# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_acidocaldarius_DSM_639_uid58379/NC_007181.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_acidocaldarius_DSM_639_uid58379/NC_007181.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Sulfolobus_acidocaldarius_DSM_639_uid58379/NC_007181.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|70605854|ref|YP_254724.1|  [L=386]
Description: cell division control protein 6-like protein 3 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   50.9   0.0    2.4e-13   49.9   0.0    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain
    2.3e-09   37.6   0.0    7.5e-09   36.0   0.0    1.8  2  AAA_22           AAA domain
    1.3e-05   25.6   0.0    4.1e-05   24.0   0.0    1.9  2  AAA              ATPase family associated with various cellul
     0.0028   16.9   0.0     0.0049   16.1   0.0    1.4  1  NB-ARC           NB-ARC domain
     0.0083   16.5   0.0      0.027   14.9   0.0    1.9  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.019   14.2   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.012   15.4   0.0      0.036   13.8   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.033   14.5   0.1       0.11   12.9   0.1    1.9  1  AAA_assoc_2      AAA C-terminal domain
      0.035   13.6   0.1       0.17   11.3   0.0    1.9  2  AAA_7            P-loop containing dynein motor region
      0.093   12.7   0.3       0.27   11.2   0.0    1.9  2  Microtub_bd      Microtubule binding
        0.1   12.6   0.0       0.37   10.8   0.0    2.0  2  ResIII           Type III restriction enzyme, res subunit
       0.11   12.2   0.0        6.9    6.4   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   1.6e-16   2.4e-13      21      82 ..     311     371 ..     303     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.6e-16
                                   HHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                        Cdc6_C  21 vyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                   +++ Y++lC+++  +pl+ r++sd++seL+m gi++++  +kGr++g ++ i++  d+++++
  gi|70605854|ref|YP_254724.1| 311 AHKIYSDLCNEYKQKPLSYRRFSDVISELDMFGIIKVKIINKGRAGGIKKTIEVA-DKEKIT 371
                                   6899*************************************************94.555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0     5e-12   7.5e-09       8     135 ..      57     187 ..      54     189 .. 0.81
   2 ?   -1.8   0.0       2.4   3.5e+03      45      70 ..     303     328 ..     275     345 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5e-12
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst.sskdllrellralglelka.erlsseellealeq 84 
                                   ++  G +GtGKT+++  ++++ +e++k +     +++++v++ + + +++ +l+++ + ++ e     + ++ e++e++ +
  gi|70605854|ref|YP_254724.1|  57 TLFLGLTGTGKTFVAMYMFNEIQEVKKEDGeyGVVSQAYVNCREVGgTPQAVLSAITQRITGEEVPkHGINLGEYIERIKE 137
                                   56779******************999999988888888*******99**********9988777666889999******** PP

                        AAA_22  85 alraravielliiDEaqhlr..s..eealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                   +l ++++  l+ +DE++ l+  +  + +l +L  ++n    ++++i+v    ++r+
  gi|70605854|ref|YP_254724.1| 138 NLVDKKA--LIYLDEVDTLIkrRggDIVLYQL-LRAN---ADISVIMVSNDiNIRD 187
                                   *****99..*********98752544444444.2333...6677777766656655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
                        AAA_22  45 vtlpsstsskdllrellralglelka 70 
                                   ++++   +  +++++l+++++++  +
  gi|70605854|ref|YP_254724.1| 303 MQASDVITAHKIYSDLCNEYKQKPLS 328
                                   44444448888999999998876554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.8e-08   4.1e-05       2      91 ..      58     169 ..      57     203 .. 0.73
   2 ?   -2.5   0.0       4.3   6.5e+03      65      92 ..     230     257 ..     229     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.8e-08
                                   EEESSTTSSHHHHHHHHHHHH....THE.......................EEEEETTTCSSSSTTHHHHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakel....gve.......................fleisgsellskyvgesekkirelfkeake 55 
                                   l+ G  GtGKT +a  + +e+    + e                       +l+    +++ + v +   ++ e+++++ke
  gi|70605854|ref|YP_254724.1|  58 LFLGLTGTGKTFVAMYMFNEIqevkK-EdgeygvvsqayvncrevggtpqaVLSAITQRITGEEVPKHGINLGEYIERIKE 137
                                   899*****************844430.144444444445555555555555666666666666888999999*******99 PP

                                   TS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHH CS
                           AAA  56 ka..kpsilfiDEidalaksrsgseseeeervvnqLlt 91 
                                   +   k+  + +DE+d l+k+r       ++ v+ qLl+
  gi|70605854|ref|YP_254724.1| 138 NLvdKKALIYLDEVDTLIKRR------GGDIVLYQLLR 169
                                   99*888***************......44444455544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                                   ETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                           AAA  65 DEidalaksrsgseseeeervvnqLlte 92 
                                   DEi + + + s +e+++++++vn L+++
  gi|70605854|ref|YP_254724.1| 230 DEILSYIAAISAKEHGDARKAVNLLFRA 257
                                   6666666666777888888888888765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.3e-06    0.0049      16     113 ..      51     152 ..      40     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                                   TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC...CBTEEEEEEEESXX...HHHHHHHXXHHHHHCCCTTSSSS-STT CS
                        NB-ARC  16 delqslvvalvGmgGvGKttlakqilnksdeveg...rFdsvawvvvsktd...kseeiletilkeLslseddleekeeve 90 
                                   ++++ +   + G  G GKt +a  ++n+ +ev++   ++ +v +  v       + + +l +i +++  +e   +  + +e
  gi|70605854|ref|YP_254724.1|  51 NNMK-FSTLFLGLTGTGKTFVAMYMFNEIQEVKKedgEYGVVSQAYVNCREvggTPQAVLSAITQRITGEEVPKHGINLGE 130
                                   5555.555678******************9998644489988888776544122567899999999999988888888888 PP

                                   SHHHHHHHHCCCTTEEEEEEEE- CS
                        NB-ARC  91 slkrklvrlLltkrfllvlDDVw 113
                                      +++ + L +k+ l+ lD V 
  gi|70605854|ref|YP_254724.1| 131 -YIERIKENLVDKKALIYLDEVD 152
                                   .9******************995 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.027       4      78 ..      33     118 ..      31     179 .. 0.72
   2 ?   -2.1   0.0         3   4.5e+03      94      94 ..     277     277 ..     211     333 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                        AAA_16   4 GReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd......ggif..lrgkcdqlesaipy...sal 72 
                                    Re+ l++++ a++  v+ +   ++l+ G  G+GK+ ++   ++++++       +g++  ++ +c++   ++p    sa+
  gi|70605854|ref|YP_254724.1|  33 FREDILREVAIAVRyFVKNNMKFSTLFLGLTGTGKTFVAMYMFNEIQEVkkedgeYGVVsqAYVNCREV-GGTPQavlSAI 112
                                   599999999999998788888899***************999998877677788545555666667666.22331111334 PP

                        AAA_16  73 aqalar 78 
                                   +q ++ 
  gi|70605854|ref|YP_254724.1| 113 TQRITG 118
                                   444433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                        AAA_16  94 l 94 
                                    
  gi|70605854|ref|YP_254724.1| 277 I 277
                                   2 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.019       8      98 ..      61     152 ..      57     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                       DUF2075   8 GvaGtGKtvvllnllael....eddeeertavylsvNhplvlvlrealakke....ekkkkkeafeklssfinnlsefkka 80 
                                   G +GtGKt v++ +++e+    ++d e+  +  ++vN ++v    +a+ +      ++++  +   +l ++i++++     
  gi|70605854|ref|YP_254724.1|  61 GLTGTGKTFVAMYMFNEIqevkKEDGEYGVVSQAYVNCREVGGTPQAVLSAItqriTGEEVPKHGINLGEYIERIK----- 136
                                   889***************7766556666777777777777764444444433011144444444444445555544..... PP

                       DUF2075  81 eekkeepkedvvivDEAh 98 
                                     ++  +k  ++  DE  
  gi|70605854|ref|YP_254724.1| 137 --ENLVDKKALIYLDEVD 152
                                   ..5555555555556555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-05     0.036      20      51 ..      52      83 ..      33     110 .. 0.73
   2 ?   -3.7   0.0       5.7   8.5e+03      95     105 ..     144     154 ..     142     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                                  TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
               Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkek 51
                                  +++ s+l +G +GtGK+++a  ++++ ++ +k
  gi|70605854|ref|YP_254724.1| 52 NMKFSTLFLGLTGTGKTFVAMYMFNEIQEVKK 83
                                  344889******************96554333 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.7
                                   SEEEEETGGGS CS
               Sigma54_activat  95 GtlfLDeigel 105
                                     ++LDe+ +l
  gi|70605854|ref|YP_254724.1| 144 ALIYLDEVDTL 154
                                   6799***9877 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.1e-05      0.11       7      55 ..     228     276 ..     225     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                                   XXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX CS
                   AAA_assoc_2   7 leddalealaela...dGDaRkaLnlLElaaeaaeakegkieitledleeal 55 
                                   ++d++l+++a+++   +GDaRka nlL  aa+ a+   g+  i +e++++a+
  gi|70605854|ref|YP_254724.1| 228 YTDEILSYIAAISakeHGDARKAVNLLFRAAQLAS---GEGMIRKEHVDRAI 276
                                   57888888888884446***********9999997...56777777776655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.17      32      59 ..      53      80 ..      35      93 .. 0.80
   2 ?   -0.7   0.0      0.57   8.5e+02      99     142 ..     141     184 ..     137     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldk 59
                                   k ++l+ G tGtGKt +++ +++++++
  gi|70605854|ref|YP_254724.1| 53 MKFSTLFLGLTGTGKTFVAMYMFNEIQE 80
                                  45679*************9999888774 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.57
                         AAA_7  99 gkklvvFvDDlnmpakekygaqppiellRqlldyggwYdrkkle 142
                                    kk ++++D+++   k + g+    +llR   d + +   ++++
  gi|70605854|ref|YP_254724.1| 141 DKKALIYLDEVDTLIKRRGGDIVLYQLLRANADISVIMVSNDIN 184
                                   6999999*****99999999999999999988877666555555 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.27      58     101 ..      28      72 ..      25      88 .. 0.82
   2 ?   -2.8   0.1       3.7   5.5e+03     133     148 ..     172     188 ..     168     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                   EECTTHCCCCCCCCHHHHHHHH.TT--EEEEEEES.......... CS
                   Microtub_bd  58 feseseqeevfeeisqlvqsal.dgynvcifaygqTGsGKtyTme 101
                                   f+     e++  e++  v   + +++ ++ +++g TG GKt+  +
  gi|70605854|ref|YP_254724.1|  28 FKDIPFREDILREVAIAVRYFVkNNMKFSTLFLGLTGTGKTFVAM 72 
                                   55556679999***********99******************644 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                   EEEEEEEEESS.-EEET CS
                   Microtub_bd 133 ielqfveiyne.kvqDl 148
                                    ++++++++n+ +++D 
  gi|70605854|ref|YP_254724.1| 172 ADISVIMVSNDiNIRDY 188
                                   6789999***9999997 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.37      20      53 ..      50      83 ..      20      96 .. 0.79
   2 ?   -2.7   0.0       3.5   5.2e+03      53      76 ..     357     380 ..     344     385 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                  ...TTSEEEEEESTTSTHHHHHHHHHHHH-S... CS
                        ResIII 20 kskrdkrglikmaTGtGKTlvaaklierllkkgk 53
                                  k++ +   l+   TGtGKT+va+ +  ++++ +k
  gi|70605854|ref|YP_254724.1| 50 KNNMKFSTLFLGLTGTGKTFVAMYMFNEIQEVKK 83
                                  4355668889999*********988888776554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                                   ...-EEEEESSHHHHHHHHHHGGG CS
                        ResIII  53 keekflflvprkslleqtleefkk 76 
                                   +++k++ +++++++++ ++e+++ 
  gi|70605854|ref|YP_254724.1| 357 GIKKTIEVADKEKITKALEEAMQL 380
                                   556777777777777777666655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0046       6.9      43      67 ..      48      74 ..      28      83 .. 0.76
   2 ?    3.3   0.1      0.04        60     104     154 ..     137     188 ..     127     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0046
                     IstB_IS21 43 fiekke..nivllGpsGvGKshlaial 67
                                  f++++   + ++lG +G+GK+++a+ +
  gi|70605854|ref|YP_254724.1| 48 FVKNNMkfSTLFLGLTGTGKTFVAMYM 74
                                  5555441145899**********9865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.04
                     IstB_IS21 104 krll.kvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaew 154
                                   ++l+ k +l+ lD++ +l   +    +l++++ +  + + i+++ ++++ ++
  gi|70605854|ref|YP_254724.1| 137 ENLVdKKALIYLDEVDTLIKRRGGDIVLYQLLRANADISVIMVSNDINIRDY 188
                                   44441568899************************99999999988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 2252.44
//
Query:       gi|70605855|ref|YP_254725.1|  [L=111]
Description: hypothetical protein Saci_0002 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.02   15.1   0.1    1.1  1  bMG6           Bacterial macroglobulin domain 6
      0.038   14.5   1.1       0.15   12.6   0.1    2.2  2  MerR-DNA-bind  MerR, DNA binding
      0.046   13.6   2.2       0.27   11.2   0.1    2.2  2  Nas2_N         Nas2 N_terminal domain
       0.08   13.4   1.5       0.93   10.0   0.3    2.1  2  NPV_P10        Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> bMG6  Bacterial macroglobulin domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   4.4e-06      0.02      15      85 ..      14      84 ..       8      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.4e-06
                          bMG6 15 seaefeivavdadgkkvatkelkvklyreerdyqWeyssdggwryestekdkpvasgtvdlsaegkaklsl 85
                                  s+   ei+ +++  +++++ +l+ k+++ +++y+ +y ++g+ r+++  kd +  +++ ++++e+k kl+ 
  gi|70605855|ref|YP_254725.1| 14 SKLDTEIAELQKVLDTLPNGHLEEKVVKGKKYYYLRYWENGRLRSKYLGKDVTEIKEKFKIATETKIKLNR 84
                                  56678999999999*************************************************99988875 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.4e-05      0.15      39      62 ..       7      30 ..       2      32 .. 0.90
   2 ?    0.5   0.1      0.21   9.4e+02      10      44 ..      58      89 ..      56     102 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.4e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHH CS
                 MerR-DNA-bind 39 allarklaeleeriaeLqalraeL 62
                                  ++l++++ +l+  iaeLq++ ++L
  gi|70605855|ref|YP_254725.1|  7 KVLEERRSKLDTEIAELQKVLDTL 30
                                  69******************9998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                                  HHHTT--HHHHHHHHHHHHSTTTBHHHHHHHHHHH CS
                 MerR-DNA-bind 10 arrlGFsLdeIrelLalyddrappcqdvrallark 44
                                   + lG  + eI+e + +    + ++ ++++l++++
  gi|70605855|ref|YP_254725.1| 58 SKYLGKDVTEIKEKFKI---ATETKIKLNRLIEER 89
                                  55666666666666655...455555555555554 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.1e-05      0.27       2      34 ..       7      40 ..       6      45 .. 0.79
   2 ?    2.1   0.2      0.04   1.8e+02       1      25 [.      82     106 ..      82     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.1e-05
                        Nas2_N  2 keLekkkdeiekeieelsevLe.sqnvgmdgplv 34
                                  k Le+++++++ ei+el++vL+  +n  ++++ v
  gi|70605855|ref|YP_254725.1|  7 KVLEERRSKLDTEIAELQKVLDtLPNGHLEEKVV 40
                                  679******************9655555666555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.04
                        Nas2_N   1 lkeLekkkdeiekeieelsevLesq 25 
                                   l++L +++++i + ++++s++L ++
  gi|70605855|ref|YP_254725.1|  82 LNRLIEERNRIVRILDKISKILVEN 106
                                   5789999999999999999999754 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.043   1.9e+02      22      66 ..      15      28 ..       3      40 .. 0.50
   2 ?   10.0   0.3   0.00021      0.93      23      66 ..      61     104 ..      57     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.043
                       NPV_P10 22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                   l+++++++q                               ++L 
  gi|70605855|ref|YP_254725.1| 15 KLDTEIAELQ-------------------------------KVLD 28
                                  3333333332...............................2222 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                       NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   l + v++++e+++  te + kL+++ ++ + +   +++I++iL 
  gi|70605855|ref|YP_254725.1|  61 LGKDVTEIKEKFKIATETKIKLNRLIEERNRIVRILDKISKILV 104
                                   678899************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 753.29
//
Query:       gi|70605856|ref|YP_254726.1|  [L=279]
Description: hypothetical protein Saci_0003 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-12   47.3  14.4    2.8e-10   40.0   4.8    5.0  5  TM_helix   Conserved TM helix


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   4.8   1.6e-14   2.8e-10       3      44 ..      21      62 ..      19      63 .. 0.95
   2 ?   -2.7   0.3      0.33   5.9e+03      40      42 ..      82      84 ..      72      95 .. 0.56
   3 !   20.1   2.0   2.6e-08   0.00047       2      39 ..     100     137 ..      99     141 .. 0.91
   4 ?   -0.0   0.5      0.05     9e+02      10      23 ..     187     200 ..     183     204 .. 0.75
   5 ?   -2.7   3.7      0.34   6.1e+03      16      26 ..     223     233 ..     214     246 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.6e-14
                                  XXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      TM_helix  3 lnnllnellsflPnLvgAilILlvGwiiAkfvsrlvtkllak 44
                                  l+nl +e+++++P ++++++I ++G+i+A +v+ +v+++l++
  gi|70605856|ref|YP_254726.1| 21 LSNLATEIINAIPSIILFVIIVIIGYIVADIVASIVGRVLRS 62
                                  89*************************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.33
                                  HHH CS
                      TM_helix 40 kll 42
                                   l+
  gi|70605856|ref|YP_254726.1| 82 ALI 84
                                  332 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 2.6e-08
                                   XXXSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      TM_helix   2 plnnllnellsflPnLvgAilILlvGwiiAkfvsrlvt 39 
                                   p+n+ ++ ++++lP L gAil+L +G  +++++ + ++
  gi|70605856|ref|YP_254726.1| 100 PANTYISAIATYLPYLAGAILLLTLGITLINILLDYIS 137
                                   899*****************************987775 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.05
                                   HHTTHSHHHHHHHH CS
                      TM_helix  10 llsflPnLvgAilI 23 
                                   l++fl+ L+ +++I
  gi|70605856|ref|YP_254726.1| 187 LIGFLVLLFSFVII 200
                                   67777777777776 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHH CS
                      TM_helix  16 nLvgAilILlv 26 
                                    ++ Ai IL+ 
  gi|70605856|ref|YP_254726.1| 223 FILYAIFILVA 233
                                   34555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 1812.43
//
Query:       gi|70605857|ref|YP_254727.1|  [L=185]
Description: hypothetical protein Saci_0004 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1459.31
//
Query:       gi|70605858|ref|YP_254728.1|  [L=239]
Description: hypothetical protein Saci_0005 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1795.81
//
Query:       gi|70605859|ref|YP_254729.1|  [L=83]
Description: ArsR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   50.6   0.0    1.8e-13   50.1   0.0    1.2  1  HTH_5            Bacterial regulatory protein, arsR family
    2.6e-10   40.2   0.0    3.5e-10   39.8   0.0    1.2  1  HTH_20           Helix-turn-helix domain
    3.6e-08   33.2   0.3      5e-08   32.7   0.3    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.2e-05   24.8   0.0    3.5e-05   23.3   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.2e-05   24.3   0.1    3.1e-05   23.8   0.1    1.3  1  HTH_11           HTH domain
    6.4e-05   22.9   0.4    8.6e-05   22.5   0.4    1.2  1  HTH_45           Winged helix-turn-helix
    0.00058   20.2   0.2    0.00088   19.6   0.2    1.3  1  Penicillinase_R  Penicillinase repressor
    0.00058   19.6   0.0     0.0008   19.2   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
     0.0012   18.8   0.1     0.0017   18.2   0.1    1.4  1  HTH_12           Ribonuclease R winged-helix domain
     0.0033   17.3   0.0     0.0045   16.8   0.0    1.1  1  MarR_2           MarR family
      0.004   17.3   0.2     0.0049   17.0   0.2    1.2  1  HTH_34           Winged helix DNA-binding domain
     0.0048   16.8   0.0     0.0056   16.6   0.0    1.2  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
     0.0074   16.6   0.0      0.011   16.0   0.0    1.2  1  DUF2513          Hypothetical protein (DUF2513)
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.012   15.3   0.0    1.1  1  DUF4423          Domain of unknown function (DUF4423)
      0.011   15.6   0.1      0.011   15.6   0.1    1.1  1  TFIIE_alpha      TFIIE alpha subunit
      0.016   14.8   0.2      0.018   14.7   0.2    1.1  1  ArsR             ArsR transcriptional regulator
      0.027   14.1   0.1       0.14   11.8   0.1    2.0  1  Sigma70_r4_2     Sigma-70, region 4
       0.03   14.5   0.1      0.039   14.1   0.1    1.2  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.064   13.2   0.0      0.084   12.8   0.0    1.2  1  MarR             MarR family
      0.067   13.2   0.1       0.34   10.9   0.1    1.9  1  PadR             Transcriptional regulator PadR-like family
      0.078   13.5   0.1       0.11   13.0   0.1    1.2  1  HTH_27           Winged helix DNA-binding domain
      0.087   12.6   0.0       0.15   11.9   0.0    1.4  1  HTH_10           HTH DNA binding domain
      0.095   13.1   0.0       0.13   12.6   0.0    1.2  1  Rrf2             Transcriptional regulator
        0.1   12.9   0.1       0.12   12.7   0.1    1.1  1  MazG-like        MazG-like family
       0.15   12.5   0.1       0.18   12.2   0.1    1.2  1  FaeA             FaeA-like protein
        0.2   11.5   0.0       0.22   11.3   0.0    1.1  1  DUF742           Protein of unknown function (DUF742)


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.7e-16   1.8e-13       3      46 ..      17      60 ..      16      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.7e-16
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  tR+kIL +L+e+++++ el++el+l+ stv++HL  L++ G+V+
  gi|70605859|ref|YP_254729.1| 17 TRRKILESLSEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVK 60
                                  9*****************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   5.1e-13   3.5e-10      11      60 ..      17      65 ..      16      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.1e-13
                                  HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  +Rr+il  L ++++ ta el ++ldl  +t++yHL+ Le+ g+v+ ++++
  gi|70605859|ref|YP_254729.1| 17 TRRKILESL-SEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARKTK 65
                                  8********.***********************************99875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.3   7.2e-11     5e-08      18      64 ..      25      71 ..      20      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.2e-11
                                  HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                          TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                  l+++p+ta+e+++el++ +s+v   L+ Le+ G+V+ +k ++++Y++
  gi|70605859|ref|YP_254729.1| 25 LSEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARKTKKYVYEV 71
                                  6899*****************************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     5e-08   3.5e-05       3      48 .]      16      60 ..      16      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5e-08
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +t+rkILe L ++p++ + eL+++l+l  stv+++l+ Le+ G++k
  gi|70605859|ref|YP_254729.1| 16 DTRRKILESLSEKPKTAY-ELSKELDLNYSTVRYHLELLEKFGFVK 60
                                  699************999.9********************988876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   4.5e-08   3.1e-05       2      44 ..      18      58 ..      17      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.5e-08
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  +++ile L e+ +  ++ eL++eL++  +tvr +++ Le+ g+
  gi|70605859|ref|YP_254729.1| 18 RRKILESLSEKPK--TAYELSKELDLNYSTVRYHLELLEKFGF 58
                                  799*****55555..**************************93 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.4   1.2e-07   8.6e-05      10      57 ..      20      68 ..      16      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYv 57
                                   ILe++se+ ++  ++ ++ +L+y++++  L+ L + g++k  +++kYv
  gi|70605859|ref|YP_254729.1| 20 KILESLSEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKArKTKKYV 68
                                  69****99999999**************************663444554 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   1.3e-06   0.00088      26      75 ..      34      82 ..      29      83 .] 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                  T--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXX CS
               Penicillinase_R 26 eleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasa 75
                                  el++e +l+ysTV+  l+ L+k g+++++k  ++++Y    +  e+ +++
  gi|70605859|ref|YP_254729.1| 34 ELSKELDLNYSTVRYHLELLEKFGFVKARK-TKKYVYEVSFKNLEFYSNQ 82
                                  799************************998.899***9998887777665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0008       8      49 ..      21      60 ..      20      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                  HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  iL+ l+e p      el+++++l+ Stv+ +L  L++ G+v+
  gi|70605859|ref|YP_254729.1| 21 ILESLSEKPKT--AYELSKELDLNYSTVRYHLELLEKFGFVK 60
                                  9999****995..9***************************8 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.5e-06    0.0017      19      50 ..      31      61 ..      19      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                        HTH_12 19 iaeeLkkr.gydigeravRyrLrkleergltrr 50
                                   a eL k  + ++   +vRy+L  le+ g+++ 
  gi|70605859|ref|YP_254729.1| 31 TAYELSKElDLNY--STVRYHLELLEKFGFVKA 61
                                  3556665556677..89*************974 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.5e-06    0.0045       7      55 ..      18      63 ..      16      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-06
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   + +L  L   p    t+ el ++l+l  s+v ++l+ L++ G+v  r+
  gi|70605859|ref|YP_254729.1| 18 RRKILESLSEKPK---TAYELSKELDLNYSTVRYHLELLEKFGFVKARK 63
                                  5778999999998...****************************98774 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   7.2e-06    0.0049       4      51 ..      20      66 ..      17      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.2e-06
                        HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                                  ++l +L+++ + ++ el+++l ++++    hl+ Lek g+++ +k++k
  gi|70605859|ref|YP_254729.1| 20 KILESLSEKPK-TAYELSKELDLNYSTVRYHLELLEKFGFVKARKTKK 66
                                  67777777666.5669*****************************986 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.1e-06    0.0056      51      92 ..      27      68 ..      16      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
               Phage_rep_org_N 51 nipytaemlalifnreletvrlaLkvlkdlelieisedkvik 92
                                  + p ta +l+ +++ + +tvr  L++l++++ ++  ++k + 
  gi|70605859|ref|YP_254729.1| 27 EKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARKTKKYV 68
                                  5699******************************98777653 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05     0.011       4      65 ..      15      69 ..      14      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                       DUF2513  4 mdlvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss 65
                                  +d  R+iL  l e++++  +l+ e      + + +  ++ yhl+ll++ g+++a k+k++  
  gi|70605859|ref|YP_254729.1| 15 WDTRRKILESLSEKPKTAYELSKE------L-DLNYSTVRYHLELLEKFGFVKARKTKKYVY 69
                                  677799999999888888887773......3.4667789****************9998754 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.8e-05     0.012      32      80 ..      25      71 ..      17      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                       DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqte 80
                                  l ++ ++  el+k l   ++ + v+  le+L+k g++k  + +ky+  +
  gi|70605859|ref|YP_254729.1| 25 LSEKPKTAYELSKELD--LNYSTVRYHLELLEKFGFVKARKTKKYVYEV 71
                                  556667899*******..**********************999987655 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1   1.6e-05     0.011      16      64 ..      19      66 ..       6      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
                   TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd 64
                                   ++l++L ek +++  +l+kel ++   +r  L  L + ++vk ++ + 
  gi|70605859|ref|YP_254729.1| 19 RKILESLSEKPKTA-YELSKELDLNYSTVRYHLELLEKFGFVKARKTKK 66
                                  68999999888876.57****************************9986 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   2.6e-05     0.018       9      60 ..       8      62 ..       2      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                          ArsR  9 pllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsq 60
                                   l+ + + +t +k++e+ls++ +t+ el+++l+ +   v+  l+lL+k +++  +
  gi|70605859|ref|YP_254729.1|  8 ELMSLPGWDTRRKILESLSEKPKTAYELSKELDLNystVRYHLELLEKFGFVKAR 62
                                  56666777899********************99876668899*********9876 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00021      0.14       5      29 ..      19      43 ..      18      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                  HHHHTTS-HHHHHHHHHHHTS---H CS
                  Sigma70_r4_2  5 realaeLperqreifllryleglsy 29
                                  r+ l++L+e+ +++++l+ + +l y
  gi|70605859|ref|YP_254729.1| 19 RKILESLSEKPKTAYELSKELDLNY 43
                                  5789******************988 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.7e-05     0.039      19      58 ..      26      65 ..      19      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                  ++k+ +  +l+++L+   s+V   l+ Lek G+v+  k k
  gi|70605859|ref|YP_254729.1| 26 SEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARKTK 65
                                  455556679*************************988865 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.084       8      49 ..      21      61 ..      16      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  iL++l+e+ p +  eL k l ++ stv   l  Lek G+++ 
  gi|70605859|ref|YP_254729.1| 21 ILESLSEK-PKTAYELSKELDLNYSTVRYHLELLEKFGFVKA 61
                                  67777665.57899*************************975 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00049      0.34       1      53 [.      21      65 ..      21      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE- CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewee 53
                                  iL+ l+e+p   ye+ kel+          ++++   L+ Lek g+v++++++
  gi|70605859|ref|YP_254729.1| 21 ILESLSEKPKTAYELSKELDLN--------YSTVRYHLELLEKFGFVKARKTK 65
                                  89999********999998755........55666678888888888888766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00016      0.11       9      51 ..      22      62 ..      19      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                        HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                  L+++   + +k++ +l++ l++++s++ y l+ L++ G+v+  
  gi|70605859|ref|YP_254729.1| 22 LESLS--EKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKAR 62
                                  56666..789999***************************322 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.15      24      45 ..      30      51 ..      25      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                        HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                   t+ eL+kel++  st+ +hL+
  gi|70605859|ref|YP_254729.1| 30 KTAYELSKELDLNYSTVRYHLE 51
                                  5788*****************7 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.13      23      59 ..      27      63 ..      19      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                  CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  e+p ++ e++++ +++ s ++  l+ L+k g+vk+++
  gi|70605859|ref|YP_254729.1| 27 EKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARK 63
                                  3567999***************************986 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00017      0.12      29      81 ..      16      67 ..       2      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                     MazG-like 29 gseeeildeLAdviiylylLAdrlGidfeeideklkkklkkypvekehglekk 81
                                  +++ +il++L++   ++y L ++l++++++++ +l+  +k  +  k+++++k+
  gi|70605859|ref|YP_254729.1| 16 DTRRKILESLSEKPKTAYELSKELDLNYSTVRYHLELLEK-FGFVKARKTKKY 67
                                  78899******************************99888.999999888776 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.18       4      47 ..      20      61 ..      17      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                  HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                          FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikr 47
                                  +Ile l +   p +  e+ + l l    +Ry Le Lek g +k 
  gi|70605859|ref|YP_254729.1| 20 KILESLSE--KPKTAYELSKELDLNYSTVRYHLELLEKFGFVKA 61
                                  57777777..78888899999999999*************9985 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.22      44      93 ..      17      67 ..       8      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                        DUF742 44 ehrailr.LcreplsVaelaAelklPvgvvrvLlsdLldaglltvrapvtd 93
                                   +r+il+ L ++p++  el+ el+l  ++vr  l  L + g +++r++  +
  gi|70605859|ref|YP_254729.1| 17 TRRKILEsLSEKPKTAYELSKELDLNYSTVRYHLELLEKFGFVKARKTKKY 67
                                  567888636666*********************************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 632.99
//
Query:       gi|70605860|ref|YP_254730.1|  [L=84]
Description: hypothetical protein Saci_0007 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.4    8.7   3.9        0.4   10.5   0.6    1.8  2  T_cell_tran_alt  T-cell leukemia translocation-altered
        3.1    7.3   9.0        4.1    6.9   9.0    1.2  1  DUF1700          Protein of unknown function (DUF1700)


Domain annotation for each model (and alignments):
>> T_cell_tran_alt  T-cell leukemia translocation-altered
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   4.5e-05       0.4      23      58 ..       1      37 [.       1      42 [. 0.77
   2 ?   -1.0   0.2      0.18   1.6e+03      32      44 ..      45      57 ..      39      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
               T_cell_tran_alt 23 mrvaifklllswlvlslva.ihlawkvyGstvndlyy 58
                                  m +++f lll +l+lsl++ i l   +  s++n +y 
  gi|70605860|ref|YP_254730.1|  1 METVLFLLLLLFLILSLLSpIFLIPAIGLSALNTMYD 37
                                  7789*************98355555555577888885 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
               T_cell_tran_alt 32 lswlvlslvaihl 44
                                  ls ++l l++ih 
  gi|70605860|ref|YP_254730.1| 45 LSLILLLLLGIHE 57
                                  7778888888884 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.0   0.00045       4.1     106     169 ..       5      68 ..       1      80 [. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00045
                       DUF1700 106 lvlsllvvalallvsplvllvksllkgfeelslnvfvsigllglGllllivayylvkilykltv 169
                                   l l ll++ +++l+sp++l+ ++ l++  +++ + f+ i l  + llll +  y +  ++ lt+
  gi|70605860|ref|YP_254730.1|   5 LFLLLLLFLILSLLSPIFLIPAIGLSALNTMYDKYFLPIPLSLILLLLLGIHEYYTYAVITLTL 68 
                                   556677788899*************************998876666665555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 633.74
//
Query:       gi|70605861|ref|YP_254731.1|  [L=271]
Description: carbon-nitrogen hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-26   91.0   0.0    9.6e-26   90.7   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   5.4e-30   9.6e-26       4     254 ..       7     246 ..       4     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 5.4e-30
                                   EEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEE CS
                  CN_hydrolase   4 vvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavviglie 84 
                                   ++Q+++k  d e+nl k+le+++      a+ +v+PEl++tgy+ ++ ++e    +   +  +l ++a++    +++g+i 
  gi|70605861|ref|YP_254731.1|   7 LAQISSKLGDVEYNLNKHLEILQT---SSAECVVFPELSLTGYVLKDLVYE----VYKDSENALNKIAENARGCIIVGFIK 80 
                                   78999*******************...99**************77777775....55588899*****************9 PP

                                   EECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS...S-EEEETTEEEEEEEGGGGGSHHHH CS
                  CN_hydrolase  85 reltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg...ipvfdtpvgkiGaaiCyeigfpell 162
                                   +   +g l   nta ++ +++      +K  L    p+ + + er +f+pg+    + +f+ ++ ++G+ +C++ ++ e +
  gi|70605861|ref|YP_254731.1|  81 EV-RPGIL--RNTAGVILNSQI--NYVYKFYL----PTYGLFEERRYFQPGNPirdLNIFEYKGLRFGVIVCEDAWHYEPI 152
                                   94.78888..888888755554..67899997....78999*********995555666666666**************** PP

                                   HHHHHTT-SEEEE....BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEEC CS
                  CN_hydrolase 163 ralalkgaeilvn....lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilagl 239
                                    al   ga+ ++      + r + +k   ++ we+l +a++l ng++++ +n+vg   q+   ++g+S++++p G+i a++
  gi|70605861|ref|YP_254731.1| 153 EALTMLGADAIFIpsasPMRRLTSHKLFIQDNWEALLKAHSLINGIWTLFSNSVGS--QEEEYFWGGSMAVSPLGEIKAKA 231
                                   *************98774468899********************************..*********************** PP

                                   CSSSTEEEEEEEEHH CS
                  CN_hydrolase 240 geeeegvliaeidla 254
                                     +ee+ +i ei+ +
  gi|70605861|ref|YP_254731.1| 232 KLFEEDRIIIEININ 246
                                   **********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1710.61
//
Query:       gi|70605862|ref|YP_254732.1|  [L=279]
Description: NAD synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-76  254.4   0.0    8.6e-76  254.2   0.0    1.0  1  NAD_synthase   NAD synthase
    0.00023   20.1   0.0     0.0071   15.2   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
     0.0024   17.5   0.0     0.0038   16.9   0.0    1.2  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.031   13.8   0.2       0.13   11.8   0.1    2.0  3  Sigma70_r4     Sigma-70, region 4
      0.033   13.8   0.0      0.037   13.7   0.0    1.1  1  Asn_synthase   Asparagine synthase
      0.093   12.2   0.0       0.28   10.7   0.0    1.8  2  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.2   0.0   2.9e-79   8.6e-76       2     242 .]      17     258 ..      16     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 2.9e-79
                                   HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHH...HHHHHTSEEEE- CS
                  NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedala...laenlgievkti 79 
                                    e+lv+ +k+y++++g +g ++GlSGG+DSs++++l  ka   en++ ll+Pss +++ed+ +a +   l++  + +++ i
  gi|70605862|ref|YP_254732.1|  17 TEYLVKRIKDYINNSGKSGGIIGLSGGIDSSVASVLLSKAT--ENFHVLLMPSSSTPKEDLDHAFMilrLINATESKYTII 95 
                                   578999**********************************9..9********************762226778889999** PP

                                   --HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHH CS
                  NAD_synthase  80 dikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevk 160
                                   +i+piv  f+ ++k +  ++ +gN+kaR Rm++lya+a+k+n+lv+gTg+ksEl++GyfTkyGDg++d++p+++l+Kt+v+
  gi|70605862|ref|YP_254732.1|  96 NIDPIVDQFRLAVKTND-KIISGNIKARSRMILLYAFAQKFNYLVVGTGDKSELMLGYFTKYGDGGVDILPLGDLYKTQVR 175
                                   *********99998887.*************************************************************** PP

                                   HHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGS CS
                  NAD_synthase 161 eLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkksehKrk 240
                                    L ++l+vPe ++kkpPs  L++gqt e e+g+ Y+++D iL   +e+ +s++ei +  ++p + v++i+++vk s+hKr 
  gi|70605862|ref|YP_254732.1| 176 MLGRYLGVPEDIVKKPPSPALWEGQTAEGEIGLDYETIDSILYlRFEEMRSENEISALVNVPIDLVRRIVRMVKISQHKRL 256
                                   *******************************************779**********************************7 PP

                                   SS CS
                  NAD_synthase 241 lp 242
                                   +p
  gi|70605862|ref|YP_254732.1| 257 PP 258
                                   76 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.4e-06    0.0071       4      37 ..      37      70 ..      36     103 .. 0.86
   2 ?    2.9   0.0     0.013        39     165     191 ..     163     191 ..     161     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-06
                 tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigvflklwee 37
                                  +++lSgG+DSsva +ll ++  +   + +  +++
  gi|70605862|ref|YP_254732.1| 37 IIGLSGGIDSSVASVLLSKATENFHVLLMPSSST 70
                                  589****************999998888877665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                 tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekk 191
                                   ++Plg+l K++vr + +  g++  + +k+
  gi|70605862|ref|YP_254732.1| 163 ILPLGDLYKTQVRMLGRYLGVPedIVKKP 191
                                   69************999888775555655 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.3e-06    0.0038       8     115 ..      38     143 ..      32     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                          ThiI   8 aLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkeklt 88 
                                     lSgGiDS Va+ ll k   + +++ +  +  t++e  +   ++ +l++  ++    k+++++ ++++++ +  vk + +
  gi|70605862|ref|YP_254732.1|  38 IGLSGGIDSSVASVLLSKATENFHVLLMP-SSSTPKEDLDHAFMILRLINATES----KYTIINIDPIVDQFRLAVKTNDK 113
                                   558**********9999988888888885.777888888888888888887765....88888888888888877776666 PP

                          ThiI  89 iv...l.lkrkmlriAekvaeeegakalvtG 115
                                   i+   +  +  m+ +    a+++++  + tG
  gi|70605862|ref|YP_254732.1| 114 IIsgnIkARSRMI-LLYAFAQKFNYLVVGTG 143
                                   6522121222232.33335555555555555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   3.3e+03       7      21 ..     121     135 ..     119     141 .. 0.76
   2 ?   -3.9   0.0       3.4     1e+04      27      36 ..     178     187 ..     177     189 .. 0.75
   3 ?   11.8   0.1   4.4e-05      0.13      12      42 ..     216     246 ..     214     247 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHTTT- CS
                    Sigma70_r4   7 ererevlelrfgegl 21 
                                   +r r++l + f ++ 
  gi|70605862|ref|YP_254732.1| 121 ARSRMILLYAFAQKF 135
                                   689999999986655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.4
                                   HHHHTS-HHH CS
                    Sigma70_r4  27 gerlgiSrer 36 
                                   g+ lg+++  
  gi|70605862|ref|YP_254732.1| 178 GRYLGVPEDI 187
                                   8899999865 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 4.4e-05
                                   HHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4  12 vlelrfgeglTleEIgerlgiSrerVrqiek 42 
                                   +l+lrf+e ++  EI++  +++   Vr+i +
  gi|70605862|ref|YP_254732.1| 216 ILYLRFEEMRSENEISALVNVPIDLVRRIVR 246
                                   9***************************975 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.037      24     136 ..      40     153 ..      37     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                  Asn_synthase  24 LSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgte.htelvlteeelldalpdviyhlee..pfad 101
                                   LSGG+DSS+ + l+++ ++ +++   +  ++   +++++a  + + ++       +++ + ++d+++ +++  ++     +
  gi|70605862|ref|YP_254732.1|  40 LSGGIDSSVASVLLSKATE-NFHVLLMPSSSTPKEDLDHAFMILRLINATeSKYTIINIDPIVDQFRLAVKTNDKiiSGNI 119
                                   9********9999999886.5555555556788999999988888887662455566777788889999998888654445 PP

                  Asn_synthase 102 rsaiplyllsrlakrkgvkvvLsGeGaDElfgGYp 136
                                   ++   + ll+  a++ ++ vv +G+ + El+ GY 
  gi|70605862|ref|YP_254732.1| 120 KARSRMILLYAFAQKFNYLVVGTGDKS-ELMLGYF 153
                                   555555666655555555566666655.6666665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.3e-05      0.28       3      57 ..      37      91 ..      35     136 .. 0.80
   2 ?   -2.2   0.0      0.82   2.4e+03     157     176 ..     165     184 ..     161     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.3e-05
                                  EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EE CS
                          QueC  3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehk 57
                                  ++ lSGG+DS+++ +l +k+ ++ ++l +   +  k++l+ a  i + ++ +e+k
  gi|70605862|ref|YP_254732.1| 37 IIGLSGGIDSSVASVLLSKATENFHVLLMPSSSTPKEDLDHAFMILRLINATESK 91
                                  6789********************9999988888888888888888877776554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.82
                                   TTTT--HHHHHHHHHHTTHH CS
                          QueC 157 PlidlsKaeivklgkelgvp 176
                                   Pl dl K+++  lg  lgvp
  gi|70605862|ref|YP_254732.1| 165 PLGDLYKTQVRMLGRYLGVP 184
                                   99*************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1688.84
//
Query:       gi|70605863|ref|YP_254733.1|  [L=506]
Description: hypothetical protein Saci_0010 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 3200.85
//
Query:       gi|70605864|ref|YP_254734.1|  [L=172]
Description: putative NTPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-50  171.4   0.1    1.8e-50  171.1   0.1    1.0  1  NTPase_1         NTPase
    5.2e-05   22.8   0.2      0.002   17.6   0.2    2.2  1  Pox_A32          Poxvirus A32 protein
    0.00017   22.0   0.0    0.00026   21.4   0.0    1.5  1  AAA              ATPase family associated with various cellul
    0.00079   19.2   0.7     0.0059   16.4   0.2    2.1  2  AAA_24           AAA domain
     0.0016   18.3   0.1     0.0034   17.3   0.1    1.7  1  NACHT            NACHT domain
     0.0021   18.1   0.0     0.0038   17.3   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0021   18.5   0.0      0.003   18.0   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0031   17.3   0.0     0.0049   16.6   0.0    1.3  1  AAA_30           AAA domain
     0.0048   16.1   0.0      0.037   13.2   0.0    1.9  2  DAP3             Mitochondrial ribosomal death-associated pro
     0.0063   16.8   0.1      0.024   14.9   0.1    1.9  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.018   15.0   0.5      0.044   13.7   0.4    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
      0.019   15.0   0.6       0.45   10.6   0.6    2.2  1  AAA_14           AAA domain
      0.023   15.2   0.1      0.047   14.2   0.0    1.6  1  ABC_tran         ABC transporter
      0.024   15.0   0.0       0.19   12.1   0.0    2.0  2  AAA_19           AAA domain
      0.024   14.5   0.2      0.064   13.1   0.0    1.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.025   15.0   0.0      0.092   13.1   0.0    1.9  2  RNA_helicase     RNA helicase
       0.03   13.9   0.0      0.072   12.7   0.0    1.6  1  DUF2478          Protein of unknown function (DUF2478)
      0.036   14.0   0.0      0.057   13.3   0.0    1.3  1  APS_kinase       Adenylylsulphate kinase
      0.037   13.2   0.0      0.069   12.3   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.037   14.6   0.2      0.049   14.2   0.2    1.7  1  AAA_18           AAA domain
      0.052   13.8   0.0       0.09   13.0   0.0    1.4  1  AAA_28           AAA domain
      0.077   12.7   0.0       0.32   10.6   0.0    1.8  2  Thymidylate_kin  Thymidylate kinase
      0.084   12.5   0.1      0.096   12.3   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.3   0.0        6.7    6.4   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
       0.12   12.5   0.0        2.8    8.1   0.0    2.2  2  AAA_33           AAA domain
       0.19   11.6   0.0       0.25   11.2   0.0    1.2  1  Ploopntkinase3   P-loop Nucleotide Kinase3


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.1   2.6e-53   1.8e-50       1     168 []       6     162 ..       6     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 2.6e-53
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHH CS
                      NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesf 81 
                                   +++iTG+pG+GKtTl+ ++++ lk+++++++Gfy++evr +++r+gFki ++ sg+e++Larv+a++++r+gky+v +   
  gi|70605864|ref|YP_254734.1|   6 RIYITGKPGIGKTTLLFNIYRILKEKNWRITGFYCPEVRVNNTRMGFKIKSVLSGKEAWLARVDARSGIRIGKYYVVL--- 83 
                                   699**************************************************************************5... PP

                                   HHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTTT CS
                      NTPase_1  82 eelalealrkal.seadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevteenrd 161
                                   e+ ++++l++++ s +d+i+iDEiG+mEl+s ++k+ ++++L+s+ pv+av+hr+        i+   d++++evt +nrd
  gi|70605864|ref|YP_254734.1|  84 EDNFVRQLEEEIfSFPDIILIDEIGPMELSSVSLKNLINKILTSNYPVIAVVHRS--------IKF-DDGVIYEVTIQNRD 155
                                   7788999999888******************************************........554.59************ PP

                                   THHHHHH CS
                      NTPase_1 162 alleeil 168
                                    lleeil
  gi|70605864|ref|YP_254734.1| 156 ILLEEIL 162
                                   *****97 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   2.9e-06     0.002      11     136 ..       2     136 ..       1     161 [. 0.59

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-06
                       Pox_A32  11 kkpFrlalvGgsGsGktvyLlsLlrtlvkkykhif.Lltp..vknseYdkyvwPdhinkvtseee.........leYsLsa 79 
                                   +kpFr+ ++G+ G Gkt+ L +++r l +k   i     p    n+   ++     i+ v s +e             + +
  gi|70605864|ref|YP_254734.1|   2 DKPFRIYITGKPGIGKTTLLFNIYRILKEKNWRITgFYCPevRVNNTRMGF----KIKSVLSGKEawlarvdarSGIRIGK 78 
                                   68*************************998744430333353223333333....44444444443322211111112222 PP

                       Pox_A32  80 tkekieklakkeknqk.eaerfLlilDDlGdkqtksktLlellnvgRhlnvsiilLcq 136
                                   +   +e+   ++ +++  ++  ++++D++G +++ s  L +l+n    +n  +i +++
  gi|70605864|ref|YP_254734.1|  79 YYVVLEDNFVRQLEEEiFSFPDIILIDEIGPMELSSVSLKNLINKILTSNYPVIAVVH 136
                                   2222222222122222134445666777777777777777777777666666666666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   3.7e-07   0.00026       1      74 [.       7     114 ..       7     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.7e-07
                                   EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCS.SS................................STTHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakelg...vefleisgsell.sk................................yvgesekk 45 
                                   ++++G pG+GKT+l   + + l+    ++  + ++e++ ++                                yv    + 
  gi|70605864|ref|YP_254734.1|   7 IYITGKPGIGKTTLLFNIYRILKeknWRITGFYCPEVRvNNtrmgfkiksvlsgkeawlarvdarsgirigkyYVVLEDNF 87 
                                   5899**********99999998544466777777777755578888899999999999999*******9999888888888 PP

                                   HHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                           AAA  46 irelfkeakekakpsilfiDEidalaksr 74 
                                   +r+l +e+ +   p i++iDEi  +  s+
  gi|70605864|ref|YP_254734.1|  88 VRQLEEEIFSF--PDIILIDEIGPMELSS 114
                                   99999998876..7********9886555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   8.5e-06    0.0059       3      27 ..       5      28 ..       3     107 .. 0.92
   2 ?    1.6   0.0      0.27   1.9e+02     112     138 ..     118     144 ..     114     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.5e-06
                        AAA_24  3 lkiliyGpsgiGKTtlakelgpkpl 27
                                   +i i+G++giGKTtl+ ++ +++l
  gi|70605864|ref|YP_254734.1|  5 FRIYITGKPGIGKTTLLFNI-YRIL 28
                                  5899*************999.6654 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                        AAA_24 112 rrllkklqelrknvifiahektrkded 138
                                   ++l++k+   ++ vi++ h  ++ d+ 
  gi|70605864|ref|YP_254734.1| 118 KNLINKILTSNYPVIAVVHRSIKFDDG 144
                                   6899*****************999986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.9e-06    0.0034       3      28 ..       7      32 ..       6     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                                  EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                  + ++G++G+GKTtLl  + + ++e++
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKN 32
                                  679***************99999876 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.5e-06    0.0038       4     110 ..       9     133 ..       7     151 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-06
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH.............CCHCCCHHHHHHCHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxx RF
                          CbiA   4 astkGGvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep.............dlkrllellealgkkk 70 
                                   + +k G GKTtl+ n+ r+l+++++r+  +    +  nn++  +g +++                + +r+++   +l  ++
  gi|70605864|ref|YP_254734.1|   9 ITGKPGIGKTTLLFNIYRILKEKNWRITGFYcPEVRVNNTR--MGFKIKSVLsgkeawlarvdarSGIRIGKYYVVLEDNF 87 
                                   56899***********************9984467777776..44444444444555666676663334444444444444 PP

                                   HHH.......EEEEEEEEESS...-TTCHHHHHHHHHHC...TS-EEE CS
                                   xxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                          CbiA  71 all.....lkiagvvlnrvdgeneetllkealeelkqry...gvpvlg 110
                                     +     + +  ++l    g+   +l + +l++l+ ++   + pv++
  gi|70605864|ref|YP_254734.1|  88 VRQleeeiFSFPDIILIDEIGP--MELSSVSLKNLINKIltsNYPVIA 133
                                   4444444533333333333333..334444444444433444555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.3e-06     0.003      27      63 ..       7      43 ..       2      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.3e-06
                        AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  ++++G +G+GK++l+  ++r l+++++  +   c + 
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKNWRITGFYCPEV 43
                                  689****************999999888777777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.2e-06    0.0049      22     120 ..       8     132 ..       4     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.2e-06
                        AAA_30  22 vltGpAGtGKttalkalreaweaaggrvigl.AptgkaAkv.Laeelgieastiakllkrlk................... 81 
                                    +tG +G GKtt+l  + +++++++ r+ g+  p+ ++ ++ ++ ++    s  + +l r +                   
  gi|70605864|ref|YP_254734.1|   8 YITGKPGIGKTTLLFNIYRILKEKNWRITGFyCPEVRVNNTrMGFKIKSVLSGKEAWLARVDarsgirigkyyvvlednfv 88 
                                   589**********************99997526666665555777777666677777777778888999999999999999 PP

                        AAA_30  82 ...grarlepgtllivDEagmv..dtkqlaallkaaekagakvi 120
                                      +++ ++  +++++DE+g +  ++ +l++l++++ +++  vi
  gi|70605864|ref|YP_254734.1|  89 rqlEEEIFSFPDIILIDEIGPMelSSVSLKNLINKILTSNYPVI 132
                                   99854455556999999999885566677777777766665555 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.3e-05     0.037      22      65 ..       3      46 ..       1      58 [. 0.81
   2 ?    0.9   0.0      0.29     2e+02      85     107 ..     116     138 ..     113     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                  ---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-GGGGTS CS
                          DAP3 22 kvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpeaedlvn 65
                                  k  r+++tG++g GK++lL  +  +  ek+w +   + +e  vn
  gi|70605864|ref|YP_254734.1|  3 KPFRIYITGKPGIGKTTLLFNIYRILKEKNWRITGFYCPEVRVN 46
                                  6779****************999999999997766655555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.29
                                   HHHHHHHHHTTSSHHHHTT-EE- CS
                          DAP3  85 ataalLsrilkaNeevLkklkls 107
                                   ++++l+++il++N +v++ ++ s
  gi|70605864|ref|YP_254734.1| 116 SLKNLINKILTSNYPVIAVVHRS 138
                                   6799***********99988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.5e-05     0.024       8      49 ..       7      42 ..       6     140 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-05
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                  +++tG +G+GKTtll ++ + l+e       + ++  +++p+
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEK------NWRITGFYCPE 42
                                  79*************9999988654......33333333333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   6.4e-05     0.044      23      68 ..       7      53 ..       2     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                      ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldef 68
                                  ++i+G  g+GKt+Ll +i+  l++k+     +y +  +++++++  +
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKNWrITGFYCPEVRVNNTRMGFK 53
                                  79********************8888744456666666665555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00065      0.45       6      29 ..       8      31 ..       5     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00065
                        AAA_14  6 vitGaRrvGKTtllkqlikellvk 29
                                   itG   +GKTtll+++++ l  k
  gi|70605864|ref|YP_254734.1|  8 YITGKPGIGKTTLLFNIYRILKEK 31
                                  799999***********9766633 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.8e-05     0.047      13      42 ..       6      35 ..       3      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-05
                                  EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei 42
                                  ++ i+G+ G GK+tLl  +++ lk ++ +i
  gi|70605864|ref|YP_254734.1|  6 RIYITGKPGIGKTTLLFNIYRILKEKNWRI 35
                                  5789*****************999876555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00027      0.19      13      38 ..       7      32 ..       3      42 .. 0.88
   2 ?    0.6   0.0      0.93   6.4e+02      98     129 ..      94     128 ..      70     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                        AAA_19 13 llvtaGpGtGKTrvlkhivallvelg 38
                                  + +t+ pG GKT++l  i ++l+e +
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKN 32
                                  679***************99999865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.93
                        AAA_19  98 kklqeeellivDEfqdvd...elqyrLlkallgek 129
                                   + +   +++++DE+  ++      ++L++++l+++
  gi|70605864|ref|YP_254734.1|  94 EIFSFPDIILIDEIGPMElssVSLKNLINKILTSN 128
                                   44434569999*99765521344566777776555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-05     0.064       2      31 ..       7      36 ..       6      38 .. 0.93
   2 ?   -2.4   0.0       5.9   4.1e+03      16      40 ..     117     141 ..     115     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvg 31
                                  + i+gk g GKTtLl ++ ++lk++++r+ 
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKNWRIT 36
                                  6799***********************995 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                          MobB  16 leklipelkarglrvgtiKhahhgf 40 
                                   l++li+++  +++ v ++ h + +f
  gi|70605864|ref|YP_254734.1| 117 LKNLINKILTSNYPVIAVVHRSIKF 141
                                   5678888888888888877776666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.092       1      25 [.       7      31 ..       7      54 .. 0.82
   2 ?   -0.9   0.0         3   2.1e+03      51      83 ..     100     130 ..      80     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                  i+++G++g+GK+tl  ++ + l +k
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEK 31
                                  79***************77776644 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                  RNA_helicase  51 evvvidDfgqvkdeenps.dlaelirlvsstpyp 83 
                                   ++++id++g ++ +   s  l++li+ + + +yp
  gi|70605864|ref|YP_254734.1| 100 DIILIDEIGPMELS---SvSLKNLINKILTSNYP 130
                                   67777777777766...44666666666666665 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.072       7     133 ..      12     138 ..       7     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                       DUF2478   7 adgeavdalLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdlgsgsqgCrLdpeaL...aeaaa 84 
                                   ++g    +lL ++ + l+++ +r+ G+   + +  ++++   +++ + +g++  + +    + +g r+    +    + ++
  gi|70605864|ref|YP_254734.1|  12 KPGIGKTTLLFNIYRILKEKNWRITGFYCPEVR-VNNTRMGFKIKSVLSGKEAWLARV--DARSGIRIGKYYVvleDNFVR 89 
                                   555556667777777777777777777755554.445566777777777777766543..334466666655422234678 PP

                       DUF2478  85 averalaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsek 133
                                   ++e+++ + +d++++   G  E +   l + i+++l+++ Pv+ +V+++
  gi|70605864|ref|YP_254734.1|  90 QLEEEIFSFPDIILIDEIGPMELSSVSLKNLINKILTSNYPVIAVVHRS 138
                                   8999999***************************************986 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.3e-05     0.057       2      44 ..       4      46 ..       3      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-05
                                  -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                    APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg 44
                                  ++ +++tG  g GK+t+ +++ + L+ek+ +++     +vR +
  gi|70605864|ref|YP_254734.1|  4 PFRIYITGKPGIGKTTLLFNIYRILKEKNWRITGFYCPEVRVN 46
                                  688**************************99999888888876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001     0.069      23      46 ..       7      30 ..       2      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                  EEEEESTTSSHHHHHHHHCCSHCC CS
                        NB-ARC 23 valvGmgGvGKttlakqilnksde 46
                                  + + G++G+GKttl+ +i++ ++e
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKE 30
                                  789***************987665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   7.2e-05     0.049       1      25 [.       7      44 ..       7     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-05
                        AAA_18  1 IlltGtpGvGKttlakeL....skrlgf...........g 25
                                  I +tG+pG GKttl  ++    +++  +            
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIyrilKEK--NwritgfycpevR 44
                                  78************99983333333..1233433444441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013      0.09       1      24 [.       6      33 ..       6      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                        AAA_28  1 kivitGgestGKTtll....eaLaargy 24
                                  +i+itG ++ GKTtll    + L+++++
  gi|70605864|ref|YP_254734.1|  6 RIYITGKPGIGKTTLLfniyRILKEKNW 33
                                  79*************9555555555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047      0.32       3      50 ..      11      62 ..       9      69 .. 0.82
   2 ?   -0.6   0.0       1.3   9.2e+02     105     128 ..      86     109 ..      77     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                  ESTTSSHHHHHHHHHHHHHHTTE..EEEESSS...TTSHHHHHHHHHHHTCS CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vvltrep...ggteiGekirelllkee 50
                                  G  G GKtt + ++++ lke+  + + +  ++    +t++G ki+++l+ +e
  gi|70605864|ref|YP_254734.1| 11 GKPGIGKTTLLFNIYRILKEKNWRiTGFYCPEvrvNNTRMGFKIKSVLSGKE 62
                                  5669*****************9998777777644479**********99444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                   HHHHHHGGGTTSE-SEEEEEESSH CS
               Thymidylate_kin 105 dlvlslnedvllkPdltflldvdp 128
                                   ++v++l+e+++  Pd++++ ++ p
  gi|70605864|ref|YP_254734.1|  86 NFVRQLEEEIFSFPDIILIDEIGP 109
                                   7999999999999**999988765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014     0.096       3      28 ..       7      32 ..       5     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                  EEEEESTTCCHHHHHHHHHCT--SS- CS
                          cobW  3 tvltGflGsGKTtLlnhllenraglk 28
                                  + +tG +G GKTtLl ++ +  ++++
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKN 32
                                  579************99985444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0098       6.7      50      77 ..       7      34 ..       1      47 [. 0.79
   2 ?    4.0   0.0     0.055        38     108     139 ..      98     130 ..      82     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0098
                     IstB_IS21 50 ivllGpsGvGKshlaialgveavragls 77
                                  i ++G +G+GK+ l   + +   +++++
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKNWR 34
                                  789*********9987776666666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.055
                     IstB_IS21 108 kvdllilDdlgllpldqaeaellf.eviekrye 139
                                    +d++++D++g  +l++ + ++l  +++ + y 
  gi|70605864|ref|YP_254734.1|  98 FPDIILIDEIGPMELSSVSLKNLInKILTSNYP 130
                                   359************998876664267777775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0041       2.8       2      20 ..       7      25 ..       7      37 .. 0.83
   2 ?    2.0   0.0      0.32   2.2e+02      10      74 ..      59     132 ..      59     135 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                        AAA_33  2 vllvGlpGsGKstlaerll 20
                                  +++ G pG GK+tl+ +++
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIY 25
                                  5788**********87765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                        AAA_33  10 sGKstlaerllkklg.....avllssdtlrrrlfg..tdqqskt....dytrvldrlyqilnelarkalsagrnvi 74 
                                   sGK  ++ r+ ++ g     ++++ +d++ r+l++       +     d +   +     l++l++k l+++++vi
  gi|70605864|ref|YP_254734.1|  59 SGKEAWLARVDARSGirigkYYVVLEDNFVRQLEEeiF--SFPDiiliDEIGPMELSSVSLKNLINKILTSNYPVI 132
                                   78888888887777788888888888888888876331..211111121111222233455666666666666666 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00037      0.25       6      43 ..       7      44 ..       2      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                Ploopntkinase3  6 iylvGqPGaGkstlmaeltkgfdrskveqeeetvphdv 43
                                  iy+ G+PG Gk+tl+ ++ + ++ ++++ +    p+  
  gi|70605864|ref|YP_254734.1|  7 IYITGKPGIGKTTLLFNIYRILKEKNWRITGFYCPEVR 44
                                  9***************9999999888876655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 1227.57
//
Query:       gi|70605865|ref|YP_254735.1|  [L=222]
Description: hypothetical protein Saci_0012 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-47  160.1   0.1    8.2e-47  159.3   0.0    1.4  2  Chlor_dismutase  Chlorite dismutase
     0.0031   17.7   0.1      0.012   15.8   0.0    1.8  2  Darcynin         Darcynin, domain of unknown function
  ------ inclusion threshold ------
       0.13   10.8   0.2        1.8    6.9   0.2    2.0  2  Aldedh           Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.05     3e+02     109     127 ..      13      31 ..       4      32 .. 0.76
   2 !  159.3   0.0   1.4e-50   8.2e-47       1     192 [.      26     213 ..      26     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.05
                                   EE-EEGGGS-HHHHHHHHH CS
               Chlor_dismutase 109 sksreWYllpeeeRrelma 127
                                   + + eW+  + + Rr++++
  gi|70605865|ref|YP_254735.1|  13 KFNNEWWSTSLQTRRNILN 31 
                                   44678***********996 PP

  == domain 2  score: 159.3 bits;  conditional E-value: 1.4e-50
                                   HHHHHHHHHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS CS
               Chlor_dismutase   1 reeaveelealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkee 81 
                                   r+++++++e+l ++++++ l+al ++++lr d++l++w+ + ++++l++++ +l + +  ++le++ +++s++++s Y   
  gi|70605865|ref|YP_254735.1|  26 RRNILNRIEELEARSKND-LVALKRFISLRYDGHLLYWVSDFDTSKLNNLRYSLIS-SGEGFLEEKLTLFSYFKPSPY--- 101
                                   778999999999999999.************************************9.7899*****************... PP

                                   -GGGHHHC.HHHHS----SSSEEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTT...EEEEEEE-TTTSSSSEEEEE CS
               Chlor_dismutase  82 deenkshv.earlapelpkkkyvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgk...VrqiitgsfGldDyEwgval 158
                                        +++ +   + +l++ +y+++YPm+ks eWYllp+eeR+e+m+eH+ei++++++   +r+++t+sfG++DyE++v +
  gi|70605865|ref|YP_254735.1| 102 ---IGGSAdKLASYLRLEPLRYFIAYPMKKSPEWYLLPFEERKEIMDEHIEIAKTHPDnqgIRSYTTYSFGIADYEFVVIY 179
                                   ...33333255566777789************************************76699******************** PP

                                   EESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEE CS
               Chlor_dismutase 159 eaddleefkdlvyelRfdeasakvaeegpfyvGr 192
                                   ea+dl+++ ++v++lR+++a+++v +e+p++vG+
  gi|70605865|ref|YP_254735.1| 180 EAPDLSKWINVVERLREAKARKWVVSEEPILVGE 213
                                   *********************************8 PP

>> Darcynin  Darcynin, domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.32   1.9e+03      22      42 ..      12      32 ..       3      57 .. 0.70
   2 !   15.8   0.0     2e-06     0.012      22      94 ..     126     198 ..     111     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.32
                      Darcynin 22 vktspewlaltveervdllee 42
                                   k   ew + +++ r ++l+ 
  gi|70605865|ref|YP_254735.1| 12 AKFNNEWWSTSLQTRRNILNR 32
                                  467789999999999888765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2e-06
                      Darcynin  22 vktspewlaltveervdlleeqvlpilekraagvrlrfydv.efyaarvtdlwvweaedhhayqllvedlreta 94 
                                   +k spew  l+ eer ++++e +  i +++  +  +r y +  f  a    + ++ea d   +  +ve lre+ 
  gi|70605865|ref|YP_254735.1| 126 MKKSPEWYLLPFEERKEIMDEHI-EIAKTHPDNQGIRSYTTySFGIADYEFVVIYEAPDLSKWINVVERLREAK 198
                                   699***************99986.678899999999999872455566677999*****************975 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2   0.00031       1.8      42      74 ..      14      47 ..       8      50 .. 0.87
   2 ?    1.6   0.0     0.013        76      40      68 ..     127     155 ..     119     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00031
                                  HH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHH CS
                        Aldedh 42 fk.awaklpaeeRaeiLrkaadlleerkeelael 74
                                  f+ +w ++++++R++iL+++ +l ++ k++l++l
  gi|70605865|ref|YP_254735.1| 14 FNnEWWSTSLQTRRNILNRIEELEARSKNDLVAL 47
                                  4448*******************99999999887 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.013
                                   HHHHHHTTS-HHHHHHHHHHHHHHHHHTH CS
                        Aldedh  40 eafkawaklpaeeRaeiLrkaadlleerk 68 
                                   ++ ++w  lp+eeR+ei+ +  ++ +++ 
  gi|70605865|ref|YP_254735.1| 127 KKSPEWYLLPFEERKEIMDEHIEIAKTHP 155
                                   56689*************99988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1527.07
//
Query:       gi|70605866|ref|YP_254736.1|  [L=175]
Description: ADP-ribose pyrophosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-14   54.2   0.1      2e-14   53.8   0.1    1.2  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1   1.1e-18     2e-14       4     120 ..      33     145 ..      29     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.1e-18
                                   EEEEEEEEETTSEEEEEEESSSSTTT.E..ESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.W..elPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygd 80 
                                    +v +  + + ++++l++++ +p  g W  e+P+G++e+gE+   +ArREleEE+G+ + +l ++l       +y  p   
  gi|70605866|ref|YP_254736.1|  33 GSVVIAPFLGPERIILIKQY-RPILGkWlyEFPAGTIEEGESEDLTARRELEEEIGYVPlKLFKVLK------FYVSPGI- 105
                                   3444445555557*******.9999999777**********999************98889999999......4444555. PP

                                   EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHT CS
                         NUDIX  81 eheilyvfl.eevegelepndenevsevrwvpleellkekl 120
                                    +e+++++   +++ + +  +e ev e   ++++e+  +++
  gi|70605866|ref|YP_254736.1| 106 ATELMHLYIaTNLTKTTQKLEEYEVIEPFELTIDEA-IKMI 145
                                   566777777545555545446888888877888888.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1185.26
//
Query:       gi|70605867|ref|YP_254737.1|  [L=202]
Description: hypothetical protein Saci_0014 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-06   27.8   2.9    2.7e-06   27.8   2.9    1.8  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   2.9   1.5e-10   2.7e-06      14     113 ..      40     143 ..      14     148 .. 0.79
   2 ?   -2.2   0.9      0.31   5.5e+03      15      35 ..     162     182 ..     149     185 .. 0.61

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.5e-10
                   SNARE_assoc  14 f.......glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygf.lallllrllpivPrd.lv 85 
                                   +       +++++++++ lga l+++l+y+lg +l  k lrr    +k+++ l+++++ + f ++l++l ++p +P+d ++
  gi|70605867|ref|YP_254737.1|  40 IknginieNFVIAIVISGLGAALAKTLTYALGFVLR-KPLRR----NKNIDILSKFSRSRYFkILLFILSVIPLLPFDdYL 115
                                   244444479999********************7665.55555....77777766666655553889**********86267 PP

                   SNARE_assoc  86 nyvaGltrvsfkrFflatfiGsipwalv 113
                                    +  G+++vs+ + + ++++G++ ++ v
  gi|70605867|ref|YP_254737.1| 116 FIGGGVAKVSILNMLKVSILGKLTKSAV 143
                                   7999******************998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.31
                   SNARE_assoc  15 glllgtlvtslgallGaslay 35 
                                   g l+ tl+ s++ ++ +++ +
  gi|70605867|ref|YP_254737.1| 162 GALTLTLIFSIAFIVLGVVLF 182
                                   445555666665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1371.11
//
Query:       gi|70605868|ref|YP_254738.1|  [L=277]
Description: endonuclease IV [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-26   93.2   0.0    1.9e-26   92.8   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    0.00018   20.9   0.0    0.00026   20.3   0.0    1.3  1  UvdE          UV-endonuclease UvdE
  ------ inclusion threshold ------
      0.014   15.5   0.4      0.033   14.3   0.4    1.6  1  DUF3973       Domain of unknown function (DUF3973)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.1e-30   1.9e-26       2     206 ..      25     228 ..      24     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.1e-30
                                   HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHH CS
                  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaL 82 
                                   + ++e+G +++E+ + ++v++s   +e+++e+ + ++elg+r++++ ++  +  ++ed   ++ ++s++++ +++++a+ +
  gi|70605868|ref|YP_254738.1|  25 KTVKELGLNAMEVEFVQGVKMS---KETAEEVGRVAKELGVRLSVHAPYFINLCSEED---EKVQASKKRILDTADRAESM 99 
                                   6789*****************8...79***************************9885...335899************** PP

                                   TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT...SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEE CS
                  AP_endonuc_2  83 GapllvlhpGtagagpkgseeeawerlaeslneladyaekeg...vklalEtlagsgvelgdeelarlldavdspnvgvcl 160
                                   Ga+ + +h+    +++k  +ee++ ++ + l e++d a+ +g   vk+++Et+a+++++   +e+  + ++++   v  ++
  gi|70605868|ref|YP_254738.1| 100 GADAIAIHIA---FYGKMKPEECYGKIKSELGEVVDSARSNGiknVKFGVETMAKETAFGSLDEVISISKEIKG--VIPYI 175
                                   ********99...****************************9999************99999***********7..***** PP

                                   EHHHHHHH...TTTHHHHHHHHHGGEEEEEE.EESS....TTTTSSTTEESTT CS
                  AP_endonuc_2 161 DtgHllia...eedvddalraladrikhvHikDakg....dlgagrdrhvpig 206
                                   D++H++ +   + d+++++++l + + ++Hi+  +      +g+  d+h pi+
  gi|70605868|ref|YP_254738.1| 176 DWAHTFGRlggKIDYEEIINRLVKELNLIHINSHFEslifKNGKYIDEHIPID 228
                                   *******************************7666677777777777777765 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.4e-08   0.00026      84     138 ..      45      93 ..      33     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-08
                          UvdE  84 alaeeleevGelakelglRltfHPeqftllnSdrkevtesairdlayHdklldal 138
                                   + +e+ eevG++akelg+Rl++H   f+ l S+ +e ++ +       +++ld+ 
  gi|70605868|ref|YP_254738.1|  45 MSKETAEEVGRVAKELGVRLSVHAPYFINLCSEEDEKVQASK------KRILDTA 93 
                                   5567889*************************9988766553......3444444 PP

>> DUF3973  Domain of unknown function (DUF3973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   5.5e-06     0.033      10      30 ..     204     224 ..     201     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-06
                       DUF3973  10 vHeektkndkiFkngfYIdpf 30 
                                   +H +++ ++ iFkng YId+ 
  gi|70605868|ref|YP_254738.1| 204 IHINSHFESLIFKNGKYIDEH 224
                                   899****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1797.00
//
Query:       gi|70605869|ref|YP_254739.1|  [L=225]
Description: hypothetical protein Saci_0016 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-26   91.6   0.2    6.7e-17   62.1   0.1    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    2.8e-09   36.9   0.0    2.7e-06   27.1   0.0    2.2  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    1.7e-06   27.3   0.0      0.028   13.6   0.0    2.3  2  Trehalose_PPase  Trehalose-phosphatase
    0.00048   20.0   0.0    0.00065   19.6   0.0    1.1  1  DUF4832          Domain of unknown function (DUF4832)
     0.0022   18.4   0.0      0.049   14.0   0.0    2.5  2  HAD              haloacid dehalogenase-like hydrolase
     0.0061   16.9   0.0       0.01   16.2   0.0    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.056   13.3   0.0    1.5  1  DUF934           Bacterial protein of unknown function (DUF93


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   3.3e-10   8.5e-07       2     111 ..       8     116 ..       7     136 .. 0.83
   2 !   62.1   0.1   2.6e-20   6.7e-17     170     255 .]     129     213 ..     110     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.3e-10
                                   EEEIIIIIS-TTS-..--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B- CS
                   Hydrolase_3   2 alDlDGTLlnsdkk..isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstis 80 
                                   ++D D TL +++++  i+++ +++++ ++ k + +++ TGR+ +++  ++ el+  +  i  NGal  + +g+++y+ + s
  gi|70605869|ref|YP_254739.1|   8 VSDYDRTLSSEKNNfrIDKEVARIVNDFS-KTYPFFVVTGREKKFIDILAPELK-PTGWILENGALM-YVNGELIYNIQPS 85 
                                   89******986555459999999999998.99**********************.669*********.9999999887777 PP

                                   .HHHHHHHHHHHHHTTCEEEEEESSEEEESTT CS
                   Hydrolase_3  81 .kedvkeiikllkennveillytedkvyvlnk 111
                                     ++ k+iik+l ++n+++ l ++  vyv ++
  gi|70605869|ref|YP_254739.1|  86 wFDTRKNIIKILDNYNISYSL-GNVIVYVDKA 116
                                   6999************99985.4666777666 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 2.6e-20
                                   EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTH CS
                   Hydrolase_3 170 titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedG 250
                                   ++++++++   i+pkgv+Kg+a+ +l ++l++   +++a+GD+eNDi+M+ +a++ v ++na + +k+++  + ++ + +G
  gi|70605869|ref|YP_254739.1| 129 ATVEWNRNDAMILPKGVDKGSAVIQLRERLGYRG-KIVAIGDSENDISMFRVADIRVSVANALPMIKEISELILEKEDGEG 208
                                   55667777789********************975.799******************************************* PP

                                   HHHHH CS
                   Hydrolase_3 251 Vakal 255
                                   V ++l
  gi|70605869|ref|YP_254739.1| 209 VKEFL 213
                                   *9886 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00073       1.9       3      73 ..       5      73 ..       3      88 .. 0.73
   2 !   27.1   0.0   1.1e-09   2.7e-06     158     212 ..     139     192 ..     100     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00073
                                  EEEEE-TBTTTB..S-HHHH.HHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEE CS
                          S6PP  3 lllvsdLDntlv.dgdneal.arlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiy 73
                                   ++vsd D tl  +++n  + ++  ++++ + +k   + ++TGR+ +    l  e   lkP  +i + G+ +y
  gi|70605869|ref|YP_254739.1|  5 IIFVSDYDRTLSsEKNNFRIdKEVARIVN-DFSKTYPFFVVTGREKKFIDILAPE---LKPTGWILENGALMY 73
                                  689*********65555555245666666.9*************98776666555...466666666666555 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.1e-09
                                   EEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HH CS
                          S6PP 158 DvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqee 212
                                    +lPk+ +kg+A+  L ++l++   +i+  Gds+nD+++++     V V+na + 
  gi|70605869|ref|YP_254739.1| 139 MILPKGVDKGSAVIQLRERLGYR-GKIVAIGDSENDISMFRVADIRVSVANALPM 192
                                   59*******************96.68**************888888*****9886 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   2.8e-05     0.072       3      79 ..      10      81 ..       8     139 .. 0.78
   2 !   13.6   0.0   1.1e-05     0.028     152     202 ..     135     181 ..     113     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                                  ETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHH.HHHHH---SSEEEEGGGTEEE-TT--EEE- CS
               Trehalose_PPase  3 DydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslke.eellvkvpelglaaeHGaeirspsgedwen 79
                                  Dyd Tls   +   + ++++e+ +++++ ++ ++   ++v+Gr++k+   l  +++  g + e+Ga +  +++   +n
  gi|70605869|ref|YP_254739.1| 10 DYDRTLSSEKN---NFRIDKEVARIVNDFSKTYP--FFVVTGREKKFiDILAPELKPTGWILENGALMYVNGE-LIYN 81
                                  99999987665...99******************..***********88888889999999999998877766.4444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.1e-05
                                   SSEEEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS- CS
               Trehalose_PPase 152 kkvvevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlr 202
                                   ++   + p+gv KG+av +l e+lg++      +++iGD   D +mF+v  
  gi|70605869|ref|YP_254739.1| 135 RNDAMILPKGVDKGSAVIQLRERLGYR----GKIVAIGDSENDISMFRVAD 181
                                   55556779******************8....5677*************975 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.5e-07   0.00065      30     152 ..      64     205 ..      57     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.5e-07
                       DUF4832  30 yleeetkyvpvGGEvvltcklndkeseslekalkelakmhvsy.Lnsdy........deavldkwksqgv........... 90 
                                   ++ e+ + ++v GE++++ ++++ ++   ++++k l ++ +sy L + +        ++ vl++ k+++v           
  gi|70605869|ref|YP_254739.1|  64 WILENGALMYVNGELIYNIQPSWFDT--RKNIIKILDNYNISYsLGNVIvyvdkaheYKGVLNSIKDATVewnrndamilp 142
                                   777888999**************666..6*************944443379999999999********************* PP

                       DUF4832  91 ...egrsvydyirkhLGYRfvles.sslskkvkaggtlsleltlkNeGfAalynerkvelvlrdee 152
                                      ++ s++ ++r++LGYR  +   ++ ++ ++    + +++++ N   A ++ ++  el+l++e+
  gi|70605869|ref|YP_254739.1| 143 kgvDKGSAVIQLRERLGYRGKIVAiGDSENDISMFRVADIRVSVAN---ALPMIKEISELILEKED 205
                                   ***99999***********765541344444444466666666666...55555555555555555 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   4.1e+02       2      21 ..       8      27 ..       7      40 .. 0.79
   2 !   14.0   0.0   1.9e-05     0.049     120     188 .]      98     178 ..      88     178 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                           HAD  2 lfDfDgTLldgdslelllrf 21
                                  ++D+D TL  +  ++ +++ 
  gi|70605869|ref|YP_254739.1|  8 VSDYDRTLSSEKNNFRIDKE 27
                                  89******999888877763 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.9e-05
                           HAD 120 aelgadevlatelevdd...rltgelglegkpvrgegkv.........aalrewlaaegegidleevvayGDspsDlpllr 188
                                   +++++ + l++ + ++d    ++g l  + + + ++++          ++  + ++ +++   + ++va+GDs++D+ ++r
  gi|70605869|ref|YP_254739.1|  98 DNYNISYSLGNVIVYVDkahEYKGVLNSIKDATVEWNRNdamilpkgvDKGSAVIQLRERLGYRGKIVAIGDSENDISMFR 178
                                   555555555555555555555555555555554444444334444333222335555666666778*************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.9e-06      0.01     172     210 .]     144     181 ..      90     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                                   TTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 172 akpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   +  + +++ ++ ++L g   +++++GD+ nD+++++ A+
  gi|70605869|ref|YP_254739.1| 144 GVDKGSAVIQLRERL-GYRGKIVAIGDSENDISMFRVAD 181
                                   445677788888999.677799*************9997 PP

>> DUF934  Bacterial protein of unknown function (DUF934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.2e-05     0.056      39      61 ..     151     173 ..     148     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.2e-05
                        DUF934  39 arlLRerlgykgelravGdvlrD 61 
                                     +LRerlgy+g++ a+Gd   D
  gi|70605869|ref|YP_254739.1| 151 VIQLRERLGYRGKIVAIGDSEND 173
                                   568****************8777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1673.40
//
Query:       gi|70605870|ref|YP_254740.1|  [L=140]
Description: hypothetical protein Saci_0017 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00034   20.4   0.0    0.00039   20.2   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
     0.0004   20.1   0.0    0.00057   19.6   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0024   17.4   0.0     0.0038   16.8   0.0    1.4  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.5e-08   0.00039      31      95 ..       8      73 ..       3     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.5e-08
               Methyltransf_31 31 vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl......naladpdkile 95
                                   v i+ + eai  A++ ++  ++dn eF ++d+e+le  ++ +k+D ++ n ++      +++ ++ k+l 
  gi|70605870|ref|YP_254740.1|  8 CVCIELDREAIMEAKSLLR--EFDNPEFIEADVESLE--IS-KKVDTVIQNPPFgvvkqgMDMVFLRKALS 73
                                  6779999*********977..9***************..77.9*******966666678877777777776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   9.5e-08   0.00057      79     133 ..       8      58 ..       2      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.5e-08
                                   EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
                       UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                                    ++++ldr+++  a++ +++    ++i   +ad+ +L+  +++vd+++ npP+G 
  gi|70605870|ref|YP_254740.1|   8 CVCIELDREAIMEAKSLLREFDNPEFI---EADVESLE-ISKKVDTVIQNPPFGV 58 
                                   6899************99999777655...57889999.6669***********6 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.3e-07    0.0038      58     112 ..       8      61 ..       3      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.3e-07
                                   EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCH CS
                           MTS  58 vtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagka 112
                                    ++++ d +A+  ak  l++ + + e+++ dv +    kk+d+++ NPPf   k+
  gi|70605870|ref|YP_254740.1|   8 CVCIELDREAIMEAKSLLREFD-NPEFIEADVESLEISKKVDTVIQNPPFGVVKQ 61 
                                   5788999999999999888776.48999****998778************87666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1001.20
//
Query:       gi|70605871|ref|YP_254741.1|  [L=220]
Description: hypothetical protein Saci_0018 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-12   47.9   0.0      2e-12   47.6   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.6e-11   44.9   0.0    4.5e-11   43.4   0.0    1.7  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.1e-06   26.5   0.0    1.5e-05   24.9   0.0    1.7  2  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.069   13.5   0.0       0.11   12.9   0.0    1.5  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   4.4e-16     2e-12      62     174 ..      82     188 ..       8     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 4.4e-16
                         HAD_2  62 ieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpevie 142
                                   ++e    ++ ++  +  ++y+++ ++++e ke+gykl ++T+ +++ v + ++ l+i++y+d ++ s d +  KP+p++++
  gi|70605871|ref|YP_254741.1|  82 VNE---LMKLNLLSDVWELYEDALNFVKEAKEMGYKLILITNATKS-VYRIIRDLEIDKYIDDMYASCDLGVLKPHPRIFK 158
                                   333...35566666889*************************9875.67899***************************** PP

                         HAD_2 143 kaleklklkkeeviyvGDsp.tDieaakkagik 174
                                    a+ek +     v+ +GD    D ++a +agi+
  gi|70605871|ref|YP_254741.1| 159 MAMEKHG---RPVFHIGDVYeVDYIGALRAGIN 188
                                   *****98...56999****99**********97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0     1e-14   4.5e-11       3     210 .]       4     186 ..       2     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1e-14
                                   EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH....HHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg....sehpigkalvaaakarsgaltgfatfigrgayaigkpewlta 79 
                                   ++++D+  TL+  +p  ++ i +        l       se+  ++a+ ++  +  ++   ++         i+  e+l +
  gi|70605871|ref|YP_254741.1|   4 VIFIDMGETLVSFSPKFHQPIFQF-------LKDKgyniSEKQVFRAINRQLGKKHFPDPTIGG-----LSEINYYELLYD 72 
                                   666777777776665555533333.......222234556666666666666666666666666.....666666666666 PP

                                   HHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                     Hydrolase  80 ldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddy 159
                                   l                  ++ ++  ++  +  ++d ++++++a  +v++ k++g++++l+t+  ++ ++ +++ l  d+y
  gi|70605871|ref|YP_254741.1|  73 L-------------KIFPSESLVN--ELMKLNLLSDVWELYEDALNFVKEAKEMGYKLILITNATKSVYR-IIRDLEiDKY 137
                                   6.............7777777788..9999********************************99875555.9999997888 PP

                                   ESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Hydrolase 160 fdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                   +d  +as++ +v kp+p++++ a+++  g+p  v ++GD    D  ++ +Ag
  gi|70605871|ref|YP_254741.1| 138 IDDMYASCDLGVLKPHPRIFKMAMEKH-GRP--VFHIGDVYEvDYIGALRAG 186
                                   8**************************.999..******9888877776665 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.87   3.9e+03      38      49 ..     108     119 ..     105     133 .. 0.83
   2 !   24.9   0.0   3.4e-09   1.5e-05       4      55 ..     151     200 ..     149     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.87
                                   HHHCT-EEEEES CS
                Hydrolase_like  38 AnnaGwksvLVl 49 
                                   A+++G+k +L++
  gi|70605871|ref|YP_254741.1| 108 AKEMGYKLILIT 119
                                   899999999987 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 3.4e-09
                                   TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS.SSS-T CS
                Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt.Gvtrp 55 
                                   KP+p ++++a+e++g +   v+ iGD ++ D +gA +aG++ vL  + G +++
  gi|70605871|ref|YP_254741.1| 151 KPHPRIFKMAMEKHGRP---VFHIGDVYEVDYIGALRAGINPVLLDRfGFYED 200
                                   9************8775...9**********************9887677766 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05      0.11      86     150 ..      97     169 ..       5     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                           HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.........rltgelglegkpvr 150
                                   l+++al +++++++ G+++++++++ + + +++   l +d  ++  ++++d          +++  + +g pv+
  gi|70605871|ref|YP_254741.1|  97 LYEDALNFVKEAKEMGYKLILITNATKSVYRIIR-DLEIDKYIDDMYASCDlgvlkphprIFKMAMEKHGRPVF 169
                                   559*************************999999.677666666655555555333445444444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1609.16
//
Query:       gi|70605872|ref|YP_254742.1|  [L=104]
Description: hypothetical protein Saci_0019 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00025   21.1   1.4     0.0005   20.1   1.4    1.4  1  Zn-ribbon_8     Zinc ribbon domain
    0.00052   20.0   0.5    0.00082   19.3   0.5    1.3  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
     0.0011   19.0   1.0     0.0014   18.7   1.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0048   15.7   0.4     0.0054   15.6   0.4    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
  ------ inclusion threshold ------
      0.021   14.8   4.4      0.021   14.8   4.4    1.7  2  ADK_lid         Adenylate kinase, active site lid
      0.022   14.3   0.1      0.033   13.7   0.1    1.2  1  Sigma70_r4      Sigma-70, region 4
      0.037   14.1   1.5      0.037   14.1   1.5    1.4  2  DUF1451         Zinc-ribbon containing domain
      0.047   13.7   1.0      0.078   13.0   1.0    1.3  1  z-alpha         Adenosine deaminase z-alpha domain
      0.052   13.1   4.2       0.53    9.8   1.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.079   12.9   0.2       0.13   12.2   0.2    1.3  1  HTH_11          HTH domain
       0.09   12.7   0.1       0.16   11.9   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.097   12.8   5.9       0.98    9.6   0.1    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.16   12.0   7.9       0.29   11.1   1.9    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.19   11.6   0.1       0.19   11.6   0.1    2.3  2  eIF-5_eIF-2B    Domain found in IF2B/IF5
       0.24   11.3   0.7         20    5.1   0.0    2.1  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.24   11.3   1.2         14    5.6   0.0    2.1  2  HalOD2          Halobacterial output domain 2
       0.27   11.4   2.7        3.2    7.9   0.3    2.1  2  FUR             Ferric uptake regulator family
       0.59   10.0   3.5         15    5.6   0.6    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.75    9.3   7.3        3.4    7.2   0.6    2.2  2  zf-ribbon_3     zinc-ribbon domain
        2.9    7.7   8.1        2.7    7.8   0.7    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        3.2    8.3   6.5        5.7    7.6   0.2    2.4  2  zf-H2C2_2       Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.4   5.9e-07    0.0005       7      35 ..      66      92 ..      61      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.9e-07
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.e 35
                                  +C++Cg +f++  + +   + +CPeC+s +
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYVFNIEKPRK---PSKCPECKSeN 92
                                  7*********776543...556****9966 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   9.5e-07   0.00082      12      45 ..      59      93 ..      56      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.5e-07
                      zf-C2HC5 12 pLleaapnClnCGkiiCakegls.kpCsfCgspll 45
                                  +L+ ++p C nCG +  + +  + ++C+ C+s+ +
  gi|70605872|ref|YP_254742.1| 59 KLFVYLPKCNNCGYVFNIEKPRKpSKCPECKSENI 93
                                  6999***********977766668*******8755 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1   1.6e-06    0.0014      72      98 ..      66      94 ..      25      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-06
                                  EETTTS-EEECHH.H.HHS-TTTSSS-EE CS
                          HypA 72 rCreCgkefelee.k.alrCpkCgsadve 98
                                  +C++Cg+ f++e+ +   +Cp+C+s+++e
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYVFNIEKpRkPSKCPECKSENIE 94
                                  8*********888545679******9986 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   6.3e-06    0.0054     480     531 ..      37      93 ..      20      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.3e-06
                                   -SSHHHHHHHHHHHHHTT--EEEEE--EEEETT.--EESS......SB-TTT--BE.E CS
                          NRDD 480 kknpealeklvkiakktgigYfsinpkidvCnecgykgei......ekCpkCgseeev 531
                                   kk++e++e+l +iak  +   +++   +  Cn+cgy   i       kCp+C+se+ +
  gi|70605872|ref|YP_254742.1|  37 KKEKEVYENLYHIAKSLKRKNVKLFVYLPKCNNCGYVFNIekprkpSKCPECKSEN-I 93 
                                   467899999999999999999999999999******555556999*89*****887.5 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.4   7.2e+03      11      15 ..      47      51 ..      45      58 .. 0.62
   2 ?   14.8   4.4   2.4e-05     0.021       4      30 ..      67      91 ..      66      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.4
                                  EETTT CS
                       ADK_lid 11 Yhvvf 15
                                  Yh+++
  gi|70605872|ref|YP_254742.1| 47 YHIAK 51
                                  99654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.4e-05
                                  -TTT--EEETTTB--SSTTB-TTT--. CS
                       ADK_lid  4 CpkCGrsYhvvfnpPkveglCDkCGep 30
                                  C +CG ++++++  P+++ +C +C ++
  gi|70605872|ref|YP_254742.1| 67 CNNCGYVFNIEK--PRKPSKCPECKSE 91
                                  *********666..**********986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.8e-05     0.033       5      35 ..       8      39 ..       6      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                                  S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HH CS
                    Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSre 35
                                  L+ re+ vl l +  e+lT ++I ++lgi +e
  gi|70605872|ref|YP_254742.1|  8 LTTREKIVLLLKYsQEPLTAKQIMKILGIKKE 39
                                  99***************************877 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.3   4.5e+03      77      77 ..      43      43 ..      21      61 .. 0.56
   2 ?   14.1   1.5   4.3e-05     0.037     116     141 ..      66      91 ..      64      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.3
                       DUF1451 77 l 77
                                  +
  gi|70605872|ref|YP_254742.1| 43 Y 43
                                  2 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.3e-05
                       DUF1451 116 vCekCgkelalkkteeippCpkCgat 141
                                    C++Cg   +++k+++ ++Cp+C+++
  gi|70605872|ref|YP_254742.1|  66 KCNNCGYVFNIEKPRKPSKCPECKSE 91 
                                   5**********************987 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   9.1e-05     0.078       6      48 ..      11      52 ..       8      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-05
                                  HHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHT CS
                       z-alpha  6 aekilelLeelgekkaatalalergLstpkreiNrvLydlerk 48
                                   eki+ lL+ + e   a+++ + +g+++  +e+   Ly ++++
  gi|70605872|ref|YP_254742.1| 11 REKIVLLLKYSQEPLTAKQIMKILGIKK-EKEVYENLYHIAKS 52
                                  689999*********************8.89*******99986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.039        33      22      29 ..      67      74 ..      66      79 .. 0.77
   2 ?    9.8   1.0   0.00062      0.53       2      12 ..      84      94 ..      83      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.039
                                  ESSSSBEE CS
                  TF_Zn_Ribbon 22 CtdCGlVl 29
                                  C +CG+V 
  gi|70605872|ref|YP_254742.1| 67 CNNCGYVF 74
                                  88999886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00062
                                  EETTTTCEECH CS
                  TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                  kCP+C+s+n++
  gi|70605872|ref|YP_254742.1| 84 KCPECKSENIE 94
                                  8******9964 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00016      0.13       2      27 ..      11      36 ..      10      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                        HTH_11  2 llqilelLleargpisgeeLAeeLnv 27
                                  +++i+ lL+ +++p++++++++ L++
  gi|70605872|ref|YP_254742.1| 11 REKIVLLLKYSQEPLTAKQIMKILGI 36
                                  789*********************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00018      0.16       3      28 ..      10      37 ..       9      39 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                  HHHHHHHHHTT..SSEEHHHHHHHHTS- CS
                         HTH_5  3 tRlkILklLae..gelcvcelaeelgls 28
                                  tR kI+ lL    ++l++ +++++lg+ 
  gi|70605872|ref|YP_254742.1| 10 TREKIVLLLKYsqEPLTAKQIMKILGIK 37
                                  788999999888688***********96 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0012      0.98      16      25 ..      66      75 ..      65      76 .. 0.90
   2 ?    4.6   2.3     0.041        35       2       8 ..      84      90 ..      84      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                       UPF0547 16 fCphCGyvFq 25
                                  +C  CGyvF+
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYVFN 75
                                  7999*****6 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.041
                       UPF0547  2 vCPeCea 8 
                                  +CPeC +
  gi|70605872|ref|YP_254742.1| 84 KCPECKS 90
                                  7****86 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4     0.051        43       2       9 ..      64      71 ..      63      71 .. 0.89
   2 ?   11.1   1.9   0.00033      0.29       3      12 ..      83      92 ..      79      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.051
                PhnA_Zn_Ribbon  2 lpkCplCa 9 
                                  lpkC +C+
  gi|70605872|ref|YP_254742.1| 64 LPKCNNCG 71
                                  8******5 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
                PhnA_Zn_Ribbon  3 pkCplCaSey 12
                                  +kCp+C+Se+
  gi|70605872|ref|YP_254742.1| 83 SKCPECKSEN 92
                                  8*******96 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022      0.19      19      49 ..      32      64 ..      19      66 .. 0.77
   2 ?    1.9   3.8      0.23     2e+02      84     116 ..      58      90 ..      56      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                  EEETT...EEEETTHHHHHHHHTTSHHHHHHHH CS
                  eIF-5_eIF-2B 19 kvegkk..ktvivNfeeiakaLnrdpehvlkyl 49
                                  k+ g k  k v++N+ +iak+L+r++ +++ yl
  gi|70605872|ref|YP_254742.1| 32 KILGIKkeKEVYENLYHIAKSLKRKNVKLFVYL 64
                                  3333333488****************9999997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                                   HHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  84 ieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                   ++ +V  ++C++    +++e+     kC +C++
  gi|70605872|ref|YP_254742.1|  58 VKLFVYLPKCNNCGYVFNIEKPRKPSKCPECKS 90 
                                   677999999999999999988888899999986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.024        20      11      21 ..      64      74 ..      62      74 .. 0.83
   2 ?    4.7   0.2     0.032        28      26      37 .]      83      94 ..      79      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.024
                       DUF35_N 11 gqrCpdCGtvq 21
                                  + +C +CG v+
  gi|70605872|ref|YP_254742.1| 64 LPKCNNCGYVF 74
                                  679*****885 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                       DUF35_N 26 avCphCgsddle 37
                                    Cp C s + e
  gi|70605872|ref|YP_254742.1| 83 SKCPECKSENIE 94
                                  67****999876 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.017        14      28      41 ..      61      74 ..      56      79 .. 0.78
   2 ?    3.7   1.2      0.07        60       1       9 [.      81      89 ..      81      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.017
                        HalOD2 28 GayvWkCtrCGevq 41
                                    y  kC +CG v 
  gi|70605872|ref|YP_254742.1| 61 FVYLPKCNNCGYVF 74
                                  567779*****885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.07
                        HalOD2  1 rPekCseCs 9 
                                  +P kC+eC+
  gi|70605872|ref|YP_254742.1| 81 KPSKCPECK 89
                                  69******7 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0037       3.2       9      55 ..      10      56 ..       7      61 .. 0.83
   2 ?    3.9   0.1     0.067        57      82      97 ..      66      81 ..      62     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0037
                                  HHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHT CS
                           FUR  9 qRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleea 55
                                  +Reki+ +l+ s+e l+a++++k l  ++++     +Y + k l++ 
  gi|70605872|ref|YP_254742.1| 10 TREKIVLLLKYSQEPLTAKQIMKILGIKKEKEVYENLYHIAKSLKRK 56
                                  7***********************99777776677777777777665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.067
                                  EETTT--EEEE--HHH CS
                           FUR 82 icekCgkviefkddei 97
                                   c++Cg v++++++  
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYVFNIEKPRK 81
                                  5**********99864 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.023        19      30      38 ..      66      74 ..      62      75 .. 0.86
   2 ?    5.6   0.6     0.017        15       2      10 ..      84      92 ..      83      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                       TFIIS_C 30 kCtkCghrW 38
                                  kC++Cg+ +
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYVF 74
                                  899999987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                       TFIIS_C  2 kCpkCgsre 10
                                  kCp+C+s++
  gi|70605872|ref|YP_254742.1| 84 KCPECKSEN 92
                                  8*****997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.1     0.013        11      18      25 ..      66      73 ..      65      74 .. 0.71
   2 ?    7.2   0.6    0.0039       3.4       4      14 ..      84      95 ..      83      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                   zf-ribbon_3 18 vCpyCGtk 25
                                  +C +CG++
  gi|70605872|ref|YP_254742.1| 66 KCNNCGYV 73
                                  68888876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0039
                   zf-ribbon_3  4 rCPnCGa.plss 14
                                  +CP+C++ ++++
  gi|70605872|ref|YP_254742.1| 84 KCPECKSeNIEP 95
                                  6****9999875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.7    0.0031       2.7       3      10 ..      67      74 ..      66      75 .. 0.84
   2 ?    3.7   1.4     0.061        52      16      22 ..      84      90 ..      84      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                  Rubredoxin_2  3 CsqCGfes 10
                                  C++CG+++
  gi|70605872|ref|YP_254742.1| 67 CNNCGYVF 74
                                  ******86 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.061
                  Rubredoxin_2 16 rCpsCgs 22
                                  +Cp+C+s
  gi|70605872|ref|YP_254742.1| 84 KCPECKS 90
                                  7****97 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0066       5.7      14      25 ..      60      75 ..      46      75 .. 0.62
   2 ?    2.8   2.0      0.22   1.8e+02      13      21 ..      81      89 ..      77      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0066
                     zf-H2C2_2 14 py....eCplCdkaFk 25
                                   +    +C  C+++F+
  gi|70605872|ref|YP_254742.1| 60 LFvylpKCNNCGYVFN 75
                                  3356889*******95 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.22
                     zf-H2C2_2 13 kpyeCplCd 21
                                  kp +Cp+C+
  gi|70605872|ref|YP_254742.1| 81 KPSKCPECK 89
                                  6779****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1359  (0.075799); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 681.49
//
Query:       gi|70605874|ref|YP_254743.1|  [L=340]
Description: hypothetical protein Saci_0020 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2517.55
//
Query:       gi|70605873|ref|YP_254744.1|  [L=131]
Description: hypothetical protein Saci_0021 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      0.006   16.4   0.3     0.0092   15.7   0.3    1.2  1  Calcipressin  Calcipressin


Domain annotation for each model (and alignments):
>> Calcipressin  Calcipressin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   5.1e-07    0.0092      90     103 ..      16      29 ..      12      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-07
                  Calcipressin  90 klFlISPPaSPPeg 103
                                    +FlISPP+SPP  
  gi|70605873|ref|YP_254744.1|  16 ENFLISPPGSPPTS 29 
                                   69**********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 926.60
//
Query:       gi|70605875|ref|YP_254745.1|  [L=118]
Description: hypothetical protein Saci_0022 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0076   16.1   2.5      0.009   15.9   2.5    1.1  1  DUF4268        Domain of unknown function (DUF4268)
  ------ inclusion threshold ------
      0.084   11.7   0.0       0.09   11.6   0.0    1.1  1  Viral_alk_exo  Viral alkaline exonuclease


Domain annotation for each model (and alignments):
>> DUF4268  Domain of unknown function (DUF4268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.5     1e-06     0.009      30     134 ..       5     107 ..       2     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                       DUF4268  30 WlnystgisgvslklvaskkkarvelyIskkdeeenkeifekLkeqkeeieeelgeeleWerleekkasrisriyvlkedv 110
                                   W  y++  +g  +++   k++ ++ l I     e  k +++ +++  ++i +  ge+l+W+   +kk  r s i ++ + v
  gi|70605875|ref|YP_254745.1|   5 WEYYKVIEKGTLISFEEFKNNREINLSI----REAIKFLYKLIESSASKITSSKGENLIWDLA-RKKVIRPSNIEEFIDVV 80 
                                   667777788899999999**********....6899************************544.66666666666666666 PP

                       DUF4268 111 dikdke...dwpeiiswliekmeklek 134
                                   +i  +    d + i+  l+  me le+
  gi|70605875|ref|YP_254745.1|  81 NIATRIeevDDSIIYPMLVRIMEDLED 107
                                   665554223556666677777776666 PP

>> Viral_alk_exo  Viral alkaline exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     1e-05      0.09     109     151 ..      39      85 ..      18      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                                   HHHHHH....HTTSSGTTSHHHHHHHTT-EESTTHHHHHH..H-TTG CS
                 Viral_alk_exo 109 lllliE....ketrgQsenslWelLRrglisasklyeavkgqltskk 151
                                   l +liE    k+t + +en +W+l R+++i  s + e++   ++ ++
  gi|70605875|ref|YP_254745.1|  39 LYKLIEssasKITSSKGENLIWDLARKKVIRPSNIEEFIDVVNIATR 85 
                                   5566662222689*********************9999877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 892.17
//
Query:       gi|70605876|ref|YP_254746.1|  [L=332]
Description: quinolinate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.1e-100  335.2   0.0   3.6e-100  335.0   0.0    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.0   0.0    2e-104  3.6e-100       2     298 ..      11     308 ..      10     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 335.0 bits;  conditional E-value: 2e-104
                                   HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HHH CS
                          NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsla 82 
                                   eik+lkkekna+il+HnY+e  +q ++df+GDS++La ka++t+a++ivf+GV FM e+a+ L+p+kkvl p+++agCsl+
  gi|70605876|ref|YP_254746.1|  11 EIKRLKKEKNAIILGHNYMEYGVQLVSDFTGDSFDLALKAMNTNADIIVFAGVYFMVEQAAALNPDKKVLSPEPNAGCSLS 91 
                                   8******************************************************************************** PP

                                   CT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS-SEEEEES-HHHHHHHHHHH.SEEEEES.S CS
                          NadA  83 dmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealkekkilflPDqnLgryvakklgekkiilw.k 162
                                   d+++ + ++++ke +p+a+vv Y+N+s+  Kal+d+v+TSs+a +v+e+++++ki+f PD nL+ryv++++g+k i +  +
  gi|70605876|ref|YP_254746.1|  92 DSLPVDVLKKYKEMYPGAPVVLYINTSIYAKALADYVVTSSTAIQVIERINSDKIIFGPDINLARYVESRTGKKLIKVPpD 172
                                   ************************************************************************987777636 PP

                                   SS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSE CS
                          NadA 163 gaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapeke 243
                                   g+C+vH++++++ ve +++++p+a +++HPE++ ev+eaad+vgST+q++k++k+s+++efi++Telg+++ lk ++peke
  gi|70605876|ref|YP_254746.1| 173 GKCIVHANYTKQLVELARKRYPNAILMAHPESPLEVLEAADYVGSTNQMVKFAKDSPQREFIVATELGMINALKLKVPEKE 253
                                   ********************************************************************************* PP

                                   EE.....ECS.SSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
                          NadA 244 fialsaeaae.eavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                                   f+ l ++ a+  a C++M++++le++ ++Le + + e+kv+++v ekAk+a  r +
  gi|70605876|ref|YP_254746.1| 254 FYPLVTTEACgCARCPYMAMVNLENIKRSLELEVY-EVKVPKDVGEKAKEAFLRTM 308
                                   **998655675777****************99999.**************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2106.30
//
Query:       gi|70605877|ref|YP_254747.1|  [L=374]
Description: selenocysteine lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-42  144.8   0.0    5.9e-42  143.9   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    0.00024   19.8   0.2    0.00037   19.1   0.2    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.063   12.4   0.3        3.1    6.9   0.1    2.1  2  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   9.8e-46   5.9e-42       2     371 .]      19     362 ..      18     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 9.8e-46
                                   EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCC CS
                   Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsla 82 
                                   yl  aA +++p  V  +++ y+ d    +  s+ +   e ++ +  +r+++  linae  +ei  + +t+ ++n++  +l 
  gi|70605877|ref|YP_254747.1|  19 YLNHAAISPTPLPVYFEANRYLIDVMRYG--SLADND-EESDELYHIRKNIGSLINAEA-DEISLIPNTSFGVNVISFGL- 94 
                                   89999999999999999999988665555..444444.45666778************6.****************9999. PP

                                   CC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHH CS
                   Aminotran_5  83 rslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigk 163
                                     +k+g++iv+ ++e    + p  +l+ ++g+k+k ++ +++ +++ ++l ++++ +t+lva++hvs  tG++ +v++i+k
  gi|70605877|ref|YP_254747.1|  95 -DIKEGENIVTDNLEFPTVVYPFLKLE-KKGVKIKLVKTKPD-TIE-EDLLSAIDTRTRLVAVSHVSFNTGVMVDVKKIVK 171
                                   .6************************9.66*****9999665.555.6888****************************** PP

                                   HHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET..TEEEE CS
                   Aminotran_5 164 lakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl..eettf 241
                                    +k +g ++l+D  q++g i++dvk+lgvDf++++g K l+ P+G G++yvrk l+    p+++ +++ +  ++  e+  +
  gi|70605877|ref|YP_254747.1| 172 EVKSVGGFTLLDIIQSAGAIKVDVKDLGVDFAVAGGYKwLMSPQGSGFIYVRKGLISDP-PFYGWKSTKNYLEFnpEKFEI 251
                                   *****************************************************999886.888777777777774467778 PP

                                   HCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHH CS
                   Aminotran_5 242 aeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhae 322
                                   +  p++fe GT  +a+  gl++  e++ + + e+  +  ++l++y+ + l++ + + ++ p  ++r+a+i  + +++  a+
  gi|70605877|ref|YP_254747.1| 252 EPGPRRFEIGTIDIAANLGLAKSCEII-RKHEEETYSSVQNLSDYVIK-LAEENRLDVITP--KKRKAGISIIRVNN--AK 326
                                   999************************.55556678888999999865.777778888676..56666666666654..45 PP

                                   HHHHHHHHTTEEEEE.E-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                   Aminotran_5 323 dvatlLdeegIavrs.GhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                   +v++ L e+ I v++ G              +++R+S ++ynt+ ev+ l
  gi|70605877|ref|YP_254747.1| 327 QVVQKLLEKHIVVSArG--------------EGIRISTHFYNTKREVEIL 362
                                   66666667789888755..............5789999999999999875 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   6.2e-08   0.00037      88     200 ..      96     211 ..      62     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.2e-08
                                   S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHH CS
               Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleelekaikentklvylEtptnpllkvvDiekiaklakk 165
                                   +k+G++iv+++  +      + k l+k g+++k v t   + +e+l +ai+ +t+lv +  ++  +  +vD++ki+k +k+
  gi|70605877|ref|YP_254747.1|  96 IKEGENIVTDNLEFPTVVYPFLK-LEKKGVKIKLVKTkpdTIEEDLLSAIDTRTRLVAVSHVSFNTGVMVDVKKIVKEVKS 175
                                   67888888777777555444444.556667777776644467899************************************ PP

                                   TT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTT CS
               Cys_Met_Meta_PP 166 agvlvvvDntfasp.llqrplklgaDivvhSaTKyl 200
                                   +g  +++D   +++ + +   +lg+D  v  + K+l
  gi|70605877|ref|YP_254747.1| 176 VGGFTLLDIIQSAGaIKVDVKDLGVDFAVAGGYKWL 211
                                   **************44455668**********9998 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.005        30      70     193 ..      76     189 ..      54     205 .. 0.69
   2 ?    6.9   0.1   0.00051       3.1     271     348 ..     279     350 ..     266     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.005
                                   GEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHH...HHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE CS
                 Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpdptyasyknil...rlsggevvryplyseedfhldlealeealkeapegnk 147
                                   ++ +++ ++ + +++ f l++  g++i+ +++ ++ +   +   +  g+++  ++++ ++      e+l+ a+++      
  gi|70605877|ref|YP_254747.1|  76 EISLIPNTSFGVNVISFGLDIKEGENIVTDNLEFPTVVYPFlklEKKGVKIKLVKTK-PD---TIEEDLLSAIDT------ 146
                                   555555555566777777777888888888887777654331113445555555522.22...233667777777...... PP

                                   TEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
                 Aminotran_1_2 148 ktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                                   +t++++v  ++ +tG++ + ++++k    +k+ + ++++D + +++
  gi|70605877|ref|YP_254747.1| 147 RTRLVAVSHVSFNTGVMVDVKKIVKE---VKSVGGFTLLDIIQSAG 189
                                   89****************99988887...88888888888776655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00051
                                   HHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS..CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC CS
                 Aminotran_1_2 271 qseleemrqrlqkrrkelrdeLaelglkvlasq..sgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitv 348
                                   +++ ee+ + +q++++++ +  +e  l+v++++   + +++ +++++  k++ +kLle+ +++v++    + +g +Ri+ 
  gi|70605877|ref|YP_254747.1| 279 RKHEEETYSSVQNLSDYVIKLAEENRLDVITPKkrKAGISIIRVNNA--KQVVQKLLEK-HIVVSA----RGEG-IRIST 350
                                   44777888888999999998887777777766633666666666666..9*********.888877....2233.66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2583.43
//
Query:       gi|70605878|ref|YP_254748.1|  [L=568]
Description: acetyl-coenzyme A synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-67  227.8   0.0    2.4e-67  227.4   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    5.2e-19   69.0   0.4    9.7e-19   68.1   0.4    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
      5e-15   55.2   3.1      1e-14   54.2   3.1    1.5  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.13   12.5   2.1       0.33   11.1   1.5    2.0  2  DUF211         Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.4   0.0   5.3e-71   2.4e-67      13     422 ..      65     454 ..      56     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 5.3e-71
                                   EEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHH CS
                   AMP-binding  13 alvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayil 90 
                                   alv+   + +   + ++el++ v+++++ L++lG++kg+r+ i++pns++ + +++a +++Ga+++ + ++l++e++   l
  gi|70605878|ref|YP_254748.1|  65 ALVFfpeDSKPIYVRFEELKRVVQSISSILLKLGLRKGKRITIYSPNSIQTLSTIFASARIGAIYSLIFAGLGKEAVNSRL 145
                                   45555665566778899**************************************************************** PP

                                   HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SS CS
                   AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTT 171
                                   +d ++ +++  +++  + + +++     ++k  i+  +++ ++e   ++    + ++  ++++ee+++++++ ++YTSGTT
  gi|70605878|ref|YP_254748.1| 146 QDFNPDIIV--TSKYTVRRGNKIP---LHHKGNIMFRQKDDNEE--INNLL--NMSE--DVKVEEIESSEPLKVMYTSGTT 215
                                   *********..6555534333333...23334444443332222..22222..2222..3466789*************** PP

                                   SS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHH CS
                   AMP-binding 172 GkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleliekl 252
                                   GkPKGV+l h++++   +++ ++  f+lk++d+v++++++ +i+  +  ++++ll+G+t +++++ ++ + ++l++ i+++
  gi|70605878|ref|YP_254748.1| 216 GKPKGVILPHGSWMVGDYTV-FDILFGLKPTDTVFTTADVGWITF-SRVMYGTLLHGSTFGFMEGAPDNPTDRLVKIIDEI 294
                                   **********9987775664.666799*****************9.5*******************9977899******** PP

                                   T-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE.CHCTTT CS
                   AMP-binding 253 kvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv.lpleed 332
                                   ++ v+++ P++l++l + + +       + ++++++ ++ge   ++++ ++ ++f ++v ++YG+TE + ++ +   l++ 
  gi|70605878|ref|YP_254748.1| 295 RPKVFFTSPTLLRMLRRYE-I-------RIPRVEYIATAGEIFDEQTW-EYAKRFADRVTDVYGQTELGYIIGTpYSLDDV 366
                                   ***************9952.3.......6899****************.888888999**************444445566 PP

                                   CTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEE CS
                   AMP-binding 333 kkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyl 410
                                   ++k+g +G p+pg+ v  +De+ g+ v +g++G l+ + p  + + g l+++e+  + f+ + g +  TGD++ l+   y+
  gi|70605878|ref|YP_254748.1| 367 EAKPGYAGVPFPGAVVDTLDED-GRSV-RGNPGYLVCKTPfpTQFTGILNDEERFLSYFK-KfG-YHDTGDVAILE-GNYV 442
                                   679999***************9.9999.8**********9888**************998.645.********888.458* PP

                                   EEEEECCCEEEE CS
                   AMP-binding 411 eivgRkkdlikl 422
                                   +ivgR++d+ik+
  gi|70605878|ref|YP_254748.1| 443 KIVGRADDMIKV 454
                                   ***********8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.4   2.2e-22   9.7e-19       1      76 []     463     534 ..     463     534 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.2e-22
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evE+++++ ++V+++aVvGvpdevkGe l++f+v + ++    +e+ ++vr+ lgp+   +kv+ v++lpk rsGK
  gi|70605878|ref|YP_254748.1| 463 EVENVIMEIDGVKDVAVVGVPDEVKGEKLIVFIVGNVNQ----DEITRKVRDSLGPIYIIDKVYYVKRLPKSRSGK 534
                                   8*********************************73234....********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   3.1   2.2e-18     1e-14       1      54 [.       3      56 ..       3      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 2.2e-18
                                  HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHH CS
                        ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyN 54
                                  y +ly+ ++e+pe +W++  ++l+W++p++kvl+++++  ++WF++Gk+Ni+yN
  gi|70605878|ref|YP_254748.1|  3 YFTLYQLALEKPEVYWKSFSDKLTWFTPWEKVLQQKDKYRYSWFVNGKTNISYN 56
                                  6689*******************************9999**************9 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   5.1e+03      58      76 ..      73      91 ..      48      95 .. 0.53
   2 ?   11.1   1.5   7.4e-05      0.33      13      85 ..     457     528 ..     450     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                  HHHHHHHHHCTT-EEEEEE CS
                        DUF211 58 yeeieeaieelggvihSiD 76
                                   + i    eel  v++Si 
  gi|70605878|ref|YP_254748.1| 73 SKPIYVRFEELKRVVQSIS 91
                                  3445555566666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.4e-05
                                   SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS-- CS
                        DUF211  13 hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGkkiv 85 
                                   h+++  e+ + + e++gv+ v ++ +   ++ e l + i G n++ +ei++++++  g i  iD+v   k++ 
  gi|70605878|ref|YP_254748.1| 457 HRITSGEVENVIMEIDGVKDVAVVGVPDEVKGEKLIVFIVG-NVNQDEITRKVRDSLGPIYIIDKVYYVKRLP 528
                                   88888899999********9998877778888889999998.69**********************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3627.99
//
Query:       gi|70605879|ref|YP_254749.1|  [L=158]
Description: hypothetical protein Saci_0026 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-17   63.7   0.7    2.6e-17   63.1   0.7    1.3  1  PIN_6            PIN domain of ribonuclease
     0.0071   16.5   2.8      0.017   15.3   2.8    1.6  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.056   13.2   3.5      0.085   12.6   3.5    1.3  1  zinc_ribbon_2    zinc-ribbon domain
       0.11   12.5   0.1       0.14   12.2   0.1    1.3  1  DUF5356          Family of unknown function (DUF5356)
       0.13   12.4   3.9        0.4   10.8   3.9    1.8  1  Zn-ribbon_8      Zinc ribbon domain
       0.16   12.5   4.5       0.29   11.6   4.2    1.6  1  Ribosomal_L44    Ribosomal protein L44
       0.17   12.1   1.3       0.86    9.8   0.1    2.5  3  COMM_domain      COMM domain
       0.71   10.2   3.3        3.5    8.0   3.3    2.0  1  C1_2             C1 domain
       0.95    9.9   3.1        3.7    8.0   3.1    1.9  1  DUF4379          Probable Zinc-ribbon domain
        2.2    8.3   4.2        4.3    7.4   4.2    1.5  1  ADK_lid          Adenylate kinase, active site lid
        8.6    6.1  10.4        3.4    7.4   2.6    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.7   1.6e-20   2.6e-17       1      89 []       5      90 ..       5      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.6e-20
                         PIN_6  1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellp..lelevrePspesvkkvtefakktGDlsvLSktDie 81
                                  +V+D++ +++     l+nl ek+ytt+eV++E++d k+ + lel++   ++ + eP+++s+ +vt+  +k++D+s LS+tDi+
  gi|70605879|ref|YP_254749.1|  5 IVFDTAGFLAG----LENLYEKVYTTQEVIREVKDFKSASLLELAIssNKVIIFEPTRQSLLTVTKTLNKINDIS-LSRTDIS 82
                                  79*******77....*************************999988546*************************9.******* PP

                         PIN_6 82 vlALtyeL 89
                                  v AL+++L
  gi|70605879|ref|YP_254749.1| 83 VAALALDL 90
                                  *****997 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.8     1e-05     0.017       1      34 [.     122     154 ..     122     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                  NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnktL 34 
                                   i++ k+++++C +C k++ ++ k  C+ CG+k +
  gi|70605879|ref|YP_254749.1| 122 ISKKKNYIYKCEGCGKTYMKNIK-ICEICGHKVI 154
                                   7789*************998776.6*****9876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.5   5.2e-05     0.085       1      22 [.     131     152 ..     131     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                   +C  CG++  +n k C+ CG++
  gi|70605879|ref|YP_254749.1| 131 KCEGCGKTYMKNIKICEICGHK 152
                                   7999*****************8 PP

>> DUF5356  Family of unknown function (DUF5356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.3e-05      0.14      56     102 ..      37      83 ..      31     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                       DUF5356  56 ysaelLNvkkkpnkVtVFaapekkaetvtkieeskrreelpkeadal 102
                                   +sa+lL ++   nkV +F ++++++ tvtk+ ++ +  +l + + ++
  gi|70605879|ref|YP_254749.1|  37 KSASLLELAISSNKVIIFEPTRQSLLTVTKTLNKINDISLSRTDISV 83 
                                   89****************************99998887776655444 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.9   0.00025       0.4       4      38 ..     128     155 ..     127     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                   Zn-ribbon_8   4 YeYrCeeCghefevlqsisdaplta.CPeCgsevrr 38 
                                   Y Y+Ce Cg+++ +         ++ C  Cg++v +
  gi|70605879|ref|YP_254749.1| 128 YIYKCEGCGKTYMKN--------IKiCEICGHKVIK 155
                                   99*******888733........3449999998876 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.2   0.00018      0.29      45      70 ..     121     146 ..     114     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                   -SSBB--EEEEETTT--EEE----BB CS
                 Ribosomal_L44  45 KttKKivlrleCteCkkkrlkalkRa 70 
                                   K +KK +  ++C+ C+k+ +k++k +
  gi|70605879|ref|YP_254749.1| 121 KISKKKNYIYKCEGCGKTYMKNIKIC 146
                                   99********************9865 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.6e+03      52      70 ..      15      33 ..      13      35 .. 0.81
   2 ?    9.8   0.1   0.00053      0.86      29      66 ..      41      74 ..      31      78 .. 0.91
   3 ?   -0.3   0.1      0.73   1.2e+03      22      36 ..     108     122 ..      99     129 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                   COMM_domain 52 qLqeLlneLeeiqkqlesl 70
                                   L++L++++ + q+++  +
  gi|70605879|ref|YP_254749.1| 15 GLENLYEKVYTTQEVIREV 33
                                  5899999999999988766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00053
                   COMM_domain 29 lleLklqngsgnsenvtlelskeqLqeLlneLeeiqkq 66
                                  lleL +++++     +++e +++ L +  ++L++i++ 
  gi|70605879|ref|YP_254749.1| 41 LLELAISSNKV----IIFEPTRQSLLTVTKTLNKINDI 74
                                  79999999999....********************985 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.73
                   COMM_domain  22 kvneptalleLklqn 36 
                                   ++n  ++ ++L+++ 
  gi|70605879|ref|YP_254749.1| 108 HMNIKYYSVKLNIKI 122
                                   455556666666654 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.3    0.0021       3.5       7      39 ..     118     150 ..     101     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0021
                          C1_2   7 LtlskgedssesfnCsaCgrkidgffYsCseCd 39 
                                   L+ +++++++  ++C++Cg++  ++  +C++C 
  gi|70605879|ref|YP_254749.1| 118 LNIKISKKKNYIYKCEGCGKTYMKNIKICEICG 150
                                   444488889999*********545557998895 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.1    0.0023       3.7      19      44 ..     119     144 ..     109     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0023
                       DUF4379  19 evtpgskkkvwWkCakCgheWeasvs 44 
                                   ++  ++kk++  kC++Cg+++ ++++
  gi|70605879|ref|YP_254749.1| 119 NIKISKKKNYIYKCEGCGKTYMKNIK 144
                                   56778899*************98875 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.2    0.0026       4.3       4      32 ..     132     154 ..     130     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0026
                                   -TTT--EEETTTB--SSTTB-TTT--.-B CS
                       ADK_lid   4 CpkCGrsYhvvfnpPkveglCDkCGepLv 32 
                                   C+ CG++Y       k+  +C  CG + +
  gi|70605879|ref|YP_254749.1| 132 CEGCGKTYM------KNIKICEICGHKVI 154
                                   9********......999*******9876 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.6    0.0021       3.4       3      14 ..     126     137 ..     124     140 .. 0.85
   2 ?    3.4   1.0     0.035        57       9      16 ..     146     153 ..     138     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                                   TT-EEE-TTT-- CS
               Desulfoferrod_N   3 klevYkCevCGn 14 
                                   k+ +YkCe CG 
  gi|70605879|ref|YP_254749.1| 126 KNYIYKCEGCGK 137
                                   6789*******6 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.035
                                   -TTT--EE CS
               Desulfoferrod_N   9 CevCGniV 16 
                                   Ce+CG  V
  gi|70605879|ref|YP_254749.1| 146 CEICGHKV 153
                                   *****765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1263.02
//
Query:       gi|70605880|ref|YP_254750.1|  [L=248]
Description: hypothetical protein Saci_0027 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.6e-20   71.7   0.0    1.5e-19   70.3   0.0    1.6  1  NAD_kinase  ATP-NAD kinase
     0.0022   17.6   0.1     0.0054   16.3   0.1    1.6  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.7e-23   1.5e-19      74     291 ..      32     237 ..       4     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-23
                                   TTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE. CS
                    NAD_kinase  74 fadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskge 154
                                   + d+  d+i+vvGGDGT l+ ++l +    P++g+  G+  +l ++ep + +e+l kl +++++ve+  +l+     +k +
  gi|70605880|ref|YP_254750.1|  32 VEDETEDAIVVVGGDGTLLRYVKLGK----PIIGIKSGRRSALFDVEPGQSKEMLLKLKNRDYKVEEYKLLE-----AKSK 103
                                   567788******************99....*************************************99998.....4442 PP

                                   .....EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESES CS
                    NAD_kinase 155 ediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPh 235
                                        +v ++ + n++ i +  ++t+    l  +++ ++    dg++vst  Gs a+  +a+  +++ +v+ai ++ ++ +
  gi|70605880|ref|YP_254750.1| 104 -----YV-KDIAFNDIAILFDLPETIYGSILFESNKIIF--EGDGILVSTTQGSWAWGYAANRIVVHRKVNAINVSFLNCL 176
                                   .....45.4556**************9977777777765..58************************************** PP

                                   SS----EEE-TT-EEEEEE-...SS--EEEEETTTE..EEEE-TT-EEEEEEESSEEEEEE CS
                    NAD_kinase 236 slssrpiVvssssklrirva...srseallaldGse..elelspgdevrvtasdkkfklir 291
                                   +   r ++++++++l+i+++   + +++ +++dG+    l+ +++d +++  s+kk+++ r
  gi|70605880|ref|YP_254750.1| 177 TPDIRALILPDNEELSIKLEdkgRPQSVRIVVDGETvgYLKTNEDDAITIKISEKKANILR 237
                                   ********************9888889999****97335788899***********99876 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     6e-07    0.0054      41      68 ..      10      49 ..       2      55 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-07
                                  TTHHHHHHHHHHH...........CC-.SEEEEEESHHHH CS
                      DAGK_cat 41 pgdakelakeake...........egv.dlivvaGGDGtv 68
                                  ++dake+a+++k+           +++ d+ivv+GGDGt+
  gi|70605880|ref|YP_254750.1| 10 TKDAKEIASNIKKiaidmgfkiveDETeDAIVVVGGDGTL 49
                                  5566666666666444444433334445***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1673.44
//
Query:       gi|70605881|ref|YP_254751.1|  [L=99]
Description: hypothetical protein Saci_0028 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.086   13.4   0.1       0.18   12.4   0.0    1.6  2  NPL       Nucleoplasmin-like domain


Domain annotation for each model (and alignments):
>> NPL  Nucleoplasmin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.36   6.5e+03      21      29 ..      13      21 ..       8      26 .. 0.79
   2 ?   12.4   0.0     1e-05      0.18      76     103 ..      27      54 ..      19      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.36
                                  EEEEEEE-T CS
                           NPL 21 ritmaaldp 29
                                  +it+aa++ 
  gi|70605881|ref|YP_254751.1| 13 KITKAAIEY 21
                                  699999975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1e-05
                                   E---EEEESS-EEEEEEES---EEEEEE CS
                           NPL  76 qpldltfsegeevffkvtGthtVhLtGn 103
                                   q+l++ ++++++v ++vtG++t+  tG 
  gi|70605881|ref|YP_254751.1|  27 QKLEIKLKPKQSVKIQVTGKTTILTTGW 54 
                                   89**********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 791.87
//
Query:       gi|70605882|ref|YP_254752.1|  [L=328]
Description: thioredoxin reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-30  104.1   0.8    1.1e-29  103.7   0.8    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.7e-24   86.0   1.2      1e-20   74.2   0.1    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.7e-14   54.1   0.2    3.3e-11   43.6   0.0    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.5e-09   35.9   0.0    1.1e-07   31.3   0.0    2.2  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    1.1e-06   28.8   0.2    4.1e-05   23.7   0.2    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.7e-06   25.9   0.4     0.0024   16.6   0.1    3.5  4  HI0933_like     HI0933-like protein
    0.00021   21.0   2.7       0.12   11.9   0.3    3.8  4  DAO             FAD dependent oxidoreductase
    0.00039   19.0   0.2     0.0018   16.8   0.0    1.9  2  FMO-like        Flavin-binding monooxygenase-like
    0.00042   20.7   0.2     0.0032   17.9   0.1    2.3  2  NAD_binding_7   Putative NAD(P)-binding
     0.0021   17.4   2.4       0.52    9.5   0.1    2.8  3  Thi4            Thi4 family
     0.0021   17.5   1.3      0.017   14.5   0.0    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.043   14.3   0.3       0.21   12.1   0.1    2.0  2  DUF4367         Domain of unknown function (DUF4367)
      0.056   13.4   0.2       0.16   12.0   0.0    1.8  1  DUF2103         Predicted metal-binding protein (DUF2103)
      0.071   12.5   0.1       0.26   10.6   0.1    1.9  2  Spermine_synth  Spermine/spermidine synthase domain
       0.27   10.2   3.2        3.6    6.6   0.0    3.0  2  FAD_binding_2   FAD binding domain
       0.28   11.2   1.7         28    4.7   0.1    3.3  4  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.8   9.4e-33   1.1e-29       4     290 ..       2     291 ..       1     295 [. 0.78

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 9.4e-33
                                   EEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHH...HCHHHHHHHHHHHHH........HHHHCHHHHCCCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...xxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                   Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlve..legtclnggcll...skallgvaedaeias........evvkklnqgielll 71 
                                   v+iGgGp Gl a  +++   ++ ++++  +    l+g+ +     k++  v++ + i++        e+ k ++ +i+   
  gi|70605882|ref|YP_254752.1|   2 VIIGGGPIGLYATFYAGLRDMRALVIDaqD---ELGGQLVTlypEKVVYDVGGYPGILAydlaqnliEQAKMFSPDIRINE 79 
                                   9*************************6442...333333333439999999999999999888877777777777777666 PP

                                   CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC...TCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl...gipGvaenvgklvrtldsaealklkllpkrivvvG 149
                                    +  ++  p++    + k  ++++  ++ +++++A G    ++   + +G+ e+  k+   +  + + k++   kri++vG
  gi|70605882|ref|YP_254752.1|  80 WADMIERTPDN-MWII-K--TDKGGAFKTKTILIAAGIGKIIPsrlNAKGEIEYENKG---VYYTVRRKRDFEGKRILIVG 153
                                   64455555555.3333.2..266779***********977777755777775555444...555556666667789***** PP

                                   -SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE......EEETTSC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx RF
                   Pyr_redox_2 150 gGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle......vvledge 224
                                   gG  +v+ A +l+ ++k vtl+++rd++  a++++++++ + a      +v++ ++ ke++g+g+k++        +++++
  gi|70605882|ref|YP_254752.1| 154 GGDSAVDWALTLSPVAKSVTLIHRRDQFR-AHERSVKQMFQVA------TVYTWHELKEVKGDGSKVTqavifdNRTKEEK 227
                                   ****************************5.6666666654444......678889999******95555533456667777 PP

                                   EEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 225 eidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaA 290
                                   ++d+d v++++G + +      k gl++ +++ i v+ +++tn  g+ya+GD+++++g+p+la  A
  gi|70605882|ref|YP_254752.1| 228 TLDVDAVIISIGHKGDLGNM-VKWGLNM-KGRSITVNGKMETNLAGVYAAGDIVEQEGTPKLALIA 291
                                   7***************8777.*******.********************************99877 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0002      0.22       1      40 [.       2      42 ..       2      45 .. 0.77
   2 !   74.2   0.1     9e-24     1e-20      90     305 .]      67     276 ..      57     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig.nsiyryp 40
                                  +IiG+GP+Gl a   +   ++ + l+++ + ++g + ++ yp
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLRDM-RALVIDAQdELGgQLVTLYP 42
                                  7**************999999.68999988655414445555 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 9e-24
                   Pyr_redox_3  90 vaksfelpiklfeeVesvkk.edegfevetske.tyeAkkviiAtGefd.kPnklnipGeek..lvkhyskvkefhkyagq 165
                                    ak f  +i+ +e    +++  d+  +++t+k+  +++k+++iA+G  + +P +ln +Ge +  ++ +y++v+  ++++g+
  gi|70605882|ref|YP_254752.1|  67 QAKMFSPDIRINEWADMIERtPDNMWIIKTDKGgAFKTKTILIAAGIGKiIPSRLNAKGEIEyeNKGVYYTVRRKRDFEGK 147
                                   5667777889999999999966999*******87***********997636********98644677************** PP

                   Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeyk 246
                                   +++++Gg++SavD Al l    ++Vt+++r+++ +++e ++++  +  +    +el +   +k        ++++  + ++
  gi|70605882|ref|YP_254752.1| 148 RILIVGGGDSAVDWALTLSPVAKSVTLIHRRDQFRAHERSVKQMFQVATVYTWHELKE---VKGDGS----KVTQ-AVIFD 220
                                   ************************************9988888777666666666532...343333....4443.24556 PP

                   Pyr_redox_3 247 vktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    +t+++k+++v d v++ +G k dl  + k ++  + +gr    + ++etn+ g++ aG
  gi|70605882|ref|YP_254752.1| 221 NRTKEEKTLDV-DAVIISIGHKGDLGNMVKWGL--NMKGRSITVNGKMETNLAGVYAAG 276
                                   66777666665.889999*******99985555..56899999999***********99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0035       3.9       2      35 ..       1      34 [.       1      44 [. 0.83
   2 !   43.6   0.0   2.9e-14   3.3e-11       1      78 [.     148     219 ..     148     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                                  EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkll 35
                                  +v++GgG igl +A+++a l+  +  v++++d+l 
  gi|70605882|ref|YP_254752.1|  1 MVIIGGGPIGL-YATFYAGLRdMRALVIDAQDELG 34
                                  69********9.78999998845788888888887 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 2.9e-14
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvkl 78 
                                   ++++vGgG++++++A +l+  +k+Vt+++r+d+++      a ++  +++ +   +v++ ++++e++g++++  ++v +
  gi|70605882|ref|YP_254752.1| 148 RILIVGGGDSAVDWALTLSPVAKSVTLIHRRDQFR------AHERSVKQMFQV-ATVYTWHELKEVKGDGSKvTQAVIF 219
                                   79*********************************......999999999888.8*****************6666655 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0     1e-10   1.1e-07     136     254 ..      95     205 ..      66     207 .. 0.82
   2 !    6.4   0.1    0.0039       4.3     295     340 ..     195     240 ..     185     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1e-10
                   K_oxygenase 136 eskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkk 216
                                   +    +++   +++++++++ G    iP+ l++  + e       y+ r++++ ++kri++vG+G Sa + +  l   +k 
  gi|70605882|ref|YP_254752.1|  95 K----TDKGGAFKTKTILIAAGIGKIIPSRLNAKGEIEYENKGVYYTVRRKRDFEGKRILIVGGGDSAVDWALTLSPVAK- 170
                                   3....477889*********************87754544555567778888*****************99888876655. PP

                   K_oxygenase 217 velklvtrsealeplddspfvneifsPeyvdyfyslpe 254
                                    +++l+ r++++++ + s  v+++f+ + v  +++l+e
  gi|70605882|ref|YP_254752.1| 171 -SVTLIHRRDQFRAHERS--VKQMFQVATVYTWHELKE 205
                                   .9*************999..679****99999999876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0039
                   K_oxygenase 295 lrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                   +++++ +e+++++ +g++ ++  + ++ ++ee+tl+vdav+++ G 
  gi|70605882|ref|YP_254752.1| 195 ATVYTWHELKEVKGDGSKVTQAVIFDNRTKEEKTLDVDAVIISIGH 240
                                   6788899*********99999999*****************99886 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   3.6e-08   4.1e-05       1      48 [.       3      50 ..       3      58 .. 0.91
   2 ?    2.6   0.0      0.14   1.6e+02       1      31 [.     151     181 ..     151     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.6e-08
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdyg 48
                                  I+G+G  Gl+a  ++  ++ + l+++++d lGG++ +   ++v++d+g
  gi|70605882|ref|YP_254752.1|  3 IIGGGPIGLYATFYAGLRDMRALVIDAQDELGGQLVTLYPEKVVYDVG 50
                                  9*********************************98877777777766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                   IvG+G s+   A +L+   ++v+l+ +rd++
  gi|70605882|ref|YP_254752.1| 151 IVGGGDSAVDWALTLSPVAKSVTLIHRRDQF 181
                                   9***************9999*****999987 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.2e-06    0.0024       4      38 ..       2      36 ..       1      39 [. 0.93
   2 ?    4.4   0.0     0.011        12     110     167 ..      59     117 ..      53     126 .. 0.85
   3 ?   -0.2   0.0      0.27   3.1e+02       2      34 ..     148     180 ..     147     183 .. 0.90
   4 ?   -2.5   0.1       1.4   1.5e+03     138     163 ..     214     239 ..     193     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                  EEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like  4 iviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                  ++iGgG+ Gl+a+  a+ r+ r l+++++++lg  
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLRDMRALVIDAQDELGGQ 36
                                  9****************************999965 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---.-SS- CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG.GlSi 167
                                   d+ + l++++k    ++r ++    +e++ d+   +kt+++++++++++++A G G+ i
  gi|70605882|ref|YP_254752.1|  59 DLAQNLIEQAKMFSPDIRINEWADMIERTPDNMWIIKTDKGGAFKTKTILIAAGiGKII 117
                                   666778888888888889998889999*************************9955555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.27
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                   +++++GgG + +  A++++   k+V+l+ + ++
  gi|70605882|ref|YP_254752.1| 148 RILIVGGGDSAVDWALTLSPVAKSVTLIHRRDQ 180
                                   689************************988766 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.4
                                   ETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 138 eedgkfrvktkseeeleadklvlAtG 163
                                   ++  +f  +tk+e++l  d++++++G
  gi|70605882|ref|YP_254752.1| 214 TQAVIFDNRTKEEKTLDVDAVIISIG 239
                                   34445566678899999999999988 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.3   0.00011      0.12       3      35 ..       2      35 ..       1      38 [. 0.93
   2 ?    1.5   0.0      0.15   1.7e+02     151     229 ..      63     140 ..      52     148 .. 0.55
   3 ?    1.8   0.0      0.13   1.5e+02       2      33 ..     149     182 ..     148     196 .. 0.81
   4 ?    2.7   0.0     0.067        75     168     232 ..     202     266 ..     190     287 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                  EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                  viiGGG iGl + +++  r    ++++++d++g g
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLRDmrALVIDAQDELG-G 35
                                  9***************998889********999.6 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                                   HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH.HTT..CTTTSEE.EEEEEEEEEE CS
                           DAO 151 alaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll.gll..keldlpi.spvrgqvlvl 227
                                    l ++a+    +i+ ++ +  +e++ +  w + +t +g  ++ +++ +aaG++ +++  +l  k     i +  +g ++++
  gi|70605882|ref|YP_254752.1|  63 NLIEQAKMFSPDIRINEWADMIERTPDNMWII-KTDKGGAFKTKTILIAAGIG-KIIpSRLnaK-G--EIeYENKGVYYTV 138
                                   55555555555555553333366655667888.44444443447799999977.2334333322.2..3337777777777 PP

                                   EE CS
                           DAO 228 kp 229
                                   ++
  gi|70605882|ref|YP_254752.1| 139 RR 140
                                   44 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.13
                                   EEEECTSHHHHHHHHHHH.HTT.EEEEESSSSTT CS
                           DAO   2 vviiGGGiiGlstAyeLa.rrg.Vtllekgdiag 33 
                                   ++i+GGG   +  A+ L+  ++ Vtl+ ++d++ 
  gi|70605882|ref|YP_254752.1| 149 ILIVGGGDSAVDWALTLSpVAKsVTLIHRRDQFR 182
                                   89*****9999999999643346******98875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.067
                                   CEEEEEEEETCEEEEE...EECT.EEE.EEEEEEEE--GGGHHHHHTTCTTTSEE.EEEEEEEEEEEECCT CS
                           DAO 168 evtgleeedgkvwgve...rttp.gen.daadavVnaaGawsdllgllkeldlpi.spvrgqvlvlkplse 232
                                   e ++++ ++ kv++     + t+ + + d +dav+++ G+  dl +++     +    ++g +++++ + e
  gi|70605882|ref|YP_254752.1| 202 ELKEVKGDGSKVTQAVifdNRTKeEKTlD-VDAVIISIGHKGDLGNMV-----KWgLNMKGRSITVNGKME 266
                                   44455333344444447886666455545.5*********98877444.....222678888888855444 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.6e-06    0.0018     178     216 ..     141     179 ..     122     199 .. 0.83
   2 ?   -0.3   0.1      0.24   2.7e+02     306     330 ..     214     240 ..     194     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                      FMO-like 178 pevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsG 216
                                      f+gkr+l++G G+s+ d a  ls  a+ v l  r+ 
  gi|70605882|ref|YP_254752.1| 141 KRDFEGKRILIVGGGDSAVDWALTLSPVAKSVTLIHRRD 179
                                   457*****************************9987765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                      FMO-like 306 tetsaifedgtvee...didvvifatGy 330
                                   t +++if++ t+ee   d+d+vi + G+
  gi|70605882|ref|YP_254752.1| 214 T-QAVIFDNRTKEEktlDVDAVIISIGH 240
                                   4.57999999999955568999998886 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.85   9.5e+02      10      20 ..       1      11 [.       1      73 [. 0.87
   2 !   17.9   0.1   2.9e-06    0.0032       4      46 ..     143     196 ..     142     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.85
                 NAD_binding_7 10 vlvvGgGevAa 20
                                  ++++GgG++++
  gi|70605882|ref|YP_254752.1|  1 MVIIGGGPIGL 11
                                  5899***9986 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.9e-06
                 NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapev.keele............e 46 
                                   d++gk++l+vGgG+ A   + +l +  + vt++  +  ++                
  gi|70605882|ref|YP_254752.1| 143 DFEGKRILIVGGGDSAVDWALTLSPVAKSVTLIHRRDqFR--AhersvkqmfqvaT 196
                                   799******************************9984322..22233443333332 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00047      0.52      21      55 ..       2      35 ..       1      39 [. 0.93
   2 ?   -1.4   0.0         1   1.1e+03      14      36 ..     143     165 ..     126     178 .. 0.68
   3 !    6.7   0.2    0.0034       3.8     155     225 ..     227     299 ..     193     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00047
                                  EEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 21 vivGaGssGLtaayylakkpdlkvailersvspGG 55
                                  vi+G+G+ GL a++y + + d++ ++++++  +GG
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLR-DMRALVIDAQDELGG 35
                                  9******************.********9999888 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                   HHTEEEEEEE--SHHHHHHHHHH CS
                          Thi4  14 kyaesDvvivGaGssGLtaayyl 36 
                                   ++    ++ivG+G s +  a +l
  gi|70605882|ref|YP_254752.1| 143 DFEGKRILIVGGGDSAVDWALTL 165
                                   44555677888888777666655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0034
                                   EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----E..CB-HHHHHHHHHHHECEEETTEEE-THHHHHH CS
                          Thi4 155 lvirakvvvdatGhdgeivavvvkkikleakiekvkgek..sldaekaedaivkktrevvpnlyvaGmevaev 225
                                   ++++  +v+ + Gh g+++++v   ++ + +  +v+g+    l    a  +iv++       l+++G + a++
  gi|70605882|ref|YP_254752.1| 227 KTLDVDAVIISIGHKGDLGNMVKWGLNMKGRSITVNGKMetNLAGVYAAGDIVEQEGTPKLALIATGFAQAAI 299
                                   5778889***************999999999889988541145556788899999888888999999998886 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.5e-05     0.017       3      39 ..       2      38 ..       1      74 [. 0.93
   2 ?   -0.7   0.0      0.61   6.8e+02       2      32 ..     149     179 ..     149     182 .. 0.92
   3 ?    0.4   0.1      0.28   3.1e+02      99     137 ..     194     232 ..     180     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                  FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                  v++GGgp G+ A   A  ++ + l+++ ++ lGG+l 
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLRDMRALVIDAQDELGGQLV 38
                                  8*********************************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.61
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                   +++vGGg + v  A++     ++v L+++r+
  gi|70605882|ref|YP_254752.1| 149 ILIVGGGDSAVDWALTLSPVAKSVTLIHRRD 179
                                   79************************99986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                  FAD_oxidored  99 eagvtvllntrlvevekegkriesvtveske.g.rktirAk 137
                                       tv+++++l+ev+ +g ++++ ++ +++ + +kt+  +
  gi|70605882|ref|YP_254752.1| 194 V--ATVYTWHELKEVKGDGSKVTQAVIFDNRtKeEKTLDVD 232
                                   4..689999*********98866555555554557776654 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.4   1.6e+03      81      95 ..     125     139 ..      87     149 .. 0.77
   2 ?   12.1   0.1   0.00018      0.21      47      99 ..     212     266 ..     182     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                       DUF4367  81 yvlvwedegvvytls 95 
                                     + +e++gv+yt++
  gi|70605882|ref|YP_254752.1| 125 GEIEYENKGVYYTVR 139
                                   457789999999875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                       DUF4367  47 eesqklsidtedaevekieingikatyyekedgeyvlvw..edegvvytlsgnis 99 
                                   +  q + +d+   e ++++++   + +++k+d ++++ w  +++g ++t++g+++
  gi|70605882|ref|YP_254752.1| 212 KVTQAVIFDNRTKEEKTLDVDAVIISIGHKGDLGNMVKWglNMKGRSITVNGKME 266
                                   4459999**9999***************************************997 PP

>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.16      18      70 ..      99     153 ..      90     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                       DUF2103  18 eGkkllekiakhpevkkviPgvikakg..sssggglrvkvtraderGnlrlllrd 70 
                                    G    ++i  + ++ k+iP++++akg  + +++g+  +v r+ +  + r+l+  
  gi|70605882|ref|YP_254752.1|  99 GGAFKTKTILIAAGIGKIIPSRLNAKGeiEYENKGVYYTVRRKRDFEGKRILIVG 153
                                   45555678888999*************77778999*****987665556666654 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.93     1e+03      44      68 ..      54      78 ..       2     106 .. 0.61
   2 ?   10.6   0.1   0.00024      0.26      18      57 ..     145     238 ..     136     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                                  EEEEEES-HHHHHHHHHHSHHHHTT CS
                Spermine_synth 44 kitlvdiDqkvidfskkflpslais 68
                                   i   d+ q+ i+  k+f p++ i+
  gi|70605882|ref|YP_254752.1| 54 GILAYDLAQNLIEQAKMFSPDIRIN 78
                                  4555677788888888888888877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00024
                                   ST-EEEEESSTT......................................................SHHHHHHTTSTT-SE CS
                Spermine_synth  18 npkevLiiGGgD......................................................Ggvlrevvkhntvek 44 
                                   + k++Li+GGgD                                                       +v+  v++ n  ++
  gi|70605882|ref|YP_254752.1| 145 EGKRILIVGGGDsavdwaltlspvaksvtlihrrdqfrahersvkqmfqvatvytwhelkevkgdgSKVTQAVIFDNRTKE 225
                                   789*********999999999999999999999999999999999999999999999999999886678888888888899 PP

                                   EEEEES-HHHHHH CS
                Spermine_synth  45 itlvdiDqkvidf 57 
                                       d+D  +i++
  gi|70605882|ref|YP_254752.1| 226 EKTLDVDAVIISI 238
                                   9999999988875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0032       3.6       3      39 ..       2      38 ..       1      39 [. 0.95
   2 ?    2.0   1.1      0.08        89     155     201 ..     192     240 ..     128     282 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0032
                                  EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  ++iG+G  GL A+  a  +  + +v++  +e gg+++
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYATFYAGLRDMRALVIDAQDELGGQLV 38
                                  9********************************9975 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.08
                                   T..EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE---- CS
                 FAD_binding_2 155 g..vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgG 201
                                       ++++ +e++e+  ++ +vt av+ + ++++e ++  +av++  g 
  gi|70605882|ref|YP_254752.1| 192 FqvATVYTWHELKEVKGDGSKVTQAVIFDNRTKEEKTLDVDAVIISIGH 240
                                   3445556666666665555566666666666666666666666665444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.086        97       1      13 [.       2      14 ..       2      38 .. 0.84
   2 ?    0.5   0.0      0.47   5.3e+02     120     154 ..      77     112 ..      57     114 .. 0.70
   3 ?   -2.6   0.0       4.4   4.9e+03       2      16 ..     151     165 ..     150     176 .. 0.79
   4 ?    4.7   0.1     0.025        28     123     155 ..     202     240 ..     168     241 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.086
                 NAD_binding_9  1 aivGaGprGlavl 13
                                  +i+G+Gp Gl+++
  gi|70605882|ref|YP_254752.1|  2 VIIGGGPIGLYAT 14
                                  7*********986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.47
                 NAD_binding_9 120 hraevvdleeradgqavll.adgaslaadaVvLAlG 154
                                   +++ +  +e+++d++++++ ++g  ++ + + +A G
  gi|70605882|ref|YP_254752.1|  77 INEWADMIERTPDNMWIIKtDKGGAFKTKTILIAAG 112
                                   455666789999998766526778999999999998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                 NAD_binding_9   2 ivGaGprGlavlerL 16 
                                   ivG+G +++  +  L
  gi|70605882|ref|YP_254752.1| 151 IVGGGDSAVDWALTL 165
                                   9****9998777666 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.025
                 NAD_binding_9 123 evvdleeradg......qavlladgaslaadaVvLAlGh 155
                                   e  +++ ++++      +  +++++++l++daV++ +Gh
  gi|70605882|ref|YP_254752.1| 202 ELKEVKGDGSKvtqaviFDNRTKEEKTLDVDAVIISIGH 240
                                   4445555444422111123344666789**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 2323.32
//
Query:       gi|70605883|ref|YP_254753.1|  [L=296]
Description: hypothetical protein Saci_0030 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-30  106.9   0.5    1.5e-30  106.4   0.5    1.2  1  Met_10           Met-10+ like-protein
    4.6e-07   30.5   0.0    8.5e-07   29.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.4e-06   28.0   0.1    2.2e-05   24.1   0.0    2.2  2  MTS              Methyltransferase small domain
    8.6e-06   26.3   0.0    1.9e-05   25.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    0.00062   19.2   0.0    0.00081   18.8   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0023   17.6   0.1      0.048   13.3   0.0    2.3  2  Cons_hypoth95    Conserved hypothetical protein 95
     0.0095   15.8   4.4      0.042   13.7   2.2    2.8  2  Trm5_N           tRNA methyltransferase 5 N-terminal domain
  ------ inclusion threshold ------
      0.023   15.0   0.1      0.059   13.7   0.1    1.7  1  POTRA_1          POTRA domain, FtsQ-type
      0.083   13.0   0.0        3.9    7.6   0.0    2.4  2  Sulf_coat_C      Sulfolobus virus coat protein C terminal
       0.13   12.1   0.1       0.39   10.5   0.1    1.7  2  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.5   8.6e-34   1.5e-30       2     193 ..      67     254 ..      66     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 8.6e-34
                                   EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                        Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                   ++ +iGd++++  + ++++  ++++++i++++ ++k+v+ +++ v+ge+R+ ++e   G+++t+ti kEng +f +D+ kv
  gi|70605883|ref|YP_254753.1|  67 SYYVIGDIALVTPKINIDK--ELLAKTIMETNpRIKSVFIRKK-VKGELRVNQIEFAGGENKTQTIYKENGLKFLVDINKV 144
                                   799*******998888876..9****************99875.6************************************ PP

                                   ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG CS
                        Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgre 162
                                   y ++  ++Er+++++ +e g++ vd+f G G  ai +a+  k   ++a dln e   +lke i+ Nk++  + +++ D++ 
  gi|70605883|ref|YP_254753.1| 145 YVNPSMSNERQKIVNEIECGKI-VDLFTGYGAIAIHLAR--KCGYIVAGDLNLEGLLLLKESINYNKLKGEIDVVNYDAKY 222
                                   ******************9985.6**************9..**************************************99 PP

                                   ---.TT-EEEEEE--TTTGGGGHHHHHHHEEE CS
                        Met_10 163 vir.eqladrvvmnlpksaieFldkvlaalkd 193
                                   +   ++++d  + + p+   +F ++++++ k+
  gi|70605883|ref|YP_254753.1| 223 LPFrDKTFDLGIADNPTIVSQFKEEICRVCKE 254
                                   87558899999999999999998888877765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.8e-10   8.5e-07       1      94 [.     166     253 ..     166     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.8e-10
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                   ++dl +G G ++++la+++  + +++ D++ e l   +e ++ ++l  ++++v+ da+ lpf d++fDl ++ +   ++  
  gi|70605883|ref|YP_254753.1| 166 IVDLFTGYGAIAIHLARKC--GYIVAGDLNLEGLLLLKESINYNKLkgEIDVVNYDAKYLPFRDKTFDLGIADNP-TIV-- 241
                                   79****************9..8*******************9999999*********************999433.333.. PP

                                   HHHHHHHHHHHHHEE CS
               Methyltransf_25  80 edlekalkeiarvLk 94 
                                       ++ +ei+rv+k
  gi|70605883|ref|YP_254753.1| 242 ---SQFKEEICRVCK 253
                                   ...355566666665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.1   1.8e+02      90     109 ..      38      55 ..      24      63 .. 0.81
   2 !   24.1   0.0   1.2e-08   2.2e-05      31     112 ..     162     245 ..     141     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                                   TTTSTTS-EEEEEE---STT CS
                           MTS  90 leeveekkfdlivsNPPfha 109
                                   +ee++   +d+i +NPP ++
  gi|70605883|ref|YP_254753.1|  38 YEEIS--GYDIIECNPPRKT 55 
                                   56666..89********665 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.2e-08
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-ST.TTTSTTS-EEE.EEE---S CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdv.leeveekkfdl.ivsNPPf 107
                                   + gk++Dl +G+G+++++la+++    +++ d + + l + ke ++ nkl+  ++vv+ d+ +  + +k fdl i  NP +
  gi|70605883|ref|YP_254753.1| 162 ECGKIVDLFTGYGAIAIHLARKCGY--IVAGDLNLEGLLLLKESINYNKLKgeIDVVNYDAkYLPFRDKTFDLgIADNPTI 240
                                   5689******************999..9***********************666666666535567799999867789988 PP

                                   TTTCH CS
                           MTS 108 hagka 112
                                    ++ +
  gi|70605883|ref|YP_254753.1| 241 VSQFK 245
                                   77755 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.1e-08   1.9e-05       5      69 ..     171     237 ..     167     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse 69 
                                   +G G++a +la++++ +v+ Dl+ e l l ke ++ ++l  ++++v  da+ lpf+d++fDl ++ +
  gi|70605883|ref|YP_254753.1| 171 TGYGAIAIHLARKCGYIVAGDLNLEGLLLLKESINYNKLkgEIDVVNYDAKYLPFRDKTFDLGIADN 237
                                   799**********************************99**9*******************988765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.5e-07   0.00081      40     119 ..     155     232 ..     110     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.5e-07
                                   HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEE CS
               Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDv 119
                                   +k+v++ +  k++D+ +G g +a++l++   + g +v  D+n + L   ++ ++ +  + +i+ ++ +a+ Lpf d++fD+
  gi|70605883|ref|YP_254753.1| 155 QKIVNEIECGKIVDLFTGYGAIAIHLAR---KCGYIVAGDLNLEGLLLLKESINYNKLKgEIDVVNYDAKYLPFRDKTFDL 232
                                   5778888889**************9976...56789******998888888887666656********************6 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.089   1.6e+02     104     159 ..      35      88 ..       6     103 .. 0.74
   2 !   13.3   0.0   2.7e-05     0.048      37     120 ..     158     236 ..     136     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.089
                                   HCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEEECCSSS- CS
                 Cons_hypoth95 104 llklakkkeefdivflDPPyakellieevlelleekkllkenalvvvetekekelp 159
                                   ++   ++ + +di+  +PP ++ +l +e+++ +++  ++ + alv+ + + +kel+
  gi|70605883|ref|YP_254753.1|  35 IPVY-EEISGYDIIECNPPRKTPKL-NEIINGVRSYYVIGDIALVTPKINIDKELL 88 
                                   5444.455668********999995.********9999999999987776666655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.7e-05
                                   CCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                 Cons_hypoth95  37 aaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                    +eie  +++Dlf G Ga+++  l R++  +v+ + + e + +lke ++  kl++e+++++ da+    +     + fd+ 
  gi|70605883|ref|YP_254753.1| 158 VNEIECGKIVDLFTGYGAIAIH-LARKCGYIVAGDLNLEGLLLLKESINYNKLKGEIDVVNYDAKYLPFRD----KTFDLG 233
                                   456888999************6.99***************************9999999988876543333....446655 PP

                                   EE- CS
                 Cons_hypoth95 118 flD 120
                                     D
  gi|70605883|ref|YP_254753.1| 234 IAD 236
                                   555 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.2   2.4e-05     0.042       1      47 []       3      45 ..       3      45 .. 0.94
   2 ?   -1.6   0.0       1.4   2.6e+03      14      30 ..      85     101 ..      83     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                  EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HHHH CS
                        Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepegye 47
                                  cikV+k e +kv+k        ++ +K+  + dy yIPv ee++gy+
  gi|70605883|ref|YP_254753.1|  3 CIKVHKDELNKVIKQI----HVNPFFKVYYSKDYAYIPVYEEISGYD 45
                                  9***********9988....5899********************996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                   HHHHHTT-B-TTS--EE CS
                        Trm5_N  14 kkLlekglLdrnyKIks 30 
                                   k+Ll+k ++  n +Iks
  gi|70605883|ref|YP_254753.1|  85 KELLAKTIMETNPRIKS 101
                                   67888888888888887 PP

>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.3e-05     0.059      29      65 ..      78     115 ..      70     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                                   T-GGGS-HHHHHHHHHH.-TTEEEEEEEEETTTEEEEE CS
                       POTRA_1  29 tslfsldleaieqrlek.lpwvksasVrrqwPntleit 65 
                                   t+ + +d+e +++++++ +p++ks+ +r++    l+++
  gi|70605883|ref|YP_254753.1|  78 TPKINIDKELLAKTIMEtNPRIKSVFIRKKVKGELRVN 115
                                   677899************************99998885 PP

>> Sulf_coat_C  Sulfolobus virus coat protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0022       3.9      35      50 ..      55      70 ..      49      78 .. 0.89
   2 ?    2.6   0.0     0.079   1.4e+02      15      40 ..     127     152 ..     116     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                   Sulf_coat_C 35 GpalvnminGlksyyi 50
                                   p l ++inG++syy+
  gi|70605883|ref|YP_254753.1| 55 TPKLNEIINGVRSYYV 70
                                  589999*********8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.079
                   Sulf_coat_C  15 raiyqGfGlkiaralnriGsGpalvn 40 
                                   ++iy+  Glk    +n++   p++ n
  gi|70605883|ref|YP_254753.1| 127 QTIYKENGLKFLVDINKVYVNPSMSN 152
                                   58***************999999877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   2.3e+03      75     126 ..      44      96 ..      35     134 .. 0.47
   2 ?   10.5   0.1   0.00022      0.39       6      90 ..     165     245 ..     163     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
               Methyltransf_31  75 fDlilsnevlnaladpdkileeiervlkpggi.lliedprllaelp.akveees 126
                                   +D+i +n +   ++ +++i++++ ++   g i l++  +++ +el+ + + e++
  gi|70605883|ref|YP_254753.1|  44 YDIIECN-PPRKTPKLNEIINGVRSYYVIGDIaLVTPKINIDKELLaKTIMETN 96 
                                   5666664.4445666666666666655433330222233355555543333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00022
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevln 85 
                                   +++Dl +G G++++ la++ g    +v  D + e + l +e    ++l+ ++ +   d+  l+  + d++fDl +++++  
  gi|70605883|ref|YP_254753.1| 165 KIVDLFTGYGAIAIHLARKCG---YIVAGDLNLEGLLLLKESINYNKLKgEIDVVNYDAKYLP--FRDKTFDLGIADNPTI 240
                                   689**************6654...5****************9999999999************..********77765543 PP

               Methyltransf_31  86 aladp 90 
                                      ++
  gi|70605883|ref|YP_254753.1| 241 VSQFK 245
                                   33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2269.90
//
Query:       gi|70605884|ref|YP_254754.1|  [L=160]
Description: hypothetical protein Saci_0031 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-51  173.9   0.8    1.8e-51  173.6   0.8    1.1  1  DUF371        Domain of unknown function (DUF371)
  ------ inclusion threshold ------
       0.06   13.5   0.0      0.083   13.0   0.0    1.2  1  SKI           Shikimate kinase
        0.1   12.5   0.2       0.22   11.4   0.2    1.6  1  MEF2_binding  MEF2 binding


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.6   0.8   3.1e-55   1.8e-51       1     130 [.       7     136 ..       7     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 3.1e-55
                                   EEEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE--TT-- CS
                        DUF371   1 ikarGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGspklt 81 
                                   ika+GH nv+a+h++Tleitkdd+ltprgdCIig+ +dk+a+d+see k+ lk++e++++++++v++l+d i+grGs+kl+
  gi|70605884|ref|YP_254754.1|   7 IKAKGHFNVRAKHRTTLEITKDDYLTPRGDCIIGILSDKGAKDISEETKKLLKRDETYVYLVIHVEGLTDIIRGRGSSKLK 87 
                                   79******************************************************************************* PP

                                   ---SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEE CS
                        DUF371  82 lenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltvel 130
                                   l++++++++RkS+y++++T+++++dk+a+d++re+v++L+++++ +v +
  gi|70605884|ref|YP_254754.1|  88 LTDPNRMIFRKSNYICEATVMINSDKSAKDINREIVRKLRTDQSNMVAI 136
                                   *****************************************98887776 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05     0.083      74     157 ..      50     126 ..      40     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                   GSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHH CS
                           SKI  74 lseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeil 154
                                   +see+ +llk+ ++ +yL +++e l + ++ + +   l+  ++     + ++ r+++y   a+v++++++++ + + +ei+
  gi|70605884|ref|YP_254754.1|  50 ISEETKKLLKRDETYVYLVIHVEGLTDIIRGRGS-SKLKLTDP----NRMIF-RKSNYICEATVMINSDKSA-KDINREIV 123
                                   6899**************************9999.44555555....34555.9999999889999988888.89999998 PP

                                   HHH CS
                           SKI 155 eal 157
                                   ++l
  gi|70605884|ref|YP_254754.1| 124 RKL 126
                                   876 PP

>> MEF2_binding  MEF2 binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.7e-05      0.22       2      18 ..      41      59 ..      40      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                  MEF2_binding  2 LLSPKGS..ISEETKQKLK 18
                                  +LS KG   ISEETK  LK
  gi|70605884|ref|YP_254754.1| 41 ILSDKGAkdISEETKKLLK 59
                                  589999666******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1177.27
//
Query:       gi|70605885|ref|YP_254755.1|  [L=87]
Description: hypothetical protein Saci_0032 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-14   53.6   1.8      2e-14   53.5   1.8    1.1  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   1.8   1.1e-18     2e-14       7      82 ..       4      78 ..       1      80 [. 0.88

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.1e-18
                     CRS1_YhbY  7 rrLrhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkcegppalnmkrmaeiLeektgglviqrsgtsivL 82
                                  ++  ++    +p ++iGk+G+++++v+ei+++lk++++vk+++   + +++k  a+++++k+++++i+++g +++L
  gi|70605885|ref|YP_254755.1|  4 KEIVKRVKASHPDIRIGKKGLNEGMVNEIKRRLKEHKVVKIRIG-ADVEDRKSFAKEVADKVNAKLIEVRGYTFIL 78
                                  5555666777899******************************6.44566***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 647.01
//
Query:       gi|70605886|ref|YP_254756.1|  [L=118]
Description: hypothetical protein Saci_0033 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-10   39.4   0.4    8.2e-10   38.8   0.4    1.3  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
       0.42   10.5   4.2       0.22   11.4   1.6    1.9  2  Ribosomal_L40e  Ribosomal L40e family


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.4   9.1e-14   8.2e-10      13      90 .]      24      89 ..      13      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 9.1e-14
                                  HHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                          Rpr2 13 laeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                  ++++  +l+r + k + + s+k + ++p ++kr++C+kC   l+ g+t + r++n            +v++ tCl Cg
  gi|70605886|ref|YP_254756.1| 24 TKNREYQLAREYTKLAITYSRKFRFKIPIEYKRSICRKCYVPLVIGLTERRRIKN------------KVVIRTCLLCG 89
                                  6788899**********************************************86............36789*****7 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.6   2.5e-05      0.22      14      27 ..      54      67 ..      51      77 .. 0.80
   2 ?   -1.5   0.0      0.27   2.4e+03      14      22 ..      77      85 ..      65      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.5e-05
                Ribosomal_L40e 14 cdKmiCrkCYArlp 27
                                   +++iCrkCY  l 
  gi|70605886|ref|YP_254756.1| 54 YKRSICRKCYVPLV 67
                                  5899******8775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.27
                Ribosomal_L40e 14 cdKmiCrkC 22
                                   +K + r C
  gi|70605886|ref|YP_254756.1| 77 KNKVVIRTC 85
                                  367788888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 898.76
//
Query:       gi|70605887|ref|YP_254757.1|  [L=219]
Description: ribosome biogenesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-44  151.1   0.1    3.2e-44  150.9   0.1    1.0  1  EMG1      EMG1/NEP1 methyltransferase


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9   0.1   1.8e-48   3.2e-44       2     191 ..       6     212 ..       5     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 1.8e-48
                                   EEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEEE CS
                          EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqvy 66 
                                   +L +++Lelv+++                k +++LL+ + h+k++k+l++++k++RpDIvH++Ll +l     ++ + + +
  gi|70605887|ref|YP_254757.1|   6 ILLDSALELVPREivshpavvknavrrgkKAENTLLDISLHYKAMKNLENANKRGRPDIVHFALLLFLTLE--EEIRGDLF 84 
                                   899*************************99***********************************999755..5555588* PP

                                   EEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC.SEEEEE-TTSEE-....... CS
                          EMG1  67 ihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlppgskiillsesaekklvdleef 147
                                   iht ++++I v+ q+R P++++rF+gLm+qLL +++i++++++ +L+++++ +++d+ ++ s +i+lses++k+  ++ ++
  gi|70605887|ref|YP_254757.1|  85 IHTIDGKIIFVDRQMRPPKNYNRFVGLMEQLLLEGKIPPKGDR-TLMEITNLKLKDLSRKYSSLIVLSESGRKV--NPADL 162
                                   ****************************************998.****************************44..45555 PP

                                   .........EEEE-SSSS....---HH...EEESSSS---HHHHHHHHHH CS
                          EMG1 148 v...vkpvvfvigamskgsvkidykee...eisisnypLsaavvcskilt 191
                                   +   +++v f +ga+++g+ + ++ke+    +sis++ L++++v++++  
  gi|70605887|ref|YP_254757.1| 163 CklmHENVLFGVGAFAHGDFSSEVKESasdFLSISKNVLETHQVICRVSI 212
                                   555499************666666663555****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1592.97
//
Query:       gi|70605888|ref|YP_254758.1|  [L=193]
Description: hypothetical protein Saci_0035 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.053   13.4   0.0    1.7  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
       0.19   11.7   0.1       0.19   11.7   0.1    2.0  3  RHH_1     Ribbon-helix-helix protein, copG family
        0.2   11.5   1.1         18    5.3   0.1    3.0  3  YppF      YppF-like protein


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.9e-06     0.053       2      41 ..       2      44 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-06
                         RHH_5  2 kRvnvtLPeelleeLeewAdeegRs...vSnlaafLvekalre 41
                                   R+n+   e+l +eLe++A++ g +   v nla + + +alre
  gi|70605888|ref|YP_254758.1|  2 GRINIAADEKLVKELEQEAKKKGYTmyaVTNLAIQAMVEALRE 44
                                  69999999***************9855579***********97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.1e-05      0.19       1      22 [.       3      24 ..       3      26 .. 0.93
   2 ?   -3.4   0.1       1.8   1.1e+04      10      16 ..      38      44 ..      36      44 .. 0.60
   3 ?   -3.1   0.0       1.5   8.9e+03      26      36 ..     156     166 ..     156     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                                  EEEEEEEHHHHHHHHHHHHHHT CS
                         RHH_1  1 rvsirldeellerLdelarrrg 22
                                  r++i  de+l+++L++ a++ g
  gi|70605888|ref|YP_254758.1|  3 RINIAADEKLVKELEQEAKKKG 24
                                  89****************9966 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                  HHHHHHH CS
                         RHH_1 10 llerLde 16
                                  ++e+L+e
  gi|70605888|ref|YP_254758.1| 38 MVEALRE 44
                                  6677665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHH CS
                         RHH_1  26 SelIReAlrey 36 
                                   S ++R  l+ey
  gi|70605888|ref|YP_254758.1| 156 SVIFRKILEEY 166
                                   67899999987 PP

>> YppF  YppF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.015        87      35      52 ..       2      19 ..       1      24 [. 0.88
   2 ?    5.3   0.1     0.003        18      37      51 ..      51      65 ..      48      67 .. 0.89
   3 ?   -0.4   0.0      0.18   1.1e+03      30      40 ..      70      80 ..      68      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.015
                          YppF 35 geisiaeYrnlvreLeaq 52
                                  g i+ia+  +lv+eLe+ 
  gi|70605888|ref|YP_254758.1|  2 GRINIAADEKLVKELEQE 19
                                  789999999*******96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.003
                          YppF 37 isiaeYrnlvreLea 51
                                  +s+ eY+++v++Le 
  gi|70605888|ref|YP_254758.1| 51 LSLIEYYKIVKDLEL 65
                                  7899*********96 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.18
                          YppF 30 klYlqgeisia 40
                                   +Yl++ i ia
  gi|70605888|ref|YP_254758.1| 70 TWYLENLIRIA 80
                                  59*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1209.72
//
Query:       gi|70605889|ref|YP_254759.1|  [L=48]
Description: hypothetical protein Saci_0036 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 315.71
//
Query:       gi|70605890|ref|YP_254760.1|  [L=351]
Description: hypothetical protein Saci_0037 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   11.5   0.1        1.8    7.6   0.1    2.2  2  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0    0.0063   1.1e+02      30      45 ..      33      48 ..      20     123 .. 0.88
   2 ?    7.6   0.1    0.0001       1.8     257     325 ..     267     336 ..     183     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.0063
                                  HHHHHHHHHHHHHTTT CS
                 Amidinotransf 30 aqkEHdafvqvLrekG 45
                                  +++E+++++ vL+e+G
  gi|70605890|ref|YP_254760.1| 33 VRREFENLISVLKENG 48
                                  799***********99 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0001
                                   -HHHHHHHHTT-SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHH.HHHHHHHTT-EEEEE-HTTTG CS
                 Amidinotransf 257 kereavaqaLkekgleiIeigeeeqwnfggNvLelkpgvvvaydrntv.tnekleeagievievpisele 325
                                   k ++ +++ L + +l+iI+++ +++++    +Le+++++ ++ d +++ ++e  +  g+e++++++++l 
  gi|70605890|ref|YP_254760.1| 267 KGKTSLREFLRKVNLKIIDVSVQDINKGLLSFLEVNDKRLLVKDLKDDgSHEIFKNLGYEIVKIQMDNLA 336
                                   4456777888888***********************999988877766256777888********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2295.23
//
Query:       gi|70605891|ref|YP_254761.1|  [L=288]
Description: hypothetical protein Saci_0038 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-64  216.3   0.0    6.1e-64  216.1   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.1   0.0   3.4e-68   6.1e-64       1     266 []       4     275 ..       4     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.1 bits;  conditional E-value: 3.4e-68
                                   EEEEEESSHHHHHHHHHHHTTSS..SGCC.EEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESS CS
                VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegle.veivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrv 80 
                                   +++G +++++dl++f++L+eg+v+ eg++   +++ +++++n+++l++++Dva+ S+a+y++i++dy++L ++++sa++ +
  gi|70605891|ref|YP_254761.1|   4 IKIGPLADSGDLYPFIPLIEGMVKPEGINlEFEIISTVQDTNEKVLKKDVDVAVPSAAMYPYIQNDYYILGEAVASAIDGI 84 
                                   689***********************8886667899********************************************* PP

                                   SSEEEEESS-CCC-SSS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTSSEEEEECCHHHTGGGG CS
                VitK2_biosynth  81 ygvllvskvpleelegelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlegedagLlIgesaltyaee 161
                                   +g+ ++s +p++ +e + ++r++++g++tT+++L++ll+ ++   k  +++  +dei+a  +eg d++++++e +++ya e
  gi|70605891|ref|YP_254761.1|  85 TGMPVISINPIKVDEIK-NSRLIVHGHNTTAFTLYKLLIGKYR--KLVIIKNVLDEIKALGKEG-DVLVAVHELKMMYALE 161
                                   *******8888887755.9***********************7..445555559****988888.**************** PP

                                   TT....EEEEEHHHHHHHHHS.S-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHH...HHCCSTTS.H..H CS
                VitK2_biosynth 162 gl....kkvlDLgelWeeltg.lPlvlglwvvrrdlaaeaakeleealreSveyalahldevaey...aaeraqemdd..e 232
                                   +l    ++++++++lW++l+g +P+++gl+v+++d+++e a++++ea+ +S++ya++h+de+++    ++++a+ ++   e
  gi|70605891|ref|YP_254761.1| 162 KLgvkvNRIISMWDLWKQLAGdTPMPMGLVVISKDIGRELAMKFKEAYVKSKHYAEKHIDEIIKIdakIMADAHKTNLdeE 242
                                   *99999**************66*****************************************98888555555554444* PP

                                   HHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHHC CS
                VitK2_biosynth 233 vlekhlelYvnelsydlgeegragleeflelaae 266
                                   +++k+++++++e+++ l +e ++gle+f+++++e
  gi|70605891|ref|YP_254761.1| 243 IIRKTIWADIQEYNVPL-PEVKRGLEKFYSITHE 275
                                   *****************.9**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2090.63
//
Query:       gi|70605892|ref|YP_254762.1|  [L=169]
Description: hypothetical protein Saci_0039 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-47  160.2   0.0      4e-47  160.0   0.0    1.0  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   0.0   2.3e-51     4e-47       1     162 [.       6     164 ..       6     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 2.3e-51
                                   S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET....TEEE CS
                    NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleeklldv 81 
                                   gSkN+vK+eAv+ea+ ++  ++ev +v+v+ +v+ qP+g ++t+ GA+nRa + l++++  d+g+G+EgGv+  e++l+++
  gi|70605892|ref|YP_254762.1|   6 GSKNKVKIEAVREAIMRIGLNAEVISVEVSPEVPLQPFG-HQTFIGARNRAFKSLKETD-SDIGIGIEGGVFSYENRLMAF 84 
                                   8**************************************.*****************77.********************* PP

                                   EEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHHHHHHTHHH CS
                    NTPase_I-T  82 awaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqavilAlipf 162
                                   a+++ vd++g +++++s sf+lP ++++++ +g+elge++d +f+ +++k++eGaig+lT ++++R++ly q vi Al+pf
  gi|70605892|ref|YP_254762.1|  85 AVVYAVDRNGLENFSFSTSFTLPTSITSLIFQGKELGEATDIVFSAKGSKENEGAIGYLT-KVINRKELYVQPVIAALYPF 164
                                   ************************************************************.79*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1106.90
//
Query:       gi|70605893|ref|YP_254763.1|  [L=193]
Description: hypothetical protein Saci_0040 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1304.85
//
Query:       gi|70605894|ref|YP_254764.1|  [L=112]
Description: thioredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-28   99.1   0.0    1.4e-28   98.9   0.0    1.0  1  Thioredoxin    Thioredoxin
    2.5e-09   37.6   0.1    2.2e-07   31.3   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
    3.6e-06   26.6   0.1    5.6e-06   25.9   0.1    1.3  1  OST3_OST6      OST3 / OST6 family, transporter family
    5.5e-06   26.6   0.1      0.073   13.4   0.0    2.2  2  Thioredoxin_8  Thioredoxin-like
      1e-05   25.3   0.2      0.079   12.7   0.0    2.1  2  Redoxin        Redoxin
    0.00012   21.9   0.0    0.00013   21.7   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    0.00016   21.6   0.0    0.00022   21.2   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
    0.00032   19.7   0.0    0.00033   19.7   0.0    1.1  1  Phosducin      Phosducin
    0.00033   20.6   0.0    0.00044   20.2   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE
    0.00044   20.2   0.1       0.27   11.1   0.1    2.1  2  AhpC-TSA       AhpC/TSA family
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.016   15.1   0.0    1.1  1  TraF           F plasmid transfer operon protein
      0.021   14.7   0.0      0.038   13.9   0.0    1.3  1  Thioredoxin_6  Thioredoxin-like domain
      0.023   13.7   0.0      0.023   13.7   0.0    1.1  1  Calsequestrin  Calsequestrin
      0.056   13.5   0.0      0.087   12.9   0.0    1.3  1  DUF2456        Protein of unknown function (DUF2456)
       0.16   11.7   0.4       0.79    9.5   0.0    1.9  2  DSBA           DSBA-like thioredoxin domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   1.1e-31   1.4e-28       2     102 ..       9     107 ..       8     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 1.1e-31
                                   EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                   Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                   v++l+++nF++ v++ +k  +v+F+A+wC++C  l+P +e+la+e++ ++ + kv++den+d+a+++++ ++Pt+++fkng
  gi|70605894|ref|YP_254764.1|   9 VIELNSSNFNSFVES-HKIAVVDFWAEWCAPCFVLSPIIEELASEYT-QIGFGKVNADENSDIANQFGIMSLPTVLIFKNG 87 
                                   7899***********.*******************************.********************************* PP

                                   EEEEEEESS-HHHHHHHHHH CS
                   Thioredoxin  83 kevkkyegarekeklaaflk 102
                                   k v++++ga ++++++++lk
  gi|70605894|ref|YP_254764.1|  88 KVVDTIVGAVPRDTIENKLK 107
                                   ****************9987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   1.8e-10   2.2e-07       4     108 ..      23     105 ..      21     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.8e-10
                 Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt. 83 
                                   ++k  +v+f++++C  C  l   ++el                  ++++i   k  +      +en++ a+++g+ ++Pt 
  gi|70605894|ref|YP_254764.1|  23 SHKIAVVDFWAEWCAPCFVLSPIIEEL----------------ASEYTQIGFGKVNA------DENSDIANQFGIMSLPTv 81 
                                   68999**************99999999................12344444444443......56789************8 PP

                 Thioredoxin_2  84 ivfldgkeivarlpGyvpaeeleal 108
                                   ++f +gk +v++++G+vp++ +e  
  gi|70605894|ref|YP_254764.1|  82 LIFKNGK-VVDTIVGAVPRDTIENK 105
                                   88*****.***********999876 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   4.7e-09   5.6e-06       9     105 ..       5      87 ..       2     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.7e-09
                     OST3_OST6   9 ksngviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFq 89 
                                   ks+ vi+ln++n++++++       vv + a+     C++C  + p +e +a+ +++          F+kv+ de++d+ +
  gi|70605894|ref|YP_254764.1|   5 KSSPVIELNSSNFNSFVE--SHKIAVVDFWAE----WCAPCFVLSPIIEELASEYTQI--------GFGKVNADENSDIAN 71 
                                   4569*************5..222334445554....7****************99988........5************** PP

                     OST3_OST6  90 klglnsaPhlllfppk 105
                                   ++g+ s+P +l+f+  
  gi|70605894|ref|YP_254764.1|  72 QFGIMSLPTVLIFKNG 87 
                                   *************974 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   6.1e-05     0.073       2      31 ..      25      54 ..      24      62 .. 0.78
   2 !   11.6   0.0   0.00023      0.27      66      94 ..      61      88 ..      56      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                                  SEEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                 Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklk 31
                                  k+ ++ f+a+wc+pc    p + el +++ 
  gi|70605894|ref|YP_254764.1| 25 KIAVVDFWAEWCAPCFVLSPIIEELASEYT 54
                                  7899***********777777777766665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00023
                                  E-TT-HHHHTT-S--TT-SEEEEE-TT-B CS
                 Thioredoxin_8 66 fddkkrnklkkkynvkaiPtlvvldknge 94
                                  ++ ++++ ++++++++++Pt+++  kng+
  gi|70605894|ref|YP_254764.1| 61 VNADENSDIANQFGIMSLPTVLIF-KNGK 88
                                  5778899*************6665.5554 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   6.6e-05     0.079      29      66 ..      25      61 ..      10      66 .. 0.84
   2 !   11.9   0.0   0.00011      0.13      90     145 ..      62     108 ..      59     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.6e-05
                                  SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEE CS
                       Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvv 66
                                  k +vv f++  +c +C    p +e+la ++ + g+ +v
  gi|70605894|ref|YP_254764.1| 25 KIAVVDFWAE-WCAPCFVLSPIIEELASEYTQIGFGKV 61
                                  448999****.*******************99999874 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                   EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.STTSHHH CS
                       Redoxin  90 lsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.eesnaea 145
                                    +D++++++ ++G  +         +  +++i ++gkvv ++v++ p++  e+++++
  gi|70605894|ref|YP_254764.1|  62 NADENSDIANQFG--I--------MSLPTVLIFKNGKVVDTIVGAVPRDtIENKLKS 108
                                   6799999999999..4........455578999*************97665555555 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.1e-07   0.00013      43     108 ..      26      88 ..      10     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                                   EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT- CS
                 Thioredoxin_9  43 lkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeeg 108
                                   + ++ + ++wC  + v  P+++++a++  +i +  +  den ++ +q+   g  + Pt++i++++ 
  gi|70605894|ref|YP_254764.1|  26 IAVVDFWAEWCAPCFVLSPIIEELASEYTQIGFGKVNADENSDIANQF---GIMSLPTVLIFKNGK 88 
                                   555557789***************************************...889****99997763 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.8e-07   0.00022       9      67 ..      35      99 ..      24     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-07
                                  SSTTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEEEC..TTCEE..EESS--- CS
                 Thioredoxin_3  9 gCakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPalvi..dgkvv..vsGkvps 67
                                   Ca C  l+ +++e+a e  +i +  +++ ++++i +++g+ms P+++i  +gkvv  ++G+vp 
  gi|70605894|ref|YP_254764.1| 35 WCAPCFVLSPIIEELASEYtQIGFGKVNADENSDIaNQFGIMSLPTVLIfkNGKVVdtIVGAVPR 99
                                  5******************77***999999999999***********66559**97557887775 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.7e-07   0.00033     150     215 ..      28      94 ..       5     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-07
                                   EEEEE-TTSTTHHHHHHHHHHHHHH-TTSEEEEEEHH.HH--TTSS-TTT-SEEEEEETTEEEEEET CS
                     Phosducin 150 vvhiyedgvkgtealnssliclaaeyptvkfckvkas.vigasdrfsrdvlpallvykagellsnfv 215
                                   vv  + +    +  l   +  la+ey  + f kv+a  +   +++f    lp++l++k g+++  +v
  gi|70605894|ref|YP_254764.1|  28 VVDFWAEWCAPCFVLSPIIEELASEYTQIGFGKVNADeNSDIANQFGIMSLPTVLIFKNGKVVDTIV 94 
                                   555666666666677777778**************96367889******************998877 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.7e-07   0.00044      49     101 ..      45      95 ..       4     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.7e-07
                                   HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEEES CS
                          HyaE  49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvlak 101
                                   ++ El  ++++     v a  ++++ +a++fg++  P++l++++g+++ ++ +
  gi|70605894|ref|YP_254764.1|  45 IIEELASEYTQIGFGKVNA--DENSDIANQFGIMSLPTVLIFKNGKVVDTIVG 95 
                                   7999*******99999999..67788********************9998865 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00023      0.27      23      58 ..      20      56 ..       5      61 .. 0.77
   2 !    7.5   0.0     0.003       3.6      87     122 ..      62      90 ..      55      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                  H..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCT CS
                      AhpC-TSA 23 y..kgkpvvlffypkdwcpvCttelpalaklyeefker 58
                                  +  + k++v+ f+++ wc +C    p +++l+ e+++ 
  gi|70605894|ref|YP_254764.1| 20 FveSHKIAVVDFWAE-WCAPCFVLSPIIEELASEYTQI 56
                                  4434599********.*****88888888887777665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                                   EE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
                      AhpC-TSA  87 lsDeegkvakaygvlkeekglalratfvidkegkir 122
                                    +De++++a+++g++       l+++ ++++ gk++
  gi|70605894|ref|YP_254764.1|  62 NADENSDIANQFGIM------SLPTVLIFKN-GKVV 90 
                                   58*************......9998888775.5554 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.3e-05     0.016     131     222 ..      26     105 ..      17     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                          TraF 131 ygLlfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpva 210
                                    + + F ++ c  c  ++pi++++a +y ++    V+ d++ +  ++n         ++g+ + P++++++    kvv   
  gi|70605894|ref|YP_254764.1|  26 IAVVDFWAEWCAPCFVLSPIIEELASEYtQIGFGKVNADENSD--IAN---------QFGIMSLPTVLIFKNG--KVVDTI 93 
                                   5666788999******************99***********88..999.........************9988..555555 PP

                          TraF 211 aGllsldeleer 222
                                   +G++  d++e++
  gi|70605894|ref|YP_254764.1|  94 VGAVPRDTIENK 105
                                   677777777766 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-05     0.038      77     160 ..       7      86 ..       3      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                   -SEEE-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEE CS
                 Thioredoxin_6  77 plvreltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivi 157
                                   ++v el++ n++ + e+  +++++ f  +       l+ +ie++a e +++i f  ++a+++ ++ +++g+   +lP++ i
  gi|70605894|ref|YP_254764.1|   7 SPVIELNSSNFNSFVESH-KIAVVDFWAEWCAPCFVLSPIIEELASE-YTQIGFGKVNADENSDIANQFGIM--SLPTVLI 83 
                                   5799*********99999.8899999976555555666667888855.566*********************..******9 PP

                                   EES CS
                 Thioredoxin_6 158 vds 160
                                   +++
  gi|70605894|ref|YP_254764.1|  84 FKN 86 
                                   983 PP

>> Calsequestrin  Calsequestrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.023      75     143 ..      40     106 ..       5     112 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                   HHHHHHHHHHHHHHCCCCTEEEEEEETTTTHHHHHCCT--STTEEEEEETTCEEE.E-S--SHHHHHHHH CS
                 Calsequestrin  75 felkelvlelvaqvledkdvgfvlvdakkeaklakklgldevdslyvlkgdevie.ydgefaadvlvefl 143
                                   f l  ++ el++   e  ++gf+ v+a+ ++ +a+++g+    ++ ++k  +v++   g    d++ + l
  gi|70605894|ref|YP_254764.1|  40 FVLSPIIEELAS---EYTQIGFGKVNADENSDIANQFGIMSLPTVLIFKNGKVVDtIVGAVPRDTIENKL 106
                                   666677777765...6789******************************999997246777777776655 PP

>> DUF2456  Protein of unknown function (DUF2456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-05     0.087      25      64 ..      15      54 ..       3      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                       DUF2456 25 wlvskairglllsviiflvlWpvtigilagigkklgsdyy 64
                                    +++++++  ++v+ f++ W++   +l +i ++l+s+y 
  gi|70605894|ref|YP_254764.1| 15 SNFNSFVESHKIAVVDFWAEWCAPCFVLSPIIEELASEYT 54
                                  55678899999*************************9996 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.3   3.6e+02       2      30 ..      29      56 ..      28      62 .. 0.81
   2 ?    9.5   0.0   0.00066      0.79     153     192 ..      63     106 ..      57     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.3
                                  EEEEEBTTBHHHHHHHHHHHHHHHHCCTE CS
                          DSBA  2 vdeffDvlCPyCylgkerleklaarspdv 30
                                  vd++ +  C  C++ ++ +e+la+ ++++
  gi|70605894|ref|YP_254764.1| 29 VDFWAEW-CAPCFVLSPIIEELASEYTQI 56
                                  7777774.888***********9999766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                          DSBA 153 vrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                    +en + a++ g+  +Ptv++  +gk   +++Ga + dt++++l
  gi|70605894|ref|YP_254764.1|  63 ADENSDIANQFGIMSLPTVLIfkNGKvvDTIVGAVPRDTIENKL 106
                                   579999****************99988999**********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 754.77
//
Query:       gi|70605895|ref|YP_254765.1|  [L=237]
Description: hypothetical protein Saci_0042 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-54  184.7   0.0    1.7e-54  184.5   0.0    1.0  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase
  ------ inclusion threshold ------
      0.095   12.6   0.0       0.36   10.8   0.0    1.9  3  DELLA           Transcriptional regulator DELLA protein N ter


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   0.0   1.9e-58   1.7e-54       4     204 ..      38     234 ..      35     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 1.9e-58
                                   --SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS-----S CS
                tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelkv 84 
                                   + d+i+++S+H+s+s++p+LTvH+ Gn++++ lGG+pe+l++a Prll+a++r+++k+       + tlEatHHGPt  kv
  gi|70605895|ref|YP_254765.1|  38 RGDAIVIFSKHQSSSKTPALTVHYPGNPSSQVLGGEPEKLGVAFPRLLTAIFREINKLD---IPVQKTLEATHHGPTYQKV 115
                                   6699*******************************************************...899**************** PP

                                   -EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--..----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--HH CS
                tRNA_deacylase  85 PslFvEiGSteeeWkdedaaeavaeavlellese..eekekvlvgiGGgHYaprftklvletevavGhilskyaleelkee 163
                                   P++FvE+GS+ ++W +e+ ++ ++e+ l+++++     +e+ +vg+GG HYap f+kl   ++v++Ghi+sky+l+++k++
  gi|70605895|ref|YP_254765.1| 116 PIVFVEVGSDPTYWGNEKIVKSLVESTLSAIDKVssLYCEEIIVGFGGPHYAPYFSKLG--EKVCIGHIISKYYLASIKDT 194
                                   *******************************999887799*****************98..59****************** PP

                                   HHHHHHHHH..T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                tRNA_deacylase 164 vikqaleks.egadvalidkkslkseqkeaieelleelgiev 204
                                   +i q++ek+ e++d++++d  s+  + ++++ ++l+++++++
  gi|70605895|ref|YP_254765.1| 195 TIIQTVEKCmENVDTVVFD--SVPLSVRDKVMHVLKDRNLKF 234
                                   *******************..9****************9985 PP

>> DELLA  Transcriptional regulator DELLA protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     4e-05      0.36       4      51 ..      17      66 ..      14      70 .. 0.92
   2 ?   -2.3   0.0      0.47   4.2e+03      54      66 ..     136     148 ..     124     151 .. 0.77
   3 ?   -3.3   0.0      0.99   8.9e+03      21      30 ..     202     211 ..     197     228 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
                         DELLA  4 LavlGYkvrssdladVAqkLEqLemvlgaaqedglsqlasdtvhy..nPS 51
                                  + +lGYk    d  +V  ++E+ + +++ +++++ s+    tvhy  nPS
  gi|70605895|ref|YP_254765.1| 17 IKKLGYKFEEIDEDEVDFRFERGDAIVIFSKHQSSSKTPALTVHYpgNPS 66
                                  5689*****************************************77787 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.47
                         DELLA  54 sswvesmLselna 66 
                                    s ves Ls +++
  gi|70605895|ref|YP_254765.1| 136 KSLVESTLSAIDK 148
                                   6789999998876 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.99
                         DELLA  21 qkLEqLemvl 30 
                                   + +E+ ++v+
  gi|70605895|ref|YP_254765.1| 202 KCMENVDTVV 211
                                   4455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1582.42
//
Query:       gi|70605896|ref|YP_254766.1|  [L=208]
Description: phosphoglycerate mutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-35  121.2   0.0      5e-35  121.0   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)
    0.00076   19.3   0.1     0.0021   17.8   0.0    1.6  2  AAA_24      AAA domain
      0.003   17.6   0.0      0.005   16.9   0.0    1.4  1  DUF1435     Protein of unknown function (DUF1435)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   8.3e-39     5e-35       1     184 [.       4     183 ..       4     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 8.3e-39
                                   EEEEE---BTTB--....TT.----B-HHHHHHHHHHHHHHTT...S---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGG CS
                    His_Phos_1   1 lyLvRHGetewnaegrlqgr.tdvpLteeGreqAealaerlag...epidaiysSplkRarqTaeliaealglpveldegL 77 
                                   ++++RH+++ +n++++l+   +  pLt+eG++qA+++ + +++    ++++iy+Sp+ Ra+qTa +++e l+l   +d++L
  gi|70605896|ref|YP_254766.1|   4 IVFIRHAQSNANTQQILSDDiNSYPLTDEGQRQAKRAVDEVRKiifLNFSKIYTSPILRAYQTASILSEGLNLVTVIDDRL 84 
                                   79**************666516679******************99999********************************* PP

                                   S----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHH CS
                    His_Phos_1  78 rEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarl 158
                                   +E+ +G++ ++ + ++ e +++  e++++ p+d      Es++++++R+ ++ e ++++ e+  v+vVsH  +i++l++++
  gi|70605896|ref|YP_254766.1|  85 KERRLGELNNK-KVNMIELMKKIAENRSNTPKD-----LESWDELTKRIINFTETILSTREN--VIVVSHHDPIKSLITYI 157
                                   ***********.999999999999999999996.....9********************986..***************** PP

                                   HT--GGGGGGB---TT-EEEEEE-SS CS
                    His_Phos_1 159 lglpleelrrleldnaslsvlefdeg 184
                                   l+l+      + l+nas+++l++ ++
  gi|70605896|ref|YP_254766.1| 158 LDLDEFSGLGVILPNASMTILKCFNQ 183
                                   *998888888888********87654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.34     2e+03     125     154 ..       4      33 ..       3      57 .. 0.62
   2 !   17.8   0.0   3.5e-07    0.0021      79     132 ..      94     148 ..      88     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.34
                        AAA_24 125 vifiahektrkdedpegeakytrlepklgk 154
                                   ++fi h++ + ++++  ++ +++++++ + 
  gi|70605896|ref|YP_254766.1|   4 IVFIRHAQSNANTQQILSDDINSYPLTDEG 33 
                                   788888888888777666555555544433 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.5e-07
                        AAA_24  79 elclaevirqnekaesk.edkgdgkGygelaeefrrllkklqelrknvifiahek 132
                                   + +++++  ++++ae++ +  +d+  ++el+++++++ +++ ++r+nvi+++h +
  gi|70605896|ref|YP_254766.1|  94 NKKVNMIELMKKIAENRsNTPKDLESWDELTKRIINFTETILSTRENVIVVSHHD 148
                                   56667777888888777566889999***************************86 PP

>> DUF1435  Protein of unknown function (DUF1435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.3e-07     0.005       8      48 ..     164     204 ..     158     208 .] 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.3e-07
                       DUF1435   8 sgWgvlLPavliallalaelsldqlrviivlallltvvmLy 48 
                                   sg gv+LP + +++l   + ++++ r++ + al lt  +L 
  gi|70605896|ref|YP_254766.1| 164 SGLGVILPNASMTILKCFNQNVKDCRLVSIGALTLTNEILM 204
                                   99**********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1468.40
//
Query:       gi|70605897|ref|YP_254767.1|  [L=164]
Description: hypothetical protein Saci_0044 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-26   92.0   0.8      5e-12   46.1   0.1    2.2  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.048   13.2   0.2      0.077   12.6   0.2    1.5  1  DisA_N    DisA bacterial checkpoint controller nucleotide-bin
      0.057   13.7   0.0         16    5.9   0.0    2.2  2  DUF1840   Domain of unknown function (DUF1840)
       0.18   10.8   0.0       0.18   10.8   0.0    1.1  1  TctC      Tripartite tricarboxylate transporter family recept


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   1.1e-15     5e-12       6      56 ..      10      60 ..       4      61 .. 0.92
   2 !   44.6   0.0   3.3e-15   1.5e-11       1      55 [.      68     122 ..      68     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.1e-15
                                  BSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  6 trdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                  ++ v+++++d++++ a+e+m+++++++l V+d+ gk+ Gi+t+rDl+ra++
  gi|70605897|ref|YP_254767.1| 10 NKTVHVIREDDSVRFAAEEMKKHNIGSLIVIDNRGKVSGIITERDLVRAIA 60
                                  67789***************9999****889******************97 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 3.3e-15
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+ +mtr+v+ v+++ +  +al+ m ++g+++lP++ +dg++ Gi++ rDl+r l
  gi|70605897|ref|YP_254767.1|  68 VSNYMTRNVIGVTENFDPNQALQVMLDHGFRHLPIIGKDGRVKGILSIRDLARTL 122
                                   7789************************************************987 PP

>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.7e-05     0.077       3      30 ..      25      52 ..      23     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                  HHHHHHHHT--EEEEEESSSCCCTTCCT CS
                        DisA_N  3 aveelskkkiGaliviereeelkeiiet 30
                                  a+ee++k++iG livi+++ +++ ii++
  gi|70605897|ref|YP_254767.1| 25 AAEEMKKHNIGSLIVIDNRGKVSGIITE 52
                                  899*****************98766633 PP

>> DUF1840  Domain of unknown function (DUF1840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0035        16      24      48 ..      37      61 ..      24      73 .. 0.85
   2 ?    5.8   0.0    0.0038        17      15      45 ..      91     121 ..      83     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0035
                       DUF1840 24 lkllgkslterGaitaedlpaaiak 48
                                  l +++++++++G+it+ dl  aia+
  gi|70605897|ref|YP_254767.1| 37 LIVIDNRGKVSGIITERDLVRAIAE 61
                                  56889999***************86 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0038
                       DUF1840  15 mfedvakqllkllgkslterGaitaedlpaa 45 
                                   ++ d++ + l ++gk++ ++G+++  dl   
  gi|70605897|ref|YP_254767.1|  91 VMLDHGFRHLPIIGKDGRVKGILSIRDLART 121
                                   56678888899*************9999765 PP

>> TctC  Tripartite tricarboxylate transporter family receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     4e-05      0.18       3      53 ..      23      74 ..      21     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
                          TctC  3 Rvvakklse.klgqpvvveNkagaGgiigtdlvakaapDGytillvatslav 53
                                  R +a+++++ ++g  +v++N+    gii+   + +a ++G     v++ +++
  gi|70605897|ref|YP_254767.1| 23 RFAAEEMKKhNIGSLIVIDNRGKVSGIITERDLVRAIAEGNINSTVSNYMTR 74
                                  88999998736**********************9**9999765555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1119.57
//
Query:       gi|70605898|ref|YP_254768.1|  [L=113]
Description: hypothetical protein Saci_0045 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 745.41
//
Query:       gi|70605899|ref|YP_254769.1|  [L=581]
Description: hypothetical protein Saci_0046 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0004   19.2  24.1     0.0004   19.2  24.1    3.4  3  AAA_13          AAA domain
     0.0012   18.8   0.7     0.0012   18.8   0.7    2.1  2  FdhE            Protein involved in formate dehydrogenase for
     0.0059   16.8   0.0      0.051   13.8   0.0    2.4  2  SbcCD_C         Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.013   14.9  21.0      0.076   12.4  19.6    2.8  2  SMC_N           RecF/RecN/SMC N terminal domain
      0.017   15.2  16.8      0.017   15.2  16.8    4.4  4  Mod_r           Modifier of rudimentary (Mod(r)) protein
      0.021   15.1  54.7       0.13   12.5   9.2    6.9  8  ABC_tran_CTD    ABC transporter C-terminal domain
      0.023   14.0  33.4       0.35   10.2  12.2    3.4  3  DUF4407         Domain of unknown function (DUF4407)
       0.05   13.6   0.2       0.13   12.4   0.2    1.7  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.086   12.2  59.9        1.2    8.4  23.0    4.1  3  GAS             Growth-arrest specific micro-tubule binding
       0.12   10.3  34.2      0.017   13.1  13.6    2.3  2  Prominin        Prominin
        0.3   11.1  34.4       0.46   10.5   6.3    4.8  4  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.32   11.3  47.8       0.82   10.0   2.9    5.1  4  BLOC1_2         Biogenesis of lysosome-related organelles com
       0.33   11.4  18.4        1.6    9.2   6.4    3.4  2  T3SSipB         Type III cell invasion protein SipB
       0.95    9.9  76.9    2.4e+03   -1.2   0.1    4.3  1  AAA_23          AAA domain
        1.1    8.1  62.4       0.66    8.8  25.0    3.4  3  Spc7            Spc7 kinetochore protein
        2.1    8.9  36.0         42    4.7   1.4    6.3  5  NPV_P10         Nucleopolyhedrovirus P10 protein
        2.2    7.8  57.6         19    4.7  25.0    3.6  2  Filament        Intermediate filament protein
        2.6    8.4  34.6        8.7    6.7   0.4    6.1  6  DUF948          Bacterial protein of unknown function (DUF948
        2.7    8.0  18.9        0.2   11.7   6.5    3.3  4  Serine_rich     Serine rich protein interaction domain
        5.2    6.2  45.1      0.073   12.3   5.7    4.3  4  TMPIT           TMPIT-like protein
        9.2    6.5  22.1          2    8.6   0.8    4.7  4  PI_PP_I         Phosphoinositide phosphatase insertion domain
        9.2    6.6  15.5         11    6.3   3.8    4.4  4  HTH_57          ThcOx helix turn helix domain


Domain annotation for each model (and alignments):
>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.57   4.6e+02      25      44 ..      30      49 ..      25      58 .. 0.84
   2 ?    4.2  22.8     0.017        14     336     453 ..     132     255 ..      73     266 .. 0.68
   3 !   19.2  24.1   4.9e-07    0.0004     305     511 ..     292     512 ..     249     531 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.57
                        AAA_13 25 NGaGKTtLSrllrslelget 44
                                  N  GKT+LS++l sl ++e+
  gi|70605899|ref|YP_254769.1| 30 NAYGKTSLSKALVSLLTNEI 49
                                  677*********99977765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.017
                        AAA_13 336 qLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk 415
                                   +Lk  ++ l  K +e+ ++ + l ++ ++i++i +++++in  i++  +  +n++ ++e+  k  ++ ++ e+++ +++  
  gi|70605899|ref|YP_254769.1| 132 ELKRRRESLIMKLEEVKSNYNnLLRTYDDIKKIANELENINLEIERLEKEKENVTVQTEQTIKITRQNRIVEIRERIQAKI 212
                                   355555566666666666555467777777777777777777777777777777777777777777777777777777777 PP

                        AAA_13 416 kkykklekaieklekelkeeeaelk.....kleeeikeLekql 453
                                   k++k+ e++i+kl++el+e + +++     kl +ei+e+ ++l
  gi|70605899|ref|YP_254769.1| 213 KELKEKETKIQKLTQELEELKGKANielkdKLTKEIQEIDREL 255
                                   7777777777777777776665432111114455555555554 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 4.9e-07
                        AAA_13 305 klkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekv 385
                                      + ++ +  + +fe  k+++++  ++ ++ +++++++  ++ + + k  e+e++++ i + +k+++++n   +  N+++
  gi|70605899|ref|YP_254769.1| 292 VCGSKVEPDLWKVRFETVKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERTEELIAQKSKALENLNIEASVINRTI 372
                                   223333335555566777777777777777777776666555555555555688888888888888888888888888888 PP

                        AAA_13 386 anleeekeeakkklelhl.veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                   + l+++ +++++ +e  + ve+ ++++d   k +++l k  ++le +l++     kk++eei+ L+kq+ d+++ +++in+
  gi|70605899|ref|YP_254769.1| 373 EALQKQLKSLEERVESTYeVESKDNDID---KRIEELRKRRSDLELQLQQLGIP-KKVAEEIESLKKQIDDINKQIDDINR 449
                                   8888888888888887552433333333...44444444555555444444332.33344444444444444444444443 PP

                        AAA_13 466 e..............LkafGlgeleLkfeee.kkgYrivrkg.gsqaa.etLSeGEktaIafl 511
                                   e              L++  l+ele+++++e ++ Yr+v+k+ g + + + LS+ Ekt  a++
  gi|70605899|ref|YP_254769.1| 450 EyirrltvvkeefetLSNSILKELEFNYTAEiDEKYRLVIKKdGVTMElRRLSTSEKTTLALI 512
                                   321111111111111222225566666666688888887665244444578888888888877 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.7   1.5e-06    0.0012      31     177 ..     151     296 ..     125     299 .. 0.67
   2 ?   -0.7   1.7       1.3   1.1e+03      21     112 ..     346     435 ..     314     474 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                   THHHHHHHHHHHHHHHHHHCS---..--HHHHH....HHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-SSHHHHHHH CS
                          FdhE  31 ladYLrflaalaeaqqkvlaaekplaldaeaie....raqehgmpplaakalerdeawqelLqallealkeelpealreal 107
                                    ++ Lr   ++ ++ +++     +++l+ e++e    + + ++ + ++ ++ +r  +++e +qa +++lke+ ++ ++++ 
  gi|70605899|ref|YP_254769.1| 151 YNNLLRTYDDIKKIANELE----NINLEIERLEkekeNVTVQTEQTIKITRQNRIVEIRERIQAKIKELKEKETK-IQKLT 226
                                   5555555555555555544....3333333333100123334555777777788889999999999999987655.99999 PP

                                   HHHHH--HHHHHHHHHHHHTT-GGGS-GGGHHHHHHHHHHHHHH.HHHT--TTSSS-.-TT-SS-TTT--- CS
                          FdhE 108 erlrkadaeelealadallageleavdaakavfvaaAlqvvwtk.laaaldakalaelaeekglCPvCgsa 177
                                   ++l++++ ++  +l d+l ++e+++ d +   +++   ++ +++ + +++ ++ +++ + ++++CPvCgs+
  gi|70605899|ref|YP_254769.1| 227 QELEELKGKANIELKDKL-TKEIQEIDRELDSLINRQNSIEIEQgVLTRILQDIQEAERIHSSMCPVCGSK 296
                                   999999988888887776.5678999999999999999998877345666666666667789*******96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                   HHHHH.HTT-TTHHHHHHHHHHHHHHHHHHCS---...--HHHHHHHHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-S CS
                          FdhE  21 RLrqL.aeehpladYLrflaalaeaqqkvlaaekpla.ldaeaieraqehgmpplaakalerdeawqelLqallealkeel 99 
                                   R ++L a++++  + L++ a++++   ++l+++ ++  ++ e++  + e++ + +++ ++e+ ++ ++ L+      +  +
  gi|70605899|ref|YP_254769.1| 346 RTEELiAQKSKALENLNIEASVINRTIEALQKQLKSLeERVESTY-EVESKDNDIDK-RIEELRKRRSDLELQ--LQQLGI 422
                                   444431333445555555555555555555322222212222222.11111112221.111112222222222..223344 PP

                                   SHHHHHHHHHHHH CS
                          FdhE 100 pealrealerlrk 112
                                   p++++e +e l+k
  gi|70605899|ref|YP_254769.1| 423 PKKVAEEIESLKK 435
                                   5555555555544 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.9   1.5e+03      45      77 ..      36      67 ..      32      76 .. 0.77
   2 !   13.8   0.0   6.3e-05     0.051      24      89 ..     492     549 ..     472     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                       SbcCD_C 45 alaaalaalyssaegrepalrlvfLDEAFsklD 77
                                   l  al++l++++  + ++l  vf DE+F ++ 
  gi|70605899|ref|YP_254769.1| 36 SLSKALVSLLTNEI-TAEDLLNVFSDEGFVEIE 67
                                  56678888888854.4788899999****8765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.3e-05
                       SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     +  + ++lS+ ek +la + ++ +l  +++          ++++DE F + D+++ +++l++l+
  gi|70605899|ref|YP_254769.1| 492 DGVTMELRRLSTSEKTTLALILILVGLKEYFKAP--------FFIIDESFMTFDQKRFSRVLKYLN 549
                                   346778899**********************994........9*******************9985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.45   3.7e+02      16      49 ..      13      46 ..       2      57 .. 0.84
   2 ?   12.4  19.6   9.3e-05     0.076      59     203 ..     345     565 ..     120     576 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.45
                                  EEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 16 ktvilpfsksftaivGpNGSGKsnlldAilFvLG 49
                                  ++ +l ++k++t+   pN  GK++l  A+  +L 
  gi|70605899|ref|YP_254769.1| 13 RELVLSLEKGITIYRAPNAYGKTSLSKALVSLLT 46
                                  67788999999*99**************976665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.3e-05
                                   HCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE.TTSEEEEEETTEEE-HHHHHHHHHCTT-STT CS
                                   xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  59 eklsdlihk...skekasvkkaeveitfdnedkklkiekeevsisrrvk.rkgeseykingkevtkkevsellesagiske 135
                                   e++++li +     e+ +++   ++ t++  +k+lk  +e+v+ + +v+ ++++ + +i++ + ++++++ +l++ gi k+
  gi|70605899|ref|YP_254769.1| 345 ERTEELIAQkskALENLNIEASVINRTIEALQKQLKSLEERVESTYEVEsKDNDIDKRIEELRKRRSDLELQLQQLGIPKK 425
                                   456677776321112223334444556677777777777776666665514555788888888888888888888888888 PP

                                   ..........................................................................CS-HHHH CS
                                   ..........................................................................xxxxxxx RF
                         SMC_N 136 ..........................................................................lLSgGek 142
                                                                                                              LS  ek
  gi|70605899|ref|YP_254769.1| 426 vaeeieslkkqiddinkqiddinreyirrltvvkeefetlsnsilkelefnytaeidekyrlvikkdgvtmelrRLSTSEK 506
                                   ********************************************************************************* PP

                                   HHHHHHHHHH.HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                   xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 143 tLvalaLlfA.iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                   t +al L++  ++++ +ap++++De  +  D+k+ ++v ++l+       +++i+ ++e+l+
  gi|70605899|ref|YP_254769.1| 507 TTLALILILVgLKEYFKAPFFIIDESFMTFDQKRFSRVLKYLNGIV---DYVIITKSDETLQ 565
                                   *****999877******************************98765...5555555555554 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.6    0.0014       1.1      10      86 ..     112     191 ..     109     193 .. 0.71
   2 ?   15.2  16.8   2.1e-05     0.017      10     114 ..     153     258 ..     148     269 .. 0.85
   3 ?   -0.6   9.6       1.5   1.3e+03      59     115 ..     333     389 ..     300     411 .. 0.42
   4 ?    3.4  11.9      0.09        74       8     119 ..     358     474 ..     354     486 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                         Mod_r  10 elledeeklealvktlpevkqlkeekeellaenesla...eknlslepeleelrselqekleelkelekefeekeqelde 86 
                                   ++++ +e +e ++++++++++lk ++e+l+ + e++    ++ l   +++++  +el++   e+++leke e+ + + ++
  gi|70605899|ref|YP_254769.1| 112 RIITGDENIEWFISSTSRIDELKRRRESLIMKLEEVKsnyNNLLRTYDDIKKIANELENINLEIERLEKEKENVTVQTEQ 191
                                   567788999*****9**************999888862222233334477777777777777777777777766666555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                         Mod_r  10 elledeeklealvktlpe....vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqelde 86 
                                    ll   + +++++++l++    +++l++eke++  ++e++ +  + +++++ e r+++q+k++elke e++ ++++qel+e
  gi|70605899|ref|YP_254769.1| 153 NLLRTYDDIKKIANELENinleIERLEKEKENVTVQTEQTIK--ITRQNRIVEIRERIQAKIKELKEKETKIQKLTQELEE 231
                                   567777777777776644455589999999999999999988..999********************************** PP

                         Mod_r  87 llqkfspdallarLqtavaeaeeeSeal 114
                                   l  k +   l+++L ++++e++ e ++l
  gi|70605899|ref|YP_254769.1| 232 LKGKANI-ELKDKLTKEIQEIDRELDSL 258
                                   9988876.59************998886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.5
                         Mod_r  59 lrselqekleelkelekefeekeqeldell.qkfspdallarLqtavaeaeeeSeala 115
                                    rsel +k +e+++ e+   +k + l++l  +    + + + Lq++++  ee  e+  
  gi|70605899|ref|YP_254769.1| 333 RRSELLQKVKEIERTEELIAQKSKALENLNiEASVINRTIEALQKQLKSLEERVES-T 389
                                   23333333333333333333333333333322222223333333333333333333.2 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.09
                         Mod_r   8 Lqelledeeklealvktl.pevkqlkeekeellaeneslaeknlsl.epeleelrselqeklee...lkelekefeekeqe 83 
                                   L+ l  + + +++ ++ l +++k+l+e+ e+   e es  ++ +++  +el++ rs+l+ +l++    k++ +e e ++++
  gi|70605899|ref|YP_254769.1| 358 LENLNIEASVINRTIEALqKQLKSLEERVEST-YEVESK-DNDIDKrIEELRKRRSDLELQLQQlgiPKKVAEEIESLKKQ 436
                                   66666666777777877767777777777777.444444.445555477**************956558888899999999 PP

                         Mod_r  84 ldellqkfspd..allarLqtavaeaeeeSealaeefl 119
                                    d++ ++ ++      +rL +  +e e +S+++ +e+ 
  gi|70605899|ref|YP_254769.1| 437 IDDINKQIDDInrEYIRRLTVVKEEFETLSNSILKELE 474
                                   98888777654335678999999999999999888775 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.4      0.02        16      14      61 ..     138     179 ..     125     179 .. 0.71
   2 ?   12.5   9.2   0.00016      0.13       7      62 ..     165     220 ..     162     221 .. 0.94
   3 ?    5.9   8.1     0.019        16       8      63 ..     213     261 ..     213     266 .. 0.70
   4 ?    3.3   3.3      0.12        97       9      65 ..     305     359 ..     303     363 .. 0.78
   5 ?    3.8   8.1     0.086        70      14      62 ..     341     391 ..     331     392 .. 0.76
   6 ?    7.5   6.2    0.0059       4.8      12      60 ..     367     413 ..     356     421 .. 0.74
   7 ?   10.5   4.1   0.00068      0.55      12      59 ..     398     446 ..     389     453 .. 0.90
   8 ?    7.1   0.9     0.008       6.6      13      56 ..     426     468 ..     424     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.02
                  ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeely 61 
                                   e+ I +LEe +++ ++ l         + ++++ +ele+++ e+e+l+
  gi|70605899|ref|YP_254769.1| 138 ESLIMKLEEVKSNYNNLLRTY------DDIKKIANELENINLEIERLE 179
                                   555666666666666666643......568999999999999999875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                  ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelye 62 
                                    +ele++  eIe+LE+e+++++ + ++    ++++++ e+ +++++  +eL+e++ 
  gi|70605899|ref|YP_254769.1| 165 ANELENINLEIERLEKEKENVTVQTEQTIKITRQNRIVEIRERIQAKIKELKEKET 220
                                   68************************99888**********************985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.019
                  ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                   +el+e e +I++L +e++el  + +        e   +l++e++e++ eL+ l  r
  gi|70605899|ref|YP_254769.1| 213 KELKEKETKIQKLTQELEELKGKANI-------ELKDKLTKEIQEIDRELDSLINR 261
                                   56777777777777777777776664.......44567888888888888887766 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.12
                  ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWe 65 
                                   ++e++ ++I++L+  + ++ + +++     +  +l +  +e+e+ e+ ++++    e
  gi|70605899|ref|YP_254769.1| 305 RFETVKKDINELDRTKNDIINNINKKK--MRRSELLQKVKEIERTEELIAQKSKALE 359
                                   68999*******************999..4455566666888888888888765555 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.086
                  ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelye 62 
                                    +eIe+ Ee ia+  ++l++ ++ +     ++ +l+++l+ le+  e  ye
  gi|70605899|ref|YP_254769.1| 341 VKEIERTEELIAQKSKALENLNIEASVinRTIEALQKQLKSLEERVESTYE 391
                                   578888888888888888888877666656699999999999999998887 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0059
                  ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                    + ++IeaL++++++le+++++   y+ + k +++ +++eel++    l
  gi|70605899|ref|YP_254769.1| 367 VINRTIEALQKQLKSLEERVEST--YEVESKDNDIDKRIEELRKRRSDL 413
                                   58899*************99954..677777778888877777665444 PP

  == domain 7  score: 10.5 bits;  conditional E-value: 0.00068
                  ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleaeLee 59 
                                    ++++Ie+L ++ ++le +l++ ++ ++  e++  l +++++++++++ 
  gi|70605899|ref|YP_254769.1| 398 DIDKRIEELRKRRSDLELQLQQLGIPKKVaEEIESLKKQIDDINKQIDD 446
                                   589***********************9999****************986 PP

  == domain 8  score: 7.1 bits;  conditional E-value: 0.008
                  ABC_tran_CTD  13 leaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleae 56 
                                   + +eIe+L ++i ++++++ d +    +  +l+ + +e e+l + 
  gi|70605899|ref|YP_254769.1| 426 VAEEIESLKKQIDDINKQIDDIN--REYiRRLTVVKEEFETLSNS 468
                                   56899************999887..88888999999998888765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  12.2   0.00043      0.35     117     247 ..     144     275 ..      78     292 .. 0.70
   2 ?    9.1   9.0   0.00093      0.76     113     234 ..     272     414 ..     266     421 .. 0.74
   3 ?    4.1   0.3      0.03        24     131     168 ..     426     463 ..     414     486 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                       DUF4407 117 qeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk....gtgttgvaGkgpaakekkaqld 193
                                    ee+k++ ++l  ++ ++++++ +++++++ ei+ +e++ ++ + + ++ ++ t+     +  ++++ k ++ kek+++++
  gi|70605899|ref|YP_254769.1| 144 LEEVKSNYNNLLRTY-DDIKKIANELENINLEIERLEKEKENVTVQTEQTIKITRqnriVEIRERIQAKIKELKEKETKIQ 223
                                   333333333333332.34444444444444444444444444444444444444444553333457788899999999999 PP

                       DUF4407 194 aaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarl 247
                                   ++++el+elk+k  + +  ++l +e++e+++e+++ ++++++ ++  +G+l+r+
  gi|70605899|ref|YP_254769.1| 224 KLTQELEELKGK-ANIELKDKLTKEIQEIDRELDSLINRQNS-IEIEQGVLTRI 275
                                   9999***99999.56666678999999999999999999987.77789999987 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00093
                       DUF4407 113 aeeqqeeakelkeqlaaa....................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.. 171
                                    ++  ++++e+ e++ ++                     +++++el++  +++ ++i++++ r+++l ++++ e++ t   
  gi|70605899|ref|YP_254769.1| 272 LTRILQDIQEA-ERIHSSmcpvcgskvepdlwkvrfetVKKDINELDRTKNDIINNINKKKMRRSELLQKVK-EIERTEel 350
                                   55555555555.333333456667777777777777778999****************************99.88877677 PP

                       DUF4407 172 .gtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasq 234
                                     ++ ++ +    +a   ++ ++a+q++l++l++++++t +++++++ +++  +e++k+r++ +
  gi|70605899|ref|YP_254769.1| 351 iAQKSKALENLNIEASVINRTIEALQKQLKSLEERVESTYEVESKDNDIDKRIEELRKRRSDLE 414
                                   7555566777777788899999999999999999999888888888888888888888887765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.03
                       DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeld 168
                                     +e++ l++qi++++++id  ++++ +  + +++e +
  gi|70605899|ref|YP_254769.1| 426 VAEEIESLKKQIDDINKQIDDINREYIRRLTVVKEEFE 463
                                   55677777777777777777777777777776666654 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00015      0.13       2      10 ..     290     298 ..     289     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                DNA_ligase_ZBD   2 CPvCGsavv 10 
                                   CPvCGs+v+
  gi|70605899|ref|YP_254769.1| 290 CPVCGSKVE 298
                                   ********8 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.8    0.0034       2.8      47     110 ..     128     191 ..     125     210 .. 0.90
   2 ?    8.4  23.0    0.0015       1.2      25     177 ..     209     366 ..     202     371 .. 0.84
   3 ?    5.2  24.8     0.014        11      23     160 ..     325     464 ..     321     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                           GAS  47 kelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                    +++e++ + ++l  +L++++ + ++L +   + +k  ++l+n++ ++++leke ++++++ e+
  gi|70605899|ref|YP_254769.1| 128 SRIDELKRRRESLIMKLEEVKSNYNNLLRTYDDIKKIANELENINLEIERLEKEKENVTVQTEQ 191
                                   67899999*************************************************9999886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                           GAS  25 LelIkslKeeieelkkkeernekelseisqenk.rlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                    ++Ik+lKe+ ++++k  ++ e +  +++ e k +l++++++ ++e++ L ++ +  e ++  l+++ + ++e+e+  +++
  gi|70605899|ref|YP_254769.1| 209 QAKIKELKEKETKIQKLTQELEELKGKANIELKdKLTKEIQEIDRELDSLINRQNSIEIEQGVLTRILQDIQEAERIHSSM 289
                                   579*********************99999996538****************************************998775 PP

                           GAS 105 ......kwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevlaaanldpa 177
                                         k+e +  + rfe+v+k+++el ++ ++ i+ + +k   ++ lL+ k+k+++ + E+  aq +++l++ n++++
  gi|70605899|ref|YP_254769.1| 290 cpvcgsKVEPDLWKVRFETVKKDINELDRTKNDIINNINKKKMRRSELLQ-KVKEIE-RTEELIAQKSKALENLNIEAS 366
                                   4444549********************************99888888885.677764.445556666666666666654 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.014
                           GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                   nN+++ k  ++e+ ++ k+ er+e ++++ s+  ++l+ +    ++ +e L+kqlk  e+  +s  +++++ ++ +k +++
  gi|70605899|ref|YP_254769.1| 325 NNINKKKMRRSELLQKVKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQLKSLEERVESTYEVESKDNDIDKRIEE 405
                                   89******************************************************************************* PP

                           GAS 104 lkwehevleqrfekvek..erdelykkfeaaiqevqqktglknllLekklkalqeelEk 160
                                   l+     le +++++    +  e  ++ ++ i+++ ++++  n    ++l+ ++ee E 
  gi|70605899|ref|YP_254769.1| 406 LRKRRSDLELQLQQLGIpkKVAEEIESLKKQIDDINKQIDDINREYIRRLTVVKEEFET 464
                                   *************9875114455556788889999999999999999999999998886 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  12.6     0.026        21     623     730 ..     151     262 ..     126     282 .. 0.71
   2 ?   13.1  13.6   2.1e-05     0.017     204     351 ..     306     460 ..     300     511 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.026
                      Prominin 623 kvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlp......lessvkklkksvkkldeensdlqesikkl 697
                                     nl  + ++++++anel+n   nl+ +  ++ ++  ++q+e++++      + ++ + ++ ++k+l+e+++++q+ +++l
  gi|70605899|ref|YP_254769.1| 151 YNNLLRTYDDIKKIANELENI--NLEIERLEKEKENVTVQTEQTIKitrqnrIVEIRERIQAKIKELKEKETKIQKLTQEL 229
                                   457888888899999999887..4443333333333333333333311111166667788999999999999999999999 PP

                      Prominin 698 laaveraenflkkngseiinneskklldrileq 730
                                    +   +a+ +lk++ ++ i++  ++l + i+ q
  gi|70605899|ref|YP_254769.1| 230 EELKGKANIELKDKLTKEIQEIDRELDSLINRQ 262
                                   999999999999999999999999999988876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.1e-05
                      Prominin 204 yeelekhvsddLddagkhlgldladt..lesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrd 282
                                   +e+++ + +++Ld +++ ++++++++   +s++l++++e+er  e + + +++Le++n   + +  + + L++ l++  ++
  gi|70605899|ref|YP_254769.1| 306 FETVK-KDINELDRTKNDIINNINKKkmRRSELLQKVKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQLKSLEER 385
                                   77887.66799************9862258999************************************************ PP

                      Prominin 283 lnqalsnlCqseeCskilssleiekldtskcldql...pnvdevlealeevle...tnlssivkeglarlneipe 351
                                   ++++ + + ++++ +k  ++l++ + d++ +l+ql   ++v e++e+l++ ++   ++++ i +e + rl  ++e
  gi|70605899|ref|YP_254769.1| 386 VESTYEVESKDNDIDKRIEELRKRRSDLELQLQQLgipKKVAEEIESLKKQIDdinKQIDDINREYIRRLTVVKE 460
                                   *******99999****99***9999*******9995544445555554444320002233333333333333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.4     0.034        27      47      99 ..     130     180 ..     118     188 .. 0.67
   2 ?    6.4   8.3     0.011       8.7      30     101 ..     185     262 ..     180     285 .. 0.64
   3 ?    1.4   6.9      0.36   2.9e+02      32     100 ..     313     385 ..     262     389 .. 0.86
   4 ?   10.5   6.3   0.00057      0.46      25     105 ..     358     448 ..     351     469 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.034
                  Baculo_PEP_C  47 LnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                   +++l+ + +sl+ +l+ +++++ +nL ++   ++ ++ neL+n+n ++  L  
  gi|70605899|ref|YP_254769.1| 130 IDELKRRRESLIMKLE-EVKSNYNNLLRTYDDIK-KIANELENINLEIERLEK 180
                                   4555555555555444.46666666666666666.899999999998888765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                  Baculo_PEP_C  30 vqilaqlatlld.aietqLnalsedlksllaeldt......rldtlltnLtdaln.alqdtlrneLtnlnsiltnLlssv 101
                                   v++  q +++++ + ++++ ++ e++++ ++el++      +l++ l++L+ + n +l+d+l++e++ ++ +l +L +  
  gi|70605899|ref|YP_254769.1| 185 VTV--QTEQTIKiTRQNRIVEIRERIQAKIKELKEketkiqKLTQELEELKGKANiELKDKLTKEIQEIDRELDSLINRQ 262
                                   444..444443315689999999999999999998666444444444444444333455*************99997643 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.36
                  Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldt..rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                   i ++l +++++i +++n+ + + ++ll+++++  r ++l+++ ++al +l+     ++  +++l+++l +L   
  gi|70605899|ref|YP_254769.1| 313 I-NELDRTKNDIINNINKKKMRRSELLQKVKEieRTEELIAQKSKALENLNieaSVINRTIEALQKQLKSLEER 385
                                   5.788889999999999988888999999998888999999999999999998888888899999999888765 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00057
                  Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldt..........rldtlltnLtdalnalq..dtlrneLtnlnsi 93 
                                   + ++n++  + ++++++a+++qL++l+e+++s   e+++          +l +  + L+ +l++l   +++ +e+++l+++
  gi|70605899|ref|YP_254769.1| 358 LENLNIEA-SVINRTIEALQKQLKSLEERVESTY-EVESkdndidkrieELRKRRSDLELQLQQLGipKKVAEEIESLKKQ 436
                                   44445544.568899999*******999999954.4555567777766666666777777777777999************ PP

                  Baculo_PEP_C  94 ltnLlssvtNin 105
                                   + +++ ++  in
  gi|70605899|ref|YP_254769.1| 437 IDDINKQIDDIN 448
                                   ***999999988 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.8    0.0012      0.99      32      85 ..     126     179 ..     124     185 .. 0.91
   2 ?    4.4   9.1     0.056        46      11      77 ..     187     258 ..     181     266 .. 0.73
   3 ?    3.8   9.5     0.085        69      23      95 ..     314     386 ..     303     388 .. 0.53
   4 ?   10.0   2.9     0.001      0.82      33      77 ..     400     447 ..     388     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                       BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                   +++++++lk++ +sl  kle++++ y++l    + i++i ++++ +   +++L+
  gi|70605899|ref|YP_254769.1| 126 STSRIDELKRRRESLIMKLEEVKSNYNNLLRTYDDIKKIANELENINLEIERLE 179
                                   5789999***********************************999998888887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.056
                       BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkd...vaaslekkleklnekye.elqpyl.qqidqiekqvteL 77 
                                   ++ e ++  +  + + ++ e+ ++k+k+lk+   ++++l+++le+l+ k + el+ +l ++i++i++++++L
  gi|70605899|ref|YP_254769.1| 187 VQTEQTIKITRQNRIVEIRERIQAKIKELKEketKIQKLTQELEELKGKANiELKDKLtKEIQEIDRELDSL 258
                                   556666666666777777777777777776522268888999999999998888766527899999999988 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.085
                       BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   + L +  +  +++++k k + ++l +k++++++++e ++++ + +++++ + + +  ++++L +  k+LE+++
  gi|70605899|ref|YP_254769.1| 314 NELDRTKNDIINNINKKKMRRSELLQKVKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQLKSLEERV 386
                                   5555555555555555555555555555555555555555555555555555555555555555555555554 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.001
                       BLOC1_2  33 sekykklkdvaaslekklekl...nekyeelqpylqqidqiekqvteL 77 
                                    +++++l+++ ++le +l++l   ++  ee++++++qid+i+kq++++
  gi|70605899|ref|YP_254769.1| 400 DKRIEELRKRRSDLELQLQQLgipKKVAEEIESLKKQIDDINKQIDDI 447
                                   57889999999999999999966667888****************986 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   4.1     0.099        81      74     141 ..     149     216 ..     118     283 .. 0.50
   2 ?    9.2   6.4    0.0019       1.6      43     151 ..     333     444 ..     319     448 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.099
                                   HHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       T3SSipB  74 saadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqadealqKkldaasklsekakake 141
                                   s+++++ +  d+++k  +eL+  + e  +le++++ ++ + + + +    ++ +++ ++++ k k+++
  gi|70605899|ref|YP_254769.1| 149 SNYNNLLRTYDDIKKIANELENINLEIERLEKEKENVTVQTEQTIKITRQNRIVEIRERIQAKIKELK 216
                                   55555555555555544444444444444444444444333333222223333333333333332222 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                                   ---STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHHHH.H CS
                       T3SSipB  43 klSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqade.a 122
                                   + S+ lq  ++e +   + + ++ +++++++ +a   ++ +++ qk+lk+L+       ++e + +   ++ + l + +  
  gi|70605899|ref|YP_254769.1| 333 RRSELLQ-KVKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQLKSLEERVESTYEVESKDNDIDKRIEELRKRRsD 412
                                   4555555.4688999999999999999999999999999999999999999555555556666666666554444443312 PP

                                   H...HHHHHHHHHHHHHHHHHHHHHHTXXXXX CS
                       T3SSipB 123 l...qKkldaasklsekakakekevDdisakv 151
                                   l     +l + +k++e+  +++k++Ddi  ++
  gi|70605899|ref|YP_254769.1| 413 LelqLQQLGIPKKVAEEIESLKKQIDDINKQI 444
                                   33334678999999999999999999998887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         3   2.4e+03     103     115 ..     480     492 ..     444     573 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3
                        AAA_23 103 ttkkaklelleid 115
                                   +++++ +  +++d
  gi|70605899|ref|YP_254769.1| 480 EIDEKYRLVIKKD 492
                                   1222222222222 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  25.0   0.00081      0.66     141     258 ..     137     256 ..     126     269 .. 0.78
   2 ?    4.1  19.4     0.022        18     144     248 ..     309     415 ..     300     421 .. 0.36
   3 ?    5.4   8.1    0.0089       7.3     158     265 ..     392     496 ..     389     508 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00081
                          Spc7 141 kegleenlegleedkelLekqeeeldellpeleeeka...eleeeleklqeaaeelesid.keeLeelreelaelkaeiee 217
                                   +e+l  +le++++ +++L +  + ++++ +ele+      +le+e e+   + e+  +i+ ++++ e+re++++  +e++e
  gi|70605899|ref|YP_254769.1| 137 RESLIMKLEEVKSNYNNLLRTYDDIKKIANELENINLeieRLEKEKENVTVQTEQTIKITrQNRIVEIRERIQAKIKELKE 217
                                   67889999999999999999999999999999887661114555555555455555556669******************* PP

                          Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                   k++++++l+++leel+ k     e k++l +ei+e +r l+
  gi|70605899|ref|YP_254769.1| 218 KETKIQKLTQELEELKGKA--NIELKDKLTKEIQEIDRELD 256
                                   ***************9987..56888888899888777654 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.022
                          Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkel 222
                                   +++ +++l++ k+ + ++ ++ +    el ++ +e+e++ e + ++++ le+  i+   ++ + e+l+++ + +ee+ + +
  gi|70605899|ref|YP_254769.1| 309 VKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERTEELIAQKSKALENlnIEASVINRTIEALQKQLKSLEERVEST 389
                                   223333333333333333333333333333333333333333333333333322223333333333333333333333344 PP

                          Spc7 223 aelqeqleeleekieelkeqkselee 248
                                    e++++ ++++++ieel++++s+le 
  gi|70605899|ref|YP_254769.1| 390 YEVESKDNDIDKRIEELRKRRSDLEL 415
                                   44444444444444444444444444 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0089
                          Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael....qeqleelee 234
                                   +e++ + +d+  +el++++++le +l++l   +        ee+e+l++++++++++i+  ++e+ ++    +e+ e+l++
  gi|70605899|ref|YP_254769.1| 392 VESKDNDIDKRIEELRKRRSDLELQLQQLGIPK-----KVAEEIESLKKQIDDINKQIDDINREYIRRltvvKEEFETLSN 467
                                   456666677777777777777777777776533.....3478999999999999999998887755540000555555555 PP

                          Spc7 235 kieelkeqkseleeeiaeaervleeckgwse 265
                                   +i  lke   ++ +ei e+ r++ ++ g++ 
  gi|70605899|ref|YP_254769.1| 468 SI--LKELEFNYTAEIDEKYRLVIKKDGVTM 496
                                   55..667777788999999888887777664 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.4     0.052        42       4      38 ..     152     186 ..     127     206 .. 0.62
   2 ?    4.7   4.0     0.052        42       9      48 ..     208     245 ..     198     266 .. 0.44
   3 ?    3.1   0.0      0.17   1.4e+02       3      16 ..     269     282 ..     267     292 .. 0.89
   4 ?    4.0   5.1     0.088        72      12      61 ..     340     389 ..     302     401 .. 0.77
   5 ?    2.9   6.9      0.18   1.5e+02      39      39 ..     425     425 ..     365     481 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.052
                       NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpdvt 38 
                                   n Ll   +dik++ + ++ ++ ++++++++ ++vt
  gi|70605899|ref|YP_254769.1| 152 NNLLRTYDDIKKIANELENINLEIERLEKEKENVT 186
                                   33444455555555555555555555555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.052
                       NPV_P10   9 Iradikavd...dkVdalqqqvddvqenlpdvtelnekLdaqs 48 
                                   I a ik+++   +k++ l q++++++ + +   el++kL   +
  gi|70605899|ref|YP_254769.1| 208 IQAKIKELKekeTKIQKLTQELEELKGKANI--ELKDKL---T 245
                                   3344444430003333333444444333222..233332...2 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.17
                       NPV_P10   3 qniLlvIradikav 16 
                                   q +L+ I++di++ 
  gi|70605899|ref|YP_254769.1| 269 QGVLTRILQDIQEA 282
                                   789********985 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.088
                       NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                    +k+++   + + q+ + +++   + + +n  ++a+++qL++le+ ve+ 
  gi|70605899|ref|YP_254769.1| 340 KVKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQLKSLEERVEST 389
                                   44444444444444445554433455889999999999999999999865 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.18
                       NPV_P10  39 e 39 
                                   +
  gi|70605899|ref|YP_254769.1| 425 K 425
                                   2 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9  40.8      0.33   2.7e+02      38     279 ..     137     387 ..     129     389 .. 0.78
   2 ?    4.7  25.0     0.024        19      53     200 ..     341     484 ..     313     500 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.33
                                   XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Filament  38 eekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatla 118
                                   +e    + +++k+ y++ l+   + ++++++e ++++le+++l++e e++  +  +e++ + +  + ++++r  ++++  +
  gi|70605899|ref|YP_254769.1| 137 RESLIMKLEEVKSNYNNLLRT-YDDIKKIANELENINLEIERLEKEKENVTVQ--TEQTIKITRQNRIVEIRERIQAKIKE 214
                                   444455566677777777665.57899****************9999998765..56667778899*************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXX...XXXXXXXXX CS
                      Filament 119 rvdLekkvesLkeelaflkkvheeEvke.lqkqvseqvlvevdaarkld.........Lteilkeiraq...yeelaeknr 186
                                     + e+k+++L++el+ lk   + E+k+ l+k++ +++  e+d+  +           Lt+il++i++    + ++     
  gi|70605899|ref|YP_254769.1| 215 LKEKETKIQKLTQELEELKGKANIELKDkLTKEI-QEIDRELDSLINRQnsieieqgvLTRILQDIQEAeriHSSMCPVCG 294
                                   *********************9999986255556.55555555532222234477**********9875344777777777 PP

                                   XXXX.XXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 187 eeae.ewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklse 266
                                   +++e + +k ++e++++ +++ + + +   ++i++ +++  +l  ++++++ +++ + ++ + l e+l+ e++ +++++++
  gi|70605899|ref|YP_254769.1| 295 SKVEpDLWKVRFETVKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERTEELIAQKSKAL-ENLNIEASVINRTIEA 374
                                   88875689***********999999999999999999999999999998888877666665555.5678889999999999 PP

                                   HHHHHHHHHHHHH CS
                      Filament 267 leeelaeireema 279
                                   l+++l+++ e+++
  gi|70605899|ref|YP_254769.1| 375 LQKQLKSLEERVE 387
                                   9999988877665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Filament  53 ekeleelrkqldeltkerarlqleldnlreeledlrkk...yekelnkreevEaelkalrkdldeatlarvdLekkvesLk 130
                                    ke+e   + + + +k+ ++l++e + ++ ++e l+k+   +e+ +++  evE++ +++ k ++e+  +r+dLe ++++L 
  gi|70605899|ref|YP_254769.1| 341 VKEIERTEELIAQKSKALENLNIEASVINRTIEALQKQlksLEERVESTYEVESKDNDIDKRIEELRKRRSDLELQLQQL- 420
                                   35677777777777777777888777777777776654111566777888999999*********************976. PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Filament 131 eelaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeiraqyeelaeknreeaeewykskleel 200
                                       + kkv  eE++ l+kq+ ++++ ++d+  + +  + l  +++++e+l ++  +e+e +y + ++e 
  gi|70605899|ref|YP_254769.1| 421 ---GIPKKV-AEEIESLKKQI-DDINKQIDDI-NREYIRRLTVVKEEFETLSNSILKELEFNYTAEIDEK 484
                                   ...566776.689********.9*******65.556777899**********************999875 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.4   3.3e+02      32      62 ..     127     157 ..     121     172 .. 0.56
   2 ?    4.2   7.8     0.063        51      21      87 ..     161     232 ..     160     234 .. 0.89
   3 ?    2.1   0.2      0.29   2.3e+02      36      67 ..     242     269 ..     235     289 .. 0.67
   4 ?    6.5   1.0     0.013        10      43      83 ..     307     347 ..     303     362 .. 0.88
   5 ?    4.3   0.7     0.059        48      31      72 ..     361     401 ..     349     420 .. 0.53
   6 ?    6.7   0.4     0.011       8.7      23      48 ..     425     450 ..     398     471 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                        DUF948  32 aatieelekqvdpilkevedllakvnelled 62 
                                   +++i+el+++ ++++ ++e++ ++ n+ll  
  gi|70605899|ref|YP_254769.1| 127 TSRIDELKRRRESLIMKLEEVKSNYNNLLRT 157
                                   4566666666666666666666666664432 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.063
                        DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvne.....lledvneklekvdplteavadlgesvsel 87 
                                   ++k+++ l++++  ie lek+ ++++ ++e++++ +++     + e ++ k++++++  +++++l++ ++el
  gi|70605899|ref|YP_254769.1| 161 IKKIANELENINLEIERLEKEKENVTVQTEQTIKITRQnriveIRERIQAKIKELKEKETKIQKLTQELEEL 232
                                   578999999************************999998888888999999999999999999999888877 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.29
                        DUF948  36 eelekqvdpilkevedllakvnelledvnekl 67 
                                   ++l+k++++i +e++ l++  n     ++ + 
  gi|70605899|ref|YP_254769.1| 242 DKLTKEIQEIDRELDSLINRQNS----IEIEQ 269
                                   57888888888888888888888....33333 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.013
                        DUF948  43 dpilkevedllakvnelledvneklekvdplteavadlges 83 
                                   + + k++++l ++ n++ +++n+k  +  +l ++v+++ ++
  gi|70605899|ref|YP_254769.1| 307 ETVKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERT 347
                                   56789999999999999999999999999999999999875 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.059
                        DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdp 72 
                                   ++    ++++ ++++ k+++ l + v+  + +v++k +++d+
  gi|70605899|ref|YP_254769.1| 361 LNIEASVINRTIEALQKQLKSLEERVES-TYEVESKDNDIDK 401
                                   4444444444444444444444444443.4444444444443 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.011
                        DUF948  23 klkktldeaaatieelekqvdpilke 48 
                                   k+++ +++++++i++++kq+d i +e
  gi|70605899|ref|YP_254769.1| 425 KVAEEIESLKKQIDDINKQIDDINRE 450
                                   44555555555555555555555554 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.5   0.00024       0.2      10     131 ..     130     261 ..     125     280 .. 0.79
   2 ?    2.7   1.1      0.14   1.2e+02      80     116 ..     335     371 ..     303     396 .. 0.75
   3 ?    0.2   3.3       0.8   6.5e+02      84     117 ..     339     372 ..     332     449 .. 0.66
   4 ?   -0.7   0.1       1.5   1.2e+03      33      53 ..     428     448 ..     397     470 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                   Serine_rich  10 larlqqevesavskLlsfvssk...WRskenl...eanlqeirlavdrlrtslrefleFargalanaaklsdknlqtkLrk 84 
                                   +++l+++ es + kL ++ s+     R+++ +    ++l++i l ++rl++  ++++  +++++    + +  ++ ++++ 
  gi|70605899|ref|YP_254769.1| 130 IDELKRRRESLIMKLEEVKSNYnnlLRTYDDIkkiANELENINLEIERLEKEKENVTVQTEQTIKITRQNRIVEIRERIQA 210
                                   5556666666666665555332334677666522266788889999999999999*99*********************** PP

                   Serine_rich  85 qlqkledsdqilqetsqeLdsceWslealasdkkqek....pddlDrlvmv 131
                                   ++++l++++  +q+ +qeL++ + +++   +dk +++    + +lD+l+  
  gi|70605899|ref|YP_254769.1| 211 KIKELKEKETKIQKLTQELEELKGKANIELKDKLTKEiqeiDRELDSLINR 261
                                   **************************9999999998877777788888865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                   Serine_rich  80 tkLrkqlqkledsdqilqetsqeLdsceWslealasd 116
                                     L ++++++e +++++ + s++L++ + +++++ ++
  gi|70605899|ref|YP_254769.1| 335 SELLQKVKEIERTEELIAQKSKALENLNIEASVINRT 371
                                   5678889999999999999999999998888877665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.8
                   Serine_rich  84 kqlqkledsdqilqetsqeLdsceWslealasdk 117
                                   ++++++e +++++ + s++L++ + +++++ ++ 
  gi|70605899|ref|YP_254769.1| 339 QKVKEIERTEELIAQKSKALENLNIEASVINRTI 372
                                   5566666666666666666666655555554433 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.5
                   Serine_rich  33 Rskenleanlqeirlavdrlr 53 
                                      e+l++++++i +++d+++
  gi|70605899|ref|YP_254769.1| 428 EEIESLKKQIDDINKQIDDIN 448
                                   345666777777777766664 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   4.0      0.12        96      10      72 ..     129     194 ..     121     206 .. 0.62
   2 ?   -0.6  14.1      0.76   6.2e+02       5      84 ..     176     257 ..     174     296 .. 0.55
   3 ?    7.0   6.9    0.0036       2.9      17      89 ..     305     379 ..     295     382 .. 0.85
   4 ?   12.3   5.7   8.9e-05     0.073       3      88 ..     371     450 ..     364     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.12
                         TMPIT  10 efkeleetakeykqkleelsklqskcske...ikkqkkrlkelksslkklkksvkeeeeeeveelk 72 
                                   +++el+ + ++++ klee+++  +++ ++   ikk  ++l++++ ++++l+k++++ + ++ +++k
  gi|70605899|ref|YP_254769.1| 129 RIDELKRRRESLIMKLEEVKSNYNNLLRTyddIKKIANELENINLEIERLEKEKENVTVQTEQTIK 194
                                   567888888899999999999888776651115555556666677777777775433333333332 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                         TMPIT   5 eelekefkeleeta..keykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                   e+leke +++  +   +  +++ +++ +  ++++ +ik+ k++ +++++  ++l++ +++ + e  ++l++e++e+++ l+
  gi|70605899|ref|YP_254769.1| 176 ERLEKEKENVTVQTeqTIKITRQNRIVEIRERIQAKIKELKEKETKIQKLTQELEELKGKANIELKDKLTKEIQEIDRELD 256
                                   556665555443330033334455555666666655555555544444444444444444556666666666666555544 PP

                         TMPIT  84 e 84 
                                   +
  gi|70605899|ref|YP_254769.1| 257 S 257
                                   2 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0036
                         TMPIT  17 takeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvlkevesll 89 
                                   +++++k++++el + ++++ ++i+k+k r +el +++k+++++ +  +++++++e+l+ e + ++++++ +++ l
  gi|70605899|ref|YP_254769.1| 305 RFETVKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERTEEliAQKSKALENLNIEASVINRTIEALQKQL 379
                                   56789************************************9966667888888888888888877777766655 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 8.9e-05
                         TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                    +e l+k++k+lee+     +++ e+++  +++ k+i++ +kr ++l+ +l++l     ++ +ee+e+lk+++++++k+++
  gi|70605899|ref|YP_254769.1| 371 TIEALQKQLKSLEERV----ESTYEVESKDNDIDKRIEELRKRRSDLELQLQQLGIP--KKVAEEIESLKKQIDDINKQID 445
                                   5667777777777777....6777899999************************987..7899****************** PP

                         TMPIT  84 evesl 88 
                                   +++  
  gi|70605899|ref|YP_254769.1| 446 DINRE 450
                                   99865 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.8    0.0025         2      20      71 ..     138     185 ..     121     209 .. 0.67
   2 ?    6.4   1.7     0.013        10      13      96 ..     209     289 ..     198     290 .. 0.75
   3 ?    0.5   0.7      0.87   7.1e+02      20      61 ..     307     348 ..     299     362 .. 0.69
   4 ?    3.3   0.4      0.11        93      12      57 ..     375     420 ..     368     442 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0025
                                   -TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS CS
                       PI_PP_I  20 eskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnel 71 
                                   es  ++l+++k++ n++l ++++ikk + +L    ++i+ + + l +  +++
  gi|70605899|ref|YP_254769.1| 138 ESLIMKLEEVKSNYNNLLRTYDDIKKIANEL----ENINLEIERLEKEKENV 185
                                   55567899*****************887544....33433333333333444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                                   HHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHHT.T..SCCCHH CS
                       PI_PP_I  13 qaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvlaeaklsveeid 93 
                                   qa   +l+ ke++++kl+q+l ++  k ++i+ +  +L++++++i+ +  +l +  n+++ +q  l r+l +   ++e+i+
  gi|70605899|ref|YP_254769.1| 209 QAKIKELKEKETKIQKLTQELEELKGK-ANIELKD-KLTKEIQEIDRELDSLINRQNSIEIEQGVLTRILQDI-QEAERIH 286
                                   555556666777777777777776655.3444333.789999****************************966.7888888 PP

                                   HHH CS
                       PI_PP_I  94 skl 96 
                                   s++
  gi|70605899|ref|YP_254769.1| 287 SSM 289
                                   765 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.87
                                   -TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT- CS
                       PI_PP_I  20 eskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannk 61 
                                   e+ ++++++l +  n+++ + ++ k + ++L +  ++i+  +
  gi|70605899|ref|YP_254769.1| 307 ETVKKDINELDRTKNDIINNINKKKMRRSELLQKVKEIERTE 348
                                   445556666666677777777777777777888888777655 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.11
                                   HHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHH CS
                       PI_PP_I  12 qqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnki 57 
                                    q  + +le + +s+ +++++ n++ ++ ee++k+ ++Le +L+++
  gi|70605899|ref|YP_254769.1| 375 LQKQLKSLEERVESTYEVESKDNDIDKRIEELRKRRSDLELQLQQL 420
                                   5667899************************************986 PP

>> HTH_57  ThcOx helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.12     1e+02      40      69 ..      36      65 ..      29      83 .. 0.72
   2 ?    6.3   3.8     0.014        11      15      72 ..     178     239 ..     171     254 .. 0.73
   3 ?    1.7   0.4       0.4   3.3e+02      12      52 ..     340     379 ..     308     410 .. 0.61
   4 ?   -0.9   0.0       2.5     2e+03      29      59 ..     482     512 ..     462     523 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                                  HHHHHHHHHHHT-B-HHHHHHHHHHHH-HH CS
                        HTH_57 40 gikaAleqLkagnaTeekLselvlekdgve 69
                                   + +Al +L ++++T+e+L ++ +++  ve
  gi|70605899|ref|YP_254769.1| 36 SLSKALVSLLTNEITAEDLLNVFSDEGFVE 65
                                  5789****************9887764444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                   EEE-SSEEEEE.....-SS-EEEEES--HHHHHHHHHHHHT-B-HHHHHHHHHHHH-HHHHH CS
                        HTH_57  15 vieeedklilqs....spdaslklaapspgikaAleqLkagnaTeekLselvlekdgveale 72 
                                   +++e++++++q+    + + + ++ +  ++i+a +++Lk++++  +kL++ ++e  g+++ e
  gi|70605899|ref|YP_254769.1| 178 LEKEKENVTVQTeqtiKITRQNRIVEIRERIQAKIKELKEKETKIQKLTQELEELKGKANIE 239
                                   6788899999984443233333455567899999**********************998754 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.4
                                   T-EEEE-SSEEEEE.-SS-EEEEES--HHHHHHHHHHHHT- CS
                        HTH_57  12 dvqvieeedklilqsspdaslklaapspgikaAleqLkagn 52 
                                   +v+ ie +++li q + +a  +l+   + i+  +e L+++ 
  gi|70605899|ref|YP_254769.1| 340 KVKEIERTEELIAQ-KSKALENLNIEASVINRTIEALQKQL 379
                                   34444555555555.33333334444444555555555444 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.5
                                   S-EEEEES--HHHHHHHHHHHHT-B-HHHHH CS
                        HTH_57  29 daslklaapspgikaAleqLkagnaTeekLs 59 
                                   d++ +l   + g+ + l  L ++++T+  L 
  gi|70605899|ref|YP_254769.1| 482 DEKYRLVIKKDGVTMELRRLSTSEKTTLALI 512
                                   4455555556899999999999988876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3319  (0.185119); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                       166  (0.00925874); expected 17.9 (0.001)
Passed Fwd filter:                        98  (0.005466); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 1.75u 0.42s 00:00:02.17 Elapsed: 00:00:00.60
# Mc/sec: 2911.06
//
Query:       gi|70605900|ref|YP_254770.1|  [L=308]
Description: nucleoside hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-73  247.0   0.0    3.6e-73  246.8   0.0    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
  ------ inclusion threshold ------
       0.15   12.5   0.1       0.32   11.4   0.1    1.7  1  FERM_C        FERM C-terminal PH-like domain


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   0.0     4e-77   3.6e-73       1     305 []       4     299 ..       4     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 4e-77
                                   EEEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S-SHHH CS
                  IU_nuc_hydro   1 rkvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.kaaaei 80 
                                   rkvi+D D+  DD +Al+la      +e++g+t+vaGnv+ e+ +rnal +l +++g +dipv++G+++p+l + ++ +e+
  gi|70605900|ref|YP_254770.1|   4 RKVIFDSDTASDDTIALMLASD---FFEVKGVTIVAGNVKFENEIRNALFTL-EYSGLSDIPVFVGSNRPILGKwRTVEEV 80 
                                   69******************74...48*************************.9999999**************888888* PP

                                   HTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE---SSS--S CS
                  IU_nuc_hydro  81 hGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGGaftarGN 161
                                   hG++G+gd +++ep++k+ese+a+da+i++    +ey+ge+ ++a+ plTN+Ala+ +d++l+k++++++iMGGaf+ +GN
  gi|70605900|ref|YP_254770.1|  81 HGKNGMGDWKISEPTKKPESEHAIDAIIRLS---KEYNGELEILAVSPLTNLALAYLKDHDLVKRIRKVWIMGGAFS-KGN 157
                                   ************************9998888...999999***********************************99.*** PP

                                   SSSSS-HHHHHSHHHHHHHHHT.S-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHHHHHHHHHHHHHHHHHHHHSSE CS
                  IU_nuc_hydro 162 vtpvaEfNifvDPeAAkiVles.apvkitlvpldvthkvqalltseeveelaalekglgafladllefyikaykeaegsdg 241
                                   +tp+aEfN++vDPeAA+iV+++  +  it+vp++vt++    +  +e e++++l++  ++f+ ++ +   + y+++ gs+g
  gi|70605900|ref|YP_254770.1| 158 TTPLAEFNFWVDPEAANIVVSAgFD--ITVVPWEVTEESA-TIYDNEWEKIEKLGNRRSEFFINVNRVLRE-YSKSVGSKG 234
                                   ********************86655..5********9444.555555566555433333355554444443.444556999 PP

                                   EE-HHHHHHHHHH-GGGEEE.EEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEEE-HHHHHH CS
                  IU_nuc_hydro 242 aplhDplavavaldpelvtt.krlavdveleggltrGrtvvdlrrl.kkaknvkvatevdverfle 305
                                    +  D l+v +a d++l        ++ve+ +  +rG+++vd+ ++ k++++++++ + d+++f++
  gi|70605900|ref|YP_254770.1| 235 SVHPDSLTVSIAYDNSLALSyVYKSISVETCS-DSRGAMLVDWYNQfKDRNSIQIVLKADEKKFKQ 299
                                   *************9977743344567888875.69*****************************85 PP

>> FERM_C  FERM C-terminal PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.6e-05      0.32      29      63 ..     198     244 ..     179     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                                   EEEEGGGEEEEEEETTEEEEEES...............STTS--.EE CS
                        FERM_C  29 lafpWreieklsfkdkkfsielr............seeqkkreells 63 
                                      +W++iekl  ++ +f+i+++            + + ++++ ++s
  gi|70605900|ref|YP_254770.1| 198 YDNEWEKIEKLGNRRSEFFINVNrvlreysksvgsKGSVHPDSLTVS 244
                                   5568******************9777666666666444445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1941.19
//
Query:       gi|70605901|ref|YP_254771.1|  [L=140]
Description: ferric uptake regulation protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-21   75.6   0.1    4.1e-21   75.4   0.1    1.1  1  FUR              Ferric uptake regulator family
      0.001   19.1   0.0     0.0017   18.4   0.0    1.4  1  HTH_20           Helix-turn-helix domain
     0.0028   17.6   0.1     0.0047   16.9   0.1    1.4  1  PadR             Transcriptional regulator PadR-like family
     0.0031   17.9   0.0     0.0097   16.3   0.0    1.8  2  Penicillinase_R  Penicillinase repressor
     0.0046   16.8   0.0       0.09   12.7   0.0    2.4  1  HTH_5            Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.014   15.2   0.0    1.4  1  HxlR             HxlR-like helix-turn-helix
       0.03   14.2   0.0       0.12   12.2   0.0    2.0  2  TrmB             Sugar-specific transcriptional regulator Trm
       0.05   13.6   0.1       0.22   11.5   0.0    2.2  2  HTH_11           HTH domain
       0.14   12.4   0.1          6    7.2   0.0    2.2  2  HTH_Tnp_Tc3_2    Transposase
       0.21   12.2   0.0       0.39   11.4   0.0    1.5  1  HTH_32           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1   2.3e-24   4.1e-21       2     117 ..      12     122 ..      11     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 2.3e-24
                                   TTHCHHHHHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEEEEE CS
                           FUR   2 aglklTkqRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhdhli 82 
                                   +glk+T+qR  il++  ++  h++ e++y+elk+ +p+isl+TVY+tL+ le+agl++++e+  g + ye++ ++ h ++ 
  gi|70605901|ref|YP_254771.1|  12 HGLKATPQRISILKL-VHNGGHFNGEQIYNELKKIEPTISLSTVYNTLNALEKAGLLNSFEVG-GVTWYEMK-RDLHVNVY 89 
                                   69***********96.56788*****************************************9.99*****9.7******* PP

                                   ETTT--EEEE--HHHHHHHHHHHHHTT-EEEEEEE CS
                           FUR  83 cekCgkviefkddeiekiqeeiaekegfklvshrl 117
                                   ce+ +++i+++ + ++++ ++  e +g+ ++s ++
  gi|70605901|ref|YP_254771.1|  90 CEDLNTIIDVDIN-LDQVYKQLIE-KGIDVKSLNI 122
                                   *********9876.7777777775.7888877665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.5e-07    0.0017      10      55 ..      18      68 ..       7      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.5e-07
                                  HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 10 PvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLve 55
                                  P R  il++ + ++ +  +++  +l      +s +t+++ L++Le+agL+ 
  gi|70605901|ref|YP_254771.1| 18 PQRISILKLVHNGGHFNGEQIYNELkkiepTISLSTVYNTLNALEKAGLLN 68
                                  7788888888777777778888888554455******************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.6e-06    0.0047       1      51 [.      23      71 ..      23      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                  HHHHHCC.S-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEE CS
                          PadR  1 iLallee.qpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesew 51
                                  iL+l+ + +   G +i +el++   +  ++s +++Y +L+ Lek gl++s +
  gi|70605901|ref|YP_254771.1| 23 ILKLVHNgGHFNGEQIYNELKKI--E-PTISLSTVYNTLNALEKAGLLNSFE 71
                                  788887767889***********..4.79*******************9865 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.89   1.6e+03       4      21 ..       1      19 [.       1      22 [. 0.79
   2 !   16.3   0.0   5.4e-06    0.0097       4      63 ..      19      79 ..      16      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.89
                                  S-SHHHHHHHHHS-.EEHH CS
               Penicillinase_R  4 lEaevmeilwekge.atvk 21
                                  +Eae++++l+++g  at +
  gi|70605901|ref|YP_254771.1|  1 MEAEIINVLRTHGLkATPQ 19
                                  599*******999766655 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.4e-06
                                  S-SHHHHHHHHHS-EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE CS
               Penicillinase_R  4 lEaevmeilwekgeatvkevveeleee.kelaysTVktllrrLvkKgllsrekegrafiYs 63
                                  +   +++++++ g+ + +++ +el++   + + sTV  +l+ L+k gll++ + g  + Y 
  gi|70605901|ref|YP_254771.1| 19 QRISILKLVHNGGHFNGEQIYNELKKIePTISLSTVYNTLNALEKAGLLNSFEVGGVTWYE 79
                                  556899*******************984556********************9999888885 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0     5e-05      0.09       2      47 .]      18      69 ..      17      69 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                  HHHHHHHHHHTT.SSEEHHHHHHHHT.....S-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  2 ptRlkILklLae.gelcvcelaeelg.....lsqstvShHLkkLreaGLVek 47
                                  p+R+ ILkl+ + g     ++ +el+     +s stv   L++L++aGL+++
  gi|70605901|ref|YP_254771.1| 18 PQRISILKLVHNgGHFNGEQIYNELKkieptISLSTVYNTLNALEKAGLLNS 69
                                  7788888888885445555688888722222455666688*********986 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     8e-06     0.014      15      51 ..      33      69 ..      19      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                  TTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
                          HxlR 15 lkgkkRfselkralpkisqkmLaqrLreLeqdglier 51
                                  ++g++ ++elk++ p+is ++  ++L +Le+ gl++ 
  gi|70605901|ref|YP_254771.1| 33 FNGEQIYNELKKIEPTISLSTVYNTLNALEKAGLLNS 69
                                  679999****************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05      0.12      34      56 ..      49      71 ..      23      82 .. 0.76
   2 ?   -1.3   0.0       1.2   2.1e+03      12      21 ..     105     114 ..     104     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                                  SSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 34 vprskvYevLrsLedkGlVerek 56
                                  ++ s+vY++L+ Le++Gl +  +
  gi|70605901|ref|YP_254771.1| 49 ISLSTVYNTLNALEKAGLLNSFE 71
                                  7789*************987655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                   CHCHHHHHHC CS
                          TrmB  12 kvYlaLlklg 21 
                                   +vY+ L+++g
  gi|70605901|ref|YP_254771.1| 105 QVYKQLIEKG 114
                                   5677777654 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.22       4      43 ..      22      65 ..      19      76 .. 0.83
   2 ?   -2.3   0.0       2.6   4.6e+03      37      48 ..     108     119 ..     104     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        HTH_11  4 qilelLleargpisgeeLAeeLn.....vSrrtvrrdIkaLeelg 43
                                  +il+l+ ++ g+++ge++  eL+     +S +tv++ + aLe++g
  gi|70605901|ref|YP_254771.1| 22 SILKLV-HNGGHFNGEQIYNELKkieptISLSTVYNTLNALEKAG 65
                                  688888.8889999999999997777779**************99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                        HTH_11  37 kaLeelgvpIes 48 
                                   k+L e+g+++ s
  gi|70605901|ref|YP_254771.1| 108 KQLIEKGIDVKS 119
                                   556677766665 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.045        80      35      48 ..       5      18 ..       2      29 .. 0.82
   2 ?    7.2   0.0    0.0033         6       4      40 ..      23      59 ..      20      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.045
                 HTH_Tnp_Tc3_2 35 irrrLrkaglkkrk 48
                                  i ++Lr++glk++ 
  gi|70605901|ref|YP_254771.1|  5 IINVLRTHGLKATP 18
                                  789********975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0033
                 HTH_Tnp_Tc3_2  4 IvrlvrkdPritlreLanelkeeGksvsreTirrrLr 40
                                  I++lv +  +   +++ nelk+ + ++s +T+ ++L 
  gi|70605901|ref|YP_254771.1| 23 ILKLVHNGGHFNGEQIYNELKKIEPTISLSTVYNTLN 59
                                  6666666666777899****888**********9996 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.39      45      73 .]      18      58 ..       1      58 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                        HTH_32 45 p.............rWsprqlaarlaeregvkvShstvyriL 73
                                  p             +++ +q+  +l ++ + ++S stvy+ L
  gi|70605901|ref|YP_254771.1| 18 PqrisilklvhnggHFNGEQIYNEL-KKIEPTISLSTVYNTL 58
                                  14455555555556***********.555588*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 917.15
//
Query:       gi|70605902|ref|YP_254772.1|  [L=153]
Description: hypothetical protein Saci_0049 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.024   14.3   0.0    1.3  1  RGS-like  Regulator of G protein signalling-like domain


Domain annotation for each model (and alignments):
>> RGS-like  Regulator of G protein signalling-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-06     0.024      28      67 ..      60      97 ..      56     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-06
                                  HS--HHHHHHHHHHHHTTS-TTHHHHHHHHHHHHHTSTT- CS
                      RGS-like 28 qfdPsallfylitdlykqgtsKetrrvaleifstFlekna 67
                                  ++dP ++l+y++   y +    ++rrva+++f++ l   +
  gi|70605902|ref|YP_254772.1| 60 EMDPHPILCYICP--YFSLRQDDSRRVAFDLFEILLYYES 97
                                  58*********96..88999*************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1171.96
//
Query:       gi|70605903|ref|YP_254773.1|  [L=332]
Description: putative 5'-3' nuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-37  128.7   4.8    3.5e-37  128.4   4.8    1.1  1  NurA       NurA domain
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.037   14.0   0.1    1.5  1  MetOD1     Metanogen output domain 1
      0.095   11.7   0.0       0.14   11.2   0.0    1.1  1  Phage-Gp8  Bacteriophage T4, Gp8


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   4.8   5.9e-41   3.5e-37       2     242 .]      52     305 ..      51     305 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 5.9e-41
                                   EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEE CS
                          NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedll 82 
                                   + +A+DG+++v++++ g+++i++a a+v  g +++++ +++ +  + + +++ ++ri+llm++lEl+  + l+  +++d++
  gi|70605903|ref|YP_254773.1|  52 KLLAIDGGMWVKETRQGVIFIVNAKAIVFEGINEINSEGKVLVHIFSPGNYA-KERIELLMQLLELQ--LALKLVENVDYV 129
                                   579*****************************************99776666.**************..************ PP

                                   EEECSHHCCCH....................HHHHHHHHHHHHHHHHHHHHHTT-......TTCEEEEESS-SCTCCHCCC CS
                          NurA  83 llDGsligslv....................efdelheeleyeeylyslsrllea......glnlvgvaKsfrskellnll 137
                                   llDGs++ +l                      ++e+++e+ +++ l + ++l+ +      + +l++++K+++s++l++ +
  gi|70605903|ref|YP_254773.1| 130 LLDGSFSKKLGrhkselkvdllddivsidkiLSLEEKDEDNMLRFLIAENQLVLSelvsryKDKLLFISKNSKSSDLFKQA 210
                                   *****************************************************999************************* PP

                                   ......S--HHHHCCHHCCHCH---STTS-HHHHTT....-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHH CS
                          NurA 138 letlligesisDiallgallrkpgytspllkilrek....pllrealidkeiyfaYvrlegggsilrleipaevstakded 214
                                            +sDi++l+  ++++gy++ l k  +e      + +++l+ +++yf+++rle++++++rl+   ++ ++k+ +
  gi|70605903|ref|YP_254773.1| 211 ---------YSDITILELFTQNCGYSKILEKKIDENyilsRKASKLLSGLNYYFTNLRLEPSERLFRLD---FFNADKIFE 279
                                   .........****************98777777777***999999999999******************...5568***** PP

                                   HHHHHH..TTB-SSSBCCHHHHHHHHCC CS
                          NurA 215 vlsllasqrlsisGYprpLalAhelaki 242
                                   +l  l   + s +GYp+pL ++h+ +++
  gi|70605903|ref|YP_254773.1| 280 YLKVLK--PVSLKGYPYPLIKVHKDVRV 305
                                   ******..******************96 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   6.2e-06     0.037      55     135 ..      11      92 ..       1      96 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-06
                        MetOD1  55 keaekeeeda....ekvlkayiewlnqlfanfgiktekkedeknvlleftnCpWgeearknPifCllcraivsrsftwtgl 131
                                   k++ek   d+    +++ +   ++ln+l  n+  +     + ++ ll ++   W +e r+  if ++ +aiv   ++  ++
  gi|70605903|ref|YP_254773.1|  11 KMKEKIMRDSytihKELSESVESILNELWINYSPESV---EHSKKLLAIDGGMWVKETRQGVIFIVNAKAIVFEGINEINS 88 
                                   3444444444000045555556666666666666665...344557999******************************** PP

                        MetOD1 132 kgsv 135
                                   +g+v
  gi|70605903|ref|YP_254773.1|  89 EGKV 92 
                                   9998 PP

>> Phage-Gp8  Bacteriophage T4, Gp8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.4e-05      0.14     196     280 ..      27     115 ..      16     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                                   HHHHHHT--SSEEEE--HHHHHHSTGGGT-TT-STHHHHTT-HHHHTT--EEEEEE....EEEGGGSCTTSSTTHS-EEEE CS
                     Phage-Gp8 196 pdevltrvtqeyivvpfpeelkedrvawglednlvfnedddeliyrvkavtlrfka....kldsvdfielalpgnkgyrqi 272
                                    +e+++ + +e  +   pe + + +    ++  +  +e  +++i+ v+a+ + f      + ++  +++++ pgn    +i
  gi|70605903|ref|YP_254773.1|  27 LSESVESILNELWINYSPESVEHSKKLLAIDGGMWVKETRQGVIFIVNAKAIVFEGineiNSEGKVLVHIFSPGNYAKERI 107
                                   47899999****9999**************************************8622114567899*********99999 PP

                                   EEEES-BB CS
                     Phage-Gp8 273 slvtnpll 280
                                    l+ + l+
  gi|70605903|ref|YP_254773.1| 108 ELLMQLLE 115
                                   99887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2503.71
//
Query:       gi|70605904|ref|YP_254774.1|  [L=886]
Description: DNA double-strand break repair rad50 ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-20   72.4  13.8    1.6e-11   44.1   3.8    4.3  4  SMC_N          RecF/RecN/SMC N terminal domain
    2.6e-19   70.5  19.7    2.6e-19   70.5  19.7    6.8  1  AAA_23         AAA domain
    8.7e-18   65.2  83.4    9.1e-18   65.1  21.7    3.3  2  AAA_15         AAA ATPase domain
    5.9e-12   45.2   1.7    5.9e-12   45.2   1.7   10.0 11  Rad50_zn_hook  Rad50 zinc hook motif
    1.3e-07   30.7 104.2    0.00035   19.4  22.8    5.6  4  AAA_13         AAA domain
    1.4e-05   25.2   0.0    4.3e-05   23.7   0.0    1.8  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
    1.6e-05   24.5   0.0    3.3e-05   23.5   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
    8.2e-05   22.6   1.9    8.2e-05   22.6   1.9    4.5  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    0.00015   22.3   2.3    0.00015   22.3   2.3    5.5  2  ABC_tran       ABC transporter
     0.0018   18.2   0.1     0.0018   18.2   0.1    4.7  5  RsgA_GTPase    RsgA GTPase
     0.0086   16.1   7.2     0.0086   16.1   7.2    7.7  6  TPR_MLP1_2     TPR/MLP1/MLP2-like protein
  ------ inclusion threshold ------
      0.016   15.6  12.7      0.016   15.6  12.7    9.8  3  ZapB           Cell division protein ZapB
       0.53    9.6 123.5       0.12   11.7  19.1    5.9  6  GAS            Growth-arrest specific micro-tubule binding
       0.99    8.7  62.3        3.6    6.8  10.8    4.7  4  DUF4407        Domain of unknown function (DUF4407)
        1.1    9.5 114.0      0.021   15.0   8.2    8.7  7  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
        1.2    9.6  55.0        2.3    8.8   0.4    9.4  9  NPV_P10        Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   2.4   3.5e-14     4e-11       2      99 ..       3      91 ..       2     128 .. 0.79
   2 ?    0.6   1.4      0.29   3.3e+02      91     151 ..     204     264 ..     158     291 .. 0.75
   3 ?   -2.8   3.3       3.2   3.6e+03      52     124 ..     448     519 ..     444     588 .. 0.73
   4 !   44.1   3.8   1.4e-14   1.6e-11      52     216 ..     658     874 ..     647     878 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.5e-14
                                  EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfd 84
                                  +++++++nF s   + ++++f+ s+++i+G+NG+GKs+++d ilF L +r+++ + +   ++li+k       k+++v+i f+
  gi|70605904|ref|YP_254774.1|  3 IREIRLQNFLSH--EDTTVKFEGSINVIIGNNGAGKSSIIDGILFGLFKRTNRDIGK--NEELIKK-----GKKSGQVSIKFE 76
                                  899*********..78999*****************************999988865..579**98.....667889999998 PP

                                  ETTEESSSSSSCEEE CS
                                  xxxxxxxxxxxxxxx RF
                         SMC_N 85 nedkklkiekeevsi 99
                                   ++++  i+++  ++
  gi|70605904|ref|YP_254774.1| 77 INGDTYLIDRNVGET 91
                                  888875555544444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.29
                                   SSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  91 kiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlf 151
                                   +ie+ +v+++    + +e e ++n+ + +++ ++e+  + +i + +LS  +k++  +aL++
  gi|70605904|ref|YP_254774.1| 204 EIEEIKVKLENIEREAKEKEDELNQYNTEFNRIKEIKVQYDILSGELSVVNKKIEEIALRL 264
                                   2333333333333444456679999999999999999999999999999999999999986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.2
                                   TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         SMC_N  52 sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk.kevs 124
                                   ++ k+r+e   +l+   +++  + +a+++ ++++ ++  + ++++++++ ++ +k++  y+ + ke ++ +e +
  gi|70605904|ref|YP_254774.1| 448 HKAKIREEIKVQLLEL-NKQITALQARINSLIKEREEL-EATRNKLQLELQKRSKEKGIYEAKLKELQRlEEEK 519
                                   5557888888888887.788888888998887777665.55555666655555555555555444443323333 PP

  == domain 4  score: 44.1 bits;  conditional E-value: 1.4e-14
                                   TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  52 sakklrseklsdlihk...skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevselles 129
                                    +++ r ++l+++i k     ++ +++k++++  ++++ k+  ie++e +i+    + +e e k+n    + ++++e+l +
  gi|70605904|ref|YP_254774.1| 658 GYSEKRYKQLEEIIDKlskILSGIEADKGKIKGSLEEKIKN--IEEKERNIEELRNKMNE-ESKLNLGISKLQKLREVLDN 735
                                   44555889999999997555577889999999988777777..77777777776666666.7799999999999******* PP

                                   TT-STT..................................................CS-HHHHHHHHHHHHHHHHC..CS- CS
                                   xxxxxx..................................................xxxxxxxxxxxxxxxxxxxx..xxx RF
                         SMC_N 130 agiske..................................................lLSgGektLvalaLlfAiqk..vkp 158
                                   ++++++                                                  +LSgGe+  +alaL++Ai k  +++
  gi|70605904|ref|YP_254774.1| 736 KHLQSHimnivrnqiennvneviakfdlsfsaveidfvgkselyvytasgqkihinALSGGERISIALALRLAIAKalMNQ 816
                                   ****999******************************************************************99833467 PP

                                   -SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 159 aplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtkven 216
                                    +  +lDe   +LDe ++k++ ++++++ +   Q+i +++++e+++  d +++v k + 
  gi|70605904|ref|YP_254774.1| 817 FSTLILDEPTVNLDEYRRKELIDVIRSAIEIvPQIILVTHDQELIQAGDYIIRVEK-KG 874
                                   77799*********************9988758*********************98.43 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5  19.7   2.3e-22   2.6e-19       2     197 ..       6     231 ..       5     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2.3e-22
                        AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenk 82 
                                   ++++nf s++d+++ F+  +++I+G+NGaGK++i+d i ++L+ +t   +r    ++ k++  i++ gk++++v+++fe +
  gi|70605904|ref|YP_254774.1|   6 IRLQNFLSHEDTTVKFEGSINVIIGNNGAGKSSIIDGILFGLFKRT---NR----DIGKNEELIKK-GKKSGQVSIKFEIN 78 
                                   99*****************************************954...33....45567766665.59999******999 PP

                        AAA_23  83 dgrytrsiererelskkkgkttkkaklellei.....deleqfisellgskkiilnlilflgqer................ 142
                                   +++  + i  +r++ +++ +t++  k+ ++ +     ++ +++i+e+lg + +il    ++gq++                
  gi|70605904|ref|YP_254774.1|  79 GDT--YLI--DRNVGETSRDTISLLKEGKIITlarqsTTVNNKIKEILGFDHKILMSTTIIGQGSvesvfsdfpevmkell 155
                                   996..455..44444444444444433333333445588899999999999999999999999999888887776654443 PP

                        AAA_23 143 ..feefelkdkke.......................rleelekeleeledekkllekl.....eqekekekeleeleeele 193
                                     +         +                        l+++++ l+ +e+e++ l+k+      ++++ e e +e+e+el+
  gi|70605904|ref|YP_254774.1| 156 kiN---------KlemlresngpihslikvltdrirSLQSIKDILKREEAEIDRLKKEieeikVKLENIEREAKEKEDELN 227
                                   331.........144555566778887777777555666666666666666666666554444344444445556666666 PP

                        AAA_23 194 eilk 197
                                   +++ 
  gi|70605904|ref|YP_254774.1| 228 QYNT 231
                                   6555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1  21.7   8.1e-21   9.1e-18       1     298 [.       1     413 [.       1     428 [. 0.69
   2 ?   -2.5  54.8       2.9   3.3e+03      66     369 .]     534     861 ..     416     861 .. 0.53

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 8.1e-21
                        AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl..FlnnkekknkkvikiekedleifeniseskdikI 79 
                                   M+I++i+++NF s++d++++++ +++v+iG N++GKSsi++ + +  F+ +    n +  k e+   + +++ + s++++I
  gi|70605904|ref|YP_254774.1|   1 MIIREIRLQNFLSHEDTTVKFEGSINVIIGNNGAGKSSIIDGILFglFKRT----NRDIGKNEELIKKGKKSGQVSIKFEI 77 
                                   9****************************************9943314443....45555666777777778888888888 PP

                        AAA_15  80 dvef............................................................................. 83 
                                   +                                                                                
  gi|70605904|ref|YP_254774.1|  78 NGDTylidrnvgetsrdtisllkegkiitlarqsttvnnkikeilgfdhkilmsttiigqgsvesvfsdfpevmkellkin 158
                                   87778**************************************************************************** PP

                        AAA_15  84 ............................aekekakeyektlkskekkkadlllkkkesdlkktikd...kklklkknelsd 133
                                                               +      +++   ++ e++  ++++++++ +l ++ ++   k+ +l+++++  
  gi|70605904|ref|YP_254774.1| 159 klemlresngpihslikvltdrirslqsI------KDILKREEAEIDRLKKEIEEIKVKLENIEREakeKEDELNQYNTEF 233
                                   ***************99999985544431......4444444444444444444444444444433000333333333333 PP

                        AAA_15 134 ekisvekkkskkelpkekeeklekekeelkid.kedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd..eds 211
                                   ++i+  k +      +++  +++ e+  l ++ +e+++k ++k+e+ +k+ +       ++ +k+ +is+ +++    +  
  gi|70605904|ref|YP_254774.1| 234 NRIKEIKVQYDILSGELSVVNKKIEEIALRLKdFEEKEKRYNKIETEVKELD-------ENREKINTISSFKSILVqiDSL 307
                                   3333333333333344444444444444444478888888888888887777.......4555555555555554433333 PP

                        AAA_15 212 ekkssllgklkekileealqekl...eeelteklkeiqeklkeidkklaeelk......kilkkkidkikkfnykgkknee 283
                                   +++ ++ ++ +++++e+ +++k    +e++ e++++ +++l+e++k+++e +k      k+++   ++i+k+ny   ++ e
  gi|70605904|ref|YP_254774.1| 308 KSQINVVENDLKRKKEKLKRKKEleeKEKQYEEIEKRKKELEEKEKQYEEIEKrltyvlKNIERQKNEIEKLNYVDTQDLE 388
                                   444444444444444433333334446666677777777777777777666667777776688888888888888888888 PP

                        AAA_15 284 ieik..........ddeelplnknG 298
                                    +ik          ++ +  l+++G
  gi|70605904|ref|YP_254774.1| 389 NKIKdvsdrinqidNELKGLLDRRG 413
                                   8888887777777655555555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.9
                        AAA_15  66 eifeniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskke 146
                                   ++feni+e+ +  Id+++                                                               
  gi|70605904|ref|YP_254774.1| 534 QEFENIAEKEKELIDYHE--------------------------------------------------------------- 551
                                   122222222222222222............................................................... PP

                        AAA_15 147 lpkekeeklekekeelkidkedlkklikkleeslkkee.....................elknvlksaiiklllisakRnv 206
                                        e+ ++                           +                     el++++++   k+++ +a+ ++
  gi|70605904|ref|YP_254774.1| 552 -----EYLKN-----S---------------------DileediqeqeqrlnelnsklsELEKSYNDYKAKYQFLPADLKS 601
                                   .....11111.....1.....................01111111111222222222223333333333333333333333 PP

                        AAA_15 207 sdedsekkssllgklkekileealqekl..................................................... 234
                                     +++e ++  +++l + ++e+   e+l                                                     
  gi|70605904|ref|YP_254774.1| 602 LVSLEERIRRRISELEKLKIEY---ERLkeeitrmkglkeeyeklkeeedallnriselgysekrykqleeiidklskils 679
                                   3333333333333333333332...11122233333333333333333333333333333333333333555444455555 PP

                        AAA_15 235 ............eeelteklkeiqeklkeidkklaeelk.................kilkkkidkikkfnykgkkneeiei 286
                                                ee++++++e + +++e+ +k++ee k                 k+l++ i +i+  ++ ++ n     
  gi|70605904|ref|YP_254774.1| 680 gieadkgkikgsLEEKIKNIEEKERNIEELRNKMNEESKlnlgisklqklrevldnKHLQSHIMNIVRNQIENNVN----- 755
                                   5555555565666666666666677777777777777777777777777775555533333333333333333333..... PP

                        AAA_15 287 k...........................ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqa 340
                                   +                           +++++ +n  + G +  + l+l ++ a+      ++  +l+++EP ++L    
  gi|70605904|ref|YP_254774.1| 756 EviakfdlsfsaveidfvgkselyvytaSGQKIHINALSGGERISIALALRLAIAKAL---MNQFSTLILDEPTVNLDEYR 833
                                   24445578888888*******************************************9...99999*************** PP

                        AAA_15 341 qkvlikllkelandnktQviitTHSphii 369
                                    k+li+ ++++++    Q+i+ TH   +i
  gi|70605904|ref|YP_254774.1| 834 RKELIDVIRSAIEIVP-QIILVTHDQELI 861
                                   ***************9.*******98765 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       8.5   9.6e+03      36      48 ..     172     184 ..     170     186 .. 0.79
   2 ?    1.2   0.4      0.31   3.4e+02       2      16 ..     195     209 ..     194     212 .. 0.90
   3 ?   -1.1   0.0       1.6   1.8e+03       2      16 ..     247     261 ..     246     262 .. 0.84
   4 !   45.2   1.7   5.3e-15   5.9e-12       1      52 []     415     467 ..     415     467 .. 0.96
   5 ?   -3.7   0.3       9.9   1.1e+04      32      40 ..     517     525 ..     512     528 .. 0.53
   6 ?    0.2   0.4      0.62   6.9e+02       2      18 ..     568     584 ..     568     586 .. 0.82
   7 ?   -3.1   1.0       6.6   7.4e+03      38      51 ..     616     629 ..     606     630 .. 0.62
   8 ?   -3.1   0.5       6.8   7.6e+03       8      18 ..     636     646 ..     633     648 .. 0.49
   9 ?   -3.2   0.3       7.2     8e+03       4      16 ..     663     675 ..     661     677 .. 0.67
  10 ?    0.4   0.7      0.55   6.2e+02      34      51 ..     685     702 ..     682     703 .. 0.85
  11 ?   -0.8   0.0       1.3   1.4e+03      29      50 ..     829     850 ..     828     852 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 8.5
                                   HHHHHHHHHHHHH CS
                 Rad50_zn_hook  36 eLikelqsklerl 48 
                                   +Lik l +++++l
  gi|70605904|ref|YP_254774.1| 172 SLIKVLTDRIRSL 184
                                   6899999999887 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                                   HHHHHHHHHHHHHHT CS
                 Rad50_zn_hook   2 hqeteelnkkieelk 16 
                                   ++e+++l+k iee+k
  gi|70605904|ref|YP_254774.1| 195 EAEIDRLKKEIEEIK 209
                                   68999*******998 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHT CS
                 Rad50_zn_hook   2 hqeteelnkkieelk 16 
                                   ++e +  nkkiee++
  gi|70605904|ref|YP_254774.1| 247 SGELSVVNKKIEEIA 261
                                   6788899******97 PP

  == domain 4  score: 45.2 bits;  conditional E-value: 5.3e-15
                                   HHHHHHHHHHHHHHHTT-SE.E-TTT--EE-HHHHHHHHHHHHHHHHHHH... CS
                 Rad50_zn_hook   1 lhqeteelnkkieelkeakg.cCPlCgReldeehrseLikelqsklerlpeel 52 
                                   l++++e+  k++++l++ ++ +CP CgR+ld+eh++++ +e++ +l +l++++
  gi|70605904|ref|YP_254774.1| 415 LNGRKEQTLKIYNNLNSIEDdRCPICGRPLDSEHKAKIREEIKVQLLELNKQI 467
                                   68999********************************************9986 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 9.9
                                   HHHHHHHHH CS
                 Rad50_zn_hook  32 ehrseLike 40 
                                   e++++L++e
  gi|70605904|ref|YP_254774.1| 517 EEKNKLQNE 525
                                   344444444 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.62
                                   HHHHHHHHHHHHHHTT- CS
                 Rad50_zn_hook   2 hqeteelnkkieelkea 18 
                                   +q+ +eln k++el+++
  gi|70605904|ref|YP_254774.1| 568 EQRLNELNSKLSELEKS 584
                                   57889999999999875 PP

  == domain 7  score: -3.1 bits;  conditional E-value: 6.6
                                   HHHHHHHHHHHH.. CS
                 Rad50_zn_hook  38 ikelqsklerlpee 51 
                                   +++l+ + erl+ee
  gi|70605904|ref|YP_254774.1| 616 LEKLKIEYERLKEE 629
                                   35666666666666 PP

  == domain 8  score: -3.1 bits;  conditional E-value: 6.8
                                   HHHHHHHHTT- CS
                 Rad50_zn_hook   8 lnkkieelkea 18 
                                   l++ +e+lke+
  gi|70605904|ref|YP_254774.1| 636 LKEEYEKLKEE 646
                                   34444555554 PP

  == domain 9  score: -3.2 bits;  conditional E-value: 7.2
                                   HHHHHHHHHHHHT CS
                 Rad50_zn_hook   4 eteelnkkieelk 16 
                                   + ++l+++i++l+
  gi|70605904|ref|YP_254774.1| 663 RYKQLEEIIDKLS 675
                                   5677777777775 PP

  == domain 10  score: 0.4 bits;  conditional E-value: 0.55
                                   HHHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook  34 rseLikelqsklerlpee 51 
                                   + ++   l++k+++++e+
  gi|70605904|ref|YP_254774.1| 685 KGKIKGSLEEKIKNIEEK 702
                                   7799999*******9997 PP

  == domain 11  score: -0.8 bits;  conditional E-value: 1.3
                                   E-HHHHHHHHHHHHHHHHHHH. CS
                 Rad50_zn_hook  29 ldeehrseLikelqsklerlpe 50 
                                   lde +r+eLi+ ++s +e +p+
  gi|70605904|ref|YP_254774.1| 829 LDEYRRKELIDVIRSAIEIVPQ 850
                                   88889********999998775 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2     0.001       1.1      10      32 ..      17      39 ..       8     102 .. 0.86
   2 ?   -1.5  46.7      0.64   7.1e+02     280     469 ..     200     407 ..     156     427 .. 0.68
   3 !   19.4  22.8   3.1e-07   0.00035     255     463 ..     434     630 ..     420     635 .. 0.81
   4 !   15.0  13.6   6.4e-06    0.0071     368     586 ..     661     873 ..     633     882 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                        AAA_13 10 aeledfkriNliYGwNGaGKTtL 32
                                  ++++  + iN+i G NGaGK+++
  gi|70605904|ref|YP_254774.1| 17 TTVKFEGSINVIIGNNGAGKSSI 39
                                  44444468*************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                        AAA_13 280 efeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkg...lqraleaKrkepfk.sve 356
                                   + ++++e+++ ++e++e++ +e  ++l++  +e ++ ++ + +++ l+ e++++++++++     +  e+K k+  k + e
  gi|70605904|ref|YP_254774.1| 200 RLKKEIEEIKVKLENIEREAKEKEDELNQYNTEFNRIKEIKVQYDILSGELSVVNKKIEEialRLKDFEEKEKRYNKiETE 280
                                   345566666666666666666666666666666666666666677777788888888777322234446777777665455 PP

                        AAA_13 357 lesvkakie......sikklvaeineliakhNekvanleeekeeakkklelhlv.......eeleseldeykkkykkleka 424
                                   +++++++ e      s+k+++ +i  l ++ N   ++l+++ke++k k el +        e+ ++el+e +k+y+++ek 
  gi|70605904|ref|YP_254774.1| 281 VKELDENREkintisSFKSILVQIDSLKSQINVVENDLKRKKEKLKRKKELEEKekqyeeiEKRKKELEEKEKQYEEIEKR 361
                                   555555443555666666666666666677777777777777777766666666112222255555555555667777777 PP

                        AAA_13 425 ieklekelkeeeaelkkleee.ikeLekqlrdekpaaeeinkeLka 469
                                   ++ + k+++ +++e++kl+    ++Le++++d+   +++i +eLk 
  gi|70605904|ref|YP_254774.1| 362 LTYVLKNIERQKNEIEKLNYVdTQDLENKIKDVSDRINQIDNELKG 407
                                   777777777777777777653599********************86 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 3.1e-07
                        AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealee 335
                                    d Cp Cg+pl++e ka++ + +  +  e    L+k i+ ++ ++++l   +k+  + +  +++ + + ++ ++e+   e+
  gi|70605904|ref|YP_254774.1| 434 DDRCPICGRPLDSEHKAKIREEIKVQLLE----LNKQITALQARINSL---IKEREELEATRNKLQLELQKRSKEKGIYEA 507
                                   589***************99877775555....555555555555433...44444555556678899999********** PP

                        AAA_13 336 qLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykk 416
                                   +Lk+lqr  e+K k      e+ s+ +  ++++++ ++ +eli  h e+ +n +  +e+++++ ++  ++el+s+l+e++k
  gi|70605904|ref|YP_254774.1| 508 KLKELQRLEEEKNKLQN---EILSLLSYHQEFENIAEKEKELIDYHEEYLKNSDILEEDIQEQEQR--LNELNSKLSELEK 583
                                   *****998888886555...56666666666778899999******************99998776..999********** PP

                        AAA_13 417 kykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeei 463
                                    y++ +++ + l ++lk   +  + ++ +i+eLek   + ++  eei
  gi|70605904|ref|YP_254774.1| 584 SYNDYKAKYQFLPADLKSLVSLEERIRRRISELEKLKIEYERLKEEI 630
                                   **********************************9776666655555 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 6.4e-06
                        AAA_13 368 kklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleee..i 446
                                   +k  ++++e+i k  ++ + +e++k ++k +le  + + +    +e ++++++l +++++   +l+   ++l+kl+e    
  gi|70605904|ref|YP_254774.1| 661 EKRYKQLEEIIDKLSKILSGIEADKGKIKGSLEEKIKN-I----EEKERNIEELRNKMNEES-KLNLGISKLQKLREVldN 735
                                   46778999***********************9995532.3....333445555555544433.455556666666665334 PP

                        AAA_13 447 keLekqlrde.kpaa.eeinkeLkaf..GlgeleLkfeeekkgYrivrkggsqaaetLSeGEktaIaflYFlkslkeddse 523
                                   k L+  + ++ ++ + +++n+ +++f   ++  e++f+ + + Y  + +g++ + + LS GE+  Ia+   l+  k   ++
  gi|70605904|ref|YP_254774.1| 736 KHLQSHIMNIvRNQIeNNVNEVIAKFdlSFSAVEIDFVGKSELYVYTASGQKIHINALSGGERISIALALRLAIAKALMNQ 816
                                   7899999887333442689999999988899*****************9998888**************999999955555 PP

                        AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntkrkrk 586
                                   +    + ++D P   LD       +  i+s +   + + Q+++ TH  e+ +  ++ ++ ++k
  gi|70605904|ref|YP_254774.1| 817 F---STLILDEPTVNLDEYRRKELIDVIRSAI---EIVPQIILVTHDQELIQAGDYIIRVEKK 873
                                   5...99**************************...99**********9998877776665544 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.8e-08   4.3e-05      29      89 ..     789     842 ..     772     843 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.8e-08
                       SbcCD_C  29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   ++++lSGGe+ + ++lal +a+a ++ +      ++++++LDE   +lDe ++++l+++++
  gi|70605904|ref|YP_254774.1| 789 HINALSGGER-ISIALALRLAIAKALMN------QFSTLILDEPTVNLDEYRRKELIDVIR 842
                                   6889******.99999999999999999......59*********************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     3e-08   3.3e-05       3      44 ..       5      45 ..       3      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-08
                        AAA_29  3 rlqlvNWgtfdghtieidlkg.atlltGpsGsGKSTllDAiqa 44
                                  +++l N  + +++t++++  g + +++G++G+GKS+++D i +
  gi|70605904|ref|YP_254774.1|  5 EIRLQNFLSHEDTTVKFE--GsINVIIGNNGAGKSSIIDGILF 45
                                  667777777778888888..779****************9976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   1.9   7.3e-08   8.2e-05       1      26 [.      25      74 ..      25     127 .. 0.59
   2 !    9.1  15.0   0.00092         1     124     302 ..     551     861 ..     465     862 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.3e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl........................d 26
                                  +nv+iG Ng+GKS+++d + +  +                          
  gi|70605904|ref|YP_254774.1| 25 INVIIGNNGAGKSSIIDGILFGLFKrtnrdigkneelikkgkksgqvsiK 74
                                  7******************8775423333333333333333333333332 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00092
                        AAA_21 124 vfslkelsvsepndlqfgkaltditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvrslklveielsdlg 203
                                   +++lk++ + e+++++++++l+++ s +++l+++ +      +  +++++ad+    ++ ++++r++++l +  ie++ l+
  gi|70605904|ref|YP_254774.1| 551 EEYLKNSDILEEDIQEQEQRLNELNSKLSELEKSYN----DyKAKYQFLPADLKSLVSLEERIRRRISELEKLKIEYERLK 627
                                   444444444444444444444444444443332222....22444444444444444444444444444444444444443 PP

                        AAA_21 204 egeeliasvderlrer................................................................. 219
                                   e +            r                                                                 
  gi|70605904|ref|YP_254774.1| 628 EEIT-----------Rmkglkeeyeklkeeedallnriselgysekrykqleeiidklskilsgieadkgkikgsleekik 697
                                   2222...........022222222444555666666666666666666666666666666666666666666666666666 PP

                        AAA_21 220 ..............................................................................gvv 222
                                                                                                                    
  gi|70605904|ref|YP_254774.1| 698 nieekernieelrnkmneesklnlgisklqklrevldnkhlqshimnivrnqiennvneviakfdlsfsaveidfvgkSEL 778
                                   666666666667777777777777777777777777777888888899999999999999999999999999999999888 PP

                        AAA_21 223 flengdgqelparelSdGtkrllalltallralkkg.....sllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   ++   +gq++ ++ lS G +  +al++ l+ a   +     s+l++DEp  +L+  + ++l+++++++ +   Q+il+TH+
  gi|70605904|ref|YP_254774.1| 779 YVYTASGQKIHINALSGGERISIALALRLAIAK--AlmnqfSTLILDEPTVNLDEYRRKELIDVIRSAIEIVPQIILVTHD 857
                                   888999****************88887777766..34599*************************66666579******** PP

                        AAA_21 299 plll 302
                                    +l+
  gi|70605904|ref|YP_254774.1| 858 QELI 861
                                   9997 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  12.8     0.014        16      10      43 ..      22      76 ..      15     284 .. 0.72
   2 !   22.3   2.3   1.4e-07   0.00015      29     136 ..     676     826 ..     673     827 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                                  TTSEEEEEESTTSSHHHHHH.HHTTSS--SEEEE....................E CS
                                  xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx....................x RF
                      ABC_tran 10 egekvaivGenGaGKStLlk.llagllkpteGei....................l 43
                                  eg++ +i+G+nGaGKS+++  +l gl k t+ +i                    +
  gi|70605904|ref|YP_254774.1| 22 EGSINVIIGNNGAGKSSIIDgILFGLFKRTNRDIgkneelikkgkksgqvsikfE 76
                                  79999**************857789999999999444443333333333333332 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.4e-07
                                   HHHTTSS--SEEEEEET.TCEGGG...............B-HHHCCHCEEEE-SS--S-TTSBHHHH.............. CS
                                   xxxxxxxxxxxxxxxxx.xxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                      ABC_tran  29 kllagllkpteGeilld.gkdlke...............qeleslrkeigvlpqepqlfpeltvren.............. 79 
                                   k+l+g +  ++G+i+   ++++k+               +e+++l+  i+ l+             +              
  gi|70605904|ref|YP_254774.1| 676 KILSGIEA-DKGKIKGSlEEKIKNieekernieelrnkmNEESKLNLGISKLQ-------------Klrevldnkhlqshi 742
                                   56666554.67777333333333322222111112222222222222333332.............133334445555557 PP

                                   ......HHHTCHHHHHHHSTTGG.................TTCBGESTTSGGS-HHHHH......HHHHHHHHHHTSSEEE CS
                                   ......xxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ......esdeeiekalsklglke.................lkdtvvksspssLSgGqkq......rvalarallkkpklll 131
                                         + +++++++++k++l+                     +++  + + LSgG++       r+a+a+al+++ + l+
  gi|70605904|ref|YP_254774.1| 743 mnivrnQIENNVNEVIAKFDLSFsaveidfvgkselyvytASGQKI--HINALSGGERIsialalRLAIAKALMNQFSTLI 821
                                   7777668888899999999999999999999999997754333333..5699****99777777799************** PP

                                   EESTT CS
                                   xxxxx RF
                      ABC_tran 132 lDEpt 136
                                   lDEpt
  gi|70605904|ref|YP_254774.1| 822 LDEPT 826
                                   ****9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.6e-06    0.0018      91     157 ..      15      85 ..       4      87 .. 0.84
   2 ?    0.1   0.6      0.57   6.4e+02      57      96 ..     189     229 ..     172     237 .. 0.84
   3 ?   -0.5   0.3      0.92     1e+03      46      93 ..     247     294 ..     226     308 .. 0.69
   4 ?   -2.3   3.8       3.1   3.5e+03      55      98 ..     321     363 ..     296     379 .. 0.71
   5 ?   -2.1   0.2       2.7     3e+03      87     119 ..     664     696 ..     608     736 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.6e-06
                                   HHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT....-----S--------------SEEEEEETTTEEEES CS
                   RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallpe....lelktgevseklgrGkhTTtavellelaegglliD 157
                                   e+ + ++++++ v++G+ G+GKS++i+ +l      ++  +g+  e  ++Gk   + +  +e++ +++liD
  gi|70605904|ref|YP_254774.1|  15 EDTTVKFEGSINVIIGNNGAGKSSIIDGILFGlfkrTNRDIGKNEELIKKGKKSGQVSIKFEINGDTYLID 85 
                                   5666778999****************9877542222678888889999**********************9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.57
                                   GG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                   RsgA_GTPase  57 Dlleeee.eleelkeelealgyevllvsaktkegleelkel 96 
                                   D+l++ee e+++lk+e+e++ +++  ++ + ke+ +el+++
  gi|70605904|ref|YP_254774.1| 189 DILKREEaEIDRLKKEIEEIKVKLENIEREAKEKEDELNQY 229
                                   55555555899****************99999999999876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.92
                                   T-EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHH CS
                   RsgA_GTPase  46 giepvivlnKiDlleeee.eleelkeelealgyevllvsaktkegleel 93 
                                     e+ +v  Ki+ +  +  ++ee +++++++++ev  ++++ +e+++++
  gi|70605904|ref|YP_254774.1| 247 SGELSVVNKKIEEIALRLkDFEEKEKRYNKIETEVKELDEN-REKINTI 294
                                   55666666777666544347999999999999999999666.5566655 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3.1
                                   -GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                   RsgA_GTPase  55 KiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                   K + l++++elee ++++e+++ +   +++k ++++ee++++l+
  gi|70605904|ref|YP_254774.1| 321 KKEKLKRKKELEEKEKQYEEIEKRKKELEEK-EKQYEEIEKRLT 363
                                   4455555557888888888888888777655.667777777664 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 2.7
                                   HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHH CS
                   RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinal 119
                                    ++lee+ ++l++ +s +    G  K +L +++
  gi|70605904|ref|YP_254774.1| 664 YKQLEEIIDKLSKILSGIEADKGKIKGSLEEKI 696
                                   334444444444433333334444444444444 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   7.2   7.7e-06    0.0086      55     123 ..     180     247 ..     176     253 .. 0.93
   2 ?    0.4  18.1      0.57   6.3e+02      29     117 ..     265     350 ..     249     351 .. 0.48
   3 ?    2.2   9.0      0.16   1.8e+02      78     121 ..     339     382 ..     338     390 .. 0.89
   4 ?   -0.5  19.4         1   1.2e+03       7     109 ..     509     617 ..     500     618 .. 0.80
   5 ?    0.7  20.6      0.45     5e+02       8     116 ..     548     658 ..     541     669 .. 0.71
   6 ?   -0.1   4.7      0.78   8.8e+02      66     109 ..     671     714 ..     659     741 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.7e-06
                    TPR_MLP1_2  55 dvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLh 123
                                    +++lq++++ l++ +aei  lk+e e+ k +le+ e + +e+++el +  +e++ ri++++ q ++L 
  gi|70605904|ref|YP_254774.1| 180 RIRSLQSIKDILKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDELNQYNTEFN-RIKEIKVQYDILS 247
                                   6899*************************************************95.9*******99996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                    TPR_MLP1_2  29 edlekqaeiakeaqqkYerelvkhaedvkelqalreel...nelkaeiaelkaeaesakaeleeseesweeqkeelekels 106
                                   +d e++++++++ +    +el ++ e +++++++++ l   ++lk++i+ +++++++ k++l++++e  e+     ek+ +
  gi|70605904|ref|YP_254774.1| 265 KDFEEKEKRYNKIETE-VKELDENREKINTISSFKSILvqiDSLKSQINVVENDLKRKKEKLKRKKELEEK-----EKQYE 339
                                   4444444444444442.245555555555555555533333555555555555555555555554432222.....22334 PP

                    TPR_MLP1_2 107 elekriedlne 117
                                   e+ekr ++l+e
  gi|70605904|ref|YP_254774.1| 340 EIEKRKKELEE 350
                                   55555555544 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.16
                    TPR_MLP1_2  78 aeaesakaeleeseesweeqkeelekelselekriedlneqNkl 121
                                   +e e+ k+elee+e++ ee +++l   l+++e++ +++++ N +
  gi|70605904|ref|YP_254774.1| 339 EEIEKRKKELEEKEKQYEEIEKRLTYVLKNIERQKNEIEKLNYV 382
                                   578999********************************999965 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1
                    TPR_MLP1_2   7 eeeikslkeekeeaeaklqklqedlekqaeiakeaqq..kYerelvkhaedvke.lqalreelnelkaeiaelkaeaesak 84 
                                    +e+++l+eek+++++++ +l +  ++ ++ia++ ++  +Y++e +k+++ ++e +q+  ++lnel+++++el+++ ++ k
  gi|70605904|ref|YP_254774.1| 509 LKELQRLEEEKNKLQNEILSLLSYHQEFENIAEKEKEliDYHEEYLKNSDILEEdIQEQEQRLNELNSKLSELEKSYNDYK 589
                                   57899999**********999999999999999888767899***999999864499999999***********9999999 PP

                    TPR_MLP1_2  85 aele...eseesweeqkeelekelsele 109
                                   a+ +   +  +s+ + +e++++++sele
  gi|70605904|ref|YP_254774.1| 590 AKYQflpADLKSLVSLEERIRRRISELE 617
                                   9866222445555566666666666665 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.45
                    TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaq...qkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                   + +++++++++ +e+++q+ ++ l++  + ++e +   ++Y+   +   +d+k+l +l e++ +  +e+++lk e e++k+
  gi|70605904|ref|YP_254774.1| 548 DYHEEYLKNSDILEEDIQEQEQRLNELNSKLSELEksyNDYKAKYQFLPADLKSLVSLEERIRRRISELEKLKIEYERLKE 628
                                   55555555555555555555555555555554444111456666777789************9999999999999999999 PP

                    TPR_MLP1_2  86 eleeseesweeqkeelekelselekriedln 116
                                   e+ + +  ++e+ e+l++e + l +ri +l 
  gi|70605904|ref|YP_254774.1| 629 EITRMKG-LKEEYEKLKEEEDALLNRISELG 658
                                   9987765.77788888888888888888875 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.78
                    TPR_MLP1_2  66 lnelkaeiaelkaeaesakaeleeseesweeqkeelekelsele 109
                                   +++l + ++ ++a+  + k +lee+ +++ee++ ++e+  ++++
  gi|70605904|ref|YP_254774.1| 671 IDKLSKILSGIEADKGKIKGSLEEKIKNIEEKERNIEELRNKMN 714
                                   33333333333333334444444444444444333333322222 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.6     4e+03      18      44 ..      94     121 ..      94     141 .. 0.85
   2 ?    1.2  20.6      0.47   5.3e+02      19      67 ..     466     531 ..     455     535 .. 0.69
   3 ?   15.6  12.7   1.4e-05     0.016       4      65 ..     600     657 ..     597     683 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                          ZapB  18 dtitlLqm.eieeLkeeneelkeenrel 44 
                                   dti+lL++ +i  L +++ + +++++e+
  gi|70605904|ref|YP_254774.1|  94 DTISLLKEgKIITLARQSTTVNNKIKEI 121
                                   8999998768999999999999988886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.47
                          ZapB  19 titlLqmeieeLkeeneelkeenrele.................eeneqlkeereawqerlkkLLg 67 
                                   +it+Lq +i  L +e eel+   ++l+                 +e+++l+ee++++q+ + +LL 
  gi|70605904|ref|YP_254774.1| 466 QITALQARINSLIKEREELEATRNKLQlelqkrskekgiyeaklKELQRLEEEKNKLQNEILSLLS 531
                                   45555555555555555555555555555555557778888999999**************99995 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.4e-05
                          ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                     L  LE++i   i ++++L+ e+e+Lkee   +k     l+ee e+lkee  a+ +r++ L
  gi|70605904|ref|YP_254774.1| 600 KSLVSLEERIRRRISELEKLKIEYERLKEEITRMKG----LKEEYEKLKEEEDALLNRISEL 657
                                   56889**************************99998....99****************9876 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.8    0.0049       5.5      75     130 ..     172     227 ..     157     229 .. 0.76
   2 ?    7.7  19.4    0.0018         2      38     141 ..     187     289 ..     172     303 .. 0.70
   3 ?    2.3  27.9     0.081        91      32     134 ..     321     424 ..     301     429 .. 0.79
   4 ?    3.9  20.4     0.027        31      95     191 ..     454     548 ..     446     556 .. 0.71
   5 ?   11.7  19.1   0.00011      0.12      29     133 ..     544     651 ..     537     656 .. 0.85
   6 ?    2.6  15.7     0.066        74      72     191 ..     635     755 ..     631     762 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0049
                           GAS  75 kqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfe 130
                                     +k       sl+++k  lk+ e e+ +lk e e  + ++e++e+e +e +++ +
  gi|70605904|ref|YP_254774.1| 172 SLIKVLTDRIRSLQSIKDILKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDELN 227
                                   55555555667999999999999999999999999999999999999998777665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                           GAS  38 lkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekv 118
                                   +k   +r e e++ +++e +++k +L++ e+e +e + +l++y+ +++++k++k ++  l  el+ +  + e    r++  
  gi|70605904|ref|YP_254774.1| 187 IKDILKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDELNQYNTEFNRIKEIKVQYDILSGELSVVNKKIEEIALRLKDF 267
                                   455567778888888888888888888888888888888888888888888888888888877777777777777777776 PP

                           GAS 119 ekerdelykkfeaaiqevqqktg 141
                                   e+ +++ y+k e+ ++e+ ++ +
  gi|70605904|ref|YP_254774.1| 268 EE-KEKRYNKIETEVKELDENRE 289
                                   53.44556666666666555544 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.081
                           GAS  32 KeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlk.arlkelekelkdlkwehevl 111
                                   K+e  + kk+ e++ek+ +ei++++k+l+e+ k+ ee  ++L   lkn e++k+++++l+    ++le+++kd++   ++ 
  gi|70605904|ref|YP_254774.1| 321 KKEKLKRKKELEEKEKQYEEIEKRKKELEEKEKQYEEIEKRLTYVLKNIERQKNEIEKLNyVDTQDLENKIKDVSDRINQI 401
                                   555555666777888999999999999999999999999999999999999999999887356788999999999999999 PP

                           GAS 112 eqrfekvekerdelykkfeaaiq 134
                                     +++ + + r +l+ + e++++
  gi|70605904|ref|YP_254774.1| 402 DNELKGLLDRRGDLNGRKEQTLK 424
                                   99999888888888888888765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.027
                           GAS  95 kelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevlaaanld 175
                                   +e + +l +l  +   l+ r++++ ker+el+++ ++   e+q++++ k  + e klk+lq   E+k++  +e+l+  +  
  gi|70605904|ref|YP_254774.1| 454 EEIKVQLLELNKQITALQARINSLIKEREELEATRNKLQLELQKRSKEKG-IYEAKLKELQRLEEEKNKLQNEILSLLSYH 533
                                   45666777788888888888888888888888888888888888877665.578888888888888888888888777766 PP

                           GAS 176 paalsavsekleevle 191
                                    ++ ++++ek +e+++
  gi|70605904|ref|YP_254774.1| 534 -QEFENIAEKEKELID 548
                                   .666777776666665 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00011
                           GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehe 109
                                   k+l + +ee  k+ +  e +++e +q+ ++l+ +L ++e+  +  +++ ++   d +sl +l++r+++  +el++lk e+e
  gi|70605904|ref|YP_254774.1| 544 KELIDYHEEYLKNSDILEEDIQEQEQRLNELNSKLSELEKSYNDYKAKYQFLPADLKSLVSLEERIRRRISELEKLKIEYE 624
                                   55666678889999999**************************************************************** PP

                           GAS 110 vleqrfekvek...erdelykkfeaai 133
                                    l++++++++    e+++l+++ +a +
  gi|70605904|ref|YP_254774.1| 625 RLKEEITRMKGlkeEYEKLKEEEDALL 651
                                   ***987776541117777776666555 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.066
                           GAS  72 eLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklk 152
                                    L+++ ++ +++  +l n  ++l  +ek +k+l++  + l++ ++ +e+++ +++ + e++i+ + +k  + + l  k+ +
  gi|70605904|ref|YP_254774.1| 635 GLKEEYEKLKEEEDALLNRISELGYSEKRYKQLEEIIDKLSKILSGIEADKGKIKGSLEEKIKNIEEKERNIEELRNKMNE 715
                                   578888888888888888888888999999999999999999999999999999999999999999999999999999999 PP

                           GAS 153 alqeelEkke.aqleevlaaanldpaalsavsekleevle 191
                                   + + +l  ++ ++l+evl +++l+ + ++ v++++e+ ++
  gi|70605904|ref|YP_254774.1| 716 ESKLNLGISKlQKLREVLDNKHLQSHIMNIVRNQIENNVN 755
                                   9999998777477999999999999999999999988665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.7    0.0042       4.7     134     233 ..     190     288 ..     161     299 .. 0.58
   2 ?    5.9  11.8    0.0065       7.2     140     246 ..     302     411 ..     295     421 .. 0.79
   3 ?    6.1  16.1    0.0055       6.1     121     231 ..     446     583 ..     442     587 .. 0.60
   4 ?    6.8  10.8    0.0032       3.6     113     233 ..     540     692 ..     525     744 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0042
                       DUF4407 134 elaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld....ata 210
                                    l+++ea+i++l++ei++ + +l++ ++ea+++ d    ++    + +  + ke k q+d ++ el  +++k++    + +
  gi|70605904|ref|YP_254774.1| 190 ILKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDE--LNQ---YNTEFNRIKEIKVQYDILSGELSVVNKKIEeialRLK 265
                                   456666666666666666666666666666655443..222...3334666777777777777777777777776666333 PP

                       DUF4407 211 rlaalraelaeleaerakeraas 233
                                   ++++++++++++e+e ++  ++ 
  gi|70605904|ref|YP_254774.1| 266 DFEEKEKRYNKIETEVKELDENR 288
                                   33333333333333333333322 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0065
                       DUF4407 140 aqiaalqaeidaaearldalraeaqkeldgtk.gtgttgvaGkgpaakekkaqldaaqaelaelkakld.atarlaalr.a 217
                                    qi++l+++i+  e++l++++++++++ + +   ++ + ++ + ++ +ek++q+++++++l+ + ++++ ++ ++++l+  
  gi|70605904|ref|YP_254774.1| 302 VQIDSLKSQINVVENDLKRKKEKLKRKKELEEkEKQYEEIEKRKKELEEKEKQYEEIEKRLTYVLKNIErQKNEIEKLNyV 382
                                   589999999999999999999999866554444556677888889999999999999999999999988877777776524 PP

                       DUF4407 218 elaeleaerakeraasqaaaaaddGllar 246
                                     ++le+++++  ++ ++  ++ +Gll+r
  gi|70605904|ref|YP_254774.1| 383 DTQDLENKIKDVSDRINQIDNELKGLLDR 411
                                   67788899999999999999999999998 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0055
                       DUF4407 121 kelkeqlaaaltaelaeleaqiaalqaeidaaearldal...raeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                   +e+k++++++ + +l el++qi+alqa i+++ +++++l   r+++q el+  +         +  ++++k ++l+++++e
  gi|70605904|ref|YP_254774.1| 446 SEHKAKIREEIKVQLLELNKQITALQARINSLIKEREELeatRNKLQLELQKRS--------KEKGIYEAKLKELQRLEEE 518
                                   567778888877788888888888888888776555444000555555555422........2344566666666666666 PP

                       DUF4407 199 laelkakld................................atarlaalraelaeleaerakera 231
                                    ++l++++                                  ++++++++++l+el++++++ ++
  gi|70605904|ref|YP_254774.1| 519 KNKLQNEILsllsyhqefeniaekekelidyheeylknsdiLEEDIQEQEQRLNELNSKLSELEK 583
                                   66666665566666667777777777777777777776666666666666666666666555544 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0032
                       DUF4407 113 aeeqqeeakelkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.................... 171
                                   ae+ +e ++ ++e l+++  l+++++e e+++++l+++++++e+ +++ +a++q      k                    
  gi|70605904|ref|YP_254774.1| 540 AEKEKELIDYHEEYLKNSdiLEEDIQEQEQRLNELNSKLSELEKSYNDYKAKYQFLPADLKslvsleerirrriseleklk 620
                                   344444444444444444899999999999999999999999999999999999887765578888888888888888888 PP

                       DUF4407 172 ......gtgttgvaGkgpaakekkaqldaaqaelaelkakld....atarlaalraelaeleaerakeraas 233
                                         ++++t+++G  +++++ k++ da+ +++ el  + +     ++ +++l + l+++ea++ k++ + 
  gi|70605904|ref|YP_254774.1| 621 ieyerlKEEITRMKGLKEEYEKLKEEEDALLNRISELGYSEKrykqLEEIIDKLSKILSGIEADKGKIKGSL 692
                                   888888788888888888888888888888888888776644666644444444444444444444444444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.9    0.0011       1.3      62     101 ..     191     230 ..     177     236 .. 0.86
   2 ?    2.6   4.4      0.14   1.6e+02      39      94 ..     237     292 ..     233     295 .. 0.86
   3 ?   10.7  16.7   0.00041      0.46      39     104 ..     298     369 ..     292     371 .. 0.91
   4 ?    4.4   1.1     0.039        44      68     100 ..     375     408 ..     367     415 .. 0.52
   5 ?    7.2  13.4    0.0052       5.8      26      89 ..     462     525 ..     446     531 .. 0.81
   6 ?    2.8  15.5      0.12   1.4e+02      14     100 ..     495     581 ..     492     595 .. 0.88
   7 ?   15.0   8.2   1.9e-05     0.021      25      99 ..     596     673 ..     586     682 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                                   CCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  62 akkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                   +k++++++++l++e++e+k +l+++e e ke e+el+++ 
  gi|70605904|ref|YP_254774.1| 191 LKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDELNQYN 230
                                   455669*******************************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                   +e++v+ + l  e   ++k+I+++  + +d ee  ++ +++ +e+k+l+++ ++++
  gi|70605904|ref|YP_254774.1| 237 KEIKVQYDILSGELSVVNKKIEEIALRLKDFEEKEKRYNKIETEVKELDENREKIN 292
                                   77888888888888899999999999999999999999999999999999988875 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00041
                                   HHHHHHHHHHHHHHHHHHHHCCCCCCTT......S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkk......edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                   +++ v++++l+++ N + +  +++k+k       e++e+  +e+++ k+el+++e++ +e+e++l+ +l +i
  gi|70605904|ref|YP_254774.1| 298 KSILVQIDSLKSQINVVENDLKRKKEKLkrkkelEEKEKQYEEIEKRKKELEEKEKQYEEIEKRLTYVLKNI 369
                                   78999**************999988765677799*********************************99987 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.039
                                   -TCCCC.CCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  68 daeeli.aevkelkeelkaleaelkeleaelekl 100
                                   ++e+l   ++++l +++k+++++ +++++el+ l
  gi|70605904|ref|YP_254774.1| 375 EIEKLNyVDTQDLENKIKDVSDRINQIDNELKGL 408
                                   3333321345556666666666666666666554 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0052
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleae 89 
                                   ++ +++ +l+++  +l++e eel a rN+l+ e +k +k+k   e+ ++e + l ee ++l++e
  gi|70605904|ref|YP_254774.1| 462 ELNKQITALQARINSLIKEREELEATRNKLQLELQKRSKEKGIYEAKLKELQRLEEEKNKLQNE 525
                                   5668999**********************************77777788888888777777665 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.12
                                   HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkaleaelkel 93 
                                   ++++ k++g ++a+++el  l+e++ +lq+e+ +l + + e   +I+++ k+  +  ee ++ ++ l e++++ e++l+el
  gi|70605904|ref|YP_254774.1| 495 LQKRSKEKGIYEAKLKELQRLEEEKNKLQNEILSLLSYHQEFE-NIAEKEKELiDYHEEYLKNSDILEEDIQEQEQRLNEL 574
                                   5788899999****************************99985.6888888888888999999999999999999999999 PP

                                   HHHHHHH CS
                  Seryl_tRNA_N  94 eaelekl 100
                                   +++l +l
  gi|70605904|ref|YP_254774.1| 575 NSKLSEL 581
                                   9988765 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 1.9e-05
                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHH...HHHHHHHHHHHHH CS
                  Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkal...eaelkeleaelek 99 
                                   +ad+++l++l+e+ r+ ++ele+l+ e  +l +eI ++k  ke+ e+l++e ++l +++++l   e++ k+le+ ++k
  gi|70605904|ref|YP_254774.1| 596 PADLKSLVSLEERIRRRISELEKLKIEYERLKEEITRMKGLKEEYEKLKEEEDALLNRISELgysEKRYKQLEEIIDK 673
                                   7899******************************************************99983333333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.5   8.4e+03      47      61 ..     107     121 ..      93     126 .. 0.68
   2 ?    5.8   3.3     0.017        19       9      66 ..     170     227 ..     169     239 .. 0.85
   3 ?    6.4   0.3     0.011        13      25      62 ..     224     261 ..     219     265 .. 0.91
   4 ?    6.7   0.7    0.0091        10      18      64 ..     248     294 ..     240     301 .. 0.82
   5 ?    1.6   2.4      0.36     4e+02      15      61 ..     269     314 ..     262     320 .. 0.59
   6 ?    6.7   0.8    0.0092        10       9      45 ..     452     492 ..     450     501 .. 0.78
   7 ?    5.2   0.2     0.026        29      34      63 ..     554     583 ..     545     599 .. 0.75
   8 ?    5.6   0.3     0.019        22      11      54 ..     562     605 ..     557     622 .. 0.68
   9 ?    8.8   0.4     0.002       2.3       6      49 ..     674     718 ..     671     745 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.5
                       NPV_P10  47 qsaqLaeletkvenI 61 
                                   ++ q +++++k+++I
  gi|70605904|ref|YP_254774.1| 107 LARQSTTVNNKIKEI 121
                                   555666666666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                       NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   I + ik + d++ +lq+  d ++ +  +++ l+++++++  +L+++e + ++ +d Ln
  gi|70605904|ref|YP_254774.1| 170 IHSLIKVLTDRIRSLQSIKDILKREEAEIDRLKKEIEEIKVKLENIEREAKEKEDELN 227
                                   5666999999999999999999999999999999999999999999998777777776 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.011
                       NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                   +++++ +++++ ++e++ + d +s +L  +++k+e+I 
  gi|70605904|ref|YP_254774.1| 224 DELNQYNTEFNRIKEIKVQYDILSGELSVVNKKIEEIA 261
                                   578899999***************************96 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0091
                       NPV_P10  18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                     ++++++++++++  l+d++e +++ +++ ++++el+++ e+I+ i
  gi|70605904|ref|YP_254774.1| 248 GELSVVNKKIEEIALRLKDFEEKEKRYNKIETEVKELDENREKINTI 294
                                   56788999999999999999999999999999999999965555554 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.36
                       NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                   + +++ + ++++v++++en ++++ +++ + ++  q+++l+++++ +
  gi|70605904|ref|YP_254774.1| 269 EKEKRYNKIETEVKELDENREKINTISS-FKSILVQIDSLKSQINVV 314
                                   5555666778888888888888776654.455555555555554444 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.0092
                       NPV_P10   9 Iradik....avddkVdalqqqvddvqenlpdvtelnekLd 45 
                                   Ir++ik    +++++++alq++++++ ++ ++++   +kL+
  gi|70605904|ref|YP_254774.1| 452 IREEIKvqllELNKQITALQARINSLIKEREELEATRNKLQ 492
                                   555554333389**************999999888887775 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.026
                       NPV_P10  34 lpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   l++ + l+e +++q + L+el++k+++ ++
  gi|70605904|ref|YP_254774.1| 554 LKNSDILEEDIQEQEQRLNELNSKLSELEK 583
                                   667677788888888888888888877665 PP

  == domain 8  score: 5.6 bits;  conditional E-value: 0.019
                       NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                   +di++ +++++ l++++ ++++  +d +   + L a  ++L +l
  gi|70605904|ref|YP_254774.1| 562 EDIQEQEQRLNELNSKLSELEKSYNDYKAKYQFLPADLKSLVSL 605
                                   68888888888888888888888888554444444444444444 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.002
                       NPV_P10   6 LlvIradikavddkVd.alqqqvddvqenlpdvtelnekLdaqsa 49 
                                   L  I++ i+a + k++ +l++++++++e+ ++++el +k+++ s+
  gi|70605904|ref|YP_254774.1| 674 LSKILSGIEADKGKIKgSLEEKIKNIEEKERNIEELRNKMNEESK 718
                                   678999999999999758**********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3719  (0.207429); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                       311  (0.0173462); expected 17.9 (0.001)
Passed Fwd filter:                       172  (0.0095934); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 3.82u 0.42s 00:00:04.24 Elapsed: 00:00:00.83
# Mc/sec: 3216.89
//
Query:       gi|70605905|ref|YP_254775.1|  [L=382]
Description: DNA double-strand break repair Mre11 nuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-14   53.0   0.4    1.1e-13   52.1   0.4    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    6.8e-11   42.6   0.0    1.5e-10   41.5   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
        2.3    8.9   6.7        2.4    8.8   1.6    2.8  3  ATP-cone       ATP cone domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.4   1.9e-17   1.1e-13       1     203 [.       1     190 [.       1     191 [. 0.77

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.9e-17
                                   EEEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH...TSEEEE CS
                   Metallophos   1 lrilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky...pipvyl 69 
                                   + +l+i+D+Hl        +++   +d++ +l+d +++e  + +v+++GDl+d ++++++     +++l ++   +ip+++
  gi|70605905|ref|YP_254775.1|   1 MQLLHISDTHLgkrqynleSREKDVYDTFTQLIDIAINE-HVKAVIHTGDLFDVNNPPNRAKLHaIKELKRLkdhNIPFIC 80 
                                   5789***************9999**********777777.***************66665555557777777888****** PP

                                   EC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCH CS
                   Metallophos  70 llGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGgspellvsldklgslnleleapepgd 148
                                   ++G H+    + ++k   ++i+++ +    e fn + + + +++   l+ + ++G               +++ +++   +
  gi|70605905|ref|YP_254775.1|  81 IAGDHD----SPKRK---EEIYPQRI---LEEFNLIKILQKIDNRvkLENVEVYGI--------------SHISNVSV--N 135
                                   ******....44444...44555555...8889*******9999566555555555..............44444444..3 PP

                                   HHHHH.HHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 149 ewlkd.lekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                   ++ ++ ++ + +++  i++ H ++   + ++ g  ++e     +g  l+  GH H 
  gi|70605905|ref|YP_254775.1| 136 DLKEQlSKVKPETRKSILMLHQGIR-TYLPYQGAWQIELSDLPKGFSLYAVGHLHS 190
                                   333334446999*************.777777777777557788899999999995 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.6e-14   1.5e-10       1     153 [.       1     215 [.       1     223 [. 0.72

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                 Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep......evleellela....pvlaV 57 
                                   M+l++iSD+H             + +d   ++++++ ++ v a+ih+GDl    +p      ++++el++l+    p++ +
  gi|70605905|ref|YP_254775.1|   1 MQLLHISDTHlgkrqynlesrekDVYDTFTQLIDIAINEHVKAVIHTGDLfDVNNPpnraklHAIKELKRLKdhniPFICI 81 
                                   9**************99999999899999999****9*99*********87334444444445666666666888****** PP

                 Metallophos_2  58 rGNnD................................eevveedvlreaaelgtdlpeeaelel...agek..vlliHgdp 101
                                    G++D                                e+v++  +++ ++   +dl+e+   ++      +  +l++H+  
  gi|70605905|ref|YP_254775.1|  82 AGDHDspkrkeeiypqrileefnlikilqkidnrvklENVEVYGISHISNVSVNDLKEQ-LSKVkpeT--RksILMLHQG- 158
                                   *********99999888888888887777776666655555555566666666666422.22223223..2469999998. PP

                 Metallophos_2 102 l....gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvv.nPGsvgeprdgd 153
                                         ++ a +  l++  +g  ++++GH H ++++  +g  ++  +Gs+   r ++
  gi|70605905|ref|YP_254775.1| 159 IrtylPYQGAWQIELSDLPKGFSLYAVGHLHSRRKDYLDGGALIeIAGSPDIMREEE 215
                                   45988555555555555334455**********999886554443799988777665 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.068   4.1e+02      11      48 ..     101     141 ..      98     150 .. 0.66
   2 ?    8.8   1.6    0.0004       2.4       2      64 ..     242     310 ..     241     329 .. 0.70
   3 ?   -2.3   0.0       1.2   7.1e+03      56      66 ..     335     345 ..     313     374 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.068
                                   EE--HHHHHHHHHHHHHH-HHH...HHHHHHHHHHHHHHHH CS
                      ATP-cone  11 epfdvekIkraiekAcegseee...ideiaeeveaevrkrl 48 
                                   e+f+  kI + i + ++ ++ e   i+ i++  +++++++l
  gi|70605905|ref|YP_254775.1| 101 EEFNLIKILQKIDNRVKLENVEvygISHISNVSVNDLKEQL 141
                                   89**********99865533332246666555556666655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0004
                                   EEE-TTS-EEE--HHHHHHHHHHHHHH.....-HHHHHHHHHHHHHHHHHHHIIT.-BHHHHHHHHHHH CS
                      ATP-cone   2 kViKRdGtvepfdvekIkraiekAceg.....seeeideiaeeveaevrkrlrdg.isteeIqdlvekt 64 
                                   +V  Rd+ v +++v+kI+++ie   ++     ++++   +  e+e  v +r++    + + ++d ve++
  gi|70605905|ref|YP_254775.1| 242 NVNIRDQLVLDINVDKIEQSIESVIQKlkenvKNDKKPILHIELEGTVPIRKDVLmTKLQALRDYVEHY 310
                                   56679999*******************776654444334444666666666555534455566666654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHH CS
                      ATP-cone  56 eIqdlvektli 66 
                                    + d+++++l+
  gi|70605905|ref|YP_254775.1| 335 SLNDIIADYLK 345
                                   44455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1456  (0.0812092); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2609.18
//
Query:       gi|70605906|ref|YP_254776.1|  [L=495]
Description: hypothetical protein Saci_0053 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-48  166.2   3.7    1.8e-48  165.6   3.7    1.3  1  DUF87          Helicase HerA, central domain
    1.3e-12   47.7   1.0    3.9e-12   46.1   0.0    2.4  2  HAS-barrel     HAS barrel domain
    2.6e-12   46.1   0.0    9.3e-07   27.8   0.0    2.3  2  DUF853         Bacterial protein of unknown function (DUF853)
    0.00033   19.7   0.0     0.0019   17.2   0.0    2.0  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00056   19.3   0.1      0.029   13.7   0.0    2.4  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0044   16.0   0.2       0.52    9.2   0.2    2.3  2  AAA_10         AAA-like domain
     0.0048   15.6   1.0     0.0076   14.9   1.0    1.3  1  DHC_N1         Dynein heavy chain, N-terminal region 1
      0.006   15.8   1.0       0.01   15.1   1.0    1.3  1  Dynamin_M      Dynamin central region
     0.0072   16.1   0.2       0.14   12.0   0.1    2.6  2  IF2_N          Translation initiation factor IF-2, N-terminal
  ------ inclusion threshold ------
       0.04   13.9   1.3        2.2    8.3   1.3    2.7  1  ResIII         Type III restriction enzyme, res subunit
      0.071   12.9   0.8         11    5.7   0.1    2.6  2  DEAD           DEAD/DEAH box helicase
       0.11   12.2   0.3        0.2   11.4   0.3    1.4  1  DUF1848        Domain of unknown function (DUF1848)
       0.13   12.8   1.6       0.28   11.7   1.6    1.6  1  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   3.7   1.3e-51   1.8e-48       1     227 []     121     331 ..     121     331 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 1.3e-51
                         DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitp 81 
                                   ++iG+l+ gs+v+v+++ln l +rHlAil+ TGsGKSntva+L ++l+ + g++ili+D HGEY++ +     +++++i+p
  gi|70605906|ref|YP_254776.1| 121 VRIGKLI-GSNVEVKIRLNPL-SRHLAILAATGSGKSNTVAILSQRLV-EIGGSILIFDYHGEYYDST----LPNLNIIEP 194
                                   68****7.999*******888.**************************.*******************....********* PP

                         DUF87  82 spsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka....keekeklssdepveklleelk..kekee 156
                                            k+np  l+++e+++lle+  +++a++q+++++++++q+k+    + +++k+s +e+  +++e lk  +e+e+
  gi|70605906|ref|YP_254776.1| 195 ---------KLNPLYLSVNEFATLLEI--RENANIQYRIIRRTFNQLKEeinnEIKEGKTSLAELNSNFFERLKvkIEEEG 264
                                   .........9*****************..**********************999999999*************9999999* PP

                         DUF87 157 lrklknqaiarlldkledllrkggsf.snsstdliallleklekegkitiidlsgvdelaqqlvvsvilrri 227
                                   +++++++++ ++l+k+ed+ ++++++ + +  d+i+++     k gki++++ls++de+a +++v+++lrri
  gi|70605906|ref|YP_254776.1| 265 RNEKRKESKDEVLNKVEDFAERYSDIiDITFGDVINKI-----KLGKINVVNLSSLDEDAIDAIVAHYLRRI 331
                                   **************************99999*******.....***************************97 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   2.8e-15   3.9e-12       1      90 [.       3      87 ..       3      89 .. 0.91
   2 ?   -2.6   0.1       4.5   6.2e+03      65      81 ..     266     282 ..     257     303 .. 0.58

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.8e-15
                    HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn...selsndlalvlsleeleeangddevalate 80
                                  iG++ig++t+++ ++ +e   +++ G yV+ e++ g+++lG++t++ +g+   ++++nd ++v+++++le++    ++++a +
  gi|70605906|ref|YP_254776.1|  3 IGYIIGSATINEATAILEQ--KIRAGYYVILEYD-GDKILGLITNVYTGSpllDDNLNDVKFVQRIKQLEANKIP-FFIKARI 81
                                  8*****************9..*************.**********************************988765.6666666 PP

                    HAS-barrel 81 dtgvkvlGev 90
                                      k+l+++
  gi|70605906|ref|YP_254776.1| 82 ----KLLCKL 87
                                  ....777766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.5
                    HAS-barrel  65 eleeangddevalated 81 
                                   +++++++ dev+ ++ed
  gi|70605906|ref|YP_254776.1| 266 NEKRKESKDEVLNKVED 282
                                   45555555555555543 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.6e-06    0.0035      10      60 ..     130     180 ..     125     188 .. 0.92
   2 !   27.8   0.0   6.7e-10   9.3e-07     262     361 ..     353     447 ..     305     464 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.6e-06
                        DUF853  10 eqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGd 60 
                                   + e++++l+   rh  i  atG Gk  t+ +l++ l e+G ++++ d  G+
  gi|70605906|ref|YP_254776.1| 130 NVEVKIRLNPLSRHLAILAATGSGKSNTVAILSQRLVEIGGSILIFDYHGE 180
                                   56788999999************************************9987 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 6.7e-10
                        DUF853 262 ffdeahLLfndapkallekv.eqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfra 341
                                     +eah+L+ + +++l +k   ++ r  r  GvG+  v+q P  l +++L+q+ n++   l+   p d+k v  ++d +  
  gi|70605906|ref|YP_254776.1| 353 VVEEAHVLLSKDTNTLTKKWaGRIAREGRKFGVGLIIVSQRPKGLDENILSQMTNKI--ILKIVEPSDKKYVLETSDNLS- 430
                                   468****999999999998626899*******************************9..5999********999988665. PP

                        DUF853 342 npefdveeaiteLgvGealv 361
                                       d+++ +++L++Gea++
  gi|70605906|ref|YP_254776.1| 431 ---EDLADGLSSLDTGEAII 447
                                   ...5899***********98 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0019      15      58 ..     141     184 ..     131     239 .. 0.89
   2 ?   -0.2   0.0      0.26   3.5e+02     265     296 ..     377     408 ..     374     434 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                 TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGafvsr 58 
                                    +h++i+ +tGsGK++++  l + + + g  ++++D +G++++ 
  gi|70605906|ref|YP_254776.1| 141 SRHLAILAATGSGKSNTVAILSQRLVEIGGSILIFDYHGEYYDS 184
                                   69***************************************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                 TrwB_AAD_bind 265 laegRkfGgavvlglqsiaqlrevYGedaaqs 296
                                   + egRkfG+ +++  q  + l e   +++++ 
  gi|70605906|ref|YP_254776.1| 377 AREGRKFGVGLIIVSQRPKGLDENILSQMTNK 408
                                   6799*******999999998875333333333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.1e-05     0.029      17      59 ..     118     161 ..     104     166 .. 0.77
   2 ?    1.9   0.0     0.085   1.2e+02     210     241 ..     363     394 ..     351     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                                   TTEEEEEEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  17 qlpvalgkei.sgnplvldlkkmashllvaGatgsGKStalntL 59 
                                    + v +gk i s+  +++ l++   hl ++ atgsGKS+++  L
  gi|70605906|ref|YP_254776.1| 118 AGDVRIGKLIgSNVEVKIRLNPLSRHLAILAATGSGKSNTVAIL 161
                                   556677777767777777777777***************99755 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.085
                                   HH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                  FtsK_SpoIIIE 210 kdssvlvedaivRlarkgraaglHlllatqrl 241
                                   kd + l ++ + R+ar gr+ g+ l++  qr+
  gi|70605906|ref|YP_254776.1| 363 KDTNTLTKKWAGRIAREGRKFGVGLIIVSQRP 394
                                   66688999999******************998 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00037      0.52      22      83 ..     142     204 ..     135     317 .. 0.63
   2 ?    4.4   0.0     0.011        15     262     314 ..     373     424 ..     346     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                        AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe...iakkinvvtLdse 83 
                                    + +i+  +G GKS ++ +l   ++ +gg +li D   e   +  tlp+   i  k+n + L+ +
  gi|70605906|ref|YP_254776.1| 142 RHLAILAATGSGKSNTVAILSQRLVEIGGSILIFDYHGE--YYDSTLPNlniIEPKLNPLYLSVN 204
                                   578999********************************9..444455443336667777777633 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                        AAA_10 262 lkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvLe 314
                                      + R GR++   +++v+q ++ ++++    ++  k++ + ++ +++k vLe
  gi|70605906|ref|YP_254776.1| 373 AGRIAREGRKFGVGLIIVSQRPKGLDENI-LSQMTNKIILKIVEPSDKKYVLE 424
                                   44689******************987654.45566677777777777776665 PP

>> DHC_N1  Dynein heavy chain, N-terminal region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.0   5.5e-06    0.0076     165     232 ..     227     294 ..     211     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.5e-06
                        DHC_N1 165 fgqeveeaikklkeaielleawkeeyeektrekleespkekpwefdeksiFarldafleRlekllelf 232
                                   f+q +ee+ + +ke ++ l++ ++ ++e+++ k+ee++++++ + ++  ++++++ f+eR  ++++++
  gi|70605906|ref|YP_254776.1| 227 FNQLKEEINNEIKEGKTSLAELNSNFFERLKVKIEEEGRNEKRKESKDEVLNKVEDFAERYSDIIDIT 294
                                   556678********************99*******99988888888889****************985 PP

>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.0   7.3e-06      0.01      68     131 ..     217     294 ..     212     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
                     Dynamin_M  68 qiLvehIrkslPelkkkineklqklekeleelg.............eskpsde.ektklllqlitkfkedfkklieGe 131
                                   +i++++Ir+++ +lk++in+++++ +  l+el              e+++++  e +  +l+++++f+e ++++i+ +
  gi|70605906|ref|YP_254776.1| 217 NIQYRIIRRTFNQLKEEINNEIKEGKTSLAELNsnfferlkvkieeEGRNEKRkESKDEVLNKVEDFAERYSDIIDIT 294
                                   6899*************************************999874444444799999***************9854 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.25   3.5e+02       4      16 ..     201     213 ..     199     218 .. 0.86
   2 !   12.0   0.1    0.0001      0.14       6      52 ..     280     328 ..     278     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.25
                         IF2_N   4 irVyeLAkeLgvk 16 
                                   ++V+e+A  L ++
  gi|70605906|ref|YP_254776.1| 201 LSVNEFATLLEIR 213
                                   69********986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                         IF2_N   6 VyeLAkeLg....vkskevikkLfkelGievkshsssLDeetaeliaeefg 52 
                                   V ++A++      ++  +vi k  k lG+  +   ssLDe+++ +i+ ++ 
  gi|70605906|ref|YP_254776.1| 280 VEDFAERYSdiidITFGDVINKI-K-LGKINVVNLSSLDEDAIDAIVAHYL 328
                                   666666666666677789*****.*.***********************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.3    0.0016       2.2      25      75 ..     142     243 ..     124     387 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                                   SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG............................... CS
                        ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef............................... 74 
                                   +++ i +aTG+GK+ + a l +rl + g+   +l++    + ++ tl ++                               
  gi|70605906|ref|YP_254776.1| 142 RHLAILAATGSGKSNTVAILSQRLVEIGG--SILIFDYHGEYYDSTLPNLniiepklnplylsvnefatlleirenaniqy 220
                                   6778999**********999999998877..55555555555555554444444444444444444455555555555555 PP

                                   ......................G CS
                        ResIII  75 ......................k 75 
                                                         +
  gi|70605906|ref|YP_254776.1| 221 riirrtfnqlkeeinneikegkT 243
                                   55555554444444444444440 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.015        21      15      33 ..     142     160 ..     134     194 .. 0.85
   2 ?    5.7   0.1    0.0079        11      84     150 ..     305     377 ..     267     391 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                                   CEEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          DEAD  15 gdvlvaaeTGsGKTlafli 33 
                                   +++ + a+TGsGK+   +i
  gi|70605906|ref|YP_254776.1| 142 RHLAILAATGSGKSNTVAI 160
                                   567789********98776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0079
                                   TSSHHHHHHHHHTT.CSEEEEEH.HHHHHHHHCTSSH....CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                   xxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  84 gvaardqlskldng.vdivvgtp.grlddllstgkln....lsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                   g+    +ls ld++ +d +v+    r++   +++k++    l+   + V+ Ea+ ll+++     ++ + +++
  gi|70605906|ref|YP_254776.1| 305 GKINVVNLSSLDEDaIDAIVAHYlRRILTSRKENKIKkdsgLKFPILTVVEEAHVLLSKDTNTLTKKWAGRIA 377
                                   45555666777655577777666133333335555556555777777************98888888777775 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00014       0.2     125     231 ..     216     333 ..     191     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                       DUF1848 125 ekltvelhlekfeklaeelkgytekvviSfvdlykkvkrnlkk...klelrelseeekeelaeelaeiakkl....glela 198
                                   ++++ +  +++f++l ee+++ +++  +S+++l +++ ++lk    +   +e ++e+k+e++++++++a+++    +++  
  gi|70605906|ref|YP_254776.1| 216 ANIQYRIIRRTFNQLKEEINNEIKEGKTSLAELNSNFFERLKVkieEEGRNEKRKESKDEVLNKVEDFAERYsdiiDITFG 296
                                   4577778889***********************999888886433225667777888889999999998766332367888 PP

                       DUF1848 199 tCaekedlselgieknkCidkellerllgkkl....k 231
                                      +k++l ++++ + + +d++ +  ++ + l    +
  gi|70605906|ref|YP_254776.1| 297 DVINKIKLGKINVVNLSSLDEDAIDAIVAHYLrrilT 333
                                   8899999999999999999999999888766544441 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.6    0.0002      0.28      11      43 ..     141     212 ..     129     296 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                   TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.......................................E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................x RF
                      ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei.......................................l 43 
                                   ++ +ai+  +G+GKS  +++l++ l    G+i                                        
  gi|70605906|ref|YP_254776.1| 141 SRHLAILAATGSGKSNTVAILSQRLVEIGGSIlifdyhgeyydstlpnlniiepklnplylsvnefatlleI 212
                                   56799***************************6666666666666666666666555555555555554431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3249.16
//
Query:       gi|70605907|ref|YP_254777.1|  [L=138]
Description: hypothetical protein Saci_0054 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00067   19.6   2.3       0.18   11.6   0.3    2.1  2  Phyto-Amp     Antigenic membrane protein of phytoplasma
    0.00086   19.7   9.5      0.073   13.5   3.0    2.1  2  Rubrerythrin  Rubrerythrin
     0.0022   17.8   0.0          3    7.8   0.0    2.5  2  Big_2         Bacterial Ig-like domain (group 2)
     0.0028   17.3   0.5     0.0038   16.9   0.5    1.3  1  BURP          BURP domain
     0.0038   17.2   8.6       0.13   12.3   1.1    2.1  2  DUF892        Domain of unknown function (DUF892)
  ------ inclusion threshold ------
      0.012   15.5   4.5       0.52   10.2   0.5    2.1  2  Ferritin      Ferritin-like domain
      0.013   15.9   0.7        4.1    7.9   0.1    2.4  2  TRCF          TRCF domain
       0.26   11.4   3.6        3.4    7.8   0.9    2.2  3  CDC37_C       Cdc37 C terminal domain


Domain annotation for each model (and alignments):
>> Phyto-Amp  Antigenic membrane protein of phytoplasma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   7.9e-05      0.18     107     167 ..      23      83 ..      15      93 .. 0.79
   2 !    8.1   0.1   0.00096       2.2     121     158 ..      97     135 ..      92     138 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                     Phyto-Amp 107 ilnlvgvcelnkltlgtekkltltvk.dgkvdaeaglkalkeagakvpatvnkddvtftvgk 167
                                   il+   + e +   + t +k+++t k +g  d ea l a+ e  ak+  tv k    + v k
  gi|70605907|ref|YP_254777.1|  23 ILEEFSIKEGE-EHISTYNKIAMTAKaEGYADIEAMLCAFAEEEAKIAETVGKVATELKVKK 83 
                                   55555555544.56789999***9985799**********************9888777766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00096
                     Phyto-Amp 121 lgtekkltltvk.dgkvdaeaglkalkeagakvpatvnk 158
                                   + t +k+++t k +g  d ea l a+ e  ak+  tv k
  gi|70605907|ref|YP_254777.1|  97 ISTYNKIAMTAKaEGYADIEAMLCAFAEEEAKIAETVGK 135
                                   5688999999985799********************987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.0   3.3e-05     0.073       6      66 ..      28      90 ..      22      96 .. 0.84
   2 !   10.5   1.2   0.00028      0.62      11      44 ..      94     128 ..      83     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                  HHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SS CS
                  Rubrerythrin  6 AiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepele.levke 66
                                  +i+  ++ ++ Y+ +a  ak egy +i++++ ++AeeE++ a+ + k+  +l+ ++   ++ +
  gi|70605907|ref|YP_254777.1| 28 SIKEGEEHISTYNKIAMTAKaEGYADIEAMLCAFAEEEAKIAETVGKVATELKVKKLlSDFAT 90
                                  6666678899******************************99999999999998877555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00028
                                   HHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHH CS
                  Rubrerythrin  11 ssarrlYkelaekak.egypqiaelFeelAeeEre 44 
                                   ++ ++ Y+ +a  ak egy +i++++ ++AeeE++
  gi|70605907|ref|YP_254777.1|  94 EEHISTYNKIAMTAKaEGYADIEAMLCAFAEEEAK 128
                                   45678899999999999999999999999999987 PP

>> Big_2  Bacterial Ig-like domain (group 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0014         3      49      68 ..      39      58 ..      26      68 .. 0.82
   2 !    7.7   0.0    0.0015       3.3      50      68 ..     101     119 ..      89     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                                  ETCCEECCCSSEEEEEEEEE CS
                         Big_2 49 satGlVtavaaGkatitats 68
                                   +++ +ta+a+G a+i+a+ 
  gi|70605907|ref|YP_254777.1| 39 YNKIAMTAKAEGYADIEAML 58
                                  38999*************86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                   TCCEECCCSSEEEEEEEEE CS
                         Big_2  50 atGlVtavaaGkatitats 68 
                                   +++ +ta+a+G a+i+a+ 
  gi|70605907|ref|YP_254777.1| 101 NKIAMTAKAEGYADIEAML 119
                                   8999*************86 PP

>> BURP  BURP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   1.7e-06    0.0038      31     115 ..       5      92 ..       2     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                          BURP  31 lprkvadsipfsskklpeilktfsikegsaeakeiketleeCeappikg.ekkaCatSles..mvdfaasvlgtkdvrals 108
                                   lp++ + +ip+ s+k+++il+ fsikeg+++ ++ ++   + +a+  ++ e+  Ca   e+  +++ + +v  + +v+ l 
  gi|70605907|ref|YP_254777.1|   5 LPSDYSLRIPMISSKVEKILEEFSIKEGEEHISTYNKIAMTAKAEGYADiEAMLCAFAEEEakIAETVGKVATELKVKKLL 85 
                                   88899999***********************9999998888888886666******9888622345554544455666666 PP

                          BURP 109 tevekes 115
                                   +++++++
  gi|70605907|ref|YP_254777.1|  86 SDFATKE 92 
                                   6665552 PP

>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.1   5.8e-05      0.13     110     156 ..      36      82 ..      28      85 .. 0.92
   2 !    9.5   1.2   0.00043      0.96     110     150 ..      97     137 ..      88     138 .] 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                                   HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892 110 iAsYgtLialAeqlgekeaaklLeqtleeekatdekltelaeslvnq 156
                                   i++Y+ ++  A++ g++++ ++L +  eee + +e++ ++a++l  +
  gi|70605907|ref|YP_254777.1|  36 ISTYNKIAMTAKAEGYADIEAMLCAFAEEEAKIAETVGKVATELKVK 82 
                                   99**************************************9987655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00043
                                   HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF892 110 iAsYgtLialAeqlgekeaaklLeqtleeekatdekltela 150
                                   i++Y+ ++  A++ g++++ ++L +  eee + +e++ ++a
  gi|70605907|ref|YP_254777.1|  97 ISTYNKIAMTAKAEGYADIEAMLCAFAEEEAKIAETVGKVA 137
                                   99*********************************998876 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00023      0.52      87     139 ..      27      79 ..      10      82 .. 0.84
   2 ?    7.4   0.3    0.0017       3.8      93     133 ..      94     134 ..      81     138 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                   HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  87 aalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                     ++  ++ ++++++++  a++eg    + +l  f ee+ + ++++ ++ ++l
  gi|70605907|ref|YP_254777.1|  27 FSIKEGEEHISTYNKIAMTAKAEGYADIEAMLCAFAEEEAKIAETVGKVATEL 79 
                                   46777789999****************************99999998887776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  93 kkvteslrelielaeeegDpatadfledfleeqeehewele 133
                                   ++ ++++++++  a++eg    + +l  f ee+ + ++++ 
  gi|70605907|ref|YP_254777.1|  94 EEHISTYNKIAMTAKAEGYADIEAMLCAFAEEEAKIAETVG 134
                                   67788899999999999999999999999999888777765 PP

>> TRCF  TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0018       4.1       4      41 ..      21      58 ..      18      61 .. 0.85
   2 ?    6.3   0.0    0.0054        12      11      41 ..      89     119 ..      79     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                          TRCF  4 dalipeeYipdeserlelYkriasieteeeldeleeeL 41
                                  + ++ e  i++ +e +++Y++ia  ++ e + ++e+ L
  gi|70605907|ref|YP_254777.1| 21 EKILEEFSIKEGEEHISTYNKIAMTAKAEGYADIEAML 58
                                  5566666699999*******************999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0054
                          TRCF  11 YipdeserlelYkriasieteeeldeleeeL 41 
                                     ++ +e +++Y++ia  ++ e + ++e+ L
  gi|70605907|ref|YP_254777.1|  89 ATKEGEEHISTYNKIAMTAKAEGYADIEAML 119
                                   55677899*****************999876 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0015       3.4      37      68 ..      19      50 ..      17      78 .. 0.75
   2 ?    4.2   0.5     0.021        47      60      89 ..      76     105 ..      52     116 .. 0.63
   3 ?    3.8   0.1     0.028        64      37      63 ..      80     106 ..      75     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                       CDC37_C 37 evnkvlakmkveeAeeilellgeagilsleel 68
                                  +v+k+l++ +++e ee+++  ++  +    e+
  gi|70605907|ref|YP_254777.1| 19 KVEKILEEFSIKEGEEHISTYNKIAMTAKAEG 50
                                  799****************9999887754444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.021
                       CDC37_C  60 agilsleellvdatteegekelkeleeekk 89 
                                   a  l++++ll d +t+ege++++  ++ + 
  gi|70605907|ref|YP_254777.1|  76 ATELKVKKLLSDFATKEGEEHISTYNKIAM 105
                                   455667777777777777777766655444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.028
                       CDC37_C  37 evnkvlakmkveeAeeilellgeagil 63 
                                   +v k l++   +e ee+++  ++  + 
  gi|70605907|ref|YP_254777.1|  80 KVKKLLSDFATKEGEEHISTYNKIAMT 106
                                   466666666667777766666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 979.48
//
Query:       gi|70605908|ref|YP_254778.1|  [L=135]
Description: hypothetical protein Saci_0055 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.4   0.1      0.019   14.2   0.1    1.0  1  FTR1      Iron permease FTR1 family
       0.13   12.9   7.7        1.1    9.8   7.7    2.2  1  FliL      Flagellar basal body-associated protein FliL


Domain annotation for each model (and alignments):
>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.1e-06     0.019      35     114 ..      42     126 ..      17     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-06
                          FTR1  35 k....lqvwagialavllalaigqafasitaalqkdkalieeellegvlsliavvviswmilwmrrv.gkklkeeveqkla 110
                                   k    + v++g a ++l++++ + +++ it  ++++ ++ +e+l e ++  + v ++s ++ + +    ++l++++++k +
  gi|70605908|ref|YP_254778.1|  42 KirekALVELGHARGILEKMIKYLGLEYITNWFEELNKKESEQLKEKFMLTATVYMLSKLLAEKLPErKNELETKSKEKYE 122
                                   1335599***************************75555555555555555556689999888776668888888888888 PP

                          FTR1 111 kava 114
                                   +a++
  gi|70605908|ref|YP_254778.1| 123 EAKK 126
                                   8764 PP

>> FliL  Flagellar basal body-associated protein FliL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.7   0.00013       1.1      42      79 ..      15      52 ..       2     135 .] 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                          FliL 42 epeirdailsllssktaeelstpegkekLkeelleeln 79
                                  ++  +d +l l+ss++ ee++++e  ek++e+ l el 
  gi|70605908|ref|YP_254778.1| 15 MANSEDHLLLLFSSQKLEEVNKKEESEKIREKALVELG 52
                                  6677899*************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1440  (0.0803168); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 958.52
//
Query:       gi|70605909|ref|YP_254779.1|  [L=503]
Description: hypothetical protein Saci_0057 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-54  184.8   0.1    2.5e-54  184.4   0.1    1.2  1  Carb_kinase   Carbohydrate kinase
      3e-39  134.7   0.0    5.2e-39  133.9   0.0    1.4  1  YjeF_N        YjeF-related protein N-terminus
    3.7e-07   29.8   0.1    9.9e-07   28.4   0.0    1.7  2  HK            Hydroxyethylthiazole kinase family
     0.0002   20.8   0.0    0.00037   19.9   0.0    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.057   13.3   0.0    1.4  1  KR            KR domain


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.1   6.9e-58   2.5e-54       1     244 []     235     483 ..     235     483 .. 0.94

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 6.9e-58
                                   EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEEE-TT CS
                   Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavviGpG 76 
                                   vl+igG  +++GA+ l+al+alr ga+lv va  +e ++v+ s +p++i  +l+    ++++  +  +  +++d+vv+GpG
  gi|70605909|ref|YP_254779.1| 235 VLIIGGNFTFSGAPTLSALGALRTGADLVYVASPEETAKVISSFSPDLISIKLKgkniSTDNLdELKPWIDKADVVVVGPG 315
                                   79***************************************************998885555557788899********** PP

                                   -SSSHCHHH....HCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHHHHHH CS
                   Carb_kinase  77 Lgrdekikk....lleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlelarelaq 152
                                   +g++ ++      ++++  +k++p viDAd+L+ +a      e   + ++TPh++Efk  +++    +  +r e ++e + 
  gi|70605909|ref|YP_254779.1| 316 MGQERETVDasieIVRYLKAKNKPSVIDADALKSVAGM----ELFPNAVITPHAGEFKIYSGVQPDsNMRKRIEQVKECSL 392
                                   ***9877666999************************5....677899************9998776999*********** PP

                                   HHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS- CS
                   Carb_kinase 153 klnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgm 233
                                   k+n+vvllkg +d+i++ ++e ++n+tg++++a+GG+GD+L+G+i++++aq+ +++ +a  +a+++g a+  a ek g+ +
  gi|70605909|ref|YP_254779.1| 393 KCNCVVLLKGYVDIIAE-KEEFKLNKTGNPGMAVGGTGDTLTGIIASFMAQKLSPFTSAYLGAFVNGLAGSIAYEKLGAHL 472
                                   ***************99.99************************************************************* PP

                                   HCHHHHHHHCH CS
                   Carb_kinase 234 latelskiipr 244
                                    at++++ ip+
  gi|70605909|ref|YP_254779.1| 473 VATDIIENIPK 483
                                   *******9985 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.0   1.5e-42   5.2e-39       4     171 .]      24     188 ..      21     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.5e-42
                        YjeF_N   4 LmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggk 84 
                                   Lmenagr+v + + ++l n + +kkv+v++G g  Ggdgl++ArhLa+eg +V+vlll e  + + da  +l++  ++  +
  gi|70605909|ref|YP_254779.1|  24 LMENAGRSVKDEIMKRL-NLDYSKKVVVFAGTGGKGGDGLVVARHLASEGSEVHVLLLGE--NKHPDAIINLNAIYEMDYS 101
                                   9****************.899**********************************98865..6788999999999999999 PP

                        YjeF_N  85 vveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadvtvtf 165
                                   + e k  +d +e    ++d++iDA+lG+g++g++re++ ++i+ +n+s+ + +++DiPSG++ad+ + +g+ v +d++vtf
  gi|70605909|ref|YP_254779.1| 102 IREVKLIKDTDELQPVKADVLIDAMLGTGFSGKVREPFRTAIRVFNQSSGFKVSIDIPSGINADDEEQQGEHVIPDLIVTF 182
                                   99988888887777799**************************************************************** PP

                        YjeF_N 166 gapkrg 171
                                   + +k+g
  gi|70605909|ref|YP_254779.1| 183 HDLKPG 188
                                   ***997 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.45   1.6e+03      35      86 ..     292     344 ..     271     353 .. 0.67
   2 !   28.4   0.0   2.8e-10   9.9e-07     126     226 ..     369     467 ..     357     487 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.45
                                   EE--STTTHHHHHHTSSEEEEE-TT--H.HHHHHHHHHHHHHHHTT--EEEE- CS
                            HK  35 imseaeeEvselakianaLllNiGtlee.kaiealkaAvksakevnrPvvlDP 86 
                                   i +++ +E++     a+ +++  G  +e ++++a ++ v+  k++n+P v+D 
  gi|70605909|ref|YP_254779.1| 292 ISTDNLDELKPWIDKADVVVVGPGMGQErETVDASIEIVRYLKAKNKPSVIDA 344
                                   55556666666666666666666655441467888888999999999999985 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.8e-10
                                   CCSCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHH CS
                            HK 126 lkvkGvDskeaataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkll 206
                                       Gv   ++  + +++v++   k+++vv++ G vD++++ ++    k G++ ++ + ++G +l+ ++a+f+a k  + +
  gi|70605909|ref|YP_254779.1| 369 KIYSGVQPDSNMRKRIEQVKECSLKCNCVVLLKGYVDIIAEKEEFKLNKTGNPGMA-VGGTGDTLTGIIASFMAQKLSPFT 448
                                   556789888888889**************************999999999***996.9******************99999 PP

                                   HHHHHHHHHHHHH.HHHHHH CS
                            HK 207 aaveavllykvAgkeaaars 226
                                   +a  +  +  +Ag  a  ++
  gi|70605909|ref|YP_254779.1| 449 SAYLGAFVNGLAGSIAY-EK 467
                                   99666677788884443.33 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     1e-07   0.00037      97     221 ..     335     450 ..     330     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-07
                                   SCTSSSBSSHHHHHHHH.HHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH...TT-SEEEEEEGGS-SSSEEE CS
                  Phos_pyr_kin  97 aksgselleeeavealk.eeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk...lgakaVlikGghlegeeavv 173
                                   ak+  ++++++a+++++  eL+p   vitP   E +  +g   +  ++m++  +++ +    +   Vl+kG          
  gi|70605909|ref|YP_254779.1| 335 AKNKPSVIDADALKSVAgMELFPN-AVITPHAGEFKIYSGV--QPDSNMRKRIEQVKEcslKCNCVVLLKGYV-------- 404
                                   677788899999888762468886.59***********994..444444444444444320455677889864........ PP

                                   EEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHH CS
                  Phos_pyr_kin 174 tdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAv 221
                                    d++ ++ee+ +l++   +     GtG+tl   ia+ +a++ s+ ++ 
  gi|70605909|ref|YP_254779.1| 405 -DIIAEKEEF-KLNKTGNPGMAVGGTGDTLTGIIASFMAQKLSPFTSA 450
                                   .888777765.55566666699******************99987765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05     0.057       6      60 ..      54     107 ..      50     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                   ETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE--- CS
                            KR   6 tGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaa 60 
                                   tGG Gg Gl++ar+la++g + h++ll+ ++  ++d+  +++++ +++ +++ v++
  gi|70605909|ref|YP_254779.1|  54 TGGKGGDGLVVARHLASEGsEVHVLLLGENK--HPDAIINLNAIYEMDYSIREVKL 107
                                   9******************889*******94..55555567777777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3058.74
//
Query:       gi|70605910|ref|YP_254780.1|  [L=153]
Description: 2-cys peroxiredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-38  131.8   0.0    1.4e-38  131.6   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    2.4e-26   92.2   0.0    2.8e-26   92.0   0.0    1.0  1  Redoxin        Redoxin
      2e-05   24.9   0.0    2.8e-05   24.4   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
      0.007   16.5   0.0     0.0099   16.0   0.0    1.3  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.028   14.0   0.0      0.032   13.8   0.0    1.0  1  DUF899         Bacterial protein of unknown function (DUF899)
      0.086   13.0   0.1          1    9.6   0.0    2.2  2  Costars        Costars


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6   0.0   4.6e-42   1.4e-38       2     123 ..       6     127 ..       5     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 4.6e-42
                                   TSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                      AhpC-TSA   2 gdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                   g++apdfe+  +  ++ +ls y+g ++vvl+fypk+++p+Ct+e  ++ +ly++fk++++evigvsvd++ ++k+f++k +
  gi|70605910|ref|YP_254780.1|   6 GNEAPDFEGDSTI-GKLKLSSYRGkSVVVLYFYPKAFTPGCTRETIKFGQLYDQFKQLNAEVIGVSVDTVSTQKSFADKCG 85 
                                   899******9776.9*******99899****************************************************** PP

                                   .SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  82 lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                     fp++sD+++++ak ygvl+e+   a+r tf+id++gki +
  gi|70605910|ref|YP_254780.1|  86 ARFPIVSDSNKQIAKLYGVLNEKGSSAQRVTFIIDENGKIIE 127
                                   ***************************************975 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.0   9.4e-30   2.8e-26       2     130 ..       5     128 ..       4     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 9.4e-30
                                   TTSBB---ECCEETTCEEEEEHHHHTTSE.EEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkk.vvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwg 81 
                                   +g++aPdf+    ++   +++ls+++gk+ vv++f+p af+P C++e++++ +l++++k+ + +v++v++d+ + +k+f++
  gi|70605910|ref|YP_254780.1|   5 KGNEAPDFEG---DSTIGKLKLSSYRGKSvVVLYFYPKAFTPGCTRETIKFGQLYDQFKQLNAEVIGVSVDTVSTQKSFAD 82 
                                   79*******4...4888999********95666************************************************ PP

                                   HTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEE CS
                       Redoxin  82 keglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvyl 130
                                   k g  fp++sD +++++k +G+  +e+ s+  + + +++ide+gk++++
  gi|70605910|ref|YP_254780.1|  83 KCGARFPIVSDSNKQIAKLYGVL-NEKGSS--AQRVTFIIDENGKIIEV 128
                                   *********************55.443333..8999**********987 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   9.3e-09   2.8e-05       2      95 .]      30     125 ..      28     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.3e-09
                                   SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--T CS
                 Thioredoxin_8   2 kvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvk 81 
                                   +vv+Lyf+ + + p c++ t k  +ly+++k + + e++ vs+d    +++k +++      ++p  ++++++++k y+v 
  gi|70605910|ref|YP_254780.1|  30 SVVVLYFYPKaFTPGCTRETIKFGQLYDQFK-QLNAEVIGVSVDT--VSTQKSFADK--CGARFPIVSDSNKQIAKLYGVL 105
                                   689999997647888***************9.7***********8..4777777777..6777999999999999999998 PP

                                   T......-SEEEEE-TT-BE CS
                 Thioredoxin_8  82 a......iPtlvvldkngev 95 
                                   +         ++++d ng++
  gi|70605910|ref|YP_254780.1| 106 NekgssaQRVTFIIDENGKI 125
                                   77777766777888888876 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.3e-06    0.0099       6      55 ..      56     106 ..      52     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.3e-06
                    AhpC-TSA_2   6 kpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqalglkr 55 
                                    +++++ + ++++++++++s  k+F++  g  f+++ D ++++ ++ g+ +
  gi|70605910|ref|YP_254780.1|  56 YDQFKQLNAEVIGVSVDTVStQKSFADKCGARFPIVSDSNKQIAKLYGVLN 106
                                   6789999************77*******************99988888755 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.032      65     186 ..      27     140 ..       8     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                        DUF899  65 egrsqLivyhfmfgpdaeegCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdf 145
                                   +g+s +++  +++ ++ + gC+  ++   ++  + ++L+a+   ++ vs  ++   +++ ++ G ++p+vs+ +++  + +
  gi|70605910|ref|YP_254780.1|  27 RGKSVVVL--YFYPKAFTPGCTRETIKFGQLYDQFKQLNAE---VIGVSVDTVSTQKSFADKCGARFPIVSDSNKQIAKLY 102
                                   45544443..3555566766666666666665566666555...8999999****************************** PP

                        DUF899 146 nvsleeeqaseelpglsvflrddgrvfhtYstyaRgleell 186
                                   +v  e++   ++++ ++  + ++g++ +  s  + + e+ +
  gi|70605910|ref|YP_254780.1| 103 GVLNEKG---SSAQRVTFIIDENGKIIEVLSGLGNAEEHAN 140
                                   *977765...4444444444445888887776666666555 PP

>> Costars  Costars
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00034         1      26      46 ..      49      69 ..      42      71 .. 0.91
   2 ?    1.2   0.0      0.15   4.4e+02       3      24 ..      95     116 ..      93     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00034
                       Costars 26 vvtFGeLfekytniseklvGt 46
                                  +++FG+L++++++ + +++G+
  gi|70605910|ref|YP_254780.1| 49 TIKFGQLYDQFKQLNAEVIGV 69
                                  69****************996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                       Costars   3 dkeileLcevIkelGeknddgk 24 
                                   +k+i +L  v++e G++ +  +
  gi|70605910|ref|YP_254780.1|  95 NKQIAKLYGVLNEKGSSAQRVT 116
                                   7899999999999998655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 986.14
//
Query:       gi|70605911|ref|YP_254781.1|  [L=523]
Description: phosphoenolpyruvate carboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   7.8e-215  714.0   1.3   8.8e-215  713.9   1.3    1.0  1  PEPcase_2  Phosphoenolpyruvate carboxylase


Domain annotation for each model (and alignments):
>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.9   1.3  4.9e-219  8.8e-215       1     494 []      16     523 .]      16     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 713.9 bits;  conditional E-value: 4.9e-219
                                   --SEEEE--ST-.......SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TTTSSEE CS
                     PEPcase_2   1 iprtmsTQHPDnakvPefaeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlGedvfl 81 
                                   iprtmsTQHPDnakvPe+++ e isge+E+ EAy a+s++gv+EvMwD+EGK+vd+hvvrklls+y+eff++++lG+d+fl
  gi|70605911|ref|YP_254781.1|  16 IPRTMSTQHPDNAKVPEWNQGEAISGENEIIEAYLAFSRYGVEEVMWDAEGKDVDTHVVRKLLSQYPEFFRHRILGKDIFL 96 
                                   9******************************************************************************** PP

                                   EEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH....SS-S-SEEEESS--SHHHHHHHHHHHHHHHH..........HH CS
                     PEPcase_2  82 tlRvPnpkvEkaerkvlaetlesipnsydlaekf...eetkpifevilPmttsaeelievakyyekvvagkeelelad.lk 158
                                   t+RvPnpk+E+aerkv+aetl++ip++ydlaekf   + ++p+fevilP+tts+eeli+v k+yekv+ ++++++l+d ++
  gi|70605911|ref|YP_254781.1|  97 TYRVPNPKIEGAERKVFAETLNTIPITYDLAEKFygeNPNPPVFEVILPFTTSYEELIAVIKFYEKVIVNSDNTKLVDdTY 177
                                   **********************************99559****************************************** PP

                                   HHH-SS---TTSSEEEEEE-SHHHHHTHHHHHHHHHHHT--SEEEEEEESHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT CS
                     PEPcase_2 159 vkelvgelkpesievIPLiEdkesllnideiveeyvkekklkelRvflarSDpAlnyGlisavllvkvAlselykleeelg 239
                                   vk+++ge++p++ievIPLiEd++s+l+id+iv +y++ +++ +lRvflarSDpA+nyGl+savl+vk+Als+l+k+e+ +g
  gi|70605911|ref|YP_254781.1| 178 VKDIIGETNPKKIEVIPLIEDRDSMLRIDTIVGKYIEIERPPYLRVFLARSDPAMNYGLLSAVLSVKYALSRLSKMEKIYG 258
                                   ********************************************************************************* PP

                                   -EEEEEEE-BSSGGGT---TTGHHHHHHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG-------HHHHHHHHHHH CS
                     PEPcase_2 240 vkiyPilGvGslpfRGhlspenveevleeYagvkTfTvQSafkYdyeeeevkeairkineaevkkprelseeeeelllevi 320
                                   vki+P+lGvGslpfRGh+sp nve++l+eY+g++TfTvQSafkYdye++ v++ai+k+n ++v+++ elsee+ee++++v+
  gi|70605911|ref|YP_254781.1| 259 VKIFPLLGVGSLPFRGHFSPYNVENTLNEYRGIYTFTVQSAFKYDYEDDLVISAIKKVNGTNVTEKIELSEEDEEIISNVT 339
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--HE---HHHHHHHHHHTT--GGGTTHHHHHHHHHHH CS
                     PEPcase_2 321 eklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieevelPRAIsftgalYsiGlPpellgissllelaeee 401
                                   +k+++ Yq+kie+ladvin+va l+p+rRaRklhiglfgYsR++++v+lPRAIsf+g+lY+iG+Ppe++g+ssl++++++e
  gi|70605911|ref|YP_254781.1| 340 RKYTQGYQNKIEALADVINKVALLLPRRRARKLHIGLFGYSRSTGKVTLPRAISFVGSLYTIGIPPEIIGLSSLSKMTDQE 420
                                   ********************************************************************************* PP

                                   HHHHHHHSTTHHHHHHHHHTT--SS.....TTTTTS-HHHHHHHHHHHHHHHHHTT--.....HHHHHHH-HHHHHHHHHH CS
                     PEPcase_2 402 levllevykalkedlaeaarylnle.....ksklkldeetvkkikedleiveeildlk.....yeeeeheeltsellkalk 472
                                   l++++++yk+lk+dl++aar++n e     k+ +++d+e vk+iked++++e++l+++     y++++h  l++ +l ++k
  gi|70605911|ref|YP_254781.1| 421 LNAIFNNYKYLKNDLQFAARFVNFEalqllKDIWNIDAEVVKAIKEDIDYAENSLGIRigesdYMSKKHVLLSTLALLSIK 501
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHTS-- CS
                     PEPcase_2 473 ekkdeelkelilemaklRkflG 494
                                   e k +e+k++i ema +R+++G
  gi|70605911|ref|YP_254781.1| 502 EGKLDEAKTYIKEMAIVRRAIG 523
                                   *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3517.94
//
Query:       gi|70605912|ref|YP_254782.1|  [L=271]
Description: hypothetical protein Saci_0060 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   11.6   0.0       0.13   11.0   0.0    1.1  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.2e-06      0.13     130     208 ..      94     175 ..      89     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-06
                           DCD 130 agYkGplyleisprsFsilvr..kGsrLsqirfrrgeaklsdeelkelhaeeklvkae.keklvieeGvalsvdLsgeeed 207
                                    gY+ +ly ei+++  ++++r   G+++s + +++ ++ ++d+ ++++++ +k++ka   +k++++e +  s d+s+ +++
  gi|70605912|ref|YP_254782.1|  94 LGYNVRLYKEIITNGLPVMIRlyDGNAVSHLVLEKFSELVTDSLVEKIESLSKVLKAIrVPKEKLNEIINYSPDISDISTQ 174
                                   69****************999667*******************99999998888877646777778777777777666555 PP

                           DCD 208 e 208
                                   +
  gi|70605912|ref|YP_254782.1| 175 K 175
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1740.74
//
Query:       gi|70605913|ref|YP_254783.1|  [L=319]
Description: hypothetical protein Saci_0061 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-85  285.2   0.1    4.3e-85  284.9   0.1    1.0  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.1e-07   31.7   0.6      1e-06   28.4   0.6    2.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    4.2e-05   23.8   0.0    9.7e-05   22.7   0.0    1.5  1  AAA_22           AAA domain
    4.6e-05   23.6   1.0    0.00016   21.8   0.1    1.9  2  DUF87            Helicase HerA, central domain
    5.7e-05   23.0   0.0    0.00013   21.8   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00028   20.6   0.0      0.053   13.2   0.0    2.2  2  SRP54            SRP54-type protein, GTPase domain
     0.0003   20.7   0.1     0.0008   19.4   0.1    1.7  1  NTPase_1         NTPase
    0.00035   20.2   0.0       0.19   11.3   0.0    2.3  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    0.00054   19.2   0.0    0.00097   18.4   0.0    1.4  1  NB-ARC           NB-ARC domain
    0.00099   18.4   0.0    0.00099   18.4   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain
     0.0011   17.9   0.0     0.0017   17.3   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0015   18.4   1.9     0.0067   16.3   0.1    2.5  3  RsgA_GTPase      RsgA GTPase
     0.0016   18.2   0.0     0.0043   16.9   0.0    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0018   18.8   0.1     0.0044   17.5   0.1    1.6  1  ABC_tran         ABC transporter
     0.0019   18.6   0.1     0.0054   17.1   0.0    1.7  2  AAA_16           AAA ATPase domain
     0.0019   18.7   0.2     0.0064   17.0   0.1    1.9  2  AAA_18           AAA domain
     0.0029   17.4   0.0     0.0057   16.4   0.0    1.4  1  AAA_30           AAA domain
     0.0036   17.0   0.2      0.034   13.9   0.4    2.3  2  AAA_29           P-loop containing region of AAA domain
     0.0041   17.5   0.1       0.02   15.2   0.0    1.9  2  AAA_19           AAA domain
     0.0044   16.4   0.0      0.008   15.5   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0071   16.4   0.2      0.023   14.8   0.2    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0092   15.3   0.0      0.017   14.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.011   15.5   0.1       0.02   14.7   0.1    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.014   15.5   0.0      0.022   14.8   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.016   14.4   0.0      0.031   13.4   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.017   15.5   0.0      0.039   14.4   0.0    1.6  1  AAA_17           AAA domain
      0.022   14.1   0.0      0.044   13.1   0.0    1.5  1  MipZ             ATPase MipZ
      0.031   13.9   0.0      0.056   13.0   0.0    1.4  1  AAA_25           AAA domain
      0.036   12.9   0.1      0.056   12.2   0.1    1.2  1  Adeno_IVa2       Adenovirus IVa2 protein
      0.038   14.2   0.1      0.076   13.3   0.1    1.5  1  AAA_28           AAA domain
      0.039   13.2   0.0      0.067   12.4   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.042   13.8   0.0      0.084   12.8   0.0    1.5  1  NACHT            NACHT domain
      0.045   13.7   0.0      0.075   12.9   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.046   13.5   0.1      0.079   12.7   0.1    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.073   13.1   0.3       0.18   11.9   0.0    1.8  1  AAA_14           AAA domain
      0.098   11.7   0.5        0.2   10.6   0.1    1.7  2  T2SSE            Type II/IV secretion system protein
       0.11   12.6   0.1       0.22   11.7   0.1    1.5  1  AAA_33           AAA domain
       0.18   11.2   1.1       0.37   10.2   0.0    1.8  2  KTI12            Chromatin associated protein KTI12


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.9   0.1   9.1e-88   4.3e-85       2     256 ..      16     271 ..      15     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.9 bits;  conditional E-value: 9.1e-88
                                   HHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------------- CS
                          MeaB   2 araitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklR 82 
                                   +r++t +e  +pe  + le+l++++G+a+v+G+tG+PG+Gkstl+++l+ e+ +rG+rv+v+ +DPsspf+ Gs +G+++R
  gi|70605913|ref|YP_254783.1|  16 GRLLTKIEYLTPEGLDALEQLMKNSGKAHVIGITGSPGSGKSTLISKLVSEYLNRGHRVGVILIDPSSPFSLGSFMGNRIR 96 
                                   799****************************************************************************** PP

                                   -HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--C CS
                          MeaB  83 leelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikk 163
                                   l+e +  e vfiRs+ srG lGG++ +++ +v+ l+++GfD +l+etvG+Gq +++v++ v+t+ vl++p++GD++q++k+
  gi|70605913|ref|YP_254783.1|  97 LSEDEFGEKVFIRSIGSRGYLGGISSEALMLVEALDGLGFDRILVETVGAGQTDTEVIDTVHTISVLTTPGTGDDIQALKA 177
                                   ********************************************************************************* PP

                                   CCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCSTT.BTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                          MeaB 164 GileiaDiivvnkaDkkeaekaarelraaleleeek.ekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrr 243
                                   Gi+ei+Di+v+nk+Dk+e+e a +++r+a+e  e + +++W+p+++kt a +g Gi el+da  eh ++l  + ++e + +
  gi|70605913|ref|YP_254783.1| 178 GIMEIGDIYVINKSDKPETELAYNTIRFAIETAEGEyKDGWKPRIVKTIAIKGVGISELIDAFDEHLRFLIGNRKFEFKVE 258
                                   *******************************999886999*********************************99999999 PP

                                   HHHHHHHHHHHHH CS
                          MeaB 244 erakeelrelved 256
                                   +r+++ l  l + 
  gi|70605913|ref|YP_254783.1| 259 NRRVKILELLLKR 271
                                   9998877665544 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.6   2.2e-09     1e-06       2     156 ..      45     197 ..      44     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.2e-09
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCC....HCCCT.......EEEETTTTECCHCTT-HH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaell....retgve......ivelenGciCctlredll 70 
                                   v+++tG++GsGK+tL+++l+    ++g ++ vi+ + ++    ++++    r +++e      i ++   +    +++++l
  gi|70605913|ref|YP_254783.1|  45 VIGITGSPGSGKSTLISKLVseYLNRGHRVGVILIDPSSPFSLGSFMgnriRLSEDEfgekvfIRSIGSRGYLGGISSEAL 125
                                   789*****************887789********998874444555523333332225566666666655555569***** PP

                                   HHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                          cobW  71 kelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                   + +eal  +   +d+il+Et+G  +  +           +   +++ v+        +++i+ +    ++  d+ v+nK D
  gi|70605913|ref|YP_254783.1| 126 MLVEALDGLG--FDRILVETVGAGQTDTE---------VIDTVHTISVLTT---PGTGDDIQALKAGIMEIGDIYVINKSD 192
                                   *********9..**********8776555.........4555556666666...567889999999999999999999999 PP

                                   HHCHC CS
                          cobW 152 lldee 156
                                     ++e
  gi|70605913|ref|YP_254783.1| 193 KPETE 197
                                   76655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.1e-07   9.7e-05       5      58 ..      43      92 ..      38     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.1e-07
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllr 58
                                  a ++ +tG +G+GK+tl+ +l++++ ++     +r++v++++++s+ s+ +++ 
  gi|70605913|ref|YP_254783.1| 43 AHVIGITGSPGSGKSTLISKLVSEYLNR----GHRVGVILIDPSSPFSLGSFMG 92
                                  567789******************9654....47************99988865 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.5e-07   0.00016      26      62 ..      46      83 ..      35     121 .. 0.87
   2 ?    0.4   0.1       1.2   5.6e+02     110     173 ..     192     278 ..     155     317 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.5e-07
                         DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDpHG 62
                                  ++i gs GsGKS++++ L++e l+  +++ ++++Dp +
  gi|70605913|ref|YP_254783.1| 46 IGITGSPGSGKSTLISKLVSEYLNrGHRVGVILIDPSS 83
                                  699********************999999******976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                         DUF87 110 dkpaaavqrsvleealdqaka............keekeklssdepveklleelk..............kekeelrklknqa 164
                                   dkp+++  ++ ++ a+++a+             +  ++ + + e++  + e+l+              +    ++ l   +
  gi|70605913|ref|YP_254783.1| 192 DKPETELAYNTIRFAIETAEGeykdgwkprivkTIAIKGVGISELIDAFDEHLRflignrkfefkvenR---RVKILELLL 269
                                   555555566666666666555555566666666666677777777777777777666666665543331...222222222 PP

                         DUF87 165 iarlldkle 173
                                   +++++  +e
  gi|70605913|ref|YP_254783.1| 270 KRSINTIIE 278
                                   222222222 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.9e-07   0.00013       1      33 [.      45      77 ..      45      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.9e-07
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrvgti 33
                                  v+gi+g  gsGK tL++kl++e  +rg rvg+i
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLISKLVSEYLNRGHRVGVI 77
                                  799****************************98 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00011     0.053       3      38 ..      45      80 ..      43      84 .. 0.91
   2 ?    5.3   0.0     0.029        14      77     113 ..     129     165 ..     102     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  vi + G  G+GK t ++KL   + ++g++v ++  D
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLISKLVSEYLNRGHRVGVILID 80
                                  777899************************998777 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                                   HHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHS CS
                         SRP54  77 ekakeekidvvlvDTaGrlqndkelmeelkkikkvvk 113
                                   e+ +  ++d +lv T G  q+d+e+++ +++i+  ++
  gi|70605913|ref|YP_254783.1| 129 EALDGLGFDRILVETVGAGQTDTEVIDTVHTISVLTT 165
                                   55566789*******************9999987665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.7e-06    0.0008       2      31 ..      46      75 ..      45      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-06
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                  + iTG+pG+GK+Tl++k++++  ++g +vg
  gi|70605913|ref|YP_254783.1| 46 IGITGSPGSGKSTLISKLVSEYLNRGHRVG 75
                                  78***************9998889998885 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.012       5.5       5      26 ..      45      66 ..      42      74 .. 0.86
   2 !   11.3   0.0    0.0004      0.19     122     192 ..     181     244 ..     165     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                                  EEEEEESTTSSHHHHHHHHHHH CS
                      GTP_EFTU  5 nigiighvDhGKtTLtdrLlyk 26
                                   igi g   +GK+TL+ +L+ +
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLISKLVSE 66
                                  589****************975 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                                   TTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                      GTP_EFTU 122 gvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                                   ++  i +iNK D++++el         +        e    +g  +  +v + a+kg g+++l++a++e+l
  gi|70605913|ref|YP_254783.1| 181 EIGDIYVINKSDKPETELAYNTIRFAIET------AEGEYKDG-WKPRIVKTIAIKGVGISELIDAFDEHL 244
                                   444799********999988877777666......44444444.3667********************998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06   0.00097       9      44 ..      33      67 ..      30     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                                  HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlakqilnks 44
                                   e+L++ ++ +  v+++ G +G+GK+tl+++ ++++
  gi|70605913|ref|YP_254783.1| 33 LEQLMK-NSGKAHVIGITGSPGSGKSTLISKLVSEY 67
                                  578995.555558******************99984 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.1e-06   0.00099      13      49 ..      38      81 ..      30     295 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                    KAP_NTPase 13 septlatpivvgLygkWGsGKssllnkledelkefa.........k 49
                                  + + +++  v+g++g  GsGKs+l+ kl +e+ ++           
  gi|70605913|ref|YP_254783.1| 38 K-N-SGKAHVIGITGSPGSGKSTLISKLVSEYLNRGhrvgvilidP 81
                                  3.3.38999*******************999988854444444440 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.7e-06    0.0017      12      52 ..      39      82 ..      31      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                 TrwB_AAD_bind 12 eretqh.ilivGttGsGKtqalekllrairargdra..ivlDlt 52
                                  ++ ++h i i+G+ GsGK++ ++kl+ +  +rg+r+  i +D++
  gi|70605913|ref|YP_254783.1| 39 NSGKAHvIGITGSPGSGKSTLISKLVSEYLNRGHRVgvILIDPS 82
                                  555566257************************99633667776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05    0.0067      77     123 ..      17      67 ..       5      77 .. 0.73
   2 ?    0.7   0.0      0.95   4.5e+02      50     106 ..     185     249 ..     175     251 .. 0.68
   3 ?   -2.6   0.2       9.6   4.5e+03      43      63 ..     273     293 ..     257     315 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                                   SEEEE--TTTHTTHHHHHHHCTT....SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  77 yevllvsaktkegleelkellkd....ktsvlvGqSGvGKStLinallpel 123
                                     +++++  t egl++l++l+k+    +++ + G+ G GKStLi +l++e 
  gi|70605913|ref|YP_254783.1|  17 RLLTKIEYLTPEGLDALEQLMKNsgkaHVIGITGSPGSGKSTLISKLVSEY 67 
                                   555566667778888888777764423566689**************9974 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.95
                                   EEEEE-GGG--HHH.......HHHHHHHHHH.HTTSEEEE--TTTHTTHHHHHHHCTTSEEEEEC CS
                   RsgA_GTPase  50 vivlnKiDlleeee.......eleelkeele.algyevllvsaktkegleelkellkdktsvlvG 106
                                   + v+nK D  e+e        ++e+ + e++  +  +++++ a ++ g++el +++++++ +l+G
  gi|70605913|ref|YP_254783.1| 185 IYVINKSDKPETELayntirfAIETAEGEYKdGWKPRIVKTIAIKGVGISELIDAFDEHLRFLIG 249
                                   56788888877777666666666666666542466777777777777888888888877777777 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.6
                                   HHTT-EEEEEEE-GGG--HHH CS
                   RsgA_GTPase  43 eekgiepvivlnKiDlleeee 63 
                                    ++ ie  i+ nK ++  e +
  gi|70605913|ref|YP_254783.1| 273 INTIIERFIIQNKNEIDVELN 293
                                   444455556666655544444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.1e-06    0.0043       1      35 [.      48      82 ..      48      86 .. 0.93
   2 ?   -2.9   0.0       9.6   4.6e+03     195     215 ..     224     244 ..     179     253 .. 0.42

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.1e-06
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPA 35
                                  ++G +GsGK+t++++l++ + +rg +v v+ +DP 
  gi|70605913|ref|YP_254783.1| 48 ITGSPGSGKSTLISKLVSEYLNRGHRVGVILIDPS 82
                                  68**************999999************7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.6
                    ATP_bind_1 195 ekykklaeaiaelleefalvl 215
                                   +  +     i+el++ f+++l
  gi|70605913|ref|YP_254783.1| 224 KTIAIKGVGISELIDAFDEHL 244
                                   333333334444555554444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   9.4e-06    0.0044      11      37 ..      43      69 ..      34     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.4e-06
                                  TSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 11 gekvaivGenGaGKStLlkllagllkp 37
                                   ++++i+G+ G+GKStL++ l  ++ +
  gi|70605913|ref|YP_254783.1| 43 AHVIGITGSPGSGKSTLISKLVSEYLN 69
                                  5789***************99999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.1e-05    0.0054      10      51 ..      31      70 ..      28      99 .. 0.76
   2 ?   -2.0   0.0       8.5     4e+03      72     105 ..     236     268 ..     216     293 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-05
                        AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                  ++L+++++  +sg  +++ ++G +G+GKs+l+ +l  ++  +
  gi|70605913|ref|YP_254783.1| 31 DALEQLMK--NSGKAHVIGITGSPGSGKSTLISKLVSEYLNR 70
                                  44444444..566669****************8887766666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.5
                        AAA_16  72 laqalareellrqlldeaesaeleawrekleeal 105
                                   l++a+++ +l   +++++ + ++e  r k++e l
  gi|70605913|ref|YP_254783.1| 236 LIDAFDE-HLRFLIGNRKFEFKVENRRVKILELL 268
                                   3444422.44333444433334444444444433 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.4e-05    0.0064       1      24 [.      46      70 ..      46      86 .. 0.76
   2 ?   -1.7   0.0       8.4   3.9e+03      42      42 ..     258     258 ..     227     302 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf 24
                                  I++tG pG+GK+tl   L ++  + 
  gi|70605913|ref|YP_254783.1| 46 IGITGSPGSGKSTLISKLVSEYlNR 70
                                  89**************997764244 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.4
                        AAA_18  42 d 42 
                                   +
  gi|70605913|ref|YP_254783.1| 258 E 258
                                   1 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0057       7      49 ..      30      74 ..      25      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                        AAA_30  7 aaavealltsgdr..vavltGpAGtGKttalkalreaweaaggrv 49
                                   +a+e+l++++ +  v  +tG +G+GK+t++++l+  + ++g+rv
  gi|70605913|ref|YP_254783.1| 30 LDALEQLMKNSGKahVIGITGSPGSGKSTLISKLVSEYLNRGHRV 74
                                  5677777776554116668***************99999998877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.4   7.1e-05     0.034      24      39 ..      45      60 ..      29      64 .. 0.81
   2 ?   -0.6   0.0       2.4   1.1e+03      32      42 ..     230     240 ..     228     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.1e-05
                        AAA_29 24 atlltGpsGsGKSTll 39
                                  ++ +tG  GsGKSTl+
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLI 60
                                  4569***********8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                        AAA_29  32 GsGKSTllDAi 42 
                                   G+G S l+DA+
  gi|70605913|ref|YP_254783.1| 230 GVGISELIDAF 240
                                   89999****97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.2e-05      0.02       9      39 ..      42      72 ..      34      83 .. 0.84
   2 ?   -0.1   0.0       2.2   1.1e+03      69      78 ..     154     169 ..     122     289 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.2e-05
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelgg 39
                                  k++v+ +t+ pG+GK++++ + v++++++g+
  gi|70605913|ref|YP_254783.1| 42 KAHVIGITGSPGSGKSTLISKLVSEYLNRGH 72
                                  678999*****************99988775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.2
                        AAA_19  69 atTiHrlal......l 78 
                                   ++T+H +++       
  gi|70605913|ref|YP_254783.1| 154 IDTVHTISVlttpgtG 169
                                   5555555553333220 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05     0.008      39      81 ..      42      83 ..      23      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                                  -.SEE.EE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTS CS
                  FtsK_SpoIIIE 39 ashll.vaGatgsGKStalntLilSlatthtPeeVqliliDykg 81
                                   +h++ + G++gsGKSt +  L+   +     ++V  iliD+++
  gi|70605913|ref|YP_254783.1| 42 KAHVIgITGSPGSGKSTLISKLVSEYLN--RGHRVGVILIDPSS 83
                                  3688779***************998665..99*********986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   4.9e-05     0.023       2      22 ..      46      66 ..      45      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-05
                                  EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                  ++i G p +GKStLi++l+ e
  gi|70605913|ref|YP_254783.1| 46 IGITGSPGSGKSTLISKLVSE 66
                                  89****************986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.7e-05     0.017      12      44 ..      39      71 ..      30      82 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqg 44
                                  ++ +  +i + G+pG+GKs+l+++l  e  ++g
  gi|70605913|ref|YP_254783.1| 39 NSGKAHVIGITGSPGSGKSTLISKLVSEYLNRG 71
                                  45666788899***********99988865443 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.2e-05      0.02       3      25 ..      48      68 ..      46      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-05
               Viral_helicase1  3 vhGvpGcGKStlirkllrtslil 25
                                  + G pG+GKStli kl+++   l
  gi|70605913|ref|YP_254783.1| 48 ITGSPGSGKSTLISKLVSE--YL 68
                                  789**************98..33 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.7e-05     0.022       6      55 ..      50     198 ..      45     316 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-05
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH............................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx............................... RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep............................... 54 
                                   ++ G+GK+tl  +L     +rg+rV ++  Dp ++ +   ++g+++++ +                               
  gi|70605913|ref|YP_254783.1|  50 GSPGSGKSTLISKLVSEYLNRGHRVGVILIDPSSPFSLGsFMGNRIRLSEdefgekvfirsigsrgylggissealmlvea 130
                                   5669***********999999************998875788888887778888899999999999999999988888888 PP

                                   ...................................................................C CS
                                   ...................................................................x RF
                          CbiA  55 ...................................................................d 55 
                                                                                                       
  gi|70605913|ref|YP_254783.1| 131 ldglgfdrilvetvgagqtdtevidtvhtisvlttpgtgddiqalkagimeigdiyvinksdkpeteL 198
                                   88887777777777777777776666666666666666665555555444444444444444444440 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.6e-05     0.031      43      85 ..      32      77 ..      11      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.6e-05
                        DUF815 43 nteqflegl.pannvLLwGarGtGKSslvkallneyaeeg..Lrli 85
                                    eq++++  +a+ + ++G+ G+GKS+l+  l++ey ++g  + +i
  gi|70605913|ref|YP_254783.1| 32 ALEQLMKNSgKAHVIGITGSPGSGKSTLISKLVSEYLNRGhrVGVI 77
                                  55666666515666669********************999444445 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.3e-05     0.039       1      19 [.      49      67 ..      49      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.3e-05
                                  EE-TTSSHHHHHHHHHHHH CS
                        AAA_17  1 lGgPGsGKgtqceklveky 19
                                  +G PGsGK+t+++klv +y
  gi|70605913|ref|YP_254783.1| 49 TGSPGSGKSTLISKLVSEY 67
                                  699*************998 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.3e-05     0.044      10      55 ..      52      98 ..      44     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                                  TTSSHHHHHHHHHHHHHTTT--EEEEE--TTT.-HHHHHHHHHHHHH CS
                          MipZ 10 GGsGksttavhvavaLlkkGarvaaidldlrq.rtlarylenraata 55
                                   GsGkst    ++   l++G+rv++i +d     +l  +++nr    
  gi|70605913|ref|YP_254783.1| 52 PGSGKSTLISKLVSEYLNRGHRVGVILIDPSSpFSLGSFMGNRIRLS 98
                                  49***************************765269999****98765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.056      22      62 ..      33      73 ..      26      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                        AAA_25 22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkp 62
                                  +++l+k+   + +++ ++G pg+GK+tl + l+ +++ +G+ 
  gi|70605913|ref|YP_254783.1| 33 LEQLMKNS-GKAHVIGITGSPGSGKSTLISKLVSEYLnRGHR 73
                                  67777777.68889999****************999987775 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012     0.056      82     126 ..      39      82 ..      20      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                    Adeno_IVa2  82 nyglqPviGviyGPtGsGksqllrnlissklisPiPetvifitPe 126
                                   n g+  viG+  G  GsGks l+ +l+s  l       vi+i P 
  gi|70605913|ref|YP_254783.1|  39 NSGKAHVIGI-TGSPGSGKSTLISKLVSEYLNRGHRVGVILIDPS 82 
                                   889999***6.6778**************9999999999999886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00016     0.076       2      21 ..      46      65 ..      45      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                        AAA_28  2 ivitGgestGKTtlleaLaa 21
                                  i itG +++GK+tl+++L +
  gi|70605913|ref|YP_254783.1| 46 IGITGSPGSGKSTLISKLVS 65
                                  569**************974 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.067       2      25 ..      44      67 ..      43      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                  +v+ +tG +G+GK+ + ++l+ e+
  gi|70605913|ref|YP_254783.1| 44 HVIGITGSPGSGKSTLISKLVSEY 67
                                  6888*****************998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00018     0.084       2      23 ..      45      66 ..      44      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                                  CEEEEC-TTTCHHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                  ++ ++G +GsGK+tL+ kl+++
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLISKLVSE 66
                                  6779***************987 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00016     0.075       4      28 ..      44      68 ..      41      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                Ploopntkinase3  4 rliylvGqPGaGkstlmaeltkgfd 28
                                   +i + G+PG+Gkstl+++l + + 
  gi|70605913|ref|YP_254783.1| 44 HVIGITGSPGSGKSTLISKLVSEYL 68
                                  678899**************98774 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00017     0.079       1      23 [.      45      67 ..      45      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                           PRK  1 vIgvagsSGaGkttvarklekif 23
                                  vIg++gs G+Gk+t+  kl++  
  gi|70605913|ref|YP_254783.1| 45 VIGITGSPGSGKSTLISKLVSEY 67
                                  8**************99998754 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00037      0.18       3      32 ..      44      72 ..      42     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkes 32
                                  +++ itG   +GK+tl+ +l++e+l ++ +
  gi|70605913|ref|YP_254783.1| 44 HVIGITGSPGSGKSTLISKLVSEYL-NRGH 72
                                  6899*******************99.4444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00043       0.2     116     159 ..      31      73 ..       7      82 .. 0.74
   2 ?   -2.8   0.1       5.7   2.7e+03      52      77 ..     271     295 ..     248     303 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                         T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksder 159
                                   ++++++++++  +  +i ++G  gsGK+tl+  l++e  ++ +r
  gi|70605913|ref|YP_254783.1|  31 DALEQLMKNS-GKAHVIGITGSPGSGKSTLISKLVSEYLNRGHR 73 
                                   5566666666.5667788*************9998876555454 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                         T2SSE  52 sriaalakldiseerplqdarlpekg 77 
                                   + i +  ++ i +++  +d +l+ k+
  gi|70605913|ref|YP_254783.1| 271 RSINTIIERFIIQNKNEIDVELN-KN 295
                                   33444444444444444555554.44 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00046      0.22       4      22 ..      48      66 ..      45      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00046
                        AAA_33  4 lvGlpGsGKstlaerllkk 22
                                  + G pGsGKstl+ +l+ +
  gi|70605913|ref|YP_254783.1| 48 ITGSPGSGKSTLISKLVSE 66
                                  68************99865 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00079      0.37       5      35 ..      47      77 ..      44      90 .. 0.81
   2 ?   -0.9   0.3       1.9   9.1e+02     176     212 ..     282     318 ..     258     319 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00079
                                  EEE--TTSSHHHHHHHHHHHHHHTT--EEEE CS
                         KTI12  5 vltGlPssGKstrakeLakaleeekrsvvvi 35
                                   +tG P sGKst+ ++L ++  +++ +v vi
  gi|70605913|ref|YP_254783.1| 47 GITGSPGSGKSTLISKLVSEYLNRGHRVGVI 77
                                  59***********999998887777776655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                   --SSSTT-------HHHHHHHHHHHHHHHHHHH.... CS
                         KTI12 176 kpnqatlskplaeanflqeLdketseivkeileaqks 212
                                    +n++ +   l+++  ++ L ++ ++i+ +ile+q++
  gi|70605913|ref|YP_254783.1| 282 IQNKNEIDVELNKNHRIKLLIEKYTKIIGSILENQQK 318
                                   5677777888888888999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2075.69
//
Query:       gi|70605914|ref|YP_254784.1|  [L=140]
Description: methylmalonyl-CoA mutase C-terminal domain/subunit, partial [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-23   80.8   0.5    9.5e-23   80.5   0.5    1.1  1  B12-binding    B12 binding domain
     0.0011   18.0   0.2     0.0014   17.7   0.2    1.1  1  IMPDH          IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.011   15.4   0.0        1.7    8.3   0.0    2.1  2  TPP_enzyme_N   Thiamine pyrophosphate enzyme, N-terminal TPP 
       0.11   12.8   0.6         35    4.8   0.0    2.7  3  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.5   2.1e-26   9.5e-23       1     113 [.       4     114 ..       4     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 2.1e-26
                   B12-binding   1 ikvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel.lkrirp 80 
                                   ikvl+a++g d h++G++v+a+al+dag+eV+++g+ +++e+iv+a+++e++dv+g+S+l+++++e +  lv++ + ++ +
  gi|70605914|ref|YP_254784.1|   4 IKVLVAKLGLDGHDRGAKVVARALKDAGMEVVYTGLRQTPEQIVKAAIQEDVDVIGVSILSGAHIELISMLVKEmKDKKLN 84 
                                   589***********************************************************************9777889 PP

                   B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgeg 113
                                   +v +vvGG++p  d    l+ +lg +d v+  g
  gi|70605914|ref|YP_254784.1|  85 DVGLVVGGVIPPQDIPA-LK-QLG-VDEVFLPG 114
                                   9*******987666665.33.399.55577666 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   3.1e-07    0.0014     100     170 ..      38     110 ..      18     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-07
                                   -SSTTHHHHHHHHHHTT-SEEEEE-STSSSHH.HHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 100 gvkedalervkalveagvdvlvvdsahghsek.vleavkeikkkvee.veviaGnvataegakaLieagadav 170
                                   g ++  ++ vka ++++vdv+ v +  g   + +   vke+k+k  + v +++G v   + + aL + g+d v
  gi|70605914|ref|YP_254784.1|  38 GLRQTPEQIVKAAIQEDVDVIGVSILSGAHIElISMLVKEMKDKKLNdVGLVVGGVIPPQDIPALKQLGVDEV 110
                                   56667788899*************9777665505556999*9876555***********************87 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00037       1.7       2      44 ..      18      59 ..      17      67 .. 0.86
   2 ?    5.2   0.0    0.0033        15      10      36 ..     101     126 ..      99     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                                  EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE CS
                  TPP_enzyme_N  2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvl 44
                                  ++a++++raLk++g e+v++   ++  ++++a+ +e+ ++v+ 
  gi|70605914|ref|YP_254784.1| 18 RGAKVVARALKDAGMEVVYTGLRQTPEQIVKAAIQED-VDVIG 59
                                  689*****************99999999999999986.76665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0033
                                   HHHHCT--EEEE---CCCHHHHCCHHC CS
                  TPP_enzyme_N  10 aLkalgvehvfgvpGsrilplldalse 36 
                                   aLk+lgv++vf +pGs+++++++++ +
  gi|70605914|ref|YP_254784.1| 101 ALKQLGVDEVF-LPGSSLKEITEKIIK 126
                                   79********9.7****9999998765 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0078        35      37      61 ..      14      38 ..       3      39 .. 0.78
   2 ?    0.5   0.0      0.17   7.5e+02      42      59 ..      42      59 ..      38      71 .. 0.83
   3 ?    3.9   0.0     0.015        69      53      94 ..      84     125 ..      75     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0078
                                  CTSSCSSTHHHHHHHHTT-SEEEES CS
                 Nitro_FeMo-Co 37 daegggggklaqllaeegvdvvivg 61
                                  d++ +g + +a+ l+++g++vv++g
  gi|70605914|ref|YP_254784.1| 14 DGHDRGAKVVARALKDAGMEVVYTG 38
                                  5666777778888888******986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                  SSTHHHHHHHHTT-SEEE CS
                 Nitro_FeMo-Co 42 gggklaqllaeegvdvvi 59
                                   ++++++ + +e+vdv+ 
  gi|70605914|ref|YP_254784.1| 42 TPEQIVKAAIQEDVDVIG 59
                                  678999999999999985 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.015
                                   TT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHHH CS
                 Nitro_FeMo-Co  53 egvdvvivgkiGpralakleaagievykgaggtveealkevl 94 
                                   ++v +v+ g i p+ + +l++ g++ +  +g +++e+ ++++
  gi|70605914|ref|YP_254784.1|  84 NDVGLVVGGVIPPQDIPALKQLGVDEVFLPGSSLKEITEKII 125
                                   89**********************988889999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 885.90
//
Query:       gi|70605915|ref|YP_254785.1|  [L=66]
Description: DNA-binding protein 7e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-41  138.3   4.2    6.8e-41  138.1   4.2    1.0  1  7kD_DNA_binding  7kD DNA-binding domain


Domain annotation for each model (and alignments):
>> 7kD_DNA_binding  7kD DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   4.2   3.8e-45   6.8e-41       1      58 []       3      60 ..       3      60 .. 0.99

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 3.8e-45
                                  EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSEEEEEEETTTS-CHHHHHHTT CS
               7kD_DNA_binding  1 kvkfkykGeekevdiskikkvWrvGkmvsftyddnGktGrGavsekdaPkelldmlek 58
                                  kvkfkykGeekevd+skikkvWrvGkmvsftyddnGktGrGavsekdaPkelldml++
  gi|70605915|ref|YP_254785.1|  3 KVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLAR 60
                                  8*******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 449.22
//
Query:       gi|70605916|ref|YP_254786.1|  [L=111]
Description: hypothetical protein Saci_0065 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0015   18.3   0.0     0.0025   17.5   0.0    1.4  1  HTH_38         Helix-turn-helix domain
     0.0052   16.4   0.1     0.0096   15.6   0.1    1.3  1  Sigma70_r4_2   Sigma-70, region 4
     0.0069   15.9   0.0      0.011   15.2   0.0    1.4  1  Sigma70_r4     Sigma-70, region 4
     0.0079   16.3   0.0      0.011   15.8   0.0    1.3  1  Trp_repressor  Trp repressor protein
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.026   14.3   0.0    1.5  1  HTH_23         Homeodomain-like domain
       0.02   14.7   0.1      0.035   14.0   0.1    1.4  1  Terminase_5    Putative ATPase subunit of terminase (gpP-like
      0.023   14.7   0.1      0.037   14.1   0.1    1.3  1  HTH_3          Helix-turn-helix
      0.049   13.2   0.0      0.082   12.5   0.0    1.4  1  GerE           Bacterial regulatory proteins, luxR family
        0.1   12.7   0.0       0.15   12.2   0.0    1.3  1  HTH_28         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0025      15      42 ..      27      54 ..      22      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                        HTH_38 15 rllaeGlslreIArrLgrspsTIsRElk 42
                                   l+a+G+++++I+ +Lg+s + I++ ++
  gi|70605916|ref|YP_254786.1| 27 NLYAKGYTYKQIGEILGVSATEINYLIR 54
                                  69******************98888776 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.8e-06    0.0096      23      47 ..      29      53 ..      28      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                                  HTS---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 23 yleglsykEIAellgisegtVksrl 47
                                  y +g++yk+I e+lg+s + +++ +
  gi|70605916|ref|YP_254786.1| 29 YAKGYTYKQIGEILGVSATEINYLI 53
                                  779**************98887765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.5e-06     0.011      18      35 ..      30      47 ..      13      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                                  TTT--HHHHHHHHTS-HH CS
                    Sigma70_r4 18 geglTleEIgerlgiSre 35
                                   +g+T+++Ige+lg+S  
  gi|70605916|ref|YP_254786.1| 30 AKGYTYKQIGEILGVSAT 47
                                  689*************75 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.5e-06     0.011      41      86 ..      24      68 ..      15      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
                 Trp_repressor 41 vvkeLLkeelsqreIaeelgvSiAtItRvsrsLktgsdeykavLkr 86
                                  ++++L  +++++++I e lgvS++ I    r L+ g++e +++Lk+
  gi|70605916|ref|YP_254786.1| 24 IANNLYAKGYTYKQIGEILGVSATEINYLIRGLR-GTNELRDILKK 68
                                  889999********************99999998.78888888876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.026      13      31 ..      28      46 ..      23      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                        HTH_23 13 llaeGlsvreIAreLgvsr 31
                                  l+a+G+++++I ++Lgvs 
  gi|70605916|ref|YP_254786.1| 28 LYAKGYTYKQIGEILGVSA 46
                                  7899*************95 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.035       5      30 ..      24      49 ..      21      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                   Terminase_5  5 qArlLYwqGyrvaeIAeelglkeatV 30
                                   A  LY +Gy+ ++I e lg++   +
  gi|70605916|ref|YP_254786.1| 24 IANNLYAKGYTYKQIGEILGVSATEI 49
                                  6999****************996655 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.8e-05     0.037       7      34 ..      30      57 ..      26      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                  HTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                         HTH_3  7 qlglsqeeLAeklGvsrstisriEnGer 34
                                  ++g++ +++ e lGvs + i+ +++G r
  gi|70605916|ref|YP_254786.1| 30 AKGYTYKQIGEILGVSATEINYLIRGLR 57
                                  68************************66 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.1e-05     0.082      13      36 ..      28      51 ..      27      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                  HHCTTS-HHHHHHHHTS-HHHHHH CS
                          GerE 13 llaeGksnkeIAeelniSekTVkv 36
                                  l a+G++ k+I+e+l++S++ +++
  gi|70605916|ref|YP_254786.1| 28 LYAKGYTYKQIGEILGVSATEINY 51
                                  579***************998876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05      0.15       8      38 ..      28      58 ..      24      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                        HTH_28  8 llaaGhsvreaArelgisrrtvyrWikryee 38
                                  l+a+G +++++ ++lg+s + +  +i+ ++ 
  gi|70605916|ref|YP_254786.1| 28 LYAKGYTYKQIGEILGVSATEINYLIRGLRG 58
                                  79****************9999888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 828.17
//
Query:       gi|70605917|ref|YP_254787.1|  [L=500]
Description: lysyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-80  269.1   0.2    5.6e-80  268.7   0.2    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.2e-10   40.4   0.3    4.3e-10   39.4   0.3    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    9.1e-09   35.2   0.3    7.4e-06   25.6   0.1    3.0  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
      0.077   12.8   0.1       0.46   10.3   0.0    2.4  2  SAP              SAP domain
       0.09   12.9   0.1       0.25   11.5   0.1    1.7  1  Med2             Mediator complex subunit 2


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.7   0.2   1.6e-83   5.6e-80       2     313 ..     152     492 ..     151     493 .. 0.93

  Alignments for each domain:
  == domain 1  score: 268.7 bits;  conditional E-value: 1.6e-83
                                   CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2   2 eelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspql 81 
                                    e+r+ +ry+d+  ++  ++++++r + ++ +r++l ++gf+e+etPiL+   +++ a++F+ +++  +++++ L++s +l
  gi|70605917|ref|YP_254787.1| 152 PEFRYAHRYVDFlYNDLARRNMEIRYSTIRRIREFLYSKGFMEVETPILQPVYGGALAKPFMSHVNYLNENWY-LRISLEL 231
                                   58899******999******************************************************99***.******* PP

                                   HHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  82 ylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnsk 162
                                   yl+++iv+g+++vf+i+++FR+Ed++ ++++ EFt +e+++++++++dim+++ee+++++vk++ ++s  +i+  i  ++ 
  gi|70605917|ref|YP_254787.1| 232 YLKRYIVGGFNKVFEIGKVFRNEDIDVTHNP-EFTLLELYWAYADYNDIMRLTEEMLQDVVKNINNDS--KIKYSIGGKEY 309
                                   *******************************.********************************5555..55555555555 PP

                                   E-SSS.-EEEEHHHHHHHHHTS-SS.--HHHHHHHHH..........................HS--SEEEEEEEBGGGST CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 163 dlkkp.fkrltykeaieklneigkd.ldkaderalvk..........................keknepvfvtdfPaelkp 215
                                   +++ + f+++t+ ++++++ +++ d ++ ++++ l++                           +  +p+fv d+P e++p
  gi|70605917|ref|YP_254787.1| 310 TIEFSqFRKITMIDSLTEVLGKDVDkMSDEELKSLMDknglkprgnmyirglmieklfdklvtPTLIQPTFVLDYPVETTP 390
                                   555555**********9988665442667788999989*************************9***************** PP

                                   TCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH.....SSSGGGGHHHHHHHHCT--SEEEEEEEH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 216 FyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld.....eeaeekfswylealeyGapphgGlglGl 291
                                   ++++++++ + l+e+++l++ g+El++++++++dp ++   +k+++       eea+  + ++++al+yG+pp+gGlg+G+
  gi|70605917|ref|YP_254787.1| 391 LCKPHRSK-QGLVERFELYVAGMELANAYTELNDPIIQDMLFKQEQEMfkrgdEEAHPYDVDFVRALSYGMPPTGGLGIGI 470
                                   ********.9**********************************9999999*999999999******************** PP

                                   HHHHHHHCT-SSGGGCSSS-XX CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 292 dRlvmlllgsesIrdviaFPkl 313
                                   dRl+mll+++ sI+++i++P l
  gi|70605917|ref|YP_254787.1| 471 DRLIMLLTNNMSIKEIIPYPML 492
                                   ********************75 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.3   1.2e-13   4.3e-10       2      75 ..      61     136 ..      60     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.2e-13
                                   EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
               tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                   + aGrv +i  r +gk++f+d+ D+  r+q+ l      + ++k++e +++Gd+++v+G +  + +gel+l ++++ l
  gi|70605917|ref|YP_254787.1|  61 STAGRVANI--RRHGKISFVDIFDEGERLQLQLRVnelgDRYDKFFEIVDRGDILGVKGDLLYTIKGELTLRIKDYVL 136
                                   569******..***************98888777777***************************9999*****99876 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.11   4.1e+02      15      43 ..     172     200 ..     161     206 .. 0.81
   2 !   25.6   0.1   2.1e-09   7.4e-06     103     169 ..     243     310 ..     240     330 .. 0.82
   3 !    5.1   0.0    0.0039        14     213     234 ..     465     486 ..     455     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
                                   B-SHHHHHHHHHHHHHHCTTCEESSTTSE CS
                  tRNA-synt_2d  15 klhpltkvleeikeiflelgfeevegpev 43 
                                   ++++  +++++i+e++ + gf eve p +
  gi|70605917|ref|YP_254787.1| 172 NMEIRYSTIRRIREFLYSKGFMEVETPIL 200
                                   566667899***************99876 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.1e-09
                                   EEEEEEEEEBSST-SSSB-SEEEEEEEEEE..ETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTE CS
                  tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvv..denvsladlkgvleellkklfgaevkvrfrpsyfpft 169
                                   k++ ig+vfR++++D th +eF+ +e  ++  d n  ++    +l++++k++ +++ k+++      +t
  gi|70605917|ref|YP_254787.1| 243 KVFEIGKVFRNEDIDVTHNPEFTLLELYWAyaDYNDIMRLTEEMLQDVVKNI-NNDSKIKYSIGGKEYT 310
                                   89************************98762255666888899999999999.6666888876655555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0039
                                   EEEEEHHHHHHHHHT-SSGHHH CS
                  tRNA-synt_2d 213 afGlGveRlamlkygieDiRel 234
                                   ++G+G++Rl ml ++   i+e+
  gi|70605917|ref|YP_254787.1| 465 GLGIGIDRLIMLLTNNMSIKEI 486
                                   79***********998888876 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   6.8e+03       6      11 ..      19      24 ..      18      27 .. 0.67
   2 ?   10.3   0.0   0.00013      0.46       2      23 ..     334     355 ..     333     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                                  HHHHHH CS
                           SAP  6 VaeLKe 11
                                  V+eLK+
  gi|70605917|ref|YP_254787.1| 19 VDELKS 24
                                  677775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                   TT--HHHHHHHHHHTT--TTS- CS
                           SAP   2 skltVaeLKeeLkkrGLptsGk 23 
                                    k++  eLK+++ k+GL+  G+
  gi|70605917|ref|YP_254787.1| 334 DKMSDEELKSLMDKNGLKPRGN 355
                                   69****************9997 PP

>> Med2  Mediator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.1e-05      0.25      10      36 ..     276     301 ..     274     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                          Med2  10 lddiLkvsgemlvqeqlktiqldsnvv 36 
                                   ++di+++  eml q+++k+i  ds++ 
  gi|70605917|ref|YP_254787.1| 276 YNDIMRLTEEML-QDVVKNINNDSKIK 301
                                   69**********.***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3584.57
//
Query:       gi|70605918|ref|YP_254788.1|  [L=358]
Description: hypothetical protein Saci_0068 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-22   78.0   4.2    6.4e-22   78.0   4.2    1.6  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
      0.049   13.5   0.0       0.29   11.0   0.0    2.2  2  PDZ_6          PDZ domain
       0.06   13.7   0.0       0.24   11.8   0.0    1.9  2  PDZ_2          PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.75   4.5e+03     179     204 ..      51      76 ..      47      79 .. 0.77
   2 !   78.0   4.2   1.1e-25   6.4e-22       1     248 [.     114     347 ..     114     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.75
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 179 laseaaeaglssflqllalisvnLgi 204
                                   +a + a   ++++  +l +is+ Lg+
  gi|70605918|ref|YP_254788.1|  51 FARKRAYKIFDKIAVVLGVISLVLGL 76 
                                   66677777888888899999998886 PP

  == domain 2  score: 78.0 bits;  conditional E-value: 1.1e-25
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflk 81 
                                   +++l++gi+v++HEl+H++ A  +g+kv++ ++++               ++++p G++V+ ++ee            f++
  gi|70605918|ref|YP_254788.1| 114 YILLAIGISVTLHELAHAISATSNGIKVRSGGLLL---------------LIFFP-GAFVEPDEEE------------FKS 166
                                   5799**************************99999...............9****.**********............*** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX.....................-EEECECTTTSCEE-SEEEC-XXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  82 kspwqrllivlAGplanfilailvfvv.....................pkkskeseeekrgviGvspkpvkkegllealke 141
                                   +s ++rl i+ AG+++n+ila ++f +                     p++++ s   +  +++v     ++ ++ ++l++
  gi|70605918|ref|YP_254788.1| 167 ASSISRLKIISAGIAVNLILAAIFFPLanflpanlsqgllivgekqyfPAYNA-SIPVNSIILKVDG---NAVKVPQQLSY 243
                                   *************************9988887777777776665555532222.2233333334433...55889999999 PP

                                   XXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 142 gvektlkvvvltvk...algklitgklslktlggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghll 219
                                   ++++  + + +++    +++++  ++ + +++g+ i+ +   +     gl +f+ +++ ++++L++lN  P+ + DGg+++
  gi|70605918|ref|YP_254788.1| 244 YLDQGRTHILTLLYpngSINSITINTTQTHQIGVYITYYFPQG---LLGLLQFITWMFTVNFSLALLNGAPLIITDGGKVF 321
                                   999988888877777889***************9999888876...78999****************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 220 falleairrkplserkeevanlvglalll 248
                                    ++  ++    l  r+  +++ v  ++l+
  gi|70605918|ref|YP_254788.1| 322 TEITRKLG---LGDRESYLIQSVFTVILI 347
                                   99988777...999999999999998887 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.27   1.6e+03      34      49 ..     124     139 ..     120     142 .. 0.74
   2 ?   11.0   0.0   4.9e-05      0.29      10      50 ..     215     253 ..     214     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                         PDZ_6  34 sladvaallrgsages 49 
                                   +l+++a+++ +  + +
  gi|70605918|ref|YP_254788.1| 124 TLHELAHAISATSNGI 139
                                   7899*****9766655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                         PDZ_6  10 PAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesv 50 
                                   PA++A + v+ iil+v+G  v  + +++++ +l +   +++
  gi|70605918|ref|YP_254788.1| 215 PAYNASIPVNSIILKVDGNAV--KVPQQLSYYLDQGRTHIL 253
                                   9********************..*999***99985544444 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.7   4.2e+03       3      62 ..     119     138 ..     118     145 .. 0.50
   2 ?   11.8   0.0     4e-05      0.24      13      57 ..     202     246 ..     179     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.7
                                   ..XX------..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT CS
                         PDZ_2   3 lGvsvsdeedtggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpG 62 
                                   +G+sv+ +e                                          ++++++++G
  gi|70605918|ref|YP_254788.1| 119 IGISVTLHEL----------------------------------------AHAISATSNG 138
                                   6666666655........................................3333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4e-05
                                   ..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHH CS
                         PDZ_2  13 tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislll 57 
                                   ++g+l+v  k+  Pa +a +  + +ilkvdg++vk  ++l  +l 
  gi|70605918|ref|YP_254788.1| 202 SQGLLIVGEKQYFPAYNASIPVNSIILKVDGNAVKVPQQLSYYLD 246
                                   6788888888999*********************98888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2513.11
//
Query:       gi|70605919|ref|YP_254789.1|  [L=221]
Description: hypothetical protein Saci_0069 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-07   29.9   0.3    1.1e-06   28.8   0.1    1.8  1  NTP_transf_2  Nucleotidyltransferase domain
    2.7e-05   24.2   0.0    5.8e-05   23.1   0.0    1.8  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   1.3e-10   1.1e-06      15      62 ..      32      72 ..      18     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.3e-10
                                  SEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCC CS
                  NTP_transf_2 15 akvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikf 62
                                   + +++GS+arG+ +k+SDiD++++ p+         gl+ ++++ kf
  gi|70605919|ref|YP_254789.1| 32 MEGFVYGSVARGDVNKESDIDIVIFNPNI-------LGLDLISCDHKF 72
                                  56689*******************99887.......344444444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.5e-09   5.8e-05      17      42 ..      35      60 ..      17     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.5e-09
                                  TEEEEEE-S------EEEEEEEESS- CS
                       Polbeta 17 ylFGSrakgkareeSDiDlavllkek 42
                                  +++GS+a+g+ ++eSDiD+ ++  + 
  gi|70605919|ref|YP_254789.1| 35 FVYGSVARGDVNKESDIDIVIFNPNI 60
                                  79*****************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1488.10
//
Query:       gi|70605920|ref|YP_254790.1|  [L=177]
Description: hypothetical protein Saci_0070 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-65  220.4   0.4    1.3e-65  220.1   0.4    1.1  1  DUF1122   Protein of unknown function (DUF1122)


Domain annotation for each model (and alignments):
>> DUF1122  Protein of unknown function (DUF1122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.1   0.4   7.4e-70   1.3e-65       2     175 ..       9     168 ..       8     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.1 bits;  conditional E-value: 7.4e-70
                                   EEEEE..EEEE-SSTTEEEEEEEETT....EEEEEEEEE--BTTB--EEEEES--G.......GGHHHHTTSHHHHHHHHH CS
                       DUF1122   2 elklea.evkqgrfkeevnlevyverdeakkellalkvFeGRdlyrpWiEifniswlreveldsltavffgskvEeelldl 81 
                                   +l +e+ +vk++++ke++++ +yv+     ++++++++F+GR++y pWiEi++ +wlre++             E +l+++
  gi|70605920|ref|YP_254790.1|   9 KLVIESiDVKDTQIKELKTFILYVNG----RKVGRTFYFTGREYYLPWIEIDYDPWLREIDG------------EVDLFNF 73 
                                   6889999*******************....*******************************9............99***** PP

                                   HTTT-S...EEEEE-TT-HHHHHHHHTT--GGGSHHHHHHHHTT--EEEEEES-TTTSSS-EEEEEE--SSHHHHHHHHHH CS
                       DUF1122  82 lsevlgpgerlfveYvkDketlkelekgipaaltrLGfeLlkrGftwFkdWYfpEGfmEGspkiqaekPldeeeekrqlee 162
                                   +++vl+pg++lfv+Y++Dket+++l++g+++a+t+LGf+Llk+GftwFk+WYfpEG++EG+pkiqa+kPl++++++rql+e
  gi|70605920|ref|YP_254790.1|  74 IYNVLPPGGKLFVTYIRDKETADMLYQGFSPADTPLGFSLLKAGFTWFKNWYFPEGGNEGAPKIQANKPLNDTDMIRQLRE 154
                                   ********************************************************************************* PP

                                   HHHHHH.HHHHH-- CS
                       DUF1122 163 llkeve.efikkve 175
                                   ll+ev+ +++k+++
  gi|70605920|ref|YP_254790.1| 155 LLDEVKrNEVKAFI 168
                                   ******9***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1271.18
//
Query:       gi|70605921|ref|YP_254791.1|  [L=337]
Description: hypothetical protein Saci_0071 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-11   42.7   0.1    3.9e-08   33.8   0.0    2.6  3  Radical_SAM  Radical SAM superfamily
    2.3e-08   34.2   0.0    4.1e-08   33.4   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
    2.8e-06   27.6   0.0    5.7e-06   26.6   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   6.6e-12   3.9e-08       3     106 ..      32     137 ..      30     141 .. 0.89
   2 !    6.4   0.0    0.0018        11     128     164 ..     143     177 ..     135     179 .. 0.86
   3 ?   -2.1   0.0      0.74   4.4e+03     124     142 ..     218     236 ..     201     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 6.6e-12
                                   EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEE CS
                                   xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgiri 80 
                                   +t  C  +C +C+++e   +++   + + + e++++ + e+ +++++ +  ++gg+pl + d+v+ l +  k +   +++i
  gi|70605921|ref|YP_254791.1|  32 ITGECGDNCYYCPVSEQrfGKDKAFANEAPAENLVDFIYEA-YRMRALGAGITGGDPLIRIDKVVSLIKKFKDEfGQEFHI 111
                                   5778************8777777777777888888888888.7999*********************99999999****** PP

                                   EEEECSSCHGHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpdeeklerllelgvdrvs 106
                                   ++ t+g  +++++l +l ++g+d + 
  gi|70605921|ref|YP_254791.1| 112 HLYTSGRYVTKDVLSELERAGLDEIR 137
                                   *********************99876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 128 eevlealeklreagikrvvdrivglpGendeeleell 164
                                    e+l+a+ek+ + +++ v + ++ +pG+  e le+l+
  gi|70605921|ref|YP_254791.1| 143 REYLRAIEKAVQFNFD-VGIEVPAIPGQEQE-LEKLI 177
                                   799*************.**********9887.77765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.74
                                   TSHHHHHHHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 124 ghtfeevlealeklreagi 142
                                   +++fe  +++l+kl+e  i
  gi|70605921|ref|YP_254791.1| 218 NGSFETAYATLRKLHEEKI 236
                                   4566666666666666544 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   6.9e-12   4.1e-08       2      92 ..      31     120 ..      29     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6.9e-12
                       Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlkeey.p 79 
                                   f+ ++ C  +C  C  +e +++   k +++e   + l     +++++++ g  +tGG+PL   + ++++ l+k+ k+e+ +
  gi|70605921|ref|YP_254791.1|  31 FI-TGECGDNCYYCPVSE-QRFGKDKAFANEAPAENLVdfIYEAYRMRALGAGITGGDPL--IRIDKVVSLIKKFKDEFgQ 107
                                   66.9**********9777.6776666766666655555122556666667789*******..789**************99 PP

                       Fer4_14  80 ekkiwletngtle 92 
                                   e++i+l+t+g + 
  gi|70605921|ref|YP_254791.1| 108 EFHIHLYTSGRYV 120
                                   9********9876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   9.5e-10   5.7e-06       5      96 ..      25     119 ..      21     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 9.5e-10
                       Fer4_12   5 Gvrlslf.vsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesi...egltllGGEPllpenaeallelvkevk 80 
                                   G+ l++f ++ C  +C +C   + ++f + k f  ++ +e++++ + + ++    g  ++GG+Pl     +++++l+k++k
  gi|70605921|ref|YP_254791.1|  25 GGKLVVFiTGECGDNCYYCP-VSEQRFGKDKAFAnEAPAENLVDFIYEAYRmraLGAGITGGDPLI--RIDKVVSLIKKFK 102
                                   67788885778*******98.6667777777774366677777777664444448899********..9************ PP

                       Fer4_12  81 eekp.ekdiwlytgytl 96 
                                    e+  e  i lyt   +
  gi|70605921|ref|YP_254791.1| 103 DEFGqEFHIHLYTSGRY 119
                                   ***97777778876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2358.14
//
Query:       gi|70605922|ref|YP_254792.1|  [L=342]
Description: hypothetical protein Saci_0072 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-24   84.0   1.6    1.1e-23   83.6   0.7    1.6  2  eRF1_1           eRF1 domain 1
    4.5e-21   75.4   5.2    2.5e-20   73.1   0.3    2.7  2  eRF1_3           eRF1 domain 3
      4e-06   27.2   0.5    2.2e-05   24.8   0.2    2.3  2  eRF1_2           eRF1 domain 2
     0.0029   17.7   0.0     0.0043   17.1   0.0    1.2  1  baeRF_family2    Bacterial archaeo-eukaryotic release factor 
  ------ inclusion threshold ------
      0.013   14.8   0.9      0.021   14.1   0.9    1.3  1  MobL             MobL relaxases
      0.074   12.7   0.2       0.37   10.4   0.0    2.0  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.14   11.8   0.8       0.62    9.7   0.8    2.0  1  Maelstrom        piRNA pathway germ-plasm component


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.7   4.3e-27   1.1e-23      10     127 ..       7     120 ..       1     121 [. 0.93
   2 ?   -3.0   0.0       2.7   6.9e+03       7      32 ..     306     330 ..     303     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 4.3e-27
                                   TTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEG CS
                        eRF1_1  10 kdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlrisGkviee 90 
                                   +d++gs++L +e+++dlw l  +i++gd++ a+t+r +        ++s+r+ ++++++ve ++f++ + +lri+G + + 
  gi|70605922|ref|YP_254792.1|   7 NDKRGSLKLHVENEDDLWLLHIIIKKGDRIVAKTTRDISM-----GKDSRRIPMTIELQVEYTEFQNFTTRLRIHGLILDA 82 
                                   5789**********************************66.....678********************************9 PP

                                   GGG.--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHH CS
                        eRF1_1  91 neh.vklgafhtldlelkrpftiikeewdsfalerLke 127
                                    e    +ga+ht++l++++++ iike+w+++ le+++e
  gi|70605922|ref|YP_254792.1|  83 PERfGIKGAHHTVNLDIGDEVIIIKEQWSNYELEKIRE 120
                                   9986789***************************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.7
                                   CTBTTSCCEEEEEE-SCHHHHHHHHH CS
                        eRF1_1   7 dlekdgsgsvtLipeddedlwhlynl 32 
                                   d+e +++g + ++p+d+   +++ nl
  gi|70605922|ref|YP_254792.1| 306 DIE-KKKGKIMIVPKDSPIYYQVKNL 330
                                   566.5589999999998888888776 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.8     0.032        82      42      89 ..     105     192 ..      85     196 .. 0.67
   2 !   73.1   0.3   9.6e-24   2.5e-20       1     113 []     245     341 ..     245     341 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.032
                                   EEEHCHHTSSSH.HHHHS......................................-HHH-HHHHHH.HHHHHHHHHHHTT CS
                        eRF1_3  42 Lvseelersrdt.lkekv......................................ketgeelelve.lieelvenveesg 82 
                                   ++ e+  +++ + ++e++                                      k++ + +e +e +++e+++ v+ +g
  gi|70605922|ref|YP_254792.1| 105 IIKEQWSNYELEkIREQEekkgkllialvdvdeyiiallmkqgvkilaekslqtpgKDNDVVNENIEeMANEIISFVKLTG 185
                                   555555555555455555556666666666666666666666667777777744444444555555589999999999999 PP

                                   -EEEEE- CS
                        eRF1_3  83 akveiis 89 
                                    +v+ii 
  gi|70605922|ref|YP_254792.1| 186 VNVIIIA 192
                                   9999985 PP

  == domain 2  score: 73.1 bits;  conditional E-value: 9.6e-24
                                   HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHT CS
                        eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenvees 81 
                                   ++q+ k+le  +e+lak+tg++vYG+e+++ka+e+gAv++LL++e++ ++    +e             +i+el++++e+ 
  gi|70605922|ref|YP_254792.1| 245 IAQQLKILESIMENLAKNTGLVVYGIEDIKKANELGAVDKLLITEDYLTDT--GRE-------------IIDELLRDIEKK 310
                                   578899*****************************************9984..332.............69********** PP

                                   T-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  82 gakveiisseseeGeqlvkafgGiaaiLRykv 113
                                   ++k+ i++++s+ + q+ k+++Gi+ +LR+++
  gi|70605922|ref|YP_254792.1| 311 KGKIMIVPKDSPIYYQV-KNLTGIVSLLRFRI 341
                                   *****************.************96 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.2   8.5e-09   2.2e-05      60     126 ..     168     233 ..     127     241 .. 0.77
   2 ?   -4.0   0.0       6.5   1.7e+04      90     109 ..     297     316 ..     293     317 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.5e-09
                                   HHHHHHHHHHH.HCHTTTESEEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE.-S-TSCHHHHHHHHC CS
                        eRF1_2  60 kvaeaankafl.lvdkdklkgiilagpgfvkeefldkdlldaelkkkviklvd.vsyggesglnevlek 126
                                   + +e++ ++ +  v+   +++ii+agpg++k+   +k+   ++  +k i+ vd vs+  ++glne+l+ 
  gi|70605922|ref|YP_254792.1| 168 ENIEEMANEIIsFVKLTGVNVIIIAGPGPFKDMVNQKI---KQIDNKLIVYVDsVSSASRAGLNELLRR 233
                                   44556666667799999**************9877765...3344566666653899*********985 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.5
                                   HHHHHHHHHHHHHHTCCEEE CS
                        eRF1_2  90 eefldkdlldaelkkkvikl 109
                                   +e++d++l d e+kk +i++
  gi|70605922|ref|YP_254792.1| 297 REIIDELLRDIEKKKGKIMI 316
                                   56667777777777777766 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.7e-06    0.0043      53     147 ..     163     259 ..     153     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                 baeRF_family2  53 eeswerNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLpervrelvvevegggraagadreal..aeevaealaer 131
                                    + +++N+e+ A e+ + v+ +g++++++aG      ++ +++++   +l+v v++ + a++a   +l  ++ ++++ +e+
  gi|70605922|ref|YP_254792.1| 163 NDVVNENIEEMANEIISFVKLTGVNVIIIAGPGPFKDMVNQKIKQIDNKLIVYVDSVSSASRAGLNELlrRDIIDQVYREF 243
                                   57899**************************************************88777766655542266699999999 PP

                 baeRF_family2 132 rarrreevlerfraer 147
                                   + +++ ++le + +++
  gi|70605922|ref|YP_254792.1| 244 EIAQQLKILESIMENL 259
                                   9999999999888766 PP

>> MobL  MobL relaxases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   8.3e-06     0.021     212     304 ..     221     313 ..     198     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
                          MobL 212 kqelakisrlireklrnqkkekkrsaveskeikkllqeiykkLpkdrkkwrygsnamkearpl..iDe..lvdkylekskk 288
                                   + ++a +++l+r+ +++q  ++ + a    ++ k l+ i+++L k+  +  yg +++k+a++l  +D+  ++++yl+  + 
  gi|70605922|ref|YP_254792.1| 221 SASRAGLNELLRRDIIDQVYREFEIA----QQLKILESIMENLAKNTGLVVYGIEDIKKANELgaVDKllITEDYLTDTGR 297
                                   567789**********9977666655....*******************************9666**944589******** PP

                          MobL 289 keleellerlekeqke 304
                                   + ++ell ++ek++ +
  gi|70605922|ref|YP_254792.1| 298 EIIDELLRDIEKKKGK 313
                                   *********9998766 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.38   9.8e+02      43      88 ..      40      83 ..      24     133 .. 0.71
   2 ?   10.4   0.0   0.00014      0.37     116     188 ..     247     320 ..     232     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.38
                                  CCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE- CS
               Methyltr_RsmB-F 43 keRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaP 88
                                  ++R  ++ ++ +r+++t  i l+++ ++++++++   +  ++lDaP
  gi|70605922|ref|YP_254792.1| 40 TTRDISMGKDSRRIPMT--IELQVEYTEFQNFTTRLRIHGLILDAP 83
                                  45666667777888887..667788888888888878888888888 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHCCCE.EEEEEEEEEES--STTTTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEECTSEEE-TTT CS
               Methyltr_RsmB-F 116 lqkellsaaidll.kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeeagtlrllPht 188
                                   +q ++l+++++ l k+ G +vY    ++ + +  +++++L +++    + +e+ +    ++++++g++ ++P+ 
  gi|70605922|ref|YP_254792.1| 247 QQLKILESIMENLaKNTGLVVYGIEDIKKANELGAVDKLLITEDYLTDTGREIIDELLRDIEKKKGKIMIVPKD 320
                                   6899******999899***************************9999999999999999999999999999976 PP

>> Maelstrom  piRNA pathway germ-plasm component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.8   0.00024      0.62      50     110 ..     153     260 ..     135     336 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                   HHTT----TTS--SB--HHHHHHHHHHHHHHH..................H-SS..S-EE..................... CS
                     Maelstrom  50 detHqlplppnalgesdlkklveeilsfless..................seksneksli..................... 91 
                                   ++  q p ++n + +++++++ +ei+sf++ +                  +     k  i                     
  gi|70605922|ref|YP_254792.1| 153 EKSLQTPGKDNDVVNENIEEMANEIISFVKLTgvnviiiagpgpfkdmvnQ-----K--Ikqidnklivyvdsvssasrag 226
                                   555577888999*******************95555555444333222221.....1..1222333333444444444444 PP

                                   ...............EEE-GGGHHHHHHHHHHH- CS
                     Maelstrom  92 ...............iltkeeeisvvksclknla 110
                                                   +  ++++++ +s+++nla
  gi|70605922|ref|YP_254792.1| 227 lnellrrdiidqvyrEFEIAQQLKILESIMENLA 260
                                   4444445544443333333444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2154.82
//
Query:       gi|70605923|ref|YP_254793.1|  [L=154]
Description: acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-16   58.5   0.1    9.3e-16   58.1   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.1e-12   47.3   0.9    3.3e-12   46.6   0.9    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.1e-12   46.5   0.0    3.3e-12   46.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.7e-08   33.3   2.8    4.7e-08   33.3   2.8    1.5  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00018   21.4   0.0    0.00026   20.9   0.0    1.2  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.075   12.4   0.1       0.28   10.5   0.0    1.7  2  GNAT_acetyltr_2  GNAT acetyltransferase 2


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.1   3.1e-19   9.3e-16       3     117 .]      14     123 ..      12     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.1e-19
                                   HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHH CS
                Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLle 83 
                                   ++++ + esf  p++ + +++++ +     + ++va+ ++++iG+i + ++      +++i s+aV+++ rg+G+G++L+ 
  gi|70605923|ref|YP_254793.1|  14 EIYDVELESFDNPYPFSLLRAYYYI---SGDLFIVAKSGDKVIGYILGIIQFG---YRGHIVSIAVKKDKRGSGIGTKLIS 88 
                                   6788888888888888888886666...5668888***********9888888...9************************ PP

                                   HHHHHHHHT.TE.SEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  84 aleeraree.gi.kkivlaveedndaairlYeklGF 117
                                   +le r++    + +  +l+v   n  ai++Y k G+
  gi|70605923|ref|YP_254793.1|  89 ELENRFKLAyHCiHS-YLEVYYKNISAINFYIKNGY 123
                                   ***999999999677.***************88886 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.9   1.1e-15   3.3e-12       4      75 ..      42     124 ..      39     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.1e-15
                                   EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH.TT.....SEEEEEEEEE....THH.HHHHHHH CS
                Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea.ae.....kgiileqlel....nae.kaikfYe 70 
                                    ++Va+ ++k++G+i   ++    ++i  +aV+++ rg GiG++L+   ++      ++i  +++l    + +  ai+fY 
  gi|70605923|ref|YP_254793.1|  42 LFIVAKSGDKVIGYILGIIQFgyrGHIVSIAVKKDKRGSGIGTKLISElENrfklaYHCI--HSYLevyyK-NiSAINFYI 119
                                   6899*********9987777677666666*****************85322433333344..345533423.269****** PP

                                   HTTEE CS
                Acetyltransf_7  71 klGFe 75 
                                   k+G++
  gi|70605923|ref|YP_254793.1| 120 KNGYK 124
                                   ****8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.1e-15   3.3e-12      31     111 ..      41     130 ..       6     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.1e-15
               Acetyltransf_10  31 alllvaeeggkivGvi.elrdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnasp.yavpfYekl 104
                                    l++va+ g+k++G+i ++ + +   hi  ++V+++ rg Gig++L+ ++e++++ + + +   l+v  ++  a++fY k 
  gi|70605923|ref|YP_254793.1|  41 DLFIVAKSGDKVIGYIlGIIQFGyrgHIVSIAVKKDKRGSGIGTKLISELENRFKLAYHCIhsYLEVYYKNiSAINFYIKN 121
                                   45999********9997555555566***************************8666555578****************** PP

               Acetyltransf_10 105 GFkav..ge 111
                                   G+kav  ++
  gi|70605923|ref|YP_254793.1| 122 GYKAVriQK 130
                                   ***995444 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   3.5e+03       1      14 [.       4      17 ..       4      24 .. 0.83
   2 !   33.3   2.8   1.6e-11   4.7e-08      51     151 ..      42     140 ..      33     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                Acetyltransf_4  1 iraateeDakeila 14
                                  i++a+eeD+ ei +
  gi|70605923|ref|YP_254793.1|  4 ISDAREEDLPEIYD 17
                                  78999****99865 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 1.6e-11
                Acetyltransf_4  51 vflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfh 129
                                   +f va+  d+++Gy  +  +++ ++++  ++s+ ++ +d++  g+g +li  le+++  +++    + e++++n+++i+f+
  gi|70605923|ref|YP_254793.1|  42 LFIVAKsGDKVIGYILGI-IQF-GYRG-HIVSIAVK-KDKRGSGIGTKLISELENRFkLAYHCIHSYLEVYYKNISAINFY 118
                                   6899998899***99777.666.4455.489****8.89****************************************** PP

                Acetyltransf_4 130 kalGFelvgifkkcikkngrwi 151
                                    + G++ v+i+k+++    + i
  gi|70605923|ref|YP_254793.1| 119 IKNGYKAVRIQKDYYGREKHAI 140
                                   *************998777665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   8.7e-08   0.00026      20      80 ..      64     126 ..      49     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.7e-08
                                   TTSSEEEEEE-GGG-SSSHHHHHHHHHHHH..HHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47  20 dggelgalqvlpehrrrGlgsrlvkalake..iaergktvllvvvasNtpsirlyeklGfeki 80 
                                   + g + ++ v+++ r+ G g++l+++l ++  +a   +++ l v  +N  +i++y k G+++ 
  gi|70605923|ref|YP_254793.1|  64 YRGHIVSIAVKKDKRGSGIGTKLISELENRfkLAYHCIHSYLEVYYKNISAINFYIKNGYKAV 126
                                   459************************98622777999**********************976 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.5e-05      0.28      98     129 ..      68      99 ..      60     113 .. 0.87
   2 ?   -0.5   0.0      0.22   6.7e+02     194     226 ..     115     146 ..     103     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.5e-05
               GNAT_acetyltr_2  98 ivRiAvhpelqkmGYGsralellekyyegkls 129
                                   iv iAv+++ ++ G G++ +++le+ ++  ++
  gi|70605923|ref|YP_254793.1|  68 IVSIAVKKDKRGSGIGTKLISELENRFKLAYH 99 
                                   9***********************99987665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
               GNAT_acetyltr_2 194 lkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                   ++F+ ++g++ v +++        h++im++sl
  gi|70605923|ref|YP_254793.1| 115 INFYIKNGYKAVRIQKDYY-GREKHAIIMIKSL 146
                                   6788899999888765433.2345788888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1117.70
//
Query:       gi|70605924|ref|YP_254794.1|  [L=782]
Description: DNA polymerase II [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-44  152.3   0.2    3.2e-44  151.4   0.2    1.5  1  DNA_pol_B       DNA polymerase family B
    6.6e-40  137.3   7.5    3.3e-38  131.7   7.5    2.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    2.1e-05   24.6   0.3    0.00012   22.1   0.0    2.4  3  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.053   13.2   0.0    1.6  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
      0.035   14.4   4.8        1.9    8.9   0.6    3.7  3  DUF1947         Domain of unknown function (DUF1947)
       0.15   11.9   0.1       0.46   10.4   0.1    1.8  1  CSN7a_helixI    COP9 signalosome complex subunit 7a helix I d


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   0.2   1.1e-47   3.2e-44      11     455 ..     380     758 ..     370     761 .. 0.87

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 1.1e-47
                                   HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHC CS
                     DNA_pol_B  11 qqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeea 91 
                                   +  r+e lL+r+ k+++  +p+r+e + +++     + ++ P +gl++ +v +lDF+  YPsii+++N+++ tlv+ + ++
  gi|70605924|ref|YP_254794.1| 380 SGHRIEWLLVRESKKYNEFIPNREERRTEAS---DEGIIVPPVSGLHN-NVYMLDFSTIYPSIILKYNISPDTLVRGDCSD 456
                                   56799****************7777755555...8999********96.699***********************999885 PP

                                   CT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                     DNA_pol_B  92 keleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGv 172
                                      +          ++   ++ + ++ +gl+ ++L +l a+  + ++e+ ++ d+++++ l++   al  + Ns+Y ++  
  gi|70605924|ref|YP_254794.1| 457 CWTSL---------NG---NYKFRKDIKGLYQNVLLNLSAE-IERREEIIKTLDPEKRRRLEEELRALRSILNSFYDYIRW 524
                                   53332.........23...24458899********998655.455666666677779999********************* PP

                                   TTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHH CS
                     DNA_pol_B 173 ansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellkigkela 253
                                   +n r + ++ A++    GRe ++++ ++v++                  +++viY DTD +f + + +         k+l+
  gi|70605924|ref|YP_254794.1| 525 TNARWYVKECAEGLFEWGRELILQILKIVKES-----------------GFQVIYADTDLMFFKGENDP--------KKLE 580
                                   ******************************88.................9*********9998766543........5678 PP

                                   HHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S CS
                     DNA_pol_B 254 eevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteer 333
                                   e + +   +  l+l+f+k y+kl+L+  KK+Ya+l+ +     nk+++ G++  R ++c+l+kev ++v++++l+      
  gi|70605924|ref|YP_254794.1| 581 EDIAN---RLSLNLKFNKFYTKLILLeGKKQYAALTKD-----NKVDMVGIEDYRNNWCDLAKEVLQNVVDQVLRS----D 649
                                   88887...33468*********987726999*999999.....99*******************************....9 PP

                                   -HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS. CS
                     DNA_pol_B 334 sleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkke 414
                                   +++e+++++ks++      l+ +++++e++v  + + k+ e+yk  +lph+ +a++ +k  ++ ++ g +i Yviv+ +  
  gi|70605924|ref|YP_254794.1| 650 KINEAVRYVKSVI----YSLRRGEFKIEDLVTWNIIDKDIEEYKF-DLPHIVAARKAMKS-GHLVTRGSKIGYVIVKGSG- 723
                                   99*******9999....99************************86.56***888887776.89***************64. PP

                                   ....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHH CS
                     DNA_pol_B 415 vkkknllaseraedpeyvleknlpidieyYls.qllkevarl 455
                                         + s+rae p ++ +++ ++dieyY++ q+++ + ++
  gi|70605924|ref|YP_254794.1| 724 ------KLSNRAE-PYFMVKEKSKVDIEYYIDkQIIPSALKV 758
                                   ......6777775.89999999**************988776 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   7.5   1.1e-41   3.3e-38       3     323 ..      28     295 ..      26     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.1e-41
                                   CTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHH CS
                DNA_pol_B_exo1   3 eegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelk 83 
                                   + g++v   + +f+pyfY+ + d ++ + v++e+k+l++   +++t   ++e+ + ++++g+  k    lk+++  p  ++
  gi|70605924|ref|YP_254794.1|  28 RRGNRVTLVEKNFRPYFYAVVDDREDVSRVISEIKKLSKPS-SPIT---NIEIETDRRYFGNPLK---SLKIETVVPAYVR 101
                                   678999999**************************999555.5566...9***************...9************ PP

                                   HHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTTCCS-EEEEEE CS
                DNA_pol_B_exo1  84 kirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpkesepplrvlsF 164
                                     r+e+s+++ +  v e+d+ +++r++id++i++f w++ +++++++++  + ++ ++    +d+  +++ +ep+l+ ++F
  gi|70605924|ref|YP_254794.1| 102 IYRDEVSKIKGVKNVLEADIRFYMRYSIDKGIKPFYWIKADVEEIQPKEIFKVKSEKLYL-IKDILEIYEAEEPRLKTMAF 181
                                   *****************************************7777777666665555555.445555455555******** PP

                                   EEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHH CS
                DNA_pol_B_exo1 165 DIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaf 245
                                   +Ie++ k+g fp+  +  dpii I +  ++         k f+   ++                         +++++++f
  gi|70605924|ref|YP_254794.1| 182 SIEVYNKYG-FPNTRR--DPIIVIGVYTENGY-------KQFISSDYD-------------------------DINVIREF 227
                                   *********.******..**********8766.......678877777.........................5699**** PP

                                   HHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS.CTCEECCCCESEEEEEECEEEETTSEEEEHHHHH CS
                DNA_pol_B_exo1 246 lefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln.kggrskvseigfskqarekvkisgrihlDlyrvv 323
                                   ++f+ + +Pd+i+gYN ++FD++Y+ +Ra+ l  +        +   gr+ +se++++   ++++++ gr+++Dl  v+
  gi|70605924|ref|YP_254794.1| 228 IKFVNDFEPDIIFGYNSNSFDWRYLVERAE-LRGI--------KvAIGRKVNSEPSQG--VYGHYSVTGRLNVDLAGVF 295
                                   ******************************.4443........2389***********..***************9887 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     4e-08   0.00012      13     160 ..     195     352 ..     182     356 .. 0.71
   2 ?   -2.3   0.0       1.3   3.9e+03      53      84 ..     559     590 ..     548     613 .. 0.75
   3 ?   -2.8   0.0       1.9   5.7e+03      78     110 ..     729     759 ..     724     780 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4e-08
                     RNase_H_2  13 kknliyliGvldvdekeiekltqllaeepeeekailelflellekk..kalvtfngksFDvpflkrlf....kkyklde.. 85 
                                   +++ i++iGv+   e+ ++   q++ ++ ++ + i e++ ++++++  + +  +n +sFD+++l +++         +   
  gi|70605924|ref|YP_254794.1| 195 RRDPIIVIGVYT--ENGYK---QFISSDYDDINVIREFI-KFVNDFepDIIFGYNSNSFDWRYLVERAelrgI----KVai 265
                                   56789******5..55544...77889999999999966.9999984345778999************66442....4444 PP

                     RNase_H_2  86 .......eefrhiDLlkel...rkkkl.........esysLksvekelgierreedlsGsqavklyqeylrtgdeelleki 147
                                          +   +  ++ ++    + ++         +s sL +++  lg+  +    + +++ ++y+  +   d+++ e +
  gi|70605924|ref|YP_254794.1| 266 grkvnseP---SQGVYGHYsvtGRLNVdlagvfcssRSKSLIDLADNLGVMPK----NKREILEWYEVPRYWDDKSKREIL 339
                                   65664432...33333222111232225566677775558************9....799999999954445899999999 PP

                     RNase_H_2 148 laYNedDvralat 160
                                   l++N   + + + 
  gi|70605924|ref|YP_254794.1| 340 LKHNLSNIKSIYD 352
                                   9999988877665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                     RNase_H_2  53 ellekkkalvtfngksFDvpflkrlf.kkykld 84 
                                   +++  +++l+ f+g++ D + l++ + ++  l+
  gi|70605924|ref|YP_254794.1| 559 QVIYADTDLMFFKGEN-DPKKLEEDIaNRLSLN 590
                                   6677889999999999.9999998886555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
                     RNase_H_2  78 fkkykldeeefrhiDLlkelrkkklesysLksv 110
                                   ++ y + + e  ++D+ + + k+ + s  Lk +
  gi|70605924|ref|YP_254794.1| 729 AEPYFMVK-EKSKVDIEYYIDKQIIPS-ALKVL 759
                                   44444454.788999999999999988.88765 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.053      33      97 ..     216     281 ..     199     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                DNA_pol_B_exo2  33 eessekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnny 97 
                                   ++ ++ ++i++f+++v+  +p ++ ++n+++fD   l  ra  +g++++   + ++e  +  +  y
  gi|70605924|ref|YP_254794.1| 216 SDYDDINVIREFIKFVNDFEPDIIfGYNSNSFDWRYLVERAELRGIKVAIGRKVNSEPSQGVYGHY 281
                                   55677899*************98769***************9999998765555554455555544 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.2   6.7e+03      11      35 ..      55      78 ..      52      85 .. 0.73
   2 ?    8.9   0.6   0.00062       1.9      31      55 ..     149     173 ..     128     180 .. 0.75
   3 ?    5.0   0.0    0.0099        29      31      55 ..     550     574 ..     538     576 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.2
                                  HHHHHHHHTTT---TT--..-EEEE CS
                       DUF1947 11 keileklkekyisislesdkiEiee 35
                                   ++++++k+ +   s  ++ iEie 
  gi|70605924|ref|YP_254794.1| 55 SRVISEIKKLSKPSSPITN-IEIET 78
                                  5778888888866677776.99986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00062
                                   -EEEE-SS-EEEEETTEEEEEESSS CS
                       DUF1947  31 iEieeekkeklYlingvpilfeeek 55 
                                    Ei++ k+eklYli +++ ++e+e+
  gi|70605924|ref|YP_254794.1| 149 KEIFKVKSEKLYLIKDILEIYEAEE 173
                                   39*******************9544 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0099
                                   -EEEE-SS-EEEEETTEEEEEESSS CS
                       DUF1947  31 iEieeekkeklYlingvpilfeeek 55 
                                   + i +e ++ +++ +  +++f++e+
  gi|70605924|ref|YP_254794.1| 550 LKIVKESGFQVIYADTDLMFFKGEN 574
                                   56999****************9665 PP

>> CSN7a_helixI  COP9 signalosome complex subunit 7a helix I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00015      0.46      10      30 ..     628     648 ..     619     661 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                  CSN7a_helixI  10 qeWcdsCeaiLsciEtqverA 30 
                                   ++Wcd ++++L+++ +qv r 
  gi|70605924|ref|YP_254794.1| 628 NNWCDLAKEVLQNVVDQVLRS 648
                                   79****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 5042.83
//
Query:       gi|70605925|ref|YP_254795.1|  [L=412]
Description: DNA primase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   41.8   0.7    1.2e-09   38.4   0.1    2.6  2  Toprim_4  Toprim domain
    1.3e-05   25.5   0.2    4.8e-05   23.7   0.0    2.1  2  Toprim_2  Toprim-like
    0.00031   20.9   3.1    0.00043   20.5   0.1    2.7  3  Toprim    Toprim domain
     0.0055   15.8   0.2      0.006   15.7   0.2    1.1  1  DUF1822   Protein of unknown function (DUF1822)
  ------ inclusion threshold ------
        3.9    7.3   7.1        2.1    8.2   2.1    2.4  3  DUF2344   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.28     1e+03      30      58 ..      82     113 ..      74     113 .. 0.81
   2 !   38.4   0.1   3.5e-13   1.2e-09       2      75 ..     166     229 ..     165     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.28
                      Toprim_4  30 alspldgirpeklktenlve....aekkvkevi 58 
                                    ++++d+++p + +  +l++    +e+k+k++i
  gi|70605925|ref|YP_254795.1|  82 MIENVDKVGPYNAEF-KLIDivdiREEKIKKII 113
                                   567889999999999.6777888*999999998 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 3.5e-13
                      Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlg..galspldgirpeklktenlveaekkvkevilaldgDaeGeataerla 75 
                                   e+iiVEg+aDv++l ++g+knv+av g  g + p+  +     k+          k vi +ldgD+ G+   ++l+
  gi|70605925|ref|YP_254795.1| 166 ELIIVEGRADVINLLRYGYKNVIAVEGatGKI-PQTLVD--LTKQ---------KKAVIAFLDGDHGGDLILKELL 229
                                   69*************************77777.555555..4444.........379**********998777765 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.3e-08   4.8e-05       1      68 [.     168     232 ..     168     251 .. 0.81
   2 ?   -2.0   0.1       1.4   5.1e+03      20      29 ..     288     297 ..     262     314 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                      Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGt..alteaalkllerypekkvvlalDnDkaGrkaakrlaell 68 
                                   +++Eg  D++ l+++g k   nv+a+ G   ++++++++l +++  k v+  lD D  G+   k+l +  
  gi|70605925|ref|YP_254795.1| 168 IIVEGRADVINLLRYGYK---NVIAVEGAtgKIPQTLVDLTKQK--KAVIAFLDGDHGGDLILKELLSSN 232
                                   69***************9...*******9988889999988888..9999**********9999887554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                      Toprim_2  20 ktnvvalgGt 29 
                                   +t +v++ +t
  gi|70605925|ref|YP_254795.1| 288 TTTAVTTTST 297
                                   3344444444 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   4.5e+03      52      66 ..      98     112 ..      59     138 .. 0.59
   2 !   20.5   0.1   1.2e-07   0.00043       1      85 [.     166     230 ..     166     250 .. 0.89
   3 ?   -0.2   0.1      0.34   1.2e+03      12      30 ..     277     294 ..     251     359 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHSEE CS
                        Toprim  52 vlkalkelakradei 66 
                                    +++++ + ++ ++i
  gi|70605925|ref|YP_254795.1|  98 LIDIVDIREEKIKKI 112
                                   333333333333333 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.2e-07
                                   EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHH CS
                        Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiaw 81 
                                   el+ivEg +d++++ ++   g+++v+a+ G   ++++                 +l  l k+ + +i  +D+D  G  i +
  gi|70605925|ref|YP_254795.1| 166 ELIIVEGRADVINLLRY---GYKNVIAVEGATGKIPQ-----------------TLVDLTKQKKAVIAFLDGDHGGDLILK 226
                                   69***************...9****************.................89999999999**************** PP

                                   HHHH CS
                        Toprim  82 elle 85 
                                   ell+
  gi|70605925|ref|YP_254795.1| 227 ELLS 230
                                   9993 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.34
                                   HHHHHTHTSTEEEEEEESS CS
                        Toprim  12 ktiakalgsgfqavtaslG 30 
                                   ++i++al  +++++ta+  
  gi|70605925|ref|YP_254795.1| 277 QAIKQALA-TETTTTAVTT 294
                                   33333333.2222332222 PP

>> DUF1822  Protein of unknown function (DUF1822)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.7e-06     0.006     252     336 ..     266     352 ..     125     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                       DUF1822 252 eilgardanhpeesiqraktidlglqlagqpvaLlvallpkpdervnvllqLepleeqevLPaglkLrlldesgqsfeeve 332
                                   +   +++++++++++q + t + + +++ ++   +v+++p++++++++ +  + +ee + LP+ l+  llde+ +++e+ +
  gi|70605925|ref|YP_254795.1| 266 AQYIKKQQEAQQAIKQALATETTTTAVTTTSTQIQVEVKPEEKKEIQITVPAQIIEEIKKLPGTLEGILLDENWNIIEKIQ 346
                                   344455666899999999999999999999*************************************************** PP

                       DUF1822 333 sra..e 336
                                    r+  +
  gi|70605925|ref|YP_254795.1| 347 VRDivQ 352
                                   999552 PP

>> DUF2344  Uncharacterized protein conserved in bacteria (DUF2344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.072   2.6e+02     119     155 ..     106     140 ..      72     154 .. 0.71
   2 ?    8.2   2.1   0.00058       2.1      90     149 ..     246     306 ..     222     327 .. 0.79
   3 ?   -3.7   0.0       2.6   9.5e+03      71      90 ..     344     363 ..     337     384 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.072
                       DUF2344 119 eealeeflaae.eilvekktkkgkkevdirplikelel 155
                                   ee++++++ +  eil      +++k++dir++i e++ 
  gi|70605925|ref|YP_254795.1| 106 EEKIKKIIGRAkEILGS---WSREKTLDIREVINEITS 140
                                   56666666443244444...456799*******99964 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00058
                       DUF2344  90 kileveeieek..akslmallaaaeYrve..eleealeeflaaeeilvekktkkgkkevdirpl 149
                                   ++ e+     k  aksl++ ++ a+Y  +  e+++a+++ la+e+ ++  +t + + +v+++p 
  gi|70605925|ref|YP_254795.1| 246 EVEEL---TGKeiAKSLSNMVTIAQYIKKqqEAQQAIKQALATETTTTAVTTTSTQIQVEVKPE 306
                                   44444...33334799**********9967899***********99999999999999999986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.6
                       DUF2344  71 evdpeevverLnaqlpegik 90 
                                   +++++++v++L++   + i+
  gi|70605925|ref|YP_254795.1| 344 KIQVRDIVQKLENISADSIR 363
                                   34444455555444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2157  (0.120308); expected 358.6 (0.02)
Passed bias filter:                     1081  (0.0602934); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2740.41
//
Query:       gi|70605926|ref|YP_254796.1|  [L=361]
Description: tyrosyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-48  163.8   0.5      3e-36  125.2   0.1    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.038   13.5   0.0      0.069   12.7   0.0    1.4  1  CNRIP1        CB1 cannabinoid receptor-interacting protein 1


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   3.4e-40     3e-36       3     200 ..      30     220 ..      28     222 .. 0.97
   2 !   36.9   0.0   2.7e-13   2.4e-09     199     292 ..     235     335 ..     230     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 3.4e-40
                                   HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                   +++l+ y G++P+g +H+G+l+  +kl +l kag+++ +l+a +hA+i+d+   +++k++ + +++ ++   +   g+d +
  gi|70605926|ref|YP_254796.1|  30 NSKLKGYIGFEPSGLFHIGWLIWAQKLKDLIKAGVDMSILVATWHAMINDKLGGDLEKIKLAGKYALEV---LEGFGVDMS 107
                                   678999**********************************************99***************...88999**** PP

                                   TEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHH CS
                  tRNA-synt_1b  84 kaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqni 164
                                   k++vv+  +  e+ +++ l+ +++k +sl+rm ++ +++ r +e+ ++ ++ ++Yp +q  Di++ + d+ +gG+DQ++  
  gi|70605926|ref|YP_254796.1| 108 KLKVVYAEDLVENIDYWSLVVKVAKNTSLARMKRALTIMGRRSEEAELDTSKLIYPAMQVSDIFFQDLDIALGGTDQRKAH 188
                                   ***************************************99999789********************************** PP

                                   HHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBT CS
                  tRNA-synt_1b 165 elgrdlarrfnkkevfkkpegltvplltgldGekKm 200
                                    l+rd+a+++++k    k+ ++ +pll+gl+G+++m
  gi|70605926|ref|YP_254796.1| 189 MLARDVAEKLQRK----KVIAIHTPLLVGLQGGQRM 220
                                   ************9....****************999 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.7e-13
                                   BTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC........SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHH CS
                  tRNA-synt_1b 199 KmSKSagnsaIfLddekesvkkkiqkavtdsde........evekllklktelsnelierleavsgkkpkreaeellaeev 271
                                   KmSKS++++aIf+ d++e v++k ++ ++  +          +++  ++  +++   ier  +++g  + +++eel+  ++
  gi|70605926|ref|YP_254796.1| 235 KMSKSKPETAIFIHDSPELVESKLKNSYCPKGVvndnpvlqINKYIIFGEQGVTL-KIERDTKYGGDIEIKSYEELERIFI 314
                                   *****************************99887744444444555566666666.999999*9999999*********** PP

                                   CCCCHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 272 tklvhggdlkkalaealnell 292
                                   ++++h+ dlk a+a++ln +l
  gi|70605926|ref|YP_254796.1| 315 EGKLHPLDLKLATARKLNDIL 335
                                   *****************9987 PP

>> CNRIP1  CB1 cannabinoid receptor-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-06     0.069      29      70 ..     282     324 ..     267     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-06
                        CNRIP1  29 Fg.qerTiKlltdskYkvevtikpaleleslsiggksleleek 70 
                                   Fg q  T+K++ d+kY  +++ik+  ele++ i+gk  +l+ k
  gi|70605926|ref|YP_254796.1| 282 FGeQGVTLKIERDTKYGGDIEIKSYEELERIFIEGKLHPLDLK 324
                                   665678******************************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2534.19
//
Query:       gi|70605927|ref|YP_254797.1|  [L=116]
Description: hypothetical protein Saci_0077 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   19.3   1.4     0.0015   19.0   1.4    1.2  1  Ribosomal_L6e  Ribosomal protein L6e
  ------ inclusion threshold ------
       0.01   15.3   1.5      0.012   15.1   1.5    1.1  1  Peptidase_C65  Peptidase C65 Otubain


Domain annotation for each model (and alignments):
>> Ribosomal_L6e  Ribosomal protein L6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.4   1.7e-07    0.0015      13      80 ..      31      93 ..      19     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-07
                 Ribosomal_L6e 13 yVIatstkvdlsgvdekipeklndeyFkkekkkkkkkkkeeelfeekkekkelseerkadqkavDkal 80
                                   +I tst++d+s++ +k+++++ +  F+ +  ++++  +e+e+f+  k +++l e+  ++  +vD  +
  gi|70605927|ref|YP_254797.1| 31 SIINTSTRIDVSEL-SKTNNQV-KFAFTDD--DEEE-MDEKEFFNFYKFTEALVEKIIQNEIDVDLIV 93
                                  58************.5555533.3445555..4443.679*****99999999999999998888655 PP

>> Peptidase_C65  Peptidase C65 Otubain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.5   1.3e-06     0.012      59     145 ..      27     113 ..      19     116 .] 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHH-HH..HHHHHHHHHHHHHHHHH...HTT--HHHHHHHHHHHHHHHHHHHTTSS-HH....HHHHHHTSH.HHH CS
                 Peptidase_C65  59 sylellleskdkaevsrikerveklkeale...slgfdeevvedfleaflellkkiekkteeseekaeellkafneq.ees 135
                                    yl+++++++ +  vs++ ++ +++k a +   + ++de+++++f++ +++l++ki +++ +     + +++ ++e+  +s
  gi|70605927|ref|YP_254797.1|  27 EYLKSIINTSTRIDVSELSKTNNQVKFAFTdddEEEMDEKEFFNFYKFTEALVEKIIQNEIDV----DLIVYDLEEKlGKS 103
                                   6999*****9999777777777777777777779**********************9555444....46777777663788 PP

                                   HHHHHHHHHH CS
                 Peptidase_C65 136 dyivvflRll 145
                                   + iv+fl+ +
  gi|70605927|ref|YP_254797.1| 104 HPIVIFLKQI 113
                                   8899999966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 764.52
//
Query:       gi|70605928|ref|YP_254798.1|  [L=134]
Description: hypothetical protein Saci_0078 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-37  126.7   0.0    5.4e-37  126.5   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0     3e-41   5.4e-37       1     114 [.      20     130 ..      20     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 3e-41
                                   E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHHH-SE CS
                       UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssllgss 80 
                                   dite+++e    +g+k+G+v vf++htt++l++nE+ ++++++D+ e+ +klvp++ +++hn + ++n++aH+ ss++g+s
  gi|70605928|ref|YP_254798.1|  20 DITEHIREN--IKGIKDGVVYVFVKHTTCALIVNEA-ESGLMKDYLEWGKKLVPPDgTFEHN-NIDNNGHAHIISSIIGNS 96 
                                   79******9..88**********************9.*************************.5667************** PP

                                   EEEEEETTEE---TTEEEEEEESS-SSEEEEEEE CS
                       UPF0047  81 ltipvedgklalGtwqsiylveldgpreRkvvvq 114
                                    ++p+++g+l+lGtwq+++l+e+dgpr+R+++v+
  gi|70605928|ref|YP_254798.1|  97 RVLPITNGELDLGTWQRVILLEFDGPRTRSILVK 130
                                   *******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 951.14
//
Query:       gi|70605929|ref|YP_254799.1|  [L=424]
Description: hypothetical protein Saci_0079 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-07   31.3   0.0    4.6e-07   30.1   0.0    1.7  1  AIRS_C    AIR synthase related protein, C-terminal domain
      1e-06   29.3   0.1    3.6e-06   27.5   0.1    2.0  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
        2.4    8.8   4.4         21    5.8   0.0    3.5  4  ATP-cone  ATP cone domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   7.7e-11   4.6e-07       6     151 ..     224     362 ..     219     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.7e-11
                                   EEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEE CS
                        AIRS_C   6 liltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvg 86 
                                   +++t+++G g ++t ++  +  +         + + +  + li  k    ++ +lv +++DvT+GG+  +++e+ p++ ++
  gi|70605929|ref|YP_254799.1| 224 IVMTEGSGGGTIATTAIYNGYYDV--------VRETISIKDLITCKIVSEEMYDLVDSMTDVTNGGIRATANEL-PEN-LS 294
                                   778888888888888888555554........6678999999999988888899********************.665.** PP

                                   EEEECG......THHHHHHHH.HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                        AIRS_C  87 aeidld......kvpifdele.splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                   + i+ +      + ++++ l+ ++++++        l++ +  ++  v+++l++ g+ +a++IG+v+ ++++
  gi|70605929|ref|YP_254799.1| 295 LAINTEsflrliNRKVLNMLNeLQIDVFGLSIDS-ILIFTDIGNE--VVSKLKSKGI-NAEIIGKVVQRQDS 362
                                   ******8777775555555545677777777777.5588888888..**********.8********99875 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1     6e-10   3.6e-06       6      92 ..     108     206 ..      98     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6e-10
                                   EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                          AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsf 80 
                                   ++++d+  + +   p+   G  a  + l+D+++ G+rP+++l  + l+       l ++ +g+ + ae l+vp+++G t +
  gi|70605929|ref|YP_254799.1| 108 LASIDGIHSRLSYFPFLA-GFHATRASLRDVMVKGGRPIGILIDIHLSddsdvgMLLDFEAGVLSVAESLNVPILSGSTLR 187
                                   556665555555555555.**********************************************************9986 PP

                                   ESS.......EEEEEEEEE CS
                          AIRS  81 sne.......ptisvtavG 92 
                                     +       ++  v+a+G
  gi|70605929|ref|YP_254799.1| 188 IGGdlvigerISGGVGAIG 206
                                   5444444445666666666 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.054   3.2e+02      17      50 ..      20      53 ..       7      62 .. 0.58
   2 ?   -0.5   0.0      0.32   1.9e+03      62      82 ..     236     256 ..     234     259 .. 0.82
   3 ?   -1.6   0.1      0.69   4.1e+03      39      62 ..     338     358 ..     325     360 .. 0.70
   4 ?    5.8   0.0    0.0034        21       8      40 ..     389     421 ..     384     424 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.054
                                  HHHHHHHHHHHH-HHH..HHHHHHHHHHHHHHHHII CS
                      ATP-cone 17 kIkraiekAcegseee..ideiaeeveaevrkrlrd 50
                                  kI++ i++   +   +  i+e+++ v++e+r++l++
  gi|70605929|ref|YP_254799.1| 20 KIEEEISFYKDNR--YpfIKELVDAVVEEARRSLEA 53
                                  4444444442222..233666666666666665544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.32
                                   HHHHHHSS-HHHHHHHHHHHH CS
                      ATP-cone  62 ektliehpdyavaaayilyrn 82 
                                   + t+i +++y+v++  i  ++
  gi|70605929|ref|YP_254799.1| 236 ATTAIYNGYYDVVRETISIKD 256
                                   6789999*******9988765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.69
                                   HHHHHHHHHHIIT-BHHHHHHHHH CS
                      ATP-cone  39 eveaevrkrlrdgisteeIqdlve 62 
                                   ev   v k + +gi+ e I+++v 
  gi|70605929|ref|YP_254799.1| 338 EV---VSKLKSKGINAEIIGKVVQ 358
                                   33...4555777899999988885 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0034
                                   S-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHH CS
                      ATP-cone   8 GtvepfdvekIkraiekAcegseeeideiaeev 40 
                                   G + p++++ I++a+e ++e++ ++++++ +++
  gi|70605929|ref|YP_254799.1| 389 GNYSPLSIGDIRKALETSFEQVKDKMEKVLKTL 421
                                   8899*****************999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2936.15
//
Query:       gi|70605930|ref|YP_254800.1|  [L=170]
Description: 30S ribosomal protein S13 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-52  175.2   0.6      8e-52  175.0   0.6    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0099   15.8   0.1      0.015   15.2   0.1    1.4  1  HHH_4          Helix-hairpin-helix containing domain
  ------ inclusion threshold ------
      0.087   11.6   0.0        0.1   11.4   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.6   1.3e-55     8e-52       1     128 []      11     139 ..      11     139 .. 1.00

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 1.3e-55
                 Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGk 80 
                                   R++g+d+dg++k+ +al++ikGiG+++a+ii++k+++d+dkr+ge+++e+i+kie++++nk+  ++pnwi nrqkd+++G+
  gi|70605930|ref|YP_254800.1|  11 RLFGQDVDGTMKLPYALAMIKGIGYNTAMIIIRKLNLDKDKRLGEISDEDIKKIENLLNNKIIPESPNWIyNRQKDYESGA 91 
                                   89******************************************************************************* PP

                 Ribosomal_S13  81 dshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                   d+h+v++dl +++r+dieR+++ rs+rG+RH+ GlkvRGQrT+ttgRt
  gi|70605930|ref|YP_254800.1|  92 DMHLVTSDLIFYVRNDIERERRSRSWRGVRHSLGLKVRGQRTRTTGRT 139
                                   ***********************************************8 PP

>> HHH_4  Helix-hairpin-helix containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.5e-06     0.015      18      69 ..       2      51 ..       1      71 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                         HHH_4 18 saklaekiykkygeealeilkenPYrliedvegigFktaDkiakklgieeds 69
                                  s+++ + i++ +g++ ++   + PY l+  ++gig++ta  i +kl++++d+
  gi|70605930|ref|YP_254800.1|  2 SQQQFKYIVRLFGQD-VDGTMKLPYALAM-IKGIGYNTAMIIIRKLNLDKDK 51
                                  677888899999998.8888889**9986.****************877764 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.7e-05       0.1     192     255 ..      26      83 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                                   HHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX....XXEE.... CS
                          FbpA 192 aLvkafqGlspllaeelleragldketsakelseedlerlyealqelleeleeekfepqlvlke 255
                                   aL+   +G++  +a  ++++++ldk++++ e+s+ed++++ + l++ + + +     p+++++ 
  gi|70605930|ref|YP_254800.1|  26 ALAMI-KGIGYNTAMIIIRKLNLDKDKRLGEISDEDIKKIENLLNNKIIPES-----PNWIYNR 83 
                                   55554.7**********************************99998776544.....5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1129.39
//
Query:       gi|70605931|ref|YP_254801.1|  [L=176]
Description: 30S ribosomal protein S4 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-15   56.1   0.1    4.9e-15   55.0   0.1    1.6  1  S4            S4 domain
    8.7e-05   23.4   1.7    0.00072   20.4   1.1    2.5  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.1   5.4e-19   4.9e-15       1      47 [.     104     150 ..     104     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 5.4e-19
                                   EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                            S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                   rRL+++++++gla ++ +ArqlI hG++ + G++v++p+y V  g++
  gi|70605931|ref|YP_254801.1| 104 RRLQTIVYKKGLARTIYQARQLITHGHIAISGRKVTSPGYVVLRGEE 150
                                   8*****************************************99986 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.1     8e-08   0.00072      36      81 ..      15      61 ..       3     107 .. 0.86
   2 ?   -0.9   0.0      0.36   3.2e+03      10      22 ..     103     123 ..      97     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8e-08
                                  --CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHHH CS
                  Ribosomal_S4 36 lseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlql 81
                                    ++ k +l ++q l+++Ygl+ +k+++ ++++ r++r ++++ Ll+l
  gi|70605931|ref|YP_254801.1| 15 SHPWIKiNLGKEQILIGKYGLRnKKEIWIAQTMIRNFR-HQARSLLAL 61
                                  4689999*******************************.******984 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                                   HCHCTS-STSSS........S CS
                  Ribosomal_S4  10 lRrvgfklflkg........r 22 
                                    Rr+++ +++kg        r
  gi|70605931|ref|YP_254801.1| 103 ERRLQTIVYKKGlartiyqaR 123
                                   577777777777765555442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1228.78
//
Query:       gi|70605932|ref|YP_254802.1|  [L=132]
Description: 30S ribosomal protein S11 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-49  166.3   2.4    2.7e-49  166.1   2.4    1.0  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1   2.4   1.5e-53   2.7e-49       1     110 []      10     128 ..      10     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 1.5e-53
                 Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                   G+a+i+as+nntiititd++Gae+++k++Gg++vka+r k+sPyaa+laa+kaa++++dkGi+a+++kv++        pG
  gi|70605932|ref|YP_254802.1|  10 GNARIYASQNNTIITITDITGAEIISKASGGMVVKADReKPSPYAAMLAANKAANDAFDKGISAIHIKVRAqggygsktPG 90 
                                   89******************************************************************************* PP

                 Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                   pG+++a+ralaraG++igriedvtP+Phd+irrp++rr
  gi|70605932|ref|YP_254802.1|  91 PGAQPAIRALARAGFIIGRIEDVTPLPHDTIRRPGGRR 128
                                   ************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 843.19
//
Query:       gi|70605933|ref|YP_254803.1|  [L=264]
Description: DNA-directed RNA polymerase subunit D [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-28   97.6   0.0    9.6e-28   96.8   0.0    1.4  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.5e-12   46.7   0.0    2.1e-12   46.3   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    0.00063   19.9   9.3     0.0017   18.5   3.9    2.3  2  Fer4_9         4Fe-4S dicluster domain
  ------ inclusion threshold ------
        0.3   11.2  12.3       0.16   12.1   1.4    3.0  3  Fer4_10        4Fe-4S dicluster domain
       0.32   12.0   7.8         13    6.8   0.0    3.2  3  Fer4_16        4Fe-4S double cluster binding domain
       0.84    9.8   8.5          1    9.5   4.1    2.6  2  Fer4_18        4Fe-4S dicluster domain
        0.9   10.2  12.0         12    6.5   1.8    2.8  3  Fer4_7         4Fe-4S dicluster domain
        5.8    7.2  18.1       0.37   10.9   1.2    3.5  3  Fer4_6         4Fe-4S binding domain
        8.3    6.6  12.2        2.6    8.2   2.1    3.0  3  Fer4_21        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   4.8e-31   9.6e-28       1     112 []      44     157 ..      44     157 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 4.8e-31
                                   EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBESSSSCEE CS
                 RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkledadvei 78 
                                   V+++en+s l+DE++aHrl+l+p+vs+++le +   +e+  e++e+++ +   ++L+v+ +++   ++++dlk+ed+ +++
  gi|70605933|ref|YP_254803.1|  44 VYFIENNSPLYDEILAHRLALVPFVSDEALEHYRPPEEC-AECKENCDGCYNRVYLDVEAKDQplmIYSRDLKSEDQMITP 123
                                   8999***************************88888888.56*************************************** PP

                                   SSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                 RNA_pol_A_bac  79 vnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                   v+  i+I+ L ++q+++lea+ + G+Gkeh k+s
  gi|70605933|ref|YP_254803.1| 124 VSGAIPIVLLGSKQKISLEARLRLGYGKEHIKYS 157
                                   ********************************97 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0     1e-15   2.1e-12       3      69 .]      16     253 ..      14     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1e-15
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
                     RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea..................................................... 30 
                                   +l+++ + + N++Rr  +  vp +a+++                                                     
  gi|70605933|ref|YP_254803.1|  16 VLENYPLEFVNSIRRASILYVPVMAVDEvyfiennsplydeilahrlalvpfvsdealehyrppeecaeckencdgcynrv 96 
                                   688999********************************************************9999999999999999999 PP

                                   .............................................................xx.................. RF
                     RNA_pol_L  31 .............................................................pv.................. 32 
                                                                                                pv                  
  gi|70605933|ref|YP_254803.1|  97 yldveakdqplmiysrdlksedqmitpvsgaipivllgskqkislearlrlgygkehikysPVsvsivryypkvtvlgnce 177
                                   999999999999999999999999997777777777776666666666666666666666622666666666667777777 PP

                                   .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  33 .......................................vkvntdkdklilevetdgslkPeealkeAlkiLkekl 69 
                                                                          v+++++++k+ile+e++gslkPe +l eA k L +kl
  gi|70605933|ref|YP_254803.1| 178 kavevcpegvfamennklvvknelscilceeclkycagsVSIESVENKFILEIESVGSLKPERILIEASKSLLRKL 253
                                   7777777777888888888888888888888888888778888****************************98886 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.024        48       5      13 ..      82      90 ..      64     109 .. 0.72
   2 !   18.5   3.9   8.4e-07    0.0017       4      47 ..     175     214 ..     174     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.024
                        Fer4_9  5 CgaCveaCp 13
                                  C +C e C 
  gi|70605933|ref|YP_254803.1| 82 CAECKENCD 90
                                  444444443 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 8.4e-07
                        Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                   +C + ve+Cp gv+ +++++  ++++     +Ci C++C++ C 
  gi|70605933|ref|YP_254803.1| 175 NCEKAVEVCPEGVFAMENNKLVVKNEL----SCILCEECLKYCA 214
                                   58888999****************987....6***********6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.051     1e+02      11      19 ..      81      89 ..      74     118 .. 0.75
   2 ?    7.8   7.6    0.0018       3.6      11      55 ..     175     213 ..     174     214 .. 0.73
   3 ?   12.1   1.4   7.8e-05      0.16       2      21 ..     196     214 ..     195     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.051
                       Fer4_10 11 rCgkCvkaC 19
                                  +C++C++ C
  gi|70605933|ref|YP_254803.1| 81 ECAECKENC 89
                                  355555544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                       Fer4_10  11 rCgkCvkaCPadltsvgakgeaseeeavrk.kvekCtgcgaCveaC 55 
                                   +C+k v++CP          +a+e+++  + +  +C+ c++C + C
  gi|70605933|ref|YP_254803.1| 175 NCEKAVEVCPE-------GVFAMENNKLVVkNELSCILCEECLKYC 213
                                   68888889999.......5555555555443888999999999988 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.8e-05
                       Fer4_10   2 vvidddtCirCgkCvkaCPa 21 
                                   vv+++ +Ci C++C k C a
  gi|70605933|ref|YP_254803.1| 196 VVKNELSCILCEECLKYC-A 214
                                   6889999***********.4 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9      0.36   7.2e+02      55      64 ..      80      89 ..      66      92 .. 0.73
   2 ?    6.8   0.0    0.0064        13       3      24 ..     174     195 ..     174     201 .. 0.79
   3 ?    6.6   0.2    0.0074        15       2      16 ..     203     217 ..     202     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.36
                       Fer4_16 55 tgCdiCqdvC 64
                                    C+ C++ C
  gi|70605933|ref|YP_254803.1| 80 EECAECKENC 89
                                  5677777777 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0064
                       Fer4_16   3 gtCgkCaevCPtnaikekkeke 24 
                                   g+C+k +evCP++++ ++++k 
  gi|70605933|ref|YP_254803.1| 174 GNCEKAVEVCPEGVFAMENNKL 195
                                   58************99986554 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0074
                       Fer4_16   2 CgtCgkCaevCPtna 16 
                                   C+ C++C++ C  ++
  gi|70605933|ref|YP_254803.1| 203 CILCEECLKYCAGSV 217
                                   9**********8765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       0.2   3.9e+02      84      96 ..      81      93 ..      68     113 .. 0.63
   2 ?    9.5   4.1   0.00052         1      63      96 ..     175     214 ..     168     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.2
                       Fer4_18 84 eciscllcidacd 96
                                  ec +c +  d c 
  gi|70605933|ref|YP_254803.1| 81 ECAECKENCDGCY 93
                                  4555555555553 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00052
                       Fer4_18  63 dcescvkvcPtgidirkGl......qleciscllcidacd 96 
                                   +ce+ v+vcP g+   +         l+ci c +c+  c 
  gi|70605933|ref|YP_254803.1| 175 NCEKAVEVCPEGVFAMENNklvvknELSCILCEECLKYCA 214
                                   69999*****999665443112222578999999999996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.6     0.016        31       4      52 .]      81     187 ..      80     187 .. 0.57
   2 ?    6.1   7.4    0.0085        17       4      48 ..     175     213 ..     174     217 .. 0.81
   3 ?    6.5   1.8    0.0062        12       1      13 [.     202     214 ..     202     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                        Fer4_7   4 gCgaCvaaCp..vkaieldeeenek............................................gtekveidpekC 38 
                                   +C  C ++C   ++ ++ld e++++                                            g+e+++++p + 
  gi|70605933|ref|YP_254803.1|  81 ECAECKENCDgcYNRVYLDVEAKDQplmiysrdlksedqmitpvsgaipivllgskqkislearlrlgyGKEHIKYSPVSV 161
                                   699999999666777776644333345555555555555555666555555555555555555555555445555554444 PP

                        Fer4_7  39 l............gCgaCvavCPtga 52 
                                   +            +C++ v+vCP g+
  gi|70605933|ref|YP_254803.1| 162 SivryypkvtvlgNCEKAVEVCPEGV 187
                                   33444444444557999999999885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0085
                        Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                   +C++ v++Cp +++ +++       + v+ ++ +C+ C++C + C
  gi|70605933|ref|YP_254803.1| 175 NCEKAVEVCPEGVFAMENN------KLVVKNELSCILCEECLKYC 213
                                   57777899******99654......447778899********999 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0062
                        Fer4_7   1 rCigCgaCvaaCp 13 
                                   +Ci C+ C ++C 
  gi|70605933|ref|YP_254803.1| 202 SCILCEECLKYCA 214
                                   5999999999996 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   4.2      0.59   1.2e+03       7      13 ..      87      93 ..      81      94 .. 0.82
   2 ?    4.7   0.3     0.017        34      13      23 ..     174     187 ..     174     188 .. 0.68
   3 ?   10.9   1.2   0.00019      0.37       4      19 ..     198     213 ..     195     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.59
                        Fer4_6  7 dkCigCg 13
                                  ++C+gC+
  gi|70605933|ref|YP_254803.1| 87 ENCDGCY 93
                                  7899997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                        Fer4_6  13 gdC...vrvCPega 23 
                                   g+C   v vCPeg+
  gi|70605933|ref|YP_254803.1| 174 GNCekaVEVCPEGV 187
                                   567444677***98 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00019
                        Fer4_6   4 idpdkCigCgdCvrvC 19 
                                    ++ +Ci C++C + C
  gi|70605933|ref|YP_254803.1| 198 KNELSCILCEECLKYC 213
                                   56779*********99 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.16   3.2e+02      11      22 ..      82      92 ..      71     108 .. 0.69
   2 ?    1.9   0.2      0.13   2.5e+02      44      56 ..     176     187 ..     171     190 .. 0.75
   3 ?    8.2   2.1    0.0013       2.6       5      22 ..     200     216 ..     195     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                       Fer4_21 11 CgkCliaCedts 22
                                  C +C   C+ ++
  gi|70605933|ref|YP_254803.1| 82 CAECKENCD-GC 92
                                  555555554.33 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                       Fer4_21  44 CnlCssvCPvedc 56 
                                   C+  ++vCP e++
  gi|70605933|ref|YP_254803.1| 176 CEKAVEVCP-EGV 187
                                   888899999.455 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0013
                       Fer4_21   5 edkCigCgkCliaCedts 22 
                                   e +Ci C++Cl+ C   s
  gi|70605933|ref|YP_254803.1| 200 ELSCILCEECLKYCAG-S 216
                                   558***********83.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1865.74
//
Query:       gi|70605934|ref|YP_254804.1|  [L=110]
Description: 50S ribosomal protein L18e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-07   31.0   0.1    4.5e-07   30.6   0.1    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
    9.1e-07   28.5   0.1      1e-06   28.3   0.1    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   5.1e-11   4.5e-07      70     127 ..      29      88 ..       2      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.1e-11
                                   ----EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  70 deaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                    +++ i++ ++ +   ++      v  Kvlg g+l ++++v a +fSk AkekI + GGkv+
  gi|70605934|ref|YP_254804.1|  29 RKRAYINIYKINRYSKANDiiV--VpgKVLGVGNLDHPVTVVALSFSKPAKEKILRSGGKVM 88 
                                   4556677777733333333433..345*********************************96 PP

>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.1e-10     1e-06      44     124 ..      18      92 ..       1     109 [. 0.80

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.1e-10
                 Ribosomal_L18  44 kvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaGGeiltlDq 124
                                     v   L   r++r+ + + ++ ++ k     + i+vv g+v+    l   P ++v+AL f++ a+++il++GG++++l +
  gi|70605934|ref|YP_254804.1|  18 VRVAEELEAPRRKRAYINIYKINRYSKA----NDIIVVPGKVLGVGNLD-HP-VTVVALSFSKPAKEKILRSGGKVMSLYK 92 
                                   457888999*************999885....69*********877665.45.89**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 854.90
//
Query:       gi|70605935|ref|YP_254805.1|  [L=148]
Description: 50S ribosomal protein L13 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-12   47.4   0.8    1.5e-10   41.4   0.8    2.3  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.8   8.4e-15   1.5e-10       3     114 ..       8     108 ..       6     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 8.4e-15
                                   EEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH..C CS
                 Ribosomal_L13   3 yviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell..e 81 
                                   +++DA++q+lgr++++iak+L+             G  v v+naek  ++g + +    y+    + +  + ++++ +   
  gi|70605935|ref|YP_254805.1|   8 VIVDATNQILGRMSTHIAKLLKS------------GKKVYVVNAEKAIISGPRSRVLEGYSLLFTV-KTMQNPYRQGIrrP 75 
                                   689******************75............6668899*****9999987766665555444.44455666644125 PP

                                   CSHHHHHHHHHHCCS-SSHHHHHHGCTEEEESS CS
                 Ribosomal_L13  82 kkpeeilekaVkgmLpknklgrrrlkrLkvyag 114
                                   ++p +i++++V+gmLpknklg++ +++Lk y g
  gi|70605935|ref|YP_254805.1|  76 RNPINIVKRTVRGMLPKNKLGKQIYRNLKAYIG 108
                                   799***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1056.25
//
Query:       gi|70605936|ref|YP_254806.1|  [L=138]
Description: 30S ribosomal protein S9 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-26   92.2   0.1    3.7e-26   92.0   0.1    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.1   2.1e-30   3.7e-26       2     121 .]      14     138 .]      13     138 .] 0.91

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 2.1e-30
                                   ECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHHHHHHH CS
                  Ribosomal_S9   2 rrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgiaraLva 80 
                                   rrK+++A ++ik+g+gk+ vn+ ++e  ++ e  r k++epl l+g +   +++ ++ ++gGG++gqa+A+r+++araLv+
  gi|70605936|ref|YP_254806.1|  14 RRKSARASCYIKPGNGKVFVNDIPIEI-IPIEVVRYKIMEPLVLAGDKItsSIEARIYTQGGGIMGQADAARMALARALVK 93 
                                   9**************************.****************987543368888999********************** PP

                                   HHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                  Ribosomal_S9  81 lekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                   +++   keL       ++++l  DpR++E  K  +  AR+  q+ +R
  gi|70605936|ref|YP_254806.1|  94 FTN--SKELVeiyksyDRTMLAGDPRQTESEKWMRYSARRWRQKAYR 138
                                   *88..455554778889***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 940.73
//
Query:       gi|70605937|ref|YP_254807.1|  [L=66]
Description: DNA-directed RNA polymerase subunit N [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-29  101.6   0.4    2.4e-29  101.4   0.4    1.0  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.4   1.3e-33   2.4e-29       1      58 [.       1      58 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.3e-33
                                  ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                     RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliek 58
                                  MiiP+rCFtCG v+++kwe + +++  ge+p+++L++Lg++ryCCrrmll+hv++i +
  gi|70605937|ref|YP_254807.1|  1 MIIPIRCFTCGAVVADKWEPFSNRVMGGEDPEKVLTELGVNRYCCRRMLLSHVNIIRE 58
                                  9******************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 445.54
//
Query:       gi|70605938|ref|YP_254808.1|  [L=225]
Description: 30S ribosomal protein S2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-27   94.6   0.0    1.9e-15   56.7   0.1    2.1  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   2.1e-13   3.7e-09       2      95 ..      37     127 ..      36     134 .. 0.94
   2 !   56.7   0.1   1.1e-19   1.9e-15     148     213 ..     135     200 ..     129     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 2.1e-13
                  Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrang 81 
                                   L+agvh+G +    +  m+++Iy +r +g +++d++k+ + lr a+k+++++  + + +l v+++  a   v++ ++ ++g
  gi|70605938|ref|YP_254808.1|  37 LSAGVHIGTH--TCTRYMERFIYRVRpEGLYVLDVRKIDERLRVAAKFISRF--RPEAVLTVASRPYAFTPVQKFSEVVRG 113
                                   79******55..5699********99779*********************87..6789*********************** PP

                  Ribosomal_S2  82 yyvnerWlgGtLTN 95 
                                     ++ r+ +GtLTN
  gi|70605938|ref|YP_254808.1| 114 KEISGRFPPGTLTN 127
                                   ************** PP

  == domain 2  score: 56.7 bits;  conditional E-value: 1.1e-19
                  Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                    P++++v+dp+ +  a+kEa+k+gip++a++Dt++  d +d +IpaN++  +s+ l++ vla++i 
  gi|70605938|ref|YP_254808.1| 135 EPEVLIVTDPRTDLQAIKEASKVGIPIVAFTDTDARVDFIDVIIPANNKGRKSLALLYWVLARQIL 200
                                   69************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1378.32
//
Query:       gi|70605939|ref|YP_254809.1|  [L=284]
Description: hypothetical protein Saci_0089 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-87  292.0   0.0    4.1e-87  291.8   0.0    1.0  1  Memo      Memo-like protein
  ------ inclusion threshold ------
       0.11   11.6   0.0       0.28   10.2   0.0    1.6  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.8   0.0   4.6e-91   4.1e-87       2     270 ..       5     280 ..       4     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 291.8 bits;  conditional E-value: 4.6e-91
                          Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei............arviisPHagyvysgevaakayaeles.skvervvil 69 
                                   +avAGsfY++d+  l+kq+e+++++ +g+k+             +r+ ++PHagy+ysg+vaa+ay++l+   ++++v+il
  gi|70605939|ref|YP_254809.1|   5 PAVAGSFYEADPVRLRKQIEWSFLHDLGPKSLpsvpqnkppqrsNRFFVVPHAGYMYSGPVAAHAYYHLSLeGSPDTVIIL 85 
                                   89****************************99999999999999999999*********************999******* PP

                          Memo  70 GpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsa 150
                                   Gp+Ht+lgs+vs++++++++TPlG++ vD e+  eLvk +ei+d+de+a+l+EHS+Evq+pfL++l+ ++ fkivPi++++
  gi|70605939|ref|YP_254809.1|  86 GPNHTGLGSYVSIWHKGKWKTPLGEVSVDDEISLELVKLTEIIDIDERAHLYEHSIEVQIPFLQYLFGQN-FKIVPIVIMM 165
                                   *********************************************************************6.********** PP

                          Memo 151 qseetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGek 229
                                   q++++a+ ++e ++k +   +  ++v++SsDl+Hy+     p++ + ++ D+ +i+++++l++++l  ++e+++ t cG++
  gi|70605939|ref|YP_254809.1| 166 QTPDVAESLAEGIYKLVSSGKkdIVVLASSDLNHYE-----PHDKTIEK-DNLAIDEIQKLDYKGLFRVVEEKDVTACGYG 240
                                   ***************999777679************.....99999999.******************************* PP

                          Memo 230 piavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                   pi+ +l ++kklg kk ++l++a+s+d+++d++svV+y+s+
  gi|70605939|ref|YP_254809.1| 241 PIMTVLILAKKLG-KKPYVLRHATSGDTSGDKSSVVGYLSV 280
                                   *************.************************986 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.2e-05      0.28      42     194 ..      78     211 ..      67     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.2e-05
                          LigB  42 sPdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmklDHGtlv 122
                                   sPdt+i+  p h+   ++v         + ++  +     + +e+ ++ e+  +++++++  +id  +  ++  ++  + +
  gi|70605939|ref|YP_254809.1|  78 SPDTVIILGPNHTGLGSYV---------SIWHKGK--WKTPLGEVSVDDEISLELVKLTEIIDIDERAHLYEHSIE--VQI 145
                                   6777777777776655544.........3444422..445677777888888888888887778776666666666..667 PP

                          LigB 123 P.LelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakada 194
                                   P L+++++   + + ++++++       ++     L e + k+v++  k +++l+s +l H+ + d++ ++d 
  gi|70605939|ref|YP_254809.1| 146 PfLQYLFG--QNFKIVPIVIMM-----QTPDVAESLAEGIYKLVSSGKKDIVVLASSDLNHYEPHDKTIEKDN 211
                                   85799999..599999999999.....455555567799*****999**************988888775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1985.56
//
Query:       gi|70605940|ref|YP_254810.1|  [L=228]
Description: hypothetical protein Saci_0090 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   12.1   0.0      0.092   11.8   0.0    1.1  1  COG4      COG4 transport protein


Domain annotation for each model (and alignments):
>> COG4  COG4 transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-06     0.092     249     307 ..      67     119 ..      38     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-06
                          COG4 249 ellssYvpLetfylrrsvekAi...qldelpslkassplissvvDDvfyilkkvlrralstg 307
                                    l s+Y+ L+++++r+++ek     +  e      +   +  ++DDv y  ++ l ral t+
  gi|70605940|ref|YP_254810.1|  67 PLSSTYIYLSELFFRKAIEKCElplT--EE-----EMWDTLKMIDDVLY--NSPLIRALRTS 119
                                   5789****************975422..22.....34569*********..99999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1562.74
//
Query:       gi|70605941|ref|YP_254811.1|  [L=303]
Description: isopentenyl pyrophosphate isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-13   48.0   0.0    1.2e-12   47.6   0.0    1.2  1  FMN_dh    FMN-dependent dehydrogenase
     0.0018   17.3   0.2       0.79    8.7   0.1    2.3  2  IMPDH     IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   1.3e-16   1.2e-12     205     343 ..     110     272 ..      45     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.3e-16
                                   HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.......................TSSTT---HHH CS
                        FMN_dh 205 wddikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG.......................Rqldgapatid 259
                                    d+i+ + +++++p+++K+    l++e + + +  G     vS  GG                          d  ++t  
  gi|70605941|ref|YP_254811.1| 110 LDKIRDVSKALSVPIIIKESsggLSKEFVSLFYSNGFRYFDVSGQGGtswvavemfrglrrnnwkaesakLFSDWGIPTAA 190
                                   457888888999******76666*********************************9997666666655434455555555 PP

                                   CHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHH CS
                        FMN_dh 260 vLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvae 340
                                   ++ e +  ++ ++ v+ +gG+r+G  v+k + lGA++ +++ p+l + a+ G+e +++ l+ +  e++++m l+G k+v++
  gi|70605941|ref|YP_254811.1| 191 TIIETRVSAP-DAFVIGSGGVRNGLEVVKSISLGANIGGFALPALKA-AIRGKEALKQFLQQVIFEIKAAMFLIGSKTVRD 269
                                   5555555554.899******************************988.99******************************9 PP

                                   HHC CS
                        FMN_dh 341 ldr 343
                                   + +
  gi|70605941|ref|YP_254811.1| 270 VYK 272
                                   866 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1   8.8e-05      0.79     188     231 ..     184     225 ..     178     228 .. 0.80
   2 !    6.3   0.0   0.00045         4     291     327 ..     236     272 ..     232     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 8.8e-05
                                   B---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 188 vGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGad 231
                                    G+p +  ++e+   ++  +  vi  GG+++  ++vk++++Ga+
  gi|70605941|ref|YP_254811.1| 184 WGIPTAATIIET--RVSAPDAFVIGSGGVRNGLEVVKSISLGAN 225
                                   577777666665..45566789*********************8 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00045
                                   EEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 291 grvpykgsvkevveqlvgglrsgmgylGaktieelke 327
                                   +++  k  +k++++q++ +++++m  +G+kt++++ +
  gi|70605941|ref|YP_254811.1| 236 AAIRGKEALKQFLQQVIFEIKAAMFLIGSKTVRDVYK 272
                                   566778899***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2031.18
//
Query:       gi|70605942|ref|YP_254812.1|  [L=330]
Description: geranylgeranyl pyrophosphate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-72  243.2   0.1    2.8e-72  242.9   0.1    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.9   0.1   1.6e-76   2.8e-72       3     249 ..      29     274 ..      27     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 1.6e-76
                                   HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHH CS
               polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklA 83 
                                    l+ea+ +l+++gGKrlRpl++  ++ +++ ++   e+a+ +++++e+lh+++LvhDDimD++++RRG p++h ++G +lA
  gi|70605942|ref|YP_254812.1|  29 KLYEASYHLFTSGGKRLRPLILTISSDLFGGQR---ERAYYAGAAIEVLHTFTLVHDDIMDQDNIRRGLPTVHVKYGLPLA 106
                                   68899999999*******************555...89******************************************* PP

                                   HHHHHHHHHHHHHHHHHHH....STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHH CS
               polyprenyl_synt  84 indgdfllarafellaklf....eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpv 159
                                   i++gd+l a+af+ll++      +++ ++++++f++ ++ + eGq++d+e e++ d++   ++eyl+++ +KTa+lf+++ 
  gi|70605942|ref|YP_254812.1| 107 ILAGDLLHAKAFQLLTQALrglpSETiIKAFDIFTRSIIIISEGQAVDMEFEDRIDIK---EQEYLDMISRKTAALFSASS 184
                                   ****************99999985557**********************999899999...******************** PP

                                   HHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTT CS
               polyprenyl_synt 160 alaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilg 240
                                    ++al+aga+d++++ ++d+g +lG+aFQi+DD+l l++d+++lgKp+ +Di+egk t++++k+lel++++++k++ ++lg
  gi|70605942|ref|YP_254812.1| 185 SIGALIAGANDNDVRLMSDFGTNLGIAFQIVDDILGLTADEKELGKPVFSDIREGKKTILVIKTLELCKEDEKKIVLKALG 265
                                   ********************************************************************************* PP

                                   SSHHHHHHH CS
               polyprenyl_synt 241 kkaekeedv 249
                                   +k++++e++
  gi|70605942|ref|YP_254812.1| 266 NKSASKEEL 274
                                   887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2229.00
//
Query:       gi|70605943|ref|YP_254813.1|  [L=328]
Description: UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-31  109.6  22.1    1.4e-31  109.6  22.1    2.4  3  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
        3.3    7.4   9.5         15    5.2   0.3    2.7  2  CbtA             Probable cobalt transporter subunit (CbtA)


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.32   2.9e+03      17      17 ..      17      17 ..       2      76 .. 0.63
   2 !  109.6  22.1   1.6e-35   1.4e-31       2     158 ..      83     239 ..      82     241 .. 0.91
   3 ?   -0.5   0.1      0.12   1.1e+03      50      76 ..     295     321 ..     263     327 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.32
               Glycos_transf_4 17 l 17
                                  +
  gi|70605943|ref|YP_254813.1| 17 V 17
                                  2 PP

  == domain 2  score: 109.6 bits;  conditional E-value: 1.6e-35
               Glycos_transf_4   2 llllltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavN 82 
                                   +++ll++l+i++lG+lDD++++++ ++ +l i+a+++lil ++++ t +++++  + +++g++++++++  ++++++Na+N
  gi|70605943|ref|YP_254813.1|  83 VSILLSSLIIGFLGLLDDIFNISQATRAFLPIFASIPLIL-YSVGHTIISIPFL-GKVNFGILFYIIILPATLTITANAFN 161
                                   67999********************************966.66799*******9.9************************* PP

               Glycos_transf_4  83 liDGldGlaagvsiiialalvvlaavd..grsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlail 158
                                   +++Gl+Gl ag+ +i+alal+++ + +  ++ +  +++++l+ +l+Gfl+fN+ypAk F G++g++f+G v++ + i 
  gi|70605943|ref|YP_254813.1| 162 MLEGLNGLGAGMGLIMALALAYIGLKSggTSFYAGIVSIILASVLFGFLIFNFYPAKTFPGNIGTYFIGSVIGSIGIS 239
                                   ************************888534444455566666688****************************99986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.12
               Glycos_transf_4  50 lgllltqvlielglilavlltllvivg 76 
                                   +g ++  +++ + + + +l+++l++v+
  gi|70605943|ref|YP_254813.1| 295 IGKFKEYHIVLIIWGIEILFAILAVVF 321
                                   333333344444555555555555554 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3    0.0017        15       7      33 ..      54      80 ..      51      83 .. 0.89
   2 ?    4.8   3.6    0.0022        20      77     132 ..     165     224 ..     151     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0017
                          CbtA  7 rgllaGllAGllaflvqrlvvePlila 33
                                  +g++aG++AG ++fl+  +  +P i++
  gi|70605943|ref|YP_254813.1| 54 IGIVAGFVAGSFTFLLTSYNLSPGIEN 80
                                  699**************9999998875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0022
                          CbtA  77 anvltgvalglllaavfallegrlgkls..aralallla..lagflavvlvPflklPpep 132
                                   +   +g+++gl++a+++a+++ + g++s  a   +++la  l+gfl + + P+  +P ++
  gi|70605943|ref|YP_254813.1| 165 GLNGLGAGMGLIMALALAYIGLKSGGTSfyAGIVSIILAsvLFGFLIFNFYPAKTFPGNI 224
                                   5556899************987777776445556777774568*********99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2234.97
//
Query:       gi|70605944|ref|YP_254814.1|  [L=216]
Description: beta-phosphoglucomutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-30  104.3   0.0    9.2e-30  104.0   0.0    1.1  1  HAD_2           Haloacid dehalogenase-like hydrolase
    3.6e-16   60.1   0.1    2.5e-11   44.2   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
    1.2e-08   35.5   0.0    2.1e-08   34.8   0.0    1.3  1  HAD             haloacid dehalogenase-like hydrolase
    6.8e-05   22.8   0.0    0.00021   21.3   0.0    1.9  2  Hydrolase_like  HAD-hyrolase-like
    0.00011   22.3   0.2      0.001   19.1   0.2    2.1  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    0.00025   20.9   0.9        2.2    7.9   0.0    3.2  3  Hydrolase_3     haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   3.1e-33   9.2e-30       1     173 [.      14     180 ..      14     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3.1e-33
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpy 81 
                                   +iFDlDgTl++t  ++ +a++++l++ g+   s+ ++++l+g ++ ++ + l+++++ +e+i+   ++y+e  k+ + +p 
  gi|70605944|ref|YP_254814.1|  14 VIFDLDGTLANTALIHKEAWEKALDRLGI--KSDVKIDNLLGRKSSDIAKLLAPNNW-SELINIKNQIYVELVKE-KASPT 90 
                                   7***********************99976..89999******************877.779****9********9.***** PP

                         HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp 162
                                   + + +lL +L+++++k +ivTs+++ +  + l++lgi+s  +v++t++dv ++KP+pe i+kal  l l+  +vi vGD+ 
  gi|70605944|ref|YP_254814.1|  91 PCALDLLSYLRKKEIKTAIVTSSNKLSSGSVLKKLGITS--EVVLTGDDVINSKPNPEGINKALSLLYLDGRDVIGVGDTE 169
                                   ************************************976..9*************************************** PP

                         HAD_2 163 tDieaakkagi 173
                                    D+ea  kag+
  gi|70605944|ref|YP_254814.1| 170 VDVEAYYKAGL 180
                                   ********997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.4e-05     0.043       1      26 [.      11      36 ..      11      66 .. 0.85
   2 !   44.2   0.0   8.5e-15   2.5e-11     110     210 .]      80     179 ..      69     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                  SSEEEEESBTTTBCHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTLttgepsvedvivsa 26
                                  +k v+fD+dGTL ++   +++++++a
  gi|70605944|ref|YP_254814.1| 11 VKGVIFDLDGTLANTALIHKEAWEKA 36
                                  689*********************99 PP

  == domain 2  score: 44.2 bits;  conditional E-value: 8.5e-15
                                   HHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 110 vftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyf.daviasdietvakpspegkvaaireLqgk 189
                                   v  ++++ ++ p a +++ +L+++ i+++++t++n+    +++++lG  +  ++v+++d++  +kp+peg ++a+  L  +
  gi|70605944|ref|YP_254814.1|  80 VELVKEKASPTPCALDLLSYLRKKEIKTAIVTSSNKLSSGSVLKKLG--ITsEVVLTGDDVINSKPNPEGINKALSLLYLD 158
                                   5666777779999**********************************..5548888888888******************* PP

                                   GGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 190 peevamVGDgvnDaaalaaAg 210
                                   +++v+ VGD+  D++a  +Ag
  gi|70605944|ref|YP_254814.1| 159 GRDVIGVGDTEVDVEAYYKAG 179
                                   ***************977765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   6.9e-12   2.1e-08       1     186 [.      14     174 ..      14     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 6.9e-12
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerfvaev 80 
                                   ++fD+DgTL ++    +l+++ ++++a++ +  ++   + +    ll ++       +++lla+ +  el++  ++++ e 
  gi|70605944|ref|YP_254814.1|  14 VIFDLDGTLANT----ALIHKEAWEKALD-RLGIKSDVKIDN---LLGRK----SSDIAKLLAPNNwSELINIKNQIYVEL 82 
                                   79**********....8888777776655.455555555555...33332....335555555666666666666666666 PP

                           HAD  81 irpkl.ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalre 160
                                   +++k+  +p al+ll+  r++ +++++v+++++     +l++lg    + +e+    +ltg      ++++ +  +  +++
  gi|70605944|ref|YP_254814.1|  83 VKEKAsPTPCALDLLSYLRKKEIKTAIVTSSNKLSSGSVLKKLG----ITSEV----VLTGD-----DVINSKPNPEGINK 150
                                   666632448***********************************....88832....67777.....33333334446666 PP

                           HAD 161 wlaaegegidleevvayGDspsDlpl 186
                                     a     +d  +v+ +GD++ D+++
  gi|70605944|ref|YP_254814.1| 151 --ALSLLYLDGRDVIGVGDTEVDVEA 174
                                   ..55557788888**********975 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.6   7.7e+03      40      51 ..     124     135 ..     121     137 .. 0.71
   2 !   21.3   0.0   6.9e-08   0.00021       3      57 ..     141     195 ..     139     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                                   HCT-EEEEESSS CS
                Hydrolase_like  40 naGwksvLVltG 51 
                                   + G++s  VltG
  gi|70605944|ref|YP_254814.1| 124 KLGITSEVVLTG 135
                                   567777777777 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.9e-08
                                   STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EE.EEESSSSS-TTT CS
                Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwks.vLVltGvtrped 57 
                                   +KP+pe +  al  l +d ++v+ +GD+ + D+++  +aG+ +  LV++Gv  +e+
  gi|70605944|ref|YP_254814.1| 141 SKPNPEGINKALSLLYLDGRDVIGVGDT-EVDVEAYYKAGLGGiYLVKSGVPFREE 195
                                   6***************************.*************9559****955554 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   3.4e-07     0.001       1      66 [.      14     141 ..      14     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-07
                                   EEEESTTTSE.............................................................ETTEE-TTHH CS
                   Hydrolase_6   1 flfDidGvLw.............................................................rgdkaipgaa 20 
                                   ++fD+dG+L                                                              ++ ++ p a 
  gi|70605944|ref|YP_254814.1|  14 VIFDLDGTLAntalihkeawekaldrlgiksdvkidnllgrkssdiakllapnnwseliniknqiyvelvkEKASPTPCAL 94 
                                   579999999999999999999999999999999999999999999999999999999999999999988888999****** PP

                                   HHHHHHHHTT-EEEEEE---SS-HHHHHHHH.HHTT----GGGEEEH CS
                   Hydrolase_6  21 ealnalraagkpvvllTNnsskseeeyakkl.eklgvditeeqvvts 66 
                                   ++l +lr+++++++++T +++ s  +++kkl    +v +t ++v+ s
  gi|70605944|ref|YP_254814.1|  95 DLLSYLRKKEIKTAIVTSSNKLSSGSVLKKLgITSEVVLTGDDVINS 141
                                   *******************************9999999999999988 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0026       7.8       1      19 [.      14      32 ..      14      76 .. 0.81
   2 !    7.9   0.0   0.00074       2.2      10      59 ..      83     132 ..      82     142 .. 0.88
   3 !    4.3   0.0    0.0097        29     191     225 ..     147     181 ..     138     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0026
                                  EEEEIIIIIS-TTS---HH CS
                   Hydrolase_3  1 ialDlDGTLlnsdkkisek 19
                                  +++DlDGTL n     +e 
  gi|70605944|ref|YP_254814.1| 14 VIFDLDGTLANTALIHKEA 32
                                  69*******9865444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00074
                                   S-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                   Hydrolase_3  10 lnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                   ++++ + ++ + + + +l++k+ik +i T  +  +  +vl++lg+++ v+
  gi|70605944|ref|YP_254814.1|  83 VKEKASPTPCALDLLSYLRKKEIKTAIVTSSNKLSSGSVLKKLGITSEVV 132
                                   56666778888999******************************997665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.0097
                                   HHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEE CS
                   Hydrolase_3 191 alkklakelnisleeviafGDgeNDieMLeaaglg 225
                                   +++k ++ l ++  +vi +GD e D+e   +aglg
  gi|70605944|ref|YP_254814.1| 147 GINKALSLLYLDGRDVIGVGDTEVDVEAYYKAGLG 181
                                   788999999*****************987777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1596.06
//
Query:       gi|70605945|ref|YP_254815.1|  [L=588]
Description: cytochrome c oxidase polypeptide I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-73  246.5  63.1    4.6e-73  246.5  63.1    2.8  3  COX1      Cytochrome C and Quinol oxidase polypeptide I
  ------ inclusion threshold ------
       0.12   12.2   0.1        0.3   11.0   0.1    1.7  1  DUF5310   Family of unknown function (DUF5310)


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.5  63.1   5.1e-77   4.6e-73       1     407 [.      22     448 ..      22     458 .. 0.86
   2 !    2.5   0.2    0.0057        51     116     144 ..     462     490 ..     452     517 .. 0.79
   3 ?   -0.9   2.6     0.064   5.7e+02      83     173 ..     532     580 ..     501     586 .. 0.48

  Alignments for each domain:
  == domain 1  score: 246.5 bits;  conditional E-value: 5.1e-77
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT........-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS- CS
                          COX1   1 kigllylilalvlllvggllgllirlqlafp........dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardl 73 
                                   +i+  +lil++v++++g++ gl++r+q  +         ++++y + +tlH+   +f+fa ++i+++++ylv +l+g ++ 
  gi|70605945|ref|YP_254815.1|  22 RIVSSMLILGVVWGALGVIDGLMVRIQESAWgiygflpfTPQEYFAGITLHAERTLFGFAQQIIFAIIIYLVIKLMGIQPR 102
                                   588899*********************96433444445889**********************999999999999866555 PP

                                   S-HHHHHHHHHHHHHHHHHHHHHHH....CS.....S-STTTTTTTC.........SHHHHHHHHHHHHHHHHHHHHHHHH CS
                          COX1  74 afprlnalsfwlvvlgvvllllsll....ga.....attgwteYapls........evdlwllglllvvvssllgainfiv 137
                                    +  l + +f+l+ ++++l+  ++l    +a      +t w+   p+          ++l+ +g++l  + ++l+++ ++ 
  gi|70605945|ref|YP_254815.1| 103 LKW-LLNTAFVLLNISMMLMEGPILiypsQAfdnyfSATIWYYLSPIGipgyslyvVSPLFFIGWILNDAFVYLAGFWIAY 182
                                   555.44455555666666666566555541166677778886666766997777778888888888888777775555555 PP

                                   HHHH.HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SS..SCE-HHHHHHHHHHHHTHHHHHHHH CS
                          COX1 138 tilk.rrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkff..spgdplldqhlfWffgHpeVyilil 215
                                    ++  +r+  +  +klp+ + ++l+ ++++++ + +++++ ++ +l     +ff   p+++ll q+ fW+fgH +Vy+l+l
  gi|70605945|ref|YP_254815.1| 183 HMYIgTRN--L-KEKLPVPLLFFLVDILIFMIGYTGVTASDVWDIL-----SFFgvVPMNALLNQIAFWIFGHSVVYMLWL 255
                                   55442432..2.568999999**********************996.....5664356*********************** PP

                                   HHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCCTTS CS
                          COX1 216 palgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatlwrg 296
                                   pa++++y ++p +a++plfs++++++++il+l++s  v +HH++t+ lp+ lk+++ ++++ +++Ps+++++n++at  + 
  gi|70605945|ref|YP_254815.1| 256 PAVAALYLLIPMLANKPLFSDRMARISAILYLVFSNNVPIHHMYTINLPVELKFVQEALTYGVVIPSFMTFLNLWATAKGA 336
                                   ******************************************************************************999 PP

                                   -CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--.HHHHH CS
                          COX1 297 sirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrml.serla 376
                                   +++++  + f++ ++   i++G+tG+ +a++s++++v n++wvvaHfH ++l+ +v +++a++y l+p++ g+m+ s ++a
  gi|70605945|ref|YP_254815.1| 337 DVKWNIITAFTVTSFAGAILAGVTGIANATVSFDFIVNNSMWVVAHFHQMILLSIVPGAMAVLYVLIPMISGKMWySSKMA 417
                                   999999999888888888*****************************************************98777***** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTTHBSSSS CS
                          COX1 377 klhfwllfiGlvlmflpmhilGllgmprraa 407
                                   ++hfw +++G+v++++++ +lG++g++rra 
  gi|70605945|ref|YP_254815.1| 418 WFHFWGYIVGVVILTVSFELLGFYGITRRAE 448
                                   *****************************97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0057
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          COX1 116 lwllglllvvvssllgainfivtilkrra 144
                                   l+  g +++ +++l ++in+i ti+k  +
  gi|70605945|ref|YP_254815.1| 462 LATAGAAIADIATLGWFINVILTIAKGSQ 490
                                   57889999*****************9653 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.064
                                   HHHHHHHHHH.HHHHHHCSS-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHH CS
                          COX1  83 fwlvvlgvvl.lllsllgaattgwteYaplsevdlwllglllvvvssllgainfivtilkrrapgmtvaklplfvwavlat 162
                                   ++l++lg+++ + +s++  a++g  +  p    +                                         w +la+
  gi|70605945|ref|YP_254815.1| 532 LVLAILGALMiVSSSII-LASAG-DATSPTDPLE-----------------------------------------WLWLAV 569
                                   33333333331222221.12222.1222212222.........................................333333 PP

                                   HHHHHHHCHHH CS
                          COX1 163 ailillalpvl 173
                                   ++l++++++v+
  gi|70605945|ref|YP_254815.1| 570 FTLGIVMVAVN 580
                                   33333333333 PP

>> DUF5310  Family of unknown function (DUF5310)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.4e-05       0.3      21      40 ..     414     433 ..     412     436 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                       DUF5310  21 SRkAFFqllgFlgscvviSl 40 
                                   S  A F++ g+++++v++++
  gi|70605945|ref|YP_254815.1| 414 SKMAWFHFWGYIVGVVILTV 433
                                   788***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3749.56
//
Query:       gi|70605946|ref|YP_254816.1|  [L=361]
Description: hypothetical protein Saci_0098 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2429.19
//
Query:       gi|70605947|ref|YP_254817.1|  [L=61]
Description: hypothetical protein Saci_0099 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 431.91
//
Query:       gi|70605948|ref|YP_254818.1|  [L=243]
Description: hypothetical protein Saci_0100 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-48  165.5   0.0    1.7e-48  165.2   0.0    1.0  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   0.0   9.5e-53   1.7e-48       1     251 [.       3     237 ..       3     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 9.5e-53
                                   EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHH CS
                    TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkela 81 
                                   +D H+H+d ++f+ dr+ +l+++e     +v++ g++ k++ ++lel kky+n v++++G+HP  v+++ +++ + l+ + 
  gi|70605948|ref|YP_254818.1|   3 VDVHAHIDVESFDGDRDLVLSECE----ITVINAGVDIKSNLKTLELYKKYNN-VIPAVGFHPEFVKDKLDEVDKCLELV- 77 
                                   7***********************....9999********************9.*********99997655554555444. PP

                                   HCCCTSEEEEEEEEEET.-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S-H CS
                    TatD_DNase  82 nvkhskvvaiGeiGLDy.ysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgsa 161
                                       ++v  i e+G+Dy + +e++ +++q e++ ++l+  ++ ++pl+iH r   +dl+++l++++   + +v+H f+gs 
  gi|70605948|ref|YP_254818.1|  78 ----DNVNIISEVGIDYfWIKEPEFRKKQLEILSKFLDKGERQRKPLIIHVRGGINDLINLLSSYN---VNFVIHAFEGSP 151
                                   ....67888********557888889**************************************94...369********* PP

                                   HHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHH CS
                    TatD_DNase 162 eeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleel 242
                                    +a+k+++lg +is++ +++   +k  +e+vk+++l+ +L+ETD+P+l p   + +rn+p+nv  +v+k+aelk+++++e+
  gi|70605948|ref|YP_254818.1| 152 SVAQKIVELGGMISIPPVIVR--DKYRQEVVKNIDLNYILTETDSPFLPP--QKMERNKPCNVIFTVKKIAELKKIEEKEV 228
                                   ******************999..66899**********************..4449************************* PP

                                   HHHHHHHHH CS
                    TatD_DNase 243 aeitaeNak 251
                                   ++++ eN+ 
  gi|70605948|ref|YP_254818.1| 229 IRQIHENFT 237
                                   *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1870.67
//
Query:       gi|70605949|ref|YP_254819.1|  [L=53]
Description: hypothetical protein Saci_0101 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-10   40.6   0.2    1.9e-10   40.4   0.2    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    0.00039   20.8   0.2    0.00045   20.6   0.2    1.1  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
    0.00095   18.9   0.2     0.0011   18.7   0.2    1.3  1  eIF-1a          Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.2   3.3e-14   1.9e-10       1      39 [.       6      44 ..       6      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3.3e-14
                                  EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCC CS
                MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilr 39
                                  +kv+++++v+iP+ +r++  ++eGd v ++ d++  +++
  gi|70605949|ref|YP_254819.1|  6 VKVSRNYQVTIPAKIRQKFQVKEGDLVRVIYDENENVVK 44
                                  69*******************************977765 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   7.5e-08   0.00045       3      40 ..       7      43 ..       5      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7.5e-08
                PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytilddgkvv 40
                                  ++ + +q tiPa +R+  ++k+  d +    +++++vv
  gi|70605949|ref|YP_254819.1|  7 KVSRNYQVTIPAKIRQKFQVKE-GDLVRVIYDENENVV 43
                                  68899****************9.678888888887776 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.9e-07    0.0011      26      51 ..      11      36 ..       3      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-07
                                  BEEEEE-HHHHCT----TT-EEEEEE CS
                        eIF-1a 26 evlaeipgkfRnkiwikrGdyVlVel 51
                                   + ++ip+k+R+k  +k+Gd V V  
  gi|70605949|ref|YP_254819.1| 11 NYQVTIPAKIRQKFQVKEGDLVRVIY 36
                                  57899*****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 398.91
//
Query:       gi|70605950|ref|YP_254820.1|  [L=126]
Description: Lrs14 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-16   57.7   0.2    1.1e-15   57.2   0.2    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.8e-06   26.7   0.8    1.2e-05   25.0   0.3    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
    6.1e-05   22.9   0.1    9.6e-05   22.2   0.1    1.3  1  MarR            MarR family
    6.8e-05   22.7   0.0    0.00011   22.0   0.0    1.4  1  MarR_2          MarR family
    8.2e-05   22.4   0.3    0.00012   21.8   0.3    1.3  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.015   15.4   2.0      0.059   13.4   0.3    2.1  2  z-alpha         Adenosine deaminase z-alpha domain
      0.022   14.5   0.2      0.052   13.3   0.0    1.7  2  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.03   14.8   0.1      0.059   13.9   0.1    1.6  1  HTH_27          Winged helix DNA-binding domain
      0.044   14.0   0.2       0.08   13.1   0.2    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.051   13.7   0.3      0.083   13.0   0.2    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.056   13.2   0.6       0.09   12.5   0.6    1.5  1  DUF4423         Domain of unknown function (DUF4423)
      0.065   13.3   0.1       0.34   11.0   0.1    2.0  2  HTH_20          Helix-turn-helix domain
      0.088   12.8   0.3       0.18   11.8   0.3    1.7  1  HTH_36          Helix-turn-helix domain
       0.13   11.9   0.8       0.23   11.1   0.1    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.2   8.6e-19   1.1e-15       1      67 [.      23      97 ..      23      98 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 8.6e-19
                                  HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE--H CS
                          TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYravdp 67
                                  L+ ++GLse++++v +aL k+g + ++e+ ++l++++++++++L++L+++Gl +r+k++       ++lY+a d+
  gi|70605950|ref|YP_254820.1| 23 LSfCYGLSETDVQVLVALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRIKESvnkagrpRYLYKARDY 97
                                  7889*************************************************************888**99775 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.3   9.5e-09   1.2e-05       3      44 ..      32      74 ..      30      76 .. 0.94
   2 ?   -0.5   0.0      0.91   1.2e+03       2      12 ..      99     109 ..      98     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.5e-09
                                  HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                         HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGL 44
                                  t +++L +La+ g +   el  +l+ls++ + + L+kL e+GL
  gi|70605950|ref|YP_254820.1| 32 TDVQVLVALAKsGAKGTEELESDLKLSKASINRSLNKLLEMGL 74
                                  6689*******999****************************9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHT CS
                         HTH_5   2 ptRlkILklLa 12 
                                   + R+kIL+ L 
  gi|70605950|ref|YP_254820.1|  99 ELRSKILSDLK 109
                                   67999998775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   7.5e-08   9.6e-05       1      53 [.      29      81 ..      29      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.5e-08
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                  l++t + +L+ l+ +g+    eL + l++sk+++ r l +L + Gl +R k  
  gi|70605950|ref|YP_254820.1| 29 LSETDVQVLVALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRIKES 81
                                  7999******************************************9998765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   8.6e-08   0.00011       2      54 ..      28      78 ..      27      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.6e-08
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  gl+ ++ +vL aL+ ++ +     el+  l+lsk++++r l++L + GL  r 
  gi|70605950|ref|YP_254820.1| 28 GLSETDVQVLVALAKSGAK--GTEELESDLKLSKASINRSLNKLLEMGLAMRI 78
                                  89999***********985..799*************************8665 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   9.7e-08   0.00012      11      83 ..      27     102 ..      18     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.7e-08
                                   S-..HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEE.CCCHCC CS
                   TFIIE_alpha  11 yg..eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrin.yeklvd 83 
                                   yg  e  v+vl +L++ g    e+l+ +lk+ +  + + Ln+L e +l+   ++  ++ +  +y ++   y++l  
  gi|70605950|ref|YP_254820.1|  27 YGlsETDVQVLVALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRIKESVNKAGRPRYLYKARdYNELRS 102
                                   555567899***************************************9766666688888888888752444333 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   4.6e-05     0.059       6      49 ..      33      73 ..      29      83 .. 0.89
   2 ?    1.6   0.1      0.22   2.9e+02       1      26 [.      96     120 ..      96     126 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                  HHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTT CS
                       z-alpha  6 aekilelLeelgekkaatalalergLstpkreiNrvLydlerkg 49
                                    ++l +L ++g  k++ +l+  ++Ls  k  iNr L +l + g
  gi|70605950|ref|YP_254820.1| 33 DVQVLVALAKSG-AKGTEELESDLKLS--KASINRSLNKLLEMG 73
                                  567999******.**************..9*******9999876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHC-TTCECCHHH CS
                       z-alpha   1 iaqeqaekilelLeelgekkaatala 26 
                                   ++ e  +kil  L++   +k a+ ++
  gi|70605950|ref|YP_254820.1|  96 DYNELRSKILSDLKDCA-DKMAKLVE 120
                                   5778899*******999.55555555 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.1e-05     0.052       4      47 ..      35      78 ..      33      83 .. 0.92
   2 ?   -2.7   0.0         4   5.1e+03       4      15 ..     114     125 ..     113     126 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.1e-05
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                  q l  l+++g   +eel   l+ S+a i R Ln+L e gl  R+
  gi|70605950|ref|YP_254820.1| 35 QVLVALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRI 78
                                  56778999999*****************************9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4
                      HTH_DeoR   4 qilellkqqgkl 15 
                                   ++ +l++q+ +l
  gi|70605950|ref|YP_254820.1| 114 KMAKLVEQEFTL 125
                                   788888887655 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.6e-05     0.059       2      50 ..      30      77 ..      29      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                        HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                  ++ +++vL  ++   + k  ++l   l++++++i  sl+kL e+GL +r
  gi|70605950|ref|YP_254820.1| 30 SETDVQVLVALA-KSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMR 77
                                  667999999999.8899999**************************855 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   6.3e-05      0.08      23      51 ..      46      74 ..      21      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.3e-05
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGy 51
                                   +t +l + L+ s++s+  +l+kL ++G+
  gi|70605950|ref|YP_254820.1| 46 KGTEELESDLKLSKASINRSLNKLLEMGL 74
                                  578899999*******************9 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   6.5e-05     0.083       8      63 ..      31      86 ..      27     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                       DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrt 63
                                  e +++vl  l+k ++     +   l++++  +++ l+kL e+GL  r ++++ k+ 
  gi|70605950|ref|YP_254820.1| 31 ETDVQVLVALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRIKESVNKAG 86
                                  56789999999999999999*************************99998887765 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6     7e-05      0.09      29      73 ..      37      80 ..      32     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                       DUF4423 29 llplkdf.kadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                  l++l +  ++ +eel+  l+  +s++ ++++l+ Ll++gl+ + ++
  gi|70605950|ref|YP_254820.1| 37 LVALAKSgAKGTEELESDLK--LSKASINRSLNKLLEMGLAMRIKE 80
                                  555444437899********..******************988776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027      0.34      18      59 ..      39      80 ..      29      81 .. 0.81
   2 ?   -0.4   0.0      0.96   1.2e+03      11      19 ..     100     108 ..      97     124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                  HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                  aLa  ++   +el   l lsk+++++ L++L e gL  + +e
  gi|70605950|ref|YP_254820.1| 39 ALAKSGAKGTEELESDLKLSKASINRSLNKLLEMGLAMRIKE 80
                                  555666666799************************888776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.96
                                   HHHHHHHHH CS
                        HTH_20  11 vRrrilraL 19 
                                    R +il+ L
  gi|70605950|ref|YP_254820.1| 100 LRSKILSDL 108
                                   566777766 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00014      0.18      28      54 ..      48      74 ..       7      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                        HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                   e l ++l+lsk ++ r +++L + G+
  gi|70605950|ref|YP_254820.1| 48 TEELESDLKLSKASINRSLNKLLEMGL 74
                                  57999*****************99886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00018      0.23      26      46 ..      54      74 ..      29      75 .. 0.76
   2 ?   -3.0   0.0       4.5   5.7e+03       3      13 ..      99     109 ..      98     113 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                        HTH_24 26 rlglSpstvnrrlkrLeeeGl 46
                                   l lS++ +nr l++L e+Gl
  gi|70605950|ref|YP_254820.1| 54 DLKLSKASINRSLNKLLEMGL 74
                                  689*****************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                        HTH_24   3 etdrkILelLq 13 
                                   e++ kIL+ L+
  gi|70605950|ref|YP_254820.1|  99 ELRSKILSDLK 109
                                   66778887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 959.18
//
Query:       gi|70605951|ref|YP_254821.1|  [L=223]
Description: hypothetical protein Saci_0103 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-56  191.8   0.2    1.2e-56  191.7   0.2    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.19   11.2   0.0    2.4  3  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   0.2   1.3e-60   1.2e-56       3     215 ..       4     220 ..       1     223 [] 0.96

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 1.3e-60
               Diphthami_syn_2   3 vavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkgtlk 82 
                                   v vlysGGkDs+++L++a+ + ++v+ L+++++  ++s+mf  +nv +++ +ae +G ++i++et+Ge++ e +dLk  ++
  gi|70605951|ref|YP_254821.1|   4 VCVLYSGGKDSTYSLHWAVFKgFDVICLITLLPRREDSWMFQYPNVIFTKKQAEVMGFEIIQQETTGEKDRELNDLKIAFE 84 
                                   789**************98766**********************************************************9 PP

               Diphthami_syn_2  83 kld...veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkkl 160
                                   k +   + ++v Ga+ s+yq+  i  + +elGlk+  PLW+kd +e++   v  +f+ i+++ +a+g   +l+G+ i+ + 
  gi|70605951|ref|YP_254821.1|  85 KAKkkgAKGIVAGALLSDYQRLNISIIAEELGLKTYTPLWRKDQKEYMYSLVRDGFKFIITSASAYGFPFELVGKVIEMED 165
                                   98777799************************************************************************* PP

               Diphthami_syn_2 161 idelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldie 215
                                   i ++   +e+yg ++a+egGeaet+v+ aPlf + l++   +   +e  + + ie
  gi|70605951|ref|YP_254821.1| 166 IKKIVYAAERYGFNPAFEGGEAETFVVYAPLFSRELKIRGHKERVSEFEWKYVIE 220
                                   ***************************************9999999999998887 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.1e-05      0.19       3      31 ..       5      33 ..       3      71 .. 0.79
   2 ?    0.8   0.0     0.032   2.8e+02      97     127 ..      74     104 ..      51     106 .. 0.86
   3 ?   -3.2   0.0      0.53   4.7e+03     141     159 ..     179     197 ..     177     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                                  EEE--SSHHHHHHHHHHHHH-SEEEEEEE CS
                          QueC  3 vvllSGGlDSttvlalakkegkevealtf 31
                                   vl SGG DSt  l +a  +g  v++l  
  gi|70605951|ref|YP_254821.1|  5 CVLYSGGKDSTYSLHWAVFKGFDVICLIT 33
                                  6899*************999888887755 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.032
                                   HHHHHHHHHHHHHHHHT-SEEEE---S-STT CS
                          QueC  97 RNliflslaasyaealgaeaiiiGvneedfs 127
                                   R l  l +a   a++ ga+ i+ G+  +d++
  gi|70605951|ref|YP_254821.1|  74 RELNDLKIAFEKAKKKGAKGIVAGALLSDYQ 104
                                   666668899999************9999985 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.53
                                   HHHHHHHHTS--EEE-TTT CS
                          QueC 141 nkalnlgedkkieieaPli 159
                                   n a + ge++++ + aPl 
  gi|70605951|ref|YP_254821.1| 179 NPAFEGGEAETFVVYAPLF 197
                                   6677888999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1602.34
//
Query:       gi|70605952|ref|YP_254822.1|  [L=155]
Description: hypothetical protein Saci_0104 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-07   30.9   0.0    9.9e-07   28.5   0.0    1.8  2  DOT1             Histone methylation protein DOT1
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.016   15.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.015   15.0   0.0      0.029   14.1   0.0    1.4  2  N6_N4_Mtase      DNA methylase
      0.017   14.2   0.0      0.022   13.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.024   14.2   0.0      0.035   13.7   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
      0.069   13.8   0.0        0.2   12.3   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
      0.089   12.3   0.0       0.13   11.8   0.0    1.2  1  MTS              Methyltransferase small domain
      0.091   12.1   0.0       0.11   11.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.097   12.8   0.0       0.14   12.2   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.12   13.1   0.0       0.26   12.0   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
       0.12   11.8   0.0       0.18   11.3   0.0    1.3  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   6.1e-10   9.9e-07      28      82 ..      10      64 ..       7      76 .. 0.87
   2 ?    0.3   0.0      0.27   4.3e+02     144     157 ..     109     122 ..      85     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.1e-10
                                  HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHH CS
                          DOT1 28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnasela 82
                                  pe+  e+l   + +++dv +DLGSG+G + + a  e+++kl++GvE+ ++ s ++
  gi|70605952|ref|YP_254822.1| 10 PEVAREMLRCADANENDVVLDLGSGMGAILNVAKKEFKVKLAIGVELDKKLSFVS 64
                                  5667789999999**********************************99988655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                   HHTT--TT-EEEES CS
                          DOT1 144 llqdlkegtkiisl 157
                                   +l  +k+g+ki+s 
  gi|70605952|ref|YP_254822.1| 109 ILGYAKKGAKIVSH 122
                                   45567999999996 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   9.9e-06     0.016       8      55 ..      11      59 ..       8     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
               Methyltransf_23  8 elsdklerllpklraggrvLdiGcGtGillevlrengf.svt.gvDlspe 55
                                  e++++ +r ++  +++  vLd+G G G  l+v++++++ +++ gv+l+ +
  gi|70605952|ref|YP_254822.1| 11 EVAREMLRCAD-ANENDVVLDLGSGMGAILNVAKKEFKvKLAiGVELDKK 59
                                  56677888886.899******************99987765559999743 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.029     175     224 ..       7      59 ..       5      66 .. 0.86
   2 ?   -3.0   0.0       2.9   4.8e+03     104     114 ..     108     118 ..      83     135 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                   ---HHHHHHHHHHH.S-TT-EEEETT-TTTHHHHHHHHTT-E..EEEEESSHH CS
                   N6_N4_Mtase 175 qkPvallerlIkls.tkkgdivlDpFaGSGtTavaakelgrk..fiGieieee 224
                                   + P + +++++++   +++d+vlD   G G ++ +ak++ +   +iG+e +++
  gi|70605952|ref|YP_254822.1|   7 PTPPEVAREMLRCAdANENDVVLDLGSGMGAILNVAKKEFKVklAIGVELDKK 59 
                                   679999999999874688*******************9976667999999886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                                   EEEEEESSTT- CS
                   N6_N4_Mtase 104 yilvfsknkky 114
                                   yil ++k++++
  gi|70605952|ref|YP_254822.1| 108 YILGYAKKGAK 118
                                   34444444444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.022      16      87 ..      10      81 ..       8     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                  HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCG CS
                        RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklskdeklkvvhqDflk 87
                                  + v+ e l+ ++ +e++ vl++g+G G+  +   k +  k    +Eld++L+ +  +  ++++ ++++  D+  
  gi|70605952|ref|YP_254822.1| 10 PEVAREMLRCADANENDVVLDLGSGMGAILNVAKKEFkvKLAIGVELDKKLSFVSYQ--ENNRDVEIICGDMIS 81
                                  57888999999****************999888888877778889******988777..689999999999875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.035      14      47 ..      25      59 ..       9      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                          MetW 14 gsrvldlGcGdGellellkeekqvd.grGleldee 47
                                  +  vldlG+G G +l++ k+e +v+ + G+eld++
  gi|70605952|ref|YP_254822.1| 25 NDVVLDLGSGMGAILNVAKKEFKVKlAIGVELDKK 59
                                  5679**************9999996589***9986 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.7   1.3e+04      75      87 ..       7      19 ..       4      23 .. 0.68
   2 ?   12.3   0.0   0.00012       0.2       1      56 [.      29      84 ..      29      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.7
                                  CCHHHHHHHHHHH CS
               Methyltransf_11 75 edpekalkeiaRv 87
                                  + p ++ +e+ R+
  gi|70605952|ref|YP_254822.1|  7 PTPPEVAREMLRC 19
                                  5667777777775 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00012
                                  EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.S CS
               Methyltransf_11  1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaekl.p 56
                                  Ld+G+G G++++  +k +  +  +gv+l+k++   ++ + ++++  ve++++d+ +l p
  gi|70605952|ref|YP_254822.1| 29 LDLGSGMGAILNVAKKEFkvKLAIGVELDKKLS-FVSYQENNRD--VEIICGDMISLaP 84
                                  8**************9999999********998.5545555555..89*****988745 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.9e-05      0.13      23      64 ..      16      57 ..      12      84 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
                                  HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESB CS
                           MTS 23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvd 64
                                  +l++ ++++++ vlDlG+G+G++  +++ke +      v+ d
  gi|70605952|ref|YP_254822.1| 16 MLRCADANENDVVLDLGSGMGAILNVAKKEFKVKLAIGVELD 57
                                  667778888999**********97766665554334444444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.8e-05      0.11     160     195 ..      23      59 ..      14      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-05
                          PrmA 160 kegeevlDvGtGSG.iLaiaaakLgakkvvavDiDev 195
                                   +e++ vlD+G G G iL +a + +  k +++v +D+ 
  gi|70605952|ref|YP_254822.1|  23 NENDVVLDLGSGMGaILNVAKKEFKVKLAIGVELDKK 59 
                                   456789******876********************74 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.6e-05      0.14      21      76 ..      24      85 ..      13     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.6e-05
                                  TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.......HHHTTEEEECS-CCCSSHH CS
                          FtsJ 21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.......aplpgvttiqgditdpeti 76
                                  +++ v+Dlg++ G+   v+ ++++  +  ++v l +        ++   v++i+gd  + +  
  gi|70605952|ref|YP_254822.1| 24 ENDVVLDLGSGMGAILNVAKKEFKV-KLAIGVELDKKlsfvsyqENNRDVEIICGDMISLAPV 85
                                  6678******************988.99******777788887556699******99776655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.26       1      58 [.      28      82 ..      28     104 .. 0.80
   2 ?   -3.1   0.0       8.5   1.4e+04      22      36 ..     117     131 ..     108     138 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                  EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGB CS
               Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedl 58
                                  vLdlG G G ++  + k+++ +  +gv++++++     +++   + +ve+++gd+ +l
  gi|70605952|ref|YP_254822.1| 28 VLDLGSGMGAILNVAKKEFKVKLAIGVELDKKLSFVSYQEN---NRDVEIICGDMISL 82
                                  9******************878889**99988754433333...34799999998665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.5
                                   SEEEEEESSHHHHHH CS
               Methyltransf_25  22 akvtgvDiseemlea 36 
                                   ak++  D++ + l+ 
  gi|70605952|ref|YP_254822.1| 117 AKIVSHDFQFQKLDL 131
                                   555555555554444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.18       2      38 ..      25      61 ..      24      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                  -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHH CS
                Methyltransf_4  2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvv 38
                                  + vvl++G+G+G +l    k++  k+ +G+E+ +k++
  gi|70605952|ref|YP_254822.1| 25 NDVVLDLGSGMGAILNVAKKEFKVKLAIGVELDKKLS 61
                                  5689********877655566667789****998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1169.30
//
Query:       gi|70605953|ref|YP_254823.1|  [L=195]
Description: hypothetical protein Saci_0105 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-14   52.4   0.0    1.2e-13   51.7   0.0    1.4  2  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   6.9e-18   1.2e-13       1     137 [.      10     128 ..      10     151 .. 0.83
   2 ?   -2.6   0.0      0.34   6.1e+03      37      49 ..     147     158 ..     126     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 6.9e-18
                                   EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalr 81 
                                   +viLAGG+S+R+g+dK+  +++ k++l+r+ +++ +    +++v  + + ++      g++v+ +     gp+++++ al 
  gi|70605953|ref|YP_254823.1|  10 VVILAGGASKRFGEDKCDHEIDCKTFLQRISENFDE----PIIVTKRIRRIK-----NGIQVLDNV--NGGPVEAIKLALP 79 
                                   69****************************999994....555555557776.....89******7..79*********** PP

                                   HH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGG CS
                  NTP_transf_3  82 aaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarl 137
                                    + +++ v+++ cD P+l++ + ++++ +    +a++ ++ +  ++ +pl+  ++l
  gi|70605953|ref|YP_254823.1|  80 YL-SKEKVFITGCDYPFLSKRIADEICSK----DAEISIVDT--GELQPLIGCYSL 128
                                   *9.9****************999999987....455555443..345777666555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.34
                                   T.-CEEEEECSHC CS
                  NTP_transf_3  37 agvdevvvvggde 49 
                                   + ++++++vg +e
  gi|70605953|ref|YP_254823.1| 147 L-AKRIYIVGTHE 158
                                   2.47889988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1385.49
//
Query:       gi|70605954|ref|YP_254824.1|  [L=389]
Description: molybdopterin biosynthesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-34  117.8   0.0    7.1e-34  116.8   0.0    1.5  1  MoeA_N         MoeA N-terminal region (domain I and II)
      8e-18   64.5   0.0    1.6e-17   63.5   0.0    1.5  2  MoCF_biosynth  Probable molybdopterin binding domain
     0.0099   16.0   2.6      0.017   15.2   0.4    2.1  2  7TMR-HDED      7TM-HD extracellular


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.0   1.2e-37   7.1e-34       1     154 [.       3     161 ..       3     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 1.2e-37
                                   B-HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--..............-S CS
                        MoeA_N   1 lsveealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep...saageepe 76 
                                   +s+eea++ii +a  +  + +  ++  +a+grv+ +d+vA++d+P+f+ SamDG+A+++++ ++  + +    +  ++++ 
  gi|70605954|ref|YP_254824.1|   3 ISLEEARKIIDNANiRNANIRsESI-YNAVGRVAGKDIVAKIDIPEFNISAMDGFAFNVSDYKKNGKLKIagkIFPSSSEI 82 
                                   689*****88777533333333455.7899**********************************98888899977777777 PP

                                   ---TT-.EEEE-TTSB--TT--EEEEGGGE...E....EETTE..S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHH CS
                        MoeA_N  77 rllpgg.avrimTGaplPegadaVvpvEdte..eeeaketvev..kavkpgenvrraGedikaGevllragtrltpaeigl 152
                                   ++l++g a++++TG+p+P+ga+a+ ++E t+  +   +++  v  + v +g++++ aGedik+G++++r+g++++  ++g+
  gi|70605954|ref|YP_254824.1|  83 PQLKEGeAYYVATGSPIPKGANAIARIEATKisG--DNQI--VfsEDVFEGKDIKFAGEDIKKGDIIVRKGEVINHYHLGV 159
                                   7777777***********************7632..2233..24589999******************************* PP

                                   HH CS
                        MoeA_N 153 la 154
                                   l 
  gi|70605954|ref|YP_254824.1| 160 LT 161
                                   96 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.4   8.4e+03      76     100 ..     110     134 ..     109     147 .. 0.77
   2 !   63.5   0.0   2.7e-21   1.6e-17       2     138 ..     177     305 ..     176     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.4
                                   HHHHHHHSEE-HHHHHHHHHHHHHH CS
                 MoCF_biosynth  76 ealaklfekelegfeeafrrvslkp 100
                                   ea++  ++ +++ +e +f++   k+
  gi|70605954|ref|YP_254824.1| 110 EATKISGDNQIVFSEDVFEGKDIKF 134
                                   6777788888888888888777665 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 2.7e-21
                                   EEEE-HHHH......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHH CS
                 MoCF_biosynth   2 vitvGdell......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpe 76 
                                   v++ Gdel        +ki D+ +p+l++ l+++gv +   ++v D +e +k +l++ +e+ d+i+++GG +++++D+ ++
  gi|70605954|ref|YP_254824.1| 177 VLASGDELCpydspeDNKIPDSISPILISILRKFGV-ANYFGIVSDHKESLKTKLESMVENCDYIVLIGGSSVGEKDYSKR 256
                                   8999***********9*******************9.66699*************9999999******************* PP

                                   HHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHH CS
                 MoCF_biosynth  77 alaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeil 138
                                   ++a+l++        +f++vs +  k  gv+ +   +   gk++i+LPG  +++ ++++e  
  gi|70605954|ref|YP_254824.1| 257 VIAELGD-------LLFEGVSVNIIKRGGVGVI---N---GKPVINLPGQVVSALTVFHEHG 305
                                   *******.......8********7554444444...4...458*************999865 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.12   6.9e+02       2      16 ..      31      45 ..      30      47 .. 0.91
   2 !   15.2   0.4   2.9e-06     0.017     190     212 ..     139     161 ..     137     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
                     7TMR-HDED  2 vGqiApqdIvAprdf 16
                                  vG +A +dIvA  d+
  gi|70605954|ref|YP_254824.1| 31 VGRVAGKDIVAKIDI 45
                                  8**********9987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.9e-06
                     7TMR-HDED 190 ikkGevIVrkGervteeqlekLe 212
                                   ikkG++IVrkGe+++  +l +L 
  gi|70605954|ref|YP_254824.1| 139 IKKGDIIVRKGEVINHYHLGVLT 161
                                   9*****************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2626.51
//
Query:       gi|70605955|ref|YP_254825.1|  [L=166]
Description: hypothetical protein Saci_0107 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-22   77.4   0.2    4.4e-21   75.2   0.2    1.9  1  MobB           Molybdopterin guanine dinucleotide synthesis p
  ------ inclusion threshold ------
       0.06   13.2   0.2         15    5.5   0.0    2.6  3  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.2   4.9e-25   4.4e-21       1     113 [.       4     107 ..       4     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 4.9e-25
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaelsl 81 
                                   ++++vgk++sGKT+ +e+ ++ lk+ g++v ++Kh+hh+  +d+pgkD++r+++AGA+ vl  +++    i   +      
  gi|70605955|ref|YP_254825.1|   4 IIQVVGKKDSGKTSAIERAVKSLKDMGYSVTVLKHSHHS--LDSPGKDTFRFKQAGADYVLFFGNDCGMFIPC-DI----- 76 
                                   799***********************************7..689******************99886666655.33..... PP

                          MobB  82 eellarlsevDlvlvEGfkkeal.pkievlrae 113
                                    +++  l ++D++++EG+k+ +l +kie+  ++
  gi|70605955|ref|YP_254825.1|  77 -NIIYLL-PTDILIIEGYKDLSLgQKIEIESPS 107
                                   .455555.9**********9876489**98765 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.066   5.9e+02      37      54 ..       3      20 ..       2      22 .. 0.79
   2 ?    5.0   0.0    0.0024        21      10      32 ..      15      37 ..       7      42 .. 0.81
   3 ?    5.5   0.0    0.0017        15      10      34 ..     105     129 ..     103     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.066
                 DAHP_snth_FXD 37 tViGviGdtskldkeqle 54
                                  ++i v+G++++ ++  +e
  gi|70605955|ref|YP_254825.1|  3 CIIQVVGKKDSGKTSAIE 20
                                  79*****99987777665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0024
                 DAHP_snth_FXD 10 teeqieevierieelGlkvhvsk 32
                                  + + ie+ ++ ++++G++v v k
  gi|70605955|ref|YP_254825.1| 15 KTSAIERAVKSLKDMGYSVTVLK 37
                                  6688**************98865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0017
                 DAHP_snth_FXD  10 teeqieevierieelGlkvhvskGe 34 
                                   +++qie+v +ri elG  ++  +G+
  gi|70605955|ref|YP_254825.1| 105 SPSQIESVSKRIVELGSLCNKLEGK 129
                                   578*************998888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1136.07
//
Query:       gi|70605956|ref|YP_254826.1|  [L=231]
Description: hypothetical protein Saci_0108 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-16   59.7   0.0    5.2e-16   59.1   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
      1e-13   51.8   0.0    1.6e-13   51.2   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    6.2e-10   39.2   0.0      1e-09   38.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.6e-09   36.8   0.1    2.4e-08   33.6   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.4e-08   33.3   0.0    1.2e-07   32.4   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    4.8e-07   29.7   0.0    8.1e-07   29.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0011   18.2   0.0     0.0015   17.7   0.0    1.3  1  DREV             DREV methyltransferase
     0.0024   17.8   0.0     0.0032   17.4   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   2.3e-19   5.2e-16       2      95 ..      88     175 ..      87     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.3e-19
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   d+G+GtG+l+ +    +  ++gvD+s ++l++ k+k ++       ++ad+ klpf+d+    v + ++lh ++    al+
  gi|70605956|ref|YP_254826.1|  88 DIGTGTGKLFDYTI--CNYCFGVDISSKFLRILKKKRPKVV----ALRADVNKLPFNDEVANGVSAMFMLHLLPSKVTALR 162
                                   9*************..7789**********99988888765....59********************************** PP

                                   HHHHHEEEEEEEE CS
               Methyltransf_11  83 eiaRvLkpgGllv 95 
                                   ei+RvLkp G++v
  gi|70605956|ref|YP_254826.1| 163 EIYRVLKPKGKFV 175
                                   **********998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   7.1e-17   1.6e-13       1      97 []      86     172 ..      86     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 7.1e-17
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   v+d+G+GtG+l  +    +      gvDis+++l++ +++     ++v  +++d+++lpf+d+  + v ++++lh+l+   
  gi|70605956|ref|YP_254826.1|  86 VIDIGTGTGKLFDYTI--C--NYCFGVDISSKFLRILKKKR----PKVVALRADVNKLPFNDEVANGVSAMFMLHLLP--S 156
                                   89*********99998..4..579***************99....9*************************99***98..4 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                     +al+ei+rvLkp+G
  gi|70605956|ref|YP_254826.1| 157 KVTALREIYRVLKPKG 172
                                   569***********99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   4.5e-13     1e-09      16     159 ..      76     211 ..      64     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.5e-13
               Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengfsvt.gvDlspeaveiae.kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                                    ++k  +g  v+diG+GtG l +   +  ++++ gvD+s++   i++ k++k +   +d ++ +++++  + ++++++l+ 
  gi|70605956|ref|YP_254826.1|  76 NAGKFVSGDTVIDIGTGTGKLFD---YTICNYCfGVDISSKFLRILKkKRPKVVALRADVNKLPFNDEVANGVSAMFMLHL 153
                                   4444556679*********5555...66898777*****9999988888899999999999******************** PP

               Methyltransf_23  95 vpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaG 159
                                   +p+   +lr i++ lkp G ++ s  +++    + l +w+ ++ +       + + + +l++e G
  gi|70605956|ref|YP_254826.1| 154 LPSKVTALREIYRVLKPKGKFVASILTRNNTVSSILASWWKIDLH-------QVEYYVQLFNEIG 211
                                   *************************99987666666666654433.......3333334555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-11   2.4e-08       7     151 ..      40     176 ..      35     193 .. 0.77
   2 ?    0.7   0.0      0.12   2.7e+02     202     223 ..     201     222 ..     195     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                                   XXXXXXXX-HHHHHHHHHHHHHTTTHHHHHH.HHHH.H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHH CS
               Ubie_methyltran   7 ekvkevfesvaskyDlmndvlslgihrlWkk.fvek.lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmL 85 
                                    k +++ e+v+  y+ + + l l +    +   +++      +g +v+D+ +Gtg l f+ +  +       ++Di+++ L
  gi|70605956|ref|YP_254826.1|  40 VKLNDILERVSGIYENIWAPLGLFVSSGHRYsEIMNnAGKFVSGDTVIDIGTGTGKL-FDYT--I--CNYCFGVDISSKFL 115
                                   566777777777777777777766655555444444044456788999999999975.2222..2..2346799******* PP

                                   HHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
               Ubie_methyltran  86 kvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                   ++ +kk       ++  l a+ ++Lpf+d+  + v   f l  ++ k +aL+e+yrvlkp G++v 
  gi|70605956|ref|YP_254826.1| 116 RILKKKRP-----KVVALRADVNKLPFNDEVANGVSAMFMLHLLPSKVTALREIYRVLKPKGKFVA 176
                                   *9988854.....577899*******************************************9985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                                   HHHHHHHHHTTEEEEEEEEEGG CS
               Ubie_methyltran 202 etlkeliedaGfksveyesltg 223
                                   e + +l+++ Gf++++y +l++
  gi|70605956|ref|YP_254826.1| 201 EYYVQLFNEIGFSNINYVRLGA 222
                                   567799***********98875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   5.3e-11   1.2e-07       2      99 .]      88     174 ..      87     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.3e-11
               Methyltransf_12   2 eiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   +iG+GtG l ++        +y+ gvDis++++   k+k  k  ++++++++l  +d     +      v a + lh l+ 
  gi|70605956|ref|YP_254826.1|  88 DIGTGTGKLFDYTIC-----NYCfGVDISSKFLRILKKKRPKVVALRADVNKLPFND-----E--VANGVSAMFMLHLLPS 156
                                   9**********9955.....5888*********666666666665555555555555.....3..7899************ PP

               Methyltransf_12  82 irevldnirklLkpgGrl 99 
                                   +  +l++i+++Lkp G++
  gi|70605956|ref|YP_254826.1| 157 KVTALREIYRVLKPKGKF 174
                                   ***************986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   3.6e-10   8.1e-07       3     110 ..      82     177 ..      81     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.6e-10
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                   +g +v+D+G+GtG+l      +       +G+Dis + ++  ++++       v   ++d+++l+  ++de  + + +   
  gi|70605956|ref|YP_254826.1|  82 SGDTVIDIGTGTGKLFDYTICN-----YCFGVDISSKFLRILKKKRP-----KVVALRADVNKLP--FNDEVANGVSAMFM 150
                                   5789********9987655523.....378*********98888544.....6999*********..99*99999999999 PP

               Methyltransf_31  84 lnaladpdkileeiervlkpggillie 110
                                   l++l+++  +l+ei rvlkp+g ++++
  gi|70605956|ref|YP_254826.1| 151 LHLLPSKVTALREIYRVLKPKGKFVAS 177
                                   9***********************976 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.7e-07    0.0015      70     190 ..      62     179 ..      20     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.7e-07
                          DREV  70 mfvlseeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynvlsale.lqetd 149
                                   +fv s +++  ++   ++ + s     +++d+G+G G++        +  +  ++s++    lkkk+ +v++    +++  
  gi|70605956|ref|YP_254826.1|  62 LFVSSGHRYSEIMNNAGK-FVS---GDTVIDIGTGTGKLFDYT--ICNYCFGVDISSKFLRILKKKRPKVVALRAdVNKLP 136
                                   566666666666554432.233...479*********998764..55679********************99754388888 PP

                          DREV 150 vkldl...ilclnlldrcfdplklledirsalepngrvivalvl 190
                                   ++ ++   ++++ +l    + ++ l++i+ +l+p+g+ + ++ l
  gi|70605956|ref|YP_254826.1| 137 FNDEVangVSAMFMLHLLPSKVTALREIYRVLKPKGKFVASI-L 179
                                   8888755689999************************88765.3 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.4e-06    0.0032     105     178 ..     122     197 ..      72     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
                                   STTEEE..S-TTS-S--TT-EE..EEEEES---SS-HHHHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHCTTE CS
                Methyltransf_8 105 nervva..cdlakvPledesvd..vavfclslmgtnladflkeanrvlkvGGllkvaevksrfesvklfaraltklGf 178
                                    ++vva   d++k+P +de ++   a+f l l+  +++  l+e++rvlk+ G + va + +r + v  ++    k+ +
  gi|70605956|ref|YP_254826.1| 122 RPKVVAlrADVNKLPFNDEVANgvSAMFMLHLLPSKVT-ALREIYRVLKPKGKF-VASILTRNNTVSSILASWWKIDL 197
                                   3455543379*********9874347999999998875.69***********85.89999999988877766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1700.42
//
Query:       gi|70605957|ref|YP_254827.1|  [L=136]
Description: hypothetical protein Saci_0109 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0075   16.4   6.2     0.0075   16.4   6.2    2.1  2  DUF4234   Domain of unknown function (DUF4234)
  ------ inclusion threshold ------
        7.1    7.1  13.1         32    5.0   6.9    2.2  2  DUF4491   Domain of unknown function (DUF4491)


Domain annotation for each model (and alignments):
>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4      0.33     3e+03      10      10 ..      39      39 ..       3      70 .. 0.64
   2 !   16.4   6.2   8.4e-07    0.0075       4      53 ..      86     131 ..      83     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
                       DUF4234 10 s 10
                                   
  gi|70605957|ref|YP_254827.1| 39 A 39
                                  1 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.4e-07
                       DUF4234   4 avvilLsivTlGIYslyWlykltrelnrlsgrkkttslllvflllslitc 53 
                                   ++ i+L ++T+GIY +++ +  ++++ +l +     +++ + ll+sli++
  gi|70605957|ref|YP_254827.1|  86 LMGIFLVFITFGIYIAVYTIFYSNAITMLVNG---LDGASF-LLFSLIIF 131
                                   4669*************************999...555555.88998876 PP

>> DUF4491  Domain of unknown function (DUF4491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.0     0.015   1.4e+02       3      61 ..      17      76 ..      15      87 .. 0.83
   2 ?    5.0   6.9    0.0036        32      20      68 ..      73     124 ..      51     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.015
                       DUF4491  3 sGliigiatfliiglfhpivikaeyylgkki.wwvflvagillivaslfvenvllsavlg 61
                                   Gl++ ++++++i  +h+ +  a y l     + + +++g+  i+ s++ +  ++s ++g
  gi|70605957|ref|YP_254827.1| 17 IGLVMFVTSLFLIINVHVGLFDAIYTLNPYPfYFLGVIVGVERIFYSITGSTKIFSLIVG 76
                                  5899999999999999****9999999654403445799**********99999999987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0036
                       DUF4491  20 pivikaeyylgkk...iwwvflvagillivaslfvenvllsavlgvlgfsll 68 
                                    iv   e +++     i+ vf+ +gi ++v ++f +n+++  v g+ g+s+l
  gi|70605957|ref|YP_254827.1|  73 LIVGEGEGFFSIAlmgIFLVFITFGIYIAVYTIFYSNAITMLVNGLDGASFL 124
                                   555556666655411145677789**********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 868.73
//
Query:       gi|70605958|ref|YP_254828.1|  [L=133]
Description: hypothetical protein Saci_0110 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0054   15.8   0.1     0.0068   15.5   0.1    1.0  1  DUF4015   Putative glycosyl hydrolase domain
  ------ inclusion threshold ------
       0.19   10.0   0.0       0.21    9.9   0.0    1.0  1  DUF5312   Family of unknown function (DUF5312)


Domain annotation for each model (and alignments):
>> DUF4015  Putative glycosyl hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.5e-07    0.0068      37      90 ..      25      78 ..      16      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-07
                                  TTS-BSS----HHHHHCT-B--S.--HHHHHHHHHHTT-EEEEEEE-S--TTHH CS
                       DUF4015 37 deGnvtyesklelaeelgaskkyisdleellkklkergiyviaRivvfkDkvla 90
                                   +Gn++  ++l ++++++  k++i dl+ ll+k  + g y  aRi ++kD+++ 
  gi|70605958|ref|YP_254828.1| 25 KNGNIEEYTTLYRTNDINELKEAIADLAYLLSKQGKYGTYDFARIYMIKDQYIG 78
                                  5799987799999*************************************9876 PP

>> DUF5312  Family of unknown function (DUF5312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   2.4e-05      0.21     419     458 ..      22      63 ..       7      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 2.4e-05
                       DUF5312 419 eFykkenriefteaf..neleklkekiakleerlspeGeiGk 458
                                    ++k+ n  e+t+ +  n++++lke+ia+l+  ls +G +G 
  gi|70605958|ref|YP_254828.1|  22 YYRKNGNIEEYTTLYrtNDINELKEAIADLAYLLSKQGKYGT 63 
                                   467888999***976669***********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 861.72
//
Query:       gi|70605959|ref|YP_254829.1|  [L=84]
Description: hypothetical protein Saci_0111 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0057   16.6   0.2     0.0074   16.2   0.2    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   4.1e-07    0.0074      10      72 ..      22      77 ..      16      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-07
                                  HHHHHHTT-SEEEEE--HHHHHHHHHHHHCTSEEEEEEECCCCCCEEEEE-BSSS-SBSSSEE CS
                  Ribosomal_S8 10 irNaekakkeevevpasklkeeilkvLkeeGyikdfeveeekkkkikielkynkkkksvikkl 72
                                   +N ++  +e+v+    ++ +++ ++L+++Gy  +fe+       ++++ k n  k++ i+++
  gi|70605959|ref|YP_254829.1| 22 EKNVQSGYHEHVSSAIDEISKNVKDILRSQGYSGKFEI------FVEVYAKENG-KSRLIQTV 77
                                  5899999*******************************......7777777777.46666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 602.21
//
Query:       gi|70605960|ref|YP_254830.1|  [L=214]
Description: iron dependent repressor [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-28   96.5   1.6    1.3e-27   95.6   0.6    1.9  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    6.1e-12   45.6   0.1      2e-11   43.9   0.0    1.9  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    5.9e-08   32.6   0.3    1.1e-07   31.7   0.3    1.5  1  HTH_45          Winged helix-turn-helix
    1.4e-06   28.1   0.0    2.5e-06   27.3   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    5.9e-06   26.1   0.0    1.5e-05   24.8   0.0    1.7  1  MarR            MarR family
    6.4e-06   26.3   0.5    1.7e-05   25.0   0.2    1.8  2  FeoA            FeoA domain
    2.3e-05   24.0   0.1    6.4e-05   22.6   0.1    1.8  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    3.5e-05   24.2   0.1    7.3e-05   23.2   0.1    1.5  1  HTH_27          Winged helix DNA-binding domain
    3.6e-05   23.2   0.1    0.00014   21.4   0.0    2.1  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0001   22.0   0.1    0.00022   21.0   0.1    1.5  1  DUF4423         Domain of unknown function (DUF4423)
    0.00012   21.9   0.0    0.00026   20.8   0.0    1.5  1  MarR_2          MarR family
    0.00021   20.9   0.0    0.00058   19.5   0.0    1.8  1  HTH_41          Helix-turn-helix domain
    0.00046   20.0   0.0    0.00098   19.0   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0018   18.3   0.0     0.0044   17.1   0.0    1.7  1  HemN_C          HemN C-terminal domain
     0.0031   17.5   0.1     0.0072   16.3   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0031   17.6   0.1      0.014   15.6   0.1    1.9  1  HTH_34          Winged helix DNA-binding domain
     0.0034   17.3   0.1      0.012   15.5   0.1    2.0  1  HTH_1           Bacterial regulatory helix-turn-helix protein
     0.0035   17.0   0.0       0.03   14.0   0.0    2.6  3  GntR            Bacterial regulatory proteins, gntR family
     0.0037   17.2   0.0     0.0066   16.4   0.0    1.4  1  HTH_36          Helix-turn-helix domain
     0.0038   17.3   0.0     0.0083   16.2   0.0    1.5  1  HTH_28          Helix-turn-helix domain
     0.0052   17.3   0.1     0.0096   16.4   0.1    1.5  1  AAA_assoc_C     C-terminal AAA-associated domain
     0.0077   16.6   0.0      0.032   14.6   0.0    2.0  1  Rrf2            Transcriptional regulator
     0.0084   16.1   0.1      0.075   13.0   0.0    2.5  2  PadR            Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.017   14.8   0.0    1.3  1  Ribosomal_S19e  Ribosomal protein S19e
      0.032   14.1   0.1       0.12   12.2   0.1    2.0  1  HxlR            HxlR-like helix-turn-helix
      0.033   14.0   0.0      0.093   12.5   0.0    1.8  1  HTH_IclR        IclR helix-turn-helix domain
      0.047   13.4   0.0       0.11   12.3   0.0    1.6  1  DUF4364         Domain of unknown function (DUF4364)
      0.052   13.6   0.2      0.098   12.8   0.2    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.053   13.5   0.6       0.24   11.4   0.1    2.3  2  HTH_11          HTH domain
      0.081   11.9   0.0       0.13   11.3   0.0    1.2  1  Topoisom_bac    DNA topoisomerase
      0.084   13.0   0.7       0.18   11.9   0.0    1.9  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.12   12.2   0.6         16    5.4   0.0    2.4  2  CvfB_WH         CvfB-like winged helix domain
       0.17   11.9   1.8         12    6.1   0.0    2.7  2  HisKA           His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.7   2.6e+03      18      33 ..       8      23 ..       5      31 .. 0.77
   2 !   95.6   0.6   2.5e-30   1.3e-27       1      69 [.      64     132 ..      64     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.7
                                  HHHHHHHHCT--CCCH CS
                 Fe_dep_repr_C 18 lerfLvdvlgvdweea 33
                                  le++L++++++++ + 
  gi|70605960|ref|YP_254830.1|  8 LENYLKEIYELEEMKG 23
                                  7999999998877555 PP

  == domain 2  score: 95.6 bits;  conditional E-value: 2.5e-30
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                   Te+Gr++A+rl++ hrl er+L+d+lg+dw +ahe A+rlEh+ +e++ie++d +l++p++cPhg+pip
  gi|70605960|ref|YP_254830.1|  64 TEEGRKIAERLIKSHRLSERLLTDILGIDWIRAHELAHRLEHIWPEDIIEKIDVMLNKPSTCPHGHPIP 132
                                   9*******************************************************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   3.6e-14     2e-11       2      56 ..       4      58 ..       3      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 3.6e-14
                                  --HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress  2 LvestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                  L+e  E+YL+ IY+l+e k+ ++++d+    n+sp ++s+ l+kLek G+++   
  gi|70605960|ref|YP_254830.1|  4 LSEPLENYLKEIYELEEMKGHARVTDIINDFNISPGTISKALSKLEKLGLIKRDN 58
                                  89999*********************************************98665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.3   2.1e-10   1.1e-07      12      75 ..      18      80 ..      10      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.1e-10
                        HTH_45 12 LeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                  Le + +g+a+ T i+ + n+s  +++k L++L + glik +++  +lTe+G+++ e+l + ++l
  gi|70605960|ref|YP_254830.1| 18 LEEM-KGHARVTDIINDFNISPGTISKALSKLEKLGLIKRDNKRLTLTEEGRKIAERLIKSHRL 80
                                  5666.99************************************************999877765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.5e-09   2.5e-06       9      46 ..      16      55 ..      12      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.5e-09
                                  HHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  9 klLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  + L+e  g + v+++ +++++s++t+S  L+kL+++GL++
  gi|70605960|ref|YP_254830.1| 16 YELEEmkGHARVTDIINDFNISPGTISKALSKLEKLGLIK 55
                                  5566776999****************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.8e-08   1.5e-05      12      49 ..      18      56 ..       9      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.8e-08
                                  HHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR 12 lyeqgp.lsvseLakklgvskstvtrvldrLekkGlieR 49
                                  l+e+ + ++v+++ + +++s++t++++l +Lek Gli+R
  gi|70605960|ref|YP_254830.1| 18 LEEMKGhARVTDIINDFNISPGTISKALSKLEKLGLIKR 56
                                  44444447899***************************9 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.3     4e+03      23      34 ..      43      54 ..      18      71 .. 0.62
   2 !   25.0   0.2   3.1e-08   1.7e-05       2      74 .]     142     212 ..     141     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.3
                                  SHHHHHHHHT-- CS
                          FeoA 23 ellrrLremGlv 34
                                  + l +L+++Gl 
  gi|70605960|ref|YP_254830.1| 43 KALSKLEKLGLI 54
                                  345666666664 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.1e-08
                                   EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEE.E-HHHHTTEEEEE CS
                          FeoA   2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrva.LgreeAqaIlVea 74 
                                    L++++ G+ ++i+ i +e++ +l+   + ++ pG++iev+ +   ++ + v+++d  ++ ++  +A +IlVe+
  gi|70605960|ref|YP_254830.1| 142 LLTEAEVGKLYKISMIVKEEEWILAMVNQKHIIPGTKIEVLGKD--QNITKVKINDR-IDeIPNVLATQILVER 212
                                   5999*************************************644..57999***985.999***********96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.2e-07   6.4e-05       3      46 ..      13      56 ..      12      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.2e-07
                      HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  ++i el + +g+ +v+++++ +++S+ Ti + L++Le+ gl++R
  gi|70605960|ref|YP_254830.1| 13 KEIYELEEMKGHARVTDIINDFNISPGTISKALSKLEKLGLIKR 56
                                  5777888889********************************99 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   1.3e-07   7.3e-05      14      68 .]      20      67 ..      11      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-07
                        HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  ++ + ++ +d++   n++  +is++l+kL++ GL+  ++d      kr++lT++G
  gi|70605960|ref|YP_254830.1| 20 EMKGHARVTDIINDFNISPGTISKALSKLEKLGLI--KRDN-----KRLTLTEEG 67
                                  77888999***************************..6666.....99*****99 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.5e-07   0.00014      14      48 .]      20      55 ..      12      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-07
                        HTH_24 14 k.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  + +++   +++    ++Sp+t+++ l +Le+ GlIk
  gi|70605960|ref|YP_254830.1| 20 EmKGHARVTDIINDFNISPGTISKALSKLEKLGLIK 55
                                  45677788999999*********************8 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1     4e-07   0.00022      26      84 ..      15      69 ..       6      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4e-07
                       DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt 84
                                  i+el ++k   a +  + + ++  is   ++kal+ L+klgl+k+d++ ++  te+  +
  gi|70605960|ref|YP_254830.1| 15 IYELEEMKGH-ARVTDIINDFN--ISPGTISKALSKLEKLGLIKRDNK-RLTLTEEGRK 69
                                  6676666666.***********..***********************8.9888887655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.7e-07   0.00026      14      53 ..      18      56 ..      14      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.7e-07
                                  HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  L    g   +v+++   +++s++++s++l +L++ GL+ r
  gi|70605960|ref|YP_254830.1| 18 LEEMKGH-ARVTDIINDFNISPGTISKALSKLEKLGLIKR 56
                                  5556664.59****************************87 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00058       8      37 ..      26      55 ..      24      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                        HTH_41  8 tIeelakeleLSvGlvQkALklLeddkais 37
                                  +++++++++ +S G++ kAL +Le+ + i+
  gi|70605960|ref|YP_254830.1| 26 RVTDIINDFNISPGTISKALSKLEKLGLIK 55
                                  799*********************999886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06   0.00098      20      58 ..      22      60 ..      15      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                  HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  +g a++++i ++ +++  ++ ++L++Le+ Gl++r  +r
  gi|70605960|ref|YP_254830.1| 22 KGHARVTDIINDFNISPGTISKALSKLEKLGLIKRDNKR 60
                                  7899******************************98776 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     8e-06    0.0044      39      65 ..      42      68 ..      32      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8e-06
                        HemN_C 39 aaaleklqeqGLLeldggrlrltprGr 65
                                   +al kl++ GL++ d++rl lt++Gr
  gi|70605960|ref|YP_254830.1| 42 SKALSKLEKLGLIKRDNKRLTLTEEGR 68
                                  567***********************8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.3e-05    0.0072      32      60 ..      35      64 ..      27      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                                  TSSHHHHHHHHHHHHHTTSEEE.TEEEEES CS
                     HTH_Crp_2 32 GltretvsrilseLkreglisr.grriril 60
                                  ++++ t+s++ls+L++ gli+r ++r++++
  gi|70605960|ref|YP_254830.1| 35 NISPGTISKALSKLEKLGLIKRdNKRLTLT 64
                                  78999****************635558776 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.5e-05     0.014      14      72 ..      24      74 ..      18      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-05
                        HTH_34 14 eadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkky 72
                                   a  +++ +  +++ g +s+ l+kLek g i++d           l++T+eGr+ +++ 
  gi|70605960|ref|YP_254830.1| 24 HARVTDIINDFNISPGTISKALSKLEKLGLIKRDN--------KRLTLTEEGRKIAERL 74
                                  57778889999********************8763........3477888888877765 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.3e-05     0.012      23      60 .]      34      68 ..      32      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                                  HTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHHH CS
                         HTH_1 23 LglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaGe 60
                                   ++s+ ++s+++++LE++    L+ R++++l+LTe+G+
  gi|70605960|ref|YP_254830.1| 34 FNISPGTISKALSKLEKL---GLIKRDNKRLTLTEEGR 68
                                  589*************86...6***************7 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   5.6e-05      0.03      29      60 ..      29      60 ..      26      63 .. 0.87
   2 ?   -1.7   0.0       4.4   2.4e+03      23      37 ..      79      92 ..      69     103 .. 0.71
   3 ?   -2.0   0.0       5.4   2.9e+03       9      24 ..     164     179 ..     161     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                          GntR 29 eLaaefgVsrttvReALrrLeaeglverrqgr 60
                                  ++   f++s  t+ +AL++Le  gl+ r ++r
  gi|70605960|ref|YP_254830.1| 29 DIINDFNISPGTISKALSKLEKLGLIKRDNKR 60
                                  67788*********************998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                                  B---HHHHHHHHTS- CS
                          GntR 23 kLPsereLaaefgVs 37
                                  +L ser L + +g++
  gi|70605960|ref|YP_254830.1| 79 RL-SERLLTDILGID 92
                                  56.666666666665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.4
                                   HHHHHHTTSS-TTSB- CS
                          GntR   9 LredIlsgelrpGdkL 24 
                                   + ++++++++ pG+k+
  gi|70605960|ref|YP_254830.1| 164 ILAMVNQKHIIPGTKI 179
                                   6678999999999998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0066      26      55 .]      25      54 ..      20      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                        HTH_36 26 psqetlakrlglsknTvsraikeLeqlGyi 55
                                  + + ++ +++++s  T+s+a+ +Le+lG+i
  gi|70605960|ref|YP_254830.1| 25 ARVTDIINDFNISPGTISKALSKLEKLGLI 54
                                  5678899999******************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05    0.0083      11      41 ..      22      53 ..      18      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                        HTH_28 11 aGh.svreaArelgisrrtvyrWikryeegGi 41
                                  +Gh +v+++ + ++is+ t+++ ++++e+ G+
  gi|70605960|ref|YP_254830.1| 22 KGHaRVTDIINDFNISPGTISKALSKLEKLGL 53
                                  6889*************************885 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.8e-05    0.0096      12      70 ..      39      95 ..      29     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-05
                   AAA_assoc_C 12 ddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaair 70
                                  + + +++  +e Lgl++ ++  ++lTe+Grk++e  ik  +  ++e+ll+ +  +++ir
  gi|70605960|ref|YP_254830.1| 39 GTISKALSKLEKLGLIKRDNKRLTLTEEGRKIAERLIKSHR--LSERLLTDILGIDWIR 95
                                  667889999*************************9998865..5666666666566555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.8e-05     0.032      21      56 ..      20      55 ..       5      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-05
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  e ++++++++i + +nisp  ++k l+kL+k gl+k
  gi|70605960|ref|YP_254830.1| 20 EMKGHARVTDIINDFNISPGTISKALSKLEKLGLIK 55
                                  34456899**************************98 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00014     0.075      19      54 ..      27      61 ..      22      73 .. 0.78
   2 ?   -0.9   0.0         3   1.6e+03      28      47 ..     145     164 ..     138     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                  HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S CS
                          PadR 19 leelsegllelseGslYpaLkrLekeglvesewees 54
                                  +++ ++  +++s+G++ +aL++Lek gl+++ +++ 
  gi|70605960|ref|YP_254830.1| 27 VTDIIND-FNISPGTISKALSKLEKLGLIKRDNKRL 61
                                  5566666.89********************998864 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3
                                   CTTHHHHHHHHHHHHHTTSE CS
                          PadR  28 elseGslYpaLkrLekeglv 47 
                                   e++ G+lY++ +  ++e+++
  gi|70605960|ref|YP_254830.1| 145 EAEVGKLYKISMIVKEEEWI 164
                                   67789999998877777776 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.1e-05     0.017      92     132 ..      37      76 ..      11      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                                   HHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XX CS
                Ribosomal_S19e  92 sgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriae 132
                                   s   i k+l +Leklgl+k+++k   +lt++G+++ +r+++
  gi|70605960|ref|YP_254830.1|  37 SPGTISKALSKLEKLGLIKRDNK-RLTLTEEGRKIAERLIK 76 
                                   5567889***********87755.89*********999876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00023      0.12      15      77 ..      21      75 ..      14      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                                  TTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                          HxlR 15 lkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77
                                  +kg+ R +++ + + +is  ++++ L +Le+ gli+r+           +lte+Gr++++ l 
  gi|70605960|ref|YP_254830.1| 21 MKGHARVTDIINDF-NISPGTISKALSKLEKLGLIKRDNKR-------LTLTEEGRKIAERLI 75
                                  78***********9.**********************9754.......457777777776665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017     0.093      14      51 ..      20      57 ..      18      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                  TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  e  +  +++++ + + +++ t +  L+ L++lG++++d
  gi|70605960|ref|YP_254830.1| 20 EMKGHARVTDIINDFNISPGTISKALSKLEKLGLIKRD 57
                                  5566679*****************************98 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.11      35      74 ..      40      75 ..      26      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                       DUF4364 35 dlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                  ++++als+L++ gli+    ++++++++Te+G++++e + 
  gi|70605960|ref|YP_254830.1| 40 TISKALSKLEKLGLIK----RDNKRLTLTEEGRKIAERLI 75
                                  6789***********9....6899***********99775 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00018     0.098      28      59 ..      30      61 ..       3      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                       DUF2250 28 iakeleipleevrellkkLeelGLlervegkt 59
                                  i + ++i+   ++++l kLe+lGL++r +++ 
  gi|70605960|ref|YP_254830.1| 30 IINDFNISPGTISKALSKLEKLGLIKRDNKRL 61
                                  67788999999****************98653 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00044      0.24       7      43 ..      16      52 ..      12      61 .. 0.83
   2 ?   -1.4   0.1       4.2   2.3e+03       4      23 ..      69      87 ..      67      91 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                        HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                    L e +g+    ++   +n+S  t+ + + +Le+lg
  gi|70605960|ref|YP_254830.1| 16 YELEEMKGHARVTDIINDFNISPGTISKALSKLEKLG 52
                                  556666777888899999******************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                        HTH_11  4 qilelLleargpisgeeLAe 23
                                  +i e+L++++  +s   L +
  gi|70605960|ref|YP_254830.1| 69 KIAERLIKSHR-LSERLLTD 87
                                  66677777665.55555555 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.13     343     391 ..      38      86 ..      27      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                  Topoisom_bac 343 paTraeiieklvergYverkkkslvptelGkalvellekfkdlvspelT 391
                                   p T+++ ++kl + g ++r++k+l  te G++++e l k ++l +  lT
  gi|70605960|ref|YP_254830.1|  38 PGTISKALSKLEKLGLIKRDNKRLTLTEEGRKIAERLIKSHRLSERLLT 86 
                                   7899***************99**************99555777766665 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00034      0.18      22      52 ..      28      58 ..      22      78 .. 0.92
   2 ?   -1.4   0.1       4.9   2.6e+03      40      53 ..     180     193 ..     148     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqs 52
                                  +d+++ ++++p  + + l +Lek gLI++ +
  gi|70605960|ref|YP_254830.1| 28 TDIINDFNISPGTISKALSKLEKLGLIKRDN 58
                                  6899***********************9965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                B-block_TFIIIC  40 ksLekkgLIvkqsi 53 
                                    +L k + I+k++i
  gi|70605960|ref|YP_254830.1| 180 EVLGKDQNITKVKI 193
                                   44555555666666 PP

>> CvfB_WH  CvfB-like winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.042        23      23      58 .]      28      63 ..       8      63 .. 0.86
   2 ?    5.4   0.0     0.029        16      40      56 ..     148     164 ..     146     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.042
                       CvfB_WH 23 eeIkavfgmSKkaFKrAvGaLlkqgkIeieedgikL 58
                                   +I + f++S  +  +A+ +L k g+I+ ++++++L
  gi|70605960|ref|YP_254830.1| 28 TDIINDFNISPGTISKALSKLEKLGLIKRDNKRLTL 63
                                  578889999999999*************99999877 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.029
                       CvfB_WH  40 vGaLlkqgkIeieedgi 56 
                                   vG+L+k  +I  ee++i
  gi|70605960|ref|YP_254830.1| 148 VGKLYKISMIVKEEEWI 164
                                   8*************998 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.021        12      32      58 ..       3      34 ..       1      41 [. 0.90
   2 ?    4.4   0.6     0.073        40      31      65 ..      61      95 ..      44     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                                  T-HSSCHHHHHHHHHHHH.....HHHHHHHHH CS
                         HisKA 32 klteelkeyletiesear.....rldhlvedl 58
                                  +l+e l+ yl+ i + ++     r++++++d+
  gi|70605960|ref|YP_254830.1|  3 ELSEPLENYLKEIYELEEmkghaRVTDIINDF 34
                                  488999*********9999************8 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.073
                                  .T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
                         HisKA 31 gklteelkeyletiesearrldhlvedlLdlsrie 65
                                    ltee ++  e+++++ r  ++l+ d+L + +i 
  gi|70605960|ref|YP_254830.1| 61 LTLTEEGRKIAERLIKSHRLSERLLTDILGIDWIR 95
                                  5789************************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1564.03
//
Query:       gi|70605961|ref|YP_254831.1|  [L=393]
Description: MOFRL family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-48  165.0   0.0    2.8e-48  164.5   0.0    1.1  1  DUF4147   Domain of unknown function (DUF4147)
    3.1e-22   78.8   0.2    5.8e-22   78.0   0.2    1.5  1  MOFRL     MOFRL family


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.0   3.1e-52   2.8e-48       5     217 ..       5     216 ..       2     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 3.1e-52
                                   HHHHHHHTTSHHHHHHTTHHHH--...........-SEEEEEESTTHHHHHHHHH..HHHGEEEEEEETT-----TT-EEE CS
                       DUF4147   5 ifeaaveavdpeklvkralslkeeeldls....kkkrvvvvgaGKAaaamaaalee.ealksgvvvvkkghaeekerievl 80 
                                   i+++ +   d + +++r+++++ ++++++    ++++ +++++GK + +ma+ + e  ++++g++v +++  ++ +++ev+
  gi|70605961|ref|YP_254831.1|   5 IVKTILSYSDSYLALSRKVEVNGNKIRINgvdyEFQNPLLISIGKSSPKMAKFFVErLKVSRGLIVSPYQ--AKVDSLEVI 83 
                                   67777777888888999998877777777888889****************7776324456******966..78899**** PP

                                   EE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHHHHHHTTBS CS
                       DUF4147  81 eaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelNtVRkhlsa 161
                                    ++hp  +e+s+ a ++i+++++  ++ d+v++l+SGG+SAl+++    + le +++++++L++sG+sI+e+NtVRkhls+
  gi|70605961|ref|YP_254831.1|  84 VSSHPKITEKSLYAGSRIVDMLR-REDYDIVIFLLSGGASALVEYSD--VPLEVLKEINDKLVTSGLSIDEINTVRKHLSK 161
                                   ***********************.5889****************997..******************************** PP

                                   STTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT-- CS
                       DUF4147 162 ikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykle 217
                                   ikGG La++ ++  +vsLi+SDV+  d+++++SGPt+ d++++ da +il+k++l+
  gi|70605961|ref|YP_254831.1| 162 IKGGWLAKYSKA-PIVSLIISDVPSSDISFVGSGPTILDKTSVIDAERILAKIGLS 216
                                   *******99875.***************************************9997 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.2   6.5e-26   5.8e-22       2     109 .]     288     385 ..     287     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 6.5e-26
                                   EEEEEE--B----S-.----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HHHH CS
                         MOFRL   2 vllsgGEttvtvkgk.GkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldakea 81 
                                   v+l+gGE+ v++++k GkGGrn e++l +++ ++     +++ l++++tDGiDG+++ aG++vd+++         +++ +
  gi|70605961|ref|YP_254831.1| 288 VILAGGEPDVKITSKaGKGGRNGEVCLGFLKYIR-----ANAKLYAVATDGIDGNSEYAGCYVDHNVKI------ENIDYY 357
                                   79**********8767***************444.....56889********************99863......36899* PP

                                   HHTT-HHHHHHHTT-EE-----S----E CS
                         MOFRL  82 LanndsyeffeklgallktgpTgtNVnD 109
                                   ++++ sye++ek+g++++tg Tg NVn+
  gi|70605961|ref|YP_254831.1| 358 VESHSSYEILEKTGNVIQTGFTGDNVNN 385
                                   **************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2661.44
//
Query:       gi|70605962|ref|YP_254832.1|  [L=253]
Description: sulfate transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-13   49.3  14.9    4.5e-13   49.3  14.9    2.2  2  BPD_transp_1   Binding-protein-dependent transport system inn


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   6.7      0.18   3.2e+03      33      72 ..       5      51 ..       1      55 [. 0.62
   2 !   49.3  14.9   2.5e-17   4.5e-13       7     178 ..      60     245 ..      51     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.18
                  BPD_transp_1 33 fvlaillvlvf.......vilsilghlilpviillllsaapyvrlir 72
                                  ++++++l+l+f       v ++++  + l+ i+l+++s+   ++li+
  gi|70605962|ref|YP_254832.1|  5 LLVIPVLFLLFygygpyfVGSTAFSRALLSSIALSFFSSSVATVLII 51
                                  34455555555555666777777777777777777777776666654 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 2.5e-17
                  BPD_transp_1   7 laalnrnkkldkllrpliivllslPsfvlaillvlvf...........vilsilghlilpviillllsaapyvrlirraal 76 
                                   ++a    +  + l+  l++++ s+P+ +++i ++++            ++   ++++ l++i++l++++ap+ ++ ++++ 
  gi|70605962|ref|YP_254832.1|  60 YLA----RHRNPLIESLVDIPASIPHPIVGIAVIFMGsplnplgrfltSLGINIYYSYLGLILALVITSAPVYIRAMQNFY 136
                                   344....444668999******************999*********99666679999************************ PP

                  BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.......lgtllleailgydy 150
                                   +slp++++e++  l  s+  +f++v++P++   ii+  + a+++++ ++  +++++   +        g+   ++++   y
  gi|70605962|ref|YP_254832.1| 137 ESLPRSYEEFSWSLRYSEVSTFFRVIFPLSTGGIISAGLTAIARAISEFGSVSIVA---PflsgwifNGDSPASVYI---Y 211
                                   *******************************************************9...333234444444444444...4 PP

                  BPD_transp_1 151 seis......nggvlalviavlllnlvadilqrl 178
                                   +e +      ++++++l+i+ lll+++++i+  +
  gi|70605962|ref|YP_254832.1| 212 NEYQtyfnaaITASATLIIFSLLLVFSTRIVKIV 245
                                   4444556886666666666666666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1582.40
//
Query:       gi|70605963|ref|YP_254833.1|  [L=102]
Description: hypothetical protein Saci_0116 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 751.81
//
Query:       gi|70605964|ref|YP_254834.1|  [L=230]
Description: triosephosphate isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-14   51.7   0.2    3.5e-13   49.5   0.0    2.0  2  TIM           Triosephosphate isomerase
    1.8e-06   27.5   0.5    2.9e-06   26.8   0.5    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
      7e-06   25.4   0.1    1.4e-05   24.5   0.1    1.4  1  Glu_synthase  Conserved region in glutamate synthase
    2.7e-05   23.4   0.1      4e-05   22.8   0.1    1.2  1  FMN_dh        FMN-dependent dehydrogenase
    0.00014   21.4   0.6      0.003   17.1   0.2    2.1  2  His_biosynth  Histidine biosynthesis protein
    0.00041   19.3   0.4    0.00082   18.3   0.4    1.4  1  Trp_syntA     Tryptophan synthase alpha chain
     0.0033   16.9   0.3     0.0033   16.9   0.3    1.5  2  NMO           Nitronate monooxygenase
     0.0066   15.5   0.6      0.011   14.8   0.6    1.3  1  IMPDH         IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.033   13.4   0.5      0.058   12.6   0.1    1.6  2  DHO_dh        Dihydroorotate dehydrogenase
      0.038   13.2   0.0      0.079   12.1   0.0    1.5  1  DUF561        Protein of unknown function (DUF561)
      0.045   13.2   2.3      0.066   12.6   0.2    2.0  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   2.1e-16   3.5e-13       2     123 ..       5     121 ..       4     125 .. 0.84
   2 ?   -0.6   0.0      0.44   7.2e+02     163     188 ..     141     169 ..     135     175 .. 0.65

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.1e-16
                                   EEEEE-TBTS-H..HHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHH CS
                           TIM   2 liagNwKmnktl..eeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlk 80 
                                   +i  N+K + +   ++  e++kk+++  ke   e+++ +p++ +++++   ees+l++ aq v+  ++Ga TG +  em+k
  gi|70605964|ref|YP_254834.1|   5 VILINYKAYENSygKKSIEITKKIEKVSKEYGTEIIVSVPATMIHRIS---EESELTVFAQHVDSGEQGARTGAILPEMIK 82 
                                   68899**9986522556677888998888899***********99865...5678************************** PP

                                   HTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE CS
                           TIM  81 dlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCv 123
                                   d+g++  ++ HsErr  + E  e     ++++   +l+ ++Cv
  gi|70605964|ref|YP_254834.1|  83 DAGARGSLLNHSERRIRLDEMAE----SLERIRVLNLESVVCV 121
                                   *****************999755....4555666677777777 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.44
                                   --GGGSSSS...----HHHHHHHHHHHHH CS
                           TIM 163 ePvWAiGtg...ktatpeqaqevhaairk 188
                                   eP   iGtg   ++a+pe + +++++i+k
  gi|70605964|ref|YP_254834.1| 141 EPPELIGTGipvSKAKPEAITKAVEEIKK 169
                                   55556999822235566667777777765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.5   1.8e-09   2.9e-06     162     226 ..     159     224 ..     143     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.8e-09
                                   S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHH.HHHHHH CS
                          ThiG 162 lnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAraf.klavea 226
                                   + ++a++ i ++ +v ++  AGi + +d+ +a+elGad++  ++av +ak+p ++ + f k a++a
  gi|70605964|ref|YP_254834.1| 159 AITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEKVVEDFvKNAIKA 224
                                   4566788899999****************************************9998873567766 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   8.4e-09   1.4e-05     251     309 ..     148     207 ..     143     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.4e-09
                                   B---HHHHHHHH.HHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHH CS
                  Glu_synthase 251 aGlPlelalaev.dqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaalia 309
                                   +G+P+  a +e+  +++ e +  + v l a  g+ tg+dv+ka+ lGAd +g ++a + a
  gi|70605964|ref|YP_254834.1| 148 TGIPVSKAKPEAiTKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKA 207
                                   79*****999973567788899999*****************************999865 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.5e-08     4e-05     261     305 ..     160     206 ..     152     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                                   HHHHHHHH....SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHH CS
                        FMN_dh 261 Lpeiveavgg..rievlvDgGirrGsDvlkAlalGAdavllGRpfly 305
                                   + + ve++++  ++ +l+  Gi++G+Dv+kA+ lGAd+++ + +++ 
  gi|70605964|ref|YP_254834.1| 160 ITKAVEEIKKtkDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMK 206
                                   444555555444799999********************998877764 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.046        75     100     152 ..      16      62 ..       7      91 .. 0.69
   2 !   17.1   0.2   1.8e-06     0.003      54     110 ..     153     209 ..     144     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.046
                                   EESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHH CS
                  His_biosynth 100 iigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavel 152
                                   + g + ++  + i+++++++g  +i+v++ a      +i+   ee++l+++  
  gi|70605964|ref|YP_254834.1|  16 SYGKKSIEITKKIEKVSKEYGT-EIIVSVPAT-----MIHRISEESELTVFAQ 62 
                                   6677778888999*********.9****9954.....4555555555555544 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.8e-06
                                   HCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                  His_biosynth  54 akegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                   +k++ ea +++veei ++ ++ +  G GI + edv +++e+gad +  ++a++k +e
  gi|70605964|ref|YP_254834.1| 153 SKAKPEAITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKE 209
                                   5667788899***********************************999999887654 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4     5e-07   0.00082     180     235 ..     154     210 ..     147     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-07
                                   SSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC CS
                     Trp_syntA 180 navaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee 235
                                   +a  + + ++ve++kk+++v ++ G Gi t e+v +++  +adG+   Sa++k+ e 
  gi|70605964|ref|YP_254834.1| 154 KAKPEAITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIeLGADGIGAASAVMKAKEP 210
                                   56678899************************99888879*****999999987552 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.9   3.1e+03     100     119 ..      22      41 ..      11      66 .. 0.56
   2 !   16.9   0.3     2e-06    0.0033     178     242 ..     156     223 ..     131     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.9
                           NMO 100 vrfyrkvevvlde.kvevvsf 119
                                   ++  +k+e v++e ++e++ +
  gi|70605964|ref|YP_254834.1|  22 IEITKKIEKVSKEyGTEII-V 41 
                                   3456677777776444433.2 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2e-06
                           NMO 178 d.kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesd..akdahkkkll 242
                                   + +  ++ v+++++  d+ ++A  Gi ++++v  a+ lGA g+  +++ + +ke +  ++d +k++++
  gi|70605964|ref|YP_254834.1| 156 KpEAITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKEPEkvVEDFVKNAIK 223
                                   34677888999999999***********************************9864336777777665 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.6   6.5e-06     0.011     192     244 ..     156     209 ..     144     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                                   HHHHHHHHHHHHCTC.T-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTT CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 192 qltAvaevaeaakka.gvpviaDGGikysgdivkAlaaGadavmlGsllagteE 244
                                   +  A+++++e  kk+ +v ++a  Gi++ +d+ kA+ +Gad +   s +   +E
  gi|70605964|ref|YP_254834.1| 156 KPEAITKAVEEIKKTkDVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKAKE 209
                                   45689998886665538***********************98866666655555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   2.1e+03      80     134 ..      24      43 ..       6      66 .. 0.53
   2 ?   12.6   0.1   3.5e-05     0.058     221     279 ..     150     207 ..     133     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-S CS
                        DHO_dh  80 vlekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSs 134
                                   +++k++k+ ke+ +                                   e+ vS 
  gi|70605964|ref|YP_254834.1|  24 ITKKIEKVSKEYGT-----------------------------------EIIVSV 43 
                                   33333333333333...................................222333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.5e-05
                                   EEEGGGHHHHH.HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                        DHO_dh 221 lsGkalkdial.kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                   +   + k+ a+ k + e++k +k ++ +++  Gi++geD++  ie GA  +   +a++++
  gi|70605964|ref|YP_254834.1| 150 IPVSKAKPEAItKAVEEIKK-TK-DVYLLAGAGITTGEDVFKAIELGADGIGAASAVMKA 207
                                   66667788886245555555.44.6***********************999888888654 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.8e-05     0.079     177     229 ..     163     216 ..     151     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                        DUF561 177 styeiskkvslPvicasGlsd.vtvplalslgasGiGigsavsklndeeemval 229
                                   ++ ei k+ ++ +++ +G+++   v  a++lga GiG  sav k ++ e++v+ 
  gi|70605964|ref|YP_254834.1| 163 AVEEIKKTKDVYLLAGAGITTgEDVFKAIELGADGIGAASAVMKAKEPEKVVED 216
                                   566788888999999999986256788********************9999863 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.36   5.9e+02      66      92 ..      31      57 ..      22      64 .. 0.54
   2 ?   12.6   0.2   4.1e-05     0.066     124     167 ..     157     200 ..     152     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                  HHH.TT-SEEEES-HHHHHHHHHTT-- CS
                  G3P_antiterm 66 lkkeikvdGiistksslikkakklgll 92
                                  ++ke++ + i+s  +++i++  +++ l
  gi|70605964|ref|YP_254834.1| 31 VSKEYGTEIIVSVPATMIHRISEESEL 57
                                  444555555555555555555554444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.1e-05
                                   SGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                  G3P_antiterm 124 PglvpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                   P  + k ++eikk+ ++ ++aG  i+t edv +a++ Ga+++ +
  gi|70605964|ref|YP_254834.1| 157 PEAITKAVEEIKKTKDVYLLAGAGITTGEDVFKAIELGADGIGA 200
                                   88999***********************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1540.04
//
Query:       gi|70605965|ref|YP_254835.1|  [L=176]
Description: hypothetical protein Saci_0118 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-09   35.8   0.1    0.00066   19.5   0.0    2.4  2  DUF429    Protein of unknown function (DUF429)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.7e-08   0.00066       1      87 [.       5      77 ..       5     119 .. 0.80
   2 !   14.7   0.1   1.1e-06      0.02     174     201 ..     112     139 ..      79     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.7e-08
                        DUF429  1 GvDlagcrtgwaavaledgrlrlvdveae.eivaalaallaaaeeaavvaiDaPiglperetggRaaDraarkllarrgasvf 82
                                  G+Dla +r+ ++av+ e+    ++dv ++ ei++  +         +++aiD P++++   +g R+ Dr++    ++ g +v+
  gi|70605965|ref|YP_254835.1|  5 GIDLAVKRPSTIAVF-ENTLIYVSDVVTDgEILSGCSGS-------KIIAIDSPLSMS---KGFRKVDRLMI---KN-GFRVL 72
                                  9****9999999997.66677777776667999999999.......***********8...8*******994...44.88888 PP

                        DUF429 83 pvpar 87
                                  p++  
  gi|70605965|ref|YP_254835.1| 73 PPSWM 77
                                  77655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-06
                        DUF429 174 keklvaadDvlDAvacaltArraarGra 201
                                   k+ +++++D lDAv+cal+A+   +G+ 
  gi|70605965|ref|YP_254835.1| 112 KDVGAKKKDELDAVICALVAYFKDKGNI 139
                                   5678899*************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1409.34
//
Query:       gi|70605966|ref|YP_254836.1|  [L=523]
Description: hypothetical protein Saci_0119 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-25   89.9  41.3    1.4e-25   89.9  41.3    2.6  2  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9  41.3   7.6e-30   1.4e-25       2     376 ..       9     357 ..       6     358 .. 0.86
   2 ?   -4.7   7.5      0.42   7.6e+03     176     226 ..     397     447 ..     385     456 .. 0.65

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 7.6e-30
                                   HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHH CS
                Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksilll 82 
                                   +l +++a+++g+ ++r+++++i++++iaGll   +gl    +s + +++ls+l + l  F++G++ld+rel+  l +++++
  gi|70605966|ref|YP_254836.1|   9 TLTLVIATIFGVALSRFRISPIPAYLIAGLLGKSFGLD--YSS-DLFNFLSTLAINLVSFNVGISLDIRELKNILSKATII 86 
                                   5566667777778************************9..777.89*********************************** PP

                                   HHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHH CS
                Na_H_Exchanger  83 allgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavll 163
                                   a++ +++ + +i+++  +    g+p+ + +++ +i  +t++ +++++   +++++ +   l+l+++ l+D++++++l v+l
  gi|70605966|ref|YP_254836.1|  87 AITEYIVGFTIISIISLI---IGLPFYDTFILTIISVTTSTTITYKLI--QNKIDDKQSGLILAVLSLEDVITFIALGVIL 162
                                   ***********9997775...699************************..9****************************77 PP

                                   HHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHH CS
                Na_H_Exchanger 164 alakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgafla 244
                                   +         + +  +  +++ +++g+l+ + +       i+r++  ++e+ ++ +++ +l+ +ll++++++ + l+ fl+
  gi|70605966|ref|YP_254836.1| 163 SSN------SNIVEIIPTSLASLGLGYLVSRTI-------INRSINTSEESVIISSIASVLSFSLLGQIFDIPSTLANFLL 230
                                   654......233333333333333444444433.......445555589******************************** PP

                                   HHHHHHHHHHTT.HHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHH CS
                Na_H_Exchanger 245 Glvlseyefsnk.lseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslre 324
                                   Gl  s   +++k +s  l++++ ++ +++fF++ G  l+l++     s l +++ i ++++l+++l+  +  +l+g ++  
  gi|70605966|ref|YP_254836.1| 231 GLGASYALKDTKkVSRILSPLI-DFSLIFFFFSAGSYLNLSL-----SSLYVLVPISLIMTLVKYLSFSTSYWLTGSNFLV 305
                                   *****655555548888*****.9***************444.....4455555555555589****************** PP

                                   HHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHH CS
                Na_H_Exchanger 325 aliigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslk 376
                                   a+  g+ +++  ++ +++a+ + ++g++++ +y+l ++ v+++  +  ++++
  gi|70605966|ref|YP_254836.1| 306 AFRSGIYMTSLSELGIIVALNAFQQGIITSLVYNLSAFLVMMSSTITSITVP 357
                                   *****************************999***99999999998888875 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 0.42
                                   TSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHH CS
                Na_H_Exchanger 176 lllllliflvvavgglllglvigwllrlitrftdddrelevllvlllalla 226
                                   +  +l ++l+ ++ ++ +  ++ +l+++++ f+   + + vl+ +llall+
  gi|70605966|ref|YP_254836.1| 397 SNFILRFILIGLITIFSASYLLIFLVSFARFFIYIAPLISVLVPFLLALLV 447
                                   334444444444555555556666666666666777888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 3627.23
//
Query:       gi|70605967|ref|YP_254837.1|  [L=321]
Description: esterase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-13   49.6   0.0    9.6e-13   48.3   0.0    1.7  1  Esterase       Putative esterase
     0.0019   17.5   0.0     0.0027   17.0   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.012   14.8   0.1      0.016   14.4   0.1    1.2  1  DUF2920        Protein of unknown function (DUF2920)
      0.057   13.1   0.0      0.084   12.5   0.0    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
       0.13   11.8   0.0       0.18   11.3   0.0    1.2  1  Esterase_phd   Esterase PHB depolymerase
       0.15   11.9   0.0       0.26   11.0   0.0    1.3  1  Abhydrolase_2  Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   3.2e-16   9.6e-13      88     242 ..      99     307 ..      19     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.2e-16
                                   CCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC............... CS
                      Esterase  88 gpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps............... 153
                                    +    ye+f+  eL p+ +++++ +    +++G S GG+gA++l++k+p+  + +  +S+ ++                 
  gi|70605967|ref|YP_254837.1|  99 SSAVGLYEDFIVRELIPYFKEKYHAQNV--VLMGKSSGGYGAMVLGMKYPNIISGIVNHSGDAYFEyiyipmfpkvlkhlr 177
                                   4445579*****************9999..*********************997777777776666*************** PP

                                   .......................................................HCHHHCTTCCHHHCC-CCCCHCHHCH CS
                      Esterase 154 .......................................................namWgqeekeawqendpvllakelsa 179
                                                                                            +W     + w e+dpv  +++ ++
  gi|70605967|ref|YP_254837.1| 178 kfsspkewlkhfwersdrkrkdlldtltlvamsafyspqdtdillpfeletgeinYNIW-----NMWLEKDPVRIVDKMYD 253
                                   *********99999999999999999999999888777777777777777777755555.....57*************** PP

                                   TTSEEEE.EEEECTTBCCCHTSCHHHHHHHHHHHCCHHHHCCCCCCTT-SCCCC--SSHHHHHH CS
                      Esterase 180 slkalri.yldvGtseddlgeqlsveilevlarnrelkeqlaargvegedheydGghsweyWra 242
                                   +l++l+  y+dvG++++ ++            + r l+e+l++ +v+++++eydGgh    +r 
  gi|70605967|ref|YP_254837.1| 254 NLRNLKLlYIDVGNKDE-FK---------LDIGLRILHEKLNKHSVNHFYEEYDGGHFNMSFRY 307
                                   ****99549*******9.33.........33455677799999**************8887775 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.1e-07    0.0027      63     131 ..     111     181 ..      97     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                   Hydrolase_4  63 aafvekvkeehpelplfllGhSmGGliallyllrypdkvaglil.saPalkikaklk.appllklllkllg 131
                                   ++++  +ke+++ ++++l+G S GG+ a+ ++ +yp+ ++g++  s+ a+    +++ +p++lk l+k+ +
  gi|70605967|ref|YP_254837.1| 111 RELIPYFKEKYHAQNVVLMGKSSGGYGAMVLGMKYPNIISGIVNhSGDAYFEYIYIPmFPKVLKHLRKFSS 181
                                   5677889999***************************9999996244455555555667777776666554 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.5e-06     0.016     173     222 ..     120     166 ..      52     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
                       DUF2920 173 rfpkeadlpviliGgsyGGYlalLiaKiaPwyvdgvlDnssvakpllayi 222
                                   ++     ++v+l+G s GGY a ++    P ++ g+++ s+ a +++ yi
  gi|70605967|ref|YP_254837.1| 120 KY---HAQNVVLMGKSSGGYGAMVLGMKYPNIISGIVNHSGDAYFEYIYI 166
                                   22...2489****************9999*****************9998 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05     0.084      54     106 ..     105     157 ..      31     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                   HSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                 Abhydrolase_1  54 ygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                   y+++ v++ + ++++++  ++++l+G S GG  a+ +  +yp+ ++++v  ++
  gi|70605967|ref|YP_254837.1| 105 YEDFIVRELIPYFKEKYHAQNVVLMGKSSGGYGAMVLGMKYPNIISGIVNHSG 157
                                   4555588888899************************************9988 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     6e-05      0.18      93     133 ..     120     160 ..      68     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                  Esterase_phd  93 rvdaarvyvaGlsaGaaladllalhypdvfaavalhsGlal 133
                                   ++ a  v + G s+G+  a +l+++yp+  + +  hsG a+
  gi|70605967|ref|YP_254837.1| 120 KYHAQNVVLMGKSSGGYGAMVLGMKYPNIISGIVNHSGDAY 160
                                   567889999*****************************998 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.8e-05      0.26      98     140 ..     117     159 ..      95     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                                   HHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES--- CS
                 Abhydrolase_2  98 lkkgipssriiigGFSqGaalalylaltlpkklggivafsgal 140
                                   +k+   +++++++G S G+  a+ l++++p+ ++giv +sg +
  gi|70605967|ref|YP_254837.1| 117 FKEKYHAQNVVLMGKSSGGYGAMVLGMKYPNIISGIVNHSGDA 159
                                   5666899*********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2244.13
//
Query:       gi|70605968|ref|YP_254838.1|  [L=153]
Description: 7,8-dihydro-8-oxoguanine-triphosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-09   38.3   0.3    1.7e-09   37.8   0.2    1.3  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   9.6e-14   1.7e-09      17     105 ..      17     100 ..       7     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 9.6e-14
                                   EEEEEES.SSSTTTEE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEECS CS
                         NUDIX  17 vLlvrrs.kkpfpgWe.lPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfl.eeveg 94 
                                   +L +r + +   +g+    gGk+++ Etp+e++ REl EE+G+++   e +g      + ++ yg+e+++++v+l  e+eg
  gi|70605968|ref|YP_254838.1|  17 FLFIR-KlRGIGTGYInSAGGKLRDTETPRECVERELYEELGIRVLSSERVG------KIEFLYGQEKYLMHVYLvTEFEG 90 
                                   34444.3355666643389***********************9554445555......4457888899999****999999 PP

                                   GCSSTSTTTEE CS
                         NUDIX  95 elepndenevs 105
                                    ++   e+ + 
  gi|70605968|ref|YP_254838.1|  91 IPRAS-EEGIP 100
                                   98877.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1125.10
//
Query:       gi|70605969|ref|YP_254839.1|  [L=438]
Description: fumarate hydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   4.5e-102  341.6   0.0   5.7e-102  341.3   0.0    1.1  1  Lyase_1      Lyase
    3.6e-13   49.7   0.5    1.3e-12   47.9   0.1    2.3  3  FumaraseC_C  Fumarase C C-terminus
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.26   11.8   0.0    3.0  3  RuvA_C       RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.3   0.0  9.5e-106  5.7e-102       1     312 []       1     315 [.       1     315 [. 0.97

  Alignments for each domain:
  == domain 1  score: 341.3 bits;  conditional E-value: 9.5e-106
                                   CEEEEETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSS CS
                       Lyase_1   1 grftvkadklmgiftersrenfrlseedikalaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlkviqe 77 
                                   +++t++a+kl++++ +r+++++ +       ++++k a+a +n+ l     e+  aii+a+++v++ g++dd+++l+v+q+
  gi|70605969|ref|YP_254839.1|   1 MKYTDTAPKLFMNTGTRFPRRIIWA------MGLIKYACARVNMNLglldREIGRAIIQAAEQVMK-GDHDDKIILDVFQT 74 
                                   589****************999888......9**************99******************.************** PP

                                   SHHHHHHHHHHHHHHHHTT....HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EE CS
                       Lyase_1  78 gsgtavnmnlnevigellg....ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvk 154
                                   gsgt +nmn+nevi+e       ++v+pnd+v+ gqSsnD+vpT++r+a++++++e+L+pal++Li++l++ka+e+kd+vk
  gi|70605969|ref|YP_254839.1|  75 GSGTGLNMNINEVIAETASkianKHVHPNDHVNLGQSSNDTVPTGIRVAAAAEVEENLIPALTKLINTLDRKAEEYKDIVK 155
                                   ***************44444556********************************************************** PP

                                   EEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSH CS
                       Lyase_1 155 iGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapns 235
                                   +GrThl+dA Pvtlgqelsay++a+++d+e+++++  ++++el  ggtavgtg+n++p f+ +v++e+++ tgl++k +n+
  gi|70605969|ref|YP_254839.1| 156 AGRTHLRDALPVTLGQELSAYSDAFKHDLENIRQTV-EYVKELPIGGTAVGTGANSHPDFQIKVIDEINNETGLGFKPANK 235
                                   ************************************.99999999************************************ PP

                                   HHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSS..C-TTSTTTEBTHHHHHHHHHHHHHHH CS
                       Lyase_1 236 feavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesep..GSSiMPgKvNPvqlElltgvagrvvG 312
                                   f+a++  ++++ l+gal++ a++L+++++D+rl++sg+ +g++e++l+ +e+  GSSiMPgK+NPv++E+  +++++vvG
  gi|70605969|ref|YP_254839.1| 236 FRAMRLLTDLLTLSGALRTSAVNLYRLGQDIRLMFSGPmTGFNEIDLPSQEEiaGSSIMPGKTNPVTVEASLLISAQVVG 315
                                   ***************************************************999************************99 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   7.6e+03      12      21 ..      90      99 ..      90     104 .. 0.80
   2 ?   -3.4   0.0       2.3   1.4e+04       7      12 ..     336     341 ..     336     345 .. 0.80
   3 !   47.9   0.1   2.3e-16   1.3e-12       1      54 []     381     432 ..     381     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                                  HHHHHHHHHH CS
                   FumaraseC_C 12 ekAakIAkeA 21
                                  e+A+kIA++ 
  gi|70605969|ref|YP_254839.1| 90 ETASKIANKH 99
                                  689****985 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                                   HHHHHH CS
                   FumaraseC_C   7 phIGYe 12 
                                   p IGY 
  gi|70605969|ref|YP_254839.1| 336 PLIGYN 341
                                   78***7 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 2.3e-16
                                   GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH. CS
                   FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMtg 54 
                                   L+T  +p+IGY+kA++I k+  k g ++rea  elg+  +e++d++ld +k+t+
  gi|70605969|ref|YP_254839.1| 381 LITIVSPVIGYDKASEIGKKLAK-GLSIREALKELGY-NDEQIDKILDLKKLTK 432
                                   89******************776.************9.**************95 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.22   1.3e+03      11      28 ..      38      55 ..      38      65 .. 0.82
   2 ?   -2.1   0.0      0.91   5.4e+03      12      18 ..     227     233 ..     226     239 .. 0.87
   3 ?   11.8   0.0   4.4e-05      0.26       6      25 ..     407     426 ..     406     432 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                                  HHCTS-HHHHHHHHHHHH CS
                        RuvA_C 11 laLGYkekeaekAvakvl 28
                                  ++LG   +e+ +A+ +++
  gi|70605969|ref|YP_254839.1| 38 MNLGLLDREIGRAIIQAA 55
                                  6899999*****997775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.91
                                   HCTS-HH CS
                        RuvA_C  12 aLGYkek 18 
                                   +LG+k++
  gi|70605969|ref|YP_254839.1| 227 GLGFKPA 233
                                   8****96 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHCTS-HHHHHHHHH CS
                        RuvA_C   6 aveALlaLGYkekeaekAva 25 
                                   + eAL+ LGY+ ++++k+++
  gi|70605969|ref|YP_254839.1| 407 IREALKELGYNDEQIDKILD 426
                                   579**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3189.60
//
Query:       gi|70605970|ref|YP_254840.1|  [L=198]
Description: hypothetical protein Saci_0123 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-27   94.4   0.2      1e-26   94.2   0.2    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00021   20.9   0.0    0.00026   20.6   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.2   1.2e-30     1e-26       2     197 .]      10     176 ..       9     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 1.2e-30
                                   CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                   Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                   g+ ++nsyl+  +++ iLiD G+++++ ++      ++ +  +++a++ TH+H+DH+ g++ + ++++vp +++++++  l
  gi|70605970|ref|YP_254840.1|  10 GDYFTNSYLVIEEDDSILIDVGGDPSEILEY-----VRTNNINLKAILATHGHFDHVIGVPLIQRHFKVPFYMNRKDEIIL 85 
                                   56789************************96.....********************************************* PP

                                   HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC. CS
                   Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridlt 163
                                   +++ +                   ++++ +l +++   +   v ++ ++gh+ g+v++ +++ lftGD+l+++++gr dl 
  gi|70605970|ref|YP_254840.1|  86 RYDSRT----------------REINVDGDLKEGVINFGKILVKVIETPGHTLGSVSFMIEDNLFTGDTLFNENIGRYDL- 149
                                   *****4................35799*****************************************************. PP

                                   TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                   Lactamase_B 164 lrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                           ++d e + +sl++l +l++ + v+ gH
  gi|70605970|ref|YP_254840.1| 150 --------GGDREYLKKSLRRLMDLEDLLNVYpGH 176
                                   ........777777777788888888888555587 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.9e-08   0.00026      30      67 ..      47      82 ..      26     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.9e-08
                                  SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHH CS
                 Lactamase_B_2 30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvl 67
                                   ++a+l th+H+DH+ g++ +++ +  k+p+y +++  
  gi|70605970|ref|YP_254840.1| 47 NLKAILATHGHFDHVIGVPLIQR-HF-KVPFYMNRKDE 82
                                  689*******************9.44.38999776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1551.72
//
Query:       gi|70605971|ref|YP_254841.1|  [L=428]
Description: hypothetical protein Saci_0124 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-18   67.0   0.1    2.6e-18   66.4   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.5e-16   61.0   0.0      2e-16   60.6   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    2.3e-12   46.7   0.0    4.4e-12   45.8   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
      5e-11   42.9   0.2      8e-11   42.2   0.2    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
      0.099   11.2   2.4        1.6    7.3   2.4    2.7  2  Chitin_synth_2   Chitin synthase
        2.6    7.2   9.5       0.57    9.3   4.8    2.2  2  STE3             Pheromone A receptor


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   8.8e-22   2.6e-18       1     167 [.      53     208 ..      53     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 8.8e-22
                                   EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
               Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                   +v ip+yNe e+  +++++s+ ++     ++ +vv Dg     ++i e+      + ++ir+ee++Gk  al +g+r+ ++
  gi|70605971|ref|YP_254841.1|  53 TVLIPVYNEvEDIFRKVIKSVSSM----GLKFVVVGDGVDQPYRAITEQN-----GGIFIRLEERRGKRFALSEGMRYIDT 124
                                   699*********************....***********77778888888.....899*********************** PP

                                   SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEE CS
               Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaall 161
                                   +++l+lD+D+ +d+  le+++ ++ + ++++v +++++ + ++  +  + +  ++ +  +  r  s++g + + +g + l+
  gi|70605971|ref|YP_254841.1| 125 RLVLLLDSDTFIDKRSLERMLSYMAE-DVGGVSPSIRVWNNGKISYYYANF--YEIMSEIVNRATSYFGRTIILSGQCVLY 202
                                   **************************.*********************987..89************************** PP

                                   EEHHHH CS
               Glycos_transf_2 162 rreale 167
                                   + +a++
  gi|70605971|ref|YP_254841.1| 203 KTSAIR 208
                                   999886 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   6.8e-20     2e-16       3     229 ..      51     273 ..      49     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 6.8e-20
               Glyco_tranf_2_3   3 dlavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   d++vl+p++ne +   ++v+ s+++   + +++vvv d+ d+  ++  e+     ++  +  +   r  +++gk+ al+e+
  gi|70605971|ref|YP_254841.1|  51 DITVLIPVYNEVEdIFRKVIKSVSS---MGLKFVVVGDGVDQPYRAITEQ----NGG--IF-I---RLEERRGKRFALSEG 118
                                   589********77355568888888...89*************9998887....344..44.3...333468********* PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfl.lnrstlvsalgalefaerhl.rflaarralgvltln 161
                                   +r ++++lvll+D+Dt +++++l+r+l ++ +++vg v  + ++ +n++  +s ++a ++++     ++a+++ +++++l+
  gi|70605971|ref|YP_254841.1| 119 MRYIDTRLVLLLDSDTFIDKRSLERMLSYM-AEDVGGVSPSIRVwNNGK--ISYYYANFYEIMSEiVNRATSYFGRTIILS 196
                                   *****************************9.********6665516666..34445544444443144555566679**** PP

               Glyco_tranf_2_3 162 Gsgslirrevlkele.........gldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                   G ++l+ ++  +++           +  +  + dD +l+ ++ ++g++   + +a+ ++  p++l++++kq  Rw++
  gi|70605971|ref|YP_254841.1| 197 GQCVLYKTSAIRNYVmsndftsskIFNISLKISDDRDLTEYIIERGYKAIKAIDAIAYTKPPENLSQFVKQVVRWTR 273
                                   ******************887653233366777******************************************87 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.5e-15   4.4e-12      16     173 .]     109     273 ..     104     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.5e-15
               Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl...ntlagvlqa 93 
                                   + K ++l+ +++++ ++l++++Dsd+++++  Le++l ++++ +vg V+  +++ +  ++    ++ +    +++ +++++
  gi|70605971|ref|YP_254841.1| 109 RGKRFALSEGMRYIDTRLVLLLDSDTFIDKRSLERMLSYMAE-DVGGVSPSIRVWNNGKISYYYANFYEimsEIVNRATSY 188
                                   5588999**********************************7.9****999998888876665555554343777888888 PP

               Glyco_transf_21  94 klsglgfavGksmalrreaLeaiG........GfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslralla 166
                                    ++++ +  G++++++++a++ +          +  ++ ++ +D  l++++ ++G+k + + ++ia t+ p+   l+++++
  gi|70605971|ref|YP_254841.1| 189 -FGRTIILSGQCVLYKTSAIRNYVmsndftssKIFNISLKISDDRDLTEYIIERGYKAIKAIDAIAYTKPPE--NLSQFVK 266
                                   .9*******************9972221111145667889**************************998775..79***** PP

               Glyco_transf_21 167 RqlrWar 173
                                   +++rW r
  gi|70605971|ref|YP_254841.1| 267 QVVRWTR 273
                                   *****86 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.2   2.7e-14     8e-11       2     181 ..     127     318 ..     126     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.7e-14
               Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrs 82 
                                   +lllD+Dt ++  +l++ ++ +a+ +v+ v+  + v+n+++ ++  +a f+ ++     + ++++gr++ + G +++   s
  gi|70605971|ref|YP_254841.1| 127 VLLLDSDTFIDKRSLERMLSYMAE-DVGGVSPSIRVWNNGK-ISYYYANFYEIMSEIVNRATSYFGRTIILSGQCVLYKTS 205
                                   89********************98.8**********97644.445556666666666667899****************** PP

               Glyco_trans_2_3  83 alqevg.........gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillvr 154
                                   a++  +          ++  +  +s+D d+   + ++Gy+ + + +++ ++k p +l  +++Q  Rw++ +   +l++l +
  gi|70605971|ref|YP_254841.1| 206 AIRNYVmsndftsskIFN-ISLKISDDRDLTEYIIERGYKAIKAIDAIAYTKPPENLSQFVKQVVRWTRAN---YLFFLRS 282
                                   ***554444444445777.557*************************9**********************6...3333333 PP

               Glyco_trans_2_3 155 ll.........gylgsllwsalplhlallllfslla 181
                                   l+          y + ++ ++++  l+++ l +l +
  gi|70605971|ref|YP_254841.1| 283 LRdgslslrgnLYVFDIIYMNFLPILVIFSLIPLQY 318
                                   333333333435566666666555555555555555 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.062   1.9e+02      26      51 ..      51      76 ..      36      87 .. 0.83
   2 ?    7.3   2.4   0.00052       1.6     204     291 ..     126     209 ..     116     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.062
                Chitin_synth_2 26 fticlvtaysegeeglrttldslast 51
                                   + +l+++y e e+ +r+ + s++s+
  gi|70605971|ref|YP_254841.1| 51 DITVLIPVYNEVEDIFRKVIKSVSSM 76
                                  456899*****************987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00052
                Chitin_synth_2 204 ivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvfGsvtclPGcfsly 284
                                    vl++d+dt +   sl+r+++ +++d    g+    ++ n+ +  +   + +e  i  + +    s fG    l G   ly
  gi|70605971|ref|YP_254841.1| 126 LVLLLDSDTFIDKRSLERMLSYMAEDV--GGVSPSIRVWNNGKISYYYANFYE--IMSEIVNRATSYFGRTIILSGQCVLY 202
                                   699*********************995..688888998877665555556666..55566666689999999999999999 PP

                Chitin_synth_2 285 rikaakg 291
                                   +  a ++
  gi|70605971|ref|YP_254841.1| 203 KTSAIRN 209
                                   9877665 PP

>> STE3  Pheromone A receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.2   3.4e+03     181     224 ..     175     218 ..     170     248 .. 0.64
   2 ?    9.3   4.8   0.00019      0.57     104     178 ..     296     387 ..     289     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
                          STE3 181 kellsssnsglnksrflRLlalalliill.tlplsiyllvsnltq 224
                                    e++s+   ++ +s f R ++l+  ++l  t  +  y++ +++t+
  gi|70605971|ref|YP_254841.1| 175 YEIMSEI-VNRATSYFGRTIILSGQCVLYkTSAIRNYVMSNDFTS 218
                                   5555553.5566677777777776655541334444555555544 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                          STE3 104 iidlliclgiPllimalhyivqghRydIiediGCvp.................alyntwlalvlvliwpliislvaavyav 167
                                   ++d++ +  +P+l+++  +++q+ R+dI++ +  +                    +  ++ +vlv+i p ++s++  v   
  gi|70605971|ref|YP_254841.1| 296 VFDIIYMNFLPILVIFSLIPLQYPRFDIFNTLSASItslerldifqlilgipiRAHLPPFDFVLVFILPRVLSIIGGVTFL 376
                                   799999*************************998889**************88777888899******************* PP

                          STE3 168 ltlrafikrrk 178
                                   l++++++++++
  gi|70605971|ref|YP_254841.1| 377 LVMIKIMEKER 387
                                   ***99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2828.92
//
Query:       gi|70605972|ref|YP_254842.1|  [L=819]
Description: hypothetical protein Saci_0125 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-50  170.5  25.4    1.8e-28   99.5  10.9    2.2  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   6.5   7.6e-26   1.4e-21     124     302 ..     289     458 ..     276     483 .. 0.89
   2 !   99.5  10.9     1e-32   1.8e-28     146     322 ..     656     815 ..     634     819 .] 0.91

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 7.6e-26
                          MMPL 124 kvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvl 204
                                   +  vtG  +++ad + ++++dl++i +vt+++++++L ++ r+lv  +l+++++v++l +a++  l ++ +lg  ++  + 
  gi|70605972|ref|YP_254842.1| 289 NYTVTGHLPVYADSASTTESDLRVIDIVTILLVAILLSVLIRALVPIILLIISAVIGLEIAYTA-LYISTFLGYSIYYISG 368
                                   5679***********************************************************9.6677888********* PP

                          MMPL 205 gllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvl 285
                                        +++++ +DY +l++ Ry ee+ +g++    + +a++ + ++++++Gl + + +l+++++  p l+++G+a+ ++ l
  gi|70605972|ref|YP_254842.1| 369 LVIPPIVFGITIDYSVLFLYRYFEEVSKGSTF--PLDKAYRNARRAILFSGLSIGLGFLSFLISPSPLLKNIGIALVIASL 447
                                   ********************************..9************************************9999555444 PP

                          MMPL 286 vdvlivlTllPAllvll 302
                                    +      l+P++l + 
  gi|70605972|ref|YP_254842.1| 448 SA------LIPSILFMK 458
                                   33......445555544 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 1e-32
                          MMPL 146 klievvtlvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRy 226
                                    ++  vt+++i + L +v++S++ ++ + lt ++s l  ++l     ++ +  +++ ++ ++++++ + G+DY ++++ R+
  gi|70605972|ref|YP_254842.1| 656 SFVLPVTILIITLYLGLVLGSIIVPIRLSLTLLLSSLFGVAL----LHIIFGSVYWLSPLIVFAIMYSLGIDYDMFIIVRI 732
                                   456789******************************999888....6888889**************************** PP

                          MMPL 227 reelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraa 306
                                    ee +++e+r   + + v stg +vtaaGl++a+a+++Lvv+++++l+++G+a++l++l+d++iv+ +l PA++++l +  
  gi|70605972|ref|YP_254842.1| 733 LEEEGNEEER---IVKSVESTGLAVTAAGLILAGAFMSLVVSNMRFLQEIGLAVGLTILFDTFIVRPILvPAVMSILKKY- 809
                                   **********...******************************************************999*******999. PP

                          MMPL 307 lakprrkrkkrwWrrl 322
                                             +wW+++
  gi|70605972|ref|YP_254842.1| 810 ----------NWWPKT 815
                                   ..........666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (819 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 5962.53
//
Query:       gi|70605973|ref|YP_254843.1|  [L=738]
Description: hypothetical protein Saci_0127 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-48  163.2   0.0      8e-48  162.6   0.0    1.3  1  Helicase_RecD    Helicase
    4.3e-30  104.8   0.0    4.8e-21   75.2   0.0    2.4  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    8.1e-21   73.8   0.0    1.9e-20   72.6   0.0    1.6  1  DUF1726          Domain of unknown function (DUF1726)
    2.8e-06   27.5   0.0    8.3e-06   26.0   0.0    1.9  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      6e-06   26.6   0.2      4e-05   24.0   0.0    2.5  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00024   20.9   0.0     0.0011   18.7   0.0    2.1  2  AAA_30           AAA domain
     0.0016   18.3   0.0     0.0038   17.2   0.0    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0036   17.6   0.2      0.086   13.1   0.0    2.9  2  AAA_22           AAA domain
     0.0037   17.0   0.0      0.007   16.1   0.0    1.4  1  tRNA_bind_2      Possible tRNA binding domain
  ------ inclusion threshold ------
      0.063   13.2   0.0       0.18   11.8   0.0    1.7  1  FR47             FR47-like protein
       0.13   12.4   0.0       0.99    9.6   0.0    2.3  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   4.9e-51     8e-48       1     177 []     225     400 ..     225     400 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 4.9e-51
                 Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke.eekkkkaekaelrvrkqrieyi 79 
                                   ++tA RGRGKS+ +Gl+l++l   +   +i++t+ps+ +  ++++fl+kgl++lg ++  +++++++ + + +   r++++
  gi|70605973|ref|YP_254843.1| 225 TITAPRGRGKSSSIGLFLSHLSTLNIsLDIIITSPSYYSSIEIISFLIKGLDQLGKRYsITRSRDGKVMGIMSGALRVKWL 305
                                   59*******************9998889***************************9996678888999999999******* PP

                 Helicase_RecD  80 apdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelreleleepiRy 160
                                   apd +++++   d++vvDEAA+i +++l+ +++++++v+l tT+hGYEGtG++f lk+l+ l+++k+ ++++++le+piRy
  gi|70605973|ref|YP_254843.1| 306 APDVAKDYQ--GDIIVVDEAASIGTETLDYIVRSWEKVILVTTIHGYEGTGKAF-LKYLNGLREDKSIKFKHVTLEKPIRY 383
                                   ******987..5******************************************.************************** PP

                 Helicase_RecD 161 aegdplEkwlndlLlLd 177
                                   a+gdp+E++++d++lLd
  gi|70605973|ref|YP_254843.1| 384 AKGDPIERFIYDVMLLD 400
                                   ***************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   2.9e-24   4.8e-21       2     121 ..     430     537 ..     429     542 .. 0.94
   2 !   27.6   0.0   1.1e-09   1.8e-06     176     227 .]     541     592 ..     536     592 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 2.9e-24
               GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipwtls 82 
                                   + ++lvs+HY+nsP+DL++l D    ++f L +           ++v qv  EG+++k ++++ l+++   +G lip++l+
  gi|70605973|ref|YP_254843.1| 430 VYGILVSAHYRNSPDDLMILGDHHFQRIFSLGK-----------IAVAQVIEEGALEKGEIDRILNGS-GLEGHLIPYKLT 498
                                   6789*******************9999999988...........89***************9988866.89********** PP

               GNAT_acetyltr_2  83 qqfqdeefaslsGaRivRiAvhpelqkmGYGsralelle 121
                                      + +ef++++G Ri+RiAv+p++q++G+Gs+ l+ + 
  gi|70605973|ref|YP_254843.1| 499 LYERLQEFGKYKGWRIMRIAVQPDVQNKGFGSKLLRSVV 537
                                   **********************************98875 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.1e-09
               GNAT_acetyltr_2 176 kpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsle 227
                                   k e +d++g+sf    + ++FW ++gf+pv+l++ +ne    +s+++l++l+
  gi|70605973|ref|YP_254843.1| 541 KREGIDWIGASFVADYRVVNFWLNNGFTPVHLSNRKNEGLNGYSIVVLKALN 592
                                   6789********************************************9875 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   1.1e-23   1.9e-20       1      91 [.      79     162 ..      79     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.1e-23
                       DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplteevkkrfnkrfir 81 
                                   y++  k+LG tyd+++ldl+++++Pn++ +lv++VrGGGlii++ ++l+++k ++++++++ +v+++       f++rf+r
  gi|70605973|ref|YP_254843.1|  79 YSNYGKILGGTYDVVILDLMDDFRPNYISALVDLVRGGGLIIMYSDDLQRNKLYKNSIQRNGIVDNY-------FEERFLR 152
                                   778889*********************************************************9988.......******* PP

                       DUF1726  82 klkehegili 91 
                                     k+++g+++
  gi|70605973|ref|YP_254843.1| 153 MAKSYPGVFL 162
                                   **99999886 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.1e-09   8.3e-06      56      97 ..     507     548 ..     473     567 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.1e-09
                                   TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                Acetyltransf_1  56 ekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                    k++ + i ++aV p+ ++kG Gs+Ll+ ++er ++egi+ i
  gi|70605973|ref|YP_254843.1| 507 GKYKGWRIMRIAVQPDVQNKGFGSKLLRSVVERGKREGIDWI 548
                                   57888999*****************************99765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.7   2.8e+03      32      38 ..     309     315 ..     286     381 .. 0.60
   2 !   24.0   0.0   2.4e-08     4e-05      25      75 ..     512     568 ..     468     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.7
                                   E-GGGTT CS
                Acetyltransf_7  32 Vdpeyrg 38 
                                   V+++y+g
  gi|70605973|ref|YP_254843.1| 309 VAKDYQG 315
                                   5555554 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.4e-08
                                   TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEEEE.EEEETHHHHHHHHHHTTEE CS
                Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLlea.ae....kgiile.qlelnaekaikfYeklGFe 75 
                                     i r+aV p+ ++kG G++Ll+  +e    +gi  +  + +++ + ++f+  +GF+
  gi|70605973|ref|YP_254843.1| 512 WRIMRIAVQPDVQNKGFGSKLLRSvVErgkrEGIDWIgASFVADYRVVNFWLNNGFT 568
                                   34567******************43232344564422344444447899*******7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.8e-07    0.0011       3     114 ..     203     340 ..     201     349 .. 0.73
   2 ?   -0.8   0.0      0.65   1.1e+03      20      34 ..     344     358 ..     342     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.8e-07
                        AAA_30   3 naeQaaavea...lltsgdrvavltGpAGtGKttalkalreaweaag.............grviglAptgkaAkvLaeelg 67 
                                   +++Qa+++++   +l++g+rv ++t+p G GK+ +++    ++ + +              ++ +++   k  ++L++   
  gi|70605973|ref|YP_254843.1| 203 TDDQAKVLDEslfILEDGRRVLTITAPRGRGKSSSIGLFLSHLSTLNisldiiitspsyySSIEIISFLIKGLDQLGKRYS 283
                                   5677777776444789***********************999998877755555555555555555555555555556666 PP

                        AAA_30  68 ieastiakllkrlk..........grarlepgtllivDEagmvdtkqlaallkaaek 114
                                   i+ s+  k++  +           + a+  +g++++vDEa+ ++t++l+ ++++ ek
  gi|70605973|ref|YP_254843.1| 284 ITRSRDGKVMGIMSgalrvkwlapDVAKDYQGDIIVVDEAASIGTETLDYIVRSWEK 340
                                   66666666665555777787888754455567*******************999877 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                        AAA_30  20 vavltGpAGtGKtta 34 
                                   v++++G+ GtGK ++
  gi|70605973|ref|YP_254843.1| 344 VTTIHGYEGTGKAFL 358
                                   7899********875 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-06    0.0038      51     117 ..     511     579 ..     504     585 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
               Acetyltransf_10  51 gshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGFkav.geeqeenG 117
                                   g++i +++V+p+ + +G g++Ll  v e+ +++gi     +  a+   v+f  + GF++v  ++++ +G
  gi|70605973|ref|YP_254843.1| 511 GWRIMRIAVQPDVQNKGFGSKLLRSVVERGKREGIDWiGASFVADYRVVNFWLNNGFTPVhLSNRKNEG 579
                                   56999*************************9**99999889999999**********999555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.3e-05     0.086       4     114 ..     220     336 ..     217     347 .. 0.75
   2 ?    1.1   0.1      0.26   4.3e+02       8      22 ..     345     359 ..     341     469 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelka.......... 70 
                                   ++++l++t++ G GK+ ++  +l+ l             +     +t ps  ss ++ + l + l++ +k+          
  gi|70605973|ref|YP_254843.1| 220 GRRVLTITAPRGRGKSSSIGLFLSHLS---------TLNIsldiIITSPSYYSSIEIISFLIKGLDQLGKRysitrsrdgk 291
                                   7899*********************94.........4444454577777777**************988889998875333 PP

                        AAA_22  71 .erlsseell.ealeqalrarav.....ielliiDEaqhlrseealeeLrs 114
                                           ++  al+  + a +v       ++++DEa  +   e l ++++
  gi|70605973|ref|YP_254843.1| 292 vM-----GIMsGALRVKWLAPDVakdyqGDIIVVDEAASI-GTETLDYIVR 336
                                   32.....3333555555555555666667***********.9999999844 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.26
                        AAA_22   8 lvvtGesGtGKTtll 22 
                                   ++++G  GtGK +l 
  gi|70605973|ref|YP_254843.1| 345 TTIHGYEGTGKAFLK 359
                                   789999999997763 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.3e-06     0.007      67     125 ..     653     708 ..     637     729 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.3e-06
                                   HHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHH CS
                   tRNA_bind_2  67 RLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddle 125
                                   ++esY + +l+Y+ + D +  +++ yF      +  L++ ++a+L+a  LQ ks  +++
  gi|70605973|ref|YP_254843.1| 653 KIESYLKGILEYNSVADGIHAVTQYYFLYP---DHFLEEREEAVLIARTLQGKSWHHIS 708
                                   68*************************864...569*****************998876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.18      24      56 ..     514     546 ..     505     557 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S- CS
                          FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergkt 56 
                                   +  + v+p+++++G+gs+l +++ ++  ++g++
  gi|70605973|ref|YP_254843.1| 514 IMRIAVQPDVQNKGFGSKLLRSVVERGKREGID 546
                                   77899*****************99887777765 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.99   1.6e+03       9      32 ..     352     377 ..     345     382 .. 0.75
   2 ?    9.6   0.0   0.00061      0.99      25      58 ..     512     545 ..     498     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.99
               Acetyltransf_CG   9 geevafleYe..vrkegvldfthTeV 32 
                                   g+ +afl+Y    r+++ ++f h+  
  gi|70605973|ref|YP_254843.1| 352 GTGKAFLKYLngLREDKSIKFKHVTL 377
                                   45579****6567888899**99865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
               Acetyltransf_CG  25 ldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                   + ++ + V++ ++ kG+++kL +++++  ++eg 
  gi|70605973|ref|YP_254843.1| 512 WRIMRIAVQPDVQNKGFGSKLLRSVVERGKREGI 545
                                   678999*********************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.39
# Mc/sec: 5610.56
//
Query:       gi|70605974|ref|YP_254844.1|  [L=326]
Description: hypothetical protein Saci_0128 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.5  12.2    1.6e-07   31.5  12.2    2.1  2  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
       0.19   11.7   0.0       0.31   11.0   0.0    1.3  1  PaREP1    Archaeal PaREP1/PaREP8 family
        2.1    8.3   9.9        1.1    9.2   0.6    2.3  2  Jagunal   Jagunal, ER re-organisation during oogenesis


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5  12.2   2.7e-11   1.6e-07       6     154 ..      15     159 ..       7     161 .. 0.64
   2 ?   -0.4   0.1      0.18   1.1e+03      52      72 ..     204     224 ..     176     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.7e-11
                        SpoIIM   6 lvgillgallaa.snfa..eqis...seskensalslflaifanNlrvalllf..llGllllgiptilvllinGfvlGava 78 
                                    ++i++g+ +   +n+a  ++++   s   +++ +s +++if +Nl +a + f  ++G     i++ + +  ++++l +va
  gi|70605974|ref|YP_254844.1|  15 ELAIFIGVSSIPyNNPAlvQEYNsmeSGIYSMPYFSQVIEIFSHNLLIATIDFipVVGA----IFFGISIGQTAYLLSVVA 91 
                                   33344444444463444553333455888899999999999999999977777333443....222333345555555553 PP

                        SpoIIM  79 alvaef....gglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakrellklllllvpllliAaliEafv 154
                                   +           l  ++ll lPh  +elp + ia+aag ++ ++ +         ++++l +  l+ + l++AaliE+ +
  gi|70605974|ref|YP_254844.1|  92 T----SrnvpSFLVAIALLTLPHSAVELPTYAIAVAAGTYVIVKRK--------DWKRYLLMYPLIPIELFLAALIESAI 159
                                   3....234457788999999*********************44442........444444455555559********865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.18
                        SpoIIM  52 fllGllllgiptilvllinGf 72 
                                   +l+G ++lg ++i++  +n f
  gi|70605974|ref|YP_254844.1| 204 VLAGTSALGSVPIYASYYNNF 224
                                   577888888888888877755 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.1e-05      0.31       6      51 ..     224     270 ..     219     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                        PaREP1   6 aekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlkll.ee 51 
                                    +  +++A ++  + d+++A + ++ Av  l+ a+a k n + + ++
  gi|70605974|ref|YP_254844.1| 224 FKNVMSQAIQYEVRSDFINAVNNYWLAVIFLIDAIATKMNMPYYtKQ 270
                                   5667889999999*************************888877443 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.9     0.012        71      84     180 ..      10     106 ..       8     112 .. 0.84
   2 ?    9.2   0.6   0.00019       1.1     103     176 ..     197     268 ..     131     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                       Jagunal  84 vwllSivpsllgllalkknkikllklyligtlvlgllpllygaveylkevleylkskeaseeitllqgfplvvlwyifvli 164
                                   ++++  +++++g+++++ n+  l++ y  +   +  +p +  ++e +++ l  ++ +      ++++g++++   y++ ++
  gi|70605974|ref|YP_254844.1|  10 IYFIIELAIFIGVSSIPYNNPALVQEYNSMESGIYSMPYFSQVIEIFSHNLLIATIDFIPVVGAIFFGISIGQTAYLLSVV 90 
                                   677778999******************999999999999999999998877777666666666899999999999999999 PP

                       Jagunal 165 alqvhlfslyfsakLl 180
                                   a   ++ s+ +++ Ll
  gi|70605974|ref|YP_254844.1|  91 ATSRNVPSFLVAIALL 106
                                   9888887777777776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                       Jagunal 103 kikllklyligtlvlgllpllygaveylkevleylkskeaseeitllqgfplvvlwyifvlialqvhlfslyfs 176
                                   k+++++ +l gt +lg +p+ ++  +++k+v++ + + e ++  ++++ +    l +if++ a+   +   y+ 
  gi|70605974|ref|YP_254844.1| 197 KTQNMQPVLAGTSALGSVPIYASYYNNFKNVMSQAIQYEVRS--DFINAVNNYWLAVIFLIDAIATKMNMPYYT 268
                                   67889999**********************998766666655..577777777888888887777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2472.33
//
Query:       gi|70605975|ref|YP_254845.1|  [L=241]
Description: exonuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-13   48.3   0.0    1.5e-12   47.5   0.0    1.4  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
    0.00013   21.8   0.0    0.00029   20.6   0.0    1.6  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.7e-16   1.5e-12       1     206 [.       4     214 ..       4     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.7e-16
                                   EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH..TTCEEEEECCHECSSSTTSSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal..ggflgasstsptgggggggnggavls 79 
                                   l+wNvng  + +l+    + +l+ ++  y  Dv++LQE++ +e   ipl  al   + +++ s+       +g+ g+ + s
  gi|70605975|ref|YP_254845.1|   4 LSWNVNGI-KAILR----KGALQPVINDY--DVIMLQEIRTNE---IPLDIALsgSNLFPFPSK------KKGYSGVLTIS 68 
                                   79*****7.77777....77788888666..*******99997...666666667777777666......5********** PP

                                   CSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE..CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos  80 rfpltslfrrtfiefndlvaalrreplaakleqlni..ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarps 158
                                   + ++ s++    i+ +d+  ++ +  l+     + +  + + d    +  ++ +l  +  +l +++ +pvi++GD+N++ +
  gi|70605975|ref|YP_254845.1|  69 KIKPLSVIKGLGINEFDEEGRVLTIELDDYFIINAYfpRAGDDLNRLDYKIKFDLEIEKFMLELRKRKPVILCGDLNVARD 149
                                   ****999888888888877777777777777777778999**************************************888 PP

                                   GGGBSCGHHHHHHCTTTH....H.............SSCESCETTTTTTTTTTTEB-BEEEEEEC CS
                                   xxxxxxxxxxxxxxxxxx....x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos 159 dddsrvlrtrglalapap....v.............glyllgggptptyvtraggsrlDrilasp 206
                                     ds ++++    l  +     +                +     + +y  ++  +r+D+ ++s+
  gi|70605975|ref|YP_254845.1| 150 KIDSTFWDEKEPGLTSEErgwiNkilstdfvdtyrfINGNKIEYSWRSYLEKWKAMRIDYCIVSS 214
                                   88888866554433333344440445555566677777777777777777777777778888876 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.3e-08   0.00029       2     119 .]      99     237 ..      98     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-08
               Exo_endo_phos_2   2 liisvYippsd.......elenlestlekllselksp.kiiilGDfNakhplWgsedtds..........sargeeL.ief 63 
                                    ii++Y p+            +++ ++ek++ el+++ ++i++GD+N+   + +s+  d+             ++ L ++f
  gi|70605975|ref|YP_254845.1|  99 FIINAYFPRAGddlnrldYKIKFDLEIEKFMLELRKRkPVILCGDLNVARDKIDSTFWDEkepgltseerGWINKILsTDF 179
                                   57777777766767665433356668999999998889*********9988877743333455675433222233344556 PP

               Exo_endo_phos_2  64 leehslsllnllksgptfkssng.....sstiDltltsdnlals.kleleeedlgSDHrpil 119
                                   ++++     n +k   +++ +++        iD +++s+++ ++ k+++  +  gSDH p++
  gi|70605975|ref|YP_254845.1| 180 VDTYRFI--NGNK--IEYSWRSYlekwkAMRIDYCIVSSEIKDRiKDSKIIKIEGSDHYPVY 237
                                   6666666..5544..3333333343665889**************999999999*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1794.95
//
Query:       gi|70605976|ref|YP_254846.1|  [L=86]
Description: hypothetical protein Saci_0130 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-15   54.6   0.5    8.5e-15   54.3   0.5    1.1  1  TusA          Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.063   13.5   0.0      0.087   13.0   0.0    1.2  1  PurS          Phosphoribosylformylglycinamidine (FGAM) syntha
       0.21   11.3   0.0       0.32   10.7   0.0    1.3  1  Sigma70_r4_2  Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.5   1.4e-18   8.5e-15       2      70 .]       4      71 ..       3      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.4e-18
                                  EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  ++D+++l CPeP++k+  +l  ++eg +++v++ dp ++  i + +k + ++++e ++++++++i+i+k
  gi|70605976|ref|YP_254846.1|  4 VIDATKLECPEPFMKTVAKLMGMKEG-TVKVMFKDPKCVDMIVEAVKLMDCNVLENTKQGDVFSITIQK 71
                                  79************************.777*************************************98 PP

>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.087      14      58 ..      37      82 ..      29      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                  -HHH.HHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHH CS
                          PurS 14 DpqG.kavkkalkslgyeevedvrvgkyieleleaedeeeaeeeve 58
                                  Dp+    + +a+k ++ +  e+ ++g ++++++++++  +  +e++
  gi|70605976|ref|YP_254846.1| 37 DPKCvDMIVEAVKLMDCNVLENTKQGDVFSITIQKTSSSKTPKEIK 82
                                  6665357999**************************9998888877 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.3e-05      0.32      31      45 ..      19      33 ..      17      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.3e-05
                                  HHHHHHT--HHHHHH CS
                  Sigma70_r4_2 31 EIAellgisegtVks 45
                                   +A+l+g++egtVk 
  gi|70605976|ref|YP_254846.1| 19 TVAKLMGMKEGTVKV 33
                                  58************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 594.19
//
Query:       gi|70605977|ref|YP_254847.1|  [L=357]
Description: hypothetical protein Saci_0131 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-10   41.0   1.4    1.7e-10   40.6   0.2    1.8  2  DUF1641         Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
      0.015   15.4   5.3        1.3    9.2   0.9    2.8  2  GED             Dynamin GTPase effector domain
      0.025   14.9   0.1         11    6.2   0.0    2.4  2  CDT1            DNA replication factor CDT1 like
      0.079   13.6  16.7       0.39   11.3   2.0    4.5  4  MgtE_N          MgtE intracellular N domain
       0.14   11.3   0.3       0.25   10.4   0.3    1.4  1  DUF1719         Domain of unknown function (DUF1719)
       0.16   12.1   3.0         15    5.8   0.0    4.5  5  DUF3847         Protein of unknown function (DUF3847)
       0.19   11.0   2.5       0.26   10.6   0.3    2.2  2  Cas_Csa4        CRISPR-associated protein (Cas_Csa4)
       0.23   11.9   3.6        2.9    8.4   0.4    2.5  2  Enkurin         Calmodulin-binding
        0.3   10.0   3.8        3.4    6.5   0.4    2.1  2  Myotub-related  Myotubularin-like phosphatase domain
        1.8    8.8   5.9         40    4.6   0.0    4.0  4  Pigment_DH      Pigment-dispersing hormone (PDH)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.3   5.8e+03      12      23 ..     284     295 ..     283     301 .. 0.75
   2 !   40.6   0.2   9.2e-14   1.7e-10       1      39 []     315     353 ..     315     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.3
                       DUF1641  12 fgLlraLrDPDV 23 
                                   ++++   +DP V
  gi|70605977|ref|YP_254847.1| 284 LKVMEVFSDPQV 295
                                   677888899998 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 9.2e-14
                       DUF1641   1 agleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                   ++l+++kpvG+fgL++aL+++DV + +G ll+l+++lGk
  gi|70605977|ref|YP_254847.1| 315 NDLPSVKPVGTFGLIGALNNKDVGYTMGALLKLAEELGK 353
                                   6899**********************************8 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0029       5.2      49      92 .]      21      64 ..      14      64 .. 0.85
   2 ?    9.2   0.9   0.00072       1.3       3      91 ..     105     185 ..     103     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0029
                                  HCCTTSGGGHHHHT---SCHCCCCHHHHHHHHHHHHHCCCCCHH CS
                           GED 49 lakLykkedldeLLkEdeeiaekRkelkkrlealkkAreilsev 92
                                  ++kL ++ +  e L E+ + ++++ +l  +l+ l +A e++++v
  gi|70605977|ref|YP_254847.1| 21 ISKLVDSLSTIEKLTEKLNEMDRKGQLDTMLNMLDQAVEVVDAV 64
                                  567777777777899999*********************99875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00072
                                   XXXTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHCCTTSGGGHHHHT---SCHCCCCHHHHHHHHHHH CS
                           GED   3 eseveeirslvksYfnivrktiadqiPkaimhllvneakeslqkellakLykkedldeLLkEdeeiaekRkelkkrlealk 83 
                                   +++v+++ + +++Y+  v+k  +d+  k+i  l ++++ +s+qk l   L k+    +L++E    +ek+ +l  ++++ +
  gi|70605977|ref|YP_254847.1| 105 TLDVDNLLNVLEKYLPLVQKLTNDKTIKTIESLNLDSLMDSVQK-LAPVLNKTA---SLVDE----MEKKGQLDAMINLIQ 177
                                   6678899999*********************************9.666666665...67777....678888888888888 PP

                                   HHCCCCCH CS
                           GED  84 kAreilse 91 
                                   +A + +++
  gi|70605977|ref|YP_254847.1| 178 QAVDLIDA 185
                                   88888876 PP

>> CDT1  DNA replication factor CDT1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0075        13      44      73 ..      74     103 ..      45     155 .. 0.73
   2 ?    6.2   0.0    0.0062        11      44      74 ..     196     226 ..     168     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0075
                          CDT1  44 ksfeekhLaqiktvyPeayklkqekqlkef 73 
                                    sf ++++a+i++++P   kl  e+ l+ +
  gi|70605977|ref|YP_254847.1|  74 MSFGMDQIAKIQAIWPVIEKLTSERALTFY 103
                                   79*******************988866544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0062
                          CDT1  44 ksfeekhLaqiktvyPeayklkqekqlkefg 74 
                                    sf ++++a+i++++P   kl  ek +k ++
  gi|70605977|ref|YP_254847.1| 196 VSFGMDQIAKIQAIWPVIEKLTSEKTIKLLE 226
                                   68********************999776554 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.9      0.34     6e+02      52      71 ..      32      51 ..       8      88 .. 0.48
   2 ?    5.7   0.1     0.012        22      45      71 ..      90     116 ..      61     120 .. 0.76
   3 ?   11.3   2.0   0.00022      0.39       8      87 ..      89     165 ..      82     172 .. 0.83
   4 ?    8.4   0.2    0.0018       3.3       8      72 ..     211     270 ..     204     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                                  HHHHHHHCCS-HHHHHHHHC CS
                        MgtE_N 52 eelaelleeldsDdaadlle 71
                                  e+l+e l+e+d   + d + 
  gi|70605977|ref|YP_254847.1| 32 EKLTEKLNEMDRKGQLDTML 51
                                  33333333333333333211 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                   HHHCS-HHHHHHHHCCS-HHHHHHHHC CS
                        MgtE_N  45 liealsdeelaelleeldsDdaadlle 71 
                                   +ie+l++e++  + + ld+D++ ++le
  gi|70605977|ref|YP_254847.1|  90 VIEKLTSERALTFYQTLDVDNLLNVLE 116
                                   456666666666666666666666655 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00022
                                   HCHCCS-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHH..HHHHHHHHCS- CS
                        MgtE_N   8 elleelpeeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpe..ekveellsald 86 
                                    ++e+l++e+++++++ l+ + + +vle+        l+++l++++  + +e l+ D + d ++ l +  +k+++l+++++
  gi|70605977|ref|YP_254847.1|  89 PVIEKLTSERALTFYQTLDVDNLLNVLEKY-----LPLVQKLTNDKTIKTIESLNLDSLMDSVQKLAPvlNKTASLVDEME 164
                                   5799***********************875.....558999********************99999763455666666665 PP

                                   H CS
                        MgtE_N  87 e 87 
                                   +
  gi|70605977|ref|YP_254847.1| 165 K 165
                                   5 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0018
                                   HCHCCS-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCC CS
                        MgtE_N   8 elleelpeeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadllee 72 
                                    ++e+l++e+ ++ll+ ++ e  +++l+ l++     l+++l++e++   +++ld   +  l+e+
  gi|70605977|ref|YP_254847.1| 211 PVIEKLTSEKTIKLLESIDLESTINALTSLSP-----LFKQLTSEKVIGTISQLDINSLLLLFER 270
                                   57899999999999999999999999999987.....5777777777777777777777666665 PP

>> DUF1719  Domain of unknown function (DUF1719)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00014      0.25     122     169 ..     220     267 ..     213     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                       DUF1719 122 lmLrlsestdivgiiikclqlltphfks.taeavrkeltqLptqdfswv 169
                                    +++l es+d+   +i+ l +l+p fk+ t e+v++ ++qL+ + + ++
  gi|70605977|ref|YP_254847.1| 220 KTIKLLESIDL-ESTINALTSLSPLFKQlTSEKVIGTISQLDINSLLLL 267
                                   57899*****7.5679**********983569**********9988743 PP

>> DUF3847  Protein of unknown function (DUF3847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   2.9e+03      43      60 ..      25      42 ..      10      62 .. 0.59
   2 ?    0.3   0.0      0.44   7.8e+02      47      67 ..      82     102 ..      78     107 .. 0.84
   3 ?    1.8   0.0      0.14   2.6e+02      49      69 ..     115     135 ..     113     149 .. 0.84
   4 ?    5.8   0.0    0.0084        15      47      71 ..     204     228 ..     200     238 .. 0.88
   5 ?   -1.1   0.0       1.2   2.1e+03      48      64 ..     236     252 ..     235     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                       DUF3847 43 itrGaalEsilpeakeLt 60
                                  ++   ++E++ ++++e+ 
  gi|70605977|ref|YP_254847.1| 25 VDSLSTIEKLTEKLNEMD 42
                                  444444444444444444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.44
                       DUF3847  47 aalEsilpeakeLteeevyel 67 
                                   a +++i p +++Lt e +  +
  gi|70605977|ref|YP_254847.1|  82 AKIQAIWPVIEKLTSERALTF 102
                                   889***********9987766 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.14
                       DUF3847  49 lEsilpeakeLteeevyelle 69 
                                   lE++lp +++Lt++   + +e
  gi|70605977|ref|YP_254847.1| 115 LEKYLPLVQKLTNDKTIKTIE 135
                                   8************98877666 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0084
                       DUF3847  47 aalEsilpeakeLteeevyellekv 71 
                                   a +++i p +++Lt e   +lle++
  gi|70605977|ref|YP_254847.1| 204 AKIQAIWPVIEKLTSEKTIKLLESI 228
                                   889********************98 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.2
                       DUF3847  48 alEsilpeakeLteeev 64 
                                   al s++p  k+Lt e v
  gi|70605977|ref|YP_254847.1| 236 ALTSLSPLFKQLTSEKV 252
                                   578999*******9987 PP

>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00014      0.26     261     314 ..     124     175 ..      57     218 .. 0.82
   2 ?   -0.5   0.0      0.34   6.1e+02     270     346 ..     222     297 ..     201     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                      Cas_Csa4 261 efkvgnnqrirsfrevelsklldfiaelkardfastiklvddllre.dleillrL 314
                                   +    n   i++ + ++l++l+d++ +l+ +   +t  lvd++ ++ +l++  +L
  gi|70605977|ref|YP_254847.1| 124 KLT--NDKTIKTIESLNLDSLMDSVQKLAPV-LNKTASLVDEMEKKgQLDAMINL 175
                                   444..4455**********************.***********998423443333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.34
                      Cas_Csa4 270 irsfrevelsklldfiaelkardfa..stiklvddllredleillrLieallygdlrevysalrvlkkagvrldaelvd 346
                                   i+  + ++l++ ++++ +l    f+     k +  + + d + ll L+e ++y +  + +   r+lk  +v +d+++vd
  gi|70605977|ref|YP_254847.1| 222 IKLLESIDLESTINALTSLSPL-FKqlTSEKVIGTISQLDINSLLLLFERFTYLQKTGAL--DRLLKVMEVFSDPQVVD 297
                                   5555666666666666666554.3300345777777777888888899999887755544..45557777777777766 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4    0.0016       2.9      53      94 ..      20      61 ..       2      64 .. 0.85
   2 ?    3.9   0.2     0.041        74      34      94 ..     121     183 ..      98     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                       Enkurin 53 kweelnkeyqslpllidtlskrqrKeklEkeLkqlEkdikll 94
                                  + ++l++ ++ +  l++ l+++ rK +l+  L+ l+++++++
  gi|70605977|ref|YP_254847.1| 20 RISKLVDSLSTIEKLTEKLNEMDRKGQLDTMLNMLDQAVEVV 61
                                  55667777777778999*********************9987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                       Enkurin  34 gmrllseeerqellegLkkkweelnkeyqslp....llidtlskrqrKeklEkeLkqlEkdikll 94 
                                    ++ l++++  +++e+L  ++++l++  q+l+     ++  + ++++K +l++ ++ + +++ l+
  gi|70605977|ref|YP_254847.1| 121 LVQKLTNDKTIKTIESL--NLDSLMDSVQKLApvlnKTASLVDEMEKKGQLDAMINLIQQAVDLI 183
                                   55666666666667766..6788899999987632223444567899******999999999887 PP

>> Myotub-related  Myotubularin-like phosphatase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2    0.0075        13     183     251 ..      22      86 ..       9      92 .. 0.68
   2 ?    6.5   0.4    0.0019       3.4     173     252 ..     137     209 ..     115     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0075
                                   HHHHHHH...TSS--HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHCS---EEEE-SSSSSHHHHHHH CS
                Myotub-related 183 kklvealkdsekeasekkwlsaLekskWlkhiksiLeaaaliaksvelekssvLvhcsdGwDrtsqlss 251
                                   +klv+ l++    ++ ++ l+++++ + l+++ ++L++a+ ++++v+ ++  +    s G+D+ + + +
  gi|70605977|ref|YP_254847.1|  22 SKLVDSLSTI---EKLTEKLNEMDRKGQLDTMLNMLDQAVEVVDAVQ-KADLINALMSFGMDQIAKIQA 86 
                                   3444444333...345566789999*********************7.444444445666666666666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0019
                                   --HHHHHHHHHHHHHHH...TSS--HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHCS---EEEE-SSSSSHHHHHHHH CS
                Myotub-related 173 enihvmreslkklvealkdsekeasekkwlsaLekskWlkhiksiLeaaaliaksvelekssvLvhcsdGwDrtsqlssl 252
                                    n  ++ +s++kl  +l+++      +++++++ek + l+ + +++++a+ ++++v++ +  +    s G+D+ + + ++
  gi|70605977|ref|YP_254847.1| 137 LNLDSLMDSVQKLAPVLNKT------ASLVDEMEKKGQLDAMINLIQQAVDLIDAVQK-SDLINTLVSFGMDQIAKIQAI 209
                                   46778899999999999777......78****************************74.333333446677777776665 PP

>> Pigment_DH  Pigment-dispersing hormone (PDH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.039        70       2      10 ..      67      75 ..      66      79 .. 0.87
   2 ?    4.6   0.0     0.022        40       2      10 ..     189     197 ..     188     200 .. 0.90
   3 ?   -3.0   0.0       6.2   1.1e+04       5      11 ..     234     240 ..     233     240 .. 0.88
   4 ?   -0.0   0.6      0.68   1.2e+03       5      10 ..     261     266 ..     257     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                    Pigment_DH  2 sdLINfLLs 10
                                   dLIN L+s
  gi|70605977|ref|YP_254847.1| 67 ADLINALMS 75
                                  59*****98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                    Pigment_DH   2 sdLINfLLs 10 
                                   sdLIN L s
  gi|70605977|ref|YP_254847.1| 189 SDLINTLVS 197
                                   9******87 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.2
                    Pigment_DH   5 INfLLsL 11 
                                   IN L sL
  gi|70605977|ref|YP_254847.1| 234 INALTSL 240
                                   9*99987 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.68
                    Pigment_DH   5 INfLLs 10 
                                   IN+LL 
  gi|70605977|ref|YP_254847.1| 261 INSLLL 266
                                   9***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2712.87
//
Query:       gi|70605978|ref|YP_254848.1|  [L=152]
Description: hypothetical protein Saci_0132 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.5   0.3       0.13   12.1   0.2    1.9  2  UPF0728   Uncharacterised protein family UPF0728
      0.041   14.4   0.1       0.26   11.9   0.0    2.0  2  MucBP_2   Mucin binding domain


Domain annotation for each model (and alignments):
>> UPF0728  Uncharacterised protein family UPF0728
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.4e-05      0.13      25      68 ..      17      58 ..      12      72 .. 0.78
   2 ?   -0.1   0.0     0.094   8.4e+02      24      48 ..     100     124 ..      90     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                       UPF0728 25 erleglqavlkkdGheveLektedynvvelvvngetvfqCkite 68
                                  + +e++++ l+k+G+ v++++ ++ n++++ + +++vf+C+ +e
  gi|70605978|ref|YP_254848.1| 17 KDVEQIKRELEKQGY-VIVKEKKEKNLLKV-FDDNVVFTCNKDE 58
                                  66899*********9.56677788888885.899******9554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.094
                       UPF0728  24 terleglqavlkkdGheveLekted 48 
                                   +  l+g++++++ + +e+ Le+  +
  gi|70605978|ref|YP_254848.1| 100 IPSLKGIRETYNVSSYELFLERYLE 124
                                   5568999999999999999998766 PP

>> MucBP_2  Mucin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05      0.26      35      63 ..      20      50 ..      11      61 .. 0.79
   2 ?   -0.1   0.0      0.16   1.4e+03      50      70 ..      76      96 ..      68      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                       MucBP_2 35 dtik.aleaqgYvlvssdgfpagt..tFdndd 63
                                  ++ik +le+qgYv+v +++  ++   +Fd++ 
  gi|70605978|ref|YP_254848.1| 20 EQIKrELEKQGYVIV-KEKKEKNLlkVFDDNV 50
                                  467779*********.7777777789999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                       MucBP_2 50 sdgfpagttFdnddatdqtft 70
                                  +d+ ++ +tF++ ++t+ tf+
  gi|70605978|ref|YP_254848.1| 76 TDKLTTVITFTKRKNTSYTFK 96
                                  556666667777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1624  (0.0905795); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 905.97
//
Query:       gi|70605979|ref|YP_254849.1|  [L=136]
Description: Lrs14 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-13   49.6   0.0    3.5e-13   49.2   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.5e-09   36.9   0.0    3.9e-09   36.3   0.0    1.4  1  MarR_2          MarR family
    6.8e-08   32.3   0.0    1.1e-07   31.7   0.0    1.3  1  MarR            MarR family
    1.8e-07   30.6   0.0    2.7e-07   30.0   0.0    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.1e-05   22.6   0.0    8.5e-05   22.4   0.0    1.2  1  TFIIE_alpha     TFIIE alpha subunit
    9.6e-05   22.1   0.0    0.00016   21.4   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    0.00011   22.6   0.0    0.00019   21.8   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
    0.00037   20.4   0.0    0.00055   19.8   0.0    1.4  1  HTH_36          Helix-turn-helix domain
     0.0011   19.2   0.0     0.0016   18.6   0.0    1.2  1  HTH_34          Winged helix DNA-binding domain
     0.0013   19.3   0.0     0.0023   18.5   0.0    1.5  1  Mga             Mga helix-turn-helix domain
     0.0016   18.6   0.0     0.0026   17.9   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0024   17.7   0.0     0.0038   17.0   0.0    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0088   15.7   0.0      0.029   14.0   0.0    1.8  2  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.019   15.0   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.015   15.2   0.0      0.027   14.4   0.0    1.4  1  HTH_11          HTH domain
      0.044   13.5   0.0      0.058   13.1   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
       0.08   11.3   0.0       0.11   10.9   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
       0.09   12.9   0.0       0.13   12.5   0.0    1.2  1  DUF5062         Domain of unknown function (DUF5062)
       0.11   12.5   0.0        0.2   11.6   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.12   12.4   0.0       0.22   11.5   0.0    1.3  1  Dimerisation2   Dimerisation domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   3.9e-16   3.5e-13       1      67 [.      31     105 ..      31     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.9e-16
                                   HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE--H CS
                          TrmB   1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYravdp 67 
                                   L+ ++++s+++++v +aL+ ++ ++ d++ae+l+++++++++++++L++ G+Ver k         +++Yr +++
  gi|70605979|ref|YP_254849.1|  31 LKfCYDISDTDFQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDVsskggrpKYIYRSIPV 105
                                   7889***************************************************99666899997779*99986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   4.3e-12   3.9e-09       2      55 ..      36      87 ..      35      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 4.3e-12
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  +++ ++++vL aL  ++g+  +  +la+ l+lsk++++r +++Lv+ G+ver +
  gi|70605979|ref|YP_254849.1| 36 DISDTDFQVLKALIGSDGK--NEDDLAEQLKLSKASINRSVNKLVSLGFVERMK 87
                                  67889*************6..778***************************975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.2e-10   1.1e-07       1      56 [.      37      92 ..      37      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.2e-10
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56
                                  ++ t f +L  l  +++ +  +La++l++sk+++ r + +L+  G++eR+k+ + +
  gi|70605979|ref|YP_254849.1| 37 ISDTDFQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDVSSK 92
                                  67899999*******************************************98865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   3.1e-10   2.7e-07       2      48 .]      38      84 ..      37      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.1e-10
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++td+++L++L    + +  +LAe+l lS++ +nr +++L++ G+++
  gi|70605979|ref|YP_254849.1| 38 SDTDFQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVE 84
                                  68******************************************996 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   9.5e-08   8.5e-05      14      86 ..      40     113 ..      27     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.5e-08
                                   HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE.EECCCHCCCHH CS
                   TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywr.inyeklvdvvk 86 
                                     ++vl++L+     +e+dla++lk+ +  + + +n+L + ++v+  + +  + +  ky +r i  +kl++ + 
  gi|70605979|ref|YP_254849.1|  40 TDFQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDVSSKGGRPKYIYRsIPVDKLIERIT 113
                                   5689******99999*****************************988888888888888886466677777665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-07   0.00016       6      50 ..      42      85 ..      42      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  +++L+al   ++  +  +lA+++ l+k++  R ++ Lv lG+ve+
  gi|70605979|ref|YP_254849.1| 42 FQVLKALIGSDGK-NEDDLAEQLKLSKASINRSVNKLVSLGFVER 85
                                  6899999999998.889**************************97 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.2e-07   0.00019       6      58 ..      42      93 ..      37     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-07
                        HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                   +vL  +    ++k + dl++ l++++++i  s++kL+  G+ver++d  +++
  gi|70605979|ref|YP_254849.1| 42 FQVLKALI-GSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDVSSKG 93
                                  56666666.68999*****************************9999965554 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.2e-07   0.00055       6      54 ..      40      82 ..      35      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.2e-07
                        HTH_36  6 saklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGy 54
                                  +++ +l  l    +kn+      ++la++l+lsk ++ r +++L+ lG+
  gi|70605979|ref|YP_254849.1| 40 TDFQVLKALIGSDGKNE------DDLAEQLKLSKASINRSVNKLVSLGF 82
                                  55555555555554444......4************************7 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.7e-06    0.0016       3      53 ..      42      92 ..      40     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.7e-06
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                  ++vl  L+  d  +  +l e+l+++++ +   ++kL + g++e++k++++k
  gi|70605979|ref|YP_254849.1| 42 FQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDVSSK 92
                                  899*******************************************98765 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.6e-06    0.0023      16      55 ..      39      78 ..      11      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-06
                                  SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                           Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                  ++++q+lk l+ ++ ++  +la++l +S+++++r++++l 
  gi|70605979|ref|YP_254849.1| 39 DTDFQVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLV 78
                                  689********************************99985 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.9e-06    0.0026      25      56 ..      56      87 ..      31      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.9e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 25 tkdlaerLnvspssVsemlkkLekdGyveyek 56
                                    dlae L+ s++s+  +++kL + G+ve  k
  gi|70605979|ref|YP_254849.1| 56 EDDLAEQLKLSKASINRSVNKLVSLGFVERMK 87
                                  579*************************9765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.3e-06    0.0038       6      46 ..      43      84 ..      39      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                                  HHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  6 kILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  ++Lk+L  +  +   +lae+l+ls++ + +  +kL  +G+Ve
  gi|70605979|ref|YP_254849.1| 43 QVLKALIGSDgKNEDDLAEQLKLSKASINRSVNKLVSLGFVE 84
                                  678888886668888**************************7 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   3.2e-05     0.029      27      58 ..      56      87 ..      55      92 .. 0.91
   2 ?   -1.6   0.0       2.5   2.2e+03       6      27 ..     109     130 ..     105     136 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 27 ereLaaefgVsrttvReALrrLeaeglverrq 58
                                  e +La++++ s+ +++++ ++L++ g ver +
  gi|70605979|ref|YP_254849.1| 56 EDDLAEQLKLSKASINRSVNKLVSLGFVERMK 87
                                  789**************************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                   HHHHHHHHHTTSS-TTSB---H CS
                          GntR   6 yerLredIlsgelrpGdkLPse 27 
                                    er++ed ++     G+ LP+e
  gi|70605979|ref|YP_254849.1| 109 IERITEDFKRCAELFGAVLPKE 130
                                   4555555555555567777777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.2e-05     0.019      14      56 ..      43      85 ..      37      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   +l+aL + +g    +lae+l lsk+++++ +++L++ g+ve+
  gi|70605979|ref|YP_254849.1| 43 QVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVER 85
                                  68999999999999***************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     3e-05     0.027      17      52 ..      55      95 ..      41      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                        HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelg.....vpIesepgr 52
                                  + ++LAe+L++S++ + r + +L +lg      ++ s+ gr
  gi|70605979|ref|YP_254849.1| 55 NEDDLAEQLKLSKASINRSVNKLVSLGfvermKDVSSKGGR 95
                                  5689***********************87777777777765 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.5e-05     0.058      26      73 ..      45      88 ..      24      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                       DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkded 73
                                  + +l+      ++ + la++l+  +s++ ++++++ L++lg++++ +d
  gi|70605979|ref|YP_254849.1| 45 LKALIGSDG--KNEDDLAEQLK--LSKASINRSVNKLVSLGFVERMKD 88
                                  555554444..58899******..********************9887 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.11     468     519 ..      37      88 ..      33      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                        DUF505 468 ltryelkvlkk.iPkrgvsveelveevdeleeeevrealeklearglvevlpd 519
                                   ++ ++ +vlk  i + g   ++l e++ +l +  ++++++kl + g+ve ++d
  gi|70605979|ref|YP_254849.1|  37 ISDTDFQVLKAlIGSDGKNEDDLAEQL-KLSKASINRSVNKLVSLGFVERMKD 88 
                                   678899****9455*********9999.999*******************987 PP

>> DUF5062  Domain of unknown function (DUF5062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.13       6      59 ..      63     117 ..      54     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                       DUF5062   6 akLlkkAleigekyAkkrGyaefdktdsake.kveaiYrlLvqdKliqplpedke 59 
                                    kL k+ ++ +++     G++e  k  s+k  + ++iYr +  dKli+ ++ed +
  gi|70605979|ref|YP_254849.1|  63 LKLSKASINRSVNKLVSLGFVERMKDVSSKGgRPKYIYRSIPVDKLIERITEDFK 117
                                   578999999999999999**999888888877*****************999965 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023       0.2      25      53 ..      57      85 ..      55      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                  HHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisr 53
                                  ++lA+ l l+  +++r  ++L   g ++r
  gi|70605979|ref|YP_254849.1| 57 DDLAEQLKLSKASINRSVNKLVSLGFVER 85
                                  79**********************99985 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.22      22      68 ..      43      89 ..      38      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                 Dimerisation2 22 gvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekke 68
                                  +v  +L  ++ ++ +++ae+l++s  +++r ++ +v+Lg  er k+ 
  gi|70605979|ref|YP_254849.1| 43 QVLKALIGSDGKNEDDLAEQLKLSKASINRSVNKLVSLGFVERMKDV 89
                                  455555566778899*************************9977554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 970.15
//
Query:       gi|70605980|ref|YP_254850.1|  [L=312]
Description: hypothetical protein Saci_0134 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-10   39.4   0.1    6.8e-10   38.8   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.2e-09   35.4   0.0    6.5e-09   35.3   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
      8e-08   32.6   0.0    4.7e-07   30.1   0.0    2.1  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0055   15.9   0.0     0.0094   15.1   0.0    1.4  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.037   13.4   0.0      0.065   12.6   0.0    1.5  2  ThiF             ThiF family
       0.11   13.0   0.1       0.24   11.9   0.1    1.5  1  UN_NPL4          Nuclear pore localisation protein NPL4


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1   2.3e-13   6.8e-10       1     178 [.       3     171 ..       3     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.3e-13
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HH.HHHHHHHHHT-SEEEE--S-- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrs.alerlfkeeqpdavihlAavg 75 
                                   il+tG  Gfi s+++  l  k +++    r  +  ++   + l     + ++ld+ +++ +le+l+k    d ++++  vg
  gi|70605980|ref|YP_254850.1|   3 ILITGL-GFISSNVAYFLSPK-HDIKITYRSLNPVKELYTKILkekgvDTTKLDVINETqKLEELVK--SNDLIVNF--VG 77 
                                   899999.*****998777655.56555555444444444333366788999***99988799*****..67******..66 PP

                                   -HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHH CS
                     Epimerase  76 gvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveay 156
                                   +++    d + ++++n+++   +++a++k++   ++++s  ++YG   ++ + e+ + + l+p++++  +Kl gek + ++
  gi|70605980|ref|YP_254850.1|  78 DIQG---DEKVLYMANVEVPSIIAQACKKYNK-VMIHASG-STYGVTGKV-TIEENHGEGLNPSTAFEKTKLQGEKELLNI 152
                                   6666...6667899****************99.8888876.89**99997.5555557778******************99 PP

                                   HHHHT-EEEEEEESEEESTTS- CS
                     Epimerase 157 aaqyglnaiilrlfnlyGprng 178
                                     +   naiilr++ +yG +n 
  gi|70605980|ref|YP_254850.1| 153 LGK---NAIILRPTLVYGRFNA 171
                                   555...59**********9932 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.2e-12   6.5e-09      69     159 ..      81     173 ..       1     263 [. 0.81

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.2e-12
                                   HSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEE.EGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.H-SSEEEEE CS
                 RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLihvS.tDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.agkkalivR 147
                                    +e+  y +n+e +  +A+a+++++ ++ih S + y   G+ + + +  +  +P +++ +tKl+GE+  l+  gk+a+i+R
  gi|70605980|ref|YP_254850.1|  81 GDEKVLYMANVEVPSIIAQACKKYNKVMIHASgSTYGVTGKVTIEENHGEGLNPSTAFEKTKLQGEKELLNiLGKNAIILR 161
                                   566778999**********************854677788888878888999*****************997889****** PP

                                   E-SEESSSSS-H CS
                 RmlD_sub_bind 148 tswvygekgknf 159
                                    + vyg+ +   
  gi|70605980|ref|YP_254850.1| 162 PTLVYGRFNAHV 173
                                   ******955443 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.6e-10   4.7e-07       1      84 [.       3      84 ..       3      92 .. 0.84
   2 ?   -0.1   0.0      0.36   1.1e+03      60      83 ..      94     118 ..      87     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.6e-10
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG.G CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkegdlvvnlsppi.s 81
                                  +li G G++++ va  l+ ++d+     +  rs++ +++l  k+ +++ +++++ld+ n+++ L++l+k++dl+vn +++i  
  gi|70605980|ref|YP_254850.1|  3 ILITGLGFISSNVAYFLSPKHDI----KITYRSLNPVKELYTKIlKEKGVDTTKLDVINETQKLEELVKSNDLIVNFVGDIqG 81
                                  7999*****************98....4555666666577666668999*******************************944 PP

                                  HHH CS
               Sacchrp_dh_NADP 82 sld 84
                                  +++
  gi|70605980|ref|YP_254850.1| 82 DEK 84
                                  445 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.36
                                   HHHHHHHHTTS.SEEEE-SSGGGHH CS
               Sacchrp_dh_NADP  60 eavLaallkeg.dlvvnlsppissl 83 
                                   ++++a+++k++ ++ +++s+++++ 
  gi|70605980|ref|YP_254850.1|  94 PSIIAQACKKYnKVMIHASGSTYGV 118
                                   6778999999999999999988765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.1e-06    0.0094      78     208 ..      59     167 ..      39     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                                   HHHHHHHHHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                 NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                    ++l+el+++ d+i++  ++++ de  k+l+ +Nve    + + +kk   +kv++h S ++   + +              
  gi|70605980|ref|YP_254850.1|  59 TQKLEELVKSNDLIVNFVGDIQGDE--KVLYMANVEVPSIIAQACKKY--NKVMIHASGSTYGVTGKV------------- 122
                                   56889**************998655..6899999999999******77..447999998666666553............. PP

                                   .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                 NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                     + e+++ ++ + ++++e++K  +Ek + +     g +++i+Rp+ ++g
  gi|70605980|ref|YP_254850.1| 123 --TIEENHGEGLNPSTAFEKTKLQGEKELLNIL---GKNAIILRPTLVYG 167
                                   ..45677888889999***********999999...77899******998 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   3.6e+03      19      34 ..       1      16 [.       1      19 [. 0.85
   2 ?   12.6   0.0   2.2e-05     0.065     100     154 ..      60     127 ..      35     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                  SEEEEE--SHHHHHHH CS
                                  xxxxxxxxxxxxxxxx RF
                          ThiF 19 skvllvGaGglGsell 34
                                  +k+l+ G+G + s+++
  gi|70605980|ref|YP_254850.1|  1 MKILITGLGFISSNVA 16
                                  589******9999987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                                   CCS-HHHHTT-SEEEEE............SSSHHHHHHHHHHHHHHT-EEEE..EEEETTEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                          ThiF 100 etvleellesvDlVvda............lDniearrlvnracvkkgiplie..agtlgfegqvvviip 154
                                   +  leel++s Dl+v+             + n+e+  ++++ac k+ + +i+  ++t g+ g+v++ ++
  gi|70605980|ref|YP_254850.1|  60 Q-KLEELVKSNDLIVNFvgdiqgdekvlyMANVEVPSIIAQACKKYNKVMIHasGSTYGVTGKVTIEEN 127
                                   3.367888888888888888888888888***********************55689999999998743 PP

>> UN_NPL4  Nuclear pore localisation protein NPL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.9e-05      0.24      16      75 ..      25      84 ..      19      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.9e-05
                                  EEEEE-TTSBHHHHHHHHHHHSS-STTT-EEESSTTCGCCCSSSSSSCCCTCH--TT-EE CS
                       UN_NPL4 16 kRieisekstlktllekvaeelkfsengfslylernkttelvssssksvkevglkhGdml 75
                                  ++i+  +   +k+l+ k+ +e +++  ++ +  e +k +elv s++  v+ vg  +Gd  
  gi|70605980|ref|YP_254850.1| 25 IKITYRSLNPVKELYTKILKEKGVDTTKLDVINETQKLEELVKSNDLIVNFVGDIQGDEK 84
                                  6888899999********************************999999988887777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2236.00
//
Query:       gi|70605981|ref|YP_254851.1|  [L=267]
Description: 2,5-diketo-D-gluconic acid reductase A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-67  227.8   0.1    1.3e-65  221.5   0.1    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.5   0.1   7.3e-70   1.3e-65       2     291 ..      11     264 ..      10     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 221.5 bits;  conditional E-value: 7.3e-70
                                   EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                  Aldo_ket_red   2 lglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                   +glGtw++g++    +  +++  +e++++ +  Gin++DtAe+Yg g+ ee++G+a+++  ++re+++i+tKv      ++
  gi|70605981|ref|YP_254851.1|  11 IGLGTWKMGGDywtpGHGNDNVYIEAIKYTINKGINLIDTAEMYGGGHTEEIVGKAVAD--FDRESLFITTKV------WP 83 
                                   9***********999999999999***********************************..************......** PP

                                   SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--EE CS
                  Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvkiv 158
                                    +l+ ++ ++s  +slkrL+t+y+Dl+l+H+p+p+++ +ee+++a+e+l++ G +r iGvSnf+v+ l++a +++kk++iv
  gi|70605981|ref|YP_254851.1|  84 NHLKYDDTIKSALASLKRLNTKYIDLYLIHWPNPDVK-VEETISAMEKLIDMGVVRCIGVSNFDVKLLDQAiHSTKKYEIV 163
                                   *************************************.******************************************* PP

                                   EEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHT CS
                  Aldo_ket_red 159 avqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakeh 239
                                   a+q++y+++r   e+ ++++++k++v +iaysplg+G+++                               ++l+++a ++
  gi|70605981|ref|YP_254851.1| 164 ANQIQYSIYRLTPERDVIPFAEKNKVTIIAYSPLGQGSIS-----------------------------SESRLKDIALKY 215
                                   ****************************************.............................35679******* PP

                                   T--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                  Aldo_ket_red 240 gvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                   g++ aq+al+y+    +++i+ip+a +  ++++++d+++++l +e+++e+++
  gi|70605981|ref|YP_254851.1| 216 GKTQAQVALAYLK---RRSIPIPKAVQKTHIDEIADVMKFDLRDEDYNEIRK 264
                                   ************9...9********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1879.68
//
Query:       gi|70605982|ref|YP_254852.1|  [L=414]
Description: dihydrolipoamide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-51  175.4   1.3    1.5e-51  175.4   0.3    1.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-20   73.6   5.6    2.3e-13   50.5   0.1    4.0  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      6e-15   55.5   0.1    2.1e-14   53.7   0.1    1.9  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.4e-13   50.8   0.3    4.4e-09   36.0   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-13   49.2   6.6    6.6e-06   25.4   1.7    4.0  3  GIDA            Glucose inhibited division protein A
    1.6e-11   43.9   3.3    1.2e-06   27.9   0.1    3.4  3  FAD_binding_2   FAD binding domain
    1.2e-10   41.5   2.1    3.7e-06   27.1   0.1    2.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    8.4e-09   34.6   1.6    1.8e-06   26.9   0.1    3.4  3  HI0933_like     HI0933-like protein
    2.5e-08   33.7   0.8    4.9e-07   29.4   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    1.4e-07   31.0   2.5      0.025   13.9   0.0    3.3  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    2.3e-06   27.1   1.0       0.02   14.1   0.2    2.3  2  FAD_binding_3   FAD binding domain
    2.1e-05   24.3   6.4      0.006   16.2   0.2    3.5  4  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.017   14.0   0.4       0.41    9.4   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
      0.022   14.0   0.5       0.11   11.7   0.1    2.2  2  Thi4            Thi4 family
      0.034   13.4   0.3        2.1    7.5   0.0    3.0  4  Amino_oxidase   Flavin containing amine oxidoreductase
      0.044   13.3   2.4        0.3   10.7   0.0    3.1  4  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.087   12.8   0.1       0.43   10.5   0.0    2.2  2  Rubredoxin_C    Rubredoxin NAD+ reductase C-terminal domain
      0.089   12.7   0.0       0.17   11.8   0.0    1.4  1  Gp_UL130        HCMV glycoprotein pUL130
       0.18   10.8   3.3       0.21   10.6   0.1    2.5  4  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.3   1.6e-54   1.5e-51       2     294 .]       2     292 ..       1     293 [. 0.93
   2 ?   -3.9   0.0       6.6   6.3e+03     185     209 ..     368     392 ..     366     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 1.6e-54
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH....................H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx....................x RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias....................e 58 
                                   ++vviG+GpAGl  a+t +  g kvtlve    l+gtc++ gc++ska+l+     + ++                    +
  gi|70605982|ref|YP_254852.1|   2 RIVVIGSGPAGLYSAITSSSLGNKVTLVEkedrLGGTCVLYGCIPSKAMLHPLILSSGIEkvkgnskiefnfkeiselgiN 82 
                                   89**************************9999******************9999998888999*****************9 PP

                                   HHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  59 vvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklk 139
                                    v+++++g e++l++  v+i++g++ +k  +++e +++++  dk+++AtG  + +++++G           ++s++   l+
  gi|70605982|ref|YP_254852.1|  83 AVNRVSKGTEYMLEKYNVDIIHGRAILKG-NSVEVNGQTLSSDKIIIATG--TVKPQVQGS----------IASDDLPYLD 150
                                   9*************99********87777.7788****************..778889999..........5555555555 PP

                                   S-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvl 220
                                      +++v++GgG+ GvE+   l+ lgke+ +ve  + ll+ +d++l++ ++  ++k+G  + lg++vk+i++n+    vvl
  gi|70605982|ref|YP_254852.1| 151 RDFQKVVIIGGGVGGVEYGWLLRALGKEIFVVEKENLLLPRHDPDLRNSVTYTFRKMGFSLLLGKEVKKIERNK----VVL 227
                                   55569******************************************************************999....7** PP

                                   TTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 221 edgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   +dg+ei+ d ++++ G++++ +++    g++   + +i+v+ef++t++ g+ya+GDv+    g  +a++A+++G
  gi|70605982|ref|YP_254852.1| 228 DDGKEIEGDIILMSFGRTANVNGF---EGVPH--DKWIKVNEFMETEIRGVYAAGDVT----GSFTAHEAISKG 292
                                   ********************9886...79*98..9***********************....777788887765 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.6
                                   HHHHHHHHHHHTTEEEEESCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 185 lsaaleealekeGvevklgtsvkei 209
                                   +s+++ee +   G +++ + +vke+
  gi|70605982|ref|YP_254852.1| 368 FSERAEEIVSVLGLAIRYNIKVKEL 392
                                   7899999999999999999999986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.1e-07    0.0001       1      35 [.       2      36 ..       2      40 .. 0.95
   2 ?   -1.1   0.0       3.2     3e+03      43      65 ..      88     110 ..      85     123 .. 0.73
   3 !   50.5   0.1   2.5e-16   2.3e-13       1      70 [.     155     224 ..     155     230 .. 0.95
   4 ?   -1.8   0.0         5   4.7e+03      42      66 ..     368     392 ..     343     394 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-07
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  ++vv+G+G  gl  A + + lg+kVt+ve +d+l 
  gi|70605982|ref|YP_254852.1|  2 RIVVIGSGPAGLYSAITSSSLGNKVTLVEKEDRLG 36
                                  79******************************997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHTTEEEECSEEEEE CS
                     Pyr_redox  43 skilqeklekngievllntkvee 65 
                                   sk ++  lek ++++++++ + +
  gi|70605982|ref|YP_254852.1|  88 SKGTEYMLEKYNVDIIHGRAILK 110
                                   55666778999999999987655 PP

  == domain 3  score: 50.5 bits;  conditional E-value: 2.5e-16
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                                   kvv++GgG+ g+E++  l++lgk++ vve ++ ll+  D+++++ ++  ++k+g  +ll+++v++ie ++
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVVEKENLLLPRHDPDLRNSVTYTFRKMGFSLLLGKEVKKIERNK 224
                                   79*****************************************************************776 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5
                                   HHHHHHHHHHHTTEEEECSEEEEEE CS
                     Pyr_redox  42 askilqeklekngievllntkveei 66 
                                   +s++ +e ++ +g  +++n kv+e+
  gi|70605982|ref|YP_254852.1| 368 FSERAEEIVSVLGLAIRYNIKVKEL 392
                                   4555666667778888888888876 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1   2.2e-17   2.1e-14       3     108 ..     313     408 ..     311     410 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.2e-17
                                   EEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHHHH CS
                 Pyr_redox_dim   3 tvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelavai 83 
                                   +v++t+p++a+vG t       g   k++k+++++++ra+a++et+gfvK+ ++  ++kv+Ga  ++++a+e+++ l +ai
  gi|70605982|ref|YP_254852.1| 313 KVIYTKPQIAYVGDTT-----RG---KCVKLNMASLTRAIAEKETEGFVKVCVE--DDKVIGAVAFSERAEEIVSVLGLAI 383
                                   79***********985.....45...89***********************554..69*********************** PP

                                   HTTSBHHHHHTSBSSSSSTGGGGHC CS
                 Pyr_redox_dim  84 kagltvedladtihihPtlsealke 108
                                   +++++v++la+  ++hP++ e+++e
  gi|70605982|ref|YP_254852.1| 384 RYNIKVKELAEYPFPHPSYLETINE 408
                                   *******************999976 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1     5e-05     0.047       1      33 [.       4      36 ..       4      44 .. 0.87
   2 !   36.0   0.0   4.7e-12   4.4e-09     113     305 .]     111     277 ..      85     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.nig 33
                                  ++iG GPaGl +ai+   +g  +++ +Ek+ ++g
  gi|70605982|ref|YP_254852.1|  4 VVIGSGPAGLYSAITSSSLGN-KVTLVEKEdRLG 36
                                  79******************9.799***985555 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 4.7e-12
                   Pyr_redox_3 113 gfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvv 193
                                   g +ve + +t++++k+iiAtG      k++++G+       + +++f     qkvv+iGg+  +v++   l + g+e+ vv
  gi|70605982|ref|YP_254852.1| 111 GNSVEVNGQTLSSDKIIIATGT----VKPQVQGSIASDDLPYLDRDF-----QKVVIIGGGVGGVEYGWLLRALGKEIFVV 182
                                   5679999***************....455566665444566666666.....9**************************** PP

                   Pyr_redox_3 194 trgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsf 273
                                    +++ +  ++        pd +n +    ++  + +l  +evk+i+++    kv  +dgk++e   d++l+  G + +++ 
  gi|70605982|ref|YP_254852.1| 183 EKENLLLPRH-------DPDLRNSVTYTFRKMGFSLLLGKEVKKIERN----KVVLDDGKEIE--GDIILMsFGRTANVNG 250
                                   ****999987.......78899999988888669************97....56678998876..58888879******99 PP

                   Pyr_redox_3 274 lkkslfeldedgrpvlteeteetnvpglflaG 305
                                   ++        d++++++e  +et + g++ aG
  gi|70605982|ref|YP_254852.1| 251 FE----GVPHDKWIKVNE-FMETEIRGVYAAG 277
                                   99....445689999985.79*********99 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   1.7     7e-09   6.6e-06       2     150 ..       3     132 ..       2     146 .. 0.74
   2 !    6.2   0.0    0.0051       4.8       1      28 [.     155     182 ..     155     200 .. 0.86
   3 !   16.7   0.1   3.2e-06    0.0031     348     386 ..     264     301 ..     258     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7e-09
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEEST CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLi...thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilNr 79 
                                   ++ViG G AG+  A++++ lG kv+L+       +t++  +C ps   +   +l   i++++g       +++i+f+    
  gi|70605982|ref|YP_254852.1|   3 IVVIGSGPAGLYSAITSSSLGNKVTLVekeDRLGGTCVLYGCIPSKAMLHPLILSSGIEKVKG-------NSKIEFNF--- 73 
                                   89*************************666566778888889999887777777777777666.......55565555... PP

                                   TS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA  80 skGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                      + + +l   ++  +  ++ te++ ++ n++ii++++       +     v  +g+t+++++++iatGt
  gi|70605982|ref|YP_254852.1|  74 ---KEISEL--GINAVNRVSKGTEYMLEKYNVDIIHGRAIL--K-GN----SVEVNGQTLSSDKIIIATGT 132
                                   ...455666..5555555556666666669*****998643..2.22....456799************** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0051
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi 28 
                                   +v++iGgG  G+e  + +  lG ++  +
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVV 182
                                   69************99999999877665 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 3.2e-06
                                   TTSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHH CS
                          GIDA 348 ntLetkkvkgLflAGqinGteGYeEaaaqGllAGinaar 386
                                   + +et+ ++g+++AG+++G     Ea+++G+ AG na+ 
  gi|70605982|ref|YP_254852.1| 264 EFMETE-IRGVYAAGDVTGSFTAHEAISKGITAGYNASG 301
                                   567887.9************8899*************86 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   1.3e-09   1.2e-06       2      38 ..       3      39 ..       2      42 .. 0.94
   2 !    7.7   0.3    0.0017       1.6       2      32 ..     156     186 ..     155     188 .. 0.95
   3 !    7.1   0.0    0.0026       2.4     375     406 ..     253     283 ..     248     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-09
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                  ++ViGsG AGL +A++ +  G kv++veke++ gg+ 
  gi|70605982|ref|YP_254852.1|  3 IVVIGSGPAGLYSAITSSSLGNKVTLVEKEDRLGGTC 39
                                  79******************************99985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                   v++iG+G++G   +  ++  G+++ vveke+
  gi|70605982|ref|YP_254852.1| 156 VVIIGGGVGGVEYGWLLRALGKEIFVVEKEN 186
                                   9****************************96 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0026
                                   EEEBETTSBESTTEEESSBTEEE-STCEESSS CS
                 FAD_binding_2 375 GvetdengrvldadgqpipGLYAaGevaaggv 406
                                   Gv+ d + +v +  ++ i G YAaG v+ g++
  gi|70605982|ref|YP_254852.1| 253 GVPHDKWIKVNEFMETEIRGVYAAGDVT-GSF 283
                                   8999999999999999************.554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     4e-09   3.7e-06       1      35 [.       5      39 ..       5      42 .. 0.97
   2 !   13.0   0.2    0.0001     0.094       1      29 [.     158     186 ..     158     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                  ++G+G +Gl+ A + +  g +v+l+ek drlGG +
  gi|70605982|ref|YP_254852.1|  5 VIGSGPAGLYSAITSSSLGNKVTLVEKEDRLGGTC 39
                                  8********************************87 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                   I+G+G++G  + +lL+  g+++ ++ek +
  gi|70605982|ref|YP_254852.1| 158 IIGGGVGGVEYGWLLRALGKEIFVVEKEN 186
                                   9*************************976 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1   1.9e-09   1.8e-06       2      36 ..       2      36 ..       1      43 [. 0.93
   2 ?    1.6   0.0     0.097        91     144     164 ..     113     132 ..      90     142 .. 0.83
   3 ?    3.0   0.0     0.036        34       2      33 ..     155     186 ..     154     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.9e-09
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +++viG G+AGl+ Ai+ ++ g++V+l+ek+++lg
  gi|70605982|ref|YP_254852.1|  2 RIVVIGSGPAGLYSAITSSSLGNKVTLVEKEDRLG 36
                                  69*****************************9998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.097
                                   EEEE.TTEEEEESEEEE---- CS
                   HI0933_like 144 rvktkseeeleadklvlAtGG 164
                                   +v++ ++++l++dk+++AtG 
  gi|70605982|ref|YP_254852.1| 113 SVEV-NGQTLSSDKIIIATGT 132
                                   5778.99************96 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.036
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                   +v++iGgG  G+     +++ gk++ ++ek++
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVVEKEN 186
                                   89**********99999999999999999986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.2e-10   4.9e-07       2      39 ..       3      40 ..       2     136 .. 0.90
   2 ?    2.9   0.2     0.059        56       2      33 ..     156     187 ..     155     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.2e-10
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                  +vV+G+gpaG+  Ai++   G kv Lve++++lGG+  
  gi|70605982|ref|YP_254852.1|  3 IVVIGSGPAGLYSAITSSSLGNKVTLVEKEDRLGGTCV 40
                                  8**********************************865 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.059
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                   vv++GGg++Gv         G++  +ve+++ 
  gi|70605982|ref|YP_254852.1| 156 VVIIGGGVGGVEYGWLLRALGKEIFVVEKENL 187
                                   9**********988888888888888888765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.7e-05     0.025      30      60 ..       2      32 ..       1      36 [. 0.92
   2 !   10.6   0.0   0.00028      0.26      30      62 ..     155     187 ..     151     228 .. 0.87
   3 ?    4.4   0.9     0.022        20      17     102 ..     273     369 ..     261     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                  +++viG G aGl ++ t+++lg kVt+++++
  gi|70605982|ref|YP_254852.1|  2 RIVVIGSGPAGLYSAITSSSLGNKVTLVEKE 32
                                  79************************99876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00028
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                   kv++iGgGv G++  +  ++lg ++ v++++  
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVVEKENL 187
                                   8*************************9998765 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.022
                                   EETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-..EEEEEESSHHHHHHHHHTTTCECEE.........HCHHHHHHH CS
                   AlaDh_PNT_C  17 gtlaGgvpgvepakvlviGgGvaGlqAiatakglga..kVtvlDvrparleqleslgakfvev.........lksqeella 86 
                                   + +aG v+g   a+  +  g +aG +A  +a++     +V+v+ ++p+ +   ++  +k v++          +++ e + 
  gi|70605982|ref|YP_254852.1| 273 VYAAGDVTGSFTAHEAISKGITAGYNASGIASRYRSdgIVKVIYTKPQIAYVGDTTRGKCVKLnmasltraiAEKETEGFV 353
                                   6789999999999999999999*****99999887622699999999887777779999999999****9999999999** PP

                                   HHHHH-SEEEE---BT CS
                   AlaDh_PNT_C  87 eavkeadvvigtvlip 102
                                   + + e d vig+v+  
  gi|70605982|ref|YP_254852.1| 354 KVCVEDDKVIGAVAFS 369
                                   ************9865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   2.1e-05      0.02       4      34 ..       3      33 ..       1      37 [. 0.93
   2 !   11.3   0.0   0.00015      0.14       3      34 ..     155     186 ..     154     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                                  EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  ++++G+GpaGl +a   s+ G +v+lvek +
  gi|70605982|ref|YP_254852.1|  3 IVVIGSGPAGLYSAITSSSLGNKVTLVEKED 33
                                  78**************************976 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                   +V+I+G+G  G+  + lL+  G +  +vek +
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVVEKEN 186
                                   69***************************976 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.4e-06     0.006       1      36 [.       2      38 ..       2      41 .. 0.94
   2 ?   -1.4   0.0       1.5   1.4e+03     157     201 ..      96     131 ..      86     145 .. 0.71
   3 !    8.7   0.8    0.0012       1.2       1      29 [.     155     185 ..     155     188 .. 0.90
   4 ?   -1.6   0.0       1.6   1.5e+03     153     179 ..     201     225 ..     192     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.4e-06
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                  ++v+iG+G +Gl  A   +  g  Vtl+ek+d++g g+
  gi|70605982|ref|YP_254852.1|  2 RIVVIGSGPAGLYSAITSSSLGnkVTLVEKEDRLG-GT 38
                                  59****************99999**********99.76 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                   HHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE.EEEEEEEE--G CS
                           DAO 157 ealGveilegtevtgleeedgkvwgve.rttpgen.daadavVnaaG 201
                                   e+  v+i+ g+ + +          ve +   g++ ++ d++++a+G
  gi|70605982|ref|YP_254852.1|  96 EKYNVDIIHGRAILKG-------NSVEvN---GQTlSS-DKIIIATG 131
                                   5566777777666653.......334213...777566.99*****9 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0012
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29 
                                   +vviiGGG+ G+   + L + g  + ++ek+
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGkeIFVVEKE 185
                                   59****************66689******98 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.6
                                   HHHHHHTT-EEEESECEEEEEEEETCE CS
                           DAO 153 araaealGveilegtevtgleeedgkv 179
                                     ++++ G  +l+g ev+++e++  kv
  gi|70605982|ref|YP_254852.1| 201 TYTFRKMGFSLLLGKEVKKIERN--KV 225
                                   556899999***********774..22 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00044      0.41       1      35 [.       2      33 ..       2      75 .. 0.85
   2 ?    2.7   0.1     0.048        46       1      36 [.     155     187 ..     155     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00044
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                  +iv++G G+aG  +A++ +  +    +vtlve+e+
  gi|70605982|ref|YP_254852.1|  2 RIVVIGSGPAGLYSAITSSSLG---NKVTLVEKED 33
                                  69***************99999...57*****986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.048
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36 
                                   k+vi+GGG  G     +l+  +    e+ +ve+e++
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALG---KEIFVVEKENL 187
                                   79*********99999998888...56999999975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.11      20      65 ..       3      47 ..       1     118 [. 0.87
   2 ?   -0.4   0.0      0.58   5.5e+02      19      48 ..     155     183 ..     141     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                  EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                          Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                  +v++G+G++GL +a + +   + kv+++e++  +GG   l G + s
  gi|70605982|ref|YP_254852.1|  3 IVVIGSGPAGLYSAITSSSL-GNKVTLVEKEDRLGGTCVLYGCIPS 47
                                  9************9988877.99*************9988876654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.58
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvaile 48 
                                    vvi+G+G  G+  +  l    + ++ ++e
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRAL-GKEIFVVE 183
                                   599******999888777555.55566666 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0022       2.1       2      30 ..      11      39 ..      10      41 .. 0.91
   2 ?    1.9   0.0      0.11   1.1e+02     224     257 ..     210     239 ..     198     243 .. 0.86
   3 ?   -3.3   0.1       4.3   4.1e+03     416     447 ..     268     295 ..     263     295 .. 0.80
   4 ?   -1.0   0.0      0.89   8.4e+02     213     235 ..     372     393 ..     325     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0022
                                  HHHHHHHHHHHTTEEEEEEESSSSSBTTS CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRi 30
                                  aGL  A + +s G +Vt++E +dr+GG +
  gi|70605982|ref|YP_254852.1| 11 AGLYSAITSSSLGNKVTLVEKEDRLGGTC 39
                                  899999999999***************65 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                                   EEETSEEEEEEEEETTCEEEEETTSTEEEESEEE CS
                 Amino_oxidase 224 dirlntrVkeikregdgvtvtledgevveaDaVv 257
                                   +++l+++Vk+i+r     +v l dg+++e+D ++
  gi|70605982|ref|YP_254852.1| 210 SLLLGKEVKKIER----NKVVLDDGKEIEGDIIL 239
                                   689**********....888889******99765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.3
                                   HHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHHH CS
                 Amino_oxidase 416 pegdprlffAGehtsreypgt.vegAilSGlra 447
                                   +  + +++ AG+ t     +   + Ai+ G++a
  gi|70605982|ref|YP_254852.1| 268 T-EIRGVYAAGDVTG----SFtAHEAISKGITA 295
                                   4.6789999***999....44499999999976 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.89
                                   HHHHHHTTTTEEEETSEEEEEEE CS
                 Amino_oxidase 213 pealaeelrgldirlntrVkeik 235
                                   +e + +  +gl ir+n +Vke++
  gi|70605982|ref|YP_254852.1| 372 AEEIVS-VLGLAIRYNIKVKELA 393
                                   344445.8999999999999986 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032       0.3       1      32 [.       1      32 [.       1      35 [. 0.94
   2 ?   -1.2   0.0       1.3   1.3e+03     108     126 ..     118     136 ..      84     149 .. 0.79
   3 ?   -0.0   0.2      0.59   5.6e+02       2      31 ..     155     184 ..     154     188 .. 0.87
   4 ?   -1.7   0.0       1.9   1.8e+03      43      76 ..     341     374 ..     324     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S- CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDid 32
                                  m+i+viG+G  Gl +a+  +++g++v++v ++
  gi|70605982|ref|YP_254852.1|  1 MRIVVIGSGPAGLYSAITSSSLGNKVTLVEKE 32
                                  89**************************9876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                   HHHHHCEEEEEE-S---TT CS
                UDPG_MGDP_dh_N 108 aealkkgkvvvvkSTvpvg 126
                                   +++l+++k+++   Tv ++
  gi|70605982|ref|YP_254852.1| 118 GQTLSSDKIIIATGTVKPQ 136
                                   4566777777777777765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.59
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDi 31 
                                   k+++iG G  G+  + +l ++g+e+ +v +
  gi|70605982|ref|YP_254852.1| 155 KVVIIGGGVGGVEYGWLLRALGKEIFVVEK 184
                                   899***9988888999999*****999976 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.9
                                   S-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC CS
                UDPG_MGDP_dh_N  43 kipiyepgLeelvkkavesgrlsfttdvekavee 76 
                                      i e++ e  vk +ve++++ +   +++ +ee
  gi|70605982|ref|YP_254852.1| 341 TRAIAEKETEGFVKVCVEDDKVIGAVAFSERAEE 374
                                   4568899999999999998888888887776654 PP

>> Rubredoxin_C  Rubredoxin NAD+ reductase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.4   3.2e+03      46      69 ..     269     292 ..     265     293 .. 0.78
   2 ?   10.5   0.0   0.00045      0.43      27      55 ..     344     370 ..     325     376 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.4
                                   EEEEEEEES-HHHHHHHHHHHHTT CS
                  Rubredoxin_C  46 klvGAiliGDtkesaklkkliekk 69 
                                    + G    GD++ s +  ++i k+
  gi|70605982|ref|YP_254852.1| 269 EIRGVYAAGDVTGSFTAHEAISKG 292
                                   577777889999999999999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00045
                                   EEEE-SS-..EEEEEEETTEEEEEEEES- CS
                  Rubredoxin_C  27 lveedkekgkYkklfikngklvGAiliGD 55 
                                   + e+++e     k++++++k++GA+ + +
  gi|70605982|ref|YP_254852.1| 344 IAEKETE--GFVKVCVEDDKVIGAVAFSE 370
                                   4444444..499*************9865 PP

>> Gp_UL130  HCMV glycoprotein pUL130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.17      72     123 ..     343     394 ..     284     403 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   HHHHSSS-------HHHHHHHHHHS-SEEEEEEEEEEEETTEEEEEEEEEEE CS
                      Gp_UL130  72 rtaskpsdgnvqisvedakifgahmvpkqtkllrfvvndgtryqmcvmkles 123
                                     a k ++g v++ ved k++ga    ++++ +  v+    ry++ v +l  
  gi|70605982|ref|YP_254852.1| 343 AIAEKETEGFVKVCVEDDKVIGAVAFSERAEEIVSVLGLAIRYNIKVKELAE 394
                                   358899************************9999999999***999988765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00023      0.21       2      35 ..       3      34 ..       2      44 .. 0.91
   2 ?   -2.2   0.1       1.7   1.6e+03       2      14 ..     156     168 ..     155     191 .. 0.74
   3 ?   -0.5   0.0      0.51   4.8e+02     109     141 ..     217     244 ..     192     255 .. 0.75
   4 ?   -3.8   0.1       5.1   4.8e+03     111     132 ..     343     365 ..     331     367 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasps 35
                                  +vviG+GpAgl  A  +  +  g kv+l+e  + 
  gi|70605982|ref|YP_254852.1|  3 IVVIGSGPAGLYSAITS--SSLGNKVTLVEKEDR 34
                                  79************999..**********98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                 Lycopene_cycl   2 vvviGaGpAglsl 14 
                                   vv+iG+G  g+  
  gi|70605982|ref|YP_254852.1| 156 VVIIGGGVGGVEY 168
                                   89*****999865 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.51
                 Lycopene_cycl 109 vesveeeeageslvvleggrkirarlvvdargl 141
                                   v+++e +      vvl++g++i++ +++ + g 
  gi|70605982|ref|YP_254852.1| 217 VKKIERN-----KVVLDDGKEIEGDIILMSFGR 244
                                   4444444.....46**********999988874 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 5.1
                 Lycopene_cycl 111 sveeeea.geslvvleggrkira 132
                                   +++e+e  g + v++e+++ i a
  gi|70605982|ref|YP_254852.1| 343 AIAEKETeGFVKVCVEDDKVIGA 365
                                   44444444788999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2964.33
//
Query:       gi|70605983|ref|YP_254853.1|  [L=428]
Description: thiamine biosynthesis protein ThiC [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.2e-165  549.0   0.0   7.3e-165  548.8   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.8   0.0  4.1e-169  7.3e-165       3     415 ..       4     419 ..       2     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 548.8 bits;  conditional E-value: 4.1e-169
                  ThiC_Rad_SAM   3 leaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdieeEveKlk 82 
                                   +e+ar+giit+e++++++ e+v+pe+vr+++aeG+i++++n+++++k  v iGkgl+tk+n+niGts+++ d+++E+eK+k
  gi|70605983|ref|YP_254853.1|   4 IEEARRGIITDEIKSISKLEKVSPEKVRKRIAEGKIMLLRNVKRPSKkLVPIGKGLTTKININIGTSSEVIDLDMELEKVK 84 
                                   799*****************************************6665********************************* PP

                  ThiC_Rad_SAM  83 valkagadtvmdLstggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdfltiHag 160
                                   ++ k+g dt+mdLstggdideir+ki+++s++pvgtvp+Yqa+ +   k++  + ++e+ell+++e+q +dGv f+tiHag
  gi|70605983|ref|YP_254853.1|  85 ISNKWG-DTLMDLSTGGDIDEIRRKIIDKSDLPVGTVPVYQAFIQsfkKKSGGAYFSEDELLSIVERQLKDGVAFMTIHAG 164
                                   *****9.************************************998877777899************************** PP

                  ThiC_Rad_SAM 161 vtlellellkkekRltgivSrgGsllaawmlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaeli 241
                                   +t+el+ ++ k++R++ ivSrgG ++a wm++n+kenp+ +++ +lle++keyd t+Slgd+lRpG++aDa+de q+ eli
  gi|70605983|ref|YP_254853.1| 165 LTRELAIRALKSDRVIPIVSRGGDMIAGWMIHNGKENPYRTNWKYLLELFKEYDATISLGDALRPGATADAHDEFQIGELI 245
                                   *******9999********************************************************************** PP

                  ThiC_Rad_SAM 242 vlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPfyvlGplvtDiapgYDhitsaiGaalaaaaGadllCy 322
                                    +++lvk a ++gvqvmveGPGHvpl+e++ +vkl+kkl+ ++P+yvlGplv+D+++ YDhi+s+iGaa+a+aaGadllCy
  gi|70605983|ref|YP_254853.1| 246 ETARLVKDAINNGVQVMVEGPGHVPLNEVAWDVKLMKKLTGGVPYYVLGPLVIDVGAPYDHIASSIGAAIASAAGADLLCY 326
                                   ********************************************************************************* PP

                  ThiC_Rad_SAM 323 vtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfelaldpekareireeklpeeeea 403
                                   +tpaEHl+lP++++v+eG ia++iaaha+d++k  kk r++d+++s +R +l+w+k++e  +dpe+a +++++  + + +a
  gi|70605983|ref|YP_254853.1| 327 LTPAEHLSLPNAKQVEEGAIAYRIAAHAGDIVKLGKKVRKWDDEVSYYRGKLEWDKMIEKLIDPEQAYKVYTQFGEPNVKA 407
                                   ***************************************************************************99**** PP

                  ThiC_Rad_SAM 404 CsmCgekCavki 415
                                   C+mCg +C +  
  gi|70605983|ref|YP_254853.1| 408 CTMCGGYCPMMW 419
                                   *********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2881.27
//
Query:       gi|70605984|ref|YP_254854.1|  [L=284]
Description: hypothetical protein Saci_0138 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0028   18.0   0.3      0.084   13.3   0.3    2.6  2  GTP_EFTU_D2  Elongation factor Tu domain 2


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.018   3.3e+02      29      50 ..      38      56 ..      23      90 .. 0.77
   2 !   13.3   0.3   4.7e-06     0.084      13      67 ..     152     200 ..     151     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.018
                                  EEEEEEEEEEEEETEEESEEET CS
                   GTP_EFTU_D2 29 keivtrissletfhededeava 50
                                      + i+s++++++ +d+a+a
  gi|70605984|ref|YP_254854.1| 38 G---EHIRSILVPQKLLDQAEA 56
                                  4...789***********9954 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.7e-06
                                   EETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGS CS
                   GTP_EFTU_D2  13 lkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledai 67 
                                   +++ d++  l+++  k+   ++++s+++  ed++ + +g+++G+ ++ +++ed i
  gi|70605984|ref|YP_254854.1| 152 VRPHDKLIALPMK--KE---VEVKSIQVLDEDQEGVLPGVRIGFALKNVKIED-I 200
                                   7899999998863..67...********************************9.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2064.66
//
Query:       gi|70605985|ref|YP_254855.1|  [L=93]
Description: hypothetical protein Saci_0139 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-22   78.1   0.1    6.2e-22   77.9   0.1    1.0  1  Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
  ------ inclusion threshold ------
      0.027   14.7   0.0       0.04   14.1   0.0    1.3  1  OSR1_C       Oxidative-stress-responsive kinase 1 C-terminal 


Domain annotation for each model (and alignments):
>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.1   6.9e-26   6.2e-22       5      90 ..       3      90 ..       1      91 [. 0.97

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 6.9e-26
                   Arc_PepC_II  5 ymligyrvkvkell.kkflflleefeekdgkikrkfisvekeldeelrkelkkykkkglieet..vWvtygvPflipitaGfi 84
                                  ++++++r+kvk++l +kflf+l+ ++ek+++  r++++ve e+dee+rk +++y+ kgli e+  +Wv++gvP++++ ++G++
  gi|70605985|ref|YP_254855.1|  3 LAISARRIKVKDFLsSKFLFPLTVIDEKGNQSIRTSFDVE-EDDEEWRKLYREYVGKGLIREEdyIWVMWGVPVIPFFFLGYL 84
                                  6889*********99****************9999*****.9******************9999******************* PP

                   Arc_PepC_II 85 ialvlG 90
                                  i+lv+G
  gi|70605985|ref|YP_254855.1| 85 ISLVIG 90
                                  *****9 PP

>> OSR1_C  Oxidative-stress-responsive kinase 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.4e-06      0.04      17      55 ..      29      69 ..      22      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.4e-06
                        OSR1_C 17 qkeneaIqFeFdlgkDtae..evaqelvkaglvdeeDvkvv 55
                                  +k n+ I+ +Fd+++D+ e  +  +e v  gl+ eeD+  v
  gi|70605985|ref|YP_254855.1| 29 EKGNQSIRTSFDVEEDDEEwrKLYREYVGKGLIREEDYIWV 69
                                  799*************998778***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 673.14
//
Query:       gi|70605986|ref|YP_254856.1|  [L=279]
Description: hypothetical protein Saci_0140 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-58  197.4  29.3    5.3e-55  186.7  25.7    2.0  2  DUF973    Protein of unknown function (DUF973)
  ------ inclusion threshold ------
       0.95    8.9   2.4        1.8    8.0   2.4    1.4  1  Sec62     Translocation protein Sec62


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8     6e-07    0.0053       1      35 [.       7      41 ..       7      44 .. 0.90
   2 !  186.7  25.7   5.9e-59   5.3e-55      62     309 ..      35     276 ..      32     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-07
                        DUF973  1 eiegleklregslfliiasllaliliilvlvvlft 35
                                  ++++l+kl+++sl++ii+ +l +++ +  l+++++
  gi|70605986|ref|YP_254856.1|  7 DLDALNKLKDASLWFIIIGILYFVGFFFALIIIVP 41
                                  5789**********************999988776 PP

  == domain 2  score: 186.7 bits;  conditional E-value: 5.9e-59
                        DUF973  62 aiiliiiasvlli.lgllkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsllslilslillgviilligi 141
                                   a+i ii+ ++l++ +g+ k+r++f+ +s++g++v+ G tgl+l++ g ii++ig +l+            l+gv+++ +g+
  gi|70605986|ref|YP_254856.1|  35 ALI-IIVPLILYFvVGIPKLRDAFQAFSNLGKNVNLGLTGLNLLIYGFIIAFIGGVLTF--------LVPLAGVALVGVGV 106
                                   444.45566666515666**************************************666........345799******** PP

                        DUF973 142 ilaliGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsklrsttsqvpvlq.vpstp.... 217
                                   +l++++q+l+g++ y++G+ Yn++l++igGi+ i     +lsfIG+il+yi++++v+++ r  ++q+p++  +ps p    
  gi|70605986|ref|YP_254856.1| 107 LLIFVAQVLIGVALYNIGNSYNSSLMSIGGIVEI-----FLSFIGWILIYISIDEVINRFRGMPAQSPTTFgTPSYPsgpt 182
                                   ******************************9876.....46********************77777765532566666667 PP

                        DUF973 218 .qqvqisqvgqGtlrsnGtanltvysqvq.vqIlsAsiegtnysttsinPntLkvGnNsitinFntvlnLvpgstYtirLl 296
                                        i+qvg+  l+ nG+ ++t+ys+v   +I+sA+ie  +++tt+i+P++L++GnN+iti F tv++L+ g +Yt+ L 
  gi|70605986|ref|YP_254856.1| 183 yMPPAIYQVGTAYLKPNGELKVTLYSNVAgISIISATIEAFSITTTNISPSVLNQGNNQITILFPTVTGLSIGGNYTVALS 263
                                   66789**********************97369************************************************* PP

                        DUF973 297 Lsngqtidvevty 309
                                   Lsngq ++v+++y
  gi|70605986|ref|YP_254856.1| 264 LSNGQVVRVTAFY 276
                                   ***********99 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.4    0.0002       1.8     137     168 ..      19      51 ..      13      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0002
                         Sec62 137 vyYLSiaalgllglilalai.vRlilflivllv 168
                                    +++ i++l ++g+++al i v lil+ +v + 
  gi|70605986|ref|YP_254856.1|  19 LWFIIIGILYFVGFFFALIIiVPLILYFVVGIP 51 
                                   699*************98753789999988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1936.88
//
Query:       gi|70605987|ref|YP_254857.1|  [L=222]
Description: hypothetical protein Saci_0141 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-42  146.0   0.0    1.6e-42  145.7   0.0    1.0  1  Creatininase  Creatinine amidohydrolase
  ------ inclusion threshold ------
      0.019   14.7   0.6      0.028   14.1   0.6    1.3  1  DUF2101       Predicted membrane protein (DUF2101)


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   0.0   1.8e-46   1.6e-42      14     240 ..      12     216 ..       7     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 1.8e-46
                  Creatininase  14 eddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTislspetliavlrdiles 94 
                                   ++++a++PvGs+EqHGphlp+gtD++iae++a+rv+e+l+  +l++Pt++y +s eh+gfp    +s  t+++++ +il+s
  gi|70605987|ref|YP_254857.1|  12 QNKIALIPVGSLEQHGPHLPMGTDSIIAEEIAKRVEEELNNVVLLFPTVYYTCSMEHEGFPY-AGVSYITFASYMLEILNS 91 
                                   678************************************988*******************9.79**************** PP

                  Creatininase  95 larhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeee.gggHAgelEtSlm 174
                                   +++   ++ vlv gHgg +++++++ r+l+  + + + + t      ++            ++ ee+ ++ HAg +EtS +
  gi|70605987|ref|YP_254857.1|  92 ISKF-SKKAVLVIGHGGVVSVIDVVKRQLNFTN-KTFKVYT------FT------------VQ-EENsEDLHAGTIETSAI 151
                                   ***9.9*************************99.4443211......11............22.333499*********** PP

                  Creatininase 175 lalrpelVrmdraedpeeaklakegvstaedaeelspsGvlGdps.kataekGealleaaveelael 240
                                     ++p+lV++d+++d +   ++   v    +++e +p+G++ + +   ++ekG+ ++ + ve+l +l
  gi|70605987|ref|YP_254857.1| 152 KVINPKLVNEDKLKDVDYSFQEG--VFDIITTKESNPYGIINKGKvVIDEEKGRVFISKNVEKLKRL 216
                                   ************99988764443..67777777878*****8776489***********99999776 PP

>> DUF2101  Predicted membrane protein (DUF2101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   3.1e-06     0.028      90     159 ..      71     144 ..      52     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-06
                       DUF2101  90 f.ylavsviailaylgyvl..lrklslelyyylvyllviviv.vlvfryyfksrygrDytyGvveevkedlvkv 159
                                   f y +vs i++ +y+  +l  + k+s++++  +   +v++++ v+  ++ f ++  + yt+ v ee  edl   
  gi|70605987|ref|YP_254857.1|  71 FpYAGVSYITFASYMLEILnsISKFSKKAVLVIGHGGVVSVIdVVKRQLNFTNKTFKVYTFTVQEENSEDLHAG 144
                                   44*************99985567888888888888888877636666789*******************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1691.24
//
Query:       gi|70605988|ref|YP_254858.1|  [L=386]
Description: hypothetical protein Saci_0144 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-19   68.3  28.6    2.7e-12   46.3  16.6    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3  16.6   1.5e-16   2.7e-12       1     238 [.      10     240 ..      10     263 .. 0.81
   2 !   27.1   5.2     1e-10   1.8e-06      67     186 ..     264     379 ..     256     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.5e-16
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   l+++++++ +++++l++++pl l ++ + s + +g+ + l  l+ +++s+++Gr++dr+  r ++++ l ++++g++ll+f
  gi|70605988|ref|YP_254858.1|  10 LFIGQAFIVAGSTLLSLLYPLVLYDQTH-STALLGISMMLNELAVGLGSYVWGRIIDRVRERYIFFIILPVSGIGITLLIF 89 
                                   799*****************87777777.999***************************6666************888888 PP

                         MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                     +  l lv+ +l G+++++  p+  +l+ + f+ ++   a+++ls  + +G i+g + g + +  +     f i+a++ +
  gi|70605988|ref|YP_254858.1|  90 -DT-SLGLVGYALLGFFTALDSPIYSILLLERFSMDKAVVANSMLSQLSLAGNIIGSIMGTFKLKFFTIIIFFTIAAVLNA 168
                                   .33.37**********************************************************88888888888888888 PP

                         MFS_1 163 lafvlfllll.peepperkrkspkeeekgtgpaplvpawkallkdpvlw....illialllfffgfsglltllplylqevl 238
                                   +++     +    ++ + +r +++++      +pl++ ++++  +  ++    i l+ ll+    ++++++++ ly+ + +
  gi|70605988|ref|YP_254858.1| 169 ILIP---RYKgDIREDKVERIRDTRR----LLKPLIS-YSIFNLSAEVFyvvyIPLLNLLTLP-SWTYFVSYTILYMIDEY 240
                                   8744...4442333333333333333....6677777.6666555544324557888888887.88889999999987765 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1e-10
                         MFS_1  67 lglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllas 146
                                    g+l+ ++g +ll++ +++  l ++l +  G  + ++++a  +li +  +k +rg+ +gl+sag++l++++g  l+gl+  
  gi|70605988|ref|YP_254858.1| 264 RGFLVALVG-YLLFMKINFSfLTVLLFISFGSLYPLYNTALFSLIFKDLKK-NRGSILGLFSAGNNLASAMGSYLSGLVNP 342
                                   477777777.66665478774444444444444455555555555555555.****************************6 PP

                         MFS_1 147 slgWravfyilaivsllafvlfllllpeepperkrkspke 186
                                       +a f+ + ++sl +f+   ++ + ++++ + +++k+
  gi|70605988|ref|YP_254858.1| 343 MSISQAYFFSFFGFSLSFFI---MYDYISEKRQRVENKKK 379
                                   66678889999999999988...88888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2311.22
//
Query:       gi|70605989|ref|YP_254859.1|  [L=311]
Description: thioesterase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.5e-22   77.2   0.1    1.1e-10   41.7   0.0    2.2  2  4HBT       Thioesterase superfamily
    1.6e-05   25.4   0.0     0.0019   18.7   0.0    2.2  2  4HBT_2     Thioesterase-like superfamily
  ------ inclusion threshold ------
       0.16   12.2   0.6       0.87    9.8   0.2    2.1  2  Synuclein  Synuclein


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   6.2e-12   3.7e-08       2      78 ..      23      98 ..      22      99 .. 0.86
   2 !   41.7   0.0   1.9e-14   1.1e-10       3      76 ..     182     258 ..     180     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.2e-12
                                  SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                          4HBT  2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78
                                  G +hgGv+l++l  ++ + + + +++  +v ++ + + f++p+ lgd + vea+ +++g++s++v+ +  +++++lv
  gi|70605989|ref|YP_254859.1| 23 GRLHGGVMLNFLVDTGMMSAIRVAKG-LAVIASLDDVIFKKPISLGDNIAVEAEAEYVGNSSVEVSMRALRDEETLV 98
                                  88********8755555555555554.8*******************************************999886 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 1.9e-14
                                   SB-HHHHHHHHHHHHHHHHHHTTST...TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSC CS
                          4HBT   3 vvhgGvylallDeaagaalrslggr...gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgr 76 
                                   ++  G +l+++D  +g+++ ++ +    g++v+v+  ++ f  p+rlgd ++++a ++++g+ts+++ + v + d++
  gi|70605989|ref|YP_254859.1| 182 IISAGKLLKAMDDLGGVLCGRYIKQsepGTVVTVAVNRMSFYTPIRLGDIVEIRAGIIYVGNTSIETLINVIRIDPK 258
                                   677899*************************************************************9999988776 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.1e-07    0.0019      11     105 ..      15     108 ..      12     137 .. 0.87
   2 !    4.9   0.0    0.0058        35      45     116 ..     212     285 ..     131     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.1e-07
                        4HBT_2  11 hlnnarylrylee.arvkflertglksrsiarrgiglilssahvryrrplkfpdrltvefrvididaktliiehrflsnad 90 
                                   h ++  yl  l+  ++ +fl +tg+ s  + ++g ++i s + v +++p+ ++d + ve    ++  +++ + +r l+  d
  gi|70605989|ref|YP_254859.1|  15 HYEHINYLGRLHGgVMLNFLVDTGMMSAIRVAKGLAVIASLDDVIFKKPISLGDNIAVEAEAEYVGNSSVEVSMRALR--D 93 
                                   77778888777776889********99999999********************************************9..7 PP

                        4HBT_2  91 gkkaarveerivvmd 105
                                     +  +++ ++v +d
  gi|70605989|ref|YP_254859.1|  94 EETLVEATGTYVKID 108
                                   777666666665555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0058
                        4HBT_2  45 glilssahvryrrplkfpdrltvefrvididaktliiehrfls...nadgkk.aarveerivvmdygkrskkapvP 116
                                    + ++ ++  +  p++++d ++++  +i++  +++     +++   ++  k+   ++  ++v +d+++  k+  vP
  gi|70605989|ref|YP_254859.1| 212 VVTVAVNRMSFYTPIRLGDIVEIRAGIIYVGNTSIETLINVIRidpKTMMKEhITTGYFTYVRVDSTG--KPIRVP 285
                                   4444445899**************99999888888888777775532222334566777777777755..455555 PP

>> Synuclein  Synuclein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00014      0.87      68     120 ..      77     130 ..      68     147 .. 0.67
   2 ?    0.0   0.0      0.15   9.1e+02      35      50 ..     236     251 ..     233     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                     Synuclein  68 eavvtsvnavaektvegaeniaaatG.lvkkedlekdl..peeegeeasevedeal 120
                                   e v +s  +v++++++++e+++ atG  vk +dl k++  +++  ++++e++    
  gi|70605989|ref|YP_254859.1|  77 EYVGNSSVEVSMRALRDEETLVEATGtYVKIDDLFKPIiiENKLIADTEEEK--RR 130
                                   445556667*****************88******999843333334433322..22 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                     Synuclein  35 eGvlyvGsktkegvvq 50 
                                    G++yvG+   e +++
  gi|70605989|ref|YP_254859.1| 236 AGIIYVGNTSIETLIN 251
                                   69*****998888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2066.25
//
Query:       gi|70605990|ref|YP_254860.1|  [L=130]
Description: hypothetical protein Saci_0146 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   14.0   0.1      0.024   14.0   0.1    1.1  1  V-ATPase_C  V-ATPase subunit C
       0.15   12.2   0.4         13    6.0   0.0    2.4  2  DUF3885     Domain of unknown function (DUF3885)


Domain annotation for each model (and alignments):
>> V-ATPase_C  V-ATPase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.7e-06     0.024      89     150 ..      57     118 ..       3     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-06
                    V-ATPase_C  89 lvngkslesYltkFqWdeakypvkqslkelvdiiskevtqidedlktksaaYnelksslqal 150
                                   ++ + sle+Yl  F+ d+++++ ++  ++++++i+++ +qi  +l+  + +Y++++++  ++
  gi|70605990|ref|YP_254860.1|  57 VIISLSLEEYLPIFSADSKRIEYNEIPEDVIKVIKTNWKQILGQLRDYLLEYSKIDKKYLEV 118
                                   4445679************************************************9887655 PP

>> DUF3885  Domain of unknown function (DUF3885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0015        13       5      23 ..      52      70 ..      49      74 .. 0.90
   2 ?    4.1   0.2    0.0058        52      16      34 ..      91     109 ..      85     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0015
                       DUF3885  5 DDRGcdvisnnketlkelY 23
                                  D RG+++is + e + +++
  gi|70605990|ref|YP_254860.1| 52 DRRGVVIISLSLEEYLPIF 70
                                  78***********999997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0058
                       DUF3885  16 ketlkelYekyndWIlDYd 34 
                                   k   k++  + +d++l+Y 
  gi|70605990|ref|YP_254860.1|  91 KTNWKQILGQLRDYLLEYS 109
                                   55668899999*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 805.69
//
Query:       gi|70605991|ref|YP_254861.1|  [L=605]
Description: hypothetical protein Saci_0147 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-15   56.8   4.8    1.2e-14   54.9   3.3    2.5  2  DUF87          Helicase HerA, central domain
      3e-08   32.7   0.0     0.0045   15.6   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    3.5e-07   29.5   0.0    1.7e-06   27.2   0.0    1.9  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    5.8e-05   23.5   0.6      0.021   15.2   0.1    2.5  2  AAA            ATPase family associated with various cellular
    7.9e-05   21.7   0.1       0.54    9.1   0.0    3.1  3  AAA_10         AAA-like domain
      0.001   19.4   0.0       0.74   10.1   0.0    2.5  2  AAA_22         AAA domain
     0.0031   17.5   0.0       0.76    9.8   0.0    2.3  2  ResIII         Type III restriction enzyme, res subunit
     0.0056   16.1   0.0     0.0098   15.3   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.35   10.5   0.0    1.6  1  Zot            Zonular occludens toxin (Zot)


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   3.3   6.2e-18   1.2e-14      10     227 .]     178     460 ..     168     460 .. 0.79
   2 ?   -1.1   0.0      0.81   1.6e+03     156     197 ..     492     540 ..     465     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 6.2e-18
                         DUF87  10 sevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal..................... 68 
                                    +++v++ l+ l + H++ilg+TG+GK+ +v+  ++ +++    +++ ++D+ G+Y++ +                     
  gi|70605991|ref|YP_254861.1| 178 GNIKVSISLDDL-NYHTLILGTTGAGKTSFVKDVIAGIYSiAELTKVFVFDATGDYYHVFlppdktdknvsqslalfesly 257
                                   469******888.**************************987778************************************ PP

                         DUF87  69 .............................................ekllsekvkvitpspsa................... 85 
                                                                                +                                   
  gi|70605991|ref|YP_254861.1| 258 pklsglnlsiiyplsrkwirkytngnkdllsitnayfklyvypmiN---------------Ylskkgykfyhsvsegrivv 323
                                   9999999999977777777665555555555555555555555550...............05555555555555555556 PP

                         DUF87  86 ....kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklkn 162
                                        + e++i p  ++++e+ ++l+  ++  +++ +++l+ +l+     ++ ++++s +++ ++le++    +++ ++ +
  gi|70605991|ref|YP_254861.1| 324 snseWKSEVEIFPFYFKFDEIKKVLPRLNPYFSEQATQFLKILLK-----RKGKDYNSLASLTESLEDYD---LDNLSIHK 396
                                   6555899********************444444445555555555.....66777888887887888877...999***** PP

                         DUF87 163 qaiarlldkledllrkggsfsnsstdliallleklekegkitiidl..sgvdelaqqlvvsvilrri 227
                                   ++++++l+ l+ l ++g ++   + +++  l   l++++k+ i+dl  s++d+ aq++v+ ++l +i
  gi|70605991|ref|YP_254861.1| 397 STKENILRGLYLLRSTGLFDVGVKREPLGRL---LTSDRKLLILDLynSELDDFAQKIVTYYFLDKI 460
                                   ***********88888888877777777777...9***********555699999999999998875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.81
                         DUF87 156 elrklknqaiarlldkledllrkggsf.......snsstdlialllekl 197
                                   + ++++ ++ +++  k+++++r g+ +       ++ +tdl + +++++
  gi|70605991|ref|YP_254861.1| 492 KGSEEDANYVRKVAGKISSMMRLGRRRkigfifsTHNPTDLSDIIVQLA 540
                                   5567788899999999999999999888888888888888888876655 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-06    0.0045      10      73 ..     179     244 ..     172     255 .. 0.82
   2 !   14.9   0.0   3.8e-06    0.0075     256     314 ..     474     540 ..     442     547 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                        DUF853  10 eqelalalklanrhGliaGatGtGktvtLq.vlaeslseaGv.pvfladvkGdLsgiakaGevkdk 73 
                                   + ++ ++l+  n h li G tG+Gkt  ++ v+a  +s a    vf+ d  Gd   +  + + +dk
  gi|70605991|ref|YP_254861.1| 179 NIKVSISLDDLNYHTLILGTTGAGKTSFVKdVIAGIYSIAELtKVFVFDATGDYYHVFLPPDKTDK 244
                                   5678899999****************998736778888777526*********9988877777766 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.8e-06
                        DUF853 256 kPklvfffdeahLLf.......ndap..kallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLG 314
                                   k +lv+  deah +f       +da   + +  k+  ++rL r + +G  f t nP+dl d  + qL 
  gi|70605991|ref|YP_254861.1| 474 KERLVLIIDEAHKFFpsgkgseEDANyvRKVAGKISSMMRLGRRRKIGFIFSTHNPTDLSDI-IVQLA 540
                                   789************6555544345422456789999**********************875.55665 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   8.5e-10   1.7e-06       6      63 ..     181     240 ..     176     244 .. 0.87
   2 ?   -0.8   0.0      0.27   5.4e+02     293     312 ..     532     551 ..     529     563 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.5e-10
                 TrwB_AAD_bind   6 gvplpkeretqhilivGttGsGKtqalekllrairarg..draivlDltGafvsrfydeg 63 
                                   +v+++ ++ + h+li+GttG+GKt  +++ +++i + +   ++ v+D+tG++++ f  ++
  gi|70605991|ref|YP_254861.1| 181 KVSISLDDLNYHTLILGTTGAGKTSFVKDVIAGIYSIAelTKVFVFDATGDYYHVFLPPD 240
                                   57888888999***********************98764589************997654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                 TrwB_AAD_bind 293 aaqsilslvntklilrvsda 312
                                    ++ i++l+ntk+i+r++++
  gi|70605991|ref|YP_254861.1| 532 LSDIIVQLANTKIIFRIKPE 551
                                   67789***********9875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0071        14       2      22 ..     194     214 ..     193     236 .. 0.80
   2 !   15.2   0.1   1.1e-05     0.021      46     127 ..     463     543 ..     438     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0071
                                   EEESSTTSSHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakel 22 
                                   l+ G+ G GKT+++k v+  +
  gi|70605991|ref|YP_254861.1| 194 LILGTTGAGKTSFVKDVIAGI 214
                                   789************998765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
                           AAA  46 irelfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                                   ire   ++ + ++  +l+iDE++++++s   s+++ +  ++v+ ++ +++   ++  +k+ +i  t++p +l++ ++ + +
  gi|70605991|ref|YP_254861.1| 463 IREAQMKIGSLKERLVLIIDEAHKFFPSGkgSEEDANYVRKVAGKISSMMRLGRR--RKIGFIFSTHNPTDLSDIIV-QLA 540
                                   444444444444559**************77777777888899999998888888..58***********9999998.444 PP

                                   SEE CS
                           AAA 125 drk 127
                                   + k
  gi|70605991|ref|YP_254861.1| 541 NTK 543
                                   444 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00099         2      21      60 ..     190     231 ..     183     250 .. 0.78
   2 ?    1.2   0.0     0.068   1.3e+02     143     184 ..     360     401 ..     344     406 .. 0.82
   3 !    9.1   0.0   0.00027      0.54     262     302 ..     508     547 ..     464     571 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00099
                        AAA_10  21 asasliiGdlGnGKSvlakll..vlyisllggkaliiDpkke 60 
                                   + ++li+G +G+GK  ++k +    y  +   k+++ D + +
  gi|70605991|ref|YP_254861.1| 190 NYHTLILGTTGAGKTSFVKDViaGIYSIAELTKVFVFDATGD 231
                                   789***********8888854114566666689999998876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.068
                        AAA_10 143 lavieelrkedekvareiarhlesvvkkslaklvfsdgsvee 184
                                   ++ ++ l k++ k+ +++a + es+ +++l +l +++ + e+
  gi|70605991|ref|YP_254861.1| 360 TQFLKILLKRKGKDYNSLASLTESLEDYDLDNLSIHKSTKEN 401
                                   566677788889999999999999999999999999987554 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00027
                        AAA_10 262 lkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr 302
                                   +++++R GR  +   ++ t+++ D+++  + ++  +k++Fr
  gi|70605991|ref|YP_254861.1| 508 ISSMMRLGRRRKIGFIFSTHNPTDLSDI-IVQLANTKIIFR 547
                                   578*********************9874.567778888888 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0039       7.7       6      27 ..     191     212 ..     187     262 .. 0.83
   2 !   10.1   0.0   0.00037      0.74      84     115 ..     470     504 ..     426     555 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0039
                        AAA_22   6 gilvvtGesGtGKTtllrrlle 27 
                                   +++++ G +G+GKT  ++ +  
  gi|70605991|ref|YP_254861.1| 191 YHTLILGTTGAGKTSFVKDVIA 212
                                   6899**********99998765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00037
                        AAA_22  84 qalraravielliiDEaqhlr.....seealeeLrsl 115
                                     + +   + +liiDEa++++     see  +++r+ 
  gi|70605991|ref|YP_254861.1| 470 IGSLKE--RLVLIIDEAHKFFpsgkgSEEDANYVRKV 504
                                   333333..56*********998665447777777655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0085        17      22      58 ..     188     224 ..     158     232 .. 0.80
   2 !    9.8   0.0   0.00038      0.76     114     164 ..     457     515 ..     418     515 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0085
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58 
                                   + + + li  +TG+GKT     +i+ +++ ++  k++
  gi|70605991|ref|YP_254861.1| 188 DLNYHTLILGTTGAGKTSFVKDVIAGIYSIAELTKVF 224
                                   456699999********99888888777766655554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                                   HHHTH........HHHTTT-SEEEEETGGGTTS......T...TTHHHHHT---SEEEE CS
                        ResIII 114 ldadseeeeeeseellrdrfdviiiDEaHrlgak.....k...swreilekfkeavllg 164
                                   ld++ e +e + +  + ++ +v+iiDEaH++  +     +    +r+++ k+++ ++lg
  gi|70605991|ref|YP_254861.1| 457 LDKIFEIREAQMKIGSLKERLVLIIDEAHKFFPSgkgseEdanYVRKVAGKISSMMRLG 515
                                   444442223333333445556*********98865555404535555888888888876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.9e-06    0.0098      28      63 ..     179     214 ..     158     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                                   S-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  28 gnplvldlkkmashllvaGatgsGKStalntLilSl 63 
                                   ++++ + l     h+l++G+tg GK+ +++  i+++
  gi|70605991|ref|YP_254861.1| 179 NIKVSISLDDLNYHTLILGTTGAGKTSFVKDVIAGI 214
                                   5566666777778*****************999876 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.35      81     139 ..     476     541 ..     442     557 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                           Zot  81 gallviDEcqeifpvrakegrkd.......pevinafteh.RhlgwDivlltqdiskihkevralae 139
                                     +l+iDE++++fp  ++  ++d        + i   +++ R+     ++ t +++ + + + +la+
  gi|70605991|ref|YP_254861.1| 476 RLVLIIDEAHKFFPSGKGS-EEDanyvrkvAGKISSMMRLgRRRKIGFIFSTHNPTDLSDIIVQLAN 541
                                   4589**********99995.44556666664444333322144444457777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3663.37
//
Query:       gi|70605992|ref|YP_254862.1|  [L=362]
Description: hypothetical protein Saci_0148 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-22   78.3   0.3      9e-22   77.9   0.3    1.1  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.052   13.4   0.1       0.15   12.0   0.1    1.8  1  DUF5486   Family of unknown function (DUF5486)


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.3     1e-25     9e-22       2     241 ..      56     329 ..      55     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1e-25
                                   EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE............................ CS
                          NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel............................ 54 
                                   +v+A+DGS++++ +s g+ + +s +av+++ k + + +  l+  ++ + ++ +                            
  gi|70605992|ref|YP_254862.1|  56 EVYAIDGSSRSI-FSAGGTISISTVAVSSSNKPVYGVYPGLFGLKGLEIQKPFialapssnskgtinpylysskyimtfsl 135
                                   69**********.*********************************9999999**************************** PP

                                   ...........HHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-TTCEEEE CS
                          NurA  55 ...........errirllmetlElklgallleekgedllllDGsligslvefdelheeleyeeylyslsrlleaglnlvgv 124
                                              er+  +l+++lE +    l+  k+++l+l+DG+l++s v      +e    ++++++ ++l+   n +gv
  gi|70605992|ref|YP_254862.1| 136 dgtpfqstiepERIETELRAILETE---ALKVLKNKGLVLVDGPLFPSYV----YLPERVKTKIINERLSILD--QNFIGV 207
                                   *************************...**********************....9******************..8***** PP

                                   ESS-SCTCCHCCC...............S--HHHHCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEES.... CS
                          NurA 125 aKsfrskellnll.........letlligesisDiallgallrkpgytspllkilrekpllrealidkeiyfaYvrl.... 192
                                   +K++ +++ll ++         +++  ++  +sD a+l +   + +y  p + ++ + pl ++ ++  ++++ Y++     
  gi|70605992|ref|YP_254862.1| 208 VKRIDKSDLLIRTlssnkeltaKYKVDPRGFLSDEAYLYQFV-RFNYNPPYPTLCIG-PLVKDVNERVKVFVNYMIYpihk 286
                                   *****999988878****************************.9***********99.**********************9 PP

                                   .STTTTEEEEEHHHHHH.CCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHC CS
                          NurA 193 .egggsilrleipaevs.takdedvlsllasqrlsisGYprpLalAhelak 241
                                     ++ silr+e     s  +++ d ls+l    +  +G+p +La A++ ak
  gi|70605992|ref|YP_254862.1| 287 yVPKFSILRIE-----SiGKNAVDRLSSLK---FTTEGIPLALAVADKTAK 329
                                   99*********.....44455555555555...***************998 PP

>> DUF5486  Family of unknown function (DUF5486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.6e-05      0.15      29      52 ..      70      93 ..      67      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                       DUF5486 29 aeGtitykrikfkssnePlyGvlC 52
                                  a Gti    +   ssn P+yGv  
  gi|70605992|ref|YP_254862.1| 70 AGGTISISTVAVSSSNKPVYGVYP 93
                                  78********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2602.34
//
Query:       gi|70605993|ref|YP_254863.1|  [L=440]
Description: NADH peroxidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-45  156.2   0.3    1.3e-45  155.9   0.3    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.9e-18   65.7   0.0    9.6e-18   64.5   0.0    1.7  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.4e-11   44.7   2.0    1.4e-11   44.7   2.0    3.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.6e-10   40.1   0.2    2.5e-08   33.5   0.1    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.4e-07   31.6   0.2      0.031   14.5   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    7.2e-05   22.0   0.1      0.075   12.1   0.0    2.4  2  GIDA            Glucose inhibited division protein A
      8e-05   21.5   0.3      0.098   11.3   0.0    2.6  2  HI0933_like     HI0933-like protein
    0.00038   20.9   0.3      0.063   13.7   0.2    2.5  2  NAD_binding_7   Putative NAD(P)-binding
     0.0015   17.7   1.9       0.42    9.6   0.0    2.8  3  FAD_binding_2   FAD binding domain
     0.0038   16.6   0.4        2.1    7.6   0.1    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0072   15.4   0.3        2.9    6.9   0.0    2.6  3  Lycopene_cycl   Lycopene cyclase protein
      0.008   16.2   2.8        2.9    7.9   0.0    3.1  3  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.089   11.9   0.0    2.0  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.019   15.2   0.6       0.17   12.2   0.3    2.6  3  TrkA_N          TrkA-N domain
      0.021   14.7   0.2      0.038   13.9   0.2    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.035   13.7   7.7       0.16   11.5   0.8    3.3  4  DAO             FAD dependent oxidoreductase
      0.044   13.0   3.2        0.4    9.9   0.0    2.8  3  Thi4            Thi4 family
      0.097   12.6   0.3        2.1    8.4   0.0    2.5  2  Transposase_23  TNP1/EN/SPM transposase
        0.1   11.5   0.7       0.18   10.6   0.0    1.7  2  Trp_halogenase  Tryptophan halogenase
        0.1   11.1   0.0       0.16   10.5   0.0    1.3  1  Mqo             Malate:quinone oxidoreductase (Mqo)
       0.13   11.5   3.0       0.52    9.5   0.4    2.1  2  FAD_binding_3   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.3   1.5e-48   1.3e-45       2     294 .]       3     300 ..       2     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 1.5e-48
                                   SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTCEE CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgeevvk 77 
                                   ++vv+GgG+AG++a+ ++++   ++++ ++e+++ + +  c +++ ++g  +d++ +     ++ k + +i++ +g  +++
  gi|70605993|ref|YP_254863.1|   3 KLVVVGGGAAGMSASSKVRRlkPEMDIEVFESTKFVSHAPCGIPYFIEGLFDDESLFMtytPEFFKEKRKIDVKTGIRITE 83 
                                   78******************755*******9999999999999999999999999888***77888899999999999*** PP

                                   EEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                   Pyr_redox_2  78 idpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiGvEl 157
                                   id+  +++  e+ + +++ k +yd+l+l tG++p++  ++G  e v+  v++ ++a +l+++l   + ++++GgG  G+E+
  gi|70605993|ref|YP_254863.1|  84 IDFSGRTIYGETAN-KEKIKREYDYLLLSTGAKPKKVETEGN-ERVF-YVHHPADALELRKQLWSlNTVAIIGGGILGLEM 161
                                   *****999996655.8889999********************.6665.5588888888888777779************** PP

                                   HHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-E CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 158 Aaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGv 237
                                     al + gk+v+l++ +d ll r+ld el+++++  + k + evkl+++  e++++g   ++v +d+  +++d  vva+Gv
  gi|70605993|ref|YP_254863.1| 162 VEALVERGKKVVLIHKGDYLLnRSLDNELGKIITSIVMK-DAEVKLNERL-EVIKRGG--RLVVTDKGNYEVDGTVVAIGV 238
                                   ***********************************9999.6999999***.5555555..589999999************ PP

                                   EES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 238 rpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                   +p+ +l+  k +l+l ++g+i+vd+++rt+ +++y +GD +       g+ + +  a++A ++G
  gi|70605993|ref|YP_254863.1| 239 EPNVDLV--KGKLTLGDTGAIKVDRHMRTTLKDVYSAGDNTevvnlltGRPQWVPFAPVANKMG 300
                                   ****995..99****************************9988888888888888888888876 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.1e-20   9.6e-18       4     103 ..     323     423 ..     320     428 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.1e-20
                                   EEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHHH CS
                 Pyr_redox_dim   4 vvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelava 82 
                                   +++ d+ +a vGl+eeeA++ g  + v+++++++ +ra++y+   +++vK++ad++++k+lG +i+G +++  +i+ la +
  gi|70605993|ref|YP_254863.1| 323 TKYKDYYIARVGLNEEEARKHG--FHVISASINSKTRARYYPGgGDIYVKIIADEESRKILGGQIIGvEEVLGRINMLAGM 401
                                   7899******************..*******************************************777777******** PP

                                   HHTTSBHHH.HHTSBSSSSSTG CS
                 Pyr_redox_dim  83 ikagltved.ladtihihPtls 103
                                   + +g t++d +  ++++ P ++
  gi|70605993|ref|YP_254863.1| 402 LYKGFTIDDvFFTEMGYLPAIN 423
                                   ********65999999999887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0084       7.2       1      22 [.       3      24 ..       3      38 .. 0.80
   2 ?   -0.5   0.0       2.2   1.9e+03      51      71 ..      69      89 ..      59      97 .. 0.83
   3 !   44.7   2.0   1.7e-14   1.4e-11       2      71 ..     149     218 ..     148     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0084
                                  EEEEECSSHHHHHHHHHHHHTT CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelg 22
                                  k+vvvGgG  g+ + +  ++l+
  gi|70605993|ref|YP_254863.1|  3 KLVVVGGGAAGMSASSKVRRLK 24
                                  68***********999999987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.2
                                  HHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox 51 ekngievllntkveeiegsed 71
                                  ek++i+v ++ +++ei+ s++
  gi|70605993|ref|YP_254863.1| 69 EKRKIDVKTGIRITEIDFSGR 89
                                  5679***********996665 PP

  == domain 3  score: 44.7 bits;  conditional E-value: 1.7e-14
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsed 71 
                                   v+++GgG +glE+ +al e gkkV +++ +d ll r lD+e++ki++  + k   ev ln+++e i+  ++
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERGKKVVLIHKGDYLLnRSLDNELGKIITSIVMKD-AEVKLNERLEVIKRGGR 218
                                   89************************************************999.99999*99999987665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.02        17       1      20 [.       5      24 ..       5      41 .. 0.80
   2 !   33.5   0.1   2.9e-11   2.5e-08      92     305 .]      69     274 ..      54     274 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.02
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkag 20
                                  +++G+G+aG++a  ++++++
  gi|70605993|ref|YP_254863.1|  5 VVVGGGAAGMSASSKVRRLK 24
                                  79**********99998876 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.9e-11
                   Pyr_redox_3  92 ksfelpiklfeeVesvkke.degfevetsketye..AkkviiAtGefdkPnklnipGeek..lvkhyskvkefhk..yagq 165
                                   ++ ++++k+  ++++++ + ++ +  +++ke+++   ++++++tG   kP+k + +G e+  +v h +   e++k   + +
  gi|70605993|ref|YP_254863.1|  69 EKRKIDVKTGIRITEIDFSgRTIYGETANKEKIKreYDYLLLSTGA--KPKKVETEGNERvfYVHHPADALELRKqlWSLN 147
                                   567999***********9615667777778876511578******9..***********6333333333333322114567 PP

                   Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeyk 246
                                    v++iGg+  + ++   lv++g++V ++++g+ + ++      sl     + + ++v +   +v  n++++ ik+   +  
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHKGDYLLNR------SLDNELGKIITSIVMK-DAEVKLNERLEVIKRG-GRLV 220
                                   9******************************966665......4555555555555554.3789999999999985.5555 PP

                   Pyr_redox_3 247 vktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   v+ +   + ev d  v+a+G +p+++++k  +++l ++g ++++ + + t++++++ aG
  gi|70605993|ref|YP_254863.1| 221 VTDKG--NYEV-DGTVVAIGVEPNVDLVK-GKLTLGDTGAIKVDRH-MRTTLKDVYSAG 274
                                   55554..4455.6689************9.8888889999999875.77889****998 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.7e-05     0.031       1      27 [.       6      34 ..       6      39 .. 0.90
   2 !   14.3   0.1   4.2e-05     0.036       1      31 [.     151     181 ..     151     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                                  EE--SHHHHHHHHHHHCC..TEEEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllek 27
                                  +vG+G++G++a +  ++     d++++e+
  gi|70605993|ref|YP_254863.1|  6 VVGGGAAGMSASSKVRRLkpEMDIEVFES 34
                                  8***************975788*****97 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.2e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                   I+G+G+ Gl +  +L ++g++v+l+ k+d+l
  gi|70605993|ref|YP_254863.1| 151 IIGGGILGLEMVEALVERGKKVVLIHKGDYL 181
                                   9*************************99987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0019       1.6       2      21 ..       4      23 ..       3      43 .. 0.85
   2 !   12.1   0.0   8.8e-05     0.075       2      55 ..     149     201 ..     148     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                  EEEE-SSHHHHHHHHHHHHT CS
                          GIDA  2 viViGgGhAGceAAlaaarl 21
                                  ++V+GgG AG+ A+ ++ rl
  gi|70605993|ref|YP_254863.1|  4 LVVVGGGAAGMSASSKVRRL 23
                                  79************998886 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.8e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHH CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrE 55 
                                   v +iGgG  G+e   a+ ++G kv+Li hk d +++ s  + +g i  ++++++
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERGKKVVLI-HKGDYLLNRSLDNELGKIITSIVMKD 201
                                   89*************************.**********9999999866666654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00011     0.098       2      33 ..       3      36 ..       2      40 .. 0.82
   2 !    7.7   0.1    0.0014       1.2       2      35 ..     148     181 ..     147     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                  SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekak 33
                                  +++v+GgGaAG+ a+ ++   k + ++ ++e++k
  gi|70605993|ref|YP_254863.1|  3 KLVVVGGGAAGMSASSKVrrLKPEMDIEVFESTK 36
                                  689************9995567788888888765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   +v++iGgG  Gl   +++ +rgk+V+l+ k++ l
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHKGDYL 181
                                   699*************************998765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.041        35       9      39 ..       3      35 ..       1     104 [. 0.79
   2 !   13.7   0.2   7.4e-05     0.063       9      40 ..     148     179 ..     144     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.041
                 NAD_binding_7  9 kvlvvGgGevAa...rkvrklleagakvtvvape 39
                                  k +vvGgG  ++   +kvr+l ++  ++ v   +
  gi|70605993|ref|YP_254863.1|  3 KLVVVGGGAAGMsasSKVRRLKPE-MDIEVFEST 35
                                  789****99865444899999998.888886555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.4e-05
                 NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev 40 
                                   +v ++GgG ++++ v+ l+e g+kv+++ +  
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHKGD 179
                                   799************************99874 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00049      0.42       2      18 ..       4      20 ..       3      37 .. 0.87
   2 !    6.4   0.3    0.0048       4.1       2      33 ..     149     180 ..     148     184 .. 0.94
   3 ?   -1.6   0.0       1.3   1.1e+03     374     401 ..     255     276 ..     220     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00049
                                  EEEE--SHHHHHHHHHH CS
                 FAD_binding_2  2 viViGsGlAGLaAAlea 18
                                  ++V+G+G+AG++A+ + 
  gi|70605993|ref|YP_254863.1|  4 LVVVGGGAAGMSASSKV 20
                                  69***********8765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                   v +iG+G+ GL    ++ e+G+kv+++ k+++
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERGKKVVLIHKGDY 180
                                   89**************************9976 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.3
                                   -EEEBETTSBESTTEEESSBTEEE-STC CS
                 FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGev 401
                                   g +++d ++r+      ++++ Y aG  
  gi|70605993|ref|YP_254863.1| 255 GAIKVDRHMRT------TLKDVYSAGDN 276
                                   55889999999......99999999975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0039       3.3      30      53 ..       3      26 ..       1      38 [. 0.83
   2 !    7.6   0.1    0.0025       2.1      30      77 ..     148     196 ..     145     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                                  EEEEESTSHHHHHHHHHHHHTT-E CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgak 53
                                  k +v+GgG aG++A +  ++l+ +
  gi|70605993|ref|YP_254863.1|  3 KLVVVGGGAAGMSASSKVRRLKPE 26
                                  789***********9999998754 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHH.TTTCECEE CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparl.eqles.lgakfvev 77 
                                   +v +iGgG+ Gl+ +++ ++ g kV+++ +    l + l++ lg+  ++ 
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHKGDYLLnRSLDNeLGKI-ITS 196
                                   699*****************99999887765544414455544443.444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0033       2.9       2      32 ..       4      34 ..       3      42 .. 0.84
   2 !    5.8   0.2    0.0069       5.9       2      36 ..     149     181 ..     148     186 .. 0.89
   3 ?   -2.7   0.0       2.7   2.3e+03     227     246 ..     403     422 ..     394     430 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0033
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvliea 32
                                  +vv+G+G+Ag+s   ++ + kp++ + + e+
  gi|70605993|ref|YP_254863.1|  4 LVVVGGGAAGMSASSKVRRLKPEMDIEVFES 34
                                  79***************88888888777665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0069
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                   v++iG+G  gl + + l   + g kvvli  ++ l
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEAL--VERGKKVVLIHKGDYL 181
                                   89***************..888999****988876 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.7
                 Lycopene_cycl 227 alglkvkevveeEqgviPvt 246
                                    +g  ++ v  +E g++P +
  gi|70605993|ref|YP_254863.1| 403 YKGFTIDDVFFTEMGYLPAI 422
                                   57999999999999999974 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0034       2.9       1      37 [.       5      38 ..       5      43 .. 0.89
   2 !    6.8   0.4     0.007         6       1      20 [.     150     169 ..     150     177 .. 0.86
   3 ?   -1.3   0.0       2.3     2e+03     127     154 ..     210     237 ..     193     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0034
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                  ++vG+G++G+++  ++ +    k +++i +f+ +++ 
  gi|70605993|ref|YP_254863.1|  5 VVVGGGAAGMSASSKVRRL---KPEMDIEVFESTKFV 38
                                  69*************9998...7*********98876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.007
                 NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                   ai+G+G+ Gl ++e+L++r 
  gi|70605993|ref|YP_254863.1| 150 AIIGGGILGLEMVEALVERG 169
                                   8****************996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                 NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlG 154
                                   le  ++g +++ +d+ ++++d  v+A+G
  gi|70605993|ref|YP_254863.1| 210 LEVIKRGGRLVVTDKGNYEVDGTVVAIG 237
                                   5555667788899999999**9999999 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.69   5.9e+02     193     223 ..       3      33 ..       1      56 [. 0.77
   2 ?   11.9   0.0    0.0001     0.089     139     217 ..      95     172 ..      59     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.69
                   K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklvt 223
                                   +++VvG+G  +     ++ r +++++++++ 
  gi|70605993|ref|YP_254863.1|   3 KLVVVGGGAAGMSASSKVRRLKPEMDIEVFE 33 
                                   6789999988888777777777777776654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0001
                   K_oxygenase 139 daegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                                   +a+ e+ ++e   l+l++G +pk  e+  + +    v H +++le +++l + +++a++G+G  + e++e l++r kkv
  gi|70605993|ref|YP_254863.1|  95 TANKEKIKREYDYLLLSTGAKPKKVETEGNER-VFYVHHPADALELRKQLWSLNTVAIIGGGILGLEMVEALVERGKKV 172
                                   45666677777889999998876544433322.3456688999999999*************************98753 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.6   1.4e+03       2      20 ..       5      24 ..       4      58 .. 0.74
   2 ?   12.2   0.3    0.0002      0.17       1      35 [.     149     183 ..     149     205 .. 0.82
   3 ?   -2.3   0.0       5.9     5e+03      35      50 ..     338     353 ..     335     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                                  EEES-SHHHHHHHHHHHH.T CS
                        TrkA_N  2 iiiGlGrvGrslaeeLse.g 20
                                  +++G G  G+s   ++++ +
  gi|70605993|ref|YP_254863.1|  5 VVVGGGAAGMSASSKVRRlK 24
                                  89********9999888843 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0002
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerve 35 
                                   ++iiG G +G +++e L e+gk+vv+i k +  ++
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERGKKVVLIHKGDYLLN 183
                                   68*****************7778****98766555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.9
                                   HHHHHTTSEEEES-TT CS
                        TrkA_N  35 eelreeglevvvgdat 50 
                                   ee+r++g++v+ ++  
  gi|70605993|ref|YP_254863.1| 338 EEARKHGFHVISASIN 353
                                   7899999**9998776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   4.4e-05     0.038       1      41 [.     148     188 ..     148     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalek 41 
                                   +va+iG G++G ++ ++++++g +Vvl+   +  l+++l++
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHKGDYLLNRSLDN 188
                                   69**************************9977777766543 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5     0.068        58       2      14 ..       4      16 ..       3      42 .. 0.75
   2 ?    0.6   0.0      0.38   3.2e+02     158     204 ..      70     116 ..      47     133 .. 0.75
   3 ?   11.5   0.8   0.00019      0.16       2      30 ..     149     179 ..     148     188 .. 0.93
   4 ?   -2.6   0.0       3.7   3.1e+03     161     205 ..     202     241 ..     191     264 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.068
                                  EEEECTSHHHHHH CS
                           DAO  2 vviiGGGiiGlst 14
                                  +v++GGG +G+s+
  gi|70605993|ref|YP_254863.1|  4 LVVVGGGAAGMSA 16
                                  79*********97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                                   HTT-EEEESECEEEEEEEETCEEEEE.EECT.EEE.EEEEEEEE--GGGH CS
                           DAO 158 alGveilegtevtgleeedgkvwgve.rttp.gen.daadavVnaaGaws 204
                                   ++ +++ +g ++t+++     + +++ +t++ + + +++d++ +++Ga  
  gi|70605993|ref|YP_254863.1|  70 KRKIDVKTGIRITEIDFS---GRTIYgETANkEKIkREYDYLLLSTGAKP 116
                                   667889999999999665...45555534444555578999******975 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00019
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                   v+iiGGGi Gl    +L +rg  V+l+ kgd
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERGkkVVLIHKGD 179
                                   9*******************99*****9995 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.7
                                   -EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH CS
                           DAO 161 veilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd 205
                                   +e+ ++++ + +++    ++++ ++t+ g+  ++d  V+a G+  +
  gi|70605993|ref|YP_254863.1| 202 AEVKLNERLEVIKR----GGRL-VVTDkGNY-EVDGTVVAIGVEPN 241
                                   55666655555543....3333.35555754.56888998887654 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00047       0.4      20      49 ..       4      34 ..       1      41 [. 0.90
   2 ?    2.3   0.5     0.097        82      19     116 ..     148     245 ..     141     251 .. 0.64
   3 ?   -1.8   0.0       1.7   1.5e+03      59      78 ..     363     382 ..     361     391 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                                  EEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
                          Thi4 20 vvivGaGssGLtaayylakk.pdlkvailer 49
                                  +v+vG+G++G++a+  + +  p++ + ++e+
  gi|70605993|ref|YP_254863.1|  4 LVVVGGGAAGMSASSKVRRLkPEMDIEVFES 34
                                  79***************9978********97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.097
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS..SS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESEHH CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvailers..vspGGGawlGGqlfsaivvrkpakelLdelgikyedegdyvvvkdaa 97 
                                    v+i+G+G  GL     l ++ + kv+++ +   +         G++ + iv+++   +l + l++     +  v+ k   
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVER-GKKVVLIHKGdyLLNRSLDNELGKIITSIVMKDAEVKLNERLEVIKRGGRLVVTDKGNY 227
                                   5899**************999.99999997631122233333445666667766655555555666555444444444455 PP

                                   HHHHHHHHHHHTSTTEEEE CS
                          Thi4  98 lftstllskvlqlanvkll 116
                                   ++  t+++  ++ +nv l+
  gi|70605993|ref|YP_254863.1| 228 EVDGTVVAIGVE-PNVDLV 245
                                   666666666666.666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.7
                                   TTSTTBSEEEEETTTHHHHH CS
                          Thi4  59 lGGqlfsaivvrkpakelLd 78 
                                   +GG ++ +i+  ++++++L 
  gi|70605993|ref|YP_254863.1| 363 GGGDIYVKIIADEESRKILG 382
                                   79**************9995 PP

>> Transposase_23  TNP1/EN/SPM transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0024       2.1      19      58 ..     143     188 ..     140     190 .. 0.72
   2 ?    1.3   0.0       0.4   3.4e+02      24      44 ..     377     397 ..     371     400 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                Transposase_23  19 lisidestvVGGepLGkeyyeVvvn......vvlkrdaaLprpYdd 58 
                                   l s ++  ++GG +LG e++e +v+      ++ k d  L r++d+
  gi|70605993|ref|YP_254863.1| 143 LWSLNTVAIIGGGILGLEMVEALVErgkkvvLIHKGDYLLNRSLDN 188
                                   6789999**************9996333321223447777777765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                Transposase_23  24 estvVGGepLGkeyyeVvvnv 44 
                                   + ++ GG++ G e +  ++n+
  gi|70605993|ref|YP_254863.1| 377 SRKILGGQIIGVEEVLGRINM 397
                                   67899******9987777665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.18       1      37 [.       3      38 ..       3      44 .. 0.85
   2 ?   -2.4   0.3       1.8   1.6e+03       2      22 ..     149     169 ..     142     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                  k+v+vGGG aG  a + +++    ++++++ es ++ 
  gi|70605993|ref|YP_254863.1|  3 KLVVVGGGAAGMSASSKVRRLK-PEMDIEVFESTKFV 38
                                  689********88888888877.55*******99875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                   EEEE--SHHHHHHHHHHHHHT CS
                Trp_halogenase   2 ivivGGGtaGwlaAaalakal 22 
                                   + i+GGG+ G     al + +
  gi|70605993|ref|YP_254863.1| 149 VAIIGGGILGLEMVEALVERG 169
                                   89******9976555555555 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00018      0.16       5     105 ..       4     107 ..       1     141 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                           Mqo   5 vvliGaGimsatlgvllkelepelsievlerldkvaees.snawnnaGtGHsalcElnYtpe..kedgsidiskAvkineq 82 
                                   +v++G+G    + ++ +++l+pe++iev+e  + v++     ++   G        + Ytpe  ke+ +id++  ++i+e 
  gi|70605993|ref|YP_254863.1|   4 LVVVGGGAAGMSASSKVRRLKPEMDIEVFESTKFVSHAPcGIPYFIEGLFDDESLFMTYTPEffKEKRKIDVKTGIRITEI 84 
                                   799*****99999*******************9998765156788899999999999999985567889999999999987 PP

                           Mqo  83 fevsrqfwaylvekgllkdpkef 105
                                       r ++  + +k+++k+  ++
  gi|70605993|ref|YP_254863.1|  85 DFSGRTIYGETANKEKIKREYDY 107
                                   77788888888888888877666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.11        91       5      18 ..       5      18 ..       2      23 .. 0.86
   2 ?    9.5   0.4    0.0006      0.52       3      32 ..     148     177 ..     147     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.11
                                  EEE--SHHHHHHHH CS
                 FAD_binding_3  5 lIVGaGpaGlmlal 18
                                  ++VG+G aG+++++
  gi|70605993|ref|YP_254863.1|  5 VVVGGGAAGMSASS 18
                                  79*********986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0006
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                   +V+I+G+G  Gl     L e+G +vvl+ k
  gi|70605993|ref|YP_254863.1| 148 TVAIIGGGILGLEMVEALVERGKKVVLIHK 177
                                   699*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2953.59
//
Query:       gi|70605994|ref|YP_254864.1|  [L=144]
Description: hypothetical protein Saci_0150 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 944.90
//
Query:       gi|70605995|ref|YP_254865.1|  [L=306]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-21   75.3   0.0    2.1e-20   73.3   0.0    1.9  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    5.5e-07   29.5   0.7    4.9e-06   26.4   0.3    2.4  2  SIS         SIS domain
  ------ inclusion threshold ------
      0.037   14.2   0.5       0.56   10.5   0.1    2.6  3  PK_C        Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   3.5e-24   2.1e-20       5     151 ..     168     298 ..     165     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 3.5e-24
                                   HHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH..... CS
                    bact-PGI_C   5 akqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprv 85 
                                   + ++A+++ gk+p++y+ s  l ++A+Rfk++ nenAK+paf+++lpeanhnei ++  ++++++++  +++ +++     
  gi|70605995|ref|YP_254865.1| 168 STRIANRITGKVPIFYA-S-DLLPIAERFKQEVNENAKYPAFFSQLPEANHNEIELY--SSQQGNQFIPIVIPSDK----- 239
                                   5689*************.5.5679*********************************..67999********9666..... PP

                                   ...HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH. CS
                    bact-PGI_C  86 kkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKee 151
                                     + e++++l++        +++  +s l+ +  ++l+++++Sv+lA  +++  ++  +I +++e+
  gi|70605995|ref|YP_254865.1| 240 --IDEATASLINA-----ELIYPPYKSILKNISGMFLIAGLASVKLASQLNIKAEELRIIPKIRER 298
                                   ..67888888885.....599***************************************999986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.3   8.2e-10   4.9e-06      43      88 ..      55     101 ..      23     110 .. 0.83
   2 ?   -2.3   0.0      0.64   3.8e+03      18      50 ..     189     221 ..     187     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8.2e-10
                                   HHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE.EEEES CS
                           SIS  43 lkhgvlalideddlvilisfsgetkdlvaaaelakergaki.iaITd 88 
                                   l  +++ ++d+++ v+++s+sg+t++++a ++ a+e g+k  i+IT+
  gi|70605995|ref|YP_254865.1|  55 LFRSYKVNVDSKTTVVAVSYSGNTAETLAGVKRAQELGVKEiIVITS 101
                                   45556789******************************654499996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.64
                                   HHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG CS
                           SIS  18 aiakelalkleeiggivvevedaselkhgvlal 50 
                                   +ia+ ++  ++e +++++++++ +e  h+ + l
  gi|70605995|ref|YP_254865.1| 189 PIAERFKQEVNENAKYPAFFSQLPEANHNEIEL 221
                                   689999999999999999999999988886655 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.047   2.8e+02      18      33 ..      68      83 ..      60      86 .. 0.84
   2 ?   10.5   0.1   9.3e-05      0.56       6      27 ..      83     104 ..      78     112 .. 0.89
   3 ?   -2.4   0.0      0.92   5.5e+03      30      47 ..     170     194 ..     165     252 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.047
                                  EEEEE-SSSHHHHHHH CS
                          PK_C 18 aIvvltesGetArlis 33
                                   +v+++ sG+tA  ++
  gi|70605995|ref|YP_254865.1| 68 TVVAVSYSGNTAETLA 83
                                  68999*******8876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.3e-05
                                   HHHHHHHHHT-SEEEEE-SSSH CS
                          PK_C   6 aaveaaeelgakaIvvltesGe 27 
                                   a v++a+elg+k I+v+t+ G+
  gi|70605995|ref|YP_254865.1|  83 AGVKRAQELGVKEIIVITSGGK 104
                                   6799***************997 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.92
                                   HHHHHT-TSSEEEEEES.......H CS
                          PK_C  30 rliskyrpkvpiiavtp.......n 47 
                                   r + ++  kvpi+  ++        
  gi|70605995|ref|YP_254865.1| 170 RIANRITGKVPIFYASDllpiaerF 194
                                   5566666667776666544444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2154.73
//
Query:       gi|70605996|ref|YP_254866.1|  [L=469]
Description: cysteinyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.2e-123  410.9   0.2     5e-123  410.3   0.2    1.3  1  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    5.4e-16   58.3   1.7    1.9e-08   33.5   0.4    2.2  2  tRNA-synt_1g   tRNA synthetases class I (M)
    2.6e-07   31.0   1.2    6.8e-06   26.5   0.5    2.7  3  DALR_2         DALR domain
    9.9e-06   24.1   2.3     0.0024   16.2   0.0    3.1  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    0.00012   21.1   1.1    0.00037   19.5   0.2    2.0  2  tRNA-synt_1f   tRNA synthetases class I (K)
     0.0042   16.0   2.5      0.025   13.5   0.1    3.0  3  tRNA-synt_1c   tRNA synthetases class I (E and Q), catalytic 
  ------ inclusion threshold ------
      0.025   14.8   3.9       0.96    9.6   1.6    2.4  2  Fib_alpha      Fibrinogen alpha/beta chain family
      0.027   13.4   1.0       0.15   11.0   0.2    2.2  2  tRNA-synt_1d   tRNA synthetases class I (R)
      0.029   14.4   4.2      0.029   14.3   0.9    2.1  2  RRF            Ribosome recycling factor
      0.034   13.9   0.0        0.1   12.4   0.0    1.7  2  SH3BP5         SH3 domain-binding protein 5 (SH3BP5)
       0.11   12.5   0.3        1.2    9.1   0.1    2.3  2  TB2_DP1_HVA22  TB2/DP1, HVA22 family
       0.13   12.0   0.6        1.4    8.6   0.3    2.3  2  TIP120         TATA-binding protein interacting (TIP20)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.3   0.2  3.3e-126    5e-123       5     300 ..      20     312 ..      16     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 410.3 bits;  conditional E-value: 3.3e-126
                                   SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                  tRNA-synt_1e   5 leekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkk 85 
                                    +  +v++YvCGptvyd++h+Gh+R++v fD + r+l+ +g++v  vqn+tDidDkiikra+e +k ++e+++++ +++++
  gi|70605996|ref|YP_254866.1|  20 FDPLTVKMYVCGPTVYDYVHIGHGRAFVGFDGIVRYLKLRGFNVIRVQNITDIDDKIIKRANETGKDWREIVDYYTKDYME 100
                                   566789*************************************************************************** PP

                                   HHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT CS
                  tRNA-synt_1e  86 dleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekkdkk 166
                                    l+aL+v   + +prv+ +++eii++v+kl++kg+aY +s+g vyfdv ++++Yg ls  ++ee ++g+e+   +ekk++ 
  gi|70605996|ref|YP_254866.1| 101 SLKALKVEI-DQHPRVTSHIQEIIDFVQKLVDKGHAYITSSGSVYFDVDSFPSYGLLSGSKKEEWNQGEEI--VKEKKNPY 178
                                   *******97.99***************************************************99999887..459***** PP

                                   -EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--E CS
                  tRNA-synt_1e 167 DfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafdkqlvkyflhnghl 247
                                   DfaLWka k+gep w+sPwgkGRPGWhieCs+m++++lg+++dih+GG+DL+fPhhene aqse++ +k +vky++h  +l
  gi|70605996|ref|YP_254866.1| 179 DFALWKAWKPGEPYWESPWGKGRPGWHIECSTMSTRYLGEQFDIHGGGVDLVFPHHENERAQSESLLGKIWVKYWVHVAYL 259
                                   ********************************************************************************* PP

                                   EETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                  tRNA-synt_1e 248 kiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                   +i++ekmsksL+n+i ++++lkk+ p++lR+  ls++yr+ +d++e++le+a+
  gi|70605996|ref|YP_254866.1| 260 TINKEKMSKSLGNIIPLNEALKKWGPSVLRFWYLSTKYRNSIDYSEQTLEQAR 312
                                   **************************************************986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.4   1.3e-11   1.9e-08      12     122 ..      36     144 ..      27     150 .. 0.90
   2 !   24.1   0.0   9.2e-09   1.4e-05     318     370 ..     256     307 ..     230     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.3e-11
                                   S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETT CS
                  tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrtt 92 
                                   + +H+Gh +  +  D ++Ry +lrg +v+ v        +i  +A++ g + +e+v+ +++ + e +k l+++ d++ r t
  gi|70605996|ref|YP_254866.1|  36 DYVHIGHGRAFVGFDGIVRYLKLRGFNVIRVQNITDIDDKIIKRANETGKDWREIVDYYTKDYMESLKALKVEIDQHPRVT 116
                                   568****************************99999999****************************************99 PP

                                   SHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                  tRNA-synt_1g  93 seehkelvqeifkklkekgliyekeieqly 122
                                   s+   +   ++++kl +kg+ y +++  +y
  gi|70605996|ref|YP_254866.1| 117 SHI--QEIIDFVQKLVDKGHAYITSSGSVY 144
                                   855..55679**********9988887777 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 9.2e-09
                                   E--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHH CS
                  tRNA-synt_1g 318 heyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswed 370
                                     ylt++ +K+SkS g+++  +eal++  + +lR+++++++ + + +d+s+++
  gi|70605996|ref|YP_254866.1| 256 VAYLTINKEKMSKSLGNIIPLNEALKKWGPSVLRFWYLSTKYR-NSIDYSEQT 307
                                   579********************************98875543.446666655 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.22   3.3e+02      32      57 ..     302     327 ..     294     334 .. 0.81
   2 !   26.5   0.5   4.5e-09   6.8e-06       1      58 [.     354     412 ..     354     416 .. 0.80
   3 ?   -3.0   0.0         7     1e+04      19      34 ..     439     454 ..     438     463 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                                   TT-HHHHHHHHHHHHHHHGGGT-S-S CS
                        DALR_2  32 eedkaaasalkallrelaevLGllqe 57 
                                   + ++++++++++ l+ l++ +G+  +
  gi|70605996|ref|YP_254866.1| 302 DYSEQTLEQARSSLQRLKDAMGIIRS 327
                                   55788899999***********9876 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.5e-09
                                   HHHHHHTBT--HHHHHHHHHHHHHHHHH..HHHTT-HHHHHHHHHHHHHHHGGGT-S-S- CS
                        DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNr..alkeedkaaasalkallrelaevLGllqee 58 
                                   kF eaM +DF Ta A++ ++e+a+ + +  + +++   a  a+ +++r++  v+G++ ee
  gi|70605996|ref|YP_254866.1| 354 KFHEAMSNDFDTATALSNIYEIANLVFTkiQYTRDFMGAMLAF-DAFRQFNYVFGVMDEE 412
                                   7*************************99433333333333444.9***********9885 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7
                                   HHHHHHHHHHHHHTT- CS
                        DALR_2  19 lFelakeiNralkeed 34 
                                   +++l+ ei++ l+++ 
  gi|70605996|ref|YP_254866.1| 439 MYDLSDEIRSVLANAG 454
                                   7999999999665554 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.014        21      31     112 ..      31     110 ..      23     138 .. 0.70
   2 !   16.2   0.0   1.6e-06    0.0024     562     600 ..     264     302 ..     249     304 .. 0.89
   3 ?    3.0   0.1     0.017        25      74     186 ..     342     463 ..     338     468 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.014
                   tRNA-synt_1  31 PPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekk..erkklgreefrekvrewka 109
                                    P v   +HiGh  a +  d ++ry +++G++v +v  +      i+ k+ k+  +++k+  e  ++ +++++e  ++ k 
  gi|70605996|ref|YP_254866.1|  31 GPTVYDYVHIGHGRAFVGFDGIVRYLKLRGFNVIRVQNIT----DIDDKIIKRANETGKDwrEIVDYYTKDYMESLKALKV 107
                                   57788889*************************9886542....3444444444444443114456777777777777766 PP

                   tRNA-synt_1 110 eya 112
                                   e  
  gi|70605996|ref|YP_254866.1| 108 EID 110
                                   654 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-06
                   tRNA-synt_1 562 rKmSKslgNvidpldvikkygadalRltlilsdvgrdin 600
                                    KmSKslgN+i  ++ +kk g  +lR++ +++++ + i+
  gi|70605996|ref|YP_254866.1| 264 EKMSKSLGNIIPLNEALKKWGPSVLRFWYLSTKYRNSID 302
                                   6*******************************9987765 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.017
                   tRNA-synt_1  74 laieakvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreyl......Tldkele...eavke 145
                                   ++++ ++   +g+ ++   +++ ++    ++ e+++    +i+ +   +G+++ fd  +        +d+e++   e++++
  gi|70605996|ref|YP_254866.1| 342 ISTQREIISLIGKFHEAMSNDFDTATALSNIYEIANLVFTKIQYTRDFMGAMLAFDAFRQfnyvfgVMDEEFSpsyETMYK 422
                                   78888888899999999999999999999999999999999999999999999988643212223479***9833344667 PP

                   tRNA-synt_1 146 vfvrladkgliyrgkklvnwstklktalselEveykdkkda 186
                                   v+  +++   i r+ k+   s +++++l+++ ++  d k+ 
  gi|70605996|ref|YP_254866.1| 423 VIDSVVEIRNILRARKMYDLSDEIRSVLANAGIKILDGKEK 463
                                   7788899999*********************9987776655 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.3   4.5e+02      36      72 ..      37      73 ..      27     112 .. 0.79
   2 !   19.5   0.2   2.5e-07   0.00037     278     341 ..     262     327 ..     250     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.3
                  tRNA-synt_1f 36 liHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                                   +HiG  r  +  d ++r l+ rg +v  +  + d+D
  gi|70605996|ref|YP_254866.1| 37 YVHIGHGRAFVGFDGIVRYLKLRGFNVIRVQNITDID 73
                                  6899999999999999999999999955555554544 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.5e-07
                  tRNA-synt_1f 278 ggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf...a 341
                                   ++ekms+S Gn++ l+++l+   p vlrf +l++k +++++ + +  + ++    ++l++++    +
  gi|70605996|ref|YP_254866.1| 262 NKEKMSKSLGNIIPLNEALKKWGPSVLRFWYLSTKYRNSIDYSEQ-TLEQARSSLQRLKDAMGiirS 327
                                   456*********************************999998887.888888888888877655551 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.7e-05     0.025      47      97 ..      88     138 ..      69     142 .. 0.77
   2 ?   -0.5   0.1      0.31   4.6e+02     226     262 ..     251     284 ..     233     346 .. 0.78
   3 ?    0.1   0.0       0.2   2.9e+02     183     213 ..     413     443 ..     408     458 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
                                   C--HH.HHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                  tRNA-synt_1c  47 rekee.aeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                   re+ + +++  +e lk l+++ d++p+ +s + +e+ +++++L+ kG+AY  
  gi|70605996|ref|YP_254866.1|  88 REIVDyYTKDYMESLKALKVEIDQHPRVTS-HIQEIIDFVQKLVDKGHAYIT 138
                                   666661567899**********88776655.7888899************75 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
                                   S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT CS
                  tRNA-synt_1c 226 evppfiheylrlnlekkklSKRklsllvdekqvkewd 262
                                   +   +   ++ l+++k+k+SK  ++++  ++++k+w+
  gi|70605996|ref|YP_254866.1| 251 K---YWVHVAYLTINKEKMSKSLGNIIPLNEALKKWG 284
                                   4...444556788999999999999999999999998 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.2
                                   EEE-HHHHHHHHHHHTT-SEEEEEGGGGCCH CS
                  tRNA-synt_1c 183 iyPtYdfavvidDaleeithvlrteefldnt 213
                                    +P+Y+    + D++ ei  +lr+   +d  
  gi|70605996|ref|YP_254866.1| 413 FSPSYETMYKVIDSVVEIRNILRARKMYDLS 443
                                   57*********************98766554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.018        27      24      70 ..      89     135 ..      69     149 .. 0.83
   2 ?    9.6   1.6   0.00065      0.96      31     114 ..     295     376 ..     292     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.018
                                   HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqk 70 
                                   ++++ y kd+ ++l+ l+ e++++ + t++++e++  +++ + +  +
  gi|70605996|ref|YP_254866.1|  89 EIVDYYTKDYMESLKALKVEIDQHPRVTSHIQEIIDFVQKLVDKGHA 135
                                   56778999999999999999999999999999999999988877665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00065
                                   CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                     Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                   ++++++++  e++le++++s +  ++ +  i+++++e+ ks++ n++ i+  ++ +   i +++e +++ + +  +L n++
  gi|70605996|ref|YP_254866.1| 295 TKYRNSIDYSEQTLEQARSSLQRLKDAMGIIRSVIKEEPKSHS-NEEEISTQREIIS-LIGKFHEAMSNDFDTATALSNIY 373
                                   5778999999*****************************9999.8999999999999.*******************9999 PP

                                   HHH CS
                     Fib_alpha 112 esn 114
                                   e  
  gi|70605996|ref|YP_254866.1| 374 EIA 376
                                   855 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2    0.0001      0.15      28      68 ..      31      71 ..      19      76 .. 0.90
   2 ?    0.2   0.0      0.19   2.8e+02     131     195 ..      82     148 ..      72     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                  --BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B- CS
                  tRNA-synt_1d 28 sPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGD 68
                                   P +   +h+Gh r+ +  d ++r l + G++vir+  + D
  gi|70605996|ref|YP_254866.1| 31 GPTVYDYVHIGHGRAFVGFDGIVRYLKLRGFNVIRVQNITD 71
                                  6889999*********999*****************99887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHHHHHHHHHHHHCT---EC..--CCCCCCCHHHHHHHHHCTT-EEE.CTTCEEEEEC CS
                  tRNA-synt_1d 131 dirklwkllvditrtelqklydrldvtlie..rGeslykeslneivkelkkkglvke.sdGalvvfld 195
                                   ++ k w+ +vd+  +++ +  ++l v + +  r  s  +e   + v++l +kg +   s G    ++d
  gi|70605996|ref|YP_254866.1|  82 ETGKDWREIVDYYTKDYMESLKALKVEIDQhpRVTSHIQEI-IDFVQKLVDKGHAYItSSGSVYFDVD 148
                                   4567899***********99999999987655555555554.46777777777765414455555555 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.9     2e-05     0.029      92     152 ..      74     132 ..      63     135 .. 0.90
   2 ?    0.5   0.1      0.35   5.2e+02      92     149 ..     305     358 ..     300     368 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           RRF  92 kelvkeakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqkltdkyikeide 152
                                   ++++k+a++ ++++++ +    +d+++ lk+l+ +i  D+  ++  +iq+++d  +k +d+
  gi|70605996|ref|YP_254866.1|  74 DKIIKRANETGKDWREIVDYYTKDYMESLKALKVEI--DQHPRVTSHIQEIIDFVQKLVDK 132
                                   789**************************9887666..***************99999886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHH CS
                           RRF  92 kelvkeakkaaekakvairniRrdankklkklekkiseDdvkkaekeiqkltdkyike 149
                                   +++ ++a++  ++ k+a+  iR+ ++++ k+ ++    +++ + + ei +l+ k+ + 
  gi|70605996|ref|YP_254866.1| 305 EQTLEQARSSLQRLKDAMGIIRSVIKEEPKSHSN----EEEISTQREIISLIGKFHEA 358
                                   6778888889999999999999988888875544....44444455555555444444 PP

>> SH3BP5  SH3 domain-binding protein 5 (SH3BP5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.9e-05       0.1     108     209 ..      78     182 ..      66     184 .. 0.87
   2 ?   -2.3   0.0       2.2   3.2e+03      20      39 ..     300     319 ..     296     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                        SH3BP5 108 eeertldkawqemLnhatqkVneaeeekkeaeeehqrktkkleeaekkvqqlekklkrsikks.kpYfelka..klnkqle 185
                                   ++ ++  k+w e  +  t++ +e+ +  k    +h r+t++++e+ + vq+l  k +  i  s + Yf++ +  ++     
  gi|70605996|ref|YP_254866.1|  78 KRANETGKDWREIVDYYTKDYMESLKALKVEIDQHPRVTSHIQEIIDFVQKLVDKGHAYITSSgSVYFDVDSfpSYGLLSG 158
                                   566788899************************************************999887368***987435667778 PP

                        SH3BP5 186 eqkekveelekevkeaKaeYseaL 209
                                   ++ke+ ++ e+ vke+K+ Y  aL
  gi|70605996|ref|YP_254866.1| 159 SKKEEWNQGEEIVKEKKNPYDFAL 182
                                   999*****************9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                        SH3BP5  20 eINklEveLeearakfrell 39 
                                   +I   E  Le+ar++ ++l+
  gi|70605996|ref|YP_254866.1| 300 SIDYSEQTLEQARSSLQRLK 319
                                   56666777777777766655 PP

>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0008       1.2      17      49 ..     244     279 ..     233     293 .. 0.79
   2 ?    0.5   0.0      0.39   5.8e+02      39      74 ..     365     400 ..     355     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0008
                 TB2_DP1_HVA22  17 et.k.wltYWvvfafltvvesla.dvllswiPfYyl 49 
                                      k w++YWv +a lt+ ++ + ++l ++iP+  +
  gi|70605996|ref|YP_254866.1| 244 LLgKiWVKYWVHVAYLTINKEKMsKSLGNIIPLNEA 279
                                   45577*************988886888889998555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.39
                 TB2_DP1_HVA22  39 vllswiPfYylfKllfllwlvlpqtqgatyvYekfl 74 
                                   + +++  +Y ++ l+f+   +  ++ ga + +++f 
  gi|70605996|ref|YP_254866.1| 365 TATALSNIYEIANLVFTKIQYTRDFMGAMLAFDAFR 400
                                   55566678999999**99999999******999986 PP

>> TIP120  TATA-binding protein interacting (TIP20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3   0.00095       1.4      98     154 ..     313     369 ..     305     387 .. 0.87
   2 ?    0.7   0.0      0.25   3.8e+02      47      62 ..     417     432 ..     415     454 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00095
                        TIP120  98 evlerldelvealrktlskklkekavkqelEkqeelkrsvlrvvaalnsklesaeva 154
                                   + l+rl++ +  +r+++++++k+++ + e+ +q e++  + ++ +a+++++++a++ 
  gi|70605996|ref|YP_254866.1| 313 SSLQRLKDAMGIIRSVIKEEPKSHSNEEEISTQREIISLIGKFHEAMSNDFDTATAL 369
                                   56899******************************************9999999853 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.25
                        TIP120  47 Yetlytlletaldrld 62 
                                   Yet+y +++++++  +
  gi|70605996|ref|YP_254866.1| 417 YETMYKVIDSVVEIRN 432
                                   9********9765433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 2466.02
//
Query:       gi|70605997|ref|YP_254867.1|  [L=146]
Description: ADP-ribose pyrophosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-19   68.1   0.0    8.7e-19   67.9   0.0    1.1  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.13   12.2   0.0    1.2  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   9.7e-23   8.7e-19       4     127 ..       6     122 ..       3     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 9.7e-23
                                   EEEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdehe 83 
                                   +avg v+l +++ vLlv+r++ p +g W++PgGkve+gEt+ +A+ RE++EEt l++e +ell++++       +++  h+
  gi|70605997|ref|YP_254867.1|   6 VAVGGVILKGNK-VLLVKRRNPPNKGnWAIPGGKVEYGETLVDAVKREMKEETALDVEPIELLAVVEI------IKEGYHY 79 
                                   799999999995.*******788888*****************************9999999994432......2222344 PP

                                   EEEEEE...EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHH CS
                         NUDIX  84 ilyvfl...eevegelepndenevsevrwvpleellkeklaaesrkl 127
                                   +++      + ++gel+p+ ++   ++ ++ l+el +e+  +   ++
  gi|70605997|ref|YP_254867.1|  80 VIF--DficKVLNGELNPGSDAT--SADFLGLDELRRENVSPTTIEM 122
                                   444..355999999999994444..4556888888666666655555 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05      0.13       4      49 ..      11      59 ..       8     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                  EEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS- CS
                       NUDIX_4  4 lirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgi 49
                                  +i+++++vll kR +    +g w +Pgg+ e ge+l +a++   +ee+++
  gi|70605997|ref|YP_254867.1| 11 VILKGNKVLLVKRRNP-PNKGNWAIPGGKvEYGETLVDAVKremKEETAL 59
                                  788899***9999886.789*********999999767774333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 999.20
//
Query:       gi|70605998|ref|YP_254868.1|  [L=418]
Description: hypothetical protein Saci_0154 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2837.68
//
Query:       gi|70605999|ref|YP_254869.1|  [L=423]
Description: glutamate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-66  224.7   3.2    1.8e-66  224.3   3.2    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.3e-54  182.3   0.0    8.6e-54  180.9   0.0    1.7  2  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0029   17.0   0.4     0.0051   16.2   0.4    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.018   14.4   1.6      0.035   13.4   1.0    1.9  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.031   11.8   0.1      0.043   11.3   0.1    1.1  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
       0.11   12.5   0.9       0.34   11.0   0.9    1.8  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.3   3.2   6.1e-70   1.8e-66       1     243 []     188     421 ..     188     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.3 bits;  conditional E-value: 6.1e-70
                                   T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHH CS
                 ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieelle 81 
                                   GG  +r  +TglGv+++++ +++k+ +  +eg+rv i+G+Gnvgs++a++l+e+gak+v++sD +G +++ +G+d+++ le
  gi|70605999|ref|YP_254869.1| 188 GGLPARIYSTGLGVATTARLAAEKVLGG-IEGARVLIQGFGNVGSFTAKFLEEMGAKIVGISDIKGGVINYNGIDVKKALE 267
                                   8999********************8777.**************************************************** PP

                                   HHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHTT CS
                 ELFV_dehydrog  82 lkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileeag 162
                                   +k++++sv +y+     + ++++ne e+l  ++dil+P+A++n+i++ na  ++k  +kl+vEgAN+p+t +A+ +++++g
  gi|70605999|ref|YP_254869.1| 268 VKDNTGSVFNYP-----DGKKVTNE-EFLVSDCDILIPAAIENVIHKFNAP-KVK--AKLIVEGANGPLTADADVVMKDRG 339
                                   ************.....34899997.99999********************.999..************************ PP

                                   -EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T.HHHHHHHHHHHHHHHHHHHC CS
                 ELFV_dehydrog 163 vlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe.lvkganiagfekvaeamkaq 242
                                   ++vvpd++aNaGGV+ S++E+++n ++  ++eee ++ + ++m+++f+ v++++++ + + ++++a+++++e+v++amk +
  gi|70605999|ref|YP_254869.1| 340 IMVVPDILANAGGVVGSYVEWANNKMGEIMDEEEARKLIVSRMERAFDYVYTKYNKLGDQdMRTAAMAMAIERVVNAMKVR 420
                                   ********************************************************76656******************99 PP

                                   T CS
                 ELFV_dehydrog 243 G 243
                                   G
  gi|70605999|ref|YP_254869.1| 421 G 421
                                   8 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.0   2.9e-57   8.6e-54       1     128 [.      42     168 ..      42     170 .. 0.99
   2 ?   -3.6   0.0       3.2   9.7e+03      89     109 ..     231     250 ..     228     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 2.9e-57
                                   -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GGG CS
               ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpkk 81 
                                   perv+qv++++k ++G+++++ g+r+qh+salgP+kGG+R+hp+v++dev aL+++mt+Knal+ lp+GG+kgg+++dp+k
  gi|70605999|ref|YP_254869.1|  42 PERVIQVKIEIKGKDGQVRTFMGWRSQHNSALGPYKGGVRYHPNVTQDEVVALSMMMTWKNALLLLPYGGGKGGIRVDPSK 122
                                   89******************************************************************************* PP

                                   S-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHH CS
               ELFV_dehydrog_N  82 lseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladey 128
                                   l+++ele++ rr+v +l+ k+iG++iD+pApDv+t++++maw +dey
  gi|70605999|ref|YP_254869.1| 123 LTQDELEQLSRRYVGALY-KYIGSDIDIPAPDVNTNPQTMAWYVDEY 168
                                   ******************.***************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHG.GG-BTTTEE CS
               ELFV_dehydrog_N  89 ritrrfvrelakkfiGpgiDv 109
                                   ++t +f +e+  k++G   D+
  gi|70605999|ref|YP_254869.1| 231 SFTAKFLEEMGAKIVGI-SDI 250
                                   67889999998888765.455 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   1.7e-06    0.0051      33      67 ..     215     249 ..     202     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                    ++g +v i G+G++G+ +ak l+++g+k+++++ 
  gi|70605999|ref|YP_254869.1| 215 GIEGARVLIQGFGNVGSFTAKFLEEMGAKIVGISD 249
                                   5899***************************9876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.0   1.2e-05     0.035      19      99 ..     212     301 ..     196     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                   TTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEE.EEESSHHHHHHHHH.TTTCECEE.............HCHHHHH CS
                   AlaDh_PNT_C  19 laGgvpgvepakvlviGgGvaGlqAiatakglgakVt.vlDvrparleqles.lgakfvev.............lksqeel 84 
                                   ++Gg++    a+vl+ G G +G   ++   ++gak++ + D++  ++++    +++  +ev             +  +  +
  gi|70605999|ref|YP_254869.1| 212 VLGGIE---GARVLIQGFGNVGSFTAKFLEEMGAKIVgISDIKGGVINYNGIdVKKA-LEVkdntgsvfnypdgK--KVTN 286
                                   456666...*************************86527788888887776634444.77777777777666332..2333 PP

                                   HHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C  85 laeavkeadvvigtv 99 
                                    +  v+++d++i ++
  gi|70605999|ref|YP_254869.1| 287 EEFLVSDCDILIPAA 301
                                   333577788887776 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.4e-05     0.043    1049    1099 ..     309     359 ..     304     376 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
                       Bac_GDH 1049 vngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                     n+ +++ak + EG+N  lt  + + +  +g+ +  D + N++GV  S  E
  gi|70605999|ref|YP_254869.1|  309 FNAPKVKAKLIVEGANGPLTADADVVMKDRGIMVVPDILANAGGVVGSYVE 359 
                                    58999****************************************988666 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   0.00011      0.34      21      74 ..     216     267 ..     201     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                   -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHH CS
                 AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtlee 74 
                                   + G  +++ G+G+vG  +a+ l+++Ga+++   +  i       +G +v++  e
  gi|70605999|ref|YP_254869.1| 216 IEGARVLIQGFGNVGSFTAKFLEEMGAKIV--GISDIKGGVINYNGIDVKKALE 267
                                   56889**********************864..4444555555555666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2609.49
//
Query:       gi|70606000|ref|YP_254870.1|  [L=93]
Description: hypothetical protein Saci_0156 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-23   79.8   1.9    8.6e-23   79.8   1.9    2.1  2  DUF131           Protein of unknown function DUF131
     0.0051   16.9   3.9     0.0076   16.4   3.8    1.4  1  MpPF26           M penetrans paralogue family 26
     0.0094   15.4   0.1     0.0094   15.4   0.1    2.0  2  DUF5305          Family of unknown function (DUF5305)
  ------ inclusion threshold ------
      0.011   16.0   1.9       0.31   11.3   0.0    2.1  2  HemY_N           HemY protein N-terminus
      0.015   15.3   2.1          4    7.5   0.0    2.1  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.021   14.4   7.3       0.91    9.1   0.0    2.1  2  Baculo_11_kDa    Baculovirus 11 kDa family
      0.023   15.3   0.1      0.023   15.3   0.1    2.2  1  OAD_gamma        Oxaloacetate decarboxylase, gamma chain
      0.046   13.3   6.3       0.15   11.7   0.3    2.0  2  Saf_2TM          SAVED-fused 2TM effector domain
      0.048   13.2   1.4       0.15   11.7   0.0    1.9  2  TMEM100          Transmembrane protein 100
      0.057   13.2  12.3       0.53   10.1   0.1    3.0  2  DUF4190          Domain of unknown function (DUF4190)
        0.2   12.3   2.9       0.89   10.3   0.0    2.0  2  GRP              Glycine rich protein family
       0.26   10.0   3.2       0.32    9.7   3.2    1.2  1  DUF2207          Predicted membrane protein (DUF2207)
       0.27   12.1   8.2       0.29   12.0   0.0    2.1  2  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
       0.41   10.9  11.1        2.9    8.1  10.8    1.9  1  DUF3784          Domain of unknown function (DUF3784)
       0.42   10.4   5.5        1.1    9.0   5.3    1.8  1  TMEM51           Transmembrane protein 51
       0.43   11.1   6.4         11    6.7   6.4    2.2  1  DUF3899          Domain of unknown function (DUF3899)
       0.47   10.1   3.4        8.4    6.1   0.0    2.0  2  DUF4736          Domain of unknown function (DUF4736)
       0.58   10.2   2.5        5.3    7.1   0.0    2.5  2  FixQ             Cbb3-type cytochrome oxidase component FixQ
       0.61   10.3  10.4        9.2    6.4   9.6    2.0  1  DUF2371          Uncharacterised conserved protein (DUF2371)
        0.7    9.8   0.0        0.7    9.8   0.0    1.9  1  TarH             Tar ligand binding domain homologue
       0.72   10.2   6.3        2.9    8.2   0.1    2.1  2  Sigma_reg_N      Sigma factor regulator N-terminal
       0.75   10.0   8.8       0.24   11.6   0.2    2.2  2  Pox_A14          Poxvirus virion envelope protein A14
        1.2    8.8   5.5        3.3    7.4   5.5    1.6  1  Tetraspanin      Tetraspanin family
        1.4    9.4   4.8         14    6.1   0.0    2.1  2  DUF2681          Protein of unknown function (DUF2681)
        2.3    8.4   9.4        1.3    9.2   0.4    2.2  2  SdpI             SdpI/YhfL protein family
        3.6    7.3   8.4        3.6    7.3   0.1    2.1  2  Neurensin        Neurensin
        6.5    6.8  11.9        8.2    6.5   0.1    2.4  2  DUF4083          Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   3.7       1.1   7.6e+02      46      57 ..      12      23 ..       3      27 .. 0.56
   2 !   79.8   1.9   1.3e-25   8.6e-23       3      61 ..      28      86 ..      26      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                        DUF131 46 taiiLaIilmil 57
                                  t i+++++l+i+
  gi|70606000|ref|YP_254870.1| 12 TIIFVGLVLVIV 23
                                  344555555555 PP

  == domain 2  score: 79.8 bits;  conditional E-value: 1.3e-25
                        DUF131  3 vvlkalekeeeeaekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                   ++k+++ke++e+++ee+++++GGV++iGPIPI+FGs+k++ak+a+i+++i+++l++++
  gi|70606000|ref|YP_254870.1| 28 GIIKSSKKERNENQREETKTEYGGVIFIGPIPIVFGSNKDMAKMALIIGVIMVVLIIAF 86
                                  6899999*************************************************998 PP

>> MpPF26  M penetrans paralogue family 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.8   1.1e-05    0.0076       8      84 ..       3      84 ..       1      91 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                        MpPF26  8 ikklsltiiilyllatvlllvsllayivllskskllskeyeeesslleaelligvllillidi.....fyivnfileiiLii 84
                                  +  ls++ + ++++  vl++v++++ i+ +sk++ ++++ ee ++ + + + ig + i++ +      +++++ +++++Lii
  gi|70606000|ref|YP_254870.1|  3 TDILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREETKTEYGGVIFIGPIPIVFGSNkdmakMALIIGVIMVVLII 84
                                  566899999******************************999999999999999999999776777999***********98 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-05    0.0094     117     165 ..       8      56 ..       2      66 .. 0.79
   2 ?    0.4   2.6      0.53   3.5e+02     112     132 ..      70      89 ..      61      93 .] 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                       DUF5305 117 illiilgllaliglvvlirriiftsskaekyelelekilkeYdewIvkg 165
                                   ++++ +++++l+ ++v i++ i +ssk+e+ e+++e++  eY+ +I  g
  gi|70606000|ref|YP_254870.1|   8 AIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREETKTEYGGVIFIG 56 
                                   4566677777888888888889999999****************99765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.53
                       DUF5305 112 slaegilliilgllaliglvv 132
                                   ++a  i+++i+++l+++++v+
  gi|70606000|ref|YP_254870.1|  70 KMAL-IIGVIMVVLIIAFVVL 89 
                                   3333.6666666666666655 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00047      0.31      13      56 ..       2      45 ..       1      52 [. 0.82
   2 ?    2.8   2.3       0.2   1.3e+02      16      32 ..      73      89 ..      60      93 .] 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                        HemY_N 13 etslvvavlllvllfvllylllrllrlllrlparvrrwrrrrre 56
                                  +t ++ a+ l+++++ l+++++ +++++++++++ r+  +r   
  gi|70606000|ref|YP_254870.1|  2 STDILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREET 45
                                  5788999************************8887776555544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                        HemY_N 16 lvvavlllvllfvllyl 32
                                  l+  v+++vl+++ ++l
  gi|70606000|ref|YP_254870.1| 73 LIIGVIMVVLIIAFVVL 89
                                  44444444444333333 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.006         4      68      95 ..      12      39 ..       3      53 .. 0.56
   2 ?    6.4   1.8     0.013       8.6      31      56 ..      66      91 ..      61      93 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.006
               Phage_holin_3_6 68 aalivaavllvlagvlalvglkklkkak 95
                                    + v++vl+++++v +++  +k  +++
  gi|70606000|ref|YP_254870.1| 12 TIIFVGLVLVIVGIVSGIIKSSKKERNE 39
                                  3333666666666666666555555544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
               Phage_holin_3_6 31 kragsgagllgaagvlallalllllv 56
                                  k ++++a+++g+ +v++++a+++l+ 
  gi|70606000|ref|YP_254870.1| 66 KDMAKMALIIGVIMVVLIIAFVVLSY 91
                                  66788999999999999999999875 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0014      0.91      40      76 ..       9      45 ..       3      50 .. 0.62
   2 ?    5.6   5.1     0.017        12      39      59 ..      73      93 .]      65      93 .] 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                 Baculo_11_kDa 40 icglvvfvvivlfilLlvv.ilknaeaeeaekekrekt 76
                                  i+  ++fv +vl i+ +v+ i+k++++e+ e ++re+t
  gi|70606000|ref|YP_254870.1|  9 IGLTIIFVGLVLVIVGIVSgIIKSSKKERNE-NQREET 45
                                  6667999988888885554277766665554.344433 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                 Baculo_11_kDa 39 vicglvvfvvivlfilLlvvi 59
                                  +i g++++v+i+ f++L +v+
  gi|70606000|ref|YP_254870.1| 73 LIIGVIMVVLIIAFVVLSYVV 93
                                  577999**********98875 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   3.5e-05     0.023       6      49 ..       6      47 ..       5      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                     OAD_gamma  6 ltllGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaa 49
                                  l+ +G++++Fv+L+l +  + ++s iik  +k+ ++++ ++++ 
  gi|70606000|ref|YP_254870.1|  6 LSAIGLTIIFVGLVLVI--VGIVSGIIKSSKKERNENQREETKT 47
                                  6789*********9865..4557788888888877777777664 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00022      0.15      61      99 ..       3      41 ..       1      48 [. 0.84
   2 ?    5.0   1.2     0.026        17      51      87 ..      55      91 ..      44      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                       Saf_2TM 61 seipeivlaiilvigvllivvGavllilryvneakrqsk 99
                                   +i +++ ++i+++g +l++vG+v  i+   + ++++++
  gi|70606000|ref|YP_254870.1|  3 TDILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQ 41
                                  448899*****************9999998887777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                       Saf_2TM 51 ggslevsfssseipeivlaiilvigvllivvGavlli 87
                                   g + + f+s++ ++ +++ii vi v+li++ +vl++
  gi|70606000|ref|YP_254870.1| 55 IGPIPIVFGSNKDMAKMALIIGVIMVVLIIAFVVLSY 91
                                  5678888999998889999999999999998877765 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00022      0.15      83     121 ..       4      45 ..       1      51 [. 0.72
   2 ?    0.2   0.9      0.76     5e+02      65      78 ..      73      86 ..      61      93 .] 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                       TMEM100  83 svisvlglvLLsaGlvllassavCWkvrrrrk...kerrres 121
                                    ++s +gl ++  Glvl+++  v   ++  +k   +++r e 
  gi|70606000|ref|YP_254870.1|   4 DILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKernENQREET 45 
                                   68899*************999998877766531103444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.76
                       TMEM100 65 LvaGvvvtavaytf 78
                                  L++Gv+  +   +f
  gi|70606000|ref|YP_254870.1| 73 LIIGVIMVVLIIAF 86
                                  44444333332222 PP

>> DUF4190  Domain of unknown function (DUF4190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00079      0.53      10      38 ..      11      39 ..       4      45 .. 0.64
   2 ?    2.3   8.6      0.21   1.4e+02      41      61 ..      65      85 ..      47      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                       DUF4190 10 ilgllfl.iitgivavilGhvAlrqirrsg 38
                                  ++ ++f+ +++ iv+++ G++  ++ +r++
  gi|70606000|ref|YP_254870.1| 11 LT-IIFVgLVLVIVGIVSGIIKSSKKERNE 39
                                  22.333558999999999998666555554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                       DUF4190 41 GkglAiaGivlGwigllllvl 61
                                  +k +A  ++++G+i+++l+++
  gi|70606000|ref|YP_254870.1| 65 NKDMAKMALIIGVIMVVLIIA 85
                                  689***************986 PP

>> GRP  Glycine rich protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0013      0.89       6      47 ..      13      51 ..       8      63 .. 0.74
   2 ?    0.2   2.9       1.9   1.3e+03       4      22 ..      70      87 ..      68      92 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                           GRP  6 lilLglllaavlLissevaaaelskeeksekeeevkdekygg 47
                                  +i++gl+l++v ++s  +++    k+e++e++ e  +++ygg
  gi|70606000|ref|YP_254870.1| 13 IIFVGLVLVIVGIVSGIIKSS---KKERNENQREETKTEYGG 51
                                  688888888877777666664...456777777777777877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                           GRP  4 kalilLglllaavlLisse 22
                                  k+++++g+++ +vl+i+  
  gi|70606000|ref|YP_254870.1| 70 KMALIIGVIM-VVLIIAFV 87
                                  5667777773.34555544 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.2   0.00049      0.32     382     430 ..       5      89 ..       1      93 [] 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00049
                       DUF2207 382 klsalglgliilglilillallllvll....................................lvfllilllillliaiiv 426
                                   +lsa+gl +i++gl+l+++++++ ++                                     +  +++++ ++++++ii+
  gi|70606000|ref|YP_254870.1|   5 ILSAIGLTIIFVGLVLVIVGIVSGIIKsskkernenqreetkteyggvifigpipivfgsnkdMAKMALIIGVIMVVLIIA 85 
                                   4556666666666666666655554449********************************998444444444444444444 PP

                       DUF2207 427 lllf 430
                                   ++++
  gi|70606000|ref|YP_254870.1|  86 FVVL 89 
                                   4443 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00044      0.29       4      36 ..      13      45 ..       6      66 .. 0.62
   2 ?    0.4   6.2       1.8   1.2e+03       4      20 ..      72      88 ..      68      92 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00044
                      EphA2_TM  4 aavaglvllvilvilvlvlvrrrsknrkqksdl 36
                                  ++++glvl+++ ++  ++  +++++n++q++++
  gi|70606000|ref|YP_254870.1| 13 IIFVGLVLVIVGIVSGIIKSSKKERNENQREET 45
                                  455566666555555555555555555555432 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.8
                      EphA2_TM  4 aavaglvllvilvilvl 20
                                  a+++g++++v++++ v+
  gi|70606000|ref|YP_254870.1| 72 ALIIGVIMVVLIIAFVV 88
                                  56677777776555444 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  10.8    0.0044       2.9       3      89 ..       9      91 ..       8      93 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0044
                       DUF3784  3 lallflilGilflkgkganLiaGYntmskeekekydekklsrfmgivllligilflllgllsaiesealliialiviiiiviy 85
                                  ++l+ +++G+++        ++G    sk+e+++   +   + +g v+++ g + +++g  + + ++al+i++++v++ii+++
  gi|70606000|ref|YP_254870.1|  9 IGLTIIFVGLVLV---IVGIVSGIIKSSKKERNENQREETKTEYGGVIFI-GPIPIVFGSNKDMAKMALIIGVIMVVLIIAFV 87
                                  5666777777777...7778899999999999999999999999987765.88********9999999999999988888888 PP

                       DUF3784 86 livy 89
                                  ++ y
  gi|70606000|ref|YP_254870.1| 88 VLSY 91
                                  7765 PP

>> TMEM51  Transmembrane protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.3    0.0017       1.1       8      51 ..       6      49 ..       2      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                        TMEM51  8 lcAlGvGllaLgivmivWsvvPgeseadkpkasanssskpdkds 51
                                  l+A+G+ ++ +g+v+++  +v g  +++k + + n+ ++++++ 
  gi|70606000|ref|YP_254870.1|  6 LSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREETKTEY 49
                                  89*********************999988888888777766554 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.4     0.016        11       2      82 ..       4      86 ..       3      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.016
                       DUF3899  2 NilFllglllliigillivlnsGfFdgfsygfrklkklflkkskkddsyyeykek........kkesskkstrplliiGllli 76
                                  +il+ +gl ++++g++l+++  G+ +g++ + +k ++     +++++ + ey             +s+k  ++  liiG++ +
  gi|70606000|ref|YP_254870.1|  4 DILSAIGLTIIFVGLVLVIV--GIVSGIIKSSKKERNE----NQREETKTEYGGVifigpipiVFGSNKDMAKMALIIGVIMV 80
                                  67777777777777777776..7777777777777766....77777777777776666665533449999999999999999 PP

                       DUF3899 77 vlsivl 82
                                  vl i++
  gi|70606000|ref|YP_254870.1| 81 VLIIAF 86
                                  999887 PP

>> DUF4736  Domain of unknown function (DUF4736)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.013       8.4      33      78 ..       5      46 ..       1      55 [. 0.72
   2 ?    4.2   1.9     0.048        32      30      54 ..      68      92 ..      61      93 .] 0.67

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                       DUF4736 33 lvllilslivllililvllsyveptvlsrkirrekeelekpllevk 78
                                  ++ +i   i+++ l+lv++ +v  ++ s k +r++++ e +    k
  gi|70606000|ref|YP_254870.1|  5 ILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREET----K 46
                                  56678888888999999999999999888777776654444....4 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.048
                       DUF4736 30 slllvllilslivllililvllsyv 54
                                  + +++l+i +++v+li+  v+lsyv
  gi|70606000|ref|YP_254870.1| 68 MAKMALIIGVIMVVLIIAFVVLSYV 92
                                  3445566667777778888888986 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.008       5.3       1      39 [.       1      39 [.       1      42 [. 0.83
   2 ?   -0.5   3.8       1.9   1.3e+03      12      27 ..      74      89 ..      66      93 .] 0.52

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.008
                          FixQ  1 mtyealrgfadswgllflvllfygvviyafrpgnrkdfe 39
                                  m+ ++l++++ ++  + lvl+ +g+v  + +++++++ e
  gi|70606000|ref|YP_254870.1|  1 MSTDILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNE 39
                                  677899999999999999999999998888888877776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                          FixQ 12 swgllflvllfygvvi 27
                                  ++g +  vl+ + vv+
  gi|70606000|ref|YP_254870.1| 74 IIGVIMVVLIIAFVVL 89
                                  4444444444444443 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   9.6     0.014       9.2      42     126 ..       5      89 ..       2      91 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                       DUF2371  42 lvlllGllvllvGiamavlgywpkkaklaseekssssstaessseklglla.....rfleqylysdklkvlGPlimGiGif 117
                                   ++ ++Gl +++vG+++ ++g       ++s++++++++ +e+++e  g+++      ++ +     k+     li+G+ + 
  gi|70606000|ref|YP_254870.1|   5 ILSAIGLTIIFVGLVLVIVGIVSGII-KSSKKERNENQREETKTEYGGVIFigpipIVFGSNKDMAKM----ALIIGVIMV 80 
                                   56788999999999999999877664.34444444455555545555444311000333333333333....456666666 PP

                       DUF2371 118 lfiCanavL 126
                                   ++i a  vL
  gi|70606000|ref|YP_254870.1|  81 VLIIAFVVL 89 
                                   666665555 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0011       0.7       7      42 ..       5      40 ..       1      48 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                                  XXXXXXXXXXXXXXXXXXXXSSSSSSHHHHHHHCHH CS
                          TarH  7 IrtrLllvlallgvLllvsgglglsglsrsndalre 42
                                  I + + l+++++g+ l+++g+++ +  s+ +++ ++
  gi|70606000|ref|YP_254870.1|  5 ILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNEN 40
                                  788899**************9988776666655443 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0043       2.9      12      45 ..       5      40 ..       3      49 .. 0.55
   2 ?    3.5   2.8      0.13        87       9      28 ..      71      90 ..      67      93 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                   Sigma_reg_N 12 ilrivlislivlllifvil..vvtllylaekegnkl 45
                                  il+ + +++i++ l++vi   v+++ + ++ke n+ 
  gi|70606000|ref|YP_254870.1|  5 ILSAIGLTIIFVGLVLVIVgiVSGIIKSSKKERNEN 40
                                  566666677666555555553444444455555554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                   Sigma_reg_N  9 rksilrivlislivlllifv 28
                                    +i+ +++++li++++++ 
  gi|70606000|ref|YP_254870.1| 71 MALIIGVIMVVLIIAFVVLS 90
                                  44555555555555555543 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00037      0.24      13      41 ..      12      40 ..       3      65 .. 0.73
   2 ?    1.6   3.9      0.48   3.2e+02      12      34 ..      70      90 ..      61      92 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                       Pox_A14 13 tvliaGiiLLilacifafvdfskststtd 41
                                  t++++G++L+i+ ++   +  sk++ + +
  gi|70606000|ref|YP_254870.1| 12 TIIFVGLVLVIVGIVSGIIKSSKKERNEN 40
                                  799*******************9987633 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.48
                       Pox_A14 12 stvliaGiiLLilacifafvdfs 34
                                    +li+G+i+++l  i+afv +s
  gi|70606000|ref|YP_254870.1| 70 KMALIIGVIMVVL--IIAFVVLS 90
                                  4567777776554..55665554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.5    0.0049       3.3       6      97 ..       7      90 ..       4      93 .] 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                                  XXXXXXXXXXXXXXXXXXXXXXX.XXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  6 fffnllfwligivllavGvwlrl.khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfsllll 87
                                    + l ++ +g+vl++vG+   + k++ ++      ++++ + +        G ++f+  +  ++g+ k+   + l+  ++++
  gi|70606000|ref|YP_254870.1|  7 SAIGLTIIFVGLVLVIVGIVSGIiKSS-KKE----RNENQREETK----TEYGGVIFIGPIPIVFGSNKDMAKMALIIGVIMV 80
                                  556677888999999999666443333.222....2222222222....3357777777777778899999988888889999 PP

                                  XXXXXXXXXX CS
                                  xxxxxxxxxx RF
                   Tetraspanin 88 vlfllelaag 97
                                  vl+++++++ 
  gi|70606000|ref|YP_254870.1| 81 VLIIAFVVLS 90
                                  9988888876 PP

>> DUF2681  Protein of unknown function (DUF2681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.021        14       5      39 ..      10      44 ..       6      49 .. 0.74
   2 ?    2.7   3.4      0.25   1.7e+02       1      21 [.      68      87 ..      68      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.021
                       DUF2681  5 allvgliaavlllvaylswqlkkarkknaklqaek 39
                                   l++ ++++vl++v+ +s  +k ++k+ ++ q e+
  gi|70606000|ref|YP_254870.1| 10 GLTIIFVGLVLVIVGIVSGIIKSSKKERNENQREE 44
                                  57788999999999999998877776666655554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.25
                       DUF2681  1 mlqlallvgliaavlllvayl 21
                                  m ++al++g+i +vl++ a++
  gi|70606000|ref|YP_254870.1| 68 MAKMALIIGVIMVVLII-AFV 87
                                  789********999997.554 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.0      0.12        78      47      65 ..       8      26 ..       1      32 [. 0.61
   2 ?    9.2   0.4    0.0019       1.3      36      64 ..      55      87 ..      38      93 .] 0.45

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                          SdpI 47 avvlvllvlvlllvivpii 65
                                  a++l+++++ l+lviv+i+
  gi|70606000|ref|YP_254870.1|  8 AIGLTIIFVGLVLVIVGIV 26
                                  3445566666666666654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                          SdpI 36 aGlilllla........lgavvlvllvlvlllvivpi 64
                                  +G i ++++             l++ v++++l+i+++
  gi|70606000|ref|YP_254870.1| 55 IGPIPIVFGsnkdmakmA----LIIGVIMVVLIIAFV 87
                                  222223333568755431....222222222222222 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0054       3.6      93     130 ..       4      41 ..       2      47 .. 0.62
   2 ?    3.9   3.0     0.062        41      37      65 ..      65      93 .]      39      93 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0054
                     Neurensin  93 dtlklaGavllclGglllalsllvpalsksdkkeeele 130
                                   d+l  +G++++ +G +l++++++  ++++s+k+ +e++
  gi|70606000|ref|YP_254870.1|   4 DILSAIGLTIIFVGLVLVIVGIVSGIIKSSKKERNENQ 41 
                                   56677888888887777777765444444444444333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.062
                     Neurensin 37 esllwkvslvvgtlvlllGvtallvGylv 65
                                  +  ++k +l++g+++++l +++++++y+v
  gi|70606000|ref|YP_254870.1| 65 NKDMAKMALIIGVIMVVLIIAFVVLSYVV 93
                                  567999******************99986 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.012       8.2       4      23 ..      11      30 ..       6      45 .. 0.56
   2 ?    2.3   7.7      0.25   1.6e+02       4      20 ..      72      88 ..      71      93 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                       DUF4083  4 dliyliivivLilllvfsft 23
                                   +i+ + ++++i+++v +++
  gi|70606000|ref|YP_254870.1| 11 LTIIFVGLVLVIVGIVSGII 30
                                  44444444444555554443 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                       DUF4083  4 dliyliivivLilllvf 20
                                  +li+ +i++vLi+++v+
  gi|70606000|ref|YP_254870.1| 72 ALIIGVIMVVLIIAFVV 88
                                  6899***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1683  (0.0938703); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 636.85
//
Query:       gi|70606001|ref|YP_254871.1|  [L=495]
Description: hypothetical protein Saci_0157 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-27   94.7   9.0    2.9e-15   56.8   0.0    2.8  3  AAA_15    AAA ATPase domain
    4.7e-20   72.6   1.4    3.8e-14   53.2   0.0    2.6  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.9e-08   34.0   0.9    2.8e-07   30.2   0.9    2.2  1  SMC_N     RecF/RecN/SMC N terminal domain
    2.7e-07   31.3   0.7    2.7e-07   31.3   0.7    1.7  2  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.015   15.8   0.4        0.4   11.2   0.4    2.7  2  ABC_tran  ABC transporter
      0.055   13.2   0.0        0.1   12.2   0.0    1.4  1  UTP15_C   UTP15 C terminal
        0.1   11.8   0.3        1.5    8.0   0.1    2.3  2  DUF2813   Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   2.0   6.2e-14   1.6e-10       1      80 [.       1     105 [.       1     163 [. 0.68
   2 !   56.8   0.0   1.1e-18   2.9e-15     264     369 .]     189     285 ..     162     285 .. 0.78
   3 ?   -1.3   0.4      0.52   1.3e+03     123     158 ..     407     442 ..     345     493 .. 0.54

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 6.2e-14
                        AAA_15   1 MkIkkikikNFRslkdveid.lseeltvliGkNnsGKSsilealdlFlnnk....ekkn.....................k 55 
                                   Mk+ ++ ++NFRs+++v++  l   l++++G N+ GK+++l a++lF++n     ek n                     k
  gi|70606001|ref|YP_254871.1|   1 MKLIEFYVNNFRSISSVKLTgLGG-LNIIVGYNGYGKTNLLTAIYLFIKNLgaglEKRNiedrngeymllwrdydvskliK 80 
                                   9**************977762444.************************88655433335555555555555555544443 PP

                        AAA_15  56 kvikiekedleifeniseskdikId 80 
                                      +ie ++ e+f+n+ ++ +i+++
  gi|70606001|ref|YP_254871.1|  81 IGGVIEFNEQEVFRNTGRNGKIRVE 105
                                   2333333344444444444444433 PP

  == domain 2  score: 56.8 bits;  conditional E-value: 1.1e-18
                        AAA_15 264 lkkkidkikkfnykgkkneeieik..............ddeelplnknGsGvqrllllillileaekkdekeeknvilliE 330
                                   + + i +i               k               +  ++++ + sG+qr +l+++ ++    k        +ll+E
  gi|70606001|ref|YP_254871.1| 189 VSNTIPEI---------------KglefwdggklvlniQNLPIYIDLAASGFQRVILMLFILWLSGSK--------VLLLE 246
                                   33333333...............233334444444566899***************************........***** PP

                        AAA_15 331 EPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                   EPE++ +p +q+ +++l+ke  n++  Qv++tTHSp+i+
  gi|70606001|ref|YP_254871.1| 247 EPEVNMYPTLQSKIMRLIKEWTNNDVFQVFVTTHSPYIV 285
                                   ************************988***********7 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.52
                        AAA_15 123 klklkknelsdekisvekkkskkelpkekeekleke 158
                                   + ++++++++ + i+v k+  ++ ++ke ++  ++e
  gi|70606001|ref|YP_254871.1| 407 NREVENYYTKAKLIEVIKNFGIYPDEKELRDLTKEE 442
                                   333333333333333333333333333322222222 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   8.9e-07    0.0023       1      23 [.      25      47 ..      25      99 .. 0.81
   2 !   53.2   0.0   1.5e-17   3.8e-14     231     303 .]     215     286 ..     179     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.9e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                  ln+++G Ng GK+nLL a++l+ 
  gi|70606001|ref|YP_254871.1| 25 LNIIVGYNGYGKTNLLTAIYLFI 47
                                  79*****************9983 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 1.5e-17
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpllld 303
                                   ++ ++ + +G++r++ +l +l+   +  ++ll++EpE ++ P l++++++l+ke ++    Qv++tTHSp++++
  gi|70606001|ref|YP_254871.1| 215 PIYIDLAASGFQRVILMLFILWLSGS--KVLLLEEPEVNMYPTLQSKIMRLIKEWTNnDVFQVFVTTHSPYIVS 286
                                   67788999**************9887..7***********************999995557**********985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.9   1.1e-10   2.8e-07       3     219 ..       4     302 ..       2     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                   EEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   3 krleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf 83 
                                    ++ ++nF+s+  ++v+l    ++++ivG NG GK+nll Ai +++ ++    l +++++d     +        +v+ ++
  gi|70606001|ref|YP_254871.1|   4 IEFYVNNFRSI--SSVKLTGLGGLNIIVGYNGYGKTNLLTAI-YLFIKNLGAGLEKRNIEDRN--GEYMLLWRDYDVSKLI 79 
                                   56789******..699999999********************.77775444445444444421..2223333445555554 PP

                                   EETTEESSSSSSCEEEEEEEETTSEEEEEE.TTEEE-HHHHHHHHHCTT-STT............................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............................ RF
                         SMC_N  84 dnedkklkiekeevsisrrvkrkgeseyki.ngkevtkkevsellesagiske............................ 135
                                   +  +    ie +e ++ r+  r+g+ ++++ n  + ++k ++  les  i+                              
  gi|70606001|ref|YP_254871.1|  80 KIGGV---IEFNEQEVFRNTGRNGKIRVEVvNTLQYNNKFIEWSLESLSINGGtptkddleivkqlfsfasqaveyvpifd 157
                                   44443...5777777888888888866654277777778888888888888878888888888888888888********* PP

                                   ...............................................................CS-HHHHHHHHHHHHHHH CS
                                   ...............................................................xxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 ...............................................................lLSgGektLvalaLlfAi 153
                                                                                                  + Sg ++ +++l +l   
  gi|70606001|ref|YP_254871.1| 158 qyyfdstmkrmidmnrspinmkrkwydfvnlvsntipeikglefwdggklvlniqnlpiyidlAASGFQRVILMLFIL--- 235
                                   *************************************************************98889999988877655... PP

                                   HCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEEEETTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 154 qkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtkvengvs 219
                                      + + + ll e + ++  +  +k+ +l+ke ++n  +Q++v++++  +++ +   + ++ ++ngvs
  gi|70606001|ref|YP_254871.1| 236 -WLSGSKVLLLEEPEVNMYPTLQSKIMRLIKEWTNNdvFQVFVTTHSPYIVSSSVDSYVIMRKKNGVS 302
                                   .67788899**********************98887779************99988888888788876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.7   1.1e-10   2.7e-07       4     114 ..       8     141 ..       6     173 .. 0.76
   2 ?   -2.0   0.1       1.7   4.2e+03       4       8 ..     423     427 ..     346     492 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-10
                        AAA_23   4 ienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.......................grgfeks 61 
                                   ++nfrs++ +++    gl++I+G NG GKT +l Ai l   +  ++l++++                       g+ +e +
  gi|70606001|ref|YP_254871.1|   8 VNNFRSISSVKLTGLGGLNIIVGYNGYGKTNLLTAIYLFIKNLGAGLEKRNiedrngeymllwrdydvsklikiGGVIEFN 88 
                                   79*********99889*********************99988778887777788889998888888886666664444444 PP

                        AAA_23  62 dveiesegkvkayvelt..fenkdgrytrsiererelskkkgkttkkaklellei 114
                                   + e++ ++  ++ ++++   + + +  +++ie++ e  + +g t  k++le+++ 
  gi|70606001|ref|YP_254871.1|  89 EQEVFRNTGRNGKIRVEvvNTLQYN--NKFIEWSLESLSINGGTPTKDDLEIVKQ 141
                                   4444444444444444422333334..56***************99999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                        AAA_23   4 ienfr 8  
                                   i+nf+
  gi|70606001|ref|YP_254871.1| 423 IKNFG 427
                                   22222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00016       0.4      14      37 ..      26      49 ..      20     250 .. 0.65
   2 ?   -2.5   0.0       2.7   6.8e+03      56      68 ..     347     361 ..     308     439 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                  EEEEESTTSSHHHHHHHHTTSS-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                    ivG nG GK+ Ll +++   k+
  gi|70606001|ref|YP_254871.1| 26 NIIVGYNGYGKTNLLTAIYLFIKN 49
                                  579***************988775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.7
                                   HCCHCEEEE-SS..- CS
                                   xxxxxxxxxxxx..x RF
                      ABC_tran  56 slrkeigvlpqe..p 68 
                                    + k+ig   qe   
  gi|70606001|ref|YP_254871.1| 347 NWLKKIGLNRQElgI 361
                                   444455554444222 PP

>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.1e-05       0.1      57      99 ..     295     337 ..     274     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                       UTP15_C  57 LrhRgalraALagrdeeslepiLkfllkhitdpryvsllvdva 99 
                                   +r+++++ +A++ r ee+l+++L  l  +i+d+ + ++++ + 
  gi|70606001|ref|YP_254871.1| 295 MRKKNGVSSAISVRPEERLKKVLGLLKANISDVLFNRIIILAS 337
                                   68999******************************99998765 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00057       1.5       3      47 ..       3      48 ..       1     145 [. 0.91
   2 ?    1.7   0.0     0.046   1.2e+02     286     326 ..     242     286 ..     238     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00057
                       DUF2813  3 LerieisGFRGinrLSls.leentvLiGENaWGKSSLldALsliln 47
                                  L +  +  FR i    l+ l  +++++G N +GK  Ll A+ l+++
  gi|70606001|ref|YP_254871.1|  3 LIEFYVNNFRSISSVKLTgLGGLNIIVGYNGYGKTNLLTAIYLFIK 48
                                  55666889999*9999976999*******************99875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.046
                       DUF2813 286 illlEdpearLHPtmlaiaWellellP....lQkiltTNSveLls 326
                                   +lllE+pe ++ Pt  + + +l++        Q  +tT S  ++s
  gi|70606001|ref|YP_254871.1| 242 VLLLEEPEVNMYPTLQSKIMRLIKEWTnndvFQVFVTTHSPYIVS 286
                                   89***********99888888876543222256677777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3113.41
//
Query:       gi|70606002|ref|YP_254872.1|  [L=262]
Description: short chain dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-48  164.3   0.0    5.3e-48  163.6   0.0    1.2  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    7.6e-31  107.1   0.0    9.5e-31  106.8   0.0    1.1  1  adh_short      short chain dehydrogenase
    2.2e-05   24.4   0.0    3.8e-05   23.7   0.0    1.3  1  KR             KR domain
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.095   12.7   0.0    1.7  1  TA_inhibitor   Inhibitor of toxin/antitoxin system (Gp4.5)
      0.087   12.1   0.1       0.16   11.3   0.1    1.5  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
       0.15   11.5   0.0       0.34   10.3   0.0    1.6  2  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   0.0   1.8e-51   5.3e-48       4     232 ..      20     256 ..      16     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 1.8e-51
                                   TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGC CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapkl 83 
                                   +gIG+a+Ak++ eeGaev+++  +e++   + e+l++ ++ +++ +D t+ ++v++l++e  + +++lDi+v n g  ++ 
  gi|70606002|ref|YP_254872.1|  20 KGIGFATAKRFVEEGAEVIISSHDEKNlILAYEKLKTIGKVHYVTADLTKADDVAKLIDEGYKMLNGLDIFVYNTGSPKP- 99 
                                   8**************************7778888888777789*************************************. PP

                                   SS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTE CS
                  adh_short_C2  84 kgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgi 164
                                    g+++++++e++++a++  l s++  +++a + m++ g+i+  +s+  ++ ++n +  ++++ +l +l++ + +elgpkgi
  gi|70606002|ref|YP_254872.1| 100 -GDLMTLTDEDWRNAFNLLLMSAVVAVREAGKRMEKDGRIILATSFTLKQPMDNLDLSNVVRLSLAGLIKVASRELGPKGI 179
                                   .******************************************************************************** PP

                                   EEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                  adh_short_C2 165 RvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    vN + +g++ T+  +++ +         ++++++e+ + +pl+r+gtpeeva++++fLas +a+y++G  + vDgG
  gi|70606002|ref|YP_254872.1| 180 LVNGIMQGWTLTDRLKEVVKnraknenktEEQVIDEVTRDIPLRRFGTPEEVANVIIFLASSLATYVNGVLIPVDGG 256
                                   ************986665433444444446679999***************************************** PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   3.2e-34   9.5e-31       1     193 [.      11     200 ..      11     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 3.2e-34
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   k v+vt  s+GIG a+ak++++eGa+v++ +  e++l  ++++lk    k++++++D+t++++v +l+++  k l +ld++
  gi|70606002|ref|YP_254872.1|  11 KKVIVTASSKGIGFATAKRFVEEGAEVIISSHDEKNLILAYEKLKTI-GKVHYVTADLTKADDVAKLIDEGYKMLNGLDIF 90 
                                   789******************************************97.79******************************* PP

                                   EE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrs 162
                                   v N+G  ++g+   l++e+w++ +++ l++++ ++r++ + m   + GrI+  +S + k+p+ ++         +agl++ 
  gi|70606002|ref|YP_254872.1|  91 VYNTGSPKPGDLMTLTDEDWRNAFNLLLMSAVVAVREAGKRME--KDGRIILATSFTLKQPMDNLDLSNVVRLSLAGLIKV 169
                                   *****************************************98..99********************************** PP

                                   HHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                     adh_short 163 lakelaptgirvnavaPGlvdTdmakelrek 193
                                   +++el p+gi vn+++ G + Td  ke+ ++
  gi|70606002|ref|YP_254872.1| 170 ASRELGPKGILVNGIMQGWTLTDRLKEVVKN 200
                                   ***********************99998776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.3e-08   3.8e-05       4     109 ..      14     114 ..      12     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-..EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga..evevvaaDvsdkdavealleeikaeeppi 82 
                                   ++t    g+G ++a+  +e+ga+ ++  s +      +k+li + e+l +  +v++v aD++++d+v++l++e  +  + +
  gi|70606002|ref|YP_254872.1|  14 IVTASSKGIGFATAKRFVEEGAEVII-SSHD------EKNLILAYEKLKTigKVHYVTADLTKADDVAKLIDEGYKMLNGL 87 
                                   7888899***************9665.3444......3445555555444449**********************999*** PP

                                   -EEEE---------TTT--HHHHHHHH CS
                            KR  83 kGvihaAgvlrdklleemtaedleqvl 109
                                      +   g  + + l+++t+ed+++++
  gi|70606002|ref|YP_254872.1|  88 DIFVYNTGSPKPGDLMTLTDEDWRNAF 114
                                   ************************987 PP

>> TA_inhibitor  Inhibitor of toxin/antitoxin system (Gp4.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.095      47      79 ..     101     133 ..      82     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                  TA_inhibitor  47 qrmtltdeqalrlvnaltkaavtaiheagrvne 79 
                                   + mtltde+     n l  +av a+ eag+  e
  gi|70606002|ref|YP_254872.1| 101 DLMTLTDEDWRNAFNLLLMSAVVAVREAGKRME 133
                                   57***************************8655 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.4e-05      0.16      29     111 ..       3      83 ..       1      98 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                                   HCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-TT-E..EEE- CS
                 THF_DHG_CYH_C  29 etgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvkegav..viDv 107
                                   + +  ++gkkv+v   s+ +g + a  + e++a V +  +  k+l    ++       +Gk + ++a+  k + v  +iD 
  gi|70606002|ref|YP_254872.1|   3 KIDLGIKGKKVIVTASSKGIGFATAKRFVEEGAEVIISSHDEKNLILAYEK----LKTIGKVHYVTADLTKADDVakLIDE 79 
                                   566779*******************************99999999888877....46789999999999988755336777 PP

                                   --EE CS
                 THF_DHG_CYH_C 108 Ginr 111
                                   G++ 
  gi|70606002|ref|YP_254872.1|  80 GYKM 83 
                                   7665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.34      10      62 ..      22      79 ..      13      84 .. 0.81
   2 ?   -2.7   0.0       1.1   3.2e+03     205     226 ..     218     239 ..     194     245 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH CS
                     Epimerase 10 iGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke 62
                                  iG a++k++ e+g evi  ++++++    +  ++       + v++dlt+++++++l++e
  gi|70606002|ref|YP_254872.1| 22 IGFATAKRFVEEGAEVIISSHDEKNL--ILAYEKlktigkvHYVTADLTKADDVAKLIDE 79
                                  89********************4433..3333334688999****************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                   TST-EEEEEEHHHHHHHHHHHH CS
                     Epimerase 205 dgtalRdflyveDvaeaillvl 226
                                      +lR f+  e+va++i++++
  gi|70606002|ref|YP_254872.1| 218 RDIPLRRFGTPEEVANVIIFLA 239
                                   4446777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1861.07
//
Query:       gi|70606003|ref|YP_254873.1|  [L=213]
Description: uracil DNA glycosylase superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-48  162.3   0.0    1.1e-47  161.9   0.0    1.1  1  UDG            Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
       0.33   10.7   0.2       0.33   10.7   0.2    1.7  2  Baculo_LEF5_C  Baculoviridae late expression factor 5 C-termi


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   1.2e-51   1.1e-47       1     147 [.      27     173 ..      27     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 1.2e-51
                                   HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHH.CCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCC CS
                           UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllne.aglkrdleseqgvyitnvvkcrppgnrdtptsaeikac 80 
                                   pgeg+p+akv+++GeaPg++ed++g+pF+g ag+ll kl+++ +g+kr     ++v+itnvvkcrpp nr +p ++ei ac
  gi|70606003|ref|YP_254873.1|  27 PGEGNPKAKVMFIGEAPGETEDEEGRPFVGSAGKLLTKLIEDtLGIKR-----DEVFITNVVKCRPPNNR-DPEEDEITAC 101
                                   79**********************************************.....*****************.********** PP

                                   HHHHHHHHHHHHSSEEEEESHHHHHH.......HH.HHSCESCCCSCT......SEEEEES-SSTTTTTTTTSHHHHH CS
                           UDG  81 aplleeeiellkprlivllGktaakall.....ge.klgklrgklleak.....irvlplphPsplnrnffksnpelk 147
                                   + +l+ +i+l+kp++iv+lG++  +++l     ++ +++k rgk++e+k     i+++p++hP+++++n      +++
  gi|70606003|ref|YP_254873.1| 102 SSYLDLQIRLIKPQVIVTLGRHSTSYILskaniEFhSITKSRGKVYEWKiddhvINIFPTYHPAAALYN------PNL 173
                                   **************************9987777556888*********88899****************......333 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   3.7e-05      0.33      28      40 ..       4      16 ..       2      18 .. 0.93
   2 ?   -3.1   0.1      0.72   6.4e+03      33      40 ..      78      85 ..      76      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                 Baculo_LEF5_C 28 DEivsfvryCskC 40
                                  DEi++ +++C+kC
  gi|70606003|ref|YP_254873.1|  4 DEIANEIKVCRKC 16
                                  ************* PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.72
                 Baculo_LEF5_C 33 fvryCskC 40
                                  f++  +kC
  gi|70606003|ref|YP_254873.1| 78 FITNVVKC 85
                                  88999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1492.58
//
Query:       gi|70606004|ref|YP_254874.1|  [L=102]
Description: hypothetical protein Saci_0160 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.035   14.0   0.1      0.081   12.8   0.1    1.6  1  Terminase_5  Putative ATPase subunit of terminase (gpP-like)
      0.049   13.9   0.0       0.11   12.7   0.0    1.6  1  PAP_assoc    Cid1 family poly A polymerase
       0.17   11.2   0.0        0.2   11.0   0.0    1.1  1  GCV_T        Aminomethyltransferase folate-binding domain


Domain annotation for each model (and alignments):
>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.4e-05     0.081      25      37 ..      30      42 ..      26      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                   Terminase_5 25 lkeatVysWkkrd 37
                                  ++e+tVysW++r+
  gi|70606004|ref|YP_254874.1| 30 RNEKTVYSWVQRE 42
                                  68*********96 PP

>> PAP_assoc  Cid1 family poly A polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05      0.11       6      41 ..      43      83 ..      42      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                  HHHHHHHHHHT--TTTEEEEC.....SST-EEEHHHHCGCS CS
                     PAP_assoc  6 LigFFeyYgreFdyenvvisi.....rtggiltkkekgwes 41
                                  L gFF+ Y+++ d  n++i i     ++  i+ k+++  ++
  gi|70606004|ref|YP_254874.1| 43 LSGFFRKYSKNKDLANDIIKIqecisKEDYICLKQQLLSTK 83
                                  789****************9955553334447777666664 PP

>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.4e-05       0.2      90     125 ..       9      44 ..       3      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                         GCV_T  90 vidDlivarldedefllvvnaankekdlawlekaae 125
                                    i+D+i+a+++ ++ ll vn+ n++++++w++++  
  gi|70606004|ref|YP_254874.1|   9 LIQDMILAKTSIEKALLHVNSRNEKTVYSWVQRELS 44 
                                   589*****************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 749.33
//
Query:       gi|70606005|ref|YP_254875.1|  [L=132]
Description: iron dependent repressor [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-19   69.0   0.0    4.3e-19   68.4   0.0    1.3  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.1e-05   25.5   0.0    1.7e-05   24.9   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    1.5e-05   24.8   0.0    1.9e-05   24.4   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
    0.00011   22.1   0.0    0.00016   21.6   0.0    1.3  1  HTH_45          Winged helix-turn-helix
    0.00021   21.1   0.0     0.0004   20.3   0.0    1.4  1  MarR            MarR family
    0.00039   20.2   0.0     0.0016   18.3   0.0    2.0  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00088   19.0   0.0     0.0018   18.0   0.0    1.6  1  LexA_DNA_bind   LexA DNA binding domain
     0.0016   18.3   0.0     0.0035   17.2   0.0    1.6  1  MarR_2          MarR family
     0.0019   18.2   0.0     0.0033   17.4   0.0    1.4  1  FeoC            FeoC like transcriptional regulator
     0.0019   17.9   0.0      0.015   15.1   0.0    2.0  2  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.8   0.1      0.092   13.3   0.0    2.1  2  HTH_27          Winged helix DNA-binding domain
       0.03   13.8   0.1      0.033   13.7   0.1    1.2  1  PI-TkoII_IV     DNA polymerase II intein Domain IV
      0.031   14.0   0.0      0.047   13.4   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e
      0.034   14.1   0.0      0.068   13.1   0.0    1.5  1  HTH_12          Ribonuclease R winged-helix domain
      0.045   13.6   0.3        4.1    7.3   0.0    3.0  3  IF2_N           Translation initiation factor IF-2, N-termina
      0.047   14.0   0.0       0.13   12.6   0.0    1.7  2  Rrf2            Transcriptional regulator
       0.14   11.9   0.0       0.53   10.1   0.0    1.9  2  FtsK_gamma      Ftsk gamma domain
       0.14   12.1   0.0       0.37   10.8   0.0    1.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
       0.18   11.7   0.0       0.33   10.9   0.0    1.4  1  UBA             UBA/TS-N domain


Domain annotation for each model (and alignments):
>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   4.6e-22   4.3e-19       1      69 [.      63     130 ..      63     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 4.6e-22
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                   Te G ++ ++lvr hr+le +Lv+ +g++++ea++   +++ a+++e+i++l+e+lg+p +cPhg++ip
  gi|70606005|ref|YP_254875.1|  63 TETGIKAIEELVRAHRILEYLLVE-MGFSKDEACQFTREFDFAVPKEIIDKLYEYLGKPGKCPHGETIP 130
                                   9***********************.9******************************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.8e-08   1.7e-05       8      57 ..       9      58 ..       2      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.8e-08
                                  HHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                Fe_dep_repress  8 dYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                   YL ++ + ++++k +k + +a+ L++sp+s+ e l+ Lek+G++e +k 
  gi|70606005|ref|YP_254875.1|  9 IYLVAVRKYNDQGKQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKKE 58
                                  5888898999999********************************98875 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     2e-08   1.9e-05      22      98 ..      10      83 ..       7     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-08
                       DUF4423 22 yypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslt.tssevkseavrsyh 98
                                  y +++r+  +  +  a+ +++a+ l+  is + + + l+ L+k g+++k+++  +  te+ ++ +++ v+++ + +y 
  gi|70606005|ref|YP_254875.1| 10 YLVAVRKYNDQGKQ-AKLSWIARDLK--ISPASAFEELQHLEKKGFIEKKKE-GISITETGIKaIEELVRAHRILEYL 83
                                  56677776666666.***********..***********************9.9999999999777777777766665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.7e-07   0.00016      18      75 ..      22      79 ..      12      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.7e-07
                        HTH_45 18 geakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                  ++ak ++i  +  +s   + + L++L +kg+i+k+ke  ++Te G + +e+l + +++
  gi|70606005|ref|YP_254875.1| 22 KQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKKEGISITETGIKAIEELVRAHRI 79
                                  5677788888899999999999******************************998876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.2e-07    0.0004      18      51 ..      24      57 ..      11      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.2e-07
                                  EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 18 lsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  +++s +a+ l++s++++ + l +LekkG+ie++k
  gi|70606005|ref|YP_254875.1| 24 AKLSWIARDLKISPASAFEELQHLEKKGFIEKKK 57
                                  67888**************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0016      22      58 ..      23      59 ..      20      77 .. 0.88
   2 ?   -1.3   0.0       2.2     2e+03       3      11 ..      86      94 ..      83      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                  CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  +a+ + ia++l+++ +++ e L+ Le+kG++e++k+ 
  gi|70606005|ref|YP_254875.1| 23 QAKLSWIARDLKISPASAFEELQHLEKKGFIEKKKEG 59
                                  567778***************************9975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                  HCHHHHHCC CS
                          TrmB  3 klGLseyEa 11
                                  ++G+s+ Ea
  gi|70606005|ref|YP_254875.1| 86 EMGFSKDEA 94
                                  689999997 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-06    0.0018      31      59 ..      29      56 ..       2      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                                  HHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 31 iaralglkSpsaveehLkaLerKGyierd 59
                                  iar l+++ p+++ e L+ Le+KG+ie +
  gi|70606005|ref|YP_254875.1| 29 IARDLKIS-PASAFEELQHLEKKGFIEKK 56
                                  89999996.*****************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.8e-06    0.0035       7      55 ..       7      57 ..       2      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-06
                                  HHHHHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  7 qarvLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  ++  L a++   ++      + +ar l++s++++   l+ L+++G++e+++
  gi|70606005|ref|YP_254875.1|  7 ELIYLVAVRKYNDQgkQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKK 57
                                  555666666666656556899***************************975 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0033       2      50 ..      11      59 ..      10      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                          FeoC  2 LtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                  L+ +++y ++ +++ l+ ++r +k+sp+     L ++++kG +ek++++
  gi|70606005|ref|YP_254875.1| 11 LVAVRKYNDQGKQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKKEG 59
                                  889************************999999************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.015      17      50 ..      22      55 ..      18      57 .. 0.89
   2 ?    0.4   0.1      0.62   5.8e+02       3      12 ..      74      83 ..      73      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                  SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                     +ls +Ar + +++++++  Lq L++ G++e+
  gi|70606005|ref|YP_254875.1| 22 KQAKLSWIARDLKISPASAFEELQHLEKKGFIEK 55
                                  44699***************************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.62
                                  HHHHHHHCT- CS
                      HTH_IclR  3 dRalaiLdal 12
                                   Ra +iL++l
  gi|70606005|ref|YP_254875.1| 74 VRAHRILEYL 83
                                  6777777776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.7e-05     0.092       1      53 [.       3      58 ..       3      66 .. 0.83
   2 ?    0.7   0.0      0.82   7.8e+02      34      46 ..      65      77 ..      63      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                        HTH_27  1 ltrqqalvLhlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                  l+r + ++L  +r    ++ ++kl+ +++ l+++ +++ + l +L++kG++e+++ 
  gi|70606005|ref|YP_254875.1|  3 LSRRELIYLVAVRkynDQGKQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKKE 58
                                  577888899999998777777888***************************77654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.82
                        HTH_27 34 hisyslkkLtekG 46
                                  ++++++++L++++
  gi|70606005|ref|YP_254875.1| 65 TGIKAIEELVRAH 77
                                  5678999999873 PP

>> PI-TkoII_IV  DNA polymerase II intein Domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.5e-05     0.033      38      93 ..      15      70 ..       5     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                                  -TTHHHHHHHHHHHHTTSS-.--TTHHHHHHHHHHCTSEEE-SSSEEES-HHHHHHH CS
                   PI-TkoII_IV 38 rknffkGmlrtlrwifgeek.rirtarrylkhleklGyvklkkrGyevldweglkky 93
                                  rk   +G    l wi  + k  + +a   l+hlek G+++ kk G+ +++  g+k  
  gi|70606005|ref|YP_254875.1| 15 RKYNDQGKQAKLSWIARDLKiSPASAFEELQHLEKKGFIEKKKEGISITET-GIKAI 70
                                  5666678888999*999885256778889****************998753.44433 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     5e-05     0.047      99     131 ..      43      74 ..      21      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                                   S--SSS---SS-HHHHHTHHHHH--SS--S--X CS
                Ribosomal_S19e  99 ilqqLeklglvkkekkkgrrltkkGqrlldria 131
                                    lq+Lek g+++k+ k+g  +t++G + ++++ 
  gi|70606005|ref|YP_254875.1|  43 ELQHLEKKGFIEKK-KEGISITETGIKAIEELV 74 
                                   59*********877.56**********999876 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.2e-05     0.068      38      65 ..      43      69 ..      29      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.2e-05
                        HTH_12 38 rLrkleergltrrvgyagreltEkGlee 65
                                   L+ le++g+++++  +   +tE G++ 
  gi|70606005|ref|YP_254875.1| 43 ELQHLEKKGFIEKKKEG-ISITETGIKA 69
                                  69***********9876.99*****985 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.48   4.5e+02       9      28 ..      29      47 ..      24      72 .. 0.73
   2 ?    1.8   0.0      0.22   2.1e+02      15      33 ..      74      91 ..      63      93 .. 0.87
   3 ?    7.3   0.0    0.0043       4.1      17      31 ..     106     120 ..     105     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.48
                         IF2_N  9 LAkeLgvkskevikkLfkel 28
                                  +A+ L+++++   ++L ++l
  gi|70606005|ref|YP_254875.1| 29 IARDLKISPASAFEEL-QHL 47
                                  6888888888777777.435 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.22
                         IF2_N 15 vkskevikkLfkelGievk 33
                                  v+++++++ L  e+G++ k
  gi|70606005|ref|YP_254875.1| 74 VRAHRILEYLLVEMGFS-K 91
                                  78999*****999**98.5 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0043
                         IF2_N  17 skevikkLfkelGie 31 
                                   +ke+i+kL ++lG++
  gi|70606005|ref|YP_254875.1| 106 PKEIIDKLYEYLGKP 120
                                   69***********97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014      0.13      20      58 ..      18      56 ..       1      59 [. 0.76
   2 ?   -2.3   0.0       6.5   6.1e+03      36      52 ..     104     120 ..     102     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                  SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  ++++++++++ ia+  +isp  +   l++L+k+g+++ +
  gi|70606005|ref|YP_254875.1| 18 NDQGKQAKLSWIARDLKISPASAFEELQHLEKKGFIEKK 56
                                  3444459*****************************965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.5
                                   TS-HHHHHHHHHHHHHT CS
                          Rrf2  36 nispsylekilakLrka 52 
                                    ++++++ k+ + L k 
  gi|70606005|ref|YP_254875.1| 104 AVPKEIIDKLYEYLGKP 120
                                   58999999999999875 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00056      0.53      17      53 ..      21      57 ..      10      60 .. 0.90
   2 ?   -1.9   0.0       3.1     3e+03      35      43 ..      75      83 ..      74      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                    FtsK_gamma 17 egkaStSllQRrlriGYnRAarlidqLeeeGiVgpae 53
                                   ++a  S++ R l+i  + A + +  Le++G++++++
  gi|70606005|ref|YP_254875.1| 21 GKQAKLSWIARDLKISPASAFEELQHLEKKGFIEKKK 57
                                  57999****************************9876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                    FtsK_gamma 35 RAarlidqL 43
                                  RA r+++ L
  gi|70606005|ref|YP_254875.1| 75 RAHRILEYL 83
                                  999999976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0004      0.37      27      60 ..      29      63 ..      23      66 .. 0.86
   2 ?   -3.0   0.0       7.8   7.4e+03       2       9 ..      78      85 ..      77     106 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0004
                                  HHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES CS
                     HTH_Crp_2 27 lAsmlGltretvsrilseLkreglisrgrr.iril 60
                                  +A+ l +++ +   +l++L+++g i+++++ i i+
  gi|70606005|ref|YP_254875.1| 29 IARDLKISPASAFEELQHLEKKGFIEKKKEgISIT 63
                                  7888999*******************653349886 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.8
                                  HHHHHHHH CS
                     HTH_Crp_2  2 RlArfLlr 9 
                                  R+  +Ll 
  gi|70606005|ref|YP_254875.1| 78 RILEYLLV 85
                                  55555553 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.33       9      21 ..      84      96 ..      83      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                  HHHTTS-HHHHHH CS
                           UBA  9 LveMGFdreevve 21
                                  LveMGF+++e+++
  gi|70606005|ref|YP_254875.1| 84 LVEMGFSKDEACQ 96
                                  9********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 932.34
//
Query:       gi|70606006|ref|YP_254876.1|  [L=285]
Description: dihydrodipicolinate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-53  179.3   0.0    7.6e-53  179.1   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.0   4.3e-57   7.6e-53       3     273 ..       2     268 ..       1     281 [. 0.95

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 4.3e-57
                                   SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSHH CS
                         DHDPS   3 sgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnsts 83 
                                   +g+++a+vtpf+e+  +d+e+l+   +fl  +gv  ++ +G+tGE+++ls++ek++ +++ +e+   + +++++v  ns++
  gi|70606006|ref|YP_254876.1|   2 EGVVPAIVTPFKENEDIDFESLNLFLNFLERNGVKWIFALGSTGEFNMLSLSEKQEFIRKLREIT--KLKIVINVSENSLK 80 
                                   699************************************************************96..678899******** PP

                                   HHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE-S CS
                         DHDPS  84 eaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKeav 164
                                   + ++l+k a ++G++g+ +++P Y kps  gl+++f+++ + + lp+ +Y  p    + ++ et+ +L++ + i g+K ++
  gi|70606006|ref|YP_254876.1|  81 NTLSLGKLAFDVGMEGIALIPPIYHKPSESGLISYFEEMSKLD-LPLYVYAYP--DKVPITYETISKLVKQDIIDGIKLTT 158
                                   **************************************97776.*********..6799********************** PP

                                   S-CTHHHHH..HCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHC CS
                         DHDPS 165 gdleeviki..kkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllplikil 243
                                   ++l    k    ke+++dl i+ G d l+   l  G++G is+ +n+a+e+m   ++ ++eG+l+e  e++  + ++ +++
  gi|70606006|ref|YP_254876.1| 159 DNLPLFKKYlgLKEIKNDLKILIGSDTLFVYSLIEGGNGCISAVANVAPELMMRAYQGVREGKLNESLEIQGMISKISDAI 239
                                   ***777776335899****************************************************************** PP

                                   CCCSCCHHHHHHHHCTTSSSBB.--TTS-- CS
                         DHDPS 244 faepnvilvktalellGlvveatlrkPltp 273
                                   ++  ++++vk al++ G+ v++ +r+Pl +
  gi|70606006|ref|YP_254876.1| 240 MSGDFPSGVKVALRYRGVSVGS-VRRPLKE 268
                                   **********************.****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1809.79
//
Query:       gi|70606007|ref|YP_254877.1|  [L=142]
Description: hypothetical protein Saci_0164 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-06   27.0   0.0    5.9e-06   26.3   0.0    1.4  1  HTH_20         Helix-turn-helix domain
    1.5e-05   24.8   0.0    2.2e-05   24.3   0.0    1.3  1  MarR_2         MarR family
    0.00011   22.0   0.0     0.0002   21.1   0.0    1.4  1  LexA_DNA_bind  LexA DNA binding domain
    0.00028   20.4   0.0    0.00075   19.0   0.0    1.7  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00029   21.2   0.0    0.00046   20.6   0.0    1.2  1  HTH_27         Winged helix DNA-binding domain
     0.0033   17.3   0.0     0.0055   16.6   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
     0.0035   17.2   0.3      0.005   16.7   0.3    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.004   17.1   0.2     0.0083   16.1   0.0    1.6  2  HTH_11         HTH domain
  ------ inclusion threshold ------
      0.076   13.0   0.0       0.22   11.5   0.0    1.8  2  HTH_12         Ribonuclease R winged-helix domain
       0.17   12.0   0.0        0.3   11.3   0.0    1.3  1  HTH_28         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.3e-09   5.9e-06      19      60 ..      17      59 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.3e-09
                                  HSTCTTB-HHHHHHHHTS-HHH.HHHHHHHHHHCTTEEEECTE CS
                        HTH_20 19 Laraegltaselaerldlsknt.lsyHLrvLeeagLvevvreg 60
                                  L+++ g+t  ++ e l+ s ++ ++yH+++L+ agLve + eg
  gi|70606007|ref|YP_254877.1| 17 LKSKNGVTIRQIQEDLGFSSTSaVRYHVKKLVAAGLVEETLEG 59
                                  578899***********888877***************99887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-08   2.2e-05      14      54 ..      17      56 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                                  HHCTTTSEEEHHHHHHHHTSSH.HHHHHHHHHHHHTTSEEEE CS
                        MarR_2 14 Lgrrpgrdltvgelarrlglsk.savsrilkrLvaaGLverr 54
                                  L    g  +t++++ + lg s  sav +++k+LvaaGLve++
  gi|70606007|ref|YP_254877.1| 17 LKSKNG--VTIRQIQEDLGFSStSAVRYHVKKLVAAGLVEET 56
                                  555566..9******************************986 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.1e-07    0.0002      27      58 ..      24      55 ..      15      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                  +ir+i + lg++S+sav  h k+L   G++e 
  gi|70606007|ref|YP_254877.1| 24 TIRQIQEDLGFSSTSAVRYHVKKLVAAGLVEE 55
                                  89**************************9986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.2e-07   0.00075      11      48 .]      16      54 ..      10      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.2e-07
                        HTH_24 11 lLqknprisqreLAerlglSp.stvnrrlkrLeeeGlIk 48
                                  +L+ + + ++r++ e lg S+ s+v++++k+L+ +Gl++
  gi|70606007|ref|YP_254877.1| 16 VLKSKNGVTIRQIQEDLGFSStSAVRYHVKKLVAAGLVE 54
                                  57778999**********875389*************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.6e-07   0.00046      15      51 ..      19      56 ..      11      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.6e-07
                        HTH_27 15 rrrrkkladlcgrlnvedshis.yslkkLtekGLvert 51
                                    ++++++++ + l +++++++ y +kkL+++GLve+t
  gi|70606007|ref|YP_254877.1| 19 SKNGVTIRQIQEDLGFSSTSAVrYHVKKLVAAGLVEET 56
                                  567899*****************************987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.1e-06    0.0055      17      46 ..      24      54 ..      14      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.1e-06
                                  EHHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                         HTH_5 17 cvcelaeelgls.qstvShHLkkLreaGLVe 46
                                  ++ ++ e+lg s  s+v++H kkL  aGLVe
  gi|70606007|ref|YP_254877.1| 24 TIRQIQEDLGFSsTSAVRYHVKKLVAAGLVE 54
                                  67788888887527****************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   2.8e-06     0.005      11      57 ..      10      58 ..       2      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                                  CCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHH.HHHHHHHCTSEEEESS CS
                          TrmB 11 akvYlaLl.klgpatadeiaeelgvprskvYe.vLrsLedkGlVerekg 57
                                   +vY ++l ++   t+++i e+lg + +++ +  +++L+ +GlVe   +
  gi|70606007|ref|YP_254877.1| 10 KRVYYYVLkSKNGVTIRQIQEDLGFSSTSAVRyHVKKLVAAGLVEETLE 58
                                  5899999988899************987755516**********98765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.6e-06    0.0083       7      43 ..      14      51 ..       9      60 .. 0.84
   2 ?   -2.9   0.0         4   7.1e+03       5      14 ..      96     105 ..      94     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                        HTH_11  7 elLleargpisgeeLAeeLnv.SrrtvrrdIkaLeelg 43
                                    +l++++ +++ ++ e L+  S+++vr ++k+L ++g
  gi|70606007|ref|YP_254877.1| 14 YYVLKSKNGVTIRQIQEDLGFsSTSAVRYHVKKLVAAG 51
                                  555688888*************************9998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4
                        HTH_11   5 ilelLlearg 14 
                                   i+++L+++++
  gi|70606007|ref|YP_254877.1|  96 IIIFLISSHE 105
                                   6777766654 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.22      31      50 ..      36      55 ..      18      65 .. 0.76
   2 ?   -2.6   0.0       3.1   5.6e+03      34      40 ..     127     133 ..     125     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        HTH_12 31 geravRyrLrkleergltrr 50
                                  ++ avRy+ +kl   gl++ 
  gi|70606007|ref|YP_254877.1| 36 STSAVRYHVKKLVAAGLVEE 55
                                  489***********999986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.1
                        HTH_12  34 avRyrLr 40 
                                   a+ +++r
  gi|70606007|ref|YP_254877.1| 127 AIKRHMR 133
                                   8999998 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017       0.3      10      41 ..      20      52 ..      16      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                        HTH_28 10 aaGhsvreaArelgi.srrtvyrWikryeegGi 41
                                  ++G+++r++ + lg  s + v+  +k++ + G+
  gi|70606007|ref|YP_254877.1| 20 KNGVTIRQIQEDLGFsSTSAVRYHVKKLVAAGL 52
                                  689************666********9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1017.93
//
Query:       gi|70606008|ref|YP_254878.1|  [L=909]
Description: hypothetical protein Saci_0165 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.4   0.0      0.076   13.1   0.0    3.6  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0026   18.3   0.1      0.017   15.6   0.0    2.4  2  AAA_18    AAA domain
  ------ inclusion threshold ------
        2.9    8.4   6.4       0.49   10.9   0.7    2.7  3  DUF1878   Protein of unknown function (DUF1878)


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.2   1.3e+04      55      82 ..      10      37 ..       6      49 .. 0.63
   2 !   13.1   0.0   1.3e-05     0.076      10      55 ..     237     415 ..     236     819 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                                  CCHCCCHHHHHHCHCHHHH..EEEEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA 55 dlkrllellealgkkkalllkiagvvln 82
                                  dlk +l l e+l+k k+ +   + v+ n
  gi|70606008|ref|YP_254878.1| 10 DLKEFLALRETLKKAKKENEAKVHVIGN 37
                                  5666666667777777777444444444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                                   SSHHHHHHHHHHHHHH.TT--EEEEE.EEESSCCCCHHTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.................................. RF
                          CbiA  10 vGKTtlaanLaralar.rglrVllvD.aDpqannlaileglendiep.................................. 54 
                                   +GK+tl++ +++ l++ +  +V l+D  D ++n ++ +++ + di+                                   
  gi|70606008|ref|YP_254878.1| 237 SGKSTLSTLIMKRLKEiGFGDVKLIDyHDLEGNFAF-IKKIQDDINDgsnfrkiivltkdiyytlkprgqvieildhflss 316
                                   6***************55669*****99***99999.99999999999955555555555555555555555555555555 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|70606008|ref|YP_254878.1| 317 pnyndllkdyernifnyfynvildadpnkaiwyiplvklaeeygtpipyklglftltkngrrvgeedkdiivewfsnvned 397
                                   555555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                   .................C CS
                                   .................x RF
                          CbiA  55 .................d 55 
                                                    d
  gi|70606008|ref|YP_254878.1| 398 iktyfdddyvkesqhkvD 415
                                   555555555555555550 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.9e-06     0.017       2     105 ..     230     345 ..     229     347 .. 0.64
   2 ?   -1.4   0.0      0.53   3.1e+03      47      84 ..     377     425 ..     363     464 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                        AAA_18   2 lltGtpGvGKttlakeLskrl.gf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.....alee 73 
                                   ++ G+ ++GK+tl+  + krl ++    v+l+d++     +  +       +k+ d+ ++ ++++++    +         
  gi|70606008|ref|YP_254878.1| 230 IILGPVRSGKSTLSTLIMKRLkEIgfgDVKLIDYHDL---EGNFAFI----KKIQDDINDGSNFRKIIVLTKdiyytLKPR 303
                                   799*****************98885555555555555...4444444....444555555555555555444555553344 PP

                        AAA_18  74 gknl.vidghlaele.seaakdikk........vvLtaspee 105
                                   g+++ ++d +l+ +   + +kd+ +        v+L+a+p++
  gi|70606008|ref|YP_254878.1| 304 GQVIeILDHFLSSPNyNDLLKDYERnifnyfynVILDADPNK 345
                                   444468888888777344455555588888888888888865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                        AAA_18  47 deskrldedkldklldaleenss........aleegknl...vidghla 84 
                                   ++  ++d+d   +++++++e ++        ++ ++k+    +idg+ +
  gi|70606008|ref|YP_254878.1| 377 RRVGEEDKDIIVEWFSNVNEDIKtyfdddyvKESQHKVDldkIIDGLSS 425
                                   6667777777777777777777777777775333333323455555544 PP

>> DUF1878  Protein of unknown function (DUF1878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         3   1.8e+04      42      65 ..      10      33 ..       8      37 .. 0.72
   2 ?   10.9   0.7   8.2e-05      0.49      13      65 ..     604     660 ..     600     681 .. 0.79
   3 ?   -2.2   0.1      0.95   5.7e+03      28      65 ..     850     852 ..     814     882 .. 0.57

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3
                                  HHHHHHHHHHHHHHHHHHHHHTT- CS
                       DUF1878 42 eveeilklCekLseeleeqkaegf 65
                                  + +e+l+l e L +  +e+ a+  
  gi|70606008|ref|YP_254878.1| 10 DLKEFLALRETLKKAKKENEAKVH 33
                                  667888888888887777777655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.2e-05
                                   HHHHHHHTTS-TTT....-HHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       DUF1878  13 yyqkLllkmideek....lpfyklviekklskeeveeilklCekLseeleeqkaegf 65 
                                   yy + +++ id +     +  y+l+i+++++++e +++++l +k  +++++ k+  +
  gi|70606008|ref|YP_254878.1| 604 YYKTDMIDKIDVKDpllsTLIYSLLIDYNVRNKELNKVVTLYDKFRKNYTKPKNTQL 660
                                   666667777766532221457*****************************9998654 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.95
                                   HHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       DUF1878  28 pfyklviekklskeeveeilklCekLseeleeqkaegf 65 
                                                                        +
  gi|70606008|ref|YP_254878.1| 850 IQ-----------------------------------Y 852
                                   22...................................2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 6191.79
//
Query:       gi|70606009|ref|YP_254879.1|  [L=521]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-134  448.5   0.0   2.8e-134  448.1   0.0    1.1  1  Aldedh    Aldehyde dehydrogenase family
    2.1e-05   23.8   0.0    0.00014   21.1   0.0    2.1  1  LuxC      Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.38   10.8   0.0    1.6  1  Med28     Mediator complex subunit 28


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.1   0.0  4.7e-138  2.8e-134      19     458 ..      66     513 ..      49     516 .. 0.96

  Alignments for each domain:
  == domain 1  score: 448.1 bits;  conditional E-value: 4.7e-138
                                   EEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH CS
                        Aldedh  19 viakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearaeveeaidvlry 99 
                                    ++ +++at++++++a+++A++a+k+w+  ++++R ei ++aa+l++++k  la+++t e+Gk+  ea+aev+e+id+lry
  gi|70606009|ref|YP_254879.1|  66 RLGIFQKATENELNEAIETAENAYKEWQYSDWKDRVEIAMRAAELMARHKFALAATITFENGKNRYEAMAEVDETIDYLRY 146
                                   677799*************************************************************************** PP

                                   HHHHHHHHSEEEEEE.C...TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHH CS
                        Aldedh 100 yaelaeklegevlps.s...egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsalllaelf 176
                                   ya l+e+ +g + ++ s   ++++ +++ +P+G++ +++P+NfPl+++a +++  +++GNt ++KP+++tplsa+ l++++
  gi|70606009|ref|YP_254879.1| 147 YAYLLEENRGYIREMeSriyKNEKGYSVMRPYGTWFVVSPFNFPLAITATMTLGSVLTGNTAIVKPSSDTPLSAYNLIQIL 227
                                   **********9988854899************************************************************* PP

                                   HHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHH.HHCTTSEEEEEE---EEEEE-TTSHHHHHHHH CS
                        Aldedh 177 eeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiaka.aaknlkrvtlElGGknplivledaDldkavea 256
                                   ++aglP+gv+n++tg+gse+    +++++++ ++ftGs +vg+k+ak   + +  ++++ElGGkn++iv+++a++dkave+
  gi|70606009|ref|YP_254879.1| 228 RRAGLPDGVVNYLTGKGSEIVTPALKSKRIAGLAFTGSKDVGHKLAKDfLDVDTRPIVMELGGKNAVIVTDKANIDKAVEG 308
                                   ************************************************999999*************************** PP

                                   HHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE- CS
                        Aldedh 257 ivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakeegaklllG 337
                                   + +gafg+ GQ+C+a sr++v+ ++yd f++klv+++k+  +gdp +++t +GPli++++++k+ k+veeak+ g ++l+G
  gi|70606009|ref|YP_254879.1| 309 VFRGAFGFGGQKCSASSRIYVETNVYDTFLNKLVNRTKEAIIGDPTKKETFLGPLINSDAVSKYVKFVEEAKKGGGEILYG 389
                                   ********************************************************************************* PP

                                   TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-S CS
                        Aldedh 338 gereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraervaerlea 418
                                   g   e  + k  +v+Pt+++n++ ++ ++++E+F P++ v+k+ ++ee +++aNd eyGL+ag+f++d +++e++ +++ea
  gi|70606009|ref|YP_254879.1| 390 G---EVIDVKRRLVKPTIVSNLPLSHWLWKTELFVPIILVTKIGSLEEGVKLANDVEYGLTAGIFSEDQKEIEYFFNKIEA 467
                                   *...6678999********************************************************************** PP

                                   SEEEESSS...ST--TTT.SEB--CGGGEES..-BSHHHHHHHTEE CS
                        Aldedh 419 GnvyiNds...ttgaaea.lpfgGvkqSglG..reggkegleeyte 458
                                   G vy N++   ttga+   +pfgG+k+Sg+   + gg+++l  +++
  gi|70606009|ref|YP_254879.1| 468 GVVYANRMvgaTTGAMPGvQPFGGWKHSGWTgkNAGGPYYLLSFMR 513
                                   *******988899999999**********654566669*9999987 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-08   0.00014       7     260 ..      98     341 ..      78     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-08
                          LuxC   7 eeildlleeaaklladdeyskraierlakitgyeealleilkalaallkreeLkkvleseLgqpeiLdeflktkeksyeka 87 
                                   ++ ++++ +aa+l+a +++ + a  ++++ ++  ea++e +++ +++l+      +le++ g  + +++ ++++ek+y+ +
  gi|70606009|ref|YP_254879.1|  98 KDRVEIAMRAAELMARHKFALAATITFENGKNRYEAMAE-VDETIDYLRYY--AYLLEENRGYIREMESRIYKNEKGYSVM 175
                                   566889999999999999999988888888888899998.58899998754..5789999999999*************** PP

                          LuxC  88 qprglvlhvlsgNvpllpvmsi.lqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksgdtkleeei 167
                                   +p g  + v + N pl +   + l ++L++n  ++k+Ss+ p  a++l++ l +      ++++l      ++  ++ + +
  gi|70606009|ref|YP_254879.1| 176 RPYGTWFVVSPFNFPLAITATMtLGSVLTGNTAIVKPSSDTPLSAYNLIQILRRAGLPDGVVNYL-----TGKGSEIVTPA 251
                                   ***************98887763678**********************99988876654333333.....33333333333 PP

                          LuxC 168 v..qnaDvvvawGgeeaikaise.klkpgkq..likfGakvSfavvdkealeeealdkaaeraAkDiivfdQqAClspqvv 243
                                   +  +   +    G+++  + +++  l    +  +++ G k  + v dk+      +dka+e +      f  q C+++  +
  gi|70606009|ref|YP_254879.1| 252 LksKRIAGLAFTGSKDVGHKLAKdFLDVDTRpiVMELGGKNAVIVTDKAN-----IDKAVEGVFRGAFGFGGQKCSASSRI 327
                                   22355666666677766666665544333331144567777776666665.....77777777777777777777777777 PP

                          LuxC 244 fvekddkieidefaeaL 260
                                   +ve   ++ +d f ++L
  gi|70606009|ref|YP_254879.1| 328 YVE---TNVYDTFLNKL 341
                                   777...45666665555 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.4e-05      0.38      77     113 ..     123     159 ..      80     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                         Med28  77 lrekgqnvfgdgtkidstidyleklkqvlsdaedvyk 113
                                     e+g+n +   +++d tidyl+ +  +l++     +
  gi|70606009|ref|YP_254879.1| 123 TFENGKNRYEAMAEVDETIDYLRYYAYLLEENRGYIR 159
                                   4699***********************9999865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3283.22
//
Query:       gi|70606010|ref|YP_254880.1|  [L=213]
Description: hypothetical protein Saci_0167 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.0   0.3      0.049   13.0   0.3    1.7  2  BNR_4     BNR repeat-containing family member


Domain annotation for each model (and alignments):
>> BNR_4  BNR repeat-containing family member
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1     0.045   8.1e+02     122     158 ..      34      69 ..      26      78 .. 0.73
   2 ?   13.0   0.3   2.7e-06     0.049      80     145 ..     106     169 ..      86     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.045
                                   EEEEEETTTTEEEEEES-.SB--T.TT-EEEEEE.EE CS
                         BNR_4 122 vlneYdektdkwktlgekqlldgeegqrnaYlkglsy 158
                                   + ++Y ++tdk +++ ++q +++  +  ++Y+ +l++
  gi|70606010|ref|YP_254880.1|  34 QPTTYYTTTDKSQNITQTQTAEKP-NVVRPYIIQLNN 69 
                                   556777888888888887666665.777888777666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-06
                                   ----SS..SSS-SSEEEEEEEE-GGG-EEEEEEE-TTSS-EEEEEEEETTTTEEEEEES-.SB--T CS
                         BNR_4  80 eveemlpggekessvTYPrflstedgkLllsyRdgksgngnavlneYdektdkwktlgekqlldge 145
                                   ev++m p  ++   +TYP  + ++++++ ++y   +  n+n+ +++Y+ +   w ++ + q+l ++
  gi|70606010|ref|YP_254880.1| 106 EVNNMSPLNSSLLFYTYPNLIVAHPDSVTYFYLYCQCSNNNTLIYTYNMT--GWVEVVHDQYLGMK 169
                                   566666665666779*********************************99..88888777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1530.85
//
Query:       gi|70606011|ref|YP_254881.1|  [L=141]
Description: CoA-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-37  127.6   0.1    3.5e-37  127.4   0.1    1.1  1  CoA_binding_2  CoA binding domain
    0.00022   21.9   0.0    0.00035   21.2   0.0    1.4  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.1     4e-41   3.5e-37       1     114 [.      16     134 ..      16     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 4e-41
                                   --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH... CS
                 CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealal... 78 
                                   ++ia +G s++p+k+++ v+r+l ++g++v+pVnp+  eilg+k+y+s+ + pe++++v vf+p++++p+iv+e+l++   
  gi|70606011|ref|YP_254881.1|  16 KNIATIGFSKDPSKPAHEVPRFLISKGYNVIPVNPTVNEILGRKSYKSILDIPEKIEVVEVFRPSSEVPKIVDEVLERvkm 96 
                                   689***********************************************868**********************999888 PP

                                   ..--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHH CS
                 CoA_binding_2  79 ..gakavwlqpgsedeeaaelaeeagirvvgdrCilve 114
                                     ++k++wlq+g++++eaae+a++ag+ v++drC+  e
  gi|70606011|ref|YP_254881.1|  97 kgDVKVIWLQEGIRHDEAAEKARKAGLVVIQDRCMYKE 134
                                   756*******************************9876 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.9e-08   0.00035       4      85 ..      16      94 ..      13     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.9e-08
                                  EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHH.T CS
                   CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelve.a 85
                                  ++++ iG+++  ++ +  + + l  +   v++vnp+   +e+lg + yks+ +++ek  ++v  ++ P+ ++ ++vde++e  
  gi|70606011|ref|YP_254881.1| 16 KNIATIGFSKDPSKPAHEVPRFLISKGYNVIPVNPT--VNEILGRKSYKSILDIPEK--IEVVEVFRPSSEVPKIVDEVLErV 94
                                  799999999999999955555555566789******..9******************..99999999***********98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1104.15
//
Query:       gi|70606012|ref|YP_254882.1|  [L=60]
Description: hypothetical protein Saci_0169 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0066   16.7   3.0     0.0088   16.3   3.0    1.2  1  DUF308    Short repeat of unknown function (DUF308)
  ------ inclusion threshold ------
       0.55   10.1   6.9        1.1    9.2   6.9    1.4  1  DUF2970   Protein of unknown function (DUF2970)


Domain annotation for each model (and alignments):
>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.0   9.9e-07    0.0088      19      64 ..       7      51 ..       4      56 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-07
                        DUF308 19 aallalvllfGilllvsGivqiiaafaarkknrggrwlglllGily 64
                                  a+++++v+l+G++++vsG+++i+    + ++    + l +++G ++
  gi|70606012|ref|YP_254882.1|  7 ASVSIIVVLLGVFVFVSGLLGIVRIA-SPEFPPYLGMLLMTVGSIS 51
                                  7999******************8554.6666665555444555544 PP

>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.9   0.00012       1.1      33      54 ..      10      31 ..       4      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                       DUF2970 33 viivGlilaalfvllLillVkl 54
                                   iiv l+++++fv +L+++V++
  gi|70606012|ref|YP_254882.1| 10 SIIVVLLGVFVFVSGLLGIVRI 31
                                  59999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 496.00
//
Query:       gi|70606013|ref|YP_254883.1|  [L=100]
Description: putative DNA-directed RNA polymerase subunit M [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-24   83.1   7.0    2.8e-22   78.3   1.7    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
    8.5e-05   22.0   1.5      0.018   14.6   0.2    2.7  2  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00013   22.1   4.3      0.012   15.7   0.4    2.2  2  DUF2387          Probable metal-binding protein (DUF2387)
    0.00013   21.8   7.8     0.0011   18.8   2.1    2.4  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0016   18.4   9.2       0.28   11.1   0.4    3.4  3  zinc_ribbon_4    zinc-ribbon domain
     0.0031   17.3   6.3       0.22   11.4   0.3    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0053   17.1   8.7       0.56   10.7   0.9    3.2  3  zf-H2C2_2        Zinc-finger double domain
     0.0056   16.0   8.6       0.77    9.3   0.4    3.3  3  zf-ribbon_3      zinc-ribbon domain
     0.0061   16.4   7.0       0.33   10.9   1.3    2.7  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0064   16.4   2.2       0.56   10.1   0.2    2.2  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
     0.0092   15.6   4.7      0.033   13.8   0.3    2.4  2  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
       0.01   15.7   3.9        5.3    7.0   0.1    3.1  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
       0.01   15.9   3.1        6.4    6.9   0.1    3.1  3  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.01   15.4   8.9       0.48   10.1   0.6    3.0  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.01   15.5   3.7       0.81    9.5   0.1    2.9  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.013   15.3   4.7        3.1    7.8   0.2    3.0  3  HalOD2           Halobacterial output domain 2
      0.032   14.3   5.4        1.9    8.7   0.2    2.6  2  zf-GRF           GRF zinc finger
      0.036   14.4   2.5        2.9    8.3   0.1    2.1  2  DUF3268          zinc-finger-containing domain
      0.037   14.2  10.9          5    7.3   0.6    3.5  4  Zn-ribbon_8      Zinc ribbon domain
      0.037   12.6   4.4       0.31    9.5   0.7    2.0  2  Terminase_GpA    Phage terminase large subunit (GpA)
      0.046   13.5   9.6        1.4    8.8   0.2    3.3  3  zinc_ribbon_5    zinc-ribbon domain
      0.051   13.6   5.8          4    7.5   0.2    3.2  3  Rubredoxin       Rubredoxin
      0.068   13.2   1.7       0.15   12.1   0.0    2.3  3  DUF2752          Protein of unknown function (DUF2752)
      0.086   12.5   9.5        4.7    6.9   0.2    3.2  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.091   12.8   3.4       0.19   11.8   0.3    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.12   12.2   3.7       0.65    9.8   0.0    2.8  3  Zn_Tnp_IS1       InsA N-terminal domain
        0.2   11.4  10.1        1.8    8.4   0.3    3.2  3  Rubredoxin_2     Rubredoxin metal binding domain
       0.21   11.6   7.2        3.9    7.5   0.1    3.2  3  YhfH             YhfH-like protein
       0.22   11.7   5.5        4.7    7.5   0.3    3.1  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.29   10.9   7.3        2.4    7.9   1.0    3.4  3  Ribosomal_S27e   Ribosomal protein S27
       0.41   10.6   7.0        1.9    8.4   0.1    3.0  3  DUF3797          Domain of unknown function (DUF3797)
       0.64   10.0   5.8          2    8.5   0.1    2.7  2  RNHCP            RNHCP domain
       0.65   10.0   7.2         23    5.0   0.1    3.1  2  Nudix_N_2        Nudix N-terminal
       0.71    9.8  11.4        4.4    7.2   0.9    3.2  3  zf-HIT           HIT zinc finger
          1    9.5   8.3        5.2    7.2   2.1    2.7  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.1    9.5   6.4       0.85    9.8   2.1    2.1  2  zf-Dof           Dof domain, zinc finger
        1.1    9.4   8.9        2.5    8.3   0.1    3.2  3  UPF0547          Uncharacterised protein family UPF0547
        1.2    8.9  18.6          2    8.3   0.4    3.6  3  zinc_ribbon_2    zinc-ribbon domain
        1.8    8.3   8.5         25    4.6   0.4    3.2  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        1.8    8.7  11.1         13    6.0   0.3    3.3  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
          2    8.8   9.2          3    8.2   0.2    2.9  2  C1_2             C1 domain
        2.3    7.9   8.0        9.4    5.9   0.3    3.2  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        2.6    9.1   8.4        5.4    8.1   0.4    3.2  3  zf-C2H2_4        C2H2-type zinc finger
        3.9    7.1   6.5        3.4    7.3   0.2    2.9  3  RecR             RecR protein
        5.3    7.5  10.6        6.7    7.2   0.3    3.3  3  DUF4379          Probable Zinc-ribbon domain
        7.3    6.4  10.2         28    4.6   0.3    3.2  3  A2L_zn_ribbon    A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3    0.0065       2.5      27      36 ..       9      18 ..       4      21 .. 0.83
   2 !   78.3   1.7   7.1e-25   2.8e-22       2      39 .]      60      97 ..      59      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0065
                       TFIIS_C 27 vfykCtkCgh 36
                                  + ykC kCg+
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCGY 18
                                  78******97 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 7.1e-25
                       TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                   Cp+Cg++eayf+ lQtRsaDEp+t+fykCtkCg+ Wr
  gi|70606013|ref|YP_254883.1| 60 SCPSCGNDEAYFWILQTRSADEPATRFYKCTKCGKVWR 97
                                  7************************************8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.024       9.5      21      32 ..      12      23 ..       4      30 .. 0.77
   2 !   14.6   0.2   4.6e-05     0.018       3      29 ..      61      96 ..      59      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
                                  EESSSSBEEEEC CS
                  TF_Zn_Ribbon 21 vCtdCGlVledn 32
                                   C++CG++  +n
  gi|70606013|ref|YP_254883.1| 12 KCSKCGYIDTEN 23
                                  499999987776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.6e-05
                                  ETTTTCEE.C........HEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon  3 CPnCgstn.l........veDpergelvCtdCGlVl 29
                                  CP Cg+++ +          +p++  + Ct+CG V+
  gi|70606013|ref|YP_254883.1| 61 CPSCGNDEaYfwilqtrsADEPATRFYKCTKCGKVW 96
                                  ******99769****996666999999******998 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   3.2e-05     0.012      24      56 ..       4      36 ..       2      56 .. 0.78
   2 !    8.4   0.3    0.0059       2.3       8      37 ..      58      93 ..      51      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.2e-05
                       DUF2387 24 eedeveyrECvsCgftdelsekgqsvakelktr 56
                                  +e+++ +  C +Cg++d+ ++k+ ++ + +k  
  gi|70606013|ref|YP_254883.1|  4 KENGKTVYKCSKCGYIDTENQKEAKITTVIKHS 36
                                  578999****************77776665544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0059
                       DUF2387  8 GavCPrCsemD......kirmweedeveyrECvsCg 37
                                  G +CP C +        ++r  +e  +++  C++Cg
  gi|70606013|ref|YP_254883.1| 58 GISCPSCGNDEayfwilQTRSADEPATRFYKCTKCG 93
                                  99*****98777777666666566668999999998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.031        12      36      45 ..       9      18 ..       3      19 .. 0.82
   2 !   18.8   2.1   2.9e-06    0.0011      18      45 ..      58      94 ..      53      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.031
                 Zn_Tnp_IS1595 36 glfqCkeCrk 45
                                   +++C++C++
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCGY 18
                                  689*****86 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.9e-06
                 Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt.........rglfqCkeCrk 45
                                  g  CP Cg+++ay+             + ++C +C+k
  gi|70606013|ref|YP_254883.1| 58 GISCPSCGNDEAYFWILqtrsadepaTRFYKCTKCGK 94
                                  567*******88884333599**************97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.024       9.3      26      33 ..      11      18 ..       4      19 .. 0.73
   2 ?    5.4   0.2     0.044        17       3       9 ..      59      65 ..      58      67 .. 0.84
   3 !   11.1   0.4   0.00071      0.28      27      36 .]      88      97 ..      81      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                 zinc_ribbon_4 26 vrCskCgh 33
                                   +CskCg 
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGY 18
                                  59****96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.044
                 zinc_ribbon_4  3 itCpsCk 9 
                                  i+CpsC+
  gi|70606013|ref|YP_254883.1| 59 ISCPSCG 65
                                  8999996 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00071
                 zinc_ribbon_4 27 rCskCghvFr 36
                                  +C+kCg+v+r
  gi|70606013|ref|YP_254883.1| 88 KCTKCGKVWR 97
                                  9********7 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00056      0.22      16      30 ..       4      19 ..       1      24 [. 0.77
   2 ?    4.8   0.2     0.068        26       4       9 ..      61      66 ..      59      70 .. 0.96
   3 ?    3.2   0.1      0.21        81      20      28 ..      84      93 ..      72      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                                  CSCCCE.EEESSSS-E CS
                RNA_POL_M_15KD 16 dkegkn.feCrqCgYe 30
                                  ++ gk  + C++CgY+
  gi|70606013|ref|YP_254883.1|  4 KENGKTvYKCSKCGYI 19
                                  4555556********7 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.068
                                  ESTTTS CS
                RNA_POL_M_15KD  4 CpkCgN 9 
                                  Cp+CgN
  gi|70606013|ref|YP_254883.1| 61 CPSCGN 66
                                  *****9 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.21
                                  CE.EEESSSS CS
                RNA_POL_M_15KD 20 kn.feCrqCg 28
                                  ++ + C +Cg
  gi|70606013|ref|YP_254883.1| 84 TRfYKCTKCG 93
                                  4568999997 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.9    0.0014      0.56       7      22 ..       3      18 ..       3      18 .. 0.88
   2 ?    2.7   0.0      0.51     2e+02      16      21 ..      60      65 ..      33      68 .. 0.83
   3 ?    7.3   0.6     0.018         7      13      22 ..      85      94 ..      81      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0014
                     zf-H2C2_2  7 rkHtgekpyeCplCdk 22
                                  rk  g++ y+C++C++
  gi|70606013|ref|YP_254883.1|  3 RKENGKTVYKCSKCGY 18
                                  567899********98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.51
                     zf-H2C2_2 16 eCplCd 21
                                   Cp+C+
  gi|70606013|ref|YP_254883.1| 60 SCPSCG 65
                                  6****7 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.018
                     zf-H2C2_2 13 kpyeCplCdk 22
                                  ++y+C +C+k
  gi|70606013|ref|YP_254883.1| 85 RFYKCTKCGK 94
                                  46*******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.019       7.3       3      10 ..      11      18 ..       9      25 .. 0.74
   2 !    9.3   0.4     0.002      0.77       3      10 ..      59      66 ..      57      68 .. 0.76
   3 ?    4.7   0.3     0.053        21      18      24 ..      88      94 ..      85      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                   zf-ribbon_3  3 vrCPnCGa 10
                                  ++C++CG 
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGY 18
                                  57888885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                   zf-ribbon_3  3 vrCPnCGa 10
                                  ++CP+CG+
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGN 66
                                  67888885 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.053
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C++CG+
  gi|70606013|ref|YP_254883.1| 88 KCTKCGK 94
                                  5888886 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.4    0.0047       1.8      27      43 ..       9      25 ..       3      35 .. 0.75
   2 !   10.9   1.3   0.00086      0.33      29      56 ..      59      96 ..      27      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0047
                OrfB_Zn_ribbon 27 TSktCseCgsknkeals 43
                                  T  +Cs+Cg++++e+++
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCGYIDTENQK 25
                                  55689****99999333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00086
                OrfB_Zn_ribbon 29 ktCseCgsknke..........alsgrtfkCpnCgfea 56
                                   +C+ Cg    +          ++++r +kC++Cg ++
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAYfwilqtrsadEPATRFYKCTKCGKVW 96
                                  58*****999999999999999999**********876 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.021       8.4      89     108 ..      12      31 ..       7      44 .. 0.87
   2 !   10.1   0.2    0.0014      0.56      88     116 ..      59      94 ..      55      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
                                   STSSSTSTCEEECCSSSCEE CS
                  eIF-5_eIF-2B  89 lCkeCkspetelekeerllv 108
                                    C++C+  +te +ke ++++
  gi|70606013|ref|YP_254883.1|  12 KCSKCGYIDTENQKEAKITT 31 
                                   6**********999988764 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0014
                                   TSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                  eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCga 116
                                   + C++C++ e  + +       e  + + kC++Cg+
  gi|70606013|ref|YP_254883.1|  59 ISCPSCGNDEAYFWIlqtrsadEPATRFYKCTKCGK 94 
                                   78********9988777777766788999*****97 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.14        54      35      41 ..      11      17 ..       5      18 .. 0.83
   2 !   13.8   0.3   8.6e-05     0.033      23      41 ..      75      93 ..      58      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                 Baculo_LEF5_C 35 ryCskCg 41
                                    CskCg
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  58****9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.6e-05
                 Baculo_LEF5_C 23 QnRagDEivsfvryCskCg 41
                                  Q+R+ DE +     C kCg
  gi|70606013|ref|YP_254883.1| 75 QTRSADEPATRFYKCTKCG 93
                                  *******9999999****9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.21        81      12      18 ..      11      17 ..       9      19 .. 0.82
   2 ?    5.6   0.1     0.039        15      26      34 ..      59      67 ..      53      69 .. 0.73
   3 ?    7.0   0.1     0.014       5.3       6      20 ..      81      95 ..      78      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.21
                       DUF35_N 12 qrCpdCG 18
                                   +C++CG
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  58****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.039
                       DUF35_N 26 avCphCgsd 34
                                   +Cp Cg d
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGND 67
                                  679999876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.014
                       DUF35_N  6 egrLvgqrCpdCGtv 20
                                  e+  ++ +C++CG+v
  gi|70606013|ref|YP_254883.1| 81 EPATRFYKCTKCGKV 95
                                  55567889*****98 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.017       6.4      33      48 ..       4      19 ..       2      42 .. 0.85
   2 ?    6.7   0.0     0.019       7.2      58      75 ..      59      76 ..      54      84 .. 0.82
   3 ?    2.0   0.3      0.56   2.2e+02      39      48 ..      86      95 ..      74      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
                   Zn_Tnp_IS91 33 aalGfaryeCeeCghe 48
                                  +++G ++y+C++Cg  
  gi|70606013|ref|YP_254883.1|  4 KENGKTVYKCSKCGYI 19
                                  578999999**99965 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                   Zn_Tnp_IS91 58 rhCpsCqkkateewlekq 75
                                   +CpsC++ ++  w+ ++
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAYFWILQT 76
                                  47*********9999655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.56
                   Zn_Tnp_IS91 39 ryeCeeCghe 48
                                   y+C++Cg+ 
  gi|70606013|ref|YP_254883.1| 86 FYKCTKCGKV 95
                                  4677777764 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6    0.0012      0.48       5      15 ..       9      19 ..       5      21 .. 0.85
   2 ?    0.3   0.3       1.4   5.6e+02       9      14 ..      61      66 ..      60      67 .. 0.88
   3 ?    9.1   0.1    0.0026         1       6      15 ..      86      95 ..      82      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                                  -EEE-TTT--E CS
               Desulfoferrod_N  5 evYkCevCGni 15
                                   vYkC  CG i
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCGYI 19
                                  69*******76 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                  -TTT-- CS
               Desulfoferrod_N  9 CevCGn 14
                                  C  CGn
  gi|70606013|ref|YP_254883.1| 61 CPSCGN 66
                                  999**9 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0026
                                  EEE-TTT--E CS
               Desulfoferrod_N  6 vYkCevCGni 15
                                   YkC+ CG +
  gi|70606013|ref|YP_254883.1| 86 FYKCTKCGKV 95
                                  6*******86 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0021      0.81      36      52 ..       2      18 ..       1      20 [. 0.87
   2 ?    0.6   0.1       1.2   4.7e+02      47      51 ..      61      65 ..      52      69 .. 0.87
   3 ?    5.3   0.1     0.042        16      39      52 ..      81      94 ..      73      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                zinc_ribbon_10 36 pkeeleevkyrCpkCga 52
                                  p++e+ ++ y+C+kCg 
  gi|70606013|ref|YP_254883.1|  2 PRKENGKTVYKCSKCGY 18
                                  689999*********97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                zinc_ribbon_10 47 CpkCg 51
                                  Cp+Cg
  gi|70606013|ref|YP_254883.1| 61 CPSCG 65
                                  99998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.042
                zinc_ribbon_10 39 eleevkyrCpkCga 52
                                  e+++  y+C kCg 
  gi|70606013|ref|YP_254883.1| 81 EPATRFYKCTKCGK 94
                                  5666679*****96 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0098       3.8      28      40 ..       7      19 ..       4      27 .. 0.84
   2 ?    0.5   0.1       1.4   5.7e+02       4      11 ..      60      67 ..      57      72 .. 0.77
   3 ?    7.8   0.2     0.008       3.1      32      40 ..      87      95 ..      82      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0098
                        HalOD2 28 GayvWkCtrCGev 40
                                  G  v+kC++CG +
  gi|70606013|ref|YP_254883.1|  7 GKTVYKCSKCGYI 19
                                  7889*******76 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.4
                        HalOD2  4 kCseCsld 11
                                  +C+ C+ d
  gi|70606013|ref|YP_254883.1| 60 SCPSCGND 67
                                  68888765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.008
                        HalOD2 32 WkCtrCGev 40
                                  +kCt+CG+v
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKV 95
                                  799999998 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8     0.011       4.1      18      32 ..       3      17 ..       2      25 .. 0.86
   2 ?    8.7   0.2    0.0049       1.9       2      31 ..      60      92 ..      59      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                        zf-GRF 18 gpNkGRkFYkCpkgk 32
                                  ++++G+  YkC+k+ 
  gi|70606013|ref|YP_254883.1|  3 RKENGKTVYKCSKCG 17
                                  5899********986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0049
                        zf-GRF  2 lCk.cg.rlavlltvr.ktgpNkGRkFYkCpkg 31
                                  +C+ cg  +a   + + +   ++   FYkC k+
  gi|70606013|ref|YP_254883.1| 60 SCPsCGnDEAYFWILQtRSADEPATRFYKCTKC 92
                                  68889987777666541467899999****998 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0074       2.9      24      58 ..       4      37 ..       1      45 [. 0.79
   2 ?    6.5   0.4     0.026        10       3      37 ..      59      93 ..      57      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0074
                       DUF3268 24 rskgkllylCpkCdayvgvhkgtkiplGtlAnael 58
                                  +++gk++y C kC+ y+ ++++++  + t+ +++ 
  gi|70606013|ref|YP_254883.1|  4 KENGKTVYKCSKCG-YIDTENQKEAKITTVIKHSA 37
                                  6799*********8.88888888777777766655 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.026
                       DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                  + Cp CG+  ++    +  ++ +  + +y C+kC+
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAYFWILQTRSADEPATRFYKCTKCG 93
                                  57******9999988888888889999*******8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.018         7       6      14 ..      11      19 ..      10      31 .. 0.76
   2 ?    5.3   0.6     0.056        22      28      34 ..      60      66 ..      53      70 .. 0.78
   3 ?    5.3   0.7     0.053        21      29      34 ..      61      66 ..      57      85 .. 0.77
   4 ?    7.3   0.6     0.013         5       6      14 ..      87      95 ..      86      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                   Zn-ribbon_8  6 YrCeeCghe 14
                                  Y+C +Cg  
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGYI 19
                                  9******65 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                   Zn-ribbon_8 28 aCPeCgs 34
                                   CP+Cg 
  gi|70606013|ref|YP_254883.1| 60 SCPSCGN 66
                                  5****97 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.053
                   Zn-ribbon_8 29 CPeCgs 34
                                  CP+Cg 
  gi|70606013|ref|YP_254883.1| 61 CPSCGN 66
                                  888886 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.013
                   Zn-ribbon_8  6 YrCeeCghe 14
                                  Y+C++Cg++
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKV 95
                                  9******86 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.017       6.8     222     247 ..       5      30 ..       1      58 [. 0.83
   2 ?    9.5   0.7    0.0008      0.31     199     239 ..      59      98 ..      58     100 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
                 Terminase_GpA 222 aeekaryvCphcgslieehhkraala 247
                                   ++ k+ y C++cg + +e++k+a++ 
  gi|70606013|ref|YP_254883.1|   5 ENGKTVYKCSKCGYIDTENQKEAKIT 30 
                                   566889***************99754 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0008
                 Terminase_GpA 199 vpCphCgelqelsferlkwpegeaeekaryvCphcgsliee 239
                                   + Cp+Cg+     +  l+  + +++ +  y C +cg+++ e
  gi|70606013|ref|YP_254883.1|  59 ISCPSCGNDEAYFWI-LQTRSADEPATRFYKCTKCGKVWRE 98 
                                   57*****98776654.45544449***************98 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0035       1.4      20      34 ..       4      19 ..       3      21 .. 0.90
   2 ?    4.1   0.3       0.1        40       3       9 ..      59      65 ..      58      67 .. 0.89
   3 ?    5.5   0.4     0.037        14      27      35 ..      88      96 ..      84      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0035
                 zinc_ribbon_5 20 KksgkkV.rCakCaev 34
                                  K++gk V +C kC+ +
  gi|70606013|ref|YP_254883.1|  4 KENGKTVyKCSKCGYI 19
                                  89***9999****976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                 zinc_ribbon_5  3 irCpdCd 9 
                                  i+Cp C+
  gi|70606013|ref|YP_254883.1| 59 ISCPSCG 65
                                  8*****8 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.037
                 zinc_ribbon_5 27 rCakCaevF 35
                                  +C kC++v 
  gi|70606013|ref|YP_254883.1| 88 KCTKCGKVW 96
                                  9*****995 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2      0.01         4       2      15 ..      11      24 ..      10      31 .. 0.82
   2 ?    5.0   0.0     0.065        26      36      47 .]      60      71 ..      48      71 .. 0.83
   3 ?    3.1   0.3      0.26     1e+02       2      12 ..      87      97 ..      82     100 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                                  EEETTT-BEEETTT CS
                    Rubredoxin  2 yeCkvCgyvYdpak 15
                                  y+C+ Cgy+  +++
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGYIDTENQ 24
                                  9*******977765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.065
                                  BBTTTB-BGGGE CS
                    Rubredoxin 36 vCPdCgvekeqF 47
                                   CP+Cg +   F
  gi|70606013|ref|YP_254883.1| 60 SCPSCGNDEAYF 71
                                  7****9987766 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.26
                                  EEETTT-BEEE CS
                    Rubredoxin  2 yeCkvCgyvYd 12
                                  y+C+ Cg v+ 
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKVWR 97
                                  89999998775 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       4.4   1.7e+03       7      15 ..       9      17 ..       8      19 .. 0.84
   2 ?   12.1   0.0    0.0004      0.15       7      25 ..      56      75 ..      53      80 .. 0.82
   3 ?   -1.7   0.1       8.3   3.2e+03       9      15 ..      87      93 ..      84      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.4
                       DUF2752  7 tGipCPGCG 15
                                  t ++C  CG
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCG 17
                                  6689****9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0004
                       DUF2752  7 t.GipCPGCGltRavhallh 25
                                  t Gi+CP CG   a  ++l+
  gi|70606013|ref|YP_254883.1| 56 TrGISCPSCGNDEAYFWILQ 75
                                  559*******9999999887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.3
                       DUF2752  9 ipCPGCG 15
                                  ++C  CG
  gi|70606013|ref|YP_254883.1| 87 YKCTKCG 93
                                  6899999 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.012       4.7      10      18 ..      10      18 ..       2      23 .. 0.82
   2 ?    5.7   0.3     0.029        11       8      17 ..      57      65 ..      51      67 .. 0.80
   3 ?    4.9   0.4     0.053        21      12      17 ..      88      93 ..      84      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                       zf-tcix 10 vrkCpkCGt 18
                                  v kC+kCG 
  gi|70606013|ref|YP_254883.1| 10 VYKCSKCGY 18
                                  67******6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                       zf-tcix  8 RGvrkCpkCG 17
                                  RG+  Cp+CG
  gi|70606013|ref|YP_254883.1| 57 RGI-SCPSCG 65
                                  677.6****9 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.053
                       zf-tcix 12 kCpkCG 17
                                  kC+kCG
  gi|70606013|ref|YP_254883.1| 88 KCTKCG 93
                                  9***** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00048      0.19      68      96 ..       8      68 ..       3      80 .. 0.84
   2 ?    2.0   0.2      0.52     2e+02      71      81 ..      87      97 ..      78     100 .] 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00048
                                  --EEEETTTS-EEECHHHHH................................S-TTTSSS- CS
                          HypA 68 pvkvrCreCgkefeleekal................................rCpkCgsad 96
                                  + +++C++Cg+  ++++k++                                +Cp+Cg+ +
  gi|70606013|ref|YP_254883.1|  8 KTVYKCSKCGYIDTENQKEAkittvikhsakektlvlesdmpktgvqltrgiSCPSCGNDE 68
                                  67899*****877755542246899*********************************976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.52
                                  EEETTTS-EEE CS
                          HypA 71 vrCreCgkefe 81
                                  ++C++Cgk ++
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKVWR 97
                                  46777777665 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.44   1.7e+02      28      34 ..      10      16 ..       3      17 .. 0.79
   2 ?    9.8   0.0    0.0017      0.65       6      17 ..      59      70 ..      56      72 .. 0.87
   3 ?   -0.4   0.2       2.5   9.8e+02      29      34 ..      87      92 ..      82      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.44
                    Zn_Tnp_IS1 28 RfrCrdC 34
                                   ++C++C
  gi|70606013|ref|YP_254883.1| 10 VYKCSKC 16
                                  59****9 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0017
                    Zn_Tnp_IS1  6 ihCPrCsstdVy 17
                                  i+CP+C  ++ y
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAY 70
                                  9*****999876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                    Zn_Tnp_IS1 29 frCrdC 34
                                  ++C +C
  gi|70606013|ref|YP_254883.1| 87 YKCTKC 92
                                  799999 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0046       1.8       1       8 [.      11      18 ..      11      22 .. 0.91
   2 ?    4.4   0.2     0.079        31      17      21 ..      61      65 ..      60      72 .. 0.80
   3 ?    4.3   0.5     0.088        34       1       8 [.      87      94 ..      87      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                  Rubredoxin_2  1 YvCsqCGf 8 
                                  Y Cs+CG+
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGY 18
                                  99*****9 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.079
                  Rubredoxin_2 17 CpsCg 21
                                  CpsCg
  gi|70606013|ref|YP_254883.1| 61 CPSCG 65
                                  88887 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.088
                  Rubredoxin_2  1 YvCsqCGf 8 
                                  Y C +CG 
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGK 94
                                  99****96 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.16        61      15      22 ..      12      19 ..      10      28 .. 0.70
   2 ?    3.2   0.2      0.23        89      16      22 ..      61      67 ..      60      70 .. 0.87
   3 ?    7.5   0.1      0.01       3.9      15      25 ..      88      98 ..      87     100 .] 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                          YhfH 15 kCteCGke 22
                                  kC++CG  
  gi|70606013|ref|YP_254883.1| 12 KCSKCGYI 19
                                  7*****64 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                          YhfH 16 CteCGke 22
                                  C++CG++
  gi|70606013|ref|YP_254883.1| 61 CPSCGND 67
                                  *****85 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.01
                          YhfH 15 kCteCGkeieE 25
                                  kCt+CGk+  E
  gi|70606013|ref|YP_254883.1| 88 KCTKCGKVWRE 98
                                  7******8766 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.012       4.7      37      55 ..      12      30 ..       5      34 .. 0.69
   2 ?    3.6   0.0      0.19        75      37      47 ..      60      70 ..      53      78 .. 0.72
   3 ?    2.0   0.2      0.63   2.4e+02       1       7 [.      88      94 ..      86      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                zinc_ribbon_13 37 sCknCgYtelYkaetsegk 55
                                   C++CgY +  +++  +  
  gi|70606013|ref|YP_254883.1| 12 KCSKCGYIDTENQKEAKIT 30
                                  6888888877666665555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                zinc_ribbon_13 37 sCknCgYtelY 47
                                  sC +Cg  e Y
  gi|70606013|ref|YP_254883.1| 60 SCPSCGNDEAY 70
                                  56666555544 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.63
                zinc_ribbon_13  1 kCpKCgn 7 
                                  kC KCg+
  gi|70606013|ref|YP_254883.1| 88 KCTKCGK 94
                                  5888875 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5      0.12        46      24      34 ..       8      18 ..       5      33 .. 0.82
   2 ?    1.8   0.5      0.52     2e+02       9      16 ..      12      19 ..      11      41 .. 0.70
   3 ?    7.9   1.0    0.0063       2.4       8      35 ..      59      95 ..      57      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                                  SS-EEESSSTC CS
                Ribosomal_S27e 24 atvvkCisCgk 34
                                  +tv kC +Cg 
  gi|70606013|ref|YP_254883.1|  8 KTVYKCSKCGY 18
                                  67888888885 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.52
                                  E-TTTS-E CS
                Ribosomal_S27e  9 kCpdCene 16
                                  kC +C+ +
  gi|70606013|ref|YP_254883.1| 12 KCSKCGYI 19
                                  56666544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0063
                                  EE-TTTS-EEEEE........SS.-SS-EEESSSTCE CS
                Ribosomal_S27e  8 vkCpdCenetvvF........sh.aatvvkCisCgkv 35
                                  + Cp C+n    F        +  a +  kC +Cgkv
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAYFwilqtrsaDEpATRFYKCTKCGKV 95
                                  679999998888866665555441445789****998 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.098        38      14      36 ..      11      35 ..       4      40 .. 0.72
   2 ?    8.4   0.1     0.005       1.9      14      23 ..      59      68 ..      52      70 .. 0.86
   3 ?    0.6   0.3       1.4   5.3e+02      38      45 ..      86      93 ..      80      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.098
                       DUF3797 14 vqCPeCgNnkvlNs.egkv.iiedd 36
                                   +C +Cg +   N  e+k+  + ++
  gi|70606013|ref|YP_254883.1| 11 YKCSKCGYIDTENQkEAKItTVIKH 35
                                  4799999999888538888755555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.005
                       DUF3797 14 vqCPeCgNnk 23
                                  + CP CgN+ 
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDE 68
                                  58******95 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.4
                       DUF3797 38 fyreCkCg 45
                                  fy+  kCg
  gi|70606013|ref|YP_254883.1| 86 FYKCTKCG 93
                                  77777776 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1     0.005         2      60      82 ..       4      26 ..       1      39 [. 0.79
   2 ?    4.2   0.2      0.11        41      66      75 ..      86      95 ..      72      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.005
                         RNHCP 60 kkewvivhrCekCgelkknrvak 82
                                  k++ + v++C+kCg +++++ ++
  gi|70606013|ref|YP_254883.1|  4 KENGKTVYKCSKCGYIDTENQKE 26
                                  5667889*******998876654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                         RNHCP 66 vhrCekCgel 75
                                   ++C+kCg++
  gi|70606013|ref|YP_254883.1| 86 FYKCTKCGKV 95
                                  699****987 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.06        23      25      31 ..      13      19 ..       8      20 .. 0.84
   2 ?    4.4   2.9     0.092        36       3      31 ..      61      95 ..      60      96 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.06
                                  ETTTTEE CS
                     Nudix_N_2 25 CpaCgti 31
                                  C++Cg+i
  gi|70606013|ref|YP_254883.1| 13 CSKCGYI 19
                                  9999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.092
                                  -TTT--B-E.....EE--TT-SS-EEE.ETTTTEE CS
                     Nudix_N_2  3 CsqCGtpve.....lripdgDnreRlv.CpaCgti 31
                                  C++CG+  +     +   +++  +R+  C++Cg +
  gi|70606013|ref|YP_254883.1| 61 CPSCGNDEAyfwilQTRSADEPATRFYkCTKCGKV 95
                                  88888875556663333455666775339999977 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9     0.011       4.4      14      20 ..      11      17 ..       6      19 .. 0.88
   2 ?    2.5   0.1      0.34   1.3e+02      15      21 ..      60      66 ..      58      70 .. 0.78
   3 ?    6.0   0.6     0.028        11      14      20 ..      87      93 ..      83      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                  EE-TTT- CS
                        zf-HIT 14 YkCpkCn 20
                                  YkC+kC+
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  ******8 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.34
                                  E-TTT-- CS
                        zf-HIT 15 kCpkCnt 21
                                  +Cp C+ 
  gi|70606013|ref|YP_254883.1| 60 SCPSCGN 66
                                  6999975 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.028
                                  EE-TTT- CS
                        zf-HIT 14 YkCpkCn 20
                                  YkC kC+
  gi|70606013|ref|YP_254883.1| 87 YKCTKCG 93
                                  ******8 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4     0.073        28      12      24 ..       6      18 ..       2      24 .. 0.83
   2 ?    2.9   0.3       0.3   1.2e+02      16      23 ..      58      65 ..      21      71 .. 0.84
   3 ?    7.2   2.1     0.013       5.2       2      23 ..      61      93 ..      60      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.073
                      zf-Mss51 12 pkhvdfeCpdCGi 24
                                  + +  ++C +CG+
  gi|70606013|ref|YP_254883.1|  6 NGKTVYKCSKCGY 18
                                  56778*******7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.3
                      zf-Mss51 16 dfeCpdCG 23
                                   + Cp CG
  gi|70606013|ref|YP_254883.1| 58 GISCPSCG 65
                                  578****9 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.013
                      zf-Mss51  2 CPvpkhkqt...........apkhvdfeCpdCG 23
                                  CP + ++++           +p+   ++C +CG
  gi|70606013|ref|YP_254883.1| 61 CPSCGNDEAyfwilqtrsadEPATRFYKCTKCG 93
                                  999999998999999999999***********9 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.67   2.6e+02       3      14 ..      10      21 ..       8      25 .. 0.80
   2 ?    9.8   2.1    0.0022      0.85       4      39 ..      59      97 ..      56      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.67
                        zf-Dof  3 alkCprCestnt 14
                                  ++kC +C   +t
  gi|70606013|ref|YP_254883.1| 10 VYKCSKCGYIDT 21
                                  789999988877 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0022
                        zf-Dof  4 lkCprCestntkFcYyNNyslsqP..R.yfCkaCrryWt 39
                                  ++Cp C   +  F      s + P  R y C +C + W 
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGNDEAYFWILQTRSADEPatRfYKCTKCGKVWR 97
                                  68*******************999654578********5 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0064       2.5      16      24 ..      12      20 ..      10      22 .. 0.85
   2 ?    3.5   0.4      0.19        76      16      21 ..      60      65 ..      59      66 .. 0.63
   3 ?    1.7   0.3      0.73   2.9e+02      16      25 ..      88      97 ..      86      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0064
                       UPF0547 16 fCphCGyvF 24
                                  +C+ CGy++
  gi|70606013|ref|YP_254883.1| 12 KCSKCGYID 20
                                  7******97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                       UPF0547 16 fCphCG 21
                                  +Cp CG
  gi|70606013|ref|YP_254883.1| 60 SCPSCG 65
                                  466666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.73
                       UPF0547 16 fCphCGyvFq 25
                                  +C  CG v+ 
  gi|70606013|ref|YP_254883.1| 88 KCTKCGKVWR 97
                                  7999**8885 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4     0.005         2       8      21 ..       5      18 ..       3      19 .. 0.69
   2 ?    6.1   0.8     0.024       9.3       2       7 ..      61      66 ..      60      67 .. 0.82
   3 ?    6.4   1.3     0.019       7.5       1       7 [.      88      94 ..      88      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.005
                 zinc_ribbon_2  8 elqdnakFCpyCGt 21
                                  e+ +++  C++CG+
  gi|70606013|ref|YP_254883.1|  5 ENGKTVYKCSKCGY 18
                                  66666667888886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                 zinc_ribbon_2  2 CpnCGa 7 
                                  Cp+CG+
  gi|70606013|ref|YP_254883.1| 61 CPSCGN 66
                                  999997 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.019
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C++CG+
  gi|70606013|ref|YP_254883.1| 88 KCTKCGK 94
                                  7999997 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.065        25       1       7 [.      11      17 ..       8      29 .. 0.74
   2 ?    3.1   0.2       0.2        76      10      24 ..      53      65 ..      50      66 .. 0.78
   3 ?    4.6   0.4     0.064        25       1       8 [.      87      94 ..      87      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.065
                                  -B-SSS- CS
                DNA_RNApol_7kD  1 YiCgeCg 7 
                                  Y+C +Cg
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  6666665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                                  ----SSS----SSS- CS
                DNA_RNApol_7kD 10 vslkkgdpiRCkeCG 24
                                  v+l +g  i C  CG
  gi|70606013|ref|YP_254883.1| 53 VQLTRG--ISCPSCG 65
                                  566666..99****9 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.064
                                  -B-SSS-- CS
                DNA_RNApol_7kD  1 YiCgeCga 8 
                                  Y+C +Cg+
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGK 94
                                  88888886 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.28   1.1e+02       3       8 ..      12      17 ..      11      19 .. 0.88
   2 ?    6.0   0.6     0.034        13       2       9 ..      59      66 ..      59      66 .. 0.85
   3 ?    6.0   0.3     0.033        13       2       9 ..      87      94 ..      86      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.28
                        zf-ACC  3 KCpsCg 8 
                                  KC +Cg
  gi|70606013|ref|YP_254883.1| 12 KCSKCG 17
                                  9****8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.034
                        zf-ACC  2 tKCpsCge 9 
                                  + CpsCg+
  gi|70606013|ref|YP_254883.1| 59 ISCPSCGN 66
                                  67****96 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.033
                        zf-ACC  2 tKCpsCge 9 
                                   KC++Cg 
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGK 94
                                  59****96 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0078         3      29      40 ..       6      18 ..       2      21 .. 0.76
   2 ?    2.2   4.0      0.58   2.3e+02      30      38 ..      84      92 ..      38      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0078
                          C1_2 29 dgff.YsCseCdf 40
                                  +g+  Y+Cs+C +
  gi|70606013|ref|YP_254883.1|  6 NGKTvYKCSKCGY 18
                                  56667******87 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.58
                          C1_2 30 gffYsCseC 38
                                    fY+C++C
  gi|70606013|ref|YP_254883.1| 84 TRFYKCTKC 92
                                  234999999 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.072        28       3       9 ..      11      17 ..       9      21 .. 0.91
   2 ?    1.1   0.2      0.78     3e+02       3       9 ..      59      65 ..      57      67 .. 0.84
   3 ?    5.9   0.3     0.024       9.4       3      11 ..      87      95 ..      85      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                        zf_UBZ  3 ylCerCg 9 
                                  y C++Cg
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  99****8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.78
                        zf_UBZ  3 ylCerCg 9 
                                  + C+ Cg
  gi|70606013|ref|YP_254883.1| 59 ISCPSCG 65
                                  68****9 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.024
                        zf_UBZ  3 ylCerCgke 11
                                  y C +Cgk 
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKV 95
                                  99*****95 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.48   1.9e+02       1       7 [.      11      17 ..      11      23 .. 0.85
   2 ?    1.5   0.1       1.9   7.2e+02       2       7 ..      60      65 ..      59      69 .. 0.83
   3 ?    8.1   0.4     0.014       5.4       1      12 [.      87      98 ..      87     100 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.48
                     zf-C2H2_4  1 fkCpiCg 7 
                                  +kC+ Cg
  gi|70606013|ref|YP_254883.1| 11 YKCSKCG 17
                                  89****5 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.9
                     zf-C2H2_4  2 kCpiCg 7 
                                   Cp Cg
  gi|70606013|ref|YP_254883.1| 60 SCPSCG 65
                                  6****7 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.014
                     zf-C2H2_4  1 fkCpiCgksFss 12
                                  +kC+ Cgk+++ 
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKVWRE 98
                                  8*******9965 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0087       3.4      15      28 ..       9      22 ..       5      24 .. 0.82
   2 ?    1.5   0.2      0.57   2.2e+02      18      24 ..      60      66 ..      56      67 .. 0.88
   3 ?    0.0   0.1       1.7   6.5e+02      18      23 ..      88      93 ..      83      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0087
                                  H-EE-TTT--EESS CS
                          RecR 15 kvrhCsrCgnltee 28
                                  +v  Cs+Cg +++e
  gi|70606013|ref|YP_254883.1|  9 TVYKCSKCGYIDTE 22
                                  6889*******766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.57
                                  E-TTT-- CS
                          RecR 18 hCsrCgn 24
                                   C+ Cgn
  gi|70606013|ref|YP_254883.1| 60 SCPSCGN 66
                                  5999998 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.7
                                  E-TTT- CS
                          RecR 18 hCsrCg 23
                                   C +Cg
  gi|70606013|ref|YP_254883.1| 88 KCTKCG 93
                                  6999*8 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.1      0.11        45      24      37 ..       5      18 ..       1      39 [. 0.70
   2 ?    0.9   0.1       1.6   6.1e+02      47      56 .]      56      64 ..      49      67 .. 0.75
   3 ?    7.2   0.3     0.017       6.7      30      40 ..      87      97 ..      77      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                       DUF4379 24 skkkvwWkCakCgh 37
                                   + k   kC+kCg+
  gi|70606013|ref|YP_254883.1|  5 ENGKTVYKCSKCGY 18
                                  5678899*****95 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.6
                       DUF4379 47 tkgsskCpkC 56
                                  t+g s Cp C
  gi|70606013|ref|YP_254883.1| 56 TRGIS-CPSC 64
                                  44555.9998 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.017
                       DUF4379 30 WkCakCgheWe 40
                                   kC kCg+ W+
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGKVWR 97
                                  69********8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.072        28       4      28 ..      11      17 ..       9      21 .. 0.63
   2 ?    3.0   0.1      0.23        90      23      30 ..      60      67 ..      56      70 .. 0.79
   3 ?    3.7   1.2      0.14        54       4      11 ..      87      94 ..      86      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.072
                 A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCg 28
                                  ++Cs+C                  g
  gi|70606013|ref|YP_254883.1| 11 YKCSKC------------------G 17
                                  455555..................4 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                 A2L_zn_ribbon 23 vCieCgas 30
                                  +C+ Cg+ 
  gi|70606013|ref|YP_254883.1| 60 SCPSCGND 67
                                  7****985 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.14
                 A2L_zn_ribbon  4 kvCsvCgg 11
                                  ++C++Cg+
  gi|70606013|ref|YP_254883.1| 87 YKCTKCGK 94
                                  79****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 679.65
//
Query:       gi|70606014|ref|YP_254884.1|  [L=82]
Description: hypothetical protein Saci_0172 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 606.57
//
Query:       gi|70606015|ref|YP_254885.1|  [L=90]
Description: DNA-directed RNA polymerase subunit L [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-22   78.8   0.0    2.2e-22   78.6   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    2.2e-10   39.8   0.0      3e-10   39.4   0.0    1.2  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   2.5e-26   2.2e-22       2      70 ..      13      81 ..      12      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.5e-26
                                  EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHH CS
                   RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicd 70
                                  l+++i gE hT+gnlL+ +llk p+V+fa+Y+ pHPl+ +++++i t++s++++eaL ka++  ++  +
  gi|70606015|ref|YP_254885.1| 13 LELQIDGEEHTIGNLLKGMLLKVPGVKFAAYSLPHPLITSITIKILTDGSISAREALIKAIELAENYAN 81
                                  789**********************************************************98777665 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   3.4e-14     3e-10       1      63 [.      14      74 ..      14      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 3.4e-14
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_L  1 efllrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlk 63
                                  e +++g+ ht+gN L+ +ll +vpgv ++a     p        + +++++ tdgs++++eal +A++
  gi|70606015|ref|YP_254885.1| 14 ELQIDGEEHTIGNLLKGMLL-KVPGVKFAAyslphPL------ITSITIKILTDGSISAREALIKAIE 74
                                  5799****************.************7766......689********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 579.10
//
Query:       gi|70606016|ref|YP_254886.1|  [L=180]
Description: exosome complex RNA-binding protein Csl4 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-09   35.7   0.2    1.3e-08   34.5   0.2    1.6  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
      0.001   18.9   0.5      0.002   18.0   0.5    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0072   16.3   0.0      0.012   15.6   0.0    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0093   16.1   2.7      0.036   14.2   2.7    1.9  1  Zn-ribbon_8     Zinc ribbon domain
     0.0099   15.3   4.5       0.19   11.2   5.2    2.1  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.8   0.3      0.016   15.2   0.3    1.2  1  DZR             Double zinc ribbon
      0.014   15.1   0.9      0.028   14.2   0.9    1.4  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.021   15.4   1.0        1.5    9.5   0.2    2.3  2  EXOSC1          Exosome component EXOSC1/CSL4
      0.027   14.1   1.2      0.048   13.3   1.2    1.4  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.027   14.0   0.5      0.065   12.8   0.5    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.03   14.2   1.2      0.049   13.6   1.2    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.04   14.1   1.2      0.068   13.3   1.2    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.048   14.0   0.1       0.17   12.2   0.1    1.9  1  S1              S1 RNA binding domain
      0.053   13.7   0.2        0.1   12.7   0.2    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.099   12.3   0.0       0.13   12.0   0.0    1.1  1  CDC24_OB3       Cell division control protein 24, OB domain 3
       0.13   12.2   0.4       0.19   11.6   0.4    1.2  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.15   11.4   0.1       0.19   11.1   0.1    1.1  1  TYW3            Methyltransferase TYW3
       0.17   11.6   3.0        0.4   10.4   3.0    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.54   10.3   4.0        4.1    7.5   0.2    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.73    9.6   4.1         15    5.5   0.9    2.1  1  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.2   1.4e-11   1.3e-08       3      34 ..       1      32 [.       1      35 [. 0.96

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-11
                                  -TT-EEEETTTSEE-TTEEEETTEEEESSSEE CS
                        ECR1_N  3 tPGevlttdeefmrGhGTYvrggtiyAsvaGt 34
                                  +PGe l   eef  G+GTY+ +gt+y+sv+G 
  gi|70606016|ref|YP_254886.1|  1 MPGEELSVIEEFTTGEGTYEFNGTVYSSVVGK 32
                                  6*****************************95 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   2.2e-06     0.002      28      55 ..     140     166 ..     133     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-06
                OrfB_Zn_ribbon  28 SktCseCgsknkealsgrtfkCpnCgfe 55 
                                   S +Cs Cgs +++ ++++ +kCp+Cg  
  gi|70606016|ref|YP_254886.1| 140 SAKCSICGSPLQR-QDEEHLKCPDCGNI 166
                                   889**********.************86 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05     0.012      69      97 ..     139     168 ..      84     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                                   -EEEETTTS-EEECHHH.HHS-TTTSSS-E CS
                          HypA  69 vkvrCreCgkefeleek.alrCpkCgsadv 97 
                                   ++++C+ Cg+  + +++ +l+Cp+Cg+ ++
  gi|70606016|ref|YP_254886.1| 139 ISAKCSICGSPLQRQDEeHLKCPDCGNIET 168
                                   5789*****99997765599******9765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.7     4e-05     0.036       7      39 ..     142     171 ..     141     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                   Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.evrrv 39 
                                   +C  Cg    +lq+  d++  +CP+Cg  e+r++
  gi|70606016|ref|YP_254886.1| 142 KCSICG---SPLQR-QDEEHLKCPDCGNiETRKL 171
                                   699999...77885.4666788*********996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   5.2   0.00021      0.19       4      23 ..     142     164 ..     140     165 .. 0.87
   2 !    6.6   0.6    0.0059       5.3       3      11 ..     158     166 ..     156     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                   zf-ribbon_3   4 rCPnCGaplssddn...vCpyCG 23 
                                   +C+ CG+pl+ +d    +Cp CG
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLQRQDEehlKCPDCG 164
                                   7******9999996666*****9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0059
                   zf-ribbon_3   3 vrCPnCGap 11 
                                    +CP CG++
  gi|70606016|ref|YP_254886.1| 158 LKCPDCGNI 166
                                   578888886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   1.8e-05     0.016      14      39 ..     142     168 ..     134     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                           DZR  14 fCseCgtklkavaa.edrCpsCgekvd 39 
                                    Cs Cg++l+++ + + +Cp Cg   +
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLQRQDEeHLKCPDCGNIET 168
                                   6********98777899*****98755 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   3.1e-05     0.028       5      31 ..     142     167 ..     139     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                 A2L_zn_ribbon   5 vCsvCggngilnseqgylvCieCgasf 31 
                                   +Cs Cg++    ++  +l C++Cg+++
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLQR-QDEEHLKCPDCGNIE 167
                                   8*******999.*************98 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0016       1.5       7      50 ..      60     106 ..      56     110 .. 0.78
   2 ?    6.0   0.1      0.02        18      91     107 ..     105     121 ..      97     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                                   EEEEEEEEEESSEEEEEEEEECTB...SBCCCEEECCCTTSS--STS CS
                        EXOSC1   7 vVLarvtrlrkkqalveilsvege...nnvlsdsgvgangegavkei 50 
                                    VL+ v+ +++  a+++i s e++       +  ++++ ++++ + i
  gi|70606016|ref|YP_254886.1|  60 YVLGIVVGIKEDSAIINIQSLEDKslvTTLSGYIHISQISSKYLNTI 106
                                   59**********************66645555667777777776665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                                   -GGCTEECTTEEEEEEE CS
                        EXOSC1  91 kviemfrpGDIvraqvi 107
                                    + +++r+GDI+ra+ i
  gi|70606016|ref|YP_254886.1| 105 TISDAMRVGDIIRAKPI 121
                                   57899********9865 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.2   5.4e-05     0.048       6      30 ..     143     166 ..     143     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                 zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgle 30 
                                   C+ CG+p ++++ ++ + Cp+Cg++
  gi|70606016|ref|YP_254886.1| 143 CSICGSPLQRQDEEH-LKCPDCGNI 166
                                   999*******99987.89*****96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   7.2e-05     0.065       2      28 ..     142     166 ..     141     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                   EETTTTCEECHEETSTTCEEESSSSBE CS
                  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlV 28 
                                   kC +Cgs+ +  D+e   l C+dCG++
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLQRQDEE--HLKCPDCGNI 166
                                   8*******6666655..999*****87 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   5.4e-05     0.049       5      28 ..     141     165 ..     138     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                   Prok-RING_1   5 kkCpvCgkelkee.dDiVvCpeCgt 28 
                                    kC++Cg +l+ + +    Cp+Cg 
  gi|70606016|ref|YP_254886.1| 141 AKCSICGSPLQRQdEEHLKCPDCGN 165
                                   79********987357899****95 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.2   7.6e-05     0.068      16      40 .]     141     164 ..     138     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                 Auto_anti-p27  16 etCpvCgvPLmrdrkggkvyCvaCd 40 
                                   + C+ Cg+PL r+ +++ + C+ C+
  gi|70606016|ref|YP_254886.1| 141 AKCSICGSPLQRQ-DEEHLKCPDCG 164
                                   67**********8.78999*****6 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00019      0.17      28      59 ..      89     119 ..      55     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   EEEEEEGGGSSSSCEESCHHHCEETTEEEEEE CS
                            S1  28 vegfvpaselsrdarvedpdevlkvGdevkvk 59 
                                    +g++++s++s++     +++  +vGd +++k
  gi|70606016|ref|YP_254886.1|  89 LSGYIHISQISSK-YLNTISDAMRVGDIIRAK 119
                                   68***********.89999********99987 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00012       0.1      10      45 ..     142     179 ..     136     180 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                  NOB1_Zn_bind  10 rChaCfkvt..kdmtkkFCpkCGnktLkrvavsvdeng 45 
                                   +C  C +    +d +   Cp CGn   ++ a +v++ g
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLqrQDEEHLKCPDCGNIETRKLAFTVKKGG 179
                                   799999988435577788***************99876 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.13      86     167 ..      66     166 ..      52     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                     CDC24_OB3  86 vegecgaslvnlStlpallnSscLrklsplsdlssetssta.kevkldhfvvealiv...............itslaHssC 150
                                   v  ++++ ++n+ +l+     + L+ ++++s++ss+   t+ +++++ +++  + i                ++s+  s C
  gi|70606016|ref|YP_254886.1|  66 VGIKEDSAIINIQSLEDKSLVTTLSGYIHISQISSKYLNTIsDAMRVGDIIRAKPINyiipvpltikqrdlgVISAKCSIC 146
                                   44578899*************************9988877755566666443334448899******************** PP

                     CDC24_OB3 151 grpv...sggeleCefCqcs 167
                                   g p+   ++++l+C  C++ 
  gi|70606016|ref|YP_254886.1| 147 GSPLqrqDEEHLKCPDCGNI 166
                                   ******98899******975 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00021      0.19      11      36 ..     140     165 ..     132     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                   --B-TTT-SB--SSSS-EEEETTT-- CS
                          C1_1  11 ptfCkhCgeflwgkekqglkCswCkl 36 
                                   +++C+ Cg++l+++   +lkC +C+ 
  gi|70606016|ref|YP_254886.1| 140 SAKCSICGSPLQRQDEEHLKCPDCGN 165
                                   589********77***********85 PP

>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00021      0.19     145     187 ..      44      87 ..      36     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                                   HCT-TT-EEEEECTTEEEEEEE---EEEEEEE.......STS---HHHHH CS
                          TYW3 145 eaGfreSGivslkkkkvivairsglklevpig.......kellvseeylk 187
                                   + Gf++ Gi slkk+k+++ i +g+k ++ i        k      + ++
  gi|70606016|ref|YP_254886.1|  44 SIGFKKPGILSLKKSKYVLGIVVGIKEDSAIIniqsledK------SLVT 87 
                                   68***************************99987555541......3333 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.0   0.00045       0.4       2      24 ..     142     164 ..     142     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                                   B-SSS--B----SSS----SSS- CS
                DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCG 24 
                                   +C  Cg++ + + ++ ++C +CG
  gi|70606016|ref|YP_254886.1| 142 KCSICGSPLQRQDEEHLKCPDCG 164
                                   6999******************9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0046       4.1       2      15 ..     143     156 ..     142     157 .. 0.84
   2 ?    3.9   0.4     0.062        56       1       6 [.     159     164 ..     159     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0046
                DNA_ligase_ZBD   2 CPvCGsavvReege 15 
                                   C +CGs++ R ++e
  gi|70606016|ref|YP_254886.1| 143 CSICGSPLQRQDEE 156
                                   668*******8876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.062
                DNA_ligase_ZBD   1 hCPvCG 6  
                                   +CP CG
  gi|70606016|ref|YP_254886.1| 159 KCPDCG 164
                                   6****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9     0.016        15       1       7 [.     159     165 ..     159     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                 zinc_ribbon_2   1 fCpnCGa 7  
                                   +Cp CG+
  gi|70606016|ref|YP_254886.1| 159 KCPDCGN 165
                                   7****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1286.93
//
Query:       gi|70606017|ref|YP_254887.1|  [L=334]
Description: diphthamide synthesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-80  268.8   0.0    8.1e-80  268.5   0.0    1.1  1  Diphthamide_syn  Putative diphthamide synthesis protein
     0.0092   16.1   0.2      0.036   14.2   0.0    2.0  2  EIF_2_alpha      Eukaryotic translation initiation factor 2 a
  ------ inclusion threshold ------
      0.023   14.6   1.3        1.7    8.6   0.0    2.5  2  Phage_Mu_Gam     Bacteriophage Mu Gam like protein
      0.072   13.0   0.2       0.55   10.1   0.1    2.3  2  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
       0.11   12.1   0.0       0.17   11.4   0.0    1.3  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
       0.11   12.6   0.4        2.1    8.5   0.1    2.6  3  Y1_Tnp           Transposase IS200 like


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.5   0.0   2.7e-83   8.1e-80       1     294 [.      26     324 ..      26     331 .. 0.92

  Alignments for each domain:
  == domain 1  score: 268.5 bits;  conditional E-value: 2.7e-83
               Diphthamide_syn   1 fPegllpdsaeiadileef..gaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYvfveield... 75 
                                   fPeg++p+s  + ++l+e+  ++e+vi++D ++GaC+v e +a+ lg+dl++H+Gh++++  + ++p+l++  +++l+   
  gi|70606017|ref|YP_254887.1|  26 FPEGIKPFSIGLLERLRETakDIEFVISSDASWGACDVAEDEARTLGVDLIIHFGHTPYTWYYpKFPTLFIELKSKLNvee 106
                                   9***************77768999************************************8777************98544 PP

               Diphthamide_syn  76 ..vehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevdail 153
                                     +e+l++ +++++ + ++++l stiq++h l+++ke+++++ ++v+  +p+s   +++g++lgc+++++   ++++d+++
  gi|70606017|ref|YP_254887.1| 107 eqIEKLIQYINEKY-NPRTVSLSSTIQHSHLLPKIKEKMQSQ-FNVIiGKPSS-PFMHDGQILGCDYKAVV--NSSADVYV 182
                                   44666777777777.5677*********************77.9999555555.779*************8..569***** PP

               Diphthamide_syn 154 yigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkll 234
                                    +++g fh+l++ l+++k p++++dpy++k ++ + ++ ++l++Ry +i ka d+++++ii g +++q+r+ +v+ l+k+l
  gi|70606017|ref|YP_254887.1| 183 NVSGGVFHALGVGLTTRK-PIVKLDPYTSKNEDLTDEVYRILKIRYGKIMKALDSRNWAIIQGVKTGQNRPLMVKYLQKKL 262
                                   ****************88.************************************************************** PP

               Diphthamide_syn 235 keagkksylvlvgelnpakLanfa..eidafVlvaCprlsiddgkeFekPvltpyElevalg 294
                                   +e+g+k+++++ + ln++ L+n++  eid f++++Cprl+idd  e+ekPvltp E+++++ 
  gi|70606017|ref|YP_254887.1| 263 EEKGYKVFIITNRSLNVDALRNIDnpEIDSFIVTSCPRLPIDDLFEYEKPVLTPGEAKMIIF 324
                                   ***********************6346*******************************9875 PP

>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.2e-05     0.036      29      63 ..      98     132 ..      68     148 .. 0.79
   2 ?   -1.1   0.0      0.67     2e+03      45      60 ..     217     232 ..     170     272 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                   HHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEE CS
                   EIF_2_alpha  29 vldkleipeeveeaLveiikkklkpqkvkiradie 63 
                                     +kl+++ee +e+L+++i++k++p++v ++++i+
  gi|70606017|ref|YP_254887.1|  98 LKSKLNVEEEQIEKLIQYINEKYNPRTVSLSSTIQ 132
                                   446899***************************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.67
                                   HCTHHHHHHT-EEEEE CS
                   EIF_2_alpha  45 eiikkklkpqkvkira 60 
                                   +++ + lk++  ki  
  gi|70606017|ref|YP_254887.1| 217 DEVYRILKIRYGKIMK 232
                                   4443333333333332 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.012        36      13      49 ..      97     133 ..      95     148 .. 0.89
   2 ?    8.6   0.0   0.00055       1.7      68     126 ..     217     283 ..     204     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                  Phage_Mu_Gam  13 elkreleeieaeaneeiaaikekleaeleplkkeiey 49 
                                   elk +l+  e+++++ i+ i+ek++  + +l + i++
  gi|70606017|ref|YP_254887.1|  97 ELKSKLNVEEEQIEKLIQYINEKYNPRTVSLSSTIQH 133
                                   7888999999999************999999998886 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00055
                                   .-----EE-SS-EE---------.--TT--.........HHHHHHHHHCT-GCC--------HHHH.. CS
                  Phage_Mu_Gam  68 dgktKslklpfGkvgfrkstpkvkkrdkek.........eelLealkelgfkefIkvkeevnkeaLkk 126
                                   d+ ++ lk  +Gk+     ++     ++ k         + l ++l+e+g+k fI + +++n +aL  
  gi|70606017|ref|YP_254887.1| 217 DEVYRILKIRYGKIMKALDSRNWAIIQGVKtgqnrplmvKYLQKKLEEKGYKVFIITNRSLNVDAL-R 283
                                   555666666666665444443333333333355556666667899*********************.2 PP

>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00018      0.55      75     117 ..      99     141 ..      89     182 .. 0.81
   2 ?   -0.7   0.0      0.37   1.1e+03      82     107 ..     248     274 ..     239     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                                   TTGGG-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE.- CS
                  PhosphMutase  75 rragristeeakeLikalneeleegvevkfypgveyrhllvl.l 117
                                   ++  ++++e+ ++Li+++ne+  +  +v++ +++++ hll   +
  gi|70606017|ref|YP_254887.1|  99 KSKLNVEEEQIEKLIQYINEKY-NPRTVSLSSTIQHSHLLPKiK 141
                                   56667899**************.3569************97653 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.37
                                   -TTHHHHHHHT-EEE..TTEEEEEEE- CS
                  PhosphMutase  82 teeakeLikalneele.egvevkfypg 107
                                    ++ + ++k+l+++le +g++v + + 
  gi|70606017|ref|YP_254887.1| 248 GQNRPLMVKYLQKKLEeKGYKVFIITN 274
                                   55666789*******558898877765 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.7e-05      0.17     118     144 ..     251     278 ..     224     295 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.7e-05
                                   ECCHH.HHHHHHHHTTEEEEEEEEEECC CS
               Acid_phosphat_B 118 ipgal.elikkvverGvkiffvsgRsee 144
                                    p ++  l kk+ e+G+k+f +++Rs +
  gi|70606017|ref|YP_254887.1| 251 RPLMVkYLQKKLEEKGYKVFIITNRSLN 278
                                   344442577899*************987 PP

>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   5.3e+02      62      85 ..       5      28 ..       1      34 [. 0.85
   2 ?    8.5   0.1   0.00069       2.1      24      63 ..     106     145 ..     101     157 .. 0.92
   3 ?   -1.6   0.0      0.94   2.8e+03      88     110 ..     255     276 ..     228     280 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                        Y1_Tnp 62 lsiskivkalkgassrlinkefpe 85
                                   ++ ki++++ ++s++++  +fpe
  gi|70606017|ref|YP_254887.1|  5 FEVDKIIEEIRKRSAKKVLLQFPE 28
                                  5789************99988887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00069
                        Y1_Tnp  24 eerlkeiikeiaekkevkilelelmpDHvHllvelppkls 63 
                                   ee+++++i+ i ek++ + ++l+    H Hll ++++k++
  gi|70606017|ref|YP_254887.1| 106 EEQIEKLIQYINEKYNPRTVSLSSTIQHSHLLPKIKEKMQ 145
                                   68999********************************996 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.94
                        Y1_Tnp  88 kkklkkeslWqrgYfvstvgeas 110
                                    k+l+ ++l ++gY+v+ + + s
  gi|70606017|ref|YP_254887.1| 255 VKYLQ-KKLEEKGYKVFIITNRS 276
                                   34444.44667888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      944  (0.0526521); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2034.09
//
Query:       gi|70606018|ref|YP_254888.1|  [L=176]
Description: 50S ribosomal protein L10e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-33  114.1   0.3    5.1e-33  113.9   0.3    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e
  ------ inclusion threshold ------
      0.056   12.9   0.1       0.16   11.4   0.1    1.7  2  ArfA           Alternative ribosome-rescue factor A


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   0.3   5.7e-37   5.1e-33       4     131 ..      15     164 ..      12     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 5.7e-37
                                   SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC....EEXXSXXXXE CS
                 Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk....klwirvfphh 71 
                                   ++y++++  yi g + +k+tk+ +g+        ++L+++ekgq++++aleaar+ + +yl+kk  +    +l + ++phh
  gi|70606018|ref|YP_254888.1|  15 PAYTRRE--YIPGIPmPKITKFVMGNvngdydyeLRLITTEKGQIRHNALEAARVIALKYLSKKLASeqnfALVVTKYPHH 93 
                                   6899999..***********************8888*************************98777778899********* PP

                                   EEEE-.....SS-TTTSSSS....XEEEEEEEEEXS.SCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEE CS
                 Ribosomal_L16  72 pvtkk.....agedRmgkGk....Gkpegwvarvki.gqiifei.kagvneeiakealrraasKlpiktki 131
                                   +++++     ag+dR+++G+    Gkp g++ar ++ g+ ++ +  ++ + e akeal+ a+sKlpi+tki
  gi|70606018|ref|YP_254888.1|  94 VIRENkmmafAGADRLQDGMrlsfGKPIGTAARLEKlGELVMYVrVKKEHLEAAKEALKIASSKLPIRTKI 164
                                   **********************************877*******83445999******************8 PP

>> ArfA  Alternative ribosome-rescue factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   1.8e-05      0.16       4      16 ..      52      64 ..      50      66 .. 0.89
   2 ?   -3.2   0.0      0.67     6e+03       8      16 ..      94     102 ..      94     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.8e-05
                          ArfA  4 hgrGkIkDNalkA 16
                                  +++G+I++Nal+A
  gi|70606018|ref|YP_254888.1| 52 TEKGQIRHNALEA 64
                                  68**********9 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.67
                          ArfA   8 kIkDNalkA 16 
                                   +I++N + A
  gi|70606018|ref|YP_254888.1|  94 VIRENKMMA 102
                                   599999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1163.13
//
Query:       gi|70606019|ref|YP_254889.1|  [L=345]
Description: hypothetical protein Saci_0177 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2319.81
//
Query:       gi|70606020|ref|YP_254890.1|  [L=303]
Description: hypothetical protein Saci_0178 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-19   70.3  18.4    3.3e-19   69.6  18.4    1.3  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6  18.4   1.8e-23   3.3e-19       3     271 ..       8     260 ..       6     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.8e-23
               LPG_synthase_TM   3 lglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnnv 83 
                                   ++++ +a+++ ++   +   +l++++ s+dp +++l +l ++ + l+ a+r      s+  ++ ++++++a l g+ ++ +
  gi|70606020|ref|YP_254890.1|   8 VAVLPIAVIIGYA--LIFKIDLIDVFLSMDPVFVVLFFLSYITQCLILAYR-----DSMISKVNFFTSFKARLFGNGISLI 81 
                                   5555555555555..2335799********999999999999998899999.....455689******************* PP

               LPG_synthase_TM  84 tPgalgGevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavlallll 164
                                   +Pga+g +++ra+l ++ +g+sl ka+++ ++e ++d+ ++ +++l++++l +++l++  ++++++ +a++++++ ++++ 
  gi|70606020|ref|YP_254890.1|  82 IPGAAGPDLARAILYTK-KGISLDKAFSISLIESFFDVTVVSVMFLILFWLRFSPLLTIFVFVAFFNVAMWIAGFGYVYGT 161
                                   *****************.**************************************9888888888888888888888777 PP

               LPG_synthase_TM 165 lllrrrlarlarvlkrlarllarfarklasakr.klvlasprrlllafllslliwllealtlylllralgvdvslalllli 244
                                   +     ++  + + ++    l+r    ++  +  k  l+++++ +   +l+++ ++l+ l +yl++ ++      +++ +i
  gi|70606020|ref|YP_254890.1| 162 SHETLNRLEQKIFTFKYIKPLERAYLDSK--WLiKDRLSNVKMASFYSALTVIGYILQSLPFYLIFSSY------LKS-II 233
                                   77666666666666666666665554443..33588899999988888888888888888888888765......334.78 PP

               LPG_synthase_TM 245 llaltlvgalpplPgGlGvrEaalall 271
                                   + +++ v++l+p+P+ +G++E al+++
  gi|70606020|ref|YP_254890.1| 234 INITYQVSLLVPIPSAAGAAELALTAI 260
                                   89*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2175.77
//
Query:       gi|70606021|ref|YP_254891.1|  [L=290]
Description: dinucleotide-utilizing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-58  198.1   0.2    1.9e-58  197.7   0.2    1.0  1  ThiF            ThiF family
     0.0016   17.7   0.1     0.0024   17.2   0.1    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0035   17.3   0.0     0.0063   16.5   0.0    1.4  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0038   17.5   0.6     0.0089   16.3   0.1    1.8  2  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.013   14.9   0.3      0.043   13.2   0.1    1.9  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.025   14.2   0.1      0.048   13.3   0.0    1.6  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.033   14.7   0.6       0.17   12.5   0.6    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.05   13.2   0.2      0.077   12.6   0.2    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.054   12.7   0.1      0.073   12.3   0.1    1.2  1  FAD_binding_3   FAD binding domain
      0.055   13.3   0.2      0.097   12.6   0.0    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.13   12.5   0.8       0.36   11.1   0.6    1.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
        0.2   11.2   0.1       0.28   10.7   0.1    1.2  1  DAO             FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.2   1.2e-61   1.9e-58       1     243 [.       4     234 ..       4     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 1.2e-61
                                   THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaeal 81 
                                   y+rql +lg   qek+++ k+++vG+G+lG  l+++La++Gvgk++l+D D +e++Nl+R +lf+e+diGkpKa+v ae++
  gi|70606021|ref|YP_254891.1|   4 YARQLLVLGLGVQEKISQLKIAIVGCGALGTTLAELLARLGVGKIKLIDADIVEVTNLHRTHLFEESDIGKPKATVCAEKI 84 
                                   78******************************************************************************* PP

                                   HHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  82 qeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeC 162
                                   ++in++++ve v++ i++++ +ee+l++ D+++dalDn+  r+l+n+++vk +ipl+ +g+ g ++ v+ i+p + +c++C
  gi|70606021|ref|YP_254891.1|  85 RKINSGIKVEVVNDIIDSNN-AEEMLKDSDYIFDALDNLYYRFLLNDVAVKLRIPLVYGGVMGEYSSVMLIVPREGPCLRC 164
                                   ****************9988.79********************************************************** PP

                                   S-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEEC-T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 163 ldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakkskcl 243
                                    +   + d+ e++v++c +++g    + t++++ a+l+++ +l +l ++   +   l+++d+ e r +nv++ ++ k+  +
  gi|70606021|ref|YP_254891.1| 165 FM---NYDEHENEVNAC-ETIG---TLDTVISITASLQVQLMLNHLRNQA--NLHSLYYLDTRELRIDNVKISKNDKC--P 234
                                   *9...59999999****.9999...9********************5444..4455559*************777655..3 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.6e-06    0.0024     137     214 ..      16     104 ..      10     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                   CCSS-TSEEEEES-SHHHHHHHHHHHHHT-...........EEEEEESSSSSS.TTS-.HHHHHHHHHHHHHT.TEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxx.xxxxxxx RF
                   Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgk...........evtlveardrll.rald.kelsaaleealeke.Gvevklg 203
                                   ++k  + +i++vG G+ G+ lA  la+lg+           evt +++   +  +  + ++++ ++e+ ++ + G++v + 
  gi|70606021|ref|YP_254891.1|  16 QEKISQLKIAIVGCGALGTTLAELLARLGVgkiklidadivEVTNLHRTHLFEeSDIGkPKATVCAEKIRKINsGIKVEVV 96 
                                   56677789**********************99******9998888888666666444438888899998887789999944 PP

                                   CEEEEEEETTE CS
                                   xxxxxxxxxxx RF
                   Pyr_redox_2 204 tsvkeidgnge 214
                                      ++i++ ++
  gi|70606021|ref|YP_254891.1|  97 ---NDIIDSNN 104
                                   ...44444433 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.2e-06    0.0063       1      87 [.      23     129 ..      23     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-06
                                   -EEEE--SHHHHHHHHHHHTTT.................--EEEE-S-H.....HHHHHHHHHSSBTTTBTT----TTEEE CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaeng.................hevrlwvree.....elieeineehenvkyLpgiklpenlva 59 
                                   kia++G G+ Gt+lA +la+ g                 h+++l+  ++     +  ++  e+ +  +   ++++ +++  
  gi|70606021|ref|YP_254891.1|  23 KIAIVGCGALGTTLAELLARLGvgkiklidadivevtnlHRTHLFEESDigkpkA--TVCAEKIRKINSGIKVEVVNDIID 101
                                   79********************999999999997777777777777776887431..333333333333345778888888 PP

                                   ES-HHHHHTT--EEEE---HHHHHHHHH CS
                NAD_Gly3P_dh_N  60 ttdlaealkgadiivlvvPsqalrevlk 87 
                                   +++ +e lk++d+i+ ++   + r  l+
  gi|70606021|ref|YP_254891.1| 102 SNNAEEMLKDSDYIFDALDNLYYRFLLN 129
                                   8888888888888887776666665555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.9e-06    0.0089       1      38 [.      24      62 ..      24      69 .. 0.86
   2 ?   -2.7   0.0       4.5   6.8e+03      59      73 ..     180     194 ..     165     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.9e-06
                                  EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelr 38
                                  i+i+G+G +G++lae L + g  ++ +id d   v +l 
  gi|70606021|ref|YP_254891.1| 24 IAIVGCGALGTTLAELLARlGVGKIKLIDADIVEVTNLH 62
                                  79*****************87666*******98887765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                                   TGGGESEEEE-SSSH CS
                        TrkA_N  59 giekadaviaatgdd 73 
                                    i + d+vi  t + 
  gi|70606021|ref|YP_254891.1| 180 TIGTLDTVISITASL 194
                                   344444455444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.9e-05     0.043      32      67 ..      17      53 ..      11      72 .. 0.80
   2 ?   -1.5   0.0      0.92   1.4e+03      81      96 ..     101     116 ..      85     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                  S-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESS CS
                  2-Hacid_dh_C 32 kelsgktvGiiGlGrIGqavakrlkafgm.kviaydr 67
                                  +++s+ +++i+G+G++G+++a++l+ +g+ k+  +d 
  gi|70606021|ref|YP_254891.1| 17 EKISQLKIAIVGCGALGTTLAELLARLGVgKIKLIDA 53
                                  679999*********************9966666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
                                   EECSHHHHHHH-SEEE CS
                  2-Hacid_dh_C  81 elvsleellaesDivs 96 
                                   +  + ee+l++sD+++
  gi|70606021|ref|YP_254891.1| 101 DSNNAEEMLKDSDYIF 116
                                   56678999****9985 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.048       1      31 [.      24      55 ..      24      89 .. 0.80
   2 ?   -3.7   0.0       5.7   8.6e+03      65      90 ..     180     205 ..     172     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                  EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLak.agadvtlilrsr 31
                                  iai+G+Ga+G++la  La+    ++ li+ + 
  gi|70606021|ref|YP_254891.1| 24 IAIVGCGALGTTLAELLARlGVGKIKLIDADI 55
                                  89****************96656677777655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.7
                                   CCS-ESEEEE-SSGGGHHHHHHHHGG CS
                          ApbA  65 elepidlvivtvKayqteealeeikp 90 
                                    ++  d vi  + ++q++ +l+ +++
  gi|70606021|ref|YP_254891.1| 180 TIGTLDTVISITASLQVQLMLNHLRN 205
                                   56677777777777777777777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   0.00011      0.17       1      24 [.      23      49 ..      23     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                  EEEEETTSHHHHHHHHHHHHTTS...- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaaga...q 24
                                  ki+i+G+G +g +la+ l++ g+   +
  gi|70606021|ref|YP_254891.1| 23 KIAIVGCGALGTTLAELLARLGVgkiK 49
                                  7*********************74331 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   5.2e-05     0.077       2      43 ..      23      65 ..      22     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                  EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgk 43
                                  ki+++G G +G + a +la++g  ++ ++D d   v +l++ +
  gi|70606021|ref|YP_254891.1| 23 KIAIVGCGALGTTLAELLARLGvGKIKLIDADIVEVTNLHRTH 65
                                  8*********************77999*******999998765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.9e-05     0.073       3      32 ..      23      53 ..      21      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.9e-05
                                  EEEEE--SHHHHHHHHHHHHTTHH.EEEEES CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvek 32
                                  +++IVG G  G +la lL++ Gv    l++ 
  gi|70606021|ref|YP_254891.1| 23 KIAIVGCGALGTTLAELLARLGVGkIKLIDA 53
                                  789********************83345555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05     0.097       1      36 [.      23      59 ..      23     119 .. 0.74
   2 ?   -3.4   0.0       5.1   7.6e+03     111     131 ..     188     208 ..     179     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                  EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHH CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagl.eVvlvdiseeale 36
                                  k+a++G+G +G+ +a+++a+ g+ +++l+d +   ++
  gi|70606021|ref|YP_254891.1| 23 KIAIVGCGALGTTLAELLARLGVgKIKLIDADIVEVT 59
                                  69*******************9867899988654444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.1
                                   EE--SSS-HHHHCCCSSSGGG CS
                       3HCDH_N 111 asnTSslsiselaealkrper 131
                                   +s T sl+++ + ++l+++++
  gi|70606021|ref|YP_254891.1| 188 ISITASLQVQLMLNHLRNQAN 208
                                   566888888888888887765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6   0.00024      0.36       1      27 [.      26      53 ..      26      55 .. 0.94
   2 ?   -2.8   0.0       5.3   7.9e+03      10      24 ..      79      95 ..      77      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                  EE--SHHHHHHHHHHHCCTE.EEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllek 27
                                  IvG G+ G ++A lLa+ g+ ++ l+++
  gi|70606021|ref|YP_254891.1| 26 IVGCGALGTTLAELLARLGVgKIKLIDA 53
                                  9******************999999996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.3
                                  HHHHHHHC..CTEEEEE CS
                 NAD_binding_8 10 vaAylLak..agfdvll 24
                                  v+A  ++k   g++v++
  gi|70606021|ref|YP_254891.1| 79 VCAEKIRKinSGIKVEV 95
                                  89999999644888887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00019      0.28       1      33 [.      23      57 ..      23      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                                  EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag 33
                                  +++i+G G  G + A  Lar g   + l++++ i+ 
  gi|70606021|ref|YP_254891.1| 23 KIAIVGCGALGTTLAELLARLGvgkIKLIDAD-IVE 57
                                  59****************999888******99.765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2376.77
//
Query:       gi|70606022|ref|YP_254892.1|  [L=271]
Description: transketolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-32  113.0   0.0    3.9e-32  111.5   0.0    1.6  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    3.5e-11   42.8   0.0    4.3e-09   36.0   0.0    2.1  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    3.6e-05   23.6   0.4     0.0009   19.0   0.4    2.2  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00018   20.6   0.0    0.00025   20.1   0.0    1.2  1  E1_dh            Dehydrogenase E1 component
    0.00047   19.1   0.1     0.0006   18.7   0.1    1.2  1  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   1.1e-35   3.9e-32      21     262 ..      36     261 ..      18     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.1e-35
                                   T-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-SS--T CS
               Transketolase_N  21 ksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsledlksfrqlgsktpGhPel 101
                                   ++ h G++l+ ++i ++lf +  k   +dp  i+RD f+Ls Gha+  lY+++   G+ +s +dl + +++     GhPe 
  gi|70606022|ref|YP_254892.1|  36 QTIHVGSSLSSIEILTTLFYRYVKD-GKDP--INRDWFILSKGHAAPALYAIMSERGL-VSDDDLWKIQDISGMLQGHPE- 111
                                   56799**************999987.5555..9************************9.6679*****************. PP

                                   TTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEE CS
               Transketolase_N 102 ghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDd 182
                                   +  +gv++ tG LGqG++  +g+a+  k+                +yv++gDg   eG   ea+  a   kL++Li++ + 
  gi|70606022|ref|YP_254892.1| 112 TFIPGVDMSTGSLGQGLSFGIGVAQGIKMRGGS----------GRVYVVMGDGEQDEGQVWEAMTHAVARKLDNLIAFIEI 182
                                   789********************9988775443..........469*********************************** PP

                                   SSEETTEEGGGT-.-S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTSTTTTTSGGGTSS- CS
               Transketolase_N 183 nkisidGeteisf.tedvakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygspakagtedvhGap 262
                                   n   +d +t     +e   + ++++gW+v++ +dg+d  ++ + i+ea ++ + P +i  +tv G g p  ++t++   +p
  gi|70606022|ref|YP_254892.1| 183 NGFQLDDSTGSVKpKEFLPDVWRSVGWKVLN-CDGHDFISLISTIDEAIKA-KAPVVIFANTVRGKGFPVIENTKKQRSSP 261
                                   *******99876615667899********98.9***************998.78********************9987776 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.2e-12   4.3e-09      15     182 ..      14     194 ..       8     213 .. 0.82
   2 !    5.1   0.0     0.003        11     245     272 ..     214     241 ..     197     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.2e-12
                DXP_synthase_N  15 keeleelaeelrefliesv.sktggHlasnLgvveLtlalhyvfdt......pkDklvwDvgHqaYv.hKiltgR....kd 83 
                                    ++l+e+ae  r+++i+++   ++ H++s+L+ +e+  +l+y + +      ++D ++   gH a + + i+++R     d
  gi|70606022|ref|YP_254892.1|  14 LNKLKEIAERARRKVIRMLfYDQTIHVGSSLSSIEILTTLFYRYVKdgkdpiNRDWFILSKGHAAPAlYAIMSERglvsDD 94 
                                   46899***********987367899***************998854222222578899999**9964389****9444347 PP

                DXP_synthase_N  84 kfktlrqkgG.lsgfpkrsEseyDafeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelk.k 162
                                   ++ +++   G l+g+p++     D+ ++g  +  +s + G+a+  +++g + +v  v+GDg    G  +ea+ ++ + k +
  gi|70606022|ref|YP_254892.1|  95 DLWKIQDISGmLQGHPETFIPGVDM-STGSLGQGLSFGIGVAQGIKMRGGSGRVYVVMGDGEQDEGQVWEAMTHAVARKlD 174
                                   7888888877457888888888885.7899999*****************************************9666526 PP

                DXP_synthase_N 163 kllvilNdNemsisknvGal 182
                                   +l+  +  N    +++ G++
  gi|70606022|ref|YP_254892.1| 175 NLIAFIEINGFQLDDSTGSV 194
                                   78888888888888888876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.003
                DXP_synthase_N 245 idGhdleelikvleevkklkgpvllhvv 272
                                    dGhd+ +li++++e+ k+k pv++   
  gi|70606022|ref|YP_254892.1| 214 CDGHDFISLISTIDEAIKAKAPVVIFAN 241
                                   7**********************99865 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   2.5e-07    0.0009      20     151 ..     112     238 ..     103     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-07
                                   EEEC..ETTTS-TTTHHHHHHHHHH....HSTTSEEEEEEEHHH..HHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHH CS
                  TPP_enzyme_C  20 sylt..sgglgtmGyglpaAiGakl....akpdrevvaivGDGg..flmilqelatavrrnlpitvvvlnNegygmtggqq 92 
                                   +++   +  +g++G gl+++iG++        + +v++++GDG        +++ +av r+l+ ++  +  +g+     q 
  gi|70606022|ref|YP_254892.1| 112 TFIPgvDMSTGSLGQGLSFGIGVAQgikmRGGSGRVYVVMGDGEqdEGQVWEAMTHAVARKLDNLIAFIEINGF-----QL 187
                                   5555544556666666666666665332133457*********84456678999999*9999655554443333.....22 PP

                                   HHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                  TPP_enzyme_C  93 epfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpali 151
                                   +  +g+   +p+  ++ p     + +++G k++ ++ +d   l  +++ea++ k p++i
  gi|70606022|ref|YP_254892.1| 188 DDSTGSV--KPK--EFLP----DVWRSVGWKVLNCDGHDFISLISTIDEAIKAKAPVVI 238
                                   2222212..122..2333....6777888887777777778888888888877777776 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.9e-08   0.00025     101     226 ..     122     244 ..     103     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.9e-08
                                   SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--E.EEEEEEESEETTEEHHHH-S---GGG CS
                         E1_dh 101 givgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpv.ifvveNNkygisTeaekasaskelad 180
                                   g +g   +++ G+a   k++g    + +++GDg   +G+v+ea++ a + kl   i ++e N++ +  ++   +  + l d
  gi|70606022|ref|YP_254892.1| 122 GSLGQGLSFGIGVAQGIKMRGGSGRVYVVMGDGEQDEGQVWEAMTHAVARKLDNlIAFIEINGFQLDDSTGSVKPKEFLPD 202
                                   55666677889*****************************************987*********99877777777777889 PP

                                   ..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE-- CS
                         E1_dh 181 rargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYR 226
                                   + r vg   l+ dg D++   +   +A++     k p++i + t+R
  gi|70606022|ref|YP_254892.1| 203 VWRSVGWKVLNCDGHDFISLISTIDEAIK----AKAPVVIFANTVR 244
                                   999999999999****9999988777754....4556666666666 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.7e-07    0.0006     120     244 ..     102     226 ..      71     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-07
                         XFP_N 120 fPGGipshvaaetPGsiheGGelGyalsh....ayGavldnPdlivacvvGdGeaetGPlatswhsnkflnPaedGavlPi 196
                                   + G +  h  + +PG     G lG  ls     a G  +   +  v  v+GdGe + G +   w++      ++   ++  
  gi|70606022|ref|YP_254892.1| 102 ISGMLQGHPETFIPGVDMSTGSLGQGLSFgigvAQGIKMRGGSGRVYVVMGDGEQDEGQV---WEAMTHAVARKLDNLIAF 179
                                   567788888889999999999999888861111555668889999*************75...9999988888888999** PP

                         XFP_N 197 lelnGykisnptilarisdeelkklfeGlGyepafvededteslhkll 244
                                   +e+nG+++ + t  +  ++e l ++++ +G+++   +++d  sl  ++
  gi|70606022|ref|YP_254892.1| 180 IEINGFQLDDST-GSVKPKEFLPDVWRSVGWKVLNCDGHDFISLISTI 226
                                   ********9988.467788999****************9988765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1835.13
//
Query:       gi|70606023|ref|YP_254893.1|  [L=312]
Description: transketolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-36  124.6   0.0    5.7e-36  123.9   0.0    1.3  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.1e-30  106.0   0.0    1.4e-29  102.4   0.0    2.1  2  Transketolase_C  Transketolase, C-terminal domain
     0.0005   20.3   0.1     0.0014   18.9   0.1    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
  ------ inclusion threshold ------
       0.17   10.5   0.0       0.24   10.0   0.0    1.1  1  Peptidase_M8     Leishmanolysin


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.0   1.3e-39   5.7e-36       4     172 ..       7     166 ..       5     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 1.3e-39
                                   EHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHH CS
                  Transket_pyr   4 awrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdF 84 
                                   ++r+ +++ l e++++ +++v+i+aDv+ ++    ++ ++++   r++++gisEq ++ fa+G++++g  +++v+  F++F
  gi|70606023|ref|YP_254893.1|   7 SMRDTFGKLLVEMGEKLKDIVVITADVGDSSRASYFKEKFPD---RYFNVGISEQDMIDFAAGLSATG--FKPVVVDFAMF 82 
                                   7999**************************************...***********************..9********** PP

                                   HGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.S CS
                  Transket_pyr  85 angAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrk 164
                                   ++    +a+++ir+ +a+++l v+ vvt+ +++  +dG +hq +e+++++r +p++kv+ P+dpa++++ +   ++ e r+
  gi|70606023|ref|YP_254893.1|  83 LM----RAWEQIRNAVARMNLDVKfVVTHSGYSDSGDGSSHQCLEDISLMRVLPNMKVIIPADPADIRRSFPVIME-ELRG 158
                                   **....***************************************************************9999999.6788 PP

                                   EEEEEE-S CS
                  Transket_pyr 165 Pvvlrlpk 172
                                   P++ r  +
  gi|70606023|ref|YP_254893.1| 159 PLYYRVGR 166
                                   98877655 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.062   2.8e+02      17      62 ..      53      98 ..      51     118 .. 0.79
   2 !  102.4   0.0   3.2e-33   1.4e-29       1     124 []     183     303 ..     183     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.062
                                  ETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHS CS
               Transketolase_C 17 yGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktg 62
                                  +G   + +++ a+ L++ g +  Vvd   +    +e i+++v++ +
  gi|70606023|ref|YP_254893.1| 53 VGISEQDMIDFAAGLSATGFKPVVVDFAMFLMRAWEQIRNAVARMN 98
                                  67777788899999************99999999999998888765 PP

  == domain 2  score: 102.4 bits;  conditional E-value: 3.2e-33
                                   TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHH CS
               Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigseva 81 
                                   gka +l+eg+dv++ + G  +  al+AaeeLek+gisa+V++l ++kp+D++ti+  ++ktgr+v++ee+++ gGigs+v+
  gi|70606023|ref|YP_254893.1| 183 GKAYVLKEGDDVAIMGAGVVLWDALRAAEELEKKGISASVINLLSIKPIDEQTIEYYARKTGRIVTIEEHSIYGGIGSAVS 263
                                   89******************************************************************************* PP

                                   HHHHHCCCTTCSSEEEEEEE-SSSSSS.GHHHHHHHTT-SHHHH CS
               Transketolase_C  82 aalaeeafdgldapvkrvggpdviepg.saeelekafgldaeki 124
                                   +++ +    + ++p++ vg+  +++++ s+ +l++++g++ ++i
  gi|70606023|ref|YP_254893.1| 264 EVVVK----RYPVPMRFVGATGFGRSArSQRDLLDFYGINYKSI 303
                                   *****....8899999999998866651556********98876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     3e-07    0.0014       2      90 ..     193     278 ..     192     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3e-07
                                   SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGT CS
                       PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkksk 82 
                                   +v+i++ G v  +a +a++el ++gi++ ++ l ++ P  e+ ++ +++k+ ++v+++    +g  G  v+ev  + +   
  gi|70606023|ref|YP_254893.1| 193 DVAIMGAGVVLWDALRAAEELEKKGISASVINLLSIKPIDEQTIEYYARKTGRIVTIEEHSIYGGIGSAVSEVVVKRY--- 270
                                   899*********************************************************999999999999866544... PP

                                   SEEEEEE- CS
                       PFOR_II  83 vkvvnfva 90 
                                   + +++fv+
  gi|70606023|ref|YP_254893.1| 271 PVPMRFVG 278
                                   34555555 PP

>> Peptidase_M8  Leishmanolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   5.5e-05      0.24     151     209 ..      44     106 ..      18     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.5e-05
                  Peptidase_M8 151 fkvPekhvtvGvsdaDlvlyvasvPse...egvlawavtC.qlfsdgrpvvgvinipaasiss 209
                                    k P+++  vG+s+ D++ ++a + +    + v+ +a++   + ++ r +v+ +n++ + +++
  gi|70606023|ref|YP_254893.1|  44 EKFPDRYFNVGISEQDMIDFAAGLSATgfkPVVVDFAMFLmRAWEQIRNAVARMNLDVKFVVT 106
                                   467*****************998877655578999998751678999**********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1630.99
//
Query:       gi|70606024|ref|YP_254894.1|  [L=341]
Description: chorismate mutase/prephenate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-20   71.1   0.0    1.5e-19   70.1   0.0    1.5  1  PDH              Prephenate dehydrogenase
    8.6e-15   54.8   0.1    2.4e-14   53.4   0.1    1.8  1  CM_2             Chorismate mutase type II
    6.7e-10   39.4   0.0    1.5e-09   38.3   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.2e-06   27.8   0.0    6.2e-06   26.3   0.0    1.8  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00013   21.5   0.0     0.0003   20.4   0.0    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    0.00022   21.2   0.0     0.0012   18.8   0.0    2.1  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00097   18.5   0.0     0.0018   17.7   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.029   14.6   0.0      0.076   13.2   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.03   14.6   0.0       0.15   12.3   0.0    2.2  2  TrkA_N           TrkA-N domain
       0.11   12.8   0.0        0.2   11.9   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.12   12.0   0.0       0.22   11.1   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.14   13.0   0.0       0.33   11.8   0.0    1.8  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   9.8e-23   1.5e-19       8     231 ..     113     326 ..     106     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 9.8e-23
                                   TT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHH CS
                           PDH   8 kgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvre 88 
                                   +g +v ++g+d+ + ++ a  e   v+  ++  +a+   + v+l++ +  +   ++ + +   ++ +++D+ s+K +  r+
  gi|70606024|ref|YP_254894.1| 113 SGHNVVITGRDKRKAERLAN-EFKFVYMEEK--SALDWSEYVILSISPSGLD-YAESVLK-YAKEKVVMDIFSTKSNTFRK 188
                                   6889*********9999888.9999999999..5999*********999875.5666666.58899*************** PP

                                   HHHHCC...GCEEEEEES---S-SSGGG--TTTT.TT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHH CS
                           PDH  89 leellke.gksfvgghPmaGteksGvdaareelf.enavviLtPtektdkealekvkelleevgarvilmspeeHDrvvav 167
                                   l+ l ++   +++++hP++G+           l+  ++  +  P++k+   + + v+e+++++g + +l++peeHD+v+a+
  gi|70606024|ref|YP_254894.1| 189 LQTLSEQfSFEYISTHPLFGP----------ILYpVGERIAVIPSQKST--RTQEVIEFWRKCGLVPVLTTPEEHDKVMAI 257
                                   *99887634689*********..........455357777888999765..7889************************** PP

                                   HTHHHHHHHHHHHHHHH...CHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHHHHHHH CS
                           PDH 168 vshlphvvaialaatlk...ekkndekeirklasggfrdvt....RiaksnPelwadilleNkeavleald 231
                                   v++l h+ +  l   ++   ++ +  ++i +l   +fr ++    Ri +  P +  +i++ N +   +++d
  gi|70606024|ref|YP_254894.1| 258 VQVLAHFYMLGLLRSSNtlkKELEVGNKIDELQTTNFREISkildRINSLLPVIL-EIQKDNPY-AHKVRD 326
                                   **********99875553336666667899***********77777777777654.68888877.555555 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   1.6e-17   2.4e-14       1      74 [.       8      85 ..       8      86 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.6e-17
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH.HH...S-HHHHHHHHHHHHHHHHHHH CS
                          CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee.ga...ldeeaierifreiisasralq 74
                                  RkeI+eiD++il+L+a+R++++  +ge+K + g++v d++Re+ v e  +e g    ++e+ + ++++++is s+  q
  gi|70606024|ref|YP_254894.1|  8 RKEIEEIDSQILNLIAKRLQVSSMIGEIKGKMGFNVTDEKREEYVKEYWTEkGRrlgIPESLVSSVLTNLISYSKMFQ 85
                                  9**************************************************633678*****************9877 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   9.9e-13   1.5e-09       1      94 [.      93     178 ..      93     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 9.9e-13
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                   ++ iiG+G m+++l s +  +g   h++v++  r++ kae la+e++     ++ + a++ ++ v+l++ p+ ++ + s l
  gi|70606024|ref|YP_254894.1|  93 RVTIIGYGGMARSLSSLFHLSG---HNVVIT-GRDKRKAERLANEFK--FVYMEEKSALDWSEYVILSISPSGLDYAESVL 167
                                   689*******************...****55.*************97..777789****************9998887777 PP

                                   GHHHHTTSEEEEE CS
                 F420_oxidored  82 akdalkgklvisv 94 
                                     +  k+k+v ++
  gi|70606024|ref|YP_254894.1| 168 --KYAKEKVVMDI 178
                                   ..77899999998 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.1e-09   6.2e-06       7      74 ..      86     146 ..      81     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.1e-09
                                   HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH CS
                  Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkella 74 
                                   +++ k+++v++iG G ma+ + + ++ +g + vv+++R+ ++a++la+e+k + +e       k++l+
  gi|70606024|ref|YP_254894.1|  86 VKDSKKRRVTIIGYGGMARSLSSLFHLSGHN-VVITGRDKRKAERLANEFKFVYME------EKSALD 146
                                   447899**************99999988887.******************766322......233444 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     2e-07    0.0003       3      68 ..      90     155 ..      89     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                                   HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S CS
                          IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmili 68 
                                   k++++++iGyG  +++ +  ++ sg +vv++ r+++k  + A+e  f  ++ + a ++++ v++ i
  gi|70606024|ref|YP_254894.1|  90 KKRRVTIIGYGGMARSLSSLFHLSGHNVVITGRDKRKAERLANEFKFVYMEEKSALDWSEYVILSI 155
                                   5789********************************************************998755 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.1e-07    0.0012       2      51 ..      94     143 ..      93     198 .. 0.69
   2 ?    0.4   0.0      0.35   5.2e+02     131     176 ..     199     245 ..     161     249 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.1e-07
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                   v++iG G m +++ ++f  +g++Vv++ ++++++e+ +++ +  + + ++
  gi|70606024|ref|YP_254894.1|  94 VTIIGYGGMARSLSSLFHLSGHNVVITGRDKRKAERLANEFKFVYMEEKS 143
                                   9***********************************99998865555433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
                                   GEEEEEE-SSTTT--EEEEEE-TT--HHH.HHHHHHHHHHTT-EEEE CS
                       3HCDH_N 131 rviglHFfnPpplmkLvEvvrgekTseet.vatvvelakkigktpvv 176
                                   ++i +H++  p l ++ E ++   ++++t +++v e+ +k g +pv 
  gi|70606024|ref|YP_254894.1| 199 EYISTHPLFGPILYPVGERIAVIPSQKSTrTQEVIEFWRKCGLVPVL 245
                                   36777777777777776655444444443267888999999988886 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.2e-06    0.0018      27      99 ..      82     155 ..      71     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                                   CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhl 99 
                                   k ++ k+ ++++v iiG+G +++++  +++  g +v+++ r k+k e  ++e ++ +++ + +l +s++v+l +
  gi|70606024|ref|YP_254894.1|  82 KMFQVKDSKKRRVTIIGYGGMARSLSSLFHLSGHNVVITGRDKRKAErLANEFKFVYMEEKSALDWSEYVILSI 155
                                   567788999********************************999888556666778888899999**9999976 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-05     0.076       2     106 ..      94     195 ..      93     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82 
                                   + +iG G M +++ + +  +g++v++  r+k k+e+l++e   ++ + +++++  + vi+ ++ +    +  e++l+ ++k
  gi|70606024|ref|YP_254894.1|  94 VTIIGYGGMARSLSSLFHLSGHNVVITGRDKRKAERLANEFKFVYMEEKSALDWSEYVILSISPS--GLDYAESVLK-YAK 171
                                   789***********************************998777777778888888888887542..2333444443.456 PP

                                   T-EEEE-S---HHHHHHHHHHHHH CS
                 NAD_binding_2  83 gdilidgstsspedtrelakelke 106
                                   +++++d  +++ ++ r+l++  ++
  gi|70606024|ref|YP_254894.1| 172 EKVVMDIFSTKSNTFRKLQTLSEQ 195
                                   667777666666666666655555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.15       1      42 [.      94     136 ..      94     146 .. 0.85
   2 ?   -1.8   0.0       2.5   3.7e+03      80     110 ..     298     329 ..     295     332 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.S CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.l 42 
                                   + iiG+G ++rsl   ++  g+ +vv+  +d++++e+l++e+ +
  gi|70606024|ref|YP_254894.1|  94 VTIIGYGGMARSLSSLFHLsGH-NVVITGRDKRKAERLANEFkF 136
                                   579****************666.7**************998733 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                                   HHHHHHHTSSSEEEEEESSGG.GHHHHHHHTT CS
                        TrkA_N  80 vllakelnpkkkiiaraqdpe.haellkklga 110
                                   ++++  +n+ +++i ++q++  +a+++++lg 
  gi|70606024|ref|YP_254894.1| 298 SKILDRINSLLPVILEIQKDNpYAHKVRDLGM 329
                                   66777788889999998876526888888875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013       0.2       1      44 [.      94     134 ..      94     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka 44 
                                   v iiG+G++++++  l + +++   ++++ +r+k+k+e+la++ 
  gi|70606024|ref|YP_254894.1|  94 VTIIGYGGMARSLSSLFHLSGH---NVVITGRDKRKAERLANEF 134
                                   679********99999999987...6*************99543 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.22       1      40 [.      94     134 ..      94     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHC CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknG 40 
                                   ++i+G G++ + l    +  g++v++ +r++ ++e+l ++ 
  gi|70606024|ref|YP_254894.1|  94 VTIIGYGGMARSLSSLFHLSGHNVVITGRDKrKAERLANEF 134
                                   68*****************************8888876654 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.33       2      88 ..      93     173 ..      92     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHH CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaa 82 
                                   rv iiG+G +++    +l +  ++++vv +  +d+ +ae++a++f++  +++ ++l  ++    +++ + + ++ ++a+ +
  gi|70606024|ref|YP_254894.1|  93 RVTIIGYGGMARSLS-SLFHL-SGHNVV-ITGRDKRKAERLANEFKFVYMEEKSALDWSE----YVILSISPSGLDYAESV 166
                                   899*******99997.77777.677777.99*****************999999998855....55555555666666666 PP

                                   HHTT-.E CS
                  GFO_IDH_MocA  83 leagk.h 88 
                                   l+  k +
  gi|70606024|ref|YP_254894.1| 167 LKYAKeK 173
                                   6666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 1974.66
//
Query:       gi|70606025|ref|YP_254895.1|  [L=330]
Description: 3-deoxy-7-phosphoheptulonate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-72  241.3   0.0    1.1e-71  240.9   0.0    1.0  1  DAHP_synth_1  DAHP synthetase I family
      6e-08   32.4   0.0     0.0063   16.0   0.0    2.8  3  NeuB          NeuB family


Domain annotation for each model (and alignments):
>> DAHP_synth_1  DAHP synthetase I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.9   0.0   1.2e-75   1.1e-71       9     260 ..      79     313 ..      55     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 240.9 bits;  conditional E-value: 1.2e-75
                                   HHCCCTTTCSEEEEEEESC-S-HHHHHHHHHHHHHHHHHHTTTEEEEEESSSC-S.SSTTS-SHTTHHHTHHHHHHHHHHH CS
                  DAHP_synth_1   9 adiliGkddrllviaGPCsiedpeaaleyAerlkklgeklkddleiimrayfeKpRrstvgfkGlindpdlkilsrikkel 89 
                                   +d+ iG+d  l+v aGPC++ed+e++l++A++ k++g+k      ++++a   KpR+s+++f+Gl++ + l+il+++ +++
  gi|70606025|ref|YP_254895.1|  79 KDVEIGGDR-LVVAAGPCAVEDEEQVLTVAKAAKRAGAK-----LLRGGAL--KPRTSPYSFQGLGERG-LEILRKVGDQV 150
                                   588999775.8****************************.....99*****..*************999.*********** PP

                                   T-EEEEEESSCCTHHHHHHHESEEEE-CTCTTBHHHHHHHHTTSSEEEEEE-TTHHHHHHHHHHHHHHHTTEEE--EEEEE CS
                  DAHP_synth_1  90 glpiatevldpisvqyladvvdiiqiGArttesqdllelasglskpvglKngtdvaidemkaaaekilflgvetkgiilce 170
                                   glp+++e++d+++++++ +++d++qiGAr+ +++dll++a+++ +pv+lK+g+ +++de+  aae++l +g  + ++ lce
  gi|70606025|ref|YP_254895.1| 151 GLPVVSEIMDTRQIDMFKKYADMLQIGARNGQNFDLLKEAGKSGMPVLLKRGLGNTVDEWLLAAEYLLLEG--NGNVVLCE 229
                                   ***********************************************************************..7******* PP

                                   EEEEESTSSSSSCHCHHHHHHHHHHCTSS-EEEESCHHHTTCGGGGHHHHHHHHHHHHHTTESEEEEEBBSSCCC-SSTGG CS
                  DAHP_synth_1 171 rglrggkktnrdvedvaavkilkeetgklpvmvDvsHansrkdykrqkkvlklakaaiaaGiaGvmiEshlnpgkalsdgk 251
                                   rg+r+++k++r + d+  + ++k +t +lp+  D+sH +++++      v +la aa+aaG++ + iE+h+np+kalsd++
  gi|70606025|ref|YP_254895.1| 230 RGIRTFEKATRFTMDIGGMIAAKLQT-HLPICADPSHPAGKRE-----LVHSLALAAVAAGADMLLIEVHPNPEKALSDSE 304
                                   ***********************999.9***************.....********************************* PP

                                   GGBBCTCBH CS
                  DAHP_synth_1 252 qalkygkse 260
                                   q+l+++++e
  gi|70606025|ref|YP_254895.1| 305 QQLTPDSFE 313
                                   ****97665 PP

>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.04   3.6e+02      97     146 ..      66     118 ..       9     126 .. 0.80
   2 !   16.0   0.0   7.1e-07    0.0063      55     146 ..     137     228 ..     127     230 .. 0.88
   3 !   12.2   0.0     1e-05     0.092     186     239 ..     276     329 ..     270     330 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.04
                                   GGGTT-HHHHHHHHT...T-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEE CS
                          NeuB  97 Sgeltnlpllekiak...tgkpvilStGmatleeieeavevlreagaeklvll 146
                                   S e  + p + k+ +    g  ++++ G + +e+ e++++v+++a+++   ll
  gi|70606025|ref|YP_254895.1|  66 SNEWKKDPTIVKVKDveiGGDRLVVAAGPCAVEDEEQVLTVAKAAKRAGAKLL 118
                                   55666666665555522246789999999999999999999988877766665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.1e-07
                                   HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT-.-HHHHHHHHHH CS
                          NeuB  55 eeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSgeltnlpllekiaktgkpvilStGma.tleeieeavev 134
                                   e+  + l +  ++ g+ ++s  +d++++d+ +++  +++ i++ + +n++ll+++ k g pv+l  G+  t++e   a e+
  gi|70606025|ref|YP_254895.1| 137 ERGLEILRKVGDQVGLPVVSEIMDTRQIDMFKKY-ADMLQIGARNGQNFDLLKEAGKSGMPVLLKRGLGnTVDEWLLAAEY 216
                                   55667789999********************877.9*******************************96267888889999 PP

                                   H.HHHT--EEEE CS
                          NeuB 135 lreagaeklvll 146
                                   l  +g+ ++vl 
  gi|70606025|ref|YP_254895.1| 217 LLLEGNGNVVLC 228
                                   988888888875 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 1e-05
                                   HHHHHHHHT--E..EEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS-- CS
                          NeuB 186 vaiaAvalGAkv..iEkHftldrnlegpDhkaSlepeelkelveairnvekalgeg 239
                                   +a+aAva GA++  iE H   +++l+  D++  l+p+ ++ l+++ir++ ++lg++
  gi|70606025|ref|YP_254895.1| 276 LALAAVAAGADMllIEVHPNPEKALS--DSEQQLTPDSFELLMNRIRALANVLGRK 329
                                   689*******9655899999998775..777789*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2076.06
//
Query:       gi|70606026|ref|YP_254896.1|  [L=353]
Description: 3-dehydroquinate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-91  304.0   0.0    8.6e-91  303.7   0.0    1.1  1  DHQ_synthase  3-dehydroquinate synthase
    5.1e-06   26.4   0.0      1e-05   25.4   0.0    1.6  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    7.8e-06   24.9   0.0    0.00019   20.3   0.0    2.3  2  Fe-ADH        Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.7   0.0   1.4e-94   8.6e-91       3     261 ..      58     318 ..      56     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.7 bits;  conditional E-value: 1.4e-94
                                   EE-SSGGGCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEET CS
                  DHQ_synthase   3 vvpdgeksKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlp 83 
                                    ++dge+ K+++   ++l++l++ +++R +++ia+GGG v+D +Gf+A+ty+RG+++++vPttll++vD+++GgK+++n+ 
  gi|70606026|ref|YP_254896.1|  58 PIKDGEEAKDIQYSLELLKVLFDGGFDRGDYVIAIGGGSVTDTVGFIASTYMRGLNLINVPTTLLGMVDAGIGGKNGVNFG 138
                                   699****************************************************************************** PP

                                   TEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHH CS
                  DHQ_synthase  84 lgKNliGafaqPkavlidlevLktLperelraGlaEviKyalikdeelfelleenaeallkeeeeealeeliarsievkae 164
                                   + KN+iG+f+qP+a+++dl++L +Lp++e+r+GlaEviKy+l+ d+el++ l  n++++l++ ++e+le++++rsi+ k +
  gi|70606026|ref|YP_254896.1| 139 RIKNIIGTFYQPRAIIADLRFLISLPSEEVRKGLAEVIKYGLVLDKELYDFLALNKNSVLSK-DPESLEYVVQRSIQDKLS 218
                                   ***********************************************************995.9***************** PP

                                   HHHHCCTT.TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTT CS
                  DHQ_synthase 165 vveeDeke.kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslke 244
                                   vv+eDe+e kg+r +Ln+GHtigHaiEa +g+ ++ HG a+++Gmv++a+++e++g+ ++  ve+++++l++++lp+s++e
  gi|70606026|ref|YP_254896.1| 219 VVKEDEREtKGVRIVLNFGHTIGHAIEAGSGF-SIPHGYAISVGMVCEAKIAEEMGYSEEGVVEDTVWILSHYNLPISIDE 298
                                   ********99**********************.**********************************************99 PP

                                   T....-HHHHHHHHTTCTTX CS
                  DHQ_synthase 245 l...leveellealkkDkkv 261
                                   l   ++++e+l al+kDkkv
  gi|70606026|ref|YP_254896.1| 299 LsskIDLKEALFALSKDKKV 318
                                   98888999***********8 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.7e-09     1e-05      51     210 ..      58     234 ..      18     258 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-09
                      Fe-ADH_2  51 vveeveeeadleeveklveal...reketdlvvavGgGtiiDiakyvsak..lnvpyvsvpTaa..SvD.Gfaspgaslvv 123
                                    +++ ee++d++   +l+++l     ++ d v+a+GgG++ D++ +++++  ++++++ vpT++   vD G+   +     
  gi|70606026|ref|YP_254896.1|  58 PIKDGEEAKDIQYSLELLKVLfdgGFDRGDYVIAIGGGSVTDTVGFIASTymRGLNLINVPTTLlgMVDaGIGGKNGV-NF 137
                                   455667777777777777777554468999*****************96522899*******9733344255544433.33 PP

                      Fe-ADH_2 124 dgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklan.........evse....plaklsaamvqe 191
                                      k  + +   P a+iaDl +l   P++ ++ G+++++ ky  + d +l +                 +l     +++q+
  gi|70606026|ref|YP_254896.1| 138 GRIKNIIGTFYQPRAIIADLRFLISLPSEEVRKGLAEVI-KYGLVLDKELYDflalnknsvL--SkdpeSLEYVVQRSIQD 215
                                   334444466778*************************99.8888999988887755443321..02222444445555555 PP

                      Fe-ADH_2 192 aaeklvedkketealeell 210
                                   +++ + ed++et+ ++ +l
  gi|70606026|ref|YP_254896.1| 216 KLSVVKEDERETKGVRIVL 234
                                   5555555666666655555 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.3e-08   0.00019      82     178 ..      86     165 ..      16     176 .. 0.74
   2 !    2.4   0.0    0.0089        53     251     278 ..     237     262 ..     227     320 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.3e-08
                                   --EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS- CS
                        Fe-ADH  82 advviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpell 162
                                    d+via+GGGsv Dt   ia ++ +                +l li +PTt   G    ++      + g+ + i   +  
  gi|70606026|ref|YP_254896.1|  86 GDYVIAIGGGSVTDTVGFIASTYMR----------------GLNLINVPTTL-LGMVDAGIGGKNGVNFGRIKNIIGTFYQ 149
                                   488********************95................599******98.5533333333332333566666666777 PP

                                   -SEEEEEHHHHHHS-H CS
                        Fe-ADH 163 PdlaivDpeltltlPk 178
                                   P+++i D +++++lP+
  gi|70606026|ref|YP_254896.1| 150 PRAIIADLRFLISLPS 165
                                   7777777777777776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.0089
                                   ---HHHHHHHHHHC.CGGGGGS-HHHHH CS
                        Fe-ADH 251 glgavHalahalgalfgiphglanaill 278
                                   g ++ Ha++ + g  f iphg+a+++ +
  gi|70606026|ref|YP_254896.1| 237 GHTIGHAIEAGSG--FSIPHGYAISVGM 262
                                   3344555554443..69****9988743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2464.52
//
Query:       gi|70606027|ref|YP_254897.1|  [L=263]
Description: shikimate/quinate 5-dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-24   85.4   0.0    4.4e-24   84.5   0.0    1.5  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    3.2e-06   27.3   0.0    5.3e-06   26.5   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00038   20.2   0.0    0.00058   19.6   0.0    1.3  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
     0.0012   19.2   0.0     0.0039   17.4   0.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0013   18.4   0.0      0.002   17.8   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0021   17.4   0.0     0.0031   16.8   0.0    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0024   18.4   0.2     0.0091   16.6   0.0    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.03   14.8   0.0      0.056   13.9   0.0    1.4  1  NAD_binding_7    Putative NAD(P)-binding
      0.032   13.7   0.0      0.054   13.0   0.0    1.3  1  adh_short        short chain dehydrogenase
       0.19   11.1   0.0       0.33   10.3   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   2.4e-27   4.4e-24       1      83 []      13      94 ..      13      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 2.4e-27
                                  EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
                Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                                  v+G++i + lSPaihn+af++lg+n++y  f+v  d++++++ +l +  ++GlnvTiP+Ke+v+++l  +seeA+ igAvNti
  gi|70606027|ref|YP_254897.1| 13 VLGENIPYTLSPAIHNYAFQRLGINAVYLRFDVRRDKFHSIIIGLLN-IASGLNVTIPYKEDVVKYLYGVSEEARVIGAVNTI 94
                                  79********************************************5.99********************************8 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.9e-09   5.3e-06      16      88 ..     123     190 ..     110     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.9e-09
                                   EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                  Shikimate_DH  16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                   ++ GaG  ++  + +Ll+ g++ v v+NR+lera++l +++k+  + ++ +++     +  d+++ at  +++
  gi|70606027|ref|YP_254897.1| 123 TVFGAGGAGRASIYALLKLGCE-VYVINRSLERAQSLEKDFKEFGYDIKIISSC----KPGDIIVNATPNSSY 190
                                   689******************9.******************9985555555444....578888888876665 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.3e-07   0.00058       1      20 [.     227     246 ..     227     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                                   HHHHHHHHHHHHHHHHHS-- CS
                         SDH_C   1 GLgMLveQgaeqFelWTGre 20 
                                   GL+ Lv Q+ e+ ++W+G+ 
  gi|70606027|ref|YP_254897.1| 227 GLEILVRQAMEAERIWFGKS 246
                                   9*****************96 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.2e-06    0.0039       3      98 ..     124     226 ..     122     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                   EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..........TTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
               Sacchrp_dh_NADP   3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..........lgvrfeaialdaenyeavLaallkegdlv 73 
                                   ++GaG+ G+a +  l++ +    e+ v+ rs+e+++ l ++           ++ +   i ++a   ++ +   + +g+lv
  gi|70606027|ref|YP_254897.1| 124 VFGAGGAGRASIYALLKLGC---EVYVINRSLERAQSLEKDFkefgydikiiSSCKPGDIIVNATPNSSYVPDECIKGKLV 201
                                   89***************985...7**********99998777777877777777777777777777777777778888888 PP

                                   EE-SSGGGHHHHHHHHHHHT-EEEE CS
               Sacchrp_dh_NADP  74 vnlsppissldvlkaCietgvhyvd 98 
                                   v+l+ +    +++  + +tg++ ++
  gi|70606027|ref|YP_254897.1| 202 VDLVYNPVKTPLILKAEKTGIRSIN 226
                                   8888888777777777777777776 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06     0.002       2      52 ..     123     182 ..     122     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                   EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHH...H.HHHHCEEEEETT....CEEEE CS
                          ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rle...a.lkknGlrltseg....geeil 52 
                                   ++ GaG+ G+   + L k g++v++i+rs  r++   + +k+ G+++++ +    g+ i+
  gi|70606027|ref|YP_254897.1| 123 TVFGAGGAGRASIYALLKLGCEVYVINRSLeRAQsleKdFKEFGYDIKIISsckpGDIIV 182
                                   689************************986666511144666677766665555555555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06    0.0031      28      70 ..     119     165 ..     115     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH....T CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles....l 70 
                                   p+  +v+G+G aG ++i +  +lg +V+v++ + +r++ le+    +
  gi|70606027|ref|YP_254897.1| 119 PSICTVFGAGGAGRASIYALLKLGCEVYVINRSLERAQSLEKdfkeF 165
                                   66679***********************************9974433 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       3.4   6.1e+03       4      15 ..      54      65 ..      53      69 .. 0.87
   2 !   16.6   0.0   5.1e-06    0.0091       4      73 ..     124     189 ..     121     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                                  EETTSHHHHHHH CS
                 F420_oxidored  4 iiGaGnmgeala 15
                                  iiG  n++++l+
  gi|70606027|ref|YP_254897.1| 54 IIGLLNIASGLN 65
                                  78******9986 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.1e-06
                                   EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE-S-HHH CS
                 F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvlavkped 73 
                                   + GaG  g+a +  ll+ g    e++v+ +r+ e+a++l+++++     +k+        ++  d++v a + + 
  gi|70606027|ref|YP_254897.1| 124 VFGAGGAGRASIYALLKLG---CEVYVI-NRSLERAQSLEKDFKefgydIKI-----ISSCKPGDIIVNATPNSS 189
                                   67*****************...****99.***********999865544444.....447778888887777554 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05     0.056      10      71 ..     122     187 ..     118     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                 NAD_binding_7  10 vlvvGgGevAarkvrklleagakvtvvapevkeele..elvklaeeel....ekdlegadlviaatdd 71 
                                   + v+G+G  +   ++ ll+ g++v v+   ++++ +  +  +++e  +     ++++  d+++ at++
  gi|70606027|ref|YP_254897.1| 122 CTVFGAGGAGRASIYALLKLGCEVYVINRSLERAQSleK--DFKEFGYdikiISSCKPGDIIVNATPN 187
                                   99*************************999522222111..122222211113335556666666665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     3e-05     0.054       7      52 ..     126     170 ..     120     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                   STTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEE CS
                     adh_short   7 GassGIGraiakelakeGakvvvvdrseekleevakelkeegakal 52 
                                   G ++G Gra  ++l+k G++v+v++rs e+++ + k +ke g ++ 
  gi|70606027|ref|YP_254897.1| 126 G-AGGAGRASIYALLKLGCEVYVINRSLERAQSLEKDFKEFGYDIK 170
                                   4.56******************************999998766555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00018      0.33      40     100 ..     123     186 ..     112     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                                   EEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  40 GiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelv.sleellaesDivslhlp 100
                                    ++G+G  G+a +  l ++g++v++++rs ++ +  e++ +++ ++ ++   ++  Di+++++p
  gi|70606027|ref|YP_254897.1| 123 TVFGAGGAGRASIYALLKLGCEVYVINRSLERAQslEKDFKEFGYDiKIISSCKPGDIIVNATP 186
                                   589**************************99887554444444444455556666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1718.20
//
Query:       gi|70606028|ref|YP_254898.1|  [L=391]
Description: chorismate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.5e-125  418.2   0.0   1.8e-125  418.0   0.0    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.0   0.0  9.8e-130  1.8e-125       1     327 []      10     355 ..      10     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 418.0 bits;  conditional E-value: 9.8e-130
                                   SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS CS
               Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdq 81 
                                   +r+ttfGeShg+++g+++dgvpagl +++edi+ eL+ Rrpg+ ++ + r+EkDe ei+sGv++g+t+G+p++++i+N+d+
  gi|70606028|ref|YP_254898.1|  10 FRITTFGESHGPMIGVIVDGVPAGLYISKEDIEFELSFRRPGK-QFVSGRREKDEPEIVSGVYNGRTTGAPLTIIIRNNDV 89 
                                   89****************************************8.8************************************ PP

                                   -..SSSSSTSBE-TTSTCHHHHHHC-S...STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE....... CS
               Chorismate_synt  82 rskdyeeikevpRpgHADltyalkYgir..dlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei....... 153
                                    s+ yee+k++pRpgHADl y +kYg +  d+rgggrsSaReTa+rvaa+a+akklL  +++ i a+++s+g +       
  gi|70606028|ref|YP_254898.1|  90 ISSLYEEVKHKPRPGHADLPYIMKYGYEnwDYRGGGRSSARETASRVAASAIAKKLLMLTDTVIGAHLKSLGPVeldedvs 170
                                   *************************54445******************************************777777777 PP

                                   ...CHH..HHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEET CS
               Chorismate_synt 154 ...eke..aenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgveiG 229
                                           + +pvr+ ++  +e++ee+i++a  egds Ggv ev++ +vp+GlGepvfdkl+++Lakal+sipAv g+e+G
  gi|70606028|ref|YP_254898.1| 171 freI-FcsKYSPVRASKKWLEEKYEELIKQATVEGDSWGGVAEVIADNVPIGLGEPVFDKLKSDLAKALLSIPAVVGFEYG 250
                                   7641.243567********************************************************************** PP

                                   TGGGGGGSBHHHHS--EEEE.......SS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S- CS
               Chorismate_synt 230 sGfeaaelkGseanDeivlr.......ktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletkeevelevkgrhD 303
                                    Gf+a+++kGseanDeiv++       + n+aGGi+GG+snGe++v+r+a+Kp++si+k+qktvdl+t+ee +++v grhD
  gi|70606028|ref|YP_254898.1| 251 LGFKASKMKGSEANDEIVIKdngklgwRYNKAGGILGGLSNGEKLVLRCAFKPTSSIRKPQKTVDLRTSEESTIRVIGRHD 331
                                   ******************556667788****************************************************** PP

                                   S-THHHHHHHHHHHHHHHHHHHHH CS
               Chorismate_synt 304 pcvvpravvvveamvalvladall 327
                                   p v++r v v+eamvalvl+d++l
  gi|70606028|ref|YP_254898.1| 332 PAVAIRGVSVAEAMVALVLVDHAL 355
                                   *********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2788.16
//
Query:       gi|70606029|ref|YP_254899.1|  [L=268]
Description: shikimate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-08   35.1   0.0    2.3e-08   34.2   0.0    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00091   19.5   0.0     0.0019   18.5   0.0    1.5  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.5e-12   2.3e-08       2      66 .]      69     135 ..      68     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.5e-12
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.HHHHHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallgls.leeaklaleaerlaqggngsggDv.aasvyGg 66 
                                    +i+seiP++ GL SS+A+++al+a + + + ++ ++ +kl++    +a++  ++  D+ + s+yGg
  gi|70606029|ref|YP_254899.1|  69 AEINSEIPPKGGLKSSSAVSTALIAEIMRRYKIKdVDPPKLSAILSLKAGVSYTGAYDDaTSSYYGG 135
                                   689**************************997663355***********999999999945566665 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.1e-07    0.0019      41      83 ..     215     254 ..     210     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
                GHMP_kinases_C  41 ealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                   + +++ Gal++++sG   Gp++fa++ ++ +  +v++ +++++
  gi|70606029|ref|YP_254899.1| 215 KQALKGGALASGISGN--GPSIFAVT-KPGDEGKVIDIFSNFG 254
                                   6677889*********..*******9.7777788888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1691.95
//
Query:       gi|70606030|ref|YP_254900.1|  [L=358]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-64  218.8   0.0    1.2e-64  218.6   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.6   0.0   6.6e-69   1.2e-64      75     416 ..      18     347 ..       2     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 218.6 bits;  conditional E-value: 6.6e-69
                                   ..--EE-HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS- CS
                 EPSP_synthase  75 ggsfeapeelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lkl 154
                                   g+++ +p  + l++g s t+lr+++++l+  +gevvL+G+es+r RPi+ +++aL     +i  +++  ++p++  g lk 
  gi|70606030|ref|YP_254900.1|  18 GEKLRVP--QYLNFGGSATTLRMMIPILSVLGGEVVLDGNESLRRRPITAIVEALAG---QIRFSSN--YLPVTMTGkLKE 91 
                                   4667777..689*****************************************9974...7887777..9****9999*** PP

                                   BEEEEETSSTTHHHHHHHHHHHTTSBSEEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B CS
                 EPSP_synthase 155 kgveikaevsSqqvtsllllaallaegttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvveg 234
                                   + v+i+++ sSq+++ ++ + +l+  g++e++  l s+ +i +t+++++++g+ ++   t+++i+v+ +e  +  +  v+g
  gi|70606030|ref|YP_254900.1|  92 NYVRIRGDESSQYISGFIYAFSLVNGGDIEIIPpLSSKSYIHMTIDLINALGGSVKF--TGNRIRVERGEFRDF-RGDVPG 169
                                   **********************99888******************************..9999***98776555.89**** PP

                                   -HHHHHHHHHHHHHTT-EEEEES--GGGGH.HH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGG CS
                 EPSP_synthase 235 DassAayflvaAaitggevtvenvginslq.Gdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptla 314
                                   D+  A+++++a aitgge+ ++++   +   Gd  +++ i+++mg++ + e +++iv+g+  +k+++vd+ ++pd+ap +a
  gi|70606030|ref|YP_254900.1| 170 DYALASFYAIASAITGGEIQIKGLYSPPYYdGDHSIVK-IIKNMGVDSRVEGNSWIVSGNGIIKGIKVDVDDMPDLAPSIA 249
                                   *************************999999**88888.****************************************** PP

                                   GHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSB CS
                 EPSP_synthase 315 vlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvae 395
                                     a fa+++t+i+gi++lr ke+dr+ ++ + L+ + ++v ++ d+++i p++  l  + + + +DhRiam+  +++l+  
  gi|70606030|ref|YP_254900.1| 250 CIAPFATSETEITGIKRLRIKESDRVSTIKSTLEAFSGNVVVDTDFIKIFPSK--LTEGSIICPNDHRIAMMAGVISLRTG 328
                                   ************************************************99985..7889999999************8888 PP

                                   SEEEEETTHHHHHHSSSHHHH CS
                 EPSP_synthase 396 geveiddiectdksfpefeek 416
                                   g  ++++++c++ks p f+ +
  gi|70606030|ref|YP_254900.1| 329 G--TVENAQCVNKSNPSFWLD 347
                                   8..99*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2498.29
//
Query:       gi|70606031|ref|YP_254901.1|  [L=219]
Description: 3-dehydroquinate dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-16   61.5   0.0    1.8e-16   61.1   0.0    1.1  1  DHquinase_I  Type I 3-dehydroquinase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0     1e-20   1.8e-16      11     229 .]      18     207 ..       9     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1e-20
                                   HHHHHHHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-S CS
                   DHquinase_I  11 eilaelesgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgad 91 
                                   + l+++e + +++DlvElRlD+l++++       ++  l+s+ + +li+tlr k egg  + ++ +   + +r++ + +  
  gi|70606031|ref|YP_254901.1|  18 KDLNRIELLINDVDLVELRLDYLSKFDV------DILDLFSKYKEKLIITLRDKDEGGV-NYIDPAFKANFVRRMEREK-F 90 
                                   456778888779***********99966......777788877889************9.5888888889998888865.5 PP

                                   EEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SS..HHHHHHHHHHHH CS
                   DHquinase_I  92 yvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaks..ieDvlrllslts 170
                                   + D+E          +l+ +   +    IvS h f++ p+  e+k+++ k  +    + Kiav ak   +e  +r+l  + 
  gi|70606031|ref|YP_254901.1|  91 MYDIEAR-------FALRYQV--NVKDKIVSIHYFDNLPEFTEVKEIFDKFDEAY--LRKIAVIAKRgyRELLMRVLDNY- 159
                                   88****3.......2566666..666779***********************666..*********97677777788777. PP

                                   HHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHHH CS
                   DHquinase_I 171 eakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelreil 229
                                            + ++m mG  G+  Ri+  ++Gs +++a+++e+  +a Gql ++++r+il
  gi|70606031|ref|YP_254901.1| 160 --------DNAVVMPMGVNGV-ERIAFSLLGSKLIYAHAGEE--TAKGQLHYKDVRRIL 207
                                   ........689*********5.8***************7777..************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1577.77
//
Query:       gi|70606032|ref|YP_254902.1|  [L=100]
Description: hypothetical protein Saci_0190 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-17   61.2   0.0    8.4e-17   60.9   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
    1.1e-08   34.9   0.0    1.4e-08   34.6   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   9.4e-21   8.4e-17       7      88 ..       5      87 ..       2      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 9.4e-21
                                  EGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGG.SEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHEEE CS
                        Rieske  7 kesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplse.gkidekgvleCpcHgwayd.adGkvikgPaprplat 87
                                  k s++++g+ ++v++g+e++++l   +g++yA++ +C+H+g+ l + g +  +++l+C+cH   ++ +dG++ikg +++pl+ 
  gi|70606032|ref|YP_254902.1|  5 KRSELKPGEKKKVTIGNEEVILLYLGGGKYYAFQSRCPHLGCDLYKvGVVI-REELVCQCHFTHFSiNDGRAIKGATKKPLKL 86
                                  679****************9999999******************9989995.559************************9987 PP

                                  E CS
                        Rieske 88 y 88
                                  y
  gi|70606032|ref|YP_254902.1| 87 Y 87
                                  6 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.6e-12   1.4e-08       7     103 ..       5      98 ..       3      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.6e-12
                                   ECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS.-TT CS
                      Rieske_2   7 kledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle.dee 86 
                                   k ++l +++++ + +++++v+l++l  ++ yA + ++p  +   +  G+v  +  elv +   + ++f++++G+ ++ +++
  gi|70606032|ref|YP_254902.1|   5 KRSELKPGEKKKVTIGNEEVILLYLGGGKYYAFQSRCPHLGCDLYKVGVVIRE--ELVCQ--CHFTHFSINDGRAIKgATK 81 
                                   7799*********************************************9877..66655..5789********9985777 PP

                                   SB-BEE-EEESTSEEEE CS
                      Rieske_2  87 vslkvypvrvedgkvev 103
                                   ++lk y+v+v+++ + v
  gi|70606032|ref|YP_254902.1|  82 KPLKLYRVQVDGEDIIV 98 
                                   99***********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 668.43
//
Query:       gi|70606033|ref|YP_254903.1|  [L=96]
Description: hypothetical protein Saci_0191 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.011   16.0   0.2      0.016   15.5   0.2    1.3  1  OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   8.9e-07     0.016      13      75 ..       9      64 ..       4      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.9e-07
                    OKR_DC_1_N 13 lekegfevvgvtstdDllsvieqnsriaavvlsvddeaaelldeirernedlPvFllaetrts 75
                                  lek +++++++++ +         +++++++++    a+e+++ i+++ + l vF + +t ++
  gi|70606033|ref|YP_254903.1|  9 LEKLDYRILEINNIS-------RSADVSCIIITNRPPASEIIEDIKKTVNVLSVFSFLSTIKA 64
                                  777788888888888.......99************************999999999884433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 686.41
//
Query:       gi|70606034|ref|YP_254904.1|  [L=551]
Description: XPD/Rad3 related DNA helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-25   88.7   0.1    1.2e-24   87.4   0.0    1.7  2  Helicase_C_2   Helicase C-terminal domain
    1.3e-15   57.5   0.6    6.6e-15   55.2   0.6    2.1  1  DEAD_2         DEAD_2
    2.9e-08   33.9   0.4    1.6e-06   28.2   0.3    3.2  2  ResIII         Type III restriction enzyme, res subunit
      3e-05   23.8   0.0      0.064   13.0   0.0    3.5  4  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.032   14.5   0.7        3.8    7.8   0.3    2.9  3  AAA_22         AAA domain
      0.033   13.7   0.0       0.42   10.0   0.0    2.6  3  PhoH           PhoH-like protein
       0.12   11.9   0.0       0.29   10.7   0.0    1.5  1  AAA_25         AAA domain
        2.4    7.9   5.5        1.7    8.4   1.5    2.3  2  Iron_permease  Low affinity iron permease


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.8   8.5e+03      18      57 ..     213     256 ..     195     267 .. 0.62
   2 !   87.4   0.0   5.3e-28   1.2e-24       3     163 ..     387     540 ..     385     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.8
                  Helicase_C_2  18 Syklleevverlkeeleskkieifvee....keesrekvleeyk 57 
                                   S ++l ++ ++l+e    +++ i ve+    ++e+ e + ++y+
  gi|70606034|ref|YP_254904.1| 213 SRRILSKLLNQLREVVLPDEKYIKVENvpklSKEELEILADDYE 256
                                   55566666666666554444444444444445555555555555 PP

  == domain 2  score: 87.4 bits;  conditional E-value: 5.3e-28
                  Helicase_C_2   3 ellevvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfs.. 81 
                                   +++ + +++vlv+fpSy+++++v++r++  +       +ve++++s e++ + +++  +++ ++ +v +Gkl EGi+++  
  gi|70606034|ref|YP_254904.1| 387 KIYFQAKANVLVVFPSYEIMDRVMSRISLPK-------YVESEDSSVEDLYSAISA--NNKVLIGSVGKGKLAEGIELRnn 458
                                   56667789*****************998754.......5666999**********9..77777777778*********943 PP

                  Helicase_C_2  82 .ddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeir 161
                                      l++ v+ivg+P+p+p+d       + +  k+++++ + +++ +al +++QaiGR+iR+ +D++ + llD+Rf++  ++
  gi|70606034|ref|YP_254904.1| 459 dRSLISDVVIVGIPYPPPDDYLKI-LAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDKRFESLYWK 538
                                   2245778***********887644.4444455555468888999*******************************996665 PP

                  Helicase_C_2 162 ek 163
                                   ++
  gi|70606034|ref|YP_254904.1| 539 KN 540
                                   55 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.6     3e-18   6.6e-15      59     163 ..      88     189 ..      52     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3e-18
                                   HHHHHCCHHCCHTTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHH CS
                        DEAD_2  59 CkelkkkkaeekeekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekire 139
                                   C   +k  + +++  C++ e + ++ ++ k+  + +  + +l++ g + k+CPYy+  + l +ad+i l Y y++  ++re
  gi|70606034|ref|YP_254904.1|  88 CLYAEKGAE-SEDIPCKYCELKGSIVEV-KTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYRE 166
                                   555555554.458889999888777774.66667777799***************************************** PP

                                   HHHT..GCGCEEEECTCCCHHHHH CS
                        DEAD_2 140 slkgislknsivilDEAhNiedvc 163
                                    ++ i+l++ ++++DEAhN+++v 
  gi|70606034|ref|YP_254904.1| 167 FID-IDLREYMIVIDEAHNLDKVN 189
                                   **9.****************9874 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.3   7.3e-10   1.6e-06       2     147 ..       2     188 ..       1     212 [. 0.66
   2 ?    1.0   0.0      0.17   3.8e+02      48      78 ..     389     417 ..     380     462 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.3e-10
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   l+lr++Qe+  ++++e l  +++  + ++++TG+GKTl ++ +  +++      k+lf+v + +     +++++k+ ++ +
  gi|70606034|ref|YP_254904.1|   2 LKLRDWQEKLKDKVIEGL--RNNFLVALNAPTGSGKTLFSLLVSLEVKP-----KVLFVVRTHNEFYPIYRDLTKIREKRN 75 
                                   689***************..5888999********************99.....7*******9888888888866665554 PP

                                   ................................GEEEESSS-B--............-SEEEEEHHHHHHTH.......... CS
                        ResIII  83 ke..............................igkkvsgdkkka.....kekdstnkkilvttiqsldadseee....... 121
                                                                   +g +v+ +++++     k+ +++  +  +  + sl +++ ++       
  gi|70606034|ref|YP_254904.1|  76 ITfsflvgkpssclyaekgaesedipckycelKGSIVEVKTDDSplslvKKLKKDGLQDKFCPYYSLLNSLYKAdvialty 156
                                   334555444444433222222333333333343333444444446777766777777777777777777775555665666 PP

                                   ..........HHHTTT-S............EEEEETGGGTTS. CS
                        ResIII 122 .....eeeseellrdrfd............viiiDEaHrlgak 147
                                        +                        +i+iDEaH+l + 
  gi|70606034|ref|YP_254904.1| 157 pyffiD-----------RyrefididlreyMIVIDEAHNLDKV 188
                                   555553...........03344444444469*******99875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                                   H-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                        ResIII  48 llkkgkeekflflvprkslleqtleefkkfl 78 
                                   ++++  + ++l++ p+ +++++ +++++  +
  gi|70606034|ref|YP_254904.1| 389 YFQA--KANVLVVFPSYEIMDRVMSRISLPK 417
                                   4444..349*************998875433 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.9e-05     0.064       6      73 ..      14      73 ..       7     100 .. 0.73
   2 !    5.4   0.1    0.0064        14     124     154 ..     176     208 ..     145     229 .. 0.75
   3 ?   -1.1   0.0      0.63   1.4e+03     147     172 ..     309     329 ..     231     333 .. 0.79
   4 ?   -0.2   0.0      0.33   7.3e+02      46      71 ..     392     417 ..     379     453 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                                  HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                  ++i+ + ++  v ++a+TGsGKTl  l+  l        + +pk+l+v+ t+     ++++l+k+ ++
  gi|70606034|ref|YP_254904.1| 14 KVIEGLRNNFLVALNAPTGSGKTLFSLLVSL--------EVKPKVLFVVRTHNEFYPIYRDLTKIREK 73
                                  55666666677889**********9888777........45678888877776666666666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0064
                                   EEEEETHHHHHHT..TTHHHHHHHHHHSHHHCT CS
                                   xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          DEAD 124 flVlDEadrlldq..gfsdfinrilnqlpqitc 154
                                   ++V+DEa++l +     ++ +++i  q++ +++
  gi|70606034|ref|YP_254904.1| 176 MIVIDEAHNLDKVneLEERSLSEITIQMAIKQS 208
                                   69********98754556666777666643333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.63
                                   HHSHHHCTTSTTTSEEEEEESSBS.HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                          DEAD 147 nqlpqitcdgklqrqvivlSATlp.kd 172
                                   n l    +d +l+  +i++S Tlp ++
  gi|70606034|ref|YP_254904.1| 309 NLL----NDNELS--IILMSGTLPpRE 329
                                   333....333344..899999998665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.33
                                   TS-EEEEEESSHHHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  46 tgpkalivePtreLaeqtlnnlkkfk 71 
                                    +  +l+v P+ e++  ++++++  k
  gi|70606034|ref|YP_254904.1| 392 AKANVLVVFPSYEIMDRVMSRISLPK 417
                                   567899*********99999885333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.041        92       9      49 ..      26      57 ..      20      79 .. 0.75
   2 ?    7.8   0.3    0.0017       3.8      94     111 ..     176     198 ..     163     210 .. 0.68
   3 ?   -1.4   0.0       1.2   2.7e+03      49     103 ..     209     243 ..     194     265 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.041
                        AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                  ++ +++G+GKT+    +  +          +p+v+fv  ++
  gi|70606034|ref|YP_254904.1| 26 ALNAPTGSGKTLFSLLVSLEV---------KPKVLFVVRTH 57
                                  6779*******9988887777.........77777665555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0017
                        AAA_22  94 lliiDEaqhlr...s..eealee 111
                                   +++iDEa++l+   +  e+ l+e
  gi|70606034|ref|YP_254904.1| 176 MIVIDEAHNLDkvnEleERSLSE 198
                                   69********7433122444444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                        AAA_22  49 sstsskdllrellralglelkaerlsseellealeqalrarav..ielliiDEaqhl 103
                                   +s++s+ +l++ll+                      +lr+      + + ++++ +l
  gi|70606034|ref|YP_254904.1| 209 KSEESRRILSKLLN----------------------QLREVVLpdEKYIKVENVPKL 243
                                   33344444444444......................444433344444444444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019      0.42      10      42 ..      13      45 ..       6      52 .. 0.86
   2 ?   -0.5   0.0      0.31     7e+02     118     133 ..     172     187 ..     171     192 .. 0.84
   3 ?   -3.7   0.0       3.1   6.9e+03      46      80 ..     492     527 ..     484     537 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                  HHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHH CS
                          PhoH 10 keylealkkndivfaiGpaGtGKtylavalave 42
                                  ++++e l++n +v   +p+G+GKt++++ + +e
  gi|70606034|ref|YP_254904.1| 13 DKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE 45
                                  5788899999****************9988776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
                                   B-SEEEEE-SGGG--H CS
                          PhoH 118 lndafvilDEAQnttk 133
                                   l + ++++DEA n+ k
  gi|70606034|ref|YP_254904.1| 172 LREYMIVIDEAHNLDK 187
                                   56789********875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.1
                                   TTS-SEEEEEE-S-.-TT----SS---------TTT CS
                          PhoH  46 kkkvkriiltrpav.eageelGflpgdleekvdpyl 80 
                                   +++ +++++  pa+ ++++ +G    d+++k++++l
  gi|70606034|ref|YP_254904.1| 492 NRENEEFLFKIPALvTIKQAIGRAIRDVNDKCNVWL 527
                                   556666666666653668899999999999998886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.29      23      57 ..      13      46 ..       5      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                        AAA_25 23 rwlvkgllpagelallaGapgtGKttlaldlalav 57
                                  +++++gl+  + l++l +++g+GKt + l ++l+v
  gi|70606034|ref|YP_254904.1| 13 DKVIEGLR-NNFLVALNAPTGSGKTLFSLLVSLEV 46
                                  57899995.8*****************99998876 PP

>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.9     0.031        70      70     118 ..     167     214 ..     162     219 .. 0.82
   2 ?    8.4   1.5   0.00077       1.7      60     124 ..     205     272 ..     201     275 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                 Iron_permease  70 aiqlkLdeLirasksaknrlidleelteeeleelakeyerlaeaakeee 118
                                    i ++L+e + + ++a+n l +++el+e+ l+e++ +++ ++++++e++
  gi|70606034|ref|YP_254904.1| 167 FIDIDLREYMIVIDEAHN-LDKVNELEERSLSEITIQMAIKQSKSEESR 214
                                   57899***9999998887.5699**********9999888777777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00077
                 Iron_permease  60 iqnsqnrdskaiqlkLdeLirasksaknrlidlee...lteeeleelakeyerlaeaakeeeevkkas 124
                                   i++s++ +s+ i  kL + +r     ++++i++e+   l++eele la+ ye +++ + ++ +v+k++
  gi|70606034|ref|YP_254904.1| 205 IKQSKSEESRRILSKLLNQLREVVLPDEKYIKVENvpkLSKEELEILADDYEDIRKDSLKQGKVNKIH 272
                                   8999999*****99*99999999999999999996333789***************999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3963.84
//
Query:       gi|70606035|ref|YP_254905.1|  [L=267]
Description: hypothetical protein Saci_0193 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-09   37.4   0.0    4.2e-09   36.3   0.0    1.6  1  Thioredoxin_3  Thioredoxin domain
     0.0061   16.7   0.3      0.018   15.2   0.0    2.0  2  Glutaredoxin   Glutaredoxin
     0.0088   16.2   0.0      0.023   14.8   0.0    1.7  1  Thioredoxin_4  Thioredoxin
  ------ inclusion threshold ------
      0.013   15.9   1.0      0.036   14.4   0.0    2.2  3  TetR_C_26      Tetracyclin repressor-like, C-terminal domain
          1    9.1   5.8        2.1    8.1   0.1    2.8  3  DUF3242        Protein of unknown function (DUF3242)
        1.8    8.6   3.5       0.48   10.5   0.2    1.8  2  YhfH           YhfH-like protein


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.4e-12   4.2e-09       2      75 ..       3      75 ..       2      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.4e-12
                                  EEEEESSS.STTCHHHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                 Thioredoxin_3  2 eikvlgpg.CakCpklekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirkll 75
                                  ++++++++ C++C  l++++++  +++  k+++++++ ++ +  ++gV+s+P++++dgk+v++G v + +e+ k+l
  gi|70606035|ref|YP_254905.1|  3 KVEIFTHKtCTECGILMEFLER--NKLLGKVTIIDTELYPFLaFERGVISTPSIFVDGKLVYAG-VVDYDELLKIL 75
                                  689975555*****88777765..4556899999999999999*********************.*******9998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     6e-06     0.018       1      60 []       4      61 ..       4      61 .. 0.95
   2 ?   -3.1   0.1       3.2   9.6e+03      18      34 ..      74      87 ..      71      92 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                                  EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                  Glutaredoxin  1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                  v++ft +tC  C    ++L+++++  ++  +d   e+   l    gv + P +f+dgk+v
  gi|70606035|ref|YP_254905.1|  4 VEIFTHKTCTECGILMEFLERNKLLGKVTIIDT--ELYPFLAFERGVISTPSIFVDGKLV 61
                                  89***********************99999999..7999999999*************87 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                                  HHHHTTGGEEEEEGCCS CS
                  Glutaredoxin 18 lLkelgvkfeeidvdkd 34
                                  +L++++v    ++v+kd
  gi|70606035|ref|YP_254905.1| 74 ILQDKKVI---VEVNKD 87
                                  56666644...455555 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.8e-06     0.023     133     166 .]      43      77 ..      35      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-06
                                   HHHHT--SS-EEEETTEE.E-TT--HHHHHHHHT- CS
                 Thioredoxin_4 133 akkagiestPtfiingek.veepqtyeelkalida 166
                                   a ++g+ stP+++++g+  +++  +y+el +++++
  gi|70606035|ref|YP_254905.1|  43 AFERGVISTPSIFVDGKLvYAGVVDYDELLKILQD 77 
                                   67899************9789**********9985 PP

>> TetR_C_26  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.036      47     103 ..      69     125 ..      55     131 .. 0.87
   2 ?   -1.6   0.1       1.1   3.3e+03      42      55 ..     140     153 ..     137     197 .. 0.64
   3 ?   -2.5   0.1       2.1   6.4e+03      93      93 ..     240     240 ..     218     264 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHTTSB-TT--HHHHHHHHHHHHHHHHHHHHT.S---SS-HHHHHHHHHH CS
                     TetR_C_26  47 eelleeakkkeeireeieveataklligliEsaaEqlylydeeeeeeveekkkellk 103
                                   +ell+  ++k+ i e  + e + kl++g+++s a  ++ly +++ +++ ++k+ +l 
  gi|70606035|ref|YP_254905.1|  69 DELLKILQDKKVIVEVNKDELVNKLMFGVVNSFAATAWLYVNRDFDALMAQKDFVLA 125
                                   57889999999999999*****************************99999987765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHH CS
                     TetR_C_26  42 lYewleelleeakk 55 
                                   +Y++l++++ +  +
  gi|70606035|ref|YP_254905.1| 140 YYTYLRNIIVKEGE 153
                                   67777766655433 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.1
                                   - CS
                     TetR_C_26  93 e 93 
                                   +
  gi|70606035|ref|YP_254905.1| 240 Q 240
                                   2 PP

>> DUF3242  Protein of unknown function (DUF3242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2     6e+03      34      50 ..      28      44 ..      20      45 .. 0.81
   2 ?    2.0   1.7     0.053   1.6e+02      10     106 ..      72     167 ..      64     182 .. 0.55
   3 ?    8.1   0.1    0.0007       2.1      48      76 ..     229     257 ..     218     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                                  EEEEEEEEETTEEEEEE CS
                       DUF3242 34 kGvvavfdnkngllyvf 50
                                   G+v++ d++ + +++f
  gi|70606035|ref|YP_254905.1| 28 LGKVTIIDTELYPFLAF 44
                                  58999999999999988 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.053
                                   HHTT-BTBEEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEEESTTHHHHHHHHHT-------EEEEE-SSEEEEEEEET CS
                       DUF3242  10 lkvlenkYrLvdveeidgygdvegkGvvavfdnkngllyvfkykdeeakksWkkivkkvgivskrkyldlldsGlfsvkke 90 
                                   lk+l++k  +v+v++ d   ++++ Gvv +f ++ +l++   ++   a+k +   v  ++ v  ++  ++ ++    ++ke
  gi|70606035|ref|YP_254905.1|  72 LKILQDKKVIVEVNK-DELVNKLMFGVVNSFAATAWLYVNRDFDALMAQKDFVLAVTGLSLVDDKSADEYYTYLRNIIVKE 151
                                   566666666666665.44555666666666666655555555555555544444444444444444444444444445556 PP

                                   TEEEEEEEETTEEEEE CS
                       DUF3242  91 gkdivvWwkdnWlfiv 106
                                   g + v  wk++ l ++
  gi|70606035|ref|YP_254905.1| 152 GEKYVDEWKEKMLRVI 167
                                   6666666666655555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0007
                                   EEEEEESTTHHHHHHHHHT-------EEE CS
                       DUF3242  48 yvfkykdeeakksWkkivkkvgivskrky 76 
                                    v++y+ ++ak+ W+k+ k+ +   k++ 
  gi|70606035|ref|YP_254905.1| 229 EVYVYTLSNAKQLWDKVIKEQEELAKKSA 257
                                   589****************9988877765 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00016      0.48       4      23 ..       3      19 ..       1      22 [. 0.75
   2 ?   -3.3   0.3       3.2   9.7e+03      21      28 ..     244     251 ..     244     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                          YhfH  4 iveFfrnLPkKkCteCGkei 23
                                  +ve+f+   +K+CteCG  +
  gi|70606035|ref|YP_254905.1|  3 KVEIFT---HKTCTECGILM 19
                                  566665...6*******766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.2
                          YhfH  21 keieEqae 28 
                                   k+i+Eq+e
  gi|70606035|ref|YP_254905.1| 244 KVIKEQEE 251
                                   679***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1785.65
//
Query:       gi|70606036|ref|YP_254906.1|  [L=75]
Description: hypothetical protein Saci_0194 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   24.7   0.0    1.7e-05   24.6   0.0    1.4  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   9.3e-10   1.7e-05       2      37 ..       6      41 ..       5      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 9.3e-10
                                  EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSC CS
                          TusA  2 elDlrGlvCPePllklkkalekleegevlevladdp 37
                                  +lDlrG +C e +l++ k l ++++g++l ++ad  
  gi|70606036|ref|YP_254906.1|  6 RLDLRGKSCDEYILEISKVLVNMKPGDILNIIADKD 41
                                  69*******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 573.72
//
Query:       gi|70606037|ref|YP_254907.1|  [L=211]
Description: [Fe] superoxide dismutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-33  113.8   0.4    5.1e-33  113.3   0.4    1.2  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    2.4e-29  101.6   0.1    2.4e-29  101.6   0.1    1.6  2  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.4   5.7e-37   5.1e-33       1     102 []     102     204 ..     102     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 5.7e-37
                                   --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHT CS
                      Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyq 80 
                                   p g+la+ i++++gs+++fk+ f+++a ++ gsGw++L++d++ ++L+i+t++n+  + ++e   +L++D +ehAYyl+y+
  gi|70606037|ref|YP_254907.1| 102 PGGALADLINKQYGSFDRFKQVFSESANSLPGSGWTVLYYDNEsGNLQIMTVENHFMNHIAELPVILIVDEFEHAYYLQYK 182
                                   6799************************************98867***********9999888899*************** PP

                                   T-HHHHHHHHGGGBBHHHHHHH CS
                      Sod_Fe_C  81 nkradYieafwnvvnWkeveer 102
                                   nkr dY++a+wnvvnW+++e+r
  gi|70606037|ref|YP_254907.1| 183 NKRGDYLNAWWNVVNWDDAEKR 204
                                   ******************9987 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.1   2.7e-33   2.4e-29       1      82 []       9      93 ..       9      93 .. 0.96
   2 ?   -3.5   0.1       1.7   1.5e+04      22      30 ..     152     160 ..     147     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.7e-33
                                  S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCH...CCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakk...kleelvlkklekalrnnagghvnHslfwkn 80
                                  +ye+p+LpY++daLeP+isk+++++H++ Hhk+Yvn++N++l++le+  k   ++ +++l+++ ++l++n++gh +H+++w+n
  gi|70606037|ref|YP_254907.1|  9 RYEFPQLPYKVDALEPYISKDIIDVHYNGHHKGYVNGANSLLDRLEKLIKgdlPQGQYDLQGILRGLTFNINGHKLHAIYWNN 91
                                  59*******************************************9988877799**************************** PP

                                  B- CS
                      Sod_Fe_N 81 ls 82
                                  ++
  gi|70606037|ref|YP_254907.1| 92 MA 93
                                  96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                   HHHHHHHTH CS
                      Sod_Fe_N  22 tlelHhdkH 30 
                                   t+e H+  H
  gi|70606037|ref|YP_254907.1| 152 TVENHFMNH 160
                                   677788877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1689.37
//
Query:       gi|70606038|ref|YP_254908.1|  [L=359]
Description: mannose-1-phosphate guanyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-35  122.9   0.0    2.2e-35  122.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.9e-10   40.7   0.0      4e-10   40.3   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    4.1e-06   26.3  11.2      0.006   16.3   0.6    3.4  3  Hexapep          Bacterial transferase hexapeptide (six repea
     0.0044   16.8   0.0     0.0094   15.7   0.0    1.5  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0054   15.7   0.0     0.0095   14.9   0.0    1.4  1  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
       0.12   10.5   0.2       0.17   10.0   0.2    1.1  1  DUF4954          Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   0.0   7.4e-39   2.2e-35       2     245 ..       4     227 ..       3     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 7.4e-39
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a++LaGG+ tRL+PL+ t +k l+pvlgk +l+++tl  la+s++++ i+ + +  +  v +++k+ +  + ++  ++e++
  gi|70606038|ref|YP_254908.1|   4 AIVLAGGYATRLRPLSLTKPKALLPVLGK-PLMDYTLYSLASSDVDT-IYLSLRVMADKVLDHVKQLNLQK-NIVSVIEES 81 
                                   8****************************.*****************.99999**************9666.9999***** PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfv 163
                                   + g A++++ +    + +++   v+v+ gD++ + +++++++ +++k+    +t+ +++ve++++yGv  +d+ +r ++++
  gi|70606038|ref|YP_254908.1|  82 RLGDAGPLKFINSKYNLSDD---VIVVYGDIYAEIDFNKLLEYHQSKGC--NATLTATQVEDPSRYGVLITDG-HRLIQII 156
                                   ********999999998886...************************99..9*****************9998.699**** PP

                                   CS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHH CS
               NTP_transferase 164 EKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanek 244
                                   EKPk++  s+l+++GiYvf++e l ++ +       g +   d+lpk+l +++    +  k+   W+D+G +++++++n +
  gi|70606038|ref|YP_254908.1| 157 EKPKTPL-SNLVNAGIYVFKKELLNKI-D-------GLSISRDFLPKLLVSDTCVSVYPYKG--LWMDIGVPRDYMRINLE 226
                                   *****99.*****************99.3.......44566778888888877777779999..7************9987 PP

                                   H CS
               NTP_transferase 245 l 245
                                   l
  gi|70606038|ref|YP_254908.1| 227 L 227
                                   6 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.3e-13     4e-10       1     127 [.       4     138 ..       4     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.3e-13
                                   EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCT.....S-EEE-TTS. CS
                  NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd..eevlaalarlg.....vrvvededp. 68 
                                   a++LAGG ++R+   +   +Kallp+ gkpl++++l +l+++ vd ++++ +   ++vl+++++l+     v+v+e++   
  gi|70606038|ref|YP_254908.1|   4 AIVLAGGYATRLRplSltkPKALLPVLGKPLMDYTLYSLASSDVDTIYLSLRVmaDKVLDHVKQLNlqkniVSVIEESRLg 84 
                                   79**********7551445*******************************8776689999998886334457777777664 PP

                                   S-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                  NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                   ++gpl+ + +  +    +d v+v+ +D+    +   ++ll+ ++++g++++  +++ e 
  gi|70606038|ref|YP_254908.1|  85 DAGPLKFINSKYN---LSDDVIVVYGDIY--AEIDFNKLLEYHQSKGCNATLTATQVED 138
                                   5888888888886...469********94..4777899999999999988777766554 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   5.1   0.00015      0.44       4      34 ..     255     284 ..     254     286 .. 0.90
   2 !    5.2   1.2    0.0061        18       2      34 ..     270     301 ..     269     303 .. 0.58
   3 !   16.3   0.6     2e-06     0.006       2      35 ..     304     336 ..     303     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                   EETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   IG+n+++g ++ i  n +IG n +Ig+g+ +
  gi|70606038|ref|YP_254908.1| 255 IGDNTTVGEGSSI-RNSIIGVNNRIGNGSCV 284
                                   9************.7777**********977 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0061
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   ++IG n+ Ig+++ + +  ++ ++v +g ++ i
  gi|70606038|ref|YP_254908.1| 270 SIIGVNNRIGNGSCV-EESILMNDVMLGDFSLI 301
                                   678888899995555.44445555555555544 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2e-06
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +vIG+ v +g++  + ++++IGd+v I+  v i+
  gi|70606038|ref|YP_254908.1| 304 SVIGDEVSLGKWNRV-DGAIIGDGVLIHDQVFIN 336
                                   69*************.***********9999997 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.1e-06    0.0094       1      69 [.       2      75 ..       2      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                                  EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEE...EE-GGGHHHHHHHHGGCCEE CS
                          IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivv...vvseddteefeqllldksiq 69
                                  v +++ A G  +R++     +pK++l + g++l+  t+ +l++ + vd+i +   v+ ++  ++++ql l+k+i+
  gi|70606038|ref|YP_254908.1|  2 VSAIVLAGGYATRLRplsLTKPKALLPVLGKPLMDYTLYSLAS-SDVDTIYLslrVMADKVLDHVKQLNLQKNIV 75
                                  578999******975322799******************9988.789**99833234455679999999998765 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-06    0.0095     265     335 ..     273     340 ..     231     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
                    Fucokinase 265 nkkekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlsl 335
                                     ++ + ++++v +S+l ++v +g+ s+i++s ++++vs g++  v g  +  +   + ++d+++++   +
  gi|70606038|ref|YP_254908.1| 273 GVNNRIGNGSCVEESILMNDVMLGDFSLIKESVIGDEVSLGKWNRVDGAIIGDG---VLIHDQVFINRDTI 340
                                   233455888999999999999999999999999999999999999888888876...44777777766555 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   5.7e-05      0.17     173     265 ..     234     323 ..     228     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.7e-05
                       DUF4954 173 vGeigekvkiln.aglikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfvGqav 252
                                   +G i +++k+ + a+l    +igd +t+   s+++n  i  ++    +iG+g  +e++i+++   + d ++i+++++G  v
  gi|70606038|ref|YP_254908.1| 234 KGFISQSAKVSEkAELFPPFYIGDNTTVGEGSSIRNSIIGVNN----RIGNGSCVEESILMNDVMLGDFSLIKESVIGDEV 310
                                   6778888888642566777889999999999999998777664....6999999999999999999999999999999999 PP

                       DUF4954 253 klkkqfsaedsll 265
                                   +l+k  ++  +++
  gi|70606038|ref|YP_254908.1| 311 SLGKWNRVDGAII 323
                                   9998877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2512.13
//
Query:       gi|70606039|ref|YP_254909.1|  [L=116]
Description: hypothetical protein Saci_0197 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.042   14.1   0.6      0.068   13.5   0.6    1.3  1  MetallophosN  N terminal of Calcineurin-like phosphoesterase
        0.1   13.2   0.0       0.15   12.7   0.0    1.3  1  FecR          FecR protein


Domain annotation for each model (and alignments):
>> MetallophosN  N terminal of Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   7.5e-06     0.068      12      71 ..      11      75 ..      10      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-06
                  MetallophosN 12 gVvVsDGvnvtkTdakGrY.eLksd.....kkakfVyistPagyevptedgllpkfYkklkkkekk 71
                                  +V+V++G nv     +G Y ++ks+     ++ ++Vyi+tP g +   ++    +fY  + +++++
  gi|70606039|ref|YP_254909.1| 11 KVIVNNGSNVQIRFDNGSYiSIKSSsqflvRNDSYVYITTPIGSNSIINNV-STNFYILFVTNDSV 75
                                  599****************988855123324689*********99988887.89999877655554 PP

>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05      0.15       6      34 ..      15      43 ..      11      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                          FecR  6 gagsraeilleDgsvvrlnensslekaad 34
                                   +gs ++i++++gs +++++ s++ ++ d
  gi|70606039|ref|YP_254909.1| 15 NNGSNVQIRFDNGSYISIKSSSQFLVRND 43
                                  5799********************55544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 876.27
//
Query:       gi|70606040|ref|YP_254910.1|  [L=632]
Description: hypothetical protein Saci_0198 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-62  210.3   0.0    2.6e-62  209.6   0.0    1.3  1  Thioredox_DsbH  Protein of unknown function, DUF255
    3.4e-15   56.0   0.1    6.6e-15   55.1   0.1    1.5  1  Thioredoxin_7   Thioredoxin-like
    3.9e-05   23.6   0.2    8.3e-05   22.5   0.2    1.5  1  Thioredoxin     Thioredoxin
    5.5e-05   23.6   0.0    0.00087   19.7   0.0    2.4  2  Thioredoxin_2   Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   0.0   5.7e-66   2.6e-62       2     163 .]       2     163 ..       1     163 [. 0.99

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 5.7e-66
                Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDree 82 
                                   nrl + +s++l+  +++p+dW+pw++ea++kak+edkp+l+++G s+chWChvm++ ++ed+ev +l+n++fv++kvDr+e
  gi|70606040|ref|YP_254910.1|   2 NRLGNVSSAFLKLSSESPIDWFPWSDEAFDKAKKEDKPVLVDVGASWCHWCHVMDETTYEDKEVIDLINKNFVAIKVDRDE 82 
                                   99******************************************************************************* PP

                Thioredox_DsbH  83 rPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeellealk 163
                                    Pdld+ ++ av+ +tg++gWPl+vf+tpd+k ffggtYfp+e+++gr gf+++l++i +lw++er+++ ++a++l ++l+
  gi|70606040|ref|YP_254910.1|  83 MPDLDRRLQLAVSSITGESGWPLTVFMTPDGKVFFGGTYFPPEDSYGRVGFKRLLNEIIRLWKNERDKIFQTANSLHSSLQ 163
                                   **************************************************************************9998875 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   1.5e-18   6.6e-15       1      83 []      21     111 ..      21     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.5e-18
                                   ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.........-TT-. CS
                 Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani........lelde. 72 
                                   +w  + dea++ka+++ kpvlv++gaswc+ C+++++++ +d+ev  +++++fv  +vd +e  + +              
  gi|70606040|ref|YP_254910.1|  21 DWFPWSDEAFDKAKKEDKPVLVDVGASWCHWCHVMDETTYEDKEVIDLINKNFVAIKVDRDEMPD-LdrrlqlavS---Si 97 
                                   6999************************************99999999************55544.2222232342...13 PP

                                   ...--SSEEEEE-T CS
                 Thioredoxin_7  73 ...qgvPvvafldp 83 
                                      +g P  +f++p
  gi|70606040|ref|YP_254910.1|  98 tgeSGWPLTVFMTP 111
                                   33477888888876 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   1.8e-08   8.3e-05       6      67 ..      26      89 ..      22      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.8e-08
                                  SHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHH...HHHHHHCTTTSEEEEEETTTSHHHHHH CS
                   Thioredoxin  6 tkenFeeevakekklvlveFyApwCghCkalaPel...eklaeelkdkvklakvdvdenedlakk 67
                                  ++e+F+++ ++ +k+vlv+  A+wC  C  +  +    +++ + ++++++ +kvd de +dl ++
  gi|70606040|ref|YP_254910.1| 26 SDEAFDKAKKE-DKPVLVDVGASWCHWCHVMDETTyedKEVIDLINKNFVAIKVDRDEMPDLDRR 89
                                  57888887666.*******************8765122356666677***********9998765 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.9e-07   0.00087       1      86 [.      33     108 ..      33     129 .. 0.68
   2 ?    0.9   0.0      0.14   6.2e+02      21      59 ..     371     410 ..     368     433 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.9e-07
                 Thioredoxin_2   1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelark..ygvr 79 
                                   ak++ kpvlv++ +++C  C+ + +++ e+++v +      ++++f+++ v+ + +++  + ++       la +   g +
  gi|70606040|ref|YP_254910.1|  33 AKKEDKPVLVDVGASWCHWCHVMDETTYEDKEVIDL-----INKNFVAIKVDRDEMPDLDRRLQ-------LAVSsiTGES 101
                                   6899**************************999999.....99996666666666666554433.......3333212444 PP

                 Thioredoxin_2  80 gtPtivf 86 
                                   g P +vf
  gi|70606040|ref|YP_254910.1| 102 GWPLTVF 108
                                   4444333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                 Thioredoxin_2  21 kklkkelkelddvtvrvllfp.lkpsfepkavaiwcakek 59 
                                   k++k+ + +l+dv++r++ +   ++++ ++ +++++  + 
  gi|70606040|ref|YP_254910.1| 371 KRFKDPIGKLNDVRERLRVYReERRKYPFIDTNVYTHSNC 410
                                   789999999*******999999999999999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3997.72
//
Query:       gi|70606041|ref|YP_254911.1|  [L=234]
Description: 3-ketoacyl-ACP reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-27   95.3   0.0    5.7e-27   94.8   0.0    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.6e-21   76.7   0.2      2e-21   76.4   0.2    1.1  1  adh_short     short chain dehydrogenase
    0.00018   21.5   0.2     0.0003   20.8   0.2    1.3  1  KR            KR domain
  ------ inclusion threshold ------
      0.023   14.7   0.3       0.12   12.4   0.3    2.3  1  ADH_zinc_N    Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   1.3e-30   5.7e-27       1     233 [.      12     229 ..      11     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 1.3e-30
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                   G   g+G+a+A    +eGaevvl  ++e++   + e++++lg ++  +  DV+ ++  +++v+++ + +   D ++   g+
  gi|70606041|ref|YP_254911.1|  12 GTSTGLGYAVAYFSINEGAEVVLNARSEKK---LVEIVKSLGDKAsyVVGDVSTPQGARDVVSRAGNIT---DLVITVGGY 86 
                                   5668*********************99998...88899999977445**********999999987664...888888888 PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSB.STTTTHHHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaerv.vpnynaygaaKaalealtrylAvel 159
                                    ++     +  s +++d++l+  ++  ++l++a l+ ++eg+ iv +ss++a  + +pn+  y++aK +l + +  lA el
  gi|70606041|ref|YP_254911.1|  87 LED-----TVESPSGLDEMLKNHIKTPLYLVNASLEKLHEGSTIVMVSSTRALYTaLPNQLSYAIAKSGLTKAVEILASEL 162
                                   887.....344789************************************99865599999******************** PP

                                   GGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B.-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                  adh_short_C2 160 gpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlg.tpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                    +kgiRv  v+p++i  + + g          ++++  lg +g  pe+ a+++ +L+s+ea++++G ++ vDgG 
  gi|70606041|ref|YP_254911.1| 163 LNKGIRVVGVAPSFIMGDFVPGR--------DWRKMRKLGDAGaPPEDFAQVITWLLSNEAQWVNGVVIPVDGGA 229
                                   ***************96665554........599999999988689****************************5 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.2   4.5e-25     2e-21       2     183 ..       7     178 ..       6     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 4.5e-25
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    vl+ G s G+G+a+a+  ++eGa+vv+ +rse+kl e++k+l++   ka ++ +Dv++ + ++++v++a    g++  Lv
  gi|70606041|ref|YP_254911.1|   7 RVLIAGTSTGLGYAVAYFSINEGAEVVLNARSEKKLVEIVKSLGD---KASYVVGDVSTPQGARDVVSRA----GNITDLV 80 
                                   59****************************************997...5**********99999999999....9998888 PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAsKaavagltrs 162
                                     +G     +    s +  +++++  ++ ++ l+ a l+++   ++ +Iv vsS+ +   +++++ +Y+ +K ++++ ++ 
  gi|70606041|ref|YP_254911.1|  81 ITVGGY--LEDTVESPSGLDEMLKNHIKTPLYLVNASLEKLH--EGSTIVMVSSTRAlYTALPNQLSYAIAKSGLTKAVEI 157
                                   888883..2333345566**********************76..8889*********45579******************* PP

                                   HHHHHGGGTEEEEEEEESSBS CS
                     adh_short 163 lakelaptgirvnavaPGlvd 183
                                   la el ++girv++vaP ++ 
  gi|70606041|ref|YP_254911.1| 158 LASELLNKGIRVVGVAPSFIM 178
                                   *****************9986 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   6.6e-08    0.0003       3     161 ..       8     156 ..       7     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.6e-08
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                   +li+G   gLG ++a + +++ga+ +vl +Rs      +k+l++ +++lg + ++v  Dvs ++  + +++++ +      
  gi|70606041|ref|YP_254911.1|   8 VLIAGTSTGLGYAVAYFSINEGAE-VVLNARS------EKKLVEIVKSLGDKASYVVGDVSTPQGARDVVSRAGNI---TD 78 
                                   69********************95.89999**......4569999999**********************999733...35 PP

                                   EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHHHHH.--TT-HHHHHHHHHHHHHHH CS
                            KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSiagll.gsagqanYaaaNaflDalae 161
                                    vi   g l+d+     + + l+++l+  +k    L +++ +  ++   +v++SS  +l+   + q +Ya a + l   +e
  gi|70606041|ref|YP_254911.1|  79 LVITVGGYLEDTV---ESPSGLDEMLKNHIKTPLYLVNASLEklHEGSTIVMVSSTRALYtALPNQLSYAIAKSGLTKAVE 156
                                   5788888888876...467888999999999999999999886778899*******997615699*****99887666555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.6e-05      0.12       1      55 [.      16      84 ..      16     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                                  HHHHHHHHHHHHTT-EEEEEESSHHHH.HHHHHTT..ESEEEET....TTC.HHHHHHHHHT......T CS
                    ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseekl.elakklG..adeviny....kea.dlverikelt......g 55
                                  g+G a+  +    Gaev+  ++se+kl e++k+lG  a +v+      + a d+v+r   +t      g
  gi|70606041|ref|YP_254911.1| 16 GLGYAVAYFSINEGAEVVLNARSEKKLvEIVKSLGdkASYVVGDvstpQGArDVVSRAGNITdlvitvG 84
                                  89999999999********999999999*******9888888878888666688888888874444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1522.19
//
Query:       gi|70606042|ref|YP_254912.1|  [L=250]
Description: hypothetical protein Saci_0200 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-58  197.2   0.0      3e-58  196.9   0.0    1.0  1  NucS      Endonuclease NucS
     0.0006   20.0   0.0     0.0015   18.7   0.0    1.6  1  Cas_Cas4  Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.15   12.3   0.0    1.5  1  UPF0102   Uncharacterised protein family UPF0102
       0.11   12.8   0.0       0.27   11.5   0.0    1.7  1  DUF4263   Domain of unknown function (DUF4263)


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.0   6.6e-62     3e-58       3     212 ..      23     229 ..      21     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 6.6e-62
                          NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLkve 83 
                                   a+l + ++C++ y Graksr   + rl +ikpdG++++h   k+ePvnWqpp+s++ + +e+g l++++ r++p+e+L + 
  gi|70606042|ref|YP_254912.1|  23 ALLTIYSECEILYSGRAKSRASLSPRLTIIKPDGSVIIHGPTKREPVNWQPPGSRIEYSIESGVLTVNAERKRPKERLSIL 103
                                   5778899************************************************************************** PP

                          NucS  84 ieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrkaevda 164
                                    + v++ ++ e++   e+ l G e +  ++ii++pd+ie Gfkp+ rey ++ G vd++gkd+eg+lv++e+kr ka ++a
  gi|70606042|ref|YP_254912.1| 104 HHRVYYITSSEVKP-GEFFLVGREKDEVDFIINNPDVIEGGFKPIHREYRTPYGTVDLIGKDKEGNLVVLEFKRAKASLQA 183
                                   ********999976.578899************************************************************ PP

                          NucS 165 veqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeld 212
                                   v+qL ry+ ++ke    ++ rG+lvap i ++a +llk  +le+ ++ 
  gi|70606042|ref|YP_254912.1| 184 VSQLYRYIMYFKEIG--ENARGILVAPGISENALNLLKRLELEYVNIS 229
                                   ***********9854..599*******************999998875 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.3e-07    0.0015      54     111 ..     155     211 ..     124     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.3e-07
                      Cas_Cas4  54 sikiDvve.kekeklvvvEvKkskkkeeaaklQllyYlllLekkgveikeGvleypkek 111
                                    + +D++  +++++lvv E+K+ k+   +a  Ql  Y++++++ g +++ G+l  p   
  gi|70606042|ref|YP_254912.1| 155 YGTVDLIGkDKEGNLVVLEFKRAKASL-QAVSQLYRYIMYFKEIGENAR-GILVAPGIS 211
                                   67899999677889999******9955.5568****************9.***988765 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.4e-05      0.15      12      45 ..     142     178 ..     139     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.4e-05
                                   TT-EEEEEEEEETTEEEEEEE...TTEEEEEEEEE-. CS
                       UPF0102  12 kgyeilernwrcragEiDiia...tevlvfvEVKtRs 45 
                                    g++ ++r++r+ +g +D+i    +  lv+ E K  +
  gi|70606042|ref|YP_254912.1| 142 GGFKPIHREYRTPYGTVDLIGkdkEGNLVVLEFKRAK 178
                                   58999******************9778*****99742 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05      0.27       4      61 ..     126     184 ..     123     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                       DUF4263   4 Ekkwqkffeknpwll....ypiisefpik..evdfksDfllidslngnivlvEikkpdknlltk 61 
                                   Ek+  +f+ +np ++    +pi +e+     +v    D++ +d+  gn+v+ E+k+++ +l   
  gi|70606042|ref|YP_254912.1| 126 EKDEVDFIINNPDVIeggfKPIHREYRTPygTV----DLIGKDK-EGNLVVLEFKRAKASLQAV 184
                                   555668999999999888655555554434355....*******.************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1535.62
//
Query:       gi|70606043|ref|YP_254913.1|  [L=342]
Description: hypothetical protein Saci_0201 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-20   72.4   0.0    6.3e-20   71.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    3.1e-13   49.6   0.0    5.1e-13   48.9   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    1.1e-12   48.3   0.0    4.8e-12   46.3   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.035   13.6   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
       0.19   11.7   6.4       0.62   10.1   6.4    1.8  1  DUF1201          Protein of unknown function (DUF1201)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   1.8e-23   6.3e-20       1     168 [.      41     198 ..      41     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.8e-23
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS....-HHHHHHHHHHHH CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreen....vGkagalnaglra 77 
                                   sv+ip+     + +e l+sll+q +y+ +e+i+v D ++D  v il+++     +v+v+  ++n     Gk++a  +gl++
  gi|70606043|ref|YP_254913.1|  41 SVIIPVRGLDVNAEENLKSLLSQ-DYSAYEVIYVVDDENDPIVPILRKY-----NVKVVVSNKNcdicSGKINAQLEGLKH 115
                                   8999999999999**********.*************************.....9********999989************ PP

                                   --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
               Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                   a+gd+i+f D+D+++++ wl++lv +l +  a  v+      +   ++i           ++ + +  s+  + +f +g+ 
  gi|70606043|ref|YP_254913.1| 116 ARGDIIVFADSDTWFPKYWLKELVSPLSNYVATTVFSWAKPVRLTIGNII--------RAGFWTLGFESQAVGGTFLWGGS 188
                                   ****************************9443333333333333333333........46778888888888888888888 PP

                                   CEEEEHHHHH CS
               Glycos_transf_2 159 allrrealee 168
                                   ++++re ++e
  gi|70606043|ref|YP_254913.1| 189 MAFKREFFDE 198
                                   8888888766 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.4e-16   5.1e-13      12     142 ..      99     224 ..      87     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.4e-16
               Glyco_transf_21  12 pvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlq 92 
                                      ++ K+n++l +l+ a+ d++v++Dsd+ +++  L+el+ +l+       t ++ + + +   +++ +a + tl    q
  gi|70606043|ref|YP_254913.1|  99 CDICSGKINAQLEGLKHARGDIIVFADSDTWFPKYWLKELVSPLSN--YVATTVFSWAKPVRLTIGNIIRAGFWTLGFESQ 177
                                   445688***************************************7..344455556677777778888888877777777 PP

               Glyco_transf_21  93 aklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlk 142
                                   a ++g  f +G sma++re +++   +++l+ + ++D+ l+++ +++G+ 
  gi|70606043|ref|YP_254913.1| 178 A-VGG-TFLWGGSMAFKREFFDER-VIQELKTQWCDDCTLTRIAKERGKL 224
                                   7.666.******************.9******************999864 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.3e-15   4.8e-12       5     198 ..      41     222 ..      39     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.3e-15
               Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealra 85 
                                   +v++p+ + +   +e l sll+q+y+++ev++vvd + +  ++ ++     + +v+v+v  + ++ +s gk++a  e+l++
  gi|70606043|ref|YP_254913.1|  41 SVIIPVRGLDVNAEENLKSLLSQDYSAYEVIYVVDDENDPIVPILRK----Y-NVKVVVSNKNCDICS-GKINAQLEGLKH 115
                                   89*******99**********************************97....6.557777666788897.************ PP

               Glyco_tranf_2_3  86 vksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgvltlnGsgsl 166
                                   +++d++++ D+Dt   ++ lk l+  + +     v t vf+      ++  + ++ + + l f   ++a+g ++l G  ++
  gi|70606043|ref|YP_254913.1| 116 ARGDIIVFADSDTWFPKYWLKELVSPL-S---NYVATTVFSWAKPVRLTIGNIIRAGFWTLGFE--SQAVGGTFLWGGSMA 190
                                   **************************9.4...47777777766665555556667677777444..467777777899999 PP

               Glyco_tranf_2_3 167 irrevlkelegldplfllt.dDyelglrlrrag 198
                                   + re+++e    ++l+  + dD+ l++ ++++g
  gi|70606043|ref|YP_254913.1| 191 FKREFFDER-VIQELKTQWcDDCTLTRIAKERG 222
                                   999999999.66665555569**9999999987 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.7e-06     0.035       1      95 [.      41     131 ..      41     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-06
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddk.ayslaaarNrGaska 80 
                                   sv+ip+r  + +   ee ++   ++     e+i v d   ++    v  + + n +v +++++   + ++  a+  G ++a
  gi|70606043|ref|YP_254913.1|  41 SVIIPVRGLDVN--AEENLKSLLSQDYSAYEVIYVVDDENDP---IVPILRKYNVKVVVSNKNCDiCSGKINAQLEGLKHA 116
                                   799***999999..8999966666544899***999999999...45555566777765665544499999********** PP

               Glyco_tranf_2_2  81 esdlvlFlDaDcfis 95 
                                    +d+++F D+D ++ 
  gi|70606043|ref|YP_254913.1| 117 RGDIIVFADSDTWFP 131
                                   ***********9865 PP

>> DUF1201  Protein of unknown function (DUF1201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   6.4   0.00017      0.62       8      36 ..     268     296 ..     263     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                       DUF1201   8 ylllafGfliclflfclvvfiwfvykqil 36 
                                    ++laf fli + +f +  fi++v+k il
  gi|70606043|ref|YP_254913.1| 268 IFMLAFLFLIPFNVFAITPFIFWVFKNIL 296
                                   579*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2310.94
//
Query:       gi|70606044|ref|YP_254914.1|  [L=122]
Description: hypothetical protein Saci_0202 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.37   11.1   4.2        2.4    8.5   0.3    2.2  2  DUF3040   Protein of unknown function (DUF3040)
          5    6.9  16.8       0.62    9.8   1.5    2.2  2  FixS      Cytochrome oxidase maturation protein cbb3-type


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3    0.0064        57      50      69 ..       6      25 ..       3      30 .. 0.77
   2 ?    8.5   0.3   0.00027       2.4      46      78 ..      83     117 ..      68     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0064
                       DUF3040 50 llfvaGllllvlGvaaaavv 69
                                  ll+++G+ ll++Gva+   +
  gi|70606044|ref|YP_254914.1|  6 LLLIIGVSLLLIGVALGDFI 25
                                  57788999999998876545 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00027
                       DUF3040  46 vlavllfva.GllllvlG.vaaaavvlgvvGfvvm 78 
                                   v ++ ++   +ll +++G ++++ +++ v+G+v++
  gi|70606044|ref|YP_254914.1|  83 VKSITIIQYpPLLNIIFGiIIVSLIIVLVAGLVIL 117
                                   55555555657899****999999*******9986 PP

>> FixS  Cytochrome oxidase maturation protein cbb3-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.5   6.9e-05      0.62       3      24 ..       6      27 ..       5      29 .. 0.90
   2 ?    2.5   7.9     0.014   1.2e+02       1      22 [.      96     117 ..      96     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.9e-05
                          FixS  3 LylLiplSlllgllalaaFlWa 24
                                  L+l i++Slll+++al+ F+ +
  gi|70606044|ref|YP_254914.1|  6 LLLIIGVSLLLIGVALGDFILS 27
                                  7899*************99865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.014
                          FixS   1 siLylLiplSlllgllalaaFl 22 
                                   +i++  i++Sl+++l+a ++ l
  gi|70606044|ref|YP_254914.1|  96 NIIFGIIIVSLIIVLVAGLVIL 117
                                   79**************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 887.73
//
Query:       gi|70606045|ref|YP_254915.1|  [L=151]
Description: hypothetical protein Saci_0203 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.025   13.9   1.1       0.03   13.7   1.1    1.0  1  LETM1       LETM1-like protein
       0.71    8.6   5.9       0.86    8.3   5.9    1.1  1  Presenilin  Presenilin
       0.72    9.3   3.7       0.92    9.0   3.7    1.1  1  Sec62       Translocation protein Sec62
        7.3    5.5   5.6        9.6    5.1   5.6    1.1  1  CLN3        CLN3 protein


Domain annotation for each model (and alignments):
>> LETM1  LETM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   6.7e-06      0.03      91     208 ..      13     136 ..       9     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                         LETM1  91 kkqkeeklkkrlkarlevakfLqetlees....lkkkkkekkekaeelkeflkkvrsggepe.evsneeilkvaklFkde. 165
                                    +qk e++++++++r+e++k   ++l e+    +++k  ++++++++  e l++v+s+ +++ ev++++i  + k F d  
  gi|70606045|ref|YP_254915.1|  13 TEQKVEASEQKVESRQETSKSTTQKLAETktseTQEK-VNENDASKSPREDLEEVKSSPNSNsEVKVDNIKGIMKKFIDRd 92 
                                   5778888899999999999999999888876542222.2222244444444555555444332679*******99999887 PP

                         LETM1 166 ltLdnlsrkqlkalcklls.lqpfgtdnllryrlrkklreiked 208
                                    ++   s +    l  l+  +  f+++++ +  l++ lrei  d
  gi|70606045|ref|YP_254915.1|  93 PKIGIWSYPSFLVLQYLYHtVPGFKMSKIAKDALERGLREIYPD 136
                                   88888888888888775443777888888888888888888655 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.9   0.00019      0.86     244     299 ..      13      72 ..       4     100 .. 0.34

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00019
                    Presenilin 244 kkeeasesskeeeseeesseksaqsse....seeeseeesseaessaeesseekeseess 299
                                   ++++ + s+++ es++e+s++++q+ +    se++++ ++++a++s++e  ee +s+++s
  gi|70606045|ref|YP_254915.1|  13 TEQKVEASEQKVESRQETSKSTTQKLAetktSETQEKVNENDASKSPREDLEEVKSSPNS 72 
                                   222222222222222222222222211000011111111111111111111111111111 PP

>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.7   0.00021      0.92      24      72 ..      14      70 ..       5     114 .. 0.29

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                         Sec62 24 skkkkeklkevkkkek.aekvfkelkksqlalrveklkekekkkkkee.........kk 72
                                  ++k + ++++v+++++ +++++++l +++++ + ek +e++++k+            + 
  gi|70606045|ref|YP_254915.1| 14 EQKVEASEQKVESRQEtSKSTTQKLAETKTSETQEKVNENDASKS--PredleevksSP 70
                                  111111111111111101122222222222222222222222221..112232221111 PP

>> CLN3  CLN3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.6    0.0022       9.6     166     242 ..       8      89 ..       4      90 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0022
                          CLN3 166 lekkkskkeakaeeeeeeyekleeeeeeee.....eeseeeelleseaasaaeeeeeeesselkkslkeklklvksLllky 241
                                   l++kk++++ +a+e++ e++++++++++++     +++++e+++e++a+++ +e+ ee +s+ +++ + k++++k ++ k+
  gi|70606045|ref|YP_254915.1|   8 LNRKKTEQKVEASEQKVESRQETSKSTTQKlaetkTSETQEKVNENDASKSPREDLEEVKSSPNSNSEVKVDNIKGIMKKF 88 
                                   555555555555555432222222222222333333334444444455555555555555777777888888888888777 PP

                          CLN3 242 m 242
                                   +
  gi|70606045|ref|YP_254915.1|  89 I 89 
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3080  (0.171789); expected 358.6 (0.02)
Passed bias filter:                     1143  (0.0637515); expected 358.6 (0.02)
Passed Vit filter:                       186  (0.0103743); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 942.50
//
Query:       gi|70606046|ref|YP_254916.1|  [L=220]
Description: ParA-like ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-28   98.1   0.8    3.2e-26   92.3   0.8    2.1  1  AAA_31        AAA domain
    8.4e-14   51.7   0.0    1.2e-13   51.3   0.0    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    5.2e-12   45.8   0.8    1.5e-11   44.2   0.8    1.7  1  ParA          NUBPL iron-transfer P-loop NTPase
    1.7e-10   40.7   0.0    2.4e-10   40.1   0.0    1.4  1  MipZ          ATPase MipZ
    7.4e-07   28.6   0.1    9.5e-05   21.7   0.0    2.2  2  ArsA_ATPase   Anion-transporting ATPase
    0.00013   21.5   0.0       0.35   10.3   0.0    2.1  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.015   15.0   0.3      0.067   12.9   0.0    2.1  3  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.031   13.7   0.1      0.067   12.6   0.1    1.5  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
      0.058   13.1   0.0      0.098   12.4   0.0    1.4  1  AAA_24        AAA domain
      0.095   12.5   0.0       0.17   11.6   0.0    1.4  1  Latrotoxin_C  Latrotoxin C-terminal domain
       0.14   11.5   0.1       0.25   10.6   0.1    1.4  1  VirC1         VirC1 protein


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.8     2e-29   3.2e-26       3     168 ..       2     149 ..       1     159 [. 0.84

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 2e-29
                        AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenldl 83 
                                   +I+++nqKGGvGKTTtsvnl+++l+k+ k + l DlDp + at+++gi+++++e  l           ++     + n+++
  gi|70606046|ref|YP_254916.1|   2 IITVINQKGGVGKTTTSVNLSYTLSKN-KNTALLDLDPEGGATISFGIKREKREYPLGGK--------SVN----IFNVEV 69 
                                   8***********************975.566678**************888766555433........222....356789 PP

                        AAA_31  84 ipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllkti 164
                                     ++i L ++e +        e + + l+k+ +++D+ +iD+pP+Lg+l+++a++a d+++ p+ ++++ le +++l +++
  gi|70606046|ref|YP_254916.1|  70 FLAHIGLLKLELN-----GDIESIVSSLKKLAENFDFLVIDTPPNLGTLAVSAMIAGDKIVTPITPQPLVLEAAKNLDSRL 145
                                   99*****987644.....344445789**********************************************99998777 PP

                        AAA_31 165 eevk 168
                                   + ++
  gi|70606046|ref|YP_254916.1| 146 QGLR 149
                                   7665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   7.1e-17   1.2e-13       1      71 [.       3     100 ..       3     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 7.1e-17
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   i+++++kGGvGKTt+++nL   l++ +++++l+D+Dp++ ++   +g + ++++                           
  gi|70606046|ref|YP_254916.1|   3 ITVINQKGGVGKTTTSVNLSYTLSK-NKNTALLDLDPEGGATI-SFGIKREKREyplggksvnifnvevflahigllklel 81 
                                   79***********************.***************97.99999999999************************** PP

                                   ..CCHCCCHHHHHHCHCHH CS
                                   ..xxxxxxxxxxxxxxxxx RF
                          CbiA  55 ..dlkrllellealgkkka 71 
                                     d+++++ +l++l +++ 
  gi|70606046|ref|YP_254916.1|  82 ngDIESIVSSLKKLAENFD 100
                                   **99999999988888754 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.8   9.1e-15   1.5e-11       5     155 ..       2     140 ..       1     164 [. 0.78

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 9.1e-15
                          ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfllese 85 
                                   +i+v+  KGGVGK+t++vnl+++L+k +++++llD+D  G      +g+++e   +   + +P+  k++++  ++++l   
  gi|70606046|ref|YP_254916.1|   2 IITVINQKGGVGKTTTSVNLSYTLSK-NKNTALLDLDPEGGAT-ISFGIKRE---K---REYPLGGKSVNIFNVEVFLA-- 72 
                                   799*********************75.6899*******99765.45788886...2...347999999****9999999.. PP

                          ParA  86 deavvwrGpmkskaikqllkdvew..gelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkk 155
                                      +      +++ i+ ++++ +   ++ D+L+iD+PP  g  +l+v  ++  +++v   tpq + l+ +k 
  gi|70606046|ref|YP_254916.1|  73 --HIGLLKLELNGDIESIVSSLKKlaENFDFLVIDTPPNLG--TLAVSAMIAGDKIVTPITPQPLVLEAAKN 140
                                   ..44444555666666666655433379************9..57777788889999999****99988775 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   1.5e-13   2.4e-10       2     152 ..       2     151 ..       1     182 [. 0.77

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.5e-13
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHH...HHT------EEE-SSS-HHHHTT CS
                          MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraatae...rkglsLplpealalseaeeaeve 79 
                                   +i + n+kGG Gk+tt+v +  +L+k+ ++ a +dld    +   +   r +++     k +++      ++  a+   ++
  gi|70606046|ref|YP_254916.1|   2 IITVINQKGGVGKTTTSVNLSYTLSKN-KNTALLDLDPEGGATISFGIKREKREYplgGKSVNIFNV---EVFLAHIGLLK 78 
                                   68899******************9876.7889*****998877777655655544100344444443...44445555566 PP

                                   S-HHHHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSHHHHCCCEEE-SSS--EEEE CS
                          MipZ  80 eeeeaevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsfvdfdllgkvdpetlkvkrp 152
                                    e + +++++   +++l++++df+vidtP +  +l+ +a    d +vtP+    + ++   ++d+    +++p
  gi|70606046|ref|YP_254916.1|  79 LELNGDIESIVSSLKKLAENFDFLVIDTPPNLGTLAVSAMIAGDKIVTPITPQPLVLEAAKNLDSRLQGLRKP 151
                                   6666666799***************************************987666666666666666555555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   5.8e-08   9.5e-05       5      52 ..       5      51 ..       1      73 [. 0.76
   2 !    5.3   0.0    0.0057       9.3     122     140 ..      96     114 ..      80     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.8e-08
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--B CS
                   ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklg 52
                                  ++  KGGVGKtt s  +++ ls++ k++ l+ +DP      sf  k +
  gi|70606046|ref|YP_254916.1|  5 VINQKGGVGKTTTSVNLSYTLSKN-KNTALLDLDPEGGATISFGIKRE 51
                                  5678******************86.56677899997666666666555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0057
                                   CSSSSEEEEESBSCCHTCG CS
                   ArsA_ATPase 122 eeeydvvvlDtaPTGhtlr 140
                                   +e++d +v+Dt+P   tl 
  gi|70606046|ref|YP_254916.1|  96 AENFDFLVIDTPPNLGTLA 114
                                   689**********877765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00021      0.35       5      54 ..       4      52 ..       1      56 [. 0.82
   2 !    9.3   0.0   0.00045      0.73     101     147 ..      84     130 ..      76     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                      CBP_BcsQ  5 alqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieq 54
                                  ++   +GGvG+t+ ++ L++ l + ++  l +Dl p+   +++F ++ e+
  gi|70606046|ref|YP_254916.1|  4 TVINQKGGVGKTTTSVNLSYTLSKNKNTAL-LDLDPEGGATISFGIKREK 52
                                  555568****************99887776.6999999999998887665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00045
                      CBP_BcsQ 101 kaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvep 147
                                   + e++ + lk+l+e+++++++D p +  +l+ +++   d+ ++ ++p
  gi|70606046|ref|YP_254916.1|  84 DIESIVSSLKKLAENFDFLVIDTPPNLGTLAVSAMIAGDKIVTPITP 130
                                   56788999**********************99999989988877766 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   2.2e+03      41      57 ..       9      25 ..       4      32 .. 0.69
   2 ?   12.9   0.0   4.1e-05     0.067      17      90 ..      83     156 ..      70     166 .. 0.83
   3 ?   -1.4   0.0       1.1   1.8e+03     121     144 ..     168     191 ..     153     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                        RuvB_N 41 pPGlGkttlakiiakel 57
                                    G+Gktt +  ++  l
  gi|70606046|ref|YP_254916.1|  9 KGGVGKTTTSVNLSYTL 25
                                  56899999887666655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.1e-05
                        RuvB_N  17 eklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgP.vlekagdlaalltnleekdvlfi 90 
                                    +++ ++++ kk  e+ d +++  pP lG  +++++ia +  v+  it  P vle a++l + l+ l++  + f 
  gi|70606046|ref|YP_254916.1|  83 GDIESIVSSLKKLAENFDFLVIDTPPNLGTLAVSAMIAGDKIVTP-ITPQPlVLEAAKNLDSRLQGLRKPAIAFT 156
                                   5667788999999*************************9987765.55555278999999999999999888775 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                        RuvB_N 121 psarsikldlpkftlvgattragl 144
                                   ps +si l++p+  l + +tr g+
  gi|70606046|ref|YP_254916.1| 168 PSVKSIDLSIPQSKLFSEATRLGV 191
                                   677889999999999999998875 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.1e-05     0.067       5      40 ..       6      40 ..       2      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                     Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  i  kGG+Gk+tts nls +l+++ +   ++  DP  
  gi|70606046|ref|YP_254916.1|  6 INQKGGVGKTTTSVNLSYTLSKNKNTA-LLDLDPEG 40
                                  678*****************9875544.44566665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05     0.098      10      94 ..       9     127 ..       3     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                        AAA_24  10 psgiGKTtlakel......gpkplfidtek.Glksldadkfpdie................swedfldevvel........ 59 
                                   + g+GKTt+  +l       ++++++d++  G + + +      +                ++e fl  +  l        
  gi|70606046|ref|YP_254916.1|   9 KGGVGKTTTSVNLsytlskNKNTALLDLDPeGGATISFGI----KrekreyplggksvnifNVEVFLAHIGLLklelngdi 85 
                                   579**********777777777777766654444444433....0344579999998888877777777777799999999 PP

                        AAA_24  60 .......aaeladyktlviDtideleelclaevirqnekaes 94 
                                          ++  ++++ lviDt   l  l++  +i  +++ + 
  gi|70606046|ref|YP_254916.1|  86 esivsslKKLAENFDFLVIDTPPNLGTLAVSAMIAGDKIVTP 127
                                   999999999999*********999999999999888877665 PP

>> Latrotoxin_C  Latrotoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.17      51      84 ..      47      80 ..      40     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                  Latrotoxin_C 51 eitrtakeygltghsldidfvevqnavigliman 84
                                   i r  +ey l g+s++i  vev  a igl+  +
  gi|70606046|ref|YP_254916.1| 47 GIKREKREYPLGGKSVNIFNVEVFLAHIGLLKLE 80
                                  68999************************98654 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00015      0.25       3      39 ..       2      37 ..       1      43 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                         VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  +it+   kGG Gktt+ + l  +l s++k  al++ d
  gi|70606046|ref|YP_254916.1|  2 IITVINQKGGVGKTTTSVNLSYTL-SKNKNTALLDLD 37
                                  6999**************998777.566777888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1342.88
//
Query:       gi|70606047|ref|YP_254917.1|  [L=322]
Description: hypothetical protein Saci_0205 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.4   0.2      3e-05   24.1   0.1    2.5  2  CCG       Cysteine-rich domain
      1e-11   45.1   5.3    2.3e-11   44.0   5.3    1.6  1  Fer4_8    4Fe-4S dicluster domain
    2.4e-10   40.8   5.1    6.3e-10   39.4   5.1    1.8  1  Fer4_17   4Fe-4S dicluster domain
    4.5e-10   40.0   6.9      1e-09   38.8   6.9    1.7  1  Fer4_7    4Fe-4S dicluster domain
    5.8e-07   29.1  11.0     0.0013   18.4   2.0    2.4  2  Fer4      4Fe-4S binding domain
    6.6e-07   29.4   6.2    2.1e-06   27.8   6.2    1.9  1  Fer4_9    4Fe-4S dicluster domain
    1.3e-06   28.4   9.3    2.7e-05   24.2  10.6    2.3  2  Fer4_10   4Fe-4S dicluster domain
     0.0001   22.2   8.5     0.0034   17.4   1.5    2.7  2  Fer4_2    4Fe-4S binding domain
    0.00023   21.4  12.1       0.06   13.9   2.1    2.7  2  Fer4_4    4Fe-4S binding domain
     0.0011   18.9  13.8      0.012   15.6   2.1    2.5  2  Fer4_6    4Fe-4S binding domain
     0.0026   18.7  10.2      0.069   14.1  10.6    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.038   14.9  16.9       0.73   10.9   5.0    2.7  2  Fer4_3    4Fe-4S binding domain
      0.068   14.0   7.2        2.8    8.8   0.5    3.1  3  Fer4_22   4Fe-4S dicluster domain
       0.08   13.1  12.2        2.4    8.3  12.5    2.5  2  Fer4_21   4Fe-4S dicluster domain
       0.19   11.9   7.3       0.75   10.0   1.0    2.5  2  Fer4_18   4Fe-4S dicluster domain
        2.8    8.5   6.0         23    5.6   0.3    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   2.7e-08     3e-05       3      84 ..     123     198 ..     121     199 .. 0.86
   2 !   23.9   0.0   3.1e-08   3.5e-05       1      84 [.     226     308 ..     226     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.7e-08
                           CCG   3 yfdgChllraa.ypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCll 82 
                                   +f+gC l     ++ v+ka+k   + lg ++++   ++CCG ++ + g++++a++++++  e+++    + +v+ +++C++
  gi|70606047|ref|YP_254917.1| 123 IFPGC-LTSVIsRSSVEKAVKYF-KGLGYNVKVI--NTCCGLAHSHVGENKRAMDIVQKLREEFKG---KTVVSLSSNCSA 196
                                   79***.77777577777777666.9999999999..****************************99...689999999987 PP

                           CCG  83 ql 84 
                                    +
  gi|70606047|ref|YP_254917.1| 197 FM 198
                                   66 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.1e-08
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpg 79 
                                   v+++++Ch+     + +   ++k  e+lg+++++  +    CGagg    +++ ++ +++ r+ e +++ g++ +++++p+
  gi|70606047|ref|YP_254917.1| 226 VTIHYPCHAHVVGIEGY---IRKMAEKLGLTIMDSdDPYFECGAGGSQIFFNKqISSDVMSRKKEKVMKSGVNTVISTNPS 303
                                   799****8666664444...444444455555555555999*******999999*************************** PP

                           CCG  80 Cllql 84 
                                   C+l +
  gi|70606047|ref|YP_254917.1| 304 CTLAF 308
                                   *9876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   5.3     2e-14   2.3e-11       2      65 .]       8      67 ..       7      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2e-14
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                  + kC++Cg+C ++Cp++  t+ +++++rg+ ++ +   +     e+l++C+ c++C+ +Cp g+
  gi|70606047|ref|YP_254917.1|  8 ALKCVHCGFCLESCPTYVVTRSEIHSPRGRITAVKLGID----SEGLKTCMFCRKCEIACPSGV 67
                                  689***************************999333333....589***************986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   5.1   5.7e-13   6.3e-10       1      60 [.      10      67 ..      10      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.7e-13
                       Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                  +C +Cg+Cl++Cp+y  +++e ++++ ++++ +l+  +++e  ++C+ C++Ce +CP+g+
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYVVTRSEIHSPRGRITAVKLG--IDSEGLKTCMFCRKCEIACPSGV 67
                                  6***************************9885444..5799****************997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   6.9   9.3e-13     1e-09       1      52 []      10      67 ..      10      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 9.3e-13
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt...ekveidpe...kClgCgaCvavCPtga 52
                                  +C++Cg+C + Cp+++++  e ++++g+    k+ id+e   +C++C++C+ +CP+g+
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYVVTRSEIHSPRGRitaVKLGIDSEglkTCMFCRKCEIACPSGV 67
                                  7********************9999987544444555543338*************96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.0   1.2e-06    0.0013       7      22 ..      10      25 ..       8      27 .. 0.89
   2 !   15.4   1.9   1.1e-05     0.012       7      22 ..      52      67 ..      50      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                  TSSS-THHHHHSTTTE CS
                          Fer4  7 kCigCGaCvevCPvgA 22
                                  kC++CG C e CP+ +
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYV 25
                                  9************976 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                                  TSSS-THHHHHSTTTE CS
                          Fer4  7 kCigCGaCvevCPvgA 22
                                   C++C +C+ +CP g+
  gi|70606047|ref|YP_254917.1| 52 TCMFCRKCEIACPSGV 67
                                  5************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   6.2   1.9e-09   2.1e-06       1      49 [.      10      66 ..      10      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.........eaCigCgaCveaCpkg 49
                                  kC+ Cg C e+Cp+ vv++++ +  +   ++           + C++C++C+ aCp+g
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYVVTRSEIHSPRGR-ITAVklgidseglKTCMFCRKCEIACPSG 66
                                  7***************998887766443.33334699999**99************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  10.6   2.5e-08   2.7e-05       7      56 .]       9      64 ..       5      64 .. 0.92
   2 !   16.1   1.9   7.8e-06    0.0088       7      31 ..      51      71 ..      45      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.5e-08
                       Fer4_10  7 dtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +C++Cg C ++CP+++      +s +++  a + + ++++++ C++c +C  aCP
  gi|70606047|ref|YP_254917.1|  9 LKCVHCGFCLESCPTYVvtrseiHSPRGRITAVKLGIDSEGLKTCMFCRKCEIACP 64
                                  68*************99****9888888888899999999***************9 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.8e-06
                       Fer4_10  7 dtCirCgkCvkaCPadltsvgakge 31
                                  +tC+ C+kC  aCP+     +++ e
  gi|70606047|ref|YP_254917.1| 51 KTCMFCRKCEIACPS----GVKYSE 71
                                  79*************....333333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   3.1e-06    0.0034       8      22 .]       9      23 ..       5      23 .. 0.89
   2 !    8.3   0.9    0.0024       2.7       9      21 ..      52      64 ..      42      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                        Fer4_2  8 drCigCgaCvsaCPa 22
                                   +C++Cg C+ +CP+
  gi|70606047|ref|YP_254917.1|  9 LKCVHCGFCLESCPT 23
                                  69************7 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                        Fer4_2  9 rCigCgaCvsaCP 21
                                  +C+ C++C  aCP
  gi|70606047|ref|YP_254917.1| 52 TCMFCRKCEIACP 64
                                  7999********* PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.1   5.3e-05      0.06       3      16 ..      10      23 ..       8      27 .. 0.93
   2 !   11.8   2.6   0.00025      0.28       2      17 .]      51      66 ..      50      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                  +C++Cg C  +CP+
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPT 23
                                  7************6 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00025
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  ++C  C++C++aCP+g
  gi|70606047|ref|YP_254917.1| 51 KTCMFCRKCEIACPSG 66
                                  67889*********75 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.1   1.1e-05     0.012       8      23 ..      10      25 ..       8      26 .. 0.92
   2 !    8.1   4.2    0.0026       2.9      12      22 ..      56      66 ..      52      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        Fer4_6  8 kCigCgdCvrvCPega 23
                                  kC++Cg C   CP+++
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYV 25
                                  8************976 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                        Fer4_6 12 CgdCvrvCPeg 22
                                  C++C+++CP g
  gi|70606047|ref|YP_254917.1| 56 CRKCEIACPSG 66
                                  *********87 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  10.6   6.1e-05     0.069       1      66 [.      10      65 ..      10      66 .. 0.76
   2 ?    6.9   3.3     0.011        12       2      15 ..      53      66 ..      52      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                  +C+ Cg C+e+CPt +++     ei +++   +      +l +d+e  k    +++C++C+ +CP 
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYVVTRS---EIHSPRGRIT----AVKLGIDSEGLK---TCMFCRKCEIACPS 65
                                  5******************9...7777776443....334444444444...599**********5 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                       Fer4_16  2 CgtCgkCaevCPtn 15
                                  C  C+kC  +CP++
  gi|70606047|ref|YP_254917.1| 53 CMFCRKCEIACPSG 66
                                  88899999999987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.0   0.00065      0.73       1      13 [.      11      23 ..      11      25 .. 0.94
   2 ?    9.2   4.1    0.0023       2.6       1      14 [.      53      66 ..      53      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00065
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C++Cg C+e+CP+
  gi|70606047|ref|YP_254917.1| 11 CVHCGFCLESCPT 23
                                  ************6 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0023
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+ C+ C+ +CP+g
  gi|70606047|ref|YP_254917.1| 53 CMFCRKCEIACPSG 66
                                  99**********98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.5    0.0025       2.8       1      15 [.      10      24 ..       6      43 .. 0.76
   2 ?    7.2   0.2     0.008         9       2      16 ..      53      67 ..      44      88 .. 0.78
   3 ?   -0.0   0.0       1.4   1.6e+03      30      69 ..     147     185 ..     125     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0025
                       Fer4_22  1 rClsCgaCtlvCptC 15
                                  +C++Cg C   Cpt 
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTY 24
                                  577777777777764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.008
                       Fer4_22  2 ClsCgaCtlvCptCs 16
                                  C+ C +C ++Cp+ +
  gi|70606047|ref|YP_254917.1| 53 CMFCRKCEIACPSGV 67
                                  888888888888755 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.4
                       Fer4_22  30 egervrvwdsClleeftkvaggenvrkekkerlrqrllhk 69 
                                    g  v+v+++C+   +++v ++ +   +  ++lr+ +  k
  gi|70606047|ref|YP_254917.1| 147 LGYNVKVINTCCGLAHSHVGEN-KRAMDIVQKLREEFKGK 185
                                   5667888899998888887766.44445566666666555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  12.5    0.0022       2.4       7      52 ..      10      64 ..       6      68 .. 0.67
   2 ?    7.7   2.6    0.0035       3.9       6      20 ..      51      65 ..      45      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                       Fer4_21  7 kCigCgkCliaCedtshqaieidakt..vlkvv.......edeCvGCnlCssvCP 52
                                  kC++Cg Cl +C++  ++  ei++ +  +++v         ++C+ C  C + CP
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPTYVVTRSEIHSPRgrITAVKlgidsegLKTCMFCRKCEIACP 64
                                  8************877766554433221222212222222469************ PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                       Fer4_21  6 dkCigCgkCliaCed 20
                                  ++C+ C kC iaC+ 
  gi|70606047|ref|YP_254917.1| 51 KTCMFCRKCEIACPS 65
                                  579999999999985 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0   0.00067      0.75      58      79 ..       8      29 ..       4      34 .. 0.83
   2 ?    5.0   0.7     0.023        26      55      76 ..      47      68 ..      30      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
                       Fer4_18 58 agdcidcescvkvcPtgidirk 79
                                  a +c++c++c++ cPt +  r 
  gi|70606047|ref|YP_254917.1|  8 ALKCVHCGFCLESCPTYVVTRS 29
                                  558*************997775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                       Fer4_18 55 ekgagdcidcescvkvcPtgid 76
                                  ++g   c+ c++c   cP g+ 
  gi|70606047|ref|YP_254917.1| 47 SEGLKTCMFCRKCEIACPSGVK 68
                                  677889************9985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.1     0.035        39       5      18 ..      10      23 ..       7      27 .. 0.91
   2 ?    5.6   0.3     0.021        23       4      18 ..      51      65 ..      49      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.035
                       Fer4_13  5 tCiacgaCvelaPd 18
                                  +C+ cg C e +P 
  gi|70606047|ref|YP_254917.1| 10 KCVHCGFCLESCPT 23
                                  7************6 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  +tC+ c +C  ++P 
  gi|70606047|ref|YP_254917.1| 51 KTCMFCRKCEIACPS 65
                                  59************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2341.88
//
Query:       gi|70606048|ref|YP_254918.1|  [L=458]
Description: glycolate oxidase subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-52  177.3   0.0    5.7e-52  176.8   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    4.1e-29  101.1   0.2      6e-29  100.6   0.2    1.3  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.0   6.4e-56   5.7e-52       1     249 [.     203     439 ..     203     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 6.4e-56
                                   --SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHH CS
                 FAD-oxidase_C   1 lpearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeele 81 
                                   +p++r++++++f+++++a ka+ +i ++g+ip+ale+md+ ++ ++e+      +  +e ea+ll+e++g++ ++  ee +
  gi|70606048|ref|YP_254918.1| 203 KPKSRKSVFATFNDVKDAGKAIIDIFKKGVIPSALEMMDRYSIIAIEKSRYR--AGLPEVEAILLIELDGSEIQVKSEESR 281
                                   699***********************************************99..9999**************888888888 PP

                                   H.HHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEE CS
                 FAD-oxidase_C  82 a.lveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevv 161
                                   + +v +  +++++        ++e e++w aR++a+p    a +  ++a+++ D+ v +s+l++++++i+++  k++l ++
  gi|70606048|ref|YP_254918.1| 282 VrDVISENNGEIIN-------PKEPEKFWSARRGAFP----AMGVISPAYITLDCNVLRSNLPEVLAKIREISIKQNLYIA 351
                                   55555555555555.......58889***********....9999************************************ PP

                                   EEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT CS
                 FAD-oxidase_C 162 lfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPk 242
                                   +++Hagdgnlh++i ++++d +   +a k++de+ +l++e gG  sgEHG+G++k +yl  +++e+ l++m++iK ++D  
  gi|70606048|ref|YP_254918.1| 352 NVFHAGDGNLHPLISYNPEDFDSFVKAVKASDEIEKLVIESGGVPSGEHGIGIEKVKYLDLYYDEKSLEVMKKIKTTFDTY 432
                                   ********************************************************************************* PP

                                   --BSTT- CS
                 FAD-oxidase_C 243 giLNPgk 249
                                   g++NP k
  gi|70606048|ref|YP_254918.1| 433 GLFNPCK 439
                                   *****98 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.2   6.7e-33     6e-29       1     138 [.      35     171 ..      35     172 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 6.7e-33
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC..SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav..atggvvldlsrlnrileideeegtatveaGvtlgdlve 79 
                                   p++vv p++eee +a++r+  ++++++++rG+G+sl+g+ v  + + vv++lsrln++  i   +  ++v++G+  + + +
  gi|70606048|ref|YP_254918.1|  35 PELVVLPGNEEEAIAVIRYLIQNRRKIIIRGSGTSLSGATVpvEGDEVVVSLSRLNKVYGIR--GLEIEVGPGIANALVTK 113
                                   789*************************************9999999**************9..9**************** PP

                                   HHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  80 alaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                    + + +l++ ++p+s+  +++GG+i+  +gG ++ kyG++++ v++++v+la+G+v ++
  gi|70606048|ref|YP_254918.1| 114 SC-PPHLFYAPDPASYQVSSIGGNISHDSGGVHVVKYGPTFNSVVSVKVILANGNVEEI 171
                                   **.99999999********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3612.34
//
Query:       gi|70606049|ref|YP_254919.1|  [L=320]
Description: FAD-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-17   61.6   0.0      1e-16   61.0   0.0    1.3  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.6e-21     1e-16       6     137 ..       6     132 ..       4     134 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.6e-21
                                   EESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHTT CS
                 FAD_binding_4   6 rpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaakgl 86 
                                   +p + e +++++  a +++l+v ++G G + +g+   + ++ +++++l+rilei e++ +a v++Gv   +l+e+l++k+l
  gi|70606049|ref|YP_254919.1|   6 YPDNYEKLSEVIGEAIKRKLKVHIMGYGNHHIGKLP-KADICISTKKLDRILEIREADLYAIVQSGVDSLKLQEELEKKNL 85 
                                   799*****************************9995.********99********************************** PP

                                   ECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEE CS
                 FAD_binding_4  87 llglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvr 137
                                   ll+     + +g+vGG+   n  +  s      +d+vlg+++++++G+vv+
  gi|70606049|ref|YP_254919.1|  86 LLP----FVYDGSVGGLFGRNYPSLYSIWFPYPKDFVLGAKILTGEGTVVK 132
                                   ***....46899*************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2449.47
//
Query:       gi|70606050|ref|YP_254920.1|  [L=304]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-32  112.7   0.4    6.5e-32  110.4   0.1    1.9  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.9e-23   82.4   0.7    3.9e-23   81.4   0.7    1.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.1   7.3e-36   6.5e-32       2     153 .]      43     192 ..      42     192 .. 0.93
   2 ?    0.2   0.0     0.065   5.8e+02     127     145 ..     222     238 ..     211     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 7.3e-36
                                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvln 81 
                                   iGc+   ++++      +++  sg+++ +G+++p+A+G+kla+p+ ev++  GDG++l i   +++ + rrn++i+v+++n
  gi|70606050|ref|YP_254920.1|  43 IGCSGK-LSQY------TRIPVSGVHTLHGRAIPFAVGIKLANPSLEVIVNGGDGDLLGIgAGHFVSVGRRNVDIVVILHN 116
                                   777776.4444......344449*************************************99******************* PP

                                   -SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  82 Negygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   N++yg+t+gq   +  +g+k+ks p +++ + ++++ la a G + +ar   +dv +l+e++k+a+++kg a++++
  gi|70606050|ref|YP_254920.1| 117 NGVYGLTKGQaapTLFRGMKTKSLPRPNINDAINPVTLALASGYTfVARAYAYDVPHLKEIIKQAIKHKGLAFVDI 192
                                   **********99888899*********9*****************999999***********************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.065
                                   ESSH.HHHHHHHHHHHHCS CS
                  TPP_enzyme_C 127 vekadveeleealkealek 145
                                   v+++  +e++e+lk+a++k
  gi|70606050|ref|YP_254920.1| 222 VKSE--SEMQEKLKKAIDK 238
                                   5566..99********965 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.7   4.4e-27   3.9e-23       1      63 [.     196     266 ..     196     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 4.4e-27
                                   XTTTXSSSXSXXXXX-EEEGGGST---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerlee 63 
                                   C+t+N++nT +wY++rvyk+++  +Dp +         l+kA++k+ ewg++ip+GifYk e +ptyeer+++
  gi|70606050|ref|YP_254920.1| 196 CPTYNDINTKEWYDKRVYKMQD--MDPVVksesemqekLKKAIDKSYEWGERIPIGIFYKnELVPTYEERIKT 266
                                   *********************8..8*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2110.75
//
Query:       gi|70606051|ref|YP_254921.1|  [L=622]
Description: 2-oxoacid-ferredoxin oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-62  209.5   0.4    3.9e-61  206.8   0.0    2.0  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    1.6e-35  122.8   1.5    3.3e-35  121.8   0.8    1.9  2  POR           Pyruvate ferredoxin/flavodoxin oxidoreductase
    1.9e-05   24.9   0.1    0.00012   22.3   0.0    2.6  2  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
    0.00017   21.3   1.3     0.0085   15.7   0.7    2.8  3  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
  ------ inclusion threshold ------
       0.12   12.4   0.0        1.4    8.9   0.0    2.7  3  Nup35_RRM_2   Nup53/35/40-type RNA recognition motif
       0.13   12.3   0.0       0.34   11.0   0.0    1.7  1  DUF2164       Uncharacterized conserved protein (DUF2164)
        1.1    9.7   6.9       0.29   11.6   3.0    2.1  2  Asp23         Asp23 family, cell envelope-related function


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.16   4.1e+02     155     226 ..      88     158 ..      82     163 .. 0.76
   2 !  206.8   0.0   1.5e-64   3.9e-61       2     222 ..     236     476 ..     235     484 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.16
                                   HHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHH CS
                         POR_N 155 gfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvv 226
                                   g+ +  +ve+v+ ++ e+   + k+ + e+ +k  +   e+   rg    p++++e+ +k+ e ++   +vv
  gi|70606051|ref|YP_254921.1|  88 GVKG-TKVETVQSMESEAAERISKQLESENLPKTVEGALESAKRRGVKLIPVNYDEIAKKVAEEAKVQLSVV 158
                                   5555.6788888888887777777778888888889999999999999999999999999988777555555 PP

  == domain 2  score: 206.8 bits;  conditional E-value: 1.5e-64
                                   HHHHCTEEEEEE--BTTTCC..HHHHHCHCCCCCTT.......EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsse..iaeelaellakgev.......gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGll 73 
                                   +++++g++++++YPITP+s+  ++ e+++ + ++++       g v+vvq+e+E++a+++++GAa++G r+ TaTSg+G++
  gi|70606051|ref|YP_254921.1| 236 GKLYGGLRFQSYYPITPASDesMYIEAHQEVLMEDPktgdkkkGAVVVVQAEDELAAVNMAVGAALTGIRSSTATSGPGFS 316
                                   67899***************9**********99999999999999************************************ PP

                                   HCCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEE CS
                         POR_N  74 LmienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPv 149
                                   Lm+e +g+a+++e+Pvvi+++ R++pstgl++rt+q Dl++       +++ iv+as+++ eaf++a+  +nlAe++++Pv
  gi|70606051|ref|YP_254921.1| 317 LMVEGIGWAGMNEVPVVITYYIRGGPSTGLPTRTSQADLLFSMfaghgEFPKIVVASGTHDEAFKDAVLTLNLAERYQTPV 397
                                   ********************************************************************************* PP

                                   EEEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXX CS
                         POR_N 150 ivlfDgfllshevekvelpdee.delklikekleeyerkey........aldpekpiargtaanpdtglehrekgneaeda 221
                                   i+l++++l+ +++ +v+  d    +l++ + kl  + +++y        +++p+ p+  g+a +++tg+eh+e+g+++ed 
  gi|70606051|ref|YP_254921.1| 398 IHLVEKTLA-NSYTTVPKQDLGvGQLYADRGKLILSPPEDYarfqftedGVSPRAPL--GKALMYYTGDEHNEYGFISEDP 475
                                   *********.*********999777777777776666666677777**9*******8..******************9994 PP

                                   H CS
                         POR_N 222 a 222
                                   +
  gi|70606051|ref|YP_254921.1| 476 V 476
                                   4 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.8   1.3e-38   3.3e-35       2     177 .]       7     207 ..       4     207 .. 0.95
   2 ?   -3.1   0.0       2.7     7e+03      71      87 ..     271     287 ..     242     300 .. 0.60

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 1.3e-38
                                   TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEE CS
                           POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggii 82 
                                   G+G+ t ++i++k+++  Gyy+++nrey+s+i+G+hsy++++isd+ +v+si+ ++ad+lv +daet+ +h++++k  g+i
  gi|70606051|ref|YP_254921.1|   7 GTGIDTSANIFGKVVSTLGYYIYGNREYHSNIKGRHSYFTLTISDK-KVRSIP-EKADILVSFDAETVLQHFNEIK--GYI 83 
                                   99********************************************.9*****.**********************..*** PP

                                   EEECTCGTT-CCHHHCTS-HHHHHHH......................T-EEEEE-HHHHHHHCCC.........CCHHHH CS
                           POR  83 iynseelkpdelkkakeeerelkerl......................gvrvygvdatkiakeiggn........eraaNt 133
                                   iyn++ + +++++ + +e+ ++++ +                      gv++++v++ +iak+ + +        er++N+
  gi|70606051|ref|YP_254921.1|  84 IYNEGVKGTKVETVQSMESEAAERISkqlesenlpktvegalesakrrGVKLIPVNYDEIAKKVAEEakvqlsvvERVKNV 164
                                   **********99999998877777669***********************************7666677778888****** PP

                                   HHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                           POR 134 vmlGalaallglplealeeaikkrfpkkkeviekNlkafragye 177
                                   ++++++ +llg+ +e+l ++   +f+++    ++N+ a++++ye
  gi|70606051|ref|YP_254921.1| 165 IGIAVSTKLLGINEEHLAKVAGSTFKQE-LYRKLNVMAIKKAYE 207
                                   **************************86.67899********97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                   HHGGGEEEEEEEEEECT CS
                           POR  71 ehldglkpggiiiynse 87 
                                   +   + k+g ++++++e
  gi|70606051|ref|YP_254921.1| 271 PKTGDKKKGAVVVVQAE 287
                                   44444555555555553 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.6   9.2e+03      71      83 ..     140     152 ..     119     170 .. 0.55
   2 !   22.3   0.0   4.7e-08   0.00012       2      95 ..     511     594 ..     510     601 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                                   HHHHHHHTGGGTS CS
                       PFOR_II  71 veevkaalkkskv 83 
                                   ++e+++++ ++++
  gi|70606051|ref|YP_254921.1| 140 YDEIAKKVAEEAK 152
                                   4555555555533 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 4.7e-08
                                   SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGT CS
                       PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkksk 82 
                                   e v+++ G+  g+    +d l e +++  ll+lr++ PFP++ ++++l++ kk++  + n+ + ++G +v   k+ +    
  gi|70606051|ref|YP_254921.1| 511 ENVVITWGAPTGV---FIDILEETKLDFALLQLRMFSPFPSRFVSKFLQGRKKIIAAEGNY-LAQAGKIV---KMNT---G 581
                                   5677777777775...57888889999**********************************.44445544...3332...2 PP

                                   SEEEEEE--GGG- CS
                       PFOR_II  83 vkvvnfvaglgGr 95 
                                   +++ n++ + +Gr
  gi|70606051|ref|YP_254921.1| 582 IEATNYILKWNGR 594
                                   4455666666665 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.032        83     125     171 ..     106     150 ..      63     151 .. 0.80
   2 !   15.7   0.7   3.3e-06    0.0085      40      98 ..     281     337 ..     274     400 .. 0.76
   3 ?   -1.6   0.0      0.69   1.8e+03      65      98 ..     369     402 ..     358     414 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.032
                                   SEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EEEHH CS
                  TPP_enzyme_N 125 kyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleevded 171
                                   +   +  ++e+lp++++ A++ a  +r+g+ ++ + +d + ++v+e+
  gi|70606051|ref|YP_254921.1| 106 ERISKQLESENLPKTVEGALESA--KRRGVKLIPVNYDEIAKKVAEE 150
                                   5555666899*************..**************99999875 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.3e-06
                                   SEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEE CS
                  TPP_enzyme_N  40 irvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsg 98 
                                   + vv+a +E +a+++A+g a     +    +tsgpG+  ++ ++  A  + +P+++   
  gi|70606051|ref|YP_254921.1| 281 VVVVQAEDELAAVNMAVGAALTG--IRSSTATSGPGFSLMVEGIGWAGMNEVPVVITYY 337
                                   5689999***********98875..7778899***********************9765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.69
                                   -EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEE CS
                  TPP_enzyme_N  65 pgvvlvtsgpGatnaltalaeAkvdriPllvlsg 98 
                                   ++v+  t+  ++  a+  l  A + ++P+++l+ 
  gi|70606051|ref|YP_254921.1| 369 IVVASGTHDEAFKDAVLTLNLAERYQTPVIHLVE 402
                                   56666666667777888888999999***99986 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.69   1.8e+03      14      27 ..      69      83 ..      68     104 .. 0.84
   2 ?   -3.2   0.0       3.5   8.9e+03      19      42 ..     179     203 ..     169     204 .. 0.78
   3 ?    8.9   0.0   0.00057       1.4       9      42 ..     554     590 ..     550     595 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.69
                   Nup35_RRM_2 14 ielVlehFas.fGeI 27
                                  +e Vl+hF++  G I
  gi|70606051|ref|YP_254921.1| 69 AETVLQHFNEiKGYI 83
                                  6789****9955766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.5
                   Nup35_RRM_2  19 ehFas.fGeIvkhyvpkevsvmyvk 42 
                                   eh+a   G + k++  ++ +vm +k
  gi|70606051|ref|YP_254921.1| 179 EHLAKvAGSTFKQELYRKLNVMAIK 203
                                   6999559999998888888888776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00057
                   Nup35_RRM_2   9 ydtelielVle...hFasfGeIvkhyvpkevsvmyvk 42 
                                   + +++++++++   ++a+ G+Ivk++ ++e   +++k
  gi|70606051|ref|YP_254921.1| 554 FLQGRKKIIAAegnYLAQAGKIVKMNTGIEATNYILK 590
                                   789999999999**************99766666666 PP

>> DUF2164  Uncharacterized conserved protein (DUF2164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.34      29      56 ..      66      93 ..      59     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                       DUF2164 29 eleAeflLdffleeiGphiYNqalaDaq 56
                                  +++Ae +L+ f e  G  iYN++++  +
  gi|70606051|ref|YP_254921.1| 66 SFDAETVLQHFNEIKGYIIYNEGVKGTK 93
                                  7**********************98655 PP

>> Asp23  Asp23 family, cell envelope-related function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.0   0.00011      0.29      21      98 ..      92     170 ..      88     177 .. 0.91
   2 ?   -2.7   0.1       3.1   7.9e+03      46      66 ..     278     297 ..     268     300 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                         Asp23  21 eeveGvvgmagklkdglaellgkenltkgvkvevgeekqvavdlyvvveYGvkipevae..nvqekVkeaveemtglevs 98 
                                   ++ve v +m++++++++++ l++enl k v+   ++ k+  v+l + v+Y+   ++vae  +vq +V e+v+++ g+ vs
  gi|70606051|ref|YP_254921.1|  92 TKVETVQSMESEAAERISKQLESENLPKTVEGALESAKRRGVKL-IPVNYDEIAKKVAEeaKVQLSVVERVKNVIGIAVS 170
                                   68999**************************9999999999998.99***********7336999***********9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                         Asp23  46 ltkgvkvevgeekqvavdlyv 66 
                                    +  v v+  e++ +av++ v
  gi|70606051|ref|YP_254921.1| 278 KGAVVVVQ-AEDELAAVNMAV 297
                                   33334444.447778888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.40
# Mc/sec: 4710.27
//
Query:       gi|70606052|ref|YP_254922.1|  [L=270]
Description: hypothetical protein Saci_0210 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.4   0.0       0.11   12.8   0.0    1.8  2  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.73   1.3e+04      13      25 ..     140     152 ..     134     155 .. 0.63
   2 ?   12.8   0.0   5.9e-06      0.11       9      33 ..     161     185 ..     157     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.73
                                   HHHHHHHHTT-EE CS
                          SepF  13 qeiadalkegkiV 25 
                                   ++i+ ++++g +V
  gi|70606052|ref|YP_254922.1| 140 EDIIVEFNKGLPV 152
                                   5566666666666 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.9e-06
                                   GGGHHHHHHHHHTT-EEEEE-CCCT CS
                          SepF   9 fedaqeiadalkegkiVilnledld 33 
                                   + d +++ ++l+++k+Vi+nl+ ++
  gi|70606052|ref|YP_254922.1| 161 YTDFRNVTETLESKKPVIVNLSPTS 185
                                   89*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1773.38
//
Query:       gi|70606053|ref|YP_254923.1|  [L=238]
Description: hypothetical protein Saci_0211 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-15   56.5   0.0    4.5e-15   55.7   0.0    1.3  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.5e-19   4.5e-15      20     211 ..      13     172 ..      11     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.5e-19
                                   HHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTEEEEEEEEEE CS
                  CN_hydrolase  20 klleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvigliereltngklqayntavl 100
                                   ++lel ++A r+ga++++lPE ++      ++            l+ l++la+++  +++ g  e    + ++       +
  gi|70606053|ref|YP_254923.1|  13 LALELTENALREGAEVVLLPEKWVKTL---DELP----------LEDLRNLAKRYTAYIIPGAVED---GVSI----ISPI 73 
                                   6899********************766...7755..........89*******************7...4444....5668 PP

                                   EETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEE...BH. CS
                  CN_hydrolase 101 ldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpellralalkgaeilvn...lse 178
                                   ++ dg++ g+  K+hLf       +   r l++  +  ++f  +++kiG+ iCy+  fpe++r + lkg+ei++    +  
  gi|70606053|ref|YP_254923.1|  74 ISYDGEVKGIAKKIHLF------LEESKRLLPGTFT--TMFNFRGIKIGVVICYDADFPEVIRSMFLKGVEIVLVpskI-- 144
                                   899**************......4555555555544..899**********************************5532.. PP

                                   GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEB CS
                  CN_hydrolase 179 rapvpksmgppqwellgraralengcfviaanq 211
                                           g + w    r+r len + +i +n 
  gi|70606053|ref|YP_254923.1| 145 -----PTDGIDLWREYLRTRVLENRIAIINSNA 172
                                   .....4678899999999*****9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1728.55
//
Query:       gi|70606054|ref|YP_254924.1|  [L=377]
Description: hypothetical protein Saci_0212 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-33  113.5   4.1      2e-10   41.0   0.0    4.4  4  CBS              CBS domain
    1.8e-05   25.5   2.5    5.9e-05   23.8   2.5    1.9  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
  ------ inclusion threshold ------
       0.16   12.2   1.2        0.5   10.6   0.0    2.4  4  PBP5_C           Penicillin-binding protein 5, C-terminal dom


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-07   0.00088      11      54 ..      14      56 ..       5      59 .. 0.81
   2 !   29.4   0.1   1.4e-10   8.1e-07       4      52 ..      67     114 ..      63     119 .. 0.87
   3 !   41.0   0.0   3.3e-14     2e-10       1      55 [.     128     181 ..     128     183 .. 0.92
   4 !   22.0   0.1   2.8e-08   0.00017       1      56 [.     204     258 ..     204     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                  EEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHH CS
                           CBS 11 tvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllra 54
                                   ++  + ++e++ +mre +   + PV+ +++ lvGi++  Dll++
  gi|70606054|ref|YP_254924.1| 14 IATYGDRIREVISKMREQNQ-WVvPVL-KEKLLVGIISYNDLLKK 56
                                  5667788*********9996.776999.555488*********96 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.4e-10
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                   +m+++ ++v+ +++++ ++ ++  ++ +++PV+de +++ Givt++ +l
  gi|70606054|ref|YP_254924.1|  67 LMSPP-ISVNLNDDIGRVIAKFYTTRSRAIPVIDEKKRFTGIVTRERVL 114
                                   56555.5**************987778999***************9988 PP

  == domain 3  score: 41.0 bits;  conditional E-value: 3.3e-14
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+++m+++ +t++ +++++ a  lm +++++ lPV+   +++ Gi++ rD+l+ l
  gi|70606054|ref|YP_254924.1| 128 VREVMNSPAITIDAEDSVARARWLMSNNNITKLPVIQ-GKEVAGIISARDILNRL 181
                                   89***********************9899*******5.445***********987 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 2.8e-08
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   +++im+ +v+tv+  ++l+ a++++  +++s++PV++++  +vG+++  D l++++
  gi|70606054|ref|YP_254924.1| 204 IKEIMNYPVITVNGAENLHSAVNTLLTRKISGMPVLEGNM-IVGMFSGIDALKVIA 258
                                   589*********************76666*******5555.******999998875 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   2.5   9.9e-09   5.9e-05      16      85 ..     286     365 ..     279     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.9e-09
                                   HHHHHHHCCGGGG...-EEEEEEE........EEEEEEEEEEEC.TTEEEEEEEEESSHHHHHHHHHHHHHHHHHHCHHTT CS
               Ribosomal_S30AE  16 eyvekklekleky..fieadVtls........kkkkvevtirla.kgkviraeeesedlyaaidlavdklerqlrkykekl 85 
                                   +  e+ l+kle++  + +++V ++        k k ++vt r++ k   + a+e++ d  +a+++av+kle ++ k  +k+
  gi|70606054|ref|YP_254924.1| 286 SILERYLAKLERLteILDFKVAFKeeaksennK-KVYQVTARVStKMGEFIAKERDWDPITALRKAVEKLEDRVIKTSRKM 365
                                   4455666777777444********987765432.677777766655666778999*********************99997 PP

>> PBP5_C  Penicillin-binding protein 5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.74   4.4e+03      43      69 ..      41      67 ..      27      94 .. 0.54
   2 ?   10.6   0.0   8.3e-05       0.5      15      89 ..      94     168 ..      85     169 .. 0.87
   3 ?   -2.8   0.0       1.3   7.5e+03      35      35 ..     210     210 ..     174     251 .. 0.54
   4 ?   -3.3   0.1       1.9   1.1e+04      43      51 ..     314     322 ..     303     331 .. 0.48

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.74
                                  CCTEEEEEEESSSEESGBGTTSEEEEE CS
                        PBP5_C 43 kkklkakvelkksleapikkGqkvGkl 69
                                  +k l   +++++ l++ i+   kv+ l
  gi|70606054|ref|YP_254924.1| 41 EKLLVGIISYNDLLKKRISPESKVVNL 67
                                  444444444455555555555555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.3e-05
                                   EEEEESSSSSEEEEEESSXEEEEE.ETTHCCTEEEEEEESSSEESGBGTTSEEEEEEEEETTEEEEEEEEEESSXB CS
                        PBP5_C  15 tvsvlkgkekeVplvakediyvtv.kkgekkklkakvelkksleapikkGqkvGklkvyldgkliakvplvakedv 89 
                                    ++v+++k+++  +v+ e + + +  ++e kk k++ +++++ + +i + + v ++ +   +++i k p++  ++v
  gi|70606054|ref|YP_254924.1|  94 AIPVIDEKKRFTGIVTRERVLLQFlNEEEFKKAKVREVMNSP-AITIDAEDSVARARWLMSNNNITKLPVIQGKEV 168
                                   689*****************7766477888888888888555.58*************************999987 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.3
                                   E CS
                        PBP5_C  35 y 35 
                                   y
  gi|70606054|ref|YP_254924.1| 210 Y 210
                                   2 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 1.9
                                   CCTEEEEEE CS
                        PBP5_C  43 kkklkakve 51 
                                    ++ k++++
  gi|70606054|ref|YP_254924.1| 314 SENNKKVYQ 322
                                   333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2500.04
//
Query:       gi|70606055|ref|YP_254925.1|  [L=346]
Description: histone deacetylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-73  247.9   0.0      2e-73  247.6   0.0    1.1  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.6   0.0   1.1e-77     2e-73       4     306 ..      23     305 ..      20     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 247.6 bits;  conditional E-value: 1.1e-77
                                   GTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSSTHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl   4 npkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldddtpvs 84 
                                   ++ R   +++ l+e  g + +++++i+p  +++e+llkvHs++Y++l+++ s+e                  l d+dtp++
  gi|70606055|ref|YP_254925.1|  23 KALRETMAKKILEE-RGAF-HYMDVIKPDLISEEDLLKVHSRDYIQLVKKKSEEGTGY--------------LDDGDTPAF 87 
                                   55555534444444.4655.45668***********************9755443332..............4589***** PP

                                   TTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETT.SS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl  85 pktlkaallavgavleavdavlsgsvkaafvlv.rPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhG 164
                                   +++++ al ++ +++++++++ +     ++v++  +++HHak s asGFC++N+va+aik +q+k++  r+a +D+D HhG
  gi|70606055|ref|YP_254925.1|  88 KGMYEGALSRTSGTVTTIKLLDKY----DVVFNiGGGFHHAKYSSASGFCVFNDVALAIKIAQEKYN--RIALIDIDGHHG 162
                                   ******************999844....6666669*****************************766..************ PP

                                   HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 165 nGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPdlilvs 245
                                   +Gt+ ++ +dp+ l +S+H+y+++f+Pgtg+++++g+g+g+g  lnvpl++gtgd+eylk+f+e ++p +e +kPdli++ 
  gi|70606055|ref|YP_254925.1| 163 DGTQYMLFDDPNSLKISLHMYHRGFFPGTGNYDEIGRGRGEGLVLNVPLPPGTGDKEYLKAFTETVIPKVESYKPDLIIIL 243
                                   ********************************************************************************* PP

                                   E-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G..EEEEE-S---HHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 246 aGfDalkgdplgelnlsvegykeltkklaeladkvk.kvvllleGGYnlealaravtavlsa 306
                                    G D++ +dpl el+l+ +gy ++++ l++la++ k k+v++++GGY+ ea+a+ +   +++
  gi|70606055|ref|YP_254925.1| 244 NGGDSHFTDPLVELKLTNKGYVDVISLLKDLAQRFKsKIVMTGGGGYSYEATAKIWVLSIAT 305
                                   *********************************9966*******************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2625.88
//
Query:       gi|70606056|ref|YP_254926.1|  [L=398]
Description: phosphoribosylglycinamide formyltransferase 2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-43  146.4   0.1    1.2e-42  145.3   0.1    1.5  1  ATP-grasp        ATP-grasp domain
    6.1e-11   42.2   0.1    1.7e-10   40.8   0.0    1.7  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.5e-10   39.8   0.1    7.3e-10   38.7   0.1    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    3.7e-06   27.1   0.4      2e-05   24.7   0.4    2.1  1  ATP-grasp_3      ATP-grasp domain
    7.1e-06   25.9   0.1    4.6e-05   23.3   0.0    2.1  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    0.00071   19.7   0.1     0.0018   18.4   0.1    1.8  1  LAL_C2           L-amino acid ligase C-terminal domain 2
     0.0015   17.8   0.0     0.0098   15.2   0.1    2.1  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
     0.0017   18.0   0.0     0.0035   17.0   0.0    1.5  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
  ------ inclusion threshold ------
      0.014   14.8   0.3      0.052   13.0   0.1    2.1  2  ATP-grasp_5      ATP-grasp domain
      0.017   15.2   0.0      0.034   14.2   0.0    1.4  1  TT1725           Hypothetical protein TT1725
      0.022   15.3   1.1        5.6    7.6   0.0    3.4  3  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.11   11.9   0.0       0.17   11.3   0.0    1.3  1  LAP2alpha        Lamina-associated polypeptide 2 alpha
       0.14   12.7   0.1        1.1    9.8   0.1    2.5  2  ATPgrasp_N       ATP-grasp N-terminal domain


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.1     9e-46   1.2e-42       2     170 ..     122     300 ..     121     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 9e-46
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE----SE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefvpfek 76 
                                   ek+++p++ + +++s ee++++++++g+p+++K ++++++G+G+ v+ +e+++e+ ++++      k+++vivEe+v+ ++
  gi|70606056|ref|YP_254926.1| 122 EKVKVPTTAYGFATSPEEVKKMCKDVGYPCIIK-PQMSSSGHGHEVIYDESQVEEKFKEAlthargKSKTVIVEEYVKIDR 201
                                   6899*****************************.*********************999999****999************* PP

                                   EEEEEEEE...ETTC-.EEE--EEEEEEETTEEEE..EEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT. CS
                     ATP-grasp  77 Elsvlvvr...saeGe.tafypvvetvqedgilrl..svapaevsekaqkkaeeiakkiveeLggvGvfavElFvledge. 150
                                   El+vl+ r   s  G  t+++ +ve+ + +g++++  s+ pa+vs++   ka e+a k+v+eLgg G+f+vE+ +   g+ 
  gi|70606056|ref|YP_254926.1| 202 ELTVLTYRyplSSGGVaTKTIYPVEHQRPQGVYHYieSWHPATVSQDVISKASEYATKVVNELGGFGIFGVEIMIA--GNr 280
                                   ********986555645788999*********985449*************************************9..555 PP

                                   EEEEEEESS--GGGGGHHHH CS
                     ATP-grasp 151 llvnElapRpHnsGhvtlda 170
                                   +l+nE+apRpH++G+vtl +
  gi|70606056|ref|YP_254926.1| 281 VLFNEVAPRPHDTGLVTLVS 300
                                   *****************975 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.2e-13   1.7e-10       9      95 ..     121     203 ..     112     210 .. 0.82
   2 ?   -3.6   0.0       4.8   6.6e+03     134     176 ..     246     286 ..     236     290 .. 0.62

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.2e-13
                                   HHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE-- CS
                   CPSase_L_D2   9 lkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlveksl 89 
                                   ++k++vp+   + + +++ ee+ ++ k++gyP+iik+ ++  G+G  v+++e++++e +k+al++a+    +k+v ve+++
  gi|70606056|ref|YP_254926.1| 121 AEKVKVPT--TAYGFATSPEEVKKMCKDVGYPCIIKPQMSSSGHGHEVIYDESQVEEKFKEALTHAR--GKSKTVIVEEYV 197
                                   44555554..344445799***********************************************7..56789******* PP

                                   SSSEEE CS
                   CPSase_L_D2  90 kgpkei 95 
                                   k  +e+
  gi|70606056|ref|YP_254926.1| 198 KIDREL 203
                                   988875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                                   -HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEE CS
                   CPSase_L_D2 134 tdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEv 176
                                   +++  ++  e a kvv+e+g  g   ve ++    ++  + Ev
  gi|70606056|ref|YP_254926.1| 246 SQDVISKASEYATKVVNELGGFGIFGVEIMIA--GNRVLFNEV 286
                                   55555556666777777777666666666665..355555555 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   5.3e-13   7.3e-10      26     176 ..     138     290 ..     123     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 5.3e-13
                                   HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGG....HHHHHHHHHTT-SCEEEEE--ES.EEEEEEEEE....TSS.. CS
               Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseee....lkeaieeafkydekvlvEeaieg.reievavlg....nek.. 95 
                                   e ++k+++ +gyp+++Kp  + S  G + +  e++    +kea+ +a  + ++v+vEe++++ re++v        ++   
  gi|70606056|ref|YP_254926.1| 138 EEVKKMCKDVGYPCIIKPQMSSSGHGHEVIYDESQveekFKEALTHARGKSKTVIVEEYVKIdRELTVLTYRyplsSGGva 218
                                   678999**************99999998887765500015666666777789********652788876544333222211 PP

                                   CEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS- CS
               Dala_Dala_lig_C  96 levsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlP 176
                                   +++   +e++  +g+y y +           pa+++++v +k +e+a k+ + l++ G+  v +++   +++++nEv + P
  gi|70606056|ref|YP_254926.1| 219 TKTIYPVEHQRPQGVYHYIES--------WHPATVSQDVISKASEYATKVVNELGGFGIFGVEIMIA-GNRVLFNEVAPRP 290
                                   333444455555566665555........57**********************************98.8999*****9888 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.4   1.4e-08     2e-05      10     159 ..     118     291 ..     110     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.4e-08
                                   HHTTT.S---.............-EESS--SSSEEEEESS-------B--SS--TTE.................EEEE--- CS
                   ATP-grasp_3  10 kLkeagvkvP.........tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..........lvqefie 71 
                                   ++ +++vkvP          +  ++ ++ + +++++Kp  ++ g++  v+ ++ + e++++e            +v e+++
  gi|70606056|ref|YP_254926.1| 118 RFAAEKVKVPttaygfatsPEEVKKMCKDVGYPCIIKPQMSSSGHGHEVIYDESQVEEKFKEALthargksktvIVEEYVK 198
                                   444555888876665443222233344555****************99999999998888876567788888888888887 PP

                                   .SEEEEEEEEE.SSSEEEEEEEEEE.EET.........TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEEE CS
                   ATP-grasp_3  72 .GkplSvsllsdgekvlvlavnrql.iekaeke.....fvyaGnvtpietel..keevvelaeevvekleglaGyvGvDlv 143
                                     ++l+v +         +a+   + +e+   +     + y  +  p+ +++   +++ e a +vv++l g +G++Gv+++
  gi|70606056|ref|YP_254926.1| 199 iDRELTVLTYRYPLSSGGVATKTIYpVEH---QrpqgvYHYIESWHPATVSQdvISKASEYATKVVNEL-GGFGIFGVEIM 275
                                   34567776644332222233222221222...14556799999999999888667999***********.*********** PP

                                   ESS.SEEEEEEESS-- CS
                   ATP-grasp_3 144 lkdeepyviEvNPRlt 159
                                   ++ +   + Ev PR+ 
  gi|70606056|ref|YP_254926.1| 276 IAGNRVLFNEVAPRPH 291
                                   **************85 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.63   8.7e+02      76     105 ..      19      45 ..      11      66 .. 0.71
   2 !   23.3   0.0   3.3e-08   4.6e-05      11      96 ..     122     205 ..     116     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.63
                                   TCCCCSSEEEEE---SEEEEEEEEECTTEE CS
                        GARS_A  76 fGeagekvviEelleGeEvsllalvdgktv 105
                                   +Ge g+++viE +  G E  +   +d +++
  gi|70606056|ref|YP_254926.1|  19 GGELGKEMVIEAQRMGVETVV---IDRYDL 45 
                                   5899999****9999999755...444444 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.3e-08
                                   HHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---. CS
                        GARS_A  11 kkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelle. 90 
                                   +k+++pt+ y   t+pee+k++ ++++ +  ++K++  ++g g  v  +e++  +  ke l+ ++ G  +++v++Ee+++ 
  gi|70606056|ref|YP_254926.1| 122 EKVKVPTTAYGFATSPEEVKKMCKDVGYPC-IIKPQMSSSGHGHEVIYDESQVEEKFKEALT-HARG-KSKTVIVEEYVKi 199
                                   6899**************************.******************************7.7777.5789*****9973 PP

                                   SEEEEE CS
                        GARS_A  91 GeEvsl 96 
                                     E+++
  gi|70606056|ref|YP_254926.1| 200 DRELTV 205
                                   356665 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-06    0.0018      40      73 ..     362     395 ..     345     398 .] 0.92

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                        LAL_C2  40 rpprssgdrlGyviatgdtaeeaeaaaeeaaaei 73 
                                   +p++ +  r G v+atg++ eea++ +++a a+i
  gi|70606056|ref|YP_254926.1| 362 KPVTYNERRMGIVLATGNSVEEAKEKVRKASALI 395
                                   5789999************************998 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   7.1e-06    0.0098      16     138 ..     107     208 ..      95     210 .. 0.73
   2 ?   -0.6   0.0      0.47   6.4e+02     226     259 ..     251     283 ..     241     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.1e-06
                   ATPgrasp_ST  16 fplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksal 96 
                                   +++  d +  +++  ++ +kvp++   +    + +e+++++k++    +iKp+ +s+G+G  vi +        +s+++ +
  gi|70606056|ref|YP_254926.1| 107 VKICMDRIELRRF-AAEKVKVPTTAYGFA--TSPEEVKKMCKDVGYPCIIKPQMSSSGHGHEVIYD--------ESQVEEK 176
                                   5666667777777.456688888655554..566789999*999555*****************55........3333333 PP

                   ATPgrasp_ST  97 ldelerhvsnilagLyslggkpdvalveelikqdpeleklsp 138
                                   ++e   h            gk+++++vee++k d el+ l++
  gi|70606056|ref|YP_254926.1| 177 FKEALTHAR----------GKSKTVIVEEYVKIDRELTVLTY 208
                                   333333433..........78999*************99987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.47
                   ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgpll 259
                                   +++ e a k+ ++l g g++G+ i ++ ++ +l 
  gi|70606056|ref|YP_254926.1| 251 SKASEYATKVVNELGGFGIFGVEIMIAGNR-VLF 283
                                   567788889999999999999999999888.555 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.5e-06    0.0035       9      56 .]     337     387 ..     332     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-06
                        PurK_C   9 edae...ekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeeleer 56 
                                   e++     + +++l+ipg+++ l gK  + + R mG + ++g+s ee++e+
  gi|70606056|ref|YP_254926.1| 337 EKWApkyINVDKALEIPGVQVRLFGKPVTYNERRMGIVLATGNSVEEAKEK 387
                                   555544446677***********************************9986 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.8e-05     0.052      21     119 ..     123     209 ..     111     212 .. 0.78
   2 ?   -3.4   0.0       3.9   5.4e+03      20      41 ..     312     333 ..     308     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                   ATP-grasp_5  21 aygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvl 101
                                    + +p++   +a+s+ee+ ++++ +gyp+ +K +  +  h     G ++ + d+++v+++++e l++++      + + v+
  gi|70606056|ref|YP_254926.1| 123 KVKVPTTAYGFATSPEEVKKMCKDVGYPCIIKPQMSSSGH-----GHEV-IYDESQVEEKFKEALTHARG-----KSKTVI 192
                                   44556666666*********************98776666.....5555.88999999999999999877.....456688 PP

                   ATP-grasp_5 102 VqemakrggrElivgvte 119
                                   V+e +k   rEl v  ++
  gi|70606056|ref|YP_254926.1| 193 VEEYVK-IDRELTVLTYR 209
                                   888888.78888876665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.9
                   ATP-grasp_5  20 eaygipvvetrlassaeeavea 41 
                                   +a+g+p+++ ++++ a++ v +
  gi|70606056|ref|YP_254926.1| 312 SALGLPTPDVKVVTPAAAHVIL 333
                                   7899999999999888776655 PP

>> TT1725  Hypothetical protein TT1725
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.034      14      69 ..      72     125 ..      66     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                   -S-HHHHHHHHHHHHTTTEEEEEEEETTEEEES--S------SEEEEEEEE-SSS- CS
                        TT1725  14 ekdpeelaekleklaeeelkLkmitnrGvkvyPegleetfctdhwrcRfvakegkk 69 
                                   +++p+++ +++e++++e  +L+ i   G+kv P+    ++c+d   +R  a+e+ k
  gi|70606056|ref|YP_254926.1|  72 KERPDAVIAEIEAINTE--TLSKIEMDGIKVMPNARAVKICMDRIELRRFAAEKVK 125
                                   6789999999****999..99************************99765554444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.004       5.6       3      32 ..      15      44 ..      13      62 .. 0.91
   2 ?    3.3   0.1      0.09   1.2e+02      41      66 ..      84     109 ..      66     116 .. 0.83
   3 ?    0.9   0.0       0.5   6.9e+02      47      72 ..     365     390 ..     358     397 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                                  EEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                     Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversd 32
                                  + +GgG +g E+  +++++g ++ v++r d
  gi|70606056|ref|YP_254926.1| 15 LWLGGGELGKEMVIEAQRMGVETVVIDRYD 44
                                  568***********************9966 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                                   HHHHHHHHHHHHTTEEEECSEEEEEE CS
                     Pyr_redox  41 easkilqeklekngievllntkveei 66 
                                   ++ +++  k+e  gi+v+ n+++++i
  gi|70606056|ref|YP_254926.1|  84 AINTETLSKIEMDGIKVMPNARAVKI 109
                                   5667777788888*********9987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.5
                                   HHHHHHTTEEEECSEEEEEEEEETTS CS
                     Pyr_redox  47 qeklekngievllntkveeiegsedg 72 
                                   + + +++gi + ++++vee +++ ++
  gi|70606056|ref|YP_254926.1| 365 TYNERRMGIVLATGNSVEEAKEKVRK 390
                                   5556788************9988776 PP

>> LAP2alpha  Lamina-associated polypeptide 2 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.17      41      69 ..     190     218 ..     159     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                   HHHHHHCCGSSS-----TTTS--B-HHHH CS
                     LAP2alpha  41 kvveeewqqvdrqlpslackypvssieaa 69 
                                    v+ ee+ ++dr+l  l+ +yp+ss   a
  gi|70606056|ref|YP_254926.1| 190 TVIVEEYVKIDRELTVLTYRYPLSSGGVA 218
                                   5899********************97544 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00082       1.1       3      39 ..      29      62 ..      27     100 .. 0.61
   2 ?   -1.5   0.0       2.8   3.8e+03      24      41 ..     232     249 ..     217     269 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00082
                                  HHHHTT-EEEEEEETTS----S-TT.EEEEEEE-TTT CS
                    ATPgrasp_N  3 aAkaLGikvvlvdeedewapeelaelvekfipldlaq 39
                                  +A+++G+++v++d+ d  ap++  +  +k+ ++++ +
  gi|70606056|ref|YP_254926.1| 29 EAQRMGVETVVIDRYD-LAPAMHVA-HRKY-VVNMHD 62
                                  69************98.55544443.2333.356653 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                   S-TT.EEEEEEE-TTT-H CS
                    ATPgrasp_N  24 elaelvekfipldlaqdp 41 
                                    + + +e  +p +++qd 
  gi|70606056|ref|YP_254926.1| 232 GVYHYIESWHPATVSQDV 249
                                   344458888888888873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2856.54
//
Query:       gi|70606057|ref|YP_254927.1|  [L=204]
Description: hypothetical protein Saci_0215 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.0   0.5        1.7    8.5   0.0    2.3  2  TPD       Protein of unknown function TPD sequence-motif


Domain annotation for each model (and alignments):
>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   9.3e-05       1.7      25      76 ..      88     146 ..      65     149 .. 0.85
   2 ?    5.0   0.3    0.0011        20      96     119 ..     150     174 ..     143     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 9.3e-05
                           TPD  25 airssvGeeyEellekllkekgiafkteedlrekgldk.......tPDvkLevpvaveg 76 
                                   + ++ +G  +E+ + ++l ++g++++ ++d r   l k        PD+++e+ +a+e 
  gi|70606057|ref|YP_254927.1|  88 KLNQLIGLVFEDYVYNQLLNTGLRVERNNDKRVLSLPKlgakthnKPDFLVENKIAIEA 146
                                   456799**************************98888888888889********99986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0011
                           TPD  96 kylkkQlssYvnrfGpGlviY.wfG 119
                                    y  +Q+++Y++ +  G+v++ w G
  gi|70606057|ref|YP_254927.1| 150 YYSYEQIEDYEKIYDIGAVVFpWSG 174
                                   57789***************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1552.23
//
Query:       gi|70606058|ref|YP_254928.1|  [L=216]
Description: hypothetical protein Saci_0216 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1501.44
//
Query:       gi|70606059|ref|YP_254929.1|  [L=208]
Description: hypothetical protein Saci_0217 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1575.55
//
Query:       gi|70606060|ref|YP_254930.1|  [L=146]
Description: hypothetical protein Saci_0218 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1093.11
//
Query:       gi|70606061|ref|YP_254931.1|  [L=332]
Description: hypothetical protein Saci_0219 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-12   45.4   0.0    2.7e-07   30.5   0.0    2.1  2  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.092   13.0   0.1    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.035   14.0   0.0       0.06   13.2   0.0    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.081   13.5   0.0       0.21   12.2   0.0    1.7  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
       0.13   12.5   0.0       0.26   11.6   0.0    1.5  1  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.5e-05     0.053       1      29 [.       2      32 ..       2      36 .. 0.93
   2 !   30.5   0.0   7.5e-11   2.7e-07     180     350 ..     143     300 ..      98     302 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                  +v++iG Gi G+s+ + L +rg  V ++e+g
  gi|70606061|ref|YP_254931.1|  2 KVLVIGKGILGSSIYHLLKERGheVSVVESG 32
                                  59****************99999******98 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 7.5e-11
                                   EEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEET CS
                           DAO 180 wgverttpgendaadavVnaaGawsd.llgllkeldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprk 259
                                   +++ +++   ++++d  +++aGaw +  +   + l  +  p++++++      ++l+++ +++ v+ + d + g+y +p  
  gi|70606061|ref|YP_254931.1| 143 VTL-DNN-DVTSRYDIFILTAGAWNTlSI---NGL--R-LPLKSYYCWS---WLTLNRNSLLDKVF-IYDYELGYYSRPFM 211
                                   222.222.22235688********87555...666..5.8899999777...45566677888898.78889*******74 PP

                                   TS....EEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGGGCGEEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEEC CS
                           DAO 260 dg....rvlvGgtad.eesgdddpevdeedidellealrklfPqlgdvlrkwaGlrp.lpdglpligetpgvkglylatGh 334
                                    g      +vG  ++ e s +d    d +++++  +++ klfP   + +    G+   +pd  p+ ge   +++ly+a G 
  gi|70606061|ref|YP_254931.1| 212 -GiglpLSIVGDGDViECSPFDKKIGDKKAVEKAESRVGKLFPIY-RGE----GYCEgTPDMRPIYGEI--TERLYFAGGL 284
                                   .4333234556666699999999999*****************94.222....4444467********5..79******** PP

                                   TTTHHHHHHHHHHHHH CS
                           DAO 335 sghGltlapatGklla 350
                                    g G   +p+++ ll+
  gi|70606061|ref|YP_254931.1| 285 DGYGAEIGPGIANLLV 300
                                   ************9987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05     0.092       1      28 [.       5      32 ..       5      34 .. 0.95
   2 ?   -1.9   0.0       1.1   4.1e+03      24      42 ..     121     139 ..     120     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                  ++G G+ G+++ +lL+++g++v ++e++
  gi|70606061|ref|YP_254931.1|  5 VIGKGILGSSIYHLLKERGHEVSVVESG 32
                                  89***********************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                   EE-SSSSSSGGG-EECETT CS
                 NAD_binding_8  24 llekrdrlGGraasyevpg 42 
                                   l+++ ++++G+++ + +++
  gi|70606061|ref|YP_254931.1| 121 LIDSVPKISGNVSVEVNDN 139
                                   7899999999998776654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05      0.06       1      29 [.       2      30 ..       2      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvd 29
                                  kv viG G++G++i +++ ++g+eV +v+
  gi|70606061|ref|YP_254931.1|  2 KVLVIGKGILGSSIYHLLKERGHEVSVVE 30
                                  689***********************997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.8e-05      0.21       1      30 [.       2      31 ..       2      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                  kv+v+G G +g      l+e g++V+vve 
  gi|70606061|ref|YP_254931.1|  2 KVLVIGKGILGSSIYHLLKERGHEVSVVES 31
                                  79**************************96 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-05      0.26       1      29 [.       3      31 ..       3      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                                  EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29
                                  +++iG G +G+s+++ L+e g+ +v+v+++
  gi|70606061|ref|YP_254931.1|  3 VLVIGKGILGSSIYHLLKErGH-EVSVVES 31
                                  68*****************555.7****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2489.07
//
Query:       gi|70606062|ref|YP_254932.1|  [L=265]
Description: hypothetical protein Saci_0220 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1762.64
//
Query:       gi|70606063|ref|YP_254933.1|  [L=178]
Description: molybdopterin-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-32  111.7   0.1    2.5e-32  111.5   0.1    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.052   13.6   0.0       0.07   13.2   0.0    1.3  1  B12-binding    B12 binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.1   2.8e-36   2.5e-32       2     144 .]      19     170 ..      18     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 2.8e-36
                                   EEEE-HHHH.....TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS..SEEEEESS-SSSTT--HH CS
                 MoCF_biosynth   2 vitvGdell.....sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea..dviittGGtGptpdDvtp 75 
                                   vit++++++     +++i+D++g+ ++e + + g++v  yt++pD++ +i +a+ +al++   dvii+tGGtG +  Dvt+
  gi|70606063|ref|YP_254933.1|  19 VITISTSRYekfikRETIVDESGDAIKESIISEGYKVVGYTLIPDNKIKILRAFSEALDNPdvDVIISTGGTGYSTTDVTV 99 
                                   8********99999999*************************************777777678****************** PP

                                   HHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHGGHHH CS
                 MoCF_biosynth  76 ealaklfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillpaleh 144
                                   e+++k+f++e+eg + +fr+vs++  k   v  + +ls+++    g++ ++ LPGsp avk a++e++lp++ h
  gi|70606063|ref|YP_254933.1| 100 ETIRKIFDREIEGYGDVFRMVSYNDPK---VRSASYLSKSTagiiGDKvVFLLPGSPDAVKLAMKELILPEIGH 170
                                   ************************988...666667788778899666599*****************999876 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-06      0.07      41      95 ..      42      96 ..       9     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-06
                   B12-binding 41 edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldp 95
                                  ++i ++i++e + vvg ++++  ++   ++  e+l   + +v++ +GG++ s++ 
  gi|70606063|ref|YP_254933.1| 42 DAIKESIISEGYKVVGYTLIPDNKIKILRAFSEALDNPDVDVIISTGGTGYSTTD 96
                                  89999********************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1263.44
//
Query:       gi|70606064|ref|YP_254934.1|  [L=161]
Description: hypothetical protein Saci_0222 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.2e-43  145.1   5.6    1.3e-42  144.6   5.6    1.2  1  DUF1286     Protein of unknown function (DUF1286)
    3.7e-05   23.1   1.2    5.8e-05   22.5   1.2    1.4  1  YdjM        LexA-binding, inner membrane-associated putative 
  ------ inclusion threshold ------
       0.12   12.4   0.2       0.12   12.4   0.2    2.8  3  OppC_N      N-terminal TM domain of oligopeptide transport pe
        1.4    9.3   7.6        1.4    9.3   2.8    2.7  2  ATP-synt_I  ATP synthase I chain


Domain annotation for each model (and alignments):
>> DUF1286  Protein of unknown function (DUF1286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   5.6   2.9e-46   1.3e-42       1     112 []       1     112 [.       1     112 [. 0.98

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 2.9e-46
                       DUF1286   1 mrlrthyvfsiGlltliesvlvs.....nflealilsgivsvlgnsliDrlGhkeiktrrGkipvrtPlthtlprsvvwgl 76 
                                   mrl++hyvf+iG+l++i+s+lv+     n++++l+++g++sv++n+liDrlGh+    +rGk+++rtP+tht+prs++w+l
  gi|70606064|ref|YP_254934.1|   1 MRLYAHYVFTIGVLVFINSFLVTplsppNYYDSLFYGGLLSVFSNTLIDRLGHE----IRGKYISRTPTTHTFPRSMLWSL 77 
                                   9*********************99999***************************....99********************* PP

                       DUF1286  77 lssvlvllllyyllskkvlllillsGvivGpshmlL 112
                                   l+svl+++l ++++++++++++l++Gvi+Gpshm+L
  gi|70606064|ref|YP_254934.1|  78 LVSVLLSFL-FFYVRHTIPYYLLIDGVIAGPSHMVL 112
                                   *******96.999*********************98 PP

>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.2   1.3e-08   5.8e-05      67     121 ..      62     122 ..      28     160 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-08
                          YdjM  67 R.gftHSllflallalvlllllrlfgrsalrlgll...lllg.....vlsHlllDlltkyGvpl 121
                                   R   tH+++  +l++l++++ll +++ ++ r +++   l          sH++lD++t +G+ +
  gi|70606064|ref|YP_254934.1|  62 RtPTTHTFPRSMLWSLLVSVLLSFLFFYV-RHTIPyylL--IdgviaGPSHMVLDIFTERGIYV 122
                                   42579****************99999995.444442223..244333556***********965 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.11   4.9e+02      23      41 ..      11      30 ..       2      47 .. 0.60
   2 ?   -1.4   0.8      0.54   2.4e+03      23      32 ..      77      86 ..      72     105 .. 0.52
   3 ?   12.4   0.2   2.7e-05      0.12       2      29 ..     127     155 ..     126     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                        OppC_N 23 lllllli.aifaPliaPydp 41
                                  + +l++i +++   ++P+++
  gi|70606064|ref|YP_254934.1| 11 IGVLVFInSFLVTPLSPPNY 30
                                  34444443455444445544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.54
                        OppC_N 23 lllllliaif 32
                                  ll+ +l++++
  gi|70606064|ref|YP_254934.1| 77 LLVSVLLSFL 86
                                  4444444433 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 2.7e-05
                        OppC_N   2 lwqda.wrrFkrNklAvvglvilllllli 29 
                                   +w+++ +  F++N  Av gl++ll ll +
  gi|70606064|ref|YP_254934.1| 127 RWKRFaLAHFRYNNPAVNGLAVLLGLLMM 155
                                   577765789***************99876 PP

>> ATP-synt_I  ATP synthase I chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.8   0.00031       1.4       4      86 ..       9      94 ..       3     108 .. 0.59
   2 ?    1.4   0.2     0.094   4.2e+02      25      41 ..     144     160 ..     131     161 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                    ATP-synt_I  4 liqlvllavlalgwlltgsasvalsallGglisvlpfalfalrvfrfsgalar...kkkkivrslylgeairlaltiallila 83
                                  ++  vl+++ +++   ++ +++  s+++Ggl+sv++++l  +   +++g+  +   + +++ rs++ + ++ ++l ++ +++ 
  gi|70606064|ref|YP_254934.1|  9 FTIGVLVFINSFLVTPLSPPNYYDSLFYGGLLSVFSNTLIDRLGHEIRGKYISrtpTTHTFPRSMLWSLLVSVLLSFLFFYVR 91
                                  344444444444444445777999**************998877666654322112444444555555555555555555555 PP

                    ATP-synt_I 84 lkl 86
                                   ++
  gi|70606064|ref|YP_254934.1| 92 HTI 94
                                  555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.094
                    ATP-synt_I  25 valsallGglisvlpfa 41 
                                    +l +llG+l+ ++p++
  gi|70606064|ref|YP_254934.1| 144 NGLAVLLGLLMMLVPLY 160
                                   47788999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1178.44
//
Query:       gi|70606065|ref|YP_254935.1|  [L=123]
Description: hypothetical protein Saci_0223 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-29  102.3   2.7    1.6e-29  102.1   2.7    1.0  1  PaREP1    Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.049   13.8   2.5        0.1   12.7   2.5    1.5  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   2.7   1.8e-33   1.6e-29       4     115 .]       8     115 ..       5     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.8e-33
                        PaREP1   4 eeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlkll.eeaeekerwstkellkavaklleelgdkevvdlw 83 
                                   ++ +++++eA+ellekGd++qA+eK+ykA+++++k+l++  nlk + e+ + ++rw++ +l++a+++++      e++ +w
  gi|70606065|ref|YP_254935.1|   8 SLILEWIREADELLEKGDIVQASEKYYKAAEEAIKLLVKTLNLKDIiEKVKVNRRWTSSLLFDAARRIS-----PEMYVIW 83 
                                   67899****************************************************************.....9999*** PP

                        PaREP1  84 klAldLHeyqfheaklelsdveskeeavkdlv 115
                                     A+ LH y+fhe kl++ + ++  + v++++
  gi|70606065|ref|YP_254935.1|  84 VDAWYLHIYGFHEMKLDYYEAKKLSKSVHEII 115
                                   ***********************999999885 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.5   1.2e-05       0.1      10     117 ..      12     120 ..      11     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC...CHHHT...-HHHHHHHHHHHCCCHHC CS
                          HEPN  10 edleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle...elkkelkeseelreeleeLekayies 87 
                                   e +++A +lle+gd   a  +++ aae a+K l  +++ +     d++e ++   +    l  ++  r++  e+  +++++
  gi|70606065|ref|YP_254935.1|  12 EWIREADELLEKGDIVQASEKYYKAAEEAIKLLVKTLNLK-----DIIEKVKvnrRWTSSLL-FDAARRISPEMYVIWVDA 86 
                                   56789999**********************9666666665.....56655552224444444.9***************** PP

                                   CCTSS--S....--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  88 rYpdakee....yteedaeealkdaeevlelvee 117
                                    Y + + +    ++  +a+++ k ++e+++++++
  gi|70606065|ref|YP_254935.1|  87 WYLHIYGFhemkLDYYEAKKLSKSVHEIIDILNK 120
                                   ******99*********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 929.59
//
Query:       gi|70606066|ref|YP_254936.1|  [L=127]
Description: hypothetical protein Saci_0224 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-26   90.0   2.4    1.1e-25   89.8   2.4    1.2  1  PaREP1    Archaeal PaREP1/PaREP8 family


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   2.4     6e-30   1.1e-25       3      88 ..       7      93 ..       5     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 6e-30
                        PaREP1  3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlkll.eeaeekerwstkellkavaklleelgdkevvdlwk 84
                                  l+++ ++++eA+ellekGd++qA+eK+ykA+++++k+l++  nlk + e+ +e++ ws + l +av++++++l d+e++dlwk
  gi|70606066|ref|YP_254936.1|  7 LSASDVLIREADELLEKGDIVQASEKYYKAAEEAIKLLVKTLNLKDIiEKVKEEGYWSLGVLHDAVTEIAKRLSDEEIIDLWK 89
                                  778999***************************************************************************** PP

                        PaREP1 85 lAld 88
                                  +A+ 
  gi|70606066|ref|YP_254936.1| 90 SAIV 93
                                  **85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 891.65
//
Query:       gi|70606067|ref|YP_254937.1|  [L=288]
Description: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-41  140.0   0.0    7.1e-41  139.8   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.095   13.2   0.0       0.19   12.3   0.0    1.4  1  NuDC      Nuclear distribution C domain


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   7.9e-45   7.1e-41       4     287 ..       2     277 ..       1     279 [. 0.93

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 7.9e-45
                                   EEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSHHH CS
                         DHDPS   4 giitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnstse 84 
                                    ii++++tpfd++gk++  al++ ++ l++kg+d+++v GttG  + ls +ek q ++   ++     ++i +vGs ++++
  gi|70606067|ref|YP_254937.1|   2 EIISPIITPFDKQGKVNVDALKTHAKNLLEKGIDAIFVNGTTGLGPALSKDEKRQNLNALYDVTH---KLIFQVGSLNLND 79 
                                   589****************************************************9998777655...8************ PP

                                   HHHHHHCCCCCT-SEEEEE---SS---HHH.HHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE-S CS
                         DHDPS  85 aiklakkaeeaGadgvlavtPYYnkpsqeg.lyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKeav 164
                                    ++l k ++e+ + gv++  PYY +  +e  l +++++i+   +  + +Yn p+ tg d+ p  +k L     + g+K++ 
  gi|70606067|ref|YP_254937.1|  80 VMELVKFSNEMDILGVSSHSPYYFPRLPEKfLAKYYEEIARISSHSLYIYNYPAATGYDIPPSILKSL----PVKGIKDTN 156
                                   ***********************9776655389******************************99999....599****** PP

                                   S-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCCC CS
                         DHDPS 165 gdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllplikilfa 245
                                   +dl +  + k +  + + +y+G + l+  +  l  dGv+++  n+++e + +  +++k+G+l+ a  l+e +++l +il +
  gi|70606067|ref|YP_254937.1| 157 QDLAHSLEYKLN-LPGVKVYNGSNTLI-YYSLLSLDGVVASFTNFIPEVIVKQRDLIKQGKLDDALRLQELINRLADILRK 235
                                   ***999888888.89*******97665.5667889********************************************** PP

                                   CSCCHHHHHHH.HCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                         DHDPS 246 epnvilvktal.ellGlvveatlrkPltpleeeekeeleallk 287
                                    + ++ +   + e  G +v++  r+P+ pl++ee  +l++ ++
  gi|70606067|ref|YP_254937.1| 236 YGSISAIYVLVnEFQGYDVGY-PRPPIFPLTDEEALSLKREIE 277
                                   *******98872567999999.*************99998775 PP

>> NuDC  Nuclear distribution C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.1e-05      0.19       7      30 ..     259     282 ..     256     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                          NuDC   7 pkIkELTDeEAekLQlElDqkKkk 30 
                                   p I  LTDeEA  L +E++  K k
  gi|70606067|ref|YP_254937.1| 259 PPIFPLTDEEALSLKREIEPLKRK 282
                                   67888**************88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2028.37
//
Query:       gi|70606068|ref|YP_254938.1|  [L=311]
Description: 2-keto-3-deoxygluconate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-41  140.0   0.0    1.1e-40  139.8   0.0    1.0  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   6.1e-45   1.1e-40       3     300 ..       3     297 ..       1     299 [. 0.92

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 6.1e-45
                                   EEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEE CS
                          PfkB   3 kvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvk 83 
                                   k+ ++Ge+l++++a   +    l + + +ek+ +G+ aN + a  ++g++   i +vGdD+fG  ++e+l+  gvd++++k
  gi|70606068|ref|YP_254938.1|   3 KLIALGEILVQFNALAVG---PLRHINYFEKHIAGSEANYCIAFIKQGNECGIIARVGDDEFGYNIIEWLRGQGVDVSGIK 80 
                                   78899***********99...888********************************************************* PP

                                   EESSSEEEEEEEEETTT..SEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES..EECTTSHHHHHHHHHHHHHHTTE CS
                          PfkB  84 idedtrtglalivvded..gertivfnrgaaadltkeeleededlleeadllyisg..llsselpeavleelaeaaknggt 160
                                   +d++  tg++++  +    ++ +++++r+ +a  + ++ + +e+++++ad+++ sg  l  s+   +++ +++++ak    
  gi|70606068|ref|YP_254938.1|  81 VDPESFTGIYFVQRSHPvpNRSSMLYFRKGSAGSRLSPEDVSENYIKSADIVHSSGitLAISDTARDAVFRAFSLAKIRS- 160
                                   ***************9896777788888888888888888****************997777777888888888999999. PP

                                   EEEEECESSSHH..HHHHHHHHH..CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEET CS
                          PfkB 161 fdpnlldplgaq..fkeallell..aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvek 237
                                   fd n++ +l++   +k+++++ll   ++d+l++  ++ +++ ge+  d+e+al+ l +    + + vv++lG++Ga v+ +
  gi|70606068|ref|YP_254938.1| 161 FDTNIRLRLWSAekAKSEIMRLLneFKPDFLITDPDDSKIIIGES--DPEKALKILSN----YSRIVVMKLGARGAMVY-S 234
                                   9*********99***********55589*****************..*********99....99***************.6 PP

                                   TEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSC CS
                          PfkB 238 dgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslp 300
                                   dg++++++ ++v+v D++GAGD+  g fl+ +l+g ++++al +   ++ l+v  +g +++lp
  gi|70606068|ref|YP_254938.1| 235 DGSIYFSPGYQVQVEDVIGAGDALGGTFLSLYLKGFNVKKALDYSIVASTLNVMIRGDQENLP 297
                                   66666666699*************************************999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2166.44
//
Query:       gi|70606069|ref|YP_254939.1|  [L=507]
Description: glyceraldehyde-3-phosphate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.1e-111  371.4   0.0   6.1e-111  371.2   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    7.9e-08   31.8   0.0    1.2e-07   31.2   0.0    1.2  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.2   0.0  6.8e-115  6.1e-111       8     462 .]      39     494 ..      33     494 .. 0.95

  Alignments for each domain:
  == domain 1  score: 371.2 bits;  conditional E-value: 6.8e-115
                                   EEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH.HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHH CS
                        Aldedh   8 tievinPatgeviakvpaataedvdaavaaAkeafk.awaklpaeeRaeiLrkaadlleerkeelaeletletGkplaear 87 
                                     +v +P++ ev a+vp+ + e +d+++a+ + + + + +++p e+R ++  ++a+ll + +e+++++++  +Gk++++ar
  gi|70606069|ref|YP_254939.1|  39 FENVKSPIDLEVYARVPRLNYEMIDSVIANIHYKGRwEIRDIPGEKRLKLYDRIANLLDKYREDFIQVLVVGNGKTVSSAR 119
                                   357889***********************9998777799****************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-T CS
                        Aldedh  88 aeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPae 163
                                   +ev+ +i+ l  +   ++kl+ge +p +      +++a++rrePlG+v+aItP+N+Pl+ ++ k++   +aGN++vlKPa 
  gi|70606069|ref|YP_254939.1| 120 GEVNASIERLLRADLDVRKLYGEYVPGDwssesLESEAIIRREPLGIVLAITPFNYPLFDVVNKFVYSTVAGNAFVLKPAI 200
                                   ************************99976777778899******************************************* PP

                                   TSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE CS
                        Aldedh 164 etplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpliv 244
                                    tp+ a+++a+l+e ag+Pk++l v+t +g+e+ + +++++++ ++s+tGste+g++i+k  +  +k+ ++ElGG +++iv
  gi|70606069|ref|YP_254939.1| 201 STPIPAIMFAKLAEIAGFPKNALAVITLPGKEMDK-VIQDKRLSVISITGSTETGEHIMKVGG--IKQYIMELGGGDSVIV 278
                                   ******************************99866.56789*******************999..9*************** PP

                                   -TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHH CS
                        Aldedh 245 ledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyve 325
                                   + daD+ +++++iv+g+++++GQ+C +++ ++ +++iy+++ ++l+e++kk+kvgdp+d+++++GP+i+++ ++++e  ++
  gi|70606069|ref|YP_254939.1| 279 MRDADIASTAQKIVTGITSYSGQRCDSIKFIFAESEIYEKLKSALIEELKKIKVGDPRDPNVNMGPIIDSKTVDEFEFSLK 359
                                   ********************************************************************************* PP

                                   HHHHTTSEEEE-TTE.SB-SSST.TEE--EEEES-T...TTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE CS
                        Aldedh 326 eakeegaklllGgereeaglekg.yfvePtvlanvt...pdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvf 402
                                   + +e+g  +l+Gg      ++ g  ++ePt+++  +   +d  ++++E+F  +++++k++d+ eai++ N+ +yGL a++f
  gi|70606069|ref|YP_254939.1| 360 DVVEKGGVILYGG------KRLGpTYIEPTLVEADKskvKDLYLYKKEVFLSIAVLVKVNDISEAISLSNERRYGLDAAIF 434
                                   *************......344449*******976511246679************************************* PP

                                   -SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 403 tkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   ++d+++++r+++ le+G vyiNd  ++ +  +pfgG k+Sg+Greg  + +e++t++kt+
  gi|70606069|ref|YP_254939.1| 435 GSDINEIRRAIRFLEVGAVYINDFPRHGIGYFPFGGRKDSGIGREGIGYTIEDVTTYKTI 494
                                   *********************************************************996 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.3e-11   1.2e-07      59     268 ..     126     331 ..      99     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.3e-11
                          LuxC  59 LkkvleseLgqpeiLdeflktke.......ksyekaqprglvlhvlsgNvpllpvm.silqglLvknvnllkvSssdpfla 131
                                   ++++l+ +L+ ++   e+++ +        +  +++ p g+vl +++ N pl  v+   + + +++n+ +lk+ +s p  a
  gi|70606069|ref|YP_254939.1| 126 IERLLRADLDVRKLYGEYVPGDWsseslesEAIIRREPLGIVLAITPFNYPLFDVVnKFVYSTVAGNAFVLKPAISTPIPA 206
                                   566666666666666666533222222334567899****************98762699****************99766 PP

                          LuxC 132 aallksladvdenhtladslsvvyfksgdtkleeeiv.qnaDvvvawGgeeaikaiseklkpgkqlikfGakvSfavvdke 211
                                   + + ++la++      +++l+v+    + +++ ++i  +   v+++ G+ e+ + i +    +  +++ G   S+ v+ ++
  gi|70606069|ref|YP_254939.1| 207 IMF-AKLAEIAG--FPKNALAVI--TLPGKEMDKVIQdKRLSVISITGSTETGEHIMKVGGIKQYIMELGGGDSVIVM-RD 281
                                   665.56777766..3578*****..788888999998677999**************999999999999*99998765.66 PP

                          LuxC 212 aleeealdkaaeraAkDiivfdQqAClspqvvfvekddkieidefaeaLaaaLekra 268
                                   a    +++++a+++ + i ++  q C s +++f e++    ++++++aL+++L+k+ 
  gi|70606069|ref|YP_254939.1| 282 A----DIASTAQKIVTGITSYSGQRCDSIKFIFAESE---IYEKLKSALIEELKKIK 331
                                   6....8*****************************66...899**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3360.40
//
Query:       gi|70606070|ref|YP_254940.1|  [L=105]
Description: hypothetical protein Saci_0228 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-09   37.7   0.0    1.7e-09   37.5   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
      0.087   12.8   0.0        0.1   12.5   0.0    1.2  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   1.9e-13   1.7e-09      20      83 ..       7      71 ..       2      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.9e-13
                                  EETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEE.TT.EEE-TTT--EEE.TTSBEEE-TTHH CS
                        Rieske 20 kvggeplvvlrdedgevyAlsdvCtHrgaplsegkid.ekgvleCpcHgwayd.adGkvikgPapr 83
                                  ++ g p++++r+ dg+ y     C+H++ p+ e++++  + +++Cp+H ++++  +G+++k P  +
  gi|70606070|ref|YP_254940.1|  7 EIEGYPIMIYRK-DGKTYTWLAGCPHKRRPILEKGVEiFDDKIKCPFHYAVFSlITGEMLKEPESK 71
                                  578899*****5.*****************988555444559*******************99876 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.2e-05       0.1      25      88 ..      12      71 ..       3      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                                  EEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS-TTSB CS
                      Rieske_2 25 qvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecledeevs 88
                                   +++ r  +++ y   + +p ++  +l +G+      +  +++P +  +f+L tGe+l+++e +
  gi|70606070|ref|YP_254940.1| 12 PIMIYRK-DGKTYTWLAGCPHKRRPILEKGVEIF---DDKIKCPFHYAVFSLITGEMLKEPESK 71
                                  5555555.77888888888887777777775222...3579*****************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 689.39
//
Query:       gi|70606071|ref|YP_254941.1|  [L=187]
Description: hypothetical protein Saci_0229 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1405.49
//
Query:       gi|70606072|ref|YP_254942.1|  [L=312]
Description: hypothetical protein Saci_0230 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-26   93.8   3.1      1e-26   93.8   3.1    1.8  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
        1.3    8.0   8.4        3.6    6.5   8.6    1.3  1  PHO4        Phosphate transporter family


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.1       0.2   1.8e+03       2      27 ..       2      27 ..       1      30 [. 0.81
   2 !   93.8   3.1   1.1e-30     1e-26       3     201 ..      80     294 ..      78     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.2
                                  .HHHHHHHHHHHHHHHHTTT--SCCH CS
                    MS_channel  2 kilkiliivvgilivlsllgvnvsal 27
                                  k+ k++ii++  ++++ ++++ +  l
  gi|70606072|ref|YP_254942.1|  2 KLQKFIIILLSSIVAFGVINYILRVL 27
                                  57799999999999999999877665 PP

  == domain 2  score: 93.8 bits;  conditional E-value: 1.1e-30
                                   HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS............. CS
                    MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig............. 70 
                                    +kil ++++i++++s+lgv+ s++la+  ++gl++glal+ ++ n++aGi++++++ + +GD v+i              
  gi|70606072|ref|YP_254942.1|  80 TVKILGYIITIVVAISTLGVSASTVLASGVFGGLVIGLALQPILGNFFAGILIILTRYITVGDQVRILssqipygvaslpa 160
                                   689****************************************************************99************ PP

                                   ...........SEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS..SSEEEEEEEEEE-TTS-...HHHHHHH CS
                    MS_channel  71 ...........dieGtVediglrttkirtfdgrivtiPnsslvtsnieNlsr.esgtrrikvsigvtyssdvkklekvlee 139
                                              + +GtV+di l++t+i t dg+++ +Pn  +++s+i  ++   s+++ + +++++++s     +e++   
  gi|70606072|ref|YP_254942.1| 161 ykyfsteridtGYKGTVVDIDLFFTRIITDDGNELRVPNLVVLNSSILDYTTrFSDQKVFGLRVEFPLSLG---VEEIENA 238
                                   **************************************************994555555555555555555...4443333 PP

                                   HHHHHHH-TTB-TTS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHH CS
                    MS_channel 140 lkealkekpevlkdkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkilee 201
                                   +++++ +++ev+   + + + ++f+ +++ + vr+ v++   e++ +v+se+ +r  k+ +e
  gi|70606072|ref|YP_254942.1| 239 VNQVV-KDYEVE---NGPYFNEQFDKEYVAVLVRIKVRN--GEDWRKVKSEVLKRLLKVRQE 294
                                   33333.455566...6889********************..8***********998776655 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.6    0.0004       3.6      59     153 ..      39     147 ..       4     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0004
                          PHO4  59 pselm...lgmlaallgaavwlllatvl.......glPvStthslvGaliGaalaa....egg.eavkwkklvkivlswvl 124
                                   p++++   lg++ al     w l  +v         + + tt+ + G +i + +a+     ++ +++  + ++  v+++ l
  gi|70606072|ref|YP_254942.1|  39 PDNILwirLGLILALGFLLSWSLGEVVReikipnvAYQIATTVKILGYIITIVVAIstlgVSAsTVLASGVFGGLVIGLAL 119
                                   44444445455555555555555554432211111455789999999999999998555422213444467888******* PP

                          PHO4 125 sPllggiiaallfllvkrlilvkeklkna 153
                                    P+lg ++a +l++l++++ +  ++++  
  gi|70606072|ref|YP_254942.1| 120 QPILGNFFAGILIILTRYITV-GDQVRIL 147
                                   *****************9944.2333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2039.25
//
Query:       gi|70606073|ref|YP_254943.1|  [L=355]
Description: hypothetical protein Saci_0231 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   60.9   0.0    1.7e-16   60.3   0.0    1.3  1  Linocin_M18   Encapsulating protein for peroxidase
     0.0014   19.0   0.7     0.0014   19.0   0.7    1.6  2  Rubrerythrin  Rubrerythrin
     0.0032   17.4   0.7     0.0075   16.2   0.7    1.6  1  Ferritin      Ferritin-like domain


Domain annotation for each model (and alignments):
>> Linocin_M18  Encapsulating protein for peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   2.9e-20   1.7e-16     100     243 ..     197     328 ..     155     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2.9e-20
                                   --HHHHHHHHHHHHHHHHHHHT--TTTT---STT-GG.GBE---..SSHHHHHHHHHHHHHHHHTT---SSEEEEEEHHHH CS
                   Linocin_M18 100 dlsavaeAArklAlaEdrlifeGlaeagieGlleakgkkklklsdwakagnileavleAlekLreaGvegpyalvlspelY 180
                                    l+ + +A+ k +l+Ed+l++  ++      l   +  +k k+sdw+ +g i+++v+++++ L+ +G++ p+++ +spelY
  gi|70606073|ref|YP_254943.1| 197 TLNIIHRAGVKYSLMEDELLLSKHP------LSIIERGRKEKASDWDIPGSIANDVIRGIQILETNGYTDPVTI-ISPELY 270
                                   4778899******************......9999999*********************************985.7***** PP

                                   HHHHHHSSS.SS-HHHHHHHHTS-EEEEESS-SS.EEEEETTSSSEEEEESS-SEEEEEEE-S CS
                   Linocin_M18 181 tklfrvsentgypeiehikelvdggvikapalkgdavlvstrggdfeLtvgqDlsigYlshea 243
                                   t+lfrv++++g++ei+ +k+ +  ++i +p +kg   +vs++g  f ++  +  ++++l++e 
  gi|70606073|ref|YP_254943.1| 271 TRLFRVYDKSGTYEIKLVKHAT--EIIVSPLIKG-LAVVSKKG--FYVMENTPAKVEFLGREG 328
                                   *********************6..**********.99999988..555555555555555555 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.7   2.4e-07    0.0014       3      58 ..      24      77 ..      22     100 .. 0.89
   2 ?   -2.5   0.1         1   6.2e+03      63      63 ..     134     134 ..     103     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-07
                                  HHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCST CS
                  Rubrerythrin  3 LekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklep 58
                                  L  A+ +E +a+++Y    + ++  +++++++ e++A+eE  H + + +ll ++ +
  gi|70606073|ref|YP_254943.1| 24 LRGALMAELDAINYYLQQGKLFE--NEHLKKVHEDIAKEEIAHFGEFLRLLYEVSK 77
                                  77899******************..******************9999999877655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                                   B CS
                  Rubrerythrin  63 e 63 
                                   +
  gi|70606073|ref|YP_254943.1| 134 Y 134
                                   1 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   1.3e-06    0.0075       3      53 ..      23      70 ..      21      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklae 53
                                  aL+ +l +el+a+++yl+    +++++l++++e   + a+ee  h+ +++ 
  gi|70606073|ref|YP_254943.1| 23 ALRGALMAELDAINYYLQQGKLFENEHLKKVHE---DIAKEEIAHFGEFLR 70
                                  7888999************************97...778888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2624.74
//
Query:       gi|70606074|ref|YP_254944.1|  [L=196]
Description: hypothetical protein Saci_0232 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1338.53
//
Query:       gi|70606075|ref|YP_254945.1|  [L=286]
Description: hypothetical protein Saci_0233 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-45  154.7  17.7      2e-45  154.7  17.7    2.0  2  Lys_export  Lysine exporter LysO
     0.0014   18.0   4.7     0.0014   18.0   4.7    2.6  3  Sbt_1       Na+-dependent bicarbonate transporter superfamily
  ------ inclusion threshold ------
          7    6.9   8.5        0.2   11.9   0.4    2.6  3  DUF3270     Protein of unknown function (DUF3270)


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   4.6     0.054   3.2e+02       5      78 ..      13      80 ..       8      96 .. 0.62
   2 !  154.7  17.7   3.3e-49     2e-45       2     189 ..     100     283 ..      99     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.054
                    Lys_export  5 iaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaal 78
                                  ++ ++lG +++l++      +s+ +++  +f + +  gs+   +e + ++ l+lll  ++t+++  l gl++  
  gi|70606075|ref|YP_254945.1| 13 VIALILGRYIKLPK-----GVSDAIILTVIFTIAFWGGSQIAGIELVDSILLSLLLALVITVVTYAL-GLFTVS 80
                                  66677777777766.....567777777777777777777666777777777776665555554444.444333 PP

  == domain 2  score: 154.7 bits;  conditional E-value: 3.3e-49
                    Lys_export   2 laliaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaalllgl 82 
                                   + l++G+++Glll++++     ++++y Ly+L +++Gi++gs  +l++   k+++ +++  ++ +++++l++l+++ ++  
  gi|70606075|ref|YP_254945.1| 100 IPLVLGFVVGLLLRVNI--PFGNIIDYELYILALVIGIDVGSAISLKTL-MKMSKVAIFAVIIDVISAVLVALIISPVI-- 175
                                   5689*******999987..689*********************996665.66777777777999999999999999997.. PP

                    Lys_export  83 slkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakr.fgklaaisvaGatsmDttLPiitks 162
                                   +lke+l + +G GwYS++g++++ ++g+++G i++l+n+lRE+la++l+p++ k+  +++ ai+v+GatsmD+tLP++ ++
  gi|70606075|ref|YP_254945.1| 176 NLKEGLMIMLGSGWYSYTGPFVARYYGPVAGIIGFLVNFLREQLAFVLVPIFLKFrPTPVGAIAVGGATSMDVTLPLYVEV 256
                                   57****************************************************9566789******************** PP

                    Lys_export 163 sgkevvvlaivhGvilsllvPilvslf 189
                                    g+e+++ a+v+Gvil+++vPi+++l+
  gi|70606075|ref|YP_254945.1| 257 LGNEYMIGAMVSGVILTIAVPIILPLV 283
                                   ************************997 PP

>> Sbt_1  Na+-dependent bicarbonate transporter superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.7   2.3e-07    0.0014       7      79 ..      10      82 ..       6      98 .. 0.87
   2 !    5.8   5.8    0.0012       6.9       6      82 ..     102     177 ..      97     181 .. 0.72
   3 ?   -3.6   0.0      0.87   5.2e+03     288     306 ..     238     256 ..     236     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-07
                         Sbt_1  7 ilGllaallksdLeiPealykllslyLLlaiGlkGGvelaeselsaelllallaavvlgllipllaflilrkl 79
                                   + ++a +l   +++P+ +++++ l ++++i + GG ++a  el  ++ll+ll+a+v+ +++  l+ +++++l
  gi|70606075|ref|YP_254945.1| 10 SVYVIALILGRYIKLPKGVSDAIILTVIFTIAFWGGSQIAGIELVDSILLSLLLALVITVVTYALGLFTVSRL 82
                                  555788899999********************************99999999999999999999998888875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0012
                         Sbt_1   6 filGllaa.llksdLeiPealykllslyLLlaiGlkGGvelaeselsaelllallaavvlgllipllaflilrkltkl 82 
                                   ++lG+++  ll++++ + + +   l ++  l iG+  G +++ ++l +++   +++av++ ++  +l+ li++ + +l
  gi|70606075|ref|YP_254945.1| 102 LVLGFVVGlLLRVNIPFGNIIDYELYIL-ALVIGIDVGSAISLKTL-MKMSKVAIFAVIIDVISAVLVALIISPVINL 177
                                   5666666514677888887777766654.45699999999999999.8899999999998888888777777665555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.87
                         Sbt_1 288 lgitfpfniligiPlYlal 306
                                   ++++    + +++PlY+++
  gi|70606075|ref|YP_254945.1| 238 IAVGGATSMDVTLPLYVEV 256
                                   6777777788899999876 PP

>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.89   5.3e+03      45      72 ..       9      36 ..       7      58 .. 0.65
   2 ?   -2.6   1.1       1.1   6.4e+03      70      82 ..      57      69 ..      33      82 .. 0.66
   3 ?   11.9   0.4   3.4e-05       0.2      34      71 ..     141     178 ..     136     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.89
                       DUF3270 45 iAvFsvitvlvsfillalklatllAfll 72
                                  i+v+ + ++l  +i l   ++ ++ + +
  gi|70606075|ref|YP_254945.1|  9 ISVYVIALILGRYIKLPKGVSDAIILTV 36
                                  6677777777777777665555443333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                       DUF3270 70 fllAilislails 82
                                  +ll++l+ l+i++
  gi|70606075|ref|YP_254945.1| 57 ILLSLLLALVITV 69
                                  3333333333333 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 3.4e-05
                       DUF3270  34 aklkeLlFFariAvFsvitvlvsfillalklatllAfl 71 
                                   + lk L+   ++A+F+vi+ ++s +l+al +++++ + 
  gi|70606075|ref|YP_254945.1| 141 ISLKTLMKMSKVAIFAVIIDVISAVLVALIISPVINLK 178
                                   6789999999***********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2148.30
//
Query:       gi|70606076|ref|YP_254946.1|  [L=165]
Description: hypothetical protein Saci_0236 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.21   11.7   0.0    1.4  1  DUF4167   Domain of unknown function (DUF4167)
       0.15   12.2   0.0       0.19   11.8   0.0    1.2  1  US10      Viral unique short region 10


Domain annotation for each model (and alignments):
>> DUF4167  Domain of unknown function (DUF4167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.21      20      56 ..       8      44 ..       2      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                       DUF4167 20 dsngpdvkvrGtAqqliekYkqLardaqssgDrVlaE 56
                                  + ++  v +rG  q+l+ek  + ard+  +  +V+ +
  gi|70606076|ref|YP_254946.1|  8 EEKKKSVTIRGIDQDLYEKMVNFARDSGRTVGEVMNQ 44
                                  55666789******************98887777765 PP

>> US10  Viral unique short region 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.2e-05      0.19      84     127 ..       8      51 ..       1      66 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                          US10  84 rprnysatltlasrdcyerfvcpvydsgtpmgvlmnltylwylg 127
                                     ++ s t+    +d ye++v    dsg  +g +mn +   +lg
  gi|70606076|ref|YP_254946.1|   8 EEKKKSVTIRGIDQDLYEKMVNFARDSGRTVGEVMNQAMSSFLG 51 
                                   5567899999999***********************99998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1095.80
//
Query:       gi|70606077|ref|YP_254947.1|  [L=324]
Description: hypothetical protein Saci_0237 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.7e-15   55.1   0.0    1.5e-14   54.6   0.0    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   8.2e-19   1.5e-14     199     279 .]     128     201 ..     113     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 8.2e-19
                                   EE-HHHHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE-- CS
                     PmbA_TldD 199 vlspeavgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkn 278
                                   +l+pea +  +h++v   l +d  +        +lGek++s+ ++++d+p++ + lg++ fDdEG pt+r+++I +G + +
  gi|70606077|ref|YP_254947.1| 128 ILDPEASAHVFHNLV-EFLKGDQPR-----I--RLGEKILSDEISVYDNPLNnYLLGFSVFDDEGYPTKRKEIIADGTVSS 200
                                   89**********988.566666666.....4..8*****************99*************************998 PP

                                   - CS
                     PmbA_TldD 279 y 279
                                   y
  gi|70606077|ref|YP_254947.1| 201 Y 201
                                   8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2337.52
//
Query:       gi|70606078|ref|YP_254948.1|  [L=251]
Description: 3-ketoacyl-ACP reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-62  211.2   0.3      2e-62  210.8   0.3    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.2e-52  178.3   1.6    1.4e-52  178.0   1.6    1.1  1  adh_short        short chain dehydrogenase
    4.6e-13   49.5   0.1    6.8e-13   48.9   0.1    1.2  1  KR               KR domain
    6.2e-06   25.8   0.1    9.6e-06   25.2   0.1    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00098   18.3   0.6     0.0011   18.1   0.6    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.001   18.3   0.0     0.0013   17.9   0.0    1.3  1  NAD_binding_4    Male sterility protein
      0.005   16.4   1.4     0.0074   15.9   0.8    1.6  2  NmrA             NmrA-like family
     0.0052   16.7   0.0      0.007   16.3   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
     0.0064   15.8   0.2       0.21   10.9   0.0    2.4  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
      0.017   14.5   0.2      0.036   13.4   0.2    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.05   13.9   0.1       0.13   12.6   0.1    1.7  2  TrkA_N           TrkA-N domain
      0.051   13.7   0.1       0.11   12.6   0.1    1.5  2  OTCace           Aspartate/ornithine carbamoyltransferase, As


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   0.3   1.3e-65     2e-62       3     232 ..      13     242 ..      11     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 1.3e-65
                                   TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGC CS
                  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapkl 83 
                                    +gIGraiA+++++ Ga+v + +++ e+  +++el+++ g   ++c+V++++qv ++ ++v+e ++++D++vnnag++ + 
  gi|70606078|ref|YP_254948.1|  13 TRGIGRAIAERFNSLGAKVFVLYASSES--QAKELESK-GIVTIKCNVSKRDQVIEASKKVREITNNVDVIVNNAGVMYT- 89 
                                   69*************************8..57777664.4445*************************************. PP

                                   SS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSB.STTTTHHHHHHHHHHHHHHHHHHHHGGG CS
                  adh_short_C2  84 kgpfletsreefdraldvnlyslfllakaalplmkeg.gsivnlssvgaerv.vpnynaygaaKaalealtrylAvelgpk 162
                                     pf+e+++e+++r++d+nl++++++++ +lp mke+ g ivn++s ++  +   +++ y+++K a++ ltr lA elg++
  gi|70606078|ref|YP_254948.1|  90 -MPFEEFDEEKYRRMMDINLNGTIYVIHTFLPFMKERgGVIVNIASNAGIGTsAVGTTFYAITKSAVIMLTRRLAFELGKY 169
                                   .*******************************8887769********99877355666*********************** PP

                                   TEEEEEEEE--BHCTG...GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                  adh_short_C2 163 giRvNavspgpikTla...asgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                   +iRvNav+pg+++T++    ++ ++++++++++++r+ l+ +g+pe++a ++ fL sd+a+yitGq++v+DgG
  gi|70606078|ref|YP_254948.1| 170 NIRVNAVAPGWVETDLtvsGKSPEETEKIKQWFRDRTVLHTTGRPEDIAGIVTFLSSDDAKYITGQVIVADGG 242
                                   **************99543344455889********************************************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.0   1.6   9.6e-56   1.4e-52       1     189 [.       5     188 ..       5     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.0 bits;  conditional E-value: 9.6e-56
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                   k v++tG+++GIGraia+++ + Gakv+v +++se++    akel+++   +++i+++v++r++v ++ +k+++ + ++dv
  gi|70606078|ref|YP_254948.1|   5 KNVVITGGTRGIGRAIAERFNSLGAKVFVlYASSESQ----AKELESK--GIVTIKCNVSKRDQVIEASKKVREITNNVDV 79 
                                   789**************************55555554....5888875..4****************************** PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAsKaavaglt 160
                                   +vnNAG+  + pf+e++ee+++r++++Nl+g++ +++++lp m+ +++G Ivn++S+ag   +  g++ Y+ +K av++lt
  gi|70606078|ref|YP_254948.1|  80 IVNNAGVMYTMPFEEFDEEKYRRMMDINLNGTIYVIHTFLPFMK-ERGGVIVNIASNAGiGTSAVGTTFYAITKSAVIMLT 159
                                   ******************************************77.99************6667778899************ PP

                                   HHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                     adh_short 161 rslakelaptgirvnavaPGlvdTdmake 189
                                   r la el +++irvnavaPG v+Td++ +
  gi|70606078|ref|YP_254948.1| 160 RRLAFELGKYNIRVNAVAPGWVETDLTVS 188
                                   *************************9865 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   4.5e-16   6.8e-13       3     144 ..       7     142 ..       6     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.5e-16
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                   ++itGG+ g+G+++a+   + ga+  vl + s       +++ +ele++g  + ++++ vs++d+v ++ +++++ ++++ 
  gi|70606078|ref|YP_254948.1|   7 VVITGGTRGIGRAIAERFNSLGAKVFVLYASS-------ESQAKELESKG--IVTIKCNVSKRDQVIEASKKVREITNNVD 78 
                                   58***************************999.......34568999987..789************************** PP

                                   EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--T CS
                            KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsa 144
                                    +++ Agv+ + ++ee ++e++++++   ++G+  + +++ +   e+  ++v ++S ag+  sa
  gi|70606078|ref|YP_254948.1|  79 VIVNNAGVMYTMPFEEFDEEKYRRMMDINLNGTIYVIHTFLPfmkERGGVIVNIASNAGIGTSA 142
                                   *********************************9877776655668888889999988875554 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   6.4e-09   9.6e-06       1     102 [.       7     118 ..       7     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.4e-09
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HHHHHHHHHH.....HT-SEEEE--S-- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrsalerlfke.....eqpdavihlAavg 75 
                                   +++tG+t  iG+a+++++++ g +v +l   s++++++++ +    +++++ +r+++ ++ k+     +++d++++ A+v 
  gi|70606078|ref|YP_254948.1|   7 VVITGGTRGIGRAIAERFNSLGAKVFVLYASSESQAKELESKGiVTIKCNVSKRDQVIEASKKvreitNNVDVIVNNAGVM 87 
                                   68**********************999999977777766665579999999999988777775222223799999999954 PP

                                   -HH..HHH..HSHHHHHHHHTHHHHHHHHHH CS
                     Epimerase  76 gva..ass..edpadfieknlqgtlnlleaa 102
                                     +  +++  e+  +++++nl+gt  +++  
  gi|70606078|ref|YP_254948.1|  88 YTMpfEEFdeEKYRRMMDINLNGTIYVIHTF 118
                                   4441133311333457888999998888865 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.6   7.7e-07    0.0011       1     113 [.       7     116 ..       7     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.7e-07
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   v++tG++  iG+++ +++ +  +k  +l+ ++E +  e+e++   +     +k+++ +    ++ +++++++ +  +vdv+
  gi|70606078|ref|YP_254948.1|   7 VVITGGTRGIGRAIAERFNSLGAKVFVLYASSESQAKELESKGIVT-----IKCNVSKRDQVIEASKKVREITN--NVDVI 80 
                                   79***************************************95333.....33343344455788899999999..99998 PP

                                   EE---.---HHHHHH...SHHHHHHHHHHHHHHHHH CS
               Polysacc_synt_2  82 fhaAA.lKhVPlvee...npleaiktNvlgtenvie 113
                                   ++ A  +  +P  e+   +   +++ N  gt  vi+
  gi|70606078|ref|YP_254948.1|  81 VNNAGvMYTMPFEEFdeeKYRRMMDINLNGTIYVIH 116
                                   887751566777654111455667778888877776 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   8.8e-07    0.0013      58     119 ..      46     115 ..       9     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.8e-07
                                   HTTTEEEEE--TTSGGGG--H.HHHHHHHHH--EEEE--SS-...S.ST....TSSEEHHHHHHHHHHHH CS
                 NAD_binding_4  58 laerikvveGDlseprlGLse.edlqelaeevdviihsaAtv...nfde....pykellrvNveGtrevl 119
                                    ++ i+ ++ ++s+ +  +++ ++++e++++vdvi+++a+ +    f+e    +y++++++N++Gt  v+
  gi|70606078|ref|YP_254948.1|  46 ESKGIVTIKCNVSKRDQVIEAsKKVREITNNVDVIVNNAGVMytmPFEEfdeeKYRRMMDINLNGTIYVI 115
                                   3555888999999999999862579***************87322233244469************9887 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8     5e-06    0.0074       1      68 [.       7      73 ..       7      87 .. 0.88
   2 ?   -3.0   0.0         3   4.4e+03     181     205 ..     212     237 ..     187     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                  EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEE CS
                          NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvv 68
                                  ++++G+T  +G+++++ + + g kv++l   ++  +ak+l+++G +++k ++  ++ + ea k+v  +
  gi|70606078|ref|YP_254948.1|  7 VVITGGTRGIGRAIAERFNSLGAKVFVLYASSE-SQAKELESKGIVTIKCNVSKRDQVIEASKKVREI 73
                                  6899************************97765.579***********99999999999999988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3
                                   -HHHHHHHHHHHHHHHHHHH.TTEEE CS
                          NmrA 181 daeeDiGafvikilkdprkl.kgkri 205
                                   +  eDi+ +v  + +d +k+  g++i
  gi|70606078|ref|YP_254948.1| 212 GRPEDIAGIVTFLSSDDAKYiTGQVI 237
                                   56678888888888887777666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.7e-06     0.007       1      66 [.      11      82 ..      11     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                                  TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT.......T-SEEEE CS
                NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk.......gadaVvs 66
                                  G+t ++Gr+++++  + g    ++++ ++++++ele ++g+ +++ +v++ +++ ea k       ++d++v 
  gi|70606078|ref|YP_254948.1| 11 GGTRGIGRAIAERFNSLGAKVFVLYASSESQAKELE-SKGIVTIKCNVSKRDQVIEASKkvreitnNVDVIVN 82
                                  99***************7445578899999*****8.69*************999999844444445555555 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00014      0.21      35      85 ..       3      53 ..       1      66 [. 0.91
   2 ?    2.3   0.1     0.062        93      69      93 ..      66      90 ..      54     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                  TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE CS
                 THF_DHG_CYH_C 35 egkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvv 85
                                  +gk+vv+ G  + +g+++a  +++ +a V v+  ++++ a+ +++  iv +
  gi|70606078|ref|YP_254948.1|  3 KGKNVVITGGTRGIGRAIAERFNSLGAKVFVLYASSESQAKELESKGIVTI 53
                                  8*********************************99999999999888865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.062
                                  TSCCHHHHHCCSSEEEE-SS-TT-B CS
                 THF_DHG_CYH_C 69 ktkdlaeitreadivvvavGkpeli 93
                                  ++k+++eit++ d++v  +G+   +
  gi|70606078|ref|YP_254948.1| 66 ASKKVREITNNVDVIVNNAGVMYTM 90
                                  68999************99987665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.4e-05     0.036      35      79 ..       3      49 ..       1      84 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                  TTSEEEEES.-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHT CS
                  2-Hacid_dh_C 35 sgktvGiiG.lGrIGqavakrlkafgmkviaydrskkkee.eeeelg 79
                                  +gk v i G +  IG+a+a+r++++g+kv++   s ++++ e e++g
  gi|70606078|ref|YP_254948.1|  3 KGKNVVITGgTRGIGRAIAERFNSLGAKVFVLYASSESQAkELESKG 49
                                  6788888862556***************9876555443332444444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.5e-05      0.13       3      58 ..       9      66 ..       7      73 .. 0.84
   2 ?   -3.1   0.0       6.1   9.1e+03      60      78 ..     214     232 ..     192     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                                  EES-SH.HHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHT CS
                        TrkA_N  3 iiGlGr.vGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeea 58
                                  i G  r +Gr++ae++++ g k +v+  ++e++++el+ +g+ +++ ++++++ + ea
  gi|70606078|ref|YP_254948.1|  9 ITGGTRgIGRAIAERFNSlGAKVFVLYASSESQAKELESKGIVTIKCNVSKRDQVIEA 66
                                  55544449**********88887888899999****************9999877665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.1
                                   GGGESEEEE-SSSHHHHHH CS
                        TrkA_N  60 iekadaviaatgddeanil 78 
                                    e++ ++++ +++d+a+ +
  gi|70606078|ref|YP_254948.1| 214 PEDIAGIVTFLSSDDAKYI 232
                                   4566666666766666555 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.4e-05      0.11       1     103 [.       3     110 ..       3     115 .. 0.77
   2 ?   -3.0   0.0       4.4   6.6e+03      54      69 ..     187     202 ..     166     211 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.4e-05
                                   CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TT....SSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                        OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkg....lepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                   kg+++++ G+    + ++ ++ ++ lg++v ++   +     e + + +  +k n++k  + i+ ++++ e  +++Dv++ 
  gi|70606078|ref|YP_254948.1|   3 KGKNVVITGGT-RGIGRAIAERFNSLGAKVFVLYASSesqaKELESKGIVTIKCNVSKRDQVIEASKKVREITNNVDVIVN 82 
                                   68999999955.789999999999999995554444434544457778889999999999********************9 PP

                                   --SS..ETTCCGGHHHHHHHHCCCSB-H CS
                        OTCace  78 dvwv..smgeekereerlkklkdyqvte 103
                                   +  v   m  e+  ee+++ ++d+ ++ 
  gi|70606078|ref|YP_254948.1|  83 NAGVmyTMPFEEFDEEKYRRMMDINLNG 110
                                   8655004445777779999999988875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                                   HHT-EEEEESSCHHHH CS
                        OTCace  54 ksggsititedleeav 69 
                                    sg+s + te++++ +
  gi|70606078|ref|YP_254948.1| 187 VSGKSPEETEKIKQWF 202
                                   3344444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1535.43
//
Query:       gi|70606079|ref|YP_254949.1|  [L=215]
Description: haloacid dehalogenase-like hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-13   49.1   0.0    9.9e-13   48.5   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.3e-09   38.7   0.0    1.9e-09   38.1   0.0    1.5  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00035   20.4   1.9      0.023   14.6   0.3    2.6  2  LisH            LisH
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.049   13.7   0.0    1.5  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.046   13.8   0.0      0.088   12.9   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
       0.27   10.3   1.8        4.5    6.4   0.2    2.4  2  LisH_2          LisH


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   3.3e-16   9.9e-13      54     174 ..      64     186 ..       7     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.3e-16
                         HAD_2  54 eseeeee.....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtse 129
                                   +++   e     + e+l +k+ +     e ++yd+++++Le+L+++gyk ++v++ +   +++ +  lg+++y+d  + s 
  gi|70606079|ref|YP_254949.1|  64 VKDFLYElgldpSNEKLTKKISSISRGSEYHIYDDAIDFLEYLRSEGYKTALVSNATP-RARNVVYSLGLHKYLDILIFSF 143
                                   3333333555556777778888888778899***********************9876.5799****************** PP

                         HAD_2 130 dvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagik 174
                                   +v+  KP+p+++  + ekl+      +  GD    Di++ak+a +k
  gi|70606079|ref|YP_254949.1| 144 EVGVVKPNPKIFTYVREKLGE---PDFHLGDIAeMDIQGAKRATLK 186
                                   *******************94...45779**999********9876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   6.4e-13   1.9e-09     101     209 ..      79     183 ..       3     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 6.4e-13
                                   HHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 101 allqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkv 180
                                    l   +    +    ++ ++++a +++++L++ g++++l+++  p+  + +   lG ++y+d+ i s +++v kp+p+++ 
  gi|70606079|ref|YP_254949.1|  79 KLT--KKISSISRGSEYHIYDDAIDFLEYLRSEGYKTALVSNATPRARN-VVYSLGlHKYLDILIFSFEVGVVKPNPKIFT 156
                                   555..55555566678899*************************98777.55556766888******************** PP

                                   HHHHHHTSTGGGEEEEESSHH.HHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                     Hydrolase 181 aaireLqgkpeevamVGDgvn.DaaalaaA 209
                                   ++ ++L g+p    + GD +  D++++++A
  gi|70606079|ref|YP_254949.1| 157 YVREKL-GEP--DFHLGDIAEmDIQGAKRA 183
                                   ******.555..59*************998 PP

>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   7.8e-06     0.023       4      19 ..      21      36 ..      21      39 .. 0.87
   2 ?    4.7   0.1     0.011        32       8      17 ..     103     112 ..     103     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.8e-06
                                  HHHHHHHHHHCT-HHH CS
                          LisH  4 NrLIydYLvkeGyeet 19
                                  ++LIyd+L+ +Gy+ +
  gi|70606079|ref|YP_254949.1| 21 YQLIYDFLRDNGYNLS 36
                                  69***********966 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.011
                                   HHHHHHCT-H CS
                          LisH   8 ydYLvkeGye 17 
                                   ++YL+ eGy+
  gi|70606079|ref|YP_254949.1| 103 LEYLRSEGYK 112
                                   68*******8 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.049      13      46 ..      93     126 ..      62     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                   TEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHH CS
                   Hydrolase_6  13 dkaipgaaealnalraagkpvvllTNnsskseee 46 
                                   +++++ a ++l++lr++g++++l++N + + ++ 
  gi|70606079|ref|YP_254949.1|  93 YHIYDDAIDFLEYLRSEGYKTALVSNATPRARNV 126
                                   67899**********************9998764 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.088       4      44 ..     149     186 ..     147     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                   TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-E CS
                Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwk 44 
                                   KP+p ++ + +e+lg++    +  GD  + Di+gA++a +k
  gi|70606079|ref|YP_254949.1| 149 KPNPKIFTYVREKLGEPD---FHLGDIAEMDIQGAKRATLK 186
                                   9*************9997...999*************9776 PP

>> LisH_2  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0015       4.5       4      19 ..      23      38 ..      22      38 .. 0.94
   2 ?    2.9   0.1     0.019        56       7      14 ..     104     111 ..     102     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                        LisH_2  4 LvaeYLqsqgYnYTLS 19
                                  L+ ++L+ +gYn +LS
  gi|70606079|ref|YP_254949.1| 23 LIYDFLRDNGYNLSLS 38
                                  899*********9998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
                        LisH_2   7 eYLqsqgY 14 
                                   eYL+s gY
  gi|70606079|ref|YP_254949.1| 104 EYLRSEGY 111
                                   9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1474.07
//
Query:       gi|70606080|ref|YP_254950.1|  [L=528]
Description: hypothetical protein Saci_0240 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-15   56.6   0.0    1.2e-13   51.8   0.0    2.7  3  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.15   2.7e+03     127     127 ..     120     120 ..      48     155 .. 0.55
   2 !   51.8   0.0   6.4e-18   1.2e-13       2     166 ..     213     394 ..     212     395 .. 0.83
   3 ?    1.4   0.0      0.02   3.6e+02      96     164 ..     430     499 ..     403     502 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.15
                                   H CS
                                   x RF
                   Radical_SAM 127 f 127
                                   +
  gi|70606080|ref|YP_254950.1| 120 W 120
                                   2 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 6.4e-18
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerlakla 74 
                                    vtrgC+++C+fC+++      ++ rs++++ i++ev+++  + g + v +  ++ lly         d ++ l+ ++ + 
  gi|70606080|ref|YP_254950.1| 213 QVTRGCPRGCRFCSITP-----ETFRSIPIDVIKKEVEIN-MKGGWRRVEFITDDILLYgsqklrtnHDAIVNLFSEVMKM 287
                                   79**************5.....9*****************.7999**************7777766644444444444444 PP

                                   ..CCTEEEEEEECSSCHG...HHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHH........HHHHHHHHHHHH CS
                                   ..xxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                   Radical_SAM  75 ..vpgiritvetngtlpd...eeklerllelg...vdrvslgleaaddekvlklmnrghtf........eevlealeklre 139
                                     +     ++++++++ +    + + +++ ++        +gle+++ + + k+m + + f        + +l+a+ ++++
  gi|70606080|ref|YP_254950.1| 288 gvDGIWFPHISAPAVRESpktVKAMSEIASYNfdrAAAPVVGLESGSLKIIEKYM-PAKAFpwtprdwrDVILDATAIMND 367
                                   8889999999999999997778888888888855555566788888888777777.6666678889999************ PP

                                   TTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 140 agikrvvdrivglpGendeeleellel 166
                                   + i +++++++g p e++e++++ ++l
  gi|70606080|ref|YP_254950.1| 368 NYIYPCYTMTIGYPEETEEDVDQSISL 394
                                   **999****************999877 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.02
                                   HHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  96 rllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivglpGendeeleell 164
                                   +l +  +d ++l  +   +  +++l+ +  t++ + ++++k+ + +i++   ++d++++   e++ e+ +++
  gi|70606080|ref|YP_254950.1| 430 KLPKNYWDLLYLAWNYDLKI-TRQLI-PVITNSMRNKLVRKIVQTMIDKifsSIDFVFMQLKETKGEHAKIY 499
                                   55555566666666666665.77777.88888888888888888888888889***********99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3884.80
//
Query:       gi|70606081|ref|YP_254951.1|  [L=114]
Description: hypothetical protein Saci_0241 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.14   11.8  26.5       0.22   11.2  26.5    1.3  1  Yip1          Yip1 domain
       0.57   10.5  19.3       0.91    9.8  19.3    1.4  1  TctB          Tripartite tricarboxylate transporter TctB fami
        2.5    7.5  16.4          7    6.1  14.6    2.0  2  DUF1129       Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  26.5   3.7e-05      0.22      63     153 ..       4     109 ..       1     113 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                          Yip1  63 lgaiiggylglllgllllalllhliakllggkgsfkq.....tlsvvgya...llPlilgaliaillllllgt.......l 128
                                   ++ +i++++ +l+g+++l+  ++l++k+   + sf+      ++s+v+y    ++  ++ga+i+i+++ll +        +
  gi|70606081|ref|YP_254951.1|   4 ISNLIILLISFLIGWIILSIPVWLASKAVSRRSSFGNamivsLVSIVVYVvlsTFLHFIGAIIGIIIILLIIReiynvgwG 84 
                                   55689999999*******************777777755444777777778889999999999999999988899999995 PP

                          Yip1 129 lllvgllaliWslvllylglkaahn 153
                                   +++v+ ++++  +v+++l l a+h 
  gi|70606081|ref|YP_254951.1|  85 GAIVIGVLSLVIFVIIALILGALHL 109
                                   5555555555555555555555554 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  19.3   0.00015      0.91      41     130 ..      15     104 ..       2     109 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                          TctB  41 llgllllv..aadgekeekearedwrkllklvlallaalllyallleplGfilata.lflllll....greerkwlkalil 114
                                   l+g ++++  +      +++a ++  ++   +++ l+++++y++l ++l fi a++ ++++ll+        +  +  +i+
  gi|70606081|ref|YP_254951.1|  15 LIG-WIILsiP---VWLASKAVSRRSSFGNAMIVSLVSIVVYVVLSTFLHFIGAIIgIIIILLIireiY---NVGWGGAIV 88 
                                   222.2222321...33344555566667777888899***********999888887333333346642...333444444 PP

                          TctB 115 avvlallvyllFtklL 130
                                     vl+l+++++ + +L
  gi|70606081|ref|YP_254951.1|  89 IGVLSLVIFVIIALIL 104
                                   4455555566666655 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  14.6    0.0012         7     114     175 ..       7      67 ..       1     101 [. 0.89
   2 ?   -0.0   1.6     0.086   5.1e+02     149     168 ..      86     105 ..      77     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0012
                       DUF1129 114 itlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviN 175
                                   + +ll++++ G++++ +  +l   k  ++r ++ + ++++l+++vv++vl t++ ++ a i 
  gi|70606081|ref|YP_254951.1|   7 LIILLISFLIGWIILSIPVWLAS-KAVSRRSSFGNAMIVSLVSIVVYVVLSTFLHFIGAIIG 67 
                                   56899****************98.9*****************************99988775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.086
                       DUF1129 149 rllilllllvvwlvlftlva 168
                                    ++i +l+lv+++++ ++++
  gi|70606081|ref|YP_254951.1|  86 AIVIGVLSLVIFVIIALILG 105
                                   55666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 763.05
//
Query:       gi|70606082|ref|YP_254952.1|  [L=274]
Description: cation efflux integral membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-17   62.2  23.6    6.4e-17   61.9  23.6    1.1  1  Cation_efflux  Cation efflux family
     0.0015   18.6   0.9      0.014   15.5   0.5    2.2  2  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
        4.4    7.4   6.0        4.6    7.3   2.2    2.2  2  Vma12          Endoplasmic reticulum-based factor for assembl


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9  23.6   1.1e-20   6.4e-17       3     199 .]       3     187 ..       1     187 [. 0.86

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.1e-20
                 Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglav 83 
                                   + l++  ++++  li+ +++nS  l+ + +hsl+dl+   +++ al+++ +  d ++++G++rle + +l+++ +++++ v
  gi|70606082|ref|YP_254952.1|   3 RILICFSLITASLLITSIFANSALLFTEFIHSLVDLIPIAFAFYALRIIDRI-DSKYTYGLHRLEIVSSLFNIFTVVAGSV 82 
                                   45555556889999*********************************99985.99************************** PP

                 Cation_efflux  84 fllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillfn 164
                                   f+++ +   li  ++   +  l+l+ + ++l ++l+            ++  ++++ lh++ D+l+ + +++s+l+i++++
  gi|70606082|ref|YP_254952.1|  83 FSVYISTVELI--EGSRGDFLLVLISSSIALSLSLVASTDKS------EEGRVSGSKLHAIQDSLAYILAVISSLLIIIMK 155
                                   ***********..66666666666666555555555555444......5566999999**********************7 PP

                 Cation_efflux 165 lksgplaDpvaslligliilysalkllkeslseLl 199
                                    +    +Dpv ++++  ++++++l+ lk s  +L+
  gi|70606082|ref|YP_254952.1| 156 IYF---IDPVSAYILNGVLVITSLSPLKFSYNILM 187
                                   776...*****************999999988886 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.037   2.2e+02      56      76 ..     195     213 ..     194     216 .. 0.84
   2 !   15.5   0.5   2.4e-06     0.014      34      77 ..     221     263 ..     205     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                                   HHHHHHHHHH-TT--EEEEEE CS
                      ZT_dimer  56 devekrikeefpgvadvliHv 76 
                                   + ve ++++ fp+v++  iHv
  gi|70606082|ref|YP_254952.1| 195 KSVETELQSIFPQVHH--IHV 213
                                   679**********977..665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.4e-06
                                   -EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                      ZT_dimer  34 ifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                    ++ lh++ ++dl+++e  +  +  ek ++e+f g+++v+i  e
  gi|70606082|ref|YP_254952.1| 221 NVATLHVRENPDLTLRELDKKREYAEKVLREKF-GITHVTIQFE 263
                                   45689****************************.99*****987 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.2   0.00077       4.6      77     111 ..      68     112 ..      63     120 .. 0.72
   2 ?    1.2   0.2     0.058   3.4e+02      63      97 ..     125     159 ..     112     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00077
                         Vma12  77 lilvlNiliSvvavffavwialrsartp..........slpvrvl 111
                                   +++ +Ni+  v++++f+v+i +  +++           s ++ + 
  gi|70606082|ref|YP_254952.1|  68 VSSLFNIFTVVAGSVFSVYISTVELIEGsrgdfllvliSSSIALS 112
                                   7899****************9988866645555555554455555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.058
                         Vma12  63 deltaqelkevnrqlilvlNiliSvvavffavwia 97 
                                     +++++l++++  l  +l ++ S ++ ++ ++++
  gi|70606082|ref|YP_254952.1| 125 GRVSGSKLHAIQDSLAYILAVISSLLIIIMKIYFI 159
                                   45667889999999999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1963.16
//
Query:       gi|70606083|ref|YP_254953.1|  [L=328]
Description: citrate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-92  309.8   0.0    2.6e-92  309.7   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.05   13.3   0.1        0.9    9.3   0.0    2.7  3  DUF4325       STAS-like domain of unknown function (DUF4325)
      0.074   13.0   0.0       0.17   11.9   0.0    1.5  1  TraI_2_C      Putative conjugal transfer nickase/helicase Tra


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.7   0.0   4.4e-96   2.6e-92      46     361 .]       1     310 [.       1     310 [. 0.95

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 4.4e-96
                                   HHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHH CS
                  Citrate_synt  46 LltgelPtkeelkefkeelaearklpekvlealealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAkl 126
                                   +l+gelP+k+ l+++k++l e+ ++p++ ++ + +lpk+++ +  + aa+ +l+a ++ + +k++ ++ a++    ++Ak 
  gi|70606083|ref|YP_254953.1|   1 MLYGELPKKSDLQRVKNKLDESFEVPDQAINLIYSLPKESETIGLMEAAFGVLAAIYNPTWEKAKNKDIAIE----IVAKT 77 
                                   58***********************************99*****************9877777776676666....***** PP

                                   HHHHHHHHHHHTTS.-----TTSSHHHHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHH CS
                  Citrate_synt 127 ptiaaaiyrarlgreplepddklsyaenflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaa 207
                                   +ti+a+iyra++g +p  p++++s+a++fl++ +g + +++ +k++d+al+l+ DHe+ aST a  v+aStl+dlys+i+a
  gi|70606083|ref|YP_254953.1|  78 ATILANIYRAKEGLKPRIPQPSESLARSFLEAAFGGHVEDKKVKAMDIALILYTDHEVPASTTAGLVAASTLSDLYSCIVA 158
                                   *************877788888************98999****************************************** PP

                                   HHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTC.HTHHHH CS
                  Citrate_synt 208 gigalkGplhgganeavlkmleeigsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaee.kgkdpl 287
                                   +++alkGplhgga e++ k + eigs+e +v+e+ ++++  +k+rl+GfGHrvy+++DpR ki+k++aeela+  ++ +++
  gi|70606083|ref|YP_254953.1| 159 ALSALKGPLHGGAAEEAFKQFVEIGSPE-KVDEWFKTNILDKKKRLMGFGHRVYRTFDPRGKIFKKYAEELASGnEQVKKY 238
                                   ***************************9.******99888779*****************************99888899* PP

                                   HHHHHHHHHHHHHHHHCHHGCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH.HT------E CS
                  Citrate_synt 288 lklaeeleevapevlkekeeknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql.adnkiiRPr 361
                                   l++ae+le++  e  +++  k++ypN Dfysg++++ +g+p  +ft +fa+sR++GwlAh +e+  +++++iRPr
  gi|70606083|ref|YP_254953.1| 239 LDIAERLEKLGVE--TFSG-KGVYPNTDFYSGIVFYGIGFPIYMFTGIFALSRTLGWLAHFIEYVeEQHRLIRPR 310
                                   **********999..7779.*******************************************987889*****8 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.42   2.5e+03      36      48 ..      47      59 ..      46      75 .. 0.71
   2 ?    9.3   0.0   0.00015       0.9      28      50 ..     100     122 ..      99     132 .. 0.81
   3 ?    0.0   0.0      0.12   6.9e+02      35      53 ..     172     190 ..     172     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.42
                       DUF4325 36 deaFgglirefge 48
                                  ++aFg+l+  +++
  gi|70606083|ref|YP_254953.1| 47 EAAFGVLAAIYNP 59
                                  7899999866655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00015
                       DUF4325  28 esigssFldeaFgglirefgeee 50 
                                   es++ sFl++aFgg +++ + ++
  gi|70606083|ref|YP_254953.1| 100 ESLARSFLEAAFGGHVEDKKVKA 122
                                   68999*********998877655 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.12
                       DUF4325  35 ldeaFgglirefgeeeisk 53 
                                   ++eaF ++++ +++e++++
  gi|70606083|ref|YP_254953.1| 172 AEEAFKQFVEIGSPEKVDE 190
                                   69******99888777665 PP

>> TraI_2_C  Putative conjugal transfer nickase/helicase TraI C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.8e-05      0.17      41      76 ..     219     254 ..     216     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                   THHHHHHHHHHHHHHHTT-TT-TTEEEEEEB--HHH CS
                      TraI_2_C  41 giFkrYaqealakeedkekwkkvqkrfeklklhrkk 76 
                                   +iFk+Ya+e +  +e+ +k  ++ +r+ekl+++  +
  gi|70606083|ref|YP_254953.1| 219 KIFKKYAEELASGNEQVKKYLDIAERLEKLGVETFS 254
                                   7********99********************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2328.96
//
Query:       gi|70606084|ref|YP_254954.1|  [L=280]
Description: carboxyvinyl-carboxyphosphonate phosphorylmutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-55  188.3   0.1    1.6e-55  188.1   0.1    1.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    9.6e-14   50.7   0.2    1.4e-13   50.3   0.2    1.2  1  ICL         Isocitrate lyase family
      0.009   15.5   0.6      0.018   14.5   0.1    1.8  2  ComA        (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   0.1   2.8e-59   1.6e-55       3     236 ..       3     239 ..       1     242 [. 0.93

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 2.8e-59
                    PEP_mutase   3 aLhakgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGyges 83 
                                   +L +k++ l++p ++++ +a ++e+ gfka+ +s+ a++ slG+pD  +++l+el  ++r+i ev+++P+ivD+++G+ge 
  gi|70606084|ref|YP_254954.1|   3 ELLRKADFLLIPGVFNPFTALLAEQVGFKAVYLSGGAYTSSLGMPDLGIITLDELAWIIRRIREVTDIPIIVDADTGFGE- 82 
                                   5667779************************************************************************9. PP

                    PEP_mutase  84 peevaetvrrliaaGvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeai 159
                                   + +v ++v+ l++aG+ ++ iED+    k++  ++++++ ++++++ki+aa +a +e  ++i+ARtd+    a +gl++ai
  gi|70606084|ref|YP_254954.1|  83 VLNVYRAVKVLESAGANAIQIEDQvlpkKCGHlDGKEVVHPRDMVSKIKAALKARKE--MLIIARTDSR---AVNGLDDAI 158
                                   99***********************98666666999999************999877..*********3...6789***** PP

                    PEP_mutase 160 eRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp.l.kgt..lsvaelaelGvarislgnhllraalaalreaae 236
                                   +Ra+ Y+eAGAd +f   +++++e ++++++v++pl + + + ++t  ++ +e++e+G + +++   ++r+a +a+++a+e
  gi|70606084|ref|YP_254954.1| 159 QRAKTYLEAGADIIFPEAMESKDEFQKFAKEVKAPLLANMtEfGKTpyITAKEFREMGYKYVIFPVTIFRVAAKAMKDALE 239
                                   ***********************************9999944544467*****************************9987 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.2   2.3e-17   1.4e-13     151     253 ..      71     168 ..      64     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 2.3e-17
                                   -EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE- CS
                           ICL 151 piiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvart 231
                                   pii dadtG+G +  v + +k++   Ga  i iedq    kkcGh+ Gk +v  ++ + ++ a+         ++l++art
  gi|70606084|ref|YP_254954.1|  71 PIIVDADTGFGEVLNVYRAVKVLESAGANAIQIEDQV-LPKKCGHLDGKEVVHPRDMVSKIKAALK----ARKEMLIIART 146
                                   9***********************************7.579***********99998888765433....36799****** PP

                                   -GGGEEEES-TT-GGGGGGEEE CS
                           ICL 232 dseaatlitstidtrdhafilG 253
                                   ds a + +  +i++   ++  G
  gi|70606084|ref|YP_254954.1| 147 DSRAVNGLDDAIQRAKTYLEAG 168
                                   ******9999998776666555 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     3e-06     0.018     115     188 ..     125     196 ..      75     204 .. 0.74
   2 ?   -2.8   0.0      0.59   3.6e+03     119     137 ..     232     250 ..     210     266 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                                   HHHHHHCCTTSEEEEEES-SSH.HHHTT--CCHHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HHHHH CS
                          ComA 115 rliekakkeglkvlpevgkkdg.elesesdveklieeakrdleaGaekviiEaresGitegvydekgevrtdvve 188
                                   ++++k+k++ lk+  e+ +    + ++   +++ i++ak  leaGa+ +  Ea es    ++ +  +ev++ +++
  gi|70606084|ref|YP_254954.1| 125 DMVSKIKAA-LKARKEMLIIARtDSRAVNGLDDAIQRAKTYLEAGADIIFPEAMESKD--EFQKFAKEVKAPLLA 196
                                   567777777.88888877754413455599************************9765..444556666665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.59
                                   HHCCTTSEEEEEES-SSHH CS
                          ComA 119 kakkeglkvlpevgkkdge 137
                                   ka k+ l+vl++ g +++ 
  gi|70606084|ref|YP_254954.1| 232 KAMKDALEVLMKEGTQKSL 250
                                   3333334444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1453.71
//
Query:       gi|70606085|ref|YP_254955.1|  [L=431]
Description: MmgE family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-94  315.1   0.0    7.6e-94  314.7   0.0    1.0  1  MmgE_PrpD  MmgE/PrpD family
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.057   13.3   0.0    1.6  1  UBA_6      UBA-like domain
      0.053   13.4   2.6      0.078   12.8   0.4    2.4  2  IF2_N      Translation initiation factor IF-2, N-terminal reg


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.7   0.0   1.3e-97   7.6e-94       3     415 ..       6     403 ..       4     412 .. 0.93

  Alignments for each domain:
  == domain 1  score: 314.7 bits;  conditional E-value: 1.3e-97
                                   HHHHHHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHHHHHHHH CS
                     MmgE_PrpD   3 qlaefvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfvnGaaih 83 
                                   ++aef+++++  +++++vv+++k+++lD+++vala+++++++k a e +k  + pg+a+++ +g ++sp  A f n  +i+
  gi|70606085|ref|YP_254955.1|   6 TIAEFASSVT--KVSDDVVKEVKKRVLDSIAVALASINSQPAKVAQETAK--YFPGEAPML-NGMKASPDFASFYNTLLIR 81 
                                   6788888765..5667*******************************766..666788877.599**************** PP

                                   CTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHHHHHHHHHT CS
                     MmgE_PrpD  84 alDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfgaaaaaakLl 164
                                   +lDf+Dt+l+ e  hpsd+++++l +A   + +g+dl++Ai+vGyEv+++l++  s+++ g +d+v ++++gaaa++a Ll
  gi|70606085|ref|YP_254955.1|  82 YLDFNDTYLSLEPLHPSDMIGGLLTLASIFDLKGEDLIRAIAVGYEVGVNLCDTTSLRKKG-FDHVNFLGIGAAAGMANLL 161
                                   *************************************************************.******************* PP

                                   T--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHHHHSTT-----S CS
                     MmgE_PrpD 165 gLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGflavlsggkdlele 245
                                    Ld+e+  nA++++++ + +lr++r ++ +++k+ a++ A+rn+v+a l+Ak+GftGp+  + g  Gf  +++++ d ++ 
  gi|70606085|ref|YP_254955.1| 162 SLDKEKAKNAISLTIVPHVALRETRSGKLSMWKAGATAEAVRNAVFATLMAKNGFTGPELPFSGVFGFSTIIAKDMDSSKF 242
                                   *************************************************************************99666655 PP

                                   .S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC---S...---SHHHHCT-C CS
                     MmgE_PrpD 246 vkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkkg...ppenradadhSl 323
                                    k     e  +i+++++K+yp+e+h+ a ++a +k+  e +     I++i+++t+ea   i+ +++   +p+n+++adhS+
  gi|70606085|ref|YP_254955.1| 243 -KLT---EGKAILRTMLKKYPVEYHAEALVEAGMKINYEGE-----IKKIVVETYEAGKSILADTEdkwKPRNKETADHSI 314
                                   .433...479**************************98887.....8*****************999************** PP

                                   CHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS-B---EEESS-TTSGGHHHH CS
                     MmgE_PrpD 324 qyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdggrtleerveypkGhprnpls 404
                                   ++++ v ll++ + l++++   +  +e+ +L+++vevve +++t+ y+ + +++v+v++  + +++++v  p+Gh +np+s
  gi|70606085|ref|YP_254955.1| 315 PFIITVTLLKKYLWLDSYNL--IGYKELEELMKRVEVVEREDYTKVYARELPTKVTVITS-KGEYSAEVRVPRGHYANPMS 392
                                   ******************86..5689*********************9999975555544.45689*************** PP

                                   HHHHHHHHHHH CS
                     MmgE_PrpD 405 reeleeKfrrl 415
                                   ++e++eK ++l
  gi|70606085|ref|YP_254955.1| 393 EDEVVEKAKKL 403
                                   *******9987 PP

>> UBA_6  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-06     0.057       5      23 ..     397     415 ..     394     416 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-06
                         UBA_6   5 ldfflKLGYseeqvqavLe 23 
                                   ++++ KLG se+q+  vL+
  gi|70606085|ref|YP_254955.1| 397 VEKAKKLGMSEKQINSVLQ 415
                                   9****************97 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.34     2e+03       5      24 ..       6      25 ..       6      28 .. 0.84
   2 ?   12.8   0.4   1.3e-05     0.078      15      45 ..     391     420 ..     389     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
                         IF2_N  5 rVyeLAkeLgvkskevikkL 24
                                  ++ e+A    + s +v+k+ 
  gi|70606085|ref|YP_254955.1|  6 TIAEFASSVTKVSDDVVKEV 25
                                  78999999999999999987 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.3e-05
                         IF2_N  15 vkskevikkLfkelGievkshsssLDeetae 45 
                                   ++  ev++k+ k+lG++ k+++s L  +t++
  gi|70606085|ref|YP_254955.1| 391 MSEDEVVEKA-KKLGMSEKQINSVLQLDTIK 420
                                   5789******.55************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2430.80
//
Query:       gi|70606086|ref|YP_254956.1|  [L=306]
Description: lactate/malate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-33  115.7   0.4    3.1e-33  114.8   0.4    1.4  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
    8.6e-07   29.0   0.1    1.3e-06   28.4   0.1    1.2  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
     0.0011   19.5   0.1     0.0046   17.5   0.0    2.1  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0016   18.4   0.3       0.04   13.9   0.0    2.7  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0023   18.1   0.0     0.0095   16.1   0.0    2.1  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0023   17.8   0.0      0.005   16.8   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.046   14.2   1.4        0.6   10.6   0.1    3.0  3  RuvA_C          RuvA, C-terminal domain


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8   0.4   1.2e-36   3.1e-33       1     134 [.       2     135 ..       2     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.2e-36
                                   EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S-S CS
                       Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitagvp 80 
                                   vkva +G+ G +Gq++a++   +++ade+ L+D+++e  e    ++ h+ + l vk++  + ++ +++++ad+vvitag p
  gi|70606086|ref|YP_254956.1|   2 VKVAFIGV-GRVGQTIAYNTIVNGYADEVMLYDVVPELPEKFEHEIRHALAALRVKTELLStNNIDDISGADIVVITAGKP 81 
                                   69******.************************************************99988999**************** PP

                                   S-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS CS
                       Ldh_1_N  81 rkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasgl 134
                                   rkpG++R+dL+ +NakI+ ++++++ k ++ a++++v+NPvd++++v+ k+sg 
  gi|70606086|ref|YP_254956.1|  82 RKPGMSRRDLFIDNAKIMIDLAKKLPKKNKGAMYIMVANPVDMMASVFMKYSGE 135
                                   **************************************************9986 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   5.2e-10   1.3e-06       5     164 ..     146     298 ..     143     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.2e-10
                                   HHHHHHHHHHHHTS-GGGEE--EEBSSST........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSS CS
                       Ldh_1_C   5 ivRaktflaekagvtprsvkvtViGgHsg........vtiipllsqvkellklsekqleeliervqnggdevvkakkGags 77 
                                   ++R++  +a+k ++ + +v  +V G+H++        vt+ ++  ++ e+l ++   ++e  + v++ ++e++      g 
  gi|70606086|ref|YP_254956.1| 146 TMRMRSYIAKKLNIPAYEVGGYVGGEHGEaamvlwstVTVKGK--PFSESLGVN---KAEVEDYVKKIAAEIIRVL---GG 218
                                   78***************************66666655333333..445555555...556667888889*******...99 PP

                                   S-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHH CS
                       Ldh_1_C  78 atlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkk 158
                                   +t + ++ + ++++++  +++++  ++v  + +++    ei+ +s Pvv+g   v   l    l++  + +l +++ke  +
  gi|70606086|ref|YP_254956.1| 219 TTWGPGADIEEVIRSVALNEGKV--MSVAFPHKYED---EIIHISEPVVVG-RTVGPALT-SALDENDKARLSQAIKEVYN 292
                                   ***********************..77776666654...57**********.55555555.58999999999999999988 PP

                                   HHHHHH CS
                       Ldh_1_C 159 eiekgl 164
                                    ++  l
  gi|70606086|ref|YP_254956.1| 293 VYKSNL 298
                                   877665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0046       1      68 [.       3      77 ..       3     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvla 68
                                  k+++iG G++g+++a + + +g  + e+++  +  pe  e+++ e+           ++ +++n + ++ ad+vv++
  gi|70606086|ref|YP_254956.1|  3 KVAFIGVGRVGQTIAYNTIVNG-YADEVMLY-DVVPELPEKFEHEIRhalaalrvkTELLSTNNIDDISGADIVVIT 77
                                  79********************.88888854.888888888888888888888888556666899999999999886 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.6e-05      0.04       1      78 [.       3      79 ..       3     129 .. 0.79
   2 ?   -0.9   0.0      0.55   1.4e+03      63      91 ..     106     134 ..      94     172 .. 0.79
   3 ?    1.4   0.0      0.11   2.7e+02      66     124 ..     235     293 ..     225     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                                  -EEEE--SHHHHHHHHHHHTTT..--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaeng..hevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78
                                  k+a++G G  G ++A     ng   ev+l+   +el e+++  he  + L  +++ ++l  t+++++ ++gadi+v+   
  gi|70606086|ref|YP_254956.1|  3 KVAFIGVGRVGQTIAYNTIVNGyaDEVMLYDVVPELPEKFE--HEIRHALAALRVKTELLSTNNIDD-ISGADIVVITAG 79
                                  79*************9888888779*************995..77788999**********999987.688999998654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.55
                                   HHHHHTT--EEEE---HHHHHHHHHHHCC CS
                NAD_Gly3P_dh_N  63 laealkgadiivlvvPsqalrevlkklkg 91 
                                   l +  kga +i+++ P  ++++v+ k +g
  gi|70606086|ref|YP_254956.1| 106 LPKKNKGAMYIMVANPVDMMASVFMKYSG 134
                                   55566788888999999988888877765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                                   HHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S CS
                NAD_Gly3P_dh_N  66 alkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelke 124
                                   al++ +++ ++ P+++  e+++  ++++  +++   l+  + e+ + +ls++i+e+ + 
  gi|70606086|ref|YP_254956.1| 235 ALNEGKVMSVAFPHKYEDEIIHISEPVVVGRTVGPALTSALDENDKARLSQAIKEVYNV 293
                                   56677888899999999999999999999999999999999999*********998765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.7e-06    0.0095       1     115 [.       3     121 ..       3     124 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                                   EEEEE--SHHHHHHHHHHHHTT-..EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHS.. CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagy..kvavynrtkekveelvaegakaaesieelvasl..dvvitmvkagkavdevieg.. 75 
                                   k++fiG+G  G+ +a n + +gy  +v++y++ +e  e++ +e  +a++ ++  ++ l  + +  +   g+++  ++ g  
  gi|70606086|ref|YP_254956.1|   3 KVAFIGVGRVGQTIAYNTIVNGYadEVMLYDVVPELPEKFEHEIRHALAALRVKTELLstNNIDDIS--GADIVVITAGkp 81 
                                   69****************99998557*******9999999887644444443333332212222222..222222222234 PP

                                   HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEE CS
                 NAD_binding_2  76 llealkkgdilidgstsspedtrelakelkekglkfldaP 115
                                    ++ +++ d++id + + ++ +++l k+ k +   ++  P
  gi|70606086|ref|YP_254956.1|  82 RKPGMSRRDLFIDNAKIMIDLAKKLPKKNKGAMYIMVANP 121
                                   6667777777777777777777777766666655555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06     0.005       1      54 [.       3      58 ..       3      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                  EEEEE--SCCHHHHHHHHHHTT-..EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTS CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagl..eVvlvdiseealekalekieksleklvekgk 54
                                  kva iG G +G+ ia+ ++ +g+  eV l+d+ +e  ek +++i++ l+ l  k +
  gi|70606086|ref|YP_254956.1|  3 KVAFIGVGRVGQTIAYNTIVNGYadEVMLYDVVPELPEKFEHEIRHALAALRVKTE 58
                                  79********************9777*******************99988754433 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.71   1.8e+03      18      27 ..      44      53 ..      43      62 .. 0.74
   2 ?   10.6   0.1   0.00023       0.6      12      41 ..     193     233 ..     192     234 .. 0.93
   3 ?    0.1   0.0      0.46   1.2e+03      22      41 ..     269     289 ..     266     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.71
                                  HHHHHHHHHH CS
                        RuvA_C 18 keaekAvakv 27
                                  +e+++A+a++
  gi|70606086|ref|YP_254956.1| 44 HEIRHALAAL 53
                                  6778887776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                                   HCTS-HHHHHHHHHHHHC...........-TTS-HHHHHHH CS
                        RuvA_C  12 aLGYkekeaekAvakvla...........npgasveelIra 41 
                                   +LG +++e+e  v+k++a           +pga++ee+Ir 
  gi|70606086|ref|YP_254956.1| 193 SLGVNKAEVEDYVKKIAAeiirvlggttwGPGADIEEVIRS 233
                                   89999***********9999999999*************95 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.46
                                   HHHHHHHC.-TTS-HHHHHHH CS
                        RuvA_C  22 kAvakvla.npgasveelIra 41 
                                    A++++l+ n+ a  +++I++
  gi|70606086|ref|YP_254956.1| 269 PALTSALDeNDKARLSQAIKE 289
                                   677788877888889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1930.75
//
Query:       gi|70606087|ref|YP_254957.1|  [L=299]
Description: D-isomer specific 2-hydroxyacid dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-33  115.0   0.0    3.7e-33  114.4   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    6.6e-10   38.8   0.0    8.1e-10   38.5   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0003   20.9   0.0    0.00051   20.1   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   6.1e-37   3.7e-33      21     178 .]     101     260 ..      82     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 6.1e-37
                                   TCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  21 gewksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlp 100
                                   g  k++++++ + l+g  + ++G G IG++va++ k +f+m vi+++rs k+ e   +++ +  +l++++ ++Di++ +lp
  gi|70606087|ref|YP_254957.1| 101 GIGKRDRTFRPYPLTGVNLMVLGGGGIGSEVARIGKmGFNMYVIGVSRSFKRPE-LFDEKHNISELKDIIGKADIIVDTLP 180
                                   4446788899999************************************99888.555566899***************** PP

                                   -STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTC..HHHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 101 ltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplped..spllelpnviltPHia 178
                                   lt+ t +++n ++l+++k++ai++N++RG++v ee++++ Lk++k   +++Dvf+     ed  s+l+el+n++ tPH++
  gi|70606087|ref|YP_254957.1| 181 LTKLTDGILNYDMLSRVKENAIIVNVGRGETVVEEDVYRLLKERKDVRFGTDVFWRKNGVEDfnSKLWELDNFTGTPHTG 260
                                   ********************************************************9777665589************87 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.4e-13   8.1e-10      35     133 ..      27     293 ..       6     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.4e-13
                                   HHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                    2-Hacid_dh  35 ekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt............. 102
                                   +++++ad+l+++  +   + +l +++++k ++++++GvD + ++++  +G+ V++  g+++ svAE++             
  gi|70606087|ref|YP_254957.1|  27 DDVPKADILMLWPLQ--AKVFLPKAKSVKAVQTFSAGVDDFPFSLLP-KGVDVFSNAGAYSVSVAEHAfalimtlakgigk 104
                                   568889999999877..66677**********************998.58******************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|70606087|ref|YP_254957.1| 105 rdrtfrpypltgvnlmvlggggigsevarigkmgfnmyvigvsrsfkrpelfdekhniselkdiigkadiivdtlpltklt 185
                                   ********************************************************************************* PP

                                   .............................................................................T-BH CS
                                   .............................................................................xxxx RF
                    2-Hacid_dh 103 .............................................................................aaTe 106
                                                                                                                +  +
  gi|70606087|ref|YP_254957.1| 186 dgilnydmlsrvkenaiivnvgrgetvveedvyrllkerkdvrfgtdvfwrkngvedfnsklweldnftgtphtggaYGND 266
                                   ****************************************************************************66677 PP

                                   HHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 107 eaqeniaeeaaenlvaflkgespanav 133
                                       n+  ea++n+ ++++ ++++n v
  gi|70606087|ref|YP_254957.1| 267 VVKTNAIIEACKNVYNYITSGKAENKV 293
                                   7788999***************99988 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.6e-08   0.00051      25     133 ..     118     229 ..     111     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.6e-08
                                   EEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHH.HHHCTT-EE--HHHCTTT-SEEEE-...SS.SSSSB-HHHHCCS CS
                 AdoHcyase_NAD  25 vavvaGyGdvGkGcaaslkglGarvivtevdPical.qaameGfevvtleevvkkadivvtt...tG.nkdiitlehlkkm 100
                                   + +v G G +G   a+ + ++G  ++v  v           e +++ +l++++ kadi+v t   t  ++ i++ ++l+++
  gi|70606087|ref|YP_254957.1| 118 NLMVLGGGGIGSEVAR-IGKMGFNMYVIGVSRSFKRpELFDEKHNISELKDIIGKADIIVDTlplTKlTDGILNYDMLSRV 197
                                   5556666666655543.4456666666666544333033446789***************873334414568999****** PP

                                   -TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEET CS
                 AdoHcyase_NAD 101 kddaivcniGhfdseidvaaleanalkkeevkp 133
                                   k++ai+ n+G  ++ ++ +  +   +++++v+ 
  gi|70606087|ref|YP_254957.1| 198 KENAIIVNVGRGETVVEEDVYRLL-KERKDVRF 229
                                   *********998776554433333.34555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1974.02
//
Query:       gi|70606088|ref|YP_254958.1|  [L=149]
Description: hypothetical protein Saci_0248 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   77.3   0.0    1.3e-21   77.1   0.0    1.0  1  EVE       EVE domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   7.5e-26   1.3e-21       1     145 []       2     142 ..       2     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 7.5e-26
                                   -EEEEEEBHHTSHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEE.....ETSSSS-EEEEEEEEECEEEE-GGGG- CS
                           EVE   1 ayWllksepdefsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfY.....hsgeklqaivgiaeVvseaypdetqfd 76 
                                   +yW++++++d   ++ +  ++ +++ g+++   ++++r++kkGDl++fY     +++ +  ++vgi++V+s++y+d+t++ 
  gi|70606088|ref|YP_254958.1|   2 TYWIIPVQED--FWEAV--SSLNVF-GHNK---ERATRYIKKGDLLIFYvnkyyAKRLG-GMFVGIYRVSSDWYTDTTPLF 73 
                                   6*********..*****..99****.9888...889999**********9887666666.9******************** PP

                                   TTSTT--TTTBTTS--EEEEEEEEEEEEEEEEHHHHTT.....HGTCTTSHHHHCC..T-SEEEE-HHHHHHHHHH CS
                           EVE  77 pkskyydpkskkekpwlrvdvkpvkklkrplslkelka.....epelegmkllrkg..rlsvrpvteedwelilel 145
                                   p++k +++ ++    ++r++++p+  l+ +++++++ +     e++++  k+lr+   +l  rpv+ +d++li+e+
  gi|70606088|ref|YP_254958.1|  74 PDEKLQNKVIH----TYRINIEPL--LAGKCPVRDILYelsfiEDKFQFSKFLRNVpgNLR-RPVPVSDAKLIEEC 142
                                   **********9....9********..999999999999444433577888899*9998888.***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1098.63
//
Query:       gi|70606089|ref|YP_254959.1|  [L=387]
Description: aspartate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-39  135.2   0.0    3.5e-39  134.8   0.0    1.1  1  Aminotran_5  Aminotransferase class-V
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.091   12.8   0.0    1.8  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   3.9e-43   3.5e-39      33     342 ..      28     334 ..      14     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 3.9e-43
                                   SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHH CS
                   Aminotran_5  33 svhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrt 112
                                   +v+  ++e+ +a++ + ++ ++l+ ++++++   + G+++ a++ v  s+   l ++++++v +++  + +  w+++ kr 
  gi|70606089|ref|YP_254959.1|  28 NVGFSSEEFVQAFQFCLKETRKLFRVDNSYQPFIIPGSGTsAMESVT-SF---LGKDNKVLVASNGVFGDR--WVNIFKRY 102
                                   5566688999999999***********99998888888862444443.44...79****************..******** PP

                                   TEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTE CS
                   Aminotran_5 113 gakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgv 192
                                    +kv+++  + +  + +d++e++++ ek++lv++thv+++tG+ qp+ee +k+++++  l++vD++++vg  ++  k++gv
  gi|70606089|ref|YP_254959.1| 103 PLKVDYLGSEVGDYVSVDKIEEKVRkEKYDLVTLTHVETSTGVRQPIEETVKRIRDYVDLIVVDGVSSVGAEEVRAKDWGV 183
                                   ********************9999769****************************************************** PP

                                   SEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET..TEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHC CS
                   Aminotran_5 193 DflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl..eettfaeapskfeaGTpnvagiiglgaaleylee 270
                                   D++   ++K + +P+G+G+l++++++ e+++   + g++++  +     + +++    + a Tp+v  i  l++a+++++e
  gi|70606089|ref|YP_254959.1| 184 DIYLTASQKaIGAPPGLGILVASEKAMESIKGDSVAGYYLDLRNWlpVMRNMEDGKGSYFA-TPPVHTIFMLAQAFKLIQE 263
                                   *********8889*************************99988765555556666666666.******************* PP

                                   HHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT CS
                   Aminotran_5 271 igleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca 342
                                    gl++  k++++ a+ ++++++s++   +++ +++  +++++ + +++v ae+v + + +eg+++  G h a
  gi|70606089|ref|YP_254959.1| 264 EGLDNRIKRHEKVAKVIRAGIESMGLRLVAK-RPESYSNTVTGVILNKVRAEEVLKEIVNEGVELAPGVHPA 334
                                   ************************9999966.899999******************************9988 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.091      29      98 ..     104     176 ..      88     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                   B12-binding  29 feVqllganven....edivaairaekpdvvglSal..ltsqleavkelvellkrirprv.kvvvGGahpsldpeet 98 
                                    +V++lg +v +    ++i++++r+ek+d+v l+ +  +t   + ++e+   +krir+ v  +vv G+  s+ +ee+
  gi|70606089|ref|YP_254959.1| 104 LKVDYLGSEVGDyvsvDKIEEKVRKEKYDLVTLTHVetSTGVRQPIEET---VKRIRDYVdLIVVDGV-SSVGAEEV 176
                                   5799998888888888*****************9843333333444444...5555554414444443.35555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2979.18
//
Query:       gi|70606090|ref|YP_254960.1|  [L=221]
Description: NADH dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-29  103.5   0.0    1.9e-29  102.9   0.0    1.3  1  Nitroreductase   Nitroreductase family
      1e-08   35.0   1.0      0.054   13.1   0.0    3.4  3  TM1586_NiRdase   Putative TM nitroreductase
  ------ inclusion threshold ------
      0.052   13.9   0.1      0.089   13.2   0.1    1.3  1  DUF1104          Protein of unknown function (DUF1104)
       0.12   11.5   1.1       0.13   11.5   0.0    1.5  2  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   4.2e-33   1.9e-29       1     170 []       7     174 ..       7     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 4.2e-33
                                   HHH--B--.-B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHHH CS
                Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeelk 80 
                                   i+kRr +R  ++++p+p+e+l+kil aa+ aPs g +qpw+f++++d e+r+k++e+++++    ++q+++ +++     +
  gi|70606090|ref|YP_254960.1|   7 IKKRRDVRsYYRKDPIPDEVLAKILMAAHLAPSVGFSQPWNFIIIRDIEKRKKIKELVQKERENFRQQLSEERKEI---FD 84 
                                   89******9999999******************************************************9998875...** PP

                                   HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHH...H.HHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S CS
                Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayrya...l.ldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp 157
                                     + +a+ + p+ i +  t+d ++  ++  +++++   +  ++ +a++nl+La ta+G+g+ ++++f +++  v+++l++p
  gi|70606090|ref|YP_254960.1|  85 RIKIEAILDTPINIAV--TCDPQRFGPNVLGRSTMpylCqYSTVLAIENLWLASTAEGIGVGWVSFFHKED--VKRILNIP 161
                                   ****************..6666665555555554422232599****************************..******** PP

                                   ..SEEEEEEEEE- CS
                Nitroreductase 158 deeeivvliavGy 170
                                   d  ++v+ +++Gy
  gi|70606090|ref|YP_254960.1| 162 DSVDLVAYLTLGY 174
                                   *9**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.5   4.1e-05      0.18       1      28 [.       2      30 ..       2      33 .. 0.85
   2 !   10.5   0.1   7.3e-05      0.33     158     186 ..      25      53 ..      19      73 .. 0.79
   3 !   13.1   0.0   1.2e-05     0.054      88     137 ..     129     179 ..     126     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                                  -HHHHHHH--B---B-.-S---HHHHHHH CS
                TM1586_NiRdase  1 nlyeaiekRhsvRkYk.dealeeelleel 28
                                  +lyeai+kR+ vR+Y  + ++++e+l ++
  gi|70606090|ref|YP_254960.1|  2 DLYEAIKKRRDVRSYYrKDPIPDEVLAKI 30
                                  69************873678999999887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.3e-05
                                   HHHHHHHHHHHTS--GGG----EEE.E-S CS
                TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdd 186
                                   e + +il aa lAPs   +qpw f +  d
  gi|70606090|ref|YP_254960.1|  25 EVLAKILMAAHLAPSVGFSQPWNFIIIRD 53 
                                   56789*******************97665 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS--- CS
                TM1586_NiRdase  88 geqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktkl 137
                                    e+l L  ta+G+g  Wv++ +k+ +k  ++++++ +lv+ ++lGy+++  
  gi|70606090|ref|YP_254960.1| 129 IENLWLASTAEGIGVGWVSFFHKEdVKRILNIPDSVDLVAYLTLGYVTHFP 179
                                   58999**************98888777779****************98655 PP

>> DUF1104  Protein of unknown function (DUF1104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     2e-05     0.089      28      62 ..      55      89 ..      36      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                  HHHHHHHHS-HHHHHHHHHHHHHHHHHHHTTS-HH CS
                       DUF1104 28 evaKrlkslkekekkkfkkklkeaaeknlekmtvk 62
                                  e +K++k+l +ke+++f+++l e++++ +++++++
  gi|70606090|ref|YP_254960.1| 55 EKRKKIKELVQKERENFRQQLSEERKEIFDRIKIE 89
                                  668999*********************99998876 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3      0.98   4.4e+03      41      57 ..      53      68 ..      49      73 .. 0.72
   2 ?   11.5   0.0   2.8e-05      0.13     134     177 ..     121     164 ..     118     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.98
               Beta_lactamase3 41 tfekrkkklkleiikvk 57
                                  ++ekr kk+k  + k++
  gi|70606090|ref|YP_254960.1| 53 DIEKR-KKIKELVQKER 68
                                  67777.88888888854 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.8e-05
               Beta_lactamase3 134 iryneliyfddltieakaagtflGWvnyllevekkkilayissl 177
                                    +y  ++ +++l +   a g+++GWv +  + + k+il +  s+
  gi|70606090|ref|YP_254960.1| 121 CQYSTVLAIENLWLASTAEGIGVGWVSFFHKEDVKRILNIPDSV 164
                                   689999******************************99887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1385.97
//
Query:       gi|70606091|ref|YP_254961.1|  [L=77]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 541.26
//
Query:       gi|70606092|ref|YP_254962.1|  [L=161]
Description: 3-isopropylmalate dehydratase small subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-21   77.1   0.0    2.2e-21   76.6   0.0    1.3  1  Aconitase_C    Aconitase C-terminal domain
     0.0011   18.7   1.8      0.065   12.8   1.8    2.2  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus
     0.0036   16.9   0.1     0.0054   16.3   0.1    1.2  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   3.6e-25   2.2e-21      61     129 ..      38     106 ..       5     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 3.6e-25
                                   EHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                   Aconitase_C  61 dvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                     ++  e ykk+ + ++++agk fG GSSRe+AA+al++ G+ka+iaeSF+rIf +n+i+ngl  ++++
  gi|70606092|ref|YP_254962.1|  38 MEPLDPEFYKKASSGVIIVAGKVFGMGSSREQAAMALKAAGVKAIIAESFARIFFRNAINNGLPVITLQ 106
                                   445556779999999***********************************************9777765 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   1.8   1.1e-05     0.065      51     149 ..      49     137 ..       6     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                                   TTSS-EEEEEEEEEES---THHHHHHHHHHSEEETTEEEEEE--EEEEEEE-HHHHHHHHHTT..-EEEE---TT--TT-E CS
                 Aconitase_2_N  51 kkgvplayvgdvvGtGssRksavnsvlWtigedipyvPnkraggvvlGgkiaPiFfntvedsG..alpieadvskletGdv 129
                                   +++  ++  g v G GssR  a  ++  +                ++  + a iFf  + + G   + ++   +++++Gd 
  gi|70606092|ref|YP_254962.1|  49 ASSGVIIVAGKVFGMGSSREQAAMALKAAG------------VKAIIAESFARIFFRNAINNGlpVITLQNATKEINQGDL 117
                                   444456677888888888887765442222............1246788899****9999888333556677899****** PP

                                   EEEETTTTEEEETT--EEEE CS
                 Aconitase_2_N 130 ieikpkegkikkeegevvse 149
                                   ++++  +g+i  +  +v++ 
  gi|70606092|ref|YP_254962.1| 118 VRVNVETGEIVVNGSKVLKG 137
                                   **********9966666554 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     9e-07    0.0054       9      60 ..      60     111 ..      55     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9e-07
                                   EES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT CS
                          IlvN   9 viGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkk 60 
                                   v G+Gs  +  a+ l+ +g++ +++    +  +++A ++g+ v+t+++a+k+
  gi|70606092|ref|YP_254962.1|  60 VFGMGSSREQAAMALKAAGVKAIIAESFARIFFRNAINNGLPVITLQNATKE 111
                                   89***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1098.68
//
Query:       gi|70606093|ref|YP_254963.1|  [L=414]
Description: 3-isopropylmalate dehydratase large subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-80  270.1   0.3    6.4e-78  262.8   0.3    2.4  1  Aconitase  Aconitase family (aconitate hydratase)
    3.9e-05   22.5   0.0    5.5e-05   22.1   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.3   7.2e-82   6.4e-78      15     461 .]      25     406 ..       7     406 .. 0.88

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 7.2e-82
                     Aconitase  15 ayvpdrvllqdvtgvqalvdlaaa.reavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaa 94 
                                   + ++d v+ +d tg  +++ ++   + +v + ++ +   dhl+p       +v               r++e   +++++ 
  gi|70606093|ref|YP_254963.1|  25 EIKVDLVAFHDLTGYHVIEVMEDVgTLKVFDREKLVIAFDHLAPPP-----DV---------------RSAEIQGQIRNFV 85 
                                   4447888888888888888886551445566777777777777766.....22...............2234445677778 PP

                     Aconitase  95 kafgi.rvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGk 174
                                   k+  + +++++++GI Hq+++E  +a pg+++v+ DSHT++ g++G++a G G ++++a+ ++ ++++ +p+  +++l+Gk
  gi|70606093|ref|YP_254963.1|  86 KKTSVpNFYDINSGILHQIMIER-YANPGQVIVAADSHTSTSGAVGAFAQGLGASDVAAAVITGKTWVMVPQPFKITLEGK 165
                                   88866589***************.********************************************************* PP

                     Aconitase 175 lkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavl 255
                                      ++  kD++l++ g ++++  +g  +E f +  ++ +++ raT++NM++E+ A + +f +d++t++Y+k t r +++  
  gi|70606093|ref|YP_254963.1| 166 PARWINGKDIALKILGDFKADYFNGMSLEIFVKEPSAVPMDFRATVSNMGIEMNADALMFVPDQETFNYIK-TARGYEP-- 243
                                   ***********************************************************************.99*9999.. PP

                     Aconitase 256 veaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkd 336
                                           ++  ++ d+da+y +++++dls+l p va p++++++ ++ ++                           ++ 
  gi|70606093|ref|YP_254963.1| 244 --------QM--VTPDSDAKYVDEYNIDLSKLDPLVAAPHSVDNVKSV-NE---------------------------VEG 286
                                   ........22..468999************************998888.22...........................345 PP

                     Aconitase 337 gkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig 417
                                   ++vd+++igSCTN++++d+++aa++l+     g+kvk+  +t+v P+S +  +++ + G+ ++L +aG+ ++   C++C+g
  gi|70606093|ref|YP_254963.1| 287 TPVDQVFIGSCTNGRISDLEMAAKILK-----GKKVKT--RTIVIPASYQLFKKALELGYVQTLADAGAIITYGTCGPCLG 360
                                   6799***********************.....******..***************************************** PP

                     Aconitase 418 .nsdrleegeaivsssNRNFegRqg.pntrayLaSPelvvaaAlaG 461
                                      + + +ge+i+s+s RNF+gR+g p+++ yL  P++++a+Al+G
  gi|70606093|ref|YP_254963.1| 361 gHFGIAGPGETIISTSSRNFKGRMGsPDAKVYLSGPAVAAATALEG 406
                                   8888889*****************8799999*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.1e-09   5.5e-05     282     357 ..     280     355 ..     243     377 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.1e-09
                        DUF521 282 elskakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtC 357
                                   ++++ + ++vd v++G c    +++l+  a++lkgkk+ +++++++ +s+++ ++a +lg+v++l +aG+ +   tC
  gi|70606093|ref|YP_254963.1| 280 SVNEVEGTPVDQVFIGsCTNGRISDLEMAAKILKGKKV-KTRTIVIPASYQLFKKALELGYVQTLADAGAIITYGTC 355
                                   34566888999999996778899**********66555.566778889***************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2575.56
//
Query:       gi|70606094|ref|YP_254964.1|  [L=278]
Description: translocase 6TM [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-45  153.8  19.6    6.4e-45  153.5  19.6    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5  19.6   3.6e-49   6.4e-45       1     196 [.      16     237 ..      16     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 3.6e-49
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHH......................HH..HCCHHHHC.CTTS-EE--SSS-HH CS
                          TatC   1 ehLeeLrkrlirallavaiafiitfvfaeel......................ia..fllepleeaeeevelivlspleaf 57 
                                   eh++eL +r  r+++ ++++++i  +f+ +                       +   +l++p+ +   +  li+lsp+ea+
  gi|70606094|ref|YP_254964.1|  16 EHIRELLRRTRRVIISFLVFLTIYTTFGITTikigtysipilyptlydsisvqFTrvVLMRPIPK---DLILITLSPFEAL 93 
                                   8**********************988844432334444444444444443433224566677655...46699******** PP

                                   HHHHHHHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTT CS
                          TatC  58 llklkvslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seevepl 134
                                   l+ + vs++++++ ++P++l ++wafv+pgLy+he+r ++++++  +llf++G afayf++lp++l f++    s +vep+
  gi|70606094|ref|YP_254964.1|  94 LTTITVSVYLSIFSSLPILLREFWAFVSPGLYEHEKRTFRKLVTPGMLLFVAGSAFAYFMLLPFMLIFIYrldvSLGVEPT 174
                                   **********************************************************************88887778*** PP

                                   EEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S.. CS
                          TatC 135 lslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.p 196
                                   l  ++y+s+++ll+ ++giaFe+Pl++++l+ +gl++++t+ k++r+ ++++++va +++P +
  gi|70606094|ref|YP_254964.1| 175 LGFNSYISTIILLMAGTGIAFEMPLIMYMLTLVGLIKSSTWFKNWRWGVLISFIVAYIISPgT 237
                                   *************************************************************43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1810.70
//
Query:       gi|70606095|ref|YP_254965.1|  [L=127]
Description: hypothetical protein Saci_0255 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0018   17.6   7.9     0.0025   17.2   7.9    1.2  1  GAS              Growth-arrest specific micro-tubule binding
     0.0091   16.9   4.7      0.012   16.5   4.7    1.2  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
  ------ inclusion threshold ------
      0.016   15.0   4.3        1.2    9.0   0.4    2.1  2  CdvA             CdvA-like coiled-coil domain
       0.02   14.5   2.8      0.056   13.0   1.0    1.9  2  SLATT_6          SMODS and SLOG-associating 2TM effector doma
      0.021   14.8   5.7       0.07   13.1   5.3    1.8  2  ArAE_1_C         Putative aromatic acid exporter C-terminal d
      0.026   14.6   7.5        1.5    9.0   0.4    2.2  2  bZIP_1           bZIP transcription factor
      0.029   13.7   0.7       0.04   13.3   0.7    1.1  1  PhoU_div         Protein of unknown function DUF47
      0.035   14.0   1.1       0.61   10.0   0.1    2.0  2  STAT_alpha       STAT protein, all-alpha domain
      0.038   14.3   0.6      0.038   14.3   0.6    1.8  2  Bac_RepA_C       Replication initiator protein A C-terminal d
      0.042   14.0   2.3        2.7    8.3   0.5    2.1  2  Lipoprotein_3    Lipoprotein
      0.052   13.4   5.7        1.3    8.8   0.9    2.1  2  Dynactin_p22     Dynactin subunit p22
      0.052   13.1   1.4       0.79    9.3   0.1    2.0  2  PspA_IM30        PspA/IM30 family
       0.07   13.1   0.1       0.13   12.2   0.1    1.4  1  Sugarporin_N     Maltoporin periplasmic N-terminal extension
      0.075   13.7   1.7       0.47   11.1   0.2    2.0  2  CdiI_2           CdiI immunity protein
      0.076   10.7   0.2      0.092   10.4   0.2    1.1  1  ACR_tran         AcrB/AcrD/AcrF family
       0.11   12.7   2.2        3.1    8.1   2.0    2.1  1  DUF948           Bacterial protein of unknown function (DUF94
       0.11   12.5   5.5       0.53   10.4   0.7    2.1  2  BRE1             BRE1 E3 ubiquitin ligase
       0.12   12.9   2.6        1.8    9.0   2.6    2.1  1  DUF4140          N-terminal domain of unknown function (DUF41
       0.12   12.4   0.4       0.12   12.4   0.4    2.1  2  SAB              SAB domain
       0.12   12.8   5.2        1.5    9.3   0.4    2.2  2  Snapin_Pallidin  Snapin/Pallidin
       0.13   12.1   2.7       0.17   11.8   0.8    2.0  2  HSBP1            Heat shock factor binding protein 1
       0.13   12.4   6.2        0.2   11.8   6.2    1.3  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.14   11.5   3.2       0.32   10.3   3.2    1.5  1  DUF3450          Protein of unknown function (DUF3450)
       0.15   11.2   0.3       0.25   10.5   0.1    1.4  1  AI-2E_transport  AI-2E family transporter
       0.15   12.5   8.7          1    9.8   0.6    2.8  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.15   12.6   0.6       0.15   12.6   0.6    2.2  2  GTP-bdg_M        GTP-binding GTPase Middle Region
       0.16   11.8   9.9       0.74    9.6   1.6    2.3  2  DivIC            Septum formation initiator
       0.17   12.2   3.2       0.54   10.6   1.0    2.5  2  DUF1149          Protein of unknown function (DUF1149)
        0.2   11.7   7.5       0.39   10.7   7.5    1.4  1  Prefoldin_2      Prefoldin subunit
        0.2   12.1   7.1        2.8    8.4   0.6    2.2  2  ZapB             Cell division protein ZapB
       0.35   11.0   5.0        9.4    6.4   0.2    2.4  2  Mst1_SARAH       C terminal SARAH domain of Mst1
       0.53   10.5   5.3        4.6    7.5   0.8    2.1  2  Med21            Subunit 21 of Mediator complex
       0.63    7.9   4.4       0.75    7.6   4.4    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.67   10.0  10.0       0.65   10.0   2.0    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.76    9.7   4.8       0.86    9.5   0.5    2.4  2  Rad50_zn_hook    Rad50 zinc hook motif
        1.2    8.4   6.3        4.2    6.6   0.8    2.0  2  FAM76            FAM76 protein
        1.2    9.8   6.7         36    5.1   6.9    2.2  1  Occludin_ELL     Occludin homology domain
        1.3    9.0  13.5       0.23   11.4   1.9    2.8  2  Pox_A_type_inc   Viral A-type inclusion protein repeat
        1.3    9.0   7.9        4.1    7.3   0.9    2.1  2  Prefoldin        Prefoldin subunit
        1.6    8.6   6.6       0.26   11.2   1.3    2.2  2  WD40_alt         Alternative WD40 repeat motif
        3.4    7.9   9.5        4.6    7.5   1.6    2.1  2  Spc24            Spc24 subunit of Ndc80
        3.9    7.7   6.9        1.3    9.3   1.0    2.4  2  XhlA             Haemolysin XhlA
        4.5    7.0   7.0         12    5.6   1.0    2.0  2  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
        5.6    6.9  11.4          1    9.3   3.1    2.6  2  PKcGMP_CC        Coiled-coil N-terminus of cGMP-dependent pro


Domain annotation for each model (and alignments):
>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.9   6.2e-06    0.0025      23     108 ..      24     115 ..      22     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.2e-06
                           GAS  23 nNLelIkslKeeieelkkkeer....nekelseisqenkrlkepLkkaeeev..eeLrkqlknyekdkqslknlkarlkel 97 
                                   n +++Ik+  +  +el++k+++     ++e++ei+q n++++ pL ++ + +  e  +    ny+ +  +++ l++r+kel
  gi|70606095|ref|YP_254965.1|  24 NSISTIKNVVKTYNELRRKQTEivneLKREFNEIAQSNEEIVRPLSEVSRTMyyETTNDTPVNYSIKDYKMDMLEQRIKEL 104
                                   67889999999999999999752222688899****************99864367777899******************* PP

                           GAS  98 ekelkdlkweh 108
                                   ekel++lk + 
  gi|70606095|ref|YP_254965.1| 105 EKELNELKKNR 115
                                   *******9875 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.7     3e-05     0.012       2      86 ..      36     121 ..      25     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-05
                PRKG1_interact   2 YkkLYeeekeenerLkreLeelekelselkseleklkqq.rqesvskrssllelekrerrslerkiseleeelkeleeLra 81 
                                   Y +L  ++ e  ++Lkre +e+ ++ +e+   l++++++   e ++++    ++++ +   le++i+ele+el+el++ r 
  gi|70606095|ref|YP_254965.1|  36 YNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRTmYYETTNDTPVNYSIKDYKMDMLEQRIKELEKELNELKKNRG 116
                                   5555566666678899999999999999998888887664456889999999***********************999876 PP

                PRKG1_interact  82 enqrL 86 
                                     + L
  gi|70606095|ref|YP_254965.1| 117 VDNEL 121
                                   65555 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0068       2.8      18      47 ..      34      63 ..      24      81 .. 0.64
   2 ?    9.0   0.4    0.0029       1.2      43      62 ..      95     114 ..      92     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0068
                          CdvA 18 styeeikekleealkklkekakelkeklkk 47
                                  +ty+e+++k +e +++lk++ +e+++  ++
  gi|70606095|ref|YP_254965.1| 34 KTYNELRRKQTEIVNELKREFNEIAQSNEE 63
                                  566666666666666666666666554444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                          CdvA  43 eklkkrlkeledqiksleka 62 
                                   ++l++r+kele+++++l+k 
  gi|70606095|ref|YP_254965.1|  95 DMLEQRIKELEKELNELKKN 114
                                   799*************9986 PP

>> SLATT_6  SMODS and SLOG-associating 2TM effector domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.0   0.00014     0.056      63     118 ..      10      70 ..       7      83 .. 0.81
   2 ?    1.8   0.1      0.38   1.6e+02      99     129 ..      73     103 ..      68     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                       SLATT_6  63 lliiigiialy.....isayekdkekYekagkeltklfneLkelysevksseeedlsklea 118
                                   ++i++gii l      is+ ++  ++Y++   + t++ neLk+ ++e+ +s+ee +++l++
  gi|70606095|ref|YP_254965.1|  10 IIIVLGIILLAgdknsISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSE 70 
                                   78999**999644444888999999***********************9988887766654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                       SLATT_6  99 kelysevksseeedlskleaelkeieaefke 129
                                   +++y+e+ ++ + ++s ++ +++ +e+++ke
  gi|70606095|ref|YP_254965.1|  73 RTMYYETTNDTPVNYSIKDYKMDMLEQRIKE 103
                                   7899999999999999999888888887765 PP

>> ArAE_1_C  Putative aromatic acid exporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.3   0.00017      0.07      58     124 ..      23      90 ..      18     113 .. 0.74
   2 ?    1.0   0.3      0.89   3.6e+02      42      58 ..      97     113 ..      85     123 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                                   CCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS--HH.HHHHHHHHHHHHH----TTHHHHHHH CS
                      ArAE_1_C  58 eNtllsneeyylkYfemRekQlevLkrmleelskieetveq.akiiaelleelaesvheendaeelle 124
                                   +N++   ++   +Y e+R+kQ e+++++++e+++i ++ e+  ++++e+ +++  + +++  ++  ++
  gi|70606095|ref|YP_254965.1|  23 KNSISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEiVRPLSEVSRTMYYETTNDTPVNYSIK 90 
                                   789999999999***********************988765245677776666666666555555444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHHHHHCCC CS
                      ArAE_1_C  42 leellkeakklayrnle 58 
                                   le+++ke +k+  +  +
  gi|70606095|ref|YP_254965.1|  97 LEQRIKELEKELNELKK 113
                                   33333333333333333 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0036       1.5      20      52 ..      39      71 ..      24      79 .. 0.83
   2 ?    9.0   1.8    0.0036       1.5      28      47 ..      94     113 ..      90     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0036
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 20 sRqRKqaeieeLerrvkaLekeNksLkseleel 52
                                   R++  + ++eL+r++ ++ + N++    l+e 
  gi|70606095|ref|YP_254965.1| 39 LRRKQTEIVNELKREFNEIAQSNEEIVRPLSEV 71
                                  67777777899*************877666665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  28 ieeLerrvkaLekeNksLks 47 
                                   ++ Le+r k+Leke  +Lk+
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNELKK 113
                                   44555555555555555554 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   9.7e-05      0.04      95     167 ..      30     114 ..      23     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.7e-05
                      PhoU_div  95 ediamlv...tlrkvefpeelkdeflallkktveaiealaevieeleklletalskk........div.eeieslEdeiDq 163
                                   +++++++   + ++ e+ +elk ef ++++ + e+++ l ev + +     ++   +        d++ + i++lE+e  +
  gi|70606095|ref|YP_254965.1|  30 KNVVKTYnelRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRTMYYETTNDTPVNysikdykmDMLeQRIKELEKELNE 110
                                   4455544211567899******************************97666666555889999996662579999999998 PP

                      PhoU_div 164 lqrk 167
                                   l+++
  gi|70606095|ref|YP_254965.1| 111 LKKN 114
                                   8876 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0015      0.61      57      94 ..      28      65 ..      20      71 .. 0.85
   2 ?    3.2   0.1      0.18        75      52      72 ..      95     115 ..      75     120 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                    STAT_alpha 57 qkellqqmlnaLdqkRkelvdklkellnlleslqekll 94
                                    +++ ++ n+L +k+ e+v++lk+ +n++ +  e+++
  gi|70606095|ref|YP_254965.1| 28 TIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIV 65
                                  557788899***********************999987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                    STAT_alpha  52 kelkkqkellqqmlnaLdqkR 72 
                                     l+++ ++l++ ln+L++ R
  gi|70606095|ref|YP_254965.1|  95 DMLEQRIKELEKELNELKKNR 115
                                   335555555555555555555 PP

>> Bac_RepA_C  Replication initiator protein A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   9.4e-05     0.038      23      74 ..      14      65 ..       9      80 .. 0.81
   2 ?    0.0   0.1       2.8   1.1e+03      47      73 ..      91     116 ..      71     121 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.4e-05
                    Bac_RepA_C 23 igiilkA..kyavekaervlgvailldeeelqelitktLrrffnslrisknkkv 74
                                  +giil A  k +    ++v+ ++  l     q++i ++L+r fn +  s+++ v
  gi|70606095|ref|YP_254965.1| 14 LGIILLAgdKNSISTIKNVVKTYNELR--RKQTEIVNELKREFNEIAQSNEEIV 65
                                  79****997778888888888888886..77999*************6665554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.8
                    Bac_RepA_C  47 d.eeelqelitktLrrffnslrisknkk 73 
                                   d + ++ e+  k+L + +n l+  kn+ 
  gi|70606095|ref|YP_254965.1|  91 DyKMDMLEQRIKELEKELNELK--KNRG 116
                                   3355565666677788888877..5555 PP

>> Lipoprotein_3  Lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5    0.0066       2.7       7      41 ..      24      58 ..      21      70 .. 0.89
   2 ?    6.3   0.1     0.027        11      37      77 ..      77     117 ..      56     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0066
                 Lipoprotein_3  7 sslsslqkyaeknkelelnKknlitiLkeayesdp 41
                                  +s+s ++++++  +el +++ ++++ Lk  +++ +
  gi|70606095|ref|YP_254965.1| 24 NSISTIKNVVKTYNELRRKQTEIVNELKREFNEIA 58
                                  599****************************9755 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                 Lipoprotein_3  37 yesdpkgtvkvLldgWkytLldqkiLekeldvsrFvkaFGs 77 
                                   ye+  ++ v+  ++ +k  +l+q+i e e++    +k  G 
  gi|70606095|ref|YP_254965.1|  77 YETTNDTPVNYSIKDYKMDMLEQRIKELEKELNELKKNRGV 117
                                   677777789****************9999998888887765 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0099         4     117     160 ..      27      70 ..      21      74 .. 0.83
   2 ?    8.8   0.9    0.0033       1.3       2      27 ..      94     119 ..      93     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0099
                  Dynactin_p22 117 pelkekLekLsqihlkqqeeveelseevkkllekYnklvltlsk 160
                                   ++ k+ +++ ++   kq+e v+el++e++++ ++ +++v+ ls+
  gi|70606095|ref|YP_254965.1|  27 STIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSE 70 
                                   45566666777788999*****************9999999997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0033
                  Dynactin_p22   2 ldaLEeriaeLEkrvlGeekekeked 27 
                                   +d LE+ri+eLEk +   +k++  ++
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNELKKNRGVDN 119
                                   789************99999887766 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.15        60      93     126 ..      26      59 ..      24      70 .. 0.83
   2 ?    9.3   0.1    0.0019      0.79      25      45 ..      93     114 ..      85     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.15
                     PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealet 126
                                   i + ++ ++ ++++  +q + v +l+++ ++ ++
  gi|70606095|ref|YP_254965.1|  26 ISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQ 59 
                                   6788999999999999999999999998777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                     PspA_IM30  25 e.kileqairdmqselakarqa 45 
                                   + ++leq i+++++el++++++
  gi|70606095|ref|YP_254965.1|  93 KmDMLEQRIKELEKELNELKKN 114
                                   558****************987 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00033      0.13      25      41 ..      94     110 ..      86     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00033
                  Sugarporin_N  25 sltiEaRLaaLEkrLqe 41 
                                   ++ +E+R+  LEk+L+e
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNE 110
                                   5668***********98 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.61   2.5e+02      23      55 ..      28      62 ..      22      83 .. 0.72
   2 ?   11.1   0.2    0.0012      0.47      20      57 ..      80     118 ..      73     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.61
                        CdiI_2 23 sieeiledY..vssespeevaelideieellassl 55
                                  +i+++++ Y  ++  + e v+el +e++e+ +s++
  gi|70606095|ref|YP_254965.1| 28 TIKNVVKTYneLRRKQTEIVNELKREFNEIAQSNE 62
                                  46677777744355667788888888888888776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0012
                        CdiI_2  20 egds.ieeiledYvssespeevaelideieellasslde 57 
                                    +d+ ++  ++dY+ ++ +++++el +e++el +++  +
  gi|70606095|ref|YP_254965.1|  80 TNDTpVNYSIKDYKMDMLEQRIKELEKELNELKKNRGVD 118
                                   556668889***********************9987754 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00023     0.092     630     711 ..      40     123 ..      10     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                                   GGSHHHHHHHHHHHCTTSTSSEEEEEETTSSCC..CSSSSCEEEEEEE.SSSSHHHHHHHHHHHHHHHHCCSTTEEEEEES CS
                      ACR_tran 630 eksvealierlrkelkkipganvellapiqlre..letlsgvrselqvklfgddleaLseaaeqllaalkelpelsdvrse 708
                                   + ++++++++l++e+++i + n e++ p +         +  ++ +++ +    ++ L++  ++l ++l+el++   v  e
  gi|70606095|ref|YP_254965.1|  40 RRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSrtMYYETTNDTPVNYSIKDYKMDMLEQRIKELEKELNELKKNRGVDNE 120
                                   56899****************9999877654442355667889999**9***********************999999888 PP

                                   S-S CS
                      ACR_tran 709 qqe 711
                                    +e
  gi|70606095|ref|YP_254965.1| 121 LSE 123
                                   766 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0    0.0077       3.1      16      73 ..      17      74 ..       7     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0077
                        DUF948 16 flivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73
                                  +l    ++  +t++++ +t +el+++ ++i++e+++  +++ +  e++ + l +v + 
  gi|70606095|ref|YP_254965.1| 17 ILLAGDKNSISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRT 74
                                  3333334556788888888888888888888888877777777777666666665554 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0013      0.53      52      90 ..      24      62 ..      23      73 .. 0.80
   2 ?    4.7   0.3     0.077        32       5      24 ..      94     113 ..      86     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                          BRE1 52 rskdalenelkkLnkllsKsselieqLkelekefvrklk 90
                                  +s+ +++n +k+ n+l  K++e++++Lk   +e+ ++ +
  gi|70606095|ref|YP_254965.1| 24 NSISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNE 62
                                  578899**********************95555555444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.077
                          BRE1   5 Lvklekafeelseqlskkvk 24 
                                   ++ le+ ++el+++l++++k
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNELKK 113
                                   45566666666666666655 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.6    0.0045       1.8      65      90 ..      79     117 ..      19     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0045
                       DUF4140  65 e.............elkalraeleeledelaaledelaa 90 
                                   +             +++ l+++++ele+el++l++ + +
  gi|70606095|ref|YP_254965.1|  79 TtndtpvnysikdyKMDMLEQRIKELEKELNELKKNRGV 117
                                   044444666777778999***************998766 PP

>> SAB  SAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4    0.0003      0.12       7      31 ..      34      59 ..      28      69 .. 0.81
   2 ?   -1.7   0.1       7.8   3.2e+03      19      23 ..     108     112 ..      98     117 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                           SAB  7 ktqdelLKHqasI.sELKRtfmEsns 31
                                  kt +el + q+ I +ELKR f E  +
  gi|70606095|ref|YP_254965.1| 34 KTYNELRRKQTEIvNELKREFNEIAQ 59
                                  888899999999769*******9765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.8
                           SAB  19 IsELK 23 
                                    +ELK
  gi|70606095|ref|YP_254965.1| 108 LNELK 112
                                   35555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4    0.0036       1.5      14      49 ..      28      63 ..      24      75 .. 0.88
   2 ?    5.1   0.5     0.075        31       9      27 ..      95     113 ..      93     117 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0036
               Snapin_Pallidin 14 kldeldeklkelrqsQeeLleqldrlnekLkeleea 49
                                  +++++ ++ +elr++Q+e  ++l+r+ +++++ +e+
  gi|70606095|ref|YP_254965.1| 28 TIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEE 63
                                  789999999****************99999887764 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.075
               Snapin_Pallidin   9 ellepkldeldeklkelrq 27 
                                   ++le  ++el+++l+el++
  gi|70606095|ref|YP_254965.1|  95 DMLEQRIKELEKELNELKK 113
                                   4555555555555555554 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.6     1e+03      12      34 ..      48      73 ..      39      75 .. 0.75
   2 ?   11.8   0.8   0.00041      0.17      28      50 ..      93     115 ..      88     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.6
                         HSBP1 12 qqlqdkFqtm...sdqilsriDdMss 34
                                  ++l+  F+++    ++i+  + + s+
  gi|70606095|ref|YP_254965.1| 48 NELKREFNEIaqsNEEIVRPLSEVSR 73
                                  77888888886656778888877775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00041
                         HSBP1  28 riDdMssriDdLEksiadlmtqa 50 
                                   ++D +++ri +LEk +++l ++ 
  gi|70606095|ref|YP_254965.1|  93 KMDMLEQRIKELEKELNELKKNR 115
                                   9*****************98765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.2    0.0005       0.2      27      99 ..      37     110 ..      22     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0005
                                   CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHCCCHHHHHHHC CS
                     Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkss.keleeeilrlketida 99 
                                   ++ +++ ++ +++l++e++ei++s++e+ +  +e++ ++  + +++++ +  ik+++ ++le++i +l++++++
  gi|70606095|ref|YP_254965.1|  37 NELRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRTMYYETTNDTPVNYSIKDYKmDMLEQRIKELEKELNE 110
                                   45566777788999999999999999998888888888888888888888888888746788888888887765 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2   0.00078      0.32      63     137 ..      29     103 ..      22     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00078
                       DUF3450  63 levyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPflleeRqarlakLkelmdr 137
                                   ++   + +++l ++q + +++l+++ +ei + ++e+v  l ++  ++    ++d+P + +  + +++ L++ +++
  gi|70606095|ref|YP_254965.1|  29 IKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRTMYYETTNDTPVNYSIKDYKMDMLEQRIKE 103
                                   555567777888889999999999999999999999999999999999999999999555444444444444333 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00061      0.25      59     119 ..       9      65 ..       7      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00061
               AI-2E_transport  59 lllvllvllvlllvplliaqltqlvkslpayidslqnilnelpslleelenliqalkqsls 119
                                   l++++l +++l+  +  i++++++vk++  +  +  +i+nel+++++e      +++ ++ 
  gi|70606095|ref|YP_254965.1|   9 LIIIVLGIILLAGDKNSISTIKNVVKTYNELRRKQTEIVNELKREFNEIA----QSNEEIV 65 
                                   6777778888888899*****************************99994....4444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.0     0.041        17       7      35 ..      37      66 ..      24      79 .. 0.83
   2 ?    9.8   0.6    0.0025         1       1      21 [.      93     113 ..      88     122 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                     FlaC_arch  7 nklsklst.eletvkkeneelsksveelke 35
                                  n+l + +t  ++ +k+e++e+ +s ee+ +
  gi|70606095|ref|YP_254965.1| 37 NELRRKQTeIVNELKREFNEIAQSNEEIVR 66
                                  677777773468999******999999965 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0025
                     FlaC_arch   1 ridelEnklsklsteletvkk 21 
                                   ++d lE+++++l+ el+ +kk
  gi|70606095|ref|YP_254965.1|  93 KMDMLEQRIKELEKELNELKK 113
                                   444455555555555544444 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3      0.97   3.9e+02      51      73 ..      40      62 ..      24      66 .. 0.74
   2 ?   12.6   0.6   0.00038      0.15      51      74 ..      94     117 ..      88     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.97
                                  HHHHHHHHHHHHHHHHHHHHHHH CS
                     GTP-bdg_M 51 rrlireriaklkkeLekvkkkre 73
                                  rr+  e +++lk+e +++++++e
  gi|70606095|ref|YP_254965.1| 40 RRKQTEIVNELKREFNEIAQSNE 62
                                  56666677888888888887765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHHHHHHHHHHHHHH. CS
                     GTP-bdg_M  51 rrlireriaklkkeLekvkkkrel 74 
                                     ++++ri++l+keL+++kk+r +
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNELKKNRGV 117
                                   56899****************976 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.6     0.011       4.5       3      56 ..      10      63 ..       8      83 .. 0.61
   2 ?    9.6   1.6    0.0018      0.74      30      53 ..      91     114 ..      77     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                                  XXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                         DivIC  3 llfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56
                                  ++++l +i++++  ++++ +k+ +++ ++   k+++  +eL++e ++  ++ + 
  gi|70606095|ref|YP_254965.1| 10 IIIVLGIILLAGDKNSISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEE 63
                                  555556666655555555555555555555555555555555555555444333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHHHHHHHCC-XXX CS
                         DivIC  30 qaelaklkaeneeLeaevkdLksd 53 
                                     +++ l ++++eLe+e+++Lk++
  gi|70606095|ref|YP_254965.1|  91 DYKMDMLEQRIKELEKELNELKKN 114
                                   567888999999999999999875 PP

>> DUF1149  Protein of unknown function (DUF1149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.0    0.0013      0.54      76     113 ..      45      81 ..       7      87 .. 0.88
   2 ?   -0.6   0.1       3.8   1.5e+03      11      36 ..      90     111 ..      83     125 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                                   EEET---S-GGGS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                       DUF1149  76 qikdrlveeqeeleqeeveeLarPlldiikrLtYevte 113
                                   +i + l  e +e++q++ ee++rPl ++ +++ Ye+t+
  gi|70606095|ref|YP_254965.1|  45 EIVNELKREFNEIAQSN-EEIVRPLSEVSRTMYYETTN 81 
                                   56777888899998876.89***************996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.8
                                   EEEEEEE-HHHH-----EEEEEEEEE CS
                       DUF1149  11 eayhydarekengepetelevelqkv 36 
                                   + y+ d+ e+  +e e+    el+++
  gi|70606095|ref|YP_254965.1|  90 KDYKMDMLEQRIKELEK----ELNEL 111
                                   55555654444333333....33333 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   7.5   0.00095      0.39       3      84 ..      32     114 ..      30     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00095
                                   HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHH.HHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   3 linkfqqlqqqlqqlaqqik.qletqlkelelvleelelldedtkvyklvGdvlvkqdkeevk.eeLeerketlekeiktl 81 
                                    ++ +++l+ +++++++++k + ++  + +e++   l+++   t+ y+   d+ v  + ++ k ++Le+r+++leke+++l
  gi|70606095|ref|YP_254965.1|  32 VVKTYNELRRKQTEIVNELKrEFNEIAQSNEEIVRPLSEVSR-TMYYETTNDTPVNYSIKDYKmDMLEQRIKELEKELNEL 111
                                   577899999999999877541233333444555555555555.599***********998887589*************** PP

                                   HHH CS
                   Prefoldin_2  82 ekq 84 
                                   +k+
  gi|70606095|ref|YP_254965.1| 112 KKN 114
                                   997 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6    0.0069       2.8      13      44 ..      29      64 ..      25      78 .. 0.62
   2 ?    7.1   1.1     0.018       7.2      22      42 ..      96     115 ..      91     125 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0069
                          ZapB 13 iqkaidtitlLqme....ieeLkeeneelkeenrel 44
                                  i++ + t+ +L+ +    + eLk+e +e ++ n+e+
  gi|70606095|ref|YP_254965.1| 29 IKNVVKTYNELRRKqteiVNELKREFNEIAQSNEEI 64
                                  677788888887773333345555555555555554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.018
                          ZapB  22 lLqmeieeLkeeneelkeenr 42 
                                    L ++i+eL++e +elk+ nr
  gi|70606095|ref|YP_254965.1|  96 MLEQRIKELEKELNELKK-NR 115
                                   455666666666666665.33 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.023       9.4       8      32 ..      35      59 ..      30      70 .. 0.92
   2 ?    6.2   1.0     0.026        11       5      31 ..      90     112 ..      87     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                    Mst1_SARAH  8 svdeLqqrlasLDpeMEqEieelrk 32
                                  +++eL+++ +++ +e+ +E +e+++
  gi|70606095|ref|YP_254965.1| 35 TYNELRRKQTEIVNELKREFNEIAQ 59
                                  699*******************987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.026
                    Mst1_SARAH   5 kflsvdeLqqrlasLDpeMEqEieelr 31 
                                   k++ +d L+qr+++    +E+E++el+
  gi|70606095|ref|YP_254965.1|  90 KDYKMDMLEQRIKE----LEKELNELK 112
                                   67777888888865....567777776 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3      0.05        20     101     132 ..      41      72 ..      26      76 .. 0.86
   2 ?    7.5   0.8     0.011       4.6     103     121 ..      97     115 ..      90     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.05
                         Med21 101 eeqeerikeLeeelreveeereekvkekeell 132
                                   ++q e ++eL++e +e+++  ee v+   e+ 
  gi|70606095|ref|YP_254965.1|  41 RKQTEIVNELKREFNEIAQSNEEIVRPLSEVS 72 
                                   6899999************9999999877765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                         Med21 103 qeerikeLeeelreveeer 121
                                    e+rikeLe+el+e +++r
  gi|70606095|ref|YP_254965.1|  97 LEQRIKELEKELNELKKNR 115
                                   589***********99987 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.4    0.0018      0.75      33      92 ..      37     115 ..      23     123 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                    V_ATPase_I  33 demerklrfleeeieklekavikeeea...................eesleapeekeldeleeelekleeelkelnenl 92 
                                   +e+ rk + + +e++++ +++++++e+                   +  + + +++++d le+++++le+el+el++n 
  gi|70606095|ref|YP_254965.1|  37 NELRRKQTEIVNELKREFNEIAQSNEEivrplsevsrtmyyettndTPVNYSIKDYKMDMLEQRIKELEKELNELKKNR 115
                                   4444444444444444322222222223444444444444433322334455667778888888888888888888774 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.3     0.068        28      34      68 ..      28      62 ..      23      72 .. 0.55
   2 ?   10.0   2.0    0.0016      0.65      35      54 ..      94     113 ..      88     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.068
                    TMF_DNA_bd 34 tikkLrkknkelekeikelkkkleklekeleelee 68
                                  tik+  k+ +el  +++e  ++l+++  e+++ +e
  gi|70606095|ref|YP_254965.1| 28 TIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNE 62
                                  55666666666655544444444444444433333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                    TMF_DNA_bd  35 ikkLrkknkelekeikelkk 54 
                                   +++L + +keleke++elkk
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNELKK 113
                                   56677777777777777743 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.54   2.2e+02       6      18 ..      48      60 ..      36      63 .. 0.66
   2 ?    9.5   0.5    0.0021      0.86       1      20 [.      97     116 ..      97     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.54
                                  HHHHHHHHHHTT- CS
                 Rad50_zn_hook  6 eelnkkieelkea 18
                                  +el++  +e++++
  gi|70606095|ref|YP_254965.1| 48 NELKREFNEIAQS 60
                                  4555555666555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHHHHHTT-SE CS
                 Rad50_zn_hook   1 lhqeteelnkkieelkeakg 20 
                                   l+q+++el+k ++elk+++g
  gi|70606095|ref|YP_254965.1|  97 LEQRIKELEKELNELKKNRG 116
                                   79**************9986 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5      0.03        12     243     298 ..      19      74 ..      16      76 .. 0.80
   2 ?    6.6   0.8      0.01       4.2     275     298 ..      91     114 ..      75     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                         FAM76 243 lekdkk.itelkaellekekelreklkelekeakekieklekkirellkevaelskk 298
                                   l+ dk+ i+++k + +++ +elr+k +e+ +e k++ +++ + ++e+ + ++e+s++
  gi|70606095|ref|YP_254965.1|  19 LAGDKNsISTIK-NVVKTYNELRRKQTEIVNELKREFNEIAQSNEEIVRPLSEVSRT 74 
                                   555554144444.57788899**************************9999999875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                         FAM76 275 kekieklekkirellkevaelskk 298
                                   + k+++le++i+el ke+ el+k+
  gi|70606095|ref|YP_254965.1|  91 DYKMDMLEQRIKELEKELNELKKN 114
                                   5699*****************997 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.9     0.089        36      21      94 ..      36     113 ..      21     114 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.089
                  Occludin_ELL  21 YkeYkelhael.eevskkfseLe....relkelkegsk.eykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKk 94 
                                   Y+e ++ ++e+ +e++++f+e+     + ++ l+e s+  y +++++   +y+ +  d +    ++r+++L+++L+ +Kk
  gi|70606095|ref|YP_254965.1|  36 YNELRRKQTEIvNELKREFNEIAqsneEIVRPLSEVSRtMYYETTNDTPVNYSIK--DYKMDMLEQRIKELEKELNELKK 113
                                   4444433333224445555555422222222233333345555555545555544..77778888999999999999997 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.9     0.043        18       2      19 ..      38      56 ..      37      56 .. 0.84
   2 ?   11.4   1.9   0.00056      0.23       3      19 ..      94     110 ..      94     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.043
                Pox_A_type_inc  2 EmsrlRsRIs.DLErqLse 19
                                  E++r++++I+ +L+r+ +e
  gi|70606095|ref|YP_254965.1| 38 ELRRKQTEIVnELKREFNE 56
                                  99******97689998665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00056
                Pox_A_type_inc   3 msrlRsRIsDLErqLse 19 
                                   m+ l  RI +LE++L+e
  gi|70606095|ref|YP_254965.1|  94 MDMLEQRIKELEKELNE 110
                                   666778**********9 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.0     0.039        16      78     113 ..      25      60 ..      22      66 .. 0.82
   2 ?    7.3   0.9      0.01       4.1      83     106 ..      91     114 ..      88     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.039
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  78 Aiellkkkleelekqlekleeeleklkdqittlean 113
                                   +i ++k+ ++++++ ++k +e +++lk++ +++ + 
  gi|70606095|ref|YP_254965.1|  25 SISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQS 60 
                                   678889999999999999999999999999998775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  83 kkkleelekqlekleeeleklkdq 106
                                   + k++ le+ +++le+el++lk++
  gi|70606095|ref|YP_254965.1|  91 DYKMDMLEQRIKELEKELNELKKN 114
                                   678888888888888888888875 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       3.4   1.4e+03       8      27 ..      31      50 ..      25      64 .. 0.59
   2 ?   11.2   1.3   0.00063      0.26      14      32 ..      95     113 ..      93     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.4
                      WD40_alt  8 nvlGdqeqlkvrvseLeeEV 27
                                  nv+   ++l+ + +e  +E+
  gi|70606095|ref|YP_254965.1| 31 NVVKTYNELRRKQTEIVNEL 50
                                  55555555555544444443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00063
                      WD40_alt  14 eqlkvrvseLeeEVrtLrK 32 
                                   ++l  r+ eLe E++ L+K
  gi|70606095|ref|YP_254965.1|  95 DMLEQRIKELEKELNELKK 113
                                   89999*************9 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.6     0.011       4.6       3      44 ..      22      69 ..      20      94 .. 0.72
   2 ?    5.5   1.5     0.047        19      14      33 ..      95     114 ..      86     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                         Spc24  3 dnekfriakelsdleseleslesel.aelkeeleeleeesee.....k 44
                                  d++ ++++k++ ++ +el + ++e  +elk+e++e+ +++ee     +
  gi|70606095|ref|YP_254965.1| 22 DKNSISTIKNVVKTYNELRRKQTEIvNELKREFNEIAQSNEEivrplS 69
                                  6778999999999999999999885389********999998666552 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.047
                         Spc24  14 sdleselesleselaelkee 33 
                                   + le+ +++le+el+elk++
  gi|70606095|ref|YP_254965.1|  95 DMLEQRIKELEKELNELKKN 114
                                   45666666666666666654 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6      0.88   3.6e+02       6      35 ..      26      51 ..      23      70 .. 0.61
   2 ?    9.3   1.0    0.0032       1.3      26      47 ..      93     114 ..      86     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.88
                          XhlA  6 lerietkldnlee.rvdkleekaaeaeekik 35
                                  + +i++ +++++e r     +k++e  +++k
  gi|70606095|ref|YP_254965.1| 26 ISTIKNVVKTYNElR-----RKQTEIVNELK 51
                                  667777777777764.....55554444443 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0032
                          XhlA  26 kaaeaeekiknleedlkklesn 47 
                                   k++  e++ik+le++l++l++n
  gi|70606095|ref|YP_254965.1|  93 KMDMLEQRIKELEKELNELKKN 114
                                   5677889999999999999887 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.7     0.043        17      15      68 ..      11      64 ..       3      90 .. 0.77
   2 ?    5.6   1.0     0.028        12      39      66 ..      89     116 ..      81     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.043
                    EMC3_TMCO1 15 Pivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdkl 68
                                   iv+ i+l++  +  +s++ + + ++ +  +k  ++ +el++++ e  ++++++
  gi|70606095|ref|YP_254965.1| 11 IIVLGIILLAGDKNSISTIKNVVKTYNELRRKQTEIVNELKREFNEIAQSNEEI 64
                                  466777777777889999999999999988899999999999999988877654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.028
                    EMC3_TMCO1  39 idkkkmekeqkrekelqkrarelqkngd 66 
                                   i   km++ ++r kel+k+  el+kn++
  gi|70606095|ref|YP_254965.1|  89 IKDYKMDMLEQRIKELEKELNELKKNRG 116
                                   44445********************876 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7      0.33   1.4e+02      17      29 ..      39      52 ..      37      55 .. 0.71
   2 ?    9.3   3.1    0.0025         1       6      28 ..      90     112 ..      88     114 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.33
                     PKcGMP_CC 17 laekdeEI.qELrs 29
                                  l++k  EI +EL++
  gi|70606095|ref|YP_254965.1| 39 LRRKQTEIvNELKR 52
                                  77777776479998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0025
                     PKcGMP_CC   6 KDERIRELEkrlaekdeEIqELr 28 
                                   KD +   LE+r++e ++E +EL+
  gi|70606095|ref|YP_254965.1|  90 KDYKMDMLEQRIKELEKELNELK 112
                                   55555556667777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2737  (0.152658); expected 358.6 (0.02)
Passed bias filter:                     1360  (0.0758548); expected 358.6 (0.02)
Passed Vit filter:                       223  (0.0124379); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 872.06
//
Query:       gi|70606096|ref|YP_254966.1|  [L=96]
Description: hypothetical protein Saci_0256 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   42.3   6.3    1.9e-10   39.9   6.3    2.0  1  MttA_Hcf106    mttA/Hcf106 family
     0.0025   17.8   1.2     0.0031   17.5   1.2    1.1  1  DUF4446        Protein of unknown function (DUF4446)
      0.004   17.0   7.0     0.0048   16.7   7.0    1.0  1  FAM184         Family with sequence similarity 184, A and B
      0.004   18.1   0.4     0.0053   17.7   0.4    1.1  1  DUF4834        Domain of unknown function (DUF4834)
  ------ inclusion threshold ------
       0.03   13.2   0.9       0.03   13.2   0.9    1.1  1  DUF3573        Protein of unknown function (DUF3573)
      0.038   14.4   2.9      0.049   14.1   2.9    1.1  1  DUF4140        N-terminal domain of unknown function (DUF4140
       0.04   13.3   2.7      0.041   13.3   2.7    1.1  1  HNOBA          Heme NO binding associated
      0.072   14.2   2.6      0.084   14.0   2.6    1.1  1  DUF5320        Family of unknown function (DUF5320)
       0.09   12.6   1.2       0.13   12.1   1.2    1.2  1  CHD5           CHD5-like protein
        1.4    9.4  15.1       0.51   10.8  10.4    1.9  2  ZapB           Cell division protein ZapB
        1.8    8.6   7.7        2.5    8.2   7.7    1.2  1  DUF4337        Domain of unknown function (DUF4337)
        3.2    7.8  13.7          1    9.4   5.8    2.1  2  Ribosomal_L29  Ribosomal L29 protein


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   6.3   1.2e-13   1.9e-10       5      47 ..      10      61 ..       6      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.2e-13
                                  HHHHHHHHH.HHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH-........- CS
                   MttA_Hcf106  5 elliIlvVa.lllFGpkkLPEvaraLGktLreFkkavkeleee........n 47
                                  +ll++l+Va +l FG+ kLPE+ r+LGk+  eFkk   e+e+e        +
  gi|70606096|ref|YP_254966.1| 10 QLLVVLIVAaILFFGATKLPELFRSLGKSVGEFKKGKMEAEMElmqmqqaqQ 61
                                  67888888527789***************************99666655440 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2     2e-06    0.0031       4      78 ..      12      86 ..      10      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                       DUF4446  4 lvlavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkks 78
                                  lv+++++ il++ +  l   +++l k++ ++ kgk ++++e + +++ ++ ++  ++++el+k+i++l+++l++ 
  gi|70606096|ref|YP_254966.1| 12 LVVLIVAAILFFGATKLPELFRSLGKSVGEFKKGKMEAEMELMQMQQAQQAQQPVDKEAELQKKIQDLQRELEEL 86
                                  5677888888888888888999************************************************99875 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   7.0   3.2e-06    0.0048      55     111 ..      32      89 ..      25      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                        FAM184  55 iaeleesleqhekekrqalae.feqykrrveerelkleaehsqkvvelsreveevkrk 111
                                     +l +s+ +++k k +a +e +++++ + +++ + +eae ++k++ l+re+ee+k++
  gi|70606096|ref|YP_254966.1|  32 FRSLGKSVGEFKKGKMEAEMElMQMQQAQQAQQPVDKEAELQKKIQDLQRELEELKKQ 89 
                                   568899999******9998883566777777788999******************997 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.4   3.5e-06    0.0053       7      79 ..      13      86 ..      10      95 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                       DUF4834  7 ilifiiailviglsilsvilrtv......fglgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeersekea 79
                                  +++++ ail++g++ l  ++r++      f +g+ + +++ +q q++++ +++ +k+      + +++i++ +r+ +e 
  gi|70606096|ref|YP_254966.1| 13 VVLIVAAILFFGATKLPELFRSLgksvgeFKKGKMEAEMELMQMQQAQQAQQPVDKEA-----ELQKKIQDLQRELEEL 86
                                  47888999***************55544444555555554444444444444433333.....2223333333333222 PP

>> DUF3573  Protein of unknown function (DUF3573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9     2e-05      0.03      32      69 ..      58      93 ..       9      96 .] 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                       DUF3573 32 eqtsksnlidkelilklqkqikelqaeinhlketknsn 69
                                  +  +  + +dke   +lqk+i++lq e+++lk++k+  
  gi|70606096|ref|YP_254966.1| 58 QAQQAQQPVDKE--AELQKKIQDLQRELEELKKQKQQS 93
                                  222223445555..69*****************99854 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.9   3.3e-05     0.049      46      89 ..      48      91 ..      39      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                       DUF4140 46 aatildvqvervpnreaeeeelkalraeleeledelaaledela 89
                                  +a    +q ++ ++ +++ ++ ++l+++++ l++el++l+++++
  gi|70606096|ref|YP_254966.1| 48 EAEMELMQMQQAQQAQQPVDKEAELQKKIQDLQRELEELKKQKQ 91
                                  567777899999999999999*******************9987 PP

>> HNOBA  Heme NO binding associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.7   2.8e-05     0.041     165     204 ..      50      92 ..      19      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                         HNOBA 165 elvlagiqqsaelelaldql...eeksaeLeesmkeleeekkr 204
                                   e+ l ++qq+++++   d++   ++k ++L+++++el+++k++
  gi|70606096|ref|YP_254966.1|  50 EMELMQMQQAQQAQQPVDKEaelQKKIQDLQRELEELKKQKQQ 92 
                                   6777788888888877766500055555555555556666655 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.6   5.6e-05     0.084      56      97 ..      48      91 ..      22      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                       DUF5320 56 aggarla..aaetaeaskeeekelLeeqaeaLeeeleaikkrlk 97
                                     ++l+  +++++++++ ++++ L+++++ L++ele++kk+ +
  gi|70606096|ref|YP_254966.1| 48 EAEMELMqmQQAQQAQQPVDKEAELQKKIQDLQRELEELKKQKQ 91
                                  222222255677888899999999*****************976 PP

>> CHD5  CHD5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   8.6e-05      0.13       4      91 ..      11      93 ..      10      96 .] 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-05
                          CHD5  4 fllvlvtkllntigkstiknllwllylkkvssksakeqrklkkellklkeelnsisaqDefAkWaKlnRkldkleeeleklkk 86
                                  +l+vl++  + ++g++ + +l   l +++ + k+   + +   el+++++ ++   aq    k a l+ k+++l+ ele+lkk
  gi|70606096|ref|YP_254966.1| 11 LLVVLIVAAILFFGATKLPELFRSLGKSVGEFKK--GKMEAEMELMQMQQAQQ---AQQPVDKEAELQKKIQDLQRELEELKK 88
                                  5788888999999999999997665544333332..33444445555555555...455555566688888888888888888 PP

                          CHD5 87 elsas 91
                                  + ++s
  gi|70606096|ref|YP_254966.1| 89 QKQQS 93
                                  88776 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.1       0.1   1.6e+02      30      59 ..      35      64 ..      25      66 .. 0.73
   2 ?   10.8  10.4   0.00034      0.51      13      44 ..      62      93 ..      59      96 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                          ZapB 30 Lkeeneelkeenreleeeneqlkeereawq 59
                                  L + + e k+ + e e e+ q+++ ++a+q
  gi|70606096|ref|YP_254966.1| 35 LGKSVGEFKKGKMEAEMELMQMQQAQQAQQ 64
                                  556666777777888888888888888886 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00034
                          ZapB 13 iqkaidtitlLqmeieeLkeeneelkeenrel 44
                                   q+ +d+ ++Lq++i++L++e eelk+++++ 
  gi|70606096|ref|YP_254966.1| 62 AQQPVDKEAELQKKIQDLQRELEELKKQKQQS 93
                                  68899***********************9986 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.7    0.0016       2.5      54      95 ..      50      92 ..      41      96 .] 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                       DUF4337 54 eleleqlelllkak.aeelaaavdkkiakykkkiarykkekke 95
                                  e+el q++ +++a+ + +++a+ +kki++++++ ++ kk+k++
  gi|70606096|ref|YP_254966.1| 50 EMELMQMQQAQQAQqPVDKEAELQKKIQDLQRELEELKKQKQQ 92
                                  3333333333333345566666666666666666666666655 PP

>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.2     0.045        68       6      34 ..      37      65 ..      35      69 .. 0.85
   2 ?    9.4   5.8    0.0007         1       8      31 ..      69      92 ..      67      96 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.045
                                  S-HHHHHHHHHHHHHHHHHHHHHHHHTSS CS
                 Ribosomal_L29  6 lsdeeLkeklkelkkeLfnLrfqkatgql 34
                                  +s+ e k+   e++ eL+++  +++++q+
  gi|70606096|ref|YP_254966.1| 37 KSVGEFKKGKMEAEMELMQMQQAQQAQQP 65
                                  8888999999999*******999998854 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0007
                                  HHHHHHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  8 deeLkeklkelkkeLfnLrfqkat 31
                                  ++eL++k+++l++eL +L+ qk+ 
  gi|70606096|ref|YP_254966.1| 69 EAELQKKIQDLQRELEELKKQKQQ 92
                                  68*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3543  (0.197613); expected 358.6 (0.02)
Passed bias filter:                     1394  (0.0777511); expected 358.6 (0.02)
Passed Vit filter:                       201  (0.0112109); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 743.24
//
Query:       gi|70606097|ref|YP_254967.1|  [L=238]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-28  100.4   0.0    1.6e-28   99.9   0.0    1.2  1  ABC_tran     ABC transporter
    4.7e-06   26.6   2.4      0.028   14.2   0.3    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0012   19.3   0.3     0.0031   17.9   0.3    1.8  1  AAA_16       AAA ATPase domain
     0.0015   18.4   0.1     0.0029   17.6   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
      0.008   16.1   0.2       0.02   14.8   0.1    1.9  2  Rad17        Rad17 P-loop domain
       0.01   16.1   0.2      0.051   13.8   0.2    2.2  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.032   14.0   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.027   13.9   0.1        4.6    6.6   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.031   14.3   0.1      0.099   12.7   0.1    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
      0.052   14.1   0.0       0.08   13.4   0.0    1.5  1  AAA_23       AAA domain
      0.057   12.2   0.0        6.6    5.4   0.0    2.8  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.076   12.7   0.0       0.14   11.9   0.0    1.4  1  AAA_24       AAA domain
       0.12   12.3   0.3       0.51   10.2   0.1    1.9  2  NACHT        NACHT domain
       0.12   11.5   0.0       0.23   10.6   0.0    1.4  1  NB-ARC       NB-ARC domain
       0.14   12.3   0.0       0.25   11.5   0.0    1.6  1  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   1.3e-31   1.6e-28       4     136 ..       1     137 [.       1     138 [. 0.95

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.3e-31
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                      ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..... 79 
                                   ++l+ +e+e+v ivG++G GKStLl++l g + pteGe++l+g+++++        +i+ ++q    fp +t+ +n     
  gi|70606097|ref|YP_254967.1|   1 MNLETHENELVSIVGPSGIGKSTLLRILGGFTLPTEGEVRLEGNKITK-----PTPKISLIHQSIVTFPWMTALDNvklgl 76 
                                   578999************************************999998.....999************************* PP

                                   ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                           e+++ ++++l+ +gl+++++       ++LSgG++qrva+aral+ +p +ll+DEp+
  gi|70606097|ref|YP_254967.1|  77 kyrklpkeEENKIAKRMLELVGLSGFENFYP----KQLSGGMRQRVAIARALVADPLVLLMDEPF 137
                                   *****9866666699**********999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   2.3e-05     0.028       3      22 ..      12      31 ..      10      56 .. 0.80
   2 !   12.5   0.1   7.9e-05     0.095     230     299 ..     103     173 ..      59     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                        AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++Gp g GKS+LL++l ++
  gi|70606097|ref|YP_254967.1| 12 SIVGPSGIGKSTLLRILGGF 31
                                  59***************765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.9e-05
                        AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllell.kelsrngaQviltTHSp 299
                                    ++ + +lS G+++  a++ al +++    +ll DEp ++L+      l  ++++ll +e+   +  v+l++H+ 
  gi|70606097|ref|YP_254967.1| 103 ENFYPKQLSGGMRQRVAIARALVADP---LVLLMDEPFSHLDEltaeGLRQEIYQLLfSEEVP-LKSVVLVSHNL 173
                                   57788899*******99999999999...89***********977777777777777755555.78999999994 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   2.6e-06    0.0031      21      45 ..       5      29 ..       2     169 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                        AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                  +++ elv ++G+sG+GKs+l+r l 
  gi|70606097|ref|YP_254967.1|  5 THENELVSIVGPSGIGKSTLLRILG 29
                                  455699***************8665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.4e-06    0.0029      98     131 ..       7      40 ..       3      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevs 131
                                   +++++ +vG+SG+GKStL+  l + +    gev+
  gi|70606097|ref|YP_254967.1|   7 ENELVSIVGPSGIGKSTLLRILGGFTLPTEGEVR 40 
                                   568899*************999776555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.6e-05      0.02      39      67 ..       2      30 ..       1     142 [. 0.79
   2 ?   -1.2   0.0       1.3   1.6e+03     137     165 ..     131     161 ..      99     181 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                         Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   Le ++++++ i GPsG gkst +++L  
  gi|70606097|ref|YP_254967.1|  2 NLETHENELVSIVGPSGIGKSTLLRILGG 30
                                  68899999******************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                         Rad17 137 lvedlP.nkfyrds.dalrevirkylrssea 165
                                   l+ d P ++    + + lr+ i + l s+e 
  gi|70606097|ref|YP_254967.1| 131 LLMDEPfSHLDELTaEGLRQEIYQLLFSEEV 161
                                   3333332333333335555555555555553 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   4.3e-05     0.051       6      25 ..       9      28 ..       4     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                        AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                   ++ ++G+sG+GK+tllr l
  gi|70606097|ref|YP_254967.1|  9 ELVSIVGPSGIGKSTLLRIL 28
                                  5678*************976 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.7e-05     0.032      19      39 ..       5      25 ..       1      28 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                        AAA_29 19 idlkgatlltGpsGsGKSTll 39
                                   ++++ + ++GpsG GKSTll
  gi|70606097|ref|YP_254967.1|  5 THENELVSIVGPSGIGKSTLL 25
                                  55556889************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0082       9.8      23      42 ..       7      26 ..       2      48 .. 0.82
   2 ?    6.6   0.0    0.0038       4.6     130     170 ..     103     146 ..      70     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0082
                                  TSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsnlld 42
                                  ++++ +ivGp G GKs ll 
  gi|70606097|ref|YP_254967.1|  7 ENELVSIVGPSGIGKSTLLR 26
                                  567889**********9986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0038
                                   TT-STTCS-HHHHHHHHHHHHHH...HHCCS--SEEEECTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                         SMC_N 130 agiskelLSgGektLvalaLlfA...iqkvkpaplyllDeidaa 170
                                   +++++++LSgG ++ va+a  +    +     +p+  lDe+ a+
  gi|70606097|ref|YP_254967.1| 103 ENFYPKQLSGGMRQRVAIARALVadpLVLLMDEPFSHLDELTAE 146
                                   678999*****999999885443377777778888888888775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.3e-05     0.099       2      22 ..      11      38 ..      10     171 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.3e-05
                                  EEEEESTTSSHHHHHHHHHT.......S CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg.......e 22
                                  v ivG +  GKStL++ l g       e
  gi|70606097|ref|YP_254967.1| 11 VSIVGPSGIGKSTLLRILGGftlptegE 38
                                  78**************997654444431 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.7e-05      0.08      19      39 ..       8      28 ..       2     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                        AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                  + l+ I+Gp G GK+T+l+ +
  gi|70606097|ref|YP_254967.1|  8 NELVSIVGPSGIGKSTLLRIL 28
                                  67899*************866 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.029        34     246     264 ..      10      28 ..       6      30 .. 0.86
   2 ?    5.4   0.0    0.0055       6.6     318     414 ..     105     189 ..      98     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.029
                                   EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 246 vtlIvGggfhGKsTLLeAl 264
                                   ++ IvG+   GKsTLL+ l
  gi|70606097|ref|YP_254967.1|  10 LVSIVGPSGIGKSTLLRIL 28 
                                   678*************865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0055
                                   EEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--.HHHCHHHHHHHH--EEEEEESS CS
                    ABC_ATPase 318 fstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitp.lvdrvrelykklgvstilvvgg 397
                                   f  ++ SG + q ++i++al a+  +lL+DE  s    +    + qe++       +  +++ v         s++lv+  
  gi|70606097|ref|YP_254967.1| 105 FYPKQLSGGMRQRVAIARALVADPLVLLMDEPFSHLDELTAEGLRQEIY-------QLlFSEEVP------LKSVVLVSHN 172
                                   6667789999999999999999999999999766443333333333222.......110112221......1355666666 PP

                                   -GCCTTT-SEEEEEETT CS
                    ABC_ATPase 398 sgdyldvAdtvilmeey 414
                                   +++ +++Ad+v  ++ +
  gi|70606097|ref|YP_254967.1| 173 LNEVVELADRVYILNGF 189
                                   66666666666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14       6      47 ..      12      50 ..       8      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                        AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie 47
                                   i+GpsgiGK+tl++ l    + + te+ + +l+++k+ +++
  gi|70606097|ref|YP_254967.1| 12 SIVGPSGIGKSTLLRIL--GGFTLPTEGEV-RLEGNKITKPT 50
                                  699***********999..33445555533.66666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00043      0.51       2      18 ..      10      26 ..       9      29 .. 0.88
   2 ?   -0.4   0.0      0.77   9.3e+02      72     123 ..     118     167 ..     107     191 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                                  CEEEEC-TTTCHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlq 18
                                  lv + G++G+GK+tLl+
  gi|70606097|ref|YP_254967.1| 10 LVSIVGPSGIGKSTLLR 26
                                  6889***********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.77
                                   CHHHHCCSCCCEEEEEE-....STT-SS-TCH.........HHHHH.CTTTTT--EE CS
                         NACHT  72 vwavllelperlLlilDg....lDelvtdlgqkekqpvrtlLseli.rkkllpeasl 123
                                   v + ++ +++ l+l++D     lDel +       + +r+ + +l+ +++++ ++ +
  gi|70606097|ref|YP_254967.1| 118 VAIARALVADPLVLLMDEpfshLDELTA-------EGLRQEIYQLLfSEEVPLKSVV 167
                                   5556666677777777632222333333.......3334444443303333333333 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.23      16      38 ..       6      26 ..       2      28 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                  TTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC 16 delqslvvalvGmgGvGKttlak 38
                                  +e +  +v++vG  G+GK+tl++
  gi|70606097|ref|YP_254967.1|  6 HENE--LVSIVGPSGIGKSTLLR 26
                                  4555..9*************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.25       1      18 [.      10      27 ..      10     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                        AAA_33  1 lvllvGlpGsGKstlaer 18
                                  lv +vG++G GKstl++ 
  gi|70606097|ref|YP_254967.1| 10 LVSIVGPSGIGKSTLLRI 27
                                  6889***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1533.35
//
Query:       gi|70606098|ref|YP_254968.1|  [L=543]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-22   80.2  55.5    3.9e-14   52.8  17.9    3.2  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8  18.9   2.1e-14   3.8e-10       2     182 ..      26     214 ..      25     217 .. 0.85
   2 ?   -0.5   2.5      0.05     9e+02      43      87 ..     284     331 ..     221     334 .. 0.68
   3 !   52.8  17.9   2.2e-18   3.9e-14       2     173 ..     338     524 ..     337     534 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 2.1e-14
                  BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrsl 79 
                                   i++G++++    ++ ++ ++   li+++ s+P+f ++++++ +fv+  +   +i   v++l+++  ++ + + +++a +++
  gi|70606098|ref|YP_254968.1|  26 IITGWFLGylAIKSHVVENIYVSLIEIFESVPVFSFLPIVLIFFVFTIGGNLGIQLaVLFLVFTAVVWNIWMGIYQAYKTI 106
                                   788999999888999***********************999777555555566777355555555555555669******* PP

                  BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG........lgtllleailgydyse 152
                                   p+d  e+++ +  s    f k  +P ++p i++ l+ +f+++l   ++ e +    G        +g+l+  + ++  y+ 
  gi|70606098|ref|YP_254968.1| 107 PQDMLEVSENYRFSLMDKFSKLYIPYSMPRIASNLFPSFVNALFYITVSEVFS-I-GnsqyqvfgIGSLINYFVNNGLYND 185
                                   ******************************************99888888655.2.2346788889999999999999999 PP

                  BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldpr 182
                                   ++ +g+++l+i v++++lv++ l++++  r
  gi|70606098|ref|YP_254968.1| 186 AL-IGIVILIIWVIIFTLVLRELAEYIISR 214
                                   99.*****************9999998777 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.05
                  BPD_transp_1  43 f...vilsilghlilpviillllsaapyvrlirraalrslpkdlveaa 87 
                                        ils + ++ ++vii + l +  y + ++  al s+  d++++a
  gi|70606098|ref|YP_254968.1| 284 SisvLILSFILYGSISVIISVPLATWSYLVSNTPFALLSIAVDYIRVA 331
                                   033345677778888888888888888888888888888888888777 PP

  == domain 3  score: 52.8 bits;  conditional E-value: 2.2e-18
                  BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...vilsilg.hlilp.viillllsaapyvrlirraa 75 
                                   +l+ i+++     +k++ ++++pli+++ ++P  v +++l++ f   +i+  +g +++   v++l++ls++ y ++ ++ +
  gi|70606098|ref|YP_254968.1| 338 LLITIFLGyfIVVHKRIERVILPLIQIVAAIPAPVYFPFLYA-FsisFISHLFGaFTNEFyVLLLGFLSTFYYSFFSYYIG 417
                                   56778888887899*********************9999985.559966666666555555******************** PP

                  BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.. 154
                                   + s+p +++e ++ + +s wq +r+++lP+++p++itg+  ++ + +gg +++e+  + +   +l +++ l++d+ + +  
  gi|70606098|ref|YP_254968.1| 418 VTSMPVQFWEIMKNYELSFWQKLRQIILPSTMPYLITGITSTVNSTWGGLAIAEYWPNITQDHNLYVRTGLMKDIVLFTnq 498
                                   *******************************************************98888855555555555555544444 PP

                  BPD_transp_1 155 .......nggvlalviavlllnlvad 173
                                          ++++++++++v+  +l+++
  gi|70606098|ref|YP_254968.1| 499 geialasWFSLIFAIVVVVYSILFTR 524
                                   45443334444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3460.16
//
Query:       gi|70606099|ref|YP_254969.1|  [L=510]
Description: pyruvate carboxylase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-60  203.6   0.0    3.8e-60  203.0   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.4e-46  156.8   0.3    4.4e-46  156.0   0.3    1.4  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    8.8e-36  122.3   0.0    1.6e-35  121.5   0.0    1.4  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    6.4e-06   25.8   0.0    1.4e-05   24.7   0.0    1.5  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00043   19.9   0.1     0.0015   18.1   0.0    1.9  2  ATP-grasp        ATP-grasp domain
     0.0022   18.0   0.0      0.006   16.6   0.0    1.7  1  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.049   12.4   0.0      0.079   11.7   0.0    1.3  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.097   12.1   0.0       0.36   10.2   0.0    1.9  2  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.0   0.0   1.7e-63   3.8e-60       6     209 ..     122     325 ..     117     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 1.7e-63
                                   HHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEE CS
                   CPSase_L_D2   6 kealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlve 86 
                                   k+++k+ +vp+ p+s++pve+l+ea++ia++igyP+++kaa+g+GG+G   ++++e+l+e+ ++  + a  afg++ +++e
  gi|70606099|ref|YP_254969.1| 122 KRLAKASGVPISPGSDGPVENLDEAIKIADRIGYPIMVKAAYGGGGTGITKVDSQEQLIEVWERNKRLAYQAFGKADLYIE 202
                                   6778999************************************************************************** PP

                                   E--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETT CS
                   CPSase_L_D2  87 kslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpk 167
                                   k   +p++iE++++ D++gn ++  ere+ +q+r+qk+ie+APs++++ eer+++ e  +k  + + + + gt+e +++  
  gi|70606099|ref|YP_254969.1| 203 KAAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPSPVVKMEERERMFEPIMKFGQLIRYHTLGTFETVFSDV 283
                                   ********************************************************************************* PP

                                   TTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GC CS
                   CPSase_L_D2 168 skeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLe 209
                                   s+e+y++E+N Rl+ve++++e++  +dlvk ++++a+ e+L+
  gi|70606099|ref|YP_254969.1| 284 SREFYFLELNKRLQVEHPITETIFRIDLVKLQIRLAADEHLP 325
                                   **************************************9996 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.3     2e-49   4.4e-46       2     110 .]       4     112 ..       3     112 .. 0.99

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 2e-49
                                   --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE--S CS
                 Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpGy 82 
                                   + kvl+anrGeiA+r+++av+e+g+++vavyse+d+nslhv++adea+ +gp++a +sYlnie+i+++a+++++davhpGy
  gi|70606099|ref|YP_254969.1|   4 FGKVLVANRGEIAIRVMKAVKEMGMKAVAVYSEADKNSLHVKYADEAYYIGPSPAIQSYLNIESIISVAEKAHVDAVHPGY 84 
                                   679****************************************************************************** PP

                                   STTTT-HHHHHHHHHTT-EESSS-HHHH CS
                 Biotin_carb_N  83 GflsEnaefaeaveeagivfiGPsaeal 110
                                   GflsE+a+faeave+ag+vfiGPs++a+
  gi|70606099|ref|YP_254969.1|  85 GFLSERADFAEAVEKAGVVFIGPSPHAM 112
                                   *************************998 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.0   7.1e-39   1.6e-35       1     107 [.     341     447 ..     341     448 .. 0.99

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 7.1e-39
                                   EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS- CS
                 Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvk 81 
                                   e Rin+Edp ++f+ ssG++t++e+p+gpgvRvdsg++ gs v+p+yDsl+aKliv+ge+r +al+  +raL++++i Gvk
  gi|70606099|ref|YP_254969.1| 341 EYRINSEDPMSDFSGSSGTITYYEEPSGPGVRVDSGITLGSYVPPFYDSLIAKLIVYGEDRISALQSGQRALSDFKIGGVK 421
                                   79******************************************************************************* PP

                                   BSHHHHHHHHH-HHHHHT---TTTCC CS
                 Biotin_carb_C  82 tnieflrailedeefakgeldtkfle 107
                                   t+ie+++ i+++e+f++++++t++++
  gi|70606099|ref|YP_254969.1| 422 TTIELYKWITREEDFVNAKFTTAYIS 447
                                   ************************97 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.4e-09   1.4e-05      29      94 ..     147     219 ..     136     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.4e-09
                                   HHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-......SCEEEEE--.ESEEEEEEEEETS CS
               Dala_Dala_lig_C  29 ekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd......ekvlvEeai.egreievavlgne 94 
                                    k+ +++gyp++VK+a  G   G++kv s+e+l e  e+  +        ++  +E+a  + r ie  ++g+ 
  gi|70606099|ref|YP_254969.1| 147 IKIADRIGYPIMVKAAYGGGGTGITKVDSQEQLIEVWERNKRLAyqafgkADLYIEKAAvNPRHIEFQLIGDK 219
                                   57999****************************9998876554400111135568876558888888888854 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.97   2.2e+03     124     150 ..      14      40 ..       9      45 .. 0.79
   2 !   18.1   0.0   6.6e-07    0.0015      14     115 ..     140     249 ..     126     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                                   HHHHHHHHHHTSSEEEEEEEEEETTCT CS
                     ATP-grasp 124 eiakkiveeLggvGvfavElFvledge 150
                                   eia ++++++  +G+ av ++  +d++
  gi|70606099|ref|YP_254969.1|  14 EIAIRVMKAVKEMGMKAVAVYSEADKN 40 
                                   688899999999999999998877665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.6e-07
                                   ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEET CS
                     ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsa 86 
                                   ve+ +e+ ++a+++g+p++vK +  g  G G + v s+e+l +++e          ++  +++E+ +   + +    + ++
  gi|70606099|ref|YP_254969.1| 140 VENLDEAIKIADRIGYPIMVK-AAYGGGGTGITKVDSQEQLIEVWERNkrlayqafGKADLYIEKAAVNPRHIEFQLIGDK 219
                                   78999****************.7777799999*************999899999999999999999888888888888888 PP

                                   TC-.EEE--EEEEEEETTEEEEEEECEE-S CS
                     ATP-grasp  87 eGe.tafypvvetvqedgilrlsvapaevs 115
                                    G+ +++++   t+q+++   +  ap++v 
  gi|70606099|ref|YP_254969.1| 220 YGNyVVAWERECTIQRRNQKLIEEAPSPVV 249
                                   887567788888888888777777776655 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06     0.006      25     159 ..     148     297 ..     122     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                   EESS--SSSEEEEESS-------B--SS--TTE....................EEEE---SEEEEEEEEE.SSSEEEEEEE CS
                   ATP-grasp_3  25 eeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.............lvqefieGkplSvsllsdgekvlvlavn 92 
                                   + +++  +++ vK ++G+gg+++++v+ +e++ +  e ++             + ++ ++ +++  +l++d+  ++v+a  
  gi|70606099|ref|YP_254969.1| 148 KIADRIGYPIMVKAAYGGGGTGITKVDSQEQLIEVWERNKrlayqafgkadlyIEKAAVNPRHIEFQLIGDKYGNYVVAWE 228
                                   45677899************************999999999**************************************** PP

                                   EEEEET....TEEEEEEES-.---HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS-- CS
                   ATP-grasp_3  93 rqliekaekefvyaGnvtpi.etelkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRlt 159
                                   r+   +++++       +p+ ++e++e+++e + +  + +     +   + v +d   e y++E N Rl+
  gi|70606099|ref|YP_254969.1| 229 RECTIQRRNQKLIEEAPSPVvKMEERERMFEPIMKFGQLI-RYHTLGTFETVFSDvsREFYFLELNKRLQ 297
                                   *998877766555555555414455777777777777777.44444445888888888999999999987 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.5e-05     0.079     274     317 ..       6      49 ..       5     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                   EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHH CS
                Oxidored_nitro 274 rvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkae 317
                                   +v+++  +++++ +++++ke+Gm+ va+ +e  ++ ++ +  +e
  gi|70606099|ref|YP_254969.1|   6 KVLVANRGEIAIRVMKAVKEMGMKAVAVYSEADKNSLHVKYADE 49 
                                   7999***************************9999988544443 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.93   2.1e+03     122     142 ..       3      23 ..       2      38 .. 0.81
   2 ?   10.2   0.0   0.00016      0.36      13      53 ..     119     161 ..     110     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.93
                   ATP-grasp_5 122 vFGpvilfGlGGtavevlkdv 142
                                    FG v++   G +a+ v+k v
  gi|70606099|ref|YP_254969.1|   3 PFGKVLVANRGEIAIRVMKAV 23 
                                   699999999999999999987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                   ATP-grasp_5  13 aeakelleaygipvvetrl..assaeeaveaaeeigypvvlKi 53 
                                    + k+l +a g+p+ +     +++ +ea+++a++igyp+ +K 
  gi|70606099|ref|YP_254969.1| 119 LDGKRLAKASGVPISPGSDgpVENLDEAIKIADRIGYPIMVKA 161
                                   567899999999999987666*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3316.73
//
Query:       gi|70606100|ref|YP_254970.1|  [L=167]
Description: hypothetical protein Saci_0261 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-18   66.0   6.3    4.1e-18   65.0   2.6    2.5  2  Biotin_lipoyl    Biotin-requiring enzyme
    7.5e-16   57.7   8.7    1.8e-08   34.1   0.2    2.8  3  Biotin_lipoyl_2  Biotin-lipoyl like
    8.5e-08   32.9   3.1      0.001   19.7   0.1    3.1  3  HlyD_3           HlyD family secretion protein
    2.7e-07   30.1   1.0     0.0054   16.0   0.1    3.0  3  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    0.00013   21.7   1.3       0.13   12.0   0.0    3.6  4  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
     0.0011   18.8   1.2     0.0052   16.7   1.2    2.0  1  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0012   18.4   0.4       0.23   11.1   0.0    2.5  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
     0.0022   17.5   0.4     0.0045   16.4   0.4    1.5  1  NQRA             Na(+)-translocating NADH-quinone reductase s
     0.0076   16.1   2.0      0.018   15.0   0.4    2.3  2  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.011   15.7   0.2       0.85    9.7   0.0    3.1  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
      0.029   13.2   3.2       0.57    9.0   0.5    2.4  2  YqfD             Putative stage IV sporulation protein YqfD
       0.04   13.9   1.0       0.09   12.7   0.9    1.9  1  DUF2118          Uncharacterized protein conserved in archaea
      0.054   13.7   1.5        7.9    6.8   0.1    2.9  1  Peptidase_M23    Peptidase family M23
       0.11   12.7   0.1        1.3    9.2   0.0    2.2  2  Pox_vIL-18BP     Orthopoxvirus interleukin 18 binding protein
       0.13   11.8   0.2       0.25   10.8   0.2    1.7  1  PS_Dcarbxylase   Phosphatidylserine decarboxylase
       0.13   12.3   1.5       0.44   10.6   0.3    2.0  2  DnaJ_C           DnaJ C terminal domain


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.16   1.8e+02      48      72 ..      51      75 ..      48      76 .. 0.89
   2 !   65.0   2.6   3.7e-21   4.1e-18       4      73 .]     102     166 ..      97     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                                  SSSEEEEEESSTTTEEE-TTCEEEE CS
                 Biotin_lipoyl 48 pkaGvvkeilvkeGdtvevgdllak 72
                                  +++G v+ + + +G  v  ++ l+k
  gi|70606100|ref|YP_254970.1| 51 KVNGEVHTVSIINGHLVIDNETLFK 75
                                  579*************999999987 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 3.7e-21
                                   EESSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                 Biotin_lipoyl   4 ksPmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                    sP  G +v+     + vk+Gd+V++gq+l+ +eamK e+ i+apk Gvvk++l+k G+ v+ gdll++i
  gi|70606100|ref|YP_254970.1| 102 VSPLQGRIVQ-----IRVKEGDAVNKGQPLLSIEAMKSETVISAPKGGVVKKVLIKPGQGVKKGDLLLII 166
                                   4555555555.....****************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3   1.4e+03       8      24 ..      51      67 ..      50      78 .. 0.76
   2 !   34.1   0.2   1.6e-11   1.8e-08       5      37 ..     101     133 ..     100     137 .. 0.90
   3 !   28.0   0.9   1.2e-09   1.4e-06       4      34 ..     137     167 .]     134     167 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
               Biotin_lipoyl_2  8 pvsGrVaqlnVkdGqrV 24
                                  +v+G V+++ +  G  V
  gi|70606100|ref|YP_254970.1| 51 KVNGEVHTVSIINGHLV 67
                                  68999999998777666 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.6e-11
               Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37 
                                   I +p+ Gr++q++Vk+G+ V++G+ L+ ++  +
  gi|70606100|ref|YP_254970.1| 101 IVSPLQGRIVQIRVKEGDAVNKGQPLLSIEAMK 133
                                   6799*************************8765 PP

  == domain 3  score: 28.0 bits;  conditional E-value: 1.2e-09
               Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34 
                                    I+ap  G+V+++++k Gq Vk+Gd+L++++
  gi|70606100|ref|YP_254970.1| 137 VISAPKGGVVKKVLIKPGQGVKKGDLLLIIE 167
                                   599**************************95 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.98   1.1e+03       5      30 ..      51      76 ..      49      81 .. 0.85
   2 !   19.7   0.1   9.3e-07     0.001       2      32 ..     101     131 ..     100     136 .. 0.92
   3 !   11.8   0.1   0.00028      0.31       1      30 [.     137     166 ..     137     167 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.98
                        HlyD_3  5 pvdGvvvelnveegevvqagdellei 30
                                   v G+v+ +++ +g+ v  +++l+++
  gi|70606100|ref|YP_254970.1| 51 KVNGEVHTVSIINGHLVIDNETLFKV 76
                                  5899*******999999888888876 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.3e-07
                        HlyD_3   2 lrApvdGvvvelnveegevvqagdelleiip 32 
                                   + +p +G++v++ v+eg+ v++g++ll+i  
  gi|70606100|ref|YP_254970.1| 101 IVSPLQGRIVQIRVKEGDAVNKGQPLLSIEA 131
                                   89**************************975 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00028
                        HlyD_3   1 tlrApvdGvvvelnveegevvqagdellei 30 
                                   ++ Ap +Gvv+++ +++g+ v +gd ll i
  gi|70606100|ref|YP_254970.1| 137 VISAPKGGVVKKVLIKPGQGVKKGDLLLII 166
                                   588**********************99866 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.085        95     115     140 ..      52      77 ..      47      81 .. 0.88
   2 !   16.0   0.1   4.8e-06    0.0054      22      53 ..     101     131 ..      96     137 .. 0.74
   3 !   10.2   0.1   0.00028      0.32     105     139 ..     132     166 ..     129     167 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.085
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 115 isGvVteknvreGqyvqpgdtlftia 140
                                   ++G V + ++++G  v  ++tlf++ 
  gi|70606100|ref|YP_254970.1|  52 VNGEVHTVSIINGHLVIDNETLFKVD 77 
                                   789999999************99986 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.8e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23  22 vsarveGwveklyvnatgdkVkkGqpLaelys 53 
                                   + + ++G++ +++v+ +gd+V+kGqpL+++++
  gi|70606100|ref|YP_254970.1| 101 IVSPLQGRIVQIRVK-EGDAVNKGQPLLSIEA 131
                                   556678888888888.8888888888888765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00028
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 105 vqktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                                   +++++ ++ap  GvV +  +  Gq v++gd l+ i
  gi|70606100|ref|YP_254970.1| 132 MKSETVISAPKGGVVKKVLIKPGQGVKKGDLLLII 166
                                   56677888999999999999999999999888766 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.083        93      76     105 ..      49      78 ..      45      90 .. 0.88
   2 ?    3.2   0.0     0.061        69      36      51 ..      97     112 ..      81     113 .. 0.79
   3 !   12.0   0.0   0.00012      0.13      79     105 ..     105     131 ..     101     140 .. 0.88
   4 ?    3.6   0.0     0.046        51      85     101 ..     148     164 ..     134     167 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.083
                                   TTTTTTTTEEES----SEE-SEEEEEEE-H CS
                    PTS_EIIA_1  76 tvklkgegFellvkegdkVkagdklvevdl 105
                                    vk++ge+ ++ + +g+ V  +++l++vd 
  gi|70606100|ref|YP_254970.1|  49 LVKVNGEVHTVSIINGHLVIDNETLFKVDR 78 
                                   6999***********************996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.061
                                   -SSEEEES--EEEEE- CS
                    PTS_EIIA_1  36 segkvvapvdGkvekv 51 
                                   +eg++v+p++G+++++
  gi|70606100|ref|YP_254970.1|  97 KEGEIVSPLQGRIVQI 112
                                   5688999999998876 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00012
                                   TTTTTEEES----SEE-SEEEEEEE-H CS
                    PTS_EIIA_1  79 lkgegFellvkegdkVkagdklvevdl 105
                                   l+g+  ++ vkegd V++g++l++++ 
  gi|70606100|ref|YP_254970.1| 105 LQGRIVQIRVKEGDAVNKGQPLLSIEA 131
                                   789999****************99865 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.046
                                   EES----SEE-SEEEEE CS
                    PTS_EIIA_1  85 ellvkegdkVkagdklv 101
                                   ++l+k g+ Vk+gd+l+
  gi|70606100|ref|YP_254970.1| 148 KVLIKPGQGVKKGDLLL 164
                                   7899**********997 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.2   4.6e-06    0.0052      39      81 ..     107     150 ..      96     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.6e-06
                        RnfC_N  39 GapakplvkvgdkVlkGqkiaeaegfvsap.vhasvsGtVkaie 81 
                                   G   ++ vk+gd V+kGq + + e++ s   + a+  G Vk++ 
  gi|70606100|ref|YP_254970.1| 107 GRIVQIRVKEGDAVNKGQPLLSIEAMKSETvISAPKGGVVKKVL 150
                                   5667899****************997665516688899999875 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0002      0.23      35      59 ..     111     135 ..     110     143 .. 0.82
   2 ?    5.0   0.1     0.017        19      36      53 ..     149     166 ..     140     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                   EES--TT-EEBTTSEEEEEEESSSC CS
                        PYNP_C  35 elhkklGdkVkkGeplatiYankee 59 
                                   ++ +k Gd+V+kG+pl+ i a k+e
  gi|70606100|ref|YP_254970.1| 111 QIRVKEGDAVNKGQPLLSIEAMKSE 135
                                   67899************99777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                                   ES--TT-EEBTTSEEEEE CS
                        PYNP_C  36 lhkklGdkVkkGeplati 53 
                                   + +k+G+ VkkG+ l+ i
  gi|70606100|ref|YP_254970.1| 149 VLIKPGQGVKKGDLLLII 166
                                   5689**********9976 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   4.1e-06    0.0045      41      79 ..     110     149 ..     101     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.1e-06
                          NQRA  41 pklkvkegdkVkkGqvlfe.dKknpgvlftspasGevvei 79 
                                    ++ vkegd V+kGq+l+  +  +++ ++ +p  G+v+++
  gi|70606100|ref|YP_254970.1| 110 VQIRVKEGDAVNKGQPLLSiEAMKSETVISAPKGGVVKKV 149
                                   6789************9872556779999********987 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.73   8.2e+02      58      87 ..      51      82 ..      45      94 .. 0.69
   2 !   15.0   0.4   1.6e-05     0.018      30      73 ..     106     148 ..      96     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.73
                                  S-EEEEE..-SSSEEEEEE-GGGTT-TTHHHH CS
                         GCV_H 58 Kaasevy..apvsGevvevNekleeepeliNk 87
                                  K  +ev   + ++G++v  Ne l +   +i +
  gi|70606100|ref|YP_254970.1| 51 KVNGEVHtvSIINGHLVIDNETLFKVDRVIEE 82
                                  45555531156888888888888777766665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                                   H-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                         GCV_H  30 lgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73 
                                    g++v ++++e g++v+kg++l ++E+ K+ + + ap  G v +
  gi|70606100|ref|YP_254970.1| 106 QGRIVQIRVKE-GDAVNKGQPLLSIEAMKSETVISAPKGGVVKK 148
                                   699******86.99******************999998887754 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.54   6.1e+02      55      74 ..      40      59 ..      23      62 .. 0.73
   2 ?    9.7   0.0   0.00075      0.85      47      69 ..     109     131 ..      99     140 .. 0.85
   3 ?    1.5   0.0      0.28   3.1e+02      48      68 ..     147     167 .]     133     167 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                                  T-EEETTEEEEEEEEEHHHH CS
                     QRPTase_N 55 GervekgdvlleieGnaral 74
                                  G+  ++g+ l+++ G+++++
  gi|70606100|ref|YP_254970.1| 40 GAGWREGEHLVKVNGEVHTV 59
                                  77778999999999999875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00075
                                   EEEESS-TT-EEETTEEEEEEEE CS
                     QRPTase_N  47 evellvkDGervekgdvlleieG 69 
                                    v++ vk+G+ v+kg+ ll ie+
  gi|70606100|ref|YP_254970.1| 109 IVQIRVKEGDAVNKGQPLLSIEA 131
                                   58999***************997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.28
                                   EEESS-TT-EEETTEEEEEEE CS
                     QRPTase_N  48 vellvkDGervekgdvlleie 68 
                                    ++l+k G+ v+kgd ll ie
  gi|70606100|ref|YP_254970.1| 147 KKVLIKPGQGVKKGDLLLIIE 167
                                   4688999*********99875 PP

>> YqfD  Putative stage IV sporulation protein YqfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   0.00051      0.57     205     233 ..     112     138 ..      96     149 .. 0.75
   2 ?    5.0   0.7    0.0083       9.3     189     219 ..     140     163 ..     129     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                          YqfD 205 plvkegdtVkkGdvLIsgvieekegktry 233
                                     vkegd+V+kG+ L s +    + +t +
  gi|70606100|ref|YP_254970.1| 112 IRVKEGDAVNKGQPLLSIEAM--KSETVI 138
                                   57**************98877..444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0083
                          YqfD 189 AkkdGvItkvivesGeplvkegdtVkkGdvL 219
                                   A k Gv++kv       l+k+g+ VkkGd+L
  gi|70606100|ref|YP_254970.1| 140 APKGGVVKKV-------LIKPGQGVKKGDLL 163
                                   5566666665.......57888888888887 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9     8e-05      0.09      81     138 ..      97     154 ..      30     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-05
                       DUF2118  81 dklkli.pvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepa 138
                                   ++ +++ p++g  v++ v++Gd v++g++l  + + k e+  + ap+ gvV  +  +p 
  gi|70606100|ref|YP_254970.1|  97 KEGEIVsPLQGRIVQIRVKEGDAVNKGQPLLSIEAMKSET-VISAPKGGVVKKVLIKPG 154
                                   4444443789999**************************8.799******987776665 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0071       7.9      53      69 ..     110     126 ..      93     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0071
                                   SEESS-TTEEE-TTCEE CS
                 Peptidase_M23  53 skisvkegqkVkaGqvI 69 
                                    +i+vkeg+ V++Gq++
  gi|70606100|ref|YP_254970.1| 110 VQIRVKEGDAVNKGQPL 126
                                   5789***********97 PP

>> Pox_vIL-18BP  Orthopoxvirus interleukin 18 binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0012       1.3      56      94 ..      23      62 ..      13      81 .. 0.83
   2 ?    1.0   0.0      0.42   4.7e+02      73      92 ..      95     113 ..      77     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                  Pox_vIL-18BP 56 akdmksdedakf.iehlgegikedetvrtidgrivtlrkv 94
                                   kd+   e a f +e+lg g +e e +  ++g++ t+  +
  gi|70606100|ref|YP_254970.1| 23 NKDLMKAEGAEFeVEYLGAGWREGEHLVKVNGEVHTVSII 62
                                  58888889999879*******************9998654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.42
                  Pox_vIL-18BP  73 egikedetvrtidgrivtlr 92 
                                   +g ke e v+ ++griv +r
  gi|70606100|ref|YP_254970.1|  95 KG-KEGEIVSPLQGRIVQIR 113
                                   44.78888888888888776 PP

>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00023      0.25     144     198 ..     107     163 ..      50     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                PS_Dcarbxylase 144 vgsivlnvlkgdelkkGeelGyFqf.GStvvlvfeag.kfieslvekgqkvkmGekl 198
                                    + ++++v++gd ++kG+ l  ++   S++v+  ++g    + l+++gq vk G+ l
  gi|70606100|ref|YP_254970.1| 107 GRIVQIRVKEGDAVNKGQPLLSIEAmKSETVISAPKGgVVKKVLIKPGQGVKKGDLL 163
                                   445666788999999999888888779999999998875567788999988888765 PP

>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.46   5.1e+02      38      66 ..      39      68 ..       6      80 .. 0.66
   2 ?   10.6   0.3   0.00039      0.44       6      68 ..      87     166 ..      83     167 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.46
                                  E-TT--TT-E.EEETT-SSSS..S---EEE CS
                                  xxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C 38 ipaGikdgqk.irlegeGdeeggepGDliv 66
                                    aG+++g++ ++++ge +     +G l++
  gi|70606100|ref|YP_254970.1| 39 LGAGWREGEHlVKVNGEVHTVSIINGHLVI 68
                                  457777777734566666655577777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00039
                                   EE-HHHHHH-.EEE.EEEE............................TEEEEEE-TT--TT-EEEETT-SSSS..S---EE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaJ_C   6 eisleelykGktkkikikrnvi.....................kkekktlevkipaGikdgqkirlegeGdeeggepGDli 65 
                                   ++s+eel+kGk+ +i    + +                     +  k++  ++ p+G   ++ ++ +g+G    +++GDl+
  gi|70606100|ref|YP_254970.1|  87 KVSFEELFKGKEGEIVSPLQGRivqirvkegdavnkgqpllsiEAMKSETVISAPKGGVVKKVLIKPGQG----VKKGDLL 163
                                   79************99887777888999999999999999997444446789999999999999999999....6789999 PP

                                   EEE CS
                                   xxx RF
                        DnaJ_C  66 vti 68 
                                   ++i
  gi|70606100|ref|YP_254970.1| 164 LII 166
                                   988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1175.58
//
Query:       gi|70606101|ref|YP_254971.1|  [L=511]
Description: propionyl-CoA carboxylase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.7e-180  600.3   1.7     3e-180  600.1   1.7    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    0.00057   19.5   0.4     0.0022   17.5   0.0    2.0  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.1   1.7  3.4e-184    3e-180       2     494 .]      23     509 ..      22     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 600.1 bits;  conditional E-value: 3.4e-184
                                   SCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEE CS
                Carboxyl_trans   2 ehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpakgek 81 
                                   +h++Gkltarer++ll+d + F e+  ++  ++te+g+ k+k+++dgvvtg+G+v+Gr+v+ +aqd+  lgg+lg+++++k
  gi|70606101|ref|YP_254971.1|  23 QHDKGKLTARERLSLLFDGNTFQEFMGFATTKATEFGLdKNKVYGDGVVTGWGKVEGRTVFAYAQDFISLGGTLGEVHANK 103
                                   8**************************************9***************************************** PP

                                   ECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETT CS
                Carboxyl_trans  82 llkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimvee 162
                                   + ++ e+a+k+g+p++gindsgGa  riqeg ++l+g+G +f+ n+ asg+Ipqi+++ g++aGg++Y+pal+d++im+++
  gi|70606101|ref|YP_254971.1| 104 IARVYELALKTGAPVVGINDSGGA--RIQEGAVALEGYGAVFKMNVMASGVIPQITIMAGPAAGGAVYSPALTDFIIMIKG 182
                                   ************************..******************************************************* PP

                                   .EEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGS CS
                Carboxyl_trans 163 .tskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadep 242
                                      ++f+tGp++ k +lg eev+ ++lgGa +h tksGv+h++ae++++a+++++kllsylP   snn+e++P ++t d+ 
  gi|70606101|ref|YP_254971.1| 183 dAYYMFVTGPEITKVALG-EEVSYQDLGGAIVHSTKSGVIHFMAENEQDAINITKKLLSYLP---SNNMEEPPYIDTGDAA 259
                                   999***************.*******************************************...999************* PP

                                   SSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHH CS
                Carboxyl_trans 243 drd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavKaa 320
                                   drd   +++i+P+++ kpy +re+i r+vd+geF E+++ +A+++++GfAr+gG  vG+vAn+++ ++G  ++ d+a+Kaa
  gi|70606101|ref|YP_254971.1| 260 DRDvsgANDIIPTDPVKPYSMRELIYRTVDNGEFMEVHKYWANNMIIGFARIGGNVVGIVANNPEEFGG-AIDVDAADKAA 339
                                   ***88777********************************************************99999.*********** PP

                                   HHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEEETT CS
                Carboxyl_trans 321 rfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlvaawp 401
                                   rfir+cda+n+Pl+ l+d++G+ +G++qey+gi++hGak+++a+aea+vPkitvilrk+yGGa+++m+ k +gadlv+awp
  gi|70606101|ref|YP_254971.1| 340 RFIRFCDAFNIPLISLVDTPGYVPGTEQEYKGIIRHGAKMLYAFAEATVPKITVILRKSYGGAHIAMSIKSLGADLVYAWP 420
                                   ********************************************************************************* PP

                                   T-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEEHGGG CS
                Carboxyl_trans 402 tariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvialelewkk 482
                                   +a+iaV gpegav il+++++++ +    +++  +k+k++ey++ ++npy aa+ g++D+vi+p++tr+ +  ale++++k
  gi|70606101|ref|YP_254971.1| 421 NAEIAVTGPEGAVRILYKRDLQKMS----NPEDYIKQKIEEYRRLFANPYWAAEKGLIDDVIEPKDTRRIIYSALEMLKNK 497
                                   ********************99998....89999*********************************************** PP

                                   HHHHHHHHHHHH CS
                Carboxyl_trans 483 arklparkrrni 494
                                   +++++++k++ni
  gi|70606101|ref|YP_254971.1| 498 REYRYPKKHGNI 509
                                   **********97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.21   1.9e+03      94     111 ..     104     121 ..      95     142 .. 0.84
   2 !   17.5   0.0   2.5e-07    0.0022      62     152 ..     347     437 ..     297     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHT--EEEE CS
                          MdcE  94 lakalarArlaGhpvigl 111
                                   +a ++ +A   G+pv+g+
  gi|70606101|ref|YP_254971.1| 104 IARVYELALKTGAPVVGI 121
                                   688999999999999997 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.5e-07
                                   SS--EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EE CS
                          MdcE  62 aekrpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqv 139
                                   a + p++ lvD+++   g  +E  Gi    a +  a+a A     p i+++  k+  Ga +a++   l a+ + a p++++
  gi|70606101|ref|YP_254971.1| 347 AFNIPLISLVDTPGYVPGTEQEYKGIIRHGAKMLYAFAEAT---VPKITVILRKSYGGAHIAMSiksLGADLVYAWPNAEI 424
                                   45679*********************988887777777776...59****************862226799********** PP

                                   ESS-HHHHHHHHT CS
                          MdcE 140 avmdkasaArvTk 152
                                   av +   a r+  
  gi|70606101|ref|YP_254971.1| 425 AVTGPEGAVRILY 437
                                   ****999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3435.97
//
Query:       gi|70606102|ref|YP_254972.1|  [L=705]
Description: DNA helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-23   83.1   0.0    7.5e-22   77.9   0.0    2.9  3  DEAD             DEAD/DEAH box helicase
    2.3e-12   47.2   0.0    1.2e-11   45.0   0.0    2.0  2  ResIII           Type III restriction enzyme, res subunit
    2.2e-09   37.6   0.2    1.5e-07   31.7   0.4    3.4  3  Helicase_C       Helicase conserved C-terminal domain
      7e-05   23.4   0.3     0.0004   20.9   0.1    2.5  2  HHH_5            Helix-hairpin-helix domain
     0.0065   16.3   0.0      0.023   14.5   0.0    1.9  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
      0.013   14.2   0.0        0.1   11.3   0.0    2.1  2  SNF2_N           SNF2 family N-terminal domain
      0.051   13.8   0.0       0.13   12.5   0.0    1.7  1  Cdd1             Pathogenicity locus
      0.062   12.6   0.0       0.14   11.5   0.0    1.5  1  ATPase           KaiC
       0.15   12.0   0.0       0.55   10.2   0.0    2.0  1  HHH              Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   3.7e-25   7.5e-22       2     170 ..      29     183 ..      28     190 .. 0.85
   2 ?    1.2   0.0      0.13   2.6e+02      45      92 ..     246     293 ..     235     312 .. 0.73
   3 ?   -2.0   0.0       1.3   2.6e+03      62     112 ..     629     688 ..     626     698 .. 0.60

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 3.7e-25
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   + Q ea++  l +++ +l+  +T+sGKTl++ + ++++++    ++g ka++v+P+r+L+ + ++++k + k ++ +v ++
  gi|70606102|ref|YP_254972.1|  29 PPQTEAVKKGLiEDKRLLITTPTASGKTLMAELGMISHLL----NKGGKAIYVTPLRALTSEKYSTFKDWEK-LGFKVGVT 104
                                   669999999888999************************6....5777************************.56677644 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                    g  +++ +   l ++ di+v+t ++ld+l +     l+++ ++VlDE + + d ++++ ++ ++ +        k q ++
  gi|70606102|ref|YP_254972.1| 105 SG--DYDTDDPWL-RNFDIIVTTYEKLDSLWRHSAEWLKDIDYFVLDEFHYMNDGDRGPVVEGVAVRA-------KRQGTI 175
                                   44..455566677.88*************98544445**************************99999.......44555* PP

                                   EEEESSBS CS
                                   xxxxxxxx RF
                          DEAD 163 ivlSATlp 170
                                   ++lSAT+ 
  gi|70606102|ref|YP_254972.1| 176 LALSATIG 183
                                   ******97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                   STS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqls 92 
                                   ++g ++++   +r+ ae t+ ++++++++++l  + +++  ++ ++++
  gi|70606102|ref|YP_254972.1| 246 SKGGQVIVFRSSRKYAETTAMKISQYMNFVKLDDKKLLETAERIKEVE 293
                                   56779***********************98866665555554444444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
                                   HHHHHHHHHTTTST.......SEEEEE..ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH CS
                                   xxxxxxxxxxxxxx.......xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  62 qtlnnlkkfkkyid.......lrvlli..iggvaardqlskldngvdivvgtpgrlddll 112
                                   q+ + l+k+ k i        l+++ +  ig  +ar   ++  ++++ +v+ p+r+ +ll
  gi|70606102|ref|YP_254972.1| 629 QHTSVLEKLHKRIAdgvkeelLELVRVpgIGRARARLLFNQGIKRPEDIVMKPERVKSLL 688
                                   666666666666444644443222222335555555555555577888999999999887 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   5.8e-15   1.2e-11       2     169 ..      25     182 ..      24     184 .. 0.85
   2 ?   -0.6   0.0      0.58   1.2e+03     141     170 ..     313     343 ..     246     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 5.8e-15
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                   ++l++ Q+ea+++ l      +dkr+li  +T +GKTl+a + +i +ll+kg+  k++ + p ++l++  +++fk++ +  
  gi|70606102|ref|YP_254972.1|  25 KKLNPPQTEAVKKGL-----IEDKRLLITTPTASGKTLMAeLGMISHLLNKGG--KAIYVTPLRALTSEKYSTFKDWEKLG 98 
                                   578999999999998.....479****************************99..9***********************99 PP

                                   ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHH.HHT-- CS
                        ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swrei.lekfk 158
                                   +  + +++sgd ++       n +i+vtt+++ld+        +     + +d+++ DE H +++ +    ++ + +++ +
  gi|70606102|ref|YP_254972.1|  99 F--KVGVTSGDYDTD-DPWLRNFDIIVTTYEKLDSLW-----RHSAEWLKDIDYFVLDEFHYMNDGDrgpVVEGVaVRAKR 171
                                   8..566666666666.66999****************.....56666677899************8555556665345556 PP

                                   -SEEEEEESS- CS
                        ResIII 159 eavllglTATp 169
                                   + ++l+l+AT+
  gi|70606102|ref|YP_254972.1| 172 QGTILALSATI 182
                                   7999*****97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.58
                                   GGGTTS.TTTHHHHHT.---SEEEEEESS-S CS
                        ResIII 141 aHrlgakkswreilek.fkeavllglTATpe 170
                                    H++g +k  r i+e+ f+e ++  +TATp 
  gi|70606102|ref|YP_254972.1| 313 FHHAGLSKGLRDIIEAsFRERIIKVITATPT 343
                                   5999998999997555267777777899995 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   2.4e+03       7      51 ..      65     109 ..      56     113 .. 0.68
   2 !   31.7   0.4   7.7e-11   1.5e-07      13     111 .]     276     390 ..     236     390 .. 0.75
   3 ?   -2.3   0.0       2.7   5.5e+03      16      43 ..     394     419 ..     392     429 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                   HHHHHHTTTTSEEEEEESSHH.HHHHHHHHHHHT..TSTEEEESTTST CS
                    Helicase_C   7 lellkleeeggkilifvntid.rlekvklllekk..gikvavlhgelp 51 
                                    +l    ++ggk++ +++ +  + ek + ++  +  g+kv v  g+  
  gi|70606102|ref|YP_254972.1|  65 SHL---LNKGGKAIYVTPLRAlTSEKYSTFKDWEklGFKVGVTSGDYD 109
                                   344...4899*******9999766655555333356888888877765 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 7.7e-11
                                   TTTTSEEEEEESSHHHHHH.....HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTES CS
                    Helicase_C  13 eeeggkilifvntidrlek.....vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvn 86 
                                   + +++k l  +++i+++e+      ++l   +     va +h+ l++  r+ i ++f++  ++v+ at  ++ G+++p   
  gi|70606102|ref|YP_254972.1| 276 KLDDKKLLETAERIKEVEDagsneKEVLY--NliVRGVAFHHAGLSKGLRDIIEASFRERIIKVITATPTLAAGVNLPARA 354
                                   34555666666666666555555444443..145789999******************99999***************999 PP

                                   EEE..ESSSSSSH.........HHHHHHHTTSSSTT CS
                    Helicase_C  87 lVi..nfdlprnv.........tsyiqriGRtgRag 111
                                   +Vi  ++ + r++          +y q++GR+gR g
  gi|70606102|ref|YP_254972.1| 355 VVIgdIYRFNRKIvgftemistMEYRQMSGRAGRPG 390
                                   9999878888665566666676************75 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                                   TSEEEEEESSHHHHHH..HHHHHHHTTSTE CS
                    Helicase_C  16 ggkilifvntidrlek..vklllekkgikv 43 
                                   +g+++i v+++ +++k   k+l    +  +
  gi|70606102|ref|YP_254972.1| 394 HGEAIILVRSKVEVDKviDKYL----HSDI 419
                                   6789999999999995544444....4444 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         9   1.8e+04       9      21 ..     598     610 ..     591     618 .. 0.72
   2 !   20.9   0.1     2e-07    0.0004       3      55 ..     651     700 ..     647     702 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9
                                   T--HHHHHHHHTT CS
                         HHH_5   9 GiGpktAlallsa 21 
                                   GiG  + +a++++
  gi|70606102|ref|YP_254972.1| 598 GIGSGDLRAIIDT 610
                                   6777777777665 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2e-07
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                   eL +v+GiG+++A+ l ++Gi+ +ed++ + +e++ ++  +G+ + e+i+ e+
  gi|70606102|ref|YP_254972.1| 651 ELVRVPGIGRARARLLFNQGIKRPEDIVMK-PERVKSL--LGQNLGEKIVKEA 700
                                   7889**********************9986.8888888..6777777776665 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.7   1.1e+04      25      39 ..      15      31 ..      14      32 .. 0.75
   2 !   14.5   0.0   1.2e-05     0.023       3      31 ..     652     680 ..     651     690 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.7
               DNA_pol_lambd_f 25 ledlra..krakLtreq 39
                                  ++d+ +  + +kL++ q
  gi|70606102|ref|YP_254972.1| 15 VKDIIKsrGIKKLNPPQ 31
                                  57888877778999987 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
               DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlrak 31 
                                   + +v G+G+++A+ ++++Gi+  ed++ k
  gi|70606102|ref|YP_254972.1| 652 LVRVPGIGRARARLLFNQGIKRPEDIVMK 680
                                   789**********************9874 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05       0.1     143     191 ..     111     155 ..      74     180 .. 0.85
   2 ?    0.2   0.0      0.12   2.5e+02       3      54 ..     470     520 ..     468     523 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                   ---------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 143 apklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkn 191
                                   ++ +l+++d+++ttY++l   + ++++ + lk++  ++ vlDE h ++ 
  gi|70606102|ref|YP_254972.1| 111 DDPWLRNFDIIVTTYEKLD--SLWRHSAEWLKDI--DYFVLDEFHYMND 155
                                   566899*************..779999***9986..5789****99876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.12
                                   HHHHHHH.......................................HHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N   3 keavkwmlkReqnlqdleaalrkllktldgekiyvnpatgevveesaeakqs 54 
                                   ++a+ w+  + ++ + +  +l+  + + ++   y+np+t+ ++++++e+ +s
  gi|70606102|ref|YP_254972.1| 470 NNAIDWL-SKNEFIKSNDDRLQLTKFGRRVSDLYLNPFTAVTIKNYLERAES 520
                                   68999*9.777788888899999999999**************999988765 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-05      0.13       3      38 ..     647     681 ..     645     697 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                          Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedp 38 
                                   ++l el ++P+iG+a a+ l + Gi+++e++ ++ p
  gi|70606102|ref|YP_254972.1| 647 EELLELVRVPGIGRARARLLFNQGIKRPEDIVMK-P 681
                                   67899*************************9764.4 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.9e-05      0.14      10      55 ..      33      78 ..      21      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                        ATPase 10 eilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvt 55
                                  e +k G+ e++  lit  + +GKt++a+  +i+ + ++g + ++vt
  gi|70606102|ref|YP_254972.1| 33 EAVKKGLIEDKRLLITTPTASGKTLMAELGMISHLLNKGGKAIYVT 78
                                  45689****************************************9 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00028      0.55      12      26 ..     651     665 ..     651     668 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                                   HHHTSTT-SHHHHHH CS
                           HHH  12 eLlalPGVGpktAea 26 
                                   eL+ +PG+G+++A+ 
  gi|70606102|ref|YP_254972.1| 651 ELVRVPGIGRARARL 665
                                   899**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4716.06
//
Query:       gi|70606103|ref|YP_254973.1|  [L=65]
Description: hypothetical protein Saci_0264 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-09   38.0   0.1    1.5e-09   37.4   0.1    1.3  1  RHH_1           Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.01   16.0   0.2      0.015   15.5   0.2    1.4  1  RHH_8           Ribbon-Helix-Helix transcriptional regulator 
       0.05   13.5   0.2        0.1   12.5   0.2    1.6  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.1   2.6e-13   1.5e-09       2      37 ..      22      58 ..      21      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.6e-13
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                  +s++ld++ l ++d+++r +g  +rS+lIR+A++ey+
  gi|70606103|ref|YP_254973.1| 22 ISFKLDDDFLQEVDKMVRLLGyTNRSDLIRDAILEYI 58
                                  89**********************************7 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.2   2.4e-06     0.015      10      46 ..      26      62 ..      17      65 .] 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-06
                         RHH_8 10 lgvvDLgqiDlLveeGfYsnRtDlirtairaqLakhd 46
                                  l+   L ++D +v+   Y+nR+Dlir ai + +++ +
  gi|70606103|ref|YP_254973.1| 26 LDDDFLQEVDKMVRLLGYTNRSDLIRDAILEYISELE 62
                                  555558899999*9999************88776655 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.7e-05       0.1       7      38 ..      26      60 ..      20      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                  XXXXXXXXX...XXXXXXXXXXXXXXXXXXX---- CS
                VapB_antitoxin  7 iDDeLlaeA...irltglktKrEaVnlALreLiqr 38
                                  +DD+ l+e+   +rl g++ ++ +++ A+ e+i +
  gi|70606103|ref|YP_254973.1| 26 LDDDFLQEVdkmVRLLGYTNRSDLIRDAILEYISE 60
                                  8*****99966678888999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 482.33
//
Query:       gi|70606104|ref|YP_254974.1|  [L=323]
Description: phosphate transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-24   85.8  40.7    1.4e-22   80.2  38.1    2.9  1  PHO4       Phosphate transporter family
  ------ inclusion threshold ------
      0.076   13.3   0.5         29    5.0   0.0    3.2  3  MazG-like  MazG-like family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2  38.1   1.6e-26   1.4e-22       1     337 []      23     310 ..      23     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.6e-26
                          PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllat 81 
                                   +G n  a + +  v++++++ +  ++++ai  flGa +   ++ +   +giv++   d+ +  ++++++l+++++  +  +
  gi|70606104|ref|YP_254974.1|  23 VGGNNSAISLGILVSTNVMKRKYSYLVSAISIFLGASVGSLTMFKS-VHGIVNT--SDELIAKVIIVCILFSSILSFFYLN 100
                                   699*********************************7754555555.5679843..35444449***************** PP

                          PHO4  82 vlglPvStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvl 162
                                    +g+P+  ++ +  +l+ ++l++    a  w++++  ++sw++sPl+++i a ll+ lv+++ l     kn + ++     
  gi|70606104|ref|YP_254974.1| 101 RMGVPTALSQMIYPSLAVISLVT--RIAFLWSAFLVTLVSWMVSPLVAIISALLLYRLVHVF-L-----KNTKGII----- 168
                                   **********************5..35789********************************.3.....3222222..... PP

                          PHO4 163 vtiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevplw.vlllgglai 242
                                                        e+ k ++++ ++++al sf  Gan v  +i+  l al          p + ++ + +la 
  gi|70606104|ref|YP_254974.1| 169 ---------------------EQVKYYRVIILIASALTSFVTGANAVGIIISTGLFAL----------PEYiIVPCYALAA 218
                                   .....................345679******************8887777776666..........655266677899* PP

                          PHO4 243 alGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwklvrniv 323
                                   a+G++l  +r + tvG ++t kl ++++ +a +++al+  +++ + +P+S T++++g+++G ++    +s ++ k +++i 
  gi|70606104|ref|YP_254974.1| 219 AIGIYLSSWRAVITVGFRVT-KLGYASASSALIGSALVSEVFTVFSVPISITQTVMGGIIGLSFRS-LTSDIE-KQLKQIG 296
                                   ********************.6*****************************************999.445554.6789*** PP

                          PHO4 324 laWvlTlpvsalls 337
                                    +W+l+  +s+++s
  gi|70606104|ref|YP_254974.1| 297 RGWLLSPTFSIIVS 310
                                   *********99987 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.015   1.3e+02      36      50 ..      78      92 ..      64      98 .. 0.84
   2 ?    1.4   0.1     0.044   3.9e+02      41      57 ..     209     225 ..     208     233 .. 0.85
   3 ?    5.0   0.0    0.0032        29      42      71 ..     267     296 ..     265     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.015
                     MazG-like 36 deLAdviiylylLAd 50
                                  + +A+vii+++l+  
  gi|70606104|ref|YP_254974.1| 78 ELIAKVIIVCILFSS 92
                                  679********9875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.044
                     MazG-like  41 viiylylLAdrlGidfe 57 
                                   +i+ +y LA ++Gi ++
  gi|70606104|ref|YP_254974.1| 209 IIVPCYALAAAIGIYLS 225
                                   7889*********9776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0032
                     MazG-like  42 iiylylLAdrlGidfeeideklkkklkkyp 71 
                                    i+  +++  +G++f+++   ++k+lk+++
  gi|70606104|ref|YP_254974.1| 267 SITQTVMGGIIGLSFRSLTSDIEKQLKQIG 296
                                   577889********************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2005.09
//
Query:       gi|70606105|ref|YP_254975.1|  [L=220]
Description: hypothetical protein Saci_0266 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-09   36.5  10.8    5.9e-09   35.6  10.8    1.4  1  PhoU_div     Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.013   15.1   4.6       0.12   12.0   4.6    2.0  1  FANCI_S1     FANCI solenoid 1
      0.014   15.6   2.4      0.037   14.2   0.3    2.7  3  TruB_C_2     tRNA pseudouridylate synthase B C-terminal domai
       0.31   11.0   2.6         24    5.0   0.1    3.5  4  hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6  10.8   1.3e-12   5.9e-09       6     213 ..      10     216 ..       5     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-12
                      PhoU_div   6 gsspekslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelves 86 
                                   +++++++l++  e++  t   l +l++all +d    ++ l +i +l ++   +++e    +++ +flP   e++++l + 
  gi|70606105|ref|YP_254975.1|  10 EQEVFDKLIKIGEDLKTTAEALRQLINALLVKDDDMKNSSLIKIKSLNEKISMTREELLSVIYSEAFLPDFKEAIVMLTQD 90 
                                   789999999999********************9899999999*************************************** PP

                      PhoU_div  87 lDeildvlediamlvtlrkv..efpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlq 165
                                   l  +  +++d++  +t r v  +    lk+ +l ++++ +ea  ++  ++  l k++++al+   + +e++ lE   D+++
  gi|70606105|ref|YP_254975.1|  91 LYRASASAKDAGRALTARRVdeKCLTTLKESLLSYISIILEASDKVVLMLSLLPKDIASALK---VGKEVQMLERSGDEIK 168
                                   ***********9998888651157789***********************************...89************** PP

                      PhoU_div 166 rklikklfsredasnplevlllveiieklenvsdraedvadrisiill 213
                                     +i+ l+  ed    +  l   + i  l  + d +e +   i+i+++
  gi|70606105|ref|YP_254975.1| 169 DMIITRLYDMEDSLHLITLLQTRDAIFFLDDILDSMESAVLSIKILYA 216
                                   ************9999999999999999999***99999999999876 PP

>> FANCI_S1  FANCI solenoid 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.6   2.6e-05      0.12       2     106 ..       8     179 ..       7     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                      FANCI_S1   2 akrlevvkvvlqliesgelseklasdlislLlleldklsgdhlvelvelcldaikegd....................... 59 
                                   ++ +ev   ++++ e+ + +++ + +li+ Ll+  d++++++l+++ +l  ++i   +                       
  gi|70606105|ref|YP_254975.1|   8 NREQEVFDKLIKIGEDLKTTAEALRQLINALLVKDDDMKNSSLIKIKSL-NEKISMTReellsviyseaflpdfkeaivml 87 
                                   68899999999999999999*************************9776.666766667789******************* PP

                      FANCI_S1  60 ..............................................akfgkvlelLPk.vLsvlaeeetlnaekgelsGee 93 
                                                                                 +k + +l+lLPk + s+l+  ++  ++  e sG e
  gi|70606105|ref|YP_254975.1|  88 tqdlyrasasakdagraltarrvdekclttlkesllsyisiileasDKVVLMLSLLPKdIASALKVGKE--VQMLERSGDE 166
                                   *******************************************9999999*******845577776563..4556669*** PP

                      FANCI_S1  94 yksqvinslcssr 106
                                    k+++i++l +++
  gi|70606105|ref|YP_254975.1| 167 IKDMIITRLYDME 179
                                   *********9997 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   1.3e+03      32      32 ..      49      49 ..      19      85 .. 0.59
   2 ?   -1.3   0.0      0.57   2.5e+03      19      41 ..      90     112 ..      79     130 .. 0.59
   3 ?   14.2   0.3   8.4e-06     0.037       5      63 ..     145     208 ..     142     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                                  . CS
                      TruB_C_2 32 d 32
                                   
  gi|70606105|ref|YP_254975.1| 49 S 49
                                  3 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.57
                                   EEEEEEETTEGG-..B-HHHHHH CS
                      TruB_C_2  19 eLRRtrvgpfdeedmvtledLed 41 
                                   +L R ++++ d+ +++t   + +
  gi|70606105|ref|YP_254975.1|  90 DLYRASASAKDAGRALTARRVDE 112
                                   45555555555555555555555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 8.4e-06
                                   HHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.....HHHHEEEGGGGG CS
                      TruB_C_2   5 dDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.....LdrlllPlesal 63 
                                   +Di+ aL +g  v++L R    ++++  + +l d+ed+++l +           Ld++l ++esa+
  gi|70606105|ref|YP_254975.1| 145 KDIASALKVGKEVQMLERSGD-EIKDMIITRLYDMEDSLHLITLlqT-RdaiffLDDILDSMESAV 208
                                   7*****************864.4566667888888888777666641.2458************98 PP

>> hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0053        24       7      38 ..      28      59 ..      25      63 .. 0.92
   2 ?    3.1   0.0     0.021        93      17      34 ..     103     120 ..     101     122 .. 0.88
   3 ?   -1.4   0.0      0.52   2.3e+03      26      42 ..     134     150 ..     131     163 .. 0.73
   4 ?   -0.3   0.0      0.24   1.1e+03      28      55 ..     181     208 ..     173     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0053
                   hnRNP_Q_AcD  7 aekLdelfrsgkltasdlDeraleaLkslpee 38
                                  ae+L +l+++  ++ +d+ + +l  +ksl+e+
  gi|70606105|ref|YP_254975.1| 28 AEALRQLINALLVKDDDMKNSSLIKIKSLNEK 59
                                  899**************************997 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.021
                   hnRNP_Q_AcD  17 gkltasdlDeraleaLks 34 
                                   + lta ++De++l  Lk+
  gi|70606105|ref|YP_254975.1| 103 RALTARRVDEKCLTTLKE 120
                                   568999********9996 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.52
                   hnRNP_Q_AcD  26 eraleaLkslpeegAla 42 
                                   ++++ +L+ lp++ A+a
  gi|70606105|ref|YP_254975.1| 134 DKVVLMLSLLPKDIASA 150
                                   56777899999887654 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.24
                   hnRNP_Q_AcD  28 aleaLkslpeegAlaVlkqfkesdlskv 55 
                                   +l  +  l+  +A + l+ +++s  s v
  gi|70606105|ref|YP_254975.1| 181 SLHLITLLQTRDAIFFLDDILDSMESAV 208
                                   5677889999999999999999876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1489.57
//
Query:       gi|70606106|ref|YP_254976.1|  [L=377]
Description: hypothetical protein Saci_0267 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.6e-125  416.6   0.0   6.6e-125  416.4   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)
  ------ inclusion threshold ------
       0.38    8.3   2.0       0.51    7.8   2.0    1.1  1  CLAG      Cytoadherence-linked asexual protein


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.4   0.0  7.3e-129  6.6e-125       1     312 []       5     335 ..       5     335 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.4 bits;  conditional E-value: 7.3e-129
                        DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkealkse 81 
                                   GiadLpLh+gkvP wl++ m++Lskai+++++ e+g+++++erls+PlwFq+++n++GmdWdsSGsTtv+lg+lke++k e
  gi|70606106|ref|YP_254976.1|   5 GIADLPLHTGKVPYWLASIMRRLSKAIIDVMIIEWGPDKVVERLSNPLWFQGFNNIIGMDWDSSGSTTVTLGILKEVIKPE 85 
                                   89******************************************************************************* PP

                        DUF763  82 elgilvaGGkGkksrktpeeleklaeklgldeeklvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviqQGmneeer 162
                                   e gi+v+GGkGk+++k+p+el++l  k++++ ek+ +asrlvakvd++++qdg++lY+h+++vse+gkw +iqQGmn e+r
  gi|70606106|ref|YP_254976.1|  86 EEGIAVLGGKGKNALKVPDELNSLRGKFSVNLEKIERASRLVAKVDSTLIQDGHTLYHHSVLVSESGKWGIIQQGMNLETR 166
                                   ********************************************************************************* PP

                        DUF763 163 lARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekklklpakh 243
                                   +ARRYhwl  ++e+f+ eph+gi+g  k+e ++n v+k+ e++rk+++dl+ke pekl++++ ++++++kg+++l+ p+  
  gi|70606106|ref|YP_254976.1| 167 FARRYHWL--STENFLVEPHKGIMG-VKQEIAINAVDKNVENTRKLMVDLLKEPPEKLINDVVKAENMIKGQTTLDNPSAF 244
                                   ********..899************.77778********************************************777777 PP

                        DUF763 244 ev................lekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPv.......kysfa 301
                                   +v                ++++l+k+ye++p+++ee ll +g+Gp++ raL lva+liy+e++s++DPv       ky++a
  gi|70606106|ref|YP_254976.1| 245 KVdikkrriymkpieiskIRQILHKVYEVNPSNLEEALL-HGLGPSSTRALYLVADLIYNEPPSYNDPVnmpydpfKYAYA 324
                                   777777777888888888******************998.9**************************************** PP

                        DUF763 302 vGgKdgvPypv 312
                                   +GgKdg+P+pv
  gi|70606106|ref|YP_254976.1| 325 IGGKDGIPFPV 335
                                   **********8 PP

>> CLAG  Cytoadherence-linked asexual protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.0   5.7e-05      0.51      73     137 ..     218     283 ..     190     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 5.7e-05
                          CLAG  73 vdasvediikyehilkeqviekykseisdlikkkilivrtlkiiklmliPlnaykkk.kdlkeale 137
                                   ++  ++d++k e+++k q + +  s     ikk+ + ++ + i k+ +i  + y+ + ++l+eal 
  gi|70606106|ref|YP_254976.1| 218 PEKLINDVVKAENMIKGQTTLDNPSAFKVDIKKRRIYMKPIEISKIRQILHKVYEVNpSNLEEALL 283
                                   45679********************************************99999865378888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2639.71
//
Query:       gi|70606107|ref|YP_254977.1|  [L=220]
Description: hypothetical protein Saci_0268 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-10   40.1   0.0    1.5e-09   38.3   0.0    1.7  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.9e-09   37.8   0.2    3.5e-09   37.5   0.2    1.1  1  Metallophos    Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.6e-13   1.5e-09       1     134 [.       1     196 [.       1     208 [. 0.74

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.6e-13
                 Metallophos_2   1 MklaiiSDlH..snldaleavlealkevgvdaiihaGDl....eeeepevleellelapvlaVrGNnD............. 62 
                                   M +a+ SD+H  + l +  a ++ +++ ++d  ++aGDl    e ++++ ++++l++++ +aV+GN D             
  gi|70606107|ref|YP_254977.1|   1 MLIAATSDIHspRYLTQFFASFNLIRNLSIDIFLLAGDLanegEYIHFKPVYDVLKRFRTIAVFGNEDfrenrdsyketyp 81 
                                   99********44444444566999**************985444455689******************************* PP

                 Metallophos_2  63 ...................eevveedvlreaaelgtdl............p.eeaelel.....agekvlliHgdpl.... 102
                                                      +++  + vl+e++++++              + e+    l     +++k+ll+H+       
  gi|70606107|ref|YP_254977.1|  82 dikwleedivefelgdilvSIIGSDGVLEEPTKWQKLNgidenyyrekarKiED----LlckarGDVKLLLTHYACTfmtv 158
                                   *********999999998833355555555555555555555556654443344....2445578889******9669*99 PP

                 Metallophos_2 103 .....gvkdalaellke.aeegsdvvvcGHtHvpevek 134
                                        +   +l +++ e +++   ++++GH H  +v++
  gi|70606107|ref|YP_254977.1| 159 qgekkSIFPHLGYRILEeTSCLPHLAIHGHAHHSKVTQ 196
                                   997765555555555553344555*********99887 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.2   3.9e-13   3.5e-09       2     203 ..       2     191 ..       1     192 [. 0.69

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.9e-13
                                   EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHHHHH CS
                   Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfeeell 82 
                                    i+ ++D+H    +  l ++ + ++ +++   +d++llaGDl ++g++ + +   ++ l ++  + +++ GN + f+e   
  gi|70606107|ref|YP_254977.1|   2 LIAATSDIH---SPRYLTQFFASFNLIRNL-SIDIFLLAGDLANEGEYIH-FKPVYDVLKRF--RTIAVFGNED-FRE--- 71 
                                   599******...666666666666666666.***************9999.88889999996..88********.444... PP

                                   HHHHHHHHH.HHHHEHH...HCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC..HHHHHHHHHH CS
                   Metallophos  83 nkygylgif.sepwrsd...aevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg..dewlkdlekr 157
                                   n+  y++++    w  +      ++ + ++ +gs+   vl  +         ++kl++++ +   +  +  +++l +    
  gi|70606107|ref|YP_254977.1|  72 NRDSYKETYpDIKWLEEdivEFELGDILVSIIGSD--GVLEEPTK-------WQKLNGIDENYYREKARkiEDLLCK---- 139
                                   44444444444555554321122222222223333..55555555.......8888888888877776566555555.... PP

                                   TTCSEEEEEESSESS....CSSSCSCCHHHHHHHHHHTT..ESEEEEESSSS CS
                   Metallophos 158 ekadwvivlgHsply....rgsgylfgdealedllkkyg..vdlvisGHtHv 203
                                   +++d++++l+H   +     g  ++  ++   ++l++    ++l i+GH H+
  gi|70606107|ref|YP_254977.1| 140 ARGDVKLLLTHYACTfmtvQGEKKSIFPHLGYRILEETSclPHLAIHGHAHH 191
                                   8*************999985555555555555677777777999*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1459.51
//
Query:       gi|70606108|ref|YP_254978.1|  [L=273]
Description: putative inactivated transposase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-19   69.9   0.0    2.4e-19   69.0   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0012   18.0   0.1        3.1    6.9   0.0    3.0  3  RuvC_1          RuvC nuclease domain
     0.0085   16.3   0.0      0.017   15.3   0.0    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.025   14.6   0.8      0.044   13.8   0.8    1.4  1  DZR             Double zinc ribbon
      0.036   13.8   2.0        5.6    6.8   0.1    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.071   12.5   2.4        3.2    7.3   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.082   12.6   4.4        0.6    9.9   4.9    2.0  2  Rubredoxin_2    Rubredoxin metal binding domain
        1.3    9.1   3.9         21    5.3   0.1    2.3  2  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0   1.1e-22   2.4e-19       3      67 ..     203     266 ..     201     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.1e-22
                OrfB_Zn_ribbon   3 klkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                   ++++ le    ++G+k+ +  p+yTSk Cs+Cg +  e + g +f+Cp+Cg++adrD+nAa+N++
  gi|70606108|ref|YP_254978.1| 203 TVEKELESHLYRKGVKFRKLPPYYTSKICSNCGFRRGE-VMGPLFVCPSCGYKADRDFNAAYNLA 266
                                   678899999*****************************.*************************8 PP

>> RuvC_1  RuvC nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0014       3.1       6      41 ..      93     128 ..      89     134 .. 0.87
   2 !    6.2   0.0    0.0022         5      80     140 ..     156     215 ..     151     220 .. 0.84
   3 ?    1.2   0.0     0.079   1.8e+02     191     208 ..     251     268 ..     222     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        RuvC_1   6 nvNkkvneklkeskdvkiiGidRgeknLlYvsvvde 41 
                                   ++ ++v+  l+ +k   i+Gid g ++L+ v+ + e
  gi|70606108|ref|YP_254978.1|  93 EFSDDVRVFLAYEKPKSIVGIDIGVRHLITVVSIRE 128
                                   6788999999999****************9988766 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0022
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        RuvC_1  80 iekikelKegYlsqvvhkiaklaikyn.aivvlEdLnlgFkrgrqkvekqvyqkfEkaLidk 140
                                   +++i+ +K g + ++++ +++ +++ n  +v +EdL++ F  +     + v +++E++L  k
  gi|70606108|ref|YP_254978.1| 156 VSEIRTIK-GKIGNIIRDVVSFIQDLNpKVVAIEDLEY-FESKIGSALRTVEKELESHLYRK 215
                                   66777776.889************999899******97.88888888888988888888765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.079
                                   xxxxxxxxxxxxxxxxxx RF
                        RuvC_1 191 lslpedadaNgayniark 208
                                   +  + d d N+ayn+a++
  gi|70606108|ref|YP_254978.1| 251 CGYKADRDFNAAYNLALQ 268
                                   5567899*********87 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.8e-06     0.017      10      34 ..     102     126 ..      82     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.8e-06
                    OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvte 34 
                                   l+ +k+++ +giD+G+++L+tvv  
  gi|70606108|ref|YP_254978.1| 102 LAYEKPKSIVGIDIGVRHLITVVSI 126
                                   67799*****************975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8     2e-05     0.044      12      44 ..     228     261 ..     221     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                           DZR  12 arfCseCgtklkavaa.edrCpsCgekvdpearf 44 
                                   ++ Cs+Cg +  +v     +CpsCg+k+d +++ 
  gi|70606108|ref|YP_254978.1| 228 SKICSNCGFRRGEVMGpLFVCPSCGYKADRDFNA 261
                                   789*****997666555889*********99986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0045        10      13      21 ..     228     236 ..     227     237 .. 0.76
   2 ?    6.8   0.1    0.0025       5.6       2       8 ..     248     254 ..     247     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0045
                 zinc_ribbon_2  13 akFCpyCGt 21 
                                   +k C++CG+
  gi|70606108|ref|YP_254978.1| 228 SKICSNCGF 236
                                   678999996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0025
                 zinc_ribbon_2   2 CpnCGae 8  
                                   Cp+CG++
  gi|70606108|ref|YP_254978.1| 248 CPSCGYK 254
                                   8888887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2    0.0078        18      17      23 ..     229     235 ..     227     237 .. 0.65
   2 ?    7.3   0.2    0.0014       3.2      18      25 ..     247     254 ..     246     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0078
                   zf-ribbon_3  17 nvCpyCG 23 
                                   ++C +CG
  gi|70606108|ref|YP_254978.1| 229 KICSNCG 235
                                   4677777 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                   zf-ribbon_3  18 vCpyCGtk 25 
                                   vCp+CG+k
  gi|70606108|ref|YP_254978.1| 247 VCPSCGYK 254
                                   68888876 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.9   0.00027       0.6       2      21 ..     230     252 ..     230     253 .. 0.93
   2 ?    5.2   0.4    0.0077        17       1      10 [.     246     255 ..     246     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                  Rubredoxin_2   2 vCsqCGfesakwfG...rCpsCg 21 
                                   +Cs+CGf+   ++G    CpsCg
  gi|70606108|ref|YP_254978.1| 230 ICSNCGFRRGEVMGplfVCPSCG 252
                                   5*************8888****8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0077
                  Rubredoxin_2   1 YvCsqCGfes 10 
                                   +vC +CG+++
  gi|70606108|ref|YP_254978.1| 246 FVCPSCGYKA 255
                                   8999999986 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0092        21      15      22 ..     229     236 ..     227     237 .. 0.87
   2 ?    4.5   0.9     0.016        36      16      22 ..     247     253 ..     246     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0092
                       UPF0547  15 qfCphCGy 22 
                                   ++C+ CG+
  gi|70606108|ref|YP_254978.1| 229 KICSNCGF 236
                                   89*****9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.016
                       UPF0547  16 fCphCGy 22 
                                   +Cp CGy
  gi|70606108|ref|YP_254978.1| 247 VCPSCGY 253
                                   5999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1886.63
//
Query:       gi|70606109|ref|YP_254979.1|  [L=237]
Description: hypothetical protein Saci_0270 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-08   31.6   0.0      1e-07   31.2   0.0    1.1  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   5.6e-12     1e-07       1     166 [.       1     172 [.       1     186 [. 0.73

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.6e-12
                      GATase_4   1 mceLLgmssnvptdisfsftgf..aarggltd...ahadGwGia..fyegkaarv..fkdpepsaesp....laelvreyp 68 
                                   mc+LLg+s++ ++d    ++++  aar  + +   +h  GwGi+   y +++ rv  fk p p  + p    +a l++   
  gi|70606109|ref|YP_254979.1|   1 MCRLLGFSVKGEVDHK-ALKSLidAARNDVFSrylNHPHGWGISaiIYRDNKPRVlhFKSPIPIYDDPtfydIASLLKG-- 78 
                                   9********9999976.3455511334333322337*******955577666555116777777766522226777776.. PP

                      GATase_4  69 iksknvvaHiRkatqGev.klenthpFvRelwgrewifAHnGdlkeykpklegrfePvGsTDsElafCelleelasrfeka 148
                                       + + H+R+a +G     +  hp+    ++ ++ fAHnG++++ k   +++  P  sTDs l + e+++++++++ + 
  gi|70606109|ref|YP_254979.1|  79 -DRVIGMIHVRRAGKGFLlGVRHNHPYHVRTKNLDIYFAHNGSISR-KAFEDPN-YP--STDSYLFLQEIIKNIDRNNLDV 154
                                   .4456679********75268899********************76.2333333.34..9****************99888 PP

                      GATase_4 149 epsaeeleralaelakei 166
                                   +++ ee    l+e++  +
  gi|70606109|ref|YP_254979.1| 155 KRAYEETIIKLSEFSVTL 172
                                   888888877777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1665.26
//
Query:       gi|70606110|ref|YP_254980.1|  [L=231]
Description: hypothetical protein Saci_0271 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-16   58.1   0.0    1.2e-15   57.6   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    2.5e-11   44.0   0.1    1.1e-10   41.9   0.1    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00073   19.5   0.0     0.0012   18.7   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0     2e-19   1.2e-15      28     201 .]      49     205 ..      35     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2e-19
                                   ..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTE CS
                 Lactamase_B_2  28 lppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggl 103
                                   l +  a+++th H+DH++g+++        + p ++++  p+g++++l++  + +  + +    ++e ++++  ++g  +l
  gi|70606110|ref|YP_254980.1|  49 LVDFSAIFVTHLHIDHINGIPDHLIyrrifGLP-DVEIRSPPGLYEILSSYQKWNGINIK---LIEESKPKG--KVG--DL 121
                                   567789***************987755564333.59999***********9665555555...555555555..566..57 PP

                                   EEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSH CS
                 Lactamase_B_2 104 eitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeea 184
                                   +i  ++a h+            ++++i++++++++y+gDt +  e i e++++adl+++++ ++e+ +   + gH ++++ 
  gi|70606110|ref|YP_254980.1| 122 NIYSVEACHAIYA---------VSYVITDNKRKIVYTGDTSQPCEPIMEEIKDADLVIHEASCLEECS---KYGHTSVKQL 190
                                   7999999998887.........*******************999**********************99...89******** PP

                                   HHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 185 veaaadlgakrlvliHi 201
                                   + ++   ++++lv++Hi
  gi|70606110|ref|YP_254980.1| 191 LSMFS--SPSKLVMTHI 205
                                   *9997..4788888887 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   1.8e-14   1.1e-10       7     173 ..      21     169 ..      16     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.8e-14
                                   EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGG.GCTTHHCCEETCCEHHHHCCHCHH CS
                   Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglg.glveatdvpvgavaeeapalfmee 86 
                                   +s+++ g +g +L D G+++++++        +l++ d +a+++THlH+DHi g + +l+ ++ +    v++  p +++e 
  gi|70606110|ref|YP_254980.1|  21 SSIYVKGSEGSLLLDLGSGASFKLD-------DLELVDFSAIFVTHLHIDHINGIPdHLIYRRIFGLPDVEIRSPPGLYEI 94 
                                   688999******************6.......9**********************74799999999999999999999999 PP

                                   HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCE CS
                   Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrga 167
                                   +  ++ ++        ++ + + e    g +g+   + v  +++  ++++v+++  +k+++tGD++ ++e ++ +      
  gi|70606110|ref|YP_254980.1|  95 LSSYQ-KW------NGINIKLIEESKPKGKVGDLNIYSVEACHAIYAVSYVITDNKRKIVYTGDTSQPCEPIMEEI----- 163
                                   95543.33......44666778888888888899999999****************************99999888..... PP

                                   EE-SHC CS
                   Lactamase_B 168 evrdps 173
                                   ++ d +
  gi|70606110|ref|YP_254980.1| 164 KDADLV 169
                                   555544 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     2e-07    0.0012       8     133 ..      21     170 ..      19     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-07
                 Lactamase_B_3   8 nsflletagarilvDPfka..nlgyeppaeeaDlvlisqaledHahletlkql............................ 58 
                                   +s+ +++++ ++l+D +++   +  + + ++  ++ +++ + dH +  ++  +                            
  gi|70606110|ref|YP_254980.1|  21 SSIYVKGSEGSLLLDLGSGasFKLDDLELVDFSAIFVTHLHIDHINGIPDHLIyrrifglpdveirsppglyeilssyqkw 101
                                   788888888999999887553333344458888999999999998888888877777777777776666666666666655 PP

                 Lactamase_B_3  59 .aenvkvleeges.levggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                      n+k++ee +   +vg+l+i +v++ h           + +++++++ +i++ G++++ + ++  +e++++D+v+
  gi|70606110|ref|YP_254980.1| 102 nGINIKLIEESKPkGKVGDLNIYSVEACH-------AIYAVSYVITDNKRKIVYTGDTSQ-PCEPIMEEIKDADLVI 170
                                   55555555554332667777777777777.......456799*****************8.799***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1486.69
//
Query:       gi|70606111|ref|YP_254981.1|  [L=288]
Description: ribokinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-52  177.2   0.0    6.9e-52  176.6   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase
    4.3e-08   32.9   0.0    6.1e-08   32.3   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
      0.041   13.4   0.0      0.061   12.8   0.0    1.2  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   1.1e-55   6.9e-52       4     295 ..       2     273 ..       1     279 [. 0.93

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 1.1e-55
                                   EEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTE CS
                          PfkB   4 vvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyv 82 
                                   +vv+G+ ++d+  ++ ++  ege+v    v    GG+g N+Av ++rlg++v++i+avG+D+fG++ ++ +++e +d++yv
  gi|70606111|ref|YP_254981.1|   2 IVVVGSYNVDFLIKVRDFpsEGETVFSDGVYIDHGGKGSNQAVSASRLGGNVRLISAVGNDEFGKRAIKFWEDERLDVAYV 82 
                                   89*****************9************************************************************* PP

                                   EEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEE CS
                          PfkB  83 kidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtfdp 163
                                   k  +++ tg a+iv d+ g++ iv+nrga+a l+++    d+d + ++d+l        e++e v++++ +  +  g  + 
  gi|70606111|ref|YP_254981.1|  83 K-IKNALTGSAYIVFDRRGRNFIVVNRGANALLSED----DLDGCLNGDILLTQL----EVNENVVKKALK--EFPG--V- 149
                                   *.5566*****************************7....67*********8886....999999998765..5555..3. PP

                                   EECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEE CS
                          PfkB 164 nlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvp 244
                                    +l+p++a  +    +ll+++d+l+pne E+++ltg +  d +  +++l k   k ++ v+vtlG++Ga++ +++  + +p
  gi|70606111|ref|YP_254981.1| 150 KVLNPAPA--VLNDNSLLEYVDILTPNEIEFKELTGTQ--DLNYGIDLLLK---KVKRAVIVTLGERGAYIGTRERRILIP 223
                                   47888885..66678899********************..********999...889************************ PP

                                   E.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSS CS
                          PfkB 245 avpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkga 295
                                   ++ +v+++DttGAGD f++++++ l +g sle+a+r+ n ++a ++++ ga
  gi|70606111|ref|YP_254981.1| 224 TL-AVDAIDTTGAGDVFNASLAVYLEKGYSLERAVRISNIISAYSTTRIGA 273
                                   *6.6*******************************************9998 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0     1e-11   6.1e-08     107     224 ..     155     260 ..     132     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1e-11
                                   HHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEE CS
                  Phos_pyr_kin 107 eavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveele 187
                                       +  ++Ll+ ++++tPN  E ++L+g     ++d++   + llk  ++aV+++ g+     a    ++ ++e+ + ++
  gi|70606111|ref|YP_254981.1| 155 APAVLNDNSLLEYVDILTPNEIEFKELTG-----TQDLNYGIDLLLKKVKRAVIVTLGER---GA----YIGTRERRILIP 223
                                   555556789********************.....89********************9983...23....466999999*** PP

                                   EE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                  Phos_pyr_kin 188 aerietknthGtGCtlssaiaaelakgesleeAvkkA 224
                                   +  ++  +t G+G+++ +++a +l kg+sle Av+ +
  gi|70606111|ref|YP_254981.1| 224 TLAVDAIDTTGAGDVFNASLAVYLEKGYSLERAVRIS 260
                                   **********************************975 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.061     118     220 ..     167     266 ..     155     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                   SSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTTS.EEEECTTEEEEE----GGG-STTHHHHHHHHH CS
                   Carb_kinase 118 aeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgekd.vivspegevlinstgssalakGGsGDvLaGli 197
                                      iLTP+  Efk L++  +        +   l +   av++  ge    i + e  +li      a  + G GDv   ++
  gi|70606111|ref|YP_254981.1| 167 YVDILTPNEIEFKELTGTQD----LNYGIDLLLKKVKRAVIVTLGERGaYIGTRERRILIPTLAVDAIDTTGAGDVFNASL 243
                                   5569************9988....34444555556666788888876515666788888888888899999*****99999 PP

                                   HHHHHCTSSHHHHHHHHHHHHHH CS
                   Carb_kinase 198 galLaqneasyeaaiaaawlhga 220
                                   +  L   ++   a+  + ++ ++
  gi|70606111|ref|YP_254981.1| 244 AVYLEKGYSLERAVRISNIISAY 266
                                   98888888666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1713.53
//
Query:       gi|70606112|ref|YP_254982.1|  [L=402]
Description: phosphomethylpyrimidine kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-82  274.6   0.4    1.1e-81  273.9   0.4    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.8e-14   53.1   0.1    2.8e-14   53.1   0.1    1.5  2  PfkB          pfkB family carbohydrate kinase
    3.9e-08   33.1   0.9    6.7e-08   32.3   0.9    1.5  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.9   0.4   1.8e-85   1.1e-81       1     246 []      14     254 ..      14     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.9 bits;  conditional E-value: 1.8e-85
                                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHH CS
                  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaek 81 
                                   Ds+GGAG+qADlktf++lgv+g+ v+t ltaqntkgv +v ++p+++ve+q++ +++d+k++ +K+Gmla++ i+evv +k
  gi|70606112|ref|YP_254982.1|  14 DSGGGAGLQADLKTFTTLGVFGTVVVTGLTAQNTKGVFKVLEVPPDFVESQIDVIMTDLKPEYAKTGMLANSRIVEVVRKK 94 
                                   9******************************************************************************** PP

                                   HHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEE CS
                  Phos_pyr_kin  82 lkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlik 162
                                   +++y++++VlDPVmvaksg+ l++e++v+alke L++++ ++tPN +Eae+++g+ki++  d+k+ a+++       V++k
  gi|70606112|ref|YP_254982.1|  95 VREYNIRLVLDPVMVAKSGDLLVTEDTVSALKE-LIRESIILTPNKFEAEKIVGRKIENILDLKNTAREIYTKYGVDVVVK 174
                                   ********************************8.**************************************77778999* PP

                                   EGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS- CS
                  Phos_pyr_kin 163 GghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkgag 243
                                   Gg         +d+ + ++e++el+++++etknthG+G+++s++++a+lakg++++eAvk+Ake+v+++i+++l+lg+g+g
  gi|70606112|ref|YP_254982.1| 175 GGGS--LGG--IDYAIVQGEEIELQSKKMETKNTHGSGDVFSASLTAYLAKGHKIKEAVKMAKEFVSKSIEYSLDLGEGNG 251
                                   9974..344..5999999999************************************************************ PP

                                   B-- CS
                  Phos_pyr_kin 244 pvn 246
                                   pv+
  gi|70606112|ref|YP_254982.1| 252 PVD 254
                                   *96 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.2       1.3   7.7e+03     225     248 ..      29      52 ..      27      56 .. 0.74
   2 !   53.1   0.1   4.6e-18   2.8e-14     162     292 ..     105     242 ..      88     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.3
                                   EEEGGGEEEEEETTEEEEEEE.SS CS
                          PfkB 225 vtlGkeGalvvekdgelkvpavpk 248
                                    tlG+ G++vv++ + ++ + v+k
  gi|70606112|ref|YP_254982.1|  29 TTLGVFGTVVVTGLTAQNTKGVFK 52 
                                   699999999999776666666655 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 4.6e-18
                                   EEEECESSSHH.....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGGG.EEEEE CS
                          PfkB 162 dpnlldplgaq.....fkeallellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGke.Galvv 235
                                   dp++++++g+      +++al+el++ + +l+pn  E+e+++g+k+e+i ++++ + ++ +k+  ++vv   G+  G  ++
  gi|70606112|ref|YP_254982.1| 105 DPVMVAKSGDLlvtedTVSALKELIRESIILTPNKFEAEKIVGRKIENILDLKNTAREIYTKYGvDVVVKGGGSLgGIDYA 185
                                   56666666644666668899*****************************************99955555555666345555 PP

                                   E.TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTS CS
                          PfkB 236 e.kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqk 292
                                     +++e++ ++ +k +  +t G GD f ++++a l++g++++ea+++a ++ + ++++
  gi|70606112|ref|YP_254982.1| 186 IvQGEEIELQS-KKMETKNTHGSGDVFSASLTAYLAKGHKIKEAVKMAKEFVSKSIEY 242
                                   57999999999.************************************9887777765 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.9   1.1e-11   6.7e-08     104     218 ..     115     236 ..       7     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.1e-11
                                   GGSGGGG.....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTT.....SEEEECTTEEEEE CS
                   Carb_kinase 104 Lnllaqkne..lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgek.....dvivspegevlin 177
                                   L + ++     +   ++ +iLTP+k E +++++  +++  d  ++are+  k+++ v++kg       d  + +++e+ + 
  gi|70606112|ref|YP_254982.1| 115 LLVTEDTVSalKELIRESIILTPNKFEAEKIVGRKIENILDLKNTAREIYTKYGVDVVVKGGGslggiDYAIVQGEEIELQ 195
                                   333333333567778899******************999*********************86522333789999******* PP

                                   ----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHH CS
                   Carb_kinase 178 stgssalakGGsGDvLaGligalLaqneasyeaaiaaawlh 218
                                   s+    + + GsGDv + ++ a La  ++ +ea+  a + +
  gi|70606112|ref|YP_254982.1| 196 SKKMETKNTHGSGDVFSASLTAYLAKGHKIKEAVKMAKEFV 236
                                   ***************************99999987777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2817.69
//
Query:       gi|70606113|ref|YP_254983.1|  [L=203]
Description: hypothetical protein Saci_0274 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-13   51.6   1.6      4e-10   40.0   0.8    2.5  2  PDDEXK_1      PD-(D/E)XK nuclease superfamily
    4.3e-09   36.7   0.0    5.7e-09   36.3   0.0    1.2  1  Cas_Cas4      Domain of unknown function DUF83
      8e-08   32.7   0.1    1.6e-07   31.7   0.1    1.5  1  PDDEXK_3      PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
       0.09   12.2   0.0       0.14   11.6   0.0    1.4  1  Chordopox_G2  Chordopoxvirus protein G2
       0.13   11.9   0.1       0.23   11.0   0.1    1.4  1  AHJR-like     REase_AHJR-like


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00013      0.45       9      49 ..      28      70 ..      25      85 .. 0.78
   2 !   40.0   0.8   1.1e-13     4e-10     119     255 .]      80     198 ..      73     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                      PDDEXK_1  9 tfleCplrfflryllgl.reeeeleap.dlGtlvHaaleefye 49
                                  ++l+Cp++ +++   +    +e+++++  lG lvH  l+ef +
  gi|70606113|ref|YP_254983.1| 28 DLLRCPMKLRFETMYKEiALSEAFTPAtMLGDLVHLGLQEFIK 70
                                  6899***999998887744488888888*************99 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.1e-13
                      PDDEXK_1 119 le....lefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalyl 195
                                   +e    + ++g+++++kGr D + + ++e +i++ K+ +    + +l    +  Ql +Yl++   +        ++ ++y+
  gi|70606113|ref|YP_254983.1|  80 VEgektIPVDGKEIKIKGRADAIIQINDEKVIVEIKSAR---ADRSLPHEHHKYQLQIYLWLFGIK--------RGLLVYI 149
                                   333233444489************888889******998...455545889999**********99........8999999 PP

                      PDDEXK_1 196 rleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskkCeyCpyksvCr 255
                                           d+ +  ++ +++ee + +     +laee l+ ++++r s +CeyC++k +C+
  gi|70606113|ref|YP_254983.1| 150 TP------DRVTEYSVNEPAEEVTII-----RLAEETLKAKIAPRYSWECEYCAFKTLCP 198
                                   99......666666666666666444.....444555666777999999**********7 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.6e-12   5.7e-09       5     160 ..      26     197 ..      22     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.6e-12
                      Cas_Cas4   5 iqyyliCkrklwlish..eitleensetvel.Gkllhe............esyerek.............kevelsesiki 57 
                                   +  +l C+ kl +  +  ei l+e  + + + G l+h             +     +             ke+++  +++ 
  gi|70606113|ref|YP_254983.1|  26 VTDLLRCPMKLRFETMykEIALSEAFTPATMlGDLVHLglqefiksvypnS-----QievegektipvdgKEIKI--KGRA 99 
                                   556677777777755444777777666554337877777777777554441.....2222334122233355555..9*** PP

                      Cas_Cas4  58 DvvekekeklvvvEvKkskkk....eeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeie 134
                                   D + + +++ v+vE+K+ +++    +e +k+Ql+ Yl+l+      ik+G l y++  + +e +++e  +e   ++i+ +e
  gi|70606113|ref|YP_254983.1| 100 DAIIQINDEKVIVEIKSARADrslpHEHHKYQLQIYLWLFG-----IKRGLLVYITPDRVTEYSVNEPAEEV--TIIRLAE 173
                                   ****9**************9977877889**********86.....7889************9998887774..6999999 PP

                      Cas_Cas4 135 eiissekppkvkkkkiCkkCayaelC 160
                                   e ++ +  p+   +  C+ Ca++ lC
  gi|70606113|ref|YP_254983.1| 174 ETLKAKIAPRY--SWECEYCAFKTLC 197
                                   99999877765..667********** PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   4.3e-11   1.6e-07      37     105 ..      75     148 ..      66     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.3e-11
                      PDDEXK_3  37 krglkveeqvelpvvYkgkevgeeyrlDllv...eekvivElKa...veel.keeheaqllnYlkltklklGlliN 105
                                   + +++ve ++++pv  k+ +++   r+D ++   +ekvivE+K+    ++l +e+h+ ql+ Yl l+++k Gll+ 
  gi|70606113|ref|YP_254983.1|  75 NSQIEVEGEKTIPVDGKEIKIKG--RADAIIqinDEKVIVEIKSaraDRSLpHEHHKYQLQIYLWLFGIKRGLLVY 148
                                   57899*********988888877..9****999999*******943334553567889****************85 PP

>> Chordopox_G2  Chordopoxvirus protein G2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.8e-05      0.14      57     122 ..      36     104 ..      24     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                  Chordopox_G2  57 leckdlleEiale..f.pddilrelvrlrlrkfsktvkrsykLtaeakGialvkdrevavrrandelle 122
                                   l+ +++ +Eial+  f p ++l +lv+l l++f k+v +  +++ e +  + v+++e+++    d++++
  gi|70606113|ref|YP_254983.1|  36 LRFETMYKEIALSeaFtPATMLGDLVHLGLQEFIKSVYPNSQIEVEGEKTIPVDGKEIKIKGRADAIIQ 104
                                   67788999999854473557899************************************9888888776 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.4e-05      0.23      44      65 ..      98     119 ..      84     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                     AHJR-like  44 rpDliarkdeeaviiEvksrrs 65 
                                   r D+i++ ++e+vi+E+ks r 
  gi|70606113|ref|YP_254983.1|  98 RADAIIQINDEKVIVEIKSARA 119
                                   78****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1398.30
//
Query:       gi|70606114|ref|YP_254984.1|  [L=391]
Description: N-acetylglucosaminyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-33  116.3   0.0    2.5e-33  115.9   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    7.6e-27   94.2   0.1    1.1e-26   93.7   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    7.8e-24   84.7   0.4    1.2e-23   84.0   0.4    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    7.6e-13   48.3   0.0    1.9e-12   47.0   0.0    1.6  2  Glyco_transf_21  Glycosyl transferase family 21
      2e-06   27.5   0.4    2.8e-05   23.8   0.4    2.0  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    7.7e-06   26.3   0.0    1.6e-05   25.3   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
     0.0013   17.6   0.1     0.0019   17.0   0.1    1.1  1  GNT-I            GNT-I family
  ------ inclusion threshold ------
       0.24   11.8   0.1       0.24   11.8   0.1    2.0  2  DNA_PPF          DNA polymerase processivity factor


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   1.1e-36   2.5e-33       3     230 .]      42     269 ..      40     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 1.1e-36
               Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqey..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                   ++++lVp+ nee+vlg++l+ l++qey  + +e++vv d+s++ t + ++  ++++++v  r+v  ++   ++gksraln 
  gi|70606114|ref|YP_254984.1|  42 TFSILVPAKNEEKVLGRLLDRLINQEYdkSKYEIIVVEDGSTDRTFQICKNYEENYDNV--RCVKLDKSNVPNGKSRALNY 120
                                   59************************97555*************************885..9*99999999********** PP

               Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg.vltl 160
                                   a++ +k+d++ ++D+Dt    d+l ++   f +++v av+++    + r++ +++   le +  + +    r ++g +++l
  gi|70606114|ref|YP_254984.1| 121 AMKLAKFDIIGVFDADTFPRLDVLSYVSGSFDSDNVVAVQGKLiPINVRESIIARFASLE-ELFNEYSIGGRARFGlFVPL 200
                                   *******************************999******99956677999999999988.44455556677777868*** PP

               Glyco_tranf_2_3 161 nGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                    G+++++  ++ +e +g+ +  +lt+D++l++ l +ag+++ y p ++ +++  ssl  +ikqr Rw++g
  gi|70606114|ref|YP_254984.1| 201 EGTCTFVKKSIIEEMGGWNE-YSLTEDLDLSVKLTSAGYKIMYNPNVVAWREVASSLRWLIKQRLRWYRG 269
                                   ********************.***********************************************86 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   4.7e-30   1.1e-26       1     168 [.      44     214 ..      44     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 4.7e-30
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESS.S-..HHHHHHHHHHHH CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirree.nv..Gkagalnaglra 77 
                                   s+ +p+ Neek l ++l++l++q ++++++eiivv DgStD+t +i++++ +++++vr +++++ nv  Gk++aln +++ 
  gi|70606114|ref|YP_254984.1|  44 SILVPAKNEEKVLGRLLDRLINQeYDKSKYEIIVVEDGSTDRTFQICKNYEENYDNVRCVKLDKsNVpnGKSRALNYAMKL 124
                                   89**************************************************99999999998743355************ PP

                                   --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
               Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                   a+ d+i ++DaD+ p  d l+ + + ++ d++ +v g+   i++ +  i r     e+    + ++ r ++g      g++
  gi|70606114|ref|YP_254984.1| 125 AKFDIIGVFDADTFPRLDVLSYVSGSFDSDNVVAVQGKLIPINVRESIIARFASL-EELFNEYSIGGRARFGLFVPLEGTC 204
                                   ********************************99999999988888888876552.3334444444444555555556666 PP

                                   CEEEEHHHHH CS
               Glycos_transf_2 159 allrrealee 168
                                   + ++++++ee
  gi|70606114|ref|YP_254984.1| 205 TFVKKSIIEE 214
                                   6666666655 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.4   5.5e-27   1.2e-23       1     184 [.     129     327 ..     129     366 .. 0.74

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 5.5e-27
               Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlv.mnvanwleelaalf..faedhgkdilvrealgrvvpsvGsgaf 78 
                                   ii + DaDt +  d+l ++   ++s++v +vqg+ ++ + + ++++++a l+  f+e  +     r+++g +vp+ G ++f
  gi|70606114|ref|YP_254984.1| 129 IIGVFDADTFPRLDVLSYVSGSFDSDNVVAVQGKLIPiNVRESIIARFASLEelFNEYSI---GGRARFGLFVPLEGTCTF 206
                                   68899*******************99********99835779999999999987777544...46889************* PP

               Glyco_trans_2_3  79 lrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....el........ 146
                                   +  s ++e+ggw+  e s++ED+d++++l ++Gy++ + p ++ ++++ ++lr  ++Qr Rw++G      ++        
  gi|70606114|ref|YP_254984.1| 207 VKKSIIEEMGGWN--EYSLTEDLDLSVKLTSAGYKIMYNPNVVAWREVASSLRWLIKQRLRWYRGHfeislSMpkkidpri 285
                                   *************..**************************************************8876551144554455 PP

               Glyco_trans_2_3 147 eklillv.rllgylgsllwsalplhl.allllfslla..lal 184
                                   +  ill+  ++ +l++l+  +l+l + + l++  +++  +a+
  gi|70606114|ref|YP_254984.1| 286 FDGILLIgTPIFMLMNLVNYSLVLIYqTPLFVVTMVIvsTAT 327
                                   444444434445555555444443222222222222221111 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   2.6e+03      23      38 ..      65      80 ..      63      82 .. 0.89
   2 !   47.0   0.0   8.4e-16   1.9e-12      10     173 .]     106     268 ..      97     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
               Glyco_transf_21 23 lqaleaakydllvisD 38
                                  +q +++ ky+++v+ D
  gi|70606114|ref|YP_254984.1| 65 NQEYDKSKYEIIVVED 80
                                  6889*********998 PP

  == domain 2  score: 47.0 bits;  conditional E-value: 8.4e-16
               Glyco_transf_21  10 gdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVts..lpvgsdakglaaaleaaflntla 88 
                                   +++   n K  +l++a++ ak d++ + D+d++ + d L  + +++ +++v  V++  +p    ++++ a+++++   ++ 
  gi|70606114|ref|YP_254984.1| 106 DKSNVPNGKSRALNYAMKLAKFDIIGVFDADTFPRLDVLSYVSGSFDSDNVVAVQGklIP-INVRESIIARFASLEELFNE 185
                                   66777899***********************************************96344.45555777777666653333 PP

               Glyco_transf_21  89 gvlqa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaR 167
                                   + +    +++ +    G +  ++++++e++GG ++  + L eD+ l+  l++aG+k++  p+++a+ +v   sslr l ++
  gi|70606114|ref|YP_254984.1| 186 YSIGGraRFGLFVPLEGTCTFVKKSIIEEMGGWNE--YSLTEDLDLSVKLTSAGYKIMYNPNVVAWREVA--SSLRWLIKQ 262
                                   3332223699*************************..9****************************9996..59******* PP

               Glyco_transf_21 168 qlrWar 173
                                    lrW r
  gi|70606114|ref|YP_254984.1| 263 RLRWYR 268
                                   ****75 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.4   1.2e-08   2.8e-05       4     123 ..      47     168 ..      44     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
               Glyco_tranf_2_2   4 iplraseerhyieerv..lqkakyyd.eeielivvddgSsekfleevssiidlnllvylkdeddk..ayslaaarNrGask 79 
                                   +p +++e+   +  r+  +++++ yd  + e+ivv+dgS++ + +  ++  +   +v   + d+     ++++a N  ++ 
  gi|70606114|ref|YP_254984.1|  47 VPAKNEEK---VLGRLldRLINQEYDkSKYEIIVVEDGSTDRTFQICKNYEENYDNVRCVKLDKSnvPNGKSRALNYAMKL 124
                                   55555444...4555556566667762689********************9998888555554442378899999****** PP

               Glyco_tranf_2_2  80 aesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpv 123
                                   a+ d++   DaD f  +D +  +     + ++  +   ++ + v
  gi|70606114|ref|YP_254984.1| 125 AKFDIIGVFDADTFPRLDVLSYVSGSFDSDNVVAVQGKLIPINV 168
                                   ******************99877665666665555555555544 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   7.1e-09   1.6e-05       1      83 [.      50     138 ..      50     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.1e-09
               Glyco_tranf_2_4   1 rneadiLpeflahhlalgfdr....ilvydndstDgtrailkel.pevkllhvdksyederrq...vellkallaryaead 73 
                                   +ne+++L++ l+ + +  +d+    i+v++++stD+t +i+k++ ++++ ++++k  ++ + +    ++l+ +++  a+ d
  gi|70606114|ref|YP_254984.1|  50 KNEEKVLGRLLDRLINQEYDKskyeIIVVEDGSTDRTFQICKNYeENYDNVRCVKLDKS-NVPngkSRALNYAMKL-AKFD 128
                                   79**********9999999755667******************8566999999986654.3331113466666654.589* PP

               Glyco_tranf_2_4  74 wvlvvDaDEf 83 
                                    + v+DaD f
  gi|70606114|ref|YP_254984.1| 129 IIGVFDADTF 138
                                   ********77 PP

>> GNT-I  GNT-I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   8.5e-07    0.0019      89     176 ..      37     125 ..      29     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.5e-07
                         GNT-I  89 kqakdviavlvlacsradavrrtvekllkyrpsaekfPlivsqdcsneevkkevlsygdkvtyikhldlesiavePde.rk 168
                                   +   +  ++lv a +  +++ r +++l++ +  ++k+ +iv  d+s + + +  ++y ++ + ++ + l++ +v+ ++ r 
  gi|70606114|ref|YP_254984.1|  37 EYSDKTFSILVPAKNEEKVLGRLLDRLINQEYDKSKYEIIVVEDGSTDRTFQICKNYEENYDNVRCVKLDKSNVPNGKsRA 117
                                   556677899****************************************************99998766666666444033 PP

                         GNT-I 169 ltayykia 176
                                   l+   k+a
  gi|70606114|ref|YP_254984.1| 118 LNYAMKLA 125
                                   43334555 PP

>> DNA_PPF  DNA polymerase processivity factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011      0.24       9      74 ..       5      71 ..       2     102 .. 0.76
   2 ?   -2.0   0.7       2.1   4.7e+03      10      46 ..     316     352 ..     311     367 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                  HHHHHHHHH-SSEEE-SE.EE..EEEE-TTSSEEEEEEEEEEE-S-EEESTHHHHHHHHTTS-TT.. CS
                       DNA_PPF  9 lllvlsslinsvgllgak.qvvditnrlnktatyseaemsvvvpadsditdvnqltsilapaknded 74
                                  ++  +s+l++s  ++++  ++ ++t r+n++  ys  + s++vpa  + + +  l + l   ++d++
  gi|70606114|ref|YP_254984.1|  5 IVVFFSILVSSWNIYNSAlSFYGLTWRVNQKIEYSDKTFSILVPAKNEEKVLGRLLDRLINQEYDKS 71
                                  567789999**9***8653899**********************98776655555555555555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                   HHHHHHHH-SSEEE-SEEE..EEEE-TTSSEEEEEEE CS
                       DNA_PPF  10 llvlsslinsvgllgakqvvditnrlnktatyseaem 46 
                                     v  ++++  +ll +   v+i+ +   + +ys  ++
  gi|70606114|ref|YP_254984.1| 316 FVVTMVIVSTATLLSFITAVGISRKHLIEYQYSILSL 352
                                   5567778888889999888888888777777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2350.12
//
Query:       gi|70606115|ref|YP_254985.1|  [L=87]
Description: hypothetical protein Saci_0276 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 635.85
//
Query:       gi|70606116|ref|YP_254986.1|  [L=309]
Description: hypothetical protein Saci_0277 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-08   32.5   0.6    3.6e-06   27.1   0.5    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-06   28.7   0.0    1.6e-06   28.1   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00014   21.4   0.0    0.00026   20.6   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.065   13.5   1.3       0.33   11.2   1.3    2.1  1  DHH            DHH family


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.5     8e-10   3.6e-06       6      57 ..      15      78 ..      11      79 .. 0.87
   2 ?    3.6   0.0     0.013        59     133     163 ..     159     234 ..     114     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8e-10
                                  SEEEEEEETTCEEEES--SCHHHHHHHH............HHHHHTSGGGGEEEEE-SBSSHHH CS
                   Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal............elaalglkpkdvdavilTHlHlDH 57
                                  + ++l+e+++  iLiD+ +s +  r+ l            + ++++ + k  d +i+TH+H+DH
  gi|70606116|ref|YP_254986.1| 15 SQATLVETKDVRILIDPAVSLAPRRFGLpphqievdrlteLAKKIYEEAKIADIIIITHYHYDH 78
                                  679************************************55555555555557778******** PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                                   CCEEEEEETTCCEEEECTTTSSHHCCCCCC.............................................. CS
                   Lactamase_B 133 hghgvveygggkvlftGDallagetgridl.............................................t 163
                                    +++ + +++ ++lft D   a+++ +id+                                              
  gi|70606116|ref|YP_254986.1| 159 VIQVAINDKDSTILFTSDIEGAPKNSHIDFiksvrpnfliidgplsyllgralsqdeldteiknmeevvrnglqyA 234
                                   567899999********************98877777766666666666655555555555555555555555555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.7e-10   1.6e-06       9     127 ..      17     190 ..      13     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.7e-10
                 Lactamase_B_3   9 sflletagarilvDPf....................ka.nlgyeppaeeaDlvlisqaledHahletlkql.......... 58 
                                   + l+et+++ril+DP                     ++  ++ +++a+ aD+++i++ + dH ++  + +l          
  gi|70606116|ref|YP_254986.1|  17 ATLVETKDVRILIDPAvslaprrfglpphqievdrlTElAKKIYEEAKIADIIIITHYHYDHHDPGYVIPLdiyqnktvyi 97 
                                   6799************9999999999999999888733467788888************************9997777776 PP

                 Lactamase_B_3  59 .............aenvkvlee.......geslevggleiravatshdavggsergenngflleq....dgltiyhlGhla 115
                                                 + ++++++        es++ + +++ +++ +  + +++  +e  g+++++    ++ ti++  ++ 
  gi|70606116|ref|YP_254986.1|  98 kdpqnfinpsqkfRRAPRFIKTitgkpktMESADGKVVKYGSTTIQFSKAVPHGADERLGYVIQVaindKDSTILFTSDIE 178
                                   544444444444423333333343342221222222333333333335556666677788888774433377777777777 PP

                 Lactamase_B_3 116 helsseelkelg 127
                                     +++++++ ++
  gi|70606116|ref|YP_254986.1| 179 GAPKNSHIDFIK 190
                                   777766666665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.7e-08   0.00026       2     148 ..      26     182 ..      25     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.7e-08
                                   EEEES--TT..............HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHH CS
                 Lactamase_B_2   2 riLiDagpd..............lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvl 67 
                                   riLiD+  +              +     r+ + ++   +e +  d +++th HyDH  +   + +     l++y +k v+
  gi|70606116|ref|YP_254986.1|  26 RILIDPAVSlaprrfglpphqieV----DRLTELAKkIYEEAKIADIIIITHYHYDHH-DPGYVIP-----LDIYQNKTVY 96 
                                   899999999888887766554321....33332233467888899************9.6666666.....6788888888 PP

                                   HHCCTTCGHHHCHTT..........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE....CTT CS
                 Lactamase_B_2  68 avleanfvylaleee..........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie....ggg 134
                                    +  +nf+   ++            ++ ++ e + g+ ++ g++ +++   +++h++     +     lG++i+    +++
  gi|70606116|ref|YP_254986.1|  97 IKDPQNFINPSQKFRraprfiktitGKPKTMESADGKVVKYGSTTIQFSK-AVPHGAD----E----RLGYVIQvainDKD 168
                                   88888887776666643333334333333333334444444533322222.2333333....3....55555555555999 PP

                                   EEEEEESS-S---H CS
                 Lactamase_B_2 135 krvyyigDtgyipe 148
                                    +++++ D +  p+
  gi|70606116|ref|YP_254986.1| 169 STILFTSDIEGAPK 182
                                   99******998874 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.3   7.3e-05      0.33      25      82 ..     212     271 ..      53     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.3e-05
                                   ECS--TCGGCGCCHHCCCSEEEEEEE-S---S..S---SS--EEEE-SSS-HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  25 lvDhneksqavegeakeeaedviiiDHHrlge..efetlapilflnepvgstaeivaell 82 
                                     D  +++ +  +e+ +++ +  iiDHH l +    + l+p+  + ++vg+ +  + e+l
  gi|70606116|ref|YP_254986.1| 212 SQDELDTEIKNMEEVVRNGLQYAIIDHHVLRDpnYESVLKPVKEVANSVGCKVISASEYL 271
                                   44444444444555679************9984323334455555555555555455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2066.30
//
Query:       gi|70606117|ref|YP_254987.1|  [L=252]
Description: hypothetical protein Saci_0278 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-47  161.8   0.9    2.4e-47  161.6   0.9    1.0  1  VIT1      VIT family
  ------ inclusion threshold ------
      0.044   12.6   0.0       0.29    9.9   0.0    1.9  2  DUF4781   Domain of unknown function (DUF4781)
       0.21   10.3   2.7       0.17   10.6   1.5    1.5  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.9   4.1e-51   2.4e-47       2     214 ..      24     237 ..      23     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 4.1e-51
                          VIT1   2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleedpeege 82 
                                   r  v+G++DGL+ + al+ G s+ s +++ +vl++Gl   +A a+SMg+GeY+s++  ++++++e k+e+ e+e++p e+e
  gi|70606117|ref|YP_254987.1|  24 RTKVFGIQDGLIGVGALISGASGYS-HDPLIVLVTGLLATIAQAFSMGVGEYISTRVRSQIIENEIKKEKFEIENYP-EKE 102
                                   788********************99.6**************************************************.889 PP

                          VIT1  83 aeelaeilearglseelaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliGgliPllpylfve... 160
                                   +eel++ ++++gl+e++a+++a+++++n+  +l+ ml +el++++ ee +sp+k ++ +++  ++Gg+iPl+p+++     
  gi|70606117|ref|YP_254987.1| 103 KEELKSFYMQKGLTESEAEKIANKIMTNKYVVLQEMLIHELKMTP-EEFESPVKLGFLMSFYLIVGGIIPLIPFILGMffs 182
                                   9*********************************99999**9886.5668************************6533343 PP

                          VIT1 161 .svglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaaylig 214
                                        ++v s+av l++l++fG++++++tg+sk ++a++++  G++A + +y+ g
  gi|70606117|ref|YP_254987.1| 183 iPFLYLVVSSMAVILVTLAIFGVLSTKYTGLSKSRGAFEQIGTGLIALIGSYFAG 237
                                   56888888899****************************************9987 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.8e-05      0.29      79     154 ..      20      96 ..      10     129 .. 0.88
   2 ?    0.2   0.2     0.045   2.7e+02     110     134 ..     188     212 ..     172     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.8e-05
                       DUF4781  79 acrlkskilnvlDvvstvvglva.avpvgaaalatPvaapvllaalvvgvgsavYstgRsiqrLvDrstHeesislt 154
                                   a  +++k++ + D +++v+ l++ a + +   l++ v + +++ a + ++g + Y  +R  +++++ ++++e  +++
  gi|70606117|ref|YP_254987.1|  20 ADIFRTKVFGIQDGLIGVGALISgASGYSHDPLIVLVTGLLATIAQAFSMGVGEYISTRVRSQIIENEIKKEKFEIE 96 
                                   555789****************96777766669999********************************999986665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.045
                       DUF4781 110 latPvaapvllaalvvgvgsavYst 134
                                   l++   a++l+++++ gv s+ Y+ 
  gi|70606117|ref|YP_254987.1| 188 LVVSSMAVILVTLAIFGVLSTKYTG 212
                                   5666679999**9********9985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.5   2.9e-05      0.17     335     441 ..      90     210 ..      73     222 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.9e-05
                       DUF2207 335 s.lkeikkyakkskkkakkfkkalkkwksavkkkergyfdkkg.....................kkklkklsalglgliil 393
                                   + + ei+ y +k+k++ k+f+ ++   +s+ +k +++ +++k                       k  + +s+++++++i+
  gi|70606117|ref|YP_254987.1|  90 KeKFEIENYPEKEKEELKSFYMQKGLTESEAEKIANKIMTNKYvvlqemlihelkmtpeefespVKLGFLMSFYLIVGGII 170
                                   245578888888888888888888888888888444444444455555555555443322222222222222222222222 PP

                       DUF2207 394 glilillallllvlllvfllilllillliaiivlllfsrllgrrteeG 441
                                    li ++l         +f++i++l l++ +++v+l+  +++g ++ ++
  gi|70606117|ref|YP_254987.1| 171 PLIPFIL--------GMFFSIPFLYLVVSSMAVILVTLAIFGVLSTKY 210
                                   2222222........455555555555555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1428  (0.0796475); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1691.40
//
Query:       gi|70606118|ref|YP_254988.1|  [L=156]
Description: hypothetical protein Saci_0279 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-28   97.5   0.8    8.3e-28   97.3   0.2    1.4  2  AAA_assoc_C     C-terminal AAA-associated domain
      0.005   16.4   0.0     0.0068   15.9   0.0    1.1  1  Glyco_hydro_80  Glycosyl hydrolase family 80 of chitosanase A


Domain annotation for each model (and alignments):
>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   1.3e+04      17      29 ..       9      21 ..       6      22 .. 0.75
   2 !   97.3   0.2   9.3e-32   8.3e-28       1     119 []      33     149 ..      33     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                   AAA_assoc_C 17 iveaaelLglvev 29
                                   +++a lLgl++v
  gi|70606118|ref|YP_254988.1|  9 DARVADLLGLLSV 21
                                  5678999999876 PP

  == domain 2  score: 97.3 bits;  conditional E-value: 9.3e-32
                   AAA_assoc_C   1 yeLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLderenkrl 81 
                                   y L++ele+++d+L+pi++aa+++g++++ egd ++T++G++f++++ik+rKe++re+l +++p+++a +        kr+
  gi|70606118|ref|YP_254988.1|  33 YVLEKELEVDIDELMPILYAANSMGFINLVEGDTIITDKGIEFIKGNIKRRKELLRESLDRIEPFKTAKDL-------KRF 106
                                   679****************************************************************9987.......9** PP

                   AAA_assoc_C  82 peerfldeLeek.ls...eeeaertletai.eWgrYaelfeyd 119
                                   + e++l+ Leek ++   +++  r+le+++ eWg+Y+++++ d
  gi|70606118|ref|YP_254988.1| 107 KTEDLLKSLEEKgITlysSPSGLRDLEIILtEWGIYSNFLKKD 149
                                   ***********98667779***********9*******99987 PP

>> Glyco_hydro_80  Glycosyl hydrolase family 80 of chitosanase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.6e-07    0.0068     146     194 ..      13      61 ..       8      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-07
                                   HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHTHHHHHHHHHHTT---- CS
                Glyco_hydro_80 146 aaltkicqalqsdfdnrqakyvmshyahidsdkllpvldalkkigftsf 194
                                   a l  + + l   fd + + yv+ +   +d d l+p+l a + +gf ++
  gi|70606118|ref|YP_254988.1|  13 ADLLGLLSVLYNTFDGKADVYVLEKELEVDIDELMPILYAANSMGFINL 61 
                                   556667788999**********************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1025.41
//
Query:       gi|70606119|ref|YP_254989.1|  [L=462]
Description: hypothetical protein Saci_0280 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-60  202.2   0.0    9.6e-60  201.7   0.0    1.2  1  QueC            Queuosine biosynthesis protein QueC
    1.6e-15   57.1   0.0    4.5e-15   55.6   0.0    1.8  1  GATase_7        Glutamine amidotransferase domain
    4.7e-10   39.8   0.0      1e-09   38.7   0.0    1.5  1  GATase_6        Glutamine amidotransferase domain
    2.5e-08   33.8   0.1    1.2e-07   31.5   0.1    2.1  1  ThiI            Thiamine biosynthesis protein (ThiI)
    9.5e-07   27.9   0.0    3.3e-06   26.1   0.0    1.9  2  tRNA_Me_trans   tRNA methyl transferase
     0.0022   17.8   0.0     0.0036   17.1   0.0    1.3  1  ATP_bind_3      PP-loop family
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.023   14.4   0.0    1.2  1  Asn_synthase    Asparagine synthase
      0.055   13.5   0.3       0.21   11.6   0.1    1.9  2  Glyco_transf_4  Glycosyltransferase Family 4
      0.057   13.3   0.0      0.097   12.6   0.0    1.3  1  YjeF_N          YjeF-related protein N-terminus
       0.14   11.9   0.0       0.23   11.2   0.0    1.4  1  TpcC            Conjugative transposon protein TcpC
       0.14   12.5   0.0       0.28   11.5   0.0    1.4  1  TetR_C_25       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.7   0.0   5.9e-63   9.6e-60       2     208 ..     242     451 ..     241     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 201.7 bits;  conditional E-value: 5.9e-63
                                   EEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG------.-- CS
                          QueC   2 avvllSGGlDSttvlalakkegkevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeie.vp 80 
                                   ++v+ SGGlDSt+++++  ++g+ev++l+f+Y+++ ++ke ea++ki++ l+v     +d+dl+k +g+s+L++++   + 
  gi|70606119|ref|YP_254989.1| 242 ILVVASGGLDSTVAATYLVRQGHEVTLLHFNYHHKaEEKEREAVRKISEYLNV-PFVEIDTDLFKIVGHSTLIKGSSGeIV 321
                                   79*********************************99****************.*******************98865555 PP

                                   -..--...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH..HTS--EEE-T CS
                          QueC  81 k..eeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg..edkkieieaP 157
                                   k  +  e +e+ +++VpaRNlif+s+a++ aea+g +ai+ G+n e++ +YPD+++efv+++ +++ ++   +kk+e+ +P
  gi|70606119|ref|YP_254989.1| 322 KdrKGEEGAEFAHEWVPARNLIFFSVALAMAEAYGFDAIASGINLEEAGAYPDNEMEFVRMFSRLVPYAvgPNKKVEVLMP 402
                                   5356667799********************************************************99988889******* PP

                                   TTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHH CS
                          QueC 158 lidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfee 208
                                   + +l K+eivklg ++++pl++t+sCYeg+++  +Cg+C  C +Rk +fe 
  gi|70606119|ref|YP_254989.1| 403 VGNLVKHEIVKLGVQIDAPLHLTWSCYEGGNK--HCGKCGPCYMRKVAFEV 451
                                   *****************************666..***************86 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   2.8e-18   4.5e-15       8     121 ..      91     203 ..      84     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.8e-18
                      GATase_7   8 dseagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea......ewgeealerlnGmfAfai 82 
                                   ++e++ QP+    ++r+v+++nG i N  el+++++ +     ++ D++vl  +l++      + + e+l+ ++G+fA++i
  gi|70606119|ref|YP_254989.1|  91 KTENDIQPFE---GERFVVTHNGIIANDMELEKKYKVS---KLSRIDSSVLPPVLDRswngnlDSLSEILNSIRGSFALVI 165
                                   78999****9...699******************9765...5799***********999999999**************** PP

                      GATase_7  83 wdeeek.rlllaRDrlGikPLyygedk.gdallfaSelkal 121
                                    d+++  r+++a++   +kP+y+++d+  +a++f+S  +++
  gi|70606119|ref|YP_254989.1| 166 GDKKNPdRIFIAQN---FKPVYMMYDRdLGAVFFTSLDDYF 203
                                   **887669******...9********985599999987766 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   6.2e-13     1e-09      27     125 ..      91     188 ..      60     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 6.2e-13
                      GATase_6  27 aeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.eelG......eevlerlrGmfafa 99 
                                   + +e + qPf  e +r++++hNG i n+ el ++++    l+   r D+ vl  +l +++       +e l+++rG fa +
  gi|70606119|ref|YP_254989.1|  91 K-TENDiQPF--EGERFVVTHNGIIANDMELEKKYKV-SKLS---RIDSSVLPPVLdRSWNgnldslSEILNSIRGSFALV 164
                                   2.44557***..********************99999.7777...9********77688888999*9************** PP

                      GATase_6 100 iwdk.rentlilardrlgvkplyyavd 125
                                   i dk  ++++++a    + kp y+ +d
  gi|70606119|ref|YP_254989.1| 165 IGDKkNPDRIFIA---QNFKPVYMMYD 188
                                   ****9*******9...45578888776 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   7.3e-11   1.2e-07       5      59 ..     241     295 ..     238     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.3e-11
                          ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaey 59 
                                   ++l++ SgG+DS Vaa  l++ G +v l+h++ +   +e+++e v+k+ e l+  
  gi|70606119|ref|YP_254989.1| 241 RILVVASGGLDSTVAATYLVRQGHEVTLLHFNYHHKAEEKEREAVRKISEYLNVP 295
                                   678899*************************877888888999999999988754 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     2e-09   3.3e-06       1      69 [.     240     300 ..     240     305 .. 0.84
   2 ?   -2.6   0.0       1.1   1.8e+03     163     180 ..     398     415 ..     393     421 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2e-09
                 tRNA_Me_trans   1 kkvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvd 69 
                                   k+++v  SgG DS+vaa+ l +qg+ev+ ++++ +++++e++         + +++++e l++p+  +d
  gi|70606119|ref|YP_254989.1| 240 KRILVVASGGLDSTVAATYLVRQGHEVTLLHFNYHHKAEEKE--------REAVRKISEYLNVPFVEID 300
                                   5899****************************9998855554........5677888888888887776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                 tRNA_Me_trans 163 kllfPlgeltKeevrkiA 180
                                   ++l+P+g+l K+e+ k+ 
  gi|70606119|ref|YP_254989.1| 398 EVLMPVGNLVKHEIVKLG 415
                                   5789********998775 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.2e-06    0.0036       2      62 ..     242     297 ..     241     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEE CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikle 62 
                                   +lv  SgGlDS++    l+++    g++++++h++++ ++e  +e+e+v+++++ ln++++
  gi|70606119|ref|YP_254989.1| 242 ILVVASGGLDSTVAATYLVRQ----GHEVTLLHFNYHHKAEE-KEREAVRKISEYLNVPFV 297
                                   78899********99999988....569********988765.567889999999998875 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.4e-05     0.023      24      77 ..     246     299 ..     238     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                  Asn_synthase  24 LSGGlDSSliaalaarqsksplktFsigfee.kgsdeakyakevaehlgtehtel 77 
                                    SGGlDS++ a ++ rq + +++  +  +++ ++ +e+++ ++++e+l+++ +e+
  gi|70606119|ref|YP_254989.1| 246 ASGGLDSTVAATYLVRQGH-EVTLLHFNYHHkAEEKEREAVRKISEYLNVPFVEI 299
                                   5****************98.99999999955599**************9986655 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   2.1e+03     143     166 ..      87     111 ..      66     114 .. 0.68
   2 ?   11.6   0.1   0.00013      0.21      12      42 ..     256     287 ..     254     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                Glyco_transf_4 143 atadelreryg.vppekitVipnGv 166
                                   ++++  +   + ++ e+ +V +nG+
  gi|70606119|ref|YP_254989.1|  87 YVRRKTENDIQpFEGERFVVTHNGI 111
                                   4444444433336679999999998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                Glyco_transf_4  12 araLarrGheVtvvtpgddgpleeev.elvvr 42 
                                   a +L r+GheVt++ +++ +++ee++ e v+ 
  gi|70606119|ref|YP_254989.1| 256 ATYLVRQGHEVTLLHFNYHHKAEEKErEAVRK 287
                                   789***********999999999997522222 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.097      22      81 ..     235     291 ..     219     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                        YjeF_N  22 nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkka 81 
                                   ++ ++k++lv++++   G d  +aA +L ++g++Vt+l+++  +k +e+ ++a+++  ++
  gi|70606119|ref|YP_254989.1| 235 KEKNKKRILVVASG---GLDSTVAATYLVRQGHEVTLLHFNYHHKAEEKEREAVRKISEY 291
                                   56678888888876...5799****************99999999888888888776655 PP

>> TpcC  Conjugative transposon protein TcpC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.23      59     113 ..     245     316 ..     199     335 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                          TpcC  59 vekk.edkeysvtyevrye...............qeeeeekkektrylrVpV.tdkggklvivglPtivaip 113
                                   v +   d+++ +ty+vr+                ++e e+  + + yl+Vp+ + + + ++ivg  t+++  
  gi|70606119|ref|YP_254989.1| 245 VASGgLDSTVAATYLVRQGhevtllhfnyhhkaeEKEREAVRKISEYLNVPFvEIDTDLFKIVGHSTLIKGS 316
                                   333334445555555555555555555555555599****************78888889999988877744 PP

>> TetR_C_25  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.28      50     101 ..     251     301 ..     246     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                     TetR_C_25  50 dpkarArylalsslGalllelqlheeedptdlravlreylermvlPalElyt 101
                                   d +  A+yl+ ++   +ll +++h+ + ++  r+++r+++e + +P +E+ t
  gi|70606119|ref|YP_254989.1| 251 DSTVAATYLVRQGHEVTLLHFNYHH-KAEEKEREAVRKISEYLNVPFVEIDT 301
                                   77889*******************9.88888999***************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3179.52
//
Query:       gi|70606120|ref|YP_254990.1|  [L=746]
Description: DEAD/DEAH box helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-23   83.8   0.0      1e-22   80.7   0.0    2.1  2  DEAD        DEAD/DEAH box helicase
    4.7e-21   75.2   0.0    4.2e-18   65.7   0.0    2.6  2  Helicase_C  Helicase conserved C-terminal domain
      2e-11   44.5   0.1    8.6e-11   42.5   0.1    2.2  1  DUF1998     Domain of unknown function (DUF1998)
    6.9e-07   29.4   0.0    1.9e-06   28.0   0.0    1.7  2  ResIII      Type III restriction enzyme, res subunit
    3.8e-05   23.1   0.0    6.8e-05   22.3   0.0    1.3  1  SecA_DEAD   SecA DEAD-like domain
  ------ inclusion threshold ------
       0.19   12.0   0.0       0.41   11.0   0.0    1.6  1  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   3.5e-26     1e-22       2     170 ..      60     220 ..      59     224 .. 0.86
   2 ?    0.2   0.0      0.18   5.5e+02      44     106 ..     271     334 ..     257     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.5e-26
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                   + Q+ea++ i +g++v++   TG+GKT+aflip+l+        +g + ++v Pt++La+++l++++++ +++++++  ++
  gi|70606120|ref|YP_254990.1|  60 KFQEEAYNKISHGNNVMIVSGTGTGKTEAFLIPLLDLA-----LKGERSVLVYPTKALARDQLERVRRLASPLGVEM-GVF 134
                                   68*********************************888.....468899***********************99555.578 PP

                                   TTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH.....HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.....xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  83 ggvaardqlskldng.vdivvgtpgrlddll.....stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                    g++ ++++++l ++ ++i++++p++++  l          +  ++    +V+DE++ +     + +i+ i  +l++ t+ 
  gi|70606120|ref|YP_254990.1| 135 DGDTPEKERKRLYENpPHILITNPDMIHIGLplsyrF----RrlIRTADHFVFDEVHSYDGV-LGSHIRMISDRLRELTD- 209
                                   8899999999995445*********999977765322....233888899***********8.************65544. PP

                                   STTTSEEEEEESSBS CS
                                   xxxxxxxxxxxxxxx RF
                          DEAD 156 gklqrqvivlSATlp 170
                                        +vi  SAT+ 
  gi|70606120|ref|YP_254990.1| 210 ----YHVIGSSATID 220
                                   ....45*******97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                                   TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEEEHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvgtpg 106
                                    k+g k+l  + ++++ae +++ + +f+++ ++ v+ + i+++++ +  + +++g ++ v++tp 
  gi|70606120|ref|YP_254990.1| 271 VKEGYKVLTFVDSQQMAELIAKITARFGEE-NIHVHrAGINKEDRLKVEESIKSGkIKGVIATPT 334
                                   578899999999999999999999999997.3455546677777777777777667999999994 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0     0.003       8.9       6      61 ..      90     149 ..      85     157 .. 0.80
   2 !   65.7   0.0   1.4e-21   4.2e-18       5     109 ..     265     368 ..     261     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.003
                                   HHHHHHHTTTTSEEEEEESSHH....HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                    Helicase_C   6 llellkleeeggkilifvntid....rlekvklllekkgikvavlhgelpqnereeileq 61 
                                   l+ ll+l  +g++++++ +t+     +le+v+ l +  g+++ v++g++p +er++  e+
  gi|70606120|ref|YP_254990.1|  90 LIPLLDLALKGERSVLVYPTKAlardQLERVRRLASPLGVEMGVFDGDTPEKERKRLYEN 149
                                   56677888999*********996555555477776666****************998775 PP

  == domain 2  score: 65.7 bits;  conditional E-value: 1.4e-21
                                   HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                    Helicase_C   5 allellkleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                   +l+++l   +eg+k+l fv +++++e +  ++ ++ + ++ v+ + +++++r+++ e+ ++g+++ +iat  +e Gidi +
  gi|70606120|ref|YP_254990.1| 265 YLTAFL--VKEGYKVLTFVDSQQMAELIAKITARFgEENIHVHRAGINKEDRLKVEESIKSGKIKGVIATPTLELGIDIGD 343
                                   566675..89*************9987666667776788888889************************************ PP

                                   ESEEEESSSSSSHHHHHHHHTTSSS CS
                    Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgR 109
                                   +++Vi+ + p n+t+y qr+GR+gR
  gi|70606120|ref|YP_254990.1| 344 LDVVIMAENPPNYTKYLQRAGRAGR 368
                                   ************************* PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1   2.9e-14   8.6e-11       2      83 .]     631     703 ..     630     703 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.9e-14
                       DUF1998   2 ehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaGCpaC 82 
                                   eh+li+ + ++++ +  dl++ ++            ++iyd+v gG+G+++ +++ lee  +  +++  +cdCe +GCp+C
  gi|70606120|ref|YP_254990.1| 631 EHVLISSARVVAGASMTDLAGISY--------PTGHVVIYDSVVGGSGVSKLLYDRLEEAYDISIDITGKCDCE-DGCPKC 702
                                   79*********************8........4689*************************************8.****** PP

                       DUF1998  83 l 83 
                                   +
  gi|70606120|ref|YP_254990.1| 703 I 703
                                   7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.3e-10   1.9e-06       4     169 ..      58     219 ..      51     221 .. 0.79
   2 ?   -2.6   0.0       1.6   4.9e+03      48      87 ..     270     309 ..     261     333 .. 0.50

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.3e-10
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke 84 
                                   l++ Qeea +++       + ++++i+  TGtGKT   +     l+ kg+  + +++ p+k+l    le++++++s+    
  gi|70606120|ref|YP_254990.1|  58 LYKFQEEAYNKIS------HGNNVMIVSGTGTGKTEAFLIPLLDLALKGE--RSVLVYPTKALARDQLERVRRLASPLGV- 129
                                   6677788877774......7789************987666666666655..9**********************99754. PP

                                   GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTTHHH...HHT-- CS
                        ResIII  85 igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..kswrei...lekfk 158
                                   ++++++gd+ ++  k+  ++  +il+t+ ++++  ++   +++ + l  + d +++DE+H + +   +++r i   l+ + 
  gi|70606120|ref|YP_254990.1| 130 EMGVFDGDTPEKerKRLYENPPHILITNPDMIHIGLPL--SYRFRRLIRTADHFVFDEVHSYDGVlgSHIRMIsdrLRELT 208
                                   7778888877776677788999************9955..666677788899********999865557777744444445 PP

                                   -SEEEEEESS- CS
                        ResIII 159 eavllglTATp 169
                                   ++ ++g +AT+
  gi|70606120|ref|YP_254990.1| 209 DYHVIGSSATI 219
                                   58888888886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                                   H-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEE CS
                        ResIII  48 llkkgkeekflflvprkslleqtleefkkflseayke..igk 87 
                                   l k+g+  k+l +v+++++ e   +  ++f +e+ +   +g 
  gi|70606120|ref|YP_254990.1| 270 LVKEGY--KVLTFVDSQQMAELIAKITARFGEENIHVhrAGI 309
                                   445555..8888888886665555444444444433332222 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.3e-08   6.8e-05      98     166 ..      80     148 ..      46     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.3e-08
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SecA_DEAD  98 kTGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerreaYe 166
                                    TG GKt +  +p++  al+g+   +v     La+ + e ++++ + lG+++gv + ++ ++er++ Ye
  gi|70606120|ref|YP_254990.1|  80 GTGTGKTEAFLIPLLDLALKGERSVLVYPTKALARDQLERVRRLASPLGVEMGVFDGDTPEKERKRLYE 148
                                   59******************************************************************8 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.41       1      62 [.      62     120 ..      62     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                        AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                   q+ea +  ++ ++++++ G GtGKT+     +  l   g    e+ +lv +t+  a+   er+
  gi|70606120|ref|YP_254990.1|  62 QEEAYNkISHGNNVMIVSGTGTGKTEAFLIPLLDLALKG----ERSVLVYPTKALARDQLERV 120
                                   8999987899999************97655544444444....45556666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4906.40
//
Query:       gi|70606121|ref|YP_254991.1|  [L=285]
Description: hypothetical protein Saci_0282 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-44  152.7  25.2    1.5e-44  152.4  25.2    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.42   10.0   0.0       0.42   10.0   0.0    2.2  3  DUF3482   Domain of unknown function (DUF3482)


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4  25.2   1.6e-48   1.5e-44       2     236 .]      11     276 ..      10     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.6e-48
                          TauE   2 llagllaGfvagllGiGggliavPlLlll..lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallG 80 
                                   ll   +aGfv++l+G+Gg++++vP+ +l+  +p ++a+++sl++ +ats ++a a+++ +  ++r+++ l +++ +Ga++G
  gi|70606121|ref|YP_254991.1|  11 LLSSTVAGFVGSLTGLGGATVLVPIYTLFlgIPLPYATGASLISTIATSSGSASAYIKDKITNVRIGMSLEIATTLGAIVG 91 
                                   678899*********************96366***************************9899****************** PP

                          TauE  81 allllllp....sellkllfgvlllllallmllrkkr..........................srakgrerrptaillvli 131
                                   +l+++ +     +++l ++fg+++l +++  l+++k                           +++  + ++ +++l  +i
  gi|70606121|ref|YP_254991.1|  92 SLIANIIYkmhlEDILFIIFGIVILSSVYVQLTKAKDelpknvkpdwttklfklygsyydqalKTE-VEYHAIRWWLGEII 171
                                   *****888444455799****9999999999998877899******99999999998888764222.46667777766677 PP

                          TauE 132 gglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarl 212
                                   ++++Gl+sGllGiG G+l v+ + + ++lplk+++ ts+++i v+++++   y+++g++ + l+++ ++g+l+Gal G+++
  gi|70606121|ref|YP_254991.1| 172 MFVAGLISGLLGIGSGALKVIGMDWAMNLPLKVSTTTSNFMIGVTAATSSSLYWVFGYIEPVLAGVTAIGVLIGALAGTKV 252
                                   666****************************************************************************** PP

                          TauE 213 arrlsertlrrlfallllvlgvkl 236
                                     r+ + ++r +f++ll++lgv +
  gi|70606121|ref|YP_254991.1| 253 LVRIRNSRIRFIFIALLIILGVEM 276
                                   *********************987 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.2   2.9         2   1.8e+04     171     189 ..       8      26 ..       6      30 .. 0.83
   2 ?   10.0   0.0   4.6e-05      0.42     169     190 ..      76      97 ..      71     106 .. 0.86
   3 ?   -1.1   0.2      0.11   9.9e+02     177     189 ..     238     250 ..     233     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: -6.2 bits;  conditional E-value: 2
                       DUF3482 171 ltLGaaaaiGalaGglaat 189
                                   ltL + +++ +++G+l ++
  gi|70606121|ref|YP_254991.1|   8 LTLLLSSTVAGFVGSLTGL 26 
                                   7999999999999998765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 4.6e-05
                       DUF3482 169 gGltLGaaaaiGalaGglaatl 190
                                    G++L +a+++Ga++G+l+a++
  gi|70606121|ref|YP_254991.1|  76 IGMSLEIATTLGAIVGSLIANI 97 
                                   6*****************9987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.11
                       DUF3482 177 aaiGalaGglaat 189
                                   +aiG l+G+la+t
  gi|70606121|ref|YP_254991.1| 238 TAIGVLIGALAGT 250
                                   5666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1948.44
//
Query:       gi|70606122|ref|YP_254992.1|  [L=122]
Description: hypothetical protein Saci_0283 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-27   93.0   8.6    1.1e-26   92.8   8.6    1.0  1  DUF1634      Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
      0.015   13.7   0.4      0.015   13.7   0.4    1.7  2  Mem_trans    Membrane transport protein
      0.086   12.4   0.0      0.086   12.4   0.0    2.1  2  Saf_2TM      SAVED-fused 2TM effector domain
        6.3    6.4  10.2         31    4.2  10.2    1.8  1  Tetraspanin  Tetraspanin family
        8.2    6.6  12.7    4.8e+02    1.0  12.7    2.5  1  SdpI         SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   8.6   3.2e-30   1.1e-26       2     102 .]       8     115 ..       7     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.2e-30
                       DUF1634   2 gklLriGvllsaavvllGlilllvkhgs.......sesenseltslseilegllelkglaiiqlGllvLiatPvlrVvlsl 75 
                                   +++Lr+Gv++s+a+++lG+ill    ++       +++ n++ +s+ ++l+gl +++g ++i++Gl++LiatPv+rV+l l
  gi|70606122|ref|YP_254992.1|   8 SYTLRVGVIISIALIILGFILLAQDPTAlqrlasrHSTFNTSRVSPIQVLQGLNRFDGVDYILFGLIILIATPVIRVILGL 88 
                                   899******************999999777777664489999*************************************** PP

                       DUF1634  76 iaFlkekdilyviitliVLliLllsll 102
                                     F++e+++ly++it+iVLl Ll++++
  gi|70606122|ref|YP_254992.1|  89 AGFIAERNKLYIVITFIVLLDLLIAIF 115
                                   ************************996 PP

>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   4.1e-06     0.015      71     146 ..      15      85 ..       4      97 .. 0.88
   2 ?   -1.2   1.5      0.14   5.1e+02      50      76 ..      91     117 ..      74     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-06
                     Mem_trans  71 klivlillllgallskifkgslewtitlfslstlpNtlvlgipllkalygeygvslmvqvvvlqciiiytlllflf 146
                                   ++i ++l++lg++l    + +   ++++   st+ ++ v +i +l++l + +gv ++++  +   i+i t++++++
  gi|70606122|ref|YP_254992.1|  15 VIISIALIILGFILLA--QDPTALQRLASRHSTFNTSRVSPIQVLQGLNRFDGVDYILFGLI---ILIATPVIRVI 85 
                                   7899999*******88..99999***********************************9988...77777777665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.14
                     Mem_trans  50 fisqnnpyemllrfiladvlvklivli 76 
                                   fi++ n++ ++++fi+++ l ++i++i
  gi|70606122|ref|YP_254992.1|  91 FIAERNKLYIVITFIVLLDLLIAIFII 117
                                   677777777777777777777777666 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.086      63     103 ..       6      46 ..       2      50 .. 0.86
   2 ?   -1.8   2.2      0.58   2.1e+03      29      49 ..      72      92 ..      60     119 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                       Saf_2TM  63 ipeivlaiilvigvllivvGavllilryvneakrqskkkvi 103
                                   +++++l + ++i+++li++G++ll ++    ++  s+  ++
  gi|70606122|ref|YP_254992.1|   6 VMSYTLRVGVIISIALIILGFILLAQDPTALQRLASRHSTF 46 
                                   6778889999*****************99999998887766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.58
                       Saf_2TM 29 gvalllailgtdwalkialkl 49
                                  g  +l+a+++   +l +a  +
  gi|70606122|ref|YP_254992.1| 72 GLIILIATPVIRVILGLAGFI 92
                                  445555555544444444433 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  10.2    0.0086        31      13      95 ..      15     117 ..       5     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0086
                                   XXXXXXXXXXXXXXXX.......................XXX.....................XXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  13 wligivllavGvwlrl.......................khaeaalacllsesaedpailaillivvGvllfllgflGcig 70 
                                   ++i+i+l+++G+ l+                         +   +  +  +  +       i+li++ v+ ++lg++G+i+
  gi|70606122|ref|YP_254992.1|  15 VIISIALIILGFILLAqdptalqrlasrhstfntsrvspIQV-LQGLNRFDGVDYILFG-LIILIATPVIRVILGLAGFIA 93 
                                   677777777775554467777777777777777776654222.1222222222333333.36799999999*******886 PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  71 alkenkcllltfsllllvlfllela 95 
                                     +++  +  tf++ll +l++++++
  gi|70606122|ref|YP_254992.1|  94 -ERNKLYIVITFIVLLDLLIAIFII 117
                                   .566667777888887777776665 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0  12.7      0.13   4.8e+02      34      66 ..      69     121 ..       5     122 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                          SdpI  34 iiaGlilllla....................lgavvlvllvlvlllvivpiiy 66 
                                   i+ Gli+l+++                    + ++++vll l+++++i+p++y
  gi|70606122|ref|YP_254992.1|  69 ILFGLIILIATpvirvilglagfiaernklyIVITFIVLLDLLIAIFIIPLVY 121
                                   56666666666666666667777777998885566677777788888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 828.91
//
Query:       gi|70606123|ref|YP_254993.1|  [L=167]
Description: hypothetical protein Saci_0284 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1241.58
//
Query:       gi|70606124|ref|YP_254994.1|  [L=145]
Description: hypothetical protein Saci_0285 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.2   3.1      0.086   12.8   3.1    1.3  1  Fig1      Ca2+ regulator and membrane fusion protein Fig1
        1.1    9.2   7.1        7.5    6.6   2.2    2.4  2  SecE      SecE/Sec61-gamma subunits of protein translocation 
        1.2    9.3   8.8       0.27   11.4   5.6    1.7  2  Pox_A14   Poxvirus virion envelope protein A14
        2.6    6.7   6.7        3.6    6.2   6.7    1.3  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.1   1.9e-05     0.086      78     150 ..       9      81 ..       2     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                          Fig1  78 hpyllmvaiiLtlllfllllyfplgseipllPfkska.vskvalvlsflllllwlv..galwqhvassaastlvee 150
                                   ++y+l+++ iL+++++++  + p   + + ++ +s+  +  v l++s+++ll++++  ++++    s a++ ++ +
  gi|70606124|ref|YP_254994.1|   9 YSYVLIFSSILIIIGLVFGGFTP---INEQVATPSYDlALPVSLSFSAFILLIIFIfsSIILWGSKSLASNLIIDS 81 
                                   68*****************9999...44566666666589999999999877766522445444455566655555 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0049        22      21      43 ..       4      26 ..       2      33 .. 0.84
   2 ?    6.6   2.2    0.0017       7.5      26      51 ..      53      78 ..      47      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0049
                                  HHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE 21 EllkttvvVlvfvvimglflflv 43
                                  + +++   Vl+f+ i+ +++ ++
  gi|70606124|ref|YP_254994.1|  4 QIVSYYSYVLIFSSILIIIGLVF 26
                                  67889999999999999998775 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                  HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE 26 tvvVlvfvvimglflflvDlvfskli 51
                                  +++ l+++++ +++l++ +++ s+li
  gi|70606124|ref|YP_254994.1| 53 AFILLIIFIFSSIILWGSKSLASNLI 78
                                  56778888999999999888888877 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.6   6.1e-05      0.27       6      65 ..       4      67 ..       1      94 [. 0.79
   2 ?   -2.8   0.0       1.6   7.3e+03      47      47 ..     129     129 ..     110     142 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.1e-05
                       Pox_A14  6 llknyystvliaGiiLLilacifa.fvdfskstst..tdkaw.ralsivsFilgivillglllf 65
                                   + +yys+vli+  iL+i+ ++f  f  +  +  t   d a+  +ls  +Fil i+ + + ++ 
  gi|70606124|ref|YP_254994.1|  4 QIVSYYSYVLIFSSILIIIGLVFGgFTPINEQVATpsYDLALpVSLSFSAFILLIIFIFSSIIL 67
                                  6899******************964777776655522444443479999****99999988774 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                       Pox_A14  47 l 47 
                                   +
  gi|70606124|ref|YP_254994.1| 129 I 129
                                   1 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.7   0.00081       3.6     379     433 ..       8      73 ..       1      87 [. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00081
                       DUF2207 379 klkklsalglgliilglilillallllvll..............lvfllilllillliaiivlllfsrl 433
                                   ++ ++ +++ +lii+gl+++ ++ +                   l+f +++lli++++++i+l+ +++l
  gi|70606124|ref|YP_254994.1|   8 YYSYVLIFSSILIIIGLVFGGFTPIN---EqvatpsydlalpvsLSFSAFILLIIFIFSSIILWGSKSL 73 
                                   34444444444444444444444444...2666**********99999999999999999999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1038.69
//
Query:       gi|70606125|ref|YP_254995.1|  [L=190]
Description: DedA family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-17   62.1   5.6    6.6e-17   62.1   5.6    1.6  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   5.6   3.7e-21   6.6e-17       1     119 [.      23     149 ..      23     150 .. 0.92
   2 ?   -2.6   0.3      0.41   7.4e+03       9      14 ..     171     176 ..     156     186 .. 0.49

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.7e-21
                   SNARE_assoc   1 lPsevllvaaGvlf.....glllgtlvtslgallGaslayllgrylgr....kalrrkllsekrvkalerlverygflall 72 
                                   +Psev++  +G+       +l+lg++v  lg+l+G+++ y+++ +lg     ++++   l +kr+++l+ ++++yg +a++
  gi|70606125|ref|YP_254995.1|  23 IPSEVIMPYTGYYSrtgnmDLFLGIIVGTLGSLVGSIIDYYIAFKLGLpflkRYGKLFRLTSKRLDRLNGWFKKYGNYAVF 103
                                   79999999999999888888999******************99999978887777777889999999************** PP

                   SNARE_assoc  73 llrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                    +r++p + r+l++++aGl+ +++ +F++ tf+G ++w   +a lG+
  gi|70606125|ref|YP_254995.1| 104 GFRFVPEI-RALISFPAGLAAMNIFNFLILTFLGHLIWDSTLAILGY 149
                                   ********.*****************************999999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.41
                   SNARE_assoc   9 aaGvlf 14 
                                    aGv++
  gi|70606125|ref|YP_254995.1| 171 GAGVII 176
                                   222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1279.56
//
Query:       gi|70606126|ref|YP_254996.1|  [L=169]
Description: hypothetical protein Saci_0287 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.0   0.1       0.29   11.0   0.0    2.0  2  DUF1981   Domain of unknown function (DUF1981)


Domain annotation for each model (and alignments):
>> DUF1981  Domain of unknown function (DUF1981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.064   1.2e+03      42      56 ..      15      29 ..       3      32 .. 0.79
   2 ?   11.0   0.0   1.6e-05      0.29      35      80 ..     118     165 ..      84     169 .] 0.62

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.064
                       DUF1981 42 eqliqsraeniksGW 56
                                  +++ + +++ i +GW
  gi|70606126|ref|YP_254996.1| 15 NSIAKFKVQRILQGW 29
                                  678889999999999 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.6e-05
                       DUF1981  35 elvlecveqliqsraeniksGWktifgvltaaa...keeneslvrlafq 80 
                                     + +c+ + i+ + +niksG k i++ +++     + ++e+  ++a +
  gi|70606126|ref|YP_254996.1| 118 LRIKDCCVS-IRVNETNIKSGLKLILNAFRLYYkiiEAQEETALSIAQK 165
                                   344444444.67899*************998663334555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1171.73
//
Query:       gi|70606127|ref|YP_254997.1|  [L=131]
Description: hypothetical protein Saci_0288 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-28   96.9   6.8      2e-13   50.6   0.7    2.1  2  CBS              CBS domain
  ------ inclusion threshold ------
      0.036   14.3   0.5       0.32   11.3   0.1    2.3  3  IF3_N            Translation initiation factor IF-3, N-termin
       0.16   11.5   0.0         10    5.7   0.0    2.0  2  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.7   3.3e-17     2e-13       1      56 [.       3      58 ..       3      59 .. 0.93
   2 !   50.0   0.7   4.9e-17   2.9e-13       1      55 [.      67     121 ..      67     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3.3e-17
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                  V+++ +r++vtv+  t++++a + mr++gv++l +Vd+d ++vGivt+rD++ a++
  gi|70606127|ref|YP_254997.1|  3 VSQLVSRKPVTVDLKTSIKDATKVMRREGVGSLVIVDNDFRPVGIVTERDIVYAIA 58
                                  7999*****************************7798888***********99885 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 4.9e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   +++im+rd+v+++  ++++ea+ lm+++g+++l V++++g+ +G+++ rD+++a+
  gi|70606127|ref|YP_254997.1|  67 ISEIMSRDPVSINGGSDVSEAVALMTSRGIRHLVVINNEGRTIGVISVRDVVKAV 121
                                   589**********************9999****667*9**************986 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   8.9e+02      23      45 ..      18      41 ..       6      48 .. 0.78
   2 ?   -0.5   0.0      0.26   1.5e+03      12      30 ..      37      55 ..      31      64 .. 0.71
   3 ?   11.3   0.1   5.3e-05      0.32       8      39 ..      97     128 ..      85     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                                  EEHHHHHHHHHHHTS.EEEEEESS CS
                         IF3_N 23 istreAlrlaeekgl.dLVevspn 45
                                   s+++A + ++++g+  LV v+++
  gi|70606127|ref|YP_254997.1| 18 TSIKDATKVMRREGVgSLVIVDND 41
                                  588999999999987457777655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
                                  EE-SSS-EEEEEEHHHHHH CS
                         IF3_N 12 lvdedGeqlGvistreAlr 30
                                  +vd+d   +G+++ r+++ 
  gi|70606127|ref|YP_254997.1| 37 IVDNDFRPVGIVTERDIVY 55
                                  5666667889999888764 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.3e-05
                                   SEEEEE-SSS-EEEEEEHHHHHHHHHHHTSEE CS
                         IF3_N   8 revrlvdedGeqlGvistreAlrlaeekgldL 39 
                                   r+  +++++G  +Gvis+r++++      ldL
  gi|70606127|ref|YP_254997.1|  97 RHLVVINNEGRTIGVISVRDVVKAVGAIALDL 128
                                   67889*****************9998888888 PP

>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0052        31      59      93 ..      15      49 ..      10      76 .. 0.82
   2 ?    5.7   0.0    0.0018        10      61      93 ..      81     113 ..      76     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0052
                                  TTTTHHHHHHHHHHHH-.EEEEEE--TTTTTHHHH CS
               GTP_cyclohydro2 59 dcgeqldealeliaeegrGvlvylrqegrgiglln 93
                                  d + ++++a + +++eg G lv +++  r +g++ 
  gi|70606127|ref|YP_254997.1| 15 DLKTSIKDATKVMRREGVGSLVIVDNDFRPVGIVT 49
                                  56778899*****99*********99999888875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0018
                                   TTHHHHHHHHHHHH-.EEEEEE--TTTTTHHHH CS
               GTP_cyclohydro2  61 geqldealeliaeegrGvlvylrqegrgiglln 93 
                                   g+ ++ea++l++++g   lv +++egr ig+++
  gi|70606127|ref|YP_254997.1|  81 GSDVSEAVALMTSRGIRHLVVINNEGRTIGVIS 113
                                   677899*****8799999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 839.57
//
Query:       gi|70606128|ref|YP_254998.1|  [L=341]
Description: hypothetical protein Saci_0289 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-11   43.5   0.3    6.6e-11   42.6   0.3    1.5  1  ATPase_2  ATPase domain predominantly from Archaea
    1.2e-10   41.5   0.1    4.9e-10   39.6   0.1    1.9  1  AAA_14    AAA domain
    2.7e-07   30.9   0.0    6.8e-07   29.6   0.0    1.7  1  AAA_22    AAA domain
      4e-06   27.3   0.0    7.9e-06   26.3   0.0    1.6  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.012   15.9   0.2      0.097   13.0   0.2    2.2  1  AAA_19    AAA domain
      0.017   14.5   0.5       0.34   10.3   0.5    2.2  1  TniB      Bacterial TniB protein
      0.073   12.5   0.0       0.19   11.2   0.0    1.6  2  PhoH      PhoH-like protein
       0.14   12.6   0.0       0.34   11.4   0.0    1.7  1  RuvA_C    RuvA, C-terminal domain
       0.15   12.4   0.0       0.46   10.9   0.0    1.8  2  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.3   3.3e-14   6.6e-11       1     221 [.      27     224 ..      27     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 3.3e-14
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81 
                                   Ffd e+ l+e+e++++  +  +++  Gp++ GKt++lk ++++l     + iy++a + +si+++ e + e++++ +l+  
  gi|70606128|ref|YP_254998.1|  27 FFDSEEILNEVEKLVQG-KFWPLL-IGPKRTGKTSILKIVANEL-----NGIYVDATNIRSIKQFGEELIESSVSLRLSLD 100
                                   9**************99.455555.5****************99.....67*****9999999998885555555444444 PP

                      ATPase_2  82 lgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvvi 162
                                   l  +v + e+       +k   k + +ll+k+  k    ii++De+q+++            ++l+l+ + ++e ++++v+
  gi|70606128|ref|YP_254998.1| 101 L--KVLRIEI-------QKTPLKGVRSLLKKLDHK----IILVDEVQNVV----S------PWFLTLLSNVYNESEIRFVF 158
                                   3..5555555.......455568888888888888....99*********....3......5899999999999******* PP

                      ATPase_2 163 clsSeglfie.....rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfeeiyr 221
                                    +s  gl+       +   +s l+g+    i++ ++  e  + flk g++   ++ls++++ee + 
  gi|70606128|ref|YP_254998.1| 159 TGSMIGLSKAlsgegKGKVSSVLKGKPILsIEIYPFSEELGRRFLKIGSERCgIKLSEDEIEESVT 224
                                   ***99999885554555668999***9999**********************999**999987554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.1   2.4e-13   4.9e-10       6     126 ..      48     195 ..      46     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.4e-13
                        AAA_14   6 vitGaRrvGKTtllkqlikell...vkkesilyinldderd...............kkladpekllelileklke...... 62 
                                   ++ G++r+GKT +lk +++el    v++ +i  i+   e++                +++ +            +      
  gi|70606128|ref|YP_254998.1|  48 LLIGPKRTGKTSILKIVANELNgiyVDATNIRSIKQFGEELiessvslrlsldlkvLRIEIQ------------Ktplkgv 116
                                   589***********999988878887777777776555555344444333333222111111............1223334 PP

                        AAA_14  63 ......ekktylflDEiqev..pewekalkslvdegknldvivtGSnskllskeiatslagrva.........eielypls 126
                                          ++++++ DE+q+v  p + + l ++++e+ ++++++tGS  +l  k ++ +  g+v+         +ie+yp+s
  gi|70606128|ref|YP_254998.1| 117 rsllkkLDHKIILVDEVQNVvsPWFLTLLSNVYNES-EIRFVFTGSMIGLS-KALSGEGKGKVSsvlkgkpilSIEIYPFS 195
                                   44554478999********95444666666677766.*********98776.55777777777766666666788888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.4e-10   6.8e-07       9     135 ..      48     167 ..      44     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.4e-10
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrar 89 
                                   +++G++ tGKT  l+ ++++l             ++v++++  s k++ +el +   + + +  l+++ l+  +++   + 
  gi|70606128|ref|YP_254998.1|  48 LLIGPKRTGKTSILKIVANEL-----------NGIYVDATNIRSIKQFGEELIESSVSLRLS--LDLKVLRIEIQKTPLKG 115
                                   69*****************99...........679*************88888888877777..55555554444443333 PP

                        AAA_22  90 av.......ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                    +       ++++++DE+q++ s+  l+ L++ +n  ++ +++++ G   +l k
  gi|70606128|ref|YP_254998.1| 116 VRsllkkldHKIILVDEVQNVVSPWFLTLLSNVYN--ESEIRFVFTGSMiGLSK 167
                                   3335555555**********6599999999999**..**********8777766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     4e-09   7.9e-06       2      72 ..      48     138 ..      47     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4e-09
                                   EEESSTTSSHHHHHHHHHHHHT........HEEEEEETTTCSSS....................STTHHHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavakelg........vefleisgsellsk....................yvgesekkirelfkeak 54 
                                   ll+Gp+ tGKT++ k va+el+        ++ ++  g     +                    +++   k +r l+k++ 
  gi|70606128|ref|YP_254998.1|  48 LLIGPKRTGKTSILKIVANELNgiyvdatnIRSIKQFGE----EliessvslrlsldlkvlrieIQKTPLKGVRSLLKKL- 123
                                   89******************9543322211333333333....1333467777777777776657777777777777654. PP

                                   HTSTSEEEEEETGGGHHH CS
                           AAA  55 ekakpsilfiDEidalak 72 
                                       ++i+++DE+ ++++
  gi|70606128|ref|YP_254998.1| 124 --D-HKIILVDEVQNVVS 138
                                   ..4.68*******98865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   4.9e-05     0.097      16     133 ..      50     157 ..      37     161 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                        AAA_19  16 taGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllt.ealelle.ea 94 
                                   +++  tGKT +lk + ++l        + i++ a + r+ k+  e+l     e +   rl+ ld++ l    + + l+  +
  gi|70606128|ref|YP_254998.1|  50 IGPKRTGKTSILKIVANEL--------NGIYVDATNIRSIKQFGEEL----IESSVSLRLS-LDLKVLRIeIQKTPLKgVR 117
                                   5555566666666554443........34455566667777777666....2222222222.2222221101122233333 PP

                        AAA_19  95 eeekklqeeellivDEfqdvd.elqyrLlkallgek.kkll 133
                                   +  kkl ++++++vDE+q+v  +   +Ll+++++e+  +++
  gi|70606128|ref|YP_254998.1| 118 SLLKKL-DHKIILVDEVQNVVsPWFLTLLSNVYNESeIRFV 157
                                   445677.899*********999**********977633344 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00017      0.34     107     161 ..     112     160 ..      29     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                          TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvG 161
                                     + v +ll++l+ +++++DE++n++         fl +l +  ne +i +v  G
  gi|70606128|ref|YP_254998.1| 112 PLKGVRSLLKKLDHKIILVDEVQNVV------SPWFLTLLSNVYNESEIRFVFTG 160
                                   3456889*****************99......56777777777777777777776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   3.4e+03      24      35 ..      49      60 ..      38      68 .. 0.79
   2 ?   11.2   0.0   9.3e-05      0.19     108     176 ..     111     182 ..      98     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                  EE--TTSSTTHH CS
                          PhoH 24 aiGpaGtGKtyl 35
                                   iGp  tGKt +
  gi|70606128|ref|YP_254998.1| 49 LIGPKRTGKTSI 60
                                  689999***987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.3e-05
                                   EEGGGGTT..--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-..EEEEEE--------.------THHHHHHTT CS
                          PhoH 108 aplaymRG..rTlndafvilDEAQnttkeqmkmfltRlGens..kvvvtGdvtqidlp.kgkksGlaealevlk 176
                                   +pl+ +R   + l+++++++DE Qn+ +    ++l+ + ++s  ++v+tG++       +g+ +G  ++ +vlk
  gi|70606128|ref|YP_254998.1| 111 TPLKGVRSllKKLDHKIILVDEVQNVVSPWFLTLLSNVYNESeiRFVFTGSMIGLSKAlSGEGKG--KVSSVLK 182
                                   5555555444679***********************99877744789999987777663334444..4444444 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.34      12      32 ..     241     264 ..     240     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                   HCTS-HHHHHHHHHHHHC...-TT CS
                        RuvA_C  12 aLGYkekeaekAvakvla...npg 32 
                                   +LGY+ + a+ +v+kv++   +++
  gi|70606128|ref|YP_254998.1| 241 NLGYSHNKAKDMVKKVAEgviKEE 264
                                   8***************88665444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.46      28      84 ..      48      91 ..      30     145 .. 0.69
   2 ?   -2.2   0.0       2.4   4.7e+03      84     100 ..     263     279 ..     220     323 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                        AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrq 84
                                  ll+G++ +GK+s+++ ++++l+   gi++ +++ ++         ++++  eel++ 
  gi|70606128|ref|YP_254998.1| 48 LLIGPKRTGKTSILKIVANELN---GIYVDATNIRS---------IKQF-GEELIES 91
                                  79***************99888...33444444444.........4555.3355554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.4
                        AAA_16  84 qlldeaesaeleawrek 100
                                   ++l ++++++++  r  
  gi|70606128|ref|YP_254998.1| 263 EELGRLSDTQRAILRSL 279
                                   44444333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2517.99
//
Query:       gi|70606129|ref|YP_254999.1|  [L=243]
Description: electron transfer flavoprotein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-34  117.5   0.2    8.3e-34  117.1   0.2    1.1  1  ETF              Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.074   13.6   2.3        3.5    8.3   0.3    3.7  2  POTRA            Surface antigen variable number repeat
       0.15   10.5   0.1       0.24    9.9   0.1    1.2  1  Nucleoporin_FG2  Nucleoporin FG repeated region
       0.15   11.8   0.0       0.39   10.5   0.0    1.6  1  DUF3104          Protein of unknown function (DUF3104)


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.2   1.8e-37   8.3e-34       8     180 ..      26     198 ..      20     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.8e-37
                                   C.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC CS
                           ETF   8 gvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalikke 88 
                                   +v++k++ +d++a+e+A r+kek+gg+ +++++G+    +a+reala mG+d+vi +d  +    d + ta+++a+ +k++
  gi|70606129|ref|YP_254999.1|  26 NVPAKISTYDKSAIEEAIRIKEKHGGKAIGITAGN-TDRKAIREALA-MGLDEVIAIDMKEQ---DIYSTANMIADQLKQL 101
                                   4799*******************************.666779*****.*********99987...79999*********** PP

                                   --SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTSS--... CS
                           ETF  89 dpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpgafep... 163
                                   +pdlv+  + ++    + +++ lA lLg+pli++v ++++eg+k++++R + +   + e+vea+lp v++v  +++ p   
  gi|70606129|ref|YP_254999.1| 102 NPDLVIGSEATTdSsgGIFPAYLAGLLGLPLISYVKSITIEGKKIRAERNLIS--ST-EIVEAELPLVISVVGEINTPrip 179
                                   ********99995598999999*******************999*********..88.*********************** PP

                                   ..--S-TT---EEEE--HH CS
                           ETF 164 ..aaimaakkkeveeveva 180
                                     ++i ++ kk+v++v++ 
  gi|70606129|ref|YP_254999.1| 180 tvKQILESSKKPVKSVNAN 198
                                   ***************9985 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.096   4.3e+02      23      39 ..      80      96 ..      15     101 .. 0.64
   2 ?    8.3   0.3   0.00078       3.5       2      53 ..     135     242 ..     134     243 .] 0.60

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.096
                                  TSSSTTSBHCHHHHHHH CS
                         POTRA 23 lelkegdvynpeklead 39
                                  + +ke d+y+++++ ad
  gi|70606129|ref|YP_254999.1| 80 IDMKEQDIYSTANMIAD 96
                                  13377777777766555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00078
                                   EEEEEEEES........SSS-HHHHHTTTSS.................................................S CS
                         POTRA   2 kikkinfeG.......nkktkdeelrrelel.................................................k 26 
                                   ++k+i++eG       n   ++e +++el+l                                                 +
  gi|70606129|ref|YP_254999.1| 135 YVKSITIEGkkiraerNLISSTEIVEAELPLvisvvgeintpriptvkqilesskkpvksvnanvkplvklasvspyviqR 215
                                   688888888555555554555555666666556656655555555555555555444444444444444444444444433 PP

                                   TTSBHCHHHHHHHHHHHHHHHHCTT-E CS
                         POTRA  27 egdvynpekleadkealksryanlGyf 53 
                                   +  + + +k+e+++++l s+++++G++
  gi|70606129|ref|YP_254999.1| 216 KKIIIDGSKMEEAVDKLLSYLRQEGVI 242
                                   447889999999999999999999986 PP

>> Nucleoporin_FG2  Nucleoporin FG repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   5.4e-05      0.24     270     315 ..     184     229 ..     176     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.4e-05
               Nucleoporin_FG2 270 isrmsskailkvqddikalkqllsvaasGlqrnslaidklkletaq 315
                                   i   s k +  v+ ++k l +l sv+   +qr+ + id  k+e a 
  gi|70606129|ref|YP_254999.1| 184 ILESSKKPVKSVNANVKPLVKLASVSPYVIQRKKIIIDGSKMEEAV 229
                                   55567889999*******************************9885 PP

>> DUF3104  Protein of unknown function (DUF3104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.7e-05      0.39      30      63 ..     165     198 ..     159     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.7e-05
                       DUF3104  30 liihvvggardPsiptLFqvadiDtGvvkvvnAD 63 
                                   l+i+vvg    P+ipt+ q+ +     vk vnA 
  gi|70606129|ref|YP_254999.1| 165 LVISVVGEINTPRIPTVKQILESSKKPVKSVNAN 198
                                   69******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1678.68
//
Query:       gi|70606130|ref|YP_255000.1|  [L=281]
Description: electron transfer flavoprotein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-32  111.6   0.3    1.8e-31  108.0   0.1    2.4  2  ETF_alpha       Electron transfer flavoprotein FAD-binding do
    1.1e-12   48.2   0.1    1.7e-12   47.6   0.1    1.3  1  ETF             Electron transfer flavoprotein domain
     0.0037   17.8   0.2      0.073   13.6   0.0    2.6  2  Usp             Universal stress protein family
  ------ inclusion threshold ------
      0.015   14.1   0.0      0.024   13.4   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
        0.1   12.2   0.0       0.19   11.4   0.0    1.4  1  DUF2244         Integral membrane protein (DUF2244)


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.12   4.4e+02       5      19 ..      96     111 ..      92     133 .. 0.76
   2 !  108.0   0.1     5e-35   1.8e-31       1      84 []     157     241 ..     157     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                                   T-S-EEEE-GGGSS.G CS
                     ETF_alpha   5 eakvvvsgGrGlks.k 19 
                                   +ak+vv  G+G+++ +
  gi|70606130|ref|YP_255000.1|  96 KAKRVVYSGMGIAElE 111
                                   7999*******98733 PP

  == domain 2  score: 108.0 bits;  conditional E-value: 5e-35
                                   .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTT.TSS-CCCB-SSSS-----S-EEEES----HHHHGG CS
                     ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvda.gwipeerqvGqtGktvaPklyiavGisGaiqhlaG 80 
                                   vdL++a+++vs+GrG++sken++ ++ela+a+g+a+g sR+++ + gw+pe+rq+G +G +v+Pk+y+a+GisG+ qhlaG
  gi|70606130|ref|YP_255000.1| 157 VDLSSAQIIVSVGRGIGSKENIKFADELARAIGGALGGSRPITADlGWLPEDRQIGLSGLKVKPKVYFALGISGQPQHLAG 237
                                   69***************************************99887*********************************** PP

                                   GTT- CS
                     ETF_alpha  81 mkes 84 
                                   +k+s
  gi|70606130|ref|YP_255000.1| 238 IKDS 241
                                   **97 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   4.8e-16   1.7e-12      79     175 ..      48     138 ..      23     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 4.8e-16
                                   HHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TT CS
                           ETF  79 kalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpg 159
                                   +a+a+ +++++pdl ++g+t  +k v++  A lL++p++ dv+e+  +    +++R +++g g+ae +  ++p v+++ ++
  gi|70606130|ref|YP_255000.1|  48 EAIAKYLASLKPDLLITGSTKRDKVVGAYAAGLLKYPILPDVIEISGN----KAKRVVYSGMGIAELEF-NTPIVVSISKK 123
                                   68999999***************************************9....8***********88766.5********** PP

                                   SS----S-TT---EEE CS
                           ETF 160 afepaaimaakkkeve 175
                                    +e+++ ++++kk+v+
  gi|70606130|ref|YP_255000.1| 124 NVEAKE-RQTQKKNVN 138
                                   ****76.555777665 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     2e-05     0.073      81     117 ..      36      72 ..       9      83 .. 0.89
   2 ?    1.2   0.2      0.14   4.9e+02      57      92 ..     127     157 ..     111     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                   EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTT CS
                           Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsgl 117
                                   + e++v+++   e+i+++  ++++dl+++Gs++r+++
  gi|70606130|ref|YP_255000.1|  36 ADELHVVDKMDEEAIAKYLASLKPDLLITGSTKRDKV 72 
                                   5689*****************************9876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHH CS
                           Usp  57 eeleleeaeleadaakaaaeaggvkvevvveegdpa 92 
                                   + + +++++     +  ++e++++k ev++++g++ 
  gi|70606130|ref|YP_255000.1| 127 AKERQTQKK-----NVNLEEGKVKKIEVKQKGGEGV 157
                                   222222222.....4467889999999999988875 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.8e-06     0.024     303     353 ..      18      69 ..      12      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-06
                                   ESSS-HHHHHHHHHHS.TT..SEEEES.CHHHHHHHHHHHT-SEEEE-CCHH CS
                Oxidored_nitro 303 tetahrddeerlkaeleeg.epeviddadleeleelikelkpdlllggsker 353
                                   +++++++  +    + + + e +v+d+ d+e +++++  lkpdll++gs +r
  gi|70606130|ref|YP_255000.1|  18 SYFPNEKIVAVSTSDTKYAdELHVVDKMDEEAIAKYLASLKPDLLITGSTKR 69 
                                   55555555533333344445569*************************9876 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.4e-05      0.19      74     139 .]     126     188 ..     115     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                       DUF2244  74 tvervsprgrerewefnpywvrveleedeeege.rltLssrgrevevGrfLspeeRaelakeLrraL 139
                                   + +    ++++++  +n    +v+  e +++g   + Lss +  v vGr ++ +e  ++a+eL ra+
  gi|70606130|ref|YP_255000.1| 126 EAK----ERQTQKKNVNLEEGKVKKIEVKQKGGeGVDLSSAQIIVSVGRGIGSKENIKFADELARAI 188
                                   333....3445555555555555555555555559*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1952.57
//
Query:       gi|70606131|ref|YP_255001.1|  [L=407]
Description: dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-15   55.0   1.3    9.2e-07   28.8   1.0    2.1  2  DAO             FAD dependent oxidoreductase
    1.3e-13   51.1   0.0    2.1e-13   50.4   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    9.1e-12   44.8   0.6    1.5e-11   44.1   0.6    1.3  1  FAD_binding_2   FAD binding domain
    1.4e-09   37.2   0.4    3.8e-09   35.7   0.1    1.8  2  HI0933_like     HI0933-like protein
    5.8e-08   32.3   0.4    9.4e-06   25.1   0.5    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      7e-08   32.1   0.0    1.1e-07   31.5   0.0    1.3  1  FAD_binding_3   FAD binding domain
    4.3e-07   30.1   2.5    8.4e-06   25.9   1.6    2.9  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.6e-06   27.2   1.5    0.00024   20.1   0.0    2.9  3  Trp_halogenase  Tryptophan halogenase
    3.9e-06   26.4   2.3     0.0049   16.2   1.8    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-06   25.4   0.8    1.8e-05   24.1   0.8    1.6  1  Thi4            Thi4 family
    2.6e-05   23.5   1.0    5.4e-05   22.5   1.0    1.5  1  GIDA            Glucose inhibited division protein A
    3.8e-05   22.9   1.2    0.00039   19.6   1.2    2.0  1  Lycopene_cycl   Lycopene cyclase protein
     0.0028   18.2   3.2      0.021   15.4   1.4    3.0  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0072   15.6   0.8      0.017   14.4   0.3    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   1.0   7.2e-10   9.2e-07       1      47 [.       6      52 ..       6      95 .. 0.74
   2 !   24.6   0.0   1.3e-08   1.7e-05     146     348 ..     104     307 ..      96     309 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.2e-10
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsg 47
                                  dv+++GGG  Gls+A  +a++g  V++le+g + + ga   ++g  + +
  gi|70606131|ref|YP_255001.1|  6 DVIVVGGGLGGLSAAITAAKEGlsVIVLERG-DYS-GAKNVSGGRMYIH 52
                                  9******************************.888.9999999866443 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.3e-08
                                   HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHHHTT..CTT..TSEEEE CS
                           DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdllgll..kel..dlpisp 219
                                   ak+ ++la++ae+lGv i + t vt+ ++e g+  ++  +t+ g+    +a  v+ a G+ s  ++ l  +++  d + + 
  gi|70606131|ref|YP_255001.1| 104 AKFDRWLASEAENLGVLISYSTLVTNAQRETGG-INL--ETNrGN---LRAplVIDASGVTSVVFRYLglRKFtpD-KWML 177
                                   68999*********************9876433.555..566586...44445******99864444433333433.3344 PP

                                   EEEEEEEE.EECCTHSTGSG.CSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG CS
                           DAO 220 vrgqvlvl.kplseklvspa.ailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPq 298
                                      +++ +  +l+e + + +  +++v  +   g+g +v+  k +++ vG       ++d+++ +e  + +l ea r+ +  
  gi|70606131|ref|YP_255001.1| 178 GAKEIIKTdVNLPEDEGEVRtIVAAV--KGVKGGG-FVYTNK-DTLSVGMA----VTFDSLPKSEVPAKDLVEAFREKLGI 250
                                   55566666233333222222133333..5555555.777776.66999986....58889788888889999999999988 PP

                                   GCGEE...E...EEEEEEEE.T..TS.SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHH CS
                           DAO 299 lgdvl...r...kwaGlrpl.p..dg.lpligetpgvkglylatGhsghGltlapatGkl 348
                                    g++l        + G+r l p  d+ l  +g    + g++++ G+  +G+ la+++G +
  gi|70606131|ref|YP_255001.1| 251 EGEILeysAhaiPYFGYRNLpPlyDNnLIAVGD---SAGFLINDGFTIRGMDLAIGSGMI 307
                                   777663321345777888853244552555555...68*******************986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   1.7e-16   2.1e-13       1     147 [.       6     159 ..       6     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.7e-16
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee............qvvtgiareflerlrq 69 
                                   Dv+VvGGg++G+ AAi+Aa++G +v+++e+ ++ G    sg+++ +   +  +            + +t+   ef+  +++
  gi|70606131|ref|YP_255001.1|   6 DVIVVGGGLGGLSAAITAAKEGLSVIVLERGDYSGAKNVSGGRMYIHALQ--KlipdalerapleRPITKETFEFYCSNDR 84 
                                   9*******************************999999999999988844..22345666676664444444455555544 PP

                  FAD_oxidored  70 rggarlkkrskwntfepevakavleeml....aeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgdG 146
                                   + + + +++ k      ++++a ++ +l    ++ gv + + t ++++++e     ++++e+  +r ++rA+++iDA+g  
  gi|70606131|ref|YP_255001.1|  85 KLSFSFEEKGK--KNSYSILRAKFDRWLaseaENLGVLISYSTLVTNAQRE---TGGINLET--NRGNLRAPLVIDASGVT 158
                                   22223333333..3678999999*****98533345555566666777776...57999987..489***********966 PP

                  FAD_oxidored 147 d 147
                                    
  gi|70606131|ref|YP_255001.1| 159 S 159
                                   5 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.6   1.1e-14   1.5e-11       1      48 [.       6      52 ..       6      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.1e-14
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-T CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidav 48
                                  DviV+G+Gl+GL+AA++aa++Gl+v+v+e +++ +ga   s+G + + 
  gi|70606131|ref|YP_255001.1|  6 DVIVVGGGLGGLSAAITAAKEGLSVIVLERGDY-SGAKNVSGGRMYIH 52
                                  9*******************************9.99999999988665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1     3e-12   3.8e-09       2     167 ..       6     160 ..       5     162 .. 0.85
   2 ?   -2.8   0.0       1.5   1.9e+03     101     126 ..     370     395 ..     366     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3e-12
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES...STTTTHHHHHHS-HHHH CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGrcNvTnlseepeellsrypenpkflksalsrftnedl 82 
                                   dviv+GgG  Gl aAi+aak+g +V++le+++  g K  +sG Gr+ +  l++ +++ l+r p ++   k+ ++ + ++d 
  gi|70606131|ref|YP_255001.1|   6 DVIVVGGGLGGLSAAITAAKEGLSVIVLERGDYSGAK-NVSG-GRMYIHALQKLIPDALERAPLERPITKETFEFYCSND- 83 
                                   8************************************.5665.8****99999999999998888888888888887766. PP

                                   HHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like  83 ialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                         +++ +  e++g+    s   ++  + l +e+++ gv + ++t v+++++e++g ++++t ++++l+a  ++ A+G
  gi|70606131|ref|YP_255001.1|  84 ------RKLSFSFEEKGKKNSYSILRAKFDRWLASEAENLGVLISYSTLVTNAQRETGG-INLET-NRGNLRAPLVIDASG 156
                                   ......44445555555555555556778899*********************998888.9****.9**********9*99 PP

                                   -SS- CS
                   HI0933_like 164 GlSi 167
                                    +S+
  gi|70606131|ref|YP_255001.1| 157 VTSV 160
                                   9886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                                   EEETT.-CHHHHHHHHHHHHHHT-EE CS
                   HI0933_like 101 lFpvsdkaedivdallkelkeagvkl 126
                                   +F+v+++ ++++++ l++lke++++l
  gi|70606131|ref|YP_255001.1| 370 MFTVTEERKPLMEVALQRLKEKDISL 395
                                   9999999*************999987 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.5   7.3e-09   9.4e-06       2      38 ..       6      47 ..       5      99 .. 0.70
   2 ?    4.8   0.0     0.011        14     182     238 ..     103     158 ..      91     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 7.3e-09
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclng 38
                                  dv+v+GgG +Gl+aa+t+a+ g+ v+++e       +++ +g
  gi|70606131|ref|YP_255001.1|  6 DVIVVGGGLGGLSAAITAAKEGLSVIVLErgdysGAKNVSGG 47
                                  8***************************76666533333333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                   -HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 182 dkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvr 238
                                     ++ ++l+ + e+ Gv +   t v+++++++  + ++++ g+ + a lv+ a Gv+
  gi|70606131|ref|YP_255001.1| 103 RAKFDRWLASEAENLGVLISYSTLVTNAQRETGGINLETNRGN-LRAPLVIDASGVT 158
                                   5789999*************************98888888888.7999999888876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   8.5e-11   1.1e-07       2     180 ..       5     173 ..       4     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.5e-11
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                   +dV++VG+G+ Gl++a   ++ G +v+++e+ +   +++  ++ +    ++ l    le+  l++  ++e++++  +n+  
  gi|70606131|ref|YP_255001.1|   5 ADVIVVGGGLGGLSAAITAAKEGLSVIVLERGDYSgAKNVSGGRMYIHALQKLIPDALERAPLERPITKETFEFYCSND-- 83 
                                   79*****************************875415556777788888888888889999999998888777666666.. PP

                                   CCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE-- CS
                 FAD_binding_3  82 dtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaD 162
                                     +k +   e e + ++ + +   +++r L+++ae+ g+ +  +t v++ ++++ g++ e      ++  ++ra  ++ a 
  gi|70606131|ref|YP_255001.1|  84 --RKLSFSFE-EKGKKNSYSILRAKFDRWLASEAENLGVLISYSTLVTNAQRETGGINLET-----NR-GNLRAPLVIDAS 155
                                   ..56666666.88999999999**************************7766666643332.....22.379********* PP

                                   GTT-HHHHHHTGGEEEEE CS
                 FAD_binding_3 163 GgrStvrktlgiefegee 180
                                   G+ S v + lg++  +++
  gi|70606131|ref|YP_255001.1| 156 GVTSVVFRYLGLRKFTPD 173
                                   ***********9843333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.6   6.6e-09   8.4e-06       1      33 [.       9      41 ..       9      57 .. 0.91
   2 ?    0.1   0.0      0.77   9.8e+02      41      66 ..     251     275 ..     243     276 .. 0.81
   3 ?   -0.2   0.0      0.96   1.2e+03       2      17 ..     302     317 ..     302     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.6e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  +vG+Gl+Gl+aA ++ak+g++v +le++d+ G 
  gi|70606131|ref|YP_255001.1|  9 VVGGGLGGLSAAITAAKEGLSVIVLERGDYSGA 41
                                  8****************************9985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.77
                                   TTCEECTS---EEETTHHHHCHHHHC CS
                 NAD_binding_8  41 pgvrvdygahifhgsgyypnvrrllr 66 
                                   +g +++y ah++  +g y+n+  l++
  gi|70606131|ref|YP_255001.1| 251 EGEILEYSAHAIPYFG-YRNLPPLYD 275
                                   57899*******9998.899887776 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.96
                                   E--SHHHHHHHHHHHC CS
                 NAD_binding_8   2 vGaGlsGlvaAylLak 17 
                                   +G+G+ + +aA  L++
  gi|70606131|ref|YP_255001.1| 302 IGSGMIAGLAAKKLKE 317
                                   8***999999998876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.7      0.14   1.7e+02       1      32 [.       6      34 ..       6      41 .. 0.85
   2 !   20.1   0.0   1.8e-07   0.00024     117     213 ..      69     161 ..      41     171 .. 0.81
   3 ?    1.2   0.0       0.1   1.3e+02     313     328 ..     273     288 ..     237     290 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                  ++++vGGG  G  aA++ ak +   l+v ++e
  gi|70606131|ref|YP_255001.1|  6 DVIVVGGGLGGLSAAITAAKEG---LSVIVLE 34
                                  699************9998887...7777777 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.8e-07
                                   S-HHHHH-SCHHHHHTTB-SB-TTS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-E CS
                Trp_halogenase 117 eeledysleavaakakkfsprekdglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgre 197
                                   +++++ ++e    +++k+s   ++  ++ + +y++ +a+++++L   ae+ Gv +   + v+  ++e+g ++ l+++ g+ 
  gi|70606131|ref|YP_255001.1|  69 RPITKETFEFYCSNDRKLSFSFEE--KGKKNSYSILRAKFDRWLASEAENLGVLISYSTLVTNAQRETGGIN-LETNRGN- 145
                                   455555555555556666555555..788899**************************************96.9999999. PP

                                   EE-SEEEE-SGGG-II CS
                Trp_halogenase 198 veadlfiDcsGfrgll 213
                                   + a l+iD+sG  + +
  gi|70606131|ref|YP_255001.1| 146 LRAPLVIDASGVTSVV 161
                                   ***********99876 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.1
                                   SEETTEEE-CCCTEE- CS
                Trp_halogenase 313 awvknvvalGlasgfv 328
                                    + +n++a+G+++gf+
  gi|70606131|ref|YP_255001.1| 273 LYDNNLIAVGDSAGFL 288
                                   5789***********7 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.8   3.8e-06    0.0049       1      31 [.       8      37 ..       8      42 .. 0.93
   2 !    8.5   0.0   0.00081         1      78     134 ..     101     157 ..      71     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                  i++G+G  Gl+aai++ k gl ++++lE+g 
  gi|70606131|ref|YP_255001.1|  8 IVVGGGLGGLSAAITAAKEGL-SVIVLERGD 37
                                  89*******************.7******96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00081
                   Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                   + r+++ ++l++ a++  + i + + V++ ++e +g ++et++++++A+ vi A G 
  gi|70606131|ref|YP_255001.1| 101 ILRAKFDRWLASEAENLGVLISYSTLVTNAQRETGGINLETNRGNLRAPLVIDASGV 157
                                   45666777888888899999*********************************9995 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.8   1.4e-08   1.8e-05      17      65 ..       4      51 ..       2      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                  ++Dv++vG+G  GL+aa + ak+ +l v++ler    G     GG+++ 
  gi|70606131|ref|YP_255001.1|  4 DADVIVVGGGLGGLSAAITAAKE-GLSVIVLERGDYSGAKNVSGGRMYI 51
                                  68*********************.*********9999999999998874 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.0   4.2e-08   5.4e-05       1      28 [.       6      33 ..       6      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.2e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                  dviV+GgG+ G+ AA++aa+ G++v+ +
  gi|70606131|ref|YP_255001.1|  6 DVIVVGGGLGGLSAAITAAKEGLSVIVL 33
                                  8************************987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.2   3.1e-07   0.00039       1     143 [.       6     159 ..       6     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga..........leecvehsWsgtivyldd 71 
                                   Dv+v+G+G+ gls A     ak gl+v+++e ++ +   n     ++ ++l++          le+ +++  +  + y+ +
  gi|70606131|ref|YP_255001.1|   6 DVIVVGGGLGGLSAAITA--AKEGLSVIVLERGDYSGAKNVSGGRMYIHALQKlipdalerapLERPITK--ETFEFYCSN 82 
                                   9************99877..***********999884443336666667777666677666665555554..345556665 PP

                 Lycopene_cycl  72 gkkillg......raYgrvsskrlkeellerlvengvklleak.vesveeeeageslvvleggr.kirarlvvdarglas 143
                                   ++k   +      ++  ++ ++++ + l+ +  + gv    ++ v++++ e+     + le +r ++ra+lv+da+g+ s
  gi|70606131|ref|YP_255001.1|  83 DRKLSFSfeekgkKNSYSILRAKFDRWLASEAENLGVLISYSTlVTNAQRETG---GINLETNRgNLRAPLVIDASGVTS 159
                                   55555554455553344678889999999998887887766662555555555...8999999999**********9655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.4   1.6e-05     0.021       2      33 ..       7      38 ..       6      46 .. 0.93
   2 ?   -0.4   0.0       1.3   1.7e+03      42      76 ..     106     137 ..      98     144 .. 0.79
   3 ?   -0.8   0.0       1.8   2.3e+03       5      22 ..     302     319 ..     300     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                  v+vvGgG+ gl +A ++a+ g +V v+er+d 
  gi|70606131|ref|YP_255001.1|  7 VIVVGGGLGGLSAAITAAKEGLSVIVLERGDY 38
                                  89***************************996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                     Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesv 76 
                                   + ++l+ + e++g+ + ++t v++ + ++ g   +
  gi|70606131|ref|YP_255001.1| 106 FDRWLASEAENLGVLISYSTLVTNAQRETGG---I 137
                                   6688999999999999999999998877766...4 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.8
                                   ECSSHHHHHHHHHHHHTT CS
                     Pyr_redox   5 vGgGyiglElAgalaelg 22 
                                   +G+G i+  +A+ l+e++
  gi|70606131|ref|YP_255001.1| 302 IGSGMIAGLAAKKLKEIN 319
                                   9******99999999987 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   1.3e-05     0.017      29      59 ..       5      35 ..       3      64 .. 0.90
   2 ?   -2.5   0.0         2   2.5e+03      89     109 ..     295     315 ..     293     320 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                  -EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDv 59
                                  a v+v+GgG  Gl+A+ ta++ g +V vl+ 
  gi|70606131|ref|YP_255001.1|  5 ADVIVVGGGLGGLSAAITAAKEGLSVIVLER 35
                                  89************************99986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                                   HHH-SEEEE---BTTSS---S CS
                   AlaDh_PNT_C  89 vkeadvvigtvlipGkkaPkL 109
                                   ++ +d+ ig+  i G +a kL
  gi|70606131|ref|YP_255001.1| 295 IRGMDLAIGSGMIAGLAAKKL 315
                                   677888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2654.71
//
Query:       gi|70606132|ref|YP_255002.1|  [L=89]
Description: ferredoxin-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-07   29.0   6.7    1.1e-06   28.6   6.7    1.1  1  Fer4_10   4Fe-4S dicluster domain
    1.8e-06   28.0   4.5    2.5e-06   27.5   4.5    1.2  1  Fer4_9    4Fe-4S dicluster domain
      2e-06   28.3   5.4      0.015   15.9   2.1    2.1  2  Fer4_7    4Fe-4S dicluster domain
    5.7e-06   26.4   0.8    6.4e-06   26.2   0.8    1.1  1  Fer4_11   4Fe-4S dicluster domain
    5.7e-06   26.1   9.2    0.00018   21.4   3.1    2.3  2  Fer4_2    4Fe-4S binding domain
    0.00018   21.4  10.8     0.0066   16.5   2.3    2.8  2  Fer4_6    4Fe-4S binding domain
    0.00019   21.5   4.6    0.00083   19.5   4.6    1.8  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
    0.00052   19.8   5.8     0.0061   16.3   1.8    2.1  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
     0.0055   17.6   3.0        2.5    9.1   0.7    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.014   15.5   8.8       0.94    9.7   3.2    2.0  2  Fer4_21   4Fe-4S dicluster domain
      0.014   15.8   2.3        1.8    9.0   0.5    2.1  2  Fer4_8    4Fe-4S dicluster domain
       0.07   13.7  11.3       0.31   11.7   2.2    2.7  2  Fer4_4    4Fe-4S binding domain
        0.1   12.5  15.4       0.39   10.6   2.6    4.0  3  Fer4      4Fe-4S binding domain
       0.64   11.1  12.1        3.7    8.7   4.1    2.3  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   6.7   8.7e-10   1.1e-06       1      56 []      20      71 ..      20      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.7e-10
                       Fer4_10  1 kvvidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  ++++++d C+ C+   Cv++CPa      +++e se++++ + +e+C +cg  + +CP
  gi|70606132|ref|YP_255002.1| 20 HIQVNTDICLTCKdkPCVASCPA------GTYEPSEDGRIIVHYERCLECGGAIVICP 71
                                  67899*******9999*******......99999999999999**************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   4.5     2e-09   2.5e-06       2      51 .]      28      75 ..      27      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2e-09
                        Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  C  C+   Cv++Cpag++++++ +r++ + +    +C++Cg  + +Cp gai
  gi|70606132|ref|YP_255002.1| 28 CLTCKDkpCVASCPAGTYEPSEDGRIIVHYE----RCLECGGAIVICPFGAI 75
                                  99**8667********************976....6************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1   1.2e-05     0.015      27      51 ..      17      43 ..       6      44 .. 0.83
   2 !   13.9   0.1   4.7e-05      0.06      29      52 .]      51      74 ..      44      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                        Fer4_7 27 gtekveidpekClgCga..CvavCPtg 51
                                   + +++++ + Cl+C+   Cva CP+g
  gi|70606132|ref|YP_255002.1| 17 NKSHIQVNTDICLTCKDkpCVASCPAG 43
                                  347899*********9999******98 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.7e-05
                        Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                   ++ +++e+Cl Cg  +  CP+ga
  gi|70606132|ref|YP_255002.1| 51 GRIIVHYERCLECGGAIVICPFGA 74
                                  577899****************98 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.8     5e-09   6.4e-06       5      62 ..      23      78 ..      19      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5e-09
                       Fer4_11  5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkn 62
                                  +  ++C  C ++pCvas+p+   ++  e+G ++++ +++  e+   +  cP+ ++  n
  gi|70606132|ref|YP_255002.1| 23 VNTDICLTCKDKPCVASCPA-GTYEPSEDGRIIVHYERCL-ECGGAIVICPFGAITFN 78
                                  56789**************7.7889999***********7.999999*****998776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   3.1   1.4e-07   0.00018       2      22 .]      20      42 ..      19      42 .. 0.92
   2 !    8.5   0.4    0.0018       2.3       3      16 ..      53      70 ..      51      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                        Fer4_2  2 pvvvdtdrCigCg..aCvsaCPa 22
                                  +++v+td+C+ C+  +Cv +CPa
  gi|70606132|ref|YP_255002.1| 20 HIQVNTDICLTCKdkPCVASCPA 42
                                  79**********777*******8 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                        Fer4_2  3 vvvdtdrCigCg....aC 16
                                  + v  +rC++Cg    +C
  gi|70606132|ref|YP_255002.1| 53 IIVHYERCLECGgaivIC 70
                                  677899*****9555555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.3   5.1e-06    0.0066       2      22 ..      21      43 ..      20      45 .. 0.90
   2 !    8.9   1.4    0.0013       1.7       5      24 .]      56      75 ..      52      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                        Fer4_6  2 veidpdkCigCgd..CvrvCPeg 22
                                  ++++ d C+ C d  Cv+ CP+g
  gi|70606132|ref|YP_255002.1| 21 IQVNTDICLTCKDkpCVASCPAG 43
                                  789********8889******98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                        Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                   +++C+ Cg  +++CP+gai
  gi|70606132|ref|YP_255002.1| 56 HYERCLECGGAIVICPFGAI 75
                                  5677777777799*****98 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   4.6   6.5e-07   0.00083      31     101 ..      21      86 ..      10      89 .] 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.5e-07
                                   TTHHHHTHHHHHS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C- CS
                        ETF_QO  31 aevavkvnlekyagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGggGP 101
                                    +v+++++l+  ++p+   CPag ye  ed      ++ +  + C+ C    +  p   i+++ PeGg   
  gi|70606132|ref|YP_255002.1|  21 IQVNTDICLTCKDKPCVASCPAGTYEPSEDG-----RIIVHYERCLECGGAIVICPFGAITFNFPEGGISY 86 
                                   45667788888999************98776.....8999***************************9665 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.8   4.8e-06    0.0061      14      40 ..      18      44 ..      10      48 .. 0.80
   2 !    6.0   0.1    0.0076       9.8      17      39 ..      53      73 ..      44      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                                  HHHHHHHHTT----TT-HHHHCSTT-- CS
                       Fer4_20 14 eeealeeAsRClqCkkapcvkgCPvei 40
                                  +++++ + + Cl+Ck++pcv++CP+ +
  gi|70606132|ref|YP_255002.1| 18 KSHIQVNTDICLTCKDKPCVASCPAGT 44
                                  5567778889**************976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                                  HHHHHTT----TT-HHHHCSTT- CS
                       Fer4_20 17 aleeAsRClqCkkapcvkgCPve 39
                                  ++   +RCl+C  a ++  CP  
  gi|70606132|ref|YP_255002.1| 53 IIVHYERCLECGGAIVI--CPFG 73
                                  566779*****887766..8875 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.7     0.002       2.5       2      20 ..      28      48 ..      14      56 .. 0.85
   2 !    9.0   0.1     0.002       2.6       1      20 [.      59      78 ..      59      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                       Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                  C tC+   C+ +CP++  +  
  gi|70606132|ref|YP_255002.1| 28 CLTCKDkpCVASCPAGTYEPS 48
                                  99999888******9876655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  rC +Cg  + +CP +ai+ +
  gi|70606132|ref|YP_255002.1| 59 RCLECGGAIVICPFGAITFN 78
                                  6****************976 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.2   0.00073      0.94      28      53 ..      15      42 ..       9      46 .. 0.81
   2 ?    8.7   8.9    0.0015       1.9       5      58 ..      25      76 ..      24      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00073
                       Fer4_21 28 idaktvlkvvedeCvGCn..lCssvCPv 53
                                  +++k++++v +d C  C+   C++ CP 
  gi|70606132|ref|YP_255002.1| 15 VNNKSHIQVNTDICLTCKdkPCVASCPA 42
                                  67889999*********6336*****95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                       Fer4_21  5 edkCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                   d C+ C+   C+ +C+ ++++    +++ ++ v  ++C  C   + +CP  ++i+
  gi|70606132|ref|YP_255002.1| 25 TDICLTCKDkpCVASCPAGTYE---PSEDGRIIVHYERCLECGGAIVICPF-GAIT 76
                                  678****7445******76654...56678889999**************7.8887 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0014       1.8      47      64 ..      24      43 ..       4      44 .. 0.78
   2 ?    6.9   0.1    0.0068       8.6       3      21 ..      58      76 ..      56      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                        Fer4_8 47 alwsCttcga..CtevCpvg 64
                                  + + C+tc+   C+  Cp g
  gi|70606132|ref|YP_255002.1| 24 NTDICLTCKDkpCVASCPAG 43
                                  4678****9999******86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0068
                        Fer4_8  3 ekCieCgaCqsaCpvlrrt 21
                                  e+C eCg     Cp+   t
  gi|70606132|ref|YP_255002.1| 58 ERCLECGGAIVICPFGAIT 76
                                  79*****999999987655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.2   0.00024      0.31       3      17 .]      27      43 ..      24      46 .. 0.86
   2 ?    6.2   1.9     0.013        17       1      15 [.      57      71 ..      57      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                        Fer4_4  3 rCigCgs..CvaaCPqg 17
                                   C+ C+   Cva+CP g
  gi|70606132|ref|YP_255002.1| 27 ICLTCKDkpCVASCPAG 43
                                  5*****779******65 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.013
                        Fer4_4  1 qerCigCgsCvaaCP 15
                                  +erC++Cg  + +CP
  gi|70606132|ref|YP_255002.1| 57 YERCLECGGAIVICP 71
                                  69*****97666666 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.16     2e+02       1      11 [.      21      31 ..      21      33 .. 0.84
   2 ?    5.1   0.6     0.017        22      14      21 ..      36      43 ..      34      46 .. 0.87
   3 ?   10.6   2.6   0.00031      0.39       1      24 []      53      76 ..      53      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                                  EEEETTTSSS- CS
                          Fer4  1 vvideekCigC 11
                                  ++++++ C  C
  gi|70606132|ref|YP_255002.1| 21 IQVNTDICLTC 31
                                  5799****999 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.017
                                  HHHHSTTT CS
                          Fer4 14 CvevCPvg 21
                                  Cv  CP g
  gi|70606132|ref|YP_255002.1| 36 CVASCPAG 43
                                  ******98 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00031
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  +++++e+C  CG  + +CP+gAIt
  gi|70606132|ref|YP_255002.1| 53 IIVHYERCLECGGAIVICPFGAIT 76
                                  57999********9********97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.1    0.0029       3.7       1      14 [.      28      43 ..      28      44 .. 0.85
   2 ?    7.3   1.0    0.0081        10       1      15 []      60      74 ..      60      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                        Fer4_3  1 CtgCg..aCvevCPvg 14
                                  C+ C   +Cv +CP g
  gi|70606132|ref|YP_255002.1| 28 CLTCKdkPCVASCPAG 43
                                  999*7669******65 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0081
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+ Cg   + CP gA
  gi|70606132|ref|YP_255002.1| 60 CLECGGAIVICPFGA 74
                                  999*99*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 568.51
//
Query:       gi|70606133|ref|YP_255003.1|  [L=493]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   47.2   0.1    1.2e-11   43.7   0.0    2.1  2  Phosphorylase    Carbohydrate phosphorylase
    2.7e-09   36.8   0.0    6.7e-09   35.5   0.0    1.6  1  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.1    0.0027        24     364     408 ..     241     286 ..     204     327 .. 0.67
   2 !   43.7   0.0   1.3e-15   1.2e-11     421     649 ..     271     475 ..     264     490 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0027
                                   E----B-CHHHCCCTSHHHHHHHHHHCSSGGCCSGGGGGGG.GGGC CS
                 Phosphorylase 364 nktnGitprrwlllanpelaelitekigeewvkdleeLkkL.ekla 408
                                     tnG+++ rw+++  +++ ++ +   ge+ vk  ++L +L +k++
  gi|70606133|ref|YP_255003.1| 241 PLTNGVSFDRWMHEEVKKIYNTGKGSFGEARVKARNDLLSLlRKYK 286
                                   4689999999999888888888888888666655544433303333 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 1.3e-15
                                   HHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT-HHHHH CS
                 Phosphorylase 421 kqenKerlaelikekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapgYalAkk 501
                                   + + +++l +l+++    e+d+++l+ v  +R+  YkR  +    +  l +e+ ++      + +++++gka p    A  
  gi|70606133|ref|YP_255003.1| 271 RVKARNDLLSLLRKY--KEIDQDKLIVVWARRMTRYKRPYF----VSRLIREMGKD-----LNVVFVIAGKAHPRD--AEG 338
                                   555666666666665..467778888888888888888764....23333333333.....567788888888854..455 PP

                                   HHHHHHHHHHHHCC-TTTCCCEE.EEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEESSTCHHH CS
                 Phosphorylase 502 iiklinsvaevvnndpevkdklk.vvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtlDGanvE 581
                                   i+ +        n+ + ++++lk v+++++y+ ++a+ i+++ dl      +g eA GT+ mk  +nG  t+++ DG  +E
  gi|70606133|ref|YP_255003.1| 339 IVYM--------NEFNWLSKELKnVIYIHDYSLTNAKYILSGGDLLLFTPFSGWEACGTSYMKAGINGVPTLSSKDGGTLE 411
                                   5432........3334445555449******************************************************** PP

                                   HHHHH-GGGSEEES-BHHHHHHHHHHT.--HHHHHHH-HHHHHHHHHHHCTTTTTTSTTTTHHHHHHHC CS
                 Phosphorylase 582 iaeevgeenifiFGltaeeveelkkkg.ynpkelyekdpelkevldalesgtfsekekeefkelvdsll 649
                                   i +     n ++FG +  e  +++++   ++ +  +  + +++ l  +++    e++++ fk+l ++ +
  gi|70606133|ref|YP_255003.1| 412 IIKD--GYNGYFFGEDIREFVDIYNSPkAKEIDSRDYVDFVNKFLYIINKA---ESDRDWFKNLSENTF 475
                                   *986..568899*******99999884222222222222233333333332...334456666665554 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   7.4e-13   6.7e-09       8     142 ..     285     424 ..     281     440 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.4e-13
                                   HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES........STTHHHHHHHHHHHCTTCGGGEEECC CS
               Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.......ngeeekelkklaeelelsdnviflgev 81 
                                    ++++++k i++   r++++K++  + +++++  k  + nv++viaG       +g    +  ++  + el +nvi++   
  gi|70606133|ref|YP_255003.1| 285 YKEIDQDKLIVVWARRMTRYKRPYFVSRLIREMGK--DLNVVFVIAGkahprdaEGIVYMNEFNW-LSKEL-KNVIYIHDY 361
                                   567899999**********************9965..7*************99733333334444.55555.579999998 PP

                                   HSSSHHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-T CS
               Glycos_transf_1  82 sredleellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkp 142
                                   s ++ + +l+  d+++++  s  E+ G++ + A   g+p+++s+ gg +e++kdg +G+++ +
  gi|70606133|ref|YP_255003.1| 362 SLTNAKYILSGGDLLLFTPFSgwEACGTSYMKAGINGVPTLSSKDGGTLEIIKDGYNGYFFGE 424
                                   88889999999999999877777************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3271.47
//
Query:       gi|70606134|ref|YP_255004.1|  [L=416]
Description: hypothetical protein Saci_0295 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-27   93.8  41.9    8.6e-21   74.2  23.7    2.0  2  MFS_1           Major Facilitator Superfamily
    2.5e-12   46.4  27.5    1.3e-11   44.1  27.5    1.9  1  MFS_1_like      MFS_1 like family
    4.3e-05   22.6  29.2    0.00025   20.1  16.7    2.4  2  Sugar_tr        Sugar (and other) transporter
  ------ inclusion threshold ------
       0.01   14.3   8.3       0.23    9.8   2.6    2.3  2  MFS_3           Transmembrane secretion effector
        1.8    8.2   8.0       0.24   11.1   1.8    2.5  3  TMEM72          Transmembrane protein family 72


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2  23.7   2.4e-24   8.6e-21      15     299 ..      22     333 ..       8     337 .. 0.76
   2 !   32.1  21.0   1.5e-11   5.5e-08       1     166 [.     236     408 ..     236     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 2.4e-24
                         MFS_1  15 lgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvl 94 
                                   l+++++l +   +lg ++ e+   ++l  l+ ++as+++G+++drf rr+ +l++  +++l l+l++++ s++l+ +  ++
  gi|70606134|ref|YP_255004.1|  22 LSTLITLqI--LNLGGNAIEVAYTVSLGNLVLIIASMFWGYVADRFDRRKQILISTGGTSLPLFLMMMSRSIPLISLNYAF 100
                                   444555423..4788888899999999***********************************5555575666688888888 PP

                         MFS_1  95 qGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                   + +++ a+++  + l+ + + k++ g+ ++ +s+++s+G+++g l++ +l+++l  +++  ilai+sl  f+l + ++p +
  gi|70606134|ref|YP_255004.1| 101 AVFMSTASTTPFNLLVMETTDKKHWGSLFSRYSLFSSIGVLVGLLISTFLITYLEISLIEGILAIISLSTFILCFRFIPKP 181
                                   88888999****************************************************************956666555 PP

                         MFS_1 176 pperkrkspkeee.................kgtgpaplvpawkallkdpvlw..illialllfffgfsglltllplylqev 237
                                   +++ +r s +  +                  +   +++++ +k l+++ v +  +l i+l++f +   ++ t  p      
  gi|70606134|ref|YP_255004.1| 182 QVSFERTSLIHNKesffsrirqipliflhlPSIHSFKIFS-LKRLKTPHVNYvpLLYIGLIIFYISSGIFNTVYPA-GLYK 260
                                   5555555555554788888777776666655555555555.77777777554545666666666555557777777.7999 PP

                         MFS_1 238 lgls..glllaglllallalvgailallagrls.dr...........lgrrrrlllallllllaalglallavtss 299
                                   +gl+   +ll++l+ +l+++vg   + +++rl+ +r           l   ++++++l+  +++ + ++l+++ts 
  gi|70606134|ref|YP_255004.1| 261 RGLTenEVLLVTLVGMLIQIVG---FQFSSRLLeNRkeeklahlsllLRGGNYIIIGLIMQFFVGIPVLLAGLTSY 333
                                   9999655555555566666666...889999997778998888888766688999999999999998888888843 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 1.5e-11
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                   l++++++ +++++i+++++p  l    g+++ e+ l++ + +l ++v+  + +rl ++    ++  l+lll +   ++++l
  gi|70606134|ref|YP_255004.1| 236 LYIGLIIFYISSGIFNTVYPAGL-YKRGLTENEVLLVTLVGMLIQIVGFQFSSRLLENRKEEKLAHLSLLLRGGNyIIIGL 315
                                   57999***************844.455799***************************999999999999999988333333 PP

                         MFS_1  81 .fa..sslwlllvlrv....lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                    +    ++++ll++       +G++++++++++ +li ++  ++++g ++g++s+ ++++   g l++g++++++++   f
  gi|70606134|ref|YP_255004.1| 316 iMQffVGIPVLLAGLTsyplAAGIAYAIFYSSSTTLIFKILGGRHQGAGLGIYSTVVGVALFAGSLISGYITHYFSYGIDF 396
                                   52244888866666666888************************************************************* PP

                         MFS_1 155 yilaivsllafv 166
                                   +i++++++++  
  gi|70606134|ref|YP_255004.1| 397 MIAGVLLIICSR 408
                                   *********954 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1  27.5   3.5e-15   1.3e-11      11     381 ..      15     394 ..       4     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3.5e-15
                    MFS_1_like  11 ffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippsker 91 
                                   f a++g l   +t+ + + g +a e++  +++  l+ i+++ +wg +aDrf +rk+++i +   s+ lfl+++        
  gi|70606134|ref|YP_255004.1|  15 FNASTGPLSTLITLQILNLGGNAIEVAYTVSLGNLVLIIASMFWGYVADRFDRRKQILISTGGTSLPLFLMMM-------- 87 
                                   567888888888888889999999*****************************************99999555........ PP

                    MFS_1_like  92 qeesklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedr.kd.yGrqrlfGsvGyaifafitGilid 170
                                                   + ++ ++ l  ++a f++ a+ + ++ ++++++ +++ +  ++r  lf+s+G  +   i+ +li+
  gi|70606134|ref|YP_255004.1|  88 ----------------SRSIPLISLNYAFAVFMSTASTTPFNLLVMETTDKKHwGSlFSRYSLFSSIGVLVGLLISTFLIT 152
                                   ................7889999999999********************55541335************************ PP

                    MFS_1_like 171 hysvnllp.ysallyvlaallvisllvvlilnetekesklkvtksl.......................qvllnilknpev 227
                                   +++++l++ +  l+++ ++ +++ + + +  ++ + e+   + + +                          l+ lk p+v
  gi|70606134|ref|YP_255004.1| 153 YLEISLIEgI--LAIISLSTFILCFRF-IPKPQVSFERTSLIHNKEsffsrirqipliflhlpsihsfkIFSLKRLKTPHV 230
                                   *****98843..233333333333333.33444444444444433378899****************98445788999998 PP

                    MFS_1_like 228 ii...fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfl 305
                                    +   + + ++i  +s+gi+++ +   L + g ++  +  ++ +g++ +i+ f f+++lle    +kl  ++ll+    ++
  gi|70606134|ref|YP_255004.1| 231 NYvplLYIGLIIFYISSGIFNTVYPAGLYKRGLTENEVLLVTLVGMLIQIVGFQFSSRLLENRKEEKLAHLSLLLRGGNYI 311
                                   65221566678999999****9999889889999888889999*****************988888888888888777777 PP

                    MFS_1_like 306 lyaii........enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlks 378
                                   ++++i          +  +    +  gi++++++++ ++ + ki + ++++ g g++s++ +g+  + Gsli+G++  ++s
  gi|70606134|ref|YP_255004.1| 312 IIGLImqffvgipVLLAGLTSYPLAAGIAYAIFYSSSTTLIFKILGGRHQGAGLGIYSTV-VGVALFAGSLISGYITHYFS 391
                                   77777333333322222233345567899*****************************98.9*************988887 PP

                    MFS_1_like 379 aif 381
                                     +
  gi|70606134|ref|YP_255004.1| 392 YGI 394
                                   655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  16.7   6.9e-08   0.00025      46     363 ..      38     345 ..      15     358 .. 0.72
   2 !    8.0   4.6   0.00032       1.1      51      92 ..     368     409 ..     359     415 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.9e-08
                                   .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmy 126
                                   + +  +vs+ +++ ii s+f g+++drf+R+k +li++  ++   +l++++    s+ ++ +   ++ +   + ++   ++
  gi|70606134|ref|YP_255004.1|  38 IEVAYTVSLGNLVLIIASMFWGYVADRFDRRKQILISTGGTSLPLFLMMMSR---SIPLISLNYAFAVFMSTASTTPFNLL 115
                                   5667899999******************************************...88888888888888888888889*** PP

                                   HHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHH CS
                      Sugar_tr 127 isEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeea 207
                                   + E + kk+ g l s y l+ ++G lv+  + ++l ++ + +     l++ ++++  +++++ f+P  P   +e++     
  gi|70606134|ref|YP_255004.1| 116 VMETTDKKHWGSLFSRYSLFSSIGVLVGLLISTFLITYLEISLIEGILAIISLST--FILCFRFIP-KPQVSFERTSLIHN 193
                                   ***********************************99999444445555544444..555556777.33333333333333 PP

                                   HHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-TH CS
                      Sugar_tr 208 kevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsk 288
                                   ke++        + r++  ++  l    + +  s+k+l++   v +  l+ ++l if   +Gi+ ++ y+  +++    ++
  gi|70606134|ref|YP_255004.1| 194 KESF------FSRIRQIPLIFLHLPSIHSFKIFSLKRLKTP-HVNYVPLLYIGLIIFYISSGIF-NTVYPAGLYKRGLTEN 266
                                   3333......4578888888888888866653344444443.4778888888999999999965.6777777777755555 PP

                                   H.HHHHHHHHHHHHHHHHHHHHHHH.....HS-SHHHHHHH...HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHH CS
                      Sugar_tr 289 s.llvtiivgvvnfvatfvaiflvd.....rfGRRtllllG...aagmaicfvilgivalllvakskaasivaivfialfi 360
                                   + llvt++ + +++v   ++  l +     ++    lll G   +++++i+ +++gi++ll   +        +++ + ++
  gi|70606134|ref|YP_255004.1| 267 EvLLVTLVGMLIQIVGFQFSSRLLEnrkeeKLAHLSLLLRGgnyIIIGLIMQFFVGIPVLLAGLT-----SYPLAAGIAYA 342
                                   57888888888888877777766651111145555555555666677777777777444443333.....23333333444 PP

                                   HHH CS
                      Sugar_tr 361 alf 363
                                   +++
  gi|70606134|ref|YP_255004.1| 343 IFY 345
                                   444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00032
                                   HHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  51 ivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavl 92 
                                      ++ v  ++Gsl++g+++++f++   ++ia+vl++i++ +
  gi|70606134|ref|YP_255004.1| 368 YSTVVGVALFAGSLISGYITHYFSYGIDFMIAGVLLIICSRI 409
                                   45556677899***************************9876 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3   0.00032       1.1      46      83 ..      39      76 ..      29     114 .. 0.70
   2 ?    9.8   2.6   6.5e-05      0.23     268     390 ..     280     410 ..     264     415 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00032
                         MFS_3 46 mvAlvqaaatLPifllsilaGalaDnfdrRkvllavql 83
                                   vA     + L +++ s++ G +aD fdrRk +l+   
  gi|70606134|ref|YP_255004.1| 39 EVAYTVSLGNLVLIIASMFWGYVADRFDRRKQILISTG 76
                                  56666666788899999999*********998887653 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.5e-05
                         MFS_3 268 ilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWi....talstlnvavqlavPrWvvgR. 343
                                   i+g  ++srL e  ++e+l +l+ +      ++++l  + +v ++vll g +++     +a++ + ++  +++ + + gR 
  gi|70606134|ref|YP_255004.1| 280 IVGFQFSSRLLENRKEEKLAHLSLLLRGGNYIIIGLIMQFFVGIPVLLAGLTSYPlaagIAYAIFYSSSTTLIFKILGGRh 360
                                   677788899999999999999999999999999999999999999998875554311113455555555555555555543 PP

                         MFS_3 344 ...alavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaail 390
                                      +l +Y tv+  +l aGsl+ G +++  s  +  ++a+++l++   i+
  gi|70606134|ref|YP_255004.1| 361 qgaGLGIYSTVVGVALFAGSLISGYITHYFSYGIDFMIAGVLLIICSRIF 410
                                   3228***************************************9988776 PP

>> TMEM72  Transmembrane protein family 72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   6.6e-05      0.24      37     132 ..      77     176 ..      70     197 .. 0.76
   2 ?   -1.4   0.0      0.44   1.6e+03     107     127 ..     266     286 ..     263     302 .. 0.71
   3 ?   -1.5   0.2      0.47   1.7e+03     113     129 ..     397     413 ..     367     416 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                        TMEM72  37 fkslavylllsgvavsvlEisyfvalllevclrckeesllfelwkkvrrlggfqkfllYvllsvacflhpv..lvw...hv 112
                                    +sl ++l++++ ++ ++ + y+ a++++++ + +++ l+ e  +k  +   f +  l+  + v++ l     l+     +
  gi|70606134|ref|YP_255004.1|  77 GTSLPLFLMMMSRSIPLISLNYAFAVFMSTASTTPFNLLVMETTDKKHWGSLFSRYSLFSSIGVLVGLLIStfLITyleIS 157
                                   48999**************************************************88887777765332220022111124 PP

                        TMEM72 113 tipGtmLvilgllylllskr 132
                                    i G+ L i +l  ++l +r
  gi|70606134|ref|YP_255004.1| 158 LIEGI-LAIISLSTFILCFR 176
                                   55554.56667777777776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.44
                        TMEM72 107 vlvwhvtipGtmLvilgllyl 127
                                   ++v +vt +G+++ i+g+   
  gi|70606134|ref|YP_255004.1| 266 NEVLLVTLVGMLIQIVGFQFS 286
                                   689999****99999998654 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.47
                        TMEM72 113 tipGtmLvilgllylll 129
                                   +i+G++L+i + + + l
  gi|70606134|ref|YP_255004.1| 397 MIAGVLLIICSRIFAYL 413
                                   57888888877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2997.42
//
Query:       gi|70606135|ref|YP_255005.1|  [L=339]
Description: Fe-S oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      8e-33  113.1   2.8    1.3e-32  112.4   2.8    1.3  1  DUF3463      Domain of unknown function (DUF3463)
    4.9e-16   59.6   0.0    1.9e-15   57.7   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    1.5e-08   35.0   0.1    5.9e-07   29.8   0.0    2.4  2  Fer4_12      4Fe-4S single cluster domain
     0.0012   19.0   1.1      0.012   15.7   0.0    2.5  3  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.078   13.0   0.1       0.17   11.9   0.1    1.5  1  MraZ         MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   2.8   3.5e-36   1.3e-32       1     132 [.     188     323 ..     188     325 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 3.5e-36
                       DUF3463   1 itvspgysYekapdqdlflerektkelfrkilelkkkkyklnesplyldflag...kq.eykCtpWgnptrnvlG.wqkPC 76 
                                   ++v+++y+Y++a  ++l++er+k+ e+++ ++elk+k+y ++esp+y++ +++   k  +++C+pW+ ++++++G ++ PC
  gi|70606135|ref|YP_255005.1| 188 VSVQVEYDYSTA--EKLSPERKKLLEVLNLLIELKRKGYPIVESPEYFQSIINswyKGvNWRCKPWMLINIDPQGrIVLPC 266
                                   579*********..9**************************************887446********************** PP

                       DUF3463  77 Ylleegyaktfk.......elleetdwekygkgkdpkCanCmvhsgyEasavsdtvksllkal 132
                                   Y+l ++y+ +         +l+++++we+y+     kC++C++++++E+s++s+t+ ++++++
  gi|70606135|ref|YP_255005.1| 267 YVL-NEYNGDKLvwetnivKLWNSYPWEQYE-----KCNKCALACYLEPSLFSWTNFNMVNER 323
                                   ***.888887667889999************.....**********************99876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   5.2e-19   1.9e-15       6     166 ..      35     180 ..      31     192 .. 0.91
   2 ?   -3.5   0.0       3.3   1.2e+04      86     115 ..     283     317 ..     272     327 .. 0.59

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 5.2e-19
                                   EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 
                                    CnlrC+ C+++    r+++++ ls+ee +  +k l ++ gv ++ + ggepll++d+ ++le+   +    + ++++tng
  gi|70606135|ref|YP_255005.1|  35 TCNLRCKMCPFW----RRKDEKLLSLEEEILMLKTL-EKSGVLFMGFEGGEPLLRRDLDQILEESYSR----FYTSLVTNG 106
                                   7***********....6*******************.89888888888**********9999999995....********* PP

                                   SCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  87 tlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                                    l+ ++ ++ + e+  d++ ++++ + +  v+++++  +++f++ +e+++ + ++ ++  v+  + +  en +++ ++lel
  gi|70606135|ref|YP_255005.1| 107 WLL-RDRVKYISEYL-DYLFVSIDGIGE--VHDRIRgIPGSFDRAVEGIKEAVRY-LP--VSLSFTITRENYDQVLDVLEL 180
                                   ***.*********99.************..666666688****************.**..677777777999988888775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                                   SSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHH CS
                                   xxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   Radical_SAM  86 gtlpd....eeklerllelg.vdrvslgleaadde 115
                                    +++     +e+ e+  +     +++ +l +++++
  gi|70606135|ref|YP_255005.1| 283 IVKLWnsypWEQYEKCNKCAlACYLEPSLFSWTNF 317
                                   44444555566666666666666666666666665 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.6e-10   5.9e-07      12     118 ..      33     130 ..      25     139 .. 0.92
   2 ?    2.3   0.1     0.052   1.8e+02      67     116 ..     169     218 ..     164     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.6e-10
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   +  Cnl+Ck C     w+ k +k  + e +  +++ l+k+ +  + + GGEPll   +++l ++++e +++++  + ++++
  gi|70606135|ref|YP_255005.1|  33 LYTCNLRCKMCP---FWRRKDEKLLSLEEEILMLKTLEKSGVLFMGFEGGEPLL---RRDLDQILEESYSRFY--TSLVTN 105
                                   578*******76...9**********999999**********************...9***************..789*** PP

                       Fer4_12  93 gytleelskkekeellkeidvlvdGk 118
                                   g  l +  k + +e l+++ v +dG 
  gi|70606135|ref|YP_255005.1| 106 GWLLRDRVK-YISEYLDYLFVSIDGI 130
                                   *****9986.79************95 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.052
                       Fer4_12  67 enaeallelvkevkeekp.ekdiwlytgytleelskkekeellkeidvlvd 116
                                   en++++l++++  ++ ++   + ++y  +t e+ls++ +++ll+ ++ l+ 
  gi|70606135|ref|YP_255005.1| 169 ENYDQVLDVLELSRKLGVtVSVQVEYDYSTAEKLSPE-RKKLLEVLNLLIE 218
                                   5777777777777777775567899999999999985.8899998888875 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.4e-06     0.012       7      73 ..      35      93 ..      32     129 .. 0.65
   2 ?    1.3   0.1       0.1   3.6e+02      62     109 ..     169     214 ..     166     222 .. 0.77
   3 ?   -3.4   0.1       2.8     1e+04       5      12 ..     298     305 ..     283     318 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-06
                       Fer4_14  7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkr 73
                                   Cnl Ck+C     ++++l   ++e l+   lk l+ks +   ++ + GGePL+    ++l++++++
  gi|70606135|ref|YP_255005.1| 35 TCNLRCKMCPFWRRKDEKLLSLEEEILM---LKTLEKSGV--LFMGFEGGEPLLR---RDLDQILEE 93
                                  6********9766555555555555555...666677777..7899*******76...445554444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                       Fer4_14  62 enkkellklvkrlkeeypekkiwletngtleielektpdlkekleals 109
                                   en +++l++++  ++ + ++++++e  ++ + +l   p+ k+ le+l+
  gi|70606135|ref|YP_255005.1| 169 ENYDQVLDVLELSRKLGVTVSVQVEYDYSTAEKLS--PERKKLLEVLN 214
                                   67789999999999999999999999999996666..77777777666 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.8
                       Fer4_14   5 lsgCnlsC 12 
                                    ++C l+C
  gi|70606135|ref|YP_255005.1| 298 CNKCALAC 305
                                   34555555 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.7e-05      0.17       8      54 ..     254     297 ..     252     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                                   EEB-TTSEEE--CHHHHHTTSCSEEEEEECCSEEEEEEHHHHHHHHH CS
                          MraZ   8 velDakGRlllPaklreeaklekevvviGvsncLeiwpraeWekyee 54 
                                   +++D +GR+ lP   ++e +++k+v      n+  +w    We+ye+
  gi|70606135|ref|YP_255005.1| 254 INIDPQGRIVLPCYVLNEYNGDKLVW---ETNIVKLWNSYPWEQYEK 297
                                   79****************99997665...678899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2091.49
//
Query:       gi|70606136|ref|YP_255006.1|  [L=102]
Description: hypothetical protein Saci_0297 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.13   12.2   0.3        3.1    7.7   0.1    2.2  2  Deltameth_res  Deltamethrin resistance
          3    8.1  10.0       0.99    9.6   3.6    2.9  2  ATPase_gene1   Putative F0F1-ATPase subunit Ca2+/Mg2+ transpo


Domain annotation for each model (and alignments):
>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00035       3.1      21      51 ..      11      39 ..       4      39 .. 0.85
   2 ?    2.6   0.0     0.014   1.3e+02       3      36 ..      52      85 ..      52      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00035
                 Deltameth_res 21 YNavLaaGiviligTialakesglinlnysp 51
                                  Y   La+G ++ + T++++ + +l+ l y+p
  gi|70606136|ref|YP_255006.1| 11 Y--ALALGALSGVTTLFFFLSLDLYALLYGP 39
                                  4..58********************999875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.014
                 Deltameth_res  3 lPvPeGdwkeqysakqrkYNavLaaGiviligTi 36
                                  lPv  G++   + +k+ k+   L + +v+ ++++
  gi|70606136|ref|YP_255006.1| 52 LPVIIGSFIAYFLTKKFKFSLRLSSVLVSCVISL 85
                                  5777799999999999999999888888887776 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4      0.24   2.2e+03      42      51 ..      15      24 ..      12      30 .. 0.55
   2 ?    9.6   3.6   0.00011      0.99       9      31 ..      48      70 ..      40     102 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.24
                  ATPase_gene1 42 lGlaaGfynv 51
                                  lG  +G+ ++
  gi|70606136|ref|YP_255006.1| 15 LGALSGVTTL 24
                                  5555555444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                  ATPase_gene1  9 ielvapillggllGywLDkkfgt 31
                                  + +v+p+++g ++ y+L kkf+ 
  gi|70606136|ref|YP_255006.1| 48 TRFVLPVIIGSFIAYFLTKKFKF 70
                                  569****************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 765.48
//
Query:       gi|70606137|ref|YP_255007.1|  [L=282]
Description: hypothetical protein Saci_0298 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.4   0.2       0.28   11.3   0.1    2.1  2  DUF1694   Protein of unknown function (DUF1694)
       0.12   12.1   0.1         14    5.4   0.0    2.1  2  ALO       D-arabinono-1,4-lactone oxidase


Domain annotation for each model (and alignments):
>> DUF1694  Protein of unknown function (DUF1694)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.18   1.6e+03      54      75 ..     167     189 ..     161     207 .. 0.74
   2 ?   11.3   0.1   3.1e-05      0.28      50     116 ..     209     278 ..     196     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                                   HHHHC-SSEEEEEETTS-.HHHH CS
                       DUF1694  54 ealkkkkalkllingkld.edil 75 
                                   ++l + +++ l+i+g+l+  +++
  gi|70606137|ref|YP_255007.1| 167 KQLPTTTEKGLIISGNLPkLNFT 189
                                   67788889999999999834444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHC..-SSEEEEEETTS-HHHHHHHHHHHHHTT--EEEE---.SS--SEEEEEEESS----S-- CS
                       DUF1694  50 keleealkk..kkalkllingkldedilskyiklakkenikftivnde.eaesdiglvvasdeAvnkeei 116
                                   ++l+++lk+   +  +l i g+  +++   +i   + +n+ + ++  e +++  +g++++s++ v ++ei
  gi|70606137|ref|YP_255007.1| 209 DKLTKLLKRflFETDNLTITGNFVYKNSTFVIYSLNVNNTTYALLGAEdHNDMITGVIIVSNSSVSVNEI 278
                                   5677777877778999****************************99886888889**********99988 PP

>> ALO  D-arabinono-1,4-lactone oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0025        23      56     107 ..      31      82 ..      20      97 .. 0.75
   2 ?    5.4   0.0    0.0015        14      64     105 ..     184     225 ..     163     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0025
                           ALO  56 teepeeskprkslkdellgrlvyeallalsrif..psltplverfvfklqygkg 107
                                   +  ++ ++++++++ ++lg + + +++ ls++f  p++t++++ f  + +y   
  gi|70606137|ref|YP_255007.1|  31 SPSND-QSSASQVTYKVLGTIYVYNVSYLSNYFmnPNVTKYINTFGSGVFYA-I 82 
                                   33344.6788999999**************65444**********9999998.2 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0015
                           ALO  64 prkslkdellgrlvyeallalsrifpsltplverfvfklqyg 105
                                   p+ +++++l+++ v+ ++  +++ f++lt+l++rf+f++   
  gi|70606137|ref|YP_255007.1| 184 PKLNFTGKLVNNQVILNFNYTGNNFDKLTKLLKRFLFETDNL 225
                                   6678999******************************97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1870.61
//
Query:       gi|70606138|ref|YP_255008.1|  [L=440]
Description: D-lactate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-45  153.7   0.0    1.1e-44  153.0   0.0    1.3  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    8.2e-44  148.7   0.0    1.7e-43  147.7   0.0    1.6  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.021   14.8   0.0       0.11   12.5   0.0    2.1  2  Phage_Arf      Accessory recombination function protein
      0.058   13.1   0.0       0.12   12.1   0.0    1.5  1  DUF4872        Domain of unknown function (DUF4872)


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.0   2.4e-48   1.1e-44       6     249 ..     203     428 ..     197     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 2.4e-48
                                   EEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHHHHH CS
                 FAD-oxidase_C   6 avalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelealvea 86 
                                    ++l+  +s+e+ +++++++++++i p   e++d + +++ +++++a    + + + +l++ +e d        le ++ +
  gi|70606138|ref|YP_255008.1| 203 YTILAYTDSLEDTAEVIVSLRKNKIMPELAEFVDYQVINALNKHLNA-GLEEVRDGGALIISVEEDY-------LE-ELKK 274
                                   345666799**************************************.888999999******9999.......55.4444 PP

                                   TTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEEEEEEEEE CS
                 FAD-oxidase_C  87 ileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglevvlfgHag 167
                                   il++      +v+ + +eae+++ +R  a      al+++g ++++eD++vPvsrl +++r+++++ ++y++++ +++H+g
  gi|70606138|ref|YP_255008.1| 275 ILGNK----KYVVAEGEEAERIYSLRAQAAI----ALKAEGKTMYIEDIVVPVSRLVEAIRRLREIERAYNVKMPTIAHIG 347
                                   44443....3445667888*********999....9********************************************* PP

                                   TTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....--------THHHHHHHHHHHH-TT-- CS
                 FAD-oxidase_C 168 dgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....ylerekgeeglalmrriKaalDPkgi 244
                                   dgnlh+++++     ++ +  +k+++ev+++a+elgGs+sgEHG+G++k++     +  ++g+e l+lm+riK+++DP +i
  gi|70606138|ref|YP_255008.1| 348 DGNLHPNVIY-----DDPKVGKKVFEEVAKVAIELGGSVSGEHGIGIQKAKllgdQIISHNGKEVLELMKRIKDLFDPYDI 423
                                   **********.....446666677***************************666666789********************* PP

                                   BSTT- CS
                 FAD-oxidase_C 245 LNPgk 249
                                   +NP k
  gi|70606138|ref|YP_255008.1| 424 MNPNK 428
                                   ***98 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   3.9e-47   1.7e-43       1     138 [.      23     160 ..      23     161 .. 0.98

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 3.9e-47
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                   p+++v+p++ee+v++++++a+e+++p+++ G+G+sl+g+ +++g+++ld++ +++i+ei+e +++a+v+aGv+l++l+++l
  gi|70606138|ref|YP_255008.1|  23 PKMIVYPRTEEDVVKIVNYARETKTPIVTWGAGTSLSGHLICDGCILLDMKYMDNIIEINEIDWYARVQAGVNLERLDKEL 103
                                   789*************************************99********77***************************** PP

                                   HHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  82 aakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                   +++g++l+++p+s+  ++vGGa+a+ +gG++  kyG+++d+vl l+vvl++G+vv++
  gi|70606138|ref|YP_255008.1| 104 EKRGFFLPPDPASFFLCSVGGATANSSGGMRGVKYGTFKDWVLALKVVLPNGKVVKI 160
                                   *******************************************************97 PP

>> Phage_Arf  Accessory recombination function protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05      0.11      14      39 ..      27      52 ..      24      56 .. 0.92
   2 ?   -1.5   0.0      0.57   2.5e+03      14      26 ..     227     239 ..     225     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                     Phage_Arf 14 isPEiEEEvEqqinLAAERqnPiitW 39
                                  + P  EE+v + +n A E + Pi+tW
  gi|70606138|ref|YP_255008.1| 27 VYPRTEEDVVKIVNYARETKTPIVTW 52
                                  67999********************* PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.57
                     Phage_Arf  14 isPEiEEEvEqqi 26 
                                   i PE+ E v+ q+
  gi|70606138|ref|YP_255008.1| 227 IMPELAEFVDYQV 239
                                   7899999999885 PP

>> DUF4872  Domain of unknown function (DUF4872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.8e-05      0.12      74     170 ..     235     336 ..     225     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                       DUF4872  74 kgakdlelalrqlvrmiEkaGTGGglFRrLyadFlqeaaellgdealael.seamteaadaWtelAalaaeasksrear.. 151
                                    + + +++  ++l +  E+ + GG+l     +d+l+e++++lg+++   +  e+++++ ++  ++A ++++ +k+  ++  
  gi|70606138|ref|YP_255008.1| 235 VDYQVINALNKHLNAGLEEVRDGGALIISVEEDYLEELKKILGNKKYVVAeGEEAERIYSLRAQAAIALKAEGKTMYIEdi 315
                                   56666777788999999****************************966551578999999999999999999999999899 PP

                       DUF4872 152 ..dlaeaadaleelaelEeel 170
                                      + ++ +a+++l+e E+++
  gi|70606138|ref|YP_255008.1| 316 vvPVSRLVEAIRRLREIERAY 336
                                   999999***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2872.53
//
Query:       gi|70606139|ref|YP_255009.1|  [L=175]
Description: nicotinamide-nucleotide adenylyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-14   51.9   0.0    1.2e-13   51.4   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.029   13.6   0.0        2.1    7.5   0.0    2.2  2  HIGH_NTase1      HIGH Nucleotidyl Transferase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.4e-17   1.2e-13       1     142 [.       4     134 ..       4     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.4e-17
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   l++G+F+p+HlGHl++++++++  ee li+++ s +++++   ++++a eRl m+++   +   i  ++ ++ + v++++ 
  gi|70606139|ref|YP_255009.1|   4 LFPGRFQPFHLGHLQVVKWLLDRYEE-LIIMIGSGQESHSP-YNPFTAGERLVMVKESLAETG-IDLRKVVIFP-VMESFT 80 
                                   799***********************.************99.****************66666.9999999997.999999 PP

                                   TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                   ++   +++  ++++      +++ i++ ++lv  + +e  + v   ++ ++  + +t+ir+
  gi|70606139|ref|YP_255009.1|  81 SK--NWIRIVEMYSP-----HFDVIISGNPLVYTVAKEAGYMVERVPMFNRDIYNATRIRK 134
                                   99..99999999998.....89999999999999999999999999999999999999996 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0025        23      10      39 ..       9      37 ..       8      38 .. 0.76
   2 ?    7.5   0.0   0.00023       2.1     200     239 ..     123     160 ..     103     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0025
                   HIGH_NTase1 10 YNPfHnGHlyhlekakeltgadvviavmSG 39
                                  + PfH GHl  ++       ++++i++ SG
  gi|70606139|ref|YP_255009.1|  9 FQPFHLGHLQVVKWLLDR-YEELIIMIGSG 37
                                  67*******998887776.45677777776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00023
                   HIGH_NTase1 200 eeeiaSAtaiRkalkeekkleelkklvPestleilkeelk 239
                                   +++i  At iRk++ e+    +  ++vP+s+ +++++   
  gi|70606139|ref|YP_255009.1| 123 NRDIYNATRIRKLIMEN--DLKWMECVPKSVSQFIRDIKG 160
                                   458999********776..46799********99987633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1284.40
//
Query:       gi|70606140|ref|YP_255010.1|  [L=203]
Description: hypothetical protein Saci_0301 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-54  184.5  19.8      2e-54  184.4  19.8    1.0  1  DUF981       Protein of unknown function (DUF981)
  ------ inclusion threshold ------
      0.027   14.2   0.7      0.027   14.2   0.7    2.5  2  Tetraspanin  Tetraspanin family
       0.19   11.1  15.8       0.19   11.1   9.3    2.1  2  TssN         Type VI secretion system, TssN
       0.37   10.5   0.0       0.37   10.5   0.0    3.3  4  DUF3188      Protein of unknown function (DUF3188)


Domain annotation for each model (and alignments):
>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4  19.8   4.4e-58     2e-54       1     186 [.       1     194 [.       1     195 [. 0.99

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 4.4e-58
                        DUF981   1 Ma.Fidyltlmlitlgagllllayyvlkal.....eerekkeankalaapflivGllalitGlhmtltWPlpgsYnilfgd 75 
                                   Ma Fid+lt +li+l+ ++l+lay ++k++     + +e +e+ ++l++p+l++G +++itGl++ l+WPlpgsYnilf+d
  gi|70606140|ref|YP_255010.1|   1 MAlFIDPLTSQLIVLASSFLVLAYGFIKTYftvhsSIQEYRESLRSLYMPLLVMGSFMAITGLYGLLVWPLPGSYNILFYD 81 
                                   999*******************************99********************************************* PP

                        DUF981  76 pallfGvllllaavalykkaklkalgilalflGlilivygvailklgLtaePlaalllyilvGLagllsplvllkldksrs 156
                                    ++++G+ l+++a++l++++kl+ +g+lal+lGl++i+ygv+++  gLt+eP+a+l+ly+lvGLa+ ++++v +  d++++
  gi|70606140|ref|YP_255010.1|  82 LYPILGLGLMGIAFSLKNNYKLELFGFLALILGLVTIYYGVQGYFKGLTTEPIALLGLYTLVGLASFFFYPVSIFVDNASK 162
                                   ****************************************************************************99987 PP

                        DUF981 157 ..vllvlaavlliiagllalliGieavyeHla 186
                                     ++l++  v+li+++lla +i++eav++Hl+
  gi|70606140|ref|YP_255010.1| 163 gkIFLIIDSVFLILSALLAGYIALEAVPAHLS 194
                                   88****************************95 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   5.9e-06     0.027      10      69 ..      12      67 ..       8      71 .. 0.76
   2 ?   -1.4   8.8      0.34   1.5e+03       3      90 ..     101     148 ..      77     189 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.9e-06
                                  XXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin 10 llfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGci 69
                                  l+++  + ++la+G+  +    + + ++  +e  e+ ++l+++l+v+G++++++g+ G++
  gi|70606140|ref|YP_255010.1| 12 LIVLASSFLVLAYGFIKT----YFTVHSSIQEYRESLRSLYMPLLVMGSFMAITGLYGLL 67
                                  788889999999993332....2233344555678899999*****************86 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                   Tetraspanin   3 yllfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcig.alkenkcllltf 82 
                                   y l +f +l +++g+v + +G                                         + G +     e + ll+++
  gi|70606140|ref|YP_255010.1| 101 YKLELFGFLALILGLVTIYYG-----------------------------------------VQGYFKgLTTEPIALLGLY 140
                                   444455555555555555555.........................................4443321444444444444 PP

                                   XXXXXXXX CS
                                   xxxxxxxx RF
                   Tetraspanin  83 sllllvlf 90 
                                    l+ l  f
  gi|70606140|ref|YP_255010.1| 141 TLVGLASF 148
                                   43333333 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.4    0.0049        22       6      57 ..      20      71 ..      15      88 .. 0.67
   2 ?   11.1   9.3   4.1e-05      0.19      33     153 ..      77     192 ..      70     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0049
                          TssN  6 llpllavilllilsliakknkllkkkkliiyiLlaglvlalpgllgflknef 57
                                  l+++  +i + +++  + ++   + ++l++ +L++g ++a++gl g+l   +
  gi|70606140|ref|YP_255010.1| 20 LVLAYGFIKTYFTVHSSIQEYRESLRSLYMPLLVMGSFMAITGLYGLLVWPL 71
                                  555555555555555555555667899*******************976554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.1e-05
                          TssN  33 liiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkffkelkekkilfeilltlivillglvlfvl 113
                                   +++y L  +l l+l+g+   lkn++    + l+ +l+l+lG++ +y+ ++ +fk l++++  + +l + + + l++++f+ 
  gi|70606140|ref|YP_255010.1|  77 ILFYDLYPILGLGLMGIAFSLKNNYK---LELFGFLALILGLVTIYYGVQGYFKGLTTEP--IALLGLYTLVGLASFFFYP 152
                                   56777777777777777777777766...556677899**********************..7788888888999999999 PP

                          TssN 114 vfnllselqygvwaatsllvfiipllflktykallsIPve 153
                                   v  ++ + + g   +    vf+i + +l  y al ++P++
  gi|70606140|ref|YP_255010.1| 153 VSIFVDNASKGKIFLIIDSVFLILSALLAGYIALEAVPAH 192
                                   9999999998888888889999999999999999999986 PP

>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.2e-05      0.37      23      43 ..      45      65 ..      39      67 .. 0.86
   2 ?   -0.3   0.6      0.21   9.3e+02      24      45 ..     105     126 ..      85     128 .. 0.50
   3 ?    0.6   0.8      0.11   4.7e+02       7      35 ..     112     140 ..     107     151 .. 0.60
   4 ?   -3.6   0.4       2.1   9.5e+03       4      11 ..     173     180 ..     166     181 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.2e-05
                       DUF3188 23 rlqslPallvGlgLivsgavg 43
                                  r  ++P+l++G++  ++g++g
  gi|70606140|ref|YP_255010.1| 45 RSLYMPLLVMGSFMAITGLYG 65
                                  6679**************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                       DUF3188  24 lqslPallvGlgLivsgavgrg 45 
                                   l+ + al  Gl+ i  g+ g++
  gi|70606140|ref|YP_255010.1| 105 LFGFLALILGLVTIYYGVQGYF 126
                                   4444455666666666666665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.11
                       DUF3188   7 llgllillysqrqgsdrlqslPallvGlg 35 
                                    lgl+ + y+     ++l   P++l Gl 
  gi|70606140|ref|YP_255010.1| 112 ILGLVTIYYGVQGYFKGLTTEPIALLGLY 140
                                   35666666665555555777788888875 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.1
                       DUF3188   4 lLillgll 11 
                                   +Lil +ll
  gi|70606140|ref|YP_255010.1| 173 FLILSALL 180
                                   66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1515.12
//
Query:       gi|70606141|ref|YP_255011.1|  [L=206]
Description: haloacid dehalogenase-like hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-12   45.3   0.2    2.4e-11   44.1   0.2    1.6  1  HAD_2           Haloacid dehalogenase-like hydrolase
     0.0088   16.1   0.0      0.016   15.3   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
       0.03   13.0   0.1       0.04   12.6   0.1    1.1  1  PSII            Photosystem II protein
      0.042   14.1   0.0        1.3    9.3   0.0    2.1  2  Hydrolase       haloacid dehalogenase-like hydrolase
      0.069   13.7   0.4        3.9    8.1   0.0    2.5  2  SF3A3           Pre-mRNA-splicing factor SF3A3, of SF3a compl


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.2   6.6e-15   2.4e-11       3     178 .]      10     172 ..       8     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 6.6e-15
                         HAD_2   3 FDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpydg 83 
                                   FD+ gT+ld + +i ++ ++ le  +l    + +++++ +++   l + l+++ e+e+  eel +k+n+   +   k +++
  gi|70606141|ref|YP_255011.1|  10 FDVFGTILDLSSIIQEFRRKQLEYTWL-LTILGKFATFEEITKLALQSTLTSRGEMEKFNEEL-NKWNNLRSHSDAKYLQD 88 
                                   9999******************88877.55566777777777766666667766666566666.55555544447888888 PP

                         HAD_2  84 vkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptD 164
                                   + e+++            +++s ++v ++le++g+ ++F+ +v++e+v+  KP+p v++ ++++      ++  v  +p+D
  gi|70606141|ref|YP_255011.1|  89 MSEIVDIY--------ALSNGSMKEVSMHLEHNGLLKFFKGVVSAEEVKVYKPSPLVYKHFMKSVTP---NAYLVSSNPFD 158
                                   88877654........579*******************************************98754...5678999**** PP

                         HAD_2 165 ieaakkagikviav 178
                                   +++ak+ag+ +i v
  gi|70606141|ref|YP_255011.1| 159 VIGAKNAGMGAIYV 172
                                   *********99865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.4e-06     0.016       4      74 ..     132     195 ..     130     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
                                   TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                   KP+p +y+  ++ ++    + +++  +   D++gA+naG+  + V + +   + l    ++p+ v++d+ e
  gi|70606141|ref|YP_255011.1| 132 KPSPLVYKHFMKSVTP---NAYLVSSN-PFDVIGAKNAGMGAIYVNRFNQPIDPL---GYQPDLVVKDFHE 195
                                   9*******99998755...78******.9****************9866555554...4899999999877 PP

>> PSII  Photosystem II protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.1e-05      0.04      12      53 ..      98     139 ..      95     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                          PSII  12 vindsGrllavHlaHtalvagwaGsmalfelavfdpsdpvlk 53 
                                   + n s + +++Hl H++l+ ++ G +   e+ v++ps  v k
  gi|70606141|ref|YP_255011.1|  98 LSNGSMKEVSMHLEHNGLLKFFKGVVSAEEVKVYKPSPLVYK 139
                                   567888999****************************33333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.028     1e+02       4      26 ..       8      30 ..       7      80 .. 0.73
   2 ?    9.3   0.0   0.00036       1.3     129     210 .]      85     166 ..      81     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.028
                                  EEEESBTTTBCHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  4 vvfDkdGTLttgepsvedvivsa 26
                                  ++fD+ GT+++ ++ + ++ ++ 
  gi|70606141|ref|YP_255011.1|  8 LAFDVFGTILDLSSIIQEFRRKQ 30
                                  89********9886666655554 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                                   HHHHT.TE.EEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHH CS
                                   xxxxx.xx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 129 sLkaa.gi.evvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaal 206
                                   +L+++  i +++ l++++ + +   +++ G  ++f++v+++++++v kpsp  +++ ++     p +   V  ++ D+ ++
  gi|70606141|ref|YP_255011.1|  85 YLQDMsEIvDIYALSNGSMKEVSMHLEHNGlLKFFKGVVSAEEVKVYKPSPLVYKHFMKSV--TP-NAYLVSSNPFDVIGA 162
                                   6788888889*************999999988999*******************9999988..22.367777777777777 PP

                                   HHTT CS
                                   xxxx RF
                     Hydrolase 207 aaAg 210
                                   ++Ag
  gi|70606141|ref|YP_255011.1| 163 KNAG 166
                                   7765 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       3.9       8      45 ..      13      50 ..      10      61 .. 0.79
   2 ?    3.3   0.1     0.033   1.2e+02      10      44 ..      63      95 ..      56     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                         SF3A3  8 yGkylDLnelyeeylnlkeikldYlqYLesfdkf...seip 45
                                  +G +lDL+++ +e+   +   l+Y++ L+ + kf   +ei+
  gi|70606141|ref|YP_255011.1| 13 FGTILDLSSIIQEFRRKQ---LEYTWLLTILGKFatfEEIT 50
                                  89************9988...69999999998883334444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.033
                         SF3A3 10 kylDLnelyeeylnlkeikldYlqYLesfdkfsei 44
                                  ++  +ne  ++++nl     +  +YL++++++ +i
  gi|70606141|ref|YP_255011.1| 63 EMEKFNEELNKWNNLRS--HSDAKYLQDMSEIVDI 95
                                  55566777889999996..4445555555544332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1644.17
//
Query:       gi|70606142|ref|YP_255012.1|  [L=103]
Description: MIase like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-18   64.1   0.0    1.2e-17   63.8   0.0    1.1  1  MIase           Muconolactone delta-isomerase
     0.0045   16.9   0.0     0.0046   16.9   0.0    1.2  1  GYD             GYD domain
  ------ inclusion threshold ------
      0.096   12.8   0.3       0.16   12.0   0.1    1.6  1  SAM_Exu         Exuperantia SAM-like domain
       0.12   12.4   0.0       0.17   11.9   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   2.6e-21   1.2e-17       1      87 [.       1      91 [.       1      93 [. 0.95

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.6e-21
                         MIase  1 mlFlvemtvklpedlpaeevaelkarekaraqelqrqGklvrlwrvvgeyanisifdvedndeLhelLssLPlfp....ymti 79
                                  mlFl+ ++vk pe+++++++ e++++e+++a    + Gk++ l++v g++++++i+dv++++eL+e+L++LP++      +++
  gi|70606142|ref|YP_255012.1|  1 MLFLLWFKVKQPESIDQKKLMEIWTKEAEAALSAVKGGKIKGLYKVSGKREVVAILDVSSHEELDEILETLPITRelghSVNV 83
                                  9************************************************************************9988778888 PP

                         MIase 80 evtpLarH 87
                                  +v p++ +
  gi|70606142|ref|YP_255012.1| 84 DVFPIHPY 91
                                  88888877 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-06    0.0046      20      63 ..      23      66 ..       7      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                           GYD 20 erreeakealvesl.GgkleslyatlGeyDvvvivEapDdetaaa 63
                                   + +ea++al +++ Ggk++ ly + G+  vv+i+++  +e+   
  gi|70606142|ref|YP_255012.1| 23 IWTKEAEAAL-SAVkGGKIKGLYKVSGKREVVAILDVSSHEELDE 66
                                  4456777777.7777**********************99987655 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.7e-05      0.16      29      71 ..      14      57 ..       8      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                       SAM_Exu 29 gidyesLkeiweekkkeGlekllkekitsl.keedkeeLlelLd 71
                                   id ++L eiw+++ +++l ++   ki+ l k + k e++ +Ld
  gi|70606142|ref|YP_255012.1| 14 SIDQKKLMEIWTKEAEAALSAVKGGKIKGLyKVSGKREVVAILD 57
                                  58889******************9***9974678999*****98 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.17      12      56 ..      24      70 ..      14      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                  HHHHHHHHHHTST..TEEEEEEESSSSSEEEEEEESSHHHHHHHHHH CS
                AsnC_trans_reg 12 qleefeealaelp..eVvecyrvtGdydyllkvvvrdlealerflre 56
                                  +++e+e+al +++   ++ +y+v+G    +++  v + e+l+++l++
  gi|70606142|ref|YP_255012.1| 24 WTKEAEAALSAVKggKIKGLYKVSGKREVVAILDVSSHEELDEILET 70
                                  56666777777552259999************************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 655.85
//
Query:       gi|70606143|ref|YP_255013.1|  [L=184]
Description: hypothetical protein Saci_0304 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        5.6    6.5  14.2       0.16   11.5   4.2    2.9  3  Smim3      Small integral membrane protein 3


Domain annotation for each model (and alignments):
>> Smim3  Small integral membrane protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2     0.066   1.2e+03      22      34 ..      73      82 ..      64      89 .. 0.55
   2 ?   11.5   4.2   8.7e-06      0.16      10      47 ..     106     142 ..      97     156 .. 0.77
   3 ?    1.1   0.2     0.015   2.8e+02      13      34 ..     160     182 ..     150     184 .] 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.066
                         Smim3 22 vivLiiLativim 34
                                  v   i L  i i+
  gi|70606143|ref|YP_255013.1| 73 V---IFLVIIHIL 82
                                  3...333333333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.7e-06
                         Smim3  10 evvLPkhiLDiWvivLiiLativimtsLlLCPatavii 47 
                                   + ++   iL + vi+LiiLa i++ t  +  P    i+
  gi|70606143|ref|YP_255013.1| 106 KSTFLNSILQMNVILLIILA-IIVNTLFVFLPVGVFIV 142
                                   55666789***********9.66789999999766555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.015
                         Smim3  13 LPkhiLD.iWvivLiiLativim 34 
                                   L k   D i+ + L+iLa  v++
  gi|70606143|ref|YP_255013.1| 160 LTKFNFDyIYSVTLLILALAVLL 182
                                   56666665899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1166.77
//
Query:       gi|70606144|ref|YP_255014.1|  [L=466]
Description: selenium-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.2e-205  682.8   0.0   2.5e-205  682.6   0.0    1.0  1  SBP56      56kDa selenium binding protein (SBP56)
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.24   11.5   0.0    1.3  1  Rad54_N    Rad54 N terminal
       0.21   10.8   0.0          2    7.6   0.0    2.3  3  Lactonase  Lactonase, 7-bladed beta-propeller


Domain annotation for each model (and alignments):
>> SBP56  56kDa selenium binding protein (SBP56)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.6   0.0  4.1e-209  2.5e-205       2     454 .]      11     464 ..      10     464 .. 0.99

  Alignments for each domain:
  == domain 1  score: 682.6 bits;  conditional E-value: 4.1e-209
                         SBP56   2 kadPg.yasPkeaikapreklayvaaleanteiekpDalavvdvdpesetyskvvhrvelpnlgdelhhfGWnaCss..ch 79 
                                   k+dP+ y+sPk+ai++p+e+layva+l+++t+i++pD++avvdv+p+sety+kvv +velp++gdelhhfGWnaCss  c+
  gi|70606144|ref|YP_255014.1|  11 KRDPTfYPSPKMAINSPPEDLAYVACLYVGTKINRPDYIAVVDVNPKSETYTKVVAKVELPYTGDELHHFGWNACSSslCP 91 
                                   78*************************************************************************999*** PP

                         SBP56  80 aedaskerrylivPglrssriyvvdtktdprkpklvkviepeevaektglsrphtvhClpegeilisalgdaeGegkggil 160
                                   ++++++err+l+vPglrssriy++dtk dprkp++vkvi+pee+++ tg+sr htvhC+p++ i+isalg++ Ge++ggil
  gi|70606144|ref|YP_255014.1|  92 NGRPNVERRFLVVPGLRSSRIYIIDTKLDPRKPNIVKVIQPEEIKKVTGYSRLHTVHCGPDA-IYISALGNEVGEEPGGIL 171
                                   **************************************************************.****************** PP

                         SBP56 161 lldketfevkgrWekdrekqelaYDfwyqlrkdvmvsseWgaPkafekGldledleegkyGkrlhvwdleerkllqtidlg 241
                                   +ld+ +fe+ g+We+ re+q+l+YDfw++l +++mv+seW++P+++e+Gl++e+l+e+ yG+r+h+wdl++rk++++i+lg
  gi|70606144|ref|YP_255014.1| 172 MLDHYSFEPLGKWEIYREDQKLSYDFWWNLPNEIMVTSEWATPTTIENGLNPEHLKEK-YGNRIHFWDLRKRKKISSITLG 251
                                   *******************************************************986.********************** PP

                         SBP56 242 eegqlvlevrflhdPkkaegfvgvv.....Lsssvfrfykeedekweaekvieipakkvegeelpel.......pglvtDi 310
                                   ee++++le+r+lhdP+k +gf+++v     Lsss++ ++  ed+kw+a+kvi+ipa+++eg+ lp++       p+lvtDi
  gi|70606144|ref|YP_255014.1| 252 EENRMALELRPLHDPTKLMGFINLVvslkdLSSSIWLWFF-EDGKWQAQKVIDIPAEPAEGN-LPDIlkpfkavPPLVTDI 330
                                   ************************99**************.99*****************97.888889999*9******* PP

                         SBP56 311 llslDDrflyvsnWltGdlrqydisdpkkPkltgqvrlGGiirkaehpavkgrkleggPqmvelslDGkrlYvtnsLysaw 391
                                   +lslDD+flyvs W+tG+lrqyd+s+p+kP+ltg+v+lGGi+ +a+hp+ +  kl+g+Pqmve+s+DG+r+YvtnsLys+w
  gi|70606144|ref|YP_255014.1| 331 DLSLDDKFLYVSLWGTGELRQYDVSNPFKPVLTGKVKLGGILYRADHPSGN--KLTGAPQMVEISRDGRRIYVTNSLYSSW 409
                                   ***********************************************9866..**************************** PP

                         SBP56 392 ddqfypelvkkgsvllkidvdtekGglsldknflvdfgkepegparahevryegGDassDiyi 454
                                   d+qfype+v  +++l+k+++++e Ggl++dk+f+vdfg+     arah++r++gGDassD+y+
  gi|70606144|ref|YP_255014.1| 410 DNQFYPEGV--KGWLVKLNANPE-GGLDIDKEFFVDFGE-----ARAHQTRLRGGDASSDSYC 464
                                   *********..************.***************.....8*****************8 PP

>> Rad54_N  Rad54 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.1e-05      0.24     104     127 ..     244     267 ..     237     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                       Rad54_N 104 lrppptLGtrkkvilvprpLhDPt 127
                                   +++ +tLG  +++ l+ rpLhDPt
  gi|70606144|ref|YP_255014.1| 244 KISSITLGEENRMALELRPLHDPT 267
                                   34899******************8 PP

>> Lactonase  Lactonase, 7-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         1     6e+03     313     334 ..      47      68 ..      37      72 .. 0.55
   2 ?    7.6   0.0   0.00033         2     209     275 ..     280     356 ..     275     374 .. 0.74
   3 ?    0.0   0.0     0.067     4e+02      37      55 ..     385     403 ..     366     430 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1
                                   TEEEEEEEETTTTEEEEESEEE CS
                     Lactonase 313 dnvtvferdaetGkLtelgkdi 334
                                   d ++v+ +++++   t++++++
  gi|70606144|ref|YP_255014.1|  47 DYIAVVDVNPKSETYTKVVAKV 68 
                                   3455555555555555555554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00033
                                   ETTTTEEEEEEEE-TTTEEEEEEEEESS-TSS-S-............--EEEEEE-TTSSEEEEEETSSTEEEEEEE-T CS
                     Lactonase 209 nELsstvsvfsydeatgaleelqtvstlpegftgk............nsaaeIrlspdgkflyvSnRgadsiavfavde 275
                                   + Lss++  + ++  +g+++  + ++  +e ++g+                +I ls d+kflyvS  g+ ++  ++v++
  gi|70606144|ref|YP_255014.1| 280 KDLSSSIWLWFFE--DGKWQAQKVIDIPAEPAEGNlpdilkpfkavpPLVTDIDLSLDDKFLYVSLWGTGELRQYDVSN 356
                                   6788888888888..666654444433333455556677888887776899***************9999999999954 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.067
                                   S---SEEE-TTSSEEEEEE CS
                     Lactonase  37 enPsyLalspdgktlYavn 55 
                                   + P+ +++s+dg+++Y+ n
  gi|70606144|ref|YP_255014.1| 385 GAPQMVEISRDGRRIYVTN 403
                                   4555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3282.33
//
Query:       gi|70606145|ref|YP_255015.1|  [L=665]
Description: acetyl-CoA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-90  303.0   0.0    3.4e-90  302.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      2e-28   99.2   4.5      5e-28   97.9   1.3    2.5  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.4e-20   71.7   2.1      8e-20   70.5   2.1    1.7  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.7   0.0   5.7e-94   3.4e-90       3     423 .]      85     534 ..      83     534 .. 0.89

  Alignments for each domain:
  == domain 1  score: 302.7 bits;  conditional E-value: 5.7e-94
                                   HHHHHST.TSEEEEE..........CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT CS
                   AMP-binding   3 eqaaktp.dkvalvd..........sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaG 71 
                                   ++a+ ++ +kva+ +           +e ++lTY++l+++vnr+A  L+ +  +kkgd++ai+lp+ pe+ + +la++++G
  gi|70606145|ref|YP_255015.1|  85 RHAKSWRkNKVAILWegepvdergnPKEVRKLTYHDLYKEVNRVAYLLKeKYKLKKGDTIAIYLPMIPELPIFMLAAARLG 165
                                   6666666699999889999999999899*********************999***************************** PP

                                   -EEEEEETTS-HHHHHHHHHHHTESEEE.......E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCC CS
                   AMP-binding  72 avvvplnptltaeelayiledseakvli.......a..tvdselleklleaaakleavklvivldadellkeeelkeeees 143
                                   +v  ++ ++++a++la  ++d+eak+++       +   v+    + +++a +k ++vk viv+ + + + + ++  ++  
  gi|70606145|ref|YP_255015.1| 166 VVFTVVFSGFSADALANRINDAEAKLVVtadggwrRgkIVEL--KQIVDKALEKTPTVKDVIVVRRTGHKVNMMEGRDKYF 244
                                   *****************************9998862533222..45567777777899999***99999988777766655 PP

                                   SCTTS......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHH CS
                   AMP-binding 144 eekae......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifgli 218
                                   +e+ +        +e+e+lk++d++yi+YTSGTTGkPKG+++  + + + +++  ++  f++++dd +++++++ +++g++
  gi|70606145|ref|YP_255015.1| 245 DEVIKdipqnvY-VEPERLKSEDPLYILYTSGTTGKPKGIVHDIGGYETLLHAT-MRWVFDIRDDDIYWCTADIGWVTGHS 323
                                   554425667753.467799***************************98888885.555588889***************** PP

                                   HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHH CS
                   AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspe 298
                                   + ++++l+ Gat v++++  + ++p++++  ie+++vt++++ P++++ +++ g++  ++k++d s +rl+ ++gep++pe
  gi|70606145|ref|YP_255015.1| 324 YIVFGPLTEGATTVMYEGALDyPQPDRWVSIIERHSVTILYTSPTAIRTFMKFGEE--WVKKHDTSTVRLIHSVGEPINPE 402
                                   *******************99777****************************5444..57889****************** PP

                                   HHHHHHHHHTC...EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET CS
                   AMP-binding 299 llrffralfge...evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp 372
                                   +++++ +l+g+   ++  ++++TEt+g+++     l+l     k+g+ G p+ gve+ +v+++ g+p   +  G l+++ p
  gi|70606145|ref|YP_255015.1| 403 AQDWMWKLVGReeiPFGSTWWMTETGGIMIShlpgLYLIPM--KPGTNGMPIMGVEADVVNDD-GKPSNLEDRGYLVIKNP 480
                                   *****************************555777332233..589****************9.****************9 PP

                                   ..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEET CS
                   AMP-binding 373 ..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdliklr 423
                                     g+    +k+pe+  ++++s+ ++++  GD ++ d+dGy++i+gR++++ik++
  gi|70606145|ref|YP_255015.1| 481 wpGMPLTIYKDPERYVKVYWSKfPGMFYAGDYAVKDRDGYFWILGRADEVIKVS 534
                                   778*****************86778***************************85 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.096   5.8e+02      42      67 ..     203     228 ..     187     233 .. 0.69
   2 !   97.9   1.3   8.3e-32     5e-28       1      76 []     542     620 ..     542     620 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.096
                                   HHHHHHHHHHHHT-TTTS-SEEEE-S CS
                 AMP-binding_C  42 leeeLkahvrkelgpyavpkkvvfvd 67 
                                      eLk+ v k+l++  + k+v++v 
  gi|70606145|ref|YP_255015.1| 203 KIVELKQIVDKALEKTPTVKDVIVVR 228
                                   46789999999999888888888774 PP

  == domain 2  score: 97.9 bits;  conditional E-value: 8.3e-32
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+Esal++hpaVaeaaVvGvpd+vkGe++ afVvl++g+++   l +e+ + vr+++gp+av +kv fv++lpktrsGK
  gi|70606145|ref|YP_255015.1| 542 ELESALIEHPAVAEAAVVGVPDPVKGEVPYAFVVLRSGQTPsqqLTQEILKTVREKVGPIAVVDKVFFVSKLPKTRSGK 620
                                   89*********************************988522357**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   2.1   1.3e-23     8e-20       1      54 [.      28      81 ..      28      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 1.3e-23
                                  HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHH CS
                        ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyN 54
                                  yke++ + ++++  FWa++a+el+W+kp++kvld+s++pf+kWF+GG++N++y 
  gi|70606145|ref|YP_255015.1| 28 YKEIHSQTVKEYRNFWASVASELEWFKPWEKVLDDSNPPFYKWFVGGEINASYL 81
                                  99**************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4071.91
//
Query:       gi|70606146|ref|YP_255016.1|  [L=248]
Description: biotin/lipoate A/B protein ligase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0017   18.2   0.1     0.0026   17.7   0.1    1.3  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.4e-07    0.0026      12     129 ..      49     157 ..      37     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-07
                                   HH..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TT CS
                 BPL_LplA_LipB  12 lkeslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegip 92 
                                   +k+++n++ +++ g+ v+rr tgG  v+h+  g+ +y+++l+ ++  ++ + + ++   l   +++al       +i g  
  gi|70606146|ref|YP_255016.1|  49 VKDEVNIEVTNQLGIPVIRRITGGGTVYHD-MGNFNYTVILENKD--VKVKGIDFLYGFLLKGTINAL------ERIIGDR 120
                                   578999999*********************.***********777..554466666555555677777......5777888 PP

                                   EEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEE CS
                 BPL_LplA_LipB  93 vfikwpnDlyvngrKlaGiavtstrgktlhhivigvg 129
                                   v+     D+ ++  K++G a     +k l h++++++
  gi|70606146|ref|YP_255016.1| 121 VETYNQTDIAYKHYKISGNAGYISNNKYLLHGTLLIN 157
                                   8866888999999999887777666677777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1912.16
//
Query:       gi|70606147|ref|YP_255017.1|  [L=82]
Description: hypothetical protein Saci_0308 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-12   47.1   1.1    2.3e-12   46.6   1.1    1.2  1  Biotin_lipoyl    Biotin-requiring enzyme
    3.2e-08   33.3   4.2     0.0006   19.6   1.7    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0033   17.3   0.2     0.0038   17.1   0.2    1.2  1  GCV_H            Glycine cleavage H-protein
     0.0076   15.5   0.3       0.19   10.9   0.2    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0077   16.0   0.2        3.1    7.6   0.1    2.0  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.021   14.8   0.2    1.4  1  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.017   15.8   1.5        3.5    8.4   0.1    2.2  2  HlyD_3           HlyD family secretion protein


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   1.1   8.9e-16   2.3e-12      15      71 ..      20      77 ..      16      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 8.9e-16
                                  ..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEE CS
                 Biotin_lipoyl 15 g.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdlla 71
                                  g vv+v+v +G+ V  ++ +aeve  K++ +i ++++G+v ++lv++Gd+v  g++la
  gi|70606147|ref|YP_255017.1| 20 GeVVSVYVREGSYVDFDDLVAEVEIEKVVLKILSQVKGRVLKVLVNQGDKVGPGSILA 77
                                  55889***************************************************98 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   8.3e-06     0.021      10      33 ..      19      42 ..      15      47 .. 0.87
   2 !   19.6   1.7   2.3e-07    0.0006       2      31 ..      48      77 ..      41      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.3e-06
               Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLael 33
                                  +G V++++V++G +V   d+ ae 
  gi|70606147|ref|YP_255017.1| 19 DGEVVSVYVREGSYVDFDDLVAEV 42
                                  9**************988887775 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.3e-07
               Biotin_lipoyl_2  2 vvsIaapvsGrVaqlnVkdGqrVkaGdvLa 31
                                  v +I ++v GrV +++V +G+ V  G +La
  gi|70606147|ref|YP_255017.1| 48 VLKILSQVKGRVLKVLVNQGDKVGPGSILA 77
                                  47899*********************9998 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.5e-06    0.0038      31      74 ..      20      62 ..      15      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                  -SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                         GCV_H 31 gdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74
                                  g+vv+v ++ +g  v+ ++ +a vE  K + ++ ++v+G v++v
  gi|70606147|ref|YP_255017.1| 20 GEVVSVYVR-EGSYVDFDDLVAEVEIEKVVLKILSQVKGRVLKV 62
                                  788999887.59*****************************886 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0078        20     115     139 ..      18      42 ..       6      48 .. 0.75
   2 !   10.9   0.2   7.4e-05      0.19      16      51 ..      45      79 ..      37      82 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0078
                                   XXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 115 isGvVteknvreGqyvqpgdtlfti 139
                                    +G V++  vreG+yv+ +d ++++
  gi|70606147|ref|YP_255017.1|  18 WDGEVVSVYVREGSYVDFDDLVAEV 42 
                                   5788888888888888877776665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 16 errlarvsarveGwveklyvnatgdkVkkGqpLael 51
                                  e+ + ++ ++v+G+v k+ vn  gdkV  G  La +
  gi|70606147|ref|YP_255017.1| 45 EKVVLKILSQVKGRVLKVLVN-QGDKVGPGSILALV 79
                                  456677888899999999999.89999999888766 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0012       3.1      80     109 ..      19      48 ..      15      55 .. 0.89
   2 !    7.4   0.0    0.0014       3.6      78     103 ..      54      79 ..      50      82 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                   TTTTEEES----SEE-SEEEEEEE-HHHHG CS
                    PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleaik 109
                                   +ge+ +++v+eg+ V   d+++ev++e++ 
  gi|70606147|ref|YP_255017.1|  19 DGEVVSVYVREGSYVDFDDLVAEVEIEKVV 48 
                                   79999*********************9985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                                   TTTTTTEEES----SEE-SEEEEEEE CS
                    PTS_EIIA_1  78 klkgegFellvkegdkVkagdklvev 103
                                   ++kg++ ++lv++gdkV  g+ l+ v
  gi|70606147|ref|YP_255017.1|  54 QVKGRVLKVLVNQGDKVGPGSILALV 79 
                                   6899***************9988766 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   8.1e-06     0.021      20      59 ..      38      77 ..      25      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.1e-06
                        RnfC_N 20 pieklplpkelvlplsqhiGapakplvkvgdkVlkGqkia 59
                                   +++++++k ++  lsq  G   k+lv++gdkV  G ++a
  gi|70606147|ref|YP_255017.1| 38 LVAEVEIEKVVLKILSQVKGRVLKVLVNQGDKVGPGSILA 77
                                  57889999999999********************999887 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0014       3.5       6      31 ..      18      43 ..      17      49 .. 0.90
   2 ?    6.9   0.1     0.004        10       2      28 ..      51      77 ..      50      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                        HlyD_3  6 vdGvvvelnveegevvqagdelleii 31
                                   dG+vv++ v+eg++v   d ++e+ 
  gi|70606147|ref|YP_255017.1| 18 WDGEVVSVYVREGSYVDFDDLVAEVE 43
                                  59*********************985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.004
                        HlyD_3  2 lrApvdGvvvelnveegevvqagdell 28
                                  + + v G+v ++ v++g+ v +g  l+
  gi|70606147|ref|YP_255017.1| 51 ILSQVKGRVLKVLVNQGDKVGPGSILA 77
                                  7899******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 645.07
//
Query:       gi|70606148|ref|YP_255018.1|  [L=286]
Description: lipoyl synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-16   59.9   0.1    7.4e-16   59.0   0.0    1.5  2  Radical_SAM      Radical SAM superfamily
     0.0019   18.0   0.4      0.009   15.9   0.1    2.3  3  DUF3198          Protein of unknown function (DUF3198)
     0.0098   15.8   0.0      0.044   13.7   0.0    2.0  2  Myb_DNA-bind_7   Myb DNA-binding like
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.29   11.2   0.1    1.8  2  Phage_int_SAM_6  Phage integrase SAM-like domain
       0.11   12.9   0.1        0.3   11.5   0.1    1.7  1  LIAS_N           N-terminal domain of lipoyl synthase of Radi


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   2.1e-19   7.4e-16       4     167 .]      52     209 ..      49     209 .. 0.94
   2 ?   -3.0   0.0       2.3   8.3e+03     127     143 ..     238     254 ..     228     279 .. 0.53

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.1e-19
                                   ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpgiri 80 
                                   +  C+++C+fC++++     g++  l+ ee ++ +++++ e+g ++v++++ + ++ +d     +  + +a    +p++ +
  gi|70606148|ref|YP_255018.1|  52 GDICTRGCRFCYVKK-----GKPVLLDHEEPIKVAEAVR-EMGLDYVVITSVDRDDLADGGASHFSQVVKAvkemNPDVIV 126
                                   678***********5.....9*****************5.*******************************9999999999 PP

                                   EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeel 160
                                    v t+ ++ ++e +e+    gvd++++++e++ +     l++  + ++e+ l++l +++++ +k  ++ i+++ Ge+ ee+
  gi|70606148|ref|YP_255018.1| 127 EVLTPDFMGNKELVEKVIGSGVDVFAHNVETVRS--LTPLVRdARASYEQSLRVLSYAKNV-VK--KSSILLGLGESLEEV 202
                                   9999999999************************..577777777****************.99..8************** PP

                                   HHHHHHH CS
                                   xxxxxxx RF
                   Radical_SAM 161 eellell 167
                                   +e++++l
  gi|70606148|ref|YP_255018.1| 203 VETMKDL 209
                                   ***9875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHTTSE CS
                                   xxxxxxxxxxxxxxxxx RF
                   Radical_SAM 127 feevlealeklreagik 143
                                    ee++e+ +++ ++g+ 
  gi|70606148|ref|YP_255018.1| 238 MEEYKELEKIAYSLGFS 254
                                   34444333333333333 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.6   9.3e+03      20      29 ..      11      20 ..      11      24 .. 0.74
   2 ?   -2.3   0.0       1.2   4.2e+03      19      40 ..     155     176 ..     152     177 .. 0.82
   3 !   15.9   0.1   2.5e-06     0.009      15      48 ..     234     267 ..     231     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
                                  HHHHHHHHHH CS
                       DUF3198 20 knlkeLekia 29
                                  +n k+L +i 
  gi|70606148|ref|YP_255018.1| 11 ENFKKLSRIV 20
                                  5889998885 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHH-SHHHHHH CS
                       DUF3198  19 vknlkeLekiarklGssYqqrL 40 
                                   v+ +++L  + r+   sY+q L
  gi|70606148|ref|YP_255018.1| 155 VETVRSLTPLVRDARASYEQSL 176
                                   6778899999999999999977 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.5e-06
                                   HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH- CS
                       DUF3198  15 KstFvknlkeLekiarklGssYqqrLeeakekWk 48 
                                   K+  ++  keLekia+ lG sY   L  a+  ++
  gi|70606148|ref|YP_255018.1| 234 KRYNMEEYKELEKIAYSLGFSYVVALPHARTSYR 267
                                   5566999***************999888887776 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.58   2.1e+03      12      35 ..      73      96 ..      63      99 .. 0.74
   2 !   13.7   0.0   1.2e-05     0.044      20      63 ..     206     250 ..     198     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.58
                Myb_DNA-bind_7 12 skeetekFYkaLsqfGtDFsliak 35
                                  ++ee  k  +a++++G D+ +i++
  gi|70606148|ref|YP_255018.1| 73 DHEEPIKVAEAVREMGLDYVVITS 96
                                  566777777899999999999875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.2e-05
                Myb_DNA-bind_7  20 YkaLsqfGtDFsliaklf.pkrtrrqlKlKFkkEerknpelieka 63 
                                    k L+++G D  ++++++ p+ ++ ++K++++ Ee k+ e+i  +
  gi|70606148|ref|YP_255018.1| 206 MKDLRNVGVDILVLSQYMrPSIKQLEVKKRYNMEEYKELEKIAYS 250
                                   56799*********99973668999***************99866 PP

>> Phage_int_SAM_6  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.9   1.1e+04      87     103 ..     114     130 ..     107     131 .. 0.71
   2 ?   11.2   0.1   8.1e-05      0.29      47      95 ..     196     246 ..     175     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
               Phage_int_SAM_6  87 laslkeideellsefla 103
                                   ++ +ke++ +++ e+l+
  gi|70606148|ref|YP_255018.1| 114 VKAVKEMNPDVIVEVLT 130
                                   56678888888888876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.1e-05
               Phage_int_SAM_6  47 vksieelekivkeaRniG..liGintyanPllklyeyliklelaslkeide 95 
                                    +s+ee+ +++k+ Rn+G  ++ ++ y++P +k  e+ +++++++ ke+++
  gi|70606148|ref|YP_255018.1| 196 GESLEEVVETMKDLRNVGvdILVLSQYMRPSIKQLEVKKRYNMEEYKELEK 246
                                   47899*************44467899**************99999998876 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.3e-05       0.3      82     108 .]       8      34 ..       2      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-05
                        LIAS_N  82 PlGknynkikndlreLnLhtvCeeaRC 108
                                    + +n++k+   + e  ++tvCeea C
  gi|70606148|ref|YP_255018.1|   8 RINENFKKLSRIVSEKGISTVCEEALC 34 
                                   5789*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1960.80
//
Query:       gi|70606149|ref|YP_255019.1|  [L=265]
Description: biotin/lipoate A/B protein ligase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-13   49.2   0.0    6.7e-13   48.7   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   3.7e-17   6.7e-13      16     130 ..      56     177 ..      44     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.7e-17
                                   GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH..........HHTT- CS
                 BPL_LplA_LipB  16 lnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealg...y.rdskpgieg 90 
                                   ++++e +  g ++vrr+tgG +++h    e+tys++ls + +  +  v e    +   ++++l+ +g   + +d   +++ 
  gi|70606149|ref|YP_255019.1|  56 VKIEEIKRLGFKLVRRPTGGGALLHPENDEITYSVVLSLDNQLAKIPVDESAssIAKGIIDALQIIGssaKvKDFGDKEKH 136
                                   6778889999****************999*********9985555555555555666666666666664325556677888 PP

                                   TTEEEE.TTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEE CS
                 BPL_LplA_LipB  91 ipvfik.wpnDlyvngrKlaGiavtstrgktlhhivigvgv 130
                                     ++ + +++D+ ++g+K++G+a+ ++  + l+h+++++++
  gi|70606149|ref|YP_255019.1| 137 DLCYLRrGSSDVILGGKKISGSAQVRNDKALLQHGTLLLRF 177
                                   8999999****************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1908.59
//
Query:       gi|70606150|ref|YP_255020.1|  [L=73]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.024   14.5   0.9      0.032   14.1   0.9    1.2  1  DUF5325     Family of unknown function (DUF5325)
      0.035   13.0   0.0      0.035   13.0   0.0    1.0  1  MFS_1_like  MFS_1 like family
      0.064   13.2   0.0        0.1   12.5   0.0    1.3  1  DUF4083     Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> DUF5325  Family of unknown function (DUF5325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.9   5.3e-06     0.032       9      52 ..       8      53 ..       4      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-06
                       DUF5325  9 llyAilAvaslmgiGia..igersilgiiiaivalivvmGlGFktK 52
                                  ll+ +++v++l g+Gia  +  + ++g +++++a + ++ + F +K
  gi|70606150|ref|YP_255020.1|  8 LLFGLAGVIFLEGLGIAldVVGQYAIGSVLIVIATVWILSIYFFMK 53
                                  89**************955456788999999******999988777 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.9e-06     0.035     152     207 ..       9      61 ..       2      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.9e-06
                    MFS_1_like 152 lfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekes 207
                                   lfG  G +if   +Gi++d +    ++   +l+v+a ++++s+ ++++  e++  +
  gi|70606150|ref|YP_255020.1|   9 LFGLAG-VIFLEGLGIALDVVGQYAIG--SVLIVIATVWILSIYFFMKYIEKKDSE 61 
                                   666555.689999**********9977..799**********99976665554433 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05       0.1      10      40 ..      36      66 ..      28      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                       DUF4083 10 ivivLilllvfsftlfiRrvvsrsaakkkks 40
                                  ++iv+    + s+++f+ ++  + + +++++
  gi|70606150|ref|YP_255020.1| 36 VLIVIATVWILSIYFFMKYIEKKDSENEENE 66
                                  66777778899**********9988655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 479.41
//
Query:       gi|70606151|ref|YP_255021.1|  [L=270]
Description: citryl-CoA lyase subunit beta-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-32  112.0   0.0      2e-30  105.6   0.0    2.1  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    2.3e-17   63.2   0.1    2.1e-09   37.0   0.0    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
  ------ inclusion threshold ------
      0.018   14.6   0.1      0.067   12.7   0.0    1.8  2  RexA            Intracellular sensor of Lambda phage, Abi com
      0.072   12.9   0.1       0.17   11.7   0.1    1.6  1  BH4             Bcl-2 homology region 4
      0.085   13.3   2.1        7.6    7.1   0.2    2.7  2  PhoU            PhoU domain


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   0.0   5.6e-34     2e-30       1     221 []       4     208 ..       4     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 5.6e-34
                                   EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG.H CS
                     HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle.v 80 
                                   r+ l++p+ ++++++k    +aDs+++DlEdav  ++K++AR+l+ +++++l+   +   e++VR+nsl+ + + +d+  +
  gi|70606151|ref|YP_255021.1|   4 RSQLYVPSISEKMIRKSIELKADSIVFDLEDAVPPEDKEKARELLVKLINELEW-GKR--ELCVRMNSLQLVDAYRDIVtI 81 
                                   789***************************************************.655..9***********999999975 PP

                                   HHT.TSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHHHTT- CS
                     HpcH_HpaI  81 ldl.gaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsadlgt 160
                                    ++ +++ ++vPk e   +++ + +a+ +             l+  iE+ +g+  +e+I+ +eg+ gv  G +Dls ++g 
  gi|70606151|ref|YP_255021.1|  82 SRIdKISCIVVPKAEG--DLSFLHKATGK------------DLIPLIETGKGLIRVEDIVRSEGVVGVSYGIADLSLSVGG 148
                                   554278999***9875..55555555443............57889*********************************98 PP

                                   TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHHHH CS
                     HpcH_HpaI 161 krspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgkllinp 221
                                     +   ++  +++  ++t+a+a +++ +d v++d ++++gf++e +++++lGf gk++i+p
  gi|70606151|ref|YP_255021.1| 149 DYNFY-EKNEFVKTYVVTTAKAYDVDPIDKVYFDLKNVDGFRRECEEAKKLGFVGKQVIHP 208
                                   76433.33448999**********************************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   4.5e-09   1.6e-05      10     110 ..       6      96 ..       5     120 .. 0.77
   2 !   37.0   0.0   5.8e-13   2.1e-09     247     326 ..     182     264 ..     149     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.5e-09
                C-C_Bond_Lyase  10 tLYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelaeaekekekeelpllFvRvRspeql... 87 
                                    LY+P  +e++++k ++ k   + s+v++lEDav  e+ e+A e l++l++el+  ++     e   l vR+ s + +   
  gi|70606151|ref|YP_255021.1|   6 QLYVPSISEKMIRKSIELK---ADSIVFDLEDAVPPEDKEKARELLVKLINELEWGKR-----E---LCVRMNSLQLVday 75 
                                   69******99988888866...679****************************98433.....3...44555555444000 PP

                C-C_Bond_Lyase  88 kellerlgealelltGfvlPkft 110
                                   ++++++   +++ ++ +v+Pk +
  gi|70606151|ref|YP_255021.1|  76 RDIVTIS--RIDKISCIVVPKAE 96 
                                   5555554..88999999999975 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 5.8e-13
                C-C_Bond_Lyase 247 ekdldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldilesakg....gvfkseyankmnEvkphraWA 323
                                    k++dg+ rE +  k+ G+vGK vIhP+q+++ +++++ ++ee e A++++e+ ++    g  + +  +k+++   h++ A
  gi|70606151|ref|YP_255021.1| 182 LKNVDGFRRECEEAKKLGFVGKQVIHPTQVEIANQVFSPTAEEIEWARRVIEAYDNakreGRGAIRLDDKLVDY-VHYKIA 261
                                   4789***********************************************98443122344444444666643.455556 PP

                C-C_Bond_Lyase 324 eki 326
                                   ++i
  gi|70606151|ref|YP_255021.1| 262 KRI 264
                                   655 PP

>> RexA  Intracellular sensor of Lambda phage, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.36   1.3e+03      51      83 ..      91     125 ..      47     130 .. 0.56
   2 ?   12.7   0.0   1.9e-05     0.067      56     123 ..     158     227 ..     143     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.36
                          RexA  51 ylvkvdgntylfiktrdnelvkkinra..tlkved 83 
                                    + k  g++ ++ k+  ++l+  i+     ++ved
  gi|70606151|ref|YP_255021.1|  91 VVPKAEGDLSFLHKATGKDLIPLIETGkgLIRVED 125
                                   33344555666666666666666665433455555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.9e-05
                          RexA  56 dgntylfiktrdnel..vkkinratlkvedlkkkLgedesiGfaSyifvepdrigfaskvfaPkaealkd 123
                                     +ty++++++  ++  + k+     +v+  +++ +e++++Gf    ++ p ++ +a +vf+P+ae++++
  gi|70606151|ref|YP_255021.1| 158 FVKTYVVTTAKAYDVdpIDKVYFDLKNVDGFRRECEEAKKLGFVGKQVIHPTQVEIANQVFSPTAEEIEW 227
                                   457888888776653224444444556777899*********************************9987 PP

>> BH4  Bcl-2 homology region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.7e-05      0.17      10      20 ..     253     263 ..     253     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHT CS
                           BH4  10 vDYvsYKLsQr 20 
                                   vDYv+YK+++r
  gi|70606151|ref|YP_255021.1| 253 VDYVHYKIAKR 263
                                   9********98 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0081        29      10      71 ..      27      84 ..      11      87 .. 0.80
   2 ?    7.1   0.2    0.0021       7.6      13      50 ..     229     266 ..     225     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0081
                                  HHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHH CS
                          PhoU 10 emlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllri 71
                                  +++ d+ +a+  +d+e are+  + + i++le   ++ ++++    q +++ +r+++++ ri
  gi|70606151|ref|YP_255021.1| 27 SIVFDLEDAVPPEDKEKAREL--LVKLINELEWGKRELCVRMN-SLQLVDA-YRDIVTISRI 84
                                  5667888999999********..699*****999888877655.4567776.8888777666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0021
                                   HHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  13 ddalealeekdtelarevierddeidrlekeierslle 50 
                                   ++++ea+ +  +e   +++ +d+ +d  +++i +++le
  gi|70606151|ref|YP_255021.1| 229 RRVIEAYDNAKREGRGAIRLDDKLVDYVHYKIAKRILE 266
                                   67999**99999999*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1989.38
//
Query:       gi|70606152|ref|YP_255022.1|  [L=134]
Description: hypothetical protein Saci_0313 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-15   57.4   0.0    1.7e-15   57.1   0.0    1.1  1  4HBT      Thioesterase superfamily
    1.1e-05   25.9   0.0    1.3e-05   25.6   0.0    1.1  1  4HBT_3    Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.021   15.0   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   2.9e-19   1.7e-15       1      79 []      47     123 ..      47     123 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.9e-19
                                   TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEEE CS
                          4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlva 79 
                                   gG +hgG +++++D a+++a+ sl    ++ v++el+++fl+p+  g ++tvea+v++ g++ ++v++  +d+d +l+a
  gi|70606152|ref|YP_255022.1|  47 GGMLHGGIMFSAMDYAGSMAVLSLSEV-KDEVTAELKVNFLKPMNKG-PFTVEAKVVNKGNKLVTVQIYAYDGDKELCA 123
                                   599***********************8.*******************.**************************99986 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.2e-09   1.3e-05      11      82 ..      50     128 ..      42     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.2e-09
                                   .-HHHHHHHHHHHHHHT.......-S.SS.EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEETTE.EEEEEEEE CS
                        4HBT_3  11 gyGGyvlAlalraaqrtv......pdprl.hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqggr.piftatas 82 
                                    +GG + + +  a   +v      +d ++ + l v+Fl+p + gp+++++++v  G +  t+++ ++ g++  +++++ +
  gi|70606152|ref|YP_255022.1|  50 LHGGIMFSAMDYAGSMAVlslsevKD-EVtAELKVNFLKPMNKGPFTVEAKVVNKGNKLVTVQIYAYDGDKeLCAVGLGT 128
                                   48888888888888877667766655.45689**********************************99865267777666 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.5e-06     0.021      16     124 ..      18     123 ..      16     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                                   GGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-.--S-EEEE CS
                       DUF4442  16 fgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak.atgdltav 95 
                                   f  +g+r+e++e g+  +++   +r+    g +H++ ++++++ a G +a  +l + +  +    +v++l++  +g  t +
  gi|70606152|ref|YP_255022.1|  18 FNFIGIRFEKVENGYSLLKFDFDKRLTRLGGMLHGGIMFSAMDYA-GSMAVLSLSEVKDEVTAELKVNFLKPmNKGPFTVE 97 
                                   56699**************************************97.6778889999999999**********789999999 PP

                                   EE-TTS-TT--EEEEEEEEEEETTE.EEE CS
                       DUF4442  96 aelepedvgekeelvvevevrdekgeevv 124
                                   a++ ++    ++ ++v+++++d ++e  +
  gi|70606152|ref|YP_255022.1|  98 AKVVNKG---NKLVTVQIYAYDGDKELCA 123
                                   9887654...4588999999998886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1070.80
//
Query:       gi|70606153|ref|YP_255023.1|  [L=140]
Description: hypothetical protein Saci_0314 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.1   0.4      0.033   14.1   0.1    1.6  2  KH_7      KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.9e-06     0.033       2      40 ..      14      52 ..      13      63 .. 0.90
   2 ?   -2.6   0.0      0.31   5.5e+03      33      44 ..     125     136 ..     125     140 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-06
                          KH_7  2 evleelkekieeklPkevkitdveFEGPelViYtknpkl 40
                                  e+ +e+k+++ +++P+ev++  ve+  P++  Y+++ ++
  gi|70606153|ref|YP_255023.1| 14 EIRDEIKRRLGKQTPEEVTVRFVEYLPPQILGYVRDGDY 52
                                  6789*******************************9765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.31
                          KH_7  33 iYtknpklfaen 44 
                                   +Y kn ++f   
  gi|70606153|ref|YP_255023.1| 125 VYLKNSQKFGRP 136
                                   799999999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 931.74
//
Query:       gi|70606154|ref|YP_255024.1|  [L=609]
Description: electron transfer flavoprotein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-89  298.4   0.2    7.5e-46  156.3   0.6    2.1  2  ETF        Electron transfer flavoprotein domain
    1.1e-32  111.9   0.1    3.1e-32  110.5   0.1    1.8  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
  ------ inclusion threshold ------
      0.029   14.3   0.2       0.19   11.6   0.2    2.1  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3   0.6   1.3e-49   7.5e-46       3     181 ..      27     211 ..      25     212 .. 0.95
   2 !  139.8   0.0   1.4e-44   8.5e-41       1     181 [.     287     467 ..     287     468 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 1.3e-49
                                   EEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHH CS
                           ETF   3 vlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaa 83 
                                    l+++gv++++np d +a+e+A rlke+ gg+  ++++Gp +ae+alreala mG+d+++l++d+a+ag+d++at++++a+
  gi|70606154|ref|YP_255024.1|  27 NLVREGVPAVINPPDYHAIEEAIRLKERFGGKTMVLTMGPGQAEVALREALA-MGIDEAYLISDRAMAGADTWATSYTVAK 106
                                   68999***********************88**********************.**************************** PP

                                   HHHHC.--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEE.ETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TT CS
                           ETF  84 likke.dpdlvlagatai.g..kqvaprlAalLgvplitdvtelev.eggkltvtRpieggnglaevveadlpavltvrpg 159
                                   +++ + ++d++l+g++a+ g   qv+p+++ +Lg+p++++v e+ + e+gk++v+R +e      ev e++lpav+t+ ++
  gi|70606154|ref|YP_255024.1| 107 AVQRLgGADIILFGRRAVdGetEQVGPQTGKWLGIPVVAYVREIRSiENGKAVVVRTTEF--EE-EVIEVPLPAVFTILET 184
                                   *****88***********99*************************98888899***9999..55.**************** PP

                                   SS--.....--S-TT---EEEE--HHH CS
                           ETF 160 afep.....aaimaakkkeveevevad 181
                                   a++p     +   +ak+++v++++ +d
  gi|70606154|ref|YP_255024.1| 185 ANKPrqpdiLSLIKAKTAKVTVWNKDD 211
                                   ****99888778899********9887 PP

  == domain 2  score: 139.8 bits;  conditional E-value: 1.4e-44
                                   EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHH CS
                           ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakal 81 
                                   ++v+++h  + ++n+++le l++Arr+++ ++++v++vv+G ++ +  + e +  +Gadkv+++++  ++ yd e ++kal
  gi|70606154|ref|YP_255024.1| 287 IWVYIDH-IGDRINKASLEILSEARRIADLMDTSVAGVVIGGESVKGIINEVYE-YGADKVYFAETKGYDRYDNEVYTKAL 365
                                   5999***.6********************888**********888888888888.************************** PP

                                   HHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC.EEEEEECCCCTEEEEEE-T.SSSEEEEE-TTS CS
                           ETF  82 aalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk.ltvtRpieggnglaevvea.dlpavltvrpga 160
                                   a+l+kk++p+ ++++ t   +++a   A   +++li+d+t+++v++++ l +tRp +gg+ ++++v++ ++p+++t+r+g+
  gi|70606154|ref|YP_255024.1| 366 AKLAKKYKPEGIFFPGTRAARELASTSAIEIDTGLIADCTNFDVDDKGvLLATRPDFGGKEMSTIVCPrHRPVMVTTRAGV 446
                                   ********************************************95559******************************** PP

                                   S----S-TT---EEEE--HHH CS
                           ETF 161 fepaaimaakkkeveevevad 181
                                   f p+++m+ +++e+ + e +d
  gi|70606154|ref|YP_255024.1| 447 FMPLPRMPGRTGELIKEEIED 467
                                   **************9988776 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.1   5.1e-36   3.1e-32       3      83 ..     486     566 ..     484     567 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.1e-36
                                   TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHGGGTT CS
                     ETF_alpha   3 LeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhlaGmke 83 
                                   L+ea++vv++GrG+ks+en++ +ee+a+alg+ +g+s++++d+gw+p++rq+GqtG+t++Pk+yia+G+sGa+qhl+G+ +
  gi|70606154|ref|YP_255024.1| 486 LTEADIVVGVGRGIKSPENIKKFEEFATALGGVLGVSKPLADMGWYPKDRQIGQTGTTIRPKVYIALGVSGAVQHLVGILS 566
                                   89****************************************************************************966 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   3.1e-05      0.19       6     100 ..     242     367 ..     240     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                                   HHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCS...............................STTHHHHHHHHHH.HHT CS
                     GatB_Yqey   6 vvkegadaklaanwllnellgelnkegleieel...............................kltpeqlaellkl.iae 54 
                                   +++  +d+++aa+w+ln++ ++l++ + +++e+                                 +++++a+l++  +a 
  gi|70606154|ref|YP_255024.1| 242 IIDGKKDPEKAAEWFLNKIYESLKEAESSLKEYvkpkakvkvnseiwvyidhigdrinkasleiLSEARRIADLMDTsVAG 322
                                   5666789*************************9889999999999999999999988888887666678888888764777 PP

                                   TSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHH CS
                     GatB_Yqey  55 gkIskkiakevleelleegkspeeiieekgLkqisdeeeleklvee 100
                                     I ++++k +++e++e g +     e kg+    + e  +k++++
  gi|70606154|ref|YP_255024.1| 323 VVIGGESVKGIINEVYEYGADKVYFAETKGYDRYDN-EVYTKALAK 367
                                   788889999999999888888888888888877754.666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4162.51
//
Query:       gi|70606155|ref|YP_255025.1|  [L=394]
Description: hypothetical protein Saci_0316 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-14   52.9   1.0    1.4e-06   28.1   0.2    2.3  2  DAO            FAD dependent oxidoreductase
    1.2e-10   40.7   5.1      2e-08   33.3   1.2    2.2  2  HI0933_like    HI0933-like protein
    9.6e-10   38.4   1.0    1.3e-09   37.9   1.0    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    4.6e-09   35.9   4.5      1e-07   31.5   4.5    2.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    9.6e-09   34.8   1.7    1.9e-08   33.8   1.7    1.5  1  FAD_binding_2  FAD binding domain
    2.2e-07   30.3   3.2    6.5e-07   28.8   3.2    1.7  1  GIDA           Glucose inhibited division protein A
    1.2e-06   28.0   3.0    5.1e-06   26.0   3.0    1.9  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-06   27.7   0.1    4.6e-06   26.8   0.1    1.4  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      2e-05   24.0   1.1    0.00042   19.7   1.5    2.3  2  FAD_binding_3  FAD binding domain
    6.4e-05   22.2   1.6    0.00017   20.8   1.6    1.6  1  Lycopene_cycl  Lycopene cyclase protein
    8.1e-05   22.0   0.1    0.00015   21.1   0.1    1.5  1  Thi4           Thi4 family
     0.0002   20.7   0.1    0.00068   19.0   0.1    1.8  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00037   21.0   1.2       0.28   11.8   0.1    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.059   13.4   1.8       0.94    9.4   0.1    2.2  2  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   1.1e-09   1.4e-06       1      44 [.       4      47 ..       4      59 .. 0.86
   2 !   23.2   0.0   3.6e-08   4.6e-05     147     219 ..      98     166 ..      94     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-09
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEE CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgll 44
                                  dv++iG+G +G+++A+ +a+ g  V+llekg+++g  +   +++++
  gi|70606155|ref|YP_255025.1|  4 DVIVIGAGPAGSAAALTAAKGGakVLLLEKGPEPG--SKNVSGAMI 47
                                  9*****************9988*********8887..555555555 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 3.6e-08
                                   HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT..CTTTSEEEE CS
                           DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll..keldlpisp 219
                                   kl +++a++ae++G+ ++++t++ g+e+ dg  ++v  +t+ g+++   +vV+a G+ + ++ g+   ++l    +p
  gi|70606155|ref|YP_255025.1|  98 KLDKWMAQQAEKAGAVLVTKTTALGVEK-DGEKYKV--VTDrGSISG-SKVVLAEGVNALISmGMKirPDL----EP 166
                                   6779**********************76.5555888..666698754.78******998533444444444....33 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   1.2   1.6e-11     2e-08       1      38 [.       3      40 ..       3      45 .. 0.94
   2 !    9.0   0.1    0.0004      0.51     115     171 ..     103     157 ..      98     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-11
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                  +dviviG+G+AG  aA++aak g++Vlllek++++g+K
  gi|70606155|ref|YP_255025.1|  3 FDVIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGSK 40
                                  59***********************************9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0004
                                   HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT CS
                   HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklG 171
                                   + +++++ag  l ++t+  +vek+ ++ ++v t ++++++ +k+vlA G +++ ++G
  gi|70606155|ref|YP_255025.1| 103 MAQQAEKAGAVLVTKTTALGVEKDGEK-YKVVT-DRGSISGSKVVLAEGVNALISMG 157
                                   678999***************997777.99999.9**************99888877 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   1.0     1e-12   1.3e-09       1     124 [.       4     134 ..       4     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1e-12
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga...rlkkr 78 
                                   Dv+V+G+gpaG aAA++Aa+ GakvlL+e+ +  G    sg++   ++     +v       f +++++ +     +    
  gi|70606155|ref|YP_255025.1|   4 DVIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGSKNVSGAMIRTEEIA---KVFDTSSMPFERKVKNVDLIfmdS---- 77 
                                   9**********************************877777754444433...677777777777776622222211.... PP

                  FAD_oxidored  79 skwn.......tfepevakavleeml....aeagvtvllntrlvevekegkriesvt 124
                                   ++++       +   +v +  l++++    ++ag  ++++t++ +vek+g++ + vt
  gi|70606155|ref|YP_255025.1|  78 TGKVrisvdisSGLINVGRLKLDKWMaqqaEKAGAVLVTKTTALGVEKDGEKYKVVT 134
                                   111112233445556666666666666665667888888888888888876665555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   4.5     8e-11     1e-07       1     113 [.       3     154 ..       3     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8e-11
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias.................... 57 
                                   +dv+viG+GpAG aaalt+a+ gakv+l+e     +   + g ++ ++++++v                            
  gi|70606155|ref|YP_255025.1|   3 FDVIVIGAGPAGSAAALTAAKGGAKVLLLEkgpePGSKNVSGAMIRTEEIAKVF------Dtssmpferkvknvdlifmds 77 
                                   69***************************5444333333333333333333333......2444567888999999***99 PP

                                   ...........................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE CS
                                   ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ...........................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssp 111
                                                              +  +  ++g  l++++++++++++ +k+k+ +++     +i   k+vlA G ++
  gi|70606155|ref|YP_255025.1|  78 tgkvrisvdissglinvgrlkldkwmaQ--QAEKAGAVLVTKTTALGVEKDGEKYKVVTDR----GSISGSKVVLAEGVNA 152
                                   9999999999999999999999998752..3344555666666799999999999995544....48999******99776 PP

                                   -B CS
                                   xx RF
                   Pyr_redox_2 112 rd 113
                                    +
  gi|70606155|ref|YP_255025.1| 153 LI 154
                                   55 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   1.7   1.5e-11   1.9e-08       1      36 [.       4      39 ..       4      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.5e-11
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  DviViG+G AG aAAl+aa+ G+kv+++ek++e g+
  gi|70606155|ref|YP_255025.1|  4 DVIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGS 39
                                  9*******************************9666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   3.2   5.1e-10   6.5e-07       1     159 [.       4     157 ..       4     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.1e-10
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE..............ES-GGGTT--SSSSEEE-T...THHHHHHHHHHHT-SHH CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..............thkldtiaelsCnpsiggi...akgllvrEidalgglii 64 
                                   dviViG+G AG++AAl+aa+ GakvlL+                ++++ia+         +   ++    r +++++ + +
  gi|70606155|ref|YP_255025.1|   4 DVIVIGAGPAGSAAALTAAKGGAKVLLLekgpepgsknvsgaMIRTEEIAK---------VfdtSSMPFERKVKNVDLIFM 75 
                                   8***************************66665544433333222222222.........244355556666666666666 PP

                                   HHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEE CS
                          GIDA  65 kaadkagiqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavv 145
                                     + k +i ++i          +l + v r +  k++ ++ e+   + + + ++  ++  +++   vvt++g+ i+ ++vv
  gi|70606155|ref|YP_255025.1|  76 DSTGKVRISVDIS--------SGL-INVGRLKLDKWMAQQAEKAGAVLVTKTTALGVEK-DGEKYKVVTDRGS-ISGSKVV 145
                                   6666666644441........222.4566666666666666666666666666666633.4444444444443.4556666 PP

                                   E--TT-BT-EEEET CS
                          GIDA 146 iatGtflkgkihig 159
                                   +a G   ++ i +g
  gi|70606155|ref|YP_255025.1| 146 LAEGV--NALISMG 157
                                   66666..5555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   3.0     4e-09   5.1e-06       1     134 [.       6     150 ..       6     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4e-09
                   Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg......nignsiyrypkemtfispsftsekleipdlnaiseets..pafsl 73 
                                   i+iGaGPaG aaa+++ k g  ++l lEkg      n++ ++ r  +  +++++s    + +++++  i+ ++    ++s+
  gi|70606155|ref|YP_255025.1|   6 IVIGAGPAGSAAALTAAKGGA-KVLLLEKGpepgskNVSGAMIRTEEIAKVFDTSSMPFERKVKNVDLIFMDSTgkVRISV 85 
                                   89******************9.7******7622222455567777888899998876555556666666655551144433 PP

                   Pyr_redox_3  74 k..ee..klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                   +  +   ++ r ++ +++++ a++      ++++   v+k++e+++v t++++++ +kv++A G 
  gi|70606155|ref|YP_255025.1|  86 DisSGliNVGRLKLDKWMAQQAEKAGAVLVTKTTALGVEKDGEKYKVVTDRGSISGSKVVLAEGV 150
                                   321223377889999***********************************************997 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   3.6e-09   4.6e-06       1      32 [.       7      38 ..       7      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.6e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  ++GaG +G++aA ++ak g++vlllek++ +G
  gi|70606155|ref|YP_255025.1|  7 VIGAGPAGSAAALTAAKGGAKVLLLEKGPEPG 38
                                  8******************************9 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.5   3.2e-07   0.00042       2     138 ..       3     130 ..       2     152 .. 0.61
   2 ?   -3.8   0.0       4.5   5.7e+03     283     292 ..     280     289 ..     244     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.2e-07
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                    dV+++GaGpaG  +al  ++ G +v+l+ek  +   +   + +   rt e+ +         ++  ++++  +++  +  
  gi|70606155|ref|YP_255025.1|   3 FDVIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGSKNvSGAM--IRTEEIAKVFDTSSMPFERK-VKNVDLIFMDST-- 78 
                                   79*****************************8776443312222..23333333322222222222.233333333333.. PP

                                   CCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCC CS
                 FAD_binding_3  82 dtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegv 138
                                      k+r+ +++    +   +++  +l++ ++++ae++g+ +  kt  +++e+d+e+ 
  gi|70606155|ref|YP_255025.1|  79 --GKVRISVDI---SSGLINVGRLKLDKWMAQQAEKAGAVLVTKTTALGVEKDGEKY 130
                                   ..344444442...2344556666777777777777776666666666677776665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.5
                                   ETTEEE-GGG CS
                 FAD_binding_3 283 kgrvflaGDA 292
                                   +g++ laGD+
  gi|70606155|ref|YP_255025.1| 280 SGKIYLAGDS 289
                                   6899999997 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.6   1.3e-07   0.00017       1     142 [.       4     151 ..       4     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga........leecvehsWsgtivylddgk 73 
                                   Dv+viGaGpAg + A     ak g kv+l+e +p++   n    +   e++ +        +e+   ++ +   + +d   
  gi|70606155|ref|YP_255025.1|   4 DVIVIGAGPAGSAAALTA--AKGGAKVLLLEKGPEPGSKNVSGAMIRTEEIAKvfdtssmpFER---KVKNVDLIFMDSTG 79 
                                   9**********9777655..**************994444444455555555544444222222...33333445555554 PP

                 Lycopene_cycl  74 killg....raYgrvsskrlkeellerlveng.vklleakvesveeeeageslvvleggrkirarlvvdargla 142
                                   k+ ++         v + +l + ++++  ++g v  ++ ++  ve++ +  ++ v+ +   i ++ vv a g+ 
  gi|70606155|ref|YP_255025.1|  80 KVRISvdisSGLINVGRLKLDKWMAQQAEKAGaVLVTKTTALGVEKDGE--KYKVVTDRGSISGSKVVLAEGVN 151
                                   4444433445666777888888999998855404555666666665554..55555566678888888888854 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.2e-07   0.00015      16      63 ..       1      47 [.       1      66 [. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                  TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
                          Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                                  +e Dv+++GaG++G +aa + ak  + kv++le+   pG     G ++
  gi|70606155|ref|YP_255025.1|  1 MEFDVIVIGAGPAGSAAALTAAKG-GAKVLLLEKGPEPGSKNVSGAMI 47
                                  689***********9999999988.*********99999887777765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   5.3e-07   0.00068      30      95 ..       4      73 ..       2      81 .. 0.83
   2 ?   -2.0   0.0       1.4   1.8e+03     176     202 ..     320     346 ..     301     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.3e-07
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH....TTTCECEEHCHHHHHHHHHHHH-SEE CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles....lgakfvevlksqeellaeavkeadvv 95
                                   v+viG+G aG +A+ ta++ gakV +l++ p+   +  s      +++ +v   ++  ++++vk++d++
  gi|70606155|ref|YP_255025.1|  4 DVIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGSKNVSgamiRTEEIAKVFDTSSMPFERKVKNVDLI 73
                                  599***************************9987665555466545555667888888899999999987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                   HHHHHHHHHCHHHTCCHHHCTSHHHHC CS
                   AlaDh_PNT_C 176 ntlpyleelladkglkkalkedealrk 202
                                   + ++y eel++dk++k ++k+++ +++
  gi|70606155|ref|YP_255025.1| 320 ECFKYEEELMKDKEIKGVVKARPLIQE 346
                                   567899999999999999998888876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00022      0.28       2      36 ..       5      41 ..       4      59 .. 0.86
   2 !    7.4   0.1    0.0049       6.3      42      78 ..      99     134 ..      93     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..T CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll..r 36
                                  v+v+G+G  g  +A ++a+ g+kV ++e ++++   +
  gi|70606155|ref|YP_255025.1|  5 VIVIGAGPAGSAAALTAAKGGAKVLLLEKGPEPGskN 41
                                  89*****************************998533 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0049
                                   HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvkl 78 
                                   + k+++++ ek g  ++++t++  +e+++++ ++v++
  gi|70606155|ref|YP_255025.1|  99 LDKWMAQQAEKAGAVLVTKTTALGVEKDGEK-YKVVT 134
                                   679************************9997.55665 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.058        75       2      32 ..       7      32 ..       6      50 .. 0.70
   2 ?    9.4   0.1   0.00074      0.94     107     154 ..     103     149 ..      98     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.058
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfd 32
                                  ++GaGp+G a++   ++        ++ l +
  gi|70606155|ref|YP_255025.1|  7 VIGAGPAGSAAALTAAKG-----GAKVLLLE 32
                                  8*******9987654433.....45555555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00074
                 NAD_binding_9 107 llarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   +++++++   v v +++++ +e+++++++v  +d  s+   +VvLA G
  gi|70606155|ref|YP_255025.1| 103 MAQQAEKAGAVLVTKTTALGVEKDGEKYKV-VTDRGSISGSKVVLAEG 149
                                   4556677778999***************99.566778999******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2787.40
//
Query:       gi|70606156|ref|YP_255026.1|  [L=96]
Description: ferredoxin-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-13   48.1   1.4    1.2e-12   47.9   1.4    1.0  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
    3.2e-07   30.4   9.7      6e-07   29.5   9.8    1.4  1  Fer4_9    4Fe-4S dicluster domain
    1.6e-06   28.6  23.9    0.00022   21.7  13.1    2.2  3  Fer4_7    4Fe-4S dicluster domain
    1.7e-06   27.6  18.3      3e-06   26.8   4.2    3.1  3  Fer4      4Fe-4S binding domain
    3.2e-06   26.9  12.4    0.00012   21.9   3.1    2.3  2  Fer4_2    4Fe-4S binding domain
    1.4e-05   25.1  12.3    4.5e-05   23.5  12.5    1.7  1  Fer4_10   4Fe-4S dicluster domain
    2.2e-05   24.6  11.3    6.5e-05   23.1   2.0    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00016   22.0   4.6     0.0041   17.5   0.5    2.3  2  Fer4_8    4Fe-4S dicluster domain
    0.00022   21.1  19.3     0.0046   17.0   4.2    2.8  2  Fer4_6    4Fe-4S binding domain
     0.0051   16.9  11.9      0.013   15.6  11.9    1.8  1  Fer4_21   4Fe-4S dicluster domain
     0.0058   17.5  12.1       0.25   12.4   3.7    2.4  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   16.5   0.9      0.012   16.5   0.9    3.0  3  Fer4_16   4Fe-4S double cluster binding domain
      0.031   14.8   2.1      0.031   14.8   2.1    2.3  3  Fer4_17   4Fe-4S dicluster domain
        5.7    7.0   7.3        1.3    9.0   3.5    2.1  2  DUF723    Protein of unknown function (DUF723)


Domain annotation for each model (and alignments):
>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   1.4     9e-16   1.2e-12      18     101 ..      12      91 ..       5      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 9e-16
                                   --SSS--SEEESSTTHHHH.THHHHHS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---ST CS
                        ETF_QO  18 heedqpvhLklkdaevavk.vnlekyagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeG 97 
                                   ++ d++ hL++ ++++++k  +++   +p+  +CPa+vy +v+++     +++++ +nCv C +C i  p +ni+w+ P  
  gi|70606156|ref|YP_255026.1|  12 YKRDEKPHLSIIEPNKCQKcAEINGVPEPCIVVCPANVYSWVDNN-----RIVVSYENCVECGACRIACPFDNISWKYPRY 87 
                                   6789999***9988765552689999****************777.....8****************************98 PP

                                   T-C- CS
                        ETF_QO  98 ggGP 101
                                   g G 
  gi|70606156|ref|YP_255026.1|  88 GLGV 91 
                                   8775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   9.8   4.7e-10     6e-07       1      49 [.      27      78 ..      26      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.7e-10
                        Fer4_9  1 kCtgCga.......CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                  kC +C +       C+ +Cpa+v++  +++r++   +    +C++CgaC  aCp +
  gi|70606156|ref|YP_255026.1| 27 KCQKCAEingvpepCIVVCPANVYSWVDNNRIVVSYE----NCVECGACRIACPFD 78
                                  79***555555666******************99865....7************76 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   2.1   0.00018      0.24      27      52 .]      16      49 ..       4      49 .. 0.68
   2 !   21.7  13.1   1.7e-07   0.00022       1      51 [.      27      78 ..      27      79 .. 0.85
   3 !   18.4   3.0   1.9e-06    0.0025       2      21 ..      65      84 ..      64      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                        Fer4_7 27 gtekvei.dpekClgC.......gaCvavCPtga 52
                                  +++++ i +p+kC+ C       + C+ vCP+++
  gi|70606156|ref|YP_255026.1| 16 EKPHLSIiEPNKCQKCaeingvpEPCIVVCPANV 49
                                  4556664279******544444445******986 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.7e-07
                        Fer4_7  1 rCigCg.......aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                  +C +C         C ++Cp+++ ++ +        ++++++e+C+ CgaC  +CP++
  gi|70606156|ref|YP_255026.1| 27 KCQKCAeingvpePCIVVCPANVYSWVDN------NRIVVSYENCVECGACRIACPFD 78
                                  68999445555559************986......469******************96 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.9e-06
                        Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                  C++CgaC  aCp + i++++
  gi|70606156|ref|YP_255026.1| 65 CVECGACRIACPFDNISWKY 84
                                  ****************9986 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.039        50       2      11 ..      22      31 ..      21      33 .. 0.83
   2 ?    5.7   1.7     0.011        13      14      22 ..      41      49 ..      40      51 .. 0.89
   3 !   26.8   4.2   2.4e-09     3e-06       1      23 [.      58      80 ..      58      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.039
                                  EEETTTSSS- CS
                          Fer4  2 videekCigC 11
                                  +i ++kC +C
  gi|70606156|ref|YP_255026.1| 22 IIEPNKCQKC 31
                                  5889999999 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                                  HHHHSTTTE CS
                          Fer4 14 CvevCPvgA 22
                                  C+ vCP ++
  gi|70606156|ref|YP_255026.1| 41 CIVVCPANV 49
                                  ******997 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 2.4e-09
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  +v+ +e C+ CGaC  +CP++ I
  gi|70606156|ref|YP_255026.1| 58 IVVSYENCVECGACRIACPFDNI 80
                                  6899****************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.9   0.00048      0.62       5      22 .]      23      47 ..      19      47 .. 0.79
   2 !   21.9   3.1   9.5e-08   0.00012       3      21 ..      58      76 ..      56      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                        Fer4_2  5 vdtdrCigC....g...aCvsaCPa 22
                                  +++++C  C    g   +C+ +CPa
  gi|70606156|ref|YP_255026.1| 23 IEPNKCQKCaeinGvpePCIVVCPA 47
                                  67889999966662666*******8 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 9.5e-08
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  +vv  ++C++CgaC+ aCP
  gi|70606156|ref|YP_255026.1| 58 IVVSYENCVECGACRIACP 76
                                  78899************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5  12.5   3.5e-08   4.5e-05       3      56 .]      22      76 ..      20      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.5e-08
                       Fer4_10  3 vidddtCirCg.......kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +i++++C +C+        C  +CPa      + +   +++++ + +e+C +cgaC  aCP
  gi|70606156|ref|YP_255026.1| 22 IIEPNKCQKCAeingvpePCIVVCPA------NVYSWVDNNRIVVSYENCVECGACRIACP 76
                                  7999******988888889*******......88889999999999**************9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.1     0.011        14       1      16 [.      25      47 ..      25      51 .. 0.89
   2 !   23.1   2.0   5.1e-08   6.5e-05       1      16 [.      62      77 ..      62      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                        Fer4_4  1 qerCigCgs.......CvaaCPq 16
                                  +++C+ C         C+ +CP 
  gi|70606156|ref|YP_255026.1| 25 PNKCQKCAEingvpepCIVVCPA 47
                                  589*****9999999*******6 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.1e-08
                        Fer4_4  1 qerCigCgsCvaaCPq 16
                                  +e+C++Cg+C++aCP+
  gi|70606156|ref|YP_255026.1| 62 YENCVECGACRIACPF 77
                                  599************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.3    0.0093        12      48      65 .]      25      49 ..       2      49 .. 0.74
   2 !   17.5   0.5   3.2e-06    0.0041       3      17 ..      63      77 ..      61      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0093
                        Fer4_8 48 lwsCttcga.......CtevCpvgi 65
                                   ++C+ c +       C +vCp ++
  gi|70606156|ref|YP_255026.1| 25 PNKCQKCAEingvpepCIVVCPANV 49
                                  5677777777779999******986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.2e-06
                        Fer4_8  3 ekCieCgaCqsaCpv 17
                                  e+C+eCgaC+ aCp+
  gi|70606156|ref|YP_255026.1| 63 ENCVECGACRIACPF 77
                                  689999999999995 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   7.2    0.0015         2       4      23 ..      23      49 ..      21      50 .. 0.90
   2 !   17.0   4.2   3.6e-06    0.0046       2      23 ..      58      79 ..      57      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                        Fer4_6  4 idpdkCigCgd.......CvrvCPega 23
                                  i p+kC  C +       C++vCP+++
  gi|70606156|ref|YP_255026.1| 23 IEPNKCQKCAEingvpepCIVVCPANV 49
                                  679******999*************98 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.6e-06
                        Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                  +++ +++C+ Cg+C ++CP++ 
  gi|70606156|ref|YP_255026.1| 58 IVVSYENCVECGACRIACPFDN 79
                                  78999**************975 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  11.9     1e-05     0.013       2      56 ..      22      79 ..      21      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                       Fer4_21  2 ridedkCigCgk.......CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56
                                  +i+++kC +C +       C+++C+ + +      +++++ v  ++Cv C  C + CP  d 
  gi|70606156|ref|YP_255026.1| 22 IIEPNKCQKCAEingvpepCIVVCPANVYS---WVDNNRIVVSYENCVECGACRIACPF-DN 79
                                  5889999999654455555******75555...5557888999***************8.44 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.3    0.0012       1.5       1      13 [.      28      47 ..      27      49 .. 0.84
   2 !   12.4   3.7   0.00019      0.25       1      13 [.      65      77 ..      65      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                        Fer4_3  1 CtgCg.......aCvevCPv 13
                                  C+ C        +C +vCP 
  gi|70606156|ref|YP_255026.1| 28 CQKCAeingvpePCIVVCPA 47
                                  8899778888889******6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00019
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C+ CgaC  +CP 
  gi|70606156|ref|YP_255026.1| 65 CVECGACRIACPF 77
                                  ************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   5.9       1.4   1.8e+03      58      67 .]      39      48 ..       7      48 .. 0.56
   2 ?    1.1   5.0      0.61   7.8e+02       8      16 ..      41      49 ..      24      62 .. 0.75
   3 ?   16.5   0.9   9.5e-06     0.012       1      20 [.      64      83 ..      64      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                       Fer4_16 58 diCqdvCPan 67
                                    C  vCPan
  gi|70606156|ref|YP_255026.1| 39 EPCIVVCPAN 48
                                  2566666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.61
                       Fer4_16  8 CaevCPtna 16
                                  C+ vCP+n+
  gi|70606156|ref|YP_255026.1| 41 CIVVCPANV 49
                                  777777775 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 9.5e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg+C  +CP + i+ k
  gi|70606156|ref|YP_255026.1| 64 NCVECGACRIACPFDNISWK 83
                                  6************9999855 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.8      0.12   1.5e+02      39      60 ..      24      49 ..       2      50 .. 0.61
   2 ?    2.1   1.5      0.23   2.9e+02       2      14 ..      28      47 ..      26      62 .. 0.53
   3 ?   14.8   2.1   2.4e-05     0.031      42      58 ..      61      77 ..      47      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                       Fer4_17 39 keekaslCieCge....CerkCPqgl 60
                                  + +k+++C+e+++    C  +CP+++
  gi|70606156|ref|YP_255026.1| 24 EPNKCQKCAEINGvpepCIVVCPANV 49
                                  44667777777644444777777765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                       Fer4_17  2 CiqCgy.......ClpeCps 14
                                  C++C+        C+ +Cp 
  gi|70606156|ref|YP_255026.1| 28 CQKCAEingvpepCIVVCPA 47
                                  44444333333334446664 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.4e-05
                       Fer4_17 42 kaslCieCgeCerkCPq 58
                                    ++C+eCg C+ +CP 
  gi|70606156|ref|YP_255026.1| 61 SYENCVECGACRIACPF 77
                                  5789***********96 PP

>> DUF723  Protein of unknown function (DUF723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.5    0.0011       1.3      20      60 .]      30      69 ..      13      69 .. 0.71
   2 ?   -2.4   0.1       3.6   4.6e+03      31      37 ..      71      77 ..      70      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                        DUF723 20 klveFegvakPvvinCPlHGnvtystykal..ikSkyGCPeCa 60
                                  k  e +gv +P+ ++CP     +ys  ++   + S   C eC+
  gi|70606156|ref|YP_255026.1| 30 KCAEINGVPEPCIVVCPAN---VYSWVDNNriVVSYENCVECG 69
                                  567899***********74...333333322266666777775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                        DUF723 31 vvinCPl 37
                                  + i CP 
  gi|70606156|ref|YP_255026.1| 71 CRIACPF 77
                                  6789995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 678.14
//
Query:       gi|70606157|ref|YP_255027.1|  [L=253]
Description: formate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-74  248.9   0.0    5.8e-74  248.8   0.0    1.0  1  FdhD-NarQ  FdhD/NarQ family
      0.005   16.7   0.3          2    8.4   0.0    3.3  3  DUF1125    Protein of unknown function (DUF1125)
  ------ inclusion threshold ------
      0.075   12.6   0.0       0.15   11.7   0.0    1.4  1  FcoT       FcoT-like thioesterase domain


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.8   0.0   9.6e-78   5.8e-74       1     236 [.      24     251 ..      24     252 .. 0.94

  Alignments for each domain:
  == domain 1  score: 248.8 bits;  conditional E-value: 9.6e-78
                                   E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S.........------------ CS
                     FdhD-NarQ   1 veEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatrakaedkeerrtakrvvtsg 81 
                                   ++Eepl+i+vn+++la++m+tp+++ el lGfl+ e +i+s +d+e+i++ +d+ +++v+  + +    e+r++  v++s+
  gi|70606157|ref|YP_255027.1|  24 AVEEPLQIFVNEKNLAIIMRTPGNDLELTLGFLYYEDYINSLRDVEEISMLSDN-EIHVRLTNGKF--VETRNF--VINSS 99 
                                   58************************************************9886.77777666444..468999..***** PP

                                   ---.---...--H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHHHHH CS
                     FdhD-NarQ  82 CglcgkesleelletlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkviGa 162
                                   Cg+cg+ +l    +++el++sd+k s+e +++l+++lr++q +f+ tgg+Haaalf+ +gel+ ++eDvGRHnA+Dk+iG 
  gi|70606157|ref|YP_255027.1| 100 CGICGRGFL----NAIELLKSDAKTSNEVIISLPEKLRSNQGVFNITGGLHAAALFTLSGELISIYEDVGRHNAVDKIIGS 176
                                   *******98....667888899*********************************************************** PP

                                   HHT.TSS.-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE-GGGE CS
                     FdhD-NarQ 163 allegld.lsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtgaeRi 236
                                   ++ ++   ++++il vsgR+ +e+v Ka++agip++ ++sapts+a+e+Ae+ag tlvgfvrg++fnvYt++eRi
  gi|70606157|ref|YP_255027.1| 177 LIHKRRLpFTEGILQVSGRIGYEIVSKAIKAGIPIISGISAPTSKAIEIAEDAGATLVGFVRGNSFNVYTHPERI 251
                                   *9976655******************************************************************9 PP

>> DUF1125  Protein of unknown function (DUF1125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0067        40      32      42 ..       4      14 ..       1      26 [. 0.88
   2 !    8.4   0.0   0.00033         2       4      38 ..      31      64 ..      29      78 .. 0.77
   3 ?   -0.9   0.0      0.26   1.6e+03      43      52 ..     155     164 ..     153     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0067
                       DUF1125 32 rkikiikiknG 42
                                  rk+ki k+k+G
  gi|70606157|ref|YP_255027.1|  4 RKVKISKVKDG 14
                                  9********99 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
                       DUF1125  4 ilkteknriivqfecGndieafscGflyrkikiik 38
                                  i+  ekn  i+    Gnd+e ++ Gfly    i  
  gi|70606157|ref|YP_255027.1| 31 IFVNEKNLAIIMRTPGNDLE-LTLGFLYYEDYINS 64
                                  56689**************9.689****8765555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.26
                       DUF1125  43 seliailedt 52 
                                    eli+i ed 
  gi|70606157|ref|YP_255027.1| 155 GELISIYEDV 164
                                   59******95 PP

>> FcoT  FcoT-like thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.15      16      55 ..      77     113 ..      58     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                   EEEEEETTEETTS.EEEEEEE--SS-SSCS--SS--CHHH CS
                          FcoT  16 aevesesdavdegkavakgeFeipescYiddtGHfnavEl 55 
                                    e++ +   + +gk v + +F i+ sc i   G +na+El
  gi|70606157|ref|YP_255027.1|  77 NEIHVR---LTNGKFVETRNFVINSSCGICGRGFLNAIEL 113
                                   444443...45789999**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1708.83
//
Query:       gi|70606158|ref|YP_255028.1|  [L=121]
Description: hypothetical protein Saci_0319 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-13   49.7   0.2    3.8e-13   49.1   0.2    1.4  1  DUF1641         Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
      0.023   14.7   0.1      0.028   14.4   0.2    1.2  1  Thioredoxin_14  Thioredoxin-like domain
      0.085   13.2   0.0       0.17   12.3   0.0    1.4  1  Radical_SAM     Radical SAM superfamily
        0.1   12.6   0.0        4.1    7.5   0.0    2.2  2  Cdc6_C          CDC6, C terminal winged helix domain


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   8.5e-17   3.8e-13       1      39 []      75     113 ..      75     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 8.5e-17
                       DUF1641   1 agleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                   ag+ee+k + l +++r+L+DPDV+rGL++ll+lLKa+G+
  gi|70606158|ref|YP_255028.1|  75 AGKEEVKDIKLSEIVRELNDPDVRRGLYLLLKLLKAIGS 113
                                   589***********************************6 PP

>> Thioredoxin_14  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   6.3e-06     0.028     166     213 ..      13      65 ..       2      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-06
                                   ..TTHHHHHHHHHHHHHT.T--SSS-EEEE.TTEEEESSSSH.....HHHHHHH CS
                Thioredoxin_14 166 tseydealkasrefikrl.glkeaqepvfllNGvvlpfdekw.....eqallae 213
                                    +e++e+++a ++f+k + +l +++  +fl NGv+++fde++     ++++l +
  gi|70606158|ref|YP_255028.1|  13 IEELTESREALEQFLKLInALHKTGILQFL-NGVLMKFDENLtflaeQNSMLIR 65 
                                   344555566666666644444444366777.*********99888777766655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05      0.17     108     151 ..       5      47 ..       3      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                   EEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 108 gleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                   g++++d   + +l++ ++ +e++l+++ +l++ gi    +++++
  gi|70606158|ref|YP_255028.1|   5 GIQTFDRL-IEELTESREALEQFLKLINALHKTGILQFLNGVLM 47 
                                   89*****9.******99******************964444444 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.021        93      40      56 ..      24      40 ..      10      44 .. 0.87
   2 ?    7.5   0.0   0.00091       4.1      13      48 ..      59      94 ..      53     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.021
                                  HHHHHHHHHHHHTTSEE CS
                        Cdc6_C 40 revsdllseLemlgile 56
                                  +++++l++ L++ gil+
  gi|70606158|ref|YP_255028.1| 24 EQFLKLINALHKTGILQ 40
                                  79*************97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00091
                                  SS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHH CS
                        Cdc6_C 13 keevttgevyevYkslCesegvdpltqrevsdllse 48
                                  ++++ ++ v+e Y+ l+ +e+v+ ++ +e+++ l++
  gi|70606158|ref|YP_255028.1| 59 QNSMLIRNVNEIYSILAGKEEVKDIKLSEIVRELND 94
                                  6788899********************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 789.19
//
Query:       gi|70606159|ref|YP_255029.1|  [L=976]
Description: formate dehydrogenase subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-87  294.2   0.0    2.1e-87  293.9   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    6.7e-20   71.2   0.0    1.3e-19   70.2   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    7.4e-19   67.5   0.3    7.4e-19   67.5   0.3    2.4  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    1.5e-12   47.4   0.1    3.8e-12   46.1   0.1    1.7  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
      4e-11   42.3  17.7    4.4e-06   26.3   3.5    3.5  3  Fer4             4Fe-4S binding domain
    7.5e-10   38.2   0.9    7.5e-10   38.2   0.9    2.1  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    4.9e-09   35.9  13.0    0.00027   20.9   3.3    2.9  2  Fer4_6           4Fe-4S binding domain
    1.3e-08   34.8   6.3    1.3e-08   34.8   6.3    2.4  1  Fer4_21          4Fe-4S dicluster domain
    2.9e-05   24.6  12.9    2.9e-05   24.6  12.9    3.8  5  Fer4_7           4Fe-4S dicluster domain
    4.2e-05   23.6  17.2      0.012   15.7   0.2    3.1  2  Fer4_10          4Fe-4S dicluster domain
    0.00011   22.3  23.2    0.00011   22.3  12.3    3.7  4  Fer4_9           4Fe-4S dicluster domain
    0.00014   21.7   0.2    0.00014   21.7   0.2    2.6  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
     0.0003   20.5   0.3       0.71    9.6   0.0    3.2  3  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
     0.0044   17.9  18.7      0.029   15.3   5.6    4.0  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0057   17.1  10.9     0.0057   17.1  10.9    3.1  3  Fer4_8           4Fe-4S dicluster domain
     0.0062   16.6  15.4     0.0084   16.2   5.8    3.3  2  Fer4_2           4Fe-4S binding domain
     0.0067   17.0   6.7       0.59   10.7   0.1    2.8  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
       0.16   12.7   7.3        0.7   10.7   1.6    2.9  2  Fer4_15          4Fe-4S single cluster domain
       0.16   12.2  13.4      0.066   13.4   0.7    2.8  2  Fer4_18          4Fe-4S dicluster domain
       0.45   11.1  19.6       0.18   12.4  11.5    3.3  4  Fer4_17          4Fe-4S dicluster domain
       0.93   10.2  21.6      0.061   13.9   3.7    3.2  2  Fer4_4           4Fe-4S binding domain
          4    8.6  31.1      0.067   14.2   7.8    3.2  2  Fer4_3           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.9   0.0   2.6e-90   2.1e-87       1     431 [.     312     734 ..     312     735 .. 0.94

  Alignments for each domain:
  == domain 1  score: 293.9 bits;  conditional E-value: 2.6e-90
                                   B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCG CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwya 81 
                                   Rl++P++R   +  +kF++++W+eA  li++++k++++kygpd++  +++++ ms+e+ ++++k+++++ g  ++++d+ a
  gi|70606159|ref|YP_255029.1| 312 RLTKPLIR---E-GDKFREATWEEAISLISRKFKEIKEKYGPDAIG-VIASDKMSNEEAYLAQKFARAVLG--TNNVDNSA 385
                                   9*******...6.89******************************9.8899********************..9******* PP

                                   GGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGC CS
                 Molybdopterin  82 dlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfa 158
                                   +++ a a     +t+g +       s ++ d+e +dli+++G+N  e +p+  +++ +a + ++ak++vi+ r +e+++ a
  gi|70606159|ref|YP_255029.1| 386 RYCQAPATvglwRTVGFGAD-----SGTIRDIESADLIVVIGHNTTESHPVIGSKVKRAKKIRGAKIAVIDVRRHEIAEWA 461
                                   ***99988777755555433.....55899**********************999999998889*************9*** PP

                                   SEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEE CS
                 Molybdopterin 159 dewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksm 239
                                   d+ ++ kpg+da ++++ +++il+++++dkef+r++ +g+e++++ +++   + ++  ++v+++++++la+ +++++    
  gi|70606159|ref|YP_255029.1| 462 DLFIKSKPGNDAIILAGVAKYILDNGWEDKEFIRNRVNGFEKFKESIEGFNLDYVESVTGVPKEQIIKLAELIHNAKN-VV 541
                                   ***********************************************************************9999999.** PP

                                   EEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT..HHHHHCCCTTTC CS
                 Molybdopterin 240 iivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke..ekikfaaeqpgn 318
                                   +++G+g++++ +g+++  ++ nL+ll+gn+g+pg+g   ++G ++++g  ++ g lp   + ++  e    +kf  +++ +
  gi|70606159|ref|YP_255029.1| 542 VLWGMGITQHVNGADTSTMISNLLLLTGNYGRPGTGAYPMRGHNNVQG-VSDFGCLPNYFPGYQKFEegVIKKFEENWKAK 621
                                   ******************************************999999.66777777666665555556677899999*** PP

                                   STSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEE CS
                 Molybdopterin 319 lgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedly 399
                                   l+ +p+ ++ ++++ + +++++ ly++g++ ++ +  + ++ kale +d+vvv d+++t+ta+ aD++LP a+ +Ek++++
  gi|70606159|ref|YP_255029.1| 622 LNEKPGLQIPQMIEGVLEGKIHGLYIIGEDTVMVDCGTPLTRKALEEADFVVVQDMFMTETAKLADVVLPVASNLEKDGTF 702
                                   ****************************99999999999****************************************** PP

                                   E-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                 Molybdopterin 400 tndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                   +n+e+r+q++ +a++p geak dw+I++ +a+
  gi|70606159|ref|YP_255029.1| 703 VNTERRIQRFYKAMEPIGEAKADWEIIQMIAN 734
                                   ***************************99986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.0   1.6e-22   1.3e-19       2     111 .]     818     926 ..     817     926 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.6e-22
                                   EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTE.EEEEEEEEESSB-TTEEEEESSH CS
               Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrG.svevrakvtervrpGvvfmpfgw 80 
                                   +L++gr+l+++h + +tr+v  l  + p  +ve++ e A+++ i++Gdl+ v+s++G ++++ra vt+rv+ + +f+p  +
  gi|70606159|ref|YP_255029.1| 818 TLNSGRVLEHFHVGNMTRRVAGLTGRVPeTFVEVSKELAQKYSINTGDLIMVKSKFGgEIRARALVTDRVQGDEIFIPLYA 898
                                   79******************************************************99*********************99 PP

                                   CC.....S-GHCTS--SCSTTT--CSTT-EE CS
               Molydop_binding  81 weagekggnaNaltddatdplsgtpefksva 111
                                    +    ++ +N lt++ +d+ sgtp +k+++
  gi|70606159|ref|YP_255029.1| 899 SD---PSKGVNILTAPIIDKGSGTPGYKDTP 926
                                   77...***********************985 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.3     9e-22   7.4e-19       2      55 .]     256     309 ..     255     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 9e-22
                                   EEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                Molybdop_Fe4S4   2 kvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55 
                                   k +kt+C+yCgvgC++ev++k+ ki k+e+ p++p+n   +CvKG++++++v++
  gi|70606159|ref|YP_255029.1| 256 KRTKTVCTYCGVGCSFEVWTKGRKILKIEPKPESPANGILTCVKGKFGWDFVNS 309
                                   89**************************************************96 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   4.6e-15   3.8e-12       3      80 ..       3      75 ..       2      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.6e-15
                        Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvetq 80
                                  +v++++DGkev+     ++a Al++ g +vp+ c++      l+++ +C +C+Vev+g+  vr+c +++ +G++++ +
  gi|70606159|ref|YP_255029.1|  3 SVRVKVDGKEVELNTELSLALALMEKGFYVPHVCYN----TGLTPIQSCDTCIVEVNGKL-VRSCAIKAVEGMSINVN 75
                                  5899********************************....99****************87.*************9765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.8   4.4e-08   3.6e-05       2      19 ..     139     156 ..     138     160 .. 0.90
   2 !   26.3   3.5   5.4e-09   4.4e-06       6      23 ..     186     203 ..     182     204 .. 0.90
   3 ?    0.0   0.2       1.1   8.6e+02       7      12 ..     261     266 ..     257     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                                   EEETTTSSS-THHHHHST CS
                          Fer4   2 videekCigCGaCvevCP 19 
                                   ++d++ Ci CG+Cve+C 
  gi|70606159|ref|YP_255029.1| 139 TYDPSQCILCGRCVEACQ 156
                                   79***************6 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 5.4e-09
                                   TTSSS-THHHHHSTTTEE CS
                          Fer4   6 ekCigCGaCvevCPvgAI 23 
                                   + C++CG+Cv vCPv+A+
  gi|70606159|ref|YP_255029.1| 186 SSCVNCGTCVTVCPVNAL 203
                                   78***************7 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.1
                                   TSSS-T CS
                          Fer4   7 kCigCG 12 
                                    C++CG
  gi|70606159|ref|YP_255029.1| 261 VCTYCG 266
                                   6****9 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.9   9.2e-13   7.5e-10       1      39 [.      83     122 ..      83     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 9.2e-13
               NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdkn.GnCeLQdlayelgvees 39 
                                   Rkt++  +L  H l+C++C++n G+CeL++ + +l+++ +
  gi|70606159|ref|YP_255029.1|  83 RKTAVSRILRYHKLYCTICENNnGDCELHEAVIKLNINSQ 122
                                   9***********************************9976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.2   1.2e-06   0.00096       3      19 ..     139     155 ..     139     159 .. 0.95
   2 !   20.9   3.3   3.4e-07   0.00027       7      24 .]     186     203 ..     185     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                        Fer4_6   3 eidpdkCigCgdCvrvC 19 
                                   ++dp+ Ci Cg+Cv +C
  gi|70606159|ref|YP_255029.1| 139 TYDPSQCILCGRCVEAC 155
                                   68*************** PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.4e-07
                        Fer4_6   7 dkCigCgdCvrvCPegai 24 
                                   ++C+ Cg Cv+vCP +a+
  gi|70606159|ref|YP_255029.1| 186 SSCVNCGTCVTVCPVNAL 203
                                   79*************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   6.3   1.6e-11   1.3e-08       4      55 ..     141     202 ..     139     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.6e-11
                       Fer4_21   4 dedkCigCgkCliaCedtshqai..........eidaktvlkvvedeCvGCnlCssvCPved 55 
                                   d+++Ci Cg+C+ aC+d +++ +          ++  ++  ++ +++Cv C  C++vCPv+ 
  gi|70606159|ref|YP_255029.1| 141 DPSQCILCGRCVEACQDFAVNEViwidwnlnppRVVWDNGNPIGNSSCVNCGTCVTVCPVNA 202
                                   789**************999877677775555444445555999****************54 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   2.2       6.5   5.3e+03      10      43 ..      60     103 ..      45     111 .. 0.59
   2 !    9.8   6.4    0.0015       1.2      27      48 ..     134     155 ..      96     159 .. 0.57
   3 !   24.6  12.9   3.5e-08   2.9e-05       1      52 []     144     202 ..     144     202 .. 0.68
   4 !   12.3  11.2   0.00025       0.2       1      44 [.     187     269 ..     187     272 .. 0.50
   5 ?    1.2   0.6      0.69   5.6e+02       4      18 ..     261     275 ..     259     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                        Fer4_7  10 aaCpvkaieldeeenekgt..........ekveidpekClgCga 43 
                                   + C  ka+e    ++++++          + ++++  +C+ C++
  gi|70606159|ref|YP_255029.1|  60 RSCAIKAVEGMSINVNSPRalnarktavsRILRYHKLYCTICEN 103
                                   55666666666544444222222222333556889999999976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                        Fer4_7  27 gtekveidpekClgCgaCvavC 48 
                                   + + +++dp++C+ Cg+Cv++C
  gi|70606159|ref|YP_255029.1| 134 TGPFYTYDPSQCILCGRCVEAC 155
                                   2267799**************9 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 3.5e-08
                        Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgtekv....eidpekClgCgaCvavCPtga 52 
                                   +Ci Cg+Cv+aC     +++i +d   n+++   +     i  ++C++Cg Cv+vCP++a
  gi|70606159|ref|YP_255029.1| 144 QCILCGRCVEACQdfavNEVIWIDWNLNPPR-VVWdngnPIGNSSCVNCGTCVTVCPVNA 202
                                   6***********7555444444444444443.2333232467799*************97 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00025
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek......................................gtekveidpekClgCga 43 
                                   +C++Cg Cv +Cpv+a++ +    e+                                      +  +++   + C++Cg+
  gi|70606159|ref|YP_255029.1| 187 SCVNCGTCVTVCPVNALMEKSMLGEAgfftwinkdlkrkaieaigkaednfsllmtfseleskaRETQIKRTKTVCTYCGV 267
                                   5***************99775444442222222222222233333333333333333333321122333445566999988 PP

                        Fer4_7  44 .C 44 
                                    C
  gi|70606159|ref|YP_255029.1| 268 gC 269
                                   77 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.69
                        Fer4_7   4 gCgaCvaaCpvkaie 18 
                                    C +C + C+ ++ +
  gi|70606159|ref|YP_255029.1| 261 VCTYCGVGCSFEVWT 275
                                   599999999877654 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.5e-05     0.012       4      19 ..     140     155 ..     137     172 .. 0.84
   2 !   15.1   5.9   2.2e-05     0.018       6      24 ..     185     241 ..     182     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                       Fer4_10   4 idddtCirCgkCvkaC 19 
                                   +d+++Ci Cg+Cv+aC
  gi|70606159|ref|YP_255029.1| 140 YDPSQCILCGRCVEAC 155
                                   7899999999999999 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadl......................................t 24 
                                    ++C++Cg+Cv++CP+++                                       
  gi|70606159|ref|YP_255029.1| 185 NSSCVNCGTCVTVCPVNAlmeksmlgeagfftwinkdlkrkaieaigkaednfsllM 241
                                   579*************88888888888888777766666665555555555555553 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   4.2   5.4e-05     0.044       2      48 ..      98     157 ..      96     160 .. 0.60
   2 !   22.3  12.3   1.3e-07   0.00011       1      50 [.     144     202 ..     144     203 .. 0.68
   3 !   14.5   2.9   3.7e-05      0.03       2      20 ..     188     206 ..     187     212 .. 0.76
   4 ?    3.7   0.3     0.087        71       5      27 ..     262     284 ..     260     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.4e-05
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpk 48 
                                   Ct C +    C+ + +v + + +  ++  +++             ++Ci Cg+CveaC+ 
  gi|70606159|ref|YP_255029.1|  98 CTICENNNGDCELHEAVIKLNINSQKYVDKGYalddtgpfytydpSQCILCGRCVEACQD 157
                                   55554434445444443333333333333333556677788999999***********86 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                        Fer4_9   1 kCtgCgaCveaC....pagvvvedaaerkarlraase.........eaCigCgaCveaCpkga 50 
                                   +C+ Cg+CveaC     ++v+  d++ +  r+              ++C+ Cg+Cv +Cp +a
  gi|70606159|ref|YP_255029.1| 144 QCILCGRCVEACqdfaVNEVIWIDWNLNPPRV----VwdngnpignSSCVNCGTCVTVCPVNA 202
                                   6***********55552333333333333333....134457888889************986 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.7e-05
                        Fer4_9   2 CtgCgaCveaCpagvvved 20 
                                   C++Cg+Cv++Cp ++ +e+
  gi|70606159|ref|YP_255029.1| 188 CVNCGTCVTVCPVNALMEK 206
                                   8888888888888887776 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.087
                        Fer4_9   5 CgaCveaCpagvvvedaaerkar 27 
                                   C++C   C ++v+++ ++  k++
  gi|70606159|ref|YP_255029.1| 262 CTYCGVGCSFEVWTKGRKILKIE 284
                                   ************99888766665 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.7e-07   0.00014       2      55 ..       7      62 ..       6      77 .. 0.78
   2 ?    0.2   0.7      0.88   7.2e+02      39      46 ..     190     197 ..     180     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-07
                                  ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSS......SSSSTTEEEEEESCECTT CS
                          Fer2  2 tidgkevevevadgettlldaaeenggidipysCgg......ggCgtClvevlegevqsd 55
                                  ++dgkeve++   + + l  a+ e  g  +p+ C++       +C tC vev+ + v+s+
  gi|70606159|ref|YP_255029.1|  7 KVDGKEVELNT--ELS-LALALMEK-GFYVPHVCYNtgltpiQSCDTCIVEVNGKLVRSC 62
                                  78999888865..555.88888888.**************9555********94433444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.88
                                   SSSTTEEE CS
                          Fer2  39 gCgtClve 46 
                                   +CgtC++ 
  gi|70606159|ref|YP_255029.1| 190 NCGTCVTV 197
                                   4****975 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00088      0.71      64     118 ..     401     459 ..     356     471 .. 0.74
   2 !    6.8   0.0    0.0064       5.2       3      25 ..     529     551 ..     527     565 .. 0.85
   3 ?   -0.6   0.0       1.2   9.9e+02      67      83 ..     658     674 ..     652     700 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00088
                                   GGGSCHHHHHHHHH-SEEEEES-SSSTCCC..TT.TTTTTTTT...-EEEEEESSCCCCTT CS
                  TPP_enzyme_M  64 glhgskaanealeeaDlvlalGarfddirt..tg.sepefape...akiihididpaeigk 118
                                   g+ +++ + + +e+aDl++++G + ++ ++   g +  + a++   aki  id+ ++ei  
  gi|70606159|ref|YP_255029.1| 401 GFGADSGTIRDIESADLIVVIGHNTTE-SHpvIGsK-VKRAKKirgAKIAVIDVRRHEIAE 459
                                   44456666677899********88766.33234432.23333334259*******999975 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0064
                                   HHHHHHHH-SSEEEEE-CHHCHT CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvars 25 
                                   k+ael+++ak++v+l G g+ ++
  gi|70606159|ref|YP_255029.1| 529 KLAELIHNAKNVVVLWGMGITQH 551
                                   79*****************9755 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.2
                                   SCHHHHHHHHH-SEEEE CS
                  TPP_enzyme_M  67 gskaanealeeaDlvla 83 
                                   g++ +++aleeaD+v++
  gi|70606159|ref|YP_255029.1| 658 GTPLTRKALEEADFVVV 674
                                   6788999*******986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4       3.6   2.9e+03      34      62 ..      73     103 ..      44     104 .. 0.54
   2 !    9.4   0.5    0.0024         2       1      19 [.     144     162 ..     144     174 .. 0.83
   3 !   15.3   5.6   3.6e-05     0.029       2      23 ..     188     207 ..     187     272 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.6
                       Fer4_16  34 ntaekkdlaedeekck..kqeaitgCdiCqd 62 
                                   n++  + l+ ++ +     +++  +C iC++
  gi|70606159|ref|YP_255029.1|  73 NVNSPRALNARKTAVSriLRYHKLYCTICEN 103
                                   3333333333333333113455688999975 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0024
                       Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                   +C+ Cg+C+e+C   a++e
  gi|70606159|ref|YP_255029.1| 144 QCILCGRCVEACQDFAVNE 162
                                   5***********8777665 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3.6e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkek 23 
                                   C++Cg C+ vCP+na+ ek   
  gi|70606159|ref|YP_255029.1| 188 CVNCGTCVTVCPVNALMEK--S 207
                                   ****************998..2 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   9.8      0.43   3.5e+02      46      61 ..     140     155 ..      45     159 .. 0.74
   2 !   17.1  10.9     7e-06    0.0057       3      64 ..     143     201 ..     141     202 .. 0.70
   3 !   10.1   6.0    0.0011      0.87       4      64 ..     187     201 ..     184     273 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.43
                        Fer4_8  46 ealwsCttcgaCtevC 61 
                                   +   +C  cg+C+e+C
  gi|70606159|ref|YP_255029.1| 140 YDPSQCILCGRCVEAC 155
                                   5556677777777766 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7e-06
                        Fer4_8   3 ekCieCgaCqsaCp...vlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   ++Ci Cg+C +aC    v +    +++l+++  + + + +        +  sC++cg C++vCpv+
  gi|70606159|ref|YP_255029.1| 143 SQCILCGRCVEACQdfaVNEVIWiDWNLNPPRVVWD-NGNPI------GNSSCVNCGTCVTVCPVN 201
                                   68***********73322222223555556665555.44444......58**************97 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0011
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +C++Cg C + Cp                                              v+
  gi|70606159|ref|YP_255029.1| 187 SCVNCGTCVTVCP----------------------------------------------VN 201
                                   5666666666666..............................................43 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.0   2.4e-05     0.019       3      20 ..     138     155 ..     136     156 .. 0.92
   2 !   16.2   5.8     1e-05    0.0084       9      21 ..     187     199 ..     181     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                        Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                   + +d+  Ci Cg Cv aC
  gi|70606159|ref|YP_255029.1| 138 YTYDPSQCILCGRCVEAC 155
                                   789*************** PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1e-05
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   +C++Cg+Cv++CP
  gi|70606159|ref|YP_255029.1| 187 SCVNCGTCVTVCP 199
                                   7************ PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   2.2    0.0072       5.9       2      18 ..     141     157 ..     141     162 .. 0.90
   2 !   10.7   0.1   0.00072      0.59       4      17 ..     186     199 ..     183     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0072
                       Fer4_13   2 DrdtCiacgaCvelaPd 18 
                                   D ++Ci cg Cve++ d
  gi|70606159|ref|YP_255029.1| 141 DPSQCILCGRCVEACQD 157
                                   6789***********88 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00072
                       Fer4_13   4 dtCiacgaCvelaP 17 
                                   ++C++cg+Cv ++P
  gi|70606159|ref|YP_255029.1| 186 SSCVNCGTCVTVCP 199
                                   79************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00086       0.7       3      24 ..     140     161 ..     139     163 .. 0.87
   2 ?    4.0   0.4       0.1        86       6      19 ..     186     199 ..     183     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00086
                       Fer4_15   3 vDrdaCigcglCvaeapevfel 24 
                                   +D ++Ci cg+Cv++++++ ++
  gi|70606159|ref|YP_255029.1| 140 YDPSQCILCGRCVEACQDFAVN 161
                                   7999************998765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                       Fer4_15   6 daCigcglCvaeap 19 
                                   + C  cg Cv+++p
  gi|70606159|ref|YP_255029.1| 186 SSCVNCGTCVTVCP 199
                                   68***********8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.4    0.0087       7.1      84      97 ..     144     157 ..     141     166 .. 0.87
   2 ?   13.4   0.7   8.1e-05     0.066      57      74 ..     184     201 ..     175     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0087
                       Fer4_18  84 eciscllcidacdk 97 
                                   +ci c++c++ac++
  gi|70606159|ref|YP_255029.1| 144 QCILCGRCVEACQD 157
                                   7***********86 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.1e-05
                       Fer4_18  57 gagdcidcescvkvcPtg 74 
                                   g++ c++c++cv+vcP++
  gi|70606159|ref|YP_255029.1| 184 GNSSCVNCGTCVTVCPVN 201
                                   6789************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.9    0.0071       5.8      21      57 ..     120     156 ..      96     159 .. 0.49
   2 ?   12.4  11.5   0.00022      0.18       1      58 [.     144     200 ..     144     203 .. 0.74
   3 ?    3.9   8.8     0.099        81       2      18 ..     188     204 ..     187     273 .. 0.63
   4 ?   -1.1   0.3       3.5   2.8e+03       5      19 ..     262     276 ..     260     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0071
                       Fer4_17  21 epkkllraaklglleeaeke...........ekaslCieCgeCerkCP 57 
                                   + +k++ +                          s+Ci Cg+C+++C 
  gi|70606159|ref|YP_255029.1| 120 NSQKYVDK-----------GyalddtgpfytYDPSQCILCGRCVEACQ 156
                                   33333333...........2222223444435789************5 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke...ekaslCieCgeCerkCPq 58 
                                   +Ci Cg C+++C  ++ ++     +  +++l+  + + ++      s+C++Cg C+++CP 
  gi|70606159|ref|YP_255029.1| 144 QCILCGRCVEACQDFAVNEV----IWIDWNLNPPRVVWDNgnpIGNSSCVNCGTCVTVCPV 200
                                   5************9999665....5555555444444333332589**************6 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.099
                       Fer4_17   2 CiqCgyClpeCpsyeay 18 
                                   C +Cg C+ +Cp ++ +
  gi|70606159|ref|YP_255029.1| 188 CVNCGTCVTVCPVNALM 204
                                   77777777777776554 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.5
                       Fer4_17   5 CgyClpeCpsyeayd 19 
                                   C yC   C++  +++
  gi|70606159|ref|YP_255029.1| 262 CTYCGVGCSFEVWTK 276
                                   888888888776654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.0     0.023        19       4      14 ..     145     155 ..     142     157 .. 0.90
   2 ?   13.9   3.7   7.5e-05     0.061       3      17 .]     187     201 ..     185     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                        Fer4_4   4 CigCgsCvaaC 14 
                                   Ci Cg+Cv aC
  gi|70606159|ref|YP_255029.1| 145 CILCGRCVEAC 155
                                   *********** PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.5e-05
                        Fer4_4   3 rCigCgsCvaaCPqg 17 
                                   +C++Cg Cv +CP++
  gi|70606159|ref|YP_255029.1| 187 SCVNCGTCVTVCPVN 201
                                   7************75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.7     0.003       2.4       1      11 [.     145     155 ..     145     157 .. 0.96
   2 ?   14.2   7.8   8.2e-05     0.067       1      15 []     188     202 ..     188     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                        Fer4_3   1 CtgCgaCvevC 11 
                                   C+ Cg+Cve+C
  gi|70606159|ref|YP_255029.1| 145 CILCGRCVEAC 155
                                   *********** PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.2e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C++Cg+Cv vCPv+A
  gi|70606159|ref|YP_255029.1| 188 CVNCGTCVTVCPVNA 202
                                   *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (976 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.50
# Mc/sec: 5889.76
//
Query:       gi|70606160|ref|YP_255030.1|  [L=380]
Description: hypothetical protein Saci_0321 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-11   41.8   0.0    1.5e-10   41.2   0.0    1.2  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
  ------ inclusion threshold ------
      0.096   12.8   0.1       0.41   10.8   0.0    2.0  2  FtsK_alpha       FtsK alpha domain


Domain annotation for each model (and alignments):
>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   1.6e-14   1.5e-10      12     121 ..      19     136 ..       6     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.6e-14
               2_5_RNA_ligase2  12 lrrslydkayprwp.pHitLlypfvededl..adlaellsrlaketepfevrldgfgvFehkks.vvylsvsdsealqalr 88 
                                   lr +++ ++++ +  pHitL+y f++++    +++ + +s++a  +e +++ +dg++  ++ k+ v+  ++s+s +l+al+
  gi|70606160|ref|YP_255030.1|  19 LR-KFRFHLHNTHKiPHITLIYSFKPKPLVkiSEISQIISDVAGKYEDLRFLFDGISIKRGSKGlVLAFNISPSMELVALQ 98 
                                   44.666777666667*************99*****************************998888**************** PP

               2_5_RNA_ligase2  89 aallealpeagdkeds.....geftPHlTiaqsadsts 121
                                   ++l++ l++    e       +   +H+ i+   ++++
  gi|70606160|ref|YP_255030.1|  99 RELYQRLKPLIKIERGkekfsESLWFHAAISFGTTEKE 136
                                   ******99873333223444677777766666555555 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.5e-05      0.41      26      75 ..      12      60 ..       9      68 .. 0.85
   2 ?   -2.1   0.0      0.47   4.3e+03      32      54 ..     335     358 ..     326     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.5e-05
                    FtsK_alpha 26 aklieetleefgieakvveisvGPvvtq.yevepapgvkvskiaaleddla 75
                                  ++++++ l++f  +  + ++++ P++t  y ++p+p vk+s+i ++ +d+a
  gi|70606160|ref|YP_255030.1| 12 KHRLKQFLRKFRFH--LHNTHKIPHITLiYSFKPKPLVKISEISQIISDVA 60
                                  67888888888765..6788999***966*****************99988 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.47
                    FtsK_alpha  32 tleefg.ieakvveisvGPvvtqy 54 
                                    l+ef  +++++ +i+vG  vt++
  gi|70606160|ref|YP_255030.1| 335 RLREFPfVNGELKTINVGVDVTKF 358
                                   566664377788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2576.13
//
Query:       gi|70606161|ref|YP_255031.1|  [L=80]
Description: hypothetical protein Saci_0322 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.1   0.7      0.028   14.0   0.1    1.7  2  DUF2067   Uncharacterized protein conserved in archaea (DUF20
      0.077   12.7   0.2      0.099   12.3   0.2    1.2  1  YkyA      Putative cell-wall binding lipoprotein
      0.077   13.5   1.5        1.6    9.2   1.6    2.3  2  CBS       CBS domain
       0.23   11.7   3.0          7    6.9   0.3    2.0  2  LPD14     Large polyvalent protein-associated domain 14


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   6.2e-06     0.028     151     186 .]       8      45 ..       2      45 .. 0.87
   2 ?   -0.6   0.0      0.19   8.6e+02     153     176 ..      51      76 ..      47      80 .] 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.2e-06
                       DUF2067 151 tgldpdevieellekGlLe..eeegkivlrkewkkalk 186
                                      d+ ev+ee+++ G+ +  +e ++i++rk ++++++
  gi|70606161|ref|YP_255031.1|   8 VNDDINEVAEEMIRLGIARskNEAFNIMIRKGLNEVKR 45 
                                   566899*************999**********999875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.19
                       DUF2067 153 ldpdevieellekGl.Le.eeegkiv 176
                                   +++ e++e+  ++Gl  e  +++ki 
  gi|70606161|ref|YP_255031.1|  51 KKVNELVERWQREGLpIElPNSNKII 76 
                                   66788888888888875556666665 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.2e-05     0.099      18      65 ..      10      59 ..       4      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                          YkyA 18 kefeeqqekLtel..ekkeqelyeeiielgmdefdkikklsdealenvee 65
                                  ++++e +e++ +l   + ++e ++ +i +g +e ++i+++ +++ e+ve 
  gi|70606161|ref|YP_255031.1| 10 DDINEVAEEMIRLgiARSKNEAFNIMIRKGLNEVKRIVDKRKKVNELVER 59
                                  6677778888776335889***************************9984 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.6   0.00037       1.6       8      29 ..       2      23 ..       1      59 [. 0.87
   2 ?   -0.7   0.1      0.46   2.1e+03      30      30 ..      53      53 ..      38      76 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                                  SCEEEETTSBHHHHHHHHHHHT CS
                           CBS  8 dvvtvppdttleealelmrekg 29
                                  +vvt++ ++++ e++e+m++ g
  gi|70606161|ref|YP_255031.1|  2 RVVTIKVNDDINEVAEEMIRLG 23
                                  689***************8744 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                                  S CS
                           CBS 30 v 30
                                  v
  gi|70606161|ref|YP_255031.1| 53 V 53
                                  3 PP

>> LPD14  Large polyvalent protein-associated domain 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0016         7      66      80 ..       6      20 ..       3      22 .. 0.89
   2 ?    6.3   0.2    0.0024        11      34      78 ..      21      63 ..      19      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                         LPD14 66 tgvngyvgEvlEEva 80
                                  ++vn+ ++Ev+EE++
  gi|70606161|ref|YP_255031.1|  6 IKVNDDINEVAEEMI 20
                                  69***********86 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                         LPD14 34 rlggvlsratgkalslikdksiikqltdianrtgvngyvgEvlEE 78
                                  rlg  + r++ +a+++++ k   +  + + +r +vn+ v+ +  E
  gi|70606161|ref|YP_255031.1| 21 RLG--IARSKNEAFNIMIRKGLNEVKRIVDKRKKVNELVERWQRE 63
                                  788..99********6666655555566679999***99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 533.34
//
Query:       gi|70606162|ref|YP_255032.1|  [L=132]
Description: hypothetical protein Saci_0323 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-15   58.3   1.3    1.1e-15   58.1   1.3    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   1.3   6.4e-20   1.1e-15       1     119 [.       3     123 ..       3     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 6.4e-20
                                   EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBC.HHHH CS
                           PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpid.aeia 78 
                                   +++DTsvlia++ ++++++e ++  + + +e ++s++v  El+ v +r  k+++e++++lv    l+ ++k  ++d  +++
  gi|70606162|ref|YP_255032.1|   3 YYIDTSVLIAYVnEKDPNHELSLMVVPKEGERIISDIVELELYSVFSRtLKLSEEELDALVNYTVLKGNCKKEELDfNKLF 83 
                                   79******************999999999*******************999999999999999999********7725689 PP

                                   HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                           PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                   e+a+ +a+  +l+++D+l+++  +  +++li t D++++++
  gi|70606162|ref|YP_255032.1|  84 ETAKSLANITKLKSLDLLHLSASILLNCELI-TLDKELENA 123
                                   99*****************************.****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 953.73
//
Query:       gi|70606163|ref|YP_255033.1|  [L=283]
Description: hypothetical protein Saci_0324 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-50  172.6  37.6    1.2e-50  172.4  37.6    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.4  37.6   6.7e-55   1.2e-50       2     236 .]      18     276 ..      16     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 6.7e-55
                          TauE   2 llagllaGfvagllGiGggliavPlLllll..............ppavavatsllavvatslsgalahrrrgnvdwrllll 68 
                                   ++ g+++G++ gl+G+Gg+++avPlLl+++                +++++ts+lav++++ ++++ h+r+gnv++  +++
  gi|70606163|ref|YP_255033.1|  18 VVSGFIIGLILGLIGGGGSILAVPLLLYFVglgndsssfgnysnITHLVLGTSALAVGLNAYINSFIHWRKGNVKVFEGVV 98 
                                   689*************************74569**********98899********************************* PP

                          TauE  69 lllgsliGallGallllllpsellkllfgvlllllallmllrkkr.......srak.....grerrptaillvligglvGl 137
                                   ++++++iG++lGa++  l+ ++l++++fg++++l++l+m+ +k +          +      +++ +  i ++ +g+lvGl
  gi|70606163|ref|YP_255033.1|  99 FTIPGVIGSILGAYFGYLTTGNLILIMFGIVMILIGLRMIKSKCKegsnetkG--SgdtgvVKSKDRINIRIIYTGFLVGL 177
                                   ***************************************99444446666551..15555533333444446777999*** PP

                          TauE 138 lsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlse 218
                                   +sG+lGiGgGfl+vp+ll+ + +++  a++tsl+ + +++l++al+ya+ g +d+ l l+ll+g++ G+++G+ la++ ++
  gi|70606163|ref|YP_255033.1| 178 ASGFLGIGGGFLIVPALLFSTSMSIISAIGTSLISVGTFGLSTALTYASYGEIDYILSLILLAGGVGGGYIGTLLASKSPR 258
                                   ********************************************************************************* PP

                          TauE 219 rtlrrlfallllvlgvkl 236
                                    tlr++f+++l+v+++++
  gi|70606163|ref|YP_255033.1| 259 STLRKVFGVVLIVVAIYI 276
                                   ***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1941.81
//
Query:       gi|70606164|ref|YP_255034.1|  [L=303]
Description: heterodisulfide reductase B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-29  101.2   0.1      2e-16   60.0   0.0    2.6  3  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.0   1.1e-20     2e-16       1      84 [.       8      90 ..       8      91 .. 0.98
   2 ?   -3.3   0.0      0.63   1.1e+04      13      30 ..      99     116 ..      95     120 .. 0.76
   3 !   38.8   0.0   4.6e-14   8.3e-10       2      79 ..     155     244 ..     154     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.1e-20
                           CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCllq 83
                                  +a+++gC +l++  + ++ +lk + + lg+ l++ e+ +CCGa  ++++++   + l +rn++ a+e+gada+v+acpgC+++
  gi|70606164|ref|YP_255034.1|  8 IAFYPGC-ALDGLGKTYEVSLKLVAQDLGIPLDRIEDYNCCGALEVKNVNTMAGLLLPARNLSLAREMGADAVVSACPGCHYS 89
                                  69*****.*************************************************************************98 PP

                           CCG 84 l 84
                                  l
  gi|70606164|ref|YP_255034.1| 90 L 90
                                  7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.63
                           CCG  13 aypevrkalkkllealgv 30 
                                   +yp+vr++  + le++g+
  gi|70606164|ref|YP_255034.1|  99 KYPKVREKANNYLEKMGT 116
                                   588888888888888875 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 4.6e-14
                           CCG   2 ayfdgChllraa............ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetg 69 
                                   a ++gC + r++             pe +  + ++l+a g+e++++ +k +CCG ++++s+ e +a+ l +r +++a++ g
  gi|70606164|ref|YP_255034.1| 155 APYYGCLYSRPKqylltgmaplkdDPERPFFMDEILKAIGAEVVPFeAKTMCCGGPHVYSDVE-VAMHLEARILKEARRNG 234
                                   6688997777778889999999889999999******************************99.9**************** PP

                           CCG  70 adaivtacpg 79 
                                   a+++vt cp 
  gi|70606164|ref|YP_255034.1| 235 AEVLVTDCPL 244
                                   ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1966.30
//
Query:       gi|70606165|ref|YP_255035.1|  [L=230]
Description: 4Fe-4S ferredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   35.5   6.3    1.8e-08   34.7   6.3    1.4  1  Fer4_8    4Fe-4S dicluster domain
    1.3e-08   34.9  10.0      1e-07   32.0  11.0    1.9  2  Fer4_9    4Fe-4S dicluster domain
      1e-06   29.2   6.7    2.2e-06   28.1   6.9    1.5  1  Fer4_17   4Fe-4S dicluster domain
    1.4e-06   28.7   6.2    2.3e-06   28.1   6.2    1.4  1  Fer4_7    4Fe-4S dicluster domain
    2.4e-05   25.2   3.0     0.0024   18.7   0.3    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0016   18.5  10.5     0.0064   16.6  10.7    1.8  1  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.7   3.8        0.7   10.8   0.2    2.3  2  Fer4_22   4Fe-4S dicluster domain
       0.04   14.4  13.9       0.46   11.1   3.5    2.2  2  Fer4_4    4Fe-4S binding domain
      0.046   13.9   9.1       0.26   11.5   9.1    2.0  1  Fer4_21   4Fe-4S dicluster domain
      0.048   13.4   1.1      0.048   13.4   1.1    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.17   12.0  13.2       0.13   12.5   1.6    2.4  2  Fer4_2    4Fe-4S binding domain
       0.49   10.3  13.6       0.74    9.7   2.8    2.3  2  Fer4      4Fe-4S binding domain
        4.4    7.5   8.4       0.76   10.0   0.9    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   6.3   1.3e-11   1.8e-08       3      65 .]      61     123 ..      59     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-11
                        Fer4_8   3 ekCieCgaCqsaCpvlrr......tkkhlldargeaaedvqeeqvlee.eealwsCttcgaCtevCpvgi 65 
                                   ++C +Cg C+s C ++r+       +k++  ar++ ++      +l + +++lw+C++c++Ct +Cp+g+
  gi|70606165|ref|YP_255035.1|  61 SACWQCGTCTSGC-TMREydpdfgPRKFIDLARKGDKQ------ALIQlQDSLWRCVSCQKCTHRCPKGV 123
                                   79***********.455523333333444444444444......33234568***************986 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   3.0   2.1e-05     0.029      33      48 ..      50      75 ..      31      78 .. 0.70
   2 !   32.0  11.0   7.5e-11     1e-07       1      50 [.      62     123 ..      62     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                        Fer4_9 33 e..........eaCigCgaCveaCpk 48
                                  e          +aC++Cg+C+  C  
  gi|70606165|ref|YP_255035.1| 50 EvantlegvtiSACWQCGTCTSGCTM 75
                                  2334445556678***********75 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 7.5e-11
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpkga 50 
                                   +C++Cg+C++ C +  + +d ++rk    a++             ++C++C++C+++Cpkg+
  gi|70606165|ref|YP_255035.1|  62 ACWQCGTCTSGCTMREYDPDFGPRKFIDLARKGdkqaliqlqdslWRCVSCQKCTHRCPKGV 123
                                   6***********9999999888888776555557899999999*****************95 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   6.9   1.6e-09   2.2e-06       1      60 [.      62     123 ..      62     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.6e-09
                       Fer4_17   1 rCiqCgyClpeCpsyeayd.nepkkllraaklglleeaek.eekaslCieCgeCerkCPqgl 60 
                                   +C qCg C+  C + e  + + p+k++  a+ g++++ ++ ++   +C++C++C+++CP+g+
  gi|70606165|ref|YP_255035.1|  62 ACWQCGTCTSGCTMREYDPdFGPRKFIDLARKGDKQALIQlQDSLWRCVSCQKCTHRCPKGV 123
                                   5************8777551579999999999999998772579***************987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   6.2   1.7e-09   2.3e-06       1      52 []      62     123 ..      62     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-09
                        Fer4_7   1 rCigCgaCvaaC..........pvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   +C +Cg C++ C          p k i+l  + +++   +++ + ++C++C++C  +CP+g+
  gi|70606165|ref|YP_255035.1|  62 ACWQCGTCTSGCtmreydpdfgPRKFIDLARKGDKQALIQLQDSLWRCVSCQKCTHRCPKGV 123
                                   5***********9999999999999999999988888888888999*************996 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.2    0.0099        14       2      13 ..      63      74 ..      47      99 .. 0.84
   2 !   18.7   0.3   1.8e-06    0.0024       1      21 [.     108     128 ..     108     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0099
                       Fer4_16  2 CgtCgkCaevCP 13
                                  C +Cg C++ C 
  gi|70606165|ref|YP_255035.1| 63 CWQCGTCTSGCT 74
                                  777777777774 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.8e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                   rC++C+kC+  CP +++ e+ 
  gi|70606165|ref|YP_255035.1| 108 RCVSCQKCTHRCPKGVMVEEV 128
                                   6****************9984 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  10.7   4.7e-06    0.0064       7      56 .]      61     120 ..      57     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.7e-06
                       Fer4_10   7 dtCirCgkCvkaCPadl............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   + C +Cg+C++ C  ++                 kg +    + ++ +++C  c +C+  CP
  gi|70606165|ref|YP_255035.1|  61 SACWQCGTCTSGC--TMreydpdfgprkfIDLARKGDKQALIQLQDSLWRCVSCQKCTHRCP 120
                                   57***********..6668********98777777777777888889**************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.4    0.0083        12      78      93 ..      59      74 ..      33      77 .. 0.67
   2 ?   10.8   0.2   0.00051       0.7       1      14 [.     108     121 ..      93     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0083
                       Fer4_22 78 gesgCvGCgRCieacp 93
                                    s+C  Cg C++ c+
  gi|70606165|ref|YP_255035.1| 59 TISACWQCGTCTSGCT 74
                                  5556666666666664 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00051
                       Fer4_22   1 rClsCgaCtlvCpt 14 
                                   rC+sC++Ct  Cp 
  gi|70606165|ref|YP_255035.1| 108 RCVSCQKCTHRCPK 121
                                   46666666666654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.5   0.00034      0.46       3      16 ..      62      75 ..      60      76 .. 0.88
   2 ?    8.6   2.8    0.0021         3       3      16 ..     108     121 ..     106     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                   C +Cg C++ C +
  gi|70606165|ref|YP_255035.1| 62 ACWQCGTCTSGCTM 75
                                  7***********75 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0021
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   rC+ C +C+  CP 
  gi|70606165|ref|YP_255035.1| 108 RCVSCQKCTHRCPK 121
                                   8*********9996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   9.1   0.00019      0.26       6      52 ..      61     120 ..      57     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                       Fer4_21   6 dkCigCgkCliaCedtshqai...........eidaktvlkvved..eCvGCnlCssvCP 52 
                                   + C +Cg C+  C    ++             ++d+++ ++++++  +Cv C+ C++ CP
  gi|70606165|ref|YP_255035.1|  61 SACWQCGTCTSGCTMREYDPDfgprkfidlarKGDKQALIQLQDSlwRCVSCQKCTHRCP 120
                                   68***********98888765566666677766667777777765568************ PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.1       0.1   1.4e+02      65      88 ..      53      76 ..      44      82 .. 0.71
   2 ?   13.4   1.1   3.5e-05     0.048      22      53 ..     107     136 ..      84     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.1
                                  -S-HHHHHHHS-GGGTGCCS-GGG CS
                       Fer4_20 65 nslpavcgrvCpqeelCegaCvle 88
                                  n+l  v+   C q  +C + C+++
  gi|70606165|ref|YP_255035.1| 53 NTLEGVTISACWQCGTCTSGCTMR 76
                                  666667777777777777777774 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.5e-05
                                   TT----TT-HHHHCSTT---HHHHHHHHHTT- CS
                       Fer4_20  22 sRClqCkkapcvkgCPveidipefikkiaegn 53 
                                    RC++C  ++c++ CP  + ++e +++i++  
  gi|70606165|ref|YP_255035.1| 107 WRCVSC--QKCTHRCPKGVMVEEVVHSIHNYF 136
                                   5*****..89*****************99865 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.3      0.03        41      10      20 ..      63      73 ..      59      75 .. 0.86
   2 ?   12.5   1.6   9.1e-05      0.13       9      21 ..     108     120 ..     101     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                        Fer4_2 10 CigCgaCvsaC 20
                                  C +Cg+C+s C
  gi|70606165|ref|YP_255035.1| 63 CWQCGTCTSGC 73
                                  668******99 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.1e-05
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   rC++C +C++ CP
  gi|70606165|ref|YP_255035.1| 108 RCVSCQKCTHRCP 120
                                   9***********9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.2    0.0085        12       6      18 ..      61      73 ..      58      74 .. 0.88
   2 ?    9.7   2.8   0.00053      0.74       7      22 ..     108     123 ..     108     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0085
                                  TTSSS-THHHHHS CS
                          Fer4  6 ekCigCGaCvevC 18
                                  + C  CG+C + C
  gi|70606165|ref|YP_255035.1| 61 SACWQCGTCTSGC 73
                                  58*******9877 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00053
                                   TSSS-THHHHHSTTTE CS
                          Fer4   7 kCigCGaCvevCPvgA 22 
                                   +C+ C +C   CP g+
  gi|70606165|ref|YP_255035.1| 108 RCVSCQKCTHRCPKGV 123
                                   7************997 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2      0.21   2.9e+02      57      72 ..      59      74 ..      18      79 .. 0.72
   2 ?   10.0   0.9   0.00055      0.76      53      77 ..     101     125 ..      76     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.21
                       Fer4_18 57 gagdcidcescvkvcP 72
                                  + + c +c++c + c 
  gi|70606165|ref|YP_255035.1| 59 TISACWQCGTCTSGCT 74
                                  4455666666666554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00055
                       Fer4_18  53 rkekgagdcidcescvkvcPtgidi 77 
                                   + +++   c++c++c + cP g+ +
  gi|70606165|ref|YP_255035.1| 101 QLQDSLWRCVSCQKCTHRCPKGVMV 125
                                   45667778*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1640.71
//
Query:       gi|70606166|ref|YP_255036.1|  [L=227]
Description: hypothetical protein Saci_0327 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1588.89
//
Query:       gi|70606167|ref|YP_255037.1|  [L=364]
Description: heterodisulfide reductase A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   63.6   0.0    2.3e-17   63.2   0.0    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    8.1e-09   35.2   0.3    1.7e-08   34.1   0.3    1.5  2  FAD_binding_3  FAD binding domain
    3.7e-08   32.9   0.0    0.00065   18.9   0.0    2.2  2  GIDA           Glucose inhibited division protein A
    1.6e-07   30.8   0.2      6e-06   25.6   0.2    2.1  2  FAD_binding_2  FAD binding domain
    4.7e-07   29.5   0.0    9.3e-07   28.5   0.0    1.5  1  FAD_oxidored   FAD dependent oxidoreductase
    5.5e-07   28.6   0.2     0.0011   17.7   0.1    2.1  2  HI0933_like    HI0933-like protein
    8.7e-07   29.1   0.1    1.8e-06   28.1   0.1    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    7.7e-06   25.3   0.0    1.2e-05   24.7   0.0    1.3  1  Thi4           Thi4 family
    9.1e-06   26.2   0.8    0.00066   20.2   0.0    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.3e-05   23.3   0.7    0.00096   18.5   0.1    2.1  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.7   0.1     0.0058   16.0   0.0    2.4  3  Amino_oxidase  Flavin containing amine oxidoreductase
    0.00012   21.8   0.7    0.00063   19.4   0.1    2.2  2  DAO            FAD dependent oxidoreductase
    0.00053   20.0   0.0       0.14   12.1   0.0    2.9  3  NAD_binding_9  FAD-NAD(P)-binding
     0.0028   16.8   0.0     0.0039   16.3   0.0    1.2  1  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.027   13.8   0.0      0.056   12.7   0.0    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.064   12.6   0.1        0.1   11.9   0.1    1.3  1  ThiF           ThiF family
        0.1   11.7   0.1       0.99    8.5   0.0    2.1  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
        0.1   13.0   0.1       0.23   11.9   0.1    1.7  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   2.3e-20   2.3e-17       1     292 [.       3     336 ..       3     338 .. 0.66

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.3e-20
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH............HHHHCHHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias............evvkklnqgiel 69 
                                   k+v+v+G+GpAGl+aa++l++ g++ +lv +++  l+g++   k    +  ++e +             e     n ++++
  gi|70606167|ref|YP_255037.1|   3 KSVLVVGAGPAGLSAAKELSRMGVDLILV-ERESYLGGTPKKLK---YSLLFPELRPasevldplvksvE----ENGNVRV 75 
                                   589**************************.66666666555533...33333333333335687765441....3455777 PP

                                   CHC...CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC..TCT.TC.TTBEECCSECHHHHHHCCSS-T.. CS
                                   xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                   Pyr_redox_2  70 llg...eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl..gip.Gvaenvgklvrtldsaealklkllp.. 142
                                   l++   e+  ++  +  +v +++kk g+ ++ + ++++ A+G++ +d   + + G   + + ++  + + e++ ++++   
  gi|70606167|ref|YP_255037.1|  76 LTEsiiENMKNV-SDGFEVGIKDKK-GNLKTEKVNAIIAASGFEHFDSrrKYEyGY--GLIPNIYQISDIEGMLHENKLvt 152
                                   777333333344.333366664444.8999999************99944333533..22333333344444444444455 PP

                                   ................SEEEEES-SHHHHHHHHHHHHHT-........EEEEEESSSSSS....TTS-HHHHHHHHHHHHH CS
                                   ................xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 143 ................krivvvGgGyiGvElAaalaklgk........evtlveardrll....raldkelsaaleealek 195
                                                    r + vG+ y++ +++a   k +                  +++    r+++ +  + +++a  +
  gi|70606167|ref|YP_255037.1| 153 tkgtppkrvaillcvgSRDATVGNTYCSRVCCAISIKQAMeikqripdA------IVHIYymdiRTYGLMEDKLYWKAQLD 227
                                   6666785555555555555***************544444232233322......3333333446788899999******* PP

                                   TTEEEEESCEEEEEEETTEEEEEEETTSCE........EEESEEEE-S-EEES-HHCS..HCCT-EEEETTEE.E--TTS. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxx. RF
                   Pyr_redox_2 196 eGvevklgtsvkeidgngeklevvledgee........idadlvvvavGvrpstelle..eklglelderggi.vvdefl. 264
                                     v +  + ++ e+ + ++  +v+ + +++        +++d+v++a G++     ++  + lglel+e+g++   d+   
  gi|70606167|ref|YP_255037.1| 228 YRVGFI-RGRISEFMRGPN-DTVIIKGEDTmnlnralvVPYDMVILANGMELGLGSKQvaKVLGLELEEHGFVkPLDPDRl 306
                                   ******.556666666555.233333333344666666*************877666677*************75666655 PP

                                   ..BESSTTEEE-GGGCTECCSS--HHHHHH CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 265 ..rtnvpgiyaiGDvaggkggpelaqaAvq 292
                                     +++ +g++++G+++g+kg+ +++++  +
  gi|70606167|ref|YP_255037.1| 307 pvQSTRKGVFLAGAITGPKGISDSITEGYA 336
                                   78999***********99999988887665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.3   1.7e-11   1.7e-08       3      35 ..       4      36 ..       2      46 .. 0.90
   2 ?   -2.8   0.0       2.8   2.8e+03     100     163 ..      52     115 ..      43     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.7e-11
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                  +Vl+VGaGpaGl++a++Ls+ Gv+ +lve+ s 
  gi|70606167|ref|YP_255037.1|  4 SVLVVGAGPAGLSAAKELSRMGVDLILVERESY 36
                                  69****************************875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                   EE--HHHHHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                 FAD_binding_3 100 tvypqteleriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                   ++ p +e++  Lv++ ee g ++v  +  +e++++  +g +  ++dk+ g+ +t + + +++a G
  gi|70606167|ref|YP_255037.1|  52 ELRPASEVLDPLVKSVEENGnVRVLTESIIENMKNVSDGFEVGIKDKK-GNLKTEKVNAIIAASG 115
                                   566778888889999888888888888888888888888888888875.4333444444666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   6.6e-07   0.00065       2      29 ..       5      32 ..       4      46 .. 0.87
   2 !   11.8   0.0   9.4e-05     0.094     354     388 ..     311     345 ..     292     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                                  EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLit 29
                                  v V+G+G AG+ AA +++r+G++ +L+ 
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKELSRMGVDLILVE 32
                                  89*********************99993 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.4e-05
                                   SSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHH CS
                          GIDA 354 kvkgLflAGqinGteGYeEaaaqGllAGinaarka 388
                                   ++kg+flAG i+G +G  +++  G  A++ a +++
  gi|70606167|ref|YP_255037.1| 311 TRKGVFLAGAITGPKGISDSITEGYAAALKAYQYV 345
                                   589**************************998776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   6.1e-09     6e-06       2      37 ..       5      40 ..       4      47 .. 0.95
   2 ?    3.2   0.0     0.039        39     139     206 ..      55     119 ..      49     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.1e-09
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                  v+V+G+G AGL+AA e+++ G + ++ve e++ gg+
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKELSRMGVDLILVERESYLGGT 40
                                  9*******************************9996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.039
                                   HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.. CS
                 FAD_binding_2 139 tghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgral 206
                                   +  ++l +lv+s++++g v+++++  ++++   ++   G +v  ++++++ + +  + ++a+ Gf++ +
  gi|70606167|ref|YP_255037.1|  55 PASEVLDPLVKSVEENGnVRVLTESIIENM---KNVSDGFEVGIKDKKGNLKTEKVNAIIAASGFEH-F 119
                                   567899************************...7899999**99999999998878**********8.2 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   9.3e-10   9.3e-07       2      37 ..       5      40 ..       4      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9.3e-10
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGl 37
                                  v+VvG+gpaG+ AA    r+G   +Lve++ +lGG+
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKELSRMGVDLILVERESYLGGT 40
                                  9**********************************7 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.1e-06    0.0011       2      36 ..       4      38 ..       3      47 .. 0.88
   2 !    9.1   0.0   0.00046      0.46     101     161 ..      49     112 ..      42     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +v+v+G+G+AGl aA ++++ g + +l+e+++ lg
  gi|70606167|ref|YP_255037.1|  4 SVLVVGAGPAGLSAAKELSRMGVDLILVERESYLG 38
                                  699**************************998777 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00046
                                   EEETT.-CHHHHHHHHHHHHHH.T-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEE..EE- CS
                   HI0933_like 101 lFpvsdkaedivdallkelkea.gvklrletevksvekeedgkfrvkt.kseeeleadkl..vlA 161
                                   lFp+ + a++++d l+k ++e+ +v++ +e+ ++++++ +dg f+v + +++++l+++k+  ++A
  gi|70606167|ref|YP_255037.1|  49 LFPELRPASEVLDPLVKSVEENgNVRVLTESIIENMKNVSDG-FEVGIkDKKGNLKTEKVnaIIA 112
                                   8******************996269***********888888.9999966777887776533554 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   1.8e-09   1.8e-06       1      33 [.       7      39 ..       7      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.8e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  +vGaG +Gl+aA +L++ g+d  l+e+ ++lGG
  gi|70606167|ref|YP_255037.1|  7 VVGAGPAGLSAAKELSRMGVDLILVERESYLGG 39
                                  8*******************************9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.2e-05      18      97 ..       3      80 ..       1      96 [. 0.76

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT..TTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESEHH CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw..lGGqlfsaivvrkpakelLdelgikyedegdyvvvkdaa 97
                                    v++vGaG++GL+aa+ l++  ++ ++++er+  +GG         lf ++   +pa+e+Ld l    e++g+  v  +++
  gi|70606167|ref|YP_255037.1|  3 KSVLVVGAGPAGLSAAKELSRM-GVDLILVERESYLGGTPKklKYSLLFPEL---RPASEVLDPLVKSVEENGNVRVLTESI 80
                                  6799******************.**********9999874311344555554...788888888877777777766666655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.6e-07   0.00066       1      35 [.       4      38 ..       4      45 .. 0.92
   2 ?    4.1   0.1     0.067        67      46      76 ..      63      93 ..      56     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.6e-07
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  +v+vvG+G  gl +A++l+++g +  +ver++ l 
  gi|70606167|ref|YP_255037.1|  4 SVLVVGAGPAGLSAAKELSRMGVDLILVERESYLG 38
                                  699***************************99886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.067
                                  HHHHHHHT.TEEEECSEEEEEEEEETTSEEEE CS
                     Pyr_redox 46 lqeklekn.gievllntkveeiegsedgvesv 76
                                  l +++e+n +++vl+++ +e+++  +dg+e v
  gi|70606167|ref|YP_255037.1| 63 LVKSVEENgNVRVLTESIIENMKNVSDGFE-V 93
                                  6788999999*************9999843.3 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   9.7e-07   0.00096       1      31 [.       6      35 ..       6      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.7e-07
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                  +++GaGPaGl+aa el ++g+ d++ +E+++
  gi|70606167|ref|YP_255037.1|  6 LVVGAGPAGLSAAKELSRMGV-DLILVERES 35
                                  69*******************.799999974 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   5.9e-06    0.0058       2      28 ..      13      39 ..      12      41 .. 0.97
   2 ?   -2.8   0.0       2.8   2.8e+03     210     262 ..      61     116 ..      53     126 .. 0.71
   3 ?    3.0   0.0     0.051        51     410     448 ..     305     338 ..     297     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                  HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                  aGL+aA++L++ G+d++++E ++ +GG
  gi|70606167|ref|YP_255037.1| 13 AGLSAAKELSRMGVDLILVERESYLGG 39
                                  9*************************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                   HHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEE....EESEEEE-S-H CS
                 Amino_oxidase 210 sqlpealaeelrgldirlntrVkeikregdgvtvtledgevv....eaDaVvvTvpl 262
                                   + l+++++e  +++++++++   ++k  +dg  v ++d + +    ++ a++ ++ +
  gi|70606167|ref|YP_255037.1|  61 DPLVKSVEE-NGNVRVLTESIIENMKNVSDGFEVGIKDKKGNlkteKVNAIIAASGF 116
                                   567777777.99999999999999999555544444444444447788887777766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.051
                                   HHHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHH CS
                 Amino_oxidase 410 ydplakpegdprlffAGehtsreypgtvegAilSGlraA 448
                                   + p++++  ++++f+AG+ t    p ++ + i  G  aA
  gi|70606167|ref|YP_255037.1| 305 RLPVQST--RKGVFLAGAITG---PKGISDSITEGYAAA 338
                                   3445555..**********99...999999999999998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.4e-07   0.00063       2      36 ..       5      40 ..       4      44 .. 0.93
   2 ?   -0.4   0.0      0.68   6.8e+02     148     201 ..      59     115 ..      41     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.4e-07
                                  EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                  v+++G+G +Gls+A eL+r g   +l+e+++ +g g+
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKELSRMGvdLILVERESYLG-GT 40
                                  99***************999**********9999.87 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.68
                                   HHHHHHHHHHHTT.-EEEESECEEEEEE.EETCEEEEEEECT.EEE.EEEEEEEE--G CS
                           DAO 148 ltaalaraaealG.veilegtevtglee.edgkvwgverttp.gen.daadavVnaaG 201
                                   ++  l + +e++G v++l+++ +++ ++  dg  +g+ ++++ + + ++++a++ a G
  gi|70606167|ref|YP_255037.1|  59 VLDPLVKSVEENGnVRVLTESIIENMKNvSDGFEVGI-KDKKgNLKtEKVNAIIAASG 115
                                   5556788888998899999988888866344555666.44442333447789999988 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00014      0.14       2      39 ..       7      39 ..       6      48 .. 0.85
   2 ?    4.0   0.0     0.046        46     101     154 ..      57     115 ..      56     117 .. 0.74
   3 ?   -0.4   0.0         1     1e+03     135     155 ..     255     275 ..     220     276 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                 NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                  +vGaGp+Gl+++++L +       +++ l++++++ g g
  gi|70606167|ref|YP_255037.1|  7 VVGAGPAGLSAAKELSRM-----GVDLILVERESYlG-G 39
                                  8**************999.....59999999977734.4 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.046
                 NAD_binding_9 101 rdlfeellarlpegvtvevhraevv.dleeradgqavlladg....aslaadaVvLAlG 154
                                   +++++ l+++++e+ +v+v++++++ ++++  dg++v  +d+    ++ +++a++ A G
  gi|70606167|ref|YP_255037.1|  57 SEVLDPLVKSVEENGNVRVLTESIIeNMKNVSDGFEVGIKDKkgnlKTEKVNAIIAASG 115
                                   578999*************98877637999****9877655422333557777777766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1
                 NAD_binding_9 135 avlladgaslaadaVvLAlGh 155
                                   ++ l++   + +d V+LA G+
  gi|70606167|ref|YP_255037.1| 255 TMNLNRALVVPYDMVILANGM 275
                                   344555667899******996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.9e-06    0.0039       2      32 ..       5      33 ..       4      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvliea 32
                                  v+v+GaGpAgls A++l  +++g+ ++l+e 
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKEL--SRMGVDLILVER 33
                                  89***************..*********986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05     0.056      30      59 ..       4      33 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                   vlv+G+G aGl+A++  +++g +  +++ 
  gi|70606167|ref|YP_255037.1|  4 SVLVVGAGPAGLSAAKELSRMGVDLILVER 33
                                  69********************98877665 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001       0.1      18      45 ..       2      29 ..       1      32 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                  TSEEEEE--SHHHHHHHHHHHHHTTTEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 18 dskvllvGaGglGsellknLalsGvgkl 45
                                  +++vl+vGaG  G  ++k+L ++Gv  +
  gi|70606167|ref|YP_255037.1|  2 NKSVLVVGAGPAGLSAAKELSRMGVDLI 29
                                  578*********************9755 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.24   2.4e+02       5      33 ..       5      31 ..       2      38 .. 0.59
   2 ?    8.5   0.0     0.001      0.99     287     342 .]      65     118 ..      61     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                   K_oxygenase  5 ligiGiGpsnLsLailleevkkelkalfl 33
                                  +  +G+Gp+ Ls a  l+ +   ++ + +
  gi|70606167|ref|YP_255037.1|  5 VLVVGAGPAGLSAAKELSRMG--VDLILV 31
                                  445677777777666666555..555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                   K_oxygenase 287 qkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYrr 342
                                   ++v+++ ++r+l+++ +e++++ ++ ++e+ +++ ++g+ +t++v+a++ A G+++
  gi|70606167|ref|YP_255037.1|  65 KSVEENGNVRVLTESIIENMKNVSD-GFEVGIKD-KKGNLKTEKVNAIIAASGFEH 118
                                   56778889***************97.******99.889999************985 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00023      0.23       7      40 ..       2      35 ..       1     122 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                 NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                  +k+vlvvG+G+ +++ ++ l + g ++++v  e+
  gi|70606167|ref|YP_255037.1|  2 NKSVLVVGAGPAGLSAAKELSRMGVDLILVERES 35
                                  799**************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2361.08
//
Query:       gi|70606168|ref|YP_255038.1|  [L=438]
Description: hypothetical protein Saci_0329 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-08   34.5   0.0      9e-07   29.0   0.0    2.9  2  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.012   2.2e+02       4      54 ..      92     143 ..      90     169 .. 0.75
   2 !   29.0   0.0     5e-11     9e-07       2      85 .]     235     333 ..     234     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.012
                           CCG   4 fdgChllraaypevrkalkkllealgveleel.ekesCCGagggrsgkee.la 54 
                                   + +C  + ++ p ++ ++  ++++l +++ +   + sC G+    sg  + +a
  gi|70606168|ref|YP_255038.1|  92 HKSC-GQCGHIPGYPTSVFWIMNKLEIDYLDEpHQTSCTGWNYHASGASNpVA 143
                                   6777.666778888888889999999999999899999998887777766544 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 5e-11
                           CCG   2 ayfdgChllraa...........ypevrkalkkllealgveleel.ekesCCGagggrsgkee...laealakrnvetaee 67 
                                   a++++Ch+++             +   + a    ++ lg++l+++  +  CCG+g ++  +e+   +++al k+ + ++ee
  gi|70606168|ref|YP_255038.1| 235 AVHTPCHIYKLVpedtiydpevyQGRRPAAPSGTVKNLGAKLVDYsTWWDCCGFGFRHILTEReftRSFALFKKVIPAVEE 315
                                   7899999888777788888888656666677778899*********************99999888889************ PP

                           CCG  68 tgadaivtacpgCllqlk 85 
                                     ad+ vt + gC ++l+
  gi|70606168|ref|YP_255038.1| 316 GHADVFVTSDTGCVTTLD 333
                                   *************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2686.80
//
Query:       gi|70606169|ref|YP_255039.1|  [L=77]
Description: hypothetical protein Saci_0330 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-13   48.1   0.0    8.5e-13   47.9   0.0    1.0  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   4.7e-17   8.5e-13       1      70 []       8      77 .]       8      77 .] 0.97

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.7e-17
                                  EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  +elDl+  +C +P+ +l   +++l++ge ++v++ d+a+++di  +ak++g ++v+ e+e+ ++ ++i+k
  gi|70606169|ref|YP_255039.1|  8 KELDLTSSSCAGPIGELSGVIDELQDGEAVKVILGDEATKKDITLWAKRRGVKIVKEEQEGSKHILFITK 77
                                  69******************************************************99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 541.15
//
Query:       gi|70606170|ref|YP_255040.1|  [L=385]
Description: pyridine nucleotide-disulfide oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-12   47.5   0.0    1.8e-11   43.9   0.0    2.0  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   9.8e-16   1.8e-11       2     278 ..       4     295 ..       3     317 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 9.8e-16
                                   SEEEE--SHHHHHHHHHHHH........HTS-EEEEETTHCHHHC.SHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCC CS
                                   xxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq........agakvtlvelegtclng.gcllskallgvaedaeiasevvkklnqgielllge 73 
                                   +++v Gg+++G+  a +laq         +++++++++++ + +  g ll   + g + ++e ++++ + l + i++++ge
  gi|70606170|ref|YP_255040.1|   4 RIIVAGGNIGGTIIANRLAQkldhelhkGEVEIVVLNKNDDHIYYpGQLL--LAYGLETPPELMKKESELLDHRIKFIHGE 82 
                                   899*******************9999433666666675444444403333..45555555555556556677789999997 PP

                                   T..CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SH CS
                                   x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  74 e..vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGy 152
                                   +  ++k+dp+++ v+       d+ +  yd+lv+ tG +     ipG   + + +  ++++a +++++l++       gG 
  gi|70606170|ref|YP_255040.1|  83 KgtITKFDPANHSVVT-----ADGVSHSYDYLVITTGVEYSWDEIPGYRAGSVNF-YEYEDALKMREALNN-----FQGGT 152
                                   766999*****99999.....567789**********8887779****6666666.788899988888887.....44699 PP

                                   HHHHHHHHHHHHT-....................EEEEEESSSSSSTTS-.HHHHHHHHHHHHHTTEEEEESCEEEEEEET CS
                                   xxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 153 iGvElAaalaklgk....................evtlveardrllrald.kelsaaleealekeGvevklgtsvkeidgn 212
                                   i v +A   +++ +                    ++ +++  +     ++ +   +++ + +e++G+ev+   +v+++++ 
  gi|70606170|ref|YP_255040.1| 153 IVVNTARLPHRCPVaplentlvlddylrkrgirdKTKIIYTYPVQG-VFGrPITNKFMLKLFEERGIEVHSPFTVTNVNPT 232
                                   9999999987776667777888888888777787666777766654.566245568899999999**************** PP

                                   TEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--TTS.BES.STTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxx RF
                   Pyr_redox_2 213 geklevvledgeeidadlvvvavGvrpstelle..eklglelderggivvdefl.rtn.vpgiyaiGDva 278
                                   ++    + ++g ++++dl++      p+    +   ++gl  d+r+++ +d+f  r + + ++y+ GD +
  gi|70606170|ref|YP_255040.1| 233 EK--IIESQEGGKLKYDLLIAIP---PNMGA-KvvGDSGLG-DRRRWLPTDKFTlRMKdHSNVYVMGDAT 295
                                   98..68999999*****987543...44433.336999997.7*********98788779********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2587.69
//
Query:       gi|70606171|ref|YP_255041.1|  [L=126]
Description: hypothetical protein Saci_0332 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.9   0.0    2.8e-10   40.6   0.0    1.1  1  DrsE      DsrE/DsrF-like family
    6.8e-07   29.3   0.6    2.3e-06   27.6   0.6    1.7  2  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   3.1e-14   2.8e-10       1     104 [.       1     113 [.       1     123 [. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.1e-14
                                   -EEEEEE-S-TTTBSHHHHHHHHHHHH..HTTT-EEEEEE-GGGGGGGBS..........---TGGGTS---GGGGGGCGG CS
                          DrsE   1 kkvfilvtggpygseaarealelalaa..aalghevsvffygdGvllllk..........gqtanpadeknlaellkalke 69 
                                   +k+ i+v     ++e++r+ + + +++  +++g ev vf+++d v++++k           +t  ++++++++ l+k++k+
  gi|70606171|ref|YP_255041.1|   1 MKLGIIVG----TNERSRLTYAAMNSVisSSMGDEVFVFLTMDSVRAFTKnpevkdsdvsSKTMVEKKDEDFTGLFKKAKK 77 
                                   89999999....9********999999556666***************************888999999************ PP

                                   GT.-EEEEEHHHHHHTT--GGG..E-T--EEEE-HHHH CS
                          DrsE  70 yg.vklyvCgqaakargldede..dlgvgvevsglgel 104
                                    g vk+y+C  a k +++++++  d  +  e++g++++
  gi|70606171|ref|YP_255041.1|  78 SGkVKIYACSYASKLFNYSKADynD--LVDEIAGITTF 113
                                   999****************887743..45788888877 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.042   3.7e+02      27      40 ..      25      38 ..       2      51 .. 0.68
   2 !   27.6   0.6   2.6e-10   2.3e-06      72     149 ..      42     121 ..      19     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.042
                                  HHHTT-EEEEEE-G CS
                        DrsE_2 27 AaalglevtiFftF 40
                                    ++g ev +F t 
  gi|70606171|ref|YP_255041.1| 25 SSSMGDEVFVFLTM 38
                                  56899999999995 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.6e-10
                                   --SSS-GGGHHHHHHHHHHHHCT---HHHHHHHHHHTT.-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-S CS
                        DrsE_2  72 klskmnmagigtkmmkkvmkekgvasleeLleaakeag.vklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeead 149
                                        n +   + +  k+m ek+ +  + L ++ak++g vk++aC  +  l++++k +  d v eiag +t++ ++e ++
  gi|70606171|ref|YP_255041.1|  42 RAFTKNPEVKDSDVSSKTMVEKKDEDFTGLFKKAKKSGkVKIYACSYASKLFNYSKADYNDLVdEIAGITTFMMDVEGGQ 121
                                   445556677778889999999999***********9977**********************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 895.83
//
Query:       gi|70606172|ref|YP_255042.1|  [L=306]
Description: hypothetical protein Saci_0333 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-15   57.2   2.5      7e-14   51.4   0.1    3.5  4  DUF1641     Protein of unknown function (DUF1641)
    0.00067   20.0   4.5       0.45   10.9   0.2    3.5  3  Syntaxin_2  Syntaxin-like protein
  ------ inclusion threshold ------
      0.041   14.1   2.1       0.71   10.2   0.1    3.1  4  ARTD15_N    ARTD15 N-terminal domain
      0.096   11.5   0.0        1.6    7.5   0.0    2.1  2  UbiD        3-octaprenyl-4-hydroxybenzoate carboxy-lyase
       0.11   12.6   0.4          1    9.4   0.1    2.4  2  Birna_VP3   Birnavirus VP3 protein
       0.18   10.5   4.1        4.1    6.0   0.4    2.2  2  DUF773      CDK5 regulatory subunit-associated protein 3
       0.24   10.8   1.7        2.5    7.5   0.1    2.7  3  DUF4527     Protein of unknown function (DUF4527)
       0.49   10.6   9.7        1.4    9.2   0.5    4.1  5  DUF3886     Protein of unknown function (DUF3886)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.1   9.1e+03      10      18 ..      30      38 ..      29      38 .. 0.63
   2 ?   -3.0   0.0       3.1   6.9e+03      30      37 ..     153     160 ..     153     162 .. 0.50
   3 !    6.7   0.0    0.0029       6.6      14      27 ..     250     263 ..     247     264 .. 0.93
   4 !   51.4   0.1   3.1e-17     7e-14       2      39 .]     262     299 ..     261     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                       DUF1641 10 GlfgLlraL 18
                                  +l++Ll+ L
  gi|70606172|ref|YP_255042.1| 30 TLTELLKKL 38
                                  677777755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                       DUF1641  30 llalLKal 37 
                                   ll++L+++
  gi|70606172|ref|YP_255042.1| 153 LLEILREM 160
                                   45555544 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0029
                       DUF1641  14 LlraLrDPDVqrGL 27 
                                   ++ a++ +DV+++L
  gi|70606172|ref|YP_255042.1| 250 MMNAMKSEDVRKAL 263
                                   79***********8 PP

  == domain 4  score: 51.4 bits;  conditional E-value: 3.1e-17
                       DUF1641   2 gleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                   +le+p++v++ gL+++L+DP+Vq GLG+l++++Ka+Gk
  gi|70606172|ref|YP_255042.1| 262 ALESPPKVSISGLIKQLSDPEVQVGLGVLFSVIKAIGK 299
                                   79***********************************8 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.034        77      30      72 ..      12      61 ..       2      68 .. 0.70
   2 !   10.9   0.2    0.0002      0.45       4      46 ..      68     113 ..      65     124 .. 0.89
   3 ?    5.5   0.0      0.01        23      29      86 ..     158     222 ..     126     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                    Syntaxin_2 30 elreklhelieeinelikktnellkklsqldnsssds.......qqklqk 72
                                  +l++k  +  +e+ el  + +ellkkl++l++s+  +         k++k
  gi|70606172|ref|YP_255042.1| 12 KLDQKRIDALSELVELTPTLTELLKKLDELKESGTLDalinyayIGKTMK 61
                                  66677777778888888899999999999999875445555555555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                    Syntaxin_2   4 nlqkinsnvstleklvkqLgtk...kdteelreklhelieeineli 46 
                                    lq++++ vs+l +l+k L+ +   ++t++l ++++ l + +++l 
  gi|70606172|ref|YP_255042.1|  68 ALQNLSNTVSSLLELTKVLSRPdtfHNTMRLMNNIDALADVTSKLR 113
                                   69*******************966677********99999998875 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.01
                    Syntaxin_2  29 eelreklhelieeinelikktnellkklsqldnsssds.......qqklqkekLkkdfkealqeF 86 
                                   +e++++   + ++i + +k++  l+ +l++l+ns+  +       + k++k+ L++d  + + ++
  gi|70606172|ref|YP_255042.1| 158 REMDDNSVRSLKSILRRAKTIDGLMVRLEELENSGALDvllnlayAGKTMKDMLNDDALAEIGKY 222
                                   577899999999999******************99877899999999999999999988877776 PP

>> ARTD15_N  ARTD15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00032      0.71      37      70 ..      10      43 ..       8      52 .. 0.87
   2 ?   -0.8   0.0      0.83   1.9e+03      46      67 ..      67      88 ..      54     102 .. 0.56
   3 ?    1.9   0.1      0.12   2.6e+02      34      60 ..      89     117 ..      77     172 .. 0.85
   4 ?   -3.1   0.0       4.3   9.6e+03      43      48 ..     176     181 ..     155     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                      ARTD15_N 37 fisesekdidaLlsvvenlpslkellkslqelde 70
                                  f++ ++k idaL++ ve  p l+ellk+l+el+e
  gi|70606172|ref|YP_255042.1| 10 FSKLDQKRIDALSELVELTPTLTELLKKLDELKE 43
                                  666789*******************998888775 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.83
                      ARTD15_N 46 daLlsvvenlpslkellkslqe 67
                                  daL++  +++ sl el k l++
  gi|70606172|ref|YP_255042.1| 67 DALQNLSNTVSSLLELTKVLSR 88
                                  4555555555555555333333 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                      ARTD15_N  34 Ppqfises..ekdidaLlsvvenlpslke 60 
                                   P +f ++     +idaL  v+++l  +ke
  gi|70606172|ref|YP_255042.1|  89 PDTFHNTMrlMNNIDALADVTSKLRTMKE 117
                                   66777766677899999999999999887 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 4.3
                      ARTD15_N  43 kdidaL 48 
                                   k id L
  gi|70606172|ref|YP_255042.1| 176 KTIDGL 181
                                   333333 PP

>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.011        24       6      97 ..      65     168 ..      60     188 .. 0.71
   2 ?    7.5   0.0   0.00072       1.6      23      87 ..     168     231 ..     152     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                   CTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBT............TB.TT-EEEE-TTS-HCHHHHHHTS-GHHH CS
                          UbiD   6 kagelvrikeevdpelEiaeiarrvleeggpallFenvk............gkgskfpvltnlfgtrervalalglsslee 74 
                                   +++ l+  +  v+  lE+++++ r    +    l +n++            ++++   vl+n   t + ++ +l+ ++l +
  gi|70606172|ref|YP_255042.1|  65 NDDALQNLSNTVSSLLELTKVLSRPDTFHNTMRLMNNIDaladvtsklrtmKEDGTLDVLMNTAYTIRTFRDMLNDEALAN 145
                                   567788888889999999999999855556666677766666666777785446899*****************9988899 PP

                                   HHHHHHHHHHS..----EE--GC CS
                          UbiD  75 ileklaellepkppippkvvese 97 
                                   i + +++lle   ++  + v+s 
  gi|70606172|ref|YP_255042.1| 146 ISRYTSNLLEILREMDDNSVRSL 168
                                   99888888885334555555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00072
                                   HHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS.. CS
                          UbiD  23 iaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkp 87 
                                   +  i+rr++  +g  +  e+ +++ ++  vl nl    + ++ +l+ ++l ei++ l++ le  p
  gi|70606172|ref|YP_255042.1| 168 LKSILRRAKTIDGLMVRLEELENS-GALDVLLNLAYAGKTMKDMLNDDALAEIGKYLSQFLEAYP 231
                                   567999999999*********744.79*******************999***********99644 PP

>> Birna_VP3  Birnavirus VP3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00047         1      23     104 ..      18     102 ..      13     128 .. 0.78
   2 ?    0.9   0.1      0.18   4.1e+02      44      66 ..     239     261 ..     112     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00047
                     Birna_VP3  23 velllsaaqtdPleeailsllswlegrglinalvkfaltderaqRlrn..kLrnleneGsk.sqrskvesrGpipeedeel 100
                                   +++l ++ +  P   ++l  l  l++ g ++al+++a  ++  + + n   L+nl n  s   + +kv sr  + ++   l
  gi|70606172|ref|YP_255042.1|  18 IDALSELVELTPTLTELLKKLDELKESGTLDALINYAYIGKTMKDMLNddALQNLSNTVSSlLELTKVLSRPDTFHNTMRL 98 
                                   68899999999******************************99999764479***99866515678999988777755555 PP

                     Birna_VP3 101 amri 104
                                     +i
  gi|70606172|ref|YP_255042.1|  99 MNNI 102
                                   5455 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                     Birna_VP3  44 swlegrglinalvkfaltderaq 66 
                                   s  +g+gl+  +++  ++++ ++
  gi|70606172|ref|YP_255042.1| 239 SVTDGNGLVSRMMNAMKSEDVRK 261
                                   34467777777777776666665 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0032       7.2     457     489 ..      11      43 ..       4      59 .. 0.89
   2 ?    6.0   0.4    0.0018       4.1     374     447 ..     114     190 ..      97     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0032
                        DUF773 457 kdleekreelqeelselepkleklvkktrelkk 489
                                   ++l++kr ++ +el el p+l++l+kk  elk+
  gi|70606172|ref|YP_255042.1|  11 SKLDQKRIDALSELVELTPTLTELLKKLDELKE 43 
                                   6899*************************9997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0018
                        DUF773 374 Elsnest.svlslq..qfqsapevlqsqtkeeiekmlsaveealslltnkklqqLiliktspryvdrlvasLeqklk 447
                                    ++++ t +vl  +  ++ ++ ++l+++  ++i  + s+  e+l ++ ++ ++ L  i+   + +d l+  Le+ ++
  gi|70606172|ref|YP_255042.1| 114 TMKEDGTlDVLMNTayTIRTFRDMLNDEALANISRYTSNLLEILREMDDNSVRSLKSILRRAKTIDGLMVRLEELEN 190
                                   55555554444333114566789999********************************************9998765 PP

>> DUF4527  Protein of unknown function (DUF4527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.14     3e+02      95     130 ..      36      75 ..      14      94 .. 0.73
   2 ?    0.3   0.1      0.17   3.8e+02      98     126 ..     112     145 ..     105     178 .. 0.68
   3 ?    7.5   0.1    0.0011       2.5      83     137 ..     171     232 ..     163     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                       DUF4527  95 thLLqelhrhglenllls.....etarsmvdDvAlAeYaat 130
                                    + L el+  g+ + l++     +t+++m++D Al + + t
  gi|70606172|ref|YP_255042.1|  36 KK-LDELKESGTLDALINyayigKTMKDMLNDDALQNLSNT 75 
                                   33.66777788777775433333788999999998877666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                       DUF4527  98 Lqelhrhglenlllse.....tarsmvdDvAlAe 126
                                   L+ ++  g+ + l+++     t r+m++D AlA+
  gi|70606172|ref|YP_255042.1| 112 LRTMKEDGTLDVLMNTaytirTFRDMLNDEALAN 145
                                   5566666666666553222226799******997 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0011
                       DUF4527  83 LvqkCreRnhlithLLqelhrhglenllls.....etarsmvdDvAlAe...YaatFlapgvp 137
                                   + ++ +  + l+ + L+el+  g+ + ll+     +t+++m++D AlAe   Y + Fl +  +
  gi|70606172|ref|YP_255042.1| 171 ILRRAKTIDGLMVR-LEELENSGALDVLLNlayagKTMKDMLNDDALAEigkYLSQFLEAYPR 232
                                   55555666677777.89*********999755555799**********866688888876555 PP

>> DUF3886  Protein of unknown function (DUF3886)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       3.4   7.7e+03      15      28 ..      33      42 ..      29      44 .. 0.48
   2 ?    9.2   0.5   0.00062       1.4       7      27 ..      59      79 ..      57      83 .. 0.89
   3 ?   -2.0   0.1       1.9   4.3e+03      14      25 ..     106     117 ..     103     118 .. 0.84
   4 ?    0.2   0.0      0.39   8.7e+02       7      20 ..     133     146 ..     130     155 .. 0.77
   5 ?    4.0   0.0     0.026        58       6      18 ..     205     217 ..     202     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                       DUF3886 15 dvlekLkakkkeLk 28
                                  ++l+kL +    Lk
  gi|70606172|ref|YP_255042.1| 33 ELLKKLDE----LK 42
                                  34444444....44 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00062
                       DUF3886  7 tLkDlLnedvlekLkakkkeL 27
                                  t+kD+Ln+d+l+ L ++ ++L
  gi|70606172|ref|YP_255042.1| 59 TMKDMLNDDALQNLSNTVSSL 79
                                  89************9998887 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                       DUF3886  14 edvlekLkakkk 25 
                                   +dv  kL+ +k+
  gi|70606172|ref|YP_255042.1| 106 ADVTSKLRTMKE 117
                                   59999**99987 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.39
                       DUF3886   7 tLkDlLnedvlekL 20 
                                   t  D+Ln+++l+  
  gi|70606172|ref|YP_255042.1| 133 TFRDMLNDEALANI 146
                                   678******99866 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.026
                       DUF3886   6 vtLkDlLnedvle 18 
                                    t+kD+Ln+d+l+
  gi|70606172|ref|YP_255042.1| 205 KTMKDMLNDDALA 217
                                   589*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2192.15
//
Query:       gi|70606173|ref|YP_255043.1|  [L=280]
Description: metabolism heterodisulfide reductase C [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-08   33.5  14.2    2.3e-06   27.9   7.9    2.2  2  Fer4_8    4Fe-4S dicluster domain
    9.8e-08   32.4   7.0    2.2e-07   31.3   7.0    1.6  1  Fer4_17   4Fe-4S dicluster domain
    1.3e-06   28.4   6.2    2.6e-06   27.4   6.2    1.5  1  Fer4_10   4Fe-4S dicluster domain
    2.1e-06   27.8   8.5    2.5e-05   24.3   9.6    2.0  2  Fer4_9    4Fe-4S dicluster domain
    2.4e-05   24.8   8.8    5.8e-05   23.6   9.0    1.6  1  Fer4_7    4Fe-4S dicluster domain
    0.00053   20.9   8.4     0.0018   19.1   8.4    2.0  1  Fer4_16   4Fe-4S double cluster binding domain
     0.0021   18.1  13.4      0.025   14.7   3.6    2.3  2  Fer4_2    4Fe-4S binding domain
     0.0026   18.1  10.7     0.0044   17.4   1.1    2.3  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.047   13.4   2.6      0.061   13.1   1.2    2.0  2  SHOCT     Short C-terminal domain
      0.056   13.2   6.4      0.077   12.8   0.3    2.3  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.14   12.3  10.4        1.6    8.9  10.5    2.1  2  Fer4_21   4Fe-4S dicluster domain
       0.17   12.0  12.9        1.1    9.5   2.1    2.3  2  Fer4_6    4Fe-4S binding domain
       0.37   10.7  16.9       0.17   11.8   2.8    2.3  2  Fer4      4Fe-4S binding domain
          2    8.7   5.5         14    5.9   0.5    2.4  2  Fer4_18   4Fe-4S dicluster domain
        5.3    7.9  12.2        3.7    8.5   1.8    2.4  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   5.8e-06     0.007      25      63 ..      37      78 ..      18      81 .. 0.72
   2 !   27.9   7.9   1.9e-09   2.3e-06       2      64 ..      63     125 ..      62     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                        Fer4_8 25 lldargeaaedvqeeqvlee....eealwsCttcgaCtevCpv 63
                                  +l +++e+++  + ++++++    +e+l  C++cg Ct+ Cp 
  gi|70606173|ref|YP_255043.1| 37 NL-KPDEREAAIRFWEAVKSdfrfNEYLRGCLNCGVCTSGCPA 78
                                  33.33333433666666555888899***************96 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 1.9e-09
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   l+ C +Cg C+s Cp+++  +  + +  +  + d +++  + +++ +w+C++c  C+ +Cp +
  gi|70606173|ref|YP_255043.1|  63 LRGCLNCGVCTSGCPAAKFYDFGPREMIQYMMRDSVDKIWEFTNKKVWACVQCYTCSMRCPFN 125
                                   578************8888774444443333442333333334899***************87 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   7.0   1.8e-10   2.2e-07       2      58 ..      66     124 ..      65     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.8e-10
                       Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaeke..ekaslCieCgeCerkCPq 58 
                                   C +Cg C+  Cp  + yd+ p+++++ ++  +++++ +   +k+  C++C  C+++CP 
  gi|70606173|ref|YP_255043.1|  66 CLNCGVCTSGCPAAKFYDFGPREMIQYMMRDSVDKIWEFtnKKVWACVQCYTCSMRCPF 124
                                   **********************999998888899975534489***************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   6.2   2.2e-09   2.6e-06       8      56 .]      65     123 ..      61     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.2e-09
                       Fer4_10   8 tCirCgkCvkaCPadl..........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    C++Cg C++ CPa            + +     +++ e  +kkv++C +c  C   CP
  gi|70606173|ref|YP_255043.1|  65 GCLNCGVCTSGCPAAKfydfgpremiQYMMRDSVDKIWEFTNKKVWACVQCYTCSMRCP 123
                                   6*************66*******99777777777888889999***************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.1   3.3e-05     0.039      33      48 ..      52      78 ..      31      81 .. 0.69
   2 !   24.3   9.6   2.1e-08   2.5e-05       2      48 ..      66     124 ..      65     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                        Fer4_9 33 e...........eaCigCgaCveaCpk 48
                                  +             C+ Cg C+  Cp 
  gi|70606173|ref|YP_255043.1| 52 AvksdfrfneylRGCLNCGVCTSGCPA 78
                                  345555555566679999999999996 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.1e-08
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase............eaCigCgaCveaCpk 48 
                                   C +Cg C++ Cpa  + +   ++++++ +++             +aC++C +C  +Cp 
  gi|70606173|ref|YP_255043.1|  66 CLNCGVCTSGCPAAKFYDFGPREMIQYMMRDSvdkiweftnkkvWACVQCYTCSMRCPF 124
                                   ***********888888777777777766666888888888888*************95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   9.0   4.8e-08   5.8e-05       2      51 ..      66     125 ..      65     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-08
                        Fer4_7   2 CigCgaCvaaCp.vkaieldeeenekgt......ekv...eidpekClgCgaCvavCPtg 51 
                                   C +Cg C++ Cp +k  ++ ++e  + +      + +   + + + C++C+ C  +CP++
  gi|70606173|ref|YP_255043.1|  66 CLNCGVCTSGCPaAKFYDFGPREMIQYMmrdsvdKIWeftNKKVWACVQCYTCSMRCPFN 125
                                   ************5566667666544433343333222333777889************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   8.4   1.5e-06    0.0018       2      67 .]      66     125 ..      65     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPan 67 
                                   C +Cg C++ CP++ +         +re i+y    +   ++ e+++kk +a+  C +C + CP+n
  gi|70606173|ref|YP_255043.1|  66 CLNCGVCTSGCPAAKFYDF-----GPREMIQY-MMRDSVDKIWEFTNKKVWACVQCYTCSMRCPFN 125
                                   99**********9987666.....67788888.45555666667777778***************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.6   2.1e-05     0.025      10      22 .]      66      78 ..      61      78 .. 0.93
   2 !    8.7   2.3    0.0017         2       9      21 ..     111     123 ..     107     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                        Fer4_2 10 CigCgaCvsaCPa 22
                                  C++Cg C+s CPa
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCPA 78
                                  ************8 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0017
                        Fer4_2   9 rCigCgaCvsaCP 21 
                                   +C++C +C   CP
  gi|70606173|ref|YP_255043.1| 111 ACVQCYTCSMRCP 123
                                   7*******999*9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.1   3.7e-06    0.0044       4      16 ..      66      78 ..      60      88 .. 0.91
   2 ?    5.2   2.8      0.03        36       4      17 .]     112     125 ..     106     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                        Fer4_4  4 CigCgsCvaaCPq 16
                                  C++Cg+C++ CP 
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCPA 78
                                  ************4 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.03
                        Fer4_4   4 CigCgsCvaaCPqg 17 
                                   C++C  C   CP++
  gi|70606173|ref|YP_255043.1| 112 CVQCYTCSMRCPFN 125
                                   *******9999975 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.16   1.9e+02      20      27 ..     249     256 ..     249     257 .. 0.92
   2 ?   13.1   1.2   5.1e-05     0.061       1      19 [.     254     272 ..     254     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                         SHOCT  20 FeakKakL 27 
                                   +e++K++L
  gi|70606173|ref|YP_255043.1| 249 YEERKQQL 256
                                   9******9 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.1e-05
                         SHOCT   1 daLekLkeLyarGeIteEE 19 
                                   ++Le+Lke  ++Ge++e+E
  gi|70606173|ref|YP_255043.1| 254 QQLEELKEKWEKGELNEDE 272
                                   69****************9 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.3     0.066        79      24      39 ..      66      79 ..      49     109 .. 0.83
   2 ?   12.8   0.3   6.5e-05     0.077      24      58 ..     112     144 ..     103     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.066
                                  ----TT-HHHHCSTT- CS
                       Fer4_20 24 ClqCkkapcvkgCPve 39
                                  Cl+C    c++gCP+ 
  gi|70606173|ref|YP_255043.1| 66 CLNC--GVCTSGCPAA 79
                                  ****..79******85 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.5e-05
                                   ----TT-HHHHCSTT---HHHHHHHHHTT-HHHHH CS
                       Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnleeaa 58 
                                   C+qC   +c+  CP +++i + i  ++e  ++ a+
  gi|70606173|ref|YP_255043.1| 112 CVQC--YTCSMRCPFNNEIAGLIMLLREYAVKFAL 144
                                   9***..78******************999988776 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.2    0.0064       7.6      41      52 ..      66      77 ..      45      83 .. 0.72
   2 ?    8.9  10.5    0.0013       1.6       8      57 ..      66     128 ..      59     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0064
                       Fer4_21 41 CvGCnlCssvCP 52
                                  C  C +C+s CP
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCP 77
                                  555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0013
                       Fer4_21   8 CigCgkCliaCedtshqaieidaktvl...............kvvedeCvGCnlCssvCPvedci 57 
                                   C++Cg C+  C+ +     ++ +++++               +     Cv C  Cs  CP ++ i
  gi|70606173|ref|YP_255043.1|  66 CLNCGVCTSGCPAAK--FYDFGPREMIqymmrdsvdkiweftNKKVWACVQCYTCSMRCPFNNEI 128
                                   ************654..3333333322222333334444332223458************98776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.4    0.0031       3.7       9      21 ..      66      78 ..      66      81 .. 0.94
   2 ?    9.5   2.1   0.00092       1.1       8      22 ..     111     125 ..     111     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                        Fer4_6  9 CigCgdCvrvCPe 21
                                  C+ Cg C++ CP+
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCPA 78
                                  9***********8 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00092
                        Fer4_6   8 kCigCgdCvrvCPeg 22 
                                   +C++C+ C + CP++
  gi|70606173|ref|YP_255043.1| 111 ACVQCYTCSMRCPFN 125
                                   6************85 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.4     0.029        34       8      20 ..      66      78 ..      65      79 .. 0.93
   2 ?   11.8   2.8   0.00014      0.17       8      21 ..     112     125 ..     111     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.029
                                  SSS-THHHHHSTT CS
                          Fer4  8 CigCGaCvevCPv 20
                                  C +CG C + CP 
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCPA 78
                                  99**********5 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00014
                                   SSS-THHHHHSTTT CS
                          Fer4   8 CigCGaCvevCPvg 21 
                                   C+ C +C + CP++
  gi|70606173|ref|YP_255043.1| 112 CVQCYTCSMRCPFN 125
                                   ************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4     0.032        38      54      73 ..      59      78 ..      42      80 .. 0.76
   2 ?    5.9   0.5     0.011        14      54      77 ..     105     128 ..      81     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.032
                       Fer4_18 54 kekgagdcidcescvkvcPt 73
                                   ++    c++c++c + cP 
  gi|70606173|ref|YP_255043.1| 59 FNEYLRGCLNCGVCTSGCPA 78
                                  55556679999999999985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                       Fer4_18  54 kekgagdcidcescvkvcPtgidi 77 
                                   ++k++  c++c +c   cP + +i
  gi|70606173|ref|YP_255043.1| 105 TNKKVWACVQCYTCSMRCPFNNEI 128
                                   5677788************88666 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.8    0.0031       3.7       2      19 ..      66      83 ..      65     102 .. 0.83
   2 ?    4.8   2.6     0.043        51      81      93 ..     111     123 ..      85     126 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                       Fer4_22  2 ClsCgaCtlvCptCsCfd 19
                                  Cl+Cg Ct  Cp+   +d
  gi|70606173|ref|YP_255043.1| 66 CLNCGVCTSGCPAAKFYD 83
                                  ************987665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.043
                       Fer4_22  81 gCvGCgRCieacp 93 
                                   +Cv C  C+++cp
  gi|70606173|ref|YP_255043.1| 111 ACVQCYTCSMRCP 123
                                   5666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1857.06
//
Query:       gi|70606174|ref|YP_255044.1|  [L=80]
Description: hypothetical protein Saci_0335 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-25   87.9   0.0    3.2e-25   87.7   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.028   14.3   0.0    1.6  1  DUF2249   Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   3.6e-29   3.2e-25       1      70 []       9      78 ..       9      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 3.6e-29
                                  EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
                          TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                                  ++lD+rG+ CP+P+l++ ka+++++ gevlevla+dpaa+ di+++a+++gh++++++++++  ri+i++
  gi|70606174|ref|YP_255044.1|  9 KTLDARGMYCPGPVLETAKAIKQIQVGEVLEVLATDPAAKPDIEAWARRTGHQILDIQQQGDATRILIKR 78
                                  69******************************************************************85 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-06     0.028       1      34 [.      10      43 ..      10      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-06
                       DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvnd 34
                                  tlD+R++  p +   + +a+++++ Ge+le+++ 
  gi|70606174|ref|YP_255044.1| 10 TLDARGMYCPGPVLETAKAIKQIQVGEVLEVLAT 43
                                  79****************************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 637.79
//
Query:       gi|70606175|ref|YP_255045.1|  [L=143]
Description: hypothetical protein Saci_0336 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   96.0   0.5    3.7e-26   91.8   0.5    1.9  1  DrsE_2    DsrE/DsrF/DrsH-like family
    5.2e-10   39.7   0.0    1.4e-09   38.3   0.0    1.6  1  DrsE      DsrE/DsrF-like family
  ------ inclusion threshold ------
       0.13   12.1   0.1       0.26   11.1   0.1    1.4  1  SinI      Anti-repressor SinI


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.5   6.3e-30   3.7e-26       2     149 ..       6     138 ..       5     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 6.3e-30
                                   T-EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--HHHHHHHHHS-SS--SSS-GGGHH CS
                        DrsE_2   2 kkklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkkslekmamkmvtrksklskmnmagig 82 
                                   kkkl+ii+++gt dk ++  il s+Aaa g+ev++FftFwGL+ + k++ ++++   ++k   +m               g
  gi|70606175|ref|YP_255045.1|   6 KKKLSIIVFSGTIDKLMPVGILSSAAAAGGYEVNLFFTFWGLQSITKRSIHSQQPPQIDKNYEQM---------------G 71 
                                   89*********************************************999999998888877765...............4 PP

                                   HHHHHHHHHHCT---HHHHHHHHHHT.T-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-S CS
                        DrsE_2  83 tkmmkkvmkekgvasleeLleaakea.gvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeead 149
                                   + m  + m+e + ++ ++L+++ake  +vk++aC  tm+ +g+k+e+l + v  ++gaat+l++ae + 
  gi|70606175|ref|YP_255045.1|  72 PIM-MQRMQEMKYPMWHQLVQQAKEVgEVKVYACSTTMEFFGVKREDLAEFVdDVVGAATFLDRAE-GG 138
                                   445.567899999***********9736***********************************885.44 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   2.3e-13   1.4e-09      13     102 ..      16     130 ..       7     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.3e-13
                                   TBSHHHHHHHHHHHHHTTT.-EEEEEE-GGGGGGGBS...---TGGGTS---...................GGGGGGCGGG CS
                          DrsE  13 gseaarealelalaaaalg.hevsvffygdGvllllk...gqtanpadeknl...................aellkalkey 70 
                                   g+ +   +  +  +aaa+g +ev++ff+  G + ++k   + +++p+ +kn+                   ++l++++ke 
  gi|70606175|ref|YP_255045.1|  16 GTIDKLMPVGILSSAAAAGgYEVNLFFTFWGLQSITKrsiHSQQPPQIDKNYeqmgpimmqrmqemkypmwHQLVQQAKEV 96 
                                   66666677777777777777********************5555666666666777777777777777777*********8 PP

                                   T.-EEEEEHHHHHHTT--GGGE-..T--EEEE-HH CS
                          DrsE  71 g.vklyvCgqaakargldededl..gvgvevsglg 102
                                   g vk+y+C ++++ +g++  edl  +v+ +v++++
  gi|70606175|ref|YP_255045.1|  97 GeVKVYACSTTMEFFGVK-REDLaeFVDDVVGAAT 130
                                   88****************.6677566666666554 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.3e-05      0.26       5      16 ..      86      97 ..      86      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                                  HHHHHHHHHHHT CS
                          SinI  5 WveLikEAkesG 16
                                  W++L+++Ake+G
  gi|70606175|ref|YP_255045.1| 86 WHQLVQQAKEVG 97
                                  **********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 919.51
//
Query:       gi|70606176|ref|YP_255046.1|  [L=133]
Description: hypothetical protein Saci_0337 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-21   75.3   0.0    5.6e-21   75.1   0.0    1.0  1  DrsE      DsrE/DsrF-like family
    1.9e-14   53.8   0.6    3.9e-06   26.8   0.2    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   6.3e-25   5.6e-21       1     117 []      15     133 .]      15     133 .] 0.97

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.3e-25
                                   -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS..---TGGGTS---GGGGGGCGGGT-EEEEEHH CS
                          DrsE   1 kkvfilvtggpygseaarealelalaaaalghevsvffygdGvllllk..gqtanpadeknlaellkalkeygvklyvCgq 79 
                                   kk++i+vt+gp + ++++++l +a + a++++e svff+ +G +ll k  ++++  +++++++  + ++ke+gvk+yvC+q
  gi|70606176|ref|YP_255046.1|  15 KKILIVVTHGPDDIDRTYAPLFMASISASMEYETSVFFMIKGPKLLDKkwQEEERRKGGNPFIRFFDMAKENGVKMYVCVQ 95 
                                   89************************************************999999************************* PP

                                   HHHHTT--GGGE-T-.-EEEE-HHHHHHHHHH-SEEEE- CS
                          DrsE  80 aakargldededlgv.gvevsglgelaelqnegdrvitf 117
                                   ++k +   +++d+ v gve++g ++l++l  ++dr + f
  gi|70606176|ref|YP_255046.1|  96 SLKDMCHMNESDI-VdGVEIVGGSTLIDLTMDADRSLFF 133
                                   ********99999.77******************98765 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   7.9e-10   7.1e-06       2      53 ..      14      67 ..      13      78 .. 0.86
   2 !   26.8   0.2   4.4e-10   3.9e-06     100     153 .]      78     132 ..      69     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.9e-10
                                  T-EEEEEE----H...HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG-- CS
                        DrsE_2  2 kkklaiifskgtld..kalaalilAsgAaalglevtiFftFwGLnilrkeekkk 53
                                  kkk+ i++++g +d  + +a+l +As  a++++e+++Ff   G ++l k+ +++
  gi|70606176|ref|YP_255046.1| 14 KKKILIVVTHGPDDidRTYAPLFMASISASMEYETSVFFMIKGPKLLDKKWQEE 67
                                  79999999999887669***********************99999998876554 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 4.4e-10
                                   HHHHHHHHTT-EEEEEHHHH.HHHT--GGGB-TT-EEE-HHHHHHHHHC-SEEEE CS
                        DrsE_2 100 eLleaakeagvklvaCqmtm.dlmglkkeelidgveiagaatylkeaeeadvnLf 153
                                    + ++ake+gvk++ C  ++ d+  +++ +++dgvei+g  t+++  ++ad  Lf
  gi|70606176|ref|YP_255046.1|  78 RFFDMAKENGVKMYVCVQSLkDMCHMNESDIVDGVEIVGGSTLIDLTMDADRSLF 132
                                   6789************99976999***************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 950.01
//
Query:       gi|70606177|ref|YP_255047.1|  [L=444]
Description: dihydrolipoamide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-44  151.0   2.0    5.4e-44  150.6   2.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.3e-20   71.0   3.7      2e-15   57.1   0.1    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.9e-17   62.9   0.0    5.3e-16   58.8   0.0    2.6  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.7e-16   60.4   0.4    4.5e-16   59.0   0.4    1.6  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-09   37.4   6.2    9.1e-05   21.7   0.2    3.5  4  GIDA            Glucose inhibited division protein A
    2.5e-09   37.0   0.3    6.2e-07   29.1   0.0    2.4  3  FAD_oxidored    FAD dependent oxidoreductase
    2.7e-09   37.1   8.5      0.011   15.4   0.0    3.2  3  DAO             FAD dependent oxidoreductase
    3.8e-09   35.7   4.0     0.0033   16.2   0.4    4.2  4  HI0933_like     HI0933-like protein
    7.2e-08   31.7   0.1      6e-05   22.1   0.1    2.2  2  Trp_halogenase  Tryptophan halogenase
    2.7e-07   30.1   1.1    0.00045   19.5   0.0    2.8  3  Thi4            Thi4 family
    3.1e-07   30.0   0.7    0.00012   21.4   0.2    2.2  2  FAD_binding_3   FAD binding domain
    7.5e-07   28.6   5.5    0.00014   21.1   1.6    2.9  3  FAD_binding_2   FAD binding domain
    1.7e-06   28.1   2.1     0.0021   18.3   0.3    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    7.3e-05   22.2   2.9      0.035   13.4   0.2    2.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00057   19.0   0.7      0.072   12.1   0.0    2.2  2  Lycopene_cycl   Lycopene cyclase protein
     0.0085   14.7   0.1      0.013   14.1   0.1    1.2  1  GDI             GDP dissociation inhibitor
  ------ inclusion threshold ------
      0.017   15.0   0.5        4.1    7.2   0.0    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.032   14.6   0.9        3.3    8.2   0.0    2.6  2  NAD_binding_7   Putative NAD(P)-binding
       0.17   12.1   3.6        1.6    9.0   0.0    3.0  3  TrkA_N          TrkA-N domain
       0.34   10.5   4.9         21    4.8   0.0    3.5  4  ApbA            Ketopantoate reductase PanE/ApbA
        2.3    8.2   3.5         48    3.9   0.1    3.7  4  NAD_binding_9   FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   2.0   6.3e-47   5.4e-44       1     291 [.       3     302 ..       3     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 6.3e-47
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias..................... 57 
                                   +dvvv+GgG AG+ a   la++g kv++ e    +g c+n gc++s  +  v  + +  +                     
  gi|70606177|ref|YP_255047.1|   3 YDVVVVGGGTAGYIAGSILARKGKKVLVTErerFGGVCVNYGCVPSIFFYDVTYFLNRGKeignylgieietkeskrfflr 83 
                                   69***************************99999***********9877666666665556669999*9999999999999 PP

                                   ..HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHH CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ..evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaeal 136
                                     e v+ l+   ++l ++ + + + g+ ++  +++++ ++++i+++++++A+G +p ++ i+G  en+      + ++ea+
  gi|70606177|ref|YP_255047.1|  84 rdELVSYLSDAGKRLIENAGGDTEIGETRILTNNRVKVNGKEIDFKRIIIASGTKPLKPEIQGI-ENA------ISEDEAV 157
                                   9866666666666666656777778888888889999***************************.777......78899** PP

                                   CCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle 217
                                   +l+  p ++v++GgG+ G+ElA+++++l+++vtl+ ++++l r++++++ ++l++ le +Gv++  +t+v++i ++     
  gi|70606177|ref|YP_255047.1| 158 RLNYIPSSVVIIGGGFAGIELAQYFSRLNSNVTLITRGKIL-RTFPEDAVNFLRQSLEFDGVKLIENTRVTNISKR----- 232
                                   ***********************************998777.8***************************999933..... PP

                                   EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAv 291
                                    v++++  ++ + vv+a+G++p+ +  + e++++ +  ++g+ ++e+lr   +++ya+GDv+  ++  ++a+ A+
  gi|70606177|ref|YP_255047.1| 233 IVETNKGNFEGEVVVYATGREPDLPK-GiENIKVIT-GKNGVITNERLRA-GENVYAVGDVV--DKANKTAHSAM 302
                                   56777777***************866.669999977.677777*****98.8**********..77777777776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.9     8e-05     0.068       2      31 ..       5      34 ..       4      37 .. 0.94
   2 !   57.1   0.1   2.4e-18     2e-15       1      68 [.     165     231 ..     165     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-05
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                  vvvvGgG+ g  ++++la+ gkkV v er+
  gi|70606177|ref|YP_255047.1|  5 VVVVGGGTAGYIAGSILARKGKKVLVTERE 34
                                  8***********************999986 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 2.4e-18
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeieg 68 
                                   +vv++GgG+ g+ElA+++++l+++Vt++ r+ k+lr ++e+a + l+++le  g++++ nt+v++i +
  gi|70606177|ref|YP_255047.1| 165 SVVIIGGGFAGIELAQYFSRLNSNVTLITRG-KILRTFPEDAVNFLRQSLEFDGVKLIENTRVTNISK 231
                                   69***************************99.5556*****************************985 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.63   5.4e+02      22      60 ..     100     138 ..      95     141 .. 0.89
   2 !   58.8   0.0   6.2e-19   5.3e-16       1     108 [.     325     424 ..     325     426 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.63
                                   HHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTT CS
                 Pyr_redox_dim  22 kaagieikvgkfpfkangralayaetkgfvKlvadaktg 60 
                                   ++ag++ ++g++++  n+r ++++++  f ++++   t+
  gi|70606177|ref|YP_255047.1| 100 ENAGGDTEIGETRILTNNRVKVNGKEIDFKRIIIASGTK 138
                                   678999*******************99999999998886 PP

  == domain 2  score: 58.8 bits;  conditional E-value: 6.2e-19
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   ip+v++tdp+++ +G   +        +k g fpf+a++ra+++++++g+vK+ +++k++ v G  ++G++a+eli+ l++
  gi|70606177|ref|YP_255047.1| 325 IPRVLYTDPQIGVIGDINDA-------VKFGYFPFNASTRAIISGNREGYVKIGINEKNEIVFG-EVIGEKAEELINILTL 397
                                   79*************65443.......46667*********************99998887777.89************** PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHC CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealke 108
                                   a++ ++tve+l    ++hP+lsea+ +
  gi|70606177|ref|YP_255047.1| 398 AVNSKMTVEQLSLIPFVHPSLSEAILN 424
                                   ***********************9965 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.4   5.3e-19   4.5e-16       1     281 [.       6     267 ..       6     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 5.3e-19
                   Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfi...spsftsekleipdlnaiseetspafslkeekl 78 
                                   +++G+G aG  a+  l ++g  ++l+ E+++ g    +y     ++    + f +++ ei++   i+ et++    k+  l
  gi|70606177|ref|YP_255047.1|   6 VVVGGGTAGYIAGSILARKGK-KVLVTERERFGGVCVNYGCVPSIFfydVTYFLNRGKEIGNYLGIEIETKE---SKRFFL 82 
                                   79******************9.7****************98877762322456688999***********97...4888** PP

                   Pyr_redox_3  79 srkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkef 159
                                   +r+e+++Yl+   k+   +   ++e+ +     ++ +v+ + +++  k++iiA G   kP k++i+G e +++   +   +
  gi|70606177|ref|YP_255047.1|  83 RRDELVSYLSDAGKRLIENAGGDTEIGETRI-LTNNRVKVNGKEIDFKRIIIASGT--KPLKPEIQGIE-NAISEDEAVRL 159
                                   ************9999889999999977544.46679999***************9..**********9.89999888888 PP

                   Pyr_redox_3 160 hkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeike 240
                                    +y    vv+iGg+  +++ A  + r +++Vt++trg+ +++           d  n l++ ++ + +k+++n++v++i++
  gi|70606177|ref|YP_255047.1| 160 -NYIPSSVVIIGGGFAGIELAQYFSRLNSNVTLITRGKILRTFP--------EDAVNFLRQSLEFDGVKLIENTRVTNISK 231
                                   .8999********************************9766664........455667766666567*************8 PP

                   Pyr_redox_3 241 keeeykvktedgkkvevkddvvlatGykpdlsf.lkkslfel 281
                                   +     v+t++g+ + + + vv+atG +pdl   +++ ++ +
  gi|70606177|ref|YP_255047.1| 232 R----IVETNKGN-F-EGEVVVYATGREPDLPKgIENIKVIT 267
                                   6....56677764.3.45899********9844376654444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.2   1.1e-07   9.1e-05       1      44 [.       4      49 ..       4      52 .. 0.91
   2 ?   -1.0   0.0      0.84   7.1e+02     132     150 ..     119     137 ..      96     156 .. 0.76
   3 !   15.9   0.2     6e-06    0.0051       2      30 ..     166     194 ..     165     239 .. 0.91
   4 ?    0.4   0.1      0.31   2.6e+02     116     176 ..     224     278 ..     206     324 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsi 44
                                  dv+V+GgG AG+ A   +ar+G kvl        + +++ +C psi
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGKKVLVTerERFGGVCVNYGCVPSI 49
                                  79***********************99975566778999*****98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                                   EETTS-EEEECEEEE--TT CS
                          GIDA 132 vtedgetikakavviatGt 150
                                   v+ +g++i  k ++ia+Gt
  gi|70606177|ref|YP_255047.1| 119 VKVNGKEIDFKRIIIASGT 137
                                   4567888888899999998 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 6e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                   v++iGgG AG+e A   +rl+ +v+Lit 
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNSNVTLITR 194
                                   9*************************963 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.31
                                   S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B-TH CS
                          GIDA 116 eeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlgeltsegl 176
                                    +v++++      k +v +++  ++ ++vv atG   +    i + ++ +G++g +t+e+l
  gi|70606177|ref|YP_255047.1| 224 TRVTNIS------KRIVETNKGNFEGEVVVYATGREPDLPKGIENIKVITGKNGVITNERL 278
                                   3455553......478888888999999999999722333334444445555555555555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   7.3e-10   6.2e-07       1      45 [.       4      47 ..       4      81 .. 0.84
   2 !    5.7   0.0    0.0092       7.9       2      33 ..     166     197 ..     165     198 .. 0.93
   3 ?   -3.0   0.0       4.1   3.5e+03      89     143 ..     205     250 ..     202     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.3e-10
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvat 45
                                  DvvVvGGg+aG++A    ar+G+kvl++e++++ GG   + +  +
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGKKVLVTERERF-GGVCVNYGCVP 47
                                  9***********************998887765.77766655544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0092
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                   vv++GGg aG+  A    r   +v L+ + + 
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNSNVTLITRGKI 197
                                   9**************************99876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.1
                  FAD_oxidored  89 akavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDAT 143
                                   a + l + l+ +gv+++ ntr++++ k+      v++    ++ +++++v++ AT
  gi|70606177|ref|YP_255047.1| 205 AVNFLRQSLEFDGVKLIENTRVTNISKR-----IVET----NKGNFEGEVVVYAT 250
                                   5666677777777777777777777664.....1222....24455555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   2.2   0.00019      0.17       1      33 [.       4      37 ..       4      44 .. 0.92
   2 !   12.7   0.1   8.2e-05      0.07       2      31 ..     166     197 ..     165     200 .. 0.90
   3 !   15.4   0.0   1.2e-05     0.011     145     203 ..     202     253 ..     199     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                  dvv++GGG +G  +   Lar+g  V++ e++ ++g
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGkkVLVTERE-RFG 37
                                  9********************99*******9.555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.2e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdi 31 
                                   vviiGGG +G+  A + +r +  Vtl+ +g+i
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNsnVTLITRGKI 197
                                   9****************998679****99965 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                           DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                   p+ ++++l++ +e  Gv+++e+t+vt++++       v  +t+ g+ ++ + vV a+G  
  gi|70606177|ref|YP_255047.1| 202 PEDAVNFLRQSLEFDGVKLIENTRVTNISK-----RIV--ETNkGN-FEGEVVVYATGRE 253
                                   78899***********************54.....345..555575.45589*****955 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   3.8e-06    0.0033       1      32 [.       3      34 ..       3      39 .. 0.93
   2 ?    3.5   0.0     0.028        24      89     165 ..      68     138 ..      62     142 .. 0.88
   3 !    8.9   0.0   0.00062      0.53       2      33 ..     165     196 ..     164     202 .. 0.91
   4 !    5.4   0.0    0.0072       6.1     110     163 ..     204     251 ..     198     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                  +dv+v+GgG AG  a   +a++gk+Vl+ e++
  gi|70606177|ref|YP_255047.1|  3 YDVVVVGGGTAGYIAGSILARKGKKVLVTERE 34
                                  59**************************9986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
                                   TT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like  89 lgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                   lg+e+++++s r+F ++    ++v+ l  + k+   +   +te+ + +  +++  rvk+ +++e+  +++++A+G +
  gi|70606177|ref|YP_255047.1|  68 LGIEIETKESKRFFLRR---DELVSYLSDAGKRLIENAGGDTEIGETRILTNN--RVKV-NGKEIDFKRIIIASGTK 138
                                   79999999999999999...899999999999999999999999999887777..8999.99************976 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00062
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                   +v++iGgG AG+  A   ++ +++V+l+ ++k
  gi|70606177|ref|YP_255047.1| 165 SVVIIGGGFAGIELAQYFSRLNSNVTLITRGK 196
                                   69**************************8875 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0072
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   d v++l + l+  gvkl  +t+v++++k       v+t +++++e + +v AtG
  gi|70606177|ref|YP_255047.1| 204 DAVNFLRQSLEFDGVKLIENTRVTNISK-----RIVET-NKGNFEGEVVVYATG 251
                                   57999*********************44.....47889.99***********99 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1     7e-08     6e-05       1      49 [.       4      49 ..       4      58 .. 0.93
   2 !    7.7   0.0    0.0017       1.4       2      38 ..     166     199 ..     165     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7e-08
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THH CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsi 49
                                  ++v+vGGGtaG++a ++la+ +k   +v++ e e +g v v  + +psi
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGK---KVLVTERERFGGVCVNYGCVPSI 49
                                  69********************4...6**************99999998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlveseeigt 38 
                                   +vi+GGG aG   A ++++      +vtl+   +i +
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLN---SNVTLITRGKILR 199
                                   9******************99...6899999888765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.3e-07   0.00045      16      55 ..       1      38 [.       1      85 [. 0.84
   2 !    8.5   0.0    0.0012       1.1      13      47 ..     159     192 ..     149     196 .. 0.84
   3 ?   -2.2   0.1       2.3   1.9e+03     160     178 ..     244     262 ..     213     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.3e-07
                                  TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                  +e Dvv+vG+G++G  a+ +la+k + kv++ er+  +GG
  gi|70606177|ref|YP_255047.1|  1 MEYDVVVVGGGTAGYIAGSILARK-GKKVLVTERER-FGG 38
                                  689*********************.*******9974.555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                                   HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEE CS
                          Thi4  13 lkyaesDvvivGaGssGLtaayylakkpdlkvail 47 
                                   l+y+ s vvi+G+G +G+  a+y+++  + +v+++
  gi|70606177|ref|YP_255047.1| 159 LNYIPSSVVIIGGGFAGIELAQYFSRL-NSNVTLI 192
                                   6899*******************9997.5566555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                                   EEEEE--GSSSTTTTHHHH CS
                          Thi4 160 kvvvdatGhdgeivavvvk 178
                                   +vvv atG + ++ + ++ 
  gi|70606177|ref|YP_255047.1| 244 EVVVYATGREPDLPKGIEN 262
                                   5666666666655544433 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.4e-07   0.00012       1      33 [.       2      34 ..       2      36 .. 0.94
   2 !    6.7   0.0    0.0043       3.7       3      32 ..     165     194 ..     164     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                                  EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                  e+dV++VG+G aG +++++L+++G +v++ e+ 
  gi|70606177|ref|YP_255047.1|  2 EYDVVVVGGGTAGYIAGSILARKGKKVLVTERE 34
                                  589**************************9996 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0043
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32 
                                   +V+I+G+G aG+ la+  s+   +v+l+++
  gi|70606177|ref|YP_255047.1| 165 SVVIIGGGFAGIELAQYFSRLNSNVTLITR 194
                                   69***************9999888888877 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.6   1.7e-07   0.00014       1      32 [.       4      35 ..       4      42 .. 0.92
   2 !    7.6   0.0     0.002       1.7       2      32 ..     166     196 ..     165     201 .. 0.90
   3 ?   -0.6   0.0      0.61   5.2e+02     374     402 ..     270     291 ..     262     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.7e-07
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                  Dv+V+G+G AG+ A+  +a++G+kv+v e e 
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGKKVLVTERER 35
                                  9**************************99876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                   v++iG+G+AG   A   ++ + +v++++ ++
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNSNVTLITRGK 196
                                   9*************99999999999999875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.61
                                   -EEEBETTSBESTTEEESSBTEEE-STCE CS
                 FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGeva 402
                                    Gv t+e++r+        ++ YA+G v 
  gi|70606177|ref|YP_255047.1| 270 NGVITNERLRA-------GENVYAVGDVV 291
                                   59999999999.......899*****987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   2.4e-06    0.0021       1      35 [.       7      40 ..       7      57 .. 0.91
   2 !    9.1   0.1    0.0017       1.5       1      26 [.     168     193 ..     168     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                  +vG+G +G  a + La++g++vl+ e+ +r+GG +
  gi|70606177|ref|YP_255047.1|  7 VVGGGTAGYIAGSILARKGKKVLVTER-ERFGGVC 40
                                  8************************98.5999977 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                                   EE--SHHHHHHHHHHHCCTEEEEEE- CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvllle 26 
                                   I+G+G++G  +A++ ++ + +v+l+ 
  gi|70606177|ref|YP_255047.1| 168 IIGGGFAGIELAQYFSRLNSNVTLIT 193
                                   9*********************9985 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.2    0.0013       1.1      30      59 ..       4      33 ..       2      36 .. 0.91
   2 !   13.4   0.2   4.1e-05     0.035      28      58 ..     163     193 ..     156     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                   v+v+GgG+aG  A ++ ++ g kV v++ 
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGKKVLVTER 33
                                  59***********************99876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.1e-05
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlD 58 
                                   p+ v++iGgG aG++ ++  ++l+ +Vt++ 
  gi|70606177|ref|YP_255047.1| 163 PSSVVIIGGGFAGIELAQYFSRLNSNVTLIT 193
                                   789************************9874 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.012       9.9       1      29 [.       4      30 ..       4      42 .. 0.79
   2 !   12.1   0.0   8.4e-05     0.072       2      34 ..     166     196 ..     165     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvl 29
                                  Dvvv+G+G Ag      l  a++g kv++
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSIL--ARKGKKVLV 30
                                  9**********8766666..666666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.4e-05
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasp 34 
                                   vv+iG+G Ag+ lA+    ++ + +v+li  ++
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYF--SRLNSNVTLITRGK 196
                                   8****************..*********96554 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.5e-05     0.013       4      40 ..       2      38 ..       1      47 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                  EECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSC CS
                           GDI  4 eydvivlGtGlkecilsGllsvdgkkvlhldrndyyG 40
                                  eydv+v+G G    i   +l+ +gkkvl+ +r+ + G
  gi|70606177|ref|YP_255047.1|  2 EYDVVVVGGGTAGYIAGSILARKGKKVLVTERERFGG 38
                                  8******************************998755 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.014        12       2      31 ..       5      34 ..       4      36 .. 0.93
   2 ?    7.2   0.0    0.0049       4.1       2      36 ..     166     207 ..     165     240 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                  v v+G Gt G    +++a++g +V +++++
  gi|70606177|ref|YP_255047.1|  5 VVVVGGGTAGYIAGSILARKGKKVLVTERE 34
                                  89***********************99875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0049
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S.......-HHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi.......seeale 36 
                                   v +iG G  G ++a+ f + + +V+l+ +        e+a++
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNSNVTLITRgkilrtfPEDAVN 207
                                   89************************9885554444444444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.065        56       9      38 ..       4      33 ..       2      50 .. 0.88
   2 ?    8.2   0.0    0.0039       3.3       9      46 ..     165     216 ..     159     275 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.065
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvap 38
                                   v+vvGgG+ ++   + l+++g+kv v   
  gi|70606177|ref|YP_255047.1|  4 DVVVVGGGTAGYIAGSILARKGKKVLVTER 33
                                  59**********999999999999998655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                 NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev..keele............e 46 
                                   +v+++GgG  + + ++ + + + +vt+++       + e            +
  gi|70606177|ref|YP_255047.1| 165 SVVIIGGGFAGIELAQYFSRLNSNVTLITRGKilRTFPEdavnflrqslefD 216
                                   79**************************998655333342333333333341 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.14   1.2e+02       1      29 [.       5      33 ..       5      36 .. 0.83
   2 ?    9.0   0.0    0.0018       1.6       1      29 [.     166     194 ..     166     255 .. 0.89
   3 ?   -2.7   0.0       7.8   6.7e+03      15      36 ..     276     296 ..     267     317 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEES CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidk 29
                                  ++++G G+ G+     L ++gk+v+v ++
  gi|70606177|ref|YP_255047.1|  5 VVVVGGGTAGYIAGSILARKGKKVLVTER 33
                                  79***************997766877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEES CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidk 29 
                                   ++iiG G  G +la+++s+ ++ +v++i +
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRlNS-NVTLITR 194
                                   79*****************766.6***986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.8
                                   HHHHHTTEEEEEEESSHHHHHH CS
                        TrkA_N  15 eeLseggkdvvvidkdeervee 36 
                                   e+L++g+ +v+++ +  +++++
  gi|70606177|ref|YP_255047.1| 276 ERLRAGE-NVYAVGDVVDKANK 296
                                   4455544.24444333333333 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.8      0.14   1.2e+02       1      31 [.       5      35 ..       5      41 .. 0.90
   2 ?    3.1   0.0      0.08        68       9      98 ..      64     157 ..      63     159 .. 0.76
   3 ?    4.8   0.0     0.024        21       1      37 [.     166     202 ..     166     239 .. 0.83
   4 ?   -2.9   0.0       5.6   4.8e+03      95     113 ..     262     280 ..     258     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  ++++G G  G + +  La++g +v +  r+r
  gi|70606177|ref|YP_255047.1|  5 VVVVGGGTAGYIAGSILARKGKKVLVTERER 35
                                  689********************99888875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.08
                                   HHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETT.CEEEEEECEEECCH...SCCCCS-ESEEEE-SSGGGHHHHH CS
                          ApbA   9 iGsllaakLakagadvtlilrsrrlealkknGlrltseg.geeilrppealsae...ekselepidlvivtvKayqteeal 85 
                                   iG +l+ ++  +  +  ++ r++ +  l+++G rl ++  g++ + ++  l++     + +  ++  +i++  + +++  +
  gi|70606177|ref|YP_255047.1|  64 IGNYLGIEIETKESKRFFLRRDELVSYLSDAGKRLIENAgGDTEIGETRILTNNrvkVNGKEIDFKRIIIASGTKPLKPEI 144
                                   899999999776666666666668888*******99998877777777777777654334455667799999999999999 PP

                                   HHHGGGECTCEEE CS
                          ApbA  86 eeikplldpntvv 98 
                                   + i++++ ++ +v
  gi|70606177|ref|YP_255047.1| 145 QGIENAISEDEAV 157
                                   9999888887655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.024
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHH CS
                          ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealk 37 
                                   ++i+G G  G  la + ++ + +vtli+r++ l ++ 
  gi|70606177|ref|YP_255047.1| 166 VVIIGGGFAGIELAQYFSRLNSNVTLITRGKILRTFP 202
                                   689**************************99555555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.6
                                   CEEEEEESSSSCHHHHHTT CS
                          ApbA  95 ntvvlllqNGlgheeelre 113
                                   n +v++  NG+ + e+lr+
  gi|70606177|ref|YP_255047.1| 262 NIKVITGKNGVITNERLRA 280
                                   5578888999999999886 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.45   3.8e+02       1      37 [.       6      37 ..       6      50 .. 0.73
   2 ?    0.5   0.0      0.61   5.2e+02      90     154 ..      81     136 ..      54     138 .. 0.61
   3 ?    3.9   0.1     0.057        48       1      19 [.     167     185 ..     167     199 .. 0.83
   4 ?   -0.5   0.0       1.3   1.1e+03     127     155 ..     224     252 ..     194     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.45
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                  ++vG+G +G  +   L+++       ++ + +++ +g
  gi|70606177|ref|YP_255047.1|  6 VVVGGGTAGYIAGSILARK-----GKKVLVTERERFG 37
                                  69*******7766666655.....4566777777666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.61
                 NAD_binding_9  90 fvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   f++R  +  Yl+d+ ++l++++  ++++    ++++      ++   ++ +g++++++++++A G
  gi|70606177|ref|YP_255047.1|  81 FLRRDELVSYLSDAGKRLIENAGGDTEIGE--TRIL-----TNN--RVKVNGKEIDFKRIIIASG 136
                                   566666666777777776666654432221..1211.....111..1234677777777777776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.057
                 NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                   +i+G+G++G+ +++ + + 
  gi|70606177|ref|YP_255047.1| 167 VIIGGGFAGIELAQYFSRL 185
                                   7*********999887776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.3
                 NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlGh 155
                                    + ++ + +++++++ +++ + Vv A+G 
  gi|70606177|ref|YP_255047.1| 224 TRVTNISKRIVETNKGNFEGEVVVYATGR 252
                                   33344445688888888999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3104.00
//
Query:       gi|70606178|ref|YP_255048.1|  [L=113]
Description: hypothetical protein Saci_0339 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 771.38
//
Query:       gi|70606179|ref|YP_255049.1|  [L=183]
Description: hypothetical protein Saci_0340 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-11   41.7   0.3    1.7e-10   40.8   0.1    1.6  2  Thioredoxin_3  Thioredoxin domain
     0.0012   19.2   0.1     0.0022   18.3   0.1    1.5  1  DUF836         Glutaredoxin-like domain (DUF836)
     0.0032   17.4   0.1      0.023   14.7   0.0    2.1  2  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.032   14.4   0.5      0.075   13.3   0.5    1.6  1  Glutaredoxin   Glutaredoxin
      0.037   14.5   0.8       0.25   11.9   0.0    2.2  2  Csd3_N         Csd3 N-terminal
      0.088   12.6   0.0       0.15   11.8   0.0    1.4  1  Thioredoxin_9  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   5.7e+03      16      30 ..      28      42 ..      22      65 .. 0.53
   2 !   40.8   0.1   5.8e-14   1.7e-10       2      72 ..     101     174 ..     100     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                                  HHHHHHHHCHCCTCE CS
                 Thioredoxin_3 16 lekavkeaaaekgik 30
                                  l + +k ++ +k+++
  gi|70606179|ref|YP_255049.1| 28 LINYLKDVVVTKQLE 42
                                  555555555555443 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 5.8e-14
                                   EEEE.ESSSSTTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHH CS
                 Thioredoxin_3   2 eikv.lgpgCakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeir 72 
                                   +ik  ++p C+kCp +++++ ++++ + ++++e+ +vt++e   eky+V svP++v +++ ++ G  ps+  ++
  gi|70606179|ref|YP_255049.1| 101 NIKLfVTPDCTKCPITAEFLYQLVQINpDVTLEIFDVTEYEYEkEKYRVLSVPKIVFNERTEIPGGFPSTIILK 174
                                   699989********999999999988868************999*********************999976655 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   7.5e-07    0.0022       2      59 ..     102     161 ..     101     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.5e-07
                                   EEEEE-TT-HHHHHHHHHHHH.HCCCTTEEEEEEETTT-CCCHCCCCT.TTTEEEECTTC CS
                        DUF836   2 ltLyskpgChlCeqakekLke.lkleegleleviDIakdeeleakYgl.eipvlalegvk 59 
                                   + L+++p C  C    e L + ++++ +++le  D+++ e+ ++kY +  +p++++++ +
  gi|70606179|ref|YP_255049.1| 102 IKLFVTPDCTKCPITAEFLYQlVQINPDVTLEIFDVTEYEYEKEKYRVlSVPKIVFNERT 161
                                   78*****************99999**********************96379***999844 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   5.5e+02      47     100 ..      14      73 ..       3      76 .. 0.56
   2 !   14.7   0.0   7.6e-06     0.023      25      83 ..     105     162 ..      87     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                   CTTTSEEEEEETTTSHHHHHHTT-S......SSSEEEEEETTEEEEEEESS-HHHHHHHH CS
                   Thioredoxin  47 lkdkvklakvdvdenedlakkyeve......giPtlklfkngkevkkyegarekeklaaf 100
                                   +k +++++ +d +e  +  k++ v+      + P +k+ k++++  +y g  ++++l  f
  gi|70606179|ref|YP_255049.1|  14 IKSNITIYYCDGEELINYLKDVVVTkqleecQKPLIKVQKDNRTYFTYYGIPTANELWPF 73 
                                   444666666665555444444433311111134778888888887777777777777655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.6e-06
                                   EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                   Thioredoxin  25 FyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                   F  p C++C   a +l +l +    +v+l   dv+e e   +ky v ++P++++ +  +
  gi|70606179|ref|YP_255049.1| 105 FVTPDCTKCPITAEFLYQLVQINP-DVTLEIFDVTEYEYEKEKYRVLSVPKIVFNERTE 162
                                   88999*****99999999999888.***************************9876655 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   2.5e-05     0.075       1      57 [.     102     159 ..     102     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                   EEEEESTSSHHHHHHHHHHHHTT.....GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                  Glutaredoxin   1 vvlftkptCpyCkkakrlLkelg.....vkfeeidvdkdeeireelkelsgvrtvPqvfidg 57 
                                   + lf++p C  C+ + ++L +l      v  e++dv++ e    + ke+  v +vP +++++
  gi|70606179|ref|YP_255049.1| 102 IKLFVTPDCTKCPITAEFLYQLVqinpdVTLEIFDVTEYE----YEKEKYRVLSVPKIVFNE 159
                                   689****************777665566889999999984....444445788999999987 PP

>> Csd3_N  Csd3 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.2   5.9e+02      33      60 ..       9      34 ..       3      66 .. 0.62
   2 ?   11.9   0.0   8.3e-05      0.25      17      77 ..      78     148 ..      63     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
                        Csd3_N 33 ellseiragvkyyelrddkgellqalip 60
                                  e++  i++++++y   +  +el++ l +
  gi|70606179|ref|YP_255049.1|  9 EYTRAIKSNITIYYCDG--EELINYLKD 34
                                  77888888888777655..444444433 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.3e-05
                        Csd3_N  17 nnipeklyynldeedkellseiragvkyyelrd.....dkgellqalipvneelQihifkd......kdkYr 77 
                                   ++i++++  +ld+++ el++ ir ++k++++ d        e l  l+++n ++ + if        k+kYr
  gi|70606179|ref|YP_255049.1|  78 ARISNDI-VQLDQKEIELAKGIRGNIKLFVTPDctkcpITAEFLYQLVQINPDVTLEIFDVteyeyeKEKYR 148
                                   4566665.58***********************98888677888889************6532333355555 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.1e-05      0.15      25     104 ..      84     158 ..      69     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                   HHHHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE CS
                 Thioredoxin_9  25 kvelseeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliil 104
                                    v+l+++++e +k i+ ++k++v  ++ C  + ++  +l ++ ++np+++++i+   e++   ++y+     ++P++++ 
  gi|70606179|ref|YP_255049.1|  84 IVQLDQKEIELAKGIRGNIKLFV--TPDCTKCPITAEFLYQLVQINPDVTLEIFDVTEYEYEKEKYRV---LSVPKIVFN 158
                                   47899999999999999999887..688************************************9966...888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1228.81
//
Query:       gi|70606180|ref|YP_255050.1|  [L=112]
Description: hypothetical protein Saci_0341 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00068   19.1   0.3    0.00082   18.8   0.3    1.3  1  PIN_5     PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   4.6e-08   0.00082     161     197 ..      72     108 ..      38     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-08
                         PIN_5 161 dvllLAkELdaavvssDeGikkwaeklGlrlveakkf 197
                                   + ++ A EL+a +v++   +kk a +lG+r+++++++
  gi|70606180|ref|YP_255050.1|  72 EAIMVAVELNALLVTDNDDVKKKALDLGVRVMSSQEL 108
                                   6899****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 871.70
//
Query:       gi|70606181|ref|YP_255051.1|  [L=277]
Description: hypothetical protein Saci_0342 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   25.3   0.0    2.2e-05   24.6   0.0    1.3  1  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.2e-09   2.2e-05       4      86 ..      25     118 ..      23     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-09
                                   SSEEEEETTT-EEEESSSEEEEEEEEET..........TTEEEEEEEECTCEEEEEEEESEESS-TTEEE-TTCEEEEEBS CS
                 Peptidase_M23   4 kGidiaapkgtpVlAaadGtVvfagkke..........gyGnvviidhgdgystlyahlskisvkegqkVkaGqvIGtvgs 74 
                                   k+id++ p   + +++ +G+V+  +k +           y+ v++i++++g +  ++h+     ++g++Vk+Gq++G+   
  gi|70606181|ref|YP_255051.1|  25 KAIDVSSPDFHTFYSPVEGEVIDTEKIRvgrpnrfaevDYDYVILIRQSNGNMVKILHVRP-FTEKGEYVKEGQPLGEFIL 104
                                   789999999999*********99999555678999*99*********************99.589*************986 PP

                                   TSSCS..SSEEEEE CS
                 Peptidase_M23  75 tgrst..gphLhfe 86 
                                   t  +    ph h+e
  gi|70606181|ref|YP_255051.1| 105 TPYTGgdFPHAHIE 118
                                   66433346777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 2267.73
//
Query:       gi|70606182|ref|YP_255052.1|  [L=351]
Description: radical SAM domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-12   48.3   0.4      5e-12   46.5   0.1    1.9  2  Radical_SAM  Radical SAM superfamily
     0.0055   17.0   0.0      0.011   15.9   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.083   12.8   0.1       0.12   12.3   0.1    1.2  1  TarH         Tar ligand binding domain homologue
       0.12   13.1   0.0       0.36   11.6   0.0    1.8  2  YukD         WXG100 protein secretion system (Wss), protein Y


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   1.1e-15     5e-12       5     161 ..      46     217 ..      44     221 .. 0.85
   2 ?   -1.3   0.0      0.54   2.4e+03      10      23 ..     304     318 ..     302     341 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.1e-15
                                   SEESS--TTTSCCTT........HHHHHHHHHHHHHHHHHHHHHHH..HHTTSEEEEEE.SSTGGGSTTHHHHHHHHHHTC CS
                                   xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   5 rgCnlrCsfCarpet........vrregrgrslsveeileevkelk..aekgvkevilg.ggepllypdfvellerlakla 74 
                                    gC  +Cs+C + +            ++ +  ++++e+++ +k      + g   + +g   +p + pd +e+++r+++  
  gi|70606182|ref|YP_255052.1|  46 DGCKANCSYCGQAREvaqgpeckTLIRVEWPLRPLDEVIKRIKDRQgdIRYGLQRICVGqLAHPRASPDAIEITRRIREA- 125
                                   69*********************889999*************888666788855555553899****************8. PP

                                   CCTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEE CS
                                   xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                   Radical_SAM  75 vpgiritvetngtlpd..eeklerllelgvdrvslgleaadde....kvlklmnrghtfeevlealeklreagikr.vvdr 148
                                     gi++ ++   t  +  ++++ +++++g + + + ++aa++e    +  kl++ +h+++++++a++ + e+ +k+   + 
  gi|70606182|ref|YP_255052.1| 126 --GIELQISELVTATYtyKRHMIEMKRAGANMIDVAIDAANKElfdqVRGKLVRSMHSWDRYIQAIDEAVEVFGKKnAGIH 204
                                   ..7776666555554466****************************98899999*****************9777695566 PP

                                   EEEBTTTSHHHHH CS
                                   xxxxxxxxxxxxx RF
                   Radical_SAM 149 ivglpGendeele 161
                                   ++++ Ge++++  
  gi|70606182|ref|YP_255052.1| 205 LIVGLGETERDAI 217
                                   6666679998865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.54
                                   --TTTSCCTT.HHHH CS
                                   xxxxxxxxxx.xxxx RF
                   Radical_SAM  10 rCsfCarpet.vrre 23 
                                   +C+ C+rp++ +r++
  gi|70606182|ref|YP_255052.1| 304 GCPGCNRPYSnERPG 318
                                   7999***99743333 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.6e-06     0.011      11     117 ..      44     162 ..      36     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-06
                       Fer4_12  11 fvsgCnlsCkgCfnketwsfk........sgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81 
                                   +  gC+ +C++C +                +++    +e++++i ++  + +     ++ G   +p   ++ +e+ ++++e
  gi|70606182|ref|YP_255052.1|  44 YPDGCKANCSYCGQAREVAQGpecktlirVEWPLRplDEVIKRIKDRQGDIRYGLQRICVGQLAHPRASPDAIEITRRIRE 124
                                   568*********987666444445555334444433455555555555444444556888********************* PP

                       Fer4_12  82 ekp..ekdiwlytgytleelskkekeellkeidvlvdG 117
                                   +++  + + +++  yt++ ++ + k+   ++idv++d 
  gi|70606182|ref|YP_255052.1| 125 AGIelQISELVTATYTYKRHMIEMKRAGANMIDVAIDA 162
                                   **94445556788999999999999999999**99996 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.7e-05      0.12      50     107 ..     130     188 ..     120     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSS.SHHHHHHHHHHHHHHHHHHHHHTS CS
                          TarH  50 qqaaLaearvsllqaRltLnragiaaladeaeda.kellaraeeslaqseeawkaYlal 107
                                   q+++L  a+ +  +  + + rag+ +++ + + a kel ++++  l +s  +w++Y ++
  gi|70606182|ref|YP_255052.1| 130 QISELVTATYTYKRHMIEMKRAGANMIDVAIDAAnKELFDQVRGKLVRSMHSWDRYIQA 188
                                   77888888899999999***********9999999*********************875 PP

>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         4   1.8e+04      12      19 ..     155     162 ..     151     167 .. 0.59
   2 ?   11.6   0.0     8e-05      0.36       9      31 ..     279     301 ..     274     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4
                                   EEEEEEET CS
                          YukD  12 rvDlaLPa 19 
                                    +D+a+ a
  gi|70606182|ref|YP_255052.1| 155 MIDVAIDA 162
                                   55666554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8e-05
                                   TTTEEEEEEETTSBTTHHHHHHH CS
                          YukD   9 gnrrvDlaLPadvpvaellpalv 31 
                                   +++ vD+++P d++v+el pa++
  gi|70606182|ref|YP_255052.1| 279 EGKLVDIEIPSDLTVEELAPAFM 301
                                   5789****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2342.24
//
Query:       gi|70606183|ref|YP_255053.1|  [L=325]
Description: radical SAM domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-12   46.3   0.1    1.7e-11   44.8   0.0    1.8  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.029   14.2   0.2        2.1    8.2   0.1    2.2  2  zf-ZPR1       ZPR1 zinc-finger domain
       0.13   12.5   0.0       0.25   11.6   0.0    1.4  1  Fer4_12       4Fe-4S single cluster domain
       0.22   11.3   0.0       0.32   10.7   0.0    1.3  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   3.7e-15   1.7e-11       2     152 ..      54     198 ..      53     213 .. 0.85
   2 ?    1.3   0.0     0.086   3.9e+02      78     105 ..     194     221 ..     190     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.7e-15
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgirit 81 
                                   v+++ C+++C++C r+     e      s e++ +e++++ ++ g k++il+gg  + + d   +    +  +  ++++i 
  gi|70606183|ref|YP_255053.1|  54 VTGKYCAFNCKHCGRRV---LETMIDGSSEEKLTRELERA-VKAGDKGIILSGG-STIRGDVPLWKYGHVISKyADKLTII 129
                                   56789***********9...9*******************.999*777777777.55544443333333333335778888 PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                     t  ++   +++ +l+e+gv +  l+  + +   +++ ++ + t++++l+++++l++agik v ++ivgl
  gi|70606183|ref|YP_255053.1| 130 AHTGVVRS-QDIAVKLKEAGVKVALLDMVSDNTT-IKEVLRQPFTVDDYLNSFKYLKQAGIKIVPHVIVGL 198
                                   88888887.************************9.*****9889************************998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.086
                                   EEEEEEECSSCHGHHHHHHHHHTT-SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpdeeklerllelgvdrv 105
                                   + + ++t g++ d e +++l+e ++d +
  gi|70606183|ref|YP_255053.1| 194 VIVGLSTKGIKGDLEAIRLLKEVEPDAI 221
                                   5678899999999999999999986654 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00046       2.1      29      53 ..      59      83 ..      56     106 .. 0.85
   2 ?    3.9   0.0      0.01        45      69     105 ..     133     169 ..     123     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00046
                       zf-ZPR1 29 msfeCehCgyknnevksageieekG 53
                                  ++f+C+hCg +  e+++ g+ eek 
  gi|70606183|ref|YP_255053.1| 59 CAFNCKHCGRRVLETMIDGSSEEKL 83
                                  68*************9999999864 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.01
                       zf-ZPR1  69 qvlkSetatveipeleleippgtlegrlttvEGlLeq 105
                                    v++S+  +v+++e ++++      ++ tt+  +L+q
  gi|70606183|ref|YP_255053.1| 133 GVVRSQDIAVKLKEAGVKVALLDMVSDNTTIKEVLRQ 169
                                   69*******************99************98 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.6e-05      0.25       9      62 ..      53     104 ..      46     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                       Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGE 62 
                                   s+  + C ++Ck C  + + +       +++l +e+ + + k  ++g++l+GG 
  gi|70606183|ref|YP_255053.1|  53 SVTGKYCAFNCKHCG-RRVLETMIDGSSEEKLTRELERAV-KAGDKGIILSGGS 104
                                   666778*********.555555556666778887776666.9999********5 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.1e-05      0.32      73     117 ..      58     101 ..      46     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.1e-05
                                   HHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEE CS
                  Amidohydro_2  73 vlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrln 117
                                   ++a  +k+++r+v    ++  ++e+ ++elerav ++g kG+ l+
  gi|70606183|ref|YP_255053.1|  58 YCAFNCKHCGRRVLETMIDGSSEEKLTRELERAV-KAGDKGIILS 101
                                   567779****************************.******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2509.18
//
Query:       gi|70606184|ref|YP_255054.1|  [L=344]
Description: protein ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-06   26.6   0.0    1.5e-05   24.9   0.0    1.9  2  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family
    3.9e-05   23.6   1.0    8.4e-05   22.5   0.1    2.0  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
  ------ inclusion threshold ------
        0.1   12.5   0.0        3.5    7.6   0.0    2.3  2  Picorna_P3A     Picornaviridae P3A protein


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.5e-09   1.5e-05      10     131 .]      51     161 ..      47     161 .. 0.82
   2 ?   -2.8   0.0      0.93   5.6e+03     103     114 ..     322     333 ..     297     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.5e-09
                                   HHHH..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT- CS
                 BPL_LplA_LipB  10 tllkeslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgieg 90 
                                   +++++++n++e+  ++ +v+rr+tgG  +  +p +  + + ++++   + +       ++l +  v+++l       g  g
  gi|70606184|ref|YP_255054.1|  51 QTVEQEVNLEEVRRKNWDVGRRPTGGGTIIMGPWQLGWEIYADKSLLGETP----DNAMRLGAEGVIRTL-------GKLG 120
                                   4567899****************************9999999998875544....445555555566666.......5557 PP

                                   TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  91 ipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                   i+++ + +nD+ ++grK++Gi+  s  +     ++i+++++
  gi|70606184|ref|YP_255054.1| 121 ISANFRPKNDVEIKGRKISGIGAFSEGRYMGVTGTILLDFD 161
                                   7777778******************9999999999999886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.93
                                   ETTEEEEEEEEE CS
                 BPL_LplA_LipB 103 vngrKlaGiavt 114
                                   +++ K+ Gi ++
  gi|70606184|ref|YP_255054.1| 322 YKNVKILGITQE 333
                                   378888888887 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.53   3.2e+03      18      50 ..     157     188 ..     152     223 .. 0.63
   2 !   22.5   0.1   1.4e-08   8.4e-05       8      84 ..     261     338 ..     259     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.53
                                   EEEEEEETTEEEEEEEEESBSSSSHCHHHHHHH CS
                Lip_prot_lig_C  18 evrldvekgiIkdikiyGDffgpkdieeleekL 50 
                                    + +dv+  +++ +k+++  +++k  ++++++L
  gi|70606184|ref|YP_255054.1| 157 LLDFDVD-AMVSVLKLTSEKLKDKLSKDFKDRL 188
                                   5555553.3455555555555555555555555 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.4e-08
                                   EEEEETTEEEEEEEEE.ETTEEEEEEEEESBS..SSSHCHHHHHHHTTSBSSHHHHHHHHHTSCHHHHCCTHHHHHHHHH CS
                Lip_prot_lig_C   8 kkkrfdwGtvevrldv.ekgiIkdikiyGDff..gpkdieeleekLigvkyekeaieealekidlseyfggieleellel 84 
                                   +++++++G v+v++++  +++I+++ i+GDff      i +le++L+  + e   i + ++++  +  + gi++e+l++l
  gi|70606184|ref|YP_255054.1| 261 LERKLPGGLVKVQIKLaGENLIQSVLITGDFFvePRTAIYDLEARLKWSRVED--IDNEIKEWYKNVKILGITQEDLINL 338
                                   57899***********7788************5446778********998874..555555555444489*******998 PP

>> Picorna_P3A  Picornaviridae P3A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00058       3.5      22      64 ..     162     204 ..     148     231 .. 0.83
   2 ?    2.5   0.0     0.022   1.3e+02      13      53 ..     285     324 ..     274     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00058
                   Picorna_P3A  22 iepkasvfkcaasrvvdklkeasrevlkwfddklksmlsfver 64 
                                   ++   sv+k  + ++ dkl +  ++ l w ++ l s +++v+ 
  gi|70606184|ref|YP_255054.1| 162 VDAMVSVLKLTSEKLKDKLSKDFKDRLTWINKELTSSIDMVDL 204
                                   67889*******************************9998875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.022
                   Picorna_P3A  13 alieqmeafiepkasvfkcaasrvvdklkeasrevlkwfdd 53 
                                    l    + f+ep++++++  a     ++ +  +e+  w+++
  gi|70606184|ref|YP_255054.1| 285 VL-ITGDFFVEPRTAIYDLEARLKWSRVEDIDNEIKEWYKN 324
                                   33.45678**********99998899999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2275.86
//
Query:       gi|70606185|ref|YP_255055.1|  [L=55]
Description: hypothetical protein Saci_0346 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-06   28.2   0.4    2.6e-06   27.4   0.4    1.4  1  YHS         YHS domain
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.017   15.5   0.1    1.2  1  ADAM17_MPD  Membrane-proximal domain, switch, for ADAM17
      0.017   14.6   0.1      0.021   14.4   0.1    1.1  1  FAP206      Domain of unknown function
       0.11   12.2   0.0       0.11   12.2   0.0    1.0  1  POR_N       Pyruvate flavodoxin/ferredoxin oxidoreductase, th


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.4   5.7e-10   2.6e-06       4      45 ..       6      47 ..       3      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.7e-10
                           YHS  4 PvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYa 45
                                  Pvc    + e +++  +++   YyF++e C+ +F++ePe+++
  gi|70606185|ref|YP_255055.1|  6 PVCNRLFEAECTPYRQSHQEILYYFDTEICMLAFLKEPERFV 47
                                  7888888888899999************************97 PP

>> ADAM17_MPD  Membrane-proximal domain, switch, for ADAM17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   3.7e-06     0.017      18      54 ..       4      39 ..       1      45 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-06
                    ADAM17_MPD 18 sCkvCCrrekngtCkpvedaeesflilrdgkpCtvGf 54
                                   C vC  r  ++ C+p++++++++l+  d + C+  f
  gi|70606185|ref|YP_255055.1|  4 VCPVCN-RLFEAECTPYRQSHQEILYYFDTEICMLAF 39
                                  688887.9999**********************9766 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.6e-06     0.021     227     257 ..      22      52 ..      20      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-06
                        FAP206 227 kykdkyyaFsseeaareFaadpdrfieavke 257
                                   ++++ +y F +e ++++F+++p+rf+++ ++
  gi|70606185|ref|YP_255055.1|  22 SHQEILYYFDTEICMLAFLKEPERFVYKCRK 52 
                                   6899**********************99876 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05      0.11      89     125 ..       3      39 ..       1      48 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                   EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE- CS
                         POR_N  89 vvivvvaRalpstglsirtdqsDlmaardtglivlas 125
                                   vv  v +R   ++ +++r++++++++  dt++++la 
  gi|70606185|ref|YP_255055.1|   3 VVCPVCNRLFEAECTPYRQSHQEILYYFDTEICMLAF 39 
                                   788999****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 372.58
//
Query:       gi|70606186|ref|YP_255056.1|  [L=116]
Description: hypothetical protein Saci_0347 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   14.9   0.8      0.014   14.8   0.8    1.1  1  AGOG      N-glycosylase/DNA lyase
      0.064   13.6   0.1       0.11   12.8   0.1    1.4  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
       0.18   11.8   1.1       0.24   11.4   0.3    1.7  2  SapB_1    Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8   2.3e-06     0.014      94     155 ..      37     101 ..       2     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHHHHHCCHHHTTTHHHHHHHH.HT.....HHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHH CS
                          AGOG  94 reakikRiekivefledleleelksyl.en.....leelleelakilgskkesKTvvFavKmlyYalr 155
                                   +    +R++++++ +e le+ +l++y  e+     +++++ el   l+s  e+  v F++ ++ Y  +
  gi|70606186|ref|YP_255056.1|  37 IY---QRLKQAKTKSEILEILQLNQYDmEKttmndMSRMITELISKLNSYDEDTAVKFTIEVFRYLQI 101
                                   33...45666555555555555554432223434699999999**********************876 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.9e-05      0.11      22      63 ..      37      78 ..      32      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                                  HHHH-SSSS-HHHHHHHHH.HHCT--HHHHHHHHHHHHHHHHC CS
                          PqqD 22 iWklldgersveeivaala.eeydvdeeeaeadvlafldqLre 63
                                  i ++l + ++ +ei ++l+ ++yd + ++  +d  +++++L +
  gi|70606186|ref|YP_255056.1| 37 IYQRLKQAKTKSEILEILQlNQYDME-KTTMNDMSRMITELIS 78
                                  88999999**********99*****9.7899*******99976 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   4.1e-05      0.24       9      30 ..      33      54 ..      31      55 .. 0.93
   2 ?   -3.4   0.0       1.8   1.1e+04      26      30 ..      76      80 ..      73      90 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
                                  HHHHHHHHH-SS--HHHHHHHH CS
                        SapB_1  9 vVkeveklLkdNkTeeeIieaL 30
                                  vV ++++ Lk+ kT++eI+e L
  gi|70606186|ref|YP_255056.1| 33 VVIKIYQRLKQAKTKSEILEIL 54
                                  899****************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                  HHHHH CS
                        SapB_1 26 IieaL 30
                                  +i+ L
  gi|70606186|ref|YP_255056.1| 76 LISKL 80
                                  33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 897.26
//
Query:       gi|70606187|ref|YP_255057.1|  [L=164]
Description: hypothetical protein Saci_0348 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00039   20.6   0.0    0.00051   20.2   0.0    1.2  1  HAD_2     Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.088   12.3   0.1       0.13   11.8   0.1    1.3  1  DUF553    Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.7e-08   0.00051      79     171 ..      38     123 ..      12     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.7e-08
                         HAD_2  79 kpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvG 159
                                   ++y++ + l e++   + kl++ +  ++ +++e l+++++    +  ++ ++++k KP+ e++e + + ++ ++ +v+++G
  gi|70606187|ref|YP_255057.1|  38 EVYEDWHTLYEQV---KDKLAVLSPYDSVTTDELLKRINV----SPLYVVSNTGKTKPSKEPFEILFKITEWDPLDVVMIG 111
                                   4555555555555...449********************7....5667888999*************************** PP

                         HAD_2 160 DsptDieaakka 171
                                    sp D+ +a+ +
  gi|70606187|ref|YP_255057.1| 112 SSPLDLLSARFF 123
                                   *********866 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.5e-05      0.13      57     103 ..      36      83 ..      12      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                        DUF553  57 dskilklietpkeilktkkgiCrDYaiLTa.alLlnlniskvylvsvt 103
                                    +++++  +t++e +k k ++ + Y   T   lL   n+s+ y+vs t
  gi|70606187|ref|YP_255057.1|  36 TYEVYEDWHTLYEQVKDKLAVLSPYDSVTTdELLKRINVSPLYVVSNT 83 
                                   445555566****************877661677789********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1033.30
//
Query:       gi|70606188|ref|YP_255058.1|  [L=146]
Description: glycine cleavage H-protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-28   99.3   0.3    1.5e-28   99.1   0.3    1.1  1  GCV_H          Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.028   14.3   0.1       0.09   12.6   0.0    1.9  2  Biotin_lipoyl  Biotin-requiring enzyme
      0.035   14.4   0.0       0.24   11.7   0.0    2.3  1  DPBB_1         Lytic transglycolase


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.3   2.6e-32   1.5e-28       4     110 ..      16     123 ..      12     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 2.6e-32
                                   -TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---.TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT-TT CS
                         GCV_H   4 tkehewvkveedgvatvGitdfaqeelgdvvfvelpe.vgtkvkkgeslaavEsvKaasevyapvsGevvevNekleeepe 83 
                                    ++h w+kvee++v++vG+td++q  +g++  v++p  vg++v++   l +vEs K+++++  +++Gevv++Ne + ++p 
  gi|70606188|ref|YP_255058.1|  16 PERHVWIKVEENKVVSVGMTDLGQYLAGKIFQVSVPRrVGERVNNRTILFSVESAKWIGKIRLQIEGEVVDINERVIKNPS 96 
                                   45677******************************9548****************************************** PP

                                   HHHH-TTTTT--EEEEES-GGGGGG.SE CS
                         GCV_H  84 liNkdpyeegWliklklsnleelee.Ll 110
                                   +iN+dpy  +W+ik+ +++++ ++    
  gi|70606188|ref|YP_255058.1|  97 IINEDPY-GSWIIKVSVTDVDLVKRaFK 123
                                   *******.79*********998877444 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05      0.09       3      57 ..      32      88 ..      30      94 .. 0.85
   2 ?   -1.6   0.0      0.42   2.5e+03       3      28 ..      92     119 ..      90     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                  EEESSSEEEEEE..ECSESS..STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEES CS
                 Biotin_lipoyl  3 iksPmiGesveeg.vvevlv..kvGdkVkagqvlaeveamKmemeieapkaGvvkeil 57
                                  + + ++G++ + g + +v v   vG+ V+   +l  ve+ K   +i  + +G v++i 
  gi|70606188|ref|YP_255058.1| 32 VGMTDLGQYLA-GkIFQVSVprRVGERVNNRTILFSVESAKWIGKIRLQIEGEVVDIN 88
                                  67888899998.556665554489******************************9985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                                   EEESSSEEEEEE...ECSESSSTTCEE- CS
                 Biotin_lipoyl   3 iksPmiGesveeg..vvevlvkvGdkVk 28 
                                   ik P+i +   +g  +++v v + d Vk
  gi|70606188|ref|YP_255058.1|  92 IKNPSIINEDPYGswIIKVSVTDVDLVK 119
                                   6777777777777777888887777765 PP

>> DPBB_1  Lytic transglycolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.24      35      65 ..      20      50 ..      12     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                                  -EEEETT--EEEEEEEE----STTECEEE-H CS
                        DPBB_1 35 tycrvlsgksvtVtitDrgpfppgrhiDLSk 65
                                  + ++v+++k v V  tD g + +g+++ +S 
  gi|70606188|ref|YP_255058.1| 20 VWIKVEENKVVSVGMTDLGQYLAGKIFQVSV 50
                                  45888669*************8888887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 994.65
//
Query:       gi|70606189|ref|YP_255059.1|  [L=149]
Description: glycine cleavage system protein H [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-42  143.3   1.2    3.7e-42  143.1   1.2    1.1  1  GCV_H          Glycine cleavage H-protein
    3.3e-05   23.6   1.7    9.6e-05   22.1   0.7    2.1  2  Biotin_lipoyl  Biotin-requiring enzyme
     0.0057   16.6   1.2     0.0089   16.0   0.2    1.8  2  RnfC_N         RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.015   14.6   0.4      0.067   12.4   0.0    2.2  3  HlyD_D23       Barrel-sandwich domain of CusB or HlyD membran
       0.17   11.8   3.4       0.33   10.9   3.4    1.4  1  Nup54_C        Nup54 C-terminal interacting domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.1   1.2     1e-45   3.7e-42       2     121 ..      15     136 ..      13     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 1e-45
                                   EE-TTSE..EEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT CS
                         GCV_H   2 yytkehe..wvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNeklee 80 
                                   yy++ ++  wvk e++++a vGitd+aq+++g++v ++++++g kv+ g ++a++Es+K+a++v+apvsGevv+ N+++e+
  gi|70606189|ref|YP_255059.1|  15 YYIDGKNtvWVKIEGSDIAVVGITDLAQTMAGKIVKIRIKKKGIKVERGRPVATLESGKWAGPVPAPVSGEVVDSNSEVEK 95 
                                   344433368************************************************************************ PP

                                   -TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHHH CS
                         GCV_H  81 epeliNkdpyeegWliklklsnleeleeLlsaeeyekllke 121
                                   +p ++N+dpy++gW++k+k+sn+ee+++Ll+ +++ ++lke
  gi|70606189|ref|YP_255059.1|  96 SPVILNRDPYGQGWIAKIKISNQEEVKQLLTGQQAIQKLKE 136
                                   *********************************99999887 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.7   2.7e-08   9.6e-05       6      54 ..      43      87 ..      34     101 .. 0.85
   2 ?   -0.3   0.0      0.27   9.7e+02      50      65 ..     107     122 ..     104     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-08
                                  SSSEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEE CS
                 Biotin_lipoyl  6 PmiGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvk 54
                                   m+G++v+      ++k+G kV+ g ++a++e+ K   +++ap++G v+
  gi|70606189|ref|YP_255059.1| 43 TMAGKIVK----IRIKKKGIKVERGRPVATLESGKWAGPVPAPVSGEVV 87
                                  46677776....467899****************************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.27
                                   SEEEEEESSTTTEEE- CS
                 Biotin_lipoyl  50 aGvvkeilvkeGdtve 65 
                                   +G +++i++++ ++v+
  gi|70606189|ref|YP_255059.1| 107 QGWIAKIKISNQEEVK 122
                                   6999999999988886 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   2.5e-06    0.0089      45      80 ..      53      89 ..      27     102 .. 0.83
   2 ?   -1.2   0.1      0.56     2e+03      15      38 ..     115     138 ..     109     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-06
                        RnfC_N 45 lvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80
                                  + k+g kV++G  +a+ e+  ++ pv a+vsG+V++ 
  gi|70606189|ref|YP_255059.1| 53 IKKKGIKVERGRPVATLESgKWAGPVPAPVSGEVVDS 89
                                  668999*********9986699************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.56
                        RnfC_N  15 lskekpieklplpkelvlplsqhi 38 
                                    s+++++++l   ++ +  l+  i
  gi|70606189|ref|YP_255059.1| 115 ISNQEEVKQLLTGQQAIQKLKEII 138
                                   577777777777777766666554 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.45   1.6e+03     137     150 ..      15      28 ..      10      36 .. 0.80
   2 ?   12.4   0.0   1.9e-05     0.067      21      57 ..      39      75 ..      31      80 .. 0.91
   3 ?   -1.4   0.0      0.32   1.1e+03      27      44 ..     107     123 ..     101     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.45
                                   XXXXXXXXXXXXXX CS
                      HlyD_D23 137 ftiadlstVWveae 150
                                   + i   +tVWv++e
  gi|70606189|ref|YP_255059.1|  15 YYIDGKNTVWVKIE 28 
                                   66788899**9876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.9e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      HlyD_D23 21 rvsarveGwveklyvnatgdkVkkGqpLaelyspelv 57
                                  +++++++G + k++++  g kV++G p+a+l+s +++
  gi|70606189|ref|YP_255059.1| 39 DLAQTMAGKIVKIRIKKKGIKVERGRPVATLESGKWA 75
                                  667899***************************9986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.32
                                   XXXXXXXXXXXXXXXXXX CS
                      HlyD_D23  27 eGwveklyvnatgdkVkk 44 
                                   +Gw+ k++++   ++Vk+
  gi|70606189|ref|YP_255059.1| 107 QGWIAKIKIS-NQEEVKQ 123
                                   6888888887.6666664 PP

>> Nup54_C  Nup54 C-terminal interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.4   9.1e-05      0.33       3      30 ..     113     139 ..     112     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.1e-05
                       Nup54_C   3 mdadlqeeIKQfLkqqQeGlkhLIeIIk 30 
                                   + ++ qee+KQ L+ qQ ++++L eII 
  gi|70606189|ref|YP_255059.1| 113 IKISNQEEVKQLLTGQQ-AIQKLKEIIT 139
                                   56778********9877.8999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1092.97
//
Query:       gi|70606190|ref|YP_255060.1|  [L=365]
Description: biotin/lipoate A/B protein ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-05   22.3   0.9    0.00021   21.2   0.3    1.9  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
  ------ inclusion threshold ------
      0.016   15.1   0.1      0.028   14.3   0.1    1.4  1  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       1.8   1.6e+04      44      52 ..     202     210 ..     199     213 .. 0.74
   2 !   21.2   0.3   2.3e-08   0.00021      18      83 ..     282     350 ..     280     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.8
                                   HHHHHHHTT CS
                Lip_prot_lig_C  44 eeleekLig 52 
                                   ee+e+kL++
  gi|70606190|ref|YP_255060.1| 202 EEIEKKLKD 210
                                   678888764 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.3e-08
                                   EEEEEEETTEEEEEEEEESBS...SSSHCHHHHHHHTTSBSSHHHHHHHHHTSC.H.HHHCCTHHHHHHHH CS
                Lip_prot_lig_C  18 evrldvekgiIkdikiyGDff...gpkdieeleekLigvkyekeaieealekid.l.seyfggieleelle 83 
                                    + + + + ++++i+i+GDff    ++ +e+lee L+gv+ +   i++++++i  + +  + g+++++l++
  gi|70606190|ref|YP_255060.1| 282 RITMRIVEKKVDEISISGDFFvmnPKNFLEKLEESLRGVEVNN--INSVVRRIFeTeKPVIFGFSENDLIN 350
                                   577889999************77335555**********9875..77777655422033444777777776 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.2e-06     0.028      21     114 ..      63     144 ..      51     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-06
                                   --TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTEEEETTTEE CS
                 BPL_LplA_LipB  21 lesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipvfikwpnDl 101
                                    ++ ++ vvrr  gG  v++ p+   +++++  +e    + r+ + +   +   v+++l     k +  +++ +     D+
  gi|70606190|ref|YP_255060.1|  63 AKQNNITVVRRDIGGGTVVITPGEHDYFIVVRAEEV---P-RNPSQLYEKFLTPVVNVL-----KSYGLNANLR---DQDI 131
                                   5778999*********99999877777777777564...5.444555566777777777.....4567778888...79** PP

                                   EETTEEEEEEEEE CS
                 BPL_LplA_LipB 102 yvngrKlaGiavt 114
                                   +vng+K++G +  
  gi|70606190|ref|YP_255060.1| 132 VVNGKKISGNGAS 144
                                   ********97655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2243.31
//
Query:       gi|70606191|ref|YP_255061.1|  [L=149]
Description: hypothetical protein Saci_0352 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.016   15.0   0.1      0.021   14.7   0.1    1.2  1  DUF3490    Domain of unknown function (DUF3490)
       0.08   13.2   0.0        0.2   11.9   0.0    1.6  1  PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> DUF3490  Domain of unknown function (DUF3490)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.3e-06     0.021      73     107 ..     105     139 ..      58     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-06
                       DUF3490  73 lkalrreremlakqlqkklskeereelyakwgiel 107
                                      ++r  e l  +l++ ++++er++ly+k+gie 
  gi|70606191|ref|YP_255061.1| 105 STVITRQIERLEEKLNRTFNEKERTDLYIKYGIEA 139
                                   34578888999**********************85 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.2e-05       0.2       8      34 ..     112     138 ..     106     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                     PhetRS_B1   8 keaLfkalgkelteeeledllfefGlE 34 
                                    e+L ++l+++++e+e +dl +++G+E
  gi|70606191|ref|YP_255061.1| 112 IERLEEKLNRTFNEKERTDLYIKYGIE 138
                                   5899**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1069.26
//
Query:       gi|70606192|ref|YP_255062.1|  [L=141]
Description: hypothetical protein Saci_0353 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-20   72.3   0.0    5.6e-20   71.7   0.0    1.2  1  OsmC        OsmC-like protein
  ------ inclusion threshold ------
      0.046   13.5   0.0        3.2    7.6   0.0    2.3  2  DUF2080     Putative transposon-encoded protein (DUF2080)
       0.17   12.3   0.0       0.26   11.7   0.0    1.3  1  E3_binding  e3 binding domain


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   9.3e-24   5.6e-20       5      99 ..      36     133 ..      32     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 9.3e-24
                                   SB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT.......CEEEEEEEEEEE-SS-H..HHHHHHH CS
                          OsmC   5 gpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak.......giteirlkvevkipgadseeklkkll 78 
                                    + Peel+la+  sC+++t+  +ak+kg++++++e  +e++ dp+g++       g+ e++++++vk+   d   k+++++
  gi|70606192|ref|YP_255062.1|  36 YVKPEELCLASALSCLILTVNYIAKEKGVDVKGIEGYIEGKLDPDGFQgknsvppGLLEVNYHISVKSN--D--TKINEVI 112
                                   679**************************************************9999999999999744..3..79***** PP

                                   HHHHHHSHHHHHHCT-SSSEE CS
                          OsmC  79 ekaekrCpvsntlkngvkvel 99 
                                   e+ae+rCp+++tl++g+kv++
  gi|70606192|ref|YP_255062.1| 113 EEAERRCPMKDTLTRGIKVNI 133
                                   *******************97 PP

>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.01        62      36      49 ..      11      24 ..      10      25 .. 0.90
   2 ?    7.6   0.0   0.00053       3.2       3      34 ..      58      89 ..      57      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.01
                       DUF2080 36 eylGkkvylvIldd 49
                                  e+ G kv ++I+dd
  gi|70606192|ref|YP_255062.1| 11 EFSGDKVTITIMDD 24
                                  788*********98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00053
                       DUF2080  3 IrkktwlkvkeilpffegkVkpfGnSAkvsiP 34
                                  I k++ + vk i++ +egk  p G  +k s+P
  gi|70606192|ref|YP_255062.1| 58 IAKEKGVDVKGIEGYIEGKLDPDGFQGKNSVP 89
                                  7899999***************9999998888 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.26       7      23 ..      55      71 ..      54      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                                  HHHHHHHCT--TTTS-- CS
                    E3_binding  7 aRklAkelGidLsdvkG 23
                                  + ++Ake+G+d + + G
  gi|70606192|ref|YP_255062.1| 55 VNYIAKEKGVDVKGIEG 71
                                  679*******9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1052.18
//
Query:       gi|70606193|ref|YP_255063.1|  [L=107]
Description: hypothetical protein Saci_0354 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   13.5   0.1       0.26   11.8   0.0    1.8  2  SF3A3     Pre-mRNA-splicing factor SF3A3, of SF3a complex, Pr


Domain annotation for each model (and alignments):
>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.5e-05      0.26      48      72 ..       9      33 ..       2      38 .. 0.83
   2 ?   -1.0   0.0      0.15   2.6e+03       8      13 ..      64      69 ..      52     106 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                         SF3A3 48 qkkskeYkeYlkeLleYLesfikrt 72
                                  +++ +e   Y++ Ll+YL++fi++ 
  gi|70606193|ref|YP_255063.1|  9 ERERNEIIAYIQVLLDYLNDFISKH 33
                                  567778889*************996 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.15
                         SF3A3  8 yGkylD 13
                                  +G+y D
  gi|70606193|ref|YP_255063.1| 64 MGEYWD 69
                                  444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 800.14
//
Query:       gi|70606194|ref|YP_255064.1|  [L=269]
Description: hypothetical protein Saci_0355 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-20   71.0   1.3    1.1e-11   44.1   0.2    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
    6.9e-15   54.6   0.4    7.5e-08   32.1   0.1    2.7  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    6.9e-06   25.9   0.2    0.00026   20.9   0.0    2.3  2  HTH_11         HTH domain
    4.6e-05   23.4   0.0       0.12   12.4   0.0    2.9  3  HTH_Mga        M protein trans-acting positive regulator (MGA
    0.00062   19.7   0.1       0.01   15.8   0.0    2.2  2  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00087   19.1   0.1      0.072   13.0   0.0    2.4  2  HTH_5          Bacterial regulatory protein, arsR family
     0.0025   17.7   0.1          1    9.3   0.0    2.4  2  MarR           MarR family
     0.0049   16.9   0.0        1.2    9.3   0.0    2.3  2  HTH_20         Helix-turn-helix domain
     0.0051   16.7   0.0       0.55   10.2   0.0    2.2  2  MarR_2         MarR family
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.097   13.0   0.0    2.1  2  Rrf2           Transcriptional regulator
      0.015   15.4   0.0        1.1    9.5   0.0    2.3  2  HTH_28         Helix-turn-helix domain
       0.02   14.7   0.0        9.5    6.2   0.0    2.3  2  HTH_23         Homeodomain-like domain
      0.072   12.9   0.1        2.1    8.2   0.0    2.2  2  HTH_10         HTH DNA binding domain
       0.22   11.7   0.2          6    7.1   0.0    2.2  2  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.2   8.6e-15   1.1e-11       1      48 []       1      48 [.       1      48 [. 0.97
   2 !   25.9   0.1   4.3e-09   5.5e-06       4      41 ..     132     169 ..     130     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8.6e-15
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +d+ d++IL+   k++risqr +A  l+l+p+ +n+r ++L+++ ++k
  gi|70606194|ref|YP_255064.1|  1 MDIVDKRILSFFLKDGRISQRRIASLLNLTPASLNYRFRKLIDSNILK 48
                                  799****************************************99976 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 4.3e-09
                        HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrL 41 
                                   +d+kI e L+++pr+  +e++++lg+    + ++++ +
  gi|70606194|ref|YP_255064.1| 132 LDKKIVEMLKEDPRLASSEISKKLGINTRVIEKHIRHM 169
                                   79********************************9987 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   5.9e-11   7.5e-08       1      41 [.       1      41 [.       1      42 [. 0.98
   2 ?   -1.8   0.0       2.2   2.8e+03      28      42 .]      96     110 ..      96     110 .. 0.86
   3 !   19.9   0.0   3.7e-07   0.00047       4      31 ..     132     159 ..     130     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.9e-11
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +D +D++IL+   +d+Ris +++A  ++l+++    R r+L
  gi|70606194|ref|YP_255064.1|  1 MDIVDKRILSFFLKDGRISQRRIASLLNLTPASLNYRFRKL 41
                                  9**************************************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                 HTH_AsnC-type  28 GlSestvlrRvrrLe 42 
                                   G S+++   R++ ++
  gi|70606194|ref|YP_255064.1|  96 GSSQTELKDRIEYMR 110
                                   6799999****9886 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 3.7e-07
                 HTH_AsnC-type   4 iDrkILeaLqedaRisyaeLAervGlSe 31 
                                   +D+kI+e L ed+R+  +e+++++G+ +
  gi|70606194|ref|YP_255064.1| 132 LDKKIVEMLKEDPRLASSEISKKLGINT 159
                                   8************************876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.088   1.1e+02       4      30 ..       7      32 ..       5      51 .. 0.83
   2 !   20.9   0.0   2.1e-07   0.00026       3      44 ..     134     174 ..     133     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.088
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrr 30
                                   il ++  ++g is  ++A  Ln++ +
  gi|70606194|ref|YP_255064.1|  7 RILSFF-LKDGRISQRRIASLLNLTPA 32
                                  688888.67778***********9876 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.1e-07
                        HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                   ++i+e+L ++++ + ++e++++L++ +r++ ++I+ ++  g+
  gi|70606194|ref|YP_255064.1| 134 KKIVEML-KEDPRLASSEISKKLGINTRVIEKHIRHMRFRGM 174
                                   69*****.88888*********************99887775 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0027       3.4       8      38 ..       6      35 ..       2      42 .. 0.89
   2 ?   -2.5   0.0       4.3   5.5e+03      30      47 ..      95     112 ..      94     116 .. 0.76
   3 !   12.4   0.0   9.7e-05      0.12       6      54 ..     132     177 ..     128     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                       HTH_Mga  8 lkLlelLteneksltldelakeLglseltlq 38
                                   ++l+++++ +++++   +a+ L+l+  +l+
  gi|70606194|ref|YP_255064.1|  6 KRILSFFLK-DGRISQRRIASLLNLTPASLN 35
                                  689******.****************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                       HTH_Mga  30 LglseltlqsdiseLnel 47 
                                   +g s  +l+++i+ ++ +
  gi|70606194|ref|YP_255064.1|  95 YGSSQTELKDRIEYMRKE 112
                                   678888999999887755 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 9.7e-05
                       HTH_Mga   6 rklkLlelLteneksltldelakeLglseltlqsdiseLnelFpeelsi 54 
                                    + k++e L e +++l  +e++k+Lg+  + + + i++++  F + ++i
  gi|70606194|ref|YP_255064.1| 132 LDKKIVEMLKE-DPRLASSEISKKLGINTRVIEKHIRHMR--FRGMILI 177
                                   57899999999.****************************..9988887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     8e-06      0.01      21      52 ..      17      48 ..       6      55 .. 0.87
   2 ?    1.6   0.0      0.22   2.8e+02      21      52 ..     145     176 ..     131     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                  +++q+ +As+l+lt+ +++  +++L + ++++
  gi|70606194|ref|YP_255064.1| 17 RISQRRIASLLNLTPASLNYRFRKLIDSNILK 48
                                  79*************************99997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis 52 
                                   +l   e++  lG++   + + +++++ +g+i 
  gi|70606194|ref|YP_255064.1| 145 RLASSEISKKLGINTRVIEKHIRHMRFRGMIL 176
                                   5677899999****************999985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.042        54      17      45 ..      19      47 ..       6      48 .. 0.79
   2 !   13.0   0.0   5.6e-05     0.072       6      43 ..     135     173 ..     134     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.042
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLV 45
                                  +   +a  l+l+++ + + ++kL +++++
  gi|70606194|ref|YP_255064.1| 19 SQRRIASLLNLTPASLNYRFRKLIDSNIL 47
                                  5566999*****************99986 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.6e-05
                                   HHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                         HTH_5   6 kILklLaege.lcvcelaeelglsqstvShHLkkLreaG 43 
                                   kI+ +L e + l ++e++++lg++   +  H + +r  G
  gi|70606194|ref|YP_255064.1| 135 KIVEMLKEDPrLASSEISKKLGINTRVIEKHIRHMRFRG 173
                                   8*********9**************99999999888555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00081         1      16      46 ..      16      46 ..       7      48 .. 0.91
   2 !    6.0   0.0    0.0088        11       8      47 ..     136     175 ..     133     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                                  TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          MarR 16 gplsvseLakklgvskstvtrvldrLekkGl 46
                                  g +s+  +a+ l+++++++    ++L++ + 
  gi|70606194|ref|YP_255064.1| 16 GRISQRRIASLLNLTPASLNYRFRKLIDSNI 46
                                  7899**********************99876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0088
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47 
                                   i+++l+e + l  se+ kklg+++  + + ++++  +G+i
  gi|70606194|ref|YP_255064.1| 136 IVEMLKEDPRLASSEISKKLGINTRVIEKHIRHMRFRGMI 175
                                   78899******************99999999998777776 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00092       1.2      28      55 ..      21      48 ..       4      49 .. 0.79
   2 ?    5.4   0.0     0.015        20      14      55 ..     135     176 ..     130     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00092
                                  HHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 28 selaerldlskntlsyHLrvLeeagLve 55
                                    +a +l l++++l+y++r+L +  +++
  gi|70606194|ref|YP_255064.1| 21 RRIASLLNLTPASLNYRFRKLIDSNILK 48
                                  5699*****************9988775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                                   +i  +L+++  l  se+ + l++    + +H+r ++  g + 
  gi|70606194|ref|YP_255064.1| 135 KIVEMLKEDPRLASSEISKKLGINTRVIEKHIRHMRFRGMIL 176
                                   79999*99999999*******************997677765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00043      0.55      16      47 ..      14      43 ..       2      48 .. 0.82
   2 ?    4.4   0.0     0.028        35      17      55 ..     142     179 ..     136     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                                  CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                        MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLva 47
                                    ++  ++++ +a  l+l++++++++ ++L +
  gi|70606194|ref|YP_255064.1| 14 KDGR--ISQRRIASLLNLTPASLNYRFRKLID 43
                                  4444..9**********************987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.028
                                   TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                   +++r l+ +e+ ++lg+    + ++++ +  +G++  +p
  gi|70606194|ref|YP_255064.1| 142 EDPR-LASSEISKKLGINTRVIEKHIRHMRFRGMILIVP 179
                                   4544.************9999999999998888886665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.79     1e+03      24      56 ..      16      48 ..       9      51 .. 0.84
   2 ?   13.0   0.0   7.6e-05     0.097      21      55 ..     141     175 ..     135     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.79
                                  C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvk 56
                                  + +s + ia+  n+ p  l   ++kL  ++++k
  gi|70606194|ref|YP_255064.1| 16 GRISQRRIASLLNLTPASLNYRFRKLIDSNILK 48
                                  4489999**********9999999999888876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.6e-05
                                   STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          Rrf2  21 eeeepvsseeiaerqnispsylekilakLrkaglv 55 
                                   +e+  ++s+ei+++ +i+ +++ek ++++r  g++
  gi|70606194|ref|YP_255064.1| 141 KEDPRLASSEISKKLGINTRVIEKHIRHMRFRGMI 175
                                   4555699***********************99988 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00083       1.1       9      34 ..      13      40 ..       6      44 .. 0.85
   2 ?    3.5   0.0      0.06        77       5      37 ..     136     170 ..     134     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00083
                        HTH_28  9 laaGh.svreaArelgisrrtv.yrWik 34
                                  l++G+ s+r +A +l++++ ++ yr +k
  gi|70606194|ref|YP_255064.1| 13 LKDGRiSQRRIASLLNLTPASLnYRFRK 40
                                  679*****************99888776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
                        HTH_28   5 iikllaaG.h.svreaArelgisrrtvyrWikrye 37 
                                   i++ l++  + + +e++++lgi+ r + + i+  +
  gi|70606194|ref|YP_255064.1| 136 IVEMLKEDpRlASSEISKKLGINTRVIEKHIRHMR 170
                                   555555443456789********999999998766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0085        11      10      35 ..       8      35 ..       6      43 .. 0.78
   2 ?    6.2   0.0    0.0074       9.5      10      35 ..     136     163 ..     135     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0085
                        HTH_23 10 illllae..GlsvreIAreLgvsrrTvy 35
                                  il  +++  ++s+r+IA +L+ ++  + 
  gi|70606194|ref|YP_255064.1|  8 ILSFFLKdgRISQRRIASLLNLTPASLN 35
                                  5556665689************998765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0074
                        HTH_23  10 illllae..GlsvreIAreLgvsrrTvy 35 
                                   i+ +l+e  +l  +eI+++Lg++ r + 
  gi|70606194|ref|YP_255064.1| 136 IVEMLKEdpRLASSEISKKLGINTRVIE 163
                                   7889998899999**********99776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.11   1.4e+02      23      47 ..      17      41 ..      11      47 .. 0.87
   2 ?    8.2   0.0    0.0016       2.1      25      46 ..     147     168 ..     142     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                        HTH_10 23 rvtlkeLAkelGIskstlsehLrka 47
                                  r++ + +A  l++++++l ++ rk 
  gi|70606194|ref|YP_255064.1| 17 RISQRRIASLLNLTPASLNYRFRKL 41
                                  788999***************9985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                        HTH_10  25 tlkeLAkelGIskstlsehLrk 46 
                                    ++e++k+lGI    +++h+r 
  gi|70606194|ref|YP_255064.1| 147 ASSEISKKLGINTRVIEKHIRH 168
                                   5689****************96 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.16   2.1e+02      17      42 ..       7      32 ..       3      37 .. 0.89
   2 ?    7.1   0.0    0.0047         6      17      45 ..     135     163 ..     132     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                                  HHHHHHHHHSSBEHHHHHHHHSSTHH CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsld 42
                                  ++ ++ l+ gr + r ++++++L++ 
  gi|70606194|ref|YP_255064.1|  7 RILSFFLKDGRISQRRIASLLNLTPA 32
                                  789999***************99875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0047
                                   HHHHHHHHHSSBEHHHHHHHHSSTHHHHH CS
                         HTH_9  17 kVvetLlrkgrltlrelvkktkLsldqVk 45 
                                   k+ve+L +  rl ++e++kk++++ + + 
  gi|70606194|ref|YP_255064.1| 135 KIVEMLKEDPRLASSEISKKLGINTRVIE 163
                                   9********************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2040.99
//
Query:       gi|70606195|ref|YP_255065.1|  [L=67]
Description: hypothetical protein Saci_0356 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-24   83.4   0.4    1.1e-23   83.2   0.4    1.0  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.4     6e-28   1.1e-23       1      56 []      10      66 ..      10      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 6e-28
                       DUF1059  1 mkefkCgDvgpdCgfei.taeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                                  ++ef+C +vg++Cgfe+ +a++e+Evl+ ++ Hak+aHg++eip +++ekik++Ik+
  gi|70606195|ref|YP_255065.1| 10 KYEFSCSSVGMNCGFEVkNASSEQEVLEILKVHAKTAHGMKEIPSDVAEKIKQNIKK 66
                                  79*****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 454.03
//
Query:       gi|70606196|ref|YP_255066.1|  [L=119]
Description: hypothetical protein Saci_0357 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-50  168.4   0.1    1.4e-25   89.2   0.0    2.0  2  DUF1059       Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.069   13.6   0.5        9.2    6.8   0.0    2.1  2  YlbE          YlbE-like protein
      0.084   13.1   0.1        8.2    6.7   0.0    2.3  2  DUF3216       Protein of unknown function (DUF3216)
       0.12   12.5   0.0       0.31   11.2   0.0    1.6  2  Helicase_C_3  Helicase conserved C-terminal domain
       0.13   11.9   0.1        7.7    6.3   0.1    2.6  2  LRRNT         Leucine rich repeat N-terminal domain
       0.24   11.5   3.0       0.37   10.9   0.1    2.1  2  zf-GRF        GRF zinc finger


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.0   4.8e-29   1.4e-25       1      56 []       3      59 ..       3      59 .. 0.98
   2 !   77.7   0.0   1.9e-25   5.8e-22       1      55 [.      62     117 ..      62     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 4.8e-29
                       DUF1059  1 mkefkCgDvgpdCgfei.taeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                                  +++fkC+Dvg+dCgfei +a++e+E+l++++ Hak++Hglt+ipp+lv+kik++Ik+
  gi|70606196|ref|YP_255066.1|  3 KYTFKCADVGMDCGFEIvNAGSEDELLEALKSHAKMSHGLTSIPPDLVNKIKQNIKK 59
                                  69*****************************************************97 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 1.9e-25
                       DUF1059   1 mkefkCgDvgpdCgfei.taeteeEvlrkvaeHakaaHglteippelvekiksaIk 55 
                                   ++ f+C +vg+dCgfei  a++e+E+l+++++Hak++Hglt+ip+++++kik++Ik
  gi|70606196|ref|YP_255066.1|  62 KYYFACSSVGMDCGFEIkAASSEQELLEELMAHAKMSHGLTSIPQDTLNKIKQNIK 117
                                   689**************999***********************************8 PP

>> YlbE  YlbE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0031       9.2      22      51 ..      27      58 ..      24      59 .. 0.88
   2 ?    5.3   0.1    0.0093        28      21      52 ..      85     118 ..      81     119 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0031
                          YlbE 22 eelkelekemkekYkkt..ipdkvekisnslq 51
                                  e l++l++ +k++ ++t  +pd v+ki+++++
  gi|70606196|ref|YP_255066.1| 27 ELLEALKSHAKMSHGLTsiPPDLVNKIKQNIK 58
                                  78999***********96569********995 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0093
                          YlbE  21 peelkelekemkekYkkt..ipdkvekisnslqm 52 
                                   +e l+el   +k++ ++t  ++d ++ki++++++
  gi|70606196|ref|YP_255066.1|  85 QELLEELMAHAKMSHGLTsiPQDTLNKIKQNIKV 118
                                   67899999999999999955589********985 PP

>> DUF3216  Protein of unknown function (DUF3216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0027       8.2       7      32 ..      19      44 ..      17      60 .. 0.86
   2 ?    4.4   0.0     0.014        43      12      35 ..      83     106 ..      76     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0027
                                  HHHCTT-HHHHHHHHHHHHHTTTHHH CS
                       DUF3216  7 llleleeenllkaleafvrltgGlek 32
                                  +++   e++ll+al+   ++++Gl +
  gi|70606196|ref|YP_255066.1| 19 IVNAGSEDELLEALKSHAKMSHGLTS 44
                                  56777899***************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                                   T-HHHHHHHHHHHHHTTTHHHHH- CS
                       DUF3216  12 eeenllkaleafvrltgGlekkrG 35 
                                    e++ll+ l a  ++++Gl +   
  gi|70606196|ref|YP_255066.1|  83 SEQELLEELMAHAKMSHGLTSIPQ 106
                                   6889**************988655 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.31      57     119 ..      24      98 ..      20     103 .. 0.80
   2 ?    1.7   0.0     0.092   2.7e+02      56     119 ..      82      98 ..      78     116 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                  Helicase_C_3  57 taeeiiefLerlsky.....pvPqaleylirdvarryGklrlgl.......easlvlrsddpalleelladkkia 119
                                   + +e++e+L++++k+     ++P  l+  i++ +++ Gk  +         + ++   s++++lleel+a+ k++
  gi|70606196|ref|YP_255066.1|  24 SEDELLEALKSHAKMshgltSIPPDLVNKIKQNIKKSGKYYFACssvgmdcGFEIKAASSEQELLEELMAHAKMS 98 
                                   57899******9987788889******************988766776655445555667888999998888775 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.092
                  Helicase_C_3  56 ltaeeiiefLerlskypvPqaleylirdvarryGklrlgleaslvlrsddpalleelladkkia 119
                                    + +e++e L +++k                                               ++
  gi|70606196|ref|YP_255066.1|  82 SSEQELLEELMAHAK-----------------------------------------------MS 98 
                                   344455555555554...............................................43 PP

>> LRRNT  Leucine rich repeat N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0026       7.7      17      27 ..      39      49 ..      39      49 .. 0.90
   2 ?    2.8   0.0     0.033        97      17      25 ..      98     106 ..      98     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0026
                                  SST-SS--STS CS
                         LRRNT 17 ergLtavPrdl 27
                                  ++gLt++P+dl
  gi|70606196|ref|YP_255066.1| 39 SHGLTSIPPDL 49
                                  59*******97 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.033
                                   SST-SS--S CS
                         LRRNT  17 ergLtavPr 25 
                                   ++gLt++P 
  gi|70606196|ref|YP_255066.1|  98 SHGLTSIPQ 106
                                   59******6 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.23   6.8e+02      26      38 ..       6      17 ..       3      17 .. 0.81
   2 ?   10.9   0.1   0.00012      0.37      14      38 ..      54      76 ..      48      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                        zf-GRF 26 YkCpkgkekqCgF 38
                                  +kC+     +CgF
  gi|70606196|ref|YP_255066.1|  6 FKCADVGM-DCGF 17
                                  78998875.8**9 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                        zf-GRF 14 vrktgpNkGRkFYkCpkgkekqCgF 38
                                   + + +  G+ +++C+     +CgF
  gi|70606196|ref|YP_255066.1| 54 KQ-NIKKSGKYYFACSSVGM-DCGF 76
                                  43.66789********9985.8**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 957.16
//
Query:       gi|70606197|ref|YP_255067.1|  [L=132]
Description: hypothetical protein Saci_0358 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00053   19.7   0.3    0.00053   19.7   0.3    2.5  3  DUF3953   Protein of unknown function (DUF3953)


Domain annotation for each model (and alignments):
>> DUF3953  Protein of unknown function (DUF3953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       0.2   3.6e+03      31      36 ..      51      56 ..      50      62 .. 0.61
   2 ?   -1.8   0.8      0.15   2.7e+03      27      37 ..      75      85 ..      73      86 .. 0.72
   3 !   19.7   0.3   2.9e-08   0.00053      13      38 ..      97     122 ..      96     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.2
                       DUF3953 31 aalfvl 36
                                  ++lfv+
  gi|70606197|ref|YP_255067.1| 51 ISLFVI 56
                                  455555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.15
                       DUF3953 27 llilaalfvlf 37
                                   +++++ f+lf
  gi|70606197|ref|YP_255067.1| 75 YAFIISPFLLF 85
                                  57888888887 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 2.9e-08
                       DUF3953  13 GieEfkkenkfsGillilaalfvlfV 38 
                                   G+ Ef+++ +f+++l+il+ lf+++V
  gi|70606197|ref|YP_255067.1|  97 GLVEFRRRMRFVSVLYILVTLFLFYV 122
                                   99***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1126.24
//
Query:       gi|70606198|ref|YP_255068.1|  [L=275]
Description: hypothetical protein Saci_0359 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-58  197.7  14.3    3.1e-58  197.0  14.3    1.3  1  DUF929         Domain of unknown function (DUF929)
  ------ inclusion threshold ------
      0.049   14.1   0.0       0.28   11.6   0.0    2.2  2  Thioredoxin_2  Thioredoxin-like domain
      0.092   12.9   0.0       0.27   11.5   0.0    1.9  2  Thioredoxin_7  Thioredoxin-like


Domain annotation for each model (and alignments):
>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.0  14.3   5.2e-62   3.1e-58       1     249 []       6     227 ..       6     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.0 bits;  conditional E-value: 5.2e-62
                        DUF929   1 skliviaiivliivvivvvslsai...........vsnalvelskqvyaseplstkfvkvsnqdlasngkvevyfvswegC 70 
                                   +k+ivi+++v+i  vi+ vsls+            ++ +lvelskq+y+ ++++ + ++v + +++s+gk++v++v++e+C
  gi|70606198|ref|YP_255068.1|   6 YKIIVIVLLVIITGVIIGVSLSSSnnssslgknisIYPELVELSKQGYNVQAYP-TNLQVLPLNFSSEGKPAVIYVGAEWC 85 
                                   599***************************************************.8************************* PP

                        DUF929  71 PvgaaesWaLyiaLsryGnl.nlephySdpsdeypniPgLiFknftpnskvefysiYiyneylnas.rngtpinselvsvg 149
                                   P++a e+WaL++aL+r+Gn+ +le+++S+++d+ypn+P+++F ++      +++s+Yi++ +++++ rng+++        
  gi|70606198|ref|YP_255068.1|  86 PYCAVERWALILALLRFGNFtGLEYMQSSSTDVYPNTPTFTFVKA------NYTSPYISFIGIEYEaRNGSQL-------- 152
                                   *********************************************......9*********************........ PP

                        DUF929 150 lqeLkeelpssvynlvkkYetesliqetsepsaylvsppHivttiiitGpkGtyilvgysinPsllsgyspeyvlkqleng 230
                                        e +p+++y+++++Y++++                     i+++ ++G+y++vg+sinP+l+sg++++yv++ql+++
  gi|70606198|ref|YP_255068.1| 153 -----EPVPTNIYQMWTQYGKGQ---------------------IPFI-IIGYYYQVGTSINPGLMSGHDWNYVISQLNDP 206
                                   .....******************.....................9999.99****************************** PP

                        DUF929 231 nsksa..IlsaanlitqiIqe 249
                                   ns+ +  ++++anlit++I++
  gi|70606198|ref|YP_255068.1| 207 NSQIYlqVYAQANLITKYICQ 227
                                   **999**************96 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.44   2.6e+03      68      84 ..      44      62 ..      23      68 .. 0.76
   2 ?   11.6   0.0   4.7e-05      0.28       3      21 ..      71      89 ..      69      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.44
                 Thioredoxin_2 68 envelark.ygvrgtPt.i 84
                                  e vel+++ y+v++ Pt +
  gi|70606198|ref|YP_255068.1| 44 ELVELSKQgYNVQAYPTnL 62
                                  5578888889999999954 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.7e-05
                 Thioredoxin_2  3 gngkpvlvvftdpdCpyCk 21
                                  ++gkp ++++ +++CpyC+
  gi|70606198|ref|YP_255068.1| 71 SEGKPAVIYVGAEWCPYCA 89
                                  689***************7 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.4e-05      0.27      15      34 ..      71      90 ..      68     141 .. 0.82
   2 ?   -2.1   0.0      0.76   4.5e+03      58      79 ..     142     175 ..     123     176 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                  HHT--EEEEE--TT-HHHHH CS
                 Thioredoxin_7 15 ergkpvlvffgaswcftCqa 34
                                  ++gkp  +++ga+wc++C +
  gi|70606198|ref|YP_255068.1| 71 SEGKPAVIYVGAEWCPYCAV 90
                                  589***************64 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.76
                                   ESS--S-GGG.........-TT---....SSEEE CS
                 Thioredoxin_7  58 vdvterdani........leldeqg....vPvva 79 
                                   ++++ r++++        +++ +q+    +P+++
  gi|70606198|ref|YP_255068.1| 142 IEYEARNGSQlepvptniYQMWTQYgkgqIPFII 175
                                   4455555555444443333333333444566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2164.75
//
Query:       gi|70606199|ref|YP_255069.1|  [L=362]
Description: hypothetical protein Saci_0360 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        1.5    7.7   7.6        2.1    7.2   7.6    1.1  1  DUF677        Protein of unknown function (DUF677)
        2.8    7.0   8.8        4.5    6.3   8.8    1.3  1  SprA-related  SprA-related family
        6.9    7.1  10.3        6.3    7.2   7.7    2.2  2  Wzz           Chain length determinant protein


Domain annotation for each model (and alignments):
>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.6   0.00035       2.1     177     251 ..       6      82 ..       2      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00035
                        DUF677 177 ktkraisnvvfvaafvaVlvlSvvlaalaa.pavvavagalavPleavgkwva.sawkkyeealkrqkeivssmekg 251
                                   k+ ra+sn+vfva  v+ +++  v  al a  +  +   +++vP  +v++     + + +++++   +++ s+  + 
  gi|70606199|ref|YP_255069.1|   6 KNTRAVSNAVFVAVAVILIIIAAVGFALYAtKPSTTSTVTTTVPTTVVSTVTTpGMTTTSTQTVTATQTVTSTQTQT 82 
                                   6789*********8888888887777765514555577799********8776656667777777766666654444 PP

>> SprA-related  SprA-related family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.8   0.00076       4.5      37      97 ..      36      96 ..       6     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00076
                  SprA-related 37 dtrsvasvvsstnsssvdatisdatsinstvktardatasastsesgsvsdtikpssaeqa 97
                                  +++s  s+v++t + +v  t++  + ++ +++t++ +++ +st  + ++s   kp++++ +
  gi|70606199|ref|YP_255069.1| 36 TKPSTTSTVTTTVPTTVVSTVTTPGMTTTSTQTVTATQTVTSTQTQTVTSTLTKPVTVNSS 96
                                  566777888888888888888899999999*************************999865 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.7    0.0011       6.3      16      82 ..      14      86 ..      11      95 .. 0.75
   2 ?   -1.1   0.0       0.4   2.4e+03      30      52 ..      97     120 ..      87     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                                  XXXXXXXXXXXXXXXXXXX.XXXXX-EEEEEEEES--CHHH..HHHHHHCC...HHHHHHHHHHHHHHHHHSS CS
                           Wzz 16 kklIilvtllfallaviya.flatpkYtataqilvpekkqv..eassltaq...dvqanlqlasteieilkSr 82
                                   + +++ ++l +++av++a ++ +p  t+t + +vp+      +++++t      v+a+ +++st++++ +S+
  gi|70606199|ref|YP_255069.1| 14 AVFVAVAVILIIIAAVGFAlYATKPSTTSTVTTTVPTTVVStvTTPGMTTTstqTVTATQTVTSTQTQTVTST 86
                                  56788899999999999999999**************987554223333334446666667777777777776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.4
                                   XXXXX.XXXXX-EEEEEEEES--C CS
                           Wzz  30 aviya.flatpkYtataqilvpek 52 
                                   +++y   + t +Yta+ + ++p  
  gi|70606199|ref|YP_255069.1|  97 GAFYNgQVITFQYTAQFMCTPPAT 120
                                   667777788889999999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2535.89
//
Query:       gi|70606200|ref|YP_255070.1|  [L=467]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.9e-101  340.2   0.0   2.6e-101  339.8   0.0    1.2  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   0.0  1.4e-105  2.6e-101       1     451 []      40     456 ..      40     456 .. 0.92

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 1.4e-105
                                   HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS- CS
                       Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekD 81 
                                   +l+++ l+++++  ek n+++t++++eal++A+kl+++++rg ++gpL G+Pi+vKDni +kg++tt +sk++ ++++ ++
  gi|70606200|ref|YP_255070.1|  40 DLIQHTLDKMKTDAEKFNSYITIIKDEALRHAEKLEEHIKRGIPTGPLSGLPIAVKDNIFTKGIRTTIASKIFREFYPNYN 120
                                   589999*************************************************************************** PP

                                   -HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHH CS
                       Amidase  82 atvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsf 162
                                   atv+ +L +a+a+i+gk n++ fa g+s   s fgptrNP+d++r+ GGSSGGsA+ vA g vp+++GtDt GS+R+PAsf
  gi|70606200|ref|YP_255070.1| 121 ATVINKLLEADAIIVGKNNLHAFASGVSNLVSEFGPTRNPLDTERITGGSSGGSASSVAFGSVPISLGTDTVGSVRVPASF 201
                                   ********************************************************************************* PP

                                   CTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEE CS
                       Amidase 163 cglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvv 243
                                   cg++G KP+ g+vSr+g+ + ++sld++G+l+++v d+al+   i+g+d++ds++ +ip+ + d  + ++ +++ +  G++
  gi|70606200|ref|YP_255070.1| 202 CGVIGYKPSNGLVSRYGLFPTAWSLDTIGVLSKTVLDVALISYFIMGYDENDSSTVNIPRINIDNVA-QGVEPRRITLGIL 281
                                   ***********************************************************55544444.4445588999999 PP

                                   GGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHH CS
                       Amidase 244 kedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpks 324
                                    + + +++++e    +++++ +L ++G++ + v++  +e  +++ ++i +aea++                   ++ l+ s
  gi|70606200|ref|YP_255070.1| 282 VQESQTEVEKE---FLDNVVSKLDSEGFKTERVNFD-IETSHKITTTIRLAEAAAF------------------HKDLFMS 340
                                   99996444444...456789*******999999985.6677777889999999854..................8999*** PP

                                   HHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGC CS
                       Amidase 325 raellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynl 405
                                   r++++ + v   i  g    ++e     y+++   r+ l+ +f ++f+++D++++Pt+p+ +p+ +e     ++    + +
  gi|70606200|ref|YP_255070.1| 341 REDDYPRDVAELIRNGMSIPAHE-----YIQSMISRKYLISDFLRLFNHVDAVITPTVPILPPKTNEIMG--KELDYRRTI 414
                                   **********9999999999988.....7888888889**************************998864..445556667 PP

                                   CTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                       Amidase 406 ldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                   +++t    +vnl g pa+s+p+ k  +glP+G+q+igk +++e+lL
  gi|70606200|ref|YP_255070.1| 415 IKYT---GFVNLLGFPAISIPSVKL-SGLPIGLQIIGKIYHDEALL 456
                                   7777...99*************987.5****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3278.01
//
Query:       gi|70606201|ref|YP_255071.1|  [L=65]
Description: DNA-bindign protein 7e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-41  138.5   4.0    5.8e-41  138.3   4.0    1.0  1  7kD_DNA_binding  7kD DNA-binding domain


Domain annotation for each model (and alignments):
>> 7kD_DNA_binding  7kD DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.3   4.0   3.2e-45   5.8e-41       1      58 []       3      60 ..       3      60 .. 0.99

  Alignments for each domain:
  == domain 1  score: 138.3 bits;  conditional E-value: 3.2e-45
                                  EEEEESSSSEEEEETTTEEEEEESSSSEEEEEE-SSSEEEEEEETTTS-CHHHHHHTT CS
               7kD_DNA_binding  1 kvkfkykGeekevdiskikkvWrvGkmvsftyddnGktGrGavsekdaPkelldmlek 58
                                  kv+fkykGeekevd+skikkvWrvGkmvsftyddnGktGrGavsekdaPkel+dml++
  gi|70606201|ref|YP_255071.1|  3 KVRFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELMDMLAR 60
                                  89******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 475.06
//
Query:       gi|70606202|ref|YP_255072.1|  [L=583]
Description: molybdopterin oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-07   30.8   0.0    0.00017   20.7   0.0    2.1  2  Molybdopterin    Molybdopterin oxidoreductase
      0.003   17.5   0.0      0.013   15.5   0.0    2.1  2  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
       0.11   12.2   0.4        1.7    8.3   0.0    2.7  3  HTH_50           Helix-turn-helix domain
       0.11   11.5   0.0       0.52    9.3   0.0    1.9  2  LuxC             Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00025       1.1     102     256 ..     128     269 ..      64     290 .. 0.69
   2 !   20.7   0.0   3.9e-08   0.00017     334     401 ..     321     389 ..     312     406 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00025
                                   -SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHH CS
                 Molybdopterin 102 ssnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilq 182
                                   ++   e++e+ d ++ wGs  +            ++l++k k i ++ r +e++++ d++  ++pg+d+ la++ ++ i +
  gi|70606202|ref|YP_255072.1| 128 FGALPEEFEKYDSVVFWGSESAVSFIHG-----WKLLQSKYK-ITVDVRISETARRSDKYYLVRPGSDGFLAVGVMKRIFA 202
                                   3333348999999999999988877666.....345554443.799****************************9999999 PP

                                   CCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHH CS
                 Molybdopterin 183 elkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiy 256
                                    +  +   l+   + +e++++++  + e      ++   + + el + +++ ++  + i+G  l + + g +++
  gi|70606202|ref|YP_255072.1| 203 RGVSAD-ILDDEATLREYVNSYTWDEIES----VTGLNRKYIEELGDLYYDRRP--LTIIGFALGRTYYGGDAV 269
                                   887777.7788888888877777666555....334444455566666666655..666666666666655555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.9e-08
                                   HHTTSSSEEEEESH.HHHHSTTSCCCHCHHH.CSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE- CS
                 Molybdopterin 334 lkssgkkvlyllgnnpevdhadenevekale.kldlvvvldgrltstalyaDiiLPaatwyEkedlytn 401
                                   ++++++kv++  ++np+++ ++  ++++a +    ++++ d +++++++ ++++ P+ t++Ek+d++ +
  gi|70606202|ref|YP_255072.1| 321 VEKGNIKVIFAWNSNPIHSLPNSDRIVEAIKeGRLTLIMHDPFINESVKLSNVVIPSPTFLEKRDVVYS 389
                                   57899***********************999655678999*************************9876 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.67     3e+03      65      83 ..     317     336 ..     311     377 .. 0.65
   2 !   15.5   0.0     3e-06     0.013      52     108 ..     519     574 ..     518     577 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.67
                                   EESSB-TTEEEEESSHCC.. CS
               Molydop_binding  65 vtervrpGvvfmpfgwwe.a 83 
                                   v e+v +G + + f+w++ +
  gi|70606202|ref|YP_255072.1| 317 VGEEVEKGNIKVIFAWNSnP 336
                                   66777777777777776641 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3e-06
                                   EEETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHCTS--SCSTTT--CSTT CS
               Molydop_binding  52 vesrrGsvevrakvtervrpGvvfmpfgwweagekggnaNaltddatdplsgtpefk 108
                                   +es++G+++v  k++erv++Gv +m+        + +++N++++ a+ ++ gtp+ +
  gi|70606202|ref|YP_255072.1| 519 LESDFGKIRVIFKISERVPKGVYYMYKSGLF-DLDDKPVNSIVNNAINEYGGTPQIN 574
                                   689***********************98766.67899****************9876 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.6     7e+03       2      13 ..      57      68 ..      56      70 .. 0.82
   2 ?    0.6   0.0     0.094   4.2e+02       1      11 [.     213     223 ..     213     232 .. 0.81
   3 ?    8.3   0.0   0.00038       1.7      26      37 ..     413     424 ..     412     427 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                        HTH_50  2 gsLkeyveefEr 13
                                   sL++ v+++ +
  gi|70606202|ref|YP_255072.1| 57 TSLEDSVKYISK 68
                                  79*****99976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.094
                        HTH_50   1 egsLkeyveef 11 
                                   e++L+eyv+++
  gi|70606202|ref|YP_255072.1| 213 EATLREYVNSY 223
                                   589******98 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00038
                        HTH_50  26 tRklAkrLGvSh 37 
                                   +R++Ak+LG+Sh
  gi|70606202|ref|YP_255072.1| 413 MRLIAKQLGISH 424
                                   59********** PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.13     6e+02      53     104 ..      38      90 ..      20      97 .. 0.83
   2 ?    9.3   0.0   0.00012      0.52     163     204 ..     131     172 ..     123     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.13
                          LuxC  53 llkreeLkkvleseL.gqpeiLdeflktkeksyekaqprglvlhv.lsgNvpll 104
                                    l+r+++++vl   + g++ +L++ +k    + +k  p+ +++hv   gN  ll
  gi|70606202|ref|YP_255072.1|  38 DLRRNKINRVLSPLVeGKETSLEDSVKYIS-KIIKETPKDKIIHVeYDGNQGLL 90 
                                   589999****99999999999*99998888.8************9445666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00012
                          LuxC 163 leeeivqnaDvvvawGgeeaikaise.klkpgkqlikfGakvS 204
                                   l ee+ ++ D vv wG+e+a++ i + kl ++k  i  + ++S
  gi|70606202|ref|YP_255072.1| 131 LPEEF-EKYDSVVFWGSESAVSFIHGwKLLQSKYKITVDVRIS 172
                                   67777.899****************988888888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3595.48
//
Query:       gi|70606203|ref|YP_255073.1|  [L=398]
Description: transporter protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-44  152.6  56.5    1.5e-44  152.4  56.5    1.0  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        6.6    6.3  10.3       0.99    8.9   5.4    2.2  2  Cytochrome-c551  Photosystem P840 reaction-centre cytochrome 


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4  56.5   1.7e-48   1.5e-44      10     379 ..      17     389 ..       8     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 1.7e-48
                                   HHHH.....HHHHTTSXHHHHHHHHHHHHTTTTTS..............HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTH CS
                Na_H_Exchanger  10 lvgl.....larrlklpeivgliiaGlllGpsglg.lieps........eedlevlselglilllFlaGleldlrelrknl 76 
                                   l+++     l+r++ +p +v++ii+G+++ p+ lg +i++         +  + +++++ +ill+F+aGl+  +++lr+ +
  gi|70606203|ref|YP_255073.1|  17 LALAqggrlLLRKYFIPALVAEIIVGIVFSPYALGgVINSIlqvnlfsiNNYVVLFANFSVILLIFAAGLSHGFKNLRSSG 97 
                                   22223334259************************74555577778888899***************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCC CS
                Na_H_Exchanger  77 ksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavv 157
                                      +l a+lg +i++ l  +++ +   l ++   all+ga+ +at+++++++i+ e+++ +e++ +ll++++ ++D+va++
  gi|70606203|ref|YP_255073.1|  98 FLGFLAATLGAVIPTYL--VFVVF--SLVYDTQVALLMGAASAATSLAATVSIVDEYKLYRENFSRLLISAAAIDDVVALI 174
                                   *****************..55553..4568*************************************************** PP

                                   CCHHHHHHTX.XXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXH CS
                Na_H_Exchanger 158 llavllalak.eeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsg 237
                                   +l+ +++l++ ++   + + l +l   l ++v+++++ ++i+ +l +++        +   ++l+++++++l++ ++g+s 
  gi|70606203|ref|YP_255073.1| 175 ILSTVVELITlGSLPLVQTTLRVLELSLAWIVIFFVAVFLIPKILTVVRDE------IVDNISLVILFVLVLIMLVVGFSP 249
                                   *********775555555556666666666666666666666666666665......33344566666667777789**** PP

                                   HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTX CS
                Na_H_Exchanger 238 ilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrll 318
                                   +++af+aG++++e+ +s++++  +e ++ ++f plfFv+vG+++++ +++ +l+ l+l ll+ ++ ++g+i +++++++++
  gi|70606203|ref|YP_255073.1| 250 VIAAFIAGVAIAESVKSKRVNGFTETLI-SIFGPLFFVYVGMETPFYIFF-NLNDLLLGLLLSFLAIVGKIFGILPVAYFY 328
                                   *******************999999999.9***************88885.56666666655555558************* PP

                                   SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                Na_H_Exchanger 319 glslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                    ++l++++i ++g+++rg++ l++a +g + ++l+   y+ +++++l+t+++   ++++l 
  gi|70606203|ref|YP_255073.1| 329 TKNLKQSIITAVGMIPRGEIGLVVATVGLSGNVLDVSQYSQIVIMALITTFLGSYIFSTLI 389
                                   ***************************************************8887777765 PP

>> Cytochrome-c551  Photosystem P840 reaction-centre cytochrome c-551
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.4   0.00011      0.99      10      93 ..     127     211 ..     123     229 .. 0.80
   2 ?   -3.4   0.0      0.68   6.1e+03      79     101 ..     304     326 ..     301     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00011
                                   XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX CS
               Cytochrome-c551  10 ialaigGavlmGalffgvsfltGykvpaenisavltplksfmGwflliffasli.ilglGklsskisdkwflsfplsilvi 89 
                                   +al +g a +  +l  +vs++  yk+  en+s +l    ++     li++++++ +++lG l    +   +l + l+ +vi
  gi|70606203|ref|YP_255073.1| 127 VALLMGAASAATSLAATVSIVDEYKLYRENFSRLLISAAAIDDVVALIILSTVVeLITLGSLPLVQTTLRVLELSLAWIVI 207
                                   799999999***********************************9999998877578999998776666677777766666 PP

                                   XXXX CS
               Cytochrome-c551  90 vavm 93 
                                     v 
  gi|70606203|ref|YP_255073.1| 208 FFVA 211
                                   4432 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.68
                                   XXXXXXXXXXXXXXXXXXXXXXX CS
               Cytochrome-c551  79 flsfplsilvivavmfvslevvw 101
                                   +l + ls l+iv  +f +l v +
  gi|70606203|ref|YP_255073.1| 304 LLGLLLSFLAIVGKIFGILPVAY 326
                                   56778899999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2283.61
//
Query:       gi|70606204|ref|YP_255074.1|  [L=320]
Description: hypothetical protein Saci_0365 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.29   11.0   3.1         15    5.4   0.0    2.4  2  PRP38     PRP38 family


Domain annotation for each model (and alignments):
>> PRP38  PRP38 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0   0.00085        15      99     131 ..      58      90 ..      51     105 .. 0.88
   2 ?    5.1   1.2     0.001        19      83     156 ..     175     260 ..     142     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00085
                         PRP38  99 lYlRlvlepkelykllepllnDyrklkrrekdg 131
                                    Y Rl  + +++ k +e+l+++ +k+k r +++
  gi|70606204|ref|YP_255074.1|  58 PYGRLDGKFNDFEKAFEKLYQEIEKIKDRGLKQ 90 
                                   699************************998776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.001
                         PRP38  83 elln...........nedskYiralgllYlRlvlepkelykllepllnDyr..klkrrekdgevdpk.gvkliti.delvd 148
                                   e  n           ++d k+++ ++  Y+R  +  +++y++ +++ +D+   k+ ++ + + ++ k ++k+i +  e  +
  gi|70606204|ref|YP_255074.1| 175 EAYNwlysefhakydTKDRKFLTDIASYYMRRFF--QQVYDVAKDYTTDKLegKIAIIPLVE-SKAKkDGKIIDVwREDLR 252
                                   33336666677777799**************876..5899******9997411555555554.333335555543234455 PP

                         PRP38 149 dLltkdri 156
                                   dLl++ r+
  gi|70606204|ref|YP_255074.1| 253 DLLEQARY 260
                                   66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1852.79
//
Query:       gi|70606205|ref|YP_255075.1|  [L=239]
Description: glutaconate CoA-transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-23   82.3   0.0    3.9e-23   82.0   0.0    1.1  1  CoA_trans       Coenzyme A transferase
  ------ inclusion threshold ------
      0.024   14.6   0.3      0.062   13.3   0.1    1.7  1  CspB_prodomain  Csp protease B prodomain
       0.15   11.7   0.0       0.35   10.5   0.0    1.6  1  40S_S4_C        40S ribosomal protein S4 C-terminus


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   6.5e-27   3.9e-23       1     216 [.       3     201 ..       3     202 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 6.5e-27
                                   CCHHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBCEHHH CS
                     CoA_trans   1 vetaaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetvnprf 81 
                                   ve++a+a+a+ ++dG+ v+vG   +  +P al  +lar+ + +++ i + a + +   ++++ s+++ ++    +  +p+f
  gi|70606205|ref|YP_255075.1|   3 VEHMAKAIAEILEDGEKVYVG--LNSILP-ALGSFLARDVYHKNIRIYGVAEADNPLDITISPSTGDPML---AQ-YTPVF 76 
                                   689******************..8888**.***********************78777888888888888...55.46666 PP

                                   HHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTTESEEEEETTEEEEEEESSSEEEEEEECCEEETT CS
                     CoA_trans  82 gkqflsgelefellpqgtlaerlraGgaglpelgfltntgigtlvapklkkvpgfgGaeyilepalkadvalikaskadee 162
                                   ++        f+ l q++ ++++++G+ +++e+ + + ++ig +++pk  ++pg+  + + +    k ++++ ++++ ++ 
  gi|70606205|ref|YP_255075.1|  77 TTV-----DLFD-LVQKGKLDVMFLGPIQIDEEINANVSVIGSYEKPK-VRLPGGAATAFMMPLIRKLILWNFRHNRQSFP 150
                                   666.....3555.99*********************************.6******************************* PP

                                   CSEESSGGGHTTHSHHHHHHEEEEEEEEEEEECTTSSECCCESBTGGGHSEEEE CS
                     CoA_trans 163 gnlvfeksagnfnkpaiaeaakvtileveeivekgkldpekvliPgvlvdavve 216
                                   ++++f + +++ +k+ +    +vt+l+v+++ ++++++ + vl+P++ +++++ 
  gi|70606205|ref|YP_255075.1| 151 KRVDFVTGTAKHSKNEVY---VVTNLGVLHFNREKNRWEVIVLYPWSNINEIKS 201
                                   ************977766...9*****************************986 PP

>> CspB_prodomain  Csp protease B prodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     1e-05     0.062      15      57 ..     164     208 ..     159     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                CspB_prodomain  15 eeerekseelsv.gydeeentwelivkys.gdleeleeelgieve 57 
                                   ++e   + +l v  +++e+n+we+iv+y   +++e++++ g+ v+
  gi|70606205|ref|YP_255075.1| 164 KNEVYVVTNLGVlHFNREKNRWEVIVLYPwSNINEIKSNTGFDVY 208
                                   566667788888899*************63788888877777665 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.9e-05      0.35      12      30 ..     106     124 ..     105     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.9e-05
                                   GGEEE--STTS-SS---SS CS
                      40S_S4_C  12 sNvFvIGkgnkpwvsLPkg 30 
                                   +Nv vIG  +kp v LP g
  gi|70606205|ref|YP_255075.1| 106 ANVSVIGSYEKPKVRLPGG 124
                                   6****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 1367.39
//
Query:       gi|70606206|ref|YP_255076.1|  [L=251]
Description: coenzyme A transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-29  102.8   0.0      2e-29  102.6   0.0    1.0  1  CoA_trans  Coenzyme A transferase


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   1.1e-33     2e-29       3     215 ..       6     222 ..       4     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 1.1e-33
                                   HHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHTTTSEEEEESTTTEECCHHHHHTTTEEEEEESCTTBBC...EHH CS
                     CoA_trans   3 taaeavakeikdGmtvavGGFgligiPealiaalarsgvkdltviiseagvlglgplllngsvkkviasyggetv...npr 80 
                                   +++ a++  +k+G+ + ++G    + P+ +i+al++s+v++l ++  e g+ gl  ll+++ vkk  a     +    +++
  gi|70606206|ref|YP_255076.1|   6 SLDRAIK-LVKEGDWITISGISFHRSPMGFIFALVNSDVRNLGFVDREPGL-GLEILLKHNVVKKIRAAMATLEWlgiPSN 84 
                                   6889999.*******************************************.***************85555444799*** PP

                                   HHHHHHTTSSEEEEHHHHHHHHHHHHHHHTEETTEEEESTTTT.SHGGTT....ESEEEEETTEEEEEEESSSEEEEEEEC CS
                     CoA_trans  81 fgkqflsgelefellpqgtlaerlraGgaglpelgfltntgig.tlvapk....lkkvpgfgGaeyilepalkadvalika 156
                                   f+k+++sge+ef + + g  +  +raG+ g+p+ ++    g++   +++k    +   + f G+e++l++a+++dva+i+ 
  gi|70606206|ref|YP_255076.1|  85 FRKKVESGEVEFLEDSCGAFIAGIRAGAFGIPFMPVKGVLGSDlVKLHEKvgswRVAKDPFSGEEVLLVKAITPDVAIIHV 165
                                   *************************************99999976677779*9966999********************** PP

                                   CEEETTCSEESSGGGHTTHSHHHHHHEEEEEEEEEEEECTTSSECCCESBTGGGHSEEE CS
                     CoA_trans 157 skadeegnlvfeksagnfnkpaiaeaakvtileveeivekgkldpekvliPgvlvdavv 215
                                   +kadeegn+ +++  + f++ + a+a k++i + eeiv+      ++ +i+  +v avv
  gi|70606206|ref|YP_255076.1| 166 HKADEEGNAEIIG--PLFEDEFKAKASKTVIITAEEIVPRSYFYGKRPTINADYVTAVV 222
                                   *************..9999999999*************877666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1661.73
//
Query:       gi|70606207|ref|YP_255077.1|  [L=505]
Description: 5-oxoprolinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-170  568.5   0.0   1.3e-170  568.3   0.0    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.3   0.0    7e-175  1.3e-170       4     515 ..       3     503 ..       1     504 [. 0.97

  Alignments for each domain:
  == domain 1  score: 568.3 bits;  conditional E-value: 7e-175
                Hydantoinase_B   4 tlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfegelkpGDvl 84 
                                   t ev+ ++   iaeemg +l+++a Spni+er+D sca++d++g++vaqa+hipvhlgs++ av +vl+++ +e+kpG+ +
  gi|70606207|ref|YP_255077.1|   3 TWEVIDKATTFIAEEMGVMLKKSALSPNIRERMDHSCAIIDNQGRIVAQAEHIPVHLGSFKVAVVNVLKYLGDEIKPGENY 83 
                                   789*****************************************************************99988******** PP

                Hydantoinase_B  85 ltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegeleedvlell 165
                                   + NdPy  gtHl+D+ ++tP+ +eg++v++v+++aH++D+GG  pGs++p a++++eEG++ippvkl      +e+v++++
  gi|70606207|ref|YP_255077.1|  84 IFNDPYISGTHLNDVGLLTPIDYEGKIVGYVVNKAHQVDVGGPIPGSLNPLAKTLYEEGIVIPPVKL------DERVIKII 158
                                   ******************************************************************9......669***** PP

                Hydantoinase_B 166 lanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgtyeaedyl...ddgip 243
                                   ++n ++pe  +gDl+Aq++an +g  r+++lie+yGl++v + +de ++++++ v + ++ +++g+y+aedyl   d+ +p
  gi|70606207|ref|YP_255077.1| 159 KENFKMPEVSIGDLRAQLSANSLGVIRVRQLIEKYGLQNVVEGWDETIEYTRNVVSN-IN-WKEGDYRAEDYLeweDKLLP 237
                                   **************************************************9988776.54.9***********6633359* PP

                Hydantoinase_B 244 ikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpsepaavvgg 324
                                   ik+t+++++d++t Df+gt+ q++g++Na++ vt+sav +++r+ +++ + +NeG+++ ++vk+ eg+l+np +pa+v+gg
  gi|70606207|ref|YP_255077.1| 238 IKLTLKVRKDRVTADFSGTHGQIDGPLNAVYGVTYSAVSFAIRSALGKSVSTNEGFYSFVQVKADEGTLVNPVKPAPVSGG 318
                                   ********************************************************************************* PP

                Hydantoinase_B 325 nvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdGasavhvhmtntrntd 405
                                   nvetsqr++dv +  l+++lp  v+Aas+gtm n+++gg  +  g++++yyeti+gG+GArp  dG+savh++mtnt nt+
  gi|70606207|ref|YP_255077.1| 319 NVETSQRIADVTFLSLSKFLP--VPAASSGTMMNIMMGGFYK--GRYWSYYETIGGGSGARPSEDGISAVHSNMTNTLNTP 395
                                   ******************995..****************998..99*********************************** PP

                Hydantoinase_B 406 vEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGepGargrvvlnllvr..g 484
                                   +E+ E+ yP+l++++ +r +sgG+Gky+GGdG++r++++l+p ++++++++r  + pwGl+GGe G++g++++    +  +
  gi|70606207|ref|YP_255077.1| 396 IEVAESVYPLLFTSYTVRVGSGGKGKYKGGDGIIRSFKVLSP-TRLALMADRFIIGPWGLNGGERGKPGKATV---RKrsD 472
                                   *****************************************9.***************************654...33358 PP

                Hydantoinase_B 485 eeenlggkatvelkagdvlvietpGGGGyGd 515
                                   e ++l++k+ vel++gd ++ietpGGGGyG+
  gi|70606207|ref|YP_255077.1| 473 ELVSLKSKCVVELDEGDEVIIETPGGGGYGS 503
                                   8999999999********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2988.94
//
Query:       gi|70606208|ref|YP_255078.1|  [L=640]
Description: 5-oxoprolinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-98  328.1   0.2      7e-96  320.9   0.1    2.2  2  Hydantoinase_A  Hydantoinase/oxoprolinase
      7e-50  169.2   0.0    1.2e-49  168.4   0.0    1.4  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
     0.0003   19.5   0.1       0.45    9.0   0.0    2.2  2  MutL            MutL protein
      0.002   17.7   0.8     0.0037   16.8   0.1    1.8  3  ROK             ROK family
  ------ inclusion threshold ------
      0.046   13.2   0.0       0.16   11.4   0.0    1.9  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
       0.22   11.1   0.1       0.64    9.5   0.0    1.7  2  FGGY_N          FGGY family of carbohydrate kinases, N-termin


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0034        10      81      98 ..       2      19 ..       1      50 [. 0.87
   2 !  320.9   0.1   2.3e-99     7e-96       1     286 [.     192     474 ..     192     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0034
                Hydantoinase_A 81 vItfDmGGTstDvslikd 98
                                  ++ +D+GGT tD+++i++
  gi|70606208|ref|YP_255078.1|  2 IVAVDVGGTFTDAIAIDE 19
                                  689************983 PP

  == domain 2  score: 320.9 bits;  conditional E-value: 2.3e-99
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   rt+t+v+nA+l+pi+++yles++k +        l++m+s+Gglv++de++k+pv++i+SGPaaGvvga+ +s+l g ++v
  gi|70606208|ref|YP_255078.1| 192 RTSTTVINAMLMPIVSRYLESISKDIPS------LYIMSSSGGLVDVDEVKKRPVQIIESGPAAGVVGAQVFSQLLGISNV 266
                                   89************************88......9********************************************** PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagad 150
                                   I fDmGGT++++  i ++e+e+++e+e+            +g++vr+p++d+++v+agGg+i+++degg+lrvgp sagad
  gi|70606208|ref|YP_255078.1| 267 ISFDMGGTTAKAGSIVNNEIEITSEYEVggkahhgrlvkgSGYPVRFPFIDLAEVSAGGGTIIWRDEGGALRVGPISAGAD 347
                                   ********************************************************************************* PP

                Hydantoinase_A 151 pgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrk 231
                                   pgp++y kGg+++t+TDanlvLGr+++  +l   +g+++ldve ar  +e+l++++     ev+++++++a+ +ma+a+r 
  gi|70606208|ref|YP_255078.1| 348 PGPIAYMKGGDKPTLTDANLVLGRINEY-LL---SGNMRLDVEGARSGLEKLGDPI-----EVSYQAVKLASIEMARAIRL 419
                                   **************************98.67...7*********************.....9******************* PP

                Hydantoinase_A 232 lsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAd 286
                                   ++vergldp+e+tl++fGGaG+q a  +aeelg+k++ivpp++g++sal++++ d
  gi|70606208|ref|YP_255078.1| 420 VTVERGLDPTEFTLFAFGGAGPQWAVDVAEELGIKRIIVPPHPGLFSALSLLAVD 474
                                   *************************************************998765 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   0.0     4e-53   1.2e-49       2     177 ..       3     173 ..       2     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 4e-53
                    Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg...erv 79 
                                   +++DvGGTfTDa+a+de+ + ++ +K lstp++++ g+r+a+ee+       + k+d v+++TTvatNa+l + +   +++
  gi|70606208|ref|YP_255078.1|   3 VAVDVGGTFTDAIAIDEN-GNIKYYKGLSTPRNPEVGLRKAIEEL-------NVKVDRVIHATTVATNAFLGQLNlelPKT 75 
                                   79**************99.99***********************9.......789******************99999*** PP

                    Hydant_A_N  80 aLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvll 158
                                   aLittkgf+d++eigrqnrp+l+++ ++  kplv++e ++ev+er+ +dg+vl +l+  e+ e++ +lk+  ves+av++l
  gi|70606208|ref|YP_255078.1|  76 ALITTKGFKDIIEIGRQNRPELYDMYFHkpKPLVPRELRFEVNERTLFDGKVLVKLNPLEIDEIAVRLKD--VESVAVSFL 154
                                   ************************9999999*************************************96..8******** PP

                    Hydant_A_N 159 hSylnpehElrvaeiarei 177
                                   hSy+npe+E  ++e+++++
  gi|70606208|ref|YP_255078.1| 155 HSYANPENEDVAKEVLSKH 173
                                   **************99876 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00022      0.65       1      66 [.       2      61 ..       2      72 .. 0.70
   2 !    9.0   0.0   0.00015      0.45     213     273 ..     232     290 ..     190     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00022
                          MutL  1 ilviDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgktevdevlat 66
                                  i+++D+G t+T ++++d++    ++    + ++t    +   Gl++a+eel+ k ++   ++ +at
  gi|70606208|ref|YP_255078.1|  2 IVAVDVGGTFTDAIAIDENG---NIK-YYKGLSTPR--NPEVGLRKAIEELNVKVDRVIHATTVAT 61
                                  689***************54...444.445555553..4568999999999998776555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00015
                          MutL 213 lskleelvsaeimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekek 273
                                   ++++++   + i   PaA + +++++++    g+ +++ +D+GG+T    s+++++ e+++
  gi|70606208|ref|YP_255078.1| 232 VDEVKKRPVQIIESGPAAGVVGAQVFSQ--LLGISNVISFDMGGTTAKAGSIVNNEIEITS 290
                                   455556666778899*************..55778****************9877766554 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.2e-06    0.0037       2      56 ..       3      56 ..       2      81 .. 0.85
   2 ?   -3.2   0.0       1.5   4.5e+03     191     219 ..     130     158 ..     124     169 .. 0.87
   3 ?   -3.4   0.0       1.8   5.3e+03       2      25 ..     267     291 ..     266     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                                  EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTE CS
                           ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkade 56
                                  +++d+Ggt + ++ +de+g+i + + +  +  ++e +l++ai+el  + +r  ++
  gi|70606208|ref|YP_255078.1|  3 VAVDVGGTFTDAIAIDENGNIKYYKGL-STPRNPEVGLRKAIEELNVKVDRVIHA 56
                                  79*************************.55568999*********9999888773 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                                   CGTTS-HHHHHHHHCTT-HHHHHHHHHHH CS
                           ROK 191 kgekleakeiiklaekgdevaeevverla 219
                                   k++ le++ei ++ +  ++va+ +++++a
  gi|70606208|ref|YP_255078.1| 130 KLNPLEIDEIAVRLKDVESVAVSFLHSYA 158
                                   678899999*9999999999999999887 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.8
                                   EEEEE-SSEEEEE.EEETTS-EEEE CS
                           ROK   2 igidiGgtkiala.lvdeegeilar 25 
                                   i+ d+Ggt +++  +v++e ei ++
  gi|70606208|ref|YP_255078.1| 267 ISFDMGGTTAKAGsIVNNEIEITSE 291
                                   6789999998875266777777665 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.3e-05      0.16       3      52 ..       5      54 ..       3     174 .. 0.89
   2 ?   -1.2   0.0      0.38   1.1e+03       4      70 ..     270     439 ..     269     442 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                                  EEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH.........HHHHHHH CS
                   BcrAD_BadFG  3 iDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaaekvleealteal 52
                                  +D+G+T t a+ +de+g+    +g+++++n e v+ ++a + l+  ++ ++
  gi|70606208|ref|YP_255078.1|  5 VDVGGTFTDAIAIDENGNiKYYKGLSTPRNPE-VGLRKAIEELNVKVDRVI 54
                                  9*****************66789999999988.887777777666555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                                   EE-SSEEEE.EEEETTTEEEEEEEE--...................................................... CS
                   BcrAD_BadFG   4 DgGsTttka.vlmdekgevlgrgitns...................................................... 29 
                                   D+G+Tt ka  +++++ e+  ++  ++                                                      
  gi|70606208|ref|YP_255078.1| 270 DMGGTTAKAgSIVNNEIEITSEYEVGGkahhgrlvkgsgypvrfpfidlaevsagggtiiwrdeggalrvgpisagadpgp 350
                                   777777777334444444444433333444444555555555555555555555555555555555555555555555555 PP

                                   ................................................TTS-HHH.........HHHHHHHHHHT--GGGE CS
                   BcrAD_BadFG  30 ................................................anlesvrfeaaekvleealtealerageeeadi 62 
                                                                                    +++   ++ a   + +a++ ++ + g++++++
  gi|70606208|ref|YP_255078.1| 351 iaymkggdkptltdanlvlgrineyllsgnmrldvegarsgleklgdpIEVSYQAVKLASIEMARAIRLVTVERGLDPTEF 431
                                   555555555555555555555555555555555555555555555533222222333344444566667777777666666 PP

                                   CEE..EEE CS
                   BcrAD_BadFG  63 eetylvgt 70 
                                      +++g+
  gi|70606208|ref|YP_255078.1| 432 TLFAFGGA 439
                                   66666665 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00021      0.64       1      24 [.       1      24 [.       1      84 [. 0.79
   2 ?   -1.9   0.0      0.67     2e+03       2      25 ..     266     290 ..     266     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                                  EEEEEEEESSEEEEEEEETTS-EE CS
                        FGGY_N  1 lilglDcGttstkaivldekgkvv 24
                                  +i+++D+G+t+t ai++de+g++ 
  gi|70606208|ref|YP_255078.1|  1 MIVAVDVGGTFTDAIAIDENGNIK 24
                                  79*******************995 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.67
                                   EEEEEEESSEEEEE.EEETTS-EEE CS
                        FGGY_N   2 ilglDcGttstkai.vldekgkvva 25 
                                   ++++D+G+t  ka  +++++ ++ +
  gi|70606208|ref|YP_255078.1| 266 VISFDMGGTTAKAGsIVNNEIEITS 290
                                   5899********9636667766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3844.00
//
Query:       gi|70606209|ref|YP_255079.1|  [L=199]
Description: hypothetical protein Saci_0370 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-14   51.7   0.0    1.3e-13   51.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    6.1e-12   46.1   0.0    1.2e-11   45.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
      6e-11   43.0   0.0    9.3e-11   42.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.3e-09   37.8   0.0    3.6e-09   37.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.1e-08   32.4   0.0    7.7e-08   32.1   0.0    1.2  1  MTS              Methyltransferase small domain
    1.6e-06   27.6   0.0      2e-06   27.3   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    3.1e-06   27.1   0.0    4.1e-06   26.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.6e-05   24.5   0.0    2.2e-05   24.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00022   21.2   0.0    0.00029   20.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0016   18.1   0.0     0.0019   17.9   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0026   17.6   0.0     0.0048   16.7   0.0    1.4  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0089   15.5   0.1      0.071   12.6   0.2    2.0  2  CheR             CheR methyltransferase, SAM binding domain
  ------ inclusion threshold ------
       0.02   14.4   0.1      0.062   12.8   0.0    1.7  2  DOT1             Histone methylation protein DOT1
      0.045   13.2   0.0      0.083   12.4   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
      0.052   12.9   0.0      0.064   12.6   0.0    1.1  1  NAS              Nicotianamine synthase protein
      0.077   13.3   0.0       0.12   12.7   0.0    1.3  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   1.1e-16   1.3e-13       2     108 ..      39     150 ..      38     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 1.1e-16
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseea......ielArenaqklgld.nveFeqgdieeleklledekf 75 
                                   dk+++vlD+GCG G+l+++   + +pka++ GiD  e++       ++A+en ++lg+  +v F++ ++ ++    e   f
  gi|70606209|ref|YP_255079.1|  39 DKEISVLDVGCGLGFLSYVVT-QYFPKAKILGIDTFENSslldsdMRKAEENMEHLGIRdRVFFKRLNVLDIT--EELGHF 116
                                   7899*****************.889*********98876555555799**********99***********77..34588* PP

               Methyltransf_31  76 Dlilsnevl.naladpdkileeiervlkpggill 108
                                   D+++sn v+ n+     +++e+i++v+kp + ++
  gi|70606209|ref|YP_255079.1| 117 DIVVSNLVFhNLGRRRFEAYEKITKVMKPSSFFI 150
                                   *********88889999************99887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.1e-14   1.2e-11       1      95 [.      44     145 ..      44     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.1e-14
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHH......HHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseeml......eaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga 73 
                                   vLd+GcG G l+  + + ++kak++g+D  e+        ++a+e++e+ g+  +v f + ++ d+ +e g+fD+vvs+ +
  gi|70606209|ref|YP_255079.1|  44 VLDVGCGLGFLSYVVTQYFPKAKILGIDTFENSSlldsdmRKAEENMEHLGIrdRVFFKRLNVLDITEELGHFDIVVSNLV 124
                                   9******************99*******97665334544478888888888899************************777 PP

                                   GGGSSHHHHHHHHHHHHHHEEE CS
               Methyltransf_25  74 lhhlsdedlekalkeiarvLkp 95 
                                   +h l +++  +a+++i +v+kp
  gi|70606209|ref|YP_255079.1| 125 FHNLGRRR-FEAYEKITKVMKP 145
                                   99999655.669*********9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   8.3e-14   9.3e-11       1      96 [.      45     146 ..      45     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.3e-14
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsai......edakeklakrennnnnnvelealdlldldgg.ssfDlvvasn 74 
                                   L++GcG G l+ ++ +++p ++++g+D  +++        +a+e + + + ++  +v ++ l++ld  ++ ++fD+vv++ 
  gi|70606209|ref|YP_255079.1|  45 LDVGCGLGFLSYVVTQYFPKAKILGIDTFENSSlldsdmRKAEENMEHLGIRD--RVFFKRLNVLDITEElGHFDIVVSNL 123
                                   8****************************999889997666666666666555..55555555554444456********* PP

               Methyltransf_12  75 vlhhlkdir.evldnirklLkpg 96 
                                   v+h+l  +r e+ ++i k++kp 
  gi|70606209|ref|YP_255079.1| 124 VFHNLGRRRfEAYEKITKVMKPS 146
                                   *****55555***********95 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   3.2e-12   3.6e-09       1      95 [.      45     150 ..      45     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 3.2e-12
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHH......HHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskeml......klakekaseegl....kvefvvadaeklpfednsfDlvvsse 69 
                                   LdvGcG G l+  +++++  a+++g+D+ ++        + a+e+ +   l    +v f + ++ ++  e + fD+vvs+ 
  gi|70606209|ref|YP_255079.1|  45 LDVGCGLGFLSYVVTQYFpkAKILGIDTFENSSlldsdmRKAEENMEH--LgirdRVFFKRLNVLDITEELGHFDIVVSNL 123
                                   8**************999************999776643334444444..3669988899999999998999********* PP

                                   -CCC-.CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  70 vlhhv.edpekalkeiaRvLkpgGllv 95 
                                   v+h++  ++ +a ++i +v+kp  +++
  gi|70606209|ref|YP_255079.1| 124 VFHNLgRRRFEAYEKITKVMKPSSFFI 150
                                   *****999**************87765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.9e-11   7.7e-08      25     123 ..      34     141 ..      23     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.9e-11
                                   HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEES..BHHHHHH....HHHHHHHTTGC..EEEEE-STTTTSTT.S CS
                           MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdv..darAles....akenleankle..vevvasdvleevee.k 96 
                                   + lp +++ +vlD+GcG G+l+ ++ +  p+a++  +d   +   l+s    a+en+e+ +++  v +   +vl+ +ee +
  gi|70606209|ref|YP_255079.1|  34 TGLPRDKEISVLDVGCGLGFLSYVVTQYFPKAKILGIDTfeNSSLLDSdmrkAEENMEHLGIRdrVFFKRLNVLDITEElG 114
                                   4577778888***********************999996224444555111155555555555875555666666665336 PP

                                   -EEEEEE---STTTCHCHHHHHHHHHH CS
                           MTS  97 kfdlivsNPPfhagkatelavaeelia 123
                                   +fd++vsN  fh+    + ++ e++ +
  gi|70606209|ref|YP_255079.1| 115 HFDIVVSNLVFHNLGRRRFEAYEKITK 141
                                   ************988888888777765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.7e-09     2e-06      65     170 ..      43     157 ..      16     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                                   EEEEES-TTSHHHHHHHHHH.--EEEEE......ES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---...--SEEEEES CS
                          CMAS  65 tlLdiGcGWGslvrravery.dvkvvgl......TlSkeqaklakkrvdeldlerkvevklldyedlde...kvdrvvsvg 135
                                    +Ld+GcG G l     + +  +k++g+       l +  +++a++++++l+++++v  k l+  d+ e   ++d vvs  
  gi|70606209|ref|YP_255079.1|  43 SVLDVGCGLGFLSYVVTQYFpKAKILGIdtfensSLLDSDMRKAEENMEHLGIRDRVFFKRLNVLDITEelgHFDIVVSNL 123
                                   69********9876655555779****94222222445578899999**********9999999999998999******** PP

                                   -GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE- CS
                          CMAS 136 afehvgkenydtffkklkkllkedGllllhtitsl 170
                                   +f  +g ++++++ +k++k++k+   +++  i+  
  gi|70606209|ref|YP_255079.1| 124 VFHNLGRRRFEAY-EKITKVMKPSSFFINGDIFFG 157
                                   ************9.678899999988888777654 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   3.7e-09   4.1e-06      13      95 ..      31     128 ..      16     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-09
               Methyltransf_23  13 lerllpklraggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiaekakkaqkdqfdeq................ 74 
                                    ++++  +++  +vLd+GcG G +l++   +++   ++ g+D  ++ + +    + ++k  ++ +                
  gi|70606209|ref|YP_255079.1|  31 FMKTGLPRDKEISVLDVGCGLG-FLSYVvTQYFPkaKILGIDTFENSSLLD---SDMRKAEENMEhlgirdrvffkrlnvl 107
                                   444444488899**********.6666624444368*******86654443...333333332223445555555556666 PP

               Methyltransf_23  75 eaaepqgkfdlIvlrevlehv 95 
                                   +++e+ g+fd++v++ v++++
  gi|70606209|ref|YP_255079.1| 108 DITEELGHFDIVVSNLVFHNL 128
                                   8888999*********99986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.9e-08   2.2e-05     158     257 ..      25     150 ..       3     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.9e-08
                          PrmA 158 l............vkegeevlDvGtGSGiLa.iaaakLgakkvvavDiDevA......vkvakeNaelNkveakleva..l 217
                                                  ++ +vlDvG+G G L+ ++ + +  +k++++D+ e +      ++ a+eN+e  ++++++  +  +
  gi|70606209|ref|YP_255079.1|  25 ElffqafmktglpRDKEISVLDVGCGLGFLSyVVTQYFPKAKILGIDTFENSslldsdMRKAEENMEHLGIRDRVFFKrlN 105
                                   2455555555543334449************5667789999******8765433333378999999999999988442112 PP

                          PrmA 218 seellk.eekadvivaNILaevl....ielaedikklvkegglli 257
                                     ++++  +++d++v+N + + l     e +e+i+k++k+++ +i
  gi|70606209|ref|YP_255079.1| 106 VLDITEeLGHFDIVVSNLVFHNLgrrrFEAYEKITKVMKPSSFFI 150
                                   3344434689*******9988873322345677777777777776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.6e-07   0.00029      16      66 ..      31      81 ..      17     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-07
               Methyltransf_32 16 llkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgida..keelvek 66
                                  ++k+   ++++++v+DvG+G g+Ls v+ +      k k++gid+  +++l ++
  gi|70606209|ref|YP_255079.1| 31 FMKTGLPRDKEISVLDVGCGLGFLSYVVTQ---YfPKAKILGIDTfeNSSLLDS 81
                                  55555677899*****************99...43799******9333344444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0019      89     129 ..      83     123 ..      29     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE-- CS
                       UPF0020  89 vqgareNaekagvgdliefsqadaakLrlkegevdvivtnp 129
                                   +++a+eN e+ g+ d++ f+ +++ +++++ g +d++v+n+
  gi|70606209|ref|YP_255079.1|  83 MRKAEENMEHLGIRDRVFFKRLNVLDITEELGHFDIVVSNL 123
                                   689*************************9999********7 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.3e-06    0.0048      64     124 ..      31      96 ..      21     115 .. 0.73
   2 ?   -3.0   0.0       4.6   5.1e+03       6      26 ..     124     144 ..     119     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-06
                                   HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHH..H....HHHHHHHHHHCTTC CS
                          PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierike..l....veeakrnlkkldle 124
                                   ++   l  +k  +vL+vG+G G+l+ v+++++ + +++++i+  ++  l    +++a++n+++l+++
  gi|70606209|ref|YP_255079.1|  31 FMKTGLPRDKEISVLDVGCGLGFLSYVVTQYFPK-AKILGIDTFENssLldsdMRKAEENMEHLGIR 96 
                                   5555566688899******************965.569***98764224222245666666666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                                   HHHHHHHTTS---HHHHHHHH CS
                          PCMT   6 lieelkkkgviksdkvaeale 26 
                                   ++++l ++++ + +k++++++
  gi|70606209|ref|YP_255079.1| 124 VFHNLGRRRFEAYEKITKVMK 144
                                   678899999999999999996 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.26     3e+02      29      47 ..      38      56 ..      15      73 .. 0.74
   2 !   12.6   0.2   6.4e-05     0.071     115     172 ..      94     150 ..      60     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.26
                                  TSSSEEEEEES-TTTHHHH CS
                          CheR 29 nekrvriwsagcssGeEpY 47
                                  + k+++++ +gc+ G  +Y
  gi|70606209|ref|YP_255079.1| 38 RDKEISVLDVGCGLGFLSY 56
                                  348999******9996555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.4e-05
                                   HHHTTEEEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEE CS
                          CheR 115 eikelvkFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLl 172
                                    i+++v F++ln+l+  + lg++D++++  v+  +   ++ + +e++ + +kp+++ +
  gi|70606209|ref|YP_255079.1|  94 GIRDRVFFKRLNVLDITEELGHFDIVVSNLVFHNLG-RRRFEAYEKITKVMKPSSFFI 150
                                   599************999********9866655554.456778888888888888766 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05     0.062      43     100 ..      41      97 ..      16     125 .. 0.81
   2 ?   -0.7   0.0      0.74   8.3e+02     106     160 ..     129     183 ..     107     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                   T-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB-- CS
                          DOT1  43 edvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkkl 100
                                   e   +D G G+G +   ++ ++  ++ +G++  +n s l  + ++  ++ ++++G++ 
  gi|70606209|ref|YP_255079.1|  41 EISVLDVGCGLGFLSYVVTQYFPKAKILGIDTFENSSLLDSD-MRKAEENMEHLGIRD 97 
                                   34568*****************************98877655.566788999999985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                                   ESS-STT-HHHHHHGGG-SEEEE--TT--HHHHHHHHHHHTT--TT-EEEESS-S CS
                          DOT1 106 irksFvenekveeiieeadvilvNNfaFdaelnkqlkellqdlkegtkiislksl 160
                                    r+ F   ek++++++ ++  +   + F++e +k+ +  +  l +  k+i +k l
  gi|70606209|ref|YP_255079.1| 129 GRRRFEAYEKITKVMKPSSFFINGDIFFGSEPEKSFEADISRLSKIFKLIFSKRL 183
                                   3677777788888866655544445667777777777777777777777777665 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.4e-05     0.083       3      38 ..      42      77 ..      40     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.4e-05
                                  EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHH CS
                Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvv 38
                                    vl++GcG G +     + +P+ ++lGi+  ++++
  gi|70606209|ref|YP_255079.1| 42 ISVLDVGCGLGFLSYVVTQYFPKAKILGIDTFENSS 77
                                  679***************************988764 PP

>> NAS  Nicotianamine synthase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.064     134     224 ..      53     147 ..      24     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                           NAS 134 ltslvlaskhlskti...fdnlDkdglandkasklvs..adedlssrmsfhtadvldvteelkaydvvflAAlvGmakeeK 209
                                   + s v+ ++  +k+    +d++++ +l ++  +k  +  +  +++ r+ f+  +vld teel ++d+v+         + +
  gi|70606209|ref|YP_255079.1|  53 FLSYVVTQY-FPKAKilgIDTFENSSLLDSDMRKAEEnmEHLGIRDRVFFKRLNVLDITEELGHFDIVVSNLVFHNLGRRR 132
                                   445444433.343330113444444443333333333112345689*********************97554444555677 PP

                           NAS 210 akviehlakkmakGa 224
                                    ++ e+++k+m++ +
  gi|70606209|ref|YP_255079.1| 133 FEAYEKITKVMKPSS 147
                                   788888888888766 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.12      45      77 ..      27      59 ..       6      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                  AdoMet_MTase 45 ylivlwkktrseeketsfvdvgcgngllvyvla 77
                                  ++  + k     +ke s  dvgcg g+l yv++
  gi|70606209|ref|YP_255079.1| 27 FFQAFMKTGLPRDKEISVLDVGCGLGFLSYVVT 59
                                  55555556666799****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1234.78
//
Query:       gi|70606210|ref|YP_255080.1|  [L=372]
Description: hypothetical protein Saci_0371 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-25   89.9  61.1    5.6e-21   74.9  28.4    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        2.6    8.0   5.3         36    4.4   2.5    3.1  2  SafA      Two-component-system connector protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9  28.4   6.2e-25   5.6e-21       8     293 ..      13     276 ..       6     276 .. 0.81
   2 !   28.7  24.6   6.6e-11   5.9e-07      15     172 ..     204     363 ..     190     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 6.2e-25
                         MFS_1   8 salarsi...lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fass 84 
                                   +++  si    + al ++l++ +++s  ++ l +tl+++++++a++++G+++d+ G++r+ +++ +l+++g +l++ ++++
  gi|70606210|ref|YP_255080.1|  13 IMCFNSIyqySWNALQPLLKSGFNVSLVQVALGFTLFSIFSSLAQPLGGHFADKQGPKRIGIIAGILSSIG-FLGTyLSPN 92 
                                   22222222436666766999***************************************999999999999.666636699 PP

                         MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                   +++++ ++ + ++g+g+l+ ++a l+ +wf + ++g a+g++s+g ++G++l  ++ ++ +   ++  + + +++  ++++
  gi|70606210|ref|YP_255080.1|  93 IYVFYTVWSIGSAGEGILYGIAANLAMKWFED-KKGVATGVVSMGLGIGSALLNPFIAMAT---SYKTITLGIGLTEVIVL 169
                                   99*****************************9.*****************99988888777...89999999999999996 PP

                         MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevlglsglll 245
                                       +ll+ ++ ++  + ++++              ++ +   +w l+++++++ ++ ++ +++ l +      g +   +
  gi|70606210|ref|YP_255080.1| 170 P---ILLWLSDYPKLLSGQAPR--------------QIITTTRFW-LIYVSFVTVLVPFSvISSQLSV---LGKGVP-QQE 228
                                   6...556666666666544444..............677788899.6666666644444426666666...477777.566 PP

                         MFS_1 246 aglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                                   + +l++ll l++ +l++++g ++drlg  r++l+  l ++l+al+l+l
  gi|70606210|ref|YP_255080.1| 229 LITLISLLPLLSGGLRPFFGMVADRLGIIRTTLILDLTITLGALFLLL 276
                                   6666*****************************999999999999875 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 6.6e-11
                         MFS_1  15 lgpalpl.alaedlg.....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlll 89 
                                   +++++p   ++++l      +  +e+ +l++l  l+++ + +++G ++dr+G  r+ l+  l+  lg+l+ll+ ++   ++
  gi|70606210|ref|YP_255080.1| 204 VTVLVPFsVISSQLSvlgkgVPQQELITLISLLPLLSGGLRPFFGMVADRLGIIRTTLILDLTITLGALFLLL-NQ---IA 280
                                   3334444455555444444499999999************************999666666666666466665.77...** PP

                         MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav...fyilaivsllafvl 167
                                   ++ +l Gl +g+++++   ++ ++f  +  +   g+l++g +lG  lg ++ ++l+ s++ +++    +i++i+++la++l
  gi|70606210|ref|YP_255080.1| 281 ISTILVGLSGGSMITLYFNVAGEIFGTRFSTVNSGILYTGKALGGTLGSVVFAILY-SINLQLSemySLICGIIGILALLL 360
                                   ********************************************************.666444433367777777777665 PP

                         MFS_1 168 fllll 172
                                     +++
  gi|70606210|ref|YP_255080.1| 361 --VVF 363
                                   ..333 PP

>> SafA  Two-component-system connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.016   1.5e+02      23      42 ..      38      57 ..      31      60 .. 0.81
   2 ?    4.4   2.5     0.004        36      25      47 ..     261     283 ..     253     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                          SafA 23 ivvvllltltliaifsaidq 42
                                   +v + l +tl +ifs++ q
  gi|70606210|ref|YP_255080.1| 38 SLVQVALGFTLFSIFSSLAQ 57
                                  556778999*******9877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.004
                          SafA  25 vvllltltliaifsaidqlsise 47 
                                   ++l lt+tl a+f  ++q++is 
  gi|70606210|ref|YP_255080.1| 261 LILDLTITLGALFLLLNQIAIST 283
                                   57889****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2415.49
//
Query:       gi|70606211|ref|YP_255081.1|  [L=782]
Description: leucyl aminopeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-83  280.2   2.1    1.6e-83  279.6   2.1    1.3  1  Peptidase_M1    Peptidase family M1 domain
      4e-35  121.7   0.1    8.3e-35  120.7   0.1    1.6  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
    3.9e-31  108.8   0.6    5.8e-31  108.2   0.6    1.3  1  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.053   12.9   0.1        0.1   12.0   0.1    1.3  1  Aminopep        Putative aminopeptidase
       0.18   11.6   0.1       0.36   10.6   0.1    1.5  1  DUF2807         Putative auto-transporter adhesin, head GIN d


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.6   2.1   4.5e-87   1.6e-83       1     218 []     202     418 ..     202     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 279.6 bits;  conditional E-value: 4.5e-87
                                   HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBT CS
                  Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfG 81 
                                   ++lev+kk+++f++eyf+++Y+lpk +l+a+p+f++gAMEnwg+it+re++ll+d e+ss  ++ +vaev+aHElaHqWfG
  gi|70606211|ref|YP_255081.1| 202 FSLEVGKKVINFYNEYFGIKYQLPKEHLIAIPEFAFGAMENWGAITFRETALLAD-EKSSVIQRMRVAEVVAHELAHQWFG 281
                                   789****************************************************.777888999**************** PP

                                   TTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHH CS
                  Peptidase_M1  82 nlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKG 162
                                   +lVtmkwWddlwLnE+fat+++y+ +d+l+p+w++  +++ +e++ a+ +d+l+++hpi+ +v++p+ei+++Fd i+Y KG
  gi|70606211|ref|YP_255081.1| 282 DLVTMKWWDDLWLNESFATFMSYKAIDHLFPNWDMFGDFIHSETSGAMLRDSLSTTHPIEAHVKSPEEIEQIFDDISYGKG 362
                                   ********************************************************************************* PP

                                   HHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                  Peptidase_M1 163 asllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                   as+lrm+e ++g+e Fqkg+++Yl+++k++nae +d+w++l+ea+++ i +v++ w
  gi|70606211|ref|YP_255081.1| 363 ASILRMIEGYMGKEAFQKGIQNYLQKYKFSNAEGQDFWNSLQEASGLPIADVVKDW 418
                                   *****************************************************999 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.1   2.3e-38   8.3e-35       4     186 .]       5     168 ..       2     168 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.3e-38
                                   EEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETTC CS
                Peptidase_M1_N   4 hYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqts 84 
                                   +Y++ l+ d+k+ +++G+ +i  +l    +e+vlda  + i      ++v++++++id   +++d+e+l+ik+ +      
  gi|70606211|ref|YP_255081.1|   5 KYEVYLDFDFKNLSYRGKEKIYCSLD---DELVLDAIGFSI------HSVRINGKEID---YNYDGEKLRIKTGK-----F 68 
                                   7************************9...************......88899999999...789******99998.....4 PP

                                   EEEEEEEEEEE-.BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCE CS
                Peptidase_M1_N  85 kytLeieyegel.ndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeees 164
                                     t+e++++g++ + +l G+yk  Y  +g+k+++v+Tqfe+ +AR+++PC+D Ps+KA f+i+++++k+  ++Snmp++++
  gi|70606211|ref|YP_255081.1|  69 DGTIEVDFTGKVrERELVGIYKAPY--DGGKNYIVSTQFESNHARKFIPCVDHPSYKAVFKIQVRVDKDLDVISNMPIQKV 147
                                   68**********8889******886..78899***********************************************99 PP

                                   EEETTCEEEEEEEEEESBEGGG CS
                Peptidase_M1_N 165 eklengqkiteFeqtpkmstYL 186
                                   +++++ +k +eF +tpkmstYL
  gi|70606211|ref|YP_255081.1| 148 TEEGD-KKLVEFYETPKMSTYL 168
                                   99985.77*************9 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.6   1.6e-34   5.8e-31       2     314 ..     487     776 ..     486     777 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 1.6e-34
                                   EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHHH CS
                       ERAP1_C   2 vllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqalsq 82 
                                   +++N d  G+yrV Y  ++l+++l+ ++++     +R gl++d ++l  ag++s++ + + ++ ++ n+++ylv++++ +q
  gi|70606211|ref|YP_255081.1| 487 LKVNLDRVGFYRVEY--DNLDLFLN-ANPN---HYERWGLLDDYYNLLLAGRISYEVYENAVKELM-NDDNYLVVDEIRGQ 560
                                   599************..68****99.5555...99****************************995.************** PP

                                   HHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-H CS
                       ERAP1_C  83 latlksllsadplyaalkaflrklleplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawlegddlipp 163
                                   l  l ++  +++ y+ + +fl+  l +  ++       ++l + +  +ll+ +++ + ++  + +   f+++ +   +++p
  gi|70606211|ref|YP_255081.1| 561 LFFLWTV--NPSKYTLITDFLELQLPKWSKRT------DDLSQRVYGNLLRSFAYVD-DRFAQGLSISFDNY-D---SLNP 628
                                   ***8655..45557677766666665555544......4499999999999996666.569999999*****.4...5*** PP

                                   HHHHHHHHHHHHHS-HHHHHHHHHHHHC-S.SHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HST CS
                       ERAP1_C 164 dlrwavycalaanggeaewdallerykdts.apsekeaalralaatpdpellerllnfvlesdevrnqdlrallaglannp 243
                                   +l+ av  a a + ge+++d+ll +y++++ + +ek+++l+a+ ++++p l+  +l ++l ++e++ qd+  ++   + np
  gi|70606211|ref|YP_255081.1| 629 NLKEAVAIAYAITQGENGYDELLRKYREEKfD-EEKQRILNAMLSFREPYLVVNTLSLAL-NGEIKRQDTARIIPLASANP 707
                                   ******99999889************999955.***************************.99*********96544559* PP

                                   THHHHHHHHHHHCHCCHHHHTSSTSCHHHHHHHHHTT--SHHHHHHHHHHHCHTT--GGGHHHHHHHHHHH CS
                       ERAP1_C 244 egrellwefvkenwdalakrwsggeildrivkgllpgftseeelaeieaffadkdtpglrrtlkqaletvr 314
                                     r ++w + k++ + l ++++g+ il+r  +g++p +    ++ e+e++f++++ p+ +  +k ale ++
  gi|70606211|ref|YP_255081.1| 708 YSRFAVWRWTKTYMEFLRSIYAGTGILGRSFRGAIPYLG--LNIPEVEEYFTSNKFPEMEVEIKSALEILK 776
                                   **********************988***********999..89*****************99999999876 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.8e-05       0.1     146     185 ..     263     308 ..     258     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                      Aminopep 146 seeelarlifHElaHq......vlYvkgdtafnEsfAtaVeregve 185
                                   ++ ++a+++ HElaHq      ++   +d   nEsfAt++  +++ 
  gi|70606211|ref|YP_255081.1| 263 QRMRVAEVVAHELAHQwfgdlvTMKWWDDLWLNESFATFMSYKAID 308
                                   57899**********9444433334569***********9887765 PP

>> DUF2807  Putative auto-transporter adhesin, head GIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0001      0.36      33      97 ..     425     495 ..     419     511 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                   CCEEEEEETTEEEEEE-.....TTTTSSB.....EEEEEEES--SEEEEECCEEEEE-S-EEEEEEEEEEECSE CS
                       DUF2807  33 ekvevevedgtLkirle.....kefestk....tlkvtvtvpnleelelsgsgsievegtlkadklelniagsg 97 
                                   + v+veve+ ++++++e     + ++ ++    +l+++v+ + +++l  + s +i+v ++   ++l++n+   g
  gi|70606211|ref|YP_255081.1| 425 PAVKVEVEGTKIRLYQErfsltP-LNENTtyliPLTLEVNGKRITQLMKEQSMTIDVGSE--VKSLKVNLDRVG 495
                                   679**************998852.33333578899************************5..555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (782 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 5025.06
//
Query:       gi|70606212|ref|YP_255082.1|  [L=942]
Description: leucyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-55  188.1   0.0    3.9e-54  183.9   0.0    2.3  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.5e-27   96.4   0.2    4.2e-14   52.1   0.0    3.5  3  tRNA-synt_1g   tRNA synthetases class I (M)
    7.5e-21   74.7   0.5    1.9e-20   73.4   0.5    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.2e-13   50.2   0.0      5e-13   49.0   0.0    1.5  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    2.7e-13   49.9   1.2      3e-05   23.5   0.1    3.2  4  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.035   13.0   0.0       0.82    8.5   0.0    2.2  2  tRNA-synt_1f   tRNA synthetases class I (K)
      0.042   13.9   0.4        0.1   12.7   0.4    1.6  1  sCache_like    Single Cache-like


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   1.5e-57   3.9e-54       1     601 [.      10     663 ..      10     664 .. 0.80

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.5e-57
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                   k+++ W+ e v+++ ++ +kek +f +++  Py +  lHiGh  + +  di  ry rmkG++vl+ + +   G +i +  +
  gi|70606212|ref|YP_255082.1|  10 KWQKVWDSERVYEADVDRTKEK-KF-ITVAFPYTNSPLHIGHGRTYITADIYARYLRMKGYNVLFPFAFQFTGTPILSIAD 88 
                                   5899***********6555544.45.566789******************************************9988776 PP

                   tRNA-synt_1  82 kklgakekke......rkkl..gr.eefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladk 153
                                   +   + +++       ++++  g+  +f +      a+++e++r++   lG s+D  re  T+d+ +e  v++ ++rl + 
  gi|70606212|ref|YP_255082.1|  89 AVK-RGDEEIistftnVYQIpiGViSKFSD-PSYLSAYFKEDMRNTALTLGLSIDRRREFTTIDPAFERFVQWQYKRLQEI 167
                                   542.22222200000023321122123333.23456788999*************************************** PP

                   tRNA-synt_1 154 gliyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv.....it 229
                                   g i + k +v +++  + ++   ++   d +  +i++     ++e+  +  aT +PeT++g +a+ +np+ dy+     ++
  gi|70606212|ref|YP_255082.1| 168 GYIKKEKAPVAYCPVDEFPVGMHDT-RGDIEPEIIDLDVIYFQGEKLLFLTATSRPETIFGAVAILINPDSDYSivvdnKN 247
                                   *************988877765544.5677777777777778888889*************************99988778 PP

                   tRNA-synt_1 230 keklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDy....evg 306
                                   +++l++     k+l  +  + + +e+++g eL+g++v++p++ +k++++  +yv++ +GtGvV   Pah++  y    e+ 
  gi|70606212|ref|YP_255082.1| 248 GKRLVMSTEAFKKLSFQM-SLTEEERKKGGELIGLNVTNPVTLKKLTVLPSKYVESKQGTGVVMAVPAHEPLHYlalsELK 327
                                   888888877777765544.23446789999********************************************4333345 PP

                   tRNA-synt_1 307 kkynlevinildedgtlteea...............................................aefeglkvfdark 340
                                   + +++ ++   ++ g++                                                   +  +g +v +ar 
  gi|70606212|ref|YP_255082.1| 328 ESFEIVPVIKSEDYGDFPAMEvletaqttsaqelkdyidtlyriefhkgsirdevvdlvpdymkqfvgERIAGKSVREARS 408
                                   567777777777788886554688899999999******************************999999999********* PP

                   tRNA-synt_1 341 kvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleniqdW 419
                                   +vve l++ g+  ++ +i     +c  + ++++    +qWf+  ++   + ++lk+++k+++ p+ +++++ +++ n++  
  gi|70606212|ref|YP_255082.1| 409 SVVELLRNLGVHGNIYEIINGPVYCRCGAEVVVKVFDDQWFIDYSNstWKSSVLKSLDKIEILPQDAKREISKIIFNMKPR 489
                                   ******************99999999999999999*******998877999****************************** PP

                   tRNA-synt_1 420 ciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfst 500
                                    + R+r  G+r+p + +++  +    +++ ++v  ++++++++       ++ l   +++   d+ vl    sS +  +  
  gi|70606212|ref|YP_255082.1| 490 PFTRSRGLGVRLP-WDDRQIIDSLS-DSTIYTVFYIVANKVKSYP-----TSIL---NER-FWDYVVLGRGDSSQL--SRE 557
                                   *************.66666554444.3444444444444433332.....3333...111.134445554444443..345 PP

                   tRNA-synt_1 501 lgypeed....teelkkffpadmlleGlDiirgWvarlillslaltgse..PfkevlvhglvrdeeGrKmSKslgNvidpl 575
                                   lg p+e+    + e++  +p d   +G D ++  +   +   + + g+   P k+++++g++r   G+KmSKs gNv   +
  gi|70606212|ref|YP_255082.1| 558 LGIPKEQleelRMEVEYWYPVDSRHSGRDLVQNHIPYYLYHHVGVLGEDkvP-KRIVLNGFIRV-GGKKMSKSFGNVYPLN 636
                                   666666511114556678***************9998888777766654326.89999****97.5*************** PP

                   tRNA-synt_1 576 dvikkygadalRltli.lsdvgrdinl 601
                                   + i++yg+d +Rl+l  +s+ + di++
  gi|70606212|ref|YP_255082.1| 637 KAIREYGVDTVRLALTsTSSLSDDIEF 663
                                   ****************67777778876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   1.6e-17   4.2e-14       2      72 ..      33     103 ..      32     110 .. 0.93
   2 !    6.4   0.0    0.0013       3.3      63     127 ..     118     184 ..     107     187 .. 0.80
   3 !   33.7   0.0   6.4e-12   1.6e-08     289     369 ..     584     666 ..     569     687 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.6e-17
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHH CS
                  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvhe 72 
                                   ++t+a+pY+n++lH+Gh +++i aDi+aRy r++g++vlf  +    Gtpi   A++ +   ee+++++++
  gi|70606212|ref|YP_255082.1|  33 FITVAFPYTNSPLHIGHGRTYITADIYARYLRMKGYNVLFPFAFQFTGTPILSIADAVKRGDEEIISTFTN 103
                                   79***************************************************999999888888887766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHTT---SEEE..ETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTT CS
                  tRNA-synt_1g  63 peelvekvheeikelfkklnisfdkyg..rttseehkelvqeifkklkekgliyekeieqlycpkde 127
                                   p+ l + ++e ++++  +l++s d     +t + + +++vq  +k+l+e g+i++++  ++ycp de
  gi|70606212|ref|YP_255082.1| 118 PSYLSAYFKEDMRNTALTLGLSIDRRRefTTIDPAFERFVQWQYKRLQEIGYIKKEKAPVAYCPVDE 184
                                   5556666677777777777777776541147788999**************************9876 PP

  == domain 3  score: 33.7 bits;  conditional E-value: 6.4e-12
                                   EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE- CS
                  tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfs 367
                                   g+d ++ H  ++     g   e k+pk++v ++++ v gkK+SkS g+v   ++a+ ++ +d++R  l+++++ ++D++fs
  gi|70606212|ref|YP_255082.1| 584 GRDLVQNHIPYYLYHHVGvlGEDKVPKRIVLNGFIRVGGKKMSKSFGNVYPLNKAIREYGVDTVRLALTSTSSLSDDIEFS 664
                                   899999999999999999888899********************************************************9 PP

                                   HH CS
                  tRNA-synt_1g 368 we 369
                                    +
  gi|70606212|ref|YP_255082.1| 665 PN 666
                                   64 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.5   7.4e-24   1.9e-20       1     145 [.     698     826 ..     698     833 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 7.4e-24
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d wi s +++++  +++++ ++++++a++ +y+ +++dl + ylel   +++s           +++ v++ ++rl+aPf+
  gi|70606212|ref|YP_255082.1| 698 DLWISSLISEYIDLIDNCLSNLDLRTAYKTIYYDIYEDL-KDYLELGNGKINS----------DIIKNVISVWIRLMAPFT 767
                                   78*************************************.********99976..........89**************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpekaeel...ekeleeeevellkeivkairklrselkikps 145
                                   P+++Eelw    ++  +++ ++++ +p+k e +      +   e+e+l+ ++ +i++++s++   p 
  gi|70606212|ref|YP_255082.1| 768 PHLAEELW----HK-LDNSLVVRQRFPSKGELQydkR--A-LLEIEYLRYTIDLINSMKSKMSKEPE 826
                                   ********....55.3556688999**7665556433..3.459999999*********99987765 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0     2e-16     5e-13      27     150 ..     219     345 ..     208     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2e-16
                 tRNA-synt_1_2  27 ttrpdtlfGvtfvalapehplvekl.aekkkelaafieevkkksesereletkekeGv.ftglkaihPitgekipiwvany 105
                                   t+rp+t+fG+  + + p+++    + +++ k+l   +e  kk s + + +e+++k+G    gl++++P+t +k+ +  ++y
  gi|70606212|ref|YP_255082.1| 219 TSRPETIFGAVAILINPDSDYSIVVdNKNGKRLVMSTEAFKKLSFQMSLTEEERKKGGeLIGLNVTNPVTLKKLTVLPSKY 299
                                   89*******************999967777888888888888887776666666655549********************* PP

                 tRNA-synt_1_2 106 vlmeygtgavmavPahdqrDfeFakkyn..lpikqvikpedeekkle 150
                                   v +++gtg+vmavPah+   +   ++ +   +i +vik+ed   ++ 
  gi|70606212|ref|YP_255082.1| 300 VESKQGTGVVMAVPAHEPLHYLALSELKesFEIVPVIKSEDYG-DFP 345
                                   *****************98876554433349999999988754.333 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.2e-08     3e-05      23      63 ..      45      85 ..      34     402 .. 0.80
   2 ?   -3.3   0.0       1.7   4.5e+03      68     107 ..     446     485 ..     437     487 .. 0.77
   3 !   23.4   0.0   1.2e-08   3.2e-05     213     284 ..     583     655 ..     570     671 .. 0.81
   4 ?   -1.0   0.0      0.35     9e+02      95     125 ..     665     695 ..     654     740 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                                  -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHH CS
                  tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiik 63
                                   h+Gh+R++++ Di +r+l+++gY+v f   +      i+ 
  gi|70606212|ref|YP_255082.1| 45 LHIGHGRTYITADIYARYLRMKGYNVLFPFAFQFTGTPILS 85
                                  7*************************986555544445554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                                   TTS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGGHHH CS
                  tRNA-synt_1e  68 eeksvkelaekfieefkkdleaLnvlkptleprvsekvde 107
                                   ++ +++   +++ ++  k l+++++l+ +++  +s+ + +
  gi|70606212|ref|YP_255082.1| 446 DQWFIDYSNSTWKSSVLKSLDKIEILPQDAKREISKIIFN 485
                                   5556666678899999999*******99999999887765 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1.2e-08
                                   EEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                  tRNA-synt_1e 213 GGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                    G DL+  h    l  +  + +  ++ k  + ng++++ g+kmsks +n+  ++++++++   ++Rl+l+s+ 
  gi|70606212|ref|YP_255082.1| 583 SGRDLVQNHIPYYLYHHVGVLGeDKVPKRIVLNGFIRVGGKKMSKSFGNVYPLNKAIREYGVDTVRLALTSTS 655
                                   57777777777777777777775666788999************************************98764 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.35
                                   -SB--BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                  tRNA-synt_1e  95 ptleprvsekvdeiielvekliekgyaYavs 125
                                   p++   + e++++i +++e+li+     ++ 
  gi|70606212|ref|YP_255082.1| 665 PNIAKSIGEQLKHIHDFIENLIKLQSVNEIR 695
                                   5666778899999999999999866555555 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.03        78       8      61 ..      17      69 ..       9      76 .. 0.83
   2 ?    8.5   0.0   0.00032      0.82     239     332 ..     582     674 ..     574     698 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.03
                  tRNA-synt_1f  8 aeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgee 61
                                  +e++ e   ++++ek+ ++v+  ++ S ++HiG  r  +tad+ ar lr +g +
  gi|70606212|ref|YP_255082.1| 17 SERVYEADVDRTKEKKFITVAFPYTNS-PLHIGHGRTYITADIYARYLRMKGYN 69
                                  467777777887799999*******99.78****************99998876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00032
                  tRNA-synt_1f 239 paGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkl 319
                                    +G+D++++   + +++++  + + + P+ +v + ++  gg+kms+S Gnv  l+++++ +  +++r+ + +     + ++
  gi|70606212|ref|YP_255082.1| 582 HSGRDLVQNHIPYYLYHHVGVLGEDKVPKRIVLNGFIRVGGKKMSKSFGNVYPLNKAIREYGVDTVRLALTS-TSSLSDDI 661
                                   566666666666666666666666678999999999999999*****************9999999998888.66666777 PP

                  tRNA-synt_1f 320 dldleilrlvdeY 332
                                   +++ +i + + e 
  gi|70606212|ref|YP_255082.1| 662 EFSPNIAKSIGEQ 674
                                   7777787776665 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   3.9e-05       0.1       5      41 ..     815     851 ..     813     855 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHHHHHHHHHHS-GGG-SSHHHHHHHHHHHH CS
                   sCache_like   5 ekleerleKEakllasllenenlkaaenkkvleease 41 
                                   +++++++ KE + ++++++++n ++++  k++e ++e
  gi|70606212|ref|YP_255082.1| 815 NSMKSKMSKEPETVIIYVNEDNTQRDLIRKAIESLKE 851
                                   689*****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (942 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 4931.62
//
Query:       gi|70606213|ref|YP_255083.1|  [L=347]
Description: hypothetical protein Saci_0374 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-09   37.1   0.1    1.2e-08   35.5   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    4.2e-07   30.3   0.2    1.1e-06   29.0   0.0    1.8  2  Fer4_12      4Fe-4S single cluster domain
    0.00029   21.0   0.0    0.00081   19.5   0.0    1.8  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0     2e-12   1.2e-08       3     151 ..       4     139 ..       2     154 .. 0.85
   2 ?   -2.1   0.0      0.74   4.4e+03       7      41 ..     281     312 ..     276     327 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2e-12
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   +t  Cnl C +C  ++ ++  + +   +v ++++ +++ +      +vi+ ggepll+p+f++ +   +k     +r  + 
  gi|70606213|ref|YP_255083.1|   4 TTGKCNLTCDYCGGSFPKEAVPWEVKYDVSKLKNVIERDS----EAVVIFYGGEPLLNPKFIMSVMDNVKA----VRWGIQ 76 
                                   6889***********9766667777777777777777776....99*********************9996....****** PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                   +ng+       ++l +  + r+++ l ++d + ++ +++++++ ++ v ++ ++ +e g++ ++ r+ +
  gi|70606213|ref|YP_255083.1|  77 SNGIGA-----KLLPDKYWKRMNIALFSIDGReEITDKHRGRGVYKVVTRNAKYVKEFGVE-TIARMAV 139
                                   *****4.....55555559*********99998899999999******************9.8888766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.74
                                   ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkel 41 
                                   C +rC +    +     g + ++ v+e+ +e  +l
  gi|70606213|ref|YP_255083.1| 281 CGGRCLYAVKEK---YWGEEGFKVVDEVTKEYLRL 312
                                   777776633332...45555555555555555444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.8e-10   1.1e-06      10     124 ..       3     109 ..       1     121 [. 0.82
   2 ?   -2.5   0.2      0.95   5.6e+03      12      36 ..     278     302 ..     272     327 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.8e-10
                       Fer4_12  10 lfvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                   l ++ Cnl C++C       +k+  +++ k    ++ + ++ +s   +++ GGEPll  n + +++++++vk+  +    +
  gi|70606213|ref|YP_255083.1|   3 LTTGKCNLTCDYCG---GSFPKEAVPWEvKYDVSKLKNVIERDSEAVVIFYGGEPLL--NPKFIMSVMDNVKAVRWG---I 75 
                                   66789*******98...7788888888866667777777888999************..****************95...8 PP

                       Fer4_12  90 lytgytleelskkekeellkeidvlvdGkfeesle 124
                                    ++g   + l +k + + ++   + +dG+ e   +
  gi|70606213|ref|YP_255083.1|  76 QSNGIGAKLLPDK-YWKRMNIALFSIDGREEITDK 109
                                   9999888877654.556678888899998876555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.95
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkef 36 
                                    s C  +C + + ++ w  ++ k +
  gi|70606213|ref|YP_255083.1| 278 KSYCGGRCLYAVKEKYWGEEGFKVV 302
                                   5677778888887777744333322 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-07   0.00081       3      76 ..       3      70 ..       1     102 [. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-07
                       Fer4_14  3 vrlsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlke 76
                                  + +++Cnl C  C     + +  ++ +++   l++++    +se     + + GGePL   n k ++ +++++k 
  gi|70606213|ref|YP_255083.1|  3 LTTGKCNLTCDYCGgSFPKEAVPWEVKYDVSKLKNVI--ERDSEA---VVIFYGGEPL--LNPKFIMSVMDNVKA 70
                                  5689*********952233466899999999999999..333333...5899******..888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2497.85
//
Query:       gi|70606214|ref|YP_255084.1|  [L=423]
Description: hypothetical protein Saci_0375 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-36  123.5   0.0    1.2e-35  123.1   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.1e-16   60.7   0.0    2.2e-16   59.7   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0   1.3e-39   1.2e-35       1     206 [.      65     419 ..      65     420 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1.3e-39
                                   EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGaka 80 
                                   l+++H+Dv+p e+ ++w++ pf + ++dGk+++rG+ d+kg ++a l+a+ +l +e+ k+k +++l  +++EE    G+++
  gi|70606214|ref|YP_255084.1|  65 LIYNHYDVQPVEPLEKWNSdPFNPVIKDGKIFARGVGDDKGTLMARLQAIIELLREN-KLKVNVKLFYEGEEE---IGSPN 141
                                   699*******999999****************************************8.88*************...67777 PP

                                   HHHHHH.TTTCESEEEEEEEESSSBTCHSTETEEEE............................................. CS
                                   xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                 Peptidase_M20  81 llegle.erekvdavfelhieepgileagklaigvv............................................. 115
                                   + + l+   + + a +  +++e+ +++ ++  + +v                                             
  gi|70606214|ref|YP_255084.1| 142 MEDFLKdYSKMLSADY--VLWEGAGKSPEG-RPEIVlgvkgllyvelrkktpkdlhsmygpiarnpawdlvyllnklrdek 219
                                   7775554444555544..445566666445.566667788***************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M20 116 ................................................................................. 115
                                                                                                                    
  gi|70606214|ref|YP_255084.1| 220 gkvlipnfydkvvwlseeekkylrtpdeylakaieqnvpgnsmiklveeptcnidgiysgytgegsktvipslafvkldfr 300
                                   ********************************************************************************* PP

                                   .....................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHHHH...TTT. CS
                                   .....................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxx. RF
                 Peptidase_M20 116 .....................kvevelleggapvtln.dsplvkalaeaaeelfgekveli.vsgpggtdarff...agi. 169
                                                        ++e+  +++ +p++++ +s++++al ++a+e+++e++ +   s+ g+  + ++   +++ 
  gi|70606214|ref|YP_255084.1| 301 lvpnqdpqeilsslkryisdpEIEIIVHGSVKPYRTSlNSEIARALIRSAKEVYNEDPVVLpNSP-GTGPMEMIaryLNVn 380
                                   *******************988999999**************************98855554888.******997776664 PP

                                   EEEEEEESSG..GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 170 ptvmifgpgs..glaHspnEyvdledlekgikvlarlle 206
                                   + ++++g ++  +++Hs nE++ ++d++kgi++ ++ll+
  gi|70606214|ref|YP_255084.1| 381 QIADGVGVDNysSNIHSFNENILVNDYYKGIEWTKSLLR 419
                                   45599**55336*********************999886 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   2.4e-20   2.2e-16       2     104 ..     176     321 ..     175     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.4e-20
                                   EB-EEEEEEEE.EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC................................... CS
                     M20_dimer   2 ghkGlaggkit.vkgkagHsgapgagaNAieklarllaeledeegdia................................. 48 
                                   g kGl+ ++++  + k++Hs ++  ++N+ + l+ ll++l+de+g++                                  
  gi|70606214|ref|YP_255084.1| 176 GVKGLLYVELRkKTPKDLHSMYGPIARNPAWDLVYLLNKLRDEKGKVLipnfydkvvwlseeekkylrtpdeylakaieqn 256
                                   679999999998889****************************99999********************************* PP

                                   ........TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSC CS
                     M20_dimer  49 .....eerslprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeileke 104
                                          + + ++t+n+ gi++G+    +k+vip+ a +k+d+Rl+p++dp+e+l  ++ ++++ 
  gi|70606214|ref|YP_255084.1| 257 vpgnsMIKLVEEPTCNIDGIYSGYtgegSKTVIPSLAFVKLDFRLVPNQDPQEILSSLKRYISDP 321
                                   *99998999999*************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2905.01
//
Query:       gi|70606215|ref|YP_255085.1|  [L=104]
Description: hypothetical protein Saci_0376 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 670.87
//
Query:       gi|70606216|ref|YP_255086.1|  [L=152]
Description: hypothetical protein Saci_0377 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-41  138.1   2.1    1.5e-40  137.5   2.1    1.3  1  PriX      Primase X


Domain annotation for each model (and alignments):
>> PriX  Primase X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.5   2.1   8.5e-45   1.5e-40       1      99 []      56     150 ..      56     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 8.5e-45
                                   -HHHHHHHHH--SSTHHHHHHHTHHHHHHHTS---HHHHHHHHHHHH....TTSSSS---HHHHHHHHHHHHHHT-----H CS
                          PriX   1 yeWiekvlekglpDgRkrlilyvisrYLvnvkklseeealkklkeflksckkkknlskiyeswirsvikgvkekglkpisl 81 
                                   y+Wi+k+lekglpD+Rkr+ilyv+srYLvnvk+lsee+++k l +f+     +++ sk+yeswirsv++gvk+k+lkp+sl
  gi|70606216|ref|YP_255086.1|  56 YDWIDKILEKGLPDARKRFILYVASRYLVNVKGLSEEDVVKILVDFY----GRHGGSKVYESWIRSVVRGVKSKNLKPWSL 132
                                   89*********************************************....99999************************* PP

                                   HHHHHH-HHHHHHHHHHH CS
                          PriX  82 kklkekdkelyeviekvl 99 
                                   kk++++dke+ye+i kvl
  gi|70606216|ref|YP_255086.1| 133 KKIESNDKEMYELILKVL 150
                                   **************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 819.58
//
Query:       gi|70606217|ref|YP_255087.1|  [L=315]
Description: PP-loop family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-14   53.3   0.0    7.2e-14   51.9   0.0    1.6  1  ATP_bind_3      PP-loop family
    0.00024   21.2   0.0    0.00047   20.2   0.0    1.5  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
     0.0005   19.7   0.0    0.00082   19.0   0.0    1.5  1  ThiI            Thiamine biosynthesis protein (ThiI)
    0.00052   18.9   0.0     0.0011   17.8   0.0    1.5  1  tRNA_Me_trans   tRNA methyl transferase
     0.0023   17.5   4.1     0.0074   15.8   1.4    2.7  2  RecR            RecR protein
     0.0024   18.4   0.0      0.058   13.9   0.0    2.9  1  Usp             Universal stress protein family
     0.0046   16.1   0.0      0.007   15.5   0.0    1.3  1  NAD_synthase    NAD synthase
  ------ inclusion threshold ------
      0.054   13.0   0.0       0.32   10.5   0.0    2.1  2  QueC            Queuosine biosynthesis protein QueC
      0.061   14.1   2.8       0.14   13.0   0.1    2.6  3  zinc_ribbon_15  zinc-ribbon family
      0.091   12.6   0.0       0.32   10.9   0.0    1.9  1  DUF2862         Protein of unknown function (DUF2862)
        4.8    7.3   7.9       0.49   10.5   1.2    2.4  3  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   4.4e-17   7.2e-14       2     167 ..      50     229 ..      49     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 4.4e-17
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS...TCHHHHHHHHHHHHHHTT-EEEEEE--H..........H CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr...eeskeeaelvkelckklnikleiekvdv..........a 69 
                                   + vAvSgG DS++Ll+l++kl++k g+++v ih++ g+      s++  e+  +  ++l++k++  +v+            
  gi|70606217|ref|YP_255087.1|  50 IGVAVSGGKDSTTLLHLMNKLAQKRGFEIVGIHIHLGIDmgkGYSDKSLEFALKNFQMLGVKYKLINVKEkygftideakF 130
                                   679**********************************98432478999999999999999999999999888887765421 PP

                                   HCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--C..CHHH-S-SEEEETTCCEE-CCCT-- CS
                    ATP_bind_3  70 kkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsgl..aglagikeaseiasirlvRPlLkvs 148
                                   k +     +    +RY  ++e++++eg++ ++++h+ +D a  +l   + g     + l  + + ++ ++++ v Pl+ ++
  gi|70606217|ref|YP_255087.1| 131 KIRRPICSTCGLVKRYS-MEEIAEEEGLDTVVTGHNLNDMAQFVLSGYFSGDVNnlSRLKPVLPPTRGYKVKKVKPLFLIY 210
                                   22233344445556775.79************************99999987642244555555555688999******** PP

                                   HHHHHHHHHHTT---B--C CS
                    ATP_bind_3 149 keeleeylkekkikwveDe 167
                                    +e+ +y+  ++i+++ D+
  gi|70606217|ref|YP_255087.1| 211 EKEILTYAILNNIPFIYDS 229
                                   ****************997 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00047       3     155 ..      51     225 ..      49     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                   EEE--SSCTCHHHHHHHHHHCTTH........EEEEEE-STB-H.HHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S CS
                   PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv........pvvfvdtghefp.etiefvdeleeryglrlkvyepeeevaekinaekhg 74 
                                    v+vsgGkds+ llhL+ k  +++          + +d+g+ ++ + +ef  +  + +g++ k+ + +e+    i ++k  
  gi|70606217|ref|YP_255087.1|  51 GVAVSGGKDSTTLLHLMNKLAQKRgfeivgihIHLGIDMGKGYSdKSLEFALKNFQMLGVKYKLINVKEKYGFTIDEAK-- 129
                                   589********************77888665445556777766525688999999999877555555554444444444.. PP

                                   -THHHC...HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S.............CEEE-CCCT- CS
                   PAPS_reduct  75 sslyee...aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek.............slrvfPllnW 139
                                     + ++     + ++K + +++  e+ + d+++tG   ++ ++     +++ d ++               + +v Pl+  
  gi|70606217|ref|YP_255087.1| 130 -FKIRRpicSTCGLVKRYSMEEIAEEEGLDTVVTGHNLNDMAQFVLSGYFSGDVNNLSrlkpvlpptrgykVKKVKPLFLI 209
                                   .2233345577***********99999*************99999999999999988899999*****99888899***** PP

                                   -HHHHHHHHHHCT--B CS
                   PAPS_reduct 140 teedvwqyilrenipy 155
                                    e+++  y+  +nip 
  gi|70606217|ref|YP_255087.1| 210 YEKEILTYAILNNIPF 225
                                   ************9985 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.1e-07   0.00082      10     127 ..      54     175 ..      46     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.1e-07
                          ThiI  10 lSgGiDSpVaayll....lkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkek 86 
                                   +SgG DS    +l+     kRG+++v +h++    +++   +k  +l   l ++q  l vk+  ++ ke     ++++k k
  gi|70606217|ref|YP_255087.1|  54 VSGGKDSTTLLHLMnklaQKRGFEIVGIHIHLGIDMGKGYSDK--SLEFALKNFQM-LGVKYKLINVKEKYGFTIDEAKFK 131
                                   79999998766655222268**********9666666666665..56666778885.667777777666665555555555 PP

                          ThiI  87 ltivllkrk.mlr..iAekvaeeegakalvtGesLgqVaSqtle 127
                                    +  ++  + +++    e++aeeeg +++vtG +L   a   l+
  gi|70606217|ref|YP_255087.1| 132 IRRPICSTCgLVKrySMEEIAEEEGLDTVVTGHNLNDMAQFVLS 175
                                   4444444332333112356899*************999876665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     7e-07    0.0011       2     124 ..      49     164 ..      48     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7e-07
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaall....keqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                   ++ va+SgG DS+  ++l+    +++g+e++g++++l  + ++      +++ l+ a +  + lg++++ ++++++y  ++
  gi|70606217|ref|YP_255087.1|  49 RIGVAVSGGKDSTTLLHLMnklaQKRGFEIVGIHIHLGIDMGKG----YSDKSLEFALKNFQMLGVKYKLINVKEKYGFTI 125
                                   799**********99987732225799********999985544....5889999999999****************8876 PP

                 tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGH 124
                                    e   +     r P  + +C   +K   + e a+e  g d+++tGH
  gi|70606217|ref|YP_255087.1| 126 DEAKFKI----RRPI-CSTC-GLVKRYSMEEIAEE-EGLDTVVTGH 164
                                   5543322....2332.6666.46787777776666.8999999998 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.21   3.4e+02      10      24 ..     126     142 ..     124     146 .. 0.65
   2 !   15.8   1.4   4.5e-06    0.0074      13      36 ..     281     306 ..     275     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                   HHHHHH-EE..-TTT-- CS
                          RecR  10 qeakekvrh..CsrCgn 24 
                                    eak k+r+  Cs Cg 
  gi|70606217|ref|YP_255087.1| 126 DEAKFKIRRpiCSTCGL 142
                                   56666666444888885 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.5e-06
                                   HHH-EE-TTT--EESSS..S-CCCCS CS
                          RecR  13 kekvrhCsrCgnlteed..lCaICsd 36 
                                    e+v+ C++Cg  t++d  +C++C+ 
  gi|70606217|ref|YP_255087.1| 281 VEEVSKCKICGRPTTKDreICSFCAT 306
                                   589********997775559****96 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.6e-05     0.058       3     112 ..      48     165 ..      46     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                                   SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..........HHH CS
                           Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..........aka 73 
                                   +rI Vav g ++s+ +l+   +la++rg e++ +h++   ++g+      ++ e +l+  ++  ++++          + +
  gi|70606217|ref|YP_255087.1|  48 DRIGVAVSGGKDSTTLLHLMNKLAQKRGFEIVGIHIHLGIDMGKGYSD--KSLEFALKNFQMLGVKYKlinvkekygfTID 126
                                   79*********************************9977766655444..4444555555555555666678888888777 PP

                                   HHHCTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESC CS
                           Usp  74 aaeaggvkvevvveegdpaeeilevaeeedadliVvGsr 112
                                   +a+ ++    + + +  ++ +  e+aeee+ d +V+G+ 
  gi|70606217|ref|YP_255087.1| 127 EAKFKIRRPICSTCGLVKRYSMEEIAEEEGLDTVVTGHN 165
                                   777788888888888888888888888888888888875 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.3e-06     0.007       7      88 ..      36     124 ..      30     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                                   HHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHH........TCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                  NAD_synthase   7 dflkeyvkkagakgvvlGlSGGvDSslvaalavkal........gkenvlalllPssvsseedvedalalaenlgievkti 79 
                                    ++++y    g++ + + +SGG DS++   l  k+         g + +l++ + ++  s++++e al+  + lg+++k i
  gi|70606217|ref|YP_255087.1|  36 RVVEKYKMFDGSDRIGVAVSGGKDSTTLLHLMNKLAqkrgfeivGIHIHLGIDM-GKGYSDKSLEFALKNFQMLGVKYKLI 115
                                   556666666677888899********9888877777677778889999******.7777889******************* PP

                                   --HHHHHHH CS
                  NAD_synthase  80 dikpivraf 88 
                                   ++k+ +   
  gi|70606217|ref|YP_255087.1| 116 NVKEKYGFT 124
                                   ***987654 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00019      0.32       4      61 ..      52     117 ..      49     131 .. 0.68
   2 ?   -0.3   0.0      0.38   6.1e+02     108     129 ..     151     172 ..     147     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                   EE--SSHHHHHHHHH....HHHH-SEEEEEEEESS....-T.TSHHHHHHHHHHHHT--.-EEEEE- CS
                          QueC   4 vllSGGlDSttvlal....akkegkevealtfdYg....qr.hkkeleaakkiakelgveehkildl 61 
                                   v +SGG DStt+l l    a+k+g e+  ++++ g    +   +k le a k ++ lgv + k +++
  gi|70606217|ref|YP_255087.1|  52 VAVSGGKDSTTLLHLmnklAQKRGFEIVGIHIHLGidmgKGySDKSLEFALKNFQMLGV-KYKLINV 117
                                   679*********98622226677888877665543111154566777777777777777.6666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                                   HHHHHT-SEEEE---S-STT-- CS
                          QueC 108 yaealgaeaiiiGvneedfsgY 129
                                    ae+ g +++++G n +d++ +
  gi|70606217|ref|YP_255087.1| 151 IAEEEGLDTVVTGHNLNDMAQF 172
                                   5899999999999999997554 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         2   3.3e+03       2      24 ..       2      22 ..       1      40 [. 0.60
   2 ?   -0.1   0.0         1   1.6e+03       2      12 ..     136     146 ..     114     155 .. 0.72
   3 ?   13.0   0.1   8.4e-05      0.14      42      85 ..     229     304 ..     201     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
                zinc_ribbon_15  2 lCpkCgklskaelvkkkkvlklf 24
                                  +C kC+   +a+++  +  ++l+
  gi|70606217|ref|YP_255087.1|  2 KCGKCD--DEAVIKIPYANISLC 22
                                  566666..344444455555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                zinc_ribbon_15   2 lCpkCgklska 12 
                                   +C++Cg ++++
  gi|70606217|ref|YP_255087.1| 136 ICSTCGLVKRY 146
                                   45555555444 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.4e-05
                zinc_ribbon_15  42 kCkslleaskelgkeiekkesse................................kkeCknCgkeveeefkyCpkC 85 
                                   +C +++     ++++i++k ++                                 + +Ck Cg+ ++++ + C++C
  gi|70606217|ref|YP_255087.1| 229 SCPHTFRVGGATQDKIRRKLEEMedeipgfmlllvqnftdkiqepleviyskveeVSKCKICGRPTTKDREICSFC 304
                                   56666666666666666554444566677777777777777777777777777889******************** PP

>> DUF2862  Protein of unknown function (DUF2862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.32      22      46 ..      30      55 ..      22      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                                  BT-..EEEEEEEEE-SSS.SEEEEEE CS
                       DUF2862 22 lkkepvgtikdfKmtDGs.giGvvvk 46
                                  l+++ + +++ +Km DGs  iGv v 
  gi|70606217|ref|YP_255087.1| 30 LENRFERVVEKYKMFDGSdRIGVAVS 55
                                  666667799********977***996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.1   6.7e+03      31      35 ..       3       7 ..       2      13 .. 0.57
   2 ?   -0.2   0.0      0.62     1e+03      14      19 ..     136     141 ..     127     147 .. 0.71
   3 ?   10.5   1.2    0.0003      0.49       1      23 [.     287     309 ..     287     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                           DZR 31 CpsCg 35
                                  C +C+
  gi|70606217|ref|YP_255087.1|  3 CGKCD 7 
                                  44443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.62
                           DZR  14 fCseCg 19 
                                    Cs+Cg
  gi|70606217|ref|YP_255087.1| 136 ICSTCG 141
                                   466665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0003
                           DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                   C+ Cg+++++d + Cs C tk+k
  gi|70606217|ref|YP_255087.1| 287 CKICGRPTTKDREICSFCATKMK 309
                                   999*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2029.25
//
Query:       gi|70606218|ref|YP_255088.1|  [L=230]
Description: hypothetical protein Saci_0379 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1600.82
//
Query:       gi|70606219|ref|YP_255089.1|  [L=247]
Description: sugar fermentation stimulation protein A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-38  132.4   0.0    1.6e-38  131.8   0.0    1.2  1  SfsA      Sugar fermentation stimulation protein RE domain
    2.9e-16   59.4   0.1    5.5e-16   58.5   0.1    1.4  1  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.8   0.0   1.7e-42   1.6e-38       2     128 ..     107     219 ..     102     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 1.7e-42
                                   HHHHHHHHHHEE..........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHH CS
                          SfsA   2 lpnklveealesglielagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLael 82 
                                   ++nk+++++l s         ++k evk++nsr+Df+ ++     ++vEVK++ l+ +g alfPdapteRg++hleeL++l
  gi|70606219|ref|YP_255089.1| 107 IHNKIARNFLPS---------DVKSEVKVNNSRLDFYYDN-----TFVEVKGCSLVVDGKALFPDAPTERGKRHLEELIKL 173
                                   567777777766.........59**************775.....7***********99********************** PP

                                   HHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEE CS
                          SfsA  83 vkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevl 128
                                   + +gyr+++l++v+r+da +f+pn+++d++f+ a+++a+e+GVev 
  gi|70606219|ref|YP_255089.1| 174 KMQGYRSLILILVMRDDAICFSPNWKTDKKFSMAFKNAVEEGVEVT 219
                                   ********************************************96 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1   6.2e-20   5.5e-16       2      62 ..      44     102 ..      44     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 6.2e-20
                                   EEEETTEEEEEEE..EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE CS
                        SfsA_N   2 rRpnRFladveldgtvHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvg 62 
                                   +R nRF++  +  + +H++++Grlkel++pG+r+l+++  +++rKt+y ++a++ +++wv+
  gi|70606219|ref|YP_255089.1|  44 ERINRFVVITQSGKLCHLHDPGRLKELIYPGNRILIRE--HKGRKTNYMVLAAHSGTGWVV 102
                                   7********998645**********************7..588****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1616.57
//
Query:       gi|162139953|ref|YP_255090.2|  [L=252]
Description: NAD-dependent deacetylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-52  177.4   0.0    3.1e-52  177.1   0.0    1.1  1  SIR2          Sir2 family
  ------ inclusion threshold ------
      0.032   14.0   0.0       0.23   11.2   0.0    2.0  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   0.0   3.4e-56   3.1e-52       1     177 []      25     197 ..      25     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 3.4e-56
                                    -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEEE CS
                           SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllrliT 80 
                                    GAGiSt+sGipdfR+ +Gl++k+++e las e++++++   ++ fy+++++ l  ea+pn aH+al++lek+g  +++iT
  gi|162139953|ref|YP_255090.2|  25 GAGISTASGIPDFRGPQGLWKKYSPE-LASIEYFQKYPDAFWQ-FYSTRMKSLF-EAKPNRAHYALAQLEKMGLIKAVIT 101
                                    9*********************9986.79**************.**99988887.8************************ PP

                                    S-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-SHHHHHHHHHH CS
                           SIR2  81 QNiDgLekkaGskkvvelHGslakakcvkcekkldkeelqeeieaekvpecekcgkllkpdvvfFGealpdklkkliekv 160
                                    QN+DgL++ aGs++v+elHG++ k  c++c  ++d  e+ +++e+ +v   ++cg++lkpdvv+FGe ++  + ++++ +
  gi|162139953|ref|YP_255090.2| 102 QNVDGLHSVAGSRNVIELHGNMRKSYCTSCLRSYDSLEVLARVEKGEVIPRCECGGILKPDVVLFGEPVH-GIYEAMRIA 180
                                    ***********************************************99999*****************9.999****** PP

                                    HH-SEEEEES--STSTT CS
                           SIR2 161 eeadlllviGtSlkVap 177
                                    +e dl+l+iG+Sl+V+p
  gi|162139953|ref|YP_255090.2| 181 NESDLVLAIGSSLTVYP 197
                                    ***************98 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.055     5e+02       2      25 ..       8      31 ..       7      38 .. 0.87
   2 ?   11.2   0.0   2.6e-05      0.23      65      90 ..     170     195 ..     147     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.055
                                   HHHHHHHHH-SSEEEEE-CHHCHT CS
                   TPP_enzyme_M  2 ekaaellkaakrpvilvGggvars 25
                                   +k+ae++ ++ + + + G g++++
  gi|162139953|ref|YP_255090.2|  8 KKVAEMILSSVNAIAFTGAGISTA 31
                                   799*****************9976 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.6e-05
                                    GGSCHHHHHHHHH-SEEEEES-SSST CS
                   TPP_enzyme_M  65 lhgskaanealeeaDlvlalGarfdd 90 
                                    +hg ++a ++++e+Dlvla+G+ ++ 
  gi|162139953|ref|YP_255090.2| 170 VHGIYEAMRIANESDLVLAIGSSLTV 195
                                    688999***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1636.52
//
Query:       gi|70606221|ref|YP_255091.1|  [L=64]
Description: hypothetical protein Saci_0382 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   17.8   2.5     0.0026   17.6   2.5    1.2  1  DUF3311   Protein of unknown function (DUF3311)
  ------ inclusion threshold ------
      0.031   13.8   2.2      0.031   13.8   2.2    2.4  3  DUF3687   D-Ala-teichoic acid biosynthesis protein


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.5   2.9e-07    0.0026      13      54 ..      23      64 .]       8      64 .] 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-07
                       DUF3311 13 lvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakr 54
                                  + p  n  + ++ Gl  fy++q  ++++++v+++++   +kr
  gi|70606221|ref|YP_255091.1| 23 IYPVFNNATMTFAGLTMFYFYQIIMLIVSTVLFVAVSLIFKR 64
                                  6688899999**************************998876 PP

>> DUF3687  D-Ala-teichoic acid biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.9      0.41   3.7e+03      16      23 ..       6      13 ..       3      24 .. 0.71
   2 ?   13.8   2.2   3.4e-06     0.031       3      25 ..      27      49 ..      25      50 .. 0.90
   3 ?   -0.6   0.1      0.11   9.8e+02      12      20 ..      50      58 ..      49      62 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.41
                       DUF3687 16 fYfaIlla 23
                                  fY a +++
  gi|70606221|ref|YP_255091.1|  6 FYIAMFIV 13
                                  67776665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.4e-06
                       DUF3687  3 kekpavkfvlkTlfYfaIllaLi 25
                                  +++ +++f + T+fYf  +++Li
  gi|70606221|ref|YP_255091.1| 27 FNNATMTFAGLTMFYFYQIIMLI 49
                                  67899***********9999997 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.11
                       DUF3687 12 lkTlfYfaI 20
                                  + T+++ a+
  gi|70606221|ref|YP_255091.1| 50 VSTVLFVAV 58
                                  679998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 496.09
//
Query:       gi|70606222|ref|YP_255092.1|  [L=519]
Description: permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-14   51.1  31.9    9.1e-14   51.1  31.9    1.5  2  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
      0.088   12.9   1.2        6.1    6.9   0.0    3.3  4  Vma12     Endoplasmic reticulum-based factor for assembly of 


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1  31.9     1e-17   9.1e-14       3     406 .]      44     450 ..      42     450 .. 0.79
   2 ?   -4.3   0.9       0.7   6.3e+03     121     142 ..     480     500 ..     465     501 .. 0.63

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1e-17
                           SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdylskRf 79 
                                   l+gr+l+++ +   ++a+   a  f+ ++  v+asG + +++++  +     + ll ++rl     + g +T +d+++ Rf
  gi|70606222|ref|YP_255092.1|  44 LGGRRLGWLLVWFLMGADLYTAYTFIAIPSGVYASG-SLFFYAVPYVAWTFGIALLTMPRLWsisrRRGYITAADFVKDRF 123
                                   89**********************************.45667766665555555666666656666*************** PP

                           SSF  80 kgkrilvylsalslllvitlklsvdlvgg.aklielalGlny..........etavlllaaltalYtviGGllAvvytdti 149
                                   +++ + v ++ +   ++   +++ +++g  a+l  l++Gl +          e a+++  +++a +t++ Gl+   +t + 
  gi|70606222|ref|YP_255092.1| 124 NNRPLSVAVALTG-AVAELPYIALQIFGMqAVLTVLLIGLGVtgtygglsvsEWALIIAFIVLAAFTITSGLRGAALTAVF 203
                                   ****888777665.5677889999999963666667777754222222222347999999999****************** PP

                           SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvagl....philvRfl 226
                                   + +l+ +  l++ i v l+ Gg++++++ + +++ k++  ++  s      p +++     l lG a++    ph +   l
  gi|70606222|ref|YP_255092.1| 204 KDILIWITVLTVIIAVPLAYGGFSHAFSAIEAIKGKGAAAYEFLS------PSAITNY-FTLALGSAMAlylyPHSINGSL 277
                                   ***********************************7766666444......3333333.34444444444445******** PP

                           SSF 227 aakdakailkgvlkltivlilvligmisiilfaiklagavpka..vgtevgvsniaypeLvvkllpnllaGlllavmlAai 305
                                   +a+d   + k+  +l+++ ++ l++   + lf+i +  + p a  +  ++++  + +p L+ + +p+++ Gl l +++   
  gi|70606222|ref|YP_255092.1| 278 SAQDTDKLKKST-SLLPLYGVGLAL---LALFGILIYAV-PSAlsIVVSNKNGALTVPSLIAATMPSWFVGLGLVAIFVGG 353
                                   *******99875.455555555544...67777755544.64401444555666789***************999999888 PP

                           SSF 306 mstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavil 386
                                   +   + + + as ++t+ +  ++++    +e +l+++++ +    ++la++ +vq+         +l  ++l    l+ + 
  gi|70606222|ref|YP_255092.1| 354 LVPAAIMAIGASNLLTRNVIGEFKKLSPRTESNLAKIISTV-FKFAALAFIFIVQATYA---VQLQLLGGILILQTLPAVF 430
                                   88888888999****************99999999887755.45678888888888777...5678899999999****** PP

                           SSF 387 lalfwkrvneqGAlagliiG 406
                                   l+l+ +++  +  +ag i+G
  gi|70606222|ref|YP_255092.1| 431 LGLYTNKLEGYSTFAGWIAG 450
                                   ****************9998 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 0.7
                           SSF 121 etavlllaaltalYtviGGllA 142
                                   +++vl la + +l tviG l+A
  gi|70606222|ref|YP_255092.1| 480 YIGVLSLA-INILVTVIGTLIA 500
                                   56665554.5567788888877 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00068       6.1     112     139 .]      11      38 ..       9      38 .. 0.92
   2 ?   -3.7   0.0       1.3   1.2e+04     112     125 ..     128     141 ..     111     144 .. 0.75
   3 ?   -2.7   0.0      0.62   5.6e+03      77     105 ..     249     282 ..     248     307 .. 0.65
   4 ?    2.8   0.1     0.013   1.2e+02      77      93 ..     484     500 ..     482     512 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00068
                         Vma12 112 lslvvallVgvAEvvvyakylrkveeak 139
                                   l+++++l V++A + +y +y+rk++ +k
  gi|70606222|ref|YP_255092.1|  11 LGVFIGLFVVFAILGFYGAYWRKGDLSK 38 
                                   899********************98776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.3
                         Vma12 112 lslvvallVgvAEv 125
                                   ls+ val  +vAE+
  gi|70606222|ref|YP_255092.1| 128 LSVAVALTGAVAEL 141
                                   68888888888886 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.62
                         Vma12  77 lilvlNiliSvvavffavwialrsartp.....s 105
                                   ++++ N +   +++++a++   +s+ +      +
  gi|70606222|ref|YP_255092.1| 249 PSAITNYFTLALGSAMALYLYPHSINGSlsaqdT 282
                                   5788888888999999999888877555555553 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.013
                         Vma12  77 lilvlNiliSvvavffa 93 
                                   l+l +Nil++v+++ +a
  gi|70606222|ref|YP_255092.1| 484 LSLAINILVTVIGTLIA 500
                                   6789*********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3423.83
//
Query:       gi|70606223|ref|YP_255093.1|  [L=121]
Description: hypothetical protein Saci_0384 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-31  108.3   0.2    2.1e-30  105.9   0.2    1.8  1  DUF2203   Uncharacterized conserved protein (DUF2203)
  ------ inclusion threshold ------
       0.12   11.2   0.1       0.14   11.1   0.1    1.0  1  DOCK_N    DOCK N-terminus


Domain annotation for each model (and alignments):
>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.2   2.4e-34   2.1e-30       2     122 .]       5     111 ..       4     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 2.4e-34
                       DUF2203   2 lFtleeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleag 82 
                                   +F+l++A++lLp+l+e+l+e++++++ +ee                 + +++++ +++ +++ +v+ei+e G++++d ++g
  gi|70606223|ref|YP_255093.1|   5 YFDLKTARELLPWLREKLKEIKRVKRLVEESL--------------VRGDKSSIFKYTVQVDMIVREITEKGIVLRDPDIG 71 
                                   8**********************999999944..............6789999**************************** PP

                       DUF2203  83 lvDFpakldgeevllCWklgEeeieywHeleeGfagRkpi 122
                                   lvDFpa +++++++lCWkl+Ee+i ywH +eeGf+gRk+i
  gi|70606223|ref|YP_255093.1|  72 LVDFPALINNKPAYLCWKLDEEDILYWHYAEEGFRGRKRI 111
                                   **************************************97 PP

>> DOCK_N  DOCK N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.6e-05      0.14      69     108 ..      23      68 ..       7      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.6e-05
                        DOCK_N  69 delkelrektvwrLvrgNk......llglDviVRdpegrgrvdtde 108
                                   +e k++++ + + Lvrg+k       ++ D+iVR+ +++g+v+ d 
  gi|70606223|ref|YP_255093.1|  23 KEIKRVKRLVEESLVRGDKssifkyTVQVDMIVREITEKGIVLRDP 68 
                                   7999********************99****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 798.52
//
Query:       gi|70606224|ref|YP_255094.1|  [L=287]
Description: 3-hydroxyisobutyrate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-34  118.9   0.2    3.4e-34  118.3   0.2    1.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.3e-26   92.4   0.0    4.3e-26   91.5   0.0    1.4  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
      1e-05   26.1   0.0    3.9e-05   24.2   0.0    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00022   21.3   0.0    0.00044   20.3   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.003   18.0   0.1      0.011   16.1   0.0    1.9  2  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.043   13.2   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.06   13.2   0.0       0.41   10.6   0.0    2.1  2  NfI_DNAbd_pre-N  Nuclear factor I protein pre-N-terminus
       0.12   12.0   0.0       0.21   11.2   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.13   12.4   0.0       0.38   10.9   0.0    1.7  1  SchA_CurD        SchA/CurD like domain
       0.14   12.9   0.0       0.35   11.7   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.2   1.9e-37   3.4e-34       5     158 .]       2     154 ..       1     154 [. 0.97

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 1.9e-37
                                   E--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT- CS
                 NAD_binding_2   5 iGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdeviegllealkkgd 84 
                                    GlG+MG  +a nl+kag   +vynrt +k+e++ +e g+k ae++++l++s+d+ itm+++++av+++i+ ll+++ k++
  gi|70606224|ref|YP_255094.1|   2 AGLGIMGYRIAANLAKAGKLNMVYNRTVSKAEQFHKEyGVKYAEDPKSLIQSVDFLITMLSDDEAVKSFITPLLPYV-KDK 81 
                                   7**********************************9956************************************88.79* PP

                                   EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEEE-E CS
                 NAD_binding_2  85 ilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvthviG 158
                                   i++d+st+sp++++ l++e++++g  ++d+PV G++   e+ +++++vGG++e+f+ v++vl++ +a+v+ ++G
  gi|70606224|ref|YP_255094.1|  82 IIVDMSTISPSTSISLSNEVSKHGGIMFDTPVIGTTIAVEQKKITVLVGGPKEKFNIVQDVLKETAANVI-YVG 154
                                   *********************************************************************9.667 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   2.4e-29   4.3e-26       1     122 []     157     278 ..     157     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 2.4e-29
                NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevina.ssgrsnalenklpqrvlsrdfdpgFaldlmlKDlgl 80 
                                   G++  +K++nnll++i + a++Ea++++++ Gldpe++  ++++ +s +s ++e klp +v+s+d+ ++Fa+++m+KDl++
  gi|70606224|ref|YP_255094.1| 157 GSALYAKIANNLLTGIYMTALAEAFTFGVRSGLDPEEIKTILSQyASVKSPFMELKLP-KVISGDYSTQFATKHMAKDLEI 236
                                   677789***********************************987478899********.5********************* PP

                NAD_binding_11  81 alelareagaplpllalaeqlyaaaaaegggdaDhsaivrll 122
                                   a+ + +++++ +pl++   qly+ a+  g gd+D++++++++
  gi|70606224|ref|YP_255094.1| 237 AVRESQNLKVITPLTSISLQLYRLADGLGYGDSDFASVIEVY 278
                                   **************************************9986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.2e-08   3.9e-05       6      94 ..       3      86 ..       1      88 [. 0.87
   2 ?   -3.5   0.0       9.3   1.7e+04      40      56 ..     228     244 ..     216     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.2e-08
                                  TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S.-HHHHHHHHHHCGHHHHT CS
                 F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav.kpedveevlselakdalk 87
                                  G G mg  +a +l++ag  + ++v   +r+ +kae++++e+gvk  + d + ++++ d+++  +   e+v+++++ l     k
  gi|70606224|ref|YP_255094.1|  3 GLGIMGYRIAANLAKAG--KLNMV--YNRTVSKAEQFHKEYGVKYAE-DPKSLIQSVDFLITMLsDDEAVKSFITPL-LPYVK 79
                                  89***************..33333..5********************.***********997761568899999999.77799 PP

                                  TSEEEEE CS
                 F420_oxidored 88 gklvisv 94
                                  +k+++++
  gi|70606224|ref|YP_255094.1| 80 DKIIVDM 86
                                  9999997 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.3
                                   HHHHHHHC-EEECECHH CS
                 F420_oxidored  40 eelaeelgvkvtavdne 56 
                                   +++a++l++ v +++n 
  gi|70606224|ref|YP_255094.1| 228 KHMAKDLEIAVRESQNL 244
                                   45566666666666555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.5e-07   0.00044      19      88 ..       3      66 ..       1      88 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                                  S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                  Shikimate_DH 19 GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88
                                  G G m+ ++a +L+++g    +v NRt+++a+++ +e++ +       e+ k+l++++d +i+  +  e+
  gi|70606224|ref|YP_255094.1|  3 GLGIMGYRIAANLAKAGKL-NMVYNRTVSKAEQFHKEYGVK-----YAEDPKSLIQSVDFLITMLSDDEA 66
                                  99************99877.589*************99444.....67899999999**99998776665 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.4e-06     0.011      20     101 ..       9      88 ..       8      91 .. 0.87
   2 ?   -2.1   0.0       2.9   5.2e+03      14      27 ..     238     251 ..     236     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EEEESS CS
                UDPG_MGDP_dh_C  20 ldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpavvfDgr 100
                                   ++i+++L+++g+   +y   v+++++ +  +e+gv++++++++ ++++d ++ +   de  +  +  l   +k+++++D+ 
  gi|70606224|ref|YP_255094.1|   9 YRIAANLAKAGKLNMVYNRTVSKAEQFH--KEYGVKYAEDPKSLIQSVDFLITMLSDDEAVKSFITPLLPYVKDKIIVDMS 87 
                                   5899*******************99887..469*****************9998877776665688899999*******87 PP

                                   S CS
                UDPG_MGDP_dh_C 101 n 101
                                    
  gi|70606224|ref|YP_255094.1|  88 T 88 
                                   5 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
                                   -TT-HHHHHHHHHH CS
                UDPG_MGDP_dh_C  14 lReSpaldiieeLl 27 
                                   +ReS+ l++i+ L+
  gi|70606224|ref|YP_255094.1| 238 VRESQNLKVITPLT 251
                                   79******998875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.4e-05     0.043      42     109 ..       2      71 ..       1      82 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                   ES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSB CS
                  2-Hacid_dh_C  42 iGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDivslhlpltpetrhli 109
                                    GlG +G ++a  l++ g   ++y+r+ +k e   +e+gv+++ + + l+++ D+++ +l   ++ + +i
  gi|70606224|ref|YP_255094.1|   2 AGLGIMGYRIAANLAKAGKLNMVYNRTVSKAEqFHKEYGVKYAeDPKSLIQSVDFLITMLSDDEAVKSFI 71 
                                   599******998888776655555555555553788999977769***********99988777666655 PP

>> NfI_DNAbd_pre-N  Nuclear factor I protein pre-N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.41       3      19 ..      63      79 ..      61      81 .. 0.87
   2 ?   -0.4   0.0      0.59   1.1e+03       9      23 ..     207     221 ..     204     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
               NfI_DNAbd_pre-N  3 qqedfhpFiEaLLPyVk 19
                                  + e + +Fi  LLPyVk
  gi|70606224|ref|YP_255094.1| 63 DDEAVKSFITPLLPYVK 79
                                  567899**********9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.59
               NfI_DNAbd_pre-N   9 pFiEaLLPyVkafaY 23 
                                   pF+E  LP V +  Y
  gi|70606224|ref|YP_255094.1| 207 PFMELKLPKVISGDY 221
                                   9*******9988777 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.21       4      43 ..       2      43 ..       1      65 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                  ES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEE CS
                          ApbA  4 lGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrl 43
                                  +G+G +G  +aa+Lakag    +++r+  ++e+  k+ G++ 
  gi|70606224|ref|YP_255094.1|  2 AGLGIMGYRIAANLAKAGKLNMVYNRTVsKAEQfHKEYGVKY 43
                                  6******************99999999999999556666665 PP

>> SchA_CurD  SchA/CurD like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.38       4      33 ..     179     209 ..     176     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                     SchA_CurD   4 aAltyrvkpGse.devaelladykrpesrvl 33 
                                   +A t+ v+ G + +e++ +l++y++++s+ +
  gi|70606224|ref|YP_255094.1| 179 EAFTFGVRSGLDpEEIKTILSQYASVKSPFM 209
                                   799*******98578************9986 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.35       5      65 ..       1      56 [.       1      70 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                  EETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESE CS
                  GFO_IDH_MocA  5 iiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeida 65
                                  + G+G +g++ +++l ++    ++  ++++  ++ae++ +++gv+  +d + l +   +d+
  gi|70606224|ref|YP_255094.1|  1 MAGLGIMGYRIAANLAKA---GKLNMVYNRTVSKAEQFHKEYGVKYAEDPKSLIQ--SVDF 56
                                  679999999998555555...89999***********************999988..5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2144.21
//
Query:       gi|70606225|ref|YP_255095.1|  [L=128]
Description: hypothetical protein Saci_0386 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 878.09
//
Query:       gi|70606226|ref|YP_255096.1|  [L=80]
Description: hypothetical protein Saci_0387 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.3   0.0    2.3e-18   66.2   0.0    1.0  1  Rdx       Rdx family


Domain annotation for each model (and alignments):
>> Rdx  Rdx family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.3e-22   2.3e-18       1      72 [.       4      73 ..       4      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.3e-22
                                  EEEEEEETTTTTHHHHHHHHHHHHHHCCCCSSEEEEEEESTT-EEEEETTEEEEEHHHHTSS--HHHHHHHH CS
                           Rdx  1 rvtIeYCtqCkwmlraaelaqellstfpeslgevalqpstgGaFeVtldgelvwsrkeeggfpetkelkqrv 72
                                  +v+I YC  C++  ra +la+ lls ++    +v+l+++++G+F V++dg+l++sr +e++fp+++e+++ +
  gi|70606226|ref|YP_255096.1|  4 NVKIVYCRPCGFLDRALNLARDLLSYYEG--VNVELEQGKNGIFDVYVDGQLIFSRFKEKRFPDSQEILKEL 73
                                  59***************************..9***********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 586.07
//
Query:       gi|70606227|ref|YP_255097.1|  [L=329]
Description: hypothetical protein Saci_0388 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-14   52.9  14.7    3.2e-14   52.9  14.7    2.4  3  ABC2_membrane    ABC-2 type transporter
    2.5e-08   33.5  31.6    4.6e-07   29.3  31.6    2.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1     0.051   4.5e+02      25      38 ..      25      38 ..       5      74 .. 0.65
   2 !   52.9  14.7   3.6e-18   3.2e-14      25     208 ..     121     294 ..      86     296 .. 0.86
   3 ?   -2.2   0.4      0.25   2.2e+03     135     145 ..     307     317 ..     297     324 .. 0.45

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.051
                 ABC2_membrane 25 rliqplllalvfgt 38
                                   +++pl+lalvf +
  gi|70606227|ref|YP_255097.1| 25 VIFFPLILALVFSL 38
                                  23333333333322 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 3.6e-18
                 ABC2_membrane  25 rliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvel 105
                                   ++++  l+++  + v +         ++ g+++ ++l ++++++t+v  +  ++ ++++r+ +spl +  + vl+ +++e+
  gi|70606227|ref|YP_255097.1| 121 SIFSSQLILTRNTPVAY---------EISGVIGVIALSNGIFGVTGV-GSGYYRDRLVDRLASSPL-RDYEWVLSLMIYEV 190
                                   33333333333333333.........459******************.888888889*********.************** PP

                 ABC2_membrane 106 pvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalaps..fedasqlaslvllpllllsGffipids 184
                                   ++++l ++++l + ++l g+++ +++ fl +l+l++l++s+lg +i  l+p+  +  a+++ +++++pl++ s +f++ + 
  gi|70606227|ref|YP_255097.1| 191 LITILSSIVVLGLGLIL-GFTPVSILEFLGVLILSTLMFSGLGAIILGLTPKdkIFLANVVPTFIVFPLMFISNAFYSSSI 270
                                   ****************9.****767*************************9633777999******************999 PP

                 ABC2_membrane 185 mpkwlqwiaylnPltyavealrsn 208
                                    p+ l  ia++ P++ + +++r++
  gi|70606227|ref|YP_255097.1| 271 FPSILGLIAEYQPVSIVNDVVRQA 294
                                   9*******************9987 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.25
                 ABC2_membrane 135 llllltalaas 145
                                   +++++++l+++
  gi|70606227|ref|YP_255097.1| 307 ITIIILTLVFL 317
                                   22222222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3  31.6   5.1e-11   4.6e-07       3     342 ..      21     316 ..      19     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.1e-11
               ABC2_membrane_3   3 fliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidgil 83 
                                   +l +++++P+il+l++ l+ +n++   ++  + +++ +   ++q++ ++++as+ ++   ++    ++       +++ ++
  gi|70606227|ref|YP_255097.1|  21 TLGFVIFFPLILALVFSLL-GNAF---QPHATVYLTGE---NAQKVGKYVNASGLFT--AYIGGSPSIV------KYEPVI 86 
                                   4445566666666655555.3444...33333344444...8999**********99..5555555553......355555 PP

               ABC2_membrane_3  84 vipkgfskdllkgesatvtvlinssnlnsskailnalnsllqqlnasalvlqseatstsaninvestql.eeelsnvasfl 163
                                    i+            ++ +v++n+  ++ +++++++lns++++++                 ++ s ql    ++ va+ +
  gi|70606227|ref|YP_255097.1|  87 FINL-----------TSKNVYYNQLEQEYVPLLQSYLNSYYTNQT-----------------SIFSSQLiLTRNTPVAYEI 139
                                   4443...........34479999****************553322.................2333333344556688889 PP

               ABC2_membrane_3 164 vgliliilifitasfiavsi.veEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgipfgnlgll 241
                                    g+i +i+++ +++ ++ ++     + r+  ++ +s+++ ++ +ls ++  +l+ +l+++++l+l  ++g  ++  +++ +
  gi|70606227|ref|YP_255097.1| 140 SGVIGVIALSNGIFGVT-GVgSGYYRDRLVDRLASSPLRDYEWVLSLMIYEVLITILSSIVVLGLglILG--FTPVSILEF 217
                                   99999998888888554.564677899***********************************99655999..********* PP

               ABC2_membrane_3 242 lllfllfglayialgyllsslfknset..aqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd 320
                                   l +++l  l+++ lg+ +  l+ + +   a+++ +++ ++l++++ ++++ + +ps+l  i+ + P + + ++  + i   
  gi|70606227|ref|YP_255097.1| 218 LGVLILSTLMFSGLGAIILGLTPKDKIflANVVPTFIVFPLMFISNAFYSSSIFPSILGLIAEYQPVSIVNDVVRQAIV-- 296
                                   *********************88776611565555555589************************************85.. PP

               ABC2_membrane_3 321 plweillsliilalfavvylll 342
                                     +++l++ i+l+ +++++l++
  gi|70606227|ref|YP_255097.1| 297 --FNVLPNPIYLITIIILTLVF 316
                                   ..44555555554444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2223.86
//
Query:       gi|70606229|ref|YP_255098.1|  [L=275]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-32  111.4   0.0    7.3e-32  110.7   0.0    1.3  1  ABC_tran         ABC transporter
    2.3e-12   47.4   0.1    2.8e-07   30.6   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.1e-05   23.5   0.0      0.044   13.5   0.2    2.2  2  AAA_15           AAA ATPase domain
    0.00018   21.0   0.3       0.22   10.9   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00073   19.3   0.0       0.02   14.6   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
     0.0015   18.5   0.2     0.0085   16.0   0.1    2.2  1  Rad17            Rad17 P-loop domain
     0.0042   16.8   0.1     0.0097   15.6   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0059   16.8   0.0      0.068   13.4   0.0    2.5  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0076   16.8   7.0       0.13   12.8   6.9    2.3  1  AAA_23           AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.2       0.07   13.4   0.2    2.3  1  AAA_22           AAA domain
      0.011   15.4   0.2       0.02   14.6   0.2    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.014   15.2   0.0      0.027   14.2   0.0    1.4  1  AAA_30           AAA domain
      0.021   15.1   0.0      0.033   14.5   0.0    1.3  1  AAA_19           AAA domain
      0.065   11.9   0.1       0.44    9.1   0.1    2.0  2  AAA_13           AAA domain
      0.067   13.1   0.0       0.13   12.2   0.0    1.5  1  Ldh_1_C          lactate/malate dehydrogenase, alpha/beta C-t
      0.079   12.7   0.1       0.26   11.0   0.0    1.9  2  AAA_24           AAA domain
      0.098   13.1   2.1          1    9.8   2.1    2.6  1  AAA              ATPase family associated with various cellul
       0.12   12.1   0.1        1.6    8.4   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
       0.12   12.2   0.6        3.1    7.7   0.1    2.7  3  RsgA_GTPase      RsgA GTPase
       0.16   12.4   0.0       0.22   11.9   0.0    1.4  1  AAA_16           AAA ATPase domain
       0.17   10.9   0.0       0.26   10.3   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.22   10.4   1.3          1    8.2   0.1    2.3  3  AAA_10           AAA-like domain
       0.23   11.2   0.9       0.44   10.3   0.2    1.8  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.38   10.8   2.8       0.42   10.7   0.5    2.1  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   9.8e-35   7.3e-32       1     136 [.      46     184 ..      46     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 9.8e-35
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+ +s++++ege+  i+G+nGaGK+t +k+l+  lkpt+G++ + g ++ + e ++ r+ ++ +pqe q f +l+vren  
  gi|70606229|ref|YP_255098.1|  46 LRGISFNVNEGEIFTILGPNGAGKTTTVKILSCVLKPTKGKVIVLGYEVPK-ECKKIREMVSSVPQEFQGFADLSVRENie 125
                                   6789********************************************999.9**************************** PP

                                   ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         ++++++e++l+ l+lke ++++     ++LSgG k+rva+a+ ++ +pk+++lDEpt
  gi|70606229|ref|YP_255098.1| 126 yfaslyKAKNKVEEVLELLDLKEHEKKRF----RNLSGGLKRRVAIACGIVGNPKIVFLDEPT 184
                                   *****9999**************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   3.2e-05     0.024       2      22 ..      59      79 ..      58      91 .. 0.86
   2 !   30.6   0.0   3.8e-10   2.8e-07     234     297 ..     154     214 ..     108     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    + GpNg+GK++  ++l+++
  gi|70606229|ref|YP_255098.1| 59 FTILGPNGAGKTTTVKILSCV 79
                                  5799**************987 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 3.8e-10
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                   +r+lS G kr  a++  +   +   +++++DEp  gL+P+  r+ ++++++l+++++ ++l+TH
  gi|70606229|ref|YP_255098.1| 154 FRNLSGGLKRRVAIACGIVGNP---KIVFLDEPTVGLDPESRRKMWDIIRALKEKKITIFLATH 214
                                   6777888888766666666555...9************************************** PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   5.9e-05     0.044      24      55 ..      56     103 ..      43     162 .. 0.58
   2 !    8.9   0.0    0.0015       1.1     298     364 ..     158     214 ..      93     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-05
                        AAA_15  24 e.ltvliGkNnsGKSsilealdlFlnnkekkn................k 55 
                                     + ++ G+N++GK++ +++l   l+ + k +                +
  gi|70606229|ref|YP_255098.1|  56 GeIFTILGPNGAGKTTTVKILSCVLKPT-KGKvivlgyevpkeckkirE 103
                                   2488999******************988.33356777666644333330 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
                        AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   + G++r + ++  i+          +++i++++EP + L p+  + +++ ++ l +++   +++ TH
  gi|70606229|ref|YP_255098.1| 158 SGGLKRRVAIACGIV---------GNPKIVFLDEPTVGLDPESRRKMWDIIRALKEKKI-TIFLATH 214
                                   555555555555444.........35778*************************99999.8999999 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1     0.002       1.5      26      48 ..      58      80 ..      46      88 .. 0.80
   2 !   10.9   0.0    0.0003      0.22     111     213 ..     131     231 ..     103     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.002
                                  EEEEEESTTSSHHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 26 ftaivGpNGSGKsnlldAilFvL 48
                                  +  i+GpNG+GK+  +  ++ vL
  gi|70606229|ref|YP_255098.1| 58 IFTILGPNGAGKTTTVKILSCVL 80
                                  5679*********9988877776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0003
                                   EEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         SMC_N 111 ykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.a 190
                                   yk ++k  +  e+ +l e+++    +LSgG k  va+a       v    +++lDe    LD + ++k+ +++++ +++  
  gi|70606229|ref|YP_255098.1| 131 YKAKNKVEEVLELLDLKEHEKKRFRNLSGGLKRRVAIACG----IVGNPKIVFLDEPTVGLDPESRRKMWDIIRALKEKkI 207
                                   44444444445555555555555569****9999988765....456667899*********************8775535 PP

                                   EEEEE-SSHHHC.CC-SCEEEEEE CS
                                   xxxxxxxxxxxx.xxxxxxxxxxx RF
                         SMC_N 191 Qfivislreeml.ekadklvgvtk 213
                                    ++  ++  +   + ad++v ++k
  gi|70606229|ref|YP_255098.1| 208 TIFLATHYLDEAeKLADRVVVIYK 231
                                   555555554444044577777766 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-05      0.02       3      78 ..      63     136 ..      61     143 .. 0.82
   2 ?    2.6   0.0      0.13        96     116     180 ..     173     237 ..     161     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                   ESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHH CS
               Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalk 78 
                                   G +GaGKtt +++l   lk  + k +vl  e    +  +kire+++ ++  e q +a l + + ie +++++k+++k
  gi|70606229|ref|YP_255098.1|  63 GPNGAGKTTTVKILSCVLKPTKGKvIVLGYEVP--KECKKIREMVS-SVPQEFQGFADLSVRENIEYFASLYKAKNK 136
                                   89*****************99999999999988..66788898888.888888888877777777777777777666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                   SE-SEEEEEESSHHHHHTSCCTTSSTT.TSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETTS-HHH CS
               Thymidylate_kin 116 lkPdltflldvdpevalkRlakrdeld.eeeeeqldflrkvrerylelak.ederiliidasksiee 180
                                   + P ++fl +  p v+l   ++r++ d     +++++   + ++yl++a+   +r+++i+  k i+e
  gi|70606229|ref|YP_255098.1| 173 GNPKIVFLDE--PTVGLDPESRRKMWDiIRALKEKKITIFLATHYLDEAEkLADRVVVIYKGKMIKE 237
                                   3788887776..9999999999999553445566666667788899999989999999987777766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.1e-05    0.0085      39      70 ..      50      81 ..      39      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                         Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                  + + ++ +i  i GP G gk+t+vk+Ls  l 
  gi|70606229|ref|YP_255098.1| 50 SFNVNEGEIFTILGPNGAGKTTTVKILSCVLK 81
                                  55556667999*****************8775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.3e-05    0.0097      17      50 ..      51      84 ..      41      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  +++++ +++ + Gp+G+GK+T +  ++ +L p+k
  gi|70606229|ref|YP_255098.1| 51 FNVNEGEIFTILGPNGAGKTTTVKILSCVLKPTK 84
                                  455544499**************99999999987 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   9.2e-05     0.068      63      89 ..     174     200 ..     132     201 .. 0.91
   2 ?   -2.6   0.0         9   6.7e+03      66      76 ..     213     222 ..     207     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-05
                       SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                   ++++vfLDE   +lD+es++++ ++++
  gi|70606229|ref|YP_255098.1| 174 NPKIVFLDEPTVGLDPESRRKMWDIIR 200
                                   5899******************99987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9
                       SbcCD_C  66 lvfLDEAFskl 76 
                                   +  LDEA +kl
  gi|70606229|ref|YP_255098.1| 213 THYLDEA-EKL 222
                                   5679999.554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   6.9   0.00017      0.13      13      43 ..      49      80 ..      41     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                        AAA_23 13 qeidF.skgltlItGpNGaGKTTildAiklaL 43
                                   +++  +  ++ I GpNGaGKTT +  +  +L
  gi|70606229|ref|YP_255098.1| 49 ISFNVnEGEIFTILGPNGAGKTTTVKILSCVL 80
                                  3444455579*************988776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   9.4e-05      0.07       6      65 ..      57     113 ..      53     252 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.4e-05
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralg 65 
                                    i ++ G+ G+GKTt+++ l   l+    +++ ++ v+ +++p+++ + +++ + + ++++
  gi|70606229|ref|YP_255098.1|  57 EIFTILGPNGAGKTTTVKILSCVLK----PTKGKVIVLGYEVPKECkKIREMVSSVPQEFQ 113
                                   68899*************9988873....44458888899999999888888888888877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.6e-05      0.02       4      34 ..      59      89 ..      57      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                  + ++G++GaGKTtt+  L+ +lk  + kv++
  gi|70606229|ref|YP_255098.1| 59 FTILGPNGAGKTTTVKILSCVLKPTKGKVIV 89
                                  6789******************999888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-05     0.027      19      52 ..      57      90 ..      49     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   + ++ Gp G+GKtt++k l  +++  +g+vi+l
  gi|70606229|ref|YP_255098.1| 57 EIFTILGPNGAGKTTTVKILSCVLKPTKGKVIVL 90
                                  578999*******************999999987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.5e-05     0.033      10      78 ..      56     156 ..      48     252 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
                        AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaf.tgrAakelrerlaalgaeatTiHrlal............ 77 
                                    +++ ++++ G GKT+++k    +l+ ++g    +++++ +   + +k++re ++++ +e + +  l++            
  gi|70606229|ref|YP_255098.1|  56 GEIFTILGPNGAGKTTTVKILSCVLKPTKG----KVIVLGYeVPKECKKIREMVSSVPQEFQGFADLSVrenieyfaslyk 132
                                   567899************999999998884....4566655157999*******999999888888887888888887755 PP

                        AAA_19  78 .......................l 78 
                                                           
  gi|70606229|ref|YP_255098.1| 133 aknkveevlelldlkehekkrfrN 156
                                   555555555554444444444440 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00059      0.44      20      39 ..      60      79 ..      53     102 .. 0.85
   2 ?   -0.1   0.0      0.35   2.6e+02     525     572 ..     173     217 ..     170     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00059
                        AAA_13 20 liYGwNGaGKTtLSrllrsl 39
                                   i G NGaGKTt  ++l+++
  gi|70606229|ref|YP_255098.1| 60 TILGPNGAGKTTTVKILSCV 79
                                  588**************997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.35
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                   g+ kiv++D P   LD +s       i++     +k   +f+ TH l+
  gi|70606229|ref|YP_255098.1| 173 GNPKIVFLDEPTVGLDPESRRKMWDIIRALK---EKKITIFLATHYLD 217
                                   67899***********999999999999986...55567999999765 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.13     116     159 ..     118     164 ..      70     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                   S....SEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHHH CS
                       Ldh_1_C 116 q....eieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkke 159
                                        +ieyf++    + n+ve+vle l l + e++++++    Lk  
  gi|70606229|ref|YP_255098.1| 118 LsvreNIEYFASLYKAK-NKVEEVLELLDLKEHEKKRFRNLSGGLKRR 164
                                   1444589***9988888.*********************999888865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035      0.26       6      32 ..      60      93 ..      56     157 .. 0.73
   2 ?   -1.3   0.0         2   1.5e+03     114     133 ..     215     234 ..     191     249 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                        AAA_24  6 liyGpsgiGKTtlakel.......gpkplfidte 32
                                   i Gp+g+GKTt++k l       + k++++  e
  gi|70606229|ref|YP_255098.1| 60 TILGPNGAGKTTTVKILscvlkptKGKVIVLGYE 93
                                  799************9988887777777777544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                        AAA_24 114 llkklqelrknvifiahekt 133
                                   +l+  ++l + v++i + k+
  gi|70606229|ref|YP_255098.1| 215 YLDEAEKLADRVVVIYKGKM 234
                                   33344444444444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.1    0.0013         1       3      38 ..      61     115 ..      59     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                                   EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSS..............S CS
                           AAA   3 lyGppGtGKTllakavakelg.....vefleisgsellsk..............y 38 
                                   + Gp G GKT+++k +   l+     v +l  ++++ ++k              +
  gi|70606229|ref|YP_255098.1|  61 ILGPNGAGKTTTVKILSCVLKptkgkVIVLGYEVPKECKKiremvssvpqefqgF 115
                                   68*************9988753222222333333333322333344444444440 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0022       1.6      33      62 ..      41      71 ..      19      81 .. 0.84
   2 ?    1.4   0.0       0.3   2.3e+02     107     147 ..     173     212 ..     134     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                     IstB_IS21 33 rkvkeLatlsf.iekkenivllGpsGvGKsh 62
                                    +++L++ sf +++ e + +lGp G+GK+ 
  gi|70606229|ref|YP_255098.1| 41 GGIEALRGISFnVNEGEIFTILGPNGAGKTT 71
                                  5688999999978899999**********95 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.3
                     IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrsiiits 147
                                    +++++ lD+  ++ ld +++++++++i +  e++ +i  +
  gi|70606229|ref|YP_255098.1| 173 GNPKIVFLDEP-TVGLDPESRRKMWDIIRALKEKKITIFLA 212
                                   55677888885.56799999999999999999999887655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0042       3.1      91     120 ..      47      77 ..      29      88 .. 0.80
   2 ?   -0.2   0.0       1.1   8.2e+02      66     109 ..     131     173 ..     116     182 .. 0.76
   3 ?    0.9   0.1      0.49   3.7e+02      21      68 ..     198     243 ..     195     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                                   HHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinall 120
                                   + ++ ++++ ++ +++G+ G+GK+t ++ l 
  gi|70606229|ref|YP_255098.1|  47 RGISFNVNEgEIFTILGPNGAGKTTTVKILS 77 
                                   556666666699*************998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                                   HHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTT CS
                   RsgA_GTPase  66 eelkeelealgyevllvsaktkegleelkellkdktsvlvGqSG 109
                                    + k+++e++ +e+l +++++k+ +++l+  lk ++++ +G  G
  gi|70606229|ref|YP_255098.1| 131 YKAKNKVEEV-LELLDLKEHEKKRFRNLSGGLKRRVAIACGIVG 173
                                   4555666666.788888999999999999999999999999777 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.49
                                   EEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHH CS
                   RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleel 68 
                                   i+ +lke++++  l + +L +ae+  ++ v+v+ K  +++e++  +el
  gi|70606229|ref|YP_255098.1| 198 IIRALKEKKITIFLATHYLDEAEKL-ADRVVVIYKGKMIKETS-PREL 243
                                   7889999999999999999999875.56677888888888877.4444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.22      20      63 ..      54     101 ..      43     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                        AAA_16  20 rsgrpelvllsGesGvGKsslv...rellralekdggif....lrgkcdql 63 
                                   ++g  e+  + G+ G GK++ v    ++l++ +++ +i+    +  +c++ 
  gi|70606229|ref|YP_255098.1|  54 NEG--EIFTILGPNGAGKTTTVkilSCVLKPTKGK-VIVlgyeVPKECKKI 101
                                   444..8999************95555666555555.444433444444444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00035      0.26     122     163 ..      49      90 ..      23     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                         T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinksderivtv 163
                                   ++  v+e  ++ + G+ g GKtt++ +l   ++ ++ +++++
  gi|70606229|ref|YP_255098.1|  49 ISFNVNEGEIFTILGPNGAGKTTTVKILSCVLKPTKGKVIVL 90 
                                   56667888899999**************99999998777765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0014         1      24      76 ..      59     113 ..      42     130 .. 0.77
   2 ?    0.8   0.1      0.25   1.8e+02     291     335 ..     120     160 ..     105     162 .. 0.70
   3 ?   -1.8   0.0       1.6   1.2e+03     139     155 ..     192     208 ..     177     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                        AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkaliiD..pkkerekfketlpeiakkin 76 
                                     i+G+ G+GK  ++k+l   +   +gk++++     ke +k +e +  ++++++
  gi|70606229|ref|YP_255098.1|  59 FTILGPNGAGKTTTVKILSCVLKPTKGKVIVLGyeVPKECKKIREMVSSVPQEFQ 113
                                   3799************************999852234677777777777777665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                        AAA_10 291 lknniglklaFretdkeeikkvLeflgldvedednkkelrelesG 335
                                    ++ni +      + k++ ++vLe+l+l     ++kk++r+l  G
  gi|70606229|ref|YP_255098.1| 120 VRENIEYFASLY-KAKNKVEEVLELLDLKE---HEKKRFRNLSGG 160
                                   556666544333.56788899999999977...578889998766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.6
                        AAA_10 139 qrgllavieelrkedek 155
                                    r+++++i+ l++++  
  gi|70606229|ref|YP_255098.1| 192 RRKMWDIIRALKEKKIT 208
                                   35666666666655433 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00059      0.44       1      29 [.      61      89 ..      61      93 .. 0.88
   2 ?   -2.3   0.0       4.2   3.1e+03     194     211 ..     129     147 ..      98     155 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvav 29
                                  ++Gp G+GKtt v+ ls +l+ ++ +v v
  gi|70606229|ref|YP_255098.1| 61 ILGPNGAGKTTTVKILSCVLKPTKGKVIV 89
                                  68*****************9988777765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                    ATP_bind_1 194 e.ekykklaeaiaelleef 211
                                   +  k k+  e++ ell++ 
  gi|70606229|ref|YP_255098.1| 129 SlYKAKNKVEEVLELLDLK 147
                                   2444455555555555554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00056      0.42      26      58 ..      59      90 ..      50      91 .. 0.89
   2 ?   -2.0   0.0       4.1     3e+03     179     193 ..     131     144 ..     104     168 .. 0.56
   3 ?   -1.7   0.0       3.3   2.5e+03     124     124 ..     219     219 ..     176     270 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                         DUF87 26 lAilgsTGsGKSntvavLleellekkgatilil 58
                                  + ilg  G+GK++tv++L   l    ++++++l
  gi|70606229|ref|YP_255098.1| 59 FTILGPNGAGKTTTVKILSCVLK-PTKGKVIVL 90
                                  679***************99999.777788876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                         DUF87 179 ggsfsnsstdliall 193
                                   ++ + n+ +++++ll
  gi|70606229|ref|YP_255098.1| 131 YKAK-NKVEEVLELL 144
                                   3322.2223333222 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.3
                         DUF87 124 a 124
                                   a
  gi|70606229|ref|YP_255098.1| 219 A 219
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 1781.55
//
Query:       gi|70606228|ref|YP_255099.1|  [L=313]
Description: hypothetical protein Saci_0390 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-10   41.5   0.0    3.2e-10   40.5   0.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    1.1e-09   38.6   0.0    1.8e-09   37.9   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   3.5e-14   3.2e-10       6      84 ..      41     121 ..      28     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.5e-14
                                   EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHHTT-EEEEEEEEEESS CS
                          AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaeelgvplvgGdtsfsne 83 
                                   v++ d    p+   + +  G+++v v+++D+ + G +   ++ +l l     l+ v++g++ea++ l++++vgG+t+ +++
  gi|70606228|ref|YP_255099.1|  41 VIHSD----PITETGKDA-GYLSVVVACNDVNMKGVECKSIITTLLLHdeeSLSPVIEGISEACNILKCKVVGGHTELTKG 116
                                   44444....444455555.********************9999999999****************************9887 PP

                                   ....E CS
                          AIRS  84 ....p 84 
                                       +
  gi|70606228|ref|YP_255099.1| 117 ldrdI 121
                                   66433 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0     2e-13   1.8e-09       2     119 ..     141     263 ..     140     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2e-13
                                   TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT.TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHHHHHHHH CS
                        AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds.avqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlgalaema 80 
                                   + d ++l g+ G+ g  +++ +  ++ + l    +++l + ++  + +  ++  a++ k+ + ++hD T+GG+  al e+a
  gi|70606228|ref|YP_255099.1| 141 ENDYIVLFGNPGIEGTWILANEYEDKLSRL--GvSRNLIERAKRFKYLIPVQDKAMKvKDYAISMHDATEGGIYQALLEVA 219
                                   6799*************9999977777764..24677777777778888888888889*********************** PP

                                   HTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEE CS
                        AIRS_C  81 pasgvgaeidldkvpifdele.....splemllsensGrllvav 119
                                   +a ++ ++++ +k+p+++e+      + + ++   +sG  +v+ 
  gi|70606228|ref|YP_255099.1| 220 QATNLRVVVEKEKIPLLEETVeitkaLNINPYTLISSGAFIVIT 263
                                   *******************9755555555555558888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2276.26
//
Query:       gi|70606230|ref|YP_255100.1|  [L=163]
Description: hypothetical protein Saci_0391 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-09   38.6   0.0    4.3e-09   36.9   0.0    1.7  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.05   13.5   0.0       0.21   11.5   0.0    1.8  2  CTP_transf_3     Cytidylyltransferase
      0.057   13.0   0.0      0.075   12.6   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
       0.11   11.6   0.1       0.21   10.8   0.0    1.5  1  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   9.5e-13   4.3e-09       1     114 [.       3     108 ..       3     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.5e-13
                                   EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd.eevlaalarlgvrvvededpgkgplaslaaal 80 
                                   a+i+AGG++sR    K+ l+++g p++ +v+++lr+  ++e++++  + +++   +  ++++ +    +g g    +  a+
  gi|70606230|ref|YP_255100.1|   3 AIIMAGGKGSRISPYKPILEICGFPMYYWVYRSLREF-AEEIYLAITPwSSLI--F--SDIPKIIT--YGNGYENDVIEAV 76 
                                   79***********************************.9******76635544..2..45555555..47899999***** PP

                                   HHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHH CS
                  NTP_transf_3  81 raaadadavlvlacDmPlltpelverllaaaaas 114
                                   +++    +v+v++ D+Pl+++++  +l++ ++a+
  gi|70606230|ref|YP_255100.1|  77 KQV--GFPVIVTPSDTPLIPKHVFMKLINDCRAQ 108
                                   998..79**********************99865 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.21       2      46 ..       3      46 ..       2      49 .. 0.85
   2 ?   -0.2   0.0      0.18     8e+02      79     117 ..      74     107 ..      69     149 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                  EEEEE-SSSSSS.TTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEE CS
                  CTP_transf_3  2 aIipARsgSkRl.pgKnlldlggkpliayvleaalkskafekviva 46
                                  aIi A  + +R+ p K++l++ g p++ +v++ +++  + e++++a
  gi|70606230|ref|YP_255100.1|  3 AIIMAGGKGSRIsPYKPILEICGFPMYYWVYRSLRE--FAEEIYLA 46
                                  688888888888789********************9..66666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                                   HHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHH CS
                  CTP_transf_3  79 evvkaflmseneeiivnlqGdnPllqeevikkaietlke 117
                                   e+vk++ +      ++ + +d Pl+++ v  k+i + + 
  gi|70606230|ref|YP_255100.1|  74 EAVKQVGFP-----VIVTPSDTPLIPKHVFMKLINDCRA 107
                                   666666666.....5556668888888887777766655 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.075       1      30 [.       2      26 ..       2      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                  EEEEE--S--GGGTTCCTTSSGGGSEETTE CS
               NTP_transferase  1 kavILaGGsGtRLwPLtrtlakklvpvlgk 30
                                  ka+I+aGG+G+R+ P     +k+ + + g 
  gi|70606230|ref|YP_255100.1|  2 KAIIMAGGKGSRISP-----YKPILEICGF 26
                                  79***********99.....5555555555 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.6e-05      0.21      73     111 ..      70     103 ..      46     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.6e-05
                          CofC  73 kdlntavekafeeieekeviiipsdiPlikkedvkdlle 111
                                   +d+ +av+++       +vi++psd Pli k++  +l++
  gi|70606230|ref|YP_255100.1|  70 NDVIEAVKQV-----GFPVIVTPSDTPLIPKHVFMKLIN 103
                                   5666666776.....348*************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1227.04
//
Query:       gi|70606231|ref|YP_255101.1|  [L=248]
Description: hypothetical protein Saci_0392 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-48  162.6  14.0    1.4e-47  161.9  14.0    1.3  1  DUF1614   Protein of unknown function (DUF1614)
  ------ inclusion threshold ------
        1.8    8.8  19.6       0.49   10.6   3.0    3.4  2  Pkr1      ER protein Pkr1
        6.8    6.7   6.4        1.1    9.2   0.1    2.9  3  Syndecan  Syndecan domain


Domain annotation for each model (and alignments):
>> DUF1614  Protein of unknown function (DUF1614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9  14.0   2.3e-51   1.4e-47       2     170 .]      61     239 ..      60     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 2.3e-51
                       DUF1614   2 lgslinipvaelkskeel.ve...vkvlgisykvpvleeeekktvvavNvGGaviPlllslylllrlavs...llaallav 75 
                                   l s++ni+v+e+++++el  e   v+v+gi+++v +l+ + +kt++a+NvGG++iPl++s+ l++ +  +   ++ +++ v
  gi|70606231|ref|YP_255101.1|  61 LFSSVNIVVKEVQRERELvPEvdvVYVFGIPLPVTRLSIKPRKTLIAINVGGCLIPLIISILLIYFAFHNlhnIILLVVDV 141
                                   679***********77442335799*************************************999887667779999999* PP

                       DUF1614  76 livaavvyllarpvpgvGivvpllipplvaalaa.lllaeeea..aavaYisgvlGtLiGadllnlkkieklgapvvsIGG 153
                                   +i++a++++++++++gvG+v++ lipp++a +++ ll+ ++ +  ++ aYis+v+GtLiGadlln+++i + + ++vsIGG
  gi|70606231|ref|YP_255101.1| 142 IILIAASKYFSKVMEGVGVVMNPLIPPIIAGIFSvLLFLHNPYlvPISAYISSVFGTLIGADLLNIRSILEANPQIVSIGG 222
                                   **********************************766666655799***********************999999****** PP

                       DUF1614 154 aGtFdGifltgilavll 170
                                   +GtFdGifl+g++++++
  gi|70606231|ref|YP_255101.1| 223 MGTFDGIFLSGLFSIII 239
                                   **************986 PP

>> Pkr1  ER protein Pkr1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   8.8      0.14   8.1e+02      22      70 ..      15      74 ..      11      77 .. 0.62
   2 ?   10.6   3.0   8.2e-05      0.49      27      59 ..     113     145 ..      99     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                          Pkr1 22 iatnvsFaaLllvllaLlvatsni......H.....fivLlllalgLwasinWFvaeLkk 70
                                   a+ ++F+aL+l +++L ++t+ +      H     f  Ll++  +L+ s+n +v+e+++
  gi|70606231|ref|YP_255101.1| 15 TAILYVFLALFLFIISLSYFTYLFrliglsHglafvFSSLLTIFSFLFSSVNIVVKEVQR 74
                                  677789999999999999998754112222322222334566666677777777777765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.2e-05
                          Pkr1  27 sFaaLllvllaLlvatsniHfivLlllalgLwa 59 
                                    ++ L++++l +++a++n+H i+Ll++ +++ +
  gi|70606231|ref|YP_255101.1| 113 CLIPLIISILLIYFAFHNLHNIILLVVDVIILI 145
                                   457799999999***************987765 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.0       0.5     3e+03      17      31 ..      15      29 ..       7      36 .. 0.59
   2 ?    9.2   0.1   0.00019       1.1       4      31 ..     101     128 ..      98     133 .. 0.84
   3 ?   -2.7   0.0      0.94   5.6e+03      12      22 ..     169     179 ..     163     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.5
                      Syndecan 17 vvgllfaillvlflv 31
                                   ++l ++  l+lf++
  gi|70606231|ref|YP_255101.1| 15 TAILYVFLALFLFII 29
                                  334444444444444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                      Syndecan   4 erpevlaaviggvvvgllfaillvlflv 31 
                                    r+ ++a  +gg+++ l++ ill+ f  
  gi|70606231|ref|YP_255101.1| 101 PRKTLIAINVGGCLIPLIISILLIYFAF 128
                                   578888889***************9975 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.94
                      Syndecan  12 viggvvvgllf 22 
                                   +i+g+   llf
  gi|70606231|ref|YP_255101.1| 169 IIAGIFSVLLF 179
                                   67777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1895.40
//
Query:       gi|70606232|ref|YP_255102.1|  [L=95]
Description: hypothetical protein Saci_0393 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   11.8   0.0       0.32   11.3   0.0    1.2  1  DUF4959   Domain of unknown function (DUF4959)


Domain annotation for each model (and alignments):
>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.32      34      60 ..      46      72 ..      38      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                       DUF4959 34 avisytlPddedLlyvkaeYklknGke 60
                                   +i+y   dded+ y++a+++  + k+
  gi|70606232|ref|YP_255102.1| 46 DIIEYARWDDEDIRYIEAVFEGGKVKM 72
                                  589*****************9655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 697.77
//
Query:       gi|70606233|ref|YP_255103.1|  [L=265]
Description: methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-45  155.6   0.7    2.2e-45  155.2   0.7    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.7   1.2e-49   2.2e-45       1     212 [.       5     212 ..       5     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 1.2e-49
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   k++++G+GpGdpel+TvrA +++++advvl+++s++   +l+++++       +++ ++++  + eei +++++++++gk 
  gi|70606233|ref|YP_255103.1|   5 KVVFIGAGPGDPELITVRAKNVIEDADVVLYAGSLVNPQVLKWARK-------DAEIVNTASLTLEEITDIMIKKANEGKL 78 
                                   799******************************9999999999976.......46667777777***************** PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeeereleal 157
                                   +++l+sGD ++yg+ +e++ al++  agi++e +PG++++ a a+ lgi+lt  + +++v+        + + + ++++ +
  gi|70606233|ref|YP_255103.1|  79 IARLKSGDFSIYGALIEEIWALQD--AGIPYELVPGITAAIATASVLGIELTLPKISQTVIitrasGAVPMEGSIKDYAPF 157
                                   ************************..************************************999844445578899999* PP

                  TP_methylase 158 langdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                   l +g +++++++++ +++++++Lke  ++d + pv+vv +a+++++++ +gt++++
  gi|70606233|ref|YP_255103.1| 158 LMKGASMAIYTGVQLIDKVVRELKEGgVPD-DMPVIVVYKATWPEQKILKGTVGDI 212
                                   **************************7776.66********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1924.89
//
Query:       gi|70606234|ref|YP_255104.1|  [L=223]
Description: cobalt-precorrin-2 C(20)-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-35  120.9   0.0    7.9e-35  120.7   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   4.4e-39   7.9e-35       2     209 ..       4     202 ..       3     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 4.4e-39
                  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvv......lgddsraleilldllaeel.eleapmgkekepleeayeeiaealaea 75 
                                   ly++G+GpGdp+l+Tvr+ ++l +a+vv       + +s+al+i++++ + e   l +pm+k+  +  ++ e i e +  +
  gi|70606234|ref|YP_255104.1|   4 LYVIGLGPGDPNLITVRGSEILSKAEVVfvpystGTNRSLALSIVEKYSKAEIvTLGFPMKKD--VDPKDLERIGEEICSK 82 
                                   9***************************665432233345******99999889999999999..5555889999999888 PP

                  TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerelea 156
                                    ++    ++++ GDP++y+t+ ++ + l   +   +ve++PGvss++a+a+++ +pl+ ++e+ +++ p+   ++ +++++
  gi|70606234|ref|YP_255104.1|  83 SKSL--SAFVTLGDPSLYSTFFRVSNYLGCFN---SVEIVPGVSSITACASKAFMPLALRNEAIAII-PA---DRLDLISK 154
                                   8886..7******************9999977...5*******************************.55...5899**** PP

                  TP_methylase 157 llangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtl 209
                                   + ++++t+++lk+ ++l+++ e+Lk+      +++ +++r+ +++e+v+  + 
  gi|70606234|ref|YP_255104.1| 155 VKQDFETIIVLKGNENLDKISEELKDD-----YDLLYARRCYLDGEKVIPWSE 202
                                   ************************776.....6789************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1616.86
//
Query:       gi|70606235|ref|YP_255105.1|  [L=192]
Description: cobalt-precorrin-6Y C(15)-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-09   37.8   0.0    2.1e-09   37.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.7e-09   36.3   0.6    1.2e-08   34.9   0.1    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.2e-07   30.3   0.1      3e-07   29.8   0.1    1.2  1  Methyltransf_3   O-methyltransferase
      4e-07   29.8   0.0    5.1e-07   29.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.7e-06   27.7   0.3    2.2e-06   27.3   0.3    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      6e-06   26.9   0.0    9.5e-06   26.2   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    8.3e-06   26.8   0.0    1.2e-05   26.3   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
    9.4e-06   25.1   0.0      1e-05   25.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.7e-05   24.4   0.0      4e-05   23.2   0.0    1.6  2  MTS              Methyltransferase small domain
    2.6e-05   23.6   0.2    3.3e-05   23.3   0.2    1.2  1  GidB             rRNA small subunit methyltransferase G
    8.4e-05   22.4   0.0    0.00011   22.0   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0002   21.2   0.0    0.00023   21.0   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00034   20.1   0.1    0.00093   18.7   0.0    1.7  2  Methyltransf_4   Putative methyltransferase
     0.0017   18.9   0.0     0.0029   18.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0024   17.2   0.0     0.0039   16.5   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0063   16.5   0.1      0.012   15.6   0.1    1.5  1  Methyltransf_18  Methyltransferase domain
     0.0074   16.1   0.0     0.0078   16.1   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.029   13.9   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.019   14.1   0.1      0.031   13.4   0.0    1.4  1  Fibrillarin      Fibrillarin
      0.019   14.6   0.0      0.055   13.1   0.0    1.7  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.02   13.9   0.0      0.034   13.2   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.031   13.8   0.0      0.048   13.2   0.0    1.2  1  DOT1             Histone methylation protein DOT1
      0.046   14.5   0.0      0.073   13.8   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      0.056   13.2   0.1       0.11   12.2   0.0    1.5  2  Methyltransf_16  Lysine methyltransferase
      0.064   12.8   0.0        0.1   12.1   0.0    1.3  1  Methyltransf_5   MraW methylase family
       0.15   11.2   0.1       0.24   10.5   0.0    1.3  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0     3e-12   2.1e-09       5     112 ..      38     140 ..      36     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 3e-12
               Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevl 84 
                                    ++lD+G+GtG  + e+   +g+k++v+ ++++++a+el r+n +k  l nve  +g++ e l+k ++ +  D     +++
  gi|70606235|ref|YP_255105.1|  38 AKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEvLNK-IN-DELDS----AFI 112
                                   579***************9******************************************7775.45.45665....444 PP

               Methyltransf_31  85 naladpdkileeiervlkpggilliedp 112
                                     +  +++i+  +++ ++ gg ++++ +
  gi|70606235|ref|YP_255105.1| 113 GGTERLEEIIPVVSEKIRRGGMIVLDAI 140
                                   5666777777777777777776666655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.8e-11   1.2e-08      70     132 ..      33      95 ..      19     102 .. 0.92
   2 ?   -0.7   0.1       1.5     1e+03      68      97 ..     139     168 ..     123     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.8e-11
                                   T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                          PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                   +l  ga+ L+vGsG+G  ++    +vgekg+v ++er ++ ve +++n++k  l+nv +++g+
  gi|70606235|ref|YP_255105.1|  33 RLFYGAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGE 95 
                                   47789******************************************************9986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                   HTT--TT-EEEEES-TTSHHHHHHHHHHCT CS
                          PCMT  68 llelkkgarvLevGsGsGyltavlarlvge 97 
                                    + ++   ++L   s  Gy++ v+  +v +
  gi|70606235|ref|YP_255105.1| 139 AILIESAVKALHTLSELGYKAEVIEVIVAK 168
                                   445667777777777788888888777765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   4.3e-10     3e-07      48     165 ..      37     147 ..      14     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.3e-10
                                   --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEE CS
                Methyltransf_3  48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfif 128
                                     + l++G  tG   +   l + e Gk+ a++ d++a+e+++k ++k ++   +e+ieg+a +vL+++ +     e+D +f
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLR-NVEIIEGEAPEVLNKIND-----ELDSAF 111
                                   44689******************************************9985.69************9854.....469*** PP

                                   E-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG CS
                Methyltransf_3 129 vDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvv 165
                                   +    +   +    + e +++Gg+i++D +L e  v 
  gi|70606235|ref|YP_255105.1| 112 IGGT-ERLEEIIPVVSEKIRRGGMIVLDAILIESAVK 147
                                   *876.4577888899999***********99998876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.5e-10   5.1e-07      40     120 ..      35     113 ..      18     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.5e-10
                                   HCC-EEEETT-TTSHHHHHH..HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                 Cons_hypoth95  40 iegarvLDlfaGsGalglEA..lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                   + ga++LD+ +G+G++++EA  +  +  k+++ve+d++av++ ++n+e++ l++ ++++  +a e l+k    + e+d  f
  gi|70606235|ref|YP_255105.1|  35 FYGAKFLDVGSGTGSVSVEAglIVGEKGKVYAVERDPQAVELTRKNVEKFSLRN-VEIIEGEAPEVLNKI---NDELDSAF 111
                                   56899***************98788889***********************997.555555555555444...55677777 PP

                                   E- CS
                 Cons_hypoth95 119 lD 120
                                   + 
  gi|70606235|ref|YP_255105.1| 112 IG 113
                                   65 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.3   3.2e-09   2.2e-06     162     278 ..      37     158 ..      23     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.2e-09
                          PrmA 162 geevlDvGtGSGiLaiaaakL.gak.kvvavDiDevAvkvakeNaelNkvea.klevalseellk..eekadvivaNIL.. 235
                                   g+++lDvG G+G  ++ a ++ g k kv+av  D++Av+ +++N+e+ ++++ ++ +  ++e+++  ++  d + +  +  
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSVEAGLIvGEKgKVYAVERDPQAVELTRKNVEKFSLRNvEI-I--EGEAPEvlNKINDELDSAFIgg 114
                                   6799************88776344348********************99998544.3..3444433323344443333423 PP

                          PrmA 236 aevlielaedikklvkeggllilSGilkekaeevaealeq.gfe 278
                                    e l e+++ +++ ++ gg+++l  il e a +  ++l++ g++
  gi|70606235|ref|YP_255105.1| 115 TERLEEIIPVVSEKIRRGGMIVLDAILIESAVKALHTLSElGYK 158
                                   57899999999999999999999999988877776666655665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.4e-08   9.5e-06       2      70 ..      41     112 ..      40     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.4e-08
                                   EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSSSTTTEEEEEE CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgda.edlpfedgsfDlvvs 70 
                                   Ld+G GtG ++ ++   +g k+kv++v+ +++++e +r+++e+ +l nve+++g+a e l+  +++ D  ++
  gi|70606235|ref|YP_255105.1|  41 LDVGSGTGSVSVEAGLIVGeKGKVYAVERDPQAVELTRKNVEKFSLrNVEIIEGEApEVLNKINDELDSAFI 112
                                   9************99888669********************998889********95557777777777766 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.7e-08   1.2e-05       3     104 ..      43     138 ..      41     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.7e-08
               Methyltransf_24   3 iGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealaslaagsiDllfiDggha 80 
                                   +G  sG  ++ + + l   ++g+++av+ dp   +a +l r+   +   ++v++i+++++e+l + + ++ D +fi g   
  gi|70606235|ref|YP_255105.1|  43 VG--SGTGSVSVEAGLIVGEKGKVYAVERDP---QAVELTRKnveKFSLRNVEIIEGEAPEVLNKIN-DELDSAFIGGT-- 115
                                   78..7777777777777777789********...66666666665577788****************.99*******98.. PP

               Methyltransf_24  81 aeavledleallprlapggvvlfd 104
                                    e+  e ++++ +++++gg++++d
  gi|70606235|ref|YP_255105.1| 116 -ERLEEIIPVVSEKIRRGGMIVLD 138
                                   .78888899**************9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.5e-08     1e-05      48     123 ..      37     113 ..      23     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-08
                                   TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--T.TT-TTS-T-EEEEEEE CS
               Ubie_methyltran  48 gakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqana.eeLpfeddsfDvvtvs 123
                                   gak+lDv +Gtg ++++    vgekgkv  ++ +++ ++ ++k +++ +  n+e + ++a e L+  +d  D+  ++
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEApEVLNKINDELDSAFIG 113
                                   89********************************************************9934578888999987775 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.9e-08     4e-05      32      89 ..      37      96 ..      24     109 .. 0.81
   2 ?   -2.2   0.0       3.8   2.7e+03      74     105 ..     151     183 ..     140     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.9e-08
                                  CSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-ST CS
                           MTS 32 sgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdv 89
                                    k lD+G+G+G +++++     e   v +v+ d +A+e++++n+e+  l+ ve+++ ++
  gi|70606235|ref|YP_255105.1| 37 GAKFLDVGSGTGSVSVEAGLIVGEKGkVYAVERDPQAVELTRKNVEKFSLRnVEIIEGEA 96
                                  5689*************9987766545*******************99998877776654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.8
                                   HHHHTTGCEEEEE-STTTTST.TS-EEEEEE-- CS
                           MTS  74 nleanklevevvasdvleeve.ekkfdlivsNP 105
                                   +l++ + ++ev++  v + ++  k + +i  NP
  gi|70606235|ref|YP_255105.1| 151 TLSELGYKAEVIEVIVAKGMKtSKGYAMISRNP 183
                                   555555566666665665555344677777777 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   4.8e-08   3.3e-05      44     146 ..      34     137 ..      22     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.8e-08
                                   CS-CCC-.EEEETSTTTTTHHHHH.HH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC..TTTTT-EEEEEE CS
                          GidB  44 llkekrdkviDvGsGaGlPGipLa.iarpelkltLleslekkiaFLeevkeelklenveivearaee..kqeeekydvvts 121
                                   l+  ++  ++DvGsG G  ++    i+ ++ k++ +e++ + ++  ++ +e++ l nvei+e +a e   + +++ d + +
  gi|70606235|ref|YP_255105.1|  34 LFYGAK--FLDVGSGTGSVSVEAGlIVGEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEvlNKINDELDSAFI 112
                                   444444..9*********99998724566678**********************************98889999******* PP

                                   C-SSSHHHHHHHHCCCEEEEEEEEE CS
                          GidB 122 RAlaslnelteillkllkegglila 146
                                    +  +l+e++ ++ ++++ gg i++
  gi|70606235|ref|YP_255105.1| 113 GGTERLEEIIPVVSEKIRRGGMIVL 137
                                   *********************9974 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.6e-07   0.00011      34     174 ..      30     166 ..      20     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.6e-07
                         GCD14  34 mkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkv 114
                                    k +l +G++ ++ G G+gs+s      v+ +G+++++e   q +e  r++ ++  l + v + + ++  e   ++++++ 
  gi|70606235|ref|YP_255105.1|  30 SKARLFYGAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRN-VEIIEGEAP-EV-LNKINDEL 107
                                   567899***********************************************999965.444433333.22.36899999 PP

                         GCD14 115 DavfLDlPaP.weaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevll 174
                                   D+ f+   +   e ip +++++ ++gg++   +  ie   ++ ++L+elg++  e++ev +
  gi|70606235|ref|YP_255105.1| 108 DSAFIGGTERlEEIIPVVSEKI-RRGGMIVLDAILIESAVKALHTLSELGYK-AEVIEVIV 166
                                   ****987665156778888888.899************************96.47777765 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.4e-07   0.00023     101     197 ..      37     135 ..      19     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-07
                                   T-EEEETT-TTTCCHHHCCH.HTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---..TT-EEEEEE--TT CS
                        Met_10 101 gevVvdvfAGiGpfaipiak.yskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir..eqladrvvmnlpk 178
                                   g   +dv  G G  ++ ++   +++ +v+a++ +P++v++ ++n++   + + v+ i++++ ev++  ++ +d   ++  +
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSVEAGLiVGEKGKVYAVERDPQAVELTRKNVEKFSLRN-VEIIEGEAPEVLNkiNDELDSAFIGGTE 116
                                   566789999*******99962478889********************99987.6799999999998777888888888888 PP

                                   TGGGGHHHHHHHEEEEEEE CS
                        Met_10 179 saieFldkvlaalkdggvi 197
                                   + +e +  v +++++gg+i
  gi|70606235|ref|YP_255105.1| 117 RLEEIIPVVSEKIRRGGMI 135
                                   8888888888888887765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.6   3.2e+03     152     167 ..      15      30 ..       9      33 .. 0.74
   2 !   18.7   0.0   1.3e-06   0.00093       5      66 ..      40     102 ..      37     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.6
                                   HCCCSSTTCCCCCCTT CS
                Methyltransf_4 152 vlriatkyeqkvqskg 167
                                    + ++tk+e +v ++ 
  gi|70606235|ref|YP_255105.1|  15 EKIPMTKEEIRVLALS 30 
                                   4568999999998765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-06
                                   EEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHH CS
                Methyltransf_4   5 vleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlrilrgdalkvlle 66 
                                   +l++G+G G++ v+      +k ++ ++E   + v+   k++e+  l+N++i++g+a +vl++
  gi|70606235|ref|YP_255105.1|  40 FLDVGSGTGSVSVEAGLIVGEKgKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEVLNK 102
                                   89***************999874788*******************************999965 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.1e-06    0.0029       1      54 [.      41      98 ..      41     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.1e-06
                                  EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC CS
               Methyltransf_11  1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaek 54
                                  LdvG+GtG+++ +    +   ++v++v+ ++++++l ++++++  l +ve+++++a +
  gi|70606235|ref|YP_255105.1| 41 LDVGSGTGSVSVEAGLIVgekGKVYAVERDPQAVELTRKNVEKFSLrNVEIIEGEAPE 98
                                  8*************94445678*******************99999999999998866 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.7e-06    0.0039      52     173 ..      26     146 ..      13     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHH...HHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----S CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrra...verydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvd 129
                                    l+l k++l  G + Ld+G G Gs+ ++a   v +   kv ++    +  +l++k+v++  l++ + ++    e l++  d
  gi|70606235|ref|YP_255105.1|  26 VLALSKARLFYGAKFLDVGSGTGSVSVEAgliVGE-KGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEVLNKIND 105
                                   57899**********************99443334.67899999999999999****999977666666666666666666 PP

                                   EEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HH CS
                          CMAS 130 rvvsvgafehvgkenydtffkklkkllkedGllllhtitslhkk 173
                                   ++ s       g+e++++ + +++++++++G+++l +i + +  
  gi|70606235|ref|YP_255105.1| 106 ELDSAF---IGGTERLEEIIPVVSEKIRRGGMIVLDAILIESAV 146
                                   665532...23999***********************9887654 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.7e-05     0.012      15     125 ..      37     147 ..      28     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
               Methyltransf_18  15 gsrvaDiGtDHgylpiyl.vkegkakkviasDinegplekakeniekagledkievrlsdGleklk..eeevdtvviaGmG 92 
                                   g++++D+G+  g +++++ +  g   kv+a++  ++++e  ++n+ek +l+ ++e++ ++  e+l+  ++e+d + i G  
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSVEAgLIVGEKGKVYAVERDPQAVELTRKNVEKFSLR-NVEIIEGEAPEVLNkiNDELDSAFIGG-- 114
                                   67899*********998734568889**********************996.466666665555543235699999985.. PP

               Methyltransf_18  93 gelileILeeakeklkkikklilqpnseaeelR 125
                                   +e   eI+   +ek ++   ++l +   ++ ++
  gi|70606235|ref|YP_255105.1| 115 TERLEEIIPVVSEKIRRGGMIVLDAILIESAVK 147
                                   677788887777777777777777665555554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0078      16      62 ..      29      85 ..      13     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
               Methyltransf_23 16 ll.pklraggrvLdiGcGtGillevlren.gf..svtgvDlspeaveiae......k 62
                                  l+ ++l+ g++ Ld+G GtG+++ ++    g   +v++v+ +p+ave+ +      +
  gi|70606235|ref|YP_255105.1| 29 LSkARLFYGAKFLDVGSGTGSVSVEAGLIvGEkgKVYAVERDPQAVELTRknvekfS 85
                                  334558999*************9999776344689************9865444440 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-05     0.029       4      67 ..      40     105 ..      38     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
               Methyltransf_15   4 ilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkl 67 
                                    lD+ sG+G  +++  l      kv+a+e +++ ++++ +N e +    ++ ++ g+  e+l+k++ 
  gi|70606235|ref|YP_255105.1|  40 FLDVGSGTGSVSVEAGLIvgeKGKVYAVERDPQAVELTRKNVEKF-SLRNVEIIEGEAPEVLNKIND 105
                                   689999999988887766544569*********************.7899*********99999764 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.031      63     108 ..      29      74 ..      23     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                   -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
                   Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                                   l++  +  g+k L +G+++G+       ivge+g+vyave  p+++
  gi|70606235|ref|YP_255105.1|  29 LSKARLFYGAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAV 74 
                                   56677788999*********99999999************988765 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     8e-05     0.055      12      76 ..      40     104 ..      34     113 .. 0.84
   2 ?   -1.6   0.0       2.5   1.7e+03     116     135 ..     117     136 ..     103     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8e-05
                                   EEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHC CS
               Methyltr_RsmB-F  12 ilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlg 76 
                                   +lD+ ++ G+       ++ +kg+v+Av+++ + ++   +n+++++++n+ ++e++a ++ + + 
  gi|70606235|ref|YP_255105.1|  40 FLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEVLNKIN 104
                                   67888888877766666799**********************************99887765555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.5
                                   HHHHHHHHHCCCEEEEEEEE CS
               Methyltr_RsmB-F 116 lqkellsaaidllkkgGvlv 135
                                   + +e++  + +++++gG++v
  gi|70606235|ref|YP_255105.1| 117 RLEEIIPVVSEKIRRGGMIV 136
                                   55688888889999999998 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     5e-05     0.034      23      83 ..      29      94 ..      22     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5e-05
                                  HHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S CS
                        RrnaAD 23 ldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklkvvhq 83
                                  l+k+ l    + l++g+G+G  ++e   ++    +v ++E d++ ++l++k+++  + +++++++ 
  gi|70606235|ref|YP_255105.1| 29 LSKARLFYGAKFLDVGSGTGSVSVEAGLIVgekGKVYAVERDPQAVELTRKNVEkfSLRNVEIIEG 94
                                  566777777899*************9999998789******************9999999999986 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-05     0.048      36      90 ..      30      85 ..      20      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                  HHTT--TT-EEEEES-TTSHHHHHHHHHH--S.EEEEEE--HHHHHHHHHHHHHHH CS
                          DOT1 36 dkvnlkkedvFvDLGSGvGnvvlqaalevgck.lsvGvEimdnaselaekqkeelk 90
                                  +k  l     F+D GSG G v + a l vg k + + vE   +a el++k+ e ++
  gi|70606235|ref|YP_255105.1| 30 SKARLFYGAKFLDVGSGTGSVSVEAGLIVGEKgKVYAVERDPQAVELTRKNVEKFS 85
                                  5667777889*******************988456899**99*****999998876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00011     0.073       1      61 [.      41     102 ..      41     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
               Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldl 61 
                                   L++G+GtGs++ +      +  ++++v+ +p+a+e +++   k + +n++ +e ea ++l++
  gi|70606235|ref|YP_255105.1|  41 LDVGSGTGSVSVEAGLIVgEKGKVYAVERDPQAVELTRKNVEKFSLRNVEIIEGEAPEVLNK 102
                                   8*******999888766699******************************999999988765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.11      46      91 ..      36      83 ..      15     102 .. 0.85
   2 ?   -2.9   0.0         7   4.8e+03     126     152 ..     136     161 ..     133     175 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
               Methyltransf_16 46 sklsvlELGsGtGlvGlavaell.peakviltDlee.llellkkniel 91
                                   + + l++GsGtG v + + + + ++ kv+   ++  ++el +kn+e 
  gi|70606235|ref|YP_255105.1| 36 YGAKFLDVGSGTGSVSVEAGLIVgEKGKVYAVERDPqAVELTRKNVEK 83
                                  567889*************99988999**998887559********97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7
               Methyltransf_16 126 aaDcvYledslelLvkvLkellkkesk 152
                                   + D +  e+++++L ++L+el  k  +
  gi|70606235|ref|YP_255105.1| 136 VLDAILIESAVKAL-HTLSELGYKAEV 161
                                   55666677777766.356666555544 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015       0.1      21      85 ..      37     104 ..      19     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                   T-EEEES--TTSHHH.HHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEES-G.GGHHHHH CS
                Methyltransf_5  21 dgvyiDaTlGaggHs.ealLeqlselrligidrDksalarakerLkefekr.ltlvkgnf.kelkeal 85 
                                   ++ ++D+  G+g  s ea L   ++ ++++++rD++a++ +++++++f  r +++++g+  + l+++ 
  gi|70606235|ref|YP_255105.1|  37 GAKFLDVGSGTGSVSvEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRnVEIIEGEApEVLNKIN 104
                                   56688888888877634556666777**********************98889999999844444444 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00035      0.24      37     120 ..      24     106 ..       7     112 .. 0.84
   2 ?   -3.7   0.0       7.1   4.9e+03     343     365 ..     150     173 ..     141     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                                   ...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC-- CS
                           TRM  37 irqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaek 117
                                   ir l+l k +l    k ld  s++G  ++   l v ++ +v+a +  ++Avel ++Nv+  +  + v+i e++A  +l+++
  gi|70606235|ref|YP_255105.1|  24 IRVLALSKARLFYGAKFLDVGSGTGSVSVEAGLIVGEKGKVYAVERDPQAVELTRKNVEKFSLRN-VEIIEGEAPEVLNKI 103
                                   566667777777778999999************************************99999998.888888999999877 PP

                                   SS- CS
                           TRM 118 kkr 120
                                   + +
  gi|70606235|ref|YP_255105.1| 104 NDE 106
                                   665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.1
                                   HHH....TT-EE-.TTSTTEEE-S CS
                           TRM 343 salkelgfevsrt.HakpkaikTn 365
                                   + l elg+++ +   +  k++kT 
  gi|70606235|ref|YP_255105.1| 150 HTLSELGYKAEVIeVIVAKGMKTS 173
                                   456666666644303455666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1360.05
//
Query:       gi|70606236|ref|YP_255106.1|  [L=355]
Description: cobalt-precorrin-6A synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-73  246.7   3.3    2.2e-73  246.7   3.3    1.4  2  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.7   3.3   1.2e-77   2.2e-73       2     252 .]      13     263 ..      12     263 .. 0.98
   2 ?   -3.4   0.1      0.26   4.6e+03     120     143 ..     328     351 ..     313     352 .. 0.61

  Alignments for each domain:
  == domain 1  score: 246.7 bits;  conditional E-value: 1.2e-77
                          CbiD   2 rsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeivaeve.. 78 
                                   r G+TtG++AaAA+ka++++l+k+e++++v+i +p g +lei++ +++++e+e  a+ +k +Gd+pD+ +g+ei+a     
  gi|70606236|ref|YP_255106.1|  13 RFGITTGATAAAASKASVIFLIKNETPKTVTIPTPIGLRLEISVGNYSRKESEfcASAKKFSGDNPDILDGLEIIACSGrs 93 
                                   89***********************************************9988*99999*****************99899 PP

                          CbiD  79 ..eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleeakegvevtisvpeGeelAkkTlNprlGivgGiS 157
                                     ++i+i++ eGvG++t+pgL+ +vg+++I+p++++mi ++v+ev+++   gv v+++vp+GeelAk+T+Np +G++gGiS
  gi|70606236|ref|YP_255106.1|  94 nsQTITITAEEGVGTITRPGLKGDVGDKSISPIAKQMIIDAVKEVVSS---GVYVKLYVPKGEELAKNTMNPLVGVEGGIS 171
                                   9*88******************************************75...9***************************** PP

                          CbiD 158 iLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkklglpeealvkvsnfvgealeeaaekgvkkvl 238
                                   iLGTtGi  p+S+e+++e+i++e  v +++g+k+lvl++Gn++ k+a++   +  ++++k+++ vg++l+ a+e g+++v+
  gi|70606236|ref|YP_255106.1| 172 ILGTTGIEYPVSDEDYIEHIKSEACVVKSTGHKTLVLAPGNTSFKFARE---IYGDKVIKIGDNVGSSLKVAEELGFSQVI 249
                                   *************************************************...7899************************* PP

                          CbiD 239 lvghiGKlvKlagG 252
                                   lv   GKlvK+a+G
  gi|70606236|ref|YP_255106.1| 250 LVSLPGKLVKVAAG 263
                                   ************99 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.26
                          CbiD 120 evleea.kegvevtisvpeGeelAk 143
                                   ++ +   k ++ v ++ ++G+ +Ak
  gi|70606236|ref|YP_255106.1| 328 KLKR-VsKLKLGVVVISEDGKIMAK 351
                                   2222.23667888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2715.01
//
Query:       gi|70606237|ref|YP_255107.1|  [L=251]
Description: precorrin-3B C(17)-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-38  132.3   0.1    2.9e-38  132.0   0.1    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
       0.13   12.3   0.3        1.4    8.9   0.0    2.4  2  RPT           A repeated domain in UCH-protein


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.1   3.2e-42   2.9e-38       1     210 [.       4     206 ..       4     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 3.2e-42
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaeal..aealra 78 
                                   kly+VGvGpG+pe  T+rA++a+k++ v+++++  + ++++dl +            ke+ +++  eei +a    e++ +
  gi|70606237|ref|YP_255107.1|   4 KLYIVGVGPGSPEMRTIRAVQAIKESNVIVAYT-TYADLVKDLTDG-----------KEVITARmKEEIYRARtaLEKAME 72 
                                   79*******************************.999999998743...........444444436666666667999999 PP

                  TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleal 157
                                   g  V l++sGDP vyg+++  +e   +++ ++++eviPGv++  aaa+rlg pl++++ + s++  l + +++  r ++a+
  gi|70606237|ref|YP_255107.1|  73 GNVVSLISSGDPQVYGMAGITLEMMYKNKIQVDFEVIPGVTAGLAAASRLGSPLSMDFASISLSdlLVPAEDILFRVRKAA 153
                                   9999*******************9999999999*******************************98444466777777776 PP

                  TP_methylase 158 langdtlvllkaprk...laelaelLkealyddttpvavveragtedervvrgtle 210
                                    a  d++++l++p +   l++++++++e+ ++++tpv +v+ a +e e+v+++tl+
  gi|70606237|ref|YP_255107.1| 154 EA--DFVIVLYNPINkplLEKAMKIISEY-RKPETPVGIVKGAYRESEEVFTTTLS 206
                                   66..**********6699***********.67788*******************97 PP

>> RPT  A repeated domain in UCH-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.063   5.7e+02      15      31 ..      26      55 ..      18      69 .. 0.60
   2 ?    8.9   0.0   0.00016       1.4      18      50 ..     156     182 ..     145     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.063
                           RPT 15 tdDdviitayqvkled.............d 31
                                  + ++ +i ay+++ +              +
  gi|70606237|ref|YP_255107.1| 26 IKESNVIVAYTTYADLvkdltdgkevitaR 55
                                  567789999999874333354333333331 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00016
                           RPT  18 dviitayqvkleddpsqkdklrrALkvIAeeRk 50 
                                   d++i  y      +p +k +l +A+k+I+e+Rk
  gi|70606237|ref|YP_255107.1| 156 DFVIVLY------NPINKPLLEKAMKIISEYRK 182
                                   4444444......599****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1836.56
//
Query:       gi|70606238|ref|YP_255108.1|  [L=340]
Description: bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-54  184.3   0.4    2.5e-54  183.9   0.4    1.1  1  CbiC      Precorrin-8X methylmutase
    4.1e-17   62.5   0.0    1.5e-16   60.6   0.0    2.0  2  CbiX      CbiX
  ------ inclusion threshold ------
      0.048   13.5   0.1         35    4.3   0.0    3.6  3  SinI      Anti-repressor SinI


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.4   4.2e-58   2.5e-54       1     195 [.     151     336 ..     151     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 4.2e-58
                                   HHHHHHHHHHHCHC-TT...S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHH CS
                          CbiC   1 eIeaeSfaiideelgeee..lseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkkrl 79 
                                   eIe++ +++i+e+l+e    +++ee ev+ R+++a+++fela+++++s da+ +gleal++g +i+tDv+mvkaGi+ ++ 
  gi|70606238|ref|YP_255108.1| 151 EIEENTMNMIREKLREIFsvFNDEELEVIARAVYASGNFELAKHVYISYDAIGSGLEALRSGISILTDVKMVKAGIRWEQ- 230
                                   69************975367********************************************************5543. PP

                                   HTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHH CS
                          CbiC  80 eklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaa 160
                                         v  +l+++   elak+ gitr+aaam++  +  +++ivviGnAPtALle+l++ ee kv   lv++ P GF +a+
  gi|70606238|ref|YP_255108.1| 231 ------VENYLDNS--SELAKKMGITRTAAAMRLGLN--SSKIVVIGNAPTALLEVLRIHEERKVDIPLVVASPPGFTNAS 301
                                   ......66789987..899****************99..569*************************************** PP

                                   HHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                          CbiC 161 esKealaesevpyitveGrkGGsavAaaivnaLle 195
                                   e Ke+l++s++p+i+v+G+ GGs++A+ai+n+L++
  gi|70606238|ref|YP_255108.1| 302 EVKEQLIKSGIPCIVVRGSYGGSNIAVAIINELIR 336
                                   *********************************86 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   2.6e-20   1.5e-16       1     105 [.      19     129 ..      19     131 .. 0.89
   2 ?   -0.5   0.0      0.26   1.6e+03      11      56 ..     123     168 ..     120     170 .. 0.70

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.6e-20
                                   -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT.... CS
                          CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeele.... 77 
                                   HGSr+++  e++ ++++++++k +  pv l ++e++ep++++ l+el + g+++++   +fl +G+hv +DI  el+    
  gi|70606238|ref|YP_255108.1|  19 HGSRRNTFVEDMGEVTSYVERKLG-IPVYLTHNEFTEPNWRTRLNELLSHGYDHFIFALAFLGRGNHVAHDIMGELNvsdf 98 
                                   ************************.***********************************************998886544 PP

                                   ..--SSSS-.....TTEEEEE---CCCSCCHHHHH CS
                          CbiX  78 ..eaeeahp.....kdveieytepLGthplvaevl 105
                                     +     +     k +  ++t+pL +++lv+ ++
  gi|70606238|ref|YP_255108.1|  99 yrWS----EttyngKRIYAYITKPLADSELVKLAI 129
                                   4344....244457888999*********998776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEE CS
                          CbiX  11 eveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkriv 56 
                                   e+ kla  +r k++fk ve g++    +++ee   ++++++ ++i+
  gi|70606238|ref|YP_255108.1| 123 ELVKLAIFYRIKSAFKDVEEGHYIEDPEEIEENTMNMIREKLREIF 168
                                   5566666677777888888888766667788887777777777775 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.015        87      10      19 ..     206     215 ..     206     215 .. 0.91
   2 ?    4.3   0.0    0.0059        35      14      27 ..     223     236 ..     222     236 .. 0.91
   3 ?    1.2   0.0     0.053   3.2e+02      12      18 ..     242     248 ..     240     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.015
                                   HHHHHHT--S CS
                          SinI  10 kEAkesGlsk 19 
                                   +EA+ sG+s+
  gi|70606238|ref|YP_255108.1| 206 LEALRSGISI 215
                                   7*******96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0059
                                   HHT--SHHHHHHHH CS
                          SinI  14 esGlskeEfReFLe 27 
                                   ++G+  e+++++L+
  gi|70606238|ref|YP_255108.1| 223 KAGIRWEQVENYLD 236
                                   68999********7 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.053
                                   HHHHT-- CS
                          SinI  12 AkesGls 18 
                                   Ak++G++
  gi|70606238|ref|YP_255108.1| 242 AKKMGIT 248
                                   9*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2301.85
//
Query:       gi|70606239|ref|YP_255109.1|  [L=211]
Description: cobalt-precorrin-6Y C(5)-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-24   86.2   0.0    3.3e-24   86.0   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.066   12.1   0.0      0.085   11.8   0.0    1.3  1  Phage_mat-A   Phage maturation protein


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.0   3.7e-28   3.3e-24       6     206 ..       2     187 ..       1     194 [. 0.88

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 3.7e-28
                  TP_methylase   6 GvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal...aealragkdVv 83 
                                   GvG Gdpel+T++Al++++++++v+g++  + +++                 ke+   +y+++ +++   ++++r+ +dV+
  gi|70606239|ref|YP_255109.1|   2 GVGAGDPELITLKALKIIEKCKIVAGWQ-SVVSRFN-------------LSGKEVVYLNYKDQDRQIpdlVKRARE-QDVA 67 
                                   9***************************.8888883.............234678888888888888885666666.58** PP

                  TP_methylase  84 llvsGDPlvy..gtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangd 162
                                   +l  GDP+v+  + ++++ e +r+   ++++ev+PG+ss+  a a +  +l++   +++++ +g  + +++e+++ +a g+
  gi|70606239|ref|YP_255109.1|  68 ILDHGDPSVSdfQFVGRIRESCRQ--FDVKYEVVPGISSVLRALALVEKDLSQVVFMTFHI-RG--ELDYTEIDKSIALGR 143
                                   **********88999999999999..7899*******************************.65..6799*****99999* PP

                  TP_methylase 163 tlvllkapr..klaelaelLkealyddttpvavveragtedervvr 206
                                    l+++  p    ++++ae+L     + + +++v+er++  de+v +
  gi|70606239|ref|YP_255109.1| 144 DLLIIPEPYsyGVKKIAERLVGL--GLNPEMVVMERLSFSDEKVNH 187
                                   *****99996559*******888..6677**************976 PP

>> Phage_mat-A  Phage maturation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.5e-06     0.085      41     103 ..      95     156 ..      71     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-06
                                   ...............-SS-B---......-EEE--EEEEE----..----------------- CS
                   Phage_mat-A  41 hcatvpiassglrpctkvwydPssllfriPesraeldvtsidaGdivykdslsstgaPkefdf 103
                                   +  +vp  ss lr  + v  d s ++f   + r+eld t id+  i+  + l   + P+ ++ 
  gi|70606239|ref|YP_255109.1|  95 KYEVVPGISSVLRALALVEKDLSQVVFMTFHIRGELDYTEIDKS-IALGRDLLIIPEPYSYGV 156
                                   4467999************************************9.**************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1334.41
//
Query:       gi|70606240|ref|YP_255110.1|  [L=325]
Description: cobalamin biosynthesis protein CbiG [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-29  101.2   0.0    5.3e-29  100.1   0.0    1.7  1  CbiG_N    Cobalamin synthesis G N-terminal
    9.1e-15   55.2   0.7    1.5e-14   54.6   0.1    1.7  2  CbiG_C    Cobalamin synthesis G C-terminus


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   5.9e-33   5.3e-29       2      82 .]      41     120 ..      40     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 5.9e-33
                                   .HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
                        CbiG_N   2 llrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82 
                                   ll +++++ydalvf++a+G vvR+++++ k+K+ Dp+V++vd++ +fvi+ll+ h  g n+lA+ei+++l+a+pviTta++
  gi|70606240|ref|YP_255110.1|  41 LLGKIWNCYDALVFVMALGGVVRTVCKYAKSKDVDPSVIAVDDSLKFVIPLLGSH-WGSNQLASEISRILNATPVITTASE 120
                                   57899**************************************************.***********************96 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.72   6.5e+03      66      93 ..     119     131 ..     102     151 .. 0.52
   2 !   54.6   0.1   1.6e-18   1.5e-14       1     116 []     207     323 ..     207     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.72
                                   HHHHCHHCSCT-CHHHCCCSSS-HHHHH CS
                        CbiG_C  66 eeLaavevpnpsefvkkevGvpsVaEaa 93 
                                   +e+++               v+sV E a
  gi|70606240|ref|YP_255110.1| 119 SEINQ---------------VTSVEELA 131
                                   33333...............33444444 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 1.6e-18
                                   EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHH..CSCT-CH CS
                        CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaave..vpnpsef 79 
                                   l+vGiG+++++s eei+eai  al + ++  ++v ++a++    +     e+ ++l++p++ ++ e++++++  + +p + 
  gi|70606240|ref|YP_255110.1| 207 LYVGIGAKKEASVEEIKEAIYFALGQLKVGLDRVLKIASVREVVE-----EVSKSLNIPFQKIDWETINSFNdeCLTPPSE 282
                                   689*************************************87655.....599******************6678899999 PP

                                   HHCCCSSS-HHHHHHHHHC....EECSCEEEE.TTEEEEEE CS
                        CbiG_C  80 vkkevGvpsVaEaaAllaa...arllvpKqak.ggvTvAia 116
                                     +e+G+++VaE +A +a    a+l+++K  + +++TvAia
  gi|70606240|ref|YP_255110.1| 283 KLEELGIKGVAEISAFIAGgpsAKLILRKISYkSKITVAIA 323
                                   999*************9954447******86569******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2232.92
//
Query:       gi|70606241|ref|YP_255111.1|  [L=284]
Description: asparaginase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-70  235.2   8.7    5.4e-39  134.0   2.0    2.0  2  Asparaginase_2  Asparaginase
  ------ inclusion threshold ------
       0.26   11.5   2.7         12    6.2   0.3    3.6  4  Flagellin_IN    Flagellin hook IN motif


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.7   2.6e-34   2.3e-30       2     123 ..      15     132 ..      14     144 .. 0.92
   2 !  134.0   2.0     6e-43   5.4e-39     171     298 ..     147     273 ..     132     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 2.6e-34
                                   EEEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEEEEE CS
                Asparaginase_2   2 vlvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAsimd 82 
                                   +l ihGGAg+  k   ++e++  +l++ale gy+  k+g s+l+aV++a+  +Ed+  f+aG Gsv +++geve+dA im 
  gi|70606241|ref|YP_255111.1|  15 ILGIHGGAGNWDK--RNHERALVELEKALERGYDEFKRG-SSLEAVVEAIAYMEDCGVFDAGVGSVKNSKGEVEMDAGIMH 92 
                                   6779*****9888..88889999************9875.78*************************************** PP

                                   TTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHH CS
                Asparaginase_2  83 gktlraGaVagvkrvknpislArlvmeksehvlLvgegAee 123
                                   g+tlr+GaVa+vk vknpi+ A +v+++ +hvlLvg+  ee
  gi|70606241|ref|YP_255111.1|  93 GNTLRVGAVASVK-VKNPIREALKVLKNGRHVLLVGNRGEE 132
                                   ************6.9********************986655 PP

  == domain 2  score: 134.0 bits;  conditional E-value: 6e-43
                                   T---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEEE-HHHHCCTTHHHHHHHHHHTTT--H CS
                Asparaginase_2 171 klgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaTGkGeeiirellaadivalmeykglsl 251
                                   +  TvGaValD+egnl a+TSTgG+  kl+GRvGDspi+GaG YA ++ +Avs+TG Ge i+r+l+a+++ +l+   g s+
  gi|70606241|ref|YP_255111.1| 147 SGDTVGAVALDKEGNLVAGTSTGGISGKLPGRVGDSPIPGAGFYA-TERVAVSSTGIGEIILRTLPAKEVDILVSL-GISI 225
                                   334******************************************.999***************************.**** PP

                                   HHHHHHHHHCHHHHTTT.-EEEEEEETTS-EEEEECSCCCEEEEEETT CS
                Asparaginase_2 252 eeAaekvieeklkrvkg.sgGviavdkkGevaaefnsegmlrayaked 298
                                   ++ + +vi++ ++ +++ ++G+i +d+kG v+a  n+ gm+r++ +++
  gi|70606241|ref|YP_255111.1| 226 DDSIRSVINKVTSIFGKdNIGMIGLDSKGFVSAYYNTIGMARGVKDSE 273
                                   *************999989************************99776 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.027   2.5e+02      17      30 ..      48      61 ..      47      62 .. 0.92
   2 ?    0.3   0.0     0.093   8.3e+02      10      27 ..     138     155 ..     131     156 .. 0.79
   3 ?    6.2   0.3    0.0014        12      12      38 ..     205     241 ..     195     241 .. 0.74
   4 ?   -3.0   0.0         1     9e+03      38      46 ..     255     263 ..     251     267 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.027
                                  ECTTTBCHHHHHHH CS
                  Flagellin_IN 17 vkagdtlddiadaI 30
                                  +k g++l+++++aI
  gi|70606241|ref|YP_255111.1| 48 FKRGSSLEAVVEAI 61
                                  788**********9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.093
                                   CS-EEEEECTTTBCHHHH CS
                  Flagellin_IN  10 ketvtisvkagdtlddia 27 
                                    +++t  + +gdt++++a
  gi|70606241|ref|YP_255111.1| 138 ETSITSPLRSGDTVGAVA 155
                                   444788999******997 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0014
                                   -.........EEEEECTTTBCHH.HHHHHHHHCCTTT CS
                  Flagellin_IN  12 t.........vtisvkagdtldd.iadaINavssktG 38 
                                   +         v+i v+ g ++dd i++ IN+v+s  G
  gi|70606241|ref|YP_255111.1| 205 IilrtlpakeVDILVSLGISIDDsIRSVINKVTSIFG 241
                                   444555555688888888899999********99776 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1
                                   TEEEEEEEE CS
                  Flagellin_IN  38 GVsAsidad 46 
                                    VsA++++ 
  gi|70606241|ref|YP_255111.1| 255 FVSAYYNTI 263
                                   599999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1914.71
//
Query:       gi|70606242|ref|YP_255112.1|  [L=396]
Description: hypothetical protein Saci_0404 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2726.59
//
Query:       gi|70606243|ref|YP_255113.1|  [L=162]
Description: hypothetical protein Saci_0405 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1228.10
//
Query:       gi|70606244|ref|YP_255114.1|  [L=206]
Description: hypothetical protein Saci_0406 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.027   14.2   0.1    1.4  1  AKAP28    28 kDa A-kinase anchor
       0.02   14.9   1.9        1.5    8.9   0.1    2.4  2  CHU_C     C-terminal domain of CHU protein family


Domain annotation for each model (and alignments):
>> AKAP28  28 kDa A-kinase anchor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     3e-06     0.027      22      69 ..      78     126 ..      73     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-06
                        AKAP28  22 twelsks.wlyliefleekeaekskiyiyrvrwSiptrrkPipratasv 69 
                                   + +++++ + y+ +f++  +++ + iy ++v +S    ++Pi +at+++
  gi|70606244|ref|YP_255114.1|  78 QVNITNAtYNYYFNFMGLAVSKTGYIYLAKVAYSYTATNNPIQNATLYI 126
                                   5666666699************************************986 PP

>> CHU_C  C-terminal domain of CHU protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3    0.0024        22      59      86 .]      79     105 ..      54     105 .. 0.83
   2 ?    8.9   0.1   0.00017       1.5      25      48 ..     118     141 ..     109     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0024
                         CHU_C  59 eklpeGtYfYvlkleegekeekkGwiyl 86 
                                    +++++tY Y++++  g   +k+G+iyl
  gi|70606244|ref|YP_255114.1|  79 VNITNATYNYYFNF-MGLAVSKTGYIYL 105
                                   56899*********.999999*****97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00017
                         CHU_C  25 kypnnsleifnrwGqlVyekknyk 48 
                                    ++n++l i n+ Gq Vy+ k   
  gi|70606244|ref|YP_255114.1| 118 PIQNATLYIMNQQGQIVYKYKLIV 141
                                   45899*************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1555.49
//
Query:       gi|70606245|ref|YP_255115.1|  [L=115]
Description: hypothetical protein Saci_0407 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 815.62
//
Query:       gi|70606246|ref|YP_255116.1|  [L=183]
Description: hypothetical protein Saci_0408 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.042   13.6   0.2       0.07   12.8   0.2    1.3  1  Rrp44_CSD1  Rrp44-like cold shock domain


Domain annotation for each model (and alignments):
>> Rrp44_CSD1  Rrp44-like cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.9e-06      0.07       8      67 ..     104     168 ..      98     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-06
                                   --HHHHHHHHHTTSEEEEEEEEE.....SSBTTEEEEE-SSSSS-EEEESHHHHTS--TT-EEEE CS
                    Rrp44_CSD1   8 ystarvmgglkngvlyqgniqis.....eynflegsvslprfskpvlivgqknlnrafngdqviv 67 
                                     t  +   l + v+   n+qis     eynf +  +s+  + kp +i+  +  n +fng   i 
  gi|70606246|ref|YP_255116.1| 104 NITLPITSNLFEYVVNSTNVQISgiiggEYNFTKFYISFSDLVKPEIILVANLYNVSFNGTYGIF 168
                                   55666667777888999999998777779********************99999******87775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1419.02
//
Query:       gi|70606247|ref|YP_255117.1|  [L=121]
Description: hypothetical protein Saci_0409 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 786.10
//
Query:       gi|70606248|ref|YP_255118.1|  [L=339]
Description: zinc-binding dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-26   92.5   1.6    2.2e-26   91.8   0.3    1.9  2  ADH_N         Alcohol dehydrogenase GroES-like domain
      8e-22   77.6   0.0    1.3e-21   76.9   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.4e-14   54.1   0.7    2.1e-14   53.5   0.7    1.2  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
     0.0044   18.1   0.0     0.0078   17.3   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
      0.006   16.2   0.5       0.12   11.9   0.0    2.3  2  DUF4147       Domain of unknown function (DUF4147)
  ------ inclusion threshold ------
      0.049   13.7   0.0        0.1   12.6   0.0    1.4  1  Shikimate_DH  Shikimate / quinate 5-dehydrogenase
      0.057   14.0   1.5      0.093   13.3   0.3    1.8  2  Fer4_17       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.3   8.8e-30   2.2e-26       2     105 ..      25     122 ..      24     125 .. 0.94
   2 ?   -1.6   0.0      0.92   2.4e+03      40      62 ..     146     167 ..     143     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 8.8e-30
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   g+++ik+ka+g+Cg+D++ l+g  ++++++p i+GHE +G++ee  ++v++lk G+rV+++++++c eC++C++g+ ++C+
  gi|70606248|ref|YP_255118.1|  25 GDIIIKMKACGLCGTDIEKLRG--QYTASQP-IIGHEPSGIIEE--SSVDSLKPGQRVFAHHHVPCYECYYCTHGSATMCP 100
                                   79*******************9..6999999.99**********..679******************************** PP

                                   TBEETTTSS-SSSBSEEEECGGG CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekk 105
                                   +++ ++++ +Ggfaey+ vp+ +
  gi|70606248|ref|YP_255118.1| 101 HYRRTNIE-PGGFAEYFRVPAWN 122
                                   ********.**********9765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.92
                                   EEEEEEESTT-CS--TT-EEEE- CS
                         ADH_N  40 vGeveevgpevkklkvGdrVvve 62 
                                     +v+ + ++v kl+ Gd+V+v 
  gi|70606248|ref|YP_255118.1| 146 LATVVRAQRRV-KLNRGDNVLVV 167
                                   66788888888.699*****986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0   5.2e-25   1.3e-21       1     127 [.     171     299 ..     171     302 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.2e-25
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   ++Gl+ v+l k  Ga ++i++d+ + ++e+a k Gad+ +n+k+ d   ++k+lt+g+gvd+++ ++G+++++ + l +++
  gi|70606248|ref|YP_255118.1| 171 PMGLLHVMLSKVNGAsKTIVTDIADFRVEYAYKVGADYSFNSKKIDTINEVKKLTDGRGVDIAIIASGAPSAILSGLLSVR 251
                                   79****************************************777************************************ PP

                                   EEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdl 127
                                   +gG++ ++G+++++++  +d+++ll +e+si+ s+ +   e+  +al++
  gi|70606248|ref|YP_255118.1| 252 KGGQVLLFGVPFKGTVlnYDISDLLNNEISIISSNAAI-EEDTVDALKI 299
                                   **********99999999***************99887.6666556655 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.7   8.3e-18   2.1e-14       6     211 ..     142     338 ..     137     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 8.3e-18
                   Glu_dehyd_C   6 LvEPisiveKaielaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvds 86 
                                   ++EP++ v +a   ++        + + +lv+GaG++GLL  ++l++  +g +++ v++     d +++   ++Ga Y   
  gi|70606248|ref|YP_255118.1| 142 FIEPLATVVRAQRRVKL------NRGDNVLVVGAGPMGLLH-VMLSK-VNGASKTIVTD---IADFRVEYAYKVGADYSF- 210
                                   55555555554433333......45689*************.55553.58888887777...57889***********85. PP

                   Glu_dehyd_C  87 retpvdeipeas.....eemdlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvN 161
                                   + +++d+i+e++     + +d+ + a G++ +++  +  ++  G + L Gvp +   ++ d+++l     l+N++ + s N
  gi|70606248|ref|YP_255118.1| 211 NSKKIDTINEVKkltdgRGVDIAIIASGAPSAILSGLLSVRKGGQVLLFGVPFKGtVLNYDISDL-----LNNEISIISSN 286
                                   355666666554111225799*******************************8762567888776.....77899999999 PP

                   Glu_dehyd_C 162 anrrhfeaavdtLaalpesl..ldelvtkvvdldeleeAfe..dddetiKtvve 211
                                   a ++  e +vd+L+ ++e+   +++lvt++ ++d+++eA +  ++ + iK++++
  gi|70606248|ref|YP_255118.1| 287 AAIE--EDTVDALKIISERKidVSKLVTHKFTIDQFNEAVRvaEEGQAIKVIIQ 338
                                   9998..688888888877764578***************973255589999986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.1e-06    0.0078       2     128 ..     205     333 ..     204     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.1e-06
                                   T-SEEEETTSTTHH....HHH-TT-EEEEEES-H.HHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE-- CS
                  ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvg.gealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyef 77 
                                   GAd  +++++ d      + t+g+gvD+++ + g   a+l+ +l+ +++gG+++  g p ++ ++l         +  ++ 
  gi|70606248|ref|YP_255118.1| 205 GADYSFNSKKIDTInevkKLTDGRGVDIAIIASGaPSAILSGLLS-VRKGGQVLLFGVP-FKGTVLNYDI-SDLLNNEISI 282
                                   99999999988888899999**************54444466654.5565999776643.4444444433.5555555555 PP

                                   GGG...-.-HHHHHHHHHHHHHHH---..-EEEEEEGGGHHHHHHHHHSS--S CS
                  ADH_zinc_N_2  78 lfsmkasaqadileelaalieeGklrp..vvdrvfpleeaaeAhrylesgrar 128
                                   +   +a + +d   + ++ i+e k+ +   v++ f++++ +eA+r  e+g+a+
  gi|70606248|ref|YP_255118.1| 283 IS-SNAAIEED-TVDALKIISERKIDVskLVTHKFTIDQFNEAVRVAEEGQAI 333
                                   55.35555555.9***********7653268888****************985 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.044   1.1e+02      23      48 ..     150     174 ..     130     236 .. 0.65
   2 !   11.9   0.0   4.6e-05      0.12     159     221 ..     248     308 ..     242     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.044
                                   HHHH--.......-SEEEEEESTTHH CS
                       DUF4147  23 lslkeeeldlskkkrvvvvgaGKAaa 48 
                                   ++  +++++l++ ++v+vvgaG   +
  gi|70606248|ref|YP_255118.1| 150 VR-AQRRVKLNRGDNVLVVGAGPMGL 174
                                   32.2346999999********96544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.6e-05
                                   TBSSTTTHHHHHHTT..SEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..- CS
                       DUF4147 159 lsaikGGrLaraaap..arvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklp 221
                                   ls  kGG+ + +  p   +v++  +SD +++++++I+S   +   ++  dal+i+ + k++  ++
  gi|70606248|ref|YP_255118.1| 248 LSVRKGGQVLLFGVPfkGTVLNYDISDLLNNEISIISSNAAIE--EDTVDALKIISERKID--VS 308
                                   677899998866666437999*****************88877..456689****999998..44 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     4e-05       0.1       3      90 ..     152     244 ..     151     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                   HHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEE...EEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHH..T-SE CS
                  Shikimate_DH   3 akkkleslkekkvlliGaGemaelvakhLlakgvkkvv...vaNRtlerakelaeelkgeeiealkleelkella..eadv 78 
                                   a+++++  ++ +vl++GaG m+ l +     +g+ k +   +a   +e a ++  +++ ++ ++ +++e+k+l +   +d+
  gi|70606248|ref|YP_255118.1| 152 AQRRVKLNRGDNVLVVGAGPMGLLHVMLSKVNGASKTIvtdIADFRVEYAYKVGADYSFNSKKIDTINEVKKLTDgrGVDI 232
                                   56667666789***********9988666666777766123456677888889888888888889999999887522689* PP

                                   EEE-SSSSS-SB CS
                  Shikimate_DH  79 visataseepil 90 
                                    i+a +++++il
  gi|70606248|ref|YP_255118.1| 233 AIIASGAPSAIL 244
                                   *****9999997 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   4.5e+03      42      50 ..      30      38 ..       9      39 .. 0.60
   2 ?   13.3   0.3   3.6e-05     0.093       2      30 ..      85     117 ..      84     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                       Fer4_17 42 kaslCieCg 50
                                  k++ C  Cg
  gi|70606248|ref|YP_255118.1| 30 KMKACGLCG 38
                                  566666665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.6e-05
                       Fer4_17   2 CiqCgyClp....eCpsyeaydnepkkllraak 30 
                                   C +C yC+     +Cp y++++ ep  +++ ++
  gi|70606248|ref|YP_255118.1|  85 CYECYYCTHgsatMCPHYRRTNIEPGGFAEYFR 117
                                   9**********************9988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2142.35
//
Query:       gi|70606249|ref|YP_255119.1|  [L=311]
Description: cobalamin biosynthesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-71  240.0   0.0    3.3e-71  239.7   0.0    1.1  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.7   0.0   1.9e-75   3.3e-71       2     251 ..       6     252 ..       5     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 239.7 bits;  conditional E-value: 1.9e-75
                     CobD_Cbib   2 llAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvallllllalaallglvlealllk 82 
                                    l++l+Dl lg+p+ ++hPvv++gk+ s+l k ++    +r++G++++++ v+++l+++++ l++   +++ l l +++lk
  gi|70606249|ref|YP_255119.1|   6 YLSILFDLTLGEPPVIIHPVVWVGKISSRLIKPFS----NRFYGIFFWIVSVVPILFILCIPLYF--PWYVELPLLVIFLK 80 
                                   6899**************************99664....579*************9999888884..344466899***** PP

                     CobD_Cbib  83 ltlalrsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflllglpgalayk 163
                                   +t++++ L++ v+k         +  R++ +++V+R++ el+e ++++A++Es+ E+++Dg+++P+f+fl+lg pgal+++
  gi|70606249|ref|YP_255119.1|  81 TTFSIKLLYSLVKKSTPVT----TYSRSYSQQLVRRNVYELSEGHVRSAVIESLFESTVDGIISPIFWFLVLGYPGALLQR 157
                                   ***********99876553....579******************************************************* PP

                     CobD_Cbib 164 avnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.........aalriarrdarkhpSpNsgwpeaalAg 235
                                   ++nT+DsmvGYk+++y++ Gw++A+lD++lnyiPAR+tall++l+         ++lri+++   k +SpN+ +p++ +  
  gi|70606249|ref|YP_255119.1| 158 LANTMDSMVGYKTPEYREQGWFSAKLDTILNYIPARITALLMLLSayllglrpkSTLRILKES--KIESPNAKYPISFASS 236
                                   ********************************************7455555554447777655..688************* PP

                     CobD_Cbib 236 algvrLggpnvYlgkl 251
                                   +l+vrL++ + Y+  l
  gi|70606249|ref|YP_255119.1| 237 ILNVRLEKIGFYNVGL 252
                                   ************5434 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2095.45
//
Query:       gi|70606250|ref|YP_255120.1|  [L=252]
Description: hypothetical protein Saci_0412 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-29  102.8  11.7    3.1e-29  102.6  11.7    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6  11.7   1.8e-33   3.1e-29       2     203 ..      12     232 ..      11     233 .. 0.72

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 1.8e-33
                          CobS   2 lsflTrlPvp.....elaralaffP.lvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglgs 74 
                                   lsf+T++P p     e+a+   + P +vG+++G++  +++ll   l   +l all++ ++ ++ g++HlDGl+D++D+l+ 
  gi|70606250|ref|YP_255120.1|  12 LSFFTIIPSPsasleEIAEFSFISPlMVGIITGIIDwFVVLLGIRL-IgSLGALLLIPTVEIIRGFHHLDGLLDMGDALMV 91 
                                   89*******9763332244444457579999999974444444444.257777776656668*****************98 PP

                          CobS  75 grdrerrleImkDsrvGafGvlalvlvlllkvaa.laala......lllapvlsRlaallaiallpyae.eglgalfaeaq 147
                                   g  +err ++++D ++G++++  +++++ + ++a l +l       +l ++vl+R++a+ ++ l+++ + + lg++f+++ 
  gi|70606250|ref|YP_255120.1|  92 G--KERRPQVLHDLQTGSGAIGLFLVYFSIFLIAtL-NLNvsnlwfFLPSEVLARASAISLLGLMKPIPgSYLGKVFHDKM 169
                                   7..9****************9999999999998853.4434566665667****************995489******965 PP

                          CobS 148 kk......lvllal.avllllla..lllaallvalllrrlarrklggvtGDvlGavieltellvl 203
                                   +       +  l++ ++++l+    l+la++++ l+++ +a+  ++g++GD++Ga+i l+  ++l
  gi|70606250|ref|YP_255120.1| 170 RDklfsikF--LLVqVFAILFSSpvLILAYVILLLVFYLMAKLVFDGMSGDIVGAIITLSFPIYL 232
                                   554543221..222322222222324455555555566788889**************9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1578.60
//
Query:       gi|70606251|ref|YP_255121.1|  [L=459]
Description: cobyrinic acid A,C-diamide synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-32  110.5   0.0    1.1e-31  110.0   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    3.2e-12   46.6   0.0      6e-12   45.7   0.0    1.4  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    4.1e-11   43.1   0.0    4.8e-08   33.1   0.0    2.2  2  AAA_26         AAA domain
     0.0051   16.7   0.0      0.008   16.0   0.0    1.3  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.042   13.6   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
       0.24   11.1   0.0        0.6    9.8   0.0    1.7  1  Peptidase_C26  Peptidase C26
       0.27   11.0   0.5       0.56   10.0   0.5    1.4  1  NqrM           (Na+)-NQR maturation NqrM


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.0   4.2e-35   1.1e-31       2     192 ..     235     409 ..     234     412 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 4.2e-35
                      GATase_3   2 iavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiC 82 
                                   + +i +p++sn++++ +L++ ++  ++fv+ k ++++ d dlvilpG+k+ti++l++l+++g+ + +k+     +pvlgiC
  gi|70606251|ref|YP_255121.1| 235 VSIIAYPQMSNFNEFYALNN-SNAHLKFVK-KPTQIT-DSDLVILPGSKNTIKSLEWLKSRGFTDFLKR-----KPVLGIC 307
                                   889***************88.56899****.999995.5************************999998.....8****** PP

                      GATase_3  83 GGlqmLGeeiedpegveg..eageveglglLdietefekekltgqvegevelaaegeevkGyEiHsGrtilkekakpllkv 161
                                   GG+q++G++++d +g  +  ++++v+glgl+ i+t++ekek+++ + ++         ++GyEi++Gr    + ++pl  +
  gi|70606251|ref|YP_255121.1| 308 GGFQIMGSKMIDNSGGLElgDVNQVDGLGLFGINTVYEKEKVVSLSSAQ-------LGIEGYEIRRGRIEYIN-EEPLTYI 380
                                   **********8877643346889********************444444.......67*********877655.8888888 PP

                      GATase_3 162 kv.ggnng.ekdGavkksedgnvlGtYlHglfd 192
                                   ++ g+ +    dG++k+      lG  +Hg ++
  gi|70606251|ref|YP_255121.1| 381 TRrGKMTVyVPDGVLKG----DKLGLSIHGSMF 409
                                   774444449******77....889999998776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   2.4e-15     6e-12       1     117 [.       3     214 ..       3     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.4e-15
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   ++iast +++GK+t++++L +++      V +++a++++ n+     + ++i+                            
  gi|70606251|ref|YP_255121.1|   3 VIIASTMSDSGKSTIVTGLSKLFH-----VKPFKAQNMSLNSYA-TLDYGEIAFiqayqsigagfsperymnplllkpsgn 77 
                                   68*******************765.....7********999984.3333344435579*********************** PP

                                   ........................................................................CCHCCCHHH CS
                                   ........................................................................xxxxxxxxx RF
                          CbiA  55 ........................................................................dlkrllell 63 
                                                                                                           d++r++ + 
  gi|70606251|ref|YP_255121.1|  78 glleviffgeskglfrpqdyystlnyfwteieknfsnefivesaggiepnfldkdlalkvsanfnvpiilvlDIDRGGAFT 158
                                   ********************************************************************************* PP

                                   HHHCHCHHHH......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CC CS
                                   xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  64 ealgkkkall....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdea 117
                                   +alg  ++l      k+ g+++n+++g+  e+ l+ +++ +++r++++ lg++p+ e+
  gi|70606251|ref|YP_255121.1| 159 SALGSYLSLPvslrEKLRGFIINKFRGD--EKFLEPGIKWVEERTNMKYLGSLPYFEE 214
                                   ****998877999***************..************************9765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.001       2.6       3      31 ..       3      31 ..       1      72 [. 0.87
   2 !   33.1   0.0   1.9e-11   4.8e-08      90     191 ..     103     212 ..      93     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvk 31
                                  +++++t  ++GK+++ +gL + ++ k +k
  gi|70606251|ref|YP_255121.1|  3 VIIASTMSDSGKSTIVTGLSKLFHVKPFK 31
                                  89*****************9888555444 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.9e-11
                        AAA_26  90 kivkelekda.divvVEGagglgvpiteellnadiaknlgapvilVarggl.gtinqllltiealr.qknvrvlGvilNkv 167
                                    ++ e+ek+  + ++VE agg+  + ++++l  ++ +n ++p+ilV+ +++ g+++ +l ++ +l  +   +++G i+Nk+
  gi|70606251|ref|YP_255121.1| 103 YFWTEIEKNFsNEFIVESAGGIEPNFLDKDLALKVSANFNVPIILVLDIDRgGAFTSALGSYLSLPvSLREKLRGFIINKF 183
                                   55667777655789***********************************99559999987777664244568********* PP

                        AAA_26 168 rnpe.....nvetlekksgipvlGvvPyl 191
                                   r +e      ++ +e+ ++++ lG++Py 
  gi|70606251|ref|YP_255121.1| 184 RGDEkflepGIKWVEERTNMKYLGSLPYF 212
                                   ***8788899*****************95 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.1e-06     0.008      14      94 ..     251     327 ..     242     410 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                                   HHHHTTSEEEEE-SGGGGCC-SEEEE-SS-HHHHHH.HHHHTT-HHHHHHHHHTT.--EEEETHHHHHH.CCEETTBSS-S CS
                           SNO  14 aikkclaenktvkrkedlaevdaliiPGGestamsk.liertglyedllefvknsekvvlGtCaGlill.skelenelvkt 92 
                                   a++++ a  k vk++ ++ + d +i+PG   t  s+  ++  g+ +    f+k+  k+vlG C G+ ++ sk ++n+   +
  gi|70606251|ref|YP_255121.1| 251 ALNNSNAHLKFVKKPTQITDSDLVILPGSKNTIKSLeWLKSRGFTD----FLKR--KPVLGICGGFQIMgSKMIDNSGGLE 325
                                   56667777799******************99977752456667555....5554..69*******9766256666664444 PP

                                   S- CS
                           SNO  93 le 94 
                                   l+
  gi|70606251|ref|YP_255121.1| 326 LG 327
                                   44 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.042      44      88 ..     272     317 ..     246     379 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                   SEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                        GATase  44 dgilvsgGpgspg..vegkieaikearenkiPiLGICLGmQllaief 88 
                                   d ++++g  ++ +     k +  + +++ ++P+LGIC G+Q+++ ++
  gi|70606251|ref|YP_255121.1| 272 DLVILPGSKNTIKslEWLKSRGFTDFLK-RKPVLGICGGFQIMGSKM 317
                                   4444444444444432223333344445.9*************8776 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00023       0.6     104     119 ..     299     314 ..     295     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                 Peptidase_C26 104 rgvPilgiCrGlqlln 119
                                   +++P+lgiC G+q++ 
  gi|70606251|ref|YP_255121.1| 299 KRKPVLGICGGFQIMG 314
                                   679***********95 PP

>> NqrM  (Na+)-NQR maturation NqrM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00022      0.56       2      20 ..     297     315 ..     297     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                          NqrM   2 ivkrKpikGSCGGLaalgi 20 
                                   ++krKp+ G CGG + +g 
  gi|70606251|ref|YP_255121.1| 297 FLKRKPVLGICGGFQIMGS 315
                                   58***********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2936.28
//
Query:       gi|70606252|ref|YP_255122.1|  [L=373]
Description: GMP synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-21   76.2   1.7      6e-18   64.7   0.2    2.8  2  GMP_synt_C       GMP synthase C terminal domain
    5.8e-13   48.5   0.2    2.4e-12   46.5   0.2    1.9  1  NAD_synthase     NAD synthase
    7.6e-08   32.3   0.0    1.2e-07   31.7   0.0    1.3  1  ATP_bind_3       PP-loop family
    8.5e-07   28.7   0.0    4.7e-05   23.0   0.0    2.2  1  QueC             Queuosine biosynthesis protein QueC
    0.00065   19.0   0.3     0.0075   15.5   0.0    2.2  2  DUF1152          Protein of unknown function (DUF1152)
  ------ inclusion threshold ------
      0.012   14.9   0.7      0.015   14.6   0.1    1.5  2  Arginosuc_synth  Arginosuccinate synthase
      0.028   14.0   0.2      0.086   12.4   0.0    2.0  2  ThiI             Thiamine biosynthesis protein (ThiI)
      0.039   12.7   0.0       0.87    8.3   0.0    2.2  2  tRNA_Me_trans    tRNA methyl transferase
       0.22   11.9   2.0        3.8    8.0   0.2    3.1  3  Latarcin         Latarcin precursor
       0.76    9.7   2.9         18    5.4   0.0    3.3  3  Tautomerase      Tautomerase enzyme


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00041      0.73       6      40 ..     245     279 ..     240     285 .. 0.81
   2 !   64.7   0.2   3.3e-21     6e-18      34      91 ..     314     371 ..     281     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00041
                                   TT-GGGSSEEEEEEEEEEE----------EEEEEE CS
                    GMP_synt_C   6 aglykkiwQafavllpvksvGvmgdkRtyeyvval 40 
                                    +l+k++        ++k++Gv+gd R+y+ v  +
  gi|70606252|ref|YP_255122.1| 245 DELSKRVGSNVFTYKKIKATGVKGDVRAYGRVAKI 279
                                   5667777777778899*************998765 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 3.3e-21
                                   -EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
                    GMP_synt_C  34 yeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpatiE 91 
                                    ey+v +Rav++eD+mta++++l+  +L+ki + i+n  k++  vvydit+kPpatiE
  gi|70606252|ref|YP_255122.1| 314 GEYTVGIRAVSTEDFMTAEITKLDRGILSKIGNEILNISKKIHEVVYDITTKPPATIE 371
                                   4799*****************************************************9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.2   1.4e-15   2.4e-12       7     177 ..      10     191 ..       6     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.4e-15
                                   HHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHH CS
                  NAD_synthase   7 dflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivra 87 
                                   d +k +++k    +++  +SGGvDS+++a+l+ k++  ++v+ +++ + +  e +ve+ +++++n  +  +++d k+    
  gi|70606252|ref|YP_255122.1|  10 DEVKPQLEKILDGKAIAAVSGGVDSTTAATLTYKLM-GDKVIPIIIDTGFLREGEVEKVKNMVKN-VLPLQVVDAKEKFLR 88 
                                   55677788888889999*******************.689*************************.899999999987655 PP

                                   HHHHHHHHH...............-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTT CS
                  NAD_synthase  88 feqelkeak...............edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiae 153
                                     + l++a+               e ++k N k  i  +i  ++ + ++   + T+++  + +G  T    g   ++p+a+
  gi|70606252|ref|YP_255122.1|  89 ALEGLSDAEekrktfrkifydilsELVRKYNAKYLIQGTIAADWVETQGG--IKTQHNVLVQLGIDTEREWGFKVVEPLAD 167
                                   44433333335578988898888777888899999998888888888887..689************9877788899**** PP

                                   S-HHHHHHHHHHTT--HHHHCS-- CS
                  NAD_synthase 154 llKtevkeLakelnvPervlkkpP 177
                                   l+K+ev++L ++l+ P+++++++P
  gi|70606252|ref|YP_255122.1| 168 LYKNEVRKLGEYLGLPKEIYNRQP 191
                                   **********************99 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   6.7e-11   1.2e-07       2     155 ..      24     176 ..      23     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.7e-11
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H.......HHCTTST CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv.......akkkgkn 75 
                                   +++AvSgG+DS++   l++kl      k++ i +d g+  e   e e vk+++k++ ++l++ +++        + +  ++
  gi|70606252|ref|YP_255122.1|  24 AIAAVSGGVDSTTAATLTYKLMG---DKVIPIIIDTGFLREG--EVEKVKNMVKNV-LPLQVVDAKEkflraleGLSDAEE 98 
                                   689***************99955...4888888888875543..455666766666.666666666555655665555778 PP

                                   CCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHH CS
                    ATP_bind_3  76 leeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvskeeleey 155
                                     ++ R++ Y++l+e+++k+++++l+ +  a D +Et     ++ +++   +gi++++e  + ++v Pl +++k+e++++
  gi|70606252|ref|YP_255122.1|  99 KRKTFRKIFYDILSELVRKYNAKYLIQGTIAADWVETQGGIKTQ-HNVLVQLGIDTERE-WGFKVVEPLADLYKNEVRKL 176
                                   888899999****************************9877766.55567889999883.4599***********99875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.6e-08   4.7e-05       1     178 [.      23     185 ..      23     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.6e-08
                                   EEEEE--SSHHHHHHHHHHHH.H-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-------- CS
                          QueC   1 kavvllSGGlDSttvlalakk.egkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievp 80 
                                   ka+  +SGG+DStt+++l  k  g++v+ + +d g  ++ e+e++k+++k++     +++d +  +++      ++ + ++
  gi|70606252|ref|YP_255122.1|  23 KAIAAVSGGVDSTTAATLTYKlMGDKVIPIIIDTGFLREGEVEKVKNMVKNV--LPLQVVDAK--EKFL-----RALEGLS 94 
                                   7999**********9987765268***********************99875..457777776..2222.....2222233 PP

                                   ---...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH....HTS--EEE-T CS
                          QueC  81 keeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg....edkkieieaP 157
                                   +     ee ++tf      if+ + + + ++++a+ +i G  + d       +    ++ n++++lg    ++  ++++ P
  gi|70606252|ref|YP_255122.1|  95 D----AEEKRKTF----RKIFYDILSELVRKYNAKYLIQGTIAADW---VETQGGIKTQHNVLVQLGidteREWGFKVVEP 164
                                   3....34556666....368999*********************95...56788888889999999988766678****** PP

                                   TTT--HHHHHHHHHHTTHHHH CS
                          QueC 158 lidlsKaeivklgkelgvple 178
                                   l dl K+e+ klg+ lg+p e
  gi|70606252|ref|YP_255122.1| 165 LADLYKNEVRKLGEYLGLPKE 185
                                   ****************99865 PP

>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.2e-06    0.0075     188     289 ..      56     156 ..      15     161 .. 0.81
   2 ?    1.3   0.0     0.092   1.7e+02     186     232 ..     271     318 ..     264     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                       DUF1152 188 ggllgilgldeedaellekileeveteAskiplaaakGlrGeveiRkgtrkveltplsalvfyldpkavaelsklaklvag 268
                                    g+l   +++ +  ++++++l   + +A +  l+a +Gl    e Rk  rk+  ++ls lv + ++k +++ + +a+ v+ 
  gi|70606252|ref|YP_255122.1|  56 TGFLREGEVE-KVKNMVKNVLPLQVVDAKEKFLRALEGLSDAEEKRKTFRKIFYDILSELVRKYNAKYLIQGTIAADWVET 135
                                   4444333332.334556666666789******************************************************* PP

                       DUF1152 269 tesleeAeerlnelgiytEld 289
                                   +  +++ ++ l +lgi tE +
  gi|70606252|ref|YP_255122.1| 136 QGGIKTQHNVLVQLGIDTERE 156
                                   ******************976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.092
                       DUF1152 186 keggllgilgldeedaellekileeve.teAskiplaaakGlrGevei 232
                                   ++ g ++ ++ +eed+e+l++++e v+ ++ +++++  a+ + Ge+++
  gi|70606252|ref|YP_255122.1| 271 RAYGRVAKIETNEEDYEKLRELMEMVTsSDVTHVVIPVARREDGEYTV 318
                                   5667888899999**********9976257888888888998888765 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   8.4e-06     0.015       3      65 ..      27      88 ..      25     151 .. 0.88
   2 ?   -3.0   0.1       1.8   3.3e+03     269     353 ..     194     280 ..     185     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
               Arginosuc_synth  3 aysGGlDtsviikllkeklgeeviavavdvGqeee.dldevkekalklgavksvvvDakeefve 65
                                  a sGG+D + + +l  + +g++vi +++d G  +e ++++vk+  +++      vvDake f +
  gi|70606252|ref|YP_255122.1| 27 AVSGGVDSTTAATLTYKLMGDKVIPIIIDTGFLREgEVEKVKNMVKNVLP--LQVVDAKEKFLR 88
                                  89*****************************7644388888888888765..789*******75 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
               Arginosuc_synth 269 apaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkealdafiektqervtG..tvrvklfkGsvvvlg 347
                                    p++lv       +ekl l r+ + + ++  + ++   Y  + f+   e+ d++ ++   +v    +++ +  kG+v+  g
  gi|70606252|ref|YP_255122.1| 194 GPGLLVRTVGKLTIEKLELVRKATTVVEKYLDGMGISQYFAFIFEAQSEKHDELSKRVGSNVFTykKIKATGVKGDVRAYG 274
                                   566666666666777777777777766666666666667777777777777777666666665411444445677777777 PP

               Arginosuc_synth 348 Resees 353
                                   R ++ +
  gi|70606252|ref|YP_255122.1| 275 RVAKIE 280
                                   766555 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05     0.086       3     116 ..      21     127 ..      19     183 .. 0.64
   2 ?   -3.8   0.0       4.3   7.8e+03      40      59 ..     280     299 ..     269     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                          ThiI   3 qgkvlaLlSgGiDSpVaaylllk.RGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilek 82 
                                    gk++a +SgG+DS  aa l  k  G +v  + ++ + +  e + ekv+++++ +   q        vvd ke     le 
  gi|70606252|ref|YP_255122.1|  21 DGKAIAAVSGGVDSTTAATLTYKlMGDKVIPIIID-TGFLREGEVEKVKNMVKNVLPLQ--------VVDAKEKFLRALEG 92 
                                   699***************99988458888888885.66677777777777666554444........44444333322222 PP

                          ThiI  83 v.kekltivllkrkmlriAekvaeeegakalvtGe 116
                                   + +++ +   +++ ++ i +++ ++++ak l++G 
  gi|70606252|ref|YP_255122.1|  93 LsDAEEKRKTFRKIFYDILSELVRKYNAKYLIQGT 127
                                   21344444456777777777777777777777775 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.3
                          ThiI  40 gtseeaiekveklaellaey 59 
                                    t+ee  ek+++l+e++++ 
  gi|70606252|ref|YP_255122.1| 280 ETNEEDYEKLRELMEMVTSS 299
                                   56777777777777776654 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00048      0.87       3      30 ..      24      52 ..      22      79 .. 0.78
   2 ?    2.1   0.0     0.037        66     163     186 ..     160     183 ..     139     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00048
                 tRNA_Me_trans  3 vvvalSgGVDSsvaaallke.qgyevigv 30
                                   ++a+SgGVDS+ aa+l  +  g +vi +
  gi|70606252|ref|YP_255122.1| 24 AIAAVSGGVDSTTAATLTYKlMGDKVIPI 52
                                  5799*********9988644145666555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.037
                 tRNA_Me_trans 163 kllfPlgeltKeevrkiAkeagla 186
                                   k++ Pl++l K+evrk+ +  gl+
  gi|70606252|ref|YP_255122.1| 160 KVVEPLADLYKNEVRKLGEYLGLP 183
                                   5677*************9999986 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0021       3.8      47      79 ..      87     116 ..      55     118 .. 0.75
   2 ?    0.5   0.1      0.45   8.1e+02      15      30 ..     282     296 ..     271     300 .. 0.69
   3 ?   -0.1   0.0      0.69   1.2e+03       7      45 ..     326     360 ..     321     364 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0021
                      Latarcin  47 lrkvedledtEEARgafkklkdkfkkmgeklkk 79 
                                   lr++e+l+d EE R    ++++ f  + ++l++
  gi|70606252|ref|YP_255122.1|  87 LRALEGLSDAEEKRK---TFRKIFYDILSELVR 116
                                   899************...777777777777766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.45
                      Latarcin  15 delergainrklmemv 30 
                                   +e e+ +  r lmemv
  gi|70606252|ref|YP_255122.1| 282 NE-EDYEKLRELMEMV 296
                                   33.3344449999998 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.69
                      Latarcin   7 eeleaeeLdelergainrklmemvnnlRkvqgRLeemve 45 
                                   e++   e++ l+ ++i   l +  n++ ++ +++ e+v 
  gi|70606252|ref|YP_255122.1| 326 EDFMTAEITKLD-RGI---LSKIGNEILNISKKIHEVVY 360
                                   788888999999.566...57777888888888888775 PP

>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.37   6.6e+02      19      41 ..     198     220 ..     197     225 .. 0.70
   2 ?    1.9   0.1      0.12   2.2e+02      11      31 ..     284     304 ..     276     311 .. 0.78
   3 ?    5.4   0.0    0.0098        18      19      38 ..     351     370 ..     350     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHHTS-GGG-EEE CS
                   Tautomerase  19 LaervTealvealgaprsaivVv 41 
                                   L++ v ++++e l + r a++Vv
  gi|70606252|ref|YP_255122.1| 198 LVRTVGKLTIEKLELVRKATTVV 220
                                   66777777777777777777765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                                   S-HHHHHHHHHHHHHHHHHHH CS
                   Tautomerase  11 rsaeqKaeLaervTealveal 31 
                                   ++ e+++eL e vT + v+++
  gi|70606252|ref|YP_255122.1| 284 EDYEKLRELMEMVTSSDVTHV 304
                                   4689**********9877765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0098
                                   HHHHHHHHHHHHHTS-GGG- CS
                   Tautomerase  19 LaervTealvealgaprsai 38 
                                   + ++++e++ +++ +p+++i
  gi|70606252|ref|YP_255122.1| 351 ISKKIHEVVYDITTKPPATI 370
                                   789**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2369.80
//
Query:       gi|70606253|ref|YP_255123.1|  [L=320]
Description: heat shock protein HtpX [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-25   88.6   0.0    1.2e-24   87.2   0.0    1.7  2  Peptidase_M48   Peptidase family M48
  ------ inclusion threshold ------
      0.018   14.3   2.3      0.033   13.4   0.2    2.1  2  Peptidase_M56   BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.17   1.5e+03     108     142 ..      34      68 ..       4      75 .. 0.57
   2 !   87.2   0.0   1.4e-28   1.2e-24       5     194 ..      72     310 ..      68     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.17
                                   HHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 108 daagafldalavliglliillflalSRkrEyqADe 142
                                     a af++  +++ +ll+ l+  a  R  E +AD 
  gi|70606253|ref|YP_255123.1|  34 TGALAFVTFFTIIQWLLGPLMIKAAYRLIEVKADD 68 
                                   22333333444444555555555888999999985 PP

  == domain 2  score: 87.2 bits;  conditional E-value: 1.4e-28
                                   SHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEE..ESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   5 aelkevveelakeaglpkpltkvyvvnspkrNAFal..gggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvs 83 
                                   +++ + v+e+a   ++   ++kvyv+  +  NAFa   + +  k +++t++L+ + l+++e++aV+GHE+GH+ hr++ + 
  gi|70606253|ref|YP_255123.1|  72 GWVYNLVQEVATYNNM--SMPKVYVAPVNFPNAFAFssPLF-GKNMAITTPLI-NILNKDEIKAVIGHEIGHLRHRDTEIL 148
                                   6888999*********..88888888888888888611455.459********.*************************** PP

                                   HHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.........HHHHHHHHHHHHHHHHTT.T.HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx.xxxxxx RF
                 Peptidase_M48  84 livsllasillllglallisraeedaagafldalavliglliillfl.........alSRkrEyqADeagvell.krakdl 154
                                   l vsl++++++ lg++l  +   +   g+  ++ + l+++ i+l  +         +l R rE +AD  ++ ++ + a +l
  gi|70606253|ref|YP_255123.1| 149 LAVSLIPTLMYWLGYSLWWGGLLGGGGGGRNSNSGLLFLIGIVLIAVsfvfnifvlFLNRMREAYADVNSALTIpNGASNL 229
                                   ***************99888877777777777777766665555555777888**************87766661567889 PP

                                   HHHHHHHHHHTT--S---HHHH.........................................HHS-SS--HHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 155 vraliklakdlerqdvsaslrs.........................................ellstHPplleRiqalke 194
                                   ++al+k++   +   v+  +++                                         +l+s HP  ++Ri+ l++
  gi|70606253|ref|YP_255123.1| 230 QTALAKIVIYTDPGIVDRVKQKsggvakmllfsgtdvsneeipsykaqelvnywrtqkvgilsDLFSDHPHPAKRIKLLDK 310
                                   99*****999999666666666677777788888888888888999999999*************************9986 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.7e-06     0.033     188     226 ..     121     159 ..     109     161 .. 0.82
   2 ?   -0.5   0.0     0.063   5.7e+02     105     130 ..     185     210 ..     179     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-06
                 Peptidase_M56 188 lkklsdeeleyillHElaHlkrkDllvnllvavlqclfw 226
                                    + l+++e++ ++ HE  Hl+++D+ + l v ++  l++
  gi|70606253|ref|YP_255123.1| 121 INILNKDEIKAVIGHEIGHLRHRDTEILLAVSLIPTLMY 159
                                   55689********************99887777766665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.063
                 Peptidase_M56 105 llliWivgalilllyliaallvlkkr 130
                                   l li iv++++ +++ i++l++ + r
  gi|70606253|ref|YP_255123.1| 185 LFLIGIVLIAVSFVFNIFVLFLNRMR 210
                                   56777777777777777777755533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2097.59
//
Query:       gi|70606254|ref|YP_255124.1|  [L=135]
Description: hypothetical protein Saci_0416 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-31  108.3   4.6    8.1e-16   58.2   0.5    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.5   4.5e-20   8.1e-16       1      55 [.      11      64 ..      11      66 .. 0.95
   2 !   52.1   0.3   3.7e-18   6.5e-14       2      56 ..      75     129 ..      74     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 4.5e-20
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  V+++m+++v++v+  t ++e++++m+ek+++++ +V e++k++Gi+t+rD++ra+
  gi|70606254|ref|YP_255124.1| 11 VKEYMRSPVISVDKKTKISEIAKIMTEKNIGSV-IVTENNKPIGIITERDIVRAI 64
                                  89*******************************.7779***************98 PP

  == domain 2  score: 52.1 bits;  conditional E-value: 3.7e-18
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   ++imt  ++t+++d++++ al lmr+ ++++lPV+++  +lvGi++ rD++ra+ 
  gi|70606254|ref|YP_255124.1|  75 EEIMTVSLITIREDSPIAGALSLMRQFNIRHLPVINDKRELVGILSIRDVARAID 129
                                   79***********************999*******98999*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 975.62
//
Query:       gi|70606255|ref|YP_255125.1|  [L=71]
Description: hypothetical protein Saci_0417 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00058   19.7   0.0    0.00071   19.4   0.0    1.2  1  RHH_4     Ribbon-helix-helix domain
  ------ inclusion threshold ------
       0.13   12.3   0.1        0.7    9.9   0.0    1.9  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     8e-08   0.00071      19      45 ..       7      33 ..       2      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8e-08
                                  HHHHHHHHHHHHHTT--HHHHHHHH.H CS
                         RHH_4 19 pafWdaLeeiArregltvnaLiaeida 45
                                  ++ +++L++iAr++++t+++Liaei +
  gi|70606255|ref|YP_255125.1|  7 KEWYEILNQIARKKHITLSNLIAEISK 33
                                  67899********************43 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   7.8e-05       0.7       4      31 ..       3      30 ..       2      31 .. 0.93
   2 ?    0.2   0.0     0.093   8.3e+02       2      12 ..      51      61 ..      50      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.8e-05
                                  EEEEHHHHHHHHHHHHHHTSSHHHHHHH CS
                         RHH_1  4 irldeellerLdelarrrgrSrSelIRe 31
                                  i++++e +e L+++ar+ + + S lI e
  gi|70606255|ref|YP_255125.1|  3 IKVPKEWYEILNQIARKKHITLSNLIAE 30
                                  89******************99999976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.093
                                  EEEEEEHHHHH CS
                         RHH_1  2 vsirldeelle 12
                                  ++++++++ +e
  gi|70606255|ref|YP_255125.1| 51 INVSIEDKQIE 61
                                  89*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 600.18
//
Query:       gi|70606256|ref|YP_255126.1|  [L=499]
Description: hypothetical protein Saci_0418 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.7   0.1       0.54   10.7   0.1    2.1  1  DUF1689   Protein of unknown function (DUF1689)


Domain annotation for each model (and alignments):
>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1     3e-05      0.54      10      91 ..     347     428 ..     339     460 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3e-05
                       DUF1689  10 aDqkLdaeDRleLakklqs.iaraqllggwlgfsavflaptayrryktgaikgvkvprsfllGlvalvvssqlaakyaykk 89 
                                    D  L +e+R +++k+++     ++ ++++ g ++ +++ ++y+   + a+ +  +++ + +  v + +ss   +k++y+ 
  gi|70606256|ref|YP_255126.1| 347 IDRALGSEERFDIKKSYTAkLNASNTIFAIIGVGISVILVYIYKGS-SPALLSSLMTIGVTVNSVWMTISSARICKSLYSM 426
                                   599**************86155556678999999999999999996.5555555688888888888999999999999988 PP

                       DUF1689  90 kl 91 
                                   k+
  gi|70606256|ref|YP_255126.1| 427 KI 428
                                   77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3403.50
//
Query:       gi|70606257|ref|YP_255127.1|  [L=379]
Description: hypothetical protein Saci_0421 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-08   34.7  12.7    1.9e-08   34.7  12.7    3.0  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.04   7.2e+02      49      68 ..       8      27 ..       1      40 [. 0.55
   2 !   34.7  12.7   1.1e-12   1.9e-08       2     152 ..      82     232 ..      81     239 .. 0.79
   3 ?   -2.1   1.8      0.23   4.1e+03      11      24 ..     315     328 ..     279     361 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.04
                         PMT_2 49 kraallaalllavvplfval 68
                                  k  +++++++la+++ +++ 
  gi|70606257|ref|YP_255127.1|  8 KYFGIISVVILATIISIYTF 27
                                  44555555555554433332 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.1e-12
                         PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfgkra.....allaalllavvplfvalsalftpdap 77 
                                   hPPl  +++alf   +g + l+ r++s ++g lti++ +l+ar+l g+++     +l+a++l+a+ p++ ++  +  +++ 
  gi|70606257|ref|YP_255127.1|  82 HPPLPKYIMALFIYALGYNPLVWRIPSWILGDLTIIIAFLMARKLIGNNVlgnvsGLIASVLIALDPNIWVMHGIAMLEIY 162
                                   9******************************************99875433333378888888888866666668888999 PP

                         PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllis.arrilkekkpyl.alllalll 152
                                     ++ +++lylll    k +        v +Gl+fl K   + lli++++yl    ++r+ +  + +l  ++++++ 
  gi|70606257|ref|YP_255127.1| 163 AGFFSLFTLYLLLSDRIKSS-------SVGLGLAFLAKESLLPLLIPYIYYLGEIvKQRTKRVIYGILiPVAIYVAF 232
                                   99999999999998777776.......599********************997664455555555455334444443 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.23
                         PMT_2  11 alftklfgfselai 24 
                                    + + +f  s ++i
  gi|70606257|ref|YP_255127.1| 315 DIKLIIFTMSAWSI 328
                                   22222222233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2837.70
//
Query:       gi|70606258|ref|YP_255128.1|  [L=257]
Description: nucleotidyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-28   98.0   0.0    7.2e-28   97.8   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    1.6e-09   38.4   0.0    1.9e-09   38.1   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.17   11.5   0.0    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
       0.11   12.3   0.0       0.16   11.8   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   1.6e-31   7.2e-28       1     242 [.       4     245 ..       4     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.6e-31
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTET.......ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSE CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgke.......rliqatlsrlansgieeiivvltqehsflveeqlkegskfgve 74 
                                   kavI a G+G+R+  +t  l+k l+p   +e       ++i+  +  l++ g+++  +++  +h  l+ ++l +       
  gi|70606258|ref|YP_255128.1|   4 KAVITAAGKGSRMKYITTVLPKALLPLFSSEngdlitrPVIDLIFDSLSSVGVKK-FCIVVGKHGKLLMDYLFDMG----- 78 
                                   79********************9998876543423445888999999999*****.77778888888888887765..... PP

                                   EEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
               NTP_transferase  75 vlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                   v+++++p +kg  dAv++a+++  ++     ++v ++D + +  y+eav  + e +   ++++++ +v+++++yG++ +++
  gi|70606258|ref|YP_255128.1|  79 VTFVFQPHPKGFGDAVLKAEDFSSNDP----FIVHADDGVLTGGYKEAVSLFDEVKP--DAVLLLREVKNPKRYGIVDVKD 153
                                   99**********************988....8*************************..9********************6 PP

                                   TS........BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE- CS
               NTP_transferase 156 eg........rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaey 228
                                   eg        rv++ +EKP++++ s++  s +Y+f +++++ l k ++  + +e e+t  ++ +++eg + + +l kd+ +
  gi|70606258|ref|YP_255128.1| 154 EGeymghkmyRVIEAQEKPQNPR-SNIGISAVYIFSPKIFQGLNK-VKVEEGKELELTYGIQNIISEGGEVYGILLKDE-K 231
                                   6667777889*************.*******************76.666667899999********************7.6 PP

                                   EEEXSSHHHHHHHH CS
               NTP_transferase 229 WsDvGtldsllean 242
                                   W  vG++ s+++a 
  gi|70606258|ref|YP_255128.1| 232 WLNVGDPVSYIDAL 245
                                   ***********986 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   4.2e-13   1.9e-09       1      95 [.       5     112 ..       5     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 4.2e-13
                                   EEEEEESS-TTTTT.....THHHHCC....CCC....CHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-T CS
                  NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl....ggk....pllervldalraagvdevvvvggd..eevlaalarlgvrvvede 66 
                                   avi A+G++sRm+      +Kallpl    +g     p+++ ++d+l+++gv++ ++v+g   + + ++l + gv++v ++
  gi|70606258|ref|YP_255128.1|   5 AVITAAGKGSRMKYittvlPKALLPLfsseNGDlitrPVIDLIFDSLSSVGVKKFCIVVGKhgKLLMDYLFDMGVTFVFQP 85 
                                   7999********9444689*******86554448999***************9888887773557889999*********9 PP

                                   TSS-SHHHHHHHHHHHH.SSSCEEEEETT CS
                  NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacD 95 
                                   +  kg + +++ a + + ++d+++v a D
  gi|70606258|ref|YP_255128.1|  86 H-PKGFGDAVLKAEDFS-SNDPFIVHADD 112
                                   6.59*********9986.77887776655 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.17       4      47 ..      44      86 ..      41      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                  HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SS CS
                  TPP_enzyme_N  4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarh 47
                                   +++++ L++ gv+++++v+G++ + l+d+l +  g+++v   h
  gi|70606258|ref|YP_255128.1| 44 IDLIFDSLSSVGVKKFCIVVGKHGKLLMDYLFDM-GVTFVFQPH 86
                                  589****************************999.698887766 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.16      52     162 ..      75     186 ..      65     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
                                   C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2  52 edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                    d +v+++ +++ +G++ a+ ++ + ++ d +++  +D + + +  ++ v  +++  +d+vl  r +++ +++ i   k  
  gi|70606258|ref|YP_255128.1|  75 FDMGVTFVFQPHPKGFGDAVLKAEDFSSNDPFIVHADDGVLTGG-YKEAVSLFDEVKPDAVLLLREVKNPKRYGIVDVKDE 154
                                   57899*************************88777777777765.89999999999**********************997 PP

                                   ..EEEECCHCCCCHCCCCCCSTTCSTCCCEEE CS
               Glycos_transf_2 133 ..generlyfkerkrslkgnlsfeigsaallr 162
                                     +   ++y+ ++ +++++n   +ig  a++ 
  gi|70606258|ref|YP_255128.1| 155 geYMGHKMYRVIEAQEKPQNPRSNIGISAVYI 186
                                   77778888888888888877777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1828.17
//
Query:       gi|70606259|ref|YP_255129.1|  [L=393]
Description: epimerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-22   79.0   0.0    5.9e-22   78.3   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.1e-19   71.1   0.0    3.1e-19   69.5   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0013   18.3   0.0     0.0025   17.4   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0014   17.8   0.0     0.0028   16.9   0.0    1.4  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0066   15.6   0.0      0.015   14.4   0.0    1.6  1  RmlD_sub_bind    RmlD substrate binding domain
  ------ inclusion threshold ------
       0.12   12.4   0.0        0.3   11.1   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0     2e-25   5.9e-22       1     233 [.       3     285 ..       3     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2e-25
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........................EEEE--TT-HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........................elveldltdrsale 57 
                                   ilV+G+ G +G  l+ +l+++g+evig+d+ls+++ +++                            +++ +d+t+   ++
  gi|70606259|ref|YP_255129.1|   3 ILVLGIDGHLGWPLALRLAKRGHEVIGIDNLSTRRFSEEVG-SdsafplpqpqervseakkhlgvdiTFYVGDITNYGFFK 82 
                                   8******************************6655444433.3599*********************************** PP

                                   HHHHHHT-SEEEE--S---HHHHHHS...HHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSS.SS....... CS
                     Epimerase  58 rlfkeeqpdavihlAavggvaassed...padfieknlqgtlnlleaarkagvk.rllflsSsevYGkdae.qp....... 126
                                   +++++++pda++h+A + + + s++d   + +++ +n + tl++++a+ + ++   +l +++   YG +a  +p       
  gi|70606259|ref|YP_255129.1|  83 DIVQRYKPDAIVHFAEQRSAPYSMIDmdhAVYTVINNEVSTLRVIQAVLEVDPTiHILKMGTMGEYGTPAFdIPesiyvea 163
                                   ****************87777776651115666669***************8888************77775476675444 PP

                                   ...BSTCSTTS--.......--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT.............S-TTSTTS CS
                     Epimerase 127 ...keettltgpl.......kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr.............ngegevsr 184
                                       +               k  s Y  +K++    +  +++ ygl ++ ++   +yG r             ++++    
  gi|70606259|ref|YP_255129.1| 164 ivnGK-------KdkiivprKAGSVYHWTKVHDTDFLLHFQELYGLTVTDIMQGPVYGTRteeiveetlrtrfDFDEVWGT 237
                                   44322.......22223345999*************************************888777766554444444455 PP

                                   HHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-S CS
                     Epimerase 185 vipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagd 233
                                   v+ ++   + +g  ++t++g+g + R f+  eD ++a+ l+le++ ++ 
  gi|70606259|ref|YP_255129.1| 238 VVNRYCVEAILGL-PLTVYGKGGQTRGFISLEDSIQALTLLLENPPKQG 285
                                   5555555555577.******************************65543 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   1.1e-22   3.1e-19       1     280 [.       4     327 ..       4     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.1e-22
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTH...........HHHHCTTT...TTGCCEEEEE--TT-HHHHHHH CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntg...........riehlakdpkeeleenlklhkgDltDssslerl 70 
                                   L+ Gi G  G  la +L ++g+ev+gi+++s+    +           + ++  ++ k++l  +++++ gD+t+    +++
  gi|70606259|ref|YP_255129.1|   4 LVLGIDGHLGWPLALRLAKRGHEVIGIDNLSTRRFSEevgsdsafplpQPQERVSEAKKHLGVDITFYVGDITNYGFFKDI 84 
                                   899************************9976654444122222222224445556677788889***************** PP

                                   HHHHT-SEEEE--S---HHHHT...TSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S....SSSB-TT CS
                 GDP_Man_Dehyd  71 laevqpdevynLAAqshVdvsf...ekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq....evpqtEt 144
                                   +++++pd+++++A q   ++s+   +++ yt+ +n + tlr+++a+ ++  +++++++ ++t   YG+++    e+ + E 
  gi|70606259|ref|YP_255129.1|  85 VQRYKPDAIVHFAEQRSAPYSMidmDHAVYTVINNEVSTLRVIQAVLEV--DPTIHILKMGTMGEYGTPAfdipESIYVEA 163
                                   *****************9999655589*******************765..689**************9763335555675 PP

                                   ..........S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS.............CCCHHHHHHH CS
                 GDP_Man_Dehyd 145 ..........tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf.............vtrkitrava 202
                                              p ++ s Y  +K+    +   ++e ygl ++       ++ r +e +                 + r+ +
  gi|70606259|ref|YP_255129.1| 164 ivngkkdkiiVPRKAGSVYHWTKVHDTDFLLHFQELYGLTVTDIMQGPVYGTRTEEIVeetlrtrfdfdevWGTVVNRYCV 244
                                   6666666666778889*************************9999999999987652222233333434434567788889 PP

                                   HHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.SS---EEE-TT..-EEEC...HHCHHCCHHCCCHHHHHH.... CS
                 GDP_Man_Dehyd 203 rialgkqevlylGnldakRdwghvkDyveamwlmlqq.dkpedyviatg..ethsv...refvelaflelgktiewegkge 277
                                   ++ lg+ + +++G++ ++R +   +D ++a+ l+l++  k+ +y +a++  e +sv    efv++a +elg ++e    ++
  gi|70606259|ref|YP_255129.1| 245 EAILGL-PLTVYGKGGQTRGFISLEDSIQALTLLLENpPKQGEYRVANQfaEIYSVkkiAEFVKKAGEELGLNVEIGSYEN 324
                                   999998.8999************************9955566777666433555552226778888888887766532222 PP

                                   ... CS
                 GDP_Man_Dehyd 278 eev 280
                                     v
  gi|70606259|ref|YP_255129.1| 325 PRV 327
                                   222 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.2e-07    0.0025       1      31 [.       1      32 [.       1      39 [. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.2e-07
                                  SEEEEE--.STTHHHHHHHHHHCTSEEEEE-S CS
                UDPG_MGDP_dh_N  1 mkisviGl.GYvGlvtaavlaeighevigvDi 31
                                  m+i v+G  G++G + a+ la++ghevig+D+
  gi|70606259|ref|YP_255129.1|  1 MRILVLGIdGHLGWPLALRLAKRGHEVIGIDN 32
                                  8999***76**********************7 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.3e-07    0.0028      47     118 ..      59     133 ..      43     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.3e-07
                                   ..-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSH...HHHHHHHHHHHHHHHHHHHHT CS
               Polysacc_synt_2  47 lkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenp...leaiktNvlgtenvieaaiea 118
                                    +kk+l v+i+  +gd+++    +++++++k+d+++h A  +  P     +   + ++ +N ++t  vi+a +e 
  gi|70606259|ref|YP_255129.1|  59 EAKKHLGVDITFYVGDITNYGFFKDIVQRYKPDAIVHFAEQRSAPYSMIDMdhaVYTVINNEVSTLRVIQAVLEV 133
                                   34567889999**********************************765544001445667889999999998765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.1e-06     0.015       1      59 [.       1      97 [.       1     108 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                                  EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................................T--TTSHHHHHH CS
                 RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre......................................eldltdaeavae 45
                                  m+ilv+G +G lG+ La +la++g+ev+++++                                         d+t+    ++
  gi|70606259|ref|YP_255129.1|  1 MRILVLGIDGHLGWPLALRLAKRGHEVIGIDNLstrrfseevgsdsafplpqpqervseakkhlgvditfyVGDITNYGFFKD 83
                                  99***************************976667889999999999999999999999999999888888888899999999 PP

                                  HHHHH--SEEEE-- CS
                 RmlD_sub_bind 46 llkeakpdvvvnaA 59
                                  +++  kpd++v+ A
  gi|70606259|ref|YP_255129.1| 84 IVQRYKPDAIVHFA 97
                                  99999999999887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0001       0.3      11      89 ..      16     107 ..      14     117 .. 0.81
   2 ?   -2.8   0.0       1.8   5.3e+03      17      55 ..     312     348 ..     308     363 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                Glyco_transf_4  11 LaraLarrGheVtvv....tpgddgpleeev............elvvrvprvplpllkrllrslaflrrlrrllkrekpDv 75 
                                   La +La+rGheV  +    t    +++ eev            e+v + ++   +    +  +++++  ++ +++r+kpD 
  gi|70606259|ref|YP_255129.1|  16 LALRLAKRGHEVIGIdnlsT----RRFSEEVgsdsafplpqpqERVSEAKKHLGVDITFYVGDITNYGFFKDIVQRYKPDA 92 
                                   7889***********65554....44444444555999999999999999999999999999******************8 PP

                Glyco_transf_4  76 v.Hahspaalgaall 89 
                                   + H     ++ ++++
  gi|70606259|ref|YP_255129.1|  93 IvHFAEQRSAPYSMI 107
                                   868877777766665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                Glyco_transf_4  17 rrGheVtvvtpgddgpleeevelvvrvprvplpllkrll 55 
                                   ++G +V++ + + ++ ++ee  ++++++r+ lp+l+ ++
  gi|70606259|ref|YP_255129.1| 312 ELGLNVEIGSYENPRVEAEE--HYYNPERKVLPSLGFYP 348
                                   56777777777777777777..56666666655554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2417.20
//
Query:       gi|70606260|ref|YP_255130.1|  [L=299]
Description: oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-42  143.3   1.5    1.2e-41  143.0   1.5    1.1  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
     0.0025   17.4   0.4       0.66    9.4   0.1    2.2  2  ROK          ROK family


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   1.5   1.3e-45   1.2e-41       1     263 [.       4     281 ..       4     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 1.3e-45
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTB CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlpekf 81 
                                   vGiD G+T+tkav ++++g+ +g+g t++ n+++v+  +a ++++ea  +a++   ee++ i         +G a+l++++
  gi|70606260|ref|YP_255130.1|   4 VGIDAGGTKTKAVAYTCDGQYIGEGETGPGNYHNVGLSKAINNIREAALKATKG--EEPDVIS--------IGAAGLDSRY 74 
                                   8************************************99999999987777664..4433333........5777777777 PP

                                   SEEE-.........HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHHHHHHT-- CS
                   BcrAD_BadFG  82 ekeiirs.......eilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgiiadelnmg 152
                                   ++e + s       ++ v++dG++al+++t    +v++i+G++s++ ++d+ +  ++++ ++ +++ G+++++++++l+++
  gi|70606260|ref|YP_255130.1|  75 DYESFNSlastvakKVIVNHDGVIALFAETLgekGVVVISGTGSVVEGYDGKDFHRIGGRGWLLSDVGSAYWVGRRALRAV 155
                                   77777777777899******************************************************************* PP

                                   TTTHHHHHTT--......................S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHH CS
                   BcrAD_BadFG 153 lreldglaekat......................kkarinstcavfaeaelrdalsggekaedIlaglhraialrvialis 211
                                   l+ +dgl++k+                       ++   + ++a +aea+ ++al g+e a++Il++ ++++a ++  +++
  gi|70606260|ref|YP_255130.1| 156 LEVMDGLRQKSNlyykvlekirvkdlddlvlwsyTSSCQADIIASVAEAVNSSALTGDELAISILKEGAEKLANQAVLMAR 236
                                   *********************************977789999*************************************** PP

                                   TT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHH CS
                   BcrAD_BadFG 212 rsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGA 263
                                   r++  t  v ++GG++k+  ++ +++++++    +         + ++ lGA
  gi|70606260|ref|YP_255130.1| 237 RLNVNT--VYMKGGMFKSPIYLATFKNYLSLYGIK-----GEVGKRNPELGA 281
                                   *****7..**********99999996666543333.....344555555555 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   7.4e-05      0.66       2      67 ..       4      70 ..       3      94 .. 0.84
   2 !    6.3   0.0   0.00065       5.8     202     256 ..     207     261 ..     195     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.4e-05
                                  EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEE..EEEEEESSE CS
                           ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeli..avgigspGl 67
                                  +gid+Ggtk+++   + +g+   + +   p +  + +l +ai+++ ++a ++++      ++ig++Gl
  gi|70606260|ref|YP_255130.1|  4 VGIDAGGTKTKAVAYTCDGQYIGEGET-GPGNYHNVGLSKAINNIREAALKATKGEEpdVISIGAAGL 70
                                  79*******************999999.899999999****999999887765533333788888886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00065
                                   HHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHH CS
                           ROK 202 klaekgdevaeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairk 256
                                     a  gde a  ++++ ae la+ ++ ++  ++ + + + Gg+ +++ +l++ ++
  gi|70606260|ref|YP_255130.1| 207 SSALTGDELAISILKEGAEKLANQAVLMARRLNVNTVYMKGGMFKSPIYLATFKN 261
                                   567789***************************************9999966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1917.86
//
Query:       gi|70606261|ref|YP_255131.1|  [L=479]
Description: gamma-glutamyltranspeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-74  251.3   0.0    2.6e-74  250.8   0.0    1.3  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.8   0.0   1.5e-78   2.6e-74       2     464 ..      23     435 ..      22     473 .. 0.89

  Alignments for each domain:
  == domain 1  score: 250.8 bits;  conditional E-value: 1.5e-78
                                   HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSGGG-B CS
               G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktgalavg 82 
                                   ++L+ GGnA+DAav ++++l+vv p+ sG+GG+gfll  + ++    a++a++   ++++ +          s + +  v 
  gi|70606261|ref|YP_255131.1|  23 KILETGGNAFDAAVGVSAVLSVVLPYTSGLGGDGFLLANTPEGLI--AYNASGWTSKNLKIQKI-------PSPRHPSTVL 94 
                                   79***********************************99999984..58999988888888888.......77788999** PP

                                   B--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTSEE--HHHH CS
               G_glu_transpept  83 VPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkagellkqpalA 163
                                   VPG v++++++ +k+ +l+++++l+pa+kla +Gf + ++l ra+++a ++ +++++l   +    +   ag+ +k  +l 
  gi|70606261|ref|YP_255131.1|  95 VPGLVDMWDYIERKFMSLDLQTVLQPAVKLATNGFYIGKELGRAISRAIDMPESWSKL---Y----KGRMAGDFIKLRELG 168
                                   ************************************************9987777665...3....34568********** PP

                                   HHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHHHHHHHHHHHHCT CS
               G_glu_transpept 164 ktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssggivllqiLnileg 244
                                   + L+ ++++ +++FY+G+l e++v  l+k+g  ++ +D+an++ e ++p++ +y ++ t+ye pp+s+gi++l+iL++ e 
  gi|70606261|ref|YP_255131.1| 169 EALKVISRN-PREFYEGKLMEEIVLGLNKQGVEMEFSDFANFRGEEVKPIKSTY-RDFTLYELPPNSQGITTLEILKLSEM 247
                                   ******987.678*****************************************.9************************* PP

                                   TTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHH..HHHHTT.BTTB..SGGGCSCGGCSC CS
               G_glu_transpept 245 fdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeya..keraklIkdkaatpsseyykaaeaa 323
                                   +++ + + ++ e+++ +v  + + y+dR+ry++Dp+f + p     +ll+++ +  k r+  I +++             +
  gi|70606261|ref|YP_255131.1| 248 VETWKHKFDDIERVKEMVKIFAIGYNDRDRYVTDPRFYS-P---EINLLDENVLrvKLREMGILPNR-------------I 311
                                   **88888888****************************7.4...67899987651133444455555.............4 PP

                                   G.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B----EE CS
               G_glu_transpept 324 eesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpspanaiePgkRplssmaPti 404
                                    + ++Tt++ v+D e n V +++++  +FGsg++v+   + +nn++  f+           +  n +eP+kRpl++++ + 
  gi|70606261|ref|YP_255131.1| 312 LRTEDTTFFVVADGE-NEVGFIQSLFFHFGSGITVK--QFPFNNRGFGFT-----------EGNNKPEPRKRPLHTLSILY 378
                                   5589**********9.99******************..599*********...........999*************9777 PP

                                   EEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEESSSSTEEEESTT CS
               G_glu_transpept 405 vlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihhqllpdkvevEeg 464
                                    +k ++  l +G aGG+  ++++++v+  + d+++++ eav+apr+     +dk+  E++
  gi|70606261|ref|YP_255131.1| 379 AEK-DDESLFIGCAGGDLRPQIHAEVFQYYADYNMEIDEAVNAPRFILL--SDKIVAEKR 435
                                   666.777899************************************963..567777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3408.51
//
Query:       gi|70606262|ref|YP_255132.1|  [L=121]
Description: hypothetical protein Saci_0426 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 934.79
//
Query:       gi|70606263|ref|YP_255133.1|  [L=83]
Description: hypothetical protein Saci_0427 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-14   51.4   0.5    1.2e-13   51.0   0.5    1.2  1  MazG       MazG nucleotide pyrophosphohydrolase domain
    5.4e-07   29.8   1.0    7.1e-07   29.4   0.1    1.5  2  MazG-like  MazG-like family
    2.6e-05   24.6   1.6    4.2e-05   23.9   1.6    1.4  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
      0.072   13.4   0.1      0.082   13.2   0.1    1.1  1  UpxZ       UpxZ family of transcription anti-terminator antag


Domain annotation for each model (and alignments):
>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.5   2.6e-17   1.2e-13       5      61 ..      27      79 ..      23      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.6e-17
                                  HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH CS
                          MazG  5 tllaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaet 61
                                  ++  +l+eEvgE+aea+ ++++d+leeEL+DvL + +++an+     gidle+++++
  gi|70606263|ref|YP_255133.1| 27 ATFTWLVEEVGELAEALLSKNKDSLEEELADVLAWTVSVANL----VGIDLEEALRK 79
                                  56789************************************9....*******9975 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.97   4.3e+03      56      65 ..       5      14 ..       3      22 .. 0.67
   2 !   29.4   0.1   1.6e-10   7.1e-07      15      62 ..      32      80 ..      30      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.97
                     MazG-like 56 feeideklkk 65
                                  ++ i+ek+k+
  gi|70606263|ref|YP_255133.1|  5 LKYIQEKMKE 14
                                  5556666664 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.6e-10
                     MazG-like 15 llksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.idek 62
                                  l+++v+el +all+++++++ +eLAdv++ ++  A+ +Gid+ee +++k
  gi|70606263|ref|YP_255133.1| 32 LVEEVGELAEALLSKNKDSLEEELADVLAWTVSVANLVGIDLEEaLRKK 80
                                  78899***************************************99988 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.6   9.4e-09   4.2e-05      27      77 ..      28      78 ..       6      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.4e-09
                                  HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHHH CS
                        PRA-PH 27 raaligEEavElleaasegdlaeladelaDllYvtygllvllGidldavfe 77
                                    ++++EE+ El ea   +++  l +elaD+l  t   + l Gidl++ ++
  gi|70606263|ref|YP_255133.1| 28 TFTWLVEEVGELAEALLSKNKDSLEEELADVLAWTVSVANLVGIDLEEALR 78
                                  6799******************************************99765 PP

>> UpxZ  UpxZ family of transcription anti-terminator antagonists
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.8e-05     0.082       4      56 ..       8      59 ..       5      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                          UpxZ  4 lqslaheLlylgedgspiysdelsrlnkevlekaealyskkgstaEeeaelcl 56
                                  +q+  +eL y+  + + +y+ +++ l +ev e+aeal+sk+ ++ Eee + +l
  gi|70606263|ref|YP_255133.1|  8 IQEKMKELYYVKDSERGVYA-TFTWLVEEVGELAEALLSKNKDSLEEELADVL 59
                                  6788999****9999****8.7******************9999999865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 667.69
//
Query:       gi|70606264|ref|YP_255134.1|  [L=772]
Description: hypothetical protein Saci_0428 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-48  165.2   0.0      2e-48  164.6   0.0    1.3  1  Helicase_RecD    Helicase
    7.4e-35  120.4   0.0      8e-26   90.8   0.0    2.3  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    2.6e-26   91.4   0.1    6.1e-26   90.2   0.1    1.7  1  DUF1726          Domain of unknown function (DUF1726)
    0.00063   19.5   0.0      0.002   17.9   0.0    1.8  2  AAA_30           AAA domain
     0.0018   18.5   0.0     0.0043   17.3   0.0    1.8  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0035   17.7   0.0      0.016   15.7   0.0    2.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.05   13.6   0.0       0.17   11.8   0.0    1.9  2  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.0   7.9e-52     2e-48       1     177 []     231     411 ..     231     411 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 7.9e-52
                 Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk......snilvtapskenvktlfeflakglealglke.eekkkkaekaelrvrkq 74 
                                   v+tA+RGRGKSa+ Gl +a li ++        +i+vtaps ++ ++ +efl++gl+alg+++ e+++  +  ++l+ ++ 
  gi|70606264|ref|YP_255134.1| 231 VITASRGRGKSAVTGLGMAGLIFKHGfrkgrkYKIIVTAPSIASSSQTMEFLKRGLDALGVEYrEKRSPMGFINSLEGEGF 311
                                   79********************99878899999****************************99677778889999****** PP

                 Helicase_RecD  75 rieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelrelele 155
                                   r+ +  p+++l+++   dllvvDEAAai + ++++ l+++k+vvl tTvhGYEG+G++f l++l++l k++k+++   e++
  gi|70606264|ref|YP_255134.1| 312 RVFFEIPEATLEHEG--DLLVVDEAAAIGIGYIDSALKTWKKVVLVTTVHGYEGSGKAF-LRYLNRLLKQRKTTVYWEEMR 389
                                   ***********9875..******************************************.********************* PP

                 Helicase_RecD 156 epiRyaegdplEkwlndlLlLd 177
                                   +p+Ryaegdp+Ekwl+d+LlLd
  gi|70606264|ref|YP_255134.1| 390 KPLRYAEGDPIEKWLYDSLLLD 411
                                   ********************97 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   3.1e-29     8e-26       2     123 ..     444     559 ..     443     564 .. 0.93
   2 !   28.7   0.0   3.1e-10   7.8e-07     174     226 ..     559     611 ..     556     612 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 3.1e-29
               GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipwtls 82 
                                   + ++lv++HY+n+PnDL+++ D  +h++  L  + +      + + vvq+a EG +s+e ++++l  g+  +Gdlip+ + 
  gi|70606264|ref|YP_255134.1| 444 VYGILVTAHYRNNPNDLMIMGDGIHHTIKGLSIEGT-----NSYIGVVQIANEGGLSDELIHSALM-GVTFDGDLIPDRMI 518
                                   6789***************************98665.....699***************9999987.569*********** PP

               GNAT_acetyltr_2  83 qqfqdeefaslsGaRivRiAvhpelqkmGYGsralelleky 123
                                   ++ +  ef++++G RivRiAv +elq +G+Gs++le++++ 
  gi|70606264|ref|YP_255134.1| 519 KHSRLIEFGKMKGWRIVRIAVMQELQDKGFGSQMLEMIIED 559
                                   ************************************99876 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.1e-10
               GNAT_acetyltr_2 174 eekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                   ++k +++d++g sf    + l+FW r+gf pv+++ ++ne  G++ +i+++++
  gi|70606264|ref|YP_255134.1| 559 DAKRQEIDWVGSSFMGDMRVLNFWIRNGFYPVHVSPKKNEKLGDYPVIVIKPI 611
                                   678899********************************************987 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.1   2.4e-29   6.1e-26       1      92 [.      87     171 ..      87     172 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.4e-29
                       DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplteevkkrfnkrfir 81 
                                   y++se++LG+t+d+++ldl+++++Pn++grlv++VrGGGliil++++l+++k +++++ ++  v ++       +++rfir
  gi|70606264|ref|YP_255134.1|  87 YSSSERYLGSTFDVAILDLVDNFEPNHIGRLVDLVRGGGLIILYTNDLKNNKIFKNSILREGKVLDV-------YETRFIR 160
                                   89***********************************************************999988.......******* PP

                       DUF1726  82 klkehegiliv 92 
                                   kl+ehegi+++
  gi|70606264|ref|YP_255134.1| 161 KLTEHEGIFVI 171
                                   ********997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.9e-07     0.002       2     113 ..     208     350 ..     207     360 .. 0.72
   2 ?   -1.0   0.0      0.47   1.2e+03      20      46 ..     355     380 ..     348     384 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.9e-07
                        AAA_30   2 lnaeQaaaveallt...sgdrvavltGpAGtGKttalkal.reaweaag......grviglAptgkaAkv.Lae.elgiea 70 
                                   l+++Q +++e++++   ++++v v+t+  G GK+ + +   + ++ ++g      +++i+ Ap+ + + + ++  + g++a
  gi|70606264|ref|YP_255134.1| 208 LSSDQNKVLESFIGmryGSRKVLVITASRGRGKSAVTGLGmAGLIFKHGfrkgrkYKIIVTAPSIASSSQtMEFlKRGLDA 288
                                   567788888877652225678*************998754366777777888889*********98887746624334444 PP

                        AAA_30  71 stiakllkrlk..................grarlepg.tllivDEagmvdtkqlaallkaae 113
                                     ++   kr                     +a+le++ +ll+vDEa+ +++  +++ lk  +
  gi|70606264|ref|YP_255134.1| 289 LGVEYREKRSPmgfinslegegfrvffeiPEATLEHEgDLLVVDEAAAIGIGYIDSALKTWK 350
                                   4444444333344555666999*******667788777**********99988877777655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                        AAA_30  20 vavltGpAGtGKttalkalreaweaag 46 
                                   v++++G+ G+GK + l+ l++++++++
  gi|70606264|ref|YP_255134.1| 355 VTTVHGYEGSGKAF-LRYLNRLLKQRK 380
                                   78999*******87.566666666655 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.7e-06    0.0043      56      94 ..     527     565 ..     441     587 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-06
                                   TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                Acetyltransf_1  56 ekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                    k + + i ++aV  e + kG Gs++le ++e a++++i
  gi|70606264|ref|YP_255134.1| 527 GKMKGWRIVRIAVMQELQDKGFGSQMLEMIIEDAKRQEI 565
                                   455778899**************************9976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.1e-06     0.016      25      74 ..     532     587 ..     508     589 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
                                   TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEE.THH.....HHHHHHHHTTE CS
                Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLleaae.....kgiileqlel.nae.....kaikfYeklGF 74 
                                     i r+aV +e + kG G+++le+++     + i     ++ + +     + ++f+ ++GF
  gi|70606264|ref|YP_255134.1| 532 WRIVRIAVMQELQDKGFGSQMLEMIIedakrQEI----DWVgS-SfmgdmRVLNFWIRNGF 587
                                   45778******************83323322222....23321.12334577889999999 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.2   8.1e+03      43      79 ..     339     375 ..     308     383 .. 0.53
   2 ?   11.8   0.0   6.7e-05      0.17      51      86 ..     531     566 ..     521     599 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.2
               Acetyltransf_10  43 vGvi..elrdgshisllfVdpeyrgqGigkaLleaveee 79 
                                   +G+i  +l++ +++ l+   + y   G gka l ++ + 
  gi|70606264|ref|YP_255134.1| 339 IGYIdsALKTWKKVVLVTTVHGY--EGSGKAFLRYLNRL 375
                                   35554333444455444444444..45555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.7e-05
               Acetyltransf_10  51 gshisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                   g++i +++V +e + +G g+++le ++e a++++i 
  gi|70606264|ref|YP_255134.1| 531 GWRIVRIAVMQELQDKGFGSQMLEMIIEDAKRQEID 566
                                   55999*************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (772 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4796.66
//
Query:       gi|70606265|ref|YP_255135.1|  [L=259]
Description: hypothetical protein Saci_0430 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    7.1  10.0        1.8    6.7  10.0    1.1  1  YfhO      Bacterial membrane protein YfhO


Domain annotation for each model (and alignments):
>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.0    0.0001       1.8     257     434 ..      42     217 ..      32     230 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0001
                          YfhO 257 inpldllsklligtfdfeqmgslpniyvgllpllllilyFvlkkiklkeklafallllllilsfllpplnlvwhgfqaPvg 337
                                    ++++ + +l + + d+e m  +    vgll+l++lil F l +i     ++f  ll +  l +l  +l ++++gf+  + 
  gi|70606265|ref|YP_255135.1|  42 WPYTRDMVHLAVRKADPEAMHRISATLVGLLSLTILILDFNLLSIAGFISVIFTALLGMATLYVLAGKLPSIFQGFHDIA- 121
                                   5566667788899999**9*************************************************************. PP

                          YfhO 338 fpyRfsfilsflllllaaealkelkql......kklkllaailllvlllliilllknkksynfltssqlllgllllllall 412
                                        ++    + ll+a+ +   +++       +  ++l  ++++ ++++++ +  + +s   ++  +  l++++++  + 
  gi|70606265|ref|YP_255135.1| 122 -----AYTTMVIYLLIAMGFDPSRFTSfiidaiTPPHFLYFVIFMGGVVTGTRK--MRFSIGDVRKPKNRLQWIWIVHSIA 195
                                   .....6665555555555554444444455532344444444444444444443..3444456666677778888877777 PP

                          YfhO 413 lllllllkkkkkklvllllllv 434
                                    ++++l+    + ++ l+l+l+
  gi|70606265|ref|YP_255135.1| 196 GVIFFLSLILLQLWIPLALALI 217
                                   7766665555556666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1777.88
//
Query:       gi|70606266|ref|YP_255136.1|  [L=106]
Description: hypothetical protein Saci_0431 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00093   19.1   0.1     0.0031   17.5   0.1    1.8  2  YfdX          YfdX protein
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.028   14.4   0.0    1.2  1  Mad3_BUB1_I   Mad3/BUB1 homology region 1
      0.022   15.0   0.0      0.034   14.4   0.0    1.3  1  UPF0253       Uncharacterised protein family (UPF0253)
      0.047   13.8   0.6       0.41   10.7   0.0    2.5  2  Exonuc_VII_S  Exonuclease VII small subunit


Domain annotation for each model (and alignments):
>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.9e-07    0.0031       1      40 [.      43      82 ..      43     100 .. 0.90
   2 ?   -0.4   0.0      0.23     1e+03     112     125 ..      92     105 ..      86     106 .] 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                                  HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHC CS
                          YfdX  1 AlrdiqkArlaldqgdtkeAkkllekAqgkleaaladdpk 40
                                  A++ i++A + +d+gd+++  kll++A +kl+ +++ +p 
  gi|70606266|ref|YP_255136.1| 43 AIKAIREAYSKIDKGDKQSSFKLLSQALEKLNSIKSNKPL 82
                                  7899******************************998875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHH CS
                          YfdX 112 typaavkkAaelle 125
                                   +++++v kA+ell+
  gi|70606266|ref|YP_255136.1|  92 EVKNNVSKAIELLK 105
                                   45566666666665 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.3e-06     0.028       5      57 ..      21      76 ..      18      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.3e-06
                                  HHHHHHHTG.....-THHHHHHHHHHHHHH-TT..-T.TT-HHHHHHHHHHHTTTS CS
                   Mad3_BUB1_I  5 efeeeleea.eegdDpLelwlryikwieesypq..sskesgllellerclkkfkdd 57
                                   fe+ l+++   +++ L+lw + ik i e+y +  +++++  ++ll ++l+k+++ 
  gi|70606266|ref|YP_255136.1| 21 DFETYLTKDgTITEEGLNLWKDAIKAIREAYSKidKGDKQSSFKLLSQALEKLNSI 76
                                  6788888876556799******************9999999********9998765 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.7e-06     0.034       6      48 ..      45      87 ..      41      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-06
                       UPF0253  6 elirelyaqIgsgdlgYipdAiscalktLdevaanealpeevr 48
                                  ++ire+y++I  gd+    + +s al+ L+++ +n+ lp + +
  gi|70606266|ref|YP_255136.1| 45 KAIREAYSKIDKGDKQSSFKLLSQALEKLNSIKSNKPLPPDAK 87
                                  579***********************************98765 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.2e-05      0.41      23      49 ..      34      60 ..      31      62 .. 0.93
   2 ?   -0.3   0.0      0.26   1.2e+03      23      37 ..      91     105 ..      86     106 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.2e-05
                  Exonuc_VII_S 23 eeslklyeeGvkLlkeCekkLdeaeqk 49
                                  ee l+l++ ++k ++e+ +k+d+ +++
  gi|70606266|ref|YP_255136.1| 34 EEGLNLWKDAIKAIREAYSKIDKGDKQ 60
                                  899*******************98876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                  Exonuc_VII_S  23 eeslklyeeGvkLlk 37 
                                   ee  + + ++++Llk
  gi|70606266|ref|YP_255136.1|  91 EEVKNNVSKAIELLK 105
                                   667778889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 655.62
//
Query:       gi|70606267|ref|YP_255137.1|  [L=466]
Description: hypothetical protein Saci_0432 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   53.7  46.5    4.6e-14   52.1  46.6    1.6  1  AA_permease_2  Amino acid permease
    4.2e-12   45.4  41.5    7.4e-12   44.6  39.5    2.1  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        4.9    7.6  16.0       0.38   11.2   0.9    4.0  4  DUF2583        Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1  46.6   7.7e-18   4.6e-14       8     393 ..      17     408 ..      15     435 .. 0.72

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 7.7e-18
                 AA_permease_2   8 alvigsvigsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf.gkkvaflsawfnwf 86 
                                   a+++++++gs +  ++ ++a++g+++++  ++a l+  l  ++++  ++ ++ + gG y++++aa+ +k va+  a++ ++
  gi|70606267|ref|YP_255137.1|  17 AMAVTAPLGSVVSTTTaAIAYAGKSVLFATLLAFLAS-LLWMFTLTKYTKKIASPGGYYTFGSAAWrSKTVAYYEAITEVI 96 
                                   68888998877666656899********999999997.89*********99***************99************* PP

                 AA_permease_2  87 ayvpvlas...ilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikes.akiqnilgilkillpliiliilg 163
                                   ay+  +a+   +++++++   ++l+ +l +   +  l +i+++  +    i++i+++ ++i +i ++l + ++l +l+  +
  gi|70606267|ref|YP_255137.1|  97 AYSSLNAVnsfSVYLLLKVTFQMLNLELPDYVLPLSL-VIGLIYPTLSSVILHIRKVlGYIVSISATLEV-IFLYVLFGYA 175
                                   **99775521155667788888888888666554444.455554444444555544449999********.5655555444 PP

                 AA_permease_2 164 litvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkkkdvpkaifigllivlvlyllvniaflgv 244
                                   ++t ++++        + + +n++++   ++  ++ s++G  +aa+  ee kk +  +++ i +++v++ +  ++ +++ v
  gi|70606267|ref|YP_255137.1| 176 VATRGFDITY-----LSPVGTNFSSL-GTAMVLTIVSIAGAGAAAYLGEETKKPTSTITTGIKIAYVVGGGAILAGTYALV 250
                                   4444444443.....44444444443.445555799*******************99***9*9999999999999999999 PP

                 AA_permease_2 245 vpdde.ianlsnlgsvaalffeavgg.kvvaiivvilial.sllgaintavigssrvlealardgvlPrffakvnkfgspi 322
                                     ++e i++lsn++   +++ + +   ++  +++++++ + sll + ++ ++g++r+l+ lar++++P++f++ n    p+
  gi|70606267|ref|YP_255137.1| 251 ALWNEpIQTLSNSP---QPLIQELYPiSFIVMLISLILSInSLLASNIGTTVGAARILFNLAREKAMPKVFSRLNSEREPL 328
                                   9996648999*998...777777762144444455444445899999999*************************888*** PP

                 AA_permease_2 323 raiiltaivslillllfllas...saaynfllsvsslgliisyllliigalilrkkrphl.kr.....pgkilvaiigal 393
                                    a++++ ++s i+++ +l+++   + a++ ++ +ssl+ +   ++  +ga + +++ ++l ++      g  +++++g++
  gi|70606267|ref|YP_255137.1| 329 IATVVVGLISAIFAISSLTYTgsaDVAFTEISFISSLFWLAGRIVDNLGAPVFYWRLRELtPKilivfLGSTTINLVGMI 408
                                   **********8888777766544444444455555555544444445555566666555533344433333444444444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6  39.5   1.2e-15   7.4e-12       6     380 ..      17     368 ..      14     402 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.2e-15
                   AA_permease   6 alggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGln.... 81 
                                   a++   ++g  v++  ++ +  + ++l a lla++ ++l m +l     ++ + gg+yt+ s  + +  ++++ ++     
  gi|70606267|ref|YP_255137.1|  17 AMAVTAPLGSVVSTTTAAIAYAGKSVLFATLLAFLASLLWMFTLTKYTKKIASPGGYYTFGSAAWRSkTVAYYEAITevia 97 
                                   6777788888888888777777779****************************************9856777777779888 PP

                   AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvt..gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiil 160
                                   y ++ +++    +  +  ++q++  + +lp  +v   ++v+ +++ +++ v +       +i+++ + + +i f+ v++ +
  gi|70606267|ref|YP_255137.1|  98 YSSLNAVNSFSVYLLLKVTFQML--NLELP-DYVLplSLVIGLIYPTLSSVILHIRKVLGYIVSISATLEVI-FLYVLFGY 174
                                   88888888888888899999999..99999.77778877777777788888777777766666655555444.44444333 PP

                   AA_permease 161 laggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvi 241
                                    +     +g       ++ +    +l+p      + +f++   ++v  +++++G ++ a++++E+k P  +i  +i+ + +
  gi|70606267|ref|YP_255137.1| 175 AVAT---RG-------FDIT----YLSPV-----GTNFSSLGTAMVLTIVSIAGAGAAAYLGEETKKPTSTITTGIKIAYV 236
                                   3333...33.......2223....44444.....567999***************************************** PP

                   AA_permease 242 ritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavi.ltaalssansslysasRvlyslakd 321
                                     + + + +++++++l++ +  +l n      sp+ ++++   +s++  li +++ + ++l s ++ ++ a R+l+ la++
  gi|70606267|ref|YP_255137.1| 237 VGGGAILAGTYALVALWNEPIQTLSN------SPQPLIQELYPISFIVMLISLILsINSLLASNIGTTVGAARILFNLARE 311
                                   *********************99999......9999************9998765155778888899999*********** PP

                   AA_permease 322 glaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivw 380
                                   +++Pkv+++++ +++Pl a +++ +is+++ + +  +++  ++   +  is ++ l+ +
  gi|70606267|ref|YP_255137.1| 312 KAMPKVFSRLNSEREPLIATVVVGLISAIFAISSLTYTG--SADVAFTEISFISSLFWL 368
                                   **************************************9..888888888888887765 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.51   3.1e+03      28      47 ..     114     133 ..     101     141 .. 0.76
   2 ?   -1.7   0.2      0.67     4e+03      16      33 ..     274     291 ..     269     302 .. 0.75
   3 ?    4.8   1.0    0.0063        38      22      63 ..     329     373 ..     327     389 .. 0.72
   4 ?   11.2   0.9   6.3e-05      0.38      18      63 ..     393     435 ..     387     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.51
                       DUF2583  28 svlnqlpelelpellaeaal 47 
                                    v+ q+ +lelp+++   +l
  gi|70606267|ref|YP_255137.1| 114 KVTFQMLNLELPDYVLPLSL 133
                                   56778999999999876665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.67
                       DUF2583  16 lGlllmvaslaysvlnql 33 
                                   + +++m++sl  s+ + l
  gi|70606267|ref|YP_255137.1| 274 ISFIVMLISLILSINSLL 291
                                   667888888888887655 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0063
                       DUF2583  22 vaslaysvlnqlpelelpellaeaal..lgi.fiGallWlaGarv 63 
                                   +a++++ +++ +++++   +  +a++    i fi +l+WlaG  v
  gi|70606267|ref|YP_255137.1| 329 IATVVVGLISAIFAISSLTYTGSADVafTEIsFISSLFWLAGRIV 373
                                   67778888888888887777655544115556**********755 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 6.3e-05
                       DUF2583  18 lllmvaslaysvlnqlpelelpellaeaallgifiGallWlaGarv 63 
                                   l+++++s + +++  + +l+ p++++ + l++++  a lW     +
  gi|70606267|ref|YP_255137.1| 393 LIVFLGSTTINLVGMIGSLQAPDMFQAVYLISVLAAATLWYI---I 435
                                   688999**********************************74...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2873.41
//
Query:       gi|70606268|ref|YP_255138.1|  [L=59]
Description: hypothetical protein Saci_0433 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   15.2   1.7     0.0089   15.1   1.7    1.0  1  PHO4      Phosphate transporter family
  ------ inclusion threshold ------
       0.22   11.2   3.3          2    8.1   0.3    2.1  2  DUF4750   Domain of unknown function (DUF4750)


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.7     1e-06    0.0089     212     261 ..      10      59 .]       3      59 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-06
                          PHO4 212 aiGpllaalisiyka..skevplwvlllgglaialGlllgGkrviktvGeki 261
                                   a+G++l+a++  +++  s+ + +w+l+l ++  ++G+l+g + +i+ +Ge++
  gi|70606268|ref|YP_255138.1|  10 AVGIILMAIL--FDYlgSSFQNIWILVLSMALAITGVLIGIRSIIEYLGERM 59 
                                   8999988774..33332336689*9999999999***************987 PP

>> DUF4750  Domain of unknown function (DUF4750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0038        34      11      25 ..       6      20 ..       5      23 .. 0.89
   2 ?    8.1   0.3   0.00023         2       1      21 [.      26      46 ..      26      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0038
                       DUF4750 11 rlllalliVlllill 25
                                  r+++a+ i+l+ il+
  gi|70606268|ref|YP_255138.1|  6 RIVFAVGIILMAILF 20
                                  799*******99987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00023
                       DUF4750  1 sweevllfvlrlllalliVll 21
                                  s++++ ++vl++ la++ Vl+
  gi|70606268|ref|YP_255138.1| 26 SFQNIWILVLSMALAITGVLI 46
                                  5899*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 404.94
//
Query:       gi|70606269|ref|YP_255139.1|  [L=216]
Description: protein-L-isoaspartate O-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-43  148.0   0.0    3.8e-43  147.7   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.8e-07   29.9   0.0    4.6e-07   29.2   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
      7e-06   25.7   0.0    9.4e-06   25.2   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.6e-05   24.7   0.0    2.1e-05   24.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.1e-05   25.2   0.0    3.7e-05   24.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0001   21.9   0.1    0.00016   21.3   0.1    1.2  1  DOT1             Histone methylation protein DOT1
    0.00012   21.6   0.0     0.0002   21.0   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00028   20.6   0.0    0.00041   20.1   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00069   19.5   0.0    0.00096   19.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
     0.0011   18.2   0.1     0.0016   17.6   0.1    1.2  1  Methyltransf_3   O-methyltransferase
     0.0013   18.7   0.0     0.0022   18.0   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0013   17.9   0.0      0.002   17.3   0.0    1.3  1  Fibrillarin      Fibrillarin
     0.0033   18.0   0.0     0.0074   16.9   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0054   16.1   0.0      0.014   14.7   0.0    1.6  2  CMAS             Mycolic acid cyclopropane synthetase
  ------ inclusion threshold ------
      0.056   13.2   0.0      0.089   12.5   0.0    1.3  1  Met_10           Met-10+ like-protein
       0.16   11.4   0.0       0.28   10.7   0.0    1.4  1  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   3.4e-46   3.8e-43       5     205 ..       8     208 ..       4     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 3.4e-46
                                   HHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTS....SS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES CS
                          PCMT   5 alieelkkkgviksdkvaealeevdReefvpesfkekaYe....daplsigynatiSaphmvalalellelkkgarvLevG 81 
                                   a++++l    ++++  v+ea+ + dR +f+p+++ + aY     d+p++i  n    a  +  ++++llelkk ++vLe+G
  gi|70606269|ref|YP_255139.1|   8 AILKYLS--TIVVNSDVLEAFMKLDRRKFLPAKYSDIAYSlkhiDQPIQITKNYNTTALGLGVKMVDLLELKKSDKVLEIG 86 
                                   5555554..4678899********************9996444488999999999************************** PP

                                   -TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHT CS
                          PCMT  82 sGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQ 162
                                   +GsGy ta++a++vg++  v +ie  +e ++ ak+nlk+  ++ +++++gDG  Gy   +PYd+i+v a++p  P al +Q
  gi|70606269|ref|YP_255139.1|  87 TGSGYYTALMAEIVGAEN-VYTIEFDEEAYNLAKNNLKE--YHGIHLIFGDGSLGYISGSPYDKIIVWASSPTFPYALYQQ 164
                                   *****************9.******************96..678999********************************** PP

                                   EEEEEEEEEEESB.SSSEEEEEEEEETTTEEEEEEEEEE---B- CS
                          PCMT 163 LkeGGrlvvPvge.eeeQvlklvdkkadgkvvikkleevrfvpl 205
                                   +ke G+++vP+ + e++Q l ++ k + g+ vi+k+++v f  l
  gi|70606269|ref|YP_255139.1| 165 MKEKGIMIVPISDnEKRQGLYRIYKGETGSPVITKVMDVYFTRL 208
                                   ************9899***********************99765 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   4.1e-10   4.6e-07      22      84 ..      70     134 ..      55     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.1e-10
                                   HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                        RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklskdeklkvvhqD 84 
                                    +d l+l+++++vleig+G G  T+ +a+++  ++v  +E de+ ++l +++l++++ + ++  D
  gi|70606269|ref|YP_255139.1|  70 MVDLLELKKSDKVLEIGTGSGYYTALMAEIVgaENVYTIEFDEEAYNLAKNNLKEYHGIHLIFGD 134
                                   68899***************************9*********************99999988776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   8.4e-09   9.4e-06     145     206 ..      59     124 ..      56     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.4e-09
                          PrmA 145 HpTTklcl..ealekl.vkegeevlDvGtGSGiL.aiaaakLgakkvvavDiDevAvkvakeNael 206
                                    +TT+l l  ++++ l +k+ ++vl +GtGSG   a+ a  +ga++v+ +  De A + ak+N++ 
  gi|70606269|ref|YP_255139.1|  59 YNTTALGLgvKMVDLLeLKKSDKVLEIGTGSGYYtALMAEIVGAENVYTIEFDEEAYNLAKNNLKE 124
                                   5688766522667776567778**********853899*************************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.9e-08   2.1e-05       2      52 ..      77     124 ..      76     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-08
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklg 52 
                                   +k  +vl++G+G+G++t  +a e+    +v+ i+++eea +lA++n++  +
  gi|70606269|ref|YP_255139.1|  77 KKSDKVLEIGTGSGYYTALMA-EIVGAENVYTIEFDEEAYNLAKNNLK--E 124
                                   67889****************.6666688****************977..4 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.3e-08   3.7e-05       1      70 [.      82     150 ..      82     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.3e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                   vL++G+G+G +t+ +a+ +g+++v+ ++++ee+ + a+++++e    ++++ gd +      + +D +++
  gi|70606269|ref|YP_255139.1|  82 VLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYNLAKNNLKEY-HGIHLIFGDGSLGYISGSPYDKIIV 150
                                   9****************************************874.3666666665443344455666655 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.4e-07   0.00016      27      97 ..      63     133 ..      52     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                                   -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTT CS
                          DOT1  27 lpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfG 97 
                                      +  +++d ++lkk+d  +++G G G  + ++a  vg ++ + +E  ++a +la+++ +e++    +fG
  gi|70606269|ref|YP_255139.1|  63 ALGLGVKMVDLLELKKSDKVLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYNLAKNNLKEYHGIHLIFG 133
                                   555667899******************************************************99988888 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-07    0.0002      23      79 ..      70     126 ..      61     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                                   HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTT CS
                           MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleank 79 
                                   +++ l+ ++s+kvl +G+G G+ +a +a+     +v  ++ d +A ++ak+nl++ +
  gi|70606269|ref|YP_255139.1|  70 MVDLLELKKSDKVLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYNLAKNNLKEYH 126
                                   56778888999******************************************9865 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.7e-07   0.00041      34      88 ..      72     125 ..      61     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.7e-07
                         GCD14  34 mkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefreh 88 
                                     Lelk+  +v+e GtGsg  +  +a  v    +++t+ef e+ ++ a+++++e 
  gi|70606269|ref|YP_255139.1|  72 DLLELKKSDKVLEIGTGSGYYTALMAEIV-GAENVYTIEFDEEAYNLAKNNLKEY 125
                                   569****************9876666655.5679****************99974 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.6e-07   0.00096      16      62 ..      73     123 ..      59     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.6e-07
               Methyltransf_23  16 llpklraggrvLdiGcGtGillevlren.gf.svtgvDlspeaveiae...k 62 
                                   ll+ l+++ +vL+iG+G+G+ + +++e  g+ +v+ ++ ++ea ++a+   k
  gi|70606269|ref|YP_255139.1|  73 LLE-LKKSDKVLEIGTGSGYYTALMAEIvGAeNVYTIEFDEEAYNLAKnnlK 123
                                   444.89999**********9999997764788999****9999998864330 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.4e-06    0.0016      42      93 ..      73     123 ..      51     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                   HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHH CS
                Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiq 93 
                                   L++l  + +vleiG+  Gy    +a  +    ++ +i+ d+eay++a++ ++
  gi|70606269|ref|YP_255139.1|  73 LLELKKSDKVLEIGTGSGYYTALMAEIVGA-ENVYTIEFDEEAYNLAKNNLK 123
                                   89999**************99999976665.58***************9776 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0022      13      87 ..      77     149 ..      69     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
               Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvv 87 
                                   +k+++v+ iGt  gy ++ +++   a++v+ ++  e++++ ak+n+++++    i+++++dG   + +++ +d ++
  gi|70606269|ref|YP_255139.1|  77 KKSDKVLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYNLAKNNLKEYHG---IHLIFGDGSLGYISGSpYDKII 149
                                   67889*******************************************975...9999999977766666577666 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06     0.002      61     107 ..      69     114 ..      58     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                                   TT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                   Fibrillarin  61 kglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                   k ++ l +kk +kvL +G++sG   + +++ivg    vy++ef + +
  gi|70606269|ref|YP_255139.1|  69 KMVDLLELKKSDKVLEIGTGSGYYTALMAEIVG-AENVYTIEFDEEA 114
                                   55777899*************************.678******8765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.6e-06    0.0074       1      42 [.      83     126 ..      83     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeg 42 
                                   L++G+G+G++++ +a+ +  ++v+++++++e+ +lak++ +e +
  gi|70606269|ref|YP_255139.1|  83 LEIGTGSGYYTALMAEIVgaENVYTIEFDEEAYNLAKNNLKEYH 126
                                   89*************88889*****************9998765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.014      54     107 ..      70     124 ..      67     130 .. 0.90
   2 ?   -2.2   0.0       1.8   2.1e+03     146     164 ..     155     173 ..     151     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                   HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHT CS
                          CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvde 107
                                   +++ lelk+ +++L+iG+G G+ +  ++e  ++ +v  + + +e ++lak++++e
  gi|70606269|ref|YP_255139.1|  70 MVDLLELKKSDKVLEIGTGSGYYTALMAEIVGAeNVYTIEFDEEAYNLAKNNLKE 124
                                   57889************************999856999***********999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHS-TT-EEEE CS
                          CMAS 146 dtffkklkkllkedGllll 164
                                   +tf  +l++ +ke G++++
  gi|70606269|ref|YP_255139.1| 155 PTFPYALYQQMKEKGIMIV 173
                                   5777789999999999987 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.9e-05     0.089      98     145 ..      76     123 ..      54     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                                   --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                        Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                    ++ + V+++  G G+++  +a    a+ v++i+ + e++++ k+n+k
  gi|70606269|ref|YP_255139.1|  76 LKKSDKVLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYNLAKNNLK 123
                                   578899**************************************9987 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00025      0.28       4      60 ..      81     135 ..      78     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60 
                                    vleiG+G+G  +  +A+     n+  iE  ++  +  l+k + +e++ +++++gd 
  gi|70606269|ref|YP_255139.1|  81 KVLEIGTGSGYYTALMAEIVGAENVYTIEFDEEAYN--LAKNNLKEYHGIHLIFGDG 135
                                   589**************************9998765..4555556677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1445.85
//
Query:       gi|70606270|ref|YP_255140.1|  [L=585]
Description: hypothetical protein Saci_0435 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-17   62.4   3.3    1.9e-16   60.8   1.0    2.4  2  DUF87     Helicase HerA, central domain
  ------ inclusion threshold ------
      0.074   13.6   0.2        2.4    8.7   0.2    2.8  2  DUF1474   Protein of unknown function (DUF1474)


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   1.0   2.1e-20   1.9e-16       4     194 ..     167     358 ..     163     368 .. 0.76
   2 ?    0.4   0.1     0.063   5.6e+02     131     151 ..     440     460 ..     363     508 .. 0.45

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.1e-20
                         DUF87   4 GrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal.ekllsekvkvitps 82 
                                   G+ + ++e++++++l k+++ H+++++ TGsGKSn+++++++++l+  k+++++i+D+  EY+ +l  +lls + +++t +
  gi|70606270|ref|YP_255140.1| 167 GKSV-NEEIDLKVNLLKAINYHIGVFAYTGSGKSNLTSLIVRRALNkYKDLKVVIIDVSMEYSILLlDELLSLNSRLVTLD 246
                                   5564.789*************************************988999***************888888888888888 PP

                         DUF87  83 psakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka.........keekeklssdepveklleelkkek 154
                                           +++ ++ld    l    +  +++++v +s+ + +++ +++         ++ +  ls+ +++e ++++++  +
  gi|70606270|ref|YP_255140.1| 247 --------RLPSNELDAGKRLLRTHVLPEELEDVRESIRKGFIKLYTEqklrrlyipPQGISYLSYGTLIEMIRSQIE--D 317
                                   ........566666655443322222222333333333333333333344446888999*******************..9 PP

                         DUF87 155 eelrklknqaiarlldkledllrkggsf.snsstdlialll 194
                                   ++++ +++ + ++ll++l++l+r++++  ++  +d+i+ ll
  gi|70606270|ref|YP_255140.1| 318 KYVSTSQKPLFMALLQSLDNLMRERKLTkDDIVDDTINPLL 358
                                   9************************9995444444444443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.063
                         DUF87 131 keekeklssdepveklleelk 151
                                    ++k  +ss   + ++l+e +
  gi|70606270|ref|YP_255140.1| 440 MRRKRAYSSLPVILFVLDEAQ 460
                                   333333444444444444444 PP

>> DUF1474  Protein of unknown function (DUF1474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.051   4.6e+02      36      70 ..      52      86 ..       8     105 .. 0.85
   2 ?    8.7   0.2   0.00027       2.4      40      70 ..     476     506 ..     463     516 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.051
                       DUF1474 36 tdsgrlkskeevlkyGykynehriyieqlidllym 70
                                   d g+l+  e ++k  y   e   yi q++ ++++
  gi|70606270|ref|YP_255140.1| 52 IDVGKLLLVETIRKGVYLILEITDYIPQHFGMINL 86
                                  47899999999999999999*********999886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00027
                       DUF1474  40 rlkskeevlkyGykynehriyieqlidllym 70 
                                      s e++l++G ky+ h    +q +  l+ 
  gi|70606270|ref|YP_255140.1| 476 SSSSVEKLLRHGRKYHLHALISTQRLAYLNT 506
                                   4568999*****************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4012.37
//
Query:       gi|70606272|ref|YP_255141.1|  [L=227]
Description: hypothetical protein Saci_0436 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-09   37.0   0.1    0.00015   21.5   0.0    2.1  2  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1     2e-06     0.036       5      89 ..      26      98 ..      23     116 .. 0.92
   2 !   21.5   0.0   8.5e-09   0.00015     166     241 ..     117     193 ..     105     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-06
                                  EEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECS CS
                          NurA  5 AvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedllllDGs 87
                                  A+DGS+  v    +  yi+++++++++ +++ + ++   +  + +     + +++ +m+++E++     + + ++dl++lD  
  gi|70606272|ref|YP_255141.1| 26 AIDGSFHTV---ANLSYIVVGIVKGEICGNEYNVKEISYKDNICE-----DCNPEDVMRKMEYE----EAQKLDVDLIFLDRK 96
                                  9********...899999999999999999999999999999999.....**************....*************88 PP

                                  HH CS
                          NurA 88 li 89
                                  l+
  gi|70606272|ref|YP_255141.1| 97 LT 98
                                  87 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 8.5e-09
                                   S-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH......TTB-SSSBCCHHHHHHHHC CS
                          NurA 166 llkilrekpllrealidkeiyfaYvrlegggsilrleipaevstakdedvlslla....sqrlsisGYprpLalAhelak 241
                                   +++i+ e+p l++ ++ ++i+  Y +l  +++++++e+ +   + ++e +lsll+    +   ++ GY++ L l++++ak
  gi|70606272|ref|YP_255141.1| 117 VPNINHETPWLVSSYERDGIRGGYFKLFSFSWVFLVEVTV---DWSWENILSLLYvlgkEPIPEALGYNYLLFLVDKVAK 193
                                   57788888*****************************444...68888888888888899999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1587.26
//
Query:       gi|70606271|ref|YP_255142.1|  [L=307]
Description: hypothetical protein Saci_0437 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-45  154.8   0.1    2.4e-45  154.1   0.1    1.3  1  ThiP_synth    Thiamine-phosphate synthase
     0.0007   19.3   0.0     0.0018   18.0   0.0    1.7  1  HTH_23        Homeodomain-like domain
    0.00071   19.7   0.1       0.01   16.0   0.1    2.5  3  RepB          RepB plasmid partitioning protein
     0.0013   18.8   0.2     0.0036   17.3   0.2    1.8  1  HTH_3         Helix-turn-helix
     0.0026   17.7   0.1     0.0054   16.7   0.1    1.5  1  HTH_37        Helix-turn-helix domain
     0.0098   15.4   0.0      0.023   14.2   0.0    1.7  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.086   12.6   0.0    2.2  1  HTH_38        Helix-turn-helix domain
      0.027   14.0   0.0       0.11   12.0   0.0    2.1  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.028   14.0   0.0      0.045   13.3   0.0    1.3  1  INTS5_N       Integrator complex subunit 5 N-terminus
      0.041   13.9   0.9      0.088   12.8   0.1    1.9  2  MA3           MA3 domain
      0.045   13.2   0.0       0.17   11.3   0.0    2.0  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.052   13.4   0.0       0.16   11.8   0.0    1.9  1  HTH_5         Bacterial regulatory protein, arsR family
      0.091   12.5   0.0       0.21   11.3   0.0    1.6  1  Sigma70_r4_2  Sigma-70, region 4
       0.13   12.2   0.0       0.28   11.1   0.0    1.6  1  Terminase_5   Putative ATPase subunit of terminase (gpP-like)
       0.22   11.9   0.0       0.49   10.8   0.0    1.5  1  HTH_31        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.1     2e-48   2.4e-45       3     164 ..     138     294 ..     136     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 2e-48
                                   HHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT--E CS
                    ThiP_synth   3 eralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevra 83 
                                   + a++l+++   +a liP+v sNiaya ++Ak+++Dv+a+pGRI+rv g ++++++p+ gas+h++r+ll + k++ ++ra
  gi|70606271|ref|YP_255142.1| 138 DIAISLIQNPI-VAPLIPQVLSNIAYAEQNAKNEDDVIAIPGRITRVLGVPTPASKPMRGASKHLSRILLGIIKKRGDIRA 217
                                   56777777766.9******************************************************************** PP

                                   EEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESSHHHHHHHHH CS
                    ThiP_synth  84 ainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkdaeevvekvl 164
                                   ++ni+yde ++  +++l+lkvv++++++  ++  + ++ ++ +a+++++  d++++ Gg+++E+++yv+g+d+ +v +kvl
  gi|70606271|ref|YP_255142.1| 218 VMNIKYDETLKTVFSQLKLKVVYVGPHDYATN--EDIAKEIVDAFTDDA--DCVVHLGGKNIEANTYVFGRDPIDVTKKVL 294
                                   ********************************..9**********9998..****************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.5e-06    0.0018       9      39 ..      20      51 ..      15      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                        HTH_23  9 rillllae.GlsvreIAreLgvsrrTvyrwlk 39
                                   +++ l+e G+++++IA++Lgvs+  + ++l 
  gi|70606271|ref|YP_255142.1| 20 FVAKKLRErGMTQSRIATLLGVSQPAIKQYLD 51
                                  566777777*****************999875 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   8.3e-06      0.01       4      43 ..      12      51 ..      10      64 .. 0.85
   2 ?    0.4   0.0      0.51   6.1e+02       9      29 ..      53      73 ..      52      92 .. 0.89
   3 ?   -0.4   0.0       0.9   1.1e+03     129     160 ..     194     227 ..     174     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.3e-06
                          RepB  4 dlsfierarfaarleerGvdreeiasalgldkqtvskmva 43
                                  dl ++ r++ a +l+erG+++++ia+ lg+++++++++++
  gi|70606271|ref|YP_255142.1| 12 DLIPVIRVFVAKKLRERGMTQSRIATLLGVSQPAIKQYLD 51
                                  67788899***************************99987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
                          RepB  9 erarfaarleerGvdreeias 29
                                  ++++++++++++G+ +eei +
  gi|70606271|ref|YP_255142.1| 53 DEQEEVNKIRKMGLNEEEIYD 73
                                  578999***********9965 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.9
                          RepB 129 peaksarlqtavlaiiedeg..rqtLalkaaeay 160
                                   +++ s+ l++ +l ii+++g  r  +++k +e+ 
  gi|70606271|ref|YP_255142.1| 194 MRGASKHLSRILLGIIKKRGdiRAVMNIKYDETL 227
                                   5888999999999*****9988889999987765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2     3e-06    0.0036       3      29 ..      23      49 ..      21      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                  HHHHHTTHHHHHHHHHHTSSHHHHHHH CS
                         HTH_3  3 elRkqlglsqeeLAeklGvsrstisri 29
                                  +++ ++g++q  +A +lGvs+ +i ++
  gi|70606271|ref|YP_255142.1| 23 KKLRERGMTQSRIATLLGVSQPAIKQY 49
                                  45556*******************998 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.5e-06    0.0054      23      56 ..      21      54 ..      16      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                                  HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                        HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                  +a+++++r+ +qs +a+llg++qP + + l+++ 
  gi|70606271|ref|YP_255142.1| 21 VAKKLRERGMTQSRIATLLGVSQPAIKQYLDEDE 54
                                  7899**********************99988765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.9e-05     0.023      18      39 ..      27      48 ..      16      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                                  TTT--HHHHHHHHTS-HHHHHH CS
                    Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                  ++g+T++ I+  lg+S+ +++q
  gi|70606271|ref|YP_255142.1| 27 ERGMTQSRIATLLGVSQPAIKQ 48
                                  89*******************9 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.2e-05     0.086      15      33 ..      24      42 ..      21      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                        HTH_38 15 rllaeGlslreIArrLgrs 33
                                  +l+++G+++++IA +Lg+s
  gi|70606271|ref|YP_255142.1| 24 KLRERGMTQSRIATLLGVS 42
                                  89***************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.4e-05      0.11      15      40 ..      27      52 ..      25      58 .. 0.89
   2 ?   -2.7   0.0       3.8   4.6e+03      18      26 ..     247     255 ..     245     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.4e-05
                        HTH_24 15 nprisqreLAerlglSpstvnrrlkr 40
                                  + +++q+ +A  lg+S+++++++l++
  gi|70606271|ref|YP_255142.1| 27 ERGMTQSRIATLLGVSQPAIKQYLDE 52
                                  679********************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                        HTH_24  18 isqreLAer 26 
                                    ++ ++A++
  gi|70606271|ref|YP_255142.1| 247 ATNEDIAKE 255
                                   6999***98 PP

>> INTS5_N  Integrator complex subunit 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.045      50     124 ..      41     115 ..      34     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                       INTS5_N  50 lfeeaveryleevetepilkesqinaeldeaieeiqtvleelveenpkawaplisaWslellgelsskkagrrgv 124
                                   + + a+++yl+e e+e+ +k  ++  +++e+   +++v e l+++n k+    i+++ l++l el   k++r+  
  gi|70606271|ref|YP_255142.1|  41 VSQPAIKQYLDEDEQEEVNKIRKMGLNEEEIYDVVNNVVELLLRNNTKSAMYYITDFGLRVLNELKLCKYHREIN 115
                                   556799****9999998899999999999999999999999999*********************9999999833 PP

>> MA3  MA3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.4e-05     0.088       7      57 ..      44      93 ..      40      95 .. 0.90
   2 ?   -3.0   0.1       5.9   7.1e+03      25      37 ..     102     114 ..      99     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.4e-05
                                  HHHHSSS...SHHHHHHHHHHTT--.TTHHHHHHHHHHHHHHS.SS--HHHH CS
                           MA3  7 liieeylssgdyeeavsklekLklp.kqeheivkillecaleesktyneyyg 57
                                    i+ yl  +d +e v k++k++l  +    +v+ ++e++l   +t++ +y 
  gi|70606271|ref|YP_255142.1| 44 PAIKQYL-DEDEQEEVNKIRKMGLNeEEIYDVVNNVVELLLRN-NTKSAMYY 93
                                  5789999.99***************899999************.99988885 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.9
                                   HHHTT--TTHHHH CS
                           MA3  25 lekLklpkqehei 37 
                                   l +Lkl k+++ei
  gi|70606271|ref|YP_255142.1| 102 LNELKLCKYHREI 114
                                   7899999999998 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.17      19      49 ..      20      51 ..      17      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                  HTH_Tnp_ISL3 19 yilellles.rsvkavArqlgvSwtTVwrild 49
                                  ++++ l+e+ ++ + +A +lgvS   ++ +ld
  gi|70606271|ref|YP_255142.1| 20 FVAKKLRERgMTQSRIATLLGVSQPAIKQYLD 51
                                  689999*****************999998887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.16       9      36 ..      23      50 ..      17      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                  HHHTTSSEEHHHHHHHHTS-HHHHHHHH CS
                         HTH_5  9 klLaegelcvcelaeelglsqstvShHL 36
                                  k L+e+ ++ + +a  lg+sq+++ ++L
  gi|70606271|ref|YP_255142.1| 23 KKLRERGMTQSRIATLLGVSQPAIKQYL 50
                                  6799999*******************99 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.21      24      47 ..      27      50 ..      24      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                  TS---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 24 leglsykEIAellgisegtVksrl 47
                                  + g+++  IA llg+s  ++k++l
  gi|70606271|ref|YP_255142.1| 27 ERGMTQSRIATLLGVSQPAIKQYL 50
                                  569*******************97 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.28      13      48 ..      29      64 ..      21      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                   Terminase_5 13 GyrvaeIAeelglkeatVysWkkrdewddldplsrv 48
                                  G +  +IA+ lg+++  +  + + de +++ ++ ++
  gi|70606271|ref|YP_255142.1| 29 GMTQSRIATLLGVSQPAIKQYLDEDEQEEVNKIRKM 64
                                  667899************************999887 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00041      0.49      10      35 ..      26      50 ..      22      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                        HTH_31 10 ReraGLsqeevAerlgvsestlsrlE 35
                                  R ++G++q   A +lgvs+  + ++ 
  gi|70606271|ref|YP_255142.1| 26 R-ERGMTQSRIATLLGVSQPAIKQYL 50
                                  4.789***************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1943.25
//
Query:       gi|70606273|ref|YP_255143.1|  [L=55]
Description: hypothetical protein Saci_0438 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 422.14
//
Query:       gi|70606274|ref|YP_255144.1|  [L=209]
Description: hypothetical protein Saci_0439 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1555.22
//
Query:       gi|70606275|ref|YP_255145.1|  [L=204]
Description: M50 family peptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-07   29.5   6.9    0.00019   20.8   2.5    3.0  3  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.07   13.1   1.4       0.18   11.8   1.4    1.7  1  DUF4492        Domain of unknown function (DUF4492)


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1   0.00026       2.3       4      39 ..      51      85 ..      48     100 .. 0.83
   2 !    3.9   0.3    0.0031        28      89     108 ..     125     144 ..     115     151 .. 0.89
   3 !   20.8   2.5   2.1e-08   0.00019     171     220 ..     136     185 ..     131     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00026
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  4 lllgilvvvHElGHflvAklcgvkveefsigfGpkl 39
                                  +  +i +v HE++H  +A++ g    +f++ f   l
  gi|70606275|ref|YP_255145.1| 51 VTATIAIVPHEIAHRQIARRYGSYS-RFALSFTGFL 85
                                  566789999*************865.9999985554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0031
                                   XXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50  89 livlAGplanfilailvfvv 108
                                    i ++Gp++n+ ++i+ f++
  gi|70606275|ref|YP_255145.1| 125 KISFGGPAVNLAVSIVSFII 144
                                   699*************9986 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 2.1e-08
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M50 171 ggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDGghllf 220
                                    ++i  + +a+ + +  +  f++ l++ +  ++++NLlPip+LDG+++++
  gi|70606275|ref|YP_255145.1| 136 AVSIVSFIIAGFTSNPLVYIFFAELYSFNAWVAFFNLLPIPPLDGFKVFR 185
                                   5555556666666777777888888999999***************9975 PP

>> DUF4492  Domain of unknown function (DUF4492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4     2e-05      0.18       9      26 ..     179     196 ..     178     204 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                       DUF4492   9 dGFrnmtlGktLwliili 26 
                                   dGF+  ++ ktLw+i li
  gi|70606275|ref|YP_255145.1| 179 DGFKVFRWNKTLWIIGLI 196
                                   9*************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1459.71
//
Query:       gi|70606276|ref|YP_255146.1|  [L=188]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-20   73.6   4.2    1.6e-20   73.6   4.2    1.7  2  Rhomboid    Rhomboid family
  ------ inclusion threshold ------
      0.021   14.5   9.3       0.15   11.7   1.7    2.7  3  DUF4203     Domain of unknown function (DUF4203)
      0.038   13.0   0.3      0.038   13.0   0.3    2.3  2  PTS_EIIC_2  Phosphotransferase system, EIIC


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.34   2.1e+03     133     140 ..      18      25 ..       4      36 .. 0.58
   2 !   73.6   4.2   2.7e-24   1.6e-20       3     149 ..      46     182 ..      44     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.34
                                   HHHHHHHH CS
                      Rhomboid 133 gGllaGll 140
                                   +G+++Gl+
  gi|70606276|ref|YP_255146.1|  18 IGFIVGLI 25 
                                   23444433 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 2.7e-24
                                   GCC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHH CS
                      Rhomboid   3 krgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgll 83 
                                    ++ +w+llts+f+  ++l  lfN++al+++     +r  +l++  ++l+sg++g+l++ll+++++  p++GaSG+ifgll
  gi|70606276|ref|YP_255146.1|  46 DYHFYWQLLTSIFVTPSILDWLFNTAALYFIYWLYKSRSAKLEI-PIFLVSGIIGNLVYLLLDPNG-PPSAGASGGIFGLL 124
                                   57899*********************************777765.789*****************8.6************* PP

                                   HHHHHHHHCCCCGS----HC...CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCCHH CS
                      Rhomboid  84 gallvlvprnrkllrkliiallllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllrra 149
                                    +++++ + ++++  +l++    ll+f+l nl+  l     +v+ +AH gG++aGlll+l+l++ +
  gi|70606276|ref|YP_255146.1| 125 SFYALNDYLEKREKNGLLLL---LLIFLLSNLFPFL-----NVNVYAHTGGVIAGLLLSLILYKTF 182
                                   **********9987766655...6666555554444.....689*****************99875 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3   0.00085       5.1      53      82 ..       8      37 ..       2      45 .. 0.87
   2 ?   11.7   1.7   2.5e-05      0.15      38     128 ..      70     160 ..      47     171 .. 0.70
   3 ?    0.0   0.2     0.095   5.7e+02      82      95 ..     166     179 ..     156     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00085
                       DUF4203 53 qgaslvaalvvGllgGllallfwelglfll 82
                                   + ++++ + +G+++Gl++ ++ ++ lfll
  gi|70606276|ref|YP_255146.1|  8 ATFFIMVLVTIGFIVGLILEFVNPFLLFLL 37
                                  56788999999*******999999999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.5e-05
                       DUF4203  38 lvlilkvvvlpsslvqgaslvaalvvGllgGllallfwelglfllgalgGlllallilsllegglitslpskaif.lvivv 117
                                   +++++ +  l++s +  + + ++lv+G++g l++ll+ + g   +ga gG+ ++ll +++l++ l + +++  ++ l+i+ 
  gi|70606276|ref|YP_255146.1|  70 TAALYFIYWLYKSRSAKLEIPIFLVSGIIGNLVYLLLDPNGPPSAGASGGI-FGLLSFYALNDYLEKREKNGLLLlLLIFL 149
                                   344433333447888999999**************************7776.67777777756666555554555688888 PP

                       DUF4203 118 lgllgavlslk 128
                                   l+ l+++l + 
  gi|70606276|ref|YP_255146.1| 150 LSNLFPFLNVN 160
                                   88888888765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.095
                       DUF4203  82 lgalgGlllallil 95 
                                   +g+++Glll+l+++
  gi|70606276|ref|YP_255146.1| 166 GGVIAGLLLSLILY 179
                                   34455555555544 PP

>> PTS_EIIC_2  Phosphotransferase system, EIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.9      0.13   7.5e+02     296     312 ..      11      27 ..       2      42 .. 0.54
   2 ?   13.0   0.3   6.4e-06     0.038     243     315 ..      87     162 ..      82     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.13
                    PTS_EIIC_2 296 lilvlfvlPlvlallis 312
                                   +i+vl+ ++++++l+++
  gi|70606276|ref|YP_255146.1|  11 FIMVLVTIGFIVGLILE 27 
                                   33333333333333332 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.4e-06
                    PTS_EIIC_2 243 ilippllasailGpvatlifklqgta.asaGmGtaGLvgplaal..eaagasavlllilvlfvlPlvlalliskvf 315
                                   + ip++l s i G +++l++  +g++ a+a  G+ GL+   a++   ++  ++ lll+l++f+l+ ++ +l  +v+
  gi|70606276|ref|YP_255146.1|  87 LEIPIFLVSGIIGNLVYLLLDPNGPPsAGASGGIFGLLSFYALNdyLEKREKNGLLLLLLIFLLSNLFPFLNVNVY 162
                                   669****************55555431455669*********9986334445577788888888777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1306.61
//
Query:       gi|70606277|ref|YP_255147.1|  [L=55]
Description: hypothetical protein Saci_0442 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 379.16
//
Query:       gi|70606278|ref|YP_255148.1|  [L=189]
Description: hypothetical protein Saci_0443 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-22   78.7   0.1      1e-21   77.9   0.0    1.4  1  AAA_18           AAA domain
    5.2e-07   30.2   0.1    1.9e-06   28.4   0.0    1.9  2  AAA              ATPase family associated with various cellul
    1.9e-06   27.9   0.0    3.4e-06   27.1   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    2.4e-06   28.0   0.0    8.2e-06   26.3   0.0    1.9  1  AAA_17           AAA domain
    7.3e-06   26.2   0.0    0.00013   22.2   0.0    2.2  1  AAA_33           AAA domain
    0.00011   22.4   0.0    0.00019   21.6   0.0    1.7  1  SKI              Shikimate kinase
    0.00067   19.9   0.5     0.0017   18.6   0.3    1.7  1  AAA_28           AAA domain
    0.00082   19.7   0.1      0.001   19.3   0.1    1.7  1  AAA_22           AAA domain
    0.00087   18.8   0.1     0.0023   17.4   0.0    1.8  2  KTI12            Chromatin associated protein KTI12
    0.00095   18.5   0.1     0.0022   17.3   0.1    1.8  1  Zeta_toxin       Zeta toxin
     0.0012   18.6   0.0     0.0058   16.4   0.0    1.9  2  Cytidylate_kin   Cytidylate kinase
     0.0029   18.0   0.1     0.0045   17.4   0.1    1.7  1  AAA_16           AAA ATPase domain
     0.0029   17.3   0.0     0.0044   16.8   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0063   15.6   0.0     0.0097   15.0   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.007   16.1   0.0      0.025   14.3   0.0    1.9  2  PRK              Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.034   14.3   0.0    1.9  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.013   15.9   0.0      0.034   14.5   0.0    1.8  1  RNA_helicase     RNA helicase
      0.014   14.7   0.0      0.016   14.4   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.014   15.7   0.0      0.024   14.9   0.0    1.4  1  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.019   14.9   2.3      0.038   13.9   0.2    2.2  2  NTPase_1         NTPase
      0.019   14.8   0.0      0.037   13.9   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
       0.02   14.8   0.2       0.13   12.1   0.1    2.1  2  APS_kinase       Adenylylsulphate kinase
      0.021   14.6   0.4      0.033   13.9   0.4    1.4  1  AAA_24           AAA domain
      0.021   14.8   0.7       0.04   14.0   0.1    1.7  2  AAA_14           AAA domain
      0.026   14.3   0.0       0.14   11.9   0.0    1.9  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.032   13.9   0.2      0.071   12.8   0.2    1.6  1  AAA_30           AAA domain
      0.034   14.5   0.1      0.091   13.1   0.1    1.7  2  AAA_19           AAA domain
      0.045   13.6   0.0      0.052   13.4   0.0    1.3  1  CPT              Chloramphenicol phosphotransferase-like prot
       0.05   13.4   1.5       0.15   11.9   0.2    2.2  2  dNK              Deoxynucleoside kinase
      0.064   12.6   0.2       0.62    9.3   0.1    2.1  2  DnaB_C           DnaB-like helicase C terminal domain
       0.08   13.0   0.1       0.24   11.5   0.0    2.0  2  ADK              Adenylate kinase
      0.084   12.6   0.4       0.39   10.4   0.1    2.0  2  Thymidylate_kin  Thymidylate kinase
      0.097   12.6   0.1       0.21   11.5   0.1    1.6  1  NACHT            NACHT domain
        0.1   12.1   0.1       0.22   11.0   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
       0.13   11.9   0.3       0.46   10.2   0.1    1.9  2  IstB_IS21        IstB-like ATP binding protein
       0.15   12.3   1.5       0.49   10.7   0.2    2.1  2  DUF4375          Domain of unknown function (DUF4375)
       0.18   11.2   0.0       0.32   10.4   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.22   11.5   0.7        0.5   10.4   0.2    1.9  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.26   10.8   0.3       0.43   10.1   0.3    1.3  1  AAA_25           AAA domain
       0.94    9.5   3.7        2.1    8.4   3.7    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   2.2e-24     1e-21       1     129 [.       3     121 ..       3     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.2e-24
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                   I+++GtpG+GKtt+ak+Ls++l++    l++ + en  ++e+d+   ++s ++dedk+ +l+++  en+       n+vi+
  gi|70606278|ref|YP_255148.1|   3 IIVAGTPGTGKTTVAKALSEKLNLnFLLLSSFIIENKAYTEYDDI--RQSYIIDEDKVFELIEKYIENNP------NVVIE 75 
                                   9*********************889********************..*****************999987......89*** PP

                        AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                    +   l++ a+k+   vvL+ +p +l e l+kR+++e ki+en eaeil
  gi|70606278|ref|YP_255148.1|  76 TIYPSLVPKADKI---VVLKRDPFILHEELKKRNWNELKIAENLEAEIL 121
                                   **********998...*******************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.2e-09   1.9e-06       1      38 [.       3      51 ..       3      88 .. 0.75
   2 ?   -0.6   0.0       3.8   1.7e+03      37      56 ..     134     157 ..     102     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.2e-09
                                  EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS...........S CS
                           AAA  1 vllyGppGtGKTllakavakelgvefleisgsellsk...........y 38
                                  +++ G+pGtGKT++aka+ ++l+ +fl +s   + +k           y
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNFLLLSSFIIENKayteyddirqsY 51
                                  5799**********************99999888887666666666543 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.8
                                   S....STTHHHHHHHHHHHHHHHT CS
                           AAA  37 k....yvgesekkirelfkeakek 56 
                                   k     + ++ + i+++++++ ++
  gi|70606278|ref|YP_255148.1| 134 KdkvcSINNTGRTISQILEKIIKN 157
                                   233335555556666666655444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.6e-09   3.4e-06       2      51 ..       3      56 ..       2      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.6e-09
                                  EEEE--SSSSHHHHHHHGGGGB.....S--EEEEE--TT--HHHHH--B--.... CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.....nreveyvqltrdtteedlkgrreikngt 51
                                  +++ G pGtgK+++a+ l++ l       + +++ ++++t+++d+++++ i+ ++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLnlnflLLSSFIIENKAYTEYDDIRQSYIID-ED 56
                                  5889******************7766666889*****************995.33 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.8e-08   8.2e-06       2      79 ..       7      77 ..       6     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.8e-08
                                  E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
                        AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdgh 79
                                  G PG GK+t+++ l ek+++ +l  ++ ++e+ +  +     d++r+ ++ +++++ +++++ i+++    +v++++ 
  gi|70606278|ref|YP_255148.1|  7 GTPGTGKTTVAKALSEKLNLNFLLLSSFIIENKAYTEY----DDIRQSYIIDEDKVFELIEKYIENN---PNVVIETI 77
                                  99***************************998555555....9999999999999999999988874...56666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.9e-07   0.00013       2      47 ..       3      51 ..       2     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.9e-07
                        AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg.tdqqsktd 47
                                  +++ G pG+GK+t+a+ l +kl   + llss ++ ++ +   d+ ++++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNlnFLLLSSFIIENKAYTeYDDIRQSY 51
                                  899********************98888888776664443244444443 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.2e-07   0.00019       1      68 [.       9      76 ..       9     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.2e-07
                                  TTSSHHHHHHHHHHHHTSEEEEHHHHH.HHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCS.SEEEEE CS
                           SKI  1 mGaGKstvGkllAkklglefiDlDeli.ekrtgksiaeifeeegeegFrelEsevlkelleee.glViat 68
                                  +G+GK+tv+k+l++kl+l+f+ l ++i e+++ ++  +i + +  ++  ++  e++++++e++ ++Vi t
  gi|70606278|ref|YP_255148.1|  9 PGTGKTTVAKALSEKLNLNFLLLSSFIiENKAYTEYDDIRQSYIIDE--DKVFELIEKYIENNpNVVIET 76
                                  69*******************99886548888899999988775544..445567889998888888877 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   3.7e-06    0.0017       2      22 ..       3      23 ..       2      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-06
                        AAA_28  2 ivitGgestGKTtlleaLaar 22
                                  i++ G+++tGKTt+++aL+++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEK 23
                                  8999**************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.3e-06     0.001       7      30 ..       2      25 ..       1     156 [. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.3e-06
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                  i++v G +GtGKTt+++ l e+l+
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLN 25
                                  799******************995 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.2e-06    0.0023       3      28 ..       2      46 ..       1      78 [. 0.68
   2 ?   -1.8   0.0       3.7   1.7e+03     165     190 ..     150     172 ..     134     186 .. 0.47

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-06
                                  EEEEE--TTSSHHHHHHHHHHHHHH...................T CS
                         KTI12  3 LvvltGlPssGKstrakeLakalee...................e 28
                                  ++++ G P +GK+t+ak L+++l+                     
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLNLnflllssfiienkayteydD 46
                                  69********************98766444444444333333333 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                                   HHHHHHHHHTS--SSSTT-------H CS
                         KTI12 165 ilkaliekkklkpnqatlskplaean 190
                                   il+++i+++    +q      ++ +n
  gi|70606278|ref|YP_255148.1| 150 ILEKIIKNE---CEQIDWLDDEKIQN 172
                                   333333222...22222233333344 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.9e-06    0.0022      18      49 ..       2      31 ..       1      80 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrl 49
                                  +i+++G pG GK+++a++l ++l  + n++ l
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKL--NLNFLLL 31
                                  79********************9..7776655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0058       3      59 ..       5      64 ..       3      76 .. 0.75
   2 ?   -0.6   0.0       2.1   9.2e+02     189     207 ..     138     156 ..     131     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                  EE-STTSSHHHHHHHHHHHHT-EEEE.HHHHHHHHHHHHHHT..T--TT-HHHHHHHHHT CS
                Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyld.tgalYRalalaalrr..kvdlldeaalvelake 59
                                  + G  g+GK +va+al+ekl+l++l  ++ +    a+   +   +  ++de++++el+++
  gi|70606278|ref|YP_255148.1|  5 VAGTPGTGKTTVAKALSEKLNLNFLLlSSFIIENKAYTEYDDirQSYIIDEDKVFELIEK 64
                                  67889*****************99751555556666666553336778888888888765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                                   EEEETTTS-HHHHHHHHHH CS
                Cytidylate_kin 189 liidtskltieevvekile 207
                                     i+ +  ti++++eki++
  gi|70606278|ref|YP_255148.1| 138 CSINNTGRTISQILEKIIK 156
                                   568889999*******997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     1e-05    0.0045      26      69 ..       2      44 ..       1     182 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-05
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy 69
                                  ++++ G +G+GK++++++l + l+ + +++l+    ++++ ++y
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLNLN-FLLLSSFIIENKAYTEY 44
                                  689******************99988.44455444444444444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.9e-06    0.0044      36      72 ..       3      39 ..       2      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.9e-06
                        RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsgPvleka 72
                                  ++++G PG Gktt+ak ++++l+ ++   s+ ++e++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNFLLLSSFIIENK 39
                                  6899**********************99999999876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-05    0.0097     131     156 ..       2      27 ..       1      74 [. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                         T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                   +i+v+G+ g+GKtt++ al +++n +
  gi|70606278|ref|YP_255148.1|   2 IIIVAGTPGTGKTTVAKALSEKLNLN 27 
                                   79******************999876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.7e-05     0.025       1      52 [.       2      55 ..       2      66 .. 0.80
   2 ?   -0.6   0.0         2     9e+02     103     125 ..      62      84 ..      46      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-05
                           PRK  1 vIgvagsSGaGkttvarklekifgrek..vkaaeiegdsflrldraekdlelee 52
                                  +I vag  G Gkttva++l + ++ +   + +  ie ++ +++d + +++ ++e
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLNLNFllLSSFIIENKAYTEYDDIRQSYIIDE 55
                                  799******************998654115566678888888888888777665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                           PRK 103 keeliegadvlviEGlhalyder 125
                                    e+ ie++  +viE +++  + +
  gi|70606278|ref|YP_255148.1|  62 IEKYIENNPNVVIETIYPSLVPK 84 
                                   57889999999999999987765 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.7e-05     0.034       1      28 [.       2      29 ..       2      69 .. 0.90
   2 ?   -2.1   0.0       7.9   3.6e+03      53      66 ..     144     157 ..     111     184 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.7e-05
               Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfy 28
                                  iI ++++ G+g++t+++aL+ekL+l+f+
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLNLNFL 29
                                  6778999*****************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.9
               Cytidylate_kin2  53 rsrlssflskllaa 66 
                                    +++s++l+k++++
  gi|70606278|ref|YP_255148.1| 144 GRTISQILEKIIKN 157
                                   33444444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.5e-05     0.034       1      38 [.       3      38 ..       3      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.5e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                  i++ G +g+GK+t+ak L+++l  ++ l   +s+++ n
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNFLLL--SSFIIEN 38
                                  6899****************999666222..3444433 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-05     0.016       3      37 ..       2      35 ..       1      90 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                       DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavyl 37
                                  +++V G +GtGKt v+ +l  +l + +    + ++
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKL-NLNFLLLSSFI 35
                                  79**************9999888.43333444444 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   5.4e-05     0.024       2      36 ..       3      37 ..       2      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.4e-05
                     Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvle 36
                                  iiv G+P +GKt+ a +L+ k +  +l + s ++e
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNFLLLSSFIIE 37
                                  9********************99999999888877 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   8.5e-05     0.038       2      24 ..       3      25 ..       2      39 .. 0.88
   2 ?    0.6   0.1       1.1   4.8e+02     108     148 ..      67     106 ..      38     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.5e-05
                                  EEEE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                  +++ G pG+GKtT+ k ++e+l+
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLN 25
                                  799*****************995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                                   GGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-T CS
                      NTPase_1 108 ElkskkfkeaveevLksekpvlavihrrkdlalveeirerk 148
                                   E + ++++e++   L ++   ++v++r  +  l ee+++r+
  gi|70606278|ref|YP_255148.1|  67 ENNPNVVIETIYPSLVPKADKIVVLKRD-PFILHEELKKRN 106
                                   5556667777777788888888888888.777778887774 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.3e-05     0.037       2      27 ..       3      28 ..       2      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.3e-05
                         AAA_3  2 vllegvPGlaktllvkalakaldlef 27
                                  +++ g+PG++kt+++kal+++l+l+f
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNF 28
                                  6899*******************998 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0003      0.13       4      27 ..       2      25 ..       1      33 [. 0.91
   2 ?   -0.0   0.0       1.6   7.2e+02      16      44 ..     145     173 ..     139     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                                  EEEEESSTTSSHHHHHHHHHHHHH CS
                    APS_kinase  4 vvwltGlsgsGKstianalekkLv 27
                                  ++ ++G  g+GK+t+a+al++kL+
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLN 25
                                  7899******************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHTT--EEEEEHHHHTTT CS
                    APS_kinase  16 stianalekkLvekgisvylLdGdnvRhg 44 
                                    ti++ lek ++++  ++  Ld +++ + 
  gi|70606278|ref|YP_255148.1| 145 RTISQILEKIIKNECEQIDWLDDEKIQNF 173
                                   4899*******9999******99998765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   7.3e-05     0.033       5      29 ..       3      26 ..       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.3e-05
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfi 29
                                  i++ G +g+GKTt+ak l  + l +
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKAL-SEKLNL 26
                                  789**************9.544444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   8.9e-05      0.04       4      65 ..       2      70 ..       1      78 [. 0.80
   2 ?   -2.1   0.0       8.1   3.6e+03      32      44 ..     153     165 ..     143     187 .. 0.45

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.9e-05
                        AAA_14  4 ilvitGaRrvGKTtllkqlikell........vkkesilyinldderdkkladpekllelileklkeekk 65
                                  i+++ G   +GKTt++k l ++l            e+  y + dd r++ + d++k+ eli + +++ + 
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLNlnflllssFIIENKAYTEYDDIRQSYIIDEDKVFELIEKYIEN-NP 70
                                  899****************988888999888866788899999999998888888888888776544.33 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.1
                        AAA_14  32 silyinldderdk 44 
                                   +i+  ++++ +  
  gi|70606278|ref|YP_255148.1| 153 KIIKNECEQIDWL 165
                                   3333333333332 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00031      0.14       1      24 [.       3      27 ..       3      58 .. 0.74
   2 ?    0.0   0.0       1.3   5.8e+02      30      70 ..     127     167 ..     112     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrts.li 24
                                  i+v+G pG GK+t+ + l ++  l+
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLnLN 27
                                  79***********888877664533 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
               Viral_helicase1  30 ptaelltegkpklpnlsvrtvdsflmalvkstkgkililDE 70 
                                   +++e++ + k  + n+++rt+ ++l++ +k    +i +lD+
  gi|70606278|ref|YP_255148.1| 127 EAIEAFGKDKVCSINNTGRTISQILEKIIKNECEQIDWLDD 167
                                   55666666668888999999999999999986688888886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00016     0.071      21      41 ..       3      23 ..       1      27 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                        AAA_30 21 avltGpAGtGKttalkalrea 41
                                   ++ G +GtGKtt+ kal e 
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEK 23
                                  6899************99875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1    0.0002     0.091      12      34 ..       2      24 ..       1      36 [. 0.84
   2 ?   -2.0   0.0       9.4   4.2e+03      44      62 ..     136     154 ..     118     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                        AAA_19 12 vllvtaGpGtGKTrvlkhivall 34
                                  +++v + pGtGKT+v k+  + l
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKL 24
                                  5789999********98876655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9.4
                        AAA_19  44 eillvaftgrAakelrerl 62 
                                   ++  +  tgr  +++ e++
  gi|70606278|ref|YP_255148.1| 136 KVCSINNTGRTISQILEKI 154
                                   5555555666666555554 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.052       2      33 ..       1      32 [.       1     110 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                  -EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                           CPT  2 riilLnGgsssGKsslaralqevldepwlhlg 33
                                  +ii+  G++ +GK+++a+al e l+  +l l 
  gi|70606278|ref|YP_255148.1|  1 MIIIVAGTPGTGKTTVAKALSEKLNLNFLLLS 32
                                  59********************9999998765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00034      0.15       1      26 [.       3      28 ..       3      52 .. 0.89
   2 ?    0.2   0.2       1.3   5.9e+02     120     143 ..      82     105 ..      33     126 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                                  EEEEESTTSSHHHHHHHHHCCSTCEE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkv 26
                                  i v G+ g GK+t++k Ls+kl+ ++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNF 28
                                  7899*****************99765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                   CCH-SEEEEEE--HHHHHHHHHHC CS
                           dNK 120 lakpdlliYLkasletclerikkR 143
                                   ++k d ++ Lk ++  + e +kkR
  gi|70606278|ref|YP_255148.1|  82 VPKADKIVVLKRDPFILHEELKKR 105
                                   233455555555555555555555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0014      0.62      21      43 ..       2      24 ..       1      41 [. 0.85
   2 ?    1.0   0.0      0.47   2.1e+02     204     236 ..      84     117 ..      46     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                                  EEEEEEXTTSSHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C 21 liiiAarpsmGktalalniaena 43
                                  +ii+A+ p++Gkt++a  + e+ 
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKL 24
                                  69*************99888765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                                   CXSEEEEEEECCHHHHHH.CHHCEEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                        DnaB_C 204 dADvvlflyrdeyykeds.eekgkaeiiiaKhRn 236
                                    AD +++l rd    +++ ++++ +e+ ia + +
  gi|70606278|ref|YP_255148.1|  84 KADKIVVLKRDPFILHEElKKRNWNELKIAENLE 117
                                   6999999999998864444778888998887755 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00054      0.24       1      30 [.       5      34 ..       5     118 .. 0.76
   2 ?   -2.1   0.0         8   3.6e+03      58      69 ..     149     160 ..     125     175 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00054
                                  EEESTTSSHHHHHHHHHHHHTSEEEEHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdl 30
                                  + G+Pg+GK t+a+ l +k++l+ l    +
  gi|70606278|ref|YP_255148.1|  5 VAGTPGTGKTTVAKALSEKLNLNFLLLSSF 34
                                  579****************99987754444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8
                                   HHHHHHHHHHHH CS
                                   xxxxxxxxxxxx RF
                           ADK  58 evvvklvkeele 69 
                                   +++ k++k+e e
  gi|70606278|ref|YP_255148.1| 149 QILEKIIKNECE 160
                                   334444444433 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00087      0.39       3      24 ..       7      28 ..       5      66 .. 0.85
   2 ?    0.4   0.0      0.99   4.4e+02     112     184 ..      79     153 ..      64     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00087
                                  ESTTSSHHHHHHHHHHHHHHTT CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeeg 24
                                  G  G+GKtt+a++l e+l+ + 
  gi|70606278|ref|YP_255148.1|  7 GTPGTGKTTVAKALSEKLNLNF 28
                                  777***************8776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.99
                                   GGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHH..HHHHHHHHHHHHHHHTTSTEEEEE.TTS-HHHHHHH CS
               Thymidylate_kin 112 edvllkPdltflldvdpevalkRlakrdeldeeeeeql..dflrkvrerylelakederiliid.asksieevhee 184
                                   +++++k d+++ l+ dp +  + l+kr+ ++ +++e+l  ++l  +++ + e++  +++++ i+ + + i ++ e+
  gi|70606278|ref|YP_255148.1|  79 PSLVPKADKIVVLKRDPFILHEELKKRNWNELKIAENLeaEILGVIEAEAIEAFG-KDKVCSINnTGRTISQILEK 153
                                   5555577777778888888888888888755555555411567778888888885.55555544044446666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00047      0.21       3      24 ..       3      24 ..       1      32 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00047
                                  EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                  +i+ G +G GKTt ++ l +++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKL 24
                                  89***************99887 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00048      0.22      36      62 ..       3      28 ..       1      55 [. 0.76
   2 ?   -3.0   0.0       9.8   4.4e+03      67      83 ..     140     156 ..     135     161 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00048
                         AAA_7 36 vllvGptGtGKtviikdllkkldkeky 62
                                  +++ G+ GtGKt+++k l +kl+ + +
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLN-F 28
                                  5789****************99943.3 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.8
                         AAA_7  67 infsaqtsanqlqdiie 83 
                                   in + +t ++ l +ii+
  gi|70606278|ref|YP_255148.1| 140 INNTGRTISQILEKIIK 156
                                   33333444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1     0.001      0.46      50      70 ..       3      23 ..       1      28 [. 0.90
   2 ?   -1.1   0.0         3   1.3e+03      30      51 ..      53      73 ..      30      76 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                     IstB_IS21 50 ivllGpsGvGKshlaialgve 70
                                  i++ G +G+GK+ +a al+ +
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEK 23
                                  7899**************876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                     IstB_IS21 30 ldkrkvkeLatlsfiekkeniv 51
                                  +d+ kv eL++ ++ie++ n+v
  gi|70606278|ref|YP_255148.1| 53 IDEDKVFELIE-KYIENNPNVV 73
                                  44444444443.3455555544 PP

>> DUF4375  Domain of unknown function (DUF4375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2    0.0011      0.49      85     117 ..      37      70 ..      15      72 .. 0.88
   2 ?    0.8   0.1       1.3   5.7e+02      78      97 ..     149     168 ..     108     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                                   HH..-GGGHHHHHHHHHHHHHHHHHHHHHHHCTH CS
                       DUF4375  85 eee.eeefdelDdefyeyeeeltellaeYvdehi 117
                                   e++ ++e d++ + ++  e++++el+ +Y+++++
  gi|70606278|ref|YP_255148.1|  37 ENKaYTEYDDIRQSYIIDEDKVFELIEKYIENNP 70 
                                   44469***************************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.3
                                   T-HHHHHHH.-GGGHHHHHH CS
                       DUF4375  78 eelealyeeeeeefdelDde 97 
                                   + le++ ++e e++d lDde
  gi|70606278|ref|YP_255148.1| 149 QILEKIIKNECEQIDWLDDE 168
                                   22444444445555555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00071      0.32      25      44 ..       3      22 ..       2      28 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00071
                  Mg_chelatase 25 lllvGppGsGKtmlakrlps 44
                                  ++++G+pG+GKt +ak+l++
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSE 22
                                  6889************9976 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2    0.0011       0.5      22      47 ..       3      29 ..       1      76 [. 0.82
   2 ?   -0.6   0.0       2.8   1.3e+03      77      98 ..     104     125 ..      58     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                  EEEEESTTSSHHHHHHHHHHHTT--.- CS
                          TsaE 22 ilLeGdLGaGKTtlvrglakalgve.e 47
                                  i+  G  G+GKTt +++l ++l+++  
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKALSEKLNLNfL 29
                                  7889999**************998743 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
                                   THHHHHCTTCCCCSTSCEEEEE CS
                          TsaE  77 eeeleelgleeyleeeavvlvE 98 
                                   +++++el++ e le+e + ++E
  gi|70606278|ref|YP_255148.1| 104 KRNWNELKIAENLEAEILGVIE 125
                                   4456666666666554455555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00096      0.43      36      53 ..       3      20 ..       1      24 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00096
                        AAA_25 36 allaGapgtGKttlaldl 53
                                  +++aG pgtGKtt+a  l
  gi|70606278|ref|YP_255148.1|  3 IIVAGTPGTGKTTVAKAL 20
                                  79************9766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.7    0.0048       2.1       1      24 [.       2      25 ..       2     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0048
                                  EEEEESSTTSSHHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  1 iaiastkGGvGKTtlaanLarala 24
                                  i+i++++ G+GKTt+a +L   l+
  gi|70606278|ref|YP_255148.1|  2 IIIVAGTPGTGKTTVAKALSEKLN 25
                                  799*************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 1252.38
//
Query:       gi|70606279|ref|YP_255149.1|  [L=295]
Description: ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-97  325.8   0.1    1.9e-97  325.5   0.1    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
      6e-13   49.0   0.0    3.1e-12   46.7   0.0    2.0  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.6e-10   40.9   0.1    3.7e-05   23.3   0.1    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    1.9e-09   37.7   0.4    6.2e-07   29.5   0.1    2.2  2  AAA_31       AAA domain
    4.3e-06   26.1   0.3    5.5e-05   22.5   0.3    2.1  2  ArsA_ATPase  Anion-transporting ATPase
    4.4e-05   22.9   0.0    6.2e-05   22.4   0.0    1.3  1  MipZ         ATPase MipZ
    0.00037   20.1   0.0    0.00062   19.4   0.0    1.4  1  AAA_25       AAA domain
    0.00038   19.5   0.1    0.00067   18.7   0.1    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0032   17.3   1.0       0.76    9.6   0.0    2.2  2  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.012   15.5   1.4      0.017   15.0   0.0    2.0  3  DUF4898      Domain of unknown function (DUF4898)
       0.19   11.4   0.0       0.35   10.6   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.5   0.1  1.2e-100   1.9e-97       2     245 ..      43     288 ..      42     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 325.5 bits;  conditional E-value: 1.2e-100
                          ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigfl 81 
                                   vk +ia+lSgKGGVGKS v++nlA+a+a++g kvg++D+D +Gps+p++lgv+++  +++++++ Pv+   +ikv+Si+fl
  gi|70606279|ref|YP_255149.1|  43 VKYKIAILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDFHGPSVPKMLGVRGQYLTADDNGINPVTGpFNIKVVSIDFL 123
                                   899****************************************************9****99******99*********** PP

                          ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiemfk 161
                                   l+++d++vvwrG++k++ai+q+l dv+wgelDyL+iD+PPGtgDe+l++aq + +l+g+viVt p ev++  vk++i+++k
  gi|70606279|ref|YP_255149.1| 124 LPKDDTPVVWRGAIKHTAIRQFLGDVNWGELDYLFIDMPPGTGDEALSIAQLIpNLTGMVIVTIPSEVSTLAVKRSINFAK 204
                                   *****************************************************889************************* PP

                          ParA 162 kvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeia 242
                                   +v++k++GvveNms+fvcp++g+++ ifg+g g+k+a+e+gvpllg++pldp i++a+d g+p+++k pes+++k++++ia
  gi|70606279|ref|YP_255149.1| 205 TVNAKIIGVVENMSHFVCPDSGKTYFIFGEGRGKKMADEMGVPLLGQVPLDPIIAKANDMGEPFFVKYPESPTSKEFMSIA 285
                                   ********************************************************************************* PP

                          ParA 243 ekv 245
                                   +k+
  gi|70606279|ref|YP_255149.1| 286 QKI 288
                                   *98 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.9e-15   3.1e-12       1     127 [.      47     267 ..      47     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.9e-15
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                   iai s+kGGvGK++++ nLa a+a  g++V  vD+D  +++     g++++  +                           
  gi|70606279|ref|YP_255149.1|  47 IAILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDFHGPSVPKMLGVRGQYLTaddnginpvtgpfnikvvsidfllpkd 127
                                   89***************************************997666666666678888888******************* PP

                                   ...................................................................CCHCCCHHHHHHCH CS
                                   ...................................................................xxxxxxxxxxxxxx RF
                          CbiA  55 ...................................................................dlkrllellealgk 68 
                                                                                                       +kr +++++++  
  gi|70606279|ref|YP_255149.1| 128 dtpvvwrgaikhtairqflgdvnwgeldylfidmppgtgdealsiaqlipnltgmvivtipsevstlAVKRSINFAKTVN- 207
                                   *******************************************************9999999886555555444444444. PP

                                   CHHHH..EEEEEEEE..ESS...-TTCHHHHHHHHHHC....TS-EEEEEE--CCHCCCCHHTS- CS
                                   xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  69 kkalllkiagvvlnr..vdgeneetllkealeelkqry....gvpvlgviprdeavaeapargep 127
                                         ki+gvv n+  +  +++ +    + e + +++    gvp+lg +p d  +a+a   gep
  gi|70606279|ref|YP_255149.1| 208 -----AKIIGVVENMshFVCPDSGKTYFIFGEGRGKKMademGVPLLGQVPLDPIIAKANDMGEP 267
                                   .....5799999886444455566666666665555556778************99999888877 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.3e-08   3.7e-05       3      40 ..      47      85 ..      45      99 .. 0.83
   2 !   15.4   0.0   5.8e-06    0.0095     194     248 ..     238     292 ..     197     295 .] 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.3e-08
                     Fer4_NifH  3 iai.yGkGGiGksttsqnlsaalaemgkkvlivGCDPka 40
                                  iai  GkGG+Gks+ s+nl++a+a+ g+kv iv  D   
  gi|70606279|ref|YP_255149.1| 47 IAIlSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDFHG 85
                                  66526*************************999988655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 5.8e-06
                     Fer4_NifH 194 ekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilenk 248
                                   +k+a+e+g+++l  vP+d i+ ka+   +  +   pes+ +ke+  +a+ki++n 
  gi|70606279|ref|YP_255149.1| 238 KKMADEMGVPLLGQVPLDPIIAKANDMGEPFFVKYPESPTSKEFMSIAQKIINNV 292
                                   6899********************999999999999999*************996 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   3.8e-10   6.2e-07       3      40 ..      46      83 ..      44      96 .. 0.94
   2 !    6.4   0.0    0.0048       7.8     107     170 ..     142     209 ..     112     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.8e-10
                        AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                   Iai   KGGvGK+  s nla+a+a +g kv +vD+D 
  gi|70606279|ref|YP_255149.1| 46 KIAILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDF 83
                                  59**********************************96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0048
                        AAA_31 107 lkellekvk.deYDyiiiDcpPsLg..lltenaLvas.dsviipvqaeayaleGleqllktieevkkk 170
                                   ++++l +v+  e Dy +iD+pP  g   l +  L+     ++i++ +++ ++  +++ +++ ++v+ k
  gi|70606279|ref|YP_255149.1| 142 IRQFLGDVNwGELDYLFIDMPPGTGdeALSIAQLIPNlTGMVIVTIPSEVSTLAVKRSINFAKTVNAK 209
                                   5566666653479*********9873344444454331346777788889999999999998888776 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   3.4e-08   5.5e-05       2      38 ..      46      82 ..      45      86 .. 0.93
   2 ?    1.4   0.0     0.093   1.5e+02     204     243 ..     177     216 ..     143     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.4e-08
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  k+ +++GKGGVGK+ vs+ +a+ ++ +g+kv ++ +D
  gi|70606279|ref|YP_255149.1| 46 KIAILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVD 82
                                  67899**************************999877 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.093
                                   TTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                   ArsA_ATPase 204 pertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                   p+ t +++V+ip ++s    +R+i+  k ++ k+  v+ N
  gi|70606279|ref|YP_255149.1| 177 PNLTGMVIVTIPSEVSTLAVKRSINFAKTVNAKIIGVVEN 216
                                   6789999999999999999999999888888777777766 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.8e-08   6.2e-05       5      54 ..      49      98 ..      45     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.8e-08
                                  E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHH CS
                          MipZ  5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraat 54
                                  +   kGG Gks ++  +a+a++++G +v+ +d+d    ++ + l+ r + 
  gi|70606279|ref|YP_255149.1| 49 ILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDFHGPSVPKMLGVRGQY 98
                                  5567********************************99999999988764 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.8e-07   0.00062      33      63 ..      45      76 ..      18     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.8e-07
                        AAA_25 33 gelallaGapgtGKttlaldlalava.tGkpw 63
                                   ++a+l G +g+GK+++ ++la a+a +G+++
  gi|70606279|ref|YP_255149.1| 45 YKIAILSGKGGVGKSFVSSNLAMAIAaSGRKV 76
                                  5789**********************988865 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   4.1e-07   0.00067       8      67 ..      24      83 ..      18      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.1e-07
                                  HH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                          MeaB  8 veserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                  v  + p+a ++  +l+ k  + +   l G  G+Gks + ++l++ +++ G++v+++ vD 
  gi|70606279|ref|YP_255149.1| 24 VQPQAPQAVDMKLQLRMKRVKYKIAILSGKGGVGKSFVSSNLAMAIAASGRKVGIVDVDF 83
                                  667788899998999999999999999*******************************94 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.3    0.0053       8.6       5      33 ..      49      77 ..      46      79 .. 0.85
   2 !    9.6   0.0   0.00046      0.76     118     195 ..     170     259 ..     161     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0053
                        AAA_26  5 vtgtdtgvGKTvvslgLvralkrkgvkvg 33
                                  + +   gvGK++vs  L+ a+ + g kvg
  gi|70606279|ref|YP_255149.1| 49 ILSGKGGVGKSFVSSNLAMAIAASGRKVG 77
                                  5566679***************9999998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00046
                        AAA_26 118 llnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNk...vrnpe...........nvetlekksgipv 184
                                   l++a+++ nl   vi+ ++++ +t+ ++  +i+++++ n +++Gv+ N    v++ +           + +++    g+p+
  gi|70606279|ref|YP_255149.1| 170 LSIAQLIPNLTGMVIVTIPSEVSTL-AVKRSINFAKTVNAKIIGVVENMshfVCP-DsgktyfifgegRGKKMADEMGVPL 248
                                   6778888888877887778777777.5899****************998554222.2344555555566666666668*** PP

                        AAA_26 185 lGvvPylpdle 195
                                   lG+vP +p + 
  gi|70606279|ref|YP_255149.1| 249 LGQVPLDPIIA 259
                                   *****999765 PP

>> DUF4898  Domain of unknown function (DUF4898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.7   9.3e+03      32      40 ..     121     129 ..     120     132 .. 0.70
   2 ?   15.0   0.0   1.1e-05     0.017       5      43 ..     192     231 ..     188     242 .. 0.91
   3 ?   -2.9   0.1       4.3   6.9e+03      16      28 ..     281     293 ..     277     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.7
                       DUF4898  32 nfilPkdkk 40 
                                    f+lPkd  
  gi|70606279|ref|YP_255149.1| 121 DFLLPKDDT 129
                                   589***954 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                       DUF4898   5 klikkskkikfvkkislkiIsdyekffnfilPkd.kkivv 43 
                                    +++ +++i+f k +++kiI  +e++  f+ P++ k +++
  gi|70606279|ref|YP_255149.1| 192 STLAVKRSINFAKTVNAKIIGVVENMSHFVCPDSgKTYFI 231
                                   56778899**************************999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.3
                       DUF4898  16 vkkislkiIsdye 28 
                                   + +i  kiI ++e
  gi|70606279|ref|YP_255149.1| 281 FMSIAQKIINNVE 293
                                   5688899999875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.35      49      80 ..      47      78 ..      13      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                     IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlf 80
                                    +l G  GvGKs+++  l+++ +++g +v  
  gi|70606279|ref|YP_255149.1| 47 IAILSGKGGVGKSFVSSNLAMAIAASGRKVGI 78
                                  45789*****************9999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2175.24
//
Query:       gi|70606280|ref|YP_255150.1|  [L=74]
Description: hypothetical protein Saci_0445 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00098   18.9   0.1     0.0011   18.8   0.1    1.1  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.013   15.8   0.3       0.59   10.5   0.2    2.1  1  Mnd1      Mnd1 HTH domain
      0.015   15.7   0.1      0.018   15.5   0.1    1.1  1  DUF1717   Viral domain of unknown function (DUF1717)


Domain annotation for each model (and alignments):
>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.8e-07    0.0011       5      58 ..      14      69 ..      10      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-07
                       DUF4364  5 ilYllkkvkfpltnsqlseiileney.tnYfdlqqalseLvesglieee.ekenkt 58
                                  il ++++ ++ +t +q+ +i++e+++  n +++ ++l++Lv +g i++e + e+k+
  gi|70606280|ref|YP_255150.1| 14 ILKIIEENRQGITSTQIRDILMEKGIqFNMVEFREILADLVREGKIKKEpDYEKKK 69
                                  7778999999*************99757*******************995545544 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   9.9e-05      0.59       1      48 [.      14      62 ..      14      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.9e-05
                          Mnd1  1 ileifqeskefytlKeleklapkekgivsqsV..kdvlqsLvdDglveve 48
                                  il+i++e+++  t  ++  ++   kgi+ + V  +++l  Lv +g++++e
  gi|70606280|ref|YP_255150.1| 14 ILKIIEENRQGITSTQIRDILME-KGIQFNMVefREILADLVREGKIKKE 62
                                  67777777777778888888877.89988776337************987 PP

>> DUF1717  Viral domain of unknown function (DUF1717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1     3e-06     0.018       8      49 ..       7      48 ..       2      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-06
                       DUF1717  8 nedisdelldcieed.kglshemieevlitkglsmvytsdfke 49
                                  +ed+  e+l  iee+ +g++   i ++l+ kg+ +    +f+e
  gi|70606280|ref|YP_255150.1|  7 KEDLKAEILKIIEENrQGITSTQIRDILMEKGIQFNM-VEFRE 48
                                  79***********98359**************97643.45665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 487.90
//
Query:       gi|70606281|ref|YP_255151.1|  [L=116]
Description: ArsR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-12   47.3   0.1      2e-12   46.8   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.6e-07   30.4   0.0      4e-07   29.8   0.0    1.3  1  MarR_2          MarR family
    9.1e-07   28.6   0.6    2.2e-05   24.2   0.3    2.6  3  HTH_5           Bacterial regulatory protein, arsR family
    2.1e-06   27.5   0.8    2.7e-06   27.2   0.8    1.1  1  TFIIE_alpha     TFIIE alpha subunit
    0.00028   20.8   0.1    0.00041   20.2   0.1    1.3  1  MarR            MarR family
    0.00035   20.7   0.2     0.0013   18.9   0.0    2.0  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00061   20.1   0.0     0.0012   19.1   0.0    1.4  1  Rrf2            Transcriptional regulator
    0.00081   19.8   0.1     0.0019   18.6   0.0    1.7  2  HTH_27          Winged helix DNA-binding domain
     0.0021   18.2   0.1     0.0034   17.5   0.1    1.4  1  HTH_34          Winged helix DNA-binding domain
     0.0022   17.9   0.0     0.0044   17.0   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
     0.0038   17.3   0.2     0.0056   16.8   0.2    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0042   16.6   0.3     0.0092   15.5   0.3    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0085   16.1   0.0      0.018   15.1   0.0    1.6  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   14.9   0.0       0.15   11.9   0.0    2.1  1  HTH_23          Homeodomain-like domain
      0.029   14.1   0.2      0.045   13.5   0.1    1.4  1  DUF4423         Domain of unknown function (DUF4423)
      0.031   13.6   0.0      0.031   13.6   0.0    1.2  1  tRNA-synt_His   Histidyl-tRNA synthetase
      0.099   12.7   0.1       0.28   11.2   0.1    1.8  1  DUF2680         Protein of unknown function (DUF2680)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.1   1.8e-15     2e-12       1      62 [.      16      86 ..      16      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.8e-15
                                  HH.HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEE CS
                          TrmB  1 Lq.klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklY 62
                                  L+ ++GLse E++++l +l +++ +++d i+ el++++s+   +L++L+d+GlV++ekg        +++Y
  gi|70606281|ref|YP_255151.1| 16 LSvAYGLSESEIDTFLRILeSKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEKGDnmkggrpKYVY 86
                                  7779***************99999**********************************9988888844466 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   3.8e-10     4e-07      14      57 ..      33      75 ..      20      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.8e-10
                                  HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                        MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                  +  + +++  + ++ ++l++sks++s ilk+L++aGLv +++g+
  gi|70606281|ref|YP_255151.1| 33 ILESKEGK-DIDAISAELKISKSRTSIILKKLSDAGLVDKEKGD 75
                                  44555544.6789***************************9985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.037        39      25      40 ..      20      35 ..      16      39 .. 0.86
   2 !   24.2   0.3   2.1e-08   2.2e-05       8      47 .]      31      71 ..      31      71 .. 0.91
   3 ?   -1.5   0.0       2.2   2.3e+03      18      25 ..     101     108 ..      85     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.037
                                  HTS-HHHHHHHHHHHH CS
                         HTH_5 25 lglsqstvShHLkkLr 40
                                   gls+s ++  L++L+
  gi|70606281|ref|YP_255151.1| 20 YGLSESEIDTFLRILE 35
                                  689************8 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.1e-08
                                  HHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  8 LklLaege.lcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  L++L+++e + +  +++el++s+s +S  LkkL +aGLV+k
  gi|70606281|ref|YP_255151.1| 31 LRILESKEgKDIDAISAELKISKSRTSIILKKLSDAGLVDK 71
                                  56788877799999*************************87 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                                   HHHHHHHH CS
                         HTH_5  18 vcelaeel 25 
                                   + el++el
  gi|70606281|ref|YP_255151.1| 101 SEELCKEL 108
                                   45677666 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.8   2.5e-09   2.7e-06       7     100 ..      19     112 ..      12     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.5e-09
                                   HHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHH CS
                   TFIIE_alpha   7 vrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkr 87 
                                   + +  + e    l +L +k     + ++ elki +     +L +L +a+lv+  +  + + +  ky + +n+e+l + +  
  gi|70606281|ref|YP_255151.1|  19 AYGLSESEIDTFLRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEKGDNMKGGRPKYVYSVNKEELKNRLIA 99 
                                   55666677777888888777777799**************************998888888899***************** PP

                                   HHHHHHHHHHHHH CS
                   TFIIE_alpha  88 kleevvkkLeekl 100
                                   k ee+ k+L++++
  gi|70606281|ref|YP_255151.1| 100 KSEELCKELNQVI 112
                                   *********9887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   3.9e-07   0.00041       9      51 ..      31      73 ..      22      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.9e-07
                                  HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  Lril+++++  +  +   l++sks ++ +l++L ++Gl++++k
  gi|70606281|ref|YP_255151.1| 31 LRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEK 73
                                  99**************************************987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0013      13      56 ..      30      73 ..      15      76 .. 0.88
   2 ?   -0.8   0.0       1.7   1.8e+03      20      34 ..      96     110 ..      83     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                  HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                   +++ e+k+      ++ +L++s+s  s  lkkL+++G+v+ ek
  gi|70606281|ref|YP_255151.1| 30 FLRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEK 73
                                  566777777777889*************************9887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                   HSSB-HHHHHHHHTS CS
                Fe_dep_repress  20 kkvvktkdlaerLnv 34 
                                   + ++k  +l ++Ln+
  gi|70606281|ref|YP_255151.1|  96 RLIAKSEELCKELNQ 110
                                   446888888888886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06    0.0012      19      62 ..      36      76 ..      26      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                  ++e+     +++i+++ +is+s  + il+kL+ aglv  ++G +
  gi|70606281|ref|YP_255151.1| 36 SKEG---KDIDAISAELKISKSRTSIILKKLSDAGLVDKEKGDN 76
                                  3333...479*******************************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.8e-06    0.0019       9      56 ..      31      78 ..      22      88 .. 0.82
   2 ?   -1.8   0.0       4.3   4.5e+03      20      29 ..     100     109 ..      94     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-06
                        HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv.ertgdead 56
                                  L+ ++   ++k + +++  l++++s +s +lkkL  +GLv +++gd + 
  gi|70606281|ref|YP_255151.1| 31 LRILE-SKEGKDIDAISAELKISKSRTSIILKKLSDAGLVdKEKGDNMK 78
                                  67777.99999*****************************666666554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                        HTH_27  20 kladlcgrln 29 
                                   k ++lc+ ln
  gi|70606281|ref|YP_255151.1| 100 KSEELCKELN 109
                                   5689999998 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.2e-06    0.0034       6      63 ..      31      90 ..      29     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.2e-06
                        HTH_34  6 lsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke..fkgkkprtllriTp 63
                                  l +L s++  d   ++++l++++++ s+ lkkL +ag +  +k+  +kg++p+ ++++ +
  gi|70606281|ref|YP_255151.1| 31 LRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEKGdnMKGGRPKYVYSVNK 90
                                  67899999**********************************963367889999998865 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.1e-06    0.0044      27      67 ..      49      90 ..      30      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-06
                                  CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESH CS
                          PadR 27 lelseGslYpaLkrLekeglvesewees.gegpprkyYrlTd 67
                                  l++s+++   +Lk+L++ glv++e+ ++ + g+p+ +Y +++
  gi|70606281|ref|YP_255151.1| 49 LKISKSRTSIILKKLSDAGLVDKEKGDNmKGGRPKYVYSVNK 90
                                  56666666669*****************99********9986 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   5.3e-06    0.0056      27      64 ..      44      81 ..      22     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.3e-06
                       DUF2250 27 siakeleipleevrellkkLeelGLlervegktikrte 64
                                   i+ el+i++++ + +lkkL ++GL+++ +g  +k  +
  gi|70606281|ref|YP_255151.1| 44 AISAELKISKSRTSIILKKLSDAGLVDKEKGDNMKGGR 81
                                  68999*************************99998655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   8.8e-06    0.0092       9      47 ..      31      69 ..      31      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                        HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  L++L+ + +  +  ++ +l +S+s ++  lk+L ++Gl+
  gi|70606281|ref|YP_255151.1| 31 LRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLV 69
                                  7899999999999************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-05     0.018      15      58 ..      30      73 ..      12      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                  HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  +lr L ++eg    ++ ++l +sk+  s  L++L++agLv+ ++
  gi|70606281|ref|YP_255151.1| 30 FLRILESKEGKDIDAISAELKISKSRTSIILKKLSDAGLVDKEK 73
                                  79999999********************************9875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.15      12      46 ..      34      68 ..       2      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                        HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  l  +eG+ + +I++eL +s++  + +lk+    Gl
  gi|70606281|ref|YP_255151.1| 34 LESKEGKDIDAISAELKISKSRTSIILKKLSDAGL 68
                                  555679999*******************9876776 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.3e-05     0.045      28      77 ..      32      78 ..      17     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                       DUF4423 28 ellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77
                                   +l+ k++ +d+++++  l+  is+++++ +l+ L ++gl++k++ ++++
  gi|70606281|ref|YP_255151.1| 32 RILESKEG-KDIDAISAELK--ISKSRTSIILKKLSDAGLVDKEKGDNMK 78
                                  47889999.***********..*********************9987765 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-05     0.031     158     206 ..      14      62 ..       1     111 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                                   HHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC... CS
                 tRNA-synt_His 158 ralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal 206
                                   r l  a+glses+ +++l++l++k+ ++++++ ae +++++ ++++ + 
  gi|70606281|ref|YP_255151.1|  14 RFLSVAYGLSESEIDTFLRILESKEGKDIDAISAELKISKSRTSIILKK 62 
                                   3344599*******************************99998887543 PP

>> DUF2680  Protein of unknown function (DUF2680)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00026      0.28      23      42 ..      59      78 ..      40      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                       DUF2680 23 ivdKyVeaGllTkeqgekik 42
                                  i +K+ +aGl  ke+g+++k
  gi|70606281|ref|YP_255151.1| 59 ILKKLSDAGLVDKEKGDNMK 78
                                  56899**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 777.76
//
Query:       gi|70606282|ref|YP_255152.1|  [L=242]
Description: 5-formyltetrahydrofolate cyclo-ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-34  118.6   0.0    3.5e-34  118.3   0.0    1.1  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
  ------ inclusion threshold ------
       0.18   11.0   0.0       0.26   10.5   0.0    1.2  1  YcaO            YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   3.9e-38   3.5e-34       1     187 []       7     198 ..       7     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 3.9e-38
                                   HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEEEEEE CS
                5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegkevllP 72 
                                   K+e+R++   ++++l+++++a+ ++++++ri+++k+s+ea  r+        a +++v+++++++++++ +l +gk vl+P
  gi|70606282|ref|YP_255152.1|   7 KAEIREK---IWSLLEDKNIASFPRPVFGRIPNFKGSKEAaLRLreiveyrkAKVLKVNPDSPQRWVREFALIDGKTVLVP 84 
                                   7899999...******************************9999************************************* PP

                                   EECSSCTEECEEEEEE.CCCCCCCCCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTS. CS
                5-FTHF_cyc-lig  73 rvrlesgslkvvrltt.lkeedslesgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkg. 151
                                   ++rl+ g+  ++ + +  ++++s++sg + l e ++ +    +  k+dlv+v++vA   +G R+GkG+Gy + ++a l++ 
  gi|70606282|ref|YP_255152.1|  85 TPRLKGGFYLLDPSKIsDYKKASTISGFIYLGELVDIYS--IP--KVDLVVVGSVALTSRGDRVGKGEGYSELEYAILREi 161
                                   ******999888765514455555555555544444444..44..8*********************************** PP

                                   T-SS--EEEEE--GGGEES.-----ST----SEEE-S CS
                5-FTHF_cyc-lig 152 gagdkpltvglaldeqlve.rlPleehDvpvdevvte 187
                                   g++d++++v++++++ ++  ++P+e +Dvpvd++vt+
  gi|70606282|ref|YP_255152.1| 162 GKIDETTPVVTTIHDIQIVdEIPTEVFDVPVDIIVTP 198
                                   ************99866555***************97 PP

>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   2.9e-05      0.26      45      95 ..      42      85 ..      24      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.9e-05
                          YcaO 45 egaldpeelglyseeekdaadfvlepfdpdrpidwvpgwsltdgeevlvPa 95
                                  e+al  +e+  y       ++ ++ +++pd+p +wv+ + l+dg++vlvP+
  gi|70606282|ref|YP_255152.1| 42 EAALRLREIVEY-------RKAKVLKVNPDSPQRWVREFALIDGKTVLVPT 85
                                  555555555444.......3456789************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1628.04
//
Query:       gi|70606283|ref|YP_255153.1|  [L=187]
Description: hypothetical protein Saci_0448 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-11   44.7  16.2    1.5e-11   44.1  16.2    1.2  1  LysE            LysE type translocator
  ------ inclusion threshold ------
       0.19   12.7   0.1       0.43   11.6   0.0    1.6  2  RALF            Rapid ALkalinization Factor (RALF)
        3.9    6.9   9.5      0.061   12.8   1.8    1.8  2  DUF1129         Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1  16.2   2.6e-15   1.5e-11       1     192 [.      15     181 ..      15     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.6e-15
                          LysE   1 lslllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrda 81 
                                   ls++++pGp n+++ +++ +r+f +gi+v++g++++d v++ + +l ++ ++  + i++ +  ++Gg+y l+l ++ lr++
  gi|70606283|ref|YP_255153.1|  15 LSIAAPPGPINAMMANES-TRSFLNGIAVGAGAMTADFVFFWITYL-FKSIIP-SNILF-VFYIVGGVYMLYLSYSVLRAK 91 
                                   58999*************.************************999.888888.55555.6689999************98 PP

                          LysE  82 kekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaarls 162
                                     +++            ++ kgl + + NP+ i +wl ++ ++l+      + ++l+ a g+++++liw+    fl +r+ 
  gi|70606283|ref|YP_255153.1|  92 QVSSS---------TGGSYVKGLSVAIVNPYQISWWLTFGISMLN------QFSVLV-APGFFIGILIWILAFPFLINRIG 156
                                   76652.........3468999************************......344444.48999999999988888887776 PP

                          LysE 163 rrlsskkvlriinvvvgvlligfavkllle 192
                                   +r  +     +++++   +l++f++++l++
  gi|70606283|ref|YP_255153.1| 157 QRYVK-----YVKIFSFTILLIFGAYILYQ 181
                                   55443.....45555666677777777765 PP

>> RALF  Rapid ALkalinization Factor (RALF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         3   1.8e+04       4      14 ..      27      37 ..      25      39 .. 0.67
   2 ?   11.6   0.0   7.3e-05      0.43      20      54 ..      82     114 ..      78     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3
                          RALF  4 lmeseisrrvl 14
                                  +m+ e++r +l
  gi|70606283|ref|YP_255153.1| 27 MMANESTRSFL 37
                                  67777777666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                          RALF  20 YisygaLrrnqvpCnkrrgasyynckprkpanpys 54 
                                   Y+sy +Lr+ qv ++   g sy +    + +npy+
  gi|70606283|ref|YP_255153.1|  82 YLSYSVLRAKQVSSS--TGGSYVKGLSVAIVNPYQ 114
                                   *********999999..9999*9866889999997 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.8     1e-05     0.061     117     204 ..       7      94 ..       3      96 .. 0.89
   2 ?   -2.0   1.1      0.35   2.1e+03      89     164 ..     139     145 ..     107     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                       DUF1129 117 llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvvryyl 197
                                   l +++++Gl +      ++  + +++ +++++ +++ ++++ + +v+f+++ l+ + i   +  + +i+ gv ++ + y +
  gi|70606283|ref|YP_255153.1|   7 LATGILMGLSIAAPPGPINAMMANESTRSFLNGIAVGAGAMTADFVFFWITYLFKSIIPSNILFVFYIVGGVYMLYLSYSV 87 
                                   67899999999999999998899*************************************************999888876 PP

                       DUF1129 198 kkkyniq 204
                                    +  ++ 
  gi|70606283|ref|YP_255153.1|  88 LRAKQVS 94 
                                   6655665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.35
                       DUF1129  89 lalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlf 164
                                   ++                                                                     +l+++
  gi|70606283|ref|YP_255153.1| 139 IG---------------------------------------------------------------------ILIWI 145
                                   22.....................................................................22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1236.17
//
Query:       gi|70606284|ref|YP_255154.1|  [L=162]
Description: SRSR-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-19   67.5   6.9      1e-09   38.0   0.1    3.5  4  HTH_38           Helix-turn-helix domain
    2.1e-14   53.3   8.8    0.00096   19.2   0.1    3.2  3  HTH_7            Helix-turn-helix domain of resolvase
    2.9e-13   49.2   1.2     0.0005   19.8   0.0    3.2  3  HTH_23           Homeodomain-like domain
    2.1e-09   36.8   1.8     0.0022   17.5   0.0    3.4  3  GerE             Bacterial regulatory proteins, luxR family
    7.6e-09   35.1   1.5     0.0072   16.0   0.0    3.2  3  Sigma70_r4_2     Sigma-70, region 4
    1.5e-08   35.2   0.5      0.001   19.5   0.0    2.2  2  GcrA             GcrA cell cycle regulator
    4.5e-08   33.0   0.1      0.038   14.0   0.0    3.3  3  HTH_29           Winged helix-turn helix
    1.3e-07   31.6   0.1       0.03   14.4   0.0    2.6  2  HTH_28           Helix-turn-helix domain
    6.2e-07   28.7   0.0    0.00043   19.6   0.0    2.7  3  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    3.6e-06   26.4   0.7       0.23   11.1   0.0    3.5  3  HTH_24           Winged helix-turn-helix DNA-binding
    6.9e-06   25.6   1.9     0.0039   16.8   0.1    2.5  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
    2.5e-05   23.7   0.8      0.035   13.6   0.0    3.2  3  Sigma70_r4       Sigma-70, region 4
    2.5e-05   24.1   0.1       0.61   10.0   0.0    3.2  3  Terminase_5      Putative ATPase subunit of terminase (gpP-li
    4.2e-05   23.1   2.5      0.068   12.8   0.0    3.2  3  HTH_50           Helix-turn-helix domain
    4.3e-05   22.7   3.8     0.0034   16.4   0.8    2.2  2  TnsD             Tn7-like transposition protein D
    0.00015   21.5   1.3       0.26   11.1   0.0    3.4  3  HTH_10           HTH DNA binding domain
    0.00035   20.4   3.3       0.44   10.5   0.1    2.9  3  Phage_antitermQ  Phage antitermination protein Q
    0.00061   20.2   1.4       0.26   11.8   0.3    2.9  2  HTH_40           Helix-turn-helix domain
    0.00063   20.1   1.2        1.7    9.1   0.0    3.0  3  Recombinase      Recombinase
     0.0011   18.5   0.1          1    9.0   0.0    2.5  2  HTH_Tnp_IS1      InsA C-terminal domain
     0.0026   17.8   3.4       0.61   10.2   0.4    3.3  3  HTH_3            Helix-turn-helix
     0.0028   17.5   0.7        1.2    9.0   0.0    2.8  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0035   17.3   1.4        5.4    7.1   0.1    3.7  4  DUF3791          Protein of unknown function (DUF3791)
     0.0076   16.5   0.1       0.33   11.3   0.0    2.6  2  HTH_Tnp_1        Transposase
     0.0088   16.1   0.3        2.9    8.0   0.0    3.0  3  HTH_35           Winged helix-turn-helix DNA-binding
     0.0091   15.9   0.2      0.056   13.4   0.1    2.2  3  PAX              'Paired box' domain
     0.0093   16.0   2.1      0.021   14.9   0.7    2.0  2  DUF2089          Protein of unknown function (DUF2089)
  ------ inclusion threshold ------
      0.011   16.3   2.8          1   10.0   0.0    2.9  3  Mga              Mga helix-turn-helix domain
      0.012   15.4   0.1        3.1    7.7   0.0    2.8  3  DUF433           Protein of unknown function (DUF433)
      0.014   15.2   0.4         15    5.6   0.0    3.6  3  HTH_5            Bacterial regulatory protein, arsR family
      0.015   15.4   0.1        2.1    8.6   0.0    2.7  2  Death            Death domain
      0.017   15.4   0.3        1.7    9.1   0.0    2.9  3  WYL_3            WYL domain
      0.023   14.6   0.5       0.99    9.3   0.1    2.5  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
      0.032   14.4   1.8        1.5    9.0   0.1    2.2  2  MRP-L20          Mitochondrial ribosomal protein subunit L20
      0.036   14.4   0.6        3.4    8.0   0.0    2.9  3  ANT              Phage antirepressor protein KilAC domain
      0.042   14.1   0.9      0.057   13.7   0.9    1.3  1  DUF3102          Protein of unknown function (DUF3102)
      0.044   13.6   0.0        1.5    8.7   0.0    2.9  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.054   13.5   0.5        6.7    6.8   0.0    3.2  3  KorB             KorB domain
      0.062   13.3   0.6        2.3    8.3   0.0    2.6  2  RWP-RK           RWP-RK domain
      0.062   13.1   0.3         11    6.0   0.0    3.6  3  Homeodomain      Homeodomain
      0.068   13.0   0.4        1.4    8.8   0.2    2.4  2  Sigma70_ECF      ECF sigma factor
      0.081   13.4   5.8       0.11   13.0   5.8    1.2  1  PIN_12           PIN domain
      0.086   12.9   0.7        2.8    8.0   0.0    2.9  3  Phage_terminase  Phage terminase small subunit
       0.11   12.4   0.1         27    4.7   0.0    2.9  3  MarR_2           MarR family
       0.11   12.5   3.5         39    4.3   0.1    3.5  3  HTH_36           Helix-turn-helix domain
       0.17   12.5   1.7        1.2    9.7   1.7    2.1  1  NPA              Nematode polyprotein allergen ABA-1
          3    8.2  11.1        2.2    8.6   0.1    3.6  3  NUMOD1           NUMOD1 domain


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   2.1e-07     8e-05       5      35 ..      22      52 ..      19      61 .. 0.82
   2 ?   -1.7   0.0       6.7   2.6e+03      15      25 ..      57      67 ..      53      70 .. 0.88
   3 !    9.7   0.4    0.0019      0.72      15      43 ..      77     105 ..      66     106 .. 0.87
   4 !   38.0   0.1   2.7e-12     1e-09       1      43 [.     111     153 ..     111     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-07
                        HTH_38  5 LsleeReeIerllaeGlslreIArrLgrsps 35
                                  ++ +   e+ rl+++G+s++ IAr+Lg s +
  gi|70606284|ref|YP_255154.1| 22 MTEASVDELKRLYNQGKSMKSIARELGISYT 52
                                  6666777999*****************9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.7
                        HTH_38 15 rllaeGlslre 25
                                  +ll++G ++r+
  gi|70606284|ref|YP_255154.1| 57 ILLNAGVNIRK 67
                                  68999999996 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0019
                        HTH_38  15 rllaeGlslreIArrLgrspsTIsRElkR 43 
                                    l ++G+s r I + L+ s s+  R lk+
  gi|70606284|ref|YP_255154.1|  77 ELAKQGHSARYISKMLKISESSALRILKK 105
                                   4779******************9999997 PP

  == domain 4  score: 38.0 bits;  conditional E-value: 2.7e-12
                        HTH_38   1 kykhLsleeReeIerllaeGlslreIArrLgrspsTIsRElkR 43 
                                   k k+Ls e+ ++I  ++ +G+s+++IA+ Lg+s++ + ++lkR
  gi|70606284|ref|YP_255154.1| 111 KIKKLSDEDINKIKEMYLKGESIYRIAKTLGKSTNLVVYHLKR 153
                                   579***************************************9 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.5e-06   0.00096       8      34 ..      24      50 ..      19      55 .. 0.88
   2 !   19.1   0.7   2.6e-06   0.00099       2      44 ..      66     105 ..      66     106 .. 0.96
   3 !   19.1   0.3   2.6e-06   0.00099       1      32 [.     109     141 ..     109     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-06
                                  HHHHGGGGSSTTTT--STTTSSSS--- CS
                         HTH_7  8 kndinrvvkLleeGisiskIAkevnis 34
                                  + + +++++L+++G s + IA+e++is
  gi|70606284|ref|YP_255154.1| 24 EASVDELKRLYNQGKSMKSIARELGIS 50
                                  55789*********************9 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.6e-06
                                   ---SS-HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS-- CS
                         HTH_7   2 RpsklskndinrvvkLleeGisiskIAkevnisRsTvYRylad 44 
                                   R++ +++   ++vv+L ++G+s++ I k ++is s+  R+l +
  gi|70606284|ref|YP_255154.1|  66 RKKRINE---QEVVELAKQGHSARYISKMLKISESSALRILKK 105
                                   99*****...9****************************9976 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 2.6e-06
                                   S--.-SS-HHHHGGGGSSTTTT--STTTSSSS- CS
                         HTH_7   1 GRp.sklskndinrvvkLleeGisiskIAkevn 32 
                                   GR+ +kls++din +++++ +G+si  IAk ++
  gi|70606284|ref|YP_255154.1| 109 GRKiKKLSDEDINKIKEMYLKGESIYRIAKTLG 141
                                   566589***********************9765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.3e-06    0.0005      12      38 ..      32      58 ..      29      61 .. 0.91
   2 !   17.1   0.3   8.9e-06    0.0034       5      41 ..      70     106 ..      66     115 .. 0.88
   3 !    9.7   0.0     0.002      0.76      12      33 ..     125     146 ..     122     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.3e-06
                        HTH_23 12 lllaeGlsvreIAreLgvsrrTvyrwl 38
                                  +l+ +G+s + IAreLg+s+  v+++l
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKSMKSIARELGISYTKVRNIL 58
                                  67889*******************996 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.9e-06
                        HTH_23   5 reRlrillllaeGlsvreIAreLgvsrrTvyrwlkry 41 
                                   ++ ++++ l+++G+s r I+++L +s++   r+lk+ 
  gi|70606284|ref|YP_255154.1|  70 INEQEVVELAKQGHSARYISKMLKISESSALRILKKH 106
                                   556789*****************************85 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.002
                        HTH_23  12 lllaeGlsvreIAreLgvsrrT 33 
                                    ++++G s+ +IA+ Lg s + 
  gi|70606284|ref|YP_255154.1| 125 EMYLKGESIYRIAKTLGKSTNL 146
                                   6999**************9875 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.9e-06    0.0022      13      36 ..      33      56 ..      30      61 .. 0.86
   2 !    9.7   0.1    0.0016      0.62       7      33 ..      72      98 ..      71     118 .. 0.91
   3 !    7.2   0.0    0.0093       3.6      12      41 ..     125     154 ..     122     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-06
                                  HHCTTS-HHHHHHHHTS-HHHHHH CS
                          GerE 13 llaeGksnkeIAeelniSekTVkv 36
                                  l  +Gks+k IA+el+iS++ V++
  gi|70606284|ref|YP_255154.1| 33 LYNQGKSMKSIARELGISYTKVRN 56
                                  5569***************98876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                                  HHHHHHHHCTTS-HHHHHHHHTS-HHH CS
                          GerE  7 ErevLrllaeGksnkeIAeelniSekT 33
                                  E+ev +l  +G s   I++ l iSe +
  gi|70606284|ref|YP_255154.1| 72 EQEVVELAKQGHSARYISKMLKISESS 98
                                  99**********************975 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0093
                                   HHHCTTS-HHHHHHHHTS-HHHHHHHHHHH CS
                          GerE  12 rllaeGksnkeIAeelniSekTVkvhksni 41 
                                   ++  +G+s   IA+ l+ S++ V +h++++
  gi|70606284|ref|YP_255154.1| 125 EMYLKGESIYRIAKTLGKSTNLVVYHLKRL 154
                                   68899*********************9985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.9e-05    0.0072      23      47 ..      34      58 ..      30      61 .. 0.88
   2 !    7.4   0.1    0.0092       3.5      15      42 ..      72      98 ..      70     101 .. 0.90
   3 !    9.6   0.0    0.0018       0.7      21      49 ..     126     153 ..     107     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-05
                                  HTS---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 23 yleglsykEIAellgisegtVksrl 47
                                  y +g+s k IA++lgis + V++ l
  gi|70606284|ref|YP_255154.1| 34 YNQGKSMKSIARELGISYTKVRNIL 58
                                  669******************9865 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0092
                                  HHHHHHHHHTS---HHHHHHHHT--HHH CS
                  Sigma70_r4_2 15 qreifllryleglsykEIAellgisegt 42
                                  ++e+++l   +g+s + I+++l+ise++
  gi|70606284|ref|YP_255154.1| 72 EQEVVELA-KQGHSARYISKMLKISESS 98
                                  78999**5.5****************97 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0018
                                   HHHTS---HHHHHHHHT--HHHHHHHHHH CS
                  Sigma70_r4_2  21 lryleglsykEIAellgisegtVksrlsR 49 
                                   + yl+g s+  IA+ lg s + V ++l+R
  gi|70606284|ref|YP_255154.1| 126 M-YLKGESIYRIAKTLGKSTNLVVYHLKR 153
                                   4.9********************999998 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2    0.0001     0.038       4      38 ..      23      56 ..      21     114 .. 0.69
   2 !   19.5   0.0   2.7e-06     0.001       4      49 ..     116     160 ..     113     162 .] 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0001
                          GcrA  4 tdErvelLkklwleGlSasqiaaqlggvsRnAViG 38
                                  t+  v++Lk+l+++G S++ ia++lg +s   V  
  gi|70606284|ref|YP_255154.1| 23 TEASVDELKRLYNQGKSMKSIARELG-ISYTKVRN 56
                                  67789*********************.55444444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.7e-06
                          GcrA   4 tdErvelLkklwleGlSasqiaaqlggvsRnAViGkvhRLglsgra 49 
                                   +dE ++++k+++l+G S+  ia+ lg  s n V+ +++RLg+ +r+
  gi|70606284|ref|YP_255154.1| 116 SDEDINKIKEMYLKGESIYRIAKTLG-KSTNLVVYHLKRLGVYKRG 160
                                   79************************.899***********98876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   9.9e-05     0.038       6      33 ..      32      58 ..      31      60 .. 0.92
   2 !   12.8   0.0   0.00024     0.091       3      40 ..      74     110 ..      73     120 .. 0.88
   3 ?    2.3   0.0      0.46   1.8e+02       8      26 ..     127     144 ..     124     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.9e-05
                        HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwl 33
                                  +l+++G s  + iA+ lg+s+++v+++l
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKS-MKSIARELGISYTKVRNIL 58
                                  68999*98.****************987 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00024
                        HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40 
                                   +++ l+++G+s  + i k+l +s+++  r+lk  + g+
  gi|70606284|ref|YP_255154.1|  74 EVVELAKQGHS-ARYISKMLKISESSALRILKKHNVGR 110
                                   6899******8.*******************9866665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.46
                        HTH_29   8 laeGvstvsqiAkllglsr 26 
                                   + +G+s + +iAk lg s 
  gi|70606284|ref|YP_255154.1| 127 YLKGES-IYRIAKTLGKST 144
                                   568998.*********986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     8e-05      0.03       7      31 ..      32      56 ..      30      60 .. 0.90
   2 !   14.4   0.0   7.9e-05      0.03       4      35 ..      74     105 ..      73     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-05
                        HTH_28  7 kllaaGhsvreaArelgisrrtvyr 31
                                  +l+ +G+s + +Arelgis++ v+ 
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKSMKSIARELGISYTKVRN 56
                                  57889****************9996 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.9e-05
                        HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWikr 35 
                                   e+++l+++Ghs+r +++ l is+++  r +k+
  gi|70606284|ref|YP_255154.1|  74 EVVELAKQGHSARYISKMLKISESSALRILKK 105
                                   89**********************99998886 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-06   0.00043      27      49 ..      36      59 ..      30      62 .. 0.86
   2 ?    6.3   0.0     0.016       6.3      17      51 ..      72     106 ..      72     107 .. 0.92
   3 ?   -1.9   0.0       6.2   2.4e+03      29      44 ..     132     147 ..     127     148 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                  HTH_Tnp_ISL3 27 s.rsvkavArqlgvSwtTVwrild 49
                                    +s+k++Ar+lg+S t V++il 
  gi|70606284|ref|YP_255154.1| 36 QgKSMKSIARELGISYTKVRNILL 59
                                  447*******************97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                  HTH_Tnp_ISL3  17 eayilelllesrsvkavArqlgvSwtTVwrildry 51 
                                   e+ ++el++++ s + ++++l +S+++  ril+ +
  gi|70606284|ref|YP_255154.1|  72 EQEVVELAKQGHSARYISKMLKISESSALRILKKH 106
                                   688999999999*******************9976 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.2
                  HTH_Tnp_ISL3  29 svkavArqlgvSwtTV 44 
                                   s+  +A+ lg S++ V
  gi|70606284|ref|YP_255154.1| 132 SIYRIAKTLGKSTNLV 147
                                   5556788888887766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00059      0.23      15      36 ..      35      56 ..      28      60 .. 0.84
   2 ?    6.8   0.1     0.012       4.7      16      40 ..      81     105 ..      77     105 .. 0.89
   3 ?    5.1   0.0     0.043        16      23      41 ..     136     154 ..     134     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00059
                        HTH_24 15 nprisqreLAerlglSpstvnr 36
                                  n + s++ +A++lg+S + v+ 
  gi|70606284|ref|YP_255154.1| 35 NQGKSMKSIARELGISYTKVRN 56
                                  8889************999976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                        HTH_24  16 prisqreLAerlglSpstvnrrlkr 40 
                                    + s r ++++l +S s  +r lk+
  gi|70606284|ref|YP_255154.1|  81 QGHSARYISKMLKISESSALRILKK 105
                                   5788899***************997 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.043
                        HTH_24  23 LAerlglSpstvnrrlkrL 41 
                                   +A+ lg S + v ++lkrL
  gi|70606284|ref|YP_255154.1| 136 IAKTLGKSTNLVVYHLKRL 154
                                   9*****************9 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     1e-05    0.0039      17      44 ..      32      59 ..      29      68 .. 0.91
   2 !    7.9   0.3    0.0061       2.3      14      46 ..      74     106 ..      72     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                                  HHHHCTT-HHHHHHHHT--CCHHHHHHH CS
                      CENP-B_N 17 qrleegeSkaelarrfnvpestlsdilk 44
                                  +++ +g+S +++ar++++  + +++il 
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKSMKSIARELGISYTKVRNILL 59
                                  6799**********************85 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0061
                                   HHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH CS
                      CENP-B_N  14 evIqrleegeSkaelarrfnvpestlsdilknK 46 
                                   ev+ +  +g S + + +++ + es + +ilk+ 
  gi|70606284|ref|YP_255154.1|  74 EVVELAKQGHSARYISKMLKISESSALRILKKH 106
                                   67778889**********************985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   9.3e-05     0.035      15      46 ..      32      63 ..      28      67 .. 0.84
   2 ?    4.7   0.1     0.058        22       9      42 ..      72     104 ..      71     106 .. 0.80
   3 ?    2.3   0.0      0.31   1.2e+02       4      34 ..     114     144 ..     112     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                                  HHHTTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Sigma70_r4 15 lrfgeglTleEIgerlgiSrerVrqiekrAlr 46
                                    + +g +++ I+++lgiS   Vr i+ +A  
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKSMKSIARELGISYTKVRNILLNAGV 63
                                  56899********************9877755 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.058
                                   HHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4   9 erevlelrfgeglTleEIgerlgiSrerVrqiek 42 
                                   e+ev+el   +g++   I+++l iS++ + +i+k
  gi|70606284|ref|YP_255154.1|  72 EQEVVELAK-QGHSARYISKMLKISESSALRILK 104
                                   788888886.5668999*********98877776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.31
                                   HS-HHHHHHHHHHHTTT--HHHHHHHHTS-H CS
                    Sigma70_r4   4 sLpererevlelrfgeglTleEIgerlgiSr 34 
                                   +L++++ + ++  +++g +   I+++lg S 
  gi|70606284|ref|YP_255154.1| 114 KLSDEDINKIKEMYLKGESIYRIAKTLGKST 144
                                   66777777788899999999********985 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0016      0.61       8      28 ..      32      52 ..      31      56 .. 0.86
   2 ?    1.8   0.0      0.58   2.2e+02      12      28 ..      81      97 ..      73     101 .. 0.88
   3 !    8.3   0.0    0.0053         2       7      36 ..     124     153 ..     120     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                   Terminase_5  8 lLYwqGyrvaeIAeelglkea 28
                                   LY qG + ++IA+elg++  
  gi|70606284|ref|YP_255154.1| 32 RLYNQGKSMKSIARELGISYT 52
                                  69***************9854 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.58
                   Terminase_5 12 qGyrvaeIAeelglkea 28
                                  qG + + I+++l ++e 
  gi|70606284|ref|YP_255154.1| 81 QGHSARYISKMLKISES 97
                                  8999*********9975 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0053
                   Terminase_5   7 rlLYwqGyrvaeIAeelglkeatVysWkkr 36 
                                   +++Y++G ++ +IA+ lg + + V +  kr
  gi|70606284|ref|YP_255154.1| 124 KEMYLKGESIYRIAKTLGKSTNLVVYHLKR 153
                                   589*****************8888776666 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00018     0.068      16      42 ..      30      56 ..      23      59 .. 0.91
   2 ?    3.7   0.1      0.12        46      24      47 ..      83     106 ..      71     109 .. 0.86
   3 ?    5.3   0.1     0.038        15      16      48 ..     123     155 ..     114     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                        HTH_50 16 ikkayekYpStRklAkrLGvShtaian 42
                                  +k++y++ +S+  +A+ LG+S t + n
  gi|70606284|ref|YP_255154.1| 30 LKRLYNQGKSMKSIARELGISYTKVRN 56
                                  799******************998755 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                        HTH_50  24 pStRklAkrLGvShtaianklrkY 47 
                                    S+R + k L +S +  ++ l+k 
  gi|70606284|ref|YP_255154.1|  83 HSARYISKMLKISESSALRILKKH 106
                                   69*************999999886 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.038
                        HTH_50  16 ikkayekYpStRklAkrLGvShtaianklrkYg 48 
                                   ik++y k  S+  +Ak LG S   ++  l++ g
  gi|70606284|ref|YP_255154.1| 123 IKEMYLKGESIYRIAKTLGKSTNLVVYHLKRLG 155
                                   788899999************999999999977 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.8   8.8e-06    0.0034     190     248 ..      29      86 ..      24     105 .. 0.78
   2 !    8.1   0.4    0.0031       1.2     162     224 ..      87     155 ..      84     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.8e-06
                          TnsD 190 rlkeLveeeglslkeiAkelgvdiktVlryakklgllkekkkqkkesrelsskdrekkr 248
                                   +lk+L++ +g+s+k iA+elg++  +V+ ++ + g + +kk  ++++ ++ +k+  ++r
  gi|70606284|ref|YP_255154.1|  29 ELKRLYN-QGKSMKSIARELGISYTKVRNILLNAGVNIRKKRINEQEVVELAKQGHSAR 86 
                                   6999***.***************************999999999888875555533333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0031
                          TnsD 162 ytrsgedlseedayrisrikkfGivweerlkeLvee..........eglslkeiAkelgvdiktVlryakklg 224
                                   y+ +  + se++a ri +  ++G    +++k+L++e          +g s+  iAk+lg +++ V+ ++k+lg
  gi|70606284|ref|YP_255154.1|  87 YISKMLKISESSALRILKKHNVG----RKIKKLSDEdinkikemylKGESIYRIAKTLGKSTNLVVYHLKRLG 155
                                   66666777888888888888888....7788888777777888899999999*****************9997 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00069      0.26      24      47 ..      38      61 ..      34      67 .. 0.86
   2 ?    3.9   0.1      0.13        48      25      46 ..      84     105 ..      79     112 .. 0.89
   3 ?    3.7   0.0      0.15        56      26      46 ..     133     153 ..     128     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00069
                        HTH_10 24 vtlkeLAkelGIskstlsehLrka 47
                                   ++k++A elGIs + + ++L +a
  gi|70606284|ref|YP_255154.1| 38 KSMKSIARELGISYTKVRNILLNA 61
                                  6789***************99988 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                        HTH_10  25 tlkeLAkelGIskstlsehLrk 46 
                                   +++ ++k l Is+s+++ +L+k
  gi|70606284|ref|YP_255154.1|  84 SARYISKMLKISESSALRILKK 105
                                   57789*************9997 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.15
                        HTH_10  26 lkeLAkelGIskstlsehLrk 46 
                                   +  +Ak+lG s + + +hL++
  gi|70606284|ref|YP_255154.1| 133 IYRIAKTLGKSTNLVVYHLKR 153
                                   5679***************97 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0012      0.44      67     103 ..      26      62 ..      15      73 .. 0.86
   2 ?    1.1   0.1      0.91   3.5e+02      77      95 ..      81      99 ..      65     108 .. 0.66
   3 !    8.3   0.1    0.0056       2.1      59      99 ..     111     151 ..     107     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
               Phage_antitermQ  67 elellvdyYvfgvskraiarklkisekevrkklqkae 103
                                    ++ l + Y  g+s ++iar+l+is ++vr+ l +a 
  gi|70606284|ref|YP_255154.1|  26 SVDELKRLYNQGKSMKSIARELGISYTKVRNILLNAG 62 
                                   56778889**********************9998875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.91
               Phage_antitermQ 77 fgvskraiarklkisekev 95
                                   g+s r i++ lkise+  
  gi|70606284|ref|YP_255154.1| 81 QGHSARYISKMLKISESSA 99
                                  4666667777777666654 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0056
               Phage_antitermQ  59 rLkkkrpeelellvdyYvfgvskraiarklkisekevrkkl 99 
                                   ++kk   e+++ + + Y++g s  +ia+ l+ s + v  +l
  gi|70606284|ref|YP_255154.1| 111 KIKKLSDEDINKIKEMYLKGESIYRIAKTLGKSTNLVVYHL 151
                                   67888899***********************9999886655 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3   0.00068      0.26       6      50 ..      31      77 ..      26     120 .. 0.69
   2 ?    6.2   0.0     0.037        14       7      35 ..     125     153 ..     120     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00068
                        HTH_40  6 lelleeglsieeIAkerglkesTIegHLaeliee..geeidlerlvs 50
                                   +l+++g+s++ IA+e g++ + + + L+++  +  +++i+ +++v+
  gi|70606284|ref|YP_255154.1| 31 KRLYNQGKSMKSIARELGISYTKVRNILLNAGVNirKKRINEQEVVE 77
                                  689******************99999998876552223344455553 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.037
                        HTH_40   7 elleeglsieeIAkerglkesTIegHLae 35 
                                   e++ +g si  IAk  g +++ ++ HL +
  gi|70606284|ref|YP_255154.1| 125 EMYLKGESIYRIAKTLGKSTNLVVYHLKR 153
                                   89*********************999966 PP

>> Recombinase  Recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0092       3.5       7      32 ..      27      52 ..      23      61 .. 0.83
   2 ?   -0.1   0.0       3.2   1.2e+03       9      29 ..      74      94 ..      65     107 .. 0.81
   3 !    9.1   0.0    0.0044       1.7       7      28 ..     120     141 ..     117     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0092
                   Recombinase  7 vrrifelylegkslksiaryLneegi 32
                                  v ++ +ly +gks+ksiar+L   + 
  gi|70606284|ref|YP_255154.1| 27 VDELKRLYNQGKSMKSIARELGISYT 52
                                  677788999***********987665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.2
                   Recombinase  9 rifelylegkslksiaryLne 29
                                  +++el+ +g+s++ i + L+ 
  gi|70606284|ref|YP_255154.1| 74 EVVELAKQGHSARYISKMLKI 94
                                  577777789999999888876 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0044
                   Recombinase   7 vrrifelylegkslksiaryLn 28 
                                   +++i e+yl+g s+ +ia++L 
  gi|70606284|ref|YP_255154.1| 120 INKIKEMYLKGESIYRIAKTLG 141
                                   7899***************996 PP

>> HTH_Tnp_IS1  InsA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0026         1      12      44 ..      73     105 ..      65     107 .. 0.91
   2 ?    7.0   0.0     0.012       4.5      12      43 ..     121     152 ..     120     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                   HTH_Tnp_IS1  12 ekIvemAfNGaGvraTARtlkvGiNTviRtLKn 44 
                                   +++ve+A  G  +r+  ++lk+     +R LK 
  gi|70606284|ref|YP_255154.1|  73 QEVVELAKQGHSARYISKMLKISESSALRILKK 105
                                   789********************9999999995 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                   HTH_Tnp_IS1  12 ekIvemAfNGaGvraTARtlkvGiNTviRtLK 43 
                                   +kI em   G      A+tl+   N v+ +LK
  gi|70606284|ref|YP_255154.1| 121 NKIKEMYLKGESIYRIAKTLGKSTNLVVYHLK 152
                                   5899***************************9 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.4    0.0016      0.61       4      31 ..      31      59 ..      29      80 .. 0.79
   2 ?    4.1   0.1      0.12        47       7      30 ..      80     103 ..      73     116 .. 0.85
   3 ?    3.0   0.0      0.28   1.1e+02      39      52 ..     131     144 ..     126     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                                  HHH.HTTHHHHHHHHHHTSSHHHHHHHHT CS
                         HTH_3  4 lRk.qlglsqeeLAeklGvsrstisriEn 31
                                  +R+  +g s++ +A++lG+s++ +++i  
  gi|70606284|ref|YP_255154.1| 31 KRLyNQGKSMKSIARELGISYTKVRNILL 59
                                  677789***************98888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                                   HTTHHHHHHHHHHTSSHHHHHHHH CS
                         HTH_3   7 qlglsqeeLAeklGvsrstisriE 30 
                                   ++g s ++++++l +s s+  ri 
  gi|70606284|ref|YP_255154.1|  80 KQGHSARYISKMLKISESSALRIL 103
                                   899999999999999999877665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHTSEH CS
                         HTH_3  39 etlkklakaLgvsl 52 
                                   e ++++ak+Lg s+
  gi|70606284|ref|YP_255154.1| 131 ESIYRIAKTLGKST 144
                                   7799*******987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0032       1.2      19      43 ..      34      58 ..      30      62 .. 0.88
   2 ?    5.6   0.1     0.037        14      19      45 ..      79     105 ..      75     105 .. 0.87
   3 ?   -1.6   0.0       6.9   2.6e+03      24      43 ..     132     151 ..     126     156 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0032
                                  HHCCCHHCHHCCCTTSSCHCHHHHH CS
                          TrmB 19 klgpatadeiaeelgvprskvYevL 43
                                   ++ ++++ ia+elg++++kv ++L
  gi|70606284|ref|YP_255154.1| 34 YNQGKSMKSIARELGISYTKVRNIL 58
                                  57788999*************9998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.037
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                          TrmB  19 klgpatadeiaeelgvprskvYevLrs 45 
                                   +++  +a+ i+++l++++s++ ++L++
  gi|70606284|ref|YP_255154.1|  79 AKQGHSARYISKMLKISESSALRILKK 105
                                   56677899*************999986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.9
                                   HHCHHCCCTTSSCHCHHHHH CS
                          TrmB  24 tadeiaeelgvprskvYevL 43 
                                   +++ ia+ lg + + v   L
  gi|70606284|ref|YP_255154.1| 132 SIYRIAKTLGKSTNLVVYHL 151
                                   56677777777666555555 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.08        30       8      29 ..      41      62 ..      39      64 .. 0.86
   2 ?   -0.6   0.0       3.6   1.4e+03      12      34 ..      66      88 ..      65      91 .. 0.78
   3 ?    7.1   0.1     0.014       5.4      11      35 ..      89     113 ..      86     120 .. 0.87
   4 ?    1.6   0.0      0.75   2.8e+02       7      31 ..     133     157 ..     132     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.08
                       DUF3791  8 eeyarklglsgkevykllkksg 29
                                   + ar+lg+s ++v ++l + g
  gi|70606284|ref|YP_255154.1| 41 KSIARELGISYTKVRNILLNAG 62
                                  689**************97665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.6
                       DUF3791 12 rklglsgkevykllkksgvldyl 34
                                  rk+ ++ +ev++l k+ +  +y+
  gi|70606284|ref|YP_255154.1| 66 RKKRINEQEVVELAKQGHSARYI 88
                                  68999999*99998876666776 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.014
                       DUF3791  11 arklglsgkevykllkksgvldyli 35 
                                   ++ l++s + ++++lkk++v + ++
  gi|70606284|ref|YP_255154.1|  89 SKMLKISESSALRILKKHNVGRKIK 113
                                   57799**************988776 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.75
                       DUF3791   7 Ieeyarklglsgkevykllkksgvl 31 
                                   I   a++lg s++ v+  lk+ gv+
  gi|70606284|ref|YP_255154.1| 133 IYRIAKTLGKSTNLVVYHLKRLGVY 157
                                   55789**************999996 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00088      0.33      17      38 ..      31      52 ..      24      56 .. 0.85
   2 ?    2.3   0.0      0.54   2.1e+02      16      38 ..     123     145 ..     109     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00088
                     HTH_Tnp_1 17 reslepgksvsevArrhgvspn 38
                                  ++ +++gks++++Ar++g+s+ 
  gi|70606284|ref|YP_255154.1| 31 KRLYNQGKSMKSIARELGISYT 52
                                  55679**************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.54
                     HTH_Tnp_1  16 VreslepgksvsevArrhgvspn 38 
                                   ++e +  g s+ ++A+ +g s n
  gi|70606284|ref|YP_255154.1| 123 IKEMYLKGESIYRIAKTLGKSTN 145
                                   689999**********9997665 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0076       2.9      11      36 ..      33      58 ..      28      67 .. 0.89
   2 ?    3.5   0.1      0.19        73      10      40 ..      77     107 ..      71     112 .. 0.89
   3 ?    1.0   0.0       1.2   4.4e+02      37      54 ..     124     143 ..     114     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0076
                        HTH_35 11 LrkrgttLaalsreaglssstlsnal 36
                                  L  +g ++++++re+g+s  +++n+l
  gi|70606284|ref|YP_255154.1| 33 LYNQGKSMKSIARELGISYTKVRNIL 58
                                  66789******************998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                        HTH_35  10 aLrkrgttLaalsreaglssstlsnaltrpw 40 
                                   +L k+g + + +s+ + +s+s+  ++l++++
  gi|70606284|ref|YP_255154.1|  77 ELAKQGHSARYISKMLKISESSALRILKKHN 107
                                   899******************9999999987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.2
                        HTH_35  37 trpwpkgEal..IAeaLgvp 54 
                                   +  + kgE +  IA++Lg +
  gi|70606284|ref|YP_255154.1| 124 KEMYLKGESIyrIAKTLGKS 143
                                   55677888654499999876 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.7   1.4e+03      29      54 ..      33      58 ..      20      63 .. 0.75
   2 !   13.4   0.1   0.00015     0.056      23      60 ..      72     109 ..      52     116 .. 0.84
   3 ?   -1.2   0.0       4.8   1.8e+03      19      48 ..     116     145 ..     109     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.7
                           PAX 29 lahsgvrpcvisrqlrvshgcvskil 54
                                  l ++g     i+r l +s   v +il
  gi|70606284|ref|YP_255154.1| 33 LYNQGKSMKSIARELGISYTKVRNIL 58
                                  45666677788888888888888877 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                           PAX  23 rqkivelahsgvrpcvisrqlrvshgcvskilgryqet 60 
                                    q++vela++g     is++l++s+    +il +++  
  gi|70606284|ref|YP_255154.1|  72 EQEVVELAKQGHSARYISKMLKISESSALRILKKHNVG 109
                                   5789***************************9987655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.8
                           PAX  19 pdsirqkivelahsgvrpcvisrqlrvshg 48 
                                    d+  +ki e+  +g     i++ l  s  
  gi|70606284|ref|YP_255154.1| 116 SDEDINKIKEMYLKGESIYRIAKTLGKSTN 145
                                   444445666666666666666666555554 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   5.4e-05     0.021      46     106 ..      34      96 ..       2     104 .. 0.63
   2 ?    0.8   0.1       1.3     5e+02      29      66 ..     110     147 ..      91     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.4e-05
                       DUF2089  46 ikarGnlkevekelgisYpTvrnrldeileaLgyeeeeeee.ee....eeerkeileklekgeisv 106
                                    ++  ++k++++elgisY+ vrn l +   ++  +  +e+e  e     ++ + i ++l+   is 
  gi|70606284|ref|YP_255154.1|  34 YNQGKSMKSIARELGISYTKVRNILLNAGVNIRKKRINEQEvVElakqGHSARYISKMLK---ISE 96 
                                   4444579****************9988888887777766442234443333444444443...444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.3
                       DUF2089  29 sefarLskeqlefvelfikarGnlkevekelgisYpTv 66 
                                    ++++Ls+e+++ ++    +  ++ +++k+lg s + v
  gi|70606284|ref|YP_255154.1| 110 RKIKKLSDEDINKIKEMYLKGESIYRIAKTLGKSTNLV 147
                                   47888999988877655555557888888888776655 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0027         1      27      53 ..      34      60 ..      19      75 .. 0.85
   2 ?    5.2   0.4     0.084        32      29      55 ..      81     107 ..      76     131 .. 0.84
   3 ?   -0.3   0.0       4.5   1.7e+03      38      55 ..     124     141 ..     119     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0027
                                  HHSEEEHHHHHHHCT--HHHHHHHHHH CS
                           Mga 27 eeeevsieelaqelyiSestlkrkike 53
                                   ++ +s++++a+el iS++++ +++ +
  gi|70606284|ref|YP_255154.1| 34 YNQGKSMKSIARELGISYTKVRNILLN 60
                                  48999****************999865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.084
                                   SEEEHHHHHHHCT--HHHHHHHHHHHH CS
                           Mga  29 eevsieelaqelyiSestlkrkikeln 55 
                                   +  s   +++ l iSes++ r++k+ n
  gi|70606284|ref|YP_255154.1|  81 QGHSARYISKMLKISESSALRILKKHN 107
                                   566777889999***********9866 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 4.5
                                   HHCT--HHHHHHHHHHHH CS
                           Mga  38 qelyiSestlkrkikeln 55 
                                   +e+y+   +++r+ k l 
  gi|70606284|ref|YP_255154.1| 124 KEMYLKGESIYRIAKTLG 141
                                   788888899999888764 PP

>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.073        28      20      53 ..      26      58 ..      22      61 .. 0.87
   2 ?    7.7   0.0    0.0081       3.1      14      46 ..      65      96 ..      63     104 .. 0.85
   3 ?   -2.0   0.0       9.1   3.5e+03      25      37 ..     124     136 ..     115     139 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                                  BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHH CS
                        DUF433 20 pVetilellaaGesieeiledyPdLtlediqaal 53
                                  +V+ +  l+++G+s + i+++  +++   +++ l
  gi|70606284|ref|YP_255154.1| 26 SVDELKRLYNQGKSMKSIAREL-GISYTKVRNIL 58
                                  7899999**************9.99998888776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0081
                                  ETTT--BTHHHHHHHHTT--HHHHHHHH.TS-H CS
                        DUF433 14 IrgtRipVetilellaaGesieeiledyPdLtl 46
                                  Ir  Ri  + ++el ++G s   i +    +++
  gi|70606284|ref|YP_255154.1| 65 IRKKRINEQEVVELAKQGHSARYISKML-KISE 96
                                  99*******************9998877.6655 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.1
                                   HHHHHTT--HHHH CS
                        DUF433  25 lellaaGesieei 37 
                                    e++ +Gesi +i
  gi|70606284|ref|YP_255154.1| 124 KEMYLKGESIYRI 136
                                   3444455555544 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.41   1.6e+02      16      33 ..      38      55 ..      30      63 .. 0.76
   2 ?    3.3   0.1       0.2        78      11      33 ..      78     100 ..      75     107 .. 0.78
   3 ?    5.6   0.0     0.039        15      19      39 ..     134     154 ..     129     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.41
                                  EEHHHHHHHHTS-HHHHH CS
                         HTH_5 16 lcvcelaeelglsqstvS 33
                                  ++   +a+elg+s  +v+
  gi|70606284|ref|YP_255154.1| 38 KSMKSIARELGISYTKVR 55
                                  667789999999977775 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                                   HTTSSEEHHHHHHHHTS-HHHHH CS
                         HTH_5  11 LaegelcvcelaeelglsqstvS 33 
                                   La++ +++  ++++l++s+s   
  gi|70606284|ref|YP_255154.1|  78 LAKQGHSARYISKMLKISESSAL 100
                                   67777778889********9764 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.039
                                   HHHHHHHTS-HHHHHHHHHHH CS
                         HTH_5  19 celaeelglsqstvShHLkkL 39 
                                     +a+ lg+s   v +HLk+L
  gi|70606284|ref|YP_255154.1| 134 YRIAKTLGKSTNLVVYHLKRL 154
                                   5699***************98 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0055       2.1       6      37 ..      32      59 ..      26      72 .. 0.81
   2 ?    4.4   0.0      0.11        43      20      39 ..     107     127 ..      89     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0055
                                  HHHCCSTCCSCCHHHHHHHTTSHHHHHHHHHH CS
                         Death  6 rildhpdplgkdWkelarkLglseeeidriek 37
                                  r+ ++    gk+ k +ar+Lg+s+++++ i  
  gi|70606284|ref|YP_255154.1| 32 RLYNQ----GKSMKSIARELGISYTKVRNILL 59
                                  45554....899***************99865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                                   HHHHHT.TSHHHHHHHHHHSS CS
                         Death  20 elarkL.glseeeidrieken 39 
                                   +++rk+ +ls+e+i+ i++ +
  gi|70606284|ref|YP_255154.1| 107 NVGRKIkKLSDEDINKIKEMY 127
                                   567888789********9988 PP

>> WYL_3  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0045       1.7       5      28 ..      27      50 ..      25      63 .. 0.85
   2 ?   -0.3   0.0       3.8   1.4e+03       5      30 ..      72      97 ..      68     115 .. 0.78
   3 ?    2.8   0.0      0.41   1.6e+02       5      29 ..     120     144 ..     119     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0045
                         WYL_3  5 kaemkkmmkdgvtkedyAkkLgIa 28
                                   +e+k++ ++g++ +  A++LgI+
  gi|70606284|ref|YP_255154.1| 27 VDELKRLYNQGKSMKSIARELGIS 50
                                  579********************8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.8
                         WYL_3  5 kaemkkmmkdgvtkedyAkkLgIadk 30
                                  ++e  ++ k+g ++    k L+I++ 
  gi|70606284|ref|YP_255154.1| 72 EQEVVELAKQGHSARYISKMLKISES 97
                                  56677788888888888888888875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.41
                         WYL_3   5 kaemkkmmkdgvtkedyAkkLgIad 29 
                                    +++k+m  +g +    Ak+Lg ++
  gi|70606284|ref|YP_255154.1| 120 INKIKEMYLKGESIYRIAKTLGKST 144
                                   6799*****************9665 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0026      0.99       5      43 ..      41      80 ..      40      83 .. 0.86
   2 ?    3.2   0.0      0.22        83       4      24 ..      85     105 ..      85     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
               HU-CCDC81_bac_2  5 nsiaeaegisyeeAlqki.ekeveelkqeLeeegrvelen 43
                                  +sia++ gisy+++++ + +  v+  k++++e++ vel +
  gi|70606284|ref|YP_255154.1| 41 KSIARELGISYTKVRNILlNAGVNIRKKRINEQEVVELAK 80
                                  79************9975267799999*********9976 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
               HU-CCDC81_bac_2   4 ansiaeaegisyeeAlqkiek 24 
                                   a +i++  +is  +Al+ ++k
  gi|70606284|ref|YP_255154.1|  85 ARYISKMLKISESSALRILKK 105
                                   679*************99987 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1     0.004       1.5      85     151 ..      21      87 ..      13      93 .. 0.72
   2 ?    5.3   0.3     0.052        20      72      99 ..     101     128 ..      79     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.004
                       MRP-L20  85 hltkedieeirrLraeDPekwsrkkLakkFgcsklfvsmvt.eapk..ekkkeveaeleavkerWgekrr 151
                                    +t++ ++e++rL+++     s+k++a++ g+s ++v+ ++ +a     kk+++e+e  ++ ++ +  r 
  gi|70606284|ref|YP_255154.1|  21 IMTEASVDELKRLYNQG---KSMKSIARELGISYTKVRNILlNAGVniRKKRINEQEVVELAKQGHSARY 87 
                                   58999*********985...69***************887745555224555555555555555555555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.052
                       MRP-L20  72 pvlkkksekekkyhltkedieeirrLra 99 
                                    +lkk++   k  +l+ edi++i+++++
  gi|70606284|ref|YP_255154.1| 101 RILKKHNVGRKIKKLSDEDINKIKEMYL 128
                                   45666555555599**********9876 PP

>> ANT  Phage antirepressor protein KilAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0088       3.4      25      56 ..      39      71 ..      27      83 .. 0.87
   2 ?    3.3   0.0      0.27     1e+02      25      49 ..      84     108 ..      74     118 .. 0.84
   3 ?   -0.5   0.0       4.1   1.6e+03      26      49 ..     133     156 ..     131     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0088
                           ANT 25 titeiAkllgigenrlfelLrekgilyrqkg.s 56
                                  +++ iA++lgi+ +++ ++L + g+ +r+k+ +
  gi|70606284|ref|YP_255154.1| 39 SMKSIARELGISYTKVRNILLNAGVNIRKKRiN 71
                                  7899************************86544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.27
                           ANT  25 titeiAkllgigenrlfelLrekgi 49 
                                   + + i k+l+i+e  + ++L+++++
  gi|70606284|ref|YP_255154.1|  84 SARYISKMLKISESSALRILKKHNV 108
                                   667899**************99876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.1
                           ANT  26 iteiAkllgigenrlfelLrekgi 49 
                                   i  iAk+lg + n ++  L++ g+
  gi|70606284|ref|YP_255154.1| 133 IYRIAKTLGKSTNLVVYHLKRLGV 156
                                   6679*****999999988888876 PP

>> DUF3102  Protein of unknown function (DUF3102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   0.00015     0.057       4      85 ..      41     124 ..      38     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                       DUF3102   4 lviaaEintikeqtkkilLtsaieiGr.rL..kEakellpyGewlkwLeesvsysqrtAerlmrlfeeyGskllasadeas 81 
                                   + ia E+ +  +++++ilL++ ++i + r+  +E+ el + G   +++++  + s+++A r+++ + + G+k ++ +de+ 
  gi|70606284|ref|YP_255154.1|  41 KSIARELGISYTKVRNILLNAGVNIRKkRIneQEVVELAKQGHSARYISKMLKISESSALRILKKH-NVGRKIKKLSDEDI 120
                                   6799***9999**************862553356789999**********************9965.56888877776555 PP

                       DUF3102  82 snse 85 
                                   ++ +
  gi|70606284|ref|YP_255154.1| 121 NKIK 124
                                   5544 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0039       1.5      19      35 ..      39      55 ..      35      56 .. 0.91
   2 ?    1.1   0.0      0.95   3.6e+02      20      36 ..      85     101 ..      83     105 .. 0.83
   3 ?   -1.6   0.0       6.4   2.5e+03      22      34 ..     135     147 ..     132     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0039
                 HTH_AsnC-type 19 syaeLAervGlSestvl 35
                                  s++ +A+++G+S + v+
  gi|70606284|ref|YP_255154.1| 39 SMKSIARELGISYTKVR 55
                                  899**********9997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.95
                 HTH_AsnC-type  20 yaeLAervGlSestvlr 36 
                                    + +++++ +Ses +lr
  gi|70606284|ref|YP_255154.1|  85 ARYISKMLKISESSALR 101
                                   566999*******9887 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.4
                 HTH_AsnC-type  22 eLAervGlSestv 34 
                                   ++A+ +G S++ v
  gi|70606284|ref|YP_255154.1| 135 RIAKTLGKSTNLV 147
                                   6899999887755 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.9   7.4e+02       2      18 ..      36      52 ..      35      77 .. 0.77
   2 ?    2.5   0.1      0.38   1.5e+02       8      48 ..      77     115 ..      70     127 .. 0.75
   3 ?    6.8   0.0     0.018       6.7       8      26 ..     135     153 ..     128     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.9
                          KorB  2 kgvkqadIAkaLGksks 18
                                  +g   + IA++LG s +
  gi|70606284|ref|YP_255154.1| 36 QGKSMKSIARELGISYT 52
                                  67788899999997655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.38
                          KorB   8 dIAkaLGksksfvslylklldvpdylrelydseviadirtL 48 
                                   + Ak+ G s  ++s  lk+ ++ + lr l + +v + i+ L
  gi|70606284|ref|YP_255154.1|  77 ELAKQ-GHSARYISKMLKISESSA-LRILKKHNVGRKIKKL 115
                                   66666.999999999999998764.6777666666666655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.018
                          KorB   8 dIAkaLGksksfvslylkl 26 
                                    IAk LGks   v  +lk 
  gi|70606284|ref|YP_255154.1| 135 RIAKTLGKSTNLVVYHLKR 153
                                   6************999985 PP

>> RWP-RK  RWP-RK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.006       2.3      13      33 ..      38      58 ..      25      64 .. 0.73
   2 ?    2.5   0.4      0.39   1.5e+02      19      40 ..      89     110 ..      84     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.006
                        RWP-RK 13 lplkeAAksLgvskttLKric 33
                                   ++k  A++Lg+s t++++i 
  gi|70606284|ref|YP_255154.1| 38 KSMKSIARELGISYTKVRNIL 58
                                  589999**********99986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.39
                        RWP-RK  19 AksLgvskttLKricRelgIsR 40 
                                   +k L++s+++  ri +++++ R
  gi|70606284|ref|YP_255154.1|  89 SKMLKISESSALRILKKHNVGR 110
                                   588999999988******9976 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.028        11       8      45 ..      23      55 ..      20      57 .. 0.74
   2 ?   -0.0   0.0       2.1   8.2e+02      26      36 ..      71      81 ..      65      99 .. 0.57
   3 ?    2.3   0.0      0.41   1.6e+02      22      38 ..     125     141 ..     111     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
                                  -HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHH CS
                   Homeodomain  8 tkeqleeLeklFeenrypsaeereeLAkklgLeerqVk 45
                                  t+  ++eL++l+++ +      ++ +A++lg++ ++V+
  gi|70606284|ref|YP_255154.1| 23 TEASVDELKRLYNQGK-----SMKSIARELGISYTKVR 55
                                  6667777777777654.....56789999999999987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.1
                                  SHHHHHHHHHH CS
                   Homeodomain 26 saeereeLAkk 36
                                  +++e  eLAk+
  gi|70606284|ref|YP_255154.1| 71 NEQEVVELAKQ 81
                                  45555555544 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.41
                                   SSS-SHHHHHHHHHHHT CS
                   Homeodomain  22 nrypsaeereeLAkklg 38 
                                   + y++ e + ++Ak lg
  gi|70606284|ref|YP_255154.1| 125 EMYLKGESIYRIAKTLG 141
                                   78999*********997 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.54   2.1e+02     147     168 ..      33      54 ..      19      59 .. 0.77
   2 ?    8.8   0.2    0.0036       1.4      97     168 ..      67     147 ..      54     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.54
                   Sigma70_ECF 147 rkleGlsveEiAeklgvskrtv 168
                                    + +G s++ iA +lg+s   v
  gi|70606284|ref|YP_255154.1|  33 LYNQGKSMKSIARELGISYTKV 54 
                                   456899************8766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                   Sigma70_ECF  97 qkRGGdvvraeldeeeds.........vdsdspdelleLdealerllsldpeqarlvelrkleGlsveEiAeklgvskrtv 168
                                   +kR  +++  el+++  s         + + s+  +l+  +   ++ +l++e   ++  ++l+G s+  iA++lg s+  v
  gi|70606284|ref|YP_255154.1|  67 KKRINEQEVVELAKQGHSaryiskmlkISESSALRILKKHNVGRKIKKLSDEDINKIKEMYLKGESIYRIAKTLGKSTNLV 147
                                   555555555555555555444444433444666667777777789999***************************998655 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.8   0.00029      0.11      25     134 ..      10     134 ..       2     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00029
                        PIN_12  25 leliesgkiklivpdivldEflknr.ekkiees.........kkle.kalks....lsklksakkklnekkkllslkeikk 90 
                                   +++i ++ ++ i+++  +dE+++ + + k  +s         +k++   l +    ++k + +++++ e+ k+  +  + +
  gi|70606284|ref|YP_255154.1|  10 KKFILKNVDSSIMTEASVDELKRLYnQGKSMKSiarelgisyTKVRnILL-NagvnIRKKRINEQEVVELAKQGHSARYIS 89 
                                   566666677779999999***99996444444469888887766663333.358886666666666666666666666666 PP

                        PIN_12  91 kieekveeslkklleklea.ikvipetndevkkilerafkkkpPf 134
                                   k+ + +e+s  ++l+k+++  k+++ ++++++ki e ++k+++ +
  gi|70606284|ref|YP_255154.1|  90 KMLKISESSALRILKKHNVgRKIKKLSDEDINKIKEMYLKGESIY 134
                                   66666788888888888888*********************9988 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0074       2.8      14      41 ..      32      56 ..      25      61 .. 0.79
   2 ?    2.0   0.0      0.57   2.2e+02      25      38 ..      85      98 ..      76     113 .. 0.86
   3 ?   -1.8   0.0       8.3   3.2e+03      12      17 ..     123     128 ..     110     147 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0074
               Phage_terminase 14 elykEsggtlklkdIAkvLdvsestvrk 41
                                  +ly    + + +k IA +L++s  +vr+
  gi|70606284|ref|YP_255154.1| 32 RLYN---QGKSMKSIARELGISYTKVRN 56
                                  5553...346789*************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.57
               Phage_terminase 25 lkdIAkvLdvsest 38
                                   + I k+L +ses 
  gi|70606284|ref|YP_255154.1| 85 ARYISKMLKISESS 98
                                  6889*******985 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.3
               Phage_terminase  12 Ayelyk 17 
                                    +e+y+
  gi|70606284|ref|YP_255154.1| 123 IKEMYL 128
                                   445554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0       0.1        38      16      41 ..      35      57 ..      22      59 .. 0.77
   2 ?    4.7   0.0     0.071        27      18      44 ..      82     105 ..      75     107 .. 0.85
   3 ?   -1.7   0.0       7.5   2.8e+03      26      45 ..     135     154 ..     129     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                                  CTTTSEEEHHHHHHHHTSSHHHHHHH CS
                        MarR_2 16 rrpgrdltvgelarrlglsksavsri 41
                                  + +    +++ +ar+lg+s   v +i
  gi|70606284|ref|YP_255154.1| 35 NQGK---SMKSIARELGISYTKVRNI 57
                                  5554...8999*******98777666 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.071
                                   TTSEEEHHHHHHHHTSSHHHHHHHHHH CS
                        MarR_2  18 pgrdltvgelarrlglsksavsrilkr 44 
                                   +    +++ + + l++s s++ rilk+
  gi|70606284|ref|YP_255154.1|  82 G---HSARYISKMLKISESSALRILKK 105
                                   4...48999****************97 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.5
                                   HHHHHHTSSHHHHHHHHHHH CS
                        MarR_2  26 elarrlglsksavsrilkrL 45 
                                    +a++lg s   v ++lkrL
  gi|70606284|ref|YP_255154.1| 135 RIAKTLGKSTNLVVYHLKRL 154
                                   68999999988899999887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1       0.1        39      27      47 ..      39      59 ..      29      61 .. 0.84
   2 ?    3.4   0.3       0.2        75      27      48 ..      84     105 ..      77     117 .. 0.87
   3 ?    3.5   0.0      0.18        68      30      49 ..     135     154 ..     130     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.1
                        HTH_36 27 sqetlakrlglsknTvsraik 47
                                  s++ +a+ lg+s  +v++++ 
  gi|70606284|ref|YP_255154.1| 39 SMKSIARELGISYTKVRNILL 59
                                  89***********99999986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.2
                        HTH_36  27 sqetlakrlglsknTvsraike 48 
                                   s ++++k l++s++++ r++k+
  gi|70606284|ref|YP_255154.1|  84 SARYISKMLKISESSALRILKK 105
                                   7899**********99999986 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.18
                        HTH_36  30 tlakrlglsknTvsraikeL 49 
                                   ++ak lg+s n v+ ++k L
  gi|70606284|ref|YP_255154.1| 135 RIAKTLGKSTNLVVYHLKRL 154
                                   79************999998 PP

>> NPA  Nematode polyprotein allergen ABA-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.7    0.0033       1.2      15     105 ..      22     125 ..      16     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0033
                           NPA  15 lteeqkaeikalkeagasseeiekkvl..............efyealeadkkeeareklkgaCkeyikkllgeeeaeelkk 81 
                                   +te    e+k+l ++g+s + i +++                   +   +++e ++   +g+  +yi+k+l+  e+  l+ 
  gi|70606284|ref|YP_255154.1|  22 MTEASVDELKRLYNQGKSMKSIARELGisytkvrnillnagVNIRKKRINEQEVVELAKQGHSARYISKMLKISESSALRI 102
                                   888889999999999999999999998889999988887763444445555666666777888888888888888888888 PP

                           NPA  82 lkesgasaeelkkkldeligeled 105
                                   l ++++   ++kk  de i+++++
  gi|70606284|ref|YP_255154.1| 103 L-KKHNVGRKIKKLSDEDINKIKE 125
                                   8.7777788888888888888865 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0059       2.2      18      37 .]      39      58 ..      38      58 .. 0.89
   2 ?    0.9   0.2       1.5   5.7e+02      18      32 ..      84      98 ..      83     103 .. 0.80
   3 ?    4.6   0.1      0.11        41      17      37 .]     131     151 ..     131     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0059
                        NUMOD1 18 SireAakyLgishntInkyl 37
                                  S+++ a+ Lgis+  +++ l
  gi|70606284|ref|YP_255154.1| 39 SMKSIARELGISYTKVRNIL 58
                                  99***********9998865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.5
                        NUMOD1 18 SireAakyLgishnt 32
                                  S r  +k L+is+++
  gi|70606284|ref|YP_255154.1| 84 SARYISKMLKISESS 98
                                  77778999****987 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.11
                        NUMOD1  17 sSireAakyLgishntInkyl 37 
                                   +Si + ak Lg+s n + ++l
  gi|70606284|ref|YP_255154.1| 131 ESIYRIAKTLGKSTNLVVYHL 151
                                   689999**********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1407  (0.0784762); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1049.41
//
Query:       gi|70606285|ref|YP_255155.1|  [L=381]
Description: tryptophanyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-25   90.0   0.0    2.5e-25   89.4   0.0    1.3  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.0   1.4e-29   2.5e-25       6     293 .]      74     349 ..      69     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1.4e-29
                                   -EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTE CS
                  tRNA-synt_1b   6 lrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpeka 85 
                                   + +y+G +P+  +H+G+l+p+    +lq+  +++v++ i D + ++ + +  ++ + ++ +  +en i  ++a+g+dp+k+
  gi|70606285|ref|YP_255155.1|  74 FFLYTGRAPSLGMHIGHLIPFIFTKWLQEkFKVNVYIEITDDEKFLRNVD-YTLDQTKEWS--YEN-ILDIIAVGFDPNKT 150
                                   568*************************7456788888888888888888.2333333333..333.4679********** PP

                                   EEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.EEEEEGGGHHHH CS
                  tRNA-synt_1b  86 evvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.lvpgGsDQkqni 164
                                    ++  +e+++++  l   +++  ++++++     ++         + ++g + Yp Lq    ++ k + l p G DQ+   
  gi|70606285|ref|YP_255155.1| 151 FIFQDTEYIKNMyPLSVKIAKKLTFNEVRATFGLDT---------SSNIGIIFYPALQIVPTMFEKRRcLIPAGIDQDPYW 222
                                   ********9987444444555555555555555555.........336899**********99999999************ PP

                                   HHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSS.BTTCETTCGC-BTTCCHHHHHHHH.HHCHCSTTC..SHHHHHHHHH CS
                  tRNA-synt_1b 165 elgrdlarrfnkkevfkkpegltvplltgldGek.KmSKSagnsaIfLddekesvkkki.qkavtdsde..evekllklkt 241
                                   +l rd+a+++++     k   +  ++l+ l+G + KmS+S++++aI+L+d++++v+ ki ++a++  ++  e+++ + +++
  gi|70606285|ref|YP_255155.1| 223 RLQRDIAESLGYF----KAAQIHSKFLPPLTGPEgKMSSSQPETAIYLTDDPKTVERKImKYAFSGGQAtvELHRKYGGNP 299
                                   ************9....888888887776666544********************999835677777779999******** PP

                                   THHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1b 242 elsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                    ++  +   ++ +   ++ +++ +++++++++ +  g+lk+ l ++ln++le
  gi|70606285|ref|YP_255155.1| 300 DIDVAFQWLYMFFEP-DD-QRIRKIEEDYRSGAMLTGELKQILVDKLNAFLE 349
                                   ****55555555555.55.6****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2537.12
//
Query:       gi|70606286|ref|YP_255156.1|  [L=214]
Description: hypothetical protein Saci_0451 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   18.5   1.1     0.0017   18.0   1.1    1.3  1  Snf7      Snf7
     0.0017   18.4   0.8     0.0039   17.2   0.6    1.7  1  LOH1CR12  Tumour suppressor protein
  ------ inclusion threshold ------
      0.047   13.8   0.1      0.083   13.0   0.1    1.4  1  BLOC1S3   Biogenesis of lysosome-related organelles complex 1


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   2.9e-07    0.0017       3      78 ..      41     116 ..      39     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlk 78 
                                   + ++r +  +ld ++ +++++ k l + + + + ++++ ra  +++++ +++k  +ql ++++ leqvsl +e+  
  gi|70606286|ref|YP_255156.1|  41 QYRVRSMVSRLDVYIGRMQERDKVLFERVVESQMSKDQSRAAMYANELAEIRKITKQLLTTQIALEQVSLRLETVT 116
                                   5677888899999***********************************************************9875 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.6   6.5e-07    0.0039      70     117 ..      72     119 ..      53     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-07
                      LOH1CR12  70 aelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelL 117
                                   +++ + q + a ya++l++++++ +ql   qi le++   lEt+ el 
  gi|70606286|ref|YP_255156.1|  72 SQMSKDQSRAAMYANELAEIRKITKQLLTTQIALEQVSLRLETVTELG 119
                                   4678889999***************************99999998875 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05     0.083     114     148 ..      81     115 ..      57     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                       BLOC1S3 114 sqvysaaskelesvtsqLnksqsaiqnashsirli 148
                                     +y +   e++++t+qL ++q a++++s  + ++
  gi|70606286|ref|YP_255156.1|  81 AAMYANELAEIRKITKQLLTTQIALEQVSLRLETV 115
                                   679**************************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1547.83
//
Query:       gi|70606287|ref|YP_255157.1|  [L=143]
Description: GtrA-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-20   71.7  10.8    8.6e-20   71.1  10.8    1.2  1  GtrA      GtrA-like protein


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1  10.8   4.8e-24   8.6e-20       1     117 []       7     142 ..       7     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 4.8e-24
                          GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglllnlli 81 
                                   ++ +vG+lg++v+ ++llll  +  l++++  a+a++ +il+nFiln++wtF+d++ +++  ++l+F++ sl+g +++++i
  gi|70606287|ref|YP_255157.1|   7 KYSLVGALGVIVNEGVLLLLRDY--LPLTVGLALAIEFSILSNFILNDIWTFRDSRVGSIGGRLLRFHVSSLVGGAVQYVI 85 
                                   799******************88..*******************************************************9 PP

                          GtrA  82 ....lwllveklgleall....................aklvgiivalvlnyvlsklfvF 117
                                       + l+v++ +l   +                     +++gi+ ++ ++++ls ++v+
  gi|70606287|ref|YP_255157.1|  86 viglVILFVNYSNL---TellfllffsslklssiylaaINFIGIVGGFGVRFILSLKYVW 142
                                   33333344444444...25559**************99999***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1102.43
//
Query:       gi|70606288|ref|YP_255158.1|  [L=317]
Description: aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-11   41.6   0.0    1.9e-09   37.2   0.0    2.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0     1e-13   1.9e-09     150     238 ..     119     204 ..      15     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1e-13
                                   EEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-E CS
                 Aminotran_1_2 150 kvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRv 230
                                    ++++ +p NPtG+   +e++ +       ++  l++De +a+  + ++    ++ +++e +nll  +s+ K+++++G+R+
  gi|70606288|ref|YP_255158.1| 119 SCVITSNPVNPTGSFVEREKIIDF---LS-NGGKLILDESFADISLIEP----NYDLASEFDNLLFISSFTKSLAIPGLRI 191
                                   489***************999888...44.5999************965....4899999999****************** PP

                                   EEEEEEH.....H CS
                 Aminotran_1_2 231 Gyilgna.....a 238
                                   G+++g+      +
  gi|70606288|ref|YP_255158.1| 192 GFTIGKRskeleD 204
                                   ****955455550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1951.57
//
Query:       gi|70606289|ref|YP_255159.1|  [L=178]
Description: HTH domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-20   72.6   0.1    2.8e-20   71.8   0.1    1.4  1  HTH_10    HTH DNA binding domain
    6.4e-06   25.6   0.3     0.0016   18.0   0.1    2.6  2  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.041   14.5   0.8       0.29   11.8   0.8    2.2  1  Mga       Mga helix-turn-helix domain
      0.055   13.5   0.3       0.15   12.2   0.1    1.9  2  HTH_3     Helix-turn-helix
       0.14   12.2   4.7       0.13   12.3   1.1    2.6  3  ENT       ENT domain
        0.2   11.6   1.7          1    9.3   0.7    2.6  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.1   9.5e-24   2.8e-20       1      53 []     118     170 ..     118     170 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 9.5e-24
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                   +T +q ++lk+A+e+GYFd PRr++l+eL+k+l+Is stl e++r+ae+++ie
  gi|70606289|ref|YP_255159.1| 118 ITGRQEQILKIALELGYFDFPRRIRLNELSKKLNISTSTLAEIIRRAERNIIE 170
                                   599************************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0044        13       2      17 ..     100     115 ..      99     117 .. 0.89
   2 !   18.0   0.1   5.3e-07    0.0016      17      43 ..     140     166 ..     122     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                        HTH_24   2 detdrkILelLqknpr 17 
                                   +++d kIL++L+++p+
  gi|70606289|ref|YP_255159.1| 100 SKIDVKILKVLKAKPS 115
                                   689*********9985 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.3e-07
                        HTH_24  17 risqreLAerlglSpstvnrrlkrLee 43 
                                   ri  +eL+++l++S st+ + ++r e+
  gi|70606289|ref|YP_255159.1| 140 RIRLNELSKKLNISTSTLAEIIRRAER 166
                                   58899*******************987 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   9.6e-05      0.29      27      60 ..     137     170 ..      87     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.6e-05
                                   HHSEEEHHHHHHHCT--HHHHHHHHHHHHHHCHC CS
                           Mga  27 eeeevsieelaqelyiSestlkrkikelnklLke 60 
                                   + +++ + el+++l iS stl  +i++ +  + e
  gi|70606289|ref|YP_255159.1| 137 FPRRIRLNELSKKLNISTSTLAEIIRRAERNIIE 170
                                   6888999******************998877765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   8.6e+03      38      49 ..     122     133 ..     121     134 .. 0.70
   2 ?   12.2   0.1   4.9e-05      0.15      12      34 ..     143     166 ..     138     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHT CS
                         HTH_3  38 letlkklakaLg 49 
                                   +e ++k+a  Lg
  gi|70606289|ref|YP_255159.1| 122 QEQILKIALELG 133
                                   577888887776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.9e-05
                                   HHHHHHHHTSSHHHHHHHHTT.SS CS
                         HTH_3  12 qeeLAeklGvsrstisriEnG.er 34 
                                   + eL++kl++s st++ i++  er
  gi|70606289|ref|YP_255159.1| 143 LNELSKKLNISTSTLAEIIRRaER 166
                                   689***************997666 PP

>> ENT  ENT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   4.3e+03      49      64 ..      38      53 ..      34      58 .. 0.53
   2 ?   -3.7   0.1       4.3   1.3e+04      34      41 ..      88      95 ..      88      95 .. 0.79
   3 ?   12.3   1.1   4.4e-05      0.13      33      56 ..     143     166 ..     104     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                           ENT 49 aelrrvksDerlktir 64
                                  +  ++v +D+  + i+
  gi|70606289|ref|YP_255159.1| 38 ESFSKVSKDTYMGIIK 53
                                  5555555555544443 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                           ENT 34 teLrkeLs 41
                                  teLrk+L+
  gi|70606289|ref|YP_255159.1| 88 TELRKLLR 95
                                  68999986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 4.4e-05
                           ENT  33 lteLrkeLsIsterHraelrrvks 56 
                                   l+eL+k L+Ist + ++++rr++ 
  gi|70606289|ref|YP_255159.1| 143 LNELSKKLNISTSTLAEIIRRAER 166
                                   56666****************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.23   6.8e+02       4      19 ..     105     121 ..     104     122 .. 0.86
   2 ?    9.3   0.7   0.00035         1      15      32 ..     140     157 ..     121     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                        HTH_11   4 qilelLleargp.isge 19 
                                   +il+ L+++ +  i+g 
  gi|70606289|ref|YP_255159.1| 105 KILKVLKAKPSSiITGR 121
                                   79****99999989885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00035
                        HTH_11  15 pisgeeLAeeLnvSrrtv 32 
                                    i  +eL+++Ln+S++t 
  gi|70606289|ref|YP_255159.1| 140 RIRLNELSKKLNISTSTL 157
                                   47789***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1375.23
//
Query:       gi|70606290|ref|YP_255160.1|  [L=104]
Description: zinc-containing ferredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-14   51.5  13.6    4.3e-07   29.5   6.0    2.2  2  Fer4      4Fe-4S binding domain
    3.5e-11   43.5  27.6    2.9e-07   30.9   9.8    1.7  3  Fer4_7    4Fe-4S dicluster domain
    7.6e-09   35.6   6.2    1.1e-08   35.1   6.2    1.2  1  Fer4_9    4Fe-4S dicluster domain
    4.5e-08   33.1   7.4    9.1e-08   32.1   7.5    1.5  1  Fer4_10   4Fe-4S dicluster domain
    9.1e-08   32.1   6.3    1.3e-07   31.6   6.3    1.3  1  Fer4_21   4Fe-4S dicluster domain
    9.6e-08   31.8  13.3    0.00025   21.0   5.5    2.2  2  Fer4_6    4Fe-4S binding domain
    2.4e-05   24.8   9.6      0.031   14.8   0.3    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    3.7e-05   24.6   8.6     0.0077   17.1   3.0    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    5.4e-05   23.0  11.0       0.03   14.4   4.3    2.4  2  Fer4_2    4Fe-4S binding domain
    7.3e-05   23.1   7.6     0.0013   19.2   8.5    2.0  2  Fer4_8    4Fe-4S dicluster domain
      9e-05   22.9   1.1       0.35   11.5   0.6    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00022   21.9  13.7      0.012   16.5   6.8    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00029   21.1   8.2      0.045   14.3   3.4    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0011   19.1   0.9     0.0012   18.9   0.9    1.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
     0.0041   17.3   9.3      0.014   15.6   2.8    2.1  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.033   14.9  11.8        0.4   11.4   0.3    2.8  2  Fer4_15   4Fe-4S single cluster domain
      0.056   13.4   0.0      0.072   13.1   0.0    1.4  1  DUF2761   Protein of unknown function (DUF2761)
        2.5    9.0   8.3          9    7.2   2.4    2.1  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.8   2.5e-09   2.5e-06       3      23 ..      41      61 ..      39      62 .. 0.91
   2 !   29.5   6.0   4.3e-10   4.3e-07       3      24 .]      79     100 ..      77     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.5e-09
                                  EETTTSSS-THHHHHSTTTEE CS
                          Fer4  3 ideekCigCGaCvevCPvgAI 23
                                  +d ++Ci+ G C+ +CPv++ 
  gi|70606290|ref|YP_255160.1| 41 VDFDLCIADGSCITACPVNVF 61
                                  8*****************985 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 4.3e-10
                                   EETTTSSS-THHHHHSTTTEEE CS
                          Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                   ++e  Ci+C+aCv+vCPv AI+
  gi|70606290|ref|YP_255160.1|  79 VNEQACIFCMACVNVCPVAAID 100
                                   899*****************95 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   2.1e-05      0.02      30      52 .]      38      60 ..      11      60 .. 0.81
   2 !   30.9   9.8     3e-10   2.9e-07       2      52 .]      46      98 ..      45      98 .. 0.82
   3 !   18.4   4.0   2.5e-06    0.0025       1      20 [.      83     102 ..      83     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                        Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                   v +d + C+  g+C+++CP+++
  gi|70606290|ref|YP_255160.1| 38 IVGVDFDLCIADGSCITACPVNV 60
                                  457899**************986 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 3e-10
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt.ekve.idpekClgCgaCvavCPtga 52
                                  Ci  g C  aCpv+++++ e   ++   +k++ ++++ C++C aCv+vCP+ a
  gi|70606290|ref|YP_255160.1| 46 CIADGSCITACPVNVFQWYETPGHPASeKKADpVNEQACIFCMACVNVCPVAA 98
                                  88889*************99866664325565357889************986 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 2.5e-06
                        Fer4_7   1 rCigCgaCvaaCpvkaield 20 
                                   +Ci C aCv++Cpv ai+++
  gi|70606290|ref|YP_255160.1|  83 ACIFCMACVNVCPVAAIDVK 102
                                   59999999999999999876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   6.2   1.1e-11   1.1e-08       2      51 .]      46      99 ..      45      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.1e-11
                        Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51
                                  C+  g+C++aCp +v++  + ++  + +++ +    +aCi+C+aCv++Cp  ai
  gi|70606290|ref|YP_255160.1| 46 CIADGSCITACPVNVFQWYETPGHPASEKKADpvneQACIFCMACVNVCPVAAI 99
                                  777799*****************9999988889**99*************9887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   7.5   9.2e-11   9.1e-08       3      56 .]      40      95 ..      38      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.2e-11
                       Fer4_10  3 vidddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +d d Ci  g C +aCP+++  +       ase++a+ ++ ++C++c aCv +CP
  gi|70606290|ref|YP_255160.1| 40 GVDFDLCIADGSCITACPVNVfqWYETPGHPASEKKADPVNEQACIFCMACVNVCP 95
                                  57899**************99986666667777888888888*************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   6.3   1.3e-10   1.3e-07       3      57 ..      41      99 ..      39     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.3e-10
                       Fer4_21  3 idedkCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedci 57
                                  +d d Ci  g+C++aC+ +  q         ++k+  +v e+ C+ C  C++vCPv  +i
  gi|70606290|ref|YP_255160.1| 41 VDFDLCIADGSCITACPVNVFQWYetpghPASEKKADPVNEQACIFCMACVNVCPV-AAI 99
                                  67899*****************995554334566677999***************9.666 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.9   1.1e-05     0.011       3      23 ..      40      60 ..      38      61 .. 0.86
   2 !   21.0   5.5   2.5e-07   0.00025       4      24 .]      79      99 ..      79      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                        Fer4_6  3 eidpdkCigCgdCvrvCPega 23
                                   +d d+Ci  g C+++CP ++
  gi|70606290|ref|YP_255160.1| 40 GVDFDLCIADGSCITACPVNV 60
                                  56779*************987 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.5e-07
                        Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                  +++++Ci C++Cv+vCP +ai
  gi|70606290|ref|YP_255160.1| 79 VNEQACIFCMACVNVCPVAAI 99
                                  799***************998 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   3.1e-05     0.031       1      20 [.      41      61 ..      41      76 .. 0.88
   2 !   13.3   4.1     9e-05      0.09       1      17 [.      79      95 ..      79     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP.dvF 20
                                  VD d Cia+g+C  ++P +vF
  gi|70606290|ref|YP_255160.1| 41 VDFDLCIADGSCITACPvNVF 61
                                  8999*************4455 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9e-05
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  V+++ Ci c+aCv+++P
  gi|70606290|ref|YP_255160.1| 79 VNEQACIFCMACVNVCP 95
                                  899*************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   8.9    0.0001     0.099       2      66 ..      46      96 ..      45      96 .. 0.70
   2 !   17.1   3.0   7.7e-06    0.0077       2      20 ..      84     102 ..      83     104 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                       Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                  C+  g C+ +CP+n+++       e++   ++   ekk  + +e+      a+++C +C++vCP+
  gi|70606290|ref|YP_255160.1| 46 CIADGSCITACPVNVFQWY-----ETPGHPAS---EKKADPVNEQ------ACIFCMACVNVCPV 96
                                  788899*******999988.....33333332...4444444444......566**********6 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.7e-06
                       Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                   C+ C +C++vCP++ai+ k
  gi|70606290|ref|YP_255160.1|  84 CIFCMACVNVCPVAAIDVK 102
                                   9***************876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.5   0.00011       0.1       3      21 ..      39      57 ..      37      58 .. 0.86
   2 !   14.4   4.3     3e-05      0.03       5      21 ..      79      95 ..      76      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  v vd d Ci+ g+C++aCP
  gi|70606290|ref|YP_255160.1| 39 VGVDFDLCIADGSCITACP 57
                                  56899999987******** PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3e-05
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                  v++++Ci C aCv++CP
  gi|70606290|ref|YP_255160.1| 79 VNEQACIFCMACVNVCP 95
                                  799************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00025      0.25      48      65 .]      43      60 ..       8      60 .. 0.86
   2 !   19.2   8.5   1.3e-06    0.0013       2      63 ..      43      96 ..      42      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                        Fer4_8 48 lwsCttcgaCtevCpvgi 65
                                  ++ C + g+C ++Cpv++
  gi|70606290|ref|YP_255160.1| 43 FDLCIADGSCITACPVNV 60
                                  689************986 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.3e-06
                        Fer4_8  2 lekCieCgaCqsaCp.vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  ++ Ci  g C +aCp  + ++ + + ++  e+++d ++eq+         C  c+aC++vCpv
  gi|70606290|ref|YP_255160.1| 43 FDLCIADGSCITACPvNVFQWYETPGHPASEKKADPVNEQA---------CIFCMACVNVCPV 96
                                  677************43566668888888887775666666.........************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00071       0.7      43      60 ..      43      60 ..      20      61 .. 0.88
   2 !   11.5   0.6   0.00035      0.35      44      57 ..      82      95 ..      62     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                       Fer4_17 43 aslCieCgeCerkCPqgl 60
                                  ++lCi  g C ++CP ++
  gi|70606290|ref|YP_255160.1| 43 FDLCIADGSCITACPVNV 60
                                  689************876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                       Fer4_17 44 slCieCgeCerkCP 57
                                  + Ci C  C+ +CP
  gi|70606290|ref|YP_255160.1| 82 QACIFCMACVNVCP 95
                                  56777777777777 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.5    0.0018       1.7       4      14 ..      46      59 ..      44      60 .. 0.75
   2 !   16.5   6.8   1.2e-05     0.012       1      14 [.      84      97 ..      84      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                        Fer4_3  4 C...gaCvevCPvg 14
                                  C   g C  +CPv+
  gi|70606290|ref|YP_255160.1| 46 CiadGSCITACPVN 59
                                  543378******98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                        Fer4_3  1 CtgCgaCvevCPvg 14
                                  C+ C+aCv+vCPv 
  gi|70606290|ref|YP_255160.1| 84 CIFCMACVNVCPVA 97
                                  ************85 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0017       1.7       2      17 .]      44      59 ..      43      63 .. 0.86
   2 !   14.3   3.4   4.5e-05     0.045       2      16 ..      82      96 ..      81      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                        Fer4_4  2 erCigCgsCvaaCPqg 17
                                  + Ci  gsC+ aCP++
  gi|70606290|ref|YP_255160.1| 44 DLCIADGSCITACPVN 59
                                  6688889*******75 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.5e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + Ci C++Cv++CP+
  gi|70606290|ref|YP_255160.1| 82 QACIFCMACVNVCPV 96
                                  689***********6 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.9   1.2e-06    0.0012      42      95 ..      48     104 .]      26     104 .] 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                                   HS-THHHH-TTS-EEEEETT...TTSSEEEEE-CCC--S--HHHHH-TT--EEE--- CS
                        ETF_QO  42 yagpeqryCPagvyeivede...eakekklqinaqnCvhCktCdikdpsqniewvvP 95 
                                    +g +   CP +v+++ e+     +++k   +n q C+ C +C    p   i+ ++P
  gi|70606290|ref|YP_255160.1|  48 ADGSCITACPVNVFQWYETPghpASEKKADPVNEQACIFCMACVNVCPVAAIDVKPP 104
                                   56778889********996642245667778************98888888887766 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5     0.011        11      58      75 ..      43      60 ..       9      63 .. 0.76
   2 !   15.6   2.8   1.4e-05     0.014      54      77 ..      77     101 ..      64     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                       Fer4_18 58 agdcidcescvkvcPtgi 75
                                     ci+ +sc++ cP+++
  gi|70606290|ref|YP_255160.1| 43 FDLCIADGSCITACPVNV 60
                                  556889999999999876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.4e-05
                       Fer4_18  54 kekgagdcidcescvkvcPt.gidi 77 
                                      ++  ci c +cv+vcP+  id+
  gi|70606290|ref|YP_255160.1|  77 DPVNEQACIFCMACVNVCPVaAIDV 101
                                   3456678************835777 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3    0.0004       0.4       1      19 [.      39      57 ..      39      68 .. 0.87
   2 ?    5.7   6.0     0.024        24       3      19 ..      79      95 ..      78     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  V vD d+Ci +g C++++p
  gi|70606290|ref|YP_255160.1| 39 VGVDFDLCIADGSCITACP 57
                                  569***************8 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
                       Fer4_15  3 vDrdaCigcglCvaeap 19
                                  v+++aCi c +Cv ++p
  gi|70606290|ref|YP_255160.1| 79 VNEQACIFCMACVNVCP 95
                                  67899**********98 PP

>> DUF2761  Protein of unknown function (DUF2761)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.2e-05     0.072      50      80 ..      31      61 ..       4      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.2e-05
                       DUF2761 50 vegvdahtagsdldvcfadgssrtvgplmtv 80
                                  v gv     g d+d+c+adgs  t  p+  +
  gi|70606290|ref|YP_255160.1| 31 VLGVHGTIVGVDFDLCIADGSCITACPVNVF 61
                                  679999999****************998765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.031        31      79      95 ..      43      59 ..      33      60 .. 0.77
   2 ?    7.2   2.4     0.009         9      78      94 ..      80      96 ..      62      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.031
                       Fer4_22 79 esgCvGCgRCieacpvk 95
                                     C+  g Ci+acpv+
  gi|70606290|ref|YP_255160.1| 43 FDLCIADGSCITACPVN 59
                                  56788888888888876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.009
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  +e++C+ C  C+++cpv
  gi|70606290|ref|YP_255160.1| 80 NEQACIFCMACVNVCPV 96
                                  56666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 763.98
//
Query:       gi|70606291|ref|YP_255161.1|  [L=409]
Description: DNA/pantothenate metabolism flavoprotein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-59  199.1   0.2    2.3e-57  193.9   0.1    2.4  2  DFP           DNA / pantothenate metabolism flavoprotein
    5.5e-40  136.7   0.4      1e-39  135.8   0.4    1.5  1  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.015   15.6   0.6        1.1    9.6   0.0    3.3  4  ATP-synt_F    ATP synthase (F/14-kDa) subunit
       0.17   11.8   0.0          1    9.4   0.0    2.2  2  FlpD          Methyl-viologen-reducing hydrogenase, delta sub


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.02        88      34      56 ..      36      58 ..      25      96 .. 0.83
   2 !  193.9   0.1     5e-61   2.3e-57       1     186 []     191     377 ..     191     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.02
                                  HHHHHHHHTT-EEEEEE-S-SS- CS
                           DFP 34 alAeaaaarGaeVtlvsgpvsle 56
                                   l +a+++rGa+V+++ ++ s++
  gi|70606291|ref|YP_255161.1| 36 DLVRALMRRGANVRVIMSKDSIR 58
                                  57899***********9986544 PP

  == domain 2  score: 193.9 bits;  conditional E-value: 5e-61
                                   TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHT CS
                           DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealk 81 
                                   l+g k++vtaGpTrE+iDpVRfisN+SSG+mG+++A++a+ rGa+V lv+gp s + ++ +++++v++++em+e+ve+ ++
  gi|70606291|ref|YP_255161.1| 191 LKGYKIVVTAGPTREYIDPVRFISNSSSGTMGVSIANEAYFRGADVILVHGPLSSSVKPYTKRIRVDTTQEMAENVEKLVR 271
                                   6899************************************************98888889*******************96 PP

                                   T-..SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S...-HHHHHHHHH CS
                           DFP  82 ea..divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e...ellenarekl 156
                                   ++   ivi a A aD++pk++a++Ki+   ++e +++ele +p+i ++l+     ++llvGF+aet +   el+e+a+ k 
  gi|70606291|ref|YP_255161.1| 272 DEkyGIVILAGAPADFKPKNTASSKIDS--HSEVPKVELETTPKISSKLS-I--YRPLLVGFSAETvNsdeELIEKAKMKK 347
                                   554599********************96..56789**************4.3..4579*******965788********** PP

                                   HHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                           DFP 157 erkgldlivaNdvskeeagfgsdenevtll 186
                                   er+++d+ivaN+v++++ gf+s+ nev+++
  gi|70606291|ref|YP_255161.1| 348 ERHKFDIIVANNVKRKDIGFSSEYNEVIVI 377
                                   ***************************986 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.4   2.3e-43     1e-39       1     146 [.      19     173 ..      19     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 2.3e-43
                                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHHCTTESEEEEEEEE CS
                  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhielrrwadllviaPas 74 
                                   kkil+g+T sv+++k l+l+++L ++g++v+v+++k++ ++i++  +++a+        +++i+h+el++++d+lviaP +
  gi|70606291|ref|YP_255161.1|  19 KKILVGVTASVSIYKSLDLVRALMRRGANVRVIMSKDSIRLINPMMFHWATgeepvvsVGGEIEHVELAEEYDALVIAPST 99 
                                   79*****************************************7755555599999999********************** PP

                                   HHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................GHH CS
                  Flavoprotein  75 antlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkmae 146
                                   ant++k+anGiad+ +tl+++   + kkp++++Pam+  mye pq ++n+ekl ++g+++i+P+  + + +++++
  gi|70606291|ref|YP_255161.1| 100 ANTISKLANGIADTSITLTALNfvGIKKPVILVPAMHLTMYEAPQFKENIEKLvKQGIEIISPE-ITRDVAHYPD 173
                                   ****************99995567999**************************99********9.4444444444 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2     1e+04      40      64 ..      88     112 ..      82     121 .. 0.73
   2 ?   -0.8   0.0      0.45     2e+03       9      45 ..     116     160 ..     109     174 .. 0.68
   3 ?    9.6   0.0   0.00024       1.1      20      48 ..     253     281 ..     229     299 .. 0.88
   4 ?    1.7   0.0      0.07   3.2e+02       7      48 ..     317     358 ..     314     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                                   TTEEEEEEEHHHHCCCHHHHHHCTC CS
                    ATP-synt_F  40 edigiilitekiaeeirelideyke 64 
                                   e++  ++i    a+ i++l + + +
  gi|70606291|ref|YP_255161.1|  88 EEYDALVIAPSTANTISKLANGIAD 112
                                   6778888888888888887776665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.45
                                   HHHHHHHTTCEEEE.........CSSHHHHHHHHHHHHHHTTEEEE CS
                    ATP-synt_F   9 tvtgfrlaGvgeve.........vtdeeeieealkelleredigii 45 
                                   t+t +  +G+++ +           ++ + +e +++l+ +++i ii
  gi|70606291|ref|YP_255161.1| 116 TLTALNFVGIKKPVilvpamhltMYEAPQFKENIEKLV-KQGIEII 160
                                   56666677777666666666666555667888888888.7777777 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00024
                                   EEECSSHHHHHHHHHHHHHHTTEEEEEEE CS
                    ATP-synt_F  20 evevtdeeeieealkelleredigiilit 48 
                                    ++v++++e++e +++l+++e++gi+++ 
  gi|70606291|ref|YP_255161.1| 253 RIRVDTTQEMAENVEKLVRDEKYGIVILA 281
                                   4568999*******************986 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.07
                                   HHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEE CS
                    ATP-synt_F   7 edtvtgfrlaGvgevevtdeeeieealkelleredigiilit 48 
                                   + +++  +l+G++  +v+++ee+ e+ k   er+++ ii+ +
  gi|70606291|ref|YP_255161.1| 317 KLSIYRPLLVGFSAETVNSDEELIEKAKMKKERHKFDIIVAN 358
                                   5567777899****9999999999999999999999999866 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00023         1      16      84 ..     199     262 ..     191     272 .. 0.73
   2 ?   -1.1   0.0      0.39   1.7e+03      77     106 ..     332     361 ..     329     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00023
                          FlpD  16 lagvsrlqyppnvriirvpCsgrvdpefilkalekGadgVlvlgChpgdChyvkGnekaerrveklkel 84 
                                   +ag +r  ++p vr+i   +sg++ +++  +a  +Gad +lv g    +      ++ ++ rv+ ++e+
  gi|70606291|ref|YP_255161.1| 199 TAGPTREYIDP-VRFISNSSSGTMGVSIANEAYFRGADVILVHGPLSSS----VKPYTKRIRVDTTQEM 262
                                   56656656666.******************************8755332....2345555555555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.39
                          FlpD  77 rveklkelleelgiepeRvrleevsaaege 106
                                   +v+  +el+e+ ++++eR ++  + a++ +
  gi|70606291|ref|YP_255161.1| 332 TVNSDEELIEKAKMKKERHKFDIIVANNVK 361
                                   6777789999********999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2794.40
//
Query:       gi|70606292|ref|YP_255162.1|  [L=168]
Description: N-acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-15   55.8   0.0    6.3e-15   55.4   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.3e-10   39.4   0.1    9.7e-10   38.7   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.9e-08   34.3   0.0    4.7e-08   33.0   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.9e-06   27.2   0.0    4.3e-06   26.6   0.0    1.3  1  FR47             FR47-like protein
    0.00089   19.3   0.0     0.0039   17.3   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0044   16.7   0.0       0.01   15.5   0.0    1.5  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.012   15.1   0.4      0.021   14.3   0.4    1.4  1  Acetyltransf_15  Putative acetyl-transferase
      0.027   14.6   1.3       0.52   10.4   1.3    2.5  1  Acetyltransf_4   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   2.8e-18   6.3e-15      23     117 .]      45     145 ..      18     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2.8e-18
                                   HHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET........TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.T CS
                Acetyltransf_1  23 efeesfsleae.gllvaeedgeliGfisllkipd........ekggvayieslaVspeyrgkGlGsaLlealeeraree.g 93 
                                   e    + +e +  ++va  +ge++G+++ ++ +            ++++i s+aV + +r+ G+G+ Ll+  ++ +++  +
  gi|70606292|ref|YP_255162.1|  45 E----HLKEYGqAFYVADLEGEVVGYVMPRIEWGfsnlkhipSLVRKGHIVSIAVLEPFRKIGVGTSLLQNSLKAMKDTyN 121
                                   2....23333348999***********99999999999999955799********************************** PP

                                   ESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  94 ikkivlaveedndaairlYeklGF 117
                                   +++++l+v+++n +ai lY+k+ F
  gi|70606292|ref|YP_255162.1| 122 AEEVYLEVRVTNYPAISLYKKFNF 145
                                   *******************88998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.1   4.3e-13   9.7e-10       4      76 .]      53     147 ..      49     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 4.3e-13
                                   EEEEEEETTEEEEEEEEEEES..............TCTEEEEE-GGGTTSSHHHHHHH..HTT....SEEEEE.EEEE... CS
                Acetyltransf_7   4 evfVaeddgkivGfialslld..............aeitrlaVdpeyrgkGiGraLle..aae....kgiile.qlel... 60 
                                    ++Va+ +g++vG++   +++              ++i  +aV++ +r+ G+G+ Ll+  +++       +   +++l   
  gi|70606292|ref|YP_255162.1|  53 AFYVADLEGEVVGYVMPRIEWgfsnlkhipslvrkGHIVSIAVLEPFRKIGVGTSLLQnsLKAmkdtY--N-AeEVYLevr 130
                                   69**********9998888889999988889887777777*****************95422233331..1.123334323 PP

                                   .THHHHHHHHHHTTEEE CS
                Acetyltransf_7  61 .naekaikfYeklGFee 76 
                                    ++ +ai++Y+k+ F+e
  gi|70606292|ref|YP_255162.1| 131 vTNYPAISLYKKFNFRE 147
                                   23349**********86 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   2.1e-11   4.7e-08      29     110 ..      50     149 ..      35     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 2.1e-11
               Acetyltransf_10  29 gealllvaeeggkivGvi..elrdgs...............hisllfVdpeyrgqGigkaLleaveeeaekdgikl..elt 90 
                                       ++va+ +g++vG++  ++  ++               hi  ++V + +r+ G+g++Ll++ ++++++  +++   l+
  gi|70606292|ref|YP_255162.1|  50 YGQAFYVADLEGEVVGYVmpRI--EWgfsnlkhipslvrkgHIVSIAVLEPFRKIGVGTSLLQNSLKAMKDTYNAEevYLE 128
                                   4566889999999999995533..33346677888888888***********************999976555555699** PP

               Acetyltransf_10  91 vnasp.yavpfYeklGFkavg 110
                                   v+ ++  a+++Y+k+ F++v+
  gi|70606292|ref|YP_255162.1| 129 VRVTNyPAISLYKKFNFREVK 149
                                   *****99***********995 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.9e-09   4.3e-06      21      80 ..      87     148 ..      83     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.9e-09
                                   TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH..S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiae..rgktvllvvvasNtpsirlyeklGfeki 80 
                                    g + ++ vl+ +r+ G g++l ++  k++    + ++v l v+ +N p+i+ly+k +f++ 
  gi|70606292|ref|YP_255162.1|  87 KGHIVSIAVLEPFRKIGVGTSLLQNSLKAMKDtyNAEEVYLEVRVTNYPAISLYKKFNFREV 148
                                   5899********************99999998778999*********************987 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0039       1     126 [.      14     146 ..      14     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                                   .EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEE.TTEEEEEEEEEEEEEEETT.EEEEE....EE CS
                Acetyltransf_9   1 eirelteedldevlellkyaFqdeespleeireyfrklleesrvlgaed.ngelvgqlallplelnvpG.ktlka....ag 75 
                                   +ir +t +d+d+++++ + a  ++ +++    ++++ l e ++++ + d +ge+vg ++  + e+ + + k ++     + 
  gi|70606292|ref|YP_255162.1|  14 QIRLATLSDIDQIIRINRSALPENYPYY----FFVEHLKEYGQAFYVADlEGEVVGYVM-PRIEWGFSNlKHIPSlvrkGH 89 
                                   59*********************99995....666666666766666666*****9664.45565555544444333339* PP

                                   EEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--......SSHHHHHTTT-E CS
                Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemree.gqplsllfP......ssipiYrrfGye 126
                                   ++++av    r+ gv ++Ll+ +l+ m++  +++ ++l        + i++Y++f ++
  gi|70606292|ref|YP_255162.1|  90 IVSIAVLEPFRKIGVGTSLLQNSLKAMKDTyNAEEVYLEVrvtnypA-ISLYKKFNFR 146
                                   ****************************9876666666443332204.7888888876 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   2.8e+03      42      59 ..      50      67 ..      42      69 .. 0.76
   2 !   15.5   0.0   4.5e-06      0.01      91     142 ..      99     150 ..      84     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                  TTEEEEEEEETTEEEEEE CS
                Acetyltransf_8 42 phsepliglldgepvgyf 59
                                    +  +++ l+ge vgy+
  gi|70606292|ref|YP_255162.1| 50 YGQAFYVADLEGEVVGYV 67
                                  556678999999999997 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.5e-06
                                   HCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEE CS
                Acetyltransf_8  91 argkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekeke 142
                                   +r+ g++t+ll+  ++ + +   ++ v +E +v+N  ai+l++k  f+++k 
  gi|70606292|ref|YP_255162.1|  99 FRKIGVGTSLLQNSLKAMKDTYNAEEVYLEVRVTNYPAISLYKKFNFREVKL 150
                                   78899*******************************************9885 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   9.2e-06     0.021      75     144 ..      90     153 ..      40     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.2e-06
               Acetyltransf_15  75 iYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkglfvks 144
                                   i ++ v e +r+ G+  +lL++slk++k  Y+++ e +l   +  +      + +lY + +Fr++  +k+
  gi|70606292|ref|YP_255162.1|  90 IVSIAVLEPFRKIGVGTSLLQNSLKAMKDTYNAE-EVYLEVRVTNY-----PAISLYKKFNFREVKLLKH 153
                                   667899**************************99.89998888775.....4778899999988877776 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00023      0.52       1     149 [.      15     160 ..      15     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvaesdrivGyaylg......qfkkr..a 73 
                                   ir+at++D+++i +i+       a+ ++y       f   l+++   ++ ++ ++ ++++vGy   +      ++k     
  gi|70606292|ref|YP_255162.1|  15 IRLATLSDIDQIIRINRS-----ALPENY---PYYFFVEHLKEY---GQAFYVADLEGEVVGYVMPRiewgfsNLKHIpsL 84 
                                   666777777777777664.....333333...122233333333...4555544448888888754411100022222222 PP

                Acetyltransf_4  74 kdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngr 149
                                    ++  ++s+ +  +  +k g+g  l++   + +   +n e+ + e+ ++n ++i ++k++ F+ v+ +k ++ ++  
  gi|70606292|ref|YP_255162.1|  85 VRKGHIVSIAVL-EPFRKIGVGTSLLQNSLKAMkDTYNAEEVYLEVRVTNYPAISLYKKFNFREVKLLKHYYADGED 160
                                   344456777776.57888889988666555555599*****************************999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1147.72
//
Query:       gi|70606293|ref|YP_255163.1|  [L=154]
Description: hypothetical protein Saci_0460 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-05   24.9   0.0    2.3e-05   24.7   0.0    1.1  1  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
    2.8e-05   23.6   0.1     0.0052   16.1   0.0    2.1  2  Metallophos_3   Metallophosphoesterase, calcineurin superfami
  ------ inclusion threshold ------
      0.054   13.3   0.7       0.63    9.9   0.0    2.6  3  Thr_dehydrat_C  C-terminal regulatory domain of Threonine deh


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.8e-09   2.3e-05      18     159 ..      15     139 ..       8     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.8e-09
                 Metallophos_2  18 avlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelgtdlpeeaelel..agekvll 96 
                                    ++e++++ +vd+++ +GD+  e p    ++l+  +++ + G +D ++   + ++  +  +++l e+ +l++  +  ++ +
  gi|70606293|ref|YP_255163.1|  15 SLIEKINSLNVDYVVGLGDV--ECP----QFLR--DFYGILGEMD-NI---TTMKYLK-NTGKLIESSFLTFstNFSNITI 82 
                                   679999*************9..555....8888..8999******.22...2233333.3333335555554324445*** PP

                 Metallophos_2  97 iHgdplgvkdalaellke...aeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpetyai 159
                                   +H  p   + ++ +l+ +    ++  ++v++GH+ v+++ + g + +v  Gs + +       y+i
  gi|70606293|ref|YP_255163.1|  83 THFPP---RLEYGSLIVRnqiLTNSPKIVFHGHSEVQKIYNLGLTKIVSIGSGEKG------YYVI 139
                                   ***85...4444444444211114444**********************9998776......5555 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0011       6.5      11      52 ..       3      44 ..       1      85 [. 0.82
   2 !   16.1   0.0   8.7e-07    0.0052     196     252 ..      90     147 ..      70     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0011
                                  EE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHH CS
                 Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvkaeakadey 52
                                  i  l  +    ++l+e+i+  ++D +v +Gd+  ++   d y
  gi|70606293|ref|YP_255163.1|  3 IMALITRLPCENSLIEKINSLNVDYVVGLGDVECPQFLRDFY 44
                                  55555566667899*****************98777666655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.7e-07
                                   --S-HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--BGGGTEEEEEETTTTEE CS
                 Metallophos_3 196 ekgsevvaelvktlnPevvvvghavkeh.eelgktlvvnPGaleeGdfavvdleekkv 252
                                   e gs +v + + t +P++v+ gh++ ++  +lg t +v+ G+ e+G + + d + +++
  gi|70606293|ref|YP_255163.1|  90 EYGSLIVRNQILTNSPKIVFHGHSEVQKiYNLGLTKIVSIGSGEKGYYVIYDSNMNEI 147
                                   568888999999************999989********************99998887 PP

>> Thr_dehydrat_C  C-terminal regulatory domain of Threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.27   1.6e+03      65      79 ..      14      28 ..      11      36 .. 0.87
   2 ?    9.9   0.0   0.00011      0.63      19      45 ..      35      61 ..      29      66 .. 0.88
   3 ?    0.2   0.1      0.11   6.3e+02      23      40 ..      69      85 ..      66      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.27
                                  XXXXXXXXXXXXXXX CS
                Thr_dehydrat_C 65 delierleklgykve 79
                                  ++lie++++l+++++
  gi|70606293|ref|YP_255163.1| 14 NSLIEKINSLNVDYV 28
                                  58999*****99987 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                                  XXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                Thr_dehydrat_C 19 eqpGaLkkFlellggrndiTlfeYrka 45
                                  e p  L+ F + lg++++iT ++Y k+
  gi|70606293|ref|YP_255163.1| 35 ECPQFLRDFYGILGEMDNITTMKYLKN 61
                                  556779******************986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.11
                                  XXXXXXXXXXXXX.XXXX CS
                Thr_dehydrat_C 23 aLkkFlellggrndiTlf 40
                                  ++++F  ++++   iT f
  gi|70606293|ref|YP_255163.1| 69 SFLTFSTNFSNIT-ITHF 85
                                  899******9999.9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1044.38
//
Query:       gi|70606294|ref|YP_255164.1|  [L=290]
Description: hypothetical protein Saci_0461 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-36  125.6   0.0    3.2e-36  125.4   0.0    1.0  1  CitG           ATP:dephospho-CoA triphosphoribosyl transferas
  ------ inclusion threshold ------
       0.13   12.5   0.1       0.34   11.1   0.1    1.8  1  Lipoprotein_3  Lipoprotein


Domain annotation for each model (and alignments):
>> CitG  ATP:dephospho-CoA triphosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   3.6e-40   3.2e-36       4     280 ..      17     272 ..      14     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 3.6e-40
                                   XXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH.---- CS
                          CitG   4 avlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaa.tggv 83 
                                   ++ A +lE+s + KPG+ +r+++   ++++f ++++Sa  +++y+++a+  G       ++++++ +l++     + t +v
  gi|70606294|ref|YP_255164.1|  17 LSNATVLEASYY-KPGNASRTRDI--KGVKFSDLVQSALLSTNYYKTACIRG------SSQEKPLYDLLYMMAKISkTLQV 88 
                                   6789********.***********..***********************555......569999*9999877666687777 PP

                                   --.HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--......---..HHHHHH..T CS
                          CitG  84 NT.hkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv......eel..kdelve.kk 153
                                   N   +G+ + l +la++ +++      +s+++l+ +a +++++l+  ++++f   +++ ++      +++      +e  +
  gi|70606294|ref|YP_255164.1|  89 NFsILGTAMQLLPLAYSSSSA------DSIGQLIFRATQLIRSLDSIESRYFkMTLETLQPsylgklDRAydY---REqDD 160
                                   7549************99966......89********************************888755222321...22357 PP

                                   T--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHH CS
                          CitG 154 sltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilrrgGaegaeevqee 234
                                   +l+l+e+l++s+ +d + +++ +g++ ++ +a  +      ++++  + ++  +l++l+elpD +i rr G  +a ev++ 
  gi|70606294|ref|YP_255164.1| 161 NLSLFEILKISA-FDSAVRNMLDGYKYSLWVAKLV------EQEGYDRGILLGFLKVLCELPDGLIFRRNGGRIAMEVSKL 234
                                   9**********9.8**************9966632......23567899******************************** PP

                                   HH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                          CitG 235 ArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfl 280
                                   A ++l++        ++ ++ ld++lv+r+++PG++AD++a+++ +
  gi|70606294|ref|YP_255164.1| 235 ACQCLSN--------EKLVSILDEYLVSRGYNPGSTADIVAVGIAI 272
                                   ******9........789*************************987 PP

>> Lipoprotein_3  Lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.8e-05      0.34      42      65 ..     174     197 ..     119     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                 Lipoprotein_3  42 kgtvkvLldgWkytLldqkiLeke 65 
                                   +++v+ +ldg+ky+L  +k++e+e
  gi|70606294|ref|YP_255164.1| 174 DSAVRNMLDGYKYSLWVAKLVEQE 197
                                   5789*****************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2049.94
//
Query:       gi|70606295|ref|YP_255165.1|  [L=304]
Description: hypothetical protein Saci_0462 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-08   34.4   0.2    4.6e-08   33.2   0.2    1.7  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.036   14.1   0.1    1.8  1  Polbeta       Polymerase beta, Nucleotidyltransferase
      0.062   13.4   0.1       0.17   12.0   0.1    1.7  1  DUF2540       Protein of unknown function (DUF2540)


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2   7.7e-12   4.6e-08      14      80 ..     121     190 ..      93     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7.7e-12
                                   TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH..HHHEHHHHHHHHCCCEEECTTEEEEEE..CEEECC CS
                  NTP_transf_2  14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre..kkeegleklaeiikfleellglevdlv..trekle 80 
                                     ++ + GS  ++t+++ SD+D+++++ +e+  +  + +eg +++ e+i+++++  gle dlv  +++ ++
  gi|70606295|ref|YP_255165.1| 121 TSRLGVSGSLLTNTYHELSDLDIVIYGCKESL-NviESFEGFNDDEEWIYETSKNYGLELDLVkkLYTRKI 190
                                   5688999***********************64.57*99*************************66333333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.1e-06     0.036      20      54 ..     128     170 ..     114     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                   EEEE-S------EEEEEEEESS-........--HHHHHHHHHH CS
                       Polbeta  20 GSrakgkareeSDiDlavllkek........ldleeelelaae 54 
                                   GS ++++++e SD+D+ ++  ++        + +++  e+  e
  gi|70606295|ref|YP_255165.1| 128 GSLLTNTYHELSDLDIVIYGCKEslnviesfEGFNDDEEWIYE 170
                                   9******************988876666444444444444444 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.8e-05      0.17      29      69 ..      94     135 ..      87     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHS---EEEEEE--HHHHHH.HHHHGGGHHHHHHHH CS
                       DUF2540  29 etlkkakeaekktkktltLsdeEkkI.vkklGkaanlLlNcv 69 
                                   e+++++++ + + k+ ltL ++ + I  ++lG + +lL N +
  gi|70606295|ref|YP_255165.1|  94 EKIREIIKHPSQSKQELTLLEIIQYIhTSRLGVSGSLLTNTY 135
                                   79***********************9669**********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2060.68
//
Query:       gi|70606296|ref|YP_255166.1|  [L=300]
Description: hypothetical protein Saci_0463 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.4e-114  380.7   0.0   6.5e-114  380.5   0.0    1.1  1  DUF1464   Protein of unknown function (DUF1464)


Domain annotation for each model (and alignments):
>> DUF1464  Protein of unknown function (DUF1464)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.5   0.0  3.6e-118  6.5e-114       1     327 []       5     288 ..       5     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 3.6e-118
                       DUF1464   1 GiDPGtksydvvvvddlgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselaereillltlaeese 81 
                                   GiDPG+++y+ ++v+++g++  + eiptd+v++++++l++++ ++r+ +va+pSG+GlP+k+i++l+e+ei+lltla++++
  gi|70606296|ref|YP_255166.1|   5 GIDPGSRTYEAISVTETGNISRKIEIPTDLVKQASYSLLRYLLDERPVAVAMPSGHGLPFKKITDLSEKEIFLLTLADPEK 85 
                                   9******************************************************************************** PP

                       DUF1464  82 eglvGLrellkelaskel..naftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeeeeyrel..sFilvEvGs 158
                                   eg+  Lr++++  +sk++  n+ftiPgVieL++vP +RK+n+iDmGtADK+asa++          yr++  +F+lvE+Gs
  gi|70606296|ref|YP_255166.1|  86 EGH--LRNFIR--SSKAYifNGFTIPGVIELDSVPVYRKINVIDMGTADKVASAFF----------YRTMydNFVLVEIGS 152
                                   ***..******..5555556************************************..........999999********* PP

                       DUF1464 159 gfnaviaVknGkivDGlGgtilpGflsaGalDgEvAyllgkvakiekslifsgGvasiageaelekklseeaferlkevvk 239
                                   +f+++++V+nG+i+DG+GgtilpGf+saG+lDgE+Ayll+k+aki+k++i+sgG                 ++er +e+++
  gi|70606296|ref|YP_255166.1| 153 NFSSILVVQNGEITDGFGGTILPGFSSAGFLDGEIAYLLCKYAKISKETIYSGG-----------------NWERGVEIIR 216
                                   ******************************************************.................9********* PP

                       DUF1464 240 svaellsskykleeiivSGrlkrikelgkklesrleevkllelaskaKeaaqGaAiianalaGgryrelvdhleiekssgt 320
                                   +++e++ssky+l+ iivSGr+k+ +++gkk+++ +            Ke+a+G+A+ian+l+Gg+yr+++d+l   ks+gt
  gi|70606296|ref|YP_255166.1| 217 IISEWYSSKYDLP-IIVSGRRKWDVDFGKKFSFPF------------KESAIGSAYIANSLYGGIYRKYIDFL---KSAGT 281
                                   *************.*********************............**************************...***** PP

                       DUF1464 321 vldyvkl 327
                                   +l++v+l
  gi|70606296|ref|YP_255166.1| 282 PLSHVRL 288
                                   *****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2354.53
//
Query:       gi|70606297|ref|YP_255167.1|  [L=164]
Description: hypothetical protein Saci_0464 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1199.67
//
Query:       gi|70606298|ref|YP_255168.1|  [L=218]
Description: hypothetical protein Saci_0465 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1656.60
//
Query:       gi|70606299|ref|YP_255169.1|  [L=122]
Description: hypothetical protein Saci_0467 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-11   43.1   3.3    2.9e-10   40.7   3.3    1.8  1  PIN              PIN domain
  ------ inclusion threshold ------
      0.018   14.8   0.1       0.03   14.1   0.1    1.4  1  DUF5615          Domain of unknown function (DUF5615)
      0.044   13.8   0.3      0.053   13.5   0.3    1.2  1  Band_7           SPFH domain / Band 7 family
      0.044   13.9   0.2      0.099   12.7   0.2    1.6  1  Ribosomal_L18A   Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18
       0.47   10.5   2.1        1.1    9.3   0.1    2.1  3  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   3.3   8.1e-14   2.9e-10       1     121 [.       2     113 ..       2     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 8.1e-14
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                   ++lD++v+i+++rg++++ ++++ +e  ++++t++  ++E+l+                ++++  + + i p++a+ a +a
  gi|70606299|ref|YP_255169.1|   2 VILDSNVIIRVMRGDKNTFKVVEEFE--DTIATTVFNVYEILRSKFG-----------YKVREHIEKMVIYPFTAREASIA 69 
                                   68****************99999999..9********9999887666...........89999999999************ PP

                                   HHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                           PIN  82 aeialkyg.....llpnDaliaAtAkehgikliatfDedfrrvak 121
                                   ++i++++      +  +D lia+  k+++  li t+D+df++++k
  gi|70606299|ref|YP_255169.1|  70 SDIYRELAsrgkiKEDIDVLIASIVKSNNEVLI-TYDKDFEDIKK 113
                                   ******999999******************999.*******9976 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.3e-06      0.03      37      61 ..      87     111 ..      57     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
                       DUF5615  37 DeeileyAkeedriivTkDkDFgel 61 
                                   D  i ++ k+++ +++T DkDF ++
  gi|70606299|ref|YP_255169.1|  87 DVLIASIVKSNNEVLITYDKDFEDI 111
                                   556778899*************997 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.5e-05     0.053      61     130 ..       2      78 ..       1     118 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                        Band_7  61 vtidvtviyrv...pddapklvaav....eresanldnlirrvlesalrevisemtleellsnreelaeelknelne 130
                                   v +d+ vi+rv    ++++k+v ++    +++  n+ +++r+++  ++re+i +m +  + +  + +a+++ +el++
  gi|70606299|ref|YP_255169.1|   2 VILDSNVIIRVmrgDKNTFKVVEEFedtiATTVFNVYEILRSKFGYKVREHIEKMVIYPFTAREASIASDIYRELAS 78 
                                   78999********************5555555555*****************9998888888878888888877775 PP

>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.8e-05     0.099      74     112 ..      46      84 ..      13      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                                   .....TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---G CS
                Ribosomal_L18A  74 rydsrsgthnfykeyrdlteegaveqvYselgsrhrakr 112
                                    y+ r++ ++++ +    +e+++ + +Y+el+sr ++k+
  gi|70606299|ref|YP_255169.1|  46 GYKVREHIEKMVIYPFTAREASIASDIYRELASRGKIKE 84 
                                   499*********************************996 PP

>> Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.13   4.6e+02     136     154 ..      15      33 ..       2      39 .. 0.59
   2 ?   -3.6   0.0       2.9   1.1e+04     104     113 ..      48      57 ..      42      57 .. 0.62
   3 ?    9.3   0.1   0.00032       1.1      87     127 ..      66     108 ..      61     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
               Spore_YhcN_YlaJ 136 drlrtgaaieevgatfkem 154
                                    + +t + +ee+++t+ ++
  gi|70606299|ref|YP_255169.1|  15 GDKNTFKVVEEFEDTIATT 33 
                                   4444444555555555554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.9
               Spore_YhcN_YlaJ 104 kVketVekvv 113
                                   kV+e +ek+v
  gi|70606299|ref|YP_255169.1|  48 KVREHIEKMV 57 
                                   6666666664 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00032
               Spore_YhcN_YlaJ  87 vlVavqtde..sdnekvkkkVketVekvvddiknVyVvtdpdv 127
                                   + +a ++ +  + + k+k+++   + ++v++ ++V ++ d+d+
  gi|70606299|ref|YP_255169.1|  66 ASIASDIYRelASRGKIKEDIDVLIASIVKSNNEVLITYDKDF 108
                                   556666666678899**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 893.85
//
Query:       gi|70606300|ref|YP_255170.1|  [L=82]
Description: hypothetical protein Saci_0468 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-24   84.0   2.8      1e-23   83.9   2.8    1.0  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
       0.01   15.3   0.6      0.011   15.1   0.6    1.0  1  DUF3387       Domain of unknown function (DUF3387)
      0.016   15.7   0.0      0.031   14.8   0.0    1.4  1  VWA_N         VWA N-terminal
      0.025   14.6   0.2      0.027   14.5   0.2    1.2  1  DUF5532       Family of unknown function (DUF5532)
      0.028   14.3   0.2      0.029   14.2   0.2    1.1  1  SKA1          Spindle and kinetochore-associated protein 1
      0.028   13.7   0.1       0.03   13.7   0.1    1.0  1  DegV          Uncharacterised protein, DegV family COG1307
      0.031   14.5   0.2       0.11   12.7   0.0    1.8  2  MatP_C        MatP C-terminal ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   2.8     4e-27     1e-23       1      69 []       3      73 ..       3      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4e-27
                  VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLle...kkkkgkkkellelfgilseeeadeiekaskelrkefk 69
                                  K I+Isd+vY+kL+klK+ g+SFs++I++L+e   k++kg+k++ll++fgil+eeea+e+ +++ ++rk+f+
  gi|70606300|ref|YP_255170.1|  3 KVITISDDVYDKLSKLKK-GRSFSETINELIEfynKNRKGNKDVLLQMFGILNEEEATEMASETLNIRKSFR 73
                                  89****************.**************************************************997 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   4.5e-06     0.011     191     242 ..      18      69 ..       7      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-06
                       DUF3387 191 lvkskkFserLeelikkYnnraltsaevieeLielakeikeekkrgeelgLs 242
                                   l k+++Fse ++eli+ Yn++   +++v+ ++  + +e ++ + + e l++ 
  gi|70606300|ref|YP_255170.1|  18 LKKGRSFSETINELIEFYNKNRKGNKDVLLQMFGILNEEEATEMASETLNIR 69 
                                   6799*********************************999999998888875 PP

>> VWA_N  VWA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.031      66     109 ..       5      51 ..       3      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                         VWA_N  66 vhvPtnvydrapevlnainwseaLdev...fkknlkedpsLkwqyFg 109
                                   + +  +vyd+ +++ +++  se ++e+   ++kn+k ++++  q+Fg
  gi|70606300|ref|YP_255170.1|   5 ITISDDVYDKLSKLKKGRSFSETINELiefYNKNRKGNKDVLLQMFG 51 
                                   567789***************99886433399**************9 PP

>> DUF5532  Family of unknown function (DUF5532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   1.1e-05     0.027      28      66 ..      30      71 ..      12      82 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                       DUF5532 28 alvenfnkesk..Ksnllkthgisl.kEAqkmLsqnLnalsl 66
                                  +l+e +nk+ k  K  ll+++gi   +EA +m s +Ln+ ++
  gi|70606300|ref|YP_255170.1| 30 ELIEFYNKNRKgnKDVLLQMFGILNeEEATEMASETLNIRKS 71
                                  45666666554337789*****987258**********8665 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.1e-05     0.029     128     187 ..       4      64 ..       1      79 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                   S----HHHHTTS-HHHHSS--HHHHHHHHHHHHHHHHHHHHHTT--TTT--.HHHHHHHHH CS
                          SKA1 128 vayiteeefesipsYmkGRLtlekiNaaidelnkaveakykilaqpkkkls.esdrelale 187
                                   v  i+++ ++++++  kGR   e iN+ i+ +nk  +++ ++l q    l+ e++ e+a+e
  gi|70606300|ref|YP_255170.1|   4 VITISDDVYDKLSKLKKGRSFSETINELIEFYNKNRKGNKDVLLQMFGILNeEEATEMASE 64 
                                   6679*************************************99999888873444555555 PP

>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.2e-05      0.03     194     249 ..      13      68 ..       3      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                   TEEEEEEEESSHHHHHHHHHHHHHHHHTTTSEEEEEEEECS-HHHHHHHHHHHCCC CS
                          DegV 194 geleplakvrgqkkaleklielikkdeeekkaervavlhagaeeeaeelkellkak 249
                                    +l++l+k r++++++++lie+ +k ++++k   + +    +eeea e++ +  + 
  gi|70606300|ref|YP_255170.1|  13 DKLSKLKKGRSFSETINELIEFYNKNRKGNKDVLLQMFGILNEEEATEMASETLNI 68 
                                   68999****************77777777777777777777999999988877665 PP

>> MatP_C  MatP C-terminal ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.2e-05      0.11      12      47 ..      10      43 ..       3      50 .. 0.79
   2 ?   -0.3   0.0      0.48   1.2e+03      35      50 ..      52      67 ..      46      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                        MatP_C 12 avWqrLsklsqrrgsTLSetivqLieeaerkekyee 47
                                   v+ +Lskl   +g+  Seti++Lie  ++++k ++
  gi|70606300|ref|YP_255170.1| 10 DVYDKLSKLK--KGRSFSETINELIEFYNKNRKGNK 43
                                  5889999995..57789*********8887776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                        MatP_C 35 Lieeaerkekyeeqvs 50
                                  +++e+e +e ++e+++
  gi|70606300|ref|YP_255170.1| 52 ILNEEEATEMASETLN 67
                                  5788888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 546.66
//
Query:       gi|70606301|ref|YP_255171.1|  [L=644]
Description: hypothetical protein Saci_0472 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   22.2   0.3    0.00035   20.7   0.1    1.9  2  DUF87     Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1     2e-08   0.00035      95     226 ..     380     512 ..     350     513 .. 0.90
   2 ?   -2.8   0.0      0.31   5.5e+03     132     141 ..     562     571 ..     517     631 .. 0.49

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2e-08
                         DUF87  95 wsldpeelldllee.ddkpaaavqrsvleealdqakakeekeklssdepveklleelk.kekeelrklknqaiarlldkle 173
                                    +l + el++ l   ++++ ++ qr ++  + +++  +e+ke++s+d++++  +++    +k+  ++ ++++   +++ l 
  gi|70606301|ref|YP_255171.1| 380 MDLGIPELITALSNgKYDTMSEPQRVAISLLARKVI-PELKEEISFDKLLNDANKQRSiFMKLLTNNVDERTVPVIIRYLI 459
                                   667788999999999999999999999999999998.7*************999999977777****************** PP

                         DUF87 174 dllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilrr 226
                                   d+  ++++++ + ++   +  ++ + ++ i+ii+l+g++++ q++v s +lr 
  gi|70606301|ref|YP_255171.1| 460 DFVGTNRNIGLELQNAHGNPIKDTNIHEGINIIQLNGLSDTMQNIVFSSVLRT 512
                                   *********999999999999999*********************99998885 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.31
                         DUF87 132 eekeklssde 141
                                    +++ + +++
  gi|70606301|ref|YP_255171.1| 562 LNIGLIGAQQ 571
                                   3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 4226.61
//
Query:       gi|70606302|ref|YP_255172.1|  [L=455]
Description: hypothetical protein Saci_0473 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00052   19.8   1.5    0.00052   19.8   1.5    1.9  2  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0     0.037   6.6e+02      76      93 ..      61      78 ..      16     163 .. 0.80
   2 !   19.8   1.5   2.9e-08   0.00052      30      94 ..     167     279 ..     147     379 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.037
                                  GCCSCEEEEECSHHCCCH CS
                          NurA 76 ekgedllllDGsligslv 93
                                  + ++dl+++DG+ ++  +
  gi|70606302|ref|YP_255172.1| 61 ATNNDLIFIDGTSRYRVI 78
                                  678999999999776655 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.9e-08
                                   CCEEECCCEEEECEBTCCHHEEEEE.........HHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCH........ CS
                          NurA  30 gggkerleealslasvdsispsdel.........errirllmetlElklgallleekgedllllDGsligslv........ 93 
                                   + + ++l+e +s  + ++i+++d           ++r+++lm+ lEl l+++l+   + +l+l+DG++ + +         
  gi|70606302|ref|YP_255172.1| 167 SDISYTLGENESGQHRQLIYREDLIssgkirqvaRNRVKELMRVLELSLLYELRQLYKDSLILMDGPIGPLIKyaglvdiy 247
                                   5566667777777777777766666888888************************************97777755555555 PP

                                   ...............................H CS
                          NurA  94 ...............................e 94 
                                                                   
  gi|70606302|ref|YP_255172.1| 248 lrevvrlrdndsnniekaydllhnvigvvkkV 279
                                   55555555555555555444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3093.55
//
Query:       gi|70606303|ref|YP_255173.1|  [L=308]
Description: hypothetical protein Saci_0474 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-16   61.0   0.0    3.1e-16   59.9   0.0    1.5  1  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil
     0.0084   15.9   0.0        0.3   10.8   0.0    2.4  3  ATP_bind_3    PP-loop family
  ------ inclusion threshold ------
      0.026   14.0   0.0       0.11   12.0   0.0    2.0  3  QueC          Queuosine biosynthesis protein QueC
       0.12   11.4   0.0        0.2   10.8   0.0    1.3  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0     7e-20   3.1e-16       6     151 ..      28     187 ..      25     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7e-20
                                   --SSCTCHHHHHHHHHHCTTH......EEEEEE-STB-HHHH.HHHHHHHHHT...T-EEEEEE-SCHHHHHHHHHH-..S CS
                   PAPS_reduct   6 vsgGkdslVllhLalkafkpv......pvvfvdtghefpeti.efvdeleery...glrlkvyepeeevaekinaekh..g 74 
                                   +sgGkds+ +l L+lka++ +       vv++dt  e+p +  e +d+le+     +++ +  +p e++  ++++ ++  +
  gi|70606303|ref|YP_255173.1|  28 FSGGKDSTTVLSLTLKAMERGamiktlYVVYADTLLEHPILRkEALDALESLKvypNVKPIRLTPIEDFISMMVERGYpaP 108
                                   9*******************77899888**********9775145566654323479996666666666666666555115 PP

                                   -THHHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEE.....E-CCCT--HHHHHHHHHH CS
                   PAPS_reduct  75 sslyeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslr.....vfPllnWteedvwqyilr 150
                                   s+ +++ + +  K++p+k+ +e+l++ + l+G+R +es++rak+  ++ + +  k +r     ++P+l+Wt edv++y+++
  gi|70606303|ref|YP_255173.1| 109 SHRFRW-CMERLKLRPMKRFMEQLGKFVQLSGVRMTESSERAKQTAYNGKHE--KIIRlgnpiIMPILDWTTEDVFRYLRS 186
                                   667777.9999***********************************998888..44442244378**************98 PP

                                   C CS
                   PAPS_reduct 151 e 151
                                   e
  gi|70606303|ref|YP_255173.1| 187 E 187
                                   6 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   6.6e-05       0.3       4      33 ..      26      57 ..      24      80 .. 0.79
   2 ?   -3.3   0.0       1.4   6.4e+03     128     158 ..     156     186 ..     141     188 .. 0.64
   3 ?    2.2   0.0      0.03   1.3e+02      70      92 ..     241     263 ..     221     269 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                                  EE--SCHHHHHHHHHHHHHCTTTTT..EEEEE CS
                    ATP_bind_3  4 vAvSgGlDSmaLllllaklkkklgi..klvai 33
                                  +++SgG DS++ l l+ k  ++ ++  +l ++
  gi|70606303|ref|YP_255173.1| 26 LGFSGGKDSTTVLSLTLKAMERGAMikTLYVV 57
                                  79************999998877764444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                                   -S-SEEEETTCCEE-CCCT--HHHHHHHHHH CS
                    ATP_bind_3 128 gikeaseiasirlvRPlLkvskeeleeylke 158
                                   g +e+  + +  ++ P+L+ + e++ +yl+ 
  gi|70606303|ref|YP_255173.1| 156 GKHEKIIRLGNPIIMPILDWTTEDVFRYLRS 186
                                   4444444455678888898888888888776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.03
                                   HCTTSTCCCHHHHHHHHHHHHCH CS
                    ATP_bind_3  70 kkkgknleeaARelRYevlkeal 92 
                                   k+  k + +  R+lRY+++++  
  gi|70606303|ref|YP_255173.1| 241 KEARKMIMDISRDLRYRIIDKNG 263
                                   3457789999********99875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.11       6      33 ..      28      55 ..      26      83 .. 0.76
   2 ?   -2.2   0.0      0.52   2.3e+03     153     194 ..     167     212 ..     147     220 .. 0.68
   3 ?   -3.0   0.0      0.91   4.1e+03     113     144 ..     275     306 ..     273     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                  --SSHHHHHHHHHHHHH-SEEEEEEEES CS
                          QueC  6 lSGGlDSttvlalakkegkevealtfdY 33
                                  +SGG DSttvl l +k++++ ++++  Y
  gi|70606303|ref|YP_255173.1| 28 FSGGKDSTTVLSLTLKAMERGAMIKTLY 55
                                  9*********988777666655555444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.52
                                   EEE-TTTT--HHHHHHHHHHTT....HHHHH-B-STTS.-BTTTTS CS
                          QueC 153 eieaPlidlsKaeivklgkelg....vpleetlsCYegeeegkaCg 194
                                    i +P++d++ +++++   +       ++++ l  Ye +e++++Cg
  gi|70606303|ref|YP_255173.1| 167 PIIMPILDWTTEDVFRYLRSERrwdgREFDYLLNLYEVKEDNDGCG 212
                                   5777888888888877665554455566777777788888888887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.91
                                   T-SEEEE---S-STT--GGGSHHHHHHHHHHH CS
                          QueC 113 gaeaiiiGvneedfsgYPDcrdefvkalnkal 144
                                   ++ +++iGv e++ +++   ++e  ++l+k++
  gi|70606303|ref|YP_255173.1| 275 EVAKVFIGVLEKEPEAFGYDTKELREKLEKVI 306
                                   67899999999998888777777777777665 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.4e-05       0.2      23      47 ..      26      50 ..       9      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.4e-05
                                  EEE-SSHHHHHHHHHHHHHHTCGEE CS
                  NAD_synthase 23 lGlSGGvDSslvaalavkalgkenv 47
                                  lG SGG DS++v  l+ ka+++  +
  gi|70606303|ref|YP_255173.1| 26 LGFSGGKDSTTVLSLTLKAMERGAM 50
                                  8*******************87554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2010.37
//
Query:       gi|70606304|ref|YP_255174.1|  [L=217]
Description: hypothetical protein Saci_0475 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.9e-107  356.4   8.0   3.4e-107  356.2   8.0    1.0  1  VirArc_Nuclease  Viral/Archaeal nuclease
  ------ inclusion threshold ------
      0.019   13.9   0.0      0.023   13.7   0.0    1.1  1  Myotub-related   Myotubularin-like phosphatase domain


Domain annotation for each model (and alignments):
>> VirArc_Nuclease  Viral/Archaeal nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.2   8.0  3.7e-111  3.4e-107       1     190 []       4     198 ..       4     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 356.2 bits;  conditional E-value: 3.7e-111
               VirArc_Nuclease   1 dfklkywansa.edfelpseylgreylvygklliklkkwkekgllkfdvyirrtgvgtltsvinedyykdlldkydltlyv 80 
                                   dfk++ywans+ ++fe+p+e+lgreyl+yg+l+iklk+wkekgl+++++y+rrtg+gtltsvin+dyykd+ldkyd+t+y+
  gi|70606304|ref|YP_255174.1|   4 DFKQRYWANSNfDGFEVPNEHLGREYLIYGLLHIKLKQWKEKGLIPDNIYLRRTGIGTLTSVINHDYYKDVLDKYDFTIYY 84 
                                   7******************************************************************************** PP

               VirArc_Nuclease  81 kak....dryypllyidvtGssfteeqskkrygeaiyailstkvevakelevlGrtifihyadredklklisalrilnlek 157
                                   ++k    dry+p+l+id+tGss+teeqs++ryge+iya+lstkv+va+e++vlGrtifihy+dredklkli+al+ilnl++
  gi|70606304|ref|YP_255174.1|  85 HYKengeDRYWPGLFIDTTGSSWTEEQSEQRYGEPIYAVLSTKVWVAQEFDVLGRTIFIHYNDREDKLKLIVALSILNLYG 165
                                   ***99999************************************************************************* PP

               VirArc_Nuclease 158 qgkikkeeiefaaksryyiiplkfWknltelrv 190
                                   q+ki+++e+e++aks+yyiip+kfWkn+telrv
  gi|70606304|ref|YP_255174.1| 166 QNKIRLNEYEYGAKSQYYIIPVKFWKNITELRV 198
                                   *******************************97 PP

>> Myotub-related  Myotubularin-like phosphatase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.5e-06     0.023     197     257 ..     103     163 ..      40     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-06
                                   -HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHCS---EEEE-SSSSSHHHHHHHHHHHHH CS
                Myotub-related 197 sekkwlsaLekskWlkhiksiLeaaaliaksvelekssvLvhcsdGwDrtsqlsslaqllL 257
                                   + ++w+++ +++++ + i ++L++++++a++ ++ ++++ +h +d  D+   +++l+ l L
  gi|70606304|ref|YP_255174.1| 103 TGSSWTEEQSEQRYGEPIYAVLSTKVWVAQEFDVLGRTIFIHYNDREDKLKLIVALSILNL 163
                                   457899999999999*****************************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1475.39
//
Query:       gi|70606305|ref|YP_255175.1|  [L=49]
Description: hypothetical protein Saci_0476 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-08   32.6   0.4    5.7e-08   32.4   0.4    1.1  1  RHH_1     Ribbon-helix-helix protein, copG family
    0.00021   21.2   0.3    0.00025   21.0   0.3    1.1  1  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.4   6.4e-12   5.7e-08       2      38 ..       4      40 ..       3      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 6.4e-12
                                  EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                  ++++ +e+l+ +Ld  a+  ++SrSe+IReAl  +le
  gi|70606305|ref|YP_255175.1|  4 INFKAEEDLVSKLDLYAINKRVSRSEIIREALQKFLE 40
                                  78999****************************9997 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   2.8e-08   0.00025      10      41 ..       9      40 ..       4      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.8e-08
                         RHH_3 10 dpelaekLkaLSekTrIprSklldeAiellLe 41
                                  +++l+ kL+ +    r+ rS++++eA+  +Le
  gi|70606305|ref|YP_255175.1|  9 EEDLVSKLDLYAINKRVSRSEIIREALQKFLE 40
                                  6899**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 337.62
//
Query:       gi|70606306|ref|YP_255176.1|  [L=86]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   17.3   1.0     0.0042   16.7   1.0    1.2  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   2.3e-07    0.0042      16      39 ..      38      60 ..      38      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-07
                          SWIM 16 tCsCpefqkngipCkHalAvllal 39
                                  +CsC + + +g +CkH+l +++++
  gi|70606306|ref|YP_255176.1| 38 SCSCEASS-YGMLCKHVLKLYNYY 60
                                  7*****99.*********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 478.38
//
Query:       gi|70606307|ref|YP_255177.1|  [L=117]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 638.90
//
Query:       gi|70606308|ref|YP_255178.1|  [L=102]
Description: hypothetical protein Saci_0479 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00086   19.8   0.0     0.0013   19.2   0.0    1.3  1  HTH_27    Winged helix DNA-binding domain
      0.001   18.9   0.1     0.0014   18.4   0.1    1.2  1  RuvB_C    RuvB C-terminal winged helix domain
     0.0032   17.4   0.3     0.0038   17.2   0.3    1.2  1  HTH_45    Winged helix-turn-helix
     0.0054   16.5   0.0     0.0064   16.3   0.0    1.2  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.036   13.9   0.2      0.071   13.0   0.2    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
        0.1   12.4   0.1       0.15   11.9   0.1    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.3e-07    0.0013      16      68 .]      33      83 ..      24      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.3e-07
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkk.LtekGLvertgdeadrrekrvrlTdkG 68
                                  +++ +l++l ++ nv+   + + ++k L + GL+   ++e+ +r+++v+lTdkG
  gi|70606308|ref|YP_255178.1| 33 EEPRTLSELWEAANVSTGIYYNTIEKnLLALGLI---KYEEKGRSTLVSLTDKG 83
                                  5777889999999998888887775549******...888889**********9 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.8e-07    0.0014      21      71 ..      33      87 ..      24      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                                  T--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEE....E-HHHHHHH CS
                        RuvB_C 21 ggpvglktlaailgeeketiedviEPyLlkeglIertsrGRi....lTkkglkyl 71
                                  ++p  l+ l +++++++    + iE  Ll  glI+  ++GR     lT+kg+k+l
  gi|70606308|ref|YP_255178.1| 33 EEPRTLSELWEAANVSTGIYYNTIEKNLLALGLIKYEEKGRStlvsLTDKGKKLL 87
                                  56888999999******************************54444899999988 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   1.3e-06    0.0038      18      72 ..      34      93 ..      21      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                        HTH_45 18 geakkTkimykanLsykllnkYLd.mLvekgli....kkskekYvlTekGlelleklkel 72
                                  +  + +++  +an s  +  + ++  L+  gli    k +++  +lT+kG++lle +ke+
  gi|70606308|ref|YP_255178.1| 34 EPRTLSELWEAANVSTGIYYNTIEkNLLALGLIkyeeKGRSTLVSLTDKGKKLLELMKEI 93
                                  555667777788888887777775269999***776444778899************997 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0064      31      74 ..      51      91 ..      25      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                       DUF4364 31 tnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                                  + Y +++   ++L+  gli+ eek  +tl ++T+kGk+ lel++
  gi|70606308|ref|YP_255178.1| 51 IYYNTIE---KNLLALGLIKYEEKGRSTLVSLTDKGKKLLELMK 91
                                  4444444...466667*************************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.4e-05     0.071      13      58 ..      25      72 ..      23      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                  HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHH.HHHHCTSEEEESST CS
                          TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLr.sLedkGlVerekgr 58
                                   Y +Ll  ++p t +e+ e+++v+    Y++++ +L+  Gl++ e++ 
  gi|70606308|ref|YP_255178.1| 25 LYRVLLaLEEPRTLSELWEAANVSTGIYYNTIEkNLLALGLIKYEEKG 72
                                  6899998899*********************9636*******988754 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.2e-05      0.15      55      88 ..      56      88 ..      45      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                       DUF1495 55 sessLielGLveeeeeseglklYklteeGieive 88
                                   e+ L++lGL++  ee+   +l +lt++G+++ e
  gi|70606308|ref|YP_255178.1| 56 IEKNLLALGLIK-YEEKGRSTLVSLTDKGKKLLE 88
                                  4889*******6.5777888899*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 568.80
//
Query:       gi|70606309|ref|YP_255179.1|  [L=96]
Description: hypothetical protein Saci_0480 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   17.9   1.5     0.0032   17.4   1.5    1.4  1  HTH_45    Winged helix-turn-helix
     0.0039   17.0   0.4     0.0046   16.7   0.4    1.1  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.029   14.2   0.7       0.16   11.8   0.1    1.9  2  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.041   13.9   0.5      0.064   13.2   0.5    1.4  1  PadR      Transcriptional regulator PadR-like family
      0.041   14.4   0.0      0.052   14.0   0.0    1.2  1  HTH_27    Winged helix DNA-binding domain
      0.056   13.7   0.0      0.074   13.3   0.0    1.2  1  DUF5493   Family of unknown function (DUF5493)
      0.089   11.6   0.0      0.092   11.6   0.0    1.0  1  NodZ      Nodulation protein Z (NodZ)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5   1.2e-06    0.0032      39      73 ..      44      82 ..      14      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                        HTH_45 39 YLdmLvekgli....kkskekYvlTekGlelleklkele 73
                                   + ++++ gli    +++k+  +lTekG++lle l+++e
  gi|70606309|ref|YP_255179.1| 44 VIPTMLKLGLIeisyENRKKIIRLTEKGRKLLEVLNDIE 82
                                  478999****9999999****************999886 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.8e-06    0.0046       9      75 ..      17      80 ..      11      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                       DUF4364  9 lkkvkfpltnsqlseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfen 75
                                  lk+v+ ++    l+e+ +++ +++   +  ++  +++ glie + ++ k+++++TekG++ le +++
  gi|70606309|ref|YP_255179.1| 17 LKHVQSEI---SLNELYTKTRIASSAFYYTVIPTMLKLGLIEISYENRKKIIRLTEKGRKLLEVLND 80
                                  55555444...455556666666666677788999999******99****************98865 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.15   3.8e+02      15      40 ..      13      38 ..       4      41 .. 0.73
   2 ?   11.8   0.1   6.1e-05      0.16      58      90 .]      47      78 ..      38      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                       DUF1495 15 llyLysiypeksnlqeisrrvrskps 40
                                  l+ ++++++++  l+e+ +++r ++s
  gi|70606309|ref|YP_255179.1| 13 LYLILKHVQSEISLNELYTKTRIASS 38
                                  44456788889999999999998765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.1e-05
                       DUF1495 58 sLielGLveeeeeseglklYklteeGieivevl 90
                                   +++lGL+e  + ++  k+ +lte+G+++ evl
  gi|70606309|ref|YP_255179.1| 47 TMLKLGLIE-ISYENRKKIIRLTEKGRKLLEVL 78
                                  6899****5.78889999**********99875 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.5e-05     0.064      19      74 ..      26      76 ..      11      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                  HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 19 leelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  l+el++  + +s +  Y++  ++ k gl+e + e+     ++k+ rlT++Gr+ l+
  gi|70606309|ref|YP_255179.1| 26 LNELYTKTRIASSAFYYTVIPTMLKLGLIEISYEN-----RKKIIRLTEKGRKLLE 76
                                  7788888888999999****************887.....8***********9876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     2e-05     0.052      11      68 .]      15      71 ..       4      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                        HTH_27 11 lir.hrrrrkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  li  h + + +l +l  ++ + +s++   ++  + + GL+ +  +e   r k +rlT+kG
  gi|70606309|ref|YP_255179.1| 15 LILkHVQSEISLNELYTKTRIASSAFYyTVIPTMLKLGLI-EISYE--NRKKIIRLTEKG 71
                                  444444467777999999999999999999**********.45555..8**********9 PP

>> DUF5493  Family of unknown function (DUF5493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.074      44      72 ..      28      58 ..      10      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                       DUF5493 44 qgytdiafssstfylgvlpll..lglvnlgy 72
                                  + yt   ++ss+fy  v+p +  lgl+++ y
  gi|70606309|ref|YP_255179.1| 28 ELYTKTRIASSAFYYTVIPTMlkLGLIEISY 58
                                  5699999************652268998887 PP

>> NodZ  Nodulation protein Z (NodZ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.6e-05     0.092      60     130 ..      22      92 ..       4      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                          NodZ  60 edigGvrvicddrinelslpgpffpawwnkpsiesvyrpdeqifrerdeldelfqaqddadantvvcdacl 130
                                    +i+  +++ + ri++ ++  +++p+  ++  ie  y + ++i+r  ++ ++l+   +d + + v+    l
  gi|70606309|ref|YP_255179.1|  22 SEISLNELYTKTRIASSAFYYTVIPTMLKLGLIEISYENRKKIIRLTEKGRKLLEVLNDIEFEKVIAKEAL 92 
                                   467777888999**************************************************999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 641.93
//
Query:       gi|70606310|ref|YP_255180.1|  [L=188]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0019   18.1   2.5      0.011   15.6   0.1    2.5  2  PadR          Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
       0.01   15.3   0.9      0.026   14.0   0.9    2.0  1  SieB          Super-infection exclusion protein B
      0.033   14.3   1.0      0.042   14.0   1.0    1.2  1  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
      0.056   13.3   2.0          1    9.2   0.2    2.3  2  HxlR          HxlR-like helix-turn-helix
      0.092   12.6   0.6       0.57   10.0   0.2    2.4  2  DUF1495       Winged helix DNA-binding domain (DUF1495)
       0.19   11.8   2.3        1.7    8.8   0.1    2.0  2  PsbP          PsbP
       0.66    9.9   5.0         11    6.0   0.1    2.5  2  DUF3116       Protein of unknown function (DUF3116)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.4e-06     0.011      14      72 ..      36      86 ..      28      88 .. 0.83
   2 ?    2.0   0.2     0.082   2.1e+02      42      65 ..     123     144 ..     120     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.4e-06
                                  HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                          PadR 14 eiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                  ++++el++l    ++    ++Yp L+r   +gl+++ ++ +    + ++Y lT++G++ 
  gi|70606310|ref|YP_255180.1| 36 ALARELAQL----INTTSNEVYPRLERYIFKGLIQKARTIN----RLNIYSLTEKGKQL 86
                                  566666666....5567789*****************9985....99*********986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.082
                                   HHTTSEEEEEE-STSSS-EEEEEE CS
                          PadR  42 ekeglveseweesgegpprkyYrl 65 
                                   e++g++e++ +es    ++ yY+l
  gi|70606310|ref|YP_255180.1| 123 EEKGYIEASSTES--VAEKVYYKL 144
                                   899*****99986..567788877 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9     1e-05     0.026      69     107 ..     101     138 ..      40     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                          SieB  69 kkvekklknLteeekavLreflnqgksvltlplndpavk 107
                                   k+++k  +nL+eeek vLr f++++  +++ + ++++++
  gi|70606310|ref|YP_255180.1| 101 KAEKKLGRNLDEEEKEVLRVFYEEK-GYIEASSTESVAE 138
                                   444555589**************95.5557777776665 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   1.6e-05     0.042      31     140 ..      39     148 ..      20     156 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-T....THHHHHHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHH CS
                  Spore_III_AB  31 eelkralellegeirygatpLpealeklaekses....plseffeevaerleekegesfeeaweeavekllkklaLkkedk 107
                                   +el ++++   +e+  + +    +++ l +k +     ++ ++ e+  + l  ++g +fee+ ++a +kl    +L++e+k
  gi|70606310|ref|YP_255180.1|  39 RELAQLINTTSNEVYPRLER--YIFKGLIQKARTinrlNIYSLTEKGKQLLFLSKGSDFEEVVKKAEKKL--GRNLDEEEK 115
                                   55666666666665544444..356666655555332333333344334444469**************9..567****** PP

                                   HHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHH CS
                  Spore_III_AB 108 eilkelgeslgysdregqlkalelaleeleeei 140
                                   e+l+ + e  gy ++ + ++  e +  +l+ + 
  gi|70606310|ref|YP_255180.1| 116 EVLRVFYEEKGYIEASSTESVAEKVYYKLKGKV 148
                                   **************9999999888888777665 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0004         1      10      72 ..      27      86 ..      21     101 .. 0.82
   2 ?    3.4   0.1     0.026        67      44      68 ..     123     147 ..     114     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0004
                                  HHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGG CS
                          HxlR 10 ilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsl 72
                                  +l  l++g+    el++ + + + +    rL +   +gli++    +      YsltekG++l
  gi|70606310|ref|YP_255180.1| 27 MLLRLVQGPALARELAQLI-NTTSNEVYPRLERYIFKGLIQKARTIN--RLNIYSLTEKGKQL 86
                                  5788999999999999999.555555678999999999998865444..4458********98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.026
                                   HHTTSEEEEEESSSS-EEEEEE-TC CS
                          HxlR  44 eqdglierevypevPpkveYsltek 68 
                                   e++g ie++  ++v +kv Y+l  k
  gi|70606310|ref|YP_255180.1| 123 EEKGYIEASSTESVAEKVYYKLKGK 147
                                   78999****************9655 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00022      0.57      60      86 ..      60      86 ..      13      88 .. 0.91
   2 ?   -2.4   0.0       1.6   4.2e+03      46      48 ..     144     146 ..     121     160 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                       DUF1495 60 ielGLveeeeeseglklYklteeGiei 86
                                  i +GL+++    + l++Y+lte+G+++
  gi|70606310|ref|YP_255180.1| 60 IFKGLIQKARTINRLNIYSLTEKGKQL 86
                                  779****9999*************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                       DUF1495  46 leG 48 
                                   l+G
  gi|70606310|ref|YP_255180.1| 144 LKG 146
                                   333 PP

>> PsbP  PsbP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00066       1.7      64     148 ..      22     107 ..       6     111 .. 0.80
   2 ?    4.3   1.2     0.016        41      66     109 ..     102     150 ..      98     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHCCCHCTSSEE.EEEEEEEEEEET.TEEEEEEEEEEEETTEEEEEEEEEEEEETT.EEEEEEEEEEHHHHCC CS
                          PsbP  64 eevaerlvkqvlassesgre.aelidaeereaddgktyYeleytvkspdeqerhqlaavavsng.kLYtltlqtpekrwek 142
                                   e++a+ l++ v+ +  + re a+li++ ++e     + Y ++  ++++++ +r ++++++ + +  L+  + +  e+ ++k
  gi|70606310|ref|YP_255180.1|  22 EKIAKMLLRLVQGPA-LARElAQLINTTSNEVYPRLERYIFKGLIQKARTINRLNIYSLTEKGKqLLFLSKGSDFEEVVKK 101
                                   455566665555444.44444************9**************************955527788888999999999 PP

                                   CHHHHH CS
                          PsbP 143 vekkle 148
                                    ekkl 
  gi|70606310|ref|YP_255180.1| 102 AEKKLG 107
                                   999885 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                                   HHHHHHHHCCCHCTSS......EEEEEEEEEEEEET.TEEEEEEEEEEEE CS
                          PsbP  66 vaerlvkqvlassesg......reaelidaeereaddgktyYeleytvks 109
                                   + ++l+++++++++ +      +e+  i+a+++e+  +k yY+l+ +vk+
  gi|70606310|ref|YP_255180.1| 102 AEKKLGRNLDEEEK-EvlrvfyEEKGYIEASSTESVAEKVYYKLKGKVKL 150
                                   56677777773333.236677777999*****************999987 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0043        11      59      80 ..      66      87 ..      48      90 .. 0.80
   2 ?    5.1   1.2    0.0079        20      40      82 ..     113     152 ..      96     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0043
                       DUF3116 59 RkeekannkkrYelTekGelly 80
                                   k  ++n    Y+lTekG++l+
  gi|70606310|ref|YP_255180.1| 66 QKARTINRLNIYSLTEKGKQLL 87
                                  44555788899********986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0079
                       DUF3116  40 tkneLLytvYWLElkgyilRkeekannkkrYelTekGellyke 82 
                                      e+L++ Y  E+kgyi   + +  ++k Y+   kG+ ++ +
  gi|70606310|ref|YP_255180.1| 113 EEKEVLRVFY--EEKGYIEASSTESVAEKVYYK-LKGKVKLYR 152
                                   5568888888..*******99999899998875.567766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1304.31
//
Query:       gi|70606311|ref|YP_255181.1|  [L=99]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00027   21.1   0.1    0.00033   20.8   0.1    1.2  1  HTH_34        Winged helix DNA-binding domain
     0.0007   19.5   0.0      0.001   19.0   0.0    1.3  1  PadR          Transcriptional regulator PadR-like family
    0.00092   19.7   0.0     0.0013   19.2   0.0    1.2  1  HTH_27        Winged helix DNA-binding domain
     0.0073   16.2   0.0       0.01   15.7   0.0    1.3  1  MarR_2        MarR family
     0.0081   16.5   0.0      0.026   14.9   0.0    1.9  1  CM_2          Chorismate mutase type II
  ------ inclusion threshold ------
       0.01   15.6   0.0       0.02   14.7   0.0    1.5  1  HTH_IclR      IclR helix-turn-helix domain
      0.013   15.4   0.1      0.021   14.7   0.0    1.4  1  TrmB          Sugar-specific transcriptional regulator TrmB
       0.16   11.4   0.2       0.57    9.6   0.1    1.8  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.5e-07   0.00033      14      74 ..      28      89 ..      16      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.5e-07
                        HTH_34 14 eadfvelkealeatdgnLsvhlkkLekagYievdkefkg.kkprtllriTpeGreafkkyvk 74
                                  e + +el++a++a+ +     + kL+  g iev+ e+   k  + + ++T++Gr  f+k ++
  gi|70606311|ref|YP_255181.1| 28 EPTLSELRDATRASWSTVHNIVPKLQGLGLIEVQEEKTRvKSVKKIAKLTDKGRMVFEKILE 89
                                  66789****************************9877651667899***********99765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.5e-07     0.001      21      74 ..      33      85 ..      25      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.5e-07
                                  CCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 21 elsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  el   ++++s +++  +  +L+  gl+e ++e+++++  +k+ +lTd+Gr  ++
  gi|70606311|ref|YP_255181.1| 33 EL-RDATRASWSTVHNIVPKLQGLGLIEVQEEKTRVKSVKKIAKLTDKGRMVFE 85
                                  55.345899999**************************************8876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.7e-07    0.0013      15      68 .]      25      80 ..      15      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.7e-07
                        HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre..krvrlTdkG 68
                                   + + +l++l++++  + s++++++ kL   GL+e ++ ++  ++  k  +lTdkG
  gi|70606311|ref|YP_255181.1| 25 LLKEPTLSELRDATRASWSTVHNIVPKLQGLGLIEVQEEKTRVKSvkKIAKLTDKG 80
                                  567899****************************6666664444477888999998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.4e-06      0.01      22      55 ..      29      62 ..       9      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.4e-06
                                  EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   t +el ++++ s s+v++i+ +L+  GL+e ++
  gi|70606311|ref|YP_255181.1| 29 PTLSELRDATRASWSTVHNIVPKLQGLGLIEVQE 62
                                  499***************************9874 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.026       6      44 ..       4      42 ..       2      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHH CS
                          CM_2  6 eiDdeileLLaeRaelakevgeyKkeeglpvydpeReae 44
                                  +i++++ eLL+  ++++  vg +K+++  +++d  R  +
  gi|70606311|ref|YP_255181.1|  4 KINEQLFELLSTEMKFVLYVGLLKEPTLSELRDATRASW 42
                                  699*********************99888****999554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   9.1e-06      0.02      18      50 ..      28      60 ..      22      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
                                  S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  e tlsel ++t  + Stvh+++  L+ lG++e 
  gi|70606311|ref|YP_255181.1| 28 EPTLSELRDATRASWSTVHNIVPKLQGLGLIEV 60
                                  459***************************985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   9.5e-06     0.021      13      60 ..      21      66 ..       8      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                                  HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                          TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                   Y+ Ll  ++ t +e+  ++  + s+v +++ +L   Gl+e+++++++
  gi|70606311|ref|YP_255181.1| 21 LYVGLL--KEPTLSELRDATRASWSTVHNIVPKLQGLGLIEVQEEKTR 66
                                  577777..667899*****************************99955 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00025      0.57      23      48 ..      25      49 ..      23      49 .. 0.90
   2 ?   -1.2   0.0       0.6   1.4e+03      28      37 ..      68      77 ..      64      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
                  HTH_Tnp_ISL3 23 lllesrsvkavArqlgvSwtTVwril 48
                                  ll+e  + ++  + ++ Sw+TV++i+
  gi|70606311|ref|YP_255181.1| 25 LLKEP-TLSELRDATRASWSTVHNIV 49
                                  78888.99****************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.6
                  HTH_Tnp_ISL3 28 rsvkavArql 37
                                  +svk +A+++
  gi|70606311|ref|YP_255181.1| 68 KSVKKIAKLT 77
                                  5999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 807.48
//
Query:       gi|70606312|ref|YP_255182.1|  [L=95]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-08   32.9   0.1    6.9e-08   32.3   0.1    1.4  1  TrmB        Sugar-specific transcriptional regulator TrmB
    2.9e-05   23.8   0.3    3.5e-05   23.6   0.3    1.2  1  HxlR        HxlR-like helix-turn-helix
     0.0002   20.9   0.1    0.00027   20.4   0.1    1.2  1  HTH_24      Winged helix-turn-helix DNA-binding
     0.0012   18.7   0.6     0.0024   17.7   0.6    1.5  1  HTH_5       Bacterial regulatory protein, arsR family
     0.0028   17.5   0.1     0.0049   16.7   0.1    1.4  1  MarR_2      MarR family
     0.0036   17.8   0.1     0.0093   16.4   0.1    1.8  1  HTH_27      Winged helix DNA-binding domain
     0.0037   17.4   0.1     0.0046   17.1   0.1    1.2  1  HTH_34      Winged helix DNA-binding domain
      0.006   16.5   0.2     0.0099   15.8   0.2    1.3  1  MarR        MarR family
  ------ inclusion threshold ------
      0.025   14.6   0.1      0.046   13.8   0.1    1.4  1  FeoC        FeoC like transcriptional regulator
      0.033   14.1   0.0      0.048   13.6   0.0    1.4  1  PadR        Transcriptional regulator PadR-like family
      0.046   13.6   0.1       0.16   11.8   0.1    1.9  1  DUF1495     Winged helix DNA-binding domain (DUF1495)
      0.067   12.8   0.1       0.12   12.0   0.1    1.4  1  GntR        Bacterial regulatory proteins, gntR family
      0.079   13.2   0.3      0.079   13.2   0.3    2.0  3  Sun2_CC2    SUN2 coiled coil domain 2
      0.087   13.0   0.0       0.13   12.4   0.0    1.2  1  MotA_activ  Transcription factor MotA, activation domain
       0.16   12.1   1.1       0.21   11.7   0.3    1.5  2  HTH_9       RNA polymerase III subunit RPC82 helix-turn-helix


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   5.8e-11   6.9e-08       5      59 ..       2      58 ..       1      66 [. 0.91

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 5.8e-11
                                  HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..T CS
                          TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..p 59
                                   Lse E ++ +aLlk++++ta+e+  ++  + s  + +L+ L++ GlV+ e++   p
  gi|70606312|ref|YP_255182.1|  2 ELSEVEQRILKALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLVNEEREHsfP 58
                                  79***********************************************99987663 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.3   2.9e-08   3.5e-05       9      85 ..       9      85 ..       4      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.9e-08
                                  HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHHHH CS
                          HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwgee 85
                                   il +llk  k+   el +a  + s+++L  +L +L + gl++ e  ++ P +    lte G++++++l e++  +e+
  gi|70606312|ref|YP_255182.1|  9 RILKALLKkDKMTARELVDAS-HSSTSVLNPSLEHLIKLGLVNEEREHSFPRRRFVILTESGKEVAQLLVEIERIVEM 85
                                  577777773445556777776.8899*********************************************9988776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.3e-07   0.00027       2      47 ..       4      49 ..       3      50 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +e + +IL++L k+ +++ reL ++++ S s +n  l+ L++ Gl+
  gi|70606312|ref|YP_255182.1|  4 SEVEQRILKALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLV 49
                                  67899***************************************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.6     2e-06    0.0024       6      46 ..       9      50 ..       7      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                                  HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +ILk+L +  ++++ el+++ + s s +   L  L ++GLV+
  gi|70606312|ref|YP_255182.1|  9 RILKALLKkDKMTARELVDASHSSTSVLNPSLEHLIKLGLVN 50
                                  7*******888******************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.1e-06    0.0049       7      55 ..       7      53 ..       2      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  + r+L aL   +   +t++el+++ + s s ++  l+ L + GLv +++
  gi|70606312|ref|YP_255182.1|  7 EQRILKALLKKDK--MTARELVDASHSSTSVLNPSLEHLIKLGLVNEER 53
                                  6799********9..******************************7764 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.7e-06    0.0093      16      68 .]      17      69 ..       3      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-06
                        HTH_27 16 rrrkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   +++++++l+++  ++++++   sl++L++ GLv +++     r+++v lT++G
  gi|70606312|ref|YP_255182.1| 17 KDKMTARELVDAS-HSSTSVLnPSLEHLIKLGLVNEEREHSFPRRRFVILTESG 69
                                  5677777777764.566777779***********555555557889******98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.8e-06    0.0046       4      70 ..       9      74 ..       6      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                        HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70
                                   +l  L+++d+++++el +a   +++ L   l+ L k g ++ + e++   +r  + +T+ G+e ++
  gi|70606312|ref|YP_255182.1|  9 RILKALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLVNEEREHSFP-RRRFVILTESGKEVAQ 74
                                  699******************************************99999.677888*****99765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   8.2e-06    0.0099       1      51 [.       3      53 ..       3      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-06
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  l++++ +iL  l  ++ ++  eL ++++ s+s +   l +L+k Gl++ ++
  gi|70606312|ref|YP_255182.1|  3 LSEVEQRILKALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLVNEER 53
                                  7889999****************************************8665 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.9e-05     0.046       6      51 ..      12      56 ..       6      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                          FeoC  6 keyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaata 51
                                  k +l ++ +   +eL  + ++s++ l++ Le++++ G v+++ + +
  gi|70606312|ref|YP_255182.1| 12 K-ALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLVNEEREHS 56
                                  4.4567788999****************************998876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05     0.048      30      73 ..      32      73 ..      10      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                                  THHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR 30 seGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  s + l p L+ L k glv++e+e s   p+r++  lT+ G++  
  gi|70606312|ref|YP_255182.1| 32 STSVLNPSLEHLIKLGLVNEEREHS--FPRRRFVILTESGKEVA 73
                                  5667889**************9985..89***********9875 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00013      0.16      58      89 ..      42      75 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                       DUF1495 58 sLielGLveeeeeseglk..lYklteeGieivev 89
                                   Li+lGLv+ee e++  +  +  lte+G+e+++ 
  gi|70606312|ref|YP_255182.1| 42 HLIKLGLVNEEREHSFPRrrFVILTESGKEVAQL 75
                                  69******9877765544324559******9985 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.12       9      56 ..       6      51 ..       4      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                  HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          GntR  9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56
                                  ++++Il+  l   dk+ + reL+++ + s+++++ +L  L   glv  
  gi|70606312|ref|YP_255182.1|  6 VEQRILK-ALLKKDKM-TARELVDASHSSTSVLNPSLEHLIKLGLVNE 51
                                  6788888.677789**.****************************975 PP

>> Sun2_CC2  SUN2 coiled coil domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.6e-05     0.079       4      27 ..       2      26 ..       1      37 [. 0.85
   2 ?   -2.5   0.0       5.4   6.4e+03       8      22 ..      40      55 ..      39      61 .. 0.57
   3 ?   -1.8   0.0       3.1   3.7e+03      48      52 ..      79      83 ..      64      90 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                      Sun2_CC2  4 eLqeLEkkILaklaeeqgksard.a 27
                                  eL e E++IL+ l ++ +++ar+ +
  gi|70606312|ref|YP_255182.1|  2 ELSEVEQRILKALLKKDKMTARElV 26
                                  799******************9954 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.4
                      Sun2_CC2  8 LEkkI.Laklaeeqgk 22
                                  LE+ I L  + ee++ 
  gi|70606312|ref|YP_255182.1| 40 LEHLIkLGLVNEEREH 55
                                  5665534445566655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                      Sun2_CC2 48 VhrIV 52
                                  ++rIV
  gi|70606312|ref|YP_255182.1| 79 IERIV 83
                                  33333 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.13      15      63 ..       4      51 ..       2      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                  -HHHHHHHHHHHHSTTB-HHHHHHT-TTS-HHHHHHHHHHHHHTTSEEE CS
                    MotA_activ 15 nektatilitiakkdfitaaevrevhpdlgnavvnsnigvlikkglvek 63
                                   e    il ++ kkd +ta e+ +       +v+n  +  lik glv+ 
  gi|70606312|ref|YP_255182.1|  4 SEVEQRILKALLKKDKMTARELVDASH-SSTSVLNPSLEHLIKLGLVNE 51
                                  566678999************887644.4689***************86 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00017      0.21      13      57 ..       5      49 ..       3      50 .. 0.93
   2 ?   -2.0   0.0       3.5   4.1e+03      35      35 ..      78      78 ..      64      94 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                  THHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 13 evvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  ev +++ + Ll+k + t+relv ++  s +    sL  Li+++lV
  gi|70606312|ref|YP_255182.1|  5 EVEQRILKALLKKDKMTARELVDASHSSTSVLNPSLEHLIKLGLV 49
                                  56689*********************9999999*********999 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                                  H CS
                         HTH_9 35 k 35
                                  +
  gi|70606312|ref|YP_255182.1| 78 E 78
                                  1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 725.29
//
Query:       gi|70606313|ref|YP_255183.1|  [L=152]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1119.71
//
Query:       gi|70606314|ref|YP_255184.1|  [L=55]
Description: hypothetical protein Saci_0485 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0041   17.0   0.1      0.006   16.5   0.1    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.14   12.0   0.1       0.14   12.0   0.1    1.1  1  AUX_IAA         AUX/IAA family


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.7e-07     0.006      12      34 ..      19      41 ..      18      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.7e-07
                                  -CCCHHHCCEECTCEEEEEECTT CS
                MazE_antitoxin 12 PkevrfelgireGdevelevdgd 34
                                  P +v+++lgi+e+de +l+v++ 
  gi|70606314|ref|YP_255184.1| 19 PIDVVRALGISENDEFVLSVENK 41
                                  99******************996 PP

>> AUX_IAA  AUX/IAA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.6e-05      0.14     188     207 ..      28      47 ..       6      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                   XXXXXXXXXXXXXXXXXXXX CS
                       AUX_IAA 188 lldgseyvltYeDkdgDwmL 207
                                   + ++ e+vl  e kdgD mL
  gi|70606314|ref|YP_255184.1|  28 ISENDEFVLSVENKDGDVML 47 
                                   55677**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 388.22
//
Query:       gi|70606315|ref|YP_255185.1|  [L=101]
Description: hypothetical protein Saci_0486 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.062   13.4   0.2      0.087   12.9   0.2    1.3  1  MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
       0.11   12.8   0.0       0.11   12.8   0.0    1.1  1  DUF3416     Domain of unknown function (DUF3416)


Domain annotation for each model (and alignments):
>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   9.7e-06     0.087      20      74 ..      10      64 ..       2      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-06
                                  EEEEEEE------------------------------------------------ CS
                    MGDG_synth 20 yqvlvkdllkelnpfllkavlksYlflvkvsalyrllyygteekiqkksilakla 74
                                   qv+vk ++ +lnp+  +a++++Y + +k  ++y ++ y  ++   + ++la  +
  gi|70606315|ref|YP_255185.1| 10 NQVKVKGSVFSLNPYSFEAIKRWYDKFLKWCENYDVMTYCQKDMEEEVEYLAEAF 64
                                  589999****************************998887665444555555544 PP

>> DUF3416  Domain of unknown function (DUF3416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05      0.11      80     138 ..      24      89 ..       3     101 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                       DUF3416  80 yef.tveAWvDpfatWrhdlekkveagqdveleleeGarlleraaeraea......aalraaaaal 138
                                   y+f +++ W D+f  W ++  +    ++d+e+e+e  a+ ++ +a ++ +      a+l++a ++ 
  gi|70606315|ref|YP_255185.1|  24 YSFeAIKRWYDKFLKWCENYDVMTYCQKDMEEEVEYLAEAFRLLAPKSLEeaeeyfAVLERAYDST 89 
                                   55535899*************************777777776666333213334555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 713.31
//
Query:       gi|70606316|ref|YP_255186.1|  [L=434]
Description: transposase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-29  102.7   0.0    2.9e-29  101.7   0.0    1.5  1  OrfB_IS605      Probable transposase
    9.6e-21   73.5   0.1    2.8e-20   72.0   0.1    1.9  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.05   13.8   0.9        7.9    6.6   0.0    2.5  2  SPT16           FACT complex subunit (SPT16/CDC68)
      0.053   14.0   0.0       0.39   11.2   0.0    2.2  2  Terminase_2     Terminase small subunit
        0.1   13.0   0.0       0.22   11.9   0.0    1.5  1  RuvX            Holliday junction resolvase
       0.13   11.9   0.4       0.34   10.6   0.0    1.9  2  DUF3562         Protein of unknown function (DUF3562)


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.0   9.6e-33   2.9e-29       1     119 [.     169     284 ..     169     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 9.6e-33
                    OrfB_IS605   1 sipvevevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                   sipvevev  +kpkgn  ag+DlGi nLatvv  d +w l+kg ++ s+y++++++ia+ q+kl+ +k  +++s++l+ l+
  gi|70606316|ref|YP_255186.1| 169 SIPVEVEV-NAKPKGNGIAGVDLGIVNLATVVFDDSSWVLFKGGSVLSEYENYSRKIAITQKKLSLHK--QERSKRLKALF 246
                                   69*****9.9**********************************************************..*********** PP

                    OrfB_IS605  82 rkrsrrrkhllhklathliktlkevgvetLnvgnmkdi 119
                                    kr+r++kh+l+++a++ ++t +e+gv+ ++vg++k+i
  gi|70606316|ref|YP_255186.1| 247 LKRKRFLKHVLNSMARKTVETAYEKGVSIIKVGYPKEI 284
                                   ***********************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   9.4e-24   2.8e-20       1      68 [.     299     367 ..     299     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 9.4e-24
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilk 68 
                                   ++ +++++++  +eyGikve+vn+ayTS  Cs Cg+ +++ + ++ +fkCp+ g + ++D+n+aiNil+
  gi|70606316|ref|YP_255186.1| 299 YNYVIRRMQEVSEEYGIKVETVNEAYTSIVCSLCGEAHENgRIHRGLFKCPHIGKVVNADLNGAINILH 367
                                   577899*************************************************************96 PP

>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0026       7.9     109     150 ..     120     165 ..     112     166 .. 0.79
   2 ?    5.1   0.2    0.0078        23      99     130 ..     217     248 ..     212     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0026
                         SPT16 109 eqekLilskskrkprLkd....lyirpniegkklaGtleaheNGlR 150
                                   ++++ ++ ++ r++ Lkd    l+ + +++ k  +G le+ +NGl 
  gi|70606316|ref|YP_255186.1| 120 RNDRYTVDENARTIYLKDfgltLHFKGKLKWKGKQGRLEIFHNGLH 165
                                   566677788889999999665566666666699***********97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0078
                         SPT16  99 aekkekedlveqekLilskskrkprLkdlyir 130
                                    e+  ++  ++q+kL l k++r++rLk l+++
  gi|70606316|ref|YP_255186.1| 217 YENYSRKIAITQKKLSLHKQERSKRLKALFLK 248
                                   5667788899******************9987 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.51   1.5e+03      14     101 ..      47      62 ..      12      92 .. 0.58
   2 ?   11.2   0.0   0.00013      0.39      21      82 ..     274     335 ..     271     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.51
                   Terminase_2  14 kdlNatqAaikAgyskktArsigselLrkpkIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseev 94 
                                   +d+N t+  + A y+                                                                  
  gi|70606316|ref|YP_255186.1|  47 VDFNDTEKVVYAKYK------------------------------------------------------------------ 61 
                                   223333322223222.................................................................. PP

                   Terminase_2  95 dkeilre 101
                                         e
  gi|70606316|ref|YP_255186.1|  62 ------E 62 
                                   ......2 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                   Terminase_2  21 AaikAgyskktArsigselLrkpkIkkaIreakaereertiieadeVlqellkiaraeitde 82 
                                   + ik+gy k+  + +g++l  +    +++ ++++e++e+ +i+ + V + +++i+    ++ 
  gi|70606316|ref|YP_255186.1| 274 SIIKVGYPKEISKHHGNKLTVNFWNYNYVIRRMQEVSEEYGIKVETVNEAYTSIVCSLCGEA 335
                                   5699*************************************************987666665 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.2e-05      0.22      38     102 ..     259     329 ..     236     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                                   HHHHHHHHHHHHTT--EEEEE------SSS---S.......STTHHHHHHHHHT..T-EEEEE--S----XX CS
                          RuvX  38 kdleelkelvkeeeveeiVvGlPlnldgsegesa.......kkvrkfaeeLakrlkklpvelvDErlttvea 102
                                   + +++  e++ e+ v+ i vG+P+++++++g++        + v + ++e+++++ +++ve+v+E +t++  
  gi|70606316|ref|YP_255186.1| 259 SMARKTVETAYEKGVSIIKVGYPKEISKHHGNKLtvnfwnyNYVIRRMQEVSEEY-GIKVETVNEAYTSIVC 329
                                   56777788899999999******99987777654111111133455567777776.*************865 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       3.4     1e+04      43      57 ..       7      21 ..       7      23 .. 0.83
   2 ?   10.6   0.0   0.00011      0.34       7      37 ..     305     335 ..     300     338 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.4
                       DUF3562 43 lpvlaarRVrealrs 57
                                  +++ + + V ++lr+
  gi|70606316|ref|YP_255186.1|  7 VRLVVSKDVGKKLRE 21
                                  788999999999996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                       DUF3562   7 iiqaiAeetdaPeelVsrlyedavaalaedA 37 
                                    +q++ ee+++  e+V++ y+ +v++l  +A
  gi|70606316|ref|YP_255186.1| 305 RMQEVSEEYGIKVETVNEAYTSIVCSLCGEA 335
                                   599***********************98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3229.11
//
Query:       gi|70606317|ref|YP_255187.1|  [L=69]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-07   29.1   0.0      1e-06   28.6   0.0    1.2  1  MarR            MarR family
    0.00023   21.0   0.3    0.00038   20.3   0.3    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00045   20.0   0.1    0.00058   19.7   0.1    1.2  1  MarR_2          MarR family
     0.0012   18.7   0.1     0.0014   18.4   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.029   13.9   0.1       0.06   12.9   0.1    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.057   13.4   0.1      0.073   13.0   0.1    1.2  1  HTH_11          HTH domain
       0.07   13.0   0.3        0.1   12.4   0.3    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.079   13.1   0.0      0.096   12.9   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.088   13.3   0.0       0.11   12.9   0.0    1.2  1  HTH_27          Winged helix DNA-binding domain
       0.11   12.5   0.1       0.23   11.5   0.1    1.7  1  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.7e-10     1e-06       6      48 ..      18      61 ..      14      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.7e-10
                                  HHHHHHHHHSTTEEHHHH.HHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  6 fviLrilyeqgplsvseL.akklgvskstvtrvldrLekkGlie 48
                                  +++L ++y+ g+++vs+L  +  g+s st+t+ +++Le  Gl++
  gi|70606317|ref|YP_255187.1| 18 LRLLLLIYSLGEATVSQLiKESGGMSASTITKYVRQLEGLGLVS 61
                                  689*************76155668******************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   2.1e-07   0.00038       6      46 ..      19      61 ..      18      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                                  HHHHHHTT.SSEEHHHHHHHH.TS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  6 kILklLae.gelcvcelaeel.glsqstvShHLkkLreaGLVe 46
                                  ++L l  + ge++v++l +e  g+s st+  + ++L+ +GLV+
  gi|70606317|ref|YP_255187.1| 19 RLLLLIYSlGEATVSQLIKESgGMSASTITKYVRQLEGLGLVS 61
                                  556666668*********98737*******************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.3e-07   0.00058       9      54 ..      19      63 ..      13      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.3e-07
                                  HHHHHHHCTTTSEEEHHHHHH.HHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelar.rlglsksavsrilkrLvaaGLverr 54
                                  r+L+ ++  ++   tv++l +   g+s s++++ ++ L+  GLv  +
  gi|70606317|ref|YP_255187.1| 19 RLLLLIYSLGE--ATVSQLIKeSGGMSASTITKYVRQLEGLGLVSVE 63
                                  88999999998..9****9996789*******************765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   7.9e-07    0.0014      18      55 ..      23      63 ..      18      69 .] 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.9e-07
                                  H..HHCCCHHCHHCCCT.TSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 18 l..klgpatadeiaeel.gvprskvYevLrsLedkGlVere 55
                                  l  +lg+at++++ +e+ g + s++ +++r+Le  GlV +e
  gi|70606317|ref|YP_255187.1| 23 LiySLGEATVSQLIKESgGMSASTITKYVRQLEGLGLVSVE 63
                                  34699*******99888469******************987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.4e-05      0.06      28      47 ..      41      60 ..      18      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                        HTH_24 28 glSpstvnrrlkrLeeeGlI 47
                                  g+S st+++++++Le  Gl+
  gi|70606317|ref|YP_255187.1| 41 GMSASTITKYVRQLEGLGLV 60
                                  7**************99987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.1e-05     0.073       8      49 ..      23      65 ..      18      68 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                        HTH_11  8 lLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49
                                  l+++  +   ++ ++e  ++S +t+ +++++Le lg v +e +
  gi|70606317|ref|YP_255187.1| 23 LIYSLGEATVSQLIKESGGMSASTITKYVRQLEGLGlVSVELT 65
                                  55555555556777888899****************9555544 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   5.8e-05       0.1       7      49 ..      19      61 ..      18      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-05
                                  HHHCT-CTTBSS-BHHHHHHHH.TS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrt.glpkStvhRlLqtLvelGyve 49
                                  ++L ++ + +++ t+s+l +++ g++ St   +++ L+ lG+v 
  gi|70606317|ref|YP_255187.1| 19 RLLLLIYSLGEA-TVSQLIKESgGMSASTITKYVRQLEGLGLVS 61
                                  566666666665.88998888846******************96 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.3e-05     0.096      20      49 ..      31      61 ..      19      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                B-block_TFIIIC 20 tqsdLakesk.qdprslfyrlksLekkgLIv 49
                                  t s+L+kes+ ++++ +++ ++ Le  gL+ 
  gi|70606317|ref|YP_255187.1| 31 TVSQLIKESGgMSASTITKYVRQLEGLGLVS 61
                                  6799*************************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.4e-05      0.11       8      48 ..      20      60 ..      15      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                        HTH_27  8 vLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLv 48
                                  +L li+  +++++    + +   +++s+i + +++L+  GLv
  gi|70606317|ref|YP_255187.1| 20 LLLLIY-SLGEATVsQLIKESGGMSASTITKYVRQLEGLGLV 60
                                  577788.78888884556667899999999************ PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.23      28      55 .]      32      60 ..      14      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                        HTH_36 28 qetlakrl.glsknTvsraikeLeqlGyi 55
                                  ++ l k + g+s +T+ ++++ Le lG++
  gi|70606317|ref|YP_255187.1| 32 VSQLIKESgGMSASTITKYVRQLEGLGLV 60
                                  5555566669*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 544.50
//
Query:       gi|70606318|ref|YP_255188.1|  [L=97]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-07   30.7   0.2    2.7e-07   30.4   0.2    1.2  1  MarR_2           MarR family
    1.1e-06   28.5   0.1    1.4e-06   28.0   0.1    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.1e-06   28.0   0.2    1.6e-06   27.6   0.2    1.2  1  HTH_24           Winged helix-turn-helix DNA-binding
      1e-05   25.5   0.2    1.6e-05   24.9   0.2    1.3  1  HTH_20           Helix-turn-helix domain
    8.5e-05   23.0   0.1    0.00016   22.1   0.1    1.5  2  HTH_27           Winged helix DNA-binding domain
    0.00077   19.3   0.1     0.0034   17.2   0.1    1.8  2  HxlR             HxlR-like helix-turn-helix
     0.0008   19.2   0.1      0.019   14.8   0.1    2.1  1  DUF1495          Winged helix DNA-binding domain (DUF1495)
     0.0018   18.0   0.1     0.0026   17.5   0.1    1.2  1  HTH_IclR         IclR helix-turn-helix domain
     0.0022   18.0   0.0     0.0037   17.3   0.0    1.3  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
     0.0043   16.9   0.1     0.0057   16.5   0.1    1.2  1  MarR             MarR family
     0.0055   16.3   0.2     0.0061   16.2   0.2    1.1  1  SMC_ScpB         Segregation and condensation complex subunit
     0.0097   16.2   0.0      0.012   16.0   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.015   15.1   0.2      0.022   14.6   0.2    1.4  1  TFIIE_alpha      TFIIE alpha subunit
       0.02   15.6   0.0      0.028   15.1   0.0    1.2  1  RPA_C            Replication protein A C terminal
      0.024   14.7   0.0      0.035   14.2   0.0    1.2  1  DprA_WH          DprA winged helix domain
      0.027   14.6   0.0      0.042   14.0   0.0    1.3  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.092   12.7   0.0       0.12   12.3   0.0    1.3  1  PadR             Transcriptional regulator PadR-like family
      0.099   12.8   0.0       0.15   12.2   0.0    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
        0.1   12.1   0.0       0.14   11.7   0.0    1.2  1  HTH_47           winged helix-turn-helix
       0.18   11.8   1.9        1.1    9.3   0.8    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2     3e-10   2.7e-07       7      56 ..      19      66 ..      14      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3e-10
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  + rvL +L  ++g   + +++ ++++ s+ +v+ +l++L + GLve+r+ 
  gi|70606318|ref|YP_255188.1| 19 EQRVLRFLLKNDG--TALSDIIEKTRSSPNSVTSALRELIEVGLVEERRE 66
                                  679**********..9******************************9975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.6e-09   1.4e-06       5      59 ..      14      70 ..      11      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-09
                                  HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..T CS
                          TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..p 59
                                   Lse E +v   Llk++    ++i e++  + ++v ++Lr+L++ GlVe ++++  p
  gi|70606318|ref|YP_255188.1| 14 ELSEIEQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERREEvfP 70
                                  69*************************************************998773 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   1.8e-09   1.6e-06       1      48 []      15      62 ..      15      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-09
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  l+e++ ++L+ L kn ++  +++ e++  Sp+ v+  l++L+e Gl++
  gi|70606318|ref|YP_255188.1| 15 LSEIEQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVE 62
                                  6799***************************************99996 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.8e-08   1.6e-05      13      60 ..      20      67 ..      15      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.8e-08
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   r+lr L  ++g  +s++ e  + s+n++   Lr+L e+gLve +re+
  gi|70606318|ref|YP_255188.1| 20 QRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERREE 67
                                  69********************************************95 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.7   3.3e+03      12      27 ..       6      21 ..       5      24 .. 0.78
   2 !   22.1   0.1   1.8e-07   0.00016       8      68 .]      22      81 ..      15      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.7
                        HTH_27 12 irhrrrrkkladlcgr 27
                                  i++  r k+l+++ +r
  gi|70606318|ref|YP_255188.1|  6 IEMSIRHKELSEIEQR 21
                                  6788899999998766 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.8e-07
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  vL+ +   +++ +l+d+++++  +  ++ ++l++L+e GLve+ + e   r++++ lT kG
  gi|70606318|ref|YP_255188.1| 22 VLRFLL-KNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERREEVFPRRRFLYLTGKG 81
                                  677777.899999****************************77777766666888888776 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.39   3.5e+02      49      77 ..      10      39 ..       2      44 .. 0.61
   2 !   17.2   0.1   3.8e-06    0.0034      33      82 ..      45      94 ..      21      97 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                                  EEEEEESSSS-EE.EEEE-TCGGGGHHHHH CS
                          HxlR 49 ierevypevPpkv.eYsltekGrslepvlq 77
                                  i  ++++e+ ++v  + l + G++l+++++
  gi|70606318|ref|YP_255188.1| 10 IRHKELSEIEQRVlRFLLKNDGTALSDIIE 39
                                  455555555555534666677777777765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.8e-06
                                  HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHH CS
                          HxlR 33 qkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkw 82
                                   +  ++ LreL + gl+e +  +  P +    lt kG+ +++ l+e++ +
  gi|70606318|ref|YP_255188.1| 45 PNSVTSALRELIEVGLVEERREEVFPRRRFLYLTGKGKVVAKKLDEIYSL 94
                                  4567899**************************************99876 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.1e-05     0.019       8      89 ..      16      87 ..       8      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                       DUF1495  8 SkvRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglk..lYklteeGieive 88
                                  S++ + vl +L+++    + l++i++++rs+p+ v+ al            Lie GLvee+ e+   +  +  lt +G+ +++
  gi|70606318|ref|YP_255188.1| 16 SEIEQRVLRFLLKNDG--TALSDIIEKTRSSPNSVTSALR----------ELIEVGLVEERREEVFPRrrFLYLTGKGKVVAK 86
                                  88899*******6655..99****************9995..........688888887666643332225557888877776 PP

                       DUF1495 89 v 89
                                  +
  gi|70606318|ref|YP_255188.1| 87 K 87
                                  5 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.9e-06    0.0026       7      50 ..      21      63 ..      20      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.9e-06
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++L++l + ++   ls++ ++t  ++ +v   L+ L+e G+ve 
  gi|70606318|ref|YP_255188.1| 21 RVLRFLLKNDGT-ALSDIIEKTRSSPNSVTSALRELIEVGLVEE 63
                                  699999999998.9****************************96 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.1e-06    0.0037      13      57 ..      17      61 ..      13      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.1e-06
                                  THHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 13 evvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  e+ ++V ++Ll++    l+++++kt+ s+++V ++L  Li  +lV
  gi|70606318|ref|YP_255188.1| 17 EIEQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLV 61
                                  66799***********************************99998 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   6.4e-06    0.0057       5      51 ..      19      65 ..      15      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.4e-06
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  + ++Lr l  +++  +s++ +k   s+ +vt +l++L++ Gl+e ++
  gi|70606318|ref|YP_255188.1| 19 EQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERR 65
                                  668999999**********************************9766 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.8e-06    0.0061      78     143 ..      12      80 ..       2      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-06
                      SMC_ScpB  78 ktrLsqaaletLaiIaykqpvtrae.ieeiRGvn..sdsvvrtLlerglieekgrkeepgrpilYgtTe 143
                                   +++Ls+ + ++L     ++    ++ ie+ R +   ++s++r+L+e gl+ee++++  p r +lY t +
  gi|70606318|ref|YP_255188.1|  12 HKELSEIEQRVLRFLLKNDGTALSDiIEKTRSSPnsVTSALRELIEVGLVEERREEVFPRRRFLYLTGK 80 
                                   56777777777777777776665552577786544599****************9999*******9977 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05     0.012       1      57 [.      15      67 ..      15      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                  ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
               Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57
                                  l+e E+ v++ l +++ +  ++++e+  +     +++V++ lr L + gl+++++e+
  gi|70606318|ref|YP_255188.1| 15 LSEIEQRVLRFLLKNDGTALSDIIEKTRSS----PNSVTSALRELIEVGLVEERREE 67
                                  699**********************98888....9****************999874 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   2.4e-05     0.022      15      65 ..      19      67 ..       4      97 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                                  HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEET CS
                   TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrde 65
                                     vl  Ll++  ++  d+ ++++  +n + ++L +L e +lv+ +r  +e
  gi|70606318|ref|YP_255188.1| 19 EQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERR--EE 67
                                  5689***************************************9766..44 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.1e-05     0.028      45      97 ..      13      61 ..       4      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                                  .XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                         RPA_C 45 kgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                  k l++ +q+vl ++ +    ++G  ++ i +k+r s n+v++a++eL++ G++
  gi|70606318|ref|YP_255188.1| 13 KELSEIEQRVLRFLLK----NDGTALSDIIEKTRSSPNSVTSALRELIEVGLV 61
                                  4688899999999888....9****************************9976 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.9e-05     0.035       9      49 ..      14      55 ..       9      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                       DprA_WH  9 plddlerrvLaaL.gpePvhvDqLvrrtglpaaevsaaLleL 49
                                  +l++ e+rvL  L  ++ +++ +++++t  ++ +v +aL eL
  gi|70606318|ref|YP_255188.1| 14 ELSEIEQRVLRFLlKNDGTALSDIIEKTRSSPNSVTSALREL 55
                                  789*******876488***********************998 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.6e-05     0.042      15      51 ..      28      64 ..      27      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                B-block_TFIIIC 15 RysGitqsdLakeskqdprslfyrlksLekkgLIvkq 51
                                  + +G + sd++  ++ +p+s+++ l+ L + gL++ +
  gi|70606318|ref|YP_255188.1| 28 KNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEER 64
                                  6799******************************865 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.12      17      73 ..      36      85 ..      22      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                  HHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR 17 keleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  + +e++     + s+ s+  aL++L + glve+++ee  + p+r++  lT +G+   
  gi|70606318|ref|YP_255188.1| 36 DIIEKT-----RSSPNSVTSALRELIEVGLVEERREE--VFPRRRFLYLTGKGKVVA 85
                                  444444.....6678888899*************997..79************9865 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.15       8      59 ..      17      68 ..      10      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                       DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegkt 59
                                  e + +vl+ l k +      i ++++ + + v+++l++L e+GL+e+  +++
  gi|70606318|ref|YP_255188.1| 17 EIEQRVLRFLLKNDGTALSDIIEKTRSSPNSVTSALRELIEVGLVEERREEV 68
                                  55566666666666666667889999999*****************988765 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.14      28      77 ..      14      62 ..       4      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                  -----HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 28 takqaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  + ++ e+++l +L   DG+  L di e++  + + v++++r+L e gl++
  gi|70606318|ref|YP_255188.1| 14 ELSEIEQRVLRFLLKNDGT-ALSDIIEKTRSSPNSVTSALRELIEVGLVE 62
                                  345668999*********7.69**************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.8   2.5e+03      18      29 ..       6      17 ..       2      18 .. 0.79
   2 ?    9.3   0.8    0.0012       1.1      32      55 ..      42      65 ..      20      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                                  EEEEHHHHHHHH CS
                     HTH_Crp_2 18 ielpltqeelAs 29
                                  ie+++ ++el++
  gi|70606318|ref|YP_255188.1|  6 IEMSIRHKELSE 17
                                  788999999986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                                  TSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 32 GltretvsrilseLkreglisrgr 55
                                   +++ +v+ +l+eL + gl++ +r
  gi|70606318|ref|YP_255188.1| 42 RSSPNSVTSALRELIEVGLVEERR 65
                                  68999****************554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 765.72
//
Query:       gi|70606319|ref|YP_255189.1|  [L=98]
Description: hypothetical protein Saci_0490 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.1   3.2       0.19   11.8   3.2    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.2     1e-05      0.19      18      78 ..      16      74 ..       6      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1e-05
                       Sdh_cyt 18 lgawlsilhritGvallv.glllllvwlllalslsspesfarvvallaspiklillllllla 78
                                    ++ s+l  i +++ll+  +l+++  ++l++++ s e++a++v ++a    +  l++l+++
  gi|70606319|ref|YP_255189.1| 16 FVTIYSLLESIVACILLGqQFLHFV-TSVLNPIAISVETYANIVVFYAL--IIGGLFILFWP 74
                                  5688999999********9999999.5799**9***********99973..23333555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 738.57
//
Query:       gi|70606320|ref|YP_255190.1|  [L=276]
Description: hypothetical protein Saci_0491 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1936.90
//
Query:       gi|70606321|ref|YP_255191.1|  [L=178]
Description: hypothetical protein Saci_0492 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1275.76
//
Query:       gi|70606322|ref|YP_255192.1|  [L=119]
Description: hypothetical protein Saci_0493 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 887.21
//
Query:       gi|70606323|ref|YP_255193.1|  [L=235]
Description: hypothetical protein Saci_0494 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.048   14.0   1.0       0.14   12.4   0.4    1.9  1  DUF1722   Protein of unknown function (DUF1722)
      0.055   12.6   0.3       0.83    8.7   0.1    2.2  2  phiKZ_IP  phiKZ-like phage internal head proteins


Domain annotation for each model (and alignments):
>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   1.6e-05      0.14      28     112 ..      31     114 ..      28     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                       DUF1722  28 eelaeeYeellmealskpatrkkhinvlqhilgyfkkklsaeekqelleliekYregkvplsvpltlLkhyarkydneyll 108
                                   ++++++  e+++++l  +  ++ +++v+  ++ y+ + l+ ++  ++ + ++kY  ++ +l+ + +lL+++ ++  +ey l
  gi|70606323|ref|YP_255193.1|  31 QDYVKKVDEEIKKLLDDEELKNGTLEVMSGLFSYLTT-LDIDDLTKIEDFMKKYPAKLQQLDNLYKLLENLPAEEYKEYWL 110
                                   57789999***************************76.*********************************9988888888 PP

                       DUF1722 109 eqty 112
                                     +y
  gi|70606323|ref|YP_255193.1| 111 GKYY 114
                                   7777 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.016   1.4e+02     284     301 ..      34      51 ..      27      59 .. 0.79
   2 ?    8.7   0.1   9.2e-05      0.83     129     181 ..     128     177 ..     118     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.016
                      phiKZ_IP 284 ikavddrikqlaeavrkn 301
                                   +k+vd++ik+l+++++ +
  gi|70606323|ref|YP_255193.1|  34 VKKVDEEIKKLLDDEELK 51 
                                   45566********99965 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 9.2e-05
                      phiKZ_IP 129 ilpylldnepkivgkiaenwskqllkllqklkkllnnyeledklldelaeafe 181
                                       ++++e++ v+ i+e++ k++l+ll++l + +++ye+ ++l+ + +++ +
  gi|70606323|ref|YP_255193.1| 128 M---RTIEEREGVNTIMEFYYKVFLGLLTDLVENIRRYETVERLKARDDAKLR 177
                                   4...7789999********************************9999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1513.27
//
Query:       gi|70606324|ref|YP_255194.1|  [L=282]
Description: hypothetical protein Saci_0495 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-06   28.3   2.9    2.2e-06   28.3   2.9    2.7  3  PIN_12    PIN domain
     0.0066   16.9   1.1      0.016   15.7   0.1    2.2  2  PIN       PIN domain
  ------ inclusion threshold ------
      0.072   13.2   2.5       0.12   12.5   0.1    2.5  3  Nod1      Gef2-related medial cortical node protein Nod1
       0.16   12.6   2.5       0.19   12.4   0.2    2.2  3  CdiI_2    CdiI immunity protein
       0.16   12.6   0.2        5.3    7.7   0.1    2.4  2  DUF883    Bacterial protein of unknown function (DUF883)
       0.24   11.2   6.0      0.056   13.3   1.6    2.1  2  PIN_8     PIN like domain


Domain annotation for each model (and alignments):
>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   2.9   7.4e-10   2.2e-06       3     132 ..       7     127 ..       6     151 .. 0.82
   2 ?    0.0   0.1      0.35     1e+03      88     112 ..     172     194 ..     127     227 .. 0.43
   3 ?    0.2   0.4      0.31   9.4e+02      62     106 ..     229     276 ..     214     280 .. 0.52

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 7.4e-10
                        PIN_12   3 iDTnifld...effrlseeealkklleliesgkiklivpdivldEflknrekkieeskklekalkslsklksakkklnekk 80 
                                   +DTni+ld   +f++++ + + +kl++ ++ +  ++++p+ v+ E+l+     +             + l  + +k+n  +
  gi|70606324|ref|YP_255194.1|   7 LDTNILLDyfyDFMDKNRHLQAEKLVKSLKGRSSEIYIPNTVKTEVLEITAGSFAIL---------RNSLILEMQKINWDN 78 
                                   8******9666677777779*********************************9977.........566666666555444 PP

                        PIN_12  81 kllslkeikkkieekveeslkkllekleaikvipetndevkkilerafkkkp 132
                                       + e  +k+ +++++++++l+e++ +  ++++t+ +   +++r f+k++
  gi|70606324|ref|YP_255194.1|  79 L---SIEERDKALDRIRDNFDELFENTRKKLYPDTTPGIRLFLAKRLFSKLR 127
                                   4...344444444556778**********9*******999*******99975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.35
                        PIN_12  88 ikkkieekveeslkkllekleaikv 112
                                   i+++ ee  +  l+ + ++++++k+
  gi|70606324|ref|YP_255194.1| 172 ISSSSEELMK--LNIFMRAFGKVKN 194
                                   2222222211..3444444444333 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.31
                        PIN_12  62 alks..lsklksakkklnekkkllslkeikkkieekvees.lkkllek 106
                                   ++k+  l++l+  +k++++++  ++ +e+ + i+++++ + l+++l+k
  gi|70606324|ref|YP_255194.1| 229 TIKEslLNNLNDFIKSSSNNDHRNYAEEMRDLIHSNLKVVkLEEILNK 276
                                   344444555555555555555555555555555555444455555554 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.3e-06     0.016       3      48 ..       7      65 ..       5     107 .. 0.72
   2 ?   -1.0   0.1      0.79   2.4e+03      45      45 ..     241     241 ..     197     279 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.3e-06
                                  E-HHHHHHHH...TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS......S CS
                           PIN  3 lDTsvliall...rgeekaeaarklleel....eelvtsalvlaEllyvlar......r 48
                                  lDT++l++++    +++++ +a+kl+ +l    +e+++++ v  E+l + a       +
  gi|70606324|ref|YP_255194.1|  7 LDTNILLDYFydfMDKNRHLQAEKLVKSLkgrsSEIYIPNTVKTEVLEITAGsfailrN 65
                                  8***********87777777788888777999**************9887774444440 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.79
                                   H CS
                           PIN  45 l 45 
                                    
  gi|70606324|ref|YP_255194.1| 241 F 241
                                   1 PP

>> Nod1  Gef2-related medial cortical node protein Nod1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     4e-05      0.12      44      85 ..      61     102 ..      22     109 .. 0.89
   2 ?   -2.2   0.0       1.4   4.1e+03      95     112 ..     202     218 ..     152     229 .. 0.63
   3 ?   -1.2   0.1      0.68     2e+03      46      80 ..     230     263 ..     225     277 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                          Nod1  44 ylLsekliqrLenldldlnskslkekavqqvkslleeLpesk 85 
                                    +L ++li ++++++ d+ s + + ka++++++++ eL e  
  gi|70606324|ref|YP_255194.1|  61 AILRNSLILEMQKINWDNLSIEERDKALDRIRDNFDELFENT 102
                                   599**********************************98765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                          Nod1  95 ivselllkLplkdqcetv 112
                                     se++l L+ ++ ce +
  gi|70606324|ref|YP_255194.1| 202 LFSEIFLALK-GGVCESI 218
                                   3456666666.6666655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.68
                          Nod1  46 LsekliqrLenldldlnskslkekavqqvksllee 80 
                                   ++e+l+++L++   + ++ + ++ a +++++l+++
  gi|70606324|ref|YP_255194.1| 230 IKESLLNNLNDFIKSSSNNDHRNYA-EEMRDLIHS 263
                                   5677778886655444443444444.777777654 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   6.6e+03      36      54 ..      84     102 ..      66     111 .. 0.66
   2 ?   -2.4   0.0       2.6   7.9e+03      38      70 ..     129     162 ..     122     165 .. 0.57
   3 ?   12.4   0.2   6.3e-05      0.19      16      63 ..     226     274 ..     222     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                        CdiI_2  36 speevaelideieellass 54 
                                    ++++ +++d+++el ++ 
  gi|70606324|ref|YP_255194.1|  84 RDKALDRIRDNFDELFENT 102
                                   4445556666666666544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                        CdiI_2  38 eevaelideieellassldee.leeaflaelgae 70 
                                   e++++ ++ei++++  + + +  ee +++++ +e
  gi|70606324|ref|YP_255194.1| 129 ELINRRLSEIKDFVLTENRIKdSEEYLIRRISNE 162
                                   5666777788887544333333555555555555 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 6.3e-05
                        CdiI_2  16 DydlegdsieeiledYvssespeevaelideieellassldee.leeaf 63 
                                   D   +++s+ + l+d+++s+s+++ +  ++e+++l++s+l+   lee +
  gi|70606324|ref|YP_255194.1| 226 DLATIKESLLNNLNDFIKSSSNNDHRNYAEEMRDLIHSNLKVVkLEEIL 274
                                   5556788899*****************************9765555554 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.091   2.7e+02      25      47 ..      84     106 ..      78     110 .. 0.82
   2 ?    7.7   0.1    0.0018       5.3       8      44 ..     232     269 ..     226     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.091
                        DUF883  25 ageeaeelRerleerlerarerl 47 
                                    ++ ++++R++ +e +e++r++l
  gi|70606324|ref|YP_255194.1|  84 RDKALDRIRDNFDELFENTRKKL 106
                                   56788999999999999999887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                        DUF883   8 eslladleellkeaa.deageeaeelRerleerlerar 44 
                                   esll++l++++k+++ ++ +++aee+R+ ++++l+ ++
  gi|70606324|ref|YP_255194.1| 232 ESLLNNLNDFIKSSSnNDHRNYAEEMRDLIHSNLKVVK 269
                                   78999****99987615778999***********9876 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   1.9e-05     0.056       2     110 ..       5     130 ..       4     182 .. 0.58
   2 ?   -0.6   0.2      0.33   9.9e+02      98     137 ..     233     268 ..     216     280 .. 0.38

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                         PIN_8   2 vvlDtNvLLn.lYryseetr....kdllkvlekladrlwvPhqvalE........fqrnresvis.kekkayedle.kele 67 
                                   ++lDtN+LL+ +Y++ ++ r    ++l+k l+  ++ +++P+ v  E        f   r+s+i   +k   ++l+ +e +
  gi|70606324|ref|YP_255194.1|   5 FALDTNILLDyFYDFMDKNRhlqaEKLVKSLKGRSSEIYIPNTVKTEvleitagsFAILRNSLILeMQKINWDNLSiEERD 85 
                                   89*******757999888773333577778888888*********993333333333334444443334444444453335 PP

                         PIN_8  68 klkkaaekkleealkkwakkkald.........teelrkelkkqleelkeel 110
                                   k+ +++ ++++e++++ +kk + d         +       k+ +++l++el
  gi|70606324|ref|YP_255194.1|  86 KALDRIRDNFDELFENTRKKLYPDttpgirlflA-------KRLFSKLRNEL 130
                                   5555555555567777777777775433444442.......33344444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                         PIN_8  98 elkkqleelkeelkaeleelkksskadkeedpilkkleel 137
                                   +l ++l+++ ++     ++  +++ a++ +d i+++l+ +
  gi|70606324|ref|YP_255194.1| 233 SLLNNLNDFIKSS----SNNDHRNYAEEMRDLIHSNLKVV 268
                                   2223333333222....11111111111123333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1772.47
//
Query:       gi|70606325|ref|YP_255195.1|  [L=194]
Description: hypothetical protein Saci_0496 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.034   14.1   0.0    1.2  1  Nitrate_red_del  Nitrate reductase delta subunit
      0.082   12.7   0.8       0.22   11.3   0.0    2.0  2  DUF4028          Protein of unknown function (DUF4028)
      0.084   13.2   1.5       0.94    9.9   0.2    2.5  2  SWIRM            SWIRM domain


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-06     0.034      60     107 ..      53     101 ..      21     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
               Nitrate_red_del  60 lfgest.levrefyrqaglevaeefneppDHlaveLeflahLaereaea 107
                                   ++ + + +e+ +f++++ +  a++++e +D la e  ++ + + +  ++
  gi|70606325|ref|YP_255195.1|  53 VNSKTAaQELIKFLQSWHVLSASDISESEDKLASEIRYIKFDLLKDLSN 101
                                   45554459******************************99655555443 PP

>> DUF4028  Protein of unknown function (DUF4028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.35   2.1e+03      25      54 ..      21      50 ..      10      55 .. 0.57
   2 ?   11.3   0.0   3.7e-05      0.22       5      40 ..      95     131 ..      91     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.35
                       DUF4028 25 yvkkwfrkhenneklGrptfkevekdwken 54
                                  y+k w      ++k    ++  vek   en
  gi|70606325|ref|YP_255195.1| 21 YLKIWRCCFRRDDKAYFRALDAVEKIRNEN 50
                                  555554444444444444455555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.7e-05
                       DUF4028   5 ilkdssnsflctvqnkn.GdqyvkkwfrkhenneklG 40 
                                   +lkd sn  lc  +n +  +  +kk +r+ +n e +G
  gi|70606325|ref|YP_255195.1|  95 LLKDLSNKRLCEDENLEkYEDIIKKAYRRLDNIEGVG 131
                                   79*********999954157789**********9998 PP

>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00016      0.94      33      86 ..      21      71 ..       3      74 .. 0.76
   2 ?    2.6   0.1      0.03   1.8e+02       6      33 ..      72     113 ..      70     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                         SWIRM 33 YlkiRnkiialyrenpkeyltvteaqkalkrrrltgidvnllsrihefLerwGl 86
                                  Ylki +    ++r++ k y++  +a++++++++ + +   +++++ +fL++w +
  gi|70606325|ref|YP_255195.1| 21 YLKIWRC---CFRRDDKAYFRALDAVEKIRNENDEVNSKTAAQELIKFLQSWHV 71
                                  4444333...34556689***********97777666999************86 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.03
                         SWIRM   6 FdpdslhpiEkellself...........ngk....dktpeeY 33 
                                   ++++ +++ E +l+se++           n k    d++ e+Y
  gi|70606325|ref|YP_255195.1|  72 LSASDISESEDKLASEIRyikfdllkdlsN-KrlceDENLEKY 113
                                   5678899**********9666666665542.235555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1445.83
//
Query:       gi|70606326|ref|YP_255196.1|  [L=284]
Description: hypothetical protein Saci_0497 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0018   18.8   5.7       0.22   12.1   0.0    2.7  3  DUF2408          Protein of unknown function (DUF2408)
     0.0034   17.0   3.4      0.033   13.8   0.2    2.9  3  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
  ------ inclusion threshold ------
      0.048   14.2   0.6        6.2    7.4   0.0    2.5  2  Globin           Globin
       0.11   12.4   6.6      0.064   13.1   2.3    2.2  2  CLTH             CTLH/CRA C-terminal to LisH motif domain
       0.29   11.8   0.1       0.29   11.8   0.1    3.0  3  Sas10_Utp3       Sas10/Utp3/C1D family
       0.92   10.1   7.1         11    6.7   0.3    3.4  3  DUF643           Protein of unknown function (DUF643)
        1.5    9.2   8.2       0.23   11.9   0.8    2.8  3  Snapin_Pallidin  Snapin/Pallidin


Domain annotation for each model (and alignments):
>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   8.4e-05      0.22      44     122 ..      49     132 ..      10     137 .. 0.85
   2 ?   -1.7   0.0       1.5   3.9e+03      71      96 ..     166     191 ..     157     205 .. 0.66
   3 !    7.7   1.6    0.0019       4.9       1      48 [.     229     274 ..     229     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                       DUF2408  44 lkelkeeLkkieskrdeegkFkseegkevvekgqavlngLlddcfdlvedlkaqd.......geekkvasslqpiYdrLle 117
                                   ++++ ++ +++ +  ++e+k +++ +  +++ g++ +++Ll    +l+ +lk+++        +e  +++  +  Yd+Ll+
  gi|70606326|ref|YP_255196.1|  49 VQNVINSFTNLVKDAVNEEKIAEKLK--HDPIGKSHIAELLSTTSKLMFELKQRElgrlyrrVKEYITKPPEKRRYDELLN 127
                                   55566666677777777888877765..8999****************************98666788899999******* PP

                       DUF2408 118 ikttL 122
                                   i++ L
  gi|70606326|ref|YP_255196.1| 128 IRKDL 132
                                   ***99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                       DUF2408  71 evvekgqavlngLlddcfdlvedlka 96 
                                   +++++++ ++++L+d+ + l + l++
  gi|70606326|ref|YP_255196.1| 166 QLSDEQKLIISTLIDEPYLLDQILSM 191
                                   45566667777777777766666655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0019
                       DUF2408   1 leelspelepiyekLvsirrsLlslaakskaeeakeseevkeelkelk 48 
                                   l++++++ ++i+e Lv++++++++l  + +++e    +ev+e++ +l 
  gi|70606326|ref|YP_255196.1| 229 LKDVKDHQKEILENLVELKKEISKLYKSDEFDE--YISEVEEKVRSLL 274
                                   678999999*****************9999983..3444566665554 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.047   1.2e+02      10      37 ..      49      77 ..      46      86 .. 0.83
   2 ?   -1.1   0.1       0.6   1.5e+03       1      15 [.     166     180 ..     166     182 .. 0.90
   3 !   13.8   0.2   1.3e-05     0.033       4      45 ..     234     275 ..     231     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.047
                  HrcA_DNA-bdg 10 lqaLielyrkk.kravKgeeiAevlkrne 37
                                  +q++i+ +++  k av  e+iAe+lk+++
  gi|70606326|ref|YP_255196.1| 49 VQNVINSFTNLvKDAVNEEKIAEKLKHDP 77
                                  566777777766899**********9987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                  HrcA_DNA-bdg   1 eLtsvqkeilqaLie 15 
                                   +L++ qk i+ +Li+
  gi|70606326|ref|YP_255196.1| 166 QLSDEQKLIISTLID 180
                                   59999********97 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.3e-05
                  HrcA_DNA-bdg   4 svqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlq 45 
                                   + qkeil++L+el ++ ++  K+ e  e ++  e  vR  l+
  gi|70606326|ref|YP_255196.1| 234 DHQKEILENLVELKKEISKLYKSDEFDEYISEVEEKVRSLLE 275
                                   67********************************99998876 PP

>> Globin  Globin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.017        44      56      95 ..      45      86 ..      37     100 .. 0.81
   2 ?    7.4   0.0    0.0024       6.2      23      75 ..     199     254 ..     193     269 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                                  HHHHHHHHHHHHHHHHHTTTSHHHHHHHHHH..HHHHHHCST CS
                        Globin 56 fkahakkvlaalgeavknldndealkaalkk..laarHaerg 95
                                  f +  + v+++++++vk   n+e+++++lk+  ++++H++++
  gi|70606326|ref|YP_255196.1| 45 FPRLVQNVINSFTNLVKDAVNEEKIAEKLKHdpIGKSHIAEL 86
                                  667789999999999999999999999999766788887776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0024
                                   HHHHHHHHSGGGGGGSTTT.TTTT-HHHHCTSHHHHHHHHHHHHHHHHHHHTT...T CS
                        Globin  23 ilkrlFkaypdtkklFkkf.gdlssaedlksspkfkahakkvlaalgeavknl...d 75 
                                   ++ +l+ ++  t ++ k+f ++  + ed+++ +++k+h k +l+ l e+ k++    
  gi|70606326|ref|YP_255196.1| 199 LFDYLLYTAFLTNAYIKRFtKG-RTDEDWEYLKDVKDHQKEILENLVELKKEIsklY 254
                                   5666666666677777888555.789********************99998885552 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.3   2.5e-05     0.064      28     136 ..      83     203 ..      50     214 .. 0.70
   2 ?    0.6   0.1      0.18   4.5e+02       6      36 ..     248     278 ..     243     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                          CLTH  28 kpellesnsnLeFkLkllqfielirg..........ktkdieealeyarenl.e.fendehlkelekamsLLafsdpeske 96 
                                     ell+  s+L F+Lk +++  l+r+          k + ++e+l+  ++ l + f  ++  + +  +m L + s+pe+  
  gi|70606326|ref|YP_255196.1|  83 IAELLSTTSKLMFELKQRELGRLYRRvkeyitkppeK-RRYDELLNIRKD-LvNsFSLRNLNDRILNLMRLCLLSPPEE-- 159
                                   56888999*****************887777766632.556666666666.55625555777889*********99988.. PP

                          CLTH  97 lssplknlldpsrrekvake.....fnsailkllglskespLeil 136
                                     + + ++l++++   ++++     +  +il++l l ++    +l
  gi|70606326|ref|YP_255196.1| 160 -AEGYCKQLSDEQKLIISTLidepyLLDQILSMLDLGNQKLFDYL 203
                                   .899******99965555550003344444444444455444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                          CLTH   6 qkIiklilegdlseaiewinenkpellesns 36 
                                   ++I kl ++ + +e i++++e+  +lle n+
  gi|70606326|ref|YP_255196.1| 248 KEISKLYKSDEFDEYISEVEEKVRSLLETNQ 278
                                   6788888999999999999999999999875 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.4   3.5e+03      18      46 ..      59      91 ..      48     101 .. 0.42
   2 ?   11.8   0.1   0.00011      0.29      38      85 ..     188     250 ..     153     252 .. 0.77
   3 ?    3.2   0.3     0.053   1.4e+02       3      26 ..     258     281 ..     256     284 .] 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.4
                    Sas10_Utp3 18 llskakaee...kkslsd.eklsegisllslKn 46
                                  l ++a +ee   +k + d   +s+  +lls+  
  gi|70606326|ref|YP_255196.1| 59 LVKDAVNEEkiaEKLKHDpIGKSHIAELLSTTS 91
                                  333322222233222222433333334555544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                    Sas10_Utp3  38 gisllslKnelllaYllnllly..lllklsg.............velkdhp..vvkeLvrlRvyl 85 
                                    +s+l+l n+ l  Yll+ +++  +   +++             ++ kdh   + ++Lv+l++ +
  gi|70606326|ref|YP_255196.1| 188 ILSMLDLGNQKLFDYLLYTAFLtnA--YIKRftkgrtdedweylKDVKDHQkeILENLVELKKEI 250
                                   479*******************443..45556667*********777777777********9865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.053
                    Sas10_Utp3   3 slsksldelqeslepllskakaee 26 
                                   ++++ ++e++e++++ll+ ++aee
  gi|70606326|ref|YP_255196.1| 258 EFDEYISEVEEKVRSLLETNQAEE 281
                                   78999*************766665 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0042        11      57      84 ..      48      75 ..      37      84 .. 0.90
   2 ?    0.1   0.0      0.46   1.2e+03      24      51 ..      89     117 ..      76     141 .. 0.60
   3 ?    4.7   0.4     0.018        46      12      27 ..     244     258 ..     229     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0042
                        DUF643 57 iindiiepekefikdvlkdknlikkykn 84
                                  +++++i++  +++kd + + ++ +k k 
  gi|70606326|ref|YP_255196.1| 48 LVQNVINSFTNLVKDAVNEEKIAEKLKH 75
                                  6899*********************985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.46
                        DUF643  24 eteqltleqk.kqlysavkkiqeykiktG 51 
                                   +t++l  e k ++l + +++++ey  k  
  gi|70606326|ref|YP_255196.1|  89 TTSKLMFELKqRELGRLYRRVKEYITKPP 117
                                   45556555442577788888888887754 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.018
                        DUF643  12 skdtkkeinklyeteq 27 
                                     ++kkei+kly+ ++
  gi|70606326|ref|YP_255196.1| 244 V-ELKKEISKLYKSDE 258
                                   3.589*******9765 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.22   5.5e+02      61      89 ..     121     148 ..      80     149 .. 0.72
   2 ?   -2.3   0.0       2.4   6.1e+03      20      47 ..     162     189 ..     156     197 .. 0.73
   3 ?   11.9   0.8   9.1e-05      0.23      20      66 ..     227     274 ..     219     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
               Snapin_Pallidin  61 yakKLvnikkrmsslnerlqklkkRaekL 89 
                                     + L ni+k++ + + +l++l++R+++L
  gi|70606326|ref|YP_255196.1| 121 RYDELLNIRKDLVN-SFSLRNLNDRILNL 148
                                   44678899999877.67899999999988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
               Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekLkele 47 
                                      k+l ++Q+   ++l  +   L+++ 
  gi|70606326|ref|YP_255196.1| 162 GYCKQLSDEQKLIISTLIDEPYLLDQIL 189
                                   5567888888888888887777777665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 9.1e-05
               Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLv 66 
                                   e lk+++++Q+e le+l +l++++ +l + +e +e++++++e ++ L 
  gi|70606326|ref|YP_255196.1| 227 EYLKDVKDHQKEILENLVELKKEISKLYKSDEfDEYISEVEEKVRSLL 274
                                   5799************************************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1979.90
//
Query:       gi|70606327|ref|YP_255197.1|  [L=148]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1010.80
//
Query:       gi|70606328|ref|YP_255198.1|  [L=50]
Description: hypothetical protein Saci_0499 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   2.2        1.4    8.9   0.1    2.2  2  Trm5_N    tRNA methyltransferase 5 N-terminal domain


Domain annotation for each model (and alignments):
>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3    0.0041        73       3      11 ..       2      10 ..       1      10 [. 0.92
   2 ?    8.9   0.1   7.7e-05       1.4       5      27 ..      18      41 ..      18      43 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0041
                                  EEEGGGHHH CS
                        Trm5_N  3 kVpkkegEk 11
                                  k++k+egE+
  gi|70606328|ref|YP_255198.1|  2 KIEKREGEE 10
                                  9*******6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 7.7e-05
                                  EGGGHHHHHHHHHHTT.-B-TTS- CS
                        Trm5_N  5 pkkegEkvRkkLlekg.lLdrnyK 27
                                  +k++ E+ R++L++k   L++++K
  gi|70606328|ref|YP_255198.1| 18 SKEDLEEFRQLLIKKYyELNPDRK 41
                                  5999*********98425777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 354.00
//
Query:       gi|70606329|ref|YP_255199.1|  [L=327]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   16.0   0.5      0.012   16.0   0.5    3.1  4  Snapin_Pallidin  Snapin/Pallidin
       0.18   12.1   2.3        4.4    7.7   0.1    3.1  3  Dpoe2NT          DNA polymerases epsilon N terminal
       0.21   11.8   1.7       0.48   10.7   0.2    2.6  3  GST_C_3          Glutathione S-transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.31   1.8e+03      34      51 ..      29      46 ..      18      58 .. 0.56
   2 ?   -1.0   0.2      0.42   2.5e+03      44      72 ..     150     175 ..     124     193 .. 0.49
   3 ?   -1.7   0.1      0.66     4e+03      38      45 ..     183     190 ..     160     220 .. 0.52
   4 ?   16.0   0.5     2e-06     0.012      20      67 ..     272     320 ..     262     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.31
               Snapin_Pallidin 34 eqldrlnekLkeleeaqe 51
                                  ++l++ +e++k+++ ++e
  gi|70606329|ref|YP_255199.1| 29 DRLQNKAEEVKDVRSLEE 46
                                  344555555555555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.42
               Snapin_Pallidin  44 keleeaqeaevlpdlkeyakKLvnikkrm 72 
                                   +++++  e   +p+  +  k L+ ++k++
  gi|70606329|ref|YP_255199.1| 150 DDINRFIE--KPPKD-RNYKELQDLRKKI 175
                                   33333222..33332.2233455555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.66
               Snapin_Pallidin  38 rlnekLke 45 
                                   +l++++++
  gi|70606329|ref|YP_255199.1| 183 ELSNEVTS 190
                                   33333333 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2e-06
               Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekLkeleeaqe.aevlpdlkeyakKLvn 67 
                                   + l+elr++Q+e+l++l+  +++L e++ ++e +evl+d++e a+ L +
  gi|70606329|ref|YP_255199.1| 272 KYLEELRDHQKEMLDNLKHVSDALYEIAYNDEfDEVLADIEEKARSLLK 320
                                   679**************************************99987765 PP

>> Dpoe2NT  DNA polymerases epsilon N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.021   1.3e+02      29      54 ..     134     159 ..     128     165 .. 0.87
   2 ?    7.7   0.1   0.00074       4.4       2      40 ..     168     204 ..     167     213 .. 0.87
   3 ?   -1.9   0.1      0.69   4.2e+03      41      41 ..     286     286 ..     266     315 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.021
                       Dpoe2NT  29 aevllsldeeeledwlekiieavekQ 54 
                                   +e+l +l++ el++  ++i   +ek 
  gi|70606329|ref|YP_255199.1| 134 SELLNELGQTELKKLFDDINRFIEKP 159
                                   5899***************9888885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00074
                       Dpoe2NT   2 lekLrkrivsaFklrglllrseaskylaevllsldeeel 40 
                                   l+ Lrk+i+  F lr  +l +e + +l e lls  ee  
  gi|70606329|ref|YP_255199.1| 168 LQDLRKKITVSFTLR--ELSNEVTSLLEECLLSYPEESA 204
                                   689************..5679**********99988765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.69
                       Dpoe2NT  41 e 41 
                                   +
  gi|70606329|ref|YP_255199.1| 286 D 286
                                   2 PP

>> GST_C_3  Glutathione S-transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.8e+03      17      17 ..      36      36 ..      17      63 .. 0.50
   2 ?   -2.3   0.0      0.87   5.2e+03      19      41 ..     135     157 ..     125     169 .. 0.70
   3 ?   10.7   0.2     8e-05      0.48      22      70 ..     204     249 ..     169     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                  H CS
                       GST_C_3 17 e 17
                                  e
  gi|70606329|ref|YP_255199.1| 36 E 36
                                  1 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.87
                                   HHHHHHHHHHHHCHHHHHHHHHH CS
                       GST_C_3  19 ekkkefleerlpkflkyfekvlk 41 
                                   e  +e+ +++l+k ++ ++++++
  gi|70606329|ref|YP_255199.1| 135 ELLNELGQTELKKLFDDINRFIE 157
                                   55566677788888888888877 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 8e-05
                                   HHHHHHHHHCHHHHHHHHHHCHGTSSSSTTS--HHHHHHHHHHHHHHHH CS
                       GST_C_3  22 kefleerlpkflkyfekvlkkkgggylvgdklTyADlalfqvldgleea 70 
                                   +e+ +   +k  k+++ +l+   ++yl+ + l++ Dl ++++ld+l ++
  gi|70606329|ref|YP_255199.1| 204 AEYCQALSEKDKKVLKILLD---KPYLLDQILSIMDLGVYELLDTLLYT 249
                                   55554444444444444444...89*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1318  (0.0735122); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2212.60
//
Query:       gi|70606330|ref|YP_255200.1|  [L=153]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.9   0.3        7.2    6.5   0.1    2.5  2  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.054   14.4   0.0       0.11   13.4   0.0    1.5  1  DUF4065   Protein of unknown function (DUF4065)
        2.1    8.9   5.7         23    5.6   0.2    2.9  3  PNPase    Polyribonucleotide nucleotidyltransferase, RNA bind


Domain annotation for each model (and alignments):
>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0014       8.6      57      73 ..      63      77 ..      58      90 .. 0.79
   2 ?    6.5   0.1    0.0012       7.2       8      32 ..     117     141 ..     103     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0014
                       DUF1495 57 ssLielGLveeeeeseg 73
                                  +sLielG+v  eee  +
  gi|70606330|ref|YP_255200.1| 63 NSLIELGMVDVEEE--E 77
                                  79*******75444..3 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0012
                       DUF1495   8 SkvRkkvllyLysiypeksnlqeis 32 
                                   Sk R+++l+y y+ yp  +  + i 
  gi|70606330|ref|YP_255200.1| 117 SKPRQEILTYVYRRYPDYTRYSVIR 141
                                   889*************888777665 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05      0.11      13     102 ..      34     138 ..      27     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                       DUF4065  13 lkrtgkpitglkyiawkyGPVvpevydeikelgskpieekeeeisdeklekkekkeveeleddkeae.............. 79 
                                   l++ g   +gl+++ w +GP+++ + d i+ l +    + eee+ ++ ++    + ++ ++                    
  gi|70606330|ref|YP_255200.1|  34 LEKEGGVNLGLNFEPWLFGPYSKLLQDRINSLIELGMVDVEEEEVKDVISGLTIG-IKRKY-----Vlandvkvdnvrnei 108
                                   5677777899***********9966666666555555555555555555443222.22222.....122222456778899 PP

                       DUF4065  80 .......lseeekevidkvikkykdlsase 102
                                           s+  +e++ +v+ +y d++   
  gi|70606330|ref|YP_255200.1| 109 iqffkewVSKPRQEILTYVYRRYPDYTRYS 138
                                   99*********************9999765 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0066        39      31      66 ..       2      37 ..       1      38 [. 0.85
   2 ?    5.6   0.2    0.0038        23      50      80 ..      72     102 ..      57     103 .. 0.90
   3 ?    1.1   0.1     0.093   5.6e+02      30      75 ..     101     147 ..     100     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0066
                                  HHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHH CS
                        PNPase 31 deikekvveafaaeleeedeedekeikeifkalekk 66
                                  d + + +++ +  + ee+ e+++ ++++if  lek+
  gi|70606330|ref|YP_255200.1|  2 DTVDNYILALLKVAKEENAEVTATKLQKIFFLLEKE 37
                                  566777788888888999************999985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0038
                                   TS-HHHHHHHHHHHHHHHHHHHHHHTS-TTT CS
                        PNPase  50 eedekeikeifkalekkvvRsrildegvRiD 80 
                                   +++e+e+k++ + l+  + R+ +l++ v +D
  gi|70606330|ref|YP_255200.1|  72 DVEEEEVKDVISGLTIGIKRKYVLANDVKVD 102
                                   56899***********************999 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.093
                                   HHHHHHHHHHHHH...HHSTTS-HHHHHHHHHH....HHHHHHHHHHHHT CS
                        PNPase  30 ldeikekvveafaaeleeedeedekeikeifka....lekkvvRsrilde 75 
                                   +d++++++++ f    e  ++ +++ + ++++      ++ v+R +++++
  gi|70606330|ref|YP_255200.1| 101 VDNVRNEIIQFFK---EWVSKPRQEILTYVYRRypdyTRYSVIRDKVIRG 147
                                   6677777777666...3334555555555554311114567777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1111.50
//
Query:       gi|70606331|ref|YP_255201.1|  [L=52]
Description: hypothetical protein Saci_0502 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 391.04
//
Query:       gi|70606332|ref|YP_255202.1|  [L=59]
Description: N-terminal of inactivated transposase (ISC1476-like) [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.016   14.7   0.0    1.2  1  HTH_OrfB_IS605  Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_OrfB_IS605  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.8e-07     0.016       6      33 ..      30      57 ..      27      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-07
                HTH_OrfB_IS605  6 ykyrlyPTpeQeeklartfGcvRfVYNk 33
                                  + +rl P+  Q++kl++ +++    +N 
  gi|70606332|ref|YP_255202.1| 30 IVVRLFPNGYQQRKLRKLADVTVKMWNE 57
                                  568******************9999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 424.67
//
Query:       gi|70606333|ref|YP_255203.1|  [L=331]
Description: C-terminal of inactivated transposase (ISC1476-like) [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-29  102.8   0.3    2.1e-28   99.0   0.1    2.2  2  OrfB_IS605      Probable transposase
    2.4e-06   27.4   0.0    4.7e-06   26.4   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0021   18.3   0.4     0.0048   17.2   0.4    1.5  1  TBCA            Tubulin binding cofactor A


Domain annotation for each model (and alignments):
>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.1   3.5e-32   2.1e-28      10     117 ..     152     265 ..     120     268 .. 0.92
   2 ?    1.8   0.0     0.045   2.7e+02      92     115 ..     282     306 ..     281     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 3.5e-32
                    OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn......ykkasrklarlhrkr 84 
                                      pkgnk+a++DlGin Latv + dgt  +y g  +ksdy+y++k+iael+++++++++      ++++ ++ +rl++k+
  gi|70606333|ref|YP_255203.1| 152 ISSPKGNKVASVDLGINMLATVIVDDGTVLFYRGSVVKSDYFYFQKKIAELDRLKSEAEKiqeveaREEVLEERKRLFNKL 232
                                   6789******************************************************999******************** PP

                    OrfB_IS605  85 srrrkhllhklathliktlkevgvetLnvgnmk 117
                                   +rr++h+++ la+hl+k l ++gv+t+++g+++
  gi|70606333|ref|YP_255203.1| 233 YRRLLHYYRTLASHLAKALWNLGVSTVYLGYPY 265
                                   *******************************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.045
                    OrfB_IS605  92 lhklathliktlkevgvet.Lnvgn 115
                                   ++kl  +++++l+e g++t L+v++
  gi|70606333|ref|YP_255203.1| 282 YRKLIEAIMNKLHEYGIKTfLVVEY 306
                                   7999*************99455555 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.8e-10   4.7e-06       1      40 [.     282     321 ..     282     329 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.8e-10
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke 40 
                                   +rkl+e + +k +eyGik+ +v +++TS  C+ +  ++ +
  gi|70606333|ref|YP_255203.1| 282 YRKLIEAIMNKLHEYGIKTFLVVEYNTSRYCAYHDVEVVR 321
                                   79*******************************9988877 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4     8e-07    0.0048      24      77 ..     197     249 ..     195     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8e-07
                          TBCA  24 eqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekLeellee 77 
                                   ++ a+l++lk++ ++   +++  eevlee k+++ +l++rl   +  L + l++
  gi|70606333|ref|YP_255203.1| 197 KKIAELDRLKSEAEK-IQEVEAREEVLEERKRLFNKLYRRLLHYYRTLASHLAK 249
                                   6678999****9966.9***************************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2196.76
//
Query:       gi|70606334|ref|YP_255204.1|  [L=182]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.16   11.7   0.2       0.87    9.3   0.1    2.0  2  Peptidase_M48  Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   4.9e-05      0.87      43      83 ..      46      89 ..      42     113 .. 0.72
   2 ?    0.4   0.0     0.026   4.7e+02     130     149 ..     111     132 ..      94     164 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 4.9e-05
                                  SS-EEEEEEHHHH-SS...B-HHHHHHHHHHHHHHHHTTHHHHH CS
                                  xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 43 gknkrivltdgLlkql...lseeelaaVlGHElGHikhrhsvvs 83
                                  g+++ i++++ Llk++   l+++  +++l HElGH+ +   ++ 
  gi|70606334|ref|YP_255204.1| 46 GEENAIYVNTLLLKKKiilLKRDLPETILKHELGHVEQVNIYYL 89
                                  6667888888888664333899999***********98776665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.026
                                   T..HHHHHHHHHHHHHHHHTTT CS
                                   x..xxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 130 l..alSRkrEyqADeagvellk 149
                                   +  a++ + Ey+AD+a  + lk
  gi|70606334|ref|YP_255204.1| 111 TikAIGVYLEYKADKAVGKPLK 132
                                   3456777778888876555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1337.50
//
Query:       gi|70606335|ref|YP_255205.1|  [L=95]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.18   11.5   0.0    1.3  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.8e-06      0.18      35      57 ..      12      34 ..       5      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-06
                        DUF309 35 lqglIqlAvAlyhlrrgnvrgak 57
                                   +g I++A+ +  +r+gn++ga+
  gi|70606335|ref|YP_255205.1| 12 RKGAIKIATPVLQYRKGNHDGAM 34
                                  589*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 632.95
//
Query:       gi|70606336|ref|YP_255206.1|  [L=189]
Description: conjugative plasmid membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.5   0.1      0.081   12.9   0.1    1.3  1  GRA6      Granule antigen protein (GRA6)
      0.061   14.0   1.0      0.061   14.0   1.0    2.5  3  PrgI      PrgI family protein


Domain annotation for each model (and alignments):
>> GRA6  Granule antigen protein (GRA6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.1e-06     0.081     111     169 ..      93     151 ..      86     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                          GRA6 111 gkseargPsleerieeqddrrrpssvqeaqakvsskraqkrhrliGavvlaasvallta 169
                                    k+e++    +e+i e ++ ++ +s+ e  ak   k    + r+i a v  +++a+l  
  gi|70606336|ref|YP_255206.1|  93 EKKEKKLKEEKEKIVEGKTTKKSVSLSEIIAKYKQKMLMYKKRVIRAGVSGTTLAVLLI 151
                                   46777777899**************************************9999999943 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   6.8e-06     0.061      12      83 ..      21      85 ..      13      90 .. 0.80
   2 ?   -1.2   0.0      0.39   3.5e+03      73      89 ..     120     136 ..     111     137 .. 0.62
   3 ?    4.0   5.5    0.0092        83      21      63 ..     136     178 ..     120     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-06
                          PrgI 12 kiffg.LtlRQliflvlallvaiglylllrafleelasvlvillavPvaalgfykkdglplekylkaiikfkl 83
                                   ++++  +l+Ql++++  +l  ++l+++ +++l      ++++  +P++ +  y  + +   +y+ +++kf+l
  gi|70606336|ref|YP_255206.1| 21 PLWIKqVSLKQLAVIFPSAL--LALIFFSKSIL------IAMASLIPAIYIITYDEKSMDEFQYVYHFVKFYL 85
                                  566666899*********99..56666666666......99999***99999998888888899999999984 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                          PrgI  73 kylkaiikfklrpkkrv 89 
                                   ++++++ + +l+ kkrv
  gi|70606336|ref|YP_255206.1| 120 EIIAKYKQKMLMYKKRV 136
                                   55555555558888876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0092
                          PrgI  21 QliflvlallvaiglylllrafleelasvlvillavP.vaalgf 63 
                                    +   v++  +a++l+l+ r f+ ++as l++l+av  v+a+++
  gi|70606336|ref|YP_255206.1| 136 VIRAGVSGTTLAVLLILVARDFI-TIASNLMYLVAVSiVIAVAI 178
                                   444456667789***********.88888888888883444454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1758  (0.0980534); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1380.57
//
Query:       gi|70606337|ref|YP_255207.1|  [L=101]
Description: hypothetical protein Saci_0508 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.6   6.4       0.18   11.5   6.4    1.0  1  DUF1673   Protein of unknown function (DUF1673)


Domain annotation for each model (and alignments):
>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   6.4     1e-05      0.18     110     199 ..       4      90 ..       1      96 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1e-05
                       DUF1673 110 kralvektvdkisikrilfkpvvIiikievtenenpvlrwllrllllviflliavllillsyvesiagelqlge.vvssfi 189
                                   +++++  t+++i +  ++++++ I++k   t+  n     +l+ +l+++fl+i    i+  y+  i+ +l l + v++s+i
  gi|70606337|ref|YP_255207.1|   4 RNSIIA-TAITIETATKYIRLLAIVMKSLATKMSNTARVVPLTPALITLFLYI---NIFCLYFAIISLKLTLFFvVFPSTI 80 
                                   556655.7888999999999*******************************99...5555555555555554334444444 PP

                       DUF1673 190 sgllllllwl 199
                                    ++ +++ ++
  gi|70606337|ref|YP_255207.1|  81 FSFSSFSFFS 90 
                                   4433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 741.69
//
Query:       gi|70606338|ref|YP_255208.1|  [L=51]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 374.66
//
Query:       gi|70606339|ref|YP_255209.1|  [L=140]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 992.64
//
Query:       gi|70606340|ref|YP_255210.1|  [L=51]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 425.09
//
Query:       gi|70606341|ref|YP_255211.1|  [L=139]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.42   10.0   3.3        6.3    6.2   0.0    2.0  2  DUF1122   Protein of unknown function (DUF1122)


Domain annotation for each model (and alignments):
>> DUF1122  Protein of unknown function (DUF1122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.7   0.00055       9.9     118     163 ..      36      82 ..      27      91 .. 0.82
   2 ?    6.2   0.0   0.00035       6.3      47     104 ..      75     129 ..      64     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00055
                                   H.HHHHHTT--EEEEEES-.TTTSSS-EEEEEE--SSHHHHHHHHHHH CS
                       DUF1122 118 G.feLlkrGftwFkdWYfp.EGfmEGspkiqaekPldeeeekrqleel 163
                                   G fe + r ft+  +WY+  EG+  G+  i + k +++  +  +++++
  gi|70606341|ref|YP_255211.1|  36 GtFERMGRAFTYE-KWYWDeEGLFTGGYGIVTGKKVEKRIRWDEIQDI 82 
                                   5588888999985.5888527*************99999999888887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00035
                                   -EEEEES--G.......GGHHHHTTSHHHHHHHHHHTTT-S...EEEEE-TT-HHHHH CS
                       DUF1122  47 pWiEifniswlreveldsltavffgskvEeelldllsevlgpgerlfveYvkDketlk 104
                                   +W Ei+ i +++  +++++  ++ g+   +++ d    vl +ger+ + Yv D   + 
  gi|70606341|ref|YP_255211.1|  75 RWDEIQDIVPMNVQSISAYGLNLAGT--SKTIGDW-VVVLKNGERVMIRYVLDPINMA 129
                                   79999999887777776555555444..3444444.568999**********987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 996.62
//
Query:       gi|70606342|ref|YP_255212.1|  [L=487]
Description: conjugative plasmid membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1172  (0.065369); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3144.22
//
Query:       gi|70606343|ref|YP_255213.1|  [L=87]
Description: hypothetical protein Saci_0516 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 635.08
//
Query:       gi|70606344|ref|YP_255214.1|  [L=223]
Description: conjugative plasmid protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   12.7   1.3        4.2    7.0   0.1    2.3  2  DUF1241   Protein of unknown function (DUF1241)
      0.088   12.2   0.1      0.088   12.2   0.1    1.6  2  SNAP      Soluble NSF attachment protein, SNAP


Domain annotation for each model (and alignments):
>> DUF1241  Protein of unknown function (DUF1241)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2    0.0022        20      79     111 ..      46      82 ..      24      87 .. 0.71
   2 ?    7.0   0.1   0.00047       4.2      35      73 ..      88     127 ..      83     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0022
                       DUF1241  79 ykversee.efqeLnkkara...LkkiLsriPdeind 111
                                   y+ +r+++ + ++L++k+++   L+ iLsr+ de +d
  gi|70606344|ref|YP_255214.1|  46 YSSKREKRdTNTKLHRKSTKdiiLQYILSRLCDEEKD 82 
                                   44444444556677776653333**********9877 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00047
                       DUF1241  35 lskaekesPgltqdlvkgllkkkelsvnlne.slLrlqgt 73 
                                   l+k ek+ P+l+  + + +l+k++ +vn +   +Lr +g 
  gi|70606344|ref|YP_255214.1|  88 LAKFEKQDPALLLAIFEFVLEKHGRRVNREYmEFLRQKGI 127
                                   789************************9764147777776 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.9e-06     0.088     172     228 ..      40      97 ..      30      99 .. 0.85
   2 ?   -1.9   0.1       0.2   1.8e+03      11      49 ..     159     199 ..     152     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-06
                                   HHHHHHHHHH.HHTTSS-TTTGGGHHHHHHHHHHHHHHTT-HHHHHHHHHGGG----- CS
                          SNAP 172 ekAieiyekv.akkslennllkysvkeyflkaglcrLaagDvvaakralekyeeldps 228
                                     Aie y++   k+ ++ +l + s k++ l+ +l rL+ ++     + l k+e++dp 
  gi|70606344|ref|YP_255214.1|  40 FSAIEYYSSKrEKRDTNTKLHRKSTKDIILQYILSRLCDEEKDLFYHILAKFEKQDPA 97 
                                   4699999765156678899***********************************9996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.2
                                   HHHSS---THH.HHH.--SHHHHHHHHHHHHHHHHHHHHTT CS
                          SNAP  11 ekklksssglf.slf.gsksskaeeAadlyeqAAnayklak 49 
                                   +k++k+   l+ + + g ++ k  e  +l ++  + ykl++
  gi|70606344|ref|YP_255214.1| 159 RKEAKELYTLLsKYYpGFHELKTREKLELIKKYSQDYKLRN 199
                                   44444444445444455566677777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1613.53
//
Query:       gi|70606345|ref|YP_255215.1|  [L=453]
Description: hypothetical protein Saci_0520 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-24   85.6   2.7    4.6e-24   85.6   2.7    3.1  3  ATPase_2        ATPase domain predominantly from Archaea
    4.2e-20   72.0   3.3    6.5e-20   71.4   1.1    2.4  2  DUF234          Archaea bacterial proteins of unknown functio
    4.7e-10   39.6   0.9      1e-09   38.5   0.2    2.0  2  AAA_14          AAA domain
    2.8e-05   24.6   0.1     0.0055   17.1   0.0    2.5  2  AAA_16          AAA ATPase domain
    5.9e-05   22.8   0.0    0.00017   21.4   0.0    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
    8.6e-05   22.0   0.1    0.00059   19.3   0.1    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00017   21.4   0.0    0.00038   20.3   0.0    1.5  1  MarR            MarR family
    0.00018   21.4   0.8     0.0021   18.0   0.0    3.0  3  HTH_45          Winged helix-turn-helix
    0.00049   20.4   0.1     0.0014   18.9   0.1    1.7  1  AAA_22          AAA domain
    0.00064   19.2   0.2     0.0069   15.8   0.0    2.5  3  TniB            Bacterial TniB protein
    0.00076   19.3   0.2     0.0021   17.9   0.2    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0051   16.7   0.0      0.011   15.6   0.0    1.5  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.017   15.2   0.7      0.037   14.1   0.1    1.9  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
      0.022   15.2   0.0      0.066   13.6   0.0    1.8  1  AAA             ATPase family associated with various cellula
      0.091   13.0   0.0        0.2   11.8   0.0    1.5  1  Roc             Ras of Complex, Roc, domain of DAPkinase
        0.2   11.5   0.0       0.37   10.6   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   2.7   4.1e-27   4.6e-24       1     233 []       5     207 ..       5     207 .. 0.84
   2 ?   -0.7   0.2      0.99   1.1e+03      86     113 ..     318     346 ..     235     358 .. 0.52
   3 ?   -0.6   0.9      0.93     1e+03      65      91 ..     326     356 ..     303     426 .. 0.52

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 4.1e-27
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81 
                                   F+dRe+el+ lee +++++++++ +YG++++GKt L+k++i+ +     + iy  +  +  ++++++           +++
  gi|70606345|ref|YP_255215.1|   5 FIDRERELEFLEEKYNEDKAQFIILYGRRRIGKTELVKQFIKDK-----EAIYHLSTTDGIQNNVNRL----------KET 70 
                                   99***************************************988.....6799888777777776666..........555 PP

                      ATPase_2  82 lgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvvi 162
                                   ++  ++k+ +       + l +  + ++ ++i +k  k+i+ iDe+q+li      +++ +++ +++++++++++++ + i
  gi|70606345|ref|YP_255215.1|  71 FARFTGKNYFRS----LNVLFDDLLIYFGDEIGDK--KVILAIDEFQYLI--E--ADRSIISQVQRAWDEKLRSTKIYLLI 141
                                   555555555533....3455555566666677665..89***********..5..55************************ PP

                      ATPase_2 163 clsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPkalvel 233
                                    +sS g++ + +++ +s+l+gr+++  ++  l + +   f+++       +  e++ +i++ v+G+P ++ +l
  gi|70606345|ref|YP_255215.1| 142 TGSSVGMMENeVLSTKSPLYGRRTGsWKLSALPFPSLSSFFRN-------KDIEELIKIWSTVDGIPFYILQL 207
                                   ********99567899*********999999999999999888.......3557999************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.99
                      ATPase_2  86 vpkaeleeilk.eksklvfkaiellleki 113
                                   v   e++++ +  ++ ++++++++ +ek+
  gi|70606345|ref|YP_255215.1| 318 VSDLEIDRVEEvMNRVNLEQYFSSKFEKL 346
                                   22222222222233333333333333333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.93
                      ATPase_2  65 ldefie....eeeekkklekalgiavpkael 91 
                                   ++e ++    e++ ++k+ek + + ++++++
  gi|70606345|ref|YP_255215.1| 326 VEEVMNrvnlEQYFSSKFEKLIRELIRNKTI 356
                                   2222223333444444444444333333333 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.3   2.6e+03      18      36 ..      61      79 ..      43      87 .. 0.63
   2 !   71.4   1.1   5.8e-23   6.5e-20       1      95 [.     310     397 ..     310     402 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                        DUF234 18 eevlekikeelneyvgkvF 36
                                  ++ ++++ke++ +++gk +
  gi|70606345|ref|YP_255215.1| 61 QNNVNRLKETFARFTGKNY 79
                                  2334677899999999987 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 5.8e-23
                        DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivaldeeekk 81 
                                   wfrfvy+n s++e++++eev+++++  l++y++++FE+l+rel++  nk+  lpf+++ v+++ +k+ee+Di+a  ++   
  gi|70606345|ref|YP_255215.1| 310 WFRFVYENVSDLEIDRVEEVMNRVN--LEQYFSSKFEKLIRELIR--NKTIPLPFKYEYVSKYLHKGEEVDIIAEGKDV-- 384
                                   ***********************99..*****************9..77889**********************99998.. PP

                        DUF234  82 alfgEvKwknseke 95 
                                   ++++EvKw++ + +
  gi|70606345|ref|YP_255215.1| 385 LFMAEVKWSD-NVD 397
                                   9********9.554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.2     9e-13     1e-09       3     111 ..      25     155 ..      23     175 .. 0.61
   2 ?   -2.4   0.0       4.1   4.6e+03      34      34 ..     356     356 ..     319     397 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 9e-13
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell..........vkkesilyinldderd..........kkla..dpekllelileklk 61 
                                   + +++ G Rr+GKT l+kq+ik++           +        n+++ ++           ++    +++ll ++ +++ 
  gi|70606345|ref|YP_255215.1|  25 QFIILYGRRRIGKTELVKQFIKDKEaiyhlsttdgI------QNNVNRLKEtfarftgknyFRSLnvLFDDLLIYFGDEIG 99 
                                   6799*****************998855553333320......222222222222222211111111123344444444443 PP

                        AAA_14  62 eekktylflDEiqevpewekalkslvd....eg...knldvivtGSnskllskeiat 111
                                    +kk +l +DE q++ e+ + + s v+    e+   +++ +++tGS+ +++ +e+ +
  gi|70606345|ref|YP_255215.1| 100 -DKKVILAIDEFQYLIEADRSIISQVQrawdEKlrsTKIYLLITGSSVGMMENEVLS 155
                                   .699***********7777665555553433445336788999********998764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.1
                        AAA_14  34 l 34 
                                   +
  gi|70606345|ref|YP_255215.1| 356 I 356
                                   1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.9e-06    0.0055       1      55 [.       4      52 ..       4      84 .. 0.74
   2 ?    5.1   0.1     0.024        27     133     161 ..      99     127 ..      65     141 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.9e-06
                        AAA_16  1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                  +++ Re+ele L++ ++  +    + ++l+G + +GK+ lv+++ +   ++++i+
  gi|70606345|ref|YP_255215.1|  4 QFIDRERELEFLEEKYNEDK---AQFIILYGRRRIGKTELVKQFIK---DKEAIY 52
                                  6888*****99999998554...479***************99986...333444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                        AAA_16 133 derplvlvlDdlqwadeaslqllaaLlrl 161
                                   ++++++l +D++q + ea+++++++  r+
  gi|70606345|ref|YP_255215.1|  99 GDKKVILAIDEFQYLIEADRSIISQVQRA 127
                                   3556****************999987776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.5e-07   0.00017       5      46 ..     247     288 ..     245     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                                   HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5   5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                   l IL+++++g  +v+ ++e +gl ++++  +L +L+e  +Ve
  gi|70606345|ref|YP_255215.1| 247 LSILRAVSQGYNTVSKISEVTGLDKGNLTSYLDRLEENEIVE 288
                                   56**************************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3   1.5e+03      11      21 ..     204     214 ..     203     215 .. 0.84
   2 !   19.3   0.1   5.3e-07   0.00059       8      48 .]     249     288 ..     247     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                        HTH_24  11 lLqknprisqr 21 
                                   +Lq +pr+s  
  gi|70606345|ref|YP_255215.1| 204 ILQLDPRLSVE 214
                                   7999****975 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 5.3e-07
                        HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   IL+++  ++  + + ++e +gl +++++ +l+rLee+++++
  gi|70606345|ref|YP_255215.1| 249 ILRAVS-QGYNTVSKISEVTGLDKGNLTSYLDRLEENEIVE 288
                                   444444.4999****************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.4e-07   0.00038      18      49 ..     258     289 ..     244     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.4e-07
                                   EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  18 lsvseLakklgvskstvtrvldrLekkGlieR 49 
                                    +vs++ +  g++k+++t  ldrLe+++ +eR
  gi|70606345|ref|YP_255215.1| 258 NTVSKISEVTGLDKGNLTSYLDRLEENEIVER 289
                                   5899***************************9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.8   3.2e+03      19      34 ..     215     230 ..     208     233 .. 0.68
   2 !   18.0   0.0   1.8e-06    0.0021       6      50 ..     244     288 ..     241     293 .. 0.94
   3 ?   -1.1   0.1       1.8     2e+03      37      49 ..     344     356 ..     327     385 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                        HTH_45  19 eakkTkimykanLsyk 34 
                                   e+ k kim+k n  y+
  gi|70606345|ref|YP_255215.1| 215 ENIKFKIMKKGNVLYD 230
                                   5566677777776665 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                        HTH_45   6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglik 50 
                                    ++++IL+a+s+g ++ +ki     L+  +l +YLd L e+++++
  gi|70606345|ref|YP_255215.1| 244 RVYLSILRAVSQGYNTVSKISEVTGLDKGNLTSYLDRLEENEIVE 288
                                   68899*************************************997 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.8
                        HTH_45  37 nkYLdmLvekgli 49 
                                   +k +  L+ ++ i
  gi|70606345|ref|YP_255215.1| 344 EKLIRELIRNKTI 356
                                   5555555555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06    0.0014       4     117 ..      23     129 ..      19     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelkaerlsseell.ea 81 
                                   +a++++++G   +GKT l++++ + +         ++ + + t  +    +   l + ++r++g +  +   s+  l+ ++
  gi|70606345|ref|YP_255215.1|  23 KAQFIILYGRRRIGKTELVKQFIKDK---------EAIYHLSTTDG-IqnNVNRLKETFARFTGKNYFR---SLNVLFdDL 90 
                                   799*********************86.........34444333333.2458888888888888877777...999999666 PP

                        AAA_22  82 leqalrarav.ielliiDEaqhlr..seealeeLrslln 117
                                   l    ++ ++ +++l iDE+q+l+     +++++ + ++
  gi|70606345|ref|YP_255215.1|  91 LIYFGDEIGDkKVILAIDEFQYLIeaDRSIISQVQRAWD 129
                                   6666666666889*********97653555555544343 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.2e-06    0.0069      21      64 ..      10      53 ..       3      66 .. 0.87
   2 ?   -2.1   0.0       1.9   2.1e+03     122     137 ..     104     119 ..     101     133 .. 0.80
   3 ?   -0.4   0.0       0.6   6.7e+02      78     105 ..     237     264 ..     227     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.2e-06
                          TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekd 64
                                  ++Le L e+ ++++ + ++l+G+  +GKt +v++F +++++  +
  gi|70606345|ref|YP_255215.1| 10 RELEFLEEKYNEDKAQFIILYGRRRIGKTELVKQFIKDKEAIYH 53
                                  67899999999**************************9987655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                          TniB 122 vLiiDEihnllagsar 137
                                   +L iDE++ l+++ ++
  gi|70606345|ref|YP_255215.1| 104 ILAIDEFQYLIEADRS 119
                                   789****999987655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.6
                          TniB  78 ppkpdekrlyaaiLealgaplkararvs 105
                                   +++ +e+r y +iL+a+++ +++  ++s
  gi|70606345|ref|YP_255215.1| 237 REEFKEQRVYLSILRAVSQGYNTVSKIS 264
                                   4566788889999998888887766665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.9e-06    0.0021      10      55 ..     242     290 ..     240     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                   CCCHCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB  10 EakvYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                   E +vYl +l   ++g  t+++i+e +g+++ +  ++L +Le+  +Ver+
  gi|70606345|ref|YP_255215.1| 242 EQRVYLSILravSQGYNTVSKISEVTGLDKGNLTSYLDRLEENEIVERV 290
                                   789*****99999**********************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.5e-06     0.011      21      54 ..     258     290 ..     242     297 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-06
                                   EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  21 dltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                   + tv+ + + +gl+k++++  l+rL++   ver+
  gi|70606345|ref|YP_255215.1| 258 N-TVSKISEVTGLDKGNLTSYLDRLEENEIVERV 290
                                   3.9*****************************97 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.3e-05     0.037      10      50 ..     249     289 ..     241     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                Sulfolobus_pRN  10 illilsrrcatleeleektGiekeellvyltrlykrGlisr 50 
                                   il  +s++  t+ ++ e tG++k +l  yl rl +  ++ r
  gi|70606345|ref|YP_255215.1| 249 ILRAVSQGYNTVSKISEVTGLDKGNLTSYLDRLEENEIVER 289
                                   88899****************************99999887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-05     0.066       1     120 [.      27     154 ..      27     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTS......TS CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk................yvgesekkirelfkeakeka......kp 59 
                                   ++lyG   +GKT l+k+ +k+ +  ++ +s ++ +++                y+   +  + +l+             k+
  gi|70606345|ref|YP_255215.1|  27 IILYGRRRIGKTELVKQFIKD-KEAIYHLSTTDGIQNnvnrlketfarftgknYFRSLNVLFDDLLIY----FgdeigdKK 102
                                   689******************.3334444444444222333333333332222222222222222222....022335567 PP

                                   EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                           AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                   +il iDE+  l++++        +++++q  +++d+  ++  k+ +++++ ++ ++++++l
  gi|70606345|ref|YP_255215.1| 103 VILAIDEFQYLIEAD--------RSIISQVQRAWDEKLRS-TKIYLLITGSSVGMMENEVL 154
                                   ***********9999........999*******9999996.55999999988888888776 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018       0.2       2      35 ..      27      61 ..      27      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                  EEEESSTTSSHHHHHHCHCT-CCC-EEETTT.TEE CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkfsekeksti.gvd 35
                                  ++l G  ++GKt l+k+f++dk    + st+ g++
  gi|70606345|ref|YP_255215.1| 27 IILYGRRRIGKTELVKQFIKDKEAIYHLSTTdGIQ 61
                                  7899****************998766655431554 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00033      0.37       6      50 ..     247     289 ..     245     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                   l+iL+a++++    t+s +++ tgl k +   +L  L+e  +ve+
  gi|70606345|ref|YP_255215.1| 247 LSILRAVSQGYN--TVSKISEVTGLDKGNLTSYLDRLEENEIVER 289
                                   677888888777..5*************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2860.41
//
Query:       gi|70606346|ref|YP_255216.1|  [L=99]
Description: hypothetical protein Saci_0523 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.6   0.1    2.7e-10   40.3   0.1    1.1  1  HTH_34    Winged helix DNA-binding domain
    5.2e-06   26.2   0.2    0.00035   20.4   0.0    2.3  2  HTH_5     Bacterial regulatory protein, arsR family
    0.00055   19.8   0.1    0.00078   19.4   0.1    1.2  1  PadR      Transcriptional regulator PadR-like family
     0.0053   16.8   0.0      0.015   15.3   0.0    1.8  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   6.1e-14   2.7e-10       1      76 [.      20      95 ..      20      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 6.1e-14
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76
                                  vRl++l  L+ v++a f++l e++++++++L+ hlk++ k gY++++       +r  + iT+eG + + + +k L
  gi|70606346|ref|YP_255216.1| 20 VRLGILLGLYYVKSAWFKDLIESTRLNKAELYQHLKAMHKSGYLKISYMPTPSGKRMRVVITEEGEKVAREILKLL 95
                                  8**********************************************9998888899999*****99999888877 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.7e-08   0.00035       4      45 ..      21      63 ..      19      64 .. 0.84
   2 ?    3.8   0.0     0.011        51      13      29 ..      83      99 .]      79      99 .] 0.89

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.7e-08
                                  HHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  4 RlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  Rl IL  L   +++ + +l e ++l+++ + +HLk+++++G++
  gi|70606346|ref|YP_255216.1| 21 RLGILLGLYYvKSAWFKDLIESTRLNKAELYQHLKAMHKSGYL 63
                                  66666666666677789************************97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                                  TSSEEHHHHHHHHTS-H CS
                         HTH_5 13 egelcvcelaeelglsq 29
                                  ege+ + e+ + lg+sq
  gi|70606346|ref|YP_255216.1| 83 EGEKVAREILKLLGKSQ 99
                                  79999999999999998 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.7e-07   0.00078      20      74 ..      37      89 ..      30      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-07
                                  HCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 20 eelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  ++l+e  ++l++++lY+ Lk + k+g+++ +  ++ +g++ ++  +T++G++  +
  gi|70606346|ref|YP_255216.1| 37 KDLIES-TRLNKAELYQHLKAMHKSGYLKISYMPTPSGKRMRV-VITEEGEKVAR 89
                                  566655.89************************9966666555.79999998766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.5e-06     0.015       8      55 ..      17      64 ..       4      66 .. 0.91
   2 ?   -1.6   0.0      0.63   2.8e+03      10      19 ..      86      95 ..      84      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                                  S-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  8 ahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                     vR++il  L   + + +++l e  +l k++l++HL+++ + g+++
  gi|70606346|ref|YP_255216.1| 17 NVSVRLGILLGLYYVKSAWFKDLIESTRLNKAELYQHLKAMHKSGYLK 64
                                  4489********999****************************99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.63
                                  HHHHHHHHHH CS
                        HTH_20 10 PvRrrilraL 19
                                  +v r+il++L
  gi|70606346|ref|YP_255216.1| 86 KVAREILKLL 95
                                  6789999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 626.75
//
Query:       gi|70606347|ref|YP_255217.1|  [L=164]
Description: hypothetical protein Saci_0524 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.4    9.0   2.5        2.7    8.0   2.5    1.4  1  DUF3043          Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.5   0.00015       2.7      75     132 ..      67     123 ..      63     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00015
                       DUF3043  75 rrnlgelflplalvvlvlllvslvkvpevqavvsl.lllvllllvvidgillgrkvkkk 132
                                   r+ + +++l    v+l+l+ +   + + + +++++ l+  +l+++ ++ +++  ++++k
  gi|70606347|ref|YP_255217.1|  67 RIFIRTFLLAGYAVLLLLFYL-SLHFTIL-SYLTFfLVATYLVFMSVNLWFILKTIRRK 123
                                   667777888777777777444.3445444.5555516666************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1084.49
//
Query:       gi|70606348|ref|YP_255218.1|  [L=231]
Description: hypothetical protein Saci_0525 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-21   76.5   0.0      4e-21   75.8   0.0    1.3  1  Nitroreductase  Nitroreductase family
     0.0053   16.4   0.3       0.29   10.7   0.0    2.1  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   4.4e-25     4e-21       1     169 [.      49     229 ..      49     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 4.4e-25
                                   HHH--B---B-S----HHHHHHHHHHH............HTS--GGG---EEEEEE.-CCCH.......HHHHHHHHHHHH CS
                Nitroreductase   1 irkRrSiRkFddepvpkeelekileaa............rraPsagnlqpwrfvvvqdkelr.......yklaeaalelll 62 
                                   +++R+S R+F+ e++ + +++++l+              r+ Psagnl ++++++++   +        y+  e +l+ l 
  gi|70606348|ref|YP_255218.1|  49 MKRRHSSRAFRRERINLNKISSLLWYSvgvkeiengiqfRMFPSAGNLAETEVYLIS-LYTDlekgvyhYDPVEGSLDVLS 128
                                   589*****************************************************4.33333467755555555555555 PP

                                   HHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GG CS
                Nitroreductase  63 kaeaqaelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggf 143
                                       ++ ++q        ++  + +   p++i+++  + k   k+++r++r++l+d+g++++n++L AtalGlg   iggf
  gi|70606348|ref|YP_255218.1| 129 NDLDEELMLQAI------KNSLPDITFVPLIILLTSLYWKPMVKYGNRGARFSLIDTGIVIENFYLVATALGLGISAIGGF 203
                                   555555555554......899999999****************************************************** PP

                                   GGGHHHHHHHHT-S....SEEEEEEEEE CS
                Nitroreductase 144 deaaeevrkllglp..deeeivvliavG 169
                                   +++   ++kl+g+   ++e ++++++vG
  gi|70606348|ref|YP_255218.1| 204 NDDF--FNKLIGVGmeKGEVVIGMLVVG 229
                                   ****..*****99887889999999999 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   3.2e-05      0.29       3      47 ..      46      91 ..      44     110 .. 0.87
   2 !    4.0   0.0    0.0036        32      81     107 ..     176     202 ..     160     231 .] 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.2e-05
                                  HHHHHH--B---B--S---HHHHHHHHH-----S....S-----EE CS
                TM1586_NiRdase  3 yeaiekRhsvRkYkdealeeelleelkeaieeinkes.glelqlvi 47
                                   e ++ Rhs R+++ e ++ ++++ l  +   +++ + g++++++ 
  gi|70606348|ref|YP_255218.1| 46 QEVMKRRHSSRAFRRERINLNKISSLLWYSVGVKEIEnGIQFRMFP 91
                                  589********************99999999999888799998875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHTT-EEEEES- CS
                TM1586_NiRdase  81 eekaGYygeqlvLkltalGlgtcWvgg 107
                                   +  +G + e++ L +talGlg + +gg
  gi|70606348|ref|YP_255218.1| 176 LIDTGIVIENFYLVATALGLGISAIGG 202
                                   344555566666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1669.11
//
Query:       gi|70606349|ref|YP_255219.1|  [L=434]
Description: hypothetical protein Saci_0526 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-42  145.5   0.0    2.5e-42  145.3   0.0    1.0  1  YcaO      YcaO cyclodehydratase, ATP-ad Mg2+-binding


Domain annotation for each model (and alignments):
>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.0   1.4e-46   2.5e-42       1     322 [.      74     395 ..      74     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.4e-46
                          YcaO   1 nGkGateeaArasalgEalErysaegffrgdekrvrasyrelegegaldpeelglyseeekdaadfvlepfdpdrpidwvp 81 
                                   +GkG+tee+++ +a+gE+lEr+   ++  +de+ ++++  +l ++  + p +++++s  e+ ++  ++++++++  ++ ++
  gi|70606349|ref|YP_255219.1|  74 GGKGFTEEESLEGAIGEFLERFYGAFTLFDDESIIFGRIGDLMTKYEIFPITYKFFST-EQLQKLLIFRDYNENVMLSLTR 153
                                   5*********************87778889999999********************66.7899999***********9999 PP

                          YcaO  82 gwsltdgeevlvPanlvyl.yeppegearlfletsnGlAaGntleeAilhGllEliERdafalawyerlplpridlasdpe 161
                                   +  + +g +v++P+++ yl    ++ge+ ++++t+ GlA ++++e A +hGllE++ERd +++ w +r+p++ri+l+  ++
  gi|70606349|ref|YP_255219.1| 154 AKYY-KGSDVYIPVQITYLlNLIRPGEDLIAYSTTGGLAFHKDFESAFIHGLLEYLERDTINISWISRIPPKRIRLP--ER 231
                                   9876.5666**********988888888999**********************************************..** PP

                          YcaO 162 irellerlreagievrlldatldl.gipvvaavlvdpklllvagaGahldpevAlerAltElaqsrltlisgaredpdfd. 240
                                   ir+ l+ l++  +++ +l ++ ++ g+ vv+++ + ++l +vagaGa+ + e+A+++A+ E++qs+ ++ +      + + 
  gi|70606349|ref|YP_255219.1| 232 IRRKLKVLED--RNITCLSFPGEFkGLFVVGCLGFINDL-YVAGAGADITLEEAIRKAVFEVYQSISSFSKITD--EEIKm 307
                                   ********99..689*********************664.589**************************77744..33333 PP

                          YcaO 241 eeladvatleradreallwl..peaaakrldfll........faewassgdleedletllerlkaagldvlvvdltrp.dl 310
                                   ++  +++ l+++   +l++   ++++ ++    +        ++e ++  + +  ++ l++++ ++++ +++ d++ +  l
  gi|70606349|ref|YP_255219.1| 308 ARNLKPDYLTDFGLVPLYYSfvKTNFLVE----YlrslqsitYEELER--EENLSYKSLIDIILGKNYYIIYKDFDIEkYL 382
                                   45555666666777777773333333332....123444544333333..444599****************999988899 PP

                          YcaO 311 g.lpvvkvivPgl 322
                                   g  + v+vivP l
  gi|70606349|ref|YP_255219.1| 383 GeGKLVRVIVPDL 395
                                   99*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3030.55
//
Query:       gi|70606350|ref|YP_255220.1|  [L=236]
Description: hypothetical protein Saci_0527 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.017   14.3   0.0    1.2  1  IF-2B     Initiation factor 2 subunit family
      0.021   15.6   2.5      0.027   15.2   2.5    1.3  1  DKNYY     DKNYY family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.9e-06     0.017      79     142 ..      84     148 ..      40     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-06
                                   HHHHHHHHHHH.HHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXT CS
                         IF-2B  79 liekikelike.ieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsr 142
                                     + ik++++  ++ +  +i+ + + l++++d i+T  +s+   +v++  a + ++f V+v++s+
  gi|70606350|ref|YP_255220.1|  84 SFRVIKSFQEVkDKSKIAVISSNISYLLSENDEIVTLLKSRKFEKVVIGYAMDYYRFFVYVMDSK 148
                                   566788888776888889999****************************888899********96 PP

>> DKNYY  DKNYY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.5     3e-06     0.027       3      64 ..      63     133 ..      61     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                         DKNYY   3 kdknnvYyenk..kikgaDlksFkvLnedkyakDknnvYykgkkiseidpknlkil.....esfelik..k 64 
                                    d++ +Y++ +  + k++D+ sF+v+++++ +kDk+++ +   +is++ ++n +i+     ++fe +   +
  gi|70606350|ref|YP_255220.1|  63 SDDEIIYLKVNslNFKNLDPFSFRVIKSFQEVKDKSKIAVISSNISYLLSENDEIVtllksRKFEKVVigY 133
                                   69999****774677************************99999999999998888778774444443322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1690.86
//
Query:       gi|70606351|ref|YP_255221.1|  [L=43]
Description: hypothetical protein Saci_0528 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 301.65
//
Query:       gi|70606352|ref|YP_255222.1|  [L=219]
Description: hypothetical protein Saci_0529 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1617.25
//
Query:       gi|70606353|ref|YP_255223.1|  [L=245]
Description: hypothetical protein Saci_0530 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1539.14
//
Query:       gi|70606354|ref|YP_255224.1|  [L=199]
Description: high-affinity zinc uptake system ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-18   65.7   0.0    8.3e-18   65.2   0.0    1.2  1  ABC_tran      ABC transporter
    2.3e-13   50.7   0.6    1.6e-06   28.2   0.8    2.0  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.1e-10   38.3   0.1     0.0001   21.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    4.6e-06   27.3   1.2    5.9e-06   26.9   1.1    1.4  1  AAA_23        AAA domain
    1.6e-05   23.8   0.2    0.00067   18.4   0.2    2.2  2  AAA_13        AAA domain
    0.00019   21.8   0.0    0.00031   21.2   0.0    1.4  1  AAA           ATPase family associated with various cellular 
    0.00022   20.9   0.3    0.00039   20.1   0.3    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00051   19.9   0.2     0.0049   16.6   0.4    2.0  2  AAA_15        AAA ATPase domain
     0.0014   19.1   0.1     0.0019   18.6   0.1    1.5  1  AAA_16        AAA ATPase domain
     0.0036   17.5   0.0      0.056   13.7   0.0    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.014   15.2   0.0    1.3  1  AAA_30        AAA domain
      0.015   15.2   0.8      0.025   14.5   0.8    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
       0.02   14.2   0.0       0.04   13.2   0.0    1.5  1  Zeta_toxin    Zeta toxin
      0.026   14.1   0.0      0.049   13.2   0.0    1.4  1  AAA_27        AAA domain
      0.032   14.8   0.0      0.054   14.0   0.0    1.5  1  AAA_18        AAA domain
      0.032   14.2   0.1      0.062   13.3   0.1    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.032   13.8   0.1      0.057   13.0   0.1    1.3  1  AAA_25        AAA domain
      0.035   13.8   0.1        6.8    6.4   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.044   13.2   0.0      0.074   12.4   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.046   11.2   0.3       0.06   10.9   0.3    1.1  1  DUF3584       Protein of unknown function (DUF3584)
      0.047   12.8   0.3       0.17   11.0   0.1    1.9  2  DUF815        Protein of unknown function (DUF815)
      0.052   13.6   0.1       0.11   12.5   0.1    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
      0.054   13.4   0.1      0.089   12.7   0.1    1.5  1  RsgA_GTPase   RsgA GTPase
      0.074   13.0   0.1       0.13   12.1   0.1    1.4  1  NACHT         NACHT domain
      0.089   13.1   0.2       0.12   12.6   0.2    1.7  1  AAA_22        AAA domain
        0.1   12.3   0.0       0.16   11.7   0.0    1.4  1  AAA_24        AAA domain
        0.1   12.9   0.0       0.13   12.6   0.0    1.4  1  AAA_19        AAA domain
       0.11   12.6   0.1        1.2    9.2   0.1    2.1  2  AAA_33        AAA domain
       0.16   11.0   0.8       0.28   10.2   0.8    1.3  1  T2SSE         Type II/IV secretion system protein
       0.24   11.6   0.4       0.41   10.9   0.2    1.5  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   1.4e-20   8.3e-18      10     136 ..      17     145 ..       9     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.4e-20
                                   TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH...HHHTCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                      ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvren...esdeei 85 
                                   e+++  + G nG+GK+tL+++++gl  p +G+i+++gk++++  + le + +  +v++  +++ ++ ++  +    + +e+
  gi|70606354|ref|YP_255224.1|  17 ENTVALLYGTNGSGKTTLIRAISGLI-PYSGSIKINGKEVRSakNLLEYSTNLPEVYFIGNTVLDTAKIVAElkgGDLREF 96 
                                   56788899****************96.89***********99643344444444555555556666654444355555666 PP

                                   HHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  86 ekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    ++++++gl+   ++v+++  ++LS G+++ v l  al+ kp++  lDEp 
  gi|70606354|ref|YP_255224.1|  97 LELVERFGLES--KKVINKPFYKLSTGERSLVTLSLALFAKPRVCTLDEPL 145
                                   66666666666..66665555*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.8   2.6e-09   1.6e-06       1      83 [.      20      84 ..      20     111 .. 0.63
   2 !   20.8   0.0   4.7e-07   0.00028     227     298 ..     108     173 ..      91     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.6e-09
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83
                                  +++l+G NgsGK++L++a+++l                   + + + ++++++ +++ ++  + +++ +v + ++  l+   +
  gi|70606354|ref|YP_255224.1| 20 VALLYGTNGSGKTTLIRAISGL------------------IPYSGSIKINGKEVRSAKNLLEYSTNLPEVYFIGNTVLDTAKI 84
                                  579******************9..................4444444444444444444444444444444444444444444 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.7e-07
                        AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell..kelsrngaQviltTHS 298
                                   ++  + p+++lS G ++l  l +al++ +   ++  +DEp  + +P+  +++++++  + ++      i++TH+
  gi|70606354|ref|YP_255224.1| 108 KKVINKPFYKLSTGERSLVTLSLALFAKP---RVCTLDEPLENVDPQKREKVIRVIreRVKEG-----IIVTHD 173
                                   55555699******************988...**************99999999996555555.....777887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.1e-05     0.012      19      45 ..      13      39 ..       2      57 .. 0.82
   2 !   21.8   0.0   1.7e-07    0.0001     135     204 ..      76     179 ..      43     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
                                  EEETTSSEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 19 ilpfsksftaivGpNGSGKsnlldAil 45
                                   l +++ +  ++G NGSGK+ l+ Ai+
  gi|70606354|ref|YP_255224.1| 13 NLVVENTVALLYGTNGSGKTTLIRAIS 39
                                  5567788999***************97 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.7e-07
                                   T........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                   x........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e........................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                   +                                         LS Ge++Lv l+L +    + +  ++ lDe   + D ++
  gi|70606354|ref|YP_255224.1|  76 NtvldtakivaelkggdlreflelverfgleskkvinkpfyKLSTGERSLVTLSLAL----FAKPRVCTLDEPLENVDPQK 152
                                   356666666666666666666666666666666999999999**********99963....3334479************* PP

                                   HHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 176 vkkvaellkeksknaQfivislreemlek 204
                                   ++kv ++++e+ k+   i++++++++++ 
  gi|70606354|ref|YP_255224.1| 153 REKVIRVIRERVKE--GIIVTHDKDLVKV 179
                                   ***********955..6999999998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.1   9.8e-09   5.9e-06       3      42 ..       2      41 ..       1     155 [. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.8e-09
                        AAA_23  3 kienfrsfrdqeidFskgltlItGpNGaGKTTildAikla 42
                                  ++++ r +++ ++  ++ + l++G NG+GKTT+++Ai   
  gi|70606354|ref|YP_255224.1|  2 SLKGTRILKGINLVVENTVALLYGTNGSGKTTLIRAISGL 41
                                  688999999999999**********************854 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.1e-06   0.00067      19      39 ..      21      41 ..      13      91 .. 0.81
   2 ?    3.8   0.0     0.029        18     495     510 ..     113     128 ..      97     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                        AAA_13 19 NliYGwNGaGKTtLSrllrsl 39
                                   l+YG+NG+GKTtL r+++ l
  gi|70606354|ref|YP_255224.1| 21 ALLYGTNGSGKTTLIRAISGL 41
                                  589***************988 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                        AAA_13 495 qaaetLSeGEktaIaf 510
                                   ++ ++LS+GE++++++
  gi|70606354|ref|YP_255224.1| 113 KPFYKLSTGERSLVTL 128
                                   68899*********97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.2e-07   0.00031       2      49 ..      22      84 ..      21     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.2e-07
                                  EEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSS..............STTHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavakel.gvefleisgsellsk..............yvgesekkirel 49
                                  llyG+ G GKT+l++a+   +  +  ++i+g+e++s               ++g++  +++++
  gi|70606354|ref|YP_255224.1| 22 LLYGTNGSGKTTLIRAISGLIpYSGSIKINGKEVRSAknlleystnlpevyFIGNTVLDTAKI 84
                                  9*******************9446679******994446666666666666555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.3   6.5e-07   0.00039      23      46 ..      18      42 ..       9      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-07
                        AAA_29 23 g.atlltGpsGsGKSTllDAiqalL 46
                                  + + ll G++GsGK+Tl+ Ai+ l+
  gi|70606354|ref|YP_255224.1| 18 NtVALLYGTNGSGKTTLIRAISGLI 42
                                  4489****************99876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   8.2e-06    0.0049      13      50 ..       8      45 ..       2     120 .. 0.76
   2 ?    1.6   0.0       0.3   1.8e+02     292     366 ..     113     174 ..      76     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-06
                        AAA_15 13 slkdveidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                   lk + + +++ + +l G+N+sGK+++++a+  ++  +
  gi|70606354|ref|YP_255224.1|  8 ILKGINLVVENTVALLYGTNGSGKTTLIRAISGLIPYS 45
                                  56777788888899*****************8777644 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.3
                        AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    p++k ++G ++l+ l+l ++ + +            ++EP  +  pq  + +i+ ++e ++++    ii TH  
  gi|70606354|ref|YP_255224.1| 113 KPFYKLSTGERSLVTLSLALFAKPRV---------CTLDEPLENVDPQKREKVIRVIRERVKEG----IIVTHDK 174
                                   57889999999999999887765554.........77888888888888888888888888888....7888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.2e-06    0.0019      26      69 ..      20      64 ..      12     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.2e-06
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesa.ipy 69
                                  + ll+G  G+GK++l+r++   +  +g i ++gk +++ ++ ++y
  gi|70606354|ref|YP_255224.1| 20 VALLYGTNGSGKTTLIRAISGLIPYSGSIKINGKEVRSAKNlLEY 64
                                  679******************999999999999999995444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.4e-05     0.056      24      89 ..     109     161 ..      92     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-05
                       SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   k +++ + +lS+Ge+  l++l la     l+        ++r++ LDE  +++D++++++++++++
  gi|70606354|ref|YP_255224.1| 109 KVINKPFYKLSTGER-SLVTLSLA-----LFA-------KPRVCTLDEPLENVDPQKREKVIRVIR 161
                                   447778888888888.66666665.....333.......489********************9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.3e-05     0.014      18      62 ..      18      61 ..      12     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvL 62
                                  + va+l G  G+GKtt+++a+  ++  +g ++ +   + + Ak+L
  gi|70606354|ref|YP_255224.1| 18 NTVALLYGTNGSGKTTLIRAISGLIPYSG-SIKINGKEVRSAKNL 61
                                  4699*****************99998776.666666666666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.8   4.1e-05     0.025      19      40 ..      17      38 ..       7     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                      ATPase_2 19 pneiyfiYGpegsGKtaLlkei 40
                                  +n++ ++YG  gsGKt+L++ i
  gi|70606354|ref|YP_255224.1| 17 ENTVALLYGTNGSGKTTLIRAI 38
                                  46899**************987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.7e-05      0.04      18      56 ..      20      57 ..       8      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-05
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                  + ll G  G+GK++l++++   + ++++ +++++ ++R+
  gi|70606354|ref|YP_255224.1| 20 VALLYGTNGSGKTTLIRAISGLI-PYSGSIKINGKEVRS 57
                                  67899***************998.7********999997 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.3e-05     0.049      25      49 ..      17      41 ..      10      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-05
                        AAA_27 25 eadlhliyGpNEAGKstalrAisdl 49
                                  e+ + l+yG+N +GK+t++rAis l
  gi|70606354|ref|YP_255224.1| 17 ENTVALLYGTNGSGKTTLIRAISGL 41
                                  56789*****************987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.1e-05     0.054       2      25 ..      22      49 ..      22     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.1e-05
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf....g 25
                                  ll Gt G+GKttl +++s +  +     
  gi|70606354|ref|YP_255224.1| 22 LLYGTNGSGKTTLIRAISGLIPYsgsiK 49
                                  589**************87654455552 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1    0.0001     0.062      18      40 ..      16      39 ..       4      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                  H.TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE 18 l.gdvilLeGdLGaGKTtlvrgla 40
                                  + ++v lL+G  G+GKTtl+r++ 
  gi|70606354|ref|YP_255224.1| 16 VeNTVALLYGTNGSGKTTLIRAIS 39
                                  2467899**************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.5e-05     0.057      28      50 ..      13      35 ..       6      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.5e-05
                        AAA_25 28 gllpagelallaGapgtGKttla 50
                                  +l++++++all+G  g+GKttl 
  gi|70606354|ref|YP_255224.1| 13 NLVVENTVALLYGTNGSGKTTLI 35
                                  47889****************96 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.023        14      37      67 ..       8      38 ..       2      45 .. 0.85
   2 ?    6.4   0.0     0.011       6.8     103     149 ..     130     174 ..     116     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.023
                     IstB_IS21 37 eLatlsfiekkenivllGpsGvGKshlaial 67
                                   L + + + ++   +l G  G GK+ l  a+
  gi|70606354|ref|YP_255224.1|  8 ILKGINLVVENTVALLYGTNGSGKTTLIRAI 38
                                  577778888899999***********99887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                     IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                   l+ ++k+++  lD+  l+++d +++e++ +vi +r++ + ii+t ++
  gi|70606354|ref|YP_255224.1| 130 LALFAKPRVCTLDE-PLENVDPQKREKVIRVIRERVK-EGIIVTHDK 174
                                   66678889999999.599*****************95.678888766 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.074      26      50 ..      22      46 ..      15      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                  Mg_chelatase 26 llvGppGsGKtmlakrlpsllppls 50
                                  ll+G+ GsGKt l++++++l+p   
  gi|70606354|ref|YP_255224.1| 22 LLYGTNGSGKTTLIRAISGLIPYSG 46
                                  89******************99654 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3    0.0001      0.06      21      37 ..      22      38 ..       9      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                       DUF3584 21 nieGtNaaGKTtLlrLi 37
                                   + GtN++GKTtL+r i
  gi|70606354|ref|YP_255224.1| 22 LLYGTNGSGKTTLIRAI 38
                                  578***********976 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00028      0.17      56      75 ..      21      40 ..      15      75 .. 0.79
   2 ?   -0.6   0.0         1   6.2e+02     176     188 ..      93     105 ..      49     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                        DUF815 56 vLLwGarGtGKSslvkalln 75
                                  +LL+G+ G+GK +l++a+  
  gi|70606354|ref|YP_255224.1| 21 ALLYGTNGSGKTTLIRAISG 40
                                  79***************975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                        DUF815 176 veeklsLsdRFGl 188
                                   + e l L +RFGl
  gi|70606354|ref|YP_255224.1|  93 LREFLELVERFGL 105
                                   5788999999998 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00018      0.11       3      39 ..      22      58 ..      21     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                  EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HH CS
                         AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltrdttee 39
                                  lL G  G+gK++l++ ++ ++  +  ++ + +  +++
  gi|70606354|ref|YP_255224.1| 22 LLYGTNGSGKTTLIRAISGLIPYSGSIKINGKEVRSA 58
                                  89******************98887777766666555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00015     0.089      90     121 ..       9      40 ..       1      92 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                   HHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  90 leelkellkdktsvlvGqSGvGKStLinallp 121
                                   l+ ++ ++++ +++l G  G GK+tLi a+ +
  gi|70606354|ref|YP_255224.1|   9 LKGINLVVENTVALLYGTNGSGKTTLIRAISG 40 
                                   56677789999*****************9976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00022      0.13       3      21 ..      21      39 ..      19      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +l G +GsGKTtL++ + 
  gi|70606354|ref|YP_255224.1| 21 ALLYGTNGSGKTTLIRAIS 39
                                  6899***********9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00021      0.12       6      26 ..      19      39 ..      16     184 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                        AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                  ++ +++G  G+GKTtl+r + 
  gi|70606354|ref|YP_255224.1| 19 TVALLYGTNGSGKTTLIRAIS 39
                                  6789*************9876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.16       3      22 ..      19      38 ..      17      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                     l+yG +g+GKTtl++ +
  gi|70606354|ref|YP_255224.1| 19 TVALLYGTNGSGKTTLIRAI 38
                                  5679************9876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022      0.13       7      33 ..      15      41 ..       9     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhival 33
                                   ++++v l+ +  G+GKT+++++i  l
  gi|70606354|ref|YP_255224.1| 15 VVENTVALLYGTNGSGKTTLIRAISGL 41
                                  678999***************998665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0021       1.2       1      18 [.      20      37 ..      20      48 .. 0.88
   2 ?    0.9   0.0      0.79   4.7e+02      70      95 ..     136     163 ..     120     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                        AAA_33  1 lvllvGlpGsGKstlaer 18
                                  + ll G +GsGK+tl++ 
  gi|70606354|ref|YP_255224.1| 20 VALLYGTNGSGKTTLIRA 37
                                  56889**********986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.79
                        AAA_33  70 grnvildat..nlsrrerarflklarrl 95 
                                    r + ld +  n+++++r++++++ r+ 
  gi|70606354|ref|YP_255224.1| 136 PRVCTLDEPleNVDPQKREKVIRVIRER 163
                                   456788888889999***9999998854 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   0.00047      0.28     126     156 ..      15      45 ..       4      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00047
                         T2SSE 126 vrerglilvsGgTgsGKttllyallkeinks 156
                                   v e+ + l+ G+ gsGKttl+ a+   i+ s
  gi|70606354|ref|YP_255224.1|  15 VVENTVALLYGTNGSGKTTLIRAISGLIPYS 45 
                                   5667788999**************9999865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00069      0.41       4      20 ..      23      39 ..      20      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00069
                        AAA_28  4 itGgestGKTtlleaLa 20
                                  + G+ ++GKTtl++a++
  gi|70606354|ref|YP_255224.1| 23 LYGTNGSGKTTLIRAIS 39
                                  79************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1286.43
//
Query:       gi|70606356|ref|YP_255225.1|  [L=198]
Description: hypothetical protein Saci_0532 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00026   20.0  25.0    0.00055   19.0  25.2    1.4  1  MFS_1      Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0  25.2   3.1e-08   0.00055      16     170 ..      48     192 ..      28     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.1e-08
                         MFS_1  16 gpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqG 96 
                                   ++++  +  e++g++++++g+ +++ +l++ v  +++Gr++    +r++l+ +++l +++++ll++ +   + +v+ ++++
  gi|70606356|ref|YP_255225.1|  48 ILII--YSVEHFGFDKTTLGIFYSVQTLLYTVVPPLIGRIA----SRKILISAYTLEGVSFYLLTV-TK--TTIVGFLMMA 119
                                   3333..558*******************************5....579************666664.22..4566666666 PP

                         MFS_1  97 lgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                   l   ++++  + ++ ++++   rg  +g+ls+ +s +++++ +++g+l+ +++ +++fy+  ++ +l+++ f++
  gi|70606356|ref|YP_255225.1| 120 LLVFSAIAWEVLFFGEVAKIGGRGVKFGILSGISSSSTAITLAFSGYLY-QISSTLLFYLYVLFIILSLLAFII 192
                                   66533444455566666666*****************************.666556655555555555443222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1270.03
//
Query:       gi|70606355|ref|YP_255226.1|  [L=157]
Description: hypothetical protein Saci_0533 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1214.88
//
Query:       gi|70606357|ref|YP_255227.1|  [L=60]
Description: hypothetical protein Saci_0534 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0043   15.9   1.1     0.0044   15.9   1.1    1.0  1  LacY_symp  LacY proton/sugar symporter
     0.0081   15.1   3.7     0.0084   15.1   3.7    1.0  1  MFS_1      Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.1   4.9e-07    0.0044       5      61 ..       3      58 ..       1      60 [] 0.90

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-07
                     LacY_symp  5 kntnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqp 61
                                  k+ nf++++l+ +++ f  s++  ++p+ l   +g+  t  Gi++s+i+l+ i+  p
  gi|70606357|ref|YP_255227.1|  3 KKDNFFYLGLSTSLLTFGNSLWIFYLPLILL-RIGIDVTLQGIIYSIITLLGIVSSP 58
                                  7889******************999999887.579****************998766 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.7   9.4e-07    0.0084     203     263 ..       2      59 ..       1      60 [] 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.4e-07
                         MFS_1 203 llkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailall 263
                                   ++kd+++++ l ++ll+ fg+s+  ++lpl+   + g++ + l g++++++ l+g++++++
  gi|70606357|ref|YP_255227.1|   2 IKKDNFFYLGLSTSLLT-FGNSLWIFYLPLI-LLRIGID-VTLQGIIYSIITLLGIVSSPF 59 
                                   67889887444444444.49**********7.*******.9***************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 425.41
//
Query:       gi|70606358|ref|YP_255228.1|  [L=199]
Description: hypothetical protein Saci_0535 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1436.76
//
Query:       gi|70606359|ref|YP_255229.1|  [L=134]
Description: hypothetical protein Saci_0538 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   14.0   1.1       0.14   12.5   1.1    2.0  1  ERGIC_N   Endoplasmic Reticulum-Golgi Intermediate Compartmen


Domain annotation for each model (and alignments):
>> ERGIC_N  Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   7.9e-06      0.14      20      69 ..       2      71 ..       1     117 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-06
                                  XXXXXXXXXXXXXXXXXXXXXXXX.XXX-EEEEEE-....................-S--SEEEEEEEEE CS
                       ERGIC_N 20 sGgiislvcillilfLllselteylttevkeelvvd....................ksrsekleinldit 69
                                  +G++i +++i+li+ + +  +++y+ + +++ ++v                      + ++k++i+l+i+
  gi|70606359|ref|YP_255229.1|  2 KGAVIAVIAIILIAAVAYLYFSGYFYSVTVTGVYVTyqnnllikyiktnysnttinLHGGQKFTITLNIS 71
                                  79***********************999988888876666666666665555444344457777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 901.73
//
Query:       gi|70606360|ref|YP_255230.1|  [L=367]
Description: translation initiation factor IF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-74  251.2   0.1    1.3e-74  251.0   0.1    1.1  1  IF-2B          Initiation factor 2 subunit family
  ------ inclusion threshold ------
        1.8    8.8   3.5         10    6.4   0.0    2.4  2  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.0   0.1   1.4e-78   1.3e-74       1     282 []      63     355 ..      63     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: 251.0 bits;  conditional E-value: 1.4e-78
                                   SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHH...HHHCCTTTSSHHHHHHH CS
                         IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllk...eiselksssdvkeakks 78 
                                   kvrG+pai+i+a +++  +i+d+     ++ +++l+ka + L ++rPtav+l +a  r+l+   ++ e  + ++vke k+ 
  gi|70606360|ref|YP_255230.1|  63 KVRGAPAIGITAGYGMVLAIQDSI--SLEKAISDLTKAKKILDESRPTAVNLMWATSRMLNkakDLVEQGNAKSVKELKEL 141
                                   69********************99..77777******************************887677788899999***** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH.........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HT CS
                         IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt.........vlevlraaakekkkfkVivvEsrPrlqG.rl 149
                                   l  +++++ +e  ea+ kig +++e+++dgdtilT cn++          +l+  + a   + k++Vi+ E+rP lqG rl
  gi|70606360|ref|YP_255230.1| 142 LEIEANKIFEEEYEAELKIGLYGIEKVNDGDTILTQCNAGGlatgtglgtALAPAKLANALGIKVSVIAPETRPWLQGsRL 222
                                   ****************************************999************************************** PP

                                   HHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSG CS
                         IF-2B 150 takeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqld 229
                                   t++eL++++ipvtli d+av+ vm + +v+ v+vGAdril++G ++nkiGT + Av+A+e  ip+++ a+s++f+    +d
  gi|70606360|ref|YP_255230.1| 223 TVYELMEENIPVTLIADTAVGLVMFKkMVNSVMVGADRILSDGHVFNKIGTFKEAVIAHELGIPFYALAPSSTFDMISTVD 303
                                   ************************999************************************************986666 PP

                                   GGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 230 edifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   + + ieer p+e+  i+g+ i ++e+kv+np+fDvtPp+++++iITe+G++ p
  gi|70606360|ref|YP_255230.1| 304 Q-VKIEERSPDEVRSIKGVYISPKEVKVYNPVFDVTPPKYVSAIITEYGIIYP 355
                                   6.666*********************************************976 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0012        10       6      28 ..      45      67 ..      42      70 .. 0.87
   2 ?    1.4   1.8     0.041   3.7e+02      24      65 ..     119     159 ..      85     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0012
                                  ESS-HHHHHHHHHHHTTSBHHHH CS
                 Ribosomal_L22  6 lrvsfkklrevarlIrgmkveeA 28
                                  + v + k+ ev ++Ir mkv+ A
  gi|70606360|ref|YP_255230.1| 45 IYVDVTKVEEVSDAIRTMKVRGA 67
                                  668899**************988 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.041
                                   BHHHHHHHHHT-SSTTHHHHHHHHHHHHHHHH..HT-GGGEE CS
                 Ribosomal_L22  24 kveeAlkyLkfskkkaakfvlklLknaeanaelkgldvdslv 65 
                                    +++A++  ++ + k+ k++++lL+ +ean + ++  + +l 
  gi|70606360|ref|YP_255230.1| 119 MLNKAKDLVEQGNAKSVKELKELLE-IEANKIFEEEYEAELK 159
                                   4567777777777779999999998.7888877766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2532.78
//
Query:       gi|70606361|ref|YP_255231.1|  [L=325]
Description: DHH-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-10   40.2   0.0    2.6e-09   37.6   0.0    2.2  2  DHHA1          DHHA1 domain
     0.0055   16.9   0.0       0.01   16.0   0.0    1.4  1  DHH            DHH family
  ------ inclusion threshold ------
       0.14   12.6   0.0        0.8   10.2   0.0    2.2  1  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.24   1.4e+03      29      68 ..      41      78 ..      33     105 .. 0.73
   2 !   37.6   0.0   4.3e-13   2.6e-09      26     125 ..     193     282 ..     178     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                                  HHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGB CS
                         DHHA1 29 ellekaeevkgvkvlvaevgeewdagalgiaadklksklk 68
                                  +ll+++e   g k +  ++  ++++ +l ++ ++l+   +
  gi|70606361|ref|YP_255231.1| 41 NLLKSLELR-GIKKIMIAD-IGINQSTLNEILTQLNRLQT 78
                                  555555554.777777777.78999999998888887444 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 4.3e-13
                                   HHHHHHHTCEEEC.....TCEEEEEECHCCHHH.HHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSHSS-HHHHH CS
                         DHHA1  26 kaeellekaeevk.....gvkvlvaevgeewda.galgiaadklksklkkpvivfvakeegdkvkvsarskkdgvdagela 100
                                   +++++ + ++ ++     g kv+va     w+   ++  a  +l +     +ivf++++++   ++s+rs+   +d++  a
  gi|70606361|ref|YP_255231.1| 193 EINGYSKLHKHIRvleidGRKVVVAVR---WKGpPDISYASQYLMN--RYNSIVFASVNGK---SISFRSN--IIDIRRFA 263
                                   455555555555566674555555555...6666899999999999..77*********99...*******..9******* PP

                                   HHHHHHTTCCEEEETCEEEEEEEHC CS
                         DHHA1 101 keaaaklgggGGGHdlAaGagipae 125
                                   ++      +gGGGH+lAaGag++a 
  gi|70606361|ref|YP_255231.1| 264 EK------LGGGGHPLAAGAGLNAP 282
                                   **......**************965 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06      0.01       8      94 ..       7     133 ..       4     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                                   CSSSHHHHHHHHHHHH................................CECS--TCGGCGCCH......HCCCSEEEEEEE CS
                                   xxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                           DHH   8 knpDtDsigSaialan................................llvDhneksqavege......akeeaedviiiD 50 
                                    + D D+ +Sa ++a+                                ++ D ++++ + ++       ++ e+ +++  D
  gi|70606361|ref|YP_255231.1|   7 VHNDFDGTASAAVYARavgslptkvffteptkihnllkslelrgikkiMIADIGINQSTLNEIltqlnrLQTEGAEIEWFD 87 
                                   578*******99999988888888888888888888777777777777689999988888776888888************ PP

                                   -S---S....S---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHH CS
                                   xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DHH  51 HHrlge....efetlapilflnepvgstaeivaelleekkeeiskeia 94 
                                   HH  ++    +++++  +++ +  + ++a+++ + l+  ++e+s+++a
  gi|70606361|ref|YP_255231.1|  88 HHVWKDewktKLREI-GVTVYHDVTTCGAGVINKNLN-PDDEVSSKLA 133
                                   ****99666544444.466777889999999999865.4444455555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00013       0.8      53     108 ..      51     109 ..       8     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                   ..T--EEEE-S-HHHHGGGHHHHHHH...--SEEEE-TT---HHHHHHHHHTT-EEE.E CS
                 CoA_binding_2  53 pepvdlvdvftppeatpeivkealal...gakavwlqpgsedeeaaelaeeagirvvgd 108
                                    +++ ++d+ ++++++ ei+ ++ +l   ga+  w+  +++++e   +++e g++v  d
  gi|70606361|ref|YP_255231.1|  51 IKKIMIADIGINQSTLNEILTQLNRLqteGAEIEWFDHHVWKDEWKTKLREIGVTVYHD 109
                                   457789****************988866679999*****************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2325.12
//
Query:       gi|70606362|ref|YP_255232.1|  [L=200]
Description: isochorismatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-38  132.8   0.0    1.7e-38  132.6   0.0    1.0  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6   0.0   9.4e-43   1.7e-38       1     161 [.      21     178 ..      21     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 9.4e-43
               Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelvp 80 
                                   talv++Dmqndfv  eg   +++++ +++ i+ l+++ar++g  +i+t+d h     k d++ + + +h   g++gae+++
  gi|70606362|ref|YP_255232.1|  21 TALVIVDMQNDFVrREGKLYVPNAESTINPIRSLIHKARDSGSLIIYTQDWHM----KDDPEFKIWGEHALAGSWGAEIIE 97 
                                   8****************************************************....99********************** PP

               Isochorismatase  81 elaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhdaalk 161
                                   el+p++ d++v K+r++af++++ld iL+ +gik++v++G  +++CV++ta +a+ + y+v++v+D+++a++  ++   l+
  gi|70606362|ref|YP_255232.1|  98 ELTPDKEDFIVRKYRYDAFFESPLDYILRVKGIKNVVITGTVANICVLHTAGSAALRWYNVTLVKDGISAITDFDYYSTLR 178
                                   **********************************************************************99877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1254.02
//
Query:       gi|70606363|ref|YP_255233.1|  [L=196]
Description: endonuclease V [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-34  118.0   0.1    6.2e-34  117.4   0.1    1.2  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
      0.031   14.7   1.0      0.064   13.7   1.0    1.6  1  DUF5607         Domain of unknown function (DUF5607)


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.1   6.9e-38   6.2e-34       5     180 ..      18     175 ..      15     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 6.9e-38
                                   CC-------SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS CS
                Endonuclease_5   5 kkveledklkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkq 85 
                                   k+++ +    e++k + GvD+++ k +    +a+ v++d ++     ++++  k++fpYipg+L  RE+p+++ka+e+++ 
  gi|70606363|ref|YP_255233.1|  18 KNITIKRLGIENIKNLCGVDIAY-KGNI--GYAVSVMFDGKD---YFHKYVKGKVDFPYIPGYLFMREAPLMIKAVESFQC 92 
                                   556666666677899********.3333..378888887544...4578999***************************96 PP

                                   --SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEE CS
                Endonuclease_5  86 kpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSv 166
                                     d++lvDG+G+aHpr+ G+As +Gv+ld ptiGvaKs+l+g++ e+    gs+  +v +g+++g+ +       + y S+
  gi|70606363|ref|YP_255233.1|  93 --DLILVDGHGMAHPRKSGIASVIGVILDKPTIGVAKSKLYGDIVEE----GSTNFIVVNGDKVGVKV------GKYYYSI 161
                                   ..9***************************************88754....56666776799999865......4679999 PP

                                   ECSS-HHHHHHHHH CS
                Endonuclease_5 167 Ghrisletalelvl 180
                                   G+++++++ +el +
  gi|70606363|ref|YP_255233.1| 162 GNKVDIDDVVELSR 175
                                   99999999988765 PP

>> DUF5607  Domain of unknown function (DUF5607)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.0   7.1e-06     0.064      18      48 ..     129     157 ..     112     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-06
                                   --EEEEEEE-SSEEEEE-SSEEEEEESSS-- CS
                       DUF5607  18 divGeiveeavynflidaGdkmcvGnkiGvw 48 
                                    + G+ivee   nf++  Gdk  vG k+G +
  gi|70606363|ref|YP_255233.1| 129 KLYGDIVEEGSTNFIVVNGDK--VGVKVGKY 157
                                   568******************..56677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1538.07
//
Query:       gi|70606364|ref|YP_255234.1|  [L=155]
Description: hypothetical protein Saci_0545 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-10   38.4   0.0    1.5e-09   37.8   0.0    1.3  1  DSPc             Dual specificity phosphatase, catalytic doma
    1.5e-09   37.8   0.0    1.7e-09   37.6   0.0    1.1  1  Y_phosphatase    Protein-tyrosine phosphatase
    8.1e-05   22.8   0.0    0.00014   22.0   0.0    1.4  1  PTPlike_phytase  Inositol hexakisphosphate
    0.00027   20.6   0.0    0.00034   20.3   0.0    1.2  1  CDKN3            Cyclin-dependent kinase inhibitor 3 (CDKN3)
     0.0079   16.2   0.0       0.02   14.8   0.0    1.5  2  Y_phosphatase3   Tyrosine phosphatase family


Domain annotation for each model (and alignments):
>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   4.1e-13   1.5e-09      69     120 ..      84     135 ..      73     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 4.1e-13
                                   HHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHHHHHHHHHHSTT-SST CS
                          DSPc  69 akqkgkkvlVHCqaGisRSatliiaYlmktknlslneayeflkerrpaispn 120
                                     +k k  lVHC  Gi R++t+ + Yl  ++n+s++ea+e ++  rp  +++
  gi|70606364|ref|YP_255234.1|  84 WLRKDKGNLVHCVGGIGRTGTILASYLVLEENMSAEEAIEEVRRVRPGAVQT 135
                                   456777779*************************************988776 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   4.9e-13   1.7e-09     144     231 ..      68     144 ..      38     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4.9e-13
                                   -SSSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHH CS
                 Y_phosphatase 144 pdhgvpesaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtle 224
                                   pd  +p s +++l++ + ++k+k       +VhC  G+gRtgt++a  ++l++      ++  ++++e+r+ Rpg+vqt+e
  gi|70606364|ref|YP_255234.1|  68 PDGRAP-SENQFLEIYKWLRKDK-----GNLVHCVGGIGRTGTILASYLVLEEN-----MSAEEAIEEVRRVRPGAVQTYE 137
                                   566666.589999******9999.....889*************9999998754.....55899***************** PP

                                   HHHHHHH CS
                 Y_phosphatase 225 qyiflye 231
                                   q +f+ +
  gi|70606364|ref|YP_255234.1| 138 QELFVFK 144
                                   *999876 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     4e-08   0.00014      96     152 ..      56     109 ..      37     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4e-08
                                   HHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS-TT-EEEEE-SSSSHHHHHHHHHH CS
               PTPlike_phytase  96 eelslrYaRipitdekapeeedfdalvsilkeapektalvfnCqmGrgRTTtamvia 152
                                   ++++++Y   pi+d +ap+e++f ++++ l++    +  +++C  G gRT t ++ +
  gi|70606364|ref|YP_255234.1|  56 KSFNIEYLYSPIPDGRAPSENQFLEIYKWLRKD---KGNLVHCVGGIGRTGTILASY 109
                                   67899****************998888777766...57899**********998765 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   9.5e-08   0.00034      97     168 .]      56     122 ..      26     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.5e-08
                                   HHTT-EEEE----TTS---HHHHHHHHHHHHHHHHTT--EEEE-SSSSSHHHHHHHHHHHHH-SSS-HHHHH CS
                         CDKN3  97 qqygivthhhpiadggtpdiascleimeelatclknyrktlihcygglgrsclvaaclllylsdsispeqai 168
                                   + + i   + pi+dg +p  +  lei +     l++ +  l+hc gg+gr+  + a  l  l +++s e+ai
  gi|70606364|ref|YP_255234.1|  56 KSFNIEYLYSPIPDGRAPSENQFLEIYK----WLRKDKGNLVHCVGGIGRTGTILASYL-VLEENMSAEEAI 122
                                   5566666789********9999888876....57889999***********99777654.578888888876 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.73   2.6e+03     200     213 ..      40      53 ..      37      62 .. 0.85
   2 !   14.8   0.0   5.7e-06      0.02      98     142 ..      63     110 ..      55     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.73
                Y_phosphatase3 200 aieekygsvegYlr 213
                                   +i+e +gs+e Y++
  gi|70606364|ref|YP_255234.1|  40 EIDEAWGSLEYYIS 53 
                                   58999*****9985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.7e-06
                Y_phosphatase3  98 lYrelle...sakkayrkvfealadeepvlfHCtaGKDRTGvlaalll 142
                                   lY  +++    +++++ ++ + l++++  l+HC  G  RTG + a  l
  gi|70606364|ref|YP_255234.1|  63 LYSPIPDgraPSENQFLEIYKWLRKDKGNLVHCVGGIGRTGTILASYL 110
                                   67777775444557888888999996699************9988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1149.75
//
Query:       gi|70606365|ref|YP_255235.1|  [L=261]
Description: hypothetical protein Saci_0546 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-57  194.0   0.1    2.8e-57  193.7   0.1    1.1  1  ATPase           KaiC
    1.5e-09   37.7   0.0    2.2e-09   37.2   0.0    1.2  1  AAA_25           AAA domain
    4.3e-08   32.7   0.0    6.6e-08   32.1   0.0    1.3  1  Rad51            Rad51
    3.9e-07   29.8   0.1    7.9e-07   28.8   0.0    1.4  2  RecA             recA bacterial DNA recombination protein
    1.2e-06   27.4   0.1    2.7e-06   26.3   0.1    1.7  1  GvpD             GvpD gas vesicle protein
    3.6e-05   23.2   0.0    0.00011   21.7   0.0    2.0  1  DnaB_C           DnaB-like helicase C terminal domain
    6.9e-05   22.6   0.2    0.00021   21.1   0.0    1.9  2  AAA_24           AAA domain
    0.00027   20.8   0.0    0.00042   20.2   0.0    1.4  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    0.00088   19.0   0.0     0.0018   18.0   0.0    1.6  2  IstB_IS21        IstB-like ATP binding protein
     0.0022   18.0   0.0      0.037   14.1   0.0    2.3  1  AAA_14           AAA domain
     0.0037   17.6   0.0     0.0074   16.6   0.0    1.5  1  AAA_22           AAA domain
     0.0082   15.0   0.0      0.011   14.6   0.0    1.1  1  AAA_35           AAA-like domain
  ------ inclusion threshold ------
      0.023   14.7   0.2        4.6    7.3   0.0    2.8  2  Rsbr_N           Rsbr N terminal
      0.033   13.3   0.0      0.078   12.1   0.0    1.6  1  PAXNEB           PAXNEB protein
       0.07   13.0   0.2       0.21   11.5   0.1    2.0  2  NTPase_1         NTPase
      0.095   13.1   0.1       0.26   11.7   0.1    1.9  1  AAA              ATPase family associated with various cellul
      0.097   12.6   0.5       0.31   10.9   0.5    2.1  1  NACHT            NACHT domain
       0.11   12.8   0.3       0.28   11.5   0.3    1.7  1  AAA_19           AAA domain
       0.11   12.9   0.0       0.51   10.8   0.0    2.0  2  RNA_helicase     RNA helicase
       0.12   12.1   0.0       0.21   11.3   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   0.1   3.2e-60   2.8e-57       2     228 ..       5     230 ..       4     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 3.2e-60
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegk 82 
                                   +tgI ++D++++gGip+g  v +tGepGtGKtif+l+F+ +g+++ g+p+v+vt+ee+  ++ ++ak++Gwd+e+  ++ k
  gi|70606365|ref|YP_255235.1|   5 STGIYEFDKLIEGGIPQGFFVALTGEPGTGKTIFSLHFVAQGLKE-GNPCVYVTTEESRDSIVKQAKQFGWDFEEHLDK-K 83 
                                   7*****************************************999.*********************************.9 PP

                        ATPase  83 laiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTailv 161
                                   l+iida +++++++ + ++  +eeli+++  a ++++    r+viDs+++l   +k+a+aR+i   l+rvl+k++ T   +
  gi|70606365|ref|YP_255235.1|  84 LIIIDALMKEKDDEWSLTELTAEELINKVILAKQKLGHgyARLVIDSVSAL-FLDKPALARKISYYLKRVLNKWKFTIYAT 163
                                   *********9998888999999******999999999888***********.***************************** PP

                        ATPase 162 sekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                   s+   + ++a g+gve+ ++dg+i+ ++  +++ l+R++ i kmR+t+h+k +++++I e +gi+ + 
  gi|70606365|ref|YP_255235.1| 164 SQYAITTSQAFGFGVEH-VADGIIRFRRSVKDGMLRRYILIEKMRQTNHDKYIWEIDIREgKGIVLIG 230
                                   *****************.**********************************************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.5e-12   2.2e-09      23     155 ..      12     135 ..       2     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.5e-12
                        AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal..rdda 101
                                   ++l++g +p g +++l+G pgtGKt + l+ ++    G +       e  +++yv +E+s+d + + +++ g ++   +d+
  gi|70606365|ref|YP_255235.1|  12 DKLIEGGIPQGFFVALTGEPGTGKTIFSLHFVAQ---GLK-------EGNPCVYVTTEESRDSIVKQAKQFGWDFeeHLDK 82 
                                   689*************************997655...552.......55689******************99777655688 PP

                        AAA_25 102 rllvldlagveslpLfakdrggtl.ltadvdaleaaieeveg.....vrlvviDplsral 155
                                   +l ++d+       L+++++++   ++   ++l++++  +++     ++ +viD++s+++
  gi|70606365|ref|YP_255235.1|  83 KLIIIDA-------LMKEKDDEWSlTELTAEELINKVILAKQklghgYARLVIDSVSALF 135
                                   8888884.......3333333333122223333333322222222349999999999876 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   7.3e-11   6.6e-08      16     145 ..       1     135 [.       1     155 [. 0.75

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.3e-11
                                   S-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT CS
                         Rad51  16 llqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaeryk 96 
                                   +++l+tG  ++D+l++GGi+ g    + Ge ++Gkt ++     ++q  +e     + +vy+ te +   + +v+ a++++
  gi|70606365|ref|YP_255235.1|   1 MIRLSTGIYEFDKLIEGGIPQGFFVALTGEPGTGKTIFSLH--FVAQGLKE----GNPCVYVTTEES--RDSIVKQAKQFG 73 
                                   589*********************************99865..45553222....3479******97..4679999****9 PP

                                   --HHHHGGG..EEEEE--ST.........THHHHHHH..HTHHHHHHS-EEEEEEETTTGGG CS
                         Rad51  97 ldkeevlen..vayaRayti.........ehqeellq..qaaallaedkfallivDsvtaly 145
                                    d ee l++  + ++   +             eel++   +a++   + +a l++Dsv al+
  gi|70606365|ref|YP_255235.1|  74 WDFEEHLDKklIIIDALMKEkddewslteLTAEELINkvILAKQKLGHGYARLVIDSVSALF 135
                                   99999988732233333333555555553344566663345566666778899999999998 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.8e-10   7.9e-07      34     108 ..       4      79 ..       2      90 .. 0.90
   2 ?   -3.8   0.0       7.6   6.8e+03     135     143 ..     126     134 ..     122     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.8e-10
                                   E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----H..HHHHHTT--GGG- CS
                          RecA  34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldp..kyakklGvdidel 108
                                   +s+G + +d  +  GG+p+G  + + G   +Gkt ++lh +a+  k+g+ ++++ +e + d+  k ak++G d +e 
  gi|70606365|ref|YP_255235.1|   4 LSTGIYEFDKLIE-GGIPQGFFVALTGEPGTGKTIFSLHFVAQGLKEGNPCVYVTTEESRDSivKQAKQFGWDFEEH 79 
                                   6889999998776.**********************************************96336799999998875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.6
                                   EEEE-TTT- CS
                          RecA 135 ivvdsvaal 143
                                   +v+dsv+al
  gi|70606365|ref|YP_255235.1| 126 LVIDSVSAL 134
                                   699***998 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1     3e-09   2.7e-06      14     208 ..      26     223 ..      11     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3e-09
                          GvpD  14 likGaPGtGktlftlrgl.dvlrresdvlyvstr.vddetvseay...fsgeaeldktalldllkdpleldldvdvPiekl 89 
                                    + G+PGtGkt+f l+++ + l++ ++ +yv+t  + d+ v++a     + e +ldk     ++ d+l  + d +  + +l
  gi|70606365|ref|YP_255235.1|  26 ALTGEPGTGKTIFSLHFVaQGLKEGNPCVYVTTEeSRDSIVKQAKqfgWDFEEHLDKKL---IIIDALMKEKDDEWSLTEL 103
                                   578**************83579999******9972556666666665644455577554...4568888899999999999 PP

                          GvpD  90 dlesllefv....deiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaansrleyiv 166
                                     e l++ v    +++ +   +l+i   s  l ++  a   ++   +k v n+   ++  +  +  + +  a    +e+++
  gi|70606365|ref|YP_255235.1| 104 TAEELINKVilakQKLGHGYARLVIDSVS-ALFLDKPALARKISYYLKRVLNKWK-FTIYATSQYAITTSQAFGFGVEHVA 182
                                   99988877634445566666677766666.6788888888888888999999887.55566666667777788889***** PP

                          GvpD 167 dGvvtl..nvkeddrgrlrrdlrleklrGvrignrlqPftladG 208
                                   dG++ +   vk+   g+lrr + +ek+r  + ++ +    + +G
  gi|70606365|ref|YP_255235.1| 183 DGIIRFrrSVKD---GMLRRYILIEKMRQTNHDKYIWEIDIREG 223
                                   *****9645554...7************8777665555555555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.2e-07   0.00011       2      66 ..       4      68 ..       3     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                                  BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                  xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                  lstg +++Dkl++ G+ +g ++ + + p++Gkt + l+++++  + e +p++++  e s++++v++
  gi|70606365|ref|YP_255235.1|  4 LSTGIYEFDKLIEgGIPQGFFVALTGEPGTGKTIFSLHFVAQGLK-EGNPCVYVTTEESRDSIVKQ 68
                                  689*******9972578888999*****************99886.56699999999999999986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-07   0.00021       5      77 ..      25     134 ..      22     144 .. 0.76
   2 ?   -2.2   0.0       3.1   2.8e+03     146     166 ..     214     234 ..     201     254 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                        AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie............swedfldevvel....... 59 
                                   ++++G++g+GKT + +++       g+  +++ te++ +s+     +                          +       
  gi|70606365|ref|YP_255235.1|  25 VALTGEPGTGKTIFSLHFvaqglkeGNPCVYVTTEESRDSIVKQAKQ-FGwdfeehldkkliI----------Idalmkek 94 
                                   689*********************88889999999988777665533.324444544444441..........04445555 PP

                        AAA_24  60 ......................aaeladyktlviDtidel 77 
                                                         ++  ++y  lviD+++ l
  gi|70606365|ref|YP_255235.1|  95 ddewslteltaeelinkvilakQKLGHGYARLVIDSVSAL 134
                                   55577777777777888888899999***********987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
                        AAA_24 146 trlepklgkktanelkeevDl 166
                                     +e++++++ +  l +++Dl
  gi|70606365|ref|YP_255235.1| 214 YIWEIDIREGKGIVLIGKLDL 234
                                   456666666666666555554 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.6e-07   0.00042      19      94 ..      41     115 ..      38     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.6e-07
                          MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdp...ermlealrralaka 94 
                                    f+++gl++g +++yv++++++d + ++ ++ g d ++ l+++ l i+da    +++   ++   e + e+l +++  a
  gi|70606365|ref|YP_255235.1|  41 HFVAQGLKEGNPCVYVTTEESRDSIVKQAKQFGWDFEEHLDKK-LIIIDAL---MKEKDDEWsltELTAEELINKVILA 115
                                   69**************************************999.7787754...4443333322355555555554444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0018      50     121 ..      25      94 ..      19     133 .. 0.84
   2 ?   -2.4   0.0       3.8   3.4e+03      84     115 ..     106     137 ..      95     175 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                     IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllp 121
                                   ++l+G +G+GK+ ++  +  ++ ++g   ++v++e+   ++   ++  ++    ++ l  +l+i+D l  ++
  gi|70606365|ref|YP_255235.1|  25 VALTGEPGTGKTIFSLHFVAQGLKEGNPCVYVTTEESRDSI--VKQAKQFGWDFEEHLDKKLIIIDALMKEK 94 
                                   789********************************987775..45666788889999999999999775544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                     IstB_IS21  84 edLveelkrarrdgklaralkrllkvdllilD 115
                                   e+L++++ +a+++     a   +  v+ l lD
  gi|70606365|ref|YP_255235.1| 106 EELINKVILAKQKLGHGYARLVIDSVSALFLD 137
                                   44455544444444333333333333444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.1e-05     0.037       5      81 ..      25      98 ..      21     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                        AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81
                                  +++tG   +GKT +  +++ + l + + ++y++ ++ rd+  ++ +++   + e+l   +k+++++D   + ++ e 
  gi|70606365|ref|YP_255235.1| 25 VALTGEPGTGKTIFSLHFVAQGLKEGNPCVYVTTEESRDSIVKQAKQFGWDFEEHL---DKKLIIIDALMKEKDDEW 98
                                  78999999***********99999999************88887777778888875...578999997766655554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.2e-06    0.0074       7     104 ..      24     135 ..      21     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.2e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka................ 70 
                                   ++++tGe+GtGKT     ++ q  +e      + ++v+vt  +s  s  + ++++  ++++ l++                
  gi|70606365|ref|YP_255235.1|  24 FVALTGEPGTGKTIFSLHFVAQGLKE------GNPCVYVTTEESRdSIVKQAKQFGWDFEEHLDKkliiidalmkekddew 98 
                                   679**********9888888887655......9999999998888765555666666666666666666888888888777 PP

                        AAA_22  71 ..erlsseellealeqalrarav.ielliiDEaqhlr 104
                                      +l+ eel++++  a ++ +   + l+iD +  l+
  gi|70606365|ref|YP_255235.1|  99 slTELTAEELINKVILAKQKLGHgYARLVIDSVSALF 135
                                   7766666666665554444444455567777666655 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.011      30     146 ..      21     142 ..      12     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                        AAA_35  30 pGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkflrwfcanvsrqLklenkldeyWd.eelgs 109
                                   +G  + + +   +GKt +  + +a+  ++g+  v++  ++  ++i+++ ++f   f  ++ ++L + ++l ++ d e   +
  gi|70606365|ref|YP_255235.1|  21 QGFFVALTGEPGTGKTIFSLHFVAQGLKEGNPCVYVTTEESRDSIVKQAKQFGWDFEEHLDKKLIIIDALMKEKDdEWSLT 101
                                   5778888888899***************************************************99998877776255567 PP

                        AAA_35 110 kvsctayleeylLkei...dkplvLaldevdrlf.eypeia 146
                                   + ++++ +++++L++    +    L++d v+ lf ++p++a
  gi|70606365|ref|YP_255235.1| 102 ELTAEELINKVILAKQklgHGYARLVIDSVSALFlDKPALA 142
                                   889999*******9983333456799999999983345555 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0052       4.6      72     116 ..      39      82 ..      35      99 .. 0.79
   2 ?    4.6   0.0     0.035        31      69     111 ..     174     219 ..     149     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0052
                                   -HHHHHHHHHHHHHHHHHHHHH..T--TT--HHHHHHHHHHHHHH CS
                        Rsbr_N  72 pLkyltkgLqefrkvvlellseeddvvkeeqslelleeieewidp 116
                                   +L+++++gL+e    v+ + +e+ d +  +q++++ +++ee +d+
  gi|70606365|ref|YP_255235.1|  39 SLHFVAQGLKEGNPCVYVTTEESRDSI-VKQAKQFGWDFEEHLDK 82 
                                   8**********9999999988877664.566699*******9997 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.035
                                   TT--HHHHHHHHHHHHHHHHHHHHH.....T--TT--HHHHHHHHH CS
                        Rsbr_N  69 lGwpLkyltkgLqefrkvvlellseed...dvvkeeqslelleeie 111
                                    G  ++ +++g+  fr+ v + +  +    +++++++  ++++ei+
  gi|70606365|ref|YP_255235.1| 174 FGFGVEHVADGIIRFRRSVKDGMLRRYiliEKMRQTNHDKYIWEID 219
                                   5888999****************99865455666777888888886 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.7e-05     0.078      19      84 ..       4      68 ..       2      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                        PAXNEB 19 tStGtpsLDklLgGGLplGsillie.EdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84
                                   StG+ ++Dkl+ GG+p G  + +  E gt   +++    F+A+G+ ++   ++++ ++++++++++
  gi|70606365|ref|YP_255235.1|  4 LSTGIYEFDKLIEGGIPQGFFVALTgEPGTG--KTIFSLHFVAQGLKEGNPCVYVTTEESRDSIVKQ 68
                                  6******************876554166665..5777789***************999999988875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00023      0.21       2      40 ..      25      63 ..      24     152 .. 0.81
   2 ?   -1.2   0.0       1.9   1.7e+03      37      88 ..     180     228 ..     163     253 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                  EEEE--TTSSHHHH.HHHHHHHH...GGGEEEEEEEEE-- CS
                      NTPase_1  2 vfiTGppGvGKtTl.vkkvlellkssgvkvgGfyteevre 40
                                  v++TG+pG+GKt + ++ v++ lk +g +   + tee r+
  gi|70606365|ref|YP_255235.1| 25 VALTGEPGTGKTIFsLHFVAQGLK-EGNPCVYVTTEESRD 63
                                  78**********984677888885.566666688888773 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                   EE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHHHHHHHHH CS
                      NTPase_1  37 evreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesfeelalea 88 
                                    v +g  r   ++ d    ++ iL ++   r+ +++ky  +++  e  ++  
  gi|70606365|ref|YP_255235.1| 180 HVADGIIRFRRSVKDG-MLRRYILIEKM--RQTNHDKYIWEIDIREGKGIVL 228
                                   4444444444444444.33444444444..6677777766666555555544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00029      0.26       2      42 ..      26      69 ..      25     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                  EEESSTTSSHHHH.HHHHHHHHT..HEEEEEETTTCSSSSTTHH CS
                           AAA  2 llyGppGtGKTll.akavakelg..vefleisgsellskyvges 42
                                   l+G pGtGKT++  + va+ l+   +++ +   e ++++v+++
  gi|70606365|ref|YP_255235.1| 26 ALTGEPGTGKTIFsLHFVAQGLKegNPCVYVTTEESRDSIVKQA 69
                                  699********873577888885447777777777775544443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00035      0.31       3      28 ..      25      51 ..      24     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                                  EEEEC-TTTCHHHH.HHHHHHHHCTS- CS
                         NACHT  3 vilqGeaGsGKTtL.lqklalawaegk 28
                                  v+l+Ge+G GKT++ l+ +a+ ++eg+
  gi|70606365|ref|YP_255235.1| 25 VALTGEPGTGKTIFsLHFVAQGLKEGN 51
                                  789**********95555677777776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00031      0.28      13      49 ..      25      57 ..      19     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                        AAA_19 13 llvtaGpGtGKTrvlkhivallvelggvkpeeillva 49
                                  +++t+ pGtGKT    h va  +++g    ++++ v+
  gi|70606365|ref|YP_255235.1| 25 VALTGEPGTGKTIFSLHFVAQGLKEG----NPCVYVT 57
                                  789***********999999998888....6777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00056      0.51       2      65 ..      26      97 ..      25     119 .. 0.70
   2 ?   -0.6   0.0       1.9   1.7e+03      62      94 ..     193     226 ..     141     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00056
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl.......klkkkdsvysrnpeddfwdgYt..gqevvvidDfgqvkdee 65
                                   l+G++g+GK+ ++ +++++ lk+         ++++ds+ ++++++  wd  +  +++ ++id +++ kd+e
  gi|70606365|ref|YP_255235.1| 26 ALTGEPGTGKTIFSLHFVAQGLKEGnpcvyvtTEESRDSI-VKQAKQFGWDFEEhlDKKLIIIDALMKEKDDE 97
                                  689*************999988777788888544444444.56666666653333488888888888888774 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                  RNA_helicase  62 kdee.npsdlaelirlvsstpyplnmasleekgt 94 
                                   kd++    +l e++r  +  +y+ + +  e kg+
  gi|70606365|ref|YP_255235.1| 193 KDGMlRRYILIEKMRQTNHDKYIWEIDIREGKGI 226
                                   4455444477778888888888888877777775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.21      21      67 ..      21      67 ..       2      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                  SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHH CS
               Sigma54_activat 21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelle 67
                                  +   v +tGe GtGK++++ +  ++  ++ +p v v   +  +++++
  gi|70606365|ref|YP_255235.1| 21 QGFFVALTGEPGTGKTIFSLHFVAQGLKEGNPCVYVTTEESRDSIVK 67
                                  5567899***************99**********9999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1749.06
//
Query:       gi|70606366|ref|YP_255236.1|  [L=278]
Description: quinolinate phosphoribosyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-64  216.6   0.4    2.3e-64  216.3   0.4    1.1  1  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
    3.7e-19   68.5   0.0      2e-18   66.3   0.0    2.1  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
  ------ inclusion threshold ------
      0.011   13.6   0.1      0.015   13.2   0.1    1.1  1  CCDC73           Coiled-coil domain-containing protein 73 fam
      0.016   14.5   0.1       0.28   10.5   0.1    2.3  1  TMP-TENI         Thiamine monophosphate synthase
      0.018   14.2   0.6       0.05   12.8   0.6    1.6  1  NanE             Putative N-acetylmannosamine-6-phosphate epi
      0.025   14.5   0.0      0.053   13.4   0.0    1.5  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
        0.2   12.0   0.0       0.35   11.2   0.0    1.3  1  YbfN             YbfN-like lipoprotein


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.3   0.4   8.8e-68   2.3e-64       1     169 []     106     273 ..     106     273 .. 0.99

  Alignments for each domain:
  == domain 1  score: 216.3 bits;  conditional E-value: 8.8e-68
                                   HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTT CS
                     QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdk 79 
                                   iAt t++mv+ a++   kv i++TRkttPglr++ekyA+ iGGgd hr++L+dmvlikdnhi+++g++++a+k+++e +++
  gi|70606366|ref|YP_255236.1| 106 IATETRKMVNIAREInpKVIIAGTRKTTPGLRIFEKYAIEIGGGDPHRYSLYDMVLIKDNHISIIGNVKDAIKQAKEITSF 186
                                   9*************9999*************************************************************** PP

                                   TSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHT CS
                     QRPTase_C  80 evkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalths 160
                                    +kievev++ +++ e+++a+adiimLDnfs++e+k++v+   + +++vl+e+SG +t env+eya++gvd+is+g+lths
  gi|70606366|ref|YP_255236.1| 187 SKKIEVEVSNINDAIEAYKAGADIIMLDNFSPQEVKEVVK---MLKGKVLLEASGRITPENVKEYAETGVDIISSGYLTHS 264
                                   ****************************************...77899********************************* PP

                                   B----EEEE CS
                     QRPTase_C 161 vkalDislk 169
                                   v++lD+s++
  gi|70606366|ref|YP_255236.1| 265 VRSLDLSMD 273
                                   *******97 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   7.6e-22     2e-18       4      89 .]      21     104 ..      18     104 .. 0.96
   2 ?   -1.1   0.0       0.8   2.1e+03      53      70 ..     222     239 ..     217     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 7.6e-22
                                   --HHHHHHGCTTSEEEEEEEESSS.EEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHH CS
                     QRPTase_N   4 gDlttealipeekkakaeiiakee.gvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLn 83 
                                   +D+t+   ++++ k+k+ i++ke+  ++aG +++  ++e+l gl+v+++ kDGe ++kg+ +l ++G+a+a+l +ER++Ln
  gi|70606366|ref|YP_255236.1|  21 EDITS--RVIRGVKVKGIIFSKENkSILAGNKFIIPFLEYL-GLKVDYYRKDGELFSKGENILIFQGDAEAVLGVERLVLN 98 
                                   7****..999999***9999999779***************.*************************************** PP

                                   HHHHHH CS
                     QRPTase_N  84 llqrlS 89 
                                   +l+rlS
  gi|70606366|ref|YP_255236.1|  99 MLSRLS 104
                                   ****98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.8
                                   -TT-EEETTEEEEEEEEE CS
                     QRPTase_N  53 kDGervekgdvlleieGn 70 
                                   k+  ++ kg+vlle++G+
  gi|70606366|ref|YP_255236.1| 222 KEVVKMLKGKVLLEASGR 239
                                   555567789999999997 PP

>> CCDC73  Coiled-coil domain-containing protein 73 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.9e-06     0.015     152     200 ..     161     211 ..     157     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-06
                        CCDC73 152 lvkenhekLeqnvqeaiqlnkrLsalnkkqeseicsLkk..eLkkvtsdLi 200
                                   l+k+nh  +  nv++ai++ k +++  kk e e++++ +  e  k+ +d+i
  gi|70606366|ref|YP_255236.1| 161 LIKDNHISIIGNVKDAIKQAKEITSFSKKIEVEVSNINDaiEAYKAGADII 211
                                   89**********************************987224446666655 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00011      0.28      80     175 ..     171     256 ..     165     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                      TMP-TENI  80 gqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGit 160
                                   g  + ++++a+e++  ++ i + v+++++a ea ++gad i++  + p + K+  ++l  +            + a G it
  gi|70606366|ref|YP_255236.1| 171 GNVKDAIKQAKEITSFSKKIEVEVSNINDAIEAYKAGADIIMLDNFSPQEVKEVVKMLKGKV----------LLEASGRIT 241
                                   55667889999999999999999999999999999999999999998877777664444333..........344566677 PP

                      TMP-TENI 161 lenvaevleagadgv 175
                                   +env+e +e+g+d +
  gi|70606366|ref|YP_255236.1| 242 PENVKEYAETGVDII 256
                                   777777777777765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.6     2e-05      0.05      84     173 ..     176     259 ..     166     269 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                   HHHHHHHH-...-EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHHHHHHHTT--EEEES---SHHHHHH CS
                          NanE  84 likkikeky...qllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalvkalseaglkviaeGrintPekakk 161
                                    ik+ ke     + +  ++s++++++ a+k+G+di+   l  +  +e k+      v ++++ ++ + a Gri tPe+ k+
  gi|70606366|ref|YP_255236.1| 176 AIKQAKEITsfsKKIEVEVSNINDAIEAYKAGADII--MLDNFSPQEVKE------VVKMLKGKVLLEASGRI-TPENVKE 247
                                   444444444333445567888888888888888887..455555555443......34455667777788887.7888888 PP

                                   HHTT--SEEEE- CS
                          NanE 162 aieiGvdavvvG 173
                                     e+Gvd +  G
  gi|70606366|ref|YP_255236.1| 248 YAETGVDIISSG 259
                                   888888877654 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.053      20      64 ..     179     221 ..     163     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                   EEEEEEETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTS CS
               Methyltransf_30  20 glqrlelaaeevtlklligdarealkeldekadawFlDgFsPakn 64 
                                   ++++  +++ + ++++ + ++++a+++ +  ad++ lD FsP+  
  gi|70606366|ref|YP_255236.1| 179 QAKE--ITSFSKKIEVEVSNINDAIEAYKAGADIIMLDNFSPQEV 221
                                   4444..44567899999*************************975 PP

>> YbfN  YbfN-like lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.35      30      70 ..     169     209 ..     162     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                          YbfN  30 acqtvlnvlkkekahqafaeqesvrvldyqqciearktGnd 70 
                                       v + +k+ k+   f+++ +v+v +    iea k+G+d
  gi|70606366|ref|YP_255236.1| 169 IIGNVKDAIKQAKEITSFSKKIEVEVSNINDAIEAYKAGAD 209
                                   55678899*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1916.41
//
Query:       gi|70606367|ref|YP_255237.1|  [L=188]
Description: GMP synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-35  122.3   0.0    2.5e-35  122.0   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    7.8e-10   38.9   0.2    5.1e-09   36.2   0.1    2.2  2  Peptidase_C26  Peptidase C26
      8e-06   25.8   0.1      0.035   13.9   0.0    2.1  2  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
       0.13   11.2   0.0       0.16   10.9   0.0    1.1  1  HTS            Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   0.0   5.6e-39   2.5e-35       2     188 ..       5     183 ..       4     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 5.6e-39
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLG 80 
                                   +i ++ ++++ +v+ l  lg++   +  d+s ee     k++d +++ gGp s+    +++  a  ++ + ++P LGICLG
  gi|70606367|ref|YP_255237.1|   5 VIYFGGQYNHLIVKDLKYLGLEAVAITPDKSVEEL----KEFDSVVFGGGPYSVIneLDKMGFAPDYVKSLNVPKLGICLG 81 
                                   677899**************999888889887777....69*************9989999999999999*********** PP

                                   HHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEET CS
                        GATase  81 mQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekk 161
                                   +Ql+a+ +g++v k+++ e+   t ++ d e  +l+glk++++++ +H++ev +    p+g++++a se+  ++ ++++++
  gi|70606367|ref|YP_255237.1|  82 HQLIAKVLGGEVRKANKPEYGLTTVNIVD-EDTILRGLKPSIKAWESHNDEVVR---PPSGFRILASSENA-KVQAMVNND 157
                                   ****************6666666666666.789********************9...9**********998.8******** PP

                                   TTEEEESSBTTSTTSTTHHHHHHHHHH CS
                        GATase 162 npfvgvQFHPEststpegpellfnfli 188
                                   n ++gvQFHPE+++t++g e+++nf i
  gi|70606367|ref|YP_255237.1| 158 NSIFGVQFHPEVKHTEKGIEVFKNF-I 183
                                   **********************998.4 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.31   1.4e+03     187     201 ..      27      41 ..      12      59 .. 0.57
   2 !   36.2   0.1   1.1e-12   5.1e-09     104     216 .]      71     168 ..      65     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                 Peptidase_C26 187 veAvaeDgviEaies 201
                                    +A+++D  +E ++ 
  gi|70606367|ref|YP_255237.1|  27 AVAITPDKSVEELKE 41 
                                   444445555544333 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 1.1e-12
                 Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkve.kgsllaellgseeievnslHhqaikelae 183
                                    +vP lgiC+G+ql++ +lGG++ ++ +            ++    +v+++ ++++l  l    +i+    H+  + +  +
  gi|70606367|ref|YP_255237.1|  71 LNVPKLGICLGHQLIAKVLGGEVRKANKP-----------EYG-LTTVNIVdEDTILRGLKP--SIKAWESHNDEVVRPPS 137
                                   689******************98766552...........233.456777626666666655..9999999********** PP

                 Peptidase_C26 184 elrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   ++r+ A +e   + a+  +++   ++gvQ+HPE
  gi|70606367|ref|YP_255237.1| 138 GFRILASSENAKVQAMVNNDN--SIFGVQFHPE 168
                                   ***************998885..59*******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   7.9e-06     0.035      25      89 ..      33      93 ..       9     113 .. 0.78
   2 !   10.3   0.0    0.0001      0.45     153     186 ..     151     186 ..     121     188 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-06
                                  E-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBS CS
                           SNO 25 vkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenel 89
                                   k++e+l+e d+++  GG    ++ l +++g+ +d   +vk  + + lG C G  l++k l++e 
  gi|70606367|ref|YP_255237.1| 33 DKSVEELKEFDSVVFGGGPYSVINEL-DKMGFAPD---YVKSLNVPKLGICLGHQLIAKVLGGEV 93
                                  4899***********99998888876.89998876...677777889************999883 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                   EEEEEEETTEEEESS-GGG..STTHCHHHHHHHHHH CS
                           SNO 153 eivvakqkkilatsfhPel..aeddirvhdyfveev 186
                                   + +v + + i+++ fhPe+  +e++i v + f++ +
  gi|70606367|ref|YP_255237.1| 151 QAMVNNDNSIFGVQFHPEVkhTEKGIEVFKNFIKIC 186
                                   344555779*********85578999*******987 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.6e-05      0.16     135     239 ..      73     171 ..      36     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.6e-05
                                   EEEEEETHHHHHHHHHHH----EEEEEEEEEEEEEEES.S--GGGTT--SEEEEEEEEEEE--HHHHTT-TTEEEEEEETT CS
                           HTS 135 tstlfiCwaaqaalyylygvekkklpeKlfGvfehkvlkekspllrgfddeflvphsRytevkeedieekkelevLaesee 215
                                   +  l iC++ q   + l g e +k ++  +G+ + ++  +++++lrg++ ++++  s   ev    ++  +++++La+se+
  gi|70606367|ref|YP_255237.1|  73 VPKLGICLGHQLIAKVLGG-EVRKANKPEYGLTTVNIV-DEDTILRGLKPSIKAWESHNDEV----VRPPSGFRILASSEN 147
                                   5568899998875555544.444556667898888855.55669999999999877766665....56677********** PP

                                   TEEEEEEESSSSEEEE-S-TT--T CS
                           HTS 216 aGvsllaskdkrevfvlgHpEYda 239
                                   a v+ ++++d+  + v+ HpE ++
  gi|70606367|ref|YP_255237.1| 148 AKVQAMVNNDNSIFGVQFHPEVKH 171
                                   *******9999988899***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1279.22
//
Query:       gi|70606368|ref|YP_255238.1|  [L=483]
Description: L-aspartate oxidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-74  251.3   0.0    2.5e-74  250.8   0.0    1.1  1  FAD_binding_2   FAD binding domain
    1.5e-08   34.2   0.4    0.00032   20.0   0.3    2.7  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-06   27.7   0.5    0.00014   21.6   0.5    2.3  1  DAO             FAD dependent oxidoreductase
    6.4e-06   26.2   0.1    0.00086   19.3   0.0    2.2  2  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    0.00011   21.4   0.3       0.12   11.4   0.2    2.2  2  GIDA            Glucose inhibited division protein A
     0.0014   17.5   0.5      0.029   13.1   0.2    2.7  2  HI0933_like     HI0933-like protein
     0.0047   17.1   0.7      0.012   15.8   0.7    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.045   13.4   0.2        0.1   12.2   0.2    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.099   11.9   0.9       0.18   11.1   0.9    1.4  1  FAD_binding_3   FAD binding domain
       0.12   12.4   0.0        0.2   11.6   0.0    1.3  1  DUF481          Protein of unknown function, DUF481


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.8   0.0   1.4e-77   2.5e-74       4     417 .]       4     355 ..       2     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 250.8 bits;  conditional E-value: 1.4e-77
                                   EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHHHHH CS
                 FAD_binding_2   4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqplvea 84 
                                   + GsG+AGL++A++++ aG+kv++++k+   gg+t ++ Ggi+++l       g++ds e+h++dtl ++ +l+d ++ve+
  gi|70606368|ref|YP_255238.1|   4 ILGSGIAGLSSAISLKLAGHKVTIITKKID-GGSTPIAKGGIAVPL-------GVDDSAEKHIQDTLRVGKNLCDYKIVEY 76 
                                   78***************************8.***************.......899************************* PP

                                   HHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEE CS
                 FAD_binding_2  85 fveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqertead 165
                                   +v+++ + v+ L++lg+ f++      d+r  Gg+s + r+lh  +d+      tg+++   l+++a+++++ +      +
  gi|70606368|ref|YP_255238.1|  77 VVREGLKVVEILQKLGFNFDK------DLRLEGGHSSR-RVLH-KGDE------TGREIWNFLYKKALDLHIPIVIDELTL 143
                                   *********************......***********.****.****......*************66666665555544 PP

                                   EEEECTTEEEEEEEEETTTTCEEEEEES.EEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..T CS
                 FAD_binding_2 166 eLivedgrvtGavvenpesgrevrirak.avvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrm 245
                                    L  ++++v+G   +  + gr   i+++ ++vlatgG+g            +a+t+n +++ G+g+al++ aga + d  m
  gi|70606368|ref|YP_255238.1| 144 IL-SKNNKVYGFATR--NRGR---IENIdKLVLATGGYGY----------LFAYTSNKETNLGEGIALGFKAGALVSD--M 206
                                   44.3699****9777..5555...55777**********8..........9***************************..* PP

                                   T-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH......GGGS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT. CS
                 FAD_binding_2 246 eevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm......nelasrdvvsrailekeiaeggseanvyldashg 320
                                   e++qfhPt +    dg++ L++e lrgeGgi+v+ +G+rF       +ela+rd+++rai  + i   ++  ++y+d+s+ 
  gi|70606368|ref|YP_255238.1| 207 EFIQFHPTVTS--LDGEAFLLSETLRGEGGIIVNEKGERFLykyderGELAPRDIIARAIYFEMI---NG-HKIYMDLSK- 280
                                   ********999..899999******************************************4444...44.567******. PP

                                   SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STC CS
                 FAD_binding_2 321 ldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGev 401
                                      e +e+++++    +++  +       d++   ip       ++p++hyt gG++++++g++      ++++LYA+Gev
  gi|70606368|ref|YP_255238.1| 281 --IEDFEKNFPTLSNYLRR-HG------YDHQSSLIP-------IFPGAHYTIGGLRVNLKGET------NVENLYAIGEV 339
                                   ..667*******6555555.66......899999***.......********************......*********** PP

                                   EESSSSTTS--TTHHH CS
                 FAD_binding_2 402 aaggvhganrlgGnsl 417
                                     +g+hganrl++nsl
  gi|70606368|ref|YP_255238.1| 340 SDSGLHGANRLASNSL 355
                                   **************98 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   1.8e-07   0.00032       3     114 ..       2     179 ..       1     195 [. 0.57
   2 !   10.8   0.0   0.00011       0.2     255     278 ..     317     340 ..     310     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                                   EEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHH..HCHHHHHHHHHHHHH..................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx..xxxxxxxxxxxxxxx..................... RF
                   Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve...legtclnggcll..skallgvaedaeias..................... 57 
                                   + ++G+G+AGl+ a+ l+ ag+kvt++    ++g ++  +  +  +  +  +ae++                         
  gi|70606368|ref|YP_255238.1|   2 IYILGSGIAGLSSAISLKLAGHKVTIITkkiDGGSTPIAKGGIavPLGVDDSAEKH---Iqdtlrvgknlcdykiveyvvr 79 
                                   579************************66664444443333331133333333333...1335777777778877777777 PP

                                   ...............................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEE CS
                                   ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ...............................................evvkklnqgielllgeevvkidpgkkkvklekkk 91 
                                                                                  +  k l  +i  + + e + i  ++         
  gi|70606368|ref|YP_255238.1|  80 eglkvveilqklgfnfdkdlrlegghssrrvlhkgdetgreiwnflyK--KALDLHIPIVID-ELTLILSKNN-------- 149
                                   777777666666666666666666666666655544443333333221..122222222222.3333333333........ PP

                                   C.......TCEEEEEESEEEE---EEE-BC CS
                                   x.......xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  92 e.......gdeekiaydklvlAtGssprdl 114
                                   +       + ++    dklvlAtG+   ++
  gi|70606368|ref|YP_255238.1| 150 KvygfatrNRGRIENIDKLVLATGGYGYLF 179
                                   244444446666667788888888765555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                                   TTEEE--TTSBESSTTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDva 278
                                    gg+ v+ +++tnv+++yaiG v 
  gi|70606368|ref|YP_255238.1| 317 IGGLRVNLKGETNVENLYAIGEVS 340
                                   6999******************99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.5   7.6e-08   0.00014       2     203 ..       2     175 ..       1     344 [. 0.72

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.6e-08
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS..STHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl..rylpeaselarlslealeelreleeelgid 78 
                                   + i G+Gi+Gls A  L  +g  Vt++ k+ i g g++  + g ++  l  ++ +e     +  +++l+  + l++ + i 
  gi|70606368|ref|YP_255238.1|   2 IYILGSGIAGLSSAISLKLAGhkVTIITKK-IDG-GSTPIAKGGIAVPLgvDDSAE-----KHIQDTLRVGKNLCD-YKI- 73 
                                   669**************988899*******.999.777777777776663322222.....455555554455543.233. PP

                                   TSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHT CS
                           DAO  79 idyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalpgllgalfypdtgqvdpakltaalaraaeal 159
                                   ++y  +  l +             ++ l+++g     +d++  ++le    g+    + +  g    ++  ++l+++a +l
  gi|70606368|ref|YP_255238.1|  74 VEYVVREGLKV-------------VEILQKLGFN---FDKD--LRLEG---GHSSRRVLHK-GDETGREIWNFLYKKALDL 132
                                   23322222222.............2222223332...3332..23332...1111111111.2222445556666666666 PP

                                   T-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                           DAO 160 Gveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                   ++ i+   e t +  +++kv+g   t + g+++ +d++V+a+G +
  gi|70606368|ref|YP_255238.1| 133 HIPIVID-ELTLILSKNNKVYGF-ATRNrGRIENIDKLVLATGGY 175
                                   6666655.555554444555555.333445444456666666655 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.015        28       3      28 ..     401     426 ..     399     436 .. 0.88
   2 !   19.3   0.0   4.8e-07   0.00086      63      97 ..     436     469 ..     428     481 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                                   HHHHHHHHHSSSSB-HHHHHHHHHHH CS
                Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkel 28 
                                   +++ki ++  g++R+ee +++a++  
  gi|70606368|ref|YP_255238.1| 401 DIQKINWESLGIVRNEEAIRKAIEVY 426
                                   789*******************9865 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.8e-07
                                   HHHHHHHHHHH--S-BTTBEBTTS-SEETTT-SEE CS
                Succ_DH_flav_C  63 lAeaiaksAlaRkESrGaHaredfperdDenwlkh 97 
                                   ++ +i  ++l R ESrG H+r d+pe + e+w   
  gi|70606368|ref|YP_255238.1| 436 ISHMIGLASLIRSESRGVHFRSDYPEEK-EEWNGK 469
                                   56677788999**************655.567554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   6.8e-05      0.12       2      33 ..       2      33 ..       1      40 [. 0.94
   2 !    7.8   0.0   0.00085       1.5     110     164 ..     133     188 ..     116     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.8e-05
                                  EEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkld 33
                                  + ++G G AG+  A+ ++ +G+kv++it+k+d
  gi|70606368|ref|YP_255238.1|  2 IYILGSGIAGLSSAISLKLAGHKVTIITKKID 33
                                  6799************************9998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00085
                                   TEEEEES-EEEEEECTTEEEEEEETTS-EEEEC.EEEE--TT-BT-EEEETTEEEE CS
                          GIDA 110 nleiieeeveeliveekkvkgvvtedgetikak.avviatGtflkgkihigekels 164
                                   ++ i+ +e + ++ +++kv g  t++   i++  + v+atG +     ++ +ke++
  gi|70606368|ref|YP_255238.1| 133 HIPIVIDELTLILSKNNKVYGFATRNRGRIENIdKLVLATGGYGYLFAYTSNKETN 188
                                   6889999**************7776666655544*******976655555555554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   1.6e-05     0.029       3     165 ..       2     175 ..       1     178 [. 0.73
   2 ?   -1.3   0.0      0.36   6.5e+02     373     386 ..     328     341 ..     312     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                   EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGGT-EEEETT-SGGGEEES...STTTTHHHHHHS-HHH.. CS
                   HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgGrcNvTnlseepeellsrypenpkflksalsrftned.. 81 
                                   + ++G G AGl  Ais++ +g++V+++ k+   g+     Gg  + +   + + +++ + ++ +++ +   + ++  ++  
  gi|70606368|ref|YP_255238.1|   2 IYILGSGIAGLSSAISLKLAGHKVTIITKKIDGGSTPIAKGGIAVPLGVDDSAEKHIQDTLRVGKNLCDYKIVEYVVREgl 82 
                                   569**************************9999998888888888888877777778888888888888899999766522 PP

                                   .HHHHHHHTT--EEE......-.STTE.EEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEE CS
                   HI0933_like  82 .lialveelgvelke......e.dsgr.lFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvkt.kseee 152
                                    +++++++lg ++ +      + +s r l   +++ ++i ++l k++ + ++ +  ++    + +++++++ ++t + ++ 
  gi|70606368|ref|YP_255238.1|  83 kVVEILQKLGFNFDKdlrlegGhSSRRvLHKGDETGREIWNFLYKKALDLHIPIVIDELTLIL-SKNNKVYGFATrNRGRI 162
                                   266777777776654222222213445244456678899999999999999999888766666.45666699999444444 PP

                                   EEESEEEE----S CS
                   HI0933_like 153 leadklvlAtGGl 165
                                    + dklvlAtGG 
  gi|70606368|ref|YP_255238.1| 163 ENIDKLVLATGGY 175
                                   5679999999996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.36
                                   TTSTTEEE-GGGBS CS
                   HI0933_like 373 kkvpgLffaGEvlD 386
                                    +v++L+ +GEv D
  gi|70606368|ref|YP_255238.1| 328 TNVENLYAIGEVSD 341
                                   4699*******977 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.7   6.9e-06     0.012       1      27 [.       4      30 ..       4      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-06
                                  EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                  I+G+G++Gl+ A  L+ ag++v+++ k
  gi|70606368|ref|YP_255238.1|  4 ILGSGIAGLSSAISLKLAGHKVTIITK 30
                                  89**********************966 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   5.7e-05       0.1       1      30 [.       2      31 ..       2      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrs 30
                                  i+ilG+G  G   a +L+ ag++vt+i+++
  gi|70606368|ref|YP_255238.1|  2 IYILGSGIAGLSSAISLKLAGHKVTIITKK 31
                                  89***************99*******9975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   9.8e-05      0.18       5      35 ..       3      33 ..       1      45 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                                  EEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  5 lIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   I G+G aGl++a  L+ aG +v++++k  +
  gi|70606368|ref|YP_255238.1|  3 YILGSGIAGLSSAISLKLAGHKVTIITKKID 33
                                  699***********************99755 PP

>> DUF481  Protein of unknown function, DUF481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011       0.2      62     111 ..     145     194 ..     140     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                        DUF481  62 lserlylfalgsyetDrfsgldsratlgaGlGyrlidtdktklsleaGpg 111
                                   ls+++ +++++  ++ r++++d+  ++ +G+Gy +  t + + +l+ G++
  gi|70606368|ref|YP_255238.1| 145 LSKNNKVYGFATRNRGRIENIDKLVLATGGYGYLFAYTSNKETNLGEGIA 194
                                   689999*******************************8888665554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2852.41
//
Query:       gi|70606369|ref|YP_255239.1|  [L=155]
Description: NUDIX domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-14   53.2   0.0    3.8e-14   52.9   0.0    1.1  1  NUDIX     NUDIX domain
     0.0048   16.9   0.0      0.007   16.3   0.0    1.5  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   4.2e-18   3.8e-14       5     123 ..       6     121 ..       3     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 4.2e-18
                                   EEEEEEEETTSEEEEEEES...SSSTTTE....ESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEE CS
                         NUDIX   5 avgvvllnekgevLlvrrs...kkpfpgW....elPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgp 77 
                                   a+ v l+ + g++L+++r+   ++p   W    +lPgG+ e+ E+ e +A+RE+ EE+ +++ +l+++        p    
  gi|70606369|ref|YP_255239.1|   6 AAVVALISKVGKILIIKRKekpGDP---WsghmALPGGRREDHEECESTAIRECYEEVRIKPrNLIRVGI----YSP---- 75 
                                   566669999999*******544444...544347****************************44444443....122.... PP

                                   EEE..EEEEEEEEEEEECSGCSST.STTTEEEEEEEEHHHHHHHHTHCT CS
                         NUDIX  78 ygd..eheilyvfleevegelepn.denevsevrwvpleellkeklaae 123
                                     +  +++ +  +   ve+elep  +e+e++++ w+++ +l k+ ++a+
  gi|70606369|ref|YP_255239.1|  76 --NnaPDMKVSAYISCVEEELEPIvQEEELEKAIWIRISDL-KPGDKAF 121
                                   ..2333444445556666666666689**************.4444444 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.8e-07     0.007       2      48 ..       8      58 ..       7     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.8e-07
                                  EEEEEEC.TEEEEEE--TT..SSSTT-EE-SEEE.-TTS-.HHHHHHHHHHS CS
                       NUDIX_4  2 vllirdd.grvllekRpek..gllggLwefPgge.eegee.leealareelg 48
                                  v++++ + g++l+ kR+ek  + + g + +Pgg+ e+ ee +++a+ re ++
  gi|70606369|ref|YP_255239.1|  8 VVALISKvGKILIIKRKEKpgDPWSGHMALPGGRrEDHEEcESTAI-RECYE 58
                                  67777777*********98646*********999777777444443.33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1044.78
//
Query:       gi|70606370|ref|YP_255240.1|  [L=452]
Description: TBP-interacting proten [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-138  462.0   3.8   1.9e-138  461.5   3.8    1.2  1  TIP49            TIP49 P-loop domain
    4.1e-23   81.3   2.2      2e-22   79.1   0.6    2.7  2  TIP49_C          TIP49 AAA-lid domain
    4.8e-11   43.2   3.1    1.8e-08   34.9   0.1    2.8  2  AAA              ATPase family associated with various cellul
    1.7e-08   34.4   0.6      5e-07   29.6   0.1    2.8  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.1e-08   33.3   0.4     0.0088   16.3   0.1    2.3  2  AAA_22           AAA domain
      3e-06   27.7   0.5    3.6e-05   24.2   0.5    2.2  1  AAA_16           AAA ATPase domain
    1.3e-05   24.8   0.4    0.00054   19.5   0.1    2.2  2  AAA_7            P-loop containing dynein motor region
    8.6e-05   22.6   0.2     0.0033   17.4   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00016   21.1   0.4     0.0012   18.3   0.1    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00068   19.1   0.2     0.0018   17.7   0.0    1.8  2  DnaB_C           DnaB-like helicase C terminal domain
    0.00073   19.3   0.0     0.0016   18.2   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
    0.00079   19.6   0.0     0.0017   18.6   0.0    1.6  1  AAA_33           AAA domain
    0.00092   19.0   0.0       0.23   11.2   0.0    3.1  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0012   19.0   0.2     0.0042   17.2   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0016   18.1   0.2      0.013   15.0   0.0    2.3  2  AAA_25           AAA domain
     0.0024   17.6   0.1      0.021   14.5   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0028   18.2   0.3     0.0091   16.5   0.0    2.2  1  AAA_18           AAA domain
     0.0055   17.1   0.4      0.028   14.8   0.0    2.4  2  AAA_17           AAA domain
     0.0074   16.7   0.0      0.015   15.7   0.0    1.5  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.027   14.4   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.014   14.9   0.2       0.03   13.8   0.2    1.5  1  PhoH             PhoH-like protein
      0.015   15.3   0.5       0.52   10.3   0.1    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.017   15.6   0.0      0.044   14.3   0.0    1.7  1  ABC_tran         ABC transporter
      0.022   15.1   3.8        1.1    9.6   3.8    2.5  1  AAA_19           AAA domain
      0.022   15.0   0.4       0.07   13.4   0.1    2.0  2  AAA_28           AAA domain
       0.04   13.8   0.0      0.083   12.8   0.0    1.6  1  NACHT            NACHT domain
       0.04   13.2   0.0      0.068   12.4   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.047   12.8   0.0      0.077   12.1   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.059   13.1   0.1       0.12   12.1   0.1    1.6  1  AAA_11           AAA domain
        0.1   12.6   0.1       0.26   11.3   0.1    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.16   11.6   0.7       0.88    9.3   0.1    2.3  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.5   3.8  3.2e-141  1.9e-138       2     350 ..      15     364 ..      14     365 .. 0.96

  Alignments for each domain:
  == domain 1  score: 461.5 bits;  conditional E-value: 3.2e-141
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49   2 islhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfva 82 
                                    s+hshi+gLGlde+g+a+  ++glvGq++area+g++v+li+++k+aG+++L++Gp+gtGktala+ai+kelged+pf++
  gi|70606370|ref|YP_255240.1|  15 ASIHSHITGLGLDEKGKAKFIADGLVGQVEAREASGIVVQLIRQGKMAGKGILFVGPPGTGKTALAVAIAKELGEDTPFTT 95 
                                   689****************************************************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-EEEEEE-HHH CS
                         TIP49  83 lsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakeekklklgski 162
                                   +++sevys+e+kkte+ltq +rks+gvrik +++v+eG v +++++ a++ ++ +  + +e++i+l t++ e++l++g  i
  gi|70606370|ref|YP_255240.1|  96 INASEVYSTELKKTEILTQVIRKSMGVRIKQKRTVYEGVVKDVKLKVARSRYNpYYVSPREAQIVLSTKDDERTLNVGDAI 176
                                   *********************************************999999**9999************************ PP

                                   HHHHHHHT--TT-EEEEETTT--EEE-SSS-..SS------S--------S---S----XXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49 163 aeellkekvkegDviviekesGkvkklGrse..arakefDiekdefvelPkGevekkkevvqevtLhdlDv.anarpqdll 240
                                   ae+++k +vk+gDvi i++e+G+v+k+Gr++  + ak++Die  + v++P G ++k+k+++ +vtLhdlD+  +a++ ++ 
  gi|70606370|ref|YP_255240.1| 177 AEQFMKLNVKKGDVIWIDAETGEVTKVGRAKgfEGAKSYDIEVVRQVDIPTGSIKKEKDITITVTLHDLDLnLAAQSISIT 257
                                   ****************************987225789*********************************94566667777 PP

                                   XXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 241 slllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnraleselaPivilatnrgiaki 321
                                   +l+       ++ei++++r+++++ v++ v+ g ae+vpGvlfiD++hmlDie+fs+l ++leselaPi+ilatnrgi+ki
  gi|70606370|ref|YP_255240.1| 258 ALF---SFFTEREINQDIRKQVDRLVKDMVNRGDAELVPGVLFIDDAHMLDIEAFSFLTKTLESELAPILILATNRGITKI 335
                                   777...4456789******************************************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 322 rGtdiisphGipvDlldrlliiktekytk 350
                                   rGtdi+sphGip+Dlldrllii+t++y++
  gi|70606370|ref|YP_255240.1| 336 RGTDIESPHGIPLDLLDRLLIIQTRPYNE 364
                                   ***************************97 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.4   8.1e+02      37      59 ..     320     342 ..     319     349 .. 0.87
   2 !   79.1   0.6   3.5e-25     2e-22       1      66 []     370     435 ..     370     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.4
                       TIP49_C  37 ltpasilakkrkkkevevedvee 59 
                                   l+p  ila+ r+ +++   d+e+
  gi|70606370|ref|YP_255240.1| 320 LAPILILATNRGITKIRGTDIES 342
                                   678899**************997 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 3.5e-25
                       TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                   I+kiRa+e +vklde+A+ lL+k+g+e SLRYa+qL++pa+i+a+++++++++ ed+eev++LF D
  gi|70606370|ref|YP_255240.1| 370 IVKIRANEIDVKLDEDAIVLLTKLGVENSLRYAVQLIEPAYIVAQRKGRESIKSEDIEEVSKLFSD 435
                                   89**************************************************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   3.1e-11   1.8e-08       1      43 [.      66     110 ..      66     141 .. 0.81
   2 !    8.1   0.2     0.006       3.5      36     112 ..     270     332 ..     238     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.1e-11
                                   EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHH CS
                           AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgese 43 
                                   +l++GppGtGKT+la a+akelg  ++f +i++se+ s  ++++e
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELGedTPFTTINASEVYSTELKKTE 110
                                   69********************77799*********966444333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.006
                                   SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.G CS
                           AAA  36 skyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.p 112
                                   +++ ++  + +++++++  ++  p +lfiD+++ l  +             + L + l+ +       i+i+atnr +
  gi|70606370|ref|YP_255240.1| 270 QDIRKQVDRLVKDMVNRGDAELVPGVLFIDDAHMLDIEA-----------FSFLTKTLESELA----PILILATNRgI 332
                                   446677788888888887766689*********995555...........8888888877776....38888888755 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   8.6e-10     5e-07       8      65 ..      38      95 ..      33     122 .. 0.87
   2 ?   -2.3   0.0       5.7   3.3e+03      45      63 ..     107     126 ..     102     129 .. 0.77
   3 ?    1.6   0.0      0.34     2e+02      87     115 ..     295     323 ..     281     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8.6e-10
                        RuvB_N  8 eyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkits 65
                                    +gq + +e   i+++  ++ + a   +l++GpPG Gkt+la  iakelg +   t+
  gi|70606370|ref|YP_255240.1| 38 GLVGQVEAREASGIVVQLIRQGKMAGKGILFVGPPGTGKTALAVAIAKELGEDTPFTT 95
                                  579***********************************************99877665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                        RuvB_N  45 Gktt.lakiiakelgvklki 63 
                                    kt  l+++i k +gv++k+
  gi|70606370|ref|YP_255240.1| 107 KKTEiLTQVIRKSMGVRIKQ 126
                                   56642789999999999986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.34
                        RuvB_N  87 vlfideihrlsraveevlysamedfrldi 115
                                   vlfid+ h l+ ++  +l +++e     i
  gi|70606370|ref|YP_255240.1| 295 VLFIDDAHMLDIEAFSFLTKTLESELAPI 323
                                   9*********9999888888888765555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.9e-05     0.023       8      62 ..      66     117 ..      60     149 .. 0.66
   2 !   16.3   0.1   1.5e-05    0.0088      38     134 ..     233     333 ..     205     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst....sskdllrellr 62 
                                   ++ +G++GtGKT l+  ++++l e+        ++ ++++++      + +++l+++ r
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELGED-------TPFTTINASEVYstelKKTEILTQVIR 117
                                   7889******************754.......333322222222222334444444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                        AAA_22  38 erpevvfvtlpsst...sskdl.lrellralglelka..erlsseellealeqalraravielliiDEaqhlrseealeeL 112
                                   e++ +++vtl  +      +++  ++l+++++++  +   r++ ++l++ + +  +a  v+++l iD+a+ l   ea+++L
  gi|70606370|ref|YP_255240.1| 233 EKDITITVTLHDLDlnlAAQSIsITALFSFFTEREINqdIRKQVDRLVKDMVNRGDAELVPGVLFIDDAHML-DIEAFSFL 312
                                   6777888888888887877777788888888887777555555555554444444444449***********.9******* PP

                        AAA_22 113 rsllnlsrkgvqliLvGtp.elr 134
                                    + l+  + + ++++  t+ ++ 
  gi|70606370|ref|YP_255240.1| 313 TKTLE--SELAPILILATNrGIT 333
                                   99999..8888888877776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.5   6.3e-08   3.6e-05      25     157 ..      64     314 ..      51     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.3e-08
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                     +l++G++G+GK++l+ +++++l +d   f++ ++ +         + + l++ e+l+q+ +++      + r+  e+++
  gi|70606370|ref|YP_255240.1|  64 KGILFVGPPGTGKTALAVAIAKELGED-TPFTTINASEV--------YSTELKKTEILTQVIRKSMGVRIKQKRTVYEGVV 135
                                   799************************.44444444444........4455556677777777755555555555555555 PP

                        AAA_16 106 a................................................................................ 106
                                   +                                                                                
  gi|70606370|ref|YP_255240.1| 136 Kdvklkvarsrynpyyvspreaqivlstkddertlnvgdaiaeqfmklnvkkgdviwidaetgevtkvgrakgfegaksyd 216
                                   566677777888888888888888888888888888889999999999999999999999999999999999999999999 PP

                        AAA_16 107 ...............................................avpelagaeasrllellkrllallsrderplvlv 140
                                                                                    +e+  ++++++ +l+k+++++   +  p vl+
  gi|70606370|ref|YP_255240.1| 217 ievvrqvdiptgsikkekdititvtlhdldlnlaaqsisitalfsffTEREINQDIRKQVDRLVKDMVNRGDAELVPGVLF 297
                                   999999999999999999999999888888888777777777777777777777777777777777776666666689999 PP

                        AAA_16 141 lDdlqwadeaslqllaa 157
                                   +Dd++ +d +  ++l  
  gi|70606370|ref|YP_255240.1| 298 IDDAHMLDIEAFSFLTK 314
                                   99999888755555444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   9.3e-07   0.00054      31      89 ..      61     118 ..      37     131 .. 0.78
   2 ?    3.3   0.0      0.09        52      50     117 ..     242     309 ..     235     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.3e-07
                         AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                    ++k +l+vGp GtGKt+++  + k+l  e++ ++tin s   s +  ++ i  ++ ++
  gi|70606370|ref|YP_255240.1|  61 MAGKGILFVGPPGTGKTALAVAIAKELG-EDTPFTTINASEVYSTELKKTEILTQVIRK 118
                                   56789***********************.889999999988766655544444444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                         AAA_7  50 ikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvy..gPpggkklvvFvDDlnmpakeky 117
                                   ++dl  +l   + +s+t  fs  t+ +   + i +++++  k++   g +     v+F+DD +m   e +
  gi|70606370|ref|YP_255240.1| 242 LHDLDLNLA-AQSISITALFSFFTEREI-NQDIRKQVDRLVKDMVnrGDAELVPGVLFIDDAHMLDIEAF 309
                                   555555555.555566666666665544.444677788877766511333444569********999876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.6e-06    0.0033       2      40 ..      66     105 ..      65     132 .. 0.78
   2 ?    2.5   0.0      0.23   1.3e+02      31      90 ..     258     317 ..     244     325 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-06
                                   EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteed 40 
                                   +l vGppGtgK+ la  +a+ l   +++++++ ++   +++
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELgeDTPFTTINASE-VYSTE 105
                                   799*******************9656666655554.44444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                                   E--TT--HHHHH--B--.........--------......G-SEEEEESGGG--HHHHHHHHHHHH CS
                         AAA_5  31 qltrdtteedlkgrreikngttslvdsplvraar......egeilvlDEveraesevlnsLlslle 90 
                                   +l ++ te+++ + ++      + vd  +++ ++       + +l++D+ ++++ e+++ L + le
  gi|70606370|ref|YP_255240.1| 258 ALFSFFTEREINQDIR------KQVDRLVKDMVNrgdaelVPGVLFIDDAHMLDIEAFSFLTKTLE 317
                                   5555666666666666......333333333333333467899*********99999999988887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     2e-06    0.0012      22      67 ..      63     108 ..      38     120 .. 0.80
   2 ?    0.5   0.0      0.57   3.3e+02     107     133 ..     293     319 ..     283     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                  Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkk 67 
                                   g  +l+vGppG+GKt la ++++ l + +   ++++++++s   kk
  gi|70606370|ref|YP_255240.1|  63 GKGILFVGPPGTGKTALAVAIAKELGEDTPFTTINASEVYSTELKK 108
                                   4579**********************************99987643 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.57
                  Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePledg 133
                                    GvLf+D++  ++ +++  L + le++
  gi|70606370|ref|YP_255240.1| 293 PGVLFIDDAHMLDIEAFSFLTKTLESE 319
                                   59*************999999999986 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.1e-06    0.0018      16      81 ..      60     129 ..      53     194 .. 0.75
   2 ?   -2.1   0.0       3.3   1.9e+03     109     109 ..     328     328 ..     268     382 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.1e-06
                                   BXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE....EEEEESSSXHHHHHHHHHHHHHTXXHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  16 lqkgdliiiAarpsmGktalalniaenaavkeklp....vavfslemsaeqlvqRllsseaeidskklrt 81 
                                      g+ i+  + p++Gktala+ ia++  +++  +      v+s e ++++++++++ +  +++ k+ rt
  gi|70606370|ref|YP_255240.1|  60 KMAGKGILFVGPPGTGKTALAVAIAKELGEDTPFTtinaSEVYSTELKKTEILTQVIRKSMGVRIKQKRT 129
                                   556667888899**************998744422223489*****************999888766654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                                   X CS
                                   x RF
                        DnaB_C 109 t 109
                                   t
  gi|70606370|ref|YP_255240.1| 328 T 328
                                   1 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.8e-06    0.0016      47      71 ..      63      87 ..      43     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.8e-06
                     IstB_IS21 47 kenivllGpsGvGKshlaialgvea 71
                                   ++i+++Gp+G+GK+ la+a+++e 
  gi|70606370|ref|YP_255240.1| 63 GKGILFVGPPGTGKTALAVAIAKEL 87
                                  5689*****************9875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.9e-06    0.0017       2      38 ..      66     107 ..      66     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdtlrr.rlf 38 
                                   +l+vG+pG+GK+ la  ++k+lg    +++++  ++++  l+
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELGedtpFTTINASEVYStELK 107
                                   69*********************9999888887774442444 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0004      0.23      10     141 ..      53     329 ..      45     334 .. 0.74
   2 ?    3.3   0.0      0.11        63      65     101 ..     404     439 ..     393     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
               DNA_pol3_delta2  10 skalksgrla.hayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivi.....eteeker... 81 
                                    + +++g++a + +Lf G+ g+gk +la ++ak+l  + + +t +  e  s +  +++    vi             +   
  gi|70606370|ref|YP_255240.1|  53 VQLIRQGKMAgKGILFVGPPGTGKTALAVAIAKELGEDTPFTTINASEVYSTELKKTEILTQVIRKsmgvrI-----Kqkr 128
                                   5667777776479*********************99888887765555555555555555555544222212.....1334 PP

               DNA_pol3_delta2  82 ................................................................................. 81 
                                                                                                                    
  gi|70606370|ref|YP_255240.1| 129 tvyegvvkdvklkvarsrynpyyvspreaqivlstkddertlnvgdaiaeqfmklnvkkgdviwidaetgevtkvgrakgf 209
                                   567888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

               DNA_pol3_delta2  82 .............................................................sikldqirelieelsrkpre 101
                                                                                                 i+++  r +++ ++r   e
  gi|70606370|ref|YP_255240.1| 210 egaksydievvrqvdiptgsikkekdititvtlhdldlnlaaqsisitalfsfftereinqDIRKQVDRLVKDMVNRGDAE 290
                                   888888888888888888888888888888888888888888888888888888888555444444334444444455555 PP

               DNA_pol3_delta2 102 skkkiiiiedaekmtksAaNalLktlEEPsenaifiLits 141
                                       ++ i+da +++ +A   l ktlE      i+iL t+
  gi|70606370|ref|YP_255240.1| 291 LVPGVLFIDDAHMLDIEAFSFLTKTLESE-LAPILILATN 329
                                   66678888888888888888888888854.5556666665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
               DNA_pol3_delta2  65 qgkhpDvivieteekersikldqirelieelsrkpre 101
                                   q   p +iv++ +++ +sik ++i+e+ + +s + r 
  gi|70606370|ref|YP_255240.1| 404 QLIEPAYIVAQRKGR-ESIKSEDIEEVSKLFSDSKRS 439
                                   566788899999998.9**************998765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.3e-06    0.0042       6      68 ..      66     126 ..      63     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.3e-06
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHT CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaee 68 
                                   il++gp g+Gkt la a+a+ l   ++ ++++++ase+   e  ++ +   ++ + + v+ ++
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELG--EDTPFTTINASEVYSTELKKTEILTQVIRKSMGVRIKQ 126
                                   89********************6..799**********9988777777777777777666666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.3e-05     0.013      32      65 ..      62      95 ..      51     145 .. 0.85
   2 ?    0.5   0.0      0.67   3.9e+02      62      85 ..     179     201 ..     168     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                        AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlg 65
                                  ag+ +l++G+pgtGKt+la+ +a ++ ++ p++ 
  gi|70606370|ref|YP_255240.1| 62 AGKGILFVGPPGTGKTALAVAIAKELGEDTPFTT 95
                                  688899*****************99999999877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.67
                        AAA_25  62 pwlgpvapeqgkVlyvsaEdsede 85 
                                   ++ + + +++g V++++aE +e +
  gi|70606370|ref|YP_255240.1| 179 QFMK-LNVKKGDVIWIDAETGEVT 201
                                   4555.6679999999999988744 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.7e-05     0.021      11      69 ..      52     110 ..      43     115 .. 0.78
   2 ?    0.1   0.0         1   5.8e+02      95     119 ..     294     318 ..     287     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS.-TTCHHHH CS
               Sigma54_activat  11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai.peellese 69 
                                   +++ i++       +l +G  GtGK+ la ai ++   +++pf ++n +++ ++el ++e
  gi|70606370|ref|YP_255240.1|  52 VVQLIRQGKMAGKGILFVGPPGTGKTALAVAIAKELG-EDTPFTTINASEVySTELKKTE 110
                                   556666666677889*****************98776.899******9976366665555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                                   SEEEEETGGGS-HHHHHHHHHHHHH CS
               Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                   G+lf+D+ + l++e+ + L + l++
  gi|70606370|ref|YP_255240.1| 294 GVLFIDDAHMLDIEAFSFLTKTLES 318
                                   99***********999988888876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-05    0.0091       1      24 [.      66      89 ..      66     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf 24
                                  Il  G+pG+GKt la +++k+lg 
  gi|70606370|ref|YP_255240.1| 66 ILFVGPPGTGKTALAVAIAKELGE 89
                                  8999****************9843 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       8.2   4.8e+03      65      90 ..      25      49 ..       3      61 .. 0.59
   2 !   14.8   0.0   4.9e-05     0.028       1      46 [.      69     120 ..      69     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.2
                                  HHHHHHSSEEEEEE-SEEEETTEEEE CS
                        AAA_17 65 iaeeakkkgvlvdghprikeqagfld 90
                                    +e++k +++ dg     e a++ +
  gi|70606370|ref|YP_255240.1| 25 GLDEKGKAKFIADGLVGQVE-AREAS 49
                                  45667888999999876433.33344 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.9e-05
                                   EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS..HSSHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrggl..akardem 46 
                                   +G+PG GK+ ++  +++++     ft ++a+++   e k+ +   +  r+ m
  gi|70606370|ref|YP_255240.1|  69 VGPPGTGKTALAVAIAKELgedtPFTTINASEVYSTELKKTEIltQVIRKSM 120
                                   7***************99865557*************999985322233333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05     0.015       1      43 [.      66     111 ..      66     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys.rnpeddf 43 
                                   i+++Gp+g+GK+ la  +ak+l ++    ++++++vys   +++++
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELGEDTpfTTINASEVYStELKKTEI 111
                                   6899*******************77656888889999955555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.6e-05     0.027      48     101 ..      66     120 ..      53     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-05
                         Rad17  48 LLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesr 101
                                   +L  GP+G gk+     ++kelg +     +n+ ++ +++ +k++++++++ +s 
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKELGEDTpFTTINASEVYSTELKKTEILTQVIRKSM 120
                                   5789**********9********9873589******************9999884 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   5.1e-05      0.03      22      47 ..      66      91 ..      49      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                                  EEEE--TTSSTTHHHHHHHHHHHHTT CS
                          PhoH 22 vfaiGpaGtGKtylavalavealkkk 47
                                  +  +Gp GtGKt lava+a e+ ++ 
  gi|70606370|ref|YP_255240.1| 66 ILFVGPPGTGKTALAVAIAKELGEDT 91
                                  4568**************98876665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0009      0.52      24      50 ..      63      89 ..       3     127 .. 0.87
   2 ?    2.9   0.0      0.16        94     106     146 ..     260     306 ..     212     327 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0009
                                  TSEEEEEESTTSTHHHHHHHHHHHH-S CS
                        ResIII 24 dkrglikmaTGtGKTlvaaklierllk 50
                                   k +l++ + GtGKT +a++++++l +
  gi|70606370|ref|YP_255240.1| 63 GKGILFVGPPGTGKTALAVAIAKELGE 89
                                  45788*****************99866 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                                   EEEEEHHHHHHTH...........HHHTTT-S...EEEEETGGGTTS CS
                        ResIII 106 ilvttiqsldadseee...eeeseellrdrfd...viiiDEaHrlga 146
                                   + ++t+ ++++d++++     ++  ++ d+++   v++iD aH l  
  gi|70606370|ref|YP_255240.1| 260 FSFFTEREINQDIRKQvdrLVKDMVNRGDAELvpgVLFIDDAHMLDI 306
                                   45777777888886666553334444444444889********8765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.6e-05     0.044      10      90 ..      62     145 ..      57     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.6e-05
                                   TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH.HHHTCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.xxxxxxxx RF
                      ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren.esdeeiek 87 
                                   +g+ + +vG+ G+GK+ L+ ++a++l  +    +++  ++ ++el++++   +v+ +    +++++ tv+e   +d++++ 
  gi|70606370|ref|YP_255240.1|  62 AGKGILFVGPPGTGKTALAVAIAKELGEDTPFTTINASEVYSTELKKTEILTQVIRKSmgVRIKQKRTVYEGvVKDVKLKV 142
                                   5778899*******************9988888889888888777777777777777666666666666666644444443 PP

                                   HHH CS
                                   xxx RF
                      ABC_tran  88 als 90 
                                   a+s
  gi|70606370|ref|YP_255240.1| 143 ARS 145
                                   333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.8    0.0019       1.1       8     125 ..      61     315 ..      54     326 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                        AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeill..vaftgrAakelrerlaalgae...atTiHrlal... 77 
                                   ++ k +l +++pGtGKT + ++i ++l e +        e++   +  t+  ++ +r+++ +   +    +T+ +  +   
  gi|70606370|ref|YP_255240.1|  61 MAGKGILFVGPPGTGKTALAVAIAKELGEDTPFTTinaSEVYSteLKKTEILTQVIRKSMGV---RikqKRTVYEG-Vvkd 137
                                   567778999**********9999999988764433222111110011122222222223322...12233333322.1244 PP

                        AAA_19  78 ................................................................................. 77 
                                                                                                                    
  gi|70606370|ref|YP_255240.1| 138 vklkvarsrynpyyvspreaqivlstkddertlnvgdaiaeqfmklnvkkgdviwidaetgevtkvgrakgfegaksydie 218
                                   444455555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                        AAA_19  78 .......................................................ldfddlltealelle...eaeeekkl 100
                                                                                           ++d+l+       +   + + + +l
  gi|70606370|ref|YP_255240.1| 219 vvrqvdiptgsikkekdititvtlhdldlnlaaqsisitalfsfftereinqdirKQVDRLV-------KdmvN-RGDAEL 291
                                   55555555555555555555555555555666666666666666666543322222222222.......22212.233333 PP

                        AAA_19 101 qeeellivDEfqdvdelqyrLlkal 125
                                       +l++D + ++d  ++++l + 
  gi|70606370|ref|YP_255240.1| 292 -VPGVLFIDDAHMLDIEAFSFLTKT 315
                                   .344667777777775555555554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012      0.07       2      47 ..      66     113 ..      65     136 .. 0.75
   2 ?   -2.3   0.0       7.7   4.5e+03     126     150 ..     265     289 ..     264     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalp 47 
                                   i ++G+++tGKT l+ a+a++   ++p  +  a e+++ +l+k+e  l 
  gi|70606370|ref|YP_255240.1|  66 ILFVGPPGTGKTALAVAIAKElgeDTPFTTINASEVYSTELKKTEI-LT 113
                                   789****************877767777777777777777766653.44 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.7
                        AAA_28 126 eRredleereaiderlrealrelgi 150
                                   eR+  ++ r+++d+++++++++ + 
  gi|70606370|ref|YP_255240.1| 265 EREINQDIRKQVDRLVKDMVNRGDA 289
                                   688888999*********9998655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.083       3      31 ..      66      94 ..      64     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                  EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaegklpq 31
                                  ++  G++G GKT+L+  +a ++ e++++ 
  gi|70606370|ref|YP_255240.1| 66 ILFVGPPGTGKTALAVAIAKELGEDTPFT 94
                                  6789******************9998875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012     0.068       7      65 ..      69     129 ..      64     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                       DUF2075   7 tGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakkeekkkkkeafe 65 
                                    G +GtGKt ++++++ el       +     + + + s   +  ++l + ++k+  + ++k++ +
  gi|70606370|ref|YP_255240.1|  69 VGPPGTGKTALAVAIAKELgedtpftT----INASEVYSTELKKTEILTQVIRKSM-GVRIKQKRT 129
                                   499****************65533221....3333344444444445555555554.444444444 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013     0.077     113     139 ..      62      88 ..      42     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                     Parvo_NS1 113 krntvwfyGpantGktnlaeaIakavp 139
                                       ++f+Gp+ tGkt la aIak + 
  gi|70606370|ref|YP_255240.1|  62 AGKGILFVGPPGTGKTALAVAIAKELG 88 
                                   445699*****************9765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00021      0.12      20      43 ..      66      89 ..      53     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                        AAA_11 20 tliqGPPGtgKTktivellsqlls 43
                                   l+ GPPGtgKT   v++ ++l +
  gi|70606370|ref|YP_255240.1| 66 ILFVGPPGTGKTALAVAIAKELGE 89
                                  5889**************999953 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00045      0.26      18      46 ..      62      90 ..      43     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00045
                                  HTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE 18 lgdvilLeGdLGaGKTtlvrglakalgve 46
                                  +g+ il+ G+ G+GKT+l+ ++ak+lg +
  gi|70606370|ref|YP_255240.1| 62 AGKGILFVGPPGTGKTALAVAIAKELGED 90
                                  2567*********************9864 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0015      0.88      21      46 ..      66      92 ..      53     148 .. 0.78
   2 ?   -0.2   0.0       1.2     7e+02      90     116 ..     294     320 ..     265     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                        AAA_30 21 avltGpAGtGKttalkal.reaweaag 46
                                   + +Gp+GtGKt +  a+ +e+ e+  
  gi|70606370|ref|YP_255240.1| 66 ILFVGPPGTGKTALAVAIaKELGEDTP 92
                                  5789********998888344444434 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                        AAA_30  90 tllivDEagmvdtkqlaallkaaekag 116
                                    +l +D a m+d++ +  l+k +e++ 
  gi|70606370|ref|YP_255240.1| 294 GVLFIDDAHMLDIEAFSFLTKTLESEL 320
                                   5899**********9999999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 3006.45
//
Query:       gi|70606371|ref|YP_255241.1|  [L=287]
Description: carbohydrate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  116.9   0.0    2.2e-18   66.6   0.0    2.1  2  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
        0.1   12.6   0.2        1.4    8.9   0.0    2.5  2  Diphtheria_T  Diphtheria toxin, T domain


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   8.8e-17   7.9e-13       5     144 ..       6     144 ..       2     153 .. 0.84
   2 !   66.6   0.0   2.4e-22   2.2e-18     207     298 ..     179     267 ..     153     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 8.8e-17
                                   EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEE CS
                          PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvk 83 
                                   +++G ++id+ia+ +k+   +e  +  t+e  +GGa+ N Ava+ + g++   ++++G+D + + +le +++ gv  dyv+
  gi|70606371|ref|YP_255241.1|   6 LSVGRINIDIIAKINKIpdIDEFETTDTLEILPGGAAVNYAVAINKFGHSIKILSKIGKDSLVSYVLERIAEMGVGLDYVE 86 
                                   689**************9888888********************************************************* PP

                                   EESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES.EECTTSH CS
                          PfkB  84 idedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg.llsselp 144
                                     ++ ++++ali++  +g  ++v ++g  + +  ++ e+ ++ ++  d++++++ + + +++
  gi|70606371|ref|YP_255241.1|  87 -ETNLPQSMALIFLRDNGSISMVRKLG--SSILLDK-EDIKKVFGLFDVIHFASiSPDIVVR 144
                                   .6677**********777555555555..5555543.3679999999999999954444444 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 2.4e-22
                                   HHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                          PfkB 207 ealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAa 287
                                   + + +++      a+++v+++G++Ga v ++++e ++++ + ++v DttGAGD f ++f +a+++g s+e+ lrfa++++a
  gi|70606371|ref|YP_255241.1| 179 STKVKIES---LKARLIVIKMGSKGAKVISENEECYCEPYKVQTVLDTTGAGDVFDAAFNYAYVQGYSIEDTLRFAVTASA 256
                                   33333333...23489**************9999999999999************************************** PP

                                   HHHTSSSSSTC CS
                          PfkB 288 lvvqkkgaias 298
                                   l v + g i+s
  gi|70606371|ref|YP_255241.1| 257 LKVMRIGGINS 267
                                   *******9985 PP

>> Diphtheria_T  Diphtheria toxin, T domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.047   4.2e+02     125     173 ..      85     133 ..      22     139 .. 0.56
   2 ?    8.9   0.0   0.00016       1.4      11      56 ..     177     221 ..     168     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.047
                                   -SHHHHHHHHHHHHHHHHHHHHHH-S-S-GGGGTTHHHHHHHHHHHHHH CS
                  Diphtheria_T 125 nteeivaqsialsslmvaqaiplvgelvdigfaaynfvesiinlfqvvh 173
                                     e  + qs+al  l    +i +v +l    +   + ++ +  lf+v+h
  gi|70606371|ref|YP_255241.1|  85 VEETNLPQSMALIFLRDNGSISMVRKLGSSILLDKEDIKKVFGLFDVIH 133
                                   2334456677777777777777777766666666666666667777766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHSSSHHHHHHHTS--SS--HHHHHHHHHHHH.HHHC CS
                  Diphtheria_T  11 rdktktkieslkehgpiknkmsespnktvseekakqyleefh.qtal 56 
                                   r+ tk kieslk    i  km     k +se+    y e ++ qt l
  gi|70606371|ref|YP_255241.1| 177 RESTKVKIESLKAR-LIVIKMGSKGAKVISENE-ECYCEPYKvQTVL 221
                                   899*********87.57889*99999*999875.5677776536665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1910.26
//
Query:       gi|70606372|ref|YP_255242.1|  [L=354]
Description: DNA polymerase IV [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-44  150.1   0.3    8.1e-44  149.2   0.2    1.5  2  IMS              impB/mucB/samB family
    2.2e-09   37.1   0.0    6.6e-09   35.6   0.0    1.9  1  IMS_HHH          IMS family HHH motif
    1.5e-05   25.5   0.2    4.8e-05   23.9   0.2    1.9  1  HHH_5            Helix-hairpin-helix domain
      0.002   18.5   0.2       0.17   12.3   0.2    2.9  2  DUF1805          Domain of unknown function (DUF1805)
     0.0025   18.0   0.0     0.0052   17.0   0.0    1.5  1  Cdd1             Pathogenicity locus
     0.0028   18.0   0.0      0.015   15.7   0.0    2.1  2  BAF              Barrier to autointegration factor
  ------ inclusion threshold ------
      0.021   15.5   0.6       0.35   11.6   0.6    2.4  1  IMS_C            impB/mucB/samB family C-terminal domain
      0.092   12.6   0.0       0.24   11.2   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.11   12.7   1.9          1    9.6   0.2    2.5  2  SRI              SRI (Set2 Rpb1 interacting) domain


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.2   4.1e-47   8.1e-44       1     149 [.       6     156 ..       6     157 .. 0.96
   2 ?   -3.4   0.0       4.3   8.6e+03      52      62 ..     311     321 ..     296     348 .. 0.47

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 4.1e-47
                                   EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT-EEEEEE-HHHHHHHH CS
                           IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpdlivvkvdlekyrrask 78 
                                   +D+d F+a+ve++++p+ kgkP+vv+ +s +   +g v++++yeAr+ Gvk+gm+i +a ++ p +i+v+ + + y+ +s+
  gi|70606372|ref|YP_255242.1|   6 VDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRtktSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSN 86 
                                   7************************9998888889********************************************** PP

                                   HHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                           IMS  79 kileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                   +i+++l+++ ++k+e asiDEayld+t+ +e + ++g +la++++++i e+ ++tv++G+a+nk+lAK+++
  gi|70606372|ref|YP_255242.1|  87 RIMNLLNKH-ADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIA 156
                                   *********.77****************777777778*******************************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.3
                                   BHHHHHTTHTT CS
                           IMS  52 rikeakklcpd 62 
                                   + k a++l  +
  gi|70606372|ref|YP_255242.1| 311 AYKVAEDLLRE 321
                                   22222222222 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   3.3e-12   6.6e-09       1      32 []     169     200 ..     169     200 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.3e-12
                       IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklGi 32 
                                   p +v++fL++l+i +ipGiG++l+ +L+ lGi
  gi|70606372|ref|YP_255242.1| 169 PTEVQDFLNELDIDEIPGIGSVLARRLNELGI 200
                                   679****************************9 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   2.4e-08   4.8e-05       3      42 ..     180     219 ..     178     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                                   HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTT CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipG 42 
                                   ++ +++GiG ++A++l + Gi  + d+++++ +eL ki+G
  gi|70606372|ref|YP_255242.1| 180 DIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITG 219
                                   6789**********************************88 PP

>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   8.3e-05      0.17      36      60 ..      41      65 ..      39      67 .. 0.87
   2 ?    2.9   0.0     0.068   1.4e+02      19      48 ..     193     224 ..     179     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.3e-05
                                  SB-SEE-HHHHHTT--TT-BHHHHG CS
                       DUF1805 36 apvesvteaAeelGikeGmtgkeaL 60
                                  + v+ ++ +A++lG+k Gm    a+
  gi|70606372|ref|YP_255242.1| 41 GAVATANYEARKLGVKAGMPIIKAM 65
                                  67999**************987775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.068
                                   E-....-S--SHHHHHHS...B-SEE-HHHHHT CS
                       DUF1805  19 rvivagsGVrtledllaa...pvesvteaAeel 48 
                                   r  + + G+++l d+l++   ++e++t +A++l
  gi|70606372|ref|YP_255242.1| 193 RR-LNELGIQKLRDILSKnynELEKITGKAKAL 224
                                   44.344899*******86333699999999986 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.6e-06    0.0052       8      41 ..     181     214 ..     176     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-06
                          Cdd1   8 lqdiPniGkalaedlvelGirsveelkgedpeel 41 
                                   + +iP+iG  la+ l elGi++++++  ++ +el
  gi|70606372|ref|YP_255242.1| 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNEL 214
                                   679***********************99885554 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.4e-06     0.015      13      47 ..     174     208 ..     170     217 .. 0.88
   2 ?   -1.8   0.0       2.2   4.3e+03      37      56 ..     310     329 ..     302     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.4e-06
                           BAF  13 epmgdKevtalaGigevlgkkLeekGfdkAyvvlg 47 
                                   + +++ ++++++Gig+vl+++L+e G++k   +l 
  gi|70606372|ref|YP_255242.1| 174 DFLNELDIDEIPGIGSVLARRLNELGIQKLRDILS 208
                                   56778899*********************999886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                           BAF  37 kGfdkAyvvlgqfLvlkkde 56 
                                   + ++ A+ +l + Lv +k++
  gi|70606372|ref|YP_255242.1| 310 NAYKVAEDLLRELLVRDKRR 329
                                   67889999999999998875 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00017      0.35      73     108 ..     310     342 ..     123     349 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                         IMS_C  73 sdtreileaalkLlrrlide.pglpirligvsasnlv 108
                                   ++    ++ a  Llr+l  + + +++r+igv + n+ 
  gi|70606372|ref|YP_255242.1| 310 NA----YKVAEDLLRELLVRdKRRNVRRIGVKLDNII 342
                                   33....444555555554445**************87 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.24       5      35 ..     183     214 ..     181     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
               DNA_pol_lambd_f   5 kvyGVGpktAkkwyakGirtledlrakr.akL 35 
                                   ++ G+G++ A+++ + Gi  l d++ k+ ++L
  gi|70606372|ref|YP_255242.1| 183 EIPGIGSVLARRLNELGIQKLRDILSKNyNEL 214
                                   589*********************99543555 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00051         1      11      49 ..      83     138 ..      77     161 .. 0.86
   2 ?    1.8   0.1      0.14   2.8e+02      21      52 ..     300     331 ..     295     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                           SRI  11 elakvVvnvlnkYrkklk..................kedfKklakeltkklvekElk 49 
                                    +++ ++n+lnk+ +k++                   e+  +la+++ + ++ekE k
  gi|70606372|ref|YP_255242.1|  83 AFSNRIMNLLNKHADKIEvasideayldvtnkvegnFENGIELARKIKQEILEKE-K 138
                                   799*************9999************9999899999************9.4 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.14
                           SRI  21 nkYrkklkkedfKklakeltkklvekElkkdk 52 
                                   +k+++ ++ ++ +k+a +l   l+ ++ +++ 
  gi|70606372|ref|YP_255242.1| 300 KKFKHGISIDNAYKVAEDLLRELLVRDKRRNV 331
                                   79999***************999999966543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2676.14
//
Query:       gi|70606373|ref|YP_255243.1|  [L=146]
Description: hypothetical protein Saci_0555 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.019   15.2   0.0    1.4  1  DUF4217   Domain of unknown function (DUF4217)
      0.056   13.8   1.6      0.081   13.3   1.6    1.3  1  DUF5099   Domain of unknown function (DUF5099)


Domain annotation for each model (and alignments):
>> DUF4217  Domain of unknown function (DUF4217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.1e-06     0.019       9      48 ..     105     144 ..     104     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-06
                       DUF4217   9 cakdrdlkelAqkAfvsyvraYsvhlakeiFrvkkLdlea 48 
                                   ++kd d  + ++++f+ yv aY + +++ i++  +L++e+
  gi|70606373|ref|YP_255243.1| 105 ILKDVDTSQRGVRGFINYVYAYGNPDLSKILNSLQLNVEE 144
                                   5799***************************999988875 PP

>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.6   9.1e-06     0.081       3      62 ..      44     100 ..      42     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-06
                       DUF5099   3 pklvliinkysevskeeikklkkkygikivkligekkdkvlikeeidfenksvlpdlvil 62 
                                   + lvl+++ky+e+ + +i+ +k k+ +  v  i+e+ dk+    +i+++n+sv+  + ++
  gi|70606373|ref|YP_255243.1|  44 ARLVLVLDKYNEIMN-DITAIKGKKAVVEVSAIKEDMDKLSK--IIHIDNRSVTDRIPFY 100
                                   679**********86.5889999999999*********9987..7777777766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 966.15
//
Query:       gi|70606374|ref|YP_255244.1|  [L=335]
Description: RNA 3'-terminal-phosphate cyclase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-77  258.2   0.1    5.4e-77  257.9   0.1    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    1.4e-20   73.7   0.1    2.3e-20   73.0   0.1    1.4  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.9   0.1     6e-81   5.4e-77       2     221 ..       9     323 ..       8     324 .. 0.96

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 6e-81
                                   TTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE-----.-SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                           RTC   2 gegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeik.ageyevd 81 
                                   gegGgqiLRt+l+Ls lt+kp+rI+nIRanR+kPGL++qhltav++++ +tna+v+g+ +gstel F+Pg+i+ +g++ +d
  gi|70606374|ref|YP_255244.1|   9 GEGGGQILRTSLTLSSLTKKPFRIYNIRANRPKPGLQRQHLTAVNAVKILTNATVKGDYVGSTELIFSPGDIQeKGDFVFD 89 
                                   8**********************************************************************98579***** PP

                                   EESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC  82 igtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevelev 162
                                   igtAGs+tl+lqt+lplll  k  +++t+kGgT+v+++ps+dy++ v+ ++l+r+g +++++el krG+yp+GgGe++++ 
  gi|70606374|ref|YP_255244.1|  90 IGTAGSTTLILQTILPLLLNRK--LTVTIKGGTDVPKSPSIDYIRLVFSKVLERIG-ISFNVELIKRGHYPEGGGEIRISN 167
                                   *****************99887..9*******************************.7*******************9988 PP

                                   E-.-S---EB....................................................................... CS
                                   xxxxxxxxxx....................................................................... RF
                           RTC 163 epskklkpie....................................................................... 172
                                    +  +++ ++                                                                       
  gi|70606374|ref|YP_255244.1| 168 VR-GEPQRFSitefgqlegfvgishvsslpvhiadrqkssaekilrrlkdkidirldvregeiskgsgiclsaigkygiig 247
                                   43.2344444556889***************************************************************** PP

                                   .............................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHHSS-EEE CS
                                   .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RTC 173 .............................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqflgvkfk 221
                                                                a++D+h+ d+l+l++ L +g  ++++++ltlh +t+ +vi++f+++k +
  gi|70606374|ref|YP_255244.1| 248 adalgergkraetvgeeaalklleelktnAAFDSHMGDMLMLYASLYQG--EYTASKLTLHSITNEKVIRKFIDIKGE 323
                                   ************************************************9..7*********************99865 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.1   2.6e-24   2.3e-20       2     102 ..     179     273 ..     178     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 2.6e-24
                                   S----SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE- CS
                    RTC_insert   2 drGrvkrirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealge 82 
                                   + G+++   G+++++ ++ ++a r+ ++a+++L++l  +++i +d v+eg+    s+G+gi+L a  +   +++ga+alge
  gi|70606374|ref|YP_255244.1| 179 EFGQLEGFVGISHVSSLPVHIADRQKSSAEKILRRLKDKIDIRLD-VREGE---ISKGSGICLSAIGK--YGIIGADALGE 253
                                   78*******************************************.66665...589**********6..69********* PP

                                   TT--HHHHHHHHHHHHHHHH CS
                    RTC_insert  83 kgvppedvGeeaaeeLleei 102
                                   +g+++e vGeeaa +Llee+
  gi|70606374|ref|YP_255244.1| 254 RGKRAETVGEEAALKLLEEL 273
                                   ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2341.30
//
Query:       gi|70606375|ref|YP_255245.1|  [L=334]
Description: NAD-dependent alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-26   91.6   0.7    4.6e-26   90.8   0.7    1.4  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    2.9e-16   59.6   0.0    8.3e-16   58.2   0.0    1.8  2  ADH_zinc_N       Zinc-binding dehydrogenase
    1.5e-11   45.4   0.0    2.4e-11   44.8   0.0    1.3  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
      0.003   16.9   0.0      0.005   16.2   0.0    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0056   17.1   0.0     0.0087   16.5   0.0    1.4  1  NAD_binding_7    Putative NAD(P)-binding
     0.0076   15.8   0.0      0.015   14.8   0.0    1.4  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.058   13.0   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.067   13.5   0.0       0.12   12.6   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.7   2.1e-29   4.6e-26       2     105 ..      27     131 ..      26     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 2.1e-29
                                   TEEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenl 80 
                                    evl++v+a+g+C+ D+hi+ g+  ++++v+lp+ilGHE+vG v + +   +k+k+ d V+v+ ++ c++C++Ck +e+++
  gi|70606375|ref|YP_255245.1|  27 SEVLLQVTATGLCHGDIHIAMGEwdSQIQVNLPIILGHEVVGRVLQSN--HDKIKKNDLVLVYNAFGCKNCKYCKFKEYQF 105
                                   59********************9888999****************976..568**************************** PP

                                   -TTBEETTTSS-SSSBSEEEEC.GGG CS
                         ADH_N  81 CeeakllgvsldGgfaeyvvvp.ekk 105
                                   Ce+ k++gv+l+Ggfaeyv +p  ++
  gi|70606375|ref|YP_255245.1| 106 CEKVKVIGVNLNGGFAEYVKIPdGDN 131
                                   *******************9994445 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.0   3.7e-19   8.3e-16       1     126 [.     173     295 ..     173     299 .. 0.90
   2 ?   -3.3   0.0       3.6   8.2e+03      44      57 ..     311     325 ..     303     328 .. 0.72

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 3.7e-19
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkp 81 
                                   +v l+a+ql+k  ++ v+++  ++ kl+ a+klGadevi  k+ + ++++  l  g+++d+++++vGs +tl ++  ll++
  gi|70606375|ref|YP_255245.1| 173 AVALIALQLLKLKNVDVTVIGENQLKLDSAEKLGADEVISIKR-EEDSYLSLLP-GKKFDYILDYVGSTRTLAESPWLLNK 251
                                   5889*************************************99.8899999999.88************************ PP

                                   EEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHH CS
                    ADH_zinc_N  82 gGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkeald 126
                                   +G l ++G ++g      + l+l+ ++i+G+l+gs  +++k  ld
  gi|70606375|ref|YP_255245.1| 252 KGELRIIGEFGGVLRAEEQLLVLRGLRIRGILYGS-LQDLKHILD 295
                                   ********65555545666688*************.688777666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                   C.HHHHHHHHHTTTS CS
                    ADH_zinc_N  44 a.dlverikeltgge 57 
                                     d++e+i + t+g+
  gi|70606375|ref|YP_255245.1| 311 LeDINEAITDVTEGK 325
                                   448999999999775 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.1e-14   2.4e-11       1     133 []     205     332 ..     205     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.1e-14
                                   TT-SEEEETT.STTHH.HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GG CS
                  ADH_zinc_N_2   1 lGAdevidyr.tedfe.aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflf 79 
                                   lGAdevi  + +ed   + + g+++D++ld vg++ +l++s  +l+++G l  ig+  +   l+++++    r++++  ++
  gi|70606375|ref|YP_255245.1| 205 LGADEVISIKrEEDSYlSLLPGKKFDYILDYVGSTRTLAESPWLLNKKGELRIIGE--FGGVLRAEEQLLVLRGLRIRGIL 283
                                   8******555366655799999***********88888***9888777**988886..44455555555556666666666 PP

                                   G...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                  ADH_zinc_N_2  80 smkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                   +   s  +d l+++++ + +Gk+ +  + v++le+++eA+ ++ +g+++G+ V+
  gi|70606375|ref|YP_255245.1| 284 Y--GS-LQD-LKHILDIYLKGKIDTLTT-VYKLEDINEAITDVTEGKVVGRAVI 332
                                   4..34.788.**************9997.*********************9997 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06     0.005      27      84 ..     162     219 ..     147     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                                   ---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHH CS
                   AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeel 84 
                                   e++kvl+iG G + l A++  k  + +Vtv+  ++ +l   e+lga  v  +k++e++
  gi|70606375|ref|YP_255245.1| 162 ENSKVLIIGTGAVALIALQLLKLKNVDVTVIGENQLKLDSAEKLGADEVISIKREEDS 219
                                   579******************************************9987777777655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.9e-06    0.0087       7      49 ..     163     212 ..     160     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele..........elvk 49 
                                   + kvl++G G vA+  ++ l  ++ +vtv+ ++    l+          e ++
  gi|70606375|ref|YP_255245.1| 163 NSKVLIIGTGAVALIALQLLKLKNVDVTVIGENQ---LKldsaeklgadEVIS 212
                                   789*****************99*********994...3322344444444343 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.6e-06     0.015      31     118 ..     163     246 ..     146     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.6e-06
                   Glu_dehyd_C  31 pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipea..seemdlvvEaTG 109
                                    +++l++G+G++ L+al ll++  ++++ v+v+g    +++++d  e+lGa  v s + + d+  +    +++d++++  G
  gi|70606375|ref|YP_255245.1| 163 NSKVLIIGTGAVALIALQLLKL--KNVD-VTVIGE---NQLKLDSAEKLGADEVISIKREEDSYLSLlpGKKFDYILDYVG 237
                                   5679****************98..5676.999994...789**********988776655555433311578888888888 PP

                   Glu_dehyd_C 110 sakhafeai 118
                                   s++ + e+ 
  gi|70606375|ref|YP_255245.1| 238 STRTLAESP 246
                                   888777765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.058       1      41 [.     166     207 ..     166     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                   EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCE CS
                          ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGl 41 
                                   ++i+G+Ga+  l+a +L k ++ dvt+i+ ++ +l++ +k G 
  gi|70606375|ref|YP_255245.1| 166 VLIIGTGAVA-LIALQLLKlKNVDVTVIGENQlKLDSAEKLGA 207
                                   68*******7.566666666************99998877775 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.4e-05      0.12       1      80 [.     166     239 ..     166     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80 
                                   vliiG G+v+  +++ll+ ++ v  ++tv++ ++ kl+ + +k+   ++++i+   + y + L +  k+ d +++ ++++
  gi|70606375|ref|YP_255245.1| 166 VLIIGTGAVALIALQLLKLKN-V--DVTVIGENQLKLDSA-EKLGADEVISIKREEDSYLS-LLPG-KKFDYILDYVGST 239
                                   89********99999888765.7..7**********9988.57899999999999999999.4442.6667777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2426.79
//
Query:       gi|70606376|ref|YP_255246.1|  [L=427]
Description: glutamine synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-71  239.8   0.0    1.3e-70  238.1   0.0    1.7  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    0.00011   22.0   0.0    0.00019   21.2   0.0    1.5  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain
  ------ inclusion threshold ------
      0.015   15.0   0.0       0.91    9.3   0.0    3.1  3  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
       0.19   10.4   0.1       0.29    9.8   0.1    1.1  1  RNA12         RNA12 protein


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.0     3e-74   1.3e-70       3     345 .]     107     422 ..     105     422 .. 0.95

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 3e-74
                                   -HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHHHH CS
                    Gln-synt_C   3 dPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiveale 83 
                                   + Rs+l + +++l+e Gl++ v++E+ F+l++ ++ +                pa+++++fs++ + e ++l++++++ l 
  gi|70606376|ref|YP_255246.1| 107 CSRSLLIKGIQKLEEVGLKLQVAFEPTFYLIKFKDSR--------------AVPADEARAFSLEGLMEEQNLLKDLIKNLG 173
                                   89******************************77663..............4678999*********************** PP

                                   HTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEES CS
                    Gln-synt_C  84 algieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgknl 164
                                   + +i+v+++ + +++gQ+Ei+++ +d+l+aaD++++ +++++ +Ar ++ + tFmpKp+ + + s+m + l + dkd++++
  gi|70606376|ref|YP_255246.1| 174 SSNIKVQSVNKHYGPGQYEITFSLSDVLEAADSLIFARETIRDTARLYNAYSTFMPKPFRNYPSSSMDIFLKILDKDNNPV 254
                                   ********************************************************************************* PP

                                   SB-TTSGGG..B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-TSGGCSTEEEEC CS
                    Gln-synt_C 165 fadeddeya..lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipaskekakrvElRl 243
                                     d++d+++  ls+++++fi+G+++h++++ a+++pt+nSYkR++ +   P+ +  g+ +R  +lRip + ++   +E+Rl
  gi|70606376|ref|YP_255246.1| 255 GVDANDSKGlgLSKILYNFIAGIIEHLPSIIAIASPTINSYKRFK-EVVTPTIMGVGT-ERHFVLRIPVTYKDYGIIEFRL 333
                                   *****999999*********************************9.788899988886.6********************* PP

                                   EBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHHHHH CS
                    Gln-synt_C 244 pdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasleeAlealeedellkevlgeevieayla 324
                                   +d+ aNPYL+l+ l+ +g+dGie++l+++ +           +++gi  lP+sl+eA+++l++d+ lk  lg+e+i+++++
  gi|70606376|ref|YP_255246.1| 334 ADPLANPYLLLSSLIFSGIDGIERNLDVEVN-----------QSLGI--LPTSLREAVKSLDKDTKLKYNLGQEIINTFVE 401
                                   ************************9986422...........22334..******************************** PP

                                   HHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 325 lkraEleeleeevsdwelery 345
                                   lk++E+e++e e++dwe++ y
  gi|70606376|ref|YP_255246.1| 402 LKNKEIEDYEGEITDWEINAY 422
                                   *****************9987 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.3e-08   0.00019       5     107 .]       5     104 ..       1     104 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.3e-08
                                   ......------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT.-EEE-GGGGG--TTS---TT-S-SSS--EEEEE-GGG-E CS
                  Gln-synt_N_2   5 avveqleekqveLieflyvdlaGvtrGkalplasLeekLas.GiGltkatlalserdlidevedlgpvGelrLvpdPasav 84 
                                    ++e l+  +++ ++ ++vd  G +rG++l +a++e+ L + G+ + ++ + l  rd        ++  ++   +d a++ 
  gi|70606376|ref|YP_255246.1|   5 EILELLKSGRIDYVRVVFVDILGNVRGRSLRRAEFEKVLNErGVEYSESLILLDYRDEPIR----STYADMFAQADLATFS 81 
                                   6889999999**************************9997548999888888888875433....346788889999**** PP

                                   EE---SSTTSEEEEEE-TTS-B- CS
                  Gln-synt_N_2  85 alpyaPdaaallgdlvevdgtPy 107
                                   ++py   +  +l+ l+++dg+P+
  gi|70606376|ref|YP_255246.1|  82 VIPYLERTGRVLSYLTQIDGSPH 104
                                   *********************95 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0002      0.91       2      75 ..      15      94 ..      14      99 .. 0.70
   2 ?   -0.9   0.0      0.32   1.4e+03      58      81 ..     223     247 ..     213     249 .. 0.79
   3 ?   -3.8   0.0       2.5   1.1e+04       7      25 ..     347     365 ..     346     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                                  --EEEEEEE-SSS-EEEEEEEHHHHHHHTTT.T-EEEETTSS.....TTT------EEEEEEEGGGEEE-SS-SS-..EEE CS
                    Gln-synt_N  2 vkfvdlqFtDikgklkhvtipadelsedale.egvsFDGSsi.....egfaeieeSDmlLkPdlstavidPfreek.ktar 75
                                  + +v++ F+Di g+++  ++   e+ e++l+  gv    S i     ++  +    Dm+ + dl t+ ++P+ e++ ++++
  gi|70606376|ref|YP_255246.1| 15 IDYVRVVFVDILGNVRGRSLRRAEF-EKVLNeRGVEYSESLIlldyrDEPIRSTYADMFAQADLATFSVIPYLERTgRVLS 94
                                  6789999999999999999999999.6665436667666666322222344556679999999999999999887655554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                   EGGGEEE-SS-SS-..EEEEEEEEE CS
                    Gln-synt_N  58 dlstavidPfreek.ktarvicdvy 81 
                                    +st+++ Pfr+ + + + ++ +++
  gi|70606376|ref|YP_255246.1| 223 AYSTFMPKPFRNYPsSSMDIFLKIL 247
                                   5799*******98877777777665 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.5
                                   EEEE-SSS-EEEEEEEHHH CS
                    Gln-synt_N   7 lqFtDikgklkhvtipade 25 
                                   l+F  i g  +++ +++++
  gi|70606376|ref|YP_255246.1| 347 LIFSGIDGIERNLDVEVNQ 365
                                   7899999999998887665 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   6.5e-05      0.29     399     439 ..     375     415 ..     371     418 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.5e-05
                         RNA12 399 raafkrlvsdkvlkavlelevleklikleekkikklEeElr 439
                                   r+a+k l +d++lk +l  e++++ ++l++k+i+ +E E++
  gi|70606376|ref|YP_255246.1| 375 REAVKSLDKDTKLKYNLGQEIINTFVELKNKEIEDYEGEIT 415
                                   7899***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2842.43
//
Query:       gi|70606377|ref|YP_255247.1|  [L=258]
Description: hypothetical protein Saci_0559 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-46  156.1   0.0    1.3e-45  155.6   0.0    1.1  1  Met_10       Met-10+ like-protein
     0.0085   15.2   0.0      0.013   14.6   0.0    1.3  1  Fibrillarin  Fibrillarin
  ------ inclusion threshold ------
      0.028   13.8   0.0      0.041   13.3   0.0    1.2  1  PrmA         Ribosomal protein L11 methyltransferase (PrmA)
       0.14   12.5   0.1       0.27   11.5   0.1    1.4  1  DUF4112      Domain of unknown function (DUF4112)


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.6   0.0   2.9e-49   1.3e-45       4     198 ..      16     212 ..      13     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 2.9e-49
                                   EEETTEEEEEB..-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS- CS
                        Met_10   4 eiiGdvvilnl..reelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvy 82 
                                   ei Gd++++ +  +e+l+e kk   +++ +++ vk+v+ ++  ++g +R  +  +laG+ ++eti +Engc+f lDv+kv+
  gi|70606377|ref|YP_255247.1|  16 EILGDIALIGIpfNENLEEVKKYAEQIMQNINYVKSVWGRYRDINGDYRLSTTIHLAGERRSETIYRENGCKFALDVTKVF 96 
                                   689**999765227899999999999999999************************************************* PP

                                   --GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-G.GG CS
                        Met_10  83 fsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDg.re 162
                                   fsskl+ E+ r+a+lv++ge+++++f G Gpf+i  + ++k++ v++id+nP+++ y+  n+ lNk  +v+ pi +D+ ++
  gi|70606377|ref|YP_255247.1|  97 FSSKLSYEHLRVARLVKPGETIINMFSGFGPFSIISSILGKPSVVYSIDINPYAYYYMMVNVDLNKTFNVI-PIYGDAfKK 176
                                   **********************************************************************9.999998345 PP

                                   ---TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                        Met_10 163 vireqladrvvmnlpksaieFldkvlaalkdggvih 198
                                   +    +adr++ +lp+++ e  + +++ l++ gv h
  gi|70606377|ref|YP_255247.1| 177 IYSLPVADRIISPLPERSYEAYKVAIERLRKDGVLH 212
                                   55589*****************************98 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     3e-06     0.013      68     130 ..     112     175 ..      71     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-06
                                   --TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHH.TTSTTEEEEES-TTS CS
                   Fibrillarin  68 ikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli.eva.kkRknivPileDArk 130
                                   +k+g+ ++ + ++ G   s +s i+g+ +vvy+++  p +   ++ +v  +k  n++Pi +DA k
  gi|70606377|ref|YP_255247.1| 112 VKPGETIINMFSGFGP-FSIISSILGKPSVVYSIDINPYAYYYMMvNVDlNKTFNVIPIYGDAFK 175
                                   6777777777777774.799******************9887665377625567********964 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.2e-06     0.041     157     215 ..     110     169 ..      99     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-06
                          PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakk.vvavDiDevAvkvakeNaelNkveaklev 215
                                   +lvk+ge+++ +  G G  +i ++ Lg  + v+ +Di++ A      N++lNk+ + + +
  gi|70606377|ref|YP_255247.1| 110 RLVKPGETIINMFSGFGPFSIISSILGKPSvVYSIDINPYAYYYMMVNVDLNKTFNVIPI 169
                                   679************************8762689******************99887755 PP

>> DUF4112  Domain of unknown function (DUF4112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     6e-05      0.27      30      91 ..     118     178 ..     113     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                       DUF4112  30 iigliPvvGd..visallslylvleakkaeglpkslllrmlvnialDlliglvPvvGdlfdvlf 91 
                                   ii ++ ++G+  +is +l+   v  +    ++ + +   m+vn+ l+ ++ ++P+ Gd+f+ ++
  gi|70606377|ref|YP_255247.1| 118 IINMFSGFGPfsIISSILGKPSVVYS---IDINPYAYYYMMVNVDLNKTFNVIPIYGDAFKKIY 178
                                   66666677762235556664444444...358889999**********************9777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1688.49
//
Query:       gi|70606378|ref|YP_255248.1|  [L=382]
Description: hypothetical protein Saci_0560 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.17   11.3   0.0    1.2  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 


Domain annotation for each model (and alignments):
>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.2e-06      0.17      77     133 ..     247     304 ..     242     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-06
               Chal_sti_synt_N  77 nPeltaemapsldarleivn.aevlklgkeaalkalkewGrPkskithlvfvssseve 133
                                   +P ++ +  p +d r+e+ + ++ l l+ e a ka+ ewG  + +i   vf+  s  +
  gi|70606378|ref|YP_255248.1| 247 KPSMALDLVPNFDLRHEMSVaVNRLLLTSEEAFKAVTEWGYKQLNINAGVFLKDSSAD 304
                                   68888899999******96514556789999****************99999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2425.14
//
Query:       gi|70606379|ref|YP_255249.1|  [L=177]
Description: archaemetzincin-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-36  126.8   0.9    1.4e-36  126.4   0.9    1.1  1  Peptidase_M54  Peptidase family M54
    0.00011   22.0   0.0    0.00012   21.9   0.0    1.2  1  Peptidase_M10  Matrixin
    0.00032   20.6   0.8    0.00071   19.5   0.2    1.8  2  Peptidase_M43  Pregnancy-associated plasma protein-A
    0.00065   20.2   0.0     0.0008   19.9   0.0    1.2  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0043   17.2   0.1     0.0043   17.2   0.1    1.3  1  Reprolysin_5   Metallo-peptidase family M12
     0.0074   16.0   0.0       0.01   15.5   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
     0.0086   14.7   0.1      0.012   14.3   0.1    1.1  1  Metallopep     Putative peptidase family
  ------ inclusion threshold ------
      0.021   13.8   0.0       0.03   13.3   0.0    1.2  1  Peptidase_M66  Peptidase M66
      0.024   14.6   1.5       0.09   12.7   0.1    2.0  2  Reprolysin     Reprolysin (M12B) family zinc metalloprotease
      0.063   12.9   0.1      0.096   12.3   0.1    1.3  1  Peptidase_M57  Dual-action HEIGH metallo-peptidase
      0.084   12.1   0.1       0.12   11.6   0.1    1.2  1  DUF4953        Met-zincin


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.9   8.3e-40   1.4e-36      21     193 ..      16     172 ..       3     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 8.3e-40
                                   HHHHHHHHHHHHH-S-E.EEEEE----..........GGGEETTTTEEEHHHHHHHHHT--S--..SEE........EEEE CS
                 Peptidase_M54  21 vvDrverflsdvglevkivyagrikLPpgllirveteegavkmyrleavveallgkLkemkddvndDsitkifgittlplg 101
                                   +v+ v+ +l ++g ev+ v ++  +L            + ++++r ++ +++ll+ +k   + + +D++        +++g
  gi|70606379|ref|YP_255249.1|  16 IVNSVRTHLMNMGFEVE-VNEEIFHLN----------AELFNWERWQYNADKLLQLVKLTFERYPYDAV--------IGIG 77 
                                   55555555555555555.444444444..........6899**************9999999*******........9*** PP

                                   SS-EE-TT-S-BSEEE-SSSSEEEEE-T..--.......SHHHHHHHHHHHHHHHHHHHTT----S-.TSTTS--SSHHHH CS
                 Peptidase_M54 102 srdqyidiykkvlGievsiGnyavlals..ikefyte..dkeLflervvkevlhelGhlyGLshCke.dCvmnfsndlkdv 177
                                   + d + d++++v+G++ +  +y +++ls   +efy +  +  L++er +kev+helGh++GL+hC++ +Cvmnfs +++dv
  gi|70606379|ref|YP_255249.1|  78 EADGFSDGLNFVFGLSTK--KYGLVFLSrlKEEFYGRviNSSLYIERTLKEVTHELGHTLGLGHCNNkECVMNFSVSVEDV 156
                                   ***************999..9*******98899***999****************************************** PP

                                   HHS-SS--HHHHHHHH CS
                 Peptidase_M54 178 DrkapkyCksCleklk 193
                                   D+k   +C sC  kl+
  gi|70606379|ref|YP_255249.1| 157 DKKGKYFCTSCSDKLN 172
                                   ************9985 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   7.4e-08   0.00012     113     138 ..     127     152 ..      38     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.4e-08
                                   HHHHHHHHTTBESXSSTTSTTSSSCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M10 113 aaHEiGHalGLeHssdkdalmyplyk 138
                                   ++HE+GH+lGL H ++k+ +m   ++
  gi|70606379|ref|YP_255249.1| 127 VTHELGHTLGLGHCNNKECVMNFSVS 152
                                   47*******************87665 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.96   1.6e+03     111     140 ..      32      53 ..      13      63 .. 0.52
   2 !   19.5   0.2   4.3e-07   0.00071      56     121 ..     111     175 ..     102     177 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                 Peptidase_M43 111 avnkdllnCngetinsqnfmdyngvrasft 140
                                    vn++++  n e +n++        r ++ 
  gi|70606379|ref|YP_255249.1|  32 EVNEEIFHLNAELFNWE--------RWQYN 53 
                                   34455555555555554........44444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.3e-07
                 Peptidase_M43  56 GaylaadststnksstLthelGhfLgLihtfeggCerGegDkvsDtpsedgkevsavnkdllnCng 121
                                   G+ + ++ + + +   +thelGh LgL h  + +C    +  v+D +++ gk   +  +d ln n+
  gi|70606379|ref|YP_255249.1| 111 GRVINSSLYIERTLKEVTHELGHTLGLGHCNNKECVMNFSVSVEDVDKK-GKYFCTSCSDKLNINN 175
                                   55555555666777789******************99999999999988.5555544444446655 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.9e-07    0.0008      44     123 ..      51     139 ..      14     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.9e-07
                  Reprolysin_3  44 tealdelaevtaeaergqagyDlvhlftardesgvgGlAyvgsvcnsskk...........agvnsgssvlgkvgadtvaH 113
                                   + + d+l ++++ +  +++ yD v  +++ d   + Gl +v ++++++++           +g + +ss + + + + v+H
  gi|70606379|ref|YP_255249.1|  51 QYNADKLLQLVKLT-FERYPYDAVIGIGEADG-FSDGLNFVFGLSTKKYGlvflsrlkeefYGRVINSSLYIERTLKEVTH 129
                                   44556666677666.68899999999999886.888999998888888887766666666644444555566656699*** PP

                  Reprolysin_3 114 EiGHnfganH 123
                                   E+GH +g+ H
  gi|70606379|ref|YP_255249.1| 130 ELGHTLGLGH 139
                                   *********9 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.6e-06    0.0043     139     171 ..     120     147 ..      20     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                  Reprolysin_5 139 tatevqvvaHElGHnfGavHDcdsssesqsCsl 171
                                      +++ v+HElGH++G  H  +     ++C +
  gi|70606379|ref|YP_255249.1| 120 IERTLKEVTHELGHTLGLGHCNN-----KECVM 147
                                   46778889***********9555.....35654 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.3e-06      0.01     138     166 ..     126     155 ..      93     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.3e-06
                  Reprolysin_4 138 ifAHEiGHtfGaaHdlsdegegl.ssktee 166
                                    + HE GHt+G+ H  ++e+    s+++e+
  gi|70606379|ref|YP_255249.1| 126 EVTHELGHTLGLGHCNNKECVMNfSVSVED 155
                                   489*************99998555777654 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   7.3e-06     0.012     318     336 ..     127     147 ..     119     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.3e-06
                    Metallopep 318 flHEiGHllglpHqed..Gvm 336
                                   + HE+GH+lgl+H+++   vm
  gi|70606379|ref|YP_255249.1| 127 VTHELGHTLGLGHCNNkeCVM 147
                                   78************9866777 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05      0.03     191     210 ..     122     141 ..     115     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                 Peptidase_M66 191 tltgefiHEqGHalGLpHyl 210
                                   ++ +e  HE+GH lGL+H  
  gi|70606379|ref|YP_255249.1| 122 RTLKEVTHELGHTLGLGHCN 141
                                   5678899***********44 PP

>> Reprolysin  Reprolysin (M12B) family zinc metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.18   2.9e+02      29      65 ..       7      43 ..       3      80 .. 0.79
   2 ?   12.7   0.1   5.6e-05      0.09     127     181 ..     119     169 ..      87     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                                  HHHHHHHHHHHHHCTEEEEEEEEEE-SS--SS---SS CS
                    Reprolysin 29 levvnlvnkiykelnirvvLvglEiWsdedkievskd 65
                                  ++++nl n i ++++++++ +g E+  +e+ ++++ +
  gi|70606379|ref|YP_255249.1|  7 IRLTNLDNLIVNSVRTHLMNMGFEVEVNEEIFHLNAE 43
                                  6789999999999999999999999888887776554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.6e-05
                                   SHHHHHHHHHHHHHHHCT---GHHTTS--STTS-BTTST.TTTS---C--HHHHH CS
                    Reprolysin 127 nlealavilaqeLghnlGlthdeekeCkceekgvCiMneeagsssgvkFskcsie 181
                                    +e     + +eLgh lGl h ++keC   + +v    e  + ++g+ F +++++
  gi|70606379|ref|YP_255249.1| 119 YIERTLKEVTHELGHTLGLGHCNNKECVM-NFSV--SVE-DVDKKGKYFCTSCSD 169
                                   4455556789*********9988887776.2332..222.456667767665555 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.9e-05     0.096     137     151 ..     127     141 ..     114     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                 Peptidase_M57 137 ithelGhtvGlRhsD 151
                                   +thelGht+Gl h +
  gi|70606379|ref|YP_255249.1| 127 VTHELGHTLGLGHCN 141
                                   8***********975 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.4e-05      0.12      17      29 ..     127     139 ..     114     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.4e-05
                       DUF4953  17 vaHEvGhtLGLrh 29 
                                   v+HE GhtLGL h
  gi|70606379|ref|YP_255249.1| 127 VTHELGHTLGLGH 139
                                   68*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1215.49
//
Query:       gi|70606380|ref|YP_255250.1|  [L=139]
Description: hypothetical protein Saci_0565 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-43  145.9   0.4    9.4e-43  145.8   0.4    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   0.4   5.2e-47   9.4e-43       1     138 []       4     139 .]       4     139 .] 0.97

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 5.2e-47
                                   EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----E CS
                      Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevk 81 
                                   +e++dhtAD++i a+G+sleeafesaala+fe+mtd+sk+e k e+eie  ++dle+lL+++++ ll+++d++ ++f ++k
  gi|70606380|ref|YP_255250.1|   4 FEFFDHTADIGIIAYGRSLEEAFESAALAVFEVMTDTSKIEYKVEVEIEEIGSDLENLLYRWIESLLVYYDSDLLLFGKFK 84 
                                   9*******************************************99**********************************8 PP

                                   EEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                      Archease  82 vdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                   v+   + ++++l+++a+gekf++ekhe +t vKA+Tyhe+ i+++d+++ +++vvDi
  gi|70606380|ref|YP_255250.1|  85 VSI--DLNNMTLKGKAYGEKFNPEKHERRTVVKAMTYHEMLISQNDGTYILRFVVDI 139
                                   855..4578*****************988***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1066.53
//
Query:       gi|70606381|ref|YP_255251.1|  [L=32]
Description: hypothetical protein Saci_0566 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.41
# Mc/sec: 236.42
//
Query:       gi|70606382|ref|YP_255252.1|  [L=52]
Description: hypothetical protein Saci_0567 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   13.0   0.8       0.11   12.9   0.6    1.3  1  Ycf70     Uncharacterized Ycf70-like


Domain annotation for each model (and alignments):
>> Ycf70  Uncharacterized Ycf70-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   6.2e-06      0.11      24      55 ..      19      50 ..      13      52 .] 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-06
                         Ycf70 24 ydyweellvmvsglyalfcvflvlfiffdsfk 55
                                  y y +++ ++vsg+ + + +++v+ i+f+ f 
  gi|70606382|ref|YP_255252.1| 19 YIYTKNVQILVSGITVAVIIYIVVKIIFERFV 50
                                  889999**********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 360.71
//
Query:       gi|70606383|ref|YP_255253.1|  [L=260]
Description: hypothetical protein Saci_0568 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.13   12.3   6.6        0.2   11.8   4.1    2.7  2  Insulin_TMD   Insulin receptor trans-membrane segment
       0.22   11.5   1.7       0.46   10.5   1.7    1.5  1  SLATT_fungal  SMODS and SLOG-associating 2TM effector domain


Domain annotation for each model (and alignments):
>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.76   6.8e+03      28      40 ..      84      96 ..      84      97 .. 0.80
   2 ?   11.8   4.1   2.2e-05       0.2       9      33 ..     216     240 ..     211     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.76
                   Insulin_TMD 28 lllvigavfvvvk 40
                                  +l +  +++++vk
  gi|70606383|ref|YP_255253.1| 84 ILYIEQSLYLMVK 96
                                  5677889999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.2e-05
                   Insulin_TMD   9 ldpsnivkIvigPviciillllvig 33 
                                   ++ps i   vigPvi i++l++   
  gi|70606383|ref|YP_255253.1| 216 VVPSIITSLVIGPVIYIFILVGFSM 240
                                   58999**************987554 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.7   5.1e-05      0.46      16      65 ..      78     130 ..      76     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.1e-05
                  SLATT_fungal  16 tslalnlaiglQvllgAlltaLgalss...grtqvaitvLGalnTviAglLAr 65 
                                   +s++ n++++ Q l   + t L a+++    ++ + ++ +Gal Tvi++ L++
  gi|70606383|ref|YP_255253.1|  78 FSWLNNILYIEQSLYLMVKTILTASNAvpeVSALIQVVPFGALLTVITSALTF 130
                                   689999999999877777777777755321447899999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1809.87
//
Query:       gi|70606384|ref|YP_255254.1|  [L=78]
Description: hypothetical protein Saci_0569 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.5    8.2   6.7        4.7    7.3   2.1    2.1  2  BTP       Chlorhexidine efflux transporter


Domain annotation for each model (and alignments):
>> BTP  Chlorhexidine efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.1   0.00026       4.7      27      54 ..       3      30 ..       1      32 [. 0.82
   2 ?    3.5   0.2     0.004        73      33      49 ..      54      70 ..      48      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00026
                           BTP 27 wllgvslleagvldiglslfalvwnfvy 54
                                  +++ ++ l+++v++ig slf+l+w++ +
  gi|70606384|ref|YP_255254.1|  3 LVTFIENLTSTVTEIGWSLFILAWAIGW 30
                                  55666778899*************9865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.004
                           BTP 33 lleagvldiglslfalv 49
                                  +  a+ l+ig ++f+l+
  gi|70606384|ref|YP_255254.1| 54 IIAAFFLAIGSTIFYLI 70
                                  678999********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 565.99
//
Query:       gi|70606385|ref|YP_255255.1|  [L=182]
Description: cytidylate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-21   75.2   0.4      1e-19   71.3   0.4    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    1.5e-18   67.6   0.1    1.9e-18   67.3   0.1    1.1  1  AAA_18           AAA domain
    2.2e-15   56.9   0.1    4.2e-09   36.5   0.1    2.0  2  Cytidylate_kin   Cytidylate kinase
    7.1e-11   42.7   0.0    1.3e-10   41.8   0.0    1.5  1  AAA_17           AAA domain
    5.4e-06   26.4   0.3      0.065   13.1   0.0    2.2  2  dNK              Deoxynucleoside kinase
    1.9e-05   24.8   0.5    4.3e-05   23.7   0.5    1.6  1  SKI              Shikimate kinase
    0.00013   21.8   0.3    0.00014   21.7   0.3    1.1  1  AAA_15           AAA ATPase domain
    0.00024   21.2   0.0     0.0011   19.1   0.0    2.0  2  ADK              Adenylate kinase
     0.0003   20.9   0.0      0.062   13.5   0.0    2.2  2  AAA_33           AAA domain
    0.00083   19.8   0.1     0.0015   19.0   0.1    1.6  1  AAA              ATPase family associated with various cellul
     0.0015   18.3   0.5       0.25   11.1   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0018   18.0   0.0        0.4   10.3   0.0    2.2  2  CoaE             Dephospho-CoA kinase
     0.0023   17.9   0.0     0.0032   17.4   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0062   16.2   0.2        1.1    8.9   0.1    2.4  2  Thymidylate_kin  Thymidylate kinase
     0.0065   16.8   0.1      0.012   16.0   0.1    1.5  1  RNA_helicase     RNA helicase
     0.0069   16.1   0.2      0.019   14.7   0.1    1.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0095   16.2   0.0       0.02   15.1   0.0    1.6  1  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.02   14.4   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.018   15.0   0.0      0.046   13.6   0.0    1.7  1  NTPase_1         NTPase
      0.018   15.3   0.0      0.037   14.3   0.0    1.5  1  AAA_22           AAA domain
       0.02   14.2   0.0      0.049   12.9   0.0    1.7  2  Zeta_toxin       Zeta toxin
      0.021   14.8   0.0      0.036   14.1   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.031   14.7   0.1      0.076   13.4   0.1    1.5  1  AAA_16           AAA ATPase domain
      0.039   14.5   0.5      0.057   13.9   0.4    1.4  1  ABC_tran         ABC transporter
      0.067   12.8   0.1      0.073   12.7   0.1    1.1  1  UPF0160          Uncharacterised protein family (UPF0160)
      0.068   12.9   0.0      0.083   12.6   0.0    1.3  1  AAA_24           AAA domain
       0.07   13.0   0.0       0.15   12.0   0.0    1.7  2  APS_kinase       Adenylylsulphate kinase
      0.076   12.4   0.1       0.13   11.6   0.1    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.4   1.6e-22     1e-19       2     178 ..       3     156 ..       2     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.6e-22
               Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldeklddel 81 
                                   I Is+  Gsg++ +++ L+ kL +++++   i++ +ak+++++  ++ ++ e                     d+++d+++
  gi|70606385|ref|YP_255255.1|   3 IIISGPPGSGKSSVAKILSSKLSIKYVSAgLIFRDLAKRMNIDIVKLNKLAE--D------------------DFEIDKKI 63 
                                   669**************************8899**************77777..2..................88999999 PP

               Cytidylate_kin2  82 feaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytg 162
                                      + ++i++    ++v+i    +  ++++ +  l+++l apl++r+kr+a+r ++se+ea  +i ++++ +++++ +y+g
  gi|70606385|ref|YP_255255.1|  64 DLEMFKLIKSQ---DNVIIESHIGGWLFHNLS-DLSIYLRAPLDVRAKRIASRDHISEDEAIIQIIKRERSHRERFLRYYG 140
                                   99999999987...5***************88.9*********************************************** PP

               Cytidylate_kin2 163 qdwgdaenYdlvlnts 178
                                    d+ d + +dlv+nts
  gi|70606385|ref|YP_255255.1| 141 IDILDLSVFDLVINTS 156
                                   ***************9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.1     3e-21   1.9e-18       1     118 [.       3     117 ..       3     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3e-21
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                   I+++G+pG+GK+++ak Ls++l +     g + rd+ak  ++ +   ++  ++  ++d++ + + +++++ +       +n
  gi|70606385|ref|YP_255255.1|   3 IIISGPPGSGKSSVAKILSSKLSIkyvsaGLIFRDLAKRMNIDIVKLNKLAEDDFEIDKKIDLEMFKLIKSQ-------DN 76 
                                   9********************97789***********************99999999999999999999996.......89 PP

                        AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeea 118
                                   ++i++h++ ++++++ d+  ++L+a+ +++++R++ R+  + 
  gi|70606385|ref|YP_255255.1|  77 VIIESHIGGWLFHNLSDLS-IYLRAPLDVRAKRIASRDHISE 117
                                   *******************.*****************95443 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   6.5e-12   4.2e-09       1      55 [.       3      54 ..       3      69 .. 0.82
   2 !   19.3   0.0   1.1e-06   0.00073     107     209 ..      69     171 ..      55     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 6.5e-12
                                  EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHTT--TT-HHHHHH CS
                Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrrkvdlldeaalve 55
                                  i i GP gsGKssva++l++kl++ky+++g ++R la  +   ++d+++ ++l+e
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVSAGLIFRDLAKRM---NIDIVKLNKLAE 54
                                  6799*******************************98655...677777776665 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
                                   HTT-BSSBEEEEESSIIIIISTT.-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSSS-S---T CS
                Cytidylate_kin 107 relvkkarvvveGRDigtvvfpd.aelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerevgpLklae 186
                                   + + ++++v++e   ig  +f + ++l i+l A  ++RakR ++  + +  +  ++ + +e  +R +  +   ++ L l+ 
  gi|70606385|ref|YP_255255.1|  69 KLIKSQDNVIIES-HIGGWLFHNlSDLSIYLRAPLDVRAKRIASRDHISEDEAIIQIIKRERSHRERFLRYYGIDILDLSV 148
                                   4444589999997.59999998869***************99998777777777888888888888888888899999*** PP

                                   T-EEEETTTS-HHHHHHHHHHHH CS
                Cytidylate_kin 187 daliidtskltieevvekileli 209
                                     l+i+ts+l  e+v + il  i
  gi|70606385|ref|YP_255255.1| 149 FDLVINTSYLLPEDVADIILGVI 171
                                   9****************998766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0     2e-13   1.3e-10       2     123 ..       7     113 ..       6     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2e-13
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SE CS
                        AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdghpr 81 
                                   G+PGsGK+ +++ l  k+ ++++saG ++r+ akr +  + + +++++ + e++k+++ e+ + i+    +++v+++ h  
  gi|70606385|ref|YP_255255.1|   7 GPPGSGKSSVAKILSSKLSIKYVSAGLIFRDLAKRMNIdIVKLNKLAEDDFEIDKKIDLEMFKLIKS---QDNVIIESHIG 84 
                                   9***********************************9877788889999999999999999999986...799******95 PP

                                   EEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                        AAA_17  82 ikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                            g   + +++l  d+ i+l a+ ++  +r ++++
  gi|70606385|ref|YP_255255.1|  85 ---------G---WLFHNL-SDLSIYLRAPLDVRAKRIASRD 113
                                   .........3...444555.5668888888887777777764 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0    0.0001     0.065       1      27 [.       3      29 ..       3      55 .. 0.91
   2 !   11.9   0.1   0.00024      0.15     115     151 ..      86     120 ..      58     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                  EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                           dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                  i ++G+ g+GKs+++k+Ls kl +k +
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYV 29
                                  789******************988766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                                   HHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS CS
                           dNK 115 nlleelakpdlliYLkasletclerikkRgreeekki 151
                                   +l ++l   dl iYL+a+l++  +ri  R+   e + 
  gi|70606385|ref|YP_255255.1|  86 WLFHNL--SDLSIYLRAPLDVRAKRIASRDHISEDEA 120
                                   333333..69********************9888743 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.5   6.7e-08   4.3e-05       1     132 [.       9     137 ..       9     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.7e-08
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHT.S-HHHHHHHH..HHHHH...HHHHHHHHHHHCCCSSEEEEE-TTGGGS CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtg.ksiaeifeee..geegF...relEsevlkelleeeglViatGGGavls 75 
                                   +G+GKs+v+k+l+ kl+++++ +  ++ + ++ ++i  i++ +   e+ F   ++ + e++k + ++++++i        +
  gi|70606385|ref|YP_255255.1|   9 PGSGKSSVAKILSSKLSIKYVSAGLIFRDLAKrMNID-IVKLNklAEDDFeidKKIDLEMFKLIKSQDNVIIES------H 82 
                                   69***********************998877745554.433321255555333788999999888888999987......2 PP

                                   HHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHC CS
                           SKI  76 eenrellkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplye 132
                                      + + + + ++iyL+++l++ ++r++++++   ++e++   +  + ++ +re++ +
  gi|70606385|ref|YP_255255.1|  83 IGGWLFHNLSDLSIYLRAPLDVRAKRIASRDH---ISEDEAIIQIIKRERsHRERFLR 137
                                   3333333344789****************999...55555545555555545555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   2.2e-07   0.00014      27     104 ..       4      82 ..       2     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-07
                        AAA_15  27 vliGkNnsGKSsilealdlFlnnkekkn..........kkvikiekedleifeniseskdikIdvefaek.ekakeyektl 96 
                                   ++ G+ +sGKSs++++l   l+ k               k ++i+  +l++  ++++++d kId+e  +k        k++
  gi|70606385|ref|YP_255255.1|   4 IISGPPGSGKSSVAKILSSKLSIK---YvsaglifrdlAKRMNIDIVKLNKLAEDDFEIDKKIDLEM-FKlI------KSQ 74 
                                   899**************7766666...14579999***99**************************9.4432......222 PP

                        AAA_15  97 kskekkka 104
                                   ++  +++ 
  gi|70606385|ref|YP_255255.1|  75 DNVIIESH 82 
                                   22222222 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06    0.0011       1      37 [.       5      41 ..       5      79 .. 0.85
   2 ?   -0.4   0.0       1.7   1.1e+03      43      68 ..     104     129 ..      92     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                                  EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                                  + G+Pg+GK  +a+ l +k++++ +s+G ++R+  k+
  gi|70606385|ref|YP_255255.1|  5 ISGPPGSGKSSVAKILSSKLSIKYVSAGLIFRDLAKR 41
                                  57******************************97765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                   HHHHHHHHTTSS--HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  43 keakevmdkgelvpdevvvklvkeel 68 
                                    +ak++  + ++  de +++++k e 
  gi|70606385|ref|YP_255255.1| 104 VRAKRIASRDHISEDEAIIQIIKRER 129
                                   56777777888888888888887664 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.6e-05     0.062       2      32 ..       3      33 ..       3      79 .. 0.80
   2 ?    5.6   0.0     0.025        16      96     140 ..      90     132 ..      85     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                                  +++ G+pGsGKs +a+ l  kl    +s   
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVSAGL 33
                                  6789************999999866666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                        AAA_33  96 gvpvrivvvetdeetlkeRlakRaangddrsevpeealdrqkarf 140
                                   +  ++ ++++++ ++ ++R+a R + ++d+  +  + ++r ++++
  gi|70606385|ref|YP_255255.1|  90 NLSDLSIYLRAPLDVRAKRIASRDHISEDE--AIIQIIKRERSHR 132
                                   6667889******************98774..5555555555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.3e-06    0.0015       1      28 [.       3      30 ..       3      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-06
                                  EEEESSTTSSHHHHHHHHHHHHTHEEEE CS
                           AAA  1 vllyGppGtGKTllakavakelgvefle 28
                                  ++++GppG GK+++ak + ++l++++++
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVS 30
                                  5799*****************9988765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00039      0.25       2      44 ..       3      45 ..       3      66 .. 0.76
   2 ?    5.6   0.2     0.018        11     127     155 ..      89     117 ..      60     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldra 44
                                  I ++g+ G+Gk++va+ l + +  + v a  i  d   r+++ 
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVSAGLIFRDLAKRMNID 45
                                  5699*******************99999888855555555543 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                           PRK 127 aelldlkiyvdisidlelarklqRDiaeR 155
                                   ++l dl+iy+ +  d++  r  +RD  + 
  gi|70606385|ref|YP_255255.1|  89 HNLSDLSIYLRAPLDVRAKRIASRDHISE 117
                                   6899*************999999*98763 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00062       0.4       3      47 ..       3      48 ..       1      67 [. 0.83
   2 ?    5.8   0.0     0.015       9.7     121     164 ..      91     135 ..      78     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                                  EEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHH CS
                          CoaE  3 vgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkk 47
                                  + ++G  +sGKs va+++++ l+++ v a l+ r + +  +    k
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSkLSIKYVSAGLIFRDLAKRMNIDIVK 48
                                  5688999***********999********99999988766555544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                                   GSSEEEEEE--HHHHHHHHHHCCTSTHHH.HHHHHHHS--HHHHH CS
                          CoaE 121 liervlvvdvelelqveRlvardgvseee.vkaiiaaQlseeerl 164
                                   l +  + + ++l+ + +R+ +rd +se+e + +ii+   s+ er 
  gi|70606385|ref|YP_255255.1|  91 LSDLSIYLRAPLDVRAKRIASRDHISEDEaIIQIIKRERSHRERF 135
                                   556667789999*************99772578999888888886 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.1e-06    0.0032      49      74 ..       4      29 ..       2      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.1e-06
                         Rad17 49 LisGPsGCgkstvvkvLskelgiklr 74
                                  +isGP+G gks v k+Ls +l+ik+ 
  gi|70606385|ref|YP_255255.1|  4 IISGPPGSGKSSVAKILSSKLSIKYV 29
                                  79********************9986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.028        18       2      21 ..       6      25 ..       5      37 .. 0.86
   2 !    8.9   0.1    0.0018       1.1     119     163 ..      93     139 ..      87     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.028
                                  EESTTSSHHHHHHHHHHHHH CS
               Thymidylate_kin  2 EGlDGaGKttqaellkerlk 21
                                   G  G+GK+++a++l ++l+
  gi|70606385|ref|YP_255255.1|  6 SGPPGSGKSSVAKILSSKLS 25
                                  5888************9997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                                   SEEEEEESSHHHHHTSCCTTSS..TTTSHHHHHHHHHHHHHHHHHHH CS
               Thymidylate_kin 119 dltflldvdpevalkRlakrde..ldeeeeeqldflrkvrerylela 163
                                   dl ++l  + +v++kR+a rd+  +de++ + ++  r+ rer+l+ +
  gi|70606385|ref|YP_255255.1|  93 DLSIYLRAPLDVRAKRIASRDHisEDEAIIQIIKRERSHRERFLRYY 139
                                   899*******************9778888888888899999988865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-05     0.012       1      26 [.       3      28 ..       3      82 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  i+++Gp+g GKS++ak L+++l+ k+
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKY 28
                                  789*****************999555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1     3e-05     0.019      36      66 ..       3      31 ..       1      57 [. 0.81
   2 ?   -0.6   0.0       1.6     1e+03      87     117 ..      33      63 ..      27      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                        RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkitsg 66
                                  ++++GpPG Gk+++aki++++l +k    s+
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIK--YVSA 31
                                  899****************998654..4444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                        RuvB_N  87 vlfideihrlsraveevlysamedfrldivi 117
                                   ++f d   r++  +  +   a +df++d  i
  gi|70606385|ref|YP_255255.1|  33 LIFRDLAKRMNIDIVKLNKLAEDDFEIDKKI 63 
                                   6788888888888888888888899888655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.1e-05      0.02       1      27 [.       2      29 ..       2      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
                        AAA_28  1 kivitGgestGKTtlleaLaar.gypvv 27
                                  ki+i+G++++GK+++++ L+++  +++v
  gi|70606385|ref|YP_255255.1|  2 KIIISGPPGSGKSSVAKILSSKlSIKYV 29
                                  79*****************987655544 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     3e-05      0.02       4      31 ..       3      30 ..       1      81 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT-- CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrs 31
                                  ++++G P sGKs++ak L+++l+ +  s
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVS 30
                                  89*******************9874444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.2e-05     0.046       1      52 [.       2      49 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-05
                                  EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdl 52
                                  k++i+GppG+GK+ + k ++++l+   +  +G++    r+  +r+  +iv+l
  gi|70606385|ref|YP_255255.1|  2 KIIISGPPGSGKSSVAKILSSKLSI-KYVSAGLIF---RDLAKRMNIDIVKL 49
                                  699******************9954.577778875...45556777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05     0.037       8      33 ..       3      28 ..       2      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
                        AAA_22  8 lvvtGesGtGKTtllrrlleqldeea 33
                                  +++ G++G+GK+ +++ l ++l + +
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKY 28
                                  799***************99996554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.7e-05     0.049      19      44 ..       3      29 ..       1      73 [. 0.82
   2 ?   -1.2   0.0       1.6   1.1e+03     135     161 ..      91     117 ..      89     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-05
                    Zeta_toxin 19 illgGqpGAGKselaellkdele.rqg 44
                                  i+++G pG+GKs++a+ l  +l  ++ 
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSiKYV 29
                                  89****************999865555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                    Zeta_toxin 135 lSrlgvldRyeeevaegRlvpkeehde 161
                                   lS l+++ R   +v + R+++ +++ e
  gi|70606385|ref|YP_255255.1|  91 LSDLSIYLRAPLDVRAKRIASRDHISE 117
                                   677777777777766667777766543 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.6e-05     0.036       2      24 ..       3      25 ..       2      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                  EEEE--SSSSHHHHHHHGGGGBS CS
                         AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                  +++ GppG+gKs++a+ l++ l 
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLS 25
                                  7899**************99884 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012     0.076      27      51 ..       3      27 ..       2      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                        AAA_16 27 vllsGesGvGKsslvrellralekd 51
                                  +++sG++G+GKss+++ l   l+ +
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIK 27
                                  689************9887766655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4     9e-05     0.057      13      37 ..       2      26 ..       1      77 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                                  EEEEEESTTSSHHHHHHHHTTSS-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                  k+ i G+ G+GKS+++k+l+ +l+ 
  gi|70606385|ref|YP_255255.1|  2 KIIISGPPGSGKSSVAKILSSKLSI 26
                                  57899**************988765 PP

>> UPF0160  Uncharacterised protein family (UPF0160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011     0.073      69     129 ..      18      78 ..      13     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                       UPF0160  69 etfsekaktklSSaGLvYkhfgkeiikkllkleldeeevellyeklyeefveaiDaiDnGi 129
                                   + +s+k ++k+ SaGL++++  k++   ++kl++ +e+   + +k++ e+++ i   Dn i
  gi|70606385|ref|YP_255255.1|  18 KILSSKLSIKYVSAGLIFRDLAKRMNIDIVKLNKLAEDDFEIDKKIDLEMFKLIKSQDNVI 78 
                                   56788899*****************999999996666667788999999999999999976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013     0.083       4      27 ..       2      24 ..       1      79 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                        AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                  ki+i Gp+g+GK+++ak l  + l
  gi|70606385|ref|YP_255255.1|  2 KIIISGPPGSGKSSVAKIL-SSKL 24
                                  89***************98.6555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023      0.15       5      33 ..       3      31 ..       1      85 [. 0.85
   2 ?   -2.2   0.0       5.4   3.4e+03     103     117 ..      94     108 ..      89     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                                  EEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                    APS_kinase  5 vwltGlsgsGKstianalekkLvekgisv 33
                                  + ++G  gsGKs++a+ l++kL  k +s+
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKLSIKYVSA 31
                                  789******************98776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.4
                                   EEEEEE--HHHHHHH CS
                    APS_kinase 103 ievfvdtplevceer 117
                                   + +++++pl+v+++r
  gi|70606385|ref|YP_255255.1|  94 LSIYLRAPLDVRAKR 108
                                   579999***999887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0002      0.13      25      46 ..       3      24 ..       1      34 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                  Mg_chelatase 25 lllvGppGsGKtmlakrlpsll 46
                                  +++ GppGsGK+ +ak l+s l
  gi|70606385|ref|YP_255255.1|  3 IIISGPPGSGKSSVAKILSSKL 24
                                  899*************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1228.50
//
Query:       gi|70606386|ref|YP_255256.1|  [L=87]
Description: 50S ribosomal protein L34e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-19   69.5   2.4    2.7e-19   69.3   2.4    1.1  1  Ribosomal_L34e  Ribosomal protein L34e
    0.00079   19.3   2.9      0.047   13.6   0.2    2.4  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.0   0.3      0.012   15.0   0.3    1.8  2  zf-FLZ          zinc-finger of the FCS-type, C2-C2
      0.013   15.1   1.8        2.7    7.7   0.1    2.2  2  zf-P11          P-11 zinc finger
      0.015   15.3   1.0      0.065   13.2   1.0    2.0  1  Gin             Inhibitor of sigma-G Gin
       0.14   12.0   2.2        2.1    8.2   0.0    2.2  2  zinc_ribbon_12  Probable zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   2.4     9e-23   2.7e-19      12      91 ..       5      81 ..       1      83 [. 0.90

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 9e-23
                Ribosomal_L34e 12 sYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkerivr 91
                                  + ++ s ++++vk p+gk +++y+++k + ++Cg+ckk L+G+++  +    + skt+k+++R YGg+lc+kc+++ i+ 
  gi|70606386|ref|YP_255256.1|  5 QQRSGSFRKVFVKLPSGKSTIHYERRKDNIARCGMCKKPLNGVKNNYTY---KYSKTEKRPERVYGGYLCHKCLESLIKM 81
                                  567899*************************************976655...55899******************99975 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   1.6e-05     0.047      12      37 ..      23      47 ..      22      48 .. 0.87
   2 !    5.9   0.2    0.0039        12      22      30 ..      58      74 ..      50      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                Zn_ribbon_SprT 12 reythhlsirrhnYrCrrCkgtLrgk 37
                                  +++++++++++ + rC+ Ck  L+g+
  gi|70606386|ref|YP_255256.1| 23 STIHYERRKDNIA-RCGMCKKPLNGV 47
                                  567999***9999.9******99986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0039
                Zn_ribbon_SprT 22 rhn........YrCrrC 30
                                  +++        Y C++C
  gi|70606386|ref|YP_255256.1| 58 TEKrpervyggYLCHKC 74
                                  44445569999****** PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   4.1e-06     0.012       9      36 ..      30      57 ..      22      58 .. 0.85
   2 ?   -0.8   0.2      0.37   1.1e+03      18      24 ..      70      76 ..      67      80 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-06
                        zf-FLZ  9 tahfLsaCflCkkkLgegkDiymYrGdk 36
                                  +++ +  C++Ckk L+  k+ y Y++ k
  gi|70606386|ref|YP_255256.1| 30 RKDNIARCGMCKKPLNGVKNNYTYKYSK 57
                                  5667889******************976 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.37
                        zf-FLZ 18 lCkkkLg 24
                                  lC+k L+
  gi|70606386|ref|YP_255256.1| 70 LCHKCLE 76
                                  6666654 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00091       2.7      36      45 ..      35      44 ..      31      47 .. 0.86
   2 ?    6.9   0.2    0.0016       4.9      22      33 ..      69      80 ..      64      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00091
                                  SBETTTSSB- CS
                        zf-P11 36 erCpiCkkPL 45
                                   rC +CkkPL
  gi|70606386|ref|YP_255256.1| 35 ARCGMCKKPL 44
                                  69*******9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0016
                                  EEEHHHHHHHHH CS
                        zf-P11 22 YLClrClqllLs 33
                                  YLC +Cl+ l++
  gi|70606386|ref|YP_255256.1| 69 YLCHKCLESLIK 80
                                  *******98876 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.0   2.2e-05     0.065      13      32 ..      64      83 ..      37      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                  -SSS--EEHHHHHHHHHHS- CS
                           Gin 13 iilgkfICeeCekkivntev 32
                                  +++g ++C++C + ++++++
  gi|70606386|ref|YP_255256.1| 64 RVYGGYLCHKCLESLIKMTI 83
                                  69**************9986 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0007       2.1      17      40 ..      17      43 ..      14      45 .. 0.62
   2 ?    3.3   0.5     0.024        73       8      16 ..      70      78 ..      69      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0007
                zinc_ribbon_12 17 qlP..kk.flllkkkqqklrCGaCsev 40
                                  +lP  k  +   ++k +  rCG C++ 
  gi|70606386|ref|YP_255256.1| 17 KLPsgKStIHYERRKDNIARCGMCKKP 43
                                  6666322023345577788*****985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.024
                zinc_ribbon_12  8 vCsnCfelL 16
                                   C++C+e L
  gi|70606386|ref|YP_255256.1| 70 LCHKCLESL 78
                                  6*****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 580.95
//
Query:       gi|70606387|ref|YP_255257.1|  [L=65]
Description: hypothetical protein Saci_0572 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.5    8.2   9.4       0.24   11.5   3.1    1.9  2  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)


Domain annotation for each model (and alignments):
>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.1   1.4e-05      0.24      36      59 ..       2      25 ..       1      32 [. 0.89
   2 ?    0.7   0.4     0.033   5.8e+02      41      52 ..      43      54 ..      39      57 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.4e-05
                         SPC12 36 ltlyillagvvltllvvvPpWpfY 59
                                  l++ ++++g++l l ++vPp+ ++
  gi|70606387|ref|YP_255257.1|  2 LMMATYIVGLFLILYLIVPPYVYF 25
                                  799******************998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.033
                         SPC12 41 llagvvltllvv 52
                                  +l+ +++++lv+
  gi|70606387|ref|YP_255257.1| 43 TLIVYIVSFLVF 54
                                  344444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 483.15
//
Query:       gi|70606388|ref|YP_255258.1|  [L=194]
Description: adenylate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-34  118.8   0.0    2.8e-34  118.5   0.0    1.1  1  AAA_17           AAA domain
    4.2e-07   30.6   0.0    5.5e-07   30.2   0.0    1.2  1  AAA_18           AAA domain
      1e-05   25.3   0.2      0.089   12.5   0.0    2.9  3  Thymidylate_kin  Thymidylate kinase
    0.00022   21.2   0.3    0.00042   20.3   0.3    1.4  1  NTPase_1         NTPase
    0.00022   20.9   0.1    0.00032   20.4   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
    0.00043   20.1   0.2     0.0017   18.1   0.1    2.0  2  AAA_30           AAA domain
    0.00053   20.3   0.0    0.00072   19.8   0.0    1.3  1  AAA_22           AAA domain
    0.00086   18.4   0.1     0.0014   17.7   0.1    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0024   18.3   0.0     0.0028   18.1   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0027   17.5   0.0     0.0035   17.1   0.0    1.2  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0038   16.7   0.0     0.0053   16.2   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.025   14.8   0.0    1.5  2  AAA_28           AAA domain
      0.013   15.5   0.1      0.034   14.2   0.1    1.7  1  AAA_14           AAA domain
      0.051   13.5   0.1       0.11   12.4   0.1    1.5  1  APS_kinase       Adenylylsulphate kinase
      0.072   13.2   0.1        0.2   11.8   0.1    1.8  1  AAA_33           AAA domain
      0.077   12.2   0.1      0.098   11.9   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.17   11.6   0.0       0.24   11.1   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   2.6e-37   2.8e-34       1     134 [.       7     148 ..       7     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 2.6e-37
                                   EE-TTSSHHHHHHHHHHHH.....TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH...HSSE CS
                        AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea...kkkg 73 
                                   +G+PG+GK+t+++k++e +     + +++++Gd + ++a + g ak+rdemrkl+ e++k+lq  aa+ iaeea   +++ 
  gi|70606388|ref|YP_255258.1|   7 TGIPGVGKSTVLAKVKEILdnqgiNNKIINYGDFMLATALKLGYAKDRDEMRKLSVEKQKKLQIDAAKGIAEEAragGEGY 87 
                                   7**************97444444499***********************************************96655555 PP

                                   EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHH CS
                        AAA_17  74 vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddnees 134
                                   + +d+h++i++++g+l+glp+ v++e++p++i+lleadp+ il+r ++d+tr+r d + es
  gi|70606388|ref|YP_255258.1|  88 LFIDTHAVIRTPSGYLPGLPSYVITEINPSVIFLLEADPKIILSRQKRDTTRNRNDYSDES 148
                                   8*****************************************************9998887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   5.2e-10   5.5e-07       2     120 ..       5     143 ..       5     155 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.2e-10
                        AAA_18   2 lltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpealdeskrldedkldkl.ldaleenss.. 69 
                                   ++tG+pGvGK+t+   +++ l +          g+    +a + g+  ++d+      ++l  +k++kl +da +++++  
  gi|70606388|ref|YP_255258.1|   5 IVTGIPGVGKSTVLAKVKEILDNqginnkiinyGDFMLATALKLGYAKDRDEM-----RKLSVEKQKKLqIDAAKGIAEea 80 
                                   79***************999866688889444444444444454444444444.....33333333332122222222243 PP

                        AAA_18  70 aleegknlvidghlaeleseaakdikk............vvLtaspeelleRlekRgyeeaki 120
                                   + + ++ l id h +   +  +  +              + L+a+p++ l R +++ ++++  
  gi|70606388|ref|YP_255258.1|  81 RAGGEGYLFIDTHAVIRTPSGYLPGLPsyviteinpsviFLLEADPKIILSRQKRDTTRNRND 143
                                   35888889*******99999999988799***********************88777665543 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   8.5e-05     0.089       3      26 ..       8      31 ..       6      37 .. 0.89
   2 ?    1.0   0.0      0.28     3e+02     136     175 ..      52      93 ..      39      98 .. 0.77
   3 !    8.5   0.0    0.0014       1.5     117     152 ..     115     150 ..     106     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                                  ESTTSSHHHHHHHHHHHHHHTTE. CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik 26
                                  G+ G+GK+t+++++ke l+++gi+
  gi|70606388|ref|YP_255258.1|  8 GIPGVGKSTVLAKVKEILDNQGIN 31
                                  999*******************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.28
                                   CTTSS.TTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEETT CS
               Thymidylate_kin 136 akrde.ldeeeeeqldflrkvrerylelak.ederiliidas 175
                                   ++rde ++  +e+q++ +    ++  e+a+   e +l id+ 
  gi|70606388|ref|YP_255258.1|  52 KDRDEmRKLSVEKQKKLQIDAAKGIAEEARaGGEGYLFIDTH 93 
                                   455555678899999999999999999999888888888876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0014
                                   E-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHH CS
               Thymidylate_kin 117 kPdltflldvdpevalkRlakrdeldeeeeeqldfl 152
                                    P ++fll+ dp++ l R ++  +++++++ ++++ 
  gi|70606388|ref|YP_255258.1| 115 NPSVIFLLEADPKIILSRQKRDTTRNRNDYSDESVI 150
                                   899******************999999999888765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3     4e-07   0.00042       3      29 ..       5      31 ..       4      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4e-07
                                  EEE--TTSSHHHHHHHHHHHH...GGG CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvk 29
                                  ++TG pGvGK+T++ kv e l+++g++
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKVKEILDNQGIN 31
                                  69********************99975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1     3e-07   0.00032       4      93 ..       4      94 ..       1     136 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHHHTTSS CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeavekakeekid 85
                                   ++ G+ G+GK t laK+ ++l ++g +  ++    f  a +  L    ++ +++ ++ +k+++ +++ ak   e+a++ +  
  gi|70606388|ref|YP_255258.1|  4 GIVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLATALKLGYAKDRDEMRKLSvEKQKKLQIDAAKGIAEEARAGGEG 86
                                  5789*********************9999999988888888889*999999999988866777788999999999999999** PP

                                  EEEEEE-- CS
                         SRP54 86 vvlvDTaG 93
                                  ++++DT  
  gi|70606388|ref|YP_255258.1| 87 YLFIDTHA 94
                                  ******75 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.7e-06    0.0017      20      47 ..       3      32 ..       1      85 [. 0.86
   2 ?   -0.2   0.0      0.66     7e+02     129     157 ..     164     192 ..     161     194 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                        AAA_30 20 vavltGpAGtGKttalkalreaweaag..g 47
                                  + ++tG +G GK+t+l++++e+++++g   
  gi|70606388|ref|YP_255258.1|  3 IGIVTGIPGVGKSTVLAKVKEILDNQGinN 32
                                  5699********************998553 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.66
                        AAA_30 129 asVeaGgvlrdlveaagigtaeLtevvRq 157
                                   ++V aG++++ +v+ +g +++  +e++R 
  gi|70606388|ref|YP_255258.1| 164 SAVLAGSTVKVIVNVEGDPSIAANEIIRS 192
                                   6999*********9999999999999995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.9e-07   0.00072       6      33 ..       2      29 ..       1      82 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.9e-07
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqldeea 33
                                  +i++vtG +G+GK+t+l++++e ld++ 
  gi|70606388|ref|YP_255258.1|  2 KIGIVTGIPGVGKSTVLAKVKEILDNQG 29
                                  589*******************999764 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.3e-06    0.0014      32      62 ..       3      34 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                  EE.EEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                          MeaB 32 vG.ltGvPGaGkstlvealglelrrrGkrvav 62
                                  +G +tG+PG+Gkst++ ++ + l ++G    +
  gi|70606388|ref|YP_255258.1|  3 IGiVTGIPGVGKSTVLAKVKEILDNQGINNKI 34
                                  5636*******************999976555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.7e-06    0.0028      28      91 ..       5      60 ..       2     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                        AAA_16 28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaes 91
                                  +++G +GvGKs+++ ++++ l  +g   ++ k   ++      +la+al + ++ ++ +++ + 
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKVKEILDNQG---INNKIINYGDF----MLATAL-KLGYAKDRDEMRKL 60
                                  79****************9888885...44444444222....455555.44666665555333 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0035       1      31 [.       6      36 ..       6      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                    ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvN 31
                                  v+G +G+GK+t   ++ eil+++g + +++N
  gi|70606388|ref|YP_255258.1|  6 VTGIPGVGKSTVLAKVKEILDNQGINNKIIN 36
                                  89****************************9 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06    0.0053       5      43 ..       5      43 ..       1      71 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                  EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.T CS
                         KTI12  5 vltGlPssGKstrakeLakaleeekrsvvviddeslgie 43
                                  ++tG+P +GKst+ +++++ l +++++  +i+   + ++
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKVKEILDNQGINNKIINYGDFMLA 43
                                  89****************************997666533 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-05     0.025       3      83 ..       5      95 ..       4     104 .. 0.65
   2 ?   -2.6   0.0       5.5   5.8e+03     112     127 ..     119     139 ..     110     155 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                        AAA_28  3 vitGgestGKTtlleaLa....argyp..vv...pEaareileeklakgedalpwv..edllafaervleeqleeeaaaaank 74
                                  ++tG ++ GK+t+l++ +    ++g++  ++     +  + l+ ++ak++d++++   e+  ++++   ++ ++eea+a +++
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKVKeildNQGINnkIInygDFMLATALKLGYAKDRDEMRKLsvEKQKKLQID-AAKGIAEEARAGGEG 86
                                  589***********88884444446554233332333345555555777777775423333444443.234567888889*** PP

                        AAA_28 75 vlfcDrgll 83
                                  +lf+D+ ++
  gi|70606388|ref|YP_255258.1| 87 YLFIDTHAV 95
                                  ******875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.5
                        AAA_28 112 vfllppapei.....dddgeR 127
                                   +fll+ +p+i     ++d++R
  gi|70606388|ref|YP_255258.1| 119 IFLLEADPKIilsrqKRDTTR 139
                                   677777776642222233333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.2e-05     0.034       3      71 ..       2      91 ..       1     106 [. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                        AAA_14  3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderd.................kkladpe......kllelile 58
                                  ki ++tG+  vGK+t+l ++  e l    ++++ i y ++   +                  +     +      +  + i e
  gi|70606388|ref|YP_255258.1|  2 KIGIVTGIPGVGKSTVLAKVK-EILdnqgINNKIINYGDFMLATAlklgyakdrdemrklsvE-----KqkklqiDAAKGIAE 78
                                  6789************98873.44457779999999999988877454444333333222221.....011222233344444 PP

                        AAA_14 59 klkeekktylflD 71
                                  ++++ ++ ylf+D
  gi|70606388|ref|YP_255258.1| 79 EARAGGEGYLFID 91
                                  4322566667776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001      0.11       7      52 ..       6      51 ..       2      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                                  EESSTTSSHHHHHHHHHHHHHHTT--EEEEE.HHHHTTTTTTT--SS CS
                    APS_kinase  7 ltGlsgsGKstianalekkLvekgisvylLd.GdnvRhgLnkdLgfs 52
                                  +tG+ g GKst+  ++++ L ++gi+ ++++ Gd +      +Lg+ 
  gi|70606388|ref|YP_255258.1|  6 VTGIPGVGKSTVLAKVKEILDNQGINNKIINyGDFM-LATALKLGYA 51
                                  7***********************888777625543.3344456654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00019       0.2       3      84 ..       5      98 ..       3     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                        AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt............lrrrlfg...tdqqskt..dytrvldrlyqilnelarkals 68
                                  ++ G pG+GKst++ ++ + l+ + ++  +                      +d++  +     + ++  ++  +++a++a++
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKVKEILDNQGINNKIinygdfmlatalK-----LgyaKDRDEMRklSVEKQKKLQIDAAKGIAEEARA 82
                                  678************9987777776766666666666444320.....12233333222102222334455666777777777 PP

                        AAA_33 69 agrnvildatnlsrre 84
                                   g ++++  t +  r+
  gi|70606388|ref|YP_255258.1| 83 GGEGYLFIDTHAVIRT 98
                                  7777777666554444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   9.3e-05     0.098       3      70 ..       3      68 ..       1      91 [. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-05
                       DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke.ekkkkkeafeklssf 70
                                  + +VtG +G GK+ vl ++   l   +++  ++ ++  ++++l+   +l + + +++ +k ++ek +++
  gi|70606388|ref|YP_255258.1|  3 IGIVTGIPGVGKSTVLAKVKEIL---DNQGINNKIINYGDFMLATALKLGYAKdRDEMRKLSVEKQKKL 68
                                  669*************9987777...4444555555555555555555544443355555555555544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.24       2      18 ..       5      21 ..       4      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
               Viral_helicase1  2 vvhGvpGcGKStlirkl 18
                                  +v G+pG GKSt++ k+
  gi|70606388|ref|YP_255258.1|  5 IVTGIPGVGKSTVLAKV 21
                                  8***********99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1422.99
//
Query:       gi|70606389|ref|YP_255259.1|  [L=463]
Description: preprotein translocase subunit SecY [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-56  192.2  31.1    1.7e-56  191.8  31.1    1.2  1  SecY             SecY translocase
      8e-09   35.2   2.4      8e-09   35.2   2.4    2.9  3  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8  31.1   1.8e-60   1.7e-56       1     306 []      74     442 ..      74     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.8e-60
                                   BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......HH.HHHHHH CS
                          SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg......lalllivlq 74 
                                   ++ +LGI+P+it+++i+q+l ++   kl +++ + +eg+ k++q+++ l++++++v++  + + ++      l  +++v+q
  gi|70606389|ref|YP_255259.1|  74 TLAQLGIGPVITSGLIMQILvGS---KLINVDLTTQEGKSKFTQAEKALALIFIIVESSLFGYVFTratsniLLPIIVVVQ 151
                                   789*****************888...555555459***********************765544445799997789***** PP

                                   HHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS....-HHHH........................SS... CS
                          SecY  75 ltagtvllmwLgEqite.kGiGnGisllifagivarlp.kals....gliel........................ale.. 123
                                   l+++++++++L+E+i++ +G+G+G+sl+i+agi++ ++ +++     +                            +    
  gi|70606389|ref|YP_255259.1| 152 LIIASYIILLLDEMIQKgWGLGSGVSLFIMAGIMKVIFwNMFGivsvQ---SqnlpvgffpllvsyitsgrnlqeiV-Lnt 228
                                   **************************************5555555440...14445555555555555555444431.044 PP

                                   .....THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH........... CS
                          SecY 124 ....gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla........... 189
                                        + + l+ l++t+ +++l+vy+ ++++ ipv+ ++    +g ++++Pl+++y + iP+If+s+l a           
  gi|70606389|ref|YP_255259.1| 229 ssttPYQPDLIGLIATVGLTILIVYLVNTNIYIPVTTQRL---RGIRTTVPLNFLYVSSIPVIFVSVLGAdiqlfaslans 306
                                   55554559****************************9943...49***********************9988877777777 PP

                                   ......................HHHCCCCS.TCCCS..THHHHHHHHHHHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSC CS
                          SecY 190 ......................lpstiaqfllalls..psvlyvvlyvlliifFayfyteit.fnpkevaenlkksggfip 245
                                                         +p+++  +++   +  + ++y++++++l i+F ++++ ++ ++pk  ae++ +sg+ ip
  gi|70606389|ref|YP_255259.1| 307 isnsasgiltdianafffppqgVPHSVYALVV---DpvGAAIYAAVFIVLSIVFGMLWIDVAgLDPKTQAEQMIRSGIEIP 384
                                   66666664444444443333333444433222...3556689*************************************** PP

                                   TTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                          SecY 246 gir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                   g+r + + ++ +L+k++  + ++++l+++liav++++lg+  +g  +g +lL+++++a++++
  gi|70606389|ref|YP_255259.1| 385 GMRtNPRIIEGILSKYIYALGFFSSLIVGLIAVVATFLGT--YG--TGVGLLLAITIAMQYY 442
                                   ***999**********************************..66..9************996 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   2.4   8.9e-13     8e-09       1      35 []      38      73 ..      38      73 .. 0.95
   2 ?   -3.3   0.0      0.94   8.5e+03      12      20 ..     193     201 ..     192     203 .. 0.76
   3 ?    0.1   0.3     0.084   7.5e+02       1      11 [.     251     261 ..     251     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.9e-13
                                  HHHHHHCCSB-TT--SS.S-TCCHTTTCCCCTSSTT CS
               Plug_translocon  1 llYlvlsqiPLyGisss.sssDpfywlRaifAsnrG 35
                                  ++Yl+++ iPLyG++ss s   +f   ++ifAs++G
  gi|70606389|ref|YP_255259.1| 38 IVYLLMASIPLYGVTSSnSFLSNFLAQQIIFASSQG 73
                                  79*************666*****************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.94
                                   TT--SSS-T CS
               Plug_translocon  12 yGissssss 20 
                                   +Gi+s +s+
  gi|70606389|ref|YP_255259.1| 193 FGIVSVQSQ 201
                                   9**977776 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.084
                                   HHHHHHCCSB- CS
               Plug_translocon   1 llYlvlsqiPL 11 
                                   ++Ylv ++i++
  gi|70606389|ref|YP_255259.1| 251 IVYLVNTNIYI 261
                                   79***999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3070.36
//
Query:       gi|70606390|ref|YP_255260.1|  [L=144]
Description: 50S ribosomal protein L15 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-16   59.2   6.1    1.5e-15   58.0   6.1    1.6  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.035   13.7   0.0      0.046   13.3   0.0    1.2  1  RSRP            Arginine/Serine-Rich protein 1


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   6.1   1.6e-19   1.5e-15       2     127 ..      30     139 ..      14     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.6e-19
                                   GGGTSSTTTTTTTTT-..S--........S--.........---GGG..---EEEEHHHHHHTTTTGTTS.--.----EEE CS
                Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerle.la.deaeeid 76 
                                   G +gGr + G++k ++  + k  +g +  G++         Gf+n +++k  +++ l++L+e+id+++++ ++ ++++++d
  gi|70606390|ref|YP_255260.1|  30 GAQGGR-QIGMHKEKWswTVKfGEGwY--GKH---------GFRN-PTSKLVNAIGLRKLQEYIDNDKIKiEEeNGKKVVD 97 
                                   555555.56666666654333233345..666.........***8.558999*****************9544889***** PP

                                   GGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  77 leelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   l++           g+ K+lg g+l+ +l +k+ k+++kAke++++ GG+++
  gi|70606390|ref|YP_255260.1|  98 LAKY----------GYdKLLGGGNLRLPLVIKVAKATEKAKERVKEIGGEII 139
                                   ****..........***********************************997 PP

>> RSRP  Arginine/Serine-Rich protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.2e-06     0.046      91     214 ..       8     131 ..       2     140 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-06
                          RSRP  91 rsrrrryyresryeysrryyrsPsrsrsrsrsrsrgrsyyaiarGrryyGfgrtvyPeespr..yrersrtrsrsrtpirl 169
                                   +sr+ r yr   ++   +++   ++   r     + +  +++  G+ +yG    + P  +       r          i++
  gi|70606390|ref|YP_255260.1|   8 KSRKYRGYRTHGWGTKGQHRDRGAQ-GGRQIGMHKEKWSWTVKFGEGWYGKHGFRNPTSKLVnaIGLRKLQEYIDNDKIKI 87 
                                   4444444454444444333322222.222222223444477888888888888888777655223333333444566899* PP

                          RSRP 170 sekerkelleiakanaakalGvanldlPaslrevevakeasrgav 214
                                    e++ k+++++ak    k lG  nl lP  ++ v +a e+ +  v
  gi|70606390|ref|YP_255260.1|  88 EEENGKKVVDLAKYGYDKLLGGGNLRLPLVIK-VAKATEKAKERV 131
                                   ******************************99.666666655455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 946.26
//
Query:       gi|70606391|ref|YP_255261.1|  [L=156]
Description: 50S ribosomal protein L30 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   42.8   0.0    7.3e-11   41.8   0.0    1.6  1  Ribosomal_L30  Ribosomal protein L30p/L7e
     0.0077   16.5   0.1      0.022   15.0   0.0    1.8  2  DUF4368        Domain of unknown function (DUF4368)
  ------ inclusion threshold ------
      0.013   15.3   0.3       0.12   12.2   0.1    2.4  3  DUF1421        UBA-like domain (DUF1421)


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.2e-14   7.3e-11       3      51 .]       7      55 ..       5      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.2e-14
                                  EEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                 Ribosomal_L30  3 VtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                                  V+rir+ + +p+ +++tL +L+L+  + +  ++++  si+GmL++V+ +V
  gi|70606391|ref|YP_255261.1|  7 VIRIRGWAATPWYIQDTLSMLRLKNAFnAMIYPKD-SSIQGMLNLVSSYV 55
                                  9************************9999999999.***********998 PP

>> DUF4368  Domain of unknown function (DUF4368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.7e-06     0.022      11      51 ..      43      83 ..      39      97 .. 0.85
   2 ?   -3.0   0.1       1.6   9.4e+03      33      40 ..     148     155 ..     147     156 .] 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                       DUF4368 11 dvekFlalvrkytdieeLtpeilnelIekIeVheaekkdgk 51
                                  +++  l+lv  y++  eL  e l+ l++k e++  +k +++
  gi|70606391|ref|YP_255261.1| 43 SIQGMLNLVSSYVTWGELNDEGLRLLVSKLEISRGKKVNEE 83
                                  5677799***************************9997766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                       DUF4368  33 lnelIekI 40 
                                   +nelI++ 
  gi|70606391|ref|YP_255261.1| 148 INELIRRM 155
                                   68888875 PP

>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   7.7e+03      11      21 ..      36      47 ..      34      51 .. 0.72
   2 ?    0.3   0.0      0.11   6.6e+02      29      43 ..      77      91 ..      62      92 .. 0.78
   3 ?   12.2   0.1   2.1e-05      0.12      11      26 ..     141     156 .]     138     156 .] 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                       DUF1421 11 MGfrrDq.Vrsv 21
                                  M +++D  ++++
  gi|70606391|ref|YP_255261.1| 36 MIYPKDSsIQGM 47
                                  558999766666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                       DUF1421 29 GqpvDfNvvlDkLss 43
                                  G+ v    v DkL++
  gi|70606391|ref|YP_255261.1| 77 GKKVNEEYVKDKLNV 91
                                  6666667799***97 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.1e-05
                       DUF1421  11 MGfrrDqVrsvvqrmv 26 
                                    G+r+D++ ++++rmv
  gi|70606391|ref|YP_255261.1| 141 FGYRGDKINELIRRMV 156
                                   5**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1070.51
//
Query:       gi|70606392|ref|YP_255262.1|  [L=214]
Description: 30S ribosomal protein S5 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-20   71.5   0.2    7.8e-20   70.6   0.2    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    8.9e-19   66.7   0.1    3.2e-18   64.9   0.0    1.8  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.3  1  Hs1pro-1_N      Hs1pro-1 N-terminus


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.2   1.3e-23   7.8e-20       4      65 .]      57     118 ..      54     118 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.3e-23
                                   EEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                  Ribosomal_S5   4 kvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                    +++i  vqk+t++G   ++++l+v+G+ +G++ +G+gkak+ ++Ai+kAi++Ak  ++pv+
  gi|70606392|ref|YP_255262.1|  57 DIVDIGIVQKQTDAGELSRYKVLIVMGNMDGYISYGTGKAKQLRVAIQKAIRDAKMRIIPVR 118
                                   689*********************************************************96 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.22   1.3e+03       6      19 ..     109     122 ..      93     123 .. 0.68
   2 !   64.9   0.0   5.4e-22   3.2e-18       2      65 ..     140     204 ..     139     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                                   TEEEEEEE--TT-- CS
                Ribosomal_S5_C   6 avkvllkpaprGtG 19 
                                    +k++++p  rG G
  gi|70606392|ref|YP_255262.1| 109 DAKMRIIPVRRGCG 122
                                   46777777777766 PP

  == domain 2  score: 64.9 bits;  conditional E-value: 5.4e-22
                                   EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                   gk g+v+v+l pap+GtG+++g + ++ l laG kDv+++++g + +  n++kA++ AL +++ +
  gi|70606392|ref|YP_255262.1| 140 GKAGSVEVTLLPAPKGTGLVVGSVLKTFLSLAGLKDVWSRTKGsTYTHENFIKAAYIALYNTYRF 204
                                   9******************************************9999**************9976 PP

>> Hs1pro-1_N  Hs1pro-1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.8e-06     0.029      51      93 ..     165     207 ..     150     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-06
                    Hs1pro-1_N  51 eqylrLpeLrklwksrefPeWknepllkPaLqaLeitfRlvsv 93 
                                    ++l L+ L+ +w++ +   +++e  +k a  aL  t+R+v+ 
  gi|70606392|ref|YP_255262.1| 165 KTFLSLAGLKDVWSRTKGSTYTHENFIKAAYIALYNTYRFVTP 207
                                   5799************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1519.34
//
Query:       gi|70606393|ref|YP_255263.1|  [L=197]
Description: 50S ribosomal protein L18 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-24   85.2   5.1      8e-18   65.0   1.8    2.4  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    3.8e-10   40.6   0.0    5.7e-10   40.0   0.0    1.3  1  Ribosomal_L18_c  Ribosomal L18 C-terminal region


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   1.8   8.9e-22     8e-18       2      98 ..       6      96 ..       5     101 .. 0.93
   2 !   21.3   0.1   2.3e-08   0.00021     131     161 ..     102     132 ..      96     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 8.9e-22
                 Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgltnya 83
                                  ++++kfrrrregktdYy+r   +i++         R+v r+tnk +i+ + +   +gd ++a+a+s el  kyg k   +n  
  gi|70606393|ref|YP_255263.1|  6 NYRIKFRRRREGKTDYYTRYTYVINNA-------IRFVPRLTNKYVIVSVSKFDQKGDIMIAYAHSIELVkKYGWKGDTNNTP 81
                                  599********************9765.......79********************************9549*********** PP

                 Ribosomal_L5e 84 aaYatglllarrllk 98
                                  aaY+tg+l + r++k
  gi|70606393|ref|YP_255263.1| 82 AAYLTGYLAGLRAVK 96
                                  ********9988765 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.3e-08
                 Ribosomal_L5e 131 aiLdvGLartttgakvfgalkgavdgglsip 161
                                   a+ d+GL    +g ++f+++kga+d+gl++p
  gi|70606393|ref|YP_255263.1| 102 AVSDIGLFVPVKGGRIFAVIKGAIDAGLKVP 132
                                   667***************************9 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   6.3e-14   5.7e-10       4      60 ..     139     195 ..     137     197 .] 0.96

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 6.3e-14
               Ribosomal_L18_c   4 lrkrIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIredp 60 
                                   l++r+ g h++ Y ++Lk+e++e y+k Fs+yi++g+++  l + ++++ ++I+e+ 
  gi|70606393|ref|YP_255263.1| 139 LKDRVNGSHISAYAQKLKNENQELYNKLFSSYIQRGLDPVLLPQHFEEVLNKIKENG 195
                                   799****************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1320.01
//
Query:       gi|70606394|ref|YP_255264.1|  [L=150]
Description: 50S ribosomal protein L19e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-48  164.6  10.3    1.6e-48  164.4  10.3    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4  10.3   9.1e-53   1.6e-48       2     143 ..       4     146 ..       3     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 9.1e-53
                                   THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHH.TT-S-SGGG--S CS
                Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkr.kgrrrgsGkrkG 81 
                                   ++lq+rlaa++ +vG n ++++pe+lee++eA tredi+klik+ ++i++pk+g s +r++erk+k+r kg+ r++G+rkG
  gi|70606394|ref|YP_255264.1|   4 FQLQRRLAADIAGVGLNNIKFNPERLEEVEEALTREDIKKLIKERAVIVNPKRGISSGRLKERKHKRRsKGEGRKHGSRKG 84 
                                   689************************************************************999877************ PP

                                   -HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                Ribosomal_L19e  82 tkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                   +++aR+ +ke Wi++iR++Rr++++lr+++ idk+tYr lY++akG++fkn +++k+y++++
  gi|70606394|ref|YP_255264.1|  85 KSGARTGDKEIWINKIRKIRRYIRWLRDNNVIDKHTYRLLYKRAKGNYFKNLSDVKSYLRQM 146
                                   **********************************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1108.83
//
Query:       gi|70606395|ref|YP_255265.1|  [L=131]
Description: 50S ribosomal protein L32e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-35  122.4   0.0    1.2e-35  122.1   0.0    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.0   6.9e-40   1.2e-35       3     108 .]      23     130 ..      21     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 6.9e-40
                                   ----TTTTT-TTS-S..S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EE CS
                Ribosomal_L32e   3 kFirhqsdryvklke..swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaa 81 
                                   kF r+++d+y ++++   wrkprGidn +r ++kg+++ +kiGY+++k++rgl+psG++ +lV++vk+Le+    ++ +++
  gi|70606395|ref|YP_255265.1|  23 KFLRFDWDKYYRIGRqeRWRKPRGIDNAIRLELKGYQPKVKIGYRTDKQIRGLHPSGLRPILVKSVKDLEAFAKGKQDVII 103
                                   8************97779*************************************************************** PP

                                   EE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                Ribosomal_L32e  82 eiahsVsskkrkeiverAaelgikVtN 108
                                    i+++++ +kr+e++++A+elg+k++N
  gi|70606395|ref|YP_255265.1| 104 IISSTIGLRKRIELIKKAEELGLKIAN 130
                                   *************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 935.70
//
Query:       gi|70606396|ref|YP_255266.1|  [L=186]
Description: 50S ribosomal protein L6 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-29  101.6   7.8      3e-14   53.4   0.6    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
       0.12   12.4   0.7        1.5    8.8   0.0    2.6  3  TubC_N        TubC N-terminal docking domain
       0.26   11.6   2.4          8    6.8   0.3    2.9  3  CooT          CO dehydrogenase accessory protein CooT


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.6   5.1e-18     3e-14       1      72 [.      12      81 ..      12      85 .. 0.97
   2 !   52.3   1.5   1.2e-17   6.9e-14       1      76 []      97     171 ..      97     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.1e-18
                                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHH CS
                  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikG 72
                                  iP++v+vs+++ ++++v+Gpkge+  +++++  ++++ +++k+  ++++ ++++k+ l+ ++ ++i+nmi+G
  gi|70606396|ref|YP_255266.1| 12 IPDKVKVSLEN-NVLKVKGPKGEVIKDFSYAKGIRIQLNEGKIILETTFADRRKKA-LLYSIIAHIKNMITG 81
                                  8*********5.********************************************.**************9 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 1.2e-17
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                   +P+ v+vs++++q+ + +G+k+ ++++i +gv+v+vk     +++ivv+g+d+ +v    A+i+++++++ ++ + +++g
  gi|70606396|ref|YP_255266.1|  97 FPISVKVSGDEVQVSNLIGEKNIRRAKILPGVKVTVK-----GEDIVVEGSDIYNVaqtaANIESSTKIVGYDRRIFSDG 171
                                   8**********************************99.....************************************98 PP

>> TubC_N  TubC N-terminal docking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00025       1.5      13      31 ..      16      34 ..      14      41 .. 0.89
   2 ?    1.2   0.0     0.062   3.7e+02       9      21 ..      40      52 ..      33      54 .. 0.88
   3 ?   -3.5   0.0       1.8   1.1e+04      12      20 ..     127     135 ..     127     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                        TubC_N 13 IkLwleggrLrfrApkgal 31
                                  +k++le++ L+++ pkg +
  gi|70606396|ref|YP_255266.1| 16 VKVSLENNVLKVKGPKGEV 34
                                  9****************76 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.062
                        TubC_N  9 ealgIkLwleggr 21
                                  +a+gI+++l++g+
  gi|70606396|ref|YP_255266.1| 40 YAKGIRIQLNEGK 52
                                  689********98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.8
                        TubC_N  12 gIkLwlegg 20 
                                   g+k+ ++g+
  gi|70606396|ref|YP_255266.1| 127 GVKVTVKGE 135
                                   899999997 PP

>> CooT  CO dehydrogenase accessory protein CooT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.019   1.1e+02      49      61 .]      44      56 ..      18      56 .. 0.87
   2 ?    6.8   0.3    0.0013         8      24      48 ..     100     124 ..      99     140 .. 0.89
   3 ?   -2.1   0.0      0.79   4.7e+03      24      35 ..     129     140 ..     127     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
                          CooT 49 keidLvehkiile 61
                                   +i+L+e+kiile
  gi|70606396|ref|YP_255266.1| 44 IRIQLNEGKIILE 56
                                  6899******996 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                          CooT  24 kiepeedgvvltdifGeekevegkI 48 
                                   ++++ +d+v ++++ Ge+ + ++kI
  gi|70606396|ref|YP_255266.1| 100 SVKVSGDEVQVSNLIGEKNIRRAKI 124
                                   799**************99887888 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.79
                          CooT  24 kiepeedgvvlt 35 
                                   k++++++ +v++
  gi|70606396|ref|YP_255266.1| 129 KVTVKGEDIVVE 140
                                   788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1376.90
//
Query:       gi|70606397|ref|YP_255267.1|  [L=133]
Description: 30S ribosomal protein S8 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-23   81.1   0.1      1e-22   80.4   0.1    1.4  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.1   5.8e-27     1e-22       1     127 []       5     133 .]       5     133 .] 0.86

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 5.8e-27
                                   -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEEE-SB CS
                  Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklkrvsk 77 
                                   +p+a++l+++ N+e+++++++ + paskl+ ++l+v+++eGyi +fe+  + +  k  +++ +++nk  ++ i+    +  
  gi|70606397|ref|YP_255267.1|   5 NPLANALATLYNNEMRRNKQALItPASKLIISVLRVMQKEGYIGEFEYIdDGRAGKiiVQLLGRINK--CGPISPRYPLDY 83 
                                   599**************9999999************************8555544444777778887..*****9999999 PP

                                   TTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                  Ribosomal_S8  78 pgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                    g+    ++ +     + +Gi+i+sT+kGvm++++  ++k+GG  l yv+
  gi|70606397|ref|YP_255267.1|  84 NGLLRLPDYIRKYLPSKEIGIIIISTPKGVMSHRDGIREKIGGVTLGYVY 133
                                   8887555544444446789******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 865.77
//
Query:       gi|162139952|ref|YP_255268.2|  [L=54]
Description: 30S ribosomal protein S14 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-10   39.6   3.9    3.4e-10   39.5   3.9    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
    0.00019   21.1   0.5      0.027   14.2   0.0    2.1  2  zf-HYPF        HypF finger
     0.0087   16.0   1.8      0.012   15.6   1.8    1.2  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.042   13.5   1.0      0.058   13.1   1.0    1.2  1  zf-P11         P-11 zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   3.9   7.5e-14   3.4e-10       4      53 ..       5      53 ..       3      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 7.5e-14
                                   ----SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE- CS
                  Ribosomal_S14  4 klprnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKa 53
                                   k p   + +++ + C+ +G + +vi+k+gL  +R+cfRe A+    +G++K 
  gi|162139952|ref|YP_255268.2|  5 KPPAERRFGKGVQLCKRCGSRDSVIQKYGLylCRQCFREVAYP---MGFRKT 53
                                   67888999***********************************...9*9995 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   6.1e-06     0.027       8      33 ..       3      28 ..       2      29 .. 0.90
   2 !    5.6   0.1    0.0031        14       1      13 [.      36      48 ..      36      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                                   HHC-TTSTTTT-TT---TTTS--EEE CS
                        zf-HYPF  8 EykdpldRRfhaqfisCtnCGPrlsl 33
                                   +yk p+ RRf      C++CG r s+
  gi|162139952|ref|YP_255268.2|  3 KYKPPAERRFGKGVQLCKRCGSRDSV 28
                                   5999*****************99765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0031
                                   --HHHHHHHC-TT CS
                        zf-HYPF  1 lCedClrEykdpl 13
                                   lC +C rE+  p+
  gi|162139952|ref|YP_255268.2| 36 LCRQCFREVAYPM 48
                                   7*******98886 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.8   2.7e-06     0.012      12      44 ..       9      41 ..       8      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
                  Zn_Tnp_IS1595 12 alrWpngfv.CPhCgsrkayriktrglfqCkeCr 44
                                   ++r++ g+  C +Cgsr +  i++ gl+ C+ C 
  gi|162139952|ref|YP_255268.2|  9 ERRFGKGVQlCKRCGSRDSV-IQKYGLYLCRQCF 41
                                   689****777*****88655.55569*******5 PP

>> zf-P11  P-11 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0   1.3e-05     0.058       1      28 [.      15      41 ..      15      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                                   -SSSBTTTSS--SSEEE-SSSEEEHHHH CS
                         zf-P11  1 GplsCksCWfkdksLveCsdHYLClrCl 28
                                   G + Ck C    +s+++    YLC++C+
  gi|162139952|ref|YP_255268.2| 15 GVQLCKRCGS-RDSVIQKYGLYLCRQCF 41
                                   6789****75.6799************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 397.53
//
Query:       gi|70606399|ref|YP_255269.1|  [L=178]
Description: 50S ribosomal protein L5 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-24   84.9   0.0    6.9e-24   83.8   0.0    1.6  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
    2.7e-19   69.2   0.1    5.9e-19   68.2   0.1    1.6  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   9.3e+03      11      24 ..      34      47 ..      32      60 .. 0.69
   2 !   83.8   0.0   7.8e-28   6.9e-24       1      94 []      67     166 ..      67     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                Ribosomal_L5_C 11 ekmyefldkllevv 24
                                  +k+y+++++l+ v+
  gi|70606399|ref|YP_255269.1| 34 QKAYQLVQELTGVK 47
                                  67777777776654 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 7.8e-28
                Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak... 78 
                                   piGvk tLr++ ++efl+k+l +v  rl+      +ssfd+ GnvsfGi e++ +p+ +yd+++gifGmd++i++ ++   
  gi|70606399|ref|YP_255269.1|  67 PIGVKATLRRQAAVEFLKKVLPAVNFRLK------QSSFDNYGNVSFGIAEHVLIPGTRYDPEIGIFGMDVAITLVRPgyr 141
                                   8****************************......*******************************************877 PP

                Ribosomal_L5_C  79 .tde..........earallkelgipf 94 
                                      +          ++r ++ke++i+f
  gi|70606399|ref|YP_255269.1| 142 tM-KrkrkkasiprRHR-VTKEEAINF 166
                                   41.35678889997888.999999988 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1   6.5e-23   5.9e-19       1      57 []      10      63 ..      10      63 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 6.5e-23
                                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                  NvM+ + l+K+++n+gvGe+ge+   l+ka +  +e+tG kPv tk +ksi++F++R
  gi|70606399|ref|YP_255269.1| 10 NVMRRVVLDKVTVNIGVGESGER---LQKAYQLVQELTGVKPVYTKGRKSIREFGVR 63
                                  9**********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1255.19
//
Query:       gi|70606400|ref|YP_255270.1|  [L=244]
Description: 30S ribosomal protein S4e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-19   68.5   0.9    7.9e-19   67.4   0.2    2.0  2  Ribosomal_S4e  Ribosomal family S4e
    6.7e-13   48.1   0.2    1.4e-12   47.1   0.2    1.6  1  S4             S4 domain
    2.3e-05   24.4   0.2    4.3e-05   23.5   0.2    1.5  1  RS4NT          RS4NT (NUC023) domain
     0.0021   17.8   0.0     0.0045   16.8   0.0    1.5  1  S4_2           S4 domain
     0.0035   17.1   0.2      0.016   15.1   0.0    2.1  2  Rad60-SLD      Ubiquitin-2 like Rad60 SUMO-like
  ------ inclusion threshold ------
       0.05   13.6   0.0       0.16   12.0   0.0    1.9  1  KOW            KOW motif
       0.12   12.4   0.1       0.26   11.4   0.1    1.5  1  DUF5474        Family of unknown function (DUF5474)


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2   3.1e-22   7.9e-19       6      75 .]      95     169 ..      90     169 .. 0.95
   2 ?   -1.6   0.0         1   2.6e+03      31      44 ..     194     207 ..     192     235 .. 0.58

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.1e-22
                                   EEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.....STT-STTEEEEEETTTTEE CS
                 Ribosomal_S4e   6 rllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.....dpdikvnDtvkidleenkI 75 
                                   r+++d+ ++++ ++I+ e+akyK ++i +ktt k g++ql+++dGr+i+ +     + +  +  t+ki+l+e+kI
  gi|70606400|ref|YP_255270.1|  95 RIIPDNVRYLTTINISREDAKYKFVRIMNKTTLKSGVLQLNLEDGRNILLKgeelsQYNLPTLTTLKIELPEQKI 169
                                   9***********************************************9999998866699*************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                                   EECEEEEECCCEEE CS
                 Ribosomal_S4e  31 Kikkkttvkkgipq 44 
                                   Ki k+++ k +++ 
  gi|70606400|ref|YP_255270.1| 194 KISKIQLAKYKRIK 207
                                   55666665533332 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.2   5.3e-16   1.4e-12       2      48 .]      38      85 ..      37      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 5.3e-16
                                  EHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                            S4  2 RLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                  +L ++l + l+ + + reA+++I +G+VlV+Gkv++d++y+V+ +Dv+
  gi|70606400|ref|YP_255270.1| 38 PLAILLkYYLKAVDTTREAKRIIFDGKVLVDGKVRRDYKYPVGLMDVV 85
                                  6888889889************************************98 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   1.7e-08   4.3e-05       6      36 ..       3      33 ..       2      34 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.7e-08
                                  -EETTTS-TTS---SSSSSEE----SSSS-T CS
                         RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                  H+ r+ AP +  + kke++++++ ++GPHk+
  gi|70606400|ref|YP_255270.1|  3 HITRFEAPWFLKVGKKEYKWIIRSRAGPHKI 33
                                  88899*************************8 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06    0.0045       6      64 ..      35      94 ..      32      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                          S4_2  6 eyItLgqlLKl.aglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidgetiev 64
                                  e + L  lLK+ +++v++  eaK +i +g+V+v+G+v    +  +   dvVei+  +++v
  gi|70606400|ref|YP_255270.1| 35 ESVPLAILLKYyLKAVDTTREAKRIIFDGKVLVDGKVRRDYKYPVGLMDVVEIPSADLRV 94
                                  788899999963799*********************955444444444888888877776 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.1e-06     0.016      16      60 ..      32      75 ..      31      81 .. 0.92
   2 ?   -3.0   0.1       2.6   6.7e+03       7      24 ..     111     128 ..     106     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.1e-06
                                  EEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGS CS
                     Rad60-SLD 16 kVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedl 60
                                  k++++ ++  L+++y k++++ + +  r+iFDG+ L + ++  d+
  gi|70606400|ref|YP_255270.1| 32 KIQESVPLAILLKYYLKAVDTTR-EAKRIIFDGKVLVDGKVRRDY 75
                                  7899999****************.99**********998887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                   ESSS--EEEEEETTSBHH CS
                     Rad60-SLD   7 gkdgkevkikVkptttvs 24 
                                     d k  ++++ ++tt++
  gi|70606400|ref|YP_255270.1| 111 REDAKYKFVRIMNKTTLK 128
                                   556666788888888886 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.1e-05      0.16       5      26 ..     181     202 ..     178     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                                   EEESSSTTTTCEEEEEEEETTT CS
                           KOW   5 VkVvsGphkGktGkVvkvdqhk 26 
                                    ++++G+++G  Gk+ k+   k
  gi|70606400|ref|YP_255270.1| 181 AMIIGGRNAGLHGKISKIQLAK 202
                                   69****************9877 PP

>> DUF5474  Family of unknown function (DUF5474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.26      16      51 ..     108     146 ..      99     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                       DUF5474  16 nvsk.dviysy..lmnstcsnkgtiklnlesgkrlkqeg 51 
                                   n+s+ d  y +  +mn t  + g ++lnle g+ +  +g
  gi|70606400|ref|YP_255270.1| 108 NISReDAKYKFvrIMNKTTLKSGVLQLNLEDGRNILLKG 146
                                   55542666665337******************9864443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1744.78
//
Query:       gi|70606401|ref|YP_255271.1|  [L=134]
Description: 50S ribosomal protein L24 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-30  104.4   0.5    4.8e-30  103.9   0.5    1.2  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    3.6e-07   29.9   2.3    6.9e-07   29.0   2.3    1.5  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.5   5.3e-34   4.8e-30       1      82 []       3     117 ..       3     117 .. 0.99

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 5.3e-34
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxx RF
                 Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gvtrek 49 
                                   ss+++kqrK  +n p+h r kl++a+Ls++L ++yg++++ ir                                g+t++k
  gi|70606401|ref|YP_255271.1|   3 SSKPSKQRKLVYNLPNHLRYKLLTARLSEDLEKQYGIKRISIRkgdsvklmrgsqvgyegkvvevdrkrgrvaieGLTKKK 83 
                                   89******************************************************************************* PP

                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                 Ribosomal_L26  50 angttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                   a+gt+v+v++h+Skv+Itkl+  Dk+r +++erk
  gi|70606401|ref|YP_255271.1|  84 ADGTPVYVWVHASKVIITKLDTgDKERMDAIERK 117
                                   *********************************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   2.3   7.7e-11   6.9e-07       1      31 [.      46      76 ..      46      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.7e-11
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                  +Gd Vk ++G   G +GkVv+vd+++ rV +
  gi|70606401|ref|YP_255271.1| 46 KGDSVKLMRGSQVGYEGKVVEVDRKRGRVAI 76
                                  7*************************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 964.32
//
Query:       gi|70606402|ref|YP_255272.1|  [L=138]
Description: 50S ribosomal protein L14 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-36  124.8   0.1    2.2e-36  124.6   0.1    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
      0.039   14.2   0.0      0.066   13.5   0.0    1.3  1  PAS_3          PAS fold


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.6   0.1   2.4e-40   2.2e-36       2     122 .]      18     138 .]      17     138 .] 0.94

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.4e-40
                                   .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEE CS
                 Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvir 78 
                                   +q ++ + vaDNsgake+ +i ++g++    + ++a++ d ++vsv+k++p     +++ +kav+vr+++++rr+dG++i+
  gi|70606402|ref|YP_255272.1|  18 LQHNSSVVVADNSGAKEAVIIGIYGYRgvlrRVPFANIADLVMVSVRKGSP---DVRKQKFKAVIVRQRMPFRRPDGTWIS 95 
                                   688999******************999777555******************...6777889******************** PP

                                   ESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                 Ribosomal_L14  79 fddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                   f+dna+V++n +g+p+Gt++ gp+are++e+ ++ki+s+A++v+
  gi|70606402|ref|YP_255272.1|  96 FEDNAVVIINPDGTPKGTEVRGPIAREAAER-WPKIASVATMVI 138
                                   ******************************9.********9996 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.3e-06     0.066      56      83 ..      84     111 ..      62     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-06
                         PAS_3  56 yRirrkdGeyrwveararvirdengkpv 83 
                                     +rr+dG+++ +e+ a+vi + +g p 
  gi|70606402|ref|YP_255272.1|  84 MPFRRPDGTWISFEDNAVVIINPDGTPK 111
                                   558*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 995.11
//
Query:       gi|162139951|ref|YP_255273.2|  [L=108]
Description: 30S ribosomal protein S17 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-19   70.4   0.0    1.3e-19   70.0   0.0    1.1  1  Ribosomal_S17  Ribosomal protein S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   7.3e-24   1.3e-19       1      67 [.      37     104 ..      37     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 7.3e-24
                                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                    G+ + ++ ++T +V++e+ ++++kyk+y++rr+++++h +++  vk+GD V i+e+rP++k+++fv++
  gi|162139951|ref|YP_255273.2|  37 GKLIRARANRTGTVEREYIFYDSKYKRYERRRSRIHVHIPSCLeVKEGDNVIIGESRPIAKSISFVIL 104
                                    6778999**********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 797.30
//
Query:       gi|70606404|ref|YP_255274.1|  [L=69]
Description: hypothetical protein Saci_0589 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-11   41.8   0.0    7.7e-11   41.8   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   4.3e-15   7.7e-11      17      81 ..       2      64 ..       1      67 [. 0.93

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.3e-15
                                  ECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHH CS
                       UPF0086 17 rsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadR 81
                                  ++++p+lvg +G+V+++t+n++ i + +sr  +v K++ +F+++  +   + v G++l+ +p++R
  gi|70606404|ref|YP_255274.1|  2 NHTDPTLVGKEGLVIEDTENAFMIGS-NSRKILVIKQNGLFQIST-KGKIFVVPGTKLIGKPEKR 64
                                  5789********************98.9999**************.5888**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 483.53
//
Query:       gi|70606405|ref|YP_255275.1|  [L=69]
Description: 50S ribosomal protein L29 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-18   66.3   6.6    2.1e-18   66.0   6.6    1.1  1  Ribosomal_L29  Ribosomal L29 protein
     0.0011   19.2   1.3     0.0013   19.0   1.3    1.0  1  DUF29          Domain of unknown function DUF29


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   6.6   2.4e-22   2.1e-18       2      57 .]       7      62 ..       6      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.4e-22
                                  HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHHH CS
                 Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlrer 57
                                  elr+++ ++Lke+l+el+ +L++Lr+  ++g+l+n++ i+++RkdIARi+Tv+ e+
  gi|70606405|ref|YP_255275.1|  7 ELRKMDLKQLKERLNELEMQLLKLRVESRMGTLKNTASIKNTRKDIARILTVIGEK 62
                                  9*****************************************************98 PP

>> DUF29  Domain of unknown function DUF29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.3   1.4e-07    0.0013      33      86 ..       4      57 ..       2      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-07
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTHHHHHHHHHHHHHHHHHH-. CS
                         DUF29 33 EiedlgrsekrelesrlavllehlLkwqyqpekrsrswrseireqrkeieklle 86
                                  E+++l + + ++l++rl  l ++lLk++ ++   + +  ++i++ rk+i+++l 
  gi|70606405|ref|YP_255275.1|  4 EVDELRKMDLKQLKERLNELEMQLLKLRVESRMGTLKNTASIKNTRKDIARILT 57
                                  89999*************************999999**************9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 543.09
//
Query:       gi|70606406|ref|YP_255276.1|  [L=231]
Description: 30S ribosomal protein S3 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-22   79.6   1.8    1.8e-22   79.6   1.8    1.8  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    2.8e-15   55.9   1.7    4.1e-15   55.4   0.0    2.1  3  KH_2            KH domain
     0.0056   16.5   1.2       0.04   13.7   0.2    2.5  2  KH_1            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         1     6e+03       7      32 ..      10      36 ..       4      38 .. 0.52
   2 !   79.6   1.8   3.1e-26   1.8e-22       2      83 .]     101     183 ..     100     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                  TT--HHHHHHHHH.HHHHHCC-SEEEE CS
                Ribosomal_S3_C  7 krvsfRramkkai.rramkagakGiki 32
                                  ++++++ ++ + + ++  +a+  G++i
  gi|70606406|ref|YP_255276.1| 10 QKAAIKVMVDEYLaKQFYNAEYAGVEI 36
                                  455555555444313444677777777 PP

  == domain 2  score: 79.6 bits;  conditional E-value: 3.1e-26
                                   HHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEEE CS
                Ribosomal_S3_C   2 aeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGvk 80 
                                   a +lek+++fRra+  +irr+m++ga G++++vsG+L+ +e+a+ ek+keG+v++  ++l++ id+a+  a +k G++Gv+
  gi|70606406|ref|YP_255276.1| 101 AIALEKGYHFRRAAFITIRRIMSSGAVGAEVIVSGKLT-SERAKYEKLKEGTVYKsgQQLEKIIDRAIGIAMLKPGVYGVE 180
                                   678***********************************.****************************************** PP

                                   EEE CS
                Ribosomal_S3_C  81 VwI 83 
                                   V I
  gi|70606406|ref|YP_255276.1| 181 VVI 183
                                   *98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   6.9e-19   4.1e-15       2      69 ..      18      84 ..      17      90 .. 0.95
   2 ?   -3.6   0.0       1.7     1e+04      44      58 ..     156     163 ..     152     168 .. 0.53
   3 ?   -1.8   0.1      0.48   2.9e+03      18      32 ..     193     201 ..     177     210 .. 0.49

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 6.9e-19
                                  HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                          KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69
                                  ++e+la+++++a++++veI +t+ +++++i++++p ++IGkgG++ik++ + l+k ++ le+ ++ + 
  gi|70606406|ref|YP_255276.1| 18 VDEYLAKQFYNAEYAGVEIVKTPIGTRVIIYAGRPPLIIGKGGKTIKQLAQVLEKFFG-LENPQITVT 84
                                  679******************************************************8.****99875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                                   GHHHHHHHHHHHHHH CS
                          KH_2  44 Gsnikkigkelrkdi 58 
                                   G+ ++ki       i
  gi|70606406|ref|YP_255276.1| 156 GQQLEKI-------I 163
                                   4444443.......3 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.48
                                   EEEECCSCEEEEEEE CS
                          KH_2  18 veIertanrviivir 32 
                                   +e+++       v++
  gi|70606406|ref|YP_255276.1| 193 IELKE------KVEK 201
                                   33311......2333 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   6.7e-06      0.04      12      27 ..      53      68 ..      43      70 .. 0.88
   2 ?    0.7   0.1     0.081   4.8e+02      21      32 ..     117     127 ..     116     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                                  HHHHTGGGHHHHHHHH CS
                          KH_1 12 griIGkgGsnIkeIre 27
                                  ++iIGkgG++Ik++ +
  gi|70606406|ref|YP_255276.1| 53 PLIIGKGGKTIKQLAQ 68
                                  58***********976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.081
                                   HHHHHHHHHT-E CS
                          KH_1  21 nIkeIreetgak 32 
                                   +I++I++ +ga 
  gi|70606406|ref|YP_255276.1| 117 TIRRIMS-SGAV 127
                                   7999999.7663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1743.11
//
Query:       gi|70606407|ref|YP_255277.1|  [L=156]
Description: 50S ribosomal protein L22 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-27   95.8   0.4    2.2e-27   95.3   0.4    1.2  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.046   13.1   0.1      0.082   12.3   0.0    1.4  2  Cytokin-bind   Cytokinin dehydrogenase 1, FAD and cytokinin b


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.4   2.5e-31   2.2e-27       2     102 ..      20     153 ..      19     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 2.5e-31
                                   EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST...............................THHHHHHHHHH CS
                 Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk...............................aakfvlklLkn 49 
                                    ++n+  s++ l +v+++Irgm+++eA ++L++  ++k+                               a k+vlklL n
  gi|70606407|ref|YP_255277.1|  20 VIKNIDASVRDLYNVCKAIRGMNLKEAREFLNNvlEEKEalpfwryshgtshrsnisrkwkvksgrypkkAIKYVLKLLDN 100
                                   679******************************9877779***************************************** PP

                                   HHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                 Ribosomal_L22  50 aeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                   ae+na +kgld d+l I++i ++kg  lkr++ rA Gr ++  k  +hiev+l
  gi|70606407|ref|YP_255277.1| 101 AENNANSKGLDIDNLKIVHIAAHKGLVLKRYMTRAFGRSTRKYKYLSHIEVIL 153
                                   ****************************************************8 PP

>> Cytokin-bind  Cytokinin dehydrogenase 1, FAD and cytokinin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.37   3.4e+03      93     128 ..      25      57 ..      14      67 .. 0.52
   2 ?   12.3   0.0   9.2e-06     0.082     184     244 ..      78     135 ..      72     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                   HHHHHHHHTT--S-TT-EEEEEEEHHHHHTCCHHHH CS
                  Cytokin-bind  93 dkeveellkklsfveglvfekdvsYvdFLdRVkeee 128
                                   d +v++l +  + ++g+  ++     +FL+ V ee 
  gi|70606407|ref|YP_255277.1|  25 DASVRDLYNVCKAIRGMNLKEA---REFLNNVLEEK 57 
                                   4444444444444444443322...35666665554 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.2e-06
                                   GS-TTSS----SSSEEEEEEEEE--STS.CCHHHHHHHHHHHHHHHHHHTT--EEESS--- CS
                  Cytokin-bind 184 kwdertsavlpdeevfYlvglLrsakpakaeeleeleeqneeilefcekagikvkqYlphy 244
                                   kw+ + s   p++ + Y++ lL  a++  +++ + l+  n +i++++ ++g+ +k+Y+++ 
  gi|70606407|ref|YP_255277.1|  78 KWKVK-SGRYPKKAIKYVLKLLDNAEN--NANSKGLDIDNLKIVHIAAHKGLVLKRYMTRA 135
                                   66544.567899*************96..889999**********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1009.67
//
Query:       gi|70606408|ref|YP_255278.1|  [L=140]
Description: 30S ribosomal protein S19 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-32  111.3   0.9    1.9e-32  111.0   0.9    1.1  1  Ribosomal_S19   Ribosomal protein S19
  ------ inclusion threshold ------
      0.046   12.7   0.1      0.057   12.4   0.1    1.0  1  DDR             Diol dehydratase reactivase ATPase-like domai
      0.078   12.9   0.8       0.12   12.3   0.8    1.3  1  Myb_DNA-bind_7  Myb DNA-binding like


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.9   3.1e-36   1.9e-32       1      81 []      40     122 ..      40     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 3.1e-36
                                   .HHHSS.TTCCCHHHHHHHHHH.TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS--- CS
                 Ribosomal_S19   1 rslkkg.pfvqesllkkvrkak.aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpv 79 
                                   rslk+g + +q++ll+k+rk + + k+++vikth+R+++IlPemvgl+++VynGk+fv++++ +em+G +LgE+s+T k v
  gi|70606408|ref|YP_255278.1|  40 RSLKRGfSDKQRRLLEKIRKISrEGKQNKVIKTHVRNMVILPEMVGLRFAVYNGKEFVEFQVVPEMIGRYLGEYSITTKKV 120
                                   89*****************9996677******************************************************* PP

                                   -S CS
                 Ribosomal_S19  80 kh 81 
                                   +h
  gi|70606408|ref|YP_255278.1| 121 EH 122
                                   99 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.5e-06     0.057     236     304 ..      50     116 ..      41     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-06
                           DDR 236 edlslekirsvRreaKekvfvtnalRalkkvsptgnirdidfvvlvGgsalDfE.ipelvtdalaeygiv 304
                                   ++  lekir++ re K++ +++  +R +  +        + f v  G   ++f  +pe+++  l ey+i 
  gi|70606408|ref|YP_255278.1|  50 QRRLLEKIRKISREGKQNKVIKTHVRNMVILPEMV---GLRFAVYNGKEFVEFQvVPEMIGRYLGEYSIT 116
                                   56779**********************98776555...788************9459**********996 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8     2e-05      0.12      35      69 ..      32      66 ..      27      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                Myb_DNA-bind_7 35 klfpkrtrrqlKlKFkkEerknpeliekalkkrke 69
                                  kl+p+r+rr lK+ F+  +r+  e+i+k+ ++ k+
  gi|70606408|ref|YP_255278.1| 32 KLLPSRQRRSLKRGFSDKQRRLLEKIRKISREGKQ 66
                                  799*************************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1063.92
//
Query:       gi|70606409|ref|YP_255279.1|  [L=238]
Description: 50S ribosomal protein L2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-41  141.2   2.4    3.4e-41  140.4   2.4    1.4  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    6.2e-13   48.5   0.0    2.2e-12   46.8   0.0    2.0  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.4   2.4   3.8e-45   3.4e-41       2     123 ..      89     215 ..      88     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 3.8e-45
                                   SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT---- CS
                Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklg 82 
                                   +Gn+++++++peGt+++n+e+ +g+ggk+ar+aG+ya + +k g+kv +kl+S+++ +vs+++rAt+G++++g+  ek+l+
  gi|70606409|ref|YP_255279.1|  89 NGNIVEVGQLPEGTVICNVEKLKGDGGKFARAAGSYAVISGKAGNKVLIKLSSEKIVEVSQNARATVGIIAGGGFVEKPLL 169
                                   7*****************************************9************************************** PP

                                   STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSSTEE CS
                Ribosomal_L2_C  83 kAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkapvs 123
                                   kAg+++w+      ++p vrGvamn+v HphGGG  +++sr + vs
  gi|70606409|ref|YP_255279.1| 170 KAGNNYWKyrvraVKWPVVRGVAMNAVSHPHGGGLHQSVSRPSTVS 215
                                   ***********999*********************88888866665 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   2.4e-16   2.2e-12       1      75 [.      11      79 ..      11      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.4e-16
                                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
                  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                                  Gr+   +r+++++r g   ++y+ i+      + kgk+++i ++pg +Ap+  vk+ +g ++yi a++g+ vG+++
  gi|70606409|ref|YP_255279.1| 11 GRGGInFRSPSWRRVG--PARYPNIEG-----DHKGKIIDILHNPGVTAPVVKVKLDNGLQFYIPAVQGVAVGQEI 79
                                  899988**********..********9.....789***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1604.66
//
Query:       gi|70606410|ref|YP_255280.1|  [L=82]
Description: 50S ribosomal protein L23 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-13   49.5  11.1    3.1e-12   46.7  11.1    1.8  1  Ribosomal_L23  Ribosomal protein L23
     0.0031   17.6   0.7     0.0036   17.4   0.7    1.1  1  ASL_C          Adenylosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.026   14.4   0.9      0.034   14.0   0.8    1.4  1  TusA           Sulfurtransferase TusA
      0.033   14.2   0.6      0.039   14.0   0.6    1.3  1  Ubiquitin_4    Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7  11.1   6.9e-16   3.1e-12       2      81 ..       2      69 ..       1      74 [. 0.84

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 6.9e-16
                                  SEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS CS
                 Ribosomal_L23  2 vilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkeg 81
                                  +i++ + tEk++kl e+ n+++  V+++ +K +ik+ veklF VkVek+ntl+ ++ +k+             a+V+Lk++
  gi|70606410|ref|YP_255280.1|  2 IIKEFLATEKAVKLIESqNTLTIIVNRNTTKKDIKNEVEKLFSVKVEKINTLITPKGEKK-------------AYVKLKQE 69
                                  6888899*********9789*********************************9996655.............44444433 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7     8e-07    0.0036      21      84 ..      12      75 ..       3      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8e-07
                                  HHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHHHHHHHTTS-- CS
                         ASL_C 21 ahslialksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYeklkeltrgkki 84
                                  a  li  +++l+ + + +  ++ +++++++  +v  E i t++  +g +k+Y klk+  + +++
  gi|70606410|ref|YP_255280.1| 12 AVKLIESQNTLTIIVNRNTTKKDIKNEVEKLFSVKVEKINTLITPKGEKKAYVKLKQEYKASDV 75
                                  6678899999999999999*************************************98777665 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   7.5e-06     0.034      15      50 ..       7      42 ..       6      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
                                  HHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHH CS
                          TusA 15 lklkkalekleegevlevladdpaatediprfakkl 50
                                  l + ka++ +e++++l ++++  ++++di++ ++kl
  gi|70606410|ref|YP_255280.1|  7 LATEKAVKLIESQNTLTIIVNRNTTKKDIKNEVEKL 42
                                  7899**************************998875 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   8.7e-06     0.039       9      40 ..      18      49 ..      12      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.7e-06
                   Ubiquitin_4  9 dgeslevvvkqnatvkdLkkaierkvelklkr 40
                                  ++++l ++v++n+t kd+k+ +e+ ++ k ++
  gi|70606410|ref|YP_255280.1| 18 SQNTLTIIVNRNTTKKDIKNEVEKLFSVKVEK 49
                                  5789********************99876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1786  (0.0996151); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 627.39
//
Query:       gi|70606411|ref|YP_255281.1|  [L=266]
Description: 50S ribosomal protein L4P [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-36  125.0   0.1    3.4e-36  124.7   0.1    1.1  1  Ribosomal_L4  Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.023   15.0   0.1      0.046   14.0   0.1    1.5  1  DUF2149       Uncharacterized conserved protein (DUF2149)
       0.14   12.4   0.2       0.33   11.2   0.2    1.6  1  DUF3913       Protein of unknown function (DUF3913)


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   0.1   5.7e-40   3.4e-36       1     191 [.      23     258 ..      23     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 5.7e-40
                                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT---S CS
                  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgva 73 
                                   +eL p +F+ p+r+dli+r+++++ ++  q++++++ a++++s+   +++     G ARv++++       +p ++gG+ a
  gi|70606411|ref|YP_255281.1|  23 IEL-PLFFSYPVRKDLIRRVFLSEFTKSLQPKGRDPlAGKRTSA--LSFGI--NLGIARVPRVKgsgeaalAPNTVGGRLA 98 
                                   678.889*************************************..59999..99************************** PP

                                   S---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES......---.-S.........S--HHHHHHHHHHTT-..... CS
                  Ribosomal_L4  74 hgpkperdystklnkKvrrlAlrsaLsakakqglllvvd......nleple.........esktkelvellkklgl..... 134
                                   ++p++e++  +++n K+++l++ saL+a+a+ + +++++      n   ++         +sk+ke++ +lk++g+     
  gi|70606411|ref|YP_255281.1|  99 FPPTTEKRLVEEVNLKEKKLGIISALAATADPNFVKARGhrftsnN---VPiilvddfenISKAKEIMDILKSIGVvddik 176
                                   ***************************************8544321...33668899999*************88877777 PP

                                   .....................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHH CS
                  Ribosomal_L4 135 .....................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekle 190
                                                          k++Livvs++++ +v++a n+pgv+v++++ ++v +l+++ +    +++tks ++ l+
  gi|70606411|ref|YP_255281.1| 177 rvkeskgvragkgkmrgrryqIAKGPLIVVSNHKSPVVESASNIPGVNVVSANLVSVIHLAPGGHpgrlTIYTKSSINILR 257
                                   777777777777777777777688****************************************************99887 PP

                                   H CS
                  Ribosomal_L4 191 e 191
                                   +
  gi|70606411|ref|YP_255281.1| 258 Q 258
                                   5 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.6e-06     0.046      39      90 ..     154     206 ..     139     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                       DUF2149  39 tvvkkpgkekmeiivke..geelkkakesaekasgkGerlGtayrlkdGkliyV 90 
                                   + + k+++  m i+      +++k+ kes+ +  gkG+  G  y+ ++G li+V
  gi|70606411|ref|YP_255281.1| 154 ENISKAKE-IMDILKSIgvVDDIKRVKESKGVRAGKGKMRGRRYQIAKGPLIVV 206
                                   55555444.7777543323479999***************************99 PP

>> DUF3913  Protein of unknown function (DUF3913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   5.6e-05      0.33      19      53 ..     151     185 ..     144     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.6e-05
                       DUF3913  19 dnvPtiPriGekveilktvrtvtdikyvknGnnfr 53 
                                   d+   i +  e ++ilk++  v dik vk+    r
  gi|70606411|ref|YP_255281.1| 151 DDFENISKAKEIMDILKSIGVVDDIKRVKESKGVR 185
                                   666678888999*****************977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1966.32
//
Query:       gi|70606412|ref|YP_255282.1|  [L=342]
Description: 50S ribosomal protein L3P [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-73  247.9   0.0    1.8e-73  247.7   0.0    1.0  1  Ribosomal_L3  Ribosomal protein L3
  ------ inclusion threshold ------
      0.084   13.1   0.2       0.18   12.0   0.2    1.5  1  XhlA          Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.7   0.0     2e-77   1.8e-73       1     369 []       1     342 []       1     342 [] 0.89

  Alignments for each domain:
  == domain 1  score: 247.7 bits;  conditional E-value: 2e-77
                                   XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC CS
                  Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvet 81 
                                   m hrk + pr+gs G +prkRa++ ++  k +P  + +   kl +f+GyKaGmth+   +dkp+s+  +kev  +vt+ve+
  gi|70606412|ref|YP_255282.1|   1 MGHRKLSSPRRGSAGLRPRKRADEILPTPKNWPLVNLK-EPKLLGFIGYKAGMTHVYMIDDKPTSPNYGKEVYTPVTIVES 80 
                                   99*******************************98877.56899************************************* PP

                                   --EEEEEEEEE.EEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEE CS
                  Ribosomal_L3  82 ppmvivgvvgy.vetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvvr 161
                                   pp+  +++++y ++ +  l  l + wa+   ee   ++     k k  ++   +   + k++ +li+++l++i      +r
  gi|70606412|ref|YP_255282.1|  81 PPILGLALRAYhIDSKGELSVLVDYWAN--FEEGSLKYL----KRKITSLK--VDSSKMKEKLDLIQKNLNNITY----MR 149
                                   **********9445555578899****9..444444442....33333333..3333448888999999999987....9* PP

                                   EEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----S CS
                  Ribosomal_L3 162 viahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklp 242
                                   +++ t+   ++sl +K+++++Eiq++gG+i ++l++  + l k+++v++vFr+g+l+D+igvtkGkGf+Gv+kR+ v + p
  gi|70606412|ref|YP_255282.1| 150 LLVSTQPWLVPSLGKKRPEIVEIQIGGGSIQDQLNYGLSLLGKQIPVRDVFREGQLTDIIGVTKGKGFQGVIKRYSVVEFP 230
                                   ********************************************************************************9 PP

                                   T..TTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..T CS
                  Ribosomal_L3 243 r..kthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevk 321
                                   r  k+ +g Rk++a g+  ++   s v+++Gq G+h+Rte+nk+i++ig+               +ei+P GG v+yG vk
  gi|70606412|ref|YP_255282.1| 231 RwhKHRKGSRKIGARGPS-IS-TPSYVPQPGQLGFHRRTEYNKRIIKIGD-------------NVNEINPAGGIVNYGLVK 296
                                   844556669999988764.33.34569***********************.............5689************** PP

                                   SCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                  Ribosomal_L3 322 ndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                   n +++++Gsv G +kr + lr  +++  s++  +++   +++ as++g
  gi|70606412|ref|YP_255282.1| 297 NTYLVIEGSVLGSRKRPLFLRYPIRPSWSPESAPKI--TYVNLASQQG 342
                                   ************************************..8999999987 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     2e-05      0.18      10      45 ..     111     146 ..     110     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                          XhlA  10 etkldnleervdkleekaaeaeekiknleedlkkle 45 
                                   e+ l+ l+ +++ l+ ++++++ek++ ++++l++++
  gi|70606412|ref|YP_255282.1| 111 EGSLKYLKRKITSLKVDSSKMKEKLDLIQKNLNNIT 146
                                   678899999*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2375.94
//
Query:       gi|70606413|ref|YP_255283.1|  [L=250]
Description: hypothetical protein Saci_0598 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-23   82.5   0.1    6.5e-16   58.7   0.1    2.3  2  Methyltrn_RNA_3  Putative RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   3.6e-20   6.5e-16       2     108 ..      10     113 ..       9     140 .. 0.86
   2 !   21.6   0.0   7.2e-09   0.00013     173     286 .]     149     245 ..     134     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.6e-20
               Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhke 82 
                                   +s+++ +si +  ++le++ y++g I R+++iF+V+e++ +dd +++++     + ++  + +Y+ tPpY  k+ Fp+++ 
  gi|70606413|ref|YP_255283.1|  10 LSVVLFTSIFDTEKKLEEIIYKLGFIIRTLVIFRVSEVIWLDDLKNKKN----ITRIIKDVSNYALTPPY-GKKYFPIKRT 85 
                                   79999***************************************98874....679**************.7889****** PP

               Methyltrn_RNA_3  83 lkyaglLppldaphhlrsse..egeyre 108
                                   l  +gl+pp+++p h+ s++  ege+r+
  gi|70606413|ref|YP_255283.1|  86 LSKVGLIPPINIPSHVVSNDyvEGEIRK 113
                                   ****************644435555554 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 7.2e-09
               Methyltrn_RNA_3 173 lywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkkefkhllivfGg.vrgleaaleadeelklege 252
                                   +y GYs+++     +v    +++ + + +i++s++g++++ + +++++  e++ l++v+G  + gl +++           
  gi|70606413|ref|YP_255283.1| 149 YYDGYSIKFY----DVTYLNKIK-DIENVIIASRSGKDLSLVADKISSIYEQNGLTLVIGPpKGGLLKTM----------- 213
                                   7788888887....333334443.78889999**************888899*********677777777........... PP

               Methyltrn_RNA_3 253 kaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                     e+  ++ +n+vp+qg + +r EEa+  aL+lL
  gi|70606413|ref|YP_255283.1| 214 --ETTGHMLVNFVPKQGVKDVRAEEALYGALSLL 245
                                   ..34456899*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1878.49
//
Query:       gi|70606414|ref|YP_255284.1|  [L=1050]
Description: isoleucyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.5e-183  610.6   1.3   3.5e-183  610.1   1.3    1.2  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.9e-28   98.3   2.5    9.1e-28   97.1   2.5    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.2e-18   66.2   9.7    1.7e-06   27.1   0.0    5.1  4  tRNA-synt_1g   tRNA synthetases class I (M)
    0.00014   21.4   0.0     0.0017   17.9   0.0    2.6  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    0.00024   20.1   0.0    0.00067   18.7   0.0    1.7  1  tRNA-synt_1f   tRNA synthetases class I (K)
     0.0009   19.8   0.6     0.0029   18.2   0.6    1.9  1  NID            Nmi/IFP 35 domain (NID)
      0.005   17.2   1.7      0.061   13.7   0.1    3.1  3  PDZ_4          PDZ domain
  ------ inclusion threshold ------
      0.014   15.6   1.2      0.076   13.3   0.1    2.6  3  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.1   1.3  1.6e-186  3.5e-183       2     601 ..      14     632 ..      13     633 .. 0.94

  Alignments for each domain:
  == domain 1  score: 610.1 bits;  conditional E-value: 1.6e-186
                   tRNA-synt_1   2 lyekWeeedvfkkelekeke.kkefilvdgPPyvtG.slHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                   +++ W++++++kk +e +++ +k+f ++dgPPy     +HiG +++kt+kd + ry+r+ G++v+ +pG+D++Gl+ie + 
  gi|70606414|ref|YP_255284.1|  14 VLKYWDDNNIYKKLKEINEKnHKKFLFIDGPPYPSSpIPHIGTVWNKTIKDCILRYERLMGYSVKDQPGYDTHGLPIEVET 94 
                                   6899**********9988776999*********876268****************************************** PP

                   tRNA-synt_1  81 ekklgakekke.rkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgk 160
                                   ek+lg+k k e  +k+g+++f+ k++e++ + +++ ++++++lG+ +D++++y+T+++++  + + v+++ +++gl+y+g 
  gi|70606414|ref|YP_255284.1|  95 EKRLGIKSKAEiIEKVGVDNFISKCKEFAVNNSKSLTQNFRNLGIFMDWENPYFTFNNDYISNSWAVIKKAYERGLLYKGV 175
                                   *****9988652689****************************************************************** PP

                   tRNA-synt_1 161 klvnwstklktalselEv.eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...itkeklilae 237
                                   ++++w+ +++t+l++ Ev ey+d +d++i+v+f ++++ + +lvi+TTtP+Tl++++ v +n++++y+   + +e l++a+
  gi|70606414|ref|YP_255284.1| 176 HVLHWCSRCETTLADYEVsEYRDLEDPSIYVKFRVKGEPNRYLVIWTTTPWTLPANVFVMINKDFEYAdvrVGDEILVIAK 256
                                   ********************************************************************99999******** PP

                   tRNA-synt_1 238 allkslvkke..sekkiledergkeLegkevelpl.........vnrkipiiad.dyvdkeaGtGvVkiaPahdedDyevg 306
                                   +++k+l+k+   +e+kil+ ++g+eL g+e+e+pl          n++ +++ + + v+ ++GtG+V+ aP+h++ D+e+g
  gi|70606414|ref|YP_255284.1| 257 DRVKELMKEAriKEYKILRVYKGEELLGLEYEHPLadivsaqskINNHHKVLDGgEAVTLQEGTGLVHSAPGHGDVDFEIG 337
                                   *******98876777**************************99977777777666************************** PP

                   tRNA-synt_1 307 kkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkel 387
                                   kky+++v++ ++++g++t++ ++++g +v  a + ++++lk++ +ll+a+ki h +p+c+r k+p+i ra eqWf+ v++l
  gi|70606414|ref|YP_255284.1| 338 KKYDMPVVMLVNDKGEFTQDSGKYAGKYVRSASEEIISDLKQRSALLHASKIVHRYPVCWRCKTPLILRAIEQWFIAVSKL 418
                                   ********************************************************************************* PP

                   tRNA-synt_1 388 adaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkaleke 468
                                   +d+++ ++++v+++p+++++r+ +++++++dW+iSRqr+WG+++p++v ++ ++++v+  ++el +     ++  ++l++ 
  gi|70606414|ref|YP_255284.1| 419 KDHLMGEIDRVRWIPDWGKTRIGNMVKEVRDWVISRQRFWGTPLPIWVCSNCQNIIVVGGVDELSK--ISINQVPQDLHRP 497
                                   *********************************************************998888887..3333444555666 PP

                   tRNA-synt_1 469 akdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse 545
                                    +d++    +k  ge ++++dv DvWF+Sg  +f++lg  +  ++  ++  p d++leG D++rgW+ +l+ +++ l++++
  gi|70606414|ref|YP_255284.1| 498 WIDSVvvrcEKCGGEARRISDVADVWFDSGVAFFASLG--QDWRKRWSELGPVDLVLEGHDQLRGWFFSLLRTGVILMDKA 576
                                   666666755677799***********************..44578899999****************************** PP

                   tRNA-synt_1 546 PfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdinl 601
                                   P++ vlvhg+++de+Gr m Ks gN+++p++v++kyg d lRl+l+ +++ +d ++
  gi|70606414|ref|YP_255284.1| 577 PYEAVLVHGFMLDEQGREMHKSSGNYVEPSQVVSKYGRDTLRLWLLRNTTWEDAKF 632
                                   **********************************************9888888876 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   2.5     4e-31   9.1e-28       1     150 [.     681     829 ..     681     832 .. 0.91

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 4e-31
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPf 80 
                                   d w+ls++++ +kev ea++ey+ ++ a+++  f+++d++++yl+++++r ++e +++++   ++vl++vl+  l+ll+ +
  gi|70606414|ref|YP_255284.1| 681 DIWLLSRYYRMLKEVIEAMKEYKVHELANKVTAFIIDDISRFYLRVTRKRAWNEANDPDKIaMYYVLYHVLKGSLILLSTV 761
                                   67***************************************************99988855588***************** PP

                   Anticodon_1  81 mPfitEelwqr..eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                   +Pf++E+++ +  +e++    esi++++ pe k+e+ + e+ ee++e++kei+ a  ++r++ +ik +++lk 
  gi|70606414|ref|YP_255284.1| 762 IPFTAEKIYLDfvQERL----ESISMEKIPEiKEEFINSEI-EEAFEVAKEIIDAGLNARAKAGIKLRWPLKE 829
                                   *********44443333....*********98887778888.99*************************9654 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.5e-10   1.7e-06       8     135 ..      45     193 ..      41     196 .. 0.66
   2 !   13.2   0.0   1.2e-05     0.027     166     238 ..     393     463 ..     368     476 .. 0.80
   3 !   22.8   0.1   1.5e-08   3.4e-05     289     371 ..     554     637 ..     517     645 .. 0.68
   4 ?    3.1   1.7     0.015        33     314     390 ..     651     726 ..     639     727 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.5e-10
                                   B--SS-.--HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT...........TS.......-HHHHHHH CS
                  tRNA-synt_1g   8 pYangk.lHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke...........gv.......tpeelvek 69 
                                   pY++++ +H+G + +  + D++ Ry+rl g+ v    g D+hG pie++ ek+           +v       + +e++ +
  gi|70606414|ref|YP_255284.1|  45 PYPSSPiPHIGTVWNKTIKDCILRYERLMGYSVKDQPGYDTHGLPIEVETEKRlgikskaeiieKVgvdnfisKCKEFAVN 125
                                   56655428******9999******************************998753111111111122111111123344445 PP

                                   HHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                  tRNA-synt_1g  70 vheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                   ++++ ++ f++l+i  d  + + t +++  + + +++kk +e+gl+y++     +c ++e++l+d +v
  gi|70606414|ref|YP_255284.1| 126 NSKSLTQNFRNLGIFMDweNPYFTFNNDYISNSWAVIKKAYERGLLYKGVHVLHWCSRCETTLADYEV 193
                                   55666677777777555223344555666666667788888888888888888888888888888766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                                   ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 166 npksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    p++  +++  +++  e++f  +sk++++l   i++ +   ++  k+ + +++ke ++d+ isr+  wG p+P
  gi|70606414|ref|YP_255284.1| 393 YPVCWRCKTPLILRAIEQWFIAVSKLKDHLMGEIDRVR-WIPDWGKTRIGNMVKE-VRDWVISRQRFWGTPLP 463
                                   489999***9************************3333.4555566667777777.***************99 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 1.5e-08
                                   EGGGHHHHHTHHHHHHHH...TT----S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EE CS
                  tRNA-synt_1g 289 gkdiikFHtifwPaillg...aelklpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDld 365
                                   g d ++    f+  + +g    +    ++v +h+++   +g+ + kS g+ v +++++ ++  d+lR +l++++   +D++
  gi|70606414|ref|YP_255284.1| 554 GHDQLR--GWFFSLLRTGvilMDKAPYEAVLVHGFMLdEQGREMHKSSGNYVEPSQVVSKYGRDTLRLWLLRNTT-WEDAK 631
                                   555443..4444444444443445566899****986256899****************************9875.689** PP

                                   E-HHHH CS
                  tRNA-synt_1g 366 fswedf 371
                                   fsw+++
  gi|70606414|ref|YP_255284.1| 632 FSWKSL 637
                                   ***976 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.015
                                   -EEEE--EEE--------------HHHHHHHH-HHHH.HHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH CS
                  tRNA-synt_1g 314 kvvaheyltvegkKlSkSrgvvvkakealerldadll.RYylaaeapekkDldfswedfvervNseLadklgnlvnRv 390
                                    v+a+ y+ +++ K Sk   + +k  ++l+  d  ll RYy + ++  +   +++ +++ ++v + ++d++  +  Rv
  gi|70606414|ref|YP_255284.1| 651 YVFANTYMSLDEFKYSKYSYNDIK--DYLKLEDIWLLsRYYRMLKEVIEAMKEYKVHELANKVTAFIIDDISRFYLRV 726
                                   6999************99888775..555554443334********************************99988886 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.4e-07    0.0017      11     146 ..     205     354 ..     201     386 .. 0.63
   2 ?   -2.3   0.0       1.2   2.8e+03      72     108 ..     954     990 ..     949     992 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.4e-07
                 tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl......aekkkelaafieevkkksesereletkekeGv. 83 
                                    ++f+v+++ ++ l ++tt p tl    fv++ ++ + ++           k++    ++e+ k+ ++++ +  +  +G  
  gi|70606414|ref|YP_255284.1| 205 YVKFRVKGEpNRYLVIWTTTPWTLPANVFVMINKDFEYADVRvgdeilVIAKDR----VKELMKEARIKEYKILRVYKGEe 281
                                   578888888777888888888888888888888888887765442223333344....44444444444444444444443 PP

                 tRNA-synt_1_2  84 ftglkaihPit.....gek....ipiw.vanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                     gl+  hP+      ++k      +    + v  + gtg v + P+h + Dfe  kky++p+   ++ ++e 
  gi|70606414|ref|YP_255284.1| 282 LLGLEYEHPLAdivsaQSKinnhHKVLdGGEAVTLQEGTGLVHSAPGHGDVDFEIGKKYDMPVVMLVNDKGEF 354
                                   55566666654211112222222222214578999*****************************999976643 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                 tRNA-synt_1_2  72 ereletkekeGvftglkaihPitgekipiwvanyvlm 108
                                   +++++++e eG+  +l     +  +++ + v +y+l 
  gi|70606414|ref|YP_255284.1| 954 QEMSKEEEEEGIIRDLIRRIQFMRKQLSLNVNEYILL 990
                                   4567788999******99999999****999999996 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     3e-07   0.00067     225     320 ..     537     633 ..     535     645 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-07
                  tRNA-synt_1f 225 dwamrWaalg.VdfEpaGkDhaaaGgSvdvsskiaeilggeaPek..vvYelillkggekmssSkGnvltledwlevaepe 302
                                   dw  rW+ lg Vd+   G D     g +    +   il  +aP++  +v  ++l+++g++m++S+Gn++ ++++++ + ++
  gi|70606414|ref|YP_255284.1| 537 DWRKRWSELGpVDLVLEGHDQLR--GWFFSLLRTGVILMDKAPYEavLVHGFMLDEQGREMHKSSGNYVEPSQVVSKYGRD 615
                                   9999**99988999999***999..555555555678888999872246899999************************** PP

                  tRNA-synt_1f 303 vlrflilrrkPkkakkld 320
                                   +lr+ +lr+   +  k++
  gi|70606414|ref|YP_255284.1| 616 TLRLWLLRNTTWEDAKFS 633
                                   *****9997766666665 PP

>> NID  Nmi/IFP 35 domain (NID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.6   1.3e-06    0.0029       7      82 ..     901     978 ..     896     981 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                           NID   7 eeeVaqrilkkkkhkvelekkkvrvkvspvel.kelkklqvklevskrtvllsgipdvleldeeeleDkLe.ihFqke 82 
                                    ++Vaq i++k+ h+++++++++r+ +s v+l +e++k  v+ ++sk  vll++  + +e +e  ++D +  i F ++
  gi|70606414|ref|YP_255284.1| 901 SDKVAQDIVSKGYHEFNVDSENLRLDISHVNLvEEVEKGYVSARFSKGVVLLKQEMSKEEEEEGIIRDLIRrIQFMRK 978
                                   689***************************9735788999************87665566688889999944888776 PP

>> PDZ_4  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       7.5   1.7e+04      34      56 ..      13      36 ..       8      38 .. 0.68
   2 !   13.7   0.1   2.7e-05     0.061       5      54 ..     206     270 ..     203     277 .. 0.78
   3 ?    0.6   0.0      0.32   7.1e+02      32      94 ..     279     341 ..     273     350 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7.5
                                  EEEEE.TTEEHHHHHHTTS-TT-- CS
                         PDZ_4 34 ellef.dgkpvkevveelkesehk 56
                                  e+l++ d++++   ++e++e++hk
  gi|70606414|ref|YP_255284.1| 13 EVLKYwDDNNIYKKLKEINEKNHK 36
                                  666543777787777888877776 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.7e-05
                                   -SEEEEE-TTS-EEEEEE-S................SSSSS-TT-EEEEETTEEHHHHHHTTS-TT CS
                         PDZ_4   5 LPfkvkgsaeGryfivdide................eklelkvGDellefdgkpvkevveelkese 54 
                                   + f+vkg    ry ++++++                e  +++vGDe+l +    vke+++e + +e
  gi|70606414|ref|YP_255284.1| 206 VKFRVKGE-PNRYLVIWTTTpwtlpanvfvminkdfEYADVRVGDEILVIAKDRVKELMKEARIKE 270
                                   56899995.559999997766777776666665544559********************9988766 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
                                   T-EEEEET.TEEHHHHHHTTS-TT----HHHHHHHHHHHTEEEGGGT-----SEEEEEEEETTS CS
                         PDZ_4  32 GDellefd.gkpvkevveelkesehknsatdqslaevkLtsRegalgekvPqGpveikirkkkg 94 
                                   G+ell ++ ++p+ ++v+   + +++++  d     v+L   +g + +   +G v+ +i kk +
  gi|70606414|ref|YP_255284.1| 279 GEELLGLEyEHPLADIVSAQSKINNHHKVLDGG-EAVTLQEGTGLVHSAPGHGDVDFEIGKKYD 341
                                   89999987578*******999999999988888.345666666665555558888888887765 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2     5e+03      46      55 ..     179     188 ..     170     195 .. 0.86
   2 ?   -1.3   0.0       1.3   2.8e+03      44      56 ..     392     404 ..     363     413 .. 0.75
   3 ?   13.3   0.1   3.4e-05     0.076      47      90 .]     466     510 ..     462     510 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                                   TB-TTT--B- CS
                          Rpr2  46 tvCkkCgsvl 55 
                                   + C++C++ l
  gi|70606414|ref|YP_255284.1| 179 HWCSRCETTL 188
                                   5799999987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                   CCTB-TTT--B-- CS
                          Rpr2  44 krtvCkkCgsvli 56 
                                   +  vC +C++ li
  gi|70606414|ref|YP_255284.1| 392 RYPVCWRCKTPLI 404
                                   4469*****9998 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 3.4e-05
                                   B-TTT--B--CT.TTEEEEEE-SSS-E.........EEEEETTTT CS
                          Rpr2  47 vCkkCgsvlipg.vtcsvrvenkskkkkkkkkkadvlvvtClaCg 90 
                                   vC++C+++++ g v    ++  ++ ++  ++++ d++vv+C +Cg
  gi|70606414|ref|YP_255284.1| 466 VCSNCQNIIVVGgVDELSKISINQVPQDLHRPWIDSVVVRCEKCG 510
                                   8*****99877537777888778899999***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1050 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.86u 0.30s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 6164.42
//
Query:       gi|70606415|ref|YP_255285.1|  [L=337]
Description: 3-isopropylmalate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-91  306.6   0.5    2.6e-91  306.4   0.5    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
      0.015   14.7   0.1      0.038   13.4   0.0    1.6  2  PdxA      Pyridoxal phosphate biosynthetic protein PdxA


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   0.5   2.9e-95   2.6e-91       2     348 .]       5     332 ..       4     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 2.9e-95
                                   EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSHH CS
                        Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrpe 82 
                                   +al++gdgiGpevv++ + +l  ++ek  l +e+ ev++G  + ++ g++lp+++l +i++ad++l+g+vg          
  gi|70606415|ref|YP_255285.1|   5 VALIQGDGIGPEVVSKSKTILARLNEKFSLPIEYIEVEAGDTTKNKFGDALPKDSLRVIEKADMILKGPVGETA------A 79 
                                   899*******************************************************************9888......4 PP

                                   HHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHH CS
                        Iso_dh  83 ngLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeie 163
                                     +++Lr + dl+anlrp+k+++    +++      ++vd+++vRe+t+++Y g e+++++      v v++k+++++++ 
  gi|70606415|ref|YP_255285.1|  80 DVVVKLRLMYDLYANLRPAKSLPG--LENK-----FGDVDILVVRENTEDLYKGLEHVISDG-----VTVGIKVITRAAST 148
                                   45789*****************43..3333.....567***********************7.....89************ PP

                                   HHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHH CS
                        Iso_dh 164 riaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtkNlfGD 243
                                   ria++a++ Al+r kkkv++v+K+nv++ ++ l+ + + +v++   +++e+++++vD+aa++lv++p++fdVivt+N +GD
  gi|70606415|ref|YP_255285.1| 149 RIAQVALNQALRR-KKKVVCVHKSNVMRITDgLFAESCRNVLK---GKVEYSEMYVDAAAANLVRNPQAFDVIVTENTYGD 225
                                   *************.*****************************...9********************************** PP

                                   HHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHH......TTT-HHHHHHHHHHH CS
                        Iso_dh 244 ilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLry......slgleeaAdkiekAv 318
                                   ilSDea ++ GslG+ pSa++g ++  +fE+vHG+a diagk++aNp+a +lS+ +mL         +  ++aA+ + +A+
  gi|70606415|ref|YP_255285.1| 226 ILSDEAGQIAGSLGISPSANIG-DRKSLFEPVHGAAFDIAGKNIANPTAFLLSVGMMLDRmqelsgDIRYNNAAKSLRDAI 305
                                   **********************.789********************************8711111124568999******* PP

                                   HHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                        Iso_dh 319 ekvlea.givTkDlageaakevstsefgdav 348
                                    +v  + +++T D++g++    +t+e++ a+
  gi|70606415|ref|YP_255285.1| 306 YSVYSEgKYLTPDVGGSS----TTDEMISAI 332
                                   ****998999*******9....999998876 PP

>> PdxA  Pyridoxal phosphate biosynthetic protein PdxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.26   2.3e+03      35      79 ..     165     219 ..     134     236 .. 0.49
   2 ?   13.4   0.0   4.2e-06     0.038     256     277 ..     255     276 ..     252     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.26
                                   E...TEEEEEE.S......BTTB--HHHHHHHHHHHHHHHHHHHT..TSSSEEEE CS
                          PdxA  35 s...eelkvldve...v..eagkvsaesGaaalaslekAvelake..gevdalvt 79 
                                       ++ +v++++   +     +v + + +++  ++++A++ + +  + +d++vt
  gi|70606415|ref|YP_255285.1| 165 VvcvHKSNVMRITdglFaeSCRNVLKGKVEYSEMYVDAAAANLVRnpQAFDVIVT 219
                                   2334334444442232123444445555555666666655554431135566665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.2e-06
                                   ESS-S-TTCTTTT---THHHHH CS
                          PdxA 256 vDhGtafdiagkgkadekSlle 277
                                   + hG afdiagk++a+++++l 
  gi|70606415|ref|YP_255285.1| 255 PVHGAAFDIAGKNIANPTAFLL 276
                                   66***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2290.83
//
Query:       gi|70606416|ref|YP_255286.1|  [L=200]
Description: hypothetical protein Saci_0601 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-42  144.4   0.0    3.6e-42  144.1   0.0    1.0  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.1   0.0     2e-46   3.6e-42       1     174 [.      17     188 ..      17     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.1 bits;  conditional E-value: 2e-46
                                   EEEEEEEE-TT-EEEEEEEEEESSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEETTTCTT. CS
                        DUF447   1 yEvivtTksekrpnaaPiGvivkgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdsetkpakia 81 
                                   yEvi++T++++  n++PiG+i++g+++++r+++++ T++N+++n++++in+t Dp++f+  +++++++ +f+ +++   ++
  gi|70606416|ref|YP_255286.1|  17 YEVILGTNGVR-LNLSPIGIIREGQELKSRIYEDTLTFQNVMKNNKCSINITLDPFQFYYGFTNNIDKLRFRLMEE---VP 93 
                                   8********88.***********************************************************99985...89 PP

                                   EETT-SEEEEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC...SHHHHHHHHHHHHHHHH CS
                        DUF447  82 vlksaeawveveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi...edkeklleeieylssvi 159
                                   vl+++ +++  e++ +++d+++++++++ ++++++++++++++Rgd ++++++V+++Rl+i   ++++++l  iey++++i
  gi|70606416|ref|YP_255286.1|  94 VLENSLVILS-ELTPISRDQNPIIFKYNRLHVVSNAPVHQALSRGDFLLVDLLVHMSRLHIysqDQIKQYLPVIEYEIKTI 173
                                   *****98876.566678**********************************************99**************** PP

                                   HHH--HHHHHHHHHH CS
                        DUF447 160 kktggerekealell 174
                                   k+++++ +  + el+
  gi|70606416|ref|YP_255286.1| 174 KRLSPNLSGIIQELI 188
                                   *****9998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1299.64
//
Query:       gi|70606417|ref|YP_255287.1|  [L=240]
Description: haloacid dehalogenase-like hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-24   86.8   0.1    5.9e-24   85.1   0.1    1.7  1  HAD_2           Haloacid dehalogenase-like hydrolase
    2.9e-12   47.3   0.0    1.1e-11   45.5   0.0    1.8  1  Hydrolase       haloacid dehalogenase-like hydrolase
    8.5e-10   38.6   0.0    1.5e-09   37.7   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like
    0.00028   21.3   0.0    0.00054   20.4   0.0    1.4  1  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.032   13.8   0.0    1.1  1  Exo_endo_phos   Endonuclease/Exonuclease/phosphatase family
      0.032   14.3   0.0       0.24   11.5   0.0    2.3  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.077   12.4   0.0       0.12   11.8   0.0    1.3  1  DUF4159         Domain of unknown function (DUF4159)


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.1   2.3e-27   5.9e-24       1     178 []      13     213 ..      13     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 2.3e-27
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleey......gls.elseeelrkliglslrellrklgeseeeee.............. 60 
                                   i FD+D+Tl+   e+  +a++ ++++       ++s e+s++++ +l+            ++ +e++              
  gi|70606417|ref|YP_255287.1|  13 IFFDFDNTLVSFDEVEDNALHMVAKDIynfvkdNYSsEISQDKITELVISRA--------KKMNEDGiydrkswwksvldq 85 
                                   67********999999999988888774444443333444444444444444........333333344445557888888 PP

                         HAD_2  61 .....kieellrkyneekkk.kevkpydgvkelLeeLkeagyklgivTsksre..aveekleqlgiesyFdvivt.sedve 132
                                          eel+++ +       + +py+++ +lLe+Lk++g++lgi+T+++ e    +  l+++ + +yF+ iv+ +e+  
  gi|70606417|ref|YP_255287.1|  86 lnvsaESEELYQWTQLYWSIaSQNTPYEDALDLLEYLKKKGFRLGIITNSDGEggDKRLRLSRFPLLHYFNIIVIgGENNI 166
                                   8888844455454444433345689************************9665226777889*********9986156677 PP

                         HAD_2 133 kkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                   k+KPd +++   +ek++l +++++++GD p +D  aakkag+k+i v
  gi|70606417|ref|YP_255287.1| 167 KPKPDLQPFIISCEKFGLFSSQCLMIGDDPiKDCLAAKKAGLKSILV 213
                                   78******************************************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   4.2e-15   1.1e-11       1     210 []      10     207 ..      10     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.2e-15
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHH.ETTTE.....HHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxx.....xxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar...sgaltgfat.figrg.....ayaig 72 
                                   +k+++fD+d+TL+       +v + a             h  +k + ++ k+    +++ +++++ +i r           
  gi|70606417|ref|YP_255287.1|  10 VKAIFFDFDNTLVSFD----EVEDNA------------LHMVAKDIYNFVKDNyssEISQDKITElVISRAkkmneDGIYD 74 
                                   69***********666....344444............3333555555555555432222333331111112233244444 PP

                                   HHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  73 kpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraan 153
                                   ++ w+++      l++ + sa+s+   +  +   +++ ++ +++  ++++a +++++Lk++g++++++t+++ e  ++ ++
  gi|70606417|ref|YP_255287.1|  75 RKSWWKSV-----LDQLNVSAESEELYQWTQ---LYWSIASQNT--PYEDALDLLEYLKKKGFRLGIITNSDGEGGDKRLR 145
                                   55588888.....788888888777665555...9999999999..***********************999999997777 PP

                                   HTT...GGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                   xxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                     Hydrolase 154 qlG...ddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                          +yf++++ + ++    kp+ + +   +++++   ++++m+GD +  D  a+++Ag
  gi|70606417|ref|YP_255287.1| 146 LSRfplLHYFNIIVIGGENNiKPKPDLQPFIISCEKFGLFSSQCLMIGDDPIkDCLAAKKAG 207
                                   766679999966666655556*****************9999********999*******98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     6e-13   1.5e-09       4      74 ..     169     235 ..     166     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6e-13
                                   TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                   KP    +    e++g+ ++++lmiGD++  D ++A++aG+ks+LV + ++ +     +e  ++yv+++l+e
  gi|70606417|ref|YP_255287.1| 169 KPDLQPFIISCEKFGLFSSQCLMIGDDPIKDCLAAKKAGLKSILVDRKNKVK----FAELYADYVVNNLRE 235
                                   44444466678999999****************************8765544....345678999999987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.1e-07   0.00054       1     110 [.      13     135 ..      13     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                           HAD   1 alfDfDgTLldgdsle.....lllrfllrrgaprlwralreklllal............frellrldraglaelleallag 64 
                                   ++fDfD TL+  d  e     +         a++ +  ++  +   +            ++++ ++   +++  + + l +
  gi|70606417|ref|YP_255287.1|  13 IFFDFDNTLVSFDEVEdnalhM--------VAKDIYNFVKDNYSSEIsqdkitelvisrAKKMNEDGIYDRKSWWKSVLDQ 85 
                                   79*******9999777555541........333334444444444444334444444556666666666788888889999 PP

                           HAD  65 ls.eelaaelerfv......aevirpklldpgalellaahraaGdrvvvvSgg 110
                                   l+  +  +el ++       a+  +p   +++al+ll+  +++G+r+ +++++
  gi|70606417|ref|YP_255287.1|  86 LNvSAESEELYQWTqlywsiASQNTP---YEDALDLLEYLKKKGFRLGIITNS 135
                                   99999999999999888777666666...49********************86 PP

>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.032      20      98 ..       8     159 ..       3     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCH.................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                 Exo_endo_phos  20 drladlltaydaDvlgLQEvdddelsriplllalggflgasstsp.................................... 64 
                                   +++++++  +d  ++ + Ev d++l++++     ++f+  +++s                                     
  gi|70606417|ref|YP_255287.1|   8 RDVKAIFFDFDNTLVSFDEVEDNALHMVAKDI--YNFVKDNYSSEisqdkitelvisrakkmnedgiydrkswwksvldql 86 
                                   4588899888889*******************..*********************************************** PP

                                   ..............................................ECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSS CS
                                   ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos  65 ..............................................tgggggggnggavlsrfpltslfrrtfiefndlv 98 
                                                                                 t+  g gg++   lsrfpl +        fn+ v
  gi|70606417|ref|YP_255287.1|  87 nvsaeseelyqwtqlywsiasqntpyedaldlleylkkkgfrlgiiTNSDGEGGDKRLRLSRFPLLHY-------FNIIV 159
                                   *****************************************************************666.......33333 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.7e+03       1      21 [.      13      33 ..      13      45 .. 0.77
   2 ?   11.5   0.0   9.4e-05      0.24      11      42 ..     107     138 ..     100     148 .. 0.88
   3 ?   -1.5   0.0         1   2.7e+03      80      96 ..     186     202 ..     176     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
                                  EEEESTTTSEETTEE-TTHHH CS
                   Hydrolase_6  1 flfDidGvLwrgdkaipgaae 21
                                  ++fD d +L+ +d++ ++a  
  gi|70606417|ref|YP_255287.1| 13 IFFDFDNTLVSFDEVEDNALH 33
                                  589999999988877666554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.4e-05
                                   ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS CS
                   Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNnssk 42 
                                    ++++++ a ++l++l+++g ++ ++TN+ ++
  gi|70606417|ref|YP_255287.1| 107 SQNTPYEDALDLLEYLKKKGFRLGIITNSDGE 138
                                   5789************************9765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1
                                   XXEEEEESXHHHHHHHH CS
                   Hydrolase_6  80 dkkvlvigeeglreelk 96 
                                    +++l+ig +++++ l 
  gi|70606417|ref|YP_255287.1| 186 SSQCLMIGDDPIKDCLA 202
                                   68899999999888775 PP

>> DUF4159  Domain of unknown function (DUF4159)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.12      41      82 ..      87     127 ..      72     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                                   EE-TT-TTGGG-SEEEEEESS------HHHHHHHHHHHTT-E CS
                       DUF4159  41 gvdlsddeLfeyPllYltghgnvkfssaeakaLraYlrkGGf 82 
                                   +v  +++eL+++  lY+++ + ++++ ++a  L +Yl+k Gf
  gi|70606417|ref|YP_255287.1|  87 NVSAESEELYQWTQLYWSIAS-QNTPYEDALDLLEYLKKKGF 127
                                   78899*************976.566668888899*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1561.43
//
Query:       gi|70606418|ref|YP_255288.1|  [L=724]
Description: elongation factor EF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-62  210.6   0.1    2.3e-62  210.0   0.1    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.6e-29  100.7   0.1    4.5e-28   97.5   0.0    2.6  3  EFG_IV       Elongation factor G, domain IV
    2.9e-21   75.4   0.1    7.4e-21   74.0   0.1    1.8  1  EFG_II       Elongation Factor G, domain II
    3.2e-21   75.2   0.0      1e-20   73.6   0.0    1.9  1  EFG_C        Elongation factor G C-terminus
    1.1e-11   44.9   0.0    4.8e-11   42.9   0.0    2.1  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00018   21.5   0.2    0.00047   20.2   0.2    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.083   12.7   0.0    1.5  1  RF3_C        Class II release factor RF3, C-terminal domain
      0.081   13.2   3.3       0.19   12.0   3.3    1.7  1  CdiA_C       Contact-dependent growth inhibition CdiA C-termi


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.1     1e-65   2.3e-62       2     193 ..       6     246 ..       5     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 1e-65
                                   CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEESSS CS
                      GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDtPGH 80 
                                   r+rnigii+hvDhGKtT++d+Ll+++g+is+  ++a+e+ +lD l+ E++rgiT+k+a+isl++  ++k y inliDtPGH
  gi|70606418|ref|YP_255288.1|   6 RVRNIGIIAHVDHGKTTTSDTLLAASGIISQ--KVAGEALALDYLSVEQQRGITVKAANISLYHeiDGKGYVINLIDTPGH 84 
                                   79*****************************..9999999***********************557*************** PP

                                   GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH........ CS
                      GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk........ 153
                                   vdFs  v+r+lrvlDg ++v+daveG+++qte+vlr+ l+e+v++i+fiNK+Drl++elk + +e++++l +         
  gi|70606418|ref|YP_255288.1|  85 VDFSGRVTRSLRVLDGSIVVIDAVEGIMTQTETVLRQSLEERVRPILFINKVDRLIKELKLSSQEIQKRLIDLiievnnli 165
                                   **********************************************************************55577775555 PP

                                   ....HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHH.....................................HH CS
                      GTP_EFTU 154 ....eeklekygekge.........kevpvvfgSalkgegvk.....................................tl 184
                                       e          e         +  +vvfgSa++++g++                                     +l
  gi|70606418|ref|YP_255288.1| 166 etygE--------P-EfkdqwkikpELGNVVFGSAKDKWGFSvpmagkrgvkfsdvvnaytsgdkakieelaskvpiheAL 237
                                   55552........2.13555555557889**********999999999999999999999999999999******99999* PP

                                   HHHHHHHSH CS
                      GTP_EFTU 185 lealvellp 193
                                   l+a+++++p
  gi|70606418|ref|YP_255288.1| 238 LDAVIKFVP 246
                                   ***999988 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.9   6.4e+03      20      63 ..     227     270 ..     216     283 .. 0.66
   2 ?   -0.4   0.0      0.42   9.4e+02       3      39 ..     457     487 ..     455     502 .. 0.64
   3 !   97.5   0.0     2e-31   4.5e-28      11     120 ..     505     612 ..     498     613 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                                   CCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCH CS
                        EFG_IV  20 lkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyie 63 
                                   l+ + +++    + ++++ P++++s+   + ++  g +  e+ +
  gi|70606418|ref|YP_255288.1| 227 LASKVPIHEALLDAVIKFVPNPRDSQKYRIPKIWKGDLDSEIAK 270
                                   44446666666677888888887777666666666666665555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                                   CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECC CS
                        EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileieP 39 
                                   V yrE+ir++++ +e+k  +      +  k ++++eP
  gi|70606418|ref|YP_255288.1| 457 VVYRESIRNKSQVFEGKSPN------KHNKLYISVEP 487
                                   88999999999977665444......23445555555 PP

  == domain 3  score: 97.5 bits;  conditional E-value: 2e-31
                                   S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEE CS
                        EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLl 91 
                                   ++ ke++++l +q+++d ++ak+i++i+++     n+f+d+t+g+q+++e++++  +Gf+ a+keGpla epv++vkv+L+
  gi|70606418|ref|YP_255288.1| 505 MDNKEMAKILRDQAEWDYDEAKKIVAIDEN----INVFIDATSGVQHLREIMDTLLQGFRLAMKEGPLAFEPVRGVKVVLH 581
                                   78899************************7....8********************************************** PP

                                   EEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                        EFG_IV  92 dgslhe..vdsseaafkpaarralkeallkA 120
                                   d+++he   ++++a++ pa+r+a+ +++l++
  gi|70606418|ref|YP_255288.1| 582 DAVVHEdpAHRGPAQLYPAVRNAIFAGILTS 612
                                   **************************99987 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.1   3.3e-24   7.4e-21       1      74 [.     380     453 ..     380     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.3e-24
                        EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                   ++ePv+++++ep++ +d +k+ +aL++l+ ED  l v+ +eeT+e++lsGmG lHle+ ++ lk++y+++v ++
  gi|70606418|ref|YP_255288.1| 380 ISEPVVTISVEPRNPKDLTKMIDALRKLSIEDSNLVVKINEETGEYLLSGMGFLHLEVSLQLLKENYGLDVVTT 453
                                   689*******************************************************************9875 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   4.5e-24     1e-20       2      85 ..     616     698 ..     615     702 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 4.5e-24
                                   EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE-- CS
                         EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevp 82 
                                   llEP++k++i++p ey+g+v+  ++++rG+++++ q+ ++ +++ aeiP+ e++++a+eLr+ ++G++ + +efs++++vp
  gi|70606418|ref|YP_255288.1| 616 LLEPLQKLDIRIPMEYLGNVTAVITRKRGKVINVVQT-GNVARVYAEIPVGESFELASELRASSAGRAFWGTEFSRWAPVP 695
                                   8************************************.******************************************* PP

                                   HHH CS
                         EFG_C  83 gdk 85 
                                    ++
  gi|70606418|ref|YP_255288.1| 696 DSI 698
                                   986 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   2.2e-14   4.8e-11       1      72 [.     295     360 ..     295     361 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.2e-14
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                   G va+grv+sGtl+ G+ev++  +  +++    ri ++   ++  +e+ ++ ++G+i+a+ g + a + G+t
  gi|70606418|ref|YP_255288.1| 295 GLVATGRVFSGTLRAGEEVWL--VNAKRQ---QRILQVSLYMGAIRELAEEIPVGNIAAALGMDAA-RSGET 360
                                   679******************..777677...9********************************8.99998 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   2.1e-07   0.00047       2     113 ..      10     134 ..       9     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.1e-07
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGCSSHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke.....................ielvDtpGliega 60 
                                   ++i+ +   GK+t   +l+ +   i ++ +g  +   +  v+ +  +                     i+l+DtpG ++  
  gi|70606418|ref|YP_255288.1|  10 IGIIAHVDHGKTTTSDTLLAAsGIISQKVAGEALALDYLSVEQQ--RgitvkaanislyheidgkgyvINLIDTPGHVD-- 86 
                                   788889999*********99834566888899999999999822..2344555666666666666777********666.. PP

                                   HHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  61 seekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                         g+  ++l+  d  ++v+da e+ +++ +  l + lee+ +p il +n
  gi|70606418|ref|YP_255288.1|  87 ----FSGRVTRSLRVLDGSIVVIDAVEGIMTQTETVLRQSLEERVRP-ILFIN 134
                                   ....345555555568********99554555545555555545555.55555 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.7e-05     0.083      14      91 ..     388     465 ..     381     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                   EEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EEEEEE- CS
                         RF3_C  14 rvrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpyslarwves 91 
                                   +v+ ++p    ++  +l++L+ E    v k +e++ e++l+ +G L +eV  + lk+ Yg++v +++  + +   +++
  gi|70606418|ref|YP_255288.1| 388 SVEPRNPKDLTKMIDALRKLSIEDSNLVVKINEETGEYLLSGMGFLHLEVSLQLLKENYGLDVVTTPPIVVYRESIRN 465
                                   678889999999999***************99999***************************9988765555555544 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.3   8.6e-05      0.19       9      80 ..     467     536 ..     463     537 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.6e-05
                        CdiA_C   9 GevfDvKsptsgngkniisnilkkakkQaknivlnlr.dsdlsieeikegieralkwpkkglkeliiikkdgk 80 
                                   ++vf+ Ksp+     n+++  ++  ++Q+ + + n + ++d++ +e++++++   +w+ ++ k+++ i+ + +
  gi|70606418|ref|YP_255288.1| 467 SQVFEGKSPN---KHNKLYISVEPLNNQTIDLIANGTiKEDMDNKEMAKILRDQAEWDYDEAKKIVAIDENIN 536
                                   689*******...55999999999999**********99*****************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 5007.90
//
Query:       gi|70606419|ref|YP_255289.1|  [L=236]
Description: XPF/RAD1 repair endonuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-23   82.8   0.3    5.3e-23   81.9   0.3    1.5  1  ERCC4       ERCC4 domain
    9.8e-07   28.8   0.0    3.1e-06   27.2   0.0    1.9  1  HHH_2       Helix-hairpin-helix motif
    1.4e-06   28.8   0.1      1e-05   26.1   0.0    2.4  2  HHH_5       Helix-hairpin-helix domain
    0.00013   22.5   0.4    0.00031   21.3   0.1    1.7  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.049   13.7   1.1         40    4.4   0.0    3.9  4  z-alpha     Adenosine deaminase z-alpha domain
       0.29   10.7   5.5        1.7    8.2   0.4    2.2  2  DUF5039     Domain of unknown function (DUF5039)


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.3   1.8e-26   5.3e-23       2     156 .]       7     127 ..       6     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-26
                                   EGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHH CS
                         ERCC4   2 Dsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsr 82 
                                   D re +s+++++ l+elg+ v++e+l++ dy ++   + +               + +erks++dlv+s+ d+r+++q+sr
  gi|70606419|ref|YP_255289.1|   7 DYREKASNVPDF-LRELGAVVIFENLTVADY-VI---SET---------------IGIERKSVEDLVSSVFDKRFFDQLSR 67 
                                   899977******.******************.99...888...............************************** PP

                                   HHH.H-SEEEEEEES.-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHHHH CS
                         ERCC4  83 lkrngykkpillveg.ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewlanl 156
                                   l++ +yk p++l+eg l+q +                   +k++ saLv+  +d+++++l++ +++++ae+l++l
  gi|70606419|ref|YP_255289.1|  68 LSE-SYKEPYILIEGdLSQIRFIT--------------TKWKAVNSALVSAIIDYDLRVLFSLNKKDSAEVLYKL 127
                                   ***.***********766665543..............7788******************************986 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0     1e-09   3.1e-06       7      39 ..     161     193 ..     155     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1e-09
                         HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLle 39 
                                   ++++VGek Ak+L ++F++++++ kas+ +L +
  gi|70606419|ref|YP_255289.1| 161 SLPNVGEKLAKKLLEKFNTIENICKASISDLEK 193
                                   579***************************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.86   2.6e+03      22      31 ..      43      54 ..      32      69 .. 0.66
   2 !   26.1   0.0   3.4e-09     1e-05       5      52 ..     160     205 ..     157     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.86
                                  T--..SHHHHHH CS
                         HHH_5 22 Gie..svedlaa 31
                                  Gie  svedl++
  gi|70606419|ref|YP_255289.1| 43 GIErkSVEDLVS 54
                                  333335555554 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.4e-09
                                   HTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                         HHH_5   5 lsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAerii 52 
                                    s++ +G+k+A++ll++ ++++e +++a++ +L k+ G + k+Ae i 
  gi|70606419|ref|YP_255289.1| 160 ESLPNVGEKLAKKLLEK-FNTIENICKASISDLEKALG-SRKRAEEIY 205
                                   689**************.*****************843.667777775 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.9   1.2e+04      41      49 ..     121     129 ..     114     145 .. 0.48
   2 !   21.3   0.1     1e-07   0.00031      22      74 ..     161     209 ..     158     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.9
                    5_3_exonuc  41 leeilenld 49 
                                    e +++ ++
  gi|70606419|ref|YP_255289.1| 121 AEVLYKLAE 129
                                   333333332 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1e-07
                    5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenldelkekklkekLeenkeearlskkLa 74 
                                     p +Gek A+kLl++++++e+i ++   +++  l+++L   k   +++k L 
  gi|70606419|ref|YP_255289.1| 161 SLPNVGEKLAKKLLEKFNTIENICKAS--ISD--LEKALGSRKRAEEIYKVLH 209
                                   6799*********************43..333..5666666555555555554 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.1     3e+02       1      17 [.       7      23 ..       7      31 .. 0.91
   2 ?    4.4   0.0     0.013        40      22      48 ..     104     130 ..      91     135 .. 0.84
   3 ?    1.3   0.0      0.12   3.5e+02       6      27 ..     155     176 ..     151     182 .. 0.78
   4 ?    2.1   0.3     0.066     2e+02      11      43 ..     178     209 ..     167     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                                  HHHHHHHHHHHHHHHC- CS
                       z-alpha  1 iaqeqaekilelLeelg 17
                                  +++e+a+ + ++L+elg
  gi|70606419|ref|YP_255289.1|  7 DYREKASNVPDFLRELG 23
                                  689************99 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                                   CCHHHHHHHHCC-HHHHHHHHHHHHHT CS
                       z-alpha  22 atalalergLstpkreiNrvLydlerk 48 
                                      ++l    s +k++   vLy+l++k
  gi|70606419|ref|YP_255289.1| 104 IIDYDLRVLFSLNKKDSAEVLYKLAEK 130
                                   56677777778889*********9987 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHC-TTCECCHHHH CS
                       z-alpha   6 aekilelLeelgekkaatalal 27 
                                   +  ++e L ++gek a + l++
  gi|70606419|ref|YP_255289.1| 155 QLYVVESLPNVGEKLAKKLLEK 176
                                   556999******9999887766 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.066
                                   HHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHH CS
                       z-alpha  11 elLeelgekkaatalalergLstpkreiNrvLy 43 
                                   + +e++  k +   l++++g ++ + ei +vL 
  gi|70606419|ref|YP_255289.1| 178 NTIENIC-KASISDLEKALGSRKRAEEIYKVLH 209
                                   5789999.999999999999999999**99996 PP

>> DUF5039  Domain of unknown function (DUF5039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4   0.00055       1.7     100     177 ..      45     126 ..      29     152 .. 0.79
   2 ?    5.0   0.7    0.0051        15      59     117 ..     175     233 ..     149     236 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00055
                       DUF5039 100 ekdavsaalsafykklrseeeaykelyyaerktlskyriealryvleeykekkqvvstsfikyadrs..yllqkdsa..le 176
                                   e+++v   +s+ + k+  ++ +     y+e   l +     +r++  ++k+ + ++ + +i+y  r    l +kdsa  l 
  gi|70606419|ref|YP_255289.1|  45 ERKSVEDLVSSVFDKRFFDQLSRLSESYKEPYILIEGDLSQIRFITTKWKAVNSALVSAIIDYDLRVlfSLNKKDSAevLY 125
                                   56777778888888888888888888888888899999999**********************999732355677773344 PP

                       DUF5039 177 l 177
                                   +
  gi|70606419|ref|YP_255289.1| 126 K 126
                                   4 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0051
                       DUF5039  59 aslevyrleykaakdeldkllntykeykelkkklkeavskeekdavsaalsafykklrs 117
                                   ++++++++  ka+  +l+k l + k  +e++k l+ a s ++  +   +l+ f    r 
  gi|70606419|ref|YP_255289.1| 175 EKFNTIENICKASISDLEKALGSRKRAEEIYKVLHTAYSSDNGTKKNVSLADFLAEDRN 233
                                   4556677777888899*******************999988766666667777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1515.59
//
Query:       gi|70606420|ref|YP_255290.1|  [L=125]
Description: prefoldin subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-23   82.1  17.7    2.7e-23   81.9  17.7    1.0  1  Prefoldin_2     Prefoldin subunit
     0.0088   16.3   0.2      0.022   15.0   0.2    1.6  2  DUF424          Protein of unknown function (DUF424)
  ------ inclusion threshold ------
       0.18   11.9   3.9       0.23   11.6   3.9    1.0  1  DUF87           Helicase HerA, central domain
       0.22   11.9   4.7        2.3    8.7   0.9    2.2  2  DUF3837         Domain of unknown function (DUF3837)
       0.27   11.5   5.6       0.22   11.8   1.4    2.2  2  RseA_C          Anti sigma-E protein RseA, C-terminal domain
       0.35   10.9  12.6       0.85    9.7   3.9    2.1  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
       0.43   11.2   9.6       0.11   13.1   2.6    2.2  2  SlyX            SlyX
        0.7   10.1   8.0        2.5    8.3   3.2    2.5  2  CDC37_C         Cdc37 C terminal domain
       0.91    9.5  12.9    1.9e+02    2.0  12.9    2.4  1  Prefoldin       Prefoldin subunit
        1.1    9.8  12.2       0.57   10.7   1.5    2.1  2  APG6_N          Apg6 coiled-coil region
        1.5    9.5   6.5        2.7    8.7   6.5    1.5  1  U1snRNP70_N     U1 small nuclear ribonucleoprotein of 70kDa M
        3.6    7.6  17.9       0.59   10.2   2.9    2.3  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9  17.7   1.8e-26   2.7e-23       1     105 [.      10     114 ..      10     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.8e-26
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktl 81 
                                   q ++ k+qqlq+ql  + +++  ++ ql+e+++vl+el++l++dt +yk vG++lvk++k++v++eL+++k  le +++t+
  gi|70606420|ref|YP_255290.1|  10 QTELVKLQQLQEQLNRVIAERSVIDSQLREVNKVLDELKQLPSDTIIYKIVGNLLVKVNKDNVEKELDDQKTILELRSRTY 90 
                                   67899**************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  82 ekqleklekeleelkeelqkklqq 105
                                   ++q++kl+++lee +++++++l +
  gi|70606420|ref|YP_255290.1|  91 QNQETKLRTQLEEKQKKVNEMLSK 114
                                   ********************9976 PP

>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.4e-05     0.022      22      86 ..      19      90 ..      12      93 .. 0.86
   2 ?    5.7   0.1     0.012        18      14      42 ..      68      96 ..      61     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                  EEETTEEEE--HHHH--EEE-HHHHHHHHHHH....EEEEEESHHHHHHH...HHTTSS-GGG-EEETTEEE CS
                        DUF424 22 fkegelllnvsegfyggelaseeeaikeLeka....tiaNivgeeavvla...vkaGlvdpdsVlvidgvph 86
                                  ++e+ +++  ++++++++l + +++++eL+++     i  ivg+ +v+++   v+ +l d +++l++ + ++
  gi|70606420|ref|YP_255290.1| 19 LQEQLNRVIAERSVIDSQLREVNKVLDELKQLpsdtIIYKIVGNLLVKVNkdnVEKELDDQKTILELRSRTY 90
                                  667777888899***********************88889****999864333999********99988776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                  EGGGTT-EEEETTEEEE--HHHH--EEE- CS
                        DUF424 14 dkellgktfkegelllnvsegfyggelas 42
                                  +k+ ++k+++++++ l++    y+++ ++
  gi|70606420|ref|YP_255290.1| 68 NKDNVEKELDDQKTILELRSRTYQNQETK 96
                                  45669999999999999999999999884 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.9   0.00015      0.23     103     201 ..      14     109 ..       5     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                         DUF87 103 ldllee.ddkpaaavqrsvleealdqaka.keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggs 181
                                   ++l    ++ +   ++rsv+++ l+++ +   e ++l sd++++k+  +l      ++ +k++ +++l d+++ l ++ ++
  gi|70606420|ref|YP_255290.1|  14 VKLQQLqEQLNRVIAERSVIDSQLREVNKvLDELKQLPSDTIIYKIVGNLL-----VKVNKDNVEKELDDQKTILELRSRT 89 
                                   444444334445555888888888888888788899***************.....************************* PP

                         DUF87 182 fsnsstdliallleklekeg 201
                                    +n++t+l ++l+ek +k +
  gi|70606420|ref|YP_255290.1|  90 YQNQETKLRTQLEEKQKKVN 109
                                   ************88777655 PP

>> DUF3837  Domain of unknown function (DUF3837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.021        32      45      81 ..      12      48 ..       5      55 .. 0.86
   2 ?    8.7   0.9    0.0015       2.3      41      83 ..      74     118 ..      63     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                       DUF3837 45 ekeeleelkekleeelkkvspkdekekklikllkdYe 81
                                  e  +l++l+e+l++ +++ s  d++  +++k+l++ +
  gi|70606420|ref|YP_255290.1| 12 ELVKLQQLQEQLNRVIAERSVIDSQLREVNKVLDELK 48
                                  556899************************9999865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                       DUF3837  41 peieekeeleelkekl..eeelkkvspkdekekklikllkdYepd 83 
                                   +e+++++++ el+ +   ++e k  ++ +ek+kk++++l++Y p+
  gi|70606420|ref|YP_255290.1|  74 KELDDQKTILELRSRTyqNQETKLRTQLEEKQKKVNEMLSKYYPQ 118
                                   467788888888888743444466677899999999999999886 PP

>> RseA_C  Anti sigma-E protein RseA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2      0.25   3.7e+02      31      42 ..      15      26 ..       6      28 .. 0.79
   2 ?   11.8   1.4   0.00015      0.22      25      53 ..      91     119 ..      85     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.25
                        RseA_C 31 teeqlqeqrrRi 42
                                  + +qlqeq +R+
  gi|70606420|ref|YP_255290.1| 15 KLQQLQEQLNRV 26
                                  568999999997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                        RseA_C  25 qeqqaateeqlqeqrrRinayLqdheLQr 53 
                                   q+q++    ql+e+++++n++L  +  Qr
  gi|70606420|ref|YP_255290.1|  91 QNQETKLRTQLEEKQKKVNEMLSKYYPQR 119
                                   348889999*************9997775 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.5    0.0049       7.3      56      92 ..      13      49 ..       8      52 .. 0.82
   2 ?    9.7   3.9   0.00057      0.85      77     115 ..      73     111 ..      65     118 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0049
                    TPR_MLP1_2 56 vkelqalreelnelkaeiaelkaeaesakaeleesee 92
                                  + +lq+l e+ln++ ae++ + +++ ++++ l+e ++
  gi|70606420|ref|YP_255290.1| 13 LVKLQQLQEQLNRVIAERSVIDSQLREVNKVLDELKQ 49
                                  5579999999999999999999999999998888765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
                    TPR_MLP1_2  77 kaeaesakaeleeseesweeqkeelekelselekriedl 115
                                   ++e+++ k+ le      ++q+++l+++l+e +k+++++
  gi|70606420|ref|YP_255290.1|  73 EKELDDQKTILELRSRTYQNQETKLRTQLEEKQKKVNEM 111
                                   555555555555555555555555555555555555554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.6   7.4e-05      0.11       7      53 ..       8      53 ..       1      57 [. 0.88
   2 ?    2.4   0.7      0.16   2.4e+02      29      50 ..      90     111 ..      71     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX  7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                  eL+++l  ++++ e+Ln+v+ae    id + r+++++ ++lk+l ++
  gi|70606420|ref|YP_255290.1|  8 ELQTELVKLQQLQEQLNRVIAER-SVIDSQLREVNKVLDELKQLPSD 53
                                  8******************9985.79999999999999999998776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                                   HHHHHHHHHHHHHHHHHT-XXX CS
                          SlyX  29 qqqqidrlqrqlrllaerlkel 50 
                                    q q ++l++ql++ +++++e+
  gi|70606420|ref|YP_255290.1|  90 YQNQETKLRTQLEEKQKKVNEM 111
                                   3445556666666666666655 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.025        38      20      47 ..       3      32 ..       2      36 .. 0.78
   2 ?    8.3   3.2    0.0017       2.5      33      93 ..      35      95 ..      30     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                       CDC37_C 20 eklppelqk.AlktksLd.evnkvlakmkv 47
                                  e+lppelq   +k ++L+ ++n+v+a+ +v
  gi|70606420|ref|YP_255290.1|  3 ERLPPELQTeLVKLQQLQeQLNRVIAERSV 32
                                  689*****6256889997359999998776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                       CDC37_C 33 ksLdevnkvlakmkveeAeeilellgeagilsleellvdatteegekelkeleeekkekkk 93
                                   +L evnkvl ++k    + i+ ++    ++++++  v+++ ++ +  l+    ++++++ 
  gi|70606420|ref|YP_255290.1| 35 SQLREVNKVLDELKQLPSDTIIYKIVGNLLVKVNKDNVEKELDDQKTILELRSRTYQNQET 95
                                  5799********************9999999999999888776665555555555554433 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  12.9      0.13   1.9e+02      71     111 ..      72     112 ..       8     115 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.13
                                   EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  71 veksleeAiellkkkleelekqlekleeeleklkdqittle 111
                                   vek+l++ +++l+ +  ++++q +kl  +le+++++++++ 
  gi|70606420|ref|YP_255290.1|  72 VEKELDDQKTILELRSRTYQNQETKLRTQLEEKQKKVNEML 112
                                   78999999999999999999999999999999999999886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.5   0.00038      0.57      54      96 ..       7      49 ..       2      55 .. 0.82
   2 ?    4.4   3.4     0.034        50      86     122 ..      75     111 ..      63     118 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                        APG6_N 54 eeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                   el++   + ++l+e+L+++ +er+ ++++l++  + l++l++
  gi|70606420|ref|YP_255290.1|  7 PELQTELVKLQQLQEQLNRVIAERSVIDSQLREVNKVLDELKQ 49
                                  5677777788899999999999999999999999999999987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.034
                        APG6_N  86 aleeelealeeeeerfwreynelqlelleleeeldsl 122
                                   +l  ++  le   + + ++  +l+++l+e++++ + +
  gi|70606420|ref|YP_255290.1|  75 ELDDQKTILELRSRTYQNQETKLRTQLEEKQKKVNEM 111
                                   3333334444444444555555555555555544444 PP

>> U1snRNP70_N  U1 small nuclear ribonucleoprotein of 70kDa MW N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.5    0.0018       2.7      27      91 ..      27     118 ..       3     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                   U1snRNP70_N  27 pekrkt.kkkitGvaaflselke.......................deeeqeppektetk...eekkererkekkekkeek 80 
                                   + +r+  ++++  v ++l+elk+                       ++e +++++  e +    + +e + +++ e+k++k
  gi|70606420|ref|YP_255290.1|  27 IAERSViDSQLREVNKVLDELKQlpsdtiiykivgnllvkvnkdnvEKELDDQKTILELRsrtYQNQETKLRTQLEEKQKK 107
                                   44555556677778888888888888888888888888888888885566666666665533468889999999******* PP

                   U1snRNP70_N  81 leealeeydPk 91 
                                   ++e+l++y P+
  gi|70606420|ref|YP_255290.1| 108 VNEMLSKYYPQ 118
                                   ********997 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.9   0.00039      0.59      66     106 ..      14      54 ..       2      58 .. 0.88
   2 ?    2.7   7.4     0.081   1.2e+02      62      99 ..      74     111 ..      65     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                CENP-F_leu_zip  66 eelreleldLvalrsekeeLekelqkkqervseLeslnssl 106
                                    +l++l+ +L+ +  e+  ++ +l++ ++  +eL++l s++
  gi|70606420|ref|YP_255290.1|  14 VKLQQLQEQLNRVIAERSVIDSQLREVNKVLDELKQLPSDT 54 
                                   689*********************************99886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.081
                CENP-F_leu_zip  62 eelaeelreleldLvalrsekeeLekelqkkqervseL 99 
                                   +el  + + lel   + +++  +L  +l++kq++v+e+
  gi|70606420|ref|YP_255290.1|  74 KELDDQKTILELRSRTYQNQETKLRTQLEEKQKKVNEM 111
                                   45667777788888888888899999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2768  (0.154387); expected 358.6 (0.02)
Passed bias filter:                      817  (0.0455686); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 888.65
//
Query:       gi|70606421|ref|YP_255291.1|  [L=77]
Description: hypothetical protein Saci_0606 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.058   13.4   0.2       0.12   12.4   0.1    1.5  2  DASH_Dad4  DASH complex subunit Dad4


Domain annotation for each model (and alignments):
>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.17   3.1e+03      26      36 ..       8      18 ..       4      24 .. 0.55
   2 ?   12.4   0.1   6.7e-06      0.12      20      69 ..      26      75 ..      24      77 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.17
                     DASH_Dad4 26 svvelnkelee 36
                                   ++e++++l++
  gi|70606421|ref|YP_255291.1|  8 ELKEVDQNLKD 18
                                  34444444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.7e-06
                     DASH_Dad4 20 vekLnesvvelnkeleeinkkNknvelvsqlwenYqrnvqfnLeatgelk 69
                                  vek+ e vv +n++l +i+   ++v+    ++++Y + +   Le+ ++ k
  gi|70606421|ref|YP_255291.1| 26 VEKVDERVVSINEKLGTITITSNSVSRGRAVINSYISWIYTILETLNKVK 75
                                  8**********************************998888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 565.56
//
Query:       gi|70606422|ref|YP_255292.1|  [L=199]
Description: Brix domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.069   13.2   0.0    1.5  2  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.9e-06     0.069       1      85 [.      30     114 ..      30     146 .. 0.68
   2 ?   -3.2   0.0      0.41   7.4e+03      67      77 ..     183     193 ..     152     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-06
                                   BTT--HHHHHHHHHHHHHCTTSEEEEEE.ECT-TTTHHHHHHH...-HHHHHHHH.HCTC.SEEEEEE..SSTTE..EEEE CS
                          Brix   1 grktssrlrqllkdlrslmkphtasflk.rnsnklkdlvelag...vthlellse.kndc.slfvfelskkrPng..ptle 73 
                                   +r++ssr+r++l++l  ++ p++ +  + r++++l+d+ + ++   ++ ++++s+ k++   ++v ++           + 
  gi|70606422|ref|YP_255292.1|  30 SRDSSSRIRSFLNELSYII-PDSFK--InRGRQSLDDIFKRSRlygASYIVIVSSsKGNPgRFLVYNT-----YTsiREFD 102
                                   6899***************.65555..4455567**98888888888899999887555425555555.....22113333 PP

                                   EEEECECTGGGS CS
                          Brix  74 fkvenyslmkdl 85 
                                    k++ ++l k++
  gi|70606422|ref|YP_255292.1| 103 IKIQGITLLKEI 114
                                   444466666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.41
                                   TTEEEEEEEEE CS
                          Brix  67 Pngptlefkve 77 
                                     gpt+ f v+
  gi|70606422|ref|YP_255292.1| 183 IIGPTIRFLVD 193
                                   33688888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1426.50
//
Query:       gi|70606423|ref|YP_255293.1|  [L=70]
Description: 50S ribosomal protein L37Ae [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-24   83.6   7.2    8.2e-24   83.5   7.2    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    0.00062   19.7   6.2    0.00062   19.7   4.9    1.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0064   16.2   1.4     0.0075   16.0   1.4    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
     0.0097   16.3   0.8      0.013   15.9   0.8    1.2  1  DnaJ_CXXCXGXG    DnaJ central domain
  ------ inclusion threshold ------
      0.024   14.1   0.1      0.036   13.6   0.1    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.032   13.6   0.5      0.052   12.9   0.5    1.3  1  zf-TFIIB         Transcription factor zinc-finger
      0.034   14.2   0.3      0.048   13.8   0.3    1.2  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.061   13.2   1.3      0.077   12.9   1.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.07   13.5   7.6        1.8    9.0   0.7    2.1  2  DUF4379          Probable Zinc-ribbon domain
       0.26   11.1   2.4        2.3    8.0   2.8    2.0  2  zinc_ribbon_5    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   7.2   4.6e-27   8.2e-24       3      68 ..       3      69 ..       1      70 [] 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 4.6e-27
                                  XXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSS CS
               Ribosomal_L37ae  3 kkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytp 68
                                  +++giaG++g+rYG+s rk++k+++++++  ++Cp c++t kv R a giw C+kc+ ++aG Aytp
  gi|70606423|ref|YP_255293.1|  3 RVTGIAGRFGARYGSSTRKKWKEVMERRYMPHQCPYCKTTgKVVRIASGIWYCRKCETKWAGLAYTP 69
                                  689**************************************************************98 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   2.2e+03      30      39 ..      15      24 ..       9      24 .. 0.76
   2 !   19.7   4.9   3.5e-07   0.00062      19      45 ..      34      60 ..      23      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                 Zn_Tnp_IS1595 30 yriktrglfq 39
                                  y  +tr++++
  gi|70606423|ref|YP_255293.1| 15 YGSSTRKKWK 24
                                  6667889996 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.5e-07
                 Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrglfqCkeCrk 45
                                  + CP+C+ + k+ ri++ g + C++C +
  gi|70606423|ref|YP_255293.1| 34 HQCPYCKTTgKVVRIAS-GIWYCRKCET 60
                                  45**************9.********75 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.4   4.2e-06    0.0075      17      52 ..      32      67 ..      18      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                  EEEB--STT---B-EEETTTEEEETTTTEEESS--E CS
                   Rep_fac-A_C 17 vYkACpsedCnkKvveeedgewrCekCdkeveepky 52
                                  + + Cp  +   Kvv+ ++g w+C kC+++++   y
  gi|70606423|ref|YP_255293.1| 32 MPHQCPYCKTTGKVVRIASGIWYCRKCETKWAGLAY 67
                                  557799777778****************99876655 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.8     7e-06     0.013      38      65 ..      30      60 ..      12      61 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-06
                 DnaJ_CXXCXGXG 38 qqsqstCpeCeGtGkvikekd...kCkkCkG 65
                                  + + ++Cp C+ tGkv++  +    C+kC+ 
  gi|70606423|ref|YP_255293.1| 30 RYMPHQCPYCKTTGKVVRIASgiwYCRKCET 60
                                  235679*********9988776645**9985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-05     0.036       2      28 ..      35      61 ..      34      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                  EETTTTCEECHEETSTTCEEESSSSBE CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlV 28
                                  +CP+C++t  v+  ++g  +C +C++ 
  gi|70606423|ref|YP_255293.1| 35 QCPYCKTTGKVVRIASGIWYCRKCETK 61
                                  8*****9999**************876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   2.9e-05     0.052       1      26 [.      35      59 ..      35      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                      zf-TFIIB  1 kCPkCqdeleeser.ggveidyCpqCr 26
                                  +CP C+++ + ++  +g  i+yC +C+
  gi|70606423|ref|YP_255293.1| 35 QCPYCKTTGKVVRIaSG--IWYCRKCE 59
                                  7*********9999566..*******6 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.7e-05     0.048       2      26 ..      34      60 ..      33      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                    zf-RRPl_C4  2 kkCkyCls..kklknlnetvyCeaCei 26
                                   +C+yC++  k +   +  +yC +Ce 
  gi|70606423|ref|YP_255293.1| 34 HQCPYCKTtgKVVRIASGIWYCRKCET 60
                                  58****874367889999*******97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.3   4.3e-05     0.077      24      56 ..      29      62 ..      14      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                OrfB_Zn_ribbon 24 payTSktCseCgsknke.alsgrtfkCpnCgfea 56
                                  ++y   +C+ C  ++k  + ++  ++C++C +++
  gi|70606423|ref|YP_255293.1| 29 RRYMPHQCPYCKTTGKVvRIASGIWYCRKCETKW 62
                                  5567789***********************9886 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.7   0.00099       1.8      36      56 .]      20      39 ..      15      39 .. 0.88
   2 ?    8.4   1.1    0.0015       2.8      29      39 ..      52      62 ..      48      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00099
                       DUF4379 36 gheWeasvsnrtkgsskCpkC 56
                                   ++W++ ++ r   ++ Cp+C
  gi|70606423|ref|YP_255293.1| 20 RKKWKEVMERRYMPHQ-CPYC 39
                                  579*********8898.**** PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                       DUF4379 29 wWkCakCgheW 39
                                   W C+kC+ +W
  gi|70606423|ref|YP_255293.1| 52 IWYCRKCETKW 62
                                  5********** PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.8    0.0013       2.3       4      25 ..      35      53 ..      32      60 .. 0.74
   2 ?    1.7   0.3      0.13   2.3e+02       5      11 ..      55      61 ..      52      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
                 zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkk 25
                                  +Cp C+t+ k+v      sg +
  gi|70606423|ref|YP_255293.1| 35 QCPYCKTTGKVVRIA---SGIW 53
                                  9**********9755...5555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                 zinc_ribbon_5  5 CpdCdtk 11
                                  C +C+tk
  gi|70606423|ref|YP_255293.1| 55 CRKCETK 61
                                  9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 485.26
//
Query:       gi|70606424|ref|YP_255294.1|  [L=276]
Description: exosome complex RNA-binding protein Rrp42 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-31  108.6   0.0    4.9e-31  108.0   0.0    1.3  1  RNase_PH      3' exoribonuclease family, domain 1
    2.6e-09   37.0   0.1    1.2e-08   34.8   0.0    2.1  2  RNase_PH_C    3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
      0.024   14.2   0.9      0.031   13.9   0.9    1.1  1  DUF1189       Protein of unknown function (DUF1189)
       0.14   12.1   0.0       0.23   11.4   0.0    1.3  1  Fimbrial_K88  Fimbrial, major and minor subunit


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   1.1e-34   4.9e-31       1     132 []      36     171 ..      36     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 1.1e-34
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrl 81 
                                   e+R+l++  g +++a+GSa+++lG+t vla+v+++  + p +++ +++g+l v+ve+ p+a ++++  g p++ +iel+r+
  gi|70606424|ref|YP_255294.1|  36 EYRQLKVTLGYAKKAEGSALVKLGNTLVLAGVKLEEDS-PYPDT-PNQGNLIVNVELLPLAYETFEP-GPPDENSIELARI 113
                                   79**********************************98.88884.45789***************76.9************ PP

                                   HHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  82 leralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                   ++r+lr s  +        ++k+ +t+ +d++vl++dg ++lda+++a+++A++d+++p
  gi|70606424|ref|YP_255294.1| 114 VDRSLRDSKAIdlsklviaPGKKVWTLWVDVYVLDYDG-NILDACMLASIAAIYDTKLP 171
                                   **********9999999999999***************.******************98 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.48   2.2e+03      23      50 ..      36      61 ..      34      72 .. 0.79
   2 !   34.8   0.0   2.7e-12   1.2e-08       2      53 ..     196     247 ..     195     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.48
                                  HHHHSSEEEEEEEETTSEEEEEEEECSS CS
                    RNase_PH_C 23 Eedlsegdltlavagtkevvtlmkeggs 50
                                  E  +++ ++tl +a++ e  +l k+g  
  gi|70606424|ref|YP_255294.1| 36 E--YRQLKVTLGYAKKAEGSALVKLGNT 61
                                  4..6777889999999999999998875 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 2.7e-12
                                   --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEE CS
                    RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqld 53 
                                   pv+ vt +k++ ++v+Dp+++Ee++++++l + +++ + +v l+k  +++l+
  gi|70606424|ref|YP_255294.1| 196 PVVTVTTAKIGKYVVVDPNLDEESIADAKLSISYTKEGTIVGLQKNYSGNLT 247
                                   89**************************************999986555544 PP

>> DUF1189  Protein of unknown function (DUF1189)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   6.8e-06     0.031      54     147 ..     161     265 ..     158     276 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                       DUF1189  54 qleelieeeipdFtiedGelqieeke............piiiqedgitiifDtsgetdeedlekynngililkdkivi.kn 121
                                   ++ +++++++p+ ++e +e++i+++e            +++ ++ g ++++D++   dee++++ + +i  +k+  ++  +
  gi|70606424|ref|YP_255294.1| 161 SIAAIYDTKLPKVEVEGDEIKINKEErlsiplvnypvvTVTTAKIGKYVVVDPNL--DEESIADAKLSISYTKEGTIVgLQ 239
                                   56788999*****************77778777774433333666777*****87..8899*****************999 PP

                       DUF1189 122 ggttqsysysdledqkltkedlrefl 147
                                   ++ +  +++++++ ++ t    ++fl
  gi|70606424|ref|YP_255294.1| 240 KNYSGNLTFKEIDAMESTARATSQFL 265
                                   99999999999998876666666665 PP

>> Fimbrial_K88  Fimbrial, major and minor subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.2e-05      0.23      76     125 ..     195     244 ..     189     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                  Fimbrial_K88  76 spvvtitts.tgevevigpnmpqggitdvvldvtegtggdqvaslqmqisg 125
                                    pvvt+tt+  g+  v+ pn+ +  i+d  l ++    g  +  lq + sg
  gi|70606424|ref|YP_255294.1| 195 YPVVTVTTAkIGKYVVVDPNLDEESIADAKLSISYTKEGT-IVGLQKNYSG 244
                                   59****9973699******************998777665.4567777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1796.45
//
Query:       gi|70606425|ref|YP_255295.1|  [L=243]
Description: exosome complex exonuclease Rrp41 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-37  126.7   0.0    1.2e-36  126.1   0.0    1.3  1  RNase_PH    3' exoribonuclease family, domain 1
    4.2e-13   49.1   0.0      8e-13   48.2   0.0    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.0   1.3e-40   1.2e-36       1     132 []      24     153 ..      24     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1.3e-40
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                   elR+++ie gvl++a+GSa++e+G+tkv+a+v+gp+e +p+  + +d    l v++ ++pf++ er++   ps++eiels+
  gi|70606425|ref|YP_255295.1|  24 ELRPIKIELGVLKNADGSAIFEMGNTKVIAAVYGPKEMHPRHLAlPDK-ASLRVRYHMTPFSTDERKN-PAPSRREIELSK 102
                                   79************************************8887777543.45***************65.79********** PP

                                   HHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  81 lleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                   ++ +al++ ill+ +p++ idi+++vl++d  ++  ++ +aas+ALadagip
  gi|70606425|ref|YP_255295.1| 103 VIREALESTILLNLFPRTVIDIFMEVLQADA-GTRLVALMAASMALADAGIP 153
                                   *******************************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   8.9e-17     8e-13       1      67 []     156     221 ..     156     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 8.9e-17
                                   S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                    RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                   +++++v+vgk d+++vlD++ +E+ ++e+d+++av  +   v+l++++g  ++++++ +a+elA+kg
  gi|70606425|ref|YP_255295.1| 156 DLIAGVAVGKADGSLVLDLNEQEDMWGEADMPIAVLPSLGQVVLLQLNGF-MTPDEFRRAFELAQKG 221
                                   5899**********************************************.*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1526.57
//
Query:       gi|70606426|ref|YP_255296.1|  [L=249]
Description: exosome complex RNA-binding protein Rrp4 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-06   27.2   0.1    7.8e-06   26.2   0.1    1.5  1  KH_6      KH domain
    0.00016   21.4   0.6    0.00037   20.3   0.6    1.6  1  KH_1      KH domain
     0.0015   18.9   0.0     0.0031   17.8   0.0    1.6  1  S1        S1 RNA binding domain
  ------ inclusion threshold ------
      0.027   14.3   0.1      0.059   13.2   0.1    1.6  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   1.7e-09   7.8e-06       1      44 [.     153     199 ..     153     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.7e-09
                          KH_6   1 GmlfeVslslvrRll....nhvLeeLgkagpfeiavGlNGriWvkses 44 
                                   G ++++ + +v+R++    + + e L  + ++ei v +NGri +k+ +
  gi|70606426|ref|YP_255296.1| 153 GTVMDIMPVKVPRVIgknrSMI-EVLTSESGCEIFVAQNGRIHIKCAN 199
                                   89*************6553333.44445555**************976 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.6   8.2e-08   0.00037       6      52 ..     159     197 ..     154     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-08
                                   EGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE CS
                          KH_1   6 vPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG 52 
                                    P + v+r+IGk+ s+I  + +e+g+ I v  ++        ++i+ 
  gi|70606426|ref|YP_255296.1| 159 MPVK-VPRVIGKNRSMIEVLTSESGCEIFVA-QN------GRIHIKC 197
                                   5666.************************87.33......2466655 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.9e-07    0.0031       2      75 .]      69     143 ..      68     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.9e-07
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..CEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..arvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                   p++g+ + G V +++ +G  +++    ++++pas+l  +    +ed  + l vGd v +k++ +d++   ++l++k
  gi|70606426|ref|YP_255296.1|  69 PKVGDTIIGLVEDIEIYGWVIDIKSFYSAYLPASSLLGRpiSPGEDVRRYLDVGDYVIAKIEAFDRTIS-PVLTVK 143
                                   899*********************************99999899***********************98.888775 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05     0.059      13      69 ..     143     196 ..     132     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                                   ETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                          KH_2  13 agvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                   +g++  +I   + ++++ i   +  +vIGk+ s+i+ +++e + +i + ++++++++
  gi|70606426|ref|YP_255296.1| 143 KGKGLGRI---PLGTVMDIMPVKVPRVIGKNRSMIEVLTSESGCEIFVAQNGRIHIK 196
                                   55555566...67788888888999*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1734.57
//
Query:       gi|70606427|ref|YP_255297.1|  [L=233]
Description: putative RNA-associated protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-23   80.2   0.1    1.7e-22   79.3   0.1    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.5e-21   76.6   0.4    2.3e-21   76.0   0.4    1.3  1  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
       0.07   13.2   0.0       0.29   11.2   0.0    1.9  2  EFG_C     Elongation factor G C-terminus


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.1   2.8e-26   1.7e-22       2      88 .]       7      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 2.8e-26
                                  -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--H CS
                          SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsa 84
                                  ++i+ry+++++rFei+v+++++++ r+gk++++s+ + s++i+++ +kG +as s+l+k+fgt + +ei+k+I+ kGei ++a
  gi|70606427|ref|YP_255297.1|  7 MVIARYEHSGERFEILVKPKEAMDLRNGKSVSISDAVVSDTIYKDIKKGLKASPSSLKKVFGTLDFEEIAKQIILKGEIPLTA 89
                                  5799******************************************************************************* PP

                                  HHHH CS
                          SBDS 85 eerk 88
                                  e+r+
  gi|70606427|ref|YP_255297.1| 90 EQRR 93
                                  *996 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.4   3.9e-25   2.3e-21       2     113 ..     100     215 ..      99     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 3.9e-25
                                   HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS-..-EE-EEEEEEEE-...CCCH CS
                        SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeip..iqrarmrlritcptsikdki 80 
                                   +k+ii+++++++++p+t+ p+++t+Ie a++++++++++nk +++Qal+++++L + ip  i+ra m++++    +  +ki
  gi|70606427|ref|YP_255297.1| 100 RKQIIDYISRNSIDPKTNLPIPRTRIELAMEQARIQIDPNKDVEAQALQIVRELAKLIPirIARALMEIKVG--PKFSSKI 178
                                   79*********************************************************5555666666664..3455555 PP

                                   HHHHHHH.HH.......S.EEEEEE.EEGGGHHHHHH CS
                        SBDS_C  81 lklieqv.esqk..vaekewevvvl.iePgaykelee 113
                                   ++ ++++ e++   + ++   +  l i++ga++++ +
  gi|70606427|ref|YP_255297.1| 179 KSQLANLgEVKRsnWLNDGTLIAELeIPAGAQQDVID 215
                                   5555555333222255566668888899998888766 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.48   2.9e+03      35      51 ..      72      87 ..      69      90 .. 0.78
   2 ?   11.2   0.0   4.8e-05      0.29       9      70 ..     166     226 ..     164     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                                  EEEE.TTEEEEEEEEEG CS
                         EFG_C 35 meqdasgrviieaeiPl 51
                                  +e++  +++i+++eiPl
  gi|70606427|ref|YP_255297.1| 72 FEEI-AKQIILKGEIPL 87
                                  5666.78899******8 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.8e-05
                                   EEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-E CS
                         EFG_C   9 veievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegs 70 
                                   +ei+v  ++++k+ s+l++  Ge++  +  ++g+ i e eiP+   ++  ++L+slTkGe +
  gi|70606427|ref|YP_255297.1| 166 MEIKVGPKFSSKIKSQLANL-GEVKRSNWLNDGTLIAELEIPAGAQQDVIDKLNSLTKGEVE 226
                                   67888888888888888764.8999988889999999**********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1662.76
//
Query:       gi|70606428|ref|YP_255298.1|  [L=242]
Description: proteasome subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-59  200.2   0.0    3.2e-59  199.6   0.0    1.3  1  Proteasome      Proteasome subunit
    3.9e-13   48.8   1.5    8.6e-13   47.7   0.5    2.1  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.6   0.0   3.6e-63   3.2e-59       1     189 [.      33     219 ..      33     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 3.6e-63
                                   HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                    Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                   vk+G+t++G+k+k gvvl a+kr     +ll+ + +eKif +ddh+g++faGla+D+r+l+++ar++a ++rl y++pi++
  gi|70606428|ref|YP_255298.1|  33 VKRGWTTLGVKTKSGVVLLAEKRKA--TQLLDVDGIEKIFMLDDHVGCTFAGLASDGRILIDYARSQALQHRLIYDEPISI 111
                                   79********************999..8999************************************************** PP

                                   HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                    Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                   e+l++ +++ +qaytq++g+rpfgv+l+++g+d+ ++p+L++++psG+++ + +avaiG+g + a+++lek+ykedl+ ++
  gi|70606428|ref|YP_255298.1| 112 EYLTKVISDVKQAYTQHGGVRPFGVALIVGGIDKGKQPKLLMTEPSGQFMPY-YAVAIGQGGYTATEYLEKNYKEDLDIQS 191
                                   ****************************************************.8*************************** PP

                                   HHHHHHHHHHHHHH.HBTTSCSSEEEEE CS
                    Proteasome 163 avelavkalkeale.rdklsgknievav 189
                                   ++ la++al ++l+ ++kl+ + +e+++
  gi|70606428|ref|YP_255298.1| 192 TILLALRALMATLKpGEKLNYSSVEIGY 219
                                   *************879999999999975 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.5   9.6e-17   8.6e-13       1      23 []      10      32 ..      10      32 .. 0.99
   2 ?   -1.2   0.0      0.19   1.7e+03      11      20 ..      86      94 ..      85      95 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 9.6e-17
                Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                  YDr++t+FSPdG L+QV+YA++A
  gi|70606428|ref|YP_255298.1| 10 YDRAITIFSPDGSLYQVDYAFEA 32
                                  **********************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                Proteasome_A_N 11 dGRLfQVEYA 20
                                  dGR++ ++YA
  gi|70606428|ref|YP_255298.1| 86 DGRIL-IDYA 94
                                  88886.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1933.83
//
Query:       gi|70606429|ref|YP_255299.1|  [L=140]
Description: hypothetical protein Saci_0614 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-10   40.0   0.0    5.3e-10   39.5   0.0    1.3  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0     3e-14   5.3e-10       1     100 [.      43     136 ..      43     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3e-14
                                   EEEEEEEEESS......-HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--EETT CS
                 RNase_P_Rpp14   1 RYllveilypdeeeelteksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitkieg 81 
                                   RY+++ei+ +  e +l ek l + ir++v+el G++ l  ++   +v+ ++   + +ii   r+ y+lv+a+L+++++i+g
  gi|70606429|ref|YP_255299.1|  43 RYIIIEIIGNI-E-NLGEKILEENIRNAVKELGGKVWLEIANP--RVVFIHG--NFGIISSTRAGYKLVLASLPYVKSING 117
                                   9*********9.4.5999*************************..6777766..89************************* PP

                                   EEEEEEEEEEESSHHHHHH CS
                 RNase_P_Rpp14  82 rpvvfrvvrvsGTikkaee 100
                                    +v++ + r+ G++k+a++
  gi|70606429|ref|YP_255299.1| 118 VEVLLAPKRTTGSLKRAKK 136
                                   ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1102.01
//
Query:       gi|70606430|ref|YP_255300.1|  [L=183]
Description: RNase P p30-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0017   17.8   0.8      0.055   12.9   0.8    2.1  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.037   13.6   0.1      0.052   13.1   0.1    1.3  1  Como_SCP     Small coat protein


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.8   6.2e-06     0.055      65     212 ..      31     167 ..      20     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-06
                                   .HHSSEEEEEEES-H.HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEE CS
                   RNase_P_p30  65 kllsRvtlvvsdpsklqrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEin 145
                                   + l+R t+v+++ + l +  k   k + + v+P +  al+ a+ +++v  i++  ++   + +k++++++ ++ + ++E+ 
  gi|70606430|ref|YP_255300.1|  31 QSLRRFTIVCNNTKALYNALKSTPKAT-IFVKPLSLDALKSAIIDHRVNAIILGRDN--LSLFKKTMLSLISQYNKFVEVR 108
                                   668999999999999755555555555.57999999999999999999999998876..4558999999999999999999 PP

                                   SHHHHHS-HHHHHHHHHHHHHHHHHHHH..--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTT CS
                   RNase_P_p30 146 yspllrdsglaRrnfisnarkllrltrg..kgvviSSgAesplelRnpydiinLlktlGLeedrakeav 212
                                   + ++  d             +l+  +    +  +iSS A +  e+++py  i+Ll+ lG +e++a + v
  gi|70606430|ref|YP_255300.1| 109 LNEVTFDVI----------YRLITWSSRwiRFPLISSCAAKFNEVWSPYSKISLLTSLGASESDALNWV 167
                                   988766666..........3344444444556689999999******************9999987655 PP

>> Como_SCP  Small coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.8e-06     0.052      58     121 ..     117     180 ..      94     183 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-06
                                   HHHHEEEEEEEEEEEEEEEETTS-GGG--BEEEEEEESSSSTTS-ESEEEEEBSSSEEEEEEEE CS
                      Como_SCP  58 lLrtaaWkkGtlhvklvvrGaavkrsdWastvridlrnslstesldartwviskPhaaeleFsl 121
                                   + r   W +  +++ l+ + aa     W+  ++i+l  sl++++ da +wv  +P     +F++
  gi|70606430|ref|YP_255300.1| 117 IYRLITWSSRWIRFPLISSCAAKFNEVWSPYSKISLLTSLGASESDALNWVCNTPLELISQFKV 180
                                   5677889999*******9999999999****************************988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1257.84
//
Query:       gi|70606431|ref|YP_255301.1|  [L=104]
Description: hypothetical protein Saci_0616 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-18   66.0   1.6    4.4e-18   65.7   1.6    1.2  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   1.6   2.5e-22   4.4e-18      38     119 .]       2      83 ..       1      83 [. 0.97

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 2.5e-22
                                   E-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEEEEHHHHH.TT---BESSSSEEEEEE CS
                   RNA_binding  38 eGhygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekgklylrldKQaay.lgklslvegddvIkvki 117
                                   +G+ygn+i++ e+++++k a ++++kl+++l++ ++ +L ++l+ r+d + kl++r+dKQ+++  +k+ l+egddvIk++i
  gi|70606431|ref|YP_255301.1|   2 QGYYGNRIIVTEIKIKGKLAIEAFNKLINALDKADLAILISTLNTRLD-GTKLHIRVDKQRLIyDNKIYLKEGDDVIKIII 81 
                                   8***********************************************.************866****************9 PP

                                   EE CS
                   RNA_binding 118 kv 119
                                   ++
  gi|70606431|ref|YP_255301.1|  82 SF 83 
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 782.43
//
Query:       gi|70606432|ref|YP_255302.1|  [L=217]
Description: 50S ribosomal protein L15e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-73  246.8   8.8    1.3e-73  246.8   8.8    1.5  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   8.8   7.1e-78   1.3e-73       1     186 [.       4     186 ..       4     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 7.1e-78
                                   -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS-- CS
                Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgr 81 
                                   ++y+y++++w++k  d  r +lr+rl+e+r++pa++r++rptrl+rAr+LGYkakqG+v+vrvrvrrGg +k  ++ ++gr
  gi|70606432|ref|YP_255302.1|   4 SMYHYIEQTWQNK--DWRRSILRKRLIEWRRQPAITRIDRPTRLNRARALGYKAKQGFVMVRVRVRRGGLNK--PRPNSGR 80 
                                   79*********88..89*******************************************************..******* PP

                                   -GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT CS
                Ribosomal_L15e  82 kpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrG 162
                                   +pkr+gv+ + p+k  ++iaeer++rk+pnl+vL+SY+v+eDg+ykyyEvi+vD sh++ir+d++++w+ ++v+++R++rG
  gi|70606432|ref|YP_255302.1|  81 RPKRMGVYGYGPSKGYRWIAEERAARKFPNLEVLGSYYVAEDGMYKYYEVIMVDYSHPVIRSDPELKWLQDSVNRKRVFRG 161
                                   ********************************************************************************* PP

                                   -SHHHHHHTT-S-SS..TT-TTTSS CS
                Ribosomal_L15e 163 ltsagkksRGlrkkg.lkgaekirg 186
                                   ltsag+ksRGl+k++ lkg+ ++++
  gi|70606432|ref|YP_255302.1| 162 LTSAGQKSRGLTKSRgLKGTVQRKW 186
                                   ***********76543777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 1282.54
//
Query:       gi|70606433|ref|YP_255303.1|  [L=400]
Description: translation-associated GTPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-36  123.0   1.6    1.2e-35  122.4   0.4    1.9  2  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.3e-21   76.0   1.6    2.1e-20   72.9   0.0    2.9  3  MMR_HSR1       50S ribosome-binding GTPase
    5.8e-12   45.5   0.1    1.3e-11   44.4   0.1    1.6  1  TGS            TGS domain
    1.5e-07   31.1   0.1    0.00015   21.4   0.1    3.1  3  FeoB_N         Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.011   16.0   0.1       0.33   11.2   0.0    2.5  2  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.011   15.7   0.4      0.079   13.0   0.3    2.4  2  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   3.9e+03      13      41 ..     171     197 ..     160     201 .. 0.65
   2 !  122.4   0.4   4.1e-39   1.2e-35       1     112 []     224     328 ..     224     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                    MMR_HSR1_C  13 nieklkekypkdkkvvpvsAaaElaLrka 41 
                                    ++kl       +k+ +vsA  E  L+++
  gi|70606433|ref|YP_255303.1| 171 LLSKLSGLSI--NKFHIVSALKETKLENL 197
                                   4444444433..36889999999999876 PP

  == domain 2  score: 122.4 bits;  conditional E-value: 4.1e-39
                    MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlv 81 
                                   a+NKaD++++++ ieklk+ky+    +vpvsA++ElaLr+a+k+glikY pgd++++i ++    l++kq++aL++i+++v
  gi|70606433|ref|YP_255303.1| 224 AANKADIKESRKFIEKLKQKYQ---WIVPVSAESELALRRASKAGLIKYLPGDNQIKILKE----LNQKQREALDYIQTNV 297
                                   89********************...8********************************988....**************** PP

                    MMR_HSR1_C  82 lkrygsTGVqealnaavfelldlivVYPVed 112
                                   ++ yg+TGVq+a+n av ++l++ivVYPVed
  gi|70606433|ref|YP_255303.1| 298 IDVYGGTGVQQAINIAVLDALQMIVVYPVED 328
                                   *****************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   7.1e-24   2.1e-20       2      87 ..       4     131 ..       3     165 .. 0.77
   2 ?   -0.8   0.0      0.52   1.6e+03      97     114 .]     210     227 ..     175     250 .. 0.66
   3 ?    0.8   0.1      0.16   4.9e+02      58      97 ..     347     390 ..     264     400 .] 0.63

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.1e-24
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEECGGCS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvDtpGli 57 
                                   v+++G++NvGKSt+++a t   ++++++p++T+++n g   +++                           i+lvD++Gli
  gi|70606433|ref|YP_255303.1|   4 VGLIGKTNVGKSTFFSAATLIDVEIANRPFVTINPNIGIAYVRD-TcvhtevnvkcnprnsvdmdnyryipIKLVDVAGLI 83 
                                   89************************************988543.13445555666666667777777777********** PP

                                   SHHHHHHHHHHHHHHHHC.TSEEEEEEETT.................T CS
                      MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas.................e 87 
                                    ga++++glg++fl+  + ad++++v+das                 e
  gi|70606433|ref|YP_255303.1|  84 PGAHQGRGLGNKFLDDLRkADVLIHVIDASgstneeglpiptgsrdpE 131
                                   **************96666*********99777665555554433332 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.52
                                   HHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  97 leelleeakkplilvlnk 114
                                   + + l+e  kp+++++nk
  gi|70606433|ref|YP_255303.1| 210 FTRKLREISKPIVIAANK 227
                                   222233355677777766 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                                   SHHHHHHHHHHHHHHHHC.TSEEEEEEETT.....TTCSHHHHHHH CS
                      MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas.....eeklkpldeel 97 
                                   +++s+ k+l+  ++   e a+ +l+ +da+      e++k + +++
  gi|70606433|ref|YP_255303.1| 347 KRNSTPKDLASVIHT--ElAKGFLYAIDAKkkirvGEDYKLQHRDI 390
                                   333444444444442..34788888888774444422344444444 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1   4.2e-15   1.3e-11       4      59 ..     339     394 ..     330     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.2e-15
                                   EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                           TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                   ++Pd+ +  ++r++t++D+A  Ih++lak f+yA+  +   rvg d++L++ d+++Iv
  gi|70606433|ref|YP_255303.1| 339 VLPDAIL--IKRNSTPKDLASVIHTELAKGFLYAIDAKkkIRVGEDYKLQHRDIIKIV 394
                                   4566666..9****************************766****************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   4.9e-08   0.00015       1      45 [.       2      46 ..       2      54 .. 0.88
   2 ?   -0.2   0.0      0.21   6.3e+02      77      90 ..     101     114 ..      74     161 .. 0.77
   3 !    5.5   0.0    0.0038        11      97     123 ..     210     236 ..     204     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.9e-08
                                  EEEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEET CS
                        FeoB_N  1 itvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklk 45
                                  itv l+G+ nvGk+t+f a t  + +++N p vt++ + g   ++
  gi|70606433|ref|YP_255303.1|  2 ITVGLIGKTNVGKSTFFSAATLIDVEIANRPFVTINPNIGIAYVR 46
                                  5899*******************************9888876655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                   TSSSEEEEEEEGGG CS
                        FeoB_N  77 eepdvvvnvvdatn 90 
                                   +++dv+++v+da+ 
  gi|70606433|ref|YP_255303.1| 101 RKADVLIHVIDASG 114
                                   57899******974 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0038
                                   HHHHHHHTTSSEEEEEETHHHHHHTTE CS
                        FeoB_N  97 Ltlqllelgvpvvlalnmideaekkgi 123
                                   +t +l e+++p+v+a n+ d  e+++ 
  gi|70606433|ref|YP_255303.1| 210 FTRKLREISKPIVIAANKADIKESRKF 236
                                   7889****************9888775 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.33      16      41 ..     345     370 ..     341     374 .. 0.90
   2 ?    2.1   0.1     0.074   2.2e+02      62      81 ..     374     393 ..     369     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                 YchF-GTPase_C  16 tikkgttapqaAgviHsDfekgFira 41 
                                    ik+++t ++ A viH+++ kgF+ a
  gi|70606433|ref|YP_255303.1| 345 LIKRNSTPKDLASVIHTELAKGFLYA 370
                                   58999******************977 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.074
                 YchF-GTPase_C  62 gklrlegkdyvvqdgDiilf 81 
                                   +k  + g dy +q+ Dii +
  gi|70606433|ref|YP_255303.1| 374 KKKIRVGEDYKLQHRDIIKI 393
                                   444567***********975 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.036   1.1e+02      79     103 ..     174     204 ..     151     207 .. 0.69
   2 ?   13.0   0.3   2.6e-05     0.079      15      94 ..     180     259 ..     170     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.036
                  MMR_HSR1_Xtn  79 e......pnsvviSaekelnldeLkekiwee 103
                                   +      ++  ++Sa ke++l++Lk + w+e
  gi|70606433|ref|YP_255303.1| 174 KlsglsiNKFHIVSALKETKLENLKLMQWSE 204
                                   2233344688899************999976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.6e-05
                  MMR_HSR1_Xtn  15 ldeetvkkilkeykihnaevliredvtvDdlidvieg.nrvYipclyvlNKiDl.isleeldelare.pnsvviSaekeln 92 
                                   +++ ++ + lke k+ n +++   + + Ddl ++  +     +p +++ NK+D   s + +++l+++ + +v++Sae+el 
  gi|70606433|ref|YP_255303.1| 180 INKFHIVSALKETKLENLKLM---QWSEDDLRNFTRKlREISKPIVIAANKADIkESRKFIEKLKQKyQWIVPVSAESELA 257
                                   566677888888888888876...67889999999883557789999******95677889999998357788*****998 PP

                  MMR_HSR1_Xtn  93 ld 94 
                                   l 
  gi|70606433|ref|YP_255303.1| 258 LR 259
                                   75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2257.87
//
Query:       gi|70606434|ref|YP_255304.1|  [L=405]
Description: nucleotidyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-37  129.2   0.0    2.4e-37  128.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.5e-26   91.1  12.1    8.1e-08   31.7   0.0    4.7  4  Hexapep          Bacterial transferase hexapeptide (six repea
    4.2e-14   53.2   0.0    5.7e-14   52.8   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    5.5e-07   29.2  10.5     0.0063   16.2   1.1    4.1  5  Hexapep_2        Hexapeptide repeat of succinyl-transferase
    7.1e-07   29.2   0.0    1.4e-06   28.2   0.0    1.6  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
       0.03   14.2   0.0      0.049   13.6   0.0    1.3  1  CTP_transf_3     Cytidylyltransferase
      0.075   11.2   1.6       0.31    9.1   0.3    2.1  2  DUF4954          Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0   9.3e-41   2.4e-37       1     243 [.       2     224 ..       2     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 9.3e-41
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   kavILa GsG+RL P+t+t++k+ +p+lgk +li +++++l + + +  i+v+++  ++ +e+ +++       v+ ++++
  gi|70606434|ref|YP_255304.1|   2 KAVILAAGSGERLEPVTQTRPKQFIPILGK-PLISYVIEELRKLNLDI-IIVVNNAYREYFESRIGSL------VKLVIQN 74 
                                   79****************************.***********877776.9999999*********988......6799*** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   egkgtA A+  +++ +  +++   +l + gD++ +d +  +++k i +++  + +++ v+v+++++yGv  ad++++ +++
  gi|70606434|ref|YP_255304.1|  75 EGKGTAAALNAVRNSVSGNEN---ILLMYGDVFLGD-L-GIIEKVIREES--ENVILGVRVQNPKDYGVLVADHNNELKEI 148
                                   *****************9996...***********5.4.45555555555..56789999********************* PP

                                   ECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 163 vEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   +EKP++++ s+l++ GiY   ++++++l +++++++rge e+td+++ + +++kv++ +  ++   W D+G + ++l +n+
  gi|70606434|ref|YP_255304.1| 149 IEKPENPP-SNLINGGIYKLGPDIFHYL-EKISKSPRGELELTDAVSLMSKSSKVKV-LKYEG--FWIDIGRPWDILSVNK 224
                                   ********.*******************.66******************99988886.46677..6*******99999886 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.2e-11   8.1e-08       2      35 ..     249     282 ..     248     283 .. 0.96
   2 !   17.5   0.0   9.7e-07    0.0025       8      29 ..     279     300 ..     278     302 .. 0.91
   3 !   20.0   0.3   1.6e-07    0.0004       3      36 .]     303     335 ..     301     335 .. 0.88
   4 !   30.3   2.7     9e-11   2.3e-07       1      36 []     360     395 ..     360     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.2e-11
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   ++I++++ I++f++i g++ IG++++Ig++++i+
  gi|70606434|ref|YP_255304.1| 249 VIIEEGAEIRSFSYIEGPTYIGKGCHIGPHSYIR 282
                                   79******************************97 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 9.7e-07
                                   EEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   8 vlIgpfaviggnVkIGdnvkIg 29 
                                   ++I+p++v++++VkIG ++ I 
  gi|70606434|ref|YP_255304.1| 279 SYIRPYTVLLNDVKIGTHTEIK 300
                                   68****************9996 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.6e-07
                                   EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   ++ +n++I + +++ g+ +IG++v  gag+vi++
  gi|70606434|ref|YP_255304.1| 303 IVMENSKIPHLSYV-GDSVIGEDVNFGAGTVIAN 335
                                   6889**********.5555*************85 PP

  == domain 4  score: 30.3 bits;  conditional E-value: 9e-11
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                   +++IG++v  g +++i++++kIG ++kI +g+v+++
  gi|70606434|ref|YP_255304.1| 360 GAIIGDHVRTGINVTILPGIKIGAYAKIYPGSVVNR 395
                                   589******************************985 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   2.2e-17   5.7e-14       1     116 [.       3     121 ..       3     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 2.2e-17
                                   EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC.T..S-EEE-TTSS-SHH CS
                  NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggdeevlaalarl.g..vrvvededpgkgpl 73 
                                   aviLA+G + R+    +  +K+++p+ gkpl+ +v++ lr++++d +++v+++   +++++++ g  v++v +  +gkg++
  gi|70606434|ref|YP_255304.1|   3 AVILAAGSGERLEpvtQtrPKQFIPILGKPLISYVIEELRKLNLD-IIIVVNNAY-REYFESRiGslVKLVIQN-EGKGTA 80 
                                   79**********6554245***********************985.555555532.223333323346666665.59**** PP

                                   HHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTS CS
                  NTP_transf_3  74 aslaaalraaadadavlvlacDmPlltpelverllaaaaasga 116
                                   a+l a  +++++++ +l++ +D+ l +  ++e+++++  +s++
  gi|70606434|ref|YP_255304.1|  81 AALNAVRNSVSGNENILLMYGDVFLGDLGIIEKVIRE--ESEN 121
                                   ***********************99999999999886..3333 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.2   5.5e+03       6      13 ..     120     127 ..     120     128 .. 0.75
   2 !   11.1   0.0    0.0001      0.26       1      16 [.     266     281 ..     248     283 .. 0.60
   3 !   12.0   0.0   5.1e-05      0.13       1      20 [.     266     287 ..     266     295 .. 0.73
   4 ?    4.7   0.2      0.01        26       4      16 ..     321     333 ..     320     334 .. 0.88
   5 !   16.2   1.1   2.5e-06    0.0063       3      33 ..     362     394 ..     360     395 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                                   TT-EE-TT CS
                     Hexapep_2   6 dnCliGan 13 
                                   +n+++G++
  gi|70606434|ref|YP_255304.1| 120 ENVILGVR 127
                                   68888876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                                   .EEE-TT-EE-TT-EE CS
                     Hexapep_2   1 pviIGdnCliGanagi 16 
                                   p+ IG+ C iG+ ++i
  gi|70606434|ref|YP_255304.1| 266 PTYIGKGCHIGPHSYI 281
                                   4556666666666655 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 5.1e-05
                                   .EEE-TT-EE-TT-EE.S.EEE CS
                     Hexapep_2   1 pviIGdnCliGanagi.G.vsl 20 
                                   p+ IG+ C iG+ ++i + + l
  gi|70606434|ref|YP_255304.1| 266 PTYIGKGCHIGPHSYIrPyTVL 287
                                   899************9744444 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.01
                                   E-TT-EE-TT-EE CS
                     Hexapep_2   4 IGdnCliGanagi 16 
                                   IG+++++Ga  +i
  gi|70606434|ref|YP_255304.1| 321 IGEDVNFGAGTVI 333
                                   9********9886 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 2.5e-06
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
                     Hexapep_2   3 iIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                                   iIGd +  G n +i  G+++G  +++++G+v+ 
  gi|70606434|ref|YP_255304.1| 362 IIGDHVRTGINVTIlpGIKIGAYAKIYPGSVVN 394
                                   9************99****************96 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   5.6e-10   1.4e-06       2      95 ..       2      97 ..       1     130 [. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 5.6e-10
                                  EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG.CCEEEEE--SSHHHH CS
                          IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld.ksiqlvaGGdeRaes 80
                                   +vi AAGsG+R++   + +pKqf+ + g++l++  ++ l +  ++d i+vv ++++ e+fe+  ++  ++++ + G+  a +
  gi|70606434|ref|YP_255304.1|  2 KAVILAAGSGERLEpvtQTRPKQFIPILGKPLISYVIEELRK-LNLDIIIVVNNAYR-EYFESRIGSlVKLVIQNEGKGTAAA 82
                                  69**********86433789******************9988.78888888888887.8888777762334444455555554 PP

                                  HHHHHHTTSSTTSEE CS
                          IspD 81 VlnglkalegeakfV 95
                                   ++  + ++g++++ 
  gi|70606434|ref|YP_255304.1| 83 LNAVRNSVSGNENIL 97
                                  444445555555554 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.049      16      99 ..      23     102 ..      18     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                   GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE CS
                  CTP_transf_3  16 KnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmseneeiivnl 96 
                                   K  ++++gkpli yv+e+++k  +  ++i+   +   + +   +g  v +  +++ ++t++ l++v++  +   +e i+ +
  gi|70606434|ref|YP_255304.1|  23 KQFIPILGKPLISYVIEELRKLNL--DIIIVVNNAYREYFESRIGSLVKLVIQNEGKGTAAALNAVRNSVSG--NENILLM 99 
                                   8889*****************666..5666665555555566666788888889999999999999886666..3444445 PP

                                   -TT CS
                  CTP_transf_3  97 qGd 99 
                                   +Gd
  gi|70606434|ref|YP_255304.1| 100 YGD 102
                                   555 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.031        80     322     345 ..     248     271 ..     243     281 .. 0.74
   2 ?    9.1   0.3   0.00012      0.31     175     239 ..     274     335 ..     270     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.031
                       DUF4954 322 qgiveRGskttsdsYilwPariga 345
                                   + i+e G+   s sYi  P++ig 
  gi|70606434|ref|YP_255304.1| 248 KVIIEEGAEIRSFSYIEGPTYIGK 271
                                   678888888888888888877774 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00012
                       DUF4954 175 eigekvkilnagl.ikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikd 239
                                   +ig ++ i+  ++ ++ vkig +++i+ +  +en        + +++G++Vi ed+ + +G+ i++
  gi|70606434|ref|YP_255304.1| 274 HIGPHSYIRPYTVlLNDVKIGTHTEIKESIVMENSK----IPHLSYVGDSVIGEDVNFGAGTVIAN 335
                                   588888888766515569***************955....57899***************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2413.18
//
Query:       gi|70606435|ref|YP_255305.1|  [L=197]
Description: 30S ribosomal protein S3Ae [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-67  225.0   1.5    7.7e-67  224.8   1.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.052   13.7   0.0        3.9    7.7   0.0    2.2  2  DUF3234         Protein of unknown function (DUF3234)


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   1.5   8.6e-71   7.7e-67       3     202 .]       6     195 ..       4     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 8.6e-71
                                   ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEE.EEESSE CS
                Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkie.evqgkn 82 
                                   +  ++Dk+k K+Wy ++aP++fg++ +G+t++        + +k+  r +ev+l+DLt+d+ + ++++l++ki  +++g++
  gi|70606435|ref|YP_255305.1|   6 SSTIRDKWKLKKWYVITAPKVFGEALLGSTPA-------YDINKALSRKIEVTLYDLTGDY-NLVYIHLYFKILgNISGDK 78 
                                   5679****************************.......*********************9.668*******9649***** PP

                                   EEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HH CS
                Ribosomal_S3Ae  83 altnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlk 163
                                   ++t F+g+el+rD++rslvr++ss+I+a+vdv+tkDgy+lrv+ +++T++r   a+ sqk+aIrk++ +i++++a+e+d++
  gi|70606435|ref|YP_255305.1|  79 LSTIFYGHELSRDYIRSLVRRKSSKINAVVDVTTKDGYMLRVKGLVLTTYR---AHISQKTAIRKVISDITRKKAEESDFD 156
                                   ***************************************************...*************************** PP

                                   HHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                Ribosomal_S3Ae 164 elvkklipeslgkeiekeakkIyplrnveirKvkvlkkP 202
                                   ++v+++i+ +l+++i++eakkIyplr+vei+K+k+lk+P
  gi|70606435|ref|YP_255305.1| 157 QFVQDVIFGKLSNDIFQEAKKIYPLRKVEIEKTKLLKAP 195
                                   ********77***************************98 PP

>> DUF3234  Protein of unknown function (DUF3234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0066        59       3      17 ..      17      31 ..      15      36 .. 0.90
   2 ?    7.7   0.0   0.00044       3.9      22      71 ..      75     124 ..      50     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0066
                                  SEEEEEST...T-BE CS
                       DUF3234  3 twyvledpnvaGehl 17
                                   wyv+  p+v Ge l
  gi|70606435|ref|YP_255305.1| 17 KWYVITAPKVFGEAL 31
                                  6************88 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00044
                                   TTEEEEEEBSSHHHHHHHHHTSTSS.--EEEEE-SHHHHHHHHHHHHHTT CS
                       DUF3234  22 lGqrlsliwtsreeaeaflektpaaeGmrvgalesyalkeaylvalgllk 71 
                                    G++ls+i+  +e ++ +++     +  ++ a+   + k+ y+  ++ l 
  gi|70606435|ref|YP_255305.1|  75 SGDKLSTIFYGHELSRDYIRSLVRRKSSKINAVVDVTTKDGYMLRVKGLV 124
                                   378******************99999999*99999999**9987776653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1260.53
//
Query:       gi|70606436|ref|YP_255306.1|  [L=235]
Description: SpoU rRNA methylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-29  100.9   0.0    9.3e-29  100.4   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
    0.00062   19.7   0.0      0.021   14.7   0.0    2.3  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0     1e-32   9.3e-29       2     142 .]       3     151 ..       2     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1e-32
                                   EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH..EEEESSHHHHHHHHCCCTEEEEE CS
                SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle..lkvvdsleealkelkeegfalva 80 
                                   +++v+ve+e + NlG iaR++k+f ++e ++v+p++     +ea++++a+  ev+e  +k+ +++++a+++++ + +a+ +
  gi|70606436|ref|YP_255306.1|   3 IRLVIVEPEGAYNLGFIARLVKNFLIDEFYVVNPKCD---INEAIKFSAKGSEVIEkmMKITNNFDDAIRDVDLK-IATSS 79 
                                   689*********************************7...5677888888888888788999************9.66655 PP

                                   EST.T-S....EGCCSHHH.....TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                SpoU_methylase  81 tsl.kgk....slseidlk.....ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                   +   kg+    s+++idl+     +kva++fG+E+ Gl++e++++ d l+ Ip ++e++ LN+++Av+i+ly
  gi|70606436|ref|YP_255306.1|  80 IADiKGDllrkSIRPIDLErlikdKKVAFIFGRESVGLTREEIAKSDFLLFIPANPEYPVLNLSHAVGIVLY 151
                                   544555522225557777788899***********************************************9 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.4e-06     0.021      31     177 ..      19     150 ..      12     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHTT-SEEEEE---HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS CS
               Methyltrn_RNA_4  31 iaRsartygvkkyyvvtpleaqrelverilehWtegagaeynpdRkealslvkvvesleealeeiekeegkkplvvatsAr 111
                                   iaR  + + ++++yvv+p  + +    + +++  +  g+e+        +++k+++++++a++++  +  ++  +   +  
  gi|70606436|ref|YP_255306.1|  19 IARLVKNFLIDEFYVVNPKCDIN----EAIKFSAK--GSEVI------EKMMKITNNFDDAIRDVDLKI-ATSSIADIKGD 86 
                                   88888888888888888877644....44555544..44432......257888899999999997665.44555666677 PP

                                   --SS-B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
               Methyltrn_RNA_4 112 kkentvsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                     +++++  +l++l+  ++k+v ++fG  + Gl++e ++k+d++L  i ++ ey  L    Av i+l
  gi|70606436|ref|YP_255306.1|  87 LLRKSIRPIDLERLI--KDKKVAFIFGReSVGLTREEIAKSDFLL-FIPANPEYPVLNLSHAVGIVL 150
                                   889999999******..9999******6489***********987.69999*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1826.38
//
Query:       gi|70606437|ref|YP_255307.1|  [L=200]
Description: hypothetical protein Saci_0622 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-12   47.1   0.0    2.9e-12   46.5   0.0    1.2  1  MTS              Methyltransferase small domain
    2.2e-12   47.0   0.1    2.9e-12   46.6   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      1e-05   26.1   0.0    1.5e-05   25.6   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.1e-05   25.3   0.0    1.5e-05   24.8   0.0    1.2  1  Met_10           Met-10+ like-protein
    9.9e-05   22.0   0.0    0.00015   21.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0013   18.6   0.0     0.0015   18.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0019   17.4   0.0     0.0028   16.9   0.0    1.1  1  DUF3419          Protein of unknown function (DUF3419)
     0.0021   17.9   0.0     0.0029   17.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0032   17.3   0.0     0.0043   16.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0066   15.8   0.0     0.0088   15.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0067   15.7   0.0      0.041   13.1   0.0    1.9  1  N6_Mtase         N-6 DNA Methylase
      0.007   16.3   0.0      0.026   14.4   0.0    1.8  2  Methyltransf_18  Methyltransferase domain
      0.009   16.6   0.0      0.015   16.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.018   15.2   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
      0.025   13.7   0.0      0.045   12.8   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.027   14.4   0.0      0.041   13.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.061   12.9   0.0       0.09   12.4   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.062   14.1   0.0      0.098   13.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
        0.1   12.3   0.0        0.3   10.7   0.0    1.7  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
       0.11   11.6   0.0       0.17   11.0   0.0    1.2  1  Methyltransf_3   O-methyltransferase
       0.12   11.8   0.0        0.2   11.2   0.0    1.2  1  DOT1             Histone methylation protein DOT1


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   3.3e-15   2.9e-12      20     107 ..      27     113 ..      24     121 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.3e-15
                                   HHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                           MTS  20 sklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                                   ++l++e ++ +  ++vlD+G+G+G+l+++++k   + +v  +dv+ +A +++  +l++n+++++v+++ +l+ + + kfd+
  gi|70606437|ref|YP_255307.1|  27 TELIMEMIKIKDGETVLDMGSGTGILSLHALKLGAK-RVLSIDVNPNAADATLCTLKSNGFSGNVLNCYLLDCIRNTKFDV 106
                                   8999999*999999******************9888.899***************************************** PP

                                   EEE---S CS
                           MTS 101 ivsNPPf 107
                                    + NPP+
  gi|70606437|ref|YP_255307.1| 107 AIFNPPY 113
                                   ******7 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   3.4e-15   2.9e-12     159     233 ..      36     110 ..      25     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 3.4e-15
                          PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaN 233
                                   +k ge+vlD+G G+GiL++ a+kLgak+v+ +D+++ A +++   ++ N+ + ++      + ++++k+dv + N
  gi|70606437|ref|YP_255307.1|  36 IKDGETVLDMGSGTGILSLHALKLGAKRVLSIDVNPNAADATLCTLKSNGFSGNVLNCYLLDCIRNTKFDVAIFN 110
                                   7899************************************************977444567888889***98876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.8e-08   1.5e-05       1      70 [.      42     109 ..      42     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.8e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                   vLd+G GtG l+l+++k  g+++v+ +D+++++ +a+   ++++g++ +++++ + d+   + +fD+ + 
  gi|70606437|ref|YP_255307.1|  42 VLDMGSGTGILSLHALKL-GAKRVLSIDVNPNAADATLCTLKSNGFSGNVLNCYLLDCIR-NTKFDVAIF 109
                                   9***************99.69*********************9*9999999999988764.458998887 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.8e-08   1.5e-05      95     153 ..      31      90 ..      17     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-08
                                   HTT..--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE CS
                        Met_10  95 akl..veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv 153
                                   +++  +++ge+V+d+  G G +++ + k++ akrvl+id+nP++       +k N  +  v
  gi|70606437|ref|YP_255307.1|  31 MEMikIKDGETVLDMGSGTGILSLHALKLG-AKRVLSIDVNPNAADATLCTLKSNGFSGNV 90 
                                   4443489********************976.666*********998777777777766554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.8e-07   0.00015      41     123 ..      38     113 ..      28     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                   +g++vLD+ +G+G l+l Al  gak+++ ++ +++a+ +    l++ +++        + l+ +l  + ++ +fd+  ++P
  gi|70606437|ref|YP_255307.1|  38 DGETVLDMGSGTGILSLHALKLGAKRVLSIDVNPNAADATLCTLKSNGFS-------GNVLNCYLLDCIRNTKFDVAIFNP 111
                                   5788********************************99877777776655.......4666666666667789******** PP

                                   SS CS
                 Cons_hypoth95 122 Py 123
                                   Py
  gi|70606437|ref|YP_255307.1| 112 PY 113
                                   *9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-06    0.0015       2      81 ..      37     110 ..      36     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                   ++g +vlD G+GtG l++ +  +lg  ++v +iD +++a       ++++g++  ++  +   + + +     kfD+ + n
  gi|70606437|ref|YP_255307.1|  37 KDGETVLDMGSGTGILSLHAL-KLGA-KRVLSIDVNPNAADATLCTLKSNGFS-GNVLNCYLLDcIRN----TKFDVAIFN 110
                                   7899*****************.7774.78*********988888888888887.34444455554442....567776665 PP

>> DUF3419  Protein of unknown function (DUF3419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.3e-06    0.0028      17      75 ..      25      86 ..      20      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                       DUF3419 17 EDprvdeeaLklepddrvlaItSa.GdNaLsYllaspkrihaVDlNp..aqnaLleLKlaai 75
                                  ED+++ +e++k++ +++vl + S+ G   L+ l+ ++kr+ ++D+Np  a   L+ LK  ++
  gi|70606437|ref|YP_255307.1| 25 EDTELIMEMIKIKDGETVLDMGSGtGILSLHALKLGAKRVLSIDVNPnaADATLCTLKSNGF 86
                                  9********************99646666666799**********98334678999998776 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.3e-06    0.0029      64     122 ..      29      85 ..       8      96 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-06
                                   HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCT CS
                          PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkld 122
                                   l++e++++k+g+ vL++GsG+G+l+   a  +g+k rv+si+  ++ ++++  +lk ++
  gi|70606437|ref|YP_255307.1|  29 LIMEMIKIKDGETVLDMGSGTGILSLH-ALKLGAK-RVLSIDVNPNAADATLCTLKSNG 85 
                                   689********************9754.4444555.48888888887777766666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-06    0.0043      13      58 ..      30      75 ..      20     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
               Methyltransf_23 13 lerllpklraggrvLdiGcGtGillevlrengf.svtgvDlspeave 58
                                  ++++ +  + g  vLd+G GtGil+ ++ + g+  v  +D +p+a +
  gi|70606437|ref|YP_255307.1| 30 IMEMIK-IKDGETVLDMGSGTGILSLHALKLGAkRVLSIDVNPNAAD 75
                                  555553.78899****************999987899*****99765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05    0.0088      51      99 ..      27      75 ..      23      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                  HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHH CS
                          CMAS 51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqak 99
                                  ++li+e +++k+G+t+Ld+G G G l  +a +    +v+++ +  + a 
  gi|70606437|ref|YP_255307.1| 27 TELIMEMIKIKDGETVLDMGSGTGILSLHALKLGAKRVLSIDVNPNAAD 75
                                  57899*************************9986667888877666655 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   4.8e-05     0.041      27      66 ..      19      58 ..      16     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                      N6_Mtase 27 effTPrevsklivellepksgesvyDpacGsggllvqaek 66
                                  +++ P e ++li+e+++ k+ge+v+D+ +G+g l ++a k
  gi|70606437|ref|YP_255307.1| 19 DVYIPAEDTELIMEMIKIKDGETVLDMGSGTGILSLHALK 58
                                  5899****************************88877766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-05     0.026      12      77 ..      36     101 ..      27     109 .. 0.78
   2 ?   -0.9   0.0       1.7   1.4e+03      92     131 ..     129     169 ..     129     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagled.kievrlsdGlek 77 
                                   +++g++v+D G+  g+l+++++k g ak+v+ +D+n+++ ++   +++++g++   ++++l d + +
  gi|70606437|ref|YP_255307.1|  36 IKDGETVLDMGSGTGILSLHALKLG-AKRVLSIDVNPNAADATLCTLKSNGFSGnVLNCYLLDCIRN 101
                                   56789*****************766.78*************99999999999651446666666555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
               Methyltransf_18  92 GgelileILeea.keklkkikklilqpnseaeelRkylven 131
                                   Gg+  ++IL +  +e+++    ++ ++ s++++l ++l e+
  gi|70606437|ref|YP_255307.1| 129 GGKSGIDILLSFlSEVVAGRAYVVYSSLSDEDKLMSFLKER 169
                                   66677777776646677777778888999999999988653 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05     0.015       1      41 [.      43      84 ..      43     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                  EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHH CS
               Methyltransf_11  1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekasee 41
                                  Ld+G+GtG+l+ +  k g +rv+ +D+++++ ++     + +
  gi|70606437|ref|YP_255307.1| 43 LDMGSGTGILSLHALKLGaKRVLSIDVNPNAADATLCTLKSN 84
                                  8*****************************996654444444 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.1e-05     0.018      13      72 ..      31      92 ..      27     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                  HHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEE.....CS-CCC CS
                          FtsJ 13 dekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvtti.....qgditd 72
                                   e  k +k g+tv+D g+++G  s  +l+  ga ++v+++D++p+a    + t+      g++++
  gi|70606437|ref|YP_255307.1| 31 MEMIK-IKDGETVLDMGSGTGILSLHALKL-GA-KRVLSIDVNPNAADATLCTLksngfSGNVLN 92
                                  56677.889*******************99.88.9**********87777777733333444444 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05     0.045      22      56 ..      30      65 ..      26      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                                  HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEE CS
                        RrnaAD 22 IldklnleekltvleigpGkGilTeeLakra.kqvv 56
                                  I++ +++++  tvl++g+G+Gil+ + +k   k v 
  gi|70606437|ref|YP_255307.1| 30 IMEMIKIKDGETVLDMGSGTGILSLHALKLGaKRVL 65
                                  7888999*****************998887656655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05     0.041      13      67 ..      30      77 ..      24      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
               Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelveka 67
                                  + +++    k ++ +tv+D+G+G g Ls            +v++id++ + ++++
  gi|70606437|ref|YP_255307.1| 30 IMEMI----KIKDGETVLDMGSGTGILSLHALK---LGAKRVLSIDVNPNAADAT 77
                                  44444....447889*************98777...5689********9988765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.09       2      55 ..      25      82 ..      24     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          MetW  2 adfeliaeli..kpgsrvldlGcGdGel.lellk.eekqvdgrGleldeegvaecvak 55
                                  +d eli+e+i  k+g +vld+G+G G l l+ lk   k v +  ++ +++  + c+ k
  gi|70606437|ref|YP_255307.1| 25 EDTELIMEMIkiKDGETVLDMGSGTGILsLHALKlGAKRVLSIDVNPNAADATLCTLK 82
                                  5889999996226899**********87555555245667666666666666666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.098       1      71 [.      43     108 ..      43     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv 71 
                                   L+ G+GtG l+ + l+    ++++ +D++p+a +++   l++++  + n+++   ld +      +fD+ +
  gi|70606437|ref|YP_255307.1|  43 LDMGSGTGILSLHALKL-GAKRVLSIDVNPNAADATLCTLKSNG-FSGNVLNCYLLDCIRN---TKFDVAI 108
                                   89************999.899999*********55544444444.4555555555554433...4777766 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035       0.3      12      53 ..      30      72 ..      27      86 .. 0.88
   2 ?   -1.2   0.1       1.5   1.3e+03     179     199 ..     105     125 ..      81     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                                  HHCCS-..--SEEEETT-TTSCCHHCS....SSCEEEEES-HH CS
               MethyltransfD12 12 IkelipkdkgktfvepFaGggaVffeakk.qgkkvlinDined 53
                                  I e+i+ ++g+t+ +  +G+g+++++a+k   k+vl+ D+n+ 
  gi|70606437|ref|YP_255307.1| 30 IMEMIKIKDGETVLDMGSGTGILSLHALKlGAKRVLSIDVNPN 72
                                  7888888899*******************999*********86 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                   .EEEE--S-T.S...TS--GG CS
               MethyltransfD12 179 divYlDPPYnprqytanytly 199
                                   d++ + PPY p ++  n  +y
  gi|70606437|ref|YP_255307.1| 105 DVAIFNPPYLPFEEYDNWLGY 125
                                   566667999986666665555 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.17      28      96 ..      19      85 ..       5      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                  GGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT CS
                Methyltransf_3 28 emevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkag 96
                                  ++ +++++++++  ++k+ +   vl++G  tG   L  al+l    ++l+id++++a++ +l  ++  g
  gi|70606437|ref|YP_255307.1| 19 DVYIPAEDTELIMEMIKIKDGETVLDMGSGTGILSL-HALKLGA-KRVLSIDVNPNAADATLCTLKSNG 85
                                  57899999**9999*****************98666.5889876.59***********99888777666 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023       0.2      33      82 ..      29      77 ..      20      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                  HHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHH CS
                          DOT1 33 evldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnasela 82
                                   +++ +++k+ ++ +D+GSG G +  + al++g k  + +++  na++ +
  gi|70606437|ref|YP_255307.1| 29 LIMEMIKIKDGETVLDMGSGTGILS-LHALKLGAKRVLSIDVNPNAADAT 77
                                  578899****************765.57899****999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1243.46
//
Query:       gi|70606438|ref|YP_255308.1|  [L=222]
Description: dimethyladenosine transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-20   73.0   0.8    7.1e-20   71.2   0.8    1.7  1  RrnaAD    Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.8   3.9e-24   7.1e-20       5     233 ..       2     195 ..       1     209 [. 0.89

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 3.9e-24
                                   XXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-C CS
                        RrnaAD   5 rksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDf 85 
                                   + ++gq+fl++ ++i++ ++ ++ + +  v+eig+G G+ T+     +k   ++E+d +L+++l++        +++  D+
  gi|70606438|ref|YP_255308.1|   2 KNKLGQHFLNDISIIKKLISLVDHS-TRPVIEIGSGNGVITK----FLKPDIAIEIDVSLINHLRN-------YQLIIGDG 70 
                                   789****************999965.789**********996....557889************99.......799***** PP

                                   CGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEE CS
                        RrnaAD  86 lkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftd 166
                                    +  t               vv++lPy+i+t+++   ++  +++++k +l++qk f  ++++     k  ++s l++++  
  gi|70606438|ref|YP_255308.1|  71 RYLPTTR-----------GQVVSSLPYYITTDFFHEAIK--LDNIRKLVLIVQKDFIDKITS-----KSTSISYLLNYYYK 133
                                   **99998...........57******************8..5555****************9.....7899********** PP

                                   EEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHH CS
                        RrnaAD 167 vklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpgge 233
                                   + l  +v++s+fsP+pkv s lv  +r  +     + k+ + +++++   ++k+l+++l+  + + e
  gi|70606438|ref|YP_255308.1| 134 ISLFDIVPPSAFSPNPKVFSQLVVFDRTRK-----YNKNISEIIECISKYRNKSLKNALSLCGYNFE 195
                                   *************************99888.....4688899****************985555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1438.58
//
Query:       gi|70606439|ref|YP_255309.1|  [L=208]
Description: hypothetical protein Saci_0624 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-58  197.4   3.4    2.2e-58  197.2   3.4    1.1  1  DUF655    Protein of unknown function (DUF655)
  ------ inclusion threshold ------
      0.051   13.8   0.0       0.11   12.8   0.0    1.6  1  HHH_6     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   3.4   2.5e-62   2.2e-58       1     180 [.      11     185 ..      11     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 2.5e-62
                                   X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-.TT----TT-EEE-SSS--SSEEEEEEE--GGGS-H CS
                        DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvpl.kevdilkldevaigkgksdkivkikreisyedLtd 80 
                                   le++ ++LDyl++G+p dkh+ hr+kpvvq +ge++++L+e +pl ++ +++ +++v++g+    ki   +  + yedLt 
  gi|70606439|ref|YP_255309.1|  11 LENYGYILDYLRQGNPLDKHQYHRNKPVVQLIGEDYFMLMEASPLdSKFEFQLEQRVELGSTP-LKI---DNLVIYEDLTT 87 
                                   6999****************************************97889**********9754.455...679******** PP

                                   HHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHH CS
                        DUF655  81 varaeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeil 161
                                   var+eL +v+++i+ +kE+ fv+ffn aep+t++lHaLelLp++gkk++r ileeR+++ F+s++d+++r+ g+kd+++il
  gi|70606439|ref|YP_255309.1|  88 VAREELVKVLRNIILQKEEIFVKFFNTAEPLTLKLHALELLPNIGKKTLRIILEERRKQLFTSYKDIESRI-GVKDVVNIL 167
                                   ***********************************************************************.5******** PP

                                   HHHHHHHHH-TTSS--SS- CS
                        DUF655 162 verileEiedktekYylFv 180
                                    eri++E+++  ekYylFv
  gi|70606439|ref|YP_255309.1| 168 EERIIKELQGG-EKYYLFV 185
                                   **********9.******8 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05      0.11      28      66 ..     124     160 ..     109     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                         HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvdsl 66 
                                   +L+ + ++g+++++ i++eR+ ++ f+s +d+ +r++ +
  gi|70606439|ref|YP_255309.1| 124 ALELLPNIGKKTLRIILEERR-KQLFTSYKDIESRIG-V 160
                                   5777889*************9.8************99.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 1516.67
//
Query:       gi|70606440|ref|YP_255310.1|  [L=114]
Description: DNA-directed RNA polymerase subunit F [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-07   30.1   1.4    5.7e-07   29.9   1.4    1.1  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0066   16.4   1.3      0.031   14.3   0.1    2.1  2  DUF1160       Protein of unknown function (DUF1160)
  ------ inclusion threshold ------
      0.013   15.9   2.0       0.21   12.1   0.2    2.1  2  HTH_40        Helix-turn-helix domain
      0.023   14.3   1.2      0.028   14.0   1.2    1.1  1  MICSWaP       Spore wall protein
      0.026   14.4   0.1       0.09   12.6   0.1    1.8  1  RIH_assoc     RyR and IP3R Homology associated
      0.091   13.1   1.3       0.26   11.6   0.6    1.9  2  DUF2209       Uncharacterized protein conserved in archaea (D
      0.092   12.7   1.5        2.2    8.3   0.1    2.7  3  HTH_36        Helix-turn-helix domain
       0.11   12.4   0.0       0.14   12.0   0.0    1.2  1  Arch_fla_DE   Archaeal flagella protein
       0.11   12.5   0.0       0.17   11.9   0.0    1.5  1  HTH_15        Helix-turn-helix domain of alkylmercury lyase


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.4   2.9e-10   5.7e-07      38     122 ..      28     111 ..       5     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.9e-10
                                   TCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTS.TSHHHHHHHH CS
                  RNA_pol_Rpb4  38 kgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerf.edeqleeiLd 117
                                   +g +++ ++kt +yl+   sr++ e+++++++++l+++   +  ++ l +++P++++e++++   + + + + eq+++i++
  gi|70606440|ref|YP_255310.1|  28 TGSSSNLIQKTFDYLNS-ISRCD-EDSASKIMKELEEIVKREDVRAVLASICPTTVEEVRSVLVIDPSTIySTEQIQKIIE 106
                                   45667788999*****9.9**99.999********************************98766666665599******** PP

                                   HHHHH CS
                  RNA_pol_Rpb4 118 elkev 122
                                   ++k++
  gi|70606440|ref|YP_255310.1| 107 IIKKY 111
                                   ***98 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.6e-05     0.031      38      80 ..       4      46 ..       1      91 [. 0.77
   2 ?    1.9   0.3      0.11   2.1e+02      84      95 ..     102     113 ..      60     114 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                       DUF1160 38 klvkvlkmFiereievediyeiveavdgikLtkkQidylvkqv 80
                                   l+++ + F+   i ++ i+e++++  +++L +k  dyl +  
  gi|70606440|ref|YP_255310.1|  4 SLKTIEEHFVPYSIAKKYIKELIDTGSSSNLIQKTFDYLNSIS 46
                                  6889999********************************7543 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                       DUF1160  84 ekiisilqkfvd 95 
                                   +kii+i++k+v+
  gi|70606440|ref|YP_255310.1| 102 QKIIEIIKKYVE 113
                                   578888889887 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011      0.21      25      89 .]       4      73 ..       1      73 [. 0.82
   2 ?    3.9   0.1     0.038        76      43      63 ..      90     110 ..      80     114 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                        HTH_40 25 kesTIegHLaelieegeeidlerlvse.eeekeIeeaiekvgsek......lkpikealpeevsydeIrlvl 89
                                  + +TIe+H++ +  +++   +++l+++ +  + I+++++ ++s +       ++i ++l+e v+ +++r+vl
  gi|70606440|ref|YP_255310.1|  4 SLKTIEEHFVPYSIAKK--YIKELIDTgSSSNLIQKTFDYLNSISrcdedsASKIMKELEEIVKREDVRAVL 73
                                  689************86..7899*988899999999999966444556666999999999999999999886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.038
                        HTH_40  43 idlerlvseeeekeIeeaiek 63 
                                   id + ++s+e++++I+e+i+k
  gi|70606440|ref|YP_255310.1|  90 IDPSTIYSTEQIQKIIEIIKK 110
                                   566788999*********998 PP

>> MICSWaP  Spore wall protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   1.4e-05     0.028       7      82 ..      12      89 ..       9     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                       MICSWaP  7 yiseevrekYsdkgedleskvqkvaeele..kalNkslkksnkeiriefdievsleipneieldkCgksvselaslLn 82
                                  +++   ++kY ++ +d +s  + +++     +++ +  + s ++i  e++ +v++e+++ +   +C+++v+e+ s+L 
  gi|70606440|ref|YP_255310.1| 12 FVPYSIAKKYIKELIDTGSSSNLIQKTFDylNSISRCDEDSASKIMKELEEIVKREDVRAVLASICPTTVEEVRSVLV 89
                                  78888999999999999887666665553114566669999999*******************************995 PP

>> RIH_assoc  RyR and IP3R Homology associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.5e-05      0.09      23      57 ..      16      65 ..       6     114 .] 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                     RIH_assoc 23 selqnylreQkdnktsynlvseivdllenlskat...............e 57
                                  s  ++y++e  d  +s nl+++++d+l+++s+                 +
  gi|70606440|ref|YP_255310.1| 16 SIAKKYIKELIDTGSSSNLIQKTFDYLNSISRCDedsaskimkeleeivK 65
                                  56799*************************98744444444444444440 PP

>> DUF2209  Uncharacterized protein conserved in archaea (DUF2209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.98   1.9e+03      86     101 ..      31      46 ..      26      50 .. 0.82
   2 ?   11.6   0.6   0.00013      0.26      22      63 ..      71     113 ..      67     114 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.98
                       DUF2209  86 veailkkefkyqeslg 101
                                   ++++++k f y +s++
  gi|70606440|ref|YP_255310.1|  31 SSNLIQKTFDYLNSIS 46 
                                   67889999***99998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00013
                       DUF2209  22 aVslevsadriekveqvkil.vvaseeepkledvvklieeave 63 
                                   aV +++ ++ +e+v++v ++ + +  ++ ++++++++i++ ve
  gi|70606440|ref|YP_255310.1|  71 AVLASICPTTVEEVRSVLVIdPSTIYSTEQIQKIIEIIKKYVE 113
                                   89**************98652788999************9986 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.062   1.2e+02      43      53 ..      19      29 ..      18      30 .. 0.89
   2 ?    8.3   0.1    0.0011       2.2      27      51 ..      38      62 ..      33      63 .. 0.93
   3 ?   -2.9   0.1       3.5   6.9e+03      39      46 ..      98     105 ..      96     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.062
                        HTH_36 43 sraikeLeqlG 53
                                   ++ikeL+++G
  gi|70606440|ref|YP_255310.1| 19 KKYIKELIDTG 29
                                  69******998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                        HTH_36 27 sqetlakrlglsknTvsraikeLeq 51
                                  ++++l + + ++++++s++ keLe+
  gi|70606440|ref|YP_255310.1| 38 TFDYLNSISRCDEDSASKIMKELEE 62
                                  6899*******************97 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.5
                        HTH_36  39 knTvsrai 46 
                                    ++++++i
  gi|70606440|ref|YP_255310.1|  98 TEQIQKII 105
                                   55666665 PP

>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.14       4      67 ..       3      66 ..       1      91 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                   Arch_fla_DE  4 pyLeelpedyaaelvvleWlefLvervgvena.aealdyYeeigWiseevreeLlkylkgikled 67
                                  + L++++e+++   ++ + ++ L+++++ +n+ +++ dy ++i   +e+ +++++k l+ i    
  gi|70606440|ref|YP_255310.1|  3 YSLKTIEEHFVPYSIAKKYIKELIDTGSSSNLiQKTFDYLNSISRCDEDSASKIMKELEEIVK-R 66
                                  5799**********************9998862689********************9999864.2 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-05      0.17      39      64 ..      71      96 ..      41     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                        HTH_15 39 eeLAaatgrsveevrqaLaalpstEy 64
                                  + LA +  ++veevr +L   pst y
  gi|70606440|ref|YP_255310.1| 71 AVLASICPTTVEEVRSVLVIDPSTIY 96
                                  679******************99977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 919.31
//
Query:       gi|70606441|ref|YP_255311.1|  [L=103]
Description: 50S ribosomal protein L21e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-35  120.3   2.4    2.9e-35  120.2   2.4    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   2.4   1.6e-39   2.9e-35       2      99 ..       3      97 ..       2      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 1.6e-39
                                  --S-STTTT-TTTTS--GGG-S.S--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETTE CS
                Ribosomal_L21e  2 knskglrrgtrklfskkfrkkg.vpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvggk 83
                                  ++skg+r++trkl++kk+r+kg +p+ls ++++y +G++V +ki+ps++kgmph+ryhGk+g v  v+kr++++ v++++g+k
  gi|70606441|ref|YP_255311.1|  3 ARSKGYRSKTRKLLEKKVREKGaIPKLSLLMHDYSQGEYVVVKINPSIHKGMPHRRYHGKVGLV--VGKRGKAYEVKVNIGDK 83
                                  689*******************8889**************************************..***************** PP

                                  ..EEEEEE-GGGEEE- CS
                Ribosomal_L21e 84 ileKriivriehlkks 99
                                    e+ +ivr+ehl ++
  gi|70606441|ref|YP_255311.1| 84 --ERVLIVRPEHLIPF 97
                                  ..**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 675.79
//
Query:       gi|70606442|ref|YP_255312.1|  [L=333]
Description: hypothetical protein Saci_0630 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.5    6.7   7.8        1.9    8.9   0.1    3.2  4  DUF5603   Domain of unknown function (DUF5603)


Domain annotation for each model (and alignments):
>> DUF5603  Domain of unknown function (DUF5603)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1      0.66   1.2e+04      30      38 ..      12      19 ..       3      37 .. 0.48
   2 ?    8.9   0.1    0.0001       1.9       7      24 ..      54      71 ..      48      87 .. 0.81
   3 ?    1.3   0.3     0.023   4.2e+02      63      95 ..     171     201 ..     114     206 .. 0.65
   4 ?   -2.8   0.0      0.46   8.2e+03       2      22 ..     248     268 ..     247     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.66
                                  HHHH...HH CS
                       DUF5603 30 keeklkdee 38
                                  +++  k +e
  gi|70606442|ref|YP_255312.1| 12 TDDE-KKKE 19
                                  3333.2222 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0001
                                  ES-HHHHHHHHHHTT--- CS
                       DUF5603  7 kgdlnklleelkkeglrv 24
                                  kg++n++leel keg+  
  gi|70606442|ref|YP_255312.1| 54 KGHINNVLEELNKEGVVK 71
                                  89*************854 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.023
                                   HHHHHHHHHHHHHTTSSEEEEESSHHHHHHHHH CS
                       DUF5603  63 qkkvskvldklslegkielvyygekeealrdle 95 
                                    kk  k ld+ +le  + + yy   e++ + ++
  gi|70606442|ref|YP_255312.1| 171 IKKTKKRLDENNLE--FLVFYYSTNEDSIKLMA 201
                                   35666777777775..56678888888777665 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.46
                                   -EEEEES-HHHHHHHHHHTT- CS
                       DUF5603   2 wypaikgdlnklleelkkegl 22 
                                   +yp ++ ++ ++ +e  k+g+
  gi|70606442|ref|YP_255312.1| 248 FYPLFVKKVREVRKEREKNGV 268
                                   689999999999888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2118.62
//
Query:       gi|70606443|ref|YP_255313.1|  [L=99]
Description: hypothetical protein Saci_0631 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.13   12.4   0.0    1.2  1  CppA_N    CppA N-terminal


Domain annotation for each model (and alignments):
>> CppA_N  CppA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.1e-06      0.13      72     114 ..       3      45 ..       1      55 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.1e-06
                        CppA_N  72 venpkeiekllakgaqakklfkGqnGyafetispeddlillha 114
                                   +e++ke+ +ll  + +++k  kG+ Gy + +  p+    ll a
  gi|70606443|ref|YP_255313.1|   3 TEKTKEVSQLLIPDLKIRKTNKGKKGYVYLIQLPQRFNKLLRA 45 
                                   689**************************99888876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 662.77
//
Query:       gi|70606444|ref|YP_255314.1|  [L=258]
Description: hypothetical protein Saci_0632 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.001   18.9   0.0     0.0017   18.2   0.0    1.3  1  Replicase      Replicase family
  ------ inclusion threshold ------
      0.033   14.6   0.3       0.59   10.5   0.0    2.4  2  EntA_Immun     Enterocin A Immunity
      0.041   14.0   0.0      0.053   13.7   0.0    1.1  1  RepB_primase   RepB DNA-primase from phage plasmid
       0.07   13.3   0.0       0.24   11.6   0.0    1.9  2  DOPA_dioxygen  Dopa 4,5-dioxygenase family
       0.17   10.2   0.5        4.9    5.4   0.3    2.0  2  Sec3_C         Exocyst complex component Sec3


Domain annotation for each model (and alignments):
>> Replicase  Replicase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.7e-07    0.0017      23      76 ..     147     199 ..     125     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.7e-07
                     Replicase  23 asvlvfDiDkp.dallrwedaklpkPnlivknpkngh.ahllyaletpvattenar 76 
                                    ++l +DiD+  + +lr      p+P +i  +   gh ahl+y l+  v+t+e+ +
  gi|70606444|ref|YP_255314.1| 147 CQWLFYDIDNVnETVLRNLSRLSPRPVVILYS---GHgAHLYYKLSRKVRTEEYKK 199
                                   48*********666666667777777777654...455********99*9998765 PP

>> EntA_Immun  Enterocin A Immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.12   4.1e+02      20      36 ..      29      45 ..      14      47 .. 0.79
   2 ?   10.5   0.0   0.00016      0.59      23      51 ..     205     233 ..     187     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.12
                    EntA_Immun 20 neelrevLltaknklek 36
                                  +ee+re+L++ + k+ek
  gi|70606444|ref|YP_255314.1| 29 EEEVRELLMSGLAKVEK 45
                                  3449******9999997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                    EntA_Immun  23 lrevLltaknklekgknvsvvasrLeqel 51 
                                    +  L++++nk++k+k+ + v++rL  +l
  gi|70606444|ref|YP_255314.1| 205 AKRYLTQYLNKIDKTKSGPYVLARLPGTL 233
                                   5789********************97666 PP

>> RepB_primase  RepB DNA-primase from phage plasmid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.053      61     144 ..     150     238 ..      91     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                  RepB_primase  61 lylliDdlgsaklakliaeglePaavletSPgnyqawlrvkaplshalrtaaakaLaery......GgDpaaadvsrfgRl 135
                                   l+ +iD + +  l+ l++   +P+++l +     ++ +++++ + +++ +++ +  a+ry        D++ ++    +Rl
  gi|70606444|ref|YP_255314.1| 150 LFYDIDNVNETVLRNLSRLSPRPVVILYSGH-GAHLYYKLSRKVRTEEYKKIWQRFAKRYltqylnKIDKTKSGPYVLARL 229
                                   5568***********9999999999999776.778******999999999999999999999999999************* PP

                  RepB_primase 136 PGfnnrKpk 144
                                   PG+ n+K  
  gi|70606444|ref|YP_255314.1| 230 PGTLNCKDP 238
                                   *******43 PP

>> DOPA_dioxygen  Dopa 4,5-dioxygenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.87   3.1e+03      19      47 ..      30      55 ..      11      77 .. 0.59
   2 ?   11.6   0.0   6.8e-05      0.24       3      49 ..     182     227 ..     180     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.87
                                  HHHHHHHHHHTTTT..E---BSS--TT-S CS
                 DOPA_dioxygen 19 keLrekirrefeeelrvgklaekpiGPhp 47
                                  +e+re +++ +   ++v+kl+ +  GP+ 
  gi|70606444|ref|YP_255314.1| 30 EEVRELLMSGL---AKVEKLSAHIDGPYR 55
                                  23333333333...357777777778875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.8e-05
                                   EEEEE...-GGGHHHHHHHHHHHHHHTTTT..E---BSS--TT-SSE CS
                 DOPA_dioxygen   3 vhiyylendeaekkeAkeLrekirrefeeelrvgklaekpiGPhpva 49 
                                   +h yy  + + +++e k++++++++++ ++  ++k+ +++ GP+  a
  gi|70606444|ref|YP_255314.1| 182 AHLYYKLSRKVRTEEYKKIWQRFAKRYLTQ-YLNKIDKTKSGPYVLA 227
                                   7**************************885.8************876 PP

>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.3    0.0014       4.9     631     690 ..      20      77 ..       4      87 .. 0.87
   2 ?    3.2   0.0    0.0065        23     156     183 ..     193     220 ..     190     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0014
                        Sec3_C 631 lkkilskYtakeirkgieklykrvekhfledadravleeeLlqkvwseleeefiskylrl 690
                                   l+ + ++Y+++e+r+++ + + +vek    + d + +++ L+ ++  e+  ++i+k+l l
  gi|70606444|ref|YP_255314.1|  20 LEYVKKNYKEEEVRELLMSGLAKVEKLS-AHIDGP-YRDYLVYRAIDEIDVNTIKKFLGL 77 
                                   5566689******************955.888988.*******************99866 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0065
                        Sec3_C 156 rrerYekvsssFlrrlveflekkfksae 183
                                   r e+Y+k+ ++F++r +++  +k+++++
  gi|70606444|ref|YP_255314.1| 193 RTEEYKKIWQRFAKRYLTQYLNKIDKTK 220
                                   7899*************99999997763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1698.76
//
Query:       gi|70606445|ref|YP_255315.1|  [L=533]
Description: hypothetical protein Saci_0633 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0068   16.0   0.0      0.012   15.3   0.0    1.3  1  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


Domain annotation for each model (and alignments):
>> LmjF365940-deam  A distinct subfamily of CDD/CDA-like deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.6e-07     0.012      11      93 ..     391     469 ..     383     475 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-07
               LmjF365940-deam  11 kkfranllaaiqek.kelasfwlrktkkpVlavllvekkkaelggdgreelvrgvNlEvSmPtGSlCsErnaigkalasdp 90 
                                     f ++++ ++ ++  ++ ++ l  ++k Vl  +l+++     + + +ee+  gvN++  m +GS+C E  +ig   + d 
  gi|70606445|ref|YP_255315.1| 391 SGFYDRAEVVVFKNrFNAPKYILDESEKEVLINILIRRA---QALSEKEEIHVGVNFDKFMESGSKCEE--VIGLIKSGDK 466
                                   5566666666555558899999999************87...5667899******************98..6776666666 PP

               LmjF365940-deam  91 slr 93 
                                    l 
  gi|70606445|ref|YP_255315.1| 467 ILS 469
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4093.04
//
Query:       gi|70606446|ref|YP_255316.1|  [L=216]
Description: resolvase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-39  134.8   0.1      3e-39  134.4   0.1    1.1  1  Resolvase  Resolvase, N terminal domain


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   0.1   1.7e-43     3e-39       1     145 [.       3     154 ..       3     155 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 1.7e-43
                                   EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-..TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S. CS
                     Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGak..leRpglkrllaalregkgdvlvvekldRLaRs 79 
                                   a+gYaRvS e+++  +e+Q++++ ayak+ng+++ k+f+D gvSG+k  leR+g+k+l++a +   ++++v+++l+RL+R+
  gi|70606446|ref|YP_255316.1|   3 ALGYARVSVEDER--IENQIAEISAYAKNNGIELMKIFTDVGVSGSKpaLEREGFKSLMQASELLDVKTIVIYDLTRLGRD 81 
                                   689**********..******************999***********6556*********99998889************* PP

                                   ..S-HHHHHHHHHTT-EEEESS.....SS----HHHH....HHHHHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                     Resolvase  80 vrdlltlleelrekgvslvsldeg...idtstpmgrl....llqilaalaeferelirertkeglaaakakGk 145
                                   ++dl+t++++l ekg+++ +++++   +++s+p+g++    ll +l+a+ae+er++irert +gla+aka+G+
  gi|70606446|ref|YP_255316.1|  82 LFDLVTTYKTLLEKGYNVLFVKHPelnVTQSSPIGEAlrkaLLVLLGAVAELERAFIRERTVSGLARAKAQGV 154
                                   **********************8668899999998887888999****************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1448.47
//
Query:       gi|70606447|ref|YP_255317.1|  [L=103]
Description: hypothetical protein Saci_0635 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0038   16.8   0.3     0.0063   16.1   0.3    1.4  1  STAR_dimer  Homodimerisation region of STAR domain protein
     0.0086   15.8   0.0      0.054   13.3   0.0    2.0  2  HTH_23      Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   16.2   0.1       0.69   10.5   0.0    2.1  2  Mga         Mga helix-turn-helix domain
      0.013   15.0   0.0      0.029   13.9   0.0    1.7  1  Sigma70_r4  Sigma-70, region 4
      0.021   14.9   0.4       0.16   12.0   0.0    2.4  3  HTH_22      HTH domain
      0.032   14.3   0.0      0.066   13.3   0.0    1.5  1  HTH_7       Helix-turn-helix domain of resolvase
      0.062   13.5   0.0       0.11   12.8   0.0    1.4  1  HTH_17      Helix-turn-helix domain
       0.07   13.3   0.0       0.12   12.5   0.0    1.4  1  HTH_28      Helix-turn-helix domain
      0.071   13.2   0.0       0.12   12.4   0.0    1.4  1  HTH_3       Helix-turn-helix
      0.074   13.1   0.1       0.95    9.5   0.0    2.1  2  DUF2089     Protein of unknown function (DUF2089)
      0.087   12.6   0.0       0.14   12.0   0.0    1.3  1  HTH_8       Bacterial regulatory protein, Fis family
        0.1   12.3   0.0       0.47   10.3   0.0    2.1  1  HTH_38      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> STAR_dimer  Homodimerisation region of STAR domain protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   4.2e-06    0.0063       9      41 ..      59      94 ..      52     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.2e-06
                    STAR_dimer  9 LaqLLkdKKqlaafpn...vftHlerLLdeEIsRVR 41
                                  L  LL+dK +l+ + +   vf  + r +deEI RV 
  gi|70606447|ref|YP_255317.1| 59 LFSLLSDKDKLELLLKlrgVFERVLREIDEEIARVN 94
                                  678*****99998888888****************6 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.6e-05     0.054      11      36 ..      16      43 ..       6      47 .. 0.80
   2 ?    0.4   0.1      0.41   6.2e+02       3      25 ..      64      92 ..      62      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                        HTH_23 11 llllae..GlsvreIAreLgvsrrTvyr 36
                                  +  +++  +l+v+eIA+ Lg+sr  +y+
  gi|70606447|ref|YP_255317.1| 16 VNFVLQrsKLPVTEIAESLGISRISLYK 43
                                  5556666799*************88886 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.41
                        HTH_23  3 sereRlrilllla...e...GlsvreIAr 25
                                  s +++l+ ll l+   e   +   +eIAr
  gi|70606447|ref|YP_255317.1| 64 SDKDKLELLLKLRgvfErvlREIDEEIAR 92
                                  56777888888776552456777888887 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00046      0.69      22      52 ..      16      46 ..       4      50 .. 0.91
   2 ?    3.9   0.0     0.056        84      46      68 ..      78     100 ..      75     103 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00046
                                  HHHHHHHSEEEHHHHHHHCT--HHHHHHHHH CS
                           Mga 22 lkflfeeeevsieelaqelyiSestlkrkik 52
                                  + f++++ ++ ++e+a++l iS+ +l+++ k
  gi|70606447|ref|YP_255317.1| 16 VNFVLQRSKLPVTEIAESLGISRISLYKMSK 46
                                  578999*********************9866 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.056
                                   HHHHHHHHHHHHCHCCT-EEETT CS
                           Mga  46 tlkrkikelnklLkefdleltkk 68 
                                    + r+++e+ + ++ ++l+++++
  gi|70606447|ref|YP_255317.1|  78 VFERVLREIDEEIARVNLKVNTQ 100
                                   57899*************99433 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.029       3      34 ..       5      38 ..       3      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                  HHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-H CS
                    Sigma70_r4  3 asLpererevlelrf..geglTleEIgerlgiSr 34
                                  ++L+++ere ++       +l+  EI+e lgiSr
  gi|70606447|ref|YP_255317.1|  5 KHLSPDEREFVVNFVlqRSKLPVTEIAESLGISR 38
                                  7899999999998888999**************9 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.16      44      60 ..      27      43 ..      20      44 .. 0.91
   2 ?   -0.1   0.1      0.67     1e+03      20      38 ..      63      79 ..      59      93 .. 0.72
   3 ?   -1.4   0.0       1.7   2.6e+03       6      16 ..      86      96 ..      74     103 .] 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                        HTH_22 44 vekvAekLgiSraTvYr 60
                                  v ++Ae LgiSr ++Y+
  gi|70606447|ref|YP_255317.1| 27 VTEIAESLGISRISLYK 43
                                  789*************7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.67
                        HTH_22 20 ltkeekieivraLdekGiF 38
                                  l+ ++k+e+  +   +G+F
  gi|70606447|ref|YP_255317.1| 63 LSDKDKLELLLK--LRGVF 79
                                  666777777644..46666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.7
                        HTH_22  6 ieevladlgkp 16
                                  i+e +a+++ +
  gi|70606447|ref|YP_255317.1| 86 IDEEIARVNLK 96
                                  44555555555 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.4e-05     0.066      21      40 ..      24      43 ..      19      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                                  T--STTTSSSS---SSSS-- CS
                         HTH_7 21 GisiskIAkevnisRsTvYR 40
                                  + ++++IA+ ++isR ++Y+
  gi|70606447|ref|YP_255317.1| 24 KLPVTEIAESLGISRISLYK 43
                                  5689***************9 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     7e-05      0.11       2      30 ..      25      52 ..      25      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7e-05
                        HTH_17  2 ltveEaAelLgvsrstvyrlirrgelpaa 30
                                  l v E+Ae Lg+sr ++y++ ++ge+ a 
  gi|70606447|ref|YP_255317.1| 25 LPVTEIAESLGISRISLYKM-SKGEIHAS 52
                                  5699***************6.79999554 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.3e-05      0.12       2      31 ..      12      43 ..      11      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                        HTH_28  2 RleiikllaaG.h.svreaArelgisrrtvyr 31
                                  R  ++  +++  + +v+e+A+ lgisr ++y+
  gi|70606447|ref|YP_255317.1| 12 REFVVNFVLQRsKlPVTEIAESLGISRISLYK 43
                                  77788888854157*************99995 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.1e-05      0.12       8      44 ..      23      59 ..      19      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                                  TTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                         HTH_3  8 lglsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                   +l  +e+Ae lG+sr +++++ +Ge + s +t++ l
  gi|70606447|ref|YP_255317.1| 23 SKLPVTEIAESLGISRISLYKMSKGEIHASDDTIIGL 59
                                  567789***************************9866 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00064      0.95      30      62 ..       3      37 ..       1      47 [. 0.86
   2 ?    1.8   0.1      0.16   2.4e+02      41      60 ..      68      87 ..      42      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00064
                       DUF2089 30 efarLskeqlefvelfikarGnl..kevekelgis 62
                                  ++++Ls+++ efv  f+ +r +l   e++++lgis
  gi|70606447|ref|YP_255317.1|  3 WVKHLSPDEREFVVNFVLQRSKLpvTEIAESLGIS 37
                                  6789*************999997447999****99 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                       DUF2089 41 fvelfikarGnlkevekelg 60
                                   +el++k rG +++v +e++
  gi|70606447|ref|YP_255317.1| 68 KLELLLKLRGVFERVLREID 87
                                  46888999999999888765 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.3e-05      0.14      14      40 ..      20      45 ..      18      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                                  HHHTTT-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_8 14 LertgGnkskAArlLGisRrtLyrKLk 40
                                  L+r++  +++ A+ LGisR +L +K+ 
  gi|70606447|ref|YP_255317.1| 20 LQRSKLPVTEIAESLGISRISL-YKMS 45
                                  777777899*************.6665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00031      0.47       3      34 ..       5      38 ..       4      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                        HTH_38  3 khLsleeReeIerl.la.eGlslreIArrLgrsp 34
                                  khLs++eRe      l+  +l + eIA  Lg s+
  gi|70606447|ref|YP_255317.1|  5 KHLSPDEREFVVNFvLQrSKLPVTEIAESLGISR 38
                                  8*******988777555266**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 691.73
//
Query:       gi|70606448|ref|YP_255318.1|  [L=90]
Description: hypothetical protein Saci_0636 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   12.0   0.2      0.067   11.8   0.2    1.0  1  DUF4455   Domain of unknown function (DUF4455)


Domain annotation for each model (and alignments):
>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   3.7e-06     0.067      35     120 ..       2      88 ..       1      89 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-06
                       DUF4455  35 eellkklsesdeeieklfkkleddedlekltiqelqelwdkVaee.slkrkswIkeldetLeklEkeRaeklkevlkkyve 114
                                   +el++k +e  +e+ +l++++ + +  + + +  l  +  kV+e+ +++  + I+el +++ ++E +  +++ ++++ yve
  gi|70606448|ref|YP_255318.1|   2 MELKHKKEEYAKELINLLSRFMSGKISYPVLSLRLTGIEAKVHESgFEDLVRLIHELLKAIREAERKGSNEINKLVRPYVE 82 
                                   68899999999999999999999999999999999999999988735677899**************************** PP

                       DUF4455 115 iLekia 120
                                   +Le+ia
  gi|70606448|ref|YP_255318.1|  83 KLESIA 88 
                                   ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 606.97
//
Query:       gi|70606449|ref|YP_255319.1|  [L=425]
Description: pNOB8-type integrase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-13   50.3   0.0    1.9e-12   47.3   0.0    2.4  2  Phage_integrase  Phage integrase family
    1.4e-06   28.3   2.1    0.00069   19.6   0.1    2.7  2  Phage_integr_3   Archaeal phage integrase
  ------ inclusion threshold ------
      0.067   12.8   1.2       0.32   10.7   0.1    2.5  2  Docking          Erythronolide synthase docking
      0.095   13.1   2.1        5.5    7.4   2.1    2.9  1  Radical_SAM      Radical SAM superfamily
       0.13   12.3   0.0        0.4   10.7   0.0    1.8  1  DUF3921          Protein of unknown function (DUF3921)
       0.18   11.9   1.3       0.61   10.2   0.1    2.4  2  TetR_C_8         Transcriptional regulator C-terminal region


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.28   8.2e+02      96     121 ..     129     154 ..      69     201 .. 0.65
   2 !   47.3   0.0   6.5e-16   1.9e-12       8     154 ..     231     389 ..     225     392 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.28
                                   BSSBETTSSB--HHHHHHHHHHHHHH CS
               Phage_integrase  96 llfaskrgkplsrqtvrkafkravee 121
                                    lf +  ++ +s++t++++++ ++++
  gi|70606449|ref|YP_255319.1| 129 QLFEKLLKETKSTKTAKDRLNYLKRA 154
                                   33444444444444444444444333 PP

  == domain 2  score: 47.3 bits;  conditional E-value: 6.5e-16
                                   HHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHH. CS
               Phage_integrase   8 verllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellska. 87 
                                   ++r+++++++   i  k+++ +l etGlR++E+lsL+v+++dle++vi++  +e  ++++ +  l e+ +++lke++    
  gi|70606449|ref|YP_255319.1| 231 LKRIFNNIQD---IGAKAFFLVLAETGLRTGEVLSLTVEQVDLEHRVIKLM-KENETKRAYITFLHENTAKWLKEVYLPYr 307
                                   6788888888...*************************************4.33344445555556777777777665551 PP

                                   ..........CHCCTTTSBSSBET..................TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHH CS
               Phage_integrase  88 ..........leeaeksellfask..................rgkplsrqtvrkafkraveeagiekpltpHtlRhsfata 140
                                             +            k                  +  p  + ++r  +k+a ++     +++  +lR  fa+ 
  gi|70606449|ref|YP_255319.1| 308 edfvsrylenV------------KklaeanpeqgidvtlwfnKFFPFRDDSLRFDIKNAMKRVLGR-EFRLYDLRSFFASY 375
                                   22222222220............1233333333333333444578999999999999999994444.6************* PP

                                   HHHHCTSHHHHHHH CS
               Phage_integrase 141 Lleagvdlrvvqkl 154
                                   ++++gv+++vv  l
  gi|70606449|ref|YP_255319.1| 376 MIKQGVSPMVVNIL 389
                                   *********99765 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3    0.0013       3.8       8      92 ..     230     306 ..     224     325 .. 0.74
   2 !   19.6   0.1   2.3e-07   0.00069     103     144 ..     362     406 ..     336     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTEEEEEEEE-SSS-EEEEEEESS---....-- CS
                Phage_integr_3   8 evrealeelkekseevelvykllvfsGiRLkevlklLreyDpekliveddiarYpialekgeKkafyiylptelakelerl 88 
                                    +++ ++++++    ++  +++l+++G+R  evl+l  e   + +++++     ++ +e  +K+a+  +l  + ak l+++
  gi|70606449|ref|YP_255319.1| 230 ILKRIFNNIQDI--GAKAFFLVLAETGLRTGEVLSLTVE---QVDLEHR---VIKLMKENETKRAYITFLHENTAKWLKEV 302
                                   566777777776..77899****************9877...3333332...33677888899999999988888888887 PP

                                   B--H CS
                Phage_integr_3  89 else 92 
                                   +l +
  gi|70606449|ref|YP_255319.1| 303 YLPY 306
                                   7755 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.3e-07
                                   T--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-...CCTTSCHHC CS
                Phage_integr_3 103 kvkakyiRkwvatklaelgvpeevidFiqGrkp...ssvlekhYl 144
                                   +++   +R ++a+ ++++gv+  v++ +qGr p    ++l++hY 
  gi|70606449|ref|YP_255319.1| 362 EFRLYDLRSFFASYMIKQGVSPMVVNILQGRVPpqqFRILQEHYF 406
                                   4777889************************9977789******7 PP

>> Docking  Erythronolide synthase docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.25   7.5e+02       7      14 ..       9      16 ..       6      16 .. 0.86
   2 ?   10.7   0.1   0.00011      0.32       8      19 ..     149     160 ..     148     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                       Docking  7 RdYLKRvT 14
                                  R+ LKR++
  gi|70606449|ref|YP_255319.1|  9 RELLKRAV 16
                                  999***95 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                       Docking   8 dYLKRvTaDLrq 19 
                                    YLKR+ aDL  
  gi|70606449|ref|YP_255319.1| 149 NYLKRALADLGN 160
                                   5*********65 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.1    0.0018       5.5      77     141 ..     260     325 ..      28     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                   TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH....HHHHHHTCTSHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaadde....kvlklmnrghtfeevlealeklreag 141
                                    +++tve   +    +++++++e ++ r +++  + +      +v  +  r + ++++le+++kl+ea+
  gi|70606449|ref|YP_255319.1| 260 VLSLTVEQVDLE--HRVIKLMKENETKRAYITFLHENTAkwlkEVYLPY-REDFVSRYLENVKKLAEAN 325
                                   333333333444..7999*****99*******99999998887777777.99999**********9994 PP

>> DUF3921  Protein of unknown function (DUF3921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013       0.4      15      37 ..      40      62 ..      35      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                       DUF3921 15 rtydelGkeldlqGvvvdeiqka 37
                                  r yde Gke++    +v+e+ ka
  gi|70606449|ref|YP_255319.1| 40 RGYDERGKEIEPPDEIVNEVMKA 62
                                  89*******************98 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0002      0.61      19      66 ..      84     131 ..      81     137 .. 0.92
   2 ?   -1.5   0.1      0.89   2.7e+03      16      53 ..     282     319 ..     272     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                   HHHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH-TT--S-HHHHHHH CS
                      TetR_C_8  19 dfyknllssngresfekylkelikelilkvieelsegkelseedkefi 66 
                                   d+++++++   ++sf++ +  ++++++ + i+e+++++ +++ed++ +
  gi|70606449|ref|YP_255319.1|  84 DILRVMVKASKDPSFRNIFLFFLHKYFGDLIKETAKEYIVTQEDIQLF 131
                                   78999*********************************9999999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.89
                                   HTHHHHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH- CS
                      TetR_C_8  16 enkdfyknllssngresfekylkelikelilkvieels 53 
                                   e k+ y ++l++n  + +++    + ++++ +++e+ +
  gi|70606449|ref|YP_255319.1| 282 ETKRAYITFLHENTAKWLKEVYLPYREDFVSRYLENVK 319
                                   34677888888888877777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      832  (0.0464053); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2780.26
//
Query:       gi|70606450|ref|YP_255320.1|  [L=631]
Description: metallo-beta-lactamase superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-23   82.8   0.0      4e-23   81.8   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    2.3e-20   72.3   9.6    9.7e-18   63.9   1.1    3.2  3  KH_7           KH domain
    9.8e-17   60.7   0.1    2.2e-15   56.3   0.0    2.5  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    7.6e-14   52.2   0.5    9.5e-13   48.6   0.5    2.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.2e-13   50.1   0.0    7.8e-13   48.3   0.0    1.9  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    4.9e-11   42.5   0.2    9.5e-11   41.6   0.2    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.3e-05   23.8   0.3    0.00019   21.4   0.0    2.3  2  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0034   17.2   8.9      0.039   13.8   1.8    2.9  2  KH_2           KH domain
  ------ inclusion threshold ------
      0.013   14.2   0.8      0.036   12.7   1.2    1.5  2  A-2_8-polyST   Alpha-2,8-polysialyltransferase (POLYST)
        0.5   10.2   3.5       0.55   10.1   0.1    2.7  2  KH_1           KH domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   2.2e-26     4e-23       2     109 ..     416     536 ..     415     537 .. 0.81

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2.2e-26
                                   HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH....HHHH..HH........... CS
                     Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae...........veakslewmeskkeeln........... 60 
                                   qe+++++++++k+kk  ++++p+y+ + ++ ++t+++++y+e                           +           
  gi|70606450|ref|YP_255320.1| 416 QEIMLVINDAMKNKK--IPEVPVYITG-MVDEITAIHTAYPEwlsrelreailY---------------Rdenpfmseffk 478
                                   9**********9955..6789******.********999955555444444440...............044455555555 PP

                                   .........HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                     Beta-Casp  61 .........sskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                             + +p++i+a+sgml+gG+++e +k++++d rn++++v+yqaegTlgrk
  gi|70606450|ref|YP_255320.1| 479 riegykediAQGEPSIIIATSGMLNGGPAVEFFKNMAHDTRNSIVFVSYQAEGTLGRK 536
                                   6666666666689*******************************************98 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   1.1   5.4e-21   9.7e-18       5      67 ..       5      65 ..       1      66 [. 0.93
   2 !   12.6   0.9   5.8e-05       0.1       3      49 ..      68     116 ..      66     134 .. 0.71
   3 ?   -3.3   0.0       5.2   9.2e+03      27      40 ..     338     351 ..     338     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 5.4e-21
                          KH_7  5 eelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsv 67
                                   ++ + i + +Pke+ i++++FEGPe+++Y++np+ +   g+ ++k+Ake++kR+v+++Dp+ 
  gi|70606450|ref|YP_255320.1|  5 LNIVNAIYNGMPKEAGISKIDFEGPEIAVYVRNPAVVD--GETVKKIAKEIKKRVVVKADPKS 65
                                  578899****************************9987..99*******************96 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.8e-05
                          KH_7   3 vleelkekieeklPkevkitdveF..EGPelViYtknpklfaengdlir 49 
                                    +ee+ke i++ +P+e++i d++F  E  e+ i +k p l++ +g  i+
  gi|70606450|ref|YP_255320.1|  68 DKEETKEIIKNIVPQEAQIIDIKFddELGEVLIKAKKPGLVIGKGGSIQ 116
                                   5799********************5555677777777777776655554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.2
                          KH_7  27 EGPelViYtknpkl 40 
                                   EG + V+Yt + k+
  gi|70606450|ref|YP_255320.1| 338 EGLHNVVYTGDFKY 351
                                   666679***99775 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.16     3e+02      18      33 ..      68      83 ..      64      87 .. 0.85
   2 !   56.3   0.0   1.2e-18   2.2e-15       2      55 ..     556     610 ..     555     622 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
                         RMMBL 18 dknellelirklkprn 33
                                  dk+e++e+i+ + p+ 
  gi|70606450|ref|YP_255320.1| 68 DKEETKEIIKNIVPQE 83
                                  9**********99986 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 1.2e-18
                         RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeee 55 
                                   i+v+++i  ++ fSgH+d+++ll ++r l+ ++  ++l+HGe+ a+s+++rl +  +
  gi|70606450|ref|YP_255320.1| 556 IKVNMEIGVVEgFSGHSDRRQLLAFLRNLNVKPknLVLNHGEPSAISSFKRLVE--S 610
                                   89*************************99777777****************994..2 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.5   5.3e-16   9.5e-13       4     162 ..     187     360 ..     185     400 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.3e-16
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                   ++ +++l+e++++ iL D G+ ++ +   +   ++    +k++d+dav++TH+HlDH+G ++ l +     +++    ++ 
  gi|70606450|ref|YP_255320.1| 187 VGRSAVLVETPESKILLDVGLNPSVSYGEKlfpRIDIDQVKLEDIDAVVITHAHLDHCGMVPLLFKYGYEGPVYMTPPTRD 267
                                   56789**************************************************************99999999999999 PP

                                   CHCHHHHHHHHHCCHH.......TTCHCGCCEEEEETTTEECCCT.....EEEEEHECTTSTSCCEEEEEETTCCEEEECT CS
                   Lactamase_B  82 lfmeeaddaasrkgll.......lagvsadkpdvdeeeldgnagg.....rralyvtggpghghghgvveygggkvlftGD 150
                                       +  da    + +       +++v++    + ++++ + ++        ++ + ++ g+   h++++ g  +v++tGD
  gi|70606450|ref|YP_255320.1| 268 IMALAQLDALDVAEKEgrpipytAKEVRRELLHTITLDYGEVTDIapdvkLTFYNAGHILGSAMAHLHIGEGLHNVVYTGD 348
                                   9998888777777777899***9444444444444444443333300000333444577888888999999********** PP

                                   TTSSHHCCCCCC CS
                   Lactamase_B 151 allagetgridl 162
                                   + +a+  +++  
  gi|70606450|ref|YP_255320.1| 349 FKYARTKLLDKA 360
                                   ***998888776 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   4.4e-16   7.8e-13       2     174 ..     194     361 ..     193     374 .. 0.78
   2 ?   -3.0   0.0       2.2     4e+03      23      64 ..     575     616 ..     554     622 .. 0.69

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.4e-16
                 Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekv....iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                   +e  + kiLlDvG + s vs+ ++l +  ++    ++++d+++++ha l+h G  +ll+     k++ + pvy t p+  +
  gi|70606450|ref|YP_255320.1| 194 VETPESKILLDVGLNPS-VSYGEKLFPRIDIdqvkLEDIDAVVITHAHLDHCGMVPLLF-----KYGYEGPVYMTPPTRDI 268
                                   677789*********98.6666655432222122489****************665555.....468899*****998777 PP

                 Lactamase_B_6  79 GrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki..skesekiv 157
                                     ++ ld+   ++ +g       + +++++   + +tl Y   +++     ++ +t ynaGh lG ++ ++   ++++++v
  gi|70606450|ref|YP_255320.1| 269 MALAQLDALDVAEKEGRP--IPYTAKEVRRELLHTITLDYGEVTDIAP---DVKLTFYNAGHILGSAMAHLhiGEGLHNVV 344
                                   777777666665555432..23567899**************999985...899************986652278999*** PP

                 Lactamase_B_6 158 YavdwnhakeshLngaa 174
                                   Y  d+  a+ ++L++a+
  gi|70606450|ref|YP_255320.1| 345 YTGDFKYARTKLLDKAN 361
                                   *************9985 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                 Lactamase_B_6  23 esalkelekviptvdliLLshatlehlGayallyakfkskll 64 
                                   ++ l++l++   +    +L h +++ ++++  l+ + k k +
  gi|70606450|ref|YP_255320.1| 575 RQLLAFLRNLNVKPKNLVLNHGEPSAISSFKRLVESGKIKGI 616
                                   556677777666666677899999999999998877655554 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.2   5.3e-14   9.5e-11       6     171 ..     208     381 ..     200     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5.3e-14
                                   S--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...........HCCTTC CS
                 Lactamase_B_2   6 DagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla...........vleanf 74 
                                   +++ +  + + ++         +l++idaV++thaH DH+  ++ l + ++ + p+y ++ +++           v     
  gi|70606450|ref|YP_255320.1| 208 NPSVSYGEKLFPRI---DiDQVKLEDIDAVVITHAHLDHCGMVPLLFK-YGYEGPVYMTPPTRDimalaqldaldV----- 279
                                   44444444433333...234445889**************55555555.455579998888888444442222222..... PP

                                   GHHHCHTT................TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEE CS
                 Lactamase_B_2  75 vylaleee................pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyy 139
                                          +                  +++ +ld ge ++++ +++++t+  a h  g         ++ l i++g ++v+y
  gi|70606450|ref|YP_255320.1| 280 -------AekegrpipytakevrrELLHTITLDYGEVTDIA-PDVKLTFYNAGHILGS-------AMAHLHIGEGLHNVVY 345
                                   .......22234456666656767777888888*******9.699*****99999999.......9999************ PP

                                   ESS-S---....HHHHHHHCT-SEEEEE-S-SSTTH CS
                 Lactamase_B_2 140 igDtgyip....eeigerlggadllllditayedde 171
                                   +gD +y      +++ +++  +d ++++ t+   d+
  gi|70606450|ref|YP_255320.1| 346 TGDFKYARtkllDKANDEFIRVDTMIMETTYGAHDQ 381
                                   ******997777777788888*******98755554 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.75   1.3e+03     136     160 ..      35      59 ..      30      61 .. 0.88
   2 !   21.4   0.0   1.1e-07   0.00019       6      54 ..     188     248 ..     185     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.75
                 Lactamase_B_3 136 vggpltlgqeealelakrLkpklvl 160
                                   v  p +++ e+++++ak++k ++v+
  gi|70606450|ref|YP_255320.1|  35 VRNPAVVDGETVKKIAKEIKKRVVV 59 
                                   6678999****************98 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.1e-07
                 Lactamase_B_3   6 ghnsflletagarilvDPfka.nlgyeppa...........eeaDlvlisqaledHahlet 54 
                                   g +++l+et++ +il+D + + ++ y+++            e++D+v+i++a+ dH+ + +
  gi|70606450|ref|YP_255320.1| 188 GRSAVLVETPESKILLDVGLNpSVSYGEKLfprididqvklEDIDAVVITHAHLDHCGMVP 248
                                   889**************99777888877778899999999*****************7765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.6     0.012        21       5      60 ..      10      59 ..       6      80 .. 0.81
   2 !   13.8   1.8   2.2e-05     0.039       6      45 ..      76     114 ..      71     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                                  HHHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHH CS
                          KH_2  5 slavei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdiek 60
                                  ++ + + k+ag+sk++     ++ +i +++ +p++v    G+++kki ke++k++ +
  gi|70606450|ref|YP_255320.1| 10 AIYNGMpKEAGISKIDF----EGPEIAVYVRNPAVV---DGETVKKIAKEIKKRVVV 59
                                  66666778999999999....777899999999999...99*************954 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.2e-05
                                   HHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGH CS
                          KH_2   6 lavei.kkagvskveIertanrviiviresqpgivIGkgGs 45 
                                   +++ + ++a++ +++ ++  +  ++ i++ +pg+vIGkgGs
  gi|70606450|ref|YP_255320.1|  76 IKNIVpQEAQIIDIKFDD--ELGEVLIKAKKPGLVIGKGGS 114
                                   556666788888888888..78899***************8 PP

>> A-2_8-polyST  Alpha-2,8-polysialyltransferase (POLYST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.2     2e-05     0.036     260     326 ..      44     111 ..      33     120 .. 0.90
   2 ?   -4.0   0.0       2.3   4.1e+03     182     203 ..     437     458 ..     435     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                  A-2_8-polyST 260 etlnrislriegkifiklhPkeme.nkyimslflnivkinprlvvinekdflieplikltkikgiiGl 326
                                   et+++i ++i+ ++ +k  Pk  + ++  + +  niv  + +++ i+  d l e lik  k+  +iG 
  gi|70606450|ref|YP_255320.1|  44 ETVKKIAKEIKKRVVVKADPKSRKdKEETKEIIKNIVPQEAQIIDIKFDDELGEVLIKAKKPGLVIGK 111
                                   7999*****************8751667999*******************************999996 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.3
                  A-2_8-polyST 182 ilkgyidkfdilyvafPeyakk 203
                                    + g +d+   +++a+Pe++ +
  gi|70606450|ref|YP_255320.1| 437 YITGMVDEITAIHTAYPEWLSR 458
                                   577899999*********9865 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5      0.98   1.7e+03      19      41 ..      43      66 ..      42      77 .. 0.54
   2 ?   10.1   0.1   0.00031      0.55       3      29 ..      97     123 ..      96     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.98
                                  GHHHHHHHHH.H.T-EEEEESSTT. CS
                          KH_1 19 GsnIkeIree.t.gakIkvpksede 41
                                  G+++k+I +e +  + +k + ++++
  gi|70606450|ref|YP_255320.1| 43 GETVKKIAKEiKkRVVVKAD-PKSR 66
                                  999****9852334444433.3332 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00031
                                   EEEEGGGHHHHHHTGGGHHHHHHHHHH CS
                          KH_1   3 rilvPsslvgriIGkgGsnIkeIreet 29 
                                   ++l+++++ g++IGkgGs  ++I +et
  gi|70606450|ref|YP_255320.1|  97 EVLIKAKKPGLVIGKGGSIQQKIFAET 123
                                   688999999**********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3870.97
//
Query:       gi|70606451|ref|YP_255321.1|  [L=356]
Description: NAD(P)-dependent glycerol-1-phosphate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-62  211.3   0.0    2.2e-62  211.0   0.0    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    2.4e-25   89.1   0.1    6.9e-23   81.0   0.1    2.0  2  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.1e-10   41.2   0.1    1.3e-09   37.7   0.1    2.3  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.0   0.0   3.7e-66   2.2e-62       3     250 .]      22     277 ..      20     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 211.0 bits;  conditional E-value: 3.7e-66
                      Fe-ADH_2   3 gegaleklgellkelel.kkvllvaden.tkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvva 81 
                                   g g+l++ +++l+ l+l + +l++++   ++++  +++ee++k+ +++v +v+    ++dl+e+ek+ + +r+k+++ +++
  gi|70606451|ref|YP_255321.1|  22 GYGILDNFRNYLQTLNLpQPFLVITGPViHQEIFSKRIEEHIKDFKYEVVIVN----KSDLSEAEKVEDIARQKGIKTILG 98 
                                   5689999999****997468999999874677899*************98775....899********************* PP

                      Fe-ADH_2  82 vGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDll 162
                                   vGgGt+iDiak+ ++k +++++s+pT++S+DG++sp+a+++  gk +++ ka+ Pla+i D+++la APrrl+ +G+GD l
  gi|70606451|ref|YP_255321.1|  99 VGGGTVIDIAKFTAYKIDREFISIPTSPSHDGITSPFAAIKGLGKPISI-KAKEPLAIISDVEILASAPRRLINAGIGDTL 178
                                   ************************************************9.9****************************** PP

                      Fe-ADH_2 163 gkytaladwklan........evseplaklsaamvqeaaeklvedkke.teal.eellea.lalsgigisrpaSGsEHliS 232
                                   gk+ta+ dw+la+        +++++la++sa++  ++ + + +d +  +++l e+l+++ +a++++g++rpaSGsEHl++
  gi|70606451|ref|YP_255321.1| 179 GKITAVRDWRLAHklrgeyygDYTASLALMSARHALSCTKIINKDIRAgVRVLtEALISSgVAMGMAGSTRPASGSEHLFA 259
                                   *************99998888889999999999998888888876553344441333333269999*************** PP

                      Fe-ADH_2 233 HaldmlalkqalHGeqVG 250
                                   Ha++ l+++  lHGe V+
  gi|70606451|ref|YP_255321.1| 260 HAIELLYPNLGLHGELVA 277
                                   **************9885 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.1   1.2e-26   6.9e-23       1     276 [.      16     278 ..      16     293 .. 0.82
   2 !    6.3   0.0   0.00059       3.5     314     344 ..     292     325 ..     290     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.2e-26
                                   -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT. CS
                        Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareeg 81 
                                   P++i+ g g l++  ++l+ l++ ++++v ++ +++++ + ++++e++++ + ev++++      +l+e e++ ++ar++g
  gi|70606451|ref|YP_255321.1|  16 PKHIYTGYGILDNFRNYLQTLNLPQPFLVITGPVIHQEIFSKRIEEHIKDFKYEVVIVN----KSDLSEAEKVEDIARQKG 92 
                                   899*******************88777777777788999*********99999999766....569*************** PP

                                   --EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS- CS
                        Fe-ADH  82 advviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpell 162
                                   + ++++vGGG+viD+AK  a+ +                    ++i iPT ++ +  ++p+a i     g+ +si      
  gi|70606451|ref|YP_255321.1|  93 IKTILGVGGGTVIDIAKFTAYKID------------------REFISIPTSPSHDGITSPFAAIK--GLGKPISIK--AKE 151
                                   ************************..................78*********************..555566666..889 PP

                                   -SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Fe-ADH 163 PdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsdalaleairliaknleravadgedleareq 235
                                   P ++i D e+++++P+r++ a+++D+l +       +           +++  lal ++r ++ + + + +d     a  +
  gi|70606451|ref|YP_255321.1| 152 PLAIISDVEILASAPRRLINAGIGDTLGKITAVRDWRlahklrgeYYGDYTASLALMSARHALSCTKIINKDI---RAGVR 229
                                   99*************************9999886555555676667777778888888888888888888774...33333 PP

                                   HHHHHHH.HHHHHHSS---.....HHHHHHHHHHC.C.GGG.GGS-HHH CS
                        Fe-ADH 236 mllastl.aglafsnaglg.....avHalahalgalf.gip.hglanai 276
                                   +l  +++ +g+a++ ag +       H +aha+  l+ ++  hg+++a+
  gi|70606451|ref|YP_255321.1| 230 VLTEALIsSGVAMGMAGSTrpasgSEHLFAHAIELLYpNLGlHGELVAL 278
                                   33333333555555555555555699*******9999899899999886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00059
                                   HHHHHHHHHTT---SHHHHT-TT-...HHHHHHH CS
                        Fe-ADH 314 ealrellkelglptsLselgvdee...dldklae 344
                                   +++r+ +k++glp++ +++g+++e   ++ ++a+
  gi|70606451|ref|YP_255321.1| 292 RRIRRAMKKIGLPVTSKQIGIPDEgiiKALTIAH 325
                                   689******************9983333344444 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   2.1e-13   1.3e-09      26     245 ..      91     310 ..      72     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-13
                                   TT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGG CS
                  DHQ_synthase  26 akleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLk 106
                                   +++   ++++ +GGG+v D+a f A    R  +f+ +Pt+     D       ai   lgK +     +P a++ d+e+L+
  gi|70606451|ref|YP_255321.1|  91 KGI---KTILGVGGGTVIDIAKFTAYKIDR--EFISIPTSP--SHDGITSPFAAI-KGLGKPISIKAKEPLAIISDVEILA 163
                                   333...589****************99999..9******95..455544445555.568998888999************* PP

                                   GS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......TTTHHHHHHHHHHHHHHHHHHHHHCCTTTTGGGG. CS
                  DHQ_synthase 107 tLperelraGlaEvi.Kyalikdeelfelleenaeallk.......eeeeealeeliarsievkaevveeDekekglral. 178
                                   + p+r ++aG+++ + K+++++d +l ++l+ +     +       ++++ +++++i++ i++  +v++e    +g+ +  
  gi|70606451|ref|YP_255321.1| 164 SAPRRLINAGIGDTLgKITAVRDWRLAHKLRGEYYGDYTaslalmsARHALSCTKIINKDIRAGVRVLTEALISSGVAMGm 244
                                   ************9876**************988765555577787766778889999999999999999998888765552 PP

                                   .......GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT CS
                  DHQ_synthase 179 .......LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkel 245
                                              H ++HaiE l      lHGe Va+G ++ a++    g+    + +r+++ +kk+glpv+ k+ 
  gi|70606451|ref|YP_255321.1| 245 agstrpaSGSEHLFAHAIELLYPN-LGLHGELVALGTIMMAYIH---GI----NWRRIRRAMKKIGLPVTSKQI 310
                                   22222225677********99877.89************99987...33....468999*********998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2104.50
//
Query:       gi|70606452|ref|YP_255322.1|  [L=239]
Description: peptidyl-prolyl cis-trans isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-15   56.8   0.7    6.7e-15   55.2   0.2    2.0  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    1.4e-07   31.5   1.4    3.4e-07   30.3   1.4    1.7  1  FKBP26_C  FKBP26_C-terminal
  ------ inclusion threshold ------
      0.065   13.3   0.7        1.8    8.7   0.1    2.3  2  FKBP_N_2  BDBT FKBP like N-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.2   1.1e-18   6.7e-15       6      79 ..       9      96 ..       6     155 .. 0.72
   2 ?    0.5   0.0      0.13   7.7e+02       7      33 ..     131     153 ..     125     208 .. 0.59

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.1e-18
                                  -TTCEEEEEEEEEET.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTT CS
                        FKBP_C  6 kegdtVtvhykgkle.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaYgek 74
                                  k++d+V+++y++k++  g++fd++          +s   +++p  + +G+  +i G+eea+ +m++Ge+++++ippe aYg+k
  gi|70606452|ref|YP_255322.1|  9 KDKDFVYIDYVAKVKdTGEIFDTTieeeakkaniYSnnvKYEPKLVILGEHSIISGLEEAIYQMNAGEEKEVEIPPEKAYGKK 91
                                  7899***********77*******99999998884467899*****************************************7 PP

                                  TBCTT CS
                        FKBP_C 75 glagg 79
                                  + ++ 
  gi|70606452|ref|YP_255322.1| 92 DPTKV 96
                                  76443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                                   TTCEEEEEEEEEETTSSEEEEHCCHTS CS
                        FKBP_C   7 egdtVtvhykgkledgkvfdssrsrak 33 
                                   +g +V ++++  l+d++v+ +     k
  gi|70606452|ref|YP_255322.1| 131 TGGRVVLDFNHPLADKTVIYKV----K 153
                                   5566667777777666666665....2 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   1.4   5.6e-11   3.4e-07       1      72 []     161     234 ..     161     234 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.6e-11
                                   HHHHHHHHHHHH-TT--..--EEEEE..TTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEEE CS
                      FKBP26_C   1 dkekikelIkryiPnidlekfkieie..dktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdefe 72 
                                   +k+k+k++ ++ + + +++kf ie+   +k ++I++p+ ++ +e+ ql+   +A+di++++     V+F++ f+
  gi|70606452|ref|YP_255322.1| 161 EKDKVKAVLEKWLGKNNADKFGIELGedKKNLKITVPKDYYKVEDFQLVIYMLARDIINYVLPESVVSFIENFQ 234
                                   59*************9*********977899******************************99999*****995 PP

>> FKBP_N_2  BDBT FKBP like N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0003       1.8      54     101 ..      50      95 ..      23     101 .. 0.66
   2 ?    2.9   0.0     0.019   1.2e+02      22      62 ..     141     187 ..     134     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0003
                      FKBP_N_2  54 eekeiviGealteideyierlleqmklgEtaevtikikaeesetesii 101
                                   e k + +Ge    i   +e+++ qm++gE  ev+i  +    ++++++
  gi|70606452|ref|YP_255322.1|  50 EPKLVILGE--HSIISGLEEAIYQMNAGEEKEVEIPPEKAYGKKDPTK 95 
                                   333344455..3455679***************998775555555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
                      FKBP_N_2  22 kPtevsscivlveklqnveerkdqllekle..l....eeekeiviGe 62 
                                   +P +  ++i +v+ +++++++kd+++  le  l     ++  i++Ge
  gi|70606452|ref|YP_255322.1| 141 HPLADKTVIYKVKVVKVLQDEKDKVKAVLEkwLgknnADKFGIELGE 187
                                   67777778888888888888888877766655533224444566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1661.90
//
Query:       gi|70606453|ref|YP_255323.1|  [L=61]
Description: 50S ribosomal protein L37e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-25   87.6   9.7    4.7e-25   87.5   9.7    1.0  1  Ribosomal_L37e   Ribosomal protein L37e
     0.0037   17.0   0.9     0.0045   16.7   0.9    1.3  1  Ephrin_rec_like  Putative ephrin-receptor like
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.012   15.7   0.3    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.029   14.4   1.8      0.035   14.1   1.8    1.2  1  DZR              Double zinc ribbon


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   9.7     1e-28   4.7e-25       1      53 [.       1      54 [.       1      55 [. 0.98

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1e-28
                Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                  +kGt+sfGk++k+ tH++CrrCg++s++ +k +Ca+cG+ +s+k+r+y+W++K+
  gi|70606453|ref|YP_255323.1|  1 MKGTPSFGKMNKTPTHVRCRRCGRNSFNARKGYCAACGFgRSKKIRRYSWQNKK 54
                                  7***************************************************97 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9     1e-06    0.0045       7      39 ..      15      45 ..       8      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
               Ephrin_rec_like  7 gletCipCprgtYqneegqlsClaCPlgtttkk 39
                                  ++++C  C r++++++  ++ C aC+ g++ k+
  gi|70606453|ref|YP_255323.1| 15 THVRCRRCGRNSFNAR--KGYCAACGFGRSKKI 45
                                  579**********765..568*****9998775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.3   2.6e-06     0.012      64      94 ..      10      39 ..       6      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                                  EEEE--EEEETTTS-EEECHHHHHS-TTTSS CS
                          HypA 64 ieevpvkvrCreCgkefeleekalrCpkCgs 94
                                  ++++p +vrCr+Cg++   ++k   C +Cg 
  gi|70606453|ref|YP_255323.1| 10 MNKTPTHVRCRRCGRNSFNARK-GYCAACGF 39
                                  68899*********88776644.56****85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.8   7.8e-06     0.035      22      49 .]      10      38 ..       3      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                           DZR 22 lkavaaedrCpsCgek.vdpearfCpeCG 49
                                  +++++++ rC +Cg+   ++++ +C +CG
  gi|70606453|ref|YP_255323.1| 10 MNKTPTHVRCRRCGRNsFNARKGYCAACG 38
                                  55667799*******999999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 413.11
//
Query:       gi|70606454|ref|YP_255324.1|  [L=302]
Description: spermidine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-44  149.7   0.0    8.3e-44  149.2   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
      3e-10   39.8   0.0      6e-10   38.9   0.0    1.5  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    1.9e-05   25.3   0.0    4.1e-05   24.2   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00035   20.5   0.0    0.00061   19.7   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    0.00055   19.5   0.0    0.00084   18.9   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0016   18.2   0.0     0.0025   17.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0043   17.8   0.0     0.0077   17.0   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.027   13.7   0.0    1.5  1  Methyltransf_2   O-methyltransferase domain
      0.014   16.0   0.0      0.028   15.1   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
       0.16   11.6   0.0       0.25   11.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   4.6e-47   8.3e-44       1     179 [.      60     238 ..      60     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 4.6e-47
                                   THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEEST CS
                Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgd 81 
                                   ef+y+e ++h  l + + p+++Li+GGg G +lre +++++v k+t+vdiD  vi+f k++l++ ++++f+d+r +l++gd
  gi|70606454|ref|YP_255324.1|  60 EFIYHESLVHPLLISLEDPENILILGGGEGATLREALRYKSVRKVTMVDIDPVVIKFAKQNLQEWHMGSFDDSRTNLIIGD 140
                                   79******************************************************************************* PP

                                   CHHHHCTCSS-EEEEEEECCSTTCSSCG..CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEEEE CS
                Spermine_synth  82 gfkflkayekkfdvvivdsldpvgpaen..lFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqvep 160
                                   g+kf+k++++k+ ++i d++dp+  + +  l+++ef++ lk++++++G +++qa +p + ++ +  +  ++k+vf+ +v+ 
  gi|70606454|ref|YP_255324.1| 141 GYKFVKETNEKYNAIILDLTDPIQDSPSqlLYTSEFYRDLKSIITPNGGLVTQATSPSFSLDTFAIIYSTLKTVFK-NVSA 220
                                   **********************99888888*********************************************9.**** PP

                                   EEEETTTSCSCEEEEEEEE CS
                Spermine_synth 161 savlvPtylsgminfvves 179
                                    +++vP++ +  ++f+ +s
  gi|70606454|ref|YP_255324.1| 221 GITYVPSFDGL-WGFIYAS 238
                                   *******9765.5555554 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.3e-13     6e-10       2      52 ..       6      56 ..       5      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.3e-13
                                  EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEE CS
               Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqlt 52
                                  W+ e ++p++ ++ +++ +L ee+Se+Q + + e   fGk L++Dg++q t
  gi|70606454|ref|YP_255324.1|  6 WHLEWQTPQEFHAHAIKRILIEERSEFQRVILAELFRFGKALIIDGKIQST 56
                                  *************************************************76 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.3e-08   4.1e-05       1      71 [.      81     158 ..      81     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT......TEEEEESBCCG.BSSSTTTEEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl......nvefvqgdaed.lpfedgsfDlvvss 71 
                                   +L lG G+G +++++++  +  kvt+vDi++  ++ a+++++e ++      + +++ gd  + +++ +++++++++ 
  gi|70606454|ref|YP_255324.1|  81 ILILGGGEGATLREALRYKSVRKVTMVDIDPVVIKFAKQNLQEWHMgsfddsRTNLIIGDGYKfVKETNEKYNAIILD 158
                                   7889************99658*********************97777788889999****988356788899999983 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.4e-07   0.00061      25      90 ..     128     194 ..     109     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                                   EETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGG...GCSHHHHHHHHHHEEEEEEEEES- CS
               Methyltransf_30  25 elaaeevtlklligdarealkeldekadawFlDgFsPaknPe...lwseellkelarllkkkgtlatys 90 
                                   ++  ++ + +l+igd  +++ke +ek++a+ lD   P +++    l++ e+++ l+ ++ ++g l+t +
  gi|70606454|ref|YP_255324.1| 128 SF--DDSRTNLIIGDGYKFVKETNEKYNAIILDLTDPIQDSPsqlLYTSEFYRDLKSIITPNGGLVTQA 194
                                   45..3567789**************************987533459******************99965 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.7e-07   0.00084      33     137 ..      79     192 ..      68     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.7e-07
                                   SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTST..TS-EEEEEE-. CS
                           MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvleeve..ekkfdlivsN. 104
                                   +++l lG G G+   ++++ ++  +vt+vd+d   +++ak+nl++ ++       ++++  d+++ v+  ++k+++i+   
  gi|70606454|ref|YP_255324.1|  79 ENILILGGGEGATLREALRYKSVRKVTMVDIDPVVIKFAKQNLQEWHMGsfddsrTNLIIGDGYKFVKetNEKYNAIILDl 159
                                   57999******99999999899999*******************9988778889999*******988855799****9753 PP

                                   .--STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                           MTS 105 .PPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                     P++++   +l  + e+ ++ k++ +++G L+ 
  gi|70606454|ref|YP_255324.1| 160 tDPIQDSPS-QLLYTSEFYRDLKSIITPNGGLVT 192
                                   378888776.788888999999999999998865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0025       5     113 ..      79     196 ..      75     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
               Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.....nveFeqgdiee.leklledekfDlil 79 
                                    ++l lG G+G+ + e+  +  +  +v+ +Di++ +i++A++n+q+         + ++ +gd  +  ++  + ek++ i+
  gi|70606454|ref|YP_255324.1|  79 ENILILGGGEGATLREAL-RYKSVRKVTMVDIDPVVIKFAKQNLQEWHMGsfddsRTNLIIGDGYKfVKE--TNEKYNAII 156
                                   567779************.6666778*****************998665433466777777887775443..358999999 PP

               Methyltransf_31  80 snevl......naladpdkileeiervlkpggilliedpr 113
                                    + +         l    ++++ +++ ++p+g l+++  +
  gi|70606454|ref|YP_255324.1| 157 LDLTDpiqdspSQLLYTSEFYRDLKSIITPNGGLVTQATS 196
                                   9833333333344444555666888888889888887666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.3e-06    0.0077       2      50 ..      83     131 ..      82     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnn 50 
                                    +G+G G++lr+ l++ +  ++t vDi+p +i+ ak+ l++++  +++ 
  gi|70606454|ref|YP_255324.1|  83 ILGGGEGATLREALRYKSVRKVTMVDIDPVVIKFAKQNLQEWHMGSFDD 131
                                   68*************************************9998766554 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.027      60     107 ..      75     123 ..      21     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                   GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-- CS
                Methyltransf_2  60 leglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehlsa 107
                                   le  ++++ +GGG Ga+++++ +     kv++ D+ p V++ Ak+ l+ 
  gi|70606454|ref|YP_255324.1|  75 LEDPENILILGGGEGATLREALRYKSVRKVTMVDIdPVVIKFAKQNLQE 123
                                   5666778889***********99989999******7888999*999754 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05     0.028       3      44 ..      84     133 ..      82     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                   ET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......E CS
               Methyltransf_11   3 vGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......k 44 
                                   +G G G+ +++  ++   ++v+ vD+++ ++k ak++ +e ++      +
  gi|70606454|ref|YP_255324.1|  84 LGGGEGATLREALRYKsvRKVTMVDIDPVVIKFAKQNLQEWHMgsfddsR 133
                                   799******999966677********************998866555554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.25      48     120 ..      84     158 ..      73     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                                   TT-TTSHHHHHHHH.TT-SEEEEEES-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  48 lfaGsGalglEAlS.Rgakkavlvekdkeavkilkenleelklee....etaelkedaleallklakkkeefdivflD 120
                                   l +G Ga   EAl    ++k+++v+ d+ ++k  k+nl+e ++ +    +t+ ++ d ++ ++++   +e+++ + lD
  gi|70606454|ref|YP_255324.1|  84 LGGGEGATLREALRyKSVRKVTMVDIDPVVIKFAKQNLQEWHMGSfddsRTNLIIGDGYKFVKET---NEKYNAIILD 158
                                   5689999999999536789*********************9998888888888888888888766...5567777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2131.21
//
Query:       gi|70606455|ref|YP_255325.1|  [L=415]
Description: S-adenosyl-L-homocysteine hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-76  256.2   0.0    1.1e-44  152.9   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.2e-54  184.7   1.1    2.4e-54  183.8   1.1    1.5  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.4e-08   33.1   0.2    7.3e-08   32.0   0.2    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.1e-05   25.1   0.1    2.1e-05   24.2   0.1    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00041   19.7   0.3     0.0031   16.8   0.3    2.0  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.001   19.3   0.0     0.0025   18.0   0.0    1.7  1  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.016   15.1   0.3      0.036   14.0   0.3    1.6  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.032   14.8   0.2       0.15   12.7   0.2    2.2  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.048   14.2   0.1       0.12   13.0   0.1    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.054   12.8   1.6       0.79    9.0   1.6    2.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.15   12.5   0.1       0.34   11.4   0.1    1.8  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   6.5e-48   1.1e-44       1     139 [.       2     135 ..       2     141 .. 0.97
   2 !  102.3   0.0   1.6e-32   2.6e-29     176     286 ..     137     409 ..     135     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 6.5e-48
                                   --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqd 81 
                                   dy+vkd+slae Grk+ie ae  mp+lm++r+++++ekpl+g ri   lh+t +tavL+etL+a Gae+  a  n  stqd
  gi|70606455|ref|YP_255325.1|   2 DYRVKDLSLAEQGRKQIEWAELHMPALMEIRKRFNAEKPLDGIRIGAVLHVTKETAVLVETLKAGGAEIALAGSNPLSTQD 82 
                                   8******************************************************************************** PP

                                   HHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase  82 eaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkg 139
                                   ++aa +a++g+ v+aw+get+++y + i+++lk      ep++i+DdGGDl ++vh+ 
  gi|70606455|ref|YP_255325.1|  83 DVAAGLAKNGIHVYAWRGETEKDYYDNIREILKY-----EPHVIMDDGGDLHAYVHEN 135
                                   ********************************66.....79***************94 PP

  == domain 2  score: 102.3 bits;  conditional E-value: 1.6e-32
                                   CHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH.................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                     AdoHcyase 176 llkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD.................................... 220
                                   l++ki G +eetttGv rL+ +++++ L+ p i vn++ tk  fD                                    
  gi|70606455|ref|YP_255325.1| 137 LTSKIVGGTEETTTGVIRLKAMEEEKVLKYPVIAVNNAFTKYLFDnrigtgqstidgilratniliagkvavvigygwvgr 217
                                   67899**************************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                     AdoHcyase 221 ................................................................................. 220
                                                                                                                    
  gi|70606455|ref|YP_255325.1| 218 giasrfkgmgarvivvesspfralealmdgfdvmtmnraseigdifvtatgnlnvvsrdhilrmkdgavlansghfnveid 298
                                   ********************************************************************************* PP

                                   .............................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE--C CS
                                   .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 221 .............................................hpsfvmsasftnqvlaqielfkkekkyekkvyvlpk 256
                                                                                hps vm+ sf+nq+l+  +l k++ k e+kvy +p 
  gi|70606455|ref|YP_255325.1| 299 vkglkeisvetrevrqnleeyklrngkriylladgrlvnlvaaegHPSEVMDLSFCNQALSVEHLIKNKGKLENKVYNVPI 379
                                   ********************************************************************************* PP

                                   HHHHHHHHHCCCCCT-------HHHHHCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     AdoHcyase 257 klDekvarlhleklgaklteltkeqaeyig 286
                                   ++De+varl+l++lg++++elt eq eyi+
  gi|70606455|ref|YP_255325.1| 380 EIDEQVARLKLKALGIEIEELTIEQKEYIK 409
                                   ****************************97 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.8   1.1   1.5e-57   2.4e-54       3     161 ..     184     342 ..     182     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 1.5e-57
                                   HHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEE CS
                 AdoHcyase_NAD   3 ygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivv 83 
                                    g+ +s +dgi rat++l+aGkvavv+GyG vG+G a+ +kg+Garviv e  P  al a+m+Gf+v+t++ + + +di+v
  gi|70606455|ref|YP_255325.1| 184 IGTGQSTIDGILRATNILIAGKVAVVIGYGWVGRGIASRFKGMGARVIVVESSPFRALEALMDGFDVMTMNRASEIGDIFV 264
                                   67889**************************************************************************** PP

                                   E-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS- CS
                 AdoHcyase_NAD  84 tttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgcat 161
                                   t+tGn ++++++h+ +mkd a+++n Ghf+ eidv++l++ ++++ ev+ ++++++l++gk+i lla+Grl+nl +a 
  gi|70606455|ref|YP_255325.1| 265 TATGNLNVVSRDHILRMKDGAVLANSGHFNVEIDVKGLKEISVETREVRQNLEEYKLRNGKRIYLLADGRLVNLVAAE 342
                                   **************************************************************************9886 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.2   4.4e-11   7.3e-08      33     127 ..     201     291 ..     180     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.4e-11
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHH CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaee 113
                                    ++gk   +iG+G +G+ +a r+k++g++vi+++ s+ +  e+   g+++++++ + +  Di + ++     + +++++++
  gi|70606455|ref|YP_255325.1| 201 LIAGKVAVVIGYGWVGRGIASRFKGMGARVIVVESSPFRALEALMDGFDVMTMNRASEIGDIFVTATG----NLNVVSRDH 277
                                   5899********************************99877777788888888888888887776654....899****** PP

                                   HHCSTTTEEEEESS CS
                  2-Hacid_dh_C 114 lakmkkgailiNta 127
                                   + +mk+ga+l N +
  gi|70606455|ref|YP_255325.1| 278 ILRMKDGAVLANSG 291
                                   ***********987 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.3e-08   2.1e-05       2     102 ..     202     298 ..     201     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.3e-08
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeie 82 
                                   + gk  +viGyG  G+  a  ++  g  v+v   +    + +A  +gf+v+t++ a++  d+ ++ +    + +v++++  
  gi|70606455|ref|YP_255325.1| 202 IAGKVAVVIGYGWVGRGIASRFKGMGARVIVVESSPF-RALEALMDGFDVMTMNRASEIGDIFVTATG---NLNVVSRDHI 278
                                   67888899*********************99766665.77889******************9877664...4456666666 PP

                                   GG--TT-EEEESSSHHHHTT CS
                          IlvN  83 pnlkegkalafahGfnihfg 102
                                     +k+g++la +  fn+  +
  gi|70606455|ref|YP_255325.1| 279 LRMKDGAVLANSGHFNVEID 298
                                   789*************9865 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.9e-06    0.0031      24     112 ..     192     295 ..     185     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                   HHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.............CCHHHHHCCSSEEEE-SS-TT CS
                 THF_DHG_CYH_C  24 vellketgielegkkvvvvGrsnivgkplallLleknatVtvchskt.............kdlaeitreadivvvavGkpe 91 
                                     +l++t+i ++gk +vv+G +  vg+ +a  ++  +a V v++s+                +++  +  di v+a+G+ +
  gi|70606455|ref|YP_255325.1| 192 DGILRATNILIAGKVAVVIGYG-WVGRGIASRFKGMGARVIVVESSPfralealmdgfdvMTMNRASEIGDIFVTATGNLN 271
                                   56899***************86.8************99999999986644433333322233445555679********** PP

                                   -B-GGGS...-TT-EEEE---EEC CS
                 THF_DHG_CYH_C  92 likaemv...kegavviDvGinrv 112
                                   +++++++   k+gav+ + G+ +v
  gi|70606455|ref|YP_255325.1| 272 VVSRDHIlrmKDGAVLANSGHFNV 295
                                   *****9888899999998887665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-06    0.0025       2      47 ..     208     253 ..     207     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                   EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES CS
                        TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvg 47 
                                   ++iG+G vGr +a +++  g  +v+v+++++ r+ e+  +g++v+  
  gi|70606455|ref|YP_255325.1| 208 VVIGYGWVGRGIASRFKGmGA-RVIVVESSPFRALEALMDGFDVMTM 253
                                   8*****************666.6********9999988888887765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.2e-05     0.036       3      37 ..     208     242 ..     205     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHH CS
                       3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealek 37 
                                    viG G +G+gia+ f   g +V +v+ s+ ++ +
  gi|70606455|ref|YP_255325.1| 208 VVIGYGWVGRGIASRFKGMGARVIVVESSPFRALE 242
                                   489************************98755444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   8.9e-05      0.15       2      32 ..     207     237 ..     206     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversd 32 
                                   +vv+G G++g   A+ ++ +g++V vve s+
  gi|70606455|ref|YP_255325.1| 207 AVVIGYGWVGRGIASRFKGMGARVIVVESSP 237
                                   59**************************886 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.3e-05      0.12       4      50 ..     209     250 ..     205     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-05
                                   EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                 F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50 
                                   +iG+G +g+++as++   g     ++v+ s+    +e+l + +   v
  gi|70606455|ref|YP_255325.1| 209 VIGYGWVGRGIASRFKGMG---ARVIVVESSPFRALEALMDGFD--V 250
                                   56*****************...9999996666666666666554..3 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6   0.00049      0.79      20      69 ..     203     243 ..     182     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00049
                                   TCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   AlaDh_PNT_C  20 aGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                   aG+v        +viG G +G   ++  kg+ga+V v++ +p r+  le+
  gi|70606455|ref|YP_255325.1| 203 AGKVA-------VVIGYGWVGRGIASRFKGMGARVIVVESSPFRA--LEA 243
                                   33333.......89***********************99988553..444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00021      0.34       5      49 ..     202     246 ..     199     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk 49 
                                   + gk  +v+G G v+   ++++   ga+v+vv    +++le l++
  gi|70606455|ref|YP_255325.1| 202 IAGKVAVVIGYGWVGRGIASRFKGMGARVIVVESSPFRALEALMD 246
                                   578999**************************9997666664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2899.29
//
Query:       gi|70606456|ref|YP_255326.1|  [L=215]
Description: hypothetical protein Saci_0647 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.2e-17   61.8   9.9    6.2e-17   61.8   9.9    1.9  2  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
        0.4   10.4  11.0      0.065   12.9   5.7    2.0  2  FtsK_4TM    4TM region of DNA translocase FtsK/SpoIIIE


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.6      0.26   2.3e+03       7      27 ..      19      40 ..      11      44 .. 0.53
   2 !   61.8   9.9   6.9e-21   6.2e-17      26     106 ..     127     205 ..     102     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.26
                                  HHHHHHHHHHHHTTT--.SCCH CS
                    MS_channel  7 liivvgilivlsllgvn.vsal 27
                                  +ii+v++ ++++ +  n + +l
  gi|70606456|ref|YP_255326.1| 19 TIIFVIVFVIIEAIVNNfLPSL 40
                                  3444444444444444435554 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 6.9e-21
                                   CHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-E CS
                    MS_channel  26 allavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsni 106
                                     +a+ G++g+++g+a ++++ + vaG+++l+ +pfkiGD v++g+ +G Vedi++++t i++ d+ +v iPn++l+ s+i
  gi|70606456|ref|YP_255326.1| 127 G-VALGGFIGVVIGFATQQVLGQAVAGLFVLIARPFKIGDQVNVGGDIGVVEDITTLFTIINKGDQ-LVLIPNNTLIGSKI 205
                                   3.7899*********************************************************999.**********9886 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.065   5.9e+02     134     159 ..       9      34 ..       6      45 .. 0.72
   2 ?   12.9   5.7   7.3e-06     0.065      58     149 ..      68     157 ..      64     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.065
                      FtsK_4TM 134 lstllgftGatllllvllliglslvl 159
                                   +s++l ++  t++++++++i  ++v 
  gi|70606456|ref|YP_255326.1|   9 SSKILSSVAKTIIFVIVFVIIEAIVN 34 
                                   56778888888888888887666554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.3e-06
                      FtsK_4TM  58 ll.slfGlsawllvvlllawglrllrrkslerr...llrllgalllllasaalfalrlasledelpggaGGvlGrllaaal 134
                                   ll  lfG+  +  +  +++w lr+  ++++++    ++r+lg+ +l +++a+  a  +a       +++GG++G +++ a 
  gi|70606456|ref|YP_255326.1|  68 LLsLLFGYLIITEISNVIYWNLRIKYDHPVAHSvrnVIRILGVGVLGATIAGAVAGGVA------GVALGGFIGVVIGFAT 142
                                   44379********************9998885522266666666666666666665555......589************* PP

                      FtsK_4TM 135 stllgftGatllllv 149
                                   +++lg + a l +l+
  gi|70606456|ref|YP_255326.1| 143 QQVLGQAVAGLFVLI 157
                                   *******99998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1423.54
//
Query:       gi|70606457|ref|YP_255327.1|  [L=152]
Description: hypothetical protein Saci_0650 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-33  113.6   0.1    7.1e-33  113.2   0.1    1.2  1  DUF2122      RecB-family nuclease (DUF2122)
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.023   14.7   0.0    1.2  1  TIR_3        Toll/interleukin-1 receptor domain
      0.083   13.1   0.0       0.12   12.6   0.0    1.2  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.1   1.2e-36   7.1e-33       1     105 [.      39     142 ..      39     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.2e-36
                       DUF2122   1 GaAAqsGipevlklalklgksllvlpdlkDalellkpekvlllskeegeelleeeeleekgrvllvfsgadegfskkelel 81 
                                   G A++ G+pev+kla+klgk+++ lpdlkDa+ell+p+ v+ll+++ ++++le++ +++k++++lvfsg+++gfsk +l+l
  gi|70606457|ref|YP_255327.1|  39 GVASNVGVPEVNKLAFKLGKTFISLPDLKDAIELLSPDLVILLTSQ-AQKILETQVFNDKNKIMLVFSGIENGFSKIDLSL 118
                                   78*******************************************8.********************************** PP

                       DUF2122  82 getvkvegveadvgelaelavvly 105
                                   ge++k+++++ +++++a++av++ 
  gi|70606457|ref|YP_255327.1| 119 GENYKLRNIDVEISPIASIAVIHS 142
                                   *********************975 PP

>> TIR_3  Toll/interleukin-1 receptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.8e-06     0.023      46     131 .]      58     144 ..      41     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                         TIR_3  46 eellslksskcilllLsaelleslyepkvlefLervlkppekvvvLlCGVees.elleelfkdweewkelstddepeeYis 125
                                   + + sl + k  + lLs +l+  l++++++   ++v++ ++k+  ++ G+e+  ++++  + ++ + +++  +  p + i+
  gi|70606457|ref|YP_255327.1|  58 KTFISLPDLKDAIELLSPDLVILLTSQAQKILETQVFNDKNKIMLVFSGIENGfSKIDLSLGENYKLRNIDVEISPIASIA 138
                                   56778888999999**********55555555568******************99******************99999999 PP

                         TIR_3 126 avkeii 131
                                   ++++ i
  gi|70606457|ref|YP_255327.1| 139 VIHSCI 144
                                   998876 PP

>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     2e-05      0.12       3      53 ..      79     129 ..      77     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                   EEE-HHHHHHHHHHHHCTTECEEEEEECCTSCCGGS..TT.EEEEEEEEESS CS
                   Fe-S_biosyn   3 itlteaAaeklkkllaedkkelrLdvddgggpyskgg.Csiggkyslvlvde 53 
                                   i lt +A++ l+ ++ +dk+++ L +    + +sk +  s+g +y+l+ +d 
  gi|70606457|ref|YP_255327.1|  79 ILLTSQAQKILETQVFNDKNKIMLVFSGIENGFSK-IdLSLGENYKLRNIDV 129
                                   679***************999**************.44899******98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1053.74
//
Query:       gi|70606458|ref|YP_255328.1|  [L=319]
Description: site-specific DNA methylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-51  176.0   0.0    1.5e-37  129.7   0.0    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.021   14.4   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.0   1.7e-41   1.5e-37       2     169 ..       5     188 ..       4     223 .. 0.85
   2 !   44.6   0.0   1.3e-15   1.2e-11     266     333 ..     246     313 ..     205     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 1.7e-41
                                   EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-...GS--..-SEEEE---GGGTEC CS
                 DNA_methylase   2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkk...klpe.diDlLvgGfPCqpfSv 76 
                                   k+idLf+G+GGf+lg+++  fe+ ++++i+  aa tY+ nf+   v++ Di++i+ +    l + + D+++g++PC pf  
  gi|70606458|ref|YP_255328.1|   5 KVIDLFSGAGGFSLGFNREPFEIKLSVDINHAAARTYSINFPntVVIEDDIRNITGRdirYLIGgEPDIIIGSPPCEPFTG 85 
                                   89****************************************987788889888888666444559*************99 PP

                                   TSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTE.EEEEEEEEGGGTT- CS
                 DNA_methylase  77 aGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGY.evsykllnasdyGv 149
                                   a         ++ f d+rg+L+ e+iri+ e kPk+f++ENV+ + + d       i  ++  +GY +v++++l+a+d G 
  gi|70606458|ref|YP_255328.1|  86 ANPsrrsdplERLFVDERGQLTLEFIRIVGELKPKIFIMENVPAIANIDV--IRSSIEGEFLRIGYpKVYFNILRAEDLGN 164
                                   9877777888899**********************************976..8899999*******88************* PP

                                   SB--EEEEEEEEEGGG---....- CS
                 DNA_methylase 150 pQnReRvfivgirkdleln....v 169
                                   p +R Rvf+  ++ +++++     
  gi|70606458|ref|YP_255328.1| 165 PSRRTRVFVSNVKLKQQKSarlnT 188
                                   *********998888776644430 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 1.3e-15
                                   --EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHH CS
                 DNA_methylase 266 eagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakei 333
                                   + ++l  +++ + ++i++ ++R Lt+rE arl+++Pdd  f +++ ++y q+G+sVpv   + ia+ei
  gi|70606458|ref|YP_255328.1| 246 NPYRLAPTVMGNSRFIHPFENRFLTVREQARLMSYPDDHVFVGNRDEQYNQVGESVPVVFSTTIAREI 313
                                   45677788888888***************************************************998 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-06     0.021       4      41 ..       6      44 ..       4      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-06
               Methyltransf_15  4 ilDlfsGaGGnviqfalv.fekviaieinleklacaqhN 41
                                  ++DlfsGaGG +  f ++ fe   +++in+        N
  gi|70606458|ref|YP_255328.1|  6 VIDLFSGAGGFSLGFNREpFEIKLSVDINHAAARTYSIN 44
                                  8***************99999999999998776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2278.85
//
Query:       gi|70606459|ref|YP_255329.1|  [L=168]
Description: hypothetical protein Saci_0652 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-20   71.5   5.9    4.5e-20   71.5   5.9    2.0  2  TFIIE_alpha      TFIIE alpha subunit
    0.00036   20.8   0.0    0.00056   20.2   0.0    1.4  1  Rrf2             Transcriptional regulator
     0.0018   18.4   0.1     0.0034   17.5   0.1    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0023   18.0   3.5     0.0024   17.9   0.0    2.4  3  Sigma70_r3       Sigma-70 region 3
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.039   14.0   0.0    1.8  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.014   15.4   0.0      0.024   14.7   0.0    1.4  1  HTH_20           Helix-turn-helix domain
      0.015   15.1   0.0      0.021   14.6   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.019   14.9   0.3      0.067   13.1   0.1    2.0  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
      0.035   14.0   1.4       0.04   13.8   0.2    1.7  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.039   13.9   0.0      0.078   13.0   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.047   13.9   0.1       0.22   11.8   0.0    1.9  2  DUF2316          Uncharacterized protein conserved in bacteri
       0.06   13.3   1.7        2.3    8.1   0.0    2.1  2  CemA             CemA family
       0.09   12.4   0.2       0.68    9.6   0.0    2.2  2  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   5.9   3.3e-23   4.5e-20       8     104 ..       3     100 ..       1     101 [. 0.94
   2 ?    1.7   0.4      0.17   2.3e+02      78     104 ..     138     164 ..     133     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 3.3e-23
                                   HHCS-HHHHHHHHHHH.CTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHH CS
                   TFIIE_alpha   8 rkfygeeavlvldvLl.ekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkr 87 
                                   ++  g+ea   l+ L+ +k+e+t+e++akel+ ++ne+rk L+ L + +lv y++ +d + + y yyw++n +++ +++  
  gi|70606459|ref|YP_255329.1|   3 KELVGDEALGLLKYLIgKKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKTKDKDSNLYIYYWKVNVNQINEILLS 83 
                                   5678999999999876379************************************************************** PP

                                   HHHHHHHHHHHHHCCCT CS
                   TFIIE_alpha  88 kleevvkkLeeklekee 104
                                   +++ ++ kL++  e+e+
  gi|70606459|ref|YP_255329.1|  84 RKRLILEKLRNRYEQEK 100
                                   ************99997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                                   CCCHCCCHHHHHHHHHHHHHHHHCCCT CS
                   TFIIE_alpha  78 yeklvdvvkrkleevvkkLeeklekee 104
                                    ek+   + +k++++  +++++++ e+
  gi|70606459|ref|YP_255329.1| 138 SEKARSFLEQKIKQIEEEINKEIRRES 164
                                   688889999999999999999999886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.1e-07   0.00056      10      59 ..      10      57 ..       3      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.1e-07
                                  HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                  al +l yL  +++   ++ eeia++ n++p+ ++k l  L+ +glv+ ++
  gi|70606459|ref|YP_255329.1| 10 ALGLLKYLIGKKS--EITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRK 57
                                  6666666666666..38*****************************9776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.5e-06    0.0034      19      58 ..      20      59 ..      16      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.5e-06
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                  +k+ ++  ++a++Ln +p  V + l  L++ G+v y k k
  gi|70606459|ref|YP_255329.1| 20 KKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKTK 59
                                  56778999****************************9976 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.7e-06    0.0024      22      61 ..      25      64 ..      21      66 .. 0.88
   2 ?   -2.9   0.1       5.6   7.7e+03      35      47 ..      75      87 ..      72     100 .. 0.63
   3 ?    0.1   0.3      0.64   8.8e+02       4      22 ..     147     165 ..     145     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                                  XHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTXB CS
                    Sigma70_r3 22 tpeEiAeeLglseekVrevleaarepvSldlpvgeeedte 61
                                  t+eEiA+eL+  +++Vr++l +  ++ ++ ++  +++d+ 
  gi|70606459|ref|YP_255329.1| 25 TDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKTKDKDSN 64
                                  89******************99988888888888888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                  HHHHHHHHHHXXX CS
                    Sigma70_r3 35 ekVrevleaarep 47
                                  +++ e+l   ++ 
  gi|70606459|ref|YP_255329.1| 75 NQINEILLSRKRL 87
                                  5666666655554 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.64
                                   HHHHHHHHHHHHHHSSXXX CS
                    Sigma70_r3   4 nkikraqreLeqelgrePt 22 
                                   +kik++ +e+  e  re +
  gi|70606459|ref|YP_255329.1| 147 QKIKQIEEEINKEIRRESS 165
                                   5999999999999999866 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.039      28      59 ..      24      55 ..       7      58 .. 0.88
   2 ?   -1.6   0.0       2.2     3e+03      16      33 ..      75      92 ..      73      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                  BEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                         HTH_9 28 ltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                   t  e++k+++  +++V+k L++L  h+lV+y
  gi|70606459|ref|YP_255329.1| 24 ITDEEIAKELNTKPNEVRKYLYLLSDHGLVTY 55
                                  56689**************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                  HHHHHHHHHHSSBEHHHH CS
                         HTH_9 16 akVvetLlrkgrltlrel 33
                                   ++ e Ll++ rl l +l
  gi|70606459|ref|YP_255329.1| 75 NQINEILLSRKRLILEKL 92
                                  667888999999888777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.024      21      59 ..      20      58 ..       9      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                  TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                   + + t +e+a++l +++n++++ L  L+++gLv+ +++
  gi|70606459|ref|YP_255329.1| 20 KKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKT 58
                                  55566779***************************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.021       5      50 ..      10      55 ..       8      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                  HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  al +L++l     e t  e+A+++   +  v+ +L  L  +G+v++
  gi|70606459|ref|YP_255329.1| 10 ALGLLKYLIGKKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTY 55
                                  7999****************************************86 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-05     0.067      50      89 ..      20      59 ..      12      97 .. 0.80
   2 ?   -0.8   0.0         1   1.4e+03      47      67 ..     144     164 ..     138     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
               Phage_rep_org_N 50 enipytaemlalifnreletvrlaLkvlkdlelieisedk 89
                                  ++ + t+e++a ++n + ++vr  L +l+d +l+   ++k
  gi|70606459|ref|YP_255329.1| 20 KKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKTK 59
                                  567789****************************875433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
               Phage_rep_org_N  47 ylsenipytaemlalifnrel 67 
                                   +l+++i++ +e++  +++re 
  gi|70606459|ref|YP_255329.1| 144 FLEQKIKQIEEEINKEIRRES 164
                                   678888888888888887765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.9e-05      0.04      16      59 ..      16      65 ..       8      75 .. 0.83
   2 ?   -2.2   0.1       2.8   3.9e+03      26      38 ..     154     166 ..     133     168 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                  HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....T CS
                          TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.....p 59
                                  +L+ k+ + t +eia+el+   + v ++L  L+d GlV+ +k +      
  gi|70606459|ref|YP_255329.1| 16 YLIgKKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYRKTKdkdsnL 65
                                  566788999*****************************999987666552 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                                   CHHCCCTTSSCHC CS
                          TrmB  26 deiaeelgvprsk 38 
                                   +ei +e+ ++ sk
  gi|70606459|ref|YP_255329.1| 154 EEINKEIRRESSK 166
                                   4566666666555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.6e-05     0.078      21      54 ..      23      56 ..       9      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                   +t ee+A  l++ +  v + l  L+++gl++ +
  gi|70606459|ref|YP_255329.1| 23 EITDEEIAKELNTKPNEVRKYLYLLSDHGLVTYR 56
                                  689****************************944 PP

>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.22      20      47 ..      20      47 ..      19      59 .. 0.89
   2 ?   -1.1   0.0       1.6   2.3e+03      57      70 ..     141     154 ..     131     158 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                       DUF2316 20 elsgltveevaedLnlttekvekvLelk 47
                                  ++s++t ee+a++Ln+++++v k L l 
  gi|70606459|ref|YP_255329.1| 20 KKSEITDEEIAKELNTKPNEVRKYLYLL 47
                                  5799******************999875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                       DUF2316  57 lrdyLeekikeqgk 70 
                                    r +Le+kik+ ++
  gi|70606459|ref|YP_255329.1| 141 ARSFLEQKIKQIEE 154
                                   47888888887665 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0017       2.3      63     104 ..       8      49 ..       1      56 [. 0.81
   2 ?    4.4   0.8     0.022        31      27     105 ..      85     166 ..      71     168 .] 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                          CemA  63 feekleleeligeapelseeeieeelkekaeelakeyreess 104
                                    e+   l+ lig+++e+++eei +el++k +e++k     s 
  gi|70606459|ref|YP_255329.1|   8 DEALGLLKYLIGKKSEITDEEIAKELNTKPNEVRKYLYLLSD 49 
                                   556667899************************998766655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                          CemA  27 knlvveplvdrflekeqaelfl..nkeleeealeelkefeekleleeligeapels.eeeieeelkekaeelakeyreess 104
                                   k+l++e+l +r+ ++++  +++  +++++ +    ++++ + l+  + ++++++ + ++ +e+++k+  ee++ke+r+ess
  gi|70606459|ref|YP_255329.1|  85 KRLILEKLRNRYEQEKDGLFYFcpQDNIKYSFDDAIENEFKCLKCGTSLSQYDSEKaRSFLEQKIKQIEEEINKEIRRESS 165
                                   567777777777765554433211555666666666666667777777777665441445677777777778887777776 PP

                          CemA 105 e 105
                                   +
  gi|70606459|ref|YP_255329.1| 166 K 166
                                   5 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00049      0.68      20      54 ..      20      54 ..      10      58 .. 0.88
   2 ?   -0.1   0.1      0.53   7.4e+02       6      21 ..      85     100 ..      81     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00049
                  HrcA_DNA-bdg 20 kkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                  kk+ +  eeiA+ l+ ++  vR  l  L   gLv 
  gi|70606459|ref|YP_255329.1| 20 KKSEITDEEIAKELNTKPNEVRKYLYLLSDHGLVT 54
                                  6788999*********************9999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                  HrcA_DNA-bdg   6 qkeilqaLielyrkkk 21 
                                   ++ il++L + y+++k
  gi|70606459|ref|YP_255329.1|  85 KRLILEKLRNRYEQEK 100
                                   6789********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2002  (0.111663); expected 358.6 (0.02)
Passed bias filter:                      898  (0.0500865); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1050.05
//
Query:       gi|70606460|ref|YP_255330.1|  [L=132]
Description: hypothetical protein Saci_0653 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-48  161.3   0.1    8.8e-48  161.1   0.1    1.0  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.1   4.9e-52   8.8e-48       1     119 []       4     128 ..       4     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 4.9e-52
                                   H-S-..-EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.....EEEEE------TCHHHHSSEEEESS CS
                         Trm56   1 wGge..fkvevakslkklikefkkeggivvhltmyGenieevieeikkkek....dllvvvGaekvprevyeladynvsvg 75 
                                   wGg+  fkve+ ++ kk++k+++++gg vvhltmyG+ i+++i+ei+k++k    +llvv+G+ekv+ ++y ++dyn+++g
  gi|70606460|ref|YP_255330.1|   4 WGGKsyFKVEFVDNPKKIVKSWREKGGLVVHLTMYGKMIDDMIDEITKASKnftlPLLVVIGSEKVEGWYYYNSDYNIGIG 84 
                                   9998889***************************************99888677789************************ PP

                                   SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EEE CS
                         Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkvv 119
                                   nqPhsev+alaifldr+++g+el+ +f+dak+ +iP+ +gk+vv
  gi|70606460|ref|YP_255330.1|  85 NQPHSEVSALAIFLDRIYKGEELYIHFSDAKFYIIPQLKGKRVV 128
                                   *****************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1040.15
//
Query:       gi|70606461|ref|YP_255331.1|  [L=352]
Description: GTP-binding protein hflX [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-19   69.7   0.7    4.3e-19   68.7   0.1    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    4.6e-17   62.4   1.8    7.8e-17   61.7   1.8    1.4  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    1.9e-10   41.3   0.4      4e-10   40.2   0.4    1.6  1  GTP-bdg_N     GTP-binding GTPase N-terminal
      3e-10   39.8   0.4    8.6e-10   38.4   0.4    1.8  1  FeoB_N        Ferrous iron transport protein B
      5e-07   29.4   0.6    0.00028   20.5   0.6    2.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
      2e-06   27.4   0.3    4.7e-06   26.1   0.1    1.7  1  SRPRB         Signal recognition particle receptor beta subun
    2.2e-06   27.7   3.0      0.035   14.0   0.1    2.8  3  RsgA_GTPase   RsgA GTPase
    0.00095   19.7   0.4     0.0024   18.4   0.2    1.8  2  ABC_tran      ABC transporter
     0.0017   18.3   0.3     0.0069   16.4   0.3    2.1  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.002   17.6   3.0      0.013   14.9   2.6    2.4  1  Arf           ADP-ribosylation factor family
      0.004   16.1   1.4        0.1   11.5   0.1    2.5  3  Spore_IV_A    Stage IV sporulation protein A (spore_IV_A)
     0.0089   16.1   0.2        0.2   11.7   0.1    2.6  2  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.011   16.2   4.5      0.011   16.2   4.5    2.2  2  AAA_23        AAA domain
      0.024   14.4   1.8       0.38   10.5   0.2    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.044   13.5   0.0      0.086   12.6   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.051   13.0   0.9       0.55    9.6   0.1    2.3  2  TniB          Bacterial TniB protein
      0.053   13.3   1.1      0.072   12.9   0.2    1.7  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
       0.08   12.5   4.6        1.1    8.8   0.3    2.7  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.11   12.9   3.5          1    9.7   1.6    2.9  2  NTP_transf_2  Nucleotidyltransferase domain
       0.27   11.0   2.2          2    8.1   0.4    2.4  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.2   3.8e+03      65      87 ..      73      99 ..      48     122 .. 0.57
   2 !   68.7   0.1   4.8e-22   4.3e-19       2     114 .]     179     298 ..     178     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.2
                                  HHHHHHHHHHC.TSEEEEEEETT....T CS
                      MMR_HSR1 65 glgkaflalee.adlillvvdas....e 87
                                  +l +++++ ++  d ill++++      
  gi|70606461|ref|YP_255331.1| 73 NLIRELKN-KKiLDKILLLLEIFalhaG 99
                                  44444443.3325777777776654331 PP

  == domain 2  score: 68.7 bits;  conditional E-value: 4.8e-22
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHH....HHCT CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkafla....leea 76 
                                    aivG++N+GK+tL+naltg k ++ +  +tT+ ++++ ++++g+++ lvDt+G+i     +   ++ +af       + a
  gi|70606461|ref|YP_255331.1| 179 TAIVGYTNAGKTTLFNALTGLKQKTDSSMFTTTLPKRYGISVNGDKLLLVDTVGFIR----GIppQIVEAFYVtlseAKYA 255
                                   59*********************************9999**9************886....22224444444322114449 PP

                                   SEEEEEEETT..TTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
                      MMR_HSR1  77 dlillvvdas..eeklkpldeeleellee...akkplilvlnk 114
                                   d +llvvd+s  ++ + ++  +  ++l++   ++kp+i+vlnk
  gi|70606461|ref|YP_255331.1| 256 DSLLLVVDSSveDTLFIDMILSSFKILRDigiSGKPMIIVLNK 298
                                   ********8843223333333334444448889*********8 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   1.8   8.7e-20   7.8e-17       1      76 [.      97     171 ..      97     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 8.7e-20
                                   H--SHHHHHHHHHHHHHHHHHHHCXXXXXX..XXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                     GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkel..srqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqr 76 
                                   +A +keaklQ+elA+lk++lp L++++k++  s+q+   g  G+G + +e+  rl+++ri k+++eL+++kk +e q 
  gi|70606461|ref|YP_255331.1|  97 HAGSKEAKLQIELARLKHQLPVLKDMYKRMkvSEQQ---GPLGAGVYGIESTVRLYQRRIVKIREELNNIKKIKEDQI 171
                                   9***********************999999555554...569******************************999875 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.4   4.5e-13     4e-10       2      89 .]      11      95 ..      10      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.5e-13
                     GTP-bdg_N  2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekele.vkViDRtqL 83
                                  e+ +E+++La++a ++v++ +    +kp+p++yi + k+ e+k+     ++d++i+ ++L++++  nL +el+  k++D+  L
  gi|70606461|ref|YP_255331.1| 11 EYEDEAKALAEAALYNVLEVIKLP-RKPNPNFYISQTKLLELKNNS---DVDTIIIFETLKSRHFINLIRELKnKKILDKILL 89
                                  5669*************9877766.59***************9655...579*******************97589******* PP

                     GTP-bdg_N 84 ILdIFA 89
                                   L+IFA
  gi|70606461|ref|YP_255331.1| 90 LLEIFA 95
                                  *****8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.4   9.5e-13   8.6e-10       2     154 ..     178     344 ..     177     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 9.5e-13
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                   t a+vG  n+Gkttlfnaltg kqk      +t   k+  ++++g+++ +vD  G     +  + e    ++   + +d +
  gi|70606461|ref|YP_255331.1| 178 TTAIVGYTNAGKTTLFNALTGLKQKTDSSMFTTTLPKRYGISVNGDKLLLVDTVGFIRGIPPQIVEAFYVTLSEAKYADSL 258
                                   6799*********************988777777777777888************99888888888888888888999*** PP

                                   EEEEEGGGHHHHHHHHH......HHHHT...TSSEEEEEETHHHHHHTT..EEE-HH.HHHHHHTS-...EEEEBTTTTBT CS
                        FeoB_N  83 vnvvdatnlernLyLtl......qllel...gvpvvlalnmideaekkg..ieidlk.kLsekLgvp...vvktsakkkeg 148
                                   + vvd++ +e +L++ +       l ++   g+p++++ln+ d ++++    +id++ k+ + L +p   v+++sa k+ +
  gi|70606461|ref|YP_255331.1| 259 LLVVDSS-VEDTLFIDMilssfkILRDIgisGKPMIIVLNKADLVNNSDvdQKIDITwKIVKDLYTPiydVIPISALKGYN 338
                                   *****96.4555554330111112334422268************99862257887557888888653338999*****99 PP

                                   HHHHHH CS
                        FeoB_N 149 ieellk 154
                                   i+++++
  gi|70606461|ref|YP_255331.1| 339 INTIRD 344
                                   999876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   3.1e-07   0.00028      88     191 ..     249     349 ..     174     352 .] 0.61

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.1e-07
                                   HHHHHT-SEEEEEEETTTB......STHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP_EFTU  88 irglrvlDgavlvvdaveG......vepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekyge 162
                                      ++ +D  +lvvd++        +   + ++lr +   g p+i+++NK+D ++++   ++ ++  k+      +++  +
  gi|70606461|ref|YP_255331.1| 249 LSEAKYADSLLLVVDSSVEdtlfidMILSSFKILRDIGISGKPMIIVLNKADLVNNSDVDQKIDITWKI------VKDL-Y 322
                                   3337889999999999866577554555666666666667777***********777666666677666......4444.4 PP

                                   TTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 163 kgekevpvvfgSalkgegvktllealvel 191
                                       ++ v+++Salkg +++t+ + l el
  gi|70606461|ref|YP_255331.1| 323 TP--IYDVIPISALKGYNINTIRDRLLEL 349
                                   43..689*************998887765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   5.3e-09   4.7e-06       5      91 ..     178     270 ..     174     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5.3e-09
                                   EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG....GGTT-SEEEETT-GC.CSHHHHH....HHHHHGGEEE CS
                         SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv.ksekgskltliDfPGhek.lrqklle....klkaksslkg 78 
                                   +  +vG +++GKT+lf+ Lt + ++kt  S+  +++ +++  s +g kl l+D  G  + +  +++e    +l + + + +
  gi|70606461|ref|YP_255331.1| 178 TTAIVGYTNAGKTTLFNALT-GLKQKTDSSMfTTTLPKRYgISVNGDKLLLVDTVGFIRgIPPQIVEafyvTLSEAKYADS 257
                                   5679*************996.78999*****9999999998899************8654556666611115555566999 PP

                                   EEEEEETTS-HHH CS
                         SRPRB  79 lvfvvDStidpke 91 
                                   l+ vvDS++++  
  gi|70606461|ref|YP_255331.1| 258 LLLVVDSSVEDTL 270
                                   ********98765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.5   3.1e+03       8      30 ..      49      71 ..      43      97 .. 0.67
   2 !   14.0   0.1   3.9e-05     0.035      89     127 ..     162     203 ..     123     234 .. 0.74
   3 !   13.6   0.1   5.1e-05     0.046      37      97 ..     280     346 ..     246     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.5
                                  ETTTTEES--EEEEEEESTTTT- CS
                   RsgA_GTPase  8 lvrpkvaNvdqllivvslkepel 30
                                  l  ++ + vd+++i  +lk+ ++
  gi|70606461|ref|YP_255331.1| 49 LELKNNSDVDTIIIFETLKSRHF 71
                                  55556778888888877776554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.9e-05
                                   THHHHHH....HCTTSEEEEECSTTSSHHHHHHHHCTT----- CS
                   RsgA_GTPase  89 gleelke....llkdktsvlvGqSGvGKStLinallpelelkt 127
                                   +++++ke    + + kt+++vG + +GK+tL nal++  ++kt
  gi|70606461|ref|YP_255331.1| 162 NIKKIKEdqirKTELKTTAIVGYTNAGKTTLFNALTGL-KQKT 203
                                   44444431110334499******************995.3333 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.1e-05
                                   HHHHHHHHTT-EEEEEEE-GGG--HHH.......HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                   RsgA_GTPase  37 rfLvlaeekgiepvivlnKiDlleeee.......eleelkeelealgyevllvsaktkegleelkell 97 
                                   ++L  +  +g +++ivlnK+Dl+++++       +++ +k+ ++ + y+v+ +sa ++ ++++++++l
  gi|70606461|ref|YP_255331.1| 280 KILRDIGISGKPMIIVLNKADLVNNSDvdqkidiTWKIVKDLYTPI-YDVIPISALKGYNINTIRDRL 346
                                   44555556677899***********999998887777788888888.*********999999999877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.4     4e+03      56      56 ..     121     121 ..      49     174 .. 0.57
   2 !   18.4   0.2   2.7e-06    0.0024      12      41 ..     177     206 ..     166     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.4
                                   H CS
                                   x RF
                      ABC_tran  56 s 56 
                                    
  gi|70606461|ref|YP_255331.1| 121 D 121
                                   2 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.7e-06
                                   SEEEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGe 41 
                                   +++aivG + aGK+tL+++l+gl ++t  +
  gi|70606461|ref|YP_255331.1| 177 KTTAIVGYTNAGKTTLFNALTGLKQKTDSS 206
                                   689********************9988765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   7.7e-06    0.0069      56     100 ..     290     346 ..     247     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-06
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                   +p+++vlNK+Dl++++++d+                 ++++iSa k++n++++ +++
  gi|70606461|ref|YP_255331.1| 290 KPMIIVLNKADLVNNSDVDQKIDItwkivkdlytpiYDVIPISALKGYNINTIRDRL 346
                                   699*********9999999866645778889999777*************9999876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.6   1.5e-05     0.013      14     172 ..     175     347 ..     162     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                   EEE.EEEEESTTSSHHHHHHHH...HHSSCEECSSSSSEEEEEEEETTEEEEEEEE-S.SGGGGG.GGGGGC......TTE CS
                           Arf  14 elr.illlGLDnaGKtTilkkl...kleelvttvPTigfnveeleiknlkftvwDvGG.qeklRp.lWknYf......ekt 82 
                                   el+   ++G  naGKtT+ + l   k++  +++  T+ ++   +++++ k+ + D  G  + + p + + ++      +  
  gi|70606461|ref|YP_255331.1| 175 ELKtTAIVGYTNAGKTTLFNALtglKQKTDSSMFTTTLPKRYGISVNGDKLLLVDTVGfIRGIPPqIVEAFYvtlseaKYA 255
                                   44414589**********887611155555668899999999**********99965515555542334444222222346 PP

                                   SEEEEEEETT-CTT.HHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH.HHHHHTTGGG.SSSSSSEEEEEEBTTT CS
                           Arf  83 davifvvDsadreR.leeakeeLkalleeeelkevallvlaNKqDlpealsee.elrellglee.lkgkrkleiqkcsavk 160
                                   d+++ vvDs+ ++  + ++     ++l++  ++  +++++ NK Dl +  + + ++  + ++ + l  +    ++  sa+k
  gi|70606461|ref|YP_255331.1| 256 DSLLLVVDSSVEDTlFIDMILSSFKILRDIGISGKPMIIVLNKADLVNNSDVDqKIDITWKIVKdLY-TPIYDVIPISALK 335
                                   89******9977751344555556799*******************987664414444433333254.5566788888888 PP

                                   TBTHHHHHHHHH CS
                           Arf 161 geglkeglewls 172
                                   g +++   ++l 
  gi|70606461|ref|YP_255331.1| 336 GYNINTIRDRLL 347
                                   888888777776 PP

>> Spore_IV_A  Stage IV sporulation protein A (spore_IV_A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   9.6e+02     291     346 ..      42      99 ..      13     116 .. 0.65
   2 !   11.5   0.1   0.00011       0.1     228     337 ..     118     227 ..     103     234 .. 0.89
   3 ?    2.9   0.1     0.046        41     150     195 ..     259     304 ..     256     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                    Spore_IV_A 291 liekvkleevdlgtg..svkielelkeelyykvlselvgleiedeaellkllkelaka 346
                                   +i+++kl e++ ++   ++ i  +lk++ + ++++el + +i d+  ll  +  l++ 
  gi|70606461|ref|YP_255331.1|  42 YISQTKLLELKNNSDvdTIIIFETLKSRHFINLIRELKNKKILDKILLLLEIFALHAG 99 
                                   5666666655554440034444577888999999999999998888776555555443 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                    Spore_IV_A 228 ilekvLyefpvkeielelpkwvealekdhelkkelieaikellkevkklkdvekllekleeleliekvkleevdlgtgsvk 308
                                   +l+++ +  +v+e +  l   v  +e++  l ++ i +i+e l+++kk+k+ +  +++l+++ ++  ++  ++ l +    
  gi|70606461|ref|YP_255331.1| 118 VLKDMYKRMKVSEQQGPLGAGVYGIESTVRLYQRRIVKIREELNNIKKIKEDQIRKTELKTTAIVGYTNAGKTTLFNALTG 198
                                   67777777777777777777888899999999************************************************* PP

                    Spore_IV_A 309 ielelkeelyykvlselvgleiedeaell 337
                                   ++ ++++++++++l +  g+++++++ ll
  gi|70606461|ref|YP_255331.1| 199 LKQKTDSSMFTTTLPKRYGISVNGDKLLL 227
                                   ***********************998776 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.046
                    Spore_IV_A 150 vvttDGsiteiereeyveaeervieelkeigkPfvvvlNskkpese 195
                                   ++  D s+ +    + + +  ++++++   gkP ++vlN ++  ++
  gi|70606461|ref|YP_255331.1| 259 LLVVDSSVEDTLFIDMILSSFKILRDIGISGKPMIIVLNKADLVNN 304
                                   56677788887778888888899999999**********9875544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00022       0.2       2      32 ..     180     210 ..     179     215 .. 0.79
   2 ?    1.7   0.0      0.26   2.4e+02      98     141 ..     220     267 ..     214     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                   EEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                     Dynamin_N   2 avvGsqSsGKSSvlnaLlgedilprgpnptT 32 
                                   a+vG +++GK+++ naL+g +    ++  tT
  gi|70606461|ref|YP_255331.1| 180 AIVGYTNAGKTTLFNALTGLKQKTDSSMFTT 210
                                   79*****************995555555555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.26
                                   TTS-SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS- CS
                     Dynamin_N  98 llvkgltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhd 141
                                    + ++l lvD+ G+++    +      ++ + +k ad +l+v++++++
  gi|70606461|ref|YP_255331.1| 220 VNGDKLLLVDTVGFIRGIPPQIveafYVTLSEAKYADSLLLVVDSSVE 267
                                   5667899******99965544456678888888999999999988873 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   4.7      0.84   7.5e+02     119     179 ..      70     170 ..      10     178 .. 0.47
   2 ?   16.2   4.5   1.3e-05     0.011       4      40 ..     160     197 ..     159     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.84
                        AAA_23 119 qfise..llgskki......ilnlilflgqer..................feefelkdkke.................... 153
                                    fi+   +l++kki       l+++++++ ++                  +         +                    
  gi|70606461|ref|YP_255331.1|  70 HFINLirELKNKKIldkillLLEIFALHAGSKeaklqielarlkhqlpvlK---------Dmykrmkvseqqgplgagvyg 141
                                   333322223333334444433344444444333322222222222222332.........022233333355566666666 PP

                        AAA_23 154 ...rleelekeleeledekkllekleqek 179
                                       ++ +++ + ++ +e + ++k ++ +
  gi|70606461|ref|YP_255331.1| 142 iesTVRLYQRRIVKIREELNNIKKIKEDQ 170
                                   66644444444444444444444433333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.3e-05
                        AAA_23   4 ienfrsfrdqeidF.skgltlItGpNGaGKTTildAik 40 
                                   ++n++++++ +i   + + t+I+G + aGKTT+++A++
  gi|70606461|ref|YP_255331.1| 160 LNNIKKIKEDQIRKtELKTTAIVGYTNAGKTTLFNALT 197
                                   789999988888663669******************97 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.084        75       1      26 [.     181     206 ..     181     212 .. 0.82
   2 ?   10.5   0.2   0.00043      0.38     114     176 ..     245     310 ..     218     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.084
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrs 26 
                                   +vG   +GKtt+ +al+ + +++  s
  gi|70606461|ref|YP_255331.1| 181 IVGYTNAGKTTLFNALTGLKQKTDSS 206
                                   78999**********99887776555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
                    ATP_bind_1 114 iveeLes.efalvvvyLvDsqrltdptkfisgllsalsamlrlel...PhvvvlnkfDllkek.leke 176
                                   +  +L++ ++a   + +vDs +    t fi+++ls+ +++  +++   P+++vlnk+Dl++++  +++
  gi|70606461|ref|YP_255331.1| 245 FYVTLSEaKYADSLLLVVDSSVE--DTLFIDMILSSFKILRDIGIsgkPMIIVLNKADLVNNSdVDQK 310
                                   55566666777778888888654..469***********999876666***********986653333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.6e-05     0.086      12      43 ..     166     197 ..     157     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-05
                        AAA_29  12 fdghtieidlkgatlltGpsGsGKSTllDAiq 43 
                                   +++ +i+ ++  +t ++G + +GK+Tl+ A++
  gi|70606461|ref|YP_255331.1| 166 IKEDQIRKTELKTTAIVGYTNAGKTTLFNALT 197
                                   5553333333336***************9987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.19   1.7e+02     129     152 ..      58      81 ..      17      89 .. 0.79
   2 ?    9.6   0.1   0.00061      0.55      19      63 ..     156     204 ..     142     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                          TniB 129 hnllagsarkqreflnalksLgne 152
                                   + ++  +  k r+f+n+++ L+n+
  gi|70606461|ref|YP_255331.1|  58 DTIIIFETLKSRHFINLIRELKNK 81 
                                   445556677899999999999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
                          TniB  19 ilerLeeLley....pkrkrmpnlllvGdsnnGKtmivekFarlhppek 63 
                                   i e+L+++ +      ++++ +   +vG +n GKt++++  + l+++++
  gi|70606461|ref|YP_255331.1| 156 IREELNNIKKIkedqIRKTELKTTAIVGYTNAGKTTLFNALTGLKQKTD 204
                                   555555544331111467888999*************998877776665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       4.4   3.9e+03     110     143 ..      54      87 ..      37     108 .. 0.59
   2 ?   12.9   0.2     8e-05     0.072       2      40 ..     179     216 ..     178     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                        AAA_21 110 vfnpeargirggvsvfslkelsvsepndlqfgka 143
                                   +++ +   i++++++++ ++l+++  n+++  k 
  gi|70606461|ref|YP_255331.1|  54 NSDVDTIIIFETLKSRHFINLIRELKNKKILDKI 87 
                                   4444445555555555555555555555554443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8e-05
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40 
                                   ++++G  ++GK++L+ al +l++  +d+ + t++l+++ 
  gi|70606461|ref|YP_255331.1| 179 TAIVGYTNAGKTTLFNALTGLKQ-KTDSSMFTTTLPKRY 216
                                   89*******************99.666666666555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0013       1.1       2      25 ..     178     203 ..     177     210 .. 0.80
   2 ?    4.8   0.5     0.022        19     144     162 ..     293     310 ..     214     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                                   EEEEEESTTCCHHHHHHHHH..CT-- CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enra 25 
                                   +t ++G+  +GKTtL n+l+  +++ 
  gi|70606461|ref|YP_255331.1| 178 TTAIVGYTNAGKTTLFNALTglKQKT 203
                                   5889**************99654444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
                                   EEEEE-HHHHCHC..HHHH CS
                          cobW 144 llvlnKtDlldeeallekl 162
                                   ++vlnK+Dl+++++  ++ 
  gi|70606461|ref|YP_255331.1| 293 IIVLNKADLVNNSDV-DQK 310
                                   799*******99954.443 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.6    0.0011         1      29      48 ..      51     145 ..      49     189 .. 0.59
   2 ?   -2.0   0.0       5.3   4.7e+03       7       7 ..     317     317 ..     297     347 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                   CTT.SSEEEEEEESTTCHHH............................................................. CS
                  NTP_transf_2  29 lkg.SDiDllvvlpeevsre............................................................. 47 
                                   lk+ SD+D++++++  +sr                                                              
  gi|70606461|ref|YP_255331.1|  51 LKNnSDVDTIIIFETLKSRHfinlirelknkkildkilllleifalhagskeaklqielarlkhqlpvlkdmykrmkvseq 131
                                   4555************99989777555555555555555555555555555555555555555555555555555555555 PP

                                   .............H CS
                  NTP_transf_2  48 .............k 48 
                                                +
  gi|70606461|ref|YP_255331.1| 132 qgplgagvygiesT 145
                                   55555555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.3
                                   H CS
                  NTP_transf_2   7 e 7  
                                   +
  gi|70606461|ref|YP_255331.1| 317 I 317
                                   2 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0023         2       3      25 ..     178     200 ..     176     212 .. 0.82
   2 ?    2.1   0.1      0.16   1.4e+02      64     141 ..     255     346 ..     239     348 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                     PduV-EutP   3 killiGkvgsGKttLtqalkgee 25 
                                      ++G +++GKttL +al+g +
  gi|70606461|ref|YP_255331.1| 178 TTAIVGYTNAGKTTLFNALTGLK 200
                                   56789**************9976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                     PduV-EutP  64 advialvqdateeesvfppgfasvfn.........keviGiitkidlaede...enieaveelLks..aGaekifevsave 130
                                   ad + lv+d++ e+++f + + s f+         k++i ++ k+dl++++   ++i+++ + +k     +  ++ +sa++
  gi|70606461|ref|YP_255331.1| 255 ADSLLLVVDSSVEDTLFIDMILSSFKilrdigisgKPMIIVLNKADLVNNSdvdQKIDITWKIVKDlyTPIYDVIPISALK 335
                                   566666666666666666665555533333333338889999999998654121456666666654224566777888888 PP

                     PduV-EutP 131 kegieellkyl 141
                                     +i+++++ l
  gi|70606461|ref|YP_255331.1| 336 GYNINTIRDRL 346
                                   88888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2279.34
//
Query:       gi|70606462|ref|YP_255332.1|  [L=163]
Description: HTH DNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-11   43.5   2.9    4.4e-11   42.7   2.9    1.5  1  HTH_3           Helix-turn-helix
    2.9e-08   33.9   0.0    4.5e-08   33.3   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    2.1e-07   30.7   1.3    1.1e-05   25.2   0.8    2.5  2  HTH_25          Helix-turn-helix domain
    6.6e-07   29.3   1.6    6.6e-07   29.3   1.6    2.8  3  HTH_19          Helix-turn-helix domain
    0.00073   19.6   3.8     0.0028   17.8   3.7    1.8  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0066   16.4   1.0      0.013   15.4   1.0    1.6  1  HTH_37          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.2   5.0      0.042   13.8   5.0    1.8  1  DUF4428         Domain of unknown function (DUF4428)
      0.016   15.2   0.2      0.031   14.3   0.2    1.4  1  DZR             Double zinc ribbon
      0.031   14.0   2.5       0.97    9.2   0.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.054   13.5   0.1        0.1   12.6   0.1    1.4  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.062   13.1   0.3       0.19   11.6   0.3    1.8  1  HTH_23          Homeodomain-like domain
        0.1   12.0   0.0       0.42   10.1   0.0    1.8  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.11   12.5   0.7       0.64   10.0   0.8    2.2  2  Pou             Pou domain - N-terminal to homeobox domain
       0.12   11.5   1.6       0.16   11.1   1.6    1.1  1  IF-2B           Initiation factor 2 subunit family
       0.17   11.5   3.9       0.23   11.1   3.9    1.1  1  Relaxase        Relaxase/Mobilisation nuclease domain
       0.17   12.5   2.1       0.24   12.0   2.1    1.1  1  GRDP-like       Glycine-rich domain-containing protein-like
       0.19   12.2   0.8       0.51   10.8   0.3    2.0  2  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.91    9.8   4.0        4.3    7.6   0.7    2.0  2  PIN_2           PIN domain
        6.5    6.4   6.5        5.5    6.7   0.1    3.1  3  RecR            RecR protein


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   2.9   4.7e-14   4.4e-11       1      52 [.      81     132 ..      81     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.7e-14
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                   +ke+R+ l++sq++LA++l vs + i r E+G+ +P+++ +k l++ Lg++l
  gi|70606462|ref|YP_255332.1|  81 IKEARERLKMSQQQLAQALKVSENIIKRFESGKLKPTIQQAKQLERILGIKL 132
                                   8************************************************987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   4.8e-11   4.5e-08       7      56 ..      82     130 ..      80     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.8e-11
                        HTH_31   7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56 
                                   +++Rer  +sq+++A++l vse  + r E+G+   p+ ++  +l r+lg 
  gi|70606462|ref|YP_255332.1|  82 KEARERLKMSQQQLAQALKVSENIIKRFESGKL-KPTIQQAKQLERILGI 130
                                   689******************************.6************995 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.061        57      48      61 ..      40      53 ..      38      54 .. 0.88
   2 !   25.2   0.8   1.1e-08   1.1e-05       2      36 ..      81     115 ..      80     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.061
                                  HHHHHHHTT--HHH CS
                        HTH_25 48 lrnYArlLgldpee 61
                                  ++nYA+++ l+ ee
  gi|70606462|ref|YP_255332.1| 40 IKNYAKIVNLKKEE 53
                                  89********8765 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.1e-08
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                        HTH_25   2 LraaRearglsleevaketkIrkdylealEeddfd 36 
                                    ++aRe++++s +++a+ +k+++++++++E+++++
  gi|70606462|ref|YP_255332.1|  81 IKEARERLKMSQQQLAQALKVSENIIKRFESGKLK 115
                                   589****************************9875 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.39   3.7e+02      10      35 ..      46      72 ..      38      80 .. 0.75
   2 !   29.3   1.6     7e-10   6.6e-07       2      55 ..      79     131 ..      78     136 .. 0.92
   3 ?   -1.3   0.0       2.4   2.2e+03       9      20 ..     146     157 ..     145     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.39
                        HTH_19 10 elgltqeelaerlgis.rskisaiEng 35
                                    +l++ee  +r+++s  +k+++ E +
  gi|70606462|ref|YP_255332.1| 46 IVNLKKEEDKKRIKTSpNKKYTEVELD 72
                                  557888888889999988889988876 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 7e-10
                        HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                   + +keaRe l+++q++la+ l++s + i  +E+gk  +p++   +++ ++lgi 
  gi|70606462|ref|YP_255332.1|  79 KIIKEARERLKMSQQQLAQALKVSENIIKRFESGKL-KPTIQQAKQLERILGIK 131
                                   579*******************************98.99999999999999986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.4
                        HTH_19   9 eelgltqeelae 20 
                                   + lglt+ ++++
  gi|70606462|ref|YP_255332.1| 146 KDLGLTLGDIVN 157
                                   789999999976 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.7   2.9e-06    0.0028      43     117 ..      48     124 ..       7     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                MqsA_antitoxin  43 gvldeeeedrlseellefrkkvnaelvdp..afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkll 117
                                   ++ +ee+++r+ ++  +   +v+ ++v+   + i++ r++l+++q+++a+ + +  n   r+e+Gk +p +   k l
  gi|70606462|ref|YP_255332.1|  48 NLKKEEDKKRIKTSPNKKYTEVELDIVEEyyKIIKEARERLKMSQQQLAQALKVSENIIKRFESGKLKPTIQQAKQL 124
                                   334556677888877777788888888551256899*********************************98766654 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.0   1.4e-05     0.013      20      56 ..      78     114 ..      49     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                        HTH_37  20 alaiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56 
                                    + i+e +e+++ sq+++aq+l++++  + r + gkl
  gi|70606462|ref|YP_255332.1|  78 YKIIKEARERLKMSQQQLAQALKVSENIIKRFESGKL 114
                                   44499**********************9999999987 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.0   4.4e-05     0.042       2      50 ..       9      60 ..       8      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-05
                       DUF4428  2 CaiCgkKigl..lkrlkleDg..yvCkdClkKlseflsdvkikkiltledIke 50
                                  C +Cg  i+   ++ + +e    +vC++C++K++++ + v+ kk  + ++Ik+
  gi|70606462|ref|YP_255332.1|  9 CELCGSPIKGkgFT-VSYEGSiiTVCTNCFNKIKNYAKIVNLKKEEDKKRIKT 60
                                  88888888764555.667766546************99999999988888875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.2e-05     0.031      10      42 ..       4      44 ..       2      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                           DZR 10 pdarfCseCgtklkavaa........edrCpsCgekvdpea 42
                                  ++ ++C+ Cg+++k             ++C +C  k+++ a
  gi|70606462|ref|YP_255332.1|  4 QNVKYCELCGSPIKGKGFtvsyegsiITVCTNCFNKIKNYA 44
                                  5679*********9554499*************99988766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1     0.001      0.97      11      23 .]       4      16 ..       2      16 .. 0.87
   2 ?    4.7   0.3     0.027        26       2      14 ..      33      45 ..      32      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.001
                 zinc_ribbon_2 11 dnakFCpyCGtpl 23
                                   n+k+C+ CG+p+
  gi|70606462|ref|YP_255332.1|  4 QNVKYCELCGSPI 16
                                  599*******995 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
                 zinc_ribbon_2  2 CpnCGaelqdnak 14
                                  C+nC +++++ ak
  gi|70606462|ref|YP_255332.1| 33 CTNCFNKIKNYAK 45
                                  ****999999987 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011       0.1      11      54 ..      63     109 ..      56     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                   -----HHHHHHHH.H..HHH-S---TT--HHHHHHHTT--HHHHHHH CS
                         HTH_6  11 kekltksekkiae.y..ilaspdkaielsikalAkaaavSeativrf 54 
                                    +k t+ e  i+e y  i ++  +  ++s ++lA+a++vSe  i rf
  gi|70606462|ref|YP_255332.1|  63 NKKYTEVELDIVEeYykIIKEARERLKMSQQQLAQALKVSENIIKRF 109
                                   566667777777632337778888899*****************999 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3    0.0002      0.19       8      36 ..      78     108 ..      78     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        HTH_23   8 lrillllae..GlsvreIAreLgvsrrTvyr 36 
                                   ++i++ ++e  ++s+++ A++L vs++ + r
  gi|70606462|ref|YP_255332.1|  78 YKIIKEARErlKMSQQQLAQALKVSENIIKR 108
                                   579*****99***************987765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   1.2e+03       8      27 ..      17      36 ..      17      36 .. 0.85
   2 ?   10.1   0.0   0.00045      0.42      18      46 ..      78     108 ..      77     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                  HTH_Tnp_ISL3  8 rrsriTlrleayilellles 27
                                  ++ ++T  +e  i++ ++++
  gi|70606462|ref|YP_255332.1| 17 KGKGFTVSYEGSIITVCTNC 36
                                  57799999999999999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00045
                  HTH_Tnp_ISL3  18 ayilellles..rsvkavArqlgvSwtTVwr 46 
                                   ++i+++++e+  +s ++ A+ l vS++ ++r
  gi|70606462|ref|YP_255332.1|  78 YKIIKEARERlkMSQQQLAQALKVSENIIKR 108
                                   6899999999999**************9998 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.8   0.00067      0.64       6      52 ..      74     114 ..      69     132 .. 0.76
   2 ?   -1.3   0.0       2.3   2.2e+03      24      35 ..     145     156 ..     143     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00067
                           Pou   6 leefakefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdl 52 
                                   +ee+ k  k+ R +l ++Q+++++aL+      +S   I+rFE+ +l
  gi|70606462|ref|YP_255332.1|  74 VEEYYKIIKEARERLKMSQQQLAQALK------VSENIIKRFESGKL 114
                                   68888899*****************96......67788999996443 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                           Pou  24 QadvglaLgkly 35 
                                   Q+d+gl+Lg+++
  gi|70606462|ref|YP_255332.1| 145 QKDLGLTLGDIV 156
                                   899999999865 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   0.00017      0.16      50     132 ..      34     126 ..      30     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHHHHHHCCTTTSSHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH CS
                         IF-2B  50 vslgnairrllkeiselksssdvkeakks...........liekikelikeieeadekigdiaaelikdgdtilTicnskt 119
                                   ++++n i+   k i +lk+++d k +k+s           ++e+  ++ike++e  +  +++ a+ +k +++i+   +s+ 
  gi|70606462|ref|YP_255332.1|  34 TNCFNKIKNYAK-IVNLKKEEDKKRIKTSpnkkyteveldIVEEYYKIIKEARERLKMSQQQLAQALKVSENIIKRFESGK 113
                                   688999999998.999*************6667777766677777777777666666666667777788899988888888 PP

                                   HHHHHHHHHHTTE CS
                         IF-2B 120 vlevlraaakekk 132
                                   +  ++++a++ ++
  gi|70606462|ref|YP_255332.1| 114 LKPTIQQAKQLER 126
                                   8888888887765 PP

>> Relaxase  Relaxase/Mobilisation nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.9   0.00024      0.23     134     218 ..      46     123 ..      35     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                      Relaxase 134 ndelasreglsideksprnrqseaekekaeknkssykeeirqalkkalenasdfedlkealkekglelrrktgkkltyklt 214
                                     +l+++e  +++++sp+++++e+e  ++e +++++ +e r++lk +++       l +alk  + +++r+ ++kl +  +
  gi|70606462|ref|YP_255332.1|  46 IVNLKKEEDKKRIKTSPNKKYTEVELDIVE-EYYKIIKEARERLKMSQQ------QLAQALKVSENIIKRFESGKLKPTIQ 119
                                   5679999999********************.677777777777777776......77777777777777777777776666 PP

                      Relaxase 215 denq 218
                                   +++q
  gi|70606462|ref|YP_255332.1| 120 QAKQ 123
                                   6665 PP

>> GRDP-like  Glycine-rich domain-containing protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.1   0.00026      0.24       5      92 ..      32     123 ..      29     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                     GRDP-like   5 dceslfgkiidksaidesneekaqkrteelwkrlypeepfeleskklkkeeevsessssisydlvkavkrqskfvykvs.. 83 
                                    c++ f+ki + + i + ++e+ +kr +   +++y+e ++++ ++  k+++e++e  + +++ l +a k  ++++++++  
  gi|70606462|ref|YP_255332.1|  32 VCTNCFNKIKNYAKIVNLKKEEDKKRIKTSPNKKYTEVELDIVEEYYKIIKEARERLKMSQQQLAQALKVSENIIKRFEsg 112
                                   699************999***********************998999999999999999******************9966 PP

                     GRDP-like  84 ..sphiseevf 92 
                                     +p+i++ + 
  gi|70606462|ref|YP_255332.1| 113 klKPTIQQAKQ 123
                                   66666666654 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00054      0.51       8      37 ..      87     115 ..      81     132 .. 0.76
   2 ?   -2.5   0.0       7.5   7.1e+03      50      59 ..     148     157 ..     148     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                        HTH_26   8 drgitkseLargtgisaatlsrlvkgkper 37 
                                     ++++++La+++ +s++ ++r+ +gk   
  gi|70606462|ref|YP_255332.1|  87 RLKMSQQQLAQALKVSENIIKRFESGKL-K 115
                                   5589**********************96.3 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.5
                        HTH_26  50 LgctpgDLle 59 
                                   Lg t+gD++ 
  gi|70606462|ref|YP_255332.1| 148 LGLTLGDIVN 157
                                   89999*9975 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.7    0.0046       4.3      29      88 ..      30      89 ..      10      91 .. 0.77
   2 ?    5.7   1.0     0.018        17      45      86 ..      83     124 ..      73     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0046
                         PIN_2 29 liapeeaveeiekhkealvkksk.lseeeleellelletkikiveeslyeskikeAkeria 88
                                  + ++ ++++ i+++ + +v+ +k  +++++++  ++  t++++   ++y++ ikeA+er++
  gi|70606462|ref|YP_255332.1| 30 ITVCTNCFNKIKNYAK-IVNLKKeEDKKRIKTSPNKKYTEVELDIVEEYYKIIKEARERLK 89
                                  478999********99.6665550556667777789999999999999*********9976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                         PIN_2  45 alvkksklseeeleellelletkikiveeslyeskikeAker 86 
                                   +  ++ k+s+++l+++l+  e+ ik +e+  +++ i++Ak++
  gi|70606462|ref|YP_255332.1|  83 EARERLKMSQQQLAQALKVSENIIKRFESGKLKPTIQQAKQL 124
                                   44456799*******************************986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0058       5.5      14      23 ..       4      13 ..       3      15 .. 0.89
   2 ?    1.2   0.6       0.3   2.8e+02      16      24 ..      30      38 ..      28      39 .. 0.87
   3 ?   -1.2   0.0       1.7   1.6e+03       3      10 ..      93     100 ..      93     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0058
                                  HH-EE-TTT- CS
                          RecR 14 ekvrhCsrCg 23
                                  ++v++C+ Cg
  gi|70606462|ref|YP_255332.1|  4 QNVKYCELCG 13
                                  79*******9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.3
                                  -EE-TTT-- CS
                          RecR 16 vrhCsrCgn 24
                                  ++ C +C+n
  gi|70606462|ref|YP_255332.1| 30 ITVCTNCFN 38
                                  678****99 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                                   HHHHHHHH CS
                          RecR   3 eeLaeaLq 10 
                                   ++La+aL+
  gi|70606462|ref|YP_255332.1|  93 QQLAQALK 100
                                   5899*996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2615  (0.145853); expected 358.6 (0.02)
Passed bias filter:                     1090  (0.0607954); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1044.92
//
Query:       gi|70606463|ref|YP_255333.1|  [L=396]
Description: proteasome-activating nucleotidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-43  146.9   0.1    1.4e-42  145.2   0.1    1.9  2  AAA              ATPase family associated with various cellul
    7.8e-15   54.4   0.1      2e-14   53.1   0.1    1.8  1  AAA_lid_3        AAA+ lid domain
    7.5e-10   38.6   0.2    1.8e-09   37.4   0.2    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    5.8e-07   29.8   0.0    1.5e-06   28.5   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
    1.5e-06   28.7   0.1    0.00024   21.5   0.0    2.6  2  AAA_16           AAA ATPase domain
    1.4e-05   25.1   0.2      7e-05   22.8   0.2    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    2.2e-05   24.3   0.0    5.6e-05   22.9   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.4e-05   23.9   0.1    6.8e-05   22.4   0.1    1.7  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    4.3e-05   23.8   0.3     0.0033   17.7   0.0    2.8  2  AAA_22           AAA domain
    0.00023   20.4   0.0    0.00042   19.6   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
     0.0005   20.4   0.0      0.001   19.4   0.0    1.6  1  AAA_28           AAA domain
     0.0011   18.4   0.6     0.0038   16.7   0.2    2.0  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0017   18.5   0.0     0.0057   16.8   0.0    1.9  1  AAA_33           AAA domain
     0.0018   18.8   0.0      0.006   17.1   0.0    2.1  1  AAA_18           AAA domain
     0.0018   18.0   0.0     0.0049   16.6   0.0    1.8  1  IstB_IS21        IstB-like ATP binding protein
     0.0021   17.3   0.0     0.0046   16.2   0.0    1.6  1  TIP49            TIP49 P-loop domain
      0.003   17.3   0.0       0.01   15.5   0.0    1.9  1  AAA_24           AAA domain
     0.0044   17.1   0.1      0.017   15.2   0.0    2.0  1  AAA_14           AAA domain
     0.0068   15.9   0.0      0.016   14.7   0.0    1.7  1  AAA_7            P-loop containing dynein motor region
     0.0093   15.7   0.0      0.043   13.5   0.0    2.0  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.1   0.1      0.028   13.7   0.0    1.7  2  Zeta_toxin       Zeta toxin
      0.015   15.7   0.0      0.035   14.5   0.0    1.7  1  RNA_helicase     RNA helicase
       0.02   14.2   0.3      0.042   13.2   0.0    1.7  1  ATPase           KaiC
      0.024   14.5   0.1       0.13   12.2   0.0    2.1  2  NACHT            NACHT domain
       0.03   13.8   0.0      0.087   12.3   0.0    1.8  1  PhoH             PhoH-like protein
      0.037   13.6   0.3       0.11   12.1   0.2    1.7  1  AAA_25           AAA domain
      0.043   13.8   0.0      0.085   12.9   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.049   13.3   0.7       0.15   11.7   0.3    1.9  2  ThylakoidFormat  Thylakoid formation protein
       0.05   13.3   0.2        1.8    8.2   0.0    2.9  3  Guanylate_kin    Guanylate kinase
      0.051   12.7   0.0      0.093   11.8   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.051   13.3   1.0       0.19   11.5   0.3    2.2  2  DivIC            Septum formation initiator
      0.061   12.9   0.0       0.12   12.0   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.066   13.1   4.4      0.091   12.7   0.1    3.1  3  ATPase_2         ATPase domain predominantly from Archaea
       0.07   13.6   0.0       0.32   11.5   0.0    2.1  2  ABC_tran         ABC transporter
      0.079   12.9   1.3       0.25   11.3   1.3    1.8  1  Prefoldin_2      Prefoldin subunit
      0.081   13.1   3.2       0.18   11.9   3.2    1.5  1  Tropomyosin_1    Tropomyosin like
      0.084   12.6   0.0       0.16   11.7   0.0    1.5  1  AAA_30           AAA domain
      0.087   12.0   0.0       0.42    9.7   0.0    2.0  2  NB-ARC           NB-ARC domain
      0.091   12.5   0.1       0.15   11.7   0.1    1.3  1  CCDC106          Coiled-coil domain-containing protein 106
        0.1   11.5   0.0       0.15   11.0   0.0    1.3  1  AFG1_ATPase      AFG1-like ATPase
       0.13   12.1   0.0       0.24   11.2   0.0    1.4  1  CPT              Chloramphenicol phosphotransferase-like prot
       0.18   12.2   0.8       0.53   10.7   0.0    2.3  1  AAA_17           AAA domain
       0.19   11.5   0.9       0.57    9.9   0.0    2.2  2  AAA_11           AAA domain
       0.19   11.3   1.9       0.72    9.4   1.1    2.4  2  YvrJ             YvrJ protein family
       0.34   11.0   4.1        0.5   10.5   1.8    2.4  2  bZIP_1           bZIP transcription factor
        7.6    7.0   9.3        3.5    8.1   0.4    3.0  2  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       7.7     3e+03      78      99 ..      14      35 ..       2      99 .. 0.62
   2 !  145.2   0.1   3.7e-45   1.4e-42       1     132 []     173     306 ..     173     306 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.7
                                  CCHHHHHHHHHHHHHHHHTTTS CS
                           AAA 78 eseeeervvnqLlteldgvkkk 99
                                  +++ +e++v+ L ++++ ++k+
  gi|70606463|ref|YP_255333.1| 14 NNNYDETLVKLLEEKIEALTKE 35
                                  4445555555555555544443 PP

  == domain 2  score: 145.2 bits;  conditional E-value: 3.7e-45
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgse 78 
                                   vllyGppGtGKT+lakava e++++f+ + +se+ +k+vge+++ +re+f+ a++ka psi+fiDE+da+a +r    +s 
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESNATFIHVVASEFAQKFVGEGARIVREVFELARKKA-PSIIFIDELDAIAARRidiGTSG 252
                                   79******************************************************9.*****************998889 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                   ++e +r++ qLl+e+dg+k  ++ v +i+atnr+d ldpa+lr gRfdr ie++l
  gi|70606463|ref|YP_255333.1| 253 EREIQRTLMQLLAEIDGFKALDN-VKIIAATNRIDILDPAILRpGRFDRLIEVPL 306
                                   9999****************755.***************************9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1   5.3e-17     2e-14       2      44 ..     331     373 ..     330     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 5.3e-17
                     AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                   ++++ +A++T+G+SGAD++++c eA+ +A+r+g+++i+ +d++
  gi|70606463|ref|YP_255333.1| 331 LNYDLIAQLTDGFSGADIKNVCTEAGYMAIREGRESIKFQDII 373
                                   57899*********************************99985 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   4.6e-12   1.8e-09       2      57 .]      61     115 ..      61     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4.6e-12
                                   EEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                Prot_ATP_ID_OB   2 atVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                   at+ ++l+d +++iV +ss+ + vv++a  v+ ++L+pg +Va+ ++   i ++LP
  gi|70606463|ref|YP_255333.1|  61 ATILDILPD-GKVIVRSSSGPNLVVNVATNVDVSKLKPGMSVALSQRGSTIIDILP 115
                                   79999****.********************************************99 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.8e-09   1.5e-06       6     103 ..     173     264 ..     169     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.8e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   +ll gp g+Gkt+laka+a   ++    ++i + ase+++    + + +   + ++    a ++   i+++DE+d i++ +
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESNA----TFIHVVASEFAQ----KFVGEGARIVREVFELARKKApsIIFIDELDAIAA-R 244
                                   6889******************96....************....66666666777776666666667************.7 PP

                                   --------H.HHHHHHHHHH CS
                         AAA_2  85 ssgadvSre.gVqrdLLqil 103
                                   ++    S+e ++qr L+q+l
  gi|70606463|ref|YP_255333.1| 245 RIDIGTSGErEIQRTLMQLL 264
                                   77777787669*******98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.2e-07   0.00024      24      61 ..     170     207 ..     140     215 .. 0.71
   2 ?    4.1   0.0      0.14        54     123     149 ..     218     243 ..     214     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.2e-07
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                   p  vll+G++G+GK+ l+++++ + +++ +++++ ++ 
  gi|70606463|ref|YP_255333.1| 170 PKGVLLYGPPGTGKTMLAKAVAAESNATFIHVVASEFA 207
                                   499*******************8777775666555554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                        AAA_16 123 lkrllallsrderplvlvlDdlqwade 149
                                   +++ ++l+++ + p ++++D+l+ + +
  gi|70606463|ref|YP_255333.1| 218 VREVFELARK-KAPSIIFIDELDAIAA 243
                                   5566688888.778*********6654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   1.8e-07     7e-05       1     124 [.     172     286 ..     172     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                   +vlL GppGtgK++la+ +aa  n+++  v  +++ ++    g r +          ++ + ar   ++i+++DE++ +  
  gi|70606463|ref|YP_255333.1| 172 GVLLYGPPGTGKTMLAKAVAAESNATFIHVVASEFAQKFVGEGARIV---------REVFELARkkAPSIIFIDELDAIAA 243
                                   59***********************9999999986554444444443.........3333344434789999999998888 PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                     +++  s   e ++ l+++  +++  +  +l ++ +ia++n+ d
  gi|70606463|ref|YP_255333.1| 244 RRIDIGTSGEREIQRTLMQLLAEIDGFK--ALDNVKIIAATNRID 286
                                   7777777766666666666666665433..345577777777776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.4e-07   5.6e-05      34      96 ..     171     241 ..     146     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.4e-07
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlek.agdlaalltnl......eekdvlfideihrl 96 
                                     vllyGpPG Gkt lak +a+e ++++ ++ ++   +k  g+ a ++ ++      ++  ++fide+  +
  gi|70606463|ref|YP_255333.1| 171 KGVLLYGPPGTGKTMLAKAVAAESNATFiHVVASEFAQKfVGEGARIVREVfelarkKAPSIIFIDELDAI 241
                                   679********************999861444444333324565555544311122134578999998765 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.8e-07   6.8e-05       3      47 ..      61     105 ..      60     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-07
                 Prot_ATP_OB_N   3 GtflavnsqdgtadV.lvggrrmrVavsPlvdaeeLrpGqeVlLnE 47 
                                   +t+l + + dg + V +++g  ++V+v+ +vd+++L+pG+ V L +
  gi|70606463|ref|YP_255333.1|  61 ATILDILP-DGKVIVrSSSGPNLVVNVATNVDVSKLKPGMSVALSQ 105
                                   67777775.4444442789*************************87 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.4e-06    0.0033       8      47 ..     173     203 ..     168     211 .. 0.83
   2 ?    4.0   0.0      0.15        57      56     106 ..     198     254 ..     193     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.4e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47 
                                   ++++G++GtGKT+l++ ++ +          ++++++v +
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAES---------NATFIHVVA 203
                                   689***************9998.........677776655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.15
                        AAA_22  56 llrellralglelkaerlsseellealeqalraravielliiDEaqhlr....s......e 106
                                   + + +++++ ++  +   +  ++++ + + +r++a  +++ iDE + +             
  gi|70606463|ref|YP_255333.1| 198 FIHVVASEFAQKFVG---EGARIVREVFELARKKAP-SIIFIDELDAIAarriDigtsgeR 254
                                   566666666654445...666777788888888888.*********996654403334552 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.1e-06   0.00042      50     116 ..     167     238 ..     121     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                        DUF815  50 glpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                    +p + vLL+G  GtGK  l ka+ +e +++ ++++  e +++ + e  ++v+++    +++   i+f+D L
  gi|70606463|ref|YP_255333.1| 167 IEPPKGVLLYGPPGTGKTMLAKAVAAESNATFIHVVasEFAQKFVGEGARIVREVFelaRKKAPSIIFIDEL 238
                                   367889**************************999977889999999999999876121455568*****98 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.6e-06     0.001       2      43 ..     173     219 ..     172     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakge 43 
                                   + + G+++tGKT l++a aa+     + vv  E+a +++ e+++  +
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAEsnatFIHVVaSEFAQKFVGEGARIVR 219
                                   6799***************7665545556668888888877765444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   9.6e-06    0.0038      25      43 ..     173     191 ..     164     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.6e-06
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKtmlak+++
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVA 191
                                   89*************9875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-05    0.0057       2      39 ..     173     212 ..     173     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                   vll G+pG+GK+ la+ ++++    ++++   ++ ++ +g
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESNatFIHVVASEFAQKFVG 212
                                   7899**************9999867777766665555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.5e-05     0.006       1      42 [.     173     222 ..     173     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevd 42 
                                   +ll G+pG+GKt lak+++ + +          +  ++v    +++ ev+
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESNAtfihvvasEFAQKFVGEGARIVREVF 222
                                   799***************87753357866665444444444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05    0.0049      45      72 ..     168     195 ..     155     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveav 72 
                                   e  ++++l Gp+G+GK+ la a++ e  
  gi|70606463|ref|YP_255333.1| 168 EPPKGVLLYGPPGTGKTMLAKAVAAESN 195
                                   566789****************998764 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0046      51      88 ..     171     206 ..     157     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                                   ++vLl Gp+gtGkt la a++ e +    f+++++se+
  gi|70606463|ref|YP_255333.1| 171 KGVLLYGPPGTGKTMLAKAVAAESN--ATFIHVVASEF 206
                                   89*******************9965..78999999996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-05      0.01       5      29 ..     173     199 ..     170     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-05
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi 29 
                                   +l+yGp+g+GKT+lak    + ++ fi
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVaaESNATFI 199
                                   89**************98776666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.4e-05     0.017       5      76 ..     173     241 ..     170     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT+l+k ++ e+      ++ +   +  +k   + +++ ++++e+++++  +++f+DE   +
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESN---ATFIHVVASEFAQKFVGEGARIVREVFELARKKAPSIIFIDELDAI 241
                                   7899***************9988...333333333333322233336788888886666899******9876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.1e-05     0.016      30      69 ..     167     206 ..     157     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinf 69 
                                   ++  k vll+Gp GtGKt+++k +  + + + + ++  +f
  gi|70606463|ref|YP_255333.1| 167 IEPPKGVLLYGPPGTGKTMLAKAVAAESNATFIHVVASEF 206
                                   556688*****************99888855444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00011     0.043      23      56 ..     171     201 ..     155     213 .. 0.78
   2 ?   -1.7   0.0       5.2     2e+03     134     143 ..     275     284 ..     254     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                     vl+ G  GtGK++la+a+ ++s+     f++v
  gi|70606463|ref|YP_255333.1| 171 KGVLLYGPPGTGKTMLAKAVAAESNA---TFIHV 201
                                   679*****************998874...44444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.2
                                   -EEEEEEESS CS
               Sigma54_activat 134 dvriiaatne 143
                                   +v+iiaatn+
  gi|70606463|ref|YP_255333.1| 275 NVKIIAATNR 284
                                   7999999996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-05     0.028      14      54 ..     168     206 ..     156     213 .. 0.85
   2 ?   -3.0   0.0       9.7   3.8e+03     159     189 ..     253     283 ..     236     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-05
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdl 54 
                                   e Pk +ll G pG GK+ la+++++e   +  ++++ + ++
  gi|70606463|ref|YP_255333.1| 168 EPPKGVLLYGPPGTGKTMLAKAVAAES--NATFIHVVASEF 206
                                   679***********************8..899999887665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.7
                    Zeta_toxin 159 hdeafeglresvealeeekqldrvkikdrdg 189
                                     e+++ l++ +++++  k+ld+vki+   +
  gi|70606463|ref|YP_255333.1| 253 EREIQRTLMQLLAEIDGFKALDNVKIIAATN 283
                                   4567788888888888888999999665444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     9e-05     0.035       1      50 [.     173     213 ..     173     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgq 50 
                                   ++lyGp+g+GK++lak +a++          + ++++ ++++f +++ g+
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAES---------NATFIHVVASEFAQKFVGE 213
                                   689**************55443.........4444555555555555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011     0.042      14     118 ..     165     267 ..     138     286 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                        ATPase  14 gGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg..klaiidasesa 92 
                                    Gi   + vl++G pGtGKt++a+  + ++    +   + v   e a+++  + +++  ++ +l ++   ++++id     
  gi|70606463|ref|YP_255333.1| 165 LGIEPPKGVLLYGPPGTGKTMLAKAVAAES----NATFIHVVASEFAQKFVGEGARIVREVFELARKKapSIIFIDELDAI 241
                                   58888889***************9877766....44566666666666666666666666666555431246666666666 PP

                        ATPase  93 eesaeekdkedleelieelaeaikei 118
                                   + +  + +++  +e+ ++l++ ++ei
  gi|70606463|ref|YP_255333.1| 242 AARRIDIGTSGEREIQRTLMQLLAEI 267
                                   55555555555555555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00033      0.13       3      22 ..     173     192 ..     171     200 .. 0.90
   2 ?   -0.8   0.0       3.2   1.3e+03      99     146 ..     247     266 ..     212     282 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00033
                                   EEEEC-TTTCHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                   v+l G++G GKT+L++ +a 
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAA 192
                                   799*************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.2
                                   H............HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EE CS
                         NACHT  99 q...kekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivle 146
                                       ++++++++ L +l                                +e
  gi|70606463|ref|YP_255333.1| 247 DigtSGEREIQRTLMQL-------------------------------LAE 266
                                   34444444444444444...............................444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022     0.087      22      43 ..     173     194 ..     157     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                                   EEEE--TTSSTTHHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                   v   Gp GtGKt+la a+a+e 
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAES 194
                                   7789************999875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00027      0.11      36      55 ..     173     192 ..     167     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                        AAA_25  36 allaGapgtGKttlaldlal 55 
                                   +ll+G+pgtGKt+la  +a+
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAA 192
                                   69************988876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00022     0.085      19      47 ..     170     200 ..     145     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..- CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..e 47 
                                    + +lL+G+ G+GKT+l++++a++ + +  +
  gi|70606463|ref|YP_255333.1| 170 PKGVLLYGPPGTGKTMLAKAVAAESNATfiH 200
                                   4569*****************9988766553 PP

>> ThylakoidFormat  Thylakoid formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00039      0.15     157     194 ..      16      53 ..       8      64 .. 0.86
   2 ?   -1.2   0.0       3.4   1.3e+03      55     113 ..     298     356 ..     297     383 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                                   T...THHHHHHHHGGGS-S-HHHHHHHHHHHHHHHHHH CS
               ThylakoidFormat 157 kdeekreealeklaealglskekvekDldlYrsnlekl 194
                                   + +e+  ++le+ +eal  + +k+ +Dl+ Y++ lekl
  gi|70606463|ref|YP_255333.1|  16 NYDETLVKLLEEKIEALTKEIDKLRQDLNWYKTELEKL 53 
                                   4567788999***************************8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.4
                                   HHHHTTT.-SSHHHHHHHHHHHHHHTT--HHHHHHHHHGGGGGTT-.BHHHHHHHHHTS- CS
               ThylakoidFormat  55 fdrlmeg.YkpeedkesifeAlckaveedpeqyredaeeleelakeksaeellsllkqee 113
                                   fdrl+e   ++e+ +++if+ +++ +  ++++ + +   +++l+++ s ++++++ ++++
  gi|70606463|ref|YP_255333.1| 298 FDRLIEVpLPDEKGRKEIFKIYLQRMRINEND-KLNYDLIAQLTDGFSGADIKNVCTEAG 356
                                   56666541445566788888888888877665.344456677777777777777776664 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.4   2.5e+03     128     157 ..      17      46 ..      11      65 .. 0.71
   2 ?    8.2   0.0    0.0045       1.8       4      35 ..     172     203 ..     170     214 .. 0.85
   3 ?    1.6   0.0       0.5     2e+02     113     155 ..     228     268 ..     218     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.4
                                   HHHHHTTSSSSHHHHHHHHHHHHHHHHGGG CS
                 Guanylate_kin 128 lqrrlksrgkeqeeklakrlaaaekelqey 157
                                    ++ l +  +e+ e l k++++++++l+ y
  gi|70606463|ref|YP_255333.1|  17 YDETLVKLLEEKIEALTKEIDKLRQDLNWY 46 
                                   555566667788888888888888888766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0045
                                   EEEEESTTTSSHHHHHHHHHHHSTTTEEE--E CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfgvsvs 35 
                                    v l gp g+Gk +l ka+ +e + +f   v+
  gi|70606463|ref|YP_255333.1| 172 GVLLYGPPGTGKTMLAKAVAAESNATFIHVVA 203
                                   6899*******************999976665 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.5
                                   TTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHG CS
                 Guanylate_kin 113 lspiivFikppslkelqrrlksrgkeqeeklakrlaaaekelq 155
                                    +p i+Fi    l+++  r   +g++ e++++  l ++ +e+ 
  gi|70606463|ref|YP_255333.1| 228 KAPSIIFI--DELDAIAARRIDIGTSGEREIQRTLMQLLAEID 268
                                   57999**9..777777777789**********99999888775 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024     0.093     117     138 ..     173     194 ..     168     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                   v++yGp+ tGkt+la+a a  +
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAES 194
                                   89***************98754 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00049      0.19      21      59 ..      24      61 ..      20      63 .. 0.90
   2 ?   -1.4   0.0       5.3   2.1e+03      21      44 ..     140     162 ..     134     165 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00049
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                         DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59
                                   l+++i+al++e++kl+++ +  + e+++L   + yie+
  gi|70606463|ref|YP_255333.1| 24 LLEEKIEALTKEIDKLRQDLNWYKTELEKL-LAPPYIEA 61
                                  5899*************************9.68888885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.3
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIC  21 qlkqeiaalqaelaklkaeneeLe 44 
                                    l+ +i++l  e+++l  +n++L 
  gi|70606463|ref|YP_255333.1| 140 GLEDQINELR-EVVELPLKNKKLF 162
                                   4555555553.4555555565555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0003      0.12       4      48 ..     174     220 ..     172     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                                   EEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SS..CHCCCCCCHC CS
                          cobW   4 vltGflGsGKTtLlnhllenraglklavivNefge..vsiDaellre 48 
                                   +l G++G+GKT+L +++ ++++   + v+  ef +  v++ a+++re
  gi|70606463|ref|YP_255333.1| 174 LLYGPPGTGKTMLAKAVAAESNATFIHVVASEFAQkfVGEGARIVRE 220
                                   688******************************98666666666655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       6.4   2.5e+03     138     157 ..      18      37 ..       6      49 .. 0.64
   2 ?   12.7   0.1   0.00023     0.091      17      70 ..     167     219 ..     156     286 .. 0.70
   3 ?   -2.0   0.1       6.9   2.7e+03      74     118 ..     340     384 ..     301     389 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.4
                      ATPase_2 138 aellvkeLlnliesltkekh 157
                                   +e lvk L + ie ltke +
  gi|70606463|ref|YP_255333.1|  18 DETLVKLLEEKIEALTKEID 37 
                                   45555666555555555543 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                      ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70 
                                    ep + +++YGp g GKt L k ++ +++   + ++  +++ +++  +  + ++
  gi|70606463|ref|YP_255333.1| 167 IEPPKGVLLYGPPGTGKTMLAKAVAAESNA-TFIHVVASEFAQKFVGEGARIVR 219
                                   57777899***************9999844.55555566666666665555544 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6.9
                      ATPase_2  74 ekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgk 118
                                    + +    ++++  +a   +i + +    f+ i ++++kikkk  
  gi|70606463|ref|YP_255333.1| 340 TDGFSGADIKNVCTEAGYMAIREGRESIKFQDIIRAIDKIKKKNL 384
                                   333333333555555555555554444446777777777777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         8   3.1e+03      52      69 ..      27      44 ..       8     102 .. 0.74
   2 ?   11.5   0.0   0.00082      0.32       6      37 ..     165     196 ..     163     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 8
                                  B-HHHCCHCEEEE-SS-- CS
                                  xxxxxxxxxxxxxxxxxx RF
                      ABC_tran 52 qeleslrkeigvlpqepq 69
                                  +++e l kei  l q+ +
  gi|70606463|ref|YP_255333.1| 27 EKIEALTKEIDKLRQDLN 44
                                  566666677777766633 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00082
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                   l +++ + v + G+ G+GK+ L+k++a +++ 
  gi|70606463|ref|YP_255333.1| 165 LGIEPPKGVLLYGPPGTGKTMLAKAVAAESNA 196
                                   6678888899****************999876 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.3   0.00063      0.25      71     103 ..      22      54 ..      12      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00063
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                   Prefoldin_2  71 ketlekeiktlekqleklekeleelkeelqkkl 103
                                    + le++i++l+k+++kl+++l+  k+el k+l
  gi|70606463|ref|YP_255333.1|  22 VKLLEEKIEALTKEIDKLRQDLNWYKTELEKLL 54 
                                   567899999999999999999999999999886 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.2   0.00047      0.18      22      66 ..       7      51 ..       5      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00047
                 Tropomyosin_1 22 kvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekae 66
                                  ++K+ e++n   e  +k L++k+++l +e++kl ++l+ +k+++e
  gi|70606463|ref|YP_255333.1|  7 SYKNRENNNNYDETLVKLLEEKIEALTKEIDKLRQDLNWYKTELE 51
                                  6899**********************************9999887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00042      0.16      20      45 ..     172     197 ..     158     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                        AAA_30  20 vavltGpAGtGKttalkalreaweaa 45 
                                    ++l Gp+GtGKt++ ka+++  +a 
  gi|70606463|ref|YP_255333.1| 172 GVLLYGPPGTGKTMLAKAVAAESNAT 197
                                   57899*********999997755544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011      0.42      22      44 ..     172     194 ..     157     208 .. 0.78
   2 ?   -1.4   0.0       2.7   1.1e+03      49      85 ..     296     332 ..     289     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                   EEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  22 vvalvGmgGvGKttlakqilnks 44 
                                    v l+G +G GKt lak +  +s
  gi|70606463|ref|YP_255333.1| 172 GVLLYGPPGTGKTMLAKAVAAES 194
                                   5889*************998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.7
                                   CCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSS CS
                        NB-ARC  49 grFdsvawvvvsktdkseeiletilkeLslseddlee 85 
                                   grFd+++ v + ++   +ei++  l+++  +e+d  +
  gi|70606463|ref|YP_255333.1| 296 GRFDRLIEVPLPDEKGRKEIFKIYLQRMRINENDKLN 332
                                   68999999999999999***99999999888777665 PP

>> CCDC106  Coiled-coil domain-containing protein 106
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00039      0.15      10      44 ..      21      55 ..      15      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                       CCDC106 10 qLevkkEkiswlqkriedLeeeRdFLRcqlekfis 44
                                   +++  Eki++l k i++L ++ ++ ++ lek++ 
  gi|70606463|ref|YP_255333.1| 21 LVKLLEEKIEALTKEIDKLRQDLNWYKTELEKLLA 55
                                  567889**************************985 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.15      49      80 ..     159     188 ..     135     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                   AFG1_ATPase  49 gklfgrkrksvepvrglYlwGgvGrGKtylmd 80 
                                   +klf   +   ep++g+ l+G+ G GKt+l  
  gi|70606463|ref|YP_255333.1| 159 KKLFE--ELGIEPPKGVLLYGPPGTGKTMLAK 188
                                   44444..34689*****************965 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00063      0.24       4      40 ..     173     209 ..     171     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                   +lL G + +GK+ la+a+ + ++++++h+   +f ++
  gi|70606463|ref|YP_255333.1| 173 VLLYGPPGTGKTMLAKAVAAESNATFIHVVASEFAQK 209
                                   89***************************99999876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0014      0.53       1      27 [.     176     204 ..     176     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0014
                                   EE-TTSSHHHHHHHHHHHHT..EEEEEHH CS
                        AAA_17   1 lGgPGsGKgtqceklvekyg..fthlsaG 27 
                                   +G+PG GK+ +++ ++ + +  f h+ a+
  gi|70606463|ref|YP_255333.1| 176 YGPPGTGKTMLAKAVAAESNatFIHVVAS 204
                                   7**************99886115555554 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       4.2   1.6e+03     159     187 ..      14      42 ..       5      55 .. 0.42
   2 ?    9.9   0.0    0.0015      0.57      19      41 ..     172     194 ..     152     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.2
                        AAA_11 159 skskleqerrklkkerkelskeleeaees 187
                                   +++  e+  + l+++++ l ke+++ ++ 
  gi|70606463|ref|YP_255333.1|  14 NNNYDETLVKLLEEKIEALTKEIDKLRQD 42 
                                   33333333333333333333333333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                        AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                    +l+ GPPGtgKT    ++ ++ 
  gi|70606463|ref|YP_255333.1| 172 GVLLYGPPGTGKTMLAKAVAAES 194
                                   4799*********6655555544 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1    0.0018      0.72      19      35 ..      25      41 ..      21      42 .. 0.92
   2 ?   -1.5   0.0       4.9   1.9e+03      26      35 ..     141     150 ..     138     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                          YvrJ 19 iEkkLdeLtksIeeLse 35
                                  +E+k+++Ltk I++L++
  gi|70606463|ref|YP_255333.1| 25 LEEKIEALTKEIDKLRQ 41
                                  69*************87 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.9
                          YvrJ  26 LtksIeeLse 35 
                                   L + I+eL+e
  gi|70606463|ref|YP_255333.1| 141 LEDQINELRE 150
                                   7788888876 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.8    0.0013       0.5      28      60 ..      22      54 ..      19      56 .. 0.89
   2 ?   -1.0   0.0       4.9   1.9e+03      33      48 ..     149     164 ..     128     166 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLk 60
                                  ++ Le++ +aL+ke  +L++ l+ +k e ekL+
  gi|70606463|ref|YP_255333.1| 22 VKLLEEKIEALTKEIDKLRQDLNWYKTELEKLL 54
                                  56799*********************9999997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.9
                                   HHHHHHHHHHHHHHHH CS
                        bZIP_1  33 rrvkaLekeNksLkse 48 
                                   r+v +L  +Nk+L +e
  gi|70606463|ref|YP_255333.1| 149 REVVELPLKNKKLFEE 164
                                   3455556666666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.2      0.99   3.8e+02     161     199 ..      11      50 ..       3      55 .. 0.50
   2 ?    8.1   0.4     0.009       3.5       4      40 ..     156     191 ..     153     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.99
                        AAA_23 161 eleeledekkllekl.eqekekekeleeleeeleeilkel 199
                                     + ++ ++ l++ l e+++   ke+++l+++l+ ++ el
  gi|70606463|ref|YP_255333.1|  11 RENNNNYDETLVKLLeEKIEALTKEIDKLRQDLNWYKTEL 50 
                                   3333333333333332333445566666666666555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.009
                        AAA_23   4 ienfrsfrdqeidFskgltlItGpNGaGKTTildAik 40 
                                   ++n + f++  i+  kg+ l++Gp G+GKT +  A+ 
  gi|70606463|ref|YP_255333.1| 156 LKNKKLFEELGIEPPKGV-LLYGPPGTGKTMLAKAVA 191
                                   677788888889999888.*************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1386  (0.0773049); expected 358.6 (0.02)
Passed bias filter:                     1061  (0.0591779); expected 358.6 (0.02)
Passed Vit filter:                       208  (0.0116013); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 2453.14
//
Query:       gi|70606464|ref|YP_255334.1|  [L=168]
Description: PUA domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-20   72.6   0.7      3e-20   72.0   0.7    1.3  1  PUA       PUA domain
    3.2e-14   52.8   0.0    6.2e-14   51.9   0.0    1.5  2  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    0.00012   22.3   0.4    0.00025   21.3   0.2    1.6  2  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.7     5e-24     3e-20       2      73 ..      95     166 ..      94     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 5e-24
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   rv + ++  +++l+g+++++++vv+++  ++ gd+V +vded++l+a+G+a++s+ee+++ k+g +v ++rv
  gi|70606464|ref|YP_255334.1|  95 RVMIQKEISEFILQGKNVFCKFVVDADPMIRYGDEVLVVDEDDRLLAIGRAKVSGEEIKQYKKGLAVIVKRV 166
                                   799******************************************************************998 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0     1e-17   6.2e-14       3      71 .]      20      92 ..      18      92 .. 0.93
   2 ?   -3.2   0.0       1.6   9.9e+03      37      45 ..     132     140 ..     123     144 .. 0.54

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1e-17
                        TGT_C2  3 lraiadYqFGagagdaLf..pedvtitrs.atgrirqvlv.dgerlatlraqdgrltLsleGarrlheslppP 71
                                  + +++ YqF     d++f  ++++ i+rs +t +ir +l  d + ++ lraqd++++++ ++++ ++e+ +pP
  gi|70606464|ref|YP_255334.1| 20 IYDVLSYQFSPSLSDCIFikHNKFLIQRSiNTDKIRDILTlDRKLFLVLRAQDNLFSITEASGNDIKECSKPP 92
                                  7899**************65445*****************9*****************************998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                        TGT_C2  37 vlvdgerla 45 
                                   v+++++rl+
  gi|70606464|ref|YP_255334.1| 132 VVDEDDRLL 140
                                   233445544 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.79   4.7e+03      11      27 ..      42      58 ..      39      85 .. 0.64
   2 !   21.3   0.2   4.1e-08   0.00025       4      57 ..      98     156 ..      95     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.79
                       UPF0113 11 lFLYGrdvlkesilkit 27
                                  +FL  r +  ++i+ i 
  gi|70606464|ref|YP_255334.1| 42 KFLIQRSINTDKIRDIL 58
                                  67777777777776664 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 4.1e-08
                       UPF0113   4 vkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt....k.a 57 
                                   ++++ ++ +L G++v+ + ++  ++ ++ ++ v+V++e++++l+iG+++ ++    + +
  gi|70606464|ref|YP_255334.1|  98 IQKEISEFILQGKNVFCKFVVDADPMIRYGDEVLVVDEDDRLLAIGRAKVSGeeikQyK 156
                                   55556667899*************************************99887653333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1155.01
//
Query:       gi|70606465|ref|YP_255335.1|  [L=240]
Description: hypothetical protein Saci_0658 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-35  120.6   0.0      1e-34  120.5   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   5.6e-39     1e-34       1     212 [.      20     222 ..      20     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 5.6e-39
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE...E-H CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg...rep 77 
                                   +i+Gf  iG+Vg++a+++++ +++++++g+i ++y l      +v++++e +  +p++l+++ d   +++lvl +   + p
  gi|70606465|ref|YP_255335.1|  20 FITGFRTIGEVGYIATRYIALKMKMKRIGFITTKY-LR-----DVTFLDEYGIATPFELFYDnD---NKILVLLNhllPLP 91 
                                   69*********************************.66.....66677777********66745...89******787777 PP

                                   SCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH...CT-CEEEEHHHHHHHHHHH CS
                          PAC2  78 ilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele...eseyggivgitglLlsaak 155
                                      ++ f++++++w+++++++ ++++ggld + r     t+ ek+ ++ t+++ + +l+    +++  ++g+ +l+   ++
  gi|70606465|ref|YP_255335.1|  92 REANM-FSEKIIKWLKRINISNAFYIGGLDKRYR-----TNNEKLRWIKTSNSTI-NLNfplMEKQLLMIGPLALFTIYSE 165
                                   77777.************************9888.....567799********99.3432234499999************ PP

                                   HTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                          PAC2 156 ergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                    +++pa++ll++++    dP aaa+++e l+k++g+++d+++L eda+++ee+l+++
  gi|70606465|ref|YP_255335.1| 166 IEDLPATVLLPYADRDRIDPGAAATVVEELAKIIGVNIDVTELYEDAKKIEEELQKQ 222
                                   ******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1656.81
//
Query:       gi|70606466|ref|YP_255336.1|  [L=498]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-66  222.6   0.0      1e-65  222.2   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.0   5.7e-70     1e-65       3     349 ..      14     336 ..      10     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 5.7e-70
                                   EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-S CS
                           TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsg 83 
                                   +R+G le++hg++etPaf+pv  ++  +++t +++  ++g + i++n++ ++     + + k+++lh++l+++k ++tdsg
  gi|70606466|ref|YP_255336.1|  14 GRIGILETKHGKLETPAFFPV-INPVKNEITIQDI-LSVGFESIITNAFLIK-----KYIGKEEDLHSILNYNKILMTDSG 87 
                                   8********************.8889999******.599*********9887.....5777888***************** PP

                                   HHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH.. CS
                           TGT  84 gfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah.. 162
                                   ++q+++              + G+ + +++ +++++ +kl++Di+++ld ++  +++kk++eksve T+ +++++ +    
  gi|70606466|ref|YP_255336.1|  88 AYQILQ--------------Y-GD-IDVSNVDIVNYETKLKPDIAVILDIPTGLTEDKKEAEKSVESTISRAKEASKFVel 152
                                   ***876..............4.9*.**************************************************976688 PP

                                   ...SE.EEEEE--TT-HHHHHHHHHHHH.HH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHH CS
                           TGT 163 ...qa.lfgivqGglyedlreesaeela.krdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedl 235
                                      ++ ++ ++qGg+y dl e sa+ +  ++d++++a+g+   +++  e++ l++++ ++++++ + kp +l+G g+P+ +
  gi|70606466|ref|YP_255336.1| 153 skdEIiWVHPIQGGMYLDLIEYSARIADmNQDYKMLALGSpTVLMQryEYAPLIDMIYKSKSNVSRGKPFHLFGGGHPHIF 233
                                   899777******************9887678999******655666688899***************************** PP

                                   HHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHH CS
                           TGT 236 leavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiH 316
                                   + avalGvD fd++ ++++ar++r++t+e  ++l++  y     p    CsC++C++y+++ + ++ ++++    +L+++H
  gi|70606466|ref|YP_255336.1| 234 AFAVALGVDTFDSASYILYARDHRYMTRERVYRLEELDYF----P----CSCPICSRYSPKDVMEMPEEQK---VRLIALH 303
                                   ***********************************88888....9....******99**********9988...******* PP

                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                           TGT 317 NlhyylelfkriReaIkegtfeefveefarkye 349
                                   Nl++++e+++ i++++keg++ e++++ a +++
  gi|70606466|ref|YP_255336.1| 304 NLYVIKEEINYIKQSLKEGRLFEYIQQKAYSHP 336
                                   **************************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3293.78
//
Query:       gi|70606467|ref|YP_255337.1|  [L=144]
Description: hypothetical protein Saci_0660 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-30  103.3   0.3    7.7e-30  102.5   0.3    1.4  1  Lsm_C            Lsm C-terminal
    0.00021   20.9   1.4     0.0013   18.4   1.0    2.3  2  LSM              LSM domain
     0.0017   18.4   0.2     0.0043   17.2   0.2    1.8  1  SM-ATX           Ataxin 2 SM domain
  ------ inclusion threshold ------
      0.073   12.8   0.0      0.092   12.5   0.0    1.3  1  DUF4579          Domain of unknown function (DUF4579)
       0.22   12.0   2.5        1.5    9.4   2.5    2.1  1  Phage_sheath_1N  Phage tail sheath protein beta-sandwich doma
       0.23   11.6   1.8        1.5    9.0   1.8    2.6  1  LSM14            Scd6-like Sm domain


Domain annotation for each model (and alignments):
>> Lsm_C  Lsm C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.3   2.6e-33   7.7e-30       1      63 []      79     141 ..      79     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 2.6e-33
                                   HHHHHHHHHHHS...TTTEEEETTTTEEEETTTEEEETTEEE--SHHHHHHHHHHHHHHH-.. CS
                         Lsm_C   1 areFaelvekelnlrpglVkvieeanvvvvldrikVsekGVeGsGplAervyelyeeYiekkk 63 
                                   +reFa++++kelnlr++++kv+eea+vv++ldr+kV+e+GVeGsGplA++vy+++++Yi+kkk
  gi|70606467|ref|YP_255337.1|  79 PREFADVITKELNLRTTDIKVYEEAGVVTILDRVKVTENGVEGSGPLAQKVYDIFNSYIDKKK 141
                                   79***********************************************************97 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.0   4.3e-07    0.0013       3      29 ..      11      37 ..      10      71 .. 0.78
   2 ?   -3.6   0.0       3.1   9.4e+03      35      44 ..     108     117 ..     107     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                  HHHTTTSEEEEEETTSEEEEEEEEEEE CS
                           LSM  3 lkklinkkvtvelkngrelrGtLkgfD 29
                                  l +l++k+++v+l+n+++++G+L +f+
  gi|70606467|ref|YP_255337.1| 11 LGSLLDKTIIVKLNNNKVYSGVLSSFE 37
                                  66899********************96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.1
                                   EEEEEEEEET CS
                           LSM  35 vLedveetlk 44 
                                   +L+ v++t +
  gi|70606467|ref|YP_255337.1| 108 ILDRVKVTEN 117
                                   6788887765 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.4e-06    0.0043      14      51 ..      17      53 ..      11      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                  SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                        SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                  k++ v++ n +vy+G++s++ + + f v+L +a+  ++
  gi|70606467|ref|YP_255337.1| 17 KTIIVKLNNNKVYSGVLSSFEV-SPFMVSLLNAKDNDN 53
                                  6799******************.8******99998877 PP

>> DUF4579  Domain of unknown function (DUF4579)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05     0.092     115     143 ..      43      71 ..      16     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                       DUF4579 115 iRlaaqsdgdgklyyklvlnGykieeqkl 143
                                   + l   +d d ++yyk+++nG  i e+ +
  gi|70606467|ref|YP_255337.1|  43 VSLLNAKDNDNNMYYKVIINGNMITEILV 71 
                                   5667778999***********99988654 PP

>> Phage_sheath_1N  Phage tail sheath protein beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5    0.0005       1.5      34      76 ..      85     140 ..      10     144 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
                                   EEEHSSSTTSEEEEEEETTEEEEEEEEES.SCCCTT-............BSSEEEE CS
               Phage_sheath_1N  34 vtsgaddsnqfdvivregdrivdaqilvt.gekdvvg............niavaak 76 
                                   v++++ +  + d+ v+e++ +v++ + v+ +e+ v+g            n++++ k
  gi|70606467|ref|YP_255337.1|  85 VITKELNLRTTDIKVYEEAGVVTILDRVKvTENGVEGsgplaqkvydifNSYIDKK 140
                                   66666688899**************************8888888888888888776 PP

>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8   0.00049       1.5       3      45 ..      15     123 ..      13     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00049
                         LSM14   3 IGskislisksdirYeGilceinledstiaLqn................................................ 35 
                                   + ++i ++ +++++Y G+l++ + +   ++L n                                                
  gi|70606467|ref|YP_255337.1|  15 LDKTIIVKLNNNKVYSGVLSSFEVSPFMVSLLNakdndnnmyykviingnmiteilvksaplfdprefadvitkelnlrtt 95 
                                   568999*************************99777777777777777777777777777777777777777777777777 PP

                         LSM14  36 ..................vrsfGtegrk 45 
                                                     v+ +G+eg +
  gi|70606467|ref|YP_255337.1|  96 dikvyeeagvvtildrvkVTENGVEGSG 123
                                   7777777777777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 766.60
//
Query:       gi|70606468|ref|YP_255338.1|  [L=124]
Description: DNA-directed RNA polymerase subunit G [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-49  166.4   3.9    2.6e-49  166.2   3.9    1.0  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
  ------ inclusion threshold ------
      0.069   13.7   0.1      0.097   13.2   0.1    1.2  1  RusA          Endodeoxyribonuclease RusA


Domain annotation for each model (and alignments):
>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2   3.9   2.9e-53   2.6e-49       1     119 []       4     123 ..       4     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 2.9e-53
                  RNA_pol_RpbG   1 svsleckvksieksklkdlkivkikcqne.eielDiiselnifkeedkveviisrekPeyldgkdFcghGylvtekeeen. 79 
                                   +++ +ck++siek++lk+l++vk++c+n+ +ie+Di++el+if+++++v++iisrekPey++ kdFc+hGyl+ e+++e+ 
  gi|70606468|ref|YP_255338.1|   4 MMQGTCKISSIEKGALKNLYVVKMDCDNDlKIEFDITKELSIFSKDEEVTFIISREKPEYSE-KDFCAHGYLFLERQQEDg 83 
                                   7899**********************************************************.***************999 PP

                  RNA_pol_RpbG  80 kiitliSlfGllvkisskkdllnelglkvmdkvYlcvrks 119
                                   ++i+ iSl+Gl+vki sk++l+n++ +k+md+vY+cv+k+
  gi|70606468|ref|YP_255338.1|  84 SFIDEISLYGLIVKILSKNGLINSKLFKMMDHVYYCVKKK 123
                                   **************************************96 PP

>> RusA  Endodeoxyribonuclease RusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.097      76     112 ..      17      60 ..       2      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                   .......SS---HHHHHHHHHHHH.HTTSBS-GGGEEEEEEE-- CS
                          RusA  76 k......tkkpDiDNlaKavlDal.ngivwkDDsqvvdlivekv 112
                                   +      + k+D+DN +K+ +D   +  +++ D+ v+ +i +++
  gi|70606468|ref|YP_255338.1|  17 GalknlyVVKMDCDNDLKIEFDITkELSIFSKDEEVTFIISREK 60 
                                   133346899***************9999*******998887643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 815.01
//
Query:       gi|70606469|ref|YP_255339.1|  [L=195]
Description: proteasome protease subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-50  170.8   0.2    2.6e-50  170.6   0.2    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.6   0.2   1.4e-54   2.6e-50       5     190 .]       6     183 ..       3     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.6 bits;  conditional E-value: 1.4e-54
                                   -EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHH CS
                    Proteasome   5 ttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlv 85 
                                    t++Gik+kdgvvlaa++r+++g+ +lsks ++K+fk+  + g+a aG ++D++tl+r++++e++ y++ + r+i+ +   
  gi|70606469|ref|YP_255339.1|   6 ATAIGIKTKDGVVLAAERRLSYGDFVLSKS-ARKVFKL-GRFGIAGAGIVGDIQTLTRIMNVEIKYYEMYNSRKISAR--- 81 
                                   59************************9999.7******.89*************************************... PP

                                   HHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHH CS
                    Proteasome  86 arvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavel 166
                                    ++a++l++ ++++++ p++ +ll++gvde+g p+L+ +dp+Gs+ie+ +++a+Gsg+ +a+++le+ey+e lt e a+el
  gi|70606469|ref|YP_255339.1|  82 -AAAKLLSVILYQNKVLPYISELLFGGVDEDG-PKLFILDPIGSLIED-SYAAVGSGARVAIGVLEAEYNESLTSEAAKEL 159
                                   .9999999999999***************888.***************.6******************************* PP

                                   HHHHHHHHHHHBTTSCSSEEEEEE CS
                    Proteasome 167 avkalkealerdklsgknievavi 190
                                   a+k++k+a+erd++sg++i++ +i
  gi|70606469|ref|YP_255339.1| 160 AIKSMKSAVERDVMSGDGIDILII 183
                                   *********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1232.51
//
Query:       gi|70606470|ref|YP_255340.1|  [L=428]
Description: histidyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-65  219.6   0.0    7.4e-65  219.2   0.0    1.1  1  tRNA-synt_His    Histidyl-tRNA synthetase
    5.3e-14   52.6   0.0    2.8e-13   50.2   0.0    2.1  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    1.2e-10   41.4   0.6    2.9e-10   40.2   0.6    1.7  1  HGTP_anticodon   Anticodon binding domain
    4.9e-10   39.3   0.0      5e-08   32.7   0.0    2.5  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.5e-05   23.4   0.0      6e-05   22.6   0.0    1.4  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   0.0   2.1e-68   7.4e-65       1     309 [.       9     318 ..       9     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 2.1e-68
                                   T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHH CS
                 tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaa 80 
                                   g++d + ee +ki+ +++++  ++ ++GY++V +P++E    +  ++ge+ +  ++ ++D+ +r ++lR++iTp+++R++ 
  gi|70606470|ref|YP_255340.1|   9 GMKDYYGEELNKIKFIEETFRTVVLNSGYQEVYTPIVEDFKLFSLKSGEEIRkTMYVFKDKADREVALRPEITPSIVRVYL 89 
                                   799***********************************************98578899999******************** PP

                                   HHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTS.SSEEEEEEETCHHHH CS
                 tRNA-synt_His  81 hrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagv.kelrldlghvglvra 159
                                   ++++  ++plRl Y G+v+r  + + gr re+ Q+G+El+G+++  ad+Ev+sll e+ + ++g+ +++ ++++++g++r+
  gi|70606470|ref|YP_255340.1|  90 NSMQhLPKPLRLFYVGQVYRYDEPQFGRYREFRQAGVELLGSSSSFADIEVISLLNEIYD-SLGLkDKIIIKINNIGIYRE 169
                                   ***99******************************************************8.9996489************* PP

                                   HHHHTT--HHHHHHHHHHHHCT-HH.HHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHH.HHHHHHHHHHH CS
                 tRNA-synt_His 160 lleaaglsesleeallaalarkdla.elkelaaeaglkealrellkal.elygdaevleealealaaap.alqaaldelee 237
                                   ++++ag++e+++e ll+++++ ++  +lke++++ ++k+  + l+ +l   + + ++le +++++++ + +l+  +++l  
  gi|70606470|ref|YP_255340.1| 170 IFNKAGITEEQQEHLLHLIDKGKVDdALKEFTDN-NYKDLITYLI-SLkFDKLESDKLESLRREVSKYNfNLEGEINKLSF 248
                                   ********************99997256777765.5544444444.44444456789999999887765367778888888 PP

                                   HHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS-SEEEEEECTTTGGG.T---EEEEEEEEHHH CS
                 tRNA-synt_His 238 laallealakpevrvtlDlaelrgyeYytGlvFaayaegvgqaiarGGrYdelgaaf.grarpAtGfsldlea 309
                                   + ++le+l+   v++++Dl+ +rg++YytG++F+++ ++v+  ia+GGrYd+l++ + g+  pA+Gf++ +e+
  gi|70606470|ref|YP_255340.1| 249 ISEVLEDLG---VKIKIDLGFVRGLAYYTGVIFEVIHPDVSFSIAGGGRYDNLVRLYgGADTPAIGFAIGVER 318
                                   888888885...*********************************************99**********9986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   7.7e-17   2.8e-13       1     123 [.      64     283 ..      64     327 .. 0.70

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 7.7e-17
                                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                   Y ++d+ dre +L+P+ ++ +v+++ + +    k  Pl+l++++ +yR+ ++ + G  R+reF q + +  ++ +s  d+ 
  gi|70606470|ref|YP_255340.1|  64 YVFKDKADREVALRPEITPSIVRVYLNSMQHLpK--PLRLFYVGQVYRYDEP-QFG--RYREFRQAGVELLGSSSSFADI- 138
                                   899***********************99443346..****************.89*..**************99977765. PP

                                   HHHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                  tRNA-synt_2b  81 rdlikaisriferlglefraiielmsaks.................................................... 109
                                    ++i + ++i+ +lgl+ + ii++++++                                                     
  gi|70606470|ref|YP_255340.1| 139 -EVISLLNEIYDSLGLKDKIIIKINNIGIyreifnkagiteeqqehllhlidkgkvddalkeftdnnykdlitylislkfd 218
                                   .9***************9999999875446667777777777777777777777777777777776666666666666666 PP

                                   ...................................................BTTSEEEEEEEEET CS
                                   ...................................................xxxxxxxxxxxxxx RF
                  tRNA-synt_2b 110 ...................................................adykdkkefeavse 123
                                                                                      + y+    fe++ +
  gi|70606470|ref|YP_255340.1| 219 klesdkleslrrevskynfnlegeinklsfisevledlgvkikidlgfvrgLAYYTGVIFEVIHP 283
                                   66666666666666666666666666666666666665555555555555555555555555555 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.6   8.1e-14   2.9e-10       1      93 [.     334     425 ..     334     426 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 8.1e-14
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   +++vipl + +++ + +a +l + Lr+++i  +l+ ++  + k + ++ + g++ +v +G+kele++++t++ +++req +
  gi|70606470|ref|YP_255340.1| 334 KIAVIPLIS-TKDSLSLAIRLLNILRKNNIIGVLNLKDVPLSKLMTYYVEEGYNAIVLIGKKELEENSITIKFLEKREQKT 413
                                   689*****9.66699***************999999********************************************* PP

                                   EETTHHHHHHHH CS
                HGTP_anticodon  82 vsldelveklke 93 
                                   v+l++++++l++
  gi|70606470|ref|YP_255340.1| 414 VKLEKIEDVLIN 425
                                   ********9987 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.4e-11     5e-08      14     156 ..      16     154 ..       7     165 .. 0.80
   2 !    3.7   0.0    0.0099        35     204     229 ..     303     327 ..     281     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.4e-11
                                   SB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHH CS
                  tRNA-synt_2d  14 gklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirt 94 
                                    +l+ ++ + e ++ + l+ g++ev  p ve     f+   +++ + +R    t y+ k++   ++++ LR   t+  +r+
  gi|70606470|ref|YP_255340.1|  16 EELNKIKFIEETFRTVVLNSGYQEVYTPIVE----DFKLFSLKSGEEIR---KTMYVFKDKA--DREVALRPEITPSIVRV 87 
                                   567778889999******************4....35556666666555...5666656666..889*********99997 PP

                                   H....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHH..HHHHHHHHHHHCTST CS
                  tRNA-synt_2d  95 l....ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladl..kgvleellkklfgae 156
                                        ++  +p++++ +g+v+R d+    +  eF q+   ++++  s+ad+  + +l+e++ +l g +
  gi|70606470|ref|YP_255340.1|  88 YlnsmQHLPKPLRLFYVGQVYRYDEPQFGRYREFRQAGVELLGSSSSFADIevISLLNEIYDSL-GLK 154
                                   5566588889**************************************9972245688888877.655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0099
                                   T-.TTSEEEEEEEEHHHHHHHHHT-S CS
                  tRNA-synt_2d 204 gideevsgfafGlGveRlamlkygie 229
                                   g   ++++++f +GveR+a++ ++i+
  gi|70606470|ref|YP_255340.1| 303 GG-ADTPAIGFAIGVERTALVINKIK 327
                                   33.489999***********999885 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.7e-08     6e-05      13     160 ..      16     155 ..      10     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-08
               tRNA_synthFbeta  13 gelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlarg 93 
                                   +elnk + ++++ r+++ ++G++Ev+t + v + +l  l++ ++ rk++ +    ++   +lR+ ++p+++ v  + +++ 
  gi|70606470|ref|YP_255340.1|  16 EELNKIKFIEETFRTVVLNSGYQEVYT-PIVEDFKLFSLKSGEEIRKTMYVFKDKADREVALRPEITPSIVRVYLNSMQHL 95 
                                   458999999*****************9.667777777777888999********************************999 PP

               tRNA_synthFbeta  94 nedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfyd..lkgivealleslgi.e 160
                                    + +rlF +g+v++ d  +  +++e r+ ++ l g++            +f+d  +  +++++ +slg+ +
  gi|70606470|ref|YP_255340.1|  96 PKPLRLFYVGQVYRYDePQFGRYREFRQAGVELLGSS-----------SSFADieVISLLNEIYDSLGLkD 155
                                   999*************877788***********9999...........55554114567788888888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2721.84
//
Query:       gi|70606471|ref|YP_255341.1|  [L=91]
Description: tRNA-splicing endonuclease subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-07   29.3   0.1    2.2e-06   27.6   0.1    1.8  1  tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal
  ------ inclusion threshold ------
      0.018   15.1   0.3      0.025   14.7   0.3    1.2  1  sCache_like    Single Cache-like
      0.032   14.5   0.1      0.037   14.3   0.1    1.1  1  Sen15          Sen15 protein


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.7e-10   2.2e-06      38      85 .]      33      80 ..       6      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.7e-10
                                  SSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
                 tRNA_int_endo 38 ehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85
                                  +  ey+V+v++e+ ++  ++l + +  + +++K+ ++a+vd+ gdvty
  gi|70606471|ref|YP_255341.1| 33 KDNEYVVMVLNENNKINAKELERFLSFSSKINKNSVIAVVDKYGDVTY 80
                                  6789******************************************99 PP

>> sCache_like  Single Cache-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   4.1e-06     0.025      11      59 ..      31      81 ..      24      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
                                  HHHHHHHHHHHS-GGG-SSHHHHHHHHHHHHHHT-E..EEEEETTS-EEEE CS
                   sCache_like 11 leKEakllasllenenlkaaenkkvleeasekldar..itivdadgkvlyd 59
                                  l+K+ ++++ +l+++n  +a++ +++  +s k++ +  i +vd+ g v y 
  gi|70606471|ref|YP_255341.1| 31 LIKDNEYVVMVLNENNKINAKELERFLSFSSKINKNsvIAVVDKYGDVTYY 81
                                  79*******************************87645899*******996 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.1e-06     0.037      39      92 ..      29      85 ..       3      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.1e-06
                         Sen15 39 d......elvl.PlelteklslekldkvfkelkeekserkkrivLaivddDsTvvYYkvtd 92
                                         e+v+  l+ ++k++ ++l+ +++  ++     +k+ v+a+vd+ + v YY++++
  gi|70606471|ref|YP_255341.1| 29 YilikdnEYVVmVLNENNKINAKELERFLSFSSKI----NKNSVIAVVDKYGDVTYYFLSE 85
                                  255555555550555599**********9985544....68899**************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 592.59
//
Query:       gi|70606472|ref|YP_255342.1|  [L=195]
Description: hypothetical protein Saci_0665 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-11   42.5   3.5    6.9e-11   41.5   3.5    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.023   14.4   1.1      0.044   13.5   0.8    1.6  2  Ribosomal_S27e  Ribosomal protein S27
       0.23   11.5   1.2       0.51   10.4   1.2    1.6  1  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.32   11.2   5.4       0.12   12.6   0.8    2.2  2  DUF1492         Protein of unknown function (DUF1492)
          2    8.0   5.6        6.9    6.2   1.2    2.4  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   3.5   1.9e-14   6.9e-11       1      31 [.       1      31 [.       1      41 [. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.9e-14
                                  EEETTTTCEECHEETSTTCEEESSSSBEEEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVled 31
                                  + CP+C+s+++v+D++ g+lvC++CGlVl+ 
  gi|70606472|ref|YP_255342.1|  1 MECPECKSREIVWDYKCGNLVCSNCGLVLDK 31
                                  67***************************85 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   1.2e-05     0.044       9      36 ..       2      29 ..       1      31 [. 0.94
   2 ?   -3.1   0.0       1.9   6.9e+03      15      28 ..      91     104 ..      90     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                  E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                   Cp+C+   +v++       C  Cg vL
  gi|70606472|ref|YP_255342.1|  2 ECPECKSREIVWDYKCGNLVCSNCGLVL 29
                                  6************************998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                   -EEEEESS-SS-EE CS
                Ribosomal_S27e  15 netvvFshaatvvk 28 
                                   n+ ++ s++at++k
  gi|70606472|ref|YP_255342.1|  91 NNAIIRSSSATIIK 104
                                   67788899999986 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.2   0.00014      0.51      41      64 ..       2      26 ..       1      33 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                   Zn_Tnp_IS91 41 eCeeCghe.kivyfsCksrhCpsCq 64
                                  eC+eC+++  ++ ++C++  C++C+
  gi|70606472|ref|YP_255342.1|  2 ECPECKSReIVWDYKCGNLVCSNCG 26
                                  8****866256679**********8 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.19     7e+02      32      65 ..      61      89 ..      41     122 .. 0.64
   2 ?   12.6   0.8   3.3e-05      0.12      57      94 ..     129     166 ..     115     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.19
                       DUF1492 32 ediekktaeaikkklelqrlidklensdsrsvLr 65
                                  ++      e i k   +++ + k + ++sr +L+
  gi|70606472|ref|YP_255342.1| 61 DK-----IEKIDKIIKFNSKLSKKQLPKSRKLLN 89
                                  33.....344555555666666666666666655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.3e-05
                       DUF1492  57 nsdsrsvLrmvyidkltvwqvidklnisrstyyrllrv 94 
                                    ++++  L m + dk t  +++++l+is+  + ++lr 
  gi|70606472|ref|YP_255342.1| 129 SIKYKVALAMYFYDKKTFNKIMNNLEISNKYFNKILRR 166
                                   3689999**********************988888775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.016        59       4      10 ..       2       8 ..       2      11 .. 0.81
   2 ?    6.2   1.2    0.0019       6.9      17      26 .]      20      29 ..      16      29 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                   zf-ribbon_3  4 rCPnCGa 10
                                  +CP+C++
  gi|70606472|ref|YP_255342.1|  2 ECPECKS 8 
                                  5999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0019
                   zf-ribbon_3 17 nvCpyCGtkl 26
                                   vC +CG +l
  gi|70606472|ref|YP_255342.1| 20 LVCSNCGLVL 29
                                  4899999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1749  (0.0975515); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1403.76
//
Query:       gi|70606473|ref|YP_255343.1|  [L=553]
Description: thermosome beta subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.4e-175  584.6  16.6   1.7e-175  584.4  16.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   12.8   0.1        6.7    7.2   0.0    2.7  2  BRCT_2      BRCT domain, a BRCA1 C-terminus domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.4  16.6  1.8e-179  1.7e-175       2     490 ..      43     533 ..      42     534 .. 0.97

  Alignments for each domain:
  == domain 1  score: 584.4 bits;  conditional E-value: 1.8e-179
                                   HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaeklia 82 
                                   ++++ktt+GP+GmdKmlv++ g++++TnDGatil +++++hPaakllv++a+ qdee+ DGT t+vi+ geL+++ae+l+ 
  gi|70606473|ref|YP_255343.1|  43 EEALKTTYGPRGMDKMLVDSLGDITITNDGATILDKMDLQHPAAKLLVQIAKGQDEETADGTKTAVIFSGELVKKAEELLY 123
                                   789****************************************************************************** PP

                                   CTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS..EEC CS
                    Cpn60_TCP1  83 agvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene..kel 160
                                   +++hpt i++gy+ka e+a++ ++ei+ ++s+  +d+e+L+kva tslssk ++  +e+l+++vv+A+ ++ e +     +
  gi|70606473|ref|YP_255343.1| 124 KEIHPTIIVSGYKKAEEMAIKTIEEISTKVSV--NDTEILRKVALTSLSSKAVAGAREHLADIVVKAItQVAELRGdkWYV 202
                                   **************************666665..59********************************666665558899* PP

                                   SCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHH CS
                    Cpn60_TCP1 161 dlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekql 241
                                   dl+++++vk++ggs++d+++v G+++dk+v++p mpk++enak++lld sLe ek+e +++++++d+++++k++++ee++l
  gi|70606473|ref|YP_255343.1| 203 DLDNVQIVKKHGGSINDTQIVYGIIVDKEVVHPGMPKRVENAKIALLDASLEVEKPELDAEIRINDPTQMKKFLDEEENIL 283
                                   ********************************************************************************* PP

                                   HHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECCETT CS
                    Cpn60_TCP1 242 eellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeekigs 322
                                   +e+++ki+++g+nvv+cqkgid++a+h+lak+gila+rr+kk+dle+la+atG+++vs++++lt+++lG+a  vee+kig+
  gi|70606473|ref|YP_255343.1| 284 KEKVDKIAQTGANVVICQKGIDEVAQHYLAKKGILAVRRAKKSDLEKLARATGGRVVSNIDELTSQDLGYATLVEERKIGE 364
                                   ********************************************************************************* PP

                                   CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHH CS
                    Cpn60_TCP1 323 ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaie 403
                                   +k+++ie+ k++k+++il+rg  + v+de+era++dAl  v+ +++d+++++GGGa+e+e+ak+l++ya +v g+eqlaie
  gi|70606473|ref|YP_255343.1| 365 DKMVFIEGAKNPKAVSILIRGGLERVVDETERALRDALGTVADVVRDGRAIAGGGAVETEIAKRLRKYAPQVGGKEQLAIE 445
                                   ********************************************************************************* PP

                                   HHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHH.HTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCE CS
                    Cpn60_TCP1 404 afakALevipktLaeNaGldpievlaklraah.nkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLri 483
                                   a+a+ALe+++++L+eN+G+dpie+l klr+ah n+ +k++gi+v +g+i+d+++ gv++p+ vk++a+k+Atea ++iLri
  gi|70606473|ref|YP_255343.1| 446 AYANALESLVMILIENGGFDPIELLVKLRSAHeNETNKWHGINVYTGQIQDMWSLGVIEPAVVKMNAIKAATEASTLILRI 526
                                   ********************************444558******************************************* PP

                                   EEEEXXX CS
                    Cpn60_TCP1 484 deiikak 490
                                   d+ i+a+
  gi|70606473|ref|YP_255343.1| 527 DDLISAG 533
                                   ****986 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.022     2e+02      26      48 ..     208     228 ..     200     263 .. 0.76
   2 ?    7.2   0.0   0.00075       6.7      18      40 ..     322     347 ..     311     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                        BRCT_2  26 klIeknGGevvetitsavyivia 48 
                                   ++++k+GG + +t+   vy +i+
  gi|70606473|ref|YP_255343.1| 208 QIVKKHGGSINDTQI--VYGIIV 228
                                   789*******99994..333333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00075
                        BRCT_2  18 spsreklkklIeknGGevveti...t 40 
                                   ++++++l+kl ++ GG+vv++i   t
  gi|70606473|ref|YP_255343.1| 322 RAKKSDLEKLARATGGRVVSNIdelT 347
                                   4789***************9994441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3406.10
//
Query:       gi|70606474|ref|YP_255344.1|  [L=546]
Description: hypothetical protein Saci_0667 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  126.6   1.1    1.5e-36  126.6   1.1    2.2  3  DUF87            Helicase HerA, central domain
    5.2e-08   31.9   0.0    0.00088   18.0   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
    8.8e-08   31.4   0.1    3.8e-05   22.8   0.0    2.6  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    2.9e-07   29.6   0.6    0.00096   18.1   0.0    2.7  3  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
    9.9e-06   25.3   0.0    4.5e-05   23.2   0.0    2.0  2  Zot              Zonular occludens toxin (Zot)
    5.5e-05   22.3   0.9       0.24   10.3   0.0    2.2  2  AAA_10           AAA-like domain
     0.0011   19.0   0.4     0.0041   17.1   0.1    2.0  2  TraG-D_C         TraM recognition site of TraD and TraG
     0.0016   18.9   0.7        2.4    8.6   0.2    3.2  3  AAA              ATPase family associated with various cellul
     0.0028   17.9   1.7        1.9    8.7   0.1    2.8  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.021   14.5   0.5      0.043   13.5   0.5    1.5  1  DDE_1            DDE superfamily endonuclease
      0.039   14.4   0.6          2    8.8   0.4    3.1  2  AAA_16           AAA ATPase domain
        0.1   12.7   0.4       0.72    9.9   0.0    2.4  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
        0.1   12.3   0.0        1.2    8.9   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.11   11.9   0.0       0.32   10.3   0.0    1.7  1  IPT              Isopentenyl transferase
       0.14   11.4   0.0       0.31   10.3   0.0    1.5  1  Zeta_toxin       Zeta toxin
       0.23   11.4   6.2       0.31   11.0   0.9    3.0  2  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.5     5e+03     133     133 ..      95      95 ..      49     134 .. 0.53
   2 !  126.6   1.1   1.3e-39   1.5e-36       1     223 [.     216     419 ..     216     423 .. 0.96
   3 ?   -1.6   0.5       2.2   2.4e+03     117     133 ..     452     483 ..     429     523 .. 0.42

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.5
                         DUF87 133 e 133
                                   +
  gi|70606474|ref|YP_255344.1|  95 N 95 
                                   1 PP

  == domain 2  score: 126.6 bits;  conditional E-value: 1.3e-39
                         DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitp 81 
                                   ie+G+++++ +++  ++  k v rH+ i+gsTGsGK+n +a++ +ell kkg  ++ilD+HGEY+++l     +++kv++ 
  gi|70606474|ref|YP_255344.1| 216 IELGEVINNYGIQTGFNS-KDVLRHISIFGSTGSGKTNSAALISKELL-KKGFDVVILDWHGEYKHIL-----PEFKVYSR 289
                                   79****************.899**************************.*******************.....99*****9 PP

                         DUF87  82 spsakdkelkinpwsldpeelldllee..ddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrkl 160
                                   +     + l++np  ld ++ +d++++  d+ ++++ q  +l+ +++q+k   ++ kl++d+ ++ +le+++    + +++
  gi|70606474|ref|YP_255344.1| 290 R-----NILTLNPIPLDEQDTEDIIDIfkDTLELTEPQSFILYLVIEQLK---RYRKLDTDT-LKIILESIQ----TDSYM 357
                                   8.....6*********************999******************7...8999**999.778******....***** PP

                         DUF87 161 knqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvi 223
                                    ++++ +l +kl+ l +  + +  +s d+  ++ ++ ek +  +iidls++ +l+++ + s++
  gi|70606474|ref|YP_255344.1| 358 IRDIKFALGRKLYLLTTPLARK-LFSLDTGYTYYDIGEKLSGGNIIDLSFIYNLKLRRLYSLF 419
                                   ****************999999.99******************************99987766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                         DUF87 117 qrsvleealdqaka...............kee 133
                                   + ++l++al+++++               +ee
  gi|70606474|ref|YP_255344.1| 452 KNEMLKRALQEIRKynvslciitqspssiDEE 483
                                   34444444444442111122222222222222 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   5.9e-05     0.066      14      62 ..     230     278 ..     220     291 .. 0.87
   2 !   18.0   0.0   7.8e-07   0.00088     226     325 ..     409     500 ..     360     535 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.9e-05
                        DUF853  14 alalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLs 62 
                                     + k + rh  i G+tG Gkt +  +++++l + G  v++ d  G+  
  gi|70606474|ref|YP_255344.1| 230 GFNSKDVLRHISIFGSTGSGKTNSAALISKELLKKGFDVVILDWHGEYK 278
                                   55667778***********************************999865 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 7.8e-07
                        DUF853 226 llqsPklyatfLlWllseLfeeLPevGdldkPklvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlP 306
                                    l+  +ly+ f++ +l  ++    e+ +    k+ +  +eah  fn+  ++l       ++ ir   v +  +tq+P+ + 
  gi|70606474|ref|YP_255344.1| 409 NLKLRRLYSLFMMKFLFTFY----ERSNNSDRKILLVIEEAHNYFNNKNEMLKR----ALQEIRKYNVSLCIITQSPSSID 481
                                   45556777777666655555....4555566799999*********99877654....45668999*************** PP

                        DUF853 307 dtvLaqLGnrvqhalraft 325
                                   ++v+     ++ h++++  
  gi|70606474|ref|YP_255344.1| 482 EEVIKNTNIKIIHTIKSNI 500
                                   *************998643 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   1.4e+03     315     359 ..      82     126 ..      69     127 .. 0.74
   2 !   22.8   0.0   3.4e-08   3.8e-05      11      59 ..     233     281 ..     226     305 .. 0.82
   3 !    5.8   0.0    0.0048       5.4     219     304 ..     412     499 ..     343     510 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                 TrwB_AAD_bind 315 AeelsellGeqeversteslsygannsrdgvslgrqrevrpvVla 359
                                   A    +l+G+++v++++  +s   ++  + +s ++ r+ + v+l+
  gi|70606474|ref|YP_255344.1|  82 AYIGFKLVGKKNVNDQQLDYSEELKQLVETISRHKDRRLKIVILT 126
                                   555557889999999999999777777777777777777777776 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.4e-08
                 TrwB_AAD_bind  11 keretqhilivGttGsGKtqalekllrairargdraivlDltGafvsrf 59 
                                    ++  +hi i+G+tGsGKt+ +  + +++ ++g  +++lD +G++ +  
  gi|70606474|ref|YP_255344.1| 233 SKDVLRHISIFGSTGSGKTNSAALISKELLKKGFDVVILDWHGEYKHIL 281
                                   566779*************************************997644 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0048
                 TrwB_AAD_bind 219 lrpllsawldlaikallslpesrerrlWfflDElpaL..grleelksllaegRkfGgavvlglqsiaqlrevYGedaaqsi 297
                                   lr l s+ +     +  +++++ +r++ +++ E ++   ++ e lk++l+e+Rk+ + + +  qs + + e   +++   i
  gi|70606474|ref|YP_255344.1| 412 LRRLYSLFMMKFLFTFYERSNNSDRKILLVIEEAHNYfnNKNEMLKRALQEIRKYNVSLCIITQSPSSIDEEVIKNTNIKI 492
                                   5666666666666677778999************9975578899***************9999*99999887666666666 PP

                 TrwB_AAD_bind 298 lslvntk 304
                                   + +++++
  gi|70606474|ref|YP_255344.1| 493 IHTIKSN 499
                                   6666665 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.84   9.5e+02     425     458 ..     117     157 ..      78     165 .. 0.72
   2 !   18.1   0.0   8.6e-07   0.00096      35     108 ..     219     303 ..     193     320 .. 0.75
   3 !    8.7   0.2   0.00059      0.66     279     348 ..     415     483 ..     408     507 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.84
               T4SS-DNA_transf 425 dddeeivlikgqkPikakkalYykd.......edfkaelak 458
                                   d+  +iv++++  P+    +++y +       edf +e++ 
  gi|70606474|ref|YP_255344.1| 117 DRRLKIVILTSFDPLPGSGIAFYTEvdssykdEDFIKEVNT 157
                                   34556888888888888888888776666665666655555 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.6e-07
               T4SS-DNA_transf  35 ggllntdGdf.........ehvlvvAptrsgKgvg..vviPnllkwkqsiVvlDpkgElaeltskiRkkqgrkVfvlePan 104
                                   g++ n+ G +          h+++++ t+sgK+ +  ++   llk++  +V+lD  gE   +  + +  + r++  l+P  
  gi|70606474|ref|YP_255344.1| 219 GEVINNYGIQtgfnskdvlRHISIFGSTGSGKTNSaaLISKELLKKGFDVVILDWHGEYKHILPEFKVYSRRNILTLNPIP 299
                                   44444444334446666679************9762144456677777******************************987 PP

               T4SS-DNA_transf 105 lkts 108
                                   l+++
  gi|70606474|ref|YP_255344.1| 300 LDEQ 303
                                   7765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00059
               T4SS-DNA_transf 279 llrlffnmvvellkrklpnkderpkevlflLDEfpsl..GkleileealatiagYgirltlIiQsisqlket 348
                                   l  lf+  ++   +++++n d++   +l+ + E  +    k e l+ al  i++Y+++l +I Qs s + e 
  gi|70606474|ref|YP_255344.1| 415 LYSLFMMKFLFTFYERSNNSDRK---ILLVIEEAHNYfnNKNEMLKRALQEIRKYNVSLCIITQSPSSIDEE 483
                                   55566666777777777777777...788888877753357799*********************9988775 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.6   1.8e+03       7      17 ..     244     254 ..     242     306 .. 0.82
   2 !   23.2   0.0     4e-08   4.5e-05      79     146 ..     435     496 ..     401     518 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                           Zot   7 GapGsgKtsga 17 
                                   G  GsgKt  a
  gi|70606474|ref|YP_255344.1| 244 GSTGSGKTNSA 254
                                   88999999877 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4e-08
                           Zot  79 dkgallviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiskihkevralaekavklkr 146
                                   d+  llvi E+++ f+++ + ++       a++e R+++  ++++tq +s i++ev +  +++  +  
  gi|70606474|ref|YP_255344.1| 435 DRKILLVIEEAHNYFNNKNEMLK------RALQEIRKYNVSLCIITQSPSSIDEEVIKNTNIKIIHTI 496
                                   57789***********9988644......9************************99776666665555 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00021      0.24      23      99 ..     239     315 ..     228     357 .. 0.65
   2 !   10.3   0.2   0.00022      0.24     212     293 ..     410     487 ..     405     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                        AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe..iakkinvvtLdse.eenegvLdPlvllkee 99 
                                   +  i G++G GK  +a l+   ++  g  ++i+D   e   +k+ lpe  ++++ n++tL++   +++ + d + ++k++
  gi|70606474|ref|YP_255344.1| 239 HISIFGSTGSGKTNSAALISKELLKKGFDVVILDWHGE---YKHILPEfkVYSRRNILTLNPIpLDEQDTEDIIDIFKDT 315
                                   7789*********************************9...666777655566767777653222222333444455544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                        AAA_10 212 lteekllsvavlfviaafarefassdkkefkvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelk 292
                                   l+  +l s+ ++  + +f +   +sd+k+    ++ Ea  + + +  +++lk  +   R+yn  + ++tqs++ +++e +k
  gi|70606474|ref|YP_255344.1| 410 LKLRRLYSLFMMKFLFTFYERSNNSDRKILL--VIEEAHNYFNNK--NEMLKRALQEIRKYNVSLCIITQSPSSIDEEVIK 486
                                   5667888999***********9999999987..999*98765544..57899999999******************99976 PP

                        AAA_10 293 n 293
                                   n
  gi|70606474|ref|YP_255344.1| 487 N 487
                                   5 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.8     2e+03      51      91 ..      58     101 ..      49     123 .. 0.68
   2 !   17.1   0.1   3.6e-06    0.0041       2      55 ..     438     493 ..     437     519 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.8
                      TraG-D_C  51 aetilgncdvklflg.vn.deetaeelS.kllGektvesestss 91 
                                    ++i+ n ++k  ++ +n + +t  ++  kl+G+k v+ ++   
  gi|70606474|ref|YP_255344.1|  58 TKNIILNFEIKNSINkINiNGKTIAYIGfKLVGKKNVNDQQLDY 101
                                   56777788888866655558899999986788999998655433 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.6e-06
                      TraG-D_C   2 vlfllDEfanlgki..pdleellstgrsrgislvlilQsiaqleelYgkegaetil 55 
                                   +l+++ E+ n  +   + l+++l+++r++++sl++i+Qs + ++e   k+++ +i+
  gi|70606474|ref|YP_255344.1| 438 ILLVIEEAHNYFNNknEMLKRALQEIRKYNVSLCIITQSPSSIDEEVIKNTNIKII 493
                                   5788888888876644679************************9987777764443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.49   5.5e+02      37      95 ..      96     164 ..      68     179 .. 0.67
   2 ?    5.7   0.0     0.016        18       3      28 ..     242     270 ..     240     335 .. 0.82
   3 !    8.6   0.2    0.0021       2.4      55     122 ..     432     486 ..     407     496 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.49
                                   SSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH........TTCCCHHHHHHHHHHHHHHHH CS
                           AAA  37 kyvgesekkirelfkeakeka..kpsilfiDEidalaksr........sgseseeeervvnqLlteldg 95 
                                   + + + ++++++l++++++++  + +i+++  +d l +s         s+ ++e+  + vn+L ++l+ 
  gi|70606474|ref|YP_255344.1|  96 DQQLDYSEELKQLVETISRHKdrRLKIVILTSFDPLPGSGiafytevdSSYKDEDFIKEVNTLKNMLES 164
                                   444455556666666665555544588888888877777777776665445566666777777777766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                                   EESSTTSSHHHHHHHHHHHH...THEEEE CS
                           AAA   3 lyGppGtGKTllakavakel...gvefle 28 
                                   ++G  G GKT  a  + kel   g++++ 
  gi|70606474|ref|YP_255344.1| 242 IFGSTGSGKTNSAALISKELlkkGFDVVI 270
                                   78*****************8554455554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0021
                                   HTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHST CS
                           AAA  55 eka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrg 122
                                   + +  ++  l+i+E+++ ++++            + L ++l++ +k+  +v ++++t++p+++d++++ +
  gi|70606474|ref|YP_255344.1| 432 N-NsdRKILLVIEEAHNYFNNK-----------NEMLKRALQEIRKY--NVSLCIITQSPSSIDEEVI-K 486
                                   3.245669999***********...........88888899999996..7***************998.3 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0017       1.9       6      29 ..     238     261 ..     235     338 .. 0.90
   2 !    7.9   0.0    0.0032       3.6      86     127 ..     431     472 ..     408     503 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0017
                        AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                   +++ ++G +G+GKT +++ + ++l
  gi|70606474|ref|YP_255344.1| 238 RHISIFGSTGSGKTNSAALISKEL 261
                                   5899************99988877 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                        AAA_22  86 lraravielliiDEaqh.lr.seealeeLrsllnlsrkgvqliL 127
                                   +++ +++ ll+i+Ea++ ++ ++e+l+    l+++++++v+l +
  gi|70606474|ref|YP_255344.1| 431 SNNSDRKILLVIEEAHNyFNnKNEMLKRA--LQEIRKYNVSLCI 472
                                   44444469*********776767777766..3333455555554 PP

>> DDE_1  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   3.8e-05     0.043      58     157 ..     419     529 ..     403     544 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                         DDE_1  58 ifeeWLkvfdkrleaekrkilLlldssrshe.tvel......leselqniklvflPassas....llqPldqgvvselKar 127
                                    + ++L  f +r ++ +rkilL+++++  +  + +       +e ++ n++l ++ +s +s    +++  +  +++++K++
  gi|70606474|ref|YP_255344.1| 419 FMMKFLFTFYERSNNSDRKILLVIEEAHNYFnNKNEmlkralQEIRKYNVSLCIITQSPSSideeVIKNTNIKIIHTIKSN 499
                                   57899999*****************9999874444476777778888899999986555441112588999********** PP

                         DDE_1 128 Yrrqllqalleeqnrlskeqkkltlldalk 157
                                     + ++   l +++++ +   kl + +a+ 
  gi|70606474|ref|YP_255344.1| 500 IDKRIISDSLSLDKDQLQLLDKLDVGEAIL 529
                                   ***999999999999999999999998886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0018         2      25     143 ..     238     350 ..     231     361 .. 0.57
   2 ?    0.8   0.0      0.51   5.7e+02     128     164 ..     429     465 ..     421     473 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                        AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                   + + + G  G+GK+  +  + ++l k+g  +++  +  ++       +++  ++  +  + l  ++   + e++ e + + 
  gi|70606474|ref|YP_255344.1| 238 RHISIFGSTGSGKTNSAALISKELLKKGfDVVILDWHGEY------KHILPEFKVYSRRNILTLNPIP-LDEQDTEDIIDI 311
                                   678899*******************997334466666666......3344455443444444433333.555555555555 PP

                        AAA_16 105 laavpelagaeasrllellkrllallsrderplvlvlDd 143
                                   ++++ el+  ++  l+ ++ +l ++ + d ++l ++l+ 
  gi|70606474|ref|YP_255344.1| 312 FKDTLELTEPQSFILYLVIEQLKRYRKLDTDTLKIILES 350
                                   554444444444444444444444444444444444444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                        AAA_16 128 allsrderplvlvlDdlqwadeaslqllaaLlrlles 164
                                   +++ + +r+++lv+++++       ++l+  l++   
  gi|70606474|ref|YP_255344.1| 429 ERSNNSDRKILLVIEEAHNYFNNKNEMLKRALQEIRK 465
                                   456667888*********9999999988877776554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.63   7.1e+02      58     104 ..     104     146 ..      57     171 .. 0.64
   2 ?    9.9   0.0   0.00064      0.72       6      35 ..     244     273 ..     240     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.63
                                   CCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  58 rllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry 104
                                    l++l+e+++++k    +++ v+l+ +d+     + + +++e+   y
  gi|70606474|ref|YP_255344.1| 104 ELKQLVETISRHKD--RRLKIVILTSFDPL--PGSGIAFYTEVDSSY 146
                                   44555555555543..47888888888875..566666666655555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00064
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDa 35 
                                   ++ G+GKT  aa + + l ++g++V+ +D 
  gi|70606474|ref|YP_255344.1| 244 GSTGSGKTNSAALISKELLKKGFDVVILDW 273
                                   678************************994 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011       1.2      25      57 ..     229     261 ..     220     281 .. 0.88
   2 ?    0.4   0.0      0.44   4.9e+02      85     111 ..     437     463 ..     431     491 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                        RuvB_N  25 aakkreealdhvllyGpPGlGkttlakiiakel 57 
                                   +  + ++ l h+ ++G+ G Gkt  a++i+kel
  gi|70606474|ref|YP_255344.1| 229 TGFNSKDVLRHISIFGSTGSGKTNSAALISKEL 261
                                   5556788999*********************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                        RuvB_N  85 kdvlfideihrlsraveevlysamedf 111
                                   k +l i+e h   ++ +e+l  a++++
  gi|70606474|ref|YP_255344.1| 437 KILLVIEEAHNYFNNKNEMLKRALQEI 463
                                   456889***************999764 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.32       6      34 ..     242     273 ..     238     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                           IPT   6 ifGatttGKtaeaiklake...tgapvivlDR 34 
                                   ifG+t++GKt+ a  ++ke   +g+ v+ lD 
  gi|70606474|ref|YP_255344.1| 242 IFGSTGSGKTNSAALISKEllkKGFDVVILDW 273
                                   9****************964448******995 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.31      21      63 ..     242     286 ..     234     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                    Zeta_toxin  21 lgGqpGAGKselaellkdele.rqgnvvrld.pDdlRelhPeyee 63 
                                   + G++G+GK++ a+l+ +el  ++ +vv ld   +++   Pe++ 
  gi|70606474|ref|YP_255344.1| 242 IFGSTGSGKTNSAALISKELLkKGFDVVILDwHGEYKHILPEFKV 286
                                   569****************98577788988844689999999875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.7     3e+03      87      87 ..      86      86 ..      43     126 .. 0.42
   2 ?   11.0   0.9   0.00028      0.31      25     147 ..     238     451 ..     219     476 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
                                  E CS
                        ResIII 87 k 87
                                   
  gi|70606474|ref|YP_255344.1| 86 F 86
                                  1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00028
                                   SEEEEEESTTSTHHHHHHHHHHHH-S..........................-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII  25 krglikmaTGtGKTlvaaklierllkkgkee.....................kflflvprkslleqtleefkkflseayke 84 
                                   +++ i   TG+GKT  aa + ++llkkg                        + ++  + + l eq  e++ ++++++ + 
  gi|70606474|ref|YP_255344.1| 238 RHISIFGSTGSGKTNSAALISKELLKKGFDVvildwhgeykhilpefkvysrRNILTLNPIPLDEQDTEDIIDIFKDTLEL 318
                                   46678889******************9886566666666666666666666644444455666666665554444443322 PP

                                   ..........GEEEESSS-B--.......-SEEEEEHHHHHHTH..................................... CS
                        ResIII  85 ..........igkkvsgdkkkakekdstnkkilvttiqsldadseee.................................. 121
                                             +   +++ k+ + + d+++ ki++++iq+ +  + ++                                  
  gi|70606474|ref|YP_255344.1| 319 tepqsfilylV---IEQLKRYR-KLDTDTLKIILESIQTDSYMI-RDikfalgrklyllttplarklfsldtgytyydige 394
                                   33333332221...22222222.444677777777777644444.223566666666666666666666666666666666 PP

                                   ....................................HHHTTT-SEEEEETGGGTTS. CS
                        ResIII 122 ...............................eeeseellrdrfdviiiDEaHrlgak 147
                                                                  + ++ ++ +dr+ +++i EaH++  +
  gi|70606474|ref|YP_255344.1| 395 klsggniidlsfiynlklrrlyslfmmkflfTFYERSNNSDRKILLVIEEAHNYFNN 451
                                   666666666666666666666666666666655566666666667777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.76u 0.32s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 3251.64
//
Query:       gi|70606475|ref|YP_255345.1|  [L=132]
Description: hypothetical protein Saci_0668 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 910.35
//
Query:       gi|70606476|ref|YP_255346.1|  [L=84]
Description: hypothetical protein Saci_0669 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-06   26.7   0.3    6.2e-06   26.5   0.3    1.1  1  Urm1           Urm1 (Ubiquitin related modifier)
    8.8e-06   26.3   0.0    9.5e-06   26.2   0.0    1.1  1  ThiS           ThiS family
  ------ inclusion threshold ------
      0.054   13.6   0.0      0.058   13.5   0.0    1.2  1  DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal do


Domain annotation for each model (and alignments):
>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.3     1e-09   6.2e-06      36      96 .]      29      84 .]      14      84 .] 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1e-09
                                  HHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                          Urm1 36 liayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                  l++ +k+  +++++++ ++++k+r G + Lin +D+ ll+    +lkd+D++  +   hGG
  gi|70606476|ref|YP_255346.1| 29 LLDILKE--LDKEEKLLINGNKIRSGYILLINGIDYRLLNG---KLKDGDVVDILPINHGG 84
                                  4444443..5667899**********************998...8***************9 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.6e-09   9.5e-06       5      77 .]       9      84 .]       5      84 .] 0.87

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.6e-09
                                  TCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG....TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                          ThiS  5 aelrelag.eeelelaegstvaelleaLgerypela....lerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                  + l +  g +e +    ++++ ++l++L+++ + l      + + ++++Ng + +   l+ +lkdgD+v+ilp+  GG
  gi|70606476|ref|YP_255346.1|  9 GPLATRLGrDEFVISLKADNLLDILKELDKEEKLLIngnkIRSGYILLINGIDYRL--LNGKLKDGDVVDILPINHGG 84
                                  6677777777777788899999******99996666****99**************..9**************99998 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.7e-06     0.058      55      93 ..       9      47 ..       1      63 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-06
                                  EEEESEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEEEEE CS
                 DNA_pol3_beta 55 stisaeseeeegkvlvparllldivkaLpndkkvkisvn 93
                                    ++    + e+ + ++a +lldi+k+L++++k  i+ n
  gi|70606476|ref|YP_255346.1|  9 GPLATRLGRDEFVISLKADNLLDILKELDKEEKLLINGN 47
                                  4445555578999*****************988777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 584.60
//
Query:       gi|70606477|ref|YP_255347.1|  [L=82]
Description: 30S ribosomal protein S17e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-14   54.3   0.9    1.3e-14   54.2   0.9    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.034   13.4   0.9      0.039   13.3   0.9    1.0  1  DUF3536         Domain of unknown function (DUF3536)
      0.053   13.4   1.5      0.056   13.3   1.5    1.0  1  DUF2797         Protein of unknown function (DUF2797)
      0.081   12.9   1.4       0.22   11.6   0.5    1.9  2  MinE            Septum formation topological specificity fact
        0.2   11.6   4.0       0.11   12.5   1.9    1.6  2  GP24_25         Tail assembly gene products 24 & 25
       0.82   10.2   7.9         11    6.6   7.9    2.0  1  YtxH            YtxH-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.9   4.3e-18   1.3e-14       1      68 [.       1      67 [.       1      81 [. 0.86

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 4.3e-18
                                  XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS--SS CS
                Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkgpvrg 68
                                  mg+v tk +K++ar++ +k++ + +  +++nkk+++e   ++skk++n+iaGy t+++k i k++v  
  gi|70606477|ref|YP_255347.1|  1 MGNVYTKDIKRVARELYDKFKDQASDKYDDNKKLVDEYVNVSSKKVKNRIAGYLTRYVK-ISKNKVEA 67
                                  9********************************************************97.66666643 PP

>> DUF3536  Domain of unknown function (DUF3536)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   1.3e-05     0.039      17      76 ..      13      72 ..       7      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                       DUF3536 17 rdelakvyeeeakkllkdpwaardeYievildrseenverFlkehakrelseeekvkalk 76
                                    el + ++++a++ + d ++  deY++v   + +++++ +l+++ k + ++ e ++a +
  gi|70606477|ref|YP_255347.1| 13 ARELYDKFKDQASDKYDDNKKLVDEYVNVSSKKVKNRIAGYLTRYVKISKNKVEAQEASE 72
                                  5678899**************************************999988888777765 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   1.9e-05     0.056     113     171 ..      10      74 ..       3      82 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                       DUF2797 113 RrlaglvevalketvaDktnwrkmlksevedvdlsaeaeelaeliaeeselga......eaiesl 171
                                   +r a+++  ++k++ +Dk + +k+l +e+ +v+ +++++++a ++++  ++ +      ea e+l
  gi|70606477|ref|YP_255347.1|  10 KRVARELYDKFKDQASDKYDDNKKLVDEYVNVSSKKVKNRIAGYLTRYVKISKnkveaqEASEEL 74 
                                   68899999***************************************444444222223333333 PP

>> MinE  Septum formation topological specificity factor MinE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.037   1.1e+02      35      48 ..      34      47 ..      29      51 .. 0.84
   2 ?   11.6   0.5   7.3e-05      0.22      26      52 ..      44      70 ..      41      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.037
                                  HHHHHH-..-SEEE CS
                          MinE 35 viskYveideekve 48
                                   + +Yv+++++kv+
  gi|70606477|ref|YP_255347.1| 34 LVDEYVNVSSKKVK 47
                                  6899******9998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.3e-05
                                  CHHHHHHHHHHHHHH-..-SEEEEEEE CS
                          MinE 26 eqlkeeileviskYveideekvevkle 52
                                  ++ k+ i   + +Yv+i+++kve +  
  gi|70606477|ref|YP_255347.1| 44 KKVKNRIAGYLTRYVKISKNKVEAQEA 70
                                  678999*****************9966 PP

>> GP24_25  Tail assembly gene products 24 & 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.9   3.7e-05      0.11      41      81 ..       7      47 ..       4      70 .. 0.82
   2 ?   -1.0   0.1      0.53   1.6e+03      51      63 ..      65      77 ..      52      81 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                       GP24_25 41 kkareavvellkefeeiaeleeddedeLvdeysdelekvia 81
                                  k+ +  ++el ++f++ a  + dd+ +Lvdey +   k ++
  gi|70606477|ref|YP_255347.1|  7 KDIKRVARELYDKFKDQASDKYDDNKKLVDEYVNVSSKKVK 47
                                  5667889***********9999999*******765555544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.53
                       GP24_25 51 lkefeeiaeleed 63
                                  +++ e   eleed
  gi|70606477|ref|YP_255347.1| 65 VEAQEASEELEED 77
                                  3333444444444 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.9    0.0038        11      28      73 ..       7      45 ..       2      82 .] 0.48

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0038
                          YtxH 28 kdlkekaddlkekakelleeakekakekaedlkekvkekadelkek 73
                                  kd+k+ a +l +k+       k++a++k +d k+ v+e ++  ++k
  gi|70606477|ref|YP_255347.1|  7 KDIKRVARELYDKF-------KDQASDKYDDNKKLVDEYVNVSSKK 45
                                  44555544444444.......3333444444444444442222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2094  (0.116794); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 553.58
//
Query:       gi|70606478|ref|YP_255348.1|  [L=385]
Description: hypothetical protein Saci_0671 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.5e-179  596.1   0.0   2.8e-179  595.9   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.9   0.0  1.6e-183  2.8e-179       1     361 []       2     362 ..       2     362 .. 1.00

  Alignments for each domain:
  == domain 1  score: 595.9 bits;  conditional E-value: 1.6e-183
                      FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeate 81 
                                   k+t+svikaD+GslaGh+ vh++ ++++++vl+eak+++llid+y+t+vGDD+elimtht+g+ +++vh+ aw+afkea++
  gi|70606478|ref|YP_255348.1|   2 KTTISVIKADIGSLAGHHVVHPDTMAAASKVLAEAKSQSLLIDYYITHVGDDLELIMTHTRGELDTKVHETAWNAFKEAAK 82 
                                   79******************************************************************************* PP

                      FBPase_3  82 vakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklhe 162
                                   vakel+ly+aGqDlL+d+fsGnv+GlGPgvae+e+eeR+sep+ +f+aDktepgafnlplyk+fadpfnt+Glvidp++h+
  gi|70606478|ref|YP_255348.1|  83 VAKELGLYAAGQDLLSDSFSGNVRGLGPGVAEIEVEERPSEPIAIFMADKTEPGAFNLPLYKMFADPFNTPGLVIDPTMHN 163
                                   ********************************************************************************* PP

                      FBPase_3 163 GfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRaqsgl 243
                                   GfkfevlDv++ ++++l+ap+elydllal+g+++ryvi+r+y+ +d+   avvs erl+liaGkYvGkDDPv+ivR q+gl
  gi|70606478|ref|YP_255348.1| 164 GFKFEVLDVYQGEAVVLNAPQELYDLLALIGTPSRYVIRRIYRSEDNLLGAVVSIERLNLIAGKYVGKDDPVTIVRLQHGL 244
                                   ********************************************************************************* PP

                      FBPase_3 244 PavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafdeaRekaaei 324
                                   Pa+ge+le+f+lphlv GwmrGsh+gpl+Pvs++da++trfdgppr+++lgf++k+gklvgp Dlfddpafde+R+ a++i
  gi|70606478|ref|YP_255348.1| 245 PALGEALEAFTLPHLVPGWMRGSHYGPLIPVSQRDARATRFDGPPRLIGLGFNVKNGKLVGPSDLFDDPAFDEVRRLANTI 325
                                   ********************************************************************************* PP

                      FBPase_3 325 adelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                   +d++Rr+Gpf+phrl++ e+eYttlp +lekl++rf+
  gi|70606478|ref|YP_255348.1| 326 TDYMRRHGPFMPHRLEPTEMEYTTLPIILEKLRSRFK 362
                                   ***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2631.79
//
Query:       gi|70606479|ref|YP_255349.1|  [L=604]
Description: putative ATPase RIL [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-37  129.0   0.0    4.7e-19   69.3   0.0    2.4  2  ABC_tran      ABC transporter
    1.4e-16   61.2   9.7     0.0039   17.0   0.1    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      2e-12   46.7   2.3    4.7e-12   45.5   2.3    1.7  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    1.2e-10   41.2   6.4      0.002   17.6   2.9    4.2  3  SMC_N         RecF/RecN/SMC N terminal domain
    3.9e-07   29.6   6.4    3.9e-07   29.6   6.4    2.6  3  Fer4          4Fe-4S binding domain
    8.4e-06   25.8   8.3    0.00024   21.1   1.0    2.3  2  Fer4_10       4Fe-4S dicluster domain
      1e-05   25.6   0.5       0.24   11.5   0.0    3.1  2  MMR_HSR1      50S ribosome-binding GTPase
    1.9e-05   24.7   0.8        0.2   11.7   0.0    3.0  3  AAA_14        AAA domain
    5.4e-05   23.8   2.5       0.13   12.7   0.3    2.4  2  AAA_23        AAA domain
      8e-05   23.2   0.1       0.85   10.2   0.0    3.0  2  AAA_18        AAA domain
     0.0001   22.7   0.0      0.019   15.4   0.0    2.5  2  AAA_16        AAA ATPase domain
    0.00044   20.2  12.9     0.0015   18.5   3.4    2.3  2  Fer4_6        4Fe-4S binding domain
    0.00055   19.9   0.0       0.79    9.6   0.0    2.4  2  Rad17         Rad17 P-loop domain
    0.00058   20.2   0.0       0.21   12.0   0.0    2.5  2  RNA_helicase  RNA helicase
    0.00067   19.6   1.2    0.00067   19.6   1.2    2.3  2  Fer4_2        4Fe-4S binding domain
    0.00077   19.6   8.3     0.0014   18.7   8.3    1.4  1  Fer4_21       4Fe-4S dicluster domain
    0.00089   19.8   0.7    0.00089   19.8   0.7    2.2  3  Fer4_7        4Fe-4S dicluster domain
     0.0011   18.8  10.3       0.45   10.2   0.1    3.9  4  AAA_15        AAA ATPase domain
     0.0013   18.9   0.0       0.57   10.3   0.0    2.9  2  AAA_33        AAA domain
     0.0015   18.6   6.8     0.0028   17.8   6.8    1.4  1  Fer4_9        4Fe-4S dicluster domain
     0.0019   18.0   0.0      0.098   12.4   0.0    2.4  2  AAA_24        AAA domain
     0.0038   18.1   4.0     0.0086   17.0   0.1    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
     0.0039   16.9   2.0        1.8    8.4   0.5    2.5  2  AAA_29        P-loop containing region of AAA domain
     0.0064   16.4   0.1      0.025   14.5   0.0    2.0  2  NACHT         NACHT domain
     0.0094   15.7   0.0       0.11   12.2   0.0    2.5  2  AAA_30        AAA domain
     0.0095   16.2   0.3       0.17   12.2   0.0    2.7  2  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.37   11.2   0.0    2.7  2  AAA           ATPase family associated with various cellular 
      0.013   15.7   0.0        5.7    7.2   0.0    2.5  2  AAA_28        AAA domain
      0.019   14.7   0.0        3.7    7.3   0.0    2.4  2  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
      0.024   14.4   0.0       0.87    9.3   0.0    2.3  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.051   12.7   0.3       0.33   10.1   0.0    2.1  2  NB-ARC        NB-ARC domain
      0.058   12.4   0.1        0.7    8.9   0.0    2.2  2  T2SSE         Type II/IV secretion system protein
      0.059   13.3   0.6       0.82    9.6   0.0    2.3  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.065   11.9   0.8         12    4.4   0.0    3.0  3  AAA_13        AAA domain
       0.15   12.5   0.1       0.15   12.5   0.1    1.8  1  Fer4_8        4Fe-4S dicluster domain
       0.25   11.2   3.7        2.1    8.3   0.0    3.0  3  RsgA_GTPase   RsgA GTPase
       0.27   11.8  10.9       0.16   12.6   2.3    2.3  2  Fer4_4        4Fe-4S binding domain
        1.3    9.6   6.4       0.27   11.8   1.4    2.0  2  Fer4_17       4Fe-4S dicluster domain
        2.4    8.0   6.7       0.94    9.3   0.3    2.9  2  ATPase_2      ATPase domain predominantly from Archaea
          6    8.1  11.4        0.5   11.4   2.5    2.2  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   5.1e-18   2.3e-15       9     136 ..      97     240 ..      93     241 .. 0.72
   2 !   69.3   0.0     1e-21   4.7e-19       8     136 ..     365     487 ..     354     488 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 5.1e-18
                                   ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                   k+g++++i+G+n +GKSt+l++l+g+l p+ G+            +            +  kei  ++q    +++l+v  
  gi|70606479|ref|YP_255349.1|  97 KKGSIIGILGKNSTGKSTILRILSGELIPNFGNPqevltkdqvldR------------FKGKEIYNYFQS-LYNNKLKVVH 164
                                   79***************************66654222222222333............444555555555.3333333333 PP

                                   H......................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   x......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n......................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +                      +++ +i+++ s l+l+ + ++ v    s LSgG+ q++ + ++ll++++++l+DEp+
  gi|70606479|ref|YP_255349.1| 165 KiqyveyaskylkgsvkdlltkvDQRGKIDEVKSMLNLTPFWEKDV----SVLSGGELQKLLVSASLLRDADVYLFDEPS 240
                                   3344555555555566666886666666999999999999999999....*****************************7 PP

  == domain 2  score: 69.3 bits;  conditional E-value: 1e-21
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH...HHHTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren...esdee 84 
                                    +ege+++ivG+nG GK+t++++l  + +p+ G++l +g  l++++ + + +  g++++  +++ +           s+  
  gi|70606479|ref|YP_255349.1| 365 AREGEIIGIVGPNGIGKTTFMRILVSEITPDHGNVLTEGLTLSYKPQRLAPNYEGTVQEYlENVRK------DilsSSSWF 439
                                   579********************************9999999997777777777777776434444......233256666 PP

                                   HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +e+++++l+l+ + +++v    + LSgG+ q++ +a al+k+++++++DEp+
  gi|70606479|ref|YP_255349.1| 440 FEEVIKRLNLHRILESNV----RDLSGGELQKLYVAGALAKEADIYVIDEPS 487
                                   **********99999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.0     3e-05     0.013       2      58 ..     102     137 ..     101     170 .. 0.71
   2 !   17.0   0.1   8.8e-06    0.0039     235     294 ..     211     267 ..     201     268 .. 0.90
   3 !   15.7   0.1   2.2e-05    0.0098       2      19 ..     371     388 ..     370     405 .. 0.85
   4 !   16.1   0.0   1.6e-05    0.0074     184     287 ..     400     507 ..     389     521 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipf 58 
                                    ++ G+N++GKS++L++l                     +   ip++ ++ +   ++
  gi|70606479|ref|YP_255349.1| 102 IGILGKNSTGKSTILRIL---------------------SGELIPNFGNPQEVLTKD 137
                                   689***************.....................455555555555555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.8e-06
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                   + lS G ++ l + ++llr++   +++l+DEp + L+ +    l+  ++el++++  +++
  gi|70606479|ref|YP_255349.1| 211 SVLSGGELQKLLVSASLLRDA---DVYLFDEPSSYLDIRERINLAIAIRELTKGRYTIVV 267
                                   678******************...9*************9999999999999987777665 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.2e-05
                        AAA_21   2 nvliGpNgsGKSnLLdal 19 
                                    +++GpNg GK++++++l
  gi|70606479|ref|YP_255349.1| 371 IGIVGPNGIGKTTFMRIL 388
                                   68***************9 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 1.6e-05
                        AAA_21 184 llqrlvrslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallralkk 257
                                   l+++l+ s+k++++ +  +g + e  + v  +++ +        +  l   +  e ++r+lS G ++ l+++ al+  +  
  gi|70606479|ref|YP_255349.1| 400 LTEGLTLSYKPQRLAPNYEGTVQEYLENVRKDILSSsswffeeVIKRLNLHRILESNVRDLSGGELQKLYVAGALAKEA-- 478
                                   5555566666666666666555555555555555555555554444444445556688999***************999.. PP

                        AAA_21 258 gsllliDEpEngLHPkllrrllellkelsr 287
                                    ++++iDEp + L+ +    +++ +k+ sr
  gi|70606479|ref|YP_255349.1| 479 -DIYVIDEPSSYLDVEERYIVAKAIKRVSR 507
                                   .9************9888888888877776 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   2.3     1e-14   4.7e-12       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1e-14
                                  --EEEES---------TTHHHHHTTSEEEESS--S CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                  mr+A++++d C+P+KC+  +c+ fcp+  +++g k
  gi|70606479|ref|YP_255349.1|  1 MRVAVINYDYCKPDKCRL-ECIAFCPI--NKSGSK 32
                                  9*****************.********..***975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.9   4.4e-06     0.002       6     202 ..      84     274 ..      80     290 .. 0.71
   2 ?    6.2   0.0     0.014       6.4      25      41 ..     369     385 ..     322     390 .. 0.91
   3 !   14.0   0.0   5.6e-05     0.025     121     189 ..     441     508 ..     414     532 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                                   EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N   6 eienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdne 86 
                                   ++++Fk +    +i+p + s+  i+G+N  GKs +l  ++     +   ++   + +++++k +  ++ k  e+  +f+  
  gi|70606479|ref|YP_255349.1|  84 KVNGFKLFG---MITPKKGSIIGILGKNSTGKSTILRILS----GELIPNF--GNPQEVLTKDQVLDRFKGKEIYNYFQSL 155
                                   688999996...8999999999999*******99998663....3333344..4566777776666777777777777543 PP

                                   TEE..SSSSSSCEEEEEEEETTSEEEEEET..TEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--S CS
                                   xxx..xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  87 dkk..lkiekeevsisrrvkrkgeseykin..gkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpap 160
                                    ++   +++k +++   +++ kg+ +  +   +++ +  ev+++l+ + +   + ++LSgGe +     Ll++    + a 
  gi|70606479|ref|YP_255349.1| 156 YNNklKVVHKIQYVEYASKYLKGSVKDLLTkvDQRGKIDEVKSMLNLTPFwekDVSVLSGGELQ----KLLVSASLLRDAD 232
                                   333224455666666677777777665554114556668999999888773334569****864....45555555699** PP

                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                   +yl+De  + LD +++ ++a  ++e +k    iv+ ++  +l
  gi|70606479|ref|YP_255349.1| 233 VYLFDEPSSYLDIRERINLAIAIRELTKGRYTIVVEHDLIVL 274
                                   *********************************998876555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnll 41 
                                   ++  ivGpNG GK+ ++
  gi|70606479|ref|YP_255349.1| 369 EIIGIVGPNGIGKTTFM 385
                                   5678**********987 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.6e-05
                                   HHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                   xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 121 kevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                   +ev + l+ ++i ++    LSgGe +     L +A   +k a +y++De  + LD +++ +va+ +k+ s +
  gi|70606479|ref|YP_255349.1| 441 EEVIKRLNLHRILESnvrDLSGGELQ----KLYVAGALAKEADIYVIDEPSSYLDVEERYIVAKAIKRVSRE 508
                                   55666666666654422269999987....455666667999*************************76544 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         8   3.6e+03       2       8 ..       5      11 ..       4      12 .. 0.86
   2 ?    0.4   0.2       1.5   6.5e+02      13      21 ..      19      27 ..      18      27 .. 0.86
   3 !   29.6   6.4   8.6e-10   3.9e-07       1      24 []      44      67 ..      44      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8
                                  EEETTTS CS
                          Fer4  2 videekC 8 
                                  vi+++ C
  gi|70606479|ref|YP_255349.1|  5 VINYDYC 11
                                  89***** PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                                  HHHHHSTTT CS
                          Fer4 13 aCvevCPvg 21
                                  +C+  CP +
  gi|70606479|ref|YP_255349.1| 19 ECIAFCPIN 27
                                  6******76 PP

  == domain 3  score: 29.6 bits;  conditional E-value: 8.6e-10
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  ++i ee CigCG+C++ CP++AI+
  gi|70606479|ref|YP_255349.1| 44 PIIYEETCIGCGICIKKCPFDAID 67
                                  5799******************95 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.2    0.0042       1.9       2      34 ..       4      36 ..       3      44 .. 0.70
   2 !   21.1   1.0   5.4e-07   0.00024       2      40 ..      44      83 ..      43      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0042
                       Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgease 34
                                  +vi+ d C   +C+ +C ++CP    +++++++++ 
  gi|70606479|ref|YP_255349.1|  4 AVINYDYCkpDKCRlECIAFCPI---NKSGSKAIEL 36
                                  5899999*5559999********...4444444444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.4e-07
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk 40
                                  ++i ++tCi+Cg C k CP+d+ + v+  +e+ ++e+ r 
  gi|70606479|ref|YP_255349.1| 44 PIIYEETCIGCGICIKKCPFDAiDIVNLPDEYGKDETHRY 83
                                  578899**************98655555555555555554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00053      0.24       2      42 ..     102     144 ..     101     202 .. 0.83
   2 !   10.8   0.1   0.00089       0.4       2      85 ..     371     518 ..     370     534 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00053
                                   EEEEESTTSSHHHHHHHHHTS.TEEE.SSSTTSSSSEEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaiv.sdkpgtTrdinegrvk 42 
                                   ++i+G+  +GKSt+++ l+ge      + +   T+d +  r+k
  gi|70606479|ref|YP_255349.1| 102 IGILGKNSTGKSTILRILSGElIPNFgNPQEVLTKDQVLDRFK 144
                                   89*****************995444424455667666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00089
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEEETTEE................................ CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvklkgke................................ 47 
                                   ++ivG    GK+t+++ l+ e +   ++    g T+  +  r++ +  e                                
  gi|70606479|ref|YP_255349.1| 371 IGIVGPNGIGKTTFMRILVSEiTPDHGNVLteGLTLSYKPQRLAPNY-Egtvqeylenvrkdilsssswffeevikrlnlh 450
                                   89*****************9865555554433788887777777432.134456666777777888888888888888888 PP

                                   .............................EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEET CS
                      MMR_HSR1  48 .............................ielvDtpGliegaseekglgkaflalee.adlillvvda 85 
                                                                i+++D p  + + +e+  ++ka++++ +  + + +vvd 
  gi|70606479|ref|YP_255349.1| 451 rilesnvrdlsggelqklyvagalakeadIYVIDEPSSYLDVEERYIVAKAIKRVSReRKSVTFVVDH 518
                                   88888888888888888888888888888999999996644555668888888877646889999983 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2    0.0014      0.63       3      89 ..     100     182 ..      98     189 .. 0.74
   2 !   11.7   0.0   0.00044       0.2       2      88 ..     368     458 ..     367     480 .. 0.59
   3 ?   -0.6   0.0       2.8   1.3e+03      34      79 ..     445     492 ..     430     516 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                    i+ i G   +GK+t+l+ l  el+    +++++l  +   +r+k +    +++++++++++   +++ +   iq+v+ ++
  gi|70606479|ref|YP_255349.1| 100 SIIGILGKNSTGKSTILRILSGELIpnfGNPQEVLTKDQVLDRFKGK----EIYNYFQSLYN---NKLKVVHKIQYVEYAS 173
                                   68999************999999995554445554444444444332....47899999853...57889999*****999 PP

                        AAA_14  81 kalkslvde 89 
                                   k+lk+ v++
  gi|70606479|ref|YP_255349.1| 174 KYLKGSVKD 182
                                   999998875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00044
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesily..inldderdkkladpekllelileklke..ekktylflDEiqevpe 78 
                                   ++i+ i+G+  +GKTt+++ l++e   ++ ++l   ++l  ++++ + ++e   +++le++++     +  f+ E+ +  +
  gi|70606479|ref|YP_255349.1| 368 GEIIGIVGPNGIGKTTFMRILVSEITPDHGNVLTegLTLSYKPQRLAPNYEGTVQEYLENVRKdiLSSSSWFFEEVIKRLN 448
                                   57999****************988874444554411333333333333444344444444333354455678888877777 PP

                        AAA_14  79 wekalkslvd 88 
                                   + ++l s v+
  gi|70606479|ref|YP_255349.1| 449 LHRILESNVR 458
                                   7777777666 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.8
                        AAA_14  34 lyinldderdkkladpe..kllelilek.lkeekktylflDEiqevpew 79 
                                     +nl +  +++ +d +  +l +l+ +  l  ++  + ++DE + + ++
  gi|70606479|ref|YP_255349.1| 445 KRLNLHRILESNVRDLSggELQKLYVAGaLA-KEADIYVIDEPSSYLDV 492
                                   4455555555555544444555666665333.47888999998877443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0012      0.56      20      40 ..     100     120 ..      84     222 .. 0.72
   2 !   12.7   0.3   0.00029      0.13      21      37 ..     370     386 ..     353     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                        AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                    +  I G+N +GK+Til+ + 
  gi|70606479|ref|YP_255349.1| 100 SIIGILGKNSTGKSTILRILS 120
                                   4789*************9765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00029
                        AAA_23  21 ltlItGpNGaGKTTild 37 
                                   +  I+GpNG GKTT+++
  gi|70606479|ref|YP_255349.1| 370 IIGIVGPNGIGKTTFMR 386
                                   778***********997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0019      0.85       1      44 [.     102     146 ..     102     196 .. 0.77
   2 !    9.8   0.0    0.0024       1.1       1      65 [.     371     433 ..     371     485 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0019
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpe 44 
                                   I++ G+  +GK+t+ + Ls +l  +  n ++v+++++ l+ +  +
  gi|70606479|ref|YP_255349.1| 102 IGILGKNSTGKSTILRILSGELiPNFGNPQEVLTKDQVLDRFKGK 146
                                   899***************999866677777777777766666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0024
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldale 65 
                                   I++ G+ G GKtt+ + L ++    +    ++  +gl l++ p+   ++++  ++++l+++ + + 
  gi|70606479|ref|YP_255349.1| 371 IGIVGPNGIGKTTFMRILVSEI---TPDHGNVLTEGLTLSYKPQrLAPNYEGTVQEYLENVRKDIL 433
                                   89****************9884...44444444446666666665555556666666555555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.073        33      22      51 ..      97     126 ..      89     219 .. 0.75
   2 !   15.4   0.0   4.2e-05     0.019      18      63 ..     362     407 ..     350     518 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.073
                        AAA_16  22 grpelvllsGesGvGKsslvrellralekd 51 
                                     ++++ + G   +GKs+++r l  +l  +
  gi|70606479|ref|YP_255349.1|  97 KKGSIIGILGKNSTGKSTILRILSGELIPN 126
                                   45588999************9887766666 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.2e-05
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                     ++ ++e++ ++G+ G+GK++ +r l  +++ d+g +l++  + +
  gi|70606479|ref|YP_255349.1| 362 EGNAREGEIIGIVGPNGIGKTTFMRILVSEITPDHGNVLTEGLTLS 407
                                   55666779**************************655544333333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.1     0.014       6.2       1      20 [.       3      25 ..       3      34 .. 0.84
   2 !   18.5   3.4   3.4e-06    0.0015       6      24 .]      48      66 ..      43      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                        Fer4_6  1 vveidpdkCi..gCgd.CvrvCP 20
                                  v++i++d C    C+  C++ CP
  gi|70606479|ref|YP_255349.1|  3 VAVINYDYCKpdKCRLeCIAFCP 25
                                  689******9778*777****** PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.4e-06
                        Fer4_6  6 pdkCigCgdCvrvCPegai 24
                                  ++ CigCg C++ CP++ai
  gi|70606479|ref|YP_255349.1| 48 EETCIGCGICIKKCPFDAI 66
                                  689**************98 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0063       2.8      43     105 ..      97     155 ..      81     189 .. 0.76
   2 !    9.6   0.0    0.0018      0.79      46      71 ..     366     394 ..     336     412 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0063
                         Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsq 105
                                   +k  i+ i G    gkst++++Ls el +++    np ++   d   + fkg+ + +  f+s+
  gi|70606479|ref|YP_255349.1|  97 KKGSIIGILGKNSTGKSTILRILSGELIPNF---GNPQEVLTKDQVLDRFKGKEIYNY-FQSL 155
                                   345589999*****************98865...567666666767777777766655.6655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                         Rad17  46 r...iLLisGPsGCgkstvvkvLskelgi 71 
                                   r   i+ i GP G gk+t +++L  e ++
  gi|70606479|ref|YP_255349.1| 366 RegeIIGIVGPNGIGKTTFMRILVSEITP 394
                                   2445999****************988766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.045        20       3      52 ..     104     148 ..     102     170 .. 0.76
   2 !   12.0   0.0   0.00046      0.21       3      24 ..     373     394 ..     371     420 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.045
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqev 52 
                                   + G++ +GKSt+ + L+ +l  +++++  ++v +   +d+++d ++g+e+
  gi|70606479|ref|YP_255349.1| 104 ILGKNSTGKSTILRILSGELIPNFGNP--QEVLT---KDQVLDRFKGKEI 148
                                   789****************99888444..56655...6666666666555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00046
                  RNA_helicase   3 lyGpsgeGKStlakeLakallk 24 
                                   ++Gp+g+GK+t+++ L+++++ 
  gi|70606479|ref|YP_255349.1| 373 IVGPNGIGKTTFMRILVSEITP 394
                                   89***************99983 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.3       4.6   2.1e+03       4      21 ..       5      25 ..       2      25 .. 0.63
   2 !   19.6   1.2   1.5e-06   0.00067       3      21 ..      44      62 ..      42      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.6
                        Fer4_2  4 vvdtdrCi.g.Cg.aCvsaCP 21
                                  v++ d C    C+  C+  CP
  gi|70606479|ref|YP_255349.1|  5 VINYDYCKpDkCRlECIAFCP 25
                                  566666633347778988898 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.5e-06
                        Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                  + + +++CigCg+C++ CP
  gi|70606479|ref|YP_255349.1| 44 PIIYEETCIGCGICIKKCP 62
                                  67889************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   8.3   3.1e-06    0.0014       3      58 ..       6      67 ..       4      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.1e-06
                       Fer4_21  3 idedkCi..gCg.kCliaCe..dtshqaieidak.tvlkvv.edeCvGCnlCssvCPvedcie 58
                                  i+ d C   +C  +C+  C+  +++ +aie+++  +  +++ e++C+GC +C++ CP  d+i+
  gi|70606479|ref|YP_255349.1|  6 INYDYCKpdKCRlECIAFCPinKSGSKAIELSEIvKGKPIIyEETCIGCGICIKKCPF-DAID 67
                                  555555433565359999963377999**87754144555459**************7.8886 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.3      0.99   4.4e+02      32      50 ..       5      26 ..       1      28 [. 0.72
   2 !   14.3   8.9   0.00011     0.047       4      52 .]      15      65 ..      10      65 .. 0.81
   3 !   19.8   0.7     2e-06   0.00089       1      28 [.      50      77 ..      50      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.99
                        Fer4_7 32 eidpekCl..gCga.CvavCPt 50
                                  +i++++C    C+  C+a CP 
  gi|70606479|ref|YP_255349.1|  5 VINYDYCKpdKCRLeCIAFCPI 26
                                  6777888655788789999996 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00011
                        Fer4_7  4 gCg.aCvaaCp.....vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +C+  C a Cp     +kaiel e      + k+ i +e+C+gCg C++ CP++a
  gi|70606479|ref|YP_255349.1| 15 KCRlECIAFCPinksgSKAIELSEI----VKGKPIIYEETCIGCGICIKKCPFDA 65
                                  67778*****977766777777665....345788899**************997 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2e-06
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt 28
                                  +CigCg C + Cp +ai++ +  +e g+
  gi|70606479|ref|YP_255349.1| 50 TCIGCGICIKKCPFDAIDIVNLPDEYGK 77
                                  5*****************9876665554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.1    0.0027       1.2      25      43 ..     101     119 ..      82     121 .. 0.77
   2 ?   -0.0   0.7       1.3   5.7e+02     120     229 ..     144     195 ..     122     228 .. 0.62
   3 !   10.2   0.1   0.00099      0.45      25      43 ..     370     388 ..     351     403 .. 0.80
   4 ?    2.4   0.0      0.23     1e+02     322     357 ..     476     511 ..     467     522 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                        AAA_15  25 ltvliGkNnsGKSsileal 43 
                                   +  + GkN++GKS+il++l
  gi|70606479|ref|YP_255349.1| 101 IIGILGKNSTGKSTILRIL 119
                                   56688************98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                        AAA_15 120 kdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiikllli 200
                                   k k+++++                                                          ++++++++++ +  i
  gi|70606479|ref|YP_255349.1| 144 KGKEIYNY----------------------------------------------------------FQSLYNNKLKVVHKI 166
                                   22222222..........................................................455666666666666 PP

                        AAA_15 201 sakRnvsdedsekkssllgklkekileea 229
                                   + +  +s++++ + ++ll+k++++ + + 
  gi|70606479|ref|YP_255349.1| 167 QYVEYASKYLKGSVKDLLTKVDQRGKIDE 195
                                   66666666666666666666666554444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00099
                        AAA_15  25 ltvliGkNnsGKSsileal 43 
                                   +  ++G+N++GK++++++l
  gi|70606479|ref|YP_255349.1| 370 IIGIVGPNGIGKTTFMRIL 388
                                   7789************998 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.23
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnkt 357
                                   ++ +i++i+EP  +L  +  ++++k++k+++++ k 
  gi|70606479|ref|YP_255349.1| 476 KEADIYVIDEPSSYLDVEERYIVAKAIKRVSRERKS 511
                                   4569*************************9998875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.047        21       5      40 ..     105     150 ..     101     192 .. 0.69
   2 !   10.3   0.0    0.0013      0.57       4      29 ..     373     401 ..     370     527 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.047
                        AAA_33   5 vGlpGsGKstlaerllkklg......avllssdtlrrrlfg....t 40 
                                    G + +GKst ++ l  +l        ++l++d++++r +g    +
  gi|70606479|ref|YP_255349.1| 105 LGKNSTGKSTILRILSGELIpnfgnpQEVLTKDQVLDRFKGkeiyN 150
                                   69999*********9888877888999*******999988744442 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                        AAA_33   4 lvGlpGsGKstlaerllkklg...avlls 29 
                                   +vG++G GK+t+ + l+ + +   + +l+
  gi|70606479|ref|YP_255349.1| 373 IVGPNGIGKTTFMRILVSEITpdhGNVLT 401
                                   79************999887766644444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   6.8   6.3e-06    0.0028       4      51 .]      15      66 ..      10      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.3e-06
                        Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkgai 51
                                  +C+ +C++ Cp +    +a e    ++ +     e CigCg C+++Cp +ai
  gi|70606479|ref|YP_255349.1| 15 KCRlECIAFCPINKSGSKAIELSEIVKGKPIiyeETCIGCGICIKKCPFDAI 66
                                  577569999988888777777776665544488899************9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.12        54       5      22 ..     102     119 ..      98     200 .. 0.88
   2 !   12.4   0.0   0.00022     0.098       5      23 ..     371     393 ..     367     510 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   i i G++ +GK+t+++ l
  gi|70606479|ref|YP_255349.1| 102 IGILGKNSTGKSTILRIL 119
                                   789**********99877 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00022
                        AAA_24   5 iliyGpsgiGKTtlakel....g 23 
                                   i i+Gp+giGKTt+++ l    +
  gi|70606479|ref|YP_255349.1| 371 IGIVGPNGIGKTTFMRILvseiT 393
                                   789************98755443 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.7       1.3   5.9e+02       4      15 ..      15      27 ..      10      43 .. 0.75
   2 !   17.0   0.1   1.9e-05    0.0086       1      19 [.      50      68 ..      50      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.3
                       Fer4_16  4 tCgk.CaevCPtn 15
                                  +C+  C+  CP n
  gi|70606479|ref|YP_255349.1| 15 KCRLeCIAFCPIN 27
                                  5776688888876 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.9e-05
                       Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                  +C++Cg C++ CP +ai+ 
  gi|70606479|ref|YP_255349.1| 50 TCIGCGICIKKCPFDAIDI 68
                                  5***************984 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.5     0.004       1.8      22      39 ..      98     116 ..      87     126 .. 0.82
   2 !    7.2   0.0    0.0093       4.2      23      39 ..     368     385 ..     359     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.004
                        AAA_29  22 kg.atlltGpsGsGKSTll 39 
                                   kg ++ + G++ +GKST+l
  gi|70606479|ref|YP_255349.1|  98 KGsIIGILGKNSTGKSTIL 116
                                   4457779***********8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0093
                        AAA_29  23 g.atlltGpsGsGKSTll 39 
                                   g ++ ++Gp+G GK+T++
  gi|70606479|ref|YP_255349.1| 368 GeIIGIVGPNGIGKTTFM 385
                                   446779**********97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       9.4   4.2e+03       5      20 ..     104     119 ..     101     123 .. 0.82
   2 !   14.5   0.0   5.6e-05     0.025       3      70 ..     371     437 ..     369     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.4
                                   EEC-TTTCHHHHHHHH CS
                         NACHT   5 lqGeaGsGKTtLlqkl 20 
                                   + G++  GK+t l+ l
  gi|70606479|ref|YP_255349.1| 104 ILGKNSTGKSTILRIL 119
                                   789999*****99866 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.6e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS- CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvs 70 
                                   + + G++G+GKTt+++ l++++  ++ +  +  l +  + ++l    +  +++++l  + +++ + +s
  gi|70606479|ref|YP_255349.1| 371 IGIVGPNGIGKTTFMRILVSEITPDHGNVLTEGLTLSYKPQRLAPNYEG-TVQEYLENVRKDILSSSS 437
                                   5689*****************9998888777667777766666665555.677777666666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.5   6.8e+02      20      38 ..     101     119 ..      91     134 .. 0.81
   2 !   12.2   0.0   0.00025      0.11      19     122 ..     369     515 ..     360     519 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                        AAA_30  20 vavltGpAGtGKttalkal 38 
                                   +  + G   tGK+t+l+ l
  gi|70606479|ref|YP_255349.1| 101 IIGILGKNSTGKSTILRIL 119
                                   556778888*******987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                        AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g..........grviglAptgkaAkvLa......................... 63 
                                    +  ++Gp G GKtt ++ l+  ++ + g          ++             La                         
  gi|70606479|ref|YP_255349.1| 369 EIIGIVGPNGIGKTTFMRILVSEITPDhGnvltegltlsYKPQR----------LApnyegtvqeylenvrkdilsssswf 439
                                   47789***************766666625444444444433334..........442332333322334444433333333 PP

                        AAA_30  64 eelgieastiakllkrlk.............grarlepgtllivDEagmv.dtkq...laallkaaekagakvilv 122
                                    e  i+  +++++l+++              + a  ++++++++DE +   d ++   +a+ +k+++++  +v +v
  gi|70606479|ref|YP_255349.1| 440 FEEVIKRLNLHRILESNVrdlsggelqklyvAGALAKEADIYVIDEPSSYlDVEEryiVAKAIKRVSRERKSVTFV 515
                                   2444566666666666659999999999997334445559999999665435555111333344444445556665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2       1.2   5.3e+02       5      27 ..      99     121 ..      95     189 .. 0.81
   2 !   12.2   0.0   0.00038      0.17       5      52 ..     368     416 ..     364     516 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                        AAA_22   5 agilvvtGesGtGKTtllrrlle 27 
                                    +i+ + G   tGK+t lr l  
  gi|70606479|ref|YP_255349.1|  99 GSIIGILGKNSTGKSTILRILSG 121
                                   67788899999999999987755 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00038
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsst.s 52 
                                     i+ ++G+ G+GKTt +r l+++ +  +++ +   +  +++++++ +  +
  gi|70606479|ref|YP_255349.1| 368 GEIIGIVGPNGIGKTTFMRILVSEIT--PDHGNvlTEGLTLSYKPQRLApN 416
                                   67888****************99874..33333552222233333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.51   2.3e+02       4      23 ..     105     128 ..     102     201 .. 0.73
   2 ?   11.2   0.0   0.00083      0.37       3      24 ..     373     394 ..     371     490 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.51
                                   ESSTTSSHHHHHHHHHHHH....T CS
                           AAA   4 yGppGtGKTllakavakel....g 23 
                                    G   tGK+++ + +  el    g
  gi|70606479|ref|YP_255349.1| 105 LGKNSTGKSTILRILSGELipnfG 128
                                   68999**********999744331 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00083
                                   EESSTTSSHHHHHHHHHHHHTH CS
                           AAA   3 lyGppGtGKTllakavakelgv 24 
                                   ++Gp G+GKT++++ +++e+  
  gi|70606479|ref|YP_255349.1| 373 IVGPNGIGKTTFMRILVSEITP 394
                                   68****************9742 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.013       5.7       3      23 ..     103     123 ..     101     167 .. 0.80
   2 ?    6.1   0.0     0.028        12       3      25 ..     372     394 ..     370     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                        AAA_28   3 vitGgestGKTtlleaLaarg 23 
                                    i+G  stGK+t+l+ L+ + 
  gi|70606479|ref|YP_255349.1| 103 GILGKNSTGKSTILRILSGEL 123
                                   58999***********99664 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                        AAA_28   3 vitGgestGKTtlleaLaargyp 25 
                                    i+G+ + GKTt ++ L ++ +p
  gi|70606479|ref|YP_255349.1| 372 GIVGPNGIGKTTFMRILVSEITP 394
                                   599************99866444 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.042        19       1      19 [.     106     124 ..     106     133 .. 0.88
   2 ?    7.3   0.0    0.0083       3.7       1      21 [.     375     395 ..     375     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.042
                        CLP1_P   1 GpkdsGKSTlarlLlNyal 19 
                                   G++ +GKST+ r+L  +++
  gi|70606479|ref|YP_255349.1| 106 GKNSTGKSTILRILSGELI 124
                                   8899**********99886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0083
                        CLP1_P   1 GpkdsGKSTlarlLlNyalrk 21 
                                   Gp+  GK+T++r+L+ +++  
  gi|70606479|ref|YP_255349.1| 375 GPNGIGKTTFMRILVSEITPD 395
                                   8999***********988755 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       0.2        91       1      23 [.     101     123 ..     101     160 .. 0.73
   2 ?    9.3   0.0    0.0019      0.87       1      24 [.     370     393 ..     370     409 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.2
                           PRK   1 vIgvagsSGaGkttvarklekif 23 
                                   +Ig+ g+   Gk+t+ r l   +
  gi|70606479|ref|YP_255349.1| 101 IIGILGKNSTGKSTILRILSGEL 123
                                   8**************99886555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                           PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                   +Ig+ g+ G Gktt++r l++ + 
  gi|70606479|ref|YP_255349.1| 370 IIGIVGPNGIGKTTFMRILVSEIT 393
                                   8****************9998775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.85   3.8e+02      21      38 ..     100     117 ..      89     144 .. 0.88
   2 ?   10.1   0.0   0.00073      0.33      18      43 ..     366     391 ..     350     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.85
                                   EEEEEEESTTSSHHHHHH CS
                        NB-ARC  21 lvvalvGmgGvGKttlak 38 
                                    ++++ G+   GK+t+++
  gi|70606479|ref|YP_255349.1| 100 SIIGILGKNSTGKSTILR 117
                                   599************986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00073
                                   SCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  18 lqslvvalvGmgGvGKttlakqilnk 43 
                                    +  ++++vG  G+GKtt ++  +++
  gi|70606479|ref|YP_255349.1| 366 REGEIIGIVGPNGIGKTTFMRILVSE 391
                                   45569*************99876665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43   1.9e+02     129     153 ..      98     123 ..      73     132 .. 0.80
   2 ?    8.9   0.0    0.0016       0.7     128     162 ..     367     401 ..     304     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                         T2SSE 129 rglil.vsGgTgsGKttllyallkei 153
                                   +g+i+ + G  ++GK+t+l +l  e+
  gi|70606479|ref|YP_255349.1|  98 KGSIIgILGKNSTGKSTILRILSGEL 123
                                   4444448899*********9998775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                         T2SSE 128 erglilvsGgTgsGKttllyallkeinksderivt 162
                                   e  +i + G+ g GKtt++ +l++ei  ++ +++t
  gi|70606479|ref|YP_255349.1| 367 EGEIIGIVGPNGIGKTTFMRILVSEITPDHGNVLT 401
                                   33445599******************999888876 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.52   2.3e+02       1      22 [.     101     122 ..     101     127 .. 0.84
   2 ?    9.6   0.0    0.0018      0.82       1      24 [.     370     393 ..     370     401 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.52
                          MobB   1 vlgivgksgsGKTtLleklipe 22 
                                   ++gi gk+ +GK t+l  l  e
  gi|70606479|ref|YP_255349.1| 101 IIGILGKNSTGKSTILRILSGE 122
                                   799************9877555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                          MobB   1 vlgivgksgsGKTtLleklipelk 24 
                                   ++givg +g GKTt++  l++e++
  gi|70606479|ref|YP_255349.1| 370 IIGIVGPNGIGKTTFMRILVSEIT 393
                                   799*****************9987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.099        45      21      59 ..     104     138 ..      97     166 .. 0.77
   2 ?    1.6   0.0      0.19        83      21      38 ..     373     390 ..     369     411 .. 0.87
   3 ?    4.4   0.0     0.027        12     525     580 ..     476     529 ..     465     546 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.099
                        AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfangsieitnge 59 
                                   i G+N +GK+t+ r+l+     e  p+f n++  +t+++
  gi|70606479|ref|YP_255349.1| 104 ILGKNSTGKSTILRILSG----ELIPNFGNPQEVLTKDQ 138
                                   77**********999987....35666766666555554 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.19
                        AAA_13  21 iYGwNGaGKTtLSrllrs 38 
                                   i G NG GKTt+ r+l s
  gi|70606479|ref|YP_255349.1| 373 IVGPNGIGKTTFMRILVS 390
                                   569*********999866 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.027
                        AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                   ++  i viD P S LD +  +iv+  ik +   ++  +  f+  H l  + ++ ++
  gi|70606479|ref|YP_255349.1| 476 KEADIYVIDEPSSYLDVEERYIVAKAIKRVS--RERKSVTFVVDHDLAIHDYIADR 529
                                   467899***********************98..45555569999999999888765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00034      0.15       4      17 ..      50      63 ..      48      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00034
                        Fer4_8  4 kCieCgaCqsaCpv 17
                                   Ci+Cg C ++Cp+
  gi|70606479|ref|YP_255349.1| 50 TCIGCGICIKKCPF 63
                                  7***********94 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.32   1.4e+02      99     123 ..      99     123 ..      93     139 .. 0.82
   2 ?   -1.6   0.0         5   2.2e+03      52      98 ..     156     201 ..     138     216 .. 0.76
   3 ?    8.3   0.0    0.0046       2.1      99     126 ..     368     395 ..     342     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.32
                                   TSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                   ++++ ++G+   GKSt++  l +el
  gi|70606479|ref|YP_255349.1|  99 GSIIGILGKNSTGKSTILRILSGEL 123
                                   46777999***********999885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5
                                   EEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCT CS
                   RsgA_GTPase  52 vlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellk 98 
                                   + nK+ ++++ + + e+++++ +  ++ ll++++++ +++e+k++l+
  gi|70606479|ref|YP_255349.1| 156 YNNKLKVVHKIQ-YVEYASKYLKGSVKDLLTKVDQRGKIDEVKSMLN 201
                                   567788888777.7777888888888888888888888888877764 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0046
                                   TSEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelk 126
                                   ++++ +vG+ G+GK+t++  l++e +  
  gi|70606479|ref|YP_255349.1| 368 GEIIGIVGPNGIGKTTFMRILVSEITPD 395
                                   578889***************9987655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.5      0.21        93       6      15 ..      15      25 ..       8      35 .. 0.78
   2 ?   12.6   2.3   0.00035      0.16       2      16 ..      49      63 ..      48      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.21
                        Fer4_4  6 gCg.sCvaaCP 15
                                   C+  C+a+CP
  gi|70606479|ref|YP_255349.1| 15 KCRlECIAFCP 25
                                  68855*****9 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00035
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e+CigCg C+  CP+
  gi|70606479|ref|YP_255349.1| 49 ETCIGCGICIKKCPF 63
                                  79************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.9      0.03        14      45      58 ..      50      63 ..      11      67 .. 0.72
   2 ?   11.8   1.4   0.00061      0.27       2      16 ..      51      65 ..      50      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.03
                       Fer4_17 45 lCieCgeCerkCPq 58
                                  +Ci+Cg C +kCP 
  gi|70606479|ref|YP_255349.1| 50 TCIGCGICIKKCPF 63
                                  55555555555553 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00061
                       Fer4_17  2 CiqCgyClpeCpsye 16
                                  Ci+Cg C+++Cp+ +
  gi|70606479|ref|YP_255349.1| 51 CIGCGICIKKCPFDA 65
                                  999999999999754 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.4       1.4   6.1e+02      19     118 ..      98     192 ..      89     204 .. 0.52
   2 ?    9.3   0.3    0.0021      0.94      19      44 ..     367     392 ..     358     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilkeks 99 
                                   + +i+ i G  + GK+++l+ +  +l        + ++ +    +++ + ++ +e  ++++   +++++ +   + ++  s
  gi|70606479|ref|YP_255349.1|  98 KGSIIGILGKNSTGKSTILRILSGEL-----IPNFGNPQEVLTKDQVLDRFKGKEIYNYFQSLYNNKLKVVHKIQYVEYAS 173
                                   56788888899999998887554444.....22233333332222222222333334444444444444444444445555 PP

                      ATPase_2 100 klvfkaielllekikkkgk 118
                                   k+++ ++++ll k+ ++gk
  gi|70606479|ref|YP_255349.1| 174 KYLKGSVKDLLTKVDQRGK 192
                                   5555555666666666555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienl 44 
                                   + ei+ i Gp g+GKt++++ ++++ 
  gi|70606479|ref|YP_255349.1| 367 EGEIIGIVGPNGIGKTTFMRILVSEI 392
                                   468999**************999876 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.8       1.5   6.8e+02       3      14 ..      15      27 ..      11      29 .. 0.78
   2 ?   11.4   2.5    0.0011       0.5       1      15 []      51      65 ..      51      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.5
                        Fer4_3  3 gCg.aCvevCPvg 14
                                   C+  C   CP +
  gi|70606479|ref|YP_255349.1| 15 KCRlECIAFCPIN 27
                                  58756******65 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg C + CP +A
  gi|70606479|ref|YP_255349.1| 51 CIGCGICIKKCPFDA 65
                                  ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 3838.14
//
Query:       gi|70606480|ref|YP_255350.1|  [L=34]
Description: hypothetical protein Saci_0673 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 238.05
//
Query:       gi|70606481|ref|YP_255351.1|  [L=438]
Description: hypothetical protein Saci_0675 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-26   91.6  72.0    5.7e-21   74.8  44.3    2.0  2  MFS_1      Major Facilitator Superfamily
    6.4e-21   74.7  37.3    3.9e-16   59.0  12.0    2.0  2  Sugar_tr   Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8  44.3   6.3e-25   5.7e-21       5     334 ..      27     368 ..      27     374 .. 0.82
   2 !   30.7  19.6   1.7e-11   1.5e-07      40     170 ..     287     424 ..     284     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 6.3e-25
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa... 82 
                                   +f+sa+a+s+++p +  + +++ g++     l++++ +l   ++++++G ++d+ Gr+ +l+ +lll++lg+l + ++   
  gi|70606481|ref|YP_255351.1|  27 FFISATAASTVWPYIY-FNSQNVGVALLYSLLIFSTGFLDRPIGAIIFGNIGDKRGRKETLVYTLLLMGLGTLGIGLTppy 106
                                   59999**********9.999999977777777888888888******************************4444463334 PP

                         MFS_1  83 ..ss........lw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllgglla.sslg. 149
                                     ++         + ll+++r+lqGl+ g+ + ++ ++++++++k + r++  ++++ g+ lG+i + ++  +l  s  g 
  gi|70606481|ref|YP_255351.1| 107 lsTGswpgigifAPiLLIIFRLLQGLAVGGEWGGASTIVTEYAAKsKYRAFWASWVQQGVPLGIIAASVAFIALQvSFPGk 187
                                   4322444455544445*****************************99*****************99966666555255558 PP

                         MFS_1 150 ......Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfs 224
                                         Wr ++yi a+++l+++++   + + e p  k+  +k+      + p++ ++k  ++   l  l ++++++ + f+
  gi|70606481|ref|YP_255351.1| 188 affdwgWRIAYYIGAAILLIGALI--RYRVLESPVFKKIIQKRAI---LNIPFARLIKNEWRTVLL--LALGWAYNNALFY 261
                                   888888***************998..9998888888888888882...455555556666666644..8888888888888 PP

                         MFS_1 225 glltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavlll 304
                                    + +++  y    lg++ ++ + +  + +++++g++l +l++ l+dr+gr++ ++++ l+ +++ + +++l +t++  l+ 
  gi|70606481|ref|YP_255351.1| 262 VIISFVQYY-IIALGFPqSFPQEL--ILIASIMGMFLIILGAILADRVGRKPVIIISTLVSSILIFVFFMLLNTKDIGLMF 339
                                   888888889.*******9888888..8999999999999999999*************99999999999999998888888 PP

                         MFS_1 305 lvlvliGfglgfvfpsllalasdlappeea 334
                                   l+++li++g+   ++ + a+ s+ +p++++
  gi|70606481|ref|YP_255351.1| 340 LGSILISTGYLG-YAVYSAFFSEQFPTRYR 368
                                   888888886554.57777777777777766 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.7e-11
                         MFS_1  40 lyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa...sslwlllvlrvlqGlgagalfpagaaliadwfpke 117
                                   + ++  ++++++++ l+dr+Gr++v++++ l++++ ++++++      + l++++ +l + g+ +++++  a++++ fp +
  gi|70606481|ref|YP_255351.1| 287 IASIMGMFLIILGAILADRVGRKPVIIISTLVSSILIFVFFMLlntKDIGLMFLGSILISTGY-LGYAVYSAFFSEQFPTR 366
                                   6788899*****************************44444333545566************8.****************9 PP

                         MFS_1 118 ergraigl.lsagfslGailgpllggllasslg......Wravfyilaivsllafvlfll 170
                                    r ++ ++ + +++ ++  l+p+++++++++++      W+++ +++ i +++++++  +
  gi|70606481|ref|YP_255351.1| 367 YRYSGSSFsYHLSTPISGGLAPVIASYIYALFNnnyllaWPYIALMVFIYGVISAIV--I 424
                                   999999983557*******************************99999999999884..2 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0  12.0   4.4e-20   3.9e-16       2     198 ..      13     222 ..      12     232 .. 0.87
   2 !   22.1  17.3   6.8e-09   6.1e-05     247     439 ..     237     425 ..     225     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.4e-20
                                   HHHHHHHHHHHHHHHHCGGGTHH.HHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                      Sugar_tr   2 alvaalggllfgYdtgvigaflt.llkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslli 81 
                                   a++ ++g ++++Yd+++ +++++ +  +++++ +++ ++      ++s li+s  ++ + iG++++g +gd+ GRk +l+ 
  gi|70606481|ref|YP_255351.1|  13 ATLSTIGTTIEWYDFFISATAAStVWPYIYFNSQNVGVAL-----LYSLLIFSTGFLDRPIGAIIFGNIGDKRGRKETLVY 88 
                                   67788999******98776554303344444444444443.....567********************************* PP

                                   HHHHHHHHHHHHH-TTTT...........SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS.-SCCHHHHHHHHHHHHHHH CS
                      Sugar_tr  82 aavlfvigavlqaaakgk...........nsvevlivgRvlvGigvGlasvlvPmyisEiA.pkklRgalvslyqlaitfG 150
                                   + +l+  g++ +++++ +           ++  +li+ R+l G++vG++ + +++ + E+A + k+R +  s+ q ++ +G
  gi|70606481|ref|YP_255351.1|  89 TLLLMGLGTLGIGLTPPYlstgswpgigiFAPILLIIFRLLQGLAVGGEWGGASTIVTEYAaKSKYRAFWASWVQQGVPLG 169
                                   ****************999****************************************9967799*************** PP

                                   HHHHHHHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH CS
                      Sugar_tr 151 ilvaaifglglnktsn.....adgwrillglqlvpallllilllflPESPryl 198
                                   i+ a++   +l+ +       ++gwri  ++ +++ l+ +++++ + ESP + 
  gi|70606481|ref|YP_255351.1| 170 IIAASVAFIALQVSFPgkaffDWGWRIAYYIGAAILLIGALIRYRVLESPVFK 222
                                   *****99999966666689*******************************996 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 6.8e-09
                                   HHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHH CS
                      Sugar_tr 247 ssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaa 325
                                   + +++ +r+++ ++l ++ +     +i+ +  + +  lg+ +s   +  +i +++ ++ ++ ++ l dr+GR+++ +++++
  gi|70606481|ref|YP_255351.1| 237 RLIKNEWRTVLLLALGWAYNNALFYVIISFVQYYIIALGFPQSfpQELILIASIMGMFLIILGAILADRVGRKPVIIISTL 317
                                   55556788888888888887777778888888888899****9888999999***************************** PP

                                   HHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHH.HHHHHHHHH CS
                      Sugar_tr 326 gmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnw.lanflisll 405
                                   + +i+ +++    +ll++k     i+++++  + i    lg +   ++  sE fp++ R++++++++ ++  ++  l  ++
  gi|70606481|ref|YP_255351.1| 318 VSSILIFVFF---MLLNTK----DIGLMFLGSILISTGYLGYAVYSAFF-SEQFPTRYRYSGSSFSYHLSTpISGGLAPVI 390
                                   ****999994...555555....68888888888888888998777555.****************987653666777777 PP

                                   HHHHHCHHH.T-HHHHHHHHHHHHHHHHHHHHS-- CS
                      Sugar_tr 406 fpiiteaig.ggyvflvfaglavlfiifvfffvpe 439
                                     +i    + ++   +++ +l+v+ + ++   v+ 
  gi|70606481|ref|YP_255351.1| 391 ASYIYALFNnNYLLAWPYIALMVFIYGVISAIVIS 425
                                   77777766655666777777777766665554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2901.85
//
Query:       gi|70606482|ref|YP_255352.1|  [L=36]
Description: integrase SulF [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.49
# Mc/sec: 219.01
//
Query:       gi|70606483|ref|YP_255353.1|  [L=98]
Description: hypothetical protein Saci_0678 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.033   14.2   0.4       0.29   11.2   0.1    2.0  2  RNA_GG_bind  PHAX RNA-binding domain


Domain annotation for each model (and alignments):
>> RNA_GG_bind  PHAX RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   1.6e-05      0.29      10      38 ..      18      46 ..      13      49 .. 0.89
   2 ?    1.1   0.0     0.023   4.1e+02      11      33 ..      63      85 ..      62      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                   RNA_GG_bind 10 kEpkkdliervvkvlGkekalelleetee 38
                                   E+k +l++r+v+ lG  k+ ++ +  ++
  gi|70606483|ref|YP_255353.1| 18 TEQKRQLLKRAVELLGYPKLTQITNRSKK 46
                                  59********************9988766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.023
                   RNA_GG_bind 11 EpkkdliervvkvlGkekalell 33
                                  Ep+++++ +v+k+l ++++ +++
  gi|70606483|ref|YP_255353.1| 63 EPHDEVVTEVMKALPVDEVVKIV 85
                                  8999999*******999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 631.88
//
Query:       gi|70606484|ref|YP_255354.1|  [L=381]
Description: hypothetical protein Saci_0679 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2569.01
//
Query:       gi|70606485|ref|YP_255355.1|  [L=297]
Description: hypothetical protein Saci_0680 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1949.98
//
Query:       gi|70606486|ref|YP_255356.1|  [L=91]
Description: hypothetical protein Saci_0681 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 662.48
//
Query:       gi|70606487|ref|YP_255357.1|  [L=102]
Description: 30S ribosomal protein S10P [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-28   96.5   0.1    9.1e-28   96.4   0.1    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.1   5.1e-32   9.1e-28       1      97 [.       6      99 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 5.1e-32
                                  EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHHHS CS
                 Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidtll 82
                                  rirl S +  +L+ +v++i ++a+++gi+v+gp+plPt r +v+v++ ph++ kk +e++e+++hkR+idi  a+++++++l+
  gi|70606487|ref|YP_255357.1|  6 RIRLWSSNIDSLNFVVNQIRNMAQKTGIQVSGPIPLPTTRMEVPVMRLPHGEgKKKWEHWEMKVHKRIIDI-AADERVMRQLM 87
                                  8**********************************************************************.5********** PP

                                  -...S---SS-EEEE CS
                 Ribosomal_S10 83 kllqlnlpegVsvev 97
                                  +   +++p+ V +e+
  gi|70606487|ref|YP_255357.1| 88 R---VRVPDDVYIEI 99
                                  *...*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 736.77
//
Query:       gi|70606488|ref|YP_255358.1|  [L=435]
Description: elongation factor 1-alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-54  182.5   0.1      8e-54  182.1   0.1    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.6e-36  123.5   0.1    1.1e-35  122.3   0.1    1.7  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.2e-17   64.0   5.5    2.1e-16   60.1   3.5    2.8  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    4.2e-06   26.8   0.1    2.9e-05   24.1   0.0    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00031   20.6   3.2    0.00031   20.6   3.2    2.1  2  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0014   18.1   0.1        0.8    9.1   0.0    2.3  2  SRPRB        Signal recognition particle receptor beta subuni
      0.004   16.5   0.1      0.018   14.4   0.1    1.9  1  Septin       Septin
  ------ inclusion threshold ------
      0.017   14.5   0.1      0.027   13.8   0.1    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.057   13.0   0.3       0.39   10.3   0.1    2.1  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.063   13.6   1.7        5.1    7.5   0.1    3.2  4  SepF         Cell division protein SepF
       0.08   13.0   0.0        2.3    8.3   0.0    2.4  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1   0.1   4.9e-57     8e-54       1     185 [.       4     219 ..       4     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 4.9e-57
                                   TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEETTCS CS
                      GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisleketk 68 
                                   k+++n+++ighvDhGK+TL++rLl++ g i++k+ k+ ee++             +D+lkeErerg+Ti+ + + +e  t+
  gi|70606488|ref|YP_255358.1|   4 KPHLNLIVIGHVDHGKSTLIGRLLMDRGFIDEKTVKEAEEAAkklgkdsekyaflMDRLKEERERGVTINLSFMRFE--TR 82 
                                   579*****************************88888444445799999****************************..** PP

                                   SEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESCGST.....H CS
                      GTP_EFTU  69 kylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKmDrl.....k 136
                                   ky +++iD+PGH+dF+k++i+g++++D a+lvv+a++G        e qt+e++ l +++g++ +iv+iNKmD +     +
  gi|70606488|ref|YP_255358.1|  83 KYFFTVIDAPGHRDFVKNMITGASQADAAILVVSAKKGeyeagmsAEGQTREHIILSKTMGINqVIVAINKMDLAdtpydE 163
                                   ***************************************************************************999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH...............HHH CS
                      GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk...............tll 185
                                   +++keiv++v+ k+      ++++g++ + +v++v++ a +g++v+               +ll
  gi|70606488|ref|YP_255358.1| 164 KRFKEIVDTVS-KF------MKSFGFDMN-KVKFVPVVAPDGDNVThkstkmpwyngptleELL 219
                                   9*******999.88......9******95.*************999777777677665444344 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.1   6.8e-39   1.1e-35       3     111 ..     321     427 ..     319     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 6.8e-39
                                   EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE- CS
                   GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpiale 83 
                                   + +++f+Aqv+++ +  +t++  gY+pvl+++ta+++++v e++s++d+kt+k++ek+p+f+k Gd++iv+ ++ik ++ e
  gi|70606488|ref|YP_255358.1| 321 TVADEFTAQVIVIWH--PTAVGVGYTPVLHVHTASIACRVSEITSRIDPKTGKEAEKNPQFIKAGDSAIVKFKPIKELVAE 399
                                   6789***********..**************************************************************** PP

                                   -TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                   GTP_EFTU_D3  84 kgseypqlGrFaiReggrTvaaGvvtei 111
                                   k+ e+p lGrFa+R++g+Tv++Gv+ ++
  gi|70606488|ref|YP_255358.1| 400 KFREFPALGRFAMRDMGKTVGVGVIIDV 427
                                   *************************987 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.093   1.5e+02      20      49 ..      10      40 ..       4      55 .. 0.78
   2 !   60.1   3.5   1.3e-19   2.1e-16       1      72 [.     247     312 ..     247     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.093
                                  EEEC.TCTTSEEEEEEEEEEEEETEEESEE...E CS
                   GTP_EFTU_D2 20 rilg.ndtskkeivtrissletfhededea...v 49
                                   ++g +d +k+   t i++l++ ++  de    +
  gi|70606488|ref|YP_255358.1| 10 IVIGhVDHGKS---TLIGRLLMDRGFIDEKtvkE 40
                                  45566899999...***********999985332 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 1.3e-19
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                   G+v  gr++sG+lk+Gd++++  ++++k   +++++s+et+h + d a++g+n+G++v++++ +d +++Gd+
  gi|70606488|ref|YP_255358.1| 247 GVVPVGRIESGVLKVGDKIVF--MPVGK---IGEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKD-VKRGDV 312
                                   8899*****************..55534...599*******************************.*****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.8e-08   2.9e-05       2      95 ..       9     127 ..       8     153 .. 0.67
   2 ?   -1.0   0.0       1.1   1.8e+03      31      54 ..     139     160 ..     126     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.8e-08
                                   EEEEESTTSSHHHHHHHHH..................T.............STEEESSSTTSSSSEEEEEEEETTEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinalt..................g.............ekaivsdkpgtTrdinegrvklkgkeielv 51 
                                    +++G+   GKStLi +l+                  +             ++ + +++ g+T++  + r+++++  ++++
  gi|70606488|ref|YP_255358.1|   9 LIVIGHVDHGKSTLIGRLLmdrgfidektvkeaeeaaKklgkdsekyaflmDRLKEERERGVTINLSFMRFETRKYFFTVI 89 
                                   579***************96766666666655555540555556656555458888999999999999999988889**** PP

                                   ECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHH CS
                      MMR_HSR1  52 DtpGliegaseekglgkaflaleeadlillvvdaseeklkplde 95 
                                   D pG  +    +  +++ +    +ad+++lvv+a+++++++  +
  gi|70606488|ref|YP_255358.1|  90 DAPG--H----RDFVKNMITGASQADAAILVVSAKKGEYEAGMS 127
                                   ****..4....23466666667789*******998666644322 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                   TSSSSEEEEEEEETTEEEEEEECG CS
                      MMR_HSR1  31 gtTrdinegrvklkgkeielvDtp 54 
                                    +T  in+  v+++  ++ l+Dtp
  gi|70606488|ref|YP_255358.1| 139 SKTMGINQVIVAIN--KMDLADTP 160
                                   56888888888854..58899998 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   3.2   1.9e-07   0.00031      21      84 ..     251     312 ..     235     313 .. 0.88
   2 ?   -3.1   0.1       4.5   7.4e+03      38      53 ..     413     428 ..     411     434 .. 0.50

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                                   EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                   GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                   vG ++ +Gv+k+g k++     ++Ge+++i++++ k+++a+ G++++  ++g    +++k gd+
  gi|70606488|ref|YP_255358.1| 251 VG-RIESGVLKVGDKIVFMPVGKIGEVRSIETHHTKIDKAEPGDNIGFNVRGVE-KKDVKRGDV 312
                                   77.99**********9987777****************************9965.788888885 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.5
                                   ETTE.EEEEEEEEEET CS
                   GTP_EFTU_D4  38 kedGrevGeilqiqdk 53 
                                   ++ G++vG+ + i  k
  gi|70606488|ref|YP_255358.1| 413 RDMGKTVGVGVIIDVK 428
                                   5566666554444433 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.003       4.8       5      43 ..       8      48 ..       4      62 .. 0.66
   2 !    9.1   0.0   0.00049       0.8      45     124 ..      80     156 ..      58     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.003
                                  EEEEE-STTSSHHHHHHHHHHS...S---B---SS-EEETTG CS
                         SRPRB  5 avllvGlsdsGKTslftrLttd...svkktvtSqessaalkv 43
                                  +++++G  d GK +l+ rL+ d     +ktv   +++aa+k+
  gi|70606488|ref|YP_255358.1|  8 NLIVIGHVDHGKSTLIGRLLMDrgfIDEKTVKE-AEEAAKKL 48
                                  5799****************9965333344333.34445555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00049
                                   ..GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTS CS
                         SRPRB  45 sekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqel 124
                                   ++++  +t+iD PGh  + +++++     s++ + + vv +   + e+   AE  +   +i  k+    ++++A nK +l
  gi|70606488|ref|YP_255358.1|  80 ETRKYFFTVIDAPGHRDFVKNMITG---ASQADAAILVVSAKKGEYEAGMSAEGQTREHIILSKTMGINQVIVAINKMDL 156
                                   5577789***********9999998...7778888899988888888888888877765555555566677888888876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.1e-05     0.018       4      78 ..       6     100 ..       3     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                                   EEEEEEEEBTTSSCCCCCCTTSSSS.----.....................--------------S-EEEEEEEEETTCEE CS
                        Septin   4 eftlmvvGesglGkttlintlfetd.liee.....................ekleeasekkkktveikkkkvvieedgvkl 62 
                                   +++l+v+G+   Gk+tli  l+ ++  i+e                       +++ +e+ ++ v+i+ + +  e    k 
  gi|70606488|ref|YP_255358.1|   6 HLNLIVIGHVDHGKSTLIGRLLMDRgFIDEktvkeaeeaakklgkdsekyaFLMDRLKEERERGVTINLSFMRFET--RKY 84 
                                   68****************9987665155555555566555555555543321122223333333333333333333..355 PP

                                   EEEEEE---BSSSSSH CS
                        Septin  63 nltviDtpgfGdavdn 78 
                                    +tviD pg+ d+v n
  gi|70606488|ref|YP_255358.1|  85 FFTVIDAPGHRDFVKN 100
                                   5688888888888877 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.7e-05     0.027      32     150 ..      69     183 ..      49     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                     Gtr1_RagA  32 gatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealr..qysp 110
                                   g+ti+++  ++  +++  + ++D +G ++fv+++++       ++ ++ i V+ +++ e+e  ++   ++ e++   ++  
  gi|70606488|ref|YP_255358.1|  69 GVTINLSFMRF-ETRKYFFTVIDAPGHRDFVKNMITG-----ASQADAAILVVSAKKGEYEAGMSAEGQTREHIIlsKTMG 143
                                   55666655555.3567899**************8654.....467789999*****99**999998888888765113444 PP

                     Gtr1_RagA 111 eakvfvlihKmDliqedereeifeerkeeireeiekleke 150
                                     +v v i+KmDl +    e+ f+e+ +++++ +++++++
  gi|70606488|ref|YP_255358.1| 144 INQVIVAINKMDLADTPYDEKRFKEIVDTVSKFMKSFGFD 183
                                   46899**************************999976654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.28   4.5e+02       3      23 ..       9      29 ..       7      41 .. 0.83
   2 ?   10.3   0.1   0.00024      0.39     103     170 ..      99     174 ..      89     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.28
                                  EEEEESTTCCHHHHHHHHHCT CS
                          cobW  3 tvltGflGsGKTtLlnhllen 23
                                  +++ G +  GK+tL+ +ll +
  gi|70606488|ref|YP_255358.1|  9 LIVIGHVDHGKSTLIGRLLMD 29
                                  578899999******999944 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                                   SHHHHHCCCECEEEEEEETTTH........CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCHC..HHHHHHHHHHHH CS
                          cobW 103 eeelksdltldavvavvDaknl.......eaeeekieekaedqlaaadllv.lnKtDlldeeallekleerlrqln 170
                                   ++ ++ + ++da + vv+ak+         + +++++  + + +    ++v +nK+Dl+d+  + ++++e+++ ++
  gi|70606488|ref|YP_255358.1|  99 KNMITGASQADAAILVVSAKKGeyeagmsAEGQTREHIILSKTMGINQVIVaINKMDLADTPYDEKRFKEIVDTVS 174
                                   5667788899*********9999999996555666667778888888888769********977799999998876 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.7   7.7e+03      23      38 ..      68      83 ..      58      86 .. 0.75
   2 ?    3.9   0.1     0.041        66      25      68 ..     147     196 ..     143     200 .. 0.76
   3 ?   -3.3   0.0         7   1.1e+04      18      39 ..     288     309 ..     275     309 .. 0.73
   4 ?    7.5   0.1    0.0031       5.1       5      71 ..     366     433 ..     364     434 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.7
                                  -EEEEE-CCCTCHHHH CS
                          SepF 23 kiVilnledldkeeak 38
                                  + V +nl+ +  e+ k
  gi|70606488|ref|YP_255358.1| 68 RGVTINLSFMRFETRK 83
                                  6799999999988766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.041
                                   EEEE-CCCTC.......HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-T CS
                          SepF  25 Vilnledldk.......eeakrivdflsgvvyaldGdiqkvgkkvflitPk 68 
                                   Vi+ ++++d        + +k ivd +s+ +++ + d+ kv+  v +++P+
  gi|70606488|ref|YP_255358.1| 147 VIVAINKMDLadtpydeKRFKEIVDTVSKFMKSFGFDMNKVK-FVPVVAPD 196
                                   55555555544456666999******************9998.77777776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7
                                   HHHTT-EEEEE-CCCTCHHHHH CS
                          SepF  18 alkegkiVilnledldkeeakr 39 
                                     + g+ + +n+ +++k++ kr
  gi|70606488|ref|YP_255358.1| 288 KAEPGDNIGFNVRGVEKKDVKR 309
                                   5556677778999999988887 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0031
                                   E-SSGGGHHHHHHHHHTT-EEEEE-CCCTCHHHHHHHHHHHHHHHHCT-EEEEECTT.EEEEE-TT-E CS
                          SepF   5 eprsfedaqeiadalkegkiVilnledldkeeakrivdflsgvvyaldGdiqkvgkk.vflitPknvd 71 
                                    p++ ++a++  + +k+g+  i++++ +++ +a+++ +f +   +a++   + vg + ++ + P++v+
  gi|70606488|ref|YP_255358.1| 366 DPKTGKEAEKNPQFIKAGDSAIVKFKPIKELVAEKFREFPALGRFAMRDMGKTVGVGvIIDVKPRKVE 433
                                   68999999999****************************99999999844444444414445566665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0014       2.3       2      21 ..      10      29 ..       9      38 .. 0.86
   2 ?    2.3   0.0     0.092   1.5e+02      86     137 ..      51     117 ..      30     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
                                  EEEEBTTTTHHHHHHHHHTS CS
                     Dynamin_N  2 avvGsqSsGKSSvlnaLlge 21
                                  +v+G++ +GKS+++  Ll +
  gi|70606488|ref|YP_255358.1| 10 IVIGHVDHGKSTLIGRLLMD 29
                                  8*************999865 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.092
                                   --SS..................-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEE CS
                     Dynamin_N  86 iskk..................villkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavts 137
                                   +s+k                   +++  ++  +   t++D PG  +  k   ++++ + +  ++il+v++
  gi|70606488|ref|YP_255358.1|  51 DSEKyaflmdrlkeerergvtiNLSFMRFETRKYFFTVIDAPGHRDFVK---NMITGASQADAAILVVSA 117
                                   33333333333333344444326666677777778899****9887433...467666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2812.81
//
Query:       gi|70606489|ref|YP_255359.1|  [L=195]
Description: 30S ribosomal protein S7 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-44  150.0   1.1    4.5e-44  149.7   1.1    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   1.1   2.5e-48   4.5e-44      18     149 .]      55     195 .]      45     195 .] 0.96

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 2.5e-48
                                   TTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE-HH CS
                  Ribosomal_S7  18 ynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevrpk 94 
                                    + ++ve+lin+lm+    +Gkk lA++iv++++dii+ kt+++p++vl++A+en++Pr+ev+++++GG+ y v+v+v+p+
  gi|70606489|ref|YP_255359.1|  55 SRIPIVERLINNLMRpgrnKGKKMLAYNIVKTTFDIIAVKTGQNPIQVLVRAIENAAPREEVTRIMYGGIVYYVAVDVAPQ 135
                                   6789***************************************************************************** PP

                                   HHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                  Ribosomal_S7  95 RrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                   Rr++lAlr+++++a   ++++ k+++e+LaeE+i+Aa+++  + a++k+ee++r+A ++r
  gi|70606489|ref|YP_255359.1| 136 RRVDLALRHLVTGAseaSFNNPKPIEEALAEEIIAAANNDnkSVAIRKKEEIERIALSSR 195
                                   *************998899999****************9999**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1228.19
//
Query:       gi|70606490|ref|YP_255360.1|  [L=163]
Description: hypothetical protein Saci_0687 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-05   25.1   0.3    1.6e-05   24.6   0.3    1.2  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   8.7e-10   1.6e-05      59     126 ..      85     154 ..      74     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 8.7e-10
                                   HHHHHTTEEEEEEEEEEEET..TEEEEEEEEEET---.EEEEE-HHHHHHHHHHHT--EEEEHHHHHHH-E CS
                   DNase-RNase  59 sllealgakvervvItdled..gtfyAelvlrkeeee.leidaRpSDaiaLAlrtgapIyveeevleeasi 126
                                   ++ ++++  ++r++I+d+    g++ A++ ++ +    +e    pS a+aLAl ++ pI++ +++++e++ 
  gi|70606490|ref|YP_255360.1|  85 NIKDSIKNVINRIIIDDVIReyGVYVATVEFKFDG-IiIEKKLIPSHAVALALLFDRPIFIRRKLVDEQEK 154
                                   5667788899*******955459*********853.24888889**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1065.06
//
Query:       gi|70606491|ref|YP_255361.1|  [L=147]
Description: 30S ribosomal protein S12 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-48  161.2   0.2    7.2e-48  160.9   0.2    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.9   0.2     4e-52   7.2e-48       1     113 [.      32     145 ..      32     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 4e-52
                                   --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--... CS
               Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk. 80 
                                   r+ l +k+k d+legap++rG+vlekv++e+++PnsA+Rk+vrv+L kng+ vtaf+pg+g +nf+dEhdev+++Gi+++ 
  gi|70606491|ref|YP_255361.1|  32 RRMLALKEKFDPLEGAPMARGIVLEKVGIESRQPNSAVRKAVRVQLVKNGRIVTAFVPGDGGVNFIDEHDEVVIAGIGGTl 112
                                   677899*************************************************************************99 PP

                                   ...BTTSTTEEEEBETS---TSSSTTTTT---- CS
               Ribosom_S12_S23  81 gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                   g++++DlpGvrykvv v+gvsl al+k+kk+kp
  gi|70606491|ref|YP_255361.1| 113 GRSMGDLPGVRYKVVMVNGVSLDALYKGKKQKP 145
                                   *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1137.50
//
Query:       gi|162139950|ref|YP_255362.2|  [L=143]
Description: transcription elongation factor NusA-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-20   70.4   5.0    9.6e-14   51.0   0.5    2.1  2  KH_2      KH domain
    4.3e-12   45.9   3.7    3.5e-11   43.0   0.8    2.2  2  KH_5      NusA-like KH domain
    7.4e-12   45.0   1.5      3e-06   27.0   0.2    2.1  2  KH_4      KH domain
  ------ inclusion threshold ------
      0.015   15.1   4.5       0.28   11.1   0.4    2.7  2  KH_1      KH domain
      0.039   13.8   0.0      0.098   12.5   0.0    1.7  1  HTH_ParB  HTH domain found in ParB protein


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.5   2.7e-17   9.6e-14       3      74 ..      13      96 ..      11      99 .. 0.91
   2 !   23.2   1.1   1.2e-08   4.4e-05      11      57 ..      86     134 ..      76     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.7e-17
                                   HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............EEEEEEE CS
                           KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............Vklnivk 72
                                   + sl++ i++ ++++++I++ +nr+i+ i  + +g++IGk+G n++k++k ++k +e++ +++            ++++ +k
  gi|162139950|ref|YP_255362.2| 13 YMSLFQDITGVTARDCIIDDRNNRIILLINPESMGVAIGKNGLNVRKLEKLINKSVEIVGYQEnledlvknlmspARVKTIK 94
                                   5799****************99***********************************9999988888888888887777777 PP

                                   ET CS
                           KH_2 73 Vk 74
                                   V 
  gi|162139950|ref|YP_255362.2| 95 VV 96
                                   75 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.2e-08
                                    ECETEEEEEEEC..CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHH CS
                           KH_2  11 kkagvskveIer..tanrviiviresqpgivIGkgGsnikkigkelrkd 57 
                                    + a v+ +++ +  +++ v i++    +gi+IGk+G+n+++ +  l++ 
  gi|162139950|ref|YP_255362.2|  86 SPARVKTIKVVQsnSKKTVYITVEPQDKGIAIGKNGRNVERAKLILKRY 134
                                    6677888888885455888899999****************99887765 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.8   9.8e-15   3.5e-11       3      69 .]      35      95 ..      33      95 .. 0.92
   2 ?    3.7   0.1     0.019        66       6      31 ..     105     125 ..     101     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 9.8e-15
                           KH_5  3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                   +r+++ +  +      +G ++gk+G +++++++ + ++ +++v ++e+l+ +++n++sPa+v+ +k+
  gi|162139950|ref|YP_255362.2| 35 NRIILLINPES-----MGVAIGKNGLNVRKLEKLI-NKSVEIVGYQENLEDLVKNLMSPARVKTIKV 95
                                   67777777777.....9***************999.***************************9985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                           KH_5   6 kvaVkshnpnvdpvGaivgkkGsrik 31 
                                     + V+ ++      G ++gk+G++++
  gi|162139950|ref|YP_255362.2| 105 YITVEPQD-----KGIAIGKNGRNVE 125
                                    57788888.....99********997 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   8.9e-07    0.0032      21      59 ..      27      65 ..      13      70 .. 0.85
   2 !   27.0   0.2   8.3e-10     3e-06       2      52 ..      75     125 ..      74     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.9e-07
                           KH_4 21 teeeeeeeveielnvegedlGrvIGkrGrtldAlqylvs 59
                                   ++ +++++++i l +++e +G+ IGk+G +++ l  l++
  gi|162139950|ref|YP_255362.2| 27 DCIIDDRNNRIILLINPESMGVAIGKNGLNVRKLEKLIN 65
                                   456899**********************99988888777 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 8.3e-10
                           KH_4   2 elvedilkalvddpeeve.vteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                    e +ed++k+l+ +p+ v+ +++ ++++++++ ++ve++d+G+ IGk+Gr++ 
  gi|162139950|ref|YP_255362.2|  75 ENLEDLVKNLM-SPARVKtIKVVQSNSKKTVYITVEPQDKGIAIGKNGRNVE 125
                                    6799******9.677665166669999**********************975 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   7.7e-05      0.28       4      27 ..      39      62 ..      36      94 .. 0.80
   2 ?    5.1   0.3    0.0058        21       4      23 ..     106     125 ..     103     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.7e-05
                                   EEEGGGHHHHHHTGGGHHHHHHHH CS
                           KH_1  4 ilvPsslvgriIGkgGsnIkeIre 27
                                   +l++ + +g  IGk+G n++++++
  gi|162139950|ref|YP_255362.2| 39 LLINPESMGVAIGKNGLNVRKLEK 62
                                   68888999**************98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0058
                                    EEEGGGHHHHHHTGGGHHHH CS
                           KH_1   4 ilvPsslvgriIGkgGsnIk 23 
                                    i+v  +  g  IGk+G+n+ 
  gi|162139950|ref|YP_255362.2| 106 ITVEPQDKGIAIGKNGRNVE 125
                                    66777778999******986 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05     0.098      36      51 ..      50      65 ..      44      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                       HTH_ParB 36 iieegLsVRetEklvr 51
                                   i ++gL+VR++Ekl+ 
  gi|162139950|ref|YP_255362.2| 50 IGKNGLNVRKLEKLIN 65
                                   6789**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1058.63
//
Query:       gi|70606493|ref|YP_255363.1|  [L=104]
Description: 50S ribosomal protein L30e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-20   71.0   0.0    5.6e-20   70.9   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.078   13.0   0.1       0.19   11.8   0.0    1.7  2  Sigma70_r1_1    Sigma-70 factor, region 1.1


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.0   6.2e-24   5.6e-20       3      94 ..       5      96 ..       3      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 6.2e-24
                                  HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH..HTTEEEEEESCHHHHHHHTTSSSECSEE CS
                Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck..ekevpyvkvkskkeLGelvgkkrpvsal 83
                                   e++lk+ +++gk++lG+++++k+l+ g++k v++++  +++ k + + +++k  +++++++k+++  eLG+l+gk+++vs++
  gi|70606493|ref|YP_255363.1|  5 FEGELKTLLRSGKVILGTRKTLKLLKTGKVKGVVVSSTLRQDLKDD-IMTFSKfsDIPIYLYKGSG-YELGTLCGKPFMVSVI 85
                                  67899*****************************************.******99999999*****.**************** PP

                                  EEEESTTTHHH CS
                Ribosomal_L7Ae 84 aikdegdskdl 94
                                  +i+deg+sk+l
  gi|70606493|ref|YP_255363.1| 86 GIVDEGESKIL 96
                                  *********98 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.95   8.6e+03       6      15 ..       8      17 ..       6      17 .. 0.84
   2 ?   11.8   0.0   2.1e-05      0.19       9      45 ..      27      63 ..      22      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.95
                                  HHHHHHHHHH CS
                  Sigma70_r1_1  6 avkeLikkgK 15
                                  ++k+L+  gK
  gi|70606493|ref|YP_255363.1|  8 ELKTLLRSGK 17
                                  6899999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHHHSCEEHHHHHHHGCCSS--HHHHHHHHHH CS
                  Sigma70_r1_1  9 eLikkgKkkGyLtyeEindaLpddeldseqiediiem 45
                                  +L+k+gK kG++ ++ + + L+dd+++  ++ di  +
  gi|70606493|ref|YP_255363.1| 27 KLLKTGKVKGVVVSSTLRQDLKDDIMTFSKFSDIPIY 63
                                  79***********************998888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 732.14
//
Query:       gi|70606494|ref|YP_255364.1|  [L=393]
Description: DNA-directed RNA polymerase subunit A'' [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-57  193.0   5.6    1.2e-56  192.1   5.6    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.76   10.0   0.0    2.3  2  SWM_repeat      Putative flagellar system-associated repeat
       0.32   10.9   3.1        0.2   11.5   0.5    2.0  2  DUF3052         Protein of unknown function (DUF3052)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   5.6     2e-60   1.2e-56      29     265 ..       8     338 ..       5     340 .. 0.92

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 2e-60
                                   HHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS...............B--TT-BHHHHHHHHHHHHHHCCCSSTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5  29 GYlqRrlvkaledvvvkyddtvrnsggeivqflygedg...............lvepGeavGiiaaQSiGePgTQltlnTF 94 
                                   GY+ +rl ++ + +  k ++  r + ++i+ +   e+                l+epGea+G++ aQS+GePgTQ+tl+TF
  gi|70606494|ref|YP_255364.1|   8 GYIDKRLNEIKDKIPDKLHEDLRAAIMDINGVELTEEDidriidltireyqqsLIEPGEAIGVVTAQSVGEPGTQMTLRTF 88 
                                   77777777777777777777777777777777666655688888888888888**************************** PP

                                   SSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                RNA_pol_Rpb1_5  95 HfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek......................... 150
                                   HfaG+ + nvtlG+prl ei+++ k+ +++++t++l+de++++++ka  ++++ie+                         
  gi|70606494|ref|YP_255364.1|  89 HFAGIRELNVTLGLPRLIEIVDARKVPSTPMMTIYLTDEYKTDKDKALDIARRIEYtrvenvvssvsvdisnmsitlqfdq 169
                                   ***************************************************99999************************* PP

                                   .............................................................CBTTEEEEEEEEEEEEEEET CS
                                   .............................................................xxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 151 .............................................................gikkikrilvkeaekgkeee 170
                                                                                                g+k+ikr++v+  +kg    
  gi|70606494|ref|YP_255364.1| 170 emlkdkgvsieeikkiitklklgeiriedndeysftiyfekidsimalfkmrekilntkikGVKGIKRAIVQ--KKG---- 244
                                   *******************************************99999999999988888888888888777..222.... PP

                                   EEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 171 kelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgei 251
                                   +e+v+ t+g nl+ +++v + vd+++i +n+i+e+ e+lgieaar+ + +ei++v+++qg++v+ rH+ l+ d+mt++g i
  gi|70606494|ref|YP_255364.1| 245 DEYVIITDGSNLEGIMNVTG-VDINKIQTNNIHEVEEVLGIEAARELISREIKKVLEEQGLDVDMRHIVLVSDIMTRTGDI 324
                                   4679****************.************************************************************ PP

                                   --SSTTCHCCSSSH CS
                                   xxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5 252 vavnrsGinkaels 265
                                    +++r+G++ +++s
  gi|70606494|ref|YP_255364.1| 325 RQIGRHGVTGEKSS 338
                                   *********99887 PP

>> SWM_repeat  Putative flagellar system-associated repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00013      0.76      45      80 ..     144     179 ..     111     181 .. 0.84
   2 ?   -1.8   0.0      0.61   3.7e+03      37      46 ..     341     350 ..     334     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                    SWM_repeat  45 vngaaitVtgvsvdaanktVtLtLsravangeqVtV 80 
                                      +++ V++vsvd +n ++tL  ++   +++ V++
  gi|70606494|ref|YP_255364.1| 144 YTRVENVVSSVSVDISNMSITLQFDQEMLKDKGVSI 179
                                   5567899******************99998888887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.61
                    SWM_repeat  37 aaaaFtVtvn 46 
                                   a+aaF+Vtv+
  gi|70606494|ref|YP_255364.1| 341 ARAAFEVTVK 350
                                   6789999997 PP

>> DUF3052  Protein of unknown function (DUF3052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   3.4e-05       0.2      19      50 ..      23      54 ..      16      60 .. 0.89
   2 ?   -2.4   0.1      0.72   4.3e+03      23      46 ..     289     312 ..     270     323 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                       DUF3052 19 dDvdedlreaiedligeelvdedadevvDvvl 50
                                  d   edlr+ai+d+ g el +ed d ++D+ +
  gi|70606494|ref|YP_255364.1| 23 DKLHEDLRAAIMDINGVELTEEDIDRIIDLTI 54
                                  66789************************876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.72
                       DUF3052  23 edlreaiedligeelvdedadevv 46 
                                   e ++++i+++++e+ +d d++ +v
  gi|70606494|ref|YP_255364.1| 289 ELISREIKKVLEEQGLDVDMRHIV 312
                                   556677777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2594.49
//
Query:       gi|70606495|ref|YP_255365.1|  [L=880]
Description: DNA-directed RNA polymerase subunit A' [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.5e-100  335.8   0.0   3.4e-100  335.4   0.0    1.2  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    1.9e-74  249.4   0.0    3.2e-74  248.7   0.0    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    5.4e-33  114.2   0.0      9e-33  113.4   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    4.1e-29  100.7   0.0    8.3e-29   99.7   0.0    1.5  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    6.5e-25   88.1   0.0    1.4e-24   86.9   0.0    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.076   12.5   7.7        7.5    6.1   0.3    3.6  3  zf-ribbon_3     zinc-ribbon domain
       0.16   12.2   2.0        2.6    8.3   0.1    2.8  2  HTH_17          Helix-turn-helix domain
       0.39   10.6   2.0        8.5    6.3   0.1    3.1  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.58   10.2   1.8          1    9.4   0.0    2.3  2  CpXC            CpXC protein
        3.2    7.8   6.7        9.1    6.4   0.0    3.2  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
          5    7.0   8.3        8.2    6.3   0.2    3.2  3  zinc_ribbon_2   zinc-ribbon domain
        5.1    7.1   8.6       0.47   10.4   0.1    3.2  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.4   0.0  2.3e-103  3.4e-100       2     312 .]       4     313 ..       3     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 335.4 bits;  conditional E-value: 2.3e-103
                                   E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfh 82 
                                   k i  ++fg++sp+eir++Sv+ + ++e+++e+  +P egG++D++lg+i+   +C +Cg++ + C+ghfGhieL kPv+h
  gi|70606495|ref|YP_255365.1|   4 KIIRGVKFGVLSPNEIRQMSVTAIITSEVYDEDG-TPIEGGVMDPKLGVIEPGQKCPVCGNTLAGCPGHFGHIELIKPVIH 83 
                                   78999***************************95.********************************************** PP

                                   HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC......CCHHHHHHHHCCS-BE-SSSSB-EEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1  83 igffklilkilecvckecskllldeekkkllsklkkrekleelk......krlkaieelckkinlcekCgavqpkleeege 157
                                   ig++k i+  l+++c +c+++ ++e++ + ++++ ++    +l+      + ++ i++++ k   c +Cg +q k++   e
  gi|70606495|ref|YP_255365.1|  84 IGYVKHIYDFLRSTCWRCGRIKIKEQDLERYKRIYNA---IKLRwpsaarRLVEYIKKISIKNLECPHCGEKQFKIKL--E 159
                                   *************************966434333333...333333344478888888888888999***87766643..3 PP

                                   EEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 158 klkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDltekl 238
                                   k + +++++++ +  kls++++++ l+ri+d+dve+lg ++++srPew+iltvlPVpP +iRPs+++++g r+edDlt+kl
  gi|70606495|ref|YP_255365.1| 160 KPY-NFNEERNGSIVKLSPSEIRDRLERIPDSDVELLGYDPKSSRPEWMILTVLPVPPITIRPSITIESGIRAEDDLTHKL 239
                                   433.45566665779****************************************************************** PP

                                   HHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_1 239 rdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                   +dii+ N+rLk+ +e+gap+liie+ ++lLQ+hvat+fdnei+gl+pa+++s+rpl++l qrLkGKeGrfRgnL
  gi|70606495|ref|YP_255365.1| 240 VDIIRLNERLKESIEAGAPQLIIEDLWDLLQYHVATYFDNEIPGLPPAKHRSGRPLRTLAQRLKGKEGRFRGNL 313
                                   *************************************************************************9 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.7   0.0   2.1e-77   3.2e-74       1     166 []     315     482 ..     315     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 248.7 bits;  conditional E-value: 2.1e-77
                                   SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S.. CS
                RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkr.. 79 
                                   Gkrvd+saR+vispdpnl++devg+P+++a++ltvpe+vt++ni+++r++++ngp+++Pga+yv++ dg++ +l++ k+  
  gi|70606495|ref|YP_255365.1| 315 GKRVDFSARTVISPDPNLSIDEVGIPYTIARMLTVPERVTNINIERIRQYIINGPDKWPGANYVIKPDGRRIDLRYVKDrk 395
                                   9***************************************************************************98843 PP

                                   CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHH CS
                RNA_pol_Rpb1_2  80 klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEa 160
                                   +la++++ g++verh+ dgdvvl+NRqPsLh++s+mah+v+vl+++t+rlnl+ + +yNaDFDGDemnlh+pqseea aEa
  gi|70606495|ref|YP_255365.1| 396 ELASSITAGYVVERHLVDGDVVLFNRQPSLHRISMMAHKVRVLPGRTFRLNLLDCPPYNADFDGDEMNLHVPQSEEAIAEA 476
                                   499****************************************************************************** PP

                                   HHCSBT CS
                RNA_pol_Rpb1_2 161 eelllv 166
                                   +el+lv
  gi|70606495|ref|YP_255365.1| 477 RELMLV 482
                                   ****86 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0     6e-36     9e-33       1     157 []     485     651 ..     485     651 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 6e-36
                                   CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHCCCCE CS
                RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpneiny 81 
                                   ni++p+ g P+ig  QD ++G+yll+ + ++++ ee+  +l   ++     ++ +pail pk+ +tgkq++s++lp+++n 
  gi|70606495|ref|YP_255365.1| 485 NIITPRYGGPIIGGGQDYISGAYLLSVKTTLLTVEEVATILGVTDFV---GELGEPAILAPKPYYTGKQVISLFLPKDFNF 562
                                   9****************************************999554...6799***********************9999 PP

                                   EEE.SSSS............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHC CS
                RNA_pol_Rpb1_3  82 erk.neek............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsg 149
                                    +  n++k            d++++ikng+l++Gv dkk++g+++ +s++h  ++eyg++  + ++d++ ++++++l ++g
  gi|70606495|ref|YP_255365.1| 563 HGPaNISKgprackdeicphDSFIVIKNGLLLEGVFDKKAIGNQQPESMLHWSIREYGTEYGKWLMDNVFKMFIRFLEMRG 643
                                   998755557888889****************************************************************** PP

                                   EB-TGGGG CS
                RNA_pol_Rpb1_3 150 ftigigDt 157
                                   ft+ ++D+
  gi|70606495|ref|YP_255365.1| 644 FTMTLEDI 651
                                   ******97 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   0.0   5.5e-32   8.3e-29       4     108 .]     679     782 ..     676     782 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 5.5e-32
                                   HCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCST.TTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS CS
                RNA_pol_Rpb1_4   4 aerygkledlpgksleelfeakinkilnkardkagkiasksla.asNsiliMvksGaKGsiinisqiagclGqqnvegkri 83 
                                   +++ g+le++pg++ ee++e+ i + l+k r+ ag+ia k+l+ + N+++iM+ +Ga+Gs +ni+q++++lGqq+v+g+ri
  gi|70606495|ref|YP_255365.1| 679 FNE-GQLEPIPGRTIEESLESYILDTLDKLRKVAGEIATKYLDpF-NNVYIMAITGARGSELNITQMTALLGQQSVRGERI 757
                                   555.99*************************************88.*********************************** PP

                                   --SSTSCSSTTSSSSESSTTTSSEE CS
                RNA_pol_Rpb1_4  84 pkgfsgrtlphfkkidespesrGFv 108
                                    +g+++rtl  fk  d  pe+rGFv
  gi|70606495|ref|YP_255365.1| 758 RRGYRERTLSLFKYGDIAPEARGFV 782
                                   ************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   9.5e-28   1.4e-24       1      66 [.     789     854 ..     789     873 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 9.5e-28
                                   B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                   GL++ e ffh+ ggReGL+DtAvkT++sGY+qRrl++al d+ ++yd+tvr+  g+ivq++yg+d+
  gi|70606495|ref|YP_255365.1| 789 GLSPYEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLRIEYDGTVRSLYGDIVQVVYGDDA 854
                                   9***************************************************************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.016        24       3      11 ..      56      65 ..      54      67 .. 0.79
   2 ?    4.3   0.0     0.019        29       4      16 ..      97     110 ..      96     111 .. 0.87
   3 ?    6.1   0.3     0.005       7.5       5      25 ..     146     152 ..     142     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                   zf-ribbon_3  3 vrCPnCGa.p 11
                                  ++CP CG+ +
  gi|70606495|ref|YP_255365.1| 56 QKCPVCGNtL 65
                                  68*****955 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                   zf-ribbon_3   4 rCPnCGa.plssdd 16 
                                   +C++CG  +++++d
  gi|70606495|ref|YP_255365.1|  97 TCWRCGRiKIKEQD 110
                                   6******7799987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.005
                   zf-ribbon_3   5 CPnCGaplssddnvCpyCGtk 25 
                                   CP+CG              +k
  gi|70606495|ref|YP_255365.1| 146 CPHCG--------------EK 152
                                   55555..............44 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.12   1.8e+02      33      47 ..     102     115 ..      90     116 .. 0.84
   2 ?    8.3   0.1    0.0017       2.6       1      14 [.     515     528 ..     515     529 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                        HTH_17  33 Grrwriprsdleewl 47 
                                   Gr ++i++ dle++ 
  gi|70606495|ref|YP_255365.1| 102 GR-IKIKEQDLERYK 115
                                   44.**********97 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                        HTH_17   1 lltveEaAelLgvs 14 
                                   lltveE+A +Lgv 
  gi|70606495|ref|YP_255365.1| 515 LLTVEEVATILGVT 528
                                   79**********96 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0057       8.5      18      29 ..      54      65 ..      51      67 .. 0.81
   2 ?    2.4   0.2     0.098   1.5e+02       4      26 ..     128     150 ..     127     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0057
                                  -SEE-TTT--EE CS
                 Rad50_zn_hook 18 akgcCPlCgRel 29
                                   +++CP+Cg +l
  gi|70606495|ref|YP_255365.1| 54 PGQKCPVCGNTL 65
                                  567*****9776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.098
                                   HHHHHHHHHHHHTT-SEE-TTT- CS
                 Rad50_zn_hook   4 eteelnkkieelkeakgcCPlCg 26 
                                   ++ +l ++i++++ ++  CP Cg
  gi|70606495|ref|YP_255365.1| 128 AARRLVEYIKKISIKNLECPHCG 150
                                   56788999999996666*****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   2.0       6.9     1e+04      40      46 ..      58      64 ..      56     109 .. 0.63
   2 ?    9.4   0.0   0.00069         1      23      74 ..     129     183 ..     117     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.9
                          CpXC 40 CpkCgat 46
                                  Cp Cg+t
  gi|70606495|ref|YP_255365.1| 58 CPVCGNT 64
                                  5555543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00069
                          CpXC  23 dpelkeklldgslfeatCpkCgat...akleapllyhdpekellillvpeserse 74 
                                      l+e + + s+ + +Cp+Cg++   +kle p  ++++++  ++ l p + r++
  gi|70606495|ref|YP_255365.1| 129 ARRLVEYIKKISIKNLECPHCGEKqfkIKLEKPYNFNEERNGSIVKLSPSEIRDR 183
                                   567899999999*********9852226899999999999888888888877655 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.5      0.19   2.8e+02      18      27 ..      55      64 ..      53      68 .. 0.83
   2 ?    0.0   0.1      0.57   8.5e+02       5      18 ..      89     102 ..      88     104 .. 0.78
   3 ?    6.4   0.0    0.0061       9.1      19      29 ..     144     153 ..     121     163 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                 Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                  g+ CP Cg++
  gi|70606495|ref|YP_255365.1| 55 GQKCPVCGNT 64
                                  789*****86 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.57
                 Zn_Tnp_IS1595   5 earalLealrWpng 18 
                                   +++++L + +W+ g
  gi|70606495|ref|YP_255365.1|  89 HIYDFLRSTCWRCG 102
                                   67899999999866 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0061
                 Zn_Tnp_IS1595  19 fvCPhCgsrka 29 
                                     CPhCg +  
  gi|70606495|ref|YP_255365.1| 144 LECPHCGEK-Q 153
                                   67*****54.3 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.026        39       1       9 [.      57      65 ..      57      66 .. 0.85
   2 ?   -0.3   0.2      0.67   9.9e+02       2       7 ..      98     103 ..      97     104 .. 0.88
   3 ?    6.3   0.2    0.0055       8.2      16      22 ..     146     152 ..     137     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +Cp CG++l
  gi|70606495|ref|YP_255365.1| 57 KCPVCGNTL 65
                                  799999986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.67
                 zinc_ribbon_2   2 CpnCGa 7  
                                   C++CG+
  gi|70606495|ref|YP_255365.1|  98 CWRCGR 103
                                   *****6 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0055
                 zinc_ribbon_2  16 CpyCGtp 22 
                                   Cp+CG++
  gi|70606495|ref|YP_255365.1| 146 CPHCGEK 152
                                   5555553 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00032      0.47       1      11 [.      55      65 ..      55      66 .. 0.91
   2 ?   -0.6   0.4      0.87   1.3e+03       4      16 ..      98     110 ..      96     115 .. 0.70
   3 ?   -0.7   0.3      0.89   1.3e+03       4       7 ..     146     149 ..     144     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                  TSB-TTT--BB CS
                  zf-FPG_IleRS  1 GepCpRCwryi 11
                                  G++Cp+C++++
  gi|70606495|ref|YP_255365.1| 55 GQKCPVCGNTL 65
                                  9********96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.87
                                   -TTT--BBEEEEC CS
                  zf-FPG_IleRS   4 CpRCwryiervgq 16 
                                   C RC+r+  ++  
  gi|70606495|ref|YP_255365.1|  98 CWRCGRIKIKEQD 110
                                   7799998776665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.89
                                   -TTT CS
                  zf-FPG_IleRS   4 CpRC 7  
                                   Cp+C
  gi|70606495|ref|YP_255365.1| 146 CPHC 149
                                   6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (880 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 5462.37
//
Query:       gi|70606496|ref|YP_255366.1|  [L=1126]
Description: DNA-directed RNA polymerase subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.6e-127  424.0   0.2     8e-127  423.5   0.2    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    1.1e-57  194.8   0.0    1.6e-57  194.3   0.0    1.2  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.8e-44  150.6   0.0    6.8e-44  149.8   0.0    1.4  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    1.8e-29  101.9   0.0    4.5e-29  100.7   0.0    1.7  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    5.8e-25   87.3   0.0    1.3e-24   86.1   0.0    1.7  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    4.7e-22   78.0   0.2    1.3e-21   76.7   0.2    1.8  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    5.8e-10   39.6   0.0    1.5e-09   38.2   0.0    1.7  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.5   0.2  3.1e-130    8e-127       1     390 []     649    1021 ..     649    1021 .. 0.95

  Alignments for each domain:
  == domain 1  score: 423.5 bits;  conditional E-value: 3.1e-130
                                    HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79  
                                    +a+++p++eh+qspr+++q+am+kq+lg+y+ n+  r++++ +ll+++q Plv+t+  +  ++        +++ ++G 
  gi|70606496|ref|YP_255366.1|  649 IASIIPYPEHNQSPRNTYQSAMAKQSLGLYASNYQIRTDTRAHLLHYPQMPLVQTR-MLGVIG--------YNDRPAGA 718 
                                    6999****************************************************.888888........******** PP

                                    EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-....-SS-GGGS-TTSB-- CS
                RNA_pol_Rpb2_6   80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv....seealkkLdedGivr 153 
                                    na+ A+msy+GYn+ED+ii+n+++++r++++s++++ y++e  ++++g+ ++i++    v    +++ ++ L+++G+v+
  gi|70606496|ref|YP_255366.1|  719 NAILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFFRLYSTEEVKYPGGQeDKIVTPEAGVkgykGKDYYRLLEDNGVVS 797 
                                    *************************************9999999**9996777666666699999999*********** PP

                                    SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEE CS
                RNA_pol_Rpb2_6  154 vgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkv 232 
                                    ++ evk gd+l+gkv  ++ ++ +e k+l     e+a  ++dts+ +++ge+g+Vd v +       +++ ++nklvkv
  gi|70606496|ref|YP_255366.1|  798 PEVEVKGGDVLIGKV--SPPRFLQEFKEL---SPEQA--KRDTSIVTRHGENGIVDLVLI-------TETLEGNKLVKV 862 
                                    **************9..888898666655...44444..59*******************.......899999****** PP

                                    EEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B-- CS
                RNA_pol_Rpb2_6  233 yvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdat 311 
                                    +v++ R +++GDKfa rhGqKGvv+++++q DmP++++Giv+Di+lNP+++PSRmtigq++E + gk aal+gk vdat
  gi|70606496|ref|YP_255366.1|  863 RVRDLRIPEIGDKFATRHGQKGVVGILIDQVDMPYTAKGIVPDIILNPHALPSRMTIGQIMEAIGGKYAALSGKPVDAT 941 
                                    ******************************************************************************* PP

                                    TT-...-.HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGG CS
                RNA_pol_Rpb2_6  312 vFdgake.eeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGka 389 
                                    +F ++ + +e+++++ + g   + +ev+ydGrtG+kl+++i +G++Yy+kL+h+v+dK+haR++Gp++ lt+QP++G+a
  gi|70606496|ref|YP_255366.1|  942 PFLETPKlQEMQKEILKLGHLPDSTEVVYDGRTGQKLKSRILFGIVYYQKLHHMVADKMHARARGPVQILTRQPTEGRA 1020
                                    ***99999*********9************************************************************9 PP

                                    G CS
                RNA_pol_Rpb2_6  390 q 390 
                                    +
  gi|70606496|ref|YP_255366.1| 1021 R 1021
                                    6 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   0.0   6.4e-61   1.6e-57       1     203 []      19     390 ..      19     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 6.4e-61
                                   CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTT.SCEEES.HHHHHHCTSBXEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesd.asereiyPkearlrnltYsap 80 
                                   gLv+q+ldSFn+f++++l+++i e+ +i +e++       l++k+++ir++kP+++e+d + +rei+P+earlrnltYs+p
  gi|70606496|ref|YP_255366.1|  19 GLVRQHLDSFNDFLRNKLQQVIYEQGEIVTEVPG------LKIKLGKIRYEKPSIRETDkGPMREITPMEARLRNLTYSSP 93 
                                   69*******************************7......9****************88799******************* PP

                                   EEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE...... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                RNA_pol_Rpb2_1  81 lyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek...... 155
                                   +++++  v     n+ e ++ e+yiG+lP+Ml+s a+ +s+++ ++l+e++E+p+d+GGyFi+nG+ekvi+aqe+      
  gi|70606496|ref|YP_255366.1|  94 IFLSMIPVE----NNIEGEPIEIYIGDLPIMLKSVADPTSNLPIDKLIEIGEDPKDPGGYFIVNGSEKVIIAQEDlatnrv 170
                                   *********....89****************************************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|70606496|ref|YP_255366.1| 171 lvdygksgsnithvakvtssaagyrvqvmierlkdstiqisfatvpgripfaiimralgfvtdrdivyavsldpqiqnell 251
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|70606496|ref|YP_255366.1| 252 psleqassitsaeealdfignrvaigqkrenriqkaeqvidkyflphlgtspedrkkkgyylasavnkilelylgrrepdd 332
                                   ********************************************************************************* PP

                                   ..........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 156 ..........laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpita 203
                                             laG+L++slfrv++k +++d+  +l+ks  ++++l+l++lv+a+ it+
  gi|70606496|ref|YP_255366.1| 333 kdhyankrvrLAGDLFTSLFRVAFKAFVKDLVYQLEKSKVRGRRLSLTALVRADIITE 390
                                   ********************************************************95 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   2.7e-47   6.8e-44       1     190 []     166     342 ..     166     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 2.7e-47
                                   -TSCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTT CS
                RNA_pol_Rpb2_2   1 rsngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsed 79 
                                   ++n+++v   k+ ++i  +a+vtss + +r +v+ ++ +++t+ ++  ++  +ip++i+++Alg+v+dr+I+++++    d
  gi|70606496|ref|YP_255366.1| 166 ATNRVLVDYGKSGSNIthVAKVTSSAAGYRVQVMIERLKDSTIQISFATVPGRIPFAIIMRALGFVTDRDIVYAVS---LD 243
                                   589*************999*********************************************************...7* PP

                                   HHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHHH CS
                RNA_pol_Rpb2_2  80 sqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkrlkaqd 160
                                   +q+++ell++le++++i+++eeald+ig++va+++++e+r+q+a++++         +++ l+ hlg+s +  +  +k ++
  gi|70606496|ref|YP_255366.1| 244 PQIQNELLPSLEQASSITSAEEALDFIGNRVAIGQKRENRIQKAEQVI---------DKYFLP-HLGTSPEDRK--KKGYY 312
                                   *********************************************996.........8*****.*******444..6**** PP

                                   HHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                RNA_pol_Rpb2_2 161 ilymidrLlslklgrrevDDiDhlgnkRvr 190
                                   ++++++++l+l lgrre+DD+Dh++nkRvr
  gi|70606496|ref|YP_255366.1| 313 LASAVNKILELYLGRREPDDKDHYANKRVR 342
                                   *****************************8 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   1.8e-32   4.5e-29       1      85 [.    1023    1113 ..    1023    1115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.8e-32
                                    BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHH CS
                RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlq 73  
                                    GGlrfGEMErd+li++G+a+l+k+rl+++SD+  v++c++c+ + +++       C+++ +++ +++v++++afklL+q
  gi|70606496|ref|YP_255366.1| 1023 GGLRFGEMERDCLIGFGTAMLIKDRLLDNSDKAVVYICDQCGYVGWYDrsknryVCPVHGDKSVLHPVTVSYAFKLLIQ 1101
                                    9**********************************************9*****9************************* PP

                                    HHHHTTBEEEEE CS
                RNA_pol_Rpb2_7   74 eLqslgialkll 85  
                                    eL+s+ i+++l+
  gi|70606496|ref|YP_255366.1| 1102 ELMSMVISPRLI 1113
                                    *********986 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   5.2e-28   1.3e-24       1      68 []     410     474 ..     410     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 5.2e-28
                RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                   q+ldr+n+ls lshlrrv s    l + + ++e+Rdlh ++wGr+Cp+eTPEG+n Glvk+Lalla+v
  gi|70606496|ref|YP_255366.1| 410 QLLDRTNWLSMLSHLRRVVSS---LARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALLAQV 474
                                   89*****************88...******************************************98 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.2     5e-25   1.3e-21       1      62 []     518     581 ..     518     581 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 5e-25
                                   EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT..T--EEEE-SSEEB-EEEEE-S CS
                RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek..qkevkiatDgGRvcRPliiVe 62 
                                   V++NGrllG+++d+k+l++++Re RR+gk+s+ev++++  +   +ev+i++D+GRv+RPliiV+
  gi|70606496|ref|YP_255366.1| 518 VYLNGRLLGYYEDGKELAKKIRESRRQGKLSDEVNVAYIATdyLNEVHINCDAGRVRRPLIIVN 581
                                   9************************************99987789*****************95 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.9e-13   1.5e-09       1      54 [.     602     638 ..     602     666 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.9e-13
                                   HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEE CS
                RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHc 54 
                                   +ddL+++g +E++DaeEEe+a++a+ p+dl+                   +TH+
  gi|70606496|ref|YP_255366.1| 602 FDDLVKQGKIEFIDAEEEENAYVALNPQDLTPD-----------------HTHL 638
                                   9*****************************876.................3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 7641.48
//
Query:       gi|70606497|ref|YP_255367.1|  [L=84]
Description: DNA-directed RNA polymerase subunit H [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-31  108.6   0.1    1.2e-31  108.4   0.1    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.1   6.5e-36   1.2e-31       1      73 []       9      81 ..       9      81 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 6.5e-36
                                  ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                  ++i++HelvPkhe+l+ ee+ +l+k+l+ik+eqLP+i++sDpva+ +g+k+Gd++kItrks+ +ge+vtYR+V
  gi|70606497|ref|YP_255367.1|  9 IDISNHELVPKHEILQLEEAYKLVKELGIKPEQLPWIRASDPVAKSIGAKPGDIIKITRKSPFTGESVTYRYV 81
                                  589********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 634.47
//
Query:       gi|70606498|ref|YP_255368.1|  [L=602]
Description: translation initiation factor IF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-37  125.5   5.4    2.1e-36  123.7   5.4    2.1  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      7e-34  117.1   0.1    1.9e-33  115.7   0.1    1.6  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.5e-14   54.0   2.0    4.2e-14   52.5   2.0    1.8  1  IF-2         Translation-initiation factor 2
    6.8e-11   42.4   1.3    5.9e-10   39.4   0.0    2.8  2  GTP_EFTU_D2  Elongation factor Tu domain 2
      2e-07   31.1   0.4    1.2e-06   28.5   0.1    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00013   22.2   0.0    0.00033   20.9   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0015   18.2   0.2      0.012   15.2   0.1    2.7  2  Ras          Ras family
     0.0021   17.5   0.8        1.6    8.2   0.1    3.0  2  Arf          ADP-ribosylation factor family
     0.0072   16.4   0.9      0.073   13.1   0.0    2.8  3  Dynamin_N    Dynamin family
     0.0095   15.7   0.0      0.042   13.6   0.0    2.1  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.024   13.7   1.3      0.072   12.1   0.1    2.1  2  JLPA         Adhesin from Campylobacter
      0.059   13.1   0.5          2    8.1   0.0    3.5  5  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.22   11.4   5.3        2.6    7.9   0.0    3.5  4  RsgA_GTPase  RsgA GTPase
        3.7    8.0   6.1       0.58   10.6   0.1    2.5  2  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   5.4   1.6e-39   2.1e-36       2      86 .]     469     554 ..     468     554 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.6e-39
                                   -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TTTS--T CS
                   GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vGrqike 81 
                                   Pgkiki+pg+vfrrsdp+ivGvevlgG+i+p++ lik+dGr+vGe+lqiqd++k+++ a++G+eva+si+g+i vGrq++e
  gi|70606498|ref|YP_255368.1| 469 PGKIKIIPGYVFRRSDPVIVGVEVLGGIIRPKYGLIKKDGRRVGEVLQIQDNKKSVDRASKGMEVAVSIKGNImVGRQVEE 549
                                   9******************************************************************************** PP

                                   T-EEE CS
                   GTP_EFTU_D4  82 gdily 86 
                                   g++ly
  gi|70606498|ref|YP_255368.1| 550 GEVLY 554
                                   ****9 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.1   1.4e-36   1.9e-33       5     190 ..      13     220 ..      10     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.4e-36
                                   EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHH CS
                      GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFsk 85 
                                    ++++ghvDhGKtTL+d++  ++   ++ ge ++ e    + ++     i+   +      + +   + +iDtPGH+ Fs+
  gi|70606498|ref|YP_255368.1|  13 IVVVLGHVDHGKTTLLDKIRGTAVVKKEPGEMTQ-EVGASFVPTSVIEKISEPLKKSFPI-KLEIPGLLFIDTPGHELFSN 91 
                                   589*****************88887777777664.4455666666666666544432222.355999************** PP

                                   HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHHH.. CS
                      GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsrk.. 153
                                      rg +v+D+a+lvvd+veG++ qt e ++++++++vp+iv+ NK+Dr+            ++++++ + v+++l+++  
  gi|70606498|ref|YP_255368.1|  92 LRKRGGSVADIAILVVDIVEGIQKQTLESIEILKSRKVPFIVAANKIDRIngwkaqdtysfLESINKQEQRVRDNLDKQvy 172
                                   *****************************************************9766544444444444444444433344 PP

                                   ..HHHHHHHHHTTT...................TTEEEEEEBTTTTBTHHHHHHHHHH CS
                      GTP_EFTU 154 ..eeklekygekge...................kevpvvfgSalkgegvktllealve 190
                                                                    k+v ++++Sa++geg+ ++l  l  
  gi|70606498|ref|YP_255368.1| 173 nlV----------IqlaeqgfnaerfdrirdftKTVAIIPVSAKTGEGIAEVLAILAG 220
                                   432..........0333344566688888999899***************99988765 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   2.0   3.3e-17   4.2e-14      13     105 .]     358     448 ..     343     448 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3.3e-17
                                   SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH..ST....EEEEEESSSCTHHHHHCCCCC CS
                          IF-2  13 kelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa..sn....aiiigFnvkvskkakklaeke 87 
                                   +  ++i+kaD  GsleA+ ++Le+      ++++  +++G+i+++D++ a+   ++    +ii +F vk+ + ++     e
  gi|70606498|ref|YP_255368.1| 358 SVYGIIVKADSLGSLEAIVSSLERR-----NIPIRLADIGPISKRDITEAEIvaEKakeyGIIAAFRVKPLSGIEI---PE 430
                                   6679********************8.....5*******************8866224467***********99986...57 PP

                                   TSEEEEESSHHHHHHHHH CS
                          IF-2  88 gvkirlynvIYkliddvk 105
                                   ++k+++ ++IY+l+d+++
  gi|70606498|ref|YP_255368.1| 431 KIKLISDDIIYQLMDNIE 448
                                   8**************985 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   4.6e-13   5.9e-10       1      74 []     251     330 ..     251     330 .. 0.95
   2 ?    0.7   0.2      0.56   7.2e+02      30      60 ..     507     539 ..     487     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 4.6e-13
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGSSTT CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea..........vaganaGvivaikgledaiivG 70 
                                   G +a++++y+G+l+k+d +++ g ++    +ivt++++++++++ +d+           ++ a+ Gv+v + +le+a ++G
  gi|70606498|ref|YP_255368.1| 251 GYTADVVIYEGILRKNDIIVLAGiDG----PIVTKVRAILVPRPLQDIKlaksdlaqidEVYAASGVKVYAQNLETA-LAG 326
                                   779******************99776....9*****************9***************************8.*** PP

                                   CEEE CS
                   GTP_EFTU_D2  71 dtlt 74 
                                   ++++
  gi|70606498|ref|YP_255368.1| 327 SPIY 330
                                   9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.56
                                   E..EEEEEEEEEEETEEESEEETTSEEEEEEEE CS
                   GTP_EFTU_D2  30 e..ivtrissletfhededeavaganaGvivai 60 
                                       v+++ +++ +++ +d a +g  + v +++
  gi|70606498|ref|YP_255368.1| 507 DgrRVGEVLQIQDNKKSVDRASKGMEVAVSIKG 539
                                   234789999999999999999999988888876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   9.5e-10   1.2e-06       2     114 .]      14     137 ..      13     137 .. 0.72
   2 ?   -0.9   0.0       1.3   1.7e+03      69      99 ..     431     456 ..     363     470 .. 0.48

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9.5e-10
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTS.SSSEEEEEEE...ETTEE..................EEEEECGGCSSHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgt.Trdinegrvk...lkgke..................ielvDtpGliega 60 
                                   v+++G+   GK+tL+ ++ g +a v+++pg  T+++    v    +   e                  + ++DtpG  e  
  gi|70606498|ref|YP_255368.1|  14 VVVLGHVDHGKTTLLDKIRG-TAVVKKEPGEmTQEVGASFVPtsvI---EkiseplkksfpikleipgLLFIDTPG-HE-- 87 
                                   899***************98.5778888865155554443333331...1334456666777777777********.44.. PP

                                   HHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  61 seekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                        +++  ++  + ad+++lvvd+  e+++++  e  e+l+++k p+i+++nk
  gi|70606498|ref|YP_255368.1|  88 ---L-FSNLRKRGGSvADIAILVVDIV-EGIQKQTLESIEILKSRKVPFIVAANK 137
                                   ...2.222222222348********99.7799999999999999*********98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                   HHHHHHCTSEEEEEEETTTTCSHHHHHHHHH CS
                      MMR_HSR1  69 aflaleeadlillvvdaseeklkpldeelee 99 
                                   +++ +   d+i  ++d + ek+    e+++e
  gi|70606498|ref|YP_255368.1| 431 KIKLIS-DDIIYQLMD-NIEKY---IEDIKE 456
                                   222222.266666666.32323...233333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.5e-07   0.00033       2     119 ..      14     139 ..      13     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                                   EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSGGCTTB.TTTTCEEEEE.....EEE-SGGCTTTT CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkikgvend.kkvkkvklni.....WDtaGqerfrsl 72 
                                   vv++G    GKt+ll+++    + +ke    ++ +g++f+ ++v  i+++++  kk   +kl+i      Dt G+e f++l
  gi|70606498|ref|YP_255368.1|  14 VVVLGHVDHGKTTLLDKIRGTAVVKKEpgemTQEVGASFVPTSV--IEKISEPlKKSFPIKLEIpgllfIDTPGHELFSNL 92 
                                   799**************999887665422227899****99887..444443312223366654333328*********** PP

                                   -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                           Roc  73 hplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                   ++   + a++ailv+d  +    k+ l++++   + k p+i+ +nkiD
  gi|70606498|ref|YP_255368.1|  93 RKRGGSVADIAILVVDIVEG-IQKQTLESIEILKSrKVPFIVAANKID 139
                                   ****************7543.33456888988766256899999***9 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.2e-06     0.012       3     119 ..      15     173 ..      13     223 .. 0.61
   2 ?   -3.3   0.0       4.5   5.8e+03      88     107 ..     445     465 ..     442     472 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.2e-06
                                   EEEESTTSSHHHHHHHHHHSSCSS....SCTTTSSEEEEEEEEEET.......TEEEEEEE.....EEETTSGGGHHHHHH CS
                           Ras   3 vlvGdsavGKtslllrfvkdkFke....eyesTigvdfytkeievd.......gkevklei.....wDTAGqeefkslrel 67 
                                   v++G    GKt+ll +       +    e+++ +g+ f  +++  +       +  +klei      DT G e f++lr+ 
  gi|70606498|ref|YP_255368.1|  15 VVLGHVDHGKTTLLDKIRGTAVVKkepgEMTQEVGASFVPTSVIEKiseplkkSFPIKLEIpgllfIDTPGHELFSNLRKR 95 
                                   6777777777777755433333220000334445555444444333444454444566665444448************** PP

                                   HHTTESEEEEEEETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG............................. CS
                           Ras  68 yyrdaegillvyditsresfenvk.kwveeikrvaeenvpivLvGnKvDlee............................. 118
                                     + a+ ++lv di +      ++ + +e i+  ++++vp+++ +nK+D  +                             
  gi|70606498|ref|YP_255368.1|  96 GGSVADIAILVVDIVEG-----IQkQTLESIEILKSRKVPFIVAANKIDRINgwkaqdtysflesinkqeqrvrdnldkqv 171
                                   **************865.....4436677777777888***********88877777777776666666555555555555 PP

                                   .G CS
                           Ras 119 .k 119
                                    +
  gi|70606498|ref|YP_255368.1| 172 yN 173
                                   50 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                                   HTHHHHHHHHHHHST.TTSEE CS
                           Ras  88 envkkwveeikrvae.envpi 107
                                   +n++k++e+ik+  + ++++ 
  gi|70606498|ref|YP_255368.1| 445 DNIEKYIEDIKESEKrKTLET 465
                                   689999999998877444444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0055         7      16      44 ..      13      41 ..       2      49 .. 0.84
   2 !    8.2   0.1    0.0012       1.6     104     144 ..     118     157 ..      82     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0055
                                  EEEEEESTTSSHHHHHHHHHHSSCEECSS CS
                           Arf 16 rilllGLDnaGKtTilkklkleelvttvP 44
                                   +++lG    GKtT+l k++   +v+  P
  gi|70606498|ref|YP_255368.1| 13 IVVVLGHVDHGKTTLLDKIRGTAVVKKEP 41
                                  57999*999***********999999988 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                                   HHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGG CS
                           Arf 104 LkalleeeelkevallvlaNKqDlpealseeelrellglee 144
                                   L++ +e  + ++v+++v aNK+D  +  ++++  + l+  +
  gi|70606498|ref|YP_255368.1| 118 LES-IEILKSRKVPFIVAANKIDRINGWKAQDTYSFLESIN 157
                                   333.45566789************99999998887776544 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.7e-05     0.073       1      34 [.      14      47 ..      14      49 .. 0.94
   2 ?    0.2   0.0      0.54     7e+02      96     111 ..      71      86 ..      55     138 .. 0.81
   3 ?   -3.8   0.0       9.3   1.2e+04      62      80 ..     335     353 ..     325     370 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                  EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                  ++v+G++ +GK+++l+++ g ++  ++p+ +T+ 
  gi|70606498|ref|YP_255368.1| 14 VVVLGHVDHGKTTLLDKIRGTAVVKKEPGEMTQE 47
                                  79***************************99975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.54
                                   EETTS-SEEEEE---B CS
                     Dynamin_N  96 lsllvkgltlvDlPGl 111
                                    +l  +gl ++D+PG 
  gi|70606498|ref|YP_255368.1|  71 IKLEIPGLLFIDTPGH 86 
                                   566778999*****96 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 9.3
                                   B--CHHHHHHHHHHHHHHH CS
                     Dynamin_N  62 ledfsevreeieketekia 80 
                                    e+++++++ i++e + + 
  gi|70606498|ref|YP_255368.1| 335 NEEVEKYKKIIQEEVSAVR 353
                                   3444444444544444444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   2.2e+03       1      16 [.      16      31 ..       7      44 .. 0.72
   2 !   13.6   0.0   3.3e-05     0.042      96     235 ..      81     218 ..      49     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                    ATP_bind_1  1 vvGpaGsGKttfvgal 16
                                  v+G++  GKtt+  ++
  gi|70606498|ref|YP_255368.1| 16 VLGHVDHGKTTLLDKI 31
                                  5677777777777665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.3e-05
                    ATP_bind_1  96 fDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek.lek 175
                                   +DtPG   + ++++ +         ++a +++ +vD     +     +++l ++ ++ + ++P++v+ nk+D ++   ++ 
  gi|70606498|ref|YP_255368.1|  81 IDTPGHELFSNLRKRGG--------SVADIAILVVDIVEGIQ-----KQTLESIEILKSRKVPFIVAANKIDRINGWkAQD 148
                                   55555544444444444........44555555555433333.....345666799999*************998555444 PP

                    ATP_bind_1 176 eleffedvealslllekee.............ekykklaeaiaelleefalvlrflplssekeesiedllsli 235
                                      f+e +++ ++     +              + +  +++  + + +f+ +  ++p+s++++e+i ++l+ +
  gi|70606498|ref|YP_255368.1| 149 TYSFLESINKQEQRV---RdnldkqvynlviqLAEQGFNAERFDRIRDFTKTVAIIPVSAKTGEGIAEVLAIL 218
                                   444444443333332...12245688988886444556667778899999999**************999865 PP

>> JLPA  Adhesin from Campylobacter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.6e-05     0.072     149     178 ..     148     177 ..     130     191 .. 0.85
   2 ?   -0.4   0.1      0.35   4.5e+02      58     111 ..     296     349 ..     286     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                          JLPA 149 ytlsfdnsinkqennyldnldikfynakln 178
                                    t sf +sinkqe+   dnld ++yn  ++
  gi|70606498|ref|YP_255368.1| 148 DTYSFLESINKQEQRVRDNLDKQVYNLVIQ 177
                                   4789**********************7665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.35
                          JLPA  58 ltkdnndeyqelfqaknikirsneiykgkanasisikeyyndlfknqksiqsnl 111
                                   l+k +  + +e++ a  +k+ ++++    a + i + e  +++ k +k iq ++
  gi|70606498|ref|YP_255368.1| 296 LAKSDLAQIDEVYAASGVKVYAQNLETALAGSPIYVAENNEEVEKYKKIIQEEV 349
                                   5677777889999**************************999999999999765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0016         2       4      27 ..      14      37 ..      11      51 .. 0.85
   2 ?   -2.6   0.0       3.2   4.1e+03      40      47 ..      80      87 ..      79     126 .. 0.61
   3 ?   -2.3   0.0       2.5   3.2e+03     122     141 ..     199     218 ..     177     219 .. 0.87
   4 ?   -1.4   0.0       1.4   1.7e+03      86     108 ..     353     375 ..     336     384 .. 0.74
   5 ?   -0.5   0.0      0.72   9.3e+02      93     140 ..     391     434 ..     383     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                     PduV-EutP  4 illiGkvgsGKttLtqalkgeelk 27
                                  ++++G+v+ GKttL  +++g ++ 
  gi|70606498|ref|YP_255368.1| 14 VVVLGHVDHGKTTLLDKIRGTAVV 37
                                  899***************998765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                     PduV-EutP 40 viDtPGey 47
                                  +iDtPG  
  gi|70606498|ref|YP_255368.1| 80 FIDTPGHE 87
                                  59999963 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                     PduV-EutP 122 kifevsavekegieellkyl 141
                                    i+ vsa + egi e+l+ l
  gi|70606498|ref|YP_255368.1| 199 AIIPVSAKTGEGIAEVLAIL 218
                                   58899999*****9998776 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.4
                     PduV-EutP  86 svfnkeviGiitkidlaedeeni 108
                                   +  n  v Gii k+d   + e+i
  gi|70606498|ref|YP_255368.1| 353 RYYNSSVYGIIVKADSLGSLEAI 375
                                   56788899****99987655544 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.72
                     PduV-EutP  93 iGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                                   iG i k d++    + e+v e+ k+ G+   f+v+ ++ + i e +k 
  gi|70606498|ref|YP_255368.1| 391 IGPISKRDIT----EAEIVAEKAKEYGIIAAFRVKPLSGIEIPEKIKL 434
                                   6667777777....677888999999********99999998876655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0     0.002       2.6      92     125 ..       4      37 ..       1      63 [. 0.84
   2 ?   -2.3   0.0       2.8   3.6e+03     150     162 ..      76      87 ..      70      91 .. 0.75
   3 ?    3.9   0.3     0.035        45      14      97 ..      98     178 ..      86     185 .. 0.76
   4 ?   -1.9   0.1       2.1   2.6e+03      52      99 ..     295     347 ..     292     352 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                                   HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                   RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpelel 125
                                   ++ ++l++ ++v++G+   GK+tL++++++++ +
  gi|70606498|ref|YP_255368.1|   4 QVPKRLRQPIVVVLGHVDHGKTTLLDKIRGTAVV 37 
                                   56788999********************998644 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                                   TTTEEEESS-SSS CS
                   RsgA_GTPase 150 aegglliDtPGfr 162
                                   + g l iDtPG +
  gi|70606498|ref|YP_255368.1|  76 P-GLLFIDTPGHE 87 
                                   4.6778*****65 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.035
                                   ES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHH CS
                   RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelk 94 
                                   +  d +++vv ++ + +++++l+  + ++++++++ +++ nKiD ++  + ++++ + le+++ +   v+ +  +++ +l 
  gi|70606498|ref|YP_255368.1|  98 SVADIAILVVDIV-EGIQKQTLES-IEILKSRKVPFIVAANKIDRINGWK-AQDTYSFLESINKQEQRVRDNLDKQVYNLV 175
                                   5567788888888.7888888875.677899****************999.788888888888777777666666666666 PP

                                   HHC CS
                   RsgA_GTPase  95 ell 97 
                                    +l
  gi|70606498|ref|YP_255368.1| 176 IQL 178
                                   555 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.1
                                   EEE-GGG--HHH.......HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                   RsgA_GTPase  52 vlnKiDlleeee.......eleelkeelealgyevllvsaktkegleelkellkd 99 
                                    l K Dl++ +e       ++ +++ e++ +g ++++   +++e++e+ k+ +++
  gi|70606498|ref|YP_255368.1| 295 KLAKSDLAQIDEvyaasgvKVYAQNLETALAGSPIYVA--ENNEEVEKYKKIIQE 347
                                   46666666666655444222222222222233333333..334555555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00046      0.58      18     160 ..      10     196 ..       7     231 .. 0.69
   2 ?   -2.7   2.3       5.5   7.1e+03     160     160 ..     433     433 ..     292     467 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                        AAA_23  18 skgltlItGpNGaGKTTildAikl.aLygetprlsrks.grgfeksdveiesegkvkay..velt..............fe 80 
                                    ++++++ G+   GKTT+ld i+  a   + p++ +++ g +f+  +v  + ++  k++  ++l+              f+
  gi|70606498|ref|YP_255368.1|  10 RQPIVVVLGHVDHGKTTLLDKIRGtAVVKKEPGEMTQEvGASFVPTSVIEKISEPLKKSfpIKLEipgllfidtpghelFS 90 
                                   6899*******************6255555565555555667776666544443444443677777777766666666644 PP

                        AAA_23  81 nkdgry................................trsiererelskkkgkttkkaklelleideleqfisellgskk 129
                                   n ++r                                   +i    +  + +g + +++  +l +i+++eq+++++   +k
  gi|70606498|ref|YP_255368.1|  91 NLRKRGgsvadiailvvdivegiqkqtlesieilksrkVPFIVAANKIDRINGWKAQDTYSFLESINKQEQRVRDN--LDK 169
                                   4444445667777777777766666666666666655545555555555566666677777777778888888886..456 PP

                        AAA_23 130 iilnlilflgqerfeefelkdkkerleelek 160
                                   +  nl++ l+++ f    ++++++r+++++k
  gi|70606498|ref|YP_255368.1| 170 QVYNLVIQLAEQGF----NAERFDRIRDFTK 196
                                   77788888888877....6777777777776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                        AAA_23 160 k 160
                                   k
  gi|70606498|ref|YP_255368.1| 433 K 433
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 4017.11
//
Query:       gi|70606499|ref|YP_255369.1|  [L=145]
Description: nucleoside diphosphate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-57  193.5   0.1    1.7e-57  193.2   0.1    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.1   9.2e-62   1.7e-57       1     132 [.       4     135 ..       4     137 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 9.2e-62
                                   EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHH CS
                           NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaie 81 
                                   +rt+v+iKPd+v+r+l+geiisr+e++g++i+alkm+++++++ae++Y+ehkgk ff+el++++ sgpvv++++eg+da++
  gi|70606499|ref|YP_255369.1|   4 QRTFVMIKPDGVRRRLVGEIISRFEKRGFNILALKMVHMDRATAERLYQEHKGKGFFNELINYIISGPVVCMIIEGDDAVS 84 
                                   79******************************************************************************* PP

                                   HHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTG CS
                           NDK  82 kvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFke 132
                                   +vr++iGat+p+ea+pgtiR+d+++s +eN++H+Sdsee+a+ e+++fF++
  gi|70606499|ref|YP_255369.1|  85 VVRKMIGATDPKEASPGTIRGDYALSKSENVIHASDSEEKAKTEMGIFFQD 135
                                   *************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1023.74
//
Query:       gi|70606500|ref|YP_255370.1|  [L=62]
Description: 50S ribosomal protein L24e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-22   79.9   0.4    1.3e-22   79.7   0.4    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    6.7e-07   29.1   1.7    1.1e-06   28.5   1.7    1.3  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    0.00022   20.7   0.7    0.00042   19.7   0.7    1.4  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
     0.0014   18.7   0.0     0.0027   17.8   0.0    1.5  2  YHS             YHS domain
      0.003   17.6   0.0     0.0051   16.9   0.0    1.3  1  zf-MYND         MYND finger
  ------ inclusion threshold ------
      0.017   15.6   0.0      0.017   15.5   0.0    1.1  1  HZS_alpha       Hydrazine synthase alpha subunit middle domai
      0.039   14.3   0.0      0.043   14.2   0.0    1.1  1  DUF3268         zinc-finger-containing domain
      0.048   13.5   3.3       0.27   11.1   3.3    2.0  1  VATC            Vms1-associating treble clef domain
        0.1   12.9   0.0       0.11   12.8   0.0    1.1  1  DUF2175         Uncharacterized protein conserved in archaea 


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.4   6.7e-26   1.3e-22       3      55 ..       4      57 ..       2      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 6.7e-26
                                  X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT CS
                Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkay 55
                                  t++CsF+g+ i PG+G ++vrnDg+ + F+ssKc +++ k +r P+klkWTk y
  gi|70606500|ref|YP_255370.1|  4 TRQCSFCGKDILPGTGLMYVRNDGSLLWFCSSKCrKSMLKLHRDPKKLKWTKSY 57
                                  89********************************9999**************98 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   1.7   5.5e-10   1.1e-06       3      40 ..       4      40 ..       3      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.5e-10
                        zf-FCS  3 kkrCwfCkkyikgkpeftyvlendgvvgqFCStsClds 40
                                  ++ C+fC+k+i  ++    ++ ndg+   FCS+ C++s
  gi|70606500|ref|YP_255370.1|  4 TRQCSFCGKDILPGT-GLMYVRNDGSLLWFCSSKCRKS 40
                                  689************.6899****************98 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.7   2.1e-07   0.00042      14      49 ..       5      43 ..       4      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                        zf-FLZ 14 saCflCkkkLgegkDiymYrGdka...FCSeeCRqqqie 49
                                  ++C++C k++ +g      r d     FCS+ CR+  ++
  gi|70606500|ref|YP_255370.1|  5 RQCSFCGKDILPGTGLMYVRNDGSllwFCSSKCRKSMLK 43
                                  68************9866676765777*******98766 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0027       6      35 ..      10      39 ..       9      50 .. 0.94
   2 ?   -1.9   0.0       1.9   3.7e+03       6      11 ..      47      52 ..      42      60 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                  cg+++ +++   +++ +G+   FcS +C+ 
  gi|70606500|ref|YP_255370.1| 10 CGKDILPGTGLMYVRNDGSLLWFCSSKCRK 39
                                  ****************************75 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                           YHS  6 cgmkvd 11
                                  +++k++
  gi|70606500|ref|YP_255370.1| 47 DPKKLK 52
                                  455552 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.6e-06    0.0051      10      35 ..       4      46 ..       2      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                  SCE-TTT.................S-SEESSHHHHHHCHHHHC CS
                       zf-MYND 10 lkkCagC.................ksvfYCskeCqradwksHk 35
                                  +++C+ C                 +  ++Cs++C+++  k H+
  gi|70606500|ref|YP_255370.1|  4 TRQCSFCgkdilpgtglmyvrndgSLLWFCSSKCRKSMLKLHR 46
                                  679****99999999999999998899**********999998 PP

>> HZS_alpha  Hydrazine synthase alpha subunit middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   8.8e-06     0.017      44      88 ..      18      62 .]       3      62 .] 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                     HZS_alpha 44 lGevpveeDGSavfevpadtplllqaldengkavqtmrswltvkP 88
                                   G ++v++DGS + +  ++   ++  l  + k +++++s+l +kP
  gi|70606500|ref|YP_255370.1| 18 TGLMYVRNDGSLLWFCSSKCRKSMLKLHRDPKKLKWTKSYLGAKP 62
                                  5889************************************99998 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.1e-05     0.043       2      46 ..       4      48 ..       3      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                       DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylC.pkCd.ayvgvhkgt 46
                                  t +C++CG+ + l     +Y  r+ g+ll+ C  kC  +  ++h++ 
  gi|70606500|ref|YP_255370.1|  4 TRQCSFCGKDI-LPGTGLMY-VRNDGSLLWFCsSKCRkSMLKLHRDP 48
                                  679*****986.55667889.999999*****989962556677665 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.3   0.00014      0.27       3      31 ..       4      37 ..       2      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                          VATC  3 vlrCsiCgeslegkv..yFekfdfr...YCstkC 31
                                  +++Cs+Cg+++++ +   + + d +   +Cs kC
  gi|70606500|ref|YP_255370.1|  4 TRQCSFCGKDILPGTglMYVRNDGSllwFCSSKC 37
                                  799*********96656777777655669****9 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.6e-05      0.11       4      49 ..       6      52 ..       4      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                       DUF2175  4 kCyiCgkeivegekFTft.kkgvvHyeClvekarkklkesedaaaLl 49
                                  +C++Cgk+i  g    ++ ++g+  + C  +  ++ lk + d + L+
  gi|70606500|ref|YP_255370.1|  6 QCSFCGKDILPGTGLMYVrNDGSLLWFCSSKCRKSMLKLHRDPKKLK 52
                                  7**************9999*********8877777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 423.61
//
Query:       gi|70606501|ref|YP_255371.1|  [L=84]
Description: 30S ribosomal protein S28e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-31  108.2   2.3    1.7e-31  108.0   2.3    1.1  1  Ribosomal_S28e  Ribosomal protein S28e
  ------ inclusion threshold ------
       0.24   11.4   2.4       0.64   10.1   0.1    2.3  2  KOW             KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   2.3   1.9e-35   1.7e-31       4      64 .]      20      80 ..      17      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 1.9e-35
                                  EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                   +AeVi++l rtG++GevtqVrv++leg+dkgri++RnVkGPvr GDiL+L+EterEAr+L
  gi|70606501|ref|YP_255371.1| 20 FPAEVIQILDRTGVTGEVTQVRVRVLEGRDKGRILTRNVKGPVRLGDILILRETEREARKL 80
                                  58**********************************************************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.064   5.7e+02      14      22 ..      32      40 ..      29      40 .. 0.87
   2 ?   10.1   0.1   7.1e-05      0.64       5      16 ..      42      53 ..      41      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.064
                                  TCEEEEEEE CS
                           KOW 14 GktGkVvkv 22
                                  G tG+V++v
  gi|70606501|ref|YP_255371.1| 32 GVTGEVTQV 40
                                  89****997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 7.1e-05
                                  EEESSSTTTTCE CS
                           KOW  5 VkVvsGphkGkt 16
                                  V+V+ G++kG++
  gi|70606501|ref|YP_255371.1| 42 VRVLEGRDKGRI 53
                                  9*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 602.22
//
Query:       gi|70606502|ref|YP_255372.1|  [L=216]
Description: uracil phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-53  180.8   0.0    2.6e-53  180.5   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
      2e-11   43.6   0.1    2.8e-11   43.2   0.1    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.085   12.4   0.0       0.15   11.6   0.0    1.4  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   0.0   4.4e-57   2.6e-53       1     206 [.       5     216 .]       5     216 .] 0.95

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 4.4e-57
                       UPRTase   1 vsshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysg.elldeekialVpilRaGeg 80 
                                   v+s+p+l + lt+lR++++++ +fr+ + +++r++++e+++  l +e+ +v+tplg++ +g  + d e+i++++ilRa  +
  gi|70606502|ref|YP_255372.1|   5 VLSKPILLHFLTQLRSKNIDQISFRKNLVKLGRIIGYEIVNT-LDYESIDVETPLGTKAKGiYIYDLENILIISILRAATP 84 
                                   6789*************************************9.******************6667789************* PP

                       UPRTase  81 meealrellpearvghlglqreeet........lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeek 153
                                   ++e+l+++lp+ar+g +   r+e++             yy k+P+  +++tv++ Dp+iaTG+++ +ai+ + +   + ++
  gi|70606502|ref|YP_255372.1|  85 FVEGLLKALPTARLGVIAASRKEKEvqvgypedIPVDVYYMKIPQVSHKDTVIIADPMIATGSTMRKAIKSIVN--SQPKR 163
                                   ***********************997777777433449************************************..899** PP

                       UPRTase 154 IlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                   I ++sv+ se g+krl+eefp v+++t +vD+e+d++g+i+pGlGD+GDR Fg
  gi|70606502|ref|YP_255372.1| 164 IYIASVIISEYGLKRLMEEFPFVDIFTISVDPEIDNRGFILPGLGDAGDRAFG 216
                                   ****************************************************7 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   4.7e-15   2.8e-11      26     144 ..      68     192 ..      56     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.7e-15
                                   --GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE...........EE----TTSEEEEE-SEESSSHH CS
                  Pribosyltran  26 yngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdes...rlledpagkkVliVDDildtGgT 102
                                   y+ ++ +++ i+r + pf+  l ++L +++l ++ +++++++++ + ++ + +     + +    + +V+i D +++tG+T
  gi|70606502|ref|YP_255372.1|  68 YDLENILIISILRAATPFVEGLLKALpTARLGVIAASRKEKEVQVGYPEDIPVDVyymKIPQVSHKDTVIIADPMIATGST 148
                                   57799*********************99999999999999999999986555544998999999999************** PP

                                   HHHHHHHHHCC-BSEEEEEEEE..E-HHHHHHHHHH-TTS.... CS
                  Pribosyltran 103 llaalelLkekgpeevriavlv..dkpateeevdknakrvfsls 144
                                   +++a++ + +  p+++ ia ++  + + +++ +++ ++ +f++s
  gi|70606502|ref|YP_255372.1| 149 MRKAIKSIVNSQPKRIYIASVIisEYGLKRLMEEFPFVDIFTIS 192
                                   *******************9998877777777777777777666 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.5e-05      0.15     115     156 ..     127     168 ..      69     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                      PRTase_2 115 eellaaakelvLvDDEistGktalnliralqeklprkryvvv 156
                                     ++++++++++ D  i+tG+t+ + i+++ ++ p++ y+  
  gi|70606502|ref|YP_255372.1| 127 IPQVSHKDTVIIADPMIATGSTMRKAIKSIVNSQPKRIYIAS 168
                                   456788999***********************9998766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1591.68
//
Query:       gi|70606503|ref|YP_255373.1|  [L=472]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-96  323.6   0.0    1.4e-96  323.0   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    9.9e-41  139.1   7.5    9.9e-41  139.1   7.5    2.1  2  GatB_Yqey  GatB domain
     0.0026   17.9   1.0     0.0052   16.9   1.0    1.4  1  Med7       MED7 protein


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.0   0.0  2.4e-100   1.4e-96       1     273 []       2     285 ..       2     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 323.0 bits;  conditional E-value: 2.4e-100
                                   EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TC CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfy 80 
                                   ++iGlE+H++l++ k+KlF+s++te  g++pn+ +++v+l+lPG++Pvln++av+ ai++ala+n+eia+++ + RK+yfy
  gi|70606503|ref|YP_255373.1|   2 VKIGLEVHVHLTSlKTKLFCSCPTEYVGKDPNTITCPVCLGLPGAIPVLNENAVRAAIMVALAINAEIADRVVMVRKHYFY 82 
                                   58*********999*********8889999*************************************************** PP

                                   TTCTTSEEEEESSS.....SEEEEEEEE..TEEEEEEEEEEEE---EEEE.....EETTEEEEETTSTT-EEEEEEE-STB CS
                                   xxxxxxxxxxxxxxx....xxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N  81 pdlpkgyQitqkeep....lakeGslel..ekkvrierihlEeDaaksvh.....eekeeslvdlnRaGvpLiEivtepdl 150
                                   pd++k+yQi+q++ p    + k+G ++l  +k++ri+ri++EeD ak v+      +++++l+d+nR+G pL+Eivtepd+
  gi|70606503|ref|YP_255373.1|  83 PDMAKNYQISQYDGPgsiaISKGGFIKLrdNKTIRIRRINIEEDPAKIVYptgsmLTSRYTLLDYNRSGFPLLEIVTEPDM 163
                                   ************97655436699999999899******************999873566********************** PP

                                   -SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                        GatB_N 151 rspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell.. 229
                                   ++p+ear+++eklr++l++lg+s+ ++ eG++R+D+N+S++        g+rvEiKn+ s k++e+a++yei rq +l+  
  gi|70606503|ref|YP_255373.1| 164 SDPREAREFLEKLRSILEHLGISNPDL-EGAMRADANISIEG-------GERVEIKNIGSPKEVEEALKYEIARQKALVaq 236
                                   ***************************.7************4.......49****************************** PP

                                   .....-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 .....qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                                        +eTr++d++k+ tv  Rske +edYryfp+pdlpp+++s ++ie
  gi|70606503|ref|YP_255373.1| 237 gmkvnRETRHWDNAKKVTVLTRSKELEEDYRYFPDPDLPPYTVSFDMIE 285
                                   *************************99****************998885 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.15   9.1e+02     106     131 ..     216     241 ..     207     256 .. 0.74
   2 !  139.1   7.5   1.6e-44   9.9e-41       1     148 []     324     470 ..     324     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                   HHHHHHHTTXXTTSTHHHHHHHHHTT CS
                     GatB_Yqey 106 pkavedyksgkekalkflvGqvMkkt 131
                                   pk+ve+  + +    k+lv q Mk  
  gi|70606503|ref|YP_255373.1| 216 PKEVEEALKYEIARQKALVAQGMKVN 241
                                   56677777777777788888888765 PP

  == domain 2  score: 139.1 bits;  conditional E-value: 1.6e-44
                                   HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHH CS
                     GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiie 81 
                                   d+fee++k++++ k+++n l+n+ l+ ln ++l+ +++k t ++l ell+l+++g+I+ kiake+l++++ egk p+eii+
  gi|70606503|ref|YP_255373.1| 324 DLFEETAKNYKNYKKLVNILINDYLRWLNDKNLKPSQSKATTKHLIELLTLLDNGTITIKIAKEILPQIVIEGKMPSEIIK 404
                                   79******************************************************************************* PP

                                   HCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                     GatB_Yqey  82 ekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                   ++ L +i+de+ l ++++ev++e+++ave+ k+ + k++++lvG+vMkkt  +adp +vnel+k++L
  gi|70606503|ref|YP_255373.1| 405 QNSLIAIKDEDYLINVIKEVLSEEKDAVEKAKRDP-KVINYLVGKVMKKTSKRADPYIVNELIKKEL 470
                                   *******************************9999.8****************************98 PP

>> Med7  MED7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   8.7e-07    0.0052      29     143 ..     237     372 ..     220     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.7e-07
                          Med7  29 aekeeeeeedesaae.....eqelelpkeLrvlipPeppkegeYrv.FGenwsllkdklpsLeeqgieqly.......... 93 
                                    +k + e+++ ++a+     ++++el ++ r++  P++p    Y+v F+   ++  ++lp+L +  i++l+          
  gi|70606503|ref|YP_255373.1| 237 GMKVNRETRHWDNAKkvtvlTRSKELEEDYRYFPDPDLP---PYTVsFDMIEKI-RKELPELPDIRIQRLVkeygiteyda 313
                                   444443333333333456666676777888999999999...676549999996.****************9999999999 PP

                          Med7  94 ...........eedesedrkkeLkkLlrslllnfleLlgillknPeqsefeekvedlrlll 143
                                                +e+ +  k+ kkL++ l+  +l  l++   +P+q   ++++++l  ll
  gi|70606503|ref|YP_255373.1| 314 nvlvidksladLFEETAKNYKNYKKLVNILINDYLRWLNDKNLKPSQ--SKATTKHLIELL 372
                                   99998888876334555557778999999*********999999*88..677777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3376.60
//
Query:       gi|70606504|ref|YP_255374.1|  [L=245]
Description: hypothetical protein Saci_0701 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-16   59.7   0.1    4.1e-16   58.9   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.053   13.0   0.0      0.079   12.4   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
      0.091   12.5   0.0       0.21   11.4   0.0    1.6  1  HTH_Tnp_4     Helix-turn-helix of DDE superfamily endonucleas


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.1   6.9e-20   4.1e-16       9     136 ..     100     234 ..      93     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 6.9e-20
                                   --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.................E CS
                  Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.........r 80 
                                   p++l+   ++ + ++  ++ ++d +v++a  G+pfa i + ++  pl ++ k k  +++  + +  +++es         r
  gi|70606504|ref|YP_255374.1| 100 PNLLKLLIEMFYHKYFGNRDEIDKIVTVAVNGIPFAAIASEAIAKPLIIIKKHK--DSVHISYIDENIKESegmitsiylR 178
                                   67777888888888888899***********************99998876655..445555555555555666777799* PP

                                   E----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH CS
                  Pribosyltran  81 lledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdkn 136
                                   +   ++g+kVl+VDD++ +G+T+  +++l+ +++++++++ vlv  +  + + ++ 
  gi|70606504|ref|YP_255374.1| 179 KDFVYKGEKVLVVDDVIRSGKTIYSTFRLIQKADAKVIGALVLVGVGKEWSKISNT 234
                                   ********************************************999999888774 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.079     112     157 ..     176     221 ..     140     236 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                       UPRTase 112 ynkLPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                   y  L k++  + ++vl++D vi +G+++ +  +l++++++++   lvl
  gi|70606504|ref|YP_255374.1| 176 Y--LRKDFvyKGEKVLVVDDVIRSGKTIYSTFRLIQKADAKVIGALVL 221
                                   3..44444448889***********************88765444444 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.5e-05      0.21      16      41 ..      27      52 ..      21      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.5e-05
                     HTH_Tnp_4 16 LRlnltyqdLayrFgvsestvsrifh 41
                                  L+   ty+ L+ +F++ es  +r+++
  gi|70606504|ref|YP_255374.1| 27 LKNSYTYKELSSIFNIQESLLCRYVN 52
                                  78889*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1739.15
//
Query:       gi|70606505|ref|YP_255375.1|  [L=192]
Description: hypothetical protein Saci_0702 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 1267.90
//
Query:       gi|70606506|ref|YP_255376.1|  [L=584]
Description: radical SAM superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-20   73.9   0.1    1.9e-20   73.9   0.1    1.9  2  Radical_SAM    Radical SAM superfamily
    5.9e-06   26.4   1.3    1.4e-05   25.2   0.0    2.2  2  Fer4_14        4Fe-4S single cluster domain
    6.8e-06   26.4   0.7    1.3e-05   25.5   0.0    1.9  2  Fer4_12        4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.051   12.3   0.0       0.22   10.2   0.0    1.9  3  Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
        0.1   12.1   0.0       0.24   10.9   0.0    1.5  2  HMGL-like      HMGL-like


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   2.2         5   1.8e+04       7      18 ..     122     133 ..     122     137 .. 0.88
   2 !   73.9   0.1   5.2e-24   1.9e-20       2     166 ..     142     306 ..     141     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 5
                                   ESS--TTTSCCT CS
                                   xxxxxxxxxxxx RF
                   Radical_SAM   7 CnlrCsfCarpe 18 
                                   C+++C  C+ ++
  gi|70606506|ref|YP_255376.1| 122 CPFNCGLCPMHH 133
                                   ********9998 PP

  == domain 2  score: 73.9 bits;  conditional E-value: 5.2e-24
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgirit 81 
                                   v+t+ C l C++C ++   ++ g++ + ++e+i+  v++lk +++ + ++ ++ggep+l+ d++e+++ l+++     +i 
  gi|70606506|ref|YP_255376.1| 142 VITNRCDLSCWYCFFYA--EKAGYVFEPTLEQIKFMVDQLK-RQDvTLVIQVTGGEPTLREDIIEIVRILREN--GVKHIQ 217
                                   799*************9..5********************5.777799*************************..9***** PP

                                   EEECSSCHG..........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpd..........eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                   + + g++             ++++ l+e+gv++++++ + ++ +     +n+++ +e +  +le++r+ag+ +vv + +++
  gi|70606506|ref|YP_255376.1| 218 LNSWGGTFGrmyledpeyaIKYARQLREAGVNTIYMSFDGTTRK-----TNPKNHWE-IPYTLEAFRKAGMTSVVLVPTVI 292
                                   *******99**********************************9.....76755555.5599******************* PP

                                   TTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx RF
                   Radical_SAM 153 pGendeeleellel 166
                                   + +nd++l +++++
  gi|70606506|ref|YP_255376.1| 293 KTVNDHDLGNIVRF 306
                                   ********999988 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.6       1.2   4.3e+03       6      16 ..     120     130 ..     118     137 .. 0.78
   2 !   25.2   0.0     4e-09   1.4e-05       4      87 ..     143     220 ..     141     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                       Fer4_14   6 sgCnlsCkgCd 16 
                                   s C+++C  C 
  gi|70606506|ref|YP_255376.1| 120 SPCPFNCGLCP 130
                                   67******996 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 4e-09
                       Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    +++C lsC  C+  +++   +  + t e+++ ++++lk +++    + +tGGeP +    ++++++v+ l+e++  k+i+
  gi|70606506|ref|YP_255376.1| 143 ITNRCDLSCWYCFFYAEK-AGYVFEPTLEQIKFMVDQLKRQDVTLV-IQVTGGEPTLR---EDIIEIVRILRENG-VKHIQ 217
                                   499**********88844.445555567777788899999999666.999*****955...99***********9.45555 PP

                       Fer4_14  85 let 87 
                                   l++
  gi|70606506|ref|YP_255376.1| 218 LNS 220
                                   554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       2.4   8.5e+03       3      22 ..     110     129 ..     109     135 .. 0.77
   2 !   25.5   0.0   3.5e-09   1.3e-05       9      97 ..     141     226 ..     132     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                       Fer4_12   3 GeGvrlslfvsgCnlsCkgC 22 
                                   G++v ++ + s C+++C  C
  gi|70606506|ref|YP_255376.1| 110 GPKVPYVDLKSPCPFNCGLC 129
                                   566666667788*****988 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 3.5e-09
                       Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.egltllGGEPllpenaeallelvkevkeekpekdi 88 
                                   ++ +++C+lsC +Cf   + +  +  e t e ++ ++++lk + +   + ++GGEP l   +e+++e+v+ ++e++++   
  gi|70606506|ref|YP_255376.1| 141 LVITNRCDLSCWYCF-FYAEKAGYVFEPTLEQIKFMVDQLKRQDVtLVIQVTGGEPTL---REDIIEIVRILRENGVKHIQ 217
                                   667899*********.56666677777789999999****87666477899*******...99***********9995554 PP

                       Fer4_12  89 wlytgytle 97 
                                   + + g t+ 
  gi|70606506|ref|YP_255376.1| 218 LNSWGGTFG 226
                                   555555555 PP

>> Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.38   1.4e+03     198     226 ..      23      51 ..      18      56 .. 0.80
   2 ?   10.2   0.0   6.1e-05      0.22      83     117 ..     186     219 ..     168     224 .. 0.81
   3 ?   -3.1   0.0      0.66   2.4e+03     103     121 ..     240     256 ..     237     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.38
                                   EEEEEECTSSEEEEEEEEETTSS-EEEEE CS
                 Peptidase_S13 198 kliersfgtntlkvtGslpedaeplklsl 226
                                   +  +++fg +++kv G lp+ +++ kl++
  gi|70606506|ref|YP_255376.1|  23 EKGVVKFGDREIKVGGPLPKLSDNEKLTR 51 
                                   5567899************9998888765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.1e-05
                                   CEEEEECSBTTBBHHHHHHHHHHHHHTT-SEESS- CS
                 Peptidase_S13  83 nlvlvgsGDPtLsaedldalaeelkksGvtkiege 117
                                    ++ v +G PtL +ed+ ++++ l+++Gv++i+++
  gi|70606506|ref|YP_255376.1| 186 LVIQVTGGEPTL-REDIIEIVRILRENGVKHIQLN 219
                                   35567889***9.689****************764 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.66
                                   HHHHHHTT-SEESS-EEEE CS
                 Peptidase_S13 103 aeelkksGvtkiegelvvD 121
                                   a++l+++Gv++i   +  D
  gi|70606506|ref|YP_255376.1| 240 ARQLREAGVNTI--YMSFD 256
                                   899*******99..55555 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   5.4e+03      23     165 ..     199     218 ..     188     225 .. 0.60
   2 ?   10.9   0.0   6.7e-05      0.24      25     121 ..     236     349 ..     230     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-HHH CS
                     HMGL-like  23 eeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatselh 103
                                   e+ ++i++ L e gv+                                                                 
  gi|70606506|ref|YP_255376.1| 199 EDIIEIVRILRENGVKH---------------------------------------------------------------- 215
                                   34455555555555554................................................................ PP

                                   HHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEE CS
                     HMGL-like 104 lkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatrini 165
                                                                                              i++
  gi|70606506|ref|YP_255376.1| 216 -----------------------------------------------------------IQL 218
                                   ...........................................................444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.7e-05
                                   HHHHHHHHHHHT-SEE--......................TSGGGT.THHHHHHHS---TT-B.....--EE-SSHHHHHH CS
                     HMGL-like  25 klaiakaLdeagvdeiEv......................gfpaaseddfevvraiakavkkar...ilalvrarekdika 80 
                                    +++a++L eagv+ i +                       f+ a+ +++  v +++k+v++ +   i+  + ++++++ +
  gi|70606506|ref|YP_255376.1| 236 AIKYARQLREAGVNTIYMsfdgttrktnpknhweipytleAFRKAGMTSVVLVPTVIKTVNDHDlgnIVRFAAYNMDVV-R 315
                                   6899***********************************************************9554555555555444.3 PP

                                   HHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHH CS
                     HMGL-like  81 avealkgagakrvhvfiatselhlkaklkkdreevakkaee 121
                                   av+       + v ++  +    +++k+++++ e++k++ee
  gi|70606506|ref|YP_255376.1| 316 AVN------FQPVSLTGMMKR-NMRSKFRITIPEILKNIEE 349
                                   444......677777766666.8999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3887.95
//
Query:       gi|70606507|ref|YP_255377.1|  [L=294]
Description: thiamine-monophosphate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   48.0   0.0    2.6e-12   47.2   0.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
    0.00017   21.7   0.0    0.00025   21.2   0.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   2.9e-16   2.6e-12      23      93 ..      29     112 ..       4     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.9e-16
                                   C.......HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEEEEEEESS.EEEEEEE CS
                          AIRS  23 f.......iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgGdtsfsne.ptisvta 90 
                                   f       iG+++v +++sD+++ G+ P ++l sl l+     ++e++++g+++a++ ++ + vgGdt++s++   i ++ 
  gi|70606507|ref|YP_255377.1|  29 FnflesydIGWRSVIGVISDILSKGGSPKFFLASLGLNknrlkEIENILKGISDAINYYKGSYVGGDTNSSDNnGWIDIVG 109
                                   244555556************************************************************995446677777 PP

                                   EEE CS
                          AIRS  91 vGl 93 
                                   +G+
  gi|70606507|ref|YP_255377.1| 110 IGE 112
                                   775 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.8e-08   0.00025       1     152 [.     123     276 ..     123     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.8e-08
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH....HTTECEEEE--TTHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal....kglvkaahDvTgGGLlgala 77 
                                   k Gd++i t ++G  ++  + +   +++ + +     l   l+  ++  v+++l  +     ++++   D+++ GL+++l 
  gi|70606507|ref|YP_255377.1| 123 KRGDKVIITSPIGYNSII-FISYVNNWKISIP-----LKYKLKY-KHPIVNPHLQDIfsqnCDNIHYSLDISD-GLIVSLY 195
                                   579********9999999.7777777777776.....3333333.444455555555546667999999****.8****** PP

                                   HHHHTTTEEEEEECGTHHHHHHHH........HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C  78 emapasgvgaeidldkvpifdele........splemllsensGrllvavppeea.davlaileeeglpeaavIGevtake 149
                                   ++++ s++g+ei+    p+ +e+           l++l++  ++   ++v+ +++  +++++++  gl +  v Ge+ +++
  gi|70606507|ref|YP_255377.1| 196 NLVERSKLGIEITKM--PVSEEVLniannykiRLLDLLKFSGEEYESIFVVDKDSyHKIINQMKLLGL-NPVVFGEISDRQ 273
                                   *************99..999998877777778778888888888888888888888***********9.799*****9999 PP

                                   SEE CS
                        AIRS_C 150 els 152
                                   +++
  gi|70606507|ref|YP_255377.1| 274 GVY 276
                                   765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2196.74
//
Query:       gi|70606508|ref|YP_255378.1|  [L=452]
Description: adenylosuccinate lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-48  165.2   0.0    3.4e-48  164.6   0.0    1.3  1  Lyase_1        Lyase
    1.2e-13   51.4   0.0    3.7e-13   49.8   0.0    1.9  1  ADSL_C         Adenylosuccinate lyase C-terminus
    7.8e-06   26.0   0.7    7.8e-06   26.0   0.7    1.9  2  ASL_C          Adenylosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.0   5.8e-52   3.4e-48      10     309 ..      17     294 ..      11     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 5.8e-52
                                   HHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHH CS
                       Lyase_1  10 lmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnev 90 
                                   +++ f+ +++ + + +     +++al  a+ k++++     +  +k +++++++++l+   +++  +++ g++v + l+  
  gi|70606508|ref|YP_255378.1|  17 MRQLFSRKNIVKTMAE-----VEIALLYALSKLGLIK----ETDVKKVEDIIDKIDLN---RVDELERKLGHDVMA-LTVH 84 
                                   5555555555555555.....8888899999999988....77888888888855555...888888888888877.8888 PP

                                   HHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHH CS
                       Lyase_1  91 igellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqe 171
                                   ++el+g   e+ d++h+g++snD+++T  ++++kkal e + ++l++ i++l e ++++kd++++GrTh+q+A P+tlg +
  gi|70606508|ref|YP_255378.1|  85 MAELSG---EAGDFIHFGATSNDIIDTTNAIIVKKAL-EIVKKKLRDVITILIEYSRKYKDTIMVGRTHGQHALPITLGFK 161
                                   888888...9***************************.88***************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHH CS
                       Lyase_1 172 lsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsfeavsdrDavvellga 251
                                   ++ y+ ++ r++er+ el kr++  ++ g++++ ++ + +    +++v + l+ +     ++  ++++v++rD  +el++ 
  gi|70606508|ref|YP_255378.1| 162 FANYVYEYSRSLERIYELEKRVVRIKMAGAVGTMAAWKGHGtTIEKYVSERLG-I-----PSHIITTQVTPRDGFAELISD 236
                                   ****************************9887666655554334488888888.4.....5688999************** PP

                                   HHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHH CS
                       Lyase_1 252 lkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagr 309
                                   l++l  +L +fa +lr l+  e+++  + +a +  GSS+MP+K NPv++E + g a  
  gi|70606508|ref|YP_255378.1| 237 LAILGSQLDRFALELRELMRPEIRELAEGDASKRVGSSTMPQKENPVNAEKISGLAKV 294
                                   ********************99******************************998876 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   6.2e-17   3.7e-13       1      73 []     361     440 ..     361     440 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 6.2e-17
                                   TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC...HHCHHHHHT-GGGCCTTHHHHHHHH CS
                        ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk...seeeldalfdpayylgsadeivdrv 73 
                                   Gl ++e++++ L+ +g+ R++A+el  e+++ a ++   lle+ +++++v+k   +e++++++++p++ylg+ +++++r+
  gi|70606508|ref|YP_255378.1| 361 GLTMAESLMINLTlNGMPRHKAHELTMELSRIASNTgksLLEVAKENETVMKiigDENKIKEVLNPSKYLGEYEKLIERA 440
                                   99***********99************************************66**999******************9995 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.4e+03      81      99 ..      47      65 ..      24      76 .. 0.60
   2 !   26.0   0.7   1.3e-09   7.8e-06       4     114 ..     311     429 ..     309     430 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                                  TS---HHHHHHHHHCS-S- CS
                         ASL_C 81 gkkitkeslkefieslevs 99
                                   k+++ ++++++i++++++
  gi|70606508|ref|YP_255378.1| 47 IKETDVKKVEDIIDKIDLN 65
                                  4444555555555555544 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.3e-09
                                   T--TCHHHHHTTCH.HHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-G.GGGHHHHHHHHHHTT-T..THHHHHHHHHT CS
                         ASL_C   4 QRDLtdStvlRnlg.valahslialksllkglsklevneealaedLdenw.evlaEaiqtvlrregie..kpYeklkeltr 80 
                                    RDLt+S+  R +   ++  +   l+s+lk l++l vn+++++++L  +    +aE++ + l  +g++  k++e   el r
  gi|70606508|ref|YP_255378.1| 311 ERDLTNSSSERIIIsHSFLIIDEMLDSMLKILKNLVVNQDQMQKNLSLSKgLTMAESLMINLTLNGMPrhKAHELTMELSR 391
                                   6**********863034444444678999*****************97751579***999998888753389********* PP

                                   TS---HHHHHHHHHCS....-S-HHHHHHHHC--CCC- CS
                         ASL_C  81 gkkitkeslkefiesl....evseeakeeLkaltpatY 114
                                    ++ t +sl e+ +++    ++  ++++  + l+p++Y
  gi|70606508|ref|YP_255378.1| 392 IASNTGKSLLEVAKENetvmKIIGDENKIKEVLNPSKY 429
                                   *********99999883222233344444445677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3339.55
//
Query:       gi|70606509|ref|YP_255379.1|  [L=333]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-73  243.7   0.0    1.4e-72  243.2   0.0    1.2  1  DUF1297   Domain of unknown function (DUF1297)
    9.9e-39  132.1   0.0    1.4e-38  131.5   0.0    1.2  1  DUF1246   Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
      0.063   13.0   0.0       0.12   12.1   0.0    1.4  1  GARS_A    Phosphoribosylglycinamide synthetase, ATP-grasp (A)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.2   0.0   2.3e-76   1.4e-72       1     188 []     153     333 .]     153     333 .] 0.98

  Alignments for each domain:
  == domain 1  score: 243.2 bits;  conditional E-value: 2.3e-76
                                   HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EE CS
                       DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyv 81 
                                   e++e l++l++++li  +d+++++i+eyv+G+++++++fysp+ +++e++gid+Rye+n+dgl+rlp +       +p++v
  gi|70606509|ref|YP_255379.1| 153 EVKEGLNRLISSKLI--KDVNDVIIQEYVIGVPMYFQFFYSPILNRLEITGIDIRYETNVDGLRRLPENL-----ADPTFV 226
                                   678999*********..9*************************************************873.....59**** PP

                                   EEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS CS
                       DUF1297  82 vvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfge 162
                                   vvGnip+v REsll+kv+++g +fv+++k++vppG+iGpFcL+svv++d  +vvf++s Riv+gtn+y++gspys+l+++e
  gi|70606509|ref|YP_255379.1| 227 VVGNIPAVARESLLPKVYDYGMSFVNTVKEVVPPGMIGPFCLESVVKDDGSIVVFEFSGRIVAGTNLYIAGSPYSWLYWDE 307
                                   ********************************************************************************* PP

                                   ---HHHHHHHHHHHHHHCT-GGGCEE CS
                       DUF1297 163 plsmGrrialEikeaiekdrleeivt 188
                                   p+s+Grri++Ei+ a+++++le i t
  gi|70606509|ref|YP_255379.1| 308 PMSVGRRISREIRLALNSNKLEVIFT 333
                                   **********************9976 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   2.4e-42   1.4e-38       1     122 []       4     122 ..       4     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 2.4e-42
                                   EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-H CS
                       DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfveYvgi 81 
                                   + t++SHs+lqil+gAkkegf+t+ ++ k+r ++Y++f++ide++ +++ ++ ++     +  ++   l+Phgs+veYvg 
  gi|70606509|ref|YP_255379.1|   4 VLTIGSHSSLQILHGAKKEGFKTVQITPKNRVNFYSQFSFIDEILGYNNEDEAVEFV---NKYSNRGALIPHGSLVEYVGS 81 
                                   569**************************************************9765...566788899************ PP

                                   HHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                       DUF1246  82 ekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                   e++++++++ifGnr+l+ wE++++kk+++L+++gi++P+++
  gi|70606509|ref|YP_255379.1|  82 ERVSKITTKIFGNRNLFAWESNQKKKMSLLRRSGIQVPEEF 122
                                   **************************************986 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.12      39      95 ..     130     185 ..     109     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                   SEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEE CS
                        GARS_A  39 kalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEvs 95 
                                   + ++vK  g  +gKg  +ak+++e  + ++ ++++k      + v+i e++ G  + 
  gi|70606509|ref|YP_255379.1| 130 RLVIVKLPGAKGGKGYFIAKTKSEVKEGLNRLISSKLIK-DVNDVIIQEYVIGVPMY 185
                                   4469*****************************966665.8899******9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2024.09
//
Query:       gi|70606510|ref|YP_255380.1|  [L=349]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-82  273.3   0.0    1.1e-81  272.9   0.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
    4.4e-46  155.8   0.0    6.4e-46  155.3   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.098   12.5   0.0    1.6  2  DUF4756   Domain of unknown function (DUF4756)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.9   0.0   1.8e-85   1.1e-81       1     187 [.     161     348 ..     161     349 .] 0.99

  Alignments for each domain:
  == domain 1  score: 272.9 bits;  conditional E-value: 1.8e-85
                                   HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EE CS
                       DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyv 81 
                                   +feekl++ll+ g+i++e++k+++ieey++Ga+fnlnyfyspl+e+vel++idrR++s+ld ++rlpa+ q++l++ p+y+
  gi|70606510|ref|YP_255380.1| 161 DFEEKLNTLLKVGIIDDEAIKNMIIEEYILGAHFNLNYFYSPLHERVELISIDRRIQSDLDTFYRLPAEIQIKLSRLPRYI 241
                                   89******************************************************************************* PP

                                   EEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--CCHHHTTS CS
                       DUF1297  82 vvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gspyskllfg 161
                                   +vG++p+++REsllekvfe+g +f++a+k+l ppGiiGpF+Lq++ t++l+lvvfdv++Ri+ggtn++m+ gs+yskl+fg
  gi|70606510|ref|YP_255380.1| 242 EVGHEPATIRESLLEKVFEIGYSFINATKTLEPPGIIGPFTLQAMATPELDLVVFDVAPRIGGGTNAFMGvGSQYSKLYFG 322
                                   ********************************************************************************* PP

                                   S---HHHHHHHHHHHHHHCT-GGGCE CS
                       DUF1297 162 eplsmGrrialEikeaiekdrleeiv 187
                                   +p+s+Grria+Eikeai+++rle i+
  gi|70606510|ref|YP_255380.1| 323 RPVSLGRRIAMEIKEAINNNRLELIT 348
                                   **********************9875 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.3   0.0   1.1e-49   6.4e-46       1     122 []       5     129 ..       5     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 1.1e-49
                                   EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC- CS
                       DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqeklreenailvPhgsfveYvg 80 
                                   iatlaSHsal++++gAk+egf+t+a+c+kgre++Y +f +++d++++l++fk+i +e++ + l+e+na++vP++s+++Yvg
  gi|70606510|ref|YP_255380.1|   5 IATLASHSALDVFDGAKDEGFETIALCKKGRERAYLEFkRIVDKCVLLEDFKEISSEKIDNLLVENNALMVPNRSLAVYVG 85 
                                   89************************************8889*************************************** PP

                                   HHHHHC-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                       DUF1246  81 iekieelkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                   ++++e++k+++fGnrk+lrwEer  +k++y  L++A+i++Pk++
  gi|70606510|ref|YP_255380.1|  86 YDNLEKMKTKFFGNRKILRWEERLGNKNYYkiLDHAKIKRPKIF 129
                                   *****************************************986 PP

>> DUF4756  Domain of unknown function (DUF4756)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.098     113     146 ..      26      61 ..      18      66 .. 0.89
   2 ?   -3.9   0.0       1.8   1.1e+04      56      71 ..     208     223 ..     205     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                       DUF4756 113 eivalvikqrteaalefqrsveqs..leqlshisse 146
                                   e +al +k r  a lef+r v++   le + +isse
  gi|70606510|ref|YP_255380.1|  26 ETIALCKKGRERAYLEFKRIVDKCvlLEDFKEISSE 61 
                                   78********************97558*******98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.8
                       DUF4756  56 elrrldkkrksliekf 71 
                                   el  +d++ +s +++f
  gi|70606510|ref|YP_255380.1| 208 ELISIDRRIQSDLDTF 223
                                   7888899989888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2321.57
//
Query:       gi|70606511|ref|YP_255381.1|  [L=337]
Description: adenylosuccinate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-69  233.4   0.5    1.3e-35  123.1   0.0    3.0  3  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   1.2e-27   2.2e-23       2     142 ..       4     137 ..       3     143 .. 0.90
   2 !  123.1   0.0   7.3e-40   1.3e-35     191     332 ..     144     283 ..     137     288 .. 0.92
   3 !   25.3   0.0   3.8e-10   6.7e-06     377     418 ..     286     327 ..     283     328 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.2e-27
                                   EEEE-SSS-S-HHHHHHHH..HTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHH CS
               Adenylsucc_synt   2 vvvGaqwGDEGKGkivDll..aeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEi 80 
                                   vvvG  +GDEGKGkiv +l  +++  + vR  G  nAGHtv  +g++ k++++pS  +n++v+ ++++g + +++ l++E+
  gi|70606511|ref|YP_255381.1|   4 VVVGGFFGDEGKGKIVAYLglKDSPSIGVR-TGSINAGHTVSYNGRQWKVRIIPSLFVNKNVKLFLAPGALTSINLLFNEA 83 
                                   8******************63444556666.699*********************************************** PP

                                   TTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT- CS
               Adenylsucc_synt  81 eeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarr 142
                                   +e ++       +rl+i+ ++ ++++  ++ ++  e     k+iG+T++G+G a a++v r+
  gi|70606511|ref|YP_255381.1|  84 KETDSL------DRLYIDPHVGIITDEEIKEERSDEYLI--KNIGSTGQGVGYAEAKRVLRK 137
                                   *99873......69************9999999999865..59*************999986 PP

  == domain 2  score: 123.1 bits;  conditional E-value: 7.3e-40
                                   HHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESS CS
               Adenylsucc_synt 191 aerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvG 271
                                    ++l++y++++ ++l   +++g+++L+EG qgt+l++ hG YP++Ts ntta+g+l+ +g++pk++de++ v+K+y+trvG
  gi|70606511|ref|YP_255381.1| 144 YRELEKYLINVPEELLLGIERGDNILVEGTQGTFLSLYHGEYPYTTSRNTTASGILSEAGIGPKYVDEIIVVFKSYVTRVG 224
                                   467899999999********************************************************************* PP

                                   SS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGG CS
               Adenylsucc_synt 272 eGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvl 332
                                   eGp+  e++ e+++k+    +E+ t+tgr+Rr   + + l++++ ++n++t++a+tklD++
  gi|70606511|ref|YP_255381.1| 225 EGPLEGEISWEEAQKM--GIAEVATVTGRKRRSAPFNVKLAKESLKINSATQIAITKLDTI 283
                                   *******966666666..346**************************************86 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 3.8e-10
                                   --TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-E CS
               Adenylsucc_synt 377 disgvrsfedlpenakkyvefieellgvpvkiisvGpereqt 418
                                   d +gvr++++lp+nakk++e +e +l+vp+++i++G++  ++
  gi|70606511|ref|YP_255381.1| 286 DAKGVREYQKLPSNAKKWIEELETELKVPITLIGTGEDALDV 327
                                   6799********************************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2197.41
//
Query:       gi|70606512|ref|YP_255382.1|  [L=467]
Description: hypothetical protein Saci_0710 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-15   56.8   0.1    6.4e-05   22.3   0.0    3.1  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.5e-09   37.1   0.0    8.4e-05   21.4   0.0    2.3  2  HI0933_like     HI0933-like protein
      2e-09   37.2   0.4    0.00092   18.6   0.1    3.1  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.7e-09   35.5   1.0    6.7e-05   22.1   0.0    2.9  3  GIDA            Glucose inhibited division protein A
    8.3e-06   25.6   0.1     0.0019   17.9   0.0    2.6  3  DAO             FAD dependent oxidoreductase
    0.00015   21.0   0.0    0.00046   19.3   0.0    1.7  2  Lycopene_cycl   Lycopene cyclase protein
    0.00015   22.3   0.1        1.5    9.4   0.1    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00023   20.5   0.2     0.0016   17.8   0.0    2.2  2  Thi4            Thi4 family
    0.00045   19.4   0.9     0.0013   17.9   0.0    2.1  3  FAD_binding_2   FAD binding domain
    0.00045   20.4   0.0     0.0019   18.4   0.0    2.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0025   17.8   0.0      0.066   13.2   0.0    2.2  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
       0.01   15.1   0.1      0.029   13.6   0.0    1.7  2  FAD_binding_3   FAD binding domain
      0.061   12.2   0.0       0.16   10.8   0.0    1.6  2  Trp_halogenase  Tryptophan halogenase
       0.12   11.2   0.0       0.19   10.5   0.0    1.2  1  GDC-P           Glycine cleavage system P-protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0     5e-08   6.4e-05       1      40 [.       3      51 ..       3      62 .. 0.88
   2 !   21.2   0.1   1.1e-07   0.00014     176     252 ..     148     226 ..     127     235 .. 0.82
   3 !    9.6   0.0   0.00037      0.47     258     279 ..     420     441 ..     399     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5e-08
                                  CSEEEE--SHHHHHHHHHHHH....HTS-EEEEE.....TTHCHHHCSH CS
                                  xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx.....xxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq....agakvtlve.....legtclnggc 40
                                  +dvv+iG+GpAGl aa +  +      +kv+lv+     l++tc++ ++
  gi|70606512|ref|YP_255382.1|  3 YDVVIIGAGPAGLLAAYEFTTfstkERLKVLLVDkglraLRRTCPLLTP 51
                                  69****************99988867*******9889999999998876 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.1e-07
                                   SSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                   Pyr_redox_2 176 rllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle..eklglel 252
                                   ++     +++ + +++++e++G++v   t+v ei+++ ++  ++++ +eei+a++++ a G+   + +l+  +klg+ +
  gi|70606512|ref|YP_255382.1| 148 HIGTDKTPMVIENIQKYIENNGINVAELTEVFEIQKKADHFVLKTNRKEEIEAKTILAAPGRAGAKWFLDqaKKLGVDM 226
                                   44456678888999************************966699******************99999998888888887 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00037
                                   EE--TTSBESSTTEEE-GGGCT CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 258 ivvdeflrtnvpgiyaiGDvag 279
                                    vvd++++t v++++++GD +g
  gi|70606512|ref|YP_255382.1| 420 AVVDSNMETVVDNLFVAGDGVG 441
                                   59*****************884 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.6e-08   8.4e-05       1      37 [.       3      43 ..       3      47 .. 0.88
   2 !   13.4   0.0   1.9e-05     0.024     106     163 ..     152     208 ..     146     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.6e-08
                                  -SEEEE--SHHHHHHHHHH....HHTT--EEEE-SSSSS-H CS
                   HI0933_like  1 kdviviGgGaAGlmaAisa....akrgkrVlllekakklgr 37
                                  +dv++iG+G+AGl+aA +      k+  +Vll++k+ +++r
  gi|70606512|ref|YP_255382.1|  3 YDVVIIGAGPAGLLAAYEFttfsTKERLKVLLVDKGLRALR 43
                                  59**************998777778999*******987766 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                                   .-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 106 dkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   dk   +++ ++k ++++g+++   tev +++k++d+ f +kt+ +ee+ea++++ A G
  gi|70606512|ref|YP_255382.1| 152 DKTPMVIENIQKYIENNGINVAELTEVFEIQKKADH-FVLKTNRKEEIEAKTILAAPG 208
                                   57778999************************9999.*****999****999888866 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.3e-05     0.067       1      30 [.       6      38 ..       6      42 .. 0.74
   2 !   18.6   0.1   7.2e-07   0.00092      84     134 ..     158     209 ..     117     215 .. 0.87
   3 ?    2.8   0.0     0.045        58     288     305 .]     420     437 ..     398     437 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl...edylilEkg 30
                                  +IiGaGPaGl aa+e+  +      ++l ++kg
  gi|70606512|ref|YP_255382.1|  6 VIIGAGPAGLLAAYEFTTFSTkerLKVLLVDKG 38
                                  7*************9987665211356666665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.2e-07
                   Pyr_redox_3  84 leYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGe 134
                                    e  +++ +++ +++ + +eV +++k++++f+++t+++ ++eAk+++ A G+
  gi|70606512|ref|YP_255382.1| 158 IENIQKYIENNGINVAELTEVFEIQKKADHFVLKTNRKeEIEAKTILAAPGR 209
                                   56789999***************************9755********99986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.045
                   Pyr_redox_3 288 vlteeteetnvpglflaG 305
                                   ++ ++++et v++lf+aG
  gi|70606512|ref|YP_255382.1| 420 AVVDSNMETVVDNLFVAG 437
                                   566789***********9 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00017      0.22       1      22 [.       4      25 ..       4      82 .. 0.73
   2 ?   -0.8   0.1       0.5   6.4e+02      99     150 ..     159     209 ..     148     227 .. 0.73
   3 !   22.1   0.0   5.3e-08   6.7e-05     299     387 ..     369     463 ..     362     465 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                                  CEEEE-SSHHHHHHHHHHHHTT CS
                          GIDA  1 dviViGgGhAGceAAlaaarlG 22
                                  dv++iG+G AG+ AA++     
  gi|70606512|ref|YP_255382.1|  4 DVVIIGAGPAGLLAAYEFTTFS 25
                                  79*************9865433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.5
                                   HHHHHHHHTSTTEEEEE.S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA  99 kevteklenepnleiie.eeveeliveekkvkgvvtedgetikakavviatGt 150
                                   +++++++en + +++ e  ev e+  ++    +++t+++e+i+ak++  a G 
  gi|70606512|ref|YP_255382.1| 159 ENIQKYIEN-NGINVAElTEVFEI-QKKADHFVLKTNRKEEIEAKTILAAPGR 209
                                   678888888.88888774578888.4466666788888889998888888776 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 5.3e-08
                                   EEEEET----S-HHHHHHHHTTSTT-TT--EEE--EEEEEEEE-GGGB-T.TSBB.......SSSBTEEE-CGGGTB.-SH CS
                          GIDA 299 liylvgfstslpeevqkevlrsipGLenaeivrpGyaieydyvdprqlln.tLet.......kkvkgLflAGqinGt.eGY 370
                                   ++++  +s  lp+ v   v + i+GLe+++ + pG+   ++ + +++++  +++          v++Lf+AG+  G   G 
  gi|70606512|ref|YP_255382.1| 369 EVTPGDISMGLPYRV---VSNLIEGLERLDNIAPGMYSSNTLLYAPEIKYySMKAvvdsnmeTVVDNLFVAGDGVGLsRGI 446
                                   566777888888854...456799999999999999999988888887765655311111112399***********99** PP

                                   HHHHHHHHHHHHHHHHH CS
                          GIDA 371 eEaaaqGllAGinaark 387
                                     aaa+G+lA++ + rk
  gi|70606512|ref|YP_255382.1| 447 NIAAATGILAARGIGRK 463
                                   ***********988877 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.5e-06    0.0019       1      29 [.       4      38 ..       4      48 .. 0.83
   2 ?    4.6   0.0     0.016        20     148     244 ..     157     261 ..      93     300 .. 0.64
   3 ?   -2.4   0.0       2.1   2.7e+03     324     350 ..     429     457 ..     363     458 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                  EEEEECTSHHHHHHHHHHHHTT......EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg......Vtllekg 29
                                  dvviiG+G +Gl +Aye ++        V+l++kg
  gi|70606512|ref|YP_255382.1|  4 DVVIIGAGPAGLLAAYEFTTFStkerlkVLLVDKG 38
                                  9*****************5532234588*****98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE.EEE--GGGHH.HH..HTTCTT.......TS CS
                           DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaada.vVnaaGawsd.ll..gllkel.......dl 215
                                   ++  +++ +e++G+++ e tev +++++     +   +t++ +e   ++a  ++aa   ++ ++  +++k+l       +l
  gi|70606512|ref|YP_255382.1| 157 VIENIQKYIENNGINVAELTEVFEIQKKA---DHFVlKTNRkEE---IEAkTILAAPGRAGaKWflDQAKKLgvdmapgPL 231
                                   566678889****************6643...332233333233...4455666664454443333444555443343223 PP

                                   EE.EEEEEEEEEEEECCTHSTGSGCSEEEE CS
                           DAO 216 pi.spvrgqvlvlkplseklvspaailpvp 244
                                    i + v  + +v+++l+ +   p+ il   
  gi|70606512|ref|YP_255382.1| 232 DIgVRVEVEAFVMEELTSAVWDPKVILYSK 261
                                   333445555577766666666665555444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                   TEEEEEEEEEC..TTTHHHHHHHHHHHHH CS
                           DAO 324 gvkglylatGh..sghGltlapatGklla 350
                                    v++l++a      ++G++ a+atG l+a
  gi|70606512|ref|YP_255382.1| 429 VVDNLFVAGDGvgLSRGINIAAATGILAA 457
                                   46677777544445889999999998876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.6e-07   0.00046       1      35 [.       4      40 ..       4      45 .. 0.85
   2 ?   -1.5   0.0       0.8     1e+03     109     157 ..     178     229 ..     159     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.6e-07
                 Lycopene_cycl  1 DvvviGaGpAglslAarl..teakpglkvvlieasps 35
                                  Dvv+iGaGpAgl+ A +    + k +lkv+l++ +  
  gi|70606512|ref|YP_255382.1|  4 DVVIIGAGPAGLLAAYEFttFSTKERLKVLLVDKGLR 40
                                  9****************94346899*******98755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.8
                 Lycopene_cycl 109 vesveeeeageslvvleggrkirarlvvdarglaslk....karrlglQtfyG 157
                                   v +++++ + + +  ++  ++i+a++++ a g a +k    +a++lg+ ++ G
  gi|70606512|ref|YP_255382.1| 178 VFEIQKKAD-HFVLKTNRKEEIEAKTILAAPGRAGAKwfldQAKKLGVDMAPG 229
                                   444444444.4444455555999999999999766668888888888888766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0047       6.1       2      30 ..       5      37 ..       4      47 .. 0.73
   2 !    9.4   0.1    0.0012       1.5      40      73 ..     155     189 ..     131     196 .. 0.86
   3 ?    0.9   0.0      0.54   6.9e+02      33      58 ..     202     227 ..     198     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0047
                                  EEEECSSHHHHHHHHHHHHTT....SEEEEEES CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg....kkVtvver 30
                                  vv++G+G  gl +A +++ +      kV +v+ 
  gi|70606512|ref|YP_255382.1|  5 VVIIGAGPAGLLAAYEFTTFStkerLKVLLVDK 37
                                  8****************6655222256666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                     Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedg.v 73 
                                   +++ +++q+++e+ngi+v   t+v ei++++d  v
  gi|70606512|ref|YP_255382.1| 155 PMVIENIQKYIENNGINVAELTEVFEIQKKADHfV 189
                                   567899***********************999744 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.54
                                   SSSTTSSHHHHHHHHHHHHHTTEEEE CS
                     Pyr_redox  33 kllrllDeeaskilqeklekngievl 58 
                                   ++l + +++ +k++ ++ +k+g+++ 
  gi|70606512|ref|YP_255382.1| 202 TILAAPGRAGAKWFLDQAKKLGVDMA 227
                                   56666678889************986 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.2e-06    0.0016      18      49 ..       3      37 ..       1      41 [. 0.78
   2 ?    0.1   0.1      0.31     4e+02     203     225 ..     420     443 ..     415     452 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                                  EEEEEE--SHHHHHHHHHH...HHCTTS-EEEEES CS
                          Thi4 18 sDvvivGaGssGLtaayyl...akkpdlkvailer 49
                                   Dvvi+GaG++GL aay +   ++k  lkv+++++
  gi|70606512|ref|YP_255382.1|  3 YDVVIIGAGPAGLLAAYEFttfSTKERLKVLLVDK 37
                                  6****************872224557899998876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                                   HHH.HHECEEETTEEE-THHHHHH CS
                          Thi4 203 aiv.kktrevvpnlyvaGmevaev 225
                                   a+v ++ + vv+nl+vaG  v  +
  gi|70606512|ref|YP_255382.1| 420 AVVdSNMETVVDNLFVAGDGVGLS 443
                                   6675677889*******9776655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.9e-07    0.0013       1      31 [.       4      38 ..       4      41 .. 0.80
   2 ?   -1.7   0.0      0.94   1.2e+03     183     208 ..     191     216 ..     132     257 .. 0.71
   3 ?   -2.4   0.1       1.5   1.9e+03     378     410 ..     422     447 ..     418     454 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.9e-07
                                  SEEEE--SHHHHHHHHHHHH....TTT-EEEEESS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaae....aGlkvavveke 31
                                  Dv++iG+G AGL AA+e +     + lkv++v+k+
  gi|70606512|ref|YP_255382.1|  4 DVVIIGAGPAGLLAAYEFTTfstkERLKVLLVDKG 38
                                  9***************9753322277799999986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.94
                                   TTTCEEEEEESEEEE-----GG.... CS
                 FAD_binding_2 183 esgrevrirakavvlatgGfgrallk 208
                                   ++ r+++i+ak ++ a g +g++++ 
  gi|70606512|ref|YP_255382.1| 191 KTNRKEEIEAKTILAAPGRAGAKWFL 216
                                   56677777887777777777764443 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                                   BETTSBESTTEEESSBTEEE-STCEESSSSTTS CS
                 FAD_binding_2 378 tdengrvldadgqpipGLYAaGevaaggvhgan 410
                                   +d n       ++++++L+ aG    g   g+n
  gi|70606512|ref|YP_255382.1| 422 VDSN------METVVDNLFVAGDGV-GLSRGIN 447
                                   4444......4559******99877.6666666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.5e-06    0.0019       1      28 [.       7      38 ..       7      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                  EE--SHHHHHHHHHHH....CCTEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLa....kagfdvlllekr 28
                                  I+GaG +Gl+aAy+ +    k++++vll++k+
  gi|70606512|ref|YP_255382.1|  7 IIGAGPAGLLAAYEFTtfstKERLKVLLVDKG 38
                                  9*************9844446799******97 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.1e-05     0.066       1      33 [.       6      37 ..       6      47 .. 0.91
   2 ?    2.3   0.0      0.12   1.5e+02     121     154 ..     175     208 ..     156     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp 33
                                  +i+GaGp+Gl+++ ++   + +k++l++ l+d+
  gi|70606512|ref|YP_255382.1|  6 VIIGAGPAGLLAAYEFTTFS-TKERLKVLLVDK 37
                                  7******************7.9**********8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                 NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlG 154
                                    +ev +++++ad++ + ++++++++a+ +  A G
  gi|70606512|ref|YP_255382.1| 175 LTEVFEIQKKADHFVLKTNRKEEIEAKTILAAPG 208
                                   4699**********9999999******9999988 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.029       2      20 ..       3      21 ..       2      41 .. 0.83
   2 ?   -2.8   0.0       2.2   2.8e+03     116     163 ..     166     208 ..     119     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                  EEEEEE--SHHHHHHHHHH CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallL 20
                                  +dV+I+GaGpaGl++a + 
  gi|70606512|ref|YP_255382.1|  3 YDVVIIGAGPAGLLAAYEF 21
                                  59*************9875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                   HHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--G CS
                 FAD_binding_3 116 eerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDG 163
                                   e+ g++v + tev  +++  ++        +t+++e+++ak + +a G
  gi|70606512|ref|YP_255382.1| 166 ENNGINVAELTEVFEIQKKADH-----FVLKTNRKEEIEAKTILAAPG 208
                                   4555555555555533333333.....222334445566666666666 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.16       1      33 [.       4      37 ..       4      39 .. 0.91
   2 ?   -2.4   0.0       1.3   1.6e+03     283     312 ..     325     354 ..     319     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                  EEEEE--SHHHHHHHHHHHHHTTTS.SEEEEEE- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk.levtlves 33
                                  ++vi+G+G+aG laA  + +  +++ l+v+lv++
  gi|70606512|ref|YP_255382.1|  4 DVVIIGAGPAGLLAAYEFTTFSTKErLKVLLVDK 37
                                  69****************99988878****9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                   HHHHHHHHHCT--TTTS-EEEE---EEES- CS
                Trp_halogenase 283 eAlaellaeldgkleaeprkirfttGrrkq 312
                                   + +a+l+ +l+g++   +r i f++Grr++
  gi|70606512|ref|YP_255382.1| 325 KSIARLMTRLGGEKPIIQRLIDFEKGRRST 354
                                   567899999****99***********9975 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.19     170     267 ..     129     229 ..     119     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                   HHHHHHGGGT-EEEEE-GGG--S-...S-EEEEEEEES-TTS.B----HHHHHHHHHTT-EEEEE...E-TTGGGTB--HH CS
                         GDC-P 170 vlktrakglgieivevdlteekvtdkekevagvlvqypnteG.riedlkelvekakkkkslvvva...adllaLtllkpPg 246
                                    ++ ra ++g e v    ++ ++ dk+  v   + +y + +G ++ +l+e+ e  kk +  v  +    ++ a t+l++Pg
  gi|70606512|ref|YP_255382.1| 129 EIQKRAAKVGAEFVPIRQRHIGT-DKTPMVIENIQKYIENNGiNVAELTEVFEIQKKADHFVLKTnrkEEIEAKTILAAPG 208
                                   56778888888887777555554.468999999999999999669999999999888887765441115788********* PP

                                   HHT-SEEEEE-TTTT---GGG CS
                         GDC-P 247 elgaDivvGsaqrfGvPlgyG 267
                                     ga   + +a+++Gv ++ G
  gi|70606512|ref|YP_255382.1| 209 RAGAKWFLDQAKKLGVDMAPG 229
                                   ****************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 2639.18
//
Query:       gi|70606513|ref|YP_255383.1|  [L=321]
Description: hypothetical protein Saci_0711 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-28   99.1   4.9    4.6e-15   55.5   0.1    2.9  4  AsnC_trans_reg2  AsnC-like ligand binding domain
    3.3e-10   39.6   0.0      1e-08   34.9   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00012   21.5   3.4      0.042   13.4   0.1    2.8  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00013   22.3   0.3      0.026   14.9   0.1    2.5  2  DUF2805          Protein of unknown function (DUF2805)
    0.00093   18.7   0.0      0.031   13.8   0.0    2.5  2  Sigma70_r4       Sigma-70, region 4
     0.0075   16.2   0.1        4.6    7.3   0.0    2.7  2  HTH_11           HTH domain
  ------ inclusion threshold ------
       0.02   14.8   0.1          3    7.8   0.0    2.7  2  MarR             MarR family
       0.05   13.2   0.2       0.13   11.9   0.2    1.7  1  Peptidase_C71    Pseudomurein endo-isopeptidase Pei
      0.054   12.7   0.1       0.99    8.5   0.0    2.2  2  Aldo_ket_red     Aldo/keto reductase family
      0.068   13.3   0.3       0.27   11.4   0.1    2.1  3  RelE             RelE toxin of RelE / RelB toxin-antitoxin sy
      0.069   13.6   0.0       0.27   11.7   0.0    1.9  2  HTH_27           Winged helix DNA-binding domain
       0.16   12.0   0.2        9.1    6.3   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.2   6.3e+03      61      82 .]      26      47 ..      22      47 .. 0.79
   2 !   55.5   0.1   3.1e-18   4.6e-15       3      82 .]      65     144 ..      63     144 .. 0.97
   3 ?   -2.6   0.0       4.1   6.2e+03      66      82 .]     200     216 ..     190     224 .. 0.54
   4 !   45.0   0.1     6e-15     9e-12       1      82 []     232     316 ..     232     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
               AsnC_trans_reg2 61 aeiaaatgledyevLpstrefK 82
                                  a+i +++gl++  vL  ++ +K
  gi|70606513|ref|YP_255383.1| 26 AKIGEKLGLSEELVLERIKRLK 47
                                  6788899999888998888877 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 3.1e-18
               AsnC_trans_reg2   3 GfkanalvawkvpeerveevaevvaelpevtHcYeRew.pynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                                   G++  al+a ++p e++e++ ++  e++e tH++ R++ +yn++ ++ a+++e+++e ++ + ++++++dy +L+s++++K
  gi|70606513|ref|YP_255383.1|  65 GME-GALIASNIPLEQIEKFRKIALEIKELTHNFVRNHpRYNIWYVLKAENKEKLNEKIRLLMNQVNCNDYVILYSKKTLK 144
                                   666.89******************************9989**************************************998 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.1
               AsnC_trans_reg2  66 atgledyevLpstrefK 82 
                                   + +l++ e+   ++e+K
  gi|70606513|ref|YP_255383.1| 200 KFNLTESEIVELIKELK 216
                                   55554444444444443 PP

  == domain 4  score: 45.0 bits;  conditional E-value: 6e-15
               AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevva.elpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyevLp 76 
                                   ++G+ +na+  ++   +++e+ +  +a +l+e tH+++R    ew+y +y+m+har+++ + e++++  +  ++++y++L+
  gi|70606513|ref|YP_255383.1| 232 RIGIVENAMFLLNS--DDIESSCYNIAtKLKEATHVVLReadkEWDYLCYAMIHARNKNLIFETAKKAIEISNAKSYMLLF 310
                                   589*********95..5566655554449**********77777************************************* PP

               AsnC_trans_reg2  77 strefK 82 
                                   s+ ++K
  gi|70606513|ref|YP_255383.1| 311 SLDNLK 316
                                   **9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   6.8e-12     1e-08       1      42 []       3      47 ..       3      47 .. 0.98
   2 ?    2.4   0.0     0.095   1.4e+02      19      36 ..     193     210 ..     190     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6.8e-12
                 HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                                  LD++D++++ +L+ +     +++a+++e++GlSe+ vl+R++rL+
  gi|70606513|ref|YP_255383.1|  3 LDKTDLQLIMELEYNfpvDERPFAKIGEKLGLSEELVLERIKRLK 47
                                  8******************************************95 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.095
                 HTH_AsnC-type  19 syaeLAervGlSestvlr 36 
                                   ++++++++ +l+es++ +
  gi|70606513|ref|YP_255383.1| 193 PFEKISKKFNLTESEIVE 210
                                   99************9865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       4.2   6.3e+03       1       9 [.       3      11 ..       3      15 .. 0.80
   2 !   13.4   0.1   2.8e-05     0.042      21      48 .]      26      53 ..      23      53 .. 0.89
   3 !    8.4   0.0     0.001       1.5      22      48 .]     196     222 ..     193     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.2
                        HTH_24  1 ldetdrkIL 9 
                                  ld+td++++
  gi|70606513|ref|YP_255383.1|  3 LDKTDLQLI 11
                                  799999986 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.8e-05
                        HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlIk 48
                                  + + e+lglS   v++r+krL+  ++Ik
  gi|70606513|ref|YP_255383.1| 26 AKIGEKLGLSEELVLERIKRLKHLEIIK 53
                                  5799*****************9888886 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.001
                        HTH_24  22 eLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    ++++ +l+ s + + +k+L+e+G+Ik
  gi|70606513|ref|YP_255383.1| 196 KISKKFNLTESEIVELIKELKEKGVIK 222
                                   589999********************8 PP

>> DUF2805  Protein of unknown function (DUF2805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.028        41      10      32 ..      21      43 ..      20      49 .. 0.86
   2 !   14.9   0.1   1.7e-05     0.026      12      34 ..     192     214 ..     191     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                       DUF2805 10 DRtpFeaIeeqfglsekeviklM 32
                                  D  pF  I e+ glse+ v++  
  gi|70606513|ref|YP_255383.1| 21 DERPFAKIGEKLGLSEELVLERI 43
                                  678**************998755 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                       DUF2805  12 tpFeaIeeqfglsekeviklMrk 34 
                                   +pFe I ++f+l+e+e+++l ++
  gi|70606513|ref|YP_255383.1| 192 KPFEKISKKFNLTESEIVELIKE 214
                                   6*******************974 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.1e-05     0.031      11      43 ..      10      45 ..       6      48 .. 0.83
   2 ?    2.1   0.0     0.093   1.4e+02      20      38 ..     191     209 ..     182     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                                  HHHHHHH...TTT--HHHHHHHHTS-HHHHHHHHHH CS
                    Sigma70_r4 11 evlelrf...geglTleEIgerlgiSrerVrqiekr 43
                                   ++el +   +++++++ Ige+lg+S+e V  ++kr
  gi|70606513|ref|YP_255383.1| 10 LIMELEYnfpVDERPFAKIGEKLGLSEELVLERIKR 45
                                  677888888999***************977666655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.093
                                   T--HHHHHHHHTS-HHHHH CS
                    Sigma70_r4  20 glTleEIgerlgiSrerVr 38 
                                   + ++e I+++++++++ + 
  gi|70606513|ref|YP_255383.1| 191 EKPFEKISKKFNLTESEIV 209
                                   6799**********99875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0069        10      19      42 ..      26      49 ..       8      59 .. 0.90
   2 !    7.3   0.0    0.0031       4.6      19      44 ..     195     220 ..     193     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0069
                        HTH_11 19 eeLAeeLnvSrrtvrrdIkaLeel 42
                                  +++ e+L++S+  v  +Ik+L+ l
  gi|70606513|ref|YP_255383.1| 26 AKIGEKLGLSEELVLERIKRLKHL 49
                                  6799*****************966 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                        HTH_11  19 eeLAeeLnvSrrtvrrdIkaLeelgv 44 
                                   e++++++n++++ ++  Ik+L+e+gv
  gi|70606513|ref|YP_255383.1| 195 EKISKKFNLTESEIVELIKELKEKGV 220
                                   689**********************4 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.03        45      21      49 ..      26      54 ..       4      55 .. 0.85
   2 ?    7.8   0.0     0.002         3      21      47 ..     195     221 ..     176     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR 21 seLakklgvskstvtrvldrLekkGlieR 49
                                  +++++klg+s   v + ++rL + + i+R
  gi|70606513|ref|YP_255383.1| 26 AKIGEKLGLSEELVLERIKRLKHLEIIKR 54
                                  49********************9999998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  21 seLakklgvskstvtrvldrLekkGli 47 
                                    ++ kk++++ s + +++++L +kG i
  gi|70606513|ref|YP_255383.1| 195 EKISKKFNLTESEIVELIKELKEKGVI 221
                                   49***********************98 PP

>> Peptidase_C71  Pseudomurein endo-isopeptidase Pei
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.7e-05      0.13      23      72 ..      94     146 ..      74     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                 Peptidase_C71  23 lyekvkkrckykyyyndkvpnreaik...kivtdGinctdasqlfkkvlealG 72 
                                    ++ v+++ +y+ +y  k +n+e ++   ++  + +nc d   l++k  ++l 
  gi|70606513|ref|YP_255383.1|  94 THNFVRNHPRYNIWYVLKAENKEKLNekiRLLMNQVNCNDYVILYSKKTLKLS 146
                                   3567889999*************998433456699**********98776654 PP

>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.056        83     163     180 ..     103     123 ..       5     154 .. 0.69
   2 ?    8.5   0.0   0.00066      0.99     117     150 ..     205     243 ..     185     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.056
                                   B-BTT...-HHHHTTHHHHHH CS
                  Aldo_ket_red 163 eynll...releeegllelck 180
                                   +yn++   +++++e+l e ++
  gi|70606513|ref|YP_255383.1| 103 RYNIWyvlKAENKEKLNEKIR 123
                                   444444443333333333322 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00066
                                   HHHHHHHHHHHHHTTSEEEEEEE..S--HHHHHHH...H CS
                  Aldo_ket_red 117 ieevldaleelvkeGkiraiGvS..nfsveqleka...k 150
                                     e+++ ++el+++G i+ +G +  ++ ++++e+a   +
  gi|70606513|ref|YP_255383.1| 205 ESEIVELIKELKEKGVIKDYGATvnGERIGIVENAmflL 243
                                   579******************996444488888876553 PP

>> RelE  RelE toxin of RelE / RelB toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.9   8.8e+03       8      32 ..      24      48 ..      22      59 .. 0.73
   2 ?   -2.6   0.0       3.8   5.7e+03      83     105 ..      73      95 ..      71      99 .. 0.81
   3 ?   11.4   0.1   0.00018      0.27       6      49 ..     191     234 ..     189     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.9
                          RelE  8 wfarwarkekisdeeLleaveevek 32
                                   fa++ +k ++s+e +le ++++++
  gi|70606513|ref|YP_255383.1| 24 PFAKIGEKLGLSEELVLERIKRLKH 48
                                  5888888888888888888877665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                          RelE  83 aniskkelkalkklakellalse 105
                                   +ni  ++ ++++k+a e+ +l++
  gi|70606513|ref|YP_255383.1|  73 SNIPLEQIEKFRKIALEIKELTH 95 
                                   68888899999999999888775 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00018
                          RelE   6 tkwfarwarkekisdeeLleaveevek.GlidadlGggviKkRva 49 
                                   +k f+++ +k +++++e++e ++e+++ G i  d+G+ v   R+ 
  gi|70606513|ref|YP_255383.1| 191 EKPFEKISKKFNLTESEIVELIKELKEkGVIK-DYGATVNGERIG 234
                                   588*********************97516665.******999996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.7   5.6e+03      22      47 ..      26      51 ..      19      56 .. 0.71
   2 ?   11.7   0.0   0.00018      0.27      22      56 ..     195     223 ..     188     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                        HTH_27 22 adlcgrlnvedshisyslkkLtekGL 47
                                  a + ++l ++   + + +k+L   + 
  gi|70606513|ref|YP_255383.1| 26 AKIGEKLGLSEELVLERIKRLKHLEI 51
                                  56777777777778888888876655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                        HTH_27  22 adlcgrlnvedshisyslkkLtekGLvertgdead 56 
                                   + ++++ n++ s i++ +k+L ekG++      +d
  gi|70606513|ref|YP_255383.1| 195 EKISKKFNLTESEIVELIKELKEKGVI------KD 223
                                   68999*********************9......44 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.066        98      27      54 ..      28      56 ..      26      64 .. 0.84
   2 ?    6.3   0.0    0.0061       9.1      27      54 ..     197     225 ..     194     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.066
                                  HHHHTTSSHHHHHHHHHHHHHTTSEEE.T CS
                     HTH_Crp_2 27 lAsmlGltretvsrilseLkreglisr.g 54
                                  +++ lGl+ e v   +++Lk   +i+r g
  gi|70606513|ref|YP_255383.1| 28 IGEKLGLSEELVLERIKRLKHLEIIKRiG 56
                                  78889********************9535 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0061
                                   HHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                     HTH_Crp_2  27 lAsmlGltretvsrilseLkreglis.rg 54 
                                   ++   +lt + +  +++eLk++g+i+  g
  gi|70606513|ref|YP_255383.1| 197 ISKKFNLTESEIVELIKELKEKGVIKdYG 225
                                   5666789999999************9534 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2270.82
//
Query:       gi|70606514|ref|YP_255384.1|  [L=173]
Description: prephenate dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   64.0   0.2      2e-17   63.6   0.2    1.2  1  PDT       Prephenate dehydratase
    1.5e-05   24.6   0.0    4.9e-05   23.0   0.0    1.9  3  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.2   2.2e-21     2e-17      98     181 ..       2      81 ..       1      83 [. 0.95

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.2e-21
                                   -EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EEEECS-SS-S--EEEEEEE CS
                           PDT  98 kkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkvleeniedkknntTRFlvl 178
                                   kk+yShp+a++++++ Lee     ++++vest+ Aak   as+dkdaaai+s++aa++ +l++l en+e+   n TRF+++
  gi|70606514|ref|YP_255384.1|   2 KKIYSHPHAIQEAKEKLEEL-GLHNIIPVESTSIAAKY--ASEDKDAAAICSRYAAQINNLNILLENVENG-VNLTRFVII 78 
                                   89*****************9.7777*************..*****************************97.7******** PP

                                   EET CS
                           PDT 179 ake 181
                                   +++
  gi|70606514|ref|YP_255384.1|  79 SNR 81 
                                   986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.82   7.4e+03      55      65 ..      11      21 ..       9      22 .. 0.78
   2 ?   -3.2   0.1      0.85   7.6e+03      23      32 ..      67      76 ..      67      79 .. 0.75
   3 !   23.0   0.0   5.5e-09   4.9e-05       1      65 [.      89     153 ..      89     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.82
                                  HHHHHHHHHTT CS
                           ACT 55 leevlealkkl 65
                                  ++e++e+l++l
  gi|70606514|ref|YP_255384.1| 11 IQEAKEKLEEL 21
                                  57889999887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.85
                                  HTTSEEEEEE CS
                           ACT 23 drgiNidsie 32
                                  ++g+N+++  
  gi|70606514|ref|YP_255384.1| 67 ENGVNLTRFV 76
                                  6899998865 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 5.5e-09
                                   EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                   t++++  p +PG L +v+  +  ++iN+++i +r+ + + ++++f v+ ++  + ++v  a+k++
  gi|70606514|ref|YP_255384.1|  89 TMIFFTIPHKPGSLYKVLERFYVNNINLTMIYSRPLKVEPWKYYFYVEFEGGLNEDKVDSAIKEI 153
                                   689999********************************************999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1180.43
//
Query:       gi|70606515|ref|YP_255385.1|  [L=404]
Description: threonine dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-77  259.8   0.6    3.8e-77  259.6   0.6    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
    0.00056   19.6   0.9     0.0022   17.7   0.1    2.3  2  ACT       ACT domain
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.051   13.6   0.0    1.7  1  ACT_6     ACT domain
      0.059   14.0   0.0       0.18   12.4   0.0    1.8  1  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.6   0.6   8.5e-81   3.8e-77       3     294 .]      19     305 ..      17     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: 259.6 bits;  conditional E-value: 8.5e-81
                                   GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                   + i +TPl  +  +s   g++++lK+E+l++tgSfK+Rga + l +l ++++ ++v++ s+GNh++++A+aa++lG+k+t+
  gi|70606515|ref|YP_255385.1|  19 QYIHKTPLDYSSTFSNIAGAKVYLKMENLQKTGSFKVRGAFSKLISLSQAERERGVIAVSAGNHAQGVAYAASVLGIKSTV 99 
                                   67899*****************************************99999****************************** PP

                                   EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE CS
                          PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvp 164
                                   v+p++a+ +k ++++ +Ga+v++ g+   e++++a+e+++e ++a+lv+++d+  vi+g+gt+glE+l     +pd+vvvp
  gi|70606515|ref|YP_255385.1| 100 VMPETAPISKYLATKNYGANVILHGKFLHESMKKAEEIIRE-TNAVLVHPYDDLNVILGQGTLGLELL---EAEPDVVVVP 176
                                   *****************************************.*************************5...5669****** PP

                                   -SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEH CS
                          PALP 165 vGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsd 245
                                   +GgGgli+Gi+ +lk++r + +vigv+++ s+++  s++ gr v++++s +iadg+ v++ps  + e++ +lvd+iv v+d
  gi|70606515|ref|YP_255385.1| 177 IGGGGLISGISIALKAKRNNLKVIGVQSSASPSMKVSVELGRLVEIEPSFSIADGILVKNPSKITYEVISELVDDIVLVDD 257
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                          PALP 246 eealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                   e+++ a+  l +r++ ++e ++aa++aa+    + ++++g++v+ i++g
  gi|70606515|ref|YP_255385.1| 258 EDIANAILYLLERNKTIAEGAGAASVAAI-ISGKIKVGNGKKVIPIISG 305
                                   *****************************.9999999999999999887 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.36   1.6e+03      40      58 ..     245     263 ..     237     264 .. 0.76
   2 !   17.7   0.1   4.9e-07    0.0022       3      57 ..     330     384 ..     328     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.36
                                   ECEEEEEEEEEEHHHHHHH CS
                           ACT  40 vagivfvvivvdeedleev 58 
                                   + ++v+ +++vd+ed++++
  gi|70606515|ref|YP_255385.1| 245 ISELVDDIVLVDDEDIANA 263
                                   4578888999999999887 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.9e-07
                                   EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHH CS
                           ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedlee 57 
                                   + v+vpD+PG L+rv++ +a+   N++ + + ++   v + ++ ++vv+e +++e
  gi|70606515|ref|YP_255385.1| 330 VKVLVPDKPGYLNRVLSRVAQIRGNVIDVIHDRMSTDVKPGFTKIHVVFEIPVSE 384
                                   6799***************************999999555555555555555444 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.051       5      33 ..     330     358 ..     327     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                         ACT_6   5 itvtGpdrpGltasLtsvlaefgvnilDi 33 
                                   + v+ pd+pG +++++s++a+++ n++D+
  gi|70606515|ref|YP_255385.1| 330 VKVLVPDKPGYLNRVLSRVAQIRGNVIDV 358
                                   567779**********************7 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05      0.18       7      64 ..     328     388 ..     323     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                         ACT_4   7 vrleveaedrkglLaditqviseekanivsv...naktrkkdglaeikitveVkdvehLsr 64 
                                   v+++v + d++g L+++++ +++ ++n+ +v   +++t+ k g+++i++ +e+  +e Ls+
  gi|70606515|ref|YP_255385.1| 328 VKVKVLVPDKPGYLNRVLSRVAQIRGNVIDVihdRMSTDVKPGFTKIHVVFEIPVSESLSE 388
                                   899********************99999888444677776799**********99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2453.74
//
Query:       gi|70606516|ref|YP_255386.1|  [L=172]
Description: HIT family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-15   57.0   0.0    3.2e-15   56.6   0.0    1.2  1  HIT          HIT domain
    1.9e-07   31.0   0.2    3.5e-07   30.1   0.2    1.5  1  CwfJ_C_1     Protein similar to CwfJ C-terminus 1
    1.4e-05   25.6   0.0    2.1e-05   25.0   0.0    1.2  1  DcpS_C       Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.051   13.7   0.0    1.4  1  COMM_domain  COMM domain


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   7.2e-19   3.2e-15       4      95 ..      39     131 ..      36     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 7.2e-19
                                   C-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-S CS
                           HIT   4 ipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqs 84 
                                    +++vv++  +++++l+ +p  pgh+ ++p kh+s ++ l+++el++l+++v+   k+l+++++ +g+++ in g+ ag  
  gi|70606516|ref|YP_255386.1|  39 RENKVVFRATYSYIVLNTFPYNPGHIMIVPYKHVSSVELLDDNELTELFKMVRTSIKKLRRVYSPDGFNIGINIGRVAGAG 119
                                   57899**************************************************************************99 PP

                                   S.SS-EEEEEEC CS
                           HIT  85 v.ahlHiHvipr 95 
                                   + +h+HiH++pr
  gi|70606516|ref|YP_255386.1| 120 IeQHVHIHIVPR 131
                                   9469******98 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   7.8e-11   3.5e-07       4      74 ..      16      89 ..      13     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.8e-11
                                  HHHHHHHHHH-S--...--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHH CS
                      CwfJ_C_1  4 kkrikasldsClfC...lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkf 74
                                   ++ik++ + C fC    + ++  ++ +v  +   Y+ l + p + gH++i+p +H+s++  ld+++l e+ k 
  gi|70606516|ref|YP_255386.1| 16 ASKIKNEKEPCIFCnfaYDRSRDRENKVVFRATYSYIVLNTFPYNPGHIMIVPYKHVSSVELLDDNELTELFKM 89
                                  578999999999997545777788899**************************************988887543 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.7e-09   2.1e-05       2     100 ..      26     129 ..      25     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.7e-09
                                   -HHHHHHTTSS...-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EE CS
                        DcpS_C   2 wvfnilakgke...pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevda 79 
                                   ++f+++a++++   +++vv++ +   ++    p ++ h++++p+++++s++ L++++l  l +m+++  k +++ y    +
  gi|70606516|ref|YP_255386.1|  26 CIFCNFAYDRSrdrENKVVFRATYSYIVLNTFPYNPGHIMIVPYKHVSSVELLDDNELTELFKMVRTSIKKLRRVY---SP 103
                                   78888888877443556699999999999************************99999999999998888888888...56 PP

                                   EEE--SCCCT-.....-S-S--EEEE CS
                        DcpS_C  80 eelrvgvhyqP.....svyhlHlHvi 100
                                   + +++g+++         +h+H+H++
  gi|70606516|ref|YP_255386.1| 104 DGFNIGINIGRvagagIEQHVHIHIV 129
                                   7777777777665557779*****98 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.051       9      49 ..       8      48 ..       6      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                   COMM_domain  9 WrldvqlsssslskvneptalleLklqngsgnsenvtlels 49
                                  Wr ++++s s++++ +ep++  ++  + + +++++v +  +
  gi|70606516|ref|YP_255386.1|  8 WRSKYVTSASKIKNEKEPCIFCNFAYDRSRDRENKVVFRAT 48
                                  *************************9998887777888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1143.52
//
Query:       gi|70606517|ref|YP_255387.1|  [L=321]
Description: DNA repair and recombination protein RadA [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-90  300.8   0.1    7.9e-90  300.6   0.1    1.1  1  Rad51     Rad51
    3.7e-15   56.1   0.4    5.6e-15   55.5   0.4    1.3  1  RecA      recA bacterial DNA recombination protein
    8.7e-12   45.5   0.3      4e-11   43.4   0.1    2.2  2  HHH_5     Helix-hairpin-helix domain
    4.6e-09   36.0   1.0    1.1e-08   34.7   1.0    1.6  1  ATPase    KaiC
    4.8e-08   32.8   0.0      8e-08   32.1   0.0    1.3  1  AAA_25    AAA domain
     0.0035   17.1   0.0      0.011   15.5   0.0    1.8  1  AAA_24    AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.021   15.3   0.0    1.6  1  AAA_18    AAA domain
      0.026   14.7   0.0      0.056   13.7   0.0    1.6  1  Cdd1      Pathogenicity locus
      0.034   14.0   0.0      0.068   13.0   0.0    1.4  1  Bac_DnaA  Bacterial dnaA  protein
      0.042   14.1   0.2       0.14   12.5   0.2    1.9  1  AAA_22    AAA domain
      0.074   13.2   0.1       0.22   11.7   0.1    1.8  1  HHH_2     Helix-hairpin-helix motif
       0.11   12.4   1.3          4    7.4   0.1    2.9  3  MarR_2    MarR family
       0.12   12.2   0.0       0.42   10.5   0.0    1.9  2  DUF3173   Domain of unknown function (DUF3173)
       0.13   12.1   0.0       0.23   11.3   0.0    1.3  1  BDV_P24   Borna disease virus P24 protein


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.6   0.1   6.2e-93   7.9e-90       3     254 ..      70     318 ..      68     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 300.6 bits;  conditional E-value: 6.2e-93
                                   -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS-- CS
                         Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtf 83 
                                   f +a e+ ++r +  ++ttGs++lD lLgGGiet ++te fGef+sGktqlch++++ vqlp e+gG +gkavyidtegtf
  gi|70606517|ref|YP_255387.1|  70 FKTALEVKKERMNTKKITTGSQALDGLLGGGIETRTMTEFFGEFGSGKTQLCHQISISVQLPQEKGGLNGKAVYIDTEGTF 150
                                   8899***************************************************************************** PP

                                   -GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS.-EEEEEEETTTGGGCH-------THHHHHHHH CS
                         Rad51  84 rperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaed.kfallivDsvtalyRtdfsgrgelakRqqklg 163
                                   r er+ ++a+  +l+++ +++n+ y Ra +++hq+ +++ + +l+++d  ++l+ivDs+t+++R+++ gr++la Rqqkl+
  gi|70606517|ref|YP_255387.1| 151 RWERIEAMAKGAGLESDIAMNNIYYMRAINSDHQMAIVDDLQELITKDpAIKLIIVDSITSHFRAEYPGRENLAVRQQKLN 231
                                   ********************************************99883599***************************** PP

                                   HHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEE CS
                         Rad51 164 kllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleav 244
                                   k+l++L +la+ +++av+itnqv+a++d     f +dp+  +gG+ l h   +R++l+k +g++Ri+++vd+P+lpe e+v
  gi|70606517|ref|YP_255387.1| 232 KHLHQLVRLAEMYDIAVIITNQVMARPDM----FYGDPTTAVGGHTLYHVPGIRVQLKKSRGNKRIARIVDAPHLPEGEVV 308
                                   ***************************98....************************************************ PP

                                   EEEETTEEE- CS
                         Rad51 245 faigeeGied 254
                                   fai+eeG+ d
  gi|70606517|ref|YP_255387.1| 309 FAITEEGVRD 318
                                   ********98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.4   4.4e-18   5.6e-15      23     226 ..      75     291 ..      45     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4.4e-18
                                   TS--.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----... CS
                          RecA  23 gdekeklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehald... 94 
                                     +ke+++ + i++Gs ald  lG GG+    ++e +G   sGkt l+ ++  ++q   +kg   g a++id+e ++    
  gi|70606517|ref|YP_255387.1|  75 EVKKERMNTKKITTGSQALDGLLG-GGIETRTMTEFFGEFGSGKTQLCHQISISVQlpqEKGglnGKAVYIDTEGTFRwer 154
                                   4466789999**************.**********************998877765332565222579******9886222 PP

                                   .HHHHHHTT....--GGG-EEE--SSHHHHHHHHH....HHHTTT--SEEEEE-TTT---STT-----------HHHHHHH CS
                          RecA  95 .pkyakklG....vdidellvsqpdtGeqaleiad....alvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlms 166
                                     + ak  G    + +++++  +  + ++ + i+d     +++  ai li+vds+++   +ae  G    ++++++ + + 
  gi|70606517|ref|YP_255387.1| 155 iEAMAKGAGlesdIAMNNIYYMRAINSDHQMAIVDdlqeLITKDPAIKLIIVDSITSH-FRAEYPGR---ENLAVRQQKLN 231
                                   123455555222245678988888888888887762221457889**********986.59999985...44555555678 PP

                                   HHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES--- CS
                          RecA 167 qalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeik 226
                                   + l +l    +  +++vi  nq+  +  + +g+p t+ GG++l     +r++++++   k
  gi|70606517|ref|YP_255387.1| 232 KHLHQLVRLAEMYDIAVIITNQVMARPDMFYGDPTTAVGGHTLYHVPGIRVQLKKSRGNK 291
                                   99***************************************************9987655 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   3.1e-14     4e-11       2      57 .]       9      64 ..       8      64 .. 0.97
   2 ?   -1.5   0.0       3.2   4.1e+03      37      53 ..     274     298 ..     271     299 .. 0.62

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 3.1e-14
                                  HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                  ++L ++sG+G  +  +l++aG++s+e++a a++++L+ + Gi + tA+rii e+++
  gi|70606517|ref|YP_255387.1|  9 KSLSDLSGVGQNILNKLVEAGYSSLEAVAVATPQDLSVAAGIPQTTAQRIIKEARE 64
                                  6799**************************************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                                   HHTSTTS........-HHHHHHHHH CS
                         HHH_5  37 LakipGi........GkktAeriil 53 
                                   L  +pGi        G+k+  ri++
  gi|70606517|ref|YP_255387.1| 274 LYHVPGIrvqlkksrGNKRIARIVD 298
                                   6667776444444457788888775 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   1.0   8.7e-12   1.1e-08       2     223 ..      87     315 ..      86     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 8.7e-12
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek...y..gepgvfvtveepa..edlrenakslGwdle 75 
                                    tg + lD +l gGi  ++++   Ge G+GKt ++ q  i+          + + v++ +e +   e +   ak  G + +
  gi|70606517|ref|YP_255387.1|  87 TTGSQALDGLLGGGIETRTMTEFFGEFGSGKTQLCHQISISVQLPqekGglNGKAVYIDTEGTFrwERIEAMAKGAGLESD 167
                                   7999*********************************98875433001211345589999988855555555555555555 PP

                        ATPase  76 kleeegklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitgl.aye..e......keavaReilrq 146
                                      ++  ++++ a +s+++          ++++++l+e i +  a k +++Dsit++   e         +++++ + l+q
  gi|70606517|ref|YP_255387.1| 168 IAMNN--IYYMRAINSDHQ----------MAIVDDLQELITKDPAiKLIIVDSITSHfRAEypGrenlavRQQKLNKHLHQ 236
                                   44444..888888887655..........78899999999888777**********95322122111111345556679** PP

                        ATPase 147 lvrvlkklgvTailvsekss........seeaaggygveefivdgv.ivLdlkeieeelvRtleivkmRgtkhskkehpfe 218
                                   lvr  +++++  i+++++            +a+gg+ + +  v g+ ++L++ + ++++ R+++       +    e++f 
  gi|70606517|ref|YP_255387.1| 237 LVRLAEMYDIAVIITNQVMArpdmfygdPTTAVGGHTLYH--VPGIrVQLKKSRGNKRIARIVDAP-----HLPEGEVVFA 310
                                   *****************98889999977667778888877..555436777766666777766533.....3344555555 PP

                        ATPase 219 Iteeg 223
                                   Iteeg
  gi|70606517|ref|YP_255387.1| 311 ITEEG 315
                                   55555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.3e-11     8e-08      15     188 ..      86     253 ..      72     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.3e-11
                        AAA_25  15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravge 95 
                                   + +  + ++ l++g +   + + ++G  g+GKt l+ +++++v + ++  g     +gk +y+++E++  ++ +R++a+ +
  gi|70606517|ref|YP_255387.1|  86 ITTGSQALDGLLGGGIETRTMTEFFGEFGSGKTQLCHQISISVQLPQEKGG----LNGKAVYIDTEGTF-RW-ERIEAMAK 160
                                   566667788899999999999***********************6553333....69***********9.44.699*9*99 PP

                        AAA_25  96 alrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg....densnsd...vgalv 169
                                    + + ++ +  ++  +   + + +d+++    a vd+l++ i++ + ++l+++D++++ +++     en +      ++ +
  gi|70606517|ref|YP_255387.1| 161 GAGLESDIAMNNIYYM---RAINSDHQM----AIVDDLQELITKDPAIKLIIVDSITSHFRAeypgRENLAVRqqkLNKHL 234
                                   9988888877776443...333333333....567889******999***********98886654444442234358888 PP

                        AAA_25 170 ealeriarrtgaavllvhH 188
                                    +l r+a+ +++av+++ +
  gi|70606517|ref|YP_255387.1| 235 HQLVRLAEMYDIAVIITNQ 253
                                   8999999999999998765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.3e-06     0.011       8      77 ..     110     212 ..     105     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-06
                        AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie..........................sw 49 
                                   +G+ g+GKT l+ ++               k+++idte+ +      ++   e                            
  gi|70606517|ref|YP_255387.1| 110 FGEFGSGKTQLCHQIsisvqlpqekgglNGKAVYIDTEGTF---RWERI---EamakgaglesdiamnniyymrainsdHQ 184
                                   79*************99999999999999999999999844...22222...23335778888888888888888887666 PP

                        AAA_24  50 edfldevvelaaeladyktlviDtidel 77 
                                    +++d+++el ++++ +k +++D+i+  
  gi|70606517|ref|YP_255387.1| 185 MAIVDDLQELITKDPAIKLIIVDSITSH 212
                                   6778888888***************975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.7e-05     0.021       5      91 ..     111     218 ..     108     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                        AAA_18   5 GtpGvGKttlakeL.......skrlgf..............gvnlrdvakenglllevdpealdeskrldedkldklldal 64 
                                   G  G+GKt+l++ +       ++++g+              ++++  +ak  gl+ +   + +   + ++ d +++++d l
  gi|70606517|ref|YP_255387.1| 111 GEFGSGKTQLCHQIsisvqlpQEKGGLngkavyidtegtfrWERIEAMAKGAGLESDIAMNNIYYMRAINSDHQMAIVDDL 191
                                   778***********6666666555544889999999999999999999999999999999988999999999999999999 PP

                        AAA_18  65 eenssaleegknlvidghlaeleseaa 91 
                                   +e + +    k +++d++ ++++ e+ 
  gi|70606517|ref|YP_255387.1| 192 QELITKDPAIKLIIVDSITSHFRAEYP 218
                                   9999988889999*********98875 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-05     0.056       3      42 ..       6      45 ..       4      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                          Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeely 42
                                  k++k+l d+ ++G+++ ++lve G++s+e ++  +p++l 
  gi|70606517|ref|YP_255387.1|  6 KKVKSLSDLSGVGQNILNKLVEAGYSSLEAVAVATPQDLS 45
                                  67999*******************************9985 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05     0.068      39     113 ..     109     198 ..     106     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                                   EE-SSSSSHHHHHHHHHHHHHHHSS....SS-EEEEEHH.HHHHHHHHHHHT..........T-HHHHHHHHTT-SEEEEE CS
                      Bac_DnaA  39 iygevGlGktHLlkaignevlenap....elrvvYltae.eFlnelvkalrd..........kkaeefkeklrkvDvLliD 104
                                   ++ge G Gkt L + i+  v+  ++    + + vY+ +e +F +e ++a+ +          +++  ++    +  + ++D
  gi|70606517|ref|YP_255387.1| 109 FFGEFGSGKTQLCHQISISVQLPQEkgglNGKAVYIDTEgTFRWERIEAMAKgaglesdiamNNIYYMRAINSDHQMAIVD 189
                                   69************998877643331222789****99857********99865554333333334444445567799*** PP

                                   -GGGGTT-H CS
                      Bac_DnaA 105 Diqflagke 113
                                   D+q l +k+
  gi|70606517|ref|YP_255387.1| 190 DLQELITKD 198
                                   ***999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00011      0.14       4     127 ..     103     250 ..     101     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...........erl 73 
                                   t++++  +Ge G+GKT l+ ++  + +  ++    + + v+++  +   ++ + +++++  gle +            + +
  gi|70606517|ref|YP_255387.1| 103 TRTMTEFFGEFGSGKTQLCHQISISVQLPQEKGGLNGKAVYIDTEGTFRWERI-EAMAKGAGLESDIamnniyymraiNSD 182
                                   7889999**************99997554444449999999999999988888.666666665555567888888887777 PP

                        AAA_22  74 sseellealeqalraravielliiDEaqh.lr.....s..........eealeeLrsllnlsrkgvqliL 127
                                    + ++++ l++ + +  +i+l+i+D +   +r     +          +++l +L++l++   +++++i+
  gi|70606517|ref|YP_255387.1| 183 HQMAIVDDLQELITKDPAIKLIIVDSITShFRaeypgRenlavrqqklNKHLHQLVRLAE--MYDIAVII 250
                                   777777888888888888999999988876767665415566666677777777777777..77777775 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00017      0.22      11      52 ..      17      59 ..      10      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                         HHH_2 11 VGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52
                                  VG++  ++L+++ + sl+a + a+ ++L+   +i +++Aq i+
  gi|70606517|ref|YP_255387.1| 17 VGQNILNKLVEAgYSSLEAVAVATPQDLSVAAGIPQTTAQRII 59
                                  88888888887559***************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.11   1.5e+02      39      50 ..      19      30 ..      16      30 .. 0.91
   2 ?    7.4   0.1    0.0031         4      23      48 ..      40      65 ..      33      78 .. 0.88
   3 ?   -1.6   0.0         2   2.6e+03      30      48 ..     281     299 ..     281     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                                  HHHHHHHHHTTS CS
                        MarR_2 39 srilkrLvaaGL 50
                                  ++il++Lv+aG+
  gi|70606517|ref|YP_255387.1| 19 QNILNKLVEAGY 30
                                  689********8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0031
                                  EHHHHHHHHTSSHHHHHHHHHHHHHT CS
                        MarR_2 23 tvgelarrlglsksavsrilkrLvaa 48
                                  t+++l  + g+++ +++ri+k++ +a
  gi|70606517|ref|YP_255387.1| 40 TPQDLSVAAGIPQTTAQRIIKEAREA 65
                                  99*******************99887 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                   HHTSSHHHHHHHHHHHHHT CS
                        MarR_2  30 rlglsksavsrilkrLvaa 48 
                                   r +l+ks+ +++++r v+a
  gi|70606517|ref|YP_255387.1| 281 RVQLKKSRGNKRIARIVDA 299
                                   5699999999999999986 PP

>> DUF3173  Domain of unknown function (DUF3173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         3   3.8e+03       7      18 ..      24      35 ..      23      40 .. 0.76
   2 ?   10.5   0.0   0.00033      0.42       5      29 ..      41      66 ..      37      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                       DUF3173  7 dLiklGfkehtA 18
                                   L++ G++   A
  gi|70606517|ref|YP_255387.1| 24 KLVEAGYSSLEA 35
                                  689999987766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00033
                       DUF3173  5 kkdL.iklGfkehtArdiIrqaKkil 29
                                   +dL ++ G +++tA++iI++a++ l
  gi|70606517|ref|YP_255387.1| 41 PQDLsVAAGIPQTTAQRIIKEAREAL 66
                                  5666567799************9875 PP

>> BDV_P24  Borna disease virus P24 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.23     102     165 ..      24      90 ..      10      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                       BDV_P24 102 arieagfeslsalqvetiq...taqrcdhsdsirilgenikildrsmktmmetmklmmekvdllyas 165
                                     +eag+ sl a+ v t q    a    ++ + ri+ e    ld  +kt +e  k  m+   +   s
  gi|70606517|ref|YP_255387.1|  24 KLVEAGYSSLEAVAVATPQdlsVAAGIPQTTAQRIIKEAREALDIRFKTALEVKKERMNTKKITTGS 90 
                                   458************9977333577889999***********************9999876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2001.85
//
Query:       gi|70606518|ref|YP_255388.1|  [L=165]
Description: hypothetical protein Saci_0716 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-06   28.1   0.5    4.3e-06   26.9   0.5    1.6  1  UPF0113         UPF0113 PUA domain
  ------ inclusion threshold ------
       0.05   13.7   1.1        0.7   10.0   0.1    2.1  2  Recep_L_domain  Receptor L domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.5   4.8e-10   4.3e-06       1      76 []      96     163 ..      96     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.8e-10
                       UPF0113   1 kvvvkekaeklFLYGrdvlke.silkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlRr 76 
                                   k ++k k +++++YG+ v  + + lki+e+       +V+ne+++++ +  +++    ++++i + + +DiG+YlR+
  gi|70606518|ref|YP_255388.1|  96 KLILKSKLAEKITYGKTVRLSlGSLKIKEGSY-----LVYNEKNDFICYSNVKI----DKKGIKIIPELDIGWYLRK 163
                                   6799**************65536777776666.....***************77....889***************6 PP

>> Recep_L_domain  Receptor L domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.015   1.4e+02      45      78 ..      22      53 ..      13      68 .. 0.59
   2 ?   10.0   0.1   7.8e-05       0.7      72     109 ..     110     147 ..      84     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.015
                                  SEGCGTT--EEESSSSBTTTEEEEEES-TT-SBE CS
                Recep_L_domain 45 slsflenLrvIrgrelfeskyalaildnknleeL 78
                                  + sflen  +I+ ++ fe +   +i +n++++e+
  gi|70606518|ref|YP_255388.1| 22 EYSFLENKLIIKFKSSFE-Q-IEIIENNSKVREV 53
                                  566777777777777666.2.2234555554443 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 7.8e-05
                                   -TT-SBEE-TTTSEESS..SEEEEESETTSBSTTTHSHHH CS
                Recep_L_domain  72 nknleeLglpslkeits..gsvviskNpkLCyseteidwk 109
                                    k + +L+l slk i++  + v+++kN  +Cys+ +id+k
  gi|70606518|ref|YP_255388.1| 110 GKTV-RLSLGSLK-IKEgsYLVYNEKNDFICYSNVKIDKK 147
                                   4444.89999999.8888899**************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1046.23
//
Query:       gi|70606519|ref|YP_255389.1|  [L=334]
Description: NOL1/NOP2/sun family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-53  180.8   0.0    3.4e-53  180.3   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.2e-13   51.4   0.0    2.5e-13   50.3   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
     0.0016   18.3   0.0     0.0024   17.7   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0024   18.0   0.0     0.0036   17.4   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0032   17.0   0.0     0.0054   16.2   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0064   15.6   0.0     0.0089   15.2   0.0    1.3  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.055   12.5   0.0      0.085   11.9   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.11   12.3   0.0        0.2   11.4   0.0    1.4  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   0.0   1.5e-56   3.4e-53       1     200 []     128     332 ..     128     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 1.5e-56
                                   HHHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EE CS
               Methyltr_RsmB-F   1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfD 81 
                                   a++L+p+ee+t+lD++aaPGgKTt +a+lmknkg ++A++++++R++++++n++r+  +n+i+++ Da+  +k+  +  f 
  gi|70606519|ref|YP_255389.1| 128 AYVLNPHEEDTVLDMAAAPGGKTTQLAQLMKNKGLIIATEKSRRRARSLISNINRMHARNIILIRSDASTLSKTRIK--FS 206
                                   589********************************************************************998886..** PP

                                   EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEE CS
               Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162
                                   +iLlDaPCsg g+i +d + + + + +d+++++  q  ll++  dll k+G+lvYsTCs+++eE+e v+++ +++    ++
  gi|70606519|ref|YP_255389.1| 207 KILLDAPCSGEGIIFKDTERRKKTSLSDLKNFSLTQMGLLTIGYDLLDKNGILVYSTCSIAPEEDELVVNYGIEELGFRAI 287
                                   ***********************************************************************9998643333 PP

                                   E......SSBSTTSTTSSECEEC.TSEEE-TTTTSS-SEEEEEEE CS
               Methyltr_RsmB-F 163 v......etelsepkglklgeea.gtlrllPhtenkdgffiaklk 200
                                   +      +  +se++g+k++++  + +r++Ph++ ++gff+ +l+
  gi|70606519|ref|YP_255389.1| 288 KisgypaDKGISEFRGVKFSHDVnNCIRFYPHEHGTEGFFVCALQ 332
                                   300111133456666666666546789**************9985 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   1.1e-16   2.5e-13       7      90 .]      35     125 ..      31     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.1e-16
                                   HHHHHHHGG..GHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---......TTSHHHHTT CS
               Methyltr_RsmF_N   7 ekmkellge..eaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerp...gkhplheaG 80 
                                   e++ +++++  +ae+f++++  p ++++R+N l ++++++e   e  +fele+v+w ++G+ + +++++   g ++++ +G
  gi|70606519|ref|YP_255389.1|  35 ERYIHMFDSleDAESFMRSCTVPLEESIRCNDLVTTCSTMEYRLEekNFELEKVQWLPHGYRVIKKPNKpslGATVEYLNG 115
                                   6666777777799**********************9999997666689*************99888766688********* PP

                                   S-EE--TTTH CS
               Methyltr_RsmF_N  81 lyYiQEpSam 90 
                                   +yYiQ  ++m
  gi|70606519|ref|YP_255389.1| 116 YYYIQGLASM 125
                                   *******999 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0024      72     134 ..     134     196 ..     120     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                   -TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                          PCMT  72 kkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                   ++ + vL++ +  G +t  la+l+++kg++++ e++++ +++   n+++ +++n+i++ +D  
  gi|70606519|ref|YP_255389.1| 134 HEEDTVLDMAAAPGGKTTQLAQLMKNKGLIIATEKSRRRARSLISNINRMHARNIILIRSDAS 196
                                   56789*****************************************************99976 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0036      20     143 ..     134     273 ..      87     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                                   -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...HHHTTEEEE.CS-C.CCSSHHHHHCHCHHHSSEEEEEE-- CS
                          FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...aplpgvtti.qgdi.tdpetiekikealserkvdlvvsDg 95 
                                   ++++tv+D +aaPGg +  l+q +++kg ++a         +++++++ +   +i +  + + ++++   + k++ ++ D 
  gi|70606519|ref|YP_255389.1| 134 HEEDTVLDMAAAPGGKTTQLAQLMKNKGLIIATEKSRRrarSLISNINRMhARNIiLIRSDASTLSK--TRIKFSKILLDA 212
                                   36689*******************999*****99977744423344444455555333333333333..234566666665 PP

                                   S-SS-CHHHHHHHHH...........CCCCHHHHCCHCCCCECCCEEEECCCH..CCCHHH CS
                          FtsJ  96 apdvsgvhdldeylq...........sqLllaalelalkllkpggtfvlkifr..geetea 143
                                     + +g+  +d+ ++           s   +  l+++ +ll+++g++v  ++    ee+e 
  gi|70606519|ref|YP_255389.1| 213 PCSGEGIIFKDTERRkktslsdlknfSLTQMGLLTIGYDLLDKNGILVYSTCSiaPEEDEL 273
                                   5444444444444444444444444322234456667788888888887777654444444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.4e-06    0.0054       4      65 ..     138     199 ..     135     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-06
                                   EEEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS
                Methyltransf_4   4 vvleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvll 65 
                                   +vl++  + G+ + +lA+ ++ + ++++ E+++++ + ++++i++ +++N+ ++r+da  +l+
  gi|70606519|ref|YP_255389.1| 138 TVLDMAAAPGGKTTQLAQlMKNKGLIIATEKSRRRARSLISNINRMHARNIILIRSDA-STLS 199
                                   789999999********945667799********************************.5554 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-06    0.0089      69     132 ..     134     199 ..      75     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                                   -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHT..TSTTEEEEES-TTSGG CS
                   Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievak..kRknivPileDArkPe 132
                                   ++++ vL + aa G     ++ +++++g++ a e s r  r li+  +  + +ni+ i  DA++ +
  gi|70606519|ref|YP_255389.1| 134 HEEDTVLDMAAAPGGKTTQLAQLMKNKGLIIATEKSRRRARSLISNINrmHARNIILIRSDASTLS 199
                                   46789***************************************654412578********98755 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05     0.085      26      82 ..     131     192 ..     128     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                   H-GGTTSEEEEES-TTTCCHHHHHCC-SE...EEEE-S-HHHHHHHHCHTT..TCCCEEEE- CS
                        RrnaAD  26 lnleekltvleigpGkGilTeeLakrakq...vvvlElderLakllqkkls..kdeklkvvh 82 
                                   ln+ e++tvl++++ +G  T++La+ +k+     + E+ +r a +l  +++   ++++ ++ 
  gi|70606519|ref|YP_255389.1| 131 LNPHEEDTVLDMAAAPGGKTTQLAQLMKNkglIIATEKSRRRARSLISNINrmHARNIILIR 192
                                   7999**********************977122334466555555555555554555555555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.9e-05       0.2       2     113 ..     134     265 ..     133     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   +++ +vlD +++ G +t +la+++  k+ ++  + s +  ++  +n  +    n+ + ++d+ +l+k+  + kf  il ++
  gi|70606519|ref|YP_255389.1| 134 HEEDTVLDMAAAPGGKTTQLAQLMKNKGLIIATEKSRRRARSLISNINRMHARNIILIRSDASTLSKT--RIKFSKILLDA 212
                                   67789****************99999999***9999999999999*******************9977..55699999996 PP

               Methyltransf_31  83 vl.....................naladpdkile....eiervlkpggilliedpr 113
                                   ++                       ++  +   +       ++l ++gil+ ++++
  gi|70606519|ref|YP_255389.1| 213 PCsgegiifkdterrkktslsdlKNFSLTQ---MglltIGYDLLDKNGILVYSTCS 265
                                   666655555533333333333333333333...13333447888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2429.26
//
Query:       gi|70606520|ref|YP_255390.1|  [L=185]
Description: hypothetical protein Saci_0718 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-31  108.5   4.1    4.3e-31  108.2   4.1    1.0  1  CYTH      CYTH domain
     0.0096   15.9   0.6      0.065   13.2   0.1    2.0  2  Raptor_N  Raptor N-terminal CASPase like domain
  ------ inclusion threshold ------
      0.055   13.6   1.3        1.2    9.3   0.1    2.8  3  KIP1      KIP1-like protein


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   4.1   7.2e-35   4.3e-31       2     170 ..       4     163 ..       3     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 7.2e-35
                                   EEEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEE.EEEEEECSSST...E CS
                          CYTH   2 iEvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgee.ltlKgpgvdge...r 77 
                                   iE E+K++v +   e++e+r  +++  +  + ++q d+Yy+ p rd++++deaLR+R  + +g++ lt+Kgp+ ++e   r
  gi|70606520|ref|YP_255390.1|   4 IEREIKLRVISPSLEEIEERiRNNY--TFINEEHQIDIYYNNPIRDFRKSDEALRLR--NTNGKViLTYKGPKQSKEtktR 80 
                                   699******9999999999955555..99999*************************..99************999999** PP

                                   EEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHH CS
                          CYTH  78 eevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeevkeaae 158
                                   ee+e+evs         d  ++  +l++lg+   + v+k R +yk++++ ++lD  + l ge++EiE  ++ e+e+  +++
  gi|70606520|ref|YP_255390.1|  81 EEIEVEVS---------DLHKMDLILRKLGFIRSFQVEKIRKNYKYADFIISLDSIKEL-GEFIEIEGINKTEKELISFVD 151
                                   ********.........******************************************.********************* PP

                                   HHHHHHHHTTEE CS
                          CYTH 159 kllallrelgls 170
                                   ++++++++ +++
  gi|70606520|ref|YP_255390.1| 152 EFVKKHQIQYEK 163
                                   *99998877665 PP

>> Raptor_N  Raptor N-terminal CASPase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   1.1e-05     0.065      40     103 ..      17      80 ..       3      95 .. 0.87
   2 ?    1.1   0.1     0.058   3.5e+02      39      73 ..     145     178 ..     107     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                      Raptor_N  40 leeiaknlqdqyeslqlrarykqlldptvedvkklcqslrrnakdervlfHYnGhgvprpteng 103
                                   leei++++++ y   + +++++++ +  + d++k  + lr +++++ v++ Y G    + t+ +
  gi|70606520|ref|YP_255390.1|  17 LEEIEERIRNNYTFINEEHQIDIYYNNPIRDFRKSDEALRLRNTNGKVILTYKGPKQSKETKTR 80 
                                   69************9***************************************9988887764 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.058
                      Raptor_N  39 e....leeiaknlqdqyeslqlrarykqlldptvedvkk 73 
                                   e    ++e+ k+ q qye+     ++k++l+  ve +kk
  gi|70606520|ref|YP_255390.1| 145 ElisfVDEFVKKHQIQYEK-----TIKSYLELLVEHAKK 178
                                   2333347888888888888.....777777777777776 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.044   2.7e+02      19      38 ..      16      35 ..       9      43 .. 0.86
   2 ?   -2.3   0.0      0.84     5e+03      47      64 ..      75      92 ..      70      97 .. 0.57
   3 ?    9.3   0.1   0.00021       1.2      49      72 ..     140     163 ..     132     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.044
                          KIP1 19 tlseldekvkemlklieeda 38
                                   l+e++e++++  + i+e+ 
  gi|70606520|ref|YP_255390.1| 16 SLEEIEERIRNNYTFINEEH 35
                                  799********999998875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.84
                          KIP1 47 myykkrpeLielveefyr 64
                                   + k r+e+   v ++++
  gi|70606520|ref|YP_255390.1| 75 KETKTREEIEVEVSDLHK 92
                                  445555555555555554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00021
                          KIP1  49 ykkrpeLielveefyrsyrsLaer 72 
                                   +k  +eLi++v+ef ++++  +e+
  gi|70606520|ref|YP_255390.1| 140 NKTEKELISFVDEFVKKHQIQYEK 163
                                   67889**************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1265.94
//
Query:       gi|70606521|ref|YP_255391.1|  [L=278]
Description: hypothetical protein Saci_0719 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-73  245.2   0.2    6.3e-73  245.1   0.2    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   0.2   3.5e-77   6.3e-73       1     234 [.       7     264 ..       7     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 3.5e-77
                                   EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EEEEEE CS
               SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterralvvea 81 
                                   i++lTD+G++d y g+++gvi++i+pd++i  it + ++f++ ++a+lL+++++yf k+t++l++VDpgvgt+r+a++v++
  gi|70606521|ref|YP_255391.1|   7 IAILTDYGVSDNYNGTLEGVIRKINPDIDITYITPNAKNFNIFTGAYLLNTSYRYFKKNTIFLVIVDPGVGTQRNAILVKT 87 
                                   889****************************************************************************** PP

                                   TTSEEEEESSSTTHHHH...SEEEEEEGSSCC......--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS-SSS... CS
               SAM_adeno_trans  82 kggyfvgPDNGlltlal...lleeaveieeee......ssatFhgrDvFapvaarlaagvsleelgeeldpeelvrle... 150
                                   +++yfv+PDNG+l + +   +++++++i++++       s+tFhgrD+Fapva +++ gv+l+ +gee++++e+v+l+   
  gi|70606521|ref|YP_255391.1|  88 NNYYFVAPDNGVLYPTIvedNIDKIIRISNKKfylsesISNTFHGRDIFAPVASYISVGVDLNVFGEEISKSEIVKLDfsy 168
                                   **************999888779******999***99988**************************************998 PP

                                   ...E..CSCEE..EEEEEE-TTS-EEEEEE...EHHHHHTTC..EE......EEEEESSGGGSTTTSEEEEE-TTSEEEEE CS
               SAM_adeno_trans 151 ...e..derle..gevlyvDrFGNvitniskelleelekerk..va......klkkvetyaevaegellalvnssglleia 216
                                      +  +++++  g+++y+D+FGN+ t i++  l+   +++k  v       +l++v+t+ae +e+el+++ n  g++ei 
  gi|70606521|ref|YP_255391.1| 169 tleRinENKVKacGKIVYIDHFGNIATTIRNVKLR---TGEKalVSlrdkqlELRVVRTFAEGKENELVLYSNGYGFIEIG 246
                                   8762444555466*****************44443...3333331256777777788************************ PP

                                   ETTC-HHHHHT--TT-EE CS
               SAM_adeno_trans 217 vnkgsaaellglkvgdev 234
                                   +n+ sa++ lg+k g++v
  gi|70606521|ref|YP_255391.1| 247 INMSSASNILGVKEGEDV 264
                                   **************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1915.80
//
Query:       gi|70606522|ref|YP_255392.1|  [L=171]
Description: nicotinamide-nucleotide adenylyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-17   63.1   0.1      9e-17   61.6   0.1    1.7  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.1     5e-21     9e-17       1     142 [.       5     135 ..       5     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 5e-21
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTT CS
               CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlkklk 81 
                                   l++G+F+p+H+GHl+++++  k+++e li+ + s+++++    ++++a eR+em+++  ++++ +  ++ ++ +  + ++ 
  gi|70606522|ref|YP_255392.1|   5 LYPGRFQPFHIGHLEVVKWSMKHVDE-LIIVIGSAQESHTL-SNPFTAGERIEMIRRTLDKEN-LDLSKVYIIP--IPDIM 80 
                                   699***********************.************99.****************99999.9999999998..44444 PP

                                   TTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
               CTP_transf_like  82 pdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                    +  ++v      ++f    +++ i+++++lv + ++e + +vl ++  +++++ st ir+
  gi|70606522|ref|YP_255392.1|  81 MN-SVWVSHI---KTF--APNFDVIISRNPLVNRLFKEANVEVLQPPPFDRHKYNSTLIRR 135
                                   44.2455444...444..4499***************99999999999999******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1205.53
//
Query:       gi|70606523|ref|YP_255393.1|  [L=178]
Description: hypothetical protein Saci_0721 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-17   62.1   0.0    8.1e-17   61.2   0.0    1.4  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   4.5e-21   8.1e-17       4     182 ..       5     168 ..       2     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 4.5e-21
                                   EEEEEEEEE.......-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE- CS
                         DUF99   4 rvlGiddsffe..rkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNvv 82 
                                    v G+dd++f+   k  +gk++l   ++++ + + ++ f  +tvdG D      ++ k      ++v +ldG++++gFN +
  gi|70606523|ref|YP_255393.1|   5 VVCGVDDGYFPlsYKGGKGKTILLSSFFQSFN-LIDIDFDYITVDGEDGNTIFKSITK-----GCNVTFLDGVVYGGFNYI 79 
                                   589********88556899********99997.55699**********9754444444.....57**************** PP

                                   -HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHHC- CS
                         DUF99  83 DlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleeaaklvrklt 163
                                    +++         i++++++p++ ++ +aL+khfp  +++  +i+ l ++ + + ++++++y++ + +el+  ++l+++++
  gi|70606523|ref|YP_255393.1|  80 TPDK-------NYIIFYSKMPNVASIDRALMKHFPLRRDK--IISFL-QNLTALPTRQGTVYIN-TDMELSLCKELIERYQ 149
                                   9986.......679*********************97554..45555.6778888888899997.58************** PP

                                   SSSSS-HHHHHHHHHHHHH CS
                         DUF99 164 legriPEPlRvAhliAsal 182
                                   l + +P P++v+h +As+l
  gi|70606523|ref|YP_255393.1| 150 LFTSTPIPIKVSHELASSL 168
                                   ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1297.99
//
Query:       gi|70606524|ref|YP_255394.1|  [L=397]
Description: cell division control protein 6-like protein 1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-21   75.9   0.5    6.3e-21   74.1   0.1    2.2  2  Cdc6_C           CDC6, C terminal winged helix domain
    4.4e-13   50.0   1.0    1.5e-10   41.7   0.0    2.8  3  AAA_16           AAA ATPase domain
      6e-13   49.2   0.1    2.3e-12   47.3   0.0    1.9  3  AAA_22           AAA domain
    2.6e-09   37.6   0.1    6.4e-09   36.3   0.1    1.7  1  AAA              ATPase family associated with various cellul
    3.1e-07   30.0   0.0    4.8e-07   29.4   0.0    1.2  1  TniB             Bacterial TniB protein
      3e-06   27.3   0.8    2.4e-05   24.4   0.1    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00038   19.4   0.2      0.013   14.3   0.0    2.1  2  AAA_32           AAA domain
     0.0028   18.0   0.2     0.0089   16.3   0.2    1.9  1  AAA_assoc_2      AAA C-terminal domain
     0.0031   17.2   0.0     0.0073   16.0   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0039   16.4   0.0     0.0061   15.8   0.0    1.5  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.017   15.1   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
      0.013   15.0   0.0      0.024   14.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.013   14.7   0.0      0.023   13.9   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.015   14.5   0.1       0.19   10.9   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain
      0.025   14.0   0.0      0.042   13.2   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.028   14.2   0.6        6.3    6.5   0.0    2.5  2  DEAD             DEAD/DEAH box helicase
       0.03   14.1   0.9       0.28   11.0   0.9    2.1  1  Bac_DnaA         Bacterial dnaA  protein
       0.05   13.5   0.0       0.15   12.0   0.0    1.8  2  NACHT            NACHT domain
      0.054   12.7   0.0       0.12   11.6   0.0    1.5  1  PIF1             PIF1-like helicase
      0.064   13.4   0.0       0.12   12.5   0.0    1.4  1  Torsin           Torsin
      0.077   13.0   0.0       0.15   12.1   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.082   13.0   2.6       0.93    9.6   0.1    2.9  2  E2F_TDP          E2F/DP family winged-helix DNA-binding domai
       0.15   12.2   0.0       0.35   11.0   0.0    1.6  1  AAA_lid_10       AAA lid domain
       0.17   12.0   0.0       0.28   11.3   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.2   4.7e+03      23      51 ..     232     243 ..     218     260 .. 0.59
   2 !   74.1   0.1   8.5e-24   6.3e-21       3      82 ..     305     381 ..     303     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.2
                                   HHHHHHHHHTT-----HHHHHHHHHHHHH CS
                        Cdc6_C  23 evYkslCesegvdpltqrevsdllseLem 51 
                                   e+  +lC  +                 ++
  gi|70606524|ref|YP_255394.1| 232 EEVIKLCAAL-----------------AA 243
                                   4444444444.................33 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 8.5e-24
                                   HHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
                        Cdc6_C   3 alvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                                   ++vl l+   + + ttgevy+ Y +l+ ++gv+ +tqr+vsd+++eL+m gi++++++++Gr +g+t++isL v++d v+
  gi|70606524|ref|YP_255394.1| 305 SIVLGLN--SNSTLTTGEVYDIYIKLAGKLGVESITQRRVSDIINELDMVGIITARVVNRGR-YGKTKEISLAVSKDIVI 381
                                   5665555..66788***********************************************9.**************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0     2e-13   1.5e-10       2      78 ..      33     111 ..      32     117 .. 0.91
   2 ?    5.6   0.1     0.025        19     118     160 ..     122     165 ..     110     180 .. 0.82
   3 ?   -0.5   0.1         2   1.5e+03      96     147 ..     208     279 ..     184     288 .. 0.54

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2e-13
                        AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysalaqalar 78 
                                   l+ Re+++++L ++l ++ +++  ++v+++G  G+GK+++ r +l  l+++   ++ f++ +++q+  ++py +la++l++
  gi|70606524|ref|YP_255394.1|  33 LPHREDQIRKLVEILAPITRSEKpSNVFIYGLTGTGKTAVTRFVLSNLQRKfpsKFTFIYINTRQN--DTPYRILADVLEA 111
                                   789*************88888878****************************988999********..****999998854 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                        AAA_16 118 rllellkrllallsrderplvlvlDdlq.wadeaslqllaaLlr 160
                                   + +el+kr++++l + +  ++++lD+++  ++ +  ++l+ L r
  gi|70606524|ref|YP_255394.1| 122 STAELFKRFVKRLNTFQTIVLITLDEIDaLVKKHGDDILYRLTR 165
                                   67899*****999997777*********7777788888888876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2
                        AAA_16  96 awrekleeala.....................avpelagaea..srllellkrll.allsrderplvlvlDdlqwa 147
                                   + +e+le+ l+                     a   la+ ++   r +  l r   + ++r++r  +++ Dd+ +a
  gi|70606524|ref|YP_255394.1| 208 YNAEQLEDILKqrskialnegviseeviklcaA---LAARDHgdARRALDLLRVSgEIAEREGR-DLITADDVNRA 279
                                   555555555554444444444444444443322...2222223444444444444366666444.77777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   3.1e-15   2.3e-12       5     126 ..      56     178 ..      52     184 .. 0.87
   2 ?   -2.4   0.1       6.9   5.1e+03      82     108 ..     259     288 ..     234     311 .. 0.52
   3 ?   -2.5   0.0       7.8   5.9e+03      52      70 ..     320     338 ..     271     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.1e-15
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                    + ++++G +GtGKT + r +l++l++     +   + ++++++  +  ++  +l ++l+alg +    +ls+ el++++ 
  gi|70606524|ref|YP_255394.1|  56 PSNVFIYGLTGTGKTAVTRFVLSNLQR-----KfpSKFTFIYINTRQNDTPYRILADVLEALGIRVPFTGLSTAELFKRFV 131
                                   56789*******************953.....235688999**************************************** PP

                        AAA_22  84 qalraravielliiDEaqhlr..s.eealeeL.rsllnlsrkgvqli 126
                                   + l++ ++i+l+ +DE++ l   + +++l  L r+ ++ls+++v++i
  gi|70606524|ref|YP_255394.1| 132 KRLNTFQTIVLITLDEIDALVkkHgDDILYRLtRINYDLSTSKVSVI 178
                                   *******************9875269999999555566577777776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                        AAA_22  82 leqalraravielliiDEaqhlr....seea 108
                                     + +++ ++  l+  D++ + r    ++++
  gi|70606524|ref|YP_255394.1| 259 SGEIAEREGR-DLITADDVNRARieleRDRV 288
                                   3333334444.78888888776544422444 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 7.8
                        AAA_22  52 sskdllrellralglelka 70 
                                   +  d++ +l+ +lg+e  +
  gi|70606524|ref|YP_255394.1| 320 EVYDIYIKLAGKLGVESIT 338
                                   4556777777777766555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1   8.5e-12   6.4e-09       1     119 [.      59     191 ..      59     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 8.5e-12
                                   EEEESSTTSSHHHHHHHHHHHH......THEEEEEETTTCSSS................STTHHHH.HHHHHHHHHHHTST CS
                           AAA   1 vllyGppGtGKTllakavakel......gvefleisgsellsk................yvgesek.kirelfkeakekak 58 
                                   v +yG  GtGKT++ + v ++l      +++f+ i+  +                    + g s +  ++ ++k++ + ++
  gi|70606524|ref|YP_255394.1|  59 VFIYGLTGTGKTAVTRFVLSNLqrkfpsKFTFIYINTRQNDTPyriladvlealgirvpFTGLSTAeLFKRFVKRLNTFQT 139
                                   578******************944444346677777777664489999999999998885555444044444455555446 PP

                                   SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                           AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                    + + +DEidal+k+        +++++  L +   ++++  skv vig+tn+++++++  
  gi|70606524|ref|YP_255394.1| 140 IVLITLDEIDALVKKH-------GDDILYRLTRINYDLST--SKVSVIGITNDVKMVENLD 191
                                   69999***********.......99999999999999999..69*********88877654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   6.5e-10   4.8e-07      17     158 ..      38     175 ..      30     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.5e-10
                          TniB  17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgap 97 
                                   ++i +  e L    ++++++n+ ++G + +GKt++  +F  ++ ++k +  +k+  ++++++++ +  r+ a +Lealg +
  gi|70606524|ref|YP_255394.1|  38 DQIRKLVEILAPITRSEKPSNVFIYGLTGTGKTAV-TRFVLSNLQRKFP--SKFTFIYINTRQNDTPYRILADVLEALGIR 115
                                   4444444566667889999**************86.5787777666544..56789***********************99 PP

                          TniB  98 lkara.rvskleqqvlrllrelkvrvLi.iDEihnllagsarkqreflnalksLgnelkipiv 158
                                   +  +  ++++l ++ ++ l+++++ vLi +DEi+ l++ + ++   +l  l +++ +l+ + v
  gi|70606524|ref|YP_255394.1| 116 VPFTGlSTAELFKRFVKRLNTFQTIVLItLDEIDALVKKHGDD---ILYRLTRINYDLSTSKV 175
                                   9877658899****************9978******9655554...44444444444444444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.2e-08   2.4e-05       4     133 ..      36     190 ..      34     204 .. 0.66
   2 ?    1.2   0.1       0.4     3e+02     107     154 ..     256     300 ..     200     325 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.2e-08
                      ATPase_2   4 Rekelkeleeil....erepneiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesiskl.defie...... 70 
                                   Re  +++l eil    ++e+ + +fiYG  g GKta+ + +++nl+ k       iy++  +++   ++  + +e      
  gi|70606524|ref|YP_255394.1|  36 REDQIRKLVEILapitRSEKPSNVFIYGLTGTGKTAVTRFVLSNLQRKFPskfTFIYINTRQNDTPYRIlADVLEalgirv 116
                                   77778877776533336889999*********************9554222225555555555554443133334677777 PP

                      ATPase_2  71 ......eeeekkklekal.........giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidl 133
                                         + e  k+    +            +  +e+++++k++  ++   ++++  +++ ++  +i i  ++ ++ +l
  gi|70606524|ref|YP_255394.1| 117 pftglsTAELFKR----FvkrlntfqtIVLITLDEIDALVKKHGDDILYRLTRINYDLSTSKVSVIGITNDVKMVENL 190
                                   7755542222222....2344466665334455567778888888899999999999999888888888888888754 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                      ATPase_2 107 elllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                    ++  +i ++  +  i +D++ +++ + l+  ++ v+e ++ +  ++k
  gi|70606524|ref|YP_255394.1| 256 LRVSGEIAEREGRDLITADDVNRAR-IELE--RDRVYEVISTLPFHSK 300
                                   3466789999999999********9.8887..5555555555544444 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.7e-05     0.013      29      75 ..      55     100 ..      39     106 .. 0.85
   2 ?    2.9   0.1     0.051        38     478     508 ..     250     280 ..     231     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                        AAA_32  29 kgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpee 75 
                                   k  N+f+ G +gtG+t +++ +l++ ++k p +   +Y+n  +n ++
  gi|70606524|ref|YP_255394.1|  55 KPSNVFIYGLTGTGKTAVTRFVLSNLQRKFPSKFTFIYINTRQN-DT 100
                                   556***********************************976555.44 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.051
                        AAA_32 478 seiadllrEAdywakkegaevveaehVekAl 508
                                   ++  dllr +  +a++eg+++++a++V++A 
  gi|70606524|ref|YP_255394.1| 250 RRALDLLRVSGEIAEREGRDLITADDVNRAR 280
                                   56789************************95 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.2e-05    0.0089      12      76 ..     238     295 ..     226     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHH CS
                   AAA_assoc_2  12 lealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryDkagdehYdliSAl 76 
                                   ++ala+  +GDaR+aL lL +  e ae+ eg+  it +d+++a      r++ + d  Y++iS l
  gi|70606524|ref|YP_255394.1| 238 CAALAARDHGDARRALDLLRVSGEIAER-EGRDLITADDVNRA------RIELERDRVYEVISTL 295
                                   345666668**************99986.99999*****9954......4555668899999976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.8e-06    0.0073       5      59 ..      37      96 ..      33     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.8e-06
                                  SHHHHHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTT...TS-EEEEETT CS
               Sigma54_activat  5 sealkelleqikkvaktd..lsvlitGesGtGKellaraiheaskrk...ekpfvavnca 59
                                  ++++++l+e ++ +++++  ++v+i G +GtGK+ + r + ++ +rk   +  f+ +n  
  gi|70606524|ref|YP_255394.1| 37 EDQIRKLVEILAPITRSEkpSNVFIYGLTGTGKTAVTRFVLSNLQRKfpsKFTFIYINTR 96
                                  567778888888777665559******************999777743226678888875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.2e-06    0.0061       2      81 ..      37     116 ..      36     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.2e-06
                                   HHHHHHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHH CS
                        NB-ARC   2 eksvekviekLle...kdelqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeL 76 
                                   e++++k+ e L     ++++    v+++G  G GKt + + +l++   ++++F+    ++++   ++d+ ++il ++l+ L
  gi|70606524|ref|YP_255394.1|  37 EDQIRKLVEILAPitrSEKPS--NVFIYGLTGTGKTAVTRFVLSN---LQRKFPskfTFIYINTRQNDTPYRILADVLEAL 112
                                   566666666665431155555..9*******************99...8999985444677888899999*******9999 PP

                                   HCCCT CS
                        NB-ARC  77 slsed 81 
                                   + +  
  gi|70606524|ref|YP_255394.1| 113 GIR-V 116
                                   866.4 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.3e-05     0.017       5      60 ..      36      91 ..      30     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                                  -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                        ResIII  5 reyQeeaienlleklks.krdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60
                                  re Q++ + ++l+ ++  ++  +++i   TGtGKT v   +  +l++k++  kf f+
  gi|70606524|ref|YP_255394.1| 36 REDQIRKLVEILAPITRsEKPSNVFIYGLTGTGKTAVTRFVLSNLQRKFPS-KFTFI 91
                                  6777777777777776556666999*************9999999999986.66665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05     0.024      33      77 ..      56      99 ..      46     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                         AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                    +v+++G tGtGKt++++ +l++l+ +k+ s++  +  +t  n+
  gi|70606524|ref|YP_255394.1| 56 PSNVFIYGLTGTGKTAVTRFVLSNLQ-RKFPSKFTFIYINTRQND 99
                                  56899**************9999999.555555444444444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.023      32      87 ..      35      93 ..      28     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                        DUF815 32 gidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg...Lrliev 87
                                    ++q ++lve  +   + ++ +nv+++G  GtGK ++ +++l++++++      +i +
  gi|70606524|ref|YP_255394.1| 35 HREDQIRKLVEILAPITRSEKPSNVFIYGLTGTGKTAVTRFVLSNLQRKFpskFTFIYI 93
                                  568899999999999999**************************999875545555555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.19       5      77 ..      40     112 ..      36     119 .. 0.82
   2 ?    1.2   0.4      0.24   1.8e+02     157     194 ..     123     160 ..     119     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                    KAP_NTPase   5 asaladilseptl.atpivvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkggddavaellaaL 77 
                                   + +l++il   t  ++p+ v +yg  G+GK+++  ++ ++l+ +  p +f+f+++n    ++   ++a++l+aL
  gi|70606524|ref|YP_255394.1|  40 IRKLVEILAPITRsEKPSNVFIYGLTGTGKTAVTRFVLSNLQRK-FPSKFTFIYINTRQNDTPYRILADVLEAL 112
                                   6677777765443488999******************9999988.8**********988888777777777776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.24
                    KAP_NTPase 157 veelladmektLdalqkrlVvviDdLDrceteevlqll 194
                                    +el+++++k L   q+ +++ +D++D + ++    +l
  gi|70606524|ref|YP_255394.1| 123 TAELFKRFVKRLNTFQTIVLITLDEIDALVKKHGDDIL 160
                                   56799*********999999*******98776555554 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.6e-05     0.042      36     139 ..      53     153 ..      36     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.6e-05
                                   GGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS.S-B-SHHHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  36 kkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykgvelsalediphllsvavatdperalraleeLvkem 116
                                   ++ +s++ + G tg+GK+ a+  ++lS + ++ P + ++i i       + +  ++++l+  ++  p + l++ +eL k  
  gi|70606524|ref|YP_255394.1|  53 SEKPSNVFIYGLTGTGKT-AVTRFVLSNLQRKFPSKFTFIYINTR-QNDTPYRILADVLEALGIRVPFTGLST-AELFKRF 130
                                   45679************7.78889*****************9987.345677777777776666666666665.4566666 PP

                                   HHHHHHHHHTT-SSHHHHHHHHH CS
                  FtsK_SpoIIIE 117 eeryalfreagvrsiaaydgeia 139
                                    +r + f+     +++  d+ ++
  gi|70606524|ref|YP_255394.1| 131 VKRLNTFQTIVLITLDEIDALVK 153
                                   66666666555555555555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0085       6.3      14      34 ..      56      76 ..      39     106 .. 0.74
   2 ?    5.6   0.1     0.016        12     111     155 ..     130     172 ..      99     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0085
                                  TCEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 14 ggdvlvaaeTGsGKTlaflip 34
                                    +v++ + TG+GKT++  + 
  gi|70606524|ref|YP_255394.1| 56 PSNVFIYGLTGTGKTAVTRFV 76
                                  4699***********995433 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                                   HHHCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 111 llstgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                   +++  +ln ++ + ++ lDE+d l ++  +d+i   l++++   ++
  gi|70606524|ref|YP_255394.1| 130 FVK--RLNtFQTIVLITLDEIDALVKK-HGDDILYRLTRINYDLST 172
                                   443..444488888999*********9.666666668887544444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   0.00038      0.28      36     209 ..      58     253 ..      44     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                                   -EEEE-SSSSSHHHHHHHHHHHHHHHSSSS.-EEEEEHH......HHHHHHHHHHHT.......T-HHHHHHHHTT-S... CS
                      Bac_DnaA  36 PlfiygevGlGktHLlkaignevlenapel.rvvYltae......eFlnelvkalrd.......kkaeefkeklrkvD... 99 
                                    +fiyg +G Gkt + + +  ++++++p++   +Y+++       + l+++++al         ++ae fk+++++++   
  gi|70606524|ref|YP_255394.1|  58 NVFIYGLTGTGKTAVTRFVLSNLQRKFPSKfTFIYINTRqndtpyRILADVLEALGIrvpftglSTAELFKRFVKRLNtfq 138
                                   489***********9999999999999865367899775222222467777777643345555566777887766543222 PP

                                   ..EEE.EE-GGGGTT-HHHHHHHHHH..HHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHH CS
                      Bac_DnaA 100 ..vLl.iDDiqflagkektqeelfht..fnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlail 175
                                     vL+ +D+i  l +k++ +++l+ +  +n  l ++k  v+      k +e+l+ r++s +     +   p + e   +il
  gi|70606524|ref|YP_255394.1| 139 tiVLItLDEIDALVKKHG-DDILYRLtrINYDLSTSKVSVIGITNDVKMVENLDPRVKSSLGEEE-IIFPPYNAEQLEDIL 217
                                   323333699****99984.56665442267667788888999999999***********998764.446788999999999 PP

                                   HHHHHHTT--..--TTHHHHHHHH--S-HHHHHHHH CS
                      Bac_DnaA 176 kkkieaekle..vpeevlefiaervtdnvRelegal 209
                                   k++ + +  e  + eev+++ a    ++  + + al
  gi|70606524|ref|YP_255394.1| 218 KQRSKIALNEgvISEEVIKLCAALAARDHGDARRAL 253
                                   99888776667799****999987777766666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.15       3      99 ..      59     157 ..      57     184 .. 0.68
   2 ?   -3.3   0.0       9.9   7.4e+03      72      98 ..     258     284 ..     237     305 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C...........C CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse...........v 72 
                                   v++ G  G GKT+  + + + ++++ + +  f + ++++ r+  ++   r lad+l + +                    +
  gi|70606524|ref|YP_255394.1|  59 VFIYGLTGTGKTAVTRFVLSNLQRKFPSK--FTF-IYINTRQNDTP--YRILADVLEALGIRVP----FtglstaelfkrF 130
                                   899**********9999999988777555..333.34444444443..3456666666543332....2222244666657 PP

                                   HHHHCCSCCCEEEEEE-STT-SS-TCH CS
                         NACHT  73 wavllelperlLlilDglDelvtdlgq 99 
                                   ++ l + ++ +L++lD +D lv++ g 
  gi|70606524|ref|YP_255394.1| 131 VKRLNTFQTIVLITLDEIDALVKKHGD 157
                                   77788888888899*******997766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.9
                                   CHHHHCCSCCCEEEEEE-STT-SS-TC CS
                         NACHT  72 vwavllelperlLlilDglDelvtdlg 98 
                                   v  +++e++ r L++ D++++++ +l+
  gi|70606524|ref|YP_255394.1| 258 VSGEIAEREGRDLITADDVNRARIELE 284
                                   556677777777777777776665444 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.12       9      47 ..      42      81 ..      36      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                  HHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
                          PIF1  9 vfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklr 47
                                   + +i++ +++ ek+ ++F++G  GtgKt + + +l+ l+
  gi|70606524|ref|YP_255394.1| 42 KLVEILAPITRsEKPSNVFIYGLTGTGKTAVTRFVLSNLQ 81
                                  45556665554499***************99998887776 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.12      48      92 ..      51      94 ..      37     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                  SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEH CS
                        Torsin 48 ekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfva 92
                                   +++kp  + ++G tGtGk  v++ +  nl r+   s++   ++ 
  gi|70606524|ref|YP_255394.1| 51 TRSEKPSNVFIYGLTGTGKTAVTRFVLSNLQRK-FPSKFTFIYIN 94
                                  47899999*********************9887.45565555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.15       3      59 ..      36      96 ..      34     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                  SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                          TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59
                                  +e+++++l + la  +     + ++++G  G+GKT+ +r ++++l+ +  +  TF  +++ 
  gi|70606524|ref|YP_255394.1| 36 REDQIRKLVEILAPITrsekPSNVFIYGLTGTGKTAVTRFVLSNLQRKFPSKFTFIYINTR 96
                                  56788888888888666544446*********************97653344577766665 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.23   1.7e+02       7      51 ..     229     293 ..     228     296 .. 0.67
   2 ?    9.6   0.1    0.0012      0.93      30      62 ..     329     358 ..     302     366 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.23
                       E2F_TDP   7 vltkkfvellke.......sakgtlslneaakeLv.............dkkdekvkkRRiYDilN 51 
                                   v+++++++l++        +a++ l+l  ++ e+              ++++ + ++ R+Y+++ 
  gi|70606524|ref|YP_255394.1| 229 VISEEVIKLCAAlaardhgDARRALDLLRVSGEIAeregrdlitaddvNRARIELERDRVYEVIS 293
                                   6777788887655333333234445555555555599999999998888888999999***9986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0012
                       E2F_TDP  30 akeLvdkkdekvkkRRiYDilNVLealglieKe 62 
                                   a +L+    e + +RR+ Di+N L+ +g+i+ +
  gi|70606524|ref|YP_255394.1| 329 AGKLG---VESITQRRVSDIINELDMVGIITAR 358
                                   44555...677899****************865 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047      0.35      44      80 ..     229     265 ..     197     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                                   -------HHHHHHHHHHT-TTTTHHHHHHHHHHHHHH CS
                    AAA_lid_10  44 kisddaieiasrkvAsvsgdarrAlkiCkrAvEiaek 80 
                                    is+++i++ +   A   gdarrAl + +   Eiae+
  gi|70606524|ref|YP_255394.1| 229 VISEEVIKLCAALAARDHGDARRALDLLRVSGEIAER 265
                                   489********************************97 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00038      0.28       8      66 ..      41     106 ..      36     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHC.C--TTS-EE--SSTTHHHH....-HHHHHH CS
               Sigma54_activ_2   8 qelkerLeqaa..qsklpvfltGekGsgkelvArl.Lhknsgpwleifvverlak....lpldlle 66 
                                    +l e L+ +   ++ ++vf+ G  G+gk+ v r+ L++ + + ++ f++++  +     p ++l+
  gi|70606524|ref|YP_255394.1|  41 RKLVEILAPITrsEKPSNVFIYGLTGTGKTAVTRFvLSNLQRKFPSKFTFIYINTrqndTPYRILA 106
                                   555566666652256688****************84666677777777776655322224555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2604.98
//
Query:       gi|70606525|ref|YP_255395.1|  [L=561]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3865.99
//
Query:       gi|70606526|ref|YP_255396.1|  [L=384]
Description: hypothetical protein Saci_0725 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   93.5  49.6    3.6e-16   59.1  26.0    2.2  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1  26.0     2e-20   3.6e-16       4     260 ..      17     252 ..       8     263 .. 0.80
   2 !   38.8  26.2   2.9e-14   5.2e-10       2     175 ..     203     379 ..     203     384 .] 0.85

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2e-20
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfass 84 
                                   +a+ +  + ++++++l ++ +  +g++   +g l +l + ++++++ ++ ++    +rr+v++ + +l ++  l++++  s
  gi|70606526|ref|YP_255396.1|  17 IAIANRSTNNMVTTTLAPLTKYVFGFNNFLAGVLEGLIFMATLISTSLINPVLSPSSRRKVFISCNFLISVL-LIGFY-LS 95 
                                   34444444455666665578888********************************9****************.88886.34 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                    + +++++ +++G+++g+++p+ ++ ++ + +k+   r ++l+s++ s++ i+gpll ++++s +++ +vf+++ ++s+l+
  gi|70606526|ref|YP_255396.1|  96 TPlTVWIFTAIAGVAYGLIMPNLVTSASLVENKRLAERLLSLYSTSLSISLIIGPLLESYVLSIFSYKSVFLAFLPFSILS 176
                                   5558***************************************************************************** PP

                         MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglll 245
                                   fvl   +l   p +++   +              + +al+++ ++ + ++++ +  + f++++t++++y  + lgl+    
  gi|70606526|ref|YP_255396.1| 177 FVL--SWLIKFPDAKREI-H--------------GMSALRNKGFI-SSILSITTYNIPFAAFTTFITIYGIDELGLP--KN 237
                                   997..5553333333333.2..............25567777755.366666666668888999999999******9..55 PP

                         MFS_1 246 aglllallalvgail 260
                                   +++++ ++++++ +l
  gi|70606526|ref|YP_255396.1| 238 LAYFSYIPFFITSFL 252
                                   555666666666544 PP

  == domain 2  score: 38.8 bits;  conditional E-value: 2.9e-14
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl...lltlyalgaavaslpl.Grlsdr.fGrrr.vlllglllfalgl 76 
                                   +++ +ls+++++i ++a++ +  + +g   +e+gl   l+ + ++ ++++s+++  +++ r f + r  ll+++++++lg 
  gi|70606526|ref|YP_255396.1| 203 FISSILSITTYNIPFAAFT-TFITIYG--IDELGLpknLAYFSYIPFFITSFLTrLFMTIRpFRSLRyPLLISVVITILG- 279
                                   6889999999***999999.6668888..777777776555566666777777744445567877777************. PP

                         MFS_1  77 llll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                   ++++ f+++l l l++ +l G+  g++fp++ ++ia+ ++ eer+ +++++ a +++ + + p++ g+l++ +g  ++f++
  gi|70606526|ref|YP_255396.1| 280 IIGVvFSPNLALYLIFMALLGIPHGSVFPISTIIIARATSSEERNAVNSYFLAYNNILFFIVPIVVGALSQFIGLGYAFVA 360
                                   66666867777********************************************************************** PP

                         MFS_1 157 laivsllafvlfllllpee 175
                                   l i  ++ + +f+l ++ +
  gi|70606526|ref|YP_255396.1| 361 LIIPVIITATVFFLKYWND 379
                                   *******999888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2507.44
//
Query:       gi|70606527|ref|YP_255397.1|  [L=111]
Description: hypothetical protein Saci_0726 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00091   18.8   0.6     0.0018   17.9   0.6    1.5  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.6   9.9e-08    0.0018       2      33 ..      33      68 ..      32      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.9e-08
                          SWIM  2 rVtldder..vrlnkatCsCpefqk..ngipCkHal 33
                                  +V+l++++    + +++C+Cp+f +   ++ C H++
  gi|70606527|ref|YP_255397.1| 33 FVFLGKDKdyLMVKDKYCTCPFFFFnkQKLKCYHLI 68
                                  577777777777889*******99999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 753.11
//
Query:       gi|70606528|ref|YP_255398.1|  [L=99]
Description: hypothetical protein Saci_0727 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-18   65.1   0.1    5.4e-18   64.8   0.1    1.1  1  Elf1             Transcription elongation factor Elf1 like
     0.0067   16.8   0.5     0.0093   16.3   0.5    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.035   13.5   1.0       0.37   10.3   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.099   12.9   1.7       0.39   11.0   1.7    1.9  1  Ribosomal_L32p   Ribosomal L32p protein family
       0.91    9.5   5.2          9    6.3   5.2    2.2  1  zinc_ribbon_4    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.1   1.5e-21   5.4e-18       1      77 [.       2      75 ..       2      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.5e-21
                          Elf1  1 gkRkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepvDvYskwiDace 77
                                  g Rkk++k + ++ k+k+p++F+Cp+C++    +++++ ke+ia+v C++C+++ +++v+ ++++++ Y k+iD ++
  gi|70606528|ref|YP_255398.1|  2 GGRKKRRKLQLQRPKPKIPSVFECPRCGKV---TISITVKEGIAKVMCGNCKLEDQFDVPLVYDEANAYGKFIDRYY 75
                                  67888888899*****************88...778888999********************************987 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   2.6e-06    0.0093       5      50 ..      24      66 ..      21      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
               Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.stpwfkiaedeaea 50
                                   CP Cg+  + ++ + + a     v+C +C+   + +++   dea+a
  gi|70606528|ref|YP_255398.1| 24 ECPRCGKVTISITVKEGIA----KVMCGNCKLeDQFDVPLVYDEANA 66
                                  6******************....8*******9644455555555554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0001      0.37       4      12 ..      24      33 ..      21      38 .. 0.76
   2 ?    1.9   0.1     0.044   1.6e+02      18      23 ..      45      50 ..      43      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                   zf-ribbon_3  4 rCPnCGap.l 12
                                  +CP+CG++ +
  gi|70606528|ref|YP_255398.1| 24 ECPRCGKVtI 33
                                  8*****9635 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.044
                   zf-ribbon_3 18 vCpyCG 23
                                  +C +C 
  gi|70606528|ref|YP_255398.1| 45 MCGNCK 50
                                  799996 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.7   0.00011      0.39      12      38 ..       5      34 ..       3      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                  HHHHGGGT...------EEEETTTCCEECT CS
                Ribosomal_L32p 12 rrkRrahw...klkapnlvecpncgelklp 38
                                  +++R  +    k k p++ ecp cg+++++
  gi|70606528|ref|YP_255398.1|  5 KKRRKLQLqrpKPKIPSVFECPRCGKVTIS 34
                                  3333333234599*************9875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.2    0.0025         9       3      32 ..      23      50 ..      22      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                 zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCg 32
                                  ++Cp+C+++ +i+   ++++++kv C +C+
  gi|70606528|ref|YP_255398.1| 23 FECPRCGKV-TISI-TVKEGIAKVMCGNCK 50
                                  58*****98.8988.699***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 695.13
//
Query:       gi|70606529|ref|YP_255399.1|  [L=257]
Description: geranylgeranylglyceryl phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-51  172.7   1.0    9.4e-51  172.4   1.0    1.0  1  PcrB           PcrB family
      3e-06   26.5   1.0    0.00032   19.8   0.5    2.2  2  IMPDH          IMP dehydrogenase / GMP reductase domain
    0.00029   20.4   0.3    0.00052   19.5   0.3    1.4  1  His_biosynth   Histidine biosynthesis protein
      0.004   17.6   3.1     0.0053   17.2   0.5    2.2  3  NAD_binding_7  Putative NAD(P)-binding
      0.006   15.8   1.0     0.0087   15.3   1.0    1.2  1  DHO_dh         Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.012   14.8   0.6      0.069   12.3   0.3    2.0  2  NanE           Putative N-acetylmannosamine-6-phosphate epime
      0.025   14.6   1.0      0.065   13.3   1.0    1.6  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
       0.49   10.7   5.6         12    6.3   0.1    2.5  2  BON            BON domain


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.4   1.0   4.2e-54   9.4e-51       7     225 ..      18     246 ..      12     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 4.2e-54
                                   S...EEEEE-TTS....S-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEE CS
                          PcrB   7 r...hltklDPee....enpdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDalFv 80 
                                       h  ++DP++    +   +i+  +ie gtD  +igG+ ++ +d+  ++l+  +++++P++++psnv+ ++++aDa+ +
  gi|70606529|ref|YP_255399.1|  18 GktlHFSLFDPDKifdlDSLHDIASKLIEAGTDVFLIGGTLGISQDKLDNILSILEEFSIPLIIFPSNVNLISNKADAILF 98 
                                   345699999**9855556778888899**********************99999999************************ PP

                                   EEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SEEEEE CS
                          PcrB  81 msllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglrliYlE 160
                                    sllns + ++ivga+  ++  +k++   +e+l+ +Yl++  +++++ ++ a+ ++ +  +++  + laa+++g+++iYlE
  gi|70606529|ref|YP_255399.1|  99 LSLLNSDDLYYIVGAQIVAAPIIKRIG--LEVLPTAYLIIGHGGTAGHIGRARvIPYDNIELIVSYSLAANYMGMKYIYLE 177
                                   ***************************..************************999876555555666************* PP

                                   -.TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHHHH CS
                          PcrB 161 a.sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkidailea 225
                                   a sGa+e v  e+++ +k+ +++  +ivGGG+ s+E+A++ v a AD+iv+Gnv+e +++++++ i+e 
  gi|70606529|ref|YP_255399.1| 178 AgSGASETVkpEAIKVVKNTVKDGVVIVGGGVTSEERARNLVLAgADIIVTGNVIERDHQKALKIIKEI 246
                                   *******99978888889999****************************************99999875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0049        11     107     149 ..      39      80 ..      33      96 .. 0.84
   2 !   19.8   0.5   1.4e-07   0.00032     116     173 ..     170     229 ..     163     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0049
                                   HHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 107 ervkalveagvdvlvvdsahghsekvleavkeikkkveevevi 149
                                   + +++l+eag dv ++  + g s+  l+ + +i ++++ + +i
  gi|70606529|ref|YP_255399.1|  39 DIASKLIEAGTDVFLIGGTLGISQDKLDNILSILEEFS-IPLI 80 
                                   55789***************************999994.5444 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.4e-07
                                   T-SEEEEE-STSSSHHHH.HHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 116 gvdvlvvdsahghsekvl.eavkeikkkvee.veviaGnvataegakaLieagadavkvG 173
                                   g+  + +++  g se+v  ea+k +k++v++ v +++G v+++e a++L+ agad++  G
  gi|70606529|ref|YP_255399.1| 170 GMKYIYLEAGSGASETVKpEAIKVVKNTVKDgVVIVGGGVTSEERARNLVLAGADIIVTG 229
                                   566788889999999986489*********9999*********************99766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   2.3e-07   0.00052      53     118 ..     181     245 ..     143     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.3e-07
                                   HHC.TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                  His_biosynth  53 aak.egreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                   +a+ + +++ +++v+++++     v vGGG+ s e++++l+ agad ++ g +  ++ +   +++++
  gi|70606529|ref|YP_255399.1| 181 GASeTVKPEAIKVVKNTVKD--GVVIVGGGVTSEERARNLVLAGADIIVTGNVIERDHQKALKIIKE 245
                                   44415677888999999999..999*********************999999877666655555555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.6   1.3e+03      24      40 ..      42      58 ..      41     120 .. 0.68
   2 ?   -3.9   0.1         8   1.8e+04      10      19 ..     133     142 ..     131     144 .. 0.80
   3 !   17.2   0.5   2.4e-06    0.0053       9      51 ..     201     243 ..     194     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.6
                 NAD_binding_7 24 rklleagakvtvvapev 40
                                  +kl+eag +v ++  ++
  gi|70606529|ref|YP_255399.1| 42 SKLIEAGTDVFLIGGTL 58
                                  68899999999987774 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8
                 NAD_binding_7  10 vlvvGgGevA 19 
                                    l++G G  A
  gi|70606529|ref|YP_255399.1| 133 YLIIGHGGTA 142
                                   599**99876 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.4e-06
                 NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvkla 51 
                                    v++vGgG   ++++r+l+ aga+++v  + +++ +++ +k++
  gi|70606529|ref|YP_255399.1| 201 GVVIVGGGVTSEERARNLVLAGADIIVTGNVIERDHQKALKII 243
                                   599************************8888766666665544 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.0   3.9e-06    0.0087     218     293 ..     178     248 ..     144     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-06
                                   SEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHH CS
                        DHO_dh 218 tGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkelee 293
                                   +G  + + +k+ a+kv+ +   ++k+ + i+g GG++s e a + + aGA ++  +  +  ++ + a ki+ke+++
  gi|70606529|ref|YP_255399.1| 178 AGSGASETVKPEAIKVVKN---TVKDGVVIVG-GGVTSEERARNLVLAGADIIVTGNVI-ERDHQKALKIIKEIKS 248
                                   4522446899999999864...5666666666.*******************9888766.7888899999999986 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.14   3.1e+02      10      36 ..      54      80 ..      39      88 .. 0.75
   2 ?   12.3   0.3   3.1e-05     0.069     131     191 ..     188     247 ..     160     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.14
                                  HHT-SEEEEESHHHHHHHHTT--S-EE CS
                          NanE 10 qaGavgiriegvedikaikavvdlPii 36
                                  ++G+ gi  + +++i  i ++ ++P+i
  gi|70606529|ref|YP_255399.1| 54 IGGTLGISQDKLDNILSILEEFSIPLI 80
                                  577777777778888777777777776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.1e-05
                                   S--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                          NanE 131 epDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfveaik 191
                                    + +++vk+ +++g+ vi+ G + + e+a++ +  G+d +v G  i r ++ a k +++ik
  gi|70606529|ref|YP_255399.1| 188 PEAIKVVKNTVKDGV-VIVGGGVTSEERARNLVLAGADIIVTGNVIERDHQKALKIIKEIK 247
                                   345788899888887.788999**************************9999988888887 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   2.9e-05     0.065       5      58 ..     192     248 ..     189     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                   HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEE...EEESSHHHHHHHHHHHT. CS
                  Shikimate_DH   5 kkleslkekkvlliGaGemaelvakhLlakgvkkvv...vaNRtlerakelaeelkg 58 
                                   k +++  +  v+++G G ++e+ a++L+ +g++ +v   v+ R++++a ++ +e+k+
  gi|70606529|ref|YP_255399.1| 192 KVVKNTVKDGVVIVGGGVTSEERARNLVLAGADIIVtgnVIERDHQKALKIIKEIKS 248
                                   5566677788**********************9665455678999999999999865 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.3     0.011        25      24      46 ..     194     216 ..     182     223 .. 0.82
   2 ?    6.3   0.1    0.0052        12      32      66 ..     224     257 .]     217     257 .] 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.011
                                   CEEEEETTCEEEECEEECHHHHH CS
                           BON  24 inVevenGvVtLsGtVdseaeke 46 
                                   ++ +v++GvV++ G V+se+ ++
  gi|70606529|ref|YP_255399.1| 194 VKNTVKDGVVIVGGGVTSEERAR 216
                                   5668************8887654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0052
                                   CEEEECEEECHHHHHHHHHHHHCCTTEEEEEEEEE CS
                           BON  32 vVtLsGtVdseaekekAveiarnvaGVkkVvnelk 66 
                                   +++++G+V  e + +kA +i+++++ +++  n +k
  gi|70606529|ref|YP_255399.1| 224 DIIVTGNV-IERDHQKALKIIKEIKSIRRTSNAIK 257
                                   3899****.******************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1849.67
//
Query:       gi|70606530|ref|YP_255400.1|  [L=59]
Description: preprotein translocase subunit SecG [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-15   55.4   3.0    5.1e-15   55.2   3.0    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   3.0   2.9e-19   5.1e-15       1      40 [.      15      54 ..      15      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.9e-19
                                  XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                    Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                  S+aGL+ryye +++++ki+PkvV+v+s+++ia Vi++ ++
  gi|70606530|ref|YP_255400.1| 15 SMAGLVRYYESEKEKVKISPKVVVVASIVLIAGVIIASFI 54
                                  89**********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 425.05
//
Query:       gi|70606531|ref|YP_255401.1|  [L=165]
Description: hypothetical protein Saci_0730 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-36  123.1   0.0    6.5e-36  122.9   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
      1e-12   47.6   0.3    1.5e-12   47.1   0.3    1.3  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0   7.3e-40   6.5e-36       1     126 [.      36     158 ..      36     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 7.3e-40
                                   EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT CS
                 Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilg 81 
                                   ivl+p++++v+  +D+ei+ k+g+++vd+sW++++  +fk++    +r+LP+L+A+Np+nY+ +++Ls++EA++a+lyil+
  gi|70606531|ref|YP_255401.1|  36 IVLDPFSETVVGIEDSEILIKQGLTAVDTSWNNTTINEFKST--GFHRRLPILFAGNPTNYALAYRLSTLEAISATLYILE 114
                                   8********************************988887776..699********************************** PP

                                   -HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHH CS
                 Ribo_biogen_C  82 lkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkey 126
                                   + e + ++l++ kwg++F+elnk++le+Y k k+++e++++++e+
  gi|70606531|ref|YP_255401.1| 115 HIELSFSILNTVKWGKTFYELNKDILESY-KGKKRDEIMKIENEI 158
                                   *****************************.78999*******997 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.3   1.7e-16   1.5e-12       1      32 [.       1      32 [.       1      35 [. 0.92

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.7e-16
                                  --EEEES---------TTHHHHHTTSEEEESS CS
                           RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrt 32
                                  m+++i+d++++dPKKCtgkk++r+++++  + 
  gi|70606531|ref|YP_255401.1|  1 MKIYIIDYHKDDPKKCTGKKLIRLGYAKPTNK 32
                                  9**************************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1030.79
//
Query:       gi|70606532|ref|YP_255402.1|  [L=83]
Description: hypothetical protein Saci_0731 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-14   53.2   0.5    2.4e-14   53.0   0.5    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0087   16.1   0.6      0.011   15.8   0.6    1.2  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.5   2.7e-18   2.4e-14       1      74 [.       6      76 ..       6      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 2.7e-18
                                  EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                  vl++++ g     ee+ e+l+ l eV+e++ v G yd+++k+ +  l+ l +f+ +++++lp v++t t+iv e
  gi|70606532|ref|YP_255402.1|  6 VLINTDAGG---EEEVFEKLKSLNEVTEVHIVYGVYDIVAKIEADTLDKLKDFVTNTVRKLPRVRSTLTMIVVE 76
                                  788999888...9***********************************************************86 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.2e-06     0.011       6      67 ..       6      69 ..       2      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                          NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsa 67
                                  ++++++ +  ++v ++l++l +v Evh + +   +V  iEa++ d+l d +++ +++lp V s+
  gi|70606532|ref|YP_255402.1|  6 VLINTDAGGEEEVFEKLKSLNEVtEVHIVYGVYDIVAKIEADTLDKLKDFVTNtVRKLPRVRST 69
                                  56788899999********97754*************************99876999*999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 614.68
//
Query:       gi|70606533|ref|YP_255403.1|  [L=393]
Description: hypothetical protein Saci_0732 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-32  110.9   0.0    6.2e-32  110.1   0.0    1.4  1  DUF1743          Domain of unknown function (DUF1743)
     0.0012   18.7   0.7     0.0029   17.5   0.7    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0043   17.1   0.5        1.1    9.4   0.2    2.4  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.054   13.5   4.3       0.12   12.3   4.3    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.07   13.0   4.9       0.79    9.6   3.5    2.8  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.071   13.2   0.6       0.16   12.0   0.6    1.7  1  Ribosomal_L37ae  Ribosomal L37ae protein family
        0.1   12.5   1.1       0.22   11.4   1.1    1.5  1  C1_1             Phorbol esters/diacylglycerol binding domain
        0.1   12.7   0.0        0.2   11.8   0.0    1.4  1  DUF2396          Protein of unknown function (DUF2396)
       0.11   12.4   0.0       0.21   11.5   0.0    1.5  1  Thioredoxin_15   Thioredoxin-like domain
       0.16   12.0   1.1       0.46   10.5   1.1    1.8  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.17   12.3   6.1        1.1    9.9   1.0    2.7  2  zf-H2C2_2        Zinc-finger double domain
        2.2    8.9   5.5        8.6    7.0   1.0    2.7  2  zf-C2H2          Zinc finger, C2H2 type
        6.5    6.8   6.8         38    4.3   2.7    2.5  2  zf-C2HC_2        zinc-finger of a C2HC-type


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   4.5e-35   6.2e-32       1     116 []     104     216 ..     104     216 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 4.5e-35
                                   TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEEE CS
                       DUF1743   1 grgiiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGirg 81 
                                   +rgiiG++aa+g+ +  e +tyEl++Yr+      r vd +svi+++e+ +p+tf+n+D+ +k+++++P+++dp+l+G+rg
  gi|70606533|ref|YP_255403.1| 104 DRGIIGSIAAIGYLP-IEGFTYELITYRHDASS-FRIVDVNSVIKFEERNFPKTFNNFDYIKKRLLITPQGKDPILYGVRG 182
                                   8************55.569**********9987.9********************************************** PP

                                   S-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                       DUF1743  82 edpeallkaakeilskeeeseemavfrtnqgtdah 116
                                   ++   +l+a+kei+s ++++e ++++++nqgtdah
  gi|70606533|ref|YP_255403.1| 183 NNLSVMLEALKEIRS-SNNVELAMIYKSNQGTDAH 216
                                   ***************.888899***********99 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   2.1e-06    0.0029      25      60 ..     308     343 ..     296     346 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                OrfB_Zn_ribbon  25 ayTSktCseCgsknkealsgrtfkCpnCgfeadrDv 60 
                                   +yT  +C++C +  +    ++ +kC++Cg+e+++  
  gi|70606533|ref|YP_255403.1| 308 EYTNPKCPKCNRSATSLGVKKGYKCKKCGYEFNAEK 343
                                   68999***********999**************975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.014        19      23      35 ..     308     320 ..     291     324 .. 0.65
   2 !    9.4   0.2   0.00079       1.1       6      17 ..     330     341 ..     329     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                   Zn-ribbon_8  23 dapltaCPeCgse 35 
                                   +  +++CP+C+  
  gi|70606533|ref|YP_255403.1| 308 EYTNPKCPKCNRS 320
                                   555788****984 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00079
                   Zn-ribbon_8   6 YrCeeCghefev 17 
                                   Y+C++Cg ef++
  gi|70606533|ref|YP_255403.1| 330 YKCKKCGYEFNA 341
                                   9*********84 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.3   8.8e-05      0.12      18      45 ..     311     337 ..     306     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                 Zn_Tnp_IS1595  18 gfvCPhCgsr.kayriktrglfqCkeCrk 45 
                                   ++ CP+C  + ++  +k  + ++Ck+C++
  gi|70606533|ref|YP_255403.1| 311 NPKCPKCNRSaTSLGVK--KGYKCKKCGY 337
                                   589****9555555555..69******98 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.25   3.5e+02       6      13 ..      68      75 ..      67      83 .. 0.79
   2 ?    9.6   3.5   0.00058      0.79       4      34 ..     314     342 ..     314     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                                  TTTSBEEE CS
                RNA_POL_M_15KD  6 kCgNlLlp 13
                                  +C+N L++
  gi|70606533|ref|YP_255403.1| 68 ECKNFLYN 75
                                  8*****98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00058
                                   ESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYeepad 34 
                                   CpkC+    + + k+g  + C +CgYe+ a+
  gi|70606533|ref|YP_255403.1| 314 CPKCNRSATSLGVKKG--YKCKKCGYEFNAE 342
                                   8888877777777777..89********987 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00012      0.16       5      63 ..     284     341 ..     281     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                   XX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE- CS
               Ribosomal_L37ae   5 vgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaG 63 
                                   v+   kyg  + a+ r rv ++  +++++ +Cp+c++++ +    + +kCkkcg+++ +
  gi|70606533|ref|YP_255403.1| 284 VRPSDKYGKIFEAE-RMRVLSLNYHEYTNPKCPKCNRSATSLGVKKGYKCKKCGYEFNA 341
                                   67778888888765.8889999999999999*****99999999999*******99876 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00016      0.22      12      38 ..     312     339 ..     305     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                   -B-TTT-SB--S.SSS-EEEETTT--EE CS
                          C1_1  12 tfCkhCgeflwg.kekqglkCswCkllv 38 
                                    +C +C+ +    + k g+kC+ C++ +
  gi|70606533|ref|YP_255403.1| 312 PKCPKCNRSATSlGVKKGYKCKKCGYEF 339
                                   5899999999888***********9975 PP

>> DUF2396  Protein of unknown function (DUF2396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.2       8      77 ..     313     380 ..     309     387 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                       DUF2396   8 kcPhcrqtipaltltdtylcerhG.afeadpeteelvhlqsgrkwrlwegkwyrqhthpdgirfeiheald 77 
                                   kcP+c++  ++l +   y c++ G  f+a+  t e+           ++ +++r  t+p  + ++ +e ld
  gi|70606533|ref|YP_255403.1| 313 KCPKCNRSATSLGVKKGYKCKKCGyEFNAEKVTIEIPR---FLVKDEYQSRYHRHLTKPVYLELQTQEDLD 380
                                   8*********************9933666665554433...334456677788888888877777777777 PP

>> Thioredoxin_15  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.21      46      90 ..     188     231 ..     183     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHH-TTEEEEEEE--S--SS-THHHHHHHHHTGGGGCT CS
                Thioredoxin_15  46 LleAlkflksspgvRlgiihnpssdseasslissalsaalkklkn 90 
                                   +leAlk ++ss++v+l +i+ +++ ++a+ + +   + ++++ k+
  gi|70606533|ref|YP_255403.1| 188 MLEALKEIRSSNNVELAMIYKSNQGTDAHIS-NDSKEYYYRTVKK 231
                                   789**********************886666.4444444444333 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00034      0.46       3      29 ..     312     339 ..     303     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                PhnA_Zn_Ribbon   3 pkCplCa.SeytYedgallvCpeCahEw 29 
                                   pkCp+C+ S +++  +  + C +C++E+
  gi|70606533|ref|YP_255403.1| 312 PKCPKCNrSATSLGVKKGYKCKKCGYEF 339
                                   9*****9788899999999999999997 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.047        64      16      25 ..     313     322 ..     303     323 .. 0.80
   2 ?    9.9   1.0   0.00077       1.1      12      25 ..     327     340 ..     324     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.047
                     zf-H2C2_2  16 eCplCdkaFk 25 
                                   +Cp+C+ + +
  gi|70606533|ref|YP_255403.1| 313 KCPKCNRSAT 322
                                   8****98865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00077
                     zf-H2C2_2  12 ekpyeCplCdkaFk 25 
                                   +k y+C++C++ F+
  gi|70606533|ref|YP_255403.1| 327 KKGYKCKKCGYEFN 340
                                   455*********96 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.099   1.4e+02       2      10 ..     313     321 ..     313     325 .. 0.83
   2 ?    7.0   1.0    0.0062       8.6       1      11 [.     330     340 ..     330     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.099
                                   EETTTTEEE CS
                       zf-C2H2   2 kCpdCgksF 10 
                                   kCp+C++s 
  gi|70606533|ref|YP_255403.1| 313 KCPKCNRSA 321
                                   7*****985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0062
                                   EEETTTTEEES CS
                       zf-C2H2   1 ykCpdCgksFk 11 
                                   ykC++Cg+ F+
  gi|70606533|ref|YP_255403.1| 330 YKCKKCGYEFN 340
                                   9********97 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.7     0.027        38       4      11 ..     313     320 ..     313     320 .. 0.92
   2 ?    3.9   0.1     0.036        50       4      15 ..     331     342 ..     330     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                     zf-C2HC_2   4 pCpkCgRs 11 
                                   +CpkC+Rs
  gi|70606533|ref|YP_255403.1| 313 KCPKCNRS 320
                                   6******8 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.036
                     zf-C2HC_2   4 pCpkCgRsFnpd 15 
                                   +C+kCg  Fn++
  gi|70606533|ref|YP_255403.1| 331 KCKKCGYEFNAE 342
                                   7*****999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2644.67
//
Query:       gi|70606534|ref|YP_255404.1|  [L=219]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0042   16.8  28.6      0.014   15.1   4.1    2.9  3  Yip1          Yip1 domain
     0.0087   16.2   1.1     0.0087   16.2   1.1    2.8  3  Oxidored_q4   NADH-ubiquinone/plastoquinone oxidoreductase, c
  ------ inclusion threshold ------
      0.076   11.1  10.0      0.088   10.9  10.0    1.0  1  UPF0182       Uncharacterised protein family (UPF0182)
        2.4    7.3   6.1        3.1    6.9   6.1    1.3  1  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   4.1   3.2e-06     0.014      64     120 ..      19      72 ..       4      74 .. 0.86
   2 !   12.1   9.6   2.7e-05      0.12     104     170 ..      96     173 ..      94     177 .. 0.90
   3 ?   -1.5   4.9      0.39   1.7e+03      81     121 ..     174     207 ..     160     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-06
                          Yip1  64 gaiiggylglllgllllalllhliakllggkgsfkqtlsvvgyallPlilgaliail 120
                                   g+ ++++    l++++++l +++i++l  +++sf  t  + ++ +++ ++++++++l
  gi|70606534|ref|YP_255404.1|  19 GTTFYLF---TLSFIVFGLNIYFISRLSSQNPSFLSTATFPSLVFVIAFISLIVTLL 72 
                                   4444444...59*****************************************9875 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.7e-05
                          Yip1 104 vgyallPlilgaliaillllllgt...........llllvgllaliWslvllylglkaahnlskkkallaalilllll 170
                                   +gy l+ l ++++++i++ l+lg            +l++vg l+l +s+ + ++gl+++++ s+   ++++++++ ll
  gi|70606534|ref|YP_255404.1|  96 YGYLLAYLSISLPVIIPVDLVLGLmernvlyilivVLASVGTLFLTYSISFSFTGLQRVTGSSRYPLAAYVALGISLL 173
                                   8999*************************************************************7777777744444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.39
                          Yip1  81 alllhliakllg.gkgsfkqtlsvvgyallPlilgaliaill 121
                                    l+          + + +k++l+++ y ++ l ++++ ++l+
  gi|70606534|ref|YP_255404.1| 174 YLF--------SySIVGYKELLAFLLYLSTGLTVSGISLLLV 207
                                   222........1256678888888888888888888877765 PP

>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   1.9e-06    0.0087      34      86 ..      14      66 ..       3      82 .. 0.77
   2 ?   -0.9   0.5       0.4   1.8e+03      70      82 ..     124     136 ..      86     153 .. 0.51
   3 ?   -0.8   3.6       0.4   1.8e+03      49      88 ..     165     197 ..     124     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-06
                                  -.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHH CS
                   Oxidored_q4 34 arlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillv 86
                                  ++ ++ + fyl++l F++F +++ f+   + +  +   ++++  l+F++ ++ 
  gi|70606534|ref|YP_255404.1| 14 SKRSLGTTFYLFTLSFIVFGLNIYFISRLSSQNPSFLSTATFPSLVFVIAFIS 66
                                  56677899********************9998776666666666666655443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHH CS
                   Oxidored_q4  70 glfgliemllFll 82 
                                    l+ li +l  ++
  gi|70606534|ref|YP_255404.1| 124 VLYILIVVLASVG 136
                                   2222333333333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.4
                                   HHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHH CS
                   Oxidored_q4  49 FliFDvevvflfpwavslkelglfgliemllFllillvgl 88 
                                   ++ + + +++lf +++       +g+ e+l Fll l  gl
  gi|70606534|ref|YP_255404.1| 165 YVALGISLLYLFSYSI-------VGYKELLAFLLYLSTGL 197
                                   5666666666666666.......45667777777776665 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  10.0     2e-05     0.088      45     207 ..      18     178 ..       4     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2e-05
                       UPF0182  45 lllfvvvflllalllllnlllaerlelleklerlrealekklkllllaialvlsllvglvassqwekvllflnstsfgvkD 125
                                   l++ +  f+l+++++ ln+++ +rl      ++  + l++ +   l+ + +++sl+v+l+  ++ + +l++l ++ f  ++
  gi|70606534|ref|YP_255404.1|  18 LGTTFYLFTLSFIVFGLNIYFISRL-----SSQNPSFLSTATFPSLVFVIAFISLIVTLLGDDRQSGLLEYLVAEGFTAQE 93 
                                   4556677888999999999999999.....23456666677777788888999**************************** PP

                       UPF0182 126 pifgkDisFYvFklPflelllsll...lalvllaliavllvyllsgeslgirlkfaelskaarrhlsvllallllllalsy 203
                                     +g  +++   +lP++  +  +l      vl++li+vl+       +++i+++f++l++ +    + l+a ++l ++l y
  gi|70606534|ref|YP_255404.1|  94 VYYGYLLAYLSISLPVIIPVDLVLglmERNVLYILIVVLASVGTLFLTYSISFSFTGLQRVTGSSRYPLAAYVALGISLLY 174
                                   ****************86555444110433444444333333222222245555566666666666666666666666555 PP

                       UPF0182 204 wLdr 207
                                   +++ 
  gi|70606534|ref|YP_255404.1| 175 LFSY 178
                                   5543 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.1   0.00068       3.1      31     148 ..      60     187 ..      13     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00068
                                   XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........XXXXXXXXXXXXXX CS
                  Bac_export_2  31 lvllaglllllllgpslveelae.llrevlsalelllelllallllllplllvllla..........allanllqvgflfs 100
                                   +v++++ l+++llg++  + l e l++e ++a+e++   lla l + lp+++ + l+           l++ l+ vg lf 
  gi|70606534|ref|YP_255404.1|  60 FVIAFISLIVTLLGDDRQSGLLEyLVAEGFTAQEVYYGYLLAYLSISLPVIIPVDLVlglmernvlyILIVVLASVGTLFL 140
                                   2233333333444444444433314555666677777777777766666533333333333444444999999999***** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Bac_export_2 101 tkalkpklsklnplkglkrifslrslvellksllkvvlvgavaylvlk 148
                                   t ++++ +  l+ ++g  r   l + v l  sll ++  ++v+y  l 
  gi|70606534|ref|YP_255404.1| 141 TYSISFSFTGLQRVTGSSRY-PLAAYVALGISLLYLFSYSIVGYKELL 187
                                   *****************997.5899************99999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1389.49
//
Query:       gi|70606535|ref|YP_255405.1|  [L=266]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-24   84.9   0.0    1.4e-23   83.9   0.0    1.5  1  ABC_tran     ABC transporter
    5.3e-10   39.6   0.3    9.5e-05   22.3   0.3    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-07   31.5   0.2      0.013   15.2   0.1    2.2  2  AAA_15       AAA ATPase domain
    7.8e-06   26.5   1.1    9.9e-06   26.2   1.1    1.7  1  AAA_23       AAA domain
    2.2e-05   24.0   0.1      0.022   14.2   0.1    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    8.6e-05   22.8   0.0    0.00014   22.1   0.0    1.3  1  AAA_22       AAA domain
    0.00029   20.5   0.0     0.0005   19.8   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
      0.008   16.1   0.0       0.02   14.8   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.029   13.9   0.0    1.3  1  AAA_27       AAA domain
       0.02   15.6   0.0      0.064   14.0   0.0    1.9  1  DUF4162      Domain of unknown function (DUF4162)
      0.091   13.1   0.1       0.16   12.3   0.1    1.5  1  AAA_16       AAA ATPase domain
      0.097   12.6   0.9        5.8    6.8   0.0    3.0  3  NTPase_1     NTPase
       0.12   12.1   0.0       0.16   11.7   0.0    1.3  1  AAA_30       AAA domain
       0.13   10.9   0.0       0.17   10.5   0.0    1.3  1  AAA_13       AAA domain
       0.14   12.2   0.3        1.9    8.5   0.2    2.4  2  AAA_5        AAA domain (dynein-related subfamily)
       0.14    9.6   0.1       0.21    9.1   0.1    1.2  1  DUF3584      Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   1.3e-26   1.4e-23       2     136 ..      18     141 ..      17     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.3e-26
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   +++++++ke  +++++G+nGaGK+t+l+llag lkp +G               + + +i++lp+   l pe++v+e    
  gi|70606535|ref|YP_255405.1|  18 HDLTFEIKEKGIYVLLGKNGAGKTTILRLLAGVLKPWKGLF-------------RREGSIAYLPHYIALPPEMRVKEAldf 85 
                                   789************************************99.............889***********************9 PP

                                   ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        +++ + ++++l+lk+l  +++    s LS+Gqk+rv+l r+++++++++llDEpt
  gi|70606535|ref|YP_255405.1|  86 lsrILNANYSSVIEELDLKDLLGKKI----SDLSQGQKKRVSLSRVFMREKDIYLLDEPT 141
                                   99999999*****************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   8.5e-08   9.5e-05       1      95 [.      29     119 ..      29     126 .. 0.65
   2 !   17.2   0.0     3e-06    0.0034     234     300 ..     111     173 ..      75     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.5e-08
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                   + vl G+Ng+GK+++L++l ++    +  +gl   +    g + +   +    pe++++ +++ fls+  + +y+  +e+ 
  gi|70606535|ref|YP_255405.1|  29 IYVLLGKNGAGKTTILRLLAGVL---KPWKGLFRRE----GSIAYLPHYIALPPEMRVKEALD-FLSRILNANYSSVIEEL 101
                                   579****************8883...3333333333....44445555555666666666666.88888888888888888 PP

                        AAA_21  82 qv....eeklssvetlle 95 
                                   ++    + k+s++ ++++
  gi|70606535|ref|YP_255405.1| 102 DLkdllGKKISDLSQGQK 119
                                   776666566655555555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3e-06
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpl 300
                                   +++lS+G+k+   l   + r     +++l+DEp  +L+P + +++ e + +ls+  +++ i t+H+ +
  gi|70606535|ref|YP_255405.1| 111 ISDLSQGQKKRVSLSRVFMREK---DIYLLDEPTDNLDPVFASKVREKVVSLSK--SKIvIYTSHNLY 173
                                   4567999999978888888766...*********************99999999..9999*****976 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.2e-05     0.013      18      44 ..      21      48 ..      16      54 .. 0.82
   2 !   14.0   0.0   2.8e-05     0.031     267     367 ..      85     173 ..      67     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                        AAA_15 18 eidlsee.ltvliGkNnsGKSsileald 44
                                  + +++e+ + vl GkN++GK++il++l 
  gi|70606535|ref|YP_255405.1| 21 TFEIKEKgIYVLLGKNGAGKTTILRLLA 48
                                  5566777799***************985 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.8e-05
                        AAA_15 267 kidkikkfnykgkkneeieikddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikl 347
                                   +++ i + ny ++ +e+ ++kd    ++++ ++G++  ++l   ++++++k       +i+l++EP  +L p + + + ++
  gi|70606535|ref|YP_255405.1|  85 FLSRILNANYSSVIEEL-DLKDLLGKKISDLSQGQKKRVSL--SRVFMREK-------DIYLLDEPTDNLDPVFASKVREK 155
                                   55555555565555555.44577777889999999998765..59999999.......9********************** PP

                        AAA_15 348 lkelandnktQviitTHSph 367
                                     +l++++   vi+t+H+ +
  gi|70606535|ref|YP_255405.1| 156 VVSLSKSKI--VIYTSHNLY 173
                                   ********8..******965 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   1.1   8.8e-09   9.9e-06      12      43 ..      19      51 ..      10     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.8e-09
                        AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                  d +++  +kg++++ G+NGaGKTTil+ +  +L
  gi|70606535|ref|YP_255405.1| 19 DLTFEIkEKGIYVLLGKNGAGKTTILRLLAGVL 51
                                  556666999*****************9988766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0018       2.1      23      42 ..      26      45 ..      18      61 .. 0.85
   2 !   14.2   0.1     2e-05     0.022     133     211 ..     110     184 ..      84     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                                  TSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsnlld 42
                                  +k++ +++G+NG+GK+ +l 
  gi|70606535|ref|YP_255405.1| 26 EKGIYVLLGKNGAGKTTILR 45
                                  578899**********9986 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2e-05
                                   STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                   +++ LS G+k+ v+l+ +f    ++ + +yllDe   +LD    +kv e + + sk+  +i +s++    ++  k v v
  gi|70606535|ref|YP_255405.1| 110 KISDLSQGQKKRVSLSRVF----MREKDIYLLDEPTDNLDPVFASKVREKVVSLSKSKIVIYTSHNLYEAKEIGKYVMV 184
                                   45679***********998....67889***************************999899898887666666665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-07   0.00014       3      98 ..      25     138 ..      22     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                        AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaee.erpevv...fvtlpsstsskdllrellralglelka..erlssee 77 
                                   k++gi v+ G  G+GKTt lr l+  l+ ++   + e++  +   ++ lp ++  k+ l  l r+l+ + ++  e+l++++
  gi|70606535|ref|YP_255405.1|  25 KEKGIYVLLGKNGAGKTTILRLLAGVLKPWKGLFRrEGSIAYlphYIALPPEMRVKEALDFLSRILNANYSSviEELDLKD 105
                                   489************************8887666644444449*9********7777777777777766666777****** PP

                        AAA_22  78 ll.ealeqalrarav...........ielliiD 98 
                                   ll +++ + ++ +++           + + ++D
  gi|70606535|ref|YP_255405.1| 106 LLgKKISDLSQGQKKrvslsrvfmreKDIYLLD 138
                                   **9999999999998666655555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.5e-07    0.0005      13      46 ..      18      51 ..      15      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.5e-07
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                  ++ t+ei++kg+++l G++G+GK+T+l  ++ +L
  gi|70606535|ref|YP_255405.1| 18 HDLTFEIKEKGIYVLLGKNGAGKTTILRLLAGVL 51
                                  667899********************96555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05      0.02      87     121 ..      14      49 ..       4      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                   HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    e +++l+ ++k+  + vl+G+ G+GK+t++  l++
  gi|70606535|ref|YP_255405.1|  14 LEVIHDLTFEIKEkGIYVLLGKNGAGKTTILRLLAG 49 
                                   5678899999999789***************99987 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-05     0.029      11      46 ..      11      47 ..       1      51 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                        AAA_27 11 yGkftd.rsldfsaeeadlhliyGpNEAGKstalrAi 46
                                  yG ++  + l+f+ +e+++ +++G N AGK+t+lr +
  gi|70606535|ref|YP_255405.1| 11 YGDLEViHDLTFEIKEKGIYVLLGKNGAGKTTILRLL 47
                                  66665426799999*******************9855 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.7e-05     0.064      28      75 ..     215     263 ..     195     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                                   ---EEEE-TTS-EEEEE-------------.----EEEEEEEE---HHH CS
                       DUF4162  28 pgveeveeeggelelkledeeaanellkal.tsgveirsFeeeePsLnd 75 
                                   +++ e   eg+++++kl+d +  ne++++l +++++i +++e++  L++
  gi|70606535|ref|YP_255405.1| 215 SKILEGHYEGDYFVVKLPDPSMVNEVIQKLlRENITIYEVKEMRNPLEE 263
                                   334444667799******************88**********9999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.16      24      59 ..      27      62 ..      17     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgk 59
                                   ++ +l G  G GK++++r l+  l+  +g+f r+ 
  gi|70606535|ref|YP_255405.1| 27 KGIYVLLGKNGAGKTTILRLLAGVLKPWKGLFRREG 62
                                  47889****************987777766663333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0052       5.8       3      24 ..      31      52 ..      29      61 .. 0.87
   2 ?   -0.1   0.1      0.66   7.4e+02      90     133 ..     126     170 ..     107     180 .. 0.62
   3 ?    2.8   0.1     0.085        95      22      78 ..     155     208 ..     146     229 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0052
                                  EEE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellk 24
                                  ++ G+ G GKtT+++ ++ +lk
  gi|70606535|ref|YP_255405.1| 31 VLLGKNGAGKTTILRLLAGVLK 52
                                  5679***********9999997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.66
                                   HHHHHHH-EEEE---STTGGG-HHHHHHHHH.H..HTTTSEEEEE-- CS
                      NTPase_1  90 rkalseadviviDEiGkmElkskkfkeavee.v..Lksekpvlavih 133
                                   r  ++e+d++++DE  +     ++f+++v+e v  L+++k+v+ + h
  gi|70606535|ref|YP_255405.1| 126 RVFMREKDIYLLDE--PTDNLDPVFASKVREkVvsLSKSKIVIYTSH 170
                                   33447888888888..5666666666666542211345566666655 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.085
                                   HH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-H CS
                      NTPase_1  22 llkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdv 78 
                                   ++ s   +   +yt+    + + ig  ++ +++g    L r ++  e r g+yvv +
  gi|70606535|ref|YP_255405.1| 155 KVVSLSKSKIVIYTSHNLYEAKEIGKYVMVMDNG---RLIRFCTMDELRTGEYVVGI 208
                                   3333333333345555555555555555555333...33333333466666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.16      18      43 ..      27      52 ..      21     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                        AAA_30 18 drvavltGpAGtGKttalkalreawe 43
                                  + + vl G  G+GKtt+l+ l+ +++
  gi|70606535|ref|YP_255405.1| 27 KGIYVLLGKNGAGKTTILRLLAGVLK 52
                                  55889**************9987765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.17      20      39 ..      31      50 ..      25     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                        AAA_13 20 liYGwNGaGKTtLSrllrsl 39
                                  ++ G+NGaGKTt+ rll+ +
  gi|70606535|ref|YP_255405.1| 31 VLLGKNGAGKTTILRLLAGV 50
                                  567*************9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0017       1.9       3      23 ..      31      51 ..      29      60 .. 0.87
   2 ?    1.6   0.0      0.23   2.6e+02      47      73 ..     114     139 ..      80     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                                  EEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  3 lLvGppGtgKselaerlaaal 23
                                  +L+G+ G gK+++ + la +l
  gi|70606535|ref|YP_255405.1| 31 VLLGKNGAGKTTILRLLAGVL 51
                                  79***************9988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                                   -.........--------G-SEEEEES CS
                         AAA_5  47 ikngttslvdsplvraaregeilvlDE 73 
                                   +++g++++v  + v  +re++i++lDE
  gi|70606535|ref|YP_255405.1| 114 LSQGQKKRVSLSRV-FMREKDIYLLDE 139
                                   33777777777777.899999999999 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00019      0.21      13      37 ..      23      47 ..      20      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00019
                       DUF3584 13 eldldghtnieGtNaaGKTtLlrLi 37
                                  e++ +g   + G N+aGKTt+lrL+
  gi|70606535|ref|YP_255405.1| 23 EIKEKGIYVLLGKNGAGKTTILRLL 47
                                  56666677789*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1872.61
//
Query:       gi|70606536|ref|YP_255406.1|  [L=143]
Description: hypothetical protein Saci_0735 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1090.36
//
Query:       gi|70606537|ref|YP_255407.1|  [L=247]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-09   37.4  28.6    1.7e-09   37.4  28.6    1.8  2  ABC2_membrane    ABC-2 type transporter
    2.3e-06   27.0  38.2      4e-06   26.2  38.2    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4  28.6   1.9e-13   1.7e-09      28     210 .]       2     195 ..       1     195 [. 0.77
   2 ?   -0.9   0.7       0.1     9e+02     100     117 ..     215     232 ..     202     246 .. 0.53

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.9e-13
                 ABC2_membrane  28 qplllalvfgtvfgnlgnsedgl.nr.........pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvl 98 
                                   qp+l++l +g    ++  s  +l ++         +g+ ++++l++ +++ +s+ + f      ++++l+++      ++ 
  gi|70606537|ref|YP_255407.1|   2 QPILWILTLGISLNGVT-SVTFLkQFntsfldfeiVGVPIIFALTIPLFGSFSSRLEFSNSTIYVVHLLSNRK-IIYYFMG 80 
                                   78888888888777643.2222222244556678866666666666655555553666666666667666666.8888888 PP

                 ABC2_membrane  99 akvlvelpvsllqalifllivyflv..gldlsrf.flflllllltalaasslgllisalapsfedasqla.slvllpllll 175
                                     v+++++++++ +l +  ++++l+  g+++  + + +l+l+ll +l++ slg++i +l++++   + +  sl+ ++l+l+
  gi|70606537|ref|YP_255407.1|  81 TDVIFYAIITFVNVLTVAGLSFILTseGVNV-IGlLAVLPLMLLGSLTSYSLGIIINSLFRNLSSPTSYLfSLIQVILILF 160
                                   899999**********999*****9555555.236****************************9988887477778899** PP

                 ABC2_membrane 176 sGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                   sG+++p++ +p++l+ ia ++P+++++ ++r++l+
  gi|70606537|ref|YP_255407.1| 161 SGVYYPLSYLPEYLRIIAFISPYSHLIALIRYILL 195
                                   **********99********************985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.1
                 ABC2_membrane 100 kvlvelpvsllqalifll 117
                                   +v++++ + +++++i+++
  gi|70606537|ref|YP_255407.1| 215 QVVLSISYVIVLGVILFI 232
                                   233333333333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  38.2   4.4e-10     4e-06     153     343 ..      24     234 ..      12     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.4e-10
               ABC2_membrane_3 153 eeelsnvasf.lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlsk..ilgdflvyllqlllilll..a 228
                                   ++ ++++ +f +vg+ +i++++i+++   +s +e   s i  + l+s  +++ y++    +++++++ ++ +l + +l  +
  gi|70606537|ref|YP_255407.1|  24 KQFNTSFLDFeIVGVPIIFALTIPLFGSFSSRLEFSNSTIYVVHLLS-NRKIIYYFMGtdVIFYAIITFVNVLTVAGLsfI 103
                                   55567777774555666666777777666667888888899899999.777776554424777777777777766654223 PP

               ABC2_membrane_3 229 fgl.gipfgnlglllllfllfglayialgyllsslfknsetaqil.ifivilllsgffgglfpledlpsalkwifsiiPff 307
                                   + + g+++ +l+++l l+ll++l++ +lg  + slf+n ++  +   +++ ++l++f+g+ +pl+ lp++l++i++i P +
  gi|70606537|ref|YP_255407.1| 104 LTSeGVNVIGLLAVLPLMLLGSLTSYSLGIIINSLFRNLSSPTSYlFSLIQVILILFSGVYYPLSYLPEYLRIIAFISPYS 184
                                   333689999******************************9955552777777899999999******************** PP

               ABC2_membrane_3 308 apglgllrlitgdplwe..............illsliilalfavvyllla 343
                                   +++ ++  ++ g++ ++              + ls+ + ++++v++++la
  gi|70606537|ref|YP_255407.1| 185 HLIALIRYILLGYNASDlnalwfytlpyqvqVVLSISYVIVLGVILFILA 234
                                   **********88866669999999999999999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2005.96
//
Query:       gi|70606538|ref|YP_255408.1|  [L=263]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-26   91.3   0.0    1.1e-25   90.8   0.0    1.2  1  ABC_tran     ABC transporter
    3.4e-14   53.4   3.6    2.1e-07   31.0   0.6    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    6.7e-08   32.2   1.6     0.0062   16.0   0.1    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    2.8e-05   24.0   0.2    7.8e-05   22.5   0.1    1.6  2  AAA_15       AAA ATPase domain
    6.3e-05   23.6   0.1    0.00013   22.5   0.1    1.5  1  AAA_23       AAA domain
    9.9e-05   22.0   0.2    0.00022   20.9   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0048   17.2   0.0     0.0088   16.3   0.0    1.4  1  AAA_22       AAA domain
     0.0093   15.6   0.1       0.21   11.2   0.0    2.2  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
     0.0099   15.8   0.0      0.022   14.6   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.016   15.1   0.1       0.14   12.0   0.0    2.4  3  NACHT        NACHT domain
      0.017   15.2   0.8      0.046   13.8   0.2    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
      0.027   14.9   0.0      0.048   14.1   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.029   13.1   0.0      0.036   12.7   0.0    1.1  1  AAA_13       AAA domain
      0.029   14.9   0.1       0.12   12.9   0.0    2.0  2  AAA_18       AAA domain
      0.045   13.5   0.0      0.078   12.7   0.0    1.4  1  AAA_30       AAA domain
      0.072   12.4   0.1        2.8    7.1   0.0    2.1  2  Septin       Septin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.0   9.7e-29   1.1e-25       1     136 [.      16     154 ..      16     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 9.7e-29
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk v++k + g+++ ivG+nG+GKStL+++l+  +kp++G+ l+dg++l++   +++r+ i+vl  ++ l+  l+vr++  
  gi|70606538|ref|YP_255408.1|  16 LKGVTFKAESGRVTCIVGRNGSGKSTLIRILSTSEKPDSGTALIDGTPLED--VKRVREVISVLYDKNYLDAFLRVRDSie 94 
                                   789***********************************************9..**************************** PP

                                   .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                           ++++++ ++++++l+   ++ v     +LS+G ++++al  al  ++++ llDEpt
  gi|70606538|ref|YP_255408.1|  95 ffisameIDRDKVYSLIKNFNLSLYLEKLV----FTLSKGTQRKLALTFALSLDRPVSLLDEPT 154
                                   ****99888888*****************9....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   3.7e-08   4.2e-05       1      20 [.      28      47 ..      28      75 .. 0.81
   2 !   31.0   0.6   1.9e-10   2.1e-07     234     302 ..     124     188 ..      58     189 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.7e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdald 20
                                  +++++G+NgsGKS+L+++l+
  gi|70606538|ref|YP_255408.1| 28 VTCIVGRNGSGKSTLIRILS 47
                                  699****************4 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.9e-10
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                   ++ lS Gt+r lal  al  ++   ++ l+DEp  gL+++    +++ +++++  +  +++tTH+  ++
  gi|70606538|ref|YP_255408.1| 124 VFTLSKGTQRKLALTFALSLDR---PVSLLDEPTEGLDYESKLLFVREISAHAH-DKTILMTTHDAQVV 188
                                   4567***************999...99************888888899977766.9********98765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.5e-06    0.0062      24      41 ..      26      43 ..       9      49 .. 0.84
   2 !   15.6   0.2   7.3e-06    0.0081     108     210 ..      92     196 ..      66     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.5e-06
                                  SSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxx RF
                         SMC_N 24 ksftaivGpNGSGKsnll 41
                                   ++t+ivG+NGSGKs l+
  gi|70606538|ref|YP_255408.1| 26 GRVTCIVGRNGSGKSTLI 43
                                  579************998 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.3e-06
                                   EEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 108 eseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvael 182
                                   + e++i   e+ + +v +l+++ ++s        +LS G +    laL fA+   +  p+ llDe    LD +    +++ 
  gi|70606538|ref|YP_255408.1|  92 SIEFFISAMEIDRDKVYSLIKNFNLSLYleklvfTLSKGTQR--KLALTFALSLDR--PVSLLDEPTEGLDYESKLLFVRE 168
                                   456777777777777777777777776666777789999775..677888887655..6678******************* PP

                                   HHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 183 lkeksknaQfivislreemlekadklvg 210
                                   + ++ ++  +++++++++++e a + v 
  gi|70606538|ref|YP_255408.1| 169 ISAHAHDKTILMTTHDAQVVESACEKVM 196
                                   *********************9955444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   6.9e-08   7.8e-05      23      55 ..      27      73 ..      16     139 .. 0.57
   2 ?   -2.7   0.0       3.2   3.5e+03     335     367 ..     156     186 ..     139     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.9e-08
                        AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnkekkn...................k 55
                                    +t+++G+N+sGKS+++++l    +++ek +                   +
  gi|70606538|ref|YP_255408.1| 27 R-VTCIVGRNGSGKSTLIRIL----STSEKPDsgtalidgtpledvkrvreV 73
                                  2.9*****************9....666554445556666655555444442 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                        AAA_15 335 hLHpqaqkvlikllkelandnktQviitTHSph 367
                                    L ++ +  +++ +   a d+   +++tTH   
  gi|70606538|ref|YP_255408.1| 156 GLDYESKLLFVREISAHAHDK--TILMTTHDAQ 186
                                   555556666777777777777..4999999765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.2e-07   0.00013      16      39 ..      22      46 ..       9      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.2e-07
                        AAA_23 16 dF.skgltlItGpNGaGKTTildAi 39
                                     s  +t+I+G NG+GK+T+++ +
  gi|70606538|ref|YP_255408.1| 22 KAeSGRVTCIVGRNGSGKSTLIRIL 46
                                  3355679**************9866 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     2e-07   0.00022      15      39 ..      19      43 ..      15      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                        AAA_29 15 htieidlkg.atlltGpsGsGKSTll 39
                                   t++ + +g +t ++G++GsGKSTl+
  gi|70606538|ref|YP_255408.1| 19 VTFKAE-SGrVTCIVGRNGSGKSTLI 43
                                  566666.556***************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.9e-06    0.0088       4      61 ..      25      75 ..      22     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.9e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrell 61
                                  + ++++++G  G+GK+tl+r l  + +       +++++++++ + +++ k +++ + 
  gi|70606538|ref|YP_255408.1| 25 SGRVTCIVGRNGSGKSTLIRILSTSEK-------PDSGTALIDGTPLEDVKRVREVIS 75
                                  67899***************9999875.......478888888888887777777665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00019      0.21       2      32 ..      28      59 ..      27      75 .. 0.84
   2 ?    2.3   0.0       0.1   1.1e+02      39      61 ..     181     203 ..     175     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                  EEEEEESTTCCHHHHHHHHH.CT--SS-EEEE CS
                          cobW  2 vtvltGflGsGKTtLlnhll.enraglklavi 32
                                  vt ++G  GsGK+tL++ l  +++ +  +a+i
  gi|70606538|ref|YP_255408.1| 28 VTCIVGRNGSGKSTLIRILStSEKPDSGTALI 59
                                  799*************9988777777777777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                                   CHCCCCCCHCCCT.EEEETTTTE CS
                          cobW  39 vsiDaellretgveivelenGci 61 
                                   + +Da+++++++++++ l+nG +
  gi|70606538|ref|YP_255408.1| 181 TTHDAQVVESACEKVMLLQNGQV 203
                                   789******************75 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-05     0.022      98     123 ..      25      50 ..      10      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                   TTSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                   +++++++vG  G GKStLi  l  ++
  gi|70606538|ref|YP_255408.1|  25 SGRVTCIVGRNGSGKSTLIRILSTSE 50 
                                   4599****************998865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.14       1      21 [.      27      47 ..      27      54 .. 0.88
   2 ?    0.1   0.0      0.61   6.8e+02      16      42 ..     119     143 ..     117     188 .. 0.82
   3 ?   -2.0   0.0       2.6   2.9e+03      35      89 ..     162     224 ..     147     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                  SCEEEEC-TTTCHHHHHHHHH CS
                         NACHT  1 rlvilqGeaGsGKTtLlqkla 21
                                  r+ ++ G++GsGK+tL++ l 
  gi|70606538|ref|YP_255408.1| 27 RVTCIVGRNGSGKSTLIRILS 47
                                  789*************98765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.61
                                   HHHHHHHHHCTS-SCCCC-SEEEEEET CS
                         NACHT  16 LlqklalawaegklpqgafklvFflsl 42 
                                    l+kl++++ +g++ +    l F lsl
  gi|70606538|ref|YP_255408.1| 119 YLEKLVFTLSKGTQRKL--ALTFALSL 143
                                   68899999999999885..56666665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                                   SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C......CHHHHCCSCCCEEEEEE- CS
                         NACHT  35 klvFflslrelsrsgna..rsladllfsqlpepaapvse......vwavllelperlLlilDg 89 
                                   kl+F+ + ++  +++++  ++ + ++++  +e+ +  ++       ++++ +++++ L + Dg
  gi|70606538|ref|YP_255408.1| 162 KLLFVREISAHAHDKTIlmTTHDAQVVESACEKVMLLQNgqvkpiDVKFIKRVADKYLVVNDG 224
                                   556666666666555555544444444444444444444444444445555555555555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   4.1e-05     0.046       3      22 ..      30      49 ..      28      71 .. 0.82
   2 ?   -1.2   0.0       1.9   2.1e+03      67      67 ..     181     181 ..     124     223 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                  EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                  +ivGr  +GKStLi+ l+ +
  gi|70606538|ref|YP_255408.1| 30 CIVGRNGSGKSTLIRILSTS 49
                                  89*************99865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                                   H CS
                      MMR_HSR1  67 g 67 
                                   +
  gi|70606538|ref|YP_255408.1| 181 T 181
                                   1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.3e-05     0.048      22      63 ..      24      66 ..       9     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                   +++++ ++G  G+GKs+l+r l ++ + d g + + g+  + 
  gi|70606538|ref|YP_255408.1| 24 ESGRVTCIVGRNGSGKSTLIRILSTSEKPDSGTAlIDGTPLED 66
                                  3348999**************9998877774333355555444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.036      17      43 ..      27      53 ..      20      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                        AAA_13 17 riNliYGwNGaGKTtLSrllrslelge 43
                                  r+  i G+NG+GK+tL r+l+  e+  
  gi|70606538|ref|YP_255408.1| 27 RVTCIVGRNGSGKSTLIRILSTSEKPD 53
                                  667799**************9987644 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.12       2      30 ..      30      75 ..      30     138 .. 0.71
   2 ?   -0.6   0.0       1.7   1.9e+03     106     121 ..     225     240 ..     153     248 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                        AAA_18  2 lltGtpGvGKttlakeLskrlgf.................gvnlrd 30
                                  ++ G  G+GK+tl + Ls +++                  ++++++
  gi|70606538|ref|YP_255408.1| 30 CIVGRNGSGKSTLIRILSTSEKPdsgtalidgtpledvkrVREVIS 75
                                  789999***********87753355667777444444444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                        AAA_18 106 lleRlekRgyeeakik 121
                                    + Rl  R++ + ki 
  gi|70606538|ref|YP_255408.1| 225 IKSRLVLRDEVNGKID 240
                                   2456666666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     7e-05     0.078      15      39 ..      24      47 ..      19      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                        AAA_30 15 tsgdrvavltGpAGtGKttalkalr 39
                                  +sg rv++++G+ G+GK+t+++ l 
  gi|70606538|ref|YP_255408.1| 24 ESG-RVTCIVGRNGSGKSTLIRILS 47
                                  445.6****************9885 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0025       2.8       9      32 ..      31      54 ..      26      95 .. 0.81
   2 ?    3.1   0.1     0.042        47     126     158 ..     202     234 ..     195     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                                  EEEBTTSSCCCCCCTTSSSS---- CS
                        Septin  9 vvGesglGkttlintlfetdliee 32
                                  +vG++g Gk+tli+ l +++  ++
  gi|70606538|ref|YP_255408.1| 31 IVGRNGSGKSTLIRILSTSEKPDS 54
                                  89***********99987766554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.042
                                   SS-HHHHHHHHHHTTTS-EEEEESSGGGS-HHH CS
                        Septin 126 glkpldvelmkklsekvnliPviaKaDtltkeE 158
                                   ++kp+dv+++k++++k  ++    K+  + ++E
  gi|70606538|ref|YP_255408.1| 202 QVKPIDVKFIKRVADKYLVVNDGIKSRLVLRDE 234
                                   789***********9988776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1618.75
//
Query:       gi|70606539|ref|YP_255409.1|  [L=163]
Description: hypothetical protein Saci_0738 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1207.48
//
Query:       gi|70606540|ref|YP_255410.1|  [L=104]
Description: hypothetical protein Saci_0739 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00034   20.5   0.2    0.00063   19.7   0.2    1.4  1  HTH_45    Winged helix-turn-helix
     0.0012   18.6   0.9     0.0014   18.4   0.9    1.1  1  DUF4364   Domain of unknown function (DUF4364)
     0.0085   15.6   0.0      0.021   14.4   0.0    1.7  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.018   15.2   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain
       0.12   12.5   0.1        1.8    8.8   0.0    2.5  2  LRR_6     Leucine Rich repeat


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.8e-07   0.00063      25      73 ..      32      89 ..      22      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                        HTH_45 25 imykanLsykllnkYLdmLvekgli.........kkskekYvlTekGlelleklkele 73
                                  i+ k n++   ++ Y+++L ++gli         +  k+k  +T+kG + l ++++l 
  gi|70606540|ref|YP_255410.1| 32 IIQKFNITKGGFQHYINQLCNEGLItcrnafyfvEGYKKKCNITDKGVKELFEIRDLL 89
                                  67788999999*************99999999978899***********999999875 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9     4e-07    0.0014       2      90 ..      13     102 ..      12     104 .] 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4e-07
                       DUF4364   2 KllilYllkkvkfpltnsqlseiileneytnYfdlqqalseLvesglieeeek.....enktlykiTekGketlelfenri 77 
                                    l+ilY+  +++     s+l++ii+++  ++   +q+++++L+++gli++++        k+ ++iT+kG + l ++ + +
  gi|70606540|ref|YP_255410.1|  13 TLVILYVYGEMG----FSELYNIIIQKFNITKGGFQHYINQLCNEGLITCRNAfyfveGYKKKCNITDKGVKELFEIRDLL 89 
                                   588899888888....799******************************987666666899*************9999999 PP

                       DUF4364  78 pksirekideylk 90 
                                   +  + ++ d+ ++
  gi|70606540|ref|YP_255410.1|  90 SLLVNDEGDNQVD 102
                                   9988888887766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.7e-06     0.021      23      48 .]      32      57 ..      29      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                        HTH_24 23 LAerlglSpstvnrrlkrLeeeGlIk 48
                                  + ++ +++++    ++++L++eGlI+
  gi|70606540|ref|YP_255410.1| 32 IIQKFNITKGGFQHYINQLCNEGLIT 57
                                  77999********************6 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.2e-06     0.018       1      71 [.       9      84 ..       9      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.2e-06
                        HTH_34  1 vRlavlsyLasvdeadfvelke....aleatdgnLsvhlkkLekagYievdkef..kgkkprtllriTpeGreafkk 71
                                  +R+  l +L++  e+ f+el +    + ++t+g     ++ L + g i+++ +f  +++  +  ++iT++G ++  +
  gi|70606540|ref|YP_255410.1|  9 IRIYTLVILYVYGEMGFSELYNiiiqKFNITKGGFQHYINQLCNEGLITCRNAFyfVEG-YKKKCNITDKGVKELFE 84
                                  68888999***999999998751111679**********************99742444.6789*******887655 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17     6e+02      13      21 ..      48      56 ..      48      57 .. 0.90
   2 ?    8.8   0.0   0.00052       1.8      12      23 ..      71      82 ..      70      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                         LRR_6 13 NdIgDeGae 21
                                  N++ +eG++
  gi|70606540|ref|YP_255410.1| 48 NQLCNEGLI 56
                                  99*****96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00052
                         LRR_6 12 gNdIgDeGaeaL 23
                                   ++I+D+G++ L
  gi|70606540|ref|YP_255410.1| 71 KCNITDKGVKEL 82
                                  59********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 778.04
//
Query:       gi|70606541|ref|YP_255411.1|  [L=66]
Description: hypothetical protein Saci_0742 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.1   0.0       0.04   13.8   0.0    1.1  1  DUF4898   Domain of unknown function (DUF4898)


Domain annotation for each model (and alignments):
>> DUF4898  Domain of unknown function (DUF4898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.3e-06      0.04      46      81 ..      10      45 ..       4      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-06
                       DUF4898 46 psdledekvikesvkkarsslsvtilyssKLkdksl 81
                                   +d+e+ k+  e  k ++++lsv+ l  sK++d+ l
  gi|70606541|ref|YP_255411.1| 10 AKDYEEAKILTEKFKGIFKDLSVKMLDLSKIEDRLL 45
                                  68******************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 508.79
//
Query:       gi|70606542|ref|YP_255412.1|  [L=96]
Description: hypothetical protein Saci_0743 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 693.58
//
Query:       gi|70606543|ref|YP_255413.1|  [L=284]
Description: hypothetical protein Saci_0744 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0032   17.7   0.0      0.011   16.0   0.0    2.0  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   6.1e-07     0.011       1      48 [.       4      47 ..       4      65 .. 0.79
   2 ?   -2.6   0.0      0.37   6.7e+03      23      37 ..      69      83 ..      67      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.1e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdyg 48
                                  I+GaG+sGl++      +++d  +le+++r+GG  +  e+ g+ + + 
  gi|70606543|ref|YP_255413.1|  4 ILGAGISGLLIS----SRKRDSIVLENQHRIGGVFSYDEISGFNIPLH 47
                                  89*******765....567789***********998888888776654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.37
                                  EEE-SSSSSSGGG-E CS
                 NAD_binding_8 23 lllekrdrlGGraas 37
                                  +++ek ++l+ +++ 
  gi|70606543|ref|YP_255413.1| 69 VIYEKENYLSAKLTI 83
                                  689999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1914.22
//
Query:       gi|70606544|ref|YP_255414.1|  [L=263]
Description: hypothetical protein Saci_0745 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   0.5         25    5.3   0.0    2.4  2  DUF4959   Domain of unknown function (DUF4959)


Domain annotation for each model (and alignments):
>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0014        25      37      75 ..      63     100 ..      43     106 .. 0.90
   2 ?    5.1   0.1    0.0016        28      37      77 ..     150     184 ..     145     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0014
                       DUF4959  37 sytlPddedLlyvkaeYklknGkerevkaSvykdsltve 75 
                                   +y++ +++++   k  Yk +nGk     +S+ +++l +e
  gi|70606544|ref|YP_255414.1|  63 KYKIFNSNNMTTFKLIYK-ENGKRDLLLVSMSERKLSIE 100
                                   79999*************.89***************998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0016
                       DUF4959  37 sytlPddedLlyvkaeYklknGkerevkaSvykds.ltveGF 77 
                                   +++lP + + l v+a+Y            S+y+ s l+  GF
  gi|70606544|ref|YP_255414.1| 150 QFKLPYNRNYLVVHANYDEL-------SKSMYTVSdLITTGF 184
                                   599**************943.......333443333555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1895.94
//
Query:       gi|70606545|ref|YP_255415.1|  [L=96]
Description: hypothetical protein Saci_0746 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.87   10.6   3.1         15    6.7   0.0    2.5  2  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.9    0.0078   1.4e+02       1       7 [.      34      40 ..      34      47 .. 0.79
   2 ?    6.7   0.0   0.00086        15       8      23 ..      53      68 ..      52      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0078
                     zf-C2H2_4  1 fkCpiCg 7 
                                  + CpiC 
  gi|70606545|ref|YP_255415.1| 34 YACPICA 40
                                  89****4 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00086
                     zf-C2H2_4  8 ksFsskkaLlrHlkth 23
                                  + F s ++L+ H+++h
  gi|70606545|ref|YP_255415.1| 53 AYFFSLDDLKEHVLSH 68
                                  5799**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1602  (0.0893524); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 787.65
//
Query:       gi|70606546|ref|YP_255416.1|  [L=222]
Description: hypothetical protein Saci_0747 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   59.5   0.1    6.1e-16   58.5   0.1    1.4  1  SIS       SIS domain
    9.6e-06   25.7   1.0     0.0023   18.0   0.3    2.3  2  SIS_2     SIS domain
     0.0011   18.8   0.7       0.48   10.3   0.1    2.3  2  PRMT5     PRMT5 arginine-N-methyltransferase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1     1e-19   6.1e-16       5     110 ..      63     162 ..      60     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1e-19
                                   SSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEE CS
                           SIS   5 akriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiia 85 
                                     +i+v+GaG+s+ ++k + + l ++g++v++  d+        + i e+d+ i+is sg+t+  + aae ak+ + ++i+
  gi|70606546|ref|YP_255416.1|  63 NGKILVMGAGRSGLVGKAFGMRLLHLGYNVYVLGDTIV------PAIGERDIAIAISGSGRTRLILTAAEAAKAAKSTLIS 137
                                   459**************************999877655......99*********************************** PP

                                   EESSTTSHHHHHSSEEEEEEEECHC CS
                           SIS  86 ITdskgsplareadlalyinaepet 110
                                   IT+ ++spla+ +d++++i+   ++
  gi|70606546|ref|YP_255416.1| 138 ITSYADSPLAKISDVVVEIPGRTKY 162
                                   *******************987776 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0016       9.7       9      52 ..      35      80 ..      29      90 .. 0.76
   2 !   18.0   0.3   3.8e-07    0.0023      98     138 .]     102     140 ..      90     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0016
                                  HHHHHHHHSHHHHHHHHHHHHHHHH..TT--EEEEESGGGHHHHHH CS
                         SIS_2  9 ilerivetqaeaiekaaeliadsle..nggkvlvfGsGhSaalaee 52
                                  i+++++  + e++ k +e+++++ +  ++gk+lv+G+G S +  + 
  gi|70606546|ref|YP_255416.1| 35 IMRAVRMLKPEQVSKMIEVLVNHYNqnKNGKILVMGAGRSGLVGKA 80
                                  566677778889999999999998622579**********886555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.8e-07
                                   HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                         SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                      + ++D+ + iS sG+   ++ aaeaak+   ++i +ts
  gi|70606546|ref|YP_255416.1| 102 A--IGERDIAIAISGSGRTRLILTAAEAAKAAKSTLISITS 140
                                   4..7899********************************98 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1     8e-05      0.48      50      84 ..      50      82 ..      24      96 .. 0.74
   2 !    7.0   0.1   0.00078       4.7      63      97 ..     105     139 ..      90     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8e-05
                                  HHHHHCTCCGTCC.-EEEEEEES-TTSHHHHHHHH CS
                         PRMT5 50 alsdlkkekkkksekklvilvvGaGRGplvdralk 84
                                  ++  l+++ ++  +k+  ilv+GaGR +lv +a+ 
  gi|70606546|ref|YP_255416.1| 50 MIEVLVNHYNQ--NKNGKILVMGAGRSGLVGKAFG 82
                                  33333333333..45788************99875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00078
                                   .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEE CS
                         PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvkiv 97 
                                   e+++ i++ G+GR  l+ +a +a++ +k t ++i+
  gi|70606546|ref|YP_255416.1| 105 ERDIAIAISGSGRTRLILTAAEAAKAAKSTLISIT 139
                                   56899*******************99997777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1553.40
//
Query:       gi|70606547|ref|YP_255417.1|  [L=597]
Description: hypothetical protein Saci_0748 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-11   43.5   1.1    8.7e-08   31.5   0.1    2.5  2  AAA_10           AAA-like domain
      8e-07   28.0   0.0     0.0031   16.2   0.0    2.2  2  DUF853           Bacterial protein of unknown function (DUF85
    6.7e-05   23.1   2.0    6.7e-05   23.1   2.0    2.6  2  DUF87            Helicase HerA, central domain
     0.0021   17.5   0.0       0.02   14.2   0.0    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.011   14.5   0.1      0.033   13.0   0.0    1.7  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
      0.037   13.8   0.0       0.21   11.3   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.044   14.0   0.1        2.4    8.4   0.0    2.7  2  AAA_22           AAA domain
      0.088   11.7   0.1        1.7    7.5   0.0    2.1  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


Domain annotation for each model (and alignments):
>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00011      0.25      19      68 ..     277     328 ..     270     370 .. 0.70
   2 !   31.5   0.1   3.9e-11   8.7e-08     213     339 ..     449     576 ..     427     583 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                        AAA_10  19 tnasasliiGdlGnGKS.vlakllvlyisllggkaliiDpkke.rekfketl 68 
                                     ++++liiG++G GK  +l  l v    l g  +++ D kk+   + k+  
  gi|70606547|ref|YP_255417.1| 277 VINPHALIIGPTGSGKTeFLLSLGVKTNILYGIPIVFFDVKKDiSLRLKKYG 328
                                   5699************83555666777788999*********9322232222 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 3.9e-11
                        AAA_10 213 teekllsvavlfviaafarefassdkkefkvvifDEawiftssae.GkkllkelvRiGRsynaavylvtqsadDvlkee.. 290
                                   + e+l  + +  +i +f ++   +d +   v ++DEaw++  s++   +++ +l++ GR +   ++++tq++dD+++ +  
  gi|70606547|ref|YP_255417.1| 449 KSEELRRLVMYGIIIKFINKYNIADDRLKLVLVIDEAWTLLRSEDrDYQIVADLIKRGRGFGIGIFMATQNFDDLGELSdi 529
                                   556666666667999***********************99877651679**************************665533 PP

                        AAA_10 291 lknniglklaFretdkeeikkvLeflgldvedednkkelrelesGqCLm 339
                                     +nigl    ++ dk+  ++v++f +l+ e  +  + l +l +G+ L+
  gi|70606547|ref|YP_255417.1| 530 FLENIGLLGFMNNGDKKFWNEVMRFADLNIE--ETLRSLIFLGKGEMLI 576
                                   6899999877788899999999999988885..4555666666666665 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-06    0.0031      17      80 ..     275     340 ..     262     361 .. 0.76
   2 !    9.6   0.0   0.00013       0.3     255     307 ..     474     525 ..     470     594 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                        DUF853  17 lklanrhGliaGatGtGktvtLqvlaesl.seaGvpvfladvkGdLs.giakaGevkdklaarlee 80 
                                    ++ n h li G tG Gkt  L  l  +     G+p++  dvk d+s  + k G   + +   l++
  gi|70606547|ref|YP_255417.1| 275 NRVINPHALIIGPTGSGKTEFLLSLGVKTnILYGIPIVFFDVKKDISlRLKKYGYKYKYINPLLNS 340
                                   46789****************999976551578************994466666665555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00013
                        DUF853 255 dkPklvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPd 307
                                   d+ klv+  dea  L+    +   + v  +++  r  G+G+++ tqn  dl +
  gi|70606547|ref|YP_255417.1| 474 DRLKLVLVIDEAWTLLRSEDRD-YQIVADLIKRGRGFGIGIFMATQNFDDLGE 525
                                   7789*********999887776.4789999******************99976 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.66   1.5e+03     160     199 ..      95     141 ..      37     230 .. 0.58
   2 !   23.1   2.0     3e-08   6.7e-05      13     220 ..     269     457 ..     258     464 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.66
                         DUF87 160 lknqaiarlldkledllrkggsf.......snsstdliallleklek 199
                                   l++++ + +++++ ++l+  g++       s ++++++++l++k+++
  gi|70606547|ref|YP_255417.1|  95 LSDESLRVKISSFHKVLDIAGQIdivfrksSIDKNKFLSDLFQKAQN 141
                                   44444444444444444444444333333333333344444333333 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 3e-08
                         DUF87  13 pvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsa....kdke 89 
                                    v  ++n++++ H +i+g TGsGK+ +  +L  +     g++i+ +D+  + +  l k++  k+k+i+p  ++    k  +
  gi|70606547|ref|YP_255417.1| 269 AVFWNVNRVINPHALIIGPTGSGKTEFLLSLGVKTNILYGIPIVFFDVKKDISLRL-KKYGYKYKYINPLLNSinllKFSN 348
                                   57789**********************999987777799************99999.9**********9532233332222 PP

                         DUF87  90 lkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlld 170
                                   +  ++ +++ e +++ ++          r v + +++ +   e++ +  ++ +  ++ ++++  k +++++ + +  r+ +
  gi|70606547|ref|YP_255417.1| 349 VNKDIYLIQLENIIRNSFK-------LDRFVSALLYRILL--ESISDNYYEVSWDYIIDKIE--KYDINEDVKAYLLRIVS 418
                                   2222222222222222222.......23333333333333..55555555555555555555..44667777777888888 PP

                         DUF87 171 kledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvv 220
                                   ++++l+   +++     dli+ +      ++ i+++dls++++++++ +v
  gi|70606547|ref|YP_255417.1| 419 AIKSLDAGVEDI-----DLISAI------SEGINVVDLSSIKSEELRRLV 457
                                   888888888888.....999999......888999999999999998865 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   9.1e-06      0.02      22      59 ..     260     299 ..     252     301 .. 0.68
   2 ?    0.3   0.0      0.16   3.6e+02     149     185 ..     478     518 ..     463     534 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-06
                                   EEEETTS-EEEEEGGGS-...SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  22 lgkeisgnplvldlkkma..shllvaGatgsGKStalntL 59 
                                   lg+ei ++  v+  ++    +h l++G tgsGK+++l +L
  gi|70606547|ref|YP_255417.1| 260 LGQEINDRRAVFWNVNRVinPHALIIGPTGSGKTEFLLSL 299
                                   566663333333222222346***************9766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                                   B-TT-..........................---------- CS
                  FtsK_SpoIIIE 149 vflvlDn.yddlaaene...ritsLsnqgpsygvhvlvtag 185
                                   ++lv+D+ +  l+ e+     +  L+++g  +g+ + ++++
  gi|70606547|ref|YP_255417.1| 478 LVLVIDEaWTLLRSEDRdyqIVADLIKRGRGFGIGIFMATQ 518
                                   578888724556677779966678********998876654 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.5e-05     0.033      40      82 ..     267     320 ..     244     326 .. 0.76
   2 ?   -2.5   0.0      0.73   1.6e+03     322     358 ..     500     548 ..     443     564 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
               T4SS-DNA_transf  40 tdGdf........ehvlvvAptrsgKg...vgvviPnllkwkqsiVvlDpkgEl 82 
                                   +   f        +h+l+++pt+sgK+    ++ + + + ++  iV +D+k+++
  gi|70606547|ref|YP_255417.1| 267 RRAVFwnvnrvinPHALIIGPTGSGKTeflLSLGVKTNILYGIPIVFFDVKKDI 320
                                   44444555555679*************555599******************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.73
               T4SS-DNA_transf 322 eealatiagYgirltlIiQsisqlke............tYgkegaksil 358
                                      +  ++g+gi +++  Q+   l e            +  ++g k+++
  gi|70606547|ref|YP_255417.1| 500 ADLIKRGRGFGIGIFMATQNFDDLGElsdiflenigllGFMNNGDKKFW 548
                                   4456667888899998888887776655555555555555555555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.5e-05      0.21      51      85 ..     283     318 ..     274     343 .. 0.81
   2 ?   -1.6   0.1      0.85   1.9e+03     113     136 ..     396     419 ..     392     422 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.5e-05
                     IstB_IS21  51 vllGpsGvGKshlaialgvea.vraglsvlfvrved 85 
                                   +++Gp+G GK+ +  +lgv++ +  g+ ++f+ v++
  gi|70606547|ref|YP_255417.1| 283 LIIGPTGSGKTEFLLSLGVKTnILYGIPIVFFDVKK 318
                                   79****************986377999999998853 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.85
                     IstB_IS21 113 ilDdlgllpldqaeaellfeviek 136
                                   i+D +   +++++ +++l++++++
  gi|70606547|ref|YP_255417.1| 396 IIDKIEKYDINEDVKAYLLRIVSA 419
                                   89*******************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0011       2.4       7      23 ..     281     297 ..     279     323 .. 0.86
   2 ?    2.7   0.0     0.065   1.5e+02      74     103 ..     454     488 ..     410     522 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                        AAA_22   7 ilvvtGesGtGKTtllr 23 
                                   + +++G++G+GKT  l 
  gi|70606547|ref|YP_255417.1| 281 HALIIGPTGSGKTEFLL 297
                                   689**********8765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.065
                        AAA_22  74 sseellealeqalrarav.....ielliiDEaqhl 103
                                   ++  ++  + + ++++       + +l+iDEa  l
  gi|70606547|ref|YP_255417.1| 454 RRLVMYGIIIKFINKYNIaddrlKLVLVIDEAWTL 488
                                   5555555556666666666667779******9774 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00076       1.7      16      35 ..     280     299 ..     274     304 .. 0.88
   2 ?    1.8   0.0     0.041        92     240     285 ..     473     523 ..     437     527 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00076
                 TrwB_AAD_bind  16 qhilivGttGsGKtqalekl 35 
                                    h+li+G tGsGKt+ l +l
  gi|70606547|ref|YP_255417.1| 280 PHALIIGPTGSGKTEFLLSL 299
                                   6*************999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
                 TrwB_AAD_bind 240 srerrlWfflDElpaLgrlee.....lksllaegRkfGgavvlglqsiaql 285
                                   +++ +l +++DE  +L r e+     +++l+++gR fG+ + ++ q++  l
  gi|70606547|ref|YP_255417.1| 473 DDRLKLVLVIDEAWTLLRSEDrdyqiVADLIKRGRGFGIGIFMATQNFDDL 523
                                   5566888999999888775432233399*******************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 4049.16
//
Query:       gi|70606548|ref|YP_255418.1|  [L=142]
Description: hypothetical protein Saci_0749 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   10.8   0.2       0.27   10.8   0.2    2.0  2  DUF4795   Domain of unknown function (DUF4795)


Domain annotation for each model (and alignments):
>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   1.5e-05      0.27     130     167 ..       4      40 ..       2      46 .. 0.74
   2 ?    2.2   1.1    0.0064   1.2e+02      94     144 ..      81     131 ..      75     142 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.5e-05
                       DUF4795 130 elepLkeqleerlkelqkelqeamekedkedeaaglrk 167
                                   ++e+Lk++le+++ el+kel+ + e + +  e +g ++
  gi|70606548|ref|YP_255418.1|   4 NIEELKKFLENKITELKKELEYY-EYLLSLLETEGYKN 40 
                                   89*****************9955.33333445666665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.0064
                       DUF4795  94 ekmleellekleeqeealkkaldtLqeelkekld..rlelepLkeqle.erlke 144
                                   +++   +++k+ e+e++ +k+  ++    +ek +  ++ ++++k++l  +r+k+
  gi|70606548|ref|YP_255418.1|  81 NRIYANVINKILENEKNKNKIEYNIT---FEKDElkEITIDSIKDELLyNRIKA 131
                                   67788899999999999999999999...4444444888999998876455543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1711  (0.095432); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1198.05
//
Query:       gi|70606549|ref|YP_255419.1|  [L=350]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-34  117.6   0.0    1.4e-33  115.9   0.0    1.8  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    8.2e-08   32.5   0.0    1.1e-07   32.1   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.14   12.8   0.0       0.38   11.4   0.0    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
        0.2   11.9   0.0       0.33   11.2   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   3.8e-37   1.4e-33       1     120 [.       3     141 ..       3     142 .. 0.98
   2 ?   -1.7   0.0         1   3.8e+03      10      41 ..     268     302 ..     268     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 3.8e-37
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvsk 80 
                                   +va++G++Gy+G ellrlL+ h +ve+++++s++  aGk+++  +++l++  ++++++ + +++ ++++ vflalp++vs 
  gi|70606549|ref|YP_255419.1|   3 RVAVIGGSGYTGGELLRLLAMHNKVEVTYITSREY-AGKPISIIHPNLRGFYNINFSQFSWDKIgEKAEAVFLALPHKVSV 82 
                                   7**********************************.**********************8888888**************** PP

                                   HHHHHHHHTTSEEEESSSTTTTST...................TSEBE-HHHHGGGGGG CS
                Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkd...................davyvlpevnreaikk 120
                                   +++pkl+e g++v+Dls+dfRlk+                   +avy++pe++ e++k 
  gi|70606549|ref|YP_255419.1|  83 DYVPKLLEMGLQVVDLSADFRLKNpelyklwyefdhpypdllkKAVYGIPEIHYEELKG 141
                                   ********************************************************986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                   HHHHHHHHHHHC..TSSEEEEEEEESTT.TTTSBH CS
                Semialdhyde_dh  10 yvGqellrlLee..hpevelvvllsssr.saGkkl 41 
                                   y G++++r+++   hp+ +  ++++s+  + G ++
  gi|70606549|ref|YP_255419.1| 268 YRGRKFVRVIRGniHPYPDPKYVIGSNFvDIGFAV 302
                                   56999999999989999999999998765555555 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   3.1e-11   1.1e-07      43     184 .]     185     320 ..     151     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.1e-11
                                   STTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEES...SSHH CS
               Semialdhyde_dhC  43 sdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkileftekvsatcvrVPvlrGhseavtiklk...lkdv 120
                                   ++++++g ++ +    + py  +  +++  e+++el+ + +++++++  +      + V  +rG +++v+  l    l+++
  gi|70606549|ref|YP_255419.1| 185 GAKPSEGSHHPERQNAIRPYEAE-GHRHAAEVEQELQYISKKEVKISLVP------HAVSTIRGALASVHGWLIsddLNEI 258
                                   45677788888888888888887.9*************************......79************99985443333 PP

                                   HHHHHHHHHHCSTTEEEEESS..HCHHSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
               Semialdhyde_dhC 121 eveeveellaaapevkvvvne..eedrPtpaavaggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                   e  +   ++++   ++v+v       +P p+ v+g +n+v++G + + +++ + + +++++DNl+k
  gi|70606549|ref|YP_255419.1| 259 EFWKKIIEFYRG-RKFVRVIRgnIHPYPDPKYVIG-SNFVDIG-FAVEKRVGR-ITMFSAIDNLMK 320
                                   333333455666.6666666555899********9.9******.********8.**********97 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.9e-05      0.18       2      50 ..       5      57 ..       4      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                                  EEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC...EEEE--T CS
                     Epimerase  2 lVtGatGfiGsalvkallekg.yevigldrlssasntarledl...elveldl 50
                                   V+G++G+ G  l++ l+ ++ +ev+ ++++++a++  ++ +     ++++++
  gi|70606549|ref|YP_255419.1|  5 AVIGGSGYTGGELLRLLAMHNkVEVTYITSREYAGKPISIIHPnlrGFYNINF 57
                                  69***************9999899********999987766655555555554 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.38       1      94 [.       3      98 ..       3     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                  EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSC..CCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHHHH CS
                 F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnp..ekaeelaeelg....vkvtavdneeaaeeadvvvlavkpedvee 76
                                  ++++i G+G  g  l++ l+ ++  + e++ ++sr+   + +  ++ +l     ++ ++ +  +  e+a+ v+la++ ++  +
  gi|70606549|ref|YP_255419.1|  3 RVAVIgGSGYTGGELLRLLAMHN--KVEVTYITSREYagKPISIIHPNLRgfynINFSQFSWDKIGEKAEAVFLALPHKVSVD 83
                                  699**9***********999999..77887787776411334445555546667***********************999888 PP

                                  HHHHCGHHHHTTSEEEEE CS
                 F420_oxidored 77 vlselakdalkgklvisv 94
                                   + +l   +  g  v++ 
  gi|70606549|ref|YP_255419.1| 84 YVPKL---LEMGLQVVDL 98
                                  88888...6666666666 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.2e-05      0.33       1      32 [.       4      34 ..       4     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.2e-05
                                  EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEES CS
               Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadr 32
                                  v +iG+ G++G  +++lla h++v  e+t ++ 
  gi|70606549|ref|YP_255419.1|  4 VAVIGGsGYTGGELLRLLAMHNKV--EVTYITS 34
                                  6789999*****************..7776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2554.36
//
Query:       gi|70606550|ref|YP_255420.1|  [L=261]
Description: acetylglutamate/acetylaminoadipate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-30  105.6   2.1    3.3e-30  105.4   2.1    1.0  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.22   10.8   1.2        1.7    7.9   0.2    2.3  2  ATLF       Anthrax toxin lethal factor, N- and C-terminal dom


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   2.1   3.7e-34   3.3e-30       2     239 ..       1     240 [.       1     242 [. 0.89

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3.7e-34
                                   EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHH CS
                     AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeagevat 78 
                                   ++VvK GG +l+    ++l+r+++ i +    +nk++ VhGgg ++ +l+++  g+++++ ++    + r+t +e++ev  
  gi|70606550|ref|YP_255420.1|   1 MIVVKTGGRVLK----QNLDRVVQSIIKT---NNKIIYVHGGGDQVTELSSK-LGIEPKFVTSpegiRSRYTTKEELEVFI 73 
                                   59**********....55889**999999...99******************.*********9**99999********996 PP

                                   HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..................HHHTTTCEEECCHHHHHHHTT-EEEE CS
                     AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr................degsdgnvesvdaeaieelleagvvpvl 143
                                     +++s  +r   + ++++ +++ l++a+  ++ a+r                d g++g+++++++e + ++ +  +v++l
  gi|70606550|ref|YP_255420.1|  74 --MVMSSISRNILSRVSSYRNSIALTGADGKLVLAERkkkiividergrkriiDGGYTGKIKNINKELLVTFSNLFEVIIL 152
                                   ..44444444444445566677777777777777777777*********************************9999**** PP

                                   ESEEEEETTTE.EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCH CS
                     AA_kinase 144 tgfigldeege.lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkh 223
                                   ++++ +d+++  l+++++D++a +lA al+ d li+ltdV+GV+ ++       +++++++v+ea+e  s+ +  Gm+ k+
  gi|70606550|ref|YP_255420.1| 153 SPLA-YDPDEStLLNVDGDQMAFALATALRSDNLILLTDVEGVMVDN-------KVVNKLTVEEAKE-LSKKIGPGMNRKI 224
                                   **97.999999999******************************886.......899**********.8888899****** PP

                                   HHHHHHHHCTT-EEEE CS
                     AA_kinase 224 paalaaarrggipvvI 239
                                   + a++a+++g+ +v+I
  gi|70606550|ref|YP_255420.1| 225 LMAAEAIENGVKKVII 240
                                   **********999988 PP

>> ATLF  Anthrax toxin lethal factor, N- and C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00019       1.7      98     134 ..      59      93 ..      43     146 .. 0.87
   2 ?    1.4   0.0     0.018   1.6e+02     106     139 ..     206     239 ..     189     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00019
                                   SHCCCTTSSCCCCCHHHHHHHHCTTCCGSCCTTSSSH CS
                          ATLF  98 iaedYvendekakevYyeigkglsrdilskdkelrne 134
                                   i   Y++++e  +ev+  +   +sr+ils+  + rn 
  gi|70606550|ref|YP_255420.1|  59 IRSRYTTKEE--LEVFIMVMSSISRNILSRVSSYRNS 93 
                                   5568999999..*****************99888775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.018
                                   SCCCCCHHHHHHHHCTTCCGSCCTTSSSHHHHHH CS
                          ATLF 106 dekakevYyeigkglsrdilskdkelrnefldli 139
                                    e+ake+ ++ig g+ r il   + ++n  +++i
  gi|70606550|ref|YP_255420.1| 206 VEEAKELSKKIGPGMNRKILMAAEAIENGVKKVI 239
                                   4669999999999999999988888877777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1824.47
//
Query:       gi|70606551|ref|YP_255421.1|  [L=140]
Description: Lrp-like transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-13   49.3   1.1    2.1e-12   46.4   0.3    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    4.5e-13   49.0   0.0    6.9e-13   48.4   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    5.3e-13   48.6   0.0    1.8e-12   46.9   0.1    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    6.2e-06   26.1   1.9    1.1e-05   25.3   0.2    2.2  3  HTH_11          HTH domain
    0.00037   20.3   0.0    0.00061   19.6   0.0    1.4  1  MarR_2          MarR family
     0.0015   18.4   0.1     0.0059   16.5   0.1    1.9  2  MarR            MarR family
     0.0033   17.4   0.1     0.0086   16.1   0.0    1.7  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0048   16.9   0.2     0.0082   16.2   0.2    1.4  1  NapD            NapD protein
     0.0053   16.8   0.0      0.008   16.2   0.0    1.2  1  HTH_20          Helix-turn-helix domain
      0.006   16.7   0.1      0.012   15.8   0.1    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0066   16.2   0.2      0.012   15.3   0.2    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0072   16.2   0.1      0.014   15.2   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0087   15.8   0.1      0.017   14.9   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.018   14.9   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      0.012   15.8   0.0        0.2   11.9   0.1    2.2  2  Rio2_N          Rio2, N-terminal
      0.016   15.7   0.1      0.025   15.1   0.1    1.3  1  HTH_27          Winged helix DNA-binding domain
      0.016   15.3   0.1      0.031   14.4   0.1    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.027   14.2   0.3      0.043   13.5   0.3    1.4  1  DUF4423         Domain of unknown function (DUF4423)
      0.042   14.1   0.0       0.09   13.0   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.049   13.7   0.1      0.079   13.1   0.1    1.3  1  FeoC            FeoC like transcriptional regulator
      0.057   13.3   0.6       0.95    9.4   0.6    2.1  1  PAX             'Paired box' domain
      0.069   13.3   0.1       0.11   12.6   0.1    1.5  1  DMAP1_like      Putative DMAP1-like
       0.08   13.3   0.1       0.18   12.2   0.1    1.6  1  Rrf2            Transcriptional regulator
      0.087   13.4   0.0       0.15   12.7   0.0    1.4  1  Mga             Mga helix-turn-helix domain
        0.1   12.6   0.1       0.18   11.8   0.1    1.5  1  HTH_36          Helix-turn-helix domain
       0.11   12.2   0.2       0.39   10.4   0.2    1.9  1  Sigma70_r4_2    Sigma-70, region 4
       0.13   12.1   0.0       0.87    9.5   0.1    2.1  2  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.3   3.1e-15   2.1e-12       2      48 .]       5      51 ..       4      51 .. 0.98
   2 ?    1.5   0.0      0.33   2.2e+02      12      27 ..      69      84 ..      59      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.1e-15
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  d+ d+kILe L+kn+r++ + +A++l +S ++v++r+++L++ G+Ik
  gi|70606551|ref|YP_255421.1|  5 DDSDIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIK 51
                                  899*******************************************8 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                        HTH_24 12 LqknprisqreLAerl 27
                                  ++ np i+  e+++++
  gi|70606551|ref|YP_255421.1| 69 VKTNPQIPTPEISKKI 84
                                  5669*********986 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0     1e-15   6.9e-13       1      74 [.      67     137 ..      67     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1e-15
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                   v+v+++p+   ++ e+ +++ ++p V+ +y +tGdyd l+ v+  ++ ++++ +++ ++sl gv +t+++ivl+
  gi|70606551|ref|YP_255421.1|  67 VMVKTNPQI--PTPEISKKIIKIPGVEAVYETTGDYDVLALVRGMNIISINKTIDD-IRSLQGVISTNSTIVLR 137
                                   688888777..999******************************************.***************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   2.7e-15   1.8e-12       2      41 ..       5      44 ..       4      45 .. 0.98
   2 ?   -1.6   0.0       3.7   2.5e+03      14      26 ..      71      83 ..      69      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 2.7e-15
                 HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  D+ D+kILe L+++aR++++ +A+++ +Se++v++Rv++L
  gi|70606551|ref|YP_255421.1|  5 DDSDIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKL 44
                                  999************************************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                 HTH_AsnC-type 14 edaRisyaeLAer 26
                                   ++ i+  e++++
  gi|70606551|ref|YP_255421.1| 71 TNPQIPTPEISKK 83
                                  58999999*9987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   1.7e-08   1.1e-05       4      44 ..      10      49 ..       8      58 .. 0.87
   2 ?   -1.8   0.0       4.7   3.1e+03       8      24 ..      68      83 ..      61      84 .. 0.68
   3 ?   -1.9   0.1       5.1   3.4e+03      32      42 ..     114     124 ..     111     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-08
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  +ile+L+++    +   +A+eL++S+++vr+++++L  lgv
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNAR-TPFTMIAKELKISEAAVRKRVEKLIRLGV 49
                                  8*****77776.8999**********************993 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.7
                        HTH_11  8 lLleargpisgeeLAee 24
                                  ++ +++++i+  e++++
  gi|70606551|ref|YP_255421.1| 68 MV-KTNPQIPTPEISKK 83
                                  44.66666999999887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.1
                        HTH_11  32 vrrdIkaLeel 42 
                                   + + I+++++l
  gi|70606551|ref|YP_255421.1| 114 INKTIDDIRSL 124
                                   55666666654 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   9.2e-07   0.00061       7      53 ..       8      52 ..       2      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.2e-07
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  +  +L  L+ + +     + +a++l++s +av +++++L + G + r
  gi|70606551|ref|YP_255421.1|  8 DIKILEMLRKNAR--TPFTMIAKELKISEAAVRKRVEKLIRLGVIKR 52
                                  5678999999998..89**************************9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.9e-06    0.0059       5      50 ..       8      53 ..       5      56 .. 0.94
   2 ?   -1.1   0.0       2.8   1.9e+03       4      26 ..      61      83 ..      60      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-06
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                   ++iL++l+ +     + +ak l++s ++v + + +L++ G i+R 
  gi|70606551|ref|YP_255421.1|  8 DIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKRF 53
                                  579*****************************************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.8
                                  HHHHHHHHHHHSTTEEHHHHHHH CS
                          MarR  4 tqfviLrilyeqgplsvseLakk 26
                                  +++++++++++++++   e+ kk
  gi|70606551|ref|YP_255421.1| 61 NEIKAIVMVKTNPQIPTPEISKK 83
                                  68889999999999999999887 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05    0.0086       6      44 ..       7      44 ..       5      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                       HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseL 44
                                  +++k+le L + + +++ + +akeL +se ++++++++L
  gi|70606551|ref|YP_255421.1|  7 SDIKILEMLRK-NARTPFTMIAKELKISEAAVRKRVEKL 44
                                  689********.***********************9998 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.2e-05    0.0082       8      68 ..      69     131 ..      60     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                          NapD   8 Vqarpe.rlaavkaalaalpgvEvhasdee.gklVvviEaesedeladtieaiealpgVlsas 68 
                                   V+++p+  ++++++++ ++pgvE   ++     +   + + +  ++ +ti++i++l+gV+s++
  gi|70606551|ref|YP_255421.1|  69 VKTNPQiPTPEISKKIIKIPGVEAVYETTGdYDVLALVRGMNIISINKTIDDIRSLQGVISTN 131
                                   555555347899***********6655554499****************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05     0.008      14      55 ..      10      51 ..       5      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                  +il +L+ ++   ++ +a++l +s + +++++++L + g ++
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIK 51
                                  7*****9999***************************99987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.7e-05     0.012       7      56 ..       5      54 ..       2      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                  d+ ++k+l++l+k       +iakel+i+   vr+ ++kL +lG ++r +
  gi|70606551|ref|YP_255421.1|  5 DDSDIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKRFT 54
                                  67789999999998888889**************************9976 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.8e-05     0.012       4      46 ..      10      52 ..       8      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  +ile+l++      + ++ +l++Sea +R+  ++L   g+++R
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKR 52
                                  79**************************************999 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.2e-05     0.014       8      55 ..       6      53 ..       3      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                                  HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  + ++k+   L k+ +   + ia+el+++++ v + +++L++ G+++r 
  gi|70606551|ref|YP_255421.1|  6 DSDIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKRF 53
                                  56888888888999999999*************************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.6e-05     0.017       7      50 ..      10      52 ..       9      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   iL++l++ ++   ++ +A+++ ++ ++v+  +  L++lG +++
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNART-PFTMIAKELKISEAAVRKRVEKLIRLGVIKR 52
                                  79*********8.9**************************9875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.7e-05     0.018       5      46 ..       9      51 ..       5      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +kIL +L++   + ++ +a+el++s+++v+    kL  +G+++
  gi|70606551|ref|YP_255421.1|  9 IKILEMLRKnARTPFTMIAKELKISEAAVRKRVEKLIRLGVIK 51
                                  69*******555889***************9999999999885 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0003       0.2      12      62 ..      12      58 ..       1      59 [. 0.83
   2 ?    1.8   0.0      0.43   2.9e+02      67      76 ..      96     105 ..      68     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                        Rio2_N 12 LtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakyd 62
                                  L   Em  +n    p+++i++  +++e  v+kr+++l++ + i+r t+ y+
  gi|70606551|ref|YP_255421.1| 12 L---EMLRKN-ARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKRFTIDYE 58
                                  3...666555.457*******************************999886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                        Rio2_N  67 tyeGyDyLAL 76 
                                   t + yD+LAL
  gi|70606551|ref|YP_255421.1|  96 TTGDYDVLAL 105
                                   3356999999 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   3.7e-05     0.025       5      51 ..       8      53 ..       4      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                  ++ +L+ +r  ++r   +++++ l+++ +++ + ++kL++ G+++r 
  gi|70606551|ref|YP_255421.1|  8 DIKILEMLR-KNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKRF 53
                                  566888888.8899999***************************875 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.7e-05     0.031      17      57 ..      10      50 ..       9      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-05
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  k+ e+L +++r + ++++k++k+s   V+k +  Li+++ +
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVI 50
                                  799******************************99999876 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   6.4e-05     0.043      39      72 ..      23      54 ..      10      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                       DUF4423 39 peelakrlrpkisaeevekalefLlklgllkkde 72
                                     +ak l+  is++ v+k +e L +lg++k+  
  gi|70606551|ref|YP_255421.1| 23 FTMIAKELK--ISEAAVRKRVEKLIRLGVIKRFT 54
                                  5679*****..********************965 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014      0.09      26      50 ..      24      48 ..      11      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                  HHHHHHHTS-HHHHHHHHHHHHHTT CS
                Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdG 50
                                  +++a++L++s + V + ++kL + G
  gi|70606551|ref|YP_255421.1| 24 TMIAKELKISEAAVRKRVEKLIRLG 48
                                  89*******************8877 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.079       6      46 ..      12      52 ..       9      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                          FeoC  6 keyleergrvslkeLsrhfkaspealeamLeqwvrkGrvek 46
                                   e l+++ r  +  +++++k+s++a+++ +e ++r G +++
  gi|70606551|ref|YP_255421.1| 12 LEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIKR 52
                                  57899********************************9876 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6    0.0014      0.95      25      84 ..      10      84 ..       4      92 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                           PAX 25 kivelahsgvrp..cvisrqlrvshgcvskilgryqetg.............sirpgviggskpkvatpevvkki 84
                                  ki+e+ ++ +r     i++ l++s+  v k + +    g              i+  v+  ++p++ tpe+ kki
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKNARTpfTMIAKELKISEAAVRKRVEKLIRLGvikrftidyelenEIKAIVMVKTNPQIPTPEISKKI 84
                                  788888888774235688888888888887666555555000000000000045555666667777777777776 PP

>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017      0.11      35      78 ..       3      46 ..       1      70 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                    DMAP1_like 35 eledkelkikeiinkkqsypnvfLaSslgfskstwnkkvekiLk 78
                                  +  d ++ki e++ k+   p   +a  l++s   + k vek+++
  gi|70606551|ref|YP_255421.1|  3 DVDDSDIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIR 46
                                  67899***********************************9864 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.18      18      56 ..      13      51 ..       8      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                  HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  ++ +++     + ia++ +is+  ++k ++kL + g++k
  gi|70606551|ref|YP_255421.1| 13 EMLRKNARTPFTMIAKELKISEAAVRKRVEKLIRLGVIK 51
                                  4445555578999************************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00022      0.15      18      56 ..       8      46 ..       4      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                                  HHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                           Mga 18 kyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                  ++++l+ l +++++ ++ +a+el iSe+ + + +++l  
  gi|70606551|ref|YP_255421.1|  8 DIKILEMLRKNARTPFTMIAKELKISEAAVRKRVEKLIR 46
                                  7899**************************999998865 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.18      29      55 .]      24      50 ..       9      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                        HTH_36 29 etlakrlglsknTvsraikeLeqlGyi 55
                                    +ak l++s+  v++ + +L++lG i
  gi|70606551|ref|YP_255421.1| 24 TMIAKELKISEAAVRKRVEKLIRLGVI 50
                                  67***********************76 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00058      0.39      32      47 ..      26      41 ..       9      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                                  HHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 32 IAellgisegtVksrl 47
                                  IA++l+ise++V++r+
  gi|70606551|ref|YP_255421.1| 26 IAKELKISEAAVRKRV 41
                                  9************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0013      0.87       9      39 ..      10      42 ..       9      52 .. 0.82
   2 ?   -0.1   0.0       1.3   8.6e+02       6      26 ..      61      83 ..      56      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                        HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlk 39
                                  +il +l++  + + + IA+eL +s+  v++ ++
  gi|70606551|ref|YP_255421.1| 10 KILEMLRKnaRTPFTMIAKELKISEAAVRKRVE 42
                                  6888888778999999*************5444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                        HTH_23  6 eRlrillllae..GlsvreIAre 26
                                  + ++++ +++    ++++eI+++
  gi|70606551|ref|YP_255421.1| 61 NEIKAIVMVKTnpQIPTPEISKK 83
                                  557899999988999999*9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1092.54
//
Query:       gi|70606552|ref|YP_255422.1|  [L=56]
Description: hypothetical protein Saci_0753 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   15.1   0.7      0.073   12.7   0.1    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.023   15.0   0.0      0.026   14.9   0.0    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.039   13.4   0.5       0.34   10.4   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
      0.063   13.2   0.0      0.092   12.7   0.0    1.3  1  zinc_ribbon_4    zinc-ribbon domain
      0.082   12.7   0.8        2.5    7.9   0.2    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.16   11.5   2.0       0.31   10.6   2.0    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.4e-05     0.073       8      18 ..       5      15 ..       1      18 [. 0.89
   2 ?    0.9   0.1      0.12   3.5e+02      12      20 ..      29      37 ..      19      42 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                  E-TTT--EEEE CS
               Desulfoferrod_N  8 kCevCGniVeV 18
                                  kC +CGn V+V
  gi|70606552|ref|YP_255422.1|  5 KCPICGNDVNV 15
                                  9********98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                  T--EEEECC CS
               Desulfoferrod_N 12 CGniVeVle 20
                                  CG   eV +
  gi|70606552|ref|YP_255422.1| 29 CGAQLEVFN 37
                                  666666665 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   8.7e-06     0.026       2      36 ..       2      31 ..       1      53 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.7e-06
               Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                   L+ CP Cg++  +  + ++ +     +  ++Cga
  gi|70606552|ref|YP_255422.1|  2 VLLKCPICGNDVNVPDDSLPGE-----IVEHECGA 31
                                  6899*************99995.....77789999 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00012      0.34       4      13 ..       5      16 ..       3      20 .. 0.72
   2 ?    1.3   0.0     0.083   2.5e+02       8      12 ..      29      33 ..      28      35 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                   zf-ribbon_3  4 rCPnCGa.p.ls 13
                                  +CP CG+ + + 
  gi|70606552|ref|YP_255422.1|  5 KCPICGNdVnVP 16
                                  699999977454 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.083
                   zf-ribbon_3  8 CGapl 12
                                  CGa+l
  gi|70606552|ref|YP_255422.1| 29 CGAQL 33
                                  77754 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05     0.092       4      29 ..       5      30 ..       3      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                 zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCs 29
                                   Cp C+   +++d+ lp+++v+  C 
  gi|70606552|ref|YP_255422.1|  5 KCPICGNDVNVPDDSLPGEIVEHECG 30
                                  7*******************998886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00083       2.5       1       9 [.       5      13 ..       5      19 .. 0.82
   2 ?    3.4   0.0     0.023        68       4       9 ..      28      33 ..      27      35 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00083
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +Cp CG+ +
  gi|70606552|ref|YP_255422.1|  5 KCPICGNDV 13
                                  799999976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.023
                 zinc_ribbon_2  4 nCGael 9 
                                  +CGa+l
  gi|70606552|ref|YP_255422.1| 28 ECGAQL 33
                                  699987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0    0.0001      0.31       2      31 ..       5      35 ..       4      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                  EETTTTC.EECHEETSTTCEEESSSSBEEEE CS
                  TF_Zn_Ribbon  2 kCPnCgs.tnlveDpergelvCtdCGlVled 31
                                  kCP+Cg+  n+  D   ge+v  +CG+ le 
  gi|70606552|ref|YP_255422.1|  5 KCPICGNdVNVPDDSLPGEIVEHECGAQLEV 35
                                  9******555788888899999999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 373.08
//
Query:       gi|70606553|ref|YP_255423.1|  [L=276]
Description: hypothetical protein Saci_0754 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-33  116.2   0.0      2e-33  115.6   0.0    1.2  1  RimK             RimK-like ATP-grasp domain
      8e-12   44.9   0.0    1.1e-11   44.5   0.0    1.2  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    2.2e-05   23.9   0.1     0.0011   18.3   0.0    2.3  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    4.7e-05   23.0   0.0    7.6e-05   22.3   0.0    1.2  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0002   21.4   0.0    0.00031   20.8   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
    0.00067   19.2   0.0     0.0015   18.0   0.0    1.5  2  ATP-grasp_5      ATP-grasp domain
     0.0029   17.2   0.0     0.0059   16.2   0.0    1.5  1  ATP-grasp        ATP-grasp domain
  ------ inclusion threshold ------
      0.025   14.1   0.2        1.3    8.4   0.1    2.4  2  Ins134_P3_kin    Inositol 1,3,4-trisphosphate 5/6-kinase ATP-
      0.033   13.7   0.0        0.3   10.6   0.0    2.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      0.041   13.4   0.0      0.073   12.6   0.0    1.3  1  ATP-grasp_2      ATP-grasp domain
      0.077   12.4   0.0       0.11   11.8   0.0    1.2  1  Fungal_lectin    Fungal fucose-specific lectin


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   1.2e-36     2e-33       3     186 ..      81     268 ..      79     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.2e-36
                                   -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG--.... CS
                          RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeai.... 76 
                                   +Kl +l lLak++ik+p+t ++ ++++a++l +ki  +fP v+K +egs G  v  a +e+ l + le    ++ +     
  gi|70606553|ref|YP_255423.1|  81 NKLYTLSLLAKHNIKTPRTIVTFSKDKAVDLAKKI--GFPAVIKPIEGSWGRMVAKAVDEDILYSFLEYqeyTTSQFrqiy 159
                                   8999*******************************..6*****************************99888666656669 PP

                                   EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEE.TT CS
                          RimK  77 lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllra.kr 156
                                   lvqe+++ + n+diR++v++de   ++ rv +e ++++n  +G+ a +l++++e+++lA+k+ ++m+ +++G+D+++  +r
  gi|70606553|ref|YP_255423.1| 160 LVQEFVK-KPNRDIRIFVMGDEAPVGIYRV-NERNWKTNTALGARALPLKIDDELRDLALKVRDIMGGFFLGIDIFEDpER 238
                                   ******8.5789***********9999999.8889***************************************9975389 PP

                                   EEEEEEEESS--SHHHHHHHT--HHHHHHH CS
                          RimK 157 gllvlEvnsspglekiektlgidiakklie 186
                                   g+lv Evn  p+ ++  +  + ++   l++
  gi|70606553|ref|YP_255423.1| 239 GYLVNEVNGVPEYKNTVRVNNFNVSSYLLN 268
                                   *************99999998888877765 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   6.7e-15   1.1e-11       2     154 ..      82     235 ..      81     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6.7e-15
                                   TGGGGGGC....CCS--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-T..THHHHHHHHTTTTTS-EEEE CS
                     GSH-S_ATP   2 Klaalsfp....elipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdp..nlksilellteegkepviaq 75 
                                   Kl++ls+       +p+t+v+ +k++  +++++ g  +++KP++g+ G+ v +  ++d   ++    e +t++ ++  ++q
  gi|70606553|ref|YP_255423.1|  82 KLYTLSLLakhnIKTPRTIVTFSKDKAVDLAKKIGFpAVIKPIEGSWGRMVAKAVDEDIlySFLEYQEYTTSQFRQIYLVQ 162
                                   5555554322214579*****************9988***************999987611445557899*********** PP

                                   E--GGGGG-EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                     GSH-S_ATP  76 rylpeikeGDkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                   +++++ ++ D Ri+++  e  +  + Rv  e++ ++n a g+ra   +++++ r +a ++++ +   G +f G+D+ +d
  gi|70606553|ref|YP_255423.1| 163 EFVKKPNR-DIRIFVMGDE-APVGIYRVN-ERNWKTNTALGARALPLKIDDELRDLALKVRDIM---GGFFLGIDIFED 235
                                   ****9988.****988544.4445***96.6789***************************987...899******976 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.8e-07    0.0011      10      85 ..      70     139 ..      66     170 .. 0.80
   2 ?    3.4   0.0     0.024        39     227     269 ..     211     252 ..     204     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.8e-07
                   ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                                   +N+ + +    +Kl + +l+ ++ +k+p++++++++ + ++ ++++  ++ +  viKp++gs+G+ + ++ +  ++
  gi|70606553|ref|YP_255423.1|  70 VNDATSLFKCGNKLYTLSLLAKHNIKTPRTIVTFSKDKAVDLAKKI--GF-P-AVIKPIEGSWGRMVAKAVD--ED 139
                                   78999999999*************************9999988876..45.3.49*********97777644..33 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.024
                   ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                   e+ +la k+ + ++g   lG+Di  d+e+g l+ E+N  p ++
  gi|70606553|ref|YP_255423.1| 211 ELRDLALKVRD-IMGGFFLGIDIFEDPERGYLVNEVNGVPEYK 252
                                   56689999999.889999*******************988876 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.6e-08   7.6e-05       9     109 ..      89     186 ..      82     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.6e-08
                                   HHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE-- CS
                   CPSase_L_D2   9 lkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlveksl 89 
                                   l+k n+++ +   +   + ++a+++ak+ig+P +ik+  g  G+    a +e+ l   ++   + +++ f ++  lv++++
  gi|70606553|ref|YP_255423.1|  89 LAKHNIKTPRTIVT--FSKDKAVDLAKKIGFPAVIKPIEGSWGRMVAKAVDEDILYSFLEYQ-EYTTSQF-RQIYLVQEFV 165
                                   66667777766666..899******************9999988777777777666666554.4444556.567889**** PP

                                   SSS.EEEEEEEEEETTS-EEE CS
                   CPSase_L_D2  90 kgp.keiEvevlrDakgnvit 109
                                   k+p ++i + v+ D++   i+
  gi|70606553|ref|YP_255423.1| 166 KKPnRDIRIFVMGDEAPVGIY 186
                                   *98689********9766655 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.9e-07   0.00031       1      98 [.      79     195 ..      79     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                                   HTSHHHHHHHHTTT.S---...........-EESS--....SSSEEEEESS-------B--SS--TTE............. CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleee....ekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                   + +Kl t   L ++++k+P       +    +++         + v+Kp++G+ g  v ++ +++ + +++e++e      
  gi|70606553|ref|YP_255423.1|  79 CGNKLYTLSLLAKHNIKTPrtivtfsK----DKAVDLakkiGFPAVIKPIEGSWGRMVAKAVDEDILYSFLEYQEyttsqf 155
                                   78*****************87754422....33322223347789****************************999***** PP

                                   ....EEEE---S..EEEEEEEEE.SSSEEEEEEEEEEEET CS
                   ATP-grasp_3  65 ....lvqefieG..kplSvsllsdgekvlvlavnrqliek 98 
                                       lvqef++   +++ + +++d+  v +  vn+  +++
  gi|70606553|ref|YP_255423.1| 156 rqiyLVQEFVKKpnRDIRIFVMGDEAPVGIYRVNERNWKT 195
                                   **********851144555555566566666667666655 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.5e-07    0.0015      16      52 ..      86     122 ..      81     127 .. 0.93
   2 ?   -3.0   0.0       2.5   4.1e+03      96     120 ..     155     179 ..     133     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.5e-07
                   ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                    +ll+  +i++++t++  s+++av++a++ig+p v+K
  gi|70606553|ref|YP_255423.1|  86 LSLLAKHNIKTPRTIVTFSKDKAVDLAKKIGFPAVIK 122
                                   579*********************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                   ATP-grasp_5  96 riegvlVqemakrggrElivgvteD 120
                                     + +lVqe +k+ +r++++ v  D
  gi|70606553|ref|YP_255423.1| 155 FRQIYLVQEFVKKPNRDIRIFVMGD 179
                                   3344669999887888888877666 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.6e-06    0.0059       2     156 ..      90     245 ..      89     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.6e-06
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE----.S CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefvpf.e 75 
                                   +k+++++pr ++  sk+++ ++a+++g+p+v+K ++ g+ G+      +e+ l ++le+        ++  +v efv+  +
  gi|70606553|ref|YP_255423.1|  90 AKHNIKTPRTIVTFSKDKAVDLAKKIGFPAVIK-PIEGSWGRMVAKAVDEDILYSFLEYQeyttsqFRQIYLVQEFVKKpN 169
                                   689******************************.********999888888888888887777765556667888886424 PP

                                   EEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEE CS
                     ATP-grasp  76 kElsvlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEl 156
                                   + + + v+ ++   + +y v e   + ++    +   +++ k+  + +++a k+ + +gg   +++ +F+  +   lvnE+
  gi|70606553|ref|YP_255423.1| 170 RDIRIFVMGDEAP-VGIYRVNERNWKTNT---ALGARALPLKIDDELRDLALKVRDIMGGF-FLGIDIFEDPERGYLVNEV 245
                                   5555544444333.555555544333332...23333344455566666666666666655.5566666665555666665 PP

>> Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.027        44      31      89 ..     115     181 ..      89     199 .. 0.63
   2 ?    8.4   0.1   0.00083       1.3     142     187 ..     210     253 ..     189     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.027
                                   --SSEEEEESB-S.S..T.TTTEE.....EEE-SGGGGTT--SSEEEEE----TTEEEEEEEETTEE CS
                 Ins134_P3_kin  31 LklPliakplvad.G..takshel.....slvydqeglkklkpPlvlqefvnhggvlfkvyvvGesv 89 
                                   + +P + kp+    G   ak+ +      +l y++ + ++++   ++qefv       +++v+G++ 
  gi|70606553|ref|YP_255423.1| 115 IGFPAVIKPIEGSwGrmVAKAVDEdilysFLEYQEYTTSQFRQIYLVQEFVKKPNRDIRIFVMGDEA 181
                                   556666666543212112333221111225778899999999999*******999999999999976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00083
                                   HHHHHHHHHHHHHH---EEEEEEEE-TTT.--EEEEEEEES---TT CS
                 Ins134_P3_kin 142 elleelakalrralGlrLfnldiirdaktkdrylvidinyfPGyak 187
                                   + l++la ++r  +G  ++++di  d ++   ylv ++n  P y++
  gi|70606553|ref|YP_255423.1| 210 DELRDLALKVRDIMGGFFLGIDIFEDPER--GYLVNEVNGVPEYKN 253
                                   5689********************99998..8************86 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019       0.3      30     178 ..     110     251 ..      89     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                                   HHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHH....HHTT-SCEEEEE--..ESEEEEEEEEETSSCEEEEEEEE CS
               Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeelkeaiee....afkydekvlvEeai..egreievavlgneklevsevgei 104
                                   ++ +++g+p+++Kp +      v+k+  e+ l +++e       ++ +  lv e++    r+i + v+g+e+         
  gi|70606553|ref|YP_255423.1| 110 DLAKKIGFPAVIKPIEGSWGRMVAKAVDEDILYSFLEYqeytTSQFRQIYLVQEFVkkPNRDIRIFVMGDEA--------- 181
                                   566667777777776432233344444455555555541111234444456666664335666666666443......... PP

                                   E-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS--- CS
               Dala_Dala_lig_C 105 vvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPGf 178
                                       g+y+ ++++ ++++ l  +a l+ ++ +++++lalk+ +++++  l  +D+f + e   ++nEvN +P +
  gi|70606553|ref|YP_255423.1| 182 --PVGIYRVNERNWKTNTALGARA-LPLKIDDELRDLALKVRDIMGGFFL-GIDIFEDPERGYLVNEVNGVPEY 251
                                   ..3478999999876777766665.8999999*********999998755.5*****************99965 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.5e-05     0.073       9      45 ..      87     122 ..      84     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                   HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE CS
                   ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvK 45 
                                    +lak+++k+p++ v++s+++a + akk+g  + v+K
  gi|70606553|ref|YP_255423.1|  87 SLLAKHNIKTPRTIVTFSKDKAVDLAKKIGFPA-VIK 122
                                   589***************************998.887 PP

>> Fungal_lectin  Fungal fucose-specific lectin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.1e-05      0.11      91     148 ..     145     205 ..     133     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.1e-05
                 Fungal_lectin  91 lakkkftvapysrlaav..flagtdlklrvyaqladntiqeygvdgdgWkklanlGs.alP 148
                                   l+ +++t++ + ++  v  f++ ++  +r+++   +  +  y v++ +Wk ++ lG+ alP
  gi|70606553|ref|YP_255423.1| 145 LEYQEYTTSQFRQIYLVqeFVKKPNRDIRIFVMGDEAPVGIYRVNERNWKTNTALGArALP 205
                                   667789999999886553389999999*****999999*****************963555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1868.71
//
Query:       gi|70606554|ref|YP_255424.1|  [L=387]
Description: acetylornithine aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.4e-112  374.2   0.0   8.5e-112  373.8   0.0    1.1  1  Aminotran_3    Aminotransferase class-III
    0.00039   19.7   0.0      0.001   18.4   0.0    1.6  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
       0.15   12.6   0.0       0.43   11.1   0.0    1.8  1  PC_rep         Proteasome/cyclosome repeat


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.8   0.0  1.4e-115  8.5e-112      11     402 ..      12     373 ..       7     377 .. 0.97

  Alignments for each domain:
  == domain 1  score: 373.8 bits;  conditional E-value: 1.4e-115
                                   EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEE CS
                   Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvf 91 
                                   l i k+e  y++d +g+rylD+  +i v+ lGh++P +++ +k+q++++s++s   +++    ++ + l k+ p ++d+ +
  gi|70606554|ref|YP_255424.1|  12 LTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILS-TSFSTPIKDEMLQALDKVKPDKMDNAM 91 
                                   5799*************************************************.8899999999***************** PP

                                   EESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HH CS
                   Aminotran_3  92 lansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkene 172
                                   l nsG+eAve+AlK+ark       t ++kiiafk+afHGrt g+lsvt++ kky++ f+p++ +v +l ++         
  gi|70606554|ref|YP_255424.1|  92 LLNSGTEAVEAALKTARK------ITGRKKIIAFKNAFHGRTAGSLSVTWN-KKYREPFEPLVGPVEFLTFNN-------- 157
                                   ******************......9**************************.********************6........ PP

                                   HHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS- CS
                   Aminotran_3 173 eeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvs 253
                                            +e+l  k+++e+aAvivEpiqge Gv++a+ ef+++l+e +++ + lli+DE+qtGfGrTGkl+A++h+++ 
  gi|70606554|ref|YP_255424.1| 158 ---------IEDLS-KIDNETAAVIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIV 228
                                   .........89987.899*************************************************************** PP

                                   -SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT CS
                   Aminotran_3 254 pDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalkegLeelqkk 334
                                   pD++t +Ka++gG+p+s+v+ ++ +++ l++g+hgsT+gGnp+a+a++ a+ ++ie+e+++e+a+++g+++++ L +  ++
  gi|70606554|ref|YP_255424.1| 229 PDILTAGKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQFSNILVKNLAD 309
                                   *************************************************************************99988888 PP

                                   -TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHHHH CS
                   Aminotran_3 335 yevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidelleil 402
                                    +v++evRgkGlmi+i++  +      ++lk ++ekG+l  +aG++vir+lp++ it e+++e+ + l
  gi|70606554|ref|YP_255424.1| 310 LKVVREVRGKGLMIGIDIRFQPG----QVLKYLQEKGILAVKAGSTVIRFLPSYLITYENMEEASNVL 373
                                   89****************99988....8**********************************998876 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.7e-07     0.001      63     299 ..      83     312 ..      61     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-07
                                   CHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-.THHHHHHHHTTSEEEEEEBEET..TTTEE-HHHHHHHHT CS
                 Aminotran_1_2  63 lklkreaavvvgsGagaliealifllklnpgdeilvpdpty.asyknilrlsggevvryplyse..edfhldlealeealk 140
                                   ++ k + a ++ sG+ a+ +al+++ k+   ++i++++  + +     l     + +r p+++   +   l+++++e+ l+
  gi|70606554|ref|YP_255424.1|  83 KPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFhGRTAGSLSVTWNKKYREPFEPLvgPVEFLTFNNIED-LS 162
                                   556666777777888888888888777666666666554440333333333333355555443366556778888887.44 PP

                                   THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHT.TEEEEEEETTTTCBSSSS.HTHHHHGGSTTSTTEEEEEES CS
                 Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakky.nlllfvDeaYagfvfgsl.davatranveeepnllivgsl 219
                                   +      +t  ++ve ++  +G+++   e  k l+ ++++ + ll++De+  gf  + +  a++ + n+ +++      + 
  gi|70606554|ref|YP_255424.1| 163 KIDN---ETAAVIVEPIQGESGVIPANIEFMKALKEKTENtGSLLIFDEIQTGFGRTGKlWAYK-HYNIVPDIL-----TA 234
                                   4333...5669*************98877777777777777*************9996533333.777777665.....99 PP

                                   SSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEE CS
                 Aminotran_1_2 220 sKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkv 299
                                   +Ka G  G+ v  ++  +++++ l+    + ++  ++++ a+++a+ ++ +k++ +e++ q+ q+ +  l+++La+l  kv
  gi|70606554|ref|YP_255424.1| 235 GKAIG-GGFPVSVVFLPDHIANKLEEGDHGSTYgGNPMAMAAVTAACKVIEKENVVEQANQKGQQFSNILVKNLADL--KV 312
                                   ****9.59999*****************999999****************************************654..44 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.2e-05      0.43       5      27 ..      36      58 ..      36      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.2e-05
                                  HHHHHCTTSTCHHHHHHHHHHHH CS
                        PC_rep  5 ALGlihaGsgneeaislLkpyls 27
                                  ++G++++G++n  ++++Lk++l 
  gi|70606554|ref|YP_255424.1| 36 GIGVAFLGHRNPIILEYLKNQLE 58
                                  89*****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2365.92
//
Query:       gi|70606555|ref|YP_255425.1|  [L=346]
Description: acetyl-lysine deacetylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-26   91.6   0.0    6.4e-26   91.3   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    0.00012   22.0   0.0    0.00021   21.1   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.055   13.3   0.0       0.16   11.8   0.0    1.7  1  DUF4897        Domain of unknown function (DUF4897)


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.0   1.1e-29   6.4e-26       1     206 [.      63     340 ..      63     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 1.1e-29
                                   EEEEES-BSSTTCGGGSSSTTS.EEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwttpfs.lteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGaka 80 
                                   ll +H D+Vp     g    f  ++ee   +yGrGa+d+kg +++++ a+  l+++g    +++++ +  dEE  ++Ga++
  gi|70606555|ref|YP_255425.1|  63 LLVGHVDTVP-----G----FInPKEEGEIIYGRGAVDDKGPLISMIIAASILNKNG----YSVTVGALSDEENKSKGARE 130
                                   5789******.....3....330445555***************************9....69**********988***** PP

                                   HHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE.............................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                 Peptidase_M20  81 llegleerekvdavfelhieepgileagklaigvv.............................................. 115
                                   +l     ++k d+   ++++ep++   g      v                                              
  gi|70606555|ref|YP_255425.1| 131 ILR---IGKKYDY---IIVGEPTNTF-GV-----Vveyrgvihldilcrarsehsssatsnlifeiakkiinttrintgyd 199
                                   ***...2557777...77**999999.44.....3468889**************************************** PP

                                   ................................................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHH CS
                                   ................................................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                 Peptidase_M20 116 ................................................kvevelleggapvtln.dsplvkalaeaaeelf 147
                                                                                    +e++++e+  pv+++ +s++vk++ +++ +  
  gi|70606555|ref|YP_255425.1| 200 dvsivptifksgeylnvtpsnavvhfdirysvrnskdqimseihrefeGCEIHEVEDISPVKVDvNSDIVKVFMRSIIKE- 279
                                   ***********************************************66***********************99999887. PP

                                   TSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 148 gekvelivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgikvlarlle 206
                                   ++k++   +  g++d++++  ++++ ++ +gpg+ +l H+ +E+++l+++  ++kv+ +++e
  gi|70606555|ref|YP_255425.1| 280 NYKPTILRKR-GTSDMNILkdLALKGILAYGPGNsSLEHTDHEKISLDEIFIATKVYINAIE 340
                                   8888888888.********5544455566****66**********************99986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.6e-08   0.00021       4      99 ..     157     244 ..     154     248 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.6e-08
                                   -EEEEEEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEE CS
                     M20_dimer   4 kGlaggkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiR 83 
                                   +G++   i ++ ++ Hs+ a  +    +e++ ++++  + ++g           ++ +t++++G   nv+p+ a +++diR
  gi|70606555|ref|YP_255425.1| 157 RGVIHLDILCRARSEHSSsATSNL--IFEIAKKIINTTRINTGYDD-------VSIVPTIFKSGEYLNVTPSNAVVHFDIR 228
                                   899999999999999999544444..56678888888888877655.......**************************** PP

                                   HHHHHHHHHHHHHHHH CS
                     M20_dimer  84 llpgedpeevleeiee 99 
                                    +   + ++++ ei  
  gi|70606555|ref|YP_255425.1| 229 YSVRNSKDQIMSEIHR 244
                                   *************986 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.16      28      96 ..      10      79 ..       2      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                       DUF4897 28 fkdekkeeeyieqYqkasee.tfekylsqlseevgreikvvslessateregileveEkavlkglvkven 96
                                   k ++   e++  Y+ + ee + +++++++++e++  ++v+s +s +  + +il v  + ++ g+++ ++
  gi|70606555|ref|YP_255425.1| 10 LKIKQFLPEFLSIYTPSGEEyKAKDFFEKIASELDLSLQVTSTNSYLLGDGDILLVGHVDTVPGFINPKE 79
                                  5555666788888987777778899****************************************98774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2362.58
//
Query:       gi|70606556|ref|YP_255426.1|  [L=262]
Description: undecaprenyl pyrophosphate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-67  226.2   0.0    4.2e-67  226.0   0.0    1.0  1  Prenyltransf   Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.051   13.1   0.2      0.086   12.4   0.2    1.3  1  Fzo_mitofusin  fzo-like conserved region


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.0   0.0   4.7e-71   4.2e-67       1     224 []      38     261 ..      38     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 4.7e-71
                                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGG.GS-HHHHHHHHHHHH...HHHHHHHHH CS
                  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNf.kRskeevdalmellk...eellkeelk 77 
                                   i DGNrRwA++++ ++  +G+  G+ +l+++l+++le+g+++vtv+a+S eN+ kR+++e++++++ lk   +ell+++  
  gi|70606556|ref|YP_255426.1|  38 IPDGNRRWARNNR-LPLDQGYYTGYVKLRDVLTWILEIGISTVTVFALSAENCeKRTQQELSMIFKYLKiglDELLTSD-- 115
                                   78***********.78888*********************************98899***********98776677665.. PP

                                   HHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHH CS
                  Prenyltransf  78 ellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetle 157
                                    ++k +vrv++iG l++lped+++ + ++e++t+k nk  +l +a++Yg+r+ei++a+r+++++++    + ++ide+t++
  gi|70606556|ref|YP_255426.1| 116 LVHKYQVRVKAIGMLDKLPEDLKKLVVDLESTTEKYNK-KKLILAICYGGRQEILDAIRKIMNDYKLGIIDsKSIDESTFR 195
                                   56666*****************************8877.9**********************99976555545679***** PP

                                   CTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                  Prenyltransf 158 khlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                   k+ly  ++l d+DlliR+sGe R+SnFllw+laysel+f+dv+WPdf+k dl++a++++qkr+r+fg
  gi|70606556|ref|YP_255426.1| 196 KYLYD-QELSDIDLLIRSSGEIRISNFLLWHLAYSELFFVDVYWPDFRKIDLWRAIRSFQKRKRNFG 261
                                   ****6.667*******************************************************997 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   9.6e-06     0.086      85     141 ..      83     140 ..      78     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.6e-06
                 Fzo_mitofusin  85 sltsancshqvqqelsstfarlcqqvdet.ekeleeeikelekeiekleevqkkakll 141
                                    l ++nc++  qqels  f+ l+   de  +++l ++ +   k i +l+++ + +k+l
  gi|70606556|ref|YP_255426.1|  83 ALSAENCEKRTQQELSMIFKYLKIGLDELlTSDLVHKYQVRVKAIGMLDKLPEDLKKL 140
                                   56789*******************999852789*****************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2023.22
//
Query:       gi|70606557|ref|YP_255427.1|  [L=128]
Description: 30S ribosomal protein S8e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-34  118.0   0.3    3.6e-34  117.9   0.3    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.3     2e-38   3.6e-34       5     137 .]       4     126 ..       1     126 [. 0.95

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 2e-38
                                   XXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEES.SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEECS CS
                 Ribosomal_S8e   5 rdskhkrkltGgkakllrkkrkielgrkekatklg.aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkkn 84 
                                    +++++rk+tGg++   r krk+elg ++++tk++ +++ ++ rv gG+ k r+  +++anv++p+ k++kk+kI++V + 
  gi|70606557|ref|YP_255427.1|   4 YQGNDSRKITGGQKGKNRDKRKYELGSPPTETKISdKDIKEKDRVAGGNFKLRLRYASYANVYDPQSKTAKKVKIISVLES 84 
                                   68999*****************************9445555679************************************* PP

                                   SSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                 Ribosomal_S8e  85 psnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                   p+n+ey+r+g+++Kg+ i++++++           A+vtsrPgqdG +na lL
  gi|70606557|ref|YP_255427.1|  85 PANREYARRGIIVKGTLIQTELGK-----------AKVTSRPGQDGIINALLL 126
                                   ************************...........****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.51
# Mc/sec: 761.40
//
Query:       gi|70606558|ref|YP_255428.1|  [L=92]
Description: hypothetical protein Saci_0759 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-05   24.8   0.1    4.1e-05   24.4   0.1    1.2  1  SRP19       SRP19 protein
     0.0034   17.6   0.0     0.0049   17.1   0.0    1.2  1  XRN1_D2_D3  Exoribonuclease Xrn1 D2/D3 domain


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   4.6e-09   4.1e-05       2      92 ..      13      89 ..      12      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.6e-09
                                  EECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-..........SS-CHHHH CS
                         SRP19  2 iYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvklkedgkevnekiknkkell 84
                                  i+ +Y+    +r++GR++ k    ++  ++ ++++ ++lgl+ ++  +k +Pr+ ++ G++ v++k            k++++
  gi|70606558|ref|YP_255428.1| 13 IWLAYFI-ADSREQGRKIRKI--SRKIDINILYQVSNSLGLNPLIISDKIHPRSGIQ-GMILVDKK----------AGKHHII 81
                                  7888885.4689******875..58999999***********************875.******84..........6788888 PP

                                  HHHHHHHH CS
                         SRP19 85 kkiaellk 92
                                  k+i ++l+
  gi|70606558|ref|YP_255428.1| 82 KMIRDELE 89
                                  88877776 PP

>> XRN1_D2_D3  Exoribonuclease Xrn1 D2/D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.4e-07    0.0049      27      81 ..       4      56 ..       1      61 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-07
                                  EEESSSEEEEEEEBS-SS---SHHHHHHHHHHHHS-EE------EEHHHHHHHHH CS
                    XRN1_D2_D3 27 tghsekklsvvlaklksekepefgkkrikeaeksnrYlpsfavakklglsplvLs 81
                                   +++ekk+ ++la + + + +e g+ +i++ ++++     ++v+++lgl+pl++s
  gi|70606558|ref|YP_255428.1|  4 RDYKEKKIAIWLAYFIA-DSREQGR-KIRKISRKIDINILYQVSNSLGLNPLIIS 56
                                  6899***********99.4555555.56667778888999*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.48
# Mc/sec: 577.80
//
Query:       gi|70606559|ref|YP_255429.1|  [L=308]
Description: epimerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-43  146.6   0.1    1.1e-42  146.2   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.3e-41  141.1   0.6    4.8e-40  138.0   0.6    2.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.9e-15   54.9   0.0    8.3e-15   54.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.4e-13   49.2   0.6    4.6e-13   48.8   0.6    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.8e-10   38.4   0.1    6.2e-06   25.6   0.0    2.3  2  NAD_binding_4    Male sterility protein
    8.6e-08   31.7   1.5    2.5e-06   26.8   1.5    2.7  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0007   19.5   0.1      0.028   14.3   0.1    2.2  2  KR               KR domain
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.026   14.1   0.0    1.3  1  NmrA             NmrA-like family
      0.057   13.3   0.0       0.28   11.1   0.0    1.9  1  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.2   0.1   5.4e-46   1.1e-42       2     241 .]       3     229 ..       2     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 5.4e-46
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHH CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaasse 82 
                                   ++tG++G+iG +lv+ l +++ e+i++d+ ++++  ++++     +ldl+ ++ l   +   +  + +hlAa  +v++s++
  gi|70606559|ref|YP_255429.1|   3 VITGGAGYIGGHLVDTLVNQNKEIIVIDNFTNGKYINNKA--LYLNLDLRGNNILGLKVP--KESILYHLAANPDVRDSMT 79 
                                   79****************************8888877766..677888887776554444..5689*************** PP

                                   SHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS..BSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT CS
                     Epimerase  83 dpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp..keettltgplkpnspYaaaKlageklveayaaqyg 161
                                   +  d +e +++ tln+le+ark++v  ++f+sSs+vYG++ ++p  +ee+t     +p s Y++ Kl+ge+lv +y + yg
  gi|70606559|ref|YP_255429.1|  80 NTIDHFEMDVKATLNILEVARKNDVCLFIFASSSTVYGEPSKIPtpEEEQT-----NPISNYGIFKLLGEQLVNYYSRVYG 155
                                   ******************************************874477777.....9************************ PP

                                   -EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
                     Epimerase 162 lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                                   ++ ii+rl n++G r      ++vi  +i+k+ +  + + +lg+g+++  ++y+ Dv++++  v+e+ ++ d+  +yn+G
  gi|70606559|ref|YP_255429.1| 156 IKSIIVRLANVIGGR----VTHGVIKDFINKLRSDPNRLQILGNGKQRKSYIYITDVIDGFQ-VIEK-SSIDQVSVYNLG 229
                                   ***************....8999***********999***********************98.6666.577888899987 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.0   0.6   2.4e-43   4.8e-40       2     330 ..       4     294 ..       3     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 2.4e-43
                                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                 GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynL 82 
                                   iTG+aG+iG +l++ L++++ e+++i++ ++  ++++  +l+              + Dl+ ++ l   + +      y+L
  gi|70606559|ref|YP_255429.1|   4 ITGGAGYIGGHLVDTLVNQNKEIIVIDNFTNGKYINNK-ALY-------------LNLDLRGNNILGLKVPKE--SILYHL 68 
                                   9*************************999888775554.344.............568999877776666665..457*** PP

                                   -S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHH CS
                 GDP_Man_Dehyd  83 AAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwi 163
                                   AA   V+ s+++    +e++v +tl++Le++r+      + f++aS+s+vYG+++++p  E+ +++P s Y++ Kl  +++
  gi|70606559|ref|YP_255429.1|  69 AANPDVRDSMTNTIDHFEMDVKATLNILEVARKND---VCLFIFASSSTVYGEPSKIPTPEEEQTNPISNYGIFKLLGEQL 146
                                   ********************************975...59***************************************** PP

                                   HHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC..SS- CS
                 GDP_Man_Dehyd 164 vvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq..dkp 242
                                   v  y + yg+  ++ +l n  + r    +    i +++ +   + +   +lGn+++++++ ++ D++++++ + ++  d+ 
  gi|70606559|ref|YP_255429.1| 147 VNYYSRVYGIKSIIVRLANVIGGR----VTHGVIKDFINKLRSDPNRLQILGNGKQRKSYIYITDVIDGFQVIEKSsiDQV 223
                                   ************************....45567999999999999999999*******************97655444555 PP

                                   --EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS CS
                 GDP_Man_Dehyd 243 edyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkv 323
                                   + y++++ +  sv+e++++  +el+ t                  +++v     +  pg+++ +l d++k+k +LgWkpk+
  gi|70606559|ref|YP_255429.1| 224 SVYNLGNEDWISVDEIARIVEEELKLTP----------------AHEYVDAGGGRGWPGDARYMLLDITKLK-KLGWKPKY 287
                                   5566666666666666666555555443................3456777778888**************9.9******* PP

                                   -HHHHHH CS
                 GDP_Man_Dehyd 324 sfeelvr 330
                                   s +e vr
  gi|70606559|ref|YP_255429.1| 288 SSREAVR 294
                                   *999887 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   4.2e-18   8.3e-15       4     284 ..       3     299 ..       1     302 [. 0.84

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4.2e-18
                                   EEESTTSHHHHHHHHHCTTTSEEEEEE-TT.............T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSH CS
                 RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeglevlaltre.............eldltdaeavaellkeakpdvvvnaAAytavDkaEsee 71 
                                   ++tG+ G +G +L++ l +++ e++ +++              +ldl+ ++ +   +   k ++++++AA  +v    ++ 
  gi|70606559|ref|YP_255429.1|   3 VITGGAGYIGGHLVDTLVNQNKEIIVIDNFtngkyinnkalylNLDLRGNNILGLKVP--KESILYHLAANPDVRDSMTNT 81 
                                   79************************97667899999999977777777777765555..5789***************** PP

                                   HHHHHHHTHHHHHHHHHHHHCT-EE.EEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEE CS
                 RmlD_sub_bind  72 eaayavnaeavealAeaaaavgalL.ihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkkalivR 147
                                      ++++++a+ ++ e+a++ ++ L i+ S+  V+    k p  e+++t+P++ YG  Kl+GEq v+     +g k +ivR
  gi|70606559|ref|YP_255429.1|  82 IDHFEMDVKATLNILEVARKNDVCLfIFASSSTVYGEPSKIPTPEEEQTNPISNYGIFKLLGEQLVNYysrvYGIKSIIVR 162
                                   **********************97549********999****************************98555567799**** PP

                                   E-SEE.SSSSS-HHHHHHHHH.HH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHH CS
                 RmlD_sub_bind 148 tswvy.gekgknfvktmlrla.kereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefA 224
                                    + v  g+  +  +k +++++ ++ ++l++     q  s  +  d+ +    ++ek+    ++ +vy l+ne+ +s  e+A
  gi|70606559|ref|YP_255429.1| 163 LANVIgGRVTHGVIKDFINKLrSDPNRLQILGNgkQRKSYIYITDVIDGFQ-VIEKSSI--DQVSVYNLGNEDWISVDEIA 240
                                   *****4557889999888777588899**9965227777778888888765.5555544..4689**************** PP

                                   HHHHHHHCHTT..SEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHH CS
                 RmlD_sub_bind 225 railkeagads..eevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlke 284
                                   r + +e++ ++  e v +      p  A   ++  Ld +kl++ +  +  + rea++ ++++
  gi|70606559|ref|YP_255429.1| 241 RIVEEELKLTPahEYVDAGGGRGWPGDA---RYMLLDITKLKKLGWKPKYSSREAVRLAVRD 299
                                   ********99876777777777777777...4888888888888888888888888877765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.6   2.3e-16   4.6e-13       1     220 [.       3     207 ..       3     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.3e-16
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegvdvvihlaslvdva 80 
                                   v+tGgaG++G +lv +Lv+ +  ke+ v+D  ++ +       +n+k  +++ D++ ++ l   + + +++ hla+  dv+
  gi|70606559|ref|YP_255429.1|   3 VITGGAGYIGGHLVDTLVNQN--KEIIVIDNFTNGKY------INNKAlYLNLDLRGNNILGLKVPKESILYHLAANPDVR 75 
                                   79*****************99..6******8877776......4444459******************************* PP

                     3Beta_HSD  81 g.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlka 160
                                     ++++    +  vk T n+le ++k++v  +++ Ss  v g+     +i   +Ee+   +++ + y  +K l E+lv   
  gi|70606559|ref|YP_255429.1|  76 DsMTNTIDHFEMDVKATLNILEVARKNDVCLFIFASSSTVYGE---PSKIPTPEEEQ---TNPISNYGIFKLLGEQLVNYY 150
                                   9445555577999*****************************9...66677555554...456788999999999999654 PP

                     3Beta_HSD 161 NgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgN 220
                                       +     +  + +R a + G + +  +++ ++++l    + l  +g+ ++ ++++Y   
  gi|70606559|ref|YP_255429.1| 151 SR--VY---GIKSIIVRLANVIGGRVThgVIKDFINKLRSDPNRLQILGNGKQRKSYIYITD 207
                                   33..22...24555566666666543311455566666666666666666666666666655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   9.9e-05       0.2       1      26 [.       4      27 ..       4      37 .. 0.89
   2 !   25.6   0.0   3.1e-09   6.2e-06      90     209 ..      64     188 ..      46     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.9e-05
                                  EE-TTSHHHHHHHHHHHHHS-.TEEE CS
                 NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiy 26
                                  +TG+ G++G +L+  L+++++e+  +
  gi|70606559|ref|YP_255429.1|  4 ITGGAGYIGGHLVDTLVNQNKEI--I 27
                                  8******************9964..4 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3.1e-09
                                   EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEE CS
                 NAD_binding_4  90 viihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldedera 167
                                   + +h aA+ ++ +++ +    +++ v++t ++le a+k     ++++ S+++v+ge + ++               + e++
  gi|70606559|ref|YP_255429.1|  64 ILYHLAANPDVRDSMTNtidHFEMDVKATLNILEVARKNDVC-LFIFASSSTVYGEPS-KI--------------PTPEEE 128
                                   7899999999998777633367899************99888.***************.44..............444444 PP

                                   ETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-...................- CS
                 NAD_binding_4 168 klkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg...................e 209
                                   +  +    Y   K l+E+lv+ ++r  g++ +ivR+ +++g                   +
  gi|70606559|ref|YP_255429.1| 129 QT-NPISNYGIFKLLGEQLVNYYSRVYGIKSIIVRLANVIGgrvthgvikdfinklrsdpN 188
                                   44.45557********************************976555555555555555550 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   1.5   1.3e-09   2.5e-06       2     187 ..       3     184 ..       2     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEE CS
               Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvf 82 
                                   ++tG++G iG +lv+++++++ k+ii++++  +  y  +k l          ++      d+r ++ l   +   k  +++
  gi|70606559|ref|YP_255429.1|   3 VITGGAGYIGGHLVDTLVNQN-KEIIVIDNFTNGKYINNKAL---------YLN-----LDLRGNNILGLKVP--KESILY 66 
                                   69*************998865.78999998776666444444.........233.....58899999988888..899*** PP

                                   E------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE..............GGGSS--SHHHHHHHHHHHHH CS
               Polysacc_synt_2  83 haAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt..............DKAvnPtnvmGatKrlaekll 149
                                   h AA   V    +n+++ ++  v +t n++e+a +++v  +++ S+                  nP++ +G+ K+l e+l+
  gi|70606559|ref|YP_255429.1|  67 HLAANPDVRDSMTNTIDHFEMDVKATLNILEVARKNDVCLFIFASSstvygepskiptpeEEQTNPISNYGIFKLLGEQLV 147
                                   *******************************************9973333333222222234589**************** PP

                                   HHGGG--SSS--EEEEEEE-EETTGT..TSSHHHHHHHHH CS
               Polysacc_synt_2 150 qalakeseekktkfvvvRfGNVlgSr..GSviplFkkqik 187
                                     +++       k ++vR  NV+g r    vi  F ++++
  gi|70606559|ref|YP_255429.1| 148 NYYSRVY---GIKSIIVRLANVIGGRvtHGVIKDFINKLR 184
                                   **99999...8999**********8722347777777665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.4e-05     0.028       2      30 ..       1      29 [.       1      56 [. 0.88
   2 ?    3.1   0.0      0.04        80     111     144 ..      87     119 ..      71     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                                  EEEEETTTSHHHHHHHHHHHHHHS-EEEE CS
                            KR  2 tylitGGlGgLGlelarwlaekgarhlvl 30
                                  +y+itGG+G +G +l+++l+++ ++ +v+
  gi|70606559|ref|YP_255429.1|  1 MYVITGGAGYIGGHLVDTLVNQNKEIIVI 29
                                  59*******************99888776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.04
                                   TTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                            KR 111 pKvkGawnLhelledesldffvlfSSiagllgsa 144
                                     vk++ n+ e+ +++++ +f++ SS ++++g++
  gi|70606559|ref|YP_255429.1|  87 MDVKATLNILEVARKNDVCLFIFASS-STVYGEP 119
                                   56999*********999999987766.5666665 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.026       2     101 ..       3     111 ..       2     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S.......-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG CS
                          NmrA   2 lviGaTGrqGksvvrallkaghkvralvRdt.......kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy 75 
                                   +++G++G++G+++v+ l++++ ++ ++           ++ l  +l  +G++++  ++  +++l ++  + dv  s+t++ 
  gi|70606559|ref|YP_255429.1|   3 VITGGAGYIGGHLVDTLVNQNKEIIVIDN-FtngkyinNKALYLNLDLRGNNILGLKVPKESILYHLAANPDVRDSMTNTI 82 
                                   589****************9999866544.35999999999999***********************************88 PP

                                   ...S-HHHHHHHHHHHHHHHS-SEEEEEE CS
                          NmrA  76 ...skeiedgkklvdAakeaGvkhfiySs 101
                                      ++ ++   ++ ++a +  v  fi++s
  gi|70606559|ref|YP_255429.1|  83 dhfEMDVKATLNILEVARKNDVCLFIFAS 111
                                   999***********************987 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.28       1     143 [.       6     163 ..       6     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHH.. CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk..deeg.. 77 
                                   G+ G +G +lv+ l++++  e  +++ n    + +  ++++  + +d+   + l   +   ++ +  +++ +      +  
  gi|70606559|ref|YP_255429.1|   6 GGAGYIGGHLVDTLVNQN-KE-IIVIDNFTNGKYI--NNKALYLNLDLRGNNILGLKVPKESILYHLAANPDVrdS--Mtn 80 
                                   899999999999999995.56.5778888888866..467788899998888888888888877777766665440..234 PP

                                   ...........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHH...HCCHHHHHHHHHHHHHHHH....SSSEEEE CS
                NAD_binding_10  78 ...........aknivdaakeagvkRfvlvsaigvgdevpgefgewnk...ellkaylaakraaeellra....sgldwTi 140
                                              + ni+++a++++v  f++ s+  v+ e p++ ++  +   + +++y + k   e+l++      g++  i
  gi|70606559|ref|YP_255429.1|  81 tidhfemdvkaTLNILEVARKNDVCLFIFASSSTVYGE-PSKIPTPEEeqtNPISNYGIFKLLGEQLVNYysrvYGIKSII 160
                                   44556666666************************975.444443333111456777666777666664432224566666 PP

                                   EEE CS
                NAD_binding_10 141 vrp 143
                                   vr 
  gi|70606559|ref|YP_255429.1| 161 VRL 163
                                   665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1929.82
//
Query:       gi|70606560|ref|YP_255430.1|  [L=540]
Description: thiamine pyrophosphate-requiring enzyme [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-40  137.6   0.1    5.7e-40  136.2   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    7.9e-25   87.4   0.0    1.3e-24   86.7   0.0    1.3  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      0.003   16.5   0.0     0.0052   15.8   0.0    1.3  1  PNTB          NAD(P) transhydrogenase beta subunit
  ------ inclusion threshold ------
      0.045   13.8   0.1        2.5    8.2   0.1    2.7  2  Imm30         Immunity protein 30


Domain annotation for each model (and alignments):
>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.0   1.3e-43   5.7e-40       1     137 []     203     338 ..     203     338 .. 0.95
   2 ?   -3.1   0.0       1.3   5.9e+03     103     114 ..     519     533 ..     499     534 .. 0.60

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 1.3e-43
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEE.ESGGGSCHHHHHHHHH-SE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylg.mlglhgskaanealeeaDl 80 
                                   ++k+aell+++k+pvil+G gv  sga++el elae l+iPv+ t+++kg+ip++hpl++g  lgl+++++++ ++ee+Dl
  gi|70606560|ref|YP_255430.1| 203 VAKVAELLNNSKNPVILAGYGVLASGAHKELLELAELLDIPVILTFRAKGSIPSSHPLFAGeGLGLFATEEGRHIIEESDL 283
                                   689****************************************************************************** PP

                                   EEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                  TPP_enzyme_M  81 vlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                   ++alG++f++ +t+g + +++  + ++++++d ++i+k+y +++++v+dv+ +l++L
  gi|70606560|ref|YP_255430.1| 284 IIALGTKFNQLSTAGWSMKIK--GYLVNVNVDGEDISKVYMPHVPVVADVGLFLREL 338
                                   **********77776444664..36*****************************997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                                   T..-.EEEEEESSCC CS
                  TPP_enzyme_M 103 e..a.kiihididpa 114
                                   +  + k+i++ idp+
  gi|70606560|ref|YP_255430.1| 519 NtgNlKVINVKIDPN 533
                                   232568999999985 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0     3e-28   1.3e-24       1     166 [.      15     181 ..      15     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 3e-28
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m++ ea++ +Lk+ g+++vf  +++ +l lld l + + i+  l+ + + a++ Ad y+r  + +g v+   g+ ++ a+ 
  gi|70606560|ref|YP_255430.1|  15 MKGEEAIAYTLKDIGIKEVFLTYDTPSL-LLDQLIKYE-IKPNLCNSTREAVILADSYSRENNTVGTVIQIPGVKLLEATD 93 
                                   7999********************9965.89******5.****************************************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHH...S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEE CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg...qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylel 159
                                    + +A+vd+ Pll++s  r+++++g    g l    d +++f+p+tk aerv + eel  ++++ +++als+r++P+y+e+
  gi|70606560|ref|YP_255430.1|  94 IISQAYVDSQPLLIISSLRSYRDTGksrVGELRTPDDLMEIFKPITKMAERVLNIEELIFTIEKGYKEALSNRNRPAYVEV 174
                                   *************************77666666555********************************************* PP

                                   EHHHCC- CS
                  TPP_enzyme_N 160 pkdvlle 166
                                   p+d+++ 
  gi|70606560|ref|YP_255430.1| 175 PEDLFKL 181
                                   ****986 PP

>> PNTB  NAD(P) transhydrogenase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.2e-06    0.0052     283     332 ..     191     240 ..     179     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.2e-06
                                   ....X--S-EESHHHHHHHHHC-SEEEEEE-HHHHHCTTHHHHHHHHHHH CS
                          PNTB 283 eekeekevkeisaedvaellkeakkviivPGYGlavaqAqhavaelaklL 332
                                   ++ e+k   + ++++vaell+++k+ +i  GYG+  + A +++ ela+lL
  gi|70606560|ref|YP_255430.1| 191 QKPEKKAPDKNTVAKVAELLNNSKNPVILAGYGVLASGAHKELLELAELL 240
                                   33444566788999*********************************998 PP

>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.035   1.6e+02      18      73 ..     346     401 ..     336     414 .. 0.83
   2 ?    8.2   0.1   0.00056       2.5      10      44 ..     489     523 ..     483     528 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.035
                         Imm30  18 lekllkeqnkdnledlckafdDdtedeevmFglvHlledleveeylkklvealpkl 73 
                                   +++ +k+ ++++++++ ka+   t+ e   + +v +le+++  + +  + +++ +l
  gi|70606560|ref|YP_255430.1| 346 IKEPIKRGTAEKIKKFKKAISLPTHSEIWPYDVVMALENYNFSKIFVDISSTTLDL 401
                                   56667788999*********9999999899***********999998887776666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00056
                         Imm30  10 evelFesalekllkeqnkdnledlckafdDdtede 44 
                                    +e F++ l ++ +  n  n+e+l ka++++t + 
  gi|70606560|ref|YP_255430.1| 489 QIERFDEVLTRMFNAVNVSNIEELKKAINENTGNL 523
                                   5899**************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3676.30
//
Query:       gi|70606561|ref|YP_255431.1|  [L=186]
Description: hypothetical protein Saci_0765 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-55  186.7   4.5    3.3e-55  186.5   4.5    1.0  1  DUF2204   Nucleotidyl transferase of unknown function (DUF220


Domain annotation for each model (and alignments):
>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.5   4.5   1.8e-59   3.3e-55       2     181 .]       4     181 ..       3     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.5 bits;  conditional E-value: 1.8e-59
                       DUF2204   2 lealaevlkvLeekgvkfvviGgtvvelalgrkrlekDvDlFiteksqlleedfyreiaeeedwdvgstelgtvkliakve 82 
                                   + ++ e+l++++e   +fv+iG+tvv+++lg+k +e+DvDlF++  s++++ed  r+ a e++wd+g+t ++t++li+ + 
  gi|70606561|ref|YP_255431.1|   4 FSKVGEILSEIRELT-DFVIIGDTVVDISLGKKGIESDVDLFVLSISTVIDEDKIRDFAFERGWDFGKTPIDTPRLIVGLD 83 
                                   567889999999988.9**************************************************************** PP

                       DUF2204  83 keevevdlleNildlyvpeeiLerakeveiggvevkvislEdyivlKaraareeaeeeldeiarlikelklkldvrlvkeh 163
                                    e ++vd++eNi+d++vpe+i+++ake++ig+  +k+i lEdy++lKa+a+ree+e+el+ i  +i e+kl+++++ +++h
  gi|70606561|ref|YP_255431.1|  84 AESLQVDMYENIQDFFVPEQIINSAKEIKIGKEYFKIITLEDYLLLKANAFREEDEDELRGIVSMIGEGKLSINKEYIRKH 164
                                   ********************************************************************************* PP

                       DUF2204 164 veafpeeeaelilkrLre 181
                                   + +f+e ++++i +rLr+
  gi|70606561|ref|YP_255431.1| 165 IDLFEE-NSKSIAERLRS 181
                                   ******.9********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1273.53
//
Query:       gi|70606562|ref|YP_255432.1|  [L=56]
Description: 50S ribosomal protein L40e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-09   35.0   4.6    1.1e-08   34.8   4.6    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0011   18.7   0.4     0.0016   18.3   0.4    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0044   17.0   0.3     0.0047   16.9   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.012   15.3   0.8      0.019   14.7   0.8    1.3  1  zinc_ribbon_2   zinc-ribbon domain
      0.065   12.6   2.3      0.091   12.1   2.3    1.2  1  zf-RanBP        Zn-finger in Ran binding protein and others
      0.068   12.6   1.0      0.098   12.1   1.0    1.3  1  zf-ribbon_3     zinc-ribbon domain
       0.18   12.0   2.5        1.1    9.4   2.7    1.9  2  Zn-ribbon_8     Zinc ribbon domain
       0.24   11.2   3.3       0.98    9.2   3.3    1.8  1  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   4.6   4.9e-12   1.1e-08       6      49 ..       9      49 ..       4      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.9e-12
                Ribosomal_L40e  6 rqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                   q+ q+  + K+iCr C A  ++rAt+Cr  +C hs+nlr KKk
  gi|70606562|ref|YP_255432.1|  9 LQIVQQRVFLKKICRDCGALNSIRATKCR--RC-HSSNLRAKKK 49
                                  5778888899*******************..88.*********9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4     7e-07    0.0016       9      36 ..      17      44 ..      10      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7e-07
                       DUF35_N  9 LvgqrCpdCGtvqfPPravCphCgsddl 36
                                  ++   C+dCG++   +   C++C+s++l
  gi|70606562|ref|YP_255432.1| 17 FLKKICRDCGALNSIRATKCRRCHSSNL 44
                                  55566********7777*********98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   2.1e-06    0.0047      64     100 ..      13      47 ..       2      53 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                                   EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                          HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadveiv 100
                                    ++v +k  Cr+Cg+  +++  a++C +C+s++++ +
  gi|70606562|ref|YP_255432.1|  13 QQRVFLKKICRDCGALNSIR--ATKCRRCHSSNLRAK 47 
                                   344556778*****887776..569******999875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.8   8.3e-06     0.019       2      20 ..      22      40 ..      21      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.3e-06
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                                  C  CGa ++ +a+ C +C 
  gi|70606562|ref|YP_255432.1| 22 CRDCGALNSIRATKCRRCH 40
                                  ******************6 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.3   4.1e-05     0.091       7      27 ..      22      42 ..      21      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                                  -SSS--EEESSSSB-TTT--B CS
                      zf-RanBP  7 CskClvqNfawstkCvaCqap 27
                                  C  C++ N+  +tkC +C ++
  gi|70606562|ref|YP_255432.1| 22 CRDCGALNSIRATKCRRCHSS 42
                                  999***************886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   4.4e-05     0.098       3      22 ..      20      39 ..      18      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                   zf-ribbon_3  3 vrCPnCGa.plssddnvCpyC 22
                                  + C  CGa + s ++++C  C
  gi|70606562|ref|YP_255432.1| 20 KICRDCGAlN-SIRATKCRRC 39
                                  67888***99.*******999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0067        15      26      36 ..      18      30 ..       8      33 .. 0.70
   2 ?    9.4   2.7   0.00049       1.1       8      37 ..      22      45 ..      21      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0067
                   Zn-ribbon_8 26 lta.CPeCgs.ev 36
                                  l++ C +Cg+ + 
  gi|70606562|ref|YP_255432.1| 18 LKKiCRDCGAlNS 30
                                  5566999998665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                   Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.evr 37
                                  C++Cg    +l si     t+C +C+s ++r
  gi|70606562|ref|YP_255432.1| 22 CRDCG----ALNSIR---ATKCRRCHSsNLR 45
                                  99***....666666...788******8887 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.3   0.00044      0.98       2      24 ..      21      43 ..      21      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00044
                  Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgsWn 24
                                  +C++CG+  +    +C+ C+s n
  gi|70606562|ref|YP_255432.1| 21 ICRDCGALNSIRATKCRRCHSSN 43
                                  5*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 354.77
//
Query:       gi|162139949|ref|YP_255433.2|  [L=168]
Description: transcription elongation factor NusA-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   18.4   0.1     0.0035   17.4   0.1    1.5  1  KH_5      NusA-like KH domain
  ------ inclusion threshold ------
      0.061   13.7   0.0       0.58   10.5   0.0    2.1  2  ECSIT_C   C-terminal domain of the ECSIT protein


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.9e-07    0.0035      30      68 ..      84     121 ..      81     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-07
                           KH_5  30 ikavsseLkgekidvvewseDlaefianalsPaevlsVk 68 
                                     ka+ +++ g ++++ e+s+ +++ + ++l+Pa+vl V+
  gi|162139949|ref|YP_255433.2|  84 AKALQEKI-GLRVRILEKSNSIKSTAVQLLTPARVLGVN 121
                                    57889999.*****************************8 PP

>> ECSIT_C  C-terminal domain of the ECSIT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.043   3.9e+02      98     114 ..      67      83 ..       6     104 .. 0.72
   2 ?   10.5   0.0   6.5e-05      0.58      16      61 ..     114     161 ..     106     168 .] 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.043
                        ECSIT_C  98 catgtsskdsllsWirl 114
                                     ++ ++s+ s ++Wi++
  gi|162139949|ref|YP_255433.2|  67 LIVTSGSQMSYQKWIKV 83 
                                    45667889999999975 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.5e-05
                        ECSIT_C  16 pvfveGpfkvwLrdkcvkYfvLradpk..ltppeeeededdvsnlrll 61 
                                    p  v G ++vwL d +v+Y+v  ++++    p++e++ e+ +s+++++
  gi|162139949|ref|YP_255433.2| 114 PARVLGVNTVWLPDGTVQYVVRISKQEkrFLPADETSLEEALSKIHST 161
                                    677899**************9888766445566666777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1109.25
//
Query:       gi|70606564|ref|YP_255434.1|  [L=428]
Description: aspartyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-92  307.4   0.0    1.2e-91  307.1   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
      6e-15   55.0   0.2    1.5e-14   53.7   0.2    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
        0.3   11.1   1.3       0.95    9.4   0.6    2.2  2  PUB              PUB domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1   0.0   1.9e-95   1.2e-91       3     313 ..     114     422 ..     112     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 1.9e-95
                                   CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                   tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqsp 79 
                                   ++rlk+r+ldlr+++++++l++++  +k++r+ l ++gf+e+ tP ++ s+te+ga+lF v        +f    +L+qsp
  gi|70606564|ref|YP_255434.1| 114 DTRLKERVLDLRRQEMQSILKIQNITLKSFRETLYKEGFVEVFTPKIIASATEGGAQLFSV-------IYFgetaFLAQSP 187
                                   89***********************************************************.......34445558***** PP

                                   HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrn 160
                                   qly+ell+   +++vf+ia+a+RaEds+t  hlaEF+++++em+f ++ed m++le+li ++v+ v +++a+d  +  ++n
  gi|70606564|ref|YP_255434.1| 188 QLYKELLAGV-VEKVFEIAPAWRAEDSDTPYHLAEFISMDVEMAFGNYEDAMKLLEKLIYNIVNSV-KNEASDELKILSHN 266
                                   *******999.*******************************************************.66667777777777 PP

                                   SEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 161 skdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDlli 235
                                     d+k p+krltyk+aie+l+++      g+d+ +++ r+l+++ k + +f+td+P   +pFy++++++d++++es+Dl++
  gi|70606564|ref|YP_255434.1| 267 LPDVKIPIKRLTYKDAIEILQSKgynikfGDDIGTPESRVLYNELKEDLYFITDWPTLSRPFYTKSKDTDPNVSESFDLIY 347
                                   88*******************999999999*************************************************** PP

                                   TTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 236 ngvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                   + +E+++Gs+R +++e+le++l++ gl+   +e+f+++l+ ++yG+pph G+g+G+ Rl+++l+g ++++++++FP+ 
  gi|70606564|ref|YP_255434.1| 348 RWLEIASGSTRNHKREVLEDSLRKRGLK---PENFEFFLRWFDYGMPPHTGFGMGFARLLVMLTGIHNVKEIVPFPRD 422
                                   ****************************...*********************************************96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.2   2.5e-18   1.5e-14       1      76 []      18      94 ..      18      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.5e-18
                                  EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEEE CS
               tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiell 76
                                  Vt+aG+v++i  r+ g+  f+ lrD+tg+ q+v+++ +  ++  +++  ++v+ v+G vk++   p+g +e++++e+++l
  gi|70606564|ref|YP_255434.1| 18 VTLAGWVHNI--RDLGGKKFLLLRDKTGIGQIVVDKsSPSFQEISDISQESVIMVKGVVKADnraPNG-VEVHAKEVKIL 94
                                  89********..**************************************************999999.********987 PP

>> PUB  PUB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.69   4.2e+03      44      58 ..     140     154 ..     134     176 .. 0.75
   2 ?    9.4   0.6   0.00016      0.95       4      59 ..     234     294 ..     232     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.69
                           PUB  44 legavelLealGFee 58 
                                   l+  +e L++ GF+e
  gi|70606564|ref|YP_255434.1| 140 LKSFRETLYKEGFVE 154
                                   566788888888886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00016
                           PUB   4 lkealktLrkylnNilehpteekyrrI.....rleNkafkekvlplegavelLealGFeek 59 
                                   +++a+k+L+k++ Ni+++ ++e    +     +l + ++  k l++++a+e+L++ G+++k
  gi|70606564|ref|YP_255434.1| 234 YEDAMKLLEKLIYNIVNSVKNEASDELkilshNLPDVKIPIKRLTYKDAIEILQSKGYNIK 294
                                   6789*************99999888885555555566666677789999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2767.94
//
Query:       gi|70606565|ref|YP_255435.1|  [L=373]
Description: hypothetical protein Saci_0769 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-60  205.0   0.3    5.4e-51  173.7   0.0    2.0  2  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7   0.0     3e-55   5.4e-51      20     282 ..      29     278 ..      10     290 .. 0.90
   2 !   29.6   0.0   1.7e-11   3.1e-07     348     416 .]     301     364 ..     292     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 3e-55
                          TruD  20 espeDFiV.eEieef.sge.eeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvep 97 
                                   ++pe F V eEi+e+ ++e + +++g y  + ++k+++d+ ++++ l + +   ++++++ G+KD++A+T+Q+i ++++ p
  gi|70606565|ref|YP_255435.1|  29 NRPEGFKViEEISETpVDEwKGESNGTYSAYLLTKKGIDHFSVISILKKLM---KRKIHYLGIKDANAITQQIIYVNGIPP 106
                                   689***9999**99997787999*********************9998765...689**********************99 PP

                          TruD  98 eelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGsrrpvthl 178
                                     + + + ++ e+e vg+ +r+l+   ++GN+Fei ++  ++e+e++kr+++il +    + +  y G+QRFG+rrpvth+
  gi|70606565|ref|YP_255435.1| 107 --ITSYKSEKFEIEFVGHFSRQLN---HTGNRFEIELNT-TNENELQKRLHKILTT----KFLFAYIGYQRFGTRRPVTHI 177
                                   ..668899***************6...79**********.5677767777766655....44567**************** PP

                          TruD 179 vGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdykkAlealpknL 259
                                   vGk+++ +d+ +Av+ +vg+pf++e+e+   ar+a+ e++d+e++ +++p++++ E ++lk+L++ ++d   A++++ ++ 
  gi|70606565|ref|YP_255435.1| 178 VGKYLLLKDWCQAVDWIVGHPFSTENENLIYARRAY-EQKDFETSSQLFPRKFKDEINILKSLMN-GDDCLTAIKKIVTP- 255
                                   ************************************.9***************************.**********9987. PP

                          TruD 260 qrlFvhAyqSylFNrvlseRler 282
                                   + +F++AyqS+l+N++ls+  +r
  gi|70606565|ref|YP_255435.1| 256 HTFFIEAYQSFLYNKYLSKIADR 278
                                   78****************86654 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.7e-11
                          TruD 348 eierevleeegleledFklpklpelsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                                   +  +e+++ee++e  +F++++  +++ +   R+ +++++++++++     +++FsL++G YAT+vlrEi
  gi|70606565|ref|YP_255435.1| 301 DNLKEIIREENIENRSFNIKE-LRVRLRDFSRSPFMKLRNIKIKQ----NKISFSLDRGMYATIVLREI 364
                                   56799**************99.899999999******99988555....689****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2476.95
//
Query:       gi|70606566|ref|YP_255436.1|  [L=118]
Description: peptidyl-tRNA hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-43  145.7   0.1    7.5e-43  145.5   0.1    1.0  1  PTH2          Peptidyl-tRNA hydrolase PTH2
     0.0048   16.9   0.3      0.019   14.9   0.0    1.8  2  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.075   12.1   0.1      0.092   11.8   0.1    1.1  1  FA_synthesis  Fatty acid synthesis protein


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.1   1.3e-46   7.5e-43       3     117 .]       1     118 []       1     118 [] 0.96

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.3e-46
                                   EEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CH...HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEE CS
                          PTH2   3 mvlvvrkDLkmskGkiaaqcahAavalvkkllkesne...kellkeWeeegqkkivlkveseeeLlelaakakalglpaal 80 
                                   m+++vr+DL m+kGkiaaq+ahAav+lv ++ +++++   ke+l+ W+++gq kivlkv++ +eLle ++ka + glpa++
  gi|70606566|ref|YP_255436.1|   1 MAVLVRTDLDMGKGKIAAQVAHAAVSLVLEIVQKRSKaewKEWLEMWINQGQPKIVLKVKNLDELLEKYNKALQSGLPATI 81 
                                   7899**************************999873356789*************************************** PP

                                   EEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                          PTH2  81 irDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                   i+Dag+tqiepgt T+ +igP+p++++d++tg+Lkll
  gi|70606566|ref|YP_255436.1|  82 IQDAGKTQIEPGTITCAGIGPGPEEMIDNITGDLKLL 118
                                   ***********************************97 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-06     0.019     133     201 ..      12      89 ..       1      96 [. 0.73
   2 ?    0.6   0.1     0.077   4.6e+02       2      13 ..      95     106 ..      94     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
                  TP_methylase 133 teggevlsvl...........lpglakeeereleallangdtlvllkaprklaelaelLkealyddttpvavveragted 201
                                   ++g+ + +v            ++++++e ++ le ++++g++ ++l  +++l+el+e   +al+  + p++++++ag+++
  gi|70606566|ref|YP_255436.1|  12 GKGKIAAQVAhaavslvleivQKRSKAEWKEWLEMWINQGQPKIVL-KVKNLDELLEKYNKALQSGL-PATIIQDAGKTQ 89 
                                   555555555555555666777777777778888888888*******.5556***********88756.*********964 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.077
                  TP_methylase   2 lylVGvGpGdpe 13 
                                   ++++G+GpG  e
  gi|70606566|ref|YP_255436.1|  95 ITCAGIGPGPEE 106
                                   899*****9665 PP

>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.5e-05     0.092     230     301 ..      14      89 ..       9      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHTTT----------HHCHHHH..HHHH-..GGGC--EEEETBSS-EEE--TT-- CS
                  FA_synthesis 230 gNvilktaegvakavksllkeelkkslasklgalllskalkrl..kkkld..ykeyggavllGlkgvvikshgkan 301
                                   g ++ + a ++++ v+++++++ k++++ +l+  + +++ k +  +k+ld   ++y++a+ +Gl +++i + gk +
  gi|70606566|ref|YP_255436.1|  14 GKIAAQVAHAAVSLVLEIVQKRSKAEWKEWLEMWINQGQPKIVlkVKNLDelLEKYNKALQSGLPATIIQDAGKTQ 89 
                                   56677889999************************66555544113344433579****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 783.77
//
Query:       gi|70606567|ref|YP_255437.1|  [L=70]
Description: hypothetical protein Saci_0771 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-14   53.3   6.6    1.4e-11   44.1   2.2    2.3  2  DUF1610          Domain of unknown function (DUF1610)
    2.2e-06   27.6  19.8    0.00019   21.4  11.4    2.4  2  DZR              Double zinc ribbon
    3.9e-05   23.5   8.4     0.0002   21.2   2.0    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    0.00012   21.4  16.5       0.55    9.7   5.2    3.9  3  zf-ribbon_3      zinc-ribbon domain
    0.00076   19.3   8.9        1.7    8.7   0.0    3.4  3  Nudix_N_2        Nudix N-terminal
    0.00081   19.5   7.0    0.00091   19.3   7.0    1.1  1  zf-UDP           Zinc-binding RING-finger
     0.0019   17.8  15.5      0.013   15.2   3.8    2.9  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0031   17.4   7.6      0.038   14.0   3.0    2.5  2  ADK_lid          Adenylate kinase, active site lid
     0.0034   17.4   7.8     0.0058   16.6   0.4    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0056   16.5  11.3       0.94    9.4   0.0    3.3  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0067   16.5   2.1     0.0067   16.5   2.1    2.5  2  Zn-ribbon_8      Zinc ribbon domain
     0.0083   16.6   9.2       0.16   12.4   0.3    2.0  2  zf-CHY           CHY zinc finger
     0.0092   16.1   2.2     0.0092   16.1   2.2    2.1  2  zf-MYND          MYND finger
  ------ inclusion threshold ------
      0.012   15.5   1.8      0.012   15.5   1.8    2.7  2  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
      0.013   15.5   8.3       0.44   10.7   0.6    2.9  3  DUF1272          Protein of unknown function (DUF1272)
      0.014   15.4  14.0        1.6    8.9   0.4    3.4  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.015   14.9   9.8        3.7    7.2   0.4    3.5  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.017   15.1   4.6      0.017   15.1   4.6    2.3  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.019   15.1   3.2      0.019   15.1   3.2    2.2  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
      0.021   14.8   2.6      0.021   14.8   2.6    2.4  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.022   13.7   0.1      0.025   13.5   0.1    1.2  1  tRNA-synt_1f     tRNA synthetases class I (K)
      0.025   13.4   6.4       0.03   13.1   6.4    1.2  1  Dynactin_p62     Dynactin p62 family
      0.026   14.8   8.7       0.65   10.3   2.6    3.0  2  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.027   14.6   1.7      0.027   14.6   1.7    2.6  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.029   13.9  15.1       0.18   11.3   0.3    3.3  3  TF_Zn_Ribbon     TFIIB zinc-binding
      0.031   14.4  10.8       0.47   10.6   0.7    2.3  2  zf-piccolo       Piccolo Zn-finger
      0.034   14.5  12.0       0.26   11.6   2.6    2.2  2  C1_2             C1 domain
      0.056   11.3   2.0       0.06   11.2   2.0    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
      0.076   13.0   9.1        1.2    9.2   1.2    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.08   12.7  22.3       0.58    9.9   6.8    3.9  3  zinc_ribbon_2    zinc-ribbon domain
       0.08   12.9   6.2      0.093   12.7   6.2    1.1  1  zf-RING_9        Putative zinc-RING and/or ribbon
      0.095   12.4  16.1       0.41   10.4   3.2    3.6  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
        0.2   11.8   0.8        1.8    8.8   0.0    2.2  2  FUR              Ferric uptake regulator family
        0.2   11.5  10.8        1.3    8.9   1.5    2.5  2  PHD              PHD-finger
       0.21   11.2   7.2        1.4    8.5   0.5    2.7  2  zf_C2H2_10       C2H2 type zinc-finger
       0.28   11.5  14.2       0.51   10.6   1.8    3.3  3  zinc_ribbon_9    zinc-ribbon
        0.3   10.7   6.3        1.3    8.7   6.5    2.0  2  DUF2321          Uncharacterized protein conserved in bacteri
       0.35   10.8  10.1        4.3    7.3   0.0    3.7  4  zinc_ribbon_4    zinc-ribbon domain
       0.38   10.5  11.1       0.22   11.2   2.6    2.9  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.39   11.0   0.2       0.39   11.0   0.2    3.7  2  zf-RING_7        C4-type zinc ribbon domain
       0.41   10.6   6.7       0.28   11.1   0.5    2.5  2  NinF             NinF protein
       0.52   10.4   8.7         13    5.9   0.4    3.1  3  CpXC             CpXC protein
        0.6   10.4   4.5        1.2    9.4   0.0    2.9  3  Chordopox_RPO7   Chordopoxvirus DNA-directed RNA polymerase 7
       0.71   10.0   8.2          8    6.6   0.0    2.6  2  Elf1             Transcription elongation factor Elf1 like
       0.89    9.8  10.1         21    5.4  10.1    2.2  1  IBR              IBR domain, a half RING-finger domain
       0.96    9.4  10.6       0.37   10.7   0.8    2.9  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.99   10.2  12.1         83    4.0  12.4    2.3  1  zinc_ribbon_15   zinc-ribbon family
          1    9.1   0.1          1    9.1   0.1    3.5  3  Rubredoxin_2     Rubredoxin metal binding domain
          1    9.5   6.5        1.9    8.7   1.0    2.5  2  Acetone_carb_G   Acetone carboxylase gamma subunit
          1    9.4   9.8       0.56   10.3   0.9    2.4  2  zf-C3H2C3        Zinc-finger
        1.1    9.0  12.7         13    5.5   4.5    3.0  3  Zn_ribbon_17     Zinc-ribbon, C4HC2 type
        1.2    8.7  12.8        1.4    8.5   0.1    3.9  4  Sgf11            Sgf11 (transcriptional regulation protein)
        1.6    8.3   6.8       0.57    9.8   4.4    1.3  1  DpnI             Dam-replacing family
        1.7    8.7   9.9        6.7    6.8   1.0    3.2  3  Rubredoxin       Rubredoxin
        1.8    8.9  13.6        2.2    8.6   2.3    3.5  2  zf-LITAF-like    LITAF-like zinc ribbon domain
        1.8    8.6  11.1         19    5.3  11.1    2.3  1  zf-RING_5        zinc-RING finger domain
          2    7.8   6.6        2.6    7.5   3.1    1.9  2  DUF1258          Protein of unknown function (DUF1258)
        2.1    8.1  13.1        4.4    7.0   2.1    3.1  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
        2.9    8.1  12.1         34    4.7   0.1    3.0  3  zf-AN1           AN1-like Zinc finger
        2.9    7.3  14.6    1.1e+02    2.3  14.7    2.8  1  zf-TFIIB         Transcription factor zinc-finger
        4.8    7.0  14.8        3.1    7.6   0.5    3.4  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        5.2    7.3  12.8        9.7    6.4   1.9    2.8  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        6.7    7.4  15.7         16    6.1   0.6    3.9  3  zf-C2H2          Zinc finger, C2H2 type
        8.9    6.9  19.6        2.8    8.5   1.0    4.0  2  zf-H2C2_2        Zinc-finger double domain
          9    6.4  21.2         12    5.9   0.5    3.8  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   2.2     5e-14   1.4e-11       1      23 [.      21      43 ..      21      44 .. 0.98
   2 !   11.4   0.1   0.00087      0.24      15      23 ..      58      66 ..      54      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5e-14
                       DUF1610  1 CtSCGaelaprEravvFpCPNCG 23
                                  C+SCG+ l+prE++ +F+CPNCG
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPREKGDEFYCPNCG 43
                                  *********************** PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00087
                       DUF1610 15 vvFpCPNCG 23
                                  vv+ CP+CG
  gi|70606567|ref|YP_255437.1| 58 VVYVCPKCG 66
                                  899*****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.2     2e-05    0.0055      22      49 .]      12      43 ..       9      43 .. 0.76
   2 !   21.4  11.4   6.9e-07   0.00019       1      49 []      21      66 ..      21      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-05
                           DZR 22 lkavaaedrCpsCgekvdpearf....CpeCG 49
                                  lk++ ++++C+sCg+ ++p+++     Cp+CG
  gi|70606567|ref|YP_255437.1| 12 LKEEIEPIVCSSCGKILHPREKGdefyCPNCG 43
                                  56666689999999999998775555699998 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 6.9e-07
                           DZR  1 CpqCgeelppdar....fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                  C++Cg+ l+p+ +    +C++Cg+ l      +rC  C ++v     +Cp+CG
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPREKgdefYCPNCGQVLI-----RRCYYCRKQVVVY--VCPKCG 66
                                  *******9999988889*********9.....9********9998..9****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   2.0   7.1e-07    0.0002      30      56 ..      20      46 ..      18      50 .. 0.91
   2 ?    5.5   1.5      0.06        16      43      55 ..      56      68 ..      48      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.1e-07
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                   Cs Cg+++ ++ +g++f+CpnCg ++
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREKGDEFYCPNCGQVL 46
                                  6***********************875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.06
                OrfB_Zn_ribbon 43 sgrtfkCpnCgfe 55
                                  +  +++Cp+Cgfe
  gi|70606567|ref|YP_255437.1| 56 QVVVYVCPKCGFE 68
                                  466799*****96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0024      0.67       4      15 ..      20      31 ..      18      33 .. 0.77
   2 !    9.7   5.2     0.002      0.55       3      12 ..      37      47 ..      35      56 .. 0.77
   3 !    8.0   0.4    0.0071         2      18      23 ..      61      66 ..      59      68 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                   zf-ribbon_3  4 rCPnCGaplssd 15
                                   C++CG++l ++
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPR 31
                                  699999977665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.002
                   zf-ribbon_3  3 vrCPnCGa.pl 12
                                   +CPnCG+ ++
  gi|70606567|ref|YP_255437.1| 37 FYCPNCGQvLI 47
                                  69*****9555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0071
                   zf-ribbon_3 18 vCpyCG 23
                                  vCp+CG
  gi|70606567|ref|YP_255437.1| 61 VCPKCG 66
                                  577777 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0     0.006       1.7      23      31 ..      19      27 ..       4      36 .. 0.76
   2 !    8.5   0.7    0.0069       1.9       2      13 ..      38      49 ..      38      51 .. 0.82
   3 ?    6.4   0.2     0.031       8.7      23      30 ..      60      67 ..      60      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.006
                                  EEETTTTEE CS
                     Nudix_N_2 23 lvCpaCgti 31
                                   vC++Cg i
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGKI 27
                                  689999988 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0069
                                  B-TTT--B-EEE CS
                     Nudix_N_2  2 FCsqCGtpvelr 13
                                  +C++CG+ + +r
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIRR 49
                                  9*****987665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.031
                                  EEETTTTE CS
                     Nudix_N_2 23 lvCpaCgt 30
                                  +vCp+Cg+
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGF 67
                                  69999996 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   7.0   3.3e-06   0.00091       6      56 ..      16      65 ..      11      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.3e-06
                        zf-UDP  6 lngqiCqiCgddvgltedgelFvacnecafpvcrpcyeyerkdgnqsCPqC 56
                                  ++  +C  Cg  +  +e+g+ F  c +c+  ++r cy  +++    +CP+C
  gi|70606567|ref|YP_255437.1| 16 IEPIVCSSCGKILHPREKGDEF-YCPNCGQVLIRRCYYCRKQVVVYVCPKC 65
                                  56679*****************.59************99999999****** PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.9     0.015       4.1       3      28 ..      18      43 ..      17      45 .. 0.77
   2 !   15.2   3.8   4.8e-05     0.013       4      30 ..      48      68 ..      47      70 .] 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                 A2L_zn_ribbon  3 lkvCsvCggngiln.seqgylv.CieCg 28
                                  ++vCs Cg+  il  +e+g+++ C++Cg
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGK--ILHpREKGDEFyCPNCG 43
                                  579999996..555588888866****9 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.8e-05
                 A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCgas 30
                                  + C +C++++++      +vC++Cg++
  gi|70606567|ref|YP_255437.1| 48 RRCYYCRKQVVV------YVCPKCGFE 68
                                  56**********......*******97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.0   0.00014     0.038       3      34 ..      20      49 ..      19      50 .. 0.86
   2 ?    5.5   0.1     0.059        16       3       8 ..      61      66 ..      60      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00014
                                  E-TTT--EEETTTB--S...STTB-TTT--.-B-- CS
                       ADK_lid  3 vCpkCGrsYhvvfnpPk...veglCDkCGepLvqR 34
                                  vC++CG++ h     P+    e  C +CG  L++R
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILH-----PRekgDEFYCPNCGQVLIRR 49
                                  9*********.....54334888***********9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.059
                                  E-TTT- CS
                       ADK_lid  3 vCpkCG 8 
                                  vCpkCG
  gi|70606567|ref|YP_255437.1| 61 VCPKCG 66
                                  9****9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   2.1e-05    0.0058      61      95 ..       9      45 ..       5      49 .. 0.81
   2 ?    5.1   1.8     0.082        23      72      93 ..      49      66 ..      44      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-05
                                  EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSSS CS
                          HypA 61 eLeieevpvkvrCreCgkefeleek..alrCpkCgsa 95
                                  +L+++e+   + C++Cgk  + +ek  ++ Cp+Cg+ 
  gi|70606567|ref|YP_255437.1|  9 RLSLKEEIEPIVCSSCGKILHPREKgdEFYCPNCGQV 45
                                  577777778899*********76644599*****985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.082
                                  EETTTS-EEECHHHHHS-TTTS CS
                          HypA 72 rCreCgkefeleekalrCpkCg 93
                                  rC  C+k++ +      CpkCg
  gi|70606567|ref|YP_255437.1| 49 RCYYCRKQVVVY----VCPKCG 66
                                  799999888754....8****8 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0034      0.94      13      25 ..      20      32 ..      19      34 .. 0.88
   2 ?    5.1   3.9     0.078        22      13      28 ..      38      53 ..      38      57 .. 0.72
   3 ?    5.9   0.3     0.044        12      10      18 ..      58      66 ..      54      68 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0034
                       DUF35_N 13 rCpdCGtvqfPPr 25
                                   C++CG+  +P++
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPRE 32
                                  5*********985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.078
                       DUF35_N 13 rCpdCGtvqfPPr.avC 28
                                  +Cp+CG+v   +r  +C
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQV-LIRRcYYC 53
                                  7*****99.45555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.044
                       DUF35_N 10 vgqrCpdCG 18
                                  v+  Cp+CG
  gi|70606567|ref|YP_255437.1| 58 VVYVCPKCG 66
                                  666777777 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.1   2.4e-05    0.0067       7      38 ..      20      49 ..      15      51 .. 0.84
   2 ?    5.5   0.8     0.069        19       6      12 ..      60      66 ..      57      69 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-05
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                   C +Cg+   ++ + +   +  CP+Cg+   rr
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREKGD---EFYCPNCGQvLIRR 49
                                  5*****9999999765...677******77777 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.069
                   Zn-ribbon_8  6 YrCeeCg 12
                                  Y C +Cg
  gi|70606567|ref|YP_255437.1| 60 YVCPKCG 66
                                  6666666 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.3   0.00059      0.16      50      73 ..      14      43 ..       4      45 .. 0.84
   2 !    8.6  10.6    0.0095       2.6      22      73 ..      21      66 ..      21      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00059
                        zf-CHY 50 eqekavlCkkCkk......efaeyfCpiCk 73
                                  e+ + ++C++C+k      + +e++Cp+C 
  gi|70606567|ref|YP_255437.1| 14 EEIEPIVCSSCGKilhpreKGDEFYCPNCG 43
                                  4556789****999*999989999*****7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0095
                        zf-CHY 22 CreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                  C +C +    h   r + +e+ c +C ++      C  C+k++  y+Cp+C 
  gi|70606567|ref|YP_255437.1| 21 CSSCGK--ILH--PREKGDEFYCPNCGQV--LIRRCYYCRKQVVVYVCPKCG 66
                                  556655..334..455667889****987..8899****************7 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.2   3.3e-05    0.0092       1      24 [.      21      55 ..      21      57 .. 0.75
   2 ?    5.4   3.4     0.073        20       1      16 [.      50      65 ..      50      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-05
                                  -TTT--......B-SC....E-TTT.....S-SEESSH CS
                       zf-MYND  1 CavCgk.....aealk....kCagC.....ksvfYCsk 24
                                  C++Cgk     +   k     C++C     ++++YC k
  gi|70606567|ref|YP_255437.1| 21 CSSCGKilhprE---KgdefYCPNCgqvliRRCYYCRK 55
                                  ********6542...44568*****66666666***87 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.073
                                  -TTT--.B-SC.E-TTT CS
                       zf-MYND  1 CavCgkaealk.kCagC 16
                                  C +C+k ++    C++C
  gi|70606567|ref|YP_255437.1| 50 CYYCRK-QVVVyVCPKC 65
                                  9*****.55555***** PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.8   4.2e-05     0.012       3      23 ..      21      42 ..      20      43 .. 0.85
   2 ?    1.7   0.2      0.83   2.3e+02      20      23 ..      62      65 ..      59      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-05
                                  -SSS--B--S.S-S---B-TTT CS
                    HscB_4_cys  3 CWnCGgpgap.grgdefFCpqC 23
                                  C +CG+ + p  +gdef+Cp C
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPrEKGDEFYCPNC 42
                                  779***8877257********* PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.83
                                  -TTT CS
                    HscB_4_cys 20 CpqC 23
                                  Cp+C
  gi|70606567|ref|YP_255437.1| 62 CPKC 65
                                  8888 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       1.2   3.3e+02       8      18 ..      21      31 ..      10      37 .. 0.67
   2 ?    7.5   2.1     0.016       4.4      42      54 ..      37      49 ..      17      51 .. 0.74
   3 ?   10.7   0.6    0.0016      0.44      32      48 ..      50      66 ..      49      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.2
                       DUF1272  8 CecCdkdlppd 18
                                  C  C k l+p 
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPR 31
                                  55555555544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                       DUF1272 42 nvCPncgGelvkR 54
                                    CPncg  l++R
  gi|70606567|ref|YP_255437.1| 37 FYCPNCGQVLIRR 49
                                  47*****999998 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0016
                       DUF1272 32 CaeCaeevlenvCPncg 48
                                  C  C ++v+  vCP cg
  gi|70606567|ref|YP_255437.1| 50 CYYCRKQVVVYVCPKCG 66
                                  999*************9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.028       7.7       4      12 ..      21      29 ..      19      32 .. 0.84
   2 ?    8.9   0.4    0.0058       1.6       3      13 ..      38      48 ..      37      51 .. 0.85
   3 ?    6.0   3.6     0.046        13      21      26 .]      60      65 ..      59      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.028
                        zf-ACC  4 CpsCgemly 12
                                  C sCg +l+
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILH 29
                                  9******98 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0058
                        zf-ACC  3 KCpsCgemlyk 13
                                   Cp Cg++l +
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIR 48
                                  6******9976 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.046
                        zf-ACC 21 yVCPkC 26
                                  yVCPkC
  gi|70606567|ref|YP_255437.1| 60 YVCPKC 65
                                  9***** PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.024       6.7       3      16 ..      19      32 ..      17      34 .. 0.80
   2 ?    6.8   0.1     0.018         5       1      11 [.      35      45 ..      35      48 .. 0.85
   3 ?   -2.0   0.1        10   2.7e+03       5      12 ..      50      57 ..      49      59 .. 0.68
   4 ?    7.2   0.4     0.013       3.7       3      10 ..      60      67 ..      58      70 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.024
                        zf_UBZ  3 ylCerCgkeipese 16
                                  ++C+ Cgk + + e
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGKILHPRE 32
                                  79******887766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.018
                        zf_UBZ  1 dtylCerCgke 11
                                  d + C+ Cg+ 
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCGQV 45
                                  6799*****97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 10
                        zf_UBZ  5 CerCgkei 12
                                  C  C k++
  gi|70606567|ref|YP_255437.1| 50 CYYCRKQV 57
                                  66688776 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.013
                        zf_UBZ  3 ylCerCgk 10
                                  y+C++Cg 
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGF 67
                                  9*****96 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   4.6   6.1e-05     0.017       6      36 ..      20      52 ..      15      58 .. 0.88
   2 ?    3.1   2.7      0.32        89      20      27 ..      59      66 ..      52      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.1e-05
                   Prok-RING_1  6 kCpvCgkelkee..dDiVvCpeCgtpyHraCye 36
                                   C+ Cgk l++    D   Cp+Cg +  r Cy 
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPRekGDEFYCPNCGQVLIRRCYY 52
                                  5********876559****************95 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.32
                   Prok-RING_1 20 iVvCpeCg 27
                                  + vCp+Cg
  gi|70606567|ref|YP_255437.1| 59 VYVCPKCG 66
                                  449****9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   3.2     7e-05     0.019      10      38 ..      20      51 ..      18      58 .. 0.84
   2 ?    3.5   2.8       0.3        82      10      30 ..      49      66 ..      46      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-05
                  NOB1_Zn_bind 10 rChaCfkvt...kdmtkkFCpkCGnktLkrva 38
                                   C +C k+    ++ +  +Cp+CG+  ++r+ 
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILhprEKGDEFYCPNCGQVLIRRCY 51
                                  6******996656688899*******999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.3
                  NOB1_Zn_bind 10 rChaCfkvtkdmtkkFCpkCG 30
                                  rC+ C    k+     CpkCG
  gi|70606567|ref|YP_255437.1| 49 RCYYC---RKQVVVYVCPKCG 66
                                  55555...55677788****9 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.6   7.8e-05     0.021      19      46 ..      20      48 ..      14      51 .. 0.89
   2 ?    3.6   6.2      0.23        65      20      41 ..      39      66 ..      38      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.8e-05
                      zf-C2HC5 19 nClnCGkiiCakegls.kpCsfCgsplls 46
                                   C +CGki+  +e+     C+ Cg+ l+ 
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREKGDeFYCPNCGQVLIR 48
                                  6*********999998899*****99985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.23
                      zf-C2HC5 20 ClnCGkii......CakeglskpCsfCg 41
                                  C nCG+++      C k+ ++  C+ Cg
  gi|70606567|ref|YP_255437.1| 39 CPNCGQVLirrcyyCRKQVVVYVCPKCG 66
                                  999**99767766688888889999997 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     9e-05     0.025     148     209 ..      10      69 ..       1      70 [] 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9e-05
                  tRNA-synt_1f 148 lenrekikeilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeee 209
                                   l+ +e+i+ i+ +  g+ ++ +    + +c++cg+v+  + + +   ++ + Y+c +cG+e+
  gi|70606567|ref|YP_255437.1|  10 LSLKEEIEPIVCSSCGKILHPREKGDEFYCPNCGQVLIRRCYYCR--KQVVVYVCPKCGFEG 69 
                                   56666777777777777766666777889*******999999888..9***********986 PP

>> Dynactin_p62  Dynactin p62 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   6.4   0.00011      0.03       6      37 ..      37      70 .]      30      70 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                  Dynactin_p62  6 lyCedChqirCpRC..vteeivtyyCPnCLFevp 37
                                   yC +C q+   RC      +v y CP+C Fe p
  gi|70606567|ref|YP_255437.1| 37 FYCPNCGQVLIRRCyyCRKQVVVYVCPKCGFEGP 70
                                  6********99999444689************87 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.6    0.0023      0.65      34      59 ..       7      32 ..       1      54 [. 0.77
   2 ?    1.2   5.6       1.7   4.6e+02      47      58 ..      38      49 ..      31      66 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0023
                                  HCT---SSTCCCTB-TTT--B--CTT CS
                          Rpr2 34 kaqlrlppsvkrtvCkkCgsvlipgv 59
                                    +l+l+++++  vC++Cg++l p  
  gi|70606567|ref|YP_255437.1|  7 SFRLSLKEEIEPIVCSSCGKILHPRE 32
                                  5678999***************9975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.7
                                  B-TTT--B--CT CS
                          Rpr2 47 vCkkCgsvlipg 58
                                  +C +Cg+vli  
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIRR 49
                                  788888888764 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.7   9.8e-05     0.027      17      40 .]      20      43 ..      18      43 .. 0.89
   2 ?    5.2  10.7     0.085        23      17      40 .]      38      66 ..      36      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-05
                 Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCvaCd 40
                                  +C+ Cg +L    kg + yC++C+
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREKGDEFYCPNCG 43
                                  6****99999866899*******6 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.085
                 Auto_anti-p27 17 tCpvCgvPLmrdr......kggkvyCvaCd 40
                                  +Cp+Cg +L r r      + + ++C+ C+
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIR-RcyycrkQVVVYVCPKCG 66
                                  8**********.5588775567789****6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4     0.023       6.4      20      29 ..      19      28 ..      15      32 .. 0.86
   2 ?   11.3   0.3   0.00067      0.18      19      29 ..      36      46 ..      31      49 .. 0.84
   3 ?    6.2   0.7     0.026       7.2       1      26 [.      60      66 ..      60      68 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                                  EEESSSSBEE CS
                  TF_Zn_Ribbon 20 lvCtdCGlVl 29
                                  +vC++CG +l
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGKIL 28
                                  59*****876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00067
                                  CEEESSSSBEE CS
                  TF_Zn_Ribbon 19 elvCtdCGlVl 29
                                  e++C++CG Vl
  gi|70606567|ref|YP_255437.1| 36 EFYCPNCGQVL 46
                                  89999999987 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.026
                                  EEETTTTCEECHEETSTTCEEESSSS CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCG 26
                                  y+CP+C                   G
  gi|70606567|ref|YP_255437.1| 60 YVCPKC-------------------G 66
                                  455555...................5 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7    0.0017      0.47      28      53 ..      18      42 ..      14      47 .. 0.80
   2 ?    8.3   3.9    0.0093       2.6      21      37 ..      48      68 ..      44      70 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0017
                    zf-piccolo 28 kqvCnlCGFnptphltekkeWlclnC 53
                                    vC+ CG   +p  +++ e  c nC
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGKILHPR-EKGDEFYCPNC 42
                                  57******766665.5689******* PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0093
                    zf-piccolo 21 ntCteCkkq....vCnlCGFn 37
                                  + C+ C+kq    vC +CGF+
  gi|70606567|ref|YP_255437.1| 48 RRCYYCRKQvvvyVCPKCGFE 68
                                  68*****9844445******6 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.6   0.00095      0.26       6      46 ..       9      50 ..       7      50 .. 0.77
   2 ?    7.9   4.3     0.014       3.8      19      40 ..      48      67 ..      44      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00095
                          C1_2  6 pLtlskgedssesfnCsaCgrk....idgffYsCseCdfslhvrC 46
                                  +L+l+   ++ e   Cs Cg+      +g++++C+ C  +l  rC
  gi|70606567|ref|YP_255437.1|  9 RLSLK---EEIEPIVCSSCGKIlhprEKGDEFYCPNCGQVLIRRC 50
                                  56677...7777899*******766555556******98887777 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.014
                          C1_2 19 fnCsaCgrkidgffYsCseCdf 40
                                  ++C  C++++    Y C++C f
  gi|70606567|ref|YP_255437.1| 48 RRCYYCRKQV--VVYVCPKCGF 67
                                  68*******6..56******98 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.0   0.00022      0.06     613     663 ..      13      67 ..       3      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                      PolC_DP2 613 eveiarrkCkkCgk......etlearCeeCgekteeklvCkkceeeveeekcekcek 663
                                   + ei+   C++Cgk      ++ e+ C++Cg+      +C  c+++v    c+kc+ 
  gi|70606567|ref|YP_255437.1|  13 KEEIEPIVCSSCGKilhpreKGDEFYCPNCGQVLIR--RCYYCRKQVVVYVCPKCGF 67 
                                   557777788888762222224557788888888777..8888888888888888865 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.43   1.2e+02      20      26 ..      19      25 ..      11      26 .. 0.87
   2 ?    5.2   0.1     0.073        20      19      26 ..      36      43 ..      32      44 .. 0.72
   3 ?    9.2   1.2    0.0043       1.2      19      28 ..      59      68 ..      50      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.43
                PhnA_Zn_Ribbon 20 lvCpeCa 26
                                   vC+ C+
  gi|70606567|ref|YP_255437.1| 19 IVCSSCG 25
                                  59****8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.073
                PhnA_Zn_Ribbon 19 llvCpeCa 26
                                   + Cp+C+
  gi|70606567|ref|YP_255437.1| 36 EFYCPNCG 43
                                  57799997 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0043
                PhnA_Zn_Ribbon 19 llvCpeCahE 28
                                  ++vCp+C+ E
  gi|70606567|ref|YP_255437.1| 59 VYVCPKCGFE 68
                                  89*****977 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.8    0.0021      0.58       2      21 ..      21      44 ..      20      46 .. 0.77
   2 ?    0.7   0.5       1.7   4.6e+02      16      21 ..      50      55 ..      48      57 .. 0.77
   3 ?    9.3   0.9    0.0034      0.93      16      22 ..      62      68 ..      54      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0021
                 zinc_ribbon_2  2 CpnCGael.q.d.nakF.CpyCGt 21
                                  C++CG+ l + + ++ F Cp+CG 
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILhPrEkGDEFyCPNCGQ 44
                                  9*****996554477779*****6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.7
                 zinc_ribbon_2 16 CpyCGt 21
                                  C yC+ 
  gi|70606567|ref|YP_255437.1| 50 CYYCRK 55
                                  999986 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0034
                 zinc_ribbon_2 16 CpyCGtp 22
                                  Cp+CG++
  gi|70606567|ref|YP_255437.1| 62 CPKCGFE 68
                                  7777765 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.2   0.00034     0.093     157     201 ..      20      65 ..      13      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00034
                     zf-RING_9 157 iCelCkseellfpfqlktverCekCkavfHkeClkkkekk...ecpkc 201
                                   +C+ C   ++l+p ++     C++C++v+ ++C+  +++     cpkc
  gi|70606567|ref|YP_255437.1|  20 VCSSCG--KILHPREKGDEFYCPNCGQVLIRRCYYCRKQVvvyVCPKC 65 
                                   566665..89***99999999*************7777669999**** PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.2    0.0015      0.41      17      53 ..      13      45 ..       4      46 .. 0.74
   2 ?    4.2   5.0      0.13        36      42      52 ..      57      67 ..      50      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                zinc_ribbon_10 17 aknryalICskChshnGlapkeeleevkyrCpkCgal 53
                                  ++++ +++Cs C +   l p+e+ +  +++Cp+Cg++
  gi|70606567|ref|YP_255437.1| 13 KEEIEPIVCSSCGKI--LHPREKGD--EFYCPNCGQV 45
                                  5778999***99775..33344444..79*****985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.13
                zinc_ribbon_10 42 evkyrCpkCga 52
                                   v y+CpkCg+
  gi|70606567|ref|YP_255437.1| 57 VVVYVCPKCGF 67
                                  579******96 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0064       1.8      69      90 ..       7      28 ..       3      33 .. 0.89
   2 ?    1.8   0.0      0.92   2.5e+02      76      89 ..      32      45 ..      28      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0064
                                  EEEESSSSSEEEEEETTT--EE CS
                           FUR 69 ryelakkehhdhlicekCgkvi 90
                                   ++l+ ke+++ ++c +Cgk+ 
  gi|70606567|ref|YP_255437.1|  7 SFRLSLKEEIEPIVCSSCGKIL 28
                                  6999999*************95 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.92
                                  SSEEEEEETTT--E CS
                           FUR 76 ehhdhlicekCgkv 89
                                  e+ d + c +Cg+v
  gi|70606567|ref|YP_255437.1| 32 EKGDEFYCPNCGQV 45
                                  5668899*****98 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.5    0.0048       1.3       2      21 ..      21      42 ..      10      45 .. 0.55
   2 ?    8.5  11.6    0.0066       1.8       1      50 [.      20      66 ..      20      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0048
                                  BTTTTS..TTSTTSCEEEETTT CS
                           PHD  2 CavCkk..ksdeeeelvqCdgC 21
                                  C+ C+k  +  e+++  +C +C
  gi|70606567|ref|YP_255437.1| 21 CSSCGKilHPREKGDEFYCPNC 42
                                  4444444444444444444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0066
                                  SBTTTTS..TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                           PHD  1 rCavCkk..ksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50
                                  +C+ C+k  +  e+++  +C +C++     C+   ++   +    ++C+kC 
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKilHPREKGDEFYCPNCGQVLIRRCYYCRKQ--VV---VYVCPKCG 66
                                  5********9999*********************977..33...4******5 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.023       6.4       2      12 ..      36      46 ..      35      46 .. 0.86
   2 ?    8.5   0.5     0.005       1.4       3      11 ..      60      68 ..      59      70 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.023
                    zf_C2H2_10  2 efsCPKCqekl 12
                                  ef CP C+ +l
  gi|70606567|ref|YP_255437.1| 36 EFYCPNCGQVL 46
                                  699****9875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.005
                    zf_C2H2_10  3 fsCPKCqek 11
                                  + CPKC+  
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGFE 68
                                  67****976 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.38   1.1e+02      15      28 ..      13      25 ..       6      27 .. 0.67
   2 ?   10.6   1.8    0.0019      0.51       5      29 ..      21      44 ..      20      47 .. 0.86
   3 ?    3.6   5.2       0.3        83       5      28 ..      50      66 ..      50      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.38
                 zinc_ribbon_9 15 spdedsdvlCPhCg 28
                                   ++ +++v C +Cg
  gi|70606567|ref|YP_255437.1| 13 KEEIEPIV-CSSCG 25
                                  44445556.****8 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0019
                 zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCgg 29
                                  C +C + ++++++ d+   CP+Cg+
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPREKGDEFY-CPNCGQ 44
                                  66899999*999888888.****95 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.3
                 zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCg 28
                                  C+ C++ V v       v CP Cg
  gi|70606567|ref|YP_255437.1| 50 CYYCRKQVVV------YV-CPKCG 66
                                  9****99998......56.99997 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.8     5e+02      65      74 ..      17      26 ..       4      34 .. 0.70
   2 ?    8.7   6.5    0.0047       1.3      23      47 ..      33      57 ..      16      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.8
                       DUF2321 65 vpsyCkkCgk 74
                                   p  C++Cgk
  gi|70606567|ref|YP_255437.1| 17 EPIVCSSCGK 26
                                  4667777776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0047
                       DUF2321 23 elveeyCekcGektitkcpkCstei 47
                                  +  e yC +cG+ +i++c  C+ ++
  gi|70606567|ref|YP_255437.1| 33 KGDEFYCPNCGQVLIRRCYYCRKQV 57
                                  44466****************9886 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.11        31       3      10 ..      19      26 ..      12      29 .. 0.72
   2 ?    7.3   0.0     0.016       4.3      23      34 ..      34      45 ..      30      47 .. 0.70
   3 ?   -1.5   0.3         9   2.5e+03      27      33 ..      49      55 ..      49      58 .. 0.58
   4 ?    4.1   0.4      0.16        45       5      10 ..      62      67 ..      60      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                 zinc_ribbon_4  3 itCpsCka 10
                                  i+C sC++
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGK 26
                                  56666654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.016
                 zinc_ribbon_4 23 gvkvrCskCghv 34
                                  g +  C++Cg+v
  gi|70606567|ref|YP_255437.1| 34 GDEFYCPNCGQV 45
                                  556668888876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 9
                 zinc_ribbon_4 27 rCskCgh 33
                                  rC  C++
  gi|70606567|ref|YP_255437.1| 49 RCYYCRK 55
                                  5555554 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.16
                 zinc_ribbon_4  5 CpsCka 10
                                  Cp+C++
  gi|70606567|ref|YP_255437.1| 62 CPKCGF 67
                                  888876 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.6   0.00079      0.22       6      29 ..      21      44 ..      20      46 .. 0.95
   2 ?    5.6   1.9     0.044        12       5      12 ..      38      45 ..      37      54 .. 0.82
   3 ?    4.4   0.2      0.11        29      23      28 ..      61      66 ..      60      68 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00079
                 zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCgl 29
                                  C+ CG   +p e g    Cp+Cg+
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPREKGDEFYCPNCGQ 44
                                  **********************97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.044
                 zf-NADH-PPase  5 FCgrCGap 12
                                  +C+ CG+ 
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQV 45
                                  78888875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.11
                 zf-NADH-PPase 23 vCpaCg 28
                                  vCp Cg
  gi|70606567|ref|YP_255437.1| 61 VCPKCG 66
                                  455555 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.037        10      23      33 .]      18      28 ..       9      28 .. 0.76
   2 ?   11.0   0.2    0.0014      0.39      19      30 ..      32      43 ..      31      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.037
                                  -EE-TTT--EE CS
                     zf-RING_7 23 vvtCpeCGRIL 33
                                   + C +CG IL
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGKIL 28
                                  488*****998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0014
                                  CSTB-EE-TTT- CS
                     zf-RING_7 19 agdevvtCpeCG 30
                                   +++ ++Cp+CG
  gi|70606567|ref|YP_255437.1| 32 EKGDEFYCPNCG 43
                                  56677******9 PP

>> NinF  NinF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5     0.001      0.28      12      32 ..      13      33 ..       9      44 .. 0.81
   2 ?    0.2   3.8       2.6   7.1e+02      20      43 ..      39      58 ..      35      68 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.001
                          NinF 12 kesveRaLCanCskkLevdev 32
                                  ke +e  +C  C+k L++ e 
  gi|70606567|ref|YP_255437.1| 13 KEEIEPIVCSSCGKILHPREK 33
                                  78899999**********984 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.6
                          NinF 20 CanCskkLevdevhvCeeCvaeli 43
                                  C nC++ L       C  C  +++
  gi|70606567|ref|YP_255437.1| 39 CPNCGQVLI----RRCYYCRKQVV 58
                                  888888773....33444444444 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.18        48      32      48 ..      13      29 ..       9      34 .. 0.80
   2 ?    4.5   1.5      0.13        35      37      46 ..      36      45 ..      31      54 .. 0.84
   3 ?    5.9   0.4     0.046        13      34      46 ..      56      68 ..      51      70 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.18
                          CpXC 32 dgslfeatCpkCgatak 48
                                  ++++  ++C +Cg+  +
  gi|70606567|ref|YP_255437.1| 13 KEEIEPIVCSSCGKILH 29
                                  67788899*****9766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.13
                          CpXC 37 eatCpkCgat 46
                                  e+ Cp+Cg+ 
  gi|70606567|ref|YP_255437.1| 36 EFYCPNCGQV 45
                                  789****986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.046
                          CpXC 34 slfeatCpkCgat 46
                                  ++  ++CpkCg +
  gi|70606567|ref|YP_255437.1| 56 QVVVYVCPKCGFE 68
                                  677899****986 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0045       1.2       4      14 ..      18      28 ..       8      32 .. 0.89
   2 ?    0.2   0.3       3.3   9.2e+02       6      19 ..      38      51 ..      36      60 .. 0.76
   3 ?    1.1   0.3       1.8     5e+02       3      12 ..      58      67 ..      56      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0045
                Chordopox_RPO7  4 plvCstCGrDl 14
                                  p+vCs+CG+ l
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGKIL 28
                                  79******965 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.3
                Chordopox_RPO7  6 vCstCGrDlseery 19
                                   C  CG+ l    y
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIRRCY 51
                                  59999998766555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.8
                Chordopox_RPO7  3 fplvCstCGr 12
                                     vC  CG+
  gi|70606567|ref|YP_255437.1| 58 VVYVCPKCGF 67
                                  5679*****7 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.029         8      33      53 ..       6      26 ..       2      33 .. 0.88
   2 ?    3.9   5.6       0.2        54      20      52 ..      35      66 ..      27      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.029
                          Elf1 33 vevkldkkekiaevsCkvCge 53
                                  v+ +l+ ke+i  + C++Cg+
  gi|70606567|ref|YP_255437.1|  6 VSFRLSLKEEIEPIVCSSCGK 26
                                  788999*************97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.2
                          Elf1 20 tkFdCpfCnheksvevkldkkekiaevsCkvCg 52
                                   +F Cp+C++    ++   +k ++ +  C +Cg
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCGQVLIRRCYYCRK-QVVVYVCPKCG 66
                                  589*******95555555555.67777799997 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  10.1     0.076        21      21      55 ..      21      56 ..       7      69 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.076
                           IBR 21 CprpdCeaiieksegcksvtCskCgfef...CfnCkke 55
                                  C    C++i+++ e+ ++  C++Cg+     C+ C+k+
  gi|70606567|ref|YP_255437.1| 21 CS--SCGKILHPREKGDEFYCPNCGQVLirrCYYCRKQ 56
                                  55..5666665555544445555555433335555543 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8    0.0013      0.37       4      28 ..      21      43 ..      19      45 .. 0.90
   2 ?    1.4   8.7       1.1   2.9e+02       4      31 ..      39      69 ..      36      70 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0013
                                  ESTTTSBEEEEECSCCCEEEESSSS CS
                RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCg 28
                                  C++Cg  L p+e+     f C +Cg
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILHPREKGDE--FYCPNCG 43
                                  ************9999..55****8 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                                  ESTTTSBEEEE...ECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  4 CpkCgNlLlpk...edkegknfeCrqCgYee 31
                                  Cp Cg  L+ +     k ++++ C +Cg e 
  gi|70606567|ref|YP_255437.1| 39 CPNCGQVLIRRcyyCRKQVVVYVCPKCGFEG 69
                                  ********86622234455459999999875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  12.4       0.3        83      37      86 .]      18      66 ..      11      66 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.3
                zinc_ribbon_15 37 ylacskCkslleaskelgkeiekkesse..kkeCknCgkeveeefkyCpkCg 86
                                   ++cs+C+++l+ ++ +g+e+   +  +   ++C  C+k+v   +  CpkCg
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGKILHPRE-KGDEFYCPNCGQvlIRRCYYCRKQVV--VYVCPKCG 66
                                  478999998888886.44444333222234667777776665..34577776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2       0.1        28       2       7 ..      20      25 ..      20      29 .. 0.84
   2 ?    5.3   0.3      0.06        17      17      22 ..      39      44 ..      37      45 .. 0.81
   3 ?    9.1   0.1    0.0038         1       1      10 [.      60      69 ..      60      70 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.1
                  Rubredoxin_2  2 vCsqCG 7 
                                  vCs+CG
  gi|70606567|ref|YP_255437.1| 20 VCSSCG 25
                                  799999 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.06
                  Rubredoxin_2 17 CpsCgs 22
                                  Cp+Cg+
  gi|70606567|ref|YP_255437.1| 39 CPNCGQ 44
                                  999986 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0038
                  Rubredoxin_2  1 YvCsqCGfes 10
                                  YvC +CGfe 
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGFEG 69
                                  9*******86 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0    0.0069       1.9      76      86 ..      35      45 ..      13      50 .. 0.87
   2 ?    3.6   0.6      0.25        69      75      84 ..      57      66 ..      49      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0069
                                  EEEE-TTT--E CS
                Acetone_carb_G 76 rEyycPecgtl 86
                                   E+ycP+cg++
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCGQV 45
                                  59*******86 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.25
                                  EEEEE-TTT- CS
                Acetone_carb_G 75 irEyycPecg 84
                                  ++ y+cP+cg
  gi|70606567|ref|YP_255437.1| 57 VVVYVCPKCG 66
                                  567******9 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9     0.002      0.56      11      35 .]      18      43 ..      16      43 .. 0.90
   2 ?    3.6   2.4      0.25        69      29      35 .]      60      66 ..      50      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.002
                     zf-C3H2C3 11 pfvaysCkHlvHakC.adeevCPkCk 35
                                  p+v  sC  + H    +de  CP C+
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGKILHPREkGDEFYCPNCG 43
                                  78889*******8777*********7 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.25
                     zf-C3H2C3 29 evCPkCk 35
                                   vCPkC+
  gi|70606567|ref|YP_255437.1| 60 YVCPKCG 66
                                  59****7 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.055        15      19      29 ..      19      29 ..      10      32 .. 0.87
   2 ?    5.2   1.8     0.057        16      16      33 ..      34      51 ..      31      53 .. 0.84
   3 ?    5.5   4.5     0.046        13       3      25 ..      46      66 ..      44      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.055
                  Zn_ribbon_17 19 vlcgvCeHvlH 29
                                  ++c +C+ +lH
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGKILH 29
                                  79********* PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.057
                  Zn_ribbon_17 16 grvvlcgvCeHvlHasCa 33
                                  g  ++c++C+ vl   C+
  gi|70606567|ref|YP_255437.1| 34 GDEFYCPNCGQVLIRRCY 51
                                  66799*****99999986 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.046
                  Zn_ribbon_17  3 llksCayCelavkgrvvlcgvCe 25
                                  l++ C yC  +v  +v++c++C+
  gi|70606567|ref|YP_255437.1| 46 LIRRCYYCRKQV--VVYVCPKCG 66
                                  5789****9887..79******7 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.36        99       5      12 ..      19      26 ..      16      29 .. 0.83
   2 ?    8.5   0.1    0.0052       1.4       4      12 ..      36      44 ..      33      46 .. 0.85
   3 ?    1.4   0.3      0.86   2.4e+02       6      14 ..      49      57 ..      47      59 .. 0.87
   4 ?    3.5   0.8      0.19        51       3      11 ..      58      66 ..      56      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.36
                                  EE-TTTSS CS
                         Sgf11  5 vtCpnCgR 12
                                  ++C  Cg+
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGK 26
                                  68****98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0052
                                  EEE-TTTSS CS
                         Sgf11  4 yvtCpnCgR 12
                                   + CpnCg+
  gi|70606567|ref|YP_255437.1| 36 EFYCPNCGQ 44
                                  699****96 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.86
                                  E-TTTSSEE CS
                         Sgf11  6 tCpnCgRqi 14
                                  +C +C +q+
  gi|70606567|ref|YP_255437.1| 49 RCYYCRKQV 57
                                  699***998 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.19
                                  -EEE-TTTS CS
                         Sgf11  3 eyvtCpnCg 11
                                  + ++Cp Cg
  gi|70606567|ref|YP_255437.1| 58 VVYVCPKCG 66
                                  5789****7 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.4    0.0021      0.57      30      60 ..      35      66 ..      31      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                                  HH---TTT--SS-EE.--------EEE-TTT- CS
                          DpnI 30 knlyCpkCgskklse.fennkpvaDfyCesck 60
                                  +++yCp+Cg+  +++ +   k+v+ + C +c 
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCGQVLIRRcYYCRKQVVVYVCPKCG 66
                                  579********9986588999*********95 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.45   1.2e+02       3      17 ..      20      35 ..      18      37 .. 0.76
   2 ?    6.8   1.0     0.024       6.7      33      41 ..      35      43 ..      32      51 .. 0.88
   3 ?    5.5   0.2     0.062        17      35      42 ..      60      67 ..      59      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.45
                                  EETTT-BEEET.TTBB CS
                    Rubredoxin  3 eCkvCgyvYdp.akGd 17
                                   C+ Cg +  p +kGd
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPrEKGD 35
                                  699**99988834677 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.024
                                  TT-BBTTTB CS
                    Rubredoxin 33 ddWvCPdCg 41
                                  d++ CP+Cg
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCG 43
                                  89******8 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.062
                                  -BBTTTB- CS
                    Rubredoxin 35 WvCPdCgv 42
                                  +vCP+Cg 
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGF 67
                                  78999985 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.3     0.008       2.2      53      67 ..      33      47 ..      18      49 .. 0.72
   2 ?    1.9   3.6         1   2.8e+02      49      63 ..      52      66 ..      47      68 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.008
                 zf-LITAF-like 53 kdvehyCpnCgallg 67
                                  k  e yCpnCg++l 
  gi|70606567|ref|YP_255437.1| 33 KGDEFYCPNCGQVLI 47
                                  555789****99985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1
                 zf-LITAF-like 49 vdslkdvehyCpnCg 63
                                  + + + v + Cp+Cg
  gi|70606567|ref|YP_255437.1| 52 YCRKQVVVYVCPKCG 66
                                  344555666777776 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  11.1     0.069        19       2      43 ..      21      66 ..      20      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.069
                     zf-RING_5  2 CnkCfekl...skeek...fyltsCgHif...CekClkkllekeavCpiCr 43
                                  C++C + l   +   k   fy  +Cg ++   C  C k+     +vCp C+
  gi|70606567|ref|YP_255437.1| 21 CSSCGKILhprE---KgdeFYCPNCGQVLirrCYYCRKQVV--VYVCPKCG 66
                                  ********5544...4455*********7555888888888..9******6 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.33        91      17      32 ..      19      34 ..      13      37 .. 0.85
   2 ?    7.5   3.1    0.0095       2.6      17      43 ..      37      61 ..      34      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.33
                       DUF1258 17 kfcnkcGkvvaksekc 32
                                   +c +cGk+++ +ek 
  gi|70606567|ref|YP_255437.1| 19 IVCSSCGKILHPREKG 34
                                  58******99988875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0095
                       DUF1258 17 kfcnkcGkvvaksekcelcggkvakfv 43
                                  ++c +cG+v+    +c +c ++v+ +v
  gi|70606567|ref|YP_255437.1| 37 FYCPNCGQVL--IRRCYYCRKQVVVYV 61
                                  89*****965..689********9998 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.62   1.7e+02      13      18 ..      21      26 ..      20      28 .. 0.85
   2 ?    7.0   2.1     0.016       4.4      13      28 ..      39      54 ..      38      57 .. 0.92
   3 ?    6.1   0.4      0.03       8.3      13      18 ..      62      67 ..      59      70 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.62
                       zf-tcix 13 CpkCGt 18
                                  C++CG 
  gi|70606567|ref|YP_255437.1| 21 CSSCGK 26
                                  *****5 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                       zf-tcix 13 CpkCGtyNGtRglsCk 28
                                  Cp+CG     R+  C+
  gi|70606567|ref|YP_255437.1| 39 CPNCGQVLIRRCYYCR 54
                                  *************998 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.03
                       zf-tcix 13 CpkCGt 18
                                  CpkCG 
  gi|70606567|ref|YP_255437.1| 62 CPKCGF 67
                                  *****6 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.12        34      11      21 ..      16      26 ..      11      31 .. 0.80
   2 ?    4.2   3.4      0.18        49       1      22 [.      21      45 ..      21      46 .. 0.75
   3 ?    0.6   8.3       2.4   6.5e+02       1      20 [.      50      66 ..      39      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                        zf-AN1 11 flpfkCryCgk 21
                                    p+ C++Cgk
  gi|70606567|ref|YP_255437.1| 16 IEPIVCSSCGK 26
                                  45899****98 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.18
                        zf-AN1  1 CsfksCkkkdflp......fkCryCgkv 22
                                  Cs  sC+k ++ p      f C++Cg+v
  gi|70606567|ref|YP_255437.1| 21 CS--SCGKILH-PrekgdeFYCPNCGQV 45
                                  77..7999995.3355667******985 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.4
                        zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                                  C +  C+k++  ++ C++Cg
  gi|70606567|ref|YP_255437.1| 50 CYY--CRKQVV-VYVCPKCG 66
                                  553..777665.67777776 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  14.7      0.38   1.1e+02       1      26 [.      38      66 ..      20      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.38
                      zf-TFIIB  1 kCPkCqdele...eserggveidyCpqCr 26
                                  +CP+C++ l     + r  v +++Cp+C+
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIrrcYYCRKQVVVYVCPKCG 66
                                  7******998676667799*********7 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.13        37       3      16 ..      20      33 ..      19      38 .. 0.79
   2 ?    7.6   0.5     0.011       3.1       3      14 ..      38      49 ..      36      52 .. 0.88
   3 ?    4.5   1.3      0.11        29       3       8 ..      61      66 ..      59      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.13
                                  E-SSS--EEEEEE- CS
                zf-C4_Topoisom  3 kCPkCggdLvlkrg 16
                                   C +Cg+ L+ +++
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREK 33
                                  59*****9999976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                                  E-SSS--EEEEE CS
                zf-C4_Topoisom  3 kCPkCggdLvlk 14
                                   CP Cg+ L+++
  gi|70606567|ref|YP_255437.1| 38 YCPNCGQVLIRR 49
                                  6*****999987 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.11
                                  E-SSS- CS
                zf-C4_Topoisom  3 kCPkCg 8 
                                   CPkCg
  gi|70606567|ref|YP_255437.1| 61 VCPKCG 66
                                  6****9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   6.9      0.79   2.2e+02      11      24 ..      31      44 ..      13      56 .. 0.74
   2 ?    6.4   1.9     0.035       9.7      12      24 ..      55      67 ..      49      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.79
                      zf-Mss51 11 apkhvdfeCpdCGi 24
                                   +k  +f Cp+CG 
  gi|70606567|ref|YP_255437.1| 31 REKGDEFYCPNCGQ 44
                                  466779*******6 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.035
                      zf-Mss51 12 pkhvdfeCpdCGi 24
                                  ++ v + Cp+CG+
  gi|70606567|ref|YP_255437.1| 55 KQVVVYVCPKCGF 67
                                  56689*******7 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.94   2.6e+02       2       8 ..      20      26 ..      19      30 .. 0.87
   2 ?    4.2   4.6      0.25        70       1      16 [.      37      52 ..      37      57 .. 0.83
   3 ?    6.1   0.6      0.06        16       1       8 [.      60      67 ..      60      70 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.94
                                  EETTTTE CS
                       zf-C2H2  2 kCpdCgk 8 
                                  +C+ Cgk
  gi|70606567|ref|YP_255437.1| 20 VCSSCGK 26
                                  7*****9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.25
                                  EEETTTTEEESSHHHH CS
                       zf-C2H2  1 ykCpdCgksFkrksnL 16
                                  ++Cp Cg++  r+  +
  gi|70606567|ref|YP_255437.1| 37 FYCPNCGQVLIRRCYY 52
                                  89*****998887655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.06
                                  EEETTTTE CS
                       zf-C2H2  1 ykCpdCgk 8 
                                  y+Cp+Cg 
  gi|70606567|ref|YP_255437.1| 60 YVCPKCGF 67
                                  9*****96 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1       0.2        56      14      22 ..      18      26 ..      13      27 .. 0.87
   2 ?    8.5   1.0      0.01       2.8       8      21 ..      28      43 ..      26      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.2
                     zf-H2C2_2 14 pyeCplCdk 22
                                  p  C++C+k
  gi|70606567|ref|YP_255437.1| 18 PIVCSSCGK 26
                                  789****98 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.01
                     zf-H2C2_2  8 kHtgek..pyeCplCd 21
                                   H+ ek  ++ Cp C+
  gi|70606567|ref|YP_255437.1| 28 LHPREKgdEFYCPNCG 43
                                  599898656******8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   5.0      0.24        66      20      43 ..      20      42 ..      13      43 .. 0.55
   2 ?    2.2   9.1      0.64   1.8e+02      17      46 .]      35      56 ..      30      56 .. 0.72
   3 ?    5.9   0.5     0.045        12      20      25 ..      61      66 ..      59      70 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                 Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeC 43
                                  vC  Cg+  + r k+   f C  C
  gi|70606567|ref|YP_255437.1| 20 VCSSCGKILHPREKG-DEFYCPNC 42
                                  566666653333333.45555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.64
                 Zn_Tnp_IS1595 17 ngfvCPhCgsrkayriktrglfqCkeCrkq 46
                                  + f CP+Cg      i++     C+ Crkq
  gi|70606567|ref|YP_255437.1| 35 DEFYCPNCG---QVLIRR-----CYYCRKQ 56
                                  6699*****...445554.....7777776 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.045
                 Zn_Tnp_IS1595 20 vCPhCg 25
                                  vCP+Cg
  gi|70606567|ref|YP_255437.1| 61 VCPKCG 66
                                  8****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        82  (0.0045736); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              65  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 438.70
//
Query:       gi|70606568|ref|YP_255438.1|  [L=106]
Description: elongation factor 1-beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.1   0.1    1.5e-18   66.8   0.1    1.1  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.18   11.6   0.0    1.0  1  Alpha-E   A predicted alpha-helical domain with a conserved E


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   1.7e-22   1.5e-18       2      90 .]      21     104 ..      20     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.7e-22
                                   EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEES.SS-GGGGHHHHHHTTS-S.....SE CS
                       EF1_GNE   2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvie.ddkvstdeleekieeiegeledlVq 80 
                                   v+l+v Pe+de +l +l +++k+  l++ + + +  ++epia+Glk+L  ++ ++ +++++td+lee ++ ieg     V+
  gi|70606568|ref|YP_255438.1|  21 VILKVFPESDEINLTQLSEEIKK-RLPEgYRLVK-NETEPIAYGLKALIAYIQMPeNTEGGTDKLEELVNGIEG-----VS 94 
                                   89*********************.87777****6.*******************988999**************.....** PP

                                   EEEEEEEEE- CS
                       EF1_GNE  81 sveivsfnkl 90 
                                   ++e+v++++l
  gi|70606568|ref|YP_255438.1|  95 HAEVVNVTRL 104
                                   *******997 PP

>> Alpha-E  A predicted alpha-helical domain with a conserved ER motif.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.18     201     285 ..      11      94 ..       2      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                       Alpha-E 201 iepervlelLlldednPrSlafqleeleealaalspaeseegrsseaerllgellaelrladieelleglhelldelqeel 281
                                    ++ +v++ L++ + +P S    l +l e++++  p e+ +  ++e+e ++  l+a +++ ++ e +eg  + l+el + +
  gi|70606568|ref|YP_255438.1|  11 HKVIKVADVLVILKVFPESDEINLTQLSEEIKKRLP-EGYRLVKNETEPIAYGLKALIAYIQMPENTEGGTDKLEELVNGI 90 
                                   57789**************************98767.4556799999*************999999977777777777777 PP

                       Alpha-E 282 aels 285
                                   + +s
  gi|70606568|ref|YP_255438.1|  91 EGVS 94 
                                   6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 786.22
//
Query:       gi|70606569|ref|YP_255439.1|  [L=773]
Description: SAV protein-like [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-100  332.2   0.0    5.1e-49  166.1   0.0    2.5  2  AAA              ATPase family associated with various cellul
    1.4e-33  114.4   3.6    4.7e-17   61.5   0.0    3.0  2  AAA_lid_3        AAA+ lid domain
    1.4e-32  111.7   1.8    4.7e-32  110.0   0.9    2.3  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.2e-16   60.8   0.0    4.4e-08   33.0   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.9e-16   57.8   2.2    6.9e-16   57.8   2.2    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    7.7e-15   55.7   0.3    6.9e-06   26.5   0.0    4.7  4  AAA_16           AAA ATPase domain
    1.3e-14   54.7   0.1    8.9e-07   29.2   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    4.5e-12   46.4   1.1     0.0047   17.2   0.0    4.7  4  AAA_22           AAA domain
    1.8e-11   44.2   1.3    0.00041   20.4   0.1    4.2  2  AAA_5            AAA domain (dynein-related subfamily)
    1.7e-10   40.7   0.0    0.00011   21.5   0.0    2.7  2  TIP49            TIP49 P-loop domain
    1.7e-10   41.2   0.0     0.0011   19.1   0.0    2.9  2  AAA_33           AAA domain
    8.8e-10   38.7   0.0     0.0018   18.3   0.0    2.6  2  AAA_14           AAA domain
    1.4e-08   34.6   0.0     0.0044   16.8   0.0    2.9  3  IstB_IS21        IstB-like ATP binding protein
    2.7e-08   34.4   0.0     0.0085   16.6   0.0    3.0  2  AAA_18           AAA domain
    7.8e-08   32.2   2.2    0.00016   21.6   0.1    3.2  2  Vps4_C           Vps4 C terminal oligomerisation domain
    2.8e-07   30.2   0.6     0.0078   15.6   0.1    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.9e-07   29.7   0.0      0.032   13.9   0.0    2.8  2  AAA_24           AAA domain
    8.1e-07   29.4   0.3      0.039   14.2   0.0    3.4  3  AAA_28           AAA domain
    1.4e-06   28.4   0.6      0.029   14.3   0.1    4.2  3  ATPase_2         ATPase domain predominantly from Archaea
    1.5e-06   28.6   0.0       0.04   14.3   0.0    2.9  2  RNA_helicase     RNA helicase
    3.3e-06   26.9   0.1       0.37   10.5   0.0    3.9  2  Sigma54_activat  Sigma-54 interaction domain
    6.5e-06   26.7   0.0       0.15   12.6   0.0    2.7  2  ABC_tran         ABC transporter
    9.2e-06   25.5   0.0       0.11   12.4   0.0    2.9  2  AAA_3            ATPase family associated with various cellul
    9.4e-06   25.0   0.2      0.086   12.1   0.0    3.3  3  Zeta_toxin       Zeta toxin
    1.8e-05   24.7   0.0       0.24   11.4   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.9e-05   23.9   0.0       0.24   10.5   0.0    3.6  3  DUF815           Protein of unknown function (DUF815)
    3.4e-05   23.4   0.0       0.36   10.3   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    6.7e-05   22.9   0.9       0.63    9.9   0.1    3.5  4  NACHT            NACHT domain
    0.00013   21.7   5.9       0.13   11.9   0.3    4.0  3  AAA_25           AAA domain
    0.00016   21.0   0.0       0.27   10.4   0.0    3.3  4  NB-ARC           NB-ARC domain
    0.00022   20.6   0.9        3.6    6.9   0.0    4.2  4  ATPase           KaiC
    0.00024   21.0   0.0      0.053   13.4   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
    0.00057   19.1   0.1       0.99    8.4   0.0    2.4  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00057   20.3   0.1        1.4    9.4   0.0    3.1  2  AAA_17           AAA domain
    0.00089   18.2   0.0        1.3    7.8   0.0    2.7  2  AFG1_ATPase      AFG1-like ATPase
     0.0011   18.5   0.1       0.31   10.5   0.0    2.5  2  PhoH             PhoH-like protein
     0.0025   18.2   0.2        2.7    8.3   0.0    3.1  3  AAA_19           AAA domain
     0.0036   17.0   0.2         16    5.2   0.0    4.1  4  Guanylate_kin    Guanylate kinase
     0.0066   15.9   0.0        3.4    7.1   0.0    3.1  2  TniB             Bacterial TniB protein
     0.0096   15.7   0.1        2.5    7.8   0.0    2.8  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   15.7   3.0          4    7.3   0.0    4.1  3  NTPase_1         NTPase
      0.019   14.7   0.0       0.86    9.3   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.02   14.8   0.0        6.4    6.7   0.0    2.9  2  Rad17            Rad17 P-loop domain
      0.029   14.1   0.0         11    5.8   0.0    2.6  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.035   13.9   0.0        3.2    7.5   0.0    2.4  2  AAA_11           AAA domain
      0.039   13.3   0.2        1.5    8.2   0.1    2.3  2  IPT              Isopentenyl transferase
      0.041   14.0   0.0        9.3    6.4   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.042   13.5   0.0        1.9    8.1   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.05   13.3   0.0        7.9    6.3   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.051   12.8   0.0        9.8    5.3   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.096   12.9   0.0         14    5.9   0.0    2.9  2  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.12   12.1   0.2        6.5    6.4   0.0    2.8  2  Cytidylate_kin   Cytidylate kinase
       0.15   12.1   0.0         12    5.9   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
       0.16   11.5   0.0       0.32   10.4   0.0    1.5  1  UFD1             Ubiquitin fusion degradation protein UFD1


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1   0.0   1.5e-51   5.1e-49       1     132 []     233     363 ..     233     363 .. 0.98
   2 !  163.7   0.0   8.3e-51   2.8e-48       1     131 [.     506     636 ..     506     637 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 1.5e-51
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +llyGppG+GKTllakava+e++++f +i+g+e++sk+ gese+++re+f++ak++a p i+fiDEida+a++r++   e+
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYFTSINGPEIMSKFYGESEQRLREIFEDAKKHA-PAIIFIDEIDAIAPKRDEVIGEV 312
                                   69******************************************************9.****************99***** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                   e+rvv+qLlt +dg++++ ++vivi+atnrp+ +dpal+r gRfdr+iei+l
  gi|70606569|ref|YP_255439.1| 313 ERRVVAQLLTLMDGLENR-GNVIVIAATNRPNAVDPALRRpGRFDREIEIPL 363
                                   *****************7.66****************************985 PP

  == domain 2  score: 163.7 bits;  conditional E-value: 8.3e-51
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   +ll+GppGtGKT+lakava+e+g++f+ + g+e+lsk+vgesek ire+f++a++ a p+++f+DEid++a+ r  +++s+
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAA-PTVIFFDEIDSIAPIRgLSTDSG 585
                                   69******************************************************9.****************98889** PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++er+vnqLl+e+dg +k e+ v+vi+atnrpd ldpallr gRfdr i+++
  gi|70606569|ref|YP_255439.1| 586 VTERIVNQLLAEMDGIEKLEN-VVVIAATNRPDILDPALLRpGRFDRLIYVP 636
                                   ******************865.***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   1.4e-19   4.7e-17       1      39 [.     385     423 ..     385     446 .. 0.83
   2 !   51.5   1.7     2e-16   6.5e-14       1      37 [.     659     695 ..     659     709 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.4e-19
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeit 39 
                                   dvdl++LAe+T+Gy+GADl+al+reAa++Alrr i+ i+
  gi|70606569|ref|YP_255439.1| 385 DVDLHKLAEMTHGYTGADLSALVREAAMNALRRYIQMID 423
                                   9********************************776554 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 2e-16
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgike 37 
                                   dv+l+++Ae+ eGy+GADlaa++reAal+A+r+ + e
  gi|70606569|ref|YP_255439.1| 659 DVSLEDIAEKAEGYTGADLAAVVREAALRAIREQMAE 695
                                   9********************************8764 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.9   1.4e-34   4.7e-32       2      83 ..      21     106 ..      20     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 1.4e-34
                                   EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTT....STTTTEEEE-HHHHHHHT--TTEEE CS
                       CDC48_N   2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepe....degkgiIrmdgvtRknagvsiGdkV 78 
                                   LrV ea+q+dvgrg+vrid + ++++g++pg+vve+eg+rkT+ai+wp++pe    de+k+iIrmdg+tRknagvsiGdkV
  gi|70606569|ref|YP_255439.1|  21 LRVVEAKQKDVGRGKVRIDIDLLSQIGVNPGEVVELEGQRKTAAIAWPLAPEdvlnDEDKYIIRMDGITRKNAGVSIGDKV 101
                                   9***************************************************8888789********************** PP

                                   EEEEE CS
                       CDC48_N  79 tVrka 83 
                                   +Vrk 
  gi|70606569|ref|YP_255439.1| 102 IVRKS 106
                                   ***97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.3e-10   4.4e-08      34     104 ..     231     309 ..     223     349 .. 0.86
   2 !   24.6   0.0   5.4e-08   1.8e-05      32      96 ..     502     574 ..     470     620 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.3e-10
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                                     +llyGpPG+Gkt lak +a+e ++ + +  gP +      e ++ l  ++ + +++   ++fidei  ++++ +ev+
  gi|70606569|ref|YP_255439.1| 231 KGILLYGPPGVGKTLLAKAVANETDAYFTSINGPEImskfygESEQRLREIFEDAKKHapAIIFIDEIDAIAPKRDEVI 309
                                   569*******************************994444334467799999988876336************999987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.4e-08
                        RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrl 96 
                                   +   +ll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++ + ++    v+f dei  +
  gi|70606569|ref|YP_255439.1| 502 PPKGILLFGPPGTGKTMLAKAVATESGANFIAVRGPEIlskwvgESEKAIREIFRKARQAapTVIFFDEIDSI 574
                                   55679*******************************8733333334455666666655432268888888766 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   2.2   2.1e-18   6.9e-16       2      63 ..     125     186 ..     124     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2.1e-18
                                   .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                       CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                   +d ++++y+k+++ + p+++Gd+v ++++gq+i+++Vv + P g+v+++++T+i++++kpve
  gi|70606569|ref|YP_255439.1| 125 VDPGFISYVKKKLKDTPLVEGDTVLIPVLGQAIPFTVVQVRPQGIVIVSDETSITISEKPVE 186
                                   5888999*****************************************************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.1e-08   6.9e-06      18     139 ..     224     335 ..     217     336 .. 0.72
   2 ?   -1.0   0.0         6     2e+03     106     149 ..     420     471 ..     377     483 .. 0.58
   3 !   16.3   0.0   2.9e-05    0.0097      22      57 ..     501     535 ..     491     548 .. 0.77
   4 ?    5.6   0.0     0.058        19     122     147 ..     550     574 ..     546     610 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.1e-08
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                   r+    p  +ll+G++GvGK+ l++++++   +++++f++ +  +      +s +    ++ +l +  +d+++ a +  + 
  gi|70606569|ref|YP_255439.1| 224 RLGIEPPKGILLYGPPGVGKTLLAKAVAN---ETDAYFTSINGPEI-----MSKFYGESEQ-RLREIFEDAKKHAPAIIFI 295
                                   555555699*******************7...5559*********9.....4444444422.3444444444445666666 PP

                        AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvl 139
                                   +++++ +   +e+ g+ ++r+ ++l  l++ l++++  +++
  gi|70606569|ref|YP_255439.1| 296 DEIDAIAPKRDEVIGEVERRVVAQLLTLMDGLENRGN-VIV 335
                                   667777778888888888***********99999776.443 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 6
                        AAA_16 106 a....avpelagaea.......srllellkrllallsrderplvlvlDdlqwade 149
                                   +    +++++++++         ++l ++k+++   +++ r +++ + +++w+d 
  gi|70606569|ref|YP_255439.1| 420 QmidlSQDKIPPEILekmevrmDDFLKAFKDIV---PSGLREIYIEVPEVHWFDI 471
                                   133334455555555555533344444444444...4444448888888888875 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 2.9e-05
                        AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflr 57 
                                     p  +ll G++G+GK+ l+++++++  ++ +i++r
  gi|70606569|ref|YP_255439.1| 501 EPPKGILLFGPPGTGKTMLAKAVATESGAN-FIAVR 535
                                   44699*******************876666.44444 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.058
                        AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                   +++++++++++ + p+v+++D+++ +
  gi|70606569|ref|YP_255439.1| 550 AIREIFRKARQ-AAPTVIFFDEIDSI 574
                                   6788999***9.999********954 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.7e-09   8.9e-07       6     105 ..     233     326 ..     228     344 .. 0.87
   2 !   22.0   0.0   4.2e-07   0.00014       6     103 ..     506     598 ..     501     609 .. 0.78
   3 ?   -1.8   0.1         9     3e+03      76      96 ..     645     666 ..     645     668 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.7e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp gvGkt+laka+a+  ++     ++ ++  e++     + + ++++  ++    a+++   i+++DEid i+pk 
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDA----YFTSINGPEIMS----KFYGESEQRLREIFEDAKKHApaIIFIDEIDAIAPKr 305
                                   8999******************96....************....88888888888988888888888************97 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   ++   +v r  V+  LL +++g
  gi|70606569|ref|YP_255439.1| 306 DEVIGEVERR-VVAQLLTLMDG 326
                                   7777777775.77778899987 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.2e-07
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt+laka+a    +    ++i +   e+l     + + ++++  ++   +a +    ++++DEid i+p  
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGA----NFIAVRGPEILS----KWVGESEKAIREIFRKARQAAptVIFFDEIDSIAPIr 578
                                   7899****************9996....9**********9....66666666666666666666688************85 PP

                                   ---------HHHHHHHHHHH CS
                         AAA_2  84 essgadvSregVqrdLLqil 103
                                   + s+     e +++ LL  +
  gi|70606569|ref|YP_255439.1| 579 GLSTDSGVTERIVNQLLAEM 598
                                   44444444566667666555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9
                                   TGGG----.---------HHHH CS
                         AAA_2  76 EidKihpk.essgadvSregVq 96 
                                   Ei K+h k     +dvS e++ 
  gi|70606569|ref|YP_255439.1| 645 EILKVHTKnVPLAEDVSLEDIA 666
                                   7889**9999999*******96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-05    0.0047       8      32 ..     233     257 ..     227     269 .. 0.85
   2 ?    6.5   0.0     0.028       9.4      72     117 ..     272     325 ..     262     341 .. 0.67
   3 !   16.1   0.0   3.2e-05     0.011       8      29 ..     506     527 ..     500     540 .. 0.84
   4 ?    0.7   0.0       1.8   5.9e+02      83     110 ..     552     592 ..     544     618 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldee 32 
                                   ++++G++G+GKT+l++ ++++ d++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAY 257
                                   89******************99765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.028
                        AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrslln 117
                                   + s+++l+e +e+a +++ +  ++ iDE++ +   +         +++ +L +l++
  gi|70606569|ref|YP_255439.1| 272 GESEQRLREIFEDAKKHAPA--IIFIDEIDAIApkRdevigeveRRVVAQLLTLMD 325
                                   56788888888888888877..*********9875333444444444444444444 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3.2e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                   ++++G++GtGKT+l++ ++ + 
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATES 527
                                   89**************998875 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.8
                        AAA_22  83 eqalrarav..ielliiDEaqhlr.....s......eeale 110
                                   ++ +r+++   + ++  DE++ +      s      e++++
  gi|70606569|ref|YP_255439.1| 552 REIFRKARQaaPTVIFFDEIDSIApirglStdsgvtERIVN 592
                                   3333333334447********99655444144344444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.2e-06   0.00041       2     136 ..     233     351 ..     232     352 .. 0.70
   2 !   18.9   0.1   3.4e-06    0.0011       2     134 ..     506     623 ..     505     626 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-06
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--.. CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae.. 78 
                                   +lL GppG+gK+ la+ +a  + + ++ +++++ +++  + g+ e        +  ++ + a+   ++i+++DE++ +   
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYFTSINGPEIMSK--FYGESEQ-------RLREIFEDAKkhAPAIIFIDEIDAIApk 304
                                   89*******************************8875..5555552.......23344444445689*********88722 PP

                                   .HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                         AAA_5  79 .sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                    +ev++++ +          ++ +l++  ++    ++ via++n+++     ++palr+
  gi|70606569|ref|YP_255439.1| 305 rDEVIGEVERRVVA------QLLTLMDGLENR--GNVIVIAATNRPN----AVDPALRR 351
                                   34566666444444......455555444431..2299999999998....77888876 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.4e-06
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                                   +lL GppGtgK++la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   + ++++DE++ + + 
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGANFIAVRGPE------ILSKWV---GESEKAIREIFRKARqaAPTVIFFDEIDSIAPI 577
                                   89*************************999997......777887...566666677777777688899999999988754 PP

                                   HHHHHHHHHHSSEE.E...-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                         AAA_5  81 vlnsLlslleerrl.l.leeggelvkaknddllerfrviatanpldrslnelspal 134
                                      s  s   er + + l+e+++ +k +n      + via++n++d     l+pal
  gi|70606569|ref|YP_255439.1| 578 RGLSTDSGVTERIVnQlLAEMDGIEKLEN------VVVIAATNRPD----ILDPAL 623
                                   43333343444333121344444444444......88888888888....556665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05    0.0046      51      96 ..     231     274 ..     223     299 .. 0.87
   2 !   21.5   0.0   3.3e-07   0.00011      51     106 ..     504     558 ..     496     562 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                   +++Ll Gp+g Gkt la a+++e   d  f++++g e+ s     +
  gi|70606569|ref|YP_255439.1| 231 KGILLYGPPGVGKTLLAKAVANET--DAYFTSINGPEIMSKFYGES 274
                                   89********************96..699*********99755554 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.3e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                   +++Ll Gp+gtGkt la a++ e g    f+a+ g e+ s  v  +e ++ + +rk+
  gi|70606569|ref|YP_255439.1| 504 KGILLFGPPGTGKTMLAKAVATESG--ANFIAVRGPEILSKWVGESEkAIREIFRKA 558
                                   89********************988..78**************99985688999997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.4e-06    0.0011       2      79 ..     233     340 ..     233     397 .. 0.75
   2 !   19.0   0.0   3.7e-06    0.0012       2      47 ..     506     559 ..     506     643 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   +ll G+pG+GK+ la+ ++++++  ++ ++ ++++++ +g+ +q+++                               +v+
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDayFTSINGPEIMSKFYGESEQRLReifedakkhapaiifideidaiapkrdeVIGEVE 313
                                   6789***************999997777************98888886677777777777777777766665443222344 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatn 79 
                                    r+ ++l  l +    +g+ +++ atn
  gi|70606569|ref|YP_255439.1| 314 RRVVAQLLTLMDGLENRGNVIVIAATN 340
                                   455555555554433444444445554 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.7e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt......d 47 
                                   +ll G+pG+GK+ la+ ++ + g  ++ ++ ++++++ +g+ ++ ++      +
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGanFIAVRGPEILSKWVGESEKAIReifrkaR 559
                                   6899*******************9999999999888888876665553333330 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.4e-06    0.0018       5      77 ..     233     302 ..     230     342 .. 0.72
   2 !   17.6   0.0   9.2e-06    0.0031       5      76 ..     506     574 ..     503     611 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.4e-06
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                   +++ G+  vGKT l+k +++e       +  in  +   k + ++e+ l++i+e +k++   ++f+DEi  + 
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETD---AYFTSINGPEIMSKFYGESEQRLREIFEDAKKHAPAIIFIDEIDAIA 302
                                   7899**************98888...7777777777666666666656667777666678999******9883 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 9.2e-06
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT+l+k ++ e+     +++ +   +   k   ++ek +++i++k+++   t++f+DEi  +
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESG---ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPTVIFFDEIDSI 574
                                   7899***************9999...99999999999998888877777777777656699********987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.3e-05     0.024      47      70 ..     230     253 ..     220     300 .. 0.88
   2 !   16.8   0.0   1.3e-05    0.0044      44      72 ..     500     528 ..     488     571 .. 0.86
   3 ?   -1.8   0.0       6.5   2.2e+03      28      53 ..     584     610 ..     580     613 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.3e-05
                     IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                    ++i+l Gp+GvGK+ la a++ e
  gi|70606569|ref|YP_255439.1| 230 PKGILLYGPPGVGKTLLAKAVANE 253
                                   5789**************999876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.3e-05
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgveav 72 
                                   ie  ++i+l+Gp+G+GK+ la a+++e  
  gi|70606569|ref|YP_255439.1| 500 IEPPKGILLFGPPGTGKTMLAKAVATESG 528
                                   5667899*****************98765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.5
                     IstB_IS21  28 rsldkrkvkeL.atlsfiekkenivll 53 
                                    ++ +r+v++L a+++ iek en+v++
  gi|70606569|ref|YP_255439.1| 584 SGVTERIVNQLlAEMDGIEKLENVVVI 610
                                   567889998665999*********997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.5e-05    0.0085       1      36 [.     233     276 ..     233     342 .. 0.65
   2 !   14.6   0.0   0.00011     0.035       1      27 [.     506     530 ..     506     609 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakeng 36 
                                   Ill G+pGvGKt lak++++++ ++        + ++++   ++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETdAYftsingpEIMSKFYGESEQ 276
                                   99******************997778877777333333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00011
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvn 27 
                                   Ill G+pG+GKt lak+++ +   g n
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATES--GAN 530
                                   99****************8775..333 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0049       1.6      16      44 ..     426     454 ..     419     455 .. 0.79
   2 !   21.6   0.1   4.7e-07   0.00016       4      58 ..     704     756 ..     703     758 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0049
                        Vps4_C  16 wmdipsdkllePpvtlkDflkalkkarpt 44 
                                     +ip++ l + +v+++Dflka k   p+
  gi|70606569|ref|YP_255439.1| 426 QDKIPPEILEKMEVRMDDFLKAFKDIVPS 454
                                   556886666667***********998886 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.7e-07
                        Vps4_C   4 CspgdpgaiemtwmdipsdkllePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                   C+++d +++e++++d  + k   + v++k+f+ alkk+rp+V+++ ++ ++++ +
  gi|70606569|ref|YP_255439.1| 704 CKKSDIECREKKIRDCMAGK--GRIVERKHFDVALKKVRPSVTQDMIQFYQNWLE 756
                                   77777788888888877554..5789***************************86 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00031       0.1      25      42 ..     233     250 ..     230     254 .. 0.90
   2 !   15.6   0.1   2.4e-05    0.0078      25      43 ..     506     524 ..     499     527 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                   +ll+GppG GKt+lak++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAV 250
                                   89*************987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.4e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKtmlak+++
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVA 524
                                   89*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   9.8e-05     0.032       5      77 ..     233     301 ..     230     347 .. 0.69
   2 !   12.6   0.0   0.00024     0.081       5      35 ..     506     529 ..     503     579 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-05
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...swedfldevvelaaeladyktlviDtidel 77 
                                   il+yGp+g+GKT lak          t++ + s+++ ++ +     s + +++ ++    +++   +++iD id +
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAV-----ANETDAYFTSINGPEIMSKFygeSEQRLREIFEDA--KKHAPAIIFIDEIDAI 301
                                   89*************998.....33445544444444444222332333333333333..3333466666666655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00024
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGl 35 
                                   il++Gp+g+GKT+lak          te G+
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAV-------ATESGA 529
                                   89*************998.......556655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0011      0.36       2      48 ..     233     284 ..     232     307 .. 0.75
   2 !   14.2   0.0   0.00012     0.039       2      46 ..     506     551 ..     505     570 .. 0.72
   3 ?   -0.6   0.2       4.3   1.4e+03      44      65 ..     738     760 ..     661     772 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpw 48 
                                   i + G+++ GKT l++a a++    ++ +  pE++ +++ e  ++ +++ ++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANEtdaYFTSIngPEIMSKFYGESEQRLREIFED 284
                                   7899***************765653444458888888887776666655554 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00012
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedal 46 
                                   i ++G+++tGKT l++a a + g + ++  + eil++   + e+a+
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATEsGANFIAVRGPEILSKWVGESEKAI 551
                                   789****************766777666555555555554444444 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4.3
                        AAA_28  44 dalpwv.edllafaervleeqle 65 
                                   +  p+v +d+++f +  le++++
  gi|70606569|ref|YP_255439.1| 738 KVRPSVtQDMIQFYQNWLEKARQ 760
                                   23344445555555555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   8.9e-05     0.029      15     122 ..     225     336 ..     219     345 .. 0.61
   2 ?    6.8   0.0     0.017       5.5      12      44 ..     495     527 ..     490     535 .. 0.82
   3 ?    1.1   0.0      0.94   3.1e+02     103     151 ..     548     600 ..     528     615 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.9e-05
                      ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............. 82 
                                   l  ep + +++YGp g+GKt L k ++++ +       y++++++ +i ++       e++++l++ +             
  gi|70606569|ref|YP_255439.1| 225 LGIEPPKGILLYGPPGVGKTLLAKAVANETDA------YFTSINGPEIMSKFYG----ESEQRLREIFedakkhapaiifi 295
                                   5567788899**********999999999843......5555555555555444....22222222222223444445666 PP

                      ATPase_2  83 .giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                     i+    + +e++ e  + v +++  l++ ++++g  i+i
  gi|70606569|ref|YP_255439.1| 296 dEIDAIAPKRDEVIGEVERRVVAQLLTLMDGLENRGNVIVI 336
                                   64444444455556666666666676777777777665555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                      ATPase_2  12 eeilerepneiyfiYGpegsGKtaLlkeiienl 44 
                                    e ++ ep + ++++Gp g GKt L k +++++
  gi|70606569|ref|YP_255439.1| 495 YENMSIEPPKGILLFGPPGTGKTMLAKAVATES 527
                                   5566678888899**************998765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.94
                      ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqklidlgln.......gaellvkeLlnlies 151
                                   +    +++++i +k+++    +i++De+  +  +  +         e  v++Ll  ++ 
  gi|70606569|ref|YP_255439.1| 548 E----KAIREIFRKARQaapTVIFFDEIDSIAPI--RglstdsgVTERIVNQLLAEMDG 600
                                   4....445555555555565899****9988733..22223333445555555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00012      0.04       1      34 [.     233     266 ..     233     341 .. 0.74
   2 !   11.5   0.0   0.00091       0.3       1      26 [.     506     531 ..     506     614 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00012
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsv 34 
                                   i+lyGp+g+GK++lak +a++    + +++ +++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYFTSINGPEI 266
                                   789**************99988766644444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00091
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i+l+Gp+g+GK++lak +a++   ++
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGANF 531
                                   689**************888766554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0011      0.37      23      73 ..     231     273 ..     220     349 .. 0.62
   2 !   10.3   0.0    0.0012      0.41      22      55 ..     503     533 ..     490     617 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEB CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGh 73 
                                     +l+ G  G+GK+lla+a+ +++   ++ f ++n  +i     +s+++G 
  gi|70606569|ref|YP_255439.1| 231 KGILLYGPPGVGKTLLAKAVANET---DAYFTSINGPEI-----MSKFYGE 273
                                   569****************98755...577888876654.....3445554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                                   SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfva 55 
                                   +  +l+ G  GtGK++la+a+ ++s    ++f+a
  gi|70606569|ref|YP_255439.1| 503 PKGILLFGPPGTGKTMLAKAVATESG---ANFIA 533
                                   5679****************987765...45555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.003      0.98       7      42 ..     226     261 ..     224     288 .. 0.74
   2 !   12.6   0.0   0.00046      0.15       5      74 ..     497     565 ..     496     614 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.003
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGei 42 
                                    +++ + + + G+ G GK+ L+k++a++++    +i
  gi|70606569|ref|YP_255439.1| 226 GIEPPKGILLYGPPGVGKTLLAKAVANETDAYFTSI 261
                                   6777788899*****************998866665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00046
                                   EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                      ABC_tran   5 slklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpel 74 
                                   ++++++ + + ++G+ G+GK+ L+k++a ++   +  i ++g ++ ++   +++k i+ ++ +  q  p++
  gi|70606569|ref|YP_255439.1| 497 NMSIEPPKGILLFGPPGTGKTMLAKAVATESG--ANFIAVRGPEILSKWVGESEKAIREIFRKaRQAAPTV 565
                                   5788999999******************9985..5677778888888777777777777777745555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00032      0.11       2      37 ..     233     267 ..     232     345 .. 0.72
   2 !   10.0   0.0    0.0017      0.57       2     110 ..     506     614 ..     505     626 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00032
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdll 37 
                                   +ll g PG++ktll+ka+a+  d+ f+ i   p+++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYFTSIN-GPEIM 267
                                   7999********************999986.45555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrapp....kt 78 
                                   +ll g PG++kt+l+ka+a+  +++f  ++  p++l    +G +  e++ +e+  k+      +++ dei+  +p     t
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGANFIAVR-GPEILSK-WVGES--EKAIREIFRKARQAAPTVIFFDEIDSIAPirglST 582
                                   78999****************999998776.4666543.33433..22223333333333445566666665444222235 PP

                         AAA_3  79 qsalleameerqvtvegethklpepflvlatq 110
                                   +s + e + ++ ++  +   kl++  ++ at+
  gi|70606569|ref|YP_255439.1| 583 DSGVTERIVNQLLAEMDGIEKLENVVVIAATN 614
                                   55566666555555555555665555555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0     0.004       1.3      14      41 ..     228     255 ..     219     264 .. 0.87
   2 !   12.1   0.0   0.00026     0.086      12      49 ..     499     534 ..     490     539 .. 0.84
   3 ?   -0.2   0.0       1.5     5e+02     139     171 ..     708     744 ..     700     750 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.004
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdele 41 
                                   e Pk ill G pG GK+ la+++++e++
  gi|70606569|ref|YP_255439.1| 228 EPPKGILLYGPPGVGKTLLAKAVANETD 255
                                   6799********************9986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00026
                    Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                   s e Pk ill G pG GK+ la+++++e   + n++ +
  gi|70606569|ref|YP_255439.1| 499 SIEPPKGILLFGPPGTGKTMLAKAVATES--GANFIAV 534
                                   4578************************8..7777766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.5
                    Zeta_toxin 139 gvldRyeee...vae..gRlvpkeehdeafeglresve 171
                                   +++ R+++    + +  gR+v+ +++d a +++r sv 
  gi|70606569|ref|YP_255439.1| 708 DIECREKKIrdcM-AgkGRIVERKHFDVALKKVRPSVT 744
                                   5666777665542.1459***********999888775 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0013      0.44      19      45 ..     230     256 ..     201     276 .. 0.75
   2 !   11.4   0.0   0.00071      0.24      20      51 ..     504     537 ..     474     541 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0013
                                   TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                    + ilL+G+ G+GKT l++++a++ + 
  gi|70606569|ref|YP_255439.1| 230 PKGILLYGPPGVGKTLLAKAVANETDA 256
                                   3459******************98765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00071
                                   EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   + ilL G+ G+GKT+l++++a + g +  +v+ P
  gi|70606569|ref|YP_255439.1| 504 KGILLFGPPGTGKTMLAKAVATESGANfiAVRGP 537
                                   349*******************999887777665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0066       2.2      52      81 ..     229     258 ..     220     350 .. 0.64
   2 ?    1.2   0.0       0.5   1.6e+02      59     103 ..     396     438 ..     391     451 .. 0.81
   3 !   10.5   0.0   0.00072      0.24      48     115 ..     498     570 ..     457     623 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0066
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg 81 
                                   p + +LL+G  G+GK  l ka+ ne+ +  
  gi|70606569|ref|YP_255439.1| 229 PPKGILLYGPPGVGKTLLAKAVANETDAYF 258
                                   55779******************9987654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                        DUF815  59 wGarGtGKSslvkallneyaeegLrlievekedlkelpklvellr 103
                                    G  G+  S+lv+ +  ++ ++ +++i+++++++   p+++e+++
  gi|70606569|ref|YP_255439.1| 396 HGYTGADLSALVREAAMNALRRYIQMIDLSQDKIP--PEILEKME 438
                                   58889999***********************9875..55555555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00072
                        DUF815  48 leglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellr...erperfilfvDD 115
                                   ++ +p + +LL+G  GtGK  l ka+ +e  ++   +r  e+  + + e +k ++++    +++   ++f D 
  gi|70606569|ref|YP_255439.1| 498 MSIEPPKGILLFGPPGTGKTMLAKAVATESGANFiaVRGPEILSKWVGESEKAIREIFrkaRQAAPTVIFFDE 570
                                   45567889********************999887445556777766666655554443111223345666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.36      33      61 ..     230     257 ..     220     307 .. 0.82
   2 !   10.1   0.0    0.0013      0.43      30      56 ..     500     526 ..     491     535 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkldkek 61 
                                    k +ll+Gp G+GKt+++k + ++ d   
  gi|70606569|ref|YP_255439.1| 230 PKGILLYGPPGVGKTLLAKAVANETD-AY 257
                                   5789****************999988.33 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkk 56 
                                   ++  k +ll Gp GtGKt+++k + ++
  gi|70606569|ref|YP_255439.1| 500 IEPPKGILLFGPPGTGKTMLAKAVATE 526
                                   5666889*************9986654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0029      0.96       3      23 ..     233     253 ..     231     332 .. 0.87
   2 ?   -1.5   0.0       6.3   2.1e+03      84     119 ..     292     330 ..     265     351 .. 0.56
   3 !    9.9   0.1    0.0019      0.63       3      23 ..     506     526 ..     504     530 .. 0.89
   4 ?   -1.8   0.0       7.7   2.5e+03      63      99 ..     545     580 ..     538     618 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   ++l G++G+GKT L++ +a +
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANE 253
                                   7899************99976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.3
                                   EEEEE-STT-SS-TCH............HHHHHCTTTTT CS
                         NACHT  84 LlilDglDelvtdlgq...kekqpvrtlLselirkkllp 119
                                    + +D +D ++ + ++   + +++v   L +l+ +   +
  gi|70606569|ref|YP_255439.1| 292 IIFIDEIDAIAPKRDEvigEVERRVVAQLLTLMDGLENR 330
                                   344566666666666666633333333333555554444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0019
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   ++l G++G GKT+L++ +a++
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATE 526
                                   6789************99976 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.7
                                   TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                         NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq 99 
                                    e++++++e +   ++++  +++ +D +D ++ + g 
  gi|70606569|ref|YP_255439.1| 545 GESEKAIRE-IFRKARQAAPTVIFFDEIDSIAPIRGL 580
                                   556666666.333456667777888999988887776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1     0.007       2.3      36      53 ..     233     250 ..     227     254 .. 0.87
   2 ?    1.6   0.1      0.54   1.8e+02     128     175 ..     276     323 ..     249     339 .. 0.75
   3 !   11.9   0.3   0.00038      0.13      36     147 ..     506     608 ..     500     610 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                        AAA_25  36 allaGapgtGKttlaldl 53 
                                   +ll+G+pg+GKt la  +
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAV 250
                                   69***********99655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.54
                        AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeri 175
                                   + ++++ +++++ + ++ + iD ++++ +   +   +v +++v++l  +
  gi|70606569|ref|YP_255439.1| 276 QRLREIFEDAKK-HAPAIIFIDEIDAIAPKRDEVIGEVeRRVVAQLLTL 323
                                   557788999999.77***********99995444555548888777655 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00038
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpL 116
                                   +ll+G+pgtGKt+la    +a+ +G ++   + pe    ++   E +    r+ +r++++a+  +   ++  +++  +++ 
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKA--VATESGANFIAVRGPEILSKWVGESEKAI---REIFRKARQAA--PTVIFFDEIDSIAPIR- 578
                                   69***********9864..44446777755333344444444444444...44444444444..3445555543333333. PP

                        AAA_25 117 fakdrggtlltadvdaleaaieevegvrlvv 147
                                     + +++ ++++ v++l a+++ +e+++ vv
  gi|70606569|ref|YP_255439.1| 579 -GLSTDSGVTERIVNQLLAEMDGIEKLENVV 608
                                   .344444445566777777777777665555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0008      0.27      23      45 ..     233     255 ..     220     261 .. 0.85
   2 ?   -2.1   0.0       5.2   1.7e+03     120     148 ..     358     387 ..     356     414 .. 0.86
   3 ?    5.9   0.0     0.019       6.4      23      43 ..     506     526 ..     490     534 .. 0.82
   4 ?   -1.2   0.0       2.7   9.1e+02      57     104 ..     635     725 ..     624     727 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0008
                                   EEEEESTTSSHHHHHHHHCCSHC CS
                        NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                   + l+G +GvGKt lak + n+ d
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETD 255
                                   779***************99955 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
                                   ....HHHHCHTTSEEE.EEESBCCCCCCS- CS
                        NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavs 148
                                   +i ++lp+++ rl++l + TR++ +++ v 
  gi|70606569|ref|YP_255439.1| 358 EIEIPLPDKQGRLEILqIHTRNMPLSKDVD 387
                                   7999*********99867899999888765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.019
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   + l G +G GKt lak +  +
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATE 526
                                   7799************99876 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.7
                                   E...........................................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHH CS
                        NB-ARC  57 v...........................................vvsktdkseeiletilkeLslseddleekeeveslkr 94 
                                   v                                            v ++   + i e++++ +++++++ ++ +  e +++
  gi|70606569|ref|YP_255439.1| 635 VpppdktarfeilkvhtknvplaedvslediaekaegytgadlaAVVREAALRAIREQMAECMGEANNECKKSD-IECREK 714
                                   55555555555555555555555555555555555555555555677777888888888888888866666555.444889 PP

                                   HHHHHCCCT.T CS
                        NB-ARC  95 klvrlLltk.r 104
                                   k++  + +k r
  gi|70606569|ref|YP_255439.1| 715 KIRDCMAGKgR 725
                                   99988888855 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       3.6      14      37 ..     225     248 ..     197     254 .. 0.78
   2 ?    0.9   0.0      0.73   2.4e+02     109     154 ..     276     327 ..     263     344 .. 0.69
   3 ?    6.9   0.0     0.011       3.6      22      40 ..     506     524 ..     499     536 .. 0.84
   4 ?   -0.1   0.0       1.4   4.8e+02     125     153 ..     571     600 ..     540     612 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                        ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                    Gi   + +l++G pG GKt++a+
  gi|70606569|ref|YP_255439.1| 225 LGIEPPKGILLYGPPGVGKTLLAK 248
                                   68888899**************97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.73
                        ATPase 109 eelaeaikeika...krvviDsitglayeeke...avaReilrqlvrvlkkl 154
                                   ++l+e+ ++ k      + iD i+++a + +e   +v R+ + ql++ + +l
  gi|70606569|ref|YP_255439.1| 276 QRLREIFEDAKKhapAIIFIDEIDAIAPKRDEvigEVERRVVAQLLTLMDGL 327
                                   55666665555433477999***99944444422245789999999888665 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                        ATPase  22 vlitGepGtGKtifalqFl 40 
                                   +l+ G pGtGKt++a+  +
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVA 524
                                   899***********98755 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.4
                        ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlkk 153
                                   iDsi+++   ++++ v+ +i+ ql+ ++ +
  gi|70606569|ref|YP_255439.1| 571 IDSIAPIrGLSTDSGVTERIVNQLLAEMDG 600
                                   899999988888889999999999999965 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00016     0.053      37     178 ..     233     376 ..     228     421 .. 0.73
   2 ?    4.3   0.0     0.093        31      37      63 ..     506     532 ..     496     670 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT-H... CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagke... 113
                                   +++yg+ G+Gkt L ka++ne+ + +     + +++ e ++++    +++  e f +  + +  ++ iD+i  +a k    
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYF-----TSINGPEIMSKFYGESEQRLREIFEDAKKhAPAIIFIDEIDAIAPKRdev 308
                                   79****************99876655.....55778888888888877777777777666244677899999999885222 PP

                                   ......HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHH CS
                      Bac_DnaA 114 ......ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkk 178
                                         ++  +l+++++ l + g+ +v+++   P++++    r   rf++   ++i  pd++ rl+il+ +
  gi|70606569|ref|YP_255439.1| 309 igeverRVVAQLLTLMDGLENRGNVIVIAATNRPNAVDPAL-RRPGRFDR--EIEIPLPDKQGRLEILQIH 376
                                   22111234567888889999999999999999999876543.33567776..4566778888888888643 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.093
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                   ++++g+ G Gkt L ka++ e  +n+ 
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGANFI 532
                                   799***************998766655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0042       1.4     117     141 ..     233     257 ..     227     260 .. 0.90
   2 !    8.4   0.0     0.003      0.99     117     136 ..     506     525 ..     498     530 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0042
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                   +++yGp+  Gkt la+a a+ ++ y
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAY 257
                                   89*****************988765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.003
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   ++++Gp+ tGkt+la+a a+
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVAT 525
                                   899**************987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0041       1.4       1      31 [.     236     268 ..     236     309 .. 0.76
   2 ?    7.5   0.0     0.016       5.3       1      24 [.     509     532 ..     509     568 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0041
                                   EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllr 31 
                                   +G+PG+GK+ +++ ++ +    ft ++  +++ 
  gi|70606569|ref|YP_255439.1| 236 YGPPGVGKTLLAKAVANETdaYFTSINGPEIMS 268
                                   7***********999987644688887666655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                                   EE-TTSSHHHHHHHHHHHHTEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                   +G+PG GK+ +++ ++ + g  ++
  gi|70606569|ref|YP_255439.1| 509 FGPPGTGKTMLAKAVATESGANFI 532
                                   6*************9999876655 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.004       1.3      56      80 ..     224     248 ..     205     342 .. 0.81
   2 !    7.6   0.0    0.0048       1.6      57      79 ..     498     520 ..     474     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.004
                   AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylmd 80 
                                   r   ep++g+ l+G+ G+GKt l  
  gi|70606569|ref|YP_255439.1| 224 RLGIEPPKGILLYGPPGVGKTLLAK 248
                                   44679****************9964 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0048
                   AFG1_ATPase  57 ksvepvrglYlwGgvGrGKtylm 79 
                                    s ep++g+ l G+ G GKt+l 
  gi|70606569|ref|YP_255439.1| 498 MSIEPPKGILLFGPPGTGKTMLA 520
                                   4679*****************95 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.04        13      23      40 ..     234     251 ..     227     257 .. 0.87
   2 !   10.5   0.0   0.00094      0.31      22      42 ..     506     526 ..     492     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.04
                                   EEE--TTSSTTHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavala 40 
                                      Gp G GKt+la a+a
  gi|70606569|ref|YP_255439.1| 234 LLYGPPGVGKTLLAKAVA 251
                                   578***********9998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00094
                                   EEEE--TTSSTTHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalave 42 
                                   +  +Gp GtGKt+la a+a e
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATE 526
                                   6789************99976 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.046        15      11      36 ..     231     256 ..     227     302 .. 0.74
   2 ?   -0.7   0.0       4.9   1.6e+03      97     127 ..     284     314 ..     259     325 .. 0.72
   3 !    8.3   0.0    0.0081       2.7      11      31 ..     504     524 ..     497     578 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.046
                        AAA_19  11 kvllvtaGpGtGKTrvlkhivallve 36 
                                   k +l+ ++pG GKT + k++ ++  +
  gi|70606569|ref|YP_255439.1| 231 KGILLYGPPGVGKTLLAKAVANETDA 256
                                   56899*********998887766555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.9
                        AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallg 127
                                   + k ++ +++++DE+  + +   +++ ++  
  gi|70606569|ref|YP_255439.1| 284 DAKKHAPAIIFIDEIDAIAPKRDEVIGEVER 314
                                   3333345699*****9999888888877764 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0081
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                   k +l+ ++pGtGKT + k++ 
  gi|70606569|ref|YP_255439.1| 504 KGILLFGPPGTGKTMLAKAVA 524
                                   56899*********9877665 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.095        31       4      31 ..     232     259 ..     230     266 .. 0.88
   2 ?    1.8   0.0      0.49   1.6e+02      75      99 ..     267     294 ..     261     306 .. 0.77
   3 ?    5.2   0.0     0.047        16       4      30 ..     505     531 ..     503     537 .. 0.87
   4 ?   -0.8   0.0       3.2   1.1e+03      77      96 ..     542     561 ..     535     578 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.095
                                   EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                    + l gp g+Gk  l ka+ +e   +f+
  gi|70606569|ref|YP_255439.1| 232 GILLYGPPGVGKTLLAKAVANETDAYFT 259
                                   6899****************99999996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.49
                                   TTEEEEEEHHHHHHHHHTTSE...EEEE CS
                 Guanylate_kin  75 sgnlygtsveaieevlekgki...viLD 99 
                                    ++ yg+s +  +e++e +k+   +i+ 
  gi|70606569|ref|YP_255439.1| 267 MSKFYGESEQRLREIFEDAKKhapAIIF 294
                                   5789*************99986664444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.047
                                   EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                    + l gp g+Gk +l ka+ +e   +f
  gi|70606569|ref|YP_255439.1| 505 GILLFGPPGTGKTMLAKAVATESGANF 531
                                   6899**************999988777 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.2
                                   EEEEEEHHHHHHHHHTTSEE CS
                 Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                   +  g+s +ai+e++ k++++
  gi|70606569|ref|YP_255439.1| 542 KWVGESEKAIREIFRKARQA 561
                                   56799**********99985 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.045        15      26      60 ..     221     255 ..     200     268 .. 0.78
   2 ?    7.1   0.0      0.01       3.4      28      57 ..     496     525 ..     463     534 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.045
                          TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60 
                                   L+++   + ++ +ll+G++ +GKt +++  a++  
  gi|70606569|ref|YP_255439.1| 221 LFKRLGIEPPKGILLYGPPGVGKTLLAKAVANETD 255
                                   455555566789**************998877665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                          TniB  28 eypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                   e+ + + ++ +ll+G++ +GKtm+++  a 
  gi|70606569|ref|YP_255439.1| 496 ENMSIEPPKGILLFGPPGTGKTMLAKAVAT 525
                                   44444556889*************997665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.064        21      22      40 ..     234     252 ..     222     263 .. 0.86
   2 !    7.8   0.0    0.0075       2.5      22      40 ..     507     525 ..     492     536 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.064
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+G GKt + ka+++
  gi|70606569|ref|YP_255439.1| 234 LLYGPPGVGKTLLAKAVAN 252
                                   688**********999976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0075
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+GtGKt++ ka++ 
  gi|70606569|ref|YP_255439.1| 507 LLFGPPGTGKTMLAKAVAT 525
                                   688**********999864 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.012         4       2      25 ..     233     256 ..     232     279 .. 0.82
   2 ?    0.2   0.1       1.8   6.1e+02      82     116 ..     275     310 ..     267     343 .. 0.70
   3 ?    5.1   0.0     0.056        19       2      23 ..     506     527 ..     505     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                                   EEEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                   +++ GppGvGKt l k v+++ + 
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDA 256
                                   6788************99998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHH-.EEEE---STTGGG-HHHHH CS
                      NTPase_1  82 eelalealrkalsead.viviDEiGkmElkskkfke 116
                                   e+   e+++ a ++a  +i iDEi  +  k  +++ 
  gi|70606569|ref|YP_255439.1| 275 EQRLREIFEDAKKHAPaIIFIDEIDAIAPKRDEVIG 310
                                   666667777777444448999998665555555544 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.056
                                   EEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                   +++ GppG+GKt l k v+ + 
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATES 527
                                   6788**********99998765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       0.2        67       4      71 ..     236     298 ..     233     303 .. 0.78
   2 ?    9.3   0.0    0.0026      0.86       3      71 ..     508     571 ..     506     587 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.2
               Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+ l + ++++    +t+++   e+ ++   +++++  + ++++ +++       i+++DE+
  gi|70606569|ref|YP_255439.1| 236 YGPPGVGKTLLAKAVANETdAYFTSING-PEIMSKFYGESEQRLREIFEDAKKHAP-----AIIFIDEI 298
                                   588**************99988888888.777777767777777777777777765.....48888987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
               Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + ++++ +a+       ++++DE+
  gi|70606569|ref|YP_255439.1| 508 LFGPPGTGKTMLAKAVATESgANFIAVRG-PEILSKWVGESEKAIREIFRKARQAAPT-----VIFFDEI 571
                                   5688*************999*88888888.9*******99999999999999988754.....8999997 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.11        36      48      83 ..     233     267 ..     221     299 .. 0.72
   2 ?    6.7   0.0     0.019       6.4      47      80 ..     505     538 ..     485     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslk 83 
                                   +L+ GP+G gk+   k ++ e    +   +n+ ++ 
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDA-YFTSINGPEIM 267
                                   6789********999999988654.44556655554 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                         Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpv 80 
                                    +L+ GP+G gk+   k ++ e g +++    p 
  gi|70606569|ref|YP_255439.1| 505 GILLFGPPGTGKTMLAKAVATESGANFIAVRGPE 538
                                   35678*****************999988766665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.042        14       2      28 ..     231     257 ..     230     261 .. 0.88
   2 ?    5.8   0.0     0.032        11       2      24 ..     504     526 ..     503     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.042
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                   k ill G+ g+GKt L++a+ +e+  Y
  gi|70606569|ref|YP_255439.1| 231 KGILLYGPPGVGKTLLAKAVANETDAY 257
                                   6699****************9987666 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.032
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k ill+G+ g+GKt L++a+  e
  gi|70606569|ref|YP_255439.1| 504 KGILLFGPPGTGKTMLAKAVATE 526
                                   679***************98765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.14        48      20      39 ..     233     252 ..     222     288 .. 0.80
   2 ?    7.5   0.0    0.0096       3.2      20      58 ..     506     540 ..     492     565 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.14
                        AAA_11  20 tliqGPPGtgKTktivells 39 
                                    l+ GPPG gKT    ++ +
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVAN 252
                                   5899********76665555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0096
                        AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL 58 
                                    l+ GPPGtgKT    ++  +       +  + ++p+iL
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATES----GANFIAVRGPEIL 540
                                   5889********8776666665....3334455555555 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.24        78       5      27 ..     234     256 ..     231     262 .. 0.89
   2 ?    8.2   0.1    0.0044       1.5       5      31 ..     507     533 ..     504     536 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.24
                           IPT   5 lifGatttGKtaeaiklaketga 27 
                                   l++G+ ++GKt  a ++a+et a
  gi|70606569|ref|YP_255439.1| 234 LLYGPPGVGKTLLAKAVANETDA 256
                                   89****************99965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0044
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   l+fG+ +tGKt  a ++a e ga  i+
  gi|70606569|ref|YP_255439.1| 507 LLFGPPGTGKTMLAKAVATESGANFIA 533
                                   89********************99987 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.093        31      24      80 ..     233     300 ..     228     312 .. 0.59
   2 ?    6.4   0.0     0.028       9.3      24      48 ..     506     530 ..     500     577 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.093
                                   EEEEEETT--HHHHHHCC--TTS-EE.--SSTTHHHH-H..........HHHHHHT...TTSEEEEEE-TT CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwl.eifvverlaklp..........ldlleqa...kggtLylkdiad 80 
                                   ++l G++G gk+l A++ +++      +i   e                 +++e a    ++++++ +i+ 
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANETDAYFtSINGPEIM---SkfygeseqrlREIFEDAkkhAPAIIFIDEIDA 300
                                   799*************9988754322011111111...111222223336666665444566677776665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                                   EEEEEETT--HHHHHHCC--TTS-E CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                   ++l G++G+gk++ A++ + +sg +
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGAN 530
                                   799***************9998874 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.26        85      18      65 ..     234     287 ..     231     345 .. 0.70
   2 ?    8.1   0.0    0.0059       1.9      17      78 ..     506     613 ..     500     622 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.26
                                   EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpe 65 
                                   l+ g  gvGkt +++++++++++         i     Ge ++ ++e++e+ ++
  gi|70606569|ref|YP_255439.1| 234 LLYGPPGVGKTLLAKAVANETDAYftsinGpEIMSKFYGESEQRLREIFEDAKK 287
                                   678999*************97555666642355566667777777777766665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
                                   EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE................................................E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................x RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvg................................................i 49 
                                   +l++g  g+Gkt+++++++ +s ++   i v                                                  
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATESGAN--FIAVRgpeilskwvgesekaireifrkarqaaptviffdeidsiapirglstdS 584
                                   679******************8766..343334788888866666666666666666666666666666666666666666 PP

                                   SEEHHHHHHHHHHCHHSSGGGGEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  50 Gergnevaevleefpegtimkrtvlvant 78 
                                   G  ++ v+++l e+   + ++++v++a+t
  gi|70606569|ref|YP_255439.1| 585 GVTERIVNQLLAEMDGIEKLENVVVIAAT 613
                                   66666666666666666666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.093        31      21      39 ..     230     247 ..     220     252 .. 0.76
   2 ?    6.3   0.0     0.024       7.9      19      42 ..     502     523 ..     492     525 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.093
                        AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                   +kg +ll Gp G+GK+ l 
  gi|70606569|ref|YP_255439.1| 230 PKG-ILLYGPPGVGKTLLA 247
                                   356.9**********8765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.024
                        AAA_29  19 idlkgatlltGpsGsGKSTllDAi 42 
                                     +kg +ll Gp G+GK+ l  A+
  gi|70606569|ref|YP_255439.1| 502 P-PKG-ILLFGPPGTGKTMLAKAV 523
                                   3.355.9**********9887666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.03       9.8       4      44 ..     233     266 ..     230     309 .. 0.70
   2 ?    4.8   0.0     0.043        14       6      25 ..     508     527 ..     504     561 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                   +l  G +G GKt+++ ++++e         a + s N+p++
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANET-------DAYFTSINGPEI 266
                                   6789*************99998.......455555555554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.043
                       DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                     G +GtGKt+++ ++++e 
  gi|70606569|ref|YP_255439.1| 508 LFGPPGTGKTMLAKAVATES 527
                                   5699*********9999886 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.043        14       2      33 ..     233     263 ..     232     286 .. 0.73
   2 ?    3.9   0.0      0.18        61       2      22 ..     506     526 ..     505     554 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.043
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTTT CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstig 33 
                                   ++l G  gvGKt l+k + ++  +   +s+ g
  gi|70606569|ref|YP_255439.1| 233 ILLYGPPGVGKTLLAKAVANE-TDAYFTSING 263
                                   6899********999988754.4444455555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.18
                                   EEEESSTTSSHHHHHHCHCT- CS
                           Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                   ++l G  g+GKt l+k + ++
  gi|70606569|ref|YP_255439.1| 506 ILLFGPPGTGKTMLAKAVATE 526
                                   7899**********9988765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.33   1.1e+02       3      26 ..     235     258 ..     233     262 .. 0.85
   2 ?    6.4   0.0      0.02       6.5       3      27 ..     508     532 ..     506     535 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.33
                                   EE-STTSSHHHHHHHHHHHHT-EE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglky 26 
                                   + GP g GK  +a+a+a++ ++ +
  gi|70606569|ref|YP_255439.1| 235 LYGPPGVGKTLLAKAVANETDAYF 258
                                   67***************9988755 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.02
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g+GK  +a+a+a++ g++++
  gi|70606569|ref|YP_255439.1| 508 LFGPPGTGKTMLAKAVATESGANFI 532
                                   56*****************999987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.27        90      21      46 ..     210     252 ..     197     262 .. 0.71
   2 ?    5.9   0.0     0.035        12      14      46 ..     493     525 ..     473     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.27
                                   ...................TTSEEEEEESTTSTHHHHHHHHHH CS
                        ResIII  21 s.................krdkrglikmaTGtGKTlvaaklie 46 
                                   +                 +  k +l+  + G+GKTl+a +++ 
  gi|70606569|ref|YP_255439.1| 210 ElvelplrhpelfkrlgiEPPKGILLYGPPGVGKTLLAKAVAN 252
                                   3444455555555566667888999***********9976665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
                                   HHT......TTSEEEEEESTTSTHHHHHHHHHH CS
                        ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklie 46 
                                   ++ e+++++  k +l+  + GtGKT++a +++ 
  gi|70606569|ref|YP_255439.1| 493 EVYENMSIEPPKGILLFGPPGTGKTMLAKAVAT 525
                                   44455666888999999*********9955554 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00097      0.32      79     166 ..      91     178 ..      76     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                          UFD1  79 enlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvyelkvlevkpesav 159
                                   +n g++ gd v +++ + + +++v+l p + ++   +      +k+L++ + L +gd++ i +  +   ++v++v+p+  v
  gi|70606569|ref|YP_255439.1|  91 KNAGVSIGDKVIVRKSNPKVATSVRLAPSNFSITVDPGFISYVKKKLKD-TPLVEGDTVLIPVLGQAIPFTVVQVRPQGIV 170
                                   67889999*********************88887666677788899988.5699***********************9844 PP

                          UFD1 160 sii.etdl 166
                                    +  et +
  gi|70606569|ref|YP_255439.1| 171 IVSdETSI 178
                                   44314544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.93u 0.34s 00:00:01.27 Elapsed: 00:00:00.50
# Mc/sec: 4651.48
//
Query:       gi|70606570|ref|YP_255440.1|  [L=74]
Description: hypothetical protein Saci_0774 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   14.0   0.0       0.07   13.7   0.0    1.2  1  SAS-6_N   Centriolar protein SAS N-terminal
       0.12   11.7   0.1       0.12   11.6   0.1    1.0  1  EAP30     EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> SAS-6_N  Centriolar protein SAS N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-06      0.07      20      47 ..      24      51 ..      21      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                                  EHHHHHHHHHHCTB-S-CCCHHHHHHHH CS
                       SAS-6_N 20 seedFeelkeeqnLlvdFaeFpsklikl 47
                                  ++e ++e+k++    v+F++F + l+kl
  gi|70606570|ref|YP_255440.1| 24 DQELYQEVKKSVGYEVSFSDFLKALMKL 51
                                  7899**********************97 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.4e-05      0.12     113     152 ..      18      55 ..       8      73 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.4e-05
                         EAP30 113 ngglisleelyalvnrarggvalvspdDllraiekllvlg 152
                                   + + ++ +ely+ v+++  g  +vs +D+l+a+ kl+  g
  gi|70606570|ref|YP_255440.1|  18 KRSPVTDQELYQEVKKSV-G-YEVSFSDFLKALMKLEMRG 55 
                                   556677799999999866.4.7**************6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 484.42
//
Query:       gi|70606571|ref|YP_255441.1|  [L=331]
Description: flap endonuclease-1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-27   94.9   0.1    9.2e-27   93.2   0.0    1.9  2  XPG_I            XPG I-region
    2.2e-18   66.6   0.0    5.2e-18   65.4   0.0    1.7  1  XPG_N            XPG N-terminal domain
    9.1e-07   29.4   0.5    9.1e-07   29.4   0.5    2.4  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
       0.03   14.9   0.1       0.13   12.9   0.1    2.1  1  HHH_5            Helix-hairpin-helix domain
      0.049   13.3   0.0      0.096   12.3   0.0    1.4  1  DUF3231          Protein of unknown function (DUF3231)
      0.069   13.1   0.0       0.24   11.3   0.0    1.8  1  5_3_exonuc_N     5'-3' exonuclease, N-terminal resolvase-like
      0.086   13.1   1.4       0.82    9.9   0.1    2.3  2  SMBP             Small metal-binding protein
       0.52   10.5   3.5        3.9    7.7   0.2    2.6  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
       0.97    9.6   5.6       0.18   12.0   1.0    2.1  3  COG5             Golgi transport complex subunit 5


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.3   8.5e+03      58      70 ..      80      92 ..      63     106 .. 0.57
   2 !   93.2   0.0   4.6e-30   9.2e-27       2      94 .]     123     218 ..     122     218 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.3
                                  ..EEECEEEEEEH CS
                         XPG_I 58 kekekkkvevidl 70
                                  ke+++kk+e+ +l
  gi|70606571|ref|YP_255441.1| 80 KEEAEKKLEKAKL 92
                                  3333444444444 PP

  == domain 2  score: 93.2 bits;  conditional E-value: 4.6e-30
                                   HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT- CS
                         XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelgl 79 
                                   +mgip+v+ApgE+EA++ay+++ +l +a++s+D+D+llFGa++++rn++ ++k+k    + +++ k+e i+le++lk+lg+
  gi|70606571|ref|YP_255441.1| 123 AMGIPVVQAPGEGEAEAAYINSIDLSWAAASQDYDSLLFGAKRLVRNITiSGKRKLPnkDVYVEIKPELIELESLLKKLGI 203
                                   79**********************************************9755544446689999***************** PP

                                   -HHHHHHHHHHHCET CS
                         XPG_I  80 treqlidlaillgcD 94 
                                   +reqlid+ail+g+D
  gi|70606571|ref|YP_255441.1| 204 NREQLIDIAILIGTD 218
                                   *************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   2.6e-21   5.2e-18      25     100 ..       2      82 ..       1      83 [. 0.95

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.6e-21
                                   TTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHHHHHHH CS
                         XPG_N  25 egkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrserrqe 100
                                   +gkk+ iDa+  +y+fl a+r+++g+ l       tshl glf+r++ +++ gi PifVFdgk+p+ k+ee+e+r+ +++e
  gi|70606571|ref|YP_255441.1|   2 KGKKISIDAYNTIYQFLAAIRQPDGTPLIDskgriTSHLNGLFYRTISIIESGIIPIFVFDGKPPEKKSEEIERRKRAKEE 82 
                                   689**********************998888999******************************************99987 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.9       2.1   4.1e+03      55      86 ..      78     109 ..      67     120 .. 0.52
   2 !   29.4   0.5   4.6e-10   9.1e-07       4      52 ..     206     254 ..     203     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.1
                    5_3_exonuc  55 klkekLeenkeearlskkLatiktdvplelel 86 
                                   ++ke+ e++ e+a+l  +  +i++ ++  ++l
  gi|70606571|ref|YP_255441.1|  78 RAKEEAEKKLEKAKLEGEYREIRKYAQAAVRL 109
                                   34455555555555555555555544444444 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.6e-10
                    5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld.elk 52 
                                   eq+id++ L+G    n  Gv+giG ktA +++k+y+++e+ +e+ + +l+
  gi|70606571|ref|YP_255441.1| 206 EQLIDIAILIGTDY-NPDGVKGIGVKTALRIIKKYNNIENAIEKGEiQLS 254
                                   89*********765.889************************96553332 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.5e-05      0.13       6      36 ..     223     252 ..     222     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                                   TSTT--HHHHHHHHTTT--SHHHHHHS-HHH CS
                         HHH_5   6 svsGiGpktAlallsaGiesvedlaaadvee 36 
                                   +v+GiG ktAl+++++ ++ +e  +++ + +
  gi|70606571|ref|YP_255441.1| 223 GVKGIGVKTALRIIKK-YNNIENAIEKGEIQ 252
                                   699************9.99998655554444 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05     0.096      45      83 ..      97     135 ..      93     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                       DUF3231  45 keikelleralelsnkhikelkelLkeenlpiPsgfses 83 
                                   +ei+++ + a +lsn+ ++e k+lL   ++p+ +++ e 
  gi|70606571|ref|YP_255441.1|  97 REIRKYAQAAVRLSNEMVEESKKLLDAMGIPVVQAPGEG 135
                                   79*******************************998654 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.24       5     102 ..       8     133 ..       5     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                  5_3_exonuc_N   5 iDgsslifRayyal.......lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelype........... 67 
                                   iD+ + i++   a+       l  s+g+ t+ + g++   ++++e+      ++vfD k+++ ++e ++            
  gi|70606571|ref|YP_255441.1|   8 IDAYNTIYQFLAAIrqpdgtpLIDSKGRITSHLNGLFYRTISIIESGII--PIFVFDGKPPEKKSEEIERrkrakeeaekk 86 
                                   7888888887777778888887788999999999999999999997553..6999**887777777776666666677777 PP

                  5_3_exonuc_N  68 .........YKanReetpeelk...eqlplikevlealgikvleveg 102
                                            Y++ R+ ++ +++   e ++  k++l+a+gi+v++++g
  gi|70606571|ref|YP_255441.1|  87 lekaklegeYREIRKYAQAAVRlsnEMVEESKKLLDAMGIPVVQAPG 133
                                   77777777799999877777763335667778899********9987 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.13   2.7e+02      37      64 ..      79      98 ..      50     139 .. 0.58
   2 ?    9.9   0.1   0.00041      0.82      67      91 ..     296     320 ..     277     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                                  HHHHHHTT-HHHHHHHHHHHHHHHHHH..... CS
                          SMBP 37 AvahgkaghakalveHaeealkhakaa....a 64
                                  A+            e+ae+ l++ak +    +
  gi|70606571|ref|YP_255441.1| 79 AK------------EEAEKKLEKAKLEgeyrE 98
                                  33............333333333333322220 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00041
                                   -------HHHHHHHHHHHHHHHHHC CS
                          SMBP  67 akeeekehldegikhLeeAIkhgka 91 
                                   ++  +++++++gi+ L++AIk++k 
  gi|70606571|ref|YP_255441.1| 296 NHDFNEDRVNNGIERLKKAIKEAKS 320
                                   455567899**************96 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2     0.002       3.9      26      61 ..      66      98 ..      55     134 .. 0.68
   2 ?   -3.3   0.0       4.8   9.6e+03      35      45 ..     241     251 ..     230     262 .. 0.58
   3 ?    3.1   0.1     0.053   1.1e+02      20      44 ..     295     319 ..     276     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                                  .GGHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHH CS
               PEP-utilisers_N 26 aedveaelerleeAlekvreelealaekalgeeeaa 61
                                  +e+  +e+er ++A e+++++le+++ +    e+++
  gi|70606571|ref|YP_255441.1| 66 PEKKSEEIERRKRAKEEAEKKLEKAKLEG---EYRE 98
                                  456789*****************976332...2222 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHH CS
               PEP-utilisers_N  35 rleeAlekvre 45 
                                    +e+A+ek + 
  gi|70606571|ref|YP_255441.1| 241 NIENAIEKGEI 251
                                   34444444444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.053
                                   -----G.GGHHHHHHHHHHHHHHHH CS
               PEP-utilisers_N  20 eeeeveaedveaelerleeAlekvr 44 
                                   ++++ ++++v++ +erl++A+++++
  gi|70606571|ref|YP_255441.1| 295 KNHDFNEDRVNNGIERLKKAIKEAK 319
                                   56677788899999*******9987 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.3   4.5e+03      48      51 ..     108     111 ..      74     124 .. 0.47
   2 ?   -3.2   0.0       4.4   8.8e+03      73      91 ..     183     201 ..     175     202 .. 0.76
   3 ?   12.0   1.0   8.8e-05      0.18      16      97 ..     234     317 ..     230     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.3
                                   XXXX CS
                          COG5  48 rlrq 51 
                                   rl +
  gi|70606571|ref|YP_255441.1| 108 RLSN 111
                                   3333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.4
                                   XXXXXXXXXXXXXXXXXXX CS
                          COG5  73 vlselksslesLsasyerl 91 
                                   v  e+k++l++L++ +++l
  gi|70606571|ref|YP_255441.1| 183 VYVEIKPELIELESLLKKL 201
                                   6778999999999888776 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 8.8e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-T CS
                          COG5  16 allkatnnnddteldlstplkrlnydiqeldkr.lrqlitsnhleL.lehlskskslssvlselksslesLsasyerlksk 94 
                                   +++k+ nn +++ +  +++l+++n+di+e++k  ++ ++++  + L l++ ++++  + ++++ + + +++++ +erlk+ 
  gi|70606571|ref|YP_255441.1| 234 RIIKKYNNIENAIEKGEIQLSKINFDIREIRKLfITPEVKKPTERLeLAECNEREIIELLVKNHDFNEDRVNNGIERLKKA 314
                                   67889999999********************97367777777777766777777777779999999999999999999999 PP

                                   THH CS
                          COG5  95 vle 97 
                                   + e
  gi|70606571|ref|YP_255441.1| 315 IKE 317
                                   865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1817  (0.101344); expected 358.6 (0.02)
Passed bias filter:                      921  (0.0513693); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2201.25
//
Query:       gi|70606572|ref|YP_255442.1|  [L=218]
Description: hypothetical protein Saci_0776 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-25   89.3   0.0    2.5e-25   88.9   0.0    1.2  1  NAD_binding_7  Putative NAD(P)-binding
    1.1e-05   25.7   0.0    1.7e-05   25.0   0.0    1.3  1  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.023   15.2   0.0      0.043   14.3   0.0    1.4  1  Ribosomal_S9   Ribosomal protein S9/S16
      0.036   13.4   0.0      0.082   12.2   0.0    1.5  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.11   13.3   0.0       0.17   12.7   0.0    1.2  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   7.1e-29   2.5e-25       1     103 [.      10     120 ..      10     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 7.1e-29
                 NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele....elvklaeeel....ekdlegadlviaatddre 73 
                                   lf++++g kvlvvGgG+v+++++ k++e++a v vv+ e+k+e e    ++++l+++++    e+ l+++ ++++at+d+e
  gi|70606572|ref|YP_255442.1|  10 LFINVEGLKVLVVGGGKVGTKRALKFAESKAIVYVVSLEFKDENElrlfDNIHLIKNDArylpENFLSRFNIIVVATNDKE 90 
                                   79*************************************8666668899666666555444566889************** PP

                 NAD_binding_7  74 lneriaeaakarrilvnvadkpelcdfifp 103
                                   lneri+e++k+ ++l+n  ++p+ ++fi+p
  gi|70606572|ref|YP_255442.1|  91 LNERICETCKKLGKLCNNPTNPDSSNFIVP 120
                                   *****************************9 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.9e-09   1.7e-05       1      89 [.      19     105 ..      19     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.9e-09
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   ++++G G+vG++ a ++ e + + v+v+  + +  +elr   ++ ++    d   L e  +++++++++at+d+e n  ++
  gi|70606572|ref|YP_255442.1|  19 VLVVGGGKVGTKRALKFAEsKAI-VYVVSLEFKDENELR--LFDNIHLIKNDARYLPENFLSRFNIIVVATNDKELNERIC 96 
                                   68*****************5555.999999889999987..55566666666669************************** PP

                                   HHHHHHTSS CS
                        TrkA_N  81 llakelnpk 89 
                                   +++k+l + 
  gi|70606572|ref|YP_255442.1|  97 ETCKKLGKL 105
                                   ****99876 PP

>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.043      55     100 ..      18      69 ..      10      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                   EEEEESS-HHHHHHHHHHHHHHHHHHHHH...HHHHHHC...TCCCTS-B-- CS
                  Ribosomal_S9  55 fvkvkgGGlsgqaeAirlgiaraLvalek...eekkeLk...kaglltrDpR 100
                                   +v v gGG++g  +A++ + ++a+v + +   + ++eL+   + +l+++D+R
  gi|70606572|ref|YP_255442.1|  18 KVLVVGGGKVGTKRALKFAESKAIVYVVSlefKDENELRlfdNIHLIKNDAR 69 
                                   6889*********************987666544666665557788888888 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05     0.082      26      81 ..      14      67 ..       8      95 .. 0.76
   2 ?   -2.6   0.0      0.78   2.8e+03     170     201 ..     151     182 ..     150     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                  B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHH CS
                   AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksq 81
                                  ve  kvlv+GgG +G++ +   ++ +a+V+v+ ++ +  ++l+ + +   +++k++
  gi|70606572|ref|YP_255442.1| 14 VEGLKVLVVGGGKVGTKRALKFAESKAIVYVVSLEFKDENELRLFDNI--HLIKND 67
                                  66789***********9888888889*****99999988888776554..554444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.78
                                   HHHHHHHHHHHHHHHCHHHTCCHHHCTSHHHH CS
                   AlaDh_PNT_C 170 salltnntlpyleelladkglkkalkedealr 201
                                   s++l +n+++++ ++ + k++ k++  ++ +r
  gi|70606572|ref|YP_255442.1| 151 SNILKENIFSLVDTMGKVKEILKLNVTEPSIR 182
                                   67788999999999988888888888777766 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05      0.17       1      86 [.      17     103 ..      17     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT...TESEEEE-S-G.GGHHH CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp...eidavivatpn.gthee 77 
                                   l+v+++G+Gk+g+k + ++ es     +v +++ + +   +++   +++  ++ ++ l +    + ++++vat   ++ e+
  gi|70606572|ref|YP_255442.1|  17 LKVLVVGGGKVGTKRALKFAES---KAIVYVVSLEFKDENELRLFDNIHLIKNDARYLPENflsRFNIIVVATNDkELNER 94 
                                   589*************999999...7788888888888888888999999999665555555779*******999666888 PP

                                   HHHHHHHTT CS
                  GFO_IDH_MocA  78 lakaaleag 86 
                                   +++ + + g
  gi|70606572|ref|YP_255442.1|  95 ICETCKKLG 103
                                   888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1603.30
//
Query:       gi|70606573|ref|YP_255443.1|  [L=414]
Description: glutamyl-tRNA reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-32  112.5   0.1    2.9e-32  111.4   0.1    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.3e-15   57.7   1.4    3.1e-15   56.5   0.1    2.2  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    2.2e-15   56.9   1.2      4e-15   56.0   1.2    1.5  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    1.5e-07   31.9   0.0      5e-07   30.2   0.0    2.0  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    6.7e-05   22.4   0.1    0.00012   21.5   0.1    1.3  1  ThiF             ThiF family
    0.00087   19.6   0.0     0.0025   18.0   0.0    1.8  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0014   18.8   0.0     0.0031   17.7   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0016   19.3   0.0     0.0036   18.1   0.0    1.6  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.002   18.3   0.0     0.0037   17.4   0.0    1.5  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
     0.0041   16.5   0.0     0.0075   15.6   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0049   17.1   0.0      0.014   15.7   0.0    1.8  1  TrkA_N           TrkA-N domain
     0.0053   16.4   0.0      0.013   15.2   0.0    1.7  1  ApbA             Ketopantoate reductase PanE/ApbA
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.04   14.4   0.0    1.9  1  NAD_binding_7    Putative NAD(P)-binding
      0.017   15.1   0.0      0.048   13.6   0.0    1.8  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.026   15.1   0.1       0.23   12.1   0.0    2.6  2  PglD_N           PglD N-terminal domain
      0.074   13.2   0.0       0.22   11.6   0.0    1.8  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.12   12.0   0.0       0.23   11.0   0.0    1.5  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.1   2.8e-35   2.9e-32      33     145 ..      42     153 ..      15     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 2.8e-35
                       GlutR_N  33 kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvke 113
                                   + +++ +L+TCNR+E+yl ++++ ++ +++l+ l+e++ +++++++ vl+g++a++Hl++VasGLdSl +GE +IlgQ+ke
  gi|70606573|ref|YP_255443.1|  42 SDTQVSLLQTCNRVELYLYTKDR-NKINDILSKLNETHGKDISSNAIVLRGKDAINHLYQVASGLDSLAIGEYEILGQIKE 121
                                   334899***********866554.66677888889999******************************************* PP

                       GlutR_N 114 ayelakeagtlgkvLerlfqkaikvakrvrte 145
                                   a++ +k++  +++++e lf+ aikv+++vr+ 
  gi|70606573|ref|YP_255443.1| 122 ALTSCKKHSLCNEEIELLFNAAIKVGRKVRSL 153
                                   ******************************86 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.1   2.9e-18   3.1e-15       5     136 ..     173     284 ..     169     286 .. 0.81
   2 ?   -2.3   0.1       3.9   4.1e+03      40      68 ..     303     331 ..     296     341 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.9e-18
                                   HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                  Shikimate_DH   5 kkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                   + +++l++ k+ ++GaGe+++++a +L ++g+++++++NR+l+ra el +++ g+++e l+++++    +e+d+v++a++ 
  gi|70606573|ref|YP_255443.1| 173 EVMGDLTDIKIAIVGAGEIGSKLAFMLKNNGARNLTIFNRNLDRALELSNKF-GYNAELLDFQKV----NEYDLVFIAINN 248
                                   567899**********************************************.665777777665....59*******999 PP

                                   SS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHH CS
                  Shikimate_DH  86 eepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLk 136
                                   ++p     +++ +    +kp+l++D++vP  v       ++ +++ +DdL+
  gi|70606573|ref|YP_255443.1| 249 SNPS----QLR-L----DKPKLVIDLSVPPVVY------KTSNVIYLDDLR 284
                                   8873....222.2....2578********6554......345667777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                                   EEEESSHHHHHHHHHHHT.ET-EEEEGCG CS
                  Shikimate_DH  40 vvaNRtlerakelaeelkgeeiealklee 68 
                                   +++N ++++ ++l ++++ +++  + ++e
  gi|70606573|ref|YP_255443.1| 303 AIINEEIQKFESLLNNYNMNRLVSRFMSE 331
                                   57888888888888888766555555555 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   1.2   3.8e-18     4e-15       1      96 [.     300     399 ..     300     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 3.8e-18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S.....-------.-TTHHHHHHHHHHHHHHHHH CS
                   GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla...ldgedree.lekltrslvnkllheptarL 77 
                                   kAeaiI+ee+++fe+ l++ +++ +++++ +++e +re+e++ra++++     d+++ +e ++k+t sl++k++ +  + L
  gi|70606573|ref|YP_255443.1| 300 KAEAIINEEIQKFESLLNNYNMNRLVSRFMSEIEWVREKEVDRAFNEILknyADKDNIKEiIDKMTYSLIKKVFSPILEDL 380
                                   7**********************************************99999899999999******************** PP

                                   HSS-TTTTHHHHHHHHH.. CS
                   GlutR_dimer  78 keaedeeeellealrrlFn 96 
                                   +++ +++++++e l ++F+
  gi|70606573|ref|YP_255443.1| 381 RKDPNNKKQIVEYLIEVFQ 399
                                   ***777779**99999996 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.7e-10     5e-07       1      96 [.     182     267 ..     182     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.7e-10
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81 
                                   ki+i+GaG++g+ la  l ++g  ++++++  +rn ++a el +++g +++  d +++  e d v++a+  ++     s+l
  gi|70606573|ref|YP_255443.1| 182 KIAIVGAGEIGSKLAFMLKNNG--ARNLTIF-NRNLDRALELSNKFGYNAELLDFQKVN-EYDLVFIAINNSN----PSQL 254
                                   7*********************..9999966.********************8877766.5*******98665....4455 PP

                                   GHHHHTTSEEEEESS CS
                 F420_oxidored  82 akdalkgklvisvla 96 
                                     +++k klvi+ ++
  gi|70606573|ref|YP_255443.1| 255 --RLDKPKLVIDLSV 267
                                   ..5677788887765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.1e-07   0.00012      11      48 ..     173     210 ..     161     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  11 dgqekLrdskvllvGaGglGsellknLalsGvgkltlv 48 
                                   + +  L d k+++vGaG +Gs l+ +L   G ++lt++
  gi|70606573|ref|YP_255443.1| 173 EVMGDLTDIKIAIVGAGEIGSKLAFMLKNNGARNLTIF 210
                                   66778999****************************97 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0025       1      80 [.     183     269 ..     183     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH............TTTCEEEEE--TTTHHHHHHHHHTT CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka............lgvrfeaialdaenyeavLaallke 69 
                                   + i+GaG +G+ +a +l++++    ++t+  r+++++ +l +k             ++ ++ +ia++ +n+++ L   l +
  gi|70606573|ref|YP_255443.1| 183 IAIVGAGEIGSKLAFMLKNNGAR--NLTIFNRNLDRALELSNKFgynaelldfqkvNEYDLVFIAINNSNPSQ-LR--LDK 258
                                   689*****************987..***********99998887**********99999************99.44..688 PP

                                   SSEEEE-SSGG CS
               Sacchrp_dh_NADP  70 gdlvvnlsppi 80 
                                    +lv++ls+p 
  gi|70606573|ref|YP_255443.1| 259 PKLVIDLSVPP 269
                                   89****99986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     3e-06    0.0031       1      91 [.     182     276 ..     182     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
                                   EEEEE--SHHHHHHHHHHHHTT-.EEEEE-SSHHHHHHHHHTTEEE-SSHH.HHHHHCSEEEE-SSSHHHHHHHHHS..HC CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagy.kvavynrtkekveelvaegakaaesie.elvasldvvitmvkagkavdevieg..ll 77 
                                   ki+++G G++Gs++a  l+++g  +++++nr+ +++ el ++    ae +  + v++ d+v++ ++++++ +  +++  l+
  gi|70606573|ref|YP_255443.1| 182 KIAIVGAGEIGSKLAFMLKNNGArNLTIFNRNLDRALELSNKFGYNAELLDfQKVNEYDLVFIAINNSNPSQLRLDKpkLV 262
                                   79****************99986379*************9997656665555789999********999887777666655 PP

                                   CC--TT-EEEE-S- CS
                 NAD_binding_2  78 ealkkgdilidgst 91 
                                     l+   ++  +s+
  gi|70606573|ref|YP_255443.1| 263 IDLSVPPVVYKTSN 276
                                   55555555555555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.4e-06    0.0036       1      74 [.     181     250 ..     181     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.4e-06
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGG CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngt 74 
                                   +++ai+GaG igsk +  ++ ++++++   +++++  ra +++++fg +    d++++    e d+v++a+ n+ 
  gi|70606573|ref|YP_255443.1| 181 IKIAIVGAGEIGSKLA--FMLKNNGARNLTIFNRNLDRALELSNKFGYNaELLDFQKVN---EYDLVFIAINNSN 250
                                   689***********98..555557887777*****************995555555555...59******99954 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.5e-06    0.0037       1      32 [.     181     210 ..     181     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                                   EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE CS
                       Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLl 32 
                                   +k+a+vGa G+iG++la++l+n++  + l+++
  gi|70606573|ref|YP_255443.1| 181 IKIAIVGA-GEIGSKLAFMLKNNGARN-LTIF 210
                                   59******.*************98765.5555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.1e-06    0.0075      29      73 ..     173     218 ..     141     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.1e-06
                                   GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH CS
                  2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee 73 
                                       +l++ +++i+G+G+IG+++a +lk  g+ ++++++r+ ++  
  gi|70606573|ref|YP_255443.1| 173 EVMGDLTDIKIAIVGAGEIGSKLAFMLKNNGArNLTIFNRNLDRAL 218
                                   445589999*******************999967777777766544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.3e-05     0.014       1      60 [.     183     236 ..     183     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTG CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagi 60 
                                   i+i+G+G++G++la  L++ g ++ ++  ++ +r+ el++++ +        + e+L+  ++
  gi|70606573|ref|YP_255443.1| 183 IAIVGAGEIGSKLAFMLKNnGARNLTIFNRNLDRALELSNKFgY--------NAELLDFQKV 236
                                   79*****************55588**************988834........4445555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.013       1      43 [.     183     228 ..     183     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                   EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHH.HHHHCEEE CS
                          ApbA   1 iailGaGaiGsllaakLakagad.vtlilrsr.rlea.lkknGlrl 43 
                                   iai+GaG iGs la +L+++ga   t+ +r+  r+ +  +k G++ 
  gi|70606573|ref|YP_255443.1| 183 IAIVGAGEIGSKLAFMLKNNGARnLTIFNRNLdRALElSNKFGYNA 228
                                   89***************99666548888887665544366666655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.8e-05      0.04       3      73 ..     176     250 ..     174     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                 NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagak.vtvvapevkeele..elvklaeeele.kdlegadlviaatddre 73 
                                    dl++ k+ +vG+Ge++ + +  l ++ga+ +t+   ++ ++le  +++ ++ e l+ ++++++dlv++a+++ +
  gi|70606573|ref|YP_255443.1| 176 GDLTDIKIAIVGAGEIGSKLAFMLKNNGARnLTIFNRNLDRALElsNKFGYNAELLDfQKVNEYDLVFIAINNSN 250
                                   58999*************999999999986377777775333332233444455555477999********9976 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-05     0.048       1      39 [.     182     221 ..     182     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                                   -EEEE--SHHHHHHHHHHHTTT.--EEEE-S-HHHHHHHH CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaeng.hevrlwvreeelieein 39 
                                   kia++GaG  G+ lA +l++ng  + +++ r+ + + e++
  gi|70606573|ref|YP_255443.1| 182 KIAIVGAGEIGSKLAFMLKNNGaRNLTIFNRNLDRALELS 221
                                   79*******************9677888888776655554 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.7   4.9e+03      38      51 ..     110     123 ..      77     131 .. 0.66
   2 ?   12.1   0.0   0.00022      0.23       1      68 [.     182     249 ..     182     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.7
                        PglD_N  38 vegypvlgkaiell 51 
                                   + +y++lg++ e l
  gi|70606573|ref|YP_255443.1| 110 IGEYEILGQIKEAL 123
                                   34466666665555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                        PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkktevegypvlgkaiellkslseeeye.vviAIGnn 68 
                                   ki+I+GaG  g   a ++++ng  + + ++  n + ++e  +  g   ell+  + +ey+ v+iAI n 
  gi|70606573|ref|YP_255443.1| 182 KIAIVGAGEIGSKLAFMLKNNG-ARNLTIFNRNLDRALELSNKFGYNAELLDFQKVNEYDlVFIAINNS 249
                                   79********************.78888888887665555455555567777666678886799**875 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.22       1      93 [.     181     284 ..     181     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                   EEEEEETTTSHHHHHHHHHHHHS.............TTEEEEEEEETTCSTTTTTBHH.....HHSSSS--S-BEB.SSHH CS
                        DapB_N   1 ikvavvGasGrmGkevvkaveea.............edlelvaavdrkeselegkdag.....ellglgklgvavt.ddle 62 
                                   ik+a+vGa G +G++++ +++++             + lel+  +  +               ++ + + + +a++ ++ +
  gi|70606573|ref|YP_255443.1| 181 IKIAIVGA-GEIGSKLAFMLKNNgarnltifnrnldRALELSNKFGYNA--------ElldfqKVNEYDLVFIAINnSNPS 252
                                   79*****9.*************755444444433333333333333333........133221333333333444433333 PP

                                   HH.HHH-SEEEE-S-HHHHHHHHHHHHHTT-E CS
                        DapB_N  63 ev.lekadvliDFTtpeavlenlklalekgvk 93 
                                   ++ l+k   +iD+++p +v+++ ++++    +
  gi|70606573|ref|YP_255443.1| 253 QLrLDKPKLVIDLSVPPVVYKTSNVIYLDDLR 284
                                   33145588************999988766655 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00022      0.23       2      68 ..     178     246 ..     177     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                   HHTS-EEEES-SHHHHHHHHHHHHTT-.-EEEEE-TT-HHHHHHHHTT-EEEEHH.HHHHT-SEEEE-S CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgl.dvvvglregsksvkkAkeegfevltva.eavkkadvvmili 68 
                                   l++ kia++G G  G   a  l+++g  ++++ +r+ ++ ++  ++ g++   ++ + v++ d+v+i i
  gi|70606573|ref|YP_255443.1| 178 LTDIKIAIVGAGEIGSKLAFMLKNNGArNLTIFNRNLDRALELSNKFGYNAELLDfQKVNEYDLVFIAI 246
                                   6788**********************8899999999999999999999987665435677777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1425  (0.0794802); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2840.33
//
Query:       gi|70606574|ref|YP_255444.1|  [L=336]
Description: delta-aminolevulinic acid dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.1e-140  465.7   0.9     8e-140  465.5   0.9    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
      0.035   13.6   0.0        2.5    7.5   0.0    2.4  2  ComA      (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.5   0.9  8.9e-144    8e-140       3     317 .]       8     329 ..       6     329 .. 0.97

  Alignments for each domain:
  == domain 1  score: 465.5 bits;  conditional E-value: 8.9e-144
                                   -GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEG.GGHHHHHHHHHHTT--EEEEEEE-SS-B CS
                          ALAD   3 rlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsv.delvkeveelvklgikavllFgvpeekd 82 
                                   r+rrlr+++ lr++v++t+l+a++lilp+fvk+g +e+e+i+smp+vyr++  d+l+k ve+++++gik+++lFg+p+ kd
  gi|70606574|ref|YP_255444.1|   8 RPRRLRSNKLLRDFVAQTHLNAANLILPIFVKDGISEPEQIQSMPDVYRYPPnDKLIKYVENVKEKGIKNIILFGIPAYKD 88 
                                   9*************************************************87589************************** PP

                                   SS-GGGGSTTSHHHHHHHHHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.....EEHHHHHHHHHHHHHHHHHCT-SEE CS
                          ALAD  83 eegsealnedglvqrairaikeev.pelvvitDvclceytshGhcgileeke....vdndetlellakvavsqaeaGadiv 158
                                   e +s+a+++dg++qra+++++e++ +++++i+D c +ey shGhcgi+ +++    +dnde+l++ +k+avsqaeaGad++
  gi|70606574|ref|YP_255444.1|  89 EVASSAYAKDGVIQRALKMLRESFkDQILLIADECTDEYISHGHCGIVLRRNgnlvIDNDESLRIHSKIAVSQAEAGADVI 169
                                   ************************55699*******************54445689************************* PP

                                   EE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-S CS
                          ALAD 159 apSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldleeGAD 239
                                   apS+mmDg v+air+ Ldeag+++vai++YsaKyaS+fY PFrdaa s+psfgdr+ Yqmdp+ns ea++ev+ld+eeGAD
  gi|70606574|ref|YP_255444.1| 170 APSSMMDGVVGAIRRDLDEAGYKDVAIMAYSAKYASTFYSPFRDAAYSKPSFGDRRGYQMDPRNSYEAIKEVKLDIEEGAD 250
                                   ********************************************************************************* PP

                                   BEEEES-TTGHHHHHHHHTT-.SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHHHHH. CS
                          ALAD 240 ivmvKPalaylDiirevkeef.dlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfakevakl 317
                                   ivmvKPa +ylD+ir vk+ef ++p+aay+vSGEY+mikaaa ngw+dek++vlE +++ikRAGadli+tY+a+++a++
  gi|70606574|ref|YP_255444.1| 251 IVMVKPAHTYLDVIRIVKDEFpEYPLAAYHVSGEYSMIKAAAINGWIDEKTAVLEITTAIKRAGADLIITYYAEKIAEW 329
                                   *********************99******************************************************98 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0045        41     109     155 ..      59     108 ..      56     131 .. 0.81
   2 ?    7.5   0.0   0.00028       2.5     127     164 ..     217     254 ..     201     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0045
                                   -HHHHHHHHHHHCCTTSEEEEEES-...SSHHHHTT--CCHHHHHHHHHH CS
                          ComA 109 peeeklrliekakkeglkvlpevgk...kdgelesesdveklieeakrdl 155
                                   p+++ ++++e++k++g+k +  +g+   kd+  +s+   + +i++a + l
  gi|70606574|ref|YP_255444.1|  59 PNDKLIKYVENVKEKGIKNIILFGIpayKDEVASSAYAKDGVIQRALKML 108
                                   689999******************97777776666677777777777766 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00028
                                   EEEEES-SSHHHHTT--CCHHHHHHHHHHHHTECEEEE CS
                          ComA 127 vlpevgkkdgelesesdveklieeakrdleaGaekvii 164
                                    +p +g + g + +  + ++ i+e+k d+e Ga+ v++
  gi|70606574|ref|YP_255444.1| 217 SKPSFGDRRGYQMDPRNSYEAIKEVKLDIEEGADIVMV 254
                                   57889999998888899********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2407.10
//
Query:       gi|70606575|ref|YP_255445.1|  [L=420]
Description: glutamate-1-semialdehyde aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-69  234.2   0.1    2.3e-69  234.0   0.1    1.0  1  Aminotran_3    Aminotransferase class-III
    3.1e-06   26.6   0.0    4.1e-06   26.2   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   0.1   2.6e-73   2.3e-69       7     380 ..      26     393 ..      21     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 2.6e-73
                                   --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                   Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                   ++ ++ +++aeG+yl+ +d+k+++D v ++ +++lGha+  v+k + eq++k ++     + +   ++la+k+ +++p   
  gi|70606575|ref|YP_255445.1|  26 KPYPFYVERAEGAYLYTADNKQLIDYVLGYGPLILGHANQYVTKKIIEQVNKGWLYG---TPSPIEIELARKISHHLPS-A 102
                                   556699***********************************************9988...44455689**********9.9 PP

                                   SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                   Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                   +k+ ++nsG+eA++ Al+lar+      +t ++kii+f+g++HG   + l  +gs     +   ++  ++++   +  +++
  gi|70606575|ref|YP_255445.1| 103 QKIRFVNSGTEATMLALRLARA------YTGREKIIKFHGNYHGAHDYLLLDAGS--AFTEFNVNVYNGIPKSIVNTIRIC 175
                                   **********************......9**************************..666666777889999999999999 PP

                                   B-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSSGG CS
                   Aminotran_3 169 keneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklfAl 247
                                   ++n+      +e++e+l   k++++a+vivEp+ g++Gv+ ++++fl++lre++  ++ +li+DEv tGf  G  G   A 
  gi|70606575|ref|YP_255445.1| 176 EYND------AECVEKLS--KSEDIAGVIVEPVMGNMGVILPDKDFLERLREITLTYNSVLIFDEVITGFrlGLGG---AQ 245
                                   9999......88899987..89************************************************777777...99 PP

                                   GGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                   Aminotran_3 248 ehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelgaalk 325
                                    +++v+pDl+tl+K ++gGlp+ av++++e+ ++l+p +    ++Tf +npl + + la++e++e+e++ e a+++ + + 
  gi|70606575|ref|YP_255445.1| 246 GTFNVTPDLTTLGKIIGGGLPIGAVAGKKEIIDMLTPAGkvfNAGTFNANPLTMTAGLATIEVLERENVHEVANRAVNVIL 326
                                   9************************************999999************************************** PP

                                   HHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE-EEETTT CS
                   Aminotran_3 326 egLeelqkky.evikevRgkGlmiaielkeeaevke............keilkkakekGvlilsaGdn 380
                                   e+L ++ +k+      +   G m+ + ++  ++v +            +++ + +++ Gv i ++  +
  gi|70606575|ref|YP_255445.1| 327 EELVNALDKKiPNNFVINHIGSMFQV-FFGVKKVSNateaklankemyQKFHNLLLQRGVFIPPSQFE 393
                                   **988887775555557788888877.33333333335577999888877888888999998877644 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   4.6e-10   4.1e-06      77     338 ..     111     392 ..      67     414 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.6e-10
                                   HHHHHHHHHHHHHHTTT-E..EEEEESS-THHHHHHHHTTSEEEEEEBEET........TTTE.E-HHHHHHHHTTHHCTT CS
                 Aminotran_1_2  77 agaliealifllklnpgde..ilvpdptyasyknilrlsggevvryplyse........edfh.ldlealeealkeapegn 146
                                    +++  ++ +l+++ +g+e  i  +  +++ ++  l  +g+++ +++++          ++ + +  ++ e+ ++++++ +
  gi|70606575|ref|YP_255445.1| 111 GTEATMLALRLARAYTGREkiIKFHGNYHGAHDYLLLDAGSAFTEFNVNVYngipksivNTIRiCEYNDAEC-VEKLSKSE 190
                                   455555555555555554432444455556666666666666666665554445544442222123444444.33333334 PP

                                   ETEEEEEEESS-TTT--B-.-HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSG CS
                 Aminotran_1_2 147 kktkvilvesphNPtGtva.tleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGla 226
                                     + +++ve +  + G+++ +++ le l +++  yn +l++De+  gf +g  +a+   +nv ++     +++l+K  G  
  gi|70606575|ref|YP_255445.1| 191 D-IAGVIVEPVMGNMGVILpDKDFLERLREITLTYNSVLIFDEVITGFRLGLGGAQG-TFNVTPD-----LTTLGKIIG-G 263
                                   4.68999998887777765167789**************************445544.5666665.....66******8.4 PP

                                   GG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..HHHHHH.HHHHHHHHHHHHHHHHS.....TEE CS
                 Aminotran_1_2 227 GeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs..eleemr.qrlqkrrkelrdeLael.....glk 298
                                   G+ +G+++g++++++ l+ +   f+  +  + +++++a  ++ ++ +  +++e + + ++   +el+++L+++      ++
  gi|70606575|ref|YP_255445.1| 264 GLPIGAVAGKKEIIDMLTPAGKVFNAgTFNANPLTMTAGLATIEVLEreNVHEVAnRAVNVILEELVNALDKKipnnfVIN 344
                                   8888*************999999999855555555555555555544455555540555566799*****999*9888888 PP

                                   EECCS.CSSEEEEEETHH.....CHHHHHHH....HHHTCTEEEEEGGGG CS
                 Aminotran_1_2 299 vlasq.sgmflltdlsae.....takelskk....Lleevgvyvtpgtsf 338
                                   +++s    +f +  +s++     ++ke+++k    Ll++ gv + p ++f
  gi|70606575|ref|YP_255445.1| 345 HIGSMfQVFFGVKKVSNAteaklANKEMYQKfhnlLLQR-GVFIPP-SQF 392
                                   888876666666677777555555555555599977777.999998.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2721.90
//
Query:       gi|70606576|ref|YP_255446.1|  [L=296]
Description: porphobilinogen deaminase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-59  200.5   0.2    2.6e-59  200.2   0.2    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
      1e-08   35.4   0.0    2.7e-08   34.0   0.0    1.8  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   0.2   2.9e-63   2.6e-59       1     199 [.       3     200 ..       3     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 2.9e-63
                Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlpte 80 
                                   iri++R+S L+++q+++v+++L++   e+e++ +ktk D  +dkpL+++ gkg+F ke++ea+++ge+d+aVhS+KD+ ++
  gi|70606576|ref|YP_255446.1|   3 IRIAARGSLLSRIQVKMVEDKLRNlGIETELIVVKTKADLFQDKPLNSL-GKGVFEKEVNEAVINGEADIAVHSMKDMLSD 82 
                                   89********************7667778********************.7****************************** PP

                Porphobil_deam  81 lpeglelaavlkredprDvlvvkssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAa 161
                                   ++e+l+l  vl+r++p D lv++++l ++++g+v+gTsS+RR++ ++ +r dl vkdlRGn+dtRl+k +++eyd+i++A+
  gi|70606576|ref|YP_255446.1|  83 MDEKLVLYGVLPRDSPYDSLVAEKDLFNIESGKVIGTSSIRRRSMISFYRRDLVVKDLRGNIDTRLKKYQSKEYDGIVIAE 163
                                   *********************9889******************************************************** PP

                Porphobil_deam 162 AGLkRlgleerisevlspeellpavgQGalavevrked 199
                                   A++kRl+   r  + ++p+ ++p + QG++a+  r ++
  gi|70606576|ref|YP_255446.1| 164 AAIKRLNSVVRYYK-IDPKIITPEANQGIIAIVGRVNE 200
                                   *******4444444.******************99875 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   3.1e-12   2.7e-08       2      74 ..     216     284 ..     215     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.1e-12
                                   HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHHH CS
               Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeell 74 
                                   +e+l+ER++ k L+GGC+ PiG  a++  ++e + + + +  d +k + +e   +g   ++  +G k+ +++ 
  gi|70606576|ref|YP_255446.1| 216 KEALVERTVVKLLGGGCHSPIGILASMISENEFNVISTYVISDKKK-ITIEGIYRG---DPTTVGEKVVKDMV 284
                                   5789**********************99666699999999999976.777777777...699****9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1903.65
//
Query:       gi|162139948|ref|YP_255447.2|  [L=220]
Description: hypothetical protein Saci_0781 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-16   60.5   0.0    1.9e-16   60.1   0.0    1.1  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   1.1e-20   1.9e-16      36     231 ..      37     208 ..      17     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.1e-20
                                    T.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-.-- CS
                           HEM4  36 ddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTaraLeelglrvdlvpseegtaegLaeelaesl 115
                                    + l+  ++d++ ftS+n+v + f+       d + ++  k++avG++Ta a+ + g+ ++ vp  e+t+ ++++++ ++ 
  gi|162139948|ref|YP_255447.2|  37 EILN--QIDGIGFTSVNGVMC-FK-------DFDRIRLSKIYAVGRSTAMAIMNKGFPDVKVPT-EFTVNSMIQLMLNDG 105
                                    3355..99*************.33.......444566669***********************9.*********999544 PP

                                    -EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HHHHH CS
                           HEM4 116 agkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealkagevdavvftSpstvrnllellkdegdel 195
                                      k+ +++r++ + ++  e  +    +v+ ++ Y+ ++ e + e++k ++k+ +vd+vv+tS+  +  +   ++      
  gi|162139948|ref|YP_255447.2| 106 L-KNPVVVRSKVGYERDRELIR----NVVFLVDYDLEVIEHNLERAKSLIKECRVDIVVVTSSKIASLIKDSIS------ 174
                                    4.56777799988888777774....899*********************************876655555555...... PP

                                    CTSEEEEESHHHHHHHHHTT---SEEETS--HHHHH CS
                           HEM4 196 kevkvaaiGptTaealkklglkvdvvaeeptaeglv 231
                                    + +k+++iGp+T+ al   g++++++a++++++g +
  gi|162139948|ref|YP_255447.2| 175 NCIKIVSIGPITSSAL--EGVNNIYEAKQHDINGVL 208
                                    578*************..8************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1453.36
//
Query:       gi|70606578|ref|YP_255448.1|  [L=550]
Description: hypothetical protein Saci_0782 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-33  116.7   0.1    4.1e-32  112.2   0.1    2.0  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
      0.002   17.6   0.0      0.021   14.2   0.0    2.5  3  Sulfatase      Sulfatase
     0.0047   17.0   0.0      0.029   14.5   0.0    2.1  2  PglZ           PglZ domain
  ------ inclusion threshold ------
      0.069   13.4   0.0       0.23   11.7   0.0    1.8  2  Peptidase_M23  Peptidase family M23


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.1   9.1e-36   4.1e-32       1     356 [.       3     480 ..       3     481 .. 0.73

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 9.1e-36
                                   EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEET CS
                  Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvt 81 
                                   vl++++DGl+++ ++r++++lp ++ L+++g++++ l++vfP+lT+ ++asl+TG +P+++G+ + ++y + +  + + + 
  gi|70606578|ref|YP_255448.1|   3 VLLVVIDGLSFSVFERIKDKLPVMKDLIEKGFYSK-LESVFPSLTPVALASLATGFNPKNNGVNSSKIYLKNSSLDKPLSA 82 
                                   79**************999****************.*********************************666666557777 PP

                                   TTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.................................... CS
                  Phosphodiest  82 ededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs................................... 127
                                   ++++a   ++  piw+ +ak+ g+++ ++ +p + +d+ +   lv+                                   
  gi|70606578|ref|YP_255448.1|  83 YNSKA---LKVNPIWVYLAKE-GYNVLVASFPQALPDRWNMEGLVLldpyrsrirkcsdgkvirsgenkvlgkiwlvesrh 159
                                   77775...999**********.****************9888888899999999977777777777777777666666666 PP

                                   .....................................................TBHHSBTCT.CSTTS............. CS
                  Phosphodiest 128 .....................................................etppryleddfnakv............. 142
                                                                                                                    
  gi|70606578|ref|YP_255448.1| 160 nngyyvsysspsgeksieiskgdwygpieiygkcgkneltgisflharedsiyL-------------Spvsfynkewcnkp 227
                                   666555555555555555555555555555554444444444444433333330.............03333333344444 PP

                                   .................................CHHHHHH.HHHHHHHHHCHTHSHHHHHCT...SSESEEEEEECCCHHH CS
                  Phosphodiest 143 .................................pledkvd.kavlqtwldaafakvvlekel...ekpdlllvyleetDtv 186
                                                                    ++ +++d +  + +++++ +++      l    k+dl ++yl+ +D  
  gi|70606578|ref|YP_255448.1| 228 simenvwnyvslkygmmldgdypslskgiitfeEYMKTIDlT--F-DFFKNYTKY------LldnIKWDLAITYLPIVDNL 299
                                   444444444456666666666666666666444444444421..2.344444433......345599************** PP

                                   HHHH.-TTSHH....HHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH......GEE CS
                  Phosphodiest 187 gHkf.Gpdspe....vedalrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg......llh 256
                                   +H + G+d+ +    +++ +  +D++i+  l++++         i++vSDHG++ +  +k +++n+lle+        +++
  gi|70606578|ref|YP_255448.1| 300 QHLLyGIDDDKayeyILKGYLMADEFIKLQLDYAP--------LIFIVSDHGIEKI--KKRVYVNKLLEKMNilklrsEDE 370
                                   **853887666688899999999999998777777........59***********..***********999999999888 PP

                                   EEECBHHS.SSE...EEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHST.HTTTEEEEEGGGS-GGGCHSTTS-SEEEE CS
                  Phosphodiest 257 lkdegkggakal...iainpkare.lnrvaeaeaeevyaelkakleelrkk.egealavylkeaipkrlhykkrapdlvlv 332
                                   +++++++++++    i+in+++re ++ v ++e+ + ++++ ++le l +  e  ++ +y +e +p+    ++r +d++++
  gi|70606578|ref|YP_255448.1| 371 IDWSKTKAYYVGggqIRINLRGREnRGIVSIKEFPKLVKRIVKNLENLKDEnEQIFTSIYANE-VPS----SDREGDITIM 446
                                   88888888888899******************************8988766344466666555.887....5999*****8 PP

                                   E-TTEEEESSTTCS..........SBS-SEE--S CS
                  Phosphodiest 333 adpgwsitskdkpd..........eyeikgthGy 356
                                     ++++  s+  ++           ++  g+hGy
  gi|70606578|ref|YP_255448.1| 447 GVRRYYGISSMVKAnqevlenvkpYVTATGEHGY 480
                                   8777775554444445666666555555566665 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.6e-06     0.021       3      96 ..       3     104 ..       2     177 .. 0.81
   2 ?   -0.8   0.0      0.18     8e+02     236     252 ..     329     345 ..     323     384 .. 0.81
   3 ?   -1.9   0.0      0.38   1.7e+03     296     307 ..     510     521 ..     491     523 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-06
                                   EEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTT........ CS
                     Sulfatase   3 vvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgg........ 75 
                                   v+l+++d l   ++++++      p +++l e+g+  +   +  +l+  ++a+l tg++p+n+gv s+  + +        
  gi|70606578|ref|YP_255448.1|   3 VLLVVIDGL---SFSVFERIKDKLPVMKDLIEKGFYSKLESVFPSLTPVALASLATGFNPKNNGVNSSKIYLKnssldkpl 80 
                                   899******...666777777777778888999998888888888*******************999999999******** PP

                                   ...HHCTTTS-HHHHHHHHTT-EE CS
                     Sulfatase  76 ...gglpqteatLpellkeaGYnt 96 
                                      ++++ +++ +  +l + GYn 
  gi|70606578|ref|YP_255448.1|  81 sayNSKALKVNPIWVYLAKEGYNV 104
                                   ***********************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.18
                                   TTGGGEEEEEEESSSSC CS
                     Sulfatase 236 glldntlvvftSDhgas 252
                                   +l+   l++++SDhg +
  gi|70606578|ref|YP_255448.1| 329 QLDYAPLIFIVSDHGIE 345
                                   55666689999***974 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.38
                                   GGGHHHHHHHHT CS
                     Sulfatase 296 hiDlfptildla 307
                                    iD++ptil+l+
  gi|70606578|ref|YP_255448.1| 510 IIDIAPTILSLF 521
                                   69*******997 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.4e-06     0.029       2      58 ..       2      60 ..       1      89 [. 0.83
   2 ?   -0.6   0.0      0.27   1.2e+03     148     168 ..     324     343 ..     285     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                          PglZ  2 kvfvIisDalryeaweelkqlLnked.rfeael.savlgvlPslTklgraallpgkkll 58
                                  kv ++++D+l + + e +k+ L   +  +e    s+  +v PslT ++ a+l  g +++
  gi|70606578|ref|YP_255448.1|  2 KVLLVVIDGLSFSVFERIKDKLPVMKdLIEKGFySKLESVFPSLTPVALASLATGFNPK 60
                                  89********************8655044444568899*************98887765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                          PglZ 148 elvkslleengykvlltaDHG 168
                                   e +k  l++ +  +++++DHG
  gi|70606578|ref|YP_255448.1| 324 EFIKLQLDY-APLIFIVSDHG 343
                                   555556677.88899*****9 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.1e-05      0.23      11      62 ..     127     183 ..     118     207 .. 0.69
   2 ?   -2.2   0.0       1.1   4.9e+03      30      46 ..     484     500 ..     450     507 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.1e-05
                                   TTT-EEEESSSEEEEEEEEETTTE..EEEEEEECTCEEEEEEEESE...ESS-TTEE CS
                 Peptidase_M23  11 pkgtpVlAaadGtVvfagkkegyG..nvviidhgdgystlyahlsk...isvkegqk 62 
                                   p+ + ++  +dG+V+ +g+++ +G  ++v  +h++gy+  y   s    i++++g+ 
  gi|70606578|ref|YP_255448.1| 127 PYRSRIRKCSDGKVIRSGENKVLGkiWLVESRHNNGYYVSYSSPSGeksIEISKGDW 183
                                   6667788899*********98666226788999***999998855411144667765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                   ETTTEEEEEEEECTCEE CS
                 Peptidase_M23  30 kegyGnvviidhgdgys 46 
                                   ++ yG v+i  +++++ 
  gi|70606578|ref|YP_255448.1| 484 NDLYGIVIIYSKNNNFK 500
                                   23667777766666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3607.24
//
Query:       gi|70606579|ref|YP_255449.1|  [L=227]
Description: hypothetical protein Saci_0783 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1643.75
//
Query:       gi|70606580|ref|YP_255450.1|  [L=326]
Description: hypothetical protein Saci_0787 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   24.6   0.0    3.2e-05   23.5   0.0    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.13   13.3   0.1       0.79   10.8   0.0    2.2  2  Methyltransf_24  Methyltransferase domain
       0.17   12.2   0.0         23    5.4   0.0    2.7  3  Uteroglobin      Uteroglobin family


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   5.4e-09   3.2e-05      36     173 ..      29     145 ..      28     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.4e-09
                                   -SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C CS
                 Lactamase_B_2  36 lthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhksgr 116
                                   +th H DHl+ l    + +     +++++ +++ l+  +    + +       +l+ g ++el +   +i++  a+h  g 
  gi|70606580|ref|YP_255450.1|  29 VTHFHSDHLTELEKSLKECT---SIIGTPATIEALDVLGYIVPKHK-----KFPLEYGIEIELSG--ERIKLEKAEHILGA 99 
                                   7********99987666443...599************75544444.....48999999999974..47999999999998 PP

                                   TCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHH CS
                 Lactamase_B_2 117 rldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemi 173
                                            + ++ie+++  ++y+gD  +     g+++ ++d+l++d+t+ +++  +
  gi|70606580|ref|YP_255450.1| 100 ---------AQVLIETDETEIAYTGDFREPG--KGTKILNPDILIIDATYGNPRLVR 145
                                   .........99*****************655..4678999*********98887654 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.49   2.9e+03      60      76 ..     142     157 ..      95     169 .. 0.76
   2 ?   10.8   0.0   0.00013      0.79      47     102 ..     266     324 ..     215     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.49
               Methyltransf_24  60 ealaslaagsiDllfiD 76 
                                    ++++++ +++D+lf D
  gi|70606580|ref|YP_255450.1| 142 RLVRQFK-QDVDMLFAD 157
                                   4556677.888888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
               Methyltransf_24  47 lddrvrli....kadseealaslaagsiDllfiDgghaaeavledleallprlapggvvl 102
                                   ld++  +i    +ad+ee++   ++ s Dl+++Dg+   + +++    +  ++++++vvl
  gi|70606580|ref|YP_255450.1| 266 LDQNSFVIgmssHADFEETVYYIDNTSADLIVVDGS-RSQYAKDLASYINTHMKKKAVVL 324
                                   4444444444447888999999999**********9.45555555577778899888886 PP

>> Uteroglobin  Uteroglobin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.85   5.1e+03      34      65 ..      32      47 ..      23      67 .. 0.61
   2 ?    3.4   0.0     0.016        96      23      64 ..     143     186 ..     132     189 .. 0.87
   3 ?    5.4   0.0    0.0039        23      32      59 ..     293     322 ..     279     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.85
                                  HHHS-HHHHHHHHHTT---HHHHHHHHHHHHH CS
                   Uteroglobin 34 flegseeeYkeeLqkynpdpeaeealaelKqc 65
                                  f  +  +e++++L                K+c
  gi|70606580|ref|YP_255450.1| 32 FHSDHLTELEKSL----------------KEC 47
                                  4444444444444................444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.016
                                   --HHHHHHHHHHH..HS-HHHHHHHHHTT---HHHHHHHHHHHH CS
                   Uteroglobin  23 gCpaleevvekfl..egseeeYkeeLqkynpdpeaeealaelKq 64 
                                       ++++v+ ++   +s+e +k++++ y    +++ea++ l++
  gi|70606580|ref|YP_255450.1| 143 LVRQFKQDVDMLFadYVSDELLKRPVKIYGYYGKIQEAMKILRK 186
                                   56789999*99998889*******************99998875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0039
                                   HHHH..HS-HHHHHHHHHTT---HHHHHHH CS
                   Uteroglobin  32 ekfl..egseeeYkeeLqkynpdpeaeeal 59 
                                    +++   gs ++Y ++L++y++++  ++a+
  gi|70606580|ref|YP_255450.1| 293 ADLIvvDGSRSQYAKDLASYINTHMKKKAV 322
                                   55665578***************9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2229.69
//
Query:       gi|70606581|ref|YP_255451.1|  [L=598]
Description: ATP-dependent DNA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-64  215.7   0.6    1.1e-63  214.6   0.6    1.6  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    4.2e-39  134.6   1.6    8.3e-39  133.7   1.6    1.5  1  DNA_ligase_A_N   DNA ligase N terminus
    9.3e-27   93.5   0.0    2.1e-26   92.4   0.0    1.6  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
      1e-07   32.4   1.2    1.7e-07   31.7   1.2    1.4  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.034   14.2   0.2        2.4    8.3   0.0    3.0  3  DNA_ligase_OB_2  DNA ligase OB-like domain
      0.095   12.7   0.9          3    7.9   0.1    3.1  2  TBPIP            TBPIP/Hop2 winged helix domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.6   0.6   3.6e-67   1.1e-63       1     204 []     235     435 ..     235     435 .. 0.97

  Alignments for each domain:
  == domain 1  score: 214.6 bits;  conditional E-value: 3.6e-67
                                   -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEE CS
                DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElv 81 
                                   pmLAe+l++ +++l k+ +++ iv++KyDGeRaq+hk+g+kv++fSRrl++it+++p++v+ +k+ +k +  +vil+GE+v
  gi|70606581|ref|YP_255451.1| 235 PMLAERLTDPSEILAKV-GGKGIVDYKYDGERAQIHKKGEKVYIFSRRLENITRQYPDVVEYIKNSIKSN--EVILEGEIV 312
                                   9***************9.66667********************************************997..8******** PP

                                   EEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEES CS
                DNA_ligase_A_M  82 avdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevk 162
                                   a+dke+geilpfq l++rk +k ++ e++ke+++ +++FD++y dge++t++pl +Rr++Leei+  ++d v++a+++ ++
  gi|70606581|ref|YP_255451.1| 313 AIDKESGEILPFQNLMHRK-RKNDIGEAIKEYPVNVYLFDLMYNDGEDYTQKPLPDRREKLEEIV-TQNDIVKVADHKYID 391
                                   ******************5.5566*****************************************.9************** PP

                                   SHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                DNA_ligase_A_M 163 dveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                   +v+el e +++ais+g EG++vK+   ds+Y++g r+  w+K+K
  gi|70606581|ref|YP_255451.1| 392 KVNELVEYFHQAISDGTEGVIVKSigKDSIYQAGARGFLWIKLK 435
                                   ************************999***************99 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   1.6   2.8e-42   8.3e-39       1     173 []       2     184 ..       2     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 2.8e-42
                                   BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS-.-----HHHHHHHHHHHHT--H CS
                DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgr.eygigesllakalaealglsk 76 
                                   +F+++ae f+++e+  ++r++ +a+l+++++k    +++ + ++++     l+Pd+ ++ e+g+ge+l++kal+  +++++
  gi|70606581|ref|YP_255451.1|   2 EFKLIAEYFDRLEK-ISSRIQLTALLTDLLKKS---DKDVIDKVIYItqgkLWPDFFEKpEIGLGEKLMIKALSVSTNIKE 78 
                                   59************.8899***********875...46689****************777********************* PP

                                   HHHHHHHHHHS-HHHHHHHHHCCHHHH........------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHH CS
                DNA_ligase_A_N  77 kkikdalakvgDlgevaeevlskrstl........akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEa 148
                                   ++i+++l+ +gDlgeva+++++++s++        +k ++lt+eev+e+L k+a + g+gs+d k++ l++llk+a+p+Ea
  gi|70606581|ref|YP_255451.1|  79 DEIEKQLRILGDLGEVAYKLKRTNSSQnvlsylgsTKVTKLTVEEVYESLSKIALSeGEGSRDMKIRSLAGLLKKADPLEA 159
                                   ******999************88888889************************9778************************ PP

                                   HHHHHHHCT---SS--HHHHHHHHH CS
                DNA_ligase_A_N 149 kyliriilkdlriglsektvldala 173
                                   ky+ir+i ++lr+g+++ t++dala
  gi|70606581|ref|YP_255451.1| 160 KYIIRFIDGRLRVGIGDATIMDALA 184
                                   ***********************97 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.0   6.9e-30   2.1e-26       1      99 []     460     569 ..     460     569 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 6.9e-30
                                   GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG..GGEECTTCESS---HHHHTTEEE-TT-EEEEEESEE CS
                DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk..elerkkppfaekvpeeekrdvWvePelvveVkfaei 77 
                                   rgg+++sll+++yd  ++++ +v+kv++Gfsdaelee++k+l+  +l++k+p+++++ +++     Wv+P++v+e+ +aei
  gi|70606581|ref|YP_255451.1| 460 RGGKLSSLLMAAYDpdKDTFYTVCKVASGFSDAELEEVQKMLSeaKLDKKDPRVESEIQPD----IWVKPKYVAEIIGAEI 536
                                   6899**********98888***********************8788888888886666666....9*************** PP

                                   ECTSSSTT...........EECT-EEEEE-TTS CS
                DNA_ligase_A_C  78 tasgkyka...........slRfPrfkrlReDk 99 
                                   t s+ +++           s+RfPrf+r+R+Dk
  gi|70606581|ref|YP_255451.1| 537 TLSPLHTCckgvvseeaglSIRFPRFIRWRDDK 569
                                   ********************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   1.2   5.8e-11   1.7e-07       5     159 ..     257     433 ..     254     435 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5.8e-11
                                   EEEE-SSEEEEEEEE..TTEEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.............. CS
                    RNA_ligase   5 vtEKlDGtnfriylv..kevgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig.............. 69 
                                   v  K DG++++i++   k v+++sR+ +           +r++ +  +++k+ ++++e+il GE++               
  gi|70606581|ref|YP_255451.1| 257 VDYKYDGERAQIHKKgeK-VYIFSRRLEN---------ITRQYPDVVEYIKNSIKSNEVILEGEIVAidkesgeilpfqnl 327
                                   667***********9633.*******999.........2566677788999****889*********88777666655554 PP

                                   .......SS....TTSS.EEEEEEEEEEE.CTTBECE--HHHHHHHHHCCT...B..EEEEE.SSHHHHHCCC..H.HHHT CS
                    RNA_ligase  70 ......hsi..kygglpkefyvFdifdir.dkeeqrylspdevealakglg...tvpvlyegkflaaeellell.l.skgn 136
                                         + i   ++++p + y+Fd++  + ++ +q+ l+ d++e+l++ +    +v+v+ +  +++ +el e++ +  +  
  gi|70606581|ref|YP_255451.1| 328 mhrkrkNDIgeAIKEYPVNVYLFDLMYNDgEDYTQKPLP-DRREKLEEIVTqndIVKVADHKYIDKVNELVEYFhQaIS-D 406
                                   433332222554444666********9997666777765.445555552223469999955544466677777555434.4 PP

                                   C--EEEEEES..SSSBE.TTE.BSEEE CS
                    RNA_ligase 137 krEGlVikpe..selyk.nkg.raifK 159
                                     EG+++k+   +++y+   +   ++K
  gi|70606581|ref|YP_255451.1| 407 GTEGVIVKSIgkDSIYQaGARgFLWIK 433
                                   89******8754555554444555666 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   6.1e+03      43      51 ..     256     264 ..     253     267 .. 0.82
   2 ?    8.3   0.0    0.0008       2.4       2      36 ..     456     496 ..     455     518 .. 0.79
   3 ?    2.5   0.0      0.05   1.5e+02      57      66 .]     557     566 ..     541     566 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                   EEEEEEE-T CS
               DNA_ligase_OB_2  43 iitykyqel 51 
                                   i+ yky+++
  gi|70606581|ref|YP_255451.1| 256 IVDYKYDGE 264
                                   899***997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0008
                                   ...EEEEEEEEEEEEE.T..TEE....EEE-SS--HHHHHH CS
               DNA_ligase_OB_2   2 GkGkykgmlGallvetkk..gkr....fkiGsGlsdaqRen 36 
                                   G+Gk  g+l +ll+   +  +++     k++sG+sda+ e+
  gi|70606581|ref|YP_255451.1| 456 GRGKRGGKLSSLLMAAYDpdKDTfytvCKVASGFSDAELEE 496
                                   99************997532333344589********9777 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.05
                                   -EEEEEEEE- CS
               DNA_ligase_OB_2  57 pRfPsflrvR 66 
                                    RfP+f r+R
  gi|70606581|ref|YP_255451.1| 557 IRFPRFIRWR 566
                                   6*******98 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00099         3      17      44 ..     102     130 ..      93     133 .. 0.89
   2 ?    1.8   0.1     0.078   2.3e+02      48      60 ..     411     423 ..     407     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00099
                         TBPIP  17 fsvqdvvanlqk.klgKtavqkaLdeLvd 44 
                                    s+q+v ++l++ k++K +v ++ ++L++
  gi|70606581|ref|YP_255451.1| 102 NSSQNVLSYLGStKVTKLTVEEVYESLSK 130
                                   699**********************9975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.078
                         TBPIP  48 iieKeyGKqkiYl 60 
                                   +i K +GK +iY 
  gi|70606581|ref|YP_255451.1| 411 VIVKSIGKDSIYQ 423
                                   689*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4000.62
//
Query:       gi|70606582|ref|YP_255452.1|  [L=172]
Description: deoxycytidine triphosphate deaminase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-27   95.3   0.0    2.8e-27   94.9   0.0    1.1  1  dUTPase   dUTPase
    1.9e-08   33.5   0.0    7.3e-08   31.6   0.0    2.0  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   3.2e-31   2.8e-27       3     126 ..      47     166 ..      45     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 3.2e-31
                                   CTBEBESSTT-SSEEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE- CS
                       dUTPase   3 aeiptrkspesAgyDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnl 83 
                                   ++++ +  p  +++D++  ++++++p+e+vl++t+ ++klp++++a+++ RS +a++gl+++p+++d+ ++G  ++++ + 
  gi|70606582|ref|YP_255452.1|  47 DKVFDPDNPDYSFFDVQRGEEFIISPHEHVLLVTEEYMKLPNDVMAFVNLRSTFARLGLFIPPTIVDAGFEG--QLTIEVV 125
                                   6788999999**************************************************************..7777777 PP

                                   SSS.-EEE-TT-EEEEEEEEEBECGEEEEESST.TTESSBTTXTT CS
                       dUTPase  84 tkk.dvkikkgdRiAqLifariltaeleevetl.katergeggfg 126
                                   +++ +vki +g+R+++Lifar+lt    +ve++ + +++g++g++
  gi|70606582|ref|YP_255452.1| 126 GSSfPVKIRRGTRFLHLIFARTLT----PVENPyQGKYQGQKGVT 166
                                   7777********************....8998889*******986 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   8.1e-12   7.3e-08       4     165 ..       2     149 ..       1     166 [. 0.79

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 8.1e-12
                           DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlekgcvY 84 
                                   il d++++  +e+g+ik  ep+  + +  + +DLr+g++  r +      +++  +    ++++ +++  e+ ++      
  gi|70606582|ref|YP_255452.1|   2 ILGDRDLKYYLEKGWIK-VEPIYGDSVRENGIDLRVGNEIARFKK-----TDKVFDPDNPDYSFFDVQRGEEFIISPHEHV 76 
                                   67788888888889985.567888889999999999998766543.....3455555566777777777777777766555 PP

                           DCD  85 ivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsqirfrrgea 165
                                   ++  +e ++Lp+d+ a +n +s+  Rl +f+            v+ag++G+l +e++  sF++++r+G+r   + f r+ +
  gi|70606582|ref|YP_255452.1|  77 LLVTEEYMKLPNDVMAFVNLRSTFARLGLFIPP--------TIVDAGFEGQLTIEVVGSSFPVKIRRGTRFLHLIFARTLT 149
                                   666799************************753........35889*************************9999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1153.89
//
Query:       gi|70606583|ref|YP_255453.1|  [L=235]
Description: hypothetical protein Saci_0790 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.021   14.8   0.2      0.021   14.8   0.2    2.6  2  RHH_1           Ribbon-helix-helix protein, copG family
      0.044   14.3   2.8      0.094   13.2   2.1    2.0  1  PIN_6           PIN domain of ribonuclease
      0.047   13.7   0.2       0.33   11.0   0.2    2.4  3  Nudix_hydro     Nudix hydrolase domain
      0.053   13.7  12.7       0.28   11.4  12.7    2.1  1  Uds1            Up-regulated During Septation
        0.2   12.3   9.5       0.16   12.7   3.4    2.4  2  YabA            Initiation control protein YabA
       0.25   11.7  15.2      0.039   14.3   7.0    2.3  2  Muted           Organelle biogenesis, Muted-like protein
       0.43   10.5   4.7       0.27   11.1   1.1    2.6  2  Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain o
       0.57   10.5   2.6       0.71   10.2   1.3    1.8  2  DUF4634         Domain of unknown function (DUF4634)
        0.7   10.2  13.3        1.3    9.3  13.3    1.5  1  Vfa1            AAA-ATPase Vps4-associated protein 1
       0.72    9.2   7.7       0.92    8.8   7.7    1.3  1  DUF4407         Domain of unknown function (DUF4407)
       0.86    8.2   3.8        1.1    7.8   3.8    1.1  1  Ndc1_Nup        Nucleoporin protein Ndc1-Nup
       0.94    9.6   3.8        3.9    7.6   0.2    3.1  3  PspB            Phage shock protein B
        1.1    9.1   7.2       0.37   10.6   3.6    1.9  2  Ferritin-like   Ferritin-like
        1.3    9.7   5.8        4.3    8.0   0.1    2.2  2  EST1            Telomerase activating protein Est1
          2    8.8   8.6       0.14   12.5   1.3    2.8  3  TSC22           TSC-22/dip/bun family
        2.7    8.1   9.9       0.34   11.1   2.7    2.3  2  p25-alpha       p25-alpha
        3.1    8.5   7.6        1.7    9.3   3.0    2.4  2  Sas10_Utp3      Sas10/Utp3/C1D family
        4.3    6.6  17.2        1.5    8.1   8.9    2.2  2  Rtf2            Rtf2 RING-finger
        9.7    6.4  12.5        2.3    8.4   6.2    2.3  2  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   2.2e-05     0.021       4      31 ..       6      34 ..       4      38 .. 0.89
   2 ?   -0.7   0.8       1.7   1.6e+03       8      19 ..      78      89 ..      75      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                                  EEEEHHHHHHHHHHHHHHT.SSHHHHHHH CS
                         RHH_1  4 irldeellerLdelarrrg.rSrSelIRe 31
                                  i+l+ee++++L+e+ar++g + +Se IR 
  gi|70606583|ref|YP_255453.1|  6 IKLSEEEYKQLEERARKEGyVLVSEYIRS 34
                                  99*****************9999998885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                  HHHHHHHHHHHH CS
                         RHH_1  8 eellerLdelar 19
                                  eel++++ el +
  gi|70606583|ref|YP_255453.1| 78 EELKKKIAELSE 89
                                  677777777765 PP

>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.1    0.0001     0.094       8      76 ..      69     138 ..      66     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                         PIN_6   8 liknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspe.svkkvtefakktGDlsvLS 76 
                                   +i+  +++l++l++k+  ++e ++E+ dkk +++ +++ + le+r+P+++ + k +++ + k   +++L 
  gi|70606583|ref|YP_255453.1|  69 FINPFTAQLEELKKKIAELSERIEELEDKKMEKQDQTTNKPLETRQPQSKkDDKQIQQQSPKKTAIEILT 138
                                   56666789*******************************9999999986514566777776666666665 PP

>> Nudix_hydro  Nudix hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.3     5e+03      42      56 ..       2      16 ..       1      26 [. 0.60
   2 ?   -0.4   0.0       1.3   1.2e+03       9      32 ..     140     163 ..     138     177 .. 0.78
   3 ?   11.0   0.2   0.00035      0.33      10      70 ..     165     226 ..     158     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.3
                   Nudix_hydro 42 rgvwlkvpieqselv 56
                                  + +++k++ e+ + +
  gi|70606583|ref|YP_255453.1|  2 KTIYIKLSEEEYKQL 16
                                  678888887765543 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                   Nudix_hydro   9 gGvtvdseelpedeeeFkskLkas 32 
                                   +Gv+ +se + +d+++F +kL++ 
  gi|70606583|ref|YP_255453.1| 140 QGVIFESEVKLRDPDAFFNKLERE 163
                                   588889988999999999999876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00035
                   Nudix_hydro  10 Gvtvdsee.lpedeeeFkskLkaslsqwreegkrgvwlkvpieqselvpiavkeGFefHhae 70 
                                    +++++e+ +   + eF ++ +++++q  +++k+    k+++++++l   +v+eG+ ++++e
  gi|70606583|ref|YP_255453.1| 165 AMIINTEKeRIALSREFFEEFQNKIKQIHSSDKEETASKLETREAKLFRKLVEEGLAIYNSE 226
                                   5677885525558999*****************************************99987 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  12.7   0.00029      0.28      21      70 ..      75     161 ..      73     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                          Uds1  21 eeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksak................................ 69 
                                    ++eelkk+++ L+er+e l+ k ++e++ ++  + L++++ +skk++k                                
  gi|70606583|ref|YP_255453.1|  75 AQLEELKKKIAELSERIEELEDK-KMEKQDQTTNKPLETRQPQSKKDDKqiqqqspkktaieilteqgvifesevklrdpd 154
                                   589********************.*****************8888886666666666666666666666666666655555 PP

                          Uds1  70 ......s 70 
                                         +
  gi|70606583|ref|YP_255453.1| 155 affnklE 161
                                   5554441 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.4   0.00017      0.16       4      75 ..      64     136 ..      59     144 .. 0.64
   2 ?    2.9   0.4      0.17   1.6e+02      35      83 ..     171     222 ..     145     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeL..eleneklrerleeeekkekekkkelsegkenLar 75 
                                   k+++d ++ ++ qleel+++++el e+++el ++  e   ++ n+ l +r+  ++kk++++ +++s  k+ ++ 
  gi|70606583|ref|YP_255453.1|  64 KKVIDFINPFTAQLEELKKKIAELSERIEELEDKKMEKqdQTTNKPLETRQP-QSKKDDKQIQQQSPKKTAIEI 136
                                   5577888888999999999999999999998776543311455777777773.344444444444445555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.17
                                   HHHHHHHHHH.HHHHHHHH.XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                          YabA  35 leenaeLele.neklrerl.eeeekkekekkkels.egkenLarlYeeGFHi 83 
                                    +e  +L+ e  e++++++ + ++++++e+ ++l+ +  + +++l eeG  i
  gi|70606583|ref|YP_255453.1| 171 EKERIALSREfFEEFQNKIkQIHSSDKEETASKLEtREAKLFRKLVEEGLAI 222
                                   3444444444324444444322233333333333303344567888988776 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.0   4.1e-05     0.039      47     125 ..      54     135 ..      34     142 .. 0.71
   2 ?    2.1   1.1      0.24   2.3e+02     100     130 ..     168     198 ..     156     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                         Muted  47 lvnelkeqllpkcles...mkenLselnkkleaalekverllqkeleee.krkseqlqekeeerkaeweeflkelqekkee 123
                                   l+n+l+ +l +k+++       +L+el+kk+ ++ e +e+l++k+ e++ +++++ l++++ ++k+   + +++++ kk  
  gi|70606583|ref|YP_255453.1|  54 LINQLMPKLEKKVIDFinpFTAQLEELKKKIAELSERIEELEDKKMEKQdQTTNKPLETRQPQSKKDD-KQIQQQSPKKTA 133
                                   4444444444444444444789********************99987761555666776666666655.555888888877 PP

                         Muted 124 vD 125
                                   ++
  gi|70606583|ref|YP_255453.1| 134 IE 135
                                   76 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                         Muted 100 qekeeerkaeweeflkelqekkeevDeefee 130
                                    ++e+er a   ef +e q+k +++  + +e
  gi|70606583|ref|YP_255453.1| 168 INTEKERIALSREFFEEFQNKIKQIHSSDKE 198
                                   4566777777778888888887777654333 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00029      0.27      16      44 ..      69      97 ..      52      98 .. 0.85
   2 ?   -0.9   0.1       1.7   1.6e+03      21      43 ..     186     209 ..     181     211 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil 16 FQtkVeseiqaLtqkLeavtkRlealEnk 44
                                  F +  + +++ L +k ++ ++R+e lE+k
  gi|70606583|ref|YP_255453.1| 69 FINPFTAQLEELKKKIAELSERIEELEDK 97
                                  55556788999999999999999999987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                   HHHHHHHHH.HHHHHHHHHHHHHH CS
                Matrilin_ccoil  21 eseiqaLtq.kLeavtkRlealEn 43 
                                   +++i++  +   e+ +++le+ E 
  gi|70606583|ref|YP_255453.1| 186 QNKIKQIHSsDKEETASKLETREA 209
                                   444555544234555666666665 PP

>> DUF4634  Domain of unknown function (DUF4634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.3   0.00075      0.71      61     122 ..      75     136 ..      65     144 .. 0.81
   2 ?   -1.7   0.0       3.6   3.4e+03      56      69 ..     143     156 ..     135     207 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                       DUF4634  61 drlnrldkevteavettisleteradhqkpvtvkpvtmetqsPdlndavsslqsPvslllsw 122
                                    +l++l+k++ e +e    le +++++q   t kp+ + ++  + +d   + qsP    + +
  gi|70606583|ref|YP_255453.1|  75 AQLEELKKKIAELSERIEELEDKKMEKQDQTTNKPLETRQPQSKKDDKQIQQQSPKKTAIEI 136
                                   68999******************************988766666677767778887666555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                       DUF4634  56 ifesedrlnrldke 69 
                                   ifese +l+  d  
  gi|70606583|ref|YP_255453.1| 143 IFESEVKLRDPDAF 156
                                   55665555443322 PP

>> Vfa1  AAA-ATPase Vps4-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  13.3    0.0014       1.3      64     169 ..      76     201 ..      61     212 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                          Vfa1  64 kkkeleeeiekvkkeyeekqkkkkekekkkkekd...kkdkdkkkekekdkkkekek...................eeekk 122
                                   + +el+++i+++ +++ee ++kk ek++++++k    +  + ++k+++k+ ++++ k                        
  gi|70606583|ref|YP_255453.1|  76 QLEELKKKIAELSERIEELEDKKMEKQDQTTNKPletR--QPQSKKDDKQIQQQSPKktaieilteqgvifesevkL---- 150
                                   34567888888888888888888877777755555331..2222222222222221123456666666666533321.... PP

                          Vfa1 123 kelkkaeeelee.................keeprvkkykLhkefyqsRlerkrqaeaakeneer 169
                                   +          +                 +e++   + +L++ef++  +++++q + + ++e+ 
  gi|70606583|ref|YP_255453.1| 151 R----------DpdaffnkleregamiinTEKE---RIALSREFFEEFQNKIKQIHSSDKEETA 201
                                   2..........1333333344466675434444...45*******9999998776666655544 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.7   0.00097      0.92     130     235 ..      61     198 ..      10     221 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00097
                       DUF4407 130 a...........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake..kkaqldaaqa 197
                                   +           +ta+l+el+++ia+l++ i+++e++  +++++ +++   t++ + +++  + +   +  kk++++ +++
  gi|70606583|ref|YP_255453.1|  61 KlekkvidfinpFTAQLEELKKKIAELSERIEELEDKKMEKQDQTTNKPLETRQPQSKKDDKQIQQ--QspKKTAIEILTE 139
                                   155555555555666666666666666666666666666666666555555444442222222222..1334444444444 PP

                       DUF4407 198 elaelkakld.....................atarlaalraelaeleaerakeraasqa 235
                                   +   ++++++                     +++r+a  r+  +e ++++++++++ ++
  gi|70606583|ref|YP_255453.1| 140 QGVIFESEVKlrdpdaffnkleregamiintEKERIALSREFFEEFQNKIKQIHSSDKE 198
                                   44444444336666666666666666667766666666666666666655555544443 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.8    0.0012       1.1     337     396 ..      78     164 ..      72     225 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                      Ndc1_Nup 337 keClklikeltqrinergq.papkaaps..kapknkasapvkelprlsksplkkk......dde..ifgn........... 395
                                   +e  k i+el++ri+e  + +  k+ ++  k++++++++++k+ ++++++++kk+      + +  if +           
  gi|70606583|ref|YP_255453.1|  78 EELKKKIAELSERIEELEDkKMEKQDQTtnKPLETRQPQSKKDDKQIQQQSPKKTaieiltE-QgvIFESevklrdpdaff 157
                                   56667789999999998885333333335677888899999999999999999987665531.234555344333333333 PP

                      Ndc1_Nup 396 ......s 396
                                          
  gi|70606583|ref|YP_255453.1| 158 nklereG 164
                                   3344430 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.7   2.5e+03      34      45 ..       7      18 ..       3      22 .. 0.75
   2 ?    7.6   0.2    0.0041       3.9      41      62 ..      75      96 ..      59     104 .. 0.93
   3 ?    1.3   0.1      0.38   3.6e+02      24      49 ..     193     218 ..     191     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                          PspB 34 glsaedekrLee 45
                                  +ls+e+ k+Lee
  gi|70606583|ref|YP_255453.1|  7 KLSEEEYKQLEE 18
                                  588888888876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0041
                          PspB 41 krLeellekAekleeRietLEr 62
                                   +Leel +k  +l+eRie LE+
  gi|70606583|ref|YP_255453.1| 75 AQLEELKKKIAELSERIEELED 96
                                  68******************96 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.38
                          PspB  24 HYrskkkrskglsaedekrLeellek 49 
                                   H + k++++++l+  + k  ++l+e+
  gi|70606583|ref|YP_255453.1| 193 HSSDKEETASKLETREAKLFRKLVEE 218
                                   77789999999*99999999999986 PP

>> Ferritin-like  Ferritin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.6   0.00039      0.37     136     197 ..      78     141 ..      37     161 .. 0.83
   2 ?   -0.5   0.1      0.99   9.4e+02     132     156 ..     179     203 ..     157     221 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                   HHHHHHHHHTGGG--T.SS---......------------S-HHHHH...HHHHHHHHHHHHHH CS
                 Ferritin-like 136 eaileglreleeeake.egeelfkgdp.ekqiteeesfesedellpvtdlesaleaisiIveqG 197
                                   e++++++ el+e+ +e e +++ k d+ +++  e ++++s+++  ++++++   +ai+i++eqG
  gi|70606583|ref|YP_255453.1|  78 EELKKKIAELSERIEElEDKKMEKQDQtTNKPLETRQPQSKKDDKQIQQQSPKKTAIEILTEQG 141
                                   5678889999999999877777666655999999999999***********************9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHHHTGGG--TSS--- CS
                 Ferritin-like 132 gefYeaileglreleeeakeegeel 156
                                    ef+e+ ++++++++ + kee+++ 
  gi|70606583|ref|YP_255453.1| 179 REFFEEFQNKIKQIHSSDKEETASK 203
                                   4788888888888877777744333 PP

>> EST1  Telomerase activating protein Est1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.7     0.092        87      46     110 ..      60     126 ..      14     139 .. 0.52
   2 ?    8.0   0.1    0.0046       4.3      12      59 ..     179     226 ..     176     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.092
                                   HHHHHHHHHHHHHHHHHHHHH-B-..HTT............-.....---------TTB--TTSHHH CS
                          EST1  46 vkflksaigfYqsliqrllsefel..elssvlkvilksktklpekessekseteseeeksslssseq 110
                                    k+ k++i f + +  +l++  +   els+ ++ ++ +k + ++++++++ et++ ++k+++++ +q
  gi|70606583|ref|YP_255453.1|  60 PKLEKKVIDFINPFTAQLEELKKKiaELSERIEELEDKKMEKQDQTTNKPLETRQPQSKKDDKQIQQ 126
                                   4444444444444444444442213444444444444555555555555555333333333333333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0046
                                   HHHHHHHHHHHHHHH----.---H.HHHHHHHHHHHHHHHHHHHHHHHH CS
                          EST1  12 yevikllkkqlknldsapk.kkkkpvekrklklklvkflksaigfYqsl 59 
                                    e+++++++++k++ s+ k ++  + e+r+  + ++k+  ++ ++Y+s 
  gi|70606583|ref|YP_255453.1| 179 REFFEEFQNKIKQIHSSDKeETASKLETREA-KLFRKLVEEGLAIYNSE 226
                                   57899**********7766555555566666.88************985 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.5   5.2e+03      34      52 ..      40      58 ..      37      62 .. 0.77
   2 ?   12.5   1.3   0.00015      0.14      17      35 ..      78      96 ..      75     118 .. 0.88
   3 ?   -0.9   0.3       2.2   2.1e+03      27      42 ..     198     214 ..     177     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.5
                         TSC22 34 eeENslLkalaspeqleql 52
                                  e++ ++ +a a ++ ++ql
  gi|70606583|ref|YP_255453.1| 40 ESQRTITRAEAGSDLINQL 58
                                  5566788999999999987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00015
                         TSC22 17 evLkekIkeLeernselee 35
                                  e+Lk+kI+eL er++ele 
  gi|70606583|ref|YP_255453.1| 78 EELKKKIAELSERIEELED 96
                                  99***************96 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.2
                         TSC22  27 eernsele.eENslLka 42 
                                   ee+ s+le +E +l+++
  gi|70606583|ref|YP_255453.1| 198 EETASKLEtREAKLFRK 214
                                   45555565235555554 PP

>> p25-alpha  p25-alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   3.8       1.7   1.6e+03      61     100 ..      84     118 ..      53     133 .. 0.52
   2 ?   11.1   2.7   0.00036      0.34      14      88 ..     122     197 ..     112     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                     p25-alpha  61 feqfkealeelaekkfkkkkkeeeleliekliegkgPklq 100
                                   +++  e +eel +kk++k+      + ++k +e ++P+++
  gi|70606583|ref|YP_255453.1|  84 IAELSERIEELEDKKMEKQD-----QTTNKPLETRQPQSK 118
                                   23334444444444222222.....234455555555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00036
                     p25-alpha  14 kktgkemdnknfsKlckDckiid.kkvtstdvDiiFsKvkaksarkitfeqfkealeelaekkfkkkkkeeeleli 88 
                                   k+ +++  +k+   ++++ ++i   +v+ +d D +F+K   ++a  i+ e+   al+    ++f++k k+ +++++
  gi|70606583|ref|YP_255453.1| 122 KQIQQQSPKKTAIEILTEQGVIFeSEVKLRDPDAFFNKLEREGAMIINTEKERIALSREFFEEFQNKIKQIHSSDK 197
                                   444445556666778888898888********************************99888889998887776333 PP

>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.0    0.0018       1.7       1      33 [.      77     116 ..      73     137 .. 0.71
   2 ?    0.6   0.1      0.91   8.6e+02       8      28 ..     182     203 ..     179     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                    Sas10_Utp3   1 leslsksldelqeslepllskakaee....kkslsd.......e 33 
                                   le+l+k++ el+e +e+l +k+ +++    +    +       +
  gi|70606583|ref|YP_255453.1|  77 LEELKKKIAELSERIEELEDKKMEKQdqttN----KpletrqpQ 116
                                   799***************9986665543321....123334331 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.91
                    Sas10_Utp3   8 ldelqeslepllskakaee.kk 28 
                                   ++e q+++++++s++k+e+ +k
  gi|70606583|ref|YP_255453.1| 182 FEEFQNKIKQIHSSDKEETaSK 203
                                   5778888888888777666422 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.9    0.0016       1.5     167     230 ..      69     132 ..      59     151 .. 0.77
   2 ?    3.1   1.2     0.053        50     160     206 ..     160     207 ..     147     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                          Rtf2 167 plnptkeelellkarleeekakkkkkkkakkkkkakakgskaeaeaaskssseasesskagkkk 230
                                    +np  ++le+lk+++ e +++ ++  ++k +k+++++++  e+++ ++++ +++ ++++ kk+
  gi|70606583|ref|YP_255453.1|  69 FINPFTAQLEELKKKIAELSERIEELEDKKMEKQDQTTNKPLETRQPQSKKDDKQIQQQSPKKT 132
                                   69********************999999999999999999999998877776665444444433 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.053
                          Rtf2 160 ykeedviplnptkeelellkarleeekakkkk.kkkakkkkkakakgs 206
                                   ++ e ++++n +ke  +l ++  ee + k k+ ++++k+++++k +++
  gi|70606583|ref|YP_255453.1| 160 LEREGAMIINTEKERIALSREFFEEFQNKIKQiHSSDKEETASKLETR 207
                                   56778899*****************99995551555555555544433 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.2    0.0024       2.3      22      84 ..      55     117 ..      53     152 .. 0.72
   2 ?    1.5   0.3      0.34   3.2e+02      36      73 ..     167     204 ..     152     229 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                                   HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkssk 84 
                                   +++l+ k ek+v + ++  + +lee++++  e +e ++e++d+  ekq +++++   +++ ++
  gi|70606583|ref|YP_255453.1|  55 INQLMPKLEKKVIDFINPFTAQLEELKKKIAELSERIEELEDKKMEKQDQTTNKPLETRQPQS 117
                                   567888888888888888888899999888888888888888888888887765333333222 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.34
                                   HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskk 73 
                                    +++ +++++  ++  +e ++ +k+i++s +e+ +sk 
  gi|70606583|ref|YP_255453.1| 167 IINTEKERIALSREFFEEFQNKIKQIHSSDKEETASKL 204
                                   44444444444555555556666666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3074  (0.171454); expected 358.6 (0.02)
Passed bias filter:                      949  (0.052931); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 1434.49
//
Query:       gi|70606584|ref|YP_255454.1|  [L=235]
Description: hypothetical protein Saci_0791 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-27   95.7   1.3    8.2e-15   54.6   1.1    2.3  2  Thioredoxin_3  Thioredoxin domain
    6.3e-05   22.9   0.7     0.0063   16.5   0.3    2.3  2  Thioredoxin    Thioredoxin
    0.00011   22.6   6.4      0.029   14.8   0.3    3.5  2  Thioredoxin_2  Thioredoxin-like domain
    0.00048   20.3   5.3      0.059   13.6   1.6    3.2  2  Glutaredoxin   Glutaredoxin
  ------ inclusion threshold ------
      0.011   15.9   0.4       0.25   11.6   0.1    2.5  2  Thioredoxin_7  Thioredoxin-like
      0.011   16.0   0.1        9.8    6.6   0.0    3.0  2  Thioredoxin_8  Thioredoxin-like
      0.021   14.2   0.2        0.2   11.0   0.1    1.9  2  OST3_OST6      OST3 / OST6 family, transporter family
      0.041   14.3   0.0       0.14   12.6   0.0    1.9  1  DUF2533        Protein of unknown function (DUF2533)
       0.19   11.5   1.1        2.7    7.7   0.0    2.7  3  DSBA           DSBA-like thioredoxin domain
       0.33   11.1   8.0        3.3    7.8   0.0    3.6  4  Thioredoxin_4  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0     3e-13   5.5e-10       7      76 .]      38     118 ..      27     118 .. 0.82
   2 !   54.6   1.1   4.6e-18   8.2e-15       4      74 ..     150     227 ..     147     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3e-13
                                   SSSSTTCH...HHHHHHHHHCHCCT.CEC.....EEECC..TTHHHHHHCT-SSSSEE.ECTTCEEEESS---CCHHHHHH CS
                 Thioredoxin_3   7 gpgCakCp...klekavkeaaaekg.ika.....evekv..tdfeeiekygVmsvPal.vidgkvvvsGkvpseeeirkll 75 
                                   +p C++C+   k+ ++vk a ++++  k       v+++   + +++e+++V++vP++ ++ gk++++G +p +eeir+l+
  gi|70606584|ref|YP_255454.1|  38 DPHCHYCEvteKFLNFVKDASPKDNaGKSllqvmVVDRAnpDQAKTFEEFEVTRVPTVaFLGGKLRWTG-APLGEEIRALI 117
                                   689*****9999999*******9975444698876677763444455**********************.9********99 PP

                                   H CS
                 Thioredoxin_3  76 e 76 
                                   e
  gi|70606584|ref|YP_255454.1| 118 E 118
                                   6 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 4.6e-18
                                   EEESSSSTTCH...HHHHHHHHHCHCCT.CEC..EEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCH.HHHH CS
                 Thioredoxin_3   4 kvlgpgCakCp...klekavkeaaaekg.ika..evekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseee.irkl 74 
                                    v++p+C++Cp    l+ +v+ +a + g  ++  ev++++++++i eky+VmsvP+++i++ v++ G vp ee  i+ +
  gi|70606584|ref|YP_255454.1| 150 TVVTPSCPYCPyaaLLAHMVAFEACKVGkCNVisEVVEAYENQDIaEKYQVMSVPTIAINDSVEFIG-VPYEENfINTI 227
                                   589********98745555554444433244466*********************************.99988735555 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.015        27      27      79 ..      38      98 ..      16     119 .. 0.72
   2 !   16.5   0.3   3.5e-06    0.0063      21      79 ..     150     209 ..     132     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                                  -TTSHHHHCHHHHHHHHHHHCTT........TSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                   Thioredoxin 27 ApwCghCkalaPeleklaeelkd........kvklakvdvdenedlakkyevegiPtlklf 79
                                   p C  C   + +l+ ++++  +        +v ++   + +++++ +++ev+ +Pt+ ++
  gi|70606584|ref|YP_255454.1| 38 DPHCHYCEVTEKFLNFVKDASPKdnagksllQVMVVDRANPDQAKTFEEFEVTRVPTVAFL 98
                                  566777766666666555555545566665556666656667889999*********9886 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.5e-06
                                   EEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                   Thioredoxin  21 vlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklf 79 
                                    +v    p+C+    la +++  a ++ + +v    v++ en+d+a+ky+v ++Pt+ + 
  gi|70606584|ref|YP_255454.1| 150 TVVTPSCPYCPYAALLAHMVAFEACKVGKcNVISEVVEAYENQDIAEKYQVMSVPTIAIN 209
                                   567777888999899999888777777767999999*********************875 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   1.6e-05     0.029       8     108 ..      32     116 ..      25     117 .. 0.70
   2 !    7.2   1.3    0.0037       6.6      66      90 ..     188     212 ..     141     223 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                 Thioredoxin_2   8 vlvvftdpdCpyCkklkk..elkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivf 86 
                                   ++++  dp+C yC+  +k  ++ ++ + ++       ++ +  ++  +++a+  +          +  ++++v+ +Pt+ f
  gi|70606584|ref|YP_255454.1|  32 LFIDSKDPHCHYCEVTEKflNFVKDASPKDN-----AGK-SLLQVMVVDRANPDQ---------AKTFEEFEVTRVPTVAF 97 
                                   556667*********9994444444333333.....333.455555566666554.........788999*********** PP

                 Thioredoxin_2  87 ldgkeivarlpGyvpaeeleal 108
                                   l gk   +r++G+   ee++al
  gi|70606584|ref|YP_255454.1|  98 LGGK---LRWTGAPLGEEIRAL 116
                                   ****...799998766776665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0037
                 Thioredoxin_2  66 ieenvelarkygvrgtPtivfldgk 90 
                                     en++ a+ky+v ++Pti + d  
  gi|70606584|ref|YP_255454.1| 188 AYENQDIAEKYQVMSVPTIAINDSV 212
                                   4567789************998865 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0045       8.1       6      57 ..      37     100 ..      24     103 .. 0.71
   2 !   13.6   1.6   3.3e-05     0.059       5      58 ..     152     211 ..     145     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0045
                                   S.TSSHHHHHHHHHH.........HHTTGG.EEEEEGCCSHHHHHHHHHHHTSSSSSEEEE.TT CS
                  Glutaredoxin   6 k.ptCpyCkkakrlL.........kelgvk.feeidvdkdeeireelkelsgvrtvPqvfi.dg 57 
                                   k p C yC  + ++L         ++ g +  ++  vd     +++  e  +v  vP+v + +g
  gi|70606584|ref|YP_255454.1|  37 KdPHCHYCEVTEKFLnfvkdaspkDNAGKSlLQVMVVDRANPDQAKTFEEFEVTRVPTVAFlGG 100
                                   4799***********8887777766666664577777776655555555558888888864355 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.3e-05
                                   ESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH........TSSSSSEEEETTE CS
                  Glutaredoxin   5 tkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels........gvrtvPqvfidgk 58 
                                   ++p CpyC+ a  l++   v+fe   v k   i e ++++          v++vP++ i++ 
  gi|70606584|ref|YP_255454.1| 152 VTPSCPYCPYAALLAHM--VAFEACKVGKCNVISEVVEAYEnqdiaekyQVMSVPTIAINDS 211
                                   45*******99766633..445555555544333333333333333444**********986 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.25      17      82 ..      29      99 ..      12     100 .. 0.69
   2 ?    2.1   0.0      0.12   2.2e+02      21      55 ..     168     200 ..     166     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  T--EEEEE--TT-HHHHHHHHH..HHH-HHHHH.HHHT-EEEEESS--S-GGG....-TT-...--SSEEEEE- CS
                 Thioredoxin_7 17 gkpvlvffgaswcftCqalerd..flsdeevkaalaekfvllrvdvterdani...lelde...qgvPvvafld 82
                                  +  ++++  +  c++C + e++  f +d + k   a+k  l   +v++ ++ +   +e  e   + vP+vafl+
  gi|70606584|ref|YP_255454.1| 29 QVHLFIDSKDPHCHYCEVTEKFlnFVKDASPKD-NAGKSLLQVMVVDRANPDQaktFE--EfevTRVPTVAFLG 99
                                  66899****************866888877777.566655555555666665543433..343355******96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                   EEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EE CS
                 Thioredoxin_7  21 lvffgaswcftCqalerdflsdeevkaalaekfvl 55 
                                   +v f+a   + C ++ ++++   e++  +aek+ +
  gi|70606584|ref|YP_255454.1| 168 MVAFEACKVGKCNVISEVVEAY-ENQD-IAEKYQV 200
                                   7889999999999999998887.6667.6766655 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0055       9.8      58      90 ..      67      99 ..      14     103 .. 0.78
   2 ?    6.4   0.0    0.0063        11      67      90 ..     187     210 ..     172     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0055
                                  -TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE- CS
                 Thioredoxin_8 58 kkpwlsvpfddkkrnklkkkynvkaiPtlvvld 90
                                    + + v+  ++++ k  ++++v+ +Pt+  l+
  gi|70606584|ref|YP_255454.1| 67 LLQVMVVDRANPDQAKTFEEFEVTRVPTVAFLG 99
                                  446778888888999999999999999998876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0063
                                   -TT-HHHHTT-S--TT-SEEEEE- CS
                 Thioredoxin_8  67 ddkkrnklkkkynvkaiPtlvvld 90 
                                   +  +++ +++ky+v+++Pt+ + d
  gi|70606584|ref|YP_255454.1| 187 EAYENQDIAEKYQVMSVPTIAIND 210
                                   4567999************88755 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011       0.2      33     104 ..      30     100 ..      10     149 .. 0.83
   2 ?    1.0   0.0      0.12   2.1e+02      79     101 ..     186     208 ..     175     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                     OST3_OST6  33 vvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfde..gkdvFqklglnsaPhlllfpp 104
                                   v ++++++     C+ C+  e+ ++ v ++  kd ++ ++ l  + vd ++    ++F++++++ +P + +   
  gi|70606584|ref|YP_255454.1|  30 VHLFIDSK--DPHCHYCEVTEKFLNFVKDASPKD-NAGKSLLQVMVVDRANpdQAKTFEEFEVTRVPTVAFLGG 100
                                   44444444..557*********************.899999********8777***************998765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                     OST3_OST6  79 vdfdegkdvFqklglnsaPhlll 101
                                   v+  e++d+ +k+++ s+P + +
  gi|70606584|ref|YP_255454.1| 186 VEAYENQDIAEKYQVMSVPTIAI 208
                                   67789**************9865 PP

>> DUF2533  Protein of unknown function (DUF2533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.9e-05      0.14      29      66 ..     114     151 ..     107     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                       DUF2533  29 EaaIeeavelckkgkpfsvekiNevTkeiNelakkgiv 66 
                                    a+Ie++v+l++ +  +s e++N++ +++N +++  +v
  gi|70606584|ref|YP_255454.1| 114 RALIETIVRLSQGESGLSKETVNAIKEKLNGFTRITTV 151
                                   589***************************98876554 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.1   3.8e+03       8      15 ..      39      46 ..      29      63 .. 0.63
   2 ?    1.8   0.0     0.099   1.8e+02     156     183 ..      80     108 ..      65     118 .. 0.82
   3 ?    7.7   0.0    0.0015       2.7     155     188 ..     190     223 ..     162     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                  TTBHHHHH CS
                          DSBA  8 vlCPyCyl 15
                                    C+yC +
  gi|70606584|ref|YP_255454.1| 39 PHCHYCEV 46
                                  34666655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.099
                                   HHHHHHHTT-SSSSEEEE.TTCEEEESSS CS
                          DSBA 156 ntaaaqslgvtGvPtvvv.dgkrmvfGad 183
                                   + + +++  vt vPtv + +gk  ++Ga+
  gi|70606584|ref|YP_255454.1|  80 QAKTFEEFEVTRVPTVAFlGGKLRWTGAP 108
                                   667889999999***988899999*9997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0015
                                   HHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHH CS
                          DSBA 155 entaaaqslgvtGvPtvvvdgkrmvfGadrldtl 188
                                   en++ a++++v  vPt+ +++++ + G++  +++
  gi|70606584|ref|YP_255454.1| 190 ENQDIAEKYQVMSVPTIAINDSVEFIGVPYEENF 223
                                   79999****************9999999877776 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6     0.038        68      12      35 ..      25      48 ..      23      91 .. 0.67
   2 ?    2.8   0.0     0.065   1.2e+02     129     165 ..      80     118 ..      50     119 .. 0.67
   3 ?   -1.7   0.6       1.6   2.9e+03      23      31 ..     154     162 ..     147     184 .. 0.73
   4 ?    7.8   0.0    0.0019       3.3     128     150 ..     190     212 ..     184     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.038
                                  T-SEEEEEEE-TT-HHHHHHHHHH CS
                 Thioredoxin_4 12 dApvtvieyedlrCphCakfeeev 35
                                  + +v v+++ d + phC   e + 
  gi|70606584|ref|YP_255454.1| 25 KSTVQVHLFIDSKDPHCHYCEVTE 48
                                  567889999999999998766543 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.065
                                   HHHHHHHHT--SS-EE.EETTEE.E-TT--HHHHHHHHT CS
                 Thioredoxin_4 129 eskeakkagiestPtf.iingek.veepqtyeelkalid 165
                                   + k++++ +++ +Pt+ +++g+   ++++  ee++ali+
  gi|70606584|ref|YP_255454.1|  80 QAKTFEEFEVTRVPTVaFLGGKLrWTGAPLGEEIRALIE 118
                                   445668888888888734577763445555567777765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.6
                                   TT-HHHHHH CS
                 Thioredoxin_4  23 lrCphCakf 31 
                                    +Cp+C   
  gi|70606584|ref|YP_255454.1| 154 PSCPYCPYA 162
                                   689999655 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHT--SS-EEEETTEE CS
                 Thioredoxin_4 128 aeskeakkagiestPtfiingek 150
                                   +++  a+k ++ s+Pt+ in+ +
  gi|70606584|ref|YP_255454.1| 190 ENQDIAEKYQVMSVPTIAINDSV 212
                                   678899**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1472.68
//
Query:       gi|70606585|ref|YP_255455.1|  [L=227]
Description: hypothetical protein Saci_0792 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-48  163.1   0.0    4.9e-48  162.9   0.0    1.1  1  AMMECR1   AMMECR1
  ------ inclusion threshold ------
      0.097   12.8   0.0       0.36   11.0   0.0    1.9  2  zf-NOSIP  Zinc-finger of nitric oxide synthase-interacting pr


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.0   5.5e-52   4.9e-48       2     163 ..      22     195 ..      21     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 5.5e-52
                                   HHHHHHHHHHTTSS-S-H.H---HHHHSEEEEEEEEE...EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS---- CS
                       AMMECR1   2 klareaieealkeekkle.eeakeelkekaglFVtlk...ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFspvt 78 
                                   k+ar++i++++k  +    e +++ l++++ +FVt++    ++++LRGCiG++e+  pL+e v+++A+aaAf+DpRF+p++
  gi|70606585|ref|YP_255455.1|  22 KIARDSIKNRFKLVNLNLdEYKNPVLNKRGLAFVTIEkieDERTSLRGCIGYVEAVAPLKEIVSKAAVAAAFSDPRFPPLS 102
                                   89*****99998877666688999*************7765556************************************* PP

                                   HHHHTTEEEEEEEE---EE--.......GGG--TTT-EEEEEET.TEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCC CS
                       AMMECR1  79 aeElpeleveVsvLtepepiv.......ledlevgkhGliiekg.srsatlLPqvaveqgwdkeeflasllrKaglrpdew 151
                                   ++El+++ +eV++Lt+pe+i+       ++ ++vg++Gli+e+g  +s++lLPqva+e+ wd e+fla+++ Kagl+pd+w
  gi|70606585|ref|YP_255455.1| 103 KSELNDILIEVTILTKPEEISvkdrwklPSFINVGEDGLIVEYGiMYSGLLLPQVASEYCWDSETFLAETCIKAGLKPDCW 183
                                   ********************53334444555***********755************************************ PP

                                   CSTTSEEEEE-E CS
                       AMMECR1 152 kdseikltryev 163
                                    ++++k++++++
  gi|70606585|ref|YP_255455.1| 184 LNERVKIKKFNG 195
                                   9********986 PP

>> zf-NOSIP  Zinc-finger of nitric oxide synthase-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     4e-05      0.36      25      60 ..      16      52 ..      11      61 .. 0.89
   2 ?   -1.8   0.0      0.41   3.6e+03      49      68 ..     172     191 ..     164     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                      zf-NOSIP 25 ygtqsvrlikdavkd.fdccslslqacrdpvltedgy 60
                                   g q +++++d++k+ f+   l l+  ++pvl + g 
  gi|70606585|ref|YP_255455.1| 16 IGKQLIKIARDSIKNrFKLVNLNLDEYKNPVLNKRGL 52
                                  5899**********77****************99886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                      zf-NOSIP  49 acrdpvltedgylyekeail 68 
                                   +c    l +d +l e+  i 
  gi|70606585|ref|YP_255455.1| 172 TCIKAGLKPDCWLNERVKIK 191
                                   67788899999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1502.13
//
Query:       gi|70606586|ref|YP_255456.1|  [L=155]
Description: hypothetical protein Saci_0793 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-35  120.1   7.2    3.9e-32  111.4   7.2    2.0  1  Mut7-C          Mut7-C RNAse domain
    7.6e-05   22.4   0.0    0.00013   21.6   0.0    1.4  1  DUF5615         Domain of unknown function (DUF5615)
     0.0023   18.1   1.9     0.0045   17.2   1.9    1.4  1  IBR             IBR domain, a half RING-finger domain
      0.009   15.9   0.7      0.021   14.7   0.4    1.8  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
        0.3   10.8   6.6       0.25   11.1   5.7    1.4  1  Rep_fac-A_C     Replication factor-A C terminal domain
        1.5    8.5   8.1       0.22   11.1   3.6    2.0  2  PHD_2           PHD-finger
        2.6    8.2   8.6         11    6.2   0.3    3.4  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   7.2   1.5e-35   3.9e-32       1     145 [.       4     135 ..       4     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.5e-35
                        Mut7-C   1 krfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vll.tsrdveeqlrevia 78 
                                   ++f++Damlgkl+++LR+lGyd+ly++d+ed +++++a+++ ri+lT dr+L+ rak+++   +++ t+ ++ee l+ +  
  gi|70606586|ref|YP_255456.1|   4 QKFIADAMLGKLSRWLRILGYDTLYSKDFEDWQIIKIAKNDSRIILTMDRGLCYRAKKNDLecFYVnTELNIEEILAMLAI 84 
                                   59*****************************************************9998778877779************* PP

                        Mut7-C  79 rlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                   +++++l+++p+ srC++Cng l++v+++                 ++C++C+k +WkG hw++++++
  gi|70606586|ref|YP_255456.1|  85 KYKIDLTADPNYSRCTKCNGILKKVDEN----------------RWKCTRCKKEYWKGMHWKSIQNI 135
                                   **********************998765................58*****************9986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.3e-08   0.00013       2      56 ..       5      53 ..       4      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.3e-08
                       DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                  k+++D+ l  +l ++lr +g+d+l+ ++      +D +i+++Ak++ rii+T D+
  gi|70606586|ref|YP_255456.1|  5 KFIADAMLG-KLSRWLRILGYDTLYSKD-----FEDWQIIKIAKNDSRIILTMDR 53
                                  899999999.9**************966.....56*******************7 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.9   1.8e-06    0.0045       7      48 ..      85     123 ..      80     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                           IBR   7 klkkslesdpnlkwCprpdCeaiieksegcksvtCskCgfef 48 
                                   k+k  l+ dpn+  C+  +C++i++k ++ ++ +C++C++e+
  gi|70606586|ref|YP_255456.1|  85 KYKIDLTADPNYSRCT--KCNGILKKVDE-NRWKCTRCKKEY 123
                                   56667889*******9..***99988887.889******986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.8   4.7e+03       8      24 ..      55      71 ..      51      73 .. 0.74
   2 !   14.7   0.4   8.2e-06     0.021      23      55 ..      93     122 ..      74     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                OrfB_Zn_ribbon  8 leykakeyGikveevnp 24
                                  l y ak+   +  +vn 
  gi|70606586|ref|YP_255456.1| 55 LCYRAKKNDLECFYVNT 71
                                  56888888888888875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.2e-06
                OrfB_Zn_ribbon  23 npayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                   +p+y+  +C +C  ++k+ ++++++kC++C+ e
  gi|70606586|ref|YP_255456.1|  93 DPNYS--RCTKCNGILKK-VDENRWKCTRCKKE 122
                                   56664..8**********.***********987 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.7   9.8e-05      0.25      16      57 ..      94     134 ..      77     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                                   TEEEB--STT---B-EEETTTEEEETTTTEEE.SS--EEEEEE CS
                   Rep_fac-A_C  16 lvYkACpsedCnkKvveeedgewrCekCdkev.eepkyryils 57 
                                     Y+ C   +Cn  + + ++++w+C +C+ke+ + ++++ i +
  gi|70606586|ref|YP_255456.1|  94 PNYSRCT--KCNGILKKVDENRWKCTRCKKEYwKGMHWKSIQN 134
                                   57999**..9**888888999*********9724456666555 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.81   2.1e+03      18      26 ..      56      64 ..      55      68 .. 0.73
   2 ?   11.1   3.6   8.7e-05      0.22      17      36 .]     101     120 ..      99     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.81
                         PHD_2 18 CYGvskesd 26
                                  CY+ +k++ 
  gi|70606586|ref|YP_255456.1| 56 CYRAKKNDL 64
                                  999888765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.7e-05
                         PHD_2  17 sCYGvskesdgeeWlCrrCe 36 
                                   +C G+ k+ d++ W+C rC+
  gi|70606586|ref|YP_255456.1| 101 KCNGILKKVDENRWKCTRCK 120
                                   79*********99******5 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.076   1.9e+02      10      18 ..      26      34 ..      25      34 .. 0.89
   2 ?    6.2   0.3    0.0041        11       2      13 ..      97     108 ..      96     110 .. 0.86
   3 ?    2.3   1.6     0.072   1.8e+02       2       8 ..     114     120 ..     114     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.076
                        zf-ACC 10 mlykkeLer 18
                                  +ly k++e+
  gi|70606586|ref|YP_255456.1| 26 TLYSKDFED 34
                                  79*****97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                        zf-ACC   2 tKCpsCgemlyk 13 
                                   ++C++C+ +l k
  gi|70606586|ref|YP_255456.1|  97 SRCTKCNGILKK 108
                                   58*******987 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.072
                        zf-ACC   2 tKCpsCg 8  
                                   +KC++C+
  gi|70606586|ref|YP_255456.1| 114 WKCTRCK 120
                                   6*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1113.93
//
Query:       gi|70606587|ref|YP_255457.1|  [L=83]
Description: hypothetical protein Saci_0794 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.27   11.3  10.1       0.42   10.7  10.1    1.3  1  COPI_assoc  COPI associated protein
       0.38   11.0   7.9        1.3    9.4   7.9    1.7  1  DUF5379     Family of unknown function (DUF5379)


Domain annotation for each model (and alignments):
>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.1   4.7e-05      0.42       8      84 ..       8      78 ..       6      83 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.7e-05
                    COPI_assoc  8 nlvvgglaillgisqliilfsnflsfilsiYiillgivlillEfrvpfeiykyfsfmfsylGRGlfyillgllvsyg 84
                                   +v g + i++gi +++ + + + s+i++i + ll+i+++ + fr +   ++        +GRG+ +++ + l+++ 
  gi|70606587|ref|YP_255457.1|  8 VIVRGIIGICAGIISFFLIQNILASLITPIASYLLSILIVNILFRNVS--KS----KWDLFGRGVAILFSAWLLIFL 78
                                  68999**********988755556669999999****99999888888..33....4789*********99776665 PP

>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.9   0.00014       1.3       1      88 [.       1      82 [.       1      83 [] 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                       DUF5379  1 ldlegkvailhaiggiifgylanyvytlgl.gllsglatllf.lfiglvilghlsakvlgeesltqkqwlgsgvlpfflvaiv 81
                                  ++ e k+ i++ i gi  g ++ ++ +  l  l++ +a++l+ ++i  ++        + + s ++ + +g gv + f  +++
  gi|70606587|ref|YP_255457.1|  1 MEKEDKIVIVRGIIGICAGIISFFLIQNILaSLITPIASYLLsILIVNIL--------FRNVSKSKWDLFGRGVAILFSAWLL 75
                                  677899***************99876655414666676654314444444........4444566778899999999999999 PP

                       DUF5379 82 vwilkyn 88
                                  +++  yn
  gi|70606587|ref|YP_255457.1| 76 IFLALYN 82
                                  9998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 658.69
//
Query:       gi|70606588|ref|YP_255458.1|  [L=594]
Description: hypothetical protein Saci_0795 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-30  105.7  21.6    4.9e-30  104.7  21.6    1.4  1  FbpA             Fibronectin-binding protein A N-terminus (Fb
    3.9e-25   88.6   0.4    1.2e-24   87.0   0.0    2.0  2  NFACT-R_1        NFACT protein RNA binding domain
    9.6e-05   22.5   0.0    0.00037   20.6   0.0    2.0  1  NFACT-R_2        NFACT protein RNA binding domain
     0.0032   18.1   1.2      0.014   16.0   0.1    2.3  2  Phage_ABA_S      Phage ABA sandwich domain
  ------ inclusion threshold ------
      0.039   14.0   0.1      0.082   12.9   0.1    1.6  1  DNA_primase_S    DNA primase small subunit
      0.053   13.7   0.9       0.15   12.3   0.1    2.2  2  P22_AR_C         P22AR C-terminal domain
       0.18   11.7   4.5        0.3   11.0   0.2    3.1  3  HetR_C           Heterocyst differentiation regulator C-termi
       0.48   10.3   6.5        2.8    7.8   0.9    2.3  2  Apolipoprotein   Apolipoprotein A1/A4/E domain
       0.49   10.4  11.5       0.34   10.9   0.5    2.6  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        0.6   10.9  12.2       0.17   12.6   3.0    2.9  2  Occludin_ELL     Occludin homology domain
       0.81    9.2  13.4       0.42   10.2   2.7    2.4  2  PspA_IM30        PspA/IM30 family
        1.2    9.6   5.3        1.4    9.4   2.0    2.6  3  Goodbye          fungal STAND N-terminal Goodbye domain
        2.1    8.7  10.4         45    4.4   0.8    3.9  3  TSC22            TSC-22/dip/bun family
        2.2    8.2  17.8       0.17   11.8   6.8    2.8  2  Ax_dynein_light  Axonemal dynein light chain
        3.6    7.2  13.1         41    3.7  11.7    2.8  3  DUF4795          Domain of unknown function (DUF4795)
        3.9    8.0  11.9        5.3    7.6   1.9    2.6  3  UPF0449          Uncharacterised protein family UPF0449
        4.6    7.8   9.4        8.9    6.9   1.6    3.1  2  YtxH             YtxH-like protein
        5.7    6.9  21.5        1.5    8.8   7.6    3.0  2  Prefoldin_2      Prefoldin subunit
        7.4    6.6  10.2        3.3    7.8   4.8    2.7  2  DUF1664          Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  21.6   5.2e-33   4.9e-30       2     416 ..       9     372 ..       8     393 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5.2e-33
                                   HHHHHHHHHHHHHHHTTXEEEEEEEEET.TEEEEEEEETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHT CS
                          FbpA   2 glvlaavvaELqkellggridkiyqpek.delvltlranrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLk 81 
                                   +++l a + E ++ ++g+rid++y     +   ++l++++  + L+++    ++rih+t++++e+ +e    + l+R+ +k
  gi|70606588|ref|YP_255458.1|   9 YIDLLAWITENKSIIEGSRIDNVYKISGiQAYLFKLHSKNTDKFLVVEP---GKRIHFTKYDREKSSE--GEVRLIRELVK 84 
                                   67888889999999**********98752688899**8777767*****...*********9955555..4589******* PP

                                   TXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSX CS
                          FbpA  82 garivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPp 162
                                    + i+si  lg++Ri ++++ +r         ++++E++ r + ++++d +nk++ + +  +++   +R i  g +Y +Pp
  gi|70606588|ref|YP_255458.1|  85 EKIIKSINILGNERIAKIDLIDR---------KIYIELLPR-GLLVITDGNNKVLFSTEYKEFR---DRIIRLGIEYLPPP 152
                                   ***********************.........9********.*******************999...9*********9888 PP

                                   XXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX CS
                          FbpA 163 sqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleele 243
                                   +   + Pl+++e+e   +l++  +++l+++L     G+ +++ e l  +++          s e+l+ +++++++ll+ ++
  gi|70606588|ref|YP_255458.1| 153 Q---PAPLTSDEIE---KLIN--KGNLTRIL-----GVPQEILEALNIKIN----------SLEELDGVKNRINDLLNTIR 210
                                   8...8888888855...5543..24444443.....877777777766666..........8899**************** PP

                                   ....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          FbpA 244 eekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekklkklek 324
                                    +kf  +l        +++v+p+k     e  +++s ++ald+y+++ +e+d v+    ++ k +e+e  +lek++++l+ 
  gi|70606588|ref|YP_255458.1| 211 GGKFFNCL------IRNVTVLPIKTD---ECVEYNSYNDALDDYFTQ-LEKDIVKT---EVDKNLEKEKGNLEKTIEELKS 278
                                   **999999......7889****9883...4589***********975.77788776...7889999999************ PP

                                   HHHCCGGH.HHHHCCHH-----------------------..-----------------HHHHHHHHHHHHHHHHHHHHHH CS
                          FbpA 325 elekaeka.enyrligelltaylyaikkgmsevelenyyde.geevtIpLdprkspsenAqkyfkkykKlkraveaveeqi 403
                                   ++e+ +k+  ++r+i+e + ++ + i++  ++ + +n  +   ++++I +dp++++ +nA ky++ +k   ++++++ e +
  gi|70606588|ref|YP_255458.1| 279 QIEEYAKKeSEMRQIAETIITNYELIENAIKNSNKKNSVTLkINNISIDIDPKLTVYKNASKYYDLAKEYSEKAKKAGEVL 359
                                   ***98888689***************999999999999998778************************************* PP

                                   HHHHHHHHHHHHH CS
                          FbpA 404 eetkeeleylesv 416
                                   ee +++l+ l+ +
  gi|70606588|ref|YP_255458.1| 360 EELRKKLSELQFK 372
                                   ******9998754 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       8.1   7.7e+03      62      80 ..     275     293 ..     258     324 .. 0.54
   2 !   87.0   0.0   1.3e-27   1.2e-24       1     109 []     392     502 ..     392     502 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.1
                     NFACT-R_1  62 elleeaaqlakanSiagnk 80 
                                   el +++ + ak++S++++ 
  gi|70606588|ref|YP_255458.1| 275 ELKSQIEEYAKKESEMRQI 293
                                   4444444455554444322 PP

  == domain 2  score: 87.0 bits;  conditional E-value: 1.3e-27
                     NFACT-R_1   1 kvfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnk 80 
                                   k++w ++ +g++vi+G+D+ +ne +++k l+e+d+++h+d++++a ++l+ ++g+   ++e+ + +aa +a+++S+a ++ 
  gi|70606588|ref|YP_255458.1| 392 KYHWGITRNGHIVIAGRDSDQNESIVRKLLDEKDIFLHADIQGAAATVLKANSGQ---VSEDDILDAAYIAACYSKAwKTG 469
                                   789999********************************************77777...*********************** PP

                     NFACT-R_1  81 lssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                   l svdv++v+ +++sk++p    l++Gs++++g
  gi|70606588|ref|YP_255458.1| 470 LGSVDVFWVYGNQVSKSPPsgeyLAKGSFMIYG 502
                                   ******************************986 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     4e-07   0.00037       9      73 ..     401     469 ..     397     486 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4e-07
                     NFACT-R_2   9 kaklIvgReeeEnkflkgll.kkdfvslrakshkGplvli.d...gelseedlelaarivarYskgkeee 73 
                                   +  +I gR+++ n+ + + l  ++ + +  ++++G+ + + +   g++se+d+  aa i+a Ysk+ ++ 
  gi|70606588|ref|YP_255458.1| 401 GHIVIAGRDSDQNESIVRKLlDEKDI-FLHADIQGAAATVlKansGQVSEDDILDAAYIAACYSKAWKTG 469
                                   556899********997666666666.6667777766544356789*******************87654 PP

>> Phage_ABA_S  Phage ABA sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2       1.2   1.1e+03      26      73 ..     274     323 ..     249     333 .. 0.68
   2 !   16.0   0.1   1.5e-05     0.014      18      78 ..     330     406 ..     315     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                   Phage_ABA_S  26 geflvevfeysedisaAweVveklknegiei...kvkslekkyqvlveide 73 
                                   +e   +++ey+++ s   +++e +  +++e+    +k+ +kk  v+ +i+ 
  gi|70606588|ref|YP_255458.1| 274 EELKSQIEEYAKKESEMRQIAETII-TNYELienAIKNSNKKNSVTLKINN 323
                                   5666678899999999999999999.4444434677777777777777665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                   Phage_ABA_S  18 sntevldegeflve.vfeysedisaAweVvekl.............knegiei..kvkslekkyqvlveidekrvev 78 
                                   ++ +v+++ +++++  +eyse+ ++A eV+e+l             ++e+i i  + k++ +ky++ ++++++ v++
  gi|70606588|ref|YP_255458.1| 330 PKLTVYKNASKYYDlAKEYSEKAKKAGEVLEELrkklselqfkideRKEEIRIslRKKEWYEKYHWGITRNGHIVIA 406
                                   55677777777777789**************************9984577777669999999*****9999996665 PP

>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.7e-05     0.082      41     132 ..     202     312 ..     185     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.7e-05
                                   GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH....................................HCHHHHCT CS
                 DNA_primase_S  41 fkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnlyrplhpflsrsmlkivkpvveeiileeqdpf..eikkllrl 119
                                   ++d+l + +g++ f c+++  ++ p+++ e  +  +y    + l+++++++ ++ivk++v++ + +e++    +i++l ++
  gi|70606588|ref|YP_255458.1| 202 INDLLNTIRGGKFFNCLIRNVTVLPIKTDECVEYNSY---NDALDDYFTQLEKDIVKTEVDKNLEKEKGNLekTIEELKSQ 279
                                   569999*********************9999996554...46689999999999**************999**99999999 PP

                                   --------.......................... CS
                 DNA_primase_S 120 lpdkslrekkkw.....................e 132
                                   + + +++e + +                     +
  gi|70606588|ref|YP_255458.1| 280 IEEYAKKE-SEMrqiaetiitnyelienaiknsN 312
                                   99998888.3333334444555555555334442 PP

>> P22_AR_C  P22AR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.4     7e+03      49      66 ..     278     295 ..     267     300 .. 0.66
   2 ?   12.3   0.1   0.00016      0.15      44      70 ..     338     364 ..     333     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                      P22_AR_C  49 siakEYsstlrdarrvLe 66 
                                   s+  EY +   ++r++ e
  gi|70606588|ref|YP_255458.1| 278 SQIEEYAKKESEMRQIAE 295
                                   566677777767766655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                      P22_AR_C  44 apkaYsiakEYsstlrdarrvLerlta 70 
                                   a k+Y++akEYs+ +++a +vLe+l +
  gi|70606588|ref|YP_255458.1| 338 ASKYYDLAKEYSEKAKKAGEVLEELRK 364
                                   689********************9965 PP

>> HetR_C  Heterocyst differentiation regulator C-terminal Hood domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.2   1.1e+03      31      48 ..     189     206 ..     173     210 .. 0.78
   2 ?   -0.3   0.1       1.1     1e+03      40      61 ..     265     286 ..     248     310 .. 0.72
   3 ?   11.0   0.2   0.00032       0.3      11      63 ..     336     394 ..     330     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                        HetR_C  31 lrvleeldippekleqal 48 
                                   +  leeld  ++++++ l
  gi|70606588|ref|YP_255458.1| 189 INSLEELDGVKNRINDLL 206
                                   667999999999988766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                        HetR_C  40 ppekleqaleeldeiirewadk 61 
                                    + +le+++eel   i e+a k
  gi|70606588|ref|YP_255458.1| 265 EKGNLEKTIEELKSQIEEYAKK 286
                                   4556777777777777777765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00032
                        HetR_C  11 edtaryfrlmrdwaerkpkvlrvleeldippekleqaleeldeiir......ewadkyh 63 
                                   +++++y+ l ++++e+ +k+  vleel     +l+  ++e  e ir      ew +kyh
  gi|70606588|ref|YP_255458.1| 336 KNASKYYDLAKEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEIRislrkkEWYEKYH 394
                                   57789*********************988777666666666555543333557999999 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0029       2.8       9      61 ..     235     288 ..     229     303 .. 0.68
   2 ?    5.2   0.5     0.019        18      70     109 ..     347     385 ..     333     389 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                                   HHHHHCCHHHCHHCHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH CS
                Apolipoprotein   9 lkayaeeleeqlaplaqe.lrdrlskeleelrarlraeleevrarlepyrdevq 61 
                                    ++y + l +  ++l ++ +++ + k+le+ +  l++ +ee+++++e+y+    
  gi|70606588|ref|YP_255458.1| 235 YNSYNDALDDYFTQLEKDiVKTEVDKNLEKEKGNLEKTIEELKSQIEEYAKKES 288
                                   556666666666666665566677777777777777777777777777766544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.019
                                   HHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHH CS
                Apolipoprotein  70 elrqrlapyteelrerlaadaeelqeqlavyaeelrerle 109
                                   e+ ++ + + e l e l++++ elq ++++ +ee+r +l+
  gi|70606588|ref|YP_255458.1| 347 EYSEKAKKAGEVL-EELRKKLSELQFKIDERKEEIRISLR 385
                                   3334434444333.35666666666666666666665554 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   4.7     0.099        94     110     152 ..     264     309 ..     246     311 .. 0.77
   2 ?   10.9   0.5   0.00036      0.34      93     134 ..     340     381 ..     323     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.099
                      MIP-T3_C 110 ealeplkaqlaeleeaIkdqkekisnvra...kilkNeakiqkllk 152
                                   ++  +l++ ++el+++I+++ +k s++r+   +i+ N + i++ +k
  gi|70606588|ref|YP_255458.1| 264 KEKGNLEKTIEELKSQIEEYAKKESEMRQiaeTIITNYELIENAIK 309
                                   4556789999999999999988877777544489999999987665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00036
                      MIP-T3_C  93 eyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekis 134
                                   +y   a+e +e+ +   e le+l+++l+el+ +I ++ke+i 
  gi|70606588|ref|YP_255458.1| 340 KYYDLAKEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEIR 381
                                   45556778888999999**********************996 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.0   0.00018      0.17      25      81 ..     260     316 ..     234     323 .. 0.92
   2 ?    2.3   1.9      0.31   2.9e+02      25      69 ..     346     387 ..     330     396 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                  Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkr 81 
                                   k+l++e  +++k+++eL+++++e++++++e+++i+e i+ +y+ +++  +  +kk+ 
  gi|70606588|ref|YP_255458.1| 260 KNLEKEKGNLEKTIEELKSQIEEYAKKESEMRQIAETIITNYELIENAIKNSNKKNS 316
                                   56888889999**********************************998888888876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                  Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                   ke  ++ +++ + ++eL+++l+el   + ++++++eei  +++k+
  gi|70606588|ref|YP_255458.1| 346 KEYSEKAKKAGEVLEELRKKLSEL---QFKIDERKEEIRISLRKK 387
                                   222222222222222222222222...234555555555555555 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.1     0.035        33     101     138 ..     260     297 ..     248     316 .. 0.78
   2 ?   10.2   2.7   0.00044      0.42      93     137 ..     338     382 ..     333     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.035
                     PspA_IM30 101 ealetqlaqqrsaveqlrkqlealetkieelkakkell 138
                                   ++le++  ++++++e+l+ q+e+ ++k +e+++  e++
  gi|70606588|ref|YP_255458.1| 260 KNLEKEKGNLEKTIEELKSQIEEYAKKESEMRQIAETI 297
                                   46777888888888888888888888888888766665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00044
                     PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkel 137
                                   + ++ + a++++++++++ +  e+lrk+l++l  ki+e k+++++
  gi|70606588|ref|YP_255458.1| 338 ASKYYDLAKEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEIRI 382
                                   5678899********************************999875 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.1   6.7e+03      83     111 ..     181     209 ..     176     211 .. 0.79
   2 ?    9.4   2.0    0.0015       1.4       1      70 [.     238     309 ..     238     314 .. 0.78
   3 ?   -0.4   0.1       1.6   1.5e+03      94     118 ..     345     369 ..     333     388 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.1
                       Goodbye  83 cfnAvsyLikaakkvseiydaieeLfeel 111
                                   ++ A+ + i+  ++++ + + i++L++++
  gi|70606588|ref|YP_255458.1| 181 ILEALNIKINSLEELDGVKNRINDLLNTI 209
                                   67778888888888889999999999887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                       Goodbye   1 WeeAlkeyekeTgkdl..kdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaa 70 
                                   +++Al++y ++ +kd+  ++ + +  ++  +l+k ie+ k++ ee  +k+++++++ ++i++  +l+ + ++
  gi|70606588|ref|YP_255458.1| 238 YNDALDDYFTQLEKDIvkTEVDKNLEKEKGNLEKTIEELKSQIEEYAKKESEMRQIAETIITNYELIENAIK 309
                                   678999999999999953222333334667899999999999999999999999999999999999888776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                       Goodbye  94 akkvseiydaieeLfeelsdflerl 118
                                   ak++se  ++  e++eel++ l+ l
  gi|70606588|ref|YP_255458.1| 345 AKEYSEKAKKAGEVLEELRKKLSEL 369
                                   4555555555555555555544444 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.062        59      14      41 ..     193     220 ..     189     225 .. 0.83
   2 ?    4.4   0.8     0.048        45      15      35 ..     272     292 ..     264     301 .. 0.73
   3 ?    3.4   1.3       0.1        95      14      38 ..     357     381 ..     355     387 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.062
                         TSC22  14 EeVevLkekIkeLeernseleeENslLk 41 
                                   Ee +  k++I +L+++++  +  N l +
  gi|70606588|ref|YP_255458.1| 193 EELDGVKNRINDLLNTIRGGKFFNCLIR 220
                                   999************9987776666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.048
                         TSC22  15 eVevLkekIkeLeernselee 35 
                                   ++e+Lk++I e  ++ se+++
  gi|70606588|ref|YP_255458.1| 272 TIEELKSQIEEYAKKESEMRQ 292
                                   567777777777777776654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.1
                         TSC22  14 EeVevLkekIkeLeernseleeENs 38 
                                   E  e+L++k  eL+ ++ e +eE +
  gi|70606588|ref|YP_255458.1| 357 EVLEELRKKLSELQFKIDERKEEIR 381
                                   677***************9999966 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.8   0.00018      0.17     118     180 ..     252     314 ..     235     320 .. 0.75
   2 ?    2.6   1.5      0.12   1.2e+02     122     165 ..     346     389 ..     334     400 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
               Ax_dynein_light 118 eqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeek.kheeei..eflkksnqq 180
                                   +  k+e++k   +Le+ek +lek ++elk+++e+  k+e+e rq+ e    ++e+  +++k+sn++
  gi|70606588|ref|YP_255458.1| 252 DIVKTEVDK---NLEKEKGNLEKTIEELKSQIEEYAKKESEMRQIAETiITNYELieNAIKNSNKK 314
                                   333444444...4***************************99998775145556556666666665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
               Ax_dynein_light 122 selekkikeLeeekeelekqvaelkaklealekrekerrqeeek 165
                                   +e+++k k+  e  eel+k+++el+ k+++ +++    ++++e 
  gi|70606588|ref|YP_255458.1| 346 KEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEIRISLRKKEW 389
                                   67788888899999999999999999999988887766666665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         8   7.5e+03      35      63 ..      25      53 ..      17      56 .. 0.76
   2 ?    3.7  11.7     0.043        41      76     165 ..     184     293 ..     181     388 .. 0.67
   3 ?   -0.5   2.8      0.81   7.6e+02     160     170 ..     357     367 ..     290     422 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8
                       DUF4795 35 krledkekklealkkqieelekvkadkee 63
                                  ++  d  +k+ +++ ++ +l++++ dk+ 
  gi|70606588|ref|YP_255458.1| 25 GSRIDNVYKISGIQAYLFKLHSKNTDKFL 53
                                  55567778888999999999999999875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.043
                       DUF4795  76 aLatkvsrdq.fDeakkeLekmleellek.........le.............eqeealkkaldtLqeelkekldrlelep 133
                                   aL++k++  + +D +k++++  l+ ++           ++             +  +al+    +L++++ +    ++le+
  gi|70606588|ref|YP_255458.1| 184 ALNIKINSLEeLDGVKNRINDLLNTIRGGkffnclirnVTvlpiktdecveynSYNDALDDYFTQLEKDIVKTEVDKNLEK 264
                                   666666443337777777777774443332322222223355555555555557777777777777777766666777777 PP

                       DUF4795 134 Lkeqleerlkelqkelqeamekedkedeaagl 165
                                    k +le++++el+ +++e+++ke++   +  +
  gi|70606588|ref|YP_255458.1| 265 EKGNLEKTIEELKSQIEEYAKKESE---MRQI 293
                                   7777777777777777777777654...3333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.81
                       DUF4795 160 deaaglrkkLl 170
                                   +  ++lrkkL+
  gi|70606588|ref|YP_255458.1| 357 EVLEELRKKLS 367
                                   11222222222 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.9    0.0056       5.3      49      94 ..     234     282 ..     202     289 .. 0.73
   2 ?    5.4   4.1     0.026        24      31      73 ..     245     289 ..     228     317 .. 0.53
   3 ?    4.7   2.5     0.043        40      54      99 ..     335     380 ..     300     381 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                       UPF0449  49 eeedleaeveelYeqvrtyl...elnerLeeakeeLkqkceeLktagee 94 
                                   e ++ ++  ++++ q+++ +   e++++Le++k +L++  eeLk++ ee
  gi|70606588|ref|YP_255458.1| 234 EYNSYNDALDDYFTQLEKDIvktEVDKNLEKEKGNLEKTIEELKSQIEE 282
                                   456777889999999855332336789*****************98776 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                       UPF0449  31 vftilsdsve..edkkassseeedleaeveelYeqvrtylelner 73 
                                    ft l++++   e++k+ ++e+ +le+ +eel  q+++y + + +
  gi|70606588|ref|YP_255458.1| 245 YFTQLEKDIVktEVDKNLEKEKGNLEKTIEELKSQIEEYAKKESE 289
                                   233333332223444444444445555555555555555555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.043
                       UPF0449  54 eaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeei 99 
                                    ++++++Y  +++y e  ++  e  eeL++k+ eL+   +e +eei
  gi|70606588|ref|YP_255458.1| 335 YKNASKYYDLAKEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEI 380
                                   4457788888888888888888888888888888887776666655 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.2     0.083        78      51      72 ..     252     285 ..     192     297 .. 0.67
   2 ?    6.9   1.6    0.0095       8.9      32      71 ..     336     381 ..     333     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.083
                          YtxH  51 ka............kekaedlkekvkekadelke 72 
                                                 k + e+  e++k++++e ++
  gi|70606588|ref|YP_255458.1| 252 DIvktevdknlekeKGNLEKTIEELKSQIEEYAK 285
                                   3344445555555533344444444444444333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0095
                          YtxH  32 ekaddlkekakelleeakeka......kekaedlkekvkekadelk 71 
                                   ++a+++ + ake+ e+ak+ +      ++k ++l+ k++e+ +e++
  gi|70606588|ref|YP_255458.1| 336 KNASKYYDLAKEYSEKAKKAGevleelRKKLSELQFKIDERKEEIR 381
                                   5667777777777777777777777779999999999999999875 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.6    0.0016       1.5      60      97 ..     255     292 ..     252     301 .. 0.87
   2 ?    3.7   4.9     0.062        58      64     104 ..     345     385 ..     339     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelke 97 
                                   k+ev ++Le++k +lek i++l++q+e+  k+ +e+++
  gi|70606588|ref|YP_255458.1| 255 KTEVDKNLEKEKGNLEKTIEELKSQIEEYAKKESEMRQ 292
                                   6899**********************998888888776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                   Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                                    +e  e+++++ +++++l k+l++l+ +++e kee+++ l 
  gi|70606588|ref|YP_255458.1| 345 AKEYSEKAKKAGEVLEELRKKLSELQFKIDERKEEIRISLR 385
                                   567789999999************************98775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.8    0.0035       3.3      51     105 ..     256     310 ..     237     329 .. 0.66
   2 ?    0.7   0.3      0.54   5.1e+02      91     118 ..     347     374 ..     311     382 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0035
                       DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                   ++v ++l++ k +L++ i+++ ++++e ++  +e+++  +++  + + i++ +++
  gi|70606588|ref|YP_255458.1| 256 TEVDKNLEKEKGNLEKTIEELKSQIEEYAKKESEMRQIAETIITNYELIENAIKN 310
                                   3566777777777777777777777777777777777777777777777666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.54
                       DUF1664  91 evredlseigedvesvkeavegleskle 118
                                   e +e+ ++ ge +e++++  ++l+ k++
  gi|70606588|ref|YP_255458.1| 347 EYSEKAKKAGEVLEELRKKLSELQFKID 374
                                   3334444444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2276  (0.126945); expected 358.6 (0.02)
Passed bias filter:                      766  (0.0427241); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.83u 0.33s 00:00:01.15 Elapsed: 00:00:00.47
# Mc/sec: 3819.87
//
Query:       gi|70606589|ref|YP_255459.1|  [L=286]
Description: hypothetical protein Saci_0796 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-35  120.3   0.1    9.7e-35  119.9   0.1    1.2  1  RIO1            RIO1 family
    5.6e-05   23.3   0.1    0.00011   22.3   0.1    1.6  1  Rio2_N          Rio2, N-terminal
     0.0019   18.1   0.8     0.0051   16.7   0.5    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0025   16.6   0.0     0.0031   16.4   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0034   16.8   0.2     0.0085   15.5   0.2    1.7  1  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.026   14.5   0.0    1.4  1  APH             Phosphotransferase enzyme family
      0.015   14.9   0.3       0.42   10.2   0.3    2.1  2  Choline_kinase  Choline/ethanolamine kinase
      0.018   14.8   0.7      0.037   13.8   0.1    1.8  2  UPF0137         Uncharacterised protein family (UPF0137)
      0.022   14.8   1.5      0.087   12.9   0.5    2.4  2  HTH_Mga         M protein trans-acting positive regulator (MG


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.1   4.9e-38   9.7e-35       1     180 [.     109     272 ..     109     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 4.9e-38
                                   EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETT CS
                          RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrh 81 
                                   +Vy ++++dg+ +++K +k++  ++++ kky++++          ++ + +   aekE+++Lk++++   +vP+p+    +
  gi|70606589|ref|YP_255459.1| 109 EVYIGYNFDGDPIIVKYHKLGK-SYRNYKKYREDTDS--------SWIRRTVHNAEKEYNALKCVKSNYGQVPSPLGSSLN 180
                                   59******************95.79999999999888........899999999*************************** PP

                                   EEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT..EEEE--GTTEEETTSTTH CS
                          RIO1  82 vlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded..kvviIDvsQaveldhpna 160
                                   ++ me+i   g +++k++  +     e++++++l+++r++yke++++H+DLSeyN+l++ d  + ++ID++Q++++++   
  gi|70606589|ref|YP_255459.1| 181 AIAMEYIY--GKELYKIEISD----PESALNDILSTVRIAYKECNIIHGDLSEYNILYSLDsdRSYVIDWPQSTNIQN--- 252
                                   ********..99999998888....7899****************************8755559**********9876... PP

                                   HHHHHHHHHHHHHHHHTTC- CS
                          RIO1 161 lefLerDveniikfFrrkgv 180
                                   +e+L rD++ni  +F++k+ 
  gi|70606589|ref|YP_255459.1| 253 EEILLRDITNILYYFSKKYN 272
                                   689**************986 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   5.6e-08   0.00011       5      79 ..      14      89 ..      10      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.6e-08
                        Rio2_N  5 skedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyDyLALktl 79
                                   ++d+r+L+ +      h+++  ++i+   ++++ e+ ++ls+l +  l+s+      + Y++t+ G+ +++ k l
  gi|70606589|ref|YP_255459.1| 14 GPMDYRLLKFLYEKTATHDWIKLSQISDELGISKREILSSLSKLYDLRLVSKeLVLGENAYRITFTGLNVISTKNL 89
                                  679*************************************************54557789*******999877665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   2.6e-06    0.0051      18      47 .]      36      65 ..      34      65 .. 0.95
   2 ?   -3.3   0.0       4.2   8.4e+03      17      26 ..      90      99 ..      82     100 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.6e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5 18 vcelaeelglsqstvShHLkkLreaGLVek 47
                                   +++++elg+s+  +   L+kL++++LV+k
  gi|70606589|ref|YP_255459.1| 36 LSQISDELGISKREILSSLSKLYDLRLVSK 65
                                  59**************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                  EHHHHHHHHT CS
                         HTH_5 17 cvcelaeelg 26
                                  +v  + ++lg
  gi|70606589|ref|YP_255459.1| 90 YVNKILNKLG 99
                                  5555555554 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0031     310     355 ..     202     243 ..     129     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                Pkinase_fungal 310 ealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiD 355
                                   +al D + + r  +++++i+H D Se+Nil       +++++ +iD
  gi|70606589|ref|YP_255459.1| 202 SALNDILSTVRIAYKECNIIHGDLSEYNILYS----LDSDRSYVID 243
                                   6999*************************977....4455555555 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   4.3e-06    0.0085       7     152 ..     102     254 ..      97     271 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                                   EEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH......HHHHHHHHHHHHHSCTTB--EEEEEEE.......SSEEE CS
                       Pkinase   7 lGeGsfGkVykaveketgkivAvKkikkekakkkke......kkvlrEikilkklkhpnivrlyevfee.......kdely 74 
                                   +G+G+ ++Vy +++  +g+ + vK  k  k   + +      ++ +   ++++  k  n ++++++ +        ++   
  gi|70606589|ref|YP_255459.1| 102 IGTGKESEVYIGYN-FDGDPIIVKYHKLGKSYRNYKkyredtDSSWIRRTVHNAEKEYNALKCVKSNYGqvpsplgSSLNA 181
                                   78888888888884.677777777777665555444333333222222233333333344444433333666777445555 PP

                                   EEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEESSSSC CS
                       Pkinase  75 lvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLid.ekgelKitDFGlakelesss 152
                                   + +ey+ g+el ++       + ++ ++ ++ il+ ++  + + +iiH Dl   NiL++ +++   ++D+  ++++++++
  gi|70606589|ref|YP_255459.1| 182 IAMEYIYGKELYKI-------EISDPESALNDILSTVRIAYkECNIIHGDLSEYNILYSlDSDRSYVIDWPQSTNIQNEE 254
                                   89999998866554.......556777889999999999994557**************777779999*99999999876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.026     168     193 ..     220     244 ..     199     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                   EE-SS-SGGGEEEC..TTEEEEE--- CS
                           APH 168 llHgDlhpgNllvdpddgrvtGviDf 193
                                   ++HgDl+  N+l   d +r  +viD+
  gi|70606589|ref|YP_255459.1| 220 IIHGDLSEYNILYSLDSDRS-YVIDW 244
                                   79************666774.8**** PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0091        18      16      66 ..     150     201 ..     133     205 .. 0.88
   2 ?   10.2   0.3   0.00021      0.42     120     171 ..     193     244 ..     190     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0091
                                   TCCHHHHHHHHHHHH.HHTTSSS-EEEEETTEEEEE--TCEE--TTGGGCHH CS
                Choline_kinase  16 elidretElvvfall.serglgpklygifenGrieefiesrtlstedlrepe 66 
                                   ++ + e+E + ++++ s++g  p+ +g   n+   e+i +++l + ++++pe
  gi|70606589|ref|YP_255459.1| 150 TVHNAEKEYNALKCVkSNYGQVPSPLGSSLNAIAMEYIYGKELYKIEISDPE 201
                                   5678899999999883578999**************************9997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                                   CCCTHHHHHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--G CS
                Choline_kinase 120 klinledlekelekleklleelespvvfcHnDlqegNillnkeekklvlIDF 171
                                    +i+++d e+ l+++ + +   +++ +  H Dl e Nil++ + ++ ++ID+
  gi|70606589|ref|YP_255459.1| 193 YKIEISDPESALNDILSTVRIAYKECNIIHGDLSEYNILYSLDSDRSYVIDW 244
                                   5677777788888888888888999999***********************9 PP

>> UPF0137  Uncharacterised protein family (UPF0137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.6   5.2e+03     172     194 ..      41      63 ..      34      91 .. 0.64
   2 ?   13.8   0.1   1.8e-05     0.037      94     154 ..     127     188 ..     118     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                       UPF0137 172 nynGetktelleiirktfPlldt 194
                                   +  G +k e+l+ + k + l  +
  gi|70606589|ref|YP_255459.1|  41 DELGISKREILSSLSKLYDLRLV 63 
                                   55577777777777776665544 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.8e-05
                       UPF0137  94 rikkvreiLknykegaFssWlllaygnrqtpYnflqYYe.lfsalPdklkseveslPrqavY 154
                                   ++ k  +  k+y+e + ssW+  +  n +  Yn+l+     + ++P +l s ++++  + +Y
  gi|70606589|ref|YP_255459.1| 127 KLGKSYRNYKKYREDTDSSWIRRTVHNAEKEYNALKCVKsNYGQVPSPLGSSLNAIAMEYIY 188
                                   556666677899***********************98652799*******999999998888 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   4.4e-05     0.087       9      46 ..      19      59 ..      17      68 .. 0.82
   2 ?   -1.0   0.0      0.93   1.9e+03      35      55 ..     202     222 ..     201     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
                       HTH_Mga  9 kLlelLtene...ksltldelakeLglseltlqsdiseLne 46
                                  +Ll +L+e +   ++++l+ ++ eLg+s +++ s +s+L +
  gi|70606589|ref|YP_255459.1| 19 RLLKFLYEKTathDWIKLSQISDELGISKREILSSLSKLYD 59
                                  57777777533338***********************9966 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.93
                       HTH_Mga  35 ltlqsdiseLnelFpeelsiv 55 
                                   ++l++++s ++++++e ++i+
  gi|70606589|ref|YP_255459.1| 202 SALNDILSTVRIAYKECNIIH 222
                                   689999999999999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1830.05
//
Query:       gi|70606590|ref|YP_255460.1|  [L=605]
Description: hypothetical protein Saci_0797 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-51  171.3   0.4    1.9e-50  170.3   0.4    1.6  1  DUF460        Protein of unknown function (DUF460)
  ------ inclusion threshold ------
       0.16   12.4  11.9        3.8    8.0   0.1    4.7  4  V-SNARE       Vesicle transport v-SNARE protein N-terminus
       0.16   12.3   3.9       0.13   12.6   1.4    2.2  2  Nab2          Nuclear abundant poly(A) RNA-bind protein 2 (Na
       0.17   12.5   8.0       0.82   10.3   1.9    2.7  2  SlyX          SlyX
        0.2   12.3  10.7        5.2    7.8   6.1    3.2  2  YabA          Initiation control protein YabA
        1.2    9.3  10.5       0.28   11.2   5.1    2.6  2  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
        1.2    9.6   5.8        2.2    8.7   0.0    3.4  4  DUF4258       Domain of unknown function (DUF4258)
        2.7    8.1  17.0       0.67   10.1  12.7    2.3  2  BRE1          BRE1 E3 ubiquitin ligase
        2.8    8.3   6.1        1.3    9.4   1.2    3.0  2  DUF5601       Domain of unknown function (DUF5601)
        4.4    7.1  12.0       0.72    9.6   5.5    2.2  2  Spc29         Spindle Pole Component 29


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.3   0.4     1e-53   1.9e-50       1     141 []     218     357 ..     218     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.3 bits;  conditional E-value: 1e-53
                        DUF460   1 kvkskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivA 81 
                                   k++++d+kve+++++k+kief++  k+  k++ivG+DPGi++gi+++d+ +++++l+s+r++dree+ie+i+++Gkpv++A
  gi|70606590|ref|YP_255460.1| 218 KMRGHDLKVEIKPIYKNKIEFKDS-KRLLKPVIVGVDPGIEVGISIIDIYSNPIYLDSKRNIDREEIIEIIKKYGKPVLIA 297
                                   5899*****************888.999***************************************************** PP

                        DUF460  82 tDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                   tDv+p+++tvkk++++l+++l++P+++ls++eK+el++++se++ +k++d+H RD+laAA
  gi|70606590|ref|YP_255460.1| 298 TDVNPASDTVKKISAQLRCRLFIPQNSLSIDEKTELVSRFSENHGIKINDPHVRDSLAAA 357
                                   ***********************************************************9 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.036        65      30      58 ..      91     119 ..      86     129 .. 0.76
   2 ?    8.0   0.1    0.0021       3.8      25      50 ..     359     384 ..     347     387 .. 0.88
   3 ?    2.6   0.8     0.098   1.8e+02      62      78 ..     437     453 ..     433     454 .. 0.87
   4 ?    0.9   1.2      0.34     6e+02       9      47 ..     463     503 ..     460     509 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.036
                       V-SNARE  30 iekkldeaeelldqMelEvrnlpsseras 58 
                                   ie ++++++e+l+++ +Ev++     +++
  gi|70606590|ref|YP_255460.1|  91 IEGEFKDLREILRSLGIEVQGKLNPIKTA 119
                                   89999***************652245555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0021
                       V-SNARE  25 aalreiekkldeaeelldqMelEvrn 50 
                                   +a +e+ +kl +ae +l++M+l +++
  gi|70606590|ref|YP_255460.1| 359 KAYHEVSQKLRQAEGILRRMDLDIEE 384
                                   6789******************9876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.098
                       V-SNARE  62 klreykselkklkkelk 78 
                                    l eyk+e+++lk++++
  gi|70606590|ref|YP_255460.1| 437 ELMEYKKEIERLKRKIR 453
                                   6889**********987 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.34
                       V-SNARE   9 ksklarlsslag.e.erkaalreiekkldeaeelldqMelE 47 
                                   ++kl+ ++ + + e er +++ e++ +++++++++++++l 
  gi|70606590|ref|YP_255460.1| 463 QHKLDEIRVEFNaEvERDRKIYELKLEIQNMQKVIENLNLA 503
                                   66777777555445699999999999999999999999886 PP

>> Nab2  Nuclear abundant poly(A) RNA-bind protein 2 (Nab2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9   7.1e+03      68      96 ..     429     457 ..     418     460 .. 0.69
   2 ?   12.6   1.4   7.2e-05      0.13       4      68 ..     494     560 ..     491     574 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                          Nab2  68 vqtaffalealqqGetvesivsklrgvsa 96 
                                    +t  +a e+++  +++e + +k+r++  
  gi|70606590|ref|YP_255460.1| 429 PDTYAKAEELMEYKKEIERLKRKIRELVL 457
                                   34444666777888899999999998765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.2e-05
                          Nab2   4 eqiaenlkvivaeklktlenfnedvnyv..aeyivlllsnGgtvesvvqelstlfdsvskealadvv 68 
                                   ++++enl   + +k k +en++e ++ v  +eyivl   n      +++  + lfd   ++ + + v
  gi|70606590|ref|YP_255460.1| 494 QKVIENLNLAIVNKQKIIENMTEIIDKVikSEYIVLKKDNFPIYMRLLNKKIFLFDEQISDDMIKYV 560
                                   6899**********************99566*********999999999999999964444444444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5     0.024        44      25      46 ..     437     458 ..     435     472 .. 0.83
   2 ?   10.3   1.9   0.00045      0.82       3      43 ..     481     521 ..     479     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHHHHHHHT CS
                          SlyX  25 vvaeqqqqidrlqrqlrllaer 46 
                                   +++e  ++i+rl+r++r+l+ +
  gi|70606590|ref|YP_255460.1| 437 ELMEYKKEIERLKRKIRELVLQ 458
                                   7889999*********999765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00045
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrll 43 
                                    ++ eL  ++  ++++ie Ln ++++ q+ i+ +++ ++++
  gi|70606590|ref|YP_255460.1| 481 RKIYELKLEIQNMQKVIENLNLAIVNKQKIIENMTEIIDKV 521
                                   57889999999***********************9988765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        30      28      75 ..     330     377 ..     307     381 .. 0.88
   2 ?    7.8   6.1    0.0029       5.2      15      75 ..     436     495 ..     423     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA  28 keelaelleenaeLeleneklrerleeeekkekekkkelsegkenLar 75 
                                   k+el++ + en+ ++++  ++r+ l+ + k+ +e +++l++++  L+r
  gi|70606590|ref|YP_255460.1| 330 KTELVSRFSENHGIKINDPHVRDSLAAALKAYHEVSQKLRQAEGILRR 377
                                   778889999****************99999999999998888877766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLar 75 
                                   e+l+e ++e+e+lk+++ el+ +n+ L+   +++r +++ +e ++++k  el+   +n+++
  gi|70606590|ref|YP_255460.1| 436 EELMEYKKEIERLKRKIRELVLQNTILQHKLDEIRVEFN-AEVERDRKIYELKLEIQNMQK 495
                                   6789999*****************************994.555555555566666666665 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.1   0.00016      0.28      95     128 ..     435     468 ..     403     469 .. 0.82
   2 ?   -1.1   0.2         1   1.8e+03      61      77 ..     485     501 ..     472     523 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                    TPR_MLP1_2  95 eeqkeelekelselekriedlneqNklLhdQlEs 128
                                   +e+  e++ke++ l+++i +l  qN++L  +l++
  gi|70606590|ref|YP_255460.1| 435 AEELMEYKKEIERLKRKIRELVLQNTILQHKLDE 468
                                   5667799***********************9997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                    TPR_MLP1_2  61 alreelnelkaeiaelk 77 
                                   +l+ e++++++ i++l+
  gi|70606590|ref|YP_255460.1| 485 ELKLEIQNMQKVIENLN 501
                                   33333333333333332 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.8   1.4e+04      26      55 ..      31      56 ..      27      60 .. 0.62
   2 ?    8.7   0.0    0.0012       2.2      11      27 ..     275     292 ..     274     339 .. 0.82
   3 ?    1.7   0.3      0.19   3.4e+02      13      30 ..     381     399 ..     374     441 .. 0.69
   4 ?   -3.8   0.1        10   1.8e+04      12      25 ..     550     563 ..     547     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.8
                       DUF4258 26 Geiieeys.lvlgktsegrplhvvvapdedp 55
                                  Gei  +++ +       g+ l++v+++ +++
  gi|70606590|ref|YP_255460.1| 31 GEIEYKQEgI-----NIGKLLRLVWEIRPSK 56
                                  5544444431.....3456678888887765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0012
                       DUF4258  11 eRgIseedieevle.nGe 27 
                                   +R+I++e+i e+++ +G+
  gi|70606590|ref|YP_255460.1| 275 KRNIDREEIIEIIKkYGK 292
                                   7*************8885 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.19
                       DUF4258  13 gIseedieevlenGe.iie 30 
                                   +I e +i+e++ +G  i+e
  gi|70606590|ref|YP_255460.1| 381 DIEEHEILECIIKGStINE 399
                                   5889999999999953333 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 10
                       DUF4258  12 RgIseedieevlen 25 
                                    +Is++ i++v + 
  gi|70606590|ref|YP_255460.1| 550 EQISDDMIKYVGDD 563
                                   68999999998665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       4.4     8e+03      35      48 ..     404     417 ..     396     425 .. 0.62
   2 ?   10.1  12.7   0.00037      0.67       3      88 ..     436     525 ..     434     532 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                          BRE1  35 rleaekakadqkyf 48 
                                    +e+e+ k d++++
  gi|70606590|ref|YP_255460.1| 404 EIEKEIGKSDEEIK 417
                                   45555556555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00037
                          BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekaka...dqkyfaamrskdalenelkkLnkllsKsselieqLke 80 
                                    EL + +k++e l+++++++v + til+ k+  + +e + +   d+k+++++ +++++++ + +Ln  +  ++++ie++ e
  gi|70606590|ref|YP_255460.1| 436 EELMEYKKEIERLKRKIRELVLQNTILQHKLDEIRVEFNAEverDRKIYELKLEIQNMQKVIENLNLAIVNKQKIIENMTE 516
                                   69************************************9654459***********************************9 PP

                          BRE1  81 .lekefvrk 88 
                                    ++k ++++
  gi|70606590|ref|YP_255460.1| 517 iIDKVIKSE 525
                                   766655555 PP

>> DUF5601  Domain of unknown function (DUF5601)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.2   0.00073       1.3       8      38 ..     308     348 ..     304     448 .. 0.80
   2 ?   -2.5   0.3       3.8   6.9e+03       6      24 ..     496     518 ..     490     522 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00073
                       DUF5601   8 rkis..........qrsisieelSemVqdFyqnlaerlnkt 38 
                                   +kis          q+s+si+e+ e+V+ F +n   ++n  
  gi|70606590|ref|YP_255460.1| 308 KKISaqlrcrlfipQNSLSIDEKTELVSRFSENHGIKINDP 348
                                   5555555566666699**************99977777655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.8
                       DUF5601   6 fvrkis....qrsisieelSemV 24 
                                   +++++     +++  ie++ e++
  gi|70606590|ref|YP_255460.1| 496 VIENLNlaivNKQKIIENMTEII 518
                                   44444444443333366666655 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.2    0.0095        17     112     161 ..     428     473 ..     405     476 .. 0.76
   2 ?    9.6   5.5    0.0004      0.72     107     163 ..     464     520 ..     462     535 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0095
                         Spc29 112 iyssvkkivelek..klddqkleIkeLkreleqqrtvnseLqekvaeleeev 161
                                   +      ++   k   l + k eI+ Lkr++ +    n  Lq+k++e+  e+
  gi|70606590|ref|YP_255460.1| 428 V------PDTYAKaeELMEYKKEIERLKRKIRELVLQNTILQHKLDEIRVEF 473
                                   3......333333447889999************************997665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0004
                         Spc29 107 srldsiyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkr 163
                                    +ld i+ + +  ve ++k+++ kleI+++++ +e+ +  + + q+ ++++ e +++
  gi|70606590|ref|YP_255460.1| 464 HKLDEIRVEFNAEVERDRKIYELKLEIQNMQKVIENLNLAIVNKQKIIENMTEIIDK 520
                                   579***********************************9999999999999988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1702  (0.09493); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 3903.99
//
Query:       gi|70606591|ref|YP_255461.1|  [L=403]
Description: S-adenosylmethionine synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.9e-168  559.0   4.6   5.5e-168  558.8   4.6    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.8   4.6  3.1e-172  5.5e-168       1     395 [.       3     398 ..       3     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 558.8 bits;  conditional E-value: 3.1e-172
                                   --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE CS
               AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevie 81 
                                   +ni+v++++  + ++ evE+ ErKG+GHPD+iaD+++e++sr+ls +yl+ fg+ilhhn+Dk+l+v+G+++pk++GG+v++
  gi|70606591|ref|YP_255461.1|   3 KNINVQQSHWANPDKLEVELAERKGVGHPDYIADSASEEASRKLSLYYLKAFGTILHHNLDKTLVVGGQATPKYKGGDVVQ 83 
                                   69******************************************************************************* PP

                                   -EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSE CS
               AdoMet_Synthase  82 pieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtS 158
                                   pi++++sgrat+ev    + e+ip+++i++e++k+++ken+r+ld+ek+v+vd+k+gkgs+dL+++fe++k+ vpl+NDtS
  gi|70606591|ref|YP_255461.1|  84 PIYVIVSGRATTEVktpsGVENIPIGTIIIESVKDWIKENFRYLDVEKHVVVDYKIGKGSTDLVGLFEANKQ-VPLSNDTS 163
                                   **************77777899***********************************************666.9******* PP

                                   EEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHH CS
               AdoMet_Synthase 159 fgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeevee 239
                                   fgvg+ap+s+le+lvl+terllnske+++k+pe+GeDiKvmglR++k+ielTva+a++++l++dl++Yl+vkee k+++ +
  gi|70606591|ref|YP_255461.1| 164 FGVGFAPYSTLENLVLSTERLLNSKEIRSKIPEIGEDIKVMGLRKGKEIELTVAMATISQLIDDLNHYLQVKEEAKQKILD 244
                                   ********************************************************************************* PP

                                   HHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHH CS
               AdoMet_Synthase 240 lakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvla 320
                                   la+kl+ e++v+v++Nt Dk+++++vyltvtGtsaE+gDdG++GRGNR+ Glitp+rpmslEA+aGKNPv+HvGK+Ynvla
  gi|70606591|ref|YP_255461.1| 245 LASKLAPEYSVKVNINTGDKIDKGIVYLTVTGTSAEHGDDGMTGRGNRATGLITPMRPMSLEATAGKNPVNHVGKLYNVLA 325
                                   ********************************************************************************* PP

                                   HHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHTTT CS
               AdoMet_Synthase 321 neiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteelieg 395
                                   n ia++++++v+g++ v+v++l qiG+pi++Pl+a+vq+++e+   ++e+++eve i+de l++++++ e ++e 
  gi|70606591|ref|YP_255461.1| 326 NLIAQKVHKDVKGINGVQVEILGQIGRPINDPLIANVQLAAEN--ITTEIKREVEGITDELLSSVTKLSELILES 398
                                   ***************************************6654..57899*******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2818.03
//
Query:       gi|70606592|ref|YP_255462.1|  [L=87]
Description: Sm-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-22   77.9   0.2      4e-22   77.7   0.2    1.1  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.096   12.8   0.0       0.12   12.6   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.2   4.4e-26     4e-22       2      66 ..      11      76 ..      10      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 4.4e-26
                                  HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET.EEEEEEEEEEEGGGEEEEE CS
                           LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk.ekrklglvliRGnnivlis 66
                                   lk  +nk+v+v+lkng+e++G+L+  D  mNlvL+d++e+++++   ++k+g+vliRG+ni++is
  gi|70606592|ref|YP_255462.1| 11 SLKTALNKIVLVKLKNGEEYVGRLEQSDGTMNLVLKDCTEYREGTSdPVAKYGRVLIRGSNILFIS 76
                                  799***************************************998899****************98 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05      0.12      16      51 ..      20      53 ..      14      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                  EEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                        SM-ATX 16 vevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                  v v++knGe y G +  ++    +++vLk   + ++
  gi|70606592|ref|YP_255462.1| 20 VLVKLKNGEEYVGRLEQSDG--TMNLVLKDCTEYRE 53
                                  88******************..*******9888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 642.47
//
Query:       gi|70606593|ref|YP_255463.1|  [L=98]
Description: hypothetical protein Saci_0800 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-13   47.9   0.1    1.6e-12   47.1   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    3.7e-09   36.5   0.0    5.2e-09   36.0   0.0    1.1  1  HTH_20          Helix-turn-helix domain
    1.5e-07   31.2   0.0    2.2e-07   30.7   0.0    1.3  1  MarR_2          MarR family
    1.6e-07   31.2   0.1    2.6e-07   30.5   0.1    1.4  1  MarR            MarR family
    3.5e-06   27.1   0.1    5.3e-06   26.5   0.1    1.4  1  HTH_34          Winged helix DNA-binding domain
      4e-06   26.3   0.0    6.5e-06   25.6   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.2e-05   24.2   0.1    3.9e-05   23.5   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    3.6e-05   23.7   0.1    8.9e-05   22.4   0.1    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0034   17.3   0.1     0.0052   16.7   0.1    1.4  1  HTH_11          HTH domain
     0.0041   17.2   0.0     0.0058   16.7   0.0    1.2  1  DprA_WH         DprA winged helix domain
     0.0054   16.5   0.0     0.0063   16.3   0.0    1.1  1  DUF742          Protein of unknown function (DUF742)
     0.0074   16.5   0.2      0.012   15.7   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0081   16.6   0.0      0.013   16.0   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
     0.0086   15.9   0.0      0.013   15.3   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.036   14.2   0.3      0.047   13.8   0.3    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.038   14.4   0.2       0.05   13.9   0.2    1.3  1  Rrf2            Transcriptional regulator
      0.044   13.7   0.0      0.091   12.7   0.0    1.6  1  PadR            Transcriptional regulator PadR-like family
      0.052   13.3   0.2      0.095   12.4   0.1    1.5  2  DUF4423         Domain of unknown function (DUF4423)
      0.055   13.3   0.3        0.1   12.4   0.3    1.6  1  TFIIE_alpha     TFIIE alpha subunit
        0.1   12.3   0.0       0.14   11.8   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
        0.1   12.6   0.1       0.17   11.9   0.1    1.4  1  DUF4315         Domain of unknown function (DUF4315)
       0.11   12.5   0.0       0.18   11.8   0.0    1.6  1  Cdc6_C          CDC6, C terminal winged helix domain
       0.17   11.8   0.0       0.25   11.3   0.0    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1     2e-15   1.6e-12       4      46 ..      23      65 ..      21      65 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2e-15
                                  HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  R+ ILkl+ae++++v+el+e l+++++++S +L+ L++aGL+e
  gi|70606593|ref|YP_255463.1| 23 RVNILKLVAEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  9****************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   6.7e-12   5.2e-09       3      55 ..      14      65 ..      12      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.7e-12
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                  + +AL+  +R  il++   +++++++el e l ++k ++s +L++Le+agL+e
  gi|70606593|ref|YP_255463.1| 14 VSKALSVMSRVNILKLV-AEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  67899999*********.**********************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.8e-10   2.2e-07      13      53 ..      29      66 ..      17      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.8e-10
                                  HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   ++  p   ++v+el + l+++k+++s  l++L++aGL+e 
  gi|70606593|ref|YP_255463.1| 29 LVAEKP---MSVTELSEFLHMTKGNISSQLAELEDAGLIEI 66
                                  445555...9*****************************95 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   3.3e-10   2.6e-07      15      48 ..      32      65 ..      21      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.3e-10
                                  STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  + p+sv+eL ++l+++k++++ +l +Le++Glie
  gi|70606593|ref|YP_255463.1| 32 EKPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  579******************************7 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   6.8e-09   5.3e-06       9      49 ..      29      69 ..      18      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.8e-09
                        HTH_34  9 LasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  L++++ ++ +el+e l +t+gn+s++l  Le+ag ie++ e
  gi|70606593|ref|YP_255463.1| 29 LVAEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIKYE 69
                                  677888999***************************99865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   8.3e-09   6.5e-06       8      48 .]      26      65 ..      22      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 8.3e-09
                        HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  IL+l+ +   +s +eL+e l++++++++ +l +Le++GlI+
  gi|70606593|ref|YP_255463.1| 26 ILKLVAE-KPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  6666666.569*****************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1     5e-08   3.9e-05      15      59 ..      27      80 ..      26      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5e-08
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.........T CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.........p 59
                                  l+L++++p++++e++e l   + ++ + L +Led+Gl+e++ ++         +
  gi|70606593|ref|YP_255463.1| 27 LKLVAEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIKYENgvkgikkivK 80
                                  58***************************************9997777755554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.1e-07   8.9e-05      19      53 ..      32      67 ..      13      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.r 53
                                  e p++ +el+++l +t   +s  l+eL+++gli+ +
  gi|70606593|ref|YP_255463.1| 32 EKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEiK 67
                                  459******************************954 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   6.7e-06    0.0052       5      54 ..      26      75 ..      22      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesepgr.GY 54
                                  il+l+  a++p+s  eL+e L++++  +   +++Le++g ++I  e+g+ G+
  gi|70606593|ref|YP_255463.1| 26 ILKLV--AEKPMSVTELSEFLHMTKGNISSQLAELEDAGlIEIKYENGVkGI 75
                                  77777..5667****************************9999999987775 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.4e-06    0.0058      15      56 ..      24      65 ..      14      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.4e-06
                       DprA_WH 15 rrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                    +L +++  P++v +L++ ++++ + +s++L eLE aGl+e
  gi|70606593|ref|YP_255463.1| 24 VNILKLVAEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  579***********************************9997 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.1e-06    0.0063      45      88 ..      23      67 ..       4      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                        DUF742 45 hrailrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltvr 88
                                  + +il+L++e p+sV el+  l++  g +   l++L dagl++++
  gi|70606593|ref|YP_255463.1| 23 RVNILKLVAEkPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIK 67
                                  679******99*******************************987 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05     0.012      20      59 ..      32      71 ..      25      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                  HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                Fe_dep_repress 20 kkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                  +k+ ++++l+e+L   +  +s  l +Le++G++e +   g
  gi|70606593|ref|YP_255463.1| 32 EKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIKYENG 71
                                  57899****************************9987776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05     0.013       8      49 ..      26      65 ..      22      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                  +L l++  + +++ ++l+++l +++ +is+ l +L+ +GL+e
  gi|70606593|ref|YP_255463.1| 26 ILKLVA--EKPMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  677888..89999****************************4 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.013       7      49 ..      25      65 ..      14      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   iL+++ae   +++++el++ ++++k + +  L+ L+  G++e
  gi|70606593|ref|YP_255463.1| 25 NILKLVAEK--PMSVTELSEFLHMTKGNISSQLAELEDAGLIE 65
                                  567777665..578**************************987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     6e-05     0.047      28      70 ..      40      82 ..       9      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                       DUF2250 28 iakeleipleevrellkkLeelGLlervegktikrteaklKkk 70
                                  +++ l++ + ++++ l +Le++GL+e + ++ +k  ++  K k
  gi|70606593|ref|YP_255463.1| 40 LSEFLHMTKGNISSQLAELEDAGLIEIKYENGVKGIKKIVKSK 82
                                  5667899999****************99999999998888766 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.5e-05      0.05      18      58 ..      27      67 ..      12      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                                  HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   k   e+p+s++e++e   + +  ++  la+L+ agl++ +
  gi|70606593|ref|YP_255463.1| 27 LKLVAEKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIK 67
                                  33445578*****************************9864 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.091       3      58 ..      28      74 ..      26      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                  HHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS CS
                          PadR  3 alleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegp 58
                                  +l++e+p+  +e+         ++l + +G++  +L++Le+ gl+e + e+ g+++
  gi|70606593|ref|YP_255463.1| 28 KLVAEKPMSVTELS--------EFLHMTKGNISSQLAELEDAGLIEIKYEN-GVKG 74
                                  55555554444443........45667799****************98776.4555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.76     6e+02      54      74 ..      13      33 ..      11      39 .. 0.80
   2 ?   12.4   0.1   0.00012     0.095      32      86 ..      32      82 ..      19      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.76
                       DUF4423 54 evekalefLlklgllkkdedg 74
                                  +v+kal+ + ++++lk  +++
  gi|70606593|ref|YP_255463.1| 13 KVSKALSVMSRVNILKLVAEK 33
                                  589999999999999988775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                       DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksltts 86
                                   k+   ++ el++ l+  +++  +++ l  L+++gl++ + ++ ++  +k ++++
  gi|70606593|ref|YP_255463.1| 32 EKP--MSVTELSEFLH--MTKGNISSQLAELEDAGLIEIKYENGVKGIKKIVKSK 82
                                  334..4899*******..*********************9998888888887754 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00013       0.1      17      62 ..      25      69 ..      13      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                  HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                   TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                  ++l+ ++ +  ++  +l++ l++ + ++ + L++L +a+l+++k +
  gi|70606593|ref|YP_255463.1| 25 NILKLVA-EKPMSVTELSEFLHMTKGNISSQLAELEDAGLIEIKYE 69
                                  5566555.55566779*************************99865 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.14      18      62 ..      29      72 ..      19      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                  S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEE CS
                          GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrGt 62
                                  l ++ ++ s+ eL++ ++ ++  +   L +Le +gl+e++  +G+
  gi|70606593|ref|YP_255463.1| 29 LVAEKPM-SVTELSEFLHMTKGNISSQLAELEDAGLIEIKYENGV 72
                                  7788999.*******************************988886 PP

>> DUF4315  Domain of unknown function (DUF4315)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00022      0.17      37      64 ..      25      52 ..      23      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                       DUF4315 37 eIvqlVramklspeeLaallkamkegaa 64
                                  +I++lV +  +s +eL+++l + k++  
  gi|70606593|ref|YP_255463.1| 25 NILKLVAEKPMSVTELSEFLHMTKGNIS 52
                                  799******************6665543 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.18      31      72 ..      40      79 ..      24      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                  HTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEE CS
                        Cdc6_C 31 segvdpltqrevsdllseLemlgileleksskGrregrtrki 72
                                    ++  +t   +s+ l+eLe+ g++e++ ++ G  +g ++ +
  gi|70606593|ref|YP_255463.1| 40 LSEFLHMTKGNISSQLAELEDAGLIEIKYEN-GV-KGIKKIV 79
                                  55556789999****************9764.33.3555544 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.25       4      39 ..      24      60 ..      21      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                  HHHHHHHHHHS.SHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_1  4 lrlfvavaeeg.sftrAAeeLglsqpavsrqikrLEe 39
                                  + +++ vae   s+t+  e L+++   +s q+++LE+
  gi|70606593|ref|YP_255463.1| 24 VNILKLVAEKPmSVTELSEFLHMTKGNISSQLAELED 60
                                  5677788888889999999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 715.02
//
Query:       gi|70606594|ref|YP_255464.1|  [L=529]
Description: CTP synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.3e-119  396.1   2.8   8.8e-119  395.7   2.8    1.2  1  CTP_synth_N    CTP synthase N-terminus
    6.5e-54  182.6   0.0    1.2e-53  181.7   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    3.9e-09   36.6   0.0    9.5e-09   35.3   0.0    1.6  1  Peptidase_C26  Peptidase C26
    1.7e-05   24.9   0.0    3.7e-05   23.8   0.0    1.9  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.063   12.4   1.6        1.2    8.2   0.3    2.4  2  ArsA_ATPase    Anion-transporting ATPase
       0.14   11.2   0.2       0.25   10.3   0.2    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.7   2.8  2.9e-122  8.8e-119       1     265 []       3     266 ..       3     266 .. 0.99

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 2.9e-122
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT--- CS
                   CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikl 81 
                                   kyi+vtGGv+S++GkG i+as+g llks+g++vt+ik+DPYlnvdagt++p+ hGEvfv+ddGaetDlDlG+YeRf++i++
  gi|70606594|ref|YP_255464.1|   3 KYIIVTGGVLSSVGKGTIVASIGFLLKSSGYNVTAIKVDPYLNVDAGTMNPYMHGEVFVTDDGAETDLDLGHYERFIGINT 83 
                                   8******************************************************************************** PP

                                   -GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHH CS
                   CTP_synth_N  82 tkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlkle 162
                                   t+ nnit+G++y +vi+ker+G+ylG+tvq+iphvtdeik  ++k+ + ++a+++i+eigGtvgdie+lpflea+rq+kle
  gi|70606594|ref|YP_255464.1|  84 TRYNNITAGRVYFEVIRKEREGKYLGQTVQIIPHVTDEIKGLVKKAVDDTNAEIAIIEIGGTVGDIEGLPFLEAVRQMKLE 164
                                   **********************************************9999******************************9 PP

                                   H-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-G CS
                   CTP_synth_N 163 lgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesi 243
                                     +en+++ihv+lv +l+ +gelktkp qhsv+elr++Giqpd+i++rs  +l+ee+k+kialf+nv+ + ++s+ dve +
  gi|70606594|ref|YP_255464.1| 165 E-EENLMFIHVALVEYLRVTGELKTKPLQHSVQELRRIGIQPDMIIARSILPLDEETKKKIALFTNVKPDYILSNYDVELT 244
                                   6.89***************************************************************************** PP

                                   GGHHHHHHHCTHHHHHHHHTT- CS
                   CTP_synth_N 244 yevpllleeqglaelileklkl 265
                                   yevpl+le+q+++++i +kl l
  gi|70606594|ref|YP_255464.1| 245 YEVPLILEKQNITKKIFNKLGL 266
                                   ******************9976 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.0   4.1e-57   1.2e-53       2     188 ..     301     524 ..     300     526 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 4.1e-57
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                   l+D+y s++e++ ha+++l+vk ++v++++s++e+ e    +lk+++gi+v +G+g++gvegki+aik+aren+iP+LGIC
  gi|70606594|ref|YP_255464.1| 301 LKDSYLSIKEAIYHAAAKLRVKPTLVWVESSDLEKSEdeinKLKDVNGIIVLPGFGARGVEGKIQAIKFARENNIPFLGIC 381
                                   79******************************9996676656*************************************** PP

                                   HHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEE CS
                        GATase  79 LGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevierhrH 128
                                   +GmQl++ e++r+v                        ++k+  + ggtmrlg+++           +y++ + ++erhrH
  gi|70606594|ref|YP_255464.1| 382 FGMQLAIVEYARNVLglkeanttevnpntkypiitlldNQKKIVQVGGTMRLGAQKIilkegtlaYSIYNS-PHIYERHRH 461
                                   ************9999999999999999999999****8888************666*****998888888.99******* PP

                                   EEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHH CS
                        GATase 129 ryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnfli 188
                                   ryevnp+    l + g++++++se++  l+eiie+kn + f g+Q HPE++s+p  p+++f +++
  gi|70606594|ref|YP_255464.1| 462 RYEVNPEyvdLLQKYGMIISGVSENG--LVEIIELKNhKfFLGTQAHPEYKSRPLSPSPVFLNFL 524
                                   *********6666678*******998..9********999*********************9997 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.2e-12   9.5e-09      97     216 .]     366     508 ..     361     508 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.2e-12
                 Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe................q.....saashavkvekg 156
                                    i+ a e+++P lgiC G+ql  v +  ++   ++e  ++t+  +++                q        ++++ +++g
  gi|70606594|ref|YP_255464.1| 366 AIKFARENNIPFLGICFGMQLAIVEYARNVL-GLKE-ANTTEV-NPNtkypiitlldnqkkivQvggtmRLGAQKIILKEG 443
                                   56778899*************9888776654.3333.122222.22224567888887766662555667889999999** PP

                 Peptidase_C26 157 sllaellgseeievnslHhqaike......laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                   +l +++++s +i     H+  ++          ++ ++ v+e g++E ie++++k f+lg Q HPE
  gi|70606594|ref|YP_255464.1| 444 TLAYSIYNSPHIYERHRHRYEVNPeyvdllQKYGMIISGVSENGLVEIIELKNHK-FFLGTQAHPE 508
                                   ********99999999999999888988855668999****************87.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.2e-08   3.7e-05       8      55 ..      13     148 ..       5     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                   + vGK t++a+++++l+  g++V ++++Dp  n +a   g+ n                                      
  gi|70606594|ref|YP_255464.1|  13 SSVGKGTIVASIGFLLKSSGYNVTAIKVDPYLNVDA---GTMNPYMHgevfvtddgaetdldlghyerfiginttrynnit 90 
                                   89*****************************99988...433333335666555666666666766666766666666666 PP

                                   .........................................................C CS
                                   .........................................................x RF
                          CbiA  55 .........................................................d 55 
                                                                                            d
  gi|70606594|ref|YP_255464.1|  91 agrvyfevirkeregkylgqtvqiiphvtdeikglvkkavddtnaeiaiieiggtvgD 148
                                   6666666666666666666666666666666666666666666666655555555552 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3   0.00041       1.2       2      44 ..       3      47 ..       2     161 .. 0.72
   2 ?    3.1   0.1     0.015        44     222     252 ..     190     220 ..     153     253 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00041
                                  EEEEEEES..TTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHH CS
                   ArsA_ATPase  2 kvilvgGK..GGVGKttvsaatavklsekgkkvllistDPAhsls 44
                                  k+i+v+G     VGK t+ a+++  l  +g++v  i +DP  ++ 
  gi|70606594|ref|YP_255464.1|  3 KYIIVTGGvlSSVGKGTIVASIGFLLKSSGYNVTAIKVDPYLNVD 47
                                  6777776423579***************************88775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHTT-EEEEEEEEEE-TTCSSS CS
                   ArsA_ATPase 222 EteRaikeLkkygikvdavivNkllpeeeqe 252
                                     + +++eL ++gi+ d++i   +lp +e+ 
  gi|70606594|ref|YP_255464.1| 190 PLQHSVQELRRIGIQPDMIIARSILPLDEET 220
                                   457789*****************99976664 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   8.3e-05      0.25      38      74 ..      13      49 ..       2      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.3e-05
                                  TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
                          MeaB 38 PGaGkstlvealglelrrrGkrvavlavDPsspftGG 74
                                    +Gk t+v  +g  l++ G+ v+ + vDP  ++  G
  gi|70606594|ref|YP_255464.1| 13 SSVGKGTIVASIGFLLKSSGYNVTAIKVDPYLNVDAG 49
                                  579***************************8777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3706.38
//
Query:       gi|70606595|ref|YP_255465.1|  [L=228]
Description: hypothetical protein Saci_0802 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-17   64.2   4.6    3.1e-17   63.0   4.6    1.6  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
     0.0023   17.7   1.5      0.005   16.6   1.0    1.9  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   4.6   3.4e-21   3.1e-17       3     225 .]      19     222 ..      17     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.4e-21
                                   EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHHHHSTC CS
                     OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekqatags 80 
                                   +++alD+ + +++ ++a ++ +  + +++ +++lv+++g      + ++++r+ +   +i++D K+aD+G+++ ++a+   
  gi|70606595|ref|YP_255465.1|  19 IQVALDFINIQDAEKVAIQAIKaGAGIIEAGTPLVKAEG-----IRGLKRLRELNpnGIILADTKTADAGDVEVEIAK--- 91 
                                   79***************999888****************.....88888888887778*******************8... PP

                                   HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHT CS
                     OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetl 161
                                      +  a+i+tv + +++a+++++++ a + g   l++ + ++  +   +++ + ++  v+ +  h       G+ +q+++
  gi|70606595|ref|YP_255465.1|  92 ---AGDANIMTVLGIMDDATIESAVKRAHELG--LLVQADLINVRDVIGRAQ-ELKKLQVDIIGLHV------GLDVQKKR 160
                                   ...566************************98..888888888888877777.33333333333333......55555555 PP

                                   HHHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                     OMPdecase 162 nateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaery 225
                                     ++    ++ i      ++   ++++g++++ +++l++    +i++vG +I++a dp +++e++
  gi|70606595|ref|YP_255465.1| 161 G-ISIVdLKNEIMEISNLNV-IISVAGGLNKDRIKELVNLP-INIFVVGGAITRAHDPFKATEEI 222
                                   5.111112222333333333.6899**************98.9***************9999975 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.0   5.5e-07     0.005      93     161 ..     137     212 ..      70     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-07
                                   HHHHHHHT-SEEEEES-.........-HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB CS
                     QRPTase_C  93 leevleaeadiimLDnf.........sveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsv 161
                                   ++e  + ++dii L            s  +lk+ +   +  n +v+i+v+Gg++++ ++e+ +  ++++ vg +++++
  gi|70606595|ref|YP_255465.1| 137 AQELKKLQVDIIGLHVGldvqkkrgiSIVDLKNEIM--EISNLNVIISVAGGLNKDRIKELVNLPINIFVVGGAITRA 212
                                   555555667776655432222222212222232222..233444***************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1454.48
//
Query:       gi|70606596|ref|YP_255466.1|  [L=150]
Description: hypothetical protein Saci_0803 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   10.9   3.6          4    7.5   0.0    3.1  5  DUF1128   Protein of unknown function (DUF1128)
          1    9.4   3.1        1.3    9.0   0.0    2.7  3  Spo12     Spo12 family


Domain annotation for each model (and alignments):
>> DUF1128  Protein of unknown function (DUF1128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00045         4      19      38 ..      11      30 ..       6      38 .. 0.86
   2 ?   -2.9   0.0      0.77   6.9e+03      60      70 ..      47      57 ..      43      60 .. 0.69
   3 ?   -2.3   0.0       0.5   4.5e+03      27      44 ..      69      86 ..      64      88 .. 0.77
   4 ?   -1.1   0.1      0.21   1.9e+03      18      36 ..      99     119 ..      98     126 .. 0.64
   5 ?    2.8   0.2     0.013   1.2e+02       3      21 ..     118     136 ..     116     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00045
                       DUF1128 19 kLkmvnaavlkaedfseeky 38
                                    kmvn+ v+++++++e+k 
  gi|70606596|ref|YP_255466.1| 11 DVKMVNRQVITPDALKEDKK 30
                                  579*************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.77
                       DUF1128 60 qaiveeLgrlR 70
                                  +a+v +L +l+
  gi|70606596|ref|YP_255466.1| 47 KALVAALNDLK 57
                                  46777777776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.5
                       DUF1128 27 vlkaedfseekyedlkdl 44
                                  vl ++ +s    edl+ l
  gi|70606596|ref|YP_255466.1| 69 VLGNNVYSPVLKEDLTTL 86
                                  677778888889999875 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.21
                       DUF1128  18 ekLkmvnaav..lkaedfsee 36 
                                   +kLk+ n ++  l++++ +e+
  gi|70606596|ref|YP_255466.1|  99 KKLKLTNNGLefLDSQQIEED 119
                                   799999987543666666555 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.013
                       DUF1128   3 ekseenleymieeikekLk 21 
                                   e  ++nl++ i++ik+k  
  gi|70606596|ref|YP_255466.1| 118 EDFKNNLTQKINDIKSKIT 136
                                   556789*********9975 PP

>> Spo12  Spo12 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.18   1.7e+03      15      21 ..      53      59 ..      51      61 .. 0.88
   2 ?   -2.6   0.3      0.62   5.6e+03      10      16 ..      96     102 ..      96     104 .. 0.77
   3 ?    9.0   0.0   0.00015       1.3      12      23 ..     125     136 ..     124     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.18
                         Spo12 15 LnahKsK 21
                                  Ln++K+K
  gi|70606596|ref|YP_255466.1| 53 LNDLKQK 59
                                  9****99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.62
                         Spo12  10 PCsqKLn 16 
                                   P s+KL+
  gi|70606596|ref|YP_255466.1|  96 PQSKKLK 102
                                   6699995 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00015
                         Spo12  12 sqKLnahKsKlf 23 
                                   +qK+n++KsK+ 
  gi|70606596|ref|YP_255466.1| 125 TQKINDIKSKIT 136
                                   9*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1097.10
//
Query:       gi|70606597|ref|YP_255467.1|  [L=125]
Description: hypothetical protein Saci_0804 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-50  167.8   4.4    9.3e-50  167.6   4.4    1.0  1  DUF2153   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.071   13.2   0.1      0.094   12.8   0.1    1.4  1  bMG1      Bacterial Alpha-2-macroglobulin MG1 domain
       0.11   12.7   0.1       0.15   12.2   0.0    1.3  1  OSCP      ATP synthase delta (OSCP) subunit


Domain annotation for each model (and alignments):
>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.6   4.4   1.6e-53   9.3e-50       8     122 ..       1     117 [.       1     118 [. 0.97

  Alignments for each domain:
  == domain 1  score: 167.6 bits;  conditional E-value: 1.6e-53
                       DUF2153   8 eqkelletlkkvekkve..eaDRLdlilasraafqhmmrtlkaFdqWLqdPviishmpremLldvketlreilekllelDi 86 
                                   +qk+ll+tlk+ ekk++  ++DRLdlila+r+afqh++rt+kaFdqWLqdP ii+hmp+emL+dv++t++e+le+llelDi
  gi|70606597|ref|YP_255467.1|   1 MQKNLLATLKELEKKYQnsSSDRLDLILATRVAFQHILRTIKAFDQWLQDPQIIKHMPKEMLEDVMKTTWELLENLLELDI 81 
                                   7***************97789************************************************************ PP

                       DUF2153  87 eHtsevrelleklskegklnpllalekeaeeekeer 122
                                   +Htse+++l+ klskegkl+pl+++++  e++++++
  gi|70606597|ref|YP_255467.1|  82 RHTSEFKDLVVKLSKEGKLDPLIWSRPVEEGQQPQQ 117
                                   ***************************999999886 PP

>> bMG1  Bacterial Alpha-2-macroglobulin MG1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.6e-05     0.094      53      83 ..      66      96 ..      18     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                          bMG1 53 vdGaWeLsdnlkelrlrhlePkrklvltvda 83
                                  +  +WeL +nl el +rh +  ++lv+ +++
  gi|70606597|ref|YP_255467.1| 66 MKTTWELLENLLELDIRHTSEFKDLVVKLSK 96
                                  5679*********************998765 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.15      18      75 ..      23      79 ..      16     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                          OSCP 18 aleeveeelealeavlaedkklaellsnpavsaeekkdlleelfkeklseavknflkl 75
                                  +l+ + +   a++++l++ k + ++l++p++ +   k++le+++k+   e+++n+l+l
  gi|70606597|ref|YP_255467.1| 23 RLDLILATRVAFQHILRTIKAFDQWLQDPQIIKHMPKEMLEDVMKT-TWELLENLLEL 79
                                  566666666788999******************************9.77888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 888.04
//
Query:       gi|70606598|ref|YP_255468.1|  [L=131]
Description: hypothetical protein Saci_0805 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-17   61.8   2.9    1.2e-16   61.0   2.9    1.4  1  Trm112p       Trm112p-like protein
  ------ inclusion threshold ------
      0.017   15.2   1.0      0.017   15.2   1.0    2.1  2  zf-UDP        Zinc-binding RING-finger
        0.4   10.9   3.4        1.1    9.5   0.0    3.1  3  zf-RING_7     C4-type zinc ribbon domain
       0.42   10.5   6.2        6.7    6.7   1.5    2.6  2  Prok-RING_4   Prokaryotic RING finger family 4
        1.8    8.2   4.7        1.9    8.1   0.1    2.5  3  Sgf11         Sgf11 (transcriptional regulation protein)
        2.5    7.7   8.8          5    6.7   0.2    2.9  3  zf-ribbon_3   zinc-ribbon domain
        2.5    8.0   7.4        4.6    7.1   0.1    3.0  3  PADR1         PADR1 (NUC008) domain
        2.5    8.0   7.4        3.3    7.6   1.8    2.9  3  Cys_rich_KTR  Cysteine-rich KTR


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   2.9   5.3e-20   1.2e-16       1      68 []       2      89 ..       2      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.3e-20
                                  BTGGCCC-B-TTTHH.C--HHHHHHHHH.TT---S-SS----S..................CHHTTEECCCCEEEETTTTEEE CS
                       Trm112p  1 kllllniLaCpackg.pLdwealvevaa.lglnelpkekpedy..................ellleldieegeLvCpncgraY 63
                                  k++ll++LaCp+ck+ pL++  +++++  +++++ +k+++e                    +++++++i++  L+Cpnc+r+Y
  gi|70606598|ref|YP_255468.1|  2 KYRLLDLLACPICKHfPLQYHIFSYKKIqREIKDEKKPLCEIFcsfkninineakssdlpcDECYQYEIVDALLYCPNCKRWY 84
                                  79***************************************99******************99******************** PP

                                  EEETT CS
                       Trm112p 64 pIkdG 68
                                  p+ d+
  gi|70606598|ref|YP_255468.1| 85 PVIDE 89
                                  **995 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.45     1e+03      52      57 ..      10      15 ..       1      38 [. 0.77
   2 ?   15.2   1.0   7.5e-06     0.017      37      71 ..      61      95 ..      31     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.45
                        zf-UDP 52 sCPqCk 57
                                  +CP Ck
  gi|70606598|ref|YP_255468.1| 10 ACPICK 15
                                  577776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.5e-06
                        zf-UDP 37 vcrpcyeyerkdgnqsCPqCktrykrlkgsprveg 71
                                   c  cy+ye  d+   CP+Ck  y    + pr+  
  gi|70606598|ref|YP_255468.1| 61 PCDECYQYEIVDALLYCPNCKRWYPVIDEIPRMLP 95
                                  599******************99988888887655 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.3   2.9e+03      25      29 ..      10      14 ..       6      15 .. 0.77
   2 ?   -0.1   0.2      0.49   1.1e+03      25      29 ..      61      65 ..      52      66 .. 0.80
   3 ?    9.5   0.0   0.00048       1.1      23      32 ..      74      83 ..      67      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                  E-TTT CS
                     zf-RING_7 25 tCpeC 29
                                   Cp C
  gi|70606598|ref|YP_255468.1| 10 ACPIC 14
                                  69999 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.49
                                  E-TTT CS
                     zf-RING_7 25 tCpeC 29
                                   C+eC
  gi|70606598|ref|YP_255468.1| 61 PCDEC 65
                                  6**** PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00048
                                  -EE-TTT--E CS
                     zf-RING_7 23 vvtCpeCGRI 32
                                  + +Cp+C R+
  gi|70606598|ref|YP_255468.1| 74 LLYCPNCKRW 83
                                  79******95 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.005        11      29      38 ..       7      16 ..       3      23 .. 0.82
   2 ?    6.7   1.5     0.003       6.7      21      38 ..      62      82 ..      43      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.005
                   Prok-RING_4 29 dlssCPlCqr 38
                                  dl +CP+C++
  gi|70606598|ref|YP_255468.1|  7 DLLACPICKH 16
                                  5669****86 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                   Prok-RING_4 21 CkeCfdskdls...sCPlCqr 38
                                  C+eC++ +       CP C+r
  gi|70606598|ref|YP_255468.1| 62 CDECYQYEIVDallYCPNCKR 82
                                  *******96655679****97 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.087   1.9e+02       5      11 ..       9      15 ..       6      16 .. 0.82
   2 ?   -2.5   0.1       1.8   3.9e+03       5      10 ..      60      65 ..      56      67 .. 0.72
   3 ?    8.1   0.1   0.00084       1.9       5      12 ..      75      82 ..      72      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.087
                                  EE-TTTS CS
                         Sgf11  5 vtCpnCg 11
                                    Cp+C+
  gi|70606598|ref|YP_255468.1|  9 LACPICK 15
                                  68****8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                                  EE-TTT CS
                         Sgf11  5 vtCpnC 10
                                    C+ C
  gi|70606598|ref|YP_255468.1| 60 LPCDEC 65
                                  569999 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00084
                                  EE-TTTSS CS
                         Sgf11  5 vtCpnCgR 12
                                    CpnC+R
  gi|70606598|ref|YP_255468.1| 75 LYCPNCKR 82
                                  67*****9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0022         5       5      12 ..      11      19 ..       9      20 .. 0.83
   2 ?   -2.2   0.3       1.4   3.1e+03      19      22 ..      62      65 ..      55      65 .. 0.57
   3 ?    5.7   0.2    0.0047        10       4       9 ..      76      81 ..      74      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0022
                   zf-ribbon_3  5 CPnCGa.pl 12
                                  CP C++ pl
  gi|70606598|ref|YP_255468.1| 11 CPICKHfPL 19
                                  *****9887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                   zf-ribbon_3 19 CpyC 22
                                  C  C
  gi|70606598|ref|YP_255468.1| 62 CDEC 65
                                  5555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0047
                   zf-ribbon_3  4 rCPnCG 9 
                                  +CPnC+
  gi|70606598|ref|YP_255468.1| 76 YCPNCK 81
                                  799996 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0021       4.6      13      32 ..       8      27 ..       7      28 .. 0.85
   2 ?    0.1   0.2      0.31   6.9e+02      15      23 ..      61      69 ..      60      73 .. 0.78
   3 ?    3.1   0.8     0.037        82      12      21 ..      73      82 ..      63      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0021
                         PADR1 13 lekCpeCkegqlvfdssgYk 32
                                  l  Cp Ck+  l+++   Yk
  gi|70606598|ref|YP_255468.1|  8 LLACPICKHFPLQYHIFSYK 27
                                  568*******9999987775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                         PADR1 15 kCpeCkegq 23
                                  +C eC + +
  gi|70606598|ref|YP_255468.1| 61 PCDECYQYE 69
                                  8****8655 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.037
                         PADR1 12 alekCpeCke 21
                                  al  Cp+Ck+
  gi|70606598|ref|YP_255468.1| 73 ALLYCPNCKR 82
                                  6889****95 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.054   1.2e+02       5      10 ..      10      15 ..       7      32 .. 0.78
   2 ?   -0.5   0.1      0.48   1.1e+03      28      39 ..      60      71 ..      39      74 .. 0.61
   3 ?    7.6   1.8    0.0015       3.3      25      35 ..      72      82 ..      64      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.054
                  Cys_rich_KTR  5 lcPvCg 10
                                   cP+C+
  gi|70606598|ref|YP_255468.1| 10 ACPICK 15
                                  466664 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                  Cys_rich_KTR 28 LfCPKCkqetli 39
                                  L C  C q  ++
  gi|70606598|ref|YP_255468.1| 60 LPCDECYQYEIV 71
                                  456677666666 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0015
                  Cys_rich_KTR 25 nfpLfCPKCkq 35
                                  +  L+CP Ck+
  gi|70606598|ref|YP_255468.1| 72 DALLYCPNCKR 82
                                  668*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 974.59
//
Query:       gi|70606599|ref|YP_255469.1|  [L=454]
Description: phosphoglucomutase/phosphomannomutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-42  143.9   0.0    4.9e-42  142.9   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.6e-22   80.0   0.0    3.7e-22   78.9   0.0    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    9.1e-19   67.7   0.0    1.6e-18   67.0   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    7.4e-10   38.9   0.0    2.2e-09   37.4   0.0    1.9  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.0   1.1e-45   4.9e-42       2     136 ..       3     133 ..       2     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 1.1e-45
                                   GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                     PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82 
                                   ++fgt+G+Rg ++++ l pelv+kl++ai++ + +   ++k++vGrD R+ +++  + + agl+++Gv+v+  gl+ptP +
  gi|70606599|ref|YP_255469.1|   3 KLFGTDGVRGLINKD-LSPELVLKLSRAIGSFFGK---GSKLLVGRDVRAGGDMYVKLVEAGLLSTGVDVFYGGLAPTPTL 79 
                                   68***********55.******************9...8****************************************** PP

                                   HHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT-E CS
                     PGM_PMM_I  83 sfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekeee 136
                                   ++a+++l++dag+++taSHnppeyngiKv++++G++i +e+e++Ie+i+++e++
  gi|70606599|ref|YP_255469.1|  80 QYAVKTLGYDAGVIVTASHNPPEYNGIKVIDKDGVEIRREKENEIEEILFSERF 133
                                   ************************************************998876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   8.3e-26   3.7e-22       2     103 .]     154     254 ..     153     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.3e-26
                                   HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG CS
                    PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkeg 82 
                                   +Y++++++ vd+e+i+k+g +v+id ++ +gg + + + kelg++v++ln + dp fp ++p+p+  e+lk+ ++++   +
  gi|70606599|ref|YP_255469.1| 154 TYVKGILQHVDTEKISKKGYTVLIDSANSVGGLTSPLVAKELGCKVYTLNGNLDPLFPARMPEPTF-ESLKETAKIALTLK 233
                                   6*****************************************************************.************** PP

                                   -SEEEEE-TTS-BEEEEETTE CS
                    PGM_PMM_II  83 adlglafDgDaDRlgvvderG 103
                                   adl +a+DgDaDR ++ d +G
  gi|70606599|ref|YP_255469.1| 234 ADLSIAHDGDADRAIFLDSEG 254
                                   ****************99877 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   3.5e-22   1.6e-18       3     113 ..     260     370 ..     258     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.5e-22
                                   HHHHHHHHHHHHCH.CSTTTC.EEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                   PGM_PMM_III   3 dqllallakyllee.klkpga.gvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                   d+ + ll+     + k+++g  ++v+ v++s+++e++++k+g++++ tkvG+  ++ ++++e+ + G+Ee+g++i++ +++
  gi|70606599|ref|YP_255469.1| 260 DRSGTLLSYWS--HvKNPKGSrVIVTAVSSSSLTEEYLAKYGLEVLWTKVGSVDIAHKLQDEKGLAGFEENGGFIYPPHQY 338
                                   55566665533..3345556559********************************************************** PP

                                   S--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                   PGM_PMM_III  82 tkDGilaallvleilaetgkslselleellkk 113
                                    +DG+++ +l+le +a ++ s ++l ++l+k 
  gi|70606599|ref|YP_255469.1| 339 VRDGAMSFALMLEFMASENLSSAQLFDRLPKY 370
                                   *************************9776654 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   4.8e-13   2.2e-09      24      70 ..     403     448 ..     372     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4.8e-13
                                   HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHH CS
                    PGM_PMM_IV  24 sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeeva 70 
                                    +++g+ki +ed ++l vR SGTep +r+ vEak+++++  laee+ 
  gi|70606599|ref|YP_255469.1| 403 ITIDGVKIIGEDFWFL-VRKSGTEPIIRIIVEAKDESKAMLLAEELK 448
                                   799*************.*********************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3217.93
//
Query:       gi|70606600|ref|YP_255470.1|  [L=352]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-27   96.5   0.3    1.9e-27   95.9   0.3    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-21   76.9   0.1      8e-21   74.8   0.1    2.0  1  Glyco_transf_4   Glycosyltransferase Family 4
    2.5e-15   57.1   0.1    5.7e-15   55.9   0.1    1.5  2  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-13   51.1   0.0    1.1e-11   45.4   0.0    2.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    0.00055   20.3   0.0     0.0011   19.3   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.11   12.5   0.9         22    5.1   0.4    2.9  3  SH3_18           CarS bacterial SH3 domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.3   6.2e-31   1.9e-27      15     169 ..     179     328 ..     166     330 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 6.2e-31
                                   -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
               Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                   + ++l++gr+++eK++  +i+ ++      n nvkl+++G   ++++++++  ++ el+l+d+v++lg v +e++ +l+ +
  gi|70606600|ref|YP_255470.1| 179 EDYLLYIGRISPEKNQLFAIECIK------NLNVKLILIGqvrDKDYLEKIMTRVSELGLEDKVRYLGVVTEEEKYSLMDK 253
                                   5689********************......669*******999999999999***************************** PP

                                   ESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHH CS
               Glycos_transf_1  93 adifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklledeelrerlgena 169
                                   + +++l+s  E+ Giv+ EAm  g+pvi+ n a+ ++ +vkdg++G+++ +   ++l++a++kl +d++ r+++gen 
  gi|70606600|ref|YP_255470.1| 254 SLAVILTSDIEAEGIVIKEAMVRGVPVIVGNkAKVLSTIVKDGVNGFVISSC--QDLKDAVEKL-RDPKVRKEIGENN 328
                                   ****************************************************..9999999995.7888999998885 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.1   2.7e-24     8e-21       2     167 ..      16     166 ..      15     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 2.7e-24
                Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev.....elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvH 77 
                                   GG e+hv++L+r+L ++ ++V+v t +d   ++e+       ++                 +  +r+ r ++ r  p v+H
  gi|70606600|ref|YP_255470.1|  16 GGTEVHVFNLSRELVKMSIDVEVHTTRDTYTEREKLipfeiMDG-----------------IKVVRHKRTWIYRDSPSVLH 79 
                                   9***********************99999998888444444222.................22222333333333444444 PP

                Glyco_transf_4  78 ah.........spaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelr 149
                                    h         + +++++  l +     +plV t H+ +         + + r++++l r + +r+d++iavSe++++e++
  gi|70606600|ref|YP_255470.1|  80 FHnlgrkfstwNLYTFLFFSLPS---VEAPLVMTPHHIF--------VSDQGRVINWLKRNIGKRVDKLIAVSEWEKEEMI 149
                                   44111111100444444443333...59***********........68999***************************** PP

                Glyco_transf_4 150 erygvppekitVipnGvD 167
                                     +g++ +ki+VipnGvD
  gi|70606600|ref|YP_255470.1| 150 N-LGYDGSKIVVIPNGVD 166
                                   *.***************9 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   7.4e+03      65      80 ..     147     163 ..     113     171 .. 0.56
   2 !   55.9   0.1   1.9e-18   5.7e-15       3     131 ..     181     315 ..     179     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
                                   HHHHH.HHH-SEEEE-- CS
               Glyco_trans_1_4  65 dlael.laaadvfvaPs 80 
                                   ++ +l ++ ++++v+P+
  gi|70606600|ref|YP_255470.1| 147 EMINLgYDGSKIVVIPN 163
                                   22222366666666665 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 1.9e-18
                                   EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEE CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprp...eeleelaa..gleerveftGfv..edlaellaaadvf 76 
                                    +l++Gr++ ++k++ + +e ++ l    v+l+++G+  ++   e++  +++  gle++v+++G v  e++ +l++++  +
  gi|70606600|ref|YP_255470.1| 181 YLLYIGRIS-PEKNQLFAIECIKNLN---VKLILIGQVRDKdylEKIMTRVSelGLEDKVRYLGVVteEEKYSLMDKSLAV 257
                                   69******5.56*************9...89*****654332333444466479************9777*********** PP

                                   EE--..---SHHHHHHHHTT-EEEE-TGGG.TTT--..TTSSEE--TT-HHHHHHHHHHH CS
               Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvgg.iaevv..gengllvppgdpealaeailrL 131
                                   +++s  e  g+++ Eam  g+pv++ + +  ++ +v  g+ng++++  + ++l +a+++L
  gi|70606600|ref|YP_255470.1| 258 ILTSdiEAEGIVIKEAMVRGVPVIVGNKAKvLSTIVkdGVNGFVIS--SCQDLKDAVEKL 315
                                   ****99999*****************9875256666999******9..899999999887 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   3.7e-15   1.1e-11       1     160 []      16     164 ..      16     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 3.7e-15
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahs 81 
                                   gG +++v +l+r+L++   +V+v t+++++ ++e       ++++ +  +       + +r  r ++   r  p v+h h+
  gi|70606600|ref|YP_255470.1|  16 GGTEVHVFNLSRELVKMSIDVEVHTTRDTYTERE---K---LIPFEIMDG------IKVVRHKRTWI--YRDSPSVLHFHN 82 
                                   899**********************988888773...3...333444433......34444456666..777899999999 PP

               Glyco_trans_4_4  82 pt.....aglaarlar.rrr.giplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpadrvv 155
                                   +       +l+  l   ++   +plv t+h   +    + ++r++ +l r + +r+d +++vse+e ee++ lg + +++v
  gi|70606600|ref|YP_255470.1|  83 LGrkfstWNLYTFLFFsLPSvEAPLVMTPHHIFV----SDQGRVINWLKRNIGKRVDKLIAVSEWEKEEMINLGYDGSKIV 159
                                   7656654234444444234349********9754....44789************************************** PP

               Glyco_trans_4_4 156 vvpng 160
                                   v+png
  gi|70606600|ref|YP_255470.1| 160 VIPNG 164
                                   ****8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.8e-07    0.0011      15      85 ..     270     339 ..     257     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.8e-07
               Glyco_trans_1_2  15 lfEaaacGafaltdda.egleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                   + Ea+  G+++++    + l  ++++g  ++++++ ++l +++++l ++p+ r++i+e+++    +e ++++
  gi|70606600|ref|YP_255470.1| 270 IKEAMVRGVPVIVGNKaKVLSTIVKDGVNGFVISSCQDLKDAVEKL-RDPKVRKEIGENNISI-SREWRWRN 339
                                   569******99999778***************************95.9**********99876.77888877 PP

>> SH3_18  CarS bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       5.1   1.5e+04      17      31 ..      13      27 ..      13      29 .. 0.81
   2 ?    4.6   0.0     0.011        34      20      60 ..     134     174 ..     128     179 .. 0.87
   3 ?    5.1   0.4    0.0075        22       8      36 ..     270     298 ..     251     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.1
                        SH3_18 17 PvriGekvkivstse 31
                                  Pvr G +v++ + s+
  gi|70606600|ref|YP_255470.1| 13 PVRGGTEVHVFNLSR 27
                                  899999999987766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                        SH3_18  20 iGekvkivstseddsidkrflGraGivvalvfddPelqyPr 60 
                                   + + + + + ++++ i+ ++ G   +v+    dd +  yP+
  gi|70606600|ref|YP_255470.1| 134 VDKLIAVSEWEKEEMINLGYDGSKIVVIPNGVDDMAFNYPK 174
                                   555677888999****************************8 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0075
                        SH3_18   8 ivtedveGaPvriGekvkivstseddsid 36 
                                   i    v G Pv +G+k k+ st  +d ++
  gi|70606600|ref|YP_255470.1| 270 IKEAMVRGVPVIVGNKAKVLSTIVKDGVN 298
                                   4445699*************998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2485.90
//
Query:       gi|70606601|ref|YP_255471.1|  [L=187]
Description: hypothetical protein Saci_0810 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-33  113.1   0.0    1.1e-32  112.9   0.0    1.0  1  MTS              Methyltransferase small domain
    3.5e-09   36.8   0.0    5.7e-09   36.1   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
    1.4e-08   34.6   0.0      2e-08   34.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.9e-07   30.8   0.0    2.2e-07   30.6   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.6e-07   29.3   0.0    6.3e-07   28.9   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
    5.2e-07   30.3   0.0    7.4e-07   29.8   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    1.3e-06   28.1   0.1    1.4e-06   28.0   0.1    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    3.3e-05   23.6   0.0    3.8e-05   23.4   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
    7.6e-05   22.5   0.1    8.6e-05   22.4   0.1    1.2  1  Met_10           Met-10+ like-protein
    0.00047   19.9   0.0    0.00074   19.3   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
    0.00088   20.0   0.0     0.0012   19.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00088   18.6   0.0     0.0012   18.2   0.0    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
    0.00097   19.1   0.1        1.3    9.0   0.0    2.1  2  rRNA_methylase   Putative rRNA methylase
      0.002   17.6   0.0     0.0033   16.9   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0023   17.5   0.0     0.0034   16.9   0.0    1.2  1  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
     0.0067   17.0   0.0      0.011   16.4   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.015   15.0   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
      0.025   14.0   0.3      0.045   13.2   0.1    1.5  2  TehB             Tellurite resistance protein TehB
      0.043   13.1   0.0      0.052   12.8   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.044   13.6   0.0      0.059   13.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
       0.22   11.5   0.0       0.27   11.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   1.3e-35   1.1e-32       3     167 ..      17     181 ..      15     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.3e-35
                                   EEEEETTSTTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.. CS
                           MTS   3 tlktlpgvFskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.. 81 
                                    l +  g FskdklD G+++Lle+l    +g v+D+GcG+G++g+ +a  +++++v ++dvd++A+ ++ +n+++ +l+  
  gi|70606601|ref|YP_255471.1|  17 SLESSRGLFSKDKLDLGTRILLENLVLPNHGIVADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSnr 97 
                                   577899*********************9999*********************************************99999 PP

                                   EEEEE-STTTTST.TS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEET.TSCHHHHHHHHHS--EEEE CS
                           MTS  82 vevvasdvleeve.ekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVanr.klgyeslleelfgnvevva 160
                                   ++v++s+++e+v+ + kf+ i sNPP++agk+     +e+l +eA ++L+ gG + +V+ + + ++ +  ++ +++v+v +
  gi|70606601|ref|YP_255471.1|  98 ITVIKSNLFENVPnDLKFNGIYSNPPLKAGKE----FIERLSEEAGRRLEIGGIIEVVVYKgEANVITEFSKFLNEVKVYK 174
                                   ************9677****************....*******************87766526778888************ PP

                                   EESSEEE CS
                           MTS 161 ktkkfkv 167
                                   + k++ +
  gi|70606601|ref|YP_255471.1| 175 RAKGYSL 181
                                   ****975 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   6.7e-12   5.7e-09      12      79 ..      43     110 ..      33     118 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.7e-12
               Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk 79 
                                   ++++ +vaDiG+  g + iy++  ++  kv+++D+ ++++    +n++k++l+++i+v+ s+ +e++ 
  gi|70606601|ref|YP_255471.1|  43 LPNHGIVADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNLFENVP 110
                                   456669*******************************************************9999884 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.3e-11     2e-08       7     119 ..      49     160 ..      45     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.3e-11
               Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnevln 85 
                                   v D+GCG G +++ +a +++++ +v+ iD +++ai +  +n +k +l+ ++++ +++ +e  ++   d kf+ i sn +l 
  gi|70606601|ref|YP_255471.1|  49 VADIGCGYGPIGIYIA-LVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSnRITVIKSNLFEnVPN---DLKFNGIYSNPPLK 125
                                   78**************.***************************999989**********9996...599*******7774 PP

               Methyltransf_31  86 aladpdkile.eiervlkpggilliedprllaelp 119
                                   a ++  + l  e+ r l+ ggi+ +  ++++a+++
  gi|70606601|ref|YP_255471.1| 126 AGKEFIERLSeEAGRRLEIGGIIEVVVYKGEANVI 160
                                   44333333322555555555555444444444333 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.6e-10   2.2e-07     154     254 ..      37     146 ..      34     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.6e-10
                          PrmA 154 aleklvkege.evlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelNkveaklev...alseellkeekadv 229
                                   +le+lv +++  v D+G+G G + i  a+++ + kv+ +D+D+ A+  + +N+++ +++++++v   +l e+++++ k++ 
  gi|70606601|ref|YP_255471.1|  37 LLENLVLPNHgIVADIGCGYGPIGIYIALVNQNlKVYMIDVDKKAIYFTSKNVSKYNLSNRITViksNLFENVPNDLKFNG 117
                                   58999999986788************999987659*************************999944345677777888888 PP

                          PrmA 230 ivaNILa....evlielaedikklvkegg 254
                                   i +N       e + +l e++ + ++ gg
  gi|70606601|ref|YP_255471.1| 118 IYSNPPLkagkEFIERLSEEAGRRLEIGG 146
                                   88884320111344444444444444444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   7.4e-10   6.3e-07      48     119 ..      46     118 ..      26     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 7.4e-10
                                   CC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SS.EEEEES-CCC.TTTTT-EEEE CS
                          GidB  48 krdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklen.veivearaee.kqeeekydvv 119
                                   +   v+D+G G G  Gi +a+++++lk+++++ ++k i F  + +++ +l+n ++++++++ e   +  k++ +
  gi|70606601|ref|YP_255471.1|  46 HG-IVADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNrITVIKSNLFEnVPNDLKFNGI 118
                                   33.59********************************************9986899988764425555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   8.7e-10   7.4e-07       1      97 []      49     146 ..      49     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8.7e-10
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBSSSTTTEEEEEEEST.GGGS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgda.edlpfedgsfDlvvssga.lhhl 77 
                                   v d+GcG G + +++a   ++ kv+++D++++++  + +++++ +l  ++++++ ++ e++p +d +f+ ++s+   l   
  gi|70606601|ref|YP_255471.1|  49 VADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLsnRITVIKSNLfENVP-NDLKFNGIYSN-PpLKA- 126
                                   78*********9999966569**********************99999********956666.777*******5.55887. PP

                                   SHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                    +e +e++ +e+ r L+ gG
  gi|70606601|ref|YP_255471.1| 127 GKEFIERLSEEAGRRLEIGG 146
                                   56789999999999999887 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.7e-09   1.4e-06       3      68 ..      48     116 ..      46     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.7e-09
               Methyltransf_15   3 vilDlfsGaG..GnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfell.aklkle 68 
                                   ++ D+ +G G  G  i++ ++  kv+ i+++++ ++ + +N   Y+ s++it+++ ++fe + + lk++
  gi|70606601|ref|YP_255471.1|  48 IVADIGCGYGpiGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNLFENVpNDLKFN 116
                                   677999999966667777777889***********************************9662344444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.4e-08   3.8e-05      45     138 ..      49     136 ..      38     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                                   EEETT-TTSHHHHH.HHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSS CS
                 Cons_hypoth95  45 vLDlfaGsGalglE.AlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPya 124
                                   v D+ +G G +g+  Al  +  k+++++ dk+a+   ++n+++ +l+++++++k + +e++++      +f+ ++ +PP +
  gi|70606601|ref|YP_255471.1|  49 VADIGCGYGPIGIYiALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNLFENVPND----LKFNGIYSNPPLK 125
                                   5677788888888548999999********************************9999999888....68**********9 PP

                                   TTCH.HHHHHHHHH CS
                 Cons_hypoth95 125 kellieevlellee 138
                                   +++     +e l e
  gi|70606601|ref|YP_255471.1| 126 AGKE---FIERLSE 136
                                   9964...4444433 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     1e-07   8.6e-05      65     186 ..       7     133 ..       2     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                                   EEEEETTEEEEEETTTS---GGGHHHHHHHH..TT--TT-.EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHH CS
                        Met_10  65 tihkEngcrfklDvskvyfsskleaErerla..klveege.vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylke 142
                                   +    ng+ + l+ s+ +fs+   +  +r+   +lv ++  +V d+  G Gp  i ia   ++ +v+ id++ +++ +  +
  gi|70606601|ref|YP_255471.1|   7 VNDVVNGIPLSLESSRGLFSKDKLDLGTRILleNLVLPNHgIVADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSK 87 
                                   55566777788888888888766655555431166777653899************************************* PP

                                   HHHHTT-TTCEEEEES-GGG---.TT-EEEEEE--TTTG.GGGHHH CS
                        Met_10 143 niklNkvekvvkpileDgrevir.eqladrvvmnlpksa.ieFldk 186
                                   n+   ++++++++i++   e ++ + +++ +  n p +a  eF++ 
  gi|70606601|ref|YP_255471.1|  88 NVSKYNLSNRITVIKSNLFENVPnDLKFNGIYSNPPLKAgKEFIER 133
                                   **************99875554436666666666655442456665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.6e-07   0.00074      50     114 ..      49     112 ..      43     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.6e-07
               Methyltransf_16  50 vlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleed 114
                                   v ++G G G +G+ +a+  +++kv++ D+++ ++ +  kn+   +  l+++++v + +  e++++d
  gi|70606601|ref|YP_255471.1|  49 VADIGCGYGPIGIYIALVNQNLKVYMIDVDKkAIYFTSKNVSKYN--LSNRITVIKSNLFENVPND 112
                                   6689*************************98799********955..9999988766666666555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.4e-06    0.0012       2      60 ..      51     107 ..      50     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlld 60 
                                   +iGcG G +  +++  +++++++ +D++++ai  +++  +k++    n++++ + +l++
  gi|70606601|ref|YP_255471.1|  51 DIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLS--NRITVIKSNLFE 107
                                   9*******************************9999999988864..466666666655 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-06    0.0012      58     133 ..      60     133 ..      57     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--..EEEE---TTS---TTTSS-BSEEEE---SSHHHHHHHHHH CS
                         DUF43  58 slalaLtglpkkvvvvDiDeRlikfiervakelglk..ieaivyDlrkplpeelkekFdvfitDPpetvealkaFlgR 133
                                   ++ +aL +   kv ++D+D++ i f  + + +++l+  i +i+ +l + +p++l  kF+ +  +Pp  ++a k F+ R
  gi|70606601|ref|YP_255471.1|  60 GIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSnrITVIKSNLFENVPNDL--KFNGIYSNPP--LKAGKEFIER 133
                                   7899*************************999999878**************98..6999999998..4566666665 PP

>> rRNA_methylase  Putative rRNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0015       1.3       1      33 [.      72     104 ..      72     118 .. 0.89
   2 !    8.2   0.1    0.0026       2.3      75     103 ..     137     165 ..     131     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0015
                                   EEEEES-HHHHHHHHHHHHHTT-GGSEEEEES- CS
                rRNA_methylase   1 vyafDiQeeAleatkerleeekleervelilds 33 
                                   vy +D+ ++A+  t++++++ +l++r+++i+++
  gi|70606601|ref|YP_255471.1|  72 VYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSN 104
                                   899************************999864 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                                   HHHHHEEEEEEEEEEE--STCHHHHHHHH CS
                rRNA_methylase  75 kalelLkkgGlitivvYpGheeGkeEkea 103
                                   +a + L+ gG+i +vvY G+++   E ++
  gi|70606601|ref|YP_255471.1| 137 EAGRRLEIGGIIEVVVYKGEANVITEFSK 165
                                   5667899************9887777554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.9e-06    0.0033       4      69 ..      48     114 ..      45     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.9e-06
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSS.EEEEES-CCCHHHHCS- CS
                Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkN.lrilrgdalkvllelle 69 
                                   +v++iGcG+G + + +A  n + ++  i++ +k +    k++ +++l+N + +++++ ++ +++ l+
  gi|70606601|ref|YP_255471.1|  48 IVADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNrITVIKSNLFENVPNDLK 114
                                   899*********************************************9899999998887777665 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     4e-06    0.0034       1      63 [.      49     111 ..      49     118 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4e-06
                          TrmK   1 laDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGlavlek 63 
                                   +aDiG+  + + iy+   n+   +  ++v + +     knv+k++l+++i+v++++ ++ + +
  gi|70606601|ref|YP_255471.1|  49 VADIGCGYGPIGIYIALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNLFENVPN 111
                                   69************999999999999******************************9988876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05     0.011       2      94 ..      51     148 ..      50     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                   EET-TTSHHHHHHH..HTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-.CCH CS
               Methyltransf_11   2 dvGcGtGrlaeala..krgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv.edp 77 
                                   d+GcG G +  ++a  ++  +v+ +D++k+++   ++++s+ +l  +++++++++ +   +d +f  ++s+  l    e  
  gi|70606601|ref|YP_255471.1|  51 DIGCGYGPIGIYIAlvNQNLKVYMIDVDKKAIYFTSKNVSKYNLsnRITVIKSNLFENVPNDLKFNGIYSNPPLKAGkEFI 131
                                   9****999999999666669************9999999998889999999999987434677999999998888886677 PP

                                   HHHHHHHHHHEEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGll 94 
                                   e++ +e+ R L+ gG++
  gi|70606601|ref|YP_255471.1| 132 ERLSEEAGRRLEIGGII 148
                                   88888888888888876 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-05     0.015      74     130 ..      67     123 ..      61     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                                   HHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--.GGG--STTS---EEEE--- CS
                       UPF0020  74 raelklygsDldrrvvqgareNaekagvgdliefsqad.aakLrlkegevdvivtnpP 130
                                   +++lk+y +D d++++  + +N +k++++++i++ + + + +++ ++ +++ i +npP
  gi|70606601|ref|YP_255471.1|  67 NQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNlFENVP-NDLKFNGIYSNPP 123
                                   67899***************************988776267888.7779********* PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.2e-05     0.045      32      82 ..      47      99 ..      35     124 .. 0.79
   2 ?   -2.5   0.0       3.3   2.8e+03     114     133 ..     164     183 ..     147     185 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                  -EEEEES-TTSHHHHHHHHTT-E..EEEEES-HHHHHHHHHHHHHTT-TTEEE CS
                          TehB 32 gkvldlgcgqgrnslylsllgyd..vtawdknensiafleeikekenlknist 82
                                  g v d+gcg g   +y++l+  +  v  +d ++++i f  +  +k nl+n  t
  gi|70606601|ref|YP_255471.1| 47 GIVADIGCGYGPIGIYIALVNQNlkVYMIDVDKKAIYFTSKNVSKYNLSNRIT 99
                                  5688**************98765226788******************987443 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                                   HHHHHHHHHTEEEEEEEEEE CS
                          TehB 114 psiienmqectkvggynliv 133
                                   ++ +++++ + ++ gy l++
  gi|70606601|ref|YP_255471.1| 164 SKFLNEVKVYKRAKGYSLVL 183
                                   34445555555666666665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.052      52     132 ..      35     119 ..      27     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                   HHHHTTTT--TT-EEEEES-TTSHHHHH.HHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-.GGG---..-- CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrr.averydvkvvglTlSkeqaklakkrvdeldlerkvevklld.yedlde..kv 128
                                   +++le l l +   + diGcG+G + ++ a  + + kv  + + k+    + k+v + +l+++ +v  ++ +e++++  k+
  gi|70606601|ref|YP_255471.1|  35 RILLENLVLPNHGIVADIGCGYGPIGIYiALVNQNLKVYMIDVDKKAIYFTSKNVSKYNLSNRITVIKSNlFENVPNdlKF 115
                                   567889999999999********886552445569************************9999887666537888776666 PP

                                   SEEE CS
                          CMAS 129 drvv 132
                                   + + 
  gi|70606601|ref|YP_255471.1| 116 NGIY 119
                                   6665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.9e-05     0.059      17     119 ..      42     152 ..      28     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-05
               Methyltransf_23  17 lpklraggrvLdiGcGtGillevlre..ngfsvtgvDlspeaveiae.............kakkaqkdqfdeqeaaepqg. 81 
                                   +  l+  g v diGcG+G    +++   +  +v+++D + +a+   +                  +k++    ++ +p++ 
  gi|70606601|ref|YP_255471.1|  42 V--LPNHGIVADIGCGYGPIGIYIALvnQNLKVYMIDVDKKAIYFTSknvskynlsnritV----IKSNL---FENVPNDl 113
                                   3..67888999********999997722467*******99888877677777766643332....33333...23333334 PP

               Methyltransf_23  82 kfdlIvlrevlehvpd.ppellrqiatllkpgGylllse 119
                                   kf+ I+++  l   +   ++l   +++ l+ gG +++ +
  gi|70606601|ref|YP_255471.1| 114 KFNGIYSNPPLKAGKEfIERLSEEAGRRLEIGGIIEVVV 152
                                   888888776666666424455555666666666666655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.27      28      78 ..      48      94 ..      37     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
               Methyltransf_32 28 tvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                   v+D+G+G g  +  +al  ++++lkv+ id+ ++ +  ++k  +k++  +
  gi|70606601|ref|YP_255471.1| 48 IVADIGCGYGPIGIYIAL--VNQNLKVYMIDVDKKAIYFTSKNVSKYN--L 94
                                  589***************..66799*******9999887777777666..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1179.84
//
Query:       gi|70606602|ref|YP_255472.1|  [L=319]
Description: H/ACA RNA-protein complex component Cbf5p [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-20   72.8   0.1    3.7e-20   71.8   0.1    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    5.1e-15   55.2   0.1    1.1e-14   54.1   0.1    1.6  2  PUA       PUA domain
    6.1e-12   45.4   0.0    1.6e-11   44.1   0.0    1.7  1  DKCLD     DKCLD (NUC011) domain
    1.4e-11   44.9   0.8    1.5e-06   28.7   0.1    3.7  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    0.00018   21.7   1.0      0.013   15.7   0.1    2.5  2  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.1     1e-23   3.7e-20       1      62 [.     166     231 ..     166     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1e-23
                                   HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGG CS
                      TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesa 62 
                                   R+Lc+D G   gcg h++eLRR+r+g f ++++mvtl+++ ++++ly++  de+ L+r+llP+e  
  gi|70606602|ref|YP_255472.1| 166 RKLCHDVGVIAGCGSHMRELRRIRSGIFtEKTNMVTLQEVSESLYLYRNckDESeLRRILLPMEYG 231
                                   9***************************98889*****************76669*********75 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   9.3e+03      52      64 ..     103     115 ..     103     121 .. 0.76
   2 !   54.1   0.1   3.1e-18   1.1e-14       1      73 [.     236     307 ..     236     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                   ESS-HHHHHHHCT CS
                           PUA  52 anysseelakikg 64 
                                   +n++ +el++i  
  gi|70606602|ref|YP_255472.1| 103 CNVDQKELKEIIS 115
                                   6899999999865 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 3.1e-18
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                   ++v+v d Av+a+++ga+L  pG++ ++  f++++ Va+++ +gelva+G + + s++l++ k+g +++ +r+
  gi|70606602|ref|YP_255472.1| 236 PKVIVSDTAVNAITYGAKLNLPGILAYQN-FRKNQDVAVLTLKGELVAIGESIVESKQLESGKKGEVIRPKRI 307
                                   69***********************9987.**************************************99997 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.4e-15   1.6e-11      18      57 ..      23      62 ..      14      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.4e-15
                                  S-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHH CS
                         DKCLD 18 tehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEV 57
                                  +e+ t+++ G+   kRpie++ik ++inLDKP +P+SHEV
  gi|70606602|ref|YP_255472.1| 23 REEDTEEKFGYYADKRPIESLIKNSIINLDKPPGPTSHEV 62
                                  5778999********************************9 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00018      0.65       1      18 [.      67      84 ..      67     104 .. 0.95
   2 !   28.7   0.1   4.2e-10   1.5e-06      69     149 .]     102     165 ..      89     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                                  HHHTT-S-EEESS---TT CS
                        TruB_N  1 krllkakkvGhtGtLDpl 18
                                  k+l++++k+Gh+GtL p 
  gi|70606602|ref|YP_255472.1| 67 KKLFNITKAGHGGTLEPV 84
                                  799************996 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 4.2e-10
                                   -TT--HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                        TruB_N  69 veklteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                     ++++++l+e++++f Gei+q pp+ S+vk                 r+ rk +iy++++l+++++ + l+v+  +GtY+
  gi|70606602|ref|YP_255472.1| 102 HCNVDQKELKEIISQFVGEIYQKPPVRSSVK-----------------RRIRKRRIYAIDILDMQDKLILLRVQSDAGTYM 165
                                   56899**************************.................899*****************************6 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.015        53      57      76 .]     148     167 ..     139     167 .. 0.80
   2 !   15.7   0.1   3.8e-06     0.013       1      61 [.     237     297 ..     237     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.015
                       UPF0113  57 aspgkivvknlaDiGeYlRr 76 
                                    +++ i+++ + D G+Y+R+
  gi|70606602|ref|YP_255472.1| 148 MQDKLILLRVQSDAGTYMRK 167
                                   678899999**********6 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.8e-06
                       UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt.kaspgk 61 
                                   kv+v+  a + ++YG ++   +il ++ ++++nq v+Vl  +ge+++iG ++ ++ ++++gk
  gi|70606602|ref|YP_255472.1| 237 KVIVSDTAVNAITYGAKLNLPGILAYQ-NFRKNQDVAVLTLKGELVAIGESIVESkQLESGK 297
                                   79***********************99.9999*******************99885344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2236.18
//
Query:       gi|70606603|ref|YP_255473.1|  [L=96]
Description: 50S ribosomal protein L14e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00066   19.5   0.4    0.00066   19.5   0.4    1.9  2  KOW             KOW motif
     0.0037   17.7   0.1     0.0053   17.2   0.1    1.2  1  Ribosomal_L14e  Ribosomal protein L14
     0.0083   16.5   0.1       0.01   16.2   0.1    1.1  1  XisI            XisI protein


Domain annotation for each model (and alignments):
>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   1.1e-07   0.00066       2      31 ..       7      35 ..       6      37 .. 0.88
   2 ?   -1.4   0.1      0.44   2.6e+03      19      29 ..      51      61 ..      40      65 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-07
                                  TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                           KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                  G+++  ++G+ +Gk++++v++++ + +V+v
  gi|70606603|ref|YP_255473.1|  7 GRICVKTRGREAGKKCVIVDIIDSN-FVLV 35
                                  899999******************9.4444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.44
                                  EEEEETTTTEE CS
                           KOW 19 VvkvdqhkvrV 29
                                  ++++++   +V
  gi|70606603|ref|YP_255473.1| 51 ILHIEPTDKKV 61
                                  55555555555 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   8.8e-07    0.0053       1      39 [.      45      83 ..      45      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.8e-07
                Ribosomal_L14e  1 pRqaiplkrlkLtkivlklprgartgavkkawekadvee 39
                                  +R  +++ +++ t+ ++++++ga+ + vk+a+e++++++
  gi|70606603|ref|YP_255473.1| 45 KRRRVNILHIEPTDKKVEINKGATDQEVKQAIEQSGLTD 83
                                  59999******************************9886 PP

>> XisI  XisI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.7e-06      0.01      27      88 ..      18      81 ..       7      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                                  EEEEEEEEETTTTEEEEEEEEEE..TTEEEEEEEEEEEEETTEEEEEEE-SS--HHHHHHTTT- CS
                          XisI 27 eveeelifDeerdhYlllevgwe..kkkrvygillhldikdgkiwiqedgteegiaeeLveaGv 88
                                  + ++++i+D   ++++l++   e  + kr +  +lh++  d+k+ i++  t++++ + + + G 
  gi|70606603|ref|YP_255473.1| 18 AGKKCVIVDIIDSNFVLVTGPKEinGVKRRRVNILHIEPTDKKVEINKGATDQEVKQAIEQSGL 81
                                  457889999999999999876654367899999***********************99988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 706.15
//
Query:       gi|70606604|ref|YP_255474.1|  [L=911]
Description: DEAD/DEAH box helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-31  107.0   0.0    2.2e-30  105.7   0.0    1.7  1  DEAD            DEAD/DEAH box helicase
    5.5e-23   81.4   0.1    1.1e-19   70.8   0.1    3.0  2  Helicase_C      Helicase conserved C-terminal domain
    6.7e-17   61.9   0.0    1.3e-16   61.0   0.0    1.5  1  DEAD_assoc      DEAD/H associated
    2.4e-06   27.6   0.0    1.2e-05   25.3   0.0    2.1  2  ResIII          Type III restriction enzyme, res subunit
    2.7e-05   24.5   0.0     0.0003   21.2   0.0    2.4  2  AAA_19          AAA domain
     0.0054   16.3   0.0      0.019   14.5   0.0    2.0  1  PrpR_N          Propionate catabolism activator
  ------ inclusion threshold ------
      0.011   15.9   0.4      0.097   12.9   0.4    2.5  1  AAA_22          AAA domain
       0.25   11.1   1.5       0.58    9.9   1.5    1.6  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   9.8e-34   2.2e-30       1     170 [.      21     188 ..      21     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 9.8e-34
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   t+iQ+  ip+il+g++ +v a+TG GKT+ +++pv+ ++++  + ++  a++++P+r+L ++  ++l+++++ +++++  i
  gi|70606604|ref|YP_255474.1|  21 TPIQKIGIPIILKGKNTIVIAPTGFGKTETAIFPVFYKILS-SNAEKISAIYITPLRALNRDLEDRLSRIGSALGIKIA-I 99 
                                   89************************************999.99*****************************998886.6 PP

                                   ETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                    +g+++++q++++ ++ +d++++tp+ l+ ll ++k++  l ++r++++DE +++ld++++ ++   +++l++     k +
  gi|70606604|ref|YP_255474.1| 100 RHGDSTERQRKRILEDpPDLLLTTPETLLYLLVNQKMRelLGNIRWIIIDELQEMLDEKRGYELLLAIQRLKRL---SKYE 177
                                   67788878888775556*************9966777778******************9999999999999544...4456 PP

                                   SEEEEEESSBS CS
                                   xxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlp 170
                                    q+i lSAT+ 
  gi|70606604|ref|YP_255474.1| 178 IQLIGLSATIG 188
                                   78*******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0     0.003       6.8       7      62 ..      57     116 ..      53     126 .. 0.66
   2 !   70.8   0.1     5e-23   1.1e-19       5     108 ..     241     345 ..     237     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.003
                                   HHHHHHTTTTSEEEEEESSHH...HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                    Helicase_C   7 lellkleeeggkilifvntid...rlek.vklllekkgikvavlhgelpqnereeileqf 62 
                                   +++l++++e+  ++ +++ +    +le+ ++ + +  gik+a+ hg+ + ++r++ile+ 
  gi|70606604|ref|YP_255474.1|  57 YKILSSNAEKISAIYITPLRAlnrDLEDrLSRIGSALGIKIAIRHGDSTERQRKRILEDP 116
                                   5555444444444555555554444442334444444********************986 PP

  == domain 2  score: 70.8 bits;  conditional E-value: 5e-23
                                   HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                    Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                   ++ el kl +e++ +l+f+n +++ e  ++ l + +++kv ++hg+l+ + r+e+ ++f+ g+ d Liat+ +e Gid+  
  gi|70606604|ref|YP_255474.1| 241 RIRELEKLIKENKPVLVFTNVRESTEFlASELSKLSQLKVRTHHGSLSREIRLEAEKEFKTGNLDALIATSSLELGIDVGT 321
                                   4445546779*************99666555555669******************************************** PP

                                   ESEEEESSSSSSHHHHHHHHTTSS CS
                    Helicase_C  85 vnlVinfdlprnvtsyiqriGRtg 108
                                   +n Vi++  p++v +++qriGR g
  gi|70606604|ref|YP_255474.1| 322 INAVIQYTSPKQVIRLVQRIGRSG 345
                                   **********************87 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   5.6e-20   1.3e-16       1     191 []     584     754 ..     584     754 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 5.6e-20
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll....pleerlpllldel 77 
                                   +Pt++++lvE  +d      +v+h+ +G+r n++l++ll+  l++  g+  ++  +++ i++ +    + +e++  +  ++
  gi|70606604|ref|YP_255474.1| 584 VPTKSKILVEINND-----LIVLHAGLGSRGNNTLGALLSLLLTQVKGVRTTYRSDPYHIAIASlvpvS-KEEF-TKAIKI 657
                                   8***********99.....69*****************************************8899743.3444.345679 PP

                    DEAD_assoc  78 lellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevled 158
                                   l++ls+ e+e++l++a+++s+ +k+++   A+r++l+ +++ +        +++ + Ll+++    d+++ +eav+e + +
  gi|70606604|ref|YP_255474.1| 658 LNSLSSSEFEDLLKRAIKESPQYKWKLLIEAERFGLIDKQKTD-------ITFS-QTLLKAYT---DTLVGEEAVKELMYK 727
                                   *****************************************99.......6665.66777766...9************** PP

                    DEAD_assoc 159 qlDlerlaellrriaageirvvevetprpSpfA 191
                                    +D+  l+e+l+r+     ++ e  +p +Sp+A
  gi|70606604|ref|YP_255474.1| 728 NYDVT-LREFLTRLTW---ECIE--VPGFSPLA 754
                                   ***95.9999999987...5555..66677776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   5.6e-09   1.2e-05      23     169 ..      33     187 ..       3     189 .. 0.79
   2 ?   -1.1   0.1      0.75   1.7e+03      74     117 ..     815     859 ..     772     885 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.6e-09
                                   TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                        ResIII  23 rdkrglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kek 99 
                                   + k+ ++ ++TG GKT +a + + +++l+++ e+  ++ + p ++l   ++++++++ s     +  + +gd+ ++  k++
  gi|70606604|ref|YP_255474.1|  33 KGKNTIVIAPTGFGKTETAiFPVFYKILSSNAEKiSAIYITPLRALNRDLEDRLSRIGSALGI-KIAIRHGDSTERqrKRI 112
                                   56788999***********88888888888888899********************9998753.44555555555555677 PP

                                   ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---.SEEEEEESS- CS
                        ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfke.avllglTATp 169
                                    ++  ++l+tt ++l   +    +++ + l +++  iiiDE   + ++k       +++++++  k    l+gl+AT+
  gi|70606604|ref|YP_255474.1| 113 LEDPPDLLLTTPETLLYLL---VNQKMRELLGNIRWIIIDELQEMLDEKrgyelllAIQRLKRLSKYeIQLIGLSATI 187
                                   99999***********999...9999****************999998665555555555544333348889*****7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                                   GGGGTGG........GEEEESSS-B--.......-SEEEEEHHHHHHT CS
                        ResIII  74 fkkflseayke....igkkvsgdkkkakekdstnkkilvttiqsldad 117
                                   f  +++e++ke    i+k+++g k ++   ++++k  ++ +i+s+ + 
  gi|70606604|ref|YP_255474.1| 815 FLTVTDEDDKEsveiIKKVIKGSKISK---NEKKKFEILQNISSMFST 859
                                   444555555556666556666666666...444444444455444443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-07    0.0003       7     126 ..      31     168 ..      24     183 .. 0.64
   2 ?    0.3   0.0      0.36     8e+02      43     126 ..     253     495 ..     237     505 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                        AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp..eeillvaftgrAakelrerlaalgae....atTiHrlal.... 77 
                                    lk k+ +v+a+ G GKT++      ++ ++ + ++   + + +++ +   + l++rl+ +g +    +   H+ ++    
  gi|70606604|ref|YP_255474.1|  31 ILKGKNTIVIAPTGFGKTETAIFP--VFYKILSSNAekISAIYITPLRALNRDLEDRLSRIGSAlgikIAIRHGDSTerqr 109
                                   578999************985544..4444444444005555667777777789999966655544443333433225555 PP

                        AAA_19  78 .........ldfddlltealelle............eaeeekklqeeellivDEfq.dvd.elqyrLlkall 126
                                            l                          +++ ++ l +  ++i+DE q ++d +  y+Ll a+ 
  gi|70606604|ref|YP_255474.1| 110 kriledppdL-------------LlttpetllyllvNQKMRELLGNIRWIIIDELQeMLDeKRGYELLLAIQ 168
                                   5555444441.............0344444445665667777775666*******9567889999**99887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                        AAA_19  43 eeillvaftgrAakelrerlaalg.aeatTiHrlal............................................. 77 
                                   +++l+ +  + +++ l+ +l++l  ++ +T H+  l                                             
  gi|70606604|ref|YP_255474.1| 253 KPVLVFTNVRESTEFLASELSKLSqLKVRTHHGS-Lsreirleaekefktgnldaliatsslelgidvgtinaviqytspk 332
                                   5666666666666666666655431346666643.2235555555555555555555555555555555555555555555 PP

                        AAA_19  78 ................................................................................. 77 
                                                                                                                    
  gi|70606604|ref|YP_255474.1| 333 qvirlvqrigrsghsinkvssgfllpshdifdilecksiidnlkegylekpivepkpydvmaheiaglvlegitdkkeifn 413
                                   555555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                        AAA_19  78 .............................ldfddlltealelleeaeeekklqeee..llivDEfqdvd..elqyrLlkal 125
                                                                 +++d+++ a  l ++  +++ + +    ++++D +++++   l y+++ +l
  gi|70606604|ref|YP_255474.1| 414 likssfqyndlteeefeetlsilesariiRKNKDKISPAGRLWRYYYSTNMIPDSIkdYIVIDHISNTKigTLDYEFVATL 494
                                   555555555544444444444444444433333333333333334444444444333477777777766556667776666 PP

                        AAA_19 126 l 126
                                    
  gi|70606604|ref|YP_255474.1| 495 D 495
                                   6 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.6e-06     0.019      56     109 ..     159     213 ..     157     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.6e-06
                        PrpR_N  56 sgyDilralkqakklg.ekialvgfeniikglktlselldldieiytinseeeae 109
                                   +gy++l a++++k+l+  +i l+g + +i +++  +++++ ++e+ ++n++++++
  gi|70606604|ref|YP_255474.1| 159 RGYELLLAIQRLKRLSkYEIQLIGLSATIGDIELAKRFIGRNVEVAEYNTRKDVK 213
                                   69**************658*********************************975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   4.3e-05     0.097       6     126 ..      35     181 ..      32     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.3e-05
                        AAA_22   6 gilvvtGesGtGKTtllrr.lleqldeeakaee.erpevvfvtlpsst..sskdllrellralglelka............ 70 
                                   + ++v++++G GKT ++   ++++        + e+ + +++t+      +++d l+++ +alg +               
  gi|70606604|ref|YP_255474.1|  35 KNTIVIAPTGFGKTETAIFpVFYKI----LSSNaEKISAIYITPLRALnrDLEDRLSRIGSALGIKIAIrhgdsterqrkr 111
                                   5689999999999988754233332....1222347777777765444477788888888888865555899999999999 PP

                        AAA_22  71 ........erlsseell.ealeqalrarav.ielliiDEaqh.lrseealeeLrsllnl...srkgvqli 126
                                              + e ll  +++q +r+    i+ +iiDE q  l++++ +e L  ++ l   s++ +qli
  gi|70606604|ref|YP_255474.1| 112 iledppdlLLTTPETLLyLLVNQKMRELLGnIRWIIIDELQEmLDEKRGYELLLAIQRLkrlSKYEIQLI 181
                                   999988885555555555777888888777999*********6656777777766666665566777765 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5   0.00026      0.58      17      52 ..     782     813 ..     777     815 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                zinc_ribbon_10  17 aknryalICskChshnGlapkeeleevkyrCpkCga 52 
                                    +n +++IC  C ++n ++    ++ev  rC kCg+
  gi|70606604|ref|YP_255474.1| 782 LNNKVKIICMVCGWNNIYY----AAEVPDRCTKCGS 813
                                   6899************999....7788889****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (911 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.83u 0.32s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 5107.91
//
Query:       gi|70606605|ref|YP_255475.1|  [L=446]
Description: hypothetical protein Saci_0815 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-08   32.5   1.3    1.8e-06   28.2   1.3    2.3  1  DUF87          Helicase HerA, central domain
      5e-07   29.0   0.6      8e-05   21.7   0.6    2.5  1  AAA_10         AAA-like domain
    7.8e-05   23.0   0.0       0.61   10.4   0.0    2.5  2  AAA_22         AAA domain
    0.00014   22.4   0.0    0.00065   20.2   0.0    2.1  2  AAA_18         AAA domain
     0.0059   17.1   0.1      0.012   16.1   0.1    1.5  1  ABC_tran       ABC transporter
     0.0074   16.0   0.4      0.014   15.1   0.4    1.4  1  AAA_29         P-loop containing region of AAA domain
     0.0077   16.2   0.0      0.014   15.4   0.0    1.4  1  AAA_5          AAA domain (dynein-related subfamily)
     0.0099   14.8   0.0        1.1    8.1   0.0    2.3  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.062   13.3   0.0    1.4  1  DUF3439        Domain of unknown function (DUF3439)
      0.056   13.9   0.1       0.25   11.8   0.0    2.0  2  AAA            ATPase family associated with various cellular
       0.11   12.3   0.1       0.25   11.2   0.1    1.5  1  RsgA_GTPase    RsgA GTPase
       0.13   12.2   0.1        2.2    8.2   0.1    2.2  2  NACHT          NACHT domain
       0.15   12.4   0.0       0.31   11.4   0.0    1.4  1  AAA_16         AAA ATPase domain


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   1.3   1.3e-09   1.8e-06      28     105 ..     131     208 ..     100     379 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                         DUF87  28 ilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsa......kdkelkinpwsldpeel 102
                                   i+g++GsGKS ++ ++ ++l     ++  i+D HGEY+  +   ++ +++ +t+ p +      k++ l++ + + +   l
  gi|70606605|ref|YP_255475.1| 131 IIGTSGSGKSSLATLISKKLN----VSFTIFDLHGEYSIPN--AVKIDMSKVTINPLSlfgrspKERALEVSYMLKSLFNL 205
                                   99***************9999....999**********999..33333333333332244444444444444444333333 PP

                         DUF87 103 ldl 105
                                    ++
  gi|70606605|ref|YP_255475.1| 206 GNI 208
                                   333 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.6   5.8e-08     8e-05      19     346 ..     124     436 ..     111     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.8e-08
                        AAA_10  19 tnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvllk.e 98 
                                   +++ +s+iiG  G GKS la l+      l+    i D   e     + +p+       v++d     +++++Pl+l+  +
  gi|70606605|ref|YP_255475.1| 124 SKNFNSIIIGTSGSGKSSLATLISK---KLNVSFTIFDLHGE-----YSIPN------AVKID---MSKVTINPLSLFGrS 187
                                   5666777777777777776666543...45566677777777.....44444......55555...445667777777654 PP

                        AAA_10  99 ekeaeslaedilelllgvkkkes.ekkaalsea.....veavle....gkqrgllavieelrke..dekvareiarhlesv 167
                                   +ke +     +l+ l ++ + ++ e  +++ ea     ++        ++++++ +++  l+++      +++i+++  s+
  gi|70606605|ref|YP_255475.1| 188 PKERALEVSYMLKSLFNLGNIQTiELSNLILEAymekgIDPDDMdtwkNPTPNFRDLLLLLERKkkAAITSQDISKYQ-SI 267
                                   444444444555544333322220222233333211114322112333555666666666643311233344455544.22 PP

                        AAA_10 168 vkkslaklvfsdgsveeaislekkvtvlevedLdLPdkderlerlteekllsvavlfviaafaref.assdkkefkvvifD 247
                                          + +s +     i  +++v+++++ + +   +   +  + +++++ + +  ++  + + +   +  ++ k++i+D
  gi|70606605|ref|YP_255475.1| 268 EP---YLIFLSST-----IFTQNNVNIIDILEKNCVLD---FSTIPTNEVKHIVMETILKGIQSYMyLEKFPDIRKMIIID 337
                                   22...22223332.....34456677766644333322...444444555544443344444443323456899******* PP

                        AAA_10 248 EawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvLeflgldvededn..k 326
                                   Ea  + s +  ++l++ l   GR++    + ++q +d v++  l +n  l ++ +  + +e +   +++g + +d      
  gi|70606605|ref|YP_255475.1| 338 EAPFLLSKDSSRELINRLFSEGRKFGFGFVVISQTVDYVKD--LFGNAYLTFVLNVLEPRESEYLSRYFGGQDNDMYLavY 416
                                   **********************************8866654..556667778888889999999999***99988764447 PP

                        AAA_10 327 kelrelesGqCLmkDllgrv 346
                                   + l++l  G  +++Dllgr 
  gi|70606605|ref|YP_255475.1| 417 ETLQKLPRGFFIVRDLLGRF 436
                                   88999***********9995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00044      0.61       9      30 ..     130     151 ..     102     196 .. 0.82
   2 !   10.3   0.0   0.00047      0.65      71     129 ..     302     370 ..     236     376 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                        AAA_22   9 vvtGesGtGKTtllrrlleqld 30 
                                   +++G sG+GK+ l+  + ++l+
  gi|70606605|ref|YP_255475.1| 130 IIIGTSGSGKSSLATLISKKLN 151
                                   89************99999984 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00047
                        AAA_22  71 erlsseell.ealeqalrarav.......ielliiDEaqhlr....seealeeLrsllnlsrkgvqliLvG 129
                                   ++++ ++++ e++ + +++++        ++++iiDEa +l     s e+++ L  +++ +++g+ ++++ 
  gi|70606605|ref|YP_255475.1| 302 PTNEVKHIVmETILKGIQSYMYlekfpdiRKMIIIDEAPFLLskdsSRELINRL--FSEGRKFGFGFVVIS 370
                                   455555555599999999999899999999**********55343225555555..333368888888875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.7e-07   0.00065       2      36 ..     130     164 ..     130     236 .. 0.71
   2 ?   -0.8   0.0       1.5   2.1e+03      55      92 ..     281     324 ..     248     355 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.7e-07
                        AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakeng 36 
                                   ++ Gt+G+GK++la  +sk+l++++ + d++ e  
  gi|70606605|ref|YP_255475.1| 130 IIIGTSGSGKSSLATLISKKLNVSFTIFDLHGEYS 164
                                   699*****************988555555444433 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                        AAA_18  55 dkldklldaleenss......aleegknlvidghlaeleseaak 92 
                                   ++  +++d+le+n+          e k++v++ +l    s+++ 
  gi|70606605|ref|YP_255475.1| 281 QNNVNIIDILEKNCVldfstiPTNEVKHIVMETILKGIQSYMYL 324
                                   44456666666666667777744566677777666665555544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   8.7e-06     0.012       4      36 ..     119     151 ..     118     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.7e-06
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllk 36 
                                   v+++ +++    i+G +G+GKS+L+ l++++l+
  gi|70606605|ref|YP_255475.1| 119 VNFSNSKNFNSIIIGTSGSGKSSLATLISKKLN 151
                                   567777777789****************99875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4     1e-05     0.014       7      38 ..     108     142 ..     102     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                        AAA_29   7 vNWgtfdg.htieidlkg..atlltGpsGsGKSTl 38 
                                   + W  +++   ++++ +   + +++G+sGsGKS+l
  gi|70606605|ref|YP_255475.1| 108 YKWIKLNQdFCVNFSNSKnfNSIIIGTSGSGKSSL 142
                                   5677788777888887777999***********98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     1e-05     0.014       2      33 ..     129     160 ..     128     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqlt 33 
                                    +++G +G+gKs+la  +++ ln ++++  l+
  gi|70606605|ref|YP_255475.1| 129 SIIIGTSGSGKSSLATLISKKLNVSFTIFDLH 160
                                   689**********************9998887 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.01        14      17      55 ..     128     163 ..     121     182 .. 0.72
   2 !    8.1   0.0    0.0008       1.1     231     292 ..     318     383 ..     303     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                 TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                     +i+Gt GsGK+  ++ + +++   +    ++Dl+G++
  gi|70606605|ref|YP_255475.1| 128 NSIIIGTSGSGKSSLATLISKKL---NVSFTIFDLHGEY 163
                                   5689********98665443333...4456677777776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0008
                 TrwB_AAD_bind 231 ikallslpesrerrlWfflDElpaLgrlee....lksllaegRkfGgavvlglqsiaqlrevYGed 292
                                   i++ + l++  + r   ++DE p L   ++    +++l  egRkfG  +v+  q++  +++ +G++
  gi|70606605|ref|YP_255475.1| 318 IQSYMYLEKFPDIRKMIIIDEAPFLLSKDSsrelINRLFSEGRKFGFGFVVISQTVDYVKDLFGNA 383
                                   5666678888888888999999987543322222778899*********************99986 PP

>> DUF3439  Domain of unknown function (DUF3439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.062      10     102 ..     109     202 ..     101     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                       DUF3439  10 rwikknskivkakssavdpds..akcsgsgkpvrsiicpttttttttttttmpttttlptttkmsmvkvplvppeafgrvm 88 
                                   +wik n++   + s++ + +s     sgsgk   + +        + t   +    ++p + k+ m kv + p   fgr  
  gi|70606605|ref|YP_255475.1| 109 KWIKLNQDFCVNFSNSKNFNSiiIGTSGSGKSSLATLISK-KLNVSFTIFDLHGEYSIPNAVKIDMSKVTINPLSLFGRSP 188
                                   7898888877666655555551156899999876666553.455566778899999************************9 PP

                       DUF3439  89 nacayfpsyiflhl 102
                                   ++ a   sy++  l
  gi|70606605|ref|YP_255475.1| 189 KERALEVSYMLKSL 202
                                   99999999987655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.25       2      31 ..     130     159 ..     129     190 .. 0.82
   2 ?   -0.8   0.0       1.4   1.9e+03      60      94 ..     332     360 ..     305     379 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEET CS
                           AAA   2 llyGppGtGKTllakavakelgvefleisg 31 
                                   +++G+ G GK++la  + k+l+v+f  +++
  gi|70606605|ref|YP_255475.1| 130 IIIGTSGSGKSSLATLISKKLNVSFTIFDL 159
                                   689******************988755443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                   EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                           AAA  60 silfiDEidalaksrsgseseeeervvnqLlteld 94 
                                   + ++iDE+  l +++      ++++++n L++e  
  gi|70606605|ref|YP_255475.1| 332 KMIIIDEAPFLLSKD------SSRELINRLFSEGR 360
                                   679999999998888......67777777776655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.25      99     124 ..     126     151 ..     102     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                   TSEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                   +  s+++G SG GKS+L   +  +l+
  gi|70606605|ref|YP_255475.1| 126 NFNSIIIGTSGSGKSSLATLISKKLN 151
                                   55689************998877654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0016       2.2       3      24 ..     129     150 ..     128     154 .. 0.88
   2 ?    1.6   0.0      0.16   2.2e+02      51     163 ..     284     404 ..     258     407 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   +i+ G +GsGK+ L+  +  ++
  gi|70606605|ref|YP_255475.1| 129 SIIIGTSGSGKSSLATLISKKL 150
                                   589************9998876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                                   ..-HCHHHCCCCTS--SSS-C......CHHHHCCSCCCEE...........EEEE-STT-SS-TCH.........HHHHHC CS
                         NACHT  51 arsladllfsqlpepaapvse......vwavllelperlL...........lilDglDelvtdlgqkekqpvrtlLselir 114
                                   +  ++d+l +++    +++++      v++ +l+  ++ +           +i+D +  l ++++       r+l+++l++
  gi|70606605|ref|YP_255475.1| 284 V-NIIDILEKNCVLDFSTIPTnevkhiVMETILKGIQSYMylekfpdirkmIIIDEAPFLLSKDSS------RELINRLFS 357
                                   4.5666666666655555555555555555555555555566666666666777777777776666......999999999 PP

                                   TTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHHHHHCT CS
                         NACHT 115 kkllpeasllltvrpralrdleeqleeaivlevegfsesrrkqlvrkyf 163
                                   +    +  +++++++     ++ ++  a+ + v    e+r  +++++yf
  gi|70606605|ref|YP_255475.1| 358 EGRKFGFGFVVISQTVDY--VKDLFGNAYLTFVLNVLEPRESEYLSRYF 404
                                   988888888888888888..99999999999999999999999999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.31      28      49 ..     130     151 ..     112     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                        AAA_16  28 llsGesGvGKsslvrellrale 49 
                                   +++G sG+GKssl++ + + l+
  gi|70606605|ref|YP_255475.1| 130 IIIGTSGSGKSSLATLISKKLN 151
                                   599************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2667.47
//
Query:       gi|70606606|ref|YP_255476.1|  [L=105]
Description: hypothetical protein Saci_0816 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-18   65.1   3.9    3.7e-18   65.1   3.9    2.7  3  RNA_pol_Rpo13  RNA polymerase Rpo13 subunit HTH domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpo13  RNA polymerase Rpo13 subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.5      0.14   2.5e+03       4      14 ..       7      17 ..       4      19 .. 0.75
   2 !   65.1   3.9   2.1e-22   3.7e-18       1      43 []      22      61 ..      22      61 .. 0.98
   3 ?   -2.0   1.2       0.2   3.5e+03       8      11 ..     102     105 .]      97     105 .] 0.43

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.14
                                  XXXXXXXXXXX CS
                 RNA_pol_Rpo13  4 ktvEEeEEeEv 14
                                  k++ E EE+E+
  gi|70606606|ref|YP_255476.1|  7 KKEPEPEETEA 17
                                  67778889886 PP

  == domain 2  score: 65.1 bits;  conditional E-value: 2.1e-22
                                  XXXXXXXXXXXXXXXX...XX---TTHHHHHHHHHHHTT--SS CS
                 RNA_pol_Rpo13  1 eEektvEEeEEeEvptvdrvsiadiEllvknTeiWdkLlrGki 43
                                  eE++++E++E++E++t   v+i+diE+l+k+TeiWdkLlr+++
  gi|70606606|ref|YP_255476.1| 22 EEISREEDDEGGEFST---VTISDIEMLLKDTEIWDKLLRNEL 61
                                  8***************...**********************95 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.2
                                   XXXX CS
                 RNA_pol_Rpo13   8 EeEE 11 
                                   EeEE
  gi|70606606|ref|YP_255476.1| 102 EEEE 105
                                   2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1466  (0.081767); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 722.44
//
Query:       gi|70606607|ref|YP_255477.1|  [L=250]
Description: DNA polymerase sliding clamp B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.7   1.2    0.00021   21.5   0.0    3.2  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    1.6e-05   24.6   1.3    3.4e-05   23.5   0.3    2.0  3  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
     0.0027   17.2   1.8     0.0073   15.8   0.6    2.0  2  Rad9      Rad9
  ------ inclusion threshold ------
       0.11   12.5   0.7       0.16   12.0   0.1    1.6  2  Svf1      Svf1-like N-terminal lipocalin domain
        0.3   10.4   7.6        1.2    8.4   7.9    1.8  2  DUF1235   Protein of unknown function (DUF1235)


Domain annotation for each model (and alignments):
>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.021        74      14      41 ..       8      35 ..       4      42 .. 0.89
   2 !    6.2   0.8    0.0031        11      14     102 ..      71     161 ..      66     186 .. 0.79
   3 !   21.5   0.0   5.8e-08   0.00021      71     127 ..     191     247 ..     182     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                                  EHHHHHHHHHHHTTT-SEEEEEEETTEE CS
                        PCNA_C 14 pssefaricrdlsqlsdsvvisvtkegv 41
                                  ++ +f  i++ +s++ ds+++  t e v
  gi|70606607|ref|YP_255477.1|  8 SAKDFYDIIQGVSNVTDSITLYFTEEEV 35
                                  689******************9999877 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                                   EHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEET.TEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHG.GG CS
                        PCNA_C  14 pssefaricrdlsqlsdsvvisvtkegvkfsasGd.iGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeft.ka 92 
                                      e +++     + s  ++i  t  g+k +   +  G  s +  + +++ + e+ v+ ++  ++++t +++ + +++  a
  gi|70606607|ref|YP_255477.1|  71 QLNELKKVLNKAKSKSAVINIEETDAGMKITVRDEkTGLKSSIYLKGEKITNIENVVEPKVGLTISFTCSGNIIKNVVdEA 151
                                   55677888888888888999999999999987654278777677777889999*******************998876379 PP

                                   GGC-SEEEEE CS
                        PCNA_C  93 tsLservtls 102
                                   +s+se+++++
  gi|70606607|ref|YP_255477.1| 152 SSISEQIQIE 161
                                   9******997 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 5.8e-08
                                   EEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                        PCNA_C  71 lelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                   le++ + + t++++ l +  ka++ se+ t+++ +++P+++e  ++++g l +++a+
  gi|70606607|ref|YP_255477.1| 191 LEIQSSGKSTYGVEVLKTALKASAFSENLTVRFGNNIPMKIEAPVQSGGQLIFWIAP 247
                                   788999999********************************************9998 PP

>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   9.6e-09   3.4e-05       4     109 ..       4     108 ..       1     125 [. 0.83
   2 ?   -1.2   0.0      0.42   1.5e+03      15      89 ..     147     168 ..     135     206 .. 0.59
   3 ?   -3.0   0.0       1.5   5.5e+03      34      58 ..     190     216 ..     182     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.6e-09
                                   EEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTT CS
                        PCNA_N   4 arleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcann 84 
                                   a +  a  +  +++++ ++ +++++   ++ +  + l + +  +v l++ +e +e+y  +++l + ++ln l k+l  a+ 
  gi|70606607|ref|YP_255477.1|   4 AIYGSAKDFYDIIQGVSNVTDSITLYFTEEEVMSRYLTEDKTLMVLLKISKEYMEEYIIEKPLGIKIQLNELKKVLNKAKS 84 
                                   5555666677789999999999999999**************************************************999 PP

                                   TSEEEEEEETTSSEEEEEEEECTSS CS
                        PCNA_N  85 edsvtlkaedeadtlalvfesekkd 109
                                   ++ v ++ e+++  +++++++ek+ 
  gi|70606607|ref|YP_255477.1|  85 KSAV-INIEETDAGMKITVRDEKTG 108
                                   8876.56677777788888877765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.42
                                   HHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEE CS
                        PCNA_N  15 lleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvt 89 
                                   +++    + ++++++ dd                                                     ++++
  gi|70606607|ref|YP_255477.1| 147 VVDEASSISEQIQIEGDD-----------------------------------------------------NQII 168
                                   333333333333333333.....................................................3333 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.5
                                   EEEEEEE-TTS..SEEEEEEEEGGGSS CS
                        PCNA_N  34 GislqalDssh..vaLvslelrsegfe 58 
                                   G+++q+  +s   v + +  l++++f+
  gi|70606607|ref|YP_255477.1| 190 GLEIQSSGKSTygVEVLKTALKASAFS 216
                                   555555554432244455555555554 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6     2e-06    0.0073     131     235 ..       5     104 ..       2     116 .. 0.89
   2 ?   -0.6   0.0       0.2   7.3e+02       4      33 ..     147     176 ..     144     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-06
                          Rad9 131 lriksrvLsdllehfsssleeitielakervllksyeeeekdnkkalstelsideeeFeqyqlaedveitlslkefkallv 211
                                   +  +++ + d+++  s+ ++ it+ +++e+v+ +  +e+     k+l   l+i++e  e+y +++   i + l e+k +l 
  gi|70606607|ref|YP_255477.1|   5 IYGSAKDFYDIIQGVSNVTDSITLYFTEEEVMSRYLTED-----KTLMVLLKISKEYMEEYIIEKPLGIKIQLNELKKVLN 80 
                                   56789999***********************99988875.....567799******************************* PP

                          Rad9 212 faeslsaslslafdeaGkPlllti 235
                                    a s sa ++++  +aG  +++  
  gi|70606607|ref|YP_255477.1|  81 KAKSKSAVINIEETDAGMKITVRD 104
                                   ************999998777655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                          Rad9   4 alqclsrigdelyleisedglelrtvnssr 33 
                                   ++  +s i++++ +e  ++++ ++t +s r
  gi|70606607|ref|YP_255477.1| 147 VVDEASSISEQIQIEGDDNQIIFSTEESGR 176
                                   577889999999999999999999988877 PP

>> Svf1  Svf1-like N-terminal lipocalin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.8     1e+04       3      12 ..      25      34 ..      17      40 .. 0.70
   2 ?   12.0   0.1   4.6e-05      0.16      33     119 ..      96     204 ..      84     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.8
                          Svf1  3 tqtfYftdld 12
                                  + t+Yft+++
  gi|70606607|ref|YP_255477.1| 25 SITLYFTEEE 34
                                  4577777765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.6e-05
                          Svf1  33 aqftfkifdskekkeknl.Wkstklenfe.......................idkasfyadnlsielkneegeqykikssv 89 
                                   a + + + d+k+  ++++  k  k++n+e                       +d+as  +++++ie   ++++    +++ 
  gi|70606607|ref|YP_255477.1|  96 AGMKITVRDEKTGLKSSIyLKGEKITNIEnvvepkvgltisftcsgniiknvVDEASSISEQIQIEG--DDNQIIFSTEES 174
                                   55555555666655554414566666666666888888888888777766657**************..467777788888 PP

                          Svf1  90 nkelkvdltvtrlapGfklgedgttyfgdd 119
                                       k  l +++  +G ++++ g++++g +
  gi|70606607|ref|YP_255477.1| 175 GRGYKAYLVMDKPLKGLEIQSSGKSTYGVE 204
                                   9999***********************954 PP

>> DUF1235  Protein of unknown function (DUF1235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.9   0.00034       1.2      21     128 ..      35     145 ..      16     172 .. 0.76
   2 ?    0.2   0.1       0.1   3.7e+02      38      63 ..     144     169 ..     138     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00034
                       DUF1235  21 dvkkyydsehakiilseikkyidekilvknlisikvvdkyelkkelinsnlskiivCiqsakkGGliividkelnekkilk 101
                                    + +y  ++ + ++l  i k   e+ ++++ + ik  + +elkk l + ++  +++ i+++  G  i v d+++  k  + 
  gi|70606607|ref|YP_255477.1|  35 VMSRYLTEDKTLMVLLKISKEYMEEYIIEKPLGIKI-QLNELKKVLNKAKSKSAVINIEETDAGMKITVRDEKTGLKSSIY 114
                                   3467999999999*****999888889999999998.7799*9777777777899************************** PP

                       DUF1235 102 lnvdkivilspLse....ytvskvvkGslii 128
                                   l+ +ki  ++ ++e     t+s    G++i 
  gi|70606607|ref|YP_255477.1| 115 LKGEKITNIENVVEpkvgLTISFTCSGNIIK 145
                                   **99998666555411115555555666555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                       DUF1235  38 ikkyidekilvknlisikvvdkyelk 63 
                                   ik+ +de   +++ i+i+  d++ + 
  gi|70606607|ref|YP_255477.1| 144 IKNVVDEASSISEQIQIEGDDNQIIF 169
                                   66777888888888888874444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1699.52
//
Query:       gi|70606608|ref|YP_255478.1|  [L=367]
Description: hypothetical protein Saci_0818 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-17   63.6   0.0    6.6e-15   55.3   0.0    2.1  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.049   13.0   0.1       0.39   10.0   0.0    1.9  2  TEBP_beta     Telomere-binding protein beta subunit (TEBP bet


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0   0.00051       4.6       1      59 [.      50     125 ..      50     148 .. 0.71
   2 !   55.3   0.0   7.4e-19   6.6e-15     160     323 ..     181     343 ..     169     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00051
                                   EEEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSS CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgatt 59 
                                   i++P l+++H+H  ++ + +       ++++             ++p++++ ++e++i    k G+  + d+++  
  gi|70606608|ref|YP_255478.1|  50 ILFPPLVNSHTHTADYSFPEYgirqSIKEVVgdplsqkytyfksIDPSIIRKGIENFIIDSQKFGVLAIVDFREQG 125
                                   68999********999775557776555555866666667777777777777777777766666666666666655 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 7.4e-19
                                   HHHHHHHTTTEEEETTTTSTCCHHTTTHCCEE...EHCTCEEEHH..HHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHH CS
                  Amidohydro_1 160 edaeaafgetiehgthlevaeslglldeikli...lahgvhltpt..eaellkerlkeagvahcpfsnsilrsgrealrka 235
                                    ++ +af  +i   ++ e ++++ l d  + i    + + ++++t  ++   +e   e++v+ cp+sn+  + g++++ +a
  gi|70606608|ref|YP_255478.1| 181 VEIFNAFSTKIRAVHISETLKQYLLDDF-RYItesYKPNLLIHAThfKYPDFREL--ETSVVFCPRSNMWFGVGVPRIVDA 258
                                   5556677777777777777777544444.44445566666666664544446666..889********************* PP

                                   HHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEE CS
                  Amidohydro_1 236 ldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvv 316
                                   ++++v++ +gtD +a   s+nl+ +l l+l+++r +       +   ke+lr aT+n+ k+++l  + G ie+Gk+A +v+
  gi|70606608|ref|YP_255478.1| 259 INANVNILFGTD-NAGLLSPNLWLDLELGLLITRIQEPM---SD-YSKEILRGATYNAYKQFNL--NWG-IEEGKEAKFVL 331
                                   ************.888899***********888844442...22.2468***************..***.*********** PP

                                   ECC.CT....CG CS
                  Amidohydro_1 317 vdl.di....la 323
                                   + + +i    ++
  gi|70606608|ref|YP_255478.1| 332 ISGnTIfnavNK 343
                                   *66433444444 PP

>> TEBP_beta  Telomere-binding protein beta subunit (TEBP beta)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.032   2.9e+02      58     101 ..      94     140 ..      73     145 .. 0.81
   2 ?   10.0   0.0   4.4e-05      0.39      84     134 ..     179     229 ..     166     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.032
                                   E-EEE-HHHHHHH...HHHSTT--GGG-TTSEEEEEEEEEEEEE--T CS
                     TEBP_beta  58 vapyftkeavaef...hakfpnvnivdlhdkvivinnwslelrrvns 101
                                   + p + ++ +++f    +kf  + ivd++++ i   +   elrr n 
  gi|70606608|ref|YP_255478.1|  94 IDPSIIRKGIENFiidSQKFGVLAIVDFREQGINGAKLVSELRRRND 140
                                   566777777777744458***************9999999***9986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 4.4e-05
                                   TSEEEEEEEEEEEEE--TTT-SS-BTTEEEEEEEEEEEEETTS----SS-- CS
                     TEBP_beta  84 dkvivinnwslelrrvnsaevftsyanlearlivhsfkpnlqerlnptryp 134
                                   + v + n++s ++r v  +e +  y   + r i  s+kpnl       +yp
  gi|70606608|ref|YP_255478.1| 179 ELVEIFNAFSTKIRAVHISETLKQYLLDDFRYITESYKPNLLIHATHFKYP 229
                                   567789***********************************8877777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2554.62
//
Query:       gi|70606609|ref|YP_255479.1|  [L=219]
Description: GGDN family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   82.7   0.1    1.1e-20   74.0   0.1    2.0  1  GCH_III   GTP cyclohydrolase III


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.1   5.9e-25   1.1e-20       4     236 ..       6     211 ..       1     217 [. 0.86

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 5.9e-25
                                   EEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHS.SS-EEE CS
                       GCH_III   4 iqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnry.pvtvsm 83 
                                   + + +Y++Wt+ ++ +re+ +qa+q  +   l ++la  + + +++R+D  + +  g++ +e   +   ++++y p ++++
  gi|70606609|ref|YP_255479.1|   6 LDLVGYKEWTESLGCDREWRIQAFQHYFASILYSKLADVNAFPIPIRYDSYIILVDGVKEKEVLHVIREVSEKYsPTKMQI 86 
                                   45669********************988888899****************************9999988888765899*** PP

                                   EEEEESSHHHHHHHHHHHHHHH--TT-TT----EEES---SS--EEEEEEEETTHHHHTTTTS-HHHHHHHHHHHHHHHHH CS
                       GCH_III  84 gigaaetPldaleaaseaLreagsaqdeeRkevlsvdelvtegyvqiahiDinnitgtltdivsavrtylevnkvkaklak 164
                                     g +et ++ + +  ++L ++                   ++ + +ah Din+it           +  e++++ka++  
  gi|70606609|ref|YP_255479.1|  87 CKGYGETIYESIFNCVDTLEDKP------------------DDKIVVAHYDINGIT-----RLDKRTAMQEIEELKANVFS 144
                                   ******************97753..................466889*********.....23344567899********* PP

                                   HHHTTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS--EEEEEEEESSHHHHHHHHHHHHHHHHTTS CS
                       GCH_III 165 klekegallqfiGGDnilavcneleeedvldiinevkekvdvdlkaGiGiadtaedaaaladeaLeeiRgkl 236
                                     ek g + ++ GGDn+   +++ + + +l i n +++    ++k GiGia+ +++a+  a +aLe +R ++
  gi|70606609|ref|YP_255479.1| 145 LSEKVGGIAYYFGGDNVGLFASKKDLDSMLTIAN-LND----NVKTGIGIAENPRKALMKATTALEYVRKNR 211
                                   99**************977667777777777654.444....5699***********************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1567.81
//
Query:       gi|70606610|ref|YP_255480.1|  [L=158]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-35  121.2   1.1    3.4e-35  120.9   1.1    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.012   14.9   1.3       0.84    8.9   0.3    2.1  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
      0.017   15.7   0.0      0.042   14.4   0.0    1.6  1  ADSL_C         Adenylosuccinate lyase C-terminus
      0.088   12.9   0.2       0.79    9.9   0.0    2.2  2  TM_PBP2_N      N-terminal of TM subunit in PBP-dependent ABC 


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   1.1   7.6e-39   3.4e-35       2     139 ..       9     140 ..       8     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 7.6e-39
                                   EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHH CS
                 DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyv 82 
                                   ++++iVv++fn +it+ +l++al++++ +gv+    +vv+VPG++++ +++k+l+++ +++d+v++lG+vi+Get+h+e+v
  gi|70606610|ref|YP_255480.1|   9 INLGIVVSEFNYDITSLMLQRALSHAEFLGVT--VKVVVKVPGSYDMAVIVKELLKR-DEIDGVVTLGAVIKGETKHDEIV 86 
                                   679***************************97..8899******************4.558******************** PP

                                   HHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                 DMRL_synthase  83 aeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                   a +++++lm++s+++g+Pv+ g++    t+eqa er+    +++  +a+e+a+++++ 
  gi|70606610|ref|YP_255480.1|  87 ATQTARKLMDLSVEYGKPVTLGIIGHGvTHEQAVERI----EEYSMRAVESAVKLIKR 140
                                   ***************************9*********....79999999999999986 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00019      0.84      12      60 ..      45      93 ..      37     103 .. 0.83
   2 ?    5.5   0.1     0.002       8.9     132     180 ..     102     150 ..      95     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00019
                                  E--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT- CS
                 Metallophos_3 12 sdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerr 60
                                   ++ g++++   ++e+++  + D +v +G ++k+e+k de   +q +r+
  gi|70606610|ref|YP_255480.1| 45 VKVPGSYDMAVIVKELLKRDEIDGVVTLGAVIKGETKHDEIVATQTARK 93
                                  56677788777788888888*********************98887776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.002
                                   TTEEEEEE-SEEESS--BSSSS-EEEHHHHHHHGGGGGGS---EEEEEE CS
                 Metallophos_3 132 GevliaGmGGeivdgekeeefrLkYPaweveyrLkvlkelkdrrkvlll 180
                                   G+ +  G+ G  v +e+  e+  +Y ++ ve ++k++k lk  r + l 
  gi|70606610|ref|YP_255480.1| 102 GKPVTLGIIGHGVTHEQAVERIEEYSMRAVESAVKLIKRLKKLREIDLT 150
                                   6667788889999999999999********************9999775 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.4e-06     0.042       8      48 ..     105     149 ..     101     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.4e-06
                                   HHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC CS
                        ADSL_C   8 vllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk 48 
                                   v+l  + +g++ e+A e ++e +m+a e+   l+ +L++  e+ +
  gi|70606610|ref|YP_255480.1| 105 VTLGIIgHGVTHEQAVERIEEYSMRAVESavkLIKRLKKLREIDL 149
                                   78888978*******************99***9999999877765 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   7.6e+02      42      66 ..      44      66 ..      38      81 .. 0.68
   2 ?    9.9   0.0   0.00018      0.79      25      48 ..     111     134 ..     107     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                     TM_PBP2_N 42 vkrvedskeYalsvatkgsettgdl 66
                                  v +v++s  Y+++v++k+  + +++
  gi|70606610|ref|YP_255480.1| 44 VVKVPGS--YDMAVIVKELLKRDEI 66
                                  4555554..8999999866555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00018
                     TM_PBP2_N  25 Ghrgtkeeaiaaiqassvkrveds 48 
                                   Gh  t e+a+++i+  s++ ve++
  gi|70606610|ref|YP_255480.1| 111 GHGVTHEQAVERIEEYSMRAVESA 134
                                   9*****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1121.03
//
Query:       gi|70606611|ref|YP_255481.1|  [L=156]
Description: riboflavin synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-10   40.9   0.1    1.9e-10   40.7   0.1    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.1   1.1e-14   1.9e-10      21     109 ..      19     102 ..       7     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.1e-14
                                   HHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHHHCTS-E CS
                 DMRL_synthase  21 egaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvaeavskglmrvsldtgvPv 101
                                   + a++++++    +++i+++tVPG  +lp+aak+l++s ++ d+vi+lG v +   +++ y a  +s gl+  ++ t++ v
  gi|70606611|ref|YP_255481.1|  19 AIAIKTITKEDP-DAEIVRYTVPGIKDLPVAAKRLLDS-GC-DGVITLGWVGKSMLDKYSYLA--ASIGLITTQIITSKHV 94 
                                   557788888774.59**********************5.45.*******99887777777766..5667888887777666 PP

                                   EEEEEEES CS
                 DMRL_synthase 102 ifgvltvd 109
                                   i   +  d
  gi|70606611|ref|YP_255481.1|  95 IDVTIHED 102
                                   54433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1067.07
//
Query:       gi|70606612|ref|YP_255482.1|  [L=220]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-44  150.0   0.0    6.7e-44  149.7   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   3.7e-48   6.7e-44       5     191 ..       9     215 ..       6     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 3.7e-48
                                   HHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSS.S-S...........S CS
                 DHBP_synthase   5 ealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmve.ene...........d 73 
                                   ++l++G +++++D + re+e+d+++  ekvt++ +++++++a+Glic+ ++++  +++++ +++e   +            
  gi|70606612|ref|YP_255482.1|   9 RHLEQGLPILIYDFDGREEETDMVFYGEKVTWKVINTLRTQAGGLICYVTSKDIGQQIGITFISEiI-KsnypklykrpkY 88 
                                   6799***********************************************************9750.2456777877775 PP

                                   TT---BB--EEESST-SSS-SHHHHHHHHHHHH-T.............T--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHH CS
                 DHBP_synthase  74 khktaftvsvdaaegttTGIsaaDRalTirkladp.............kakpedfrrPGhvfplrareggvleRrghTEaa 141
                                     + af+++v++  +t+TGIs++DRa+Tir+l++              ++  ++f +PGhv +l +r  g+ +R+ghTE++
  gi|70606612|ref|YP_255482.1|  89 GDEPAFSLWVNHI-DTKTGISDEDRAKTIRELHAVvelvennnideaiQKFYNEFYSPGHVPILLSR--GLSTRKGHTELT 166
                                   5679*********.9******************95679999999998866779************99..8*********** PP

                                   HHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                 DHBP_synthase 142 vdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedlie 191
                                   ++L    glk+ a+i+e+l+++  ++++d+   +++++g+++i ++++i+
  gi|70606612|ref|YP_255482.1| 167 MALFSYLGLKKSAIIAEMLDNN-ISLSKDKSLIYSRNNGFPLIDGKEIIK 215
                                   *******************777.59***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1541.46
//
Query:       gi|70606613|ref|YP_255483.1|  [L=187]
Description: hypothetical protein Saci_0823 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1283.99
//
Query:       gi|70606614|ref|YP_255484.1|  [L=254]
Description: hypothetical protein Saci_0824 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-66  223.0  23.9    4.5e-66  222.8  23.9    1.0  1  DUF2208   Predicted membrane protein (DUF2208)
     0.0012   18.6  14.8     0.0035   17.1   4.1    2.3  2  Rer1      Rer1 family
  ------ inclusion threshold ------
      0.086   12.7   5.0      0.078   12.9   0.9    2.2  2  PDR_CDR   CDR ABC transporter
        2.1    8.6   7.8        1.5    9.1   3.0    2.4  2  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


Domain annotation for each model (and alignments):
>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.8  23.9     1e-69   4.5e-66       1     231 []      14     241 ..      14     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.8 bits;  conditional E-value: 1e-69
                       DUF2208   1 kmilisqvsiilfalvlaflpqylflviilYiivimvimsvltsrs..llrerkkleevesgktLfeEknalkliekDeel 79 
                                   kmil+sq+si+++++vl+++ qy++ v+i+Y+i++++im++++ rs  +l+erk+l+e+++++t++eEk+a +li++Dee+
  gi|70606614|ref|YP_255484.1|  14 KMILLSQTSIVIISFVLSLYSQYFLPVYIAYLIIYFIIMTTIMARSnpMLSERKYLSEIVNARTILEEKKAGELIQNDEEY 94 
                                   79******************************************************************************* PP

                       DUF2208  80 qkelkeqlkasmitllllliviilffllyryiiplassllgevleeklarflaflalFealflismflrllarrvlkklvm 160
                                   +k++++++ a++ +++++++++i+++++y++++ +++s+++++     +++++fl++ ealfl+ mf++   rr++++++m
  gi|70606614|ref|YP_255484.1|  95 IKKFQAITSANLKSFGIMFVYLIVILIFYNFVVLRYVSSVTQI-----QKLIVFLVYSEALFLFGMFVN---RRIMRVQMM 167
                                   ****************************************999.....********************9...********* PP

                       DUF2208 161 limat.sykvtekGivlkkrtgikfplk..enieiklneerkfVElrstkqklktriRLYtkdpeklyeilerl 231
                                    +ma+ +yk+tekGiv+++r++++++++  +n++i+ n+++k+VE++ t+ kl++++RLY++d++++++ ++r+
  gi|70606614|ref|YP_255484.1| 168 EVMAPfTYKITEKGIVSTDRSAVFLHSRhlVNASIVENRDKKYVEISPTTLKLPYKLRLYSNDIDRILDAINRV 241
                                   ****************************9******************************************997 PP

>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.1   7.9e-07    0.0035     109     150 ..      18      59 ..      10      73 .. 0.85
   2 !    7.1   3.0   0.00089         4      27      65 ..     107     145 ..      83     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.9e-07
                          Rer1 109 lsatkailialvltffevfdvpVfwpiLlvyfivlfvltmrr 150
                                   ls t+ ++i++vl++++ + +pV+   L++yfi++++++ r+
  gi|70606614|ref|YP_255484.1|  18 LSQTSIVIISFVLSLYSQYFLPVYIAYLIIYFIIMTTIMARS 59 
                                   4678899***************************99987765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00089
                          Rer1  27 atlvllllfllriillqgfyivaYalgiylLnlllaflt 65 
                                     + +++++l+ i++  +f ++ Y+ ++  ++ l+ fl 
  gi|70606614|ref|YP_255484.1| 107 KSFGIMFVYLIVILIFYNFVVLRYVSSVTQIQKLIVFLV 145
                                   4567899*****************************985 PP

>> PDR_CDR  CDR ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.077   3.4e+02      53      68 ..      41      56 ..      35      69 .. 0.59
   2 ?   12.9   0.9   1.8e-05     0.078      24      83 ..      84     143 ..      79     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.077
                       PDR_CDR 53 liaflifflalyllat 68
                                   ia+li+++++   ++
  gi|70606614|ref|YP_255484.1| 41 YIAYLIIYFIIMTTIM 56
                                  4555555444433333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.8e-05
                       PDR_CDR  24 pGqeyVsGddYlelsfgyssshlwrnfgiliaflifflal.yllatelisaekskgevlvf 83 
                                   +G+ + + ++Y++ +f+  +s   + fgi++++li+ l++ +++++ ++s+ ++ ++ +vf
  gi|70606614|ref|YP_255484.1|  84 AGELIQNDEEYIK-KFQAITSANLKSFGIMFVYLIVILIFyNFVVLRYVSSVTQIQKLIVF 143
                                   5666667789*99.9******************9887665167888999999988888887 PP

>> DPM3  Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.072   3.2e+02       8      66 ..      38      60 ..      12      84 .. 0.48
   2 ?    9.1   3.0   0.00034       1.5       8      57 ..     113     161 ..     107     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.072
                          DPM3  8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgygvltfnd 66
                                  l + ++ l+++++                                    +++ ++  ++
  gi|70606614|ref|YP_255484.1| 38 LPVYIAYLIIYFI------------------------------------IMTTIMARSN 60
                                  2223333333333....................................3333333333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                          DPM3   8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatl 57 
                                   +++++++l+++ +++lr vs   +++q+ +v+++   al+lfG++   ++
  gi|70606614|ref|YP_255484.1| 113 FVYLIVILIFYNFVVLRYVSSV-TQIQKLIVFLVYSEALFLFGMFVNRRI 161
                                   6778889999*********766.********************9986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1373  (0.0765798); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1708.97
//
Query:       gi|70606616|ref|YP_255485.1|  [L=434]
Description: cobyrinic acid A,C-diamide synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-38  132.7   0.0    1.9e-38  132.0   0.0    1.3  1  GATase_3  CobB/CobQ-like glutamine amidotransferase domain
    2.2e-13   50.5   0.0    2.1e-08   34.3   0.0    2.4  2  AAA_26    AAA domain
    2.2e-10   40.7   0.1    8.8e-10   38.7   0.0    1.9  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.0   3.2e-42   1.9e-38       3     193 ..     242     427 ..     240     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 3.2e-42
                      GATase_3   3 avirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgi 81 
                                    v++++a+s+y+  ++d+L+++ +v+ +f+pl++++ ++++ +++++Gg+++++  +l+++++++++ik+ +e+g+++l++
  gi|70606616|ref|YP_255485.1| 242 YVAYDSAFSFYYdeNIDILKKRYDVE-FFSPLNNDAPADQPSFIYIGGGYPELHLEELENSTKTKDWIKRNVEKGVKLLAE 321
                                   589******************99887.7899899999999***************************************** PP

                      GATase_3  82 CGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel........aaegeevkGyEiHsGrtilkek 154
                                   CGG+++L++ei++++       ++ ++gl di+++ +++ ++g +e    l        +++ge ++G+E+H ++ ++  +
  gi|70606616|ref|YP_255485.1| 322 CGGFMFLSNEIINEK-------SYRMIGLYDIQIKAKDKLTIGYTE----LetekdnllSSKGESIRGHEFHVSKAVSVGD 391
                                   ************975.......9***************55555555....4445599998899*****************9 PP

                      GATase_3 155 akpllkvkvggnng.ekdGavkksedgnvlGtYlHglfdn 193
                                   ++ ++k k g+++  +kdG++ +    n lG+Y H++f +
  gi|70606616|ref|YP_255485.1| 392 VNFAFKNKHGKGIWnGKDGVYVE----NSLGSYSHFHFSR 427
                                   999999977777668******99....***********86 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   6.6e-06      0.04       3      32 ..       6      34 ..       4      40 .. 0.82
   2 !   34.3   0.0   3.4e-12   2.1e-08      95     196 ..      77     180 ..      62     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-06
                        AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkv 32
                                  i++++ + ++GKT+v++gL++ l+ k +kv
  gi|70606616|ref|YP_255485.1|  6 IIISSDRSNSGKTLVTAGLIKVLS-KRYKV 34
                                  8999999*************9995.55554 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 3.4e-12
                        AAA_26  95 lekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvet 175
                                     k  d+ ++EG+ gl +++ e+ +++++ +    p ilV++  + + +  ++   +   +n +v+Gvi+N +++++ ++ 
  gi|70606616|ref|YP_255485.1|  77 YGKHFDLGIIEGVMGLYDGLYEDYSTYKLSELTHTPLILVINCSNLSSTVGAIVKGLREYRNANVRGVIFNYIASEKHLDY 157
                                   47888999***********************************88655555555555566779*********999999999 PP

                        AAA_26 176 lekksg..ipvlGvvPylpdlea 196
                                    +k+++  ++vlG +P +++l+ 
  gi|70606616|ref|YP_255485.1| 158 CKKSIPenVEVLGYLPIDKSLSV 180
                                   999988779*********99975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.5e-13   8.8e-10       1     125 [.       6     184 ..       6     187 .. 0.90
   2 ?   -1.1   0.0      0.31   1.8e+03      94     125 ..     223     256 ..     196     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.5e-13
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx......................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep......................... 54 
                                   i+i s  +++GKT ++a+L++ l++ +++V  ++++p+    ++  +                                  
  gi|70606616|ref|YP_255485.1|   6 IIISSDRSNSGKTLVTAGLIKVLSK-RYKVRGYKVGPDFIDPMYhkIA-------Sghpvinldlwlmgesgvysslakyg 78 
                                   789999*******************.************7666653322.......13344567999999999********* PP

                                   .......................................CCHCCCHHHHHHCHCHHHH....EEEEEEEEESS...-TTCH CS
                                   .......................................xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .......................................dlkrllellealgkkkall..lkiagvvlnrvdgeneetllk 94 
                                                                          +++ l+ ++ a++k+++     ++ gv++n + +e++    k
  gi|70606616|ref|YP_255485.1|  79 khfdlgiiegvmglydglyedystyklselthtplilviNCSNLSSTVGAIVKGLREYrnANVRGVIFNYIASEKHLDYCK 159
                                   ******************************************************988899********************* PP

                                   HHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  95 ealeelkqrygvpvlgviprdeavaeaparg 125
                                   +++ e     +v+vlg +p d+++   p+r+
  gi|70606616|ref|YP_255485.1| 160 KSIPE-----NVEVLGYLPIDKSL-SVPSRH 184
                                   ***99.....9*********9998.566665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.31
                                   HHHHHHHHHHC.TS-EEE..EEE--CCHCCCCHHT CS
                                   xxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxx RF
                          CbiA  94 kealeelkqry.gvpvlg..viprdeavaeaparg 125
                                    + l+e + ++ +++v+g   + +d+a+++ + ++
  gi|70606616|ref|YP_255485.1| 223 ANELQESN-EIeERNVVGkaYVAYDSAFSFYYDEN 256
                                   33333333.22478888888899999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3043.16
//
Query:       gi|70606615|ref|YP_255486.1|  [L=260]
Description: DNA polymerase sliding clamp A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-15   54.9   0.2      2e-14   53.4   0.1    1.8  3  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    4.1e-12   46.4   0.6    3.9e-10   40.0   0.1    2.2  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    3.3e-10   39.5   0.9    1.2e-05   24.5   0.0    2.1  2  Rad1      Repair protein Rad1/Rec1/Rad17
    1.2e-07   31.4   0.4    1.7e-07   31.0   0.4    1.2  1  Rad9      Rad9
  ------ inclusion threshold ------
        1.6    8.0   8.5        0.4   10.0   3.3    2.1  2  PhoU_div  Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   5.6e-18     2e-14      12      97 ..      24     108 ..      14     121 .. 0.93
   2 ?   -2.5   0.0       1.1     4e+03      74      96 ..     161     183 ..     149     205 .. 0.64
   3 ?   -3.5   0.0       2.2     8e+03      72      90 ..     213     231 ..     210     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.6e-18
                                   HHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEE CS
                        PCNA_N  12 lkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlka 92 
                                   lk ++e++   ++e  f++ ++Gi+l a+D++hv+L+++el +e f++y  + +  +g n + l+kil +a+ ++ + +++
  gi|70606615|ref|YP_255486.1|  24 LKNIVETLTKFIDEGLFEIGQDGIRLVAVDKAHVSLINIELYKELFKEYEVEDEFKFGFNSQYLAKILSIAKRKEEISIES 104
                                   8******************************************************************************98 PP

                                   ETTSS CS
                        PCNA_N  93 edead 97 
                                   +  ++
  gi|70606615|ref|YP_255486.1| 105 DS-PE 108
                                   65.34 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                   HHHHHHTTSTTTSEEEEEEETTS CS
                        PCNA_N  74 slskilkcannedsvtlkaedea 96 
                                   +++  + +   ed+v+lk e ++
  gi|70606615|ref|YP_255486.1| 161 AVTDTVDIIAVEDKVILKGEGKE 183
                                   44444555566677777766554 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.2
                                   HHHHHHHHTTSTTTSEEEE CS
                        PCNA_N  72 lnslskilkcannedsvtl 90 
                                   +n ls il ++n +d   l
  gi|70606615|ref|YP_255486.1| 213 VNYLSDILSLTNLSDYTRL 231
                                   5666667666666655443 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0078        28      17     114 ..      23     113 ..      15     126 .. 0.72
   2 !   40.0   0.1   1.1e-13   3.9e-10       5     128 .]     139     258 ..     133     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0078
                                   HHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-S CS
                        PCNA_C  17 efaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftkatsLse 97 
                                   + + i+  l+++ d+    + ++g++ +a     +a + l + +    +e + + e+++  ++ f  +Yla++   +   e
  gi|70606615|ref|YP_255486.1|  23 DLKNIVETLTKFIDEGLFEIGQDGIRLVAV---DKAHVSLINIEL--YKELFKEYEVEDEFKFGFNSQYLAKILSIAKRKE 98 
                                   667888888888888888999999998884...455555554443..346777889999999*******999876555444 PP

                                   EEEEEEETTSEEEEEEE CS
                        PCNA_C  98 rvtlslssevPlvveyk 114
                                     ++s+ s+ P  v+ +
  gi|70606615|ref|YP_255486.1|  99 --EISIESDSPERVKIT 113
                                   ..466667777766655 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 1.1e-13
                                   SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHH CS
                        PCNA_C   5 seydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkY 85 
                                   +e++   +l+s  f+  + ++s + d+v i +  + v  + +G  Gs      +++ +++    + +e k+  +  + ++Y
  gi|70606615|ref|YP_255486.1| 139 LEFEVKASLSSKAFKTTINEISAVTDTVDIIAVEDKVILKGEGKEGSQ----IENEFSKDTGAISDMEFKNEAKSPYDVNY 215
                                   67888899*************************************998....45666778888999*************** PP

                                   HHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-BS CS
                        PCNA_C  86 laeftkatsLservtlslssevPlvveykikdvgllayllakk 128
                                   l ++   t Ls+   l +s e Pl +e++++ +g ++ylla+k
  gi|70606615|ref|YP_255486.1| 216 LSDILSLTNLSDYTRLAFSTEKPLELEFNMEGGGKVTYLLAPK 258
                                   *****************************************97 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.3e-09   1.2e-05       5     105 ..      17     106 ..      13     125 .. 0.86
   2 !   13.8   0.2   6.2e-06     0.022     166     261 ..     142     231 ..     132     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.3e-09
                          Rad1   5 tlsnvseLatlLksiafkd.kalvqissdGlkfi.vednrvlqaqafldkalFtsYtfenaqddedeedeeedsvsfevsL 83 
                                   + ++v+ L ++ ++++ +  + l +i +dG++++ v++++v  ++  l+k+lF++Y++             ed+ +f ++ 
  gi|70606615|ref|YP_255486.1|  17 VYDDVRDLKNIVETLTKFIdEGLFEIGQDGIRLVaVDKAHVSLINIELYKELFKEYEV-------------EDEFKFGFNS 84 
                                   67899*********9977648***********75389*********************.............7899999*** PP

                          Rad1  84 sallecLnifgkndssskesss 105
                                   + l++ L+i +++++ s es s
  gi|70606615|ref|YP_255486.1|  85 QYLAKILSIAKRKEEISIESDS 106
                                   ********99999988765544 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.2e-06
                          Rad1 166 vlkvilkselLhsalteLdatskklkilassekkapvfalsakgelgs.sevefpneksvlekfevsslsessessYkfal 245
                                    +k  l s+ +++ ++e++a+++++ i+a +        l+++g+ gs  e ef+++   +  +e +  +e+++  Y++++
  gi|70606615|ref|YP_255486.1| 142 EVKASLSSKAFKTTINEISAVTDTVDIIAVED----KVILKGEGKEGSqIENEFSKDTGAISDMEFK--NEAKSP-YDVNY 215
                                   578899************************95....68999***999989*****************..777777.***** PP

                          Rad1 246 lkkaakalalssKvsl 261
                                   l+ + + ++ls  + l
  gi|70606615|ref|YP_255486.1| 216 LSDILSLTNLSDYTRL 231
                                   **99999988876655 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.4   4.7e-11   1.7e-07       3     228 ..      26     247 ..      24     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.7e-11
                          Rad9   3 ralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekv 83 
                                    ++++l ++ de  +ei++dg++l +v+ ++ +   ++l k++F++y  ev++++++  +   + +++ s +   k  e++
  gi|70606615|ref|YP_255486.1|  26 NIVETLTKFIDEGLFEIGQDGIRLVAVDKAHVSLINIELYKELFKEY--EVEDEFKFGFNSQYLAKIL-SIA---KRKEEI 100
                                   6899*******************************************..8999999999999999***.777...444556 PP

                          Rad9  84 kisidekksrlivqllCkhg.vkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitielakervll 163
                                   +i+  ++  r++++l    + v    +i++   e  +++++ e    k + +s+ ++  +++ s  ++++ i + +++v+l
  gi|70606615|ref|YP_255486.1| 101 SIES-DSPERVKITLGGALNrVFIINNIQVSPPEVPEVNLEFE---VKASLSSKAFKTTINEISAVTDTVDIIAVEDKVIL 177
                                   6665.7788******9875437777788888777778887544...57789****************************** PP

                          Rad9 164 k......syeeeekdnkkalstelsideeeFeqyqlaedveitlslkefkallvfaeslsaslslafdeaG 228
                                   k      s  e+e  ++ +  +++ +++e    y+++   +i lsl ++   + +a s++ +l+l+f+  G
  gi|70606615|ref|YP_255486.1| 178 KgegkegSQIENEFSKDTGAISDMEFKNEAKSPYDVNYLSDI-LSLTNLSDYTRLAFSTEKPLELEFNMEG 247
                                   933333333333444467777888888888888888888887.8999999999999999999999998766 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3   0.00011       0.4     117     205 ..      11     101 ..       2     105 .. 0.89
   2 ?    0.5   0.2      0.09   3.2e+02     150     165 ..     155     170 ..     137     232 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                      PhoU_div 117 lallkktveaiealaevieeleklletalskk..diveeieslEdeiDqlqrklikklfsredasnplevlllveiiekle 195
                                   l ++ ++ + ++ l++++e l k ++++l +   d +  +     ++ +++++l+k+lf++ +++   ++ + +++  k+ 
  gi|70606615|ref|YP_255486.1|  11 LLIMRIVYDDVRDLKNIVETLTKFIDEGLFEIgqDGIRLVAVDKAHVSLINIELYKELFKEYEVEDEFKFGFNSQYLAKIL 91 
                                   568899999****************9999754669999999999999********************************** PP

                      PhoU_div 196 nvsdraedva 205
                                    ++ r e+++
  gi|70606615|ref|YP_255486.1|  92 SIAKRKEEIS 101
                                   *****99987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.09
                      PhoU_div 150 iveeieslEdeiDqlq 165
                                    ++ei+ + d +D++ 
  gi|70606615|ref|YP_255486.1| 155 TINEISAVTDTVDIIA 170
                                   4444444444444432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1691.17
//
Query:       gi|70606617|ref|YP_255487.1|  [L=324]
Description: 5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-20   73.3   2.3    2.4e-20   73.3   2.3    1.7  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    0.00044   19.6   0.0      0.002   17.4   0.0    2.0  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
  ------ inclusion threshold ------
      0.014   15.4   0.4      0.049   13.6   0.0    2.0  2  DUF2150      Uncharacterized protein conserved in archaea (DU
       0.11   12.5   1.4        2.6    8.0   0.1    2.4  2  Lipase_GDSL  GDSL-like Lipase/Acylhydrolase


Domain annotation for each model (and alignments):
>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.18   8.1e+02     164     195 ..      22      53 ..      18      74 .. 0.72
   2 !   73.3   2.3   5.4e-24   2.4e-20     108     310 ..      83     285 ..      76     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.18
                                   -EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT CS
                   Meth_synt_1 164 skakeekveklellekLlpvYkelleeLkeag 195
                                   s+ k++k+ek +++e+L++  k++lee+ke  
  gi|70606617|ref|YP_255487.1|  22 SRLKSGKIEKSKAYEELMKFEKRILEEVKEYE 53 
                                   66666777777777777777777777776644 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 5.4e-24
                                   EEESTTSS-EEEE-BE-SS.----S-T..HHHHHHHHH.HHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHH CS
                   Meth_synt_1 108 mtkwFntnYHYlvPelekdtefklase..klleevkea.kalgieakpvllGpltflkLskakeekveklellekLlpvYk 185
                                   + ++F+ n+ Y +  ++++  +k +++  +++++vke  k l  + k+v+lGpltfl+L++++  + +  +++++  +  +
  gi|70606617|ref|YP_255487.1|  83 LERFFDNNFYYRKIVINQKLGYKSQNDyvQYFKQVKEIsKDLKSKIKIVILGPLTFLQLAENNYYD-DVGNIIDDYAKSTN 162
                                   689********999999888888775422889*****9999***********************99.999*********** PP

                                   HHHHHHHHTT-SEEEEE-GGGGSSG.CHHHHHHHHHHHHHHTCCTTTSEEEEE--SS-.CCHHHHHTTSSTSEEEEETSS. CS
                   Meth_synt_1 186 elleeLkeagvewvqidEPalvldl.ekeelealkeaYeelakekkelklllatyFdsvaealellaelpveglglDlvr. 264
                                   +ll++L +   ++v+++EP l  +  + + l++ +++Ye+l  +  + +  + tyFd   + ++ l++lp + +g+D+++ 
  gi|70606617|ref|YP_255487.1| 163 SLLRDLIDY-YDVVEVHEPSLFQKGiKGALLQSSQQVYEKLF-NGINKEKHVLTYFDIRFDRIQYLLNLPADYFGFDVTEq 241
                                   ******998.9********998765388899**********6.6777778899*************************985 PP

                                   HCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHHH CS
                   Meth_synt_1 265 aeenlealkkaglpedkvLsaGvidGrniWradlekalelleelae 310
                                   ++++l  l   g+ +d  +++Gvid rn     +++  +++e+++e
  gi|70606617|ref|YP_255487.1| 242 NKTKLGRLY--GYMKDMNVYLGVIDSRNTKMDKISTIRRIIEKVHE 285
                                   556666555..699**************999999888888888876 PP

>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.6e-07     0.002       1     286 [.       3     283 ..       3     294 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-07
                                   S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS CS
                   Meth_synt_2   1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkn 81 
                                   + T+ +GS+P+  ++ ++  ++k+g++++ + ++ + +  ++++++ +e ++D   +g     d  +     l+g+ + + 
  gi|70606617|ref|YP_255487.1|   3 FYTALVGSYPKPVKIAKVISRLKSGKIEKSKAYEELMKFEKRILEEVKEYELDYTTDGMVGWDDIADLTTSFLEGVEKGAL 83 
                                   67999************************777777777889*****************98777777776777777633333 PP

                                   --EEEETTEEE---EE-SS-...--SS-SSTHHHHHHTTS-SS-.BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHH CS
                   Meth_synt_2  82 gwvqsygsrcvrppiivgdv...srpaamtvkesalaqsltdkp.vkglltGpvtilnwsfvrddvdraeaaaqialalrd 158
                                   +      + ++r  +i + +   s++  +++ +++   s + k+ +k ++ Gp t l+ +      d  +++ + a     
  gi|70606617|ref|YP_255487.1|  84 ERFFDN-NFYYRKIVINQKLgykSQNDYVQYFKQVKEISKDLKSkIKIVILGPLTFLQLAENNYYDDVGNIIDDYAKSTNS 163
                                   322211.12222223332220003333344444444444444445788888888888887777555666777888888888 PP

                                   HHHHHHHTT-SEEEEE-TTS.STT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEE CS
                   Meth_synt_2 159 evkdLeaaGikviQiDepal.reGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvit 238
                                    ++dL +    v+ + ep l ++G+     +     +  v + + +  +++++  v t +  +++ d ++ + +l +D   
  gi|70606617|ref|YP_255487.1| 164 LLRDLIDY-YDVVEVHEPSLfQKGIKGALLQS----SQQVYEKLFN--GINKEKHVLTYF--DIRFDRIQYLLNLPADYFG 235
                                   88888777.78888888854133333222111....1122232222..335555555544..3333444666666666666 PP

                                   ESBSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCH CS
                   Meth_synt_2 239 ieasrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikka 286
                                    +  ++++  l  l     + +v lGv+d    +++    i+ +i+k+
  gi|70606617|ref|YP_255487.1| 236 FDVTEQNKTKLGRLYGYMKDMNVYLGVIDSRNTKMDKISTIRRIIEKV 283
                                   666666666666666666666666666666666666666666666665 PP

>> DUF2150  Uncharacterized protein conserved in archaea (DUF2150)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.049      43      80 ..      15      52 ..      14      64 .. 0.88
   2 ?   -1.5   0.1      0.48   2.1e+03      61      79 ..     268     286 ..     263     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                       DUF2150 43 lavlkiikaveeeelskeeAleeleevreivleeveed 80
                                  + ++k+i+++++++++k++A eel + ++ +leev+e 
  gi|70606617|ref|YP_255487.1| 15 VKIAKVISRLKSGKIEKSKAYEELMKFEKRILEEVKEY 52
                                  5799******************************9984 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.48
                       DUF2150  61 eAleeleevreivleevee 79 
                                   + +++++++r+i+ + +e+
  gi|70606617|ref|YP_255487.1| 268 TKMDKISTIRRIIEKVHEK 286
                                   5689999999999776665 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00058       2.6      99     170 ..     109     173 ..      98     184 .. 0.66
   2 ?    3.3   0.1     0.016        73     100     130 ..     273     303 ..     181     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00058
                                   HHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCHHHHHHHHHHHHHHHHHHHHHCTEEEECHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Lipase_GDSL  99 yiknlreaikelkeegapkaivvlvsppglgpqeekdakklgekgnefvgeynqrlndlaekdgfavvDlyd 170
                                    + ++ + +ke+++ + +k+++v+++p+ + +     +++ ++++ ++++ y++  n+l++     ++D yd
  gi|70606617|ref|YP_255487.1| 109 DYVQYFKQVKEISKDLKSKIKIVILGPLTFLQ---LAENNYYDDVGNIIDDYAKSTNSLLR----DLIDYYD 173
                                   444444556777767779**************...66666666666666666666666666....3333333 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHTTEEEEEEE-SSTCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Lipase_GDSL 100 iknlreaikelkeegapkaivvlvsppglgp 130
                                   i+ +r  i+ ++e+ga+ +i+ ++s+ ++ p
  gi|70606617|ref|YP_255487.1| 273 ISTIRRIIEKVHEKGAKSLIIGNSSFNDFIP 303
                                   6789999*****************9999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2211.47
//
Query:       gi|70606618|ref|YP_255488.1|  [L=339]
Description: methionine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-64  217.1   0.0    4.6e-64  216.7   0.0    1.0  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    8.1e-14   51.8   1.6    1.2e-12   48.0   1.5    2.0  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
  ------ inclusion threshold ------
      0.079   13.4   0.2       0.23   11.9   0.1    1.9  2  DUF4830      Domain of unknown function (DUF4830)


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.7   0.0   7.8e-68   4.6e-64       1     320 [.       8     314 ..       8     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 7.8e-68
                                   S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS CS
                   Meth_synt_2   1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkn 81 
                                   lpTt+iGS+P  + +re+ +  ++g++++e+ e+a ++++ +vvr+ +e+g+Dv  +ge+ R +mve+f+e+l+gf f   
  gi|70606618|ref|YP_255488.1|   8 LPTTVIGSYPRPKWLRETIRLHRAGKVNQEDLEEAFNDAVVTVVRDHQEAGIDVPTDGEMRRDEMVEFFAERLSGFKF--Y 86 
                                   79*************************************************************************977..5 PP

                                   --EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-.BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHH CS
                   Meth_synt_2  82 gwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkp.vkglltGpvtilnwsfvrddvdraeaaaqialalrdevk 161
                                   g v   g+ ++r p + g + ++++m + e   a+s+   + +k  +tGp ti +ws+ +    ++++a+++a ++ +e+k
  gi|70606618|ref|YP_255488.1|  87 GHVRVWGDHYYRKPSVTGKIKYNNPMLLDEVNFAKSVSYTQnLKVTITGPYTISEWSYNEYYKTQRDMAFDLAKVINQEIK 167
                                   789999**************************99998766559*****************99******************* PP

                                   HHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEEESBS CS
                   Meth_synt_2 162 dLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvitieas 242
                                   +L + GikviQ+Depa+ +     k    + ++wa ++  +++++ +++++v +H+Cy e+  + +++++l+vD i++   
  gi|70606618|ref|YP_255488.1| 168 NLVDIGIKVIQVDEPAIHTR----K----EDVEWAIDS--INESIKGVNVKVVLHVCYGEYSYLEPHLDKLKVDQINLALK 238
                                   ****************9764....4....456799986..8999999*****************9**************** PP

                                   SS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHHHHHHHHHH CS
                   Meth_synt_2 243 rsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCGLktrkreearaalknmvd 320
                                   + +   ++ +++  ++r++g+Gv+d+h  +++s+ee+a+ ++k l+  + e +wvnPdCGLk ++r+ a ++l nmv+
  gi|70606618|ref|YP_255488.1| 239 NYNYTPVKLFKK--WDREIGVGVIDVHNRKIESVEEVAEDLRKLLEYFKPEMVWVNPDCGLKLLPRKIALQKLINMVK 314
                                   ***99*****99..**************************************************************97 PP

>> Meth_synt_1  Cobalamin-independent synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.022   1.3e+02      17      59 ..      23      65 ..      11      75 .. 0.83
   2 !   48.0   1.5     2e-16   1.2e-12     117     310 ..      96     282 ..      92     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                                  HHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHCTT-SBEEES CS
                   Meth_synt_1 17 kkalesywkgkiseeeLektakeLrakhwkkqkeagidlipvn 59
                                  ++++  + +gk+++e+Le+  ++   + ++  +eagid+ + +
  gi|70606618|ref|YP_255488.1| 23 RETIRLHRAGKVNQEDLEEAFNDAVVTVVRDHQEAGIDVPTDG 65
                                  5556666789****************************87655 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 2e-16
                                   EEEE-BE-SS.----S-THHHHHHHHHHHTTG..GEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT CS
                   Meth_synt_1 117 HYlvPelekdtefklaseklleevkeakalgi..eakpvllGpltflkLskakeekveklellekLlpvYkelleeLkeag 195
                                    Y +P ++   ++k+++  ll+ev+ ak+  +  + k ++ Gp+t    s ++  k ++ ++  +L +v ++ +++L + g
  gi|70606618|ref|YP_255488.1|  96 YYRKPSVTG--KIKYNNPMLLDEVNFAKSVSYtqNLKVTITGPYTISEWSYNEYYK-TQRDMAFDLAKVINQEIKNLVDIG 173
                                   467788885..699*************8776522789*************999999.8888999***************** PP

                                   -SEEEEE-GGGGSSGCHHHHHHHHHHHHHHTCCTTTSEEEEE--SS-.CCHHHHHTTSSTSEEEEETSS.HCHHHHHHHHC CS
                   Meth_synt_1 196 vewvqidEPalvldlekeelealkeaYeelakekkelklllatyFdsvaealellaelpveglglDlvr.aeenlealkka 275
                                   ++++q+dEPa+ +  e+ e+ a++++ e++  +  ++k++l+  +++ +     l +l+v+ + l l + + + ++ +kk 
  gi|70606618|ref|YP_255488.1| 174 IKVIQVDEPAIHTRKEDVEW-AIDSINESI--KGVNVKVVLHVCYGEYSYLEPHLDKLKVDQINLALKNyNYTPVKLFKK- 250
                                   **********9988665555.678888888..899*****************************9997644444444444. PP

                                   TT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHHH CS
                   Meth_synt_1 276 glpedkvLsaGvidGrniWradlekalelleelae 310
                                       d+ + +Gvid +n     +e++ e l++l e
  gi|70606618|ref|YP_255488.1| 251 ---WDREIGVGVIDVHNRKIESVEEVAEDLRKLLE 282
                                   ...79***********9999999999998888765 PP

>> DUF4830  Domain of unknown function (DUF4830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.9e-05      0.23      17      53 ..     129     168 ..     113     171 .. 0.73
   2 ?   -3.1   0.0         2   1.2e+04       4      10 ..     239     245 ..     228     279 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                       DUF4830  17 kevki..Pkefeev.yaeynelqkdiGldLekykgkevtr 53 
                                    +v+i  P +++e  y+ey ++q+d+ +dL+k+ ++e++ 
  gi|70606618|ref|YP_255488.1| 129 LKVTItgPYTISEWsYNEYYKTQRDMAFDLAKVINQEIKN 168
                                   444441245554447*********************9986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                       DUF4830   4 kygwsve 10 
                                   +y +++ 
  gi|70606618|ref|YP_255488.1| 239 NYNYTPV 245
                                   3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1032  (0.0575604); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2110.37
//
Query:       gi|70606619|ref|YP_255489.1|  [L=153]
Description: 30S ribosomal protein S15 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-23   80.2   0.1    2.7e-22   78.6   0.0    1.8  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    6.6e-14   51.9   0.1    9.4e-14   51.4   0.1    1.2  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.044   14.3   0.0      0.074   13.6   0.0    1.3  1  DUF2408          Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   4.5e-26   2.7e-22       5      60 .]       3      58 ..       1      58 [. 0.97
   2 ?   -1.5   0.0      0.45   2.7e+03      31      41 ..     114     124 ..     106     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 4.5e-26
                                  SSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
               Ribosomal_S13_N  5 hsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                  ++r kG S+S rP+r  +p+W++++ eeve l+ +lak+G++pS+IG++LRDqyGv
  gi|70606619|ref|YP_255489.1|  3 KKRAKGNSHSIRPVRSGPPKWVRFTREEVELLVEELAKRGYPPSMIGMVLRDQYGV 58
                                  4899***************************************************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.45
                                   HHHHHHHHHHH CS
               Ribosomal_S13_N  31 eeveelivkla 41 
                                   eeve++i +la
  gi|70606619|ref|YP_255489.1| 114 EEVESKIRRLA 124
                                   78999888776 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.1   1.6e-17   9.4e-14       8      80 ..      76     146 ..      69     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.6e-17
                                   HSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCTS CS
                 Ribosomal_S15   8 fqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklgl 80 
                                    + ++    ++++++ +l++r++n+++hl e +kDk+++rgL +++sk+r+l  Y+k++ +  +++ +  +k++l
  gi|70606619|ref|YP_255489.1|  76 RNMKP----KIPEDLFNLMRRAVNIRRHLFEYPKDKSAKRGLEEVESKIRRLASYYKETGKlpQEWSYDPAKAEL 146
                                   55555....899***********************************************9999*****9999887 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.074       3      67 ..      81     136 ..      80     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                       DUF2408   3 elspelepiyekLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskrdeegkFkse 67 
                                   +++++l +++ + v+irr+L+++  +++a+           l+e++++++++ s  +e+gk  +e
  gi|70606619|ref|YP_255489.1|  81 KIPEDLFNLMRRAVNIRRHLFEYPKDKSAK---------RGLEEVESKIRRLASYYKETGKLPQE 136
                                   699********************9888875.........77888888888888888887777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1070.78
//
Query:       gi|70606620|ref|YP_255490.1|  [L=123]
Description: sirohydrochlorin cobaltochelatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-27   96.5   0.1    1.2e-27   96.3   0.1    1.0  1  CbiX            CbiX
    3.8e-05   23.1   0.0    4.2e-05   23.0   0.0    1.2  1  CbiK            Cobalt chelatase (CbiK)
  ------ inclusion threshold ------
      0.036   13.1   0.0      0.036   13.1   0.0    1.3  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.1     2e-31   1.2e-27       1     107 []       9     109 ..       9     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2e-31
                                   -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SS CS
                          CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaee 81 
                                   HGS+ +e++e v + aeel+++ p   ve+gf+e++ep+++ea ++l+e+g++ ivvvPl+++aG+h+k+DIp++l+e  +
  gi|70606620|ref|YP_255490.1|   9 HGSKIKEWQEIVINYAEELKRHFP--LVEYGFIEINEPKIDEAAKKLVERGADTIVVVPLLFAAGMHFKRDIPNQLKETSN 87 
                                   9********************777..****************************************************999 PP

                                   SS-TTEEEEE---CCCSCCHHHHHHH CS
                          CbiX  82 ahpkdveieytepLGthplvaevlke 107
                                   + +    i+++ep+G +++++++lke
  gi|70606620|ref|YP_255490.1|  88 KAK----IIIAEPIGFDKRIVDILKE 109
                                   999....****************986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   7.1e-09   4.2e-05     146     220 ..       6      81 ..       3     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.1e-09
                                   EEE---SCHHHH.HHHHHHHHHHHCT-S.EEEEETT.SSS-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSS CS
                          CbiK 146 fvgHGtehesna.vyaeldkvlkekdfkqvvvgtve.gyPeveevieelkkkgikevkliPlmlvAGdHaknDmasd 220
                                   +v HG++ +  + +  +  + lk  +f  v  g +e   P+++e  ++l ++g+ ++ ++Pl++ AG H k+D+ ++
  gi|70606620|ref|YP_255490.1|   6 LVLHGSKIKEWQeIVINYAEELKR-HFPLVEYGFIEiNEPKIDEAAKKLVERGADTIVVVPLLFAAGMHFKRDIPNQ 81 
                                   566777665433033334444444.47888889998558**********************************9664 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     6e-06     0.036     241     313 ..      43     111 ..       3     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-06
                                   SSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHH CS
                Ferrochelatase 241 ePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlv 313
                                   eP++d++ ++l e+g++ ivvvp+ F++  +  + ++  +++e+ ++a++     ++ ++ +++++++l++ +
  gi|70606620|ref|YP_255490.1|  43 EPKIDEAAKKLVERGADTIVVVPLLFAA-GMHFKRDIPNQLKETSNKAKI---IIAEPIGFDKRIVDILKEKA 111
                                   7999999999999999999999998877.677888888888888888655...66666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 980.97
//
Query:       gi|70606621|ref|YP_255491.1|  [L=213]
Description: 30S ribosomal protein S6 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-23   83.6   0.8      3e-22   78.9   0.0    2.4  2  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.0   0.1    0.0054        98       1      18 [.       4      21 ..       4      52 .. 0.78
   2 !   78.9   0.0   1.7e-26     3e-22      13     113 ..     116     212 ..     109     213 .] 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0054
                                  -EEEEEETTTTEEEEEE- CS
                 Ribosomal_S6e  1 mklnisdpatgkqkliev 18
                                  +k+++sdp+t++ k+ ++
  gi|70606621|ref|YP_255491.1|  4 FKIVVSDPKTKEDKKEKL 21
                                  799******998876554 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 1.7e-26
                                   EEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSSSS-EEE CS
                 Ribosomal_S6e  13 qklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprrkGerkr 93 
                                   + ++ +d++kl +l+g +ig+ +d ++ G    + +lkitggsd++Gf m+ +v +  ++++L+s+  +gy p+++G r++
  gi|70606621|ref|YP_255491.1| 116 AFQLSLDQSKLPNLVGTKIGDVIDINVSG---VNLKLKITGGSDNSGFSMRFDVGGGAKRKILVSG-PPGYYPKEDGLRRK 192
                                   5677789**********************...899******************************9.************** PP

                                   EEEE-SB--SSEEEEEEEEE CS
                 Ribosomal_S6e  94 ksvrGcivsadisqlnlviv 113
                                   ++vrG++++ +i+q+n++++
  gi|70606621|ref|YP_255491.1| 193 RTVRGNMITPEIVQINTIMI 212
                                   ****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1564.26
//
Query:       gi|70606622|ref|YP_255492.1|  [L=416]
Description: translation initiation factor IF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-29  103.0   0.1    7.9e-29  100.6   0.1    2.0  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.5e-25   89.3   1.3    3.6e-25   88.0   1.3    1.7  1  eIF2_C       Initiation factor eIF2 gamma, C terminal
    2.5e-09   37.4   0.4    2.3e-08   34.3   0.2    2.4  2  GTP_EFTU_D2  Elongation factor Tu domain 2
      1e-05   25.5   0.0    4.3e-05   23.6   0.0    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00011   22.2   0.1     0.0054   16.7   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
     0.0055   16.5   0.2        0.6    9.8   0.0    2.4  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.1   2.6e-32   7.9e-29       4     193 ..      10     203 ..       7     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 2.6e-32
                                   EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................... CS
                      GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................... 64 
                                    nig++ghvDhGKtTL+ +L+   g+ +             +++eE +rg+Tik   ++ +                    
  gi|70606622|ref|YP_255492.1|  10 ANIGVVGHVDHGKTTLVQALT---GIWT------------SKHSEELKRGMTIKLGYAEANiglcescklpdgyvtepscs 75 
                                   69******************9...5533............356789999999999999999999999999999999***** PP

                                   ......TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.H CS
                      GTP_EFTU  65 ......ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.k 136
                                         + +  +++++iD+PGH+  + ++  g++ +Dga+lvv+a+e  ++pqt+e++  +  ++v+ ++++ NK+D + +
  gi|70606622|ref|YP_255492.1|  76 qcnsseEPKFLRKVSFIDAPGHEILMATMLSGAALMDGAILVVAANEPfPQPQTREHFVALGIVDVKrLVIVQNKVDVVsR 156
                                   99875334556799*********************************989*****************999999******99 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                      GTP_EFTU 137 aelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                   +e  ++ ++++ ++      l+  ++++    p++++S+l++ ++++++ al +++p
  gi|70606622|ref|YP_255492.1| 157 EEAIKQYKQIR-EF------LKGTWAEN---APIIPASSLHKINIDAVIGALQDHIP 203
                                   99999999999.55......56666665...6***********************98 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   1.3   1.2e-28   3.6e-25       3      86 .]     330     415 ..     328     415 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 1.2e-28
                                   EEEE.EEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-S.TTEEEEEEEEETTSEEEE CS
                        eIF2_C   3 leie.yellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcae.kgekialsRrvekrWrLi 81 
                                   ++ie ++ller+vg+ke  kv++++ kE+Lm++ Gsa+t+gv +svk+  ++v+Lk+P++ + k+ +i++sR++++rWrLi
  gi|70606622|ref|YP_255492.1| 330 VTIEnFQLLERVVGTKELVKVDSIRPKESLMISFGSATTIGVTKSVKGGRVEVELKRPIVLWdKNLRIVVSRQIGGRWRLI 410
                                   556449******************************************************997899*************** PP

                                   EEEEE CS
                        eIF2_C  82 GwGei 86 
                                   GwG+i
  gi|70606622|ref|YP_255492.1| 411 GWGII 415
                                   ***97 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.35     1e+03      13      21 ..      41      49 ..       8      57 .. 0.85
   2 !   34.3   0.2   7.8e-12   2.3e-08       1      62 [.     235     304 ..     235     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                                  EETTEEEEE CS
                   GTP_EFTU_D2 13 lkkGdevri 21
                                  lk+G+++++
  gi|70606622|ref|YP_255492.1| 41 LKRGMTIKL 49
                                  788888877 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 7.8e-12
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEE........EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke........ivtrissletfhededeavaganaGvivaikg 62 
                                   G+v++g++++G++k+Gde++il+     +k+          t+iss+  +  +++ea +g+ + +++++++
  gi|70606622|ref|YP_255492.1| 235 GGVIGGSIIQGKFKVGDEIKILPgI-RIEKPdgkaeyipLYTTISSIRFMDLEVEEAKPGGLVAIGTKLDP 304
                                   89*********************66.568889********************************9999875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.4e-08   4.3e-05       1      88 [.      11     122 ..      11     183 .. 0.65
   2 ?   -1.6   0.0      0.92   2.8e+03      29      52 ..     368     392 ..     364     393 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.4e-08
                                   EEEEEESTTSSHHHHHHHHHTS.TEEE..SSSTTSSSSEEEEEEEET..TEE...........................EE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaiv..sdkpgtTrdinegrvklk..gke...........................ie 49 
                                   ++++vG+   GK+tL++altg  +++   + k g T++  +++ +++  + +                           + 
  gi|70606622|ref|YP_255492.1|  11 NIGVVGHVDHGKTTLVQALTGIwTSKHseELKRGMTIKLGYAEANIGlcE-ScklpdgyvtepscsqcnsseepkflrkVS 90 
                                   599******************66554401556699999999988855330.1334444445555555555566666666** PP

                                   EEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTT CS
                      MMR_HSR1  50 lvDtpGliegaseekglgkaflalee.adlillvvdasee 88 
                                   ++D pG  e       l  ++l+    +d ++lvv a+ e
  gi|70606622|ref|YP_255492.1|  91 FIDAPG-HE------ILMATMLSGAAlMDGAILVVAAN-E 122
                                   ******.43......56666666555467777777755.3 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.92
                                   STTSSSSEEEEEEEETT.EEEEEEE CS
                      MMR_HSR1  29 kpgtTrdinegrvklkg.keielvD 52 
                                   + g+T+ ++ grv+++  ++i+l+D
  gi|70606622|ref|YP_255492.1| 368 TIGVTKSVKGGRVEVELkRPIVLWD 392
                                   5699*******99966558899988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.023        70     104     137 ..      14      44 ..       6      47 .. 0.84
   2 !   16.7   0.0   1.8e-06    0.0054      13      92 ..     108     193 ..      85     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.023
                                   EECSTTSSHHHHHHHHCTT-----S--------- CS
                   RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                   +vG+   GK+tL+ al++     t++ se+l+rG
  gi|70606622|ref|YP_255492.1|  14 VVGHVDHGKTTLVQALTGI---WTSKHSEELKRG 44 
                                   6788889*********986...788888888888 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.8e-06
                                   EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTTH CS
                   RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee......eleelkeelealgyevllvsaktk 87 
                                   +a +d +++vv+++ep  ++++ + f++l      ++viv nK+D++++ee      +++e+ + + a + +++  s+ +k
  gi|70606622|ref|YP_255492.1| 108 AALMDGAILVVAANEPFPQPQTREHFVALGIVDVKRLVIVQNKVDVVSREEaikqykQIREFLKGTWAENAPIIPASSLHK 188
                                   8899**********9*9999999999999999999****************555333333333333344555555555555 PP

                                   TTHHH CS
                   RsgA_GTPase  88 eglee 92 
                                    ++++
  gi|70606622|ref|YP_255492.1| 189 INIDA 193
                                   55555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0002       0.6       4      23 ..      12      31 ..       9      56 .. 0.83
   2 !    4.4   0.0    0.0094        28      88     141 ..     140     198 ..      86     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                     PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                  i ++G+v+ GKttL qal+g
  gi|70606622|ref|YP_255492.1| 12 IGVVGHVDHGKTTLVQALTG 31
                                  6689**************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0094
                     PduV-EutP  88 fnkeviGiitkidlaedeeniea...veelLksaGaek..ifevsavekegieellkyl 141
                                     k ++ +  k+d+++ ee+i++    +e+Lk   ae+  i+  s+++k++i+ ++  l
  gi|70606622|ref|YP_255492.1| 140 DVKRLVIVQNKVDVVSREEAIKQykqIREFLKGTWAENapIIPASSLHKINIDAVIGAL 198
                                   346666688999999999988751116778887777653379999*******9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2953.29
//
Query:       gi|70606623|ref|YP_255493.1|  [L=143]
Description: hypothetical protein Saci_0833 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-12   46.7   0.1    4.2e-12   46.4   0.1    1.1  1  PIN_9     PIN like domain
      1e-06   29.1   0.3    5.7e-05   23.4   0.3    2.0  1  PIN_4     PIN domain
    2.9e-06   27.8   0.6    8.8e-06   26.2   0.6    1.7  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.084   12.6   0.1       0.16   11.7   0.0    1.6  2  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.1   9.4e-16   4.2e-12       1     113 [.      13     130 ..      13     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 9.4e-16
                         PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkg.kertaakvalsL..aer..ceiveae.ee 74 
                                   +++Dtn Lm  v  g+d fe +   l  + e+ v ka + EL++  +++k+  +++ a+va+    +++   ++++   + 
  gi|70606623|ref|YP_255493.1|  13 ILVDTNILMN-VYDGIDPFELVISYLeYKPEFYVSKATIMELDKFLNEEKSvIKQKRARVAMLYleTNKssWTLIDEAdNI 92 
                                   679***9985.667**********997789*************98877777567788899865423222235566655255 PP

                         PIN_9  75 kaDdailelakeldaavlvTnDreLkkrllekgipvilL 113
                                    +D+ +lel k+++  ++ T+Dr Lk+r+l++gi+vi+L
  gi|70606623|ref|YP_255493.1|  93 LVDNLLLELCKQYNFIIF-TSDRILKNRALKEGIKVIYL 130
                                   5*************8888.*******************9 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   1.3e-08   5.7e-05       2     127 ..      14     127 ..      13     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                         PIN_4   2 VlDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsae 75 
                                    +DTn+l++  + ++ f       + + + ++   ++ ELdk+ ++++  ++ ++ r  + +l+ +++k+s++l ++++++
  gi|70606623|ref|YP_255493.1|  14 LVDTNILMNVYDGIDPFelvisylEYKPEFYVSKATIMELDKFLNEEK--SVIKQKRARVAMLYLETNKSSWTL-IDEADN 91 
                                   58**********************9**********************9..888888999999998888877777.443332 PP

                         PIN_4  76 elpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                               Dn  l+ + +        + ++++ D+ l+++A  +gi++
  gi|70606623|ref|YP_255493.1|  92 I---------LVDNLLLELCKQ-------YNFIIFTSDRILKNRALKEGIKV 127
                                   1.........345555555543.......36799999999999999999976 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.6     2e-09   8.8e-06       1     118 [.      13     118 ..      13     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2e-09
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                   i++DT++l ++++g +  e +   le   e ++s++++ El  +l+            +++ +  ++ ++  +  e  +  
  gi|70606623|ref|YP_255493.1|  13 ILVDTNILMNVYDGIDPFELVISYLEYKPEFYVSKATIMELDKFLNE-----------EKSVIKQKRARVAMLYLETNKSS 82 
                                   79**********9999999999999988*******************...........44444444444444446666666 PP

                                   HHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                           PIN  82 aeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                   + ++++++  + D l++ ++k+++++++ t D+ +++
  gi|70606623|ref|YP_255493.1|  83 WTLIDEADNILVDNLLLELCKQYNFIIF-TSDRILKN 118
                                   777777778889*************777.***98876 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   5.8e+03       2       9 ..      12      19 ..      11      24 .. 0.82
   2 ?   11.7   0.0   3.6e-05      0.16      26      62 ..      84     120 ..      68     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                       DUF5615  2 klllDenl 9 
                                  k+l+D n+
  gi|70606623|ref|YP_255493.1| 12 KILVDTNI 19
                                  89999997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.6e-05
                       DUF5615  26 hvrelglegasDeeileyAkeedriivTkDkDFgell 62 
                                   ++ ++ ++   D+  le++k+ ++ii+T D+   +++
  gi|70606623|ref|YP_255493.1|  84 TLIDEADNILVDNLLLELCKQYNFIIFTSDRILKNRA 120
                                   55566666688999****************8666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1035.19
//
Query:       gi|70606624|ref|YP_255494.1|  [L=183]
Description: DNA-directed RNA polymerase subunit E' [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   63.5   0.7    1.7e-17   63.5   0.7    1.6  2  S1             S1 RNA binding domain
    7.3e-16   58.3   0.1    1.4e-15   57.4   0.1    1.5  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
  ------ inclusion threshold ------
      0.072   13.3   0.0       0.13   12.5   0.0    1.5  1  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.9   1.1e+04      54      68 ..      23      37 ..      23      39 .. 0.80
   2 !   63.5   0.7   2.9e-21   1.7e-17       2      73 ..      79     148 ..      78     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                                  EEEEEEEEEEETTTT CS
                            S1 54 devkvkvlkvdkdrr 68
                                  de+  k+l+ +++++
  gi|70606624|ref|YP_255494.1| 23 DEIAIKILRQEYQEK 37
                                  789999999888876 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 2.9e-21
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEE CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriils 73 
                                   p ++ev+eGeV++v+++G++V++g +v+g+v++s++ +d+ ++d+++ + +G++ k+ ++k d+ r+ +i+s
  gi|70606624|ref|YP_255494.1|  79 PIIHEVIEGEVSQVDNYGVYVNMG-PVDGLVHISQITDDNLKFDSNRGILIGEKSKKSIQKGDRVRA-MIIS 148
                                   6689********************.****************************************99.6665 PP

>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   2.3e-19   1.4e-15       3      70 .]      10      77 ..       8      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.3e-19
                                  EEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                   SHS2_Rpb7-N  3 tvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                  +vr++P+y+g+ +++++ ++l++ y  k+++++Gv++ + + + ++eg ++ g+G++y++V+f++lv+
  gi|70606624|ref|YP_255494.1| 10 IVRIPPEYFGQSVDEIAIKILRQEYQEKLIKDIGVVLGIVNAKASEEGFIIFGDGATYHEVEFDMLVY 77
                                  7*****************************************************************97 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05      0.13       1      71 [.      79     146 ..      79     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                   -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEE CS
                 RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrv 71 
                                   P++ ev++g +++ ++ g+ v++g +d +    +   ++ +fd+++ + + e    ++  +++g+++r  +
  gi|70606624|ref|YP_255494.1|  79 PIIHEVIEGEVSQVDNYGVYVNMGPVDGLVHISQITDDNLKFDSNRGILIGEK---SKKSIQKGDRVRAMI 146
                                   8999**********************997666677788999999988876554...666777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1290.07
//
Query:       gi|70606625|ref|YP_255495.1|  [L=68]
Description: hypothetical protein Saci_0835 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-13   49.2   0.1    5.2e-13   48.9   0.1    1.1  1  Spt4            Spt4/RpoE2 zinc finger
     0.0031   17.4   2.1     0.0042   16.9   2.1    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0059   16.6   1.4     0.0079   16.2   1.4    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.012   16.3   1.1      0.015   16.0   1.1    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.022   14.8   3.0      0.038   14.1   3.0    1.4  1  UPF0547         Uncharacterised protein family UPF0547
      0.052   13.8   1.5      0.063   13.6   1.5    1.1  1  zf-C4H2         Zinc finger-containing protein
       0.11   12.1   1.6       0.15   11.7   1.6    1.2  1  RecR            RecR protein


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1     2e-16   5.2e-13       2      77 .]      10      68 .]       9      68 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2e-16
                          Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                  +AC++C+++++ ++   ++Cp C           +s+++s+e++G+v+il+++ S+v+++  +++++p+ YA+ v+
  gi|70606625|ref|YP_255495.1| 10 KACKNCRALVPPET---SICPLC-----------HSSSFSDEWNGMVIILNEK-SEVGQM--FGATTPWRYAIIVK 68
                                  9*************...******...........9***************987.******..***********995 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.1   1.6e-06    0.0042      14      36 ..      12      34 ..       9      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                       DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                  C++C ++ +PP+  +Cp C+s+++
  gi|70606625|ref|YP_255495.1| 12 CKNCRAL-VPPEtSICPLCHSSSF 34
                                  *******.7***9********876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.4   3.1e-06    0.0079      29      48 ..      10      29 ..       3      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-06
                           DZR 29 drCpsCgekvdpearfCpeC 48
                                  ++C +C + v+pe+++Cp C
  gi|70606625|ref|YP_255495.1| 10 KACKNCRALVPPETSICPLC 29
                                  67888888888888888888 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   1.1   5.9e-06     0.015      59      85 ..       3      29 ..       1      30 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                zinc_ribbon_15 59 kkessekkeCknCgkeveeefkyCpkC 85
                                  +k+ ++ k CknC++ v +e + Cp C
  gi|70606625|ref|YP_255495.1|  3 EKKGTSFKACKNCRALVPPETSICPLC 29
                                  45566689******************* PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.0   1.5e-05     0.038       1      20 [.      10      29 ..       6      29 .. 0.98

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                       UPF0547  1 KvCPeCeakvPvaaqfCphC 20
                                  K C+ C+a vP  + +Cp+C
  gi|70606625|ref|YP_255495.1| 10 KACKNCRALVPPETSICPLC 29
                                  89****************** PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.5   2.5e-05     0.063     178     204 ..       9      35 ..       2      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                       zf-C4H2 178 MKsClsChqqIHRNAPiCPlCKaKsRS 204
                                    K+C++C + +     iCPlC + s S
  gi|70606625|ref|YP_255495.1|   9 FKACKNCRALVPPETSICPLCHSSSFS 35 
                                   79*******************998865 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.6   5.8e-05      0.15      17      37 ..      10      32 ..       7      33 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                                  EE-TTT--E..ESSSS-CCCCST CS
                          RecR 17 rhCsrCgnl..teedlCaICsdp 37
                                  + C++C+ l   e+ +C+ C ++
  gi|70606625|ref|YP_255495.1| 10 KACKNCRALvpPETSICPLCHSS 32
                                  78*******999999*****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 547.66
//
Query:       gi|70606626|ref|YP_255496.1|  [L=164]
Description: hypothetical protein Saci_0836 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-34  117.0   0.1      5e-34  116.6   0.1    1.1  1  DUF359      Protein of unknown function (DUF359)
  ------ inclusion threshold ------
       0.93    9.5   6.0       0.71    9.9   0.2    2.7  2  Holin_BlyA  holin, BlyA family


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.1   5.6e-38     5e-34       1     125 [.      42     159 ..      42     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.6e-38
                        DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal.eseekvlilVdGEED 80 
                                   vt+++lk +ikP laivDgktkR+          ke+  ++e i+vkN++G i+ ++i++ik++l ++e++ +++VdGEED
  gi|70606626|ref|YP_255496.1|  42 VTQTILKFHIKPFLAIVDGKTKRK----LV----KENFGQFEYIKVKNEPGLIRLSTIREIKDILvHNENDKILMVDGEED 114
                                   8***********************....22....34668999***********************5555566667****** PP

                        DUF359  81 LavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                   L+v+p++++ + g++++YGqp++Gvv+   ++ +k+++ e+++kf
  gi|70606626|ref|YP_255496.1| 115 LLVIPVVIYGNFGDIIIYGQPNAGVVVTLNNDFLKRRVLEIFKKF 159
                                   *******************************************99 PP

>> Holin_BlyA  holin, BlyA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2     8e-05      0.71       5      38 ..      22      53 ..      18      63 .. 0.86
   2 ?    1.2   1.4     0.041   3.7e+02      10      21 ..      88      99 ..      84     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8e-05
                    Holin_BlyA  5 kllilLitldeiKLiilgiFvvllvlgvllllKP 38
                                  kl  +Li+  + +Li +g  v+  +l     +KP
  gi|70606626|ref|YP_255496.1| 22 KLKQFLINKSNSRLITVGDVVTQTILKF--HIKP 53
                                  8999******************999975..4566 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.041
                    Holin_BlyA 10 LitldeiKLiil 21
                                  L+t+ eiK i +
  gi|70606626|ref|YP_255496.1| 88 LSTIREIKDILV 99
                                  555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1291.77
//
Query:       gi|70606627|ref|YP_255497.1|  [L=413]
Description: cofactor-independent phosphoglycerate mutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-54  182.0   0.0    1.6e-53  181.0   0.0    1.5  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.2e-33  115.7   0.1    2.5e-33  115.5   0.1    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
      0.019   14.9   0.2      0.045   13.6   0.1    1.7  2  DUF4410        Domain of unknown function (DUF4410)
      0.073   12.6   0.0       0.13   11.8   0.0    1.6  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   3.6e-57   1.6e-53       2     170 .]      41     212 ..      41     212 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 3.6e-57
                                   HTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-.- CS
                  PhosphMutase   2 kkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragrist 82 
                                   k+++ Gl+d++++gi pgSd+++l+i+G dp kyy+GRG++EA+g+G +lk gdvafR+n++tvd ++ ++idrragr   
  gi|70606627|ref|YP_255497.1|  41 KNSIAGLMDPISPGIVPGSDTSHLAIFGIDPFKYYRGRGAFEAIGAGARLKAGDVAFRGNFATVD-NNLTVIDRRAGRK-V 119
                                   58999***********************************************************7.6***********9.9 PP

                                   TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS..SGGGHHHHHHHHHH CS
                  PhosphMutase  83 eeakeLikalneel.e.egvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellpl.kseeaketaellnel 156
                                   +eak L+++ln+++ e +gv+vkfy+g+e+r+++vl    lsdki+dtdp  +++g ++k+  ++ +++eak tae+ln+l
  gi|70606627|ref|YP_255497.1| 120 DEAKDLVQELNSKIgEiDGVQVKFYHGTEHRVAVVLsgkgLSDKISDTDP--HETGVKVKKSEATdDTREAKITAEVLNKL 198
                                   99*************899********************************..9***********9889999********** PP

                                   HHHHHHHHHHSHHH CS
                  PhosphMutase 157 ieksqeiLedhpvN 170
                                   ++++++iL++ ++N
  gi|70606627|ref|YP_255497.1| 199 TNRIYDILSSSELN 212
                                   *********99998 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.1   5.7e-37   2.5e-33       2     237 ..       5     393 ..       4     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 5.7e-37
                                   EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH............ CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 Metalloenzyme   2 kvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel............ 67 
                                   k++l + DGlG++p ++l+    ++  ++P++ +L k+       ++ g++ ++  ++ ++s+++Hl++            
  gi|70606627|ref|YP_255497.1|   5 KILLFIADGLGDRPVTKLEHktpLEAVEKPNIGELLKN-------SIAGLMDPISPGIVPGSDTSHLAIfgidpfkyyrgr 78 
                                   689************99888889***************.......89********************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Metalloenzyme  68 ................................................................................. 67 
                                                                                                                    
  gi|70606627|ref|YP_255497.1|  79 gafeaigagarlkagdvafrgnfatvdnnltvidrragrkvdeakdlvqelnskigeidgvqvkfyhgtehrvavvlsgkg 159
                                   ********************************************************************************* PP

                                   ......................................................HHHHTT-----EEEEEEEE-S---SSH CS
                                   ......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  68 ......................................................lrisetvkfahvtffwnggrsgyfnpl 94 
                                                                                         +ri++++ +a++++++++ ++ +++++
  gi|70606627|ref|YP_255497.1| 160 lsdkisdtdphetgvkvkkseatddtreakitaevlnkltnriydilssselnkKRIERGELPANIVLLRGAAQYVDLPKF 240
                                   ********************************************************************************* PP

                                   HHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHH CS
                                   xxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme  95 eereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleati 155
                                    ++++i+++ v ++ l                      ++++  +ae+a + + ++ +d+v++++k +D+++H+g++ ++ 
  gi|70606627|ref|YP_255497.1| 241 YDYTKINAAAVSATALikgicsqigmnvvtpkgatgGLDTNYIGKAEEASKLL-KE-YDMVFLHLKATDAASHDGNIDGKL 319
                                   ************************************9***********99999.66.************************ PP

                                   HHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT---.-S--S.SHHHHTT-TTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxx RF
                 Metalloenzyme 156 aaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglap.dkvke.gakfrekggLa 234
                                    ai  +D++++++ld    ++ i+++t+DH ++ ++++        Ht +pVP+l++ +     d+v   ++k  +kg+L 
  gi|70606627|ref|YP_255497.1| 320 YAISMIDKMIGRVLDI-YGSELIIAITGDHATPVEVKE--------HTGDPVPFLLYVPYNIVaDNVDDfNEKQLRKGSL- 390
                                   **************76.56666****************........**********999754414555567676668888. PP

                                   EEE CS
                                   xxx RF
                 Metalloenzyme 235 nva 237
                                   +++
  gi|70606627|ref|YP_255497.1| 391 RIK 393
                                   444 PP

>> DUF4410  Domain of unknown function (DUF4410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2   8.8e+03      55      73 ..      86     105 ..      81     107 .. 0.76
   2 ?   13.6   0.1     1e-05     0.045      12      68 ..     175     231 ..     164     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                       DUF4410  55 agt.lpkngllvegrftkvd 73 
                                   ag  l+++++  +g+f  vd
  gi|70606627|ref|YP_255497.1|  86 AGArLKAGDVAFRGNFATVD 105
                                   55568889999999999888 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1e-05
                       DUF4410  12 eiksddgseaasqqadakelvdamadaLvkeLkskglfarrsaagtlpkngllvegr 68 
                                   ++k+ ++++ +++++  +e+ ++++++++  L+s +l ++r++ g+lp+n +l++g+
  gi|70606627|ref|YP_255497.1| 175 KVKKSEATDDTREAKITAEVLNKLTNRIYDILSSSELNKKRIERGELPANIVLLRGA 231
                                   4666667899999******************************************97 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       2.1   9.3e+03      20      42 ..      32      53 ..       9      53 .. 0.80
   2 ?   11.8   0.0   2.9e-05      0.13     154     232 ..     280     348 ..     160     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 2.1
                                  TSHHHHHHHHHSEEESEEE-SSS CS
                  Phosphodiest 20 llpnlaaLakegvsapnlrpvfP 42
                                  + pn+ +L+k+++ +  ++p+ P
  gi|70606627|ref|YP_255497.1| 32 EKPNIGELLKNSIAGL-MDPISP 53
                                  7899999999999888.888766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.9e-05
                                   HHHHHCHTHSHHHHHCT..SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES- CS
                  Phosphodiest 154 qtwldaafakvvlekel..ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDH 232
                                    +++ +a+++     ++  +++d+++++l +tD+++H    +    + a++ +Dk+ig+ l+    +     + i +++DH
  gi|70606627|ref|YP_255497.1| 280 TNYIGKAEEA-----SKllKEYDMVFLHLKATDAASHDG--NIDGKLYAISMIDKMIGRVLDIYGSE-----LIIAITGDH 348
                                   3455555544.....3346******************76..43345789************999998.....889999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2766.11
//
Query:       gi|70606628|ref|YP_255498.1|  [L=747]
Description: ATP-dependent Zn protease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-100  332.1   0.0    1.6e-50  170.9   0.0    2.5  2  AAA              ATPase family associated with various cellul
    9.7e-30  102.1   0.8    3.2e-14   52.4   0.1    2.7  2  AAA_lid_3        AAA+ lid domain
    1.5e-24   85.9   2.0      4e-24   84.6   2.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    8.6e-18   63.9   0.2    1.6e-16   59.8   0.1    2.6  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.5e-16   60.3   0.0    1.8e-08   34.7   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    5.7e-16   58.7   0.0    1.6e-07   31.2   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.4e-14   54.1   0.1      2e-06   28.3   0.0    3.7  3  AAA_16           AAA ATPase domain
    3.4e-12   46.5   0.3    5.1e-05   23.3   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    6.5e-12   45.3   0.0    6.6e-05   22.3   0.0    2.7  2  TIP49            TIP49 P-loop domain
    2.1e-11   44.2   0.7     0.0014   18.9   0.0    4.2  2  AAA_22           AAA domain
      3e-11   43.7   0.0    0.00011   22.3   0.0    2.6  2  AAA_33           AAA domain
    4.3e-11   42.9   0.0    0.00033   20.7   0.0    3.4  3  AAA_14           AAA domain
    1.8e-10   40.6   3.7      2e-05   24.5   0.0    3.6  3  Vps4_C           Vps4 C terminal oligomerisation domain
    2.5e-09   37.8   0.2     0.0014   19.2   0.0    3.2  3  AAA_18           AAA domain
    4.3e-09   36.3   0.0     0.0018   18.0   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.9e-08   34.1   0.0     0.0044   17.3   0.0    2.5  2  AAA_28           AAA domain
    9.9e-08   31.6   1.0      0.008   15.6   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.5e-07   31.2   0.9       0.38   10.3   0.6    4.2  3  AAA_25           AAA domain
    3.5e-07   30.2   0.0      0.019   14.7   0.0    2.6  2  AAA_24           AAA domain
    4.9e-07   30.1   0.0      0.012   16.0   0.0    2.7  2  RNA_helicase     RNA helicase
    1.6e-06   28.1   0.3      0.048   13.7   0.0    3.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.1e-05   25.2   0.1       0.32   10.7   0.0    3.6  2  Sigma54_activat  Sigma-54 interaction domain
    1.5e-05   24.4   0.1       0.16   11.3   0.1    2.8  2  Zeta_toxin       Zeta toxin
      2e-05   24.5   0.0       0.21   11.5   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    2.5e-05   23.5   0.2      0.067   12.3   0.0    2.4  2  Parvo_NS1        Parvovirus non-structural protein NS1
    3.5e-05   23.8   1.4       0.61   10.0   0.1    3.6  4  NACHT            NACHT domain
    4.7e-05   23.0   0.0       0.42   10.1   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
      7e-05   22.1   0.0       0.13   11.4   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    0.00012   22.6   0.0          1    9.9   0.0    3.0  2  ABC_tran         ABC transporter
    0.00015   21.2   5.8       0.44    9.9   0.0    4.5  5  ATPase           KaiC
    0.00015   21.2   0.0      0.024   13.9   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00015   21.7   0.0      0.047   13.5   0.0    3.0  2  Bac_DnaA         Bacterial dnaA  protein
    0.00019   21.0   0.8       0.49    9.8   0.2    2.5  2  PhoH             PhoH-like protein
    0.00043   20.3   0.0       0.52   10.2   0.0    3.2  2  Rad17            Rad17 P-loop domain
    0.00097   19.3   0.0       0.29   11.2   0.0    2.6  2  SKI              Shikimate kinase
      0.001   18.0   0.0       0.31    9.9   0.0    2.6  3  AFG1_ATPase      AFG1-like ATPase
     0.0011   18.8   0.8        1.1    9.0   0.0    2.6  2  AAA_11           AAA domain
     0.0012   19.3   0.0        2.8    8.4   0.0    3.0  2  AAA_17           AAA domain
     0.0013   18.7   1.7       0.77    9.6   0.0    3.7  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0016   18.8   0.8        2.2    8.6   0.0    2.9  2  AAA_19           AAA domain
     0.0024   17.6   0.6        3.1    7.5   0.0    2.7  2  AAA_30           AAA domain
     0.0029   17.0   0.3        1.4    8.2   0.1    2.5  2  IPT              Isopentenyl transferase
     0.0036   17.1   0.1        2.4    7.9   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
     0.0042   16.9   0.0       0.82    9.4   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0048   17.0   0.0        3.7    7.7   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0048   16.3   0.0        1.6    8.1   0.0    3.2  2  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.012   14.6   0.0       0.57    9.1   0.0    2.5  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.012   14.7   0.0        2.1    7.3   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.013   15.2   0.2          7    6.4   0.0    2.7  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.023   14.2   0.0       0.05   13.1   0.0    1.6  1  UFD1             Ubiquitin fusion degradation protein UFD1
      0.026   13.7   0.0        7.6    5.6   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.038   14.0   0.1         12    5.9   0.0    2.8  2  ResIII           Type III restriction enzyme, res subunit
      0.041   13.6   0.0         14    5.5   0.1    2.7  2  AAA_29           P-loop containing region of AAA domain
       0.06   13.0   4.6         15    5.2   0.0    4.7  5  Guanylate_kin    Guanylate kinase
       0.13   12.5   0.8        7.4    6.8   0.0    2.8  3  Hydin_ADK        Hydin Adenylate kinase-like domain
        0.4   10.6   9.2         17    5.2   0.0    4.7  4  NTPase_1         NTPase
        1.2    9.7   3.3         44    4.5   0.0    3.5  3  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   5.2e-53   1.6e-50       1     131 [.     216     345 ..     216     346 .. 0.98
   2 !  158.7   0.0   3.1e-49   9.6e-47       1     131 [.     491     621 ..     491     622 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 5.2e-53
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +llyGppGtGKTlla+a+a+e+g++f++++g+e++sk+ gese++ire+fkea+e+a psi+fiDEida+a++r++ + e+
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYFITVNGPEIMSKFYGESEQRIREIFKEAEENA-PSIIFIDEIDAIAPKREDVTGEV 295
                                   69******************************************************9.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+rvv+qLlt +dg k + ++vivigatnrpd +dpal+r gRfdr+iei+
  gi|70606628|ref|YP_255498.1| 296 EKRVVAQLLTLMDGIKGR-GRVIVIGATNRPDAIDPALRRpGRFDREIEIR 345
                                   *****************7.77***************************986 PP

  == domain 2  score: 158.7 bits;  conditional E-value: 3.1e-49
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   +ll+GppGtGKT+lakava+e+g++f+ + g+e+lsk+vgesek ire+f++a++ a p+++f+DEid++a+ r  +++s+
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAA-PTVIFFDEIDSIAPIRgLSTDSG 570
                                   69******************************************************9.****************98889** PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++er+vnqLl+e+dg     +kv++i+atnrpd ldpallr gRfdr i+++
  gi|70606628|ref|YP_255498.1| 571 VTERIVNQLLAEMDGIVPL-NKVVIIAATNRPDILDPALLRpGRFDRLIYVP 621
                                   ****************996.77***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1     1e-16   3.2e-14       1      34 [.     368     407 ..     368     431 .. 0.77
   2 !   47.7   0.1   3.1e-15   9.7e-13       1      33 [.     644     676 ..     644     718 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1e-16
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr......g 34 
                                   dvdl++LAe+T Gy+GADlaal +eAa+ Alrr       
  gi|70606628|ref|YP_255498.1| 368 DVDLDKLAEMTYGYTGADLAALAKEAAIYALRRfvdekkL 407
                                   9********************************5544440 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 3.1e-15
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr 33 
                                   dv+l+++Ae+ eGy+GADl+al+reA ++A+r 
  gi|70606628|ref|YP_255498.1| 644 DVSLEDIAEKAEGYTGADLEALVREATINAMRS 676
                                   9******************************97 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   2.0   1.3e-26     4e-24       2      84 ..       7      89 ..       6      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.3e-26
                                  EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCC.EEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                       CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveieg.krk.TvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                  +rV+ea+q+dvg++++ri++  m++l++e gd++ei g + + + a+v+pa++   +++ Ir+dg++Rk ++v+iGd+VtVrk
  gi|70606628|ref|YP_255498.1|  7 FRVTEARQRDVGKKVARISETSMRKLNVEAGDYIEIIGqDGNsALAQVMPAYDI--SDDEIRIDGYIRKSIKVGIGDDVTVRK 87
                                  89************************************8777677*******66..68************************* PP

                                  E- CS
                       CDC48_N 83 ae 84
                                  ++
  gi|70606628|ref|YP_255498.1| 88 TN 89
                                  97 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.99   3.1e+02      30      57 ..       1      32 [.       1      38 [. 0.83
   2 !   59.8   0.1     5e-19   1.6e-16       1      63 [.     105     167 ..     105     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.99
                                  TCCCEEEEEEEECCCC....SCEEECTSCCEE CS
                       CDC48_2 30 kgqeiklvVvstePkg....pvgitetTeiel 57
                                  ++q ik++V++    +    +++i+et++ +l
  gi|70606628|ref|YP_255498.1|  1 MSQSIKFRVTEARQRDvgkkVARISETSMRKL 32
                                  5899*******999999997779999987665 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 5e-19
                                   ..SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                       CDC48_2   1 ridgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                   r+d  +++y+k+ ++++p++kG++++++  +++++l+Vv+t+P++ v +t +T ie++++pv+
  gi|70606628|ref|YP_255498.1| 105 RFDNSFVEYVKDTLMDKPLAKGETLPIPIYTGTLELTVVNTQPSNYVYVTGSTNIEIREEPVK 167
                                   699999*******************************************************98 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   5.6e-11   1.8e-08       6     105 ..     216     309 ..     211     313 .. 0.89
   2 !   21.9   0.0     5e-07   0.00016       6     101 ..     491     581 ..     487     587 .. 0.77
   3 ?   -1.8   0.1       9.1   2.9e+03      76      96 ..     630     651 ..     630     653 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.6e-11
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt+la+ala+ + +     +i+++  e++     + + ++++  ++  ++aee+   i+++DEid i+pk 
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGA----YFITVNGPEIMS----KFYGESEQRIREIFKEAEENApsIIFIDEIDAIAPKr 288
                                   8999******************96....************....********************9**************75 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   e  + +v +  V+  LL +++g
  gi|70606628|ref|YP_255498.1| 289 EDVTGEVEK-RVVAQLLTLMDG 309
                                   555555554.688889999997 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 5e-07
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt+laka+a    +    ++i +   e+l     + + ++++  ++   +a +    ++++DEid i+p  
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGA----NFIAVRGPEILS----KWVGESEKAIREIFRKARQAAptVIFFDEIDSIAPIr 563
                                   7899****************9996....9**********9....66666666666666666666688************85 PP

                                   ---------HHHHHHHHH CS
                         AAA_2  84 essgadvSregVqrdLLq 101
                                   + s+     e +++ LL 
  gi|70606628|ref|YP_255498.1| 564 GLSTDSGVTERIVNQLLA 581
                                   444444445666666665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9.1
                                   TGGG----.---------HHHH CS
                         AAA_2  76 EidKihpk.essgadvSregVq 96 
                                   Ei K+h k     +dvS e++ 
  gi|70606628|ref|YP_255498.1| 630 EILKVHTKnVPLAEDVSLEDIA 651
                                   7889**9999999*******96 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   5.1e-10   1.6e-07      35     103 ..     215     291 ..     207     338 .. 0.84
   2 !   24.3   0.0   6.9e-08   2.2e-05      35      98 ..     490     561 ..     481     615 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.1e-10
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                    +llyGpPG Gkt la+ +a+e+g+ + +  gP +      e ++ +  ++++ ee+   ++fidei  ++++ e+v
  gi|70606628|ref|YP_255498.1| 215 GILLYGPPGTGKTLLARALANEIGAYFITVNGPEImskfygESEQRIREIFKEAEENapSIIFIDEIDAIAPKREDV 291
                                   59*******************************994444434467799999998876447*********99998886 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 6.9e-08
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsr 98 
                                    +ll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++ + ++    v+f dei  +++
  gi|70606628|ref|YP_255498.1| 490 GILLFGPPGTGKTMLAKAVATESGANFIAVRGPEIlskwvgESEKAIREIFRKARQAapTVIFFDEIDSIAP 561
                                   69*******************************874333333455666677665543226888898887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   6.3e-09     2e-06      16     141 ..     205     319 ..     200     327 .. 0.71
   2 !   15.7   0.1   4.7e-05     0.015      24      57 ..     488     520 ..     478     531 .. 0.79
   3 ?    5.2   0.0     0.078        24     122     147 ..     535     559 ..     531     583 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 6.3e-09
                        AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                   ++r+  + p  +ll+G++G+GK+ l+r+l++++    ++f++ +  +      +s +      e+ +r++  eae+++++ 
  gi|70606628|ref|YP_255498.1| 205 FQRLGIDPPKGILLYGPPGTGKTLLARALANEIG---AYFITVNGPEI-----MSKFYGE--SEQRIREIFKEAEENAPSI 275
                                   56666666799*******************9777...88999999999.....3333333..3467777777755555555 PP

                        AAA_16  97 wrekleeala.avpelagaeasrllellkrllallsrderplvlvl 141
                                         +a+a    +++g+ ++r+ ++l  l++ ++ ++r  v+v+
  gi|70606628|ref|YP_255498.1| 276 IFIDEIDAIApKREDVTGEVEKRVVAQLLTLMDGIKGRGR--VIVI 319
                                   5544444444256666666669999999999988887555..5554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.7e-05
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflr 57 
                                   p  +ll G++G+GK+ l+++++++  ++ +i++r
  gi|70606628|ref|YP_255498.1| 488 PKGILLFGPPGTGKTMLAKAVATESGAN-FIAVR 520
                                   3899******************876666.44444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.078
                        AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                   +++++++++++ + p+v+++D+++ +
  gi|70606628|ref|YP_255498.1| 535 AIREIFRKARQ-AAPTVIFFDEIDSI 559
                                   6788999***9.999********954 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.6e-07   5.1e-05       2     135 ..     216     333 ..     215     335 .. 0.64
   2 !   18.1   0.1   6.5e-06     0.002       2     132 ..     491     606 ..     490     612 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                                   +lL GppGtgK+ la+ la  +++ + +v++++ +++  + g+ e      ++   +++ +a+   ++i+++DE++ + ++
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYFITVNGPEIMSK--FYGESE------QRIREIFK-EAEenAPSIIFIDEIDAIAPK 287
                                   89*******************************8875..444444......33345555.444478899999999988765 PP

                                   HHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  81 vlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                     ++   +   +++ ++++ +l++  +     r+ vi+++n++d     ++palr
  gi|70606628|ref|YP_255498.1| 288 REDVTGEV---EKRVVAQLLTLMDGIKG--RGRVIVIGATNRPD----AIDPALR 333
                                   44433221...22222233333333221..12266666666666....6666665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.5e-06
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                                   +lL GppGtgK++la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   + ++++DE++ + + 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAVRGPE------ILSKWV---GESEKAIREIFRKARqaAPTVIFFDEIDSIAPI 562
                                   89*****************99999999999987......777777...555555666666777677889999999977743 PP

                                   H.HHHHHHHHHSSEEE...-SSSEEE---......-EEEEEESS--.-TT-TTH CS
                         AAA_5  81 v.lnsLlslleerrll.leeggelvkaknddllerfrviatanpldrslnelsp 132
                                     l++   + e+   + l+e+++ v  ++      + +ia++n++d     l+p
  gi|70606628|ref|YP_255498.1| 563 RgLSTDSGVTERIVNQlLAEMDGIVPLNK------VVIIAATNRPD----ILDP 606
                                   30333333333332221233333333333......77777777776....4455 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00036      51      97 ..     214     258 ..     209     283 .. 0.88
   2 !   22.3   0.0   2.1e-07   6.6e-05      50     106 ..     488     543 ..     476     547 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                   +++Ll Gp+gtGkt la a+++e+g    f++++g e+ s     +e
  gi|70606628|ref|YP_255498.1| 214 KGILLYGPPGTGKTLLARALANEIG--AYFITVNGPEIMSKFYGESE 258
                                   89***********************..78*********997666655 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.1e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                         TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                    +++Ll Gp+gtGkt la a++ e g    f+a+ g e+ s  v  +e ++ + +rk+
  gi|70606628|ref|YP_255498.1| 488 PKGILLFGPPGTGKTMLAKAVATESG--ANFIAVRGPEILSKWVGESEkAIREIFRKA 543
                                   599********************988..78**************99985688999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.5e-06    0.0014       8      51 ..     216     248 ..     211     328 .. 0.64
   2 !   16.5   0.1   2.5e-05    0.0077       8      29 ..     491     512 ..     486     589 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.5e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                   ++++G++GtGKT+l+r l+++          ++   f+t+++++
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEI---------GAY--FITVNGPE 248
                                   89******************87.........333..33333333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.5e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                   ++++G++GtGKT+l++ ++ + 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATES 512
                                   89***************99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.7e-07   0.00011       2      47 ..     216     281 ..     216     339 .. 0.72
   2 !   18.7   0.0   4.8e-06    0.0015       2      46 ..     491     537 ..     491     628 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.7e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..................d 47 
                                   +ll G+pG+GK+ la+ l+++ g  +++++ ++++++ +g+ +q+++                   
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGayFITVNGPEIMSKFYGESEQRIReifkeaeenapsiifideI 281
                                   6789*******************99999************88888875555555555555555550 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 4.8e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                   +ll G+pG+GK+ la+ ++ + g  ++ ++ ++++++ +g+ ++ ++
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGanFIAVRGPEILSKWVGESEKAIR 537
                                   6899*******************999999999998888886666555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       4.6   1.4e+03      88     108 ..     144     164 ..     139     171 .. 0.74
   2 !   20.7   0.0     1e-06   0.00033       5     102 ..     216     323 ..     213     348 .. 0.76
   3 !   17.5   0.0     1e-05    0.0032       5      76 ..     491     559 ..     488     586 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.6
                        AAA_14  88 degknldvivtGSnskllske 108
                                   ++++   v+vtGS +  + +e
  gi|70606628|ref|YP_255498.1| 144 NTQPSNYVYVTGSTNIEIREE 164
                                   44555589*****99887665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1e-06
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev........ 76 
                                   +++ G+  +GKT l++ l++e       ++ +n  +   k + ++e ++ e+++e ++e+  +++f+DEi  +        
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIG---AYFITVNGPEIMSKFYGESEqRIREIFKE-AEENAPSIIFIDEIDAIapkredvt 292
                                   7899***************8887...88888888887776666555245555555.455699**********988888888 PP

                        AAA_14  77 ....pewekalkslvd..egknldvivtGSns 102
                                       +++   l  l+d  +g +++viv G  +
  gi|70606628|ref|YP_255498.1| 293 geveKRVVAQLLTLMDgiKG-RGRVIVIGATN 323
                                   88888888888888886444.77888888765 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT+l+k ++ e+     +++ +   +   k   ++ek +++i++k+++   t++f+DEi  +
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESG---ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPTVIFFDEIDSI 559
                                   7899***************9999...99999999999998888877777777777656699********887 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.9   3.1e+03      17      34 ..     164     181 ..     156     190 .. 0.73
   2 !   15.0   0.1   5.8e-05     0.018      18      44 ..     413     439 ..     403     443 .. 0.83
   3 !   24.5   0.0   6.3e-08     2e-05      28      59 ..     710     741 ..     687     742 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.9
                        Vps4_C  17 mdipsdkllePpvtlkDf 34 
                                   + ++++ l  P+v+ +D+
  gi|70606628|ref|YP_255498.1| 164 EPVKESSLAYPKVSWEDI 181
                                   557778888888888886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.8e-05
                        Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                    ip++ ++e +v+++Dfl+alk+ +p+
  gi|70606628|ref|YP_255498.1| 413 TIPAEIIKELKVSMNDFLNALKSIQPS 439
                                   399999********************9 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 6.3e-08
                        Vps4_C  28 pvtlkDflkalkkarptVskeDLekheeFTke 59 
                                   +v+ +Df+kal+ ++ + +++D++++e+F ke
  gi|70606628|ref|YP_255498.1| 710 KVSKEDFEKALNVVKASLTQADIQRYERFSKE 741
                                   89***************************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.5e-06    0.0014       1      67 [.     216     310 ..     216     324 .. 0.64
   2 !   14.5   0.0   0.00012     0.039       1      27 [.     491     515 ..     491     558 .. 0.79
   3 ?   -0.5   0.1       5.4   1.7e+03      88     114 ..     717     742 ..     630     746 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.......aldeskrld 53 
                                   Ill G+pG+GKt la++L+++  ++                     +++ + a en +++ + +e         d + +++
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIgAYfitvngpeimskfygeseqrIREIFKEAEENAPSIIFIDEidaiapkREDVTGEVE 296
                                   99*****************99855588888887777777777544344444444444444444445555555555556666 PP

                        AAA_18  54 edkldklldaleen 67 
                                   + ++++ll++++++
  gi|70606628|ref|YP_255498.1| 297 KRVVAQLLTLMDGI 310
                                   66666666666665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00012
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvn 27 
                                   Ill G+pG+GKt lak+++ +   g n
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATES--GAN 515
                                   99****************8775..333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 5.4
                        AAA_18  88 seaakdikk......vvLtaspeelleRlekRg 114
                                   +       k        Lt  + +++eR++k  
  gi|70606628|ref|YP_255498.1| 717 E-------KalnvvkASLTQADIQRYERFSKEL 742
                                   2.......0222333788888888888888765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.9e-05    0.0092      44      70 ..     210     236 ..     189     252 .. 0.89
   2 !   18.0   0.0   5.8e-06    0.0018      37      72 ..     478     513 ..     466     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-05
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgve 70 
                                   i+  ++i+l Gp+G+GK+ la al+ e
  gi|70606628|ref|YP_255498.1| 210 IDPPKGILLYGPPGTGKTLLARALANE 236
                                   5566789*****************976 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.8e-06
                     IstB_IS21  37 eLatlsfiekkenivllGpsGvGKshlaialgveav 72 
                                   eL t s ++  ++i+l+Gp+G+GK+ la a+++e  
  gi|70606628|ref|YP_255498.1| 478 ELFTKSGVTPPKGILLFGPPGTGKTMLAKAVATESG 513
                                   6777788888899******************98765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.4e-05    0.0044       2      39 ..     216     258 ..     215     297 .. 0.74
   2 !   14.3   0.0   0.00012     0.037       2      46 ..     491     536 ..     490     555 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileekl 39 
                                   i + G+++tGKT l++aLa++    + +v  pE++ +++ e  
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEigaYFITVngPEIMSKFYGESE 258
                                   7899***************888442334447777766664444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00012
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedal 46 
                                   i ++G+++tGKT l++a a + g + ++  + eil++   + e+a+
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATEsGANFIAVRGPEILSKWVGESEKAI 536
                                   789****************766777666555555555554444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   7.7e-05     0.024      25      43 ..     216     234 ..     213     240 .. 0.90
   2 !   15.6   0.1   2.5e-05     0.008      25      43 ..     491     509 ..     486     512 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt+la++l+
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALA 234
                                   89**************986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.5e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKtmlak+++
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVA 509
                                   89*************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0014      0.43      36      54 ..     216     234 ..     197     238 .. 0.91
   2 ?    4.6   0.0     0.067        21     127     176 ..     258     307 ..     240     322 .. 0.84
   3 !   10.3   0.6    0.0012      0.38      36      55 ..     491     510 ..     483     594 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pgtGKt la  la
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALA 234
                                   69*************8887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.067
                        AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                   ++ ++++ +++ee + +  + iD ++++ +  e+   +v +++v++l  + 
  gi|70606628|ref|YP_255498.1| 258 EQRIREIFKEAEE-NAPSIIFIDEIDAIAPKREDVTGEVeKRVVAQLLTLM 307
                                   4668899999999.77***************99999998899999887665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0012
                        AAA_25  36 allaGapgtGKttlaldlal 55 
                                   +ll+G+pgtGKt+la  +a 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVAT 510
                                   69***********9965553 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.2e-05     0.019       5      77 ..     216     284 ..     213     297 .. 0.70
   2 !   12.7   0.0   0.00025     0.078       5      35 ..     491     514 ..     488     564 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.2e-05
                        AAA_24   5 iliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                   il+yGp+g+GKT la+ l  +  +++ t +G   +    ++   s + +++ ++e +++ +  ++++iD id +
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALaNEIGAYFITVNGPEIMSKFYGE---SEQRIREIFKEAEENAP--SIIFIDEIDAI 284
                                   89**************9964444555555555555555554...66666666666666555..77777777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00025
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGl 35 
                                   il++Gp+g+GKT+lak          te G+
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAV-------ATESGA 514
                                   89*************998.......566655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.9e-05     0.012       1      26 [.     216     241 ..     216     284 .. 0.83
   2 !   11.3   0.0    0.0011      0.35       1      24 [.     491     514 ..     491     560 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i+lyGp+g+GK++la+ La+++   +
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYF 241
                                   789*****************998665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0011
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallk 24 
                                   i+l+Gp+g+GK++lak +a++   
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGA 514
                                   689**************8887654 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00015     0.048      19      51 ..     213     247 ..     182     261 .. 0.77
   2 !   11.1   0.1   0.00095       0.3      20      51 ..     489     522 ..     460     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    + ilL+G+ G+GKT l+r+la+++g    +v+ P
  gi|70606628|ref|YP_255498.1| 213 PKGILLYGPPGTGKTLLARALANEIGAYfiTVNGP 247
                                   3459********************99876667666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00095
                                   EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                   + ilL G+ G+GKT+l++++a + g +  +v+ P
  gi|70606628|ref|YP_255498.1| 489 KGILLFGPPGTGKTMLAKAVATESGANfiAVRGP 522
                                   349*******************999887777665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0     0.001      0.32      23      61 ..     214     249 ..     203     291 .. 0.80
   2 !    9.8   0.0    0.0019      0.59      23      54 ..     489     517 ..     480     601 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                     +l+ G  GtGK+llara+ ++     + f++vn  +i
  gi|70606628|ref|YP_255498.1| 214 KGILLYGPPGTGKTLLARALANEIG---AYFITVNGPEI 249
                                   569****************987654...67777776554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfv 54 
                                     +l+ G  GtGK++la+a+ ++s    ++f+
  gi|70606628|ref|YP_255498.1| 489 KGILLFGPPGTGKTMLAKAVATESG---ANFI 517
                                   569****************987765...4455 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.42      15      50 ..     212     245 ..     203     260 .. 0.86
   2 !   11.3   0.1    0.0005      0.16      14      49 ..     486     519 ..     478     524 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                    Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    Pk ill G pG GK+ la++l++e+  +  +++++
  gi|70606628|ref|YP_255498.1| 212 PPKGILLYGPPGTGKTLLARALANEI--GAYFITVN 245
                                   5999*********************9..55566555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0005
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                     Pk ill G pG GK+ la+++++e   + n++ +
  gi|70606628|ref|YP_255498.1| 486 TPPKGILLFGPPGTGKTMLAKAVATES--GANFIAV 519
                                   56999*********************8..7777766 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00065      0.21       2      30 ..     216     244 ..     215     298 .. 0.82
   2 !   10.0   0.0    0.0019       0.6       2      38 ..     491     526 ..     490     607 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00065
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   +ll g PG++ktll++ala+ +++ f  +
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYFITV 244
                                   7999******************9988766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0019
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllP 38 
                                   +ll g PG++kt+l+ka+a+  +++f  ++  p++l 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAVR-GPEILS 526
                                   78999****************999998776.455554 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00021     0.067     117     141 ..     216     240 ..     210     246 .. 0.89
   2 !    8.6   0.0    0.0027      0.86     117     136 ..     491     510 ..     480     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                   +++yGp+ tGkt la+a+a+ +  y
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAY 240
                                   89*****************988766 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   ++++Gp+ tGkt+la+a a+
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVAT 510
                                   8899*************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.002      0.62       3      24 ..     216     237 ..     214     240 .. 0.90
   2 ?   -1.5   0.0       6.4     2e+03      62     108 ..     254     303 ..     248     355 .. 0.71
   3 !   10.0   0.1    0.0019      0.61       3      23 ..     491     511 ..     489     515 .. 0.89
   4 ?   -0.9   0.0       4.2   1.3e+03      62     113 ..     529     580 ..     522     618 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   ++l G++G GKT L++ la ++
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEI 237
                                   7899**************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.4
                                   CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............. CS
                         NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtl 108
                                   + e++++++e++++  e++ ++ +i D +D ++ + +      ek+ v +l
  gi|70606628|ref|YP_255498.1| 254 YGESEQRIREIFKEAEENAPSIIFI-DEIDAIAPKREDvtgeVEKRVVAQL 303
                                   6677888888888888888888875.8888887766556663333333333 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0019
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   ++l G++G GKT+L++ +a++
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATE 511
                                   6789************99976 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 4.2
                                   CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHHHH CS
                         NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLseli 113
                                     e++++++e +   ++++  +++ +D +D ++ + g           +++  ++l+
  gi|70606628|ref|YP_255498.1| 529 VGESEKAIRE-IFRKARQAAPTVIFFDEIDSIAPIRGLstdsgV----TERIVNQLL 580
                                   5566777777.444466777888999999999998888533332....233333333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0013      0.42      33      58 ..     213     238 ..     202     286 .. 0.86
   2 !   10.1   0.0    0.0013      0.42      30      56 ..     485     511 ..     477     520 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                    k +ll+Gp GtGKt++++ l +++ 
  gi|70606628|ref|YP_255498.1| 213 PKGILLYGPPGTGKTLLARALANEIG 238
                                   5789**************99988876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkk 56 
                                   ++  k +ll Gp GtGKt+++k + ++
  gi|70606628|ref|YP_255498.1| 485 VTPPKGILLFGPPGTGKTMLAKAVATE 511
                                   5666889*************9986654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0039       1.2      52      81 ..     212     241 ..     169     284 .. 0.79
   2 !   11.4   0.0   0.00042      0.13      22      97 ..     448     534 ..     432     604 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0039
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg 81 
                                   p + +LL+G  GtGK  l +al ne+ +  
  gi|70606628|ref|YP_255498.1| 212 PPKGILLYGPPGTGKTLLARALANEIGAYF 241
                                   56789*******************987655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00042
                        DUF815  22 vdevklddLvgidkqkealvente.......qfleg..lpannvLLwGarGtGKSslvkallneyaeeg..Lrlieveked 91 
                                   v +v+++d+ g+d+ k++l e +e        f +   +p + +LL+G  GtGK  l ka+ +e  ++   +r  e+  + 
  gi|70606628|ref|YP_255498.1| 448 VPKVNWNDIGGLDNVKQQLREAVEwplrfpeLFTKSgvTPPKGILLFGPPGTGKTMLAKAVATESGANFiaVRGPEILSKW 528
                                   5678888888888888888888753331111233322357899*******************9988877334445665555 PP

                        DUF815  92 lkelpk 97 
                                   + e +k
  gi|70606628|ref|YP_255498.1| 529 VGESEK 534
                                   555444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0053       1.7       8      66 ..     210     266 ..     207     315 .. 0.75
   2 !    9.9   0.0    0.0033         1      13      67 ..     490     542 ..     482     594 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0053
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpq 66 
                                   + + + + + G+ G+GK+ L+++la++       i+++g ++ ++   +++++i+ +++
  gi|70606628|ref|YP_255498.1| 210 IDPPKGILLYGPPGTGKTLLARALANEIGA--YFITVNGPEIMSKFYGESEQRIREIFK 266
                                   556667889****************98754..345556666666555555555555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0033
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                    + ++G+ G+GK+ L+k++a ++   +  i ++g ++ ++   +++k i+ ++ +
  gi|70606628|ref|YP_255498.1| 490 GILLFGPPGTGKTMLAKAVATESG--ANFIAVRGPEILSKWVGESEKAIREIFRK 542
                                   5789***************99975..56677777777777777777777766666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0029      0.91      15      37 ..     209     231 ..     202     239 .. 0.83
   2 ?   -1.2   0.0       3.3     1e+03     110     151 ..     260     307 ..     252     319 .. 0.58
   3 !    9.9   0.0    0.0014      0.44      10      40 ..     478     509 ..     456     521 .. 0.83
   4 ?   -0.6   0.0       2.1   6.7e+02     125     152 ..     556     584 ..     526     594 .. 0.77
   5 ?   -0.1   0.2       1.5   4.7e+02      58     120 ..     645     709 ..     632     734 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0029
                        ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                   Gi   + +l++G pGtGKt++a 
  gi|70606628|ref|YP_255498.1| 209 GIDPPKGILLYGPPGTGKTLLAR 231
                                   66667789************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                        ATPase 110 elaeaikeika...krvviDsitglayeekeav....aReilrqlvrvl 151
                                   +++e+ ke ++   + + iD i+++   ++e+v     ++ + ql++ +
  gi|70606628|ref|YP_255498.1| 260 RIREIFKEAEEnapSIIFIDEIDAI-APKREDVtgevEKRVVAQLLTLM 307
                                   4555555544433488999999999.33333330111455556666555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0014
                        ATPase  10 eil.kgGipegrvvlitGepGtGKtifalqFl 40 
                                   e++ k G+   + +l+ G pGtGKt++a+  +
  gi|70606628|ref|YP_255498.1| 478 ELFtKSGVTPPKGILLFGPPGTGKTMLAKAVA 509
                                   5555689999999**************98755 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.1
                        ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlk 152
                                   iDsi+++   ++++ v+ +i+ ql+ ++ 
  gi|70606628|ref|YP_255498.1| 556 IDSIAPIrGLSTDSGVTERIVNQLLAEMD 584
                                   89999997788888889999999998886 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.5
                        ATPase  58 epaedlrenak.slGwdlekleeegklaiidasesaeesaee.kdkedleelieelaeaikeika 120
                                    + ed+ e+a+   G dle+l +e  ++ +    s+ +++++ + k ++e   ++++e ++++  
  gi|70606628|ref|YP_255498.1| 645 VSLEDIAEKAEgYTGADLEALVREATINAMRSIYSMCDKQSRdECKGNMECYQKHIKECMNKTSF 709
                                   45588888888567999999999988876665555554444347788888888888888777655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   7.7e-05     0.024       4      66 ..     216     271 ..     213     299 .. 0.74
   2 ?    4.8   0.0     0.043        14       6      25 ..     493     512 ..     489     547 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-05
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafek 66 
                                   +l  G +GtGKt+++ +l++e+        a +++vN+p+++ + + + +++  ++ +kea e+
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEI-------GAYFITVNGPEIMsKFYGESEQRI-REIFKEAEEN 271
                                   6789******************.......889999999987647777776666.4444444443 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.043
                       DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                     G +GtGKt+++ ++++e 
  gi|70606628|ref|YP_255498.1| 493 LFGPPGTGKTMLAKAVATES 512
                                   5699*********9999886 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00015     0.047      37     179 ..     216     360 ..     211     378 .. 0.76
   2 ?    4.6   0.0     0.082        26      37      65 ..     491     519 ..     486     668 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-HH.. CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagkek.. 114
                                   +++yg+ G Gkt L +a++ne+ + +     + +++ e ++++    +++  e fke   ++  ++ iD+i  +a k +  
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYF-----ITVNGPEIMSKFYGESEQRIREIFKEAEENApSIIFIDEIDAIAPKREdv 291
                                   79*****************9997665.....56889999999999999999999**98886527899*******9885322 PP

                                   .......HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHH CS
                      Bac_DnaA 115 .......tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkki 179
                                          +  +l+++++ + + g+ +v+ +   P +++    r   rf++   ++i ppd++ r +il+ + 
  gi|70606628|ref|YP_255498.1| 292 tgevekrVVAQLLTLMDGIKGRGRVIVIGATNRPDAIDPAL-RRPGRFDR--EIEIRPPDTKGRKDILQVHT 360
                                   2221111334566777777788999*********9987654.33577876..68999**********97544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.082
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                                   ++++g+ G Gkt L ka++ e  +n+ + 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAV 519
                                   789***************99877666554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0     0.003      0.95      23      40 ..     217     234 ..     210     239 .. 0.87
   2 !    9.8   0.2    0.0016      0.49      23      42 ..     492     511 ..     486     519 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.003
                                   EEE--TTSSTTHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavala 40 
                                      Gp GtGKt+la ala
  gi|70606628|ref|YP_255498.1| 217 LLYGPPGTGKTLLARALA 234
                                   578***********9998 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                                   EEE--TTSSTTHHHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavalave 42 
                                     +Gp GtGKt+la a+a e
  gi|70606628|ref|YP_255498.1| 492 LLFGPPGTGKTMLAKAVATE 511
                                   579************99976 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0016      0.52      20      78 ..     183     245 ..     167     283 .. 0.73
   2 ?    6.0   0.0     0.032        10      48      80 ..     491     523 ..     479     560 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                         Rad17  20 elavhkkkieevkew.lka....dvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewln 78 
                                   +l   k+ki+e+ ew ++     + L   + + +L+ GP+G gk+   + L+ e g  ++   n
  gi|70606628|ref|YP_255498.1| 183 DLEEAKQKIREIVEWpMRHpelfQRLGIDPPKGILLYGPPGTGKTLLARALANEIGAYFITV-N 245
                                   5666799999999995544111134444566677889*****************99877654.4 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                         Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpv 80 
                                   +L+ GP+G gk+   k ++ e g +++    p 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAVRGPE 523
                                   5778*****************999988766665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00094      0.29       1      45 [.     222     271 ..     222     272 .. 0.78
   2 ?    5.4   0.0     0.057        18       1      23 [.     497     519 ..     497     547 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00094
                                   TTSSHHHHHHHHHHHHTSEEEEHHH..HHHHHHT...S-HHHHHHHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDe..liekrtg...ksiaeifeeegee 45 
                                   +G+GK+ ++++lA+++g  fi +    +++k  g   ++i+eif+e  e+
  gi|70606628|ref|YP_255498.1| 222 PGTGKTLLARALANEIGAYFITVNGpeIMSKFYGeseQRIREIFKEAEEN 271
                                   69*******************99744255665554447899999988775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.057
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                   +G+GK+ ++k++A + g +fi +
  gi|70606628|ref|YP_255498.1| 497 PGTGKTMLAKAVATESGANFIAV 519
                                   69******************965 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.9   2.8e+03     251     285 ..      11      45 ..       3      64 .. 0.76
   2 ?    5.0   0.0     0.029       9.2      51      78 ..     204     229 ..     163     236 .. 0.79
   3 !    9.9   0.0   0.00099      0.31      31      79 ..     461     505 ..     446     511 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.9
                   AFG1_ATPase 251 klrvraaagdlvrfsfaelceaarsqsdYlalaer 285
                                   ++r r ++++++r+s +++ +   ++ dY++++ +
  gi|70606628|ref|YP_255498.1|  11 EARQRDVGKKVARISETSMRKLNVEAGDYIEIIGQ 45 
                                   56667788999999999999999999999999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                   AFG1_ATPase  51 lfgrkrksvepvrglYlwGgvGrGKtyl 78 
                                   lf+r      p++g+ l+G+ G GKt l
  gi|70606628|ref|YP_255498.1| 204 LFQRL--GIDPPKGILLYGPPGTGKTLL 229
                                   44433..568****************88 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00099
                   AFG1_ATPase  31 rlteelaaqdlarkssalgklfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                   +++++l+ + +     ++  lf++    v+p++g+ l G+ G GKt+l 
  gi|70606628|ref|YP_255498.1| 461 NVKQQLREAVEWP--LRFPELFTKS--GVTPPKGILLFGPPGTGKTMLA 505
                                   5555555544432..3466777744..689*****************95 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0034       1.1      20      41 ..     216     237 ..     206     274 .. 0.79
   2 !    7.5   0.0    0.0098       3.1      20      58 ..     491     525 ..     465     550 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0034
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                    l+ GPPGtgKT    +l +++
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEI 237
                                   5899********9999988887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0098
                        AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL 58 
                                    l+ GPPGtgKT    ++  +       +  + ++p+iL
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATES----GANFIAVRGPEIL 525
                                   5889********8776666665....3334455555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0088       2.8       1      25 [.     219     243 ..     219     294 .. 0.76
   2 ?    7.5   0.0     0.016       5.1       1      24 [.     494     517 ..     494     552 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0088
                                   EE-TTSSHHHHHHHHHHHHTEEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                   +G+PG GK+ +++ l+ ++g  +++
  gi|70606628|ref|YP_255498.1| 219 YGPPGTGKTLLARALANEIGAYFIT 243
                                   7*****************9866554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                                   EE-TTSSHHHHHHHHHHHHTEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                   +G+PG GK+ +++ ++ + g  ++
  gi|70606628|ref|YP_255498.1| 494 FGPPGTGKTMLAKAVATESGANFI 517
                                   6*************9999876655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0025      0.77      19     118 ..     212     315 ..     203     320 .. 0.53
   2 ?    5.0   0.0     0.065        20      23      44 ..     491     512 ..     482     519 .. 0.85
   3 ?    0.2   0.0       1.9   5.9e+02     103     131 ..     533     560 ..     513     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0025
                      ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..............gia 85 
                                   p + +++YGp g GKt L + ++++         y+i +++ +i ++       e+++++++ +               i+
  gi|70606628|ref|YP_255498.1| 212 PPKGILLYGPPGTGKTLLARALANEI------GAYFITVNGPEIMSKFYG----ESEQRIREIFkeaeenapsiifidEID 282
                                   5566899*************999988......345555555444444444....222222222222233333333334222 PP

                      ATPase_2  86 vpkaeleeilkeksklvfkaielllekikkkgk 118
                                       + e +  e  k v +++  l++ ik +g+
  gi|70606628|ref|YP_255498.1| 283 AIAPKREDVTGEVEKRVVAQLLTLMDGIKGRGR 315
                                   222223333445555555555555566666555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.065
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                   ++++Gp g GKt L k +++++
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATES 512
                                   789*************998765 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                      ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqkli 131
                                   +    +++++i +k+++    +i++De+  + 
  gi|70606628|ref|YP_255498.1| 533 E----KAIREIFRKARQaapTVIFFDEIDSIA 560
                                   4....4455555555555558999***98876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.018       5.6      12      32 ..     215     235 ..     210     275 .. 0.80
   2 !    8.6   0.0    0.0071       2.2      11      31 ..     489     509 ..     482     560 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                        AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                    +l+ ++pGtGKT + ++  +
  gi|70606628|ref|YP_255498.1| 215 GILLYGPPGTGKTLLARALAN 235
                                   5899*********88776655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0071
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                   k +l+ ++pGtGKT + k++ 
  gi|70606628|ref|YP_255498.1| 489 KGILLFGPPGTGKTMLAKAVA 509
                                   6689**********9877665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0      0.01       3.1      22      41 ..     217     236 ..     205     246 .. 0.85
   2 ?    7.4   0.2     0.011       3.3      22      40 ..     492     510 ..     485     521 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.01
                        AAA_30  22 vltGpAGtGKttalkalrea 41 
                                   +l Gp+GtGKt + +al++ 
  gi|70606628|ref|YP_255498.1| 217 LLYGPPGTGKTLLARALANE 236
                                   688**********9999765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+GtGKt++ ka++ 
  gi|70606628|ref|YP_255498.1| 492 LLFGPPGTGKTMLAKAVAT 510
                                   678**********999864 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.021       6.6       5      31 ..     217     243 ..     214     246 .. 0.90
   2 !    8.2   0.1    0.0045       1.4       5      31 ..     492     518 ..     489     521 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   l++G+ +tGKt  a +la+e ga  i+
  gi|70606628|ref|YP_255498.1| 217 LLYGPPGTGKTLLARALANEIGAYFIT 243
                                   89******************9987775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0045
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   l+fG+ +tGKt  a ++a e ga  i+
  gi|70606628|ref|YP_255498.1| 492 LLFGPPGTGKTMLAKAVATESGANFIA 518
                                   89********************99987 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0075       2.4       3      27 ..     218     242 ..     216     246 .. 0.89
   2 ?    6.5   0.0      0.02       6.2       3      27 ..     493     517 ..     491     520 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0075
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g+GK  +arala+++g+ ++
  gi|70606628|ref|YP_255498.1| 218 LYGPPGTGKTLLARALANEIGAYFI 242
                                   67*******************9887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.02
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g+GK  +a+a+a++ g++++
  gi|70606628|ref|YP_255498.1| 493 LFGPPGTGKTMLAKAVATESGANFI 517
                                   56*****************999987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.053        17       4      71 ..     219     281 ..     216     286 .. 0.79
   2 !    9.4   0.0    0.0026      0.82       3      71 ..     493     556 ..     491     572 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
               Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+ l r l+++   + +tvn p  e+ ++   +++++  + ++++++++       i+++DE+
  gi|70606628|ref|YP_255498.1| 219 YGPPGTGKTLLARALANEIgaYFITVNGP--EIMSKFYGESEQRIREIFKEAEENAP-----SIIFIDEI 281
                                   588**************999777777777..66666667888888888888888764.....48999997 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
               Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + ++++ +a+       ++++DE+
  gi|70606628|ref|YP_255498.1| 493 LFGPPGTGKTMLAKAVATESgANFIAVRG-PEILSKWVGESEKAIREIFRKARQAAPT-----VIFFDEI 556
                                   5688*************999*88888888.9*******99999999999999988754.....8999997 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.012       3.7      24      45 ..     216     237 ..     212     288 .. 0.81
   2 ?    6.5   0.0     0.028       8.7      24      48 ..     491     515 ..     485     562 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                   EEEEEETT--HHHHHHCC--TT CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhkns 45 
                                   ++l G++G+gk+l Ar+L+++ 
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEI 237
                                   799***************9875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.028
                                   EEEEEETT--HHHHHHCC--TTS-E CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                   ++l G++G+gk++ A++ + +sg +
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGAN 515
                                   799***************9998874 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.077        24      26      56 ..     204     234 ..     185     242 .. 0.82
   2 !    8.1   0.0    0.0052       1.6      22      57 ..     475     510 ..     465     519 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.077
                          TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                   L+++   + ++ +ll+G++ +GKt +++  a
  gi|70606628|ref|YP_255498.1| 204 LFQRLGIDPPKGILLYGPPGTGKTLLARALA 234
                                   666666677889************9988765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                          TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                   r+ eL+++   + ++ +ll+G++ +GKtm+++  a 
  gi|70606628|ref|YP_255498.1| 475 RFPELFTKSGVTPPKGILLFGPPGTGKTMLAKAVAT 510
                                   567788888888999***************997665 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0018      0.57      37      68 ..     218     249 ..     211     256 .. 0.88
   2 ?    2.4   0.0      0.19        61      37      62 ..     493     518 ..     485     560 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
                         AAA_6  37 paGpagtGKtEtvkdLakalakqvvvfncsdq 68 
                                   ++Gp gtGKt   + La++++ +++ +n  + 
  gi|70606628|ref|YP_255498.1| 218 LYGPPGTGKTLLARALANEIGAYFITVNGPEI 249
                                   68***********************9997665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.19
                         AAA_6  37 paGpagtGKtEtvkdLakalakqvvv 62 
                                   + Gp gtGKt   k +a + +  ++ 
  gi|70606628|ref|YP_255498.1| 493 LFGPPGTGKTMLAKAVATESGANFIA 518
                                   68*********999999988877765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0067       2.1     130     163 ..     214     244 ..     156     251 .. 0.87
   2 ?    4.8   0.0      0.04        13     128     152 ..     487     511 ..     385     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0067
                         T2SSE 130 glilvsGgTgsGKttllyallkeinksderivtv 163
                                   + il+ G+ g+GKt l+ al +ei ++   ++tv
  gi|70606628|ref|YP_255498.1| 214 KGILLYGPPGTGKTLLARALANEIGAY---FITV 244
                                   6699*******************9887...5555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.04
                         T2SSE 128 erglilvsGgTgsGKttllyallke 152
                                     + il+ G+ g+GKt l+ a+ +e
  gi|70606628|ref|YP_255498.1| 487 PPKGILLFGPPGTGKTMLAKAVATE 511
                                   4567999***********9998765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.022         7       2      28 ..     214     240 ..     213     245 .. 0.86
   2 ?    5.9   0.0     0.033        10       2      24 ..     489     511 ..     488     513 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                   k ill G+ g+GKt L++al +e   Y
  gi|70606628|ref|YP_255498.1| 214 KGILLYGPPGTGKTLLARALANEIGAY 240
                                   6699****************9986555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.033
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k ill+G+ g+GKt L++a+  e
  gi|70606628|ref|YP_255498.1| 489 KGILLFGPPGTGKTMLAKAVATE 511
                                   679***************98765 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016      0.05      67     167 ..      61     160 ..      17     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                          UFD1  67 eegtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvye 147
                                   +++++ +  ++ +++++  gd v++++++++ ++ v l p +   +d s   +v ++ +   + L+kg++++i     ++e
  gi|70606628|ref|YP_255498.1|  61 SDDEIRIDGYIRKSIKVGIGDDVTVRKTNVSPASKVVLAPTQPIRFDNSFVEYVKDTLMD--KPLAKGETLPIPIYTGTLE 139
                                   567788888999999*************************99988888887777666665..48***************** PP

                          UFD1 148 lkvlevkpesavsii.etdle 167
                                   l+v++++p++ v++   t++e
  gi|70606628|ref|YP_255498.1| 140 LTVVNTQPSNYVYVTgSTNIE 160
                                   **********99886245555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.024       7.6      23      43 ..     216     236 ..     202     243 .. 0.84
   2 ?    5.2   0.0     0.033        10      23      43 ..     491     511 ..     485     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.024
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   + l+G +G GKt la+   n+
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANE 236
                                   789************988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   + l G +G GKt lak +  +
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATE 511
                                   5689************99876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.037        12      22      71 ..     211     254 ..     179     296 .. 0.71
   2 ?    4.9   0.0     0.073        23      21      46 ..     468     510 ..     429     556 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.037
                                   .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl 71 
                                   +  k +l+  + GtGKTl+a +l+ ++         ++ v++ +++++ +
  gi|70606628|ref|YP_255498.1| 211 DPPKGILLYGPPGTGKTLLARALANEIGA------YFITVNGPEIMSKFY 254
                                   6678889999*********9988877654......344455555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.073
                                   ...................TTSEEEEEESTTSTHHHHHHHHHH CS
                        ResIII  21 s.................krdkrglikmaTGtGKTlvaaklie 46 
                                   +                 +  k +l+  + GtGKT++a +++ 
  gi|70606628|ref|YP_255498.1| 468 EavewplrfpelftksgvTPPKGILLFGPPGTGKTMLAKAVAT 510
                                   34444555555555555566778889999*******9955554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.071        22      20      38 ..     211     229 ..     193     235 .. 0.76
   2 ?    5.5   0.1     0.044        14      21      42 ..     488     508 ..     479     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.071
                        AAA_29  20 dlkgatlltGpsGsGKSTl 38 
                                   d+   +ll Gp G+GK+ l
  gi|70606628|ref|YP_255498.1| 211 DPPKGILLYGPPGTGKTLL 229
                                   444449**********865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.044
                        AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                   +kg +ll Gp G+GK+ l  A+
  gi|70606628|ref|YP_255498.1| 488 PKG-ILLFGPPGTGKTMLAKAV 508
                                   467.9**********9887666 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.46   1.4e+02       4      30 ..     215     241 ..     213     249 .. 0.86
   2 ?    2.3   0.0      0.39   1.2e+02      75      95 ..     250     270 ..     245     288 .. 0.79
   3 ?    5.2   0.0     0.048        15       4      30 ..     490     516 ..     488     522 .. 0.87
   4 ?   -0.7   0.0       3.2     1e+03      77      96 ..     527     546 ..     520     563 .. 0.83
   5 ?   -0.3   0.3       2.4   7.6e+02     130     180 ..     675     728 ..     661     730 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.46
                                   EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                    + l gp g+Gk  l  aL +e   +f
  gi|70606628|ref|YP_255498.1| 215 GILLYGPPGTGKTLLARALANEIGAYF 241
                                   6899***************99888777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.39
                                   TTEEEEEEHHHHHHHHHTTSE CS
                 Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                    ++ yg+s + i+e+++++ +
  gi|70606628|ref|YP_255498.1| 250 MSKFYGESEQRIREIFKEAEE 270
                                   5789************99876 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.048
                                   EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                    + l gp g+Gk +l ka+ +e   +f
  gi|70606628|ref|YP_255498.1| 490 GILLFGPPGTGKTMLAKAVATESGANF 516
                                   6899**************999988777 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 3.2
                                   EEEEEEHHHHHHHHHTTSEE CS
                 Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                   +  g+s +ai+e++ k++++
  gi|70606628|ref|YP_255498.1| 527 KWVGESEKAIREIFRKARQA 546
                                   56799**********99985 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 2.4
                                   HHHTTSSSSHHH.HHHHHHHHHHHHHGGG.C.SSEEEEESSHHHHHHHHHHHHH CS
                 Guanylate_kin 130 rrlksrgkeqee.klakrlaaaekelqey.e.fdvvivnddleealkklkelle 180
                                   r + s+ ++q++ + + +++  +k+++e+ +  ++ +  +d+e+al+ +k  l 
  gi|70606628|ref|YP_255498.1| 675 RSIYSMCDKQSRdECKGNMECYQKHIKECmNkTSFKVSKEDFEKALNVVKASLT 728
                                   4444554444441566778888888888865678889999*****999998776 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.024       7.4       2      31 ..     216     245 ..     215     271 .. 0.88
   2 ?    2.9   0.1      0.38   1.2e+02       2      30 ..     491     519 ..     490     522 .. 0.88
   3 ?   -1.5   0.2       8.2   2.6e+03      39     142 ..     666     708 ..     641     740 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiD 31 
                                   i++ G+P +GKt  a +La + +a ++t+ 
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYFITVN 245
                                   7889********************999996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.38
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                   i++ G+P +GKt  a ++a + +a ++++
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATESGANFIAV 519
                                   7789***************9998887765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 8.2
                     Hydin_ADK  39 sdgnssaGlrA.relCaeaaieqaekekeeaaeeaekkegqlsvealvkktselssaaeekaasskiskkkktsvvsgkkk 118
                                     + ++ ++r    +C + ++++                                                          
  gi|70606628|ref|YP_255498.1| 666 VREATINAMRSiYSMCDKQSRDE---------------------------------------------------------- 688
                                   33333333332123444444333.......................................................... PP

                     Hydin_ADK 119 aesegaksqkqkekktsetaqiss 142
                                     ++g+++  qk+ k+  ++  +s
  gi|70606628|ref|YP_255498.1| 689 --CKGNMECYQKHIKECMNK--TS 708
                                   ..333333333333322221..22 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.056        17       2      32 ..     216     246 ..     215     262 .. 0.79
   2 ?    0.8   0.2       1.3     4e+02      81     106 ..     257     283 ..     251     302 .. 0.74
   3 ?    5.2   0.0     0.057        18       2      23 ..     491     512 ..     490     527 .. 0.80
   4 ?    1.4   0.1      0.83   2.6e+02      46     121 ..     628     707 ..     622     740 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.056
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   +++ GppG+GKt l + +++++    ++v+G
  gi|70606628|ref|YP_255498.1| 216 ILLYGPPGTGKTLLARALANEIGAYFITVNG 246
                                   6788************999999777777777 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHH.HHH-EEEE---ST CS
                      NTPase_1  81 feelalealrkal.seadviviDEiGk 106
                                    e+ + e++++a  + + +i iDEi  
  gi|70606628|ref|YP_255498.1| 257 SEQRIREIFKEAEeNAPSIIFIDEIDA 283
                                   577778888888845566******965 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.057
                                   EEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                   +++ GppG+GKt l k v+ + 
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAVATES 512
                                   6788**********99998765 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.83
                                   EEEEEET.T--EEEEEETT...---SSEETTEEE-HHH.HHHHHHHHHHHHHHHH-EEEE---.STTGGG-HHHHHHHHHH CS
                      NTPase_1  46 gFkivdlasgeegiLarve...akreprvgkyvvdves.feelalealrkalseadviviDEi.GkmElkskkfkeaveev 121
                                    F+i ++   ++ +La+     +  e   g    d+e+ + e +++a+r  +s +d    DE+ G+mE   k++ke ++++
  gi|70606628|ref|YP_255498.1| 628 RFEILKV-HTKNVPLAEDVsleDIAEKAEGYTGADLEAlVREATINAMRSIYSMCDKQSRDECkGNMECYQKHIKECMNKT 707
                                   5777777.5566666665545444555566666777775677788899988899999999999999999999999888765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.14        44      14      39 ..     209     233 ..     203     235 .. 0.81
   2 ?    3.0   0.0      0.39   1.2e+02      22      39 ..     491     508 ..     473     510 .. 0.85
   3 ?   -0.2   0.2       3.9   1.2e+03      87     147 ..     679     742 ..     628     746 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                        AAA_23  14 eidFskgltlItGpNGaGKTTildAi 39 
                                    id  kg+ l++Gp G+GKT + +A+
  gi|70606628|ref|YP_255498.1| 209 GIDPPKGI-LLYGPPGTGKTLLARAL 233
                                   56666777.9***********99998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.39
                        AAA_23  22 tlItGpNGaGKTTildAi 39 
                                    l++Gp G+GKT +  A+
  gi|70606628|ref|YP_255498.1| 491 ILLFGPPGTGKTMLAKAV 508
                                   499**********99886 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.9
                        AAA_23  87 trsiererelskkkgkttkkaklellei...deleqfisellgskkiilnlilflgqerfeefe 147
                                    ++ +++r + k++++ ++k ++e +++   + +++ +++ l++ k++l++ +++  erf +++
  gi|70606628|ref|YP_255498.1| 679 SMCDKQSRDECKGNMECYQKHIKECMNKtsfKVSKEDFEKALNVVKASLTQADIQRYERFSKEL 742
                                   5556667777777778888887777766666777788888888888888888888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.88u 0.35s 00:00:01.23 Elapsed: 00:00:00.54
# Mc/sec: 4180.06
//
Query:       gi|70606629|ref|YP_255499.1|  [L=1048]
Description: reverse gyrase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-72  243.5   1.0      3e-71  240.6   1.0    2.4  1  Topoisom_bac  DNA topoisomerase
    9.7e-27   93.2   0.3    6.8e-26   90.5   0.0    2.5  2  Toprim        Toprim domain
  ------ inclusion threshold ------
      0.064   13.7   0.2        0.8   10.2   0.0    2.8  3  Toprim_4      Toprim domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.6   1.0     5e-75     3e-71       2     413 .]     604    1038 ..     603    1038 .. 0.79

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 5e-75
                  Topoisom_bac    2 inenlvdaaeaRrelDwliGinlsrlltk................klkg..kkvlsaGRVqtptLaliveRereienFv 62  
                                     n nlv+++ +Rr+ D++iG++ls +l++                +     +k+lsaGRVqtp+L++iv+R+ e+++ +
  gi|70606629|ref|YP_255499.1|  604 FNVNLVKSQLVRRIEDRWIGFKLSSILQTrfwpeyckslssnkqlN--CneNKNLSAGRVQTPVLSWIVDRYTEYQRNK 680 
                                    588**********************999878888777766553322..1459*************************** PP

                  Topoisom_bac   63 peeyweveatlkkekkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkk.ppplpfdtttLqkeasrkl 140 
                                    ++ y+    +l  ++         k++ + ++++   +++++          ++ e++  p p p++t+tL+++ ++ +
  gi|70606629|ref|YP_255499.1|  681 SRVYYGKIDQL--QDIVI---YVPKQDGVRKNSKIVVVFNEI----------NQLEEEFgPLP-PYTTDTLLSDSNNFF 743 
                                    ****9753232..22222...345556666667777777777..........34445554888.*************** PP

                  Topoisom_bac  141 glsakktlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeA 219 
                                    glsa +t++iaq+L+e  glitY+RTds+r+s++  ++ + ++l++  g++y +     +k ++++    ++  +aHe 
  gi|70606629|ref|YP_255499.1|  744 GLSAPETMRIAQDLFEL-GLITYHRTDSNRISNTG-ISVAENYLKDVLGDKYTN----IFK-PRSW----GDG-GAHEG 810 
                                    ****************6.****************9.999999999987766655....665.6666....455.8**** PP

                  Topoisom_bac  220 IrPteelp.klkels...............ddekklYelIvrrflaslmkdakyeettvklev..eeeefkasgktile 280 
                                    IrPt+ ++ ++  l+               +++ k+Y++I+rrf+ s++ + k+++  vk+e   e+++ k+++++ + 
  gi|70606629|ref|YP_255499.1|  811 IRPTKPIDvEQ--LRllieegelelakrltNNHFKVYDIIFRRFISSQIIPLKVRKEIVKIELygENKKEKINSNQNII 887 
                                    ******99644..3344566677788888899999**************************996544445555555555 PP

                  Topoisom_bac  281 kGfkkvy.keekkeeeee............elpelke.geevkv.keveleekkTkpp.kryteasLikamekagiGtp 343 
                                    +  + +  +   + e  +               +lke g ++++  ++e+++ + k   + yt+a+L+ +m++++iG+p
  gi|70606629|ref|YP_255499.1|  888 EVITGITlP-GIDTEISKfayvpvrnvsrsVAERLKElGRSIPTdFSIEISNSFIKSTvNLYTQADLVMEMKNKKIGRP 965 
                                    555555542.222222235567666666653333444455555435667777776654399****************** PP

                  Topoisom_bac  344 aTraeiieklvergYverk.k.kslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevld 413 
                                    +T+a+ii ++++rgYv ++ k k+l+pt+lG ++++ l e++ ++vs++ T++l + +d ++ g+++++evl+
  gi|70606629|ref|YP_255499.1|  966 STYATIIGTILRRGYVLESlKtKKLIPTRLGVEVNKYLnENYGRFVSEDRTRKLLQLMDMVEAGQEKYEEVLK 1038
                                    ****************999888****************8888****************************985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.29   1.7e+03      66      66 ..      85      85 ..      20     166 .. 0.52
   2 !   90.5   0.0   1.1e-29   6.8e-26       1     103 []     426     589 ..     426     589 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                                  E CS
                        Toprim 66 i 66
                                  +
  gi|70606629|ref|YP_255499.1| 85 V 85
                                  1 PP

  == domain 2  score: 90.5 bits;  conditional E-value: 1.1e-29
                                   EEEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS.................TTEEEEE.. CS
                        Toprim   1 elvivEgpsdaktiakalg..................sgfqavtaslGhildlet.................efkpvye.. 44 
                                   +l +vE+p++akti+++++                  ++ ++vtas Gh++dl+t                  f p+y+  
  gi|70606629|ref|YP_255499.1| 426 VLLVVESPNKAKTISSFFSrpsirqignmrvyetvlgDKVLMVTASGGHVYDLTTqdmgiygvdimkqnsslVFIPIYNsi 506
                                   699*********************************************************************666666666 PP

                                   .........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEE CS
                        Toprim  45 .........................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvef 100
                                                            +++d  k +++l+ la +ade+++ tDpD+eGe+iaw+l+ +l+++++n i+r+ef
  gi|70606629|ref|YP_255499.1| 507 kkcennhqftdffesnkcprcmttkVRYDSLKSINVLRNLAVEADEVLIGTDPDTEGEKIAWDLYLALRPYNSN-IRRAEF 586
                                   667777777788888889********************************************************.****** PP

                                   SSS CS
                        Toprim 101 sei 103
                                   +e+
  gi|70606629|ref|YP_255499.1| 587 HEV 589
                                   *96 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2     7e+03      37      63 ..     405     432 ..     396     448 .. 0.70
   2 ?   10.2   0.0   0.00013       0.8      37      87 ..     532     583 ..     528     585 .. 0.74
   3 ?   -1.2   0.0      0.48   2.8e+03      38      77 ..     998    1039 ..     971    1046 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                      Toprim_4  37 irpeklktenlve.aekkvkevilaldg 63 
                                    +++klk e  v+ a++kvk v+l++++
  gi|70606629|ref|YP_255499.1| 405 NEISKLKNEGNVApALQKVKTVLLVVES 432
                                   3344555544444899999999999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                      Toprim_4  37 irpeklktenlve.aekkvkevilaldgDaeGeataerlaellleegvkvtr 87 
                                   +r ++lk+ n+++    +++ev++ +d+D eGe+ a  l+ +l++ + +++r
  gi|70606629|ref|YP_255499.1| 532 VRYDSLKSINVLRnLAVEADEVLIGTDPDTEGEKIAWDLYLALRPYNSNIRR 583
                                   5555666644444466677****************99888877777777776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.48
                      Toprim_4   38 rpeklktenlve..aekkvkevilaldgDaeGeataerlael 77  
                                    +  k+  en+ +  +e+ ++++++++d  ++G++  e+++++
  gi|70606629|ref|YP_255499.1|  998 EVNKYLNENYGRfvSEDRTRKLLQLMDMVEAGQEKYEEVLKQ 1039
                                    444555555555778888899999999999999999998884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1048 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1322  (0.0737353); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.87u 0.30s 00:00:01.17 Elapsed: 00:00:00.50
# Mc/sec: 6260.65
//
Query:       gi|70606630|ref|YP_255500.1|  [L=297]
Description: hypothetical protein Saci_0840 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-17   61.2   0.0    1.2e-16   60.9   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
      0.062   12.6   0.1       0.18   11.1   0.1    1.7  2  TMP-TENI      Thiamine monophosphate synthase
       0.13   11.6   0.0       0.22   10.9   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0     2e-20   1.2e-16      10     249 ..      11     245 ..       2     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2e-20
                                   STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS.........SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEE CS
                  CN_hydrolase  10 kaadleanlqklleliaeAarkgadLivlPElfitgy.........keeahfleaAeaglgetlallaalarkngiavvig 81 
                                   k a+++an++k+ +li+ A++kga+L+vlP lf  g          k++  ++ +Ae+++g + + l +la +  +++ +g
  gi|70606630|ref|YP_255500.1|  11 KEASRKANIEKARRLIKVAKEKGAKLVVLPSLFPIGNlfevyenekKSRSVIRNLAEKIPGSISEMLINLAMEGEVHLMAG 91 
                                   678999*****************************99*******999999999999************************* PP

                                   .EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHHH CS
                  CN_hydrolase  82 .liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpel 161
                                    ++e+  +++k+  + t ++++++g+++gkyrK+ +       +++  r   ++g+ +p+f +   + G+   ++ + pe+
  gi|70606630|ref|YP_255500.1|  92 pILEQ--AGPKI--FLTSLIISPQGEIIGKYRKVII-------SEKDTRLGISSGK-EPMFLSLDKRYGIISEDDLFSPEI 160
                                   77777..*****..*********************6.......4555555555555.78999999999**999******** PP

                                   HHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSS CS
                  CN_hydrolase 162 lralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglgee 242
                                    r+lal     ++   +   + k+ + +    ++ +r len+++ i + +    e++++     +++++ +  +  ++ e+
  gi|70606630|ref|YP_255500.1| 161 NRILALGSSVAVIG--SIKAYSKNNSSDIIKHVAISRTLENEIPYILVGEMIEDENGDIIGSSPTFVTSVNSLVYKQAEED 239
                                   ******99999999..4468999************************9999995555555555556666555555555555 PP

                                   STEEEEE CS
                  CN_hydrolase 243 eegvlia 249
                                     +vl++
  gi|70606630|ref|YP_255500.1| 240 D-TVLYV 245
                                   4.46665 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.1e-05      0.18      28      62 ..       4      38 ..       2      41 .. 0.95
   2 ?   -2.1   0.0      0.34     2e+03     150     158 ..     200     208 ..     158     228 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.1e-05
                      TMP-TENI 28 tlvqlRekeldarellelaeklaalcrkygvplii 62
                                   l++lR ke+++++ +e+a++l ++++++g++l++
  gi|70606630|ref|YP_255500.1|  4 GLLHLRLKEASRKANIEKARRLIKVAKEKGAKLVV 38
                                  6899*****************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.34
                      TMP-TENI 150 eiPvvaiGG 158
                                   eiP + +G 
  gi|70606630|ref|YP_255500.1| 200 EIPYILVGE 208
                                   244444444 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.7e-05      0.22      64     119 ..      13      68 ..       4      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                                   S.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHH..HHHHHHHHHHHHHHHH CS
                  AP_endonuc_2  64 r.reesvdalkraielaaaLGapllvlhpGtagagpkgsee..eawerlaeslnelady 119
                                   + r++ +++++r i+ a++ Ga+l+vl++    ++ ++  e  e+ ++ +++++ la++
  gi|70606630|ref|YP_255500.1|  13 AsRKANIEKARRLIKVAKEKGAKLVVLPSL---FPIGNLFEvyENEKKSRSVIRNLAEK 68 
                                   246666**********************88...55555555558888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2110.44
//
Query:       gi|70606631|ref|YP_255501.1|  [L=109]
Description: 30S ribosomal protein S25 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-19   70.1  11.4    1.7e-19   69.9  11.4    1.0  1  Ribosomal_S25   S25 ribosomal protein
    0.00013   21.8   1.1     0.0062   16.5   0.2    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00099   18.6   0.6       0.36   10.4   0.2    2.5  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0012   18.7   1.8     0.0042   17.0   0.3    2.4  3  MarR            MarR family
      0.003   16.9   0.4     0.0046   16.3   0.4    1.3  1  EAP30           EAP30/Vps36 family
     0.0043   16.9   3.0       0.01   15.7   0.5    2.3  3  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0072   16.6   1.6       0.99    9.8   0.1    2.2  2  Rrf2            Transcriptional regulator
      0.008   16.1   0.8      0.008   16.1   0.8    2.0  3  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.011   15.6   2.5       0.66    9.8   0.2    2.4  2  IF2_N           Translation initiation factor IF-2, N-termina
      0.016   15.4   0.4      0.016   15.4   0.4    2.4  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.17   11.8   0.1       0.72    9.8   0.0    2.0  3  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9  11.4     1e-22   1.7e-19       8      99 ..      15     106 ..      10     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1e-22
                 Ribosomal_S25   8 akaaaakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLreleekglikl 88 
                                     ++ +++++k+ +K+ ++++ k+  ++ +++dk+t++k+ +e +k k+itp+++++++++++s+A+++L+ele++g++ +
  gi|70606631|ref|YP_255501.1|  15 RVKKMEEEQQKKGQKRTTSKTGKEITSKSITIDKDTVSKVQEELKKEKIITPYTLASKINVTISVAKKILEELERQGMLAK 95 
                                   3344444444555777888999*********************************************************** PP

                 Ribosomal_S25  89 vskhraqviYt 99 
                                   v k+r+ v+Y 
  gi|70606631|ref|YP_255501.1|  96 VTKNRRIVVYQ 106
                                   **********5 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0085        14      34      52 ..      47      65 ..      18      69 .. 0.84
   2 !   16.5   0.2   3.8e-06    0.0062      24      61 ..      66     106 ..      64     109 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0085
                                  SHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 34 tretvsrilseLkreglis 52
                                     tvs++  eLk+e++i+
  gi|70606631|ref|YP_255501.1| 47 DKDTVSKVQEELKKEKIIT 65
                                  5679**************8 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.8e-06
                                   HHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEEEEES- CS
                     HTH_Crp_2  24 qeelAsmlGltretvsrilseLkreglis..r.grririld 61 
                                      lAs +++t +   +il eL+r+g++   + +rri++ +
  gi|70606631|ref|YP_255501.1|  66 PYTLASKINVTISVAKKILEELERQGMLAkvTkNRRIVVYQ 106
                                   5679*************************753345599865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0053       8.7      30      44 ..       8      22 ..       4      24 .. 0.87
   2 !   10.4   0.2   0.00022      0.36      12      46 ..      58      92 ..      53      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                        HTH_24 30 SpstvnrrlkrLeee 44
                                  +++t+ +r+k++eee
  gi|70606631|ref|YP_255501.1|  8 PIGTIEKRVKKMEEE 22
                                  689**********97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
                        HTH_24 12 LqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                  L+k+  i+   LA ++++++s  ++ l++Le++G 
  gi|70606631|ref|YP_255501.1| 58 LKKEKIITPYTLASKINVTISVAKKILEELERQGM 92
                                  555555666679*********************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.88   1.4e+03      32      44 ..      10      22 ..       8      23 .. 0.82
   2 ?    0.2   0.0      0.43   7.1e+02      25      44 ..      42      61 ..      37      65 .. 0.79
   3 !   17.0   0.3   2.6e-06    0.0042      16      58 ..      62     102 ..      56     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.88
                                  HHHHHHHHHHHHT CS
                          MarR 32 stvtrvldrLekk 44
                                  +t+ + ++++e++
  gi|70606631|ref|YP_255501.1| 10 GTIEKRVKKMEEE 22
                                  6788899***986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
                                  HHHTS-HHHHHHHHHHHHHT CS
                          MarR 25 kklgvskstvtrvldrLekk 44
                                  k + ++k tv++v  +L k+
  gi|70606631|ref|YP_255501.1| 42 KSITIDKDTVSKVQEELKKE 61
                                  56889999999998888776 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 2.6e-06
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58 
                                     ++   La+k++v++s + ++l +Le++G++ +  +  +rR+
  gi|70606631|ref|YP_255501.1|  62 KIITPYTLASKINVTISVAKKILEELERQGMLAKVTK--NRRI 102
                                   5578899*************************99877..6666 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   2.8e-06    0.0046     174     232 ..      47      93 ..       8      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                         EAP30 174 ntdqvevlevakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                   ++d+  v +v ++l       ++++ +t   la++    ++++++ak+ Leeler+G+l
  gi|70606631|ref|YP_255501.1|  47 DKDT--VSKVQEEL-------KKEKIITPYTLASK---INVTISVAKKILEELERQGML 93 
                                   2222..33444444.......22257******888...*******************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.7     6e+03      33      47 ..       6      20 ..       4      22 .. 0.67
   2 ?    2.1   0.1      0.11   1.9e+02      24      48 ..      35      60 ..      30      66 .. 0.73
   3 !   15.7   0.5   6.2e-06      0.01      23      61 ..      64     102 ..      57     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                                  TSSCHCHHHHHHHHH CS
                          TrmB 33 gvprskvYevLrsLe 47
                                  + p  ++ + ++++e
  gi|70606631|ref|YP_255501.1|  6 KKPIGTIEKRVKKME 20
                                  667777777777776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                                  HHCHH.CCCTTSSCHCHHHHHHHHHH CS
                          TrmB 24 tadei.aeelgvprskvYevLrsLed 48
                                  t +ei ++ + +++ +v +v ++L++
  gi|70606631|ref|YP_255501.1| 35 TGKEItSKSITIDKDTVSKVQEELKK 60
                                  56666245678999999999888876 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 6.2e-06
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                          TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61 
                                    t +++a++++v  s + ++L++Le+ G+  ++ +++++
  gi|70606631|ref|YP_255501.1|  64 ITPYTLASKINVTISVAKKILEELERQGMLAKVTKNRRI 102
                                   6899***************************99998664 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0057       9.4      26      56 ..      34      65 ..      23      68 .. 0.79
   2 !    9.8   0.1   0.00061      0.99      30      56 ..      68      94 ..      64      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0057
                                  B-HHHHHH.HHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 26 vsseeiae.rqnispsylekilakLrkaglvk 56
                                   + +ei + +  i +  ++k+ ++L+k+++++
  gi|70606631|ref|YP_255501.1| 34 KTGKEITSkSITIDKDTVSKVQEELKKEKIIT 65
                                  455677653779****************9996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00061
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 30 eiaerqnispsylekilakLrkaglvk 56
                                  ++a++ n+  s+++kil++L+++g++ 
  gi|70606631|ref|YP_255501.1| 68 TLASKINVTISVAKKILEELERQGMLA 94
                                  699*********************986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.4   2.3e+03      31      42 ..      11      22 ..      10      27 .. 0.85
   2 ?   -2.8   0.0       3.8   6.3e+03      17      47 ..      35      40 ..      28      44 .. 0.53
   3 !   16.1   0.8   4.9e-06     0.008       5      49 ..      54      99 ..      50     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.4
                        HTH_11 31 tvrrdIkaLeel 42
                                  t+ +++k++ee 
  gi|70606631|ref|YP_255501.1| 11 TIEKRVKKMEEE 22
                                  899999999875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.8
                        HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgvpIe 47
                                  +g+e                         I+
  gi|70606631|ref|YP_255501.1| 35 TGKE-------------------------IT 40
                                  3333.........................33 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 4.9e-06
                        HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg..vpIese 49
                                  + e L ++++ i+  +LA ++nv+ ++  + +++Le +g  +++++ 
  gi|70606631|ref|YP_255501.1| 54 VQEEL-KKEKIITPYTLASKINVTISVAKKILEELERQGmlAKVTKN 99
                                  55667.66666***************************977777765 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0004      0.66      28      53 ..      35      60 ..      28      61 .. 0.89
   2 ?    5.5   0.2     0.009        15       4      33 ..      64      94 ..      62      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                         IF2_N 28 lGievkshsssLDeetaeliaeefgi 53
                                   G+e  s s ++D++t+ ++ ee++ 
  gi|70606631|ref|YP_255501.1| 35 TGKEITSKSITIDKDTVSKVQEELKK 60
                                  69999******************986 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.009
                         IF2_N  4 irVyeLAkeLgvk...skevikkLfkelGievk 33
                                  i+ y LA +++v+   +k+++++L + +G+  +
  gi|70606631|ref|YP_255501.1| 64 ITPYTLASKINVTisvAKKILEEL-ERQGML-A 94
                                  677889999997755579999999.669987.4 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   3.2e+03      38      49 ..      11      22 ..      10      25 .. 0.79
   2 ?    1.5   0.1      0.21   3.4e+02      29      49 ..      41      61 ..      28      63 .. 0.82
   3 ?   15.4   0.4   9.7e-06     0.016      19      53 ..      60      94 ..      49     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                  HHHHHHHHHHHT CS
                Fe_dep_repress 38 sVsemlkkLekd 49
                                  ++ + +kk+e++
  gi|70606631|ref|YP_255501.1| 11 TIEKRVKKMEEE 22
                                  667889999875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                                  HHHHTS-HHHHHHHHHHHHHT CS
                Fe_dep_repress 29 aerLnvspssVsemlkkLekd 49
                                  ++ + + + +Vs+  ++L+k+
  gi|70606631|ref|YP_255501.1| 41 SKSITIDKDTVSKVQEELKKE 61
                                  788999999999999998875 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 9.7e-06
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++k++++  la+ +nv  s + + l++Le++G + 
  gi|70606631|ref|YP_255501.1| 60 KEKIITPYTLASKINVTISVAKKILEELERQGMLA 94
                                  57899***************************875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   5.2e+03      37      47 ..      11      21 ..      10      22 .. 0.76
   2 ?   -0.2   0.0      0.58   9.4e+02      33      51 ..      46      64 ..      42      68 .. 0.84
   3 ?    9.8   0.0   0.00044      0.72      23      59 ..      65      99 ..      56     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                                  HHHHHHHHHHH CS
                        MarR_2 37 avsrilkrLva 47
                                  ++ +++k++++
  gi|70606631|ref|YP_255501.1| 11 TIEKRVKKMEE 21
                                  56689999987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.58
                                  SSHHHHHHHHHHHHHTTSE CS
                        MarR_2 33 lsksavsrilkrLvaaGLv 51
                                  ++k +vs++ ++L +   +
  gi|70606631|ref|YP_255501.1| 46 IDKDTVSKVQEELKKEKII 64
                                  79999*9999999887766 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00044
                                  EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                        MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                  t+  la + +++ s + +il++L+++G++ +++    
  gi|70606631|ref|YP_255501.1| 65 TPYTLASKINVTISVAKKILEELERQGMLAKVTK--N 99
                                  78889************************99865..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2633  (0.146857); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 703.45
//
Query:       gi|70606632|ref|YP_255502.1|  [L=251]
Description: hypothetical protein Saci_0842 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-19   68.7   0.1    9.5e-19   67.1   0.1    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.4e-06   27.7   0.5    4.3e-06   26.2   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00054   19.8   0.1     0.0016   18.3   0.0    1.8  2  MarR             MarR family
    0.00062   20.2   0.0     0.0013   19.2   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
     0.0038   17.0   0.1       0.01   15.7   0.1    1.7  1  TFIIE_alpha      TFIIE alpha subunit
     0.0045   17.3   0.1     0.0098   16.2   0.1    1.6  1  Penicillinase_R  Penicillinase repressor
     0.0047   17.0   0.0      0.019   15.1   0.0    1.9  2  HTH_28           Helix-turn-helix domain
     0.0072   16.3   0.0      0.018   15.0   0.0    1.6  1  PadR             Transcriptional regulator PadR-like family
     0.0072   16.5   0.0      0.017   15.3   0.0    1.5  1  HTH_34           Winged helix DNA-binding domain
     0.0092   15.9   0.0       0.02   14.8   0.0    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0097   15.8   0.0      0.016   15.1   0.0    1.3  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.042   14.2   0.0       0.13   12.7   0.0    1.8  1  Rrf2             Transcriptional regulator
      0.085   12.5   0.0       0.31   10.6   0.0    1.9  3  SMC_ScpB         Segregation and condensation complex subunit
      0.091   12.6   0.0       0.15   11.9   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
       0.15   11.0   0.0       0.21   10.5   0.0    1.3  1  TnsD             Tn7-like transposition protein D
       0.16   12.0   0.0       0.29   11.2   0.0    1.3  1  HTH_29           Winged helix-turn helix


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   8.5e-22   9.5e-19       3      66 ..      20      83 ..      19      85 .. 0.97
   2 ?   -2.7   0.0       5.1   5.7e+03      51      59 ..      98     109 ..      96     126 .. 0.53

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 8.5e-22
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                  ++G+s +E kvY+ Ll +g++ta+++++  +++++kvY++L++Le +G+++r+ ++p lY+a +
  gi|70606632|ref|YP_255502.1| 20 VFGISRNELKVYFLLLVNGKMTAKDVSNSMNISYTKVYSILSKLEARGWIKRVGKKPSLYSANP 83
                                  79**********************************************************9976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                                   SEEEESST...T CS
                          TrmB  51 lVerekgr...p 59 
                                   +Ver++++   p
  gi|70606632|ref|YP_255502.1|  98 MVERIEREliiP 109
                                   667666554441 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   3.9e-09   4.3e-06       2      48 .]      24      70 ..      23      70 .. 0.97
   2 ?   -1.6   0.2       1.8     2e+03       3      13 ..     203     213 ..     202     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.9e-09
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +++++k++ lL  n++++ ++++   ++S + v   l +Le  G+Ik
  gi|70606632|ref|YP_255502.1| 24 SRNELKVYFLLLVNGKMTAKDVSNSMNISYTKVYSILSKLEARGWIK 70
                                  5799******************************************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                        HTH_24   3 etdrkILelLq 13 
                                   +td+ IL +++
  gi|70606632|ref|YP_255502.1| 203 ITDKGILLIIK 213
                                   699****9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.5e-06    0.0016       1      49 [.      23      71 ..      23      75 .. 0.95
   2 ?   -1.9   0.0         3   3.4e+03      21      42 ..     118     139 ..     116     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  ++++++++ ++l  +g ++ ++  + +++s + v  +l +Le +G+i+R
  gi|70606632|ref|YP_255502.1| 23 ISRNELKVYFLLLVNGKMTAKDVSNSMNISYTKVYSILSKLEARGWIKR 71
                                  68899999999*************************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3
                                   HHHHHHHTS-HHHHHHHHHHHH CS
                          MarR  21 seLakklgvskstvtrvldrLe 42 
                                   + L + ++vs+ ++ +++++L 
  gi|70606632|ref|YP_255502.1| 118 TSLYNVISVSSENLPNMITQLL 139
                                   5677788999999999999986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0013      17      54 ..      38      75 ..      27      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                        HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                  ++++++d++  +n++++ + ++l+kL+++G+++r g++
  gi|70606632|ref|YP_255502.1| 38 GKMTAKDVSNSMNISYTKVYSILSKLEARGWIKRVGKK 75
                                  88999***************************999985 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   8.9e-06      0.01      10      90 ..      20     104 ..      15     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                                   CS-..HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE..TTTEEEEEEEEEECCCHCCCHH CS
                   TFIIE_alpha  10 fyg..eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd..eekswykyywrinyeklvdvvk 86 
                                   ++g   +  +v + Ll +g++t  d+++ ++i  +++ ++L +L   + +k + ++    + +  +  w   +++++d+v 
  gi|70606632|ref|YP_255502.1|  20 VFGisRNELKVYFLLLVNGKMTAKDVSNSMNISYTKVYSILSKLEARGWIKRVGKKPslYSANPVTDVWVSVKRNIMDMVE 100
                                   555445778999**************************************9988888666777777788888888888887 PP

                                   HHHH CS
                   TFIIE_alpha  87 rkle 90 
                                   r  +
  gi|70606632|ref|YP_255502.1| 101 RIER 104
                                   7555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   8.7e-06    0.0098       1      65 [.      23      82 ..      23     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.7e-06
                                  ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
               Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65
                                  ++  E++v+ +l  +g++t+k+v + ++      y+ V ++l++L+++g+++r  ++   +Ys++
  gi|70606632|ref|YP_255502.1| 23 ISRNELKVYFLLLVNGKMTAKDVSNSMNIS----YTKVYSILSKLEARGWIKRVGKK-PSLYSAN 82
                                  688999*****************9987765....******************99854.4457765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.7     3e+03      15      26 ..      14      25 ..       9      30 .. 0.81
   2 !   15.1   0.0   1.7e-05     0.019       8      41 ..      34      68 ..      32      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                        HTH_28 15 vreaArelgisr 26
                                  +  +   +gisr
  gi|70606632|ref|YP_255502.1| 14 IGKIGSVFGISR 25
                                  6678899***99 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.7e-05
                        HTH_28  8 llaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                  ll +G+ +++++++ ++is++ vy+ ++++e+ G+
  gi|70606632|ref|YP_255502.1| 34 LLVNGKmTAKDVSNSMNISYTKVYSILSKLEARGW 68
                                  5678988**************************97 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.6e-05     0.018      24      49 ..      46      71 ..      39      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                  TT-CCTTHHHHHHHHHHHHHTTSEEE CS
                          PadR 24 egllelseGslYpaLkrLekeglves 49
                                  ++ +++s++++Y +L++Le+ g++++
  gi|70606632|ref|YP_255502.1| 46 SNSMNISYTKVYSILSKLEARGWIKR 71
                                  45699*******************86 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.017       3      46 ..      28      71 ..      27      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                  l+v  +L+++ +++++++++++++++ + ++ l+kLe+ g+i++
  gi|70606632|ref|YP_255502.1| 28 LKVYFLLLVNGKMTAKDVSNSMNISYTKVYSILSKLEARGWIKR 71
                                  788889************************************85 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.8e-05      0.02      21      54 ..      39      73 ..      19      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.T CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr.g 54
                                  ++t ++ ++ ++++   v  ils+L+ +g+i+r g
  gi|70606632|ref|YP_255502.1| 39 KMTAKDVSNSMNISYTKVYSILSKLEARGWIKRvG 73
                                  7999***************************9535 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.016       2      54 ..      22      72 ..      21      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  g+++ ++ v + L  ++   +t++++   +++s   v  il +L+a+G++ r+
  gi|70606632|ref|YP_255502.1| 22 GISRNELKVYFLLLVNGK--MTAKDVSNSMNISYTKVYSILSKLEARGWIKRV 72
                                  566666666677777877..******************************997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011      0.13      24      57 ..      38      71 ..      30      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvks 57
                                  ++++++++++++nis + +  il+kL+  g++k 
  gi|70606632|ref|YP_255502.1| 38 GKMTAKDVSNSMNISYTKVYSILSKLEARGWIKR 71
                                  459*****************************85 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.31      74     131 ..      16      76 ..       2      84 .. 0.75
   2 ?   -2.6   0.0       3.2   3.6e+03     135     159 ..     110     133 ..      96     134 .. 0.71
   3 ?   -3.2   0.0       4.9   5.5e+03     111     128 ..     190     207 ..     184     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                      SMC_ScpB  74 kekkktrLsqaaletLaiIaykqpvtraeiee...iRGvnsdsvvrtLlerglieekgrke 131
                                   k  +   +s+ +l++  +  ++ + t +++++   i   +++s++++L +rg+i+++g+k+
  gi|70606632|ref|YP_255502.1|  16 KIGSVFGISRNELKVYFLLLVNGKMTAKDVSNsmnISYTKVYSILSKLEARGWIKRVGKKP 76 
                                   55555667888888888888888889988886222556779*****************875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                      SMC_ScpB 135 rpilYgtTekFleyfglksleeLpk 159
                                    +il++ T  +++ + ++s e+Lp+
  gi|70606632|ref|YP_255502.1| 110 MSILFSSTTSLYNVISVSS-ENLPN 133
                                   5788999999999998877.77876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
                      SMC_ScpB 111 sdsvvrtLlerglieekg 128
                                    ++ v++++  gli++kg
  gi|70606632|ref|YP_255502.1| 190 QKKYVNSMFGSGLITDKG 207
                                   567899999999999876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.15      17      51 ..      38      72 ..      36      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  + +t +++++   ++ ++v+ +L+ L+ +G++++ 
  gi|70606632|ref|YP_255502.1| 38 GKMTAKDVSNSMNISYTKVYSILSKLEARGWIKRV 72
                                  6799****************************986 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00019      0.21     175     227 ..       9      67 ..       1     106 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                          TnsD 175 yrisrikkfGivweerlkeLvee......eglslkeiAkelgvdiktVlryakklgllk 227
                                     i+ri k+G+v   +++eL+ +       +++ k++++ ++++  +V+++++kl+   
  gi|70606632|ref|YP_255502.1|   9 EIIGRIGKIGSVFGISRNELKVYflllvnGKMTAKDVSNSMNISYTKVYSILSKLEARG 67 
                                   5699*****************999****9*************************98655 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.29       5      41 ..      33      68 ..      32      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                        HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                  lll++  + t +++   +++s+++vy +l   e+ G+
  gi|70606632|ref|YP_255502.1| 33 LLLVNGKM-TAKDVSNSMNISYTKVYSILSKLEARGW 68
                                  66777777.9*********************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1298.74
//
Query:       gi|70606633|ref|YP_255503.1|  [L=50]
Description: hypothetical protein Saci_0843 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-09   36.7   0.0    3.1e-09   36.4   0.0    1.1  1  RHH_1            Ribbon-helix-helix protein, copG family
    4.5e-05   23.8   0.0    4.9e-05   23.7   0.0    1.1  1  ParD_antitoxin   Bacterial antitoxin of ParD toxin-antitoxin 
     0.0016   18.6   0.0     0.0018   18.5   0.0    1.1  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
     0.0018   18.1   0.0     0.0025   17.7   0.0    1.3  1  VapB_antitoxin   Bacterial antitoxin of type II TA system, Va
  ------ inclusion threshold ------
      0.084   13.0   0.0      0.094   12.8   0.0    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   8.7e-13   3.1e-09       2      38 ..       4      41 ..       4      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.7e-13
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                  ++++l+e+ le++del+  ++  SrSe+IR Al +++ 
  gi|70606633|ref|YP_255503.1|  4 ITVKLPEQFLEAIDELVNTGRyTSRSEVIRLALNDFIR 41
                                  89*******************************99875 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.4e-08   4.9e-05       6      38 ..       5      37 ..       2      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.4e-08
                                  EE---HHHHHHHHHHHCTTS-SSHHHHHHHHHH CS
                ParD_antitoxin  6 svvLgehfsafidsqvaaGrYgsaseviraaLr 38
                                   v L e f   id  v++GrY s sevir aL 
  gi|70606633|ref|YP_255503.1|  5 TVKLPEQFLEAIDELVNTGRYTSRSEVIRLALN 37
                                  5789999**********************9996 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.9e-07    0.0018       6      41 ..       4      39 ..       2      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.9e-07
                         RHH_8  6 vtinlgvvDLgqiDlLveeGfYsnRtDlirtairaq 41
                                  +t+ l    L  iD Lv+ G Y++R+++ir a+ + 
  gi|70606633|ref|YP_255503.1|  4 ITVKLPEQFLEAIDELVNTGRYTSRSEVIRLALNDF 39
                                  78888888899*******************997654 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.9e-07    0.0025      10      39 ..      14      43 ..      13      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.9e-07
                                  XXXXXXXXXXXXXXXXXXXXXXXXX----- CS
                VapB_antitoxin 10 eLlaeAirltglktKrEaVnlALreLiqrr 39
                                  e ++e +  ++++ ++E+++lAL ++i+++
  gi|70606633|ref|YP_255503.1| 14 EAIDELVNTGRYTSRSEVIRLALNDFIRKE 43
                                  56788888899****************986 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.094      92     119 ..       4      32 ..       1      35 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
               HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgfl 119
                                   i + lpe+ l+ iD++v++ + +sRS  +
  gi|70606633|ref|YP_255503.1|   4 ITVKLPEQFLEAIDELVNTGRyTSRSEVI 32 
                                   6799***************99679**987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 278.27
//
Query:       gi|70606634|ref|YP_255504.1|  [L=255]
Description: hypothetical protein Saci_0844 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-30  104.0   0.0    1.3e-29  103.6   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.4e-10   41.2   0.0    1.9e-10   40.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.6e-08   34.6   0.0    2.1e-08   34.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    4.9e-07   30.4   0.0    8.1e-07   29.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    3.4e-05   24.4   0.0    6.1e-05   23.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    7.2e-05   22.2   0.0    0.00013   21.3   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00013   21.7   0.0    0.00023   20.9   0.0    1.3  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    0.00017   21.1   0.0    0.00023   20.7   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0006   20.8   0.0      0.001   20.1   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
     0.0007   19.2   0.0     0.0041   16.7   0.0    2.0  1  MTS              Methyltransferase small domain
    0.00074   19.5   0.0    0.00093   19.2   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    0.00084   19.3   0.0     0.0018   18.2   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
     0.0081   15.4   0.0      0.013   14.7   0.0    1.2  1  Methyltransf_3   O-methyltransferase
  ------ inclusion threshold ------
      0.011   15.6   0.0        0.2   11.5   0.0    2.1  1  Methyltransf_23  Methyltransferase domain
      0.036   13.7   0.1       0.13   11.9   0.1    1.9  1  UPF0020          Putative RNA methylase family UPF0020
      0.055   12.5   0.0      0.076   12.1   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.12   12.0   0.0       0.18   11.4   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.15   11.1   0.0       0.23   10.6   0.0    1.2  1  Exonuc_X-T_C     Exonuclease C-terminal


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.3e-32   1.3e-29       3     188 ..      58     236 ..      57     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.3e-32
                         GCD14   3 vyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekare 83 
                                   +y+l+ptP      L+   q+ly +Di  ii +  ++pGs +ve+GtGsg l+ ++a  ++   ++ t++  e+  + a+ 
  gi|70606634|ref|YP_255504.1|  58 AYLLKPTPIDLYRGLKRLSQVLYPKDIGYIIYSSGVQPGSTIVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKR 138
                                   59******888899******************************************************************* PP

                         GCD14  84 efrehelsqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgf 164
                                   +    +ls+ +  + +D+ +eG  eev  +vDa+fLD+P Pw+a++ + kal k +g l  f P ++q+ + +  L++  f
  gi|70606634|ref|YP_255504.1| 139 NASYLGLSDRIIFKLKDI-REGI-EEV--NVDAIFLDMPDPWNAMETVRKAL-KPSGSLIIFVPTVNQIEKVIPSLSD--F 212
                                   *****************9.5899.889..9**********************.67777889***************87..* PP

                         GCD14 165 teietlevllrtyevrkskleeid 188
                                   +++++ e+ +r+y+++++ ++  +
  gi|70606634|ref|YP_255504.1| 213 VDVHAEELIIREYQMKENAVRPRN 236
                                   ****************98876655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.9e-13   1.9e-10       4     113 ..      96     198 ..      94     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.9e-13
               Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsne 82 
                                   g +++++G+G+G+lt+ la  lg   ++v  D  e++   A+ na+ lgl+ ++ F+  di e +e+     ++D i+   
  gi|70606634|ref|YP_255504.1|  96 GSTIVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSdRIIFKLKDIREgIEE----VNVDAIFL-- 170
                                   67899**************9999999************************99***********9996....35888888.. PP

               Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                      +++dp +++e + ++lkp g l+i  p 
  gi|70606634|ref|YP_255504.1| 171 ---DMPDPWNAMETVRKALKPSGSLIIFVPT 198
                                   ...6**********************98777 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   2.1e-11   2.1e-08      70     180 ..      92     202 ..      54     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.1e-11
                                   T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEEES CS
                          PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaihvg 149
                                    +++g+ ++e G+GsG+lt  la ++g+++++v+ +  +++++ akrn   l+l+ ++i++  D r+G ee    dai++ 
  gi|70606634|ref|YP_255504.1|  92 GVQPGSTIVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSdRIIFKLKDIREGIEEVN-VDAIFLD 171
                                   489**************************************************9889************9875.8*****9 PP

                                   SBBS.S--HHHHHTEEEEEEEEEEESBSSSEE CS
                          PCMT 150 aaap.eiPealidQLkeGGrlvvPvgeeeeQv 180
                                      p +  e+  + Lk+ G l++ v  + +Q 
  gi|70606634|ref|YP_255504.1| 172 MPDPwNAMETVRKALKPSGSLIIFVP-TVNQI 202
                                   98874677888889*******99887.55554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   8.1e-10   8.1e-07       1      97 []      99     190 ..      99     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 8.1e-10
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhls 78 
                                   ++++G+G+G ltl la  lg + k++  D+ e+m ++a+++a+  gl  ++ f  +d+++   e+  +D++++        
  gi|70606634|ref|YP_255504.1|  99 IVEAGTGSGFLTLSLAYFLGnSTKIVTYDVREDMQDIAKRNASYLGLsdRIIFKLKDIREGI-EEVNVDAIFLD------- 171
                                   789*************888559*********************99999**********9954.4568*****93....... PP

                                   HHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                    +d  +a++ ++++Lkp G
  gi|70606634|ref|YP_255504.1| 172 MPDPWNAMETVRKALKPSG 190
                                   35677899********998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   6.1e-08   6.1e-05       2      96 .]     101     194 ..     100     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.1e-08
                                   EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCH CS
               Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedp 77 
                                   ++G+G+G l+  la      +++v+ D+ + m ++ak++as  gl  ++ f   d+++  +e+  +D++++      ++dp
  gi|70606634|ref|YP_255504.1| 101 EAGTGSGFLTLSLAYFLgnsTKIVTYDVREDMQDIAKRNASYLGLsdRIIFKLKDIRE-GIEEVNVDAIFLD-----MPDP 175
                                   78************433678*************************9999999999998.9*********988.....5*** PP

                                   HHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                     a++ +++ Lkp G l+i
  gi|70606634|ref|YP_255504.1| 176 WNAMETVRKALKPSGSLII 194
                                   ****************986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.4e-07   0.00013      39     151 ..      87     194 ..      79     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                                   HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EE CS
               Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfD 118
                                   ++  ++v++g+++++  +G+g l+++l+  +g++ k+v  D+ e+m +++++ +   g + +i f      +L+   +  +
  gi|70606634|ref|YP_255504.1|  87 IIYSSGVQPGSTIVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSdRIIF------KLKDIREGIE 161
                                   56678999***********************************************9999956665......6666777777 PP

                                   EEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
               Ubie_methyltran 119 vvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                    v v   + +++D  +a++++++ lkp G l++
  gi|70606634|ref|YP_255504.1| 162 EVNVDAIFLDMPDPWNAMETVRKALKPSGSLII 194
                                   777777788999999999999999999999876 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.3e-07   0.00023       3      49 ..       2      48 ..       2      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                       GCD14_N  3 pfraGdrVqLtDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGs 49
                                  p+++Gd V +    +r + + L +++ f t++G+i+  +lIG + Gs
  gi|70606634|ref|YP_255504.1|  2 PLNEGDPVVIWVDPKRIYLVKLIQNKVFSTDKGYIDLGKLIGLEYGS 48
                                  7999999988655569**************************99886 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-07   0.00023     158     258 ..      92     194 ..      82     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                          PrmA 158 lvkegeevlDvGtGSGiLaia..aakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvivaN 233
                                    v++g++++  GtGSG L++     + +  k+v +D+ e   ++ak+Na++ ++++++ ++  +++ +   e ++d i+  
  gi|70606634|ref|YP_255504.1|  92 GVQPGSTIVEAGTGSGFLTLSlaYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSDRI-IFKLKDIREgieEVNVDAIFLD 171
                                   58999***********976651055556789*************************98.4455555542215556655544 PP

                          PrmA 234 ILaevlielaedikklvkeggllil 258
                                    + ++  + +e++ k++k++g+li+
  gi|70606634|ref|YP_255504.1| 172 -MPDPW-NAMETVRKALKPSGSLII 194
                                   .23333.445677777777777775 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     1e-06     0.001       1     102 [.     100     193 ..     100     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiDg 77 
                                   vE G+ sG+ tl l++ l +    ++v+ d  +   + + +a++    +gl+dr+ +  +d +e +++++   +D +f+D+
  gi|70606634|ref|YP_255504.1| 100 VEAGTGSGFLTLSLAYFLGNST--KIVTYDVRE---DMQDIAKRnasyLGLSDRIIFKLKDIREGIEEVN---VDAIFLDM 172
                                   89*************9999876..699999999...555666656666********************99...9******9 PP

               Methyltransf_24  78 ghaaeavledleallprlapggvvl 102
                                   +    +  +++e++++ l+p g ++
  gi|70606634|ref|YP_255504.1| 173 P----DPWNAMETVRKALKPSGSLI 193
                                   8....88888999999999877665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0041      33     104 ..      97     171 ..      90     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                                   SEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE- CS
                           MTS  33 gkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsN 104
                                    +++  G+G G+l+++la +  + + ++ +dv     ++ak+n++  +l+  + +  +d+ e +ee ++d+i   
  gi|70606634|ref|YP_255504.1|  97 STIVEAGTGSGFLTLSLAYFLGNSTkIVTYDVREDMQDIAKRNASYLGLSdrIIFKLKDIREGIEEVNVDAIFLD 171
                                   578999*************9988777***********************99999999**************9765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.4e-07   0.00093      25      94 ..      95     161 ..      73     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.4e-07
               Methyltransf_32  25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeats 94 
                                   +  t+v++G G g+L+  la+    +++k+v  d++e++ + a++ a+ lg  +++r+ f+ ++i+e ++
  gi|70606634|ref|YP_255504.1|  95 PGSTIVEAGTGSGFLTLSLAY-FLGNSTKIVTYDVREDMQDIAKRNASYLG--LSDRIIFKLKDIREGIE 161
                                   5579*****************.45699********************9999..88888887777776655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.8e-06    0.0018      11      86 ..      92     168 ..      88     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.8e-06
               Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                    v++gs+++  Gt  g+l++ l+   g+ +k++  D++e   + ak+n++  gl+d+i + l d  e ++e +vd++
  gi|70606634|ref|YP_255504.1|  92 GVQPGSTIVEAGTGSGFLTLSLAyFLGNSTKIVTYDVREDMQDIAKRNASYLGLSDRIIFKLKDIREGIEEVNVDAI 168
                                   58999***************9983479999**********************************9999998889987 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.013      51     118 ..      99     166 ..      93     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                   EEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTS CS
                Methyltransf_3  51 vleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkd 118
                                   ++e G+  G+  L++a  l +  ki++ d+ ++  +ia++     g+ ++i ++  d ++ +ee+  d
  gi|70606634|ref|YP_255504.1|  99 IVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSDRIIFKLKDIREGIEEVNVD 166
                                   7899***************************************************9999998887655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002       0.2      22     124 ..      95     201 ..      73     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
               Methyltransf_23  22 aggrvLdiGcGtGillevlren...gfsvtgvDlspeaveiae................kakkaqkdqfdeqeaaepqgkf 83 
                                   +g+ +++ G+G+G l+ +l+++    ++++ +D ++ +++ia+                k                  + +
  gi|70606634|ref|YP_255504.1|  95 PGSTIVEAGTGSGFLTLSLAYFlgnSTKIVTYDVREDMQDIAKrnasylglsdriifklK--------D-------IREGI 160
                                   567899*******88777766532167********9999998655554444332221110........1.......11233 PP

               Methyltransf_23  84 dlIvlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                   + +     +  +pdp  ++ ++++ lkp G l++ +p++++
  gi|70606634|ref|YP_255504.1| 161 EEVNVDAIFLDMPDPWNAMETVRKALKPSGSLIIFVPTVNQ 201
                                   33333344445566667777777777777777777766665 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00013      0.13      76     130 ..     120     173 ..      86     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--- CS
                       UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpP 130
                                     k++  D  + + + a++Na++ g++d+i f+ +d+++   +e +vd+i  ++P
  gi|70606634|ref|YP_255504.1| 120 STKIVTYDVREDMQDIAKRNASYLGLSDRIIFKLKDIREGI-EEVNVDAIFLDMP 173
                                   567999******************************99755.56689*9999998 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.6e-05     0.076      21      69 ..      86     137 ..      80     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                                   HHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHH CS
                        RrnaAD  21 eIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllq 69 
                                    I+  + +++  t++e g+G G+lT +La  +    + v +  +e++  + +
  gi|70606634|ref|YP_255504.1|  86 YIIYSSGVQPGSTIVEAGTGSGFLTLSLAYFLgnsTKIVTYDVREDMQDIAK 137
                                   578888899*******************988877778888888888776655 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.18       7      88 ..      94     173 ..      89     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEE.S-CTCCHHHHCC..EEEEEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivle.aDarkidkvlggelfDriLlD 86 
                                   q++ ti+++ ++ G  T  +a ++ n+ ++v  d+ +   +  ++n + Lg+ + i+++  D+r+    + +  +D i lD
  gi|70606634|ref|YP_255504.1|  94 QPGSTIVEAGTGSGFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYLGLSDRIIFKlKDIREG---IEEVNVDAIFLD 171
                                   567789999999999999***********************************7776652688877...556669****** PP

                                   E- CS
               Methyltr_RsmB-F  87 aP 88 
                                    P
  gi|70606634|ref|YP_255504.1| 172 MP 173
                                   98 PP

>> Exonuc_X-T_C  Exonuclease C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00023      0.23      32      91 ..     107     168 ..      97     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                                   EEEEEEEEE-SS-TTEEEEEETTS--HHHHHS-HHH..HHHHHTSTTTTT.TSS----EEEE CS
                  Exonuc_X-T_C  32 ialvlplawhptnknavivvDLaeDpsellelsaee..lrerlftkkeelaegeerlplkli 91 
                                     l l la+   n+++++++D++eD++++++ +a    l +r+  k +++ eg e++ +  i
  gi|70606634|ref|YP_255504.1| 107 GFLTLSLAYFLGNSTKIVTYDVREDMQDIAKRNASYlgLSDRIIFKLKDIREGIEEVNVDAI 168
                                   556788999999******************99998733589**************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1737.82
//
Query:       gi|70606635|ref|YP_255505.1|  [L=109]
Description: hypothetical protein Saci_0845 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0018   18.6   3.5     0.0025   18.2   3.5    1.3  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.012   15.1   0.7       0.53    9.7   0.1    2.2  2  ArenaCapSnatch  Arenavirus cap snatching domain
      0.033   14.2   6.7      0.073   13.2   0.7    2.3  2  DUF826          Protein of unknown function (DUF826)
      0.081   12.4   1.5      0.093   12.2   1.5    1.0  1  DIT1_PvcA       Pyoverdine/dityrosine biosynthesis protein


Domain annotation for each model (and alignments):
>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   3.5   5.7e-07    0.0025      36     103 ..      38     105 ..      12     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.7e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHH- CS
                  V-ATPase_G_2  36 eaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAvelilkaVl 103
                                   e   +++ + Ae+ + ++ ae e++ aee +++r ++ ++ ++e +++++ aea l++Av+ ++   l
  gi|70606635|ref|YP_255505.1|  38 ESLTQKLKSVAEEYVTSISAELERKYAEEANKLRLKYGEERSKEINKIKQLAEANLDKAVDFVISKLL 105
                                   5556788899***************************************************9998765 PP

>> ArenaCapSnatch  Arenavirus cap snatching domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0029        13     108     132 ..      18      42 ..       3      48 .. 0.83
   2 ?    9.7   0.1   0.00012      0.53      94     125 ..      41      72 ..      39      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0029
                                   SHHHHHHHHHHHHHHHHTTHHHHHH CS
                ArenaCapSnatch 108 spaefekkyiedlkkleqlkedlks 132
                                   + +e ekk  ed kkl  l e l++
  gi|70606635|ref|YP_255505.1|  18 NLKEIEKKIAEDGKKLILLSESLTQ 42 
                                   56799************99998865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                                   ETTEEEEEEEEE-SSHHHHHHHHHHHHHHHHT CS
                ArenaCapSnatch  94 tgnslillecfvrsspaefekkyiedlkkleq 125
                                   t++   + e +v s  ae+e+ky e+ +kl  
  gi|70606635|ref|YP_255505.1|  41 TQKLKSVAEEYVTSISAELERKYAEEANKLRL 72 
                                   5666667899*******************975 PP

>> DUF826  Protein of unknown function (DUF826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.8      0.01        46       2      28 ..      20      46 ..      19      59 .. 0.89
   2 ?   13.2   0.7   1.6e-05     0.073       9      50 ..      64     105 ..      55     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                        DUF826  2 sEIkslVtedlVKeaLrSeeVrkalKa 28
                                   EI   + ed  K +L+Se   + lK 
  gi|70606635|ref|YP_255505.1| 20 KEIEKKIAEDGKKLILLSESLTQKLKS 46
                                  599999**************9999996 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
                        DUF826   9 tedlVKeaLrSeeVrkalKaklrkdlesqiDaeVDavLaeLl 50 
                                    e++ K  L+ +e r+   +k+++  e+ +D +VD v+ +Ll
  gi|70606635|ref|YP_255505.1|  64 AEEANKLRLKYGEERSKEINKIKQLAEANLDKAVDFVISKLL 105
                                   67888888888888888889*********************8 PP

>> DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.5   2.1e-05     0.093      74     156 ..       5      91 ..       2     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                   TT--HHHHHHHHHHHHHHHHHCT-TTEEEE-GGG-GGGGGG.....................TT-HHHHHHHHHHHH---H CS
                     DIT1_PvcA  74 igvddeevdaYgeeLrelakekglediefvrlkdlleseee.aeeeseells......eeeyleeaeklrkeLlksfgede 147
                                   i+v  + v +Y+++L+e+ k+++ +  +++ l++ l+++ +   ee     +      e +y eea+klr +  ++ +++ 
  gi|70606635|ref|YP_255505.1|   5 IKVYADAVVKYETNLKEIEKKIAEDGKKLILLSESLTQKLKsVAEEYV---TsisaelERKYAEEANKLRLKYGEERSKEI 82 
                                   7888999****************9889999999999666554333333...234488899999999999998888888887 PP

                                   HHHHHHHTT CS
                     DIT1_PvcA 148 eelrkeike 156
                                   +++++  + 
  gi|70606635|ref|YP_255505.1|  83 NKIKQLAEA 91 
                                   777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1681  (0.0937587); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 640.16
//
Query:       gi|70606636|ref|YP_255506.1|  [L=319]
Description: hypothetical protein Saci_0846 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-25   88.3   5.9    7.9e-25   88.1   5.9    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.047   13.7   0.7       0.17   11.9   0.1    2.3  3  ER              Enhancer of rudimentary
      0.067   12.9   0.1         13    5.5   0.0    2.6  2  Ten1_2          Telomere-capping, CST complex subunit
       0.13   12.0   0.0       0.21   11.3   0.0    1.3  1  Rep_N           Rep protein catalytic domain like


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   5.9   1.8e-28   7.9e-25       2     335 ..       8     312 ..       7     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.8e-28
                                   HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGG.GS-H..HH CS
                vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklre.qapgp.sr 80 
                                   +A+ r+++++ Lt+++  +Ll+ ++ +d++++Lk+++       e   p+  +d e++lr+k +++++ l++   + + + 
  gi|70606636|ref|YP_255506.1|   8 TALARVYKANTLTKSTVLELLDTKNWKDAVTILKDKGLIP----EI--PSKLEDAENLLRDKAVKTVATLKQyTLNSKvAA 82 
                                   79********************************975555....33..67899*******************767777999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SS.SS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC.. CS
                vATP-synt_AC39  81 efldyllyrydidNvklllrgklsgdldleeleeklhplg.elsaldldklieaksveelyeallgtpyakyleealdele 160
                                   ++ld++     ++ + +++ + + g ++           + ++ ++ +   ++++s+e+++++++   y+++l+  ld+  
  gi|70606636|ref|YP_255506.1|  83 QILDLYEFILTLEDIEAVISASVLG-KKDGV--------NvRYLKELV--DVRPQSLEDVVSTVK-GTYKEALRFSLDKAG 151
                                   ************************5.63232........224445555..579************.5688889888*9999 PP

                                   .--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-S--HHHHH CS
                vATP-synt_AC39 161 etgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkllipggslypegle 241
                                   + +++++i + L  ++ ++l+++++++ g+ +   +ei++  +D  ++++++ +k +       r     ++ +++++ ++
  gi|70606636|ref|YP_255506.1| 152 N-KTPSRINSYLEYYFVDRLYQIISNITGDARMKAQEIICGYVDYVAVSLAFTLKEQE------R-----SICKISSDIIR 220
                                   9.9*****************************************************33......5.....568******** PP

                                   HHHTT-G.....GG.GGSSTSSTTGGGTT--S..HHHHHHHHHHHHHHHHHTTTSSSTSTHHHHHHHHHHHHHHHHHHHHH CS
                vATP-synt_AC39 242 alaeaedveellaalkyteygelleealeeags.lksledaldealvkllkkafrqqfsvgvfyaYlklkeqEirnlrwIa 321
                                   ++++++ ++el ++l++t+y++ll+ ++    + l s+ +a +    +   +af+++ sv  ++a   l + + ++l++I+
  gi|70606636|ref|YP_255506.1| 221 DIINMARPDELSNILSRTSYAKLLTLGNP--YDlLASFKRAARVLARNASINAFMNSPSVVSVLAIAELTKLDYEDLVTIL 299
                                   *************************6644..555999999997777777777***************************** PP

                                   HHHHHT--SHHHHG CS
                vATP-synt_AC39 322 egiaqglpkekIre 335
                                   +gia +++ +kI++
  gi|70606636|ref|YP_255506.1| 300 NGIALKIN-DKIKN 312
                                   ******55.89987 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.8e-05      0.17      43      88 ..      74     119 ..      57     128 .. 0.81
   2 ?   -1.1   0.0      0.42   1.9e+03      57      65 ..     164     172 ..     118     208 .. 0.61
   3 ?   -3.7   0.0       2.9   1.3e+04      19      40 ..     290     311 ..     287     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                            ER  43 npskksitYdisdLfefidsladlsaLvleketksylprdkewike 88 
                                   ++ ++++  +i dL+efi +l+d++a+++ +  ++    + +++ke
  gi|70606636|ref|YP_255506.1|  74 YTLNSKVAAQILDLYEFILTLEDIEAVISASVLGKKDGVNVRYLKE 119
                                   3445789999******************999888877777777776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.42
                            ER  57 fefidslad 65 
                                   + f+d+l +
  gi|70606636|ref|YP_255506.1| 164 YYFVDRLYQ 172
                                   333344333 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.9
                            ER  19 ldyesvkealdgicklyeeaLk 40 
                                   ldye++ + l+gi    ++++k
  gi|70606636|ref|YP_255506.1| 290 LDYEDLVTILNGIALKINDKIK 311
                                   5788888888887665555555 PP

>> Ten1_2  Telomere-capping, CST complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0061        27      14      39 ..      55      80 ..      44      84 .. 0.80
   2 ?    5.5   0.0    0.0029        13      82     112 ..      95     125 ..      83     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0061
                        Ten1_2 14 ssgslkegssvRtlGrLksydvatsr 39
                                  + ++l + ++v+t+++Lk+y ++++ 
  gi|70606636|ref|YP_255506.1| 55 DAENLLRDKAVKTVATLKQYTLNSKV 80
                                  56788999************998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0029
                        Ten1_2  82 edgeivlrARvlrcvdgldldlyekaleerr 112
                                   ed e+v+ A vl   dg++++ +++ +++r 
  gi|70606636|ref|YP_255506.1|  95 EDIEAVISASVLGKKDGVNVRYLKELVDVRP 125
                                   56789*********************99985 PP

>> Rep_N  Rep protein catalytic domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.7e-05      0.21      72     156 ..      78     171 ..      21     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.7e-05
                         Rep_N  72 a..........kyflQlEkneegfhlhvlietpgvksrvlGryvsqireklvkvlyeltepkikdkfavaktkkGGknkvv 142
                                   +          ++ l lE+ e+ ++  vl +++gv+ r l + +  +r +  ++++++++ ++k+ +  +  k G k+  +
  gi|70606636|ref|YP_255506.1|  78 SkvaaqildlyEFILTLEDIEAVISASVLGKKDGVNVRYL-KELVDVRPQSLEDVVSTVKGTYKEALRFSLDKAGNKTPSR 157
                                   2444555666689999************************.*********************************99***** PP

                         Rep_N 143 gesyipnyLlpklq 156
                                     sy+++y + +l+
  gi|70606636|ref|YP_255506.1| 158 INSYLEYYFVDRLY 171
                                   ********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2149.96
//
Query:       gi|70606637|ref|YP_255507.1|  [L=109]
Description: hypothetical protein Saci_0847 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 763.67
//
Query:       gi|70606638|ref|YP_255508.1|  [L=326]
Description: oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-47  162.4   0.0    1.8e-47  162.0   0.0    1.2  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.0     1e-51   1.8e-47       1     290 [.      15     304 ..      15     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1e-51
                                   .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE......--SS CS
                  Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv......dlrd 74 
                                   elg+G+w+l +k +  + ++a ++lrra+e Ginf+DtA+vYg+g  e +lG+++++   kr++v+i tK+      +  +
  gi|70606638|ref|YP_255508.1|  15 ELGIGLWSLVTKeWGADVNKAEDILRRAFELGINFYDTADVYGEGLGESILGKVFSS---KRDKVVILTKIgldfyhNSVN 92 
                                   69**********99*******************************************...**************9999999 PP

                                   STTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE.....S--HHHHHHHH CS
                  Aldo_ket_red  75 aeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS.....nfsveqlekak 150
                                   +++++++s + +  ++e+sl+rL+tdyvD+l +H+p+ ++ +  +++d+l+ l+k Gk+r iGv+     ++  e le++ 
  gi|70606638|ref|YP_255508.1|  93 GKYPRNYSLDYLSFAFEKSLERLNTDYVDILMIHNPKINDIKNKKLYDFLDSLRKDGKVRVIGVAlgptlGWGEEGLEAI- 172
                                   9*****************************************************************9999999*****99. PP

                                   HTTT--EEEEE-B-BTT-HHHHTTHHH..HHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHH CS
                  Aldo_ket_red 151 kkkkvkivavqveynllreleeeglle..lckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaa 229
                                      k+   +++  ynl       +l++   + +++++  +  p ++ +l + + +  + +++++r +  + ++++k+ ++ 
  gi|70606638|ref|YP_255508.1| 173 ---KMGYGSLEYIYNLI------ELRPgiEFLNYDIAHFVRVPHASDALNESKWPIYNDPKFHRRYK--DINWINKAIERS 242
                                   ...999***********......4444223344699999***********99999999999988875..558********* PP

                                   HHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HHHHHHHH CS
                  Aldo_ket_red 230 eelselakehgvslaqlalryalsqpavgivipgasnieqlednldalel.klseeevaeld 290
                                   ++l ++a+++ ++laqlal+++l++++v++vip++ +i++le+ +++ +l +l+e e+++l 
  gi|70606638|ref|YP_255508.1| 243 RDLISFARSKHMTLAQLALKFILYNKRVTSVIPNVASISELEEFAKVENLeQLTETEYDYLY 304
                                   *******************************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2336.15
//
Query:       gi|70606639|ref|YP_255509.1|  [L=191]
Description: nucleoside-triphosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-50  170.0   0.0    5.6e-50  169.9   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   3.1e-54   5.6e-50       1     186 [.       9     184 ..       9     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 3.1e-54
                                   EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGG CS
                    Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPGv 79 
                                   i+++T+N++K++e+++i ++  ++v+ l  ++ p+ +E+q +++ee+++  a  a++ ++ p++++DsgL+++aLng+PG+
  gi|70606639|ref|YP_255509.1|   9 IILVTSNENKFKEMNSIAQN--FNVS-LIWFNIPK-VEIQaDSLEEIVKFSAIIAYNqINRPLIVEDSGLFIEALNGFPGP 85 
                                   89***************854..3333.32223344.69999**********99888746889******************* PP

                                   GTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-S CS
                    Ham1p_like  80 ysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeege 160
                                   ys+++       + +++ +++ le  e++r+A+f +vla++d   ++ +lfeG+v G+i +e rg++gfGyDpiF+p++  
  gi|70606639|ref|YP_255509.1|  86 YSNYVR-----RKIGMEGIIRLLE-GEKNRKAYFSTVLAYVDS--TQLKLFEGRVYGSISTEIRGTKGFGYDPIFIPDG-V 157
                                   *****3.....4668899999997.4458************95..6669****************************65.5 PP

                                   S.BTTTS.CHHHHHHSHHHHHHHHHHH CS
                    Ham1p_like 161 k.tfaelskeeknaiShRgkAleklle 186
                                   + tf+e+s+eekn++ShR+ A++k+le
  gi|70606639|ref|YP_255509.1| 158 NlTFGEMSTEEKNKYSHRAIAFRKFLE 184
                                   55***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1231.36
//
Query:       gi|70606640|ref|YP_255510.1|  [L=219]
Description: serine/threonine protein kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-11   43.8   0.0    3.1e-11   43.2   0.0    1.3  1  RIO1            RIO1 family
    9.2e-10   38.3   0.4    1.1e-09   38.0   0.4    1.3  1  Pkinase         Protein kinase domain
    5.3e-09   35.7   0.1    9.3e-09   34.9   0.1    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    1.2e-08   35.2   0.0    0.00015   21.8   0.0    2.1  2  APH             Phosphotransferase enzyme family
    3.9e-06   26.3   0.1    6.4e-06   25.6   0.1    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
    4.1e-05   23.3   0.8    4.9e-05   23.1   0.8    1.5  1  WaaY            Lipopolysaccharide core biosynthesis protein 
      0.005   15.7   0.3     0.0056   15.5   0.3    1.2  1  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.023   14.3   0.1       0.05   13.2   0.1    1.6  1  Choline_kinase  Choline/ethanolamine kinase
      0.034   13.5   0.1      0.058   12.7   0.1    1.4  1  EcKinase        Ecdysteroid kinase
       0.16   11.3   0.6        5.5    6.2   0.0    2.5  3  DUF4135         Domain of unknown function (DUF4135)


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   1.8e-14   3.1e-11      36     155 ..      35     146 ..      19     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1.8e-14
                                   TTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEE..TTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHH CS
                          RIO1  36 krfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielk..rhvlvmefigedgvaapklkdveeeeeaeelyeev 114
                                   +     ++ +  r++ +  ++ E r++  + ++gv+vP  + +   +  +vme+i+  g+ + ++ +    ++++el +e+
  gi|70606640|ref|YP_255510.1|  35 Y-----RNDIVDRAINESRTKLEARMIYSALKSGVNVPAILLVDpiQFLIVMEYIE--GTTLRDIFNQG--RNLRELGKEM 106
                                   2.....3456778888999999*****************9888644789*******..98888888877..7888887776 PP

                                   HHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEET CS
                          RIO1 115 leemrklykeaglvHaDLSeyNvlvdedkvviIDvsQavel 155
                                      m+ l+++a+++H+DL   N++++++++++ID++ a + 
  gi|70606640|ref|YP_255510.1| 107 GL-MISLLHKANIIHGDLTTTNMIYTDEGLFLIDFGLAKKS 146
                                   55.9*******************************866543 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.4   6.3e-13   1.1e-09      69     151 ..      73     149 ..       1     168 [. 0.75

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 6.3e-13
                                   ESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                       Pkinase  69 ekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakele 149
                                   ++ ++++v+ey+eg++l d+ +     + ++++++ k++   ++ lH+++iiH Dl + N+++  ++ l ++DFGlak+ +
  gi|70606640|ref|YP_255510.1|  73 DPIQFLIVMEYIEGTTLRDIFN-----QGRNLRELGKEMGLMISLLHKANIIHGDLTTTNMIYT-DEGLFLIDFGLAKKSN 147
                                   477899***************8.....58999*****************************999.89999********987 PP

                                   SS CS
                       Pkinase 150 ss 151
                                     
  gi|70606640|ref|YP_255510.1| 148 DI 149
                                   65 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   5.2e-12   9.3e-09      37     207 .]      27     182 ..       2     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.2e-12
                           Kdo  37 rggllgklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaela 116
                                    ++ ++k +++    + +++ r   E r++    + gv+vp ++           + l+++e +eg+  L d+ ++     
  gi|70606640|ref|YP_255510.1|  27 FKKRIKKSYRNDIVDRaINESRTKLEARMIYSALKSGVNVPAILLVDP------IQFLIVMEYIEGTT-LRDIFNQ----- 95 
                                   45556666676666666999*********************9998654......5779********86.9999999..... PP

                           Kdo 117 eelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl..kiel 195
                                   ++  r+l k+ g +i+ lh+a++ H+dl   n+    e+     + liD+  a++      +   d++ L+rs++  ++++
  gi|70606640|ref|YP_255510.1|  96 GRNLRELGKEMGLMISLLHKANIIHGDLTTTNMIYTDEG-----LFLIDFGLAKKSN-DIEDFATDIHVLLRSLEsiHSHF 170
                                   99999***************************9999998.....9*****9998777.7788899********99444455 PP

                           Kdo 196 teadweallraY 207
                                   ++  +e ++++Y
  gi|70606640|ref|YP_255510.1| 171 KDEIFEGFKEGY 182
                                   555577787777 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   5.4e-05     0.097      42     108 ..      54     116 ..      42     118 .. 0.80
   2 !   21.8   0.0   8.2e-08   0.00015     166     207 ..     116     154 ..     111     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                   HHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS.HHHHHHHHHHHHHHHHHHCCHHCH CS
                           APH  42 allrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr.klsaaqlpellealgeflaalhqv 108
                                   ++     k+gv vP++l       +      ++ey++g++l++  ++ + l+el+ ++g ++  lh +
  gi|70606640|ref|YP_255510.1|  54 RMIYSALKSGVNVPAILL-----VDPIQFLIVMEYIEGTTLRDiFNQGRNLRELGKEMGLMISLLHKA 116
                                   555444578899999999.....223335789************999******************987 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 8.2e-08
                                   EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHC CS
                           APH 166 tvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlav 207
                                   + ++HgDl + N++ + d+g +  +iDf++a+ ++ + D+a+
  gi|70606640|ref|YP_255510.1| 116 ANIIHGDLTTTNMIYT-DEGLF--LIDFGLAKKSNDIEDFAT 154
                                   569*************.88999..********9999999865 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   3.6e-09   6.4e-06      51     155 ..      52     148 ..       1     171 [. 0.62

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.6e-09
                                   HHHHHHTS-BTTB--EEEEEE.SSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-S CS
                   Pkinase_Tyr  51 eakimkklkhpnivkllgvct.keepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdla 130
                                   ea+++ +   +  v++ ++ + +  + liv+ey++g +L++  ++        ++l ++  ++   ++ L++ +++H dl+
  gi|70606640|ref|YP_255510.1|  52 EARMIYSA-LKSGVNVPAILLvDPIQFLIVMEYIEGTTLRDIFNQG-------RNLRELGKEMGLMISLLHKANIIHGDLT 124
                                   33333332.3333444444443566799***************998.......5666777777888899************ PP

                                   GGGEEEEETTEEEE-STTTHEETTT CS
                   Pkinase_Tyr 131 arNvLlsenkvvkisDfGLardiek 155
                                   + N++ +++ +  + DfGLa++ ++
  gi|70606640|ref|YP_255510.1| 125 TTNMIYTDEGLF-LIDFGLAKKSND 148
                                   ***999977766.55******9843 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.8   2.7e-08   4.9e-05     117     198 ..      76     162 ..       3     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.7e-08
                          WaaY 117 vyimiieyiegielvdmpeiddevka...kikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerkakdr 192
                                    +++++eyieg  l d+ +   ++++   ++   i  lh+ +++ gd    n+i  ++++ +id  l+ k+   e  a d 
  gi|70606640|ref|YP_255510.1|  76 QFLIVMEYIEGTTLRDIFNQGRNLRElgkEMGLMISLLHKANIIHGDLTTTNMIYTDEGLFLIDfgLAKKSNDIEDFATDI 156
                                   5899**************9999988622256668999**************************944456666667777776 PP

                          WaaY 193 idlerh 198
                                     l r 
  gi|70606640|ref|YP_255510.1| 157 HVLLRS 162
                                   555554 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   3.1e-06    0.0056     321     364 ..     111     148 ..      28     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                Pkinase_fungal 321 sLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsd 364
                                   sL++ka+i+H D  + N++ t      ++  +LiD+ lak+ +d
  gi|70606640|ref|YP_255510.1| 111 SLLHKANIIHGDLTTTNMIYT------DEGLFLIDFGLAKKSND 148
                                   7888*************9999......889**********9987 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.8e-05      0.05     143     183 ..     114     152 ..      81     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                                   G-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHH CS
                Choline_kinase 143 spvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDl 183
                                   ++ +  H Dl   N+++  +++ l+lIDF  a  +    D+
  gi|70606640|ref|YP_255510.1| 114 HKANIIHGDLTTTNMIY--TDEGLFLIDFGLAKKSNDIEDF 152
                                   456677***********..99********887766655555 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.2e-05     0.058     217     285 ..     118     186 ..      97     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                      EcKinase 217 lnHGDlwvnNimfkydeegepedvilvDFQlsrygS....palDLlyflyt..steeelrkekfdellriYhesL 285
                                   + HGDl ++N+++    e     + l+DF l++ +      a D++++l +  s+++ +++e f+ + + Y + +
  gi|70606640|ref|YP_255510.1| 118 IIHGDLTTTNMIYTD--E----GLFLIDFGLAKKSNdiedFATDIHVLLRSleSIHSHFKDEIFEGFKEGYSTMM 186
                                   89**********943..3....59*******99875333378999999965447888999999998888887655 PP

>> DUF4135  Domain of unknown function (DUF4135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.74   1.3e+03     274     320 ..      15      60 ..      12      75 .. 0.71
   2 ?    2.9   0.1     0.031        56     139     171 ..     106     140 ..      79     159 .. 0.76
   3 ?    6.2   0.0    0.0031       5.5     265     292 ..     165     192 ..     141     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.74
                       DUF4135 274 ileGFreayelllkhkeellaeegpldafagsevRvvlrpTavYael 320
                                   i eG++++ +++ k++ +   ++ ++d+ a  e+R  l + ++Y+ l
  gi|70606640|ref|YP_255510.1|  15 IYEGYFAGIHAVFKKRIKKSYRNDIVDR-AINESRTKLEARMIYSAL 60 
                                   6789999999999998886666667777.445666666666666665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.031
                       DUF4135 139 aGallallyllgg..tDlheeNliasgeqpvliDl 171
                                   +G ++ ll+  ++   Dl   N+i + e ++liD+
  gi|70606640|ref|YP_255510.1| 106 MGLMISLLHKANIihGDLTTTNMIYTDEGLFLIDF 140
                                   56666666665553369*****************7 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0031
                       DUF4135 265 vspadyleeileGFreayelllkhkeel 292
                                     ++++ +ei eGF+e+y+ +++ ++ +
  gi|70606640|ref|YP_255510.1| 165 SIHSHFKDEIFEGFKEGYSTMMDSDKVI 192
                                   5578899***************887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1601.73
//
Query:       gi|70606641|ref|YP_255511.1|  [L=332]
Description: putative DNA-binding/iron metalloprotein/AP endonuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-78  261.6   0.2    1.2e-77  261.3   0.2    1.0  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   0.2   6.6e-82   1.2e-77       2     271 .]      27     299 ..      26     299 .. 0.95

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 6.6e-82
                                   CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT- CS
                 Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnk 82 
                                   +lanv  +++   +++GG+ P++ +r+H+e+ + ++++al+ea+++++d+d++av+ gPG +++LrvG+++A++lal++nk
  gi|70606641|ref|YP_255511.1|  27 ILANVKDTYI---PPQGGMKPSELARHHVEQAPIIVKKALDEAKVNMKDIDGVAVALGPGIGPALRVGATVARALALSFNK 104
                                   6777777775...******************************************************************** PP

                                   -EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..S....SCCHHHH CS
                 Peptidase_M22  83 PlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpy....pggpkie 159
                                    l++Vnh +ah++ ++++++ ++P++l++sGg+t + +  +++y+++getld+a+g+++d + r  gl      +g  +i+
  gi|70606641|ref|YP_255511.1| 105 KLIPVNHGIAHIEIGMYSTNAKDPLILYLSGGNTIISIFFDRKYRVFGETLDIALGNMIDVFVREAGLAPpyvvNGVHQID 185
                                   ***************9888889*****************99***************************9944544555*** PP

                                   HHHCTC.S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHH CS
                 Peptidase_M22 160 klakeg.kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvilGGvaankr 238
                                    +a +g +++e+p+ +kg+d+s+sGl ta+lk+l+k +  d+++s+ e ++d+l e tera++l++++e++++GGvaa   
  gi|70606641|ref|YP_255511.1| 186 ICADKGkEYVELPYIVKGQDMSYSGLLTAALKLLSKrNLPDICYSVREIAFDMLLEATERAMALTGKNEILVVGGVAASVS 266
                                   ******888*************************7657******************************************* PP

                                   HHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                 Peptidase_M22 239 LrealeeeaeelglkliiPplkyctdnaamiaw 271
                                   L+++le++a+++g++l i p++y  dn+amia+
  gi|70606641|ref|YP_255511.1| 267 LKSKLEKLAADRGAELKIVPSQYSGDNGAMIAY 299
                                   *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 2017.08
//
Query:       gi|70606642|ref|YP_255512.1|  [L=67]
Description: 30S ribosomal protein S27ae [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   53.9   1.7    1.8e-14   53.6   1.7    1.2  1  Ribosomal_S27    Ribosomal protein S27a
    0.00039   20.3   2.1    0.00055   19.9   2.1    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0015   18.4   0.2     0.0033   17.3   0.2    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.002   18.0   1.3     0.0025   17.7   1.2    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0057   16.5   0.5     0.0087   15.9   0.5    1.3  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0082   16.5   1.1       0.44   10.9   0.1    2.0  2  GFA              Glutathione-dependent formaldehyde-activatin
  ------ inclusion threshold ------
      0.016   15.6   1.1      0.031   14.6   1.1    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.025   14.5   1.9       0.08   12.9   1.9    1.8  1  Nudix_N_2        Nudix N-terminal
       0.05   12.4   0.6      0.052   12.3   0.6    1.0  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
      0.058   13.5   3.1       0.15   12.2   0.1    2.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.063   13.4   0.6      0.091   12.9   0.6    1.3  1  FAM72            FAM72 protein
      0.079   12.6   2.3       0.33   10.6   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.089   13.0   1.6       0.94    9.7   0.1    2.3  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.32   10.5   6.3       0.37   10.2   0.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.35   11.0   5.6        2.3    8.4   5.6    2.0  1  UPF0547          Uncharacterised protein family UPF0547
       0.41   10.2   2.1        8.2    6.1   0.1    2.2  2  zf_C2H2_10       C2H2 type zinc-finger
       0.78    9.5   0.1       0.78    9.5   0.1    2.7  3  zinc_ribbon_2    zinc-ribbon domain
       0.81    9.7   7.8        8.4    6.5   7.5    2.1  2  YhfH             YhfH-like protein
          1    9.2   4.8        2.6    7.9   0.2    2.3  2  zinc_ribbon_5    zinc-ribbon domain
          2    7.9   6.2       0.25   10.8   1.0    1.9  2  Mu-like_Com      Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   1.7     2e-17   1.8e-14       1      45 []      17      60 ..      17      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2e-17
                                  SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTT...EEEESSTTTE CS
                 Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkd...RkyCGkCglT 45
                                  v +yY+v++ ++++ ++k+Cpr C  G +MA+h     R++CGkCg+T
  gi|70606642|ref|YP_255512.1| 17 VRTYYEVEQ-DSIKLKNKKCPR-C--GSIMAHHMKpleRWACGKCGYT 60
                                  568******.9***********.*..*******87777*********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   2.1   6.1e-07   0.00055      20      46 .]      34      60 ..      27      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.1e-07
                 Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCrkq 46
                                   CP+Cgs  a+ +k  +++ C +C+++
  gi|70606642|ref|YP_255512.1| 34 KCPRCGSIMAHHMKPLERWACGKCGYT 60
                                  5*******999999999*******985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   3.7e-06    0.0033       4      31 ..      35      61 ..      34      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-06
                                  ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                  Cp Cg+ +    + + +  +C +CgY e
  gi|70606642|ref|YP_255512.1| 35 CPRCGSIMAHHMKPLER-WACGKCGYTE 61
                                  ****************6.8*******86 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.2   2.8e-06    0.0025      29      55 ..      33      60 ..      20      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfe 55
                                  k+C++Cgs++ +  +  +++ C +Cg++
  gi|70606642|ref|YP_255512.1| 33 KKCPRCGSIMAHhMKPLERWACGKCGYT 60
                                  89**********99999*********97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   9.7e-06    0.0087       6      37 ..      34      65 ..      34      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                Zn_ribbon_SprT  6 rCtgCgreythhlsi.rrhnYrCrrCk.gtLrgk 37
                                  +C++Cg+   hh +   r  + C++C+  ++ gk
  gi|70606642|ref|YP_255512.1| 34 KCPRCGSIMAHHMKPlER--WACGKCGyTEFIGK 65
                                  6***************99..66****98888776 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00049      0.44      33      61 ..      16      44 ..       2      48 .. 0.77
   2 ?    6.4   0.1     0.013        12      42      61 ..      44      63 ..      41      67 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                           GFA 33 elkeykktadsgnkvtrsfCpeCgsplys 61
                                   +++y + ++ + k++++ Cp+Cgs + +
  gi|70606642|ref|YP_255512.1| 16 VVRTYYEVEQDSIKLKNKKCPRCGSIMAH 44
                                  67788888899999***********9886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                           GFA 42 dsgnkvtrsfCpeCgsplys 61
                                  ++ ++++r+ C +Cg + + 
  gi|70606642|ref|YP_255512.1| 44 HHMKPLERWACGKCGYTEFI 63
                                  5678999********87665 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1   3.5e-05     0.031       3      36 ..      32      59 ..      30      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
               Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                   k CP Cg+   ++  ++ ++      +C +Cg+
  gi|70606642|ref|YP_255512.1| 32 NKKCPRCGSIMAHHMKPLERW------ACGKCGY 59
                                  599***********9999987......9*****9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   8.9e-05      0.08       3      31 ..      35      60 ..      33      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-05
                                  -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                     Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                  C+ CG+ +++++      eR  C +Cg++
  gi|70606642|ref|YP_255512.1| 35 CPRCGSIMAHHMK---PLERWACGKCGYT 60
                                  *********9995...799********97 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   5.8e-05     0.052     479     529 ..       6      61 ..       2      67 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.8e-05
                                   --SSHHHHHHHHHHHHHTT--EEEEE--EEEETT.--.EESS.......SB-TTT--BE CS
                          NRDD 479 ekknpealeklvkiakktgigYfsinpkidvCnecgy.kgei.......ekCpkCgsee 529
                                   +++n+++ +++v+++++  +   si  k + C++cg     +       + C kCg +e
  gi|70606642|ref|YP_255512.1|   6 KNNNENQSKAVVRTYYE--VEQDSIKLKNKKCPRCGSiM-AHhmkplerWACGKCGYTE 61 
                                   4589999999***8777..9999**************63.33378999*99*****554 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.15      15      34 ..      21      40 ..      18      46 .. 0.78
   2 ?    1.9   0.4      0.27   2.4e+02       7      12 ..      53      58 ..      48      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                   Zn-ribbon_8 15 fevlqsisdapltaCPeCgs 34
                                  +ev q + + ++++CP+Cgs
  gi|70606642|ref|YP_255512.1| 21 YEVEQDSIKLKNKKCPRCGS 40
                                  67888777888999*****9 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                   Zn-ribbon_8  7 rCeeCg 12
                                   C +Cg
  gi|70606642|ref|YP_255512.1| 53 ACGKCG 58
                                  488887 PP

>> FAM72  FAM72 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6    0.0001     0.091      50      81 ..      15      46 ..       6      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                         FAM72 50 dfvgslystesckcklkdiaclkcGnvvGyhv 81
                                   +v + y  e+ + klk+  c +cG ++ +h+
  gi|70606642|ref|YP_255512.1| 15 AVVRTYYEVEQDSIKLKNKKCPRCGSIMAHHM 46
                                  4566778899999****************996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00037      0.33       3      17 ..      33      47 ..      31      48 .. 0.84
   2 ?    2.1   0.2      0.16   1.5e+02       2       9 ..      51      58 ..      50      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                        zf_UBZ  3 ylCerCgkeipesel 17
                                    C+rCg+ + ++++
  gi|70606642|ref|YP_255512.1| 33 KKCPRCGSIMAHHMK 47
                                  68*******999876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                        zf_UBZ  2 tylCerCg 9 
                                   + C +Cg
  gi|70606642|ref|YP_255512.1| 51 RWACGKCG 58
                                  689****8 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.18   1.6e+02       1       8 [.      34      41 ..      34      48 .. 0.78
   2 ?    9.7   0.1    0.0011      0.94      37      47 ..      53      63 ..      51      67 .] 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                zinc_ribbon_13  1 kCpKCgnt 8 
                                  kCp+Cg+ 
  gi|70606642|ref|YP_255512.1| 34 KCPRCGSI 41
                                  6****975 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                zinc_ribbon_13 37 sCknCgYtelY 47
                                   C +CgYte+ 
  gi|70606642|ref|YP_255512.1| 53 ACGKCGYTEFI 63
                                  5********95 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00042      0.37       3      11 ..      33      41 ..      31      43 .. 0.82
   2 ?    3.1   1.0     0.073        66      18      24 ..      53      59 ..      52      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                   zf-ribbon_3  3 vrCPnCGap 11
                                  ++CP+CG++
  gi|70606642|ref|YP_255512.1| 33 KKCPRCGSI 41
                                  79*****85 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.073
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C +CG+
  gi|70606642|ref|YP_255512.1| 53 ACGKCGY 59
                                  5999997 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.6    0.0025       2.3       1      22 [.      33      59 ..      33      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                       UPF0547  1 KvCPeCeakvPvaaq.....fCphCGy 22
                                  K+CP+C ++ ++ ++     +C  CGy
  gi|70606642|ref|YP_255512.1| 33 KKCPRCGSIMAHHMKplerwACGKCGY 59
                                  9********999998666666877887 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.052        47       5      11 ..      35      41 ..      33      43 .. 0.84
   2 ?    6.1   0.1    0.0091       8.2       3      10 ..      52      59 ..      51      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.052
                    zf_C2H2_10  5 CPKCqek 11
                                  CP+C+ +
  gi|70606642|ref|YP_255512.1| 35 CPRCGSI 41
                                  ****875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0091
                    zf_C2H2_10  3 fsCPKCqe 10
                                  ++C KC++
  gi|70606642|ref|YP_255512.1| 52 WACGKCGY 59
                                  79*****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.6   2.3e+03       7      13 ..       9      15 ..       8      16 .. 0.76
   2 ?    9.5   0.1   0.00087      0.78      13      21 ..      32      40 ..      27      42 .. 0.69
   3 ?    3.3   1.8      0.08        72      16      21 ..      54      59 ..      53      60 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.6
                 zinc_ribbon_2  7 aelqdna 13
                                  +e+q +a
  gi|70606642|ref|YP_255512.1|  9 NENQSKA 15
                                  7999887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00087
                 zinc_ribbon_2 13 akFCpyCGt 21
                                  +k Cp+CG+
  gi|70606642|ref|YP_255512.1| 32 NKKCPRCGS 40
                                  667777774 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.08
                 zinc_ribbon_2 16 CpyCGt 21
                                  C +CG+
  gi|70606642|ref|YP_255512.1| 54 CGKCGY 59
                                  777776 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.5    0.0094       8.4      10      24 ..      29      43 ..      27      57 .. 0.89
   2 ?    1.1   0.9      0.45   4.1e+02      14      20 ..      52      58 ..      45      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0094
                          YhfH 10 nLPkKkCteCGkeie 24
                                  +L +KkC+ CG+ + 
  gi|70606642|ref|YP_255512.1| 29 KLKNKKCPRCGSIMA 43
                                  6899*******9885 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.45
                          YhfH 14 KkCteCG 20
                                    C +CG
  gi|70606642|ref|YP_255512.1| 52 WACGKCG 58
                                  5799999 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0029       2.6       9      34 ..      18      41 ..      17      44 .. 0.77
   2 ?    2.8   5.3      0.11     1e+02       4      32 ..      34      58 ..      33      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                 zinc_ribbon_5  9 dtkFklvdsklKksgkkVrCakCaev 34
                                  +t + + ++ +K   k  +C +C+++
  gi|70606642|ref|YP_255512.1| 18 RTYYEVEQDSIKLKNK--KCPRCGSI 41
                                  5777888888887777..59999887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                 zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkkVrCakCa 32
                                  +Cp C++        +K +  +  C+kC+
  gi|70606642|ref|YP_255512.1| 34 KCPRCGSI---MAHHMKPLERWA-CGKCG 58
                                  69999984...567778888885.99997 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00028      0.25      26      33 ..      34      41 ..      25      50 .. 0.76
   2 ?   -0.3   0.4      0.81   7.3e+02       7      10 ..      54      57 ..      47      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                   Mu-like_Com 26 KCPRCGtL 33
                                  KCPRCG +
  gi|70606642|ref|YP_255512.1| 34 KCPRCGSI 41
                                  9*****86 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                   Mu-like_Com  7 CGeC 10
                                  CG+C
  gi|70606642|ref|YP_255512.1| 54 CGKC 57
                                  7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 431.68
//
Query:       gi|70606643|ref|YP_255513.1|  [L=118]
Description: 30S ribosomal protein S24e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-17   63.0   0.1    2.5e-17   62.6   0.1    1.2  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   1.4e-21   2.5e-17       2      76 ..      33     107 ..      32     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.4e-21
                                   EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS-- CS
                Ribosomal_S24e   2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaek 76 
                                   +++ H g++tps++e+ + +a+ + + +dlvvv+++ t++G g + + +++Y+++++++k Ep++++ R + ++ 
  gi|70606643|ref|YP_255513.1|  33 IKLFHIGSGTPSRKELVKAIASTFSTAEDLVVVKKVFTNYGSGISYARVNVYKDKDSLQKLEPQYLIGRDTGQKI 107
                                   6789*****************************************************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 842.95
//
Query:       gi|70606644|ref|YP_255514.1|  [L=265]
Description: ribulose-1,5-biphosphate synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-81  272.9   4.0      2e-81  272.7   4.0    1.0  1  Thi4            Thi4 family
    8.2e-15   55.2   5.5    9.1e-09   35.3   0.5    2.3  2  DAO             FAD dependent oxidoreductase
    5.2e-10   39.4   0.6    2.2e-09   37.4   0.6    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      6e-10   39.1   3.2    7.8e-10   38.7   3.2    1.1  1  FAD_oxidored    FAD dependent oxidoreductase
    1.2e-09   37.7   6.6    1.6e-07   30.8   1.0    2.6  3  FAD_binding_2   FAD binding domain
    1.3e-09   37.7   0.4    1.6e-09   37.4   0.4    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.9e-07   29.3   0.0    7.6e-07   28.7   0.0    1.2  1  FAD_binding_3   FAD binding domain
    4.3e-06   25.7   0.1    5.9e-06   25.2   0.1    1.3  1  HI0933_like     HI0933-like protein
    1.3e-05   24.5   0.7    2.4e-05   23.6   0.7    1.4  1  GIDA            Glucose inhibited division protein A
    0.00013   21.4   0.0    0.00028   20.2   0.0    1.5  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00031   21.2   0.4     0.0013   19.2   0.4    2.1  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0029   17.0   0.1     0.0061   15.9   0.1    1.5  1  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0039   16.3   0.7       0.01   14.9   0.7    1.9  1  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.018   14.2   0.0       0.03   13.5   0.0    1.2  1  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
        0.1   12.6   1.6       0.15   12.0   0.2    2.0  2  NAD_binding_9   FAD-NAD(P)-binding
       0.11   11.3   4.9       0.19   10.6   0.7    2.4  3  Trp_halogenase  Tryptophan halogenase
       0.15   11.4   0.1       0.32   10.3   0.0    1.5  2  GMC_oxred_N     GMC oxidoreductase


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.7   4.0   1.9e-84     2e-81       1     235 []      16     244 ..      16     244 .. 0.99

  Alignments for each domain:
  == domain 1  score: 272.7 bits;  conditional E-value: 1.9e-84
                                   HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT CS
                          Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelg 81 
                                   sr i+++++ed+++++e DvvivGaG++G++aayylak+ +lk++++er++s+GGG+++G +lf+++v++ pa+e+L+e++
  gi|70606644|ref|YP_255514.1|  16 SRYIIKQTMEDWMNFVENDVVIVGAGPAGMSAAYYLAKH-GLKTLVFERRLSFGGGIGGGAMLFHKLVIESPADEVLKEMN 95 
                                   799************************************.***************************************** PP

                                   ---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETB.TEEEEEEEEEHHHHTC..TTTSS.-B-EEEEE CS
                          Thi4  82 ikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivreg.egvaGvvinwtlvela..hdtqscvDPlvira 159
                                   i++e+ +d+v++ d+a+f+++l++ +++ a++k++++v+v+D+i+re+  +vaGv ++wt+ ++a  h     vDP +i a
  gi|70606644|ref|YP_255514.1|  96 IRLEKVEDGVYIVDSAEFMAKLAASAID-AGAKIIHGVTVDDVIFRENpLRVAGVAVEWTATQMAglH-----VDPVFISA 170
                                   ****************************.******************99****************888.....******** PP

                                   EEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                          Thi4 160 kvvvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                   k+vvdatGhd+e+vav+ +ki +      ++ge+s+++e+ae+  v++t  v p+lyvaGm v+ev g++RmGpif
  gi|70606644|ref|YP_255514.1| 171 KAVVDATGHDAEVVAVASRKIPELG--IVIPGERSAYSEMAEKLTVEQTGVVAPGLYVAGMSVTEVRGLPRMGPIF 244
                                   *********************9988..68**********************************************9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.5   8.6e-12   9.1e-09       1      48 [.      34      82 ..      34     100 .. 0.85
   2 !   22.1   0.4     9e-08   9.5e-05     141     207 ..     106     185 ..      97     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 8.6e-12
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48
                                  dvvi+G+G +G+s+Ay+La++g  ++++e++  +g g  g+ + l+h  +
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHGlkTLVFERRLSFG-GGIGGGAMLFHKLV 82
                                  9******************************9999.88888888888766 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 9e-08
                                   EEEEHHHHHHHHHHHHHHTT-EEEESECEEEE..EEEETCEEEEE....EECT.EEEE.....EEEEEEE--GGGHH.HH CS
                           DAO 141 gqvdpakltaalaraaealGveilegtevtgl..eeedgkvwgve....rttp.gend.....aadavVnaaGawsd.ll 207
                                    +vd a+++a la+ a ++G++i+ g +v ++  +e+  +v+gv      t   g  +     +a+avV a+G+ +   +
  gi|70606644|ref|YP_255514.1| 106 YIVDSAEFMAKLAASAIDAGAKIIHGVTVDDVifRENPLRVAGVAvewtATQMaGLHVdpvfiSAKAVVDATGHDAEvVA 185
                                   568****************************645444488899988785333345442689997799*******998422 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.6   2.1e-12   2.2e-09       1      34 [.      37      70 ..      37      87 .. 0.94
   2 ?   -1.4   0.0       2.8     3e+03      44      57 ..     121     134 ..     110     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.1e-12
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                  IvGaG +G++aAy+Lak+g++ l++e+r ++GG 
  gi|70606644|ref|YP_255514.1| 37 IVGAGPAGMSAAYYLAKHGLKTLVFERRLSFGGG 70
                                  9*******************************95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.8
                                   EECTS---EEETTH CS
                 NAD_binding_8  44 rvdygahifhgsgy 57 
                                   ++d ga i+hg+  
  gi|70606644|ref|YP_255514.1| 121 AIDAGAKIIHGVTV 134
                                   68999999999754 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   3.2   7.4e-13   7.8e-10       1     152 [.      34     187 ..      34     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 7.4e-13
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkkrskw 81 
                                   Dvv+vG+gpaG+ AA+  a++G k+l+ e+r   GG   +g+  ++ ++     v++  a+e+l++++ r    l+k ++ 
  gi|70606644|ref|YP_255514.1|  34 DVVIVGAGPAGMSAAYYLAKHGLKTLVFERRLSFGGGIGGGA--MLFHK----LVIESPADEVLKEMNIR----LEKVEDG 104
                                   9***********************************987665..55554....59999999999999552....2222222 PP

                  FAD_oxidored  82 .n.tfepevakavleemlaeagvtvllntrlvevekeg.........kriesvtveske.grktirAkvfiDATg.dGdla 149
                                      +   e++++++   ++  g +++++ ++++v+ ++          + ++ +++        i+Ak ++DATg d++++
  gi|70606644|ref|YP_255514.1| 105 vYiVDSAEFMAKLAASAIDA-GAKIIHGVTVDDVIFREnplrvagvaVEWTATQMAGLHvDPVFISAKAVVDATGhDAEVV 184
                                   22244566666666666655.8999999999888876435555544323444444444434899**********8678888 PP

                  FAD_oxidored 150 ala 152
                                   a a
  gi|70606644|ref|YP_255514.1| 185 AVA 187
                                   877 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.0   1.5e-10   1.6e-07       1      36 [.      34      69 ..      34      76 .. 0.93
   2 !    9.2   0.2   0.00053      0.56     136     201 ..     106     179 ..      97     197 .. 0.83
   3 ?   -1.5   0.0      0.94   9.9e+02     383     410 ..     213     238 ..     208     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.5e-10
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  Dv+++G+G AG++AA+ +a++Glk++v e   +fgg
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHGLKTLVFERRLSFGG 69
                                  9***************************99888776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00053
                                   ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT..EEEEEEEEET......TTTCEE....EEEESEEEE---- CS
                 FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedg..rvtGavvenp......esgrev....rirakavvlatgG 201
                                    +v+  + +a l++sa +ag ++ +   +d++i +++  rv G+ ve             +     i akavv+atg 
  gi|70606644|ref|YP_255514.1| 106 YIVDSAEFMAKLAASAIDAGAKIIHGVTVDDVIFRENplRVAGVAVEWTatqmagL----HvdpvFISAKAVVDATGH 179
                                   567788999*************************9999*********776543333....1556599999******95 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.94
                                   BESTTEEESSBTEEE-STCEESSSSTTS CS
                 FAD_binding_2 383 rvldadgqpipGLYAaGevaaggvhgan 410
                                    v +++g + pGLY aG    + v g  
  gi|70606644|ref|YP_255514.1| 213 TV-EQTGVVAPGLYVAGMSV-TEVRGLP 238
                                   45.889999*******9776.6666655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.4   1.6e-12   1.6e-09       2      87 ..      34     131 ..      33     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.6e-12
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeias................ 57 
                                   dvv++G+GpAG++aa +la++g+k++++e          +g++l+++ ++ + + +v ++ +i++                
  gi|70606644|ref|YP_255514.1|  34 DVVIVGAGPAGMSAAYYLAKHGLKTLVFErrlsfgggiGGGAMLFHKLVIESPADEVLKEMNIRLekvedgvyivdsaefm 114
                                   8***************************88888555666666666666666666666666666658887777666555444 PP

                                   ..HHHHCHHHHCCCCHCCTCEEEEESCEEEEE CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  58 ..evvkklnqgielllgeevvkidpgkkkvkl 87 
                                                      + +id g+k ++ 
  gi|70606644|ref|YP_255514.1| 115 akL---------------AASAIDAGAKIIHG 131
                                   442...............34444444433333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   7.2e-10   7.6e-07       2      33 ..      33      64 ..      32      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 7.2e-10
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   dV+IVGaGpaG+++a  L+++G ++++ e+r
  gi|70606644|ref|YP_255514.1| 33 NDVVIVGAGPAGMSAAYYLAKHGLKTLVFERR 64
                                  59****************************97 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   5.6e-09   5.9e-06       2      37 ..      34      69 ..      33     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.6e-09
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgr 37
                                  dv+++G+G+AG+ aA  +ak+g ++l++e+  ++g 
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHGLKTLVFERRLSFGG 69
                                  8****************************9988885 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.7   2.3e-08   2.4e-05       1      29 [.      34      62 ..      34      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                  dv+++G+G AG+ AA+ +a+ G+k+l + 
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHGLKTLVFE 62
                                  79***********************9985 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.7e-07   0.00028       1      30 [.      36      64 ..      36      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                  +I+GaGPaG++aa+ l k+gl + l+ E+ 
  gi|70606644|ref|YP_255514.1| 36 VIVGAGPAGMSAAYYLAKHGL-KTLVFERR 64
                                  7********************.57999985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   1.2e-06    0.0013       2      34 ..      35      67 ..      34      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkl 34
                                  vv+vG+G  g+ +A +la++g k+ v+er+  +
  gi|70606644|ref|YP_255514.1| 35 VVIVGAGPAGMSAAYYLAKHGLKTLVFERRLSF 67
                                  8****************************9666 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   5.8e-06    0.0061       2      28 ..      43      69 ..      42      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                                  HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                  aG++aA++L+ +G++++v+E r  +GG
  gi|70606644|ref|YP_255514.1| 43 AGMSAAYYLAKHGLKTLVFERRLSFGG 69
                                  9*********************99999 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   9.6e-06      0.01       1      31 [.      34      62 ..      34     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.6e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                  Dvv++GaGpAg+s A  l  ak glk ++ e
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYL--AKHGLKTLVFE 62
                                  9*****************..99999988765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05      0.03       4      39 ..      34      67 ..      32      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                   K_oxygenase  4 DligiGiGpsnLsLailleevkkelkalflerqpef 39
                                  D++++G+Gp+ +s a  l+++   lk+l++er+ +f
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHG--LKTLVFERRLSF 67
                                  9********************9..********9988 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00014      0.15       1      40 [.      36      70 ..      36      91 .. 0.82
   2 ?   -1.5   0.1       2.1   2.2e+03     140     155 ..     164     179 ..     144     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagr 40
                                  +ivGaGp+G++++  L+++      l+  +f++  ++g g+
  gi|70606644|ref|YP_255514.1| 36 VIVGAGPAGMSAAYYLAKHG-----LKTLVFERrLSFG-GG 70
                                  7****************995.....8888888833446.54 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                 NAD_binding_9 140 dgaslaadaVvLAlGh 155
                                   d   + a+aVv A+Gh
  gi|70606644|ref|YP_255514.1| 164 DPVFISAKAVVDATGH 179
                                   4455789999999999 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   0.00018      0.19       1      22 [.      34      55 ..      34      76 .. 0.86
   2 ?    1.5   0.2     0.097     1e+02     149     212 ..     106     182 ..      87     190 .. 0.69
   3 ?   -0.0   0.1      0.29   3.1e+02      12      41 ..     167     196 ..     163     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                  EEEEE--SHHHHHHHHHHHHHT CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                  ++vivG+G+aG  aA +lak++
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHG 55
                                  69*****************987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.097
                                   EEE-HHHHHHHHHHHHHHCT-EEEE--EE.EEEE-T.TS-EEEEEETT...........S-EEE-SEEEE-SGGG-I CS
                Trp_halogenase 149 yhldaalyakfLrrvaearGvtrvegkvv.evqlde.dgrveslrled...........greveadlfiDcsGfrgl 212
                                   y +d a++   L + a ++G ++++g  v +v  +e   rv+++ +e               ++a  ++D++G+ + 
  gi|70606644|ref|YP_255514.1| 106 YIVDSAEFMAKLAASAIDAGAKIIHGVTVdDVIFREnPLRVAGVAVEWtatqmaglhvdPVFISAKAVVDATGHDAE 182
                                   88999999999999999999999999765155556556678877776544555544433333556666666666655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.29
                                   HHHHHHHHHHTTTSSEEEEEE-SSS---SS CS
                Trp_halogenase  12 wlaAaalakalkgklevtlveseeigtvgv 41 
                                   +++A a+  a+ +++ev  v s +i+ +g+
  gi|70606644|ref|YP_255514.1| 167 FISAKAVVDATGHDAEVVAVASRKIPELGI 196
                                   578889999986669999999999998886 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.1   4.3e+03       2      26 ..      34      58 ..      33      61 .. 0.79
   2 ?   10.3   0.0    0.0003      0.32     203     255 ..     122     178 ..     114     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                   GMC_oxred_N  2 delveggGsagsvvAaRLsedpsts 26
                                  d +++g+G ag   A+ L++++ ++
  gi|70606644|ref|YP_255514.1| 34 DVVIVGAGPAGMSAAYYLAKHGLKT 58
                                  6789999999999999998876665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0003
                   GMC_oxred_N 203 lerpnleiltgakaekiilegrkkravGVeasdkkgt.....vkrlvvaakevvvaaG 255
                                   + + +++i+ g++++ +i++++  r+ GV+++ + ++     v  ++++ak vv a G
  gi|70606644|ref|YP_255514.1| 122 IDA-GAKIIHGVTVDDVIFRENPLRVAGVAVEWTATQmaglhVDPVFISAKAVVDATG 178
                                   455.9***************9********99988887666777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1999.61
//
Query:       gi|70606645|ref|YP_255515.1|  [L=69]
Description: hypothetical protein Saci_0855 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00017   21.8   4.8    0.00026   21.2   4.8    1.3  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.028   14.0   0.0    1.2  1  SH3_6            SH3 domain (SH3b1 type)
      0.031   14.2   9.9      0.076   13.0   9.9    1.8  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
       0.08   13.1   0.7       0.13   12.4   0.7    1.5  1  YHS              YHS domain
      0.086   12.2   0.0       0.09   12.1   0.0    1.0  1  DUF3388          Protein of unknown function (DUF3388)
       0.21   11.2   3.6       0.24   11.1   3.6    1.2  1  zf-SNAP50_C      snRNA-activating protein of 50kDa MW C termi


Domain annotation for each model (and alignments):
>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   4.8   8.8e-08   0.00026       1      30 [.      14      45 ..      14      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.8e-08
               Arc_trans_TRASH  1 CDYCGkeivgePivykl..knkvYyvCCktCk 30
                                  C +CGk+i +ePiv+k    nk +++C   C 
  gi|70606645|ref|YP_255515.1| 14 CSWCGKVINNEPIVVKTccNNKPWVFCSRQCY 45
                                  99**************6448*******99995 PP

>> SH3_6  SH3 domain (SH3b1 type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.3e-06     0.028      23      53 .]      20      50 ..      17      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.3e-06
                                  E-TT-EEEEEEE-TTSSEEEEE-SS-EEEEE CS
                         SH3_6 23 lkagtPVlilhaSkDgaWlfVetsfasGWve 53
                                  +  ++P+++ +   ++ W+f+  + ++ Wv+
  gi|70606645|ref|YP_255515.1| 20 VINNEPIVVKTCCNNKPWVFCSRQCYNMWVR 50
                                  5679*************************96 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   9.9   2.5e-05     0.076       4      37 ..      12      44 ..      10      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                        zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsC 37
                                   rC++C+k i + p  ++ +  +++ ++FCS++C
  gi|70606645|ref|YP_255515.1| 12 VRCSWCGKVINNEP-IVVKTCCNNKPWVFCSRQC 44
                                  79************.55666667*********** PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.7   4.3e-05      0.13       5      35 ..      16      46 ..      12      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                           YHS  5 vcgmkvdkekaeekseYkGkeYyFcSegCkd 35
                                  +cg+ +++e    k+  + k + FcS +C++
  gi|70606645|ref|YP_255515.1| 16 WCGKVINNEPIVVKTCCNNKPWVFCSRQCYN 46
                                  8999999999999999999**********97 PP

>> DUF3388  Protein of unknown function (DUF3388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     3e-05      0.09      63     103 ..      18      58 ..       3      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                       DUF3388  63 PrvGktesivaasvcankrwlflsstllkqtvrsqliedey 103
                                    +v   e iv  + c nk w+f s    +  vr+ l ++e 
  gi|70606645|ref|YP_255515.1|  18 GKVINNEPIVVKTCCNNKPWVFCSRQCYNMWVRDWLKSQEQ 58 
                                   578889*******************9999999999887776 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.6   7.9e-05      0.24     141     185 ..       6      51 ..       1      65 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.9e-05
                   zf-SNAP50_C 141 kkklrrkkCkvCekfsakwvvlndkllpedpsyfCd.kCfrslhyd 185
                                   +++++  +C+ C k + +  ++ ++ ++++p  fC+ +C+++   d
  gi|70606645|ref|YP_255515.1|   6 NTNITAVRCSWCGKVINNEPIVVKTCCNNKPWVFCSrQCYNMWVRD 51 
                                   4578899*********99999999***********637**987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 444.63
//
Query:       gi|70606646|ref|YP_255516.1|  [L=220]
Description: phenylacrylic acid decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-24   86.6   0.0    1.9e-24   86.2   0.0    1.1  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   0.0   1.1e-28   1.9e-24       2     125 ..      21     186 ..      20     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 1.1e-28
                                   EEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS...................TCSSHHHHHHCT... CS
                  Flavoprotein   2 killgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaa...............redpilhielrr... 63 
                                   ++++gi+G++++i++++ ++ L++ g++ ++++++ A k+++ke  l+l +               +          +   
  gi|70606646|ref|YP_255516.1|  21 NVVVGISGASGVIYGIRTVKTLNNLGYDQEIIISNGAIKVAEKEcGLDLVStiskfvdgkiyreeeI----------Dapp 91 
                                   79******************************************96666554455655544444432..........0455 PP

                                   .......TESEEEEEEEEHHHHHHHHTT--SSHH............................HHHHHTHCCTTEEEEE.-- CS
                  Flavoprotein  64 .......wadllviaPasantlakianGiadnll............................tlilratakkpiliaPamn 109
                                          +  ++v++P+s++tla i nG++ nl+                             + lr+ ++++++++P ++
  gi|70606646|ref|YP_255516.1|  92 sssshvvKSLGMVVVPCSIKTLAEISNGLSSNLIsrtalnflrikgklvlvlretplgavelRNALRV-TNAGAIVLP-AS 170
                                   55566669*************************************************99887444444.66*******.** PP

                                   HHCCTCSTCHHHHHHH CS
                  Flavoprotein 110 pamyenpqtlknlekl 125
                                   p +y+np+t+++l+++
  gi|70606646|ref|YP_255516.1| 171 PGFYHNPKTFDDLVNF 186
                                   ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1556.44
//
Query:       gi|70606647|ref|YP_255517.1|  [L=132]
Description: hypothetical protein Saci_0857 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 959.82
//
Query:       gi|70606648|ref|YP_255518.1|  [L=181]
Description: tRNA-splicing endonuclease subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-27   94.2   0.0    7.3e-27   93.3   0.0    1.5  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    3.4e-21   74.7   0.2    1.4e-20   72.7   0.2    1.9  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0   8.2e-31   7.3e-27       1      85 []      88     173 ..      88     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 8.2e-31
                                   HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE.TTT CS
                 tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv.dae 80 
                                   f+l y+vy+dLrek +vvrsG+k+GadF++Y+  p+leh+ ylV  ++e++e++++++++ +r++hs++K+lil iv +++
  gi|70606648|ref|YP_255518.1|  88 FELLYTVYEDLREKKFVVRSGMKYGADFAIYTVAPGLEHAPYLVIAIDEEQEISPNEILGFGRVSHSTRKNLILSIVnQRN 168
                                   8899*************************************************************************6666 PP

                                   SCEEE CS
                 tRNA_int_endo  81 gdvty 85 
                                    +++y
  gi|70606648|ref|YP_255518.1| 169 RSIRY 173
                                   66766 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.2   1.5e-24   1.4e-20       1      64 [.       2      75 ..       2      78 .. 0.96
   2 ?   -0.9   0.0      0.14   1.3e+03      22      41 ..     143     164 ..     130     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.5e-24
                                  EEEEEETTEEEESSHHHHHHHHHTTT-SEE..........CCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HH CS
               tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkp..........lidepLqLslvEAlYLlekGklevvkggeplsfe 64
                                  ++ge++gd+vl++d e+ak++y+ g+YGkp          +i++pL Lsl+EAlYL +k+++ev ++g++++  
  gi|70606648|ref|YP_255518.1|  2 IQGEILGDKVLINDVEKAKEIYKLGYYGKPlditkpkspeDIKKPLILSLIEALYLSKKKIIEVIRDGKVIDDA 75
                                  699******************************************************************99865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.14
                                   HHTTT-SEE..CCTSSEEEEHH CS
               tRNA_int_endo_N  22 yekgfYGkp..lidepLqLslv 41 
                                    e  ++G+      ++L Ls+v
  gi|70606648|ref|YP_255518.1| 143 NEILGFGRVshSTRKNLILSIV 164
                                   5555788887777888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1174.33
//
Query:       gi|70606649|ref|YP_255519.1|  [L=210]
Description: hypothetical protein Saci_0859 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-08   33.1   7.8    2.4e-07   30.3   2.0    2.1  2  PhoU_div     Protein of unknown function DUF47
    7.9e-06   26.3  10.5    0.00036   20.9   3.1    2.9  3  PhoU         PhoU domain
     0.0014   18.6   2.7     0.0017   18.4   0.5    1.9  2  Vta1         Vta1 like
     0.0025   17.3   2.0      0.012   15.0   0.7    2.0  2  Tropomyosin  Tropomyosin
  ------ inclusion threshold ------
      0.014   14.6   2.3      0.064   12.4   0.2    2.3  3  RmuC         RmuC family
      0.015   15.6   0.9        2.9    8.2   0.2    2.4  2  DUF948       Bacterial protein of unknown function (DUF948)
      0.022   15.1   0.7      0.047   14.0   0.2    1.8  2  HrpJ         HrpJ-like domain
      0.026   14.5   1.4      0.095   12.6   0.1    2.1  2  PriC         Primosomal replication protein priC
      0.051   13.6   0.3       0.27   11.3   0.0    2.2  3  DUF1664      Protein of unknown function (DUF1664)
      0.081   11.8   2.6       0.17   10.8   0.3    1.9  2  T4_tail_cap  Tail-tube assembly protein
       0.12   12.8   1.4          9    6.8   0.3    3.3  2  DASH_Dad2    DASH complex subunit Dad2
       0.19   11.9   1.9       0.41   10.8   0.6    1.8  2  Interferon   Interferon alpha/beta domain
       0.54   10.3   7.2          2    8.4   0.1    2.8  3  Laminin_II   Laminin Domain II
       0.85    9.8   7.2        1.6    8.9   3.4    2.5  2  Fib_alpha    Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.4    0.0039         5     139     210 ..      29      98 ..       6     101 .. 0.75
   2 !   30.3   2.0   1.9e-10   2.4e-07     121     211 ..     116     205 ..     102     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0039
                      PhoU_div 139 klletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisi 210
                                   +  e+  +  ++ ++i+ +   + +l+ kl +  f   + +n +e  l  +i    e++s ++  +++r+ +
  gi|70606649|ref|YP_255519.1|  29 QFTENNANHTQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGINNKE--LYLDILSDFEKISQNISAASYRFGV 98 
                                   233444444489999********************9777666666..5679******************976 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 1.9e-10
                      PhoU_div 121 kktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdra 201
                                    +t + i al ++ie++  l  ++ + ++++ ++ ++E+e+D+l+r+   klf+re+ s+++ +ll ++  + le  +d  
  gi|70606649|ref|YP_255519.1| 116 TITEKLIAALMNTIEAIRLLSVSSKKASEKARNVIKIEEEVDDLYRNFEVKLFEREQ-SGIAYILLTKDVADRLEDCADLL 195
                                   4567888999999999987667777777**************************888.*********************** PP

                      PhoU_div 202 edvadrisii 211
                                    +va+ i  i
  gi|70606649|ref|YP_255519.1| 196 RNVANSILYI 205
                                   *****99877 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.3    0.0018       2.3       5      82 ..      16      89 ..      12      96 .. 0.74
   2 ?    1.0   0.1      0.48   6.1e+02      31      55 ..     104     128 ..      98     139 .. 0.73
   3 !   20.9   3.1   2.8e-07   0.00036      17      88 ..     136     201 ..     122     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                                  HHHHHHHHHHHHHHHHCT-H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  5 aeiveemlddalealeekdt...elarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82
                                  a+ ++++l+ +++ + e++        ++     ++++l +++ +++++ +   ++++        +l+i +d E i+  +
  gi|70606649|ref|YP_255519.1| 16 ANQILDQLRILYQQFTENNAnhtQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGINNKEL-------YLDILSDFEKISQNI 89
                                  66677777777888877774332333666666999***********9999955555555.......999******999766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.48
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  31 ierddeidrlekeiersllealakr 55 
                                      d+ + +l   i+++l+ al++ 
  gi|70606649|ref|YP_255519.1| 104 KVYDNVLQNLSITITEKLIAALMNT 128
                                   4569999999999999999988763 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.8e-07
                                   HHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  17 ealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaer 88 
                                   ++ ++k  e ar vi+ ++e+d+l++++e +l+e+    q+    + ++l   ++a  lE  +D  +n+a++
  gi|70606649|ref|YP_255519.1| 136 SVSSKKASEKARNVIKIEEEVDDLYRNFEVKLFERE---QSG---IAYILLTKDVADRLEDCADLLRNVANS 201
                                   23345667********************99976654...332...444555667***************986 PP

>> Vta1  Vta1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.47     6e+02      26      63 ..      14      53 ..      11     118 .. 0.50
   2 !   18.4   0.5   1.3e-06    0.0017      43     113 ..     118     196 ..     102     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.47
                          Vta1 26 yaveqilkkklk...rkdkeakefltkLldklEqlKkelke 63
                                  y+++qil+ +l+   ++ +e ++  t++  k++ +K+++++
  gi|70606649|ref|YP_255519.1| 14 YIANQILD-QLRilyQQFTENNANHTQVYSKIDGIKSSVED 53
                                  55666666.33334344456666666666666666666522 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                          Vta1  43 akefltkLldklEql........Kkelkendaiedeeaakayvenfalklfnkadkedragkatkataktflaaatlfe 113
                                   +++++ +L++++E++        K++ k  ++i+ ee+    ++nf +klf++ +  +     tk++a+ +  +a+l+ 
  gi|70606649|ref|YP_255519.1| 118 TEKLIAALMNTIEAIrllsvsskKASEKARNVIKIEEEVDDLYRNFEVKLFEREQSGIAYILLTKDVADRLEDCADLLR 196
                                   578899*******77777777768888888***********************************************97 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.14   1.8e+02     145     193 ..      18      66 ..       7      72 .. 0.82
   2 !   15.0   0.7   9.2e-06     0.012     127     212 ..      80     162 ..      71     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                   Tropomyosin 145 eLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRae 193
                                   ++ ++L++  ++  +  +++ + + + d  +  +++L+ kL e++ R  
  gi|70606649|ref|YP_255519.1|  18 QILDQLRILYQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEYIFRVA 66 
                                   5567788888888888899999999999999999999999999998865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 9.2e-06
                   Tropomyosin 127 sdLeraeeraeaaeskiveLeeeLkvvgnnlksLevs.eekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekev 206
                                   sd+e++ + + aa  +   L + +kv  n l++L +   ek  +   +  e+ir L+   k+a e+a    r+v k+e+ev
  gi|70606649|ref|YP_255519.1|  80 SDFEKISQNISAASYRFGVLNNVIKVYDNVLQNLSITiTEKLIAALMNTIEAIRLLSVSSKKASEKA----RNVIKIEEEV 156
                                   799********************************9747899999999********99988887776....99******** PP

                   Tropomyosin 207 drlede 212
                                   d+l  +
  gi|70606649|ref|YP_255519.1| 157 DDLYRN 162
                                   **9766 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2     5e-05     0.064     222     282 ..      10      70 ..       5      78 .. 0.91
   2 ?    1.1   0.1      0.13   1.7e+02     228     290 ..      82     141 ..      73     142 .. 0.79
   3 ?    1.0   0.1      0.15   1.9e+02     209     245 ..     123     159 ..      89     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                          RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklk 282
                                   e+++  a++i+++l+ ly++f +  ++ +++ +k++ +++s++++  kl + i+r ae ++
  gi|70606649|ref|YP_255519.1|  10 EQLQYIANQILDQLRILYQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGIN 70 
                                   67777899*****************************************999999998775 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                          RmuC 228 aeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvkekk 290
                                    e+i + +++   +f+ + + ++   + l++++ ++ +   kl   +++++e ++ l+v++kk
  gi|70606649|ref|YP_255519.1|  82 FEKISQNISAASYRFGVLNNVIKVYDNVLQNLSITITE---KLIAALMNTIEAIRLLSVSSKK 141
                                   56788888888888888888888888888888888887...8889999999999999988876 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                          RmuC 209 lalLrtvamlwrqeaqeknaeeiaellgelydkfekf 245
                                   +al++t++ +      +k+a+e a+ + ++ +++  +
  gi|70606649|ref|YP_255519.1| 123 AALMNTIEAIRLLSVSSKKASEKARNVIKIEEEVDDL 159
                                   3344444443333333333333333333333333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.015        19      25      85 ..      27      90 ..      12      93 .. 0.84
   2 ?    8.2   0.2    0.0023       2.9       8      79 ..     122     200 ..     120     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                        DUF948 25 kktldeaaatieelekqvdpilkevedllakvne....lledvneklekvdplteavadlgesvs 85
                                   + ++e++a  +++ +++d+i   vedl  k  e    ++e++n+k   +d + + ++++++++s
  gi|70606649|ref|YP_255519.1| 27 YQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEyifrVAEGINNKELYLD-ILSDFEKISQNIS 90
                                  567889999999999*************99999988888999999887777.5677888888887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                        DUF948   8 iAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvne.......lledvneklekvdplteavad 79 
                                   iA ++ +i  i++l   +k ++e a+ + ++e++vd + ++ e  l + ++       l++dv ++le+   l  +va+
  gi|70606649|ref|YP_255519.1| 122 IAALMNTIEAIRLLSVSSKKASEKARNVIKIEEEVDDLYRNFEVKLFEREQsgiayilLTKDVADRLEDCADLLRNVAN 200
                                   566677777788888889999999999999*********9999999999999*****9***********9999999986 PP

>> HrpJ  HrpJ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   3.7e-05     0.047     132     162 ..      13      44 ..       6      46 .. 0.86
   2 ?   -2.6   0.0       4.8   6.1e+03      39      39 ..     137     137 ..     107     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                                   C.CCTS-HHHHHHHHHHHHTS---HHHHHHHH CS
                          HrpJ 132 q.tdqlslqaLRdlYrqavsddqslsalyeal 162
                                   q   ++ l++LR lY+q+++++++++++y+++
  gi|70606649|ref|YP_255519.1|  13 QyIANQILDQLRILYQQFTENNANHTQVYSKI 44 
                                   556778899********************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.8
                                   H CS
                          HrpJ  39 v 39 
                                   v
  gi|70606649|ref|YP_255519.1| 137 V 137
                                   1 PP

>> PriC  Primosomal replication protein priC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.5e-05     0.095      64     155 ..       9      95 ..       2     112 .. 0.82
   2 ?    0.7   0.1      0.33   4.3e+02      24      57 ..     158     190 ..     119     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSST.....TTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHT....T--TH CS
                          PriC  64 aeqvaflaerlvaqieAlqrelattelrkkeakqkkksrkkshqlyqelakhqeyerrLeemiaereqqlekaqslaekqk 144
                                   +eq +++a+++ +q++ l +++++++ ++++  +k +    ++ +++   k  ey  r  e i+++e  l+  ++    +k
  gi|70606649|ref|YP_255519.1|   9 EEQLQYIANQILDQLRILYQQFTENNANHTQVYSKIDG--IKSSVEDLKYKLGEYIFRVAEGINNKELYLDILSD---FEK 84 
                                   789***********************999999887744..56666666677789999999999999999998666...445 PP

                                   HHHHHHHHHHH CS
                          PriC 145 lqqeilaleqR 155
                                   ++q+i a   R
  gi|70606649|ref|YP_255519.1|  85 ISQNISAASYR 95 
                                   57777777766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.33
                                   ---S----SS--S--SSHHHHHHHHHHHHHHHHH CS
                          PriC  24 akqarFdrqLFsqrsaklsdYleeiektlkqLek 57 
                                     +  F+ +LF+ ++ +   Y+  +++  ++Le+
  gi|70606649|ref|YP_255519.1| 158 DLYRNFEVKLFEREQ-SGIAYILLTKDVADRLED 190
                                   345567777775443.344455555555555555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.27      44     120 ..      38     113 ..      32     117 .. 0.92
   2 ?   -0.8   0.1       1.1   1.4e+03      93     107 ..     143     157 ..     110     172 .. 0.49
   3 ?   -3.7   0.0         9   1.2e+04      71      88 ..     184     201 ..     182     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                       DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   ++v ++++ +++s+++ k +L + i rv + +++ ke+  +i ++ +++++++s+ +  +  ++++++  ++ l+++
  gi|70606649|ref|YP_255519.1|  38 TQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGINN-KELYLDILSDFEKISQNISAASYRFGVLNNVIKVYDNVLQNL 113
                                   689999*************************985.799999***************************999998877 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                       DUF1664  93 redlseigedvesvk 107
                                   +e+ +++ +  e+v+
  gi|70606649|ref|YP_255519.1| 143 SEKARNVIKIEEEVD 157
                                   222222222222222 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9
                       DUF1664  71 vdkkldeqkeiskeikee 88 
                                   v ++l++++++ +++++ 
  gi|70606649|ref|YP_255519.1| 184 VADRLEDCADLLRNVANS 201
                                   556666666666666655 PP

>> T4_tail_cap  Tail-tube assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.12   1.6e+02     209     270 ..      20      82 ..       9      94 .. 0.78
   2 ?   10.8   0.3   0.00013      0.17     195     251 ..     111     167 ..     100     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.12
                   T4_tail_cap 209 Lkeiikiyelflllsygeteksttakelkgkideaykstlikkatpedasknktlgegit.sf 270
                                   L ++  +y+ f++    +t+  + ++ +k+++++   +++     + +  +nk+l+  i  +f
  gi|70606649|ref|YP_255519.1|  20 LDQLRILYQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGINNKELYLDILsDF 82 
                                   667777899999999999999999999999999988888888888899999999876655244 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                   T4_tail_cap 195 ktflyqltprsledLkeiikiyelflllsygeteksttakelkgkideaykstlikk 251
                                   +++  ++t + ++ L++ i+ ++l+++ s  ++ek++ + ++ +++d+ y++  +k 
  gi|70606649|ref|YP_255519.1| 111 QNLSITITEKLIAALMNTIEAIRLLSVSSKKASEKARNVIKIEEEVDDLYRNFEVKL 167
                                   677778899999***************************************986654 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.21   2.7e+02      16      45 ..      11      40 ..       7      45 .. 0.87
   2 ?    6.8   0.3    0.0071         9      14      65 ..      44      95 ..      35     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.21
                     DASH_Dad2 16 qlrdlsdslakqleeLeeklstladgteav 45
                                  ql+ +++++ +ql+ L +++++ + + + v
  gi|70606649|ref|YP_255519.1| 11 QLQYIANQILDQLRILYQQFTENNANHTQV 40
                                  8899999************99998887766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0071
                     DASH_Dad2 14 LkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslk 65
                                  +  +++  ++l+ +l e   ++++  ++ e   ++l+ ++++ ++is as  
  gi|70606649|ref|YP_255519.1| 44 IDGIKSSVEDLKYKLGEYIFRVAEGINNKELYLDILSDFEKISQNISAASYR 95
                                  5556666667777777777777777777777777788888888888777754 PP

>> Interferon  Interferon alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   0.00032      0.41      48     134 ..       9      94 ..       4      96 .. 0.87
   2 ?   -0.0   0.0      0.69   8.8e+02      78     125 ..     116     163 ..      97     196 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHHHHHHHHCCS--CCCT--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHH CS
                    Interferon  48 keqaalvlhemlqqifnlFstnessaawnetlleqllsgLhqqleeLeacleeeaeeeeseleeeesrlalkkYFqrisly 128
                                   +eq   + +++l q+  ++ ++ ++ + n+t++ +  +g++  +e+L+  l+e   +  + ++++e  l + + F++is+ 
  gi|70606649|ref|YP_255519.1|   9 EEQLQYIANQILDQLR-ILYQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEYIFRVAEGINNKELYLDILSDFEKISQN 88 
                                   5788889999999975.55567788888999999999********************9999******************98 PP

                                   HHHTTT CS
                    Interferon 129 LkekkY 134
                                   + +  Y
  gi|70606649|ref|YP_255519.1|  89 ISAASY 94 
                                   777666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.69
                                   HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCHHHHHHHHHHH CS
                    Interferon  78 tlleqllsgLhqqleeLeacleeeaeeeeseleeeesrlalkkYFqri 125
                                   t+ e+l + L + +e +  +  ++++ +e++++  +   ++   +++ 
  gi|70606649|ref|YP_255519.1| 116 TITEKLIAALMNTIEAIRLLSVSSKKASEKARNVIKIEEEVDDLYRNF 163
                                   555666666666666666555555555555444444444555555544 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0016         2      63      99 ..      11      51 ..       7      56 .. 0.86
   2 ?    0.4   0.1      0.46   5.9e+02      15      50 ..      78     113 ..      66     133 .. 0.71
   3 ?    3.2   2.2     0.063        81      33      77 ..     122     165 ..      97     204 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                                  XX--TTTTTGGGHHHHHHHHHH.......HHHHHHHHHHHH CS
                    Laminin_II 63 kLeklapqLldklkelkqleeasss....lsdniseikelI 99
                                  +L+  a+q+ld+l+ l q+  ++++    +  +i+ ik  +
  gi|70606649|ref|YP_255519.1| 11 QLQYIANQILDQLRILYQQFTENNAnhtqVYSKIDGIKSSV 51
                                  78889***********9998777777999999999999866 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.46
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkda 50 
                                   +l++ +++sqn++  +     +n+ ++  +++++++
  gi|70606649|ref|YP_255519.1|  78 ILSDFEKISQNISAASYRFGVLNNVIKVYDNVLQNL 113
                                   567777777777777777777776666666666555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.063
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHH CS
                    Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqLldklke 77 
                                   +  + +++e +  +  +++ka +   r+v k+e+++++L   ++ 
  gi|70606649|ref|YP_255519.1| 122 IAALMNTIEAIRLLSVSSKKASE-KARNVIKIEEEVDDLYRNFEV 165
                                   34444554444444444455554.556899999999999998762 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.4    0.0012       1.6      22     128 ..       8     120 ..       7     123 .. 0.79
   2 ?    1.9   0.1      0.18   2.3e+02      52     104 ..     154     205 ..     122     210 .] 0.53

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0012
                                   HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHCCCHHHHH CS
                     Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd......ndnvikksskeleeeilrlket 96 
                                   +++ l+   +++ ++l+ l ++++e++ +++++++ +  ik+s+++ + +  +      +    k++  ++ ++ +++ ++
  gi|70606649|ref|YP_255519.1|   8 IEEQLQYIANQILDQLRILYQQFTENNANHTQVYSKIDGIKSSVEDLKYKLGEyifrvaEGINNKELYLDILSDFEKISQN 88 
                                   66778888899999***************************9988777666664444331223333333444589999*** PP

                                   HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  97 idaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                   i+a   +  vL nv++  ++ +q+L   i++k
  gi|70606649|ref|YP_255519.1|  89 ISAASYRFGVLNNVIKVYDNVLQNLSITITEK 120
                                   *************************9999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                     Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                   +e+++l ++ + +l e+++s      ++k+++++le + ++l +++ + +  i
  gi|70606649|ref|YP_255519.1| 154 EEVDDLYRNFEVKLFEREQSGIAYILLTKDVADRLE-DCADLLRNVANSILYI 205
                                   333444444444444444444444445555555555.5555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1550  (0.0864521); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1462.73
//
Query:       gi|70606650|ref|YP_255520.1|  [L=132]
Description: hypothetical protein Saci_0860 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.033   14.3   2.1      0.062   13.4   1.5    1.7  1  EcoEI_R_C   EcoEI R protein C-terminal
      0.072   11.9   0.3      0.089   11.6   0.3    1.1  1  Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain


Domain annotation for each model (and alignments):
>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.5     7e-06     0.062       4      64 ..      12      75 ..      10     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                     EcoEI_R_C  4 vekfrkfieenkdsidaLqiiwsdreltkellkeLeekLkepppgi..tpealweayellek.k 64
                                  + +f++ iee+++++d L    + +el  e ++ L ++L++ ++ i    e + +++e++++ k
  gi|70606650|ref|YP_255520.1| 12 LLYFERVIEEHNNTLDKLENYAQIPELDTEKIDVLIRRLRRTRKEIlqGIETISNYVENVKDtK 75
                                  568***********************************99988877224577888887776644 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3     1e-05     0.089     184     264 ..      16     112 ..      12     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                    Fmp27_WPPW 184 eeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkeseesse................. 244
                                   e+ ie+++++l++le+  +     +e+++  i++l+++ ke+ + +e++++++e++k ++ ++e                 
  gi|70606650|ref|YP_255520.1|  16 ERVIEEHNNTLDKLENYAQIPeldTEKIDVLIRRLRRTRKEILQGIETISNYVENVKDTKLKEEalglinyfyvvgledee 96 
                                   67899**********998887798999******************************999887799999999998875333 PP

                    Fmp27_WPPW 245 ...eeeskskelsaastsesfse 264
                                      +       + ++++++++++
  gi|70606650|ref|YP_255520.1|  97 nvlR-------TLKERSASTDQN 112
                                   2221.......222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 945.06
//
Query:       gi|70606651|ref|YP_255521.1|  [L=122]
Description: hypothetical protein Saci_0861 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00022   21.2   0.2       0.15   12.1   0.0    2.2  2  Molydop_binding  Molydopterin dinucleotide binding domain


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2   0.00019       3.3      16      63 ..      40      89 ..      30      95 .. 0.76
   2 !   12.1   0.0   8.3e-06      0.15      27      55 ..      94     121 ..      88     122 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00019
                                  TTCGCCHHHHCSSS..-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEE CS
               Molydop_binding 16 trtrpvlrlakpep..evveinpedAaalGikdGdlVevesrrGsvevra 63
                                  +++++v  ++k+e    +v i+ + A++ + kd  ++ v+ rr +++  +
  gi|70606651|ref|YP_255521.1| 40 VKEKRVKIRKKTEVdaGTVIISSKLANEINAKDEIEISVKGRRNKFKIIV 89
                                  444455444444444589*************************9988765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.3e-06
                                   SSS-EEEEEHHHHHHHT--TT-EEEEEET CS
               Molydop_binding  27 pepevveinpedAaalGikdGdlVevesr 55 
                                   p+   ++ n ed+ +lG++d+ +V v+s+
  gi|70606651|ref|YP_255521.1|  94 PA-TEIWSNSEDMLKLGLEDNSTVSVRSS 121
                                   44.48999*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1293  (0.0721178); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 931.40
//
Query:       gi|70606652|ref|YP_255522.1|  [L=574]
Description: glycyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-18   64.5   0.0    1.7e-17   63.3   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain
    2.8e-07   30.7   0.6    1.8e-06   28.1   0.6    2.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.058   13.4   2.2       0.41   10.6   0.0    2.8  2  YokU            YokU-like protein, putative antitoxin
       0.31   10.9   2.1        1.3    9.0   0.1    2.5  2  Rad50_zn_hook   Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   3.8e-21   1.7e-17       2      92 ..     468     555 ..     467     557 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 3.8e-21
                                   EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEE CS
                HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqerv 82 
                                   +++ pl ek+e l + a+++++ L++  +++ +d +++sigk++++ d++g+p+ ++v++ +l ++tvt+rdrd+ +q+rv
  gi|70606652|ref|YP_255522.1| 468 IAIFPLLEKDE-LIKKAREIYDSLKER-YDIIFD-DSGSIGKRYARVDEIGVPYSITVDPMTLTDNTVTIRDRDSWQQIRV 545
                                   7999***9555.*************88.888887.79******************************************** PP

                                   ETTHHHHHHH CS
                HGTP_anticodon  83 sldelveklk 92 
                                    + +l+++l 
  gi|70606652|ref|YP_255522.1| 546 NITDLMNVLD 555
                                   *****99875 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.6   3.9e-10   1.8e-06      11      75 ..     160     225 ..     155     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.9e-10
                                   EEE-SSSHHHHHHHHHHHEE...EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGG CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  11 yiLkPtneetfvelirdevl...rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeas 75 
                                     L+P+  +++   ++       r+k LP+ ++qi+ + R+E s  +GL+R+reF+  + + f  ++s
  gi|70606652|ref|YP_255522.1| 160 AFLRPETAQGMFTSFKRV-YeafRQK-LPIGIAQIGKVGRNEISPRQGLIRMREFTIMEVEFFFDPNS 225
                                   579999999988888754.2233777.****************9566**************9998763 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.2e-05      0.41      33      55 ..      86     108 ..      71     111 .. 0.87
   2 ?    0.8   0.6      0.11   4.8e+02      42      70 ..     380     407 ..     375     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.2e-05
                          YokU  33 tPsieCseCglvyqeeevvkeie 55 
                                    P +eC++C+ vy+ +++v+ei 
  gi|70606652|ref|YP_255522.1|  86 DPVVECNSCHNVYRADHLVEEIA 108
                                   699******************95 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                          YokU  42 glvyqeeevvkeiedqllLvdtkklpesi 70 
                                    ++ ++ ++v+eie +++L ++k l + i
  gi|70606652|ref|YP_255522.1| 380 IMEIINTKTVEEIE-RMILNKEKVLGKDI 407
                                   5888999******9.67888888888777 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00028       1.3      16      32 ..     124     141 ..     118     149 .. 0.79
   2 ?    0.7   0.3      0.11   4.9e+02      33      50 ..     475     492 ..     471     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00028
                                   TT-SE.E-TTT--EE-HH CS
                 Rad50_zn_hook  16 keakg.cCPlCgReldee 32 
                                     +kg +CP Cg el+e 
  gi|70606652|ref|YP_255522.1| 124 IREKGiKCPKCGGELGEV 141
                                   557888*********986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHH. CS
                 Rad50_zn_hook  33 hrseLikelqsklerlpe 50 
                                   ++ eLik+ ++  ++l+e
  gi|70606652|ref|YP_255522.1| 475 EKDELIKKAREIYDSLKE 492
                                   5899******99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3935.27
//
Query:       gi|70606653|ref|YP_255523.1|  [L=296]
Description: agmatinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-70  238.1   0.0    1.6e-70  237.8   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.8   0.0   8.8e-75   1.6e-70       3     276 ..      26     284 ..      24     287 .. 0.95

  Alignments for each domain:
  == domain 1  score: 237.8 bits;  conditional E-value: 8.8e-75
                                   EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHT CS
                      Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilka 82 
                                   ++++G+P+d++ s+rpG+rf+P+ ire  + +e    y++++g+ + e+ + d+gd+ ++p + ee +++i++ v+   ++
  gi|70606653|ref|YP_255523.1|  26 FVIVGIPLDITSSFRPGSRFAPSVIREVAQYIEF---YSMRTGIdMGEIGFSDVGDIVMHPSNVEENIKRIKDVVSYFSEK 103
                                   79**************************988887...8899999999**************99999*************** PP

                                   TCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH CS
                      Arginase  83 gklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdne 163
                                   gk+++ +GG+Hsi++g+ ++  +      +v+ +DAH+Dlr+++  g +++h++++rr++ e+ +   k++ +G r+v++e
  gi|70606653|ref|YP_255523.1| 104 GKIVVSIGGEHSITVGTTEGTNAD-----CVLSIDAHLDLRDEY-MGYKYDHACVMRRIS-ERGV---KIIELGTRAVSKE 174
                                   *********************985.....7**************.9**************.5566...5************ PP

                                   HHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCH CS
                      Arginase 164 eyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaek 244
                                   e e+a++ gi +++ r+++ lg++ ++e++++ + ae++ +yl++D+D++Dpa+aPG+ tpep Gl++  +l++++++ + 
  gi|70606653|ref|YP_255523.1| 175 ELEYANQKGIMYLNPRQVNLLGIRGTAEKVKRGL-AECKRIYLTYDMDGIDPAYAPGVATPEPEGLDPTTVLEIVNMVTD- 253
                                   *****99***************************.599****************************************99. PP

                                   SEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHH CS
                      Arginase 245 lnlvgaDvvEvnPaldteaeqtarlaarlvre 276
                                   +++vg+DvvE++P+ d+++ +t+ la r++ e
  gi|70606653|ref|YP_255523.1| 254 KRIVGFDVVEISPPHDPSN-ITSVLASRFILE 284
                                   99***************55.********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2086.68
//
Query:       gi|70606654|ref|YP_255524.1|  [L=48]
Description: DNA-directed RNA polymerase subunit P [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-06   27.5   4.7    3.9e-06   26.4   4.7    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0093   16.1   0.3      0.013   15.6   0.3    1.2  1  Zn-ribbon_8     Zinc ribbon domain
     0.0095   16.2   0.2     0.0095   16.2   0.2    1.0  1  DUF2072         Zn-ribbon containing protein
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.013   15.5   0.1    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.029   13.8   2.6       0.11   12.0   0.6    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.03   14.3   0.4      0.068   13.2   0.4    1.5  1  DZR             Double zinc ribbon
      0.042   13.8   4.4      0.051   13.5   0.1    2.0  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.048   13.4   4.5       0.38   10.5   4.5    2.1  1  zinc_ribbon_2   zinc-ribbon domain
      0.058   13.2   5.5        0.7    9.7   0.0    2.4  2  zinc_ribbon_5   zinc-ribbon domain
        0.1   13.1   1.9        8.2    7.1   0.1    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.14   12.1   1.7        6.7    6.7   0.0    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.14   12.2   2.1        3.3    7.8   0.1    2.1  2  zf-BED          BED zinc finger


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   4.7   2.6e-09   3.9e-06       1      29 [.       4      35 ..       4      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-09
                                  -B-SSS--B--...--SSS----SSS-----B CS
                DNA_RNApol_7kD  1 YiCgeCgaevs...lkkgdpiRCkeCGhRilY 29
                                  Y Cg+C +e     lk    +RC +CG+Ri+Y
  gi|70606654|ref|YP_255524.1|  4 YRCGKCWKELDddqLKTLPGVRCPYCGYRIIY 35
                                  99****99987333666677***********9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   8.6e-06     0.013       6      33 ..       4      30 ..       3      34 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.6e-06
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCg 33
                                  YrC +C +e +  q  +  p + CP Cg
  gi|70606654|ref|YP_255524.1|  4 YRCGKCWKELDDDQ-LKTLPGVRCPYCG 30
                                  ***********999.57788999****9 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.4e-06    0.0095       3      37 ..       5      41 ..       3      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.4e-06
                       DUF2072  3 kCtkCekvfedgskeilkG..CpsCGgkkFlyvkeee 37
                                  +C kC k+++d + + l G  Cp CG +    v++ +
  gi|70606654|ref|YP_255524.1|  5 RCGKCWKELDDDQLKTLPGvrCPYCGYRIIYMVRKPT 41
                                  8****************9999******9988888765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   8.9e-06     0.013      69     102 ..       2      39 ..       1      47 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.9e-06
                                   -EEEETTTS-EEECHH.H...HHS-TTTSSS-EEEEES CS
                          HypA  69 vkvrCreCgkefelee.k...alrCpkCgsadveivsG 102
                                   +k+rC +C ke + ++ k    +rCp Cg + + +v+ 
  gi|70606654|ref|YP_255524.1|   2 AKYRCGKCWKELDDDQlKtlpGVRCPYCGYRIIYMVRK 39 
                                   6789********98875323445******987777765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1       0.1   1.5e+02       3      10 ..       4      11 ..       2      19 .. 0.59
   2 ?   12.0   0.6     7e-05      0.11      19      25 ..      26      32 ..      22      33 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                   zf-ribbon_3  3 vrCPnCGa 10
                                  +rC +C +
  gi|70606654|ref|YP_255524.1|  4 YRCGKCWK 11
                                  66766644 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7e-05
                   zf-ribbon_3 19 CpyCGtk 25
                                  CpyCG++
  gi|70606654|ref|YP_255524.1| 26 CPYCGYR 32
                                  7777776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   4.5e-05     0.068      15      37 ..       6      32 ..       2      37 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                           DZR 15 CseCgtklkavaa....edrCpsCgek 37
                                  C++C ++l+  +       rCp Cg+ 
  gi|70606654|ref|YP_255524.1|  6 CGKCWKELDDDQLktlpGVRCPYCGYR 32
                                  888888876433377778888888876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   1.0      0.14   2.1e+02      37      44 ..       3      10 ..       1      12 [. 0.79
   2 ?   13.5   0.1   3.4e-05     0.051      18      34 ..      23      39 ..      17      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                 Zn_Tnp_IS1595 37 lfqCkeCr 44
                                  +++C +C 
  gi|70606654|ref|YP_255524.1|  3 KYRCGKCW 10
                                  69999995 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                 Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt 34
                                  g++CP+Cg+r +y +++
  gi|70606654|ref|YP_255524.1| 23 GVRCPYCGYRIIYMVRK 39
                                  789******98888876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.5   0.00025      0.38       1      22 [.       5      32 ..       5      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                 zinc_ribbon_2  1 fCpnCGaelqdnakF......CpyCGtp 22
                                  +C +C +el+d++        CpyCG+ 
  gi|70606654|ref|YP_255524.1|  5 RCGKCWKELDDDQLKtlpgvrCPYCGYR 32
                                  599999999999999999999*****96 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   2.6     0.029        43      25      31 ..       3       9 ..       2      11 .. 0.85
   2 ?    9.7   0.0   0.00047       0.7      14      32 ..      13      30 ..      12      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.029
                 zinc_ribbon_5 25 kVrCakC 31
                                  k rC+kC
  gi|70606654|ref|YP_255524.1|  3 KYRCGKC 9 
                                  77***** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                 zinc_ribbon_5 14 lvdsklKksgkkVrCakCa 32
                                  l+d++lK + + VrC  C+
  gi|70606654|ref|YP_255524.1| 13 LDDDQLKTLPG-VRCPYCG 30
                                  89*****9987.9**9997 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.012        18       1       9 [.       4      12 ..       4      19 .. 0.87
   2 ?    7.1   0.1    0.0055       8.2       2       8 ..      25      31 ..      24      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                                  EEETTTTEE CS
                       zf-C2H2  1 ykCpdCgks 9 
                                  y+C++C k 
  gi|70606654|ref|YP_255524.1|  4 YRCGKCWKE 12
                                  9*****985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0055
                                  EETTTTE CS
                       zf-C2H2  2 kCpdCgk 8 
                                  +Cp+Cg+
  gi|70606654|ref|YP_255524.1| 25 RCPYCGY 31
                                  7****97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.4     0.011        16      46      59 ..       3      16 ..       1      21 [. 0.87
   2 ?    6.7   0.0    0.0045       6.7      29      40 ..      24      35 ..      19      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                OrfB_Zn_ribbon 46 tfkCpnCgfeadrD 59
                                  +++C +C+ e+d D
  gi|70606654|ref|YP_255524.1|  3 KYRCGKCWKELDDD 16
                                  799*******9988 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                OrfB_Zn_ribbon 29 ktCseCgsknke 40
                                   +C+ Cg++  +
  gi|70606654|ref|YP_255524.1| 24 VRCPYCGYRIIY 35
                                  579999998766 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0022       3.3      16      29 ..       3      16 ..       2      22 .. 0.81
   2 ?    4.7   0.3      0.02        30      17      24 ..      24      31 ..      18      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                                  --EETTTTEE---- CS
                        zf-BED 16 kavCryCgkilsrg 29
                                  k +C  C+k+l+++
  gi|70606654|ref|YP_255524.1|  3 KYRCGKCWKELDDD 16
                                  569*******9876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                                  -EETTTTE CS
                        zf-BED 17 avCryCgk 24
                                  ++C yCg 
  gi|70606654|ref|YP_255524.1| 24 VRCPYCGY 31
                                  89****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 295.39
//
Query:       gi|70606655|ref|YP_255525.1|  [L=99]
Description: translation initiation factor Sui1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.9e-23   80.5   0.9    1.3e-22   80.1   0.9    1.1  1  SUI1      Translation initiation factor SUI1
    0.00036   20.8   1.0    0.00047   20.4   1.0    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.9   1.4e-26   1.3e-22       3      77 .]      21      91 ..      19      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.4e-26
                          SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                  + i+i++e+r+ +K vT+v+g+ +++ +lkk+a+elk+k+a++g+v k+g   i++QGd+r++v+elL+++ g+p
  gi|70606655|ref|YP_255525.1| 21 QFIKIKVEKRRYGKEVTIVEGISNDETELKKIASELKSKLAAGGTV-KNG--KIELQGDHRDRVKELLIKM-GFP 91
                                  679******************************************9.888..7*****************9.997 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.0   5.2e-08   0.00047      20      80 .]      29      90 ..      14      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.2e-08
                          Img2 20 krggtkkltvirkieGDiaalre...dLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                  kr+  k++t++  i+ D ++l++   +L++ l+  +  + ++gkie++Gd++++vk+ L + gF
  gi|70606655|ref|YP_255525.1| 29 KRRYGKEVTIVEGISNDETELKKiasELKSKLA--AGGTVKNGKIELQGDHRDRVKELLIKMGF 90
                                  455678899999999888776542226666666..5666789*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 709.75
//
Query:       gi|70606656|ref|YP_255526.1|  [L=311]
Description: transcription initiation factor IIB [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-35  120.3   5.4    2.9e-17   62.5   0.7    2.2  2  TFIIB          Transcription factor TFIIB repeat
    2.9e-11   42.7   0.4    5.6e-11   41.8   0.4    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
      1e-05   25.2   0.1    3.1e-05   23.7   0.1    1.9  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0001   21.7   3.2     0.0006   19.3   0.2    3.3  4  Sigma70_r4     Sigma-70, region 4
    0.00062   19.8   0.1        0.4   10.8   0.0    2.3  2  Cyclin_C       Cyclin, C-terminal domain
     0.0013   18.0   0.1      0.063   12.7   0.0    3.2  4  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
     0.0028   17.2   0.6        0.7    9.5   0.1    2.5  2  DUF3562        Protein of unknown function (DUF3562)
     0.0028   17.3   0.1      0.013   15.2   0.0    2.2  2  Sigma70_r4_2   Sigma-70, region 4
     0.0028   17.2   0.1      0.011   15.2   0.1    2.1  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0056   16.6   0.2      0.012   15.6   0.2    1.6  1  HTH_11         HTH domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.046   13.7   0.0    1.7  2  RB_B           Retinoblastoma-associated protein B domain
      0.036   13.9   0.1      0.036   13.9   0.1    3.3  4  HTH_23         Homeodomain-like domain
      0.041   13.8   0.2       0.86    9.6   0.0    2.6  2  HTH_Crp_2      Crp-like helix-turn-helix domain
        0.1   12.3   0.4        2.3    7.9   0.2    2.2  2  Cyclin_N       Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.7   2.2e-20   2.9e-17       3      70 ..     131     198 ..     129     199 .. 0.93
   2 !   60.3   0.3   1.1e-19   1.4e-16       2      71 .]     224     293 ..     223     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.2e-20
                                   HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
                         TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                                   r+ + l+Lp+ V+d+A  ++++a+e++++ Grs ++++AA++y Acr+ +++rt+ ei++ ++ + k+
  gi|70606656|ref|YP_255526.1| 131 RIGNLLNLPKAVKDEAALIYRKAVEKGLVRGRSIESVVAASIYAACRRMKMARTLDEIAQFTKANRKE 198
                                   666779******************************************************99877776 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 1.1e-19
                                   HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   +r+   l L+ +  + A e++++a++ ++++G+ pag+aAA++yiA++++ ++rtqkei++v+ V+e+t+
  gi|70606656|ref|YP_255526.1| 224 TRIGTLLSLSGITMKHAAEIIEKAKNSGLTAGKDPAGLAAAAIYIAALLNDERRTQKEIAQVAGVTEVTV 293
                                   56666788999999******************************************************97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.4   4.3e-14   5.6e-11       9      43 .]      20      54 ..      17      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.3e-14
                                  EECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  9 tnlveDpergelvCtdCGlVlednsidegpewref 43
                                  +++++D+erge++Ct+ G+V+e+++id gpewr+f
  gi|70606656|ref|YP_255526.1| 20 DKIIFDEERGEYICTETGEVIEERIIDQGPEWRAF 54
                                  559******************************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   2.4e-08   3.1e-05       9      41 ..     268     300 ..     268     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                 HTH_AsnC-type   9 LeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                                   ++aL  d R++ +e+A+  G++e tv++R++ L
  gi|70606656|ref|YP_255526.1| 268 IAALLNDERRTQKEIAQVAGVTEVTVRNRYKEL 300
                                   689***************************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         4   5.1e+03       8      20 ..      98     110 ..      93     112 .. 0.66
   2 ?   -1.1   0.0       1.1   1.4e+03      23      34 ..     129     140 ..     125     141 .. 0.87
   3 ?    0.6   0.0      0.32   4.1e+02      20      31 ..     182     193 ..     176     210 .. 0.72
   4 !   19.3   0.2   4.7e-07    0.0006      18      49 ..     274     305 ..     265     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                   HHHHHHHHHHTTT CS
                    Sigma70_r4   8 rerevlelrfgeg 20 
                                   r  evl+ r ++ 
  gi|70606656|ref|YP_255526.1|  98 RRLEVLRWRKWQI 110
                                   4558999988765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHTS-H CS
                    Sigma70_r4  23 leEIgerlgiSr 34 
                                   le Ig+ l++++
  gi|70606656|ref|YP_255526.1| 129 LERIGNLLNLPK 140
                                   899*****9985 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
                                   T--HHHHHHHHT CS
                    Sigma70_r4  20 glTleEIgerlg 31 
                                    +Tl EI++   
  gi|70606656|ref|YP_255526.1| 182 ARTLDEIAQFTK 193
                                   68******9665 PP

  == domain 4  score: 19.3 bits;  conditional E-value: 4.7e-07
                                   TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                                   +e +T++EI+++ g+++ +Vr + k+  + L+
  gi|70606656|ref|YP_255526.1| 274 DERRTQKEIAQVAGVTEVTVRNRYKELTQELK 305
                                   6889*******************999877775 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00031       0.4      45      89 ..     166     209 ..     163     221 .. 0.86
   2 !    6.9   0.0    0.0051       6.5      44      88 ..     258     302 ..     228     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                      Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                   S++Aa+ ++++r++ +     +++ ++t+++ +++  c++lil  
  gi|70606656|ref|YP_255526.1| 166 SVVAASIYAACRRM-KMARTLDEIAQFTKANRKEVARCYRLILRE 209
                                   88888888888888.788889*********************875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0051
                                   HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                      Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                   p  +Aaaa+++a    ++   ++++ ++ g+++  +++ ++ + +
  gi|70606656|ref|YP_255526.1| 258 PAGLAAAAIYIAALLNDERRTQKEIAQVAGVTEVTVRNRYKELTQ 302
                                   7779**********9999999*************99999998876 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6   4.6e+03      19      29 ..     171     184 ..     169     193 .. 0.59
   2 ?    1.2   0.0      0.19   2.4e+02      28      39 ..     194     205 ..     188     205 .. 0.84
   3 ?   -1.3   0.0       1.1   1.5e+03      22      36 ..     228     243 ..     220     244 .. 0.72
   4 !   12.7   0.0     5e-05     0.063      16      51 ..     264     300 ..     247     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                  HTH_Tnp_ISL3  19 yilellles...rs 29 
                                    i+++++++   r+
  gi|70606656|ref|YP_255526.1| 171 SIYAACRRMkmaRT 184
                                   56677777752344 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                  HTH_Tnp_ISL3  28 rsvkavArqlgv 39 
                                   +++k+vAr++++
  gi|70606656|ref|YP_255526.1| 194 ANRKEVARCYRL 205
                                   389******996 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                  HTH_Tnp_ISL3  22 ellles.rsvkavArq 36 
                                   +ll  s +++k++A++
  gi|70606656|ref|YP_255526.1| 228 TLLSLSgITMKHAAEI 243
                                   55555559*****986 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 5e-05
                  HTH_Tnp_ISL3  16 leayilellles.rsvkavArqlgvSwtTVwrildry 51 
                                   ++ yi++ll +  r+ k++A+  gv++ TV+++++++
  gi|70606656|ref|YP_255526.1| 264 AAIYIAALLNDErRTQKEIAQVAGVTEVTVRNRYKEL 300
                                   5669999999999********************9976 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00055       0.7       7      40 ..     184     217 ..     180     226 .. 0.84
   2 ?    5.5   0.1      0.01        13       9      33 ..     280     304 ..     273     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00055
                       DUF3562   7 iiqaiAeetdaPeelVsrlyedavaalaedARvl 40 
                                    +++iA+ t a +++V r y  ++++l  +  v 
  gi|70606656|ref|YP_255526.1| 184 TLDEIAQFTKANRKEVARCYRLILRELDIEVPVS 217
                                   689******************9999998776664 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                       DUF3562   9 qaiAeetdaPeelVsrlyedavaal 33 
                                   ++iA+  +++e +V+  y++  ++l
  gi|70606656|ref|YP_255526.1| 280 KEIAQVAGVTEVTVRNRYKELTQEL 304
                                   68*****************999887 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.2   6.7e+03      30      43 ..     186     199 ..     184     209 .. 0.70
   2 !   15.2   0.0   9.8e-06     0.013      27      48 ..     277     298 ..     271     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.2
                                   HHHHHHHT--HHHH CS
                  Sigma70_r4_2  30 kEIAellgisegtV 43 
                                   +EIA+ ++ + + V
  gi|70606656|ref|YP_255526.1| 186 DEIAQFTKANRKEV 199
                                   68888776665555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.8e-06
                                   --HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2  27 lsykEIAellgisegtVksrls 48 
                                    ++kEIA++ g++e+tV++r++
  gi|70606656|ref|YP_255526.1| 277 RTQKEIAQVAGVTEVTVRNRYK 298
                                   589*****************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.9e-06     0.011      10      44 ..     269     303 ..     266     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.9e-06
                        HTH_24  10 elLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                                    +L  + r +q+e+A+  g++  tv+ r k+L++e
  gi|70606656|ref|YP_255526.1| 269 AALLNDERRTQKEIAQVAGVTEVTVRNRYKELTQE 303
                                   68999***************************975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   9.2e-06     0.012       7      45 ..     270     307 ..     264     311 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.2e-06
                        HTH_11   7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vp 45 
                                    lL  +++  + +e+A+  +v++ tvr++ k+L+  + ++
  gi|70606656|ref|YP_255526.1| 270 ALL--NDERRTQKEIAQVAGVTEVTVRNRYKELTQELkIQ 307
                                   444..55558***********************8776455 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.046      13      97 ..     125     207 ..     114     221 .. 0.81
   2 ?   -2.8   0.0       4.8   6.1e+03      61      80 ..     265     284 ..     262     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                          RB_B  13 aavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvy 93 
                                   a+  l+++ + L+l + +++++  + ++++  e+ l++ R ++ ++ +++Y+ ++  k+ +++ ei +  + + ++ ++ y
  gi|70606656|ref|YP_255526.1| 125 AMNELERIGNLLNLPKAVKDEAALIYRKAV--EKGLVRGRSIESVVAASIYAACRRMKMARTLDEIAQFTKANRKEVARCY 203
                                   566666677777777777777665555554..578********************************99999988888888 PP

                          RB_B  94 rsvl 97 
                                   r +l
  gi|70606656|ref|YP_255526.1| 204 RLIL 207
                                   8765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                          RB_B  61 avYvvakvtkeelsFkeiik 80 
                                   a+Y+ a +++e+++ kei +
  gi|70606656|ref|YP_255526.1| 265 AIYIAALLNDERRTQKEIAQ 284
                                   66777777766666666654 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       1.5   1.9e+03       5      15 ..      97     107 ..      93     115 .. 0.69
   2 ?    0.7   0.2       0.4   5.1e+02       6      27 ..     177     203 ..     174     205 .. 0.82
   3 ?   -3.5   0.0       7.8     1e+04      15      26 ..     232     243 ..     229     251 .. 0.66
   4 ?   13.9   0.1   2.8e-05     0.036      10      39 ..     269     298 ..     266     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                        HTH_23   5 reRlrilllla 15 
                                   ++Rl++l+  +
  gi|70606656|ref|YP_255526.1|  97 KRRLEVLRWRK 107
                                   67888887665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.4
                        HTH_23   6 eRlrillllae.....GlsvreIAreL 27 
                                   +R+++++ l+e     +++++e+Ar +
  gi|70606656|ref|YP_255526.1| 177 RRMKMARTLDEiaqftKANRKEVARCY 203
                                   7888888888777799999****9976 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7.8
                        HTH_23  15 aeGlsvreIAre 26 
                                   + G++ + +A++
  gi|70606656|ref|YP_255526.1| 232 LSGITMKHAAEI 243
                                   557777777764 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 2.8e-05
                        HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlk 39 
                                   ++ll +e+ +++eIA+  gv++ Tv++  k
  gi|70606656|ref|YP_255526.1| 269 AALLNDERRTQKEIAQVAGVTEVTVRNRYK 298
                                   5677888*******************5444 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.32   4.1e+02      20      41 ..     181     202 ..     168     209 .. 0.81
   2 ?    9.6   0.0   0.00068      0.86      23      48 ..     278     303 ..     265     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.32
                                   EEHHHHHHHHHTTSSHHHHHHH CS
                     HTH_Crp_2  20 lpltqeelAsmlGltretvsri 41 
                                   +  t +e+A++  ++r  v r 
  gi|70606656|ref|YP_255526.1| 181 MARTLDEIAQFTKANRKEVARC 202
                                   5557799**********99997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00068
                                   HHHHHHHHTTSSHHHHHHHHHHHHHT CS
                     HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkre 48 
                                   tq+e+A+  G+t +tv    +eL +e
  gi|70606656|ref|YP_255526.1| 278 TQKEIAQVAGVTEVTVRNRYKELTQE 303
                                   9***************9999999886 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0018       2.3      55     124 ..     146     212 ..     112     214 .. 0.83
   2 ?    2.4   0.0     0.098   1.3e+02      37      90 ..     222     275 ..     220     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT CS
                      Cyclin_N  55 avnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnf 124
                                   a+ ++ + ++k  v+ + ++ v+a++++ A++  ++ + +l++++  t+   +++e+ +  rliL++L+ 
  gi|70606656|ref|YP_255526.1| 146 AALIYRKAVEKGLVRGRSIESVVAASIYAACRRMKM-ARTLDEIAQFTK--ANRKEVARCYRLILRELDI 212
                                   6667777888888889999*************9888.89********88..899*************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.098
                                   HHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSS CS
                      Cyclin_N  37 wlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveei 90 
                                   +++++ + ++l+  t+ +a++++++   +  +  ++   ++a+++++Aa +++ 
  gi|70606656|ref|YP_255526.1| 222 YVTRIGTLLSLSGITMKHAAEIIEKAKNSGLTAGKDPAGLAAAAIYIAALLNDE 275
                                   56666667778888888999999999998888889999999*******987433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2207.69
//
Query:       gi|70606657|ref|YP_255527.1|  [L=91]
Description: hypothetical protein Saci_0867 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-12   46.0  10.8    3.7e-12   45.7   9.3    1.8  2  DUF131     Protein of unknown function DUF131
  ------ inclusion threshold ------
       0.24   11.6   1.7        5.5    7.2   0.1    2.1  2  Pox_A14    Poxvirus virion envelope protein A14
        1.2    9.6   5.9        5.1    7.6   5.9    1.8  1  DUF202     Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3     0.094   5.6e+02      26      34 ..      11      19 ..       7      31 .. 0.73
   2 !   45.7   9.3   6.1e-16   3.7e-12       8      61 ..      23      77 ..      15      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.094
                        DUF131 26 GVvliGPIP 34
                                  G+v+iG I 
  gi|70606657|ref|YP_255527.1| 11 GLVFIGAII 19
                                  778888664 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 6.1e-16
                        DUF131  8 lekeeeeaekeesrvkgGGVvliGPIPIiFGsdk.rlaktaiiLaIilmilllil 61
                                  +e  ++ + ++++++ +GG++liGPIPI+FGs +  l   ++ ++Iil+i+++++
  gi|70606657|ref|YP_255527.1| 23 SEVLSSPQVSGTTSSNVGGFILIGPIPIVFGSGNqALFPQLMTFGIILTIIAILF 77
                                  444455889999********************98467789*************98 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.008        48      15      38 ..       6      30 ..       2      53 .. 0.69
   2 ?    7.2   0.1   0.00092       5.5      11      32 ..      60      81 ..      56      91 .] 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.008
                       Pox_A14 15 liaGiiLL.ilacifafvdfsksts 38
                                  +++G+ L+ i a+i+af ++  s +
  gi|70606657|ref|YP_255527.1|  6 ILTGLGLVfIGAIILAFSEVLSSPQ 30
                                  5678877526799999988755544 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00092
                       Pox_A14 11 ystvliaGiiLLilacifafvd 32
                                  + +++ +GiiL i+a++f  + 
  gi|70606657|ref|YP_255527.1| 60 FPQLMTFGIILTIIAILFYVLP 81
                                  667899**********986443 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.9   0.00085       5.1      16      61 ..       8      84 ..       6      91 .] 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
                        DUF202 16 tslalialglallrffl.............................tgepsalg..kilglilivlgiltllvglvr 61
                                  t+l+l+++g+ +l+f                               +g+++ +   + +g+il +++il+ ++ ++ 
  gi|70606657|ref|YP_255527.1|  8 TGLGLVFIGAIILAFSEvlsspqvsgttssnvggfiligpipivfgSGNQALFPqlMTFGIILTIIAILFYVLPFIL 84
                                  89************977989888888777777777766666666654444443322555788888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 622.73
//
Query:       gi|70606658|ref|YP_255528.1|  [L=355]
Description: hypothetical protein Saci_0869 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-18   65.9   0.2    6.9e-18   64.8   0.2    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    2.7e-08   34.3   0.1      6e-08   33.2   0.1    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.2   7.7e-22   6.9e-18       7     168 ..     181     332 ..     175     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 7.7e-22
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsre 84 
                                     + + e++k++l+vgr+e+ K +++++ + al      ++vk vi+G   ++ + ++l kl+ + +   ++++l  + ++
  gi|70606658|ref|YP_255528.1| 181 SAYHEGEREKFFLTVGRIERGKMLENAVLVSAL------SKVKGVIVGslrEKGYYNKLLKLSRKMGA--DIHILTDLTPQ 253
                                   55667899************************5......57*******98777777777777555555..9999999999* PP

                                   SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH.HHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede.elrer 164
                                   +l +l+++a+++++p   E+fGi+++EAm+agl  ++   +g++ev  + +       +n+e++++ i++++e +   r++
  gi|70606658|ref|YP_255528.1| 254 ELVKLMSRASVYFHPTLGEHFGIPVVEAMSAGLVPVVPEESGAKEVAPEFK------YKNVEEASKLIKEAMEVDrRFRKE 328
                                   **********************************************99999......346677777777777755455555 PP

                                   HHHH CS
               Glycos_transf_1 165 lgen 168
                                   l e+
  gi|70606658|ref|YP_255528.1| 329 LHER 332
                                   5555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   6.7e-12     6e-08       4     109 ..     192     300 ..     189     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 6.7e-12
                                   EEEES---G.G.GTHHHHHHHHHHHH.HHEEEEEES---......HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
               Glyco_trans_1_4   4 ilfvGrlee.nvkgvdllleavpllrkkdvrlvivGdgprp....eeleelaagleerveftGfv..edlaellaaadvfv 77 
                                   +l+vGr+e+ +     +l+ a+ +     v+ vivG+   +    ++l +l +++ ++++++  +  ++l +l+++a+v+ 
  gi|70606658|ref|YP_255528.1| 192 FLTVGRIERgKMLENAVLVSALSK-----VKGVIVGSLR-EkgyyNKLLKLSRKMGADIHILTDLtpQELVKLMSRASVYF 266
                                   567777732222222333444444.....6689***543.23455566555556668899999998888************ PP

                                   E--..---SHHHHHHHHTT-EEEE-TGGGTTT-- CS
               Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv 109
                                    P+  e fg+ ++Eam+agl  V+ + +g++ev 
  gi|70606658|ref|YP_255528.1| 267 HPTlgEHFGIPVVEAMSAGLVPVVPEESGAKEVA 300
                                   *****9*************988888777878865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2520.84
//
Query:       gi|70606659|ref|YP_255529.1|  [L=287]
Description: hypothetical protein Saci_0870 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-11   44.6   0.0    1.8e-11   44.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.038   13.5   0.0        0.1   12.0   0.0    1.7  2  Glyco_transf_21  Glycosyl transferase family 21
      0.061   13.8   0.0       0.12   12.9   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0     3e-15   1.8e-11      10     132 ..      14     126 ..       4     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3e-15
                                   TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-..HHHHHHHHHHHH--SSEEEEEES CS
               Glycos_transf_2  10 ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv..GkagalnaglraatgdyilflDa 88 
                                    + ++e++ s+l+q   + ++++v D++++ ++ + l +la     v +i+ ++ +    a+ +n  l+ ++ d+i+ lD+
  gi|70606659|ref|YP_255529.1|  14 LEWVRESVSSALRQ---KVDRVVVYDNSERPDLGDYLSSLA-----VEYIKGPRMRkiNMAKLRNIMLSLSKDDVIIMLDS 86 
                                   6889**********...888888888888***********6.....********998999********************* PP

                                   SEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
               Glycos_transf_2  89 Ddepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                   D++++ dw ++lve++      +v  +++++ ++t+ i +++  
  gi|70606659|ref|YP_255529.1|  87 DVVIPYDWSQRLVEKIRS----GVHFTWMHYAYSTNDIMKPLAP 126
                                   *****************9....4478888888888888887765 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05       0.1      21      70 ..      70     116 ..      51     147 .. 0.73
   2 ?   -2.0   0.0      0.37   2.2e+03      58      69 ..     269     280 ..     263     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
               Glyco_transf_21  21 nllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgs 70 
                                   n+  +l+  k d+++++Dsdv+++ d  ++l++++++ +v +  + +++s
  gi|70606659|ref|YP_255529.1|  70 NI--MLSLSKDDVIIMLDSDVVIPYDWSQRLVEKIRS-GVHFTWMHYAYS 116
                                   32..3344899*************************7.776654444443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.37
               Glyco_transf_21  58 pkvglVtslpvg 69 
                                   p+ +lVtslp+g
  gi|70606659|ref|YP_255529.1| 269 PGLALVTSLPYG 280
                                   6789******98 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05      0.12      10      91 ..      20      97 ..      13     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
               Glyco_tranf_2_4 10 flahhlalgfdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaDEflvvpdsrs 91
                                   +  +l+  +dr++vydn  +++  ++l++   + + +++++   ++  ++ l++++ + +++d ++++D+D ++ +++s++
  gi|70606659|ref|YP_255529.1| 20 SVSSALRQKVDRVVVYDNSERPDLGDYLSS---LAVEYIKGPRM-RKINMAKLRNIMLSLSKDDVIIMLDSDVVIPYDWSQR 97
                                  456778889********************9...57888888764.5788998888888999***********9999998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2204.51
//
Query:       gi|70606660|ref|YP_255530.1|  [L=307]
Description: hypothetical protein Saci_0871 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-29  101.8   0.0    7.7e-29  100.9   0.0    1.4  1  Peptidase_M48    Peptidase family M48
  ------ inclusion threshold ------
      0.062   12.8  14.7      0.021   14.3   2.1    2.1  2  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
       0.11   11.6   1.8       0.12   11.6   0.4    1.8  2  Peptidase_M56    BlaR1 peptidase M56
        0.2   12.1   0.3        0.2   12.1   0.3    3.0  3  DUF3899          Domain of unknown function (DUF3899)


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.0   1.7e-32   7.7e-29       7     193 ..      72     301 ..      69     304 .. 0.79

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.7e-32
                                   HHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   7 lkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsvvsliv 86 
                                   l e+v+++a e+++  p+++v++  ++  NAFa g+  +  r+++t++Ll + l+++el+aVl+HE+GHikh ++ + +  
  gi|70606660|ref|YP_255530.1|  72 LYEIVRKIAMESKV--PTPRVFISYEEYPNAFAFGNYITGkRVAVTKPLL-DILNQDELEAVLAHEVGHIKHLDVEIGMAL 149
                                   568999********..********************99999*********.***************************999 PP

                                   HHHHHHHHHHHHHHHT.T-SHHHHHTT--S---HH.HHHHHHHHTT..........HHHHHHHHHHHHHHHHTTT.HH.HH CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx.xx RF
                 Peptidase_M48  87 sllasillllglalli.sraeedaagafldalavl.iglliillfl..........alSRkrEyqADeagvellkrak.dl 154
                                   +l+++i+ ++g +ll+ +++ ++ ag  ++ +  l +++++ +lf+          ++ R rE+ AD +++ l k+++ +l
  gi|70606660|ref|YP_255530.1| 150 GLIPTIIGYVGNFLLFtGWTLLFFAGDEVELILGLaMLAIGGVLFVltfllqifvlWFNRLRESFADFHSATLYKDKApYL 230
                                   999999999997665415666665555443333220222233333345556669******************999765389 PP

                                   HHHHHHHHHHTT-....................-S---HHHH...................HHS-SS--HHHHHHHHH CS
                                   xxxxxxxxxxxxx....................xxxxxxxxx...................xxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 155 vraliklakdler....................qdvsaslrs...................ellstHPplleRiqalk 193
                                   ++al+k++  +++                    +       +                   ++l+tHP  ++R++ l 
  gi|70606660|ref|YP_255530.1| 231 ATALAKIQIYAQNirtdpftgiiitappiklkeN-------ErdaeelvmkwlhehispfaDILMTHPHPAKRVKMLY 301
                                   99****9988888778888888888877766531.......03334457788888999999*************9986 PP

>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.0    0.0064        29     209     250 ..      10      51 ..       4      60 .. 0.80
   2 ?   14.3   2.1   4.8e-06     0.021     109     205 ..     146     245 ..     128     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0064
               LPG_synthase_TM 209 lafllslliwllealtlylllralgvdvslallllillaltl 250
                                   l fl  +l+ ++e+ ++yl++ ++g+++ +++++l++l l+ 
  gi|70606660|ref|YP_255530.1|  10 LMFLSGTLTIIAEGIITYLIVSIIGIPTIFTAIFLVILWLIQ 51 
                                   6799999*************************9955544433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.8e-06
               LPG_synthase_TM 109 alasvvverlldllal.vllgllallllggllaegaa..vllllalallllavlalllllllrrrlarlarvlkrlarlla 186
                                    +a  ++ ++++ ++  +l+++++ll++ g   e     ++l+++++l++l +l+ +++l++ r +   a ++++ + + +
  gi|70606660|ref|YP_255530.1| 146 GMALGLIPTIIGYVGNfLLFTGWTLLFFAGDEVELILglAMLAIGGVLFVLTFLLQIFVLWFNRLRESFADFHSATLYKDK 226
                                   55555666666666650556677777777776666668988889999999999999******************9999999 PP

               LPG_synthase_TM 187 rfarklasakrklvlaspr 205
                                   ++   +a ak+++++++ r
  gi|70606660|ref|YP_255530.1| 227 APYLATALAKIQIYAQNIR 245
                                   9888888887755555444 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   2.6e-05      0.12     180     216 ..     111     147 ..      34     168 .. 0.74
   2 ?   -2.2   0.0      0.41   1.9e+03     107     133 ..     185     209 ..     173     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                 Peptidase_M56 180 rIvlPadflkklsdeeleyillHElaHlkrkDllvnl 216
                                   r+ + + +l  l+++ele +l+HE  H+k+ D+ + +
  gi|70606660|ref|YP_255530.1| 111 RVAVTKPLLDILNQDELEAVLAHEVGHIKHLDVEIGM 147
                                   566666677889********************97765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.41
                 Peptidase_M56 107 liWivgalilllyliaallvlkkrfvr 133
                                   ++ ++g ++++l ++  ++vl+  f r
  gi|70606660|ref|YP_255530.1| 185 AMLAIGGVLFVLTFLLQIFVLW--FNR 209
                                   4445555555555555555555..333 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   1.3       1.9   8.7e+03       8      14 ..      41      47 ..      29      54 .. 0.49
   2 ?   -3.6   2.1       3.8   1.7e+04      11      31 ..     150     170 ..     146     173 .. 0.64
   3 ?   12.1   0.3   4.5e-05       0.2       6      56 ..     181     228 ..     180     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                       DUF3899  8 gllllii 14
                                  +++l+i+
  gi|70606660|ref|YP_255530.1| 41 AIFLVIL 47
                                  2333333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.8
                       DUF3899  11 lliigillivlnsGfFdgfsy 31 
                                    li  i+ +v n  +F+g+++
  gi|70606660|ref|YP_255530.1| 150 GLIPTIIGYVGNFLLFTGWTL 170
                                   456666667777777777765 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 4.5e-05
                       DUF3899   6 llglllliigillivlnsGfFdgfsygfrklkklflkkskkddsyyeykek 56 
                                   +lgl++l+ig++l+vl   ++++f ++f++l+++f   + +++ +y++k++
  gi|70606660|ref|YP_255530.1| 181 ILGLAMLAIGGVLFVLT-FLLQIFVLWFNRLRESFA--DFHSATLYKDKAP 228
                                   79*************96.59**************99..8888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2057.41
//
Query:       gi|70606661|ref|YP_255531.1|  [L=741]
Description: truncated copper-transporting P-type ATPase, partial [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-53  180.4   1.3    6.4e-53  179.0   1.3    1.8  1  E1-E2_ATPase   E1-E2 ATPase
      7e-32  111.4   0.7    1.5e-31  110.3   0.7    1.6  1  Hydrolase      haloacid dehalogenase-like hydrolase
    5.1e-15   55.7   9.9      3e-13   50.0   2.8    2.9  2  HMA            Heavy-metal-associated domain
    3.1e-06   27.1   5.7      0.022   14.5   0.1    3.2  4  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.017   15.1   0.0        0.6   10.2   0.0    2.5  2  NLPC_P60       NlpC/P60 family
      0.023   14.8   0.0       0.11   12.6   0.0    2.2  2  Hydrolase_6    Haloacid dehalogenase-like hydrolase
      0.024   15.0   0.0          1    9.7   0.0    2.9  2  HAD            haloacid dehalogenase-like hydrolase
      0.047   13.8   2.0       0.82    9.7   0.1    3.3  3  HAD_2          Haloacid dehalogenase-like hydrolase
       0.21   11.4   6.8        2.1    8.2   1.5    4.1  5  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
       0.41   11.3   0.1       0.41   11.3   0.1    3.1  3  ACT_4          ACT domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.0   1.3   3.5e-56   6.4e-53       1     180 [.     262     442 ..     262     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 179.0 bits;  conditional E-value: 3.5e-56
                                   SSS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                  E1-E2_ATPase   1 kllpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                   kl++ +a++i++g+e ei+++el++GD+v++k+gd++paDg++ +g+a+vdes+ TGE+lp +k+kgd v++G++v  g +
  gi|70606661|ref|YP_255531.1| 262 KLTQVKARKIENGKEYEINSNELKVGDLVVVKTGDIIPADGVVESGEATVDESIYTGEALPTTKKKGDPVIGGSIVQTGAL 342
                                   578999*************************************************************************** PP

                                   EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHHHHS-T CS
                  E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallvaaiPc 161
                                   ++ Vt+ g+  ++++++++++ea+ +k p+qk +dk+++++vp+v++i++l  ++++++++  + ++ll ++a+l +a+Pc
  gi|70606661|ref|YP_255531.1| 343 TVYVTRSGNRAYISQVVSAIKEAEFTKLPIQKLVDKVSSIFVPFVIVISVLSSIFWYYIFHADFtFSLLIGIAVLASACPC 423
                                   ************************************************************99988**************** PP

                                   THHHHHHHHHHHHHHHHHH CS
                  E1-E2_ATPase 162 aLplavplalalgarrlak 180
                                   +++la+p+a+++g+r+lak
  gi|70606661|ref|YP_255531.1| 424 GFGLATPTAIMIGIRKLAK 442
                                   ******************8 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.7   8.4e-35   1.5e-31       2     208 ..     460     648 ..     459     650 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 8.4e-35
                                   SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHETTTE........HHHHTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx........xxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.sgaltgfatfigrg........ayaigk 73 
                                   k v+fDk+GT+t g+  ++ +  + +++la ale  s+hpi+ka++    ++ + ++++f++f+g+g        ++ +gk
  gi|70606661|ref|YP_255531.1| 460 KRVIFDKTGTITSGK--IKIIKTEGDIQLASALESLSNHPIAKAIAQLHSDMtEKKIEDFTEFQGQGvygkvnghEIIVGK 538
                                   569*********999..5556666699******************888888868888************************ PP

                                   HHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  74 pewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                   +e++  +        ++++  +++ + + +++++ + ++i+d+  ++pea+ ++++Lk+ g++v ++tgd++++a+++a+ 
  gi|70606661|ref|YP_255531.1| 539 KEFVLNN-------CQTDEIVDDADILVCKDGKLEGKIWISDE--IRPEAKMVIEYLKKHGYDVEIATGDSSKFADEVAKS 610
                                   *******.......66667777777777779************..************************************ PP

                                   TTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 155 lGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                   lG           ++ +++ s e k +++re    p  ++++GDgvnDa al++
  gi|70606661|ref|YP_255531.1| 611 LG-----------VKLHKGLSAEEKAELVREK---P--TVFIGDGVNDAIALKE 648
                                   **...........888**************97...9..**************97 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   2.8   1.6e-16     3e-13       2      62 .]      12      71 ..      11      71 .. 0.96
   2 !    8.9   0.7    0.0012       2.1      14      62 .]      89     135 ..      86     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.6e-16
                           HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                  ++v gmhCa C+ +v+k++++++gV++++v+l ++++ ++ ++ + kl+ +i+ai+kagy+
  gi|70606661|ref|YP_255531.1| 12 LKVVGMHCATCVETVTKAILSVQGVKDASVNLTSGEAKIVIEDNK-KLKNVIQAIRKAGYD 71
                                  6899*************************************9998.88************7 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                           HMA  14 akvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                   +kv++ +++++gV svkv ++  +v Ve ++ s++++ i+ ++  +gyk
  gi|70606661|ref|YP_255531.1|  89 GKVKDIIENIDGVISVKVGME--RVIVEINPLSVSPEVILDELNRKGYK 135
                                   69***********99999888..88888888888889999999999996 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4         1   1.8e+03     148     189 ..      52      91 ..      27     152 .. 0.67
   2 ?   -3.6   0.0       4.2   7.5e+03      74     121 ..     493     539 ..     484     555 .. 0.59
   3 !   14.1   0.0   1.6e-05     0.029      15      56 ..     574     615 ..     572     620 .. 0.93
   4 !   14.5   0.1   1.2e-05     0.022     202     244 ..     629     671 ..     616     675 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                                   ES-HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHH CS
                   Hydrolase_3 148 lkdkekldelekelksklnklltitssskgyleimpkgvsKg 189
                                   ++d++kl+++++++++   +   it+     l+i++ ++ K 
  gi|70606661|ref|YP_255531.1|  52 IEDNKKLKNVIQAIRKAGYD--IITQEFIMKLNINQDEIGKV 91 
                                   44455555555555555433..44444444444554444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.2
                                   EEE--B-HHHHHHHHHHHHHTTCEEEEEESSEEEESTT.THHHHHHHH CS
                   Hydrolase_3  74 lykstiskedvkeiikllkennveillytedkvyvlnkeksekkkkee 121
                                   l++++i k+ ++   +  +++  ++  ++ ++vy++ +  +e ++ ++
  gi|70606661|ref|YP_255531.1| 493 LSNHPIAKAIAQLHSDMTEKKIEDFTEFQGQGVYGKVN-GHEIIVGKK 539
                                   56666666665555555555557777777777777666.444444444 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.6e-05
                                   ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                   Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                   +i +++k +i++lk++g+ v iATG s +++ +v+++lg++l
  gi|70606661|ref|YP_255531.1| 574 EIRPEAKMVIEYLKKHGYDVEIATGDSSKFADEVAKSLGVKL 615
                                   68999**********************************985 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 1.2e-05
                                   -GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE- CS
                   Hydrolase_3 202 sleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtk 244
                                     + ++ +GDg ND   L+ + +g+A+ ++++ +k a d ++ 
  gi|70606661|ref|YP_255531.1| 629 REKPTVFIGDGVNDAIALKESHVGIAISSGTDIAKYAGDIIIS 671
                                   567899*****************************99988876 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00034       0.6      28      63 ..     260     295 ..     249     303 .. 0.84
   2 ?    2.2   0.0       0.1   1.8e+02      15      93 ..     599     675 ..     588     688 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                                   T----SSHHHHCCCSEE..EEGGG--TTEEEEESGT CS
                      NLPC_P60  28 gielprssgeqeaagkkkeiskselkrGDLvffktk 63 
                                    i+l +   ++ ++gk++ei ++elk GDLv++kt+
  gi|70606661|ref|YP_255531.1| 260 VIKLTQVKARKIENGKEYEINSNELKVGDLVVVKTG 295
                                   5888888889999*******************9994 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                                   -HHHHHHHHHHTTT----SSHHHHCCCSEE..EEGGG--TTEEEEESGTGGESEEEEEEETTEEEEEETTEEEEEETTS CS
                      NLPC_P60  15 DCsglvryafakagielprssgeqeaagkkkeiskselkrGDLvffktkkgisHvgiYlgngkmlhassekvsvsslse 93 
                                   D s +   + ++ g++l++  +++e+a+      k  +  GD v  + + + sHvgi +  g+ + +  + + +s+ls+
  gi|70606661|ref|YP_255531.1| 599 DSSKFADEVAKSLGVKLHKGLSAEEKAELV--REKPTVFIGDGVNDAIALKESHVGIAISSGTDIAKYAGDIIISNLSQ 675
                                   888888888888899999988888777777..66677777888888888899*******99999998888888887765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.6   8.2e+03      43      62 ..      57      76 ..      49      84 .. 0.64
   2 ?   12.6   0.0   6.1e-05      0.11       6      55 ..     566     616 ..     564     630 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.6
                                  -HHHHHHHHHHTT----GGG CS
                   Hydrolase_6 43 seeeyakkleklgvditeeq 62
                                  + +++++ ++k g+di  ++
  gi|70606661|ref|YP_255531.1| 57 KLKNVIQAIRKAGYDIITQE 76
                                  44556666666666655544 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.1e-05
                                   TTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH.HHTT CS
                   Hydrolase_6   6 dGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl.eklg 55 
                                    G +w  d++ p+a+ ++++l+++g++v + T  ssk  +e+ak l  kl 
  gi|70606661|ref|YP_255531.1| 566 EGKIWISDEIRPEAKMVIEYLKKHGYDVEIATGDSSKFADEVAKSLgVKLH 616
                                   6899**********************************9999999976663 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.6   1.1e+03      35      78 ..     479     522 ..     456     535 .. 0.77
   2 ?    9.7   0.0   0.00056         1      86     183 ..     575     642 ..     564     647 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                           HAD  35 reklllalfrellrldraglaelleallaglseelaaelerfva 78 
                                   + + + +l++ l +l++  +a++++ l+++++e+ ++++ +f+ 
  gi|70606661|ref|YP_255531.1| 479 KTEGDIQLASALESLSNHPIAKAIAQLHSDMTEKKIEDFTEFQG 522
                                   55556677788888999999************999999999884 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00056
                           HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaeg 166
                                   ++p+a+ +++  ++ G+ v + +g  + ++ ++++ lg    +           ++          e+k+  +re      
  gi|70606661|ref|YP_255531.1| 575 IRPEAKMVIEYLKKHGYDVEIATGDSSKFADEVAKSLG----VKL--------HKG-------LSAEEKAELVRE------ 630
                                   347788888878899*******************9999....222........222.......333366666666...... PP

                           HAD 167 egidleevvayGDspsD 183
                                        + +v++GD+++D
  gi|70606661|ref|YP_255531.1| 631 -----KPTVFIGDGVND 642
                                   .....227777777777 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.26   4.7e+02      87     110 ..     125     148 ..      70     157 .. 0.81
   2 ?   -3.8   0.0       6.4   1.1e+04      30      43 ..     507     520 ..     487     546 .. 0.55
   3 ?    9.7   0.1   0.00046      0.82      81     119 ..     576     614 ..     572     655 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.26
                         HAD_2  87 lLeeLkeagyklgivTsksreave 110
                                   +L+eL+++gyk  i T k +++ e
  gi|70606661|ref|YP_255531.1| 125 ILDELNRKGYKANIETEKIAKKSE 148
                                   699***********9999877654 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.4
                         HAD_2  30 selseeelrkligl 43 
                                   s+++e++++ + ++
  gi|70606661|ref|YP_255531.1| 507 SDMTEKKIEDFTEF 520
                                   24444444444444 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00046
                         HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgie 119
                                    +++k+++e+Lk++gy + i+T  s++ ++e  + lg++
  gi|70606661|ref|YP_255531.1| 576 RPEAKMVIEYLKKHGYDVEIATGDSSKFADEVAKSLGVK 614
                                   5789***************************99999975 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.2   1.1e+04      26      39 ..      39      52 ..      35      54 .. 0.85
   2 ?   -0.7   0.0      0.72   1.3e+03      12      28 ..      56      72 ..      50      75 .. 0.86
   3 ?    8.2   1.5    0.0012       2.1       4      39 ..      78     113 ..      77     115 .. 0.96
   4 ?   -3.3   0.0       4.5   8.1e+03      17      30 ..     125     138 ..     123     139 .. 0.85
   5 ?    2.5   0.0     0.072   1.3e+02      15      35 ..     580     600 ..     576     602 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.2
                 DAHP_snth_FXD 26 lkvhvskGeertVi 39
                                   +v+++ Ge ++Vi
  gi|70606661|ref|YP_255531.1| 39 ASVNLTSGEAKIVI 52
                                  5789999*999998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                 DAHP_snth_FXD 12 eqieevierieelGlkv 28
                                  +++++vi+ i++ G+++
  gi|70606661|ref|YP_255531.1| 56 KKLKNVIQAIRKAGYDI 72
                                  67899*********975 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0012
                 DAHP_snth_FXD   4 vmkkgateeqieevierieelGlkvhvskGeertVi 39 
                                   +mk ++++++i +v + ie+ +  + v  G er+++
  gi|70606661|ref|YP_255531.1|  78 IMKLNINQDEIGKVKDIIENIDGVISVKVGMERVIV 113
                                   8*********************************98 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.5
                 DAHP_snth_FXD  17 vierieelGlkvhv 30 
                                   ++++++++G+k+++
  gi|70606661|ref|YP_255531.1| 125 ILDELNRKGYKANI 138
                                   67899******987 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.072
                 DAHP_snth_FXD  15 eevierieelGlkvhvskGee 35 
                                   + vie +++ G++v++ +G +
  gi|70606661|ref|YP_255531.1| 580 KMVIEYLKKHGYDVEIATGDS 600
                                   679**************9975 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00023      0.41      31      71 ..      27      67 ..      18      70 .. 0.87
   2 ?   -0.2   0.1      0.89   1.6e+03      59      79 ..      85     105 ..      75     105 .. 0.75
   3 ?   -3.7   0.1        10   1.8e+04      26      49 ..     255     278 ..     254     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                         ACT_4 31 kanivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71
                                  + +i sv+ +++ + +l++++ ++ ++d ++L++vi+++r+
  gi|70606661|ref|YP_255531.1| 27 TKAILSVQGVKDASVNLTSGEAKIVIEDNKKLKNVIQAIRK 67
                                  5678999999988889***********************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.89
                         ACT_4  59 vehLsrviakLraipgVisVe 79 
                                    +++ +v + +++i+gVisV+
  gi|70606661|ref|YP_255531.1|  85 QDEIGKVKDIIENIDGVISVK 105
                                   566677888888999999885 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 10
                         ACT_4  26 viseekanivsvnaktrkkdglae 49 
                                    ise+ ++++ v+a++ ++ +  e
  gi|70606661|ref|YP_255531.1| 255 KISEDVIKLTQVKARKIENGKEYE 278
                                   588899999999999877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (741 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 4830.45
//
Query:       gi|70606662|ref|YP_255532.1|  [L=55]
Description: hypothetical protein Saci_0873 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-20   70.9   3.4    7.2e-20   70.8   3.4    1.0  1  YHS              YHS domain
    9.2e-05   22.7   1.7    0.00013   22.2   1.7    1.2  1  Arc_trans_TRASH  Archaeal TRASH domain
      0.002   18.1   1.2     0.0028   17.6   1.2    1.4  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.022   14.3   0.1    1.1  1  FAP206           Domain of unknown function
       0.11   12.5   1.5       0.51   10.4   1.5    1.9  1  DUF2116          Uncharacterized protein containing a Zn-ribb


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   3.4     2e-23   7.2e-20       2      46 ..       3      46 ..       2      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2e-23
                           YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYat 46
                                  +dPvcgm v  e +++ks YkGk YyFcS++Ck +F+++P++Y+t
  gi|70606662|ref|YP_255532.1|  3 IDPVCGMEV-EENSQYKSMYKGKIYYFCSPHCKKAFDKDPQEYLT 46
                                  6********.666******************************98 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.7   3.6e-08   0.00013       4      35 ..       7      39 ..       6      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.6e-08
               Arc_trans_TRASH  4 CGkeivgePiv.yklknkvYyvCCktCkselkk 35
                                  CG e+ +++     +k k+Yy+C + Ck+ + k
  gi|70606662|ref|YP_255532.1|  7 CGMEVEENSQYkSMYKGKIYYFCSPHCKKAFDK 39
                                  99999999854145799************9987 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.2   7.8e-07    0.0028      24      41 .]      20      37 ..       6      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.8e-07
                        zf-FCS 24 endgvvgqFCStsCldsY 41
                                   ++g++++FCS +C++ +
  gi|70606662|ref|YP_255532.1| 20 MYKGKIYYFCSPHCKKAF 37
                                  478************988 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.2e-06     0.022     227     254 ..      20      47 ..      14      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-06
                        FAP206 227 kykdkyyaFsseeaareFaadpdrfiea 254
                                   +yk+k y F s+ + ++F +dp++++++
  gi|70606662|ref|YP_255532.1|  20 MYKGKIYYFCSPHCKKAFDKDPQEYLTK 47 
                                   79***********************986 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.5   0.00014      0.51      18      32 ..      27      41 ..       4      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
                       DUF2116 18 sfCsekCqeeyekkr 32
                                   fCs++C+++++k  
  gi|70606662|ref|YP_255532.1| 27 YFCSPHCKKAFDKDP 41
                                  59*********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 384.16
//
Query:       gi|70606663|ref|YP_255533.1|  [L=181]
Description: hypothetical protein Saci_0874 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-20   71.0   8.8    1.4e-19   70.1   8.8    1.5  1  Arc_trans_TRASH  Archaeal TRASH domain
      1e-07   31.8   0.7    2.6e-07   30.5   0.7    1.7  1  HTH_11           HTH domain
    1.5e-06   27.9   0.2    2.8e-06   27.1   0.2    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    6.1e-06   25.7   0.7    6.1e-06   25.7   0.7    1.8  2  HTH_24           Winged helix-turn-helix DNA-binding
    9.6e-05   22.2   0.0    0.00015   21.6   0.0    1.3  1  MarR_2           MarR family
     0.0001   22.2   0.2    0.00016   21.5   0.2    1.3  1  MarR             MarR family
    0.00018   21.3   0.2    0.00039   20.3   0.2    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.002   18.1   0.8     0.0044   17.0   0.8    1.5  1  HTH_6            Helix-turn-helix domain, rpiR family
     0.0056   16.7   0.0      0.013   15.5   0.0    1.5  1  HTH_29           Winged helix-turn helix
     0.0096   15.7   0.1       0.02   14.7   0.1    1.6  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.026   14.4   0.1    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
      0.012   16.0   0.1      0.025   14.9   0.1    1.6  1  Penicillinase_R  Penicillinase repressor
      0.017   15.1   0.6      0.037   14.0   0.6    1.5  1  HTH_36           Helix-turn-helix domain
      0.027   14.5   1.5      0.034   14.2   0.0    1.9  2  HTH_20           Helix-turn-helix domain
      0.031   14.9   1.2      0.056   14.0   0.3    1.8  2  Mga              Mga helix-turn-helix domain
      0.038   13.8   0.2       0.12   12.2   0.2    1.9  1  HTH_38           Helix-turn-helix domain
      0.045   14.2   0.1      0.072   13.6   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
      0.056   13.5   0.1       0.15   12.2   0.1    1.7  1  HTH_7            Helix-turn-helix domain of resolvase
      0.057   12.5   0.0      0.071   12.2   0.0    1.1  1  APG17            Autophagy protein Apg17
      0.061   13.4   0.2       0.14   12.2   0.2    1.7  1  HTH_22           HTH domain
      0.065   13.5   0.4       0.14   12.4   0.4    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.33   10.8   2.5       0.77    9.6   0.7    2.3  3  HTH_10           HTH DNA binding domain


Domain annotation for each model (and alignments):
>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   8.8   1.7e-22   1.4e-19       1      37 []     140     176 ..     140     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.7e-22
               Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselkkkl 37 
                                   CDYCG+ei+g+Pi++k+++++Yy+CC+tCk++l+kkl
  gi|70606663|ref|YP_255533.1| 140 CDYCGGEIKGTPITLKVRRRIYYTCCNTCKEHLRKKL 176
                                   ***********************************96 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.7   3.2e-10   2.6e-07       4      45 ..      23      63 ..      21      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.2e-10
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  ++l +L ++++  s++ +A+eL vSr+t+ + Ik+L+++ ++
  gi|70606663|ref|YP_255533.1| 23 KVLNIL-KEDSRRSASSIAKELQVSRATIAKTIKSLRSKNIK 63
                                  678889.88888*************************99854 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   3.4e-09   2.8e-06       6      42 .]      22      58 ..      17      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.4e-09
                 HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   k L++L ed+R+s + +A+++ +S++t+++ ++ L+
  gi|70606663|ref|YP_255533.1| 22 YKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLR 58
                                  688****************************999886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.7   7.5e-09   6.1e-06       3      45 ..      19      61 ..      17      62 .. 0.93
   2 ?   -2.1   0.0       3.6   2.9e+03      33      40 ..     167     174 ..     166     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.5e-09
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                   +++k+L++L++++r s + +A++l +S++t+ + +k L ++ 
  gi|70606663|ref|YP_255533.1| 19 PLEYKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLRSKN 61
                                  6789***********************************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                        HTH_24  33 tvnrrlkr 40 
                                   t++++l++
  gi|70606663|ref|YP_255533.1| 167 TCKEHLRK 174
                                   9****997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.8e-07   0.00015       3      48 ..      17      60 ..      15      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.8e-07
                                  --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48
                                  ltp ++ vL+ L    +   +++ +a++l++s++++ +++k L ++
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLNILKEDSR--RSASSIAKELQVSRATIAKTIKSLRSK 60
                                  89**********99987..5*********************99886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2     2e-07   0.00016       1      44 [.      17      60 ..      17      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-07
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekk 44
                                  lt+ ++++L il+e    s s +ak l+vs++t+ ++++ L  k
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLRSK 60
                                  8999***********************************99766 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   4.7e-07   0.00039       6      50 ..      17      61 ..      13      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.7e-07
                                  HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
                          TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkG 50
                                  L+  E kv   L +  + +a+ ia+el v+r+++ ++++sL +k 
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLRSKN 61
                                  8999*************************************9986 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   5.4e-06    0.0044      12      58 ..      15      57 ..       5      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-06
                                  ----HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHHHH--- CS
                         HTH_6 12 ekltksekkiaeyilaspdkaielsikalAkaaavSeativrfakkL 58
                                   klt+ e k++++++++     + s + +Ak+++vS+ati +  k+L
  gi|70606663|ref|YP_255533.1| 15 VKLTPLEYKVLNILKEDS----RRSASSIAKELQVSRATIAKTIKSL 57
                                  578888888888887765....567788**************99988 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.013       6      41 ..      28      62 ..      24      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                        HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                  l+ +   s  s iAk l++sr t+ +++k  + + +
  gi|70606663|ref|YP_255533.1| 28 LKEDSRRS-ASSIAKELQVSRATIAKTIKSLRSKNI 62
                                  44455555.99******************9988765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.4e-05      0.02      17      42 ..      33      58 ..      22      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                        HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryr 42
                                  + s + IA+eL vsr T+ + +k  r
  gi|70606663|ref|YP_255533.1| 33 RRSASSIAKELQVSRATIAKTIKSLR 58
                                  789999**************999865 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.2e-05     0.026       6      40 ..      23      58 ..      19      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                                  HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                         HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLr 40
                                  k+L++L e + ++++ +a+el++s++t+    k Lr
  gi|70606663|ref|YP_255533.1| 23 KVLNILKEdSRRSASSIAKELQVSRATIAKTIKSLR 58
                                  79******566****************977666666 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.1e-05     0.025       1      50 [.      17      62 ..      17      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                                  ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS CS
               Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgl 50
                                  l++lE +v++il e ++ +++++ +el+      ++T++ +++ L  K++
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLNILKEDSRRSASSIAKELQVS----RATIAKTIKSLRSKNI 62
                                  699**********************99877....9999999999999875 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   4.5e-05     0.037      27      52 ..      35      60 ..      33      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                        HTH_36 27 sqetlakrlglsknTvsraikeLeql 52
                                  s + +ak l +s+ T+ + ik+L+ +
  gi|70606663|ref|YP_255533.1| 35 SASSIAKELQVSRATIAKTIKSLRSK 60
                                  5678*******************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.2e-05     0.034      10      50 ..      19      59 ..      15      62 .. 0.91
   2 ?   -2.4   0.0       6.4   5.2e+03      39      47 ..     166     174 ..     166     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                  HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLee 50
                                  P  +++l  L+++  ++as +a++l++s++t+ + ++ L++
  gi|70606663|ref|YP_255533.1| 19 PLEYKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLRS 59
                                  667889999****************************9975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.4
                                   HHHHHHHHH CS
                        HTH_20  39 ntlsyHLrv 47 
                                   nt+  HLr+
  gi|70606663|ref|YP_255533.1| 166 NTCKEHLRK 174
                                   78999**65 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   6.9e-05     0.056      17      55 ..      20      58 ..       7      67 .. 0.90
   2 ?   -2.0   0.0       6.7   5.5e+03      52      63 ..     107     118 ..      98     133 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-05
                                  HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                           Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                  l+y++l  l e+ + s  ++a+el +S++t+ + ik l+
  gi|70606663|ref|YP_255533.1| 20 LEYKVLNILKEDSRRSASSIAKELQVSRATIAKTIKSLR 58
                                  68999*******************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.7
                                   HHHHHHCHCCT- CS
                           Mga  52 kelnklLkefdl 63 
                                   +++++ L++ ++
  gi|70606663|ref|YP_255533.1| 107 DHIQQILEQNKI 118
                                   455555544443 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00015      0.12      21      42 ..      34      55 ..      16      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                        HTH_38 21 lslreIArrLgrspsTIsRElk 42
                                   s + IA++L +s+ TI++ +k
  gi|70606663|ref|YP_255533.1| 34 RSASSIAKELQVSRATIAKTIK 55
                                  68899************99776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.9e-05     0.072       1      44 [.      17      59 ..      17      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-05
                        HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLte 44
                                  lt+++  vL+ ++ ++ r +++ +++ l+v+ ++i++ +k L  
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLNILK-EDSRRSASSIAKELQVSRATIAKTIKSLRS 59
                                  799999*******.999999********************9975 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.15      23      38 ..      35      50 ..      22      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                  -STTTSSSS---SSSS CS
                         HTH_7 23 siskIAkevnisRsTv 38
                                  s+s IAke+++sR+T+
  gi|70606663|ref|YP_255533.1| 35 SASSIAKELQVSRATI 50
                                  7899***********8 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-05     0.071      65     150 ..      28     126 ..      16     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                                   IIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS......................STGGGCS--TTTTHHHHHHHH CS
                         APG17  65 klekgkeefkdlikeldaanerLektlekLrktkvepsfrpegee...............ktLlDFvdedsveelkealke 130
                                    +e++++ + ++ kel+ + + + kt+++Lr+ +++ s+   +e                k  +  +d +sv++++ ++++
  gi|70606663|ref|YP_255533.1|  28 LKEDSRRSASSIAKELQVSRATIAKTIKSLRSKNIKFSVEYWEEGelavfaiskeclkgsKECYKLIDGRSVSIIRGSFDH 108
                                   449999********************************98877548*********************************99 PP

                                   HHHHHHHHHHHHHTTHH..H CS
                         APG17 131 sidelqaaqkkldssllefd 150
                                   +++ l+  q+k++++ll+ d
  gi|70606663|ref|YP_255533.1| 109 IQQILE--QNKIKNYLLAVD 126
                                   955555..466666666554 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00018      0.14      41      58 ..      33      50 ..      31      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                        HTH_22 41 kgavekvAekLgiSraTv 58
                                  +++++ +A++L++SraT+
  gi|70606663|ref|YP_255533.1| 33 RRSASSIAKELQVSRATI 50
                                  899**************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00017      0.14      18      48 ..      29      59 ..      23      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                  HHHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                Fe_dep_repress 18 eekkvvktkdlaerLnvspssVsemlkkLek 48
                                  +e +  + + +a++L+vs +++ +++k L++
  gi|70606663|ref|YP_255533.1| 29 KEDSRRSASSIAKELQVSRATIAKTIKSLRS 59
                                  5556667899*****************9986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.8   4.7e+03       1      10 [.      17      26 ..      17      27 .. 0.87
   2 ?    9.6   0.7   0.00095      0.77      23      50 ..      33      60 ..      29      63 .. 0.87
   3 ?   -0.4   0.0       1.3   1.1e+03      38      46 ..     166     174 ..     165     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.8
                        HTH_10  1 LTdkqlevlk 10
                                  LT+ +++vl 
  gi|70606663|ref|YP_255533.1| 17 LTPLEYKVLN 26
                                  899****996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00095
                        HTH_10 23 rvtlkeLAkelGIskstlsehLrkaesk 50
                                  r +++++Akel +s++t+ + +++  sk
  gi|70606663|ref|YP_255533.1| 33 RRSASSIAKELQVSRATIAKTIKSLRSK 60
                                  67899***************99987776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.3
                        HTH_10  38 stlsehLrk 46 
                                   +t +ehLrk
  gi|70606663|ref|YP_255533.1| 166 NTCKEHLRK 174
                                   6899****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1181.64
//
Query:       gi|70606664|ref|YP_255534.1|  [L=92]
Description: hypothetical protein Saci_0875 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.8   0.0     0.0017   18.6   0.0    1.1  1  DUF5405   Domain of unknown function (DUF5405)


Domain annotation for each model (and alignments):
>> DUF5405  Domain of unknown function (DUF5405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.3e-08    0.0017      16      72 ..      32      89 ..      15      92 .] 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.3e-08
                       DUF5405 16 faLievkldkedgareel.sviavYdsevvlvadlVselvkrevfrkqvksitellae 72
                                   + ++v++ k++  + ++ + i  Y +e++++  +V e v   +  ++ k+ite++++
  gi|70606664|ref|YP_255534.1| 32 IGVGKVNCKKNSAIIDQVlDEIYKYTNEINITILIVPEEVYSNISTGTYKKITEMMNF 89
                                  4567999************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 710.34
//
Query:       gi|70606665|ref|YP_255535.1|  [L=591]
Description: hypothetical protein Saci_0877 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-76  255.6   0.0    2.9e-37  128.1   0.0    2.6  2  AAA              ATPase family associated with various cellul
    4.6e-16   59.0   0.0    7.5e-09   35.5   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.5e-14   53.3   3.5     0.0067   16.7   0.0    5.0  4  AAA_22           AAA domain
    1.3e-13   51.2   0.3    6.1e-05   23.0   0.0    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-12   48.6   0.0    6.3e-05   23.5   0.0    2.9  2  AAA_18           AAA domain
    5.7e-12   45.8   0.0    6.7e-06   26.2   0.0    2.9  2  AAA_14           AAA domain
    5.8e-12   46.0   0.0    4.4e-05   23.7   0.0    2.4  2  AAA_33           AAA domain
    8.6e-12   44.9   0.3     0.0001   21.6   0.1    2.6  2  TIP49            TIP49 P-loop domain
    1.4e-11   45.1   0.4    4.9e-05   23.8   0.0    3.7  3  AAA_16           AAA ATPase domain
    1.4e-11   44.1   0.0    3.3e-05   23.2   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    7.3e-10   38.5   0.0    0.00092   19.0   0.0    3.1  2  AAA_lid_3        AAA+ lid domain
    3.5e-09   36.7   0.0     0.0018   18.0   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    4.1e-09   36.8   0.0    4.3e-05   23.7   0.0    2.9  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.8e-09   35.7   0.0     0.0032   17.8   0.0    3.2  2  RNA_helicase     RNA helicase
    2.1e-08   34.6   0.0     0.0078   16.5   0.0    2.6  2  AAA_28           AAA domain
    2.3e-08   34.0   0.0     0.0029   17.4   0.0    2.6  2  AAA_24           AAA domain
    3.1e-08   33.4   0.1      0.007   15.9   0.1    3.1  2  AAA_7            P-loop containing dynein motor region
      6e-08   32.2   0.0      0.002   17.4   0.0    3.0  3  Zeta_toxin       Zeta toxin
    1.3e-07   31.6   0.1      0.018   14.8   0.0    2.4  2  Cytidylate_kin   Cytidylate kinase
    3.2e-07   30.2   0.1     0.0067   16.4   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    5.4e-07   29.7   0.0      0.023   14.7   0.0    2.3  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    9.6e-07   28.4   0.0      0.036   13.4   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.1e-06   27.9   0.1      0.039   13.1   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    2.8e-06   27.9   0.0        0.1   13.1   0.0    2.5  2  ABC_tran         ABC transporter
    5.2e-06   26.6   0.0       0.11   12.6   0.0    3.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    7.8e-06   26.1   0.0       0.19   11.8   0.0    2.6  2  SKI              Shikimate kinase
    9.3e-06   25.2   2.4      0.057   12.8   0.0    4.1  4  TniB             Bacterial TniB protein
    1.4e-05   25.4   0.2       0.67   10.3   0.0    3.5  3  AAA_19           AAA domain
    1.9e-05   24.5   0.0        0.2   11.5   0.0    2.9  2  AAA_3            ATPase family associated with various cellul
    2.3e-05   24.8   0.0       0.12   12.8   0.0    2.9  2  AAA_17           AAA domain
    3.3e-05   23.9   0.0       0.43   10.5   0.0    3.3  3  Rad17            Rad17 P-loop domain
    3.9e-05   23.6   0.0       0.11   12.3   0.0    2.3  2  CPT              Chloramphenicol phosphotransferase-like prot
    5.2e-05   23.0   0.1       0.52   10.0   0.1    2.9  2  AAA_30           AAA domain
    5.5e-05   23.1   0.0      0.068   13.0   0.0    3.2  2  Bac_DnaA         Bacterial dnaA  protein
    5.7e-05   23.0   0.0       0.21   11.3   0.0    2.4  2  AAA_11           AAA domain
    5.9e-05   22.6   0.0        0.3   10.5   0.0    2.7  2  KTI12            Chromatin associated protein KTI12
    6.3e-05   23.0   1.4       0.64    9.9   0.0    4.0  4  NTPase_1         NTPase
    8.1e-05   22.6   0.5       0.55   10.1   0.1    3.5  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00014   21.5   2.0        1.2    8.7   0.1    3.7  3  AAA_25           AAA domain
    0.00016   21.5   0.0        1.2    8.8   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
    0.00016   20.8   0.0       0.22   10.4   0.0    2.2  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
    0.00018   21.0   3.0        2.6    7.3   0.1    4.3  4  ATPase           KaiC
    0.00023   21.1   0.6       0.95    9.4   0.0    3.2  3  NACHT            NACHT domain
    0.00028   20.4   0.1       0.47    9.9   0.0    2.5  2  PhoH             PhoH-like protein
    0.00054   19.9   0.0        1.5    8.7   0.0    2.8  2  RsgA_GTPase      RsgA GTPase
    0.00091   18.5   0.0          2    7.5   0.0    3.3  3  NB-ARC           NB-ARC domain
     0.0011   18.4   0.0       0.33   10.3   0.0    2.4  2  IPT              Isopentenyl transferase
     0.0015   18.3   0.0          2    8.1   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.002   18.1   0.0        3.5    7.6   0.0    2.8  2  ResIII           Type III restriction enzyme, res subunit
     0.0021   18.2   0.0        3.1    7.9   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
      0.003   17.3   0.0        2.8    7.6   0.0    2.8  2  Guanylate_kin    Guanylate kinase
     0.0035   17.7   0.1          2    8.6   0.0    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0043   17.6   0.6          5    7.6   0.1    2.9  2  AAA_23           AAA domain
     0.0046   16.2   0.0          1    8.5   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0047   16.2   0.7        2.7    7.1   0.0    3.4  4  KAP_NTPase       KAP family P-loop domain
      0.005   16.2   0.0       0.16   11.2   0.0    2.4  2  6PF2K            6-phosphofructo-2-kinase
      0.006   16.5   0.0        2.3    8.1   0.0    2.4  2  APS_kinase       Adenylylsulphate kinase
     0.0061   15.4   0.1        2.2    7.0   0.0    2.3  2  Adeno_IVa2       Adenovirus IVa2 protein
     0.0089   16.2   0.0        1.6    8.8   0.0    2.5  2  Cytidylate_kin2  Cytidylate kinase-like family
     0.0091   15.1   0.0        2.1    7.3   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   14.6   0.0        3.4    6.4   0.0    2.3  2  PPV_E1_C         Papillomavirus helicase
      0.014   15.7   0.0        6.4    7.0   0.0    2.6  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.015   15.4   0.0         11    6.1   0.0    3.2  3  ADK              Adenylate kinase
      0.015   14.9   0.1        5.6    6.5   0.0    2.7  2  SRP54            SRP54-type protein, GTPase domain
      0.016   14.9   0.1        4.1    7.2   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.018   14.9   0.1        1.2    8.9   0.0    2.4  2  dNK              Deoxynucleoside kinase
      0.026   14.6   0.0        4.1    7.5   0.0    2.3  2  Torsin           Torsin
      0.029   13.5   0.1        4.5    6.3   0.0    3.0  3  MCM              MCM P-loop domain
      0.087   12.3   0.0         17    4.8   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
       0.11   12.3   0.0         17    5.1   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   12.1   0.0         19    5.0   0.0    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.13   12.1   5.0        4.9    6.9   0.5    3.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
       0.14   11.5   0.2         19    4.5   0.0    2.9  2  Gtr1_RagA        Gtr1/RagA G protein conserved region
       0.15   11.7   0.0         12    5.5   0.0    2.4  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.29   11.2   3.6         12    6.0   0.5    3.8  3  DUF2540          Protein of unknown function (DUF2540)


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0   9.8e-39   2.4e-36       1     132 []      98     229 ..      98     229 .. 0.98
   2 !  128.1   0.0   1.2e-39   2.9e-37       1     131 [.     369     495 ..     369     496 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 9.8e-39
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   v+l+GppGtGKT++aka+a++l+ +++e+  s++lsk+ gese  ++++f++++ +  p i++iDEid ++ +r+g+ +e+
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWNYFELRSSDILSKWYGESEFLLENFFNTVELNV-PAIIVIDEIDGFTLRREGDIHEV 177
                                   68**************************************************98887.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                   + r+vn Ll+ l++  +k+ +vi+ig+tn p+++d+allr gRfd++i+++l
  gi|70606665|ref|YP_255535.1| 178 THRLVNILLNRLQDIHDKRLPVIIIGTTNLPQEIDEALLRpGRFDEIIYVPL 229
                                   ******************999****************************985 PP

  == domain 2  score: 128.1 bits;  conditional E-value: 1.2e-39
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +llyGppGtGKT++aka+a+el+++f+ +sg e+ s    ++ + i+e f  ak ++ psi+fiDEid +a++r    ++e
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFIVVSGDEISSVGPFKAGELIAEKFHIAKDNS-PSIIFIDEIDMIARTR---GENE 445
                                   69*********************************99999****************9.****************...8889 PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    + ++ +Ll+e+dg +++ ++vi+igatnrp++ldpallr gRfdr+i+++
  gi|70606665|ref|YP_255535.1| 446 WRGALTELLSEMDGIREN-EDVIIIGATNRPWDLDPALLRaGRFDRIIYVP 495
                                   999**************7.55***************************997 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.3e-06   0.00032      26      72 ..      89     135 ..      66     196 .. 0.68
   2 !   35.5   0.0   3.1e-11   7.5e-09      31     100 ..     364     441 ..     340     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-06
                        RuvB_N  26 akkreealdhvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka 72 
                                     +r++a   v+l+GpPG Gkt++ak +a++l+ + ++  s+ +l+k 
  gi|70606665|ref|YP_255535.1|  89 VMSRKRAY-GVILFGPPGTGKTSIAKALANNLKWNyFELRSSDILSKW 135
                                   44555544.68999******************9873577788887774 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 3.1e-11
                        RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvle.....kagdlaalltnleekd...vlfideihrlsrav 100
                                   +++  +llyGpPG Gkt++ak +a+el++++ + sg  ++     kag+l+a   ++ +++   ++fidei  ++r+ 
  gi|70606665|ref|YP_255535.1| 364 KPVKGILLYGPPGTGKTSIAKALANELQASFIVVSGDEISsvgpfKAGELIAEKFHIAKDNspsIIFIDEIDMIARTR 441
                                   567789*******************************998555556889998777776543333*******9998875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.8e-05    0.0067       4      32 ..      94     121 ..      91     133 .. 0.82
   2 !   13.2   0.3   0.00035     0.083      92     134 ..     155     208 ..     138     211 .. 0.72
   3 !   16.4   0.0   3.4e-05     0.008       8      31 ..     369     392 ..     366     404 .. 0.87
   4 ?    2.7   0.0      0.59   1.4e+02      86     117 ..     418     458 ..     407     474 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldee 32 
                                   +a+ ++++G++GtGKT  ++ l+++l ++
  gi|70606665|ref|YP_255535.1|  94 RAYGVILFGPPGTGKTSIAKALANNL-KW 121
                                   677789******************98.35 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00035
                        AAA_22  92 ielliiDEaqhlr..s........eealeeLrsllnl.srkgvqliLvGtpelr 134
                                   +++++iDE++ ++  +        +++++ L ++l + ++k +++i++Gt++l 
  gi|70606665|ref|YP_255535.1| 155 PAIIVIDEIDGFTlrRegdihevtHRLVNILLNRLQDiHDKRLPVIIIGTTNLP 208
                                   689********97762445545555555555333333699**********9985 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 3.4e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                                   ++++G++GtGKT  ++ l+++l++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQA 392
                                   799******************953 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.59
                        AAA_22  86 lrarav..ielliiDEaqhlr..s.....eealeeLrslln 117
                                   ++ +++  ++++ iDE++ +   +       al+eL s ++
  gi|70606665|ref|YP_255535.1| 418 FHIAKDnsPSIIFIDEIDMIArtRgenewRGALTELLSEMD 458
                                   4444445569*********9765256678777777755444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   3.1e-07   7.5e-05       1      75 [.      97     164 ..      97     218 .. 0.64
   2 !   23.0   0.0   2.5e-07   6.1e-05       2      78 ..     369     438 ..     368     484 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.1e-07
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                   +v+L GppGtgK+++a+ la  l++++++       +++d++ ++    g+ ++    + + ++   ++i+v+DE++
  gi|70606665|ref|YP_255535.1|  97 GVILFGPPGTGKTSIAKALANNLKWNYFEL------RSSDILSKWY---GESEFLLENFFNTVElnVPAIIVIDEID 164
                                   59*************************974......5556666666...4444444444444444466666666666 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.5e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae 78 
                                   +lL GppGtgK+++a+ la  l++++ +v + +  +   +k +  i        ++    + ++++i+++DE++++ 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFIVVSGDEISSVGPFKAGELI-------AEKFHIAKDNSPSIIFIDEIDMIA 438
                                   89****************************9998887777777666.......233333355599999999998765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   7.2e-07   0.00017       1      40 [.      98     140 ..      98     236 .. 0.76
   2 !   23.5   0.0   2.6e-07   6.3e-05       1      79 [.     369     469 ..     369     479 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.2e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakengllle 40 
                                   ++l G+pG+GKt++ak+L++ l+      +++d++++ + + e
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWnyfELRSSDILSKWYGESE 140
                                   79****************9998444686666666665444444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.6e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe....aldeskrldedk 56 
                                   Ill G+pG+GKt++ak+L+++l ++                      +  ++ak+n +++ + +e    a  + + + ++ 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELqASfivvsgdeissvgpfkagelIAEKFHIAKDNSPSIIFIDEidmiARTRGENEWRGA 449
                                   99*****************99955589898777777776666555444455555555555555556644444444555555 PP

                        AAA_18  57 ldklldaleenssaleegknlvi 79 
                                   l +ll++++++   +e++++++i
  gi|70606665|ref|YP_255535.1| 450 LTELLSEMDGI---RENEDVIII 469
                                   55555555554...345555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.7e-05    0.0065       5     124 ..      98     228 ..      94     233 .. 0.67
   2 !   26.2   0.0   2.8e-08   6.7e-06       5     101 ..     369     472 ..     366     496 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev......... 76 
                                   +++ G+  +GKT ++k l+++l     +++++   d   k + ++e lle +++ ++ +   ++++DEi            
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLK---WNYFELRSSDILSKWYGESEFLLENFFNTVELNVPAIIVIDEIDGFtlrregdih 175
                                   7899**************97776...5555555555555555555547777777754468899******998888888888 PP

                        AAA_14  77 .......pewekalkslvd.egknldvivtGSnskllskeiatslagrvaeielyp 124
                                          +     l++l d ++k+l vi+ G  ++    + a    gr +ei   p
  gi|70606665|ref|YP_255535.1| 176 evthrlvN---ILLNRLQDiHDKRLPVIIIGTTNLPQEIDEALLRPGRFDEIIYVP 228
                                   77763333...333444443225588888887766554444444466666666555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 2.8e-08
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek...lkeekktylflDEiqev...... 76 
                                   +++ G+  +GKT ++k l++el     s++ ++ d+ +     +     eli ek   +k++  +++f+DEi ++      
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQ---ASFIVVSGDEISSVGPFKA---GELIAEKfhiAKDNSPSIIFIDEIDMIartrge 443
                                   7899***************9988...**********999765544...45555553323447999***************9 PP

                        AAA_14  77 pewekalkslvd..eg..knldvivtGSn 101
                                   +ew+ al +l+   +g  +n dvi+ G  
  gi|70606665|ref|YP_255535.1| 444 NEWRGALTELLSemDGirENEDVIIIGAT 472
                                   99999999999955225467789888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-07   4.4e-05       2     113 ..      98     236 ..      98     239 .. 0.68
   2 !   19.8   0.0   2.8e-06   0.00067       2      65 ..     369     456 ..     369     503 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt...................lrrrlfgtdqqskt............... 46 
                                   v+l G+pG+GK+  a+ l+++l+  ++ l+s +                   +            +               
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKwnYFELRSSDilskwygesefllenffntV------------Elnvpaiivideidgf 166
                                   7899*********************7777777735555555555444444440............0444555555555555 PP

                        AAA_33  47 ......dytrvldrlyqilnelarkalsagrnvildatnlsrrer.arflklarrlgvpvrivvvetdeetlke 113
                                         d  +v++rl +il +++++   ++ +vi+  t   ++e  +++l+  r     ++i++v  ++e+++e
  gi|70606665|ref|YP_255535.1| 167 tlrregDIHEVTHRLVNILLNRLQDIHDKRLPVIIIGTTNLPQEIdEALLRPGR----FDEIIYVPLPDEKARE 236
                                   5555547788**********************8775554444444145555555....4478888888877776 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.8e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt..............lrrrlfg.tdqqskt..........dytrvldrl 55 
                                   +ll G+pG+GK+  a+ l+++l+  ++++s d+              +    f   +++s++           +tr ++++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQasFIVVSGDEissvgpfkageliaE---KFHiAKDNSPSiifideidmiARTRGENEW 446
                                   6789********************9*******9666666666664331...222233333334455555555444444445 PP

                        AAA_33  56 yqilnelark 65 
                                   ++ l el+ +
  gi|70606665|ref|YP_255535.1| 447 RGALTELLSE 456
                                   5555555544 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.5e-07    0.0002      46     111 ..      92     154 ..      77     190 .. 0.87
   2 !   21.6   0.1   4.4e-07    0.0001      51     103 ..     367     418 ..     355     422 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.5e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  46 kklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvri 111
                                   +k a  +v+l Gp+gtGkt++a a++++l     +  l +s++ s     +e l++++  ++ + +
  gi|70606665|ref|YP_255535.1|  92 RKRA-YGVILFGPPGTGKTSIAKALANNLK--WNYFELRSSDILSKWYGESEFLLENFFNTVELNV 154
                                   4444.68999******************97..8899**********************99999877 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.4e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle.vkktevltqal 103
                                   +++Ll Gp+gtGkt++a a+++el     f+++sg e+ s+   k  e++ +++
  gi|70606665|ref|YP_255535.1| 367 KGILLYGPPGTGKTSIAKALANELQ--ASFIVVSGDEISSVGpFKAGELIAEKF 418
                                   89**********************8..68*********9986244456666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.9e-05     0.016      25      50 ..      96     121 ..      77     202 .. 0.86
   2 !   23.8   0.0     2e-07   4.9e-05      25      61 ..     367     402 ..     358     420 .. 0.86
   3 ?   -0.3   0.0       5.1   1.2e+03     131     147 ..     421     437 ..     409     469 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-05
                        AAA_16  25 elvllsGesGvGKsslvrellralek 50 
                                     v+l G++G+GK+s++++l++ l+ 
  gi|70606665|ref|YP_255535.1|  96 YGVILFGPPGTGKTSIAKALANNLKW 121
                                   6799****************998764 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2e-07
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                     +ll+G++G+GK+s++++l+++l+++ +i+++g+  
  gi|70606665|ref|YP_255535.1| 367 KGILLYGPPGTGKTSIAKALANELQAS-FIVVSGDEI 402
                                   679**********************99.888888765 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 5.1
                        AAA_16 131 srderplvlvlDdlqwa 147
                                   ++d +p ++++D+++ +
  gi|70606665|ref|YP_255535.1| 421 AKDNSPSIIFIDEIDMI 437
                                   4458899******9943 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.4e-07   3.3e-05      18      80 ..      60     122 ..      50     134 .. 0.88
   2 !   18.3   0.0   4.3e-06     0.001      47     116 ..     360     434 ..     313     475 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-07
                        DUF815  18 pveevdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80 
                                    ++++ +v+++++ ++++ k++l++  +  ++ ++a  v+L+G  GtGK s+ kal n+++ +
  gi|70606665|ref|YP_255535.1|  60 KMRNIPSVSWEQIYDMKELKQKLLDISNYVMSRKRAYGVILFGPPGTGKTSIAKALANNLKWN 122
                                   46788899*************************************************998755 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 4.3e-06
                        DUF815  47 fleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelp.....klve...llrerperfilfvDDL 116
                                    l  +p + +LL+G  GtGK s+ kal ne++++ +    v+ ++++++      +l++   ++++ +   i+f+D +
  gi|70606665|ref|YP_255535.1| 360 KLGIKPVKGILLYGPPGTGKTSIAKALANELQASFIV---VSGDEISSVGpfkagELIAekfHIAKDNSPSIIFIDEI 434
                                   333467888**********************987643...33333333321111123221224667777777777765 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.9e-06   0.00092       1      43 [.     247     288 ..     247     290 .. 0.92
   2 !   15.8   0.0   3.7e-05    0.0088       4      35 ..     520     551 ..     514     566 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.9e-06
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                   +vd k LA +++  S AD+++++   ++++ ++g++  t++df
  gi|70606665|ref|YP_255535.1| 247 SVDCKLLANKSNRLSPADIKEIVESVSIECSKEGREP-TTQDF 288
                                   69*********************************99.55666 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.7e-05
                     AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgi 35 
                                   l+++ ++T++y+ ADl+ +++e  ++ l++ +
  gi|70606665|ref|YP_255535.1| 520 LNKVSRMTNNYTPADLKLVVDEIRRNLLKEAT 551
                                   78999****************98777777754 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.7e-06    0.0018      19      70 ..      64     118 ..      51     127 .. 0.72
   2 !   15.4   0.0   4.9e-05     0.012      44      71 ..     363     390 ..     345     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.7e-06
                     IstB_IS21  19 ledidfraarsldkrkvkeLatlsfi...ekkenivllGpsGvGKshlaialgve 70 
                                   + ++ +++  ++++ k k L   +++   +++ +++l+Gp+G+GK+ +a al+ +
  gi|70606665|ref|YP_255535.1|  64 IPSVSWEQIYDMKELKQKLLDISNYVmsrKRAYGVILFGPPGTGKTSIAKALANN 118
                                   45666666666666666666666676222345689*****************975 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.9e-05
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                   i+  ++i+l Gp+G+GK+ +a al+ e 
  gi|70606665|ref|YP_255535.1| 363 IKPVKGILLYGPPGTGKTSIAKALANEL 390
                                   5566789*****************9875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0037      0.88       7      82 ..      99     168 ..      94     207 .. 0.68
   2 !   23.7   0.0   1.8e-07   4.3e-05       2      83 ..     365     440 ..     364     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0037
                                   EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                         AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                   +l gp g+Gkt +akala+ l+  +  +l  +d  +     e+e l++++  + + +v      i+ +DEid  + 
  gi|70606665|ref|YP_255535.1|  99 ILFGPPGTGKTSIAKALANNLKW-NYFELRSSDILSKWY-GESEFLLENFFNTVELNV----PAIIVIDEIDGFTL 168
                                   5569*****************95.444444444433333.445555555554444444....34999999987666 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.8e-07
                                   ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG-- CS
                         AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKih 81 
                                   p+  ill gp g+Gkt +akala+ l++    ++i++   e+     v    + +++a+++ ++++++  i+++DEid i+
  gi|70606665|ref|YP_255535.1| 365 PVKGILLYGPPGTGKTSIAKALANELQA----SFIVVSGDEISS---VGPFKAGELIAEKFHIAKDNSPsIIFIDEIDMIA 438
                                   566799********************96....************...77777788888888777777766*********** PP

                                   -- CS
                         AAA_2  82 pk 83 
                                   ++
  gi|70606665|ref|YP_255535.1| 439 RT 440
                                   95 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00017     0.041       1      26 [.      98     123 ..      98     164 .. 0.79
   2 !   17.8   0.0   1.3e-05    0.0032       1      26 [.     369     394 ..     369     443 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00017
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   ++l+Gp+g+GK+++ak La++l  ++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWNY 123
                                   689**************999987443 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.3e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i+lyGp+g+GK+++ak La++l+ ++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASF 394
                                   789*******************9887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.3e-05    0.0078       2      27 ..      98     124 ..      97     141 .. 0.85
   2 !   15.4   0.0   6.9e-05     0.017       2      26 ..     369     394 ..     368     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                   ++++G+++tGKT++++aLa++ +++++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNlKWNYF 124
                                   789****************98777665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.9e-05
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypv 26 
                                   i + G+++tGKT++++aLa++ + + 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANElQASF 394
                                   7899***************8654333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00014     0.033       3      75 ..      96     164 ..      94     174 .. 0.67
   2 !   17.4   0.0   1.2e-05    0.0029       5      76 ..     369     436 ..     366     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                        AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtek..GlksldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                   + ++++Gp+g+GKT++ak l  + l  + ++  +++ l  + ++      +fl e  ++  el+   ++viD id
  gi|70606665|ref|YP_255535.1|  96 YGVILFGPPGTGKTSIAKAL-ANNLKWNYFElrSSDILSKWYGE-----SEFLLENFFNTVELNVPAIIVIDEID 164
                                   6789***************9.66555554443455555555554.....45555555555666666666666666 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.2e-05
                        AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdieswedfldevvel..aaeladyktlviDtide 76 
                                   il+yGp+g+GKT++ak l    + +++++  ++   s+ + k  +          ++e    a+++  ++++iD id 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALanelQASFIVVSGDE-ISSVGPFKAGE---------LIAEKfhIAKDNSPSIIFIDEIDM 436
                                   89***************9888778888887777.44555555441.........122222334444446666666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00016     0.039      32      60 ..      94     122 ..      83     132 .. 0.83
   2 !   15.9   0.1   2.9e-05     0.007      31      66 ..     364     398 ..     356     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                         AAA_7  32 nkkpvllvGptGtGKtviikdllkkldke 60 
                                   + + v+l Gp GtGKt+i+k l ++l+ +
  gi|70606665|ref|YP_255535.1|  94 RAYGVILFGPPGTGKTSIAKALANNLKWN 122
                                   56679*******************99844 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.9e-05
                         AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                   k  k +ll+Gp GtGKt+i+k l ++l+  ++++++
  gi|70606665|ref|YP_255535.1| 364 KPVKGILLYGPPGTGKTSIAKALANELQ-ASFIVVS 398
                                   556889*********************9.6666555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0011      0.27       3      43 ..      81     120 ..      79     131 .. 0.83
   2 ?   -0.1   0.0         2   4.8e+02      72     140 ..     174     238 ..     165     267 .. 0.81
   3 !   17.4   0.0   8.4e-06     0.002      18      57 ..     368     405 ..     353     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                    Zeta_toxin   3 ellkdkk.ypsqerPklillgGqpGAGKselaellkdelerq 43 
                                   +ll+ ++ + s++r   ++l G pG GK+++a++l+++l  +
  gi|70606665|ref|YP_255535.1|  81 KLLDISNyVMSRKRAYGVILFGPPGTGKTSIAKALANNL--K 120
                                   67778887778899999******************9998..4 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                    Zeta_toxin  72 aseltqkdaselvekllqeaiengyniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgv 140
                                     e+t++ +  l ++l q +++++  +i+ gt   p++++   eal   G+  e+++v  + e +r+++
  gi|70606665|ref|YP_255535.1| 174 IHEVTHRLVNILLNRL-QDIHDKRLPVIIIGTTNLPQEID---EALLRPGRFDEIIYVPLPDEKAREEI 238
                                   5677777777777775.6799***********99999998...66666788889999988888888766 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 8.4e-06
                    Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57 
                                    ill G pG GK+++a++l++el  q +++++++D++ + 
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALANEL--QASFIVVSGDEISSV 405
                                   58999******************..9*********98665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.4e-05     0.018       4      28 ..     101     125 ..      98     129 .. 0.91
   2 !   14.3   0.0    0.0001     0.025       3      27 ..     371     395 ..     369     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-05
                                   E-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                                    GP g+GK s+a+ala++l+++y++
  gi|70606665|ref|YP_255535.1| 101 FGPPGTGKTSIAKALANNLKWNYFE 125
                                   59*********************86 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.0001
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g+GK s+a+ala++l+++++
  gi|70606665|ref|YP_255535.1| 371 LYGPPGTGKTSIAKALANELQASFI 395
                                   67*******************9987 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0017       0.4      30      55 ..     284     309 ..     277     314 .. 0.89
   2 !   16.4   0.0   2.8e-05    0.0067      28      56 ..     559     587 ..     548     590 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0017
                        Vps4_C  30 tlkDflkalkkarptVskeDLekhee 55 
                                   t +Df++ l + +p+Vs + L k+e+
  gi|70606665|ref|YP_255535.1| 284 TTQDFIRYLDNFKPSVSIQTLIKFEN 309
                                   789******************99997 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.8e-05
                        Vps4_C  28 pvtlkDflkalkkarptVskeDLekheeF 56 
                                   +++++Df+++l+  +p+V+ e L+ +e+F
  gi|70606665|ref|YP_255535.1| 559 SLNFDDFVRVLAYIKPSVNVELLKMYEQF 587
                                   6899************************9 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00046      0.11       7      49 ..      75     127 ..      69     133 .. 0.73
   2 !   14.7   0.0   9.7e-05     0.023       8      50 ..     355     398 ..     346     400 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHCHTEE........EEEEESTTSSHHHHHHHHHHHTT--..--- CS
                          TsaE   7 tealgkklakalgdv........ilLeGdLGaGKTtlvrglakalgve..evk 49 
                                   +++l +kl +  + v        ++L G+ G+GKT ++++la++l+ +  e +
  gi|70606665|ref|YP_255535.1|  75 MKELKQKLLDISNYVmsrkraygVILFGPPGTGKTSIAKALANNLKWNyfELR 127
                                   66666666664422234455677*********************988755555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.7e-05
                                   HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--.---- CS
                          TsaE   8 ealgkklakalgdvilLeGdLGaGKTtlvrglakalgve.evkS 50 
                                   +++++kl+ +  + ilL+G+ G+GKT ++++la++l+ +  v S
  gi|70606665|ref|YP_255535.1| 355 KDIANKLGIKPVKGILLYGPPGTGKTSIAKALANELQASfIVVS 398
                                   45555555544566**********************98765655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00031     0.073      24      44 ..      97     117 ..      74     125 .. 0.87
   2 !   13.4   0.0   0.00015     0.036      24      44 ..     368     388 ..     351     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                    ++l+GppG+GKt +ak+l++
  gi|70606665|ref|YP_255535.1|  97 GVILFGPPGTGKTSIAKALAN 117
                                   689**************9975 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00015
                  Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                    +ll+GppG+GKt +ak+l++
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALAN 388
                                   58***************9976 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00023     0.056      97     138 ..      76     119 ..      68     121 .. 0.72
   2 !   13.1   0.0   0.00016     0.039     117     138 ..     369     390 ..     363     399 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                     Parvo_NS1  97 vevgqvllawlskqlgkrnt..vwfyGpantGktnlaeaIakav 138
                                    e++q ll +++ +++++ +  v ++Gp+ tGkt +a+a+a+ +
  gi|70606665|ref|YP_255535.1|  76 KELKQKLLDISNYVMSRKRAygVILFGPPGTGKTSIAKALANNL 119
                                   55566666666666666655235667***************976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                   +++yGp+ tGkt +a+a+a+ +
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANEL 390
                                   89*****************976 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0008      0.19      14      38 ..      98     122 ..      85     162 .. 0.87
   2 !   13.1   0.0   0.00042       0.1       6      37 ..     361     392 ..     358     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0008
                                   EEEEESTTSSHHHHHHHHTTSS--S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  14 vaivGenGaGKStLlkllagllkpt 38 
                                   v ++G+ G+GK++++k+la++lk++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWN 122
                                   7899****************99984 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00042
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkp 37 
                                   l +k+ + + + G+ G+GK++++k+la++l+ 
  gi|70606665|ref|YP_255535.1| 361 LGIKPVKGILLYGPPGTGKTSIAKALANELQA 392
                                   6788889999*****************99875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00047      0.11      19     118 ..      93     214 ..      71     224 .. 0.60
   2 !    8.9   0.0    0.0066       1.6      24      47 ..     369     392 ..     363     472 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00047
                                   T-SS-EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H......................HHHHHHTTTSEEEE. CS
               Sigma54_activ_2  19 qsklpvfltGekGsgkelvArlLhknsgpw.leifvverlaklp......................ldlleqakggtLyl. 75 
                                   ++   v l G++G+gk+++A++L++n   +  e+   + l+                           ++++++g tL   
  gi|70606665|ref|YP_255535.1|  93 KRAYGVILFGPPGTGKTSIAKALANNLKWNyFELRSSDILS--KwygesefllenffntvelnvpaIIVIDEIDGFTLRRe 171
                                   5667899****************987543213444444444..23344445554443333333332222333455555431 PP

                                   EE-TT--HHHHHHHHHHHHHHTTTT-EEEEEEEE-TTT..--- CS
               Sigma54_activ_2  76 kdiadlskaeqkeLlellakaeksslrlVstsskdleqlleag 118
                                    di++    +   Ll++l+    ++l ++ ++ ++l+q+++++
  gi|70606665|ref|YP_255535.1| 172 GDIHEVTHRLVNILLNRLQDIHDKRLPVIIIGTTNLPQEIDEA 214
                                   3566666666666777777777777777888877777777765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0066
                                   EEEEEETT--HHHHHHCC--TTS- CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                   ++l G++G+gk+++A++L+++ + 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQA 392
                                   799***************987554 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00079      0.19       1      23 [.     104     126 ..     104     134 .. 0.93
   2 !   11.4   0.0    0.0011      0.26       1      21 [.     375     395 ..     375     405 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00079
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                           SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                   +G+GK++++k+lA+ l++++++l
  gi|70606665|ref|YP_255535.1| 104 PGTGKTSIAKALANNLKWNYFEL 126
                                   69*****************9975 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                                   TTSSHHHHHHHHHHHHTSEEE CS
                           SKI   1 mGaGKstvGkllAkklglefi 21 
                                   +G+GK++++k+lA++l+ +fi
  gi|70606665|ref|YP_255535.1| 375 PGTGKTSIAKALANELQASFI 395
                                   69****************998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00024     0.057       3      57 ..      62     117 ..      60     130 .. 0.86
   2 ?    2.5   0.2      0.35        84     121     170 ..     156     212 ..     142     227 .. 0.62
   3 ?    6.4   0.0     0.022       5.3      35      57 ..     366     388 ..     352     401 .. 0.83
   4 ?   -1.2   0.0       4.7   1.1e+03     112     136 ..     418     442 ..     409     457 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                          TniB   3 ayiradrwigyprakeilerLeeLley.pkrkrmpnlllvGdsnnGKtmivekFar 57 
                                   + i + +w +  ++ke+ ++L ++ +y  +rkr   ++l+G++ +GKt+i++  a+
  gi|70606665|ref|YP_255535.1|  62 RNIPSVSWEQIYDMKELKQKLLDISNYvMSRKRAYGVILFGPPGTGKTSIAKALAN 117
                                   66777788899999***********995569*******************998776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.35
                          TniB 121 rvLiiDEihnll........agsarkqreflnalksLgnelkipivlvGteealralr 170
                                    +++iDEi+ +         + ++r  + +ln l+ ++++ ++p++++Gt+++ + ++
  gi|70606665|ref|YP_255535.1| 156 AIIVIDEIDGFTlrregdihEVTHRLVNILLNRLQDIHDK-RLPVIIIGTTNLPQEID 212
                                   5789999987641110000033334444455555555544.79999999998766665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.022
                          TniB  35 mpnlllvGdsnnGKtmivekFar 57 
                                   ++ +ll+G++ +GKt+i++  a+
  gi|70606665|ref|YP_255535.1| 366 VKGILLYGPPGTGKTSIAKALAN 388
                                   6789*************998776 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4.7
                          TniB 112 lrllrelkvrvLiiDEihnllagsa 136
                                    ++ ++ ++ ++ iDEi+ + + + 
  gi|70606665|ref|YP_255535.1| 418 FHIAKDNSPSIIFIDEIDMIARTRG 442
                                   566677788999*****99986654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0028      0.67      13      37 ..      98     122 ..      89     133 .. 0.83
   2 !   10.1   0.1    0.0031      0.74      12      36 ..     368     392 ..     360     404 .. 0.86
   3 ?   -0.4   0.0       5.5   1.3e+03     102     115 ..     425     438 ..     406     473 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0028
                        AAA_19  13 llvtaGpGtGKTrvlkhivallvel 37 
                                   +++ ++pGtGKT + k+  + l+++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWN 122
                                   7899**********99998888765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0031
                        AAA_19  12 vllvtaGpGtGKTrvlkhivallve 36 
                                    +l+ ++pGtGKT + k+  ++l++
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALANELQA 392
                                   5899***********9998887765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 5.5
                        AAA_19 102 eeellivDEfqdvd 115
                                   +  ++++DE+ ++ 
  gi|70606665|ref|YP_255535.1| 425 SPSIIFIDEIDMIA 438
                                   345899*****997 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0029      0.69       2      29 ..      98     125 ..      97     206 .. 0.90
   2 !   11.5   0.0   0.00085       0.2       2      28 ..     369     395 ..     368     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0029
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkr 29 
                                   v+l g PG++kt ++kala+ l+ ++  
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWNYFE 125
                                   68899****************9988765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00085
                         AAA_3   2 vllegvPGlaktllvkalakaldlefk 28 
                                   +ll g PG++kt ++kala+ l+++f 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFI 395
                                   7999******************99985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0076       1.8       1      25 [.     101     125 ..     101     150 .. 0.80
   2 !   12.8   0.0   0.00049      0.12       1      32 [.     372     404 ..     372     464 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0076
                                   EE-TTSSHHHHHHHHHHHHTEEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                   +G+PG GK+ +++ l+ +++  +++
  gi|70606665|ref|YP_255535.1| 101 FGPPGTGKTSIAKALANNLKWNYFE 125
                                   6***************999666554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00049
                                   EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllre 32 
                                   +G+PG GK+ +++ l+ ++   f ++s Gd + +
  gi|70606665|ref|YP_255535.1| 372 YGPPGTGKTSIAKALANELqaSFIVVS-GDEISS 404
                                   7*****************933444455.888765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0061       1.5      39      75 ..      89     125 ..      71     134 .. 0.70
   2 !   10.5   0.0    0.0018      0.43      40      74 ..     361     395 ..     338     414 .. 0.83
   3 ?   -1.4   0.0       7.9   1.9e+03      46      87 ..     490     529 ..     481     545 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0061
                         Rad17  39 vLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75 
                                   v+ +++   +++ GP+G gk+ + k L+ +l  ++ e
  gi|70606665|ref|YP_255535.1|  89 VMSRKRAYGVILFGPPGTGKTSIAKALANNLKWNYFE 125
                                   3333333357789***************999888765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0018
                         Rad17  40 LesrkkriLLisGPsGCgkstvvkvLskelgiklr 74 
                                   L  ++ + +L+ GP+G gk+ + k L+ el  +++
  gi|70606665|ref|YP_255535.1| 361 LGIKPVKGILLYGPPGTGKTSIAKALANELQASFI 395
                                   555666668999*****************988765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.9
                         Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn 87 
                                   ri+ +  P   g+  v+kvL+k l+++ +e ln vs + ++n
  gi|70606665|ref|YP_255535.1| 490 RIIYVPPPDYEGRVKVLKVLTKGLSVD-EEILNKVS-RMTNN 529
                                   5677777777889999*****988776.57788888.66655 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0054       1.3       4      33 ..      98     127 ..      95     138 .. 0.88
   2 !   12.3   0.0   0.00048      0.11       4      36 ..     369     401 ..     367     418 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0054
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                   ++L G + +GK+s+a+al + l+  +++l 
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKWNYFELR 127
                                   89*****************99999988876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00048
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                   ilL G + +GK+s+a+al + l+++++ +  D+
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFIVVSGDE 401
                                   89************************9998886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0025      0.59      21      40 ..      98     117 ..      85     125 .. 0.83
   2 !   10.0   0.1    0.0022      0.52      22      44 ..     370     392 ..     356     443 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                        AAA_30  21 avltGpAGtGKttalkalre 40 
                                   ++l Gp+GtGKt + kal++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALAN 117
                                   6889************9976 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0022
                        AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                   +l Gp+GtGKt + kal++ ++a
  gi|70606665|ref|YP_255535.1| 370 LLYGPPGTGKTSIAKALANELQA 392
                                   688*************9887766 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.058        14      34      68 ..      95     129 ..      82     197 .. 0.83
   2 !   13.0   0.0   0.00028     0.068      33     198 ..     365     527 ..     351     539 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.058
                                   S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EE CS
                      Bac_DnaA  34 ynPlfiygevGlGktHLlkaignevlenapelrvv 68 
                                      ++++g+ G Gkt + ka++n+++ n  elr +
  gi|70606665|ref|YP_255535.1|  95 AYGVILFGPPGTGKTSIAKALANNLKWNYFELRSS 129
                                   556899******************99888887755 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00028
                                   .S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-..HHHHHH.HHTT-SEEEEE-GGGGT CS
                      Bac_DnaA  33 kynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkk..aeefke.klrkvDvLliDDiqfla 110
                                       +++yg+ G Gkt + ka++ne+++++     + ++++e  +  v   +  +  ae+f+  k  +  ++ iD+i  +a
  gi|70606665|ref|YP_255535.1| 365 PVKGILLYGPPGTGKTSIAKALANELQASF-----IVVSGDEISS--VGPFKAGEliAEKFHIaKDNSPSIIFIDEIDMIA 438
                                   456789****************99988765.....4567777654..55555544113444430233567999*****999 PP

                                   T-HHHHH......HHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT-- CS
                      Bac_DnaA 111 gkektqe......elfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaekle 185
                                   +  + +e      el+  ++ + e++  +++ +   P++l+    r   rf++  ++ + ppd+e r+++lk  + +++l 
  gi|70606665|ref|YP_255535.1| 439 RTRGENEwrgaltELLSEMDGIRENEDVIIIGATNRPWDLDPALLR-AGRFDR--IIYVPPPDYEGRVKVLK--VLTKGLS 514
                                   887666544433367777777889999999********99865544.358876..78899*********995..6788999 PP

                                   --TTHHHHHHHH- CS
                      Bac_DnaA 186 vpeevlefiaerv 198
                                   v ee+l+ +++  
  gi|70606665|ref|YP_255535.1| 515 VDEEILNKVSRMT 527
                                   9999999998654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0038       0.9      20      41 ..      98     119 ..      78     145 .. 0.81
   2 !   11.3   0.0    0.0009      0.21      20      42 ..     369     391 ..     352     426 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0038
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                   +++ GPPGtgKT+   +l ++l
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNL 119
                                   5678*********999999988 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0009
                        AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                    l+ GPPGtgKT+   +l ++l 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQ 391
                                   5899*********9999999983 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.003      0.71       4      26 ..      98     120 ..      97     134 .. 0.89
   2 !   10.5   0.0    0.0013       0.3       4      28 ..     369     393 ..     368     469 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.003
                                   EEEE--TTSSHHHHHHHHHHHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakale 26 
                                   v+l+G P +GK+++ak La+ l+
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLK 120
                                   89*****************9997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0013
                                   EEEE--TTSSHHHHHHHHHHHHHHT CS
                         KTI12   4 vvltGlPssGKstrakeLakaleee 28 
                                   ++l G P +GK+++ak La++l+++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQAS 393
                                   799*******************984 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0     0.009       2.2       2      25 ..      98     121 ..      97     127 .. 0.87
   2 ?   -0.1   0.0       3.3   7.9e+02      94     107 ..     153     166 ..     139     189 .. 0.73
   3 !    9.9   0.0    0.0027      0.64       2      32 ..     369     399 ..     368     406 .. 0.89
   4 ?   -1.0   0.0       5.9   1.4e+03      88     105 ..     417     435 ..     401     458 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.009
                                   EEEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                   v++ GppG+GKt + k ++++lk 
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKW 121
                                   7889****************9974 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.3
                                   HHH-EEEE---STT CS
                      NTPase_1  94 seadviviDEiGkm 107
                                   + + +iviDEi  +
  gi|70606665|ref|YP_255535.1| 153 NVPAIIVIDEIDGF 166
                                   45669*****9555 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0027
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                   +++ GppG+GKt + k ++++l+ s + v+G
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFIVVSG 399
                                   6788******************999888877 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5.9
                                   HHHHHH.HHH-EEEE---S CS
                      NTPase_1  88 alrkal.seadviviDEiG 105
                                   +++ a  +++ +i iDEi 
  gi|70606665|ref|YP_255535.1| 417 KFHIAKdNSPSIIFIDEID 435
                                   44444437788******95 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0083         2      18      45 ..      93     120 ..      79     202 .. 0.80
   2 !   10.1   0.1    0.0023      0.55      16      49 ..     362     394 ..     355     469 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0083
                      ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienle 45 
                                   +++  + ++Gp g GKt++ k +++nl+
  gi|70606665|ref|YP_255535.1|  93 KRAYGVILFGPPGTGKTSIAKALANNLK 120
                                   44445678******************94 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0023
                      ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienledkdk 49 
                                     +p + +++YGp g GKt++ k ++++l+  ++
  gi|70606665|ref|YP_255535.1| 362 GIKPVKGILLYGPPGTGKTSIAKALANELQA-SF 394
                                   555666789*****************99954.44 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0057       1.4      36      54 ..      98     116 ..      78     119 .. 0.88
   2 !    8.7   0.1    0.0049       1.2      36      54 ..     369     387 ..     364     393 .. 0.90
   3 ?    0.8   0.0       1.3   3.1e+02     135     184 ..     419     469 ..     394     472 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0057
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   ++l+G+pgtGKt +a  la
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALA 116
                                   79***********998776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0049
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pgtGKt +a  la
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALA 387
                                   69***********998887 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.3
                        AAA_25 135 aaieevegvrlvviDplsralgg.densnsdv.galvealeriarrtgaavl 184
                                     +++ + +  + iD ++ + +  +en+ + + ++l++ ++ i+++ +++++
  gi|70606665|ref|YP_255535.1| 419 HIAKD-NSPSIIFIDEIDMIARTrGENEWRGAlTELLSEMDGIRENEDVIII 469
                                   45555.779999*****9998888899888888**********999888876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0     0.005       1.2      15      45 ..      85     118 ..      72     131 .. 0.71
   2 !    8.8   0.0    0.0051       1.2      24      47 ..     368     391 ..     346     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.005
                                   HHHHCTSS...S-EEEECSTTSSHHHHHHHHHHH CS
               Sigma54_activat  15 ikkvaktd...lsvlitGesGtGKellaraihea 45 
                                   i++++ ++     v++ G  GtGK+ +a+a+ ++
  gi|70606665|ref|YP_255535.1|  85 ISNYVMSRkraYGVILFGPPGTGKTSIAKALANN 118
                                   44433333344889***************99775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0051
                                   -EEEECSTTSSHHHHHHHHHHHST CS
               Sigma54_activat  24 svlitGesGtGKellaraiheask 47 
                                    +l+ G  GtGK+ +a+a+ ++ +
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALANELQ 391
                                   69***************9987554 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0055       1.3      32      60 ..      95     123 ..      87     135 .. 0.80
   2 !   10.4   0.0   0.00094      0.22      36      66 ..     370     400 ..     362     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0055
                         AAA_6  32 klggapaGpagtGKtEtvkdLakalakqv 60 
                                    +g  + Gp gtGKt   k La++l    
  gi|70606665|ref|YP_255535.1|  95 AYGVILFGPPGTGKTSIAKALANNLKWNY 123
                                   5677889***************9997655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00094
                         AAA_6  36 apaGpagtGKtEtvkdLakalakqvvvfncs 66 
                                    ++Gp gtGKt   k La++l   ++v+  +
  gi|70606665|ref|YP_255535.1| 370 LLYGPPGTGKTSIAKALANELQASFIVVSGD 400
                                   578******************9999998765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.42     1e+02      22      37 ..      98     113 ..      91     119 .. 0.83
   2 ?    1.8   0.0      0.52   1.3e+02     113     151 ..     148     185 ..     115     192 .. 0.78
   3 ?    7.3   0.1     0.011       2.6      14      37 ..     361     384 ..     336     393 .. 0.84
   4 ?    6.7   0.0     0.017       4.1      98     154 ..     404     460 ..     384     471 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.42
                        ATPase  22 vlitGepGtGKtifal 37 
                                   v + G pGtGKt +a+
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAK 113
                                   5688********9886 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.52
                        ATPase 113 eaikeikakrvviDsitglayeekeavaReilrqlvrvl 151
                                   + ++      +viD i+g+ +  +e  + e  ++lv++l
  gi|70606665|ref|YP_255535.1| 148 NTVELNVPAIIVIDEIDGF-TLRREGDIHEVTHRLVNIL 185
                                   55544445789********.9999999999999999988 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.011
                        ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                    Gi   + +l++G pGtGKt +a+
  gi|70606665|ref|YP_255535.1| 361 LGIKPVKGILLYGPPGTGKTSIAK 384
                                   68888999************9886 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.017
                        ATPase  98 ekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                   + + +++ eli+e  ++ k+   + + iD i+ +a++  e++ R  l +l++++ ++
  gi|70606665|ref|YP_255535.1| 404 SVGPFKAGELIAEKFHIAKDNSPSIIFIDEIDMIARTRGENEWRGALTELLSEMDGI 460
                                   3578899999999999***********************************999764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0082         2       3      26 ..      98     121 ..      96     131 .. 0.87
   2 ?   -1.6   0.0       9.6   2.3e+03      73     130 ..     146     206 ..     127     227 .. 0.57
   3 !    9.4   0.0     0.004      0.95       3      26 ..     369     392 ..     367     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0082
                                   EEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                   vil G++G GKT  ++ la  ++ 
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLKW 121
                                   7999***************99875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.6
                                   HHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECC CS
                         NACHT  73 wavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpr 130
                                   + + +el   + +++D +D +    +    +   ++ + L + ++  + ++ +++++ +++
  gi|70606665|ref|YP_255535.1| 146 FFNTVELNVPAIIVIDEIDGFTLRREGdihEVTHRLVNILLNRLQDIHDKRLPVIIIGTTN 206
                                   5566777778889999999876433333443333333334444444455555555555555 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.004
                                   EEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                   ++l G++G GKT  ++ la ++++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQA 392
                                   7899***************99976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.002      0.47      19      41 ..      95     117 ..      76     123 .. 0.79
   2 !    7.8   0.0    0.0086         2      22      42 ..     369     389 ..     354     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.002
                                   -SEEEEE--TTSSTTHHHHHHHH CS
                          PhoH  19 ndivfaiGpaGtGKtylavalav 41 
                                      v+ +Gp GtGKt +a ala 
  gi|70606665|ref|YP_255535.1|  95 AYGVILFGPPGTGKTSIAKALAN 117
                                   446899************99985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0086
                                   EEEE--TTSSTTHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalave 42 
                                   +   Gp GtGKt +a ala e
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANE 389
                                   5678***********999965 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0064       1.5      81     131 ..      73     127 ..      50     133 .. 0.64
   2 ?    7.9   0.0     0.011       2.7     100     131 ..     367     398 ..     336     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0064
                                   E--TTTHTTHHHHHHHCTT....SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  81 lvsaktkegleelkellkd....ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   +  ++ k++l ++++++ +      ++l G+ G GK+++ +al+++l+ +  e++
  gi|70606665|ref|YP_255535.1|  73 YDMKELKQKLLDISNYVMSrkraYGVILFGPPGTGKTSIAKALANNLKWNYFELR 127
                                   444444555555555544321114579*****************99887666655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                                   SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   k ++l G+ G GK+++ +al++el+++   vs
  gi|70606665|ref|YP_255535.1| 367 KGILLYGPPGTGKTSIAKALANELQASFIVVS 398
                                   66899*****************9988766665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.02       4.8      21      43 ..      96     118 ..      72     142 .. 0.77
   2 ?   -0.6   0.0       2.6   6.3e+02      32      89 ..     203     259 ..     202     271 .. 0.73
   3 !    7.5   0.0    0.0083         2      23      44 ..     369     390 ..     352     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                                   EEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                                     v l G +G GKt +ak   n+
  gi|70606665|ref|YP_255535.1|  96 YGVILFGPPGTGKTSIAKALANN 118
                                   34889************998887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                                   SHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-ST CS
                        NB-ARC  32 GKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeev 89 
                                   G t l ++i +      grFd +++v + ++   eei+    k Ls   + l +k+++
  gi|70606665|ref|YP_255535.1| 203 GTTNLPQEIDEA-LLRPGRFDEIIYVPLPDEKAREEIWLGYTKGLSVDCKLLANKSNR 259
                                   556666666666.445579************999999998888887776666666655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0083
                                   EEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                   + l+G +G GKt +ak   n++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANEL 390
                                   789*************999885 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.037       8.9       5      27 ..      99     121 ..      96     126 .. 0.88
   2 !   10.3   0.0    0.0014      0.33       5      32 ..     370     397 ..     366     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                           IPT   5 lifGatttGKtaeaiklaketga 27 
                                   ++fG+ +tGKt+ a +la++  +
  gi|70606665|ref|YP_255535.1|  99 ILFGPPGTGKTSIAKALANNLKW 121
                                   68****************98766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
                           IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                   l++G+ +tGKt+ a +la+e  a+ iv+
  gi|70606665|ref|YP_255535.1| 370 LLYGPPGTGKTSIAKALANELQASFIVV 397
                                   89****************9876665543 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0084         2       4      24 ..      98     118 ..      95     134 .. 0.83
   2 ?    7.6   0.0     0.012         3       2      24 ..     367     389 ..     366     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0084
                     PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                   ++l+G+ g+GKt++++al ++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANN 118
                                   89****************873 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k ill G+ g+GKt++++al +e
  gi|70606665|ref|YP_255535.1| 367 KGILLYGPPGTGKTSIAKALANE 389
                                   679*****************986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.015       3.5      21      51 ..      84     122 ..      63     225 .. 0.79
   2 ?    7.6   0.0     0.015       3.6      15      51 ..     357     393 ..     338     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                                   ..........TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                        ResIII  21 s........krdkrglikmaTGtGKTlvaaklierllkk 51 
                                   +        kr   +++  + GtGKT +a +l+ +l+ +
  gi|70606665|ref|YP_255535.1|  84 DisnyvmsrKRAYGVILFGPPGTGKTSIAKALANNLKWN 122
                                   3556666556777888999**********9999998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.015
                                   HT......TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                        ResIII  15 lleklkskrdkrglikmaTGtGKTlvaaklierllkk 51 
                                   +++kl +k  k +l+  + GtGKT +a +l+ +l+ +
  gi|70606665|ref|YP_255535.1| 357 IANKLGIKPVKGILLYGPPGTGKTSIAKALANELQAS 393
                                   5566666778899999**************9999876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.016       3.8       2      22 ..      98     118 ..      97     161 .. 0.87
   2 ?    7.9   0.0     0.013       3.1       2      23 ..     369     391 ..     368     473 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                                   EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                   v+++G p +GK+++ +al ++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANN 118
                                   789***************985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.013
                                   EEEEESTTSSHHHHHHHHHTS.T CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.k 23 
                                   ++++G p +GK+++ +al +e +
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANElQ 391
                                   6899***************9642 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.028       6.6       5      27 ..      98     120 ..      94     127 .. 0.87
   2 ?    7.6   0.0     0.012       2.8       4      31 ..     368     395 ..     366     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.028
                                   EEEESTTTSSHHHHHHHHHHHST CS
                 Guanylate_kin   5 vvlvgpsgaGksslkkaLlselp 27 
                                   v+l gp g+Gk s+ kaL ++l+
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLK 120
                                   8****************987765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                   EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                    + l gp g+Gk s+ kaL +el+ +f 
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALANELQASFI 395
                                   6899******************999985 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.035       8.4       2      22 ..      98     118 ..      97     126 .. 0.89
   2 !    8.6   0.0    0.0085         2       2      30 ..     369     397 ..     368     404 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.035
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakk 22 
                                   +i+ G+P +GKt++a +La +
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANN 118
                                   799***************975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0085
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                   i++ G+P +GKt++a +La + +a+++ +
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASFIVV 397
                                   7889****************999988765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0      0.03       7.1      23      40 ..      99     116 ..      97     156 .. 0.89
   2 ?    7.6   0.1     0.021         5      23      39 ..     370     386 ..     360     388 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.03
                        AAA_23  23 lItGpNGaGKTTildAik 40 
                                   +++Gp G+GKT+i  A+ 
  gi|70606665|ref|YP_255535.1|  99 ILFGPPGTGKTSIAKALA 116
                                   789************996 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.021
                        AAA_23  23 lItGpNGaGKTTildAi 39 
                                   l++Gp G+GKT+i  A+
  gi|70606665|ref|YP_255535.1| 370 LLYGPPGTGKTSIAKAL 386
                                   89************998 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.037       8.9       6      25 ..     100     119 ..      96     148 .. 0.76
   2 !    8.5   0.0    0.0043         1       4      33 ..     369     391 ..     367     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.037
                       DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                     G +GtGKt ++ +l+++l
  gi|70606665|ref|YP_255535.1| 100 LFGPPGTGKTSIAKALANNL 119
                                   5699************9998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeert 33 
                                   +l  G +GtGKt ++ +l++el       +
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANEL-------Q 391
                                   6778*****************9.......2 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.71   1.7e+02      18      45 ..      93     120 ..      80     125 .. 0.81
   2 ?    2.5   0.0      0.29        69     146     184 ..     128     165 ..     122     188 .. 0.76
   3 ?    7.1   0.0     0.011       2.7      23      66 ..     369     407 ..     355     428 .. 0.81
   4 ?   -0.9   0.1       3.3   7.8e+02     168     184 ..     420     436 ..     412     441 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.71
                    KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelk 45 
                                   ++ + v L g+ G+GK+s+ + l ++lk
  gi|70606665|ref|YP_255535.1|  93 KRAYGVILFGPPGTGKTSIAKALANNLK 120
                                   678889999999***********99988 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.29
                    KAP_NTPase 146 eeaplkklqteveelladmektLdalqkrlVvviDdLDr 184
                                   +++ l k   e e ll+++++t +  + + ++viD++D 
  gi|70606665|ref|YP_255535.1| 128 SSDILSKWYGESEFLLENFFNTVEL-NVPAIIVIDEIDG 165
                                   5555555556677788899999887.************5 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                    KAP_NTPase  23 vgLygkWGsGKssllnkledelkefakpvrflfaefnawsfkgg 66 
                                   + Lyg+ G+GK+s+ + l +el+       f++++ +  s+ g 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQAS-----FIVVSGDEISSVGP 407
                                   88********************998.....78777777777664 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.3
                    KAP_NTPase 168 LdalqkrlVvviDdLDr 184
                                   +++ +++ +++iD++D 
  gi|70606665|ref|YP_255535.1| 420 IAKDNSPSIIFIDEIDM 436
                                   56689999*******95 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00067      0.16      12      44 ..      94     126 ..      85     132 .. 0.85
   2 ?    2.0   0.0      0.44     1e+02      16      38 ..     369     391 ..     355     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00067
                                   S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                         6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrt 44 
                                   +   ++l G p +gKt i+k+l   lkw+ ++ 
  gi|70606665|ref|YP_255535.1|  94 RAYGVILFGPPGTGKTSIAKALANNLKWNYFEL 126
                                   55669***********************98765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.44
                                   EEEESSTTSSHHHHHHHHHHHHH CS
                         6PF2K  16 ivlvGLpargKtyiskkltrylk 38 
                                   i+l G p +gKt i+k+l   l+
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQ 391
                                   78999************988776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.051        12       5      27 ..      98     120 ..      94     129 .. 0.86
   2 !    8.1   0.0    0.0094       2.3       5      30 ..     369     394 ..     366     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.051
                                   EEEESSTTSSHHHHHHHHHHHHH CS
                    APS_kinase   5 vwltGlsgsGKstianalekkLv 27 
                                   v l G  g+GK++ia+al+++L+
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLK 120
                                   7788***************9997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0094
                                   EEEESSTTSSHHHHHHHHHHHHHHTT CS
                    APS_kinase   5 vwltGlsgsGKstianalekkLvekg 30 
                                   ++l G  g+GK++ia+al+++L+++ 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQASF 394
                                   7899***************9998753 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0092       2.2      59     108 ..      70     116 ..      58     120 .. 0.85
   2 ?    6.0   0.0     0.019       4.5      82     107 ..     360     386 ..     310     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0092
                    Adeno_IVa2  59 eevkdiekldakllrddGelsslnyglqPviGvi.yGPtGsGksqllrnli 108
                                   e+++d+++l++kll      s   + ++   Gvi +GP G+Gk+ + ++l 
  gi|70606665|ref|YP_255535.1|  70 EQIYDMKELKQKLLDI----SNYVMSRKRAYGVIlFGPPGTGKTSIAKALA 116
                                   7999********9976....8888888999998758********9999885 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                    Adeno_IVa2  82 nyglqPviGv.iyGPtGsGksqllrnl 107
                                    +g +Pv G+ +yGP G+Gk+ + ++l
  gi|70606665|ref|YP_255535.1| 360 KLGIKPVKGIlLYGPPGTGKTSIAKAL 386
                                   47899****846*********999887 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0067       1.6       8      43 ..     104     139 ..     100     203 .. 0.79
   2 ?    4.8   0.0      0.12        29       8      27 ..     375     394 ..     369     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0067
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelgls 43 
                                    G+g++ i++aLA++L++++++ +  + ++k  g s
  gi|70606665|ref|YP_255535.1| 104 PGTGKTSIAKALANNLKWNYFELRSSDILSKWYGES 139
                                   59****************999765444444444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpf 27 
                                    G+g++ i++aLA++L+  f
  gi|70606665|ref|YP_255535.1| 375 PGTGKTSIAKALANELQASF 394
                                   69**************9877 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.038       9.1     113     153 ..      77     119 ..      55     124 .. 0.65
   2 !    7.3   0.0    0.0087       2.1     129     156 ..     366     393 ..     302     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.038
                         T2SSE 113 alkekiaevlrkavr..erglilvsGgTgsGKttllyallkei 153
                                   +lk+k+ ++ ++ ++  + + +++ G+ g+GKt ++ al + +
  gi|70606665|ref|YP_255535.1|  77 ELKQKLLDISNYVMSrkRAYGVILFGPPGTGKTSIAKALANNL 119
                                   4444444443333330034557888*********999998776 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0087
                         T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                                    + il+ G+ g+GKt ++ al +e+++s
  gi|70606665|ref|YP_255535.1| 366 VKGILLYGPPGTGKTSIAKALANELQAS 393
                                   5679********************9987 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.014       3.4     242     287 ..      75     120 ..      11     133 .. 0.85
   2 ?    6.0   0.0     0.019       4.5     259     291 ..     364     395 ..     328     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                      PPV_E1_C 242 gvelisfltalkefLkgvPkknclvllGppntGkslfamslikfLk 287
                                     el + l ++ +++ ++ +   ++l+Gpp tGk+  a++l + Lk
  gi|70606665|ref|YP_255535.1|  75 MKELKQKLLDISNYVMSRKRAYGVILFGPPGTGKTSIAKALANNLK 120
                                   45555667888999999999999****************9988776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                      PPV_E1_C 259 vPkknclvllGppntGkslfamslikfLkGkvl 291
                                   +P k  ++l+Gpp tGk+  a++l + L+ + +
  gi|70606665|ref|YP_255535.1| 364 KPVK-GILLYGPPGTGKTSIAKALANELQASFI 395
                                   5555.5789***************999887655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.027       6.4       2      22 ..      98     118 ..      97     138 .. 0.89
   2 ?    5.8   0.0     0.063        15       2      22 ..     369     389 ..     368     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.027
                                   EEEESSTTSSHHHHHHCHCT- CS
                           Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                   v+l G  g+GKts++k + ++
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANN 118
                                   7999************99875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.063
                                   EEEESSTTSSHHHHHHCHCT- CS
                           Roc   2 vvlvGdsgvGKtsllkrfved 22 
                                   ++l G  g+GKts++k + ++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANE 389
                                   6899***********999864 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.046        11       1      31 [.     100     132 ..     100     164 .. 0.83
   2 ?    5.0   0.0       0.1        24       1      25 [.     371     395 ..     371     404 .. 0.82
   3 ?   -0.4   0.0       4.6   1.1e+03      53      85 ..     536     568 ..     516     575 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.046
                                   EEESTTSSHHHHHHHHHHHHTSE..EEEHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                           ADK   1 llGaPgaGKGtqaeklvkkygla..hlstGdll 31 
                                   l G+Pg+GK   a+ l+++++++  +l + d+l
  gi|70606665|ref|YP_255535.1| 100 LFGPPGTGKTSIAKALANNLKWNyfELRSSDIL 132
                                   68***************9887651156666665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.1
                                   EEESTTSSHHHHHHHHHHHHTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK   1 llGaPgaGKGtqaeklvkkyglahl 25 
                                   l G+Pg+GK   a+ l++++++  +
  gi|70606665|ref|YP_255535.1| 371 LYGPPGTGKTSIAKALANELQASFI 395
                                   67****************9987654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4.6
                                   SS--HHHHHHHHHHHHHCHGTTTEEEEESB-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ADK  53 elvpdevvvklvkeelekedkkkgfllDGfPRt 85 
                                   +lv de+  +l+ke+ ++ + ++ + +D f R 
  gi|70606665|ref|YP_255535.1| 536 KLVVDEIRRNLLKEATSTGNIRTSLNFDDFVRV 568
                                   7999**********9999999999999988886 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.055        13       4      26 ..      98     120 ..      96     127 .. 0.87
   2 ?    6.5   0.0     0.023       5.6       4      27 ..     369     392 ..     366     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.055
                                   EEEEESTTSSHHHHHHHHHHHHH CS
                         SRP54   4 illvGlqGaGKTttlaKLaallk 26 
                                   ++l+G+ G+GKT+ +  La+ lk
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNLK 120
                                   6899*********9999**9887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                                   EEEEESTTSSHHHHHHHHHHHHHH CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkk 27 
                                   ill G+ G+GKT+ +  La+ l++
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQA 392
                                   89**********999999998875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.08        19      24      42 ..      97     115 ..      84     120 .. 0.78
   2 ?    7.2   0.0     0.017       4.1      22      43 ..     367     387 ..     356     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.08
                        AAA_29  24 atlltGpsGsGKSTllDAi 42 
                                    ++l Gp G+GK+++  A+
  gi|70606665|ref|YP_255535.1|  97 GVILFGPPGTGKTSIAKAL 115
                                   5899**********98776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.017
                        AAA_29  22 kgatlltGpsGsGKSTllDAiq 43 
                                   kg +ll Gp G+GK+++  A++
  gi|70606665|ref|YP_255535.1| 367 KG-ILLYGPPGTGKTSIAKALA 387
                                   45.9************987775 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0052       1.2       5      47 ..     102     148 ..      98     152 .. 0.78
   2 ?    3.5   0.0      0.23        55       3      25 ..     371     393 ..     369     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0052
                                   ESTTSSHHHHHHHHHCCSTCEEEE-....HHHHCCSSSSHHHHHHHH CS
                           dNK   5 GnIgaGKstlvklLskklgvkvfeE....pvdkwtnvqknlLekfYk 47 
                                   G+ g GK++++k L+++l+++ fe     + +kw    + lLe+f++
  gi|70606665|ref|YP_255535.1| 102 GPPGTGKTSIAKALANNLKWNYFELrssdILSKWYGESEFLLENFFN 148
                                   7779*****************99633333788887777777777776 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.23
                                   EEESTTSSHHHHHHHHHCCSTCE CS
                           dNK   3 veGnIgaGKstlvklLskklgvk 25 
                                   + G+ g GK++++k L+++l+  
  gi|70606665|ref|YP_255535.1| 371 LYGPPGTGKTSIAKALANELQAS 393
                                   66889*************99844 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.017       4.1      51      92 ..      93     137 ..      78     154 .. 0.74
   2 ?    4.6   0.0      0.14        33      56      77 ..     369     390 ..     341     396 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.017
                                   SS-EEEEEEE-TTSSHHHHHHHHHHHH...STTGGGSTTEEEEEH CS
                        Torsin  51 kkpLvlsfhGwtGtGknfvaeiiaenl...yrdGlrsdyvkkfva 92 
                                   k++  + + G +GtGk  +a+ +a+nl   y +   sd+  k+ +
  gi|70606665|ref|YP_255535.1|  93 KRAYGVILFGPPGTGKTSIAKALANNLkwnYFELRSSDILSKWYG 137
                                   456667789****************98443444445555555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.14
                                   EEEEE-TTSSHHHHHHHHHHHH CS
                        Torsin  56 lsfhGwtGtGknfvaeiiaenl 77 
                                   + ++G +GtGk  +a+ +a++l
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANEL 390
                                   5689***************987 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.21        50      58      85 ..      96     123 ..      63     132 .. 0.84
   2 ?   -0.8   0.0       2.8   6.6e+02     124     144 ..     157     177 ..     150     182 .. 0.90
   3 ?    6.3   0.0     0.019       4.5      46      96 ..     355     406 ..     328     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                                   -EEEEEESSTSTHHHHHHHHHHHSSSEE CS
                           MCM  58 invllvgdpgtaKsqlLkyveklaprav 85 
                                     v+l g pgt+K+ + k+++++++ + 
  gi|70606665|ref|YP_255535.1|  96 YGVILFGPPGTGKTSIAKALANNLKWNY 123
                                   5699**************9998877665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                                   EEEEESGGGSTCHHHHHHHHH CS
                           MCM 124 vcciDefdkmkeedrsalhEa 144
                                   +++iDe+d  + + +  +hE+
  gi|70606665|ref|YP_255535.1| 157 IIVIDEIDGFTLRREGDIHEV 177
                                   899*********9999***98 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.019
                                   BBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE.EEEESSSSSSSH CS
                           MCM  46 kkledktklrgdinvllvgdpgtaKsqlLkyveklapra.vytsgkgssaag 96 
                                   k   +k  ++    +ll g pgt+K+ + k++++ ++ + + +sg   s++g
  gi|70606665|ref|YP_255535.1| 355 KDIANKLGIKPVKGILLYGPPGTGKTSIAKALANELQASfIVVSGDEISSVG 406
                                   445555667777789****************988777662556777777766 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0      0.07        17       5      26 ..      97     118 ..      93     133 .. 0.85
   2 ?    4.8   0.0      0.07        17       5      27 ..     368     390 ..     364     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.07
                                   EEEEE-STTSSHHHHHHHHHHS CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd 26 
                                    v+l G+  +GKTs+ + L ++
  gi|70606665|ref|YP_255535.1|  97 GVILFGPPGTGKTSIAKALANN 118
                                   69*************9998765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.07
                                   EEEEE-STTSSHHHHHHHHHHSS CS
                         SRPRB   5 avllvGlsdsGKTslftrLttds 27 
                                    +ll G+  +GKTs+ + L ++ 
  gi|70606665|ref|YP_255535.1| 368 GILLYGPPGTGKTSIAKALANEL 390
                                   699************99998873 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.084        20       4      71 ..     101     163 ..      98     167 .. 0.72
   2 ?    5.1   0.0      0.07        17       4      71 ..     372     434 ..     369     440 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.084
               Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+++ + l+++   +  + r+   +l+++  +++ l  + +++++ +  +     i+++DE+
  gi|70606665|ref|YP_255535.1| 101 FGPPGTGKTSIAKALANNLkWNYFELRS-SDILSKWYGESEFLLENFFNTVELNVPA-----IIVIDEI 163
                                   688*******999999986744444444.6777777777777777778877777543.....7777775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.07
               Viral_helicase1   4 hGvpGcGKStlirkllrtsliltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+++ + l+++       + ++++++     +  p + ++ + +  + +++  +  i+++DE+
  gi|70606665|ref|YP_255535.1| 372 YGPPGTGKTSIAKALANE------LQASFIVVSGDEisSVGPFKAGELIAEKFHIAKDN-SPSIIFIDEI 434
                                   588*******99999999......66666666655566556666666555444444443.4667777776 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.11        26       1      18 [.     102     119 ..     102     126 .. 0.89
   2 ?    5.0   0.0     0.077        19       1      18 [.     373     390 ..     373     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                        CLP1_P   1 GpkdsGKSTlarlLlNya 18 
                                   Gp  +GK+++a+ L+N++
  gi|70606665|ref|YP_255535.1| 102 GPPGTGKTSIAKALANNL 119
                                   8899************97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.077
                        CLP1_P   1 GpkdsGKSTlarlLlNya 18 
                                   Gp  +GK+++a+ L+N++
  gi|70606665|ref|YP_255535.1| 373 GPPGTGKTSIAKALANEL 390
                                   8899************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1      0.06        14       3      40 ..      99     130 ..      98     146 .. 0.69
   2 ?    6.9   0.5     0.021       4.9       3      31 ..     370     392 ..     369     441 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.06
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40 
                                   +l Gp g+GK+++ +al      +++++    el+++ 
  gi|70606665|ref|YP_255535.1|  99 ILFGPPGTGKTSIAKAL------ANNLKWNYFELRSSD 130
                                   799**************......555555444444444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.021
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdveg 31 
                                   +l+Gp g+GK+++ +al       ++++ 
  gi|70606665|ref|YP_255535.1| 370 LLYGPPGTGKTSIAKALA------NELQA 392
                                   79***************3......22222 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        33       2      22 ..      98     118 ..      97     126 .. 0.87
   2 ?    4.5   0.0     0.081        19       2      25 ..     369     392 ..     368     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                     Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdn 22 
                                   v+L G+ g GKts+ + + +n
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANN 118
                                   89************9987666 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.081
                     Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnyla 25 
                                   +LL G+ g GKts+ + + ++++a
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQA 392
                                   89************9987766665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.17        40      17      38 ..      98     119 ..      80     131 .. 0.85
   2 ?    5.5   0.0     0.051        12      17      47 ..     369     398 ..     365     488 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
                                   EEEEESTTSSHHHHHHHHHHHS CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqs 38 
                                   ++++g  g+Gkt i+++l+++ 
  gi|70606665|ref|YP_255535.1|  98 VILFGPPGTGKTSIAKALANNL 119
                                   679***************9985 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.051
                                   EEEEESTTSSHHHHHHHHHHHSSTSSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyv 47 
                                   +l+ g  g+Gkt i+++l+++ +++  i++ 
  gi|70606665|ref|YP_255535.1| 369 ILLYGPPGTGKTSIAKALANELQAS-FIVVS 398
                                   5688999**************7555.55544 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       2.4   5.7e+02      19      41 ..      60      82 ..      56      87 .. 0.91
   2 ?    2.7   0.0      0.56   1.3e+02      25      44 ..     298     317 ..     285     326 .. 0.83
   3 ?    6.0   0.5     0.051        12      23      60 ..     326     363 ..     312     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.4
                                  HGGG-----HHHHHHHHHS---E CS
                       DUF2540 19 klenlenvdvetlkkakeaekkt 41
                                  k+ n+ +v+ e++  +ke+++k+
  gi|70606665|ref|YP_255535.1| 60 KMRNIPSVSWEQIYDMKELKQKL 82
                                  89***************999885 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.56
                                   ---HHHHHHHHHS---EEEE CS
                       DUF2540  25 nvdvetlkkakeaekktkkt 44 
                                   +v+++tl k +++ kk+++ 
  gi|70606665|ref|YP_255535.1| 298 SVSIQTLIKFENLSKKYSRH 317
                                   89***************995 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.051
                                   -----HHHHHHHHHS---EEEEEE--HHHHHHHHHHGG CS
                       DUF2540  23 lenvdvetlkkakeaekktkktltLsdeEkkIvkklGk 60 
                                   + n++ + l+   e +k ++ +++L  + k I +klG+
  gi|70606665|ref|YP_255535.1| 326 IANIKWDDLGDLDEIKKVIRESVELPMKNKDIANKLGI 363
                                   689**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        75  (0.00418317); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              75  [number of targets reported over threshold]
# CPU time: 0.86u 0.32s 00:00:01.18 Elapsed: 00:00:00.46
# Mc/sec: 3881.66
//
Query:       gi|70606666|ref|YP_255536.1|  [L=185]
Description: hypothetical protein Saci_0878 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.0   1.6     0.0032   17.0   1.6    2.7  3  SPW       SPW repeat


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4      0.16   2.9e+03      35      44 ..      15      24 ..      10      35 .. 0.52
   2 !   17.0   1.6   1.8e-07    0.0032      16      46 ..     104     134 ..     100     135 .. 0.94
   3 ?   -1.8   0.1      0.14   2.4e+03      20      39 ..     142     161 ..     139     167 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.16
                           SPW 35 avvavLalaf 44
                                  +v  + ++++
  gi|70606666|ref|YP_255536.1| 15 VVFSIASYVT 24
                                  4443333333 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.8e-07
                           SPW  16 WvlGfsattgaawnnvivGavvavLalafaa 46 
                                   W +G+ + +++++n  +vG ++ vL++ f++
  gi|70606666|ref|YP_255536.1| 104 WAIGYRGLRAVMINTTVVGGLIGVLSVFFGS 134
                                   **************************99976 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.14
                           SPW  20 fsattgaawnnvivGavvav 39 
                                   +++  ++ +  vi G++ +v
  gi|70606666|ref|YP_255536.1| 142 SVPFSSLLLAYVIFGVIYFV 161
                                   55556677777888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1362.09
//
Query:       gi|70606667|ref|YP_255537.1|  [L=161]
Description: hypothetical protein Saci_0879 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.09   12.6   1.4       0.65    9.8   0.0    2.1  2  DUF4386   Domain of unknown function (DUF4386)
        2.2    9.1   8.5        1.8    9.4   2.4    2.4  2  YMF19     Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> DUF4386  Domain of unknown function (DUF4386)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5     0.018   1.6e+02      53      95 ..       3      40 ..       1      72 [. 0.70
   2 ?    9.8   0.0   7.2e-05      0.65     142     178 ..     113     149 ..      98     161 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.018
                       DUF4386 53 lmalllvvlavlLypllrrvnpglallaaafrlveaaviavgl 95
                                  + +l  +v +++Ly++ r+ n     l  +fr+++ + i++gl
  gi|70606667|ref|YP_255537.1|  3 IEFLVIIVSYIVLYVVNRE-N----FLIFTFRVLSYVNIFIGL 40
                                  5666777777777776655.3....355555555555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.2e-05
                       DUF4386 142 wllllgllllrsrllPrwlgllgllagllyllasfae 178
                                   +l l+g l+ ++++ Pr + +l+l+a++++ll s + 
  gi|70606667|ref|YP_255537.1| 113 NLKLYGNLIRKRNFKPRKIDILLLIASVSVLLVSCVY 149
                                   6678999**********************99988765 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.4    0.0002       1.8      12      47 ..       5      40 ..       3      53 .. 0.83
   2 ?    3.3   0.4     0.016   1.5e+02      22      67 ..      69     113 ..      60     138 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                         YMF19 12 ffWlclfFitlYivllknilpkiarilklrkkllss 47
                                  f+ +++ +i+lY+v  +n+l +++r+l++ + ++  
  gi|70606667|ref|YP_255537.1|  5 FLVIIVSYIVLYVVNRENFLIFTFRVLSYVNIFIGL 40
                                  55566779*****999************99988765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                         YMF19  22 lYivllknilpkiarilklrkkllsslssevsklkkeqknlivskd 67 
                                   ++ + +++ l + +r  k+r  ++++  + + +  k  ++l+vs++
  gi|70606667|ref|YP_255537.1|  69 FF-YRVSRELIFNMRARKVRFSFSNYVLPLTVQTIKVAEDLYVSYN 113
                                   33.4557777778888888888887777655555444445554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1308.23
//
Query:       gi|70606668|ref|YP_255538.1|  [L=372]
Description: ABC-type transport system [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-30  105.2   0.1    1.6e-14   54.6   0.0    3.3  3  ABC_tran         ABC transporter
    3.5e-15   56.6   8.3     0.0007   19.5   0.0    4.3  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.5e-08   33.2   0.0     0.0046   17.2   0.0    2.5  2  AAA_22           AAA domain
    1.5e-07   30.9   0.1      0.005   16.0   0.1    2.5  2  NB-ARC           NB-ARC domain
    2.7e-06   27.2   0.7     0.0081   15.8   0.2    2.4  2  SRP54            SRP54-type protein, GTPase domain
    4.7e-06   26.3   0.2      0.019   14.7   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    5.3e-06   26.3   0.2      0.069   12.9   0.0    2.8  2  AAA_24           AAA domain
      1e-05   25.1   4.8      0.096   12.1   0.1    3.8  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.6e-05   25.1   0.0      0.065   13.4   0.0    2.6  2  AAA_33           AAA domain
      2e-05   25.0   2.2      0.026   15.0   0.1    3.1  2  AAA              ATPase family associated with various cellul
      5e-05   23.3   1.8      0.098   12.6   0.0    2.6  2  NACHT            NACHT domain
    6.1e-05   22.6   0.0       0.32   10.5   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
    6.3e-05   23.0   2.9      0.054   13.5   0.1    3.3  2  AAA_14           AAA domain
      7e-05   22.7   3.3       0.21   11.5   0.2    2.7  2  MobB             Molybdopterin guanine dinucleotide synthesis
    8.7e-05   22.5   0.6      0.053   13.4   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    0.00011   22.6   0.0       0.53   10.6   0.0    2.5  2  AAA_16           AAA ATPase domain
    0.00012   22.2   0.0       0.17   12.1   0.0    2.5  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00013   21.9   4.4       0.26   11.2   0.3    3.6  3  NTPase_1         NTPase
    0.00025   20.4   0.0      0.069   12.4   0.0    2.4  2  Zeta_toxin       Zeta toxin
    0.00025   20.8   0.1       0.56    9.9   0.0    2.3  2  AAA_30           AAA domain
    0.00025   20.9  17.3      0.006   16.3   0.3    3.2  3  AAA_15           AAA ATPase domain
    0.00026   21.0   0.1       0.95    9.5   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00029   21.4  10.3       0.24   11.9   6.3    2.9  2  AAA_23           AAA domain
    0.00031   20.7   2.2       0.26   11.2   0.0    2.7  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0004   20.0   0.5      0.066   12.8   0.0    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00041   20.4   2.7       0.23   11.6   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
    0.00045   19.8   0.2       0.58    9.6   0.0    2.5  2  Pox_A32          Poxvirus A32 protein
    0.00078   19.8   0.4        2.5    8.4   0.0    3.3  2  AAA_19           AAA domain
     0.0013   19.1   0.0       0.75   10.2   0.0    2.8  2  RNA_helicase     RNA helicase
     0.0025   17.6   0.0        1.1    9.0   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0027   18.2   3.6        1.2    9.7   0.1    2.7  2  AAA_18           AAA domain
     0.0033   17.4   0.1        1.9    8.5   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0041   16.9   1.0        2.5    7.8   0.0    2.8  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0095   15.1   0.0       0.75    8.9   0.0    2.3  2  G-alpha          G-protein alpha subunit
  ------ inclusion threshold ------
      0.016   15.6   1.3        1.6    9.1   0.0    2.9  2  AAA_17           AAA domain
      0.026   14.1   0.0        3.7    7.1   0.0    2.4  2  AAA_25           AAA domain
      0.033   14.4   0.0        2.8    8.2   0.0    2.3  2  AAA_28           AAA domain
      0.048   13.2   0.0        1.3    8.6   0.0    2.3  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.051   12.5   0.2          2    7.2   0.0    2.4  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.064   13.0   0.0        3.4    7.3   0.0    2.4  2  VirE             Virulence-associated protein E
      0.078   12.2   2.8        5.3    6.2   0.2    2.8  3  Septin           Septin
      0.086   12.3   0.1        1.3    8.5   0.0    2.3  2  PhoH             PhoH-like protein
      0.088   12.5   0.1        7.3    6.3   0.0    2.5  2  IstB_IS21        IstB-like ATP binding protein
       0.19   12.0   0.0        1.1    9.6   0.0    2.2  2  SbcCD_C          Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   3.9e-17   1.6e-14       6     137 .]       8     136 ..       5     136 .. 0.79
   2 !   21.2   0.2   8.1e-07   0.00033       7      34 ..     223     250 ..     219     253 .. 0.90
   3 !   25.6   0.0   3.4e-08   1.4e-05      80     136 ..     268     320 ..     248     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.9e-17
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenesdeeie 86 
                                   l +  + +v++vG+nG+GK+tL+k  + l ++   +i ldg+d+ e  +++++k  gv+++ ++    lt++e+ + + + 
  gi|70606668|ref|YP_255538.1|   8 LVIDDNDIVGLVGKNGSGKTTLIKNALCLGQN-RFKIILDGDDFCE--HREYSKLTGVFQEPATQILALTCEEELKLRSLF 85 
                                   56778899****************98888875.66777******99..677777777666668888899999985544444 PP

                                   HHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  87 kalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   + ++    k++ ++ ++++ ++LS G k+r ++a al ++pk +llDEp+a
  gi|70606668|ref|YP_255538.1|  86 HTIDFNIAKKIMENYINRDFYTLSDGYKKRFVIASALSSNPKHILLDEPFA 136
                                   44444444556777778888*****************************85 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 8.1e-07
                                   EEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagl 34 
                                   kl+ege++ +vG+nG GK+t lk l ++
  gi|70606668|ref|YP_255538.1| 223 KLREGEILCLVGRNGVGKTTTLKKLVNK 250
                                   799*******************988765 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 3.4e-08
                                   HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    ++++ e+al+ +++k+l+++       +LS+Gqk rv +a a+++ +k++ +DEp+
  gi|70606668|ref|YP_255538.1| 268 IDEVKDEEALRLFKIKDLAEKSP----FTLSYGQKMRVLIATAFASGSKVIGFDEPS 320
                                   55666778888888888666666....*****************************6 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.8   5.4e-05     0.022       2      19 ..      16      33 ..      15      50 .. 0.82
   2 !   13.6   0.0   0.00011     0.043     222     279 ..      93     150 ..      74     167 .. 0.80
   3 !    9.5   0.2    0.0019      0.77       2      17 ..     230     245 ..     229     249 .. 0.88
   4 !   19.5   0.0   1.7e-06    0.0007     213     302 ..     269     355 ..     246     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-05
                        AAA_21  2 nvliGpNgsGKSnLLdal 19
                                   +l+G+NgsGK++L++  
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNA 33
                                  68************9855 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                        AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrll 279
                                       ++++ +++++ lSdG k+  +++++ l+ ++k   +l+DEp ++L+    kl+++++
  gi|70606668|ref|YP_255538.1|  93 AKKIMENYINRDFYTLSDGYKKR-FVIASALSSNPK--HILLDEPFANLDKystKLVKEII 150
                                   556789999**************.999999999995..6**********997777767766 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0019
                        AAA_21   2 nvliGpNgsGKSnLLd 17 
                                    +l+G+Ng+GK++ L+
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLK 245
                                   589**********997 PP

  == domain 4  score: 19.5 bits;  conditional E-value: 1.7e-06
                        AAA_21 213 derlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvi 293
                                   de+ +e+ +++++ +d  e +++ lS G+k    ++ta+++     +++ +DEp  g++ ++l ++++++k+l+++g   i
  gi|70606668|ref|YP_255538.1| 269 DEVKDEEALRLFKIKDLAEKSPFTLSYGQKMRVLIATAFASGS---KVIGFDEPSVGMDGEALLSFYQMVKILKEEGKAMI 346
                                   3333333899999***************996667777777755...9****************************99999* PP

                        AAA_21 294 ltTHSplll 302
                                   ++TH+  +l
  gi|70606668|ref|YP_255538.1| 347 IATHDEDIL 355
                                   ****98877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00017     0.068       7      70 ..      15      98 ..      10     150 .. 0.78
   2 !   17.2   0.0   1.1e-05    0.0046       4      29 ..     226     251 ..     223     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00017
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee...................erpevv.fvtlpsstsskdllrellralglelk 69
                                  i+ ++G  G+GKTtl+++ l   +++ k+                     e+++++   t+ ++ ++++l++ +  ++  +  
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNALCLGQNRFKIILdgddfcehreyskltgvfqEPATQIlALTCEEELKLRSLFHTIDFNIAKKIM 97
                                  56689***************999999998889999999999999999998666666689999999999999999888876554 PP

                        AAA_22 70 a 70
                                  +
  gi|70606668|ref|YP_255538.1| 98 E 98
                                  4 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.1e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                   +  il+++G  G+GKTt+l++l+++ 
  gi|70606668|ref|YP_255538.1| 226 EGEILCLVGRNGVGKTTTLKKLVNKV 251
                                   5679******************9986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05     0.005       8      41 ..       4      34 ..       1      44 [. 0.86
   2 !   12.4   0.0   0.00017     0.068      19      44 ..     228     251 ..     212     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                  HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                        NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqil 41
                                  + ++L+  d+ +  +v+lvG+ G+GKttl+k++l
  gi|70606668|ref|YP_255538.1|  4 INDTLV-IDDND--IVGLVGKNGSGKTTLIKNAL 34
                                  566777.78888..****************9986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00017
                                   CSEEEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  19 qslvvalvGmgGvGKttlakqilnks 44 
                                   +  ++ lvG+ GvGKtt +k+ +nk 
  gi|70606668|ref|YP_255538.1| 228 E--ILCLVGRNGVGKTTTLKKLVNKV 251
                                   3..999***************99995 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0     0.002      0.83       4      34 ..      16      45 ..      13      54 .. 0.76
   2 !   15.8   0.2     2e-05    0.0081       3      24 ..     229     250 ..     227     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                  + lvG +G+GKTt + K a  l ++  k++l
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLI-KNALCLGQNRFKIIL 45
                                  669*********987.667777777777766 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2e-05
                                   EEEEEESTTSSHHHHHHHHHHH CS
                         SRP54   3 villvGlqGaGKTttlaKLaal 24 
                                   ++ lvG +G+GKTttl KL ++
  gi|70606668|ref|YP_255538.1| 229 ILCLVGRNGVGKTTTLKKLVNK 250
                                   6789***************876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.6e-05     0.019      17      39 ..       8      30 ..       3      42 .. 0.79
   2 !    9.1   0.0    0.0025         1      17      39 ..     222     244 ..     216     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-05
                        AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                  + id ++++ l+G++GsGK+Tl+
  gi|70606668|ref|YP_255538.1|  8 LVIDDNDIVGLVGKNGSGKTTLI 30
                                  5677677889************9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0025
                        AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                   i++++ ++  l+G++G+GK+T l
  gi|70606668|ref|YP_255538.1| 222 IKLREGEILCLVGRNGVGKTTTL 244
                                   5666455999**********965 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00091      0.37       5      23 ..      16      38 ..      13      59 .. 0.80
   2 !   12.9   0.0   0.00017     0.069       5      29 ..     230     253 ..     226     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00091
                        AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                  + ++G++g+GKTtl+k++    +
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNAlclgQ 38
                                  5799************9966642 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00017
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfi 29 
                                   ++++G +g+GKTt++k+l  + ++i
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKL-VNKVYI 253
                                   79****************.766666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00023     0.096      25      52 ..      14      40 ..       3      46 .. 0.78
   2 ?    0.5   0.0      0.82   3.3e+02     162     185 ..     129     152 ..      86     180 .. 0.82
   3 ?    3.6   0.0     0.093        38      25      41 ..     228     244 ..     214     249 .. 0.82
   4 !    7.7   0.1    0.0051       2.1     136     212 ..     292     365 ..     269     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                  SEEEEEESTTSSHHHHHHHHHHHCTT.T CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAilFvLGers 52
                                   +  +vG+NGSGK+ l+     +LG++ 
  gi|70606668|ref|YP_255538.1| 14 DIVGLVGKNGSGKTTLIKNA-LCLGQNR 40
                                  56789**********99754.4898765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                                   EEECTTTTTS-HHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 162 yllDeidaaLDeknvkkvaellke 185
                                    llDe  a+LD+  +k v e++ +
  gi|70606668|ref|YP_255538.1| 129 ILLDEPFANLDKYSTKLVKEIIPK 152
                                   589**********99999998865 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.093
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N  25 sftaivGpNGSGKsnll 41 
                                   ++ ++vG+NG GK+  l
  gi|70606668|ref|YP_255538.1| 228 EILCLVGRNGVGKTTTL 244
                                   56789********9765 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0051
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                   +LS G+k  v    l+A+  ++ + +  +De    +D +    + +++k  +++   +i+ +++e++l+ +dk+v + 
  gi|70606668|ref|YP_255538.1| 292 TLSYGQKMRV----LIATAFASGSKVIGFDEPSVGMDGEALLSFYQMVKILKEEgKAMIIATHDEDILSLCDKVVNLE 365
                                   5788887555....55555556778999*********************7777747789999**********999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00016     0.065       2      35 ..      16      52 ..      15     146 .. 0.70
   2 !    9.3   0.0    0.0029       1.2       3      22 ..     231     250 ..     229     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                        AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssdtlrr 35
                                  v lvG +GsGK+tl+++ l  lg     ++l+ d++ +
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNAL-CLGqnrfKIILDGDDFCE 52
                                  5689*************64.233334677788888444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
                        AAA_33   3 llvGlpGsGKstlaerllkk 22 
                                    lvG +G+GK+t +++l++k
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNK 250
                                   689**************944 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.4     0.005       2.1       3      36 ..      18      52 ..      16     194 .. 0.84
   2 !   15.0   0.1   6.3e-05     0.026       1      66 [.     230     318 ..     230     356 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.005
                                  EESSTTSSHHHHHHHHHHHHTHEE.EEEETTTCSS CS
                           AAA  3 lyGppGtGKTllakavakelgvef.leisgsells 36
                                  l+G  G GKT+l+k      + +f + ++g ++++
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIKNALCLGQNRFkIILDGDDFCE 52
                                  89***********9766554445547777777773 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.3e-05
                                   EEEESSTTSSHHHHHHHHHHHH.......THE.................EEEEETTTCSSS..STTHHHHHHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakel.......gve.................fleisgsellsk..yvgesekkirelfkeake 55 
                                   ++l+G  G+GKT++ k +++++       + +                 +++i+      k  +     +k+r l+++a +
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKVyiifqnpDLQffkprvidevkdeealrLFKIKDLAE--KspFTLSYGQKMRVLIATAFA 308
                                   589******************7333332212222222222222222211222222222..133555555555555555555 PP

                                   TSTSEEEEEET CS
                           AAA  56 kakpsilfiDE 66 
                                   +   +++ +DE
  gi|70606668|ref|YP_255538.1| 309 SG-SKVIGFDE 318
                                   54.55666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.7    0.0032       1.3       3      18 ..      16      31 ..      14      38 .. 0.87
   2 !   12.6   0.0   0.00024     0.098       2      23 ..     229     250 ..     228     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                                  EEEEC-TTTCHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlq 18
                                  v l G++GsGKTtL++
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIK 31
                                  6689**********87 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00024
                                   CEEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   2 lvilqGeaGsGKTtLlqklala 23 
                                   +++l G++G+GKTt l+kl+ +
  gi|70606668|ref|YP_255538.1| 229 ILCLVGRNGVGKTTTLKKLVNK 250
                                   589****************976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0013      0.55      29      54 ..       9      34 ..       4      46 .. 0.79
   2 !   10.5   0.0   0.00078      0.32      30      57 ..     224     251 ..     200     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                         AAA_7 29 llknkkpvllvGptGtGKtviikdll 54
                                  +++ +  v lvG+ G+GKt++ik+ l
  gi|70606668|ref|YP_255538.1|  9 VIDDNDIVGLVGKNGSGKTTLIKNAL 34
                                  5666777889*************944 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00078
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                                   l+++  ++lvG  G+GKt+++k+l++k+
  gi|70606668|ref|YP_255538.1| 224 LREGEILCLVGRNGVGKTTTLKKLVNKV 251
                                   456667899**************99875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.4    0.0063       2.6       2      57 ..      13      64 ..      12     152 .. 0.85
   2 !   13.5   0.1   0.00013     0.054       2      33 ..     227     260 ..     226     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0063
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelil 57
                                  + i+ ++G   +GKTtl+k+ +  l    ++ + i ld +++ ++++++kl  +++
  gi|70606668|ref|YP_255538.1| 13 NDIVGLVGKNGSGKTTLIKNAL-CL---GQNRFKIILDGDDFCEHREYSKLTGVFQ 64
                                  678999***********99987.33...3677777777777766666655555554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikell....vkkesi 33 
                                   ++il+++G   vGKTt lk+l+++ +        + 
  gi|70606668|ref|YP_255538.1| 227 GEILCLVGRNGVGKTTTLKKLVNKVYiifqN--PDL 260
                                   57999*****************888855322..222 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   0.00051      0.21       1      20 [.      15      34 ..      15      44 .. 0.85
   2 !   11.1   0.3   0.00066      0.27       1      22 [.     229     250 ..     229     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00051
                          MobB  1 vlgivgksgsGKTtLlekli 20
                                  ++g+vgk+gsGKTtL+++ +
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNAL 34
                                  689*************9876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00066
                          MobB   1 vlgivgksgsGKTtLleklipe 22 
                                   +l++vg++g GKTt l+kl+++
  gi|70606668|ref|YP_255538.1| 229 ILCLVGRNGVGKTTTLKKLVNK 250
                                   799****************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.4     0.018       7.5     100     118 ..      14      32 ..       7      43 .. 0.81
   2 !   13.4   0.0   0.00013     0.053      50     122 ..     180     250 ..     158     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.018
                                   SEEEEECSTTSSHHHHHHH CS
                   RsgA_GTPase 100 ktsvlvGqSGvGKStLina 118
                                   +++ lvG+ G GK+tLi++
  gi|70606668|ref|YP_255538.1|  14 DIVGLVGKNGSGKTTLIKN 32 
                                   7888************964 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00013
                                   EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                   ++ + K  l++e+      +e l+ + ++ + ++ k+k  +e    +l++ ++ +lvG  GvGK+t +++l+++
  gi|70606668|ref|YP_255538.1| 180 IVEIEKEKLYDEKF---LREEGLRGFKLPEINIKPKDKVIFEYSWIKLREgEILCLVGRNGVGKTTTLKKLVNK 250
                                   55555555555555...44455666666666666666666665555666669*****************99886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0035       1.4      26      51 ..      15      39 ..       4      90 .. 0.68
   2 !   10.6   0.0    0.0013      0.53      23      46 ..     226     249 ..     220     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0035
                        AAA_16 26 lvllsGesGvGKsslvrellralekd 51
                                  +v l+G  G+GK++l++ +l  l ++
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNAL-CLGQN 39
                                  7789************8887.45555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0013
                        AAA_16  23 rpelvllsGesGvGKsslvrellr 46 
                                   ++e++ l+G  GvGK++ +++l +
  gi|70606668|ref|YP_255538.1| 226 EGEILCLVGRNGVGKTTTLKKLVN 249
                                   34899**************98875 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0      0.01       4.1       3      20 ..      17      34 ..      16      75 .. 0.81
   2 !   12.1   0.0   0.00043      0.17       2      30 ..     230     258 ..     229     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                                  EEESSTTSSHHHHHHCHC CS
                           Roc  3 vlvGdsgvGKtsllkrfv 20
                                   lvG++g+GKt+l+k+ +
  gi|70606668|ref|YP_255538.1| 17 GLVGKNGSGKTTLIKNAL 34
                                  59************9754 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00043
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEET CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfsekeks 30 
                                   ++lvG +gvGKt+ lk++v++ +   +++
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKVYIIFQNP 258
                                   689****************9987655555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0032       1.3       3      24 ..      17      38 ..      15      62 .. 0.80
   2 !   11.2   0.3   0.00064      0.26       3      23 ..     231     251 ..     229     302 .. 0.64
   3 ?    1.5   0.1      0.61   2.5e+02      95     152 ..     310     369 ..     291     371 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                                  EEE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellk 24
                                   + G+ G+GKtTl+k++l+l +
  gi|70606668|ref|YP_255538.1| 17 GLVGKNGSGKTTLIKNALCLGQ 38
                                  688************9987655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00064
                                   EEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   3 fiTGppGvGKtTlvkkvlell 23 
                                   ++ G+ GvGKtT +kk+++++
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNKV 251
                                   678*************99986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.61
                                   HH-EEEE--..-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EE CS
                      NTPase_1  95 eadviviDE..iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkv 152
                                   ++ vi  DE  +G       +f ++v+ +Lk ++k +++  h ++ l+l +++ + +++++
  gi|70606668|ref|YP_255538.1| 310 GSKVIGFDEpsVGMDGEALLSFYQMVK-ILKeEGKAMIIATHDEDILSLCDKVVNLEEMRI 369
                                   555666666555555555566777765.555599999999999998999999999888776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00017     0.069      18      65 ..      15      60 ..      10      78 .. 0.83
   2 ?    5.5   0.0     0.023       9.4      19      61 ..     230     267 ..     223     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                    Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeil 65
                                  ++ l+G  G+GK++l++ +     +++  + ld+Dd+ + h+ey+++ 
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNALCLG-QNRFKIILDGDDF-CEHREYSKLT 60
                                  56799************999886.5999999******.6799998865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.023
                    Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPey 61 
                                   + l+G  G GK++++++l +++     ++ ++  dl+ + P++
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKV-----YIIFQNPDLQFFKPRV 267
                                   6799*************99987.....6666666666666664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0036       1.5      16      38 ..      11      33 ..       4      44 .. 0.83
   2 !    9.9   0.0    0.0014      0.56      19      40 ..     228     249 ..     223     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                        AAA_30 16 sgdrvavltGpAGtGKttalkal 38
                                  +++ ++ l+G  G+GKtt++k +
  gi|70606668|ref|YP_255538.1| 11 DDNDIVGLVGKNGSGKTTLIKNA 33
                                  4556999************9975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                        AAA_30  19 rvavltGpAGtGKttalkalre 40 
                                    + +l+G+ G GKtt+lk+l++
  gi|70606668|ref|YP_255538.1| 228 EILCLVGRNGVGKTTTLKKLVN 249
                                   47899*************9965 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  12.4     0.053        22      22      84 ..      11     121 ..       3     220 .. 0.46
   2 !   16.3   0.3   1.5e-05     0.006      19      80 ..     222     283 ..     197     300 .. 0.61
   3 ?   -1.5   0.0         4   1.6e+03     325     368 ..     312     354 ..     293     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.053
                        AAA_15  22 see.ltvliGkNnsGKSsilealdlFlnnkekkn.................................kkvikiekedleif 68 
                                   +++ +  l+GkN+sGK+++++    + +n   ++                                 +    +e +  + f
  gi|70606668|ref|YP_255538.1|  11 DDNdIVGLVGKNGSGKTTLIKNALCLGQNR--FKiildgddfcehreyskltgvfqepatqilaltcE----EELKLRSLF 85 
                                   3334999*************9776777766..334555655555555555555555555544422221....222222333 PP

                        AAA_15  69 eniseskdikIdvef....................a 84 
                                   + i++++  kI  ++                    a
  gi|70606668|ref|YP_255538.1|  86 HTIDFNIAKKIMENYinrdfytlsdgykkrfviasA 121
                                   333333333333333444434333333333332220 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.5e-05
                        AAA_15  19 idlsee.ltvliGkNnsGKSsileal....dlFlnnkekknkkvikiekedleifeniseskdikId 80 
                                   i+l e  + +l+G+N++GK++ l+ l    +++++n      +  +++   +++ ++++  + +kI+
  gi|70606668|ref|YP_255538.1| 222 IKLREGeILCLVGRNGVGKTTTLKKLvnkvYIIFQNP-----DLQFFKPRVIDEVKDEEALRLFKIK 283
                                   44444479***************98833333444433.....3444444444444444544444444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                   +++ ++EP +    +a  ++++  k l +++k   ii TH + i
  gi|70606668|ref|YP_255538.1| 312 KVIGFDEPSVGMDGEALLSFYQMVKILKEEGK-AMIIATHDEDI 354
                                   56778888888888888888888888888887.999999*9877 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0034       1.4      19      39 ..      13      33 ..       2      43 .. 0.81
   2 !    9.5   0.0    0.0023      0.95      19      43 ..     227     251 ..     213     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                                  TEEEEEEESTTSSHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                  +d++ L G+ G+GKTtl+++ 
  gi|70606668|ref|YP_255538.1| 13 NDIVGLVGKNGSGKTTLIKNA 33
                                  67899*************975 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                                   TEEEEEEESTTSSHHHHHHHHHHHT CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakal 43 
                                   g++++L G  G+GKTt  ++l++++
  gi|70606668|ref|YP_255538.1| 227 GEILCLVGRNGVGKTTTLKKLVNKV 251
                                   789*****************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   6.3   0.00059      0.24      19      42 ..      13      37 ..       5     196 .. 0.88
   2 !   10.2   0.1    0.0019      0.76      18      36 ..     226     244 ..     194     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00059
                        AAA_23 19 kgltlItGpNGaGKTTil.dAikla 42
                                  + ++ ++G+NG+GKTT++ +A++l+
  gi|70606668|ref|YP_255538.1| 13 NDIVGLVGKNGSGKTTLIkNALCLG 37
                                  678899************9999985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0019
                        AAA_23  18 skgltlItGpNGaGKTTil 36 
                                   +  + +++G NG GKTT l
  gi|70606668|ref|YP_255538.1| 226 EGEILCLVGRNGVGKTTTL 244
                                   44588************87 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.7    0.0038       1.5      17      44 ..      10      37 ..       2     187 .. 0.76
   2 !   11.2   0.0   0.00065      0.26      14      61 ..     221     263 ..     219     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0038
                      ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienl 44
                                   + n+i+ + G  gsGKt+L+k+++   
  gi|70606668|ref|YP_255538.1| 10 IDDNDIVGLVGKNGSGKTTLIKNALCLG 37
                                  5678899999************987554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00065
                      ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialrees 61 
                                   +++  + ei+ + G+ g+GKt+ lk+++++      y+i+ ++  + +
  gi|70606668|ref|YP_255538.1| 221 WIKLREGEILCLVGRNGVGKTTTLKKLVNKV-----YIIFQNPDLQFF 263
                                   777788999********************98.....666666554444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00016     0.066       2      28 ..      15      40 ..      14      60 .. 0.78
   2 ?    5.3   0.1     0.033        14       3      23 ..     230     250 ..     228     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                                  EEEEEESTTCCHHHHHHHHH.CT--SS- CS
                          cobW  2 vtvltGflGsGKTtLlnhll.enraglk 28
                                  +++l+G  GsGKTtL+++ l     +++
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNALcL--GQNR 40
                                  57899************99842..3333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                                   EEEEESTTCCHHHHHHHHHCT CS
                          cobW   3 tvltGflGsGKTtLlnhllen 23 
                                   + l+G  G GKTt l++l+++
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNK 250
                                   6799*************9965 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.8     0.009       3.7       2      19 ..      16      34 ..      15      46 .. 0.80
   2 !   11.6   0.0   0.00056      0.23       3      26 ..     231     254 ..     229     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.009
                                  EEEEESTTSSHHHHH.HHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLi.nal 19
                                  v++vG+  +GK+tLi nal
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIkNAL 34
                                  89*************4444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00056
                                   EEEESTTSSHHHHHHHHHTSTEEE CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltgekaiv 26 
                                   ++vGr  vGK+t +++l++++ i+
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNKVYII 254
                                   79*****************97655 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0014      0.58      17      44 ..      17      44 ..       5      80 .. 0.88
   2 !    7.6   0.0    0.0055       2.2      16      39 ..     230     253 ..     216     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                       Pox_A32 17 alvGgsGsGktvyLlsLlrtlvkkykhi 44
                                   lvG+ GsGkt+ +++ l    +++k i
  gi|70606668|ref|YP_255538.1| 17 GLVGKNGSGKTTLIKNALCLGQNRFKII 44
                                  59**************998888888877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                       Pox_A32  16 lalvGgsGsGktvyLlsLlrtlvk 39 
                                   l lvG  G Gkt+ L+ L++++  
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKVYI 253
                                   789***************999765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.023       9.4      11      33 ..      14      36 ..       9     157 .. 0.66
   2 !    8.4   0.0    0.0062       2.5       9      34 ..     226     251 ..     221     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                        AAA_19 11 kvllvtaGpGtGKTrvlkhival 33
                                  +++ +++  G+GKT+++k ++ l
  gi|70606668|ref|YP_255538.1| 14 DIVGLVGKNGSGKTTLIKNALCL 36
                                  677889999******99987654 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0062
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivall 34 
                                   + ++l++++  G GKT++lk+ v+ +
  gi|70606668|ref|YP_255538.1| 226 EGEILCLVGRNGVGKTTTLKKLVNKV 251
                                   5678999*************998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.041        17       3      17 ..      18      32 ..      16      56 .. 0.85
   2 !   10.2   0.0    0.0019      0.75       1      23 [.     230     252 ..     230     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                  RNA_helicase  3 lyGpsgeGKStlake 17
                                  l+G++g GK+tl+k+
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIKN 32
                                  78**********998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0019
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   ++l+G++g+GK+t+ k+L++++ 
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKVY 252
                                   5899*************999875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0026       1.1       8      39 ..      23      48 ..      19      66 .. 0.77
   2 ?    6.3   0.0     0.018       7.2       8      40 ..     237     269 ..     232     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
               Viral_helicase1  8 GcGKStlirkllrtsliltvnrptaelltegk 39
                                  G+GK+tli+++l+       ++++++++ +g 
  gi|70606668|ref|YP_255538.1| 23 GSGKTTLIKNALCL------GQNRFKIILDGD 48
                                  9***********99......666666666655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
               Viral_helicase1   8 GcGKStlirkllrtsliltvnrptaelltegk.p 40 
                                   G GK+t ++kl+++   +   +p    +++++ +
  gi|70606668|ref|YP_255538.1| 237 GVGKTTTLKKLVNKV-YIIFQNPDLQFFKPRViD 269
                                   99***********95.333445557777777652 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.6    0.0041       1.7       1      18 [.      16      33 ..      16     132 .. 0.84
   2 !    9.7   0.1     0.003       1.2       2      22 ..     231     251 ..     230     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0041
                        AAA_18  1 IlltGtpGvGKttlakeL 18
                                  ++l G+ G+GKttl k+ 
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNA 33
                                  6899***********987 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.003
                        AAA_18   2 lltGtpGvGKttlakeLskrl 22 
                                   +l G  GvGKtt  k L ++ 
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNKV 251
                                   789999***********9984 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.022         9       4      22 ..      18      36 ..      15      51 .. 0.80
   2 !    8.5   0.0    0.0046       1.9       2      20 ..     230     248 ..     229     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                                  EE--SSSSHHHHHHHGGGG CS
                         AAA_5  4 LvGppGtgKselaerlaaa 22
                                  LvG+ G+gK++l++  + +
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIKNALCL 36
                                  9***********9987655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0046
                                   EEEE--SSSSHHHHHHHGG CS
                         AAA_5   2 vlLvGppGtgKselaerla 20 
                                   ++LvG  G+gK++  ++l 
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLV 248
                                   79***********998875 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015         6       4      19 ..      16      31 ..      13      37 .. 0.86
   2 !    7.8   0.0    0.0062       2.5       4      42 ..     230     269 ..     227     271 .. 0.70
   3 ?   -2.5   0.0       9.8     4e+03      55      75 ..     343     363 ..     339     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                     PduV-EutP  4 illiGkvgsGKttLtq 19
                                  + l+Gk gsGKttL +
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIK 31
                                  559***********87 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0062
                     PduV-EutP   4 illiGkvgsGKttLtqal.kgeelkYkktqaiefsdeviD 42 
                                   + l+G+ g+GKtt  ++l ++  ++++      f+++viD
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLvNKVYIIFQNPDLQFFKPRVID 269
                                   579********87655551556777777666666666666 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 9.8
                     PduV-EutP  55 salivtsaeadvialvqdate 75 
                                   +a+i+++++ d++ l+ ++++
  gi|70606668|ref|YP_255538.1| 343 KAMIIATHDEDILSLCDKVVN 363
                                   689999999999999988765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0018      0.75      28      52 ..      18      42 ..      11     192 .. 0.87
   2 ?    4.4   0.0     0.042        17      26      44 ..     230     248 ..     213     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                                  EEESTTSSHHHHHHHHHHHCS---- CS
                       G-alpha 28 llGqseSGKsTilkqlkllykkgfs 52
                                  l+G+++SGK+T++k+  +l ++ f+
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIKNALCLGQNRFK 42
                                  89*************9999998864 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.042
                                   EEEEESTTSSHHHHHHHHH CS
                       G-alpha  26 llllGqseSGKsTilkqlk 44 
                                   l l+G ++ GK+T+lk+l 
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLV 248
                                   6789************986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.15        63       1      15 [.      19      33 ..      19      65 .. 0.78
   2 ?    9.1   0.0    0.0039       1.6       1      21 [.     233     253 ..     233     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.15
                                  EE-TTSSHHHHHHHH CS
                        AAA_17  1 lGgPGsGKgtqcekl 15
                                  +G  GsGK+t++++ 
  gi|70606668|ref|YP_255538.1| 19 VGKNGSGKTTLIKNA 33
                                  6889*******9876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0039
                                   EE-TTSSHHHHHHHHHHHHTE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygf 21 
                                   +G  G+GK+t ++klv k+ +
  gi|70606668|ref|YP_255538.1| 233 VGRNGVGKTTTLKKLVNKVYI 253
                                   6889************99865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.067        27      31      50 ..      11      30 ..       7      36 .. 0.81
   2 ?    7.1   0.0    0.0092       3.7      30      53 ..     224     247 ..     217     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                        AAA_25 31 pagelallaGapgtGKttla 50
                                    ++++ l+G  g+GKttl 
  gi|70606668|ref|YP_255538.1| 11 DDNDIVGLVGKNGSGKTTLI 30
                                  56677789**********96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0092
                        AAA_25  30 lpagelallaGapgtGKttlaldl 53 
                                   l++ge+  l+G+ g+GKtt +  l
  gi|70606668|ref|YP_255538.1| 224 LREGEILCLVGRNGVGKTTTLKKL 247
                                   5799***************87666 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.11        46       4      18 ..      18      32 ..      15      93 .. 0.88
   2 ?    8.2   0.0    0.0069       2.8       3      33 ..     231     270 ..     229     320 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                        AAA_28  4 itGgestGKTtllea 18
                                  ++G  ++GKTtl+++
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIKN 32
                                  78999*******974 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0069
                        AAA_28   3 vitGgestGKTtlleaLaar........gypvv.pEaare 33 
                                   +++G  + GKTt+l++L ++        + + + p++  e
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNKvyiifqnpDLQFFkPRVIDE 270
                                   79999************97744444334444444555555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.34   1.4e+02       6      24 ..      16      34 ..      12      53 .. 0.84
   2 ?    8.6   0.0    0.0031       1.3       7      50 ..     231     275 ..     228     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.34
                                  EEEEESTTSSHHHHHHHHH CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLl 24
                                  +g++g   +GKtTL+ + l
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNAL 34
                                  78899999******98755 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                                   EEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHSTHCHSHHHH CS
                      GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgeka.eeervlDtlkeEr 50 
                                   +++g    GKtT++ +L+ k  +i ++   +  + rv+D  k+E+
  gi|70606668|ref|YP_255538.1| 231 CLVGRNGVGKTTTLKKLVNKVYIIFQNPDLQfFKPRVIDEVKDEE 275
                                   67888889******************99999766999***99997 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.13        53      18      36 ..      16      34 ..      11      48 .. 0.81
   2 ?    7.2   0.0     0.005         2      14      39 ..     226     251 ..     220     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                 TrwB_AAD_bind 18 ilivGttGsGKtqalekll 36
                                  + +vG  GsGKt+ +++ l
  gi|70606668|ref|YP_255538.1| 16 VGLVGKNGSGKTTLIKNAL 34
                                  5799*********999866 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.005
                 TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrai 39 
                                   e + + +vG  G GKt++l+kl++++
  gi|70606668|ref|YP_255538.1| 226 EGEILCLVGRNGVGKTTTLKKLVNKV 251
                                   6666789***************9876 PP

>> VirE  Virulence-associated protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.15        62      54      77 ..      15      41 ..      10     121 .. 0.80
   2 ?    7.3   0.0    0.0083       3.4      53      77 ..     228     252 ..     222     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                          VirE 54 vlvLvGkqgsgKstflek...lgeewf 77
                                  ++ LvGk gsgK+t++++   lg++ f
  gi|70606668|ref|YP_255538.1| 15 IVGLVGKNGSGKTTLIKNalcLGQNRF 41
                                  6789**********9985322466655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0083
                          VirE  53 fvlvLvGkqgsgKstfleklgeewf 77 
                                   ++l LvG  g+gK+t+l+kl ++ +
  gi|70606668|ref|YP_255538.1| 228 EILCLVGRNGVGKTTTLKKLVNKVY 252
                                   7999****************77755 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.024       9.6       9      25 ..      18      35 ..      14      62 .. 0.83
   2 ?   -3.2   0.1       9.5   3.9e+03     122     149 ..     151     178 ..     148     199 .. 0.56
   3 ?    6.2   0.2     0.013       5.3       7      30 ..     230     253 ..     227     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.024
                                  EEEBTTSSCCCCC.CTTS CS
                        Septin  9 vvGesglGkttli.ntlf 25
                                  +vG++g Gkttli n+l+
  gi|70606668|ref|YP_255538.1| 18 LVGKNGSGKTTLIkNALC 35
                                  79***********44565 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.5
                                   TTSSSS-HHHHHHHHHHTTTS-EEEEES CS
                        Septin 122 PtghglkpldvelmkklsekvnliPvia 149
                                   P+g  + +  ++ ++ l +kv li  i 
  gi|70606668|ref|YP_255538.1| 151 PKGSLIAEHRIKEIRDLVSKVYLIKEIN 178
                                   5555555555555555555555554443 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                                   EEEEEBTTSSCCCCCCTTSSSS-- CS
                        Septin   7 lmvvGesglGkttlintlfetdli 30 
                                   l +vG++g+Gktt ++ l+++  i
  gi|70606668|ref|YP_255538.1| 230 LCLVGRNGVGKTTTLKKLVNKVYI 253
                                   5689**************998765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0031       1.3      16      35 ..      10      29 ..       5      44 .. 0.85
   2 ?    1.0   0.0      0.61   2.5e+02      15      34 ..     223     242 ..     208     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                                  HHH-SEEEEE--TTSSTTHH CS
                          PhoH 16 lkkndivfaiGpaGtGKtyl 35
                                  +++ndiv  +G+ G+GKt l
  gi|70606668|ref|YP_255538.1| 10 IDDNDIVGLVGKNGSGKTTL 29
                                  779***************87 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.61
                                   HHHH-SEEEEE--TTSSTTH CS
                          PhoH  15 alkkndivfaiGpaGtGKty 34 
                                    l++ +i++ +G+ G GKt 
  gi|70606668|ref|YP_255538.1| 223 KLREGEILCLVGRNGVGKTT 242
                                   466889************95 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.14        59      44      64 ..      10      30 ..       3      42 .. 0.79
   2 ?    6.3   0.0     0.018       7.3      39      61 ..     217     241 ..     202     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                     IstB_IS21 44 iekkenivllGpsGvGKshla 64
                                  i++++ + l+G  G GK+ l 
  gi|70606668|ref|YP_255538.1| 10 IDDNDIVGLVGKNGSGKTTLI 30
                                  78899999**********883 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                     IstB_IS21  39 atlsfie..kkenivllGpsGvGKs 61 
                                    + s+i+  + e ++l+G  GvGK+
  gi|70606668|ref|YP_255538.1| 217 FEYSWIKlrEGEILCLVGRNGVGKT 241
                                   5678987214567999********9 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0026       1.1      61      83 ..     123     145 ..      88     151 .. 0.82
   2 ?   -1.3   0.0       6.5   2.6e+03      65      80 ..     312     327 ..     287     336 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0026
                       SbcCD_C  61 epalrlvfLDEAFsklDeesiat 83 
                                   +++++ ++LDE F++lD+ s++ 
  gi|70606668|ref|YP_255538.1| 123 SSNPKHILLDEPFANLDKYSTKL 145
                                   456889***********988765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.5
                       SbcCD_C  65 rlvfLDEAFsklDees 80 
                                   +++ +DE   ++D+e 
  gi|70606668|ref|YP_255538.1| 312 KVIGFDEPSVGMDGEA 327
                                   4556777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.39
# Mc/sec: 2840.97
//
Query:       gi|70606669|ref|YP_255539.1|  [L=419]
Description: hypothetical protein Saci_0881 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.4   2.1        0.2   11.8   0.1    2.8  3  DUF4752   Domain of unknown function (DUF4752)
        0.1   12.5   0.2       0.23   11.4   0.2    1.6  1  DUF5486   Family of unknown function (DUF5486)


Domain annotation for each model (and alignments):
>> DUF4752  Domain of unknown function (DUF4752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.075   6.7e+02      11      29 ..       9      27 ..       3      30 .. 0.79
   2 ?   11.8   0.1   2.2e-05       0.2      57      83 ..      29      55 ..      18      56 .. 0.82
   3 ?   -1.9   0.1      0.41   3.7e+03      19      33 ..     322     336 ..     303     375 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.075
                       DUF4752 11 lallgwlyimfksgrWlvs 29
                                  l l+ w++++ k++  l+ 
  gi|70606669|ref|YP_255539.1|  9 LNLVHWIFVIMKAFDLLIY 27
                                  67999*******9988775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.2e-05
                       DUF4752 57 ldslepGstirvatkgdlviliyreee 83
                                  +++++pGs i v+t+++++ili +e++
  gi|70606669|ref|YP_255539.1| 29 FEHIKPGSLIAVKTRDNFTILIKKEDD 55
                                  379*******************99875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.41
                       DUF4752  19 imfksgrWlvsvllK 33 
                                   i ++s+  l s ++ 
  gi|70606669|ref|YP_255539.1| 322 IDYQSFDKLLSNFVN 336
                                   455555555544443 PP

>> DUF5486  Family of unknown function (DUF5486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.6e-05      0.23       3      28 ..      53      79 ..      51      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                       DUF5486  3 eidynkirs.sreemmrrfkeahdkak 28
                                  e dy  i s  +e+ mr+fke ++ka 
  gi|70606669|ref|YP_255539.1| 53 EDDYTVIASiCKENNMRKFKEVYNKAT 79
                                  669999998568999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2630.71
//
Query:       gi|70606670|ref|YP_255540.1|  [L=102]
Description: hypothetical protein Saci_0882 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-28   97.8   5.4    3.2e-28   97.5   5.4    1.1  1  HTH_45        Winged helix-turn-helix
    0.00018   21.3   0.4     0.0002   21.1   0.4    1.3  1  DUF4364       Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.015   14.3   0.3       0.02   13.9   0.3    1.1  1  Topoisom_bac  DNA topoisomerase
      0.018   14.4   0.3      0.022   14.1   0.3    1.3  1  DUF2119       Uncharacterized protein conserved in archaea (D
      0.023   13.1   2.1      0.025   13.0   2.1    1.0  1  DUF505        Protein of unknown function (DUF505)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   5.4   8.8e-32   3.2e-28       1      75 [.      11      84 ..      11      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 8.8e-32
                        HTH_45  1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                  +R+++eIi+dIL ++ e++akkT++mykanLsy+l+n+Y+++Lvek+li+++++ Y+lT+kG++lle lke++++
  gi|70606670|ref|YP_255540.1| 11 KRTRYEIIHDILAQC-ENGAKKTWLMYKANLSYELTNNYINKLVEKQLISQKDGLYYLTDKGKKLLELLKEYKDK 84
                                  8**************.9******************************************************9986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.4   5.7e-08    0.0002      26      75 ..      35      80 ..      14      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-08
                       DUF4364 26 leneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfen 75
                                  + +  ++Y   ++++++Lve++li++    ++ ly +T+kGk+ lel+++
  gi|70606670|ref|YP_255540.1| 35 MYKANLSYELTNNYINKLVEKQLISQ----KDGLYYLTDKGKKLLELLKE 80
                                  56677899999**************5....88**************9986 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   5.5e-06      0.02     348     393 ..      47      94 ..      45      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                  Topoisom_bac 348 eiieklvergYverkkkslvptelGkalvellekf..kdlvspelTae 393
                                   + i+klve++ + +k + ++ t++Gk+l ell+++  k+ +   +T++
  gi|70606670|ref|YP_255540.1|  47 NYINKLVEKQLISQKDGLYYLTDKGKKLLELLKEYkdKKTALDRVTSQ 94 
                                   579***********8899**************8884444555566665 PP

>> DUF2119  Uncharacterized protein conserved in archaea (DUF2119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   6.3e-06     0.022      30      73 ..      40      83 ..       7      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.3e-06
                       DUF2119 30 edlsegllvipnlekskYiSTldkeyyeseegkklidlveklkp 73
                                    ++ +  +i++l +++ iS  d  yy +++gkkl++l++++k 
  gi|70606670|ref|YP_255540.1| 40 LSYELTNNYINKLVEKQLISQKDGLYYLTDKGKKLLELLKEYKD 83
                                  55666778999*******************************97 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.1   6.9e-06     0.025     333     406 ..       8      80 ..       4      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                        DUF505 333 GRkleempkkkeeiakkfeeakdlekWyednfdlreaLysLesfeLieseveekgkevyvlTeyGekvledqek 406
                                   GRk    ++  ++i  + e+ ++   W+  + +l  +L +    +L+e+++ ++ +  y+lT++G+k+le +++
  gi|70606670|ref|YP_255540.1|   8 GRKKRTRYEIIHDILAQCENGAKK-TWLMYKANLSYELTNNYINKLVEKQLISQKDGLYYLTDKGKKLLELLKE 80 
                                   566556666666666666665555.4998888888889888889999999988889999999999999997754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 694.62
//
Query:       gi|70606671|ref|YP_255541.1|  [L=493]
Description: ammonia transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-94  316.2  25.0      3e-94  315.9  25.0    1.1  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.9  25.0   1.7e-98     3e-94       1     399 []      56     465 ..      56     465 .. 0.92

  Alignments for each domain:
  == domain 1  score: 315.9 bits;  conditional E-value: 1.7e-98
                                   HHHHHHHHHHHHH.HHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-........... CS
               Ammonium_transp   1 aflllsaalvifm.qagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign........... 69 
                                   a++l++a lv +   +g+al++agl+++k ++n+++  + ++a+v+l++++ G+ + fg   ++ ++ g            
  gi|70606671|ref|YP_255541.1|  56 AWMLIAATLVGLQsIPGVALFYAGLTKKKYTVNTMFLIFYAFAAVLLVWIIAGFNFGFGYP-SLLSIKGLgilgypvpawq 135
                                   7************9*********************************************87.5555555556577888776 PP

                                   ......TTTTSCCGCCTTCCHHH........HHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS CS
               Ammonium_transp  70 ......lglsaagvqdetlldgl........fflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwg 136
                                         + +   +                  +++fq++faa++  +  g+v eri+ +a+++f  +++ lvy+p+a+w ++
  gi|70606671|ref|YP_255541.1| 136 glymaeQAVYGPSG--------TplnipmstYIIFQFVFAAITPILLVGSVIERINYKAWMIFVPVWSLLVYSPLAYWLFA 208
                                   65544422222222........1334455559************************************************* PP

                                   .SSHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSH CS
               Ammonium_transp 137 eggwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltank 217
                                    ggwl++lg++ Df g+ v+Hl++g+ +Laaal +g+r       e+++++hnl+++++Gt l+w+gW gFN+G   +a+ 
  gi|70606671|ref|YP_255541.1| 209 -GGWLNQLGAV-DFSGGYVIHLNAGIGALAAALAVGPRLAE----ERKLEPHNLSLILIGTGLIWLGWNGFNGGDPGGATI 283
                                   .**********.***************************75....69********************************99 PP

                                   HHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHH CS
               Ammonium_transp 218 rararaavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkek 298
                                    a+  a+++T lAaa++a+t+++++    +k++++g+a G++ GlVAiT+a+++++ wg++iiG+ +g l  l++ kl+ k
  gi|70606671|ref|YP_255541.1| 284 DAAI-AVLNTDLAAAISAITWIIMDMKFFKKPTLVGAATGAITGLVAITPAAGYIDAWGSIIIGIASGSLPWLSLYKLEPK 363
                                   9999.*********************************************************************99***** PP

                                   HTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC..SSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
               Ammonium_transp 299 lkidDsldvvavHgvgGiwGllavgifaaekvv..askisggllsgegkqlvvqligilvilayafvvtlilllllklllg 377
                                   l++dD+l+v++ Hg++G++G+l++g++a+++v   +    +g l+g+  ql++q++++l++++y+f vt+ ll+l++l++ 
  gi|70606671|ref|YP_255541.1| 364 LRVDDTLGVFSSHGIAGLVGGLLTGVLADPSVSqyILPGLTGALYGNLYQLGIQAFAALIVTIYTFFVTYGLLKLIGLFVP 444
                                   *******************************99888888999*************************************** PP

                                   SB--HHHHHHSHHHHHHSSSSB CS
               Ammonium_transp 378 LrvseeeeevglDvaehgetay 399
                                   Lr s e+e +  D   hge ay
  gi|70606671|ref|YP_255541.1| 445 LRAS-EAELKVGDYLMHGEVAY 465
                                   ***5.55555567778***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3423.06
//
Query:       gi|70606672|ref|YP_255542.1|  [L=293]
Description: serine/threonine protein phosphatase catalytic subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-26   92.1   1.1    8.9e-26   91.7   1.1    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    5.2e-06   26.8   0.0    7.1e-06   26.3   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   1.1   9.9e-30   8.9e-26       2     203 ..      31     240 ..      31     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 9.9e-30
                                   EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS...HHHHHHHHHHHHHHHH.....TSEEEEEC-TT CS
                   Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg...dlekellellaalvky.....pipvylllGNH 74 
                                   +++++gD+H     g ++ ++ +++++ +  ++dl++++GD+vdr    ++e+ l   l++l+++     ++++++l+GNH
  gi|70606672|ref|YP_255542.1|  31 KVVFVGDTH-----GAINVTEYVFRKFYD--NVDLIVFLGDYVDREpqtGVEN-LSLILKKLIESdenkgKTKIVVLRGNH 103
                                   79*******.....**********99955..59************97776666.66667777777999999999******* PP

                                   S....CHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE.......THHHHHHHHHHHSCHH CS
                   Metallophos  75 e....gfeeellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspel.......lvsldklgslnlelea 143
                                   e    +f+++ ++  + ++++  + ++++ + f+++p ++l++g   +l++hGg p         +++++++ +l++++ +
  gi|70606672|ref|YP_255542.1| 104 EspltNFHYGFFEELKIKTEDaENAYEKFRDLFSYMPYSVLVNG---YLCMHGGLPATlegdrlgITTVEDIAKLKYPDIN 181
                                   **999555544444444444456889999***********9999...*******6666688899**************999 PP

                                   HHCC...HHHHHHHHHHTTCSEEEEEESSESS.CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                   Metallophos 144 pepg...dewlkdlekrekadwvivlgHsply.rgsgylfgdealedllkkygvdlvisGHtHv 203
                                   p++    +++++d     ++d ++ +   p     + y+fg++++ ++l +++ + +i+GH+ v
  gi|70606672|ref|YP_255542.1| 182 PDDPvglQILWND-----PRDGLLDIDFLPSIrGEGIYYFGERVTNEFLSYNNFKGIIRGHEAV 240
                                   9999*********.....6666666666666666779************************975 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     8e-10   7.1e-06       2      63 ..      31     116 ..      31     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8e-10
                 Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDleeeep.......e.vleellela......pvlaVrGNnD...... 62 
                                   k++++ D+H++++ +e v++++ +  vd+i+++GD+ ++ep       + +l++l+e        ++++ rGN++      
  gi|70606672|ref|YP_255542.1|  31 KVVFVGDTHGAINVTEYVFRKFYDN-VDLIVFLGDYVDREPqtgvenlSlILKKLIESDenkgktKIVVLRGNHEspltnf 110
                                   6899******************999.9********855555445544435666666666889999**********766555 PP

                 Metallophos_2  63 .....e 63 
                                        e
  gi|70606672|ref|YP_255542.1| 111 hygffE 116
                                   433331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1990.06
//
Query:       gi|70606673|ref|YP_255543.1|  [L=395]
Description: hypothetical protein Saci_0885 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-54  185.2   0.0    1.8e-54  184.6   0.0    1.2  1  MR_MLE_C  Enolase C-terminal domain-like
    5.1e-15   55.7   0.0    9.7e-15   54.8   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.6   0.0     2e-58   1.8e-54       2     219 ..     143     365 ..     142     366 .. 0.95

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 2e-58
                                   HHHHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTE CS
                      MR_MLE_C   2 laeearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldl 74 
                                   +ae+a++ +++ g++a+K++++g+         ++e  erv+avreavg+  +vd++++ ++++++++ i +a++le +++
  gi|70606673|ref|YP_255543.1| 143 FAEKAKNVIRM-GYKALKFDPFGPyfnsidekGLQEAEERVKAVREAVGE--NVDILIEHHGRFNANASILIAKRLENYNP 220
                                   68899887777.************************************66..66**********************99*** PP

                                   SEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEE CS
                      MR_MLE_C  75 lwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvap 154
                                    ++EEPv++ +d+egl++ ++ a  +++a+gE+l +++++++++ +g vdivqpdv+++gGi+  rkv++l eaf+v++a+
  gi|70606673|ref|YP_255543.1| 221 GFMEEPVHH-EDIEGLRKYKS-AtVLKVALGERLIGVKEAANYIGDGLVDIVQPDVCNIGGISVGRKVIHLSEAFDVEIAF 299
                                   ********9.57********6.4489******************************************************* PP

                                   BSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH.TSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                      MR_MLE_C 155 Hsgsgglglaaslhlaaaipnllileyfldael.leeelleeplevedGrvtvpdgpGlGveldee 219
                                   H+  g+++ a+sl+laa +pnl +le f+d+ + ++++++ ++++ve G+v vp++pG+Gv ++e+
  gi|70606673|ref|YP_255543.1| 300 HNAFGSIQNAYSLQLAAIAPNLYFLENFYDWFPrWKRDIVYDETKVEGGYVNVPNKPGIGVSVNEK 365
                                   **658*************************9999*****************************986 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   1.1e-18   9.7e-15      14     117 .]       8     119 ..       2     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 1.1e-18
                                   CEEEETTEEEEEEE....EEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS.. CS
                      MR_MLE_N  14 rPvqlavttvqkqs....lvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg.. 88 
                                   +P++la t  + ++    ++lv++ ts+G+vG gea++   r  +++  +++ +    +gk+a++ ++  ++ +r+ ++  
  gi|70606673|ref|YP_255543.1|   8 EPIVLAQTEKGSATwasvMILVRVVTSNGMVGFGEAVPTL-RVINVYNTIKQ-VSKGYLGKEAEEPEKNYHEWYRQDFYlp 86 
                                   5777777766665422226799****************99.99999999998.99999*****************999999 PP

                                   ....CHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                      MR_MLE_N  89 ....nmsAkaaidmAlwDlkakalnlpladLlG 117
                                        ++A +aid+AlwD+++k l++p+++LlG
  gi|70606673|ref|YP_255543.1|  87 rsfeSATATSAIDQALWDILGKELGAPIYKLLG 119
                                   **9999**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2402.13
//
Query:       gi|70606674|ref|YP_255544.1|  [L=493]
Description: inorganic phosphate transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-54  185.9  23.7    1.6e-54  185.5  23.7    1.1  1  Sugar_tr        Sugar (and other) transporter
    2.1e-30  105.8  37.0    1.7e-25   89.7  32.8    2.1  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.28   11.0   5.9        1.6    8.5   0.0    2.7  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
        0.6    8.3  10.1       0.15   10.3   4.2    2.3  2  BT1             BT1 family


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5  23.7   3.6e-58   1.6e-54       7     449 ..      27     482 ..      22     484 .. 0.89

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 3.6e-58
                                   HHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH........HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                      Sugar_tr   7 lggllfgYdtgvigafltllkfaknfglsksksskee.....ssvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                   +g +   Yd+ +i+++l+++  a++++  +  + +e      ++ ++gl++s+++  aiiG+l++g++gdr+GRkk++ + 
  gi|70606674|ref|YP_255544.1|  27 MGFFTDAYDLLIISYILAVMIDAYKYYGFNMAGFTEYlignqATFWTGLLASSAIWTAIIGQLVFGYIGDRLGRKKVYGVE 107
                                   5558889**********9999999999999998888899999*************************************** PP

                                   HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnk 163
                                   a l+ +ga+l+a+++   ++ +li+ R ++G+g+G+ + ++ + +sE++  k Rg+lv l  +  ++G + a i+g++ + 
  gi|70606674|ref|YP_255544.1| 108 ASLLTAGALLSALSP---NLPLLILFRSIMGLGIGGDYPISATIMSEYSNVKDRGKLVALVFSNQALGSIAALIVGVVAAL 185
                                   ***************...9************************************************************99 PP

                                   SS-.TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH.HHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH...... CS
                      Sugar_tr 164 tsn.adgwrillglqlvpallllilllflPESPryl.vekgkeeeakevlaklrgeedadrelaeekdsleaeqeee.kas 241
                                   t   +  wr++ g+ ++pa ++++l+  +PE+Pry  + kg+ eeak+  + +  + +++++l++  +s++ +  +   ++
  gi|70606674|ref|YP_255544.1| 186 TLPpDIAWRVMAGFGAIPAATVIYLRRKVPETPRYSlIAKGDVEEAKKAAQFVGANLQVKDSLKAPNSSTKLNIMTFlRNY 266
                                   98889******************************6599*************99999999999999999998855446556 PP

                                   HTTHHHHSH......HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH....HHHHHHHHHHHHHHHHHHHHHHHHS- CS
                      Sugar_tr 242 wkellsskt...vrqrlligvvlqifqqltGinaimyysptifenlglsks....llvtiivgvvnfvatfvaiflvdrfG 315
                                      l+++ +   ++  +++g ++ +    t i+    +s+ti++ + ++ +    l + +i + v f   f a+ l+d++G
  gi|70606674|ref|YP_255544.1| 267 SLLLIGTAGtwfILDIAFYGTGVYSSSVITPIFG-SPFSSTITSITEFQSElakqLFIGGIPYLVGFPGYFTAVALIDKLG 346
                                   6666666665555556666666666666666544.35899********999999989999999****************** PP

                                   SHHHHHHHHHHHHHHHHHHH...HHHHTTSS...CHHHHHHHHHH...HHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHH CS
                      Sugar_tr 316 RRtllllGaagmaicfvilg.ivalllvakskaasivaivfialf...ialfalgwgpvpwvlvsElfpqsvRskalaiav 392
                                   R+ + + G+++m i+  i++   + ++++   + +i a+v+++l+   +++  +g +++ +v+ sE++p+++Rs++  i++
  gi|70606674|ref|YP_255544.1| 347 RKLIQVQGFIVMGILYGIVSlVLFQAGKSI--SFTIPATVAFILYsltFFFIDFGANTTTFVIPSEVYPTKFRSTGHGISA 425
                                   *******************94444444444..455555555555533278889**************************** PP

                                   HHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCG CS
                      Sugar_tr 393 avnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeie 449
                                   a+  l   ++++lfp ++ +ig   +f++ +++ ++++i + + +pe k ++le++ 
  gi|70606674|ref|YP_255544.1| 426 ASGKLGAAITTYLFPSLVASIGFRNIFVLLTAVSIIGAILTIVLIPEPKMKSLEDVA 482
                                   ******************************************************986 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7  32.8   3.7e-29   1.7e-25      30     352 ..      67     435 ..      25     436 .. 0.71
   2 !   28.0   6.8   2.1e-10   9.5e-07      66     187 ..     364     485 ..     363     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 3.7e-29
                         MFS_1  30 spse..igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaa 108
                                   + ++   gll++   ++a++++l++G+++dr+Gr++v+ + + l+ +g+ll +++++l+ll+++r ++Glg g+ +p++a+
  gi|70606674|ref|YP_255544.1|  67 NQATfwTGLLASSAIWTAIIGQLVFGYIGDRLGRKKVYGVEASLLTAGALLSALSPNLPLLILFRSIMGLGIGGDYPISAT 147
                                   222256899***************************************56666779999********************** PP

                         MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslg....Wravfyilaivsllafvlfllllpeepperkrkspk 185
                                   +++++++ ++rg+ ++l+ +  +lG+i + ++g + a  l     Wr++  + ai ++ +     ++l+++ pe +r s +
  gi|70606674|ref|YP_255544.1| 148 IMSEYSNVKDRGKLVALVFSNQALGSIAALIVGVVAALTLPpdiaWRVMAGFGAIPAATV-----IYLRRKVPETPRYSLI 223
                                   ********************8888887777776666644445666999999999999998.....5666666666666666 PP

                         MFS_1 186 eee......................kgtgpaplvp........awkallkdpvl.......willialllfffgfsglltl 229
                                    ++                      k                 + + l++   l       w++l ++++++ g+++ ++ 
  gi|70606674|ref|YP_255544.1| 224 AKGdveeakkaaqfvganlqvkdslK--------ApnsstklnIMTFLRNYSLLligtagtWFILDIAFYGT-GVYSSSVI 295
                                   66666888999888888766655432........12333445455555555544555555553333333333.44445555 PP

                         MFS_1 230 lplylqevlgls.........glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.... 297
                                   +p++  + +  +          l   +++ ++++lvg+++ + a +l+d+lgr+ + + +++++ +++ ++ l+ +     
  gi|70606674|ref|YP_255544.1| 296 TPIF-GSPFSSTitsitefqsELAKQLFIGGIPYLVGFPGYFTAVALIDKLGRKLIQVQGFIVMGILYGIVSLVLFQagks 375
                                   5554.4444444666666667577777789**********99999999*****8888888888888888888888886544 PP

                         MFS_1 298 ...ssavllll....vlvliGfglgfv....fpsllalasdlappeeagtasglfntagslggalg 352
                                      +      +    +++l++++++f+    +++ +++ s+++p++ + t  g+    g lg+a+ 
  gi|70606674|ref|YP_255544.1| 376 isfT------IpatvAFILYSLTFFFIdfgaNTTTFVIPSEVYPTKFRSTGHGISAASGKLGAAIT 435
                                   4331......134444455444444445555*******************************9985 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2.1e-10
                         MFS_1  66 llglllfalg.lllllfa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggl 143
                                   +++l+lf +g ++ ++++ +  + l  +  ++  +ga   +++  ++ ++++p + r+ + g+ +a+  lGa+++  l + 
  gi|70606674|ref|YP_255544.1| 364 IVSLVLFQAGkSISFTIPaTVAFiLYSLTFFFIDFGA---NTTTFVIPSEVYPTKFRSTGHGISAASGKLGAAITTYLFPS 441
                                   5677777777555555322334446667777888886...999********************************999999 PP

                         MFS_1 144 lasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                   l++s+g+r +f++l++vs+++++l ++l+pe++ ++  +  kee
  gi|70606674|ref|YP_255544.1| 442 LVASIGFRNIFVLLTAVSIIGAILTIVLIPEPKMKSLEDVAKEE 485
                                   999*********************88999888877777776666 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   2.9      0.03   1.3e+02      99     130 ..     375     406 ..     344     407 .. 0.83
   2 ?    8.5   0.0   0.00036       1.6      25      62 ..     422     459 ..     418     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.03
                                   HHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHH CS
                Sterol-sensing  99 galtdvpavqeFclfaavavlvdFllqitfFv 130
                                   ++++++pa  +F l++   +++dF    t Fv
  gi|70606674|ref|YP_255544.1| 375 SISFTIPATVAFILYSLTFFFIDFGANTTTFV 406
                                   456799***********************997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00036
                                   CHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHH CS
                Sterol-sensing  25 gllaylgltltliilevlPflvlavgvdnifvlvkavq 62 
                                   g+ a+ g     i++ ++P lv  +g  nifvl++av 
  gi|70606674|ref|YP_255544.1| 422 GISAASGKLGAAITTYLFPSLVASIGFRNIFVLLTAVS 459
                                   56666666677888999*****************9986 PP

>> BT1  BT1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2     0.033   1.5e+02     118     170 ..     154     206 ..     144     246 .. 0.75
   2 ?   10.3   4.2   3.3e-05      0.15     294     392 ..     379     470 ..     349     477 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.033
                           BT1 118 spkagpsLvSwiwlvsavGgiiasvlsGpLldagktrisvlvsaalqlltvvv 170
                                   + k  ++Lv +++   a+G+i a +++ + + +  + i+  v+a + ++    
  gi|70606674|ref|YP_255544.1| 154 NVKDRGKLVALVFSNQALGSIAALIVGVVAALTLPPDIAWRVMAGFGAIPAAT 206
                                   45566799999999999999755444444556667889999998888876544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 3.3e-05
                           BT1 294 alplviakanvFlyltkalylqlpgaldafylakaeClpdgPnfsyeflgtvkgvigsiagligvtlfnrllkklsyrlvf 374
                                   ++p    + ++ ly   + ++   +  ++ ++   e  p +  f  +  g+++   g+++  i++ lf  l + + +r++f
  gi|70606674|ref|YP_255544.1| 379 TIPA---TVAFILYSLTFFFIDFGA-NTTTFVIPSEVYPTK--FRSTGHGISA-ASGKLGAAITTYLFPSLVASIGFRNIF 452
                                   4444...344445555566565544.455566677888988..999999*999.99************************* PP

                           BT1 375 ivttvlqvlaglfdlilv 392
                                   ++ t ++++ ++++++l+
  gi|70606674|ref|YP_255544.1| 453 VLLTAVSIIGAILTIVLI 470
                                   ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3421.51
//
Query:       gi|70606675|ref|YP_255545.1|  [L=128]
Description: hypothetical protein Saci_0887 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-26   92.4   0.3    4.8e-26   92.0   0.3    1.2  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.3   2.7e-30   4.8e-26       4     141 .]       2     128 .]       1     128 [] 0.95

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 2.7e-30
                                   EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEE CS
                           Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvev 84 
                                   + l+a+Dgse+skkA+++ l+ +k+  +e+++++vi++ + ++     e+++++e  ++e  +              +   
  gi|70606675|ref|YP_255545.1|   2 KFLIAYDGSEQSKKAVRFLLRILKKE-DEVYVITVIKEAPRSPDQKIIEDEKKAEGLHKEVLE----------LFPSAKSA 71 
                                   78*******************99995.79***************9999999999999999755..........579999** PP

                                   EEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  85 vveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   ++e+gd+  +i+++ e+ ++d+iV+Gsrg++g++++++GSvs++++++a++p lvV+
  gi|70606675|ref|YP_255545.1|  72 IIESGDVVSTIIDYCERVNCDMIVTGSRGLTGIKKVVIGSVSSALIEKAKVPILVVK 128
                                   ********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 937.17
//
Query:       gi|70606676|ref|YP_255546.1|  [L=407]
Description: guanine deaminase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-55  189.4   0.1    1.3e-55  189.2   0.1    1.0  1  Amidohydro_1    Amidohydrolase family
    2.1e-15   57.2   0.0    2.9e-10   40.2   0.0    2.1  2  Amidohydro_3    Amidohydrolase family
      0.008   15.5   0.0      0.014   14.7   0.0    1.4  1  A_deaminase     Adenosine/AMP deaminase
  ------ inclusion threshold ------
      0.062   13.0   0.1       0.14   11.9   0.1    1.5  1  SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2   0.1   2.8e-59   1.3e-55       1     343 [.      52     384 ..      52     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 2.8e-59
                                   EEEE-EEEEEEECETTECSSS....GHHHHH.........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHH CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.........vppetaaealesgiktalksGtttvadmgattstgiealle 68 
                                   +v+PGlI+aH+H  +  +rg      l dwl         +++     ++e+ + ++l+ Gtt + dm++    + e ++e
  gi|70606676|ref|YP_255546.1|  52 VVIPGLINAHTHSGMMIFRGYyddsELADWLsriwdeerkMTQKVMNIGSEISVIEMLSKGTTGFVDMYF----NPEGVKE 128
                                   69********************************************************************....99***** PP

                                   HHHTSSSEEEEEEESSEGGS..GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                  Amidohydro_1  69 aaeelplglrilggkvsldr..gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlp 147
                                    ae++  g+r+++g+++ld   + +e++  +r+  ++             +k++++ h+ +++s ++lk a ++a++  + 
  gi|70606676|ref|YP_255546.1| 129 IAEKY--GIRVEAGYTFLDSmmEPHEVDSRQRKLSRT-----------NYFKPIVNVHSIYSTSVDTLKLAKQLAEETETR 196
                                   ****9..*******99999875444444444444433...........4567***************************** PP

                                   EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHH.SEH CS
                  Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsi.lrs 227
                                   ++iH++et++e++++++++g   ++  ++e++++l + ++    l+h  ++   e+e++       + +hcp+sn++  + 
  gi|70606676|ref|YP_255546.1| 197 IHIHVAETRNEIFQSKKKYG---KF--PVEFLHELNIVEI--SQLVHLGWVANWELEYV------EMATHCPTSNMKlATA 264
                                   ********************...55..****888777776..44666666666666663......34479*******4457 PP

                                   HHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-T CS
                  Amidohydro_1 228 grealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsiev 308
                                   g +++ +++++G++v++gtDg + +nsl++++e+++ ++lqr++++   ++ +++++al+ aT  g k +g+  k G+i++
  gi|70606676|ref|YP_255546.1| 265 GFFPFIDMIEKGKNVTIGTDGPSTNNSLDMFREMKNTVLLQRHSYW---DTRIKALHALKSATEEGYKLMGI--KGGKIKE 340
                                   9*********************************************...677********************..******* PP

                                   TSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 309 GkdADlvvvdl...di......laafvglkkdgnvkkvivkGkl 343
                                   G+ ADlv++d    ++       +++v+++   nv kvi++Gk+
  gi|70606676|ref|YP_255546.1| 341 GYMADLVLLDSdqlYPlkkdriVSNIVYNAVGENVSKVIIDGKI 384
                                   ***********76633778889********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-06     0.011       2      32 ..      45      73 ..      44     105 .. 0.79
   2 !   40.2   0.0   6.4e-14   2.9e-10     322     473 .]     231     386 ..     167     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                  Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggvnl.rllr 32
                                  +iD+++ +v+PG++ +HtH    g+++ r++ 
  gi|70606676|ref|YP_255546.1| 45 EIDCSNYVVIPGLINAHTH---SGMMIfRGYY 73
                                  8******************...5555545544 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 6.4e-14
                  Amidohydro_3 322 iervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrgge 400
                                   i+ +  l++ a +++ ++    +   + ++ ++ g +p+  ++++g +v+ g+D  +  +++d + ++  +v ++     +
  gi|70606676|ref|YP_255546.1| 231 ISQLVHLGWVANWELEYVEMATHCPTSNMKLATAGFFPFIDMIEKGKNVTIGTDgpSTNNSLDMFREMKNTVLLQR----H 307
                                   556667777777774444422233333334444555******************9778899************999....5 PP

                  Amidohydro_3 401 vlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear........vrltvvdGrvv 472
                                    + +d ++   +al+  T+++ k++g     G +++G++ADlv+ld +++  ++++++++          v+++++dG++ 
  gi|70606676|ref|YP_255546.1| 308 SY-WDTRIKALHALKSATEEGYKLMGIKG--GKIKEGYMADLVLLDsDQLYPLKKDRIVSNIvynavgenVSKVIIDGKIA 385
                                   55.5679**********************..***************766666777777776688889999*********98 PP

                  Amidohydro_3 473 y 473
                                   y
  gi|70606676|ref|YP_255546.1| 386 Y 386
                                   7 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-06     0.014     242     293 ..     252     301 ..     224     324 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                                   EE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BSCCCCT-S.HHHHHHHH CS
                   A_deaminase 242 evcPlSNvalgafleyaenPlkeflerglnvslntDDPlqfgtt.LieeYaia 293
                                   + cP+SN++l   ++    P+ + +e+g nv+++tD P   ++  +  e++ +
  gi|70606676|ref|YP_255546.1| 252 THCPTSNMKL---ATAGFFPFIDMIEKGKNVTIGTDGPSTNNSLdMFREMKNT 301
                                   56********...99999********************987765588888755 PP

>> SNCAIP_SNCA_bd  Synphilin-1 alpha-Synuclein-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.2e-05      0.14      12      29 ..     183     200 ..     175     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                SNCAIP_SNCA_bd  12 VKLTKQLkEQTaeRInlQ 29 
                                    KL KQL E T  RI + 
  gi|70606676|ref|YP_255546.1| 183 LKLAKQLAEETETRIHIH 200
                                   7**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2818.15
//
Query:       gi|70606677|ref|YP_255547.1|  [L=89]
Description: hypothetical protein Saci_0891 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-37  125.9   2.2    5.1e-37  125.8   2.2    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
      0.012   15.9   0.1       0.22   11.8   0.0    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)
      0.036   14.4   0.2      0.098   13.1   0.2    1.7  1  HEAT_2    HEAT repeats


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.8   2.2   8.6e-41   5.1e-37       1      81 []       7      87 ..       7      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 8.6e-41
                                  HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                       UPF0147  1 neekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                  ne+ki++++ +L++i++dtsvPrniRraa++a+++L+d++ s+avraa+ai iL+eis+DpnmP+h+R++iw+vvs LEt+
  gi|70606677|ref|YP_255547.1|  7 NEAKIRQAVGMLQKIVNDTSVPRNIRRAATDAIRNLQDQTLSPAVRAANAIGILEEISQDPNMPMHTRIAIWNVVSMLETV 87
                                  5899***************************************************************************97 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.22      27      58 ..      11      42 ..       5      48 .. 0.89
   2 ?    2.2   0.0     0.037   2.2e+02      30      48 ..      56      74 ..      44      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                       UPF0253 27 iscalktLdevaanealpeevrekAAyAAANL 58
                                  i+ a+  L++++++ ++p+++r  A  A  NL
  gi|70606677|ref|YP_255547.1| 11 IRQAVGMLQKIVNDTSVPRNIRRAATDAIRNL 42
                                  7789999****************999888887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.037
                       UPF0253 30 alktLdevaanealpeevr 48
                                  a+  L+e+ ++ ++p ++r
  gi|70606677|ref|YP_255547.1| 56 AIGILEEISQDPNMPMHTR 74
                                  6788999999999998776 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.6e-05     0.098      30      75 ..      12      68 ..       3      81 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                        HEAT_2 30 pealpaLvelleded..pavRraaaeaLgaigdpe.........alpaLkelldddd 75
                                  ++a+ +L ++++d++  +++Rraa +a+  ++d+          a+ +L+e+ +d++
  gi|70606677|ref|YP_255547.1| 12 RQAVGMLQKIVNDTSvpRNIRRAATDAIRNLQDQTlspavraanAIGILEEISQDPN 68
                                  577888888888877655788888888887765331111222225666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 613.38
//
Query:       gi|70606678|ref|YP_255548.1|  [L=119]
Description: hypothetical protein Saci_0892 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-14   53.6   0.2    2.6e-14   53.1   0.2    1.3  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.021   14.6   1.0      0.028   14.2   1.0    1.2  1  DUF592          Protein of unknown function (DUF592)
       0.13   12.3   0.5       0.26   11.3   0.5    1.5  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.2   4.3e-18   2.6e-14       1      40 []       8      46 ..       8      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 4.3e-18
                 Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                  kk++elL +G+tML+  CpvC++PL+r + +g+v+C++++
  gi|70606678|ref|YP_255548.1|  8 KKAAELLRQGATMLDIPCPVCNMPLFRLK-SGEVICPTHG 46
                                  799*************************6.79*****995 PP

>> DUF592  Protein of unknown function (DUF592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   4.6e-06     0.028      70     132 ..      49     116 ..      46     119 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-06
                        DUF592  70 Felkdkellnaiskvveveadseekvek......eeleDpLekkeivrlikdLqkainkvlstrlrlsn 132
                                   + +kd++  + i+ ++ +++ ++  v++      +  +Dp++ ++i ++i+ L+ ai++++ +r  l++
  gi|70606678|ref|YP_255548.1|  49 YIVKDEAEQKRIQTNFLMDSLESILVNNvekvaeKIKQDPMDTESITQIIRYLE-AIERIMRIRNGLEK 116
                                   56788888888888776555444444444445448899**************95.9*****99988875 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   4.4e-05      0.26       2      17 ..      25      41 ..      24      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                DNA_ligase_ZBD  2 CPvCGsavvR.eegeai 17
                                  CPvC+ ++ R + ge+i
  gi|70606678|ref|YP_255548.1| 25 CPVCNMPLFRlKSGEVI 41
                                  *********97888987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 950.52
//
Query:       gi|70606679|ref|YP_255549.1|  [L=194]
Description: thymidylate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-41  140.3   0.1    6.5e-41  140.0   0.1    1.0  1  Thymidylate_kin  Thymidylate kinase
    2.2e-06   27.7   4.3    7.5e-05   22.7   0.7    2.1  2  dNK              Deoxynucleoside kinase
    4.2e-05   24.1   0.0    0.00012   22.6   0.0    1.9  1  AAA_18           AAA domain
     0.0026   18.0   0.0     0.0043   17.3   0.0    1.4  1  AAA_28           AAA domain
     0.0033   17.5   0.2        0.4   10.8   0.1    2.1  2  SKI              Shikimate kinase
  ------ inclusion threshold ------
      0.019   14.3   1.7       0.41   10.0   0.1    2.2  2  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.045   13.9   0.0       0.49   10.5   0.0    2.5  2  AAA_33           AAA domain
      0.049   12.8   0.1      0.089   12.0   0.1    1.5  1  NB-ARC           NB-ARC domain
       0.05   14.0   0.2        4.6    7.7   0.0    2.6  3  AAA_17           AAA domain
       0.19   12.3   0.7       0.56   10.7   0.6    2.0  1  ABC_tran         ABC transporter


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.1   3.6e-44   6.5e-41       1     184 [.       6     182 ..       6     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 3.6e-44
                                   EEESTTSSHHHHHHHHHHHHH.HTTE...EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHH CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlk.eegik..vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalk 78 
                                   +EG+DG+GKtt++++++e+l  e g +  ++lt ep + ei ++i e+       ++ ++allf+adr++hl  + k+   
  gi|70606679|ref|YP_255549.1|   6 FEGIDGSGKTTISKIIYEKLLiEIGSNkkIILTSEPFSQEIIKLIEEIGW----KDPISLALLFTADRAYHLNLLFKQ--- 79 
                                   8****************998524444456*******************55....89*****************88887... PP

                                   TT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHH CS
               Thymidylate_kin  79 qgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrery 159
                                   + +++i+dRy++S++aYq+  + +d +++++ln+ ++ +Pdlt+lld++pe+a++R++ +  + ++  e++++l kvre+y
  gi|70606679|ref|YP_255549.1|  80 NPEIIIMDRYIDSTIAYQSSLG-IDENWIRNLNKYFP-EPDLTILLDLKPETAIARIKNKVDKFNF-DEKISTLSKVREKY 157
                                   778****************655.*************9.**********************995555.577889******** PP

                                   HHHHHTTSTEEEEETTS-HHHHHHH CS
               Thymidylate_kin 160 lelakederiliidasksieevhee 184
                                   lelak +++i i++a+ksi+e++ee
  gi|70606679|ref|YP_255549.1| 158 LELAKRNNKIRIVNAEKSIDEIVEE 182
                                   ********************99876 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.2     0.003       5.4       1      22 [.       4      25 ..       4      50 .. 0.90
   2 !   22.7   0.7   4.2e-08   7.5e-05      97     179 ..      91     173 ..      67     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                                  EEEEESTTSSHHHHHHHHHCCS CS
                           dNK  1 ivveGnIgaGKstlvklLskkl 22
                                  i+ eG  g+GK+t+ k++ +kl
  gi|70606679|ref|YP_255549.1|  4 ISFEGIDGSGKTTISKIIYEKL 25
                                  789*************998776 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 4.2e-08
                                   HTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEE CS
                           dNK  97 ekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlv 177
                                   ++ ++ ++ l i +++  nl++++++pdl i L++++et   rik++ ++++   +++ l k+ eky e  k  n++ ++ 
  gi|70606679|ref|YP_255549.1|  91 DSTIAYQSSLGIDENWIRNLNKYFPEPDLTILLDLKPETAIARIKNKVDKFNFDEKISTLSKVREKYLELAKRNNKIRIVN 171
                                   555666677777889************************************998889999999999999998877776554 PP

                                   EE CS
                           dNK 178 id 179
                                    +
  gi|70606679|ref|YP_255549.1| 172 AE 173
                                   44 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   6.7e-08   0.00012       3     113 ..       6     137 ..       4     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.7e-08
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf...........gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                     G+ G+GKtt++k + ++l +           ++  ++ + +   ++++ ++   +   l +  ++++l++l +++    
  gi|70606679|ref|YP_255549.1|   6 FEGIDGSGKTTISKIIYEKLLIeigsnkkiiltSEPFSQEIIKLIEEIGWKDP--ISLALLFTADRAYHLNLLFKQNP--- 81 
                                   68**************8887335588888888866666666666666666666..45556666667889999988876... PP

                        AAA_18  73 egknlvidghlaeleseaakdikk.................vvLtaspeelleRlekR 113
                                     + +++d  +   + ++   +                   + L+++pe+ + R+++ 
  gi|70606679|ref|YP_255549.1|  82 --EIIIMDRYIDSTIAYQSSLGIDenwirnlnkyfpepdltILLDLKPETAIARIKNK 137
                                   ..77766666666666655544446666777899*********************986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.4e-06    0.0043       4     147 ..       6     159 ..       3     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                        AAA_28   4 itGgestGKTtlleaLaar.........gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaa..aan 73 
                                   + G  ++GKTt+++ + ++         ++    E+    ++++  k  +++ w +d++ +a ++ + ++  +     +++
  gi|70606679|ref|YP_255549.1|   6 FEGIDGSGKTTISKIIYEKllieigsnkKIILTSEP----FSQEIIKLIEEIGW-KDPISLALLFTADRAYHLNLLfkQNP 81 
                                   678889999999999997766655432222222443....33333455566779.6********999998777776889** PP

                        AAA_28  74 kvlfcDrglldtlaYarayggeaeaeleaaar.ekrydlvfllppapei....dddgeRredleereaiderlrealre 147
                                   +++++Dr +  t+aY   +g++ e+ + +  + + + dl +ll+  pe+     ++++ +  ++e   +  ++re + e
  gi|70606679|ref|YP_255549.1|  82 EIIIMDRYIDSTIAYQSSLGID-ENWIRNLNKyFPEPDLTILLDLKPETaiarIKNKVDKFNFDEKISTLSKVREKYLE 159
                                   **********************.98888877756779999999977744335567777777777776666666665555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.013        24       2      16 ..      11      25 ..      10      56 .. 0.86
   2 !   10.8   0.1   0.00022       0.4      84     152 ..     116     182 ..     101     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
                                  TSSHHHHHHHHHHHH CS
                           SKI  2 GaGKstvGkllAkkl 16
                                  G+GK+t+ k++ +kl
  gi|70606679|ref|YP_255549.1| 11 GSGKTTISKIIYEKL 25
                                  9********998877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00022
                                   HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHHHHHHHH CS
                           SKI  84 ekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseeskeevaee 152
                                   e  ++i+Ld+++e+ ++r+k++ ++  + ek +    l++ + +  +l ++ +++ + ++e+s +e++ee
  gi|70606679|ref|YP_255549.1| 116 EPDLTILLDLKPETAIARIKNKVDKFNFDEKIS---TLSKVReKYLELAKRNNKIRIVNAEKSIDEIVEE 182
                                   66789*******************655555555...3333333445666666666666666666777776 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00023      0.41       6      24 ..       8      26 ..       4      51 .. 0.89
   2 ?    4.0   0.2     0.016        28     102     169 ..     119     185 ..      82     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                     Gtr1_RagA  6 GksgsGKtsmrsiiFdnyl 24
                                  G  gsGKt++ +ii++++l
  gi|70606679|ref|YP_255549.1|  8 GIDGSGKTTISKIIYEKLL 26
                                  7889************986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                     Gtr1_RagA 102 lealrqyspeakvfvlihKmDliqedereeifeerkeeireeieklekeeiqffaTSiwdeslykAfs 169
                                   l+ l + +pe  +  + +K+D+ + de+ +++++ +e++ e +++ +k +i     Si de + + +s
  gi|70606679|ref|YP_255549.1| 119 LTILLDLKPETAIARIKNKVDKFNFDEKISTLSKVREKYLELAKRNNKIRIVNAEKSI-DEIVEETWS 185
                                   567788899999999999*************999999999999987755566566666.666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00027      0.49       2      24 ..       4      26 ..       3     160 .. 0.77
   2 ?    0.7   0.0       0.3   5.5e+02      84     111 ..     153     179 ..     127     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00027
                        AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                  + + G  GsGK+t ++ +++kl 
  gi|70606679|ref|YP_255549.1|  4 ISFEGIDGSGKTTISKIIYEKLL 26
                                  6699***********98887775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.3
                        AAA_33  84 erarflklarrlgvpvrivvvetdeetl 111
                                    r+++l+la+r + ++riv  e + +++
  gi|70606679|ref|YP_255549.1| 153 VREKYLELAKRNN-KIRIVNAEKSIDEI 179
                                   5789999999999.99999888776665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     5e-05     0.089      21      43 ..       2      24 ..       1      50 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                  EEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                  +++++ G  G+GKtt++k i++k
  gi|70606679|ref|YP_255549.1|  2 FIISFEGIDGSGKTTISKIIYEK 24
                                  79******************998 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0026       4.6       2      21 ..       8      27 ..       7      51 .. 0.87
   2 ?    4.0   0.0     0.034        61     101     125 ..     116     140 ..      78     151 .. 0.75
   3 ?   -2.1   0.0       2.6   4.7e+03      45      61 ..     156     172 ..     136     183 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0026
                                  E-TTSSHHHHHHHHHHHHTE CS
                        AAA_17  2 GgPGsGKgtqceklvekygf 21
                                  G+ GsGK+t+++ + ek+ +
  gi|70606679|ref|YP_255549.1|  8 GIDGSGKTTISKIIYEKLLI 27
                                  899********999999854 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
                                   ..SEEEEEE--HHHHHHHHHHHTTS CS
                        AAA_17 101 kpdaiilleadpeeilerrlkdrtr 125
                                   +pd+ ill+ +pe+ ++r +++  +
  gi|70606679|ref|YP_255549.1| 116 EPDLTILLDLKPETAIARIKNKVDK 140
                                   489***************9987555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                                   HHCTSHHHHHHHHHHHH CS
                        AAA_17  45 emrklpleekkelqkea 61 
                                   ++ +l ++ +k    +a
  gi|70606679|ref|YP_255549.1| 156 KYLELAKRNNKIRIVNA 172
                                   33333333333333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00031      0.56      17      51 ..       7      44 ..       3     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                                  EESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG CS
                                  xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                      ABC_tran 17 vGenGaGKStLlkllagllkp...teGeilldgkdlke 51
                                   G  G+GK+t+ k+++++l      + +i l ++++++
  gi|70606679|ref|YP_255549.1|  7 EGIDGSGKTTISKIIYEKLLIeigSNKKIILTSEPFSQ 44
                                  5889************9876623344445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1332.59
//
Query:       gi|70606680|ref|YP_255550.1|  [L=363]
Description: hypothetical protein Saci_0894 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-24   87.1   0.0    1.8e-24   86.6   0.0    1.2  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.25   11.4   0.2    1.8  1  MMR_HSR1  50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0     2e-28   1.8e-24       1     187 [.      85     253 ..      85     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2e-28
                        CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtisla..lverpidveegfsldaplvyffGdtspsdnpsl 79 
                                   G+++sGK+ l+ +LlN+   +g    ++D+DvGqs++ +P ++s++   ve++++ +e      +   ffGd +p +np+l
  gi|70606680|ref|YP_255550.1|  85 GKQNSGKTYLSNMLLNM---HG--GKIIDADVGQSSLFLPTFVSISsrQVEKKLKLSER---AYESIEFFGDITPLTNPRL 157
                                   899*************9...45..4579**************99983356666655443...445579************* PP

                        CLP1_P  80 ylalvkelareveekleenkkakasgliIntpGwvkgl.gaellleliealepdvvvvldqeellnelkrdlplskvkvvk 159
                                    ++l+++l+++ +          ++ l+I+ +Gw++g+ +++++leli  l pd+++v   e+ l++l  + + +kvk++k
  gi|70606680|ref|YP_255550.1| 158 HISLIDKLYNMNK---------DEKNLVIDADGWINGFsALKHKLELIYRLDPDYILVFN-EKILSDLPIEIR-RKVKIIK 227
                                   *********9888.........5799***********9457******************9.589999999999.7777776 PP

                        CLP1_P 160 lpkspgvvqrsreerrelreerireYFy 187
                                          v+r+ ++r+++r++++r+YF+
  gi|70606680|ref|YP_255550.1| 228 PFP--LDVNRNIKTRKMYRKNKYRSYFS 253
                                   555..5569******************7 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.8e-05      0.25       1      22 [.      80     101 ..      80     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                                   EEEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge 22 
                                   +++i+G+ N+GK+ L n l++ 
  gi|70606680|ref|YP_255550.1|  80 RIIILGKQNSGKTYLSNMLLNM 101
                                   699****************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2463.47
//
Query:       gi|70606681|ref|YP_255551.1|  [L=178]
Description: hypothetical protein Saci_0895 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1112.79
//
Query:       gi|70606682|ref|YP_255552.1|  [L=172]
Description: hypothetical protein Saci_0896 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-07   30.1   0.1    4.9e-07   29.7   0.1    1.2  1  AAA_24        AAA domain
    0.00011   21.6   0.5     0.0066   15.8   0.1    2.0  2  ATPase        KaiC
     0.0018   17.9   0.0       0.14   11.7   0.0    2.2  1  AAA_25        AAA domain
     0.0055   16.2   0.0     0.0075   15.8   0.0    1.2  1  RecA          recA bacterial DNA recombination protein
     0.0073   16.7   0.0      0.011   16.1   0.0    1.3  1  AAA_16        AAA ATPase domain
     0.0082   16.6   0.1      0.011   16.2   0.1    1.4  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.017   15.7   0.1      0.024   15.1   0.1    1.3  1  ABC_tran      ABC transporter
      0.017   14.4   0.1      0.023   13.9   0.1    1.3  1  DUF2075       Uncharacterized conserved protein (DUF2075)
      0.024   13.9   0.7       0.15   11.3   0.7    2.2  1  Rad51         Rad51
      0.027   14.9   0.1      0.051   14.0   0.1    1.6  1  RNA_helicase  RNA helicase
      0.029   14.0   0.1      0.052   13.2   0.1    1.3  1  MOZART2       Mitotic-spindle organizing gamma-tubulin ring a
      0.034   13.4   0.8        0.1   11.9   0.8    1.8  1  Delta_lysin   Delta lysin family
      0.084   11.2   0.1      0.096   11.0   0.1    1.0  1  NYD-SP12_N    Spermatogenesis-associated, N-terminal
      0.085   13.4   0.0       0.12   12.9   0.0    1.3  1  AAA_18        AAA domain
      0.085   13.1   1.2       0.63   10.3   1.2    2.1  1  AAA_22        AAA domain
       0.12   12.2   0.0       0.14   11.9   0.0    1.1  1  AAA_11        AAA domain
        0.2   11.4   0.0       0.27   10.9   0.0    1.2  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   4.7e-10   4.9e-07       3      82 ..       9      97 ..       7     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.7e-10
                        AAA_24  3 lkiliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdie.......swedfldevvel.......aaeladykt 68
                                  + i iyG sg+GKT + +el    +  lfi te+ + s  + k+  ++       s +        +       ++ + + k 
  gi|70606682|ref|YP_255552.1|  9 NIISIYGASGTGKTNIGLELcqeIQPSLFISTEGKSYSSRVEKLR-LKkdilfieSSNV-------FellyalsKTTDLHVKL 83
                                  5688****************9998899*******88787777765.3235544433333.......14446667999999*** PP

                        AAA_24 69 lviDtideleelcl 82
                                  +v+Dt++++++l +
  gi|70606682|ref|YP_255552.1| 84 IVVDTVNKFYKLYR 97
                                  **********9865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.3e-06    0.0066      16      91 ..       5      75 ..       3      79 .. 0.83
   2 !    5.5   0.1    0.0087       9.2     116     189 ..      77     149 ..      61     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.3e-06
                        ATPase 16 ipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidases 91
                                  + +g+++ i+G +GtGKt ++l+       +  +p +f+++e ++ + r +  +l  d+  +e+++ + ++ a ++
  gi|70606682|ref|YP_255552.1|  5 FEKGNIISIYGASGTGKTNIGLELCQ----E-IQPSLFISTEGKSYSSRVEKLRLKKDILFIESSNVFELLYALSK 75
                                  5789*****************98543....3.4689******9998888888889999998888888888777666 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0087
                        ATPase 116 keikakrvviDsitglayeekeavaR.eilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdl 189
                                    ++++k +v+D+++ + y+   ++   e    l++ +++ gv  ++  ++s + ++++g +     +d +++L +
  gi|70606682|ref|YP_255552.1|  77 TDLHVKLIVVDTVNKF-YKLYRNKKDiELPLILLKSIADAGVKVVMLWQMSGN-NRVSGEKFMRNFSDDIMRLSK 149
                                   56889***********.444444433044456788999999999999997655.444444444447777888876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00013      0.14      31     160 ..       6      98 ..       2     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                        AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagv 111
                                    +g ++ ++Ga+gtGKt + l+l+ ++               + l++s+E++      R+++++ +    ++ l++   +v
  gi|70606682|ref|YP_255552.1|   6 EKGNIISIYGASGTGKTNIGLELCQEIQ--------------PSLFISTEGKS--YSSRVEKLRLK----KDILFIESSNV 66 
                                   5788889999999999999999987776..............45777777777..67777655444....45555554343 PP

                        AAA_25 112 eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggden 160
                                                   + + al ++ +  + v+l+v+D++++++    n
  gi|70606682|ref|YP_255552.1|  67 ---------------FELLYALSKTTDL-H-VKLIVVDTVNKFYKLYRN 98 
                                   ...............1334445555444.4.888888888887777555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.1e-06    0.0075      51     140 ..       6      89 ..       4     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                                   ETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHTT--GGG-EEE--SSHHHHHHHHHHHHTTT. CS
                          RecA  51 pkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakklGvdidellvsqpdtGeqaleiadalvrsg. 130
                                    kG ii iyG+  +Gkt + l++  e+q     + fi +e    ++  +kl ++ d l++   +     +e++ al +++ 
  gi|70606682|ref|YP_255552.1|   6 EKGNIISIYGASGTGKTNIGLELCQEIQP----SLFISTEGKSYSSRVEKLRLKKDILFIESSNV----FELLYALSKTTd 78 
                                   69*********************999996....57888888888888888888888888876554....444444444431 PP

                                   .--SEEEEE-T CS
                          RecA 131 .aidlivvdsv 140
                                     + livvd+v
  gi|70606682|ref|YP_255552.1|  79 lHVKLIVVDTV 89 
                                   15677888877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     1e-05     0.011      24      65 ..       8      47 ..       4      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqles 65
                                  ++++ ++G+sG+GK+ +  el ++++ +  +f++++ ++++s
  gi|70606682|ref|YP_255552.1|  8 GNIISIYGASGTGKTNIGLELCQEIQPS--LFISTEGKSYSS 47
                                  4899**********************99..777777777722 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     1e-05     0.011       3      69 ..      13      91 ..      11     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                  EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS..........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGG CS
                           AAA  3 lyGppGtGKTllakavakelg.vefleisgsellsk..........yvgesekkirelfkeakeka.kpsilfiDEida 69
                                  +yG  GtGKT +   +++e++ + f++++g++  s           ++ es++ ++ l +  k+   + + +++D + +
  gi|70606682|ref|YP_255552.1| 13 IYGASGTGKTNIGLELCQEIQpSLFISTEGKSYSSRveklrlkkdiLFIESSNVFELLYALSKTTDlHVKLIVVDTVNK 91
                                  79*****************984556777777776555566666666555555555555555444444446666665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.3e-05     0.024       5      41 ..       2      43 ..       1     101 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
                                  EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx RF
                      ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllkp.....teGe 41
                                  ++ +++g+++ i G +G+GK+ +   l+++ +p     teG+
  gi|70606682|ref|YP_255552.1|  2 EFIFEKGNIISIYGASGTGKTNIGLELCQEIQPslfisTEGK 43
                                  67899******************9999999998444444444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.2e-05     0.023       3      26 ..      10      38 ..       8      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                       DUF2075  3 vvlVtGvaGtGKtvvllnllael.....e 26
                                  ++ + G++GtGKt ++l+l  e+      
  gi|70606682|ref|YP_255552.1| 10 IISIYGASGTGKTNIGLELCQEIqpslfI 38
                                  6789******************9554441 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00014      0.15      35      64 ..       6      35 ..       4     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                  ESSSEEEEEESTTSSHHHHHHHHHHHTTS- CS
                         Rad51 35 etgsiteifGefrsGktqlchtlcvtvqlp 64
                                  e g+i  i+G +++Gkt +  +lc  +q  
  gi|70606682|ref|YP_255552.1|  6 EKGNIISIYGASGTGKTNIGLELCQEIQPS 35
                                  789999******************999843 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.8e-05     0.051       1      37 [.      11      47 ..      11      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysr 37
                                  i +yG+sg+GK+++  eL+++++ +l   ++++ ys 
  gi|70606682|ref|YP_255552.1| 11 ISIYGASGTGKTNIGLELCQEIQPSLFISTEGKSYSS 47
                                  569********************99877777777774 PP

>> MOZART2  Mitotic-spindle organizing gamma-tubulin ring associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.9e-05     0.052      11      56 ..      45      89 ..      35      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                       MOZART2 11 vsstvqkyavkkkkvLsaeeaeLyeLtqaaGiviDqevfkiivDLL 56
                                   ss+v+k+ + kk++L  e  +++eL  a   + D +v  i+vD +
  gi|70606682|ref|YP_255552.1| 45 YSSRVEKLRL-KKDILFIESSNVFELLYALSKTTDLHVKLIVVDTV 89
                                  5788888887.589*****************************975 PP

>> Delta_lysin  Delta lysin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   9.5e-05       0.1      13      25 .]      81      94 ..      76      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.5e-05
                   Delta_lysin 13 VKWI.IDTVNKFkK 25
                                  VK I +DTVNKF K
  gi|70606682|ref|YP_255552.1| 81 VKLIvVDTVNKFYK 94
                                  666537******87 PP

>> NYD-SP12_N  Spermatogenesis-associated, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.1e-05     0.096      43     126 ..      36     122 ..      19     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                    NYD-SP12_N  43 ikkncgekqveitaervkltksikekqsnel.ek.aalkrkaeseeksva.kkeakitelddqlitvplphiplknimdve 120
                                   + +++  k+     e+++l k i   +s+++ e   al + ++   k +     +k  +l  +   + lp i+lk+i d  
  gi|70606682|ref|YP_255552.1|  36 LFISTEGKSYSSRVEKLRLKKDILFIESSNVfELlYALSKTTDLHVKLIVvDTVNKFYKLYRNKKDIELPLILLKSIADAG 116
                                   4466778888888999999999887666554153358999999999998757789999*********************** PP

                    NYD-SP12_N 121 lklvyi 126
                                   +k+v +
  gi|70606682|ref|YP_255552.1| 117 VKVVML 122
                                   ***986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.12       1      92 [.      11      99 ..      11     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss.aleegknlvidgh 82
                                  I + G++G+GKt ++ eL ++    + + ++ +e+ ++ ++ ++ l+ +k +      +++++l + s+ +  + k +v+d +
  gi|70606682|ref|YP_255552.1| 11 ISIYGASGTGKTNIGLELCQE---IQPSLFISTEGKSYSSRVEK-LRLKKDILFIESSNVFELLYALSKtTDLHVKLIVVDTV 89
                                  6799**************777...58888888888888888888.66666666666677777777776666666777788877 PP

                        AAA_18 83 laeleseaak 92
                                     +  +++k
  gi|70606682|ref|YP_255552.1| 90 NKFYKLYRNK 99
                                  7776666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.2   0.00059      0.63       4      29 ..       7      32 ..       4     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                  + +i+ ++G sGtGKT    +l ++ 
  gi|70606682|ref|YP_255552.1|  7 KGNIISIYGASGTGKTNIGLELCQEI 32
                                  5789************8877776665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.14      13      65 ..       4      66 ..       1      90 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                        AAA_11 13 alseseitliqGPPGtgKTktivellsqllsr..........rkseeeksakpriLvCapSNa 65
                                  + ++ +i  i G  GtgKT   +el++++ ++          ++ +e+ + k+ iL   +SN+
  gi|70606682|ref|YP_255552.1|  4 IFEKGNIISIYGASGTGKTNIGLELCQEIQPSlfistegksySSRVEKLRLKKDILFIESSNV 66
                                  567778899********************8324554455444557899999999**9999996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00026      0.27      16     121 ..       7     121 ..       1     123 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                        AAA_30  16 sgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkv.Laeelg.ieastiakllkrlkgrarlepg.tll 92 
                                   +g+ +  + G+ GtGKt +  +l +e+  +   +  g + ++++ k  L++++  ie+s++ +ll++l +  + + + +l+
  gi|70606682|ref|YP_255552.1|   7 KGN-IISIYGASGTGKTNIGLELcQEIQPSLFISTEGKSYSSRVEKLrLKKDILfIESSNVFELLYALSK--TTDLHvKLI 84 
                                   444.77899*********97777355555558999999999999886698888745*********99996..345555999 PP

                        AAA_30  93 ivDEagmv........dtkqlaallkaaekagakvil 121
                                   +vD +           d++    llk++++ag+kv++
  gi|70606682|ref|YP_255552.1|  85 VVDTVNKFyklyrnkkDIELPLILLKSIADAGVKVVM 121
                                   9998877777777666666667777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1089.08
//
Query:       gi|70606683|ref|YP_255553.1|  [L=163]
Description: hypothetical protein Saci_0897 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-41  140.8   9.2    2.2e-40  138.5   9.2    1.8  1  CarS-like     CDP-archaeol synthase
    0.00049   20.2   1.9      0.028   14.6   0.1    2.7  2  DUF347        Repeat of Unknown Function (DUF347)
     0.0034   17.2   2.4     0.0034   17.2   2.4    2.0  2  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   9.2   3.6e-44   2.2e-40       1     175 []       1     163 []       1     163 [] 0.91

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 3.6e-44
                     CarS-like   1 lldlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldss 81 
                                   ++ l+l  iy++ pa van sa  +  Gtp+d+ ++l dGrr++GdG+t+ G++  +  G+ vg i   +           
  gi|70606683|ref|YP_255553.1|   1 MIGLLLGLIYYI-PALVANGSAPFIKSGTPIDFKRKLNDGRRVLGDGKTFEGLLLSLTFGTTVGAIISRF----------- 69 
                                   567888888885.*******************************************99999998764433........... PP

                     CarS-like  82 gsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgallla.ypvkllpieliilivlitlvlhlsa 161
                                      +e +i++++ ++Ga+lGd+ G+fikrr+++erG +a+ildqldf+lga ++  +  + l i  +++++++ ++lh+ +
  gi|70606683|ref|YP_255553.1|  70 -LGIEWIIIGFVESLGAMLGDMLGAFIKRRIGLERGARAPILDQLDFILGATVVLiSFNVNLNIYQVVFVCVLVIALHMFT 149
                                   .236899*******************************************98766366888999999************** PP

                     CarS-like 162 niiayklglkdvwy 175
                                   n++ay+l +k v++
  gi|70606683|ref|YP_255553.1| 150 NYVAYRLKIKSVPW 163
                                   *************9 PP

>> DUF347  Repeat of Unknown Function (DUF347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.3     0.007        42       7      25 ..      53      71 ..      52      73 .. 0.81
   2 !   14.6   0.1   4.7e-06     0.028       3      41 ..      74     145 ..      74     155 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.007
                        DUF347  7 iltttlGttaGDflsqglg 25
                                  +l+ t+Gtt+G  +s+ lg
  gi|70606683|ref|YP_255553.1| 53 LLSLTFGTTVGAIISRFLG 71
                                  68899*****988888776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4.7e-06
                        DUF347   3 WiaiiltttlGttaGDfls.....................q............glglgyavgaaifgalllv 41 
                                   Wi+i ++  lG+++GD+l                      +            +++l ++++  + ++++++
  gi|70606683|ref|YP_255553.1|  74 WIIIGFVESLGAMLGDMLGafikrriglergarapildqlDfilgatvvlisfNVNLNIYQVVFVCVLVIAL 145
                                   ******************977776666665555555544403333344444345566666666666666654 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.4   5.6e-07    0.0034     170     231 ..      46     100 ..      43     103 .. 0.94
   2 ?    0.3   0.7     0.079   4.7e+02      13      36 ..     120     143 ..     109     162 .. 0.44

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-07
                                   --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                  CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafg 231
                                   +KT eG++ +l + ++vg +++ +l+        + ++++++ sl a++GD++   +KR++g
  gi|70606683|ref|YP_255553.1|  46 GKTFEGLLLSLTFGTTVGAIISRFLGI-------EWIIIGFVESLGAMLGDMLGAFIKRRIG 100
                                   6*************************7.......57999********************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.079
                                   HHHHTTTSH.HHHHHHHHHHHHHH CS
                  CTP_transf_1  13 ivliilllgglvflllvavvvila 36 
                                   +v++i +  +l +  +v+v+v+++
  gi|70606683|ref|YP_255553.1| 120 TVVLISFNVNLNIYQVVFVCVLVI 143
                                   333333333322222222222211 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1197.46
//
Query:       gi|70606684|ref|YP_255554.1|  [L=122]
Description: hypothetical protein Saci_0898 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   14.6   8.2      0.015   14.4   8.2    1.1  1  Acyl_transf_3  Acyltransferase family
      0.096   12.7   0.3       0.18   11.8   0.3    1.4  1  MHC2-interact  CLIP, MHC2 interacting
       0.15   11.5  15.2        0.2   11.1   3.9    2.1  2  DUF3112        Protein of unknown function (DUF3112)
          1    9.4  11.2        1.3    9.1  11.2    1.1  1  MARVEL         Membrane-associating domain
        7.7    5.7   8.6       0.97    8.7   1.2    2.0  2  S_4TM          SMODS-associating 4TM effector domain
        8.9    6.4  12.9       0.53   10.3   5.5    2.2  2  DUF997         Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   8.2   5.1e-06     0.015     161     244 ..      31     113 ..      15     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 161 hlllllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsllllalillalf 241
                                   +l++ +++l+++++ +++  +++++ +  +++  +vl ++ +++G++l+ ++ + +n + g+ i++l++++ +++ +la++
  gi|70606684|ref|YP_255554.1|  31 VLVMGITILGAIAFPYYISPITYSNGGTAQAGGIAVL-AALIILGLILGVYFVENKNYDIGTPILILMLVIIVIYVWLAYG 110
                                   3445555555555555555555566666666666666.************************************9999999 PP

                                   xxx RF
                 Acyl_transf_3 242 gqt 244
                                   + +
  gi|70606684|ref|YP_255554.1| 111 SAA 113
                                   877 PP

>> MHC2-interact  CLIP, MHC2 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3     6e-05      0.18      30      60 ..      58      88 ..      51      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                 MHC2-interact 30 alkvaglsiLvalLiAGQavTaYfvyqQkgq 60
                                  +++  g+++L+al+i G  + +Yfv + + +
  gi|70606684|ref|YP_255554.1| 58 TAQAGGIAVLAALIILGLILGVYFVENKNYD 88
                                  677889*******************876655 PP

>> DUF3112  Protein of unknown function (DUF3112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.8    0.0029       8.7      12      58 ..      20      66 ..       9      77 .. 0.69
   2 ?   11.1   3.9   6.7e-05       0.2      21      76 ..      64     119 ..      62     122 .] 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0029
                       DUF3112 12 vmlllylvvigvvvmti.vasvvpylyflsekhyemckkvvkassvli 58
                                  v+  +y+++i v+vm i +  ++ + y++s+ +y++  + ++a ++ +
  gi|70606684|ref|YP_255554.1| 20 VVNNVYVIIILVLVMGItILGAIAFPYYISPITYSNGGT-AQAGGIAV 66
                                  56789******999987456789999********88654.44444332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.7e-05
                       DUF3112  21 igvvvmtivasvvpylyflsekhyemckkvvkassvliilysllavalillayllk 76 
                                   i+v++  i+  +++ +yf+++k+y+  + +   + v+i++y+ la    ++ ++++
  gi|70606684|ref|YP_255554.1|  64 IAVLAALIILGLILGVYFVENKNYDIGTPILILMLVIIVIYVWLAYGSAAIKFIFN 119
                                   578888899999***********************************999999996 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  11.2   0.00042       1.3       8     103 ..      26     119 ..      20     122 .] 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00042
                        MARVEL   8 ilrilqlvfaiiilgliasliakldqllgspssalnfavfvavfsfly.alfllvlylfknsaftsilwplidlivdalaa 87 
                                   ++ il lv++i ilg ia  +  + + ++ +++ +  a  +av++ l+   ++l +y+ +n++  +i  p++ l++  +++
  gi|70606684|ref|YP_255554.1|  26 VIIILVLVMGITILGAIAFPY--YISPITYSNGGTAQAGGIAVLAALIiLGLILGVYFVENKN-YDIGTPILILMLVIIVI 103
                                   788999**************9..4344444455555555555565555244455556666555.6999999999999**** PP

                        MARVEL  88 llwlvafialaaglrd 103
                                    +wl+ ++a  + + +
  gi|70606684|ref|YP_255554.1| 104 YVWLAYGSAAIKFIFN 119
                                   *****99998887766 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.1     0.046   1.4e+02     161     187 ..      13      39 ..      11      51 .. 0.56
   2 ?    8.7   1.2   0.00032      0.97      22      71 ..      52     106 ..      49     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.046
                         S_4TM 161 rlrrryaklllfalvlwillvlvvgli 187
                                   ++r+ y+ +  + ++++++lv+ + ++
  gi|70606684|ref|YP_255554.1|  13 EVRKTYSVVNNVYVIIILVLVMGITIL 39 
                                   677777755555544444444444444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00032
                         S_4TM  22 lYsrakrlqalrvilsvvlaivlsvlav.lvps....lktylallgllwllldvl 71 
                                   +Ys+  + qa  +++ ++l i++++l+v +v++    + t + +l+l++++++v 
  gi|70606684|ref|YP_255554.1|  52 TYSNGGTAQAGGIAVLAALIILGLILGVyFVENknydIGTPILILMLVIIVIYVW 106
                                   69999999********************666668888888888888888888854 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7      0.24     7e+02      47      62 ..      19      34 ..      16      49 .. 0.66
   2 ?   10.3   5.5   0.00018      0.53      11      68 ..      66     119 ..      61     120 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.24
                        DUF997 47 scillpilfivlvill 62
                                  s++ ++ ++i+lv ++
  gi|70606684|ref|YP_255554.1| 19 SVVNNVYVIIILVLVM 34
                                  5566656666665554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                        DUF997  11 lltllyflwwllfaYglgskeveeyyilglPlWfflscillpilfivlvillvkfvFk 68 
                                   +l++l++l  +l  Y++++k+    y +g+P  +++ +i+++ + ++   +++kf+F+
  gi|70606684|ref|YP_255554.1|  66 VLAALIILGLILGVYFVENKN----YDIGTPILILMLVIIVIYVWLAYGSAAIKFIFN 119
                                   68889999**********999....999****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1329  (0.0741257); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 958.12
//
Query:       gi|70606685|ref|YP_255555.1|  [L=73]
Description: hypothetical protein Saci_0899 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.059   13.8   0.1      0.086   13.3   0.1    1.2  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.8e-06     0.086      12      47 ..      18      53 ..      18      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                                  HHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT CS
                   FumaraseC_C 12 ekAakIAkeAlkegktlreavlelgllteeeldell 47
                                  e+A ++ +e ++++ tl +++ +lgl + ee  el+
  gi|70606685|ref|YP_255555.1| 18 ENAIRVLNEYVRTQMTLEQLARRLGLTSWEEAYELV 53
                                  7999*************************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 556.63
//
Query:       gi|70606686|ref|YP_255556.1|  [L=688]
Description: replication and repair minichromosome maintenance protein MCM [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-97  324.4   0.0    4.5e-97  323.5   0.0    1.4  1  MCM              MCM P-loop domain
    1.8e-33  115.1   0.0    3.1e-33  114.3   0.0    1.4  1  MCM_OB           MCM OB domain
    3.8e-28   97.8   0.4    8.3e-28   96.6   0.4    1.6  1  MCM_lid          MCM AAA-lid domain
    7.6e-18   65.0   1.0      2e-17   63.7   1.0    1.7  1  MCM_N            MCM N-terminal domain
    5.5e-08   32.9   0.0    1.4e-07   31.6   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-06   28.2   0.1    0.00011   21.7   0.1    2.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.7e-05   24.7   0.0    3.6e-05   23.6   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    2.5e-05   24.0   0.1    0.00037   20.3   0.1    2.3  1  Sigma54_activat  Sigma-54 interaction domain
     0.0012   18.5   0.3      0.006   16.3   0.1    2.4  2  DUF4325          STAS-like domain of unknown function (DUF432
     0.0071   15.7   0.0      0.015   14.6   0.0    1.5  1  EAP30            EAP30/Vps36 family
  ------ inclusion threshold ------
      0.025   13.6   0.0        3.3    6.6   0.0    2.2  2  DUF3987          Protein of unknown function (DUF3987)
      0.062   13.6   0.0       0.16   12.3   0.0    1.6  1  ANT              Phage antirepressor protein KilAC domain
       0.15   12.3   0.1       0.44   10.8   0.1    1.8  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.65   10.1   3.2        2.1    8.5   0.1    2.8  2  HEPN             HEPN domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.5   0.0  3.5e-100   4.5e-97       1     224 []     277     499 ..     277     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 323.5 bits;  conditional E-value: 3.5e-100
                                   HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                           MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                   ++++i+el+k++ i ek+++siapsiygh ++k+ai+l+lfgg+ k l+d+t++rgdi++l++gdpgtaKsq+L++++++a
  gi|70606686|ref|YP_255556.1| 277 DEKKIRELSKDSFIREKIISSIAPSIYGHWEIKEAIALSLFGGSPKLLPDGTRVRGDIHILIIGDPGTAKSQMLQFAARVA 357
                                   5799***************************************************************************** PP

                                   SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                           MCM  82 pravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLn 162
                                   pravyt+gkgs+aagLta+v+rd+++g+++leaGalvlad+G+++iDe+dkm+eedr+a+hEamEqqt+siaKaGiva+Ln
  gi|70606686|ref|YP_255556.1| 358 PRAVYTTGKGSTAAGLTATVTRDKNSGDYYLEAGALVLADGGIAVIDEIDKMREEDRVAIHEAMEQQTVSIAKAGIVAKLN 438
                                   ********************************************************************************* PP

                                   --EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                           MCM 163 artsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                   ar++v+aA npk gry  +++++eninl++++LsrFDlif+l+Dk+  ++De la+hi+++h
  gi|70606686|ref|YP_255556.1| 439 ARATVIAAGNPKLGRYIAERTLIENINLPPTILSRFDLIFILVDKPG-KEDELLASHILNVH 499
                                   *********************************************98.579********987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   2.4e-36   3.1e-33       2     125 ..     108     239 ..     107     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 2.4e-36
                                   XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.E.........S----SB-..TTT-HHH-EEE-GGGS CS
                        MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.v.........eleePrkCeekeCeskdpfkleteks 72 
                                   lR+lrs++ g+l++veGi ++a+  k++l+ka f++ +  +++e v          +e P+ C  ++C++ ++fk+  +ks
  gi|70606686|ref|YP_255556.1| 108 LRKLRSNYAGRLISVEGILVKATPPKERLRKAIFQHMNPDCMHEfVwppegdmgeVIEAPSVC--PACNKPGQFKFIEDKS 186
                                   8**********************************987777666446888866644555****..99************** PP

                                   EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                        MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                   +f+d+qk  +QE+pee+p+G+lPr++e+++eddlvd  +PGdrv+v+Gi++++
  gi|70606686|ref|YP_255556.1| 187 EFIDWQKAVIQERPEEIPPGQLPRQVEIVFEDDLVDISRPGDRVKVVGILEIK 239
                                   *************************************************9875 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.4   6.5e-31   8.3e-28       1      84 [.     513     596 ..     513     599 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 6.5e-31
                                   HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                   ell+kYiay+r++++Pkl +eak+ l +++ve+Rk++++s ++ i it+RqLe+liR+seA A++ l+e+v++ed+e+ai+
  gi|70606686|ref|YP_255556.1| 513 ELLKKYIAYSRKNVSPKLGDEAKKLLLDFFVEMRKKSSESPDSPIIITPRQLEALIRISEAYARMALKEEVSREDAERAIN 593
                                   68***********************************888999************************************** PP

                                   HHH CS
                       MCM_lid  82 llk 84 
                                   +++
  gi|70606686|ref|YP_255556.1| 594 IMR 596
                                   *97 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   1.0   1.6e-20     2e-17       2     102 ..      11      99 ..      10     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.6e-20
                         MCM_N   2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkkleps 82 
                                   e F +F+++f    +d++g+ +Y + ++e++ + k+++++d++dL++f++++a ++++ pke++pl e+ l ++v + +ps
  gi|70606686|ref|YP_255556.1|  11 ELFLEFISTF----HDDKGRLVYQNLINELIAYRKKSIYIDFSDLYSFNQKFATKLIDSPKEIIPLIEKKLYDYVTERDPS 87 
                                   579*******....7899*************************************************************** PP

                         MCM_N  83 ykddakefpaeltrrfqvrf 102
                                   y+d+         r+++vr+
  gi|70606686|ref|YP_255556.1|  88 YQDE--------IRELHVRI 99 
                                   **98........88888887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.1e-10   1.4e-07       1     123 [.     335     450 ..     335     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.1e-10
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraes 79 
                                   ++l++G+pGt+Ks++ +  a++  r v  +   ++ t++ l+  +  +  +g++ l+ ++lv     g i+v+DE+++++ 
  gi|70606686|ref|YP_255556.1| 335 HILIIGDPGTAKSQMLQFAARVAPRAV--YTTGKGSTAAGLTATVTRDknSGDYYLEAGALV--LADGGIAVIDEIDKMRE 411
                                   689*************98888875544..4456677778887776655669***********..99*************** PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                   e   + +  +e++++++++ g + k ++       +via++np 
  gi|70606686|ref|YP_255556.1| 412 EDRVAIHEAMEQQTVSIAKAGIVAKLNAR-----ATVIAAGNPK 450
                                   ****************9999999999886.....9*******96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   8.3e-08   0.00011      95     159 ..     386     450 ..     329     461 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.3e-08
                  Mg_chelatase  95 skpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                      + G++ la  G+ ++DE+ +++++   ++ e +e+++v+i++a   ++  ar +++aa Np 
  gi|70606686|ref|YP_255556.1| 386 YYLEAGALVLADGGIAVIDEIDKMREEDRVAIHEAMEQQTVSIAKAGIVAKLNARATVIAAGNPK 450
                                   56789**********************************************************95 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.8e-08   3.6e-05       1     112 [.     335     449 ..     335     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.8e-08
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftp.dllPsdilGtevfeekekefefkkGpvf.an..llladeinrappk 77 
                                   h+l+ g PG+ak ++ +  a++       +  t      + ++ t   ++++ ++ +++G+++ a+  + + dei++    
  gi|70606686|ref|YP_255556.1| 335 HILIIGDPGTAKSQMLQFAARVAPRA---VYTTGkGSTAAGLTATVTRDKNSGDYYLEAGALVlADggIAVIDEIDKMREE 412
                                   9**************99888876544...44443145678899999999999********976233449999********* PP

                         AAA_3  78 tqsalleameerqvtvege..thklpepflvlatqnP 112
                                    + a+ eame+++v+++++    kl+   +v+a+ nP
  gi|70606686|ref|YP_255556.1| 413 DRVAIHEAMEQQTVSIAKAgiVAKLNARATVIAAGNP 449
                                   **************9986522679************9 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.9e-07   0.00037      80     157 ..     384     463 ..     327     466 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                   TTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS-HHHHHHTTSS-HH CS
               Sigma54_activat  80 GAekekkGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatnedleeaveegkfred 157
                                   G    ++G++  adgG+  +Dei ++  e  + + +++++++  + + G  ++ ++   +iaa n +l + ++e+++ e+
  gi|70606686|ref|YP_255556.1| 384 GDYYLEAGALVLADGGIAVIDEIDKMREEDRVAIHEAMEQQTvsIAKAGIVAKLNARATVIAAGNPKLGRYIAERTLIEN 463
                                   4455678*******************************9997225799************************99998775 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.7e-06     0.006       2      39 ..      25      63 ..      24      77 .. 0.85
   2 ?   -2.7   0.0       3.8   4.8e+03       6      24 ..     523     541 ..     523     541 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                       DUF4325  2 Gerfrdkilkpllke..gekvelDFdgvesigssFldeaF 39
                                  G+ ++++++++l+ +  ++ + +DF++ +s+++ F+  ++
  gi|70606686|ref|YP_255556.1| 25 GRLVYQNLINELI-AyrKKSIYIDFSDLYSFNQKFATKLI 63
                                  7889999999994.458******************98776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                       DUF4325   6 rdkilkpllkegekvelDF 24 
                                   r+++ ++l +e +k+ lDF
  gi|70606686|ref|YP_255556.1| 523 RKNVSPKLGDEAKKLLLDF 541
                                   677888888899******9 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.015     116     232 ..     567     677 ..     538     678 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                         EAP30 116 lisleelyalvnrarggv.alvspdDllraiekl....lvlgsglsvlqvggkkvvrSvptelntdqvevlevakrlvsll 191
                                   li ++e ya++     +  ++vs +D +rai+ +    ++ g  ++  +++  +++   p++ +++ +++le++  +    
  gi|70606686|ref|YP_255556.1| 567 LIRISEAYARM-----ALkEEVSREDAERAINIMriflERVGIDVESGKIDIDTIMTGKPKSAREKMSKILEIIDTI---- 638
                                   44444444444.....4447**************7655555544444444455556666888888888888888888.... PP

                         EAP30 192 aekssgggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                     +ss+g v+ ++la+e+en g++++  ++ + ++ ++Gl+
  gi|70606686|ref|YP_255556.1| 639 --SSSEGCVKIKDLAKEAENAGIEKSSFDKLISDMRKQGLI 677
                                   ..233357*******************************97 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.01        13      30      59 ..     327     356 ..     320     361 .. 0.83
   2 ?    6.6   0.0    0.0026       3.3     277     357 ..     527     600 ..     495     602 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.01
                       DUF3987  30 gyteplnLytlvvapsGerKSpvdklvlrp 59 
                                   g+++   +++l+++++G+ KS+++++++r 
  gi|70606686|ref|YP_255556.1| 327 GTRVRGDIHILIIGDPGTAKSQMLQFAARV 356
                                   4567777899*************9998876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                       DUF3987 277 tlrlsdeAkerfneffnelesrlrpggdledirdwasKlagnvaRiAgilhllredgigeateisaetlqaAialaeylle 357
                                     +l deAk+++ +ff e+ +++ ++ d      +  +  ++++Ri    + +       ++e+s e+ ++Ai++++ +le
  gi|70606686|ref|YP_255556.1| 527 SPKLGDEAKKLLLDFFVEMRKKSSESPDS--PIIITPRQLEALIRISEAYARM-----ALKEEVSREDAERAINIMRIFLE 600
                                   55788999999****99999998555554..6788999999999999988888.....6788***************9986 PP

>> ANT  Phage antirepressor protein KilAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.16       9      53 ..     630     680 ..     623     685 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                           ANT   9 PkaeyaDrvlesdgsititeiAkllg......igenrlfelLrekgilyrq 53 
                                     +e  D++++s+g+++i+++Ak+ +       +  +l+  +r++g++y +
  gi|70606686|ref|YP_255556.1| 630 KILEIIDTISSSEGCVKIKDLAKEAEnagiekSSFDKLISDMRKQGLIYES 680
                                   557899******************888887778889999999****99985 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00035      0.44       4      52 ..     626     677 ..     624     681 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                                   HHHHHHHHHHHHHHHHHSSB-HHHHHHH...HTS-HHHHHHHHHHHHHTTSE CS
                Fe_dep_repress   4 estEdYLetIYtlseekkvvktkdlaer...LnvspssVsemlkkLekdGyv 52 
                                   e++ + Le I t+s +++ vk kdla++    ++++ss  + ++ ++k+G++
  gi|70606686|ref|YP_255556.1| 626 EKMSKILEIIDTISSSEGCVKIKDLAKEaenAGIEKSSFDKLISDMRKQGLI 677
                                   678889*******************86522279*****************96 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.31     4e+02      72     116 ..      28      74 ..       3      76 .. 0.81
   2 ?    8.5   0.1    0.0017       2.1      79     115 ..     569     602 ..     513     605 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.31
                                   HHHHHHHHHHCCCHHCCCTSS--S..--HHHHHHHHHHHHHHHHHHH CS
                          HEPN  72 elreeleeLekayiesrYpdakee..yteedaeealkdaeevlelve 116
                                    +++ ++eL  ++ +s Y d+     + ++ a ++++  +e++ l+e
  gi|70606686|ref|YP_255556.1|  28 VYQNLINELIAYRKKSIYIDFSDLysFNQKFATKLIDSPKEIIPLIE 74 
                                   5677889999999999999999888899*********9999998766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                                   HHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHH CS
                          HEPN  79 eLekayiesrYpdakeeyteedaeealkdaeevlelv 115
                                   ++++ay         ee+++edae+a+++++ +le v
  gi|70606686|ref|YP_255556.1| 569 RISEAYARMALK---EEVSREDAERAINIMRIFLERV 602
                                   444444333322...2379***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4527.09
//
Query:       gi|70606687|ref|YP_255557.1|  [L=183]
Description: hypothetical protein Saci_0901 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   41.9   0.9    1.5e-10   41.5   0.9    1.2  1  Sld5      GINS complex protein
  ------ inclusion threshold ------
      0.051   13.7   0.5       0.11   12.7   0.5    1.5  1  DUF5622   Domain of unknown function (DUF5622)


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.9   1.6e-14   1.5e-10       2     109 .]      46     159 ..      45     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.6e-14
                                   EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS.....SSSTTTTTTHHHHHHHHHHHHT.........HCHHHH CS
                          Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetks.....sdlpslpphflelavkllelard........ldelkr 69 
                                   e+ lWla +L++++ v++   +++++++l +il +e+++     s  + ++++++++ +   el +         +++  +
  gi|70606687|ref|YP_255557.1|  46 EIELWLANILRERGIVKMI--DMVTIDELGRILFQEKQTasvpaSLVKLPKDFYFKVRILFNELKKKndvatyenIKKAYQ 124
                                   789*************997..6899******************77777777888899999999998667889555555559 PP

                                   HHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHHH CS
                          Sld5  70 llrdllevRlakirkfaenledaagggggellsglseeEk 109
                                   +l +++ +R++ki ++a  + +++     +l+++++ eE+
  gi|70606687|ref|YP_255557.1| 125 MLSEIMSIRIRKIIQLAYLNVEDE-----NLMDRMTTEEI 159
                                   9****************9999999.....99999999996 PP

>> DUF5622  Domain of unknown function (DUF5622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.2e-05      0.11       9      39 ..      90     121 ..      89     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                       DUF5622   9 VeredgwYvKvRvLksree.vndpekYivlgk 39 
                                   V++ +++Y KvR+L+++ +  nd+  Y  ++k
  gi|70606687|ref|YP_255557.1|  90 VKLPKDFYFKVRILFNELKkKNDVATYENIKK 121
                                   788899********887666799999966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1153.52
//
Query:       gi|70606688|ref|YP_255558.1|  [L=169]
Description: hypothetical protein Saci_0902 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-10   39.9   0.8    5.4e-10   39.5   0.8    1.2  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.8     3e-14   5.4e-10       2     142 ..      21     152 ..      20     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 3e-14
                                   HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE.EEEEESSHHHHHHHHHHHHHHHHHH CS
                         THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipv.cevceadledileaakeivkkkfee 81 
                                   ei++++  +++n++ ve +k++i+++++  + e    l+  + ++++   +++p+   +   +  +++++   + k ++++
  gi|70606688|ref|YP_255558.1|  21 EILNRILIKDINATAVEIVKNVIILYSNLNPMEAYGLLISGPPSCVA---KIFPIhGVIDSISEAEVIRKSIDLCKNMLKN 98 
                                   7999999*********************9999999999999999988...*****87778888889999999999999988 PP

                                   CT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEE CS
                         THUMP  82 eketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisi 142
                                      tF V++  rg +  +++rei+  +G  ++   +  Vd+++P+++v+v + +dk yis 
  gi|70606688|ref|YP_255558.1|  99 ---TFYVQCYSRGVR--VNCREIEIGIGIGLRGIAK--VDFKSPELIVFVNVVRDKSYISF 152
                                   ...***********6..*******999999998766..*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1184.49
//
Query:       gi|70606689|ref|YP_255559.1|  [L=415]
Description: cell division control protein 6 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   60.4   0.0    4.3e-16   58.6   0.0    2.0  2  Cdc6_C    CDC6, C terminal winged helix domain
    4.2e-15   56.2   0.1    9.3e-15   55.1   0.1    1.5  1  AAA_22    AAA domain
    0.00013   21.4   0.0    0.00023   20.6   0.0    1.3  1  TniB      Bacterial TniB protein
     0.0047   17.3   0.8      0.095   13.1   0.3    2.8  2  AAA_16    AAA ATPase domain
     0.0055   15.9   0.0      0.011   15.0   0.0    1.4  1  NB-ARC    NB-ARC domain
  ------ inclusion threshold ------
      0.043   13.7   0.0      0.082   12.8   0.0    1.5  1  NACHT     NACHT domain
      0.071   12.6   0.0       0.19   11.2   0.0    1.7  2  AAA_7     P-loop containing dynein motor region
       0.11   11.8   0.0       0.22   10.8   0.0    1.5  1  AIG1      AIG1 family
       0.18   11.0   0.0       0.26   10.5   0.0    1.2  1  DUF2075   Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         6   1.2e+04      34      47 ..     212     225 ..     210     226 .. 0.79
   2 !   58.6   0.0   2.2e-19   4.3e-16       1      77 [.     317     392 ..     317     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6
                                   -----HHHHHHHHH CS
                        Cdc6_C  34 vdpltqrevsdlls 47 
                                   + p +++e +d+l+
  gi|70606689|ref|YP_255559.1| 212 FPPYKSTELYDILA 225
                                   57889999999986 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 2.2e-19
                                   HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSS CS
                        Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvd 77 
                                   L alvll++++g + +++g+++++Y +l +  g +p+ ++++ +++++++ +g++++++s++G+r grt+++sL ++
  gi|70606689|ref|YP_255559.1| 317 LKALVLLHDQEGIDFFPIGKIEQRYVELSKNFGEEPRRHTQIFEYVRRMKLMGLINTRQSGRGMR-GRTTLVSLPIP 392
                                   78**************************************************************7.********876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.1   4.7e-18   9.3e-15       8     128 ..      61     187 ..      59     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.7e-18
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                   lv++G +GtGK+++ +++  +l e +++e+  r e+v+v++  + ++  +l+e+ + l l+l +++lss+e ++ ++++l+
  gi|70606689|ref|YP_255559.1|  61 LVIIGRTGTGKSVTTKKFGLKLRE-IAHERnLRLEYVHVNCHRQRTLYLILQEISQGLRLQLPNRGLSSQETFRIIYDYLE 140
                                   79*******************965.555556************************************************** PP

                        AAA_22  88 aravielliiDEaqhlrs...eealeeLrsllnl...srkgvqliLv 128
                                   +r  + ++ +DE++++ s    e + +L++ ++     +k ++ i++
  gi|70606689|ref|YP_255559.1| 141 KRNIHLVITLDEFDYFVStapLEDIYFLVRVYDElnvTTKRLHYIFI 187
                                   ***************76523466666666666645656666666665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00023      13     132 ..      37     157 ..      27     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                          TniB  13 yprakeilerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLea 93 
                                    +++ke++ ++++L+ +p ++    l+++G++ +GK++  +kF  + ++  +e++ +++ ++v++  + +   + ++i + 
  gi|70606689|ref|YP_255559.1|  37 ENQIKEMTVSFRDLILNPGSSS-IRLVIIGRTGTGKSVTTKKFGLKLREIAHERNLRLEYVHVNCHRQRTLYLILQEISQG 116
                                   57889999999*******9999.5699*****************99999999***************************** PP

                          TniB  94 lgaplkara.rvskleqqvlrllrelkvrvLi.iDEihnll 132
                                   l+ +l +r  + ++  + ++ +l++ +++++i +DE++ ++
  gi|70606689|ref|YP_255559.1| 117 LRLQLPNRGlSSQETFRIIYDYLEKRNIHLVItLDEFDYFV 157
                                   ****98887344466677889******9987758**98765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   4.8e-05     0.095       2     160 ..      33     170 ..      32     187 .. 0.63
   2 ?   -0.6   0.0      0.79   1.6e+03     106     160 ..     252     322 ..     197     331 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                        AAA_16   2 lvGReeeleqLlsale..rvrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.salaqalar 78 
                                   l+ Re+++++++  ++   ++ g++   ++++G  G+GKs   +++   l++            +e+++++ ++ +++  r
  gi|70606689|ref|YP_255559.1|  33 LPHRENQIKEMTVSFRdlILNPGSSsIRLVIIGRTGTGKSVTTKKFGLKLREI----------AHERNLRLeYVHVNCH-R 102
                                   7889999999999999653444444545669************9998444433..........3333333322466777.5 PP

                        AAA_16  79 eellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade.aslqllaaL 158
                                    + l  +l+e ++ ++ + + + ++                 e+++ + ++l+++   lv++lD+++ + + a+l+ +++L
  gi|70606689|ref|YP_255559.1| 103 QRTLYLILQEISQGLRLQLPNRGLS---------------SQETFRIIYDYLEKRNIHLVITLDEFDYFVStAPLEDIYFL 168
                                   5777778777555444444443333...............34444444466666555699999999966443666667777 PP

                        AAA_16 159 lr 160
                                   +r
  gi|70606689|ref|YP_255559.1| 169 VR 170
                                   66 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.79
                        AAA_16 106 a.............avpelagaea...srllellkrllallsrderplvlvlDdlqwadeaslqllaaLlr 160
                                   +             ++ elag++a   ++   +l ++ +  s+  + l  ++D +  +d ++l +l+aL+ 
  gi|70606689|ref|YP_255559.1| 252 GfdkggsgnarisiETLELAGKIAdseNSPIVTLEHAKKANSKINPELSALIDSIKELDLHQLIFLKALVL 322
                                   34444444444444334444444455555555555555444443333777777777777777777777665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.4e-06     0.011      15     109 ..      53     148 ..      41     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.4e-06
                                   TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBT...EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSH CS
                        NB-ARC  15 kdelqslvvalvGmgGvGKttlakqilnksdevegrFd...svawvvvsktdkseeiletilkeLslseddleekeevesl 92 
                                   + ++ s+ + + G+ G GK++  k+   k+ e+ ++ +    ++ v   ++ + + il++i + L l+  ++   + +e  
  gi|70606689|ref|YP_255559.1|  53 NPGSSSIRLVIIGRTGTGKSVTTKKFGLKLREIAHERNlrlEYVHVNCHRQRTLYLILQEISQGLRLQLPNRGLSS-QE-T 131
                                   5667778899***********************99655425566777789999************98855544444.44.6 PP

                                   HHHHHHHCCCTTEEEEE CS
                        NB-ARC  93 krklvrlLltkrfllvl 109
                                    r ++ +L++++  lv+
  gi|70606689|ref|YP_255559.1| 132 FRIIYDYLEKRNIHLVI 148
                                   999******99554432 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05     0.082       3      98 ..      61     161 ..      60     208 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC.-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C....CHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqga.fklvFflslrelsrsgna.rsladllfsqlpepaapvse....vwavll 77 
                                   +++ G+ G GK++  +k+ l+++e   +++   ++v + + r+++    +   + + l+ qlp  +  ++e    +  +l 
  gi|70606689|ref|YP_255559.1|  61 LVIIGRTGTGKSVTTKKFGLKLREIAHERNLrLEYVHVNCHRQRTL-YLIlQEISQGLRLQLPNRGLSSQEtfriIYDYLE 140
                                   6899***************999998777754344444433333333.2335555555666666665555555554899999 PP

                                   CSCCCEEEEEE-STT-SS-TC CS
                         NACHT  78 elperlLlilDglDelvtdlg 98 
                                   ++   l+++lD +D++v+  +
  gi|70606689|ref|YP_255559.1| 141 KRNIHLVITLDEFDYFVSTAP 161
                                   99999**********998655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.4e-05      0.19      32      58 ..      57      83 ..      39     115 .. 0.79
   2 ?   -3.1   0.0       2.4   4.9e+03      74      90 ..     127     143 ..     124     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.4e-05
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkld 58
                                  ++  ++++G tGtGK+v++k++  kl 
  gi|70606689|ref|YP_255559.1| 57 SSIRLVIIGRTGTGKSVTTKKFGLKLR 83
                                  5677899*************9876665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                         AAA_7  74 sanqlqdiiesklekrr 90 
                                   s++++ +ii ++lekr+
  gi|70606689|ref|YP_255559.1| 127 SSQETFRIIYDYLEKRN 143
                                   7899999999****996 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.22       2      43 ..      60     104 ..      59     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                   EEEEESSTTSSHHHHHHHH...HTS--SS--TTTS---SS-EEEE CS
                          AIG1   2 tivlvGktgnGkSaTgNsi...lgkkaFesklsaqsvtkkcqkks 43 
                                   ++v++G+tg+GkS T       l++ a e +l+ + v  +c++++
  gi|70606689|ref|YP_255559.1|  60 RLVIIGRTGTGKSVTTKKFglkLREIAHERNLRLEYVHVNCHRQR 104
                                   89*************988777777777888887777777777765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.26       4      55 ..      61     114 ..      59     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                       DUF2075   4 vlVtGvaGtGKtvvllnllael..eddeeertavylsvNhplvlvlrealakke 55 
                                   +++ G++GtGK+v   ++  +l    +e++ +  y+ vN   +++l+  l++ +
  gi|70606689|ref|YP_255559.1|  61 LVIIGRTGTGKSVTTKKFGLKLreIAHERNLRLEYVHVNCHRQRTLYLILQEIS 114
                                   5789************99999977788999999*********999998886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2932.67
//
Query:       gi|70606690|ref|YP_255560.1|  [L=68]
Description: hypothetical protein Saci_0904 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00042   20.1   0.3     0.0005   19.9   0.3    1.2  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0011   19.2   0.1     0.0014   18.9   0.1    1.2  1  Rrf2         Transcriptional regulator
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.019   14.9   0.2    1.3  1  HTH_45       Winged helix-turn-helix
      0.015   15.0   0.0      0.017   14.8   0.0    1.0  1  Urocanase_N  Urocanase N-terminal domain
      0.046   13.5   0.1      0.066   13.0   0.1    1.3  1  FtsK_gamma   Ftsk gamma domain
      0.046   13.7   0.0      0.073   13.0   0.0    1.3  1  MarR         MarR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3   1.7e-07    0.0005      19      61 ..       2      44 ..       1      55 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                  ++g+ +++ +a+e+ v + k  ++L+ Le+k ++e+ +g +++
  gi|70606690|ref|YP_255560.1|  2 REGEINITRLARESHVNYKKLEKALETLERKNIIEIYEGDKTK 44
                                  579999******************************9998554 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   4.8e-07    0.0014      24      62 ..       4      42 ..       1      46 [. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.8e-07
                                  C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                          Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                  + ++++ +a++  ++ + lek l++L+++++++  +G +
  gi|70606690|ref|YP_255560.1|  4 GEINITRLARESHVNYKKLEKALETLERKNIIEIYEGDK 42
                                  4599******************************99975 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   6.5e-06     0.019      17      51 ..       3      37 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.5e-06
                        HTH_45 17 egeakkTkimykanLsykllnkYLdmLvekglikk 51
                                  ege + T++  ++  +yk l+k L++L  k++i+ 
  gi|70606690|ref|YP_255560.1|  3 EGEINITRLARESHVNYKKLEKALETLERKNIIEI 37
                                  78999***************************943 PP

>> Urocanase_N  Urocanase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.8e-06     0.017      50      94 ..      15      59 ..       7      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
                                  SHHHHHHHHHHHHH--TTEEEEEETTEEEEEEE--TTS-SEEEEE CS
                   Urocanase_N 50 nweqfelivktLkeleedetLlvqsGkpvglfksheeaPrvlian 94
                                  +  +++++ k+L++le ++ + ++ G  + l++ + ++P+v+i  
  gi|70606690|ref|YP_255560.1| 15 SHVNYKKLEKALETLERKNIIEIYEGDKTKLIRINYSNPKVIILK 59
                                  4568**************************************965 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.2e-05     0.066      16      60 ..       2      46 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                    FtsK_gamma 16 eegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegskpReV 60
                                  +eg++ +  l R+ ++ Y++  + ++ Le++ i++ +eg k + +
  gi|70606690|ref|YP_255560.1|  2 REGEINITRLARESHVNYKKLEKALETLERKNIIEIYEGDKTKLI 46
                                  6788889999*****************************998766 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.4e-05     0.073      15      48 ..       3      36 ..       2      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                                  STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  +g+++++ La+ ++v+   + ++l +Le+k+ ie
  gi|70606690|ref|YP_255560.1|  3 EGEINITRLARESHVNYKKLEKALETLERKNIIE 36
                                  699*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 450.51
//
Query:       gi|162139947|ref|YP_255561.2|  [L=148]
Description: putative molybdenum cofactor biosynthesis protein MoaC [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-49  166.2   2.6    4.5e-49  166.0   2.6    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   2.6   2.5e-53   4.5e-49       1     134 [.       6     144 ..       6     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 2.5e-53
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    m+d+s k+ + r+A+Aeg++kl+++t+e+i++++++kGdv+a+a++agi+aaKkt+el+p+cHp+pl+ ++ve+e+e  +
  gi|162139947|ref|YP_255561.2|   6 MIDISGKDIVLREAIAEGFIKLKKDTIEKITKREIEKGDVIATAKVAGILAAKKTHELLPMCHPIPLEYINVEIEIE--N 83 
                                    9*************************************************************************987..8 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                    + +++ +tv+++ +tGvemEALta+s+a+lt++DmvK+++k+       ++i+++r+v+K 
  gi|162139947|ref|YP_255561.2|  84 DGLKVVSTVRAHYRTGVEMEALTATSIALLTIWDMVKKYEKDeegqyplTEISKIRVVSKI 144
                                    9****************************************99****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1122.68
//
Query:       gi|70606692|ref|YP_255562.1|  [L=437]
Description: replication factor C large subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-18   66.8   0.5    9.4e-17   61.7   0.0    3.0  2  AAA              ATPase family associated with various cellul
    6.5e-11   42.2   0.0    1.4e-10   41.1   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.2e-08   33.0   0.0    2.1e-07   31.0   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-07   31.8   0.3    5.9e-06   26.3   0.0    2.7  2  Rad17            Rad17 P-loop domain
    4.9e-07   29.2   0.1    1.9e-06   27.3   0.0    2.0  3  DUF815           Protein of unknown function (DUF815)
      8e-07   29.2   0.0    7.6e-06   26.0   0.0    2.3  2  AAA_14           AAA domain
    8.5e-07   29.5   0.0    3.3e-06   27.6   0.0    2.2  1  AAA_16           AAA ATPase domain
    3.5e-06   27.3   0.1    7.9e-05   23.0   0.0    3.1  2  AAA_22           AAA domain
    5.3e-06   26.7   0.1    2.1e-05   24.7   0.0    2.1  1  AAA_assoc_2      AAA C-terminal domain
    9.7e-06   26.2   0.4    7.3e-05   23.3   0.0    2.7  1  AAA_18           AAA domain
    5.2e-05   23.7   0.0    0.00076   19.9   0.0    2.6  2  AAA_17           AAA domain
    0.00017   21.8   0.0     0.0013   18.9   0.0    2.3  2  AAA_2            AAA domain (Cdc48 subfamily)
    0.00021   21.1   0.0    0.00076   19.3   0.0    2.0  1  IstB_IS21        IstB-like ATP binding protein
    0.00032   20.3   0.0     0.0012   18.5   0.0    1.8  2  AAA_25           AAA domain
    0.00045   20.4   0.0     0.0017   18.5   0.0    1.9  2  AAA_33           AAA domain
    0.00071   19.9   0.0     0.0028   18.0   0.0    2.1  1  RNA_helicase     RNA helicase
    0.00085   19.3   0.2      0.029   14.3   0.0    3.1  3  NACHT            NACHT domain
    0.00086   19.1   0.0     0.0026   17.5   0.0    1.9  1  AAA_24           AAA domain
     0.0013   19.0   0.0     0.0076   16.5   0.0    2.3  2  AAA_28           AAA domain
     0.0015   17.8   0.0     0.0039   16.4   0.0    1.7  1  NB-ARC           NB-ARC domain
     0.0018   18.2   3.4     0.0023   17.9   0.1    2.9  3  ATPase_2         ATPase domain predominantly from Archaea
     0.0018   18.8   0.1      0.035   14.6   0.0    2.9  3  ABC_tran         ABC transporter
     0.0056   15.6   0.1        5.3    5.8   0.0    3.1  3  AFG1_ATPase      AFG1-like ATPase
     0.0074   15.4   0.0      0.084   11.9   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0078   16.2   0.0      0.014   15.4   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0087   16.0   0.0      0.023   14.6   0.0    1.7  1  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.1   0.0       0.67    9.3   0.0    3.2  3  TniB             Bacterial TniB protein
      0.011   15.0   0.1       0.33   10.3   0.0    2.9  3  ATPase           KaiC
      0.015   15.4   0.0      0.029   14.5   0.0    1.4  1  RFC1             Replication factor RFC1 C terminal domain
      0.017   14.9   0.2       0.38   10.5   0.0    2.8  3  DNA_pol3_delta   DNA polymerase III, delta subunit
      0.019   14.4   0.0      0.031   13.7   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.021   14.8   0.0       0.32   10.9   0.0    2.6  2  NTPase_1         NTPase
      0.033   14.0   0.0          1    9.1   0.0    2.7  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.039   13.2   0.0       0.07   12.3   0.0    1.4  1  TIP49            TIP49 P-loop domain
      0.046   13.4   0.0       0.14   11.9   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.053   13.0   0.0       0.12   11.9   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.071   13.0   0.0       0.23   11.3   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
       0.08   13.1   0.0       0.31   11.1   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain
       0.13   12.3   0.0        0.4   10.8   0.0    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
       0.16   12.3   0.1        1.2    9.5   0.0    2.3  3  AAA_19           AAA domain
       0.18   11.6   0.6       0.87    9.3   0.0    2.2  3  AAA_11           AAA domain
       0.28   11.4   0.8       0.69   10.2   0.0    1.9  2  Hydin_ADK        Hydin Adenylate kinase-like domain
       0.39   11.2   0.0       0.39   11.2   0.0    2.9  2  AAA_23           AAA domain
        1.3    9.2   3.4        0.9    9.7   0.1    2.3  2  DUF5341          Family of unknown function (DUF5341)


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.3e-19   9.4e-17       1     116 [.      44     146 ..      44     161 .. 0.89
   2 ?    1.2   0.1       1.1   4.5e+02      47      82 ..     168     198 ..     163     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.3e-19
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.....TSEEEEEETGGGHHHHHTT CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka.....kpsilfiDEidalaksrsg 76 
                                   vllyGppG+GKT+la+a+a++ + e+le+++s+ +      + ++i+++ ++a+ +      k +i+++DEid + ++   
  gi|70606692|ref|YP_255562.1|  44 VLLYGPPGVGKTTLAEALARDYKLELLEMNASDSR------NLRDIKDVAERASISGslfgiKGKIILLDEIDGIYSRA-- 116
                                   79*********************************......99*********9887789*9888***********9888.. PP

                                   CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                           AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                        +  +++++l+ +++ k       vi+++n+p++++
  gi|70606692|ref|YP_255562.1| 117 -----DAGAIPAILELIEKTKY-----PVILTANDPWDPS 146
                                   .....8999*********9988.....7*******98765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                                   HHHHHHHHHTSTSEEEEEET.GGGHHHHHTTCCCHHH CS
                           AAA  47 relfkeakekakpsilfiDE.idalaksrsgseseee 82 
                                   + l+k++ ek+  +i+ iDE +d +++++    ++++
  gi|70606692|ref|YP_255562.1| 168 KRLLKRICEKE--KIVCIDEaLDHIIEQS----EGDA 198
                                   56788888876..9******457777666....3344 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   3.5e-13   1.4e-10       2      66 ..      10      74 ..       9     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.5e-13
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsg 66
                                  rPksl+e   q++vke+lk  ie+  + e +   vllyGpPG+Gkttla+ +a++ + +l    +
  gi|70606692|ref|YP_255562.1| 10 RPKSLQEVENQDEVKEELKKWIESWLNGEPTAKAVLLYGPPGVGKTTLAEALARDYKLELLEMNA 74
                                  9*****************************************************99887654433 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   5.1e-10   2.1e-07       2      95 ..      44     134 ..      43     140 .. 0.84
   2 ?   -1.9   0.0       7.5   3.1e+03      59      73 ..     171     185 ..     160     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.1e-10
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG....G-- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve....rae 78 
                                   vlL GppG+gK++lae la+ ++ e+++++ +++ + +d+k   e     ++   ++l   + +g+i++lDE++    ra+
  gi|70606692|ref|YP_255562.1|  44 VLLYGPPGVGKTTLAEALARDYKLELLEMNASDSRNLRDIKDVAE-----RASISGSLF--GIKGKIILLDEIDgiysRAD 117
                                   8********************************999999998888.....567777887..89**********84444666 PP

                                   HHHHHHHHHHHHSSEEE CS
                         AAA_5  79 sevlnsLlslleerrll 95 
                                     ++++ l l+e+ +++
  gi|70606692|ref|YP_255562.1| 118 AGAIPAILELIEKTKYP 134
                                   66777777777777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.5
                                   ------G-SEEEEES CS
                         AAA_5  59 lvraaregeilvlDE 73 
                                   l+r +++ +i+++DE
  gi|70606692|ref|YP_255562.1| 171 LKRICEKEKIVCIDE 185
                                   67888899******9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.4e-08   5.9e-06       8      76 ..       4      72 ..       2      94 .. 0.87
   2 ?    2.6   0.0      0.28   1.1e+02      26     143 ..     350     383 ..     316     419 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-08
                         Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                  +Wf ky+P+ ++e+    +  ee+k+w+++    +   + +L+ GP+G gk+t  + L++ +  +l e 
  gi|70606692|ref|YP_255562.1|  4 QWFLKYRPKSLQEVENQDEVKEELKKWIESWLNGEPTAKAVLLYGPPGVGKTTLAEALARDYKLELLEM 72
                                  8**************9999999******99877777788999******************999888764 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.28
                         Rad17  26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesrflsqi 106
                                   +k                                                                               
  gi|70606692|ref|YP_255562.1| 350 EK------------------------------------------------------------------------------- 351
                                   33............................................................................... PP

                         Rad17 107 esfkeleLkdakylklqklGddlrtdkklilvedlP...n 143
                                           +d+    l+k G++ +t k+ +l + lP   +
  gi|70606692|ref|YP_255562.1| 352 --------RDSIETLLKKIGEKTHTSKRKVLNDTLPflaS 383
                                   ........55555666677777777777777777775533 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   4.6e-09   1.9e-06      24      99 ..      11      87 ..       3     106 .. 0.84
   2 ?   -2.8   0.0       6.7   2.7e+03      89     115 ..     115     141 ..     113     141 .. 0.85
   3 ?   -3.1   0.0       8.5   3.5e+03      81     114 ..     153     184 ..     148     212 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.6e-09
                        DUF815 24 evklddLvgidkqkealventeqfleglp.annvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklv 99
                                  + +l+++ + d+ ke+l++ +e +l+g+p a+ vLL+G  G+GK +l  al ++y+ e L +   + ++l++++++ 
  gi|70606692|ref|YP_255562.1| 11 PKSLQEVENQDEVKEELKKWIESWLNGEPtAKAVLLYGPPGVGKTTLAEALARDYKLELLEMNASDSRNLRDIKDVA 87
                                  56789999999****************985789********************998777776666666666666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.7
                        DUF815  89 kedlkelpklvellrerperfilfvDD 115
                                   + d   +p+++el++++++ +il   D
  gi|70606692|ref|YP_255562.1| 115 RADAGAIPAILELIEKTKYPVILTAND 141
                                   6677899************99997766 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 8.5
                        DUF815  81 gLrlievekedlkelpklvellrerperfilfvD 114
                                    +++ie+++     l++l++ + e+++  i+ +D
  gi|70606692|ref|YP_255562.1| 153 AVKMIELKRLGKYPLKRLLKRICEKEK--IVCID 184
                                   578888888887888888887766544..44444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.9e-08   7.6e-06       3      98 ..      42     138 ..      40     152 .. 0.76
   2 ?    0.3   0.0       1.7   6.8e+02      54      73 ..     168     186 ..     143     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.9e-08
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk.ladpekllelilek.lkeekktylflDEiqev..... 76 
                                   k++++ G+  vGKTtl++ l++++     + l++n  d r+ + ++d    +++  +  l + k ++++lDEi  +     
  gi|70606692|ref|YP_255562.1|  42 KAVLLYGPPGVGKTTLAEALARDYK---LELLEMNASDSRNLRdIKDV--AERASISGsLFGIKGKIILLDEIDGIysrad 117
                                   899******************9999...99*****9998885413332..22222222233458899******98877777 PP

                        AAA_14  77 pewekalkslvdegknldvivt 98 
                                    ++  a+ +l++++ ++ vi+t
  gi|70606692|ref|YP_255562.1| 118 AGAIPAILELIEKT-KYPVILT 138
                                   77777777777777.6677776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.7
                        AAA_14  54 elileklkeekktylflDEi 73 
                                   + +l+++ e k++++++DE+
  gi|70606692|ref|YP_255562.1| 168 KRLLKRICE-KEKIVCIDEA 186
                                   334444444.7788888885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   8.2e-09   3.3e-06      10      51 ..      25      68 ..      20     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.2e-09
                        AAA_16 10 eqLlsalervrsgrp..elvllsGesGvGKsslvrellralekd 51
                                  e+L+  +e++  g+p   +vll+G++GvGK++l+++l+r ++ +
  gi|70606692|ref|YP_255562.1| 25 EELKKWIESWLNGEPtaKAVLLYGPPGVGKTTLAEALARDYKLE 68
                                  56777889999999999*********************987765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.9e-07   7.9e-05       4      56 ..      40      83 ..      38     244 .. 0.94
   2 ?   -0.9   0.0       4.6   1.9e+03      51      79 ..     348     374 ..     323     409 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.9e-07
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                  ta+ ++++G++G+GKTtl++ l++ +         + e+++++++ s +++d+
  gi|70606692|ref|YP_255562.1| 40 TAKAVLLYGPPGVGKTTLAEALARDY---------KLELLEMNASDSRNLRDI 83
                                  57889********************9.........999999999999999887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.6
                        AAA_22  51 t.sskdllrellralglelkaerlsseell 79 
                                   t + +d  + ll+++g+++++   s++ +l
  gi|70606692|ref|YP_255562.1| 348 TkEKRDSIETLLKKIGEKTHT---SKRKVL 374
                                   323444455555555555555...333333 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   5.3e-08   2.1e-05       3      63 ..     178     232 ..     176     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 5.3e-08
                                   X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledleealqrkalryD 63 
                                   +k+ + d+al++++e ++GDaR ++n+L+ +ae         ++tl++++e++ rk +  D
  gi|70606692|ref|YP_255562.1| 178 EKIVCIDEALDHIIEQSEGDARYCINMLQGIAEGYG------KVTLDNVKELVRRKDRELD 232
                                   6788889**********************9988775......79********999987766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.8e-07   7.3e-05       1      31 [.      44      83 ..      44     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.8e-07
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf.........gvnlrdv 31
                                  +ll G+pGvGKttla++L++  ++         ++nlrd+
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARDYKLellemnasdSRNLRDI 83
                                  799***************8874445566677787777776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.9e-06   0.00076       1      26 [.      47      72 ..      47      78 .. 0.93
   2 ?    0.1   0.0       2.4   9.8e+02      52      80 ..     349     379 ..     337     399 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.9e-06
                                  EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthlsa 26
                                  +G+PG+GK+t++e l+++y+++ l++
  gi|70606692|ref|YP_255562.1| 47 YGPPGVGKTTLAEALARDYKLELLEM 72
                                  7********************99976 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHH..HSSEEEEEE-S CS
                        AAA_17  52 eekkelqkeaaekiaeea..kkkgvlvdghp 80 
                                   +ek++  +++ +ki e+   +k++vl d+ p
  gi|70606692|ref|YP_255562.1| 349 KEKRDSIETLLKKIGEKThtSKRKVLNDTLP 379
                                   3344445555556655544444556655555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.2e-06    0.0013       6     106 ..      44     131 ..      40     134 .. 0.69
   2 ?   -0.8   0.0       3.6   1.5e+03      14      63 ..     162     212 ..     153     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.2e-06
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG------ CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihpkes 85 
                                   +ll gp gvGkt la+ala+  ++    +l  ++as+     +++ + +r  ++         +G i+llDEid i ++  
  gi|70606692|ref|YP_255562.1|  44 VLLYGPPGVGKTTLAEALARDYKL----ELLEMNASDSRNLRDIKDVAERASISGSLF---GIKGkIILLDEIDGIYSR-- 115
                                   6899*****************996....555555555555444666666666654432...23335**********993.. PP

                                   -------HHHHHHHHHHHH-- CS
                         AAA_2  86 sgadvSregVqrdLLqilegg 106
                                           g   ++L ++e++
  gi|70606692|ref|YP_255562.1| 116 -----ADAGAIPAILELIEKT 131
                                   .....2335666666666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.6
                                   SSHHHHHHHHHHHTT-....-EEEEEGGG---...----THHHHHHHHHTTT- CS
                         AAA_2  14 vGktelakalaellfvkkekkliradaselle...eeevehlvsrligappgy 63 
                                    Gk  l++ l ++ +  kek +++ +a + +    e +++  +++l+g ++gy
  gi|70606692|ref|YP_255562.1| 162 LGKYPLKRLLKRICE--KEKIVCIDEALDHIIeqsEGDARYCINMLQGIAEGY 212
                                   566667777777775..566666666665544455567778888888888877 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.9e-06   0.00076      46     150 ..      40     142 ..      15     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-06
                     IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlg..llpldq 124
                                   ++++++l Gp+GvGK+ la al+++   + l++     ++ ++ +k   +  +++  l   +k ++++lD++   +   d 
  gi|70606692|ref|YP_255562.1|  40 TAKAVLLYGPPGVGKTTLAEALARDYKLELLEMNASD-SRNLRDIKDVAERASISGSLF-GIKGKIILLDEIDgiYSRADA 118
                                   46789*****************986543333333222.222333333333344443332.345577777776433566666 PP

                     IstB_IS21 125 aeaellfeviekryerrsiiitsnlp 150
                                    +   ++e+iek   + ++i+t+n p
  gi|70606692|ref|YP_255562.1| 119 GAIPAILELIEKT--KYPVILTANDP 142
                                   6666777777764..66777777765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0012      12      56 ..      17      64 ..       8      71 .. 0.80
   2 ?   -1.6   0.0       4.3   1.7e+03     144     180 ..     179     213 ..     150     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                        AAA_25 12 vadlaapppprrwlvkgll...pagelallaGapgtGKttlaldlala 56
                                  v++ +   ++++++++ +l   p  + +ll+G+pg+GKttla  la +
  gi|70606692|ref|YP_255562.1| 17 VENQDEVKEELKKWIESWLngePTAKAVLLYGPPGVGKTTLAEALARD 64
                                  5666777888899999998444567889**************999976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                        AAA_25 144 rlvviDplsralggdensnsdvgalvealeriarrtg 180
                                   + v+iD   ++ +  e+s+ d++ ++++l+ ia+ +g
  gi|70606692|ref|YP_255562.1| 179 KIVCIDE--ALDHIIEQSEGDARYCINMLQGIAEGYG 213
                                   5666663..3444478888899999999999988777 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.1e-06    0.0017       2      32 ..      44      74 ..      44     156 .. 0.83
   2 ?   -1.7   0.0         7   2.8e+03      53     114 ..     353     420 ..     333     432 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.1e-06
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt 32
                                  vll G+pG+GK+tlae l++  + +ll+ ++
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARDYKLELLEMNA 74
                                  7899***************999998887665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7
                        AAA_33  53 drlyqilnelarkalsagrnvildat......nlsr.rerarflklarrlgvpvrivvvetdeetlkeR 114
                                   d++   l+++ +k+ +++r v+ d        ++++ ++ +++l+l +  + +++ v+ +++  t +e+
  gi|70606692|ref|YP_255562.1| 353 DSIETLLKKIGEKTHTSKRKVLNDTLpflasyYTRHaEAVENYLQLTEGEK-EILNVFTQASKPTSEEK 420
                                   445555555555555555555554434444433333244566666665433.55556666666666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.9e-06    0.0028       1      26 [.      44      69 ..      44     140 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.9e-06
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                  ++lyGp+g+GK+tla+ La++   +l
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARDYKLEL 69
                                  689*****************988655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.9   3.6e+03      94     115 ..      18      37 ..      13      40 .. 0.64
   2 !   14.3   0.0   7.1e-05     0.029       3      25 ..      44      66 ..      42      98 .. 0.88
   3 ?    1.1   0.0      0.82   3.3e+02      85     162 ..     104     174 ..      82     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.9
                                   SS-TCH.........HHHHHCT CS
                         NACHT  94 vtdlgqkekqpvrtlLselirk 115
                                   +++++   k+++++++++++++
  gi|70606692|ref|YP_255562.1|  18 ENQDEV--KEELKKWIESWLNG 37 
                                   443333..77788888888875 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.1e-05
                                  EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                  v+l G++G+GKTtL++ la++ +
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARDYK 66
                                  899***************99876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.82
                                   EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHHHHHC CS
                         NACHT  85 lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegfsesrrkqlvrky 162
                                   ++lD +D + +  ++    +    + eli+k   ++ +++lt+     + l+++    +++e++ ++++  k+l+ + 
  gi|70606692|ref|YP_255562.1| 104 ILLDEIDGIYSRADA---GA-IPAILELIEK---TKYPVILTANDPWDPSLRSLRNAVKMIELKRLGKYPLKRLLKRI 174
                                   678888888886666...44.445569****...89999999877666666655555599999999988888887765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.3e-06    0.0026       2      23 ..      41      64 ..      40     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.3e-06
                        AAA_24  2 klkiliyGpsgiGKTtlakel..g 23
                                  ++ +l+yGp+g+GKTtla  l   
  gi|70606692|ref|YP_255562.1| 41 AKAVLLYGPPGVGKTTLAEALarD 64
                                  5779**************998543 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.9e-05    0.0076       2      22 ..      44      64 ..      43      83 .. 0.86
   2 ?   -1.7   0.0       7.4     3e+03      68     103 ..     365     399 ..     330     424 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-05
                        AAA_28  2 ivitGgestGKTtlleaLaar 22
                                  + + G+++ GKTtl+eaLa++
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARD 64
                                  7899***************86 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.4
                        AAA_28  68 aaaaankvlfcDrglldtlaYarayggeaeaeleaa 103
                                   +  ++++ ++ D+ ++    Y r+ +   e++l+  
  gi|70606692|ref|YP_255562.1| 365 KTHTSKRKVLNDTLPFLASYYTRHAEAV-ENYLQLT 399
                                   3345666677777777777777777665.6665444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.5e-06    0.0039       7      44 ..      26      65 ..      20      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-06
                                  HHHHHHHC..TTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                        NB-ARC  7 kviekLle..kdelqslvvalvGmgGvGKttlakqilnks 44
                                  +++++     ++e+    v l+G +GvGKttla+   +++
  gi|70606692|ref|YP_255562.1| 26 ELKKWIESwlNGEPTAKAVLLYGPPGVGKTTLAEALARDY 65
                                  44444333336888888****************9988874 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   5.7e-06    0.0023       9      44 ..      29      65 ..      24     216 .. 0.65
   2 ?   -2.1   0.0       7.2   2.9e+03     199     222 ..     261     284 ..     252     288 .. 0.85
   3 ?   -1.7   0.2       5.4   2.2e+03      53      68 ..     380     395 ..     336     429 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.7e-06
                      ATPase_2  9 keleeilerepn.eiyfiYGpegsGKtaLlkeiienl 44
                                  k +e++l+ ep  + +++YGp g+GKt+L   ++   
  gi|70606692|ref|YP_255562.1| 29 KWIESWLNGEPTaKAVLLYGPPGVGKTTLAEALARDY 65
                                  469*****9985268899***********98776554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.2
                      ATPase_2 199 nflkegfkeleelskedfeeiyry 222
                                   ++l++ f e++ l+ +++e+++r 
  gi|70606692|ref|YP_255562.1| 261 ELLMRWFDENIPLQYTSMEDVWRA 284
                                   678889999999999999999996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.4
                      ATPase_2  53 yyialreesiskldef 68 
                                   ++ +  ++  + ++++
  gi|70606692|ref|YP_255562.1| 380 FLASYYTRHAEAVENY 395
                                   2222222222222222 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.6e-05     0.035      12      39 ..      42      69 ..      39     110 .. 0.78
   2 ?   -0.9   0.0       5.2   2.1e+03     119     136 ..     170     187 ..     163     188 .. 0.84
   3 ?   -0.5   0.0         4   1.6e+03      77     115 ..     347     404 ..     319     418 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.6e-05
                                  SEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 12 ekvaivGenGaGKStLlkllagllkpte 39
                                  + v + G+ G GK+tL+++la+ +k + 
  gi|70606692|ref|YP_255562.1| 42 KAVLLYGPPGVGKTTLAEALARDYKLEL 69
                                  56889*****************998754 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.2
                                   HHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxx RF
                      ABC_tran 119 larallkkpkllllDEpt 136
                                   l + +++k k++++DE+ 
  gi|70606692|ref|YP_255562.1| 170 LLKRICEKEKIVCIDEAL 187
                                   5567899*********85 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4
                                   HHHHHHTCHHHHHHHSTTGG...................TTCBGESTTSGGS-HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  77 renesdeeiekalsklglke...................lkdtvvksspssLSgGqkq 115
                                   r++e+++ ie++l+k+g k                    +++  + ++  +L +G+k+
  gi|70606692|ref|YP_255562.1| 347 RTKEKRDSIETLLKKIGEKThtskrkvlndtlpflasyyTRHAEAVENYLQLTEGEKE 404
                                   3345555555555555555433333333333333333333333333334444444444 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.013       5.3      34      80 ..      15      59 ..       8      75 .. 0.76
   2 ?    5.8   0.0     0.013       5.4     109     135 ..     159     185 ..     146     194 .. 0.84
   3 ?   -1.3   0.0       1.8   7.5e+02     282     316 ..     208     242 ..     197     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                   AFG1_ATPase 34 eelaaqdlarkssalgklfgrkrksvepvrglYlwGgvGrGKtylmd 80
                                  +e+++qd++++   l+k +    + + +++++ l+G+ G+GKt l +
  gi|70606692|ref|YP_255562.1| 15 QEVENQDEVKEE--LKKWIESWLNGEPTAKAVLLYGPPGVGKTTLAE 59
                                  688899998885..4444443334555689*************9965 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                   AFG1_ATPase 109 klrkekdplaivadrlaeearvlCfDE 135
                                     r +k pl+  ++r++e+ +++C+DE
  gi|70606692|ref|YP_255562.1| 159 LKRLGKYPLKRLLKRICEKEKIVCIDE 185
                                   4445799*******************9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.8
                   AFG1_ATPase 282 laerfhtvlledVpvltkakedaarRfiaLvDelY 316
                                   +ae +  v l++V+ l + k+ +   f +L D ++
  gi|70606692|ref|YP_255562.1| 208 IAEGYGKVTLDNVKELVRRKDRELDPFETLRDVFW 242
                                   7899999**********999999999999999886 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00021     0.084      97     136 ..      25      63 ..       6      68 .. 0.80
   2 ?    0.7   0.1      0.54   2.2e+02      24      62 ..     330     369 ..     319     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                     Parvo_NS1  97 vevgqvllawlskqlgkrntvwfyGpantGktnlaeaIak 136
                                    e+++++  wl+ +     +v++yGp+  Gkt laea+a+
  gi|70606692|ref|YP_255562.1|  25 EELKKWIESWLNGE-PTAKAVLLYGPPGVGKTTLAEALAR 63 
                                   56777888888888.66679******************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.54
                     Parvo_NS1  24 eedWaaidsesYlr.lsrsragrrqienaleqakirmfst 62 
                                   +  W++ ++ +Y++ l r++++r +ie++l+ +  ++ ++
  gi|70606692|ref|YP_255562.1| 330 KARWVKYQFPQYIQaLARTKEKRDSIETLLKKIGEKTHTS 369
                                   568*********8736788889999***999987777665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.4e-05     0.014      11      46 ..      24      68 ..      14      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-05
                                  HHHHHHCH.........TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE 11 gkklakal.........gdvilLeGdLGaGKTtlvrglakalgve 46
                                   ++l+k +         ++++lL+G+ G+GKTtl+ +la+ +++e
  gi|70606692|ref|YP_255562.1| 24 KEELKKWIeswlngeptAKAVLLYGPPGVGKTTLAEALARDYKLE 68
                                  44444433333455555567*******************988765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.5e-05     0.023      98     135 ..      40      77 ..       8      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-05
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S------- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevseklg 135
                                   + k ++l G+ GvGK+tL +al+ + +l+  e+ ++++
  gi|70606692|ref|YP_255562.1|  40 TAKAVLLYGPPGVGKTTLAEALARDYKLELLEMNASDS 77 
                                   347889*****************999998888777665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0016      0.67      18      60 ..      22      66 ..      12      81 .. 0.73
   2 ?    0.8   0.0      0.68   2.8e+02     114     159 ..      95     137 ..      67     142 .. 0.74
   3 ?    0.1   0.0       1.2   4.7e+02     119     150 ..     177     209 ..     147     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                          TniB 18 eilerLeeLley.pk.rkrmpnlllvGdsnnGKtmivekFarlhp 60
                                  e+ e+L++ +e   + +   + +ll+G++ +GKt+++e  ar+++
  gi|70606692|ref|YP_255562.1| 22 EVKEELKKWIESwLNgEPTAKAVLLYGPPGVGKTTLAEALARDYK 66
                                  5556664433331332555689****************9999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.68
                          TniB 114 llrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                    l  +k +++++DEi+ +    +r+   ++ a+  L ++ k p++l
  gi|70606692|ref|YP_255562.1|  95 SLFGIKGKIILLDEIDGIY---SRADAGAIPAILELIEKTKYPVIL 137
                                   5556788999999999998...556666667777777777777765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.2
                          TniB 119 kvrvLiiDE.ihnllagsarkqreflnalksLg 150
                                   k +++ iDE ++++++ s  + r ++n+l+ + 
  gi|70606692|ref|YP_255562.1| 177 KEKIVCIDEaLDHIIEQSEGDARYCINMLQGIA 209
                                   568999**9569999999999999999998775 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00081      0.33      14      37 ..      36      59 ..      17      68 .. 0.86
   2 ?   -2.1   0.0         5     2e+03      76     129 ..     173     221 ..     167     232 .. 0.52
   3 ?    1.1   0.0      0.51   2.1e+02      65     133 ..     296     361 ..     289     423 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                        ATPase 14 gGipegrvvlitGepGtGKtifal 37
                                  +G p +++vl++G pG GKt++a+
  gi|70606692|ref|YP_255562.1| 36 NGEPTAKAVLLYGPPGVGKTTLAE 59
                                  78899*****************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
                        ATPase  76 kleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsit 129
                                   ++ e++k++ id + + +    e+++ d++  i+ l+ + + ++  +v +D+++
  gi|70606692|ref|YP_255562.1| 173 RICEKEKIVCIDEALDHII---EQSEGDARYCINMLQGIAEGYG--KVTLDNVK 221
                                   5555666666665544433...2335555555555555554443..34455555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.51
                        ATPase  65 enakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ay 133
                                    +ak++Gwdl  +     l+   ++   +  +++k  ++++ ++ ++ ++i+++  ++   Dsi++l ++
  gi|70606692|ref|YP_255562.1| 296 TRAKQVGWDLLSYVFD--LMGPGIAF--ASLEKKKPGYKARWVKYQFPQYIQALARTKEKRDSIETLlKK 361
                                   5667777777666655..22111111..112233455666666666666666666666666666666322 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.2e-05     0.029      15      95 ..     301     388 ..     293     413 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-05
                                   S-GGGHHHHHHHHTHHHHHTT-EE-SS..........-----SHHHHHHHHHHHHHHHHHHHTTTTT------HHHHHTTT CS
                          RFC1  15 qnWsLlpthavlssvlPaslvrgsleg..........risFpswLGknSktnKnkRllqelqshlrlktsaskselrldyl 85 
                                     W+Ll +  v+  + P+ + +  le+          +++Fp++     +t++++  +++l  ++  kt++sk+++  d+l
  gi|70606692|ref|YP_255562.1| 301 VGWDLLSY--VFDLMGPGIAFAS-LEKkkpgykarwvKYQFPQYIQALARTKEKRDSIETLLKKIGEKTHTSKRKVLNDTL 378
                                   56999999..8999999544442.33345566778889******************************************* PP

                                   HHHHHHHHS- CS
                          RFC1  86 pllkkklvkp 95 
                                   p+l  +++++
  gi|70606692|ref|YP_255562.1| 379 PFLASYYTRH 388
                                   ****999987 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   1.6e+03     127     140 ..      23      36 ..       7      39 .. 0.76
   2 ?   10.5   0.0   0.00092      0.38      59     170 ..     102     206 ..      73     209 .. 0.74
   3 ?    0.6   0.0         1   4.1e+02     130     164 ..     337     368 ..     323     400 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                                   -TTTHHHHHHHHHH CS
                DNA_pol3_delta 127 keeelkkwiqkraq 140
                                    +eelkkwi+++++
  gi|70606692|ref|YP_255562.1|  23 VKEELKKWIESWLN 36 
                                   5789*****99875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00092
                                   EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHH CS
                DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkra 139
                                   +i++l+    +   s  ++  + ++ e++++  ++   il+a++  d    ++  L + ++++e k+l +  lk+ +++++
  gi|70606692|ref|YP_255562.1| 102 KIILLDEIDGI--YSRADAGAIPAILELIEK--TKYPVILTANDPWD---PSLRSLRNAVKMIELKRLGKYPLKRLLKRIC 175
                                   55555555444..444555555555555555..44445556664455...46667788888******************** PP

                                   HHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                DNA_pol3_delta 140 qelglkiekealelLlelvennlsaikqele 170
                                   +++++   +eal+ ++e +e++ +   + l+
  gi|70606692|ref|YP_255562.1| 176 EKEKIVCIDEALDHIIEQSEGDARYCINMLQ 206
                                   *********************9888777766 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1
                                   THHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHH CS
                DNA_pol3_delta 130 elkkwiqkraqelglkiekealelLlelvennlsa 164
                                   +++++iq+ a+++    +++++e+Ll++++  + +
  gi|70606692|ref|YP_255562.1| 337 QFPQYIQALARTKE---KRDSIETLLKKIGEKTHT 368
                                   67788888887544...467777777777766654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.5e-05     0.031      24      43 ..      43      62 ..      15      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                  Mg_chelatase 24 nlllvGppGsGKtmlakrlp 43
                                   +ll+GppG GKt la++l+
  gi|70606692|ref|YP_255562.1| 43 AVLLYGPPGVGKTTLAEALA 62
                                  68**************9985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00077      0.32       2      21 ..      44      63 ..      43      73 .. 0.85
   2 ?    0.3   0.0       1.4   5.7e+02      98     155 ..     103     159 ..      91     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00077
                                  EEEE--TTSSHHHHHHHHHH CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvle 21
                                  v++ GppGvGKtTl + +++
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALAR 63
                                  6789**********998876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                   EEEE---.STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEEE- CS
                      NTPase_1  98 viviDEi.GkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkvfev 155
                                   +i++DEi G      +  + a+ e+++ ++ pv+ +   +   + ++++r+   vk++e+
  gi|70606692|ref|YP_255562.1| 103 IILLDEIdGIYSRADAGAIPAILELIEkTKYPVILTANDP-WDPSLRSLRNA--VKMIEL 159
                                   8888999667777778889999999998899999999999.55778888877..666665 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0025         1       4      42 ..      26      64 ..      23      77 .. 0.84
   2 ?    0.0   0.0       1.6   6.4e+02      85     142 ..      80     141 ..      69     162 .. 0.64
   3 ?   -0.1   0.0       1.7   6.8e+02      67     106 ..     337     373 ..     276     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
               DNA_pol3_delta2  4 ealkilskalksgrlahayLfeGdegigkkelalnlaka 42
                                  e  k +++ l+ +  a+a L++G+ g+gk +la +la+ 
  gi|70606692|ref|YP_255562.1| 26 ELKKWIESWLNGEPTAKAVLLYGPPGVGKTTLAEALARD 64
                                  5566677777788899*******************9975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.6
               DNA_pol3_delta2  85 ldqirelieelsrkpre..skkkiiiiedaekmtksAaN....alLktlEEPsenaifiLitsd 142
                                   l +i+++ e++s ++     k kii++++++ + ++A      a+L ++E    +  +iL+++d
  gi|70606692|ref|YP_255562.1|  80 LRDIKDVAERASISGSLfgIKGKIILLDEIDGIYSRADAgaipAILELIEKT--KYPVILTAND 141
                                   5566777776666655443578999999999887776422111666666654..4445555555 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.7
               DNA_pol3_delta2  67 khpDvivieteekersikldqirelieelsrkpreskkki 106
                                   ++p +i +    k    k d+i+ l +++ +k++ sk+k+
  gi|70606692|ref|YP_255562.1| 337 QFPQYIQALARTK---EKRDSIETLLKKIGEKTHTSKRKV 373
                                   5555554422222...36799999999**99999999998 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.07      49      79 ..      40      68 ..      16      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 49 aGravLlaGpsgtGktalaiaiskelgedvp 79
                                  + +avLl Gp+g Gkt la a++++    + 
  gi|70606692|ref|YP_255562.1| 40 TAKAVLLYGPPGVGKTTLAEALARDYK--LE 68
                                  569********************9864..44 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00034      0.14       6      45 ..      25      64 ..      19     101 .. 0.78
   2 ?   -2.2   0.0       7.3     3e+03      87     105 ..      94     112 ..      86     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                                  HHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
               Sigma54_activat  6 ealkelleqikkvaktdlsvlitGesGtGKellaraihea 45
                                  e+lk+ +e+  +  +t   vl+ G  G+GK++la+a+ + 
  gi|70606692|ref|YP_255562.1| 25 EELKKWIESWLNGEPTAKAVLLYGPPGVGKTTLAEALARD 64
                                  5667777777777788899****************99764 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.3
                                   HHHHHTTTSEEEEETGGGS CS
               Sigma54_activat  87 GlfekadgGtlfLDeigel 105
                                   G +   +g +++LDei  +
  gi|70606692|ref|YP_255562.1|  94 GSLFGIKGKIILLDEIDGI 112
                                   6677778899999999765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.12      33      68 ..      41      73 ..      31      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                         AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsltin 68
                                   k vll+Gp G+GKt++++ l + ++   +  l +n
  gi|70606692|ref|YP_255562.1| 41 AKAVLLYGPPGVGKTTLAEALARDYK---LELLEMN 73
                                  589***************99998877...4444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00056      0.23       2      32 ..      44      74 ..      43     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00056
                         AAA_3  2 vllegvPGlaktllvkalakaldlefkriqf 32
                                  vll g PG++kt+l++ala+  +le+  +  
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARDYKLELLEMNA 74
                                  899*****************99888766655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00077      0.31      23     111 ..      43     143 ..      23     156 .. 0.73
   2 ?   -1.6   0.0       6.4   2.6e+03      77      99 ..     158     180 ..     146     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00077
                                   -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H....HHHHHHT.........TTSEEEEEE-TT.--HHHHHHH CS
               Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgpwleifvverlaklp....ldlleqa.........kggtLylkdiad.lskaeqkeL 89 
                                    v+l G++G gk++ A++L+       e+ +++ + + +    +d+ e+a         kg +++l +i+  +s+a+   +
  gi|70606692|ref|YP_255562.1|  43 AVLLYGPPGVGKTTLAEALARDYKL--ELLEMNASDSRNlrdiKDVAERAsisgslfgiKGKIILLDEIDGiYSRADAGAI 121
                                   69*****************987766..444443333322234477777744444445559999999999973577777788 PP

                                   HHHHHHHTTTT-EEEEEEEE-T CS
               Sigma54_activ_2  90 lellakaeksslrlVstsskdl 111
                                   + +l+  ek +  ++ t    +
  gi|70606692|ref|YP_255562.1| 122 PAILELIEKTKYPVILTANDPW 143
                                   8888888888888877766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.4
                                   E-TT--HHHHHHHHHHHHHHTTT CS
               Sigma54_activ_2  77 diadlskaeqkeLlellakaeks 99 
                                   +++ l+k  +k+Ll+++ ++ek 
  gi|70606692|ref|YP_255562.1| 158 ELKRLGKYPLKRLLKRICEKEKI 180
                                   678899999999**999999875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00097       0.4       2      22 ..      44      64 ..      43     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00097
                                  EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                  v+++G p vGK+tL  al ++
  gi|70606692|ref|YP_255562.1| 44 VLLYGPPGVGKTTLAEALARD 64
                                  789***************985 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0028       1.2       9      32 ..      40      63 ..      34      78 .. 0.83
   2 ?   -1.8   0.0       8.9   3.6e+03      98     110 ..     173     185 ..     149     193 .. 0.59
   3 ?   -1.8   0.0       8.5   3.5e+03      45      75 ..     342     372 ..     331     422 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhiva 32
                                  ++k +l+ ++pG GKT++ ++  +
  gi|70606692|ref|YP_255562.1| 40 TAKAVLLYGPPGVGKTTLAEALAR 63
                                  57899***********98877665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.9
                        AAA_19  98 kklqeeellivDE 110
                                   +  ++e+++ +DE
  gi|70606692|ref|YP_255562.1| 173 RICEKEKIVCIDE 185
                                   2222333555555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.5
                        AAA_19  45 illvaftgrAakelrerlaalgaeatTiHrl 75 
                                   i ++a t+   + +++ l+++g++++T  r 
  gi|70606692|ref|YP_255562.1| 342 IQALARTKEKRDSIETLLKKIGEKTHTSKRK 372
                                   5556666666666666666666664444433 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0021      0.87       4      39 ..      25      63 ..      22      88 .. 0.76
   2 ?   -2.5   0.0       8.6   3.5e+03     216     226 ..     176     186 ..     152     261 .. 0.72
   3 ?   -1.1   0.6       3.2   1.3e+03     127     150 ..     349     400 ..     318     436 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0021
                        AAA_11  4 dsqreaiksalsese...itliqGPPGtgKTktivells 39
                                  ++ +++i+s l+ +     +l+ GPPG gKT+   +l +
  gi|70606692|ref|YP_255562.1| 25 EELKKWIESWLNGEPtakAVLLYGPPGVGKTTLAEALAR 63
                                  56677788888877777789***********87666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.6
                        AAA_11 216 kkfdvviIDEA 226
                                   +k ++v IDEA
  gi|70606692|ref|YP_255562.1| 176 EKEKIVCIDEA 186
                                   34445555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.2
                        AAA_11 127 keiskeleklakelrafeeeeek............................e 150
                                   ke+++++e+l k++ +++ ++++                            e
  gi|70606692|ref|YP_255562.1| 349 KEKRDSIETLLKKIGEKTHTSKRkvlndtlpflasyytrhaeavenylqltE 400
                                   3333333333333333333333244444444444454444444433433330 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0017      0.69       1      29 [.      43      71 ..      43      75 .. 0.90
   2 ?   -1.5   0.5       6.5   2.6e+03      79     115 ..     353     394 ..     340     436 .. 0.39

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0017
                     Hydin_ADK  1 aiivhGaPlsGKtatavtLakkYeaAllt 29
                                  a+++ G+P  GKt+ a +La+ Y+  ll 
  gi|70606692|ref|YP_255562.1| 43 AVLLYGPPGVGKTTLAEALARDYKLELLE 71
                                  78999******************988776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.5
                     Hydin_ADK  79 lsvealvkktselssaaeekaas..........skiskkkktsvvsg 115
                                    s e+l+kk+ e++ ++++k+ +          +     ++++ v++
  gi|70606692|ref|YP_255562.1| 353 DSIETLLKKIGEKTHTSKRKVLNdtlpflasyyT-----RHAEAVEN 394
                                   4555555555555555555444444444322220.....22222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00096      0.39      21      39 ..      43      61 ..      31      63 .. 0.89
   2 ?   -1.3   3.7       6.2   2.5e+03     148     169 ..     348     369 ..     318     430 .. 0.40

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00096
                        AAA_23 21 ltlItGpNGaGKTTildAi 39
                                   +l++Gp G GKTT+ +A+
  gi|70606692|ref|YP_255562.1| 43 AVLLYGPPGVGKTTLAEAL 61
                                  679***************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.2
                        AAA_23 148 lkdkkerleelekeleeledek 169
                                   +k+k + +e l k++ e++ + 
  gi|70606692|ref|YP_255562.1| 348 TKEKRDSIETLLKKIGEKTHTS 369
                                   2222222222222222222211 PP

>> DUF5341  Family of unknown function (DUF5341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.7       6.7   2.7e+03      49      86 ..     225     261 ..     188     284 .. 0.58
   2 ?    9.7   0.1    0.0022       0.9      54      95 ..     321     362 ..     313     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.7
                       DUF5341  49 kaknkslkkrtdrfeveWvSynydnsnsdlakkaeede 86 
                                   + k ++l   +   +v W  y +  +n+  ++++ ++e
  gi|70606692|ref|YP_255562.1| 225 RRKDRELDPFETLRDVFWAKYYWQAKNAV-TNSQVDYE 261
                                   44555555555555788888888876543.33333334 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                       DUF5341  54 slkkrtdrfeveWvSynydnsnsdlakkaeedeglegnfeev 95 
                                   sl+k++  +++ Wv y++ +  + la+++e+ +  e  ++++
  gi|70606692|ref|YP_255562.1| 321 SLEKKKPGYKARWVKYQFPQYIQALARTKEKRDSIETLLKKI 362
                                   799***********************9999987777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 2793.28
//
Query:       gi|70606693|ref|YP_255563.1|  [L=325]
Description: replication factor C small subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-23   82.1   1.3    1.1e-22   80.2   0.1    2.5  2  Rep_fac_C        Replication factor C C-terminal domain
    1.4e-16   61.2   0.0    3.2e-16   59.9   0.0    1.7  1  AAA              ATPase family associated with various cellul
    4.6e-14   52.5   0.1    1.4e-09   37.9   0.2    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.9e-07   31.0   0.0    6.4e-07   29.2   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.1e-07   29.8   0.0    1.2e-06   28.5   0.0    1.8  1  Rad17            Rad17 P-loop domain
    1.1e-06   28.8   0.3    4.4e-05   23.5   0.0    2.4  2  AAA_14           AAA domain
    1.1e-05   25.6   0.0     0.0001   22.4   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
    1.1e-05   25.8   0.3      0.094   13.0   0.0    3.0  3  AAA_22           AAA domain
    1.1e-05   25.9   0.0      0.019   15.3   0.0    2.5  2  AAA_16           AAA ATPase domain
    1.5e-05   24.9   0.0    2.7e-05   24.1   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    3.5e-05   24.4   0.0     0.0002   21.9   0.0    2.2  3  AAA_18           AAA domain
    4.5e-05   23.3   0.0     0.0002   21.1   0.0    2.0  2  AAA_24           AAA domain
    6.4e-05   22.3   0.0    0.00049   19.4   0.0    2.2  1  TIP49            TIP49 P-loop domain
     0.0001   22.1   0.1    0.00031   20.5   0.1    1.8  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00029   20.6   0.0    0.00051   19.8   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
    0.00062   20.1   0.0     0.0018   18.6   0.0    1.9  1  AAA_assoc_2      AAA C-terminal domain
    0.00079   19.3   0.0     0.0015   18.4   0.0    1.4  1  AAA_11           AAA domain
    0.00089   19.0   0.0     0.0075   16.0   0.0    2.2  2  AAA_30           AAA domain
     0.0009   19.2   0.2     0.0018   18.2   0.1    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
    0.00092   18.7   0.1      0.064   12.7   0.0    2.3  2  TniB             Bacterial TniB protein
     0.0018   17.9   0.0      0.003   17.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0019   18.2   0.0      0.009   16.0   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0019   17.6   0.0       0.12   11.8   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0033   16.8   0.0      0.039   13.3   0.0    2.6  4  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0046   16.4   0.0       0.35   10.3   0.0    2.4  2  PhoH             PhoH-like protein
     0.0049   16.1   0.0     0.0079   15.4   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0076   16.6   0.2       0.19   12.1   0.1    2.6  2  AAA_19           AAA domain
     0.0096   16.1   0.2      0.025   14.8   0.2    2.0  1  AAA_33           AAA domain
     0.0096   15.2   0.1       0.08   12.2   0.1    2.0  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0097   15.0   0.0      0.019   14.0   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   15.3   0.7      0.044   13.4   0.3    2.2  2  AAA_25           AAA domain
      0.014   15.1   0.0       0.38   10.4   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.017   14.9   0.1      0.053   13.3   0.0    1.8  2  Phage_T4_Ndd     T4-like phage nuclear disruption protein (Nd
       0.02   14.6   0.0      0.035   13.8   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.027   13.9   0.0      0.079   12.4   0.0    1.8  2  KTI12            Chromatin associated protein KTI12
      0.031   14.5   0.0      0.082   13.1   0.0    1.7  1  AAA_28           AAA domain
       0.04   14.3   0.0       0.18   12.2   0.0    2.2  1  RNA_helicase     RNA helicase
      0.051   13.7   0.1        0.4   10.8   0.1    2.1  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.073   12.8   0.7         14    5.4   0.0    2.7  2  DEAD             DEAD/DEAH box helicase
      0.092   12.6   0.6       0.73    9.7   0.0    2.5  2  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       4.7   2.1e+03       3      25 ..     183     204 ..     162     212 .. 0.66
   2 !   80.2   0.1   2.4e-25   1.1e-22       2      88 .]     226     313 ..     225     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.7
                                   HHHHHHHHHHHHHT-HHHHHHHH CS
                     Rep_fac_C   3 pteieeileaclngdfeeaykkl 25 
                                   p+ ie+i++   +gd ++a +++
  gi|70606693|ref|YP_255563.1| 183 PKGIETIFDIT-QGDMRKAINVI 204
                                   55566666666.66666666665 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 2.4e-25
                                   -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH-HHHH CS
                     Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGasehlq 81 
                                   +p+ei+e+l+ +l+g+f +a++klrell+++G+s+edi++q+h+ +  +  ++p+++k+ +++++ge+e+r+ eGa++++q
  gi|70606693|ref|YP_255563.1| 226 QPKEIREMLHLALSGKFLQARDKLRELLINYGLSGEDIIKQVHKELTGNeISIPDDLKVILVDYAGEVEFRIMEGADDEIQ 306
                                   79*********************************************99877***************************** PP

                                   HHHHHHH CS
                     Rep_fac_C  82 lsallar 88 
                                   lsa+la+
  gi|70606693|ref|YP_255563.1| 307 LSAFLAK 313
                                   *****96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   7.2e-19   3.2e-16       1     125 [.      41     154 ..      41     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 7.2e-19
                                   EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHT CS
                           AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksrs 75 
                                   +l+ GppGtGKT++a a++++l      ++fle+++s+ +   +    +k++e+ +++ +++ p +++++DE+d+++ +  
  gi|70606693|ref|YP_255563.1|  41 LLFAGPPGTGKTTAALALVRDLygnnyRQYFLELNASDER--GIDVIRNKVKEFARTVASNNVPfKVILLDEADNMTADA- 118
                                   699******************955433488**********..99999******999988888688***********9888. PP

                                   TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                           AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                             +++L + ++ +++   ++ +i+a+n+ +k+ +++  +R  
  gi|70606693|ref|YP_255563.1| 119 ----------QQALRRTMELYTE---TTRFILACNYLSKIIEPIQ-SRTA 154
                                   ..........*************...589***************9.8865 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00022       0.1       2      47 ..      22      66 ..      21      75 .. 0.91
   2 !   37.9   0.2   3.2e-12   1.4e-09      84     162 ..      81     161 ..      69     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
               DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                  q+e+++ l+k +k++++ h +Lf+G+ g+gk ++al+l++ l  ++
  gi|70606693|ref|YP_255563.1| 22 QKEIVERLKKFVKEKNMPH-LLFAGPPGTGKTTAALALVRDLYGNN 66
                                  8999*************99.8******************9998765 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 3.2e-12
               DNA_pol3_delta2  84 kldqirelieelsrkpresk..kkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfspl 162
                                    +d ir+  +e+ r+   ++   k+i++++a++mt+ A+ al +t+E   e + fiL  +  +k++++i+SR+  ++f pl
  gi|70606693|ref|YP_255563.1|  81 GIDVIRNKVKEFARTVASNNvpFKVILLDEADNMTADAQQALRRTMELYTETTRFILACNYLSKIIEPIQSRTALFRFYPL 161
                                   7899**99999999887765237******************************************************9987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.4e-09   6.4e-07       2      58 ..      12      63 ..      11     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.4e-09
                        RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                  rPksl+e + q+++ e+lk f++     e+++ h+l++GpPG Gktt a  + ++l 
  gi|70606693|ref|YP_255563.1| 12 RPKSLDEIVNQKEIVERLKKFVK-----EKNMPHLLFAGPPGTGKTTAALALVRDLY 63
                                  9******************9996.....67899***************999888874 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.8e-09   1.2e-06       6     117 ..       4     111 ..       1     139 [. 0.72

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.8e-09
                         Rad17   6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLske.lgiklrewlnpvslkep 85 
                                     lW eky+P+ ++e+   k+ +e +k+++k + +++     LL +GP+G gk+t+   L +  +g ++r++   ++  + 
  gi|70606693|ref|YP_255563.1|   4 EILWAEKYRPKSLDEIVNQKEIVERLKKFVKEKNMPH-----LLFAGPPGTGKTTAALALVRDlYGNNYRQYFLELN-ASD 78 
                                   558**************99999999999999887775.....6************9888877626899999876666.222 PP

                         Rad17  86 dnqksdfkgltekesrf.lsqiesfkeleLkda 117
                                   +   + ++ +++ + r   s    fk ++L +a
  gi|70606693|ref|YP_255563.1|  79 ERGIDVIRNKVKEFARTvASNNVPFKVILLDEA 111
                                   223333444444444432344444555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.079        36      70      95 ..      16      41 ..       3      46 .. 0.81
   2 !   23.5   0.0   9.8e-08   4.4e-05       5     126 ..      41     162 ..      37     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.079
                        AAA_14 70 lDEiqevpewekalkslvdegknldv 95
                                  lDEi + +e+ + lk++v+e++  ++
  gi|70606693|ref|YP_255563.1| 16 LDEIVNQKEIVERLKKFVKEKNMPHL 41
                                  9******************9944455 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.8e-08
                        AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpe..kllelileklkeekktylflDEiqev.pewe 80 
                                   l+  G+  +GKTt +  l+++l+    ++ +l++n  der  +   ++  ++ + + ++  +   ++++lDE+ ++  +++
  gi|70606693|ref|YP_255563.1|  41 LLFAGPPGTGKTTAALALVRDLYgnNYRQYFLELNASDERGIDVIRNKvkEFARTVASN--NVPFKVILLDEADNMtADAQ 119
                                   56789999***************876677788888888887553323111333333333..233578******987368** PP

                        AAA_14  81 kalkslvdeg.knldvivtGSnskllskeiatslagrvaeielypls 126
                                   +al++ ++ + +  ++i+   n   l ++i +  + r+a ++ ypl+
  gi|70606693|ref|YP_255563.1| 120 QALRRTMELYtETTRFIL-ACNY--L-SKIIEPIQSRTALFRFYPLK 162
                                   ********7734455555.4333..3.34778888888888888887 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.3e-07    0.0001       8      58 ..      22      72 ..      17      95 .. 0.92
   2 ?    0.3   0.0       1.4   6.1e+02     133     152 ..     103     124 ..      75     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-07
                                  HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                        ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                  Q+e++e+l++ +k+k+  ++l++ + GtGKT  a++l++ l+ +++++ fl
  gi|70606693|ref|YP_255563.1| 22 QKEIVERLKKFVKEKNMPHLLFAGPPGTGKTTAALALVRDLYGNNYRQYFL 72
                                  9***********999999*************************99988776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.4
                                   -SEEEEETGGGTTS...TTTHH CS
                        ResIII 133 fdviiiDEaHrlgak..kswre 152
                                   f+vi+ DEa +++a+  ++ r+
  gi|70606693|ref|YP_255563.1| 103 FKVILLDEADNMTADaqQALRR 124
                                   6699999999998853323333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00021     0.094       6      47 ..      39      74 ..      33      99 .. 0.70
   2 !   11.1   0.0    0.0008      0.36      79     128 ..      86     138 ..      59     146 .. 0.67
   3 ?   -1.9   0.0       8.5   3.8e+03      70      85 ..     247     270 ..     205     295 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47
                                   +l+  G++GtGKTt +  l++ l        ++ +++f +l
  gi|70606693|ref|YP_255563.1| 39 PHLLFAGPPGTGKTTAALALVRDLYG------NNYRQYFLEL 74
                                  578999***********999998733......2444444444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0008
                        AAA_22  79 lealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                   ++++ + +r+ a      +++++DEa+++ +++a + Lr+ ++l +  +++iL+
  gi|70606693|ref|YP_255563.1|  86 RNKVKEFARTVASnnvpFKVILLDEADNM-TADAQQALRRTMELYTETTRFILA 138
                                   3555555555555777889**********.999999999998886777777765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.5
                        AAA_22  70 a........erlsseellealeqa 85 
                                   +        ++ls e++++++++ 
  gi|70606693|ref|YP_255563.1| 247 DklrellinYGLSGEDIIKQVHKE 270
                                   023333333334444444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.3e-05     0.019       9      56 ..      26      72 ..      19      82 .. 0.68
   2 !    8.3   0.0    0.0064       2.9     117     161 ..      83     128 ..      72     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-05
                        AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggifl 56
                                  +e+L+  ++   +   + +l+ G++G+GK++ + +l r l ++  + +fl
  gi|70606693|ref|YP_255563.1| 26 VERLKKFVK---EKNMPHLLFAGPPGTGKTTAALALVRDLYGNnyRQYFL 72
                                  444544444...555589*************9988877776664335554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0064
                        AAA_16 117 srllellkrll.allsrderp.lvlvlDdlqwadeaslqllaaLlrl 161
                                     +++++k+++   +s+   p  v++lD+++   ++ +q+l+ +++l
  gi|70606693|ref|YP_255563.1|  83 DVIRNKVKEFArTVASN-NVPfKVILLDEADNMTADAQQALRRTMEL 128
                                   56778888999666777.44549******************999876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.9e-08   2.7e-05       1      88 [.      40     128 ..      40     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.9e-08
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefe..fkkGpvfanllladeinrappktq 79 
                                   h+l+ g PG++kt+++ al + l  +  r q+  +l  sd  G++v+++k kef   + +  v  +++l de +  ++ +q
  gi|70606693|ref|YP_255563.1|  40 HLLFAGPPGTGKTTAALALVRDLYGNNYR-QYFLELNASDERGIDVIRNKVKEFArtVASNNVPFKVILLDEADNMTADAQ 119
                                   99*********************999888.77789****************99962266788999**************** PP

                         AAA_3  80 salleamee 88 
                                    al  +me 
  gi|70606693|ref|YP_255563.1| 120 QALRRTMEL 128
                                   ***999985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.5e-07    0.0002       3      45 ..      43      88 ..      41     131 .. 0.79
   2 ?   -1.1   0.0       5.9   2.6e+03      25     100 ..     167     237 ..     138     253 .. 0.61
   3 ?   -1.6   0.0       8.6   3.8e+03      25      44 ..     246     265 ..     211     285 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.5e-07
                        AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe....a 45
                                   +G+pG+GKtt a +L + l +g n+r+++ e + ++e+  +    +
  gi|70606693|ref|YP_255563.1| 43 FAGPPGTGKTTAALALVRDL-YGNNYRQYFLELNASDERGIDvirnK 88
                                  79**************9998.89999999999988888777643332 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.9
                        AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikk.vvLt 100
                                   + +l+++ak++  +++      +    + ++ + k+++ ++++s+     + + ++ +   l  ++ k+i    +L 
  gi|70606693|ref|YP_255563.1| 167 VNRLIQIAKNEKVEFDPKGI--ETIFDITQGDMRKAINVIQAASA----YGKITVETVYKVLGLAQPKEIREmLHLA 237
                                   55566666666666666666..66666777777777777766655....6666666666666666666655554444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 8.6
                        AAA_18  25 gvnlrdvakenglllevdpe 44 
                                    ++lr+++ + gl+ e+  +
  gi|70606693|ref|YP_255563.1| 246 RDKLRELLINYGLSGEDIIK 265
                                   34444444444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.5e-07    0.0002       5      87 ..      41     124 ..      38     134 .. 0.85
   2 ?   -1.6   0.0       4.1   1.8e+03      53      78 ..     264     294 ..     240     304 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.5e-07
                        AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlks.ldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                   +l  Gp+g+GKTt a+ l        ++  f+ ++++  + +d+++        ++++++ ++a ++ ++k++ +D +d +
  gi|70606693|ref|YP_255563.1|  41 LLFAGPPGTGKTTAALALvrdlygnNYRQYFLELNASDERgIDVIRN-------KVKEFARTVASNNVPFKVILLDEADNM 114
                                   5678*******************999999999999977542666664.......478888888****************** PP

                        AAA_24  78 eelclaevir 87 
                                      + + ++r
  gi|70606693|ref|YP_255563.1| 115 TADAQQALRR 124
                                   9988887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                        AAA_24  53 ldevvel.....aaeladyktlviDtidele 78 
                                   +++v +         ++d+k++ +D ++e+e
  gi|70606693|ref|YP_255563.1| 264 IKQVHKEltgneISIPDDLKVILVDYAGEVE 294
                                   4444444566667788999999999988876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00049      39      87 ..      29      78 ..      17     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX CS
                         TIP49 39 ivelikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgse 87
                                  + +++kek++    +L+aGp+gtGkt  a+a+ ++l        f  l++s+
  gi|70606693|ref|YP_255563.1| 29 LKKFVKEKNMP--HLLFAGPPGTGKTTAALALVRDLYgnnYRQYFLELNASD 78
                                  66899****99..9*********************95322345688888876 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1     7e-07   0.00031      61     170 ..     106     205 ..      94     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7e-07
                                   EEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHH CS
                DNA_pol3_delta  61 vvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqe 141
                                   ++l+        ++ +++ +++L ++++ + e+t +il ++  l+   k++  +++++ ++++ +lk+e++ + + ++a++
  gi|70606693|ref|YP_255563.1| 106 ILLDE------ADNMTADAQQALRRTMELYTETTRFILACN-YLS---KIIEPIQSRTALFRFYPLKKEDVVNRLIQIAKN 176
                                   44444......47799*************************.888...8999999************************** PP

                                   TT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                DNA_pol3_delta 142 lglkiekealelLlelvennlsaikqele 170
                                   ++++++++ +e++ + + ++++ + + ++
  gi|70606693|ref|YP_255563.1| 177 EKVEFDPKGIETIFDITQGDMRKAINVIQ 205
                                   *********************99988776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06   0.00051      42     127 ..      31     121 ..      13     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                     IstB_IS21  42 sfiekke..nivllGpsGvGKshlaialgveavraglsvlfvrvedLvee...lkrarrdgklaralkrllkvdllilDdl 117
                                   +f+++k+   +++ Gp+G+GK+  a al ++   ++++ +f+ +++  e+   + r++ ++ + + +++ + +++++lD+ 
  gi|70606693|ref|YP_255563.1|  31 KFVKEKNmpHLLFAGPPGTGKTTAALALVRDLYGNNYRQYFLELNASDERgidVIRNKVKEFARTVASNNVPFKVILLDEA 111
                                   56665552258999***************************9987654432114444444444445556677799999999 PP

                     IstB_IS21 118 gllpldqaea 127
                                      + d ++a
  gi|70606693|ref|YP_255563.1| 112 DNMTADAQQA 121
                                   8888877665 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     4e-06    0.0018       2      38 ..     176     212 ..     175     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4e-06
                                   XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaae 38 
                                   ++k++++++ +e++ ++ +GD+Rka+n++++a ++ +
  gi|70606693|ref|YP_255563.1| 176 NEKVEFDPKGIETIFDITQGDMRKAINVIQAASAYGK 212
                                   6799**************************9987765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-06    0.0015      11      43 ..      30      69 ..      20     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
                        AAA_11 11 ksalsese..itliqGPPGtgKTktivellsqll.....s 43
                                  k++++e++    l+ GPPGtgKT++ ++l++ l+     +
  gi|70606693|ref|YP_255563.1| 30 KKFVKEKNmpHLLFAGPPGTGKTTAALALVRDLYgnnyrQ 69
                                  66666666566899******************96433320 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-05    0.0075      21     113 ..      41     127 ..      20     138 .. 0.74
   2 ?    0.2   0.0       1.1   5.1e+02      62     104 ..     249     297 ..     197     309 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                        AAA_30  21 avltGpAGtGKtta.lkalreaweaa..ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEag 98 
                                    +  Gp+GtGKtta l+ +r+++ ++  ++ + + A+ ++  +v+++++   a+t+a+            p ++++ DEa 
  gi|70606693|ref|YP_255563.1|  41 LLFAGPPGTGKTTAaLALVRDLYGNNyrQYFLELNASDERGIDVIRNKVKEFARTVASNN----V-----PFKVILLDEAD 112
                                   4678********97256669999988534777899***********99999999998766....3.....45888999988 PP

                        AAA_30  99 mvdtkqlaallkaae 113
                                    + ++  +al + +e
  gi|70606693|ref|YP_255563.1| 113 NMTADAQQALRRTME 127
                                   887666666665555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                        AAA_30  62 Lae...elgieastiakllkrlk..grarlepg.tllivDEagmvdtkq 104
                                   L+e   + g+ ++ i k +++    ++ ++ ++ ++++vD ag v ++ 
  gi|70606693|ref|YP_255563.1| 249 LRElliNYGLSGEDIIKQVHKELtgNEISIPDDlKVILVDYAGEVEFRI 297
                                   2222223333333333333222255445566666777777777776665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   4.1e-06    0.0018       8     131 ..      26     146 ..      20     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.1e-06
                      ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal.giavp 87 
                                   +++l++ +++++ + ++  Gp g GKt+    ++  l   + y+ y+ +l+ +++  +d      +++k++++++ +++vp
  gi|70606693|ref|YP_255563.1|  26 VERLKKFVKEKNMPHLLFAGPPGTGKTTAALALVRDLYG-NNYRQYFLELNASDERGIDVI---RNKVKEFARTVaSNNVP 102
                                   4566666666555555555******************77.55899***************9...55555555555244444 PP

                      ATPase_2  88 kaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                    + +  +l+   + ++++++a+ + +e  +++ ++ i+    l k+i
  gi|70606693|ref|YP_255563.1| 103 FKVI--LLDeadNMTADAQQALRRTMELYTET-TRFILACNYLSKII 146
                                   4333..34446588999999999988776666.66777777777776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00014     0.064      23      52 ..      26      55 ..      15      69 .. 0.84
   2 ?    3.8   0.0     0.072        32     116     143 ..      99     126 ..      67     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                          TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmiv 52
                                   e+L ++ k+k mp+ll++G++ +GKt+ +
  gi|70606693|ref|YP_255563.1| 26 VERLKKFVKEKNMPHLLFAGPPGTGKTTAA 55
                                  4677788899*****************975 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.072
                          TniB 116 relkvrvLiiDEihnllagsarkqrefl 143
                                   +++  +v+++DE +n+ a  +++ r+++
  gi|70606693|ref|YP_255563.1|  99 NNVPFKVILLDEADNMTADAQQALRRTM 126
                                   56789***********987777777665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.6e-06     0.003      32      72 ..      37      77 ..      19     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                         AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                  n  ++l+ Gp GtGKt+ +  l++ l  ++y   +++++a+
  gi|70606693|ref|YP_255563.1| 37 NMPHLLFAGPPGTGKTTAALALVRDLYGNNYRQYFLELNAS 77
                                  445899******************************99985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05     0.009       1      90 [.      40     127 ..      40     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                                   EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                   ++l  GppGtgK++ a  l + l ++++  + l  + + e  +  ++  n+ +++   ++ +++   ++++lDE +++  +
  gi|70606693|ref|YP_255563.1|  40 HLLFAGPPGTGKTTAALALVRDLyGNNYRQYFLELNASDERGIDVIR--NKVKEFARTVASNNV-PFKVILLDEADNMTAD 117
                                   6899*************999999888877777776666655444444..677777777777444.6789999999999999 PP

                                   HHHHHHHHHH CS
                         AAA_5  81 vlnsLlslle 90 
                                   ++++L + +e
  gi|70606693|ref|YP_255563.1| 118 AQQALRRTME 127
                                   9999976665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00026      0.12      24      43 ..      40      59 ..      16      80 .. 0.81
   2 ?    3.3   0.0       0.1        46     109     132 ..     105     128 ..      95     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                  Mg_chelatase 24 nlllvGppGsGKtmlakrlp 43
                                  +ll++GppG+GKt  a +l 
  gi|70606693|ref|YP_255563.1| 40 HLLFAGPPGTGKTTAALALV 59
                                  89***********9998775 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePled 132
                                   v++LDE+ ++++++ ++LR+ +e 
  gi|70606693|ref|YP_255563.1| 105 VILLDEADNMTADAQQALRRTMEL 128
                                   799*****************9995 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   8.7e-05     0.039      23      60 ..      22      59 ..       4      63 .. 0.77
   2 ?   -2.6   0.0       6.4   2.9e+03     126     164 ..      80     119 ..      77     144 .. 0.61
   3 ?   -1.8   0.0       3.5   1.6e+03     106     142 ..     139     175 ..     131     233 .. 0.63
   4 ?   -1.2   0.0       2.4   1.1e+03      69      88 ..     279     299 ..     276     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.7e-05
                                  EEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE 23 gkei.sgnplvldlkkmashllvaGatgsGKStalntLi 60
                                   kei  + +  + +k+m+ hll aG +g+GK+ta  +L+
  gi|70606693|ref|YP_255563.1| 22 QKEIvERLKKFVKEKNMP-HLLFAGPPGTGKTTAALALV 59
                                  456656666677889999.**************988876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                                   TT-SSHHH.HHHHHHHHHHTT---B-TT-........... CS
                  FtsK_SpoIIIE 126 agvrsiaa.ydgeiaedpldifgdvflvlDnyddlaaene 164
                                   +g++ i++ +++ + +++ +  ++ +++lD+ d++ a  +
  gi|70606693|ref|YP_255563.1|  80 RGIDVIRNkVKEFARTVASNNVPFKVILLDEADNMTADAQ 119
                                   5666666633333444555555666677777777666555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.5
                                   HHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHH CS
                  FtsK_SpoIIIE 106 lraleeLvkemeeryalfreagvrsiaaydgeiaedp 142
                                    + l ++++ +++r alfr    ++ ++++  i+ ++
  gi|70606693|ref|YP_255563.1| 139 CNYLSKIIEPIQSRTALFRFYPLKKEDVVNRLIQIAK 175
                                   5667777777777777777666666655333333222 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.4
                                   TTTEEEEEE-TTSS.SCGGGT CS
                  FtsK_SpoIIIE  69 PeeVqliliDykgv.elsale 88 
                                   P++++ il+Dy+g  e++ +e
  gi|70606693|ref|YP_255563.1| 279 PDDLKVILVDYAGEvEFRIME 299
                                   999********9877999887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00078      0.35       8      41 ..      21      60 ..      17      81 .. 0.78
   2 ?    4.0   0.0     0.066        29     121     137 ..     104     120 ..      82     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00078
                                  HHHHHHHHHH....H-S..EEEEE--TTSSTTHHHHHHHH CS
                          PhoH  8 eQkeylealk....knd..ivfaiGpaGtGKtylavalav 41
                                  +Qke++e lk    +++   +  +Gp GtGKt  a+al  
  gi|70606693|ref|YP_255563.1| 21 NQKEIVERLKkfvkEKNmpHLLFAGPPGTGKTTAALALVR 60
                                  799999999877753334467889*********9998755 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.066
                                   EEEEE-SGGG--HHHHH CS
                          PhoH 121 afvilDEAQnttkeqmk 137
                                   ++++lDEA n+t    +
  gi|70606693|ref|YP_255563.1| 104 KVILLDEADNMTADAQQ 120
                                   589********987654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-05    0.0079      27     104 ..      13      91 ..       3     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                        DUF815  27 lddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellre 104
                                    ++L +i +qk ++ve  ++f++ ++  ++L+ G  GtGK +   al++++  ++    ++e++ +d + ++ + ++++e
  gi|70606693|ref|YP_255563.1|  13 PKSLDEIVNQK-EIVERLKKFVKEKNMPHLLFAGPPGTGKTTAALALVRDLYGNNyrQYFLELNASDERGIDVIRNKVKE 91 
                                   56666676666.577889************************99999999888774422555555555555555555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00042      0.19       7      73 ..      35      97 ..      29     138 .. 0.65
   2 ?    0.5   0.0       1.6     7e+02      11      67 ..     200     258 ..     191     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00042
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiH 73
                                  + + ++ll  ++pGtGKT+   + v+ l  ++ ++   + l a  +r  + +r+++   ++ a+T+ 
  gi|70606693|ref|YP_255563.1| 35 EKNMPHLLFAGPPGTGKTTAALALVRDLYGNNYRQ-YFLELNASDERGIDVIRNKV---KEFARTVA 97
                                  5566677888889******9999988887776443.44455566666666666666...45555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.6
                        AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgr...Aakelrerlaalga 67 
                                    + ++ a    GK  +++++ ++l  ++  + +e+l +a+ g+   A ++lre l ++g+
  gi|70606693|ref|YP_255563.1| 200 AINVIQAASAYGKI-TVETVYKVLGLAQPKEIREMLHLALSGKflqARDKLRELLINYGL 258
                                   55566777777774.457777777777777789999999998644477777777655554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.5e-05     0.025       3      25 ..      42      69 ..      41     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-05
                        AAA_33  3 llvGlpGsGKstlaerllkklg.....a 25
                                  l+ G+pG+GK+t a  l++ l       
  gi|70606693|ref|YP_255563.1| 42 LFAGPPGTGKTTAALALVRDLYgnnyrQ 69
                                  799*************999887444441 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00018      0.08       7     102 ..      44     116 ..      40     134 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                       DUF2075   7 tGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeep 87 
                                    G +GtGKt  +l+l+ +l    +++++ +l  N +           ++    ++   +k+++f  ++          ++ 
  gi|70606693|ref|YP_255563.1|  44 AGPPGTGKTTAALALVRDL--YGNNYRQYFLELNAS----------DER---GIDVIRNKVKEFARTVA--------SNNV 101
                                   699***************9..444444444444432..........222...33344444455555555........4455 PP

                       DUF2075  88 kedvvivDEAhrllt 102
                                   +++v++ DEA  ++ 
  gi|70606693|ref|YP_255563.1| 102 PFKVILLDEADNMTA 116
                                   566666666666655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.2e-05     0.019     104     153 ..      15      62 ..       7      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                         T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                   +ld+++ +++  e++++++++   +   +l++G+ g+GKtt + al+  +
  gi|70606693|ref|YP_255563.1|  15 SLDEIVNQKEIVERLKKFVKEK--NMPHLLFAGPPGTGKTTAALALVRDL 62 
                                   6788888888888999999888..7888**************99998766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   9.8e-05     0.044      37      57 ..      42      62 ..      36     136 .. 0.90
   2 ?   -1.7   0.0       3.9   1.8e+03      79     137 ..     260     318 ..     217     323 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                        AAA_25 37 llaGapgtGKttlaldlalav 57
                                  l+aG+pgtGKtt+al l+ ++
  gi|70606693|ref|YP_255563.1| 42 LFAGPPGTGKTTAALALVRDL 62
                                  789*************99875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.9
                        AAA_25  79 aEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtl.ltadvdaleaai 137
                                   +Ed  +++++ l      ++dd ++ ++d+ag+ + ++++ ++++++ l a++++l+ ++
  gi|70606693|ref|YP_255563.1| 260 GEDIIKQVHKELTGNEISIPDDLKVILVDYAGEVEFRIME-GADDEIqLSAFLAKLALHA 318
                                   3333334444444333333666666666666663334433.3444444677777666555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00085      0.38       9      59 ..      23      77 ..      17      83 .. 0.80
   2 ?    2.2   0.0      0.28   1.3e+02      96     118 ..     105     127 ..     100     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                                  HHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH..HSTTTTS-EEEEETT CS
               Sigma54_activat  9 kelleqikkvaktd..lsvlitGesGtGKellaraihe..askrkekpfvavnca 59
                                  ke++e++kk++k +   ++l  G  GtGK++ a a+ +    ++ ++ f+++n +
  gi|70606693|ref|YP_255563.1| 23 KEIVERLKKFVKEKnmPHLLFAGPPGTGKTTAALALVRdlYGNNYRQYFLELNAS 77
                                  678888999887776568999************9998865566777788888865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                                   EEEEETGGGS-HHHHHHHHHHHH CS
               Sigma54_activat  96 tlfLDeigelplelQekLlrvlq 118
                                   +++LDe  ++++++Q+ L r ++
  gi|70606693|ref|YP_255563.1| 105 VILLDEADNMTADAQQALRRTME 127
                                   689**************999886 PP

>> Phage_T4_Ndd  T4-like phage nuclear disruption protein (Ndd)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.6   2.5e+03     112     128 ..      47      63 ..      24      77 .. 0.66
   2 ?   13.3   0.0   0.00012     0.053      78     107 ..      84     114 ..      68     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.6
                  Phage_T4_Ndd 112 tgygkgqlalaftrnhs 128
                                    g gk   ala+ r+  
  gi|70606693|ref|YP_255563.1|  47 PGTGKTTAALALVRDLY 63 
                                   47899999999999754 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                  Phage_T4_Ndd  78 hirqrrsqlartiatnnveydviyls.akkm 107
                                    ir++  ++art+a+nnv+++vi l  a++m
  gi|70606693|ref|YP_255563.1|  84 VIRNKVKEFARTVASNNVPFKVILLDeADNM 114
                                   58999999***************99536666 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.8e-05     0.035       3      72 ..      43     112 ..      41     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.8e-05
               Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegk...pklpnlsvrtv.dsflmalvkstkgkililDEyl 72 
                                    +G pG GK+t+   l+r+ l  + +r+ +  l+++     ++ +++v+ + +++ +++v +  +k+++lDE+ 
  gi|70606693|ref|YP_255563.1|  43 FAGPPGTGKTTAALALVRD-LYGNNYRQYFLELNASDergIDVIRNKVKEFaRTVASNNV-P--FKVILLDEAD 112
                                   5799***************.7778888888888888866645544444444044444444.4..9*******85 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018     0.079       1      40 [.      38      77 ..      38     103 .. 0.81
   2 ?   -2.5   0.0       5.9   2.7e+03      60      80 ..     263     283 ..     261     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                  E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                         KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                  Mp +++ G P +GK+t+a  L + l  ++++ + ++ ++ 
  gi|70606693|ref|YP_255563.1| 38 MPHLLFAGPPGTGKTTAALALVRDLYGNNYRQYFLELNAS 77
                                  999************************9999888776655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.9
                                   HHHHHHHHHTT.SEEEE-S-- CS
                         KTI12  60 lrsavkrdLskekvVIvDsln 80 
                                   ++++v+++L+ +++ I D+l 
  gi|70606693|ref|YP_255563.1| 263 IIKQVHKELTGNEISIPDDLK 283
                                   778999999999999999985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00018     0.082       4      54 ..      43     116 ..      40     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                        AAA_28   4 itGgestGKTtlleaLa...................argypvv....pEaareileeklakgedalpwvedlla 54 
                                   + G+++tGKTt + aL                    +rg+ v+    +E+ar++ +++  ++   l++++++ a
  gi|70606693|ref|YP_255563.1|  43 FAGPPGTGKTTAALALVrdlygnnyrqyflelnasdERGIDVIrnkvKEFARTVASNNVPFKVILLDEADNMTA 116
                                   78***********9999666666555555544444334666555555677777766666665555555444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0004      0.18       2      26 ..      42      66 ..      41     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0004
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                  ++ Gp+g+GK+t+a  L+++l ++ 
  gi|70606693|ref|YP_255563.1| 42 LFAGPPGTGKTTAALALVRDLYGNN 66
                                  689*****************99554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00089       0.4       8     106 ..      23     138 ..      20     157 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00089
                                   HHHHHHHHHHH..T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHH..TTT CS
               Sigma54_activ_2   8 qelkerLeqaa..qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleq..akg 70 
                                   +e+ erL++ +  +++  ++ +G++G+gk++ A +L     ++     + +l ++               ++++++  +  
  gi|70606693|ref|YP_255563.1|  23 KEIVERLKKFVkeKNMPHLLFAGPPGTGKTTAALALVRDLYGNNYRQYFLELNASDergidvirnkvkefARTVASnnVPF 103
                                   689999999875456667999************988754333322222212221111234444444433333322222455 PP

                                   SEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEE CS
               Sigma54_activ_2  71 gtLylkdiadlskaeqkeLlellakaeksslrlVst 106
                                    +++l + +++ +++q+ L   ++    +  r++ +
  gi|70606693|ref|YP_255563.1| 104 KVILLDEADNMTADAQQALRRTMELY-TETTRFILA 138
                                   56666777777777777776666655.566666655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.031        14      16      35 ..      40      59 ..      19      71 .. 0.73
   2 ?    5.0   0.0     0.041        18     121     148 ..     102     128 ..      64     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                                  EEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                          DEAD 16 dvlvaaeTGsGKTlaflipv 35
                                  ++l a++ G+GKT+a+l  v
  gi|70606693|ref|YP_255563.1| 40 HLLFAGPPGTGKTTAALALV 59
                                  67899**********87655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                                   TEEEEEEETHHHHHHTTTHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 121 qvrflVlDEadrlldqgfsdfinrilnq 148
                                    ++++ lDEad++  +  ++ ++r ++ 
  gi|70606693|ref|YP_255563.1| 102 PFKVILLDEADNMTAD-AQQALRRTMEL 128
                                   347899*******998.66777776654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0016      0.73       2      28 ..      41      67 ..      40      70 .. 0.87
   2 ?    1.0   0.0      0.77   3.4e+02      73     147 ..      69     152 ..      63     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                                  EEEE--TTSSHHHHHHHHHHHH...GG CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                  ++  GppG+GKtT    +++ l  +++
  gi|70606693|ref|YP_255563.1| 41 LLFAGPPGTGKTTAALALVRDLYGNNY 67
                                  6789************99999988877 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.77
                                   TEEE-HHHHHHHHHHHHHHHHHHH-...........EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHH CS
                      NTPase_1  73 kyvvdvesfeelalealrkalsead...........viviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalve 142
                                   +y +++++ +e +++++r++++e             vi++DE  +m   +++  +   e+ ++ + ++        ++++e
  gi|70606693|ref|YP_255563.1|  69 QYFLELNASDERGIDVIRNKVKEFArtvasnnvpfkVILLDEADNMTADAQQALRRTMELYTETTRFILACNYL--SKIIE 147
                                   67777777777777777777744333445556677788889988887777665555555555555555444444..34555 PP

                                   HHHT- CS
                      NTPase_1 143 eirer 147
                                    i++r
  gi|70606693|ref|YP_255563.1| 148 PIQSR 152
                                   55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.59
# Mc/sec: 1648.20
//
Query:       gi|70606694|ref|YP_255564.1|  [L=150]
Description: hypothetical protein Saci_0908 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-34  117.7   0.0    4.8e-34  117.5   0.0    1.0  1  PBP              Phosphatidylethanolamine-binding protein
  ------ inclusion threshold ------
        0.2   11.6   0.0       0.35   10.8   0.0    1.4  1  DNAPolymera_Pol  DNA polymerase catalytic subunit Pol


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   5.3e-38   4.8e-34       1     132 []      13     146 ..      13     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 5.3e-38
                                   B--GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC.........EE-B-TTS CS
                           PBP   1 klpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega.........vqgknslg 70 
                                   ++p+ky  +g+++sP+l+w+++p+  ksya++v+DpDap  + tf+Hwv++ni+  +++l+e+          +qg n++g
  gi|70606694|ref|YP_255564.1|  13 YIPDKYtcDGSDISPELEWDQIPN-VKSYAIIVEDPDAP-GG-TFIHWVIYNIK--QNKLEENVkkiekagvgIQGVNDFG 88 
                                   58999999***************5.**************.44.5*********9..889999889999999********** PP

                                   SCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                           PBP  71 eesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                   +    gY gpcPp  ++ HrY+f +yal+ e   +k+g t +el+++++g+ ++k  ++g+Y
  gi|70606694|ref|YP_255564.1|  89 R---VGYNGPCPPRSHQAHRYFFYVYALSSEL-PVKSGVTAEELKRMMEGYMIDKGFIMGKY 146
                                   *...************99**********9995.7999*999******************998 PP

>> DNAPolymera_Pol  DNA polymerase catalytic subunit Pol
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.8e-05      0.35      14      28 ..     118     132 ..     113     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
               DNAPolymera_Pol  14 tigaGieaEETRRkL 28 
                                   ++ +G++aEE  R++
  gi|70606694|ref|YP_255564.1| 118 PVKSGVTAEELKRMM 132
                                   799***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1082.10
//
Query:       gi|70606695|ref|YP_255565.1|  [L=203]
Description: proteasome beta subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-52  175.7   0.3    7.8e-52  175.5   0.3    1.0  1  Proteasome   Proteasome subunit
  ------ inclusion threshold ------
       0.42   10.2   2.7        0.7    9.4   0.2    2.3  2  TGF_beta_GS  Transforming growth factor beta type I GS-motif


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.5   0.3   8.7e-56   7.8e-52       3     189 ..       9     187 ..       7     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 8.7e-56
                                   HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHH CS
                    Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipver 83 
                                   kGtt+vGik kdgvvlaad+ra+ag +++ k  v+K+  ++d+ig+++aG++aD + + + +++  ++ +++ + pi+v+ 
  gi|70606695|ref|YP_255565.1|   9 KGTTTVGIKVKDGVVLAADRRASAGYYVAHKY-VRKVLYVTDNIGITTAGSVADLQFIYEALKYIYHRNSITGEGPITVK- 87 
                                   8***************************8888.9**********************************************. PP

                                   HHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHH CS
                    Proteasome  84 lvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeav 164
                                       +a+ l++ + +s+  p++v++li+gvd  ++p+Ly++d+ G+++ee+ ++a+Gsgs +a ++le++yk++++l+ea 
  gi|70606695|ref|YP_255565.1|  88 ---GIATWLANVLSSSKYFPYLVQILIGGVD--DQPRLYNLDYLGDITEEE-YTATGSGSPEALGVLEDNYKPEMSLDEAA 162
                                   ...888888888889999*************..55***************6.***************************** PP

                                   HHHHHHHHHHHHHBTTSCSSEEEEE CS
                    Proteasome 165 elavkalkealerdklsgknievav 189
                                   ela++a+ ++++rd+++g+++ v+ 
  gi|70606695|ref|YP_255565.1| 163 ELAKRAIFSSIKRDSFTGTGVIVTK 187
                                   ********************99875 PP

>> TGF_beta_GS  Transforming growth factor beta type I GS-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.067     6e+02      18      23 ..     103     108 ..     103     108 .. 0.91
   2 ?    9.4   0.2   7.8e-05       0.7       1      16 [.     125     141 ..     125     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.067
                   TGF_beta_GS  18 lPLLVQ 23 
                                   +P+LVQ
  gi|70606695|ref|YP_255565.1| 103 FPYLVQ 108
                                   5****9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 7.8e-05
                   TGF_beta_GS   1 tlkDllee.sstSGSGS 16 
                                   +l+D++ee  + +GSGS
  gi|70606695|ref|YP_255565.1| 125 YLGDITEEeYTATGSGS 141
                                   589*****5566****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1427.61
//
Query:       gi|70606696|ref|YP_255566.1|  [L=395]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-85  287.7   0.5    1.7e-83  281.1   0.5    2.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.5   9.6e-88   1.7e-83      41     451 .]      20     380 ..      13     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 9.6e-88
                                   ......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBT CS
                       Amidase  41 rgkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgptrNP 121
                                   ++++kg L  + +s+KD id+kgvpttaGs++l +y+++++a vve++ ++G  i+gkTn++efamg++  +s+fgp++NP
  gi|70606696|ref|YP_255566.1|  20 KKRDKGRLSNLKFSIKDIIDIKGVPTTAGSRILNDYIPDTNAYVVEKILEEGGEIIGKTNTHEFAMGATNTSSIFGPAKNP 100
                                   47899**************************************************************************** PP

                                   TCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHH CS
                       Amidase 122 wdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsvedlal 202
                                   +d +r++GGSSGG A+ vA glv++++GtDtGGS+RiPA++cg++G+KP+ g+++ +g++++++s+d+vG++ ++ ++l+ 
  gi|70606696|ref|YP_255566.1| 101 YDIERISGGSSGGAAVSVALGLVDVGVGTDTGGSVRIPAALCGVIGFKPSIGLIPTDGIIPFSWSIDTVGFIVKDMQTLNR 181
                                   ********************************************************************************* PP

                                   HHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGG CS
                       Amidase 203 llrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpslee 283
                                   +l+v+l + +     +            +++ ++  r+G+  + +     +ev ra++ ++++L++  + ++e++ + le+
  gi|70606696|ref|YP_255566.1| 182 VLEVTLTDKTV----L------------VSQIRRRPRVGLFLFGD-----DEVSRALKPVVDTLNNY-FDIKEIHNEILEK 240
                                   ******54433....3............24556889***986655.....8*************986.6666666666655 PP

                                   HHH.HHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHH CS
                       Amidase 284 als.lyylilvaeassnlarylgvryerlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrll 363
                                       +  +i++ ea s+                  +++ +k r++++ + v+r +e g++ l  e     y  a + r++l
  gi|70606696|ref|YP_255566.1| 241 YSGdIRRKIVLPEAYSY------------------HRKWFKERKDDYFPDVRRLLENGSKILGYE-----YVDALRSRHVL 298
                                   55558999999999988..................7789999*********************99.....9********** PP

                                   HHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEEST CS
                       Amidase 364 rrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigka 444
                                   +re+ k+f ++Dvl+sPt+   ap++ e         +l+   ++++++ ++n++g p++s+p+++ + glPvG++v g+ 
  gi|70606696|ref|YP_255566.1| 299 IREYMKIFSDVDVLISPTTKVVAPKISEVIG-----NELTFREKLVSNTEIFNVTGAPSISIPVAQLN-GLPVGLMVSGEL 373
                                   ***************************9964.....4455555555556****************986.************ PP

                                   T-HHHHH CS
                       Amidase 445 fqeetlL 451
                                   +q+ t+L
  gi|70606696|ref|YP_255566.1| 374 YQDGTVL 380
                                   *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2558.62
//
Query:       gi|70606697|ref|YP_255567.1|  [L=334]
Description: putative alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-27   95.0   0.1    4.4e-27   94.1   0.1    1.5  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    6.1e-21   74.8   0.1    9.1e-21   74.2   0.1    1.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    7.7e-10   39.9   0.0    1.4e-09   39.1   0.0    1.4  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    4.5e-05   23.1   0.8    7.5e-05   22.4   0.8    1.3  1  LDcluster4       SLOG cluster4 family
     0.0075   15.6   1.5      0.013   14.8   1.5    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.2   0.8      0.025   14.3   0.8    1.4  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
      0.021   14.6   0.1      0.047   13.5   0.1    1.5  1  E1-N             E1 N-terminal domain
       0.13   12.8   0.0       0.34   11.5   0.0    1.7  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1     2e-30   4.4e-27       2     109 .]      26     132 ..      25     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 2e-30
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   +ev+i+v  ag+C  Dl  l+g   +++k+p++lGHE+vGe+eevg++v+++k+GdrV+     ++g+C++Ck gee +C+
  gi|70606697|ref|YP_255567.1|  26 DEVVIRVVRAGLCYRDLLQLQG-YYPRMKYPVVLGHEVVGEIEEVGDNVSGFKIGDRVISLLYAPDGSCEYCKVGEEAYCK 105
                                   79********************.8********************************************************* PP

                                   TBEETTTSS-SSSBSEEEECGGGEEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvkl 109
                                   ++  ++ +ldG fae+  v+ +++vk+
  gi|70606697|ref|YP_255567.1| 106 RRLGYSEELDGFFAERAKVKVTSIVKV 132
                                   **999999************9999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.1     4e-24   9.1e-21       1     127 [.     175     295 ..     175     298 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 4e-24
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkp 81 
                                   gvG++a+q+AkalGa++i+v  se+k++  +k+ ad+vi   + +++++ +++    ++ +v+++vG   t+e++l++l+ 
  gi|70606697|ref|YP_255567.1| 175 GVGIHAIQVAKALGARTIGVTTSEDKAKVIRKY-ADHVIVG-S-KFSDEARKIG---DISLVIDTVG-TPTIEESLRSLRM 248
                                   9********************************.8999999.4.6*********...9*********.************* PP

                                   EEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHH CS
                    ADH_zinc_N  82 gGrlvvvGg..gkgeeefdlrnlllkeksilGsllgslreefkealdl 127
                                   gG+lv +G   +++  +++l++l+lk++ ++G   ++ + + ++ l+l
  gi|70606697|ref|YP_255567.1| 249 GGKLVQIGNvdPSQIYSLRLGYLILKDILLVGHASAT-KYDAEQTLKL 295
                                   ********988888888****************9999.7887777766 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   6.2e-13   1.4e-09       3     133 .]     208     332 ..     207     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.2e-13
                                   -SEEE.ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG. CS
                  ADH_zinc_N_2   3 Adevi.dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsm 81 
                                   Ad+vi  ++ ++++ +++ g+ +++v+dtvg++++ e+sl+ l+ gG+lv+ig+   ++++  +++  +   +k  +l+  
  gi|70606697|ref|YP_255567.1| 208 ADHVIvGSKfSDEA-RKI-GD-ISLVIDTVGTPTI-EESLRSLRMGGKLVQIGNV-DPSQIYSLRL--GYLILKDILLV-G 280
                                   89**9766645555.677.56.***********99.*******998*******63.4555555544..44444444444.2 PP

                                   ..-..-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                  ADH_zinc_N_2  82 kas.aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                   +as  + d  e+ ++l e G++  vv  +  l+++ e +r ++ +  +GK+ l
  gi|70606697|ref|YP_255567.1| 281 HASaTKYD-AEQTLKLTEGGNISAVVAGHVNLDNIDEGYRMIKDRNKIGKVLL 332
                                   33322555.99***************************************976 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.8   3.3e-08   7.5e-05      29      82 ..     161     214 ..     156     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.3e-08
                    LDcluster4  29 iAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyT 82 
                                   i k+++ l+tG+ +Gv   a + ak  g  t+G++ ++++ +   ky d +i+ 
  gi|70606697|ref|YP_255567.1| 161 INKNEYALVTGASGGVGIHAIQVAKALGARTIGVTTSEDKAKVIRKYADHVIVG 214
                                   7899********************************************999985 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.5   5.6e-06     0.013      20     102 ..     158     237 ..     149     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.6e-06
                                   TCEETCB---EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                   AlaDh_PNT_C  20 aGgvpgvepakvlviGg.GvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtv 99 
                                   aGg++  ++   lv G+ G +G++Ai++ak+lga++  + +++++++ ++++  + v  + s+ +  a+++ +  +vi tv
  gi|70606697|ref|YP_255567.1| 158 AGGIN--KNEYALVTGAsGGVGIHAIQVAKALGARTIGVTTSEDKAKVIRKYADH-VI-VGSKFSDEARKIGDISLVIDTV 234
                                   67777..55666788866899*****************************99999.33.3444444567788888888887 PP

                                   -BT CS
                   AlaDh_PNT_C 100 lip 102
                                     p
  gi|70606697|ref|YP_255567.1| 235 GTP 237
                                   655 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.8   1.1e-05     0.025      36      73 ..     161     196 ..     147     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                   ---.-SEEEEESTSSHHHHHHHHHHHHSS--EEEEEE- CS
               Eno-Rase_NADH_b  36 iekgpkkvLviGaStGYGLAsriaaafgagadtigVsf 73 
                                   i+ +   +Lv GaS G G+ + i +a + ga+tigV  
  gi|70606697|ref|YP_255567.1| 161 IN-KNEYALVTGASGGVGIHA-IQVAKALGARTIGVTT 196
                                   44.36789**********975.88889999******75 PP

>> E1-N  E1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.1e-05     0.047      30      64 ..     166     200 ..     156     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                          E1-N  30 avlvtaapGgkdaaavevvelllartvqvvtseae 64 
                                     lvt a Gg    a++v+++l+art++v+tse +
  gi|70606697|ref|YP_255567.1| 166 YALVTGASGGVGIHAIQVAKALGARTIGVTTSEDK 200
                                   579***************************99865 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.34      11      52 ..     174     214 ..     167     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEE CS
                 Biotin_carb_N  11 GeiAvriiravrelgietvavyseedanslhvreadeavelg 52 
                                   G + +  i+ ++ lg +t+ v ++ed+++   ++ad+++ +g
  gi|70606697|ref|YP_255567.1| 174 GGVGIHAIQVAKALGARTIGVTTSEDKAKVIRKYADHVI-VG 214
                                   667889999***************************965.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2124.84
//
Query:       gi|70606698|ref|YP_255568.1|  [L=203]
Description: hypothetical protein Saci_0912 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1428.69
//
Query:       gi|70606699|ref|YP_255569.1|  [L=163]
Description: hypothetical protein Saci_0913 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.065   13.6   0.5       0.17   12.3   0.5    1.7  1  Rep_fac_C  Replication factor C C-terminal domain


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   9.7e-06      0.17       4      65 ..      19     101 ..      17     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-06
                                   HHHHHHHHHHHH...T-HHHHHHH.............HHHHHHHC---HHHHHH.HHHHHGCCS.....S-HHH.HHHHHH CS
                     Rep_fac_C   4 teieeileacln...gdfeeaykk.............lrellvekGysaedilt.qlhrvvkeq...eelpeaq.kleile 63 
                                   +e e++++ cl+   gd+++++k+             l + l +kG s edil+  ++++  +    +  p ++ k+eil+
  gi|70606699|ref|YP_255569.1|  19 KEAEDMAKECLSslrGDVDKIRKNikeikqqvqadflLPKALRDKGVSTEDILKiSMYELARRAaifS-GPSKVkKNEILK 98 
                                   567889999988999999999999888888899999977889999********945666666655422.334334888885 PP

                                   H.H CS
                     Rep_fac_C  64 l.l 65 
                                   + l
  gi|70606699|ref|YP_255569.1|  99 YsL 101
                                   333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      883  (0.0492498); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1142.45
//
Query:       gi|70606700|ref|YP_255570.1|  [L=238]
Description: uroporphyrin-III C-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-47  162.1   0.2    2.2e-47  161.8   0.2    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   0.2   1.2e-51   2.2e-47       1     212 [.       4     208 ..       4     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 1.2e-51
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaealaealragk 80 
                                   ++y+VG+GpGdpel+T++Al++lk+advvl+d+ +++e++l  l+ e       +  ke  ++  +e+i+  l+e++r+gk
  gi|70606700|ref|YP_255570.1|   4 RVYIVGAGPGDPELITIKALNILKSADVVLYDR-LVPESILTGLKCE-----LIYVGKEIGDAYlQEKINHLLVEKAREGK 78 
                                   69*******************************.9999998776542.....222233344444577777888******** PP

                  TP_methylase  81 dVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.lpglakeeereleallan 160
                                   +Vv+l++GDP+++g+g e++  + +  +gie+e+iPGv+s+ a++  ++ip+t +  + sv+  +++  ++e   ++ + +
  gi|70606700|ref|YP_255570.1|  79 TVVRLKGGDPTIFGRGEEECIYVVE--NGIECEIIPGVTSAIAVPETAKIPVTSRLASPSVTiITATRSNGELITSDYIPK 157
                                   ********************88888..9****************************9999999666677788999999999 PP

                  TP_methylase 161 gdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                   ++tlv+l++ + ++el  +L+   ++++ pvav+e+++++d+rv+ g+leel
  gi|70606700|ref|YP_255570.1| 158 KGTLVILMGIHVIEELYGILLSV-RNKDEPVAVIEKGTLKDQRVFLGKLEEL 208
                                   ********************999.88888*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1588.62
//
Query:       gi|70606701|ref|YP_255571.1|  [L=47]
Description: hypothetical protein Saci_0915 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-20   72.4   2.9    2.5e-20   72.3   2.9    1.0  1  YHS              YHS domain
    2.1e-05   24.8   2.1    2.7e-05   24.4   2.1    1.2  1  Arc_trans_TRASH  Archaeal TRASH domain
    0.00025   20.9   1.1     0.0003   20.6   1.1    1.2  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
    0.00048   19.7   0.1    0.00053   19.6   0.1    1.1  1  FAP206           Domain of unknown function
  ------ inclusion threshold ------
      0.069   13.2   0.2       0.31   11.1   0.1    1.8  2  DUF2116          Uncharacterized protein containing a Zn-ribb
      0.093   13.1   0.2      0.096   13.0   0.2    1.1  1  NosL             NosL


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   2.9   8.3e-24   2.5e-20       3      47 ..       4      47 .]       2      47 .] 0.96

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 8.3e-24
                           YHS  3 dPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYata 47
                                  dPvcgm v +e +++k++YkGk+YyFcS+ C+ +F++ PekY ++
  gi|70606701|ref|YP_255571.1|  4 DPVCGMEV-NEDTKYKLSYKGKTYYFCSPLCMAEFKKRPEKYIQH 47
                                  9*******.999******************************986 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   2.1   9.1e-09   2.7e-05       4      36 ..       7      40 ..       6      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.1e-09
               Arc_trans_TRASH  4 CGkeiv.gePivyklknkvYyvCCktCkselkkk 36
                                  CG e+  ++ + + +k k+Yy+C + C  e+kk+
  gi|70606701|ref|YP_255571.1|  7 CGMEVNeDTKYKLSYKGKTYYFCSPLCMAEFKKR 40
                                  999997245688999*****************97 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.1     1e-07    0.0003      20      41 .]      16      37 ..       7      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                        zf-FCS 20 tyvlendgvvgqFCStsCldsY 41
                                   y l+++g++++FCS  C++++
  gi|70606701|ref|YP_255571.1| 16 KYKLSYKGKTYYFCSPLCMAEF 37
                                  3579***************998 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.8e-07   0.00053     226     254 ..      19      47 .]      14      47 .] 0.96

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.8e-07
                        FAP206 226 lkykdkyyaFsseeaareFaadpdrfiea 254
                                   l+yk+k+y F s+ ++ eF ++p+++i++
  gi|70606701|ref|YP_255571.1|  19 LSYKGKTYYFCSPLCMAEFKKRPEKYIQH 47 
                                   79*************************97 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.25   7.3e+02       7      16 ..       5      14 ..       4      18 .. 0.77
   2 ?   11.1   0.1    0.0001      0.31      18      35 ..      27      44 ..      23      47 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.25
                       DUF2116  7 ivCGkaIpld 16
                                  +vCG  +++d
  gi|70606701|ref|YP_255571.1|  5 PVCGMEVNED 14
                                  6899888776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                       DUF2116 18 sfCsekCqeeyekkrkkv 35
                                   fCs+ C  e++k+  k 
  gi|70606701|ref|YP_255571.1| 27 YFCSPLCMAEFKKRPEKY 44
                                  69***********98886 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.2e-05     0.096       9      53 ..       3      43 ..       1      47 [] 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                          NosL  9 ecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepee 53
                                  + +vCgM ++e  + k ++ y++  +   Fcs  ++ +f  +pe+
  gi|70606701|ref|YP_255571.1|  3 NDPVCGMEVNE--DTKYKLSYKG--KTYYFCSPLCMAEFKKRPEK 43
                                  6789*****97..5666789998..99*************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 353.50
//
Query:       gi|70606702|ref|YP_255572.1|  [L=280]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-48  163.2   0.0    6.8e-48  162.6   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    7.6e-28   96.7   0.3    1.1e-27   96.1   0.3    1.3  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.6   0.0   7.5e-52   6.8e-48       2     170 ..       5     168 ..       4     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.6 bits;  conditional E-value: 7.5e-52
                                   EEEEEE-SSHHHHHHHHHHCTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHHHH CS
                 FAD_binding_5   2 kfeylrpasleealallaaepdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaaeal 82 
                                   k++y+ p++++e +++l++++da+++aGg++l++ +k++++rp+ l++i++ +el++++ ++g+ +iGA++t+ ++     
  gi|70606702|ref|YP_255572.1|   5 KIGYVIPENIDETFDFLEDHEDARPLAGGHSLIPALKLRIIRPSYLVEIRRFKELNYVKFEGGKYRIGALTTHYDI----- 80 
                                   5789************************************************************************..... PP

                                   HHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-EE CS
                 FAD_binding_5  83 vrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktalepgeli 163
                                    ++ +p ls+a++kiA+pq+Rn++TiGG++ + +p++D+++ L+a+dAev+++s++ger+v +++f k++ + +l+pgel+
  gi|70606702|ref|YP_255572.1|  81 SKAGVPLLSQAATKIADPQVRNMGTIGGSISHLDPAADYPASLIAADAEVKIKSKKGERTVSFKDFAKDMFTPDLNPGELV 161
                                   67889**************************************************************************** PP

                                   EEEEEE- CS
                 FAD_binding_5 164 taveiPa 170
                                   ++v++P 
  gi|70606702|ref|YP_255572.1| 162 VEVQLPD 168
                                   ******5 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.3   1.3e-31   1.1e-27       2     101 ..     175     273 ..     174     275 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.3e-31
                                   EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHTCT CS
                 CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspasdp 81 
                                   +y kl+rr++ d+aiv++A++++l++d ++ d+ri++++v++ +vra++ae+ LiGk+ls+el+e+a +++ e ++p+sd+
  gi|70606702|ref|YP_255572.1| 175 SYeKLERRAG-DFAIVGVAVLLKLSGD-VVDDVRIGLTAVNNVAVRAKEAEEELIGKRLSQELIEKASSRAVERANPSSDI 253
                                   799*******.**************99.***************************************************** PP

                                   TC-HHHHHHHHHHHHHHHHH CS
                 CO_deh_flav_C  82 rasaeYRrslavsllfrfll 101
                                   r+saeY++++++++++r++ 
  gi|70606702|ref|YP_255572.1| 254 RGSAEYKKKMVKVMTKRAII 273
                                   *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2096.78
//
Query:       gi|70606703|ref|YP_255573.1|  [L=168]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-34  117.5   0.7    1.2e-33  115.0   0.0    2.1  2  Fer2_2    [2Fe-2S] binding domain
    3.6e-07   30.1   1.0    3.6e-07   30.1   1.0    2.0  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
    0.00024   21.1   0.8    0.00049   20.1   0.8    1.6  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3     0.093   5.6e+02      21      31 ..      46      56 ..      40      64 .. 0.83
   2 !  115.0   0.0     2e-37   1.2e-33       1      76 []      81     154 ..      81     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.093
                        Fer2_2 21 eegasqCGyCt 31
                                   ++ s CG Ct
  gi|70606703|ref|YP_255573.1| 46 GCDTSNCGACT 56
                                  578899****9 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 2e-37
                        Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAvk 76 
                                   Tvegl+++  +lhp+qeaf e++a+qCGyCtpG++m+ + ll+e+ p+pteeeire +sgnlCRCtgY++i++A+k
  gi|70606703|ref|YP_255573.1|  81 TVEGLSKD-GKLHPIQEAFWENHALQCGYCTPGMIMESYWLLKEK-PNPTEEEIREGISGNLCRCTGYQNIIKAIK 154
                                   9*****88.68*********************************9.99999***********************95 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   1.0   5.9e-11   3.6e-07       2      53 ..      15      65 ..      14      85 .. 0.85
   2 ?   -0.6   0.2      0.21   1.3e+03      40      53 ..     106     121 ..     101     144 .. 0.51

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.9e-11
                                  ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCEC CS
                          Fer2  2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegevq 53
                                   i+g+++evev +++++l  +++e g + ++++C  ++Cg+C+v ++  +v+
  gi|70606703|ref|YP_255573.1| 15 RINGETHEVEV-EPRRLLVHVLRELGYTSVHVGCDTSNCGACTVIMNGRSVK 65
                                  689******99.55555*******99******************99976664 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                                   SSTTEEEEEESCE..C CS
                          Fer2  40 CgtClvevlegev..q 53 
                                   Cg C+  +  +++   
  gi|70606703|ref|YP_255573.1| 106 CGYCTPGMIMESYwlL 121
                                   9999855554444431 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.8   8.2e-08   0.00049      20      81 ..      20      76 ..       5      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.2e-08
                        Fer2_3 20 eyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlak 81
                                  ++eve+e++  ++++L ++  +     + +  C    CG+c+v +nG++   Ct    + + 
  gi|70606703|ref|YP_255573.1| 20 THEVEVEPRRLLVHVLRELGYT-----SVHVGCDTSNCGACTVIMNGRSVKSCTVLGIEANG 76
                                  5666666666666666665555.....35689*********************987655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1276.38
//
Query:       gi|70606704|ref|YP_255574.1|  [L=187]
Description: hypothetical protein Saci_0918 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-33  116.8   0.0    1.5e-33  116.4   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    2.6e-07   30.6   0.0    4.3e-07   29.9   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00076   18.7   0.1     0.0011   18.3   0.1    1.3  1  CofC             Guanylyl transferase CofC like
     0.0078   16.2   0.0       0.01   15.8   0.0    1.2  1  CTP_transf_3     Cytidylyltransferase
  ------ inclusion threshold ------
      0.086   12.4   0.0       0.16   11.5   0.0    1.5  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   4.2e-37   1.5e-33       1     157 [.       5     157 ..       5     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 4.2e-37
                                   EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd.eevlaalarlgvrvvededpgkgplaslaaal 80 
                                   a+iLA+G+++R+gg+K+l+ ++++pl+  ++++++ +  d+vv+vg++ +e+l+ l  l+  v++++++ +g+++s++ ++
  gi|70606704|ref|YP_255574.1|   5 AIILAAGEGKRFGGNKLLATIDNTPLILKTINSVKFL--DRVVIVGKYyRELLEVL--LDEIVIYNPNWREGISSSIRLGV 81 
                                   79*********************************77..9******9988888776..5678999999************* PP

                                   HHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHCHHHH CS
                  NTP_transf_3  81 raaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrllrrl 157
                                   r  ++ d+vlvl++DmPl+t+++v++++ +++ +++ +v+p+++g rg+p+l+++ l +++  l gd gar +l +l
  gi|70606704|ref|YP_255574.1|  82 RFFSNFDGVLVLLGDMPLITENTVKKIISEFK-ENCYAVIPVHKGSRGNPVLLSRVLYEKIMNLHGDVGARMILGEL 157
                                   **99***************************7.8899***********************************99876 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.2e-10   4.3e-07       3     127 ..       5     122 ..       3     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.2e-10
                                   EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE..--SSHHHHH CS
                          IspD   3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlva..GGdeRaesV 81 
                                   ++i AAG+GkR   g +K++ ++++ +l+ +t++++     +d++v+v + ++ e  e ll +  i++ +    +  + s+
  gi|70606704|ref|YP_255574.1|   5 AIILAAGEGKRF--GGNKLLATIDNTPLILKTINSVKF---LDRVVIVGKYYR-ELLEVLLDE--IVIYNpnWREGISSSI 77 
                                   89*********8..679***************998776...********9999.666666655..4444310334457899 PP

                                   HHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSEEEEE CS
                          IspD  82 lnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqgaila 127
                                     g++  ++  + VLv  +  pl++++++++++ + ++++ ++i++
  gi|70606704|ref|YP_255574.1|  78 RLGVRFFSNF-DGVLVLLGDMPLITENTVKKIISEFKENCYAVIPV 122
                                   9999998887.6788888889*****************9*999986 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.9e-07    0.0011      35     132 ..      32     133 ..      26     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-07
                          CofC  35 ldvidalkrld.vlvvsed.eevleyaldelgvevvkek.ekdlntaveka..feeieekeviiipsdiPlikkedvkdll 110
                                   l  i+++k ld v++v++  +e+le  lde  +   + +  +++ ++++    f   +++ v+++  d+Pli++++vk+++
  gi|70606704|ref|YP_255574.1|  32 LKTINSVKFLDrVVIVGKYyRELLEVLLDEIVI--YNPNwREGISSSIRLGvrFF-SNFDGVLVLLGDMPLITENTVKKII 109
                                   456777888888888887537888888865543..33344688999998655554.69*********************** PP

                          CofC 111 elekradvviaPargG..Gtnlll 132
                                      k+    + P ++G  G  +ll
  gi|70606704|ref|YP_255574.1| 110 SEFKENCYAVIPVHKGsrGNPVLL 133
                                   998888888888888833333443 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.8e-06      0.01       2     120 ..       5     117 ..       4     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
                                   EEEEE-SSSSSST.TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHH CS
                  CTP_transf_3   2 aIipARsgSkRlp.gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevv 81 
                                   aIi+A  + kR+  +K l+ + + pli  ++      k++++v++    + ++++++ +  +++   ++ +++ +++    
  gi|70606704|ref|YP_255574.1|   5 AIILAAGEGKRFGgNKLLATIDNTPLILKTINS---VKFLDRVVIV--GKYYRELLEVLLDEIVIYNPNWREGISSSIRLG 80 
                                   799999999999637***********9666655...5669**9987..599**************************9999 PP

                                   HHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
                  CTP_transf_3  82 kaflmseneeiivnlqGdnPllqeevikkaietlkenqe 120
                                    +f ++++   ++ l Gd Pl+ e ++kk+i++ ken +
  gi|70606704|ref|YP_255574.1|  81 VRFFSNFD--GVLVLLGDMPLITENTVKKIISEFKENCY 117
                                   99998855..567789*******************9954 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05      0.16       2     129 ..       5     115 ..       4     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a+ILa G+G+R+         kl+   ++ +li +t++ +     ++ +v++ ++ ++l+e  l e+        i   + 
  gi|70606704|ref|YP_255574.1|   5 AIILAAGEGKRFG------GNKLLATIDNTPLILKTINSVKF--LDR-VVIVGKYYRELLEVLLDEIV-------IYNPNW 69 
                                   79*********95......58899999998***999998883..555.9************9999874.......333444 PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEE.EEST.THHHHHHHHHTH CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDh.likd.ayeeavkkaiek 129
                                   ++g+  +++l+++++ + +    vlvL gD+ li++ ++++++ +++e+
  gi|70606704|ref|YP_255574.1|  70 REGISSSIRLGVRFFSNFDG---VLVLLGDMpLITEnTVKKIISEFKEN 115
                                   56**************9998...88888886445544788888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1289.27
//
Query:       gi|70606705|ref|YP_255575.1|  [L=144]
Description: hypothetical protein Saci_0919 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-40  138.2   0.1    1.6e-40  138.1   0.1    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    8.6e-05   22.8   0.0    0.00013   22.1   0.0    1.3  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.031   14.1   0.0         13    5.5   0.0    2.8  3  DUF4923          Lipocalin-like domain (DUF4923)
       0.13   12.5   0.0       0.15   12.3   0.0    1.3  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.1   0.1   3.6e-44   1.6e-40       1     139 [.       5     142 ..       5     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.1 bits;  conditional E-value: 3.6e-44
                                   EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE...EEEEEE- CS
                          COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsfkarvelselekenstt.ieikGkGrg 79 
                                   Ge +v+ +++++w f++d ek+a+c+PG+ks++k g + y+v++++++G++kg++ka+v+ls+++++++   +++kG+G++
  gi|70606705|ref|YP_255575.1|   5 GELQVPFSSDKLWGFITDVEKVASCFPGLKSITKTGeNTYAVVGTAGIGFIKGEYKANVQLSNIDQSSKSLnLVAKGTGLN 85 
                                   899***************************************************************999988********* PP

                                   SSEEEEEEEEEEEEEETTEEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                          COXG  80 agvaidfalvvlveegggtrlswsakvnvggllaslGsrlidsaarklinelfecisskl 139
                                   ++++i + +++l  +    rl++sa+v+v+g+las+G+rl+dsa++kl+n+lfeci+ k+
  gi|70606705|ref|YP_255575.1|  86 SNLDITALVQLLESP---VRLKYSADVKVSGVLASIGARLMDSAVNKLLNDLFECIKLKA 142
                                   *************99...**************************************9876 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     3e-08   0.00013       1     129 [.       9     134 ..       9     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3e-08
                                   ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEEE CS
                Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfkslegkW 81 
                                   vp ++d+++ +++dve+    +p+++s + + e++  + + ++ g g ++ +++a v+l   ++                 
  gi|70606705|ref|YP_255575.1|   9 VPFSSDKLWGFITDVEKVASCFPGLKSITKTGENT--YAVVGTAGIGFIKGEYKANVQLSNIDQ----------------- 70 
                                   68899*********************866666666..55699****************999999................. PP

                                   EECTECC.......EEE..........CEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc  82 tieslpp.......nsg..........gtrtkvalevdfkfaspllgalvgqvaervldellaal 129
                                   +++sl         ns+          ++ +++ ++ d+   s++l+ +   + ++++++ll++l
  gi|70606705|ref|YP_255575.1|  71 SSKSLNLvakgtglNSNlditalvqllESPVRLKYSADV-KVSGVLASIGARLMDSAVNKLLNDL 134
                                   444443355554555557888888888888999999999.5888888888888888888888776 PP

>> DUF4923  Lipocalin-like domain (DUF4923)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.003        13     128     162 ..       5      37 ..       1      48 [. 0.77
   2 ?    0.4   0.1      0.11   4.8e+02      95     122 ..      54      80 ..      35     108 .. 0.59
   3 ?    5.1   0.0     0.004        18      44      74 ..     112     142 ..     103     144 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.003
                       DUF4923 128 nelsLlfdadkLlelltalsskssnstlktvssll 162
                                    el++ f +dkL+ ++t + +++  s +  ++s++
  gi|70606705|ref|YP_255575.1|   5 GELQVPFSSDKLWGFITDVEKVA--SCFPGLKSIT 37 
                                   689999**************999..4444444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                       DUF4923  95 tlkGtYsldakdktvtLklakllslnak 122
                                    +kG+Y+ + + ++++ + +k l+l ak
  gi|70606705|ref|YP_255575.1|  54 FIKGEYKANVQLSNIDQS-SKSLNLVAK 80 
                                   567777776666666655.223333333 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.004
                       DUF4923  44 dnllakagGaaaataveekLkeyykkvgike 74 
                                     +la +g+ ++ +av++ L++ ++ +++k+
  gi|70606705|ref|YP_255575.1| 112 SGVLASIGARLMDSAVNKLLNDLFECIKLKA 142
                                   5689*********************999985 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05      0.15       7      57 ..       6      54 ..       1     139 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                  EEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCC CS
               Polyketide_cyc2  7 svviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvgg 57
                                  + +++ + +k w +++d e++++  p++++ + +g++     v+gt   g+
  gi|70606705|ref|YP_255575.1|  6 ELQVPFSSDKLWGFITDVEKVASCFPGLKSITKTGENTY--AVVGTAGIGF 54
                                  5678999**********************9988863333..3335554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1053.25
//
Query:       gi|70606706|ref|YP_255576.1|  [L=526]
Description: GTP-binding protein 1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-22   80.3   0.0    2.4e-22   79.5   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.6e-06   26.9   0.1    1.3e-05   25.5   0.1    1.9  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.4e-05   25.1   0.0    6.7e-05   22.9   0.0    2.2  2  MMR_HSR1     50S ribosome-binding GTPase
    8.4e-05   22.3   0.7        3.3    7.4   0.0    3.4  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0022   18.3   2.5     0.0043   17.4   1.2    2.2  2  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0024   17.8   0.8       0.31   10.9   0.1    2.6  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.047   14.0   4.6       0.36   11.2   0.1    3.2  4  AlbA_2       Putative DNA-binding domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   9.2e-26   2.4e-22       4     188 ..     112     329 ..     110     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 9.2e-26
                                   EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................... CS
                      GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................... 64 
                                   +ni+++ghv++GK+TLt++L+  + ++ + + +a     + ++ +E   g T +++   l                     
  gi|70606706|ref|YP_255576.1| 112 VNIAVMGHVNAGKSTLTGALILGKLDDGNGTLRAL----IARHMHEILSGRTSSVTLRLLGldsngniinwtlrdpldeae 188
                                   79*******************99988888777664....77777777777777777666667777*************997 PP

                                   .TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHH CS
                      GTP_EFTU  65 .ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelke 141
                                    + ++++ i liD  GH+ + +++ +g     +D+++lvv a++G  +  +e+l +a+ ++ pi+++++K+D+  k++ + 
  gi|70606706|ref|YP_255576.1| 189 iTLKSSKIIRLIDLGGHERYLRTTLKGllGYEVDYVMLVVGADDGLSAMGKEHLAVASILKFPIFIVVTKVDKYsKEKTNG 269
                                   66899999*******************76689******************************************9999*** PP

                                   HHHHHHHHHHHH............HHHHHHH.HHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                      GTP_EFTU 142 iveevkqklsrk............eekleky.gekgekevpvvfgSalkgegvktlleal 188
                                   iv+++++ l+              e+ l+++ ++k+++ vp++ +S ++geg++ l++ l
  gi|70606706|ref|YP_255576.1| 270 IVNDIRNILKIPginrlvieveneEDLLNSIlAMKTKRVVPIFKVSNVTGEGLDLLMKFL 329
                                   ******999655988888888886333333333334479**************9777665 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1     5e-09   1.3e-05       2     109 ..     437     522 ..     436     525 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5e-09
                                   -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEE.ECCEEE CS
                   GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveve.likpia 81 
                                   +++ +kf+A+v++l++  +t i +gY + l++ t   + +++++ +              +++++Gd+++v+++ l +p  
  gi|70606706|ref|YP_255576.1| 437 VRSSRKFKAKVMVLHH--PTTIKEGYVATLHLYTIRQAIRFENIST--------------KYLRSGDAAEVTLSfLYRPEY 501
                                   56789***********..*********************9999922..............567778877777763457777 PP

                                   E--TTTHCCCCEEEEECTTCEEEEEEEE CS
                   GTP_EFTU_D3  82 lekgseypqlGrFaiReggrTvaaGvvt 109
                                   +ek +       F  Re grT + G+v 
  gi|70606706|ref|YP_255576.1| 502 IEKDQ------IFVFRE-GRTRGLGIVI 522
                                   77777......777776.4566777665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.6e-08   6.7e-05       1     114 []     113     258 ..     113     258 .. 0.63
   2 ?   -2.6   0.0       2.3   5.9e+03      52      74 ..     279     304 ..     260     332 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                                   EEEEEESTTSSHHHHHHHHH........TS.TEEESSST.....TSSSSEEEEEEEETTEE.................... CS
                      MMR_HSR1   1 evaivGrpNvGKStLinalt........ge.kaivsdkp.....gtTrdinegrvklkgke.................... 47 
                                   ++a++G+ N+GKStL  al+        g+ +a ++++      g T  ++ + + l   +                    
  gi|70606706|ref|YP_255576.1| 113 NIAVMGHVNAGKSTLTGALIlgklddgnGTlRALIARHMheilsGRTSSVTLRLLGL---Dsngniinwtlrdpldeaeit 190
                                   59*****************95555443312333333222122234444444444442...033456667777777788888 PP

                                   ......EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  48 ......ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                         i+l+D+ G  e     + l+ +++     e+d ++lvv a  ++l+++ +e  ++ +  k p+++v++k
  gi|70606706|ref|YP_255576.1| 191 lksskiIRLIDLGG-HE-----RYLRTTLKGllGYEVDYVMLVVGAD-DGLSAMGKEHLAVASILKFPIFIVVTK 258
                                   888888********.44.....445555555224469*******977.557776666666655567899999887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                   ECGGC....SSHHHHHHHHHHHHHHHH CS
                      MMR_HSR1  52 DtpGl....iegaseekglgkaflale 74 
                                    +pG+    i + ++e++l +++la++
  gi|70606706|ref|YP_255576.1| 279 KIPGInrlvI-EVENEEDLLNSILAMK 304
                                   4566322211.2333444555555433 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0076        19       3      21 ..     113     131 ..     111     138 .. 0.88
   2 !    7.3   0.1    0.0014       3.7      60     127 ..     217     291 ..     198     304 .. 0.76
   3 !    7.4   0.0    0.0013       3.3     104     142 ..     292     330 ..     287     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0076
                     PduV-EutP   3 killiGkvgsGKttLtqal 21 
                                   +i ++G+v++GK tLt al
  gi|70606706|ref|YP_255576.1| 113 NIAVMGHVNAGKSTLTGAL 131
                                   5889************987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
                     PduV-EutP  60 tsaeadvialvqdateeesvfppg...fasvfnkeviGiitkidlaedeen...ieaveelLksaGaeki.fevs 127
                                   + +e+d ++lv+ a++  s + ++   +as+++ ++  ++tk+d+ ++e+    ++  ++ Lk  G++++ +ev+
  gi|70606706|ref|YP_255576.1| 217 LGYEVDYVMLVVGADDGLSAMGKEhlaVASILKFPIFIVVTKVDKYSKEKTngiVNDIRNILKIPGINRLvIEVE 291
                                   5678999999999999998887752226889999**********9866654344778889999999988635555 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0013
                     PduV-EutP 104 deenieaveelLksaGaekifevsavekegieellkyle 142
                                   +ee++ ++   +k+  +  if+vs+v+ eg++ l+k+l+
  gi|70606706|ref|YP_255576.1| 292 NEEDLLNSILAMKTKRVVPIFKVSNVTGEGLDLLMKFLN 330
                                   5666666677788888999*****************997 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   8.2e+03      33      60 ..      24      50 ..      16      60 .. 0.60
   2 !   17.4   1.2   1.7e-06    0.0043       1      74 []     360     431 ..     360     431 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
                                  EEEEEEEEETEEESEEETTSEEEEEEEE CS
                   GTP_EFTU_D2 33 trissletfhededeavaganaGvivai 60
                                  tr +sl t ++ ++ ++ g+ a  i+++
  gi|70606706|ref|YP_255576.1| 24 TRLQSLATQMK-YRLEEGGGEAFYIIGV 50
                                  78888888877.4444444444444443 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.7e-06
                                   EEEEEEEEEESEEETTEEEEEEC..TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg..ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                   Gtv+lg+v++G + ++ + +i++  +   +++  ++++s+++++  +d +  g  a + + + + +  +++G++lt
  gi|70606706|ref|YP_255576.1| 360 GTVVLGSVVRGMITTNRNYYIGPtrL---GDFKEVKVKSIQVNKIFVDKVSSGTIATFAIQGLDKDI-LRKGMVLT 431
                                   9********************99544...44466********************************9.9*****96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.1    0.0086        22     102     122 ..     114     134 ..      58     177 .. 0.62
   2 !   10.9   0.1   0.00012      0.31      16      90 ..     221     296 ..     210     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0086
                                   EEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                   ++++G+  +GKStL  al+  
  gi|70606706|ref|YP_255576.1| 114 IAVMGHVNAGKSTLTGALILG 134
                                   5689**********9998653 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                                   --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEEEE--TTTHTTH CS
                   RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee...eleelkeelealgyevllvsaktkegl 90 
                                   vd +++vv+++ + ls  + +  L++a   + ++ iv++K+D +++e+    ++++++ l+  g++ l+++++++e+l
  gi|70606706|ref|YP_255576.1| 221 VDYVMLVVGAD-DGLS-AMGKEHLAVASILKFPIFIVVTKVDKYSKEKtngIVNDIRNILKIPGINRLVIEVENEEDL 296
                                   89999999999.4444.55677899**********************9776677777777778899899888876654 PP

>> AlbA_2  Putative DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00014      0.36      37      86 ..      46      92 ..       8     120 .. 0.70
   2 ?   -2.3   0.0       2.1   5.3e+03      51      69 ..     284     302 ..     243     350 .. 0.59
   3 ?   -2.4   0.0       2.2   5.7e+03      78      98 ..     387     407 ..     376     423 .. 0.77
   4 ?    3.5   0.0     0.034        87      56     116 ..     428     487 ..     404     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                        AlbA_2 37 lliGVeDdgkvvGvecsdqeedqlrlelksiikrfkpkvlpdiervelkg 86
                                   +iGV D+g+++G+  ++++ d+   + ++i++ ++ k+    + ve+k+
  gi|70606706|ref|YP_255576.1| 46 YIIGVGDNGEIIGI--ERDQLDKSIATIEKIASTINAKIVH-KRIVEVKS 92
                                  58************..4444444444444477777766432.22234444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.1
                        AlbA_2  51 ecsdqeedqlrlelksiik 69 
                                   ++   e ++++ +l+si+ 
  gi|70606706|ref|YP_255576.1| 284 NRLVIEVENEEDLLNSILA 302
                                   3333333333333333333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.2
                        AlbA_2  78 diervelkgkkvlvvkveksk 98 
                                   d+++v++k+ +v ++ v+k +
  gi|70606706|ref|YP_255576.1| 387 DFKEVKVKSIQVNKIFVDKVS 407
                                   677888888888888887765 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.034
                        AlbA_2  56 eedqlrlelksiikrfkpkvlpdiervelkgkkvlvvkvekskkkplyeneegvvyiRrgg 116
                                   +  ++ + +   +++fk kv +  ++  +k+ +v  ++ +  +++    ++ ++ y R+g+
  gi|70606706|ref|YP_255576.1| 428 MVLTNHNSKVRSSRKFKAKVMVLHHPTTIKEGYVATLHLYTIRQAI-RFENISTKYLRSGD 487
                                   555666677778999***********************99998888.66666777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3483.22
//
Query:       gi|70606707|ref|YP_255577.1|  [L=166]
Description: hypothetical protein Saci_0921 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-29  102.3   0.0    5.8e-29  101.0   0.0    1.6  1  zf-ZPR1          ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.025   14.6   0.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.017   15.5   0.1      0.028   14.8   0.1    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   9.7e-33   5.8e-29       2     159 .]      14     157 ..      13     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 9.7e-33
                       zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveipe 82 
                                    Cp C+++++  r +  + P  +  ++m feCe+Cgy+ ++vk+ +e ++   +i lkve+eedl+  +++S +a+v ipe
  gi|70606707|ref|YP_255577.1|  14 ICPVCSNNSMWIRQYSYEAPKAGVLLLMVFECESCGYRIRDVKPFEEGKP--IKIILKVENEEDLRSILYRSPYANVIIPE 92 
                                   6****988888999999*********************************..***************************** PP

                       zf-ZPR1  83 leleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegeepftlildDpagnSfie 159
                                   l++e  ++ + +g +ttvEGlLe + +++ +                ++ ++++e++++ge pftli++D++g S++e
  gi|70606707|ref|YP_255577.1|  93 LGVEALSKeAYQGVITTVEGLLEILLDNMGE-------------LCENNGCQDIEKAKKGELPFTLIIEDQSGLSYVE 157
                                   ***9877669*******************21.............112356899***********************96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   4.1e-06     0.025      15      45 ..       9      50 ..       5      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-06
                 Zn_Tnp_IS1595 15 WpngfvCPhCgsr....kayrikt.......rglfqCkeCrk 45
                                  + ++++CP C +     + y++++         +f+C++C++
  gi|70606707|ref|YP_255577.1|  9 YEGKHICPVCSNNsmwiRQYSYEApkagvllLMVFECESCGY 50
                                  567899******999999999999**9999999*******98 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.7e-06     0.028       6      37 ..      15      54 ..      13      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
               Lar_restr_allev  6 CPfCggravlersqrvvaeigq.....cvyCadCga...s 37
                                  CP C +   ++r+++  a ++      +++C+ Cg+    
  gi|70606707|ref|YP_255577.1| 15 CPVCSNNSMWIRQYSYEAPKAGvlllmVFECESCGYrirD 54
                                  **************99996555*************94331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1111.17
//
Query:       gi|70606708|ref|YP_255578.1|  [L=173]
Description: small heat shock protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-11   42.6   0.0    4.7e-11   42.1   0.0    1.3  1  ArsA_HSP20     HSP20-like domain found in ArsA
    2.8e-10   40.2   1.6    8.9e-09   35.4   1.6    2.2  1  HSP20          Hsp20/alpha crystallin family
  ------ inclusion threshold ------
      0.046   14.1   0.0      0.067   13.6   0.0    1.2  1  PIH1_CS        PIH1 CS-like domain
      0.047   13.7   0.0        0.1   12.6   0.0    1.5  1  DUF3788        Protein of unknown function (DUF3788)
       0.13   12.1   1.9       0.16   11.9   0.3    2.1  2  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain


Domain annotation for each model (and alignments):
>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   1.3e-14   4.7e-11       2      62 ..      91     156 ..      90     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.3e-14
                    ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrs..gdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIr 62 
                                    e+++ ++LP+vdk +i++ +   g+ L+I++  + R+    i LP+ +++k + +A++++gvL + 
  gi|70606708|ref|YP_255578.1|  91 EEVRVIAELPGVDKNNIKVKIIegGKKLIIQASGEDRKyykeIDLPTEVDDKSA-KASYNNGVLQVV 156
                                   588999*********999887666*********555555555**********77.*********997 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   1.6   2.5e-12   8.9e-09       2     101 ..      86     172 ..      85     173 .] 0.82

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.5e-12
                                   --SSEEEEEEEEE-TT--CCCEEEEEETTE..EEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTE CS
                         HSP20   2 ikeeeeefevkldvpglkkeelkvkvednr..vlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGv 80 
                                   ++e  ee +v +++pg++k+++kvk+ ++   +++++  e               rk+ +++ LP +vd+++ kas+++Gv
  gi|70606708|ref|YP_255578.1|  86 VIERGEEVRVIAELPGVDKNNIKVKIIEGGkkLIIQASGE--------------DRKYYKEIDLPTEVDDKSAKASYNNGV 152
                                   67889999*****************854322266666655..............4788899******************** PP

                                   EEEEEEBSS--..-------- CS
                         HSP20  81 Ltvtvpkkepekkkkerkiqi 101
                                   L+v ++k + +++ k  +i++
  gi|70606708|ref|YP_255578.1| 153 LQVVLKKLKGKEE-KGTEIKV 172
                                   *********9976.7777766 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.067      32      87 ..      92     150 ..      78     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                       PIH1_CS  32 elaieielPllksikevklrvgerrlel..eskk..akyfLslkLpYpvdedkveAkFvk 87 
                                   e ++  elP++   +++k+++ e   +l  ++ +   ky  +++Lp +vd+++++A +++
  gi|70606708|ref|YP_255578.1|  92 EVRVIAELPGV-DKNNIKVKIIEGGKKLiiQASGedRKYYKEIDLPTEVDDKSAKASYNN 150
                                   55666789999.67889999866544443354445799********************96 PP

>> DUF3788  Protein of unknown function (DUF3788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.9e-05       0.1      15      45 ..       7      37 ..       1      39 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                       DUF3788 15 keyelwdkllelleetyeepelewsyygkkk 45
                                  ++++l+d+l++++ee++e++e e+++yg ++
  gi|70606708|ref|YP_255578.1|  7 DPFDLFDELIKEIEEEFERFEREFERYGPEE 37
                                  6799***********************9766 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   5.8e+03      11      18 ..      20      27 ..      13      34 .. 0.50
   2 ?   11.9   0.3   4.3e-05      0.16      21      51 ..     102     132 ..      91     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                 DAHP_snth_FXD 11 eeqieevi 18
                                  ee+ e+  
  gi|70606708|ref|YP_255578.1| 20 EEEFERFE 27
                                  34444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.3e-05
                 DAHP_snth_FXD  21 ieelGlkvhvskGeertViGviGdtskldke 51 
                                   + + ++kv++++G ++ +i + G+++k  ke
  gi|70606708|ref|YP_255578.1| 102 VDKNNIKVKIIEGGKKLIIQASGEDRKYYKE 132
                                   57899*********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1187.76
//
Query:       gi|70606709|ref|YP_255579.1|  [L=141]
Description: hypothetical protein Saci_0923 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-21   75.9   0.0    3.1e-21   75.7   0.0    1.1  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.3e-10   40.9   0.0    2.7e-10   40.7   0.0    1.1  1  Glyoxalase_3  Glyoxalase-like domain
    2.1e-09   37.6   0.0    4.7e-09   36.5   0.0    1.6  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.064   13.4   0.0       0.11   12.7   0.0    1.4  1  Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-term


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     7e-25   3.1e-21       1     109 []       7     122 ..       7     122 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 7e-25
                                   EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT.......-THHHTS-EEEEEEE CS
                  Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp.......eflaehgeglhhlay 74 
                                   d+igi+Ve+l+  ++ +++ lG+++  r + +++++++ f+  +sg+  ieL+ep++ +       +fl+++g+glhhla+
  gi|70606709|ref|YP_255579.1|   7 DHIGIAVENLDNSIDLYTNKLGFRVVHRETLPDRGIKVVFLAGSSGETTIELMEPINHDdetntvvKFLKNRGPGLHHLAI 87 
                                   6******************************************9*9***********77778899999999********** PP

                                   EES-HHHHHHHHCTTTEEEEEEEE-GGGTT-EEEE CS
                  Glyoxalase_4  75 wvddldaavarleeqGfevvqkgvragaagrrfay 109
                                    v+d+++++ +l   G+++v+k +r+ga+g+ +a+
  gi|70606709|ref|YP_255579.1|  88 KVSDIKQSLSELNILGIQLVDKTPRVGARGHLVAF 122
                                   *******************************9998 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0     6e-14   2.7e-10       1     114 [.       6     120 ..       6     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 6e-14
                  Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmf..gdgYlElla.vdpeapaperprlfgldrlakgegl 78 
                                   +DH+++av++l++ ++ ++++lGf+v+ +   p+ g++   +    g++ +El++ ++++ ++++    +++ + ++g+gl
  gi|70606709|ref|YP_255579.1|   6 IDHIGIAVENLDNSIDLYTNKLGFRVVHRETLPDRGIKVVFLAGssGETTIELMEpINHDDETNTV---VKFLK-NRGPGL 82 
                                   7*********************************999866555543345******77888888544...44433.57**** PP

                  Glyoxalase_3  79 htlalrtddidataarlraaGvd..eagrrvrpdggdl 114
                                   h+la++++di++   +l   G++  ++  rv   g+ +
  gi|70606709|ref|YP_255579.1|  83 HHLAIKVSDIKQSLSELNILGIQlvDKTPRVGARGHLV 120
                                   ******************99998754444444444444 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0     1e-12   4.7e-09       2     109 ..       6     114 ..       5     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1e-12
                                   EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.......TSE CS
                    Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee.......tvh 75 
                                   idh+ ++v +l+ s+d Yt+ LGf++v ++    ++ g +  f+  ++g  ++ l e+ ++++       +        + 
  gi|70606709|ref|YP_255579.1|   6 IDHIGIAVENLDNSIDLYTNKLGFRVVHRET--LPDRGIKVVFLAGSSGETTIELMEPINHDDETN----TvvkflknRGP 80 
                                   9******************************..666666666666666666666666666665555....333445569** PP

                                   EEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHH CS
                    Glyoxalase  76 hvafialdvedvgkaldrlkeagvkvvaepgrhy 109
                                   +++++a +v d+ + l +l   g++ v++  r +
  gi|70606709|ref|YP_255579.1|  81 GLHHLAIKVSDIKQSLSELNILGIQLVDKTPRVG 114
                                   ***************9999999999776655544 PP

>> Glyoxalase_5  Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05      0.11      10     103 ..       6     111 ..       1     120 [. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                  Glyoxalase_5  10 fefvefaape.aealeelfeklGftavarhr..skdvtl.yrqGg.....infi..lneepd.saaakfarehGpsacala 78 
                                    + +  a ++ +++++ + +klGf+ v r     + +++ +  G+     i+++  +n++ +  ++ kf ++ Gp+   la
  gi|70606709|ref|YP_255579.1|   6 IDHIGIAVENlDNSIDLYTNKLGFRVVHRETlpDRGIKVvFLAGSsgettIELMepINHDDEtNTVVKFLKNRGPGLHHLA 86 
                                   55666666665577777778888888877652223343213222111223666655676655156889************* PP

                  Glyoxalase_5  79 frvkdakkayeralekGakpveket 103
                                   ++v d k++++++   G + v+k++
  gi|70606709|ref|YP_255579.1|  87 IKVSDIKQSLSELNILGIQLVDKTP 111
                                   *********9999888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 976.76
//
Query:       gi|70606710|ref|YP_255580.1|  [L=559]
Description: methylmalonyl-CoA mutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   7.6e-212  704.4   0.0   8.6e-212  704.2   0.0    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.032   12.7   0.1      0.044   12.2   0.1    1.2  1  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.2   0.0  9.6e-216  8.6e-212       2     513 .]      37     551 ..      36     551 .. 0.99

  Alignments for each domain:
  == domain 1  score: 704.2 bits;  conditional E-value: 9.6e-216
                 MM_CoA_mutase   2 TaegievkplYtaedleek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvafdl 81 
                                   T++gi vk+lYt+ d + +   +  +PGe+P+tRG++++myrgr Wtirqyag+++ae+tn r++klLeaGqtgls+afdl
  gi|70606710|ref|YP_255580.1|  37 TPSGILVKRLYTPLDQKGDyLSKLGFPGEYPYTRGIYPNMYRGRLWTIRQYAGYGSAEDTNYRFRKLLEAGQTGLSMAFDL 117
                                   89*************9555667778******************************************************** PP

                 MM_CoA_mutase  82 ptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgtiqnDi 162
                                   pt+ g+D+dh+ a +evG +Gv++ + ++m+ ++++i+++kv++smtina+a++ll+my+a+ae++g++ ++l+gt+qnDi
  gi|70606710|ref|YP_255580.1| 118 PTQLGLDPDHKLAFTEVGVVGVSLFHWKEMDLVMSDIPIQKVTTSMTINATAIELLSMYIATAESRGISTSELDGTVQNDI 198
                                   ********************************************************************************* PP

                 MM_CoA_mutase 163 LkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvralleaGldvdefa 243
                                   Lke++ar++yiyppe  +r ++d+iey +k++p++++is+sgyhireaGa+a+ E+AftladG+eYvr+ +e+G++vd+fa
  gi|70606710|ref|YP_255580.1| 199 LKEYIARKNYIYPPEFGIRYAVDLIEYSSKNIPNWHPISISGYHIREAGADAILEVAFTLADGIEYVRKTIERGISVDDFA 279
                                   ********************************************************************************* PP

                 MM_CoA_mutase 244 prlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilRttlealaAvlggtq 324
                                   p+lsFffa+ +++feeiAk+RAaRr+Wa+i+ke f+ak+++s++lr+h+qT+g++ltaq+p++Ni+Rttl+alaA+lggtq
  gi|70606710|ref|YP_255580.1| 280 PKLSFFFAAYTNIFEEIAKFRAARRMWAKIMKEMFNAKKPESMMLRFHTQTGGAELTAQQPEINIIRTTLQALAAILGGTQ 360
                                   ********************************************************************************* PP

                 MM_CoA_mutase 325 slhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklfqeieeaGGmlkaiesGlv 405
                                   slh+ns+Deal+lPte++a+iA ++q+++a+Esg ++++DP++GSyyvE+LTde++e+awk++ +ie++GGm+kaie G++
  gi|70606710|ref|YP_255580.1| 361 SLHVNSYDEALGLPTEKAAKIAIRVQQVIAHESGATDTIDPIAGSYYVEWLTDEIEEHAWKILYDIERMGGMMKAIEVGYP 441
                                   ********************************************************************************* PP

                 MM_CoA_mutase 406 qeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealraerdeaavkaaLaalgeaarse. 485
                                   q++iaes++r qk++e+++ v vGvN++ + +   ++ev k+++ v++r  +rl+++++erd+++v+  L++l++aa++e 
  gi|70606710|ref|YP_255580.1| 442 QAQIAESSYRIQKRLEQNDLVRVGVNMYYEPDWIGTTEVFKVNPLVRDRILQRLAKYKKERDNSKVEGSLSRLRNAADKEn 522
                                   ****************************97777899***************************************999889 PP

                 MM_CoA_mutase 486 .nllaraveaaralatlGeisdaleevfg 513
                                    n+++++++a++  at+Ge+s++l+e +g
  gi|70606710|ref|YP_255580.1| 523 vNIFPYILDAIKSGATVGEVSSVLRELWG 551
                                   **************************998 PP

>> Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     5e-06     0.044     204     309 ..     279     389 ..     261     469 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-06
                 Met_asp_mut_E 204 vksitvgygqvgnlvqDvaalraleelaeeylkkf.gy.edvvvttvlhqwmGgfPqdeak.afgvi..slgaavaalaka 279
                                   + +++  ++ ++n+  ++a  ra +++  + +k++  + +   +   +h++ Gg   + ++    +i  +l a +a l+++
  gi|70606710|ref|YP_255580.1| 279 APKLSFFFAAYTNIFEEIAKFRAARRMWAKIMKEMfNAkKPESMMLRFHTQTGGAELTAQQpEINIIrtTLQALAAILGGT 359
                                   556777889999*************99999998752331345677789*****9544333312344411556888999*** PP

                 Met_asp_mut_E 280 tkvivKtphEalgvptkeanaaglratkqv 309
                                   + + v + +Ealg pt++a   ++r+ + +
  gi|70606710|ref|YP_255580.1| 360 QSLHVNSYDEALGLPTEKAAKIAIRVQQVI 389
                                   *******************99999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3848.37
//
Query:       gi|70606711|ref|YP_255581.1|  [L=175]
Description: phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-23   82.4   0.1    3.3e-23   81.9   0.1    1.1  1  Pribosyltran  Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   1.9e-27   3.3e-23       4     150 ..       6     145 ..       3     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.9e-27
                                   HTTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE........EE-- CS
                  Pribosyltran   4 ellenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdesrlle 83 
                                   e++e       v  +a++ l++ n+ pd++v i++gGv++ak ++d+L+++ l yv+++ y + +  e ++ + ++     
  gi|70606711|ref|YP_255581.1|   6 EIEE------GVLTIAEKMLDD-NFVPDMIVSILTGGVIPAKLISDALGIKnLKYVDIRFYKGVKDRENKPIVRAI--YVN 77 
                                   4555......777788888888.*************************998788****999999999999888777..8** PP

                                   --TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS......EEEEE CS
                  Pribosyltran  84 dpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfsls.pdnfva 150
                                   d++ kkVl++DD+ dtG Tl  a ++++  +p +vr+a+l+ kp +++ +d+++k +++ + + ++++
  gi|70606711|ref|YP_255581.1|  78 DVEAKKVLVIDDVSDTGETLDFAGNIIAMFNPLVVRTATLFVKPWSRKYPDYYYKIIDKWIiFPWDKW 145
                                   **********************************************************7777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1327.05
//
Query:       gi|70606712|ref|YP_255582.1|  [L=364]
Description: hypothetical protein Saci_0926 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-17   63.4   5.0    9.9e-17   61.5   4.7    1.8  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
    1.1e-07   32.1   1.2    1.9e-07   31.4   0.1    2.0  2  PglZ           PglZ domain
    5.6e-05   22.6   0.5    8.3e-05   22.1   0.1    1.5  2  Metalloenzyme  Metalloenzyme superfamily


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   4.7   1.7e-20   9.9e-17      27     246 ..      55     259 ..      53     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.7e-20
                                   HHHHSEEESE.EE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEETTTTGGGGGCTTS-HHHHHHHTHTTC CS
                  Phosphodiest  27 Lakegvsapn.lrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvtededaprwwqgepiwdtaakarglk 106
                                   L + g+++++ +++vfP++T++ +++l T + P+eHGi g+t y + +g      +++ ++   +    + d+   + g+ 
  gi|70606712|ref|YP_255582.1|  55 LSDAGFTVDRtITTVFPSTTATTLTTLFTAQLPAEHGILGYTTYSKRLGGI----INTLKY--TYPLVDTRDIISEE-GIE 128
                                   567788899989******************************998888774....222221..12224455556666.777 PP

                                   EEEESE..TTTTSEBTTCT.SC.TBHHSBTCT..CSTTSCHHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCH CS
                  Phosphodiest 107 aaalfw..pgsevdystyyylvsetppryled.dfnakvpledkvdkavlqtwldaafakvvlekelekpdlllvyleetD 184
                                     ++f   +    +++++++   e+ p+ le+ +f++  + ++ ++k  + ++ d af +++  ++++++d++++y++++D
  gi|70606712|ref|YP_255582.1| 129 YEKAFPdvKNYLKEVRDKKTA--EVTPKGLENtQFTKLTHGRTNITKTYI-NYWD-AFTEASNILQMKEYDFVYIYIPDVD 205
                                   777877666666666655444..677777755577777777777776566.3433.23232223444************** PP

                                   HHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGG CS
                  Phosphodiest 185 tvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvieln 246
                                   +  Hk+Gp++p v++ +r++ + + +L e  ++      +++++++DHG  +v  ++ i ln
  gi|70606712|ref|YP_255582.1| 206 SLAHKHGPNHPVVKECIRDLYNGLMKLAERFKD------YTFVITADHGHVQV--NEHIALN 259
                                   ************999998888888888888775......79************..5555554 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.39   2.3e+03      35      56 ..      65      86 ..      48      93 .. 0.81
   2 !   31.4   0.1   3.2e-11   1.9e-07     105     175 ..     187     255 ..     112     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.39
                          PglZ 35 avlgvlPslTklgraallpgkk 56
                                   + +v Ps T      l+  + 
  gi|70606712|ref|YP_255582.1| 65 TITTVFPSTTATTLTTLFTAQL 86
                                  5678999999999999998665 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 3.2e-11
                          PglZ 105 rrellkdkevvyivhnkvDalgdkasteqksfeaveeslkelkelvksllee.ngykvlltaDHGfiyqrgk 175
                                       +k+++ vyi++  vD+l++   +       v+e +  l++ + +l+e+ + y+ ++taDHG ++++++
  gi|70606712|ref|YP_255582.1| 187 NILQMKEYDFVYIYIPDVDSLAH---KHGPNHPVVKECIRDLYNGLMKLAERfKDYTFVITADHGHVQVNEH 255
                                   333699*****************...55666778999999999999999999999*************9875 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0       1.4   8.5e+03       3      15 ..      42      54 ..      41      59 .. 0.78
   2 !   22.1   0.1   1.4e-08   8.3e-05     114     188 ..     176     250 ..     113     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.4
                                  EEEEEETTBB--- CS
                                  xxxxxxxxxxxxx RF
                 Metalloenzyme  3 vvlvvlDGlGeap 15
                                  ++l +lDGlG+  
  gi|70606712|ref|YP_255582.1| 42 IALTLLDGLGYTM 54
                                  78999****9865 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.4e-08
                                   --HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHH..HHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Metalloenzyme 114 mkavevaekaldailsgkfdlvvvniknaDmvGHtgdleati..aaieaaDeavkeildaieqvdgilvvtADHgna 188
                                   +++ + + +a + ++ +++d+v++ i++ D+++H+  ++  +  + i ++ + + ++ ++   +d ++v+tADHg  
  gi|70606712|ref|YP_255582.1| 176 INYWDAFTEASNILQMKEYDFVYIYIPDVDSLAHKHGPNHPVvkECIRDLYNGLMKLAERF--KDYTFVITADHGHV 250
                                   556667777888888899****************998887542267788888888888885..5667********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2558.63
//
Query:       gi|70606713|ref|YP_255583.1|  [L=51]
Description: hypothetical protein Saci_0927 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 357.80
//
Query:       gi|70606714|ref|YP_255584.1|  [L=602]
Description: SAV protein-like [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-84  279.7   0.0    8.7e-41  139.4   0.0    2.6  2  AAA              ATPase family associated with various cellul
    9.9e-27   92.5   5.1    1.6e-14   53.4   0.8    2.9  2  AAA_lid_3        AAA+ lid domain
    1.1e-16   61.4   0.0    7.2e-09   36.0   0.0    3.0  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.6e-14   51.7   0.0    1.4e-06   28.3   0.0    3.1  2  AAA_14           AAA domain
    1.4e-12   47.8   0.5    2.9e-05   24.1   0.6    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    3.9e-12   46.9   0.1    0.00047   20.6   0.1    4.4  3  AAA_16           AAA ATPase domain
    1.3e-11   44.5   0.0      2e-05   24.4   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.2e-11   43.0   3.1    0.00062   20.1   0.0    5.0  3  AAA_22           AAA domain
      2e-10   41.3   0.0     0.0003   21.3   0.0    2.8  2  AAA_18           AAA domain
    1.2e-09   37.9   0.0    3.2e-05   23.3   0.0    2.5  2  TIP49            TIP49 P-loop domain
      2e-09   37.7   0.0    0.00031   20.9   0.0    2.7  2  AAA_33           AAA domain
    2.8e-09   36.8   0.1    1.8e-05   24.7   0.0    3.2  2  Vps4_C           Vps4 C terminal oligomerisation domain
    7.2e-09   36.0   0.0      0.004   17.5   0.0    3.2  2  RNA_helicase     RNA helicase
    1.8e-08   34.5   0.2      0.013   15.5   0.0    3.2  2  Rad17            Rad17 P-loop domain
    6.1e-08   32.6   0.0      0.011   15.5   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    1.1e-07   32.4   0.2      0.017   15.5   0.0    3.4  2  AAA_17           AAA domain
    1.4e-07   31.4   0.1     0.0018   18.1   0.2    2.8  2  AAA_3            ATPase family associated with various cellul
    5.6e-07   30.0   0.0       0.05   13.8   0.0    2.7  2  AAA_28           AAA domain
    8.4e-07   29.0   0.0      0.011   15.7   0.1    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.9e-06   27.3   0.7       0.17   11.8   0.1    3.5  3  NACHT            NACHT domain
    4.5e-06   26.2   3.5     0.0093   15.4   0.5    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.6e-06   25.8   0.0        0.1   12.1   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    8.1e-06   25.5   1.3      0.097   12.2   0.6    3.3  2  AAA_25           AAA domain
    1.5e-05   24.8   0.8      0.061   13.0   0.1    3.2  3  AAA_24           AAA domain
    7.6e-05   22.6   0.0       0.17   11.6   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00011   22.8   0.1       0.39   11.2   0.0    2.9  2  ABC_tran         ABC transporter
    0.00013   22.0   0.1       0.97    9.4   0.0    3.2  3  ResIII           Type III restriction enzyme, res subunit
    0.00014   21.6   0.1       0.99    9.1   0.0    3.3  2  Sigma54_activat  Sigma-54 interaction domain
    0.00021   21.1   0.3       0.96    9.1   0.1    3.1  2  AAA_30           AAA domain
    0.00023   20.2   0.0       0.48    9.2   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
     0.0004   19.6   0.0       0.67    9.1   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
    0.00044   19.7   0.3        1.7    7.9   0.0    3.1  2  ATPase           KaiC
      0.001   19.1   2.6      0.077   12.9   0.0    3.5  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0016   17.8   0.1       0.27   10.5   0.0    2.8  2  Zeta_toxin       Zeta toxin
     0.0019   18.0   0.0        2.3    8.0   0.0    3.0  3  Bac_DnaA         Bacterial dnaA  protein
     0.0021   17.7   0.2        2.4    7.8   0.1    3.6  3  Guanylate_kin    Guanylate kinase
     0.0022   18.1   0.0        3.4    7.8   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0025   17.6   0.0        3.4    7.4   0.0    2.7  2  AAA_11           AAA domain
     0.0027   17.1   0.3        1.5    8.2   0.1    3.5  3  TniB             Bacterial TniB protein
     0.0032   16.5   0.0       0.91    8.4   0.1    2.6  2  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0032   16.7   0.1        1.5    8.0   0.1    2.7  2  NB-ARC           NB-ARC domain
     0.0082   16.0   0.9        2.8    7.7   0.1    3.5  3  dNK              Deoxynucleoside kinase
     0.0099   16.1   0.0      0.047   13.9   0.0    2.2  1  Glutaredoxin     Glutaredoxin
  ------ inclusion threshold ------
      0.011   15.9   0.5          2    8.5   0.4    2.9  2  SKI              Shikimate kinase
      0.011   15.4   0.0        1.5    8.4   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.012   15.1   0.2        3.3    7.1   0.0    3.8  4  KTI12            Chromatin associated protein KTI12
      0.014   14.7   0.8      0.022   14.0   0.8    1.2  1  MFS_Mycoplasma   Mycoplasma MFS transporter
      0.015   15.0   0.0          1    9.0   0.0    2.9  2  Cytidylate_kin   Cytidylate kinase
      0.019   15.0   0.1        5.2    7.2   0.0    3.5  3  MMR_HSR1         50S ribosome-binding GTPase
      0.019   14.9   0.2        2.1    8.2   0.1    2.9  2  NTPase_1         NTPase
      0.022   15.1   0.1        1.3    9.3   0.1    2.9  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.023   13.8   0.0        4.4    6.3   0.0    2.4  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.026   14.9   1.5        6.6    7.1   0.0    3.0  2  AAA_19           AAA domain
      0.033   13.9   0.1        1.8    8.3   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.039   13.4   0.1        4.8    6.6   0.0    3.3  3  SRPRB            Signal recognition particle receptor beta su
      0.045   12.6   0.3       0.87    8.3   0.0    2.7  3  Adeno_IVa2       Adenovirus IVa2 protein
      0.052   13.7   0.0         19    5.4   0.0    2.9  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.063   13.1   0.0        4.4    7.1   0.1    2.4  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.066   12.4   0.0        8.8    5.4   0.0    2.4  2  DAP3             Mitochondrial ribosomal death-associated pro
      0.075   12.8   0.0         19    5.1   0.0    2.6  2  AAA_29           P-loop containing region of AAA domain
      0.083   11.3   0.4       0.15   10.4   0.4    1.3  1  Zwilch           RZZ complex, subunit zwilch
      0.088   11.6   0.2        6.8    5.4   0.0    2.1  2  PPV_E1_C         Papillomavirus helicase
       0.11   13.2   3.0       0.32   11.7   3.0    1.8  1  DUF3139          Protein of unknown function (DUF3139)
       0.53    9.9   2.4         37    3.9   0.0    3.6  3  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.0   1.1e-42   2.9e-40       1     131 [.      97     227 ..      97     228 .. 0.97
   2 !  139.4   0.0   3.1e-43   8.7e-41       1     131 [.     380     508 ..     380     509 .. 0.97

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 1.1e-42
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgsese 80 
                                   +ll+GppG+GKTl+++a+a+e++++f+ +++s+++sk+ gese+++relf++a++++ p+ilf+DEid ++ +r s++ ++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSDIMSKWYGESEARLRELFANARKNS-PCILFFDEIDTIGVRReSHTGDS 176
                                   69******************************************************9.****************88999** PP

                                   HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++ r+++ +l+e+dg++ +++ +i++g tn p+ ld+allr gRfd+ i+i+
  gi|70606714|ref|YP_255584.1| 177 VTPRLLSLMLSEIDGLQGNDG-IILVGSTNIPHLLDKALLRaGRFDKLIYIG 227
                                   ******************866.***************************997 PP

  == domain 2  score: 139.4 bits;  conditional E-value: 3.1e-43
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +ll+GppG+GKT++aka+ k+lgv+f+ isg+e+l k  + + + i+e+f++a+e++ p i+++DEida+a++r ++++++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFIMISGAEILYKGYEGAVSTIKEVFNRARENK-PAIVLLDEIDAIAPRR-ENQKTD 458
                                   69*********************************99999999*************8.****************.999*** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   +++vvnqLlte+dg ++ ++ v+vi++tnr++++dpal r gRfdr+++++
  gi|70606714|ref|YP_255584.1| 459 SSKVVNQLLTEMDGIRSLKE-VVVIATTNRMEDVDPALKRpGRFDRIVYMP 508
                                   *****************865.***************************987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.8   5.8e-17   1.6e-14       1      45 []     250     299 ..     250     299 .. 0.88
   2 !   40.0   0.3   9.1e-13   2.5e-10       2      36 ..     531     565 ..     531     579 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 5.8e-17
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcr....eAallAlrrgik.eitmedfee 45 
                                   dvd+++LAe+Te ++GADla+lc+    +Aa++Al+r+ + +i+m+df++
  gi|70606714|ref|YP_255584.1| 250 DVDFDKLAEMTERFTGADLANLCQevarRAAIEALERNVErKISMQDFND 299
                                   9***********************666666688999999956******86 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 9.1e-13
                     AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                   v  +++A+ TeGySGADlaa+ reA l  lr+ i 
  gi|70606714|ref|YP_255584.1| 531 VKCDQIAKVTEGYSGADLAAIAREAKLKVLREIIR 565
                                   6789****************************776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   5.2e-07   0.00014       6      90 ..      97     176 ..      92     196 .. 0.79
   2 !   36.0   0.0   2.6e-11   7.2e-09       4     105 ..     378     472 ..     375     488 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.2e-07
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt++ +ala+  ++    ++i ++ s+++     + + +++   ++   +a ++   i+++DEid i  + 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKI----NFIYVNVSDIMS----KWYGESEARLRELFANARKNSpcILFFDEIDTIGVRr 169
                                   8899******************98....************....77777777766666666666666**********9976 PP

                                   ------- CS
                         AAA_2  84 essgadv 90 
                                   es + d 
  gi|70606714|ref|YP_255584.1| 170 ESHTGDS 176
                                   6666554 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 2.6e-11
                                   --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG---- CS
                         AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihpk 83 
                                     ill gp gvGkt++akal+++l v    k+i++   e+l  +  e  vs    ++ ++ ++e++  ivllDEid i+p+
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALSKTLGV----KFIMISGAEILY-KGYEGAVSTI--KEVFNRARENKPaIVLLDEIDAIAPR 451
                                   5699*********************8....999999999999.5666666543..3333333333335************7 PP

                                   .---------HHHHHHHHHHHH- CS
                         AAA_2  84 .essgadvSregVqrdLLqileg 105
                                    e+++ d S   V++ LL  ++g
  gi|70606714|ref|YP_255584.1| 452 rENQKTDSS--KVVNQLLTEMDG 472
                                   555555555..688888877766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   5.1e-09   1.4e-06       5      77 ..      97     179 ..      94     228 .. 0.73
   2 !   19.8   0.0   2.3e-06   0.00064       5     124 ..     380     508 ..     378     514 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5.1e-09
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev........ 76 
                                   +++ G+  +GKT +++ l++e      +++y+n+ d   k + ++e +l el+ +   ++   +lf+DEi  +        
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAK---INFIYVNVSDIMSKWYGESEaRLRELFANAR-KNSPCILFFDEIDTIgvrresht 173
                                   7899***************9888...9***********9998877635666666654.458999******98866666666 PP

                        AAA_14  77 .....p 77 
                                        p
  gi|70606714|ref|YP_255584.1| 174 gdsvtP 179
                                   555554 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.3e-06
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........p 77 
                                   +++ G+  vGKT+++k l k+l     +++ i+  +  +k ++   + +++++++++e+k  +++lDEi  +        +
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLG---VKFIMISGAEILYKGYEGAVSTIKEVFNRARENKPAIVLLDEIDAIaprrenqkT 457
                                   6899**************99999...89***********99886554555555555566999********99888888886 PP

                        AAA_14  78 ewekalkslvdeg....knldvivtGSnskllskeiatslagrvaeielyp 124
                                   + +k++++l+ e     +  +v+v    + +   + a +  gr + i  +p
  gi|70606714|ref|YP_255584.1| 458 DSSKVVNQLLTEMdgirSLKEVVVIATTNRMEDVDPALKRPGRFDRIVYMP 508
                                   666666666663311211124555555555555555555556665555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.3e-06    0.0015       2      77 ..      97     165 ..      96     184 .. 0.84
   2 !   24.1   0.6     1e-07   2.9e-05       2     135 ..     380     496 ..     379     497 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.3e-06
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEvera 77 
                                   +lL GppG+gK+ +++ la   + ++ yv+ ++      +  ++    g+ + +  +l  +ar  +++il++DE++++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSD------IMSKWY---GESEARLRELFANARknSPCILFFDEIDTI 165
                                   89*************************999876......555565...555566678887888788999999999865 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--..H CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEverae..s 79 
                                   +lL GppG+gK+++a+ l++ l+ ++ ++ + +      l  ++e   g  s  + ++ ra + +++i++lDE++ +   +
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFIMISGAE-----ILYKGYE---GAVSTIKEVFNRAREnKPAIVLLDEIDAIAprR 452
                                   89***********************99998865.....5555666...666667777776666999*********776222 PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                   e +++  s   ++ l   e+++  + k+      + viat+n+ +    +++pal+
  gi|70606714|ref|YP_255584.1| 453 ENQKTDSSKVVNQLLT--EMDGIRSLKE------VVVIATTNRME----DVDPALK 496
                                   3333333322222222..3333333333......88888888888....7777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.5e-05     0.016      24      55 ..      94     122 ..      85     135 .. 0.83
   2 ?    4.3   0.0      0.17        46     122     146 ..     141     173 ..     136     200 .. 0.73
   3 !   20.6   0.1   1.7e-06   0.00047      25     100 ..     378     448 ..     360     483 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.5e-05
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggif 55 
                                   p  +ll G++G+GK+ ++r+l+++++ +   f
  gi|70606714|ref|YP_255584.1|  94 PKGILLFGPPGCGKTLMMRALANEAKIN---F 122
                                   4789******************988866...3 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.17
                        AAA_16 122 llkrllallsrderplvlvlDdlq.........w 146
                                    l++l+a +++  +p +l++D+++          
  gi|70606714|ref|YP_255584.1| 141 RLRELFANARK-NSPCILFFDEIDtigvrreshT 173
                                   67888899999.889********96655555544 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 1.7e-06
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                   + +ll+G++GvGK+ ++++l + l  + +i ++g    +     y   ++++ +e + r+ +++++  +l++ ++ 
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALSKTLGVK-FIMISGAEILY---KGYEGAVSTI-KEVFNRARENKPAIVLLDEIDAI 448
                                   89*******************999988.88899999888...7777788888.65777777766555444444443 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-05    0.0033      34      96 ..      95     165 ..      63     181 .. 0.72
   2 !   24.4   0.0   7.2e-08     2e-05      32      73 ..     376     417 ..     341     455 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-05
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkit.sgPvlek.....agdlaalltnleekd..vlfideihrl 96 
                                     +ll+GpPG Gkt + + +a+e ++++     + +++k     ++ l  l++n +++   +lf dei  +
  gi|70606714|ref|YP_255584.1|  95 KGILLFGPPGCGKTLMMRALANEAKINFIYVnVSDIMSKwygesEARLRELFANARKNSpcILFFDEIDTI 165
                                   569*********************99975441344444321111444555555555554458888888765 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 7.2e-08
                        RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekag 73 
                                   ++  +ll+GpPG+Gkt +ak ++k lgvk+ + sg  +  +g
  gi|70606714|ref|YP_255584.1| 376 PIRGILLHGPPGVGKTMMAKALSKTLGVKFIMISGAEILYKG 417
                                   56789***************************9998876554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.2e-06   0.00062       8      51 ..      97     131 ..      91     210 .. 0.89
   2 ?   -1.3   0.0       8.9   2.5e+03      51     103 ..     265     319 ..     225     330 .. 0.68
   3 !   16.2   0.6   3.4e-05    0.0094       8      30 ..     380     402 ..     378     482 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.2e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                   ++++G++G+GKT+ +r l++++         +  +++v+++  +
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEA---------KINFIYVNVSDIM 131
                                   89*******************9.........8999999887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 8.9
                        AAA_22  51 t.sskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhl 103
                                   + ++++l++e++r    e+ +++ +++  ++ +++ +++++  + l +++E +++
  gi|70606714|ref|YP_255584.1| 265 GaDLANLCQEVARRAAIEALERNVERKISMQDFNDVIKRYKPsVTLQMLEEYEKF 319
                                   3456667777777777666664555555557777777777776666666666655 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 3.4e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                   ++++G++G+GKT+ ++ l ++l 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLG 402
                                   79****************99983 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.2e-05    0.0063       1      34 [.      97     133 ..      97     164 .. 0.84
   2 !   21.3   0.0   1.1e-06    0.0003       1      69 [.     380     450 ..     380     492 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvake 34 
                                   Ill G+pG+GKt + ++L+++ ++    vn++d+ ++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKInfiYVNVSDIMSK 133
                                   99****************9887666699999998876 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.1e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenss 69 
                                   Ill G+pGvGKt +ak+Lsk l  gv+ + +   + l+ +++ +     ++ +  r++++   +lld++++++ 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL--GVKFIMISGAEILYKGYEGAvstikEVFNRARENKPA-IVLLDEIDAIAP 450
                                   89*******************9..5555544444444444444444323333333333333.344444444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00033     0.093      51      98 ..      95     140 ..      87     151 .. 0.87
   2 !   23.3   0.0   1.1e-07   3.2e-05      43      90 ..     369     415 ..     364     481 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                   +++Ll Gp+g Gkt +  a+++e   ++ f+ ++ s++ s     +e+
  gi|70606714|ref|YP_255584.1|  95 KGILLFGPPGCGKTLMMRALANEA--KINFIYVNVSDIMSKWYGESEA 140
                                   89*******************995..6***********9987777765 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.1e-07
                                   XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  43 ikekkla.GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                   +++ k+   r++Ll Gp+g Gkt +a a+sk lg  v+f+++sg+e+  
  gi|70606714|ref|YP_255584.1| 369 MEQMKIPpIRGILLHGPPGVGKTMMAKALSKTLG--VKFIMISGAEILY 415
                                   55556541499***********************..99********843 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00016     0.044       2      47 ..      97     144 ..      97     163 .. 0.83
   2 !   20.9   0.0   1.1e-06   0.00031       2     105 ..     380     508 ..     380     527 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00016
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktd 47 
                                   +ll G+pG+GK+   + l+++ +  ++ ++  +++++ +g+ + ++++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKinFIYVNVSDIMSKWYGESEARLRE 144
                                   6899***************99999999999999999998876665554 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.1e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt...............................lrrrlfgtdqqsktdyt 49 
                                   +ll+G+pG+GK+  a+ l k lg  ++ +s  +                               ++++++++ +++ktd++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGvkFIMISGAEilykgyegavstikevfnrarenkpaivlldEIDAIAPRRENQKTDSS 460
                                   689********************9999999888888888999997777777777777777766666666666666665554 PP

                        AAA_33  50 rvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvve 105
                                   +v +    +l    +  +s +  v++  tn+++    +++ +++r g  +riv++ 
  gi|70606714|ref|YP_255584.1| 461 KVVN----QLLTEMDGIRSLKEVVVIATTNRME----DVDPALKRPGRFDRIVYMP 508
                                   4443....3335556678899999999998765....4444444444445555555 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.2e-08   1.8e-05      25      57 ..     288     320 ..     279     323 .. 0.92
   2 !    8.5   0.0    0.0072         2      27      48 ..     570     591 ..     561     600 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.2e-08
                        Vps4_C  25 lePpvtlkDflkalkkarptVskeDLekheeFT 57 
                                   +e++++++Df +++k+ +p+V+ + Le++e+F 
  gi|70606714|ref|YP_255584.1| 288 VERKISMQDFNDVIKRYKPSVTLQMLEEYEKFR 320
                                   789****************************95 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0072
                        Vps4_C  27 PpvtlkDflkalkkarptVske 48 
                                   ++++++D+++a +k +p+V +e
  gi|70606714|ref|YP_255584.1| 570 RKLSYEDLIEAASKIKPSVKQE 591
                                   689****************987 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.5e-05     0.024       1      23 [.      97     119 ..      97     160 .. 0.83
   2 !   17.5   0.0   1.4e-05     0.004       1     106 [.     380     486 ..     380     487 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.5e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   i+l+Gp+g+GK+++++ La++  
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAK 119
                                   689**************998865 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.4e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpeddfwdgYt..gqevvvidDfgqvkdeenpsdlael 73 
                                   i+l+Gp+g+GK+++ak L+k+l  k+      +   k+   + ++ +++++  +  ++++v+ d++ ++  +    + +  
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFimisgaEILYKGYEGAVSTIKEVFNRARenKPAIVLLDEIDAIAPR---RENQKT 457
                                   689*******************97776666652222222223345566666665556778888888888766...344445 PP

                  RNA_helicase  74 irlvsstpyplnmasleekgtlftSkvvivtsN 106
                                         +++ ++m+ + +     + +vvi+t+N
  gi|70606714|ref|YP_255584.1| 458 DSSKVVNQLLTEMDGIRS----LKEVVVIATTN 486
                                   555555666667777764....35677777777 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.8e-05     0.016      47      78 ..      96     126 ..      68     189 .. 0.69
   2 !   15.5   0.0   4.5e-05     0.013      46      77 ..     378     409 ..     351     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.8e-05
                         Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewln 78 
                                    +L+ GP+GCgk+ +++ L+ e  i+++ ++n
  gi|70606714|ref|YP_255584.1|  96 GILLFGPPGCGKTLMMRALANEAKINFI-YVN 126
                                   46778****************9998876.334 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.5e-05
                         Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewl 77 
                                   r +L+ GP+G gk+ + k Lsk lg+k++  +
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALSKTLGVKFIMIS 409
                                   45789*********************998655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.9e-05     0.011      44      90 ..      91     134 ..      77     173 .. 0.73
   2 !   14.4   0.0   8.2e-05     0.023      48      70 ..     378     400 ..     353     466 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-05
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90 
                                   i+  ++i+l+Gp+G GK+ +  al+ ea    ++ ++v v+d++++ 
  gi|70606714|ref|YP_255584.1|  91 IKPPKGILLFGPPGCGKTLMMRALANEA---KINFIYVNVSDIMSKW 134
                                   6667899*****************9986...6778888888888765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.2e-05
                     IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                    +i+l Gp+GvGK+ +a al++ 
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALSKT 400
                                   6799*************998653 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.1e-05     0.017       1      38 [.     100     139 ..     100     175 .. 0.80
   2 !   13.1   0.0   0.00035     0.098       2      33 ..     384     417 ..     383     487 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.1e-05
                                   EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTT CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgg 38 
                                   +G+PG+GK+ +++ l+ +   +f +++ +d++ +   +++
  gi|70606714|ref|YP_255584.1| 100 FGPPGCGKTLMMRALANEAkiNFIYVNVSDIMSKWYGESE 139
                                   6**************9654339999*******88766555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00035
                                   E-TTSSHHHHHHHHHHHHTEEE..EEHHHHHHHH CS
                        AAA_17   2 GgPGsGKgtqceklvekygfth..lsaGdllree 33 
                                   G+PG+GK+ +++ l + +g+++  +s  ++l++ 
  gi|70606714|ref|YP_255584.1| 384 GPPGVGKTMMAKALSKTLGVKFimISGAEILYKG 417
                                   9*****************7765115666666554 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0021      0.59       2      32 ..      97     127 ..      96     135 .. 0.87
   2 !   18.1   0.2   6.5e-06    0.0018       2     114 ..     380     489 ..     379     503 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0021
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqf 32 
                                   +ll g PG +ktl+++ala+  +++f  + +
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNV 127
                                   78999****************9999988765 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.5e-06
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                   +ll+g PG++kt+++kal+k+l+++f  i   +++l     G+    ++  +   ++ p    ++l dei+  +p+ +   
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFIMIS-GAEILYKGYEGAVSTIKEVFNRARENKP---AIVLLDEIDAIAPRRENQK 456
                                   79************************9886.4567766666654333333222333333...5678888887777765555 PP

                         AAA_3  83 lea..meerqvtvegethklpepflvlatqnPie 114
                                    ++  + ++ +t  +  ++l+   +v+at n +e
  gi|70606714|ref|YP_255584.1| 457 TDSskVVNQLLTEMDGIRSLK-EVVVIATTNRME 489
                                   544113344455555555554.457788888766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00026     0.073       2      27 ..      97     123 ..      96     155 .. 0.77
   2 !   13.8   0.0   0.00018      0.05       2      50 ..     380     430 ..     379     461 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00026
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv 27 
                                   i ++G++++GKT +++aLa++ +++ +
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEaKINFI 123
                                   789****************76555443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00018
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv.e 50 
                                   i + G+++ GKT +++aL+++ g++ +  ++ eil ++++    ++++v +
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTlGVKFIMISGAEILYKGYEGAVSTIKEVfN 430
                                   7899***************999***99999999999999888777777644 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0015      0.41      19      46 ..      94     121 ..      68     130 .. 0.77
   2 !   15.7   0.1   3.9e-05     0.011      21      59 ..     372     418 ..     351     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0015
                                   TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                    + ilL G+ G+GKT ++r+la++ +++
  gi|70606714|ref|YP_255584.1|  94 PKGILLFGPPGCGKTLMMRALANEAKIN 121
                                   3459*******************99886 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.9e-05
                                   E.......EEEEESTTSSHHHHHHHHHHHTT--.----TTTTSEEEE CS
                          TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgve.evkSPTFtlveeY 59 
                                   +       ilL+G+ G+GKT+++++l k+lgv+  + S    l + Y
  gi|70606714|ref|YP_255584.1| 372 MkippirgILLHGPPGVGKTMMAKALSKTLGVKfIMISGAEILYKGY 418
                                   12344455************************976666655555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0041       1.2       3      25 ..      97     119 ..      95     124 .. 0.90
   2 !   11.8   0.1   0.00061      0.17       3      24 ..     380     401 ..     378     407 .. 0.89
   3 ?    2.8   0.0      0.35        98      57     134 ..     413     490 ..     404     523 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0041
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                   ++l G++G+GKT +++ la +++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAK 119
                                   6789**************99875 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00061
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   ++l+G++G+GKT++++ l  ++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL 401
                                   89**************998876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.35
                                   HHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.........HHHHHCT....TTTT--EEEEEEECCCHH CS
                         NACHT  57 llfsqlpepaapvsevwavllelperlLlilDglDelvtdlgqkekqpvrtlLselirk....kllpeasllltvrpralr 133
                                   +l + +    ++++e + ++++  + +  +lD +D ++   ++ +k+ + ++ ++l+++     +l+e  +++++++++ +
  gi|70606714|ref|YP_255584.1| 413 ILYKGYEGAVSTIKE-VFNRARENKPAIVLLDEIDAIAPRREN-QKTDSSKVVNQLLTEmdgiRSLKE--VVVIATTNRME 489
                                   555556666666677.445666777788899******997777.555555666666655110033444..44444445555 PP

                                   H CS
                         NACHT 134 d 134
                                   d
  gi|70606714|ref|YP_255584.1| 490 D 490
                                   5 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00078      0.22      25      43 ..      97     115 ..      94     119 .. 0.90
   2 !   15.4   0.5   3.3e-05    0.0093      25      46 ..     380     401 ..     376     407 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00078
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt++ ++l+
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALA 115
                                   89************99885 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.3e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlpsll 46 
                                   +ll GppG GKtm+ak+l++ l
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL 401
                                   89***************98766 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00037       0.1      33      68 ..      94     126 ..      82     164 .. 0.82
   2 !   11.0   0.0    0.0008      0.22      22      58 ..     365     402 ..     361     414 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                         AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                    k +ll Gp G+GKt++++ l ++ +   ++++ +n
  gi|70606714|ref|YP_255584.1|  94 PKGILLFGPPGCGKTLMMRALANEAK---INFIYVN 126
                                   5789****************999877...3333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0008
                         AAA_7  22 ysyllell.lknkkpvllvGptGtGKtviikdllkkld 58 
                                   ys l+e++ +   + +ll Gp G+GKt+++k l k+l 
  gi|70606714|ref|YP_255584.1| 365 YSKLMEQMkIPPIRGILLHGPPGVGKTMMAKALSKTLG 402
                                   5555554425556789***************9999887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.022         6      36      54 ..      97     115 ..      92     117 .. 0.86
   2 !   12.2   0.6   0.00035     0.097      36     142 ..     380     475 ..     367     481 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pg+GKt +   la
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALA 115
                                   69**********9976665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00035
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpL 116
                                   +ll G+pg+GKt++a   al+ ++G ++        +  ly   E++ +++++ + +++e+   +a +l+       +++ 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAK--ALSKTLGVKFIM---ISGAEILYKGYEGAVSTIKEVFNRARENK--PAIVLLD------EIDA 447
                                   699**********985..667788999866...38999999999999999999999988884..2222222......2333 PP

                        AAA_25 117 fakdrggtl..ltadvdaleaaieeveg 142
                                   +a++r++++     +v++l  +++ +  
  gi|70606714|ref|YP_255584.1| 448 IAPRRENQKtdSSKVVNQLLTEMDGIRS 475
                                   4444444442244556666666665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.1   1.4e+03      83     115 ..      41      76 ..      20      80 .. 0.62
   2 !    8.4   0.0    0.0059       1.7       5      23 ..      97     119 ..      94     164 .. 0.83
   3 !   13.0   0.1   0.00022     0.061       5      30 ..     380     404 ..     378     493 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.1
                        AAA_24  83 aevirqnekaesked..kgdgkG.ygelaeefrrll 115
                                    +++++n++++++ d  +  + G y ++++e+++++
  gi|70606714|ref|YP_255584.1|  41 TQIQQKNQRKNDILDriNWEMIGgYEDVKKEIKEYI 76 
                                   445555555555533222223344888888888766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0059
                        AAA_24   5 iliyGpsgiGKTtlakel....g 23 
                                   il++Gp+g GKT +++ l    +
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALaneaK 119
                                   89************999855333 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00022
                        AAA_24   5 iliyGpsgiGKTtlakelgpkplfid 30 
                                   il+ Gp+g+GKT++ak l  k+l + 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKAL-SKTLGVK 404
                                   899***************.7776554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00061      0.17       3      71 ..      99     162 ..      97     165 .. 0.73
   2 !    8.5   0.0    0.0052       1.5       1      71 [.     380     445 ..     380     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00061
               Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pGcGK+ + r l+++   +  ++++   + +++  +++++  + +  + ++  +     il++DE+
  gi|70606714|ref|YP_255584.1|  99 LFGPPGCGKTLMMRALANEAkIN-FIYVNVSDIMSKWYGESEARLRELFANARKNSPC-----ILFFDEI 162
                                   5688***************9633.3455556888888877777766666666665543.....8999996 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0052
               Viral_helicase1   1 ivvhGvpGcGKStlirkllrtsliltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                   i+ hG pG GK+ + + l +t      +++ +++++ +    k     v+t++++ + + +  k  i++lDE+
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKT-----LGVK-FIMISGAEilYKGYEGAVSTIKEVFNRAREN-KPAIVLLDEI 445
                                   678***************999.....4555.7777777776666777888999988888876.6899999997 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0014      0.39       8      36 ..      91     119 ..      86     158 .. 0.84
   2 ?    8.4   0.1     0.011         3       7      37 ..     373     403 ..     370     492 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0014
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllk 36 
                                   +k+ + + ++G+ G+GK+ ++++la++ k
  gi|70606714|ref|YP_255584.1|  91 IKPPKGILLFGPPGCGKTLMMRALANEAK 119
                                   67777889****************99876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.011
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                                   k+ + + + + G+ G GK+ ++k+l++ l  
  gi|70606714|ref|YP_255584.1| 373 KIPPIRGILLHGPPGVGKTMMAKALSKTLGV 403
                                   5666677889***************998754 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.011       3.1      21      51 ..      84     121 ..      58     153 .. 0.71
   2 ?   -0.1   0.0         3   8.3e+02      65      96 ..     307     340 ..     300     363 .. 0.72
   3 !    9.4   0.0    0.0035      0.97      15      84 ..     368     435 ..     355     490 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                                   .........TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                        ResIII  21 s.......krdkrglikmaTGtGKTlvaaklierllkk 51 
                                   +       k  k +l+  + G+GKTl++ +l+ + + +
  gi|70606714|ref|YP_255584.1|  84 ElsrkygiKPPKGILLFGPPGCGKTLMMRALANEAKIN 121
                                   155555557788999999**********9998887764 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3
                                   HHHHHHHHHGGGGTGG......GEEEESSS-B-- CS
                        ResIII  65 slleqtleefkkflseayke..igkkvsgdkkka 96 
                                   s++ q+lee++kf  ++  +    +++s+d++k+
  gi|70606714|ref|YP_255584.1| 307 SVTLQMLEEYEKFRLDYERKfrGPEITSSDNEKI 340
                                   6788*********999976665445555555444 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0035
                                   HT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH...HHGGGGTGG.... CS
                        ResIII  15 lleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl...eefkkflseayke 84 
                                   l+e++k+   + +l++ + G+GKT++a +l + l       kf+++   ++l++  +   +++k++++ a+++
  gi|70606714|ref|YP_255584.1| 368 LMEQMKIPPIRGILLHGPPGVGKTMMAKALSKTLGV-----KFIMISGAEILYKGYEgavSTIKEVFNRAREN 435
                                   55666666667889***********99999988887.....79999999999887774444445555555544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0035      0.99      23      63 ..      95     132 ..      81     168 .. 0.85
   2 !    8.6   0.0    0.0048       1.4      24      44 ..     379     399 ..     360     490 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0035
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-T CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipe 63 
                                     +l+ G  G+GK+l+ ra+ ++   ++ +f+ vn+++i +
  gi|70606714|ref|YP_255584.1|  95 KGILLFGPPGCGKTLMMRALANE---AKINFIYVNVSDIMS 132
                                   679*************9998765...5589*****999854 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0048
                                   -EEEECSTTSSHHHHHHHHHH CS
               Sigma54_activat  24 svlitGesGtGKellaraihe 44 
                                    +l++G  G+GK+++a+a+ +
  gi|70606714|ref|YP_255584.1| 379 GILLHGPPGVGKTMMAKALSK 399
                                   69***************9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0066       1.9      22      40 ..      98     116 ..      92     123 .. 0.86
   2 !    9.1   0.1    0.0034      0.96      22      47 ..     381     403 ..     367     482 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0066
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+G GKt +++al++
  gi|70606714|ref|YP_255584.1|  98 LLFGPPGCGKTLMMRALAN 116
                                   578*************975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0034
                        AAA_30  22 vltGpAGtGKttalkalreaweaagg 47 
                                   +l+Gp+G GKt++ kal +++     
  gi|70606714|ref|YP_255584.1| 381 LLHGPPGVGKTMMAKALSKTLG---V 403
                                   799**********999987654...3 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0017      0.48      50      82 ..      83     114 ..      38     226 .. 0.83
   2 !    8.5   0.0     0.003      0.84      50      80 ..     367     395 ..     348     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                   AFG1_ATPase  50 klfgrkrksvepvrglYlwGgvGrGKtylmdlf 82 
                                   k + rk    +p++g+ l G+ G GKt +m   
  gi|70606714|ref|YP_255584.1|  83 KELSRKY-GIKPPKGILLFGPPGCGKTLMMRAL 114
                                   5556664.678******************9765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                   AFG1_ATPase  50 klfgrkrksvepvrglYlwGgvGrGKtylmd 80 
                                   kl+ +   +  p rg+ l+G+ G+GKt++  
  gi|70606714|ref|YP_255584.1| 367 KLMEQ--MKIPPIRGILLHGPPGVGKTMMAK 395
                                   45543..357799**************9865 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0024      0.67      23      81 ..      55     122 ..      37     163 .. 0.64
   2 !    7.7   0.0    0.0061       1.7      21      82 ..     336     406 ..     317     491 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                        DUF815  23 devklddLvgidkqkealventeqfle.........glpannvLLwGarGtGKSslvkallneyaeeg 81 
                                   d+++++ + g+++ k++++e +e  l+          +p + +LL+G  G+GK  +++al ne++ + 
  gi|70606714|ref|YP_255584.1|  55 DRINWEMIGGYEDVKKEIKEYIEFPLKykelsrkygIKPPKGILLFGPPGCGKTLMMRALANEAKINF 122
                                   556666666666666666655543332111111111357789******************99976554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0061
                        DUF815  21 evdevklddLvgidkqkealvente......qf...leglpannvLLwGarGtGKSslvkallneyaeegL 82 
                                   ++++++ldd+ g+++ k++l e  e      ++   ++  p + +LL G  G+GK  + kal +++  + +
  gi|70606714|ref|YP_255584.1| 336 DNEKITLDDIGGYNSIKKELYELLEiqlrysKLmeqMKIPPIRGILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   567888899999988888877644311111123111334467889*****************998865553 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0062       1.7      13      37 ..      88     112 ..      79     132 .. 0.83
   2 !    7.9   0.3    0.0064       1.8      16      60 ..     374     414 ..     367     497 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0062
                        ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                   k Gi   + +l+ G pG+GKt++  
  gi|70606714|ref|YP_255584.1|  88 KYGIKPPKGILLFGPPGCGKTLMMR 112
                                   568888899*************965 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0064
                        ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa 60 
                                   ip  r +l+ G pG GKt++a+    +     g + ++++  e  
  gi|70606714|ref|YP_255584.1| 374 IPPIRGILLHGPPGVGKTMMAKALSKT----LGVKFIMISGAEIL 414
                                   6777889*************9864322....36666777665554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00028     0.077      13      54 ..      87     125 ..      81     152 .. 0.75
   2 ?    2.6   0.1      0.38   1.1e+02      77     150 ..     396     471 ..     392     487 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00028
                      ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54 
                                   + +  +p + ++++Gp g+GKt +++ ++++ +    + iy+
  gi|70606714|ref|YP_255584.1|  87 RKYGIKPPKGILLFGPPGCGKTLMMRALANEAKI---NFIYV 125
                                   555556777799*************999998832...33443 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.38
                      ATPase_2  77 klekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlgln...gaellvkeLlnlie 150
                                    l+k+lg ++   ++ eil +  + + + i+++++  +++ k  i+++De+  +     n    + ++v++Ll+ ++
  gi|70606714|ref|YP_255584.1| 396 ALSKTLGVKFIMISGAEILYKGYEGAVSTIKEVFNRAREN-KPAIVLLDEIDAIAPRRENqktDSSKVVNQLLTEMD 471
                                   5667777777777778888889999999999999998877.5588899*9988874333322234556666665555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00098      0.27      14      50 ..      92     126 ..      82     133 .. 0.83
   2 ?    3.9   0.1       0.1        29      19      47 ..     380     406 ..     367     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00098
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                   + Pk ill G pG+GK+ ++++l++e   + n++ ++
  gi|70606714|ref|YP_255584.1|  92 KPPKGILLFGPPGCGKTLMMRALANEA--KINFIYVN 126
                                   5699*********************98..66666655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                    Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvv 47 
                                   ill G pG GK+ +a++l + l  + +++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL--GVKFI 406
                                   7999**************9998..55555 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         8   2.2e+03     121     160 ..      21      62 ..       3      76 .. 0.62
   2 !    8.0   0.0    0.0082       2.3      37      71 ..      97     131 ..      86     156 .. 0.86
   3 ?    6.3   0.0     0.027       7.6      37     186 ..     380     531 ..     369     547 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8
                                   HHHHHHHTTT-EEEEEESS-TT..T-SS--HHHHHHHHSSEE CS
                      Bac_DnaA 121 htfnalleegkqvvlssDrsPk..eleeledrlrsrfeaGlv 160
                                    ++  l++++ q ++ sD++ +  + ++ ++ +  r+++ ++
  gi|70606714|ref|YP_255584.1|  21 VILSLLFKKQTQKFIVSDKATQiqQKNQRKNDILDRINWEMI 62 
                                   567778888888888888875411223333445555555555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0082
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEE CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYlt 71 
                                   ++++g+ G Gkt +++a++ne++ n+    v+ + 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSDIM 131
                                   799******************99988777776665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.027
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHH.HHHHTT-SEEEEE-GGGGTT-HHHH CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeef.keklrkvDvLliDDiqflagkektq 116
                                   ++++g+ G+Gkt + ka++++        + + +++ e l +  +   ++ +e f + +  k  ++l+D+i  +a + + q
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKT-----LGVKFIMISGAEILYKGYEGAVSTIKEVFnRARENKPAIVLLDEIDAIAPRRENQ 455
                                   799*********998887655.....4566667776666655554443333334403344466788999999998655444 PP

                                   .HHHHHHHHHHHTTT......-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--.- CS
                      Bac_DnaA 117 .eelfhtfnalleeg......kqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaekle.v 186
                                    ++  +++n+ll e       k vv+ +    +++e+++  l+   +   +v +  p+ e r +il+k i  e+++ v
  gi|70606714|ref|YP_255584.1| 456 kTDSSKVVNQLLTEMdgirslKEVVVIAT--TNRMEDVDPALKRPGRFDRIVYMPLPNSEEREDILQKYIGLEECKmV 531
                                   15667788887654312222266666654..46788888888865555567777778888888888888877776644 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.076        21       4      35 ..      96     128 ..      94     133 .. 0.87
   2 ?    0.4   0.0       1.6   4.4e+02      73     101 ..     129     160 ..     124     173 .. 0.80
   3 !    7.8   0.1    0.0086       2.4       3      31 ..     378     406 ..     377     413 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.076
                                   EEEEESTTTSSHHHHHHHHHHHSTTTEE.E--E CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg.vsvs 35 
                                    + l gp g Gk  +  aL +e + +f  v vs
  gi|70606714|ref|YP_255584.1|  96 GILLFGPPGCGKTLMMRALANEAKINFIyVNVS 128
                                   6899********************999657776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                                   EETTEEEEEEHHHHHHHHHTTSE...EEEE-- CS
                 Guanylate_kin  73 efsgnlygtsveaieevlekgki...viLDvd 101
                                   +  ++ yg+s +  +e ++++++   +iL  d
  gi|70606714|ref|YP_255584.1| 129 DIMSKWYGESEARLRELFANARKnspCILFFD 160
                                   567899*************9999889998665 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0086
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                   r + l gp g+Gk ++ kaL ++l  kf 
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   56899***************999998885 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.015       4.1      24      80 ..      97     164 ..      92     171 .. 0.73
   2 ?    7.8   0.0     0.012       3.4      24      81 ..     380     448 ..     367     457 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                                   EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H........HHHHHHT...TTSEEEEEE-TT CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp........ldlleqa...kggtLylkdiad 80 
                                   ++l G++G+gk+l+ r+L++++  +   ++v + ++           +l+++a   ++ +L++ +i+ 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSDIMSKWygesearlRELFANArknSPCILFFDEIDT 164
                                   799*****************998877666665554322333444447777776666788899988886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.012
                                   EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H...........HHHHHHT...TTSEEEEEE-TT- CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp...........ldlleqa...kggtLylkdiadl 81 
                                   ++l G++G gk+++A++L+k  g     f+++++a++            ++++++a   k+++ +l +i+ +
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGV---KFIMISGAEILykgyegavstiKEVFNRArenKPAIVLLDEIDAI 448
                                   799***************998765...334445554444455555555677777765557777777777765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.012       3.4      20      43 ..      97     132 ..      83     160 .. 0.65
   2 ?    7.3   0.0     0.013       3.5      20      41 ..     380     401 ..     365     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                        AAA_11  20 tliqGPPGtgKTktivellsqll............s 43 
                                    l+ GPPG+gKT +  +l +++             s
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKinfiyvnvsdimS 132
                                   5788**********9999999865555555444441 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.013
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                    l++GPPG gKT +  +l + l
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL 401
                                   489*********7666555554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.12        34      33      58 ..      92     117 ..      74     131 .. 0.81
   2 !    8.2   0.1    0.0054       1.5      22      55 ..     364     397 ..     352     404 .. 0.85
   3 ?    0.3   0.0       1.5   4.1e+02     110     150 ..     427     467 ..     416     472 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                          TniB  33 krmpnlllvGdsnnGKtmivekFarl 58 
                                   k ++ +ll+G++ +GKt +++  a++
  gi|70606714|ref|YP_255584.1|  92 KPPKGILLFGPPGCGKTLMMRALANE 117
                                   556889***********999887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0054
                          TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekF 55 
                                   r  +L+e  k   ++ +ll+G++ +GKtm+++  
  gi|70606714|ref|YP_255584.1| 364 RYSKLMEQMKIPPIRGILLHGPPGVGKTMMAKAL 397
                                   55689999999999***************99865 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.5
                          TniB 110 qvlrllrelkvrvLiiDEihnllagsarkqreflnalksLg 150
                                   +v +  re k+ ++++DEi+ +   + +++     ++ +L 
  gi|70606714|ref|YP_255584.1| 427 EVFNRARENKPAIVLLDEIDAIAPRRENQKTDSSKVVNQLL 467
                                   5566678889999*******999888877777777766665 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.04        11      37      70 ..      99     132 ..      90     138 .. 0.90
   2 !    8.4   0.1    0.0032      0.91      34      65 ..     379     410 ..     361     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.04
                         AAA_6  37 paGpagtGKtEtvkdLakalakqvvvfncsdqld 70 
                                   + Gp g GKt  ++ La++    ++ +n+sd ++
  gi|70606714|ref|YP_255584.1|  99 LFGPPGCGKTLMMRALANEAKINFIYVNVSDIMS 132
                                   68***************************99875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0032
                         AAA_6  34 ggapaGpagtGKtEtvkdLakalakqvvvfnc 65 
                                   g  ++Gp g GKt   k L+k+l++ ++++  
  gi|70606714|ref|YP_255584.1| 379 GILLHGPPGVGKTMMAKALSKTLGVKFIMISG 410
                                   55689********************9998765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.026       7.3      23      46 ..      97     119 ..      83     136 .. 0.82
   2 !    8.0   0.1    0.0052       1.5      21      41 ..     378     398 ..     363     406 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                                   EEEEESTTSSHHHHHHHHCCSHCC CS
                        NB-ARC  23 valvGmgGvGKttlakqilnksde 46 
                                   + l G +G+GKt +++   n+ ++
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANE-AK 119
                                   6799***********999988.44 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0052
                                   EEEEEEESTTSSHHHHHHHHC CS
                        NB-ARC  21 lvvalvGmgGvGKttlakqil 41 
                                     + l+G +GvGKt +ak   
  gi|70606714|ref|YP_255584.1| 378 RGILLHGPPGVGKTMMAKALS 398
                                   45889*********9988655 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.097        27       5      51 ..     101     151 ..      97     157 .. 0.73
   2 ?   -1.4   0.0       6.4   1.8e+03     113     164 ..     210     264 ..     204     309 .. 0.64
   3 ?    7.7   0.1      0.01       2.8       1      27 [.     380     406 ..     380     411 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.097
                                   ESTTSSHHHHHHHHHCCST....CEEEE-HHHHCCSSSSHHHHHHHHSHHH CS
                           dNK   5 GnIgaGKstlvklLskklg....vkvfeEpvdkwtnvqknlLekfYkdpsr 51 
                                   G+ g+GK+ ++  L+++++    ++ ++++++kw    +  L+ ++ ++ +
  gi|70606714|ref|YP_255584.1| 101 GPPGCGKTLMMRALANEAKinfiYVNVSDIMSKWYGESEARLRELFANARK 151
                                   888*************99933333445567778877777888877777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.4
                                   HHHHHHHCCH-SEEEEEE--HHHHHHH...HHHCTTCCCTTS-HHHHHHHHHHHH CS
                           dNK 113 ldnlleelakpdlliYLkasletcler...ikkRgreeekkieldYlekLhekye 164
                                   ld++l  + ++d liY+ ++ +   +    i+ +++  e  +++d l ++ e++ 
  gi|70606714|ref|YP_255584.1| 210 LDKALLRAGRFDKLIYIGLPDKRSRREileIHCKAKPLESDVDFDKLAEMTERFT 264
                                   5666667777888888877655554432114556666666777777777766664 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.01
                                   EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                           dNK   1 ivveGnIgaGKstlvklLskklgvkvf 27 
                                   i + G+ g+GK+ ++k Lsk+lgvk++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   5678999****************9975 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00017     0.047       1      45 [.      97     146 ..      97     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00017
                                   EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.....HHHHHHHHHH CS
                  Glutaredoxin   1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde.....eireelkels 45 
                                   ++lf+ p+C+   ++++l++e +++f +++v++ +     e  + l+el 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSDIMskwygESEARLRELF 146
                                   679999**************************987667766666666665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.13        36       1      21 [.     103     123 ..     103     138 .. 0.93
   2 ?    8.5   0.4    0.0072         2       1      21 [.     386     406 ..     386     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                                   TTSSHHHHHHHHHHHHTSEEE CS
                           SKI   1 mGaGKstvGkllAkklglefi 21 
                                   +G+GK+ + ++lA++ +++fi
  gi|70606714|ref|YP_255584.1| 103 PGCGKTLMMRALANEAKINFI 123
                                   6****************9998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0072
                                   TTSSHHHHHHHHHHHHTSEEE CS
                           SKI   1 mGaGKstvGkllAkklglefi 21 
                                   +G+GK+ ++k+l+k+lg++fi
  gi|70606714|ref|YP_255584.1| 386 PGVGKTMMAKALSKTLGVKFI 406
                                   69******************8 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0055       1.5      17      50 ..      97     128 ..      94     316 .. 0.86
   2 ?    4.8   0.0     0.068        19      17      81 ..     380     488 ..     371     494 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0055
                                   EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvgiG 50 
                                   +l++g  g+Gkt ++++l+++++ +   iyv + 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKIN--FIYVNVS 128
                                   579******************8666..8888743 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.068
                                   EEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................................ESEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................xxxx RF
                   ATP-synt_ab  17 tlipgafgvGktvisqslskqsnsddaiiyvg.............................................iGer 52 
                                   +l+ g  gvGkt+++++lsk    +  i + g                                                 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVK-FIMISGaeilykgyegavstikevfnrarenkpaivlldeidaiaprrenqKTDS 459
                                   5678999**************9888.4444445777777777777777777777777777777777777777665555555 PP

                                   HHHHHHHHHHCHHSSGGGGEEEEEEETTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  53 gnevaevleefpegtimkrtvlvantsne 81 
                                   ++ v+++l+e+   + +k++v++a t  +
  gi|70606714|ref|YP_255584.1| 460 SKVVNQLLTEMDGIRSLKEVVVIATTNRM 488
                                   55555666666666677777777766655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.42   1.2e+02       4      27 ..      97     120 ..      96     144 .. 0.80
   2 ?   -0.9   0.0       3.2   8.9e+02      91     165 ..     270     345 ..     240     359 .. 0.72
   3 ?    7.1   0.0     0.012       3.3       4      27 ..     380     403 ..     379     473 .. 0.86
   4 ?   -0.1   0.0       1.8     5e+02      49      73 ..     553     577 ..     530     579 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.42
                                   EEEE--TTSSHHHHHHHHHHHHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakalee 27 
                                   ++l+G P  GK+ + + La++ + 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKI 120
                                   799***********9999987654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.2
                                   HHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHHHHH---..TTSS-GGGS-SEEEE.TTS---HHHH CS
                         KTI12  91 ciakaakttlcvvyvvapldvlvkwneereekeeyekelldaLiqRyee..PdsknrWDsPlftvlsaeeklpldei 165
                                   ++++++  + ++  + ++ +  +++++ ++  ++y++ +  ++++ ye+   d + +   P +t + ++ek+ ld+i
  gi|70606714|ref|YP_255584.1| 270 NLCQEVARRAAIEALERNVERKISMQDFNDVIKRYKPSVTLQMLEEYEKfrLDYERKFRGPEITSS-DNEKITLDDI 345
                                   555555555555555566666666666666666788888888888888733455666777777766.7777777666 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.012
                                   EEEE--TTSSHHHHHHHHHHHHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakalee 27 
                                   ++l G P +GK+ +ak L+k+l  
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGV 403
                                   7999***************99854 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.8
                                   -GGGHHHHHHHHHHHHHHHHTT.SE CS
                         KTI12  49 dsakekalRsslrsavkrdLskekv 73 
                                    +ak k lR+ +r +v+r+Ls e++
  gi|70606714|ref|YP_255584.1| 553 REAKLKVLREIIRGNVDRKLSYEDL 577
                                   6788899**************9876 PP

>> MFS_Mycoplasma  Mycoplasma MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8     8e-05     0.022      42      88 ..       8      54 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                MFS_Mycoplasma 42 iiltvlillilvilivyalfgkevdtvakkekqtkteqtlskkvsal 88
                                  ii+++l+++i++++i+ +lf k+ +++  ++k t+++q+ + k  +l
  gi|70606714|ref|YP_255584.1|  8 IIISLLGVIIFIVVILSLLFKKQTQKFIVSDKATQIQQKNQRKNDIL 54
                                  89****************************9******9888876655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.3        83       3      27 ..      99     123 ..      97     131 .. 0.82
   2 ?    9.0   0.0    0.0037         1       2      28 ..     381     407 ..     380     471 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                                   EE-STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                   + GP g GK  + rala++ +++++
  gi|70606714|ref|YP_255584.1|  99 LFGPPGCGKTLMMRALANEAKINFI 123
                                   56***************98777665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0037
                                   EEE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   2 aiDGPagsGKssvaralaeklglkyld 28 
                                    + GP g GK  +a+al+++lg+k++ 
  gi|70606714|ref|YP_255584.1| 381 LLHGPPGVGKTMMAKALSKTLGVKFIM 407
                                   578*********************974 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.018       5.2       2      23 ..      97     119 ..      96     211 .. 0.76
   2 ?   -1.5   0.0       9.4   2.6e+03      43      60 ..     335     351 ..     297     370 .. 0.61
   3 ?    3.4   0.0      0.28        79       2      22 ..     380     400 ..     379     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                                   EEEEESTTSSHHHHHHHHHTS.T CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.k 23 
                                   ++++G p  GK+ +++al +e k
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEaK 119
                                   789****************9631 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9.4
                                   ETTEEEEEEECGGCSSHH CS
                      MMR_HSR1  43 lkgkeielvDtpGliega 60 
                                    ++++i+l D+ G +++ 
  gi|70606714|ref|YP_255584.1| 335 SDNEKITLDDIGG-YNSI 351
                                   2357799999999.7522 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.28
                                   EEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                   +++ G p vGK+ + +al+++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKT 400
                                   6789*************9975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.26        72       2      24 ..      97     119 ..      96     141 .. 0.86
   2 ?    8.2   0.1    0.0074       2.1       2      28 ..     380     406 ..     379     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.26
                                   EEEE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                   +++ GppG GKt +++ ++++ k
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAK 119
                                   6788********99998888764 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0074
                                   EEEE--TTSSHHHHHHHHHHHH...GG CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgv 28 
                                   +++ GppGvGKt + k ++++l  + +
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   6899************99999955544 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0       0.7     2e+02       2      56 ..      97     149 ..      96     154 .. 0.81
   2 ?    9.3   0.1    0.0045       1.3       2      29 ..     380     407 ..     379     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.7
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgnssaGlrArelCaea 56 
                                   i++ G+P  GKt    +La + ++ ++ +   v + +s+   ++  r rel a+a
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVN--VSDIMSKWYGESEARLRELFANA 149
                                   7789***************98777776665..88888888888888888887765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0045
                     Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllt 29 
                                   i++hG+P  GKt  a +L+k+ +  ++ 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFIM 407
                                   889*****************98876665 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.043        12     117     137 ..      97     117 ..      85     129 .. 0.88
   2 ?    6.3   0.0     0.016       4.4     117     138 ..     380     401 ..     369     406 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.043
                     Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                   ++++Gp+ +Gkt + +a+a+ 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANE 117
                                   8999**************985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                   ++++Gp+  Gkt++a+a+ k++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL 401
                                   899***************9976 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.023       6.6      11      32 ..      95     116 ..      91     130 .. 0.84
   2 ?    5.0   1.0       0.1        29      13      34 ..     380     401 ..     374     540 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.023
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                   k +l+ ++pG+GKT ++++  +
  gi|70606714|ref|YP_255584.1|  95 KGILLFGPPGCGKTLMMRALAN 116
                                   56899*********99987765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.1
                        AAA_19  13 llvtaGpGtGKTrvlkhivall 34 
                                   +l+ ++pG GKT + k+  + l
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTL 401
                                   7899********9988776655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0064       1.8       2      25 ..      95     118 ..      94     130 .. 0.87
   2 ?    3.0   0.1      0.28        77       3      23 ..     379     399 ..     377     409 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0064
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkgee 25 
                                   k ill+G+ g+GKt +++al +e+
  gi|70606714|ref|YP_255584.1|  95 KGILLFGPPGCGKTLMMRALANEA 118
                                   679*****************9864 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.28
                     PduV-EutP   3 killiGkvgsGKttLtqalkg 23 
                                    ill G+ g+GKt +++al++
  gi|70606714|ref|YP_255584.1| 379 GILLHGPPGVGKTMMAKALSK 399
                                   5899**************986 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.017       4.8       5      28 ..      96     119 ..      93     142 .. 0.81
   2 ?    0.5   0.0       1.2   3.4e+02      43      70 ..     332     359 ..     315     368 .. 0.87
   3 ?    1.0   0.0      0.91   2.6e+02       5      26 ..     379     400 ..     377     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                                   EEEEE-STTSSHHHHHHHHHHSS- CS
                         SRPRB   5 avllvGlsdsGKTslftrLttdsv 28 
                                    +ll G+  +GKT+++  L ++++
  gi|70606714|ref|YP_255584.1|  96 GILLFGPPGCGKTLMMRALANEAK 119
                                   589**************9998854 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                                   G...GGTT-SEEEETT-GCCSHHHHHHH CS
                         SRPRB  43 vksekgskltliDfPGheklrqkllekl 70 
                                   ++s++++k+tl D+ G ++++++l e l
  gi|70606714|ref|YP_255584.1| 332 ITSSDNEKITLDDIGGYNSIKKELYELL 359
                                   678999*****************99864 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.91
                                   EEEEE-STTSSHHHHHHHHHHS CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd 26 
                                    +ll G+   GKT++ + L++ 
  gi|70606714|ref|YP_255584.1| 379 GILLHGPPGVGKTMMAKALSKT 400
                                   589***********99999876 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0031      0.87      78     110 ..      85     117 ..      31     128 .. 0.76
   2 ?    0.3   0.0      0.83   2.3e+02      82     107 ..     371     397 ..     343     407 .. 0.76
   3 ?   -0.9   0.0       1.9   5.4e+02       5      42 ..     421     458 ..     418     482 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                    Adeno_IVa2  78 lsslnyglqPviGvi.yGPtGsGksqllrnliss 110
                                   l s  yg +P  G++ +GP G+Gk+ ++r+l   
  gi|70606714|ref|YP_255584.1|  85 L-SRKYGIKPPKGILlFGPPGCGKTLMMRALANE 117
                                   3.568999**99*8538*************9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.83
                    Adeno_IVa2  82 nyglqPviGvi.yGPtGsGksqllrnl 107
                                    ++  P+ G++ +GP G Gk+ + ++l
  gi|70606714|ref|YP_255584.1| 371 QMKIPPIRGILlHGPPGVGKTMMAKAL 397
                                   4667899998538*******9988876 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.9
                    Adeno_IVa2   5 eveaveelydrveelkdavkslnraillkPlkdfasye 42 
                                   +v +++e+++r  e k a++ l+  ++++P ++ +  +
  gi|70606714|ref|YP_255584.1| 421 AVSTIKEVFNRARENKPAIVLLDEIDAIAPRRENQKTD 458
                                   57789999999999999999999999999998877666 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.066        19       8      55 ..     103     150 ..      97     200 .. 0.82
   2 ?    5.1   0.0     0.082        23       8      28 ..     386     406 ..     380     481 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.066
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersr 55 
                                    G+g++ + +aLA++ +++f+  ++ + ++k  g se+ + e + + +r
  gi|70606714|ref|YP_255584.1| 103 PGCGKTLMMRALANEAKINFIYVNVSDIMSKWYGESEARLrELFAN-AR 150
                                   6************************************999555544.33 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.082
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfy 28 
                                    G g++ +++aL++ Lg++f+
  gi|70606714|ref|YP_255584.1| 386 PGVGKTMMAKALSKTLGVKFI 406
                                   699****************97 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.24        67       4      39 ..      97     132 ..      95     160 .. 0.85
   2 ?    7.1   0.1     0.016       4.4       4      30 ..     380     406 ..     378     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.24
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafve 39 
                                   ilL G +  GK+ + ral + ++  ++ ++v   + 
  gi|70606714|ref|YP_255584.1|  97 ILLFGPPGCGKTLMMRALANEAKINFIYVNVSDIMS 132
                                   89******************9999999888866665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                                   EEEEE-TTSSHHHHHHHHHHHSSS-EE CS
                           CPT   4 ilLnGgsssGKsslaralqevldepwl 30 
                                   ilL+G +  GK+ +a+al ++l   ++
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   9******************99877766 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.032       8.8      13      58 ..      84     128 ..      78     141 .. 0.74
   2 ?    4.5   0.0     0.057        16      26      49 ..     380     402 ..     360     448 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                                   HHTTS-SSS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES CS
                          DAP3  13 klkkadkkkkvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvp 58 
                                   +l+++   k+ k ++l G +g+GK++++  ala  ++ +++ ++v+
  gi|70606714|ref|YP_255584.1|  84 ELSRKYGIKPPKGILLFGPPGCGKTLMMR-ALANEAKINFIYVNVS 128
                                   566666678888899*********99874.4444445566666665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.057
                                   EEEE-SSSSSTTTTHHHHHHHGGG CS
                          DAP3  26 lvltGekgsGKSvlLlqalayAle 49 
                                   ++l+G +g+GK+++ ++al   l 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMM-AKALSKTLG 402
                                   679********984.555544444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.091        26      21      42 ..      94     114 ..      86     118 .. 0.82
   2 ?    5.1   0.0     0.069        19      18      42 ..     373     397 ..     364     402 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.091
                        AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                   +kg +ll Gp G GK+ ++ A+
  gi|70606714|ref|YP_255584.1|  94 PKG-ILLFGPPGCGKTLMMRAL 114
                                   456.9**********9888776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.069
                        AAA_29  18 eidlkgatlltGpsGsGKSTllDAi 42 
                                   +i +   +ll Gp G+GK+ +  A+
  gi|70606714|ref|YP_255584.1| 373 KIPPIRGILLHGPPGVGKTMMAKAL 397
                                   44444449**********9776665 PP

>> Zwilch  RZZ complex, subunit zwilch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00055      0.15     397     464 ..     309     369 ..     304     374 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                        Zwilch 397 plelLLEiGleklrkdyinifseqelasldeleyflktvendlksrekalksssvdlqeivmrlsklh 464
                                   +l++L E   ek r dy+ +f + e++s+d ++ +l     d+  +++++k+   +l+ei  r skl 
  gi|70606714|ref|YP_255584.1| 309 TLQMLEE--YEKFRLDYERKFRGPEITSSDNEKITL-----DDIGGYNSIKKELYELLEIQLRYSKLM 369
                                   6777777..59*************************.....888*********************996 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.059        17     221     283 ..      49     115 ..      27     129 .. 0.75
   2 ?    5.4   0.0     0.024       6.8     259     291 ..     374     406 ..     341     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
                      PPV_E1_C 221 rlkevedegdWkeivkf..lryqgvelisfltalkefLkgvPkk..nclvllGppntGkslfamsli 283
                                   r +++ d  +W+ i  +  ++ +  e i+f  + ke+ ++   k  + ++l+Gpp  Gk+l+  +l 
  gi|70606714|ref|YP_255584.1|  49 RKNDILDRINWEMIGGYedVKKEIKEYIEFPLKYKELSRKYGIKppKGILLFGPPGCGKTLMMRALA 115
                                   4444456778999987744677778999999999999887544422578999********9988876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                      PPV_E1_C 259 vPkknclvllGppntGkslfamslikfLkGkvl 291
                                   +P    ++l+Gpp  Gk+++a++l k L  k +
  gi|70606714|ref|YP_255584.1| 374 IPPIRGILLHGPPGVGKTMMAKALSKTLGVKFI 406
                                   55566799******************9987766 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.0    0.0011      0.32       6      56 ..       8      57 ..       5      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0011
                       DUF3139  6 iililliillvivkvflglvgskpikkylankkldkylqekgykeddIks.i 56
                                  ii++ll ++++iv+++  l  +k+ +k+++  k  + +q+k+  ++dI + i
  gi|70606714|ref|YP_255584.1|  8 IIISLLGVIIFIVVILS-LLFKKQTQKFIVSDKATQ-IQQKNQRKNDILDrI 57
                                  67777777777655555.77888899*999876555.789999999998851 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13        37       3      26 ..      96     119 ..      94     127 .. 0.86
   2 ?    1.0   0.0      0.99   2.8e+02      20      56 ..     255     293 ..     252     323 .. 0.73
   3 ?    2.0   0.2      0.49   1.4e+02       4      24 ..     380     400 ..     378     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                                   EEEEEESTTSSHHHHHHHHHHHHH CS
                         SRP54   3 villvGlqGaGKTttlaKLaallk 26 
                                    ill+G+ G GKT  +  La+  k
  gi|70606714|ref|YP_255584.1|  96 GILLFGPPGCGKTLMMRALANEAK 119
                                   69*************999998765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.99
                                   HHHHHHHHT.TS-EEEEEESTSSTTHHHHHHHHHHH.TT CS
                         SRP54  20 KLaallkke.gkkvllvaaDtfRaaAveQLktlaek.lg 56 
                                   KLa++ ++  g +++  +  + R aA+e L+ + e+ + 
  gi|70606714|ref|YP_255584.1| 255 KLAEMTERFtGADLANLCQEVARRAAIEALERNVERkIS 293
                                   888888887799999999************999886244 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.49
                                   EEEEESTTSSHHHHHHHHHHH CS
                         SRP54   4 illvGlqGaGKTttlaKLaal 24 
                                   ill G+ G+GKT  +  L++ 
  gi|70606714|ref|YP_255584.1| 380 ILLHGPPGVGKTMMAKALSKT 400
                                   899*********987777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      858  (0.0478554); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); expected 17.9 (0.001)
Passed Fwd filter:                        65  (0.00362541); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              64  [number of targets reported over threshold]
# CPU time: 0.95u 0.31s 00:00:01.26 Elapsed: 00:00:00.48
# Mc/sec: 3762.88
//
Query:       gi|70606715|ref|YP_255585.1|  [L=267]
Description: inositol-1-monophosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-21   75.9   0.0    4.7e-21   75.5   0.0    1.1  1  Inositol_P  Inositol monophosphatase family
    4.4e-05   23.0   0.2    7.1e-05   22.4   0.2    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   5.2e-25   4.7e-21      11     226 ..       8     217 ..       3     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 5.2e-25
                                   HHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEE CS
                    Inositol_P  11 elaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivD 91 
                                   ++a++a++ + ee ++++++++ +   + +d+   +d+++e++i+++l+    +  i++ee++ + + + ++ d ++ ivD
  gi|70606715|ref|YP_255585.1|   8 KVASEASKYIYEERENKDVDRVINV--HGNDVTRIIDKRSEDFIVDRLKSLGYNILIVTEESGVIDS-YGKNYD-YIAIVD 84 
                                   4667889999999988888888888..89************************************99.889999.****** PP

                                   EEETHHHHHHT-SG-EEEEEEEE..TTEEEEEEEEET..TTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSS CS
                    Inositol_P  92 PiDGTknFvrgipqvaVsigllv..egkpvlGviaqP..llgqlysaakgkGaflngeklplsrappiseallvtlfavss 168
                                   P+DG +nFv+gip+  Vsi+++   e+ ++ + ++++  +      +++   a++ng k+   ++p  ++ ll++   +s+
  gi|70606715|ref|YP_255585.1|  85 PLDGSTNFVSGIPWSSVSIAIYNrdEEDILSSNVGAVssIFTPYTFSYDEGSAYVNGVKIAEIKKP--EKILLLA--YFSR 161
                                   **********************976666777777777643334444566667899**777777777..5665644..6677 PP

                                   SSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHH CS
                    Inositol_P 169 rkdtseasllekvesavsaegvrsvgssalklaavaeGkadaylefg.rekkWDhAAGe 226
                                    k ++ + ++ek+    +  ++rs+gs+ l++++v +G+a ++ +++ ++   D+AA +
  gi|70606715|ref|YP_255585.1| 162 SKLPNLKLFFEKIG---QGYKIRSLGSASLDMILVCTGRATMFFDIRgKLRNVDIAASS 217
                                   77777766887773...333478***********************999*******965 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   7.9e-09   7.1e-05      54     135 ..      30     111 ..      26     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-09
                        FBPase  54 eNvtGdeq.kklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSnidtnvsvGti.fsiyrk 132
                                    Nv+G+++ + +D ++++ +++ lk+ +    +v EE+  ++     k+  y+ ++DPlDGS n   ++    + ++iy++
  gi|70606715|ref|YP_255585.1|  30 INVHGNDVtRIIDKRSEDFIVDRLKSLGYNILIVTEESGVIDSY--GKNYDYIAIVDPLDGSTNFVSGIPWSSVsIAIYNR 108
                                   588986551668*************************9999999..78889*************98877655543466666 PP

                        FBPase 133 kse 135
                                   + e
  gi|70606715|ref|YP_255585.1| 109 DEE 111
                                   555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1727.88
//
Query:       gi|70606716|ref|YP_255586.1|  [L=323]
Description: thioredoxin reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-51  174.0   1.2    4.9e-51  173.7   1.2    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    6.9e-26   91.2   4.8    1.1e-25   90.5   0.7    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    5.6e-15   55.7   3.6    8.1e-15   55.2   0.6    2.5  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.9e-06   25.8   0.1      0.015   14.0   0.0    3.4  3  HI0933_like    HI0933-like protein
    6.6e-05   22.2  10.6      0.054   12.6   1.2    4.4  5  GIDA           Glucose inhibited division protein A
    0.00024   20.4   0.1       0.55    9.3   0.0    3.2  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    0.00033   19.9   2.2       0.69    8.9   0.0    3.1  3  FAD_binding_2  FAD binding domain
    0.00071   19.0   2.4      0.038   13.4   0.0    2.7  3  FAD_oxidored   FAD dependent oxidoreductase
     0.0034   17.8   0.7      0.031   14.7   0.2    2.4  2  NAD_binding_7  Putative NAD(P)-binding
     0.0091   15.3   0.7       0.96    8.6   0.0    2.6  3  Thi4           Thi4 family
  ------ inclusion threshold ------
       0.16   11.9   0.1          3    7.8   0.0    2.7  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7   1.2     3e-54   4.9e-51       1     294 []      16     305 ..      16     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 3e-54
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielllge 73 
                                   +d ++iG GpA+++aal++a+  +k++++   g++++g+   + ++  + +   i +        ++++k++  + +ll+ 
  gi|70606716|ref|YP_255586.1|  16 YDTIIIGLGPAAYSAALYAARFMLKTLVI---GETPGGQLTEAGEVDDYLGLIGINAqdmikvfnKHIEKYE--VPVLLD- 90 
                                   5899*************************...7778888888777777777776666755555666666665..445555. PP

                                   TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiG 154
                                    v ++ ++  ++++++k+   + ++++d+l+lA+G + r+l++pG++e +g++v+++  ++a   k++   +v+vGgG  +
  gi|70606716|ref|YP_255586.1|  91 IVEGFKREGDEFVVKTKR---KGEYKADTLILAIGVKRRKLNVPGENEFAGRGVSYCSICDAPLFKNRT--TVIVGGGDSA 166
                                   344444555788885544...558***************************************999998..********** PP

                                   HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxx RF
                   Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle.vvledgeeidad 229
                                   +E A  l+++  +v+lv++rd++       ++ ++ e ++k+ +ve+ l+++vkei+g++      ++   +++ +ei++ 
  gi|70606716|ref|YP_255586.1| 167 LEGAEILSRYSNKVYLVHRRDQFK------AQPIYVELVKKKpNVEIILNSVVKEIKGEKLvksvVIQnINTGETREIQTN 241
                                   ***********************7......8999999999999****************987764444888888899**** PP

                                   EEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 230 lvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    ++v +G++p t+++ ++ g+e+d++g+i+vde++rtnv+g++a+GD++g   g++++ +A +qG
  gi|70606716|ref|YP_255586.1| 242 GIFVEIGFEPPTDFA-RAHGIEVDNNGYIKVDEWMRTNVEGVFAAGDCTGMWLGFRQIITATAQG 305
                                   ***************.*********************************************9998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.042        69       1      27 [.      19      44 ..      19      53 .. 0.86
   2 !   90.5   0.7   6.9e-29   1.1e-25      81     305 .]      70     286 ..      66     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.042
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                  iIiG GPa  +aa+ + ++ l++ l++
  gi|70606716|ref|YP_255586.1| 19 IIIGLGPAAYSAALYAARFMLKT-LVI 44
                                  8********************75.555 PP

  == domain 2  score: 90.5 bits;  conditional E-value: 6.9e-29
                   Pyr_redox_3  81 kealeYlrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhyskvk 157
                                   +++ + +++  +++e+p+ l+  Ve  k+e+++f+v+t+++ +y+A+++i+A+G   k +kln+pGe++     + y  + 
  gi|70606716|ref|YP_255586.1|  70 QDMIKVFNKHIEKYEVPVLLD-IVEGFKREGDEFVVKTKRKgEYKADTLILAIGV--KRRKLNVPGENEfagRGVSYCSIC 147
                                   556666677778888888776.599*************9755*************..999********8644567888888 PP

                   Pyr_redox_3 158 efhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkei 238
                                   ++  ++++  v++Gg++Sa + A  l r+ ++V +v+r+++ ++         +p++ + +++   + +++++ n+ vkei
  gi|70606716|ref|YP_255586.1| 148 DAPLFKNRTTVIVGGGDSALEGAEILSRYSNKVYLVHRRDQFKA---------QPIYVELVKK---KPNVEIILNSVVKEI 216
                                   998999*********************************96555.........5788777776...345999999999999 PP

                   Pyr_redox_3 239 keke..eeykvk.tedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   k ++  +++ ++  ++g++ e++++ +++ +G++p ++f +++++e d++g+++++ e++ tnv+g+f aG
  gi|70606716|ref|YP_255586.1| 217 KGEKlvKSVVIQnINTGETREIQTNGIFVeIGFEPPTDFARAHGIEVDNNGYIKVD-EWMRTNVEGVFAAG 286
                                   865422444444355666666677778888************************97.69**********99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.3   2.2e+03       3      28 ..      19      44 ..      17      48 .. 0.85
   2 ?   -1.4   0.0       2.2   3.6e+03      40      60 ..      70      90 ..      64     109 .. 0.71
   3 !   55.2   0.6   4.9e-18   8.1e-15       2      79 ..     157     228 ..     156     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                                  EEECSSHHHHHHHHHHHHTTSEEEEE CS
                     Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvv 28
                                  +++G G  +  +A ++a++  k+ v+
  gi|70606716|ref|YP_255586.1| 19 IIIGLGPAAYSAALYAARFMLKTLVI 44
                                  79***********9999998887776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                  HHHHHHHHHHHHHTTEEEECS CS
                     Pyr_redox 40 eeaskilqeklekngievlln 60
                                  +++ k++ +++ek  + vll+
  gi|70606716|ref|YP_255586.1| 70 QDMIKVFNKHIEKYEVPVLLD 90
                                  577788889999999988875 PP

  == domain 3  score: 55.2 bits;  conditional E-value: 4.9e-18
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklk 79 
                                    v+vGgG+++lE A++l+++ +kV++v+r+d++       a+ i  e ++k+ ++e++ln++v+ei+g++  v+sv+++
  gi|70606716|ref|YP_255586.1| 157 TVIVGGGDSALEGAEILSRYSNKVYLVHRRDQFK------AQPIYVELVKKKpNVEIILNSVVKEIKGEKL-VKSVVIQ 228
                                   69********************************......***************************8887.9999986 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.016        26       2      31 ..      17      46 ..      16      57 .. 0.87
   2 !   14.0   0.0   9.4e-06     0.015     107     163 ..      68     122 ..      65     125 .. 0.92
   3 !    4.5   0.0    0.0073        12       2      34 ..     156     188 ..     155     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                  d+i+iG G+A   aA+ aa+   ++l++ +
  gi|70606716|ref|YP_255586.1| 17 DTIIIGLGPAAYSAALYAARFMLKTLVIGE 46
                                  89*****************99999999865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.4e-06
                                   -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   +a+d+++++ k++++ +v + l+  v+++++e d+ f vktk ++e++ad+l+lA+G
  gi|70606716|ref|YP_255586.1|  68 NAQDMIKVFNKHIEKYEVPVLLD-IVEGFKREGDE-FVVKTKRKGEYKADTLILAIG 122
                                   699*****************987.599**998888.*******************99 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0073
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                   +++++GgG + l +A+ +++  ++V l+ + ++
  gi|70606716|ref|YP_255586.1| 156 TTVIVGGGDSALEGAEILSRYSNKVYLVHRRDQ 188
                                   589************************988776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.2    0.0012       1.9       1      29 [.      17      45 ..      17      65 .. 0.85
   2 ?    2.3   0.0     0.043        70     110     167 ..      84     139 ..      64     149 .. 0.66
   3 ?    2.6   0.0     0.035        56       3      35 ..     158     189 ..     156     194 .. 0.87
   4 ?    0.4   0.1      0.16   2.6e+02      99     138 ..     193     232 ..     183     248 .. 0.67
   5 !   12.6   1.2   3.3e-05     0.054     346     391 ..     271     319 ..     216     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                  d i+iG G A + AAl aar  +k+l i 
  gi|70606716|ref|YP_255586.1| 17 DTIIIGLGPAAYSAALYAARFMLKTLVIG 45
                                  579**********************9983 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.043
                                   TEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSC CS
                          GIDA 110 nleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGr 167
                                   ++ ++ + ve  +  e+   +v+t+++ ++ka++ ++a G   + k  +  ++  aGr
  gi|70606716|ref|YP_255586.1|  84 EVPVLLDIVEGFKR-EGDEFVVKTKRKGEYKADTLILAIGV-KRRKLNVPGENEFAGR 139
                                   44444444555522.46667899*****************9.6666666555555565 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.035
                                   EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                          GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkldti 35 
                                   +++GgG + +e A  ++r   kv L+ h+ d++
  gi|70606716|ref|YP_255586.1| 158 VIVGGGDSALEGAEILSRYSNKVYLV-HRRDQF 189
                                   89***********************9.766665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.16
                                   HHHHHHHHTSTTEEEEES-E.EEEEECTTEEEEEEETTS-E CS
                          GIDA  99 kevteklenepnleiieeev.eeliveekkvkgvvtedget 138
                                     + e ++++pn+eii ++v +e+   ek vk vv ++ +t
  gi|70606716|ref|YP_255586.1| 193 PIYVELVKKKPNVEIILNSVvKEI-KGEKLVKSVVIQNINT 232
                                   45678999******9877651555.5577777777765444 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 3.3e-05
                                   B-TTSBBSSSBTEEE-CGGGTB.-SH...HHHHHHHHHHHHHHHHHHCTS CS
                          GIDA 346 llntLetkkvkgLflAGqinGt.eGY...eEaaaqGllAGinaarkakgk 391
                                   + + ++t+ v+g+f+AG+ +G+  G+   + a+aqG +A++ a ++++++
  gi|70606716|ref|YP_255586.1| 271 VDEWMRTN-VEGVFAAGDCTGMwLGFrqiITATAQGAVAAHAAFNYLNQR 319
                                   44568887.*************78973335799**********9988875 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        19       2      25 ..      15      38 ..      14      50 .. 0.78
   2 !    9.3   0.0   0.00034      0.55     133     229 ..     102     190 ..      88     194 .. 0.66
   3 ?    3.2   0.0     0.025        40     284     341 ..     194     250 ..     191     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevk 25
                                   +D i+iG+Gp++ s a+ ++   
  gi|70606716|ref|YP_255586.1| 15 KYDTIIIGLGPAAYSAALYAARFM 38
                                  69***********99988776655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00034
                   K_oxygenase 133 ltveskdaegeeeelearnlvlgvGtep...kiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                   + v++     ++ e++a +l+l++G ++   ++P   e   g   v   s        l ++++ ++vG+G Sa e +e l
  gi|70606716|ref|YP_255586.1| 102 FVVKT----KRKGEYKADTLILAIGVKRrklNVPGENEF-AG-RGVSYCSICDAP---LFKNRTTVIVGGGDSALEGAEIL 173
                                   55554....467789999999999966512235554442.22.333333333333...57888999**********88777 PP

                   K_oxygenase 211 lrrqkkvelklvtrseale 229
                                    r ++  ++ lv r+++++
  gi|70606716|ref|YP_255586.1| 174 SRYSN--KVYLVHRRDQFK 190
                                   66665..889999999887 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.025
                   K_oxygenase 284 lyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                                   +y + vk++++++++ n+ v++++ e+     + ++n ++ge+++++++ +++  G++
  gi|70606716|ref|YP_255586.1| 194 IYVELVKKKPNVEIILNSVVKEIKGEKL-VKSVVIQNINTGETREIQTNGIFVEIGFE 250
                                   67888999999************99984.888999999********999999888775 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00045      0.74       1      33 [.      17      49 ..      17      56 .. 0.89
   2 ?    0.2   0.0      0.19   3.1e+02     153     192 ..     201     240 ..      68     251 .. 0.67
   3 !    8.9   0.0   0.00042      0.69     376     405 ..     269     291 ..     251     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00045
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                  D i+iG G A ++AAl aa+  lk++v+  ++ 
  gi|70606716|ref|YP_255586.1| 17 DTIIIGLGPAAYSAALYAARFMLKTLVIGETPG 49
                                  89*************************987765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                   TCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEE CS
                 FAD_binding_2 153 kag.vdfqerteadeLivedgrvtGavvenpesgrevrira 192
                                   k + v++  +  ++e+   ++ v  +v++n ++g++++i+ 
  gi|70606716|ref|YP_255586.1| 201 KKPnVEIILNSVVKEI-KGEKLVKSVVIQNINTGETREIQT 240
                                   2223555555555555.224456666666666666666655 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00042
                                   EEBETTSBESTTEEESSBTEEE-STCEESS CS
                 FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaagg 405
                                   +++de++r+      +++G +AaG ++ g+
  gi|70606716|ref|YP_255586.1| 269 IKVDEWMRT------NVEGVFAAGDCT-GM 291
                                   566666666......***********9.44 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.3e-05     0.038       1      42 [.      17      56 ..      17      88 .. 0.91
   2 !    4.9   0.1    0.0083        14      85     132 ..     187     236 ..     163     243 .. 0.79
   3 ?   -3.8   0.0       3.8   6.1e+03     139     155 ..     298     314 ..     296     321 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42
                                  D +++G gpa + AA+ Aar   k+l++ e++  GG+lt ++
  gi|70606716|ref|YP_255586.1| 17 DTIIIGLGPAAYSAALYAARFMLKTLVIGETP--GGQLTEAG 56
                                  779*************************9987..*****987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0083
                  FAD_oxidored  85 epevakavleeml.aeagvtvllntrlvevekegkriesvtveske.g.rk 132
                                   +   a+ ++ e++ ++++v+++ln++++e++ e+  ++sv++++ + g ++
  gi|70606716|ref|YP_255586.1| 187 DQFKAQPIYVELVkKKPNVEIILNSVVKEIKGEK-LVKSVVIQNINtGeTR 236
                                   5556788999999888***************984.69***99987766455 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 3.8
                  FAD_oxidored 139 fiDATgdGdlaalaGvp 155
                                   +i AT +G +aa a  +
  gi|70606716|ref|YP_255586.1| 298 IITATAQGAVAAHAAFN 314
                                   56677777777776555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.33   5.4e+02      10      40 ..      18      48 ..      13     129 .. 0.73
   2 !   14.7   0.2   1.9e-05     0.031       5      64 ..     152     221 ..     151     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.33
                 NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev 40
                                   +++G G+ A++ +   +++  k  v+ ++ 
  gi|70606716|ref|YP_255586.1| 18 TIIIGLGPAAYSAALYAARFMLKTLVIGETP 48
                                  6799999999999999999999999998885 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                 NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele...........elvklaeeelekdlegadl 64 
                                   +k+++ ++vGgG+ A++ ++ l +++ kv +v  + + +              +v+++ + + k+++g +l
  gi|70606716|ref|YP_255586.1| 152 FKNRTTVIVGGGDSALEGAEILSRYSNKVYLVHRRDQFK-AqpiyvelvkkkPNVEIILNSVVKEIKGEKL 221
                                   689*****************************9995222.2355553333332222333333344444333 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00059      0.96      17      55 ..      15      50 ..       7      84 .. 0.84
   2 ?    4.5   0.0     0.011        18      19      49 ..     156     185 ..     144     191 .. 0.84
   3 ?   -3.0   0.1       2.1   3.4e+03     108     122 ..     214     228 ..     195     243 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00059
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                  + D +i+G G++  +aa y a+   lk++++ +  +pGG
  gi|70606716|ref|YP_255586.1| 15 KYDTIIIGLGPAAYSAALYAARF-MLKTLVIGE--TPGG 50
                                  5699*****************99.9***99976..3555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                     vivG+G s L  a +l++    kv ++ r
  gi|70606716|ref|YP_255586.1| 156 TTVIVGGGDSALEGAEILSRY-SNKVYLVHR 185
                                   579****************99.778877765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.1
                                   HTSTTEEEEESEEEE CS
                          Thi4 108 lqlanvkllnavave 122
                                    ++ + kl+++v++ 
  gi|70606716|ref|YP_255586.1| 214 KEIKGEKLVKSVVIQ 228
                                   222233333333333 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.86   1.4e+03       2      14 ..      20      32 ..      19      38 .. 0.84
   2 ?    7.8   0.0    0.0018         3     113     154 ..      81     122 ..      63     124 .. 0.83
   3 ?    0.4   0.0      0.36   5.8e+02       1      20 [.     158     177 ..     158     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.86
                 NAD_binding_9  2 ivGaGprGlavle 14
                                  i+G Gp++ +++ 
  gi|70606716|ref|YP_255586.1| 20 IIGLGPAAYSAAL 32
                                  9******999875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
                 NAD_binding_9 113 egvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   e+ +v v+ + v+  ++++d++ v ++++ +++ad ++LA+G
  gi|70606716|ref|YP_255586.1|  81 EKYEVPVLLDIVEGFKREGDEFVVKTKRKGEYKADTLILAIG 122
                                   456788888889999**************************9 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.36
                 NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                   +ivG+G ++l  +e L + +
  gi|70606716|ref|YP_255586.1| 158 VIVGGGDSALEGAEILSRYS 177
                                   69999999999988887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2035.52
//
Query:       gi|70606717|ref|YP_255587.1|  [L=502]
Description: hypothetical protein Saci_0932 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-06   28.0   0.4    1.5e-05   25.0   0.1    2.3  2  DUF4346     Domain of unknown function (DUF4346)
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.24   10.8   0.0    1.4  1  Baculo_p26  Nucleopolyhedrovirus p26 protein


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.072   6.4e+02      17      37 ..     415     433 ..     410     449 .. 0.84
   2 !   25.0   0.1   1.7e-09   1.5e-05      91     118 .]     457     484 ..     438     484 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.072
                       DUF4346  17 GYflikvdreaklivakhysn 37 
                                   GY  +k+d+++++iv+++y +
  gi|70606717|ref|YP_255587.1| 415 GY--VKIDKNDEEIVLTYYGK 433
                                   55..799***********975 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.7e-09
                       DUF4346  91 kldhaaYlGRelqraeaaLlsgkeYiqD 118
                                   + +ha+Y+G el +ae+aL  gk+YiqD
  gi|70606717|ref|YP_255587.1| 457 NTEHALYIGYELAKAEIALNLGKNYIQD 484
                                   458************************9 PP

>> Baculo_p26  Nucleopolyhedrovirus p26 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.7e-05      0.24     152     225 ..     332     403 ..     323     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.7e-05
                    Baculo_p26 152 vsGqlnvdgnvkveklrdglsvygkqqlpyekvkafalsaeanrrdlprsvavfynkkevritlvegefeisri 225
                                   + G+l v +  ++e+ +++ s y+ +    +k+ + al++++n +dl  ++ +  +kk+++ +l+e+  ei r+
  gi|70606717|ref|YP_255587.1| 332 IAGELGVANLLTMERGKTRGSSYEINTA--TKMISIALNKRKNPKDLGLDLLILKDKKKISTSLNENSGEIIRV 403
                                   6788888899999999999999999998..458899********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 4101.86
//
Query:       gi|70606718|ref|YP_255588.1|  [L=129]
Description: hypothetical protein Saci_0933 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 885.25
//
Query:       gi|70606719|ref|YP_255589.1|  [L=139]
Description: hypothetical protein Saci_0934 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.1   0.0    1.4e-21   76.7   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.074   13.3   0.0      0.095   13.0   0.0    1.1  1  DUF4826   Domain of unknown function (DUF4826)


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   1.6e-25   1.4e-21       6     119 ..      10     135 ..       5     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 1.6e-25
                                   EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-.STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS..... CS
                          PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegee.ldetgmvvdfgelkealkeileelDhkfl.naddpeleell..... 79 
                                   f+Fd+aH+  +++g   ++HGH+yk+ v++eg++ ++++g+v+df  l ++++e+++e+Dhk++    d+   el+     
  gi|70606719|ref|YP_255589.1|  10 FSFDSAHYTLSSKG-NDQIHGHTYKLSVEIEGQDvDKNSGFVIDFMILTKIIHEVIREWDHKLIiPSRDARKIELKgpfkv 89 
                                   99********8875.568***************76999**************************8756655555568**** PP

                                   .........--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEE CS
                          PTPS  80 ........spTaEnlaklifeelkerlqekevklskvrvwEtpnswae 119
                                            pT+E++ + i++ + e+l ek+ k+ +v+++E +ns+a 
  gi|70606719|ref|YP_255589.1|  90 eykiieedFPTVEYIGSEIAKDIYEKL-EKKFKV-RVKIYEGENSYAL 135
                                   ********9******************.666665.6*********996 PP

>> DUF4826  Domain of unknown function (DUF4826)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.095      18      80 ..      53     116 ..      45     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                       DUF4826  18 ylaekgilpekvlekesrylaPyvalWkledqdpkkakyWvlsGdlPt.Dhveveaakeardal 80 
                                   ++   +i++e + e++ + ++P     k+e + p k +y ++  d Pt +++  e ak+  + l
  gi|70606719|ref|YP_255589.1|  53 FMILTKIIHEVIREWDHKLIIPSRDARKIELKGPFKVEYKIIEEDFPTvEYIGSEIAKDIYEKL 116
                                   677789*****************************************85799999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 950.16
//
Query:       gi|70606720|ref|YP_255590.1|  [L=169]
Description: hypothetical protein Saci_0935 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   16.4   0.2      0.024   15.4   0.2    1.6  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
      0.043   12.4   0.0      0.062   11.9   0.0    1.2  1  Chitin_synth_2   Chitin synthase
      0.082   13.4   1.7       0.31   11.5   1.7    1.8  1  FlgN             FlgN protein


Domain annotation for each model (and alignments):
>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   4.1e-06     0.024       7      38 ..      48      86 ..      42     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                                  TS---HHHHHHHHHHHCCGGGG.....-EEEEEEE...E CS
               Ribosomal_S30AE  7 nievtdalkeyvekkleklekyf....ieadVtls...k 38
                                  +ie+ d+lk+ +e+k++ le+ +     +++V+++   +
  gi|70606720|ref|YP_255590.1| 48 QIEILDSLKSLIEEKIDTLEREIhdkvNSFNVNIEeltY 86
                                  79******************7644556999999994431 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     1e-05     0.062     175     240 ..      76     144 ..      66     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                Chitin_synth_2 175 tfdermteleyelfkkikk....viGvspdfyei.vlmvdadtkvapdsltrlvaalvkdpeilglcGetk 240
                                    f+ ++ el y ++++i +    +iG+++  +e  vl      ++   sl++++ +++kd++i++lc e +
  gi|70606720|ref|YP_255590.1|  76 SFNVNIEELTYSIYNSIENgkdyIIGHDSLKFEDkVLATGKFQEI--ISLSQVIDSIKKDKNIISLCDEIR 144
                                   599999***********8766679*****9999614444444444..59******************9976 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   5.2e-05      0.31       8     105 ..      42     152 ..      41     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTT--...........SCHHH CS
                          FlgN   8 ielleeelelleeLlelleeEteaLkagdieaLeelleekqellekl.eqleqkrakllaelgls...........aeeat 76 
                                   ie ++e++e+l++L++l+ee+ + L ++  ++ ++ + +++el   + + +e+  + ++ + +l+            e  +
  gi|70606720|ref|YP_255590.1|  42 IESFKEQIEILDSLKSLIEEKIDTLEREIHDKVNSFNVNIEELTYSIyNSIENGKDYIIGHDSLKfedkvlatgkfQEIIS 122
                                   68899**********************999999998888777755442566666666666666666677766666666666 PP

                                   HHHHHCT.TCCHHHHHHHHHHHHHHHHHHH CS
                          FlgN  77 lsellak.eedeelkelwqelkelleelke 105
                                   ls+++ + ++d+ + +l++e++ l e l e
  gi|70606720|ref|YP_255590.1| 123 LSQVIDSiKKDKNIISLCDEIRYLSESLWE 152
                                   666666677777777777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.49
# Mc/sec: 1033.45
//
Query:       gi|70606721|ref|YP_255591.1|  [L=157]
Description: hypothetical protein Saci_0936 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1065.11
//
Query:       gi|70606722|ref|YP_255592.1|  [L=136]
Description: hypothetical protein Saci_0937 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   15.9   1.2      0.022   14.9   1.2    1.5  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2   1.2e-06     0.022       2      82 ..       8      88 ..       7     133 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-06
                                  HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT....-HHHHHHHHHHHC CS
                          HEPN  2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke.seelreeleeLek 82
                                  +e+l r+ +dl++ ++++eegd   ++ + ++ +e +  ++l+ +g  ++  h   + le+l+ +  e +++l++ele Le+
  gi|70606722|ref|YP_255592.1|  8 SEFLTRSFRDLSDCKKAFEEGDLLGSLRRMYELVENISFSMLVLYGFYYKGSHK-AQFLELLRGKASEkENKLIDELELLEQ 88
                                  578999****************************************97666555.444443333222225555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 923.20
//
Query:       gi|70606723|ref|YP_255593.1|  [L=65]
Description: hypothetical protein Saci_0938 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 470.36
//
Query:       gi|70606724|ref|YP_255594.1|  [L=203]
Description: hypothetical protein Saci_0939 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-24   84.7   0.1    8.7e-24   84.1   0.1    1.2  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.027   14.5   0.1    1.5  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   9.7e-28   8.7e-24       4     167 ..      23     162 ..      18     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 9.7e-28
                    MAF_flag10   4 lknlkenlkpslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasy 83 
                                   + n +++++ +l++l++   g +++ +vgaGP Le+ +  +    ++ vii+ad+a++ L+++gI+PDivv+ lD+     
  gi|70606724|ref|YP_255594.1|  23 MINSDDYIE-ELNSLIR---G-RKVAVVGAGPNLEE-VTEI----EEDVIISADGATNYLVSKGITPDIVVTdLDG----- 88 
                                   444555554.4555555...7.************99.5556....4779***************************..... PP

                    MAF_flag10  84 evfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqa..lelleeekneilfgGgsvantaldlAvklgfkeIili 162
                                     +  + +  + ++v a+g+n++ll k k  k  + t  +q+  +  l      +lfgG++++++a+ lA  +++k+++l+
  gi|70606724|ref|YP_255594.1|  89 --ITVFPD--SLYVVLAHGDNIKLLYKAKRMKRLIGT--CQVmpFGRL------RLFGGFTDGDRAVVLAKLFNAKSVTLY 157
                                   ..555666..799************999998886544..444358888......9************************** PP

                    MAF_flag10 163 GqDla 167
                                   G+D+ 
  gi|70606724|ref|YP_255594.1| 158 GMDFD 162
                                   ***96 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     3e-06     0.027       8      44 ..      59      90 ..      55      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                 TPK_catalytic  8 aslrvcaDgGanrlyeeekerlellpdvivGDlDSir 44
                                   ++++ aDg++n l+     +++++pd++v DlD i+
  gi|70606724|ref|YP_255594.1| 59 EDVIISADGATNYLV-----SKGITPDIVVTDLDGIT 90
                                  5799***********.....9*************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1294.95
//
Query:       gi|70606725|ref|YP_255595.1|  [L=386]
Description: trans-homoaconitate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-91  305.6   0.2    4.5e-91  305.1   0.2    1.2  1  HMGL-like     HMGL-like
  ------ inclusion threshold ------
       0.13   11.7   0.1        1.4    8.3   0.1    2.7  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.15   12.4   0.0       0.33   11.3   0.0    1.5  1  EF-hand_14    EF-hand domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.1   0.2   7.6e-95   4.5e-91       1     264 []      11     271 ..      11     271 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.1 bits;  conditional E-value: 7.6e-95
                                   B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B...--EE-SSHHHHHH CS
                     HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar.ilalvrarekdika 80 
                                   kv+i+dttLRDGeqa++  l+v++k+++ak L+e+gvd+iE+gfpa+s ++fe++++i ++++++  +++l r++++di++
  gi|70606725|ref|YP_255595.1|  11 KVRIFDTTLRDGEQAPGIDLTVDQKIRVAKRLAELGVDVIEAGFPASSDGEFEATKKILSEIGDQVeVTGLSRSVKQDIDR 91 
                                   699************************************************************9977************** PP

                                   HHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-S CS
                     HMGL-like  81 avealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGat 161
                                   +++    +g  ++h+fiats++hlk+klk++reev++++ e v++a+++g  ve+s+eda+r+d efl++ v++a++aGa+
  gi|70606725|ref|YP_255595.1|  92 TID----TGLSSIHIFIATSDIHLKYKLKMTREEVLNRIYESVRYAKDHGLIVEYSPEDATRSDEEFLLKAVKTAIDAGAD 168
                                   ***....************************************************************************** PP

                                   EEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHH CS
                     HMGL-like 162 riniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaa 242
                                   rini+DtvGv+ P+++++lis++++++    i+svHcHnd+GlA+an++a+v+aGa++v +tvnG+GeraGna+lee+v+ 
  gi|70606725|ref|YP_255595.1| 169 RINIPDTVGVMHPFKFYDLISKIVKVTG-DKIVSVHCHNDFGLATANSIAGVMAGARQVHVTVNGIGERAGNASLEEVVMS 248
                                   ***************************9.7789************************************************ PP

                                   HHHTT.-B----HHHHHHHHHHH CS
                     HMGL-like 243 lealg.vdtgldlqklrsiaalv 264
                                   l++l  +d g+ ++ l++++++v
  gi|70606725|ref|YP_255595.1| 249 LKKLLgYDVGVRTYLLYEVSRYV 271
                                   *99766**************997 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00024       1.4       3     127 ..      41     140 ..      26     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00024
                                   HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHT CS
                  AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLG 83 
                                   ++ae+G+d +E  ++   +         ++ +k+l e g +            +++  +        + +k+ i+++ + G
  gi|70606725|ref|YP_255595.1|  41 RLAELGVDVIEAGFPASSDGE------FEATKKILSEIGDQ------------VEVTGL-------SRSVKQDIDRTIDTG 96 
                                   566677777777766666664......56666666666666............444323.......346999999999999 PP

                                   BSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEE CS
                  AP_endonuc_2  84 apllvlhpGtagagpkgseeeawerlaeslneladyaekegvkl 127
                                      +++++ t + + k   + ++e + +++ e ++ya+++g  +
  gi|70606725|ref|YP_255595.1|  97 LSSIHIFIATSDIHLKYKLKMTREEVLNRIYESVRYAKDHGLIV 140
                                   99999999997777777777777778888888888877778443 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.5e-05      0.33      19      60 ..     331     372 ..     326     385 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                    EF-hand_14  19 vakllkaLaetGirkdDpRLkellkklkkvekekseaeeset 60 
                                   ++ l + L+e Gi  dD  L+e+lk++k++ +  +++++++ 
  gi|70606725|ref|YP_255595.1| 331 IHGLKRLLEEQGIFLDDTQLREVLKEIKSLAEAGNKVTSADA 372
                                   5678999**********************9999876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2923.26
//
Query:       gi|70606726|ref|YP_255596.1|  [L=206]
Description: hypothetical protein Saci_0941 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-34  118.6   0.1      3e-34  118.3   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.2e-13   51.0   2.3    7.3e-10   38.7   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.1   3.3e-38     3e-34       2     163 .]       2     157 ..       1     157 [. 0.96

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 3.3e-38
                 Lactamase_B_3   2 ltwlghnsflletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevggleirav 81 
                                   ++++ h++fl++   + il+DP ++ ++g+ +p+ +a lvli++++ dH++ e ++    ++  l+e +++++++  i+++
  gi|70606726|ref|YP_255596.1|   2 IRFFLHSCFLID---KLILIDPHDGaSIGLPKPETKAPLVLITHDHYDHNAYEIIPH---ETVKLKEYGEFTFRNYTIKGF 76 
                                   67889*****96...79******999*******************************...9999***************** PP

                 Lactamase_B_3  82 atshdavggsergenngf.lleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlP 161
                                   +++hd+++g++rge  ++ +++ +g +i+hlG+++h    e+++e+++ Dv+l+Pvgg +t++++ea ++++ L+p++v+P
  gi|70606726|ref|YP_255596.1|  77 RAYHDKEKGRRRGETAIYkIITPNGNSIVHLGDIGH--VPENIEEIKNSDVLLLPVGGVITVNAKEATDIVNILRPRIVIP 155
                                   ******************555669************..69999************************************** PP

                 Lactamase_B_3 162 mh 163
                                   mh
  gi|70606726|ref|YP_255596.1| 156 MH 157
                                   *9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.7   2.1e-05      0.19      26      43 ..      32      47 ..      15      51 .. 0.67
   2 !   38.7   0.0   8.1e-14   7.3e-10      86     201 .]      56     158 ..      48     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                                  --..SEEEEE-SS--HHH CS
                 Lactamase_B_2 26 delppidaVllthaHyDH 43
                                  ++  +  +Vl+th+HyDH
  gi|70606726|ref|YP_255596.1| 32 ET--KAPLVLITHDHYDH 47
                                  34..6778********** PP

  == domain 2  score: 38.7 bits;  conditional E-value: 8.1e-14
                                   EEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S CS
                 Lactamase_B_2  86 nvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyipeeigerlggadlllldit 165
                                   ++++l+  ++f++   + +i+ + a h++++  +r++g+t+ + i   +g++++++gD g++pe i+ ++++ d+lll+++
  gi|70606726|ref|YP_255596.1|  56 ETVKLKEYGEFTFR--NYTIKGFRAYHDKEK--GRRRGETAIYKIItPNGNSIVHLGDIGHVPENIE-EIKNSDVLLLPVG 131
                                   45667777888887..689**********99..7777777777555499****************88.************* PP

                                   -SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 166 ayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                            + ++++ +ea ++++ l++++++++H+
  gi|70606726|ref|YP_255596.1| 132 ---------GVITVNAKEATDIVNILRPRIVIPMHY 158
                                   .........8999**********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1448.96
//
Query:       gi|70606727|ref|YP_255597.1|  [L=58]
Description: hypothetical protein Saci_0942 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   40.9   0.5    1.7e-10   40.4   0.5    1.3  1  RHH_1     Ribbon-helix-helix protein, copG family
    3.1e-07   30.3   1.1    4.5e-07   29.7   0.5    1.5  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.5   1.9e-14   1.7e-10       2      37 ..       4      39 ..       3      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-14
                                  EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                  v+++++e+lle+Ld+ a+++g +rSe+IR A++ ++
  gi|70606727|ref|YP_255597.1|  4 VTFKVEEDLLELLDRYAIKTGLNRSEAIRKAIEKLV 39
                                  9********************************987 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.5     5e-11   4.5e-07       5      41 ..       4      40 ..       2      41 .. 0.95
   2 ?   -1.3   0.0      0.25   2.2e+03      18      24 ..      41      47 ..      41      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5e-11
                         RHH_3  5 ttvsidpelaekLkaLSekTrIprSklldeAiellLe 41
                                  +t+ ++++l+e L+ +  kT+ +rS+ +++Aie l +
  gi|70606727|ref|YP_255597.1|  4 VTFKVEEDLLELLDRYAIKTGLNRSEAIRKAIEKLVR 40
                                  79*******************************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.25
                         RHH_3 18 kaLSekT 24
                                  +++S++T
  gi|70606727|ref|YP_255597.1| 41 DEISKET 47
                                  5789998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 442.21
//
Query:       gi|70606728|ref|YP_255598.1|  [L=104]
Description: hypothetical protein Saci_0943 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-05   23.0   0.0    9.6e-05   22.2   0.0    1.4  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
     0.0043   17.6   0.8     0.0093   16.5   0.0    1.8  2  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
  ------ inclusion threshold ------
       0.39   10.8   3.1       0.72   10.0   3.1    1.5  1  SAM_Exu         Exuperantia SAM-like domain


Domain annotation for each model (and alignments):
>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.6e-08   9.6e-05       4      40 ..       4      40 ..       1      42 [. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.6e-08
                         RHH_5  4 vnvtLPeelleeLeewAdeegRsvSnlaafLvekalr 40
                                  + ++LPe ++eeL++ Ad+ g+ +  l++f+++ +++
  gi|70606728|ref|YP_255598.1|  4 IHLSLPEWIYEELKRKADDMGVQITDLVKFFIKMGIE 40
                                  7899*****************************9986 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.6e-06    0.0093      44      77 ..       3      36 ..       1      37 [. 0.94
   2 ?   -1.6   0.4       0.7   4.2e+03       5      14 ..      85      94 ..      81      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-06
                CopG_antitoxin 44 sislrlpedlLealkekAnkrdvpyqslikelle 77
                                  +i l lpe + e+lk kA  ++v ++ l+k +++
  gi|70606728|ref|YP_255598.1|  3 TIHLSLPEWIYEELKRKADDMGVQITDLVKFFIK 36
                                  799***************************9886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.7
                CopG_antitoxin  5 efkseeeeee 14
                                  +f++e+eeee
  gi|70606728|ref|YP_255598.1| 85 KFEEEDEEEE 94
                                  7888888876 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.1   0.00012      0.72      31      71 ..      57      99 ..      50     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                       SAM_Exu 31 dyesLke..iweekkkeGlekllkekitslkeedkeeLlelLd 71
                                  +y++L+e  i+ e +++ le+l+ e i++ +eed ee +e+++
  gi|70606728|ref|YP_255598.1| 57 KYAKLEEniIYLEARMAQLETLVGELIKKFEEEDEEEEVEIIN 99
                                  6888877669***************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1610  (0.0897987); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 721.61
//
Query:       gi|70606729|ref|YP_255599.1|  [L=75]
Description: hypothetical protein Saci_0944 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-10   39.5   0.2    4.6e-10   39.3   0.2    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.041   13.4   0.0      0.049   13.1   0.0    1.0  1  DUF3829         Protein of unknown function (DUF3829)
      0.044   14.0   0.1      0.055   13.7   0.1    1.1  1  DapH_N          Tetrahydrodipicolinate succinyltransferase N-


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.2   7.8e-14   4.6e-10      15      73 ..      18      75 .]       8      75 .] 0.94

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 7.8e-14
                                  HHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                AsnC_trans_reg 15 efeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                  ++  +l+++  V+e+  v G+yd ++++v+ +l++l++++ + ++++  + rt t+iv+
  gi|70606729|ref|YP_255599.1| 18 DVSNELRKINGVKEANPVYGEYDVVAEIVADNLDELNKVIFQ-VRRNTSILRTVTLIVM 75
                                  68899*************************************.***************8 PP

>> DUF3829  Protein of unknown function (DUF3829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-06     0.049      42      94 ..      15      61 ..       4      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-06
                       DUF3829 42 kektiyglydlkecleklkaaaaskpameelDeaakkliaaleklaplldead 94
                                  ke      +d++++l+k++ +++ +p + e D  a+ +++ l++l++++ +++
  gi|70606729|ref|YP_255599.1| 15 KE------VDVSNELRKINGVKEANPVYGEYDVVAEIVADNLDELNKVIFQVR 61
                                  33......788**************************************9985 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.3e-06     0.055      18      81 ..       2      66 ..       1      68 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.3e-06
                                  EEEEEEEE.-.C.TC----.TTSEEEE-SSEEEEEEEHHHHHHHHHHTTTTEEEEEEEE--BSB-S CS
                        DapH_N 18 pvkvYvkg.elkeeelefp.eevkvfgsedsgvvfGdwkeieevleenkdkiedyevendrRnSAi 81
                                  pvk+Yv   +  ++e++++ e  k+ g ++ + v+G+++ ++e++++n d+++++ + + rRn+ i
  gi|70606729|ref|YP_255599.1|  2 PVKAYVLLvTAVGKEVDVSnELRKINGVKEANPVYGEYDVVAEIVADNLDELNKV-IFQVRRNTSI 66
                                  78888754123345555552566788999999******************99886.6677888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 555.98
//
Query:       gi|70606730|ref|YP_255600.1|  [L=393]
Description: hypothetical protein Saci_0945 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-22   79.5  43.2    2.9e-22   79.2  43.2    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.3e-05   25.3  11.0    1.3e-05   25.3  11.0    3.4  3  ABC2_membrane_4  ABC-2 family transporter protein
    2.1e-05   24.0  39.7    0.00011   21.7  39.7    2.3  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.025   14.8   7.5        1.3    9.3   0.0    3.5  3  DUF2754          Protein of unknown function (DUF2754)
        1.7    8.2  36.7        2.1    7.8  30.7    3.1  2  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2  43.2   8.1e-26   2.9e-22       1     344 [.      17     382 ..      17     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 8.1e-26
               ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsveddentpiavvdedn..sslsqqlvealeaspsvelvyevdseeeakkalkngdi 79 
                                   k++l+++++lP+il+ ++gli+ ++   ++++ i +++++    ++ + + +++e+s+ +     v + ++       ++ 
  gi|70606730|ref|YP_255600.1|  17 KRLLVSIIILPFILLPIIGLILFATL-GAQQPVIEIINQNPknIPYVNFVEKNIESSGATV----VMNSSSG------TTP 86 
                                   78999****************99999.5899999****98766666556666666666554....3444433......589 PP

               ABC2_membrane_3  80 dgilvipkgfskdllkgesatvtvli..nssnlnsskailnalns.llqqlnasalvlqseatstsaninvestql..... 152
                                   ++i+v+pk+f+++++  +++ ++vl+   ssn++++++++nal++ l +++ + +    +  + ++++++v+++ +     
  gi|70606730|ref|YP_255600.1|  87 NAIIVFPKDFYDNVTNISRQAYVVLYvvISSNQQAVNIVNNALYNlLVNISSQRIA---QLEKLANTSVSVDDIRNpiylv 164
                                   9*************95555555555557*****************88887776665...5777888999999998899999 PP

               ABC2_membrane_3 153 ...........eeelsnvasf......lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflv 216
                                              +    ++a++      lv+lil+ +++ ++++++ +i  E+e+r++e +l++++++ ++++sk+l+  l+
  gi|70606730|ref|YP_255600.1| 165 lgyktssgsttT----SSANQlaqlsrLVALILFPSVTPVVFYLLEGITGERERRTLEALLSTPLTVRSFIVSKLLTASLL 241
                                   998776643322....333335666888889999999999***************************************** PP

               ABC2_membrane_3 217 yllql....llilllafgl........gipfg.nlglll.llfllfglayialgyllsslfknsetaqilifivilllsgf 283
                                   ++l++    l ++++   +        +++ + +l++l+ + +l+ +l++ +l+++l ++f  s   +++i ++il+++++
  gi|70606730|ref|YP_255600.1| 242 GFLSSigdvLGTIIF--VSvsgiglaiNLTEMiQLLALIvITYLISILLTGSLSLALLYIFGGSIRNIQIINFLILSFGMA 320
                                   *****4444223332..22244455445555587777777999999******************99999*****9988777 PP

               ABC2_membrane_3 284 fgglfpledlp..salkwifsiiPffapglgllrlitgdplweillsliilalfavvylllal 344
                                   + ++ ++ + +  s+   + +iiP ++++lg+l+ ++g  + e + sl++  +++vv+++l++
  gi|70606730|ref|YP_255600.1| 321 SSFISLFINTAqlSFPLSLIYIIPYVQLSLGFLSYVFGS-IQESIFSLLVTTIISVVLIILVI 382
                                   777766444445888888*******************99.99999999999999999999876 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.1    0.0059        21       2      38 ..       6      44 ..       5      60 .. 0.74
   2 !   25.3  11.0   3.6e-09   1.3e-05      32     170 ..     167     308 ..     158     318 .. 0.72
   3 ?   -6.5  10.0         5   1.8e+04     102     151 ..     326     377 ..     309     389 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0059
               ABC2_membrane_4  2 iktEflKlkrskivwllvlaa..llvpllallyfnllgk 38
                                  ++ E++ ++r k ++++++++  +l+p+++l++f++lg+
  gi|70606730|ref|YP_255600.1|  6 LRKELMEIRRDKRLLVSIIILpfILLPIIGLILFATLGA 44
                                  567888899988766665544115578899999988765 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 3.6e-09
               ABC2_membrane_4  32 yfnllgktg.ldpaefyslsvfgftlllllplilgiiasyl..ifrEeqndtlknLltiPvsrtklllaKlivllllsvll 109
                                   y +  g+t+  +++++ +ls +   +l+l+p ++ ++   l  i+ E++  tl  Ll  P + ++++++Kl++  ll +l 
  gi|70606730|ref|YP_255600.1| 167 YKTSSGSTTtSSANQLAQLSRLV--ALILFPSVTPVVFYLLegITGERERRTLEALLSTPLTVRSFIVSKLLTASLLGFLS 245
                                   44444443313334444444444..5566777766654333339999********************************** PP

               ABC2_membrane_4 110 mlvtflitvlfallsgf.vgfsvklvlellkkclelgllvffavlpi.ialvllkksyvlpli 170
                                   ++  +l t++f  +sg   +++ + +++ll  ++++ l++++++  + +al +++ +++  + 
  gi|70606730|ref|YP_255600.1| 246 SIGDVLGTIIFVSVSGIgLAINLTEMIQLLALIVITYLISILLTGSLsLALLYIFGGSIRNIQ 308
                                   **********988888548899999***99999988888777766553677777777766554 PP

  == domain 3  score: -6.5 bits;  conditional E-value: 5
               ABC2_membrane_4 102 llllsvllmlvtflitvl..fallsgfvgfsvklvlellkkclelgllvffa 151
                                   l++ ++ l++ + li ++  + l +gf ++ ++++ e+++ +l+++++++++
  gi|70606730|ref|YP_255600.1| 326 LFINTAQLSFPLSLIYIIpyVQLSLGFLSYVFGSIQESIFSLLVTTIISVVL 377
                                   3333333333333333332244445555444444444444444444433333 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7  39.7     3e-08   0.00011       4     284 ..       6     386 ..       3     390 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3e-08
               ABC2_membrane_2   4 akkEfrdlvrsrrfllltvllpli......................................................... 27 
                                   ++kE+ +++r++r+l+  ++lp+i                                                         
  gi|70606730|ref|YP_255600.1|   6 LRKELMEIRRDKRLLVSIIILPFIllpiiglilfatlgaqqpvieiinqnpknipyvnfvekniessgatvvmnsssgttp 86 
                                   79***************************6666666555555555555555555555555555555444444444444444 PP

               ABC2_membrane_2  28 ..dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv.............................. 76 
                                                                                     +                              
  gi|70606730|ref|YP_255600.1|  87 naI-----------------------------------------------Ivfpkdfydnvtnisrqayvvlyvvissnqq 120
                                   440...............................................1555555555555555555555555555555 PP

               ABC2_membrane_2  77 .................................................................vstimavlipviaalf 92 
                                                                                                    + + + +l+p +  + 
  gi|70606730|ref|YP_255600.1| 121 avnivnnalynllvnissqriaqleklantsvsvddirnpiylvlgyktssgstttssanqlaqlSRLVALILFPSVTPVV 201
                                   555666666666666666666667777778888889****************************84444445555553333 PP

               ABC2_membrane_2  93 g..adaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgi..vlaledllllvvasv 169
                                         i+gE+er+Tl++lLs+P + ++ +++K++  +++   + ++ +  vl +++++ ++gi  +++l +++ l++++v
  gi|70606730|ref|YP_255600.1| 202 FylLEGITGERERRTLEALLSTPLTVRSFIVSKLLTASLL---GFLSSIGDVLGTIIFVSVSGIglAINLTEMIQLLALIV 279
                                   300467**********************************...77777777777777776666511667788888888888 PP

               ABC2_membrane_2 170 lllllv..vflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllne 248
                                   ++ l+      +l+l+l  ++  s + +++  +l++ + ++++ +++ ++ + + +            l ++ +y +l   
  gi|70606730|ref|YP_255600.1| 280 ITYLISilLTGSLSLALLYIFGGSIRNIQIINFLILSFGMASSFISLFINTAQLSFPL---------SLIYIIPYVQLSLG 351
                                   88777788669***************************99***999999988886666.........77777777777777 PP

               ABC2_membrane_2 249 ilagsdlnalgstatnllilllllavllvlgyvlFk 284
                                   +l+   + +++   ++ll++ ++ +vl++l++ +F+
  gi|70606730|ref|YP_255600.1| 352 FLSYV-FGSIQESIFSLLVTTIISVVLIILVIRSFD 386
                                   77766.334566677777777777777777778886 PP

>> DUF2754  Protein of unknown function (DUF2754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00036       1.3       6      43 ..      12      49 ..       8      54 .. 0.88
   2 ?    1.2   1.6      0.12   4.3e+02      20      56 ..     254     290 ..     249     296 .. 0.86
   3 ?    5.4   0.2    0.0059        21      16      65 ..     335     388 ..     331     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00036
                       DUF2754  6 kirrdwhyyavalGlifilnGvvGllGfeakGwqtyav 43
                                   irrd       + l fil  ++Gl+ f + G q   +
  gi|70606730|ref|YP_255600.1| 12 EIRRDKRLLVSIIILPFILLPIIGLILFATLGAQQPVI 49
                                  69****************************99997655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                       DUF2754  20 lifilnGvvGllGfeakGwqtyavGlvtwvisfwiaG 56 
                                   +if+    +Gl    ++  q  a+ ++t++is+ ++G
  gi|70606730|ref|YP_255600.1| 254 IIFVSVSGIGLAINLTEMIQLLALIVITYLISILLTG 290
                                   6788888899999999999*************99988 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0059
                       DUF2754  16 valGlifilnGvvGllGfeakGw...qtya.vGlvtwvisfwiaGliirrrpee 65 
                                   + l li+i+  v   lGf +  +   q      lvt +is  +  l+ir  + e
  gi|70606730|ref|YP_255600.1| 335 FPLSLIYIIPYVQLSLGFLSYVFgsiQESIfSLLVTTIISVVLIILVIRSFDSE 388
                                   66889999988876666665544111433314589**************87755 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.16   5.6e+02      17      32 ..      19      34 ..       6      55 .. 0.46
   2 ?    7.8  30.7   0.00059       2.1      42     198 ..     194     355 ..     182     380 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.16
               ABC2_membrane_5 17 llivllllaiiilifl 32
                                  ll+++++l++i+l ++
  gi|70606730|ref|YP_255600.1| 19 LLVSIIILPFILLPII 34
                                  2222222222222222 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00059
               ABC2_membrane_5  42 ilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlili.......liailitlllliiavlikgnvtise 115
                                   + s++ +++++l+ +  ++  ++   ll++P+t +  + sK l++ +l+       +++++i++ ++ i+  i+ + +i+ 
  gi|70606730|ref|YP_255600.1| 194 FPSVTPVVFYLLEGITGERERRTLEALLSTPLTVRSFIVSKLLTASLLGflssigdVLGTIIFVSVSGIGLAINLTEMIQL 274
                                   333333467778999999****************************99977777777777777777778888888888888 PP

               ABC2_membrane_5 116 vllsiliglvialiflaivlPlyfkfgvekgri....vliiiifgiifllvaifslsklelslidlsnyilliillviill 192
                                   + l ++ +l+ +l+ ++++l l+++fg +  +i    +li+++ ++  +++ ++++ +l++ l+ ++ +        + l 
  gi|70606730|ref|YP_255600.1| 275 LALIVITYLISILLTGSLSLALLYIFGGSIRNIqiinFLILSFGMASSFISLFINTAQLSFPLSLIYIIPY------VQLS 349
                                   888999999999999************66555544444444444444466666666655444332222211......2222 PP

               ABC2_membrane_5 193 liivSy 198
                                   l ++Sy
  gi|70606730|ref|YP_255600.1| 350 LGFLSY 355
                                   222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2449.51
//
Query:       gi|70606731|ref|YP_255601.1|  [L=248]
Description: ABC transporter ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-25   90.8   0.0    1.6e-25   90.2   0.0    1.2  1  ABC_tran  ABC transporter
    5.9e-12   46.0   1.4    9.7e-06   25.6   0.3    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00015   22.4   1.5    0.00026   21.6   1.3    1.7  1  AAA_23    AAA domain
    0.00016   21.5   0.0    0.00018   21.3   0.0    1.3  1  AAA_30    AAA domain
    0.00079   19.2   0.0    0.00099   18.9   0.0    1.3  1  AAA_15    AAA ATPase domain
     0.0053   16.2   0.3       0.26   10.7   0.1    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.028   14.2   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.018   14.6   0.0      0.032   13.8   0.0    1.3  1  AAA_27    AAA domain
      0.031   14.6   0.0      0.044   14.1   0.0    1.3  1  AAA_19    AAA domain
      0.038   13.9   0.0      0.077   12.9   0.0    1.7  1  Rad17     Rad17 P-loop domain
      0.074   12.7   0.1       0.13   11.9   0.1    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.078   13.4   0.0       0.16   12.4   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
      0.081   12.0   0.1       0.12   11.4   0.1    1.3  1  T2SSE     Type II/IV secretion system protein
       0.14   12.4   0.1       0.26   11.6   0.1    1.7  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   1.2e-28   1.6e-25       1     136 [.      22     164 ..      22     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.2e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+ +sl++++ge+ +++G+nGaGK+t l++++g lk+ eG+i + g   +e    +    i+++p++++  ++l+  en  
  gi|70606731|ref|YP_255601.1|  22 LNGISLQVYKGEVFGLIGPNGAGKTTTLRAISGILKKYEGDISIFGYTPEE---AKKLGYISYMPEDAFPYEKLSGIENle 99 
                                   789***************************************999877777...788899*******99999999888889 PP

                                   .......HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .......xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                            d+e+ek   +lg k  +  +++++++s +S G+k+r+++aral+ kp+l +lDEpt
  gi|70606731|ref|YP_255601.1| 100 vfaqiyaRGDKELEKEFLELGVKIaDLGNKIYEQTSIYSRGMKRRLMIARALMVKPRLAILDEPT 164
                                   99999984444444444444433224677778999*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.3   7.6e-09   9.7e-06       2      61 ..      35      77 ..      34     115 .. 0.68
   2 !   19.7   0.1   4.9e-07   0.00063     238     302 ..     138     200 ..      96     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.6e-09
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61
                                   +liGpNg+GK++ L+a++++                  +  + + ++++y pe++ +++
  gi|70606731|ref|YP_255601.1| 35 FGLIGPNGAGKTTTLRAISGIL-----------------KKYEGDISIFGYTPEEAKKLG 77
                                  68****************9996.................444444444444444444444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.9e-07
                        AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                   S G+kr   +++  l   +  +l ++DEp +gL+ + + r+ ++++el r  ++ +++++H+ l +
  gi|70606731|ref|YP_255601.1| 138 SRGMKRR-LMIARALMVKP--RLAILDEPTTGLDVESTVRVRRIIRELPRsINTTILFSSHNMLEV 200
                                   8999999.88888888776..**************99988888886666667899*******8765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.3     2e-07   0.00026      18      43 ..      31      56 ..      13     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2e-07
                        AAA_23 18 skgltlItGpNGaGKTTildAiklaL 43
                                  +  ++ ++GpNGaGKTT l+Ai  +L
  gi|70606731|ref|YP_255601.1| 31 KGEVFGLIGPNGAGKTTTLRAISGIL 56
                                  556999****************9887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.4e-07   0.00018      20      63 ..      34      77 ..      26     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa 63
                                  v  l Gp G+GKtt+l+a+  ++++ +g++ ++  t + Ak+L+
  gi|70606731|ref|YP_255601.1| 34 VFGLIGPNGAGKTTTLRAISGILKKYEGDISIFGYTPEEAKKLG 77
                                  77899*********************999999999999999998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.7e-07   0.00099      25      84 ..      34     134 ..      14     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.7e-07
                        AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn...........................kkvikiekedleifeniseskdik 78 
                                   +  liG+N++GK++ l+a+  +l++  + +                           +  +    e+le+f +i+   d +
  gi|70606731|ref|YP_255601.1|  34 VFGLIGPNGAGKTTTLRAISGILKKY-EGDisifgytpeeakklgyisympedafpyE--KLSGIENLEVFAQIYARGDKE 111
                                   5569****************999944.3336888999999999999999998886542..233456778888888888888 PP

                        AAA_15  79 Idvef.................a 84 
                                   +++ef                  
  gi|70606731|ref|YP_255601.1| 112 LEKEFlelgvkiadlgnkiyeqT 134
                                   88888777666444433333330 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0002      0.26      25      47 ..      33      55 ..      10      62 .. 0.79
   2 ?    3.9   0.0     0.023        30     155     204 ..     152     200 ..      96     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                  SEEEEEESTTSSHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAilFv 47
                                  ++  ++GpNG+GK+  l Ai+ +
  gi|70606731|ref|YP_255601.1| 33 EVFGLIGPNGAGKTTTLRAISGI 55
                                  45679**************9755 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                                   CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                   +vkp  l +lDe    LD + + +v ++++e   +    +   +++mle 
  gi|70606731|ref|YP_255601.1| 152 MVKP-RLAILDEPTTGLDVESTVRVRRIIRELPRSINTTILFSSHNMLEV 200
                                   4444.4899*********************99877776666666666665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.028      22      46 ..      31      56 ..      18      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                        AAA_29 22 kg.atlltGpsGsGKSTllDAiqalL 46
                                  kg ++ l+Gp+G+GK+T l Ai+ +L
  gi|70606731|ref|YP_255601.1| 31 KGeVFGLIGPNGAGKTTTLRAISGIL 56
                                  3447889************9998776 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-05     0.032      31      50 ..      37      56 ..      23      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                        AAA_27 31 iyGpNEAGKstalrAisdll 50
                                  ++GpN AGK+t+lrAis +l
  gi|70606731|ref|YP_255601.1| 37 LIGPNGAGKTTTLRAISGIL 56
                                  57**************9776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.5e-05     0.044       9      46 ..      31      64 ..      25     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeil 46
                                  k +v+ ++++ G GKT++l++i  +l++ +g     i 
  gi|70606731|ref|YP_255601.1| 31 KGEVFGLIGPNGAGKTTTLRAISGILKKYEGD----IS 64
                                  678999*****************999998854....44 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     6e-05     0.077      26      70 ..      14      57 ..       3     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-05
                         Rad17 26 kkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                  kk ++v e l+  +L+  k ++  + GP G gk+t+++ +s +l 
  gi|70606731|ref|YP_255601.1| 14 KKYKNV-EVLNGISLQVYKGEVFGLIGPNGAGKTTTLRAISGILK 57
                                  455666.46888889999999999***************998874 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.13       4      29 ..      35      60 ..      33      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                  EEEEESTTSSHHHHHHHHHHHHHHTT CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkeg 29
                                  + l+G++GaGKTttl  ++ +lkk +
  gi|70606731|ref|YP_255601.1| 35 FGLIGPNGAGKTTTLRAISGILKKYE 60
                                  5689***********99999888865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.16       3      23 ..      37      57 ..      35      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                  EESSTTSSHHHHHHHHHHHHT CS
                           AAA  3 lyGppGtGKTllakavakelg 23
                                  l+Gp G GKT++ +a+   l+
  gi|70606731|ref|YP_255601.1| 37 LIGPNGAGKTTTLRAISGILK 57
                                  89**************98876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.6e-05      0.12     130     161 ..      33      64 ..       5      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.6e-05
                         T2SSE 130 glilvsGgTgsGKttllyallkeinksderiv 161
                                    ++ + G+ g GKtt+l a+  +++k++  i 
  gi|70606731|ref|YP_255601.1|  33 EVFGLIGPNGAGKTTTLRAISGILKKYEGDIS 64 
                                   555577********************988776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0002      0.26      10      32 ..      37      59 ..      31     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        AAA_22 10 vtGesGtGKTtllrrlleqldee 32
                                  ++G+ G+GKTt+lr +   l+++
  gi|70606731|ref|YP_255601.1| 37 LIGPNGAGKTTTLRAISGILKKY 59
                                  79************987776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1663.08
//
Query:       gi|70606732|ref|YP_255602.1|  [L=230]
Description: hypothetical protein Saci_0947 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   16.1   0.2       0.04   14.3   0.1    2.0  2  UPF0176_N     UPF0176 acylphosphatase like domain
      0.027   14.5   0.8       0.61   10.2   0.7    2.4  2  Bromodomain   Bromodomain
      0.031   13.5   0.2       0.12   11.6   0.0    2.0  2  Syntaxin-5_N  Syntaxin-5 N-terminal, Sly1p-binding domain
       0.04   14.1   0.1      0.094   12.9   0.1    1.6  1  SRI           SRI (Set2 Rpb1 interacting) domain


Domain annotation for each model (and alignments):
>> UPF0176_N  UPF0176 acylphosphatase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.1   4.8e+03      60      82 ..     125     147 ..     114     150 .. 0.58
   2 ?   14.3   0.1   8.9e-06      0.04      13      57 ..     168     213 ..     159     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                     UPF0176_N  60 lrsdeelsdlelklslsseppFe 82 
                                   ++++ e+ + ++kls  +++ F+
  gi|70606732|ref|YP_255602.1| 125 IEKKLEFINRKVKLSDVDKKMFR 147
                                   34444455555555555666555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.9e-06
                     UPF0176_N  13 edpealaeelrelleelgllGr.ilvAeEGiNgtlavpeealeafl 57 
                                   e+ +++a++++++l+     Gr i+v++EGiN  l+ +e + e+ +
  gi|70606732|ref|YP_255602.1| 168 EETQEVAKRIQKILTLAYTIGRkIYVSREGINKGLSEKEGERENNY 213
                                   67899999999999988888866**********9998877666554 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.048   2.2e+02      54      75 ..      14      35 ..       2      39 .. 0.79
   2 ?   10.2   0.7   0.00014      0.61      11      62 ..     108     165 ..      94     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.048
                                  HHHHHHHHHHHHHHHHHHSHTT CS
                   Bromodomain 54 ladfeadlkllfsNarkyngeg 75
                                  l +f ++ +l++sNa++  +e+
  gi|70606732|ref|YP_255602.1| 14 LLKFADKGRLVISNAIEITEEN 35
                                  567888889*******998876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                                   TTCGGGGCSTT..-GCCSTTHHHH.SS---HHHHHHHH....HTT--SSHHHHHHHHH CS
                   Bromodomain  11 hklaepFlepv..dpeefpdyyavikkPldLstIkkkl....esnkYksladfeadlk 62 
                                    k+  +Fl++   dp+e ++  ++i+++++Ls + kk        ++++l+++++d+ 
  gi|70606732|ref|YP_255602.1| 108 PKIRLIFLKFYslDPKEIEKKLEFINRKVKLSDVDKKMfrtlIFDQISQLTELYEDAL 165
                                   4566788888888***********************8865556677778888888875 PP

>> Syntaxin-5_N  Syntaxin-5 N-terminal, Sly1p-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.7e-05      0.12       5      14 ..       5      14 ..       1      14 [. 0.86
   2 ?   -1.2   0.1      0.29   1.3e+03      15      22 ..      47      54 ..      46      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                  Syntaxin-5_N  5 SirDRTsEFq 14
                                  S+rDRT EF+
  gi|70606732|ref|YP_255602.1|  5 SVRDRTIEFL 14
                                  9********7 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                  Syntaxin-5_N 15 SivkslQk 22
                                  + v++lQ+
  gi|70606732|ref|YP_255602.1| 47 ALVERLQS 54
                                  679****8 PP

>> SRI  SRI (Set2 Rpb1 interacting) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.1e-05     0.094       4      44 ..     142     182 ..     139     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                           SRI   4 qekkfkkelakvVvnvlnkYrkklkkedfKklakeltkklv 44 
                                    +k f+ +++  + ++++ Y+++l+ e+  ++ak++ k+l+
  gi|70606732|ref|YP_255602.1| 142 DKKMFRTLIFDQISQLTELYEDALQYEETQEVAKRIQKILT 182
                                   5899**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1615.40
//
Query:       gi|70606733|ref|YP_255603.1|  [L=268]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-106  355.9   0.2   1.3e-106  355.7   0.2    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    7.4e-06   25.6   0.2     0.0019   17.7   0.0    2.5  3  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.7   0.2  1.5e-110  1.3e-106       1     258 [.       5     259 ..       5     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 355.7 bits;  conditional E-value: 1.5e-110
               Pantoate_transf   1 kvtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvva 81 
                                   kv+++d+ k+k + eki+mlTayd++tAk+++++++d iLVGDsl+mvvlgye+tl+v+++em+ h  +V+r+++r+lvva
  gi|70606733|ref|YP_255603.1|   5 KVSIRDFLKKKGK-EKITMLTAYDYPTAKIMSMTNLDGILVGDSLSMVVLGYENTLKVSMKEMLVHLDSVVRAKPRQLVVA 84 
                                   5788999998876.******************************************************************* PP

               Pantoate_transf  82 dlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaek 162
                                   d+Pf+sye+s ++a++nA+ ++++ gad+vKlegg+e+a++v+++v+agipVmgHiGltPq+  ++gg++v gk+++e+e+
  gi|70606733|ref|YP_255603.1|  85 DMPFLSYEVSANTAVKNAGLFVRH-GADSVKLEGGEEMADVVRKIVRAGIPVMGHIGLTPQRFLRIGGFRVLGKSKHEEEQ 164
                                   ***********************9.******************************************************** PP

               Pantoate_transf 163 lledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieea 243
                                   ll+da+ leeaG+f+lv+E + a++ak+itekl++ptI+IGAG++cdGq+lv+hD+lgl+ +f+p f+k y++l+e+i++a
  gi|70606733|ref|YP_255603.1| 165 LLRDAEVLEEAGIFSLVIENTYADVAKKITEKLKVPTICIGAGPYCDGQILVIHDVLGLS-EFTPYFAKAYVNLKEEIQKA 244
                                   ***********************************************************9.9******************* PP

               Pantoate_transf 244 vkaYaeevkegsFPa 258
                                   v++Y+eev+e++FP+
  gi|70606733|ref|YP_255603.1| 245 VNKYVEEVRESKFPQ 259
                                   **************7 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.1e-07    0.0019       2      72 ..       9      81 ..       8      87 .. 0.87
   2 !    5.2   0.0    0.0014        13     155     194 ..      95     134 ..      85     158 .. 0.80
   3 ?   -1.8   0.0       0.2   1.8e+03      86     107 ..     164     185 ..     158     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-07
                    PEP_mutase  2 ra.Lhakg.eplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPl 72
                                  r+ L++kg e + ++ a+D  +aki+  +  +++ ++      +lG++ + +++++e+l ++ +++++    l
  gi|70606733|ref|YP_255603.1|  9 RDfLKKKGkEKITMLTAYDYPTAKIMSMTNLDGILVGDSLSMVVLGYENTLKVSMKEMLVHLDSVVRAKPRQL 81
                                  555777663699*************************99999**********************999875444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0014
                    PEP_mutase 155 leeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavdvp 194
                                    ++a++ a +++  GAd v   g+++ a+ ++++v+a  +p
  gi|70606733|ref|YP_255603.1|  95 ANTAVKNAGLFVRHGADSVKLEGGEEMADvVRKIVRAG-IP 134
                                   57899999*******************99788888663.44 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.2
                    PEP_mutase  86 evaetvrrliaaGvvgvniEDk 107
                                   ++ +  + l++aG+  ++iE +
  gi|70606733|ref|YP_255603.1| 164 QLLRDAEVLEEAGIFSLVIENT 185
                                   5556667788888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2108.00
//
Query:       gi|70606734|ref|YP_255604.1|  [L=252]
Description: hypothetical protein Saci_0949 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-78  260.4   4.4    7.9e-78  260.0   4.4    1.2  1  PPS_PS           Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.023   14.0   0.7      0.053   12.7   0.1    1.8  2  Arabinose_Isome  L-arabinose isomerase
      0.027   14.2   0.5        0.5   10.1   0.1    2.2  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.0   4.4   1.3e-81   7.9e-78       1     176 []      64     241 ..      64     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.0 bits;  conditional E-value: 1.3e-81
                        PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleeda..ripeleseRak 79 
                                   lllak+pvisvNGN+aaLv+++iv+Lae+++ak+evNlfyrt +R++ki+e+lk+aga+evlg+ +da   ipel seR++
  gi|70606734|ref|YP_255604.1|  64 LLLAKNPVISVNGNMAALVPDDIVRLAEEINAKIEVNLFYRTLDREKKIEEVLKRAGAKEVLGVGDDAsaVIPELFSERRR 144
                                   79**************************************************************9999889********** PP

                        PPS_PS  80 vskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkskeeleeiv 160
                                   vsk+Giy aDvvlv lEDGDR+eaLvkmgKkviaiD+NPlsRt+++a++tivdn++R +p++++ +ke+kk++k+el++i+
  gi|70606734|ref|YP_255604.1| 145 VSKKGIYIADVVLVGLEDGDRTEALVKMGKKVIAIDINPLSRTSQMASLTIVDNIIRVFPKMISLAKEMKKSDKDELQKII 225
                                   ********************************************************************************* PP

                        PPS_PS 161 kefdnkkvlkealkei 176
                                   ++++nk++lke+l+ i
  gi|70606734|ref|YP_255604.1| 226 NQYNNKEILKESLRFI 241
                                   ***********99875 PP

>> Arabinose_Isome  L-arabinose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.12     7e+02      34      65 ..      92     120 ..      42     127 .. 0.55
   2 ?   12.7   0.1   8.8e-06     0.053     185     256 ..     158     230 ..     141     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.12
                                   HHHHHS--SSEEEE---B-SHHHHHHHHHHHH CS
               Arabinose_Isome  34 elnesaklpvkvvlkpvvktseeieklvkean 65 
                                   e+n  ak++v++    ++  +++ie+++k a 
  gi|70606734|ref|YP_255604.1|  92 EIN--AKIEVNLF-YRTLDREKKIEEVLKRAG 120
                                   222..22223332.234555556666666655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.8e-06
                                   -STT---HHHHHHHH--EEEEE-HHHHHHHHHTS-HHHHHHHHHHHHHHSEE-GGGSTTSTT.HHHHHHHHHH CS
               Arabinose_Isome 185 vavteGdkveaeiklGvsvntygvgdlvevveavsdeevdalveeyekkYelaeelkeeeer.eeslreaari 256
                                   v   +Gd++ea +k+G +v ++ ++ l ++ + +s + vd+ ++ + k  +la+e+k+++++  +++ ++ + 
  gi|70606734|ref|YP_255604.1| 158 VGLEDGDRTEALVKMGKKVIAIDINPLSRTSQMASLTIVDNIIRVFPKMISLAKEMKKSDKDeLQKIINQYNN 230
                                   56679************************************************99987655426777776555 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   8.3e-05       0.5       2      42 ..      58      97 ..      57     104 .. 0.91
   2 ?    2.1   0.0     0.025   1.5e+02      81     128 ..     155     197 ..     143     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.3e-05
                                  HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE CS
                  TPP_enzyme_M  2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv 42
                                  ++a+++l  ak+pvi v g +a + + +++++lae++++ +
  gi|70606734|ref|YP_255604.1| 58 KAAIAMLLLAKNPVISVNGNMA-ALVPDDIVRLAEEINAKI 97
                                  7899*************99999.99***********99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                                   EEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEEC CS
                  TPP_enzyme_M  81 vlalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivg 128
                                   v+++G  ++d   t+   +  + + k+i idi+p +   +  ++l+iv 
  gi|70606734|ref|YP_255604.1| 155 VVLVG--LEDGDRTE---ALVKMGkKVIAIDINPLSRTSQM-ASLTIVD 197
                                   44577..55533333...33333448*******97655554.5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1369  (0.0763567); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1799.05
//
Query:       gi|70606735|ref|YP_255605.1|  [L=249]
Description: hypothetical protein Saci_0950 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-05   23.4   0.3    8.5e-05   22.7   0.3    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   4.8e-09   8.5e-05       1      66 []      73     136 ..      73     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.8e-09
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                                   +i+++s +P+g G G S+++++a  + +++l   sl   +  ++a++  ++ +++ gDv a + Gg
  gi|70606735|ref|YP_255605.1|  73 KISVQSQVPLGFGYGLSGSISLAYSYLAYELGLTSL--KEALYTAHESEVVNKNGLGDVIAEYIGG 136
                                   589************************999983335..3444555555566889*****9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.55
# Mc/sec: 1355.40
//
Query:       gi|70606736|ref|YP_255606.1|  [L=141]
Description: hypothetical protein Saci_0951 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.051   13.1   0.0      0.064   12.8   0.0    1.2  1  RVT_1     Reverse transcriptase (RNA-dependent DNA polymerase


Domain annotation for each model (and alignments):
>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.6e-06     0.064      86     157 ..      35     104 ..      33     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-06
                                   -GGGGGGG-EEET..........................TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T.. CS
                         RVT_1  86 eellrkltafkvptklinliksflstrsfsvrvnge.eskgryekkglpqGsvlSPllfnlfmnellrelrkr 157
                                   e+l+r l++ k+p+k   l++++l++    +  +++ +s ++++  +lp G + S ++f  +m+ ll ++r +
  gi|70606736|ref|YP_255606.1|  35 ERLIRGLNTSKTPQK-QSLCEQILEKGY--IVTDQHiRSNTHPQLFVLPVGDNSSLITFRDTMDLLLVHFRLY 104
                                   7899999999***77.99******6666..555777789*************************999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 980.84
//
Query:       gi|70606737|ref|YP_255607.1|  [L=235]
Description: molybdenum cofactor biosynthesis protein D/E [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-18   66.5   0.2    3.7e-18   65.9   0.2    1.3  1  MoaE       MoaE protein
      2e-12   47.6   0.3    2.1e-11   44.3   0.1    2.5  2  ThiS       ThiS family
     0.0042   17.6   0.2        1.1    9.8   0.3    2.4  2  Elongin_A  RNA polymerase II transcription factor SIII (Elong
  ------ inclusion threshold ------
      0.046   13.1   0.1      0.079   12.4   0.1    1.3  1  PIN_5      PINc domain ribonuclease


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.2   8.2e-22   3.7e-18      16     112 ..     103     202 ..      90     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 8.2e-22
                                   -..-TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCC.TTSEEEEEEE-EEEETTSEEEEEEEEE CS
                          MoaE  16 a..spkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerw.elervavvHrlGelevgeasvvvavss 93 
                                   a  ++++G +v+++G+v+   +++kv eL yeay++ +ek l+ei+e++r+++ +l ++ + H + +l++g+ + +v++ +
  gi|70606737|ref|YP_255607.1| 103 AeaTEEVGSMVIYLGIVKGAIEEHKVYELRYEAYKEYTEKRLKEIIENLRTKYkDLVKMKILHVVDDLKPGDDVFLVMALG 183
                                   233789************9999*******************************88************************** PP

                                   SSHHHHHHHHHHHHHHHHH CS
                          MoaE  94 ahRkeafeaceylidelKk 112
                                   + R + ++a+e++++ +K+
  gi|70606737|ref|YP_255607.1| 184 RGRGDTLKAVEEAVELVKH 202
                                   ******************8 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   4.8e-15   2.1e-11       1      77 []       5      84 ..       5      84 .. 0.97
   2 ?    0.6   0.0       0.2   8.8e+02      20      36 ..     140     156 ..     127     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.8e-15
                                  EEETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEEST CS
                          ThiS  1 vllfaelrelag.eeelelaegstvaelleaLgerypela........lerrvavavNgeivprlwldtelkdgDevailppV 74
                                  v++fa lr+ ++ +ee+ ++e + va l+ +L++ y++++         + r++++vNg++ ++      +++gDeva+lpp 
  gi|70606737|ref|YP_255607.1|  5 VRYFALLRDYTKkNEEIIETECKDVACLVSQLEKVYGKEFgrvvregfGPVRIVILVNGKVDNE------IREGDEVALLPPP 81
                                  89**********************************************889*********9777......************* PP

                                  TC- CS
                          ThiS 75 aGG 77
                                  aGG
  gi|70606737|ref|YP_255607.1| 82 AGG 84
                                  **9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                                   STSBHHHHHHHHHHHTC CS
                          ThiS  20 egstvaelleaLgeryp 36 
                                   +++ ++e++e+L ++y+
  gi|70606737|ref|YP_255607.1| 140 TEKRLKEIIENLRTKYK 156
                                   46788999999988884 PP

>> Elongin_A  RNA polymerase II transcription factor SIII (Elongin) subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.3   0.00025       1.1      65      97 ..     127     159 ..      94     163 .. 0.77
   2 !    5.2   0.0    0.0066        29      21      51 ..     187     216 ..     177     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
                     Elongin_A  65 kswrelYeklkkereeklkeaaerLreaykklk 97 
                                   k +   Ye++k+ +e++lke  e+Lr++yk+l 
  gi|70606737|ref|YP_255607.1| 127 KVYELRYEAYKEYTEKRLKEIIENLRTKYKDLV 159
                                   455566***********************9875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0066
                     Elongin_A  21 peqLreiEensphlaeetdelWkklikrdfp 51 
                                    + L+ +Ee+  +l+++t  +Wk  i+ d  
  gi|70606737|ref|YP_255607.1| 187 GDTLKAVEEAV-ELVKHTTGIWKLEIRDDGE 216
                                   68899***999.6**********99988765 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.8e-05     0.079     111     160 ..     124     170 ..     114     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                         PIN_5 111 aEeavreaaeeseklekeeeeeevgelikklRekYrealRkGilDsaeDl 160
                                    E++v+e   e++   ke +e+ ++e+i++lR kY++ ++  il   +Dl
  gi|70606737|ref|YP_255607.1| 124 EEHKVYELRYEAY---KEYTEKRLKEIIENLRTKYKDLVKMKILHVVDDL 170
                                   4555555555544...5568999******************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1699.45
//
Query:       gi|70606738|ref|YP_255608.1|  [L=447]
Description: hypothetical protein Saci_0953 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-67  227.5   0.0    1.9e-67  227.2   0.0    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.9e-44  150.6   0.0    4.6e-44  149.9   0.0    1.3  1  ThiP_synth    Thiamine-phosphate synthase
    1.2e-06   28.0   0.0    1.7e-05   24.3   0.0    2.1  2  PfkB          pfkB family carbohydrate kinase
     0.0056   16.2   0.0     0.0097   15.4   0.0    1.3  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.2   0.0   4.3e-71   1.9e-67       1     246 []      13     255 ..      13     255 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.2 bits;  conditional E-value: 4.3e-71
                                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHH CS
                  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaek 81 
                                   D++ GAG + Dlk+++ lgv+g+ ++taltaq t+g+++v p+p+e+++ ql+++++d++++ vKiGm+++++ ++vv ++
  gi|70606738|ref|YP_255608.1|  13 DTGNGAGAESDLKVYEILGVHGVIAVTALTAQSTTGIRAVLPTPPEFLKTQLDTLFDDFEIKDVKIGMIYNNDQFAVVKDY 93 
                                   999****************************************************************************** PP

                                   HHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH.TT-SEEEE CS
                  Phos_pyr_kin  82 lkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk.lgakaVli 161
                                   l+    +vV DPV++ak+g++l+++  +e +k+++l+ +tv+tPN+pEa+ L+g ki++ e++k a+k+++k  +  +V++
  gi|70606738|ref|YP_255608.1|  94 LRD--KRVVTDPVLFAKDGTQLIKD--LEEYKRNILRNTTVLTPNIPEASYLSGLKISSIEEVKLACKTISKdFNIPYVVV 170
                                   *44..49****************99..999******************************************99******* PP

                                   EEGGS-SSSEEEEEEEE..TSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTS CS
                  Phos_pyr_kin 162 kGghlegeeavvtdvly..dgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgk 240
                                   kGgh+  e+++++dvly  +++ ++ +   r+++++thGtG ++++a+ ael+kg+++ +A+++A++ ++++i ++le+g+
  gi|70606738|ref|YP_255608.1| 171 KGGHA--EDDYSIDVLYdsNRDLYYGIGYMRLNQRHTHGTGSVFATAVSAELSKGNDILTALRHARSLLQDSIYYGLEIGH 249
                                   ****8..566667****655566788999**************************************************** PP

                                   SS-B-- CS
                  Phos_pyr_kin 241 gagpvn 246
                                   g+gp++
  gi|70606738|ref|YP_255608.1| 250 GIGPID 255
                                   ****85 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0     1e-47   4.6e-44       1     163 [.     272     440 ..     272     442 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 1e-47
                                   HHHHHHHHHHCC--.GCC--TT-B-EEEE-S..T--SGGGEEEETT-EEE-T.SSEEE-S-EEETS-CHHHHHHHHHHCC- CS
                    ThiP_synth   1 eleralelleeeeefakliPevgsNiayalp..dAksieDvaavpGRIvrvk.grvkvvgepefgasshvarvllaamkfd 78 
                                   e++r+ +++e+ ++f+kliPev+sN+a+++p  + +++eD+a+++ RIv+ + +rvkv  +  fg+ +h+ar+ll++  ++
  gi|70606738|ref|YP_255608.1| 272 EMTRFSQEVESVDGFYKLIPEVQSNLAHSIPsqYVRGLEDIATFRDRIVKNWdNRVKVGLPAVFGKPTHTARLLLSILPYE 352
                                   6899999*********************************************9**************************** PP

                                   TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC..T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSH CS
                    ThiP_synth  79 pevraainirydekilealeelglkvvefdreeepeev..gstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkda 156
                                    ++ +++nir+++ki++ l+e g+++ e++re ep +   g++m+w ++ + e++ ++p+vi+d+G +GkE+mi+ +++++
  gi|70606738|ref|YP_255608.1| 353 TKASVLMNIRFEDKIVNLLKEVGYNTLEINRELEPMSNveGKSMQWIASYIHENYgRIPNVIFDRGVKGKEAMIRFWTSSI 433
                                   ************************************988***********9999999************************ PP

                                   HHHHHHH CS
                    ThiP_synth 157 eevvekv 163
                                   +e+++++
  gi|70606738|ref|YP_255608.1| 434 DEMIDTL 440
                                   ***9987 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.7e-09   1.7e-05     156     282 ..      95     233 ..      83     236 .. 0.85
   2 ?    1.2   0.0     0.041   1.9e+02     191     231 ..     382     421 ..     355     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.7e-09
                                   HHTTE.EEEEECESSSHH....HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGGG CS
                          PfkB 156 knggt.fdpnlldplgaq....fkeallellaladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGke 230
                                   + +    dp+l ++ g q      e  +++l+ +++l+pn  E++ l+g k+ +iee++ a++++ + ++   vvv+ G  
  gi|70606738|ref|YP_255608.1|  95 RDKRVvTDPVLFAKDGTQlikdLEEYKRNILRNTTVLTPNIPEASYLSGLKISSIEEVKLACKTISKDFNiPYVVVKGGHA 175
                                   4444458999999999998886666666777**********************************999999********99 PP

                                   EEEEEE......TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                          PfkB 231 Galvve......kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfa 282
                                      ++       + + ++       ++  t G+G  f+ ++ a l++g+++ +alr a
  gi|70606738|ref|YP_255608.1| 176 EDDYSIdvlydsNRDLYYGIGYMRLNQRHTHGTGSVFATAVSAELSKGNDILTALRHA 233
                                   9999988999865555555666889*****************************9988 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.041
                                   HHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGE CS
                          PfkB 191 eeElealtgekledieealaalhklkakgaktvvvtlGkeG 231
                                    +Ele +++ ++++++ ++ ++h+ +  ++ +v++ +G++G
  gi|70606738|ref|YP_255608.1| 382 NRELEPMSNVEGKSMQWIASYIHE-NYGRIPNVIFDRGVKG 421
                                   47*********************9.44455********998 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.2e-06    0.0097      86     163 ..      93     173 ..      72     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                                   HCHHHCCCCS-EEEEGGGGGSGGGG.....TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTT.EEEEEST CS
                   Carb_kinase  86 lleevlekdeplviDAdgLnllaqkne..lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklna.vvllkge 163
                                    l+ ++   +p++   dg +l+++ +e      ++ ++LTP++ E ++L+++ + + +++  +++++++  n   v++kg 
  gi|70606738|ref|YP_255608.1|  93 YLRDKRVVTDPVLFAKDGTQLIKDLEEykRNILRNTTVLTPNIPEASYLSGLKISSIEEVKLACKTISKDFNIpYVVVKGG 173
                                   566666777888888899999999888767778999******************988899999999999888535777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3120.14
//
Query:       gi|70606739|ref|YP_255609.1|  [L=177]
Description: hypothetical protein Saci_0954 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-14   53.2   0.0    1.2e-13   51.3   0.0    1.8  1  HD_3      HD domain
    3.3e-13   49.8   0.1    6.5e-13   48.8   0.1    1.5  1  HD_2      HD containing hydrolase-like enzyme
    4.6e-06   26.9   0.0    1.3e-05   25.4   0.0    1.8  1  HD        HD domain
    0.00034   20.2   0.0    0.00048   19.6   0.0    1.2  1  HDOD      HDOD domain
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.022   14.6   0.0    1.2  1  zf-ZPR1   ZPR1 zinc-finger domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   3.4e-17   1.2e-13       5     144 ..      11     145 ..       9     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.4e-17
                          HD_3   5 KfqkRqgwlqtgrvr..eesvaeHmwrvalmalllseelkek...vdiarvikmfLiHDlvEiltgDiispdelakeekee 80 
                                   K+  R+gw+q g+     e+++ H+w   ++a+ ++ +lke+   v+ ++++  +++HD+ E+l gD++  ++ +   k+e
  gi|70606739|ref|YP_255609.1|  11 KNLVRTGWMQRGVPGgvGETISQHSWEAGVLAYYIATKLKENgvyVNAEKAVTIAVFHDIGETLLGDLPKWATEKIGNKKE 91 
                                   6778*******9732337*********************9644449**********************9999777777777 PP

                          HD_3  81 eekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqalekegdslaafea 144
                                    e ea+ ril++   +     ++l++E++  +t e+++ak  Dkl + lqal ++++ ++  e+
  gi|70606739|ref|YP_255609.1|  92 LESEAI-RILGI---G-----EELFNEYNS-TTIEGRLAKLCDKLSTYLQALRYSKQGYNVKEI 145
                                   777776.56666...3.....469****76.99*********************9998775544 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.8e-16   6.5e-13      23     162 ..      28     155 ..       6     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.8e-16
                          HD_2  23 eenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireaykevEeeaeekllel 103
                                    e++++Hs+e  ++a+ +a+  +++ g  ++ae+++++a++HD+ E++ GDlp   K a+++i +  ke+E+ea + l   
  gi|70606739|ref|YP_255609.1|  28 GETISQHSWEAGVLAYYIATKLKEN-GVYVNAEKAVTIAVFHDIGETLLGDLP---KWATEKIGN-KKELESEAIRIL--G 101
                                   599***************9955555.67*************************...999999986.588999988755..6 PP

                          HD_2 104 LpeelreeyeelladeeaeeeekklvkaaDklsalikcleelkagnke..Feeakkeieek 162
                                   + eel +ey++ +    +   e++l k +Dkls+++++l+  k+g +     e +k+ +e+
  gi|70606739|ref|YP_255609.1| 102 IGEELFNEYNSTT----I---EGRLAKLCDKLSTYLQALRYSKQGYNVkeIVENYKTELER 155
                                   8999999999887....5...899****************999986431244444443333 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.7e-09   1.3e-05       3     121 ..      33     128 ..      31     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.7e-09
                                   HHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.HH CS
                            HD   3 eHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.le 79 
                                   +Hs+e   la  +a +l+e     + e+++++a +HDiG+ + gd                k++ e++ + ++++  + + 
  gi|70606739|ref|YP_255609.1|  33 QHSWEAGVLAYYIATKLKEngvYVNAEKAVTIAVFHDIGETLLGD--------------LPKWATEKIGNKKELE--SeAI 97 
                                   8*****************************************999..............3455555555555555..2244 PP

                                   HHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  80 dvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                    ++ + +e ++  +             ++e r++kl+D+l++
  gi|70606739|ref|YP_255609.1|  98 RILGIGEELFNEYN-----------STTIEGRLAKLCDKLST 128
                                   67777777777776...........78999999999999875 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-07   0.00048      94     164 ..      30     106 ..      20     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                                   HHHHHHHHHHHHHHHHHHHTT-S-H....HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHHH--..-HHHHHHHH CS
                          HDOD  94 klwehslavAlvarelaeelgledp....eeaflaGLLhdiGklvllsllpeeleellekvaeeel..slleaeeel 164
                                   ++ +hs + +++a  +a++l+ +      e+a++ + +hdiG+ +l +l +   e++ +k + e++  + l + eel
  gi|70606739|ref|YP_255609.1|  30 TISQHSWEAGVLAYYIATKLKENGVyvnaEKAVTIAVFHDIGETLLGDLPKWATEKIGNKKELESEaiRILGIGEEL 106
                                   56799999999999999999777644566*****************9988888888887655433212555555555 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     6e-06     0.022      95     148 ..     111     165 ..      92     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6e-06
                       zf-ZPR1  95 rlttvEGlLeqikeelekeegdqaer...ed.eekekieeflekleeliegeepftli 148
                                   + tt+EG L +++++l++    qa r   +  + ke +e+  ++le++++ eepf+++
  gi|70606739|ref|YP_255609.1| 111 NSTTIEGRLAKLCDKLST--YLQALRyskQGyNVKEIVENYKTELERIVN-EEPFKIV 165
                                   679*************63..3444444434467899999999*******9.99**986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1159.57
//
Query:       gi|70606740|ref|YP_255610.1|  [L=173]
Description: inorganic pyrophosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-58  195.5   0.2    5.2e-58  195.4   0.2    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.2   2.9e-62   5.2e-58       1     159 [.      15     169 ..      15     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 2.9e-62
                                   EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEEE CS
               Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGvl 81 
                                   v+vEip+gsn+Kye+d eeg +++drvl+ts++yp+nYGfip Tle+     DgDPlDvlv+++ +l+pg+v+ev+++G+l
  gi|70606740|ref|YP_255610.1|  15 VLVEIPQGSNIKYEYDDEEGVIKVDRVLYTSMNYPFNYGFIPGTLEE-----DGDPLDVLVITNYQLYPGSVIEVRPIGIL 90 
                                   68*********************************************.....***************************** PP

                                   EEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHHH CS
               Pyrophosphatase  82 amiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeahery 159
                                    m De+++D+Ki+avp++  dp++++i+di+dlp+ ++++i hfFe+yk+le ++k vk+++w +++eA++ i+ a++r+
  gi|70606740|ref|YP_255610.1|  91 YMKDEEGEDAKIVAVPKDktDPSFSNIKDINDLPQATKNKIVHFFEHYKELE-PGKYVKISGWGSATEAKNRIQLAIKRV 169
                                   *****************999**99****************************.77999****************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1211.58
//
Query:       gi|70606741|ref|YP_255611.1|  [L=397]
Description: hypothetical protein Saci_0956 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-24   86.5   0.1    3.7e-24   85.7   0.1    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    6.1e-22   78.6   0.0    8.3e-22   78.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.8e-21   74.8   0.1    9.9e-21   74.3   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-11   44.4   0.0      3e-10   39.9   0.0    2.2  2  Glyco_transf_21  Glycosyl transferase family 21
    1.3e-07   31.4   1.1    3.7e-07   29.9   1.1    1.7  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0025   16.4   1.4     0.0045   15.5   1.4    1.4  1  Cellulose_synt   Cellulose synthase
  ------ inclusion threshold ------
       0.07   13.1   0.0       0.12   12.4   0.0    1.3  1  FIST_C           FIST C domain
       0.12   12.9   4.7        3.8    8.1   0.0    3.2  3  Ribosomal_L6e    Ribosomal protein L6e


Domain annotation for each model (and alignments):
>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.1   1.7e-27   3.7e-24       1     194 [.     102     303 ..     102     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.7e-27
               Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrr 81 
                                   + +++DaD ++++d+l ++++     ++ +++++++++  ++ ++  +a f+   +  +   r++lg +++  Gs +++rr
  gi|70606741|ref|YP_255611.1| 102 YLVFMDADARVNEDFLQRLNN----KDYVACSLKIIIYDTSTSIQSYYAEFTEKVMDMMFKGRSKLGLPIFPNGSAFSIRR 178
                                   5799**********9998854....4678899999999999********9987777777778889**************** PP

               Glyco_trans_2_3  82 salqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....el..........e 147
                                   + l ++ggw+  e +++ED+++g+r++ + ++  f+++++v+ ksp+tl++ ++Q +Rw yG      ++          +
  gi|70606741|ref|YP_255611.1| 179 DTLLSIGGWK--ENAIAEDLELGIRMYLNDLKNLFYDDVVVFLKSPYTLMDLYNQIQRWSYGSsqllkSSlkllkkgikgF 257
                                   **********..**************************************************8765541144553343333 PP

               Glyco_trans_2_3 148 klillvrllgylgsllwsalplhlallllfsllalalvlllllllaa 194
                                   + +l+ +++  +++++++  +   +l+++f+++ ++l+ll+l++++ 
  gi|70606741|ref|YP_255611.1| 258 EGLLYSQQWVIYPLFFTVLGVY-GILTPVFNITQTYLLLLILIYGIS 303
                                   3333444444444444444444.447888888888888887777665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   3.7e-25   8.3e-22       3     230 .]      20     238 ..      17     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 3.7e-25
               Glyco_tranf_2_3   3 dlavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                   +++++V+  +e++ v+++++e+l ++ y r+ev++v d ++ + +e +e +  ++p    r+++++ n  s+gk+ aln a
  gi|70606741|ref|YP_255611.1|  20 TFSIIVAIKDESKqVIESLVENLKRINYERYEVIIVSDDDESKFREYLE-I--KFPE-NFRLIRRESN--SGGKAGALNFA 94 
                                   478888887777755555666666999***********99999999885.4..9998.58***99886..55********* PP

               Glyco_tranf_2_3  83 lravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarral.gv.ltln 161
                                    r+ k+d+++++D+D++v  d+l+rl+     +++ a   +   +  st ++ ++a ef+e  +++++  r++ g  +++n
  gi|70606741|ref|YP_255611.1|  95 SRISKGDYLVFMDADARVNEDFLQRLN----NKDYVACSLKIIIYDTSTSIQSYYA-EFTEKVMDMMFKGRSKlGLpIFPN 170
                                   **********************99955....5677777788888889999998888.*******9998876654888999* PP

               Glyco_tranf_2_3 162 GsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                   Gs + irr+ l  ++g+ + + +++D+elg r+  +  +  ++ +++v   +p +l ++++q +Rw+yg
  gi|70606741|ref|YP_255611.1| 171 GSAFSIRRDTLLSIGGWKE-NAIAEDLELGIRMYLNDLKNLFYDDVVVFLKSPYTLMDLYNQIQRWSYG 238
                                   *******************.***********************************************97 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   4.4e-24   9.9e-21       1     100 [.      22     120 ..      22     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.4e-24
                                   EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH-- CS
               Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglraat 79 
                                   s+++ +  e ++ ++ ++e l+++ +y+++e+i+v D ++ + +e le     ++++r+irre n  Gkagaln + r ++
  gi|70606741|ref|YP_255611.1|  22 SIIVAIKDEsKQVIESLVENLKRI-NYERYEVIIVSDDDESKFREYLEIK--FPENFRLIRRESNSgGKAGALNFASRISK 99 
                                   89**********************.**************88888888877..58*************************** PP

                                   SSEEEEEESSEEE-TTHHHHH CS
               Glycos_transf_2  80 gdyilflDaDdepdpdwlekl 100
                                   gdy++f+DaD  +++d+l++l
  gi|70606741|ref|YP_255611.1| 100 GDYLVFMDADARVNEDFLQRL 120
                                   ******************998 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.047   1.1e+02      20      48 ..      39      67 ..      22      69 .. 0.74
   2 !   39.9   0.0   1.3e-13     3e-10      16     172 ..      85     236 ..      73     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.047
               Glyco_transf_21 20 nnllqaleaakydllvisDsdvrvkpdyL 48
                                  +  l+ +++ +y+++++sD+d    ++yL
  gi|70606741|ref|YP_255611.1| 39 VENLKRINYERYEVIIVSDDDESKFREYL 67
                                  4556667889***********87777777 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.3e-13
               Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa... 93 
                                     K  +l+ a +  k d+lv+ D+d+rv++d+L++l ++     v++   ++++    ++ +   a f + ++ ++     
  gi|70606741|ref|YP_255611.1|  85 GGKAGALNFASRISKGDYLVFMDADARVNEDFLQRLNNKD---YVACSLKIIIYDTSTSIQSYY-AEFTEKVMDMMFKgrs 161
                                   457777777777799*********************9864...477777777766665555544.3444444333333355 PP

               Glyco_transf_21  94 klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                   kl+   f +G++  +rr++L +iGG ++    +AeD++lg ++  + lk  + +++++  + p   +l +l+++  rW+
  gi|70606741|ref|YP_255611.1| 162 KLGLPIFPNGSAFSIRRDTLLSIGGWKE--NAIAEDLELGIRMYLNDLKNLFYDDVVVFLKSP--YTLMDLYNQIQRWS 236
                                   679999**********************..9************************98865554..59999********7 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   1.1   1.6e-10   3.7e-07       2     201 ..      23     204 ..      22     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.6e-10
               Glyco_tranf_2_2   2 vviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska 80 
                                   ++++++ + ++  ie  v  l++ +   e  e+i+v d    kf e ++     n +   +  + ++ ++a a N     +
  gi|70606741|ref|YP_255611.1|  23 IIVAIKDESKQ-VIESLVenLKRIN--YERYEVIIVSDDDESKFREYLEIKFPENFRLI-R-RESNSGGKAGALNFASRIS 98 
                                   55555555444.5666665333444..499*************9998886666676665.3.3356889************ PP

               Glyco_tranf_2_2  81 esdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkff 161
                                   ++d+++F+DaD  +  D ++++ +           +  v+ ++  ++ + s  ++ +   ++  +v++ ++  +s l   +
  gi|70606741|ref|YP_255611.1|  99 KGDYLVFMDADARVNEDFLQRLNN-----------KDYVACSLKIIIYDTSTSIQSYYAEFT-EKVMDMMFKGRSKLGLPI 167
                                   *****************9987766...........334455554455455555555444433.44554556678888999* PP

               Glyco_tranf_2_2 162 apssssilinrraflevGGyDErfrGhgaEDfdlllRlak 201
                                    p++s + i+r ++l +GG+ E+     aED +l +R+ +
  gi|70606741|ref|YP_255611.1| 168 FPNGSAFSIRRDTLLSIGGWKENA---IAEDLELGIRMYL 204
                                   ***********************9...7899999998754 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.4     2e-06    0.0045     416     533 ..     186     298 ..     181     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                Cellulose_synt 416 GwiyGsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkllerl 496
                                   Gw   +++ed+  G +m+ +  + ++       f   +p  l d  +q+ rw+ Gs +++ s    l       +k +e l
  gi|70606741|ref|YP_255611.1| 186 GWKENAIAEDLELGIRMYLNDLKNLFYDDVV-VFL-KSPYTLMDLYNQIQRWSYGSSQLLKSSLKLLKK----GIKGFEGL 260
                                   89999*******************9976554.444.46********************99887666555....59999999 PP

                Cellulose_synt 497 aylnv.iiypftsifllvycilpalsllsgkfivkels 533
                                    y +  +iyp+   +l vy il ++  +++ +++  + 
  gi|70606741|ref|YP_255611.1| 261 LYSQQwVIYPLFFTVLGVYGILTPVFNITQTYLLLLIL 298
                                   99764389**************9999999998775544 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-05      0.12      30      80 ..      73     123 ..      36     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                        FIST_C  30 ggdflvrhllgvdpedgslaladdveeGqrlqlmlrdaealiedlerllee 80 
                                   ++  l+r+  +   + g+l++a+++ +G+ l++m +da   ++ l+rl ++
  gi|70606741|ref|YP_255611.1|  73 ENFRLIRRESNSGGKAGALNFASRISKGDYLVFMDADARVNEDFLQRLNNK 123
                                   4455666666666789**********************9988888888533 PP

>> Ribosomal_L6e  Ribosomal protein L6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.8     0.089     2e+02      49      87 ..       7      45 ..       2      72 .. 0.58
   2 ?    2.0   0.0      0.13     3e+02       6      41 ..     117     159 ..     112     164 .. 0.71
   3 ?    8.1   0.0    0.0017       3.8      70     102 ..     310     341 ..     304     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.089
                 Ribosomal_L6e 49 kkkeeelfeekkekkelseerkadqkavDkallaaikke 87
                                  k++++  f+++k++ ++  + k + k+v ++l++++k+ 
  gi|70606741|ref|YP_255611.1|  7 KDDHKTTFNKHKKTFSIIVAIKDESKQVIESLVENLKRI 45
                                  344556666666666666667777777777776666654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
                 Ribosomal_L6e   6 LrRvnqryVIatstkvdlsgvd.......ekipeklndeyFkk 41 
                                   L+R n++  +a+s k+ + + +       ++++ek+ d +Fk 
  gi|70606741|ref|YP_255611.1| 117 LQRLNNKDYVACSLKIIIYDTStsiqsyyAEFTEKVMDMMFKG 159
                                   7888888888888888887666455556567788888888875 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0017
                 Ribosomal_L6e  70 kadqkavDkallaaikkekllkkYLkskFsLrk 102
                                   + +qk vD ++l++i     +++YLk  F+L+ 
  gi|70606741|ref|YP_255611.1| 310 VLNQKRVDIKILKTILD-ASITGYLKGLFGLKY 341
                                   568************97.67899*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.38s 00:00:01.14 Elapsed: 00:00:00.59
# Mc/sec: 2037.28
//
Query:       gi|70606742|ref|YP_255612.1|  [L=360]
Description: GTPase-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-18   65.1   0.0    8.6e-18   64.2   0.0    1.6  1  TGS            TGS domain
    1.4e-07   31.5   0.1    3.3e-07   30.3   0.1    1.7  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.011   15.9   0.1        1.9    8.7   0.0    2.5  2  YchF-GTPase_C  Protein of unknown function (DUF933)


Domain annotation for each model (and alignments):
>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   1.4e-21   8.6e-18       1      59 [.     287     358 ..     287     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.4e-21
                                   EEEEE.TTSSEEE.....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                           TGS   1 irvyt.PdGkvpd.....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                   irvyt  + ++p      ++rg+tv+++A+k+h +la+ f yA+V+G       q+vg dhvLedgd+veI 
  gi|70606742|ref|YP_255612.1| 287 IRVYTkEPKDKPSmepliVKRGTTVVEVARKLHNELAEGFGYARVWGksvkfpgQKVGADHVLEDGDIVEIH 358
                                   799997666777799*******************************************************96 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   5.5e-11   3.3e-07       3      63 ..     196     256 ..     194     286 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.5e-11
                  MMR_HSR1_Xtn   3 GikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlN 63 
                                   Gi+i +  kl +++e++v++ l+ ++i na v+i ++vt+Dd+   + g   Y+p+++v N
  gi|70606742|ref|YP_255612.1| 196 GIRIVNMGKLVNTNEDDVRRYLEGFGIRNALVKIIGEVTLDDIEREVFGTSLYKPAIIVSN 256
                                   999**999***************************************************98 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00032       1.9      17      43 ..     305     331 ..     297     337 .. 0.91
   2 ?    4.3   0.1    0.0078        46      66      81 ..     342     357 ..     335     359 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00032
                 YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraev 43 
                                   +k+gtt+ + A + H+++ +gF  a+v
  gi|70606742|ref|YP_255612.1| 305 VKRGTTVVEVARKLHNELAEGFGYARV 331
                                   799*******************99988 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0078
                 YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                   + g d+v++dgDi+++
  gi|70606742|ref|YP_255612.1| 342 KVGADHVLEDGDIVEI 357
                                   6799*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2199.29
//
Query:       gi|70606743|ref|YP_255613.1|  [L=212]
Description: ribonuclease HII [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-45  153.7   0.1      6e-45  153.5   0.1    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.1   3.4e-49     6e-45       1     196 [.       4     195 ..       4     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 3.4e-49
                                   EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-HHHHH CS
                     RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinlneik 81 
                                   +GiDEaGrG+++Gp+vva+va++ +  ++l+++gvkDSKkL+ +kre+L+  i    e++++++   ++a  +ei++ +++
  gi|70606743|ref|YP_255613.1|   4 VGIDEAGRGSLIGPMVVAGVAIDSNFLKFLSEIGVKDSKKLTRKKREYLFGVIL---EYSYAISL--VKAYPEEIDSENLN 79 
                                   6****************************************************9...55555544..44667999999999 PP

                                   HHHHHHHHHHHHHT.CEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHHHCS CS
                     RNase_HII  82 aaltlavikllekl.gvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverdeelellkrkpg 161
                                   + ++ a+i+ ++     +++ + vd v+++  +++++ +i +    ve+ ad ky+ v+aASiiAkv rd +++ lk+ +g
  gi|70606743|ref|YP_255613.1|  80 EITYRAMIQIIHSMsVYNPSIVTVDKVGNASAVEREIININS-SPRVENNADVKYVEVSAASIIAKVVRDNIINELKKTYG 159
                                   999*****988877356788999********9**99999998.6789********************************98 PP

                                   H.--TTSSTTSHHHHHHHHHHHHH...S--TTB-TTSH CS
                     RNase_HII 162 tldkgsGyasdektrallkkgats...klpdivrlsfk 196
                                     d+gsGy+ d+kt +++k+           i r+s+k
  gi|70606743|ref|YP_255613.1| 160 --DFGSGYPGDKKTVEWIKDLYSRqptYALPIIRRSWK 195
                                   ..*****************9777645534457788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1361.32
//
Query:       gi|70606744|ref|YP_255614.1|  [L=228]
Description: hypothetical protein Saci_0959 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-43  147.9   2.0    3.6e-43  147.8   2.0    1.0  1  NMD3           NMD3 family
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.11   12.7   0.0    1.4  1  PG_binding_3   Predicted Peptidoglycan domain
       0.13   12.3   0.6        2.4    8.2   0.4    2.5  2  DZR            Double zinc ribbon
        5.4    6.9   6.2         20    5.1   0.1    3.1  3  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   2.0     8e-47   3.6e-43       3     243 .]       2     228 .]       1     228 [] 0.90

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 8e-47
                          NMD3   3 rCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseeveevk 83 
                                    CGke  eli++lC dC++k +++++++++i+ ++Ck Cg+ + +gkW+k+  + ++ l++++++++ +++k++ +v++v+
  gi|70606744|ref|YP_255614.1|   2 SCGKENVELIDRLCIDCYMKIKELITVPTEIQGKYCKVCGSEWVSGKWIKS--ADQDPLTSIVYREIDRNIKTDPNVTDVE 80 
                                   7******************************************999**776..89999*********************** PP

                          NMD3  84 velvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk.relteeehk 163
                                   + +v+++ +  ++   +  + v ++g++ g  ++ ++ + ++ +kv+r  Cp+C r++++yyeai+Q+R+k  e+t++++ 
  gi|70606744|ref|YP_255614.1|  81 YTIVKQW-LDYND---HPFIDVDIRGKI-G--NRDFRLTRTISLKVERVLCPSCLRRKSRYYEAIIQLRTKtGEFTQSKRT 154
                                   **77666.44444...34579999***9.3..46799**********************************7777766666 PP

                          NMD3 164 rtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevg.gkvkeseklvsedkksgkevyrltysvrl 243
                                     + ++++        +++s++ e +eG+D+yf +k  A++lv+ l s++  +k++es +  ++  k+gk++ +l++svr+
  gi|70606744|ref|YP_255614.1| 155 VFESFFNEE-----VINNLSDVIEGREGIDYYFINKGVAKRLVSSLMSTIKdIKITESFQDERM--KNGKKSAKLVISVRI 228
                                   555555555.....5779*******************************988***********9..66************8 PP

>> PG_binding_3  Predicted Peptidoglycan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05      0.11       6      68 ..      84     149 ..      80     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                   HHHHH...T.....S---S---HHHHHHH...HHS-HHHHHHHHHHHHHHHHHHHHHHHHSTHHHH CS
                  PG_binding_3   6 lQriL...gklgydvkvDGiiGpkTlaAvearasadedaLlkainlarrefyldlaerritnerfl 68 
                                     ++L    ++  dv + G+iG++ ++  ++   + e +L+ +   ++ ++y+ +++ r++  +f 
  gi|70606744|ref|YP_255614.1|  84 VKQWLdynDHPFIDVDIRGKIGNRDFRLTRTISLKVERVLCPSCLRRKSRYYEAIIQLRTKTGEFT 149
                                   556665554466789999***********99999**********************9998877775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4   0.00054       2.4       4      37 ..       3      43 ..       1      50 [. 0.73
   2 ?    1.1   0.0     0.091   4.1e+02      28      35 ..     121     128 ..      91     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00054
                           DZR  4 Cgee.lppdarfCseCgtklkavaa......edrCpsCgek 37
                                  Cg+e ++  +r C +C  k+k+  +       + C  Cg++
  gi|70606744|ref|YP_255614.1|  3 CGKEnVELIDRLCIDCYMKIKELITvpteiqGKYCKVCGSE 43
                                  77763456788999999998766557778888999999987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.091
                           DZR  28 edrCpsCg 35 
                                      CpsC 
  gi|70606744|ref|YP_255614.1| 121 RVLCPSCL 128
                                   45677774 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0044        20       4      19 ..       2      18 ..       1      18 [. 0.84
   2 ?    3.1   0.2     0.018        83      15      21 ..      36      42 ..      35      44 .. 0.59
   3 ?    0.2   0.1      0.15   6.8e+02      16      19 ..     124     127 ..     120     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0044
                 zinc_ribbon_2  4 nCGaelqd.nakFCpyC 19
                                  +CG+e+ +  ++ C  C
  gi|70606744|ref|YP_255614.1|  2 SCGKENVElIDRLCIDC 18
                                  7*****87699999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.018
                 zinc_ribbon_2 15 FCpyCGt 21
                                  +C  CG+
  gi|70606744|ref|YP_255614.1| 36 YCKVCGS 42
                                  6666665 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.15
                 zinc_ribbon_2  16 CpyC 19 
                                   Cp C
  gi|70606744|ref|YP_255614.1| 124 CPSC 127
                                   5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1449.43
//
Query:       gi|70606745|ref|YP_255615.1|  [L=102]
Description: hypothetical protein Saci_0960 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-24   85.6   1.0    2.5e-24   85.3   1.0    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   1.4e-28   2.5e-24       5      92 .]      13     100 ..      10     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 1.4e-28
                                   TE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEE CS
                        DUF424   5 dllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvp 85 
                                   d+ +lv++c++e lgktf+e++l+l v+e+f+gg+ ++ e+a++ +++at ++ivg+++v++a+k+G+v+++ V++++g++
  gi|70606745|ref|YP_255615.1|  13 DNYTLVNICERETLGKTFEENNLRLVVNEEFFGGQEVGLEYAFSLINSATAVSIVGNKVVEEAIKRGFVAKEGVIEVKGIK 93 
                                   4559***************************************************************************** PP

                                   EEEEEE- CS
                        DUF424  86 haqigkl 92 
                                   +aqi++l
  gi|70606745|ref|YP_255615.1|  94 FAQIYNL 100
                                   *****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 740.25
//
Query:       gi|70606746|ref|YP_255616.1|  [L=141]
Description: translation initiation factor IF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-31  107.3   0.3    4.9e-31  107.0   0.3    1.1  1  eIF-5_eIF-2B    Domain found in IF2B/IF5
  ------ inclusion threshold ------
      0.014   15.3   0.1       0.47   10.4   0.0    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.016   15.7   0.0      0.029   14.9   0.0    1.5  1  SUI1            Translation initiation factor SUI1
      0.026   14.5   0.4       0.35   10.9   0.0    2.2  2  zinc_ribbon_6   Zinc-ribbon
       0.05   13.3   0.2        2.5    7.9   0.0    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.092   12.5   0.6       0.17   11.6   0.6    1.4  1  Ribosomal_S27e  Ribosomal protein S27


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.3   1.6e-34   4.9e-31       5     117 .]      24     135 ..      21     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.6e-34
                                   CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHH CS
                  eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyie 85 
                                   ++k+ + ++p+l v + g+ +t+i+Nf+e +++++r+++ +++yllkel++ gs+ eng+l+++gkf+++ ++ l++++++
  gi|70606746|ref|YP_255616.1|  24 AQKSGQQNLPNLIVLQVGN-TTIIRNFSEYCDRIRREDKLCMRYLLKELAAPGSLGENGQLVIQGKFSSQVVTMLMERFLK 103
                                   45667889***********.************************************************************* PP

                                   HHTSTSSSTSTCEEECCSSSCEEEEESSSTCE CS
                  eIF-5_eIF-2B  86 eyVlCkeCkspetelekeerllvlkCkaCgak 117
                                    yV+C++C+s +t l++++++++++C aCga+
  gi|70606746|ref|YP_255616.1| 104 MYVQCSTCRSFDTILKRDKKVWIISCLACGAQ 135
                                   ******************************85 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.05   1.5e+02      21      28 ..     105     112 ..      99     115 .. 0.78
   2 ?   10.4   0.0   0.00016      0.47      13      36 .]     118     141 .]     117     141 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.05
                                   EEEESSSS CS
                RNA_POL_M_15KD  21 nfeCrqCg 28 
                                   ++ C++C 
  gi|70606746|ref|YP_255616.1| 105 YVQCSTCR 112
                                   589****7 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                   EEECSCCCEEEESSSS-EEESSCS CS
                RNA_POL_M_15KD  13 pkedkegknfeCrqCgYeepadqf 36 
                                    k+dk++++  C  Cg+  p  qf
  gi|70606746|ref|YP_255616.1| 118 LKRDKKVWIISCLACGAQTPVKQF 141
                                   689*****************9887 PP

>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.7e-06     0.029      32      73 ..      61     100 ..      36     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.7e-06
                          SUI1  32 kklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtek 73 
                                   k  ++ l k++a+ gs  ++g  ++++QG+++ +v+ +L+e+
  gi|70606746|ref|YP_255616.1|  61 KLCMRYLLKELAAPGSLGENG--QLVIQGKFSSQVVTMLMER 100
                                   55678899*********8899..9***************997 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.35      43      58 ..     101     116 ..      96     117 .. 0.86
   2 ?    1.4   0.1      0.11   3.3e+02      26      41 ..     123     138 ..     119     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                 zinc_ribbon_6  43 fhvlglkCkeCgSYNT 58 
                                   f  ++++C++C+S++T
  gi|70606746|ref|YP_255616.1| 101 FLKMYVQCSTCRSFDT 116
                                   55689**********9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.11
                 zinc_ribbon_6  26 kkvkilCnDCekksev 41 
                                   k+  i+C  C++++ v
  gi|70606746|ref|YP_255616.1| 123 KVWIISCLACGAQTPV 138
                                   4556899999998876 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00084       2.5      16      26 ..     107     117 ..     100     119 .. 0.86
   2 ?    3.3   0.1     0.023        68       3      11 ..     129     137 ..     128     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00084
                  Rubredoxin_2  16 rCpsCgsWntl 26 
                                   +C  C+s++t+
  gi|70606746|ref|YP_255616.1| 107 QCSTCRSFDTI 117
                                   9*********8 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.023
                  Rubredoxin_2   3 CsqCGfesa 11 
                                   C +CG++++
  gi|70606746|ref|YP_255616.1| 129 CLACGAQTP 137
                                   999999986 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   5.8e-05      0.17       6      34 ..     104     134 ..      99     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                                   EEEE-TTTS-EEEEESS-SS-..EEESSSTC CS
                Ribosomal_S27e   6 ldvkCpdCenetvvFshaatv..vkCisCgk 34 
                                   + v+C  C    ++  + ++v  + C+ Cg 
  gi|70606746|ref|YP_255616.1| 104 MYVQCSTCRSFDTILKRDKKVwiISCLACGA 134
                                   569************988874449*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1073.43
//
Query:       gi|70606747|ref|YP_255617.1|  [L=421]
Description: hypothetical protein Saci_0962 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-26   91.4   0.3    4.2e-25   89.1   0.1    2.0  2  Radical_SAM  Radical SAM superfamily
    6.8e-24   83.8   0.2    1.2e-23   83.0   0.2    1.4  1  UPF0004      Uncharacterized protein family UPF0004
    6.5e-06   26.0   0.1    1.4e-05   25.0   0.1    1.5  1  TRAM         TRAM domain
     0.0082   16.3   0.1       0.12   12.6   0.0    2.5  2  TRAM_2       TRAM domain
  ------ inclusion threshold ------
       0.19   11.8   2.9       0.97    9.6   0.2    2.8  3  CDC37_C      Cdc37 C terminal domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   9.1e+02      83     105 ..      44      71 ..      21     113 .. 0.70
   2 !   89.1   0.1   1.2e-28   4.2e-25       2     166 ..     137     308 ..     136     309 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                   EECSSCHG.....HHHHHHHHHTT-SEE CS
                                   xxxxxxxx.....xxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd.....eeklerllelgvdrv 105
                                    t++++++     +  +++l++++  r+
  gi|70606747|ref|YP_255617.1|  44 NTCAVRLEteermKQRIKELKKYNDKRL 71 
                                   4444444444445556666666654333 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 1.2e-28
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.........TTHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.........pdfvellerlakl 73 
                                   ++  gC+++C+fC+++     +++ rs ++  i+e v+ + ++kg+ e+ l+g++  +y         +d+v+++ +    
  gi|70606747|ref|YP_255617.1| 137 PIADGCAGDCNFCITKL---ARRKLRSYPPHLIVESVRDA-VRKGAVEIELSGQDTAAYgldlgqiklSDLVRKVTEVEGD 213
                                   5789************9...8*******************.9******************999999988888888888888 PP

                                   CCCTEEEEEEECSSCHG..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEE CS
                                   xxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
                   Radical_SAM  74 avpgiritvetngtlpd..eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdr 148
                                       iri + t++   +  + ++e l+e      ++l+++++dd  vlklmnr++t++e++++++ +r++ ++    ++d+
  gi|70606747|ref|YP_255617.1| 214 --FMIRIGMMTPEQAMRdiDGIIEVLRETKvYKFIHLPVQSGDDN-VLKLMNRKYTVDEYKDLVKEIRKK-VPIvniTTDI 290
                                   ..7************99****************************.************************.********** PP

                                   EEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 149 ivglpGendeeleellel 166
                                   i+g+pGe +  ++++lel
  gi|70606747|ref|YP_255617.1| 291 IIGHPGEDENAFRNTLEL 308
                                   ***************987 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.2   3.4e-27   1.2e-23       1      95 [.       2      94 ..       2      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 3.4e-27
                                  XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-H CS
                       UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrek 83
                                  +v+iet+GC  N+ ds ++++lL+++g+e+v++ ++A+++++nTCavr ++e+++ q+++elk+ +  +k++vv+GC+a++e+
  gi|70606747|ref|YP_255617.1|  2 RVYIETYGCALNKGDSYIMMTLLRDKGHEIVDNIQDAEILVINTCAVRLETEERMKQRIKELKKYN--DKRLVVAGCLASAEP 82
                                  79***************************************************************9..79************* PP

                                  HHHHHH-TTS-E CS
                       UPF0004 84 eellkeepevdl 95
                                  + +++ +pe+ +
  gi|70606747|ref|YP_255617.1| 83 AVVVSLAPEASV 94
                                  999999998554 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   3.8e-09   1.4e-05      13      61 ..     373     419 ..     363     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.8e-09
                                   EEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
                          TRAM  13 eglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                                   ++ + ++g  iGrt n+ +v+++  + ++G++ +V+I ++ ++ LrGe+
  gi|70606747|ref|YP_255617.1| 373 TEYG-RKGSVIGRTLNYIPVVIRQ-NVELGKRINVRINEASFYDLRGEP 419
                                   6667.89*****************.999*******************97 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.17   6.2e+02      24      39 ..     225     241 ..     211     254 .. 0.81
   2 !   12.6   0.0   3.3e-05      0.12      34      64 .]     393     420 ..     370     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.17
                                   S-T.TTS--EEEES--- CS
                        TRAM_2  24 dAP.EvDgevyvtgaek 39 
                                   +A  ++Dg + v  ++k
  gi|70606747|ref|YP_255617.1| 225 QAMrDIDGIIEVLRETK 241
                                   67779*****9997765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.3e-05
                                   EES---T...T-EEEEEEEEEETTEEEEEE- CS
                        TRAM_2  34 vtgaeklskvGdfvkvkItdadeyDLiGevv 64 
                                   ++++   ++ G+ ++v+I +a+ yDL Ge +
  gi|70606747|ref|YP_255617.1| 393 IRQN---VELGKRINVRINEASFYDLRGEPI 420
                                   4433...236*******************87 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00027      0.97      48      89 ..      26      68 ..      19      72 .. 0.82
   2 ?   -1.5   0.1      0.79   2.8e+03      47      80 ..     267     301 ..     227     310 .. 0.55
   3 ?    0.9   0.0      0.14     5e+02       8      43 ..     337     372 ..     333     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                       CDC37_C 48 eeAeeilellgeagilsleellvdatteeg.ekelkeleeekk 89
                                  ++  ei++ +++a+il ++   v+ +tee  ++++kel++ + 
  gi|70606747|ref|YP_255617.1| 26 DKGHEIVDNIQDAEILVINTCAVRLETEERmKQRIKELKKYND 68
                                  56789*******************9998862667888887654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.79
                       CDC37_C  47 veeAeeilell.geagilsleellvdatteegeke 80 
                                   v+e +++++ + ++  i+++   ++     e+e+ 
  gi|70606747|ref|YP_255617.1| 267 VDEYKDLVKEIrKKVPIVNITTDIIIGHPGEDENA 301
                                   33333333332123344444444444444555555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.14
                       CDC37_C   8 edpeeqkkvevFeklppelqkAlktksLdevnkvla 43 
                                    dp +++++++ +kl +el   +++  L+ +  v++
  gi|70606747|ref|YP_255617.1| 337 PDPVKKERIQIANKLYEELAYEIHSDYLNSIASVIT 372
                                   599999*************99999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2556.40
//
Query:       gi|70606748|ref|YP_255618.1|  [L=392]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-87  291.1   0.6    8.4e-87  290.8   0.6    1.1  1  Thiolase_N     Thiolase, N-terminal domain
    5.4e-35  119.7   0.0    1.2e-34  118.6   0.0    1.6  1  Thiolase_C     Thiolase, C-terminal domain
    2.2e-05   24.2   1.7    4.4e-05   23.2   1.6    1.6  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.8   0.6   1.4e-90   8.4e-87       1     260 []       4     262 ..       4     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 290.8 bits;  conditional E-value: 1.4e-90
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+ivsa+rtp+gkfggslkd+s +eL++ ++++++++a+vdp+ +d vi+Gnvl ag+gq +arqa++kagip ++ a  v
  gi|70606748|ref|YP_255618.1|   4 VYIVSAVRTPLGKFGGSLKDISPSELGSVVIREAVNRAKVDPKLIDIVIMGNVLRAGHGQDLARQASIKAGIPAKTDAYCV 84 
                                   89******************************************************************************* PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEE...EHHHHHHTEETTTTSEHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekak...dllipdgladafneehmGlta 159
                                   ++vcsSg+ + ++a+q+i++ +ad+vvagG+Esms+a+ a  +++r+g+k+  +k     d++i dgl+d fn + mG  a
  gi|70606748|ref|YP_255618.1|  85 DMVCSSGMISTINAVQMIKSEDADIVVAGGMESMSRASFAIGSEIRWGTKMLMNKSLdiiDTMIIDGLTDPFNFKVMGQEA 165
                                   ***********************************************9999887765111678889*************** PP

                                   HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-B CS
                    Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvt 240
                                   +++a++++i+R+e+de+A +sh++a  a+++g FkdeivP++v+g+    +vdkde+ir+++t+ekL +lkpaF ++G  t
  gi|70606748|ref|YP_255618.1| 166 DMVAREHEITRRELDEVAYESHRRATIATEKGYFKDEIVPLNVDGR----VVDKDEGIRADTTLEKLLQLKPAFGSDGLHT 242
                                   *******************************************994....7****************************** PP

                                   TTSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 241 AgnasqisDGaaavllmses 260
                                   Agn+sqisDGaaa++++ses
  gi|70606748|ref|YP_255618.1| 243 AGNSSQISDGAAALVFVSES 262
                                   *****************996 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0     2e-38   1.2e-34       2     122 ..     270     390 ..     269     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 2e-38
                                   --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B-T CS
                    Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHPl 82 
                                   +p+a++  y+  g +  ++  +P+y +kk+l+k  + +++ d+fE nEAFa+  +  ++ l++ ++++Nv+GGaialGHP+
  gi|70606748|ref|YP_255618.1| 270 EPIARVLGYSWIGIESWKFPEAPIYSVKKLLDKINIPLSKFDYFENNEAFAVNNVLFNRYLGVSYDRLNVYGGAIALGHPI 350
                                   689****************************************************************************** PP

                                   TTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                    Thiolase_C  83 GasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                   GasG+Ri+vtll+ l+k +gk+g+a++C g g ++a+ +e
  gi|70606748|ref|YP_255618.1| 351 GASGSRILVTLLNVLRKMNGKYGIASICHGIGGSTAIAVE 390
                                   ************************************9987 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.6   7.4e-09   4.4e-05     168     216 ..      81     128 ..      63     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.4e-09
                                   EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHH CS
                 ketoacyl-synt 168 svtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsa 216
                                   +++vd  CsS+      avq+++s +ad+++aGG+e +++  ++a  s+
  gi|70606748|ref|YP_255618.1|  81 AYCVDMVCSSGMISTINAVQMIKSEDADIVVAGGME-SMSRASFAIGSE 128
                                   789********77777777*****************.555555655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3212.03
//
Query:       gi|70606749|ref|YP_255619.1|  [L=108]
Description: translation initiation factor IF-1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-23   81.1   0.3    5.2e-23   80.6   0.3    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.3   2.9e-27   5.2e-23       1      64 []      21      83 ..      21      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 2.9e-27
                                  EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                        eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                  gevi++V ++ g+ +++V ++d gke+l++ipgk+++k+wi++Gd+Vl  +++++++k++Ivyr
  gi|70606749|ref|YP_255619.1| 21 GEVICVVKKLFGGEHVQVICTD-GKERLGRIPGKLKKKVWIREGDVVLAAPWDFQPNKCDIVYR 83
                                  69******************96.****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 699.30
//
Query:       gi|70606750|ref|YP_255620.1|  [L=251]
Description: hypothetical protein Saci_0965 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-63  212.5   0.2    5.4e-63  212.0   0.2    1.2  1  RIO1            RIO1 family
     0.0041   17.1   0.0      0.018   14.9   0.0    1.9  2  APH             Phosphotransferase enzyme family
     0.0065   15.8   0.0      0.052   12.9   0.0    2.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.024   13.4   0.2      0.033   13.0   0.2    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.2   1.2e-66   5.4e-63       1     187 [.      57     243 ..      57     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 1.2e-66
                                   EEEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                          RIO1   1 nVyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                   ++y a +e+++ +a+Kiy +st++ k+ +++y+ g++rf+     +n++kl+++wa+kEf+nL++++++gv+vPkpi +++
  gi|70606750|ref|YP_255620.1|  57 KIYPALTESEEWYAVKIYYVSTASSKRaIERYTFGDPRFEGV-RASNTLKLIEVWAKKEFKNLSKMYDSGVSVPKPIYVHK 136
                                   59***********************999************77.69************************************ PP

                                   TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHH CS
                          RIO1  81 hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnal 161
                                   ++l+mefig++g++ap lk++++e+ +e+ly+++++++ ++ ++a+lvH+DLSeyN++v ++k++iIDvsQa++l+hpna+
  gi|70606750|ref|YP_255620.1| 137 NILIMEFIGDNGIRAPLLKELRSEDVNEDLYKTIIDQVVIMANKAELVHGDLSEYNIMVFDGKPYIIDVSQAIDLTHPNAR 217
                                   **********************9999******************************************************* PP

                                   HHHHHHHHHHHHHHHTTC-----HHH CS
                          RIO1 162 efLerDveniikfFrrkgvekvdeee 187
                                   efL rD++ni+ fF+++g++ ++e e
  gi|70606750|ref|YP_255620.1| 218 EFLVRDIRNINSFFMNNGINVMSETE 243
                                   *******************9887765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.3   1.4e+03      39      60 ..     113     134 ..     109     145 .. 0.79
   2 !   14.9   0.0   4.1e-06     0.018     142     192 ..     155     204 ..     145     209 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHTT-B--B-CTT CS
                           APH  39 revallrlLakagvpvPevlag 60 
                                   +e++ l  + ++gv+vP++++ 
  gi|70606750|ref|YP_255620.1| 113 KEFKNLSKMYDSGVSVPKPIYV 134
                                   677788889999*******994 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.1e-06
                                   CC.HHHHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE-- CS
                           APH 142 ld.lleeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviD 192
                                   ++ + e++ e ++ ++ + +   + ++ l+HgDl+  N++v   dg+  ++iD
  gi|70606750|ref|YP_255620.1| 155 KElRSEDVNEDLYKTIIDQVVImANKAELVHGDLSEYNIMVF--DGKP-YIID 204
                                   4444445555566666666666788899**************..6665.79*9 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.2e-05     0.052      51      99 ..     104     144 ..      72     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                           Kdo  51 fklgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterl 99 
                                   +kl +  a +Ef++l ++++ gv vpkp++            +l++e +
  gi|70606750|ref|YP_255620.1| 104 LKLIEVWAKKEFKNLSKMYDSGVSVPKPIYVHK--------NILIMEFI 144
                                   5566677899*******************9764........34555544 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   7.4e-06     0.033     322     369 ..     177     218 ..     150     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-06
                Pkinase_fungal 322 LflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddsses 369
                                   + +ka+++H D Se+Ni++       + k  +iD+  a++l ++++++
  gi|70606750|ref|YP_255620.1| 177 MANKAELVHGDLSEYNIMVF------DGKPYIIDVSQAIDLTHPNARE 218
                                   457899**************......7889999999999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1675.11
//
Query:       gi|70606751|ref|YP_255621.1|  [L=178]
Description: putative RNA-processing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00016   21.5   6.6    0.00055   19.7   1.6    2.4  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.2    0.0022        40      23      50 ..      18      39 ..      17      56 .. 0.71
   2 !   19.7   1.6   3.1e-08   0.00055      10      65 ..      96     143 ..      89     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0022
                                  HHHHHHHT-EEEEES.STT...T.-EEEE CS
                          KH_1 23 keIreetgakIkvpk.sedegsderevti 50
                                  k+I+e +++ I++++         +++++
  gi|70606751|ref|YP_255621.1| 18 KRIEEISNTTINFDEvT-------KQIRV 39
                                  89**********98422.......34444 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 3.1e-08
                                   HHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                          KH_1  10 lvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                     gr+IG +G++ + I+e tg+ + v         + e+ + G+ e+   Ak++ie
  gi|70606751|ref|YP_255621.1|  96 IKGRVIGEKGKTKRTIEEYTGVIVLVK--------DHEIGLLGNIEQLSIAKRAIE 143
                                   569***************99**87765........347999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1193.86
//
Query:       gi|70606752|ref|YP_255622.1|  [L=181]
Description: hypothetical protein Saci_0967 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.3   0.1       0.01   15.8   0.0    1.8  2  DUF3883   Domain of unknown function (DUF3883)


Domain annotation for each model (and alignments):
>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.27   4.9e+03      56      69 ..      12      25 ..       8      30 .. 0.73
   2 !   15.8   0.0   5.8e-07      0.01      27      54 ..      57      82 ..      33      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.27
                       DUF3883 56 kdfelsrnElefaq 69
                                  +++ l+  E+e+a 
  gi|70606752|ref|YP_255622.1| 12 QEYDLTDDEIEYAI 25
                                  56678888888885 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.8e-07
                       DUF3883 27 dglgYDiesvdkedgeerfIEVKttakg 54
                                  d   +Die+ +  dg++ ++EVK+t+k+
  gi|70606752|ref|YP_255622.1| 57 DLPTHDIEAEK--DGSKYYVEVKATKKS 82
                                  55679*****9..9***********954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1263.51
//
Query:       gi|70606753|ref|YP_255623.1|  [L=330]
Description: hypothetical protein Saci_0968 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     2e-115  385.0   0.1   2.3e-115  384.9   0.1    1.0  1  DUF1152   Protein of unknown function (DUF1152)
  ------ inclusion threshold ------
       0.12   12.8   0.4       0.31   11.4   0.4    1.8  1  HHH_8     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.9   0.1  2.6e-119  2.3e-115       1     294 [.       4     296 ..       4     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 384.9 bits;  conditional E-value: 2.6e-119
                       DUF1152   1 LvlgiGGGGDvvsalvlaellkklgveavlgsvvWeRlvvDplPGPisleelegveaineavaivnaesrairgarsvlpq 81 
                                   +++g+GGGGDvvsa++++e++k+lg++++lg+v+WeR+v+DplPGPi+  e+ +++++n++++++n+es++ir++r v+pq
  gi|70606753|ref|YP_255623.1|   4 FIFGLGGGGDVVSAYIAYEYYKRLGYDTILGAVTWERYVEDPLPGPIC--EFMNADNLNDVITKLNKESYSIRNGRVVIPQ 82 
                                   68**********************************************..******************************* PP

                       DUF1152  82 larvakvln.eevvlldikkgveglaealeelaeklgidliigvDvGGDvLAkGdEegLrSPLaDalslAalskleeesvl 161
                                   +++v+kvln +e ++++i++g +++a+ ++e+a k+gid+i+gvD+GGDvLAkG+Ee+L SPL+D+++l +l++++++svl
  gi|70606753|ref|YP_255623.1|  83 IVKVLKVLNiSEGYSICIREGIRKIARMIDEFALKEGIDVIVGVDAGGDVLAKGCEETLGSPLIDFIMLNVLTETKTKSVL 163
                                   *********99********************************************************************** PP

                       DUF1152 162 avaGpGsDGELseeelleriseiakeggllgilgldeedaellekileeveteAskiplaaakGlrGeveiRkgtrkvelt 242
                                   a +G+GsDGEL+++++l+ri+eia++ggl +i+g+de   ++l++il+ v+teAskipl+a++Gl+Gev+iR++tr+v +t
  gi|70606753|ref|YP_255623.1| 164 ATIGAGSDGELQQDYILRRIAEIATKGGLKDIKGIDEAISRKLDEILSVVTTEASKIPLEAFRGLYGEVSIRNNTRRVFVT 244
                                   ********************************************************************************* PP

                       DUF1152 243 plsalvfyldpkavaelsklaklvagtesleeAeerlnelgiytEldlErdl 294
                                   p+sa++f+++pk+v+e+s++ak+++++esle+A+e+ln++g+ytE+++E dl
  gi|70606753|ref|YP_255623.1| 245 PISAVMFFMEPKIVYETSPIAKVIKDSESLEDANEKLNKMGVYTEYNFELDL 296
                                   *************************************************987 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   3.4e-05      0.31      41      67 ..     185     210 ..     179     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                                   -HHHHTTHCTTSTT--HHHHHHHHHHH CS
                         HHH_8  41 eitsleeeltklpgiGkkiaakieeil 67 
                                   ei++ +++l++++gi ++i +k++eil
  gi|70606753|ref|YP_255623.1| 185 EIAT-KGGLKDIKGIDEAISRKLDEIL 210
                                   3444.668******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2443.66
//
Query:       gi|70606754|ref|YP_255624.1|  [L=178]
Description: hypothetical protein Saci_0969 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1261.57
//
Query:       gi|70606755|ref|YP_255625.1|  [L=104]
Description: hypothetical protein Saci_0970 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 684.06
//
Query:       gi|70606756|ref|YP_255626.1|  [L=373]
Description: hypothetical protein Saci_0971 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-121  404.3   0.1   4.3e-121  404.1   0.1    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.9e-10   39.9   0.1    2.5e-09   36.8   0.1    2.1  1  Aminotran_1_2    Aminotransferase class I and II
    8.7e-08   31.5   0.3    4.4e-07   29.2   0.3    2.0  1  Aminotran_5      Aminotransferase class-V
      0.007   15.7   0.0        0.1   11.9   0.0    2.1  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.018   13.5   0.2        1.1    7.7   0.2    2.1  1  Met_gamma_lyase  Methionine gamma-lyase
      0.029   13.4   0.2        0.3   10.0   0.2    2.7  1  SelA             L-seryl-tRNA selenium transferase
      0.093   11.4   0.3       0.13   10.9   0.3    1.5  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
       0.14   11.7   0.0       0.27   10.8   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.1   0.1  1.9e-124  4.3e-121      11     381 ..      12     370 ..       5     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.1 bits;  conditional E-value: 1.9e-124
                                   CHTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TT CS
               Cys_Met_Meta_PP  11 kdeqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaG 91 
                                   +de+tga+++piy+t++++f           +++ Y+R  npt+  l e ia Le++e ++++ssGm+Ai+++ ++llk  
  gi|70606756|ref|YP_255626.1|  12 TDEKTGAITTPIYQTTSFEFP--------IGEKFRYTREANPTVLKLAEMIASLEEAEMGVVFSSGMGAISTVAFTLLKPN 84 
                                   5789*****************........445699********************************************** PP

                                   EEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEE CS
               Cys_Met_Meta_PP  92 deivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvv 172
                                   + +++++d++g +++++++++k++g+++++ ++   e +eka +++ ++v++E+++np+l+vvD++++ak++k+++vl+vv
  gi|70606756|ref|YP_255626.1|  85 SSVLIHRDMFGRSYKFFTEFMKNWGVRAEVAEP--GEVIEKAKEKKYDMVFVESISNPTLRVVDLPELAKICKENNVLLVV 163
                                   ******************************999..78899***************************************** PP

                                   EGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHHHHHTTHHHHH CS
               Cys_Met_Meta_PP 173 DntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlllrGlkTLslRl 253
                                   D tfa+p++q+p+  ga ivvhS++K+++Gh+dv++Gv++ ++  el++++  + ++lG   +p++++l++rG+kTL++R+
  gi|70606756|ref|YP_255626.1| 164 DGTFATPINQKPIVQGANIVVHSGSKFIAGHNDVIIGVACGNN--ELMNKIDLTRRSLGTSADPHASYLTIRGMKTLKVRM 242
                                   ****************************************766..9*********************************** PP

                                   HHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SSSEECSS-SSSS-E CS
               Cys_Met_Meta_PP 254 erhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlklfslaeslGgvesl 334
                                   +  ++nA+k+AefL++hpk+++vyYpg++ hp++++a++ lk  ggv+sFe+k+++e + k++++l+++  a+ lGgv+s 
  gi|70606756|ref|YP_255626.1| 243 DVINSNAQKIAEFLQEHPKISRVYYPGIKVHPDYNTARRVLKANGGVVSFEIKGSQEDSIKLMNRLNVILSAQTLGGVNST 323
                                   ********************************************************************************* PP

                                   EEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
               Cys_Met_Meta_PP 335 ielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                   i++pa+m+h+s+++eer+ ag+t++++RlsvGiE+++Dli+Dl++al
  gi|70606756|ref|YP_255626.1| 324 ISHPATMSHRSLTPEERKLAGITPNMLRLSVGIEEIEDLIEDLDRAL 370
                                   **********************************************9 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   1.1e-12   2.5e-09      65     266 ..      58     237 ..      37     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.1e-12
                                   TTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHH..HHHTTHH CS
                 Aminotran_1_2  65 lkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldleale..ealkeap 143
                                   +++e  vv++sG ga+  ++++llk  p + +l+++  ++   + +        ++     +++++ +e  e  e +++a+
  gi|70606756|ref|YP_255626.1|  58 EEAEMGVVFSSGMGAISTVAFTLLK--PNSSVLIHRDMFGRSYKFF-------TEFM----KNWGVRAEVAEpgEVIEKAK 125
                                   347789******************9..9999999877665444433.......3333....44444444444225666665 PP

                                   CTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT. CS
                 Aminotran_1_2 144 egnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf. 223
                                   e++    +++ves++NPt  v +l+el k+   +k++n+ll+vD ++a+   +        + v+   n ++v s sK   
  gi|70606756|ref|YP_255626.1| 126 EKKY--DMVFVESISNPTLRVVDLPELAKI---CKENNVLLVVDGTFATPINQ-------KPIVQG-AN-IVVHSGSKFIa 192
                                   5555..9***********************...**************998888.......444444.46.78888888774 PP

                                   SSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHH CS
                 Aminotran_1_2 224 GlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsd 266
                                   G     +G ++gn ++ + +    r++    + ++++++   +++
  gi|70606756|ref|YP_255626.1| 193 GHNDVIIGVACGNNELMNKIDLTRRSLGTsaDPHASYLTIRGMKT 237
                                   555566677777777777766666655444455555555555555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.3     2e-10   4.4e-07      47     362 ..      49     357 ..      34     366 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2e-10
                                   HHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCB CS
                   Aminotran_5  47 earekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegel 127
                                   +  e +a l +ae    ++f sG + ai++va +l   lkp  ++++ +           e +k  g++ +v++    ge+
  gi|70606756|ref|YP_255626.1|  49 KLAEMIASLEEAEM--GVVFSSGMG-AISTVAFTL---LKPNSSVLIHRDMFGRSYKFFTEFMKNWGVRAEVAEP---GEV 120
                                   44555666666664..788888888.999999999...9999999998755444444688888899999988887...544 PP

                                   EGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---.HHHHTESEEEEETTT.TTSST CS
                   Aminotran_5 128 dldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipid.vkklgvDflafsghK.llgPt 206
                                       +ek+ ++k+++v++  +sn t  + +++e++k++k++++l++vD++ a +  +   v+  g+ +++ sg K + g +
  gi|70606756|ref|YP_255626.1| 121 ----IEKAKEKKYDMVFVESISNPTLRVVDLPELAKICKENNVLLVVDGTFATPINQKPiVQ--GANIVVHSGSKfIAGHN 195
                                   ....56777899*************************************9887755444044..5556*******555555 PP

                                   T..-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHH..HCHHHHHHHHHHHHH CS
                   Aminotran_5 207 G..iGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyl..eeigleaiekhekel 283
                                      iGv ++ +el +k+  +  + ++ +          ++   +      + g+  l+  ++ +  +++++++  +++ + 
  gi|70606756|ref|YP_255626.1| 196 DviIGVACGNNELMNKIDLTRRSLGTSA----------DPHASY----LTIRGMKTLKVRMDVInsNAQKIAEFLQEHPKI 262
                                   4558************944333333222..........233333....357788888888888876778899999999999 PP

                                   HHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEE....E-TTT..HHH.HHHTT.S..... CS
                   Aminotran_5 284 aeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrs....Ghhca..qpl.mkrlale..... 352
                                   +   + ++k  p+++++  ++ +++ ++vsf +kg + + + +l+++ ++ +++    G +++  +p+ m++++l+     
  gi|70606756|ref|YP_255626.1| 263 SRVYYPGIKVHPDYNTAR-RVLKANGGVVSFEIKGSQEDSI-KLMNRLNVILSAqtlgGVNSTisHPAtMSHRSLTpeerk 341
                                   999999999999999977.7999999999999998776555.567777888777777444443333321344444466666 PP

                                   ......-EEEEE--TT CS
                   Aminotran_5 353 ......gtvRaSlyiy 362
                                         +++R+S +i 
  gi|70606756|ref|YP_255626.1| 342 lagitpNMLRLSVGIE 357
                                   6666666666666665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   4.5e-05       0.1      29      86 ..      42     103 ..      12     189 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                                   T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT....-HHHHSS CS
               Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtep....ahihfde 86 
                                   + ++tv +L++ +a l ++e ++ + +G +A s    +ll+++++v+++++    +  +f+e
  gi|70606756|ref|YP_255626.1|  42 EANPTVLKLAEMIASLEEAEMGVVFSSGMGAISTVAFTLLKPNSSVLIHRDmfgrSYKFFTE 103
                                   4689******************************************9998855443333333 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00048       1.1      71     112 ..      58     102 ..      42     286 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00048
               Met_gamma_lyase  71 eaalvrpqlvsGthaiatalfgvlrpgdella...itGkPydtle 112
                                   e+a + + + sG  ai+t+ f+ l+p+  +l    + G+ y  + 
  gi|70606756|ref|YP_255626.1|  58 EEAEMGVVFSSGMGAISTVAFTLLKPNSSVLIhrdMFGRSYKFFT 102
                                   555555667777777777777777777766641112333333332 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00014       0.3     189     234 ..     165     213 ..      11     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                                   T-----BHHHHHHTT-SEEEEETTSTT-SSS...-EEEEE-HHHHHHHH CS
                          SelA 189 glskePtvqealaeGvdlvsfsGDkllGgpq...aGiivGkkelieklk 234
                                   g    P  q+ + +G+++v  sG k++ g      G+  G+ el++k++
  gi|70606756|ref|YP_255626.1| 165 GTFATPINQKPIVQGANIVVHSGSKFIAGHNdviIGVACGNNELMNKID 213
                                   55567999999****************9976222577789999999885 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   5.7e-05      0.13     147     196 ..     120     169 ..     103     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
                                   HHHCCTCCCEEEE.EECSSTTTTB----HHHHHHHHHCCT--EEEEGCCCC CS
                       SepSecS 147 iiekkreevilav.lstlsffaprspDdvkeiakiCaeydvPhlvNgAYai 196
                                   +iek +e    +v +   s  + r+ D ++e+akiC+e +v ++v g +a 
  gi|70606756|ref|YP_255626.1| 120 VIEKAKEKKYDMVfVESISNPTLRVVD-LPELAKICKENNVLLVVDGTFAT 169
                                   343333333333303344444558888.*******************9986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.27      74     126 ..     119     168 ..     101     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                   HHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBH CS
                         SRP54  74 eavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattg 126
                                   e +ekake+k+d+v+v +     n +  + +l +++k++k+++vllv+d+t  
  gi|70606756|ref|YP_255626.1| 119 EVIEKAKEKKYDMVFVES---ISNPTLRVVDLPELAKICKENNVLLVVDGTFA 168
                                   6799************97...67788888999999999***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2384.67
//
Query:       gi|70606757|ref|YP_255627.1|  [L=306]
Description: homoserine kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-13   48.7   3.4    1.8e-12   47.3   3.4    1.8  1  GHMP_kinases_N  GHMP kinases N terminal domain
    2.8e-08   34.0   0.1    9.6e-08   32.3   0.0    1.9  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   3.4     2e-16   1.8e-12       3      66 .]      78     143 ..      76     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2e-16
                                   EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                   ++ + iP g GLGSS+A ava+v+ +++ll l l++   ++ +  +e +   g+ ++++vaasvyGg
  gi|70606757|ref|YP_255627.1|  78 KVIKGIPAGLGLGSSGASAVAAVVGVNNLLKLGLDKqelVRASMIGEIASS-GSAHPDNVAASVYGG 143
                                   68899*************************9998333579*9*****7666.**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.71   6.3e+03      49      65 ..      87     100 ..      81     120 .. 0.70
   2 !   32.3   0.0   1.1e-11   9.6e-08       5      76 ..     209     275 ..     205     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.71
                GHMP_kinases_C  49 lgaklsGaGgGptvfal 65 
                                   lg + sGa   ++v+a+
  gi|70606757|ref|YP_255627.1|  87 LGLGSSGA---SAVAAV 100
                                   67777777...555555 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.1e-11
                GHMP_kinases_C   5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                   l +gd ell+ +ln+      +  + +l+p+ e+l+++  e+ a+ga++sGa  Gpt+++++++ ++ ++++
  gi|70606757|ref|YP_255627.1| 209 LVKGDRELLRLGLNDEIV---EVARSPLFPHYEKLKKISIENNAIGACVSGA--GPTIAVFVDEYSDKNKIK 275
                                   678889999999996555...559****************************..********6666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2120.19
//
Query:       gi|70606758|ref|YP_255628.1|  [L=541]
Description: putative molybdopterin biosynthesis protein MoeA/unknown domain fusion protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-35  121.7   0.0    5.4e-35  120.5   0.0    1.7  1  MoeA_N         MoeA N-terminal region (domain I and II)
    5.9e-26   90.8   0.1      1e-25   90.1   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
    6.1e-14   52.0   0.0    1.8e-13   50.4   0.0    1.8  1  MoeA_C         MoeA C-terminal region (domain IV)


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   9.1e-39   5.4e-35       4     157 .]      14     170 ..      11     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 9.1e-39
                                   HHHHHHHHHH-HH..-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............-S---T CS
                        MoeA_N   4 eealaiilaalel..eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep.saageeperllp 80 
                                   ++ala++l+++ +   e e ++l +++l+r++aed+++++++Ppf +S++DG+A++ +   g+ ++   ++ ge +e  + 
  gi|70606758|ref|YP_255628.1|  14 QDALAKFLNEFGVkqLEVErINL-EDSLNRIVAEDIISDIPLPPFSRSTVDGFAIKHDLCPGEFTVIDkIRIGEFKEIRIG 93 
                                   67888888888444645555999.99*****************************98887777666558888888888888 PP

                                   T-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                        MoeA_N  81 gg.avrimTGaplPegadaVvpvEdte.eeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                   +g av++ TG+p+Pega+aVv+vE+t  e   ++ v+v k+ + gen+  +G di +G++++r+g+rl+p +i+llas+G
  gi|70606758|ref|YP_255628.1|  94 NGeAVEVDTGSPIPEGATAVVKVENTViEG--NK-VKVsKKLSFGENIGWIGTDIPKGTLVVRRGERLNPYKIALLASIG 170
                                   888**********************96532..23.333599*************************************98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.1   1.7e-29     1e-25       2     139 ..     184     315 ..     183     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 1.7e-29
                                   EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HH CS
                 MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtp 75 
                                   +i++Gdel+       +gki+ +n+++l+++  + g++v+k+t+v Dd+e i++++l+ +e+ad++i+tGG +++++D+++
  gi|70606758|ref|YP_255628.1| 184 IIITGDELVepgkdldPGKIYESNSYYLQAYYLSKGYDVIKRTHVNDDKELIRREILEGIEKADIVIVTGGSSAGEKDYVH 264
                                   8******************************************************************************** PP

                                   HHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHH CS
                 MoCF_biosynth  76 ealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeill 139
                                   +++++ ++       +++++++ kpgkp ++a +   +   gk+++gLPG+  + +++ ee++ 
  gi|70606758|ref|YP_255628.1| 265 QVIKEEGK-------IIVHGLKIKPGKPAILAEI---K---GKPVFGLPGNITSTMVINEEVVD 315
                                   *******9.......9***********9999999...4...468********999999998874 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   3.1e-17   1.8e-13       1      71 [.     332     400 ..     332     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 3.1e-17
                                   EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                        MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                   ka++++++k+d +r+++++v l ++dg+y+a  +   +S+++  ++ A+g+i+i++g++ +e+G eV+v+l
  gi|70606758|ref|YP_255628.1| 332 KATITNEVKADYNRTTYIPVYLIKKDGKYYAIGM-PFDSYMIGVFSTADGYIIINPGEN-IEEGSEVSVYL 400
                                   688999****************************.9**********************9.*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3619.90
//
Query:       gi|70606759|ref|YP_255629.1|  [L=95]
Description: hypothetical protein Saci_0974 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-13   49.1   0.1    6.2e-13   48.8   0.1    1.2  1  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
       0.04   14.2   0.1       0.11   12.7   0.1    1.7  2  DUF4777   Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   6.9e-17   6.2e-13       5      67 .]      33      93 ..      14      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.9e-17
                                  E-SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                          PqqD  5 ldpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67
                                  l++e+  +++L ++++++W+l+dg r+v eiv++ ++ ++ + +++++ +l  ld+L+++ li
  gi|70606759|ref|YP_255629.1| 33 LSEEK--VYELAPIAYYVWELCDGNRTVTEIVDRASNDTNLPSDQVREPILTVLDELKKAALI 93
                                  45555..99**************************************************9887 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.36   3.2e+03      49      59 ..      22      32 ..       3      34 .. 0.60
   2 ?   12.7   0.1   1.3e-05      0.11      21      50 ..      57      86 ..      55      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.36
                       DUF4777 49 eaAvrhGFlkk 59
                                  + ++ +G++ k
  gi|70606759|ref|YP_255629.1| 22 KSGEEEGYVIK 32
                                  56777777765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.3e-05
                       DUF4777 21 TldEivervaerydlseeelkkvVkntLea 50
                                  T+ Eiv+r ++ ++l+++++++++  +L++
  gi|70606759|ref|YP_255629.1| 57 TVTEIVDRASNDTNLPSDQVREPILTVLDE 86
                                  899********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 644.54
//
Query:       gi|70606760|ref|YP_255630.1|  [L=146]
Description: single-stranded DNA-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-06   28.2   0.2    2.1e-06   27.6   0.2    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0081   16.1   0.5       0.01   15.8   0.5    1.2  1  REPA_OB_2        Replication protein A OB domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   2.3e-10   2.1e-06       1      70 [.      15      87 ..      15      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-10
                                  EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
               tRNA_anti-codon  1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkv 70
                                  V++  rv+  s       + +++ ++ +++ D+tgri+++l+     +la ++k G+v+++   +++ ++g+++l++
  gi|70606760|ref|YP_255630.1| 15 VNITVRVIEASeprviqtKNGTRTISEAVVGDETGRIKLTLWG----NLAGTIKSGSVIKIANAWTTAYKGKVQLNA 87
                                  56677777777777777678899********************....***************666666666699987 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   1.1e-06      0.01      13      89 ..      15      87 ..       2      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                     REPA_OB_2 13 vDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFggr.slsl 89
                                  v +   v +++e + i++k+++++++  e  + De+g+ +++tlWg+ a ++  ++ +v+ + ++  + ++g+ +l+ 
  gi|70606760|ref|YP_255630.1| 15 VNITVRVIEASEPRVIQTKNGTRTIS--EAVVGDETGR-IKLTLWGNLAGTI--KSGSVIKIANAWTTAYKGKvQLNA 87
                                  5555557788899999***9997766..5677899985.9*******99995..588999999999999999624444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 999.88
//
Query:       gi|70606761|ref|YP_255631.1|  [L=386]
Description: hypothetical protein Saci_0976 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-27   95.6   0.1    8.8e-27   93.8   0.0    2.0  3  AAA_5            AAA domain (dynein-related subfamily)
    6.4e-07   29.2   0.4    2.2e-06   27.4   0.1    2.1  2  AAA_lid_8        AAA lid domain
    1.4e-05   25.5   0.2    0.00034   21.0   0.0    2.7  3  AAA              ATPase family associated with various cellul
    2.9e-05   24.5   0.8    7.3e-05   23.2   0.1    2.0  2  AAA_16           AAA ATPase domain
    3.7e-05   23.2   0.1    0.00036   20.0   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00014   21.7   0.0    0.00023   21.0   0.0    1.3  1  AAA_3            ATPase family associated with various cellul
     0.0024   17.0   0.0     0.0083   15.3   0.0    1.8  2  MCM              MCM P-loop domain
     0.0048   16.6   0.0      0.017   14.9   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
     0.0058   16.9   0.3      0.057   13.7   0.0    2.7  2  AAA_22           AAA domain
     0.0085   16.8   0.2       0.03   15.0   0.2    2.0  1  PMC2NT           PMC2NT (NUC016) domain
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.063   12.8   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.039   14.3   0.2        8.3    6.8   0.0    2.6  2  EF-hand_14       EF-hand domain
      0.059   13.1   0.0       0.11   12.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.095   12.4   0.1       0.62    9.8   0.1    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   6.8e-30   8.8e-27       1     138 []      44     171 ..      44     171 .. 0.92
   2 ?   -2.4   0.0       3.4   4.4e+03      98     102 ..     319     323 ..     286     369 .. 0.50
   3 ?   -2.4   0.0       3.5   4.5e+03      74      91 ..     360     377 ..     356     382 .. 0.67

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 6.8e-30
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG- CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEvera 77 
                                   +v+L+G+pGt+Ks la+r a ++ +++++++lt++t++++l+g +++     +l++++++r  +    e+ei++lDE+++a
  gi|70606761|ref|YP_255631.1|  44 HVILIGEPGTAKSALARRAADLMSAKFFMYLLTKYTEPAELFGALDV----NALKQGIYKRITKdrlpESEIAFLDEIFNA 120
                                   79********************************************9....66666666666666677************* PP

                                   -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   +s++ln+Llsll+er ++  +g +++k++        ++i ++n+++ ++ e   al++R+
  gi|70606761|ref|YP_255631.1| 121 NSAILNALLSLLNERVIY--DGYNVIKVPL------RTLISASNRVP-DEPE-LDALYDRL 171
                                   ******************..**********......89*********.7777.78999985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                                   -SSSE CS
                         AAA_5  98 eggel 102
                                   e +++
  gi|70606761|ref|YP_255631.1| 319 EATKY 323
                                   22333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.5
                                   GGG--HHHHHHHHHHHHS CS
                         AAA_5  74 veraesevlnsLlsllee 91 
                                   ve+ +++v+n+  +lle+
  gi|70606761|ref|YP_255631.1| 360 VEEFSKDVINEIDKLLEK 377
                                   666677777777777765 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1   1.7e-09   2.2e-06       5      69 ..     231     293 ..     227     296 .. 0.90
   2 ?   -2.8   0.0       4.7   6.1e+03       7      35 ..     311     342 ..     307     344 .. 0.51

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-09
                     AAA_lid_8   5 lileiknkleeeeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeqkekvk 69 
                                    +l++   l  ee++i + DRR  k++k+   +A+lngr +  ++Dl++lk++  +e ++ ekv 
  gi|70606761|ref|YP_255631.1| 231 KLLKLYAML--EEKGIHLTDRRKGKVLKIAASHALLNGRLKAIEEDLIVLKYIAPKEIDDFEKVS 293
                                   577888888..889***************************************999999988886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                     AAA_lid_8   7 leiknkleeeee...aiyvSDRRwkkivkllk 35 
                                   +ei  +++e ++   a   SD R+ + ++ l+
  gi|70606761|ref|YP_255631.1| 311 NEIYSNIKEATKyvdAANESDPRLVELIRSLR 342
                                   45555554433311145667777777766666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-07   0.00034       1     116 [.      45     163 ..      45     178 .. 0.78
   2 ?    1.3   0.0      0.34   4.4e+02      64     110 ..     213     261 ..     189     276 .. 0.81
   3 ?   -2.0   0.1       3.6   4.6e+03     107     107 ..     352     352 ..     295     380 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS....STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHT CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk....yvgesekkirelfkeakeka..kpsilfiDEidalaksrs 75 
                                   v+l+G pGt K++la+  a  ++++f+   +++ ++        + ++  +++ k++ + +  +  i f+DEi + +++  
  gi|70606761|ref|YP_255631.1|  45 VILIGEPGTAKSALARRAADLMSAKFFMYLLTKYTEPaelfGALDVNALKQGIYKRITKDRlpESEIAFLDEIFNANSAI- 124
                                   68***************************999999666766445556666777888777778778********9887666. PP

                                   TCCCHHHHHHHHHHHHHHHHTTTS.........SSTEEEEEEESS.GGGST CS
                           AAA  76 gseseeeervvnqLlteldgvkkk.........eskvivigatnr.pdkld 116
                                             +n+Ll+ l++   +             ++i a+nr pd+++
  gi|70606761|ref|YP_255631.1| 125 ----------LNALLSLLNERVIYdgynvikvpL--RTLISASNRvPDEPE 163
                                   ..........999999999888887888777543..478888888666554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.34
                                   EETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEES CS
                           AAA  64 iDEidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatn 110
                                   +DE+++l+++       + + v ++Ll+    +++k        ++kv+ i+a++
  gi|70606761|ref|YP_255631.1| 213 LDELYSLIPQV------DLSAVKSKLLKLYAMLEEKgihltdrrKGKVLKIAASH 261
                                   89999999999......77777788887777777777778888888888888886 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.6
                                   E CS
                           AAA 107 g 107
                                   g
  gi|70606761|ref|YP_255631.1| 352 G 352
                                   1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   5.7e-08   7.3e-05       1      63 [.      24      81 ..      24     172 .. 0.69
   2 ?   -0.9   0.1       1.5   1.9e+03     106     107 ..     301     320 ..     228     381 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.7e-08
                        AAA_16  1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  ++vGReee + L+ al      + e v+l+Ge+G+ Ks+l+r++++ ++++ + +l +k+++ 
  gi|70606761|ref|YP_255631.1| 24 PFVGREEEARVLTLALL-----SKEHVILIGEPGTAKSALARRAADLMSAKFFMYLLTKYTEP 81
                                  69******999976665.....2389*******************988888444466666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                        AAA_16 106 a..................a 107
                                   +                  a
  gi|70606761|ref|YP_255631.1| 301 KtpikymkelneiysnikeA 320
                                   33333333333333333331 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.8e-07   0.00036       6      47 ..      26      67 ..      22      76 .. 0.93
   2 ?    0.5   0.0      0.26   3.4e+02     109     135 ..     111     137 ..     105     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                  Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                  +G+ee  r+l++a   + +++l+G pG+ K+ la+r + l++
  gi|70606761|ref|YP_255631.1| 26 VGREEEARVLTLALLSKEHVILIGEPGTAKSALARRAADLMS 67
                                  6999********************************999986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.26
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgev 135
                                   + fLDE+ + ++ +l++L + l+++ +
  gi|70606761|ref|YP_255631.1| 111 IAFLDEIFNANSAILNALLSLLNERVI 137
                                   67***************9887777655 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.8e-07   0.00023       1     105 [.      44     151 ..      44     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfee.kekefe.fkkGpv.fanllladeinrappkt 78 
                                   hv+l g PG+ak  l++  a+ ++++f    +t    P+++ G+  +++ k+  ++ ++k  +  +++ + dei  a++ +
  gi|70606761|ref|YP_255631.1|  44 HVILIGEPGTAKSALARRAADLMSAKFFMYLLTKYTEPAELFGALDVNAlKQGIYKrITKDRLpESEIAFLDEIFNANSAI 124
                                   9******************************************8655541443333134444415789999********** PP

                         AAA_3  79 qsalleameerqvtvegethklpepfl 105
                                     all  ++er +  + +  k+p   l
  gi|70606761|ref|YP_255631.1| 125 LNALLSLLNERVIYDGYNVIKVPLRTL 151
                                   **********98877766666665554 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.4e-06    0.0083      54      87 ..      39      72 ..      20      99 .. 0.77
   2 ?   -1.6   0.0      0.93   1.2e+03      66      91 ..     225     250 ..     222     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.4e-06
                                  BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE CS
                           MCM 54 lrgdinvllvgdpgtaKsqlLkyveklapravyt 87
                                  l ++ +v+l+g+pgtaKs+l +++++l++   ++
  gi|70606761|ref|YP_255631.1| 39 LLSKEHVILIGEPGTAKSALARRAADLMSAKFFM 72
                                  67889******************99988776554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                                   STSTHHHHHHHHHHHSSSEEEEESSS CS
                           MCM  66 pgtaKsqlLkyveklapravytsgkg 91 
                                    +  Ks+lLk  + l ++++  + + 
  gi|70606761|ref|YP_255631.1| 225 LSAVKSKLLKLYAMLEEKGIHLTDRR 250
                                   56778889888888877777665544 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.017      16     142 ..      36     156 ..      28     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                   HHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSS.SSSTTTSS-BEHHHHHTTTS CS
               Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhek.GaFtGAekekkGlfekadgG 95 
                                   + +  ++ +v++ Ge Gt K+ lar   +  +   ++f     ++++e    +eLFG  +  a      ++  + +  +  
  gi|70606761|ref|YP_255631.1|  36 TLALLSKEHVILIGEPGTAKSALARRAADLMS---AKFFMYLLTKYTE---PAELFGALDvNALKQGIYKRITKDRLPESE 110
                                   456678899****************9877665...5566555666655...478888754278888888888888899999 PP

                                   EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EE.EEEEES CS
               Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvr.iiaatn 142
                                   + fLDei + + ++ + Ll +l+e+ ++   + + ikv +r +i+a+n
  gi|70606761|ref|YP_255631.1| 111 IAFLDEIFNANSAILNALLSLLNERVIYD--GYNVIKVPLRtLISASN 156
                                   99**********************99975..34455555553455555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.5e-05     0.057       5      61 ..      42      89 ..      39     140 .. 0.84
   2 ?   -0.1   0.1      0.79     1e+03      56      56 ..     306     306 ..     229     377 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrell 61
                                  + +++++Ge+Gt K+ l+rr ++           +++++ + l++ t++++l+ +l 
  gi|70606761|ref|YP_255631.1| 42 KEHVILIGEPGTAKSALARRAADLM---------SAKFFMYLLTKYTEPAELFGALD 89
                                  6799*******************98.........99999999999999999987775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.79
                        AAA_22  56 l 56 
                                    
  gi|70606761|ref|YP_255631.1| 306 Y 306
                                   1 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.4e-05      0.03      26      87 ..     324     382 ..     308     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                        PMC2NT  26 aksldeqserllslinsllklaaskseisassklededdveekfksvvdvvDsllEkadtcL 87 
                                    ++ +e+  rl++li sl      ++ i    k+ + ++vee  k+v++ +D+llEk+   L
  gi|70606761|ref|YP_255631.1| 324 VDAANESDPRLVELIRSLRAT--RDRVIAL-GKESGDEKVEEFSKDVINEIDKLLEKVARKL 382
                                   456677777899999988333..3333333.588899999999999***********98766 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.9e-05     0.063      25      64 ..      34      73 ..      23      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                         AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekyls 64
                                  +l+l l +k +v+l+G+ Gt+K++++++  + ++ + +++
  gi|70606761|ref|YP_255631.1| 34 VLTLALLSKEHVILIGEPGTAKSALARRAADLMSAKFFMY 73
                                  5777888999****************99888777554444 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.026        33      18      43 ..     231     256 ..     214     277 .. 0.81
   2 ?    6.8   0.0    0.0065       8.3      33      81 ..     329     377 ..     310     385 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.026
                    EF-hand_14  18 svakllkaLaetGirkdDpRLkellk 43 
                                   ++ kl ++L+e+Gi+ +D R  ++lk
  gi|70606761|ref|YP_255631.1| 231 KLLKLYAMLEEKGIHLTDRRKGKVLK 256
                                   678999************99777765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0065
                    EF-hand_14  33 kdDpRLkellkklkkvekeks.eaeesetleldretF.kkcveenivLiak 81 
                                   ++DpRL el++ l+  +++     +es + ++  e+F k++++e   L++k
  gi|70606761|ref|YP_255631.1| 329 ESDPRLVELIRSLRATRDRVIaLGKESGDEKV--EEFsKDVINEIDKLLEK 377
                                   79************999987632222222222..33314455555555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.9e-05      0.11      46     172 ..      41     172 ..      17     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                     IstB_IS21  46 kkenivllGpsGvGKshlaialg...veavraglsvlfvrvedLveelkrar.rdgklaralk.rllkvdllilDdlgllp 121
                                   +ke ++l+G +G+ Ks la   +    +     l + ++  ++L+  l ++  ++g ++r+ k rl ++++  lD++   +
  gi|70606761|ref|YP_255631.1|  41 SKEHVILIGEPGTAKSALARRAAdlmSAKFFMYLLTKYTEPAELFGALDVNAlKQGIYKRITKdRLPESEIAFLDEI--FN 119
                                   5789**************96544110444446677899999*******9866156666665532688899999**98..56 PP

                     IstB_IS21 122 ldqaeaellfeviekr..yerrsiiitsnlpfaewdevlgdatlatAilDRlv 172
                                    ++a  + l+ ++++r  y+   +i     ++ + ++ ++d+   +A+ DRl+
  gi|70606761|ref|YP_255631.1| 120 ANSAILNALLSLLNERviYDGYNVIKVPLRTLISASNRVPDEPELDALYDRLL 172
                                   67888888999998884455555555555566666666677777777777765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00048      0.62      33     104 ..      42     128 ..      36     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00048
                        RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvkl......kitsgPvlekagdlaallt.........nleekdvlfideihrlsr 98 
                                    +hv+l+G PG  k++la+  a+ + +k+      k t    l  a d+ al +         +l e+++ f+dei   ++
  gi|70606761|ref|YP_255631.1|  42 KEHVILIGEPGTAKSALARRAADLMSAKFfmylltKYTEPAELFGALDVNALKQgiykritkdRLPESEIAFLDEIFNANS 122
                                   58****************999998888752222223444444555555555433111111111344566777777776666 PP

                        RuvB_N  99 aveevl 104
                                   a+ + l
  gi|70606761|ref|YP_255631.1| 123 AILNAL 128
                                   665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2470.81
//
Query:       gi|70606762|ref|YP_255632.1|  [L=451]
Description: hypothetical protein Saci_0977 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-09   36.4   0.1      2e-07   31.4   0.0    2.6  2  VWA            von Willebrand factor type A domain
    8.3e-07   29.1   0.0      2e-06   27.8   0.0    1.6  1  VWA_3          von Willebrand factor type A domain
    1.4e-05   25.7   0.0    0.00048   20.7   0.0    2.7  2  VWA_2          von Willebrand factor type A domain
    1.4e-05   24.6   0.0      3e-05   23.5   0.0    1.5  1  VWA_CoxE       VWA domain containing CoxE-like protein
    0.00011   22.5   0.3    0.00065   20.0   0.1    2.2  2  UvrA_DNA-bind  UvrA DNA-binding domain
  ------ inclusion threshold ------
      0.088   12.5   0.8       0.13   11.9   0.8    1.3  1  SDH_alpha      Serine dehydratase alpha chain
        1.2    9.4   4.0        2.5    8.3   3.1    2.0  2  DUF29          Domain of unknown function DUF29
        2.5    7.7   9.3        3.6    7.2   0.2    3.4  3  DUF5095        Domain of unknown function (DUF5095)


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.15   3.3e+02      41      79 ..     193     231 ..     175     248 .. 0.81
   2 !   31.4   0.0   8.9e-11     2e-07       2     154 ..     289     433 ..     289     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                                   EEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC CS
                           VWA  41 glvqfssevktefslndysskeellsalnnlkysgggtt 79 
                                   +++ f +e++++ +l + ++ +++l+ ln ++  g+ t+
  gi|70606762|ref|YP_255632.1| 193 SILNFEGEIHEVLRLARNTEIKKILEFLNGMPRLGSYTK 231
                                   58899999**********************855544443 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 8.9e-11
                                   EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGGGSSC-H CS
                           VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnl.kysgggttnt 81 
                                   i+++lD Sgsm++e++  +k  + +l ++    +e+  + +  f + +++ +++ +  + +++++ ++ + k++ggg t++
  gi|70606762|ref|YP_255632.1| 289 IYLLLDKSGSMDGEKIIWAKAVALSLYNRAR--RENRDFYIRFFDNIPYPLIKVMKNAKSKDVIKMIEYIgKIRGGGGTDI 367
                                   89*****************************..88888******************9999***********99******** PP

                                   HHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSSS CS
                           VWA  82 gkalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeqgikvfavGvgnadekelLnkiase 154
                                      +  a e + ++  +     ++ +illtdG+++    +++ ++++e++  +++v ++ + +++ L++ia +
  gi|70606762|ref|YP_255632.1| 368 SRSIISACEDIKEGHVK----GVSEVILLTDGEDKI-AETTVRRSLREANSVLISVMIRGD-NAD-LRRIADK 433
                                   *************9999....5667899******66.677777888888999999998554.566.8888765 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   8.8e-10     2e-06       3     122 ..     289     411 ..     287     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 8.8e-10
                         VWA_3   3 vvivvDvsssmsaen..klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgasnle 81 
                                   + +++D s sm +e+   + + aLs+  r+  +n  ++++ f+  p pl++  ++++++++ ++ ++i ++    g+++  
  gi|70606762|ref|YP_255632.1| 289 IYLLLDKSGSMDGEKiiWAKAVALSLYNRARRENRDFYIRFFDNIPYPLIKVMKNAKSKDVIKMIEYIGKIRG-GGGTDIS 368
                                   6799**********99988999***************************************************.******* PP

                         VWA_3  82 gaLkealr..qpakpgevrsvilltDgssaqgeervsdlisra 122
                                   +++  a +  ++ +++ v++villtDg +   e+ v  ++++a
  gi|70606762|ref|YP_255632.1| 369 RSIISACEdiKEGHVKGVSEVILLTDGEDKIAETTVRRSLREA 411
                                   *******85566999*************877777777776555 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.18     4e+02      28      74 ..     180     227 ..     158     255 .. 0.72
   2 !   20.7   0.0   2.1e-07   0.00048       2     107 .]     290     396 ..     289     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                         VWA_2  28 veallkslpgdrvglvtfsdgpevlipl..tkdkakilnalrnleakgg 74 
                                   ++++++ +   + ++++f+++ + ++ l  ++  +kil++l+++    g
  gi|70606762|ref|YP_255632.1| 180 MQRIVGGNGAGTGSILNFEGEIHEVLRLarNTEIKKILEFLNGMPRL-G 227
                                   44455555555778999999999999994447789999999988765.3 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 2.1e-07
                         VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.pgd.rvglvtfsdgpevlipl..tkdkakilnalrnleak..gggt 76 
                                    ++lD SgSm ++     ++  ak+ + +l ++  +++  + +  f++ p+ li++  +   +++ + ++ +     gggt
  gi|70606762|ref|YP_255632.1| 290 YLLLDKSGSMDGE-----KIIWAKAVALSLYNRArRENrDFYIRFFDNIPYPLIKVmkNAKSKDVIKMIEYIGKIrgGGGT 365
                                   69**********9.....799999999999995525554999999999999999884333455666666666655779*** PP

                         VWA_2  77 nlaaaLqlarkalkkrrkgekrvivlitDge 107
                                   ++   +  a + +k++  +  ++++l+tDge
  gi|70606762|ref|YP_255632.1| 366 DISRSIISACEDIKEGHVKGVSEVILLTDGE 396
                                   ***********9999987888999*****96 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.3e-08     3e-05      49     173 ..     278     408 ..     250     420 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-08
                      VWA_CoxE  49 rrkprerkprelvllvDvSgSmaaysaiflallhAllqqlp.....rtevfaFdtrlvdlTralrerDpaeaLarvsaave 124
                                   ++k+ ++   ++ ll+D SgSm+    i+++ ++  l ++      +  +  Fd     l + ++++  +++++ ++ + +
  gi|70606762|ref|YP_255632.1| 278 YQKKIKEALGPIYLLLDKSGSMDGEKIIWAKAVALSLYNRArrenrDFYIRFFDNIPYPLIKVMKNAKSKDVIKMIEYIGK 358
                                   5555566666899**********9666666544433333332433244444566665678888888888888888887777 PP

                      VWA_CoxE 125 d.lgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellael 173
                                      gGgT+i++++ ++ e ++   ++  + v+l++Dg+++ +   + + l
  gi|70606762|ref|YP_255632.1| 359 IrGGGGTDISRSIISACEDIKEGHVKGVSEVILLTDGEDKIAETTVRRSL 408
                                   757899***************9999************8876665555555 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.9e-07   0.00065       1      80 [.      79     156 ..      79     166 .. 0.90
   2 ?   -0.4   0.0      0.66   1.5e+03      81     104 ..     193     216 ..     160     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                                   -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----............... CS
                 UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyksggrkrs 80 
                                   D +lv+++++ s+a+ A+ +    + sy ++l+e++ +   ++ ++  +e+ e++++ l+ Gsg+++ +++ +++++k++
  gi|70606762|ref|YP_255632.1|  79 DSELVIKNRNYSIANSAVSMA--LSVSYIQNLIEELERIKRTSQSQEEREMAEQILNGLMKGSGGKESNTKNNEENQKME 156
                                   89****************999..7899*************************************9888777777665554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.66
                                   ....---HHHHHHHHHH------- CS
                 UvrA_DNA-bind  81 yektfeGvipnlerryreteSeav 104
                                      +feG i+++ r  r+te +++
  gi|70606762|ref|YP_255632.1| 193 SILNFEGEIHEVLRLARNTEIKKI 216
                                   55689**********999997766 PP

>> SDH_alpha  Serine dehydratase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.8   5.9e-05      0.13      26     138 ..     108     231 ..      60     238 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                     SDH_alpha  26 idakleeiwevmdeaieeglsnkaiaeegllpgelkvk.......ra.y.aalgkrlldklsaaAlavaemnaaggrvvta 97 
                                   + ++le+i+++ + + e+ ++ ++i  +gl++g+  ++       ++ + ++l+k++ +k+   A+ +ae    ++r+v  
  gi|70606762|ref|YP_255632.1| 108 LIEELERIKRTSQSQEEREMA-EQIL-NGLMKGSGGKEsntknneENqKmERLMKQVHEKALSKAVEDAEAVKNMQRIVGG 186
                                   333455555444444443333.3333.34444444443333222222233667777778********************** PP

                     SDH_alpha  98 ptsGaaGi......lPavlvalleelkas.....eellraLllaaligilik 138
                                    ++G   i      +  vl               +++l++L     +g++ k
  gi|70606762|ref|YP_255632.1| 187 NGAGTGSIlnfegeIHEVLRL-------ArnteiKKILEFLNGMPRLGSYTK 231
                                   ****99995543333333333.......112245666666665555555555 PP

>> DUF29  Domain of unknown function DUF29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.1    0.0011       2.5      27      85 ..     105     171 ..      99     183 .. 0.59
   2 ?   -2.5   0.0       2.4   5.5e+03      71     110 ..     279     322 ..     275     343 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHH.......HHHSTTTTHHHHHHHHHHHHHHHHHH- CS
                         DUF29  27 lenLieEiedlgrsekrelesrl.avllehlLk.......wqyqpekrsrswrseireqrkeiekll 85 
                                   ++nLieE+e + r+ +++ e  + +++l  l+k        ++++e++++  r   + + k ++k++
  gi|70606762|ref|YP_255632.1| 105 IQNLIEELERIKRTSQSQEEREMaEQILNGLMKgsggkesNTKNNEENQKMERLMKQVHEKALSKAV 171
                                   69**********9877666655516888888887655332112222333333333333444445555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHH-..-GGG...G--H.....HHHHHHHHHHH CS
                         DUF29  71 rseireqrkeieklledspsL...ksyleee.leeaYqdArkla 110
                                   +++i+e+   i  ll++s s+   k  ++++   + Y++Ar++ 
  gi|70606762|ref|YP_255632.1| 279 QKKIKEALGPIYLLLDKSGSMdgeKIIWAKAvALSLYNRARREN 322
                                   56667777777777777777743222223321445666666654 PP

>> DUF5095  Domain of unknown function (DUF5095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   1.2       0.4     9e+02      36      57 ..     143     164 ..     101     187 .. 0.45
   2 ?    4.2   0.1     0.013        30     120     155 ..     256     292 ..     252     298 .. 0.80
   3 ?    7.2   0.2    0.0016       3.6     112     156 ..     306     351 ..     294     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.4
                       DUF5095  36 tkekskineddflkvLikkkkk 57 
                                   ++++++ +e++ ++ L+k+ ++
  gi|70606762|ref|YP_255632.1| 143 ESNTKNNEENQKMERLMKQVHE 164
                                   2222222222222222222222 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
                       DUF5095 120 FkeykkaneeFyvkykd.ellifstelkvskklkklL 155
                                   ++e    +e Fyvk+ d +ll +++++k   +++ lL
  gi|70606762|ref|YP_255632.1| 256 YSELALPDELFYVKFADsDLLLYQKKIKEALGPIYLL 292
                                   6666666778*****8648********9988877776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0016
                       DUF5095 112 flsalk.slFkeykkaneeFyvkykdellifstelkvskklkklLe 156
                                   + +a++ sl++  +++n  Fy+++ d++ +   ++++++k k++++
  gi|70606762|ref|YP_255632.1| 306 WAKAVAlSLYNRARRENRDFYIRFFDNIPYPLIKVMKNAKSKDVIK 351
                                   77776439******************98655777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1541  (0.0859501); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2562.28
//
Query:       gi|70606763|ref|YP_255633.1|  [L=122]
Description: succinate dehydrogenase subunit D [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 912.78
//
Query:       gi|70606764|ref|YP_255634.1|  [L=290]
Description: succinate dehydrogenase subunit C [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-33  114.0   0.4      5e-16   58.7   0.1    2.2  2  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   2.8e-20     5e-16       1      82 [.       3      83 ..       3      86 .. 0.96
   2 !   53.7   0.0     1e-18   1.8e-14       1      85 []     148     238 ..     148     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.8e-20
                           CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCll 82
                                  +ay++gC  +++ +++ + a+kk++e lg++l+e ++ +CCG g + +  e  + al+ rn++ +e++g++++vt+c+ Cl 
  gi|70606764|ref|YP_255634.1|  3 YAYYPGC-TAHGLSKDIDIATKKVFETLGLKLDEVKDWNCCGGGFYDEYDEVGHVALNLRNLSIVEKMGYQKMVTPCSVCLQ 83
                                  79*****.9*************************************999999999*************************86 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 1e-18
                           CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaiv 74 
                                   v  ++gC++lr++        + +++++ l++++g++ + + + +sCCG++ + s+ + + ++la   +++a+e++ad+i+
  gi|70606764|ref|YP_255634.1| 148 VGAYYGCQMLRPEeimgfePAFNPHSMEDLIRVTGATPVSFkAAKSCCGFPLMGSNPK-VGLRLAYGVLKSAKEEQADIII 227
                                   5679**************98889999***************9***********66655.9********************* PP

                           CCG  75 tacpgCllqlk 85 
                                   ++c+ C+lql+
  gi|70606764|ref|YP_255634.1| 228 HPCSLCHLQLD 238
                                   *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2020.69
//
Query:       gi|70606765|ref|YP_255635.1|  [L=317]
Description: succinate dehydrogenase iron-sulfur subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-32  110.9   0.1    5.3e-32  110.1   0.1    1.4  1  Fer2_3         2Fe-2S iron-sulfur cluster binding domain
    3.4e-11   43.4   2.2    3.4e-11   43.4   2.2    2.1  2  Fer4_8         4Fe-4S dicluster domain
      3e-08   34.1   4.2      3e-08   34.1   4.2    2.5  2  Fer4_7         4Fe-4S dicluster domain
    1.8e-06   28.0  12.0    2.2e-05   24.5   9.5    3.0  3  Fer4_9         4Fe-4S dicluster domain
    2.4e-05   24.4  19.7    5.8e-05   23.1  10.3    2.6  3  Fer4_10        4Fe-4S dicluster domain
      7e-05   22.7  16.3     0.0011   18.9   1.1    3.2  3  Fer4_2         4Fe-4S binding domain
     0.0001   22.5   2.6       0.13   12.4   0.2    2.6  2  Fer4_18        4Fe-4S dicluster domain
    0.00053   20.5  18.0     0.0022   18.5  10.1    2.7  4  Fer4_17        4Fe-4S dicluster domain
      0.001   18.8  20.6     0.0065   16.2   3.0    3.0  3  Fer4           4Fe-4S binding domain
     0.0011   19.9   8.7     0.0011   19.9   8.7    3.0  4  Fer4_16        4Fe-4S double cluster binding domain
      0.002   18.2  11.8      0.058   13.5   0.5    3.0  3  Fer4_21        4Fe-4S dicluster domain
     0.0039   17.9   3.7        1.4    9.7   0.6    2.7  2  Fer4_15        4Fe-4S single cluster domain
     0.0041   17.6   7.2        0.2   12.3   1.9    2.9  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.027   14.2   5.9       0.46   10.3   0.3    2.8  3  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
      0.048   13.7   0.8      0.048   13.7   0.8    2.9  3  Fer4_6         4Fe-4S binding domain
      0.079   13.8   3.6        1.5    9.7   0.0    2.9  3  Fer4_22        4Fe-4S dicluster domain
       0.11   12.5   0.5       0.11   12.5   0.5    2.3  3  Fer2           2Fe-2S iron-sulfur cluster binding domain
       0.13   12.8   1.0       0.13   12.8   1.0    3.1  2  Fer4_4         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.1   5.3e-35   5.3e-32       2     108 ..      12     117 ..      11     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 5.3e-35
                        Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakq 82 
                                   +kvkR+++   ++  ++qey++++++ +++ +aL +ik+e+dptla+rasC+ ++CGsc+++inG+p+laC++ + d+ k+
  gi|70606765|ref|YP_255635.1|  12 IKVKRYTQ---EKGFYWQEYKLKVDRFTQFTEALRRIKSEQDPTLAYRASCHMAVCGSCGMKINGEPKLACKTLVLDVIKK 89 
                                   799****9...4478***************************************************************999 PP

                        Fer2_3  83 ks..eieleplpkfpvirDLvvDideml 108
                                    +   i++ep++ f++++DLvvD d+++
  gi|70606765|ref|YP_255635.1|  90 YGsnVITIEPMDYFKPVKDLVVDLDDFY 117
                                   88788********************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2         6     6e+03       5       8 ..      64      67 ..      43      70 .. 0.71
   2 !   43.4   2.2   3.4e-14   3.4e-11       2      65 .]     153     224 ..     152     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6
                        Fer4_8  5 CieC 8 
                                  C+ C
  gi|70606765|ref|YP_255635.1| 64 CGSC 67
                                  3333 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 3.4e-14
                        Fer4_8   2 lekCieCgaCqsaCpvlrr...........tk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   + +Ci Cg+C saCp++++           ++ ++l d+r+  +e ++ +      +++w+Ct c +C +vCp +i
  gi|70606765|ref|YP_255635.1| 153 FAQCIWCGLCVSACPAVQEdpeflgpaahaKGfRFLADPRDTITE-ERLKIL---IDSAWRCTYCYMCYNVCPRDI 224
                                   679***********8666633333333333666666666666666.333322...799***************986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.3   1.3e+03      27      42 ..      53      68 ..      21      82 .. 0.72
   2 !   34.1   4.2     3e-11     3e-08       1      51 [.     155     223 ..     155     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                        Fer4_7 27 gtekveidpekClgCg 42
                                     ++  ++  C +Cg
  gi|70606765|ref|YP_255635.1| 53 LAYRASCHMAVCGSCG 68
                                  3455566777777776 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 3e-11
                        Fer4_7   1 rCigCgaCvaaCpvkaield...eeenek..............gtekveid.pekClgCgaCvavCPtg 51 
                                   +Ci Cg Cv+aCp+   + +   +++++k              ++ k+ id +++C++C++C +vCP +
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPAVQEDPEflgPAAHAKgfrfladprdtiteERLKILIDsAWRCTYCYMCYNVCPRD 223
                                   6***********8555554422233333333333333343433334556654789************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1         1     1e+03      34      42 ..      57      67 ..      28      72 .. 0.66
   2 !   15.0   1.7     2e-05      0.02      33      48 ..     147     168 ..     123     171 .. 0.72
   3 !   24.5   9.5   2.3e-08   2.2e-05       1      49 [.     155     223 ..     155     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1
                        Fer4_9 34 eaCig..CgaC 42
                                   +C++  Cg+C
  gi|70606765|ref|YP_255635.1| 57 ASCHMavCGSC 67
                                  45754457777 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                        Fer4_9  33 e......eaCigCgaCveaCpk 48 
                                   +       +Ci Cg Cv aCp 
  gi|70606765|ref|YP_255635.1| 147 QkvlwkfAQCIWCGLCVSACPA 168
                                   245555689***********95 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 2.3e-08
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase....................eaCigCgaCveaCpkg 49 
                                   +C+ Cg Cv+aCpa    ++  +  a  + ++                     ++C+ C  C+++Cp++
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPAVQEDPEFLGPAAHAKGFRFladprdtiteerlkilidsaWRCTYCYMCYNVCPRD 223
                                   6***********77666666666666666666567777777777999999999***************9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       4.2   4.2e+03      47      51 ..      61      67 ..      46      70 .. 0.66
   2 !   23.1  10.3   5.8e-08   5.8e-05       7      56 .]     154     221 ..     148     221 .. 0.78
   3 !   14.2   1.9   3.5e-05     0.035       8      30 ..     209     231 ..     200     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.2
                       Fer4_10 47 g..cgaC 51
                                  +  cg+C
  gi|70606765|ref|YP_255635.1| 61 MavCGSC 67
                                  3334444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 5.8e-08
                       Fer4_10   7 dtCirCgkCvkaCPadl...................tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                                    +Ci Cg Cv+aCPa                     +  ++  +++e  ++ +   ++Ct c +C+ +CP
  gi|70606765|ref|YP_255635.1| 154 AQCIWCGLCVSACPAVQedpeflgpaahakgfrflaDPRDT--ITEERLKILIdSAWRCTYCYMCYNVCP 221
                                   68*************77***************997533333..3333333333358*************9 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.5e-05
                       Fer4_10   8 tCirCgkCvkaCPadltsvgakg 30 
                                   +C+ C  C ++CP d++ v a++
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPRDIEPVTAIK 231
                                   68888888888888774444444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.8       2.3   2.3e+03      13      16 ..      64      67 ..      55      70 .. 0.69
   2 !   18.9   1.1   1.1e-06    0.0011       9      22 .]     155     168 ..     148     168 .. 0.87
   3 !   13.4   1.3   6.5e-05     0.065       3      21 ..     202     221 ..     200     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                        Fer4_2 13 CgaC 16
                                  Cg+C
  gi|70606765|ref|YP_255635.1| 64 CGSC 67
                                  5555 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-06
                        Fer4_2   9 rCigCgaCvsaCPa 22 
                                    Ci Cg CvsaCPa
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPA 168
                                   6************8 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6.5e-05
                        Fer4_2   3 vvvdtd.rCigCgaCvsaCP 21 
                                   + +d++ rC+ C  C+++CP
  gi|70606765|ref|YP_255635.1| 202 ILIDSAwRCTYCYMCYNVCP 221
                                   6677555************* PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   0.00013      0.13      44      73 ..     139     168 ..     129     172 .. 0.74
   2 !    9.4   0.2    0.0011       1.1      57      76 ..     206     225 ..     188     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                       Fer4_18  44 kkalkekeerkekgagdcidcescvkvcPt 73 
                                   ++ lk ++++   + ++ci c+ cv+ cP 
  gi|70606765|ref|YP_255635.1| 139 EHRLKPEDQKVLWKFAQCIWCGLCVSACPA 168
                                   555666677777788899999999999985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                       Fer4_18  57 gagdcidcescvkvcPtgid 76 
                                   +a  c+ c +c +vcP +i+
  gi|70606765|ref|YP_255635.1| 206 SAWRCTYCYMCYNVCPRDIE 225
                                   5668************9986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.8   2.8e+03      42      53 ..      60      68 ..      28      70 .. 0.62
   2 !   14.4   1.0   4.3e-05     0.042      41      58 ..     151     168 ..     116     171 .. 0.72
   3 !   18.5  10.1   2.2e-06    0.0022       1      60 [.     155     224 ..     155     225 .. 0.75
   4 !    9.6   3.4    0.0013       1.3       1      17 [.     209     225 ..     209     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                       Fer4_17 42 kaslCieCgeCe 53
                                   +     Cg C 
  gi|70606765|ref|YP_255635.1| 60 HMAV---CGSCG 68
                                  3333...44444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.3e-05
                       Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                    k+ +Ci Cg+C+++CP+
  gi|70606765|ref|YP_255635.1| 151 WKFAQCIWCGLCVSACPA 168
                                   37899***********95 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.2e-06
                       Fer4_17   1 rCiqCgyClpeCpsyeaydn..epkkllraakl......glleeaeke.......ekaslCieCgeCerkCPqgl 60 
                                   +Ci Cg C+ +Cp  ++ ++   p+  ++ +++      +     ++e       + a +C+ C +C  +CP ++
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPAVQEDPEflGPAAHAKGFRFladprdT-----ITEerlkiliDSAWRCTYCYMCYNVCPRDI 224
                                   5****************88855477777777666444322.....2322445677899**************987 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0013
                       Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                   rC+ C +C ++Cp+ ++
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPRDIE 225
                                   69999999999998665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.2       4.8   4.8e+03      11      14 ..      64      67 ..      63      69 .. 0.69
   2 !   14.5   1.9   2.4e-05     0.024       7      20 ..     155     168 ..     150     169 .. 0.87
   3 !   16.2   3.0   6.5e-06    0.0065       7      21 ..     209     223 ..     209     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.8
                                  -THH CS
                          Fer4 11 CGaC 14
                                  CG C
  gi|70606765|ref|YP_255635.1| 64 CGSC 67
                                  7777 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                                   TSSS-THHHHHSTT CS
                          Fer4   7 kCigCGaCvevCPv 20 
                                    Ci CG+Cv++CP 
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPA 168
                                   5888*********5 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 6.5e-06
                                   TSSS-THHHHHSTTT CS
                          Fer4   7 kCigCGaCvevCPvg 21 
                                   +C++C  C++vCP +
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPRD 223
                                   7************87 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       4.2   4.2e+03      54      60 ..      61      67 ..      27      69 .. 0.66
   2 !   11.0   1.8   0.00066      0.65      52      66 ..     154     168 ..     122     169 .. 0.64
   3 !   19.9   8.7   1.1e-06    0.0011       1      65 [.     155     221 ..     155     223 .. 0.69
   4 !    9.4   4.2    0.0021       2.1       1      47 [.     209     252 ..     209     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.2
                       Fer4_16 54 itgCdiC 60
                                  ++ C+ C
  gi|70606765|ref|YP_255635.1| 61 MAVCGSC 67
                                  3566666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00066
                       Fer4_16  52 eaitgCdiCqdvCPa 66 
                                    +++ C+ C+ +CPa
  gi|70606765|ref|YP_255635.1| 154 AQCIWCGLCVSACPA 168
                                   555666666666664 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 1.1e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkeke..iearecisyntaekkdlaedeekck..kqeaitgCdiCqdvCP 65 
                                   +C+ Cg C+++CP+  ++e+ e+   ++  + +    + +++++e++ k    +++++t+C +C +vCP
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPA--VQEDPEFLgpAAHAKGFRFLADPRDTITEERLKILidSAWRCTYCYMCYNVCP 221
                                   5************6..555522321133344444477777777777777663367************** PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0021
                       Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeek 47 
                                   rC+ C  C +vCP +  +    + i++ + +s   ++k +++++ ek
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPRDI-EPV--TAIKKTRAFSRLAKDKTEVIKTGEK 252
                                   6999999*****9874.444..4666666666655555555555444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5       3.4   3.4e+03      15      27 ..      76      88 ..      57     101 .. 0.52
   2 !   13.5   0.5   5.8e-05     0.058      40      52 ..     155     167 ..     141     173 .. 0.65
   3 !   11.8   0.4    0.0002      0.19      39      52 ..     208     221 ..     191     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
                       Fer4_21 15 liaCedtshqaie 27
                                   +aC++   + i+
  gi|70606765|ref|YP_255635.1| 76 KLACKTLVLDVIK 88
                                  2455555555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.8e-05
                       Fer4_21  40 eCvGCnlCssvCP 52 
                                   +C+ C lC+s CP
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACP 167
                                   4555555555555 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0002
                       Fer4_21  39 deCvGCnlCssvCP 52 
                                    +C+ C +C++vCP
  gi|70606765|ref|YP_255635.1| 208 WRCTYCYMCYNVCP 221
                                   47************ PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.6    0.0014       1.4       7      23 ..     155     171 ..     154     185 .. 0.85
   2 !    8.3   0.1    0.0038       3.7       3      23 ..     204     225 ..     202     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                       Fer4_15   7 aCigcglCvaeapevfe 23 
                                   +Ci cglCv ++p v e
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPAVQE 171
                                   6************6644 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0038
                       Fer4_15   3 vD.rdaCigcglCvaeapevfe 23 
                                   +D  ++C+ c +C+ ++p+ +e
  gi|70606765|ref|YP_255635.1| 204 IDsAWRCTYCYMCYNVCPRDIE 225
                                   66568************87555 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.9    0.0002       0.2       5      19 ..     155     169 ..     154     176 .. 0.89
   2 !    7.3   0.3    0.0068       6.8       5      18 ..     209     222 ..     204     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                       Fer4_13   5 tCiacgaCvelaPdv 19 
                                   +Ci cg+Cv+++P v
  gi|70606765|ref|YP_255635.1| 155 QCIWCGLCVSACPAV 169
                                   8************98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0068
                       Fer4_13   5 tCiacgaCvelaPd 18 
                                   +C+ c  C++++P 
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPR 222
                                   7************5 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.8   2.8e+03       4      38 ..      37      69 ..      26      75 .. 0.57
   2 ?    6.2   0.1    0.0084       8.3      15      47 ..     147     177 ..     135     187 .. 0.79
   3 ?   10.3   0.3   0.00046      0.46      17      50 ..     203     234 ..     189     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.8
                                  S-S-SB----HHHHHHHHTT----TT-HHHHCSTT CS
                       Fer4_20  4 nfkevalglteeealeeAsRClqCkkapcvkgCPv 38
                                  +f+e  +++++e+  + A R  +C+ a c  +C +
  gi|70606765|ref|YP_255635.1| 37 QFTEALRRIKSEQDPTLAYR-ASCHMAVCG-SCGM 69
                                  44444445555555555555.346666665.4554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0084
                                   HHHHHHHTT----TT-HHHHCSTT---HHHHHH CS
                       Fer4_20  15 eealeeAsRClqCkkapcvkgCPveidipefik 47 
                                   +++l + + C+ C    cv++CP+  + pef+ 
  gi|70606765|ref|YP_255635.1| 147 QKVLWKFAQCIWC--GLCVSACPAVQEDPEFLG 177
                                   5556666789999..89********99999986 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00046
                                   HHHHHTT----TT-HHHHCSTT---HHHHHHHHH CS
                       Fer4_20  17 aleeAsRClqCkkapcvkgCPveidipefikkia 50 
                                    ++ A RC +C   +c + CP +i+  + ikk++
  gi|70606765|ref|YP_255635.1| 203 LIDSAWRCTYC--YMCYNVCPRDIEPVTAIKKTR 234
                                   478899*****..79********99988888765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.0       5.4   5.4e+03       9      15 ..      59      67 ..      56      70 .. 0.58
   2 ?   13.7   0.8   4.9e-05     0.048       9      21 ..     156     168 ..     149     171 .. 0.90
   3 ?    9.3   3.9    0.0012       1.2       8      20 ..     209     221 ..     209     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                        Fer4_6  9 Ci..gCgdC 15
                                  C    Cg C
  gi|70606765|ref|YP_255635.1| 59 CHmaVCGSC 67
                                  553336666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.9e-05
                        Fer4_6   9 CigCgdCvrvCPe 21 
                                   Ci Cg Cv++CP+
  gi|70606765|ref|YP_255635.1| 156 CIWCGLCVSACPA 168
                                   999*********7 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
                        Fer4_6   8 kCigCgdCvrvCP 20 
                                   +C+ C+ C++vCP
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCP 221
                                   6999********* PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         5     5e+03      80      85 ..      62      67 ..      15      75 .. 0.70
   2 ?    9.7   0.0    0.0015       1.5      61      94 ..     133     168 ..     111     170 .. 0.65
   3 ?    4.0   0.2     0.092        91       1      13 [.     209     221 ..     206     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5
                       Fer4_22 80 sgCvGC 85
                                   +C  C
  gi|70606765|ref|YP_255635.1| 62 AVCGSC 67
                                  222222 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
                       Fer4_22  61 rlrqrllhklsefkekf..gesgCvGCgRCieacpv 94 
                                    l+ +  h+l+   +k+  +  +C+ Cg C++acp+
  gi|70606765|ref|YP_255635.1| 133 VLEGKAEHRLKPEDQKVlwKFAQCIWCGLCVSACPA 168
                                   455566666665555554578889999999999986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.092
                       Fer4_22   1 rClsCgaCtlvCp 13 
                                   rC  C  C  vCp
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCP 221
                                   5888888888887 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   0.00011      0.11      29      77 ..      53      83 ..      39      84 .. 0.83
   2 ?   -0.8   0.1       1.5   1.5e+03      40      71 ..     159     188 ..     154     189 .. 0.69
   3 ?   -1.8   0.1       3.1   3.1e+03       9      44 ..     186     217 ..     180     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                  TTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                          Fer2 29 idipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                  ++ ++sC+++ Cg+C  +++            ge++      laC t+v
  gi|70606765|ref|YP_255635.1| 53 LAYRASCHMAVCGSCGMKIN------------GEPK------LACKTLV 83
                                  66789*************99............8874......8888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                   SSTTEEEEEESCECTTSSSSTHHHHHTTEEEE CS
                          Fer2  40 CgtClvevlegevqsdetelegeeldegklrl 71 
                                   Cg C+  +    vq+d+++l  +  ++g++ l
  gi|70606765|ref|YP_255635.1| 159 CGLCVSACP--AVQEDPEFLGPAAHAKGFRFL 188
                                   999997655..456667777777777776655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                                   EEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTE CS
                          Fer2   9 evevadgettlldaaeenggidipysCggggCgtCl 44 
                                   ++ +++ +t+  + ++    id  + C    C +C 
  gi|70606765|ref|YP_255635.1| 186 RFLADPRDTITEERLK-I-LIDSAWRCT--YCYMCY 217
                                   5556666664444443.3.788888887..777775 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   0.00013      0.13       4      15 ..     156     167 ..     151     177 .. 0.91
   2 ?   10.4   1.7   0.00077      0.76       3      16 ..     209     222 ..     208     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                        Fer4_4   4 CigCgsCvaaCP 15 
                                   Ci Cg Cv+aCP
  gi|70606765|ref|YP_255635.1| 156 CIWCGLCVSACP 167
                                   899********* PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00077
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   rC+ C  C+++CP 
  gi|70606765|ref|YP_255635.1| 209 RCTYCYMCYNVCPR 222
                                   8************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2073.77
//
Query:       gi|70606766|ref|YP_255636.1|  [L=566]
Description: succinate dehydrogenase flavoprotein subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.3e-110  368.7   0.3   5.2e-110  368.4   0.3    1.1  1  FAD_binding_2   FAD binding domain
    1.3e-43  148.0   0.2      2e-43  147.4   0.2    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.8e-05   24.5   1.5    0.00021   21.0   1.4    2.2  1  DAO             FAD dependent oxidoreductase
    6.8e-05   22.3   0.1    0.00012   21.5   0.1    1.3  1  FAD_binding_3   FAD binding domain
    0.00028   21.1   1.0     0.0011   19.2   1.0    2.1  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00034   19.4   1.6    0.00071   18.4   0.9    1.8  2  HI0933_like     HI0933-like protein
     0.0014   17.9   1.3     0.0044   16.3   0.3    2.2  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0092   15.1   2.6      0.025   13.7   2.4    1.8  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.015   14.6   1.0      0.065   12.5   0.2    2.4  3  Thi4            Thi4 family
      0.032   13.3   0.1       0.06   12.4   0.1    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.078   12.3   0.1       0.14   11.5   0.1    1.4  1  TMP-TENI        Thiamine monophosphate synthase
      0.099   11.9   1.3       0.12   11.6   0.2    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.4   0.3  3.5e-113  5.2e-110       1     417 []       7     386 ..       7     386 .. 0.99

  Alignments for each domain:
  == domain 1  score: 368.4 bits;  conditional E-value: 3.5e-113
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHH CS
                 FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqpl 81 
                                   D+++iG+GlAGL+AA+e+++aG + av++k++++++++a+++Ggi+a+ ++++  +  +dsp+++++dt+k++d+l dq++
  gi|70606766|ref|YP_255636.1|   7 DAVIIGAGLAGLMAAHEISKAGYSAAVISKVFPTRSHSAAAEGGIAAYVNGNS--D-PNDSPDYMAYDTIKGGDYLVDQDA 84 
                                   89**************************************************9..5.55********************** PP

                                   HHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEEES CS
                 FAD_binding_2  82 veafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdfqer 161
                                   +e+++ +++e v+ Le++g+ f+r++dg++++r +Gg++ + rt + ++d+      tg all++l+e+    g vdf+++
  gi|70606766|ref|YP_255636.1|  85 AELLAYKSGEIVELLEKWGALFNRQPDGRIALRYFGGQTYP-RTRF-VGDK------TGMALLHTLYERTSGSGkVDFYFE 157
                                   *****************************************.****.****......*************9999******* PP

                                   EEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES CS
                 FAD_binding_2 162 teadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnd 242
                                   ++a eLi+++ rv+G+v+ +++++  + ++akavv+a+gG+g            +++ttn  + tGdg a+alra++al+d
  gi|70606766|ref|YP_255636.1| 158 WFAWELIRDESRVRGVVAFDMRNMVPFFFKAKAVVIAAGGMGM----------LYRHTTNSYIGTGDGYAMALRARVALKD 228
                                   ******************************************9..........**************************** PP

                                   ..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH.HHHHTTTS..CCBEE CS
                 FAD_binding_2 243 drmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsrailekeiaeggs..eanvy 314
                                     +e+vqfhPt+l+    +s iLi+ea+rgeG++l +++G+rFm        +la+rd+vsrai+ +ei+eg++  + +v 
  gi|70606766|ref|YP_255636.1| 229 --PEFVQFHPTALY----PSDILISEAARGEGAVLKNAKGERFMtryapkkLDLAPRDIVSRAII-TEIKEGRGfpGGYVG 302
                                   ..************....***********************************************.********9999*** PP

                                   EE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTE CS
                 FAD_binding_2 315 ldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGL 395
                                   ld+sh l++e ++++l+  +e+a+++ +      +d++++ ip       ++pa+hy mgG+ +d +g+        + GL
  gi|70606766|ref|YP_255636.1| 303 LDISH-LGEEYIKERLALAYEAAKTFSG------VDATKELIP-------IRPAHHYYMGGIDVDITGKN-----PDVIGL 364
                                   *****.*******************999......*********.......*******************9.....9***** PP

                                   EE-STCEESSSSTTS--TTHHH CS
                 FAD_binding_2 396 YAaGevaaggvhganrlgGnsl 417
                                   +AaGe+a+++vhganrlg+nsl
  gi|70606766|ref|YP_255636.1| 365 FAAGEAACVSVHGANRLGSNSL 386
                                   ********************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.2   1.4e-46     2e-43       2     128 .]     442     566 .]     441     566 .] 0.97

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 1.4e-46
                                   HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTBE CS
                Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaHa 82 
                                   ++L++ m++ vg++R+e+gLk+a++e+ +lre++kn+ v dkskv+N+e+ +alel+n+++l+ +ia  Al+RkESrGaH+
  gi|70606766|ref|YP_255636.1| 442 EKLRDYMWEFVGIYRDENGLKNAVSEILKLREQMKNMYVLDKSKVYNTEFYNALELKNMIDLGLVIASTALNRKESRGAHY 522
                                   589****************************************************************************** PP

                                   BTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                Succ_DH_flav_C  83 redfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                   r+d+p+rdD+nwlkht+a+l+   ++ve++y+pv++++ kp+eR+Y
  gi|70606766|ref|YP_255636.1| 523 RTDYPKRDDQNWLKHTIAYLSG--NTVEITYKPVKMTKWKPEERVY 566
                                   ******************8775..58*******************9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.4   1.4e-07   0.00021       1      52 [.       7      61 ..       7     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS...STHH CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl...rylp 52
                                  d viiG+G +Gl +A+e +++g   +++ k  ++ +  S ++ g +++++   +  p
  gi|70606766|ref|YP_255636.1|  7 DAVIIGAGLAGLMAAHEISKAGysAAVISKV-FPTRSHSAAAEGGIAAYVngnS-DP 61
                                  78****************************9.8888999999999999776541.22 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   7.8e-08   0.00012       2      39 ..       6      43 ..       5      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.8e-08
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                  +d +I+GaG+aGlm+a++ s+aG +  ++ k   t  +
  gi|70606766|ref|YP_255636.1|  6 YDAVIIGAGLAGLMAAHEISKAGYSAAVISKVFPTRSH 43
                                  5889*************************998766655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.0   7.3e-07    0.0011       1      26 [.      10      35 ..      10      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.3e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE- CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvllle 26
                                  I+GaGl+Gl aA++++kag++  ++ 
  gi|70606766|ref|YP_255636.1| 10 IIGAGLAGLMAAHEISKAGYSAAVIS 35
                                  9*******************998875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.9   4.8e-07   0.00071       2      31 ..       7      36 ..       6      56 .. 0.93
   2 ?   -1.9   0.0      0.66   9.9e+02     153     167 ..     186     200 ..     165     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                  d ++iG+G AGlmaA +++k+g + +++ k
  gi|70606766|ref|YP_255636.1|  7 DAVIIGAGLAGLMAAHEISKAGYSAAVISK 36
                                  89***********************99976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                   EEESEEEE----SS- CS
                   HI0933_like 153 leadklvlAtGGlSi 167
                                   ++a+++v+A GG+ +
  gi|70606766|ref|YP_255636.1| 186 FKAKAVVIAAGGMGM 200
                                   689999999999865 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   2.9e-06    0.0044       1      36 [.       6      39 ..       6      63 .. 0.86
   2 ?   -3.8   0.0       3.8   5.7e+03      99     109 ..     187     197 ..     174     200 .. 0.85
   3 ?   -1.0   0.0      0.53   7.9e+02     255     278 ..     347     371 ..     314     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-06
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcl 36
                                  +d v+iG+G AGl aa+++++ag+  +++   + ++
  gi|70606766|ref|YP_255636.1|  6 YDAVIIGAGLAGLMAAHEISKAGYSAAVI--SKVFP 39
                                  588**********************9999..44454 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.8
                                   EESEEEE---E CS
                                   xxxxxxxxxxx RF
                   Pyr_redox_2  99 aydklvlAtGs 109
                                   +++++v+A G+
  gi|70606766|ref|YP_255636.1| 187 KAKAVVIAAGG 197
                                   78999999996 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.53
                                   TTEEE--TTSBES.STTEEE-GGGC CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Pyr_redox_2 255 rggivvdeflrtn.vpgiyaiGDva 278
                                    ggi vd +++   v g++a+G  a
  gi|70606766|ref|YP_255636.1| 347 MGGIDVDITGKNPdVIGLFAAGEAA 371
                                   59999**9998766********988 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   2.4   1.7e-05     0.025       1      28 [.       7      34 ..       7      58 .. 0.84
   2 ?   -1.8   0.0      0.83   1.2e+03     124     150 ..     166     197 ..     160     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                  d ++iG+G+AG+ AA +++++G++ + i
  gi|70606766|ref|YP_255636.1|  7 DAVIIGAGLAGLMAAHEISKAGYSAAVI 34
                                  579********************99988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.83
                                   CTTEEEEEEETTS-.....EEEECEEEE--TT CS
                          GIDA 124 eekkvkgvvtedge.....tikakavviatGt 150
                                   +e++v+gvv  d +      +kakavvia+G 
  gi|70606766|ref|YP_255636.1| 166 DESRVRGVVAFDMRnmvpfFFKAKAVVIAAGG 197
                                   556666666554441111157899******98 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.3e-05     0.065      17      48 ..       5      35 ..       1      52 [. 0.87
   2 ?   -2.9   0.0       2.1   3.1e+03     127     167 ..     165     196 ..     163     202 .. 0.55
   3 ?   -1.0   0.0      0.56   8.4e+02     212     233 ..     361     383 ..     351     384 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvaile 48
                                    D vi+GaG +GL aa+ ++k+ +   a++ 
  gi|70606766|ref|YP_255636.1|  5 SYDAVIIGAGLAGLMAAHEISKA-GYSAAVIS 35
                                  5699******************9.88888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                   ETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--G CS
                          Thi4 127 regegvaGvvinwtlvelahdtqscvDPlvirakvvvdatG 167
                                   r++++v+Gvv      ++       + P + +ak+vv a+G
  gi|70606766|ref|YP_255636.1| 165 RDESRVRGVVA----FDMRN-----MVPFFFKAKAVVIAAG 196
                                   55566666653....22222.....5566666666665555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.56
                                   ETTEEE-THHH.HHHHT-EB--S CS
                          Thi4 212 vpnlyvaGmev.aevdganRmGp 233
                                   v +l++aG ++   v+ganR+G+
  gi|70606766|ref|YP_255636.1| 361 VIGLFAAGEAAcVSVHGANRLGS 383
                                   568999997651689******96 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     4e-05      0.06       1      30 [.       7      34 ..       7      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvli 30
                                  D v+iGaG+Agl  A+++  +k+g +  +i
  gi|70606766|ref|YP_255636.1|  7 DAVIIGAGLAGLMAAHEI--SKAGYSAAVI 34
                                  88****************..5555555444 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.5e-05      0.14      95     140 ..       7      52 ..       1      58 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                      TMP-TENI  95 pdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgle 140
                                   + +iiG+   +l  a+e+ ++g +  +++++fpT +++ a+  g++
  gi|70606766|ref|YP_255636.1|   7 DAVIIGAGLAGLMAAHEISKAGYSAAVISKVFPTRSHSAAAEGGIA 52 
                                   678***********************************99888876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   8.1e-05      0.12       1      28 [.       9      35 ..       9      43 .. 0.87
   2 ?   -2.8   0.1       1.9   2.8e+03     123     136 ..     186     199 ..     185     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilE 28
                                  +IiGaG aGl aa+e+ kag +   ++ 
  gi|70606766|ref|YP_255636.1|  9 VIIGAGLAGLMAAHEISKAGYS-AAVIS 35
                                  7********************5.56665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                   Pyr_redox_3 123 yeAkkviiAtGefd 136
                                   ++Ak v+iA+G ++
  gi|70606766|ref|YP_255636.1| 186 FKAKAVVIAAGGMG 199
                                   689********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3704.23
//
Query:       gi|70606767|ref|YP_255637.1|  [L=263]
Description: hypothetical protein Saci_0983 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-23   80.6   0.0    1.5e-22   79.6   0.0    1.5  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    2.1e-18   66.2   0.0    5.3e-18   64.8   0.0    1.7  1  Hydrolase_like  HAD-hyrolase-like
    9.1e-06   26.1   0.0    4.3e-05   23.9   0.0    2.3  1  Hydrolase       haloacid dehalogenase-like hydrolase
    4.7e-05   23.6   0.3    0.00018   21.6   0.0    2.1  2  HAD_2           Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.13   12.5   0.3        1.8    8.8   0.0    2.6  3  UPF0180         Uncharacterised protein family (UPF0180)


Domain annotation for each model (and alignments):
>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   4.2e-26   1.5e-22       1     101 []       9     109 ..       9     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.2e-26
                                   EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHSXXX CS
                   Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkrkadk 81 
                                   +++DidGv++r++++i     a++ l +agk+v+llTNns+ s+  +  +l+ lg++i++e +vts+ta+a y+k++ + k
  gi|70606767|ref|YP_255637.1|   9 IISDIDGVILREGEPIWPNFLAIKKLSEAGKKVLLLTNNSGFSRVLLSRQLSYLGLKISPEYIVTSGTATAIYMKEQSNIK 89 
                                   689****************************************************************************** PP

                                   EEEEESXHHHHHHHHHTTXE CS
                   Hydrolase_6  82 kvlvigeeglreelkeagfk 101
                                   +v+v+geegl eelk+ gf+
  gi|70606767|ref|YP_255637.1|  90 TVFVVGEEGLIEELKNFGFE 109
                                   ******************96 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   1.5e-21   5.3e-18       2      75 .]     188     262 ..     187     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.5e-21
                                   .STTSSHHHHHHHHHH---.GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                Hydrolase_like   2 lgKPepemydfalevlgsd.peevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                   +gKP+ +m++ a +  g++ +++ +miGD+l+tDi+++ na +++vLVltG+++++dle+  +kp++v+++l+e+
  gi|70606767|ref|YP_255637.1| 188 AGKPNIWMIKVAFKIAGLKdFSRAIMIGDQLETDIKMGLNANIDTVLVLTGINTRKDLEASDIKPKFVVNTLTEL 262
                                   69**************8877****************************************99**********986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.2e-08   4.3e-05       2     210 .]       7     229 ..       6     229 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                                   SEEEEESBTTTB.CHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH..HHHHHHHHHETTTEHHHHTHHHHHHH CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   2 ktvvfDkdGTLt.tgepsvedvivsaalalaaaletgsehpigkalvaaakar..sgaltgfatfigrgayaigkpewlta 79 
                                   ++++ D+dG+++ +gep    +++                    +l +a k++    + +gf +     +++  +  +l  
  gi|70606767|ref|YP_255637.1|   7 DLIISDIDGVILrEGEPIWPNFLAIK------------------KLSEAGKKVllLTNNSGFSR-----VLLSRQLSYLGL 64 
                                   78999******988887777766666..................44444444433222244444.....444444444444 PP

                                   H......HCHHHHHHHHHHHHHHCHHHHHH.......................TTHHHHHHHHHHTHHBHTTHHHHHHHHH CS
                                   x......xxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase  80 l......dippdlgaaigsaqsqgrtvall.......................qaralavftiadplkvkpeaaeavasLk 131
                                            +    a   ++qs  +tv+++                       +   +av+   d l+ ++++  a++s  
  gi|70606767|ref|YP_255637.1|  65 KispeyiVTSGTATAIYMKEQSNIKTVFVVgeeglieelknfgfevlgireanEETPDAVVIGLDRLSTYEKLSTAMRSVY 145
                                   4444443333444444444444555555555555555555555555555666656************************66 PP

                                   HTTEEEEEEESSEHHHHH.HHHHH.TTGGGE.SEEEEHHCES........STTTSHHHHHHHHHHHTST.GGGEEEEESSH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxx.xxxxxx.xxxxxxxxxx........xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                     Hydrolase 132 aagievvlltgdnpetae.raanq.lGddyf.daviasdiet........vakpspegkvaaireLqgk.peevamVGDgv 200
                                    +g   +++t+ ++  +    ++  +G  ++ + +i     +         +kp+ ++ + a +  + k  ++ +m+GD +
  gi|70606767|ref|YP_255637.1| 146 -KGS-KFIVTNMDRLWPSkDGLKLgAG--AIaSTIIY----AlkrnpdfiAGKPNIWMIKVAFKIAGLKdFSRAIMIGDQL 218
                                   .466.89*******9999666666666..22122222....1333468899****************555*********** PP

                                   H.HHHHHHHTT CS
                                   x.xxxxxxxxx RF
                     Hydrolase 201 n.DaaalaaAg 210
                                     D++++ +A+
  gi|70606767|ref|YP_255637.1| 219 EtDIKMGLNAN 229
                                   ******98885 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.69   2.5e+03      88     127 ..      31      73 ..      26      79 .. 0.70
   2 !   21.6   0.0   5.1e-08   0.00018     130     178 .]     185     235 ..     113     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                         HAD_2  88 LeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivt 127
                                   +++L+eag k+ + T++   sr  + ++l+ lg++   + ivt
  gi|70606767|ref|YP_255637.1|  31 IKKLSEAGKKVLLLTNNsgfSRVLLSRQLSYLGLKISPEYIVT 73 
                                   7899999999999999844445556666666666666666665 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5.1e-08
                         HAD_2 130 dvekkKPdpeviekaleklklkk.eeviyvGDsp.tDieaakkagikviav 178
                                   d+   KP+  +i+ a +  +lk  +++i++GD+  tDi+ + +a+i+++ v
  gi|70606767|ref|YP_255637.1| 185 DFIAGKPNIWMIKVAFKIAGLKDfSRAIMIGDQLeTDIKMGLNANIDTVLV 235
                                   45566****************97589**********************976 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.082     3e+02      37      65 ..      70      99 ..      34     102 .. 0.83
   2 ?    8.8   0.0   0.00049       1.8      13      40 ..     100     126 ..      96     158 .. 0.79
   3 ?   -3.0   0.0       2.5   8.8e+03      33      46 ..     228     242 ..     217     256 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.082
                       UPF0180 37 aiVvtGqdtnv.mgiedtetkapvInAsgk 65
                                   iV++G  t + m+++ +   ++v+  +g+
  gi|70606767|ref|YP_255637.1| 70 YIVTSGTATAIyMKEQSNIKTVFVVGEEGL 99
                                  689999888876888889999999877765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00049
                       UPF0180  13 keaLrekGYeVvdleteedaqsvdaiVv 40 
                                    e+L++ G+eV  ++ e++++  da+V+
  gi|70606767|ref|YP_255637.1| 100 IEELKNFGFEVLGIR-EANEETPDAVVI 126
                                   589************.59999****998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.5
                       UPF0180  33 qsvdaiVv.tGqdtn 46 
                                    ++d + v tG +t+
  gi|70606767|ref|YP_255637.1| 228 ANIDTVLVlTGINTR 242
                                   455544444666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1790.24
//
Query:       gi|70606768|ref|YP_255638.1|  [L=95]
Description: hypothetical protein Saci_0984 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 656.65
//
Query:       gi|70606769|ref|YP_255639.1|  [L=528]
Description: hypothetical protein Saci_0985 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.1e-102  342.7   2.5   3.6e-102  342.5   2.5    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.5   2.5    2e-106  3.6e-102       2     563 ..       8     520 ..       7     521 .. 0.94

  Alignments for each domain:
  == domain 1  score: 342.5 bits;  conditional E-value: 2e-106
                       DUF2070   2 eklskyifrlPswk.vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflallteli 81 
                                   +k++++++rlPs++ v  +++i +all          l ++l fg+ +++ fl++l ++ ++    ++k s+fl llte++
  gi|70606769|ref|YP_255639.1|   8 RKYYSKLKRLPSFRiVFSIFAIEFALL----------LVRSLEFGILYIIPFLIYLLCVLLI--VREIKLSIFLGLLTEFV 76 
                                   69***********99999999999999..........889999************9999776..4467899********** PP

                       DUF2070  82 vviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllsl 162
                                   ++i+sl+ + ++              +a+ +  +++ ++++++ s+lk++l ++++++l  l++ l       + +ll+sl
  gi|70606769|ref|YP_255639.1|  77 YLIFSLFTSQTV--------------FAFGILAPFFGYLMLGKLSELKSTLSVFVTSFLPSLISGLN------YYVLLYSL 137
                                   **********99..............8999*********************************9999......89****** PP

                       DUF2070 163 ifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skelEeffeeigeeadvpvkvlsfrredgekallvvPniHP 242
                                   i+a++++++i++v+ +++r++g+++l ll+ Fl +++++ +k +E+f++ +g++++++v ++++     ++ ++++P+iH+
  gi|70606769|ref|YP_255639.1| 138 IIAVVFHFYIHIVNVKGERITGFKSLTLLRPFLMSVMRNdNKLVEKFLDGVGTKIVTNVGMFKI-----GNHHFIIPKIHY 213
                                   ***************************************55666********************.....************ PP

                       DUF2070 243 GPlgeiGGsnLpkilaerldelvlvlHgtatHdfNlvserevekiveavkealeeleysskaskpvrvesgd.vkllgqrf 322
                                   G  geiG+s+++++l++ +++ v+v+Hg+++H+++lv+++e++++++ + ++ ++ +  s+    ++v ++  ++ ++++f
  gi|70606769|ref|YP_255639.1| 214 GLNGEIGSSKFIYQLESIIPN-VIVFHGPGDHELDLVTSSESRRVADFIGNEIKDGKWLSQKFYGIHVWYNCgFRGVTLVF 293
                                   *******************88.***********************************6666666788888888******** PP

                       DUF2070 323 gdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevlpgsedaeeliraaekalekl.eaaee 402
                                    ds+l+++ r+  giDD+p +++++ +++       + +++D+HN++ +e+ +     +  e+++++++ a + l e + e
  gi|70606769|ref|YP_255639.1| 294 SDSTLTFLERPGLGIDDLPVKLWENSVKY-------NDYIIDCHNEYLQEELP----LNSRECIMQGINYAKNVLrERRVE 363
                                   **********************9999997.......559*************9....78899999999999999989**** PP

                       DUF2070 403 selkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealke.vdlevevmTTDtHvvngv 482
                                   + lk+ + ++++++  p egl++++i+v++l+ +++++ +v++++NN +p l + +re+l + v+    ++T+D+H+++g 
  gi|70606769|ref|YP_255639.1| 364 RALKIAIEERTISN--P-EGLCSNKIKVAALSDGNTTVGIVYLYANNADPSLTKSLRESLGKyVN-IPLLITPDDHSCTGS 440
                                   ********999995..4.8*******************************************999.**************8 PP

                       DUF2070 483 slgynpvGekvs....kdelielvlelvekAiadlepvevgyaterve.vkvfgedrfeelvstvnsvvsvakilaaalll 558
                                   +     +G+ ++      el  l++++ ++A+++l+++evg+ + +++ vkv+g+ +++++v ++++++ ++++++++ l+
  gi|70606769|ref|YP_255639.1| 441 E-----LGNLYTpaqfSPELPSLAEKTLNDALNKLQDCEVGFNRLDLKgVKVIGK-IISSFVVALEEIGGYVMKTFWIPLV 515
                                   7.....665554445589999**********************************.7************************ PP

                       DUF2070 559 laill 563
                                   l+++l
  gi|70606769|ref|YP_255639.1| 516 LPLFL 520
                                   **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3695.42
//
Query:       gi|70606770|ref|YP_255640.1|  [L=452]
Description: hypothetical protein Saci_0986 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-13   50.7   0.0      4e-07   29.9   0.0    2.1  2  DAO             FAD dependent oxidoreductase
    9.3e-12   44.7   0.1    3.3e-06   26.5   0.1    2.2  2  FAD_binding_2   FAD binding domain
    1.1e-07   31.5   0.0    6.2e-07   29.1   0.0    2.0  1  FAD_oxidored    FAD dependent oxidoreductase
    1.5e-07   31.0   0.1    3.7e-06   26.4   0.0    2.6  2  FAD_binding_3   FAD binding domain
    2.7e-07   30.0   0.0    6.5e-07   28.8   0.0    1.6  2  GIDA            Glucose inhibited division protein A
    3.9e-07   30.2   0.0    3.8e-06   27.0   0.0    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.2e-06   28.0   0.0    2.3e-06   27.1   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00012   21.4   0.0      0.001   18.3   0.0    2.1  2  Thi4            Thi4 family
    0.00012   21.1   0.0       0.02   13.7   0.0    2.3  3  Trp_halogenase  Tryptophan halogenase
    0.00057   20.4   0.0     0.0024   18.4   0.0    2.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0026   16.5   0.0     0.0044   15.8   0.0    1.3  1  HI0933_like     HI0933-like protein
     0.0035   16.4   0.0     0.0064   15.6   0.0    1.4  1  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.088   12.0   0.0       0.94    8.7   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.15   11.3   0.0       0.28   10.4   0.0    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.1e-10     4e-07       1      29 [.       7      37 ..       7      44 .. 0.95
   2 !   18.9   0.0   7.2e-07   0.00092     135     334 ..      88     309 ..      50     322 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.1e-10
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                  dv+iiGGG +G+s+Ay+L+rrg  ++l++++
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQLSRRGlkILLVDSK 37
                                  8****************************87 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.2e-07
                                   EEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEE...EECT.EEE.EEEEEEEE--GGGHHHH.H CS
                           DAO 135 lfypdtgqvdpakltaalaraaealGveilegtevtg.leeedgkvwgve...rttp.gen.daadavVnaaGawsdll.g 208
                                    ++ ++  +++  + + ++++a+++Gvei   t++ + +  edg v+g     r t+ + +  + + vV a+G +s+ +  
  gi|70606770|ref|YP_255640.1|  88 TVNGEGFELNAPLYNQRVLKEAQDRGVEIWDLTTAMKpI-FEDGYVKGAVlfnRRTNeELTvYS-KVVVEATG-YSRSFrS 165
                                   4566778889**************************966.456555555567866764655334.77*****9.7786656 PP

                                   TT.CTTTSEEEE.........EEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTS CS
                           DAO 209 ll.keldlpisp.........vrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpe 279
                                   +l +el  pi+          +  +vl +k+  e  ++ ++   + + + +g++  ++p  +++v vG         +   
  gi|70606770|ref|YP_255640.1| 166 KLpPEL--PITEdlddkdadvAYREVLLTKEDIE--DHDYLRIFIDQETSPGGYWWYFPKGKNKVNVGLGI------QGGM 236
                                   666666..44334444444448888888855444..3556666666699999999999*999999999754......3335 PP

                                   CSHHHHHHHHHHHHHHSGG.....G...........CGEEE.EEEEEEEETTSSEEEEEEE.TEEEEEEEEEC CS
                           DAO 280 vdeedidellealrklfPq.....l...........gdvlr.kwaGlrplpdglpligetp.gvkglylatGh 334
                                     +   +++ ++l k+ P+     l           +++   +w G+    d ++ + +++ g kg  + +G+
  gi|70606770|ref|YP_255640.1| 237 GYPSIHEYYKKYLDKYAPDvdkskLlvkggalvptrRPLYTmAWNGIIVIGDSGFTVNPVHgGGKGSAMISGY 309
                                   5566666666666666666431110111111111103322235555555444433333322223455554444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   2.6e-09   3.3e-06       1      32 [.       7      38 ..       7      43 .. 0.94
   2 !   16.4   0.0   2.9e-06    0.0038     146     203 ..     104     160 ..      38     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.6e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                  Dv++iG+G+AG +AA++++++Glk+++v+ ++
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQLSRRGLKILLVDSKP 38
                                  9***************************9876 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
                 FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfg 203
                                   r++++a+++gv++++ t a + i edg v Gav+ n+++ +e ++ +k vv atg ++
  gi|70606770|ref|YP_255640.1| 104 RVLKEAQDRGVEIWDLTTAMKPIFEDGYVKGAVLFNRRTNEELTVYSKVVVEATG-YS 160
                                   4445567777***************************999999988887777776.44 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   4.8e-10   6.2e-07       1     144 [.       7     158 ..       7     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.8e-10
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergv..lGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkkrs 79 
                                   Dv+++GGg aG  AA++  r+G k lLv+ +++  +G    + +v+     k      +g  +e+ ++++  + ++   ++
  gi|70606770|ref|YP_255640.1|   7 DVLIIGGGFAGSSAAYQLSRRGLKILLVDSKPWnrIGDKPCGDAVSKAHFDKLGMPYPKG--EELENKINGIKLYSPDMQT 85 
                                   9****************************9988557777776666555444433344444..6666666553334223334 PP

                  FAD_oxidored  80 kw..n.....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                    w  n        p  +++vl+e  ++ gv+++  t++ +++ e++ +++ ++ +++ + + t+ +kv++ ATg
  gi|70606770|ref|YP_255640.1|  86 VWtvNgegfeLNAPLYNQRVLKEAQDR-GVEIWDLTTAMKPIFEDGYVKGAVLFNRRtNeELTVYSKVVVEATG 158
                                   443225555567777777777777666.9999999999999999888999999999876799999999999998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.9e-09   3.7e-06       2     180 ..       6     175 ..       5     213 .. 0.80
   2 ?   -0.7   0.1      0.53   6.8e+02     283     317 ..     280     314 ..     269     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.9e-09
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                 FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                   +dVlI+G+G aG ++a  Ls++G + +lv+   ++    + +g +  +   +++lG+     +e   n+++g+ ly +   
  gi|70606770|ref|YP_255640.1|   6 YDVLIIGGGFAGSSAAYQLSRRGLKILLVDSKPWNRIGDKPCG-DAVSKAHFDKLGMPYPKGEEL-ENKINGIKLYSP--- 81 
                                   79********************************999988877.455667899999987766665.899999999999... PP

                                   CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEE.EECCEECCCCCCCEEEECCTTEEEEEEEEEEEE-- CS
                 FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfkte.vesleqdeegvtaevrdketgeeetvrakYlvGaD 162
                                     + ++  +   ++e  ++    + +r+L e+ + rg+++   t  ++ + +d+    a++ +++t+ee tv +k +v a 
  gi|70606770|ref|YP_255640.1|  82 --DMQTVWT--VNGEGFELNAPLYNQRVLKEA-QDRGVEIWDLTTaMKPIFEDGYVKGAVLFNRRTNEELTVYSKVVVEAT 157
                                   ..5555555..556666666666666777666.999999987766588888899888899999999999999999999999 PP

                                   GTT-HHHHHHTGGEEEEE CS
                 FAD_binding_3 163 GgrStvrktlgiefegee 180
                                   G+    r++l+ e++ +e
  gi|70606770|ref|YP_255640.1| 158 GYSRSFRSKLPPELPITE 175
                                   998888888887765555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.53
                                   ETTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHH CS
                 FAD_binding_3 283 kgrvflaGDAaHihpPtgGqGlNtaiqDavnLawk 317
                                    + + ++GD+  ++ P++G G  +a+   +  a++
  gi|70606770|ref|YP_255640.1| 280 WNGIIVIGDSGFTVNPVHGGGKGSAMISGYCAAKA 314
                                   567899***************99999877776665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   5.1e-10   6.5e-07       1      44 [.       7      51 ..       7      59 .. 0.92
   2 ?   -2.9   0.0       2.1   2.7e+03     133     149 ..     142     158 ..     102     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.1e-10
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsi 44
                                  dv +iGgG AG+ AA++++r+G+k+lL+  +  ++i+  +C +++
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQLSRRGLKILLVdSKPWNRIGDKPCGDAV 51
                                  799*************************76778999999998887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                   ETTS-EEEECEEEE--T CS
                          GIDA 133 tedgetikakavviatG 149
                                   t+++ t+ +k+vv atG
  gi|70606770|ref|YP_255640.1| 142 TNEELTVYSKVVVEATG 158
                                   45566677778888887 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     3e-09   3.8e-06       1      28 [.      10      37 ..      10      65 .. 0.87
   2 ?    0.2   0.0      0.72   9.3e+02      25      67 ..     206     247 ..     191     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3e-09
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                  I+G+G++G++aAy L+++g+++ll+++ 
  gi|70606770|ref|YP_255640.1| 10 IIGGGFAGSSAAYQLSRRGLKILLVDSK 37
                                  9*************************86 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.72
                                   E-SSSSSSGGG-EECETTCEECTS---EEETTHHHHCHHHHCC CS
                 NAD_binding_8  25 lekrdrlGGraasyevpgvrvdygahifhgsgyypnvrrllre 67 
                                   +++ +++GG +  +  ++++v++g  i  g+g yp + +++++
  gi|70606770|ref|YP_255640.1| 206 IDQETSPGGYWWYFPKGKNKVNVGLGIQGGMG-YPSIHEYYKK 247
                                   78999999999999998888888877777776.8999999887 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.8e-09   2.3e-06       1      31 [.       6      41 ..       6     187 .. 0.53

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.....T CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve.....l 31
                                  +dv++iGgG+AG +aa +l++ g+k++lv+     +
  gi|70606770|ref|YP_255640.1|  6 YDVLIIGGGFAGSSAAYQLSRRGLKILLVDskpwnR 41
                                  69***************************6444441 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.1e-07     0.001      17      50 ..       5      37 ..       1      44 [. 0.92
   2 ?    0.3   0.0      0.27   3.5e+02     155     172 ..     146     163 ..     132     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.1e-07
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                                  + Dv+i+G+G +G +aay l+++ +lk+++++++
  gi|70606770|ref|YP_255640.1|  5 KYDVLIIGGGFAGSSAAYQLSRR-GLKILLVDSK 37
                                  67*********************.*****99875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                                   EEEEEEEEEE--GSSSTT CS
                          Thi4 155 lvirakvvvdatGhdgei 172
                                   l++ +kvvv+atG+  ++
  gi|70606770|ref|YP_255640.1| 146 LTVYSKVVVEATGYSRSF 163
                                   7899*********98776 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.6e-05      0.02       1      39 [.       7      42 ..       7      52 .. 0.87
   2 !    4.8   0.0    0.0082        10     147     211 ..      92     161 ..      70     169 .. 0.78
   3 ?   -3.9   0.0       3.7   4.7e+03     316     350 ..     281     319 ..     272     336 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS--- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtv 39
                                  +++i+GGG aG+ aA  l++ +   l+++lv+s+   ++
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQLSRRG---LKILLVDSKPWNRI 42
                                  699*****************99...99****99865554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0082
                                   -EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.....S-EEE-SEEEE-SGGG- CS
                Trp_halogenase 147 yAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled.....greveadlfiDcsGfrg 211
                                    +++l+a ly++   + a++rGv++ + + +   + edg+v++  l +     + +v    ++ ++G+ +
  gi|70606770|ref|YP_255640.1|  92 EGFELNAPLYNQRVLKEAQDRGVEIWDLTTAMKPIFEDGYVKGAVLFNrrtneELTVYSKVVVEATGYSR 161
                                   5799**********************99999999999***998655433333366777788888888655 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.7
                                   TTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT- CS
                Trp_halogenase 316 knvvalGlasgfvePlestsihliqa....alrrLlall 350
                                   ++++ +G++   v+P+ + +   ++     a++ +l+ +
  gi|70606770|ref|YP_255640.1| 281 NGIIVIGDSGFTVNPVHGGGKGSAMIsgycAAKAILSAF 319
                                   357778888888888776543222222233555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0024       2      52 ..       8      57 ..       7      72 .. 0.81
   2 ?   -2.0   0.0       4.3   5.5e+03      44      61 ..     103     120 ..     100     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHH CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklek 52
                                  v+++GgG+ g  +A  l++ g k+ +v+ +++ +   D+ +++++ + + +
  gi|70606770|ref|YP_255640.1|  8 VLIIGGGFAGSSAAYQLSRRGLKILLVDSKPWNR-IGDKPCGDAVSKAHFD 57
                                  89****************************9988.7777777777655533 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                   HHHHHHHHHTTEEEECSE CS
                     Pyr_redox  44 kilqeklekngievllnt 61 
                                   +++ ++ +++g+e++  t
  gi|70606770|ref|YP_255640.1| 103 QRVLKEAQDRGVEIWDLT 120
                                   6788999999**998655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06    0.0044       1      32 [.       6      37 ..       6      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                  +dv++iGgG AG  aA ++++rg ++ll++++
  gi|70606770|ref|YP_255640.1|  6 YDVLIIGGGFAGSSAAYQLSRRGLKILLVDSK 37
                                  59****************************87 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     5e-06    0.0064       1      34 [.       7      38 ..       7      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                  Dv++iG+G Ag s A +l  ++ glk++l+++ p
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQL--SRRGLKILLVDSKP 38
                                  9*****************..**********8765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00073      0.94     166     200 ..       7      40 ..       2      50 .. 0.70
   2 ?    0.8   0.0      0.18   2.3e+02     242     272 ..     133     164 ..      96     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00073
                   Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseie 200
                                   +v++iGg+  +  aA++l r+g ++ +v+++  ++
  gi|70606770|ref|YP_255640.1|   7 DVLIIGGGFAGSSAAYQLSRRGLKILLVDSKP-WN 40 
                                   67777777777777777777777777766653.55 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                   Pyr_redox_3 242 eeeykvktedgkkvevkddvvla.tGykpdls 272
                                   +  +  + +++++++v+++vv+  tGy+ +++
  gi|70606770|ref|YP_255640.1| 133 KGAVLFNRRTNEELTVYSKVVVEaTGYSRSFR 164
                                   455666777788999988888766***98875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.28      30      61 ..       7      38 ..       4      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                   vl+iGgG aG +A+   ++ g k+ ++D +p
  gi|70606770|ref|YP_255640.1|  7 DVLIIGGGFAGSSAAYQLSRRGLKILLVDSKP 38
                                  69******************999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3110.69
//
Query:       gi|70606771|ref|YP_255641.1|  [L=140]
Description: hypothetical protein Saci_0987 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   11.8   0.2       0.36   10.3   0.0    1.8  2  Poty_coat  Potyvirus coat protein


Domain annotation for each model (and alignments):
>> Poty_coat  Potyvirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     2e-05      0.36      74     104 ..       6      35 ..       2      75 .. 0.79
   2 ?   -0.7   0.0     0.049   8.8e+02     117     138 ..      96     117 ..      80     136 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2e-05
                     Poty_coat  74 teeef.mstilpglivwCivngtsserskegs 104
                                   t++ f m++++p +++  ivn ts++  +   
  gi|70606771|ref|YP_255641.1|   6 TNTTFmMANLMPYSLIASIVNVTSENLDN--F 35 
                                   45555279*****************9983..3 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.049
                     Poty_coat 117 EqvlYplkPivenAqPtlRqim 138
                                     ++Y+++ i++  +   R im
  gi|70606771|ref|YP_255641.1|  96 KLLEYNIDGILIYCDEETRPIM 117
                                   3455555555554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1056.77
//
Query:       gi|70606772|ref|YP_255642.1|  [L=76]
Description: hypothetical protein Saci_0988 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 555.84
//
Query:       gi|70606773|ref|YP_255643.1|  [L=179]
Description: hypothetical protein Saci_0989 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-06   26.3   0.0    8.3e-06   26.1   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
     0.0042   16.5   0.0     0.0067   15.8   0.0    1.3  1  CCB1           Cofactor assembly of complex C subunit B


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   9.2e-10   8.3e-06      15     160 ..      16     167 ..       1     171 [. 0.71

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.2e-10
                 Metallophos_2  15 aleavlealkevgvdaiihaGD.......leeeep...evleellela...pvlaVrGNnDeevveedvlreaaelgtdl. 81 
                                   +  a+  ++k++++++i++ GD       +  e p   +vl+ ++++a   ++++++G++D   ++ ++  ++ ++++++ 
  gi|70606773|ref|YP_255643.1|  16 IESALSMIIKREEPETIVLNGDttqcywdY--ECPrviDVLYVIRSIApwaQIVYIQGDMD--PHAIKCIMAEPRYREEIl 92 
                                   445666789999**********55554332..3334445666667766999**********..433334444444444442 PP

                 Metallophos_2  82 .peeaelelagekvlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpetyail 160
                                    ++    e+  +k +++Hg+    ++++++l++++ +g    +v+G   + ev+k    +v++ G +++   +d ++y+++
  gi|70606773|ref|YP_255643.1|  93 aTTMYIAEVSSVKYFIVHGH----QNDIDQLRRSMGAGPWdWIVLGQYKRLEVDKL--ARVIYIGGITREFPSDSRGYLVI 167
                                   2255567778999*******....78888888886666656*******99999999..79999999999999999888876 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.4e-07    0.0067     103     166 ..      47     124 ..      43     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.4e-07
                          CCB1 103 vpelgnlflllvllsPlAgvfYwkkakrkeqvslkles..............eeeeseseitveahrdeleelqkelk 166
                                   +p++  +++++  ++P+A ++Y +   ++  ++  + +              +e +s +  +v++h++++++l+++++
  gi|70606773|ref|YP_255643.1|  47 CPRVIDVLYVIRSIAPWAQIVYIQGDMDPHAIKCIMAEpryreeilattmyiAEVSSVKYFIVHGHQNDIDQLRRSMG 124
                                   5777889999***************************9*************99999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1126.34
//
Query:       gi|70606774|ref|YP_255644.1|  [L=166]
Description: hypothetical protein Saci_0990 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.074   13.1   0.8      0.074   13.1   0.8    1.6  2  Neur_chan_memb  Neurotransmitter-gated ion-channel transmembr
        4.8    7.1  15.1        0.5   10.3   2.1    2.7  3  DUF1275         Protein of unknown function (DUF1275)


Domain annotation for each model (and alignments):
>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   8.3e-06     0.074      54      95 ..      16      58 ..       8      69 .. 0.80
   2 ?   -3.3   0.1      0.85   7.6e+03      38      49 ..      99     110 ..      91     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-06
                                  S-STTHHHHHHHHHHHHHHHHHHHHHHHHH.H-S-S---HHHH CS
                Neur_chan_memb 54 ipLigkYLlftmvfvtlsivetvfVlnvhh.rsprthtmpawv 95
                                  +pLi  YLl  ++fv++s + +++V+++    +  t t+ + v
  gi|70606774|ref|YP_255644.1| 16 LPLIPAYLLNFLAFVISSAIGFIIVIYIMIsNKTWTDTKNKVV 58
                                  7**************************9974444455555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.85
                                   HHHHHHHHHHHH CS
                Neur_chan_memb  38 vfllliteilPk 49 
                                    f+ll+++ilPk
  gi|70606774|ref|YP_255644.1|  99 QFILLAKDILPK 110
                                   477888888886 PP

>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7     0.047   4.2e+02      50      67 ..      22      39 ..       2      53 .. 0.55
   2 ?    3.6   3.2    0.0062        55      38      92 ..      44     101 ..      25     117 .. 0.54
   3 ?   10.3   2.1   5.6e-05       0.5     150     190 ..     119     159 ..      97     163 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.047
                       DUF1275 50 alvsllaFvlGaalagll 67
                                  +l+ +laFv+ +a++ ++
  gi|70606774|ref|YP_255644.1| 22 YLLNFLAFVISSAIGFII 39
                                  445555555555555544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0062
                       DUF1275  38 alaegna.....kaalaalvsllaFvlGaalagllarrggrrrrlvllleallllaaall 92 
                                    + ++ +     k + +++   ++F++G++l+++l+ +  +r+ ++  l  +l +++ ++
  gi|70606774|ref|YP_255644.1|  44 MISNKTWtdtknKVVGTYFS--GVFATGVVLGEFLELYSATREFAIAGLVFVLPFIVQFI 101
                                   34445553332222222333..66777777777775443233333333334444555555 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 5.6e-05
                       DUF1275 150 larnrrlaiilafllGavvGallvks.aaalwlaaallllva 190
                                   +  n +l +++ +++Ga+vG +l+ + +  ++ ++ ++++++
  gi|70606774|ref|YP_255644.1| 119 F-SNGYLPMLIVIIIGALVGRMLTSFySLIILYSGTIVVALL 159
                                   3.68999*****************998444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1117.02
//
Query:       gi|70606775|ref|YP_255645.1|  [L=332]
Description: hypothetical protein Saci_0991 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-05   23.4   0.0    7.1e-05   22.2   0.0    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.7e-05   22.9   0.1    0.00021   21.5   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00023   20.9   0.1      0.024   14.2   0.1    2.1  2  DAO            FAD dependent oxidoreductase
     0.0042   16.2   0.0     0.0089   15.1   0.0    1.5  1  GIDA           Glucose inhibited division protein A
     0.0076   15.5   0.0      0.012   14.9   0.0    1.3  1  FAD_binding_3  FAD binding domain
     0.0093   15.2   0.4       0.37   10.0   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.021   13.5   0.0      0.037   12.7   0.0    1.4  1  HI0933_like    HI0933-like protein
      0.022   13.8   0.0      0.053   12.6   0.0    1.8  2  Lycopene_cycl  Lycopene cyclase protein
       0.15   11.2   0.0        1.4    8.1   0.0    2.2  2  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.6e-08   7.1e-05       2     119 ..       2     147 ..       1     161 [. 0.68

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.6e-08
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......................... 57 
                                   dv +iGgGpAGl++a +l+  +++ t++ ++   ++ ++     ++gv+e   i +                         
  gi|70606775|ref|YP_255645.1|   2 DVSIIGGGPAGLSLAWFLKGTKYNATVY-EGLDNVGYKPCAWGLITGVEELVPISKeaiigeikrfriylngkivhdiesk 81 
                                   899*************************.6666678888888999999999998888778777777777777666555444 PP

                                   ......HHHHCHHHHCCCCHC........CTCEEEEESCEEEEETEEEC....TCEEEEEESEEEE---..EEE-BCTCTT CS
                                   ......xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                   Pyr_redox_2  58 ......evvkklnqgielllg........eevvkidpgkkkvklekkke....gdeekiaydklvlAtG..ssprdlgipG 118
                                                       +        +e+v++ +++k ++  k  +    + ++k++ d ++  tG  s ++d +ip+
  gi|70606775|ref|YP_255645.1|  82 rrlgyiV-------------DkplflrdiAEKVNVQYNSKVIER-K--GeylvNGNQKLESDMVINSTGhySLSFDQTIPA 146
                                   3333330.............133334444556666555533333.2..133565567899999999999544566667777 PP

                                   C CS
                                   x RF
                   Pyr_redox_2 119 v 119
                                    
  gi|70606775|ref|YP_255645.1| 147 I 147
                                   6 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1     1e-07   0.00021       1      32 [.       5      36 ..       5      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                  I+G+G +Gl++A++L+  +++ +++e  d +G
  gi|70606775|ref|YP_255645.1|  5 IIGGGPAGLSLAWFLKGTKYNATVYEGLDNVG 36
                                  9*************************988887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.2e-05     0.024       1      28 [.       2      31 ..       2      67 .. 0.83
   2 ?    4.3   0.0     0.013        26     160     207 ..     100     139 ..      87     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                  EEEEECTSHHHHHHHHHHHHTT....EEEEES CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllek 28
                                  dv iiGGG +Gls A++L   g     t++e 
  gi|70606775|ref|YP_255645.1|  2 DVSIIGGGPAGLSLAWFLK--GtkynATVYEG 31
                                  899***************4..33367888885 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                                   T-EEEESECEEEEEEEETCEEEEEEECTEEE..EEEEEEEE--GGGHHHH CS
                           DAO 160 Gveilegtevtgleeedgkvwgverttpgen..daadavVnaaGawsdll 207
                                    v++ ++++v +   +   +  + +   g++  ++ d v+n++G++s  +
  gi|70606775|ref|YP_255645.1| 100 KVNVQYNSKVIER--K---GEYLVN---GNQklES-DMVINSTGHYSL-S 139
                                   3777788777653..3...444423...3332224.88********83.3 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.5e-06    0.0089       1     151 [.       2     136 ..       2     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-06
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSE.EE-T......THHHHHHHHHHHT.-SHHHHHHHHEEE CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnps.iggi......akgllvrEidalg.gliikaadkagiq 73 
                                   dv +iGgG AG+  A+ ++   ++ + + + ld+++  +C    i g+      +k  +  Ei+++   l +k+   + i 
  gi|70606775|ref|YP_255645.1|   2 DVSIIGGGPAGLSLAWFLKGTKYNATVY-EGLDNVGYKPCAWGlITGVeelvpiSKEAIIGEIKRFRiYLNGKI--VHDI- 78 
                                   799***********************99.99*******997431444466666666666666666432222222..2233. PP

                                   EEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT- CS
                          GIDA  74 frilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtf 151
                                             + r l   vd+ l+ +++ ek++ + n ++ie++ e l+             +++++++ v+ +tG +
  gi|70606775|ref|YP_255645.1|  79 ---------ESKRRLGYIVDKPLFLRDIAEKVNVQYNSKVIERKGEYLVN-----------GNQKLESDMVINSTGHY 136
                                   .........5667777789****************************965...........56666666666666654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     6e-06     0.012       3      21 ..       2      20 ..       1      29 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6e-06
                                  EEEEE--SHHHHHHHHHHH CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLs 21
                                  dV I+G+GpaGl+la +L+
  gi|70606775|ref|YP_255645.1|  2 DVSIIGGGPAGLSLAWFLK 20
                                  89**************996 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00019      0.37       2      26 ..       5      28 ..       4      37 .. 0.83
   2 ?    3.3   0.1      0.02        39      96     151 ..     101     151 ..      92     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                   Pyr_redox_3  2 IiGaGPaGlaaaielkkagledyli 26
                                  IiG+GPaGl+ a  lk  + +  ++
  gi|70606775|ref|YP_255645.1|  5 IIGGGPAGLSLAWFLKGTKYN-ATV 28
                                  9***********999988874.445 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                   Pyr_redox_3  96 lpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvk 151
                                   ++++++++V    + ++++ v+  ++++e++ vi +tG ++    + ip  + + +
  gi|70606775|ref|YP_255645.1| 101 VNVQYNSKV---IERKGEYLVNG-NQKLESDMVINSTGHYSLSFDQTIPAIQ-YIT 151
                                   555666555...33456677765.5689************998888888776.544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.037       2      38 ..       2      38 ..       1      44 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                  dv +iGgG+AGl  A  ++ ++ + +++e  +++g K
  gi|70606775|ref|YP_255645.1|  2 DVSIIGGGPAGLSLAWFLKGTKYNATVYEGLDNVGYK 38
                                  899**************************99999987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05     0.053       1      26 [.       2      25 ..       2     151 .. 0.80
   2 ?   -3.7   0.0       2.4   4.8e+03     261     290 ..     229     258 ..     228     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglk 26
                                  Dv +iG+GpAglslA  l  + ++ +
  gi|70606775|ref|YP_255645.1|  2 DVSIIGGGPAGLSLAWFL--KGTKYN 25
                                  999************988..444444 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.4
                 Lycopene_cycl 261 iGaaaglvhPaTGYsvarslaeapllasai 290
                                   +G a g+v P TG  +  s+  +++la+++
  gi|70606775|ref|YP_255645.1| 229 VGEAIGAVYPLTGEGIRPSILSSKILADSL 258
                                   78999999****988888888888887766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00068       1.4      18      37 ..       1      20 [.       1      37 [. 0.85
   2 ?    0.1   0.0      0.19   3.8e+02     155     169 ..     122     136 ..      86     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00068
                                  EEEEEE--SHHHHHHHHHHH CS
                          Thi4 18 sDvvivGaGssGLtaayyla 37
                                  +Dv i+G+G++GL+ a  l 
  gi|70606775|ref|YP_255645.1|  1 MDVSIIGGGPAGLSLAWFLK 20
                                  79*************99885 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.19
                                   EEEEEEEEEE--GSS CS
                          Thi4 155 lvirakvvvdatGhd 169
                                   + +++ +v+++tGh 
  gi|70606775|ref|YP_255645.1| 122 QKLESDMVINSTGHY 136
                                   467888999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2173.43
//
Query:       gi|70606776|ref|YP_255646.1|  [L=112]
Description: transcription regulator AsnC [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-16   58.2   0.1    7.2e-16   57.9   0.1    1.1  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    0.00089   19.3   0.0     0.0013   18.7   0.0    1.2  1  NapD             NapD protein
     0.0035   17.5   0.0     0.0058   16.8   0.0    1.3  1  AsnC_trans_reg2  AsnC-like ligand binding domain
  ------ inclusion threshold ------
      0.014   16.0   0.0       0.18   12.4   0.0    2.2  2  ACT_4            ACT domain
      0.031   14.2   0.2       0.06   13.3   0.2    1.7  1  NTPase_1         NTPase
       0.18   12.0   0.0       0.48   10.6   0.0    1.6  2  MIase            Muconolactone delta-isomerase


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.1   2.4e-19   7.2e-16       1      75 []      32     102 ..      32     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.4e-19
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                   ++++ +p++   +e++ +++a ++ + e++ +tG+y  +lkv+v++ e+l ++l+e +++++gv++t t++vl+t
  gi|70606776|ref|YP_255646.1|  32 IMIKADPKR---YEQILKKIASFKSIFEVFDITGEYYSILKVRVKSREELAKILDE-IGNMEGVTSTYTMFVLRT 102
                                   789999999...********************************************.****************96 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.5e-07    0.0013       6      70 ..      32      97 ..      27      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.5e-07
                          NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70
                                  + ++a+p+r +++++++a+++ + Ev   ++e   ++ +  +s++ela+++++i +++gV s+  +
  gi|70606776|ref|YP_255646.1| 32 IMIKADPKRYEQILKKIASFKSIfEVFDITGEYYSILKVRVKSREELAKILDEIGNMEGVTSTYTM 97
                                  6799****************9855**************************************9755 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0058       2      80 ..      24     102 ..      23     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
               AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstre 80 
                                   +G +  a +++k++ +r+e++ +++a+++ +  ++    +y     v ++s+ee+ ++l+ei +  g++++++++ +r+
  gi|70606776|ref|YP_255646.1|  24 IGLNVVAFIMIKADPKRYEQILKKIASFKSIFEVFDITGEYYSILKVRVKSREELAKILDEIGNMEGVTSTYTMFVLRT 102
                                   7888889999*******************************999****************************9999886 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.18   5.5e+02      60      78 ..      39      57 ..      32      58 .. 0.86
   2 ?   12.4   0.0   6.1e-05      0.18      52      77 ..      68      93 ..      62      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                         ACT_4 60 ehLsrviakLraipgVisV 78
                                  +  +++++k+ + +++ +V
  gi|70606776|ref|YP_255646.1| 39 KRYEQILKKIASFKSIFEV 57
                                  667999*********9998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.1e-05
                         ACT_4 52 itveVkdvehLsrviakLraipgVis 77
                                  ++v Vk++e+L+++++ + +++gV+s
  gi|70606776|ref|YP_255646.1| 68 LKVRVKSREELAKILDEIGNMEGVTS 93
                                  79**********************97 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2     2e-05      0.06      92     126 ..      73     107 ..       3     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                   HHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTS CS
                      NTPase_1  92 alseadviviDEiGkmElkskkfkeaveevLksek 126
                                   + +e+   ++DEiG+mE  + ++   v +++k+ k
  gi|70606776|ref|YP_255646.1|  73 KSREELAKILDEIGNMEGVTSTYTMFVLRTIKEAK 107
                                   3344446799*************999999999766 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.42   1.3e+03      30      44 ..       2      16 ..       1      51 [. 0.69
   2 ?   10.6   0.0   0.00016      0.48      23      71 ..      34      85 ..      25      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.42
                         MIase 30 raqelqrqGklvrlw 44
                                  r+++l+++G ++ ++
  gi|70606776|ref|YP_255646.1|  2 RIRRLKEKGVIKGFY 16
                                  567888888888766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                         MIase 23 lkarekaraqelqrqGklvrlwrv...vgeyanisifdvedndeLhelLssL 71
                                  +ka+ k++ q l++   +++++ v    gey +i  ++v++++eL ++L ++
  gi|70606776|ref|YP_255646.1| 34 IKADPKRYEQILKKIASFKSIFEVfdiTGEYYSILKVRVKSREELAKILDEI 85
                                  5677777777777777777777776669*********************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 823.96
//
Query:       gi|70606777|ref|YP_255647.1|  [L=210]
Description: ribosomal protein S6 modification protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-31  107.4   0.0    7.6e-31  107.2   0.0    1.0  1  RimK            RimK-like ATP-grasp domain
    2.6e-11   43.2   0.1    9.6e-11   41.4   0.2    1.6  2  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    1.3e-08   35.0   0.1    1.9e-08   34.5   0.1    1.2  1  ATP-grasp_3     ATP-grasp domain
    3.4e-07   29.8   0.0     0.0032   16.7   0.0    2.3  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
    2.1e-05   23.9   0.0      0.072   12.3   0.0    2.3  2  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    0.00093   18.8   0.0      0.001   18.6   0.0    1.1  1  Synapsin_C      Synapsin, ATP binding domain
     0.0019   17.7   0.0       0.36   10.3   0.0    2.1  2  Ins134_P3_kin   Inositol 1,3,4-trisphosphate 5/6-kinase ATP-g


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.0     3e-34   7.6e-31       1     187 [.      18     203 ..      18     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 3e-34
                                   HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG--EE CS
                          RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeailv 78 
                                   ardK+ sl  L  a+i+vp+ta+++d+ +a +l+ k k    vv+K v gs G++ + a++++ +  v ++   +++ i +
  gi|70606777|ref|YP_255647.1|  18 ARDKFYSLVKLKNAGIPVPETAVVEDPFEAMRLVMKWK---DVVIKPVVGSLGLGSIRAEDPDIVFRVSKSllsINQPIYI 95 
                                   79***********************************7...9*********************9988866676699***** PP

                                   EEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEETTE.E CS
                          RimK  79 qeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrakrg.l 158
                                   q+yi++  ++diR++ v+d + +++ r+ ++  +++n+ +G+ +++++++++++e+ +k  k+++l++aG+D+++ + g +
  gi|70606777|ref|YP_255647.1|  96 QKYINKP-QRDIRIFAVGDRILGGIYRI-NKSSWKTNVAQGSLTQVITVNQDLEEITLKSMKVLGLDYAGIDIVEDESGdY 174
                                   ****865.69******************.555****************************************999887626 PP

                                   EEEEEESS--SHHHHHHHT--HHHHHHHH CS
                          RimK 159 lvlEvnsspglekiektlgidiakkliea 187
                                    +lEvn sp   ++   ++i+ ak ++e 
  gi|70606777|ref|YP_255647.1| 175 KILEVNGSPLWGGFYEATKINPAKYIVEH 203
                                   699*********************99986 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   3.7e-14   9.6e-11      12     155 ..      35     170 ..      26     181 .. 0.85
   2 ?    0.8   0.0      0.11   2.9e+02      82      96 ..     170     184 ..     168     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.7e-14
                                   S--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEEEET CS
                     GSH-S_ATP  12 ipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDkRillvd 92 
                                   +p+t v +d  e ++++ + +dv++KP+ g+ G g +r ++  p++   ++ +  + ++p+ +q+y+++ ++ D Ri+ v 
  gi|70606777|ref|YP_255647.1|  35 VPETAVVEDPFEAMRLVMKWKDVVIKPVVGSLGLGSIRAED--PDIVFRVSKSLLSINQPIYIQKYINKPQR-DIRIFAVG 112
                                   699****************************9999877665..66666666667777889********9988.*******9 PP

                                   TEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE CS
                     GSH-S_ATP  93 GepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk 155
                                    + +g  + R+ + +  ++n+a g+ ++  ++++  +ei+    +++k  Gl ++G+D+++d+
  gi|70606777|ref|YP_255647.1| 113 DRILG-GIYRINK-SSWKTNVAQGSLTQVITVNQDLEEITL---KSMKVLGLDYAGIDIVEDE 170
                                   99999.*****76.679*********999999999999876...577888**********984 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                                   GG-EEEEEEETTEE- CS
                     GSH-S_ATP  82 keGDkRillvdGepi 96 
                                   ++GD +il v+G+p+
  gi|70606777|ref|YP_255647.1| 170 ESGDYKILEVNGSPL 184
                                   68***********98 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   7.5e-12   1.9e-08       1     155 [.      18     180 ..      18     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 7.5e-12
                                   HTSHHHHHHHHTTT.S---..........-EESS--SSSEEEEESS-------B--SS--TTE.............EEEE- CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvP......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......lvqef 69 
                                   a dK+ +  kLk+ag++vP      +  ea++l  + k +v+Kp+ G+ g +   +e+ +  ++  +++        +q++
  gi|70606777|ref|YP_255647.1|  18 ARDKFYSLVKLKNAGIPVPetavveDPFEAMRLVMKWKDVVIKPVVGSLGLGSIRAEDPDIVFRVSKSLLsinqpiYIQKY 98 
                                   579****************99999999999999999**********9988887777766544444333335556659**** PP

                                   --SEEEEEEE..EE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.S CS
                   ATP-grasp_3  70 ieGkplSvsl..lsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkdee 148
                                   i+  +  + +  ++d     +  +n+  +++    +v +G++t++ t  +++++e+  + ++ l gl  y+G+D+v  +++
  gi|70606777|ref|YP_255647.1|  99 INKPQRDIRIfaVGDRILGGIYRINKSSWKT----NVAQGSLTQVIT-VNQDLEEITLKSMKVL-GL-DYAGIDIVEDESG 172
                                   *976666655005555555688899999987....99********95.5778999999******.76.6*******99955 PP

                                   EE.EEEEE CS
                   ATP-grasp_3 149 py.viEvN 155
                                   +y ++EvN
  gi|70606777|ref|YP_255647.1| 173 DYkILEVN 180
                                   55499*** PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06    0.0032      24      69 ..      30      75 ..       5     109 .. 0.82
   2 !   11.3   0.0   5.7e-05      0.15     182     250 ..     142     205 ..     118     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                ATPgrasp_YheCD 24 elrpyLPetellesledleemlekyksvylKpanGskGkgilriek 69
                                  ++   +Pet  +e++ +  +++ k+k+v++Kp+ Gs+G g +r e 
  gi|70606777|ref|YP_255647.1| 30 NAGIPVPETAVVEDPFEAMRLVMKWKDVVIKPVVGSLGLGSIRAED 75
                                  455669********************************99888665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.7e-05
                ATPgrasp_YheCD 182 ileeleelalelaealeesfgrlgElGlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrpl 250
                                   ++++lee++l+ +++l   +      G+D+  d++g + +lEvN  p    f ea + + a+ +v++++
  gi|70606777|ref|YP_255647.1| 142 VNQDLEEITLKSMKVLGLDY-----AGIDIVEDESGDYKILEVNGSPLWGGFYEATKINPAKYIVEHLI 205
                                   55555555555555555444.....49********************9999998887777777766666 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   2.8e-05     0.072       8      79 ..       7      73 ..       1      98 [. 0.72
   2 !    9.8   0.0   0.00016      0.42     231     266 ..     149     183 ..     132     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                   ATPgrasp_ST  8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvi 79
                                    +N   ++ +  dK+     +++ag++vp++ +v   ++ ++ +  +v ++ ++vviKp+ gs+G G + +
  gi|70606777|ref|YP_255647.1|  7 TLINRPDAMFVARDKFYSLVKLKNAGIPVPETAVV---EDPFE-AMRLVMKW-KDVVIKPVVGSLGLGSIRA 73
                                  5678888888899999555555899******4333...34444.44567778.67************96544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                   ATPgrasp_ST 231 laakaaeklpglgylGwDivldeekgplllElNarp 266
                                   ++ k  + ++gl y G+Div de+++  +lE+N  p
  gi|70606777|ref|YP_255647.1| 149 ITLKSMK-VLGLDYAGIDIVEDESGDYKILEVNGSP 183
                                   5556555.9************************876 PP

>> Synapsin_C  Synapsin, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     4e-07     0.001      51     201 ..      55     208 ..      24     210 .] 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4e-07
                    Synapsin_C  51 fpvvvklghahagmgkvkven.qydyqdiasvvalaktyataeafidskydirvqkigsnykaymrtsisgnwkantgsam 130
                                     vv+k      g+g ++ e+ +  ++   s++++ +     + +   + dir+  +g+     +       wk+n     
  gi|70606777|ref|YP_255647.1|  55 KDVVIKPVVGSLGLGSIRAEDpDIVFRVSKSLLSINQPIYIQKYINKPQRDIRIFAVGDRILGGIYRINKSSWKTNVAQGS 135
                                   46889988889999999999834567888899999998877777777899**********998887777889********* PP

                    Synapsin_C 131 leqvamseryklwvdscsemfggldicavkavhskdgkdyiievmdssmpligehvvedk....qliaelvvskm 201
                                   l qv   ++    +   s  + gld + +  v    g   i+ev  s  pl g   +  k    + i e ++ km
  gi|70606777|ref|YP_255647.1| 136 LTQVITVNQDLEEITLKSMKVLGLDYAGIDIVEDESGDYKILEVNGS--PLWGGFYEATKinpaKYIVEHLIKKM 208
                                   ****999988888888888899***************99999*9765..66665554443111145555555555 PP

>> Ins134_P3_kin  Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00014      0.36       9      89 ..      35     115 ..      28     138 .. 0.75
   2 !    5.9   0.0    0.0032       8.3     144     187 ..     146     187 ..     118     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                   ---EEEE-S-GTTHHHHHHHTT--SSEEEEESB-S...ST.TTTEEEEE-S.GGGGTT--SSEEEEE----TTEEEEEEEE CS
                 Ins134_P3_kin   9 vPkqlvvtkdasslseavakagLklPliakplvad...Gtakshelslvyd.qeglkklkpPlvlqefvnhggvlfkvyvv 85 
                                   vP+  vv  d+ + +++v k +    ++ kp v     G+ ++ +  +v+   ++l  ++ P+ +q+++n      +++ v
  gi|70606777|ref|YP_255647.1|  35 VPETAVVE-DPFEAMRLVMKWK---DVVIKPVVGSlglGSIRAEDPDIVFRvSKSLLSINQPIYIQKYINKPQRDIRIFAV 111
                                   55555555.5555555555433...45666666543338888888999996378******************99999**99 PP

                                   TTEE CS
                 Ins134_P3_kin  86 Gesv 89 
                                   G+ +
  gi|70606777|ref|YP_255647.1| 112 GDRI 115
                                   9986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0032
                                   HHHHHHHHHHHH---EEEEEEEE-TTT.--EEEEEEEES---TT CS
                 Ins134_P3_kin 144 leelakalrralGlrLfnldiirdaktkdrylvidinyfPGyak 187
                                   lee++ +  + lGl   ++di+ d+     y ++++n  P +++
  gi|70606777|ref|YP_255647.1| 146 LEEITLKSMKVLGLDYAGIDIVEDESG--DYKILEVNGSPLWGG 187
                                   67777777899***********98765..8*******9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1475.34
//
Query:       gi|70606778|ref|YP_255648.1|  [L=283]
Description: polyprenyl synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-34  117.2   0.3    9.7e-34  116.6   0.3    1.2  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.081   12.8   0.0       0.14   12.0   0.0    1.4  1  DUF4335          Domain of unknown function (DUF4335)


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.3   1.1e-37   9.7e-34       6     203 ..      32     212 ..      29     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.1e-37
                                   HHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHH CS
               polyprenyl_synt   6 ealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAind 86 
                                   e+++y++ + GKr R++l + + eal+    el++++++a ++e+lh++sL +DDi+D ++tRRG+ +a +l+ n++ ++ 
  gi|70606778|ref|YP_255648.1|  32 EVSKYIL-KDGKRYRAVLNMFFTEALG---GELSNSLDAALAIEILHSSSLALDDIVDYDTTRRGKLSAWALYTNRRVVFI 108
                                   7889999.*******************...47899********************************************** PP

                                   HHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTT CS
               polyprenyl_synt  87 gdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallag 167
                                    ++l   a+++++++  ++ ++l++  e   +t+ G + d+     + +s      yl+ ++ KT++lf l++alaa  a+
  gi|70606778|ref|YP_255648.1| 109 TNYLIPSALNIISRY--GE-NALKVSLELWKDTAVGAIKDM-FG--PATS------YLSTIELKTSSLFKLSTALAAFTAD 177
                                   ***************..77.9********************.33..5566......************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHH CS
               polyprenyl_synt 168 asdeelealkdiglelGlaFQiqDDylDlfgdpevl 203
                                     +++l+ l d+g++lG+++Q++DDy+D+ + ++  
  gi|70606778|ref|YP_255648.1| 178 R-EKDLDLLLDMGKYLGIMYQLIDDYIDCINFESGK 212
                                   7.7779***********************9766554 PP

>> DUF4335  Domain of unknown function (DUF4335)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05      0.14     114     143 ..     155     184 ..     124     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                       DUF4335 114 leieLstvqLfDLveAldqflaDsqtlpsl 143
                                   ++ieL+t+ Lf L +Al +f+aD++   +l
  gi|70606778|ref|YP_255648.1| 155 STIELKTSSLFKLSTALAAFTADREKDLDL 184
                                   68*********************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2149.58
//
Query:       gi|70606779|ref|YP_255649.1|  [L=268]
Description: hypothetical protein Saci_0996 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.37   11.0   2.8         10    6.3   2.7    2.3  1  ARA70     Nuclear coactivator


Domain annotation for each model (and alignments):
>> ARA70  Nuclear coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.7   0.00057        10      49      76 ..     147     174 ..     133     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00057
                         ARA70  49 sdfskawgqLkdlEnWLlkqqqlivrek 76 
                                    ++sk ++++++lE WL +++++ + ++
  gi|70606779|ref|YP_255649.1| 147 REISKELEEINSLEDWLKEKIKETKLGR 174
                                   5677777777777777777666654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1918.38
//
Query:       gi|70606780|ref|YP_255650.1|  [L=270]
Description: 5'-methylthioadenosine phosphorylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-47  159.7   0.0    7.8e-47  159.5   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   0.0   4.4e-51   7.8e-47       1     233 [.       9     247 ..       9     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 4.4e-51
                                   CEEEEESSHHHHHHHHHH...EEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SEE CS
                     PNP_UDP_1   1 kiaiivgspgevellaes...pleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvkai 73 
                                   ki+ii+gs+   + ++e    +   tp+g++  +  + +G+l+gk v ++ ++G    i ++ ++++a+i++lke+gvk +
  gi|70606780|ref|YP_255650.1|   9 KIGIIGGSGLYDPKILENtreIKIYTPYGEP--SDYILLGELEGKSVaFLPRHGrghrIPPHKINYRANIWALKELGVKWL 87 
                                   69*******44444444445579999*****..*********7776659******************************** PP

                                   EEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEESE CS
                     PNP_UDP_1  74 iriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.Gvvatadg 153
                                   i+++++G+l+ d+k+GD+vipd++i+++ ++++++++ + + ++ ++d+ ++ +lr+++   ++++ i++h+ G++++ +g
  gi|70606780|ref|YP_255650.1|  88 ISVSAVGSLRMDYKPGDFVIPDQFIDMTKGRDYTFFDGPVVAHVSMADP-FCNSLRKIILDIVREMKIQTHErGTYICIEG 167
                                   ***************************************999******9.*****************999999******** PP

                                   SS-CHHHHHH.HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHH CS
                     PNP_UDP_1 154 fyaeteaelr.llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllall 233
                                   ++++t+ae+r + + + ad+++M+ ++++ lA e+++++ +i++++d ++  a+ + t eev+++++e+ ++a +ll +++
  gi|70606780|ref|YP_255650.1| 168 PRFSTRAESRvWKEVFKADIIGMTLVPEVNLACEAQMCYSTIAMITD-YDVFAELPVTAEEVTKVMAENTEKARKLLYEVI 247
                                   **********8888899******************************.55569999999******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2052.66
//
Query:       gi|70606781|ref|YP_255651.1|  [L=206]
Description: purine phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-17   61.3   0.0    1.1e-16   60.8   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0006   19.3   0.0     0.0008   18.9   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
        0.1   12.7   1.2        3.7    7.7   0.0    2.9  3  KH_5          NusA-like KH domain
       0.15   11.8   0.0       0.24   11.2   0.0    1.3  1  SNF5          SNF5 / SMARCB1 / INI1


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   2.4e-20   1.1e-16      21     135 ..      23     138 ..      11     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 2.4e-20
                                   EEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--E.E........EE----TTSEEEEE-SEESSS CS
                  Pribosyltran  21 eileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgsee.aargssdesrlledpagkkVliVDDildtG 100
                                   + ++e +++pd++++iargG+++a i+ad L+  + ++++ k+++++ +  +++ +++      d++gk+Vl+VDDi dtG
  gi|70606781|ref|YP_255651.1|  23 DSIKEEGYQPDIIIAIARGGLVPARIVADVLG--VLDMLSIKVEHWVETAsQTPEAKVKYPYKLDLKGKRVLLVDDIADTG 101
                                   4445559************************9..4555555555555544044444445589******************* PP

                                   HHHHHHHHHHHCC-.BSEEEEEEEE.E-HHHHHHHHH CS
                  Pribosyltran 101 gTllaalelLkekg.peevriavlv.dkpateeevdk 135
                                    ++  a +++++   p ev++a+    ++ ++ ++d+
  gi|70606781|ref|YP_255651.1| 102 DSVVLAKKFVEDNFlPREVKTATMQyIQSVSKYKPDY 138
                                   ********998665266*****986433333333333 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.8e-07    0.0008      48     146 ..      13     113 ..       3     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-07
                       UPRTase  48 ev.tvttplgkeysgelldeekialVpilRaGegmeealrellpearvghlglqreeet.lepveyynkLPkki..aertv 124
                                   ev +  t lg++ ++e  ++   ++++i R+G+  ++ + ++l    ++ ++++   et  ++ e   k P k+  + ++v
  gi|70606781|ref|YP_255651.1|  13 EVvEWSTKLGDSIKEEGYQP--DIIIAIARGGLVPARIVADVLGVLDMLSIKVEHWVETaSQTPEAKVKYPYKLdlKGKRV 91 
                                   44467788888888877665..4789***************************996555155568888999999889999* PP

                       UPRTase 125 lllDpviaTGgsaaaaiqlLke 146
                                   ll+D +  TG s++ a + + +
  gi|70606781|ref|YP_255651.1|  92 LLVDDIADTGDSVVLAKKFVED 113
                                   *************988776655 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.78   3.5e+03      44      51 ..       8      15 ..       6      27 .. 0.58
   2 ?    2.3   0.0      0.04   1.8e+02      37      65 ..      86     121 ..      83     124 .. 0.86
   3 ?    7.7   0.0   0.00083       3.7      14      40 ..     158     183 ..     154     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.78
                          KH_5 44 vvewseDl 51
                                  vv w+e +
  gi|70606781|ref|YP_255651.1|  8 VVTWEEVV 15
                                  55555543 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.04
                          KH_5  37 LkgekidvvewseD.......laefianalsPaevl 65 
                                   Lkg+++ +v+   D        ++f+++ + P ev+
  gi|70606781|ref|YP_255651.1|  86 LKGKRVLLVDDIADtgdsvvlAKKFVEDNFLPREVK 121
                                   889999999988888999998999********9997 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00083
                          KH_5  14 pnvdpvGaivgkkGsrikavsseLkge 40 
                                   ++++ v++i+ ++Gs +k +++++ +e
  gi|70606781|ref|YP_255651.1| 158 DEINLVRKILSNGGSDVKDIERKF-EE 183
                                   6899********************.55 PP

>> SNF5  SNF5 / SMARCB1 / INI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.24     149     218 ..     102     168 ..      57     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                          SNF5 149 tpEeFAkqlcadlgLsgefvtaiaHaIrEqvlkykksllesgllvaglkkleagwrfdeelaeefepkle 218
                                        Ak++++d  L++e++ta    I+  v+kyk + +  g++v+ +k ++  w+++e++++  +  l+
  gi|70606781|ref|YP_255651.1| 102 DSVVLAKKFVEDNFLPREVKTATMQYIQ-SVSKYKPDYV--GMVVTEWKWFMYPWNYWEDEINLVRKILS 168
                                   555789****************999997.89********..*****************998776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1274.26
//
Query:       gi|70606782|ref|YP_255652.1|  [L=336]
Description: peptide chain release factor 1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-44  150.1   0.0    7.3e-44  149.3   0.0    1.4  1  eRF1_2          eRF1 domain 2
    6.2e-21   75.0   3.5    3.1e-20   72.7   1.1    2.8  2  eRF1_3          eRF1 domain 3
    1.6e-13   51.1   0.0    3.6e-13   49.9   0.0    1.6  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.9e-12   47.6   0.0      3e-12   47.0   0.0    1.3  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.049   13.6   0.0       0.08   12.9   0.0    1.4  1  eRF1_1          eRF1 domain 1


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.0     2e-47   7.3e-44       2     133 .]     107     240 ..     106     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 2e-47
                                   EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTESEEE CS
                        eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdklkgii 81 
                                   +gl++++++ Atig+lkg+++evl+++e+ vP+Kh++Ggqs+rr+eR++ee++++flk+v+e++n++fl +++ +k+kgi+
  gi|70606782|ref|YP_255652.1| 107 FGLVIVERDYATIGVLKGTKVEVLDEFEGFVPGKHMMGGQSQRRIERIIEEMYHNFLKEVGEKVNQYFLpYIEMKKMKGIL 187
                                   79******************************************************************************* PP

                                   EEESSTHHHHHHHHHHHHHHHHTCCEE.EEE-S-TSCHHHHHHHHCCHHHHCC CS
                        eRF1_2  82 lagpgfvkeefldkdlldaelkkkvik.lvdvsyggesglnevlekaaevlkd 133
                                   ++gpgf+k++++++dlld++ kk v++ l+d+ ++ge gl+e+++ka++ lk+
  gi|70606782|ref|YP_255652.1| 188 IGGPGFAKKDLYESDLLDYRVKKLVLQpLFDIPDQGEPGLKELIMKAQDILKN 240
                                   *************************999*********************9985 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   4.4e+03      61      77 ..     144     161 ..      94     171 .. 0.59
   2 !   72.7   1.1   8.6e-24   3.1e-20       2     113 .]     244     335 ..     243     335 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                   HH-HHHHHH.HHHHHHHH CS
                        eRF1_3  61 tgeelelve.lieelven 77 
                                    g+ ++++e +iee+++n
  gi|70606782|ref|YP_255652.1| 144 GGQSQRRIErIIEEMYHN 161
                                   345555566555555554 PP

  == domain 2  score: 72.7 bits;  conditional E-value: 8.6e-24
                                   HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT CS
                        eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesg 82 
                                   i+ ++l+ee   +lakd+g++vYG ee++kal++gA++ L+v+ee  ++                    +e+l +++e++g
  gi|70606782|ref|YP_255652.1| 244 IEVENLMEEIKYHLAKDDGMVVYGLEEIRKALQLGAIDALIVYEEPGSE--------------------LEKLSQEAENYG 304
                                   78899****************************************9987....................89********** PP

                                   -EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                        eRF1_3  83 akveiisseseeGeqlvkafgGiaaiLRykv 113
                                   +kv++i +e + Ge+++k+fgG ++ LR+k+
  gi|70606782|ref|YP_255652.1| 305 TKVYVIGDELPDGEWVKKTFGGAIGKLRFKI 335
                                   *****************************97 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         4   1.5e+04      57      70 ..      34      47 ..      28      63 .. 0.48
   2 !   49.9   0.0     1e-16   3.6e-13       3     125 ..     107     235 ..     105     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4
                       acVLRF1 57 alleavaeaaarll 70
                                  a  +a+++a++rl 
  gi|70606782|ref|YP_255652.1| 34 AVTTAIQAAIDRLT 47
                                  33334444444443 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1e-16
                       acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.....vv 78 
                                   +g+++v r+  ++gv++g++++   +++  v g++  GG+Sq+R +R +e+   + l++v e++++ + ++ +      ++
  gi|70606782|ref|YP_255652.1| 107 FGLVIVERDYATIGVLKGTKVEVLDEFEGFVPGKHMMGGQSQRRIERIIEEMYHNFLKEVGEKVNQYFLPYIEMkkmkgIL 187
                                   6899****************************************************************88888788899** PP

                       acVLRF1  79 lgGdrslvaevledar.laplatlareelldvpdprravLedavrrar 125
                                   +gG+  + +++ e+   + ++++l+ ++l+d+pd  +  L++ + +a+
  gi|70606782|ref|YP_255652.1| 188 IGGPGFAKKDLYESDLlDYRVKKLVLQPLFDIPDQGEPGLKELIMKAQ 235
                                   ***********9996625669999999**********99999887765 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   8.4e-16     3e-12       3     126 ..      94     224 ..      93     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 8.4e-16
                baeRF_family10   3 lapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellakl 83 
                                   ++ L + ++e+e +g+v+v+r+ a + +  + ++e  +e+eg vpg++  gg+ sq+r++r  ee+ + +lkev+e ++++
  gi|70606782|ref|YP_255652.1|  94 VEFLEDMVEENEVFGLVIVERDYATIGVLKGTKVEVLDEFEGFVPGKHMMGGQ-SQRRIERIIEEMYHNFLKEVGEKVNQY 173
                                   6678899**********************************************.**************************9 PP

                baeRF_family10  84 leerg....verlvlgGdeeetaall..drlpkalrarvvgt.lplpv.da 126
                                   + +      ++ +++gG+  +++ l   d+l  +++++v ++ +++p+ ++
  gi|70606782|ref|YP_255652.1| 174 FLPYIemkkMKGILIGGPGFAKKDLYesDLLDYRVKKLVLQPlFDIPDqGE 224
                                   976544445*********6666666423789999**999999999998444 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05      0.08      20     128 ..       3     100 ..       1     101 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                                   E-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSEEEEEEEEEEGGGG--TT CS
                        eRF1_1  20 peddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agvlrisGkvieenehvklg 97 
                                   +++   + ++ nl++++ s++ +++ k +r           v+++++  + +++  ++   +g++ ++G++ ++++     
  gi|70606782|ref|YP_255652.1|   3 IPPGRPIPDILNLLRQEASIAQNIKLKRTR---------DAVTTAIQAAIDRLTQIPKvdgNGLVIFCGENFNNED----- 69 
                                   66666677899****************999.........89*************99999999*********99888..... PP

                                   SEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                        eRF1_1  98 afhtldlelkrpftiikee.wdsfalerLkea 128
                                    f  + + +++++ ++ ++ ++ f++e L+++
  gi|70606782|ref|YP_255652.1|  70 -FKCFMFSPPEKVPLFFYRtDKFFHVEFLEDM 100
                                   .99999********999997778899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2030.33
//
Query:       gi|70606783|ref|YP_255653.1|  [L=1155]
Description: hypothetical protein Saci_1002 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.5    6.5   6.3         18    5.1   0.2    3.0  3  DUF3188   Protein of unknown function (DUF3188)


Domain annotation for each model (and alignments):
>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.8    0.0041        73      27      41 ..     328     342 ..     326     344 .. 0.91
   2 ?   -3.3   0.0      0.44   7.8e+03       9      22 ..     997    1010 ..     997    1010 .. 0.87
   3 ?    5.1   0.2     0.001        18      24      44 ..    1132    1152 ..    1113    1155 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0041
                       DUF3188  27 lPallvGlgLivsga 41 
                                   lP++lvG g ivs+a
  gi|70606783|ref|YP_255653.1| 328 LPIFLVGVGFIVSSA 342
                                   9***********986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.44
                       DUF3188    9 gllillysqrqgsd 22  
                                    g+l++ ++++q sd
  gi|70606783|ref|YP_255653.1|  997 GFLAFYVGNNQRSD 1010
                                    789999****9876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.001
                       DUF3188   24 lqslPallvGlgLivsgavgr 44  
                                    ++ +P++lvG++ ++  ++ r
  gi|70606783|ref|YP_255653.1| 1132 IYVIPIALVGIFFLIFWVLRR 1152
                                    899*********998744444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 7579.14
//
Query:       gi|70606784|ref|YP_255654.1|  [L=350]
Description: hypothetical protein Saci_1003 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.3    8.2   6.2       0.32   11.0   1.3    2.1  2  DUF1077   Protein of unknown function (DUF1077)


Domain annotation for each model (and alignments):
>> DUF1077  Protein of unknown function (DUF1077)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3      0.39     7e+03      41      62 ..      77      98 ..      73     111 .. 0.65
   2 ?   11.0   1.3   1.8e-05      0.32      29      98 ..     260     340 ..     254     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.39
                       DUF1077 41 ifsimmvlmllvnpikallsvn 62
                                  ifs+ +++  +v+ + ++++vn
  gi|70606784|ref|YP_255654.1| 77 IFSLSLTILGIVSLLLSVTNVN 98
                                  6666666666666666665555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.8e-05
                       DUF1077  29 lfmlYmsGnslqifsimmvlmllvnpikallsvnkaFkkleseksks..........klll.qklvyvllqllllalglyk 98 
                                    f+++++G+ + i++++m ++++++ + ++++ +++ ++++ ++ +           ++++  ++++ +++l+++++g  k
  gi|70606784|ref|YP_255654.1| 260 GFLFFLTGSPILIIPLVMFGITITSVVPKVFNSKNTGASINIASIEGavvpvvgtvsDYVAgGMTLFSMITLVAMYFGEKK 340
                                   5899*******************************9999998544223333333333444448888888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2427.18
//
Query:       gi|70606785|ref|YP_255655.1|  [L=70]
Description: hypothetical protein Saci_1004 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 520.62
//
Query:       gi|70606786|ref|YP_255656.1|  [L=135]
Description: ParR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-11   42.8   0.1    1.1e-10   41.3   0.0    1.8  2  PadR      Transcriptional regulator PadR-like family
    0.00078   19.6   1.0      0.001   19.2   1.0    1.2  1  DUF2120   Uncharacterized protein conserved in archaea (DUF21
     0.0016   19.1   0.0     0.0031   18.1   0.0    1.7  1  RTP       Replication terminator protein
     0.0019   18.1   0.9     0.0082   16.1   0.0    2.2  3  HTH_45    Winged helix-turn-helix
     0.0057   16.6   0.0      0.041   13.9   0.0    2.1  2  BLACT_WH  Beta-lactamase associated winged helix domain
  ------ inclusion threshold ------
      0.043   13.6   0.7      0.048   13.4   0.1    1.5  2  DUF4364   Domain of unknown function (DUF4364)
       0.14   12.0   0.1        1.6    8.6   0.0    2.5  2  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   4.3e-14   1.1e-10       1      74 [.      16      81 ..      16      82 .. 0.95
   2 ?   -2.0   0.0       1.4   3.5e+03      13      22 ..     122     131 ..     108     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.3e-14
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  iL ll ++p  G +ii+++ + s g++++s+Gs+Yp+L++L +eg v +e  ++        Y++Td+G +e++
  gi|70606786|ref|YP_255656.1| 16 ILWLLYQSPKRGIDIIDDIYKMSWGMWRPSPGSVYPLLNKLLEEGAVRKEGGDK--------YQITDKGIKEIE 81
                                  7999**********************************************9997........*******99876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                   HHHHHHHHCC CS
                          PadR  13 yeiikeleel 22 
                                   ++i k++ee 
  gi|70606786|ref|YP_255656.1| 122 LDILKKIEEV 131
                                   5566666665 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.0     4e-07     0.001      21      77 ..      79     134 ..      73     135 .] 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4e-07
                       DUF2120  21 dkeeiLivrgvsrkkeeleeleskleellekldaeevdleseeakkliekldesire 77 
                                   + e+ ++vr +s++++ +eel++ l+  +++++ ee+ l +e++ ++++k++e +r+
  gi|70606786|ref|YP_255656.1|  79 EIEHFILVRNRSKTEDAVEELRGLLD-FFKEINREELALHKENILDILKKIEEVVRN 134
                                   5678999****************998.6899************************97 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.2e-06    0.0031       3      81 ..       5      85 ..       3     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                                  S--HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT.----HHHHHHHHHHHHHTTSEEEEEEEB...TSSSSSEEEEEEE CS
                           RTP  3 llkqrAFlklylitlvekkklyglklldelkkeFkelg.ykPnhseiyralhelvedgilkrrkelk...ekaklqevviYsl 81
                                  l +qr  l+l ++ l+ ++++ g+ ++d++ k   ++g ++P++  +y  l+ l+e+g ++++   k   +++ ++e+  + l
  gi|70606786|ref|YP_255656.1|  5 LARQRGRLRLLILWLLYQSPKRGIDIIDDIYKM--SWGmWRPSPGSVYPLLNKLLEEGAVRKEGGDKyqiTDKGIKEIEHFIL 85
                                  5689999**********************9764..4556*********************99876664445555666655544 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.7   9.5e+03      62      70 ..      27      35 ..      21      38 .. 0.56
   2 !   16.1   0.0   3.2e-06    0.0082      39      68 ..      52      82 ..      48      91 .. 0.83
   3 ?   -0.4   0.1      0.46   1.2e+03       8      16 ..     121     129 ..     118     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.7
                        HTH_45 62 Glelleklk 70
                                  G ++++++ 
  gi|70606786|ref|YP_255656.1| 27 GIDIIDDIY 35
                                  555555544 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.2e-06
                        HTH_45 39 YLdmLvekgli.kkskekYvlTekGlellek 68
                                   L++L+e+g + k+ ++kY++T+kG + +e+
  gi|70606786|ref|YP_255656.1| 52 LLNKLLEEGAVrKEGGDKYQITDKGIKEIEH 82
                                  599********666999********987765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.46
                        HTH_45   8 iadILeais 16 
                                   i+dIL++i+
  gi|70606786|ref|YP_255656.1| 121 ILDILKKIE 129
                                   678888775 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.6e-05     0.041      16      43 ..      40      67 ..      29      71 .. 0.80
   2 ?   -0.1   0.2      0.38   9.7e+02      23      34 ..     119     130 ..     115     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                      BLACT_WH 16 slhpaAergvlahLeKLeeeGkVkregd 43
                                   ++++   +v+  L+KL eeG V++eg+
  gi|70606786|ref|YP_255656.1| 40 GMWRPSPGSVYPLLNKLLEEGAVRKEGG 67
                                  678888899999*************996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.38
                      BLACT_WH  23 rgvlahLeKLee 34 
                                    ++l +L+K ee
  gi|70606786|ref|YP_255656.1| 119 ENILDILKKIEE 130
                                   58999****986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.4   8.8e+03       2      11 ..      13      22 ..      13      25 .. 0.82
   2 ?   13.4   0.1   1.9e-05     0.048      39      91 ..      52     101 ..      48     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
                       DUF4364  2 KllilYllkk 11
                                  +llil+ll++
  gi|70606786|ref|YP_255656.1| 13 RLLILWLLYQ 22
                                  699**99987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                       DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfenripksirekideylke 91 
                                    l++L+e+g +++   e+ + y+iT+kG + +e f      s  e++ e l+ 
  gi|70606786|ref|YP_255656.1|  52 LLNKLLEEGAVRK---EGGDKYQITDKGIKEIEHFILVRNRSKTEDAVEELRG 101
                                   699*********7...99************99999766666666666666555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.33   8.5e+02      10      21 ..       3      14 ..       3      15 .. 0.87
   2 ?    8.6   0.0   0.00061       1.6      32      51 ..      46      65 ..      45      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                  CT-CTTBSS-BH CS
                      HTH_IclR 10 dalaeapqeltl 21
                                  ++la+++++l+l
  gi|70606786|ref|YP_255656.1|  3 ELLARQRGRLRL 14
                                  689*****9987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00061
                                  HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR 32 kStvhRlLqtLvelGyveqd 51
                                  + +v+ lL+ L e+G v+++
  gi|70606786|ref|YP_255656.1| 46 PGSVYPLLNKLLEEGAVRKE 65
                                  689***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 903.77
//
Query:       gi|70606787|ref|YP_255657.1|  [L=283]
Description: ABC transporter ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-16   59.7   0.0    7.2e-16   59.0   0.0    1.4  1  ABC_tran  ABC transporter
      6e-13   49.3   0.4    1.3e-12   48.2   0.4    1.6  1  DUF4162   Domain of unknown function (DUF4162)
    3.5e-08   33.6   0.0    4.9e-08   33.1   0.0    1.2  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   1.2e-19   7.2e-16      30     136 ..       1     115 [.       1     116 [. 0.95

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.2e-19
                                   HHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHHHHHHHSTTGGT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxx RF
                      ABC_tran  30 llagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeiekalsklglkel 97 
                                   +l+  lkp eG+  ++g d+ + + + +r++igv+pqe + +++lt  en              ++e+ +++l+ ++l++ 
  gi|70606787|ref|YP_255657.1|   1 MLTTVLKPSEGTGIVNGYDIVK-QPSLVRRSIGVVPQEFTADEDLTGWENimmmaglygipkdVANERGKELLELVELTNA 80 
                                   5788899*****99******99.78899********************************99988999999*********9 PP

                                   TCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  98 kdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   ++++v    +++SgG+++r+++a++l+++pk+l+lDEpt
  gi|70606787|ref|YP_255657.1|  81 ANRKV----ETYSGGMRRRLEIAMSLISRPKILFLDEPT 115
                                   99999....*****************************9 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.4   2.2e-16   1.3e-12       1      81 []     170     257 ..     170     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.2e-16
                                   E-HHHHHTTS-SSEEEEE-------.......---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HH CS
                       DUF4162   1 GtleeiKrsygknrieveadaeellee.....pgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLn 74 
                                   G+++e+K+++g+++i +++ + el+++     +gv+e++  +g +++k+e  ee a++++++l ++g+++ ++  +eP+L+
  gi|70606787|ref|YP_255657.1| 170 GSPKELKDKIGGDIISLSTSNNELAQQyikvvEGVKELKVMDGMIRVKVERgEEIAPKIMEELiKKGIKVGKLYITEPTLD 250
                                   99****************5555555555555688****************99***********88**************** PP

                                   HHHHHHH CS
                       DUF4162  75 dIFiekv 81 
                                   ++++e++
  gi|70606787|ref|YP_255657.1| 251 EVYMEYT 257
                                   *****86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   8.2e-12   4.9e-08     169     298 ..      37     147 ..      20     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 8.2e-12
                        AAA_21 169 lnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllallt 249
                                    + +++ +++++++ ++ +l++ +k+v +e  ++                  + ++e ++  ++ +   S G++r l ++ 
  gi|70606787|ref|YP_255657.1|  37 EFTADEDLTGWENIMMMAGLYGIPKDVANERGKE-----------------LLELVELTNAANRKVETYSGGMRRRLEIAM 100
                                   5666777899999999999999999999999999.................7888888888999999************** PP

                        AAA_21 250 allralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                   +l++++   ++l++DEp  gL+ +   ++++ + +++++ g  +++tTH 
  gi|70606787|ref|YP_255657.1| 101 SLISRP---KILFLDEPTIGLDAQTRVSIWKYIlELKKEQGMTIFVTTHY 147
                                   ******...9********************77746666699********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1898.51
//
Query:       gi|70606788|ref|YP_255658.1|  [L=282]
Description: hypothetical protein Saci_1007 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-35  120.4  21.4    6.8e-35  120.4  21.4    2.1  2  ABC2_membrane    ABC-2 type transporter
      1e-18   67.6  25.8      1e-18   67.6  25.8    1.8  2  ABC2_membrane_3  ABC-2 family transporter protein
    2.8e-08   33.4  18.2    3.8e-08   33.0  18.2    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    8.7e-05   22.6  12.6    8.7e-05   22.6  12.6    2.6  2  ABC2_membrane_4  ABC-2 family transporter protein
     0.0068   15.1   0.1     0.0068   15.1   0.1    2.2  2  EMP70            Endomembrane protein 70


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4  21.4   1.9e-38   6.8e-35       3     209 ..       7     247 ..       5     248 .. 0.90
   2 ?   -1.0   0.7      0.27   9.8e+02     102     121 ..     255     274 ..     250     279 .. 0.54

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.9e-38
                 ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr............................... 52 
                                   +++ll+re++++++d + + l+++iqp+l++ +fg +   l n  +g ++                               
  gi|70606788|ref|YP_255658.1|   7 LFTLLNRELKKWYKDIVVL-LLSIIQPILWIGLFGKAMN-LANIFSGTSFnipgldipkqvldqiaqqalaqtfgtsdyfs 85 
                                   689*************999.99*************9997.44322222224578888899999999999999********* PP

                 ABC2_membrane  53 ...pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyfl.vgldls. 128
                                      +g+l f++lf++  + +++++v++r+ gvl+r+l++p+ s++ +++akv++++++sl+q+ i+l+i+++l +++++  
  gi|70606788|ref|YP_255658.1|  86 flaAGMLSFIALFTS--MQSGMSIVWDRRLGVLDRLLTTPV-SRANILMAKVFSSVIRSLVQSSIVLAIAVLLgMSFRVGi 163
                                   ***************..9999999*****************.**************************9999732444447 PP

                 ABC2_membrane 129 ...rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealr 206
                                       f+  +++l+l+++ +ssl++++++ a++ +  + +++l+ lpll++s +f+p+dsmp wl+ +a++nPlt+  +++r
  gi|70606788|ref|YP_255658.1| 164 splDFLGSYAALFLMSFGLSSLFMMVAIRATTWQSQMAIMNLLNLPLLFTSNAFYPVDSMPWWLKPVAEVNPLTHSNSIIR 244
                                   7778899*****************************************************988889**************9 PP

                 ABC2_membrane 207 snl 209
                                   + l
  gi|70606788|ref|YP_255658.1| 245 NLL 247
                                   976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.27
                 ABC2_membrane 102 lvelpvsllqalifllivyf 121
                                   ++++++ +++ali+++i + 
  gi|70606788|ref|YP_255658.1| 255 AIDFIYLVVFALILSIIGIT 274
                                   45555555555555555444 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.1       0.2   7.1e+02     211     239 ..      22      49 ..      20      59 .. 0.66
   2 !   67.6  25.8   2.8e-22     1e-18     155     344 ..      79     273 ..      53     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
               ABC2_membrane_3 211 lgdflvyllqlllilllafglgipfgnlg 239
                                   + ++l++++q +l+++l fg +++  n++
  gi|70606788|ref|YP_255658.1|  22 IVVLLLSIIQPILWIGL-FGKAMNLANIF 49 
                                   56788999999999987.33224444443 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 2.8e-22
               ABC2_membrane_3 155 elsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afgl.. 231
                                    +s++ sfl++ +l +++++t+++  +siv +++ +++ ++l+++vs++ ++++k++++++ +l+q+ ++l++  ++g   
  gi|70606788|ref|YP_255658.1|  79 GTSDYFSFLAAGMLSFIALFTSMQSGMSIVWDRRLGVLDRLLTTPVSRANILMAKVFSSVIRSLVQSSIVLAIavLLGMsf 159
                                   4678889999977777777787778889***************************************99998766777666 PP

               ABC2_membrane_3 232 ..gipfgnlglll..llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffa 308
                                     gi+  +++     l+++ fgl++++++ ++ + + +s +a+  + +++l+l++ + +++p++++p +lk ++ ++P+++
  gi|70606788|ref|YP_255658.1| 160 rvGISPLDFLGSYaaLFLMSFGLSSLFMMVAIRATTWQSQMAI--MNLLNLPLLFTSNAFYPVDSMPWWLKPVAEVNPLTH 238
                                   7766666665444358888899999999999999999999986..9*********************************** PP

               ABC2_membrane_3 309 pglgllrlitgdplweillsliilalfavvylllal 344
                                       + +l+ g+ + ++++++i+l++fa+++ ++++
  gi|70606788|ref|YP_255658.1| 239 SNSIIRNLLLGV-PGNLAIDFIYLVVFALILSIIGI 273
                                   ************.66***************999875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0  18.2   1.1e-11   3.8e-08       2     278 ..       9     275 ..       8     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.1e-11
               ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli..dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvsti 80 
                                   +++ +E+++  ++ ++lll+++ p++   ++  +++ +  +++++++  + + +++  +++a +  ++  ++ d    s +
  gi|70606788|ref|YP_255658.1|   9 TLLNRELKKWYKDIVVLLLSIIQPILwiGLFGKAMNLANIFSGTSFNIPGLDIPKQVLDQIAQQALAQTFGTSD--YFSFL 87 
                                   5788999999************9999887788888888899999999999999999999887775555444444..47778 PP

               ABC2_membrane_2  81 mavlipviaalfgad...aiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivla 157
                                   +a+++ +ia+ ++++   +i+ ++  g l +lL++PvsR+ il++K+ ++++ +l+   + l ++vl    + +++ + ++
  gi|70606788|ref|YP_255658.1|  88 AAGMLSFIALFTSMQsgmSIVWDRRLGVLDRLLTTPVSRANILMAKVFSSVIRSLVqSSIVLAIAVL----LGMSFRVGIS 164
                                   8888888888887763337**********************************99955555555555....5667777777 PP

               ABC2_membrane_2 158 ledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsp 238
                                     d+l   +a  l+ +   + +l++++++ a + ++++a++  l + l ++ +++ y+v +++   ++ +e+n++ +  s+
  gi|70606788|ref|YP_255658.1| 165 PLDFLGSYAALFLMSF--GLSSLFMMVAIRATTWQSQMAIMNLLNLPL-LFTSNAFYPVDSMPWWLKPVAEVNPLTHSNSI 242
                                   7777777666666666..3589******99999999998888777776.99999999******999996666666665555 PP

               ABC2_membrane_2 239 tsayntllneilagsdlnalgstatnllilllllavllvl 278
                                   +++  +++   la +       +   +++ l+l ++ + l
  gi|70606788|ref|YP_255658.1| 243 IRNLLLGVPGNLAID-------FIYLVVFALILSIIGITL 275
                                   555555555555555.......344445555555555555 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6  12.6   2.4e-08   8.7e-05       3     164 ..      12     199 ..      10     214 .. 0.60
   2 ?   -0.0   0.4       0.2   7.3e+02      15     160 ..     259     275 ..     252     281 .. 0.46

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.4e-08
               ABC2_membrane_4   3 ktEflKlkrskivwllvlaallvpllallyfn...........................llgktg....ldpaefyslsvf 52 
                                     E++K+ +  i  +++l++++ p+l++ +f                            ++++++    + ++ ++s+ + 
  gi|70606788|ref|YP_255658.1|  12 NRELKKWYKD-I--VVLLLSIIQPILWIGLFGkamnlanifsgtsfnipgldipkqvldQIAQQAlaqtFGTSDYFSFLAA 89 
                                   5566666666.2..3334555566666666655666777777777778888777777663333330000223333333333 PP

               ABC2_membrane_4  53 gftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfalls..gfvgfsv 131
                                   g  +l ++ l + + ++++i   +  + l  Llt Pvsr+++l+aK++  ++ s++ + + ++i+vl+++ +  g +++++
  gi|70606788|ref|YP_255658.1|  90 G--MLSFIALFTSMQSGMSIVWDRRLGVLDRLLTTPVSRANILMAKVFSSVIRSLVQSSIVLAIAVLLGMSFrvGISPLDF 168
                                   3..44455555566799*******************************998888888877777777765544113445555 PP

               ABC2_membrane_4 132 klvlellkkclelgllvffavlpiialvllkks 164
                                    + + +l+ ++ +gl ++f++++i a ++++++
  gi|70606788|ref|YP_255658.1| 169 LGSYAALF-LMSFGLSSLFMMVAIRA-TTWQSQ 199
                                   55444443.44555555555555444.334433 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.2
               ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtkll 95 
                                   ++                                                                               
  gi|70606788|ref|YP_255658.1| 259 IY------------------------------------------------------------------------------- 260
                                   22............................................................................... PP

               ABC2_membrane_4  96 laKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvl 160
                                                                                     l+vf+++l ii ++l
  gi|70606788|ref|YP_255658.1| 261 --------------------------------------------------LVVFALILSIIGITL 275
                                   ..................................................233333333333333 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.9e-06    0.0068     397     449 ..      58     112 ..      19     121 .. 0.76
   2 ?   -8.3   9.5         5   1.8e+04     267     345 ..     134     212 ..     118     277 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-06
                         EMP70 397 i.ehpvrt.nqiprqipkqpwylkpllsvllgGilpFgaifielyfilsslwlek 449
                                     + p ++  qi++q   q + ++ ++s+l +G+l F+a+f+ ++  +s +w ++
  gi|70606788|ref|YP_255658.1|  58 GlDIPKQVlDQIAQQALAQTFGTSDYFSFLAAGMLSFIALFTSMQSGMSIVWDRR 112
                                   336677776999*99999**********************************876 PP

  == domain 2  score: -8.3 bits;  conditional E-value: 5
                         EMP70 267 lvGsGvqlllmalvtlllallgflspsnrgslltvalllyvllgliaGYvsarlyktfggekwkkntlltalllpgllf 345
                                   + +s ++ l+ + ++l++a+l  +s+    s l ++    +l+ +  G  s  ++  ++ + w++++ ++ ll   llf
  gi|70606788|ref|YP_255658.1| 134 VFSSVIRSLVQSSIVLAIAVLLGMSFRVGISPLDFLGSYAALFLMSFGLSSLFMMVAIRATTWQSQMAIMNLLNLPLLF 212
                                   4444555555555555555555555444444444443333444444444444444445555666666555554433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1990.39
//
Query:       gi|70606789|ref|YP_255659.1|  [L=704]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   9.2e-142  473.3   0.0   1.2e-141  472.9   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    7.8e-18   64.8   0.0    9.8e-09   35.6   0.0    2.6  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.9   0.0  1.3e-145  1.2e-141       5     550 .]     125     647 ..     121     647 .. 0.94

  Alignments for each domain:
  == domain 1  score: 472.9 bits;  conditional E-value: 1.3e-145
                                   -STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT--G CS
                 Ald_Xan_dh_C2   5 apdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlglpe 83 
                                    ++n+++   ++ Gdve+ f++a  v++g+++++r+   +lEt++ala +  ++g+lt ysstq  h++rr +ae+lg   
  gi|70606789|ref|YP_255659.1| 125 SQSNIVYreVFKGGDVEKIFNSAYKVIKGKLYNQRIVASPLETRGALAFY--DGGKLTFYSSTQSAHYLRRNLAEFLGF-- 201
                                   5677777777788*************************************..69************************8.. PP

                                   GGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEEEEEE CS
                 Ald_Xan_dh_C2  84 nkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvdllad 164
                                   +++rvi+p+vGG+FG+K+ ++p+e ++a ++  t++p k++ +R+e++l++g++++  +++++++d++G++++++ +l+ +
  gi|70606789|ref|YP_255659.1| 202 QDIRVIQPDVGGAFGSKIIAHPEEYALAKLSILTRKPLKWIPTRTEEFLSAGHGRDKFLEFETAVDREGNVLGIRGRLVGN 282
                                   89******************************************************************************* PP

                                   ESST.H...HHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHHH CS
                 Ald_Xan_dh_C2 165 aGay.a...dlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelRr 241
                                    Ga      d + + ++ a+ +l g Yki+ +++e+ +v tN pp++ +RG+G+p+a++++Er+m+ +A+elg+d++e+R 
  gi|70606789|ref|YP_255659.1| 283 LGAPyPdanDDELGNVQSATKMLPGIYKIKGIEIEAIAVNTNVPPTQSYRGAGRPEATYFIERIMNIVADELGIDQYEIRV 363
                                   **9633334677788899999999********************************************************* PP

                                   HHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEEE CS
                 Ald_Xan_dh_C2 242 rNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqegal 319
                                   +N+i  ++l py++p    ydsg+++ ll+ +++ +  e+++       +g     +g++ ++e +g+g+       e+a+
  gi|70606789|ref|YP_255659.1| 364 KNAI--DSL-PYTNPlgiKYDSGNVKGLLEYGRKFY--ESLK------SQG----CVGVSSYTEISGFGP------WETAR 423
                                   ****..566.999988888***********999865..3332......235....8**********8887......579** PP

                                   EEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 320 vrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrerl 400
                                   + ++ dG++t+ tg+ ++GqG  t++aqiaa+ L++p+e+++v++gdt+ + +g+gt++Sr+ +++g+Av  A ++l+++l
  gi|70606789|ref|YP_255659.1| 424 IFIKYDGKITLVTGTGPHGQGDATAFAQIAADILEIPIENIEVRWGDTEIIEDGIGTWGSRTVTIGGSAVVLATQQLKKKL 504
                                   ********************************************************************************* PP

                                   HHHHHHHCTS-CCCEEEETTEEEET..EEEECHHHHHHHHHHTTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEE CS
                 Ald_Xan_dh_C2 401 lkiaaellevspedleledgkvvvk..eksvslaelaaaaylervslsatgfyktldeetgkgppfayfaygaavaeVevD 479
                                    ++ a+ll+++ e++e+++gkv++k  ++sv+l+++a++a++ ++sl+ t+ yk       + pp  +++yg+++a V+vD
  gi|70606789|ref|YP_255659.1| 505 IEVGAKLLKADVEEVEYKQGKVIHKktGESVDLNRIARKAFSFGESLDVTSVYK------VDLPP--TTPYGVHLALVDVD 577
                                   *************************999999**********************4......44566..9************* PP

                                   TTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                 Ald_Xan_dh_C2 480 tetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                    etg+v v+++v+++DvG +iNp ++egQ+ GG+ qG+ + l+E +v++++Gqllt++++dY iPta + P
  gi|70606789|ref|YP_255659.1| 578 -ETGKVVVKKYVAIDDVGVVINPLLAEGQVIGGALQGLSQGLLEGTVFNDQGQLLTSNFQDYAIPTAVESP 647
                                   .9*****************************************************************9977 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   5.7e-10   5.1e-06       1      31 [.      17      47 ..      17      53 .. 0.95
   2 !   35.6   0.0   1.1e-12   9.8e-09      62     109 ..      58     105 ..      48     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.7e-10
                                  TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEE CS
                  Ald_Xan_dh_C  1 tGeavYvdDipapgalylafvrStkahAkiv 31
                                  tG++ YvdDi++pg+ ++af+rS+++hAki+
  gi|70606789|ref|YP_255659.1| 17 TGKGSYVDDIQIPGTHFVAFLRSQYPHAKIK 47
                                  8*****************************7 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 1.1e-12
                                   TSSS-EEEESS-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  62 siledeedallaedkvrsvgqavaavvAedeetArkAaklvkveYeel 109
                                   + +++ +d  +a+++v++vgq++a+v+A+d+++A + ++ ++veYe+l
  gi|70606789|ref|YP_255659.1|  58 NEINPGKDFPIATEEVTYVGQPIAMVIAKDRYEAYDLLENIEVEYEPL 105
                                   4566677899************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 4328.73
//
Query:       gi|70606790|ref|YP_255660.1|  [L=162]
Description: putative RNA-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-24   84.8   1.1    6.2e-24   84.1   1.1    1.3  1  DUF1947   Domain of unknown function (DUF1947)
    5.9e-14   51.8   0.4      9e-14   51.2   0.4    1.3  1  PUA       PUA domain
    0.00093   19.4   0.3     0.0014   18.9   0.3    1.3  1  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
       0.13   13.0   4.3       0.65   10.7   1.8    2.5  2  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   1.1   1.4e-27   6.2e-24       1      65 [.       2      63 ..       2      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.4e-27
                                  --EE--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEEEETTEEEEEESSSEEE-HHHHHH CS
                       DUF1947  1 kRHfLSkKeakeileklkekyisislesdkiEieeekkeklYlingvpilfeeekliPtLklLlk 65
                                  +RH+LS+K+++++l+k+k+ky +i+le++ iE+++ekke +Y++ng +++f +e++iPtL++++k
  gi|70606790|ref|YP_255660.1|  2 NRHLLSDKDKRDFLSKVKQKY-NIELEGQ-IEVGKEKKELYYFVNGLLSFF-SEEIIPTLCFVQK 63
                                  5********************.******9.*********************.**********998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.4     2e-17     9e-14       1      67 [.      69     136 ..      69     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2e-17
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHH.HHHHCTSEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanyssee.lakikggks 67 
                                   ++vvvd+gAvk ++ ga+L++pG+v+++++++egdvV ++++ + ++a+ ++ ++ +  +++ kg+ +
  gi|70606790|ref|YP_255660.1|  69 PYVVVDEGAVKRVTDGADLFVPGIVSYNCECKEGDVVLVKTKTNLPIAIIKVILNKDKaIQDKKGKFG 136
                                   68****************************************99999998887776541445555555 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   3.1e-07    0.0014       1      56 [.      70     127 ..      70     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.1e-07
                       UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k 56 
                                   +vvv+e a k+++ G d++  +i++++ ++ke++vv+V  + + p++i k++ ++   
  gi|70606790|ref|YP_255660.1|  70 YVVVDEGAVKRVTDGADLFVPGIVSYNCECKEGDVVLVKTKTNLPIAIIKVILNKdkA 127
                                   79********************************************999887776532 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.8   0.00015      0.65      40      86 ..      14      64 ..       1      64 [. 0.58
   2 ?   -2.7   0.0       2.3     1e+04      46      56 ..     103     112 ..      99     132 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                       Pre-PUA 40 llpkkeevkvvklq......gehve.lyvvdgeplffqdregellPtlytlwky 86
                                  +l k ++   + l+      +e+ e +y+v+g + ff+    e++Ptl++++ky
  gi|70606790|ref|YP_255660.1| 14 FLSKVKQKYNIELEgqievgKEKKElYYFVNGLLSFFSE---EIIPTLCFVQKY 64
                                  444433333333333444444444405677899999988...9*******9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                       Pre-PUA  46 evkvvklqgeh 56 
                                   +v++vk++ ++
  gi|70606790|ref|YP_255660.1| 103 DVVLVKTK-TN 112
                                   45555555.32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1122.24
//
Query:       gi|70606791|ref|YP_255661.1|  [L=222]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-23   82.3   0.1    6.8e-23   81.3   0.0    1.5  2  Glycos_transf_2  Glycosyl transferase family 2
     0.0011   18.9   0.0     0.0012   18.8   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
     0.0095   15.4   0.1      0.015   14.8   0.1    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.044   14.3   0.0      0.074   13.6   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   1.5e-26   6.8e-23       2     166 ..       4     158 ..       3     162 .. 0.89
   2 ?   -2.2   0.0      0.68     3e+03     108     154 ..     169     211 ..     166     217 .. 0.62

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.5e-26
                                   EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS. CS
               Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd. 81 
                                   vviptyNe+++++e++ ++++   ++d+ ii+vDD+S+D+t  i+++l    + + ++r++e+ G ++al  gl++     
  gi|70606791|ref|YP_255661.1|   4 VVIPTYNEAENIRELIPRIKEV--DKDINIIIVDDNSPDNTSGIAKQL----GAIVFVRKDER-GIGSALKFGLEQGVKMg 77 
                                   9********************9..************************....34666666655.************77777 PP

                                   ..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
               Glycos_transf_2  82 ..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                      ++++DaD+ +dp++++ l+    k +ad+v+g+r++++g   +++ ++r    + + + + +  l  n+ + ++++++
  gi|70606791|ref|YP_255661.1|  78 fkRLITMDADLSHDPKYIPALIS---K-DADLVIGSRYVKGGAIENWPLQRR--LISSGANSIARLLLRFNVRDATSGYRA 152
                                   99*************99998875...4.8899*****************998..799999999999999999999999888 PP

                                   EEEHHH CS
               Glycos_transf_2 161 lrreal 166
                                   +  +a+
  gi|70606791|ref|YP_255661.1| 153 YTPRAV 158
                                   876665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
                                   TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
               Glycos_transf_2 108 gadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                   g+   ++++++if+++ +i         +   ++++k +l+ +  f 
  gi|70606791|ref|YP_255661.1| 169 GYEFQICSVYHIFKSRLQIAEVPI----SFHDRERGKSKLDSQKIFK 211
                                   555667888999999888888754....5555555555555555555 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-07    0.0012       4     108 ..       2      98 ..       1     156 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnl.gstgksralneal 83 
                                   l v++pt+ne++ ++e++  +      ++ +++v+d+s + t   a++    l++  ++ v++++++ gs  k  +l++++
  gi|70606791|ref|YP_255661.1|   2 LGVVIPTYNEAENIRELIPRIKEV-DKDINIIIVDDNSPDNTSGIAKQ----LGA--IVFVRKDERGiGSALKF-GLEQGV 74 
                                   679**************9999974.478****************9998....555..57788877665665553.477777 PP

               Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrl 108
                                   ++   +l+  +D+D   +P ++++l
  gi|70606791|ref|YP_255661.1|  75 KMGFKRLI-TMDADLSHDPKYIPAL 98 
                                   77666665.58********999873 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   3.4e-06     0.015       2      46 ..       4      45 ..       3      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
               Glyco_tranf_2_2  2 vviplraseerhyieervlqkakyydeeielivvddgSsekflee 46
                                  vvip +++ e+  i+e + +++   d++i++i+vdd S++++   
  gi|70606791|ref|YP_255661.1|  4 VVIPTYNEAEN--IRELIPRIKEV-DKDINIIIVDDNSPDNTSGI 45
                                  9**********..*****999999.***************97543 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.074       1      50 [.       9      59 ..       9      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
               Glyco_tranf_2_4  1 rneadiLpeflahhlalgfd.rilvydndstDgtrailkelpevkllhvdk 50
                                  +nea+ + e +  +++++ d +i+++d++s D+t+ i k+l ++ +++ d+
  gi|70606791|ref|YP_255661.1|  9 YNEAENIRELIPRIKEVDKDiNIIIVDDNSPDNTSGIAKQLGAIVFVRKDE 59
                                  5899999999999999999878******************98877666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1570.04
//
Query:       gi|70606792|ref|YP_255662.1|  [L=107]
Description: hypothetical protein Saci_1012 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-06   25.8   0.2    1.1e-05   24.9   0.2    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00011   22.1   0.4    0.00035   20.4   0.1    2.0  3  HTH_11           HTH domain
     0.0017   18.3   3.3     0.0029   17.5   3.3    1.3  1  Prefoldin_2      Prefoldin subunit
     0.0021   17.8   0.0     0.0033   17.2   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
     0.0022   17.9   0.1      0.013   15.4   0.0    1.9  2  MarR             MarR family
     0.0027   17.7   1.0     0.0099   16.0   1.0    1.9  1  Med9             RNA polymerase II transcription mediator com
     0.0038   17.5   2.1      0.009   16.3   2.1    1.7  1  Csm1_N           Csm1 N-terminal domain
  ------ inclusion threshold ------
      0.013   15.2   1.3       0.02   14.5   1.3    1.3  1  NRBF2            Nuclear receptor-binding factor 2, autophagy
      0.017   14.9   2.1      0.025   14.4   0.4    1.9  2  DivIC            Septum formation initiator
      0.019   14.7   0.0      0.035   13.9   0.0    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.021   14.6   0.0      0.048   13.4   0.0    1.6  1  LexA_DNA_bind    LexA DNA binding domain
      0.021   14.9   1.4      0.059   13.4   1.0    1.7  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.034   14.0   0.0      0.046   13.6   0.0    1.3  1  MarR_2           MarR family
      0.041   13.9   0.0      0.071   13.1   0.0    1.4  1  Phage_terminase  Phage terminase small subunit
      0.047   13.8   0.0       0.09   12.9   0.0    1.5  1  FeoC             FeoC like transcriptional regulator
      0.056   13.5   0.0       0.14   12.3   0.0    1.7  1  Myc-LZ           Myc leucine zipper domain
      0.057   13.4   1.3       0.16   12.0   1.3    1.8  1  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
      0.061   13.2   0.0       0.13   12.1   0.0    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
      0.061   13.3   0.6      0.088   12.8   0.1    1.6  1  HTH_36           Helix-turn-helix domain
      0.072   13.3   0.0       0.12   12.6   0.0    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.073   13.2   1.8       0.13   12.3   1.8    1.5  1  DUF5595          Domain of unknown function (DUF5595)
      0.074   13.7   0.0       0.16   12.6   0.0    1.5  1  SlyX             SlyX
      0.095   13.1   0.0       0.17   12.2   0.0    1.5  1  Rrf2             Transcriptional regulator
      0.097   13.2   0.8       0.15   12.7   0.7    1.4  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.12   11.7   0.6       0.12   11.7   0.6    1.0  1  FAM76            FAM76 protein
       0.36   11.0   3.4       0.99    9.5   3.4    1.8  1  Cep57_CLD_2      Centrosome localisation domain of PPC89


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.5e-08   1.1e-05       6      48 .]       8      51 ..       3      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.5e-08
                        HTH_24  6 rkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +I+++L+++++  ++r+LA +l +Sp t + + ++L + G+I+
  gi|70606792|ref|YP_255662.1|  8 QDIISILKEKGGsVNIRDLALQLKISPKTAKGYARELYRLGYIE 51
                                  68*******9999******************************7 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   5.1e-07   0.00035       1      44 [.       6      49 ..       6      55 .. 0.90
   2 ?   -1.8   0.0       4.4     3e+03      38      49 ..      70      85 ..      66      88 .. 0.56
   3 ?   -1.7   0.0       4.1   2.9e+03      19      25 ..      90      96 ..      80     102 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.1e-07
                        HTH_11  1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  Rl++i+ +L+e+ g +++ +LA +L++S +t   + ++L  lg+
  gi|70606792|ref|YP_255662.1|  6 RLQDIISILKEKGGSVNIRDLALQLKISPKTAKGYARELYRLGY 49
                                  89*******888888*****************999999988883 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                        HTH_11 38 aLeelg....vpIese 49
                                  +L+++     ++Ie+ 
  gi|70606792|ref|YP_255662.1| 70 DLKKTVethtAEIEAL 85
                                  5555555555666665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.1
                        HTH_11 19 eeLAeeL 25
                                  e+L+eeL
  gi|70606792|ref|YP_255662.1| 90 EFLKEEL 96
                                  3444444 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.3   4.2e-06    0.0029      53      97 ..      57     101 ..      55     107 .] 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                                   TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelke 97 
                                   ++ +k++ +e +++L+++ et ++ei++l+k+ e l++el+ ++ 
  gi|70606792|ref|YP_255662.1|  57 NMILKRENPENITDLKKTVETHTAEIEALKKEVEFLKEELSRFRG 101
                                   68999***********************************99986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.8e-06    0.0033       7      51 ..       9      53 ..       6      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.8e-06
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  +i+ +l e ++ +++++lA ++ +++ t+ ++ + L +lGy+e d
  gi|70606792|ref|YP_255662.1|  9 DIISILKEKGGSVNIRDLALQLKISPKTAKGYARELYRLGYIEMD 53
                                  8999**************************************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.013       2      48 ..       4      51 ..       3      57 .. 0.89
   2 ?    0.2   0.0         1   7.1e+02      11      31 ..      59      79 ..      58      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                                  -HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  2 tltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                  t+   +i+ il+e+g+  ++ +La +l++s+ t+   +++L++ G+ie
  gi|70606792|ref|YP_255662.1|  4 TPRLQDIISILKEKGGsVNIRDLALQLKISPKTAKGYARELYRLGYIE 51
                                  666668999*****999******************************8 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                                  HHHHSTTEEHHHHHHHHTS-H CS
                          MarR 11 ilyeqgplsvseLakklgvsk 31
                                  il++++p ++++L k +++++
  gi|70606792|ref|YP_255662.1| 59 ILKRENPENITDLKKTVETHT 79
                                  789999999999999887765 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   1.4e-05    0.0099      39      77 ..      62     100 ..       2     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                          Med9  39 relirelpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                   re  +++ ++ ++ve+  aeie+l+++++  +e L++++
  gi|70606792|ref|YP_255662.1|  62 RENPENITDLKKTVETHTAEIEALKKEVEFLKEELSRFR 100
                                   566689999**************************9997 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.1   1.3e-05     0.009      28      61 ..      66     100 ..      54     107 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                        Csm1_N  28 ENsv.LsqkletkdqeiesLkeqlaeleekvkele 61 
                                   EN + L++++et++ eie+Lk++++ l+e++++  
  gi|70606792|ref|YP_255662.1|  66 ENITdLKKTVETHTAEIEALKKEVEFLKEELSRFR 100
                                   66443999*********************998765 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.3   2.8e-05      0.02      83     120 ..      63     100 ..      51     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                         NRBF2  83 eqatkiadLkrlvelLlaenerLrkenkqLkaekaRLq 120
                                   e   +i+dLk+ ve+ +ae e+L+ke + Lk e +R +
  gi|70606792|ref|YP_255662.1|  63 ENPENITDLKKTVETHTAEIEALKKEVEFLKEELSRFR 100
                                   55678****************************99987 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.3   8.8e+02      59      73 ..      39      55 ..      21      62 .. 0.64
   2 ?   14.4   0.4   3.6e-05     0.025      18      50 ..      67      99 ..      60     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                                  XXXXX..XXXXXXXXXX CS
                         DivIC 59 erARs..elglvkpgEt 73
                                   +AR+  +lg++  +E+
  gi|70606792|ref|YP_255662.1| 39 GYARElyRLGYIEMDEN 55
                                  55663226777766664 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                  ++ +lk+ +++ +ae+++lk+e e L++e+++ 
  gi|70606792|ref|YP_255662.1| 67 NITDLKKTVETHTAEIEALKKEVEFLKEELSRF 99
                                  456778888888888888888888888887765 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     5e-05     0.035       1      31 [.       6      37 ..       6      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                      HTH_DeoR  1 Rieqilellkqq.gklsveelvellgvSeaTi 31
                                  R++ i+  lk++ g++++ +l+ +l++S++T+
  gi|70606792|ref|YP_255662.1|  6 RLQDIISILKEKgGSVNIRDLALQLKISPKTA 37
                                  899******987369****************7 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-05     0.048       3      61 ..       2      55 ..       1      57 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                                  ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                 LexA_DNA_bind  3 kLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                  +LT+r +++++++k    e+g    ir++a +l+++ p++++   + L r Gyie+d++
  gi|70606792|ref|YP_255662.1|  2 ELTPRLQDIISILK----EKGGSVNIRDLALQLKIS-PKTAKGYARELYRLGYIEMDEN 55
                                  58888888887765....6899999*********97.*******************987 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.4   1.7e+03      29      49 ..      24      44 ..      20      46 .. 0.86
   2 ?   13.4   1.0   8.6e-05     0.059      47      89 ..      56      98 ..      51     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                    TPR_MLP1_2 29 edlekqaeiakeaqqkYerel 49
                                  +dl  q +i  +  + Y+rel
  gi|70606792|ref|YP_255662.1| 24 RDLALQLKISPKTAKGYAREL 44
                                  588899999999999999998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.6e-05
                    TPR_MLP1_2 47 relvkhaedvkelqalreelnelkaeiaelkaeaesakaelee 89
                                  + ++++ e+ +++++l++ +++ +aei+ lk+e+e +k+el++
  gi|70606792|ref|YP_255662.1| 56 ENMILKRENPENITDLKKTVETHTAEIEALKKEVEFLKEELSR 98
                                  568999999******************************9985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.7e-05     0.046      12      56 ..      12      55 ..       2      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
                                  HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                    L   +g  +++++la  l++s+ ++    ++L + G++e  ++
  gi|70606792|ref|YP_255662.1| 12 SILKEKGG-SVNIRDLALQLKISPKTAKGYARELYRLGYIEMDEN 55
                                  45555555.59*****************************97655 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.071      12      41 ..      10      39 ..       4      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
               Phage_terminase 12 AyelykEsggtlklkdIAkvLdvsestvrk 41
                                     + kE+gg ++++d+A  L +s +t ++
  gi|70606792|ref|YP_255662.1| 10 IISILKEKGGSVNIRDLALQLKISPKTAKG 39
                                  56799*********************9876 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.09       5      51 ..      10      57 ..       6      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                          FeoC  5 lkeyleer.grvslkeLsrhfkaspealeamLeqwvrkGrvekvaata 51
                                  + + l+e+ g+v++++L+ ++k+sp++ ++    + r G +e  ++++
  gi|70606792|ref|YP_255662.1| 10 IISILKEKgGSVNIRDLALQLKISPKTAKGYARELYRLGYIEMDENEN 57
                                  55555555279****************999888888888887766655 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002      0.14       8      29 ..      80     101 ..      79     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                        Myc-LZ   8 SekEqLRkrrEqLKhkLeQLrN 29 
                                   +e+E L+k+ E LK  L + r+
  gi|70606792|ref|YP_255662.1|  80 AEIEALKKEVEFLKEELSRFRG 101
                                   89***************99986 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   0.00023      0.16       2      31 ..      67      96 ..      66     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                 Bap31_Bap29_C  2 eiekLkkeLkkkkkDlealKkQaeglakEY 31
                                   i+ Lkk  ++  +++ealKk  e l+ E 
  gi|70606792|ref|YP_255662.1| 67 NITDLKKTVETHTAEIEALKKEVEFLKEEL 96
                                  6999*****************999998885 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.13       6      46 ..       9      51 ..       6      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                  HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +I+++L e  g+  + +la +l++s+ t   + + L+ +G++e
  gi|70606792|ref|YP_255662.1|  9 DIISILKEkgGSVNIRDLALQLKISPKTAKGYARELYRLGYIE 51
                                  5999*****9******************999999999999886 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.088      28      55 .]      23      50 ..       9      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                        HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                   ++la +l++s +T+  + +eL +lGyi
  gi|70606792|ref|YP_255662.1| 23 IRDLALQLKISPKTAKGYARELYRLGYI 50
                                  689************************9 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017      0.12      16      55 ..      14      53 ..       4      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                                  HHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 16 lseekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                  l+e+++ v   dla  L++sp ++    ++L + Gy+e  
  gi|70606792|ref|YP_255662.1| 14 LKEKGGSVNIRDLALQLKISPKTAKGYARELYRLGYIEMD 53
                                  5679999*****************************9875 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   0.00019      0.13      40      70 ..      69      99 ..      49     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                       DUF5595 40 skLkelynvdeaqlesleeeekrLeeEierl 70
                                  + Lk+ ++ + a++e+l++e + L+eE++r 
  gi|70606792|ref|YP_255662.1| 69 TDLKKTVETHTAEIEALKKEVEFLKEELSRF 99
                                  679*************************985 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00023      0.16      18      50 ..      67      99 ..      64     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                          SlyX 18 tieeLndvvaeqqqqidrlqrqlrllaerlkel 50
                                   i +L ++v  +  +i++l+++++ l+e+l+  
  gi|70606792|ref|YP_255662.1| 67 NITDLKKTVETHTAEIEALKKEVEFLKEELSRF 99
                                  6999************************99765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.17      19      57 ..      15      52 ..       7      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  ke++ ++v+++++a + +isp+ ++   ++L + g+++ 
  gi|70606792|ref|YP_255662.1| 15 KEKG-GSVNIRDLALQLKISPKTAKGYARELYRLGYIEM 52
                                  3444.45*****************************985 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   0.00021      0.15      29      77 ..      54     102 ..      31     106 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                  Syntaxin-6_N  29 edtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkid 77 
                                   e+++   + e  e  t+L+k++++   ++e L++ v+ ++++ s+f+ +
  gi|70606792|ref|YP_255662.1|  54 ENENMILKRENPENITDLKKTVETHTAEIEALKKEVEFLKEELSRFRGT 102
                                   333334688999999************************9999998755 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   0.00017      0.12     208     266 ..      48     106 ..       8     107 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                         FAM76 208 ksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelrek 266
                                     +++  +++++   +  e+i+ lkk++e++  e+ + +k++  lk el + + + + k
  gi|70606792|ref|YP_255662.1|  48 GYIEMDENENMILKRENPENITDLKKTVETHTAEIEALKKEVEFLKEELSRFRGTKKVK 106
                                   37888999**************************************9999988776665 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.4    0.0014      0.99      20      62 ..      51      97 ..      49     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                   Cep57_CLD_2 20 qvheeelkrLnkERdsalrqLgvAye....elneLkaevealrkELk 62
                                  ++ e e++ L +E+ + ++ L    e    e++ Lk eve+l++EL 
  gi|70606792|ref|YP_255662.1| 51 EMDENENMILKRENPENITDLKKTVEthtaEIEALKKEVEFLKEELS 97
                                  6778888889998888888887766533337899**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 704.67
//
Query:       gi|70606793|ref|YP_255663.1|  [L=317]
Description: ornithine cyclodeaminase/mu-crystallin family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-47  161.7   0.1    2.2e-46  158.3   0.1    1.9  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    2.1e-05   24.6   0.0    4.5e-05   23.5   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0059   16.2   0.1      0.012   15.2   0.1    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0073   16.5   0.0      0.011   15.9   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
  ------ inclusion threshold ------
      0.021   15.6   0.0      0.072   13.9   0.0    1.9  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.025   14.1   0.0       0.04   13.5   0.0    1.3  1  NmrA             NmrA-like family
       0.04   14.5   0.2       0.28   11.8   0.1    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.1   8.7e-50   2.2e-46       6     316 ..       5     297 ..       1     299 [. 0.88

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 8.7e-50
                                   E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTT.EEEEEEEEEETTTCCCTSSSE CS
               OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagre.llgvKlvnshpenkksglptv 85 
                                   l +v+ve++++ +d+ + +e af+ l++ ++ ++ r++  ++       vm+ + ++ + +lg+K+             + 
  gi|70606793|ref|YP_255663.1|   5 LREVDVEKLVNFKDIYDSLERAFKYLSNKNASNTKRIRTIFHG-----SVMTYQAGAFDnYLGFKVF-----------VKG 69 
                                   5678899999999999999999999999888888888888877.....6676555554457777764...........345 PP

                                   EEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHH CS
               OCD_Mu_crystall  86 talvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydrdeea 166
                                   t l+vL + + G  +++++a ll+ +RT+  s ++  yLa+k+ + ++iiG G q e+q++ ++++ +   v i ++++e+
  gi|70606793|ref|YP_255663.1|  70 TYLGVLYSLD-GDIVLVVEADLLSRIRTGILSVLVSDYLAKKNYTSVGIIGLGKQGEFQVKSFNELKK--GVTIRAISKEK 147
                                   6788998865.8999*************************************************9985..677889***** PP

                                   HHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEE.SH CS
               OCD_Mu_crystall 167 aekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkradifv.ds 246
                                   ++k +++lq ++++v  +k+ +e  +  +++vt+T +k p lk e+++ G+hina+g++ p+++eL ++++k + ++  ++
  gi|70606793|ref|YP_255663.1| 148 TDKNIKRLQSQGLNVIPAKDYKELCSTSEVIVTITSSKDPFLKLEFLNHGTHINALGSNLPERAELFPEVIKASSLIAvED 228
                                   ************************************************************************998776699 PP

                                   HHHHHHC.CCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHHCC CS
               OCD_Mu_crystall 247 eaqaree.GeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyeraee 316
                                   ++qa+ee G++ +  ek  + + +kv  + +vi+Gk+ GR+sd eit+f+s+G++ eDva++kl ye+a++
  gi|70606793|ref|YP_255663.1| 229 LEQAKEEaGDLIL-AEKMKMLDWNKVVLISDVINGKV-GRKSDDEITIFKSTGIGLEDVATMKLLYEKAKK 297
                                   9999865499888.56666777889999*******86.8*****************************986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.8e-08   4.5e-05      11      97 ..     111     196 ..     102     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
                                   TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB- CS
                  Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepile 91 
                                   +   v +iG G+ +e  +k + + +   v++   + e+ ++  ++l+++ +++++ +++kel + ++v+++ t+s++p l+
  gi|70606793|ref|YP_255663.1| 111 NYTSVGIIGLGKQGEFQVKSFNELKKG-VTIRAISKEKTDKNIKRLQSQGLNVIPAKDYKELCSTSEVIVTITSSKDPFLK 190
                                   456899**************9876655.**************************************************998 PP

                                   HHHHHC CS
                  Shikimate_DH  92 keevee 97 
                                    e +++
  gi|70606793|ref|YP_255663.1| 191 LEFLNH 196
                                   776665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   4.7e-06     0.012       6      67 ..     114     181 ..     109     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                                   -EEEES-SHHHHHHHHHHHH..TT--EE.EEE-TT-HHHHHHHHTT-EEE...EHHHHHHT-SEEEE- CS
                          IlvN   6 kiaviGyGsqGhaqalnlrd..sgldvv.vglregsksvkkAkeegfevl...tvaeavkkadvvmil 67 
                                    + +iG G qG+ q + + +   g+ +  ++ ++++k++k+ +++g++v+   +++e++++++v++++
  gi|70606793|ref|YP_255663.1| 114 SVGIIGLGKQGEFQVKSFNElkKGVTIRaISKEKTDKNIKRLQSQGLNVIpakDYKELCSTSEVIVTI 181
                                   699*********99998887224555532556666789**********97222567888888888766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.4e-06     0.011       2      67 ..     115     186 ..     114     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT......EEE-SSHHHHHHHCSEEEE-SSSHH CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg......akaaesieelvasldvvitmvkagk 67 
                                   +g+iGlG+ G+  ++ + + +  v++   +kek+++ +++       + +a++ +el+++ +v++t+ ++++
  gi|70606793|ref|YP_255663.1| 115 VGIIGLGKQGEFQVKSFNELKKGVTIRAISKEKTDKNIKRLqsqglnVIPAKDYKELCSTSEVIVTITSSKD 186
                                   8**************9966666666666666666555555334459999***************99877665 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.8e-05     0.072       3      89 ..     115     200 ..     113     203 .. 0.79
   2 ?    0.6   0.0      0.38   9.8e+02      23      59 ..     195     234 ..     183     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                   EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
                  GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpngtheelaka 81 
                                   v+iiG+Gk g+ +++++ne +++  + a+ ++++ +  +  +s g++    +d++el +      viv++ +++   l ++
  gi|70606793|ref|YP_255663.1| 115 VGIIGLGKQGEFQVKSFNELKKGVTIRAISKEKTDKNIKRLQSQGLNviPAKDYKELCS---TSEVIVTITSSKDPFLKLE 192
                                   9****************************998887766664555555448899999999...4457777777777777777 PP

                                   HHHTT-EE CS
                  GFO_IDH_MocA  82 aleagkhv 89 
                                   +l++g h+
  gi|70606793|ref|YP_255663.1| 193 FLNHGTHI 200
                                   77777776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                                   TTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHT CS
                  GFO_IDH_MocA  23 qrleevvalldpdaeraeavaesfgve...aysdleella 59 
                                   ++++++ al ++ +erae + e  +++   a++dle+ ++
  gi|70606793|ref|YP_255663.1| 195 NHGTHINALGSNLPERAELFPEVIKASsliAVEDLEQAKE 234
                                   46679999999*********99888886666666666554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05      0.04       8      60 ..     121     176 ..     116     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                   SHHHHHHHHHHHH..HT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHH CS
                          NmrA   8 GrqGksvvrallk..aghkvralvRdtkselakslkeaGvelv.kgdlddkeslve 60 
                                   G+qG++ v+ + +  +g ++ra+ ++ + +++k l+++G +++ + d ++  s +e
  gi|70606793|ref|YP_255663.1| 121 GKQGEFQVKSFNElkKGVTIRAISKEKTDKNIKRLQSQGLNVIpAKDYKELCSTSE 176
                                   999999999986666****************************8888776555444 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011      0.28       2      66 ..     115     179 ..     114     186 .. 0.69
   2 ?    0.1   0.0      0.48   1.2e+03      18      73 ..     193     247 ..     189     257 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEEETTSHHHHHHHHHHHHTTS.-GGCEEE.EEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEE CS
                 F420_oxidored   2 igiiGaGnmgealasgllaaga.qpheivv.ansrnpekaeelaeelgvkvtavdneeaaeeadvvv 66 
                                   +giiG G++ge  ++ + +  +     i+    +++ + ++ l+++    + a+d++e+++ ++v+v
  gi|70606793|ref|YP_255663.1| 115 VGIIGLGKQGEFQVKSFNELKKgV--TIRAiSKEKTDKNIKRLQSQGLNVIPAKDYKELCSTSEVIV 179
                                   8****************8887432..333303455555666665444333445599********998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.48
                                   HHHTTS-GGCEEEEEESSCCCHHHHHHHHC..-EEECECHHHHHHH-SEEEE-S-HHH CS
                 F420_oxidored  18 llaagaqpheivvansrnpekaeelaeelg..vkvtavdneeaaeeadvvvlavkped 73 
                                   +l++g   ++i   +s+ pe+ae + e ++    +   d e+a eea  ++la k+++
  gi|70606793|ref|YP_255663.1| 193 FLNHG---THINALGSNLPERAELFPEVIKasSLIAVEDLEQAKEEAGDLILAEKMKM 247
                                   56666...66665556677777666655554333333355566666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2038.62
//
Query:       gi|70606794|ref|YP_255664.1|  [L=379]
Description: aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-28   99.3   0.0    2.8e-28   99.1   0.0    1.0  1  Aminotran_1_2   Aminotransferase class I and II
    8.1e-10   38.0   0.0    1.4e-09   37.3   0.0    1.3  1  Aminotran_MocR  Alanine-glyoxylate amino-transferase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.0   3.2e-32   2.8e-28       4     363 .]      26     372 ..      23     372 .. 0.88

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 3.2e-32
                                   EESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                 Aminotran_1_2   4 inLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                   inL+s+ ++      +++e+++a  e   + g+++ +y+   g+ el++++   +   ++++   +++vvv+sGa+++ e+
  gi|70606794|ref|YP_255664.1|  26 INLASGTPDPR--LMPIKEIRQAYDEvLEEFGSKVLFYPGAGGQEELKKEIENNFL--PYIDSGIKGNVVVTSGAQHAVEL 102
                                   89999988554..67*********9977788899**********************..9*********************9 PP

                                   HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B CS
                 Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtv 164
                                   l+  +    +d i v +pt+ +  + l+l+   v +++l+   + ++ +++le +lk    g++ + + ++ ++hNP G+ 
  gi|70606794|ref|YP_255664.1| 103 LAKYFL--EDDTIAVENPTFIETFTPLKLRSNVVLPVSLD---EGGIKIDELELLLKV---GKI-RLLYVIPNCHNPAGVT 174
                                   999996..999***************************77...99*********9997...555.567799********** PP

                                   --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHH CS
                 Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrk 245
                                   + +e  + l++la+ky + ++ D+ Y   +  ++    t+  +++   ++  +s+sK   ++G+RvG+i+++++ vs   +
  gi|70606794|ref|YP_255664.1| 175 MCEERRKILVELADKYDFCILEDDPYKPIAGVTPM---TIKSLDRNGRVIYISSFSKII-APGLRVGFIVSSSEEVSNKIS 251
                                   ***************************99998653...4999999999*********88.6**********7777777777 PP

                                   HHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHHH CS
                 Aminotran_1_2 246 lsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaetakelskkL 324
                                   l  ++ + +s   ++v a l ++  +++++++  + ++++ k+l d+L ++g+k + ++  g+fll dl++      +k+ 
  gi|70606794|ref|YP_255664.1| 252 LIEQMDFsTSTINQFVIARLLKKGIVRERMKNLHSYYKEKMKTLIDSLHDKGFKDFNEPqCGFFLLLDLKKD----SWKVF 328
                                   7777777655555666666666666899***********************9987765559*********99....56664 PP

                                   HHT..CTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 325 lee..vgvyvtpgtsftv...pgrlRitvAglteeeleelveal 363
                                    e    g+  +p ++f++   ++  R++++  tee+++e v++l
  gi|70606794|ref|YP_255664.1| 329 NEAvkLGLSFVPAKPFYLrggETMARLSISVATEEQIKEGVKRL 372
                                   44322489999**********9999999999********99987 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   1.5e-13   1.4e-09     129     382 ..     115     352 ..      86     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.5e-13
                                   EEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-E CS
                Aminotran_MocR 129 vtvpGydrhfllleelGielltvdlqddGpdvdaveklvaedasvkGilavpkysnptGetiseevarrlaalkaaapdfr 209
                                   v  p +   f  l+     +l v l++ G  +d +e l  +   ++ ++++p+  np+G t+ ee+ + l+ l a   df 
  gi|70606794|ref|YP_255664.1| 115 VENPTFIETFTPLKLRSNVVLPVSLDEGGIKIDELELLL-KVGKIRLLYVIPNCHNPAGVTMCEERRKILVEL-ADKYDFC 193
                                   555666666666666666788999**********98665.6789*********************99999988.5678*** PP

                                   EEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S---HHHHH CS
                Aminotran_MocR 210 ifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkylGlqsiGpdkveql 290
                                   i+ dd y+  + v+       i    ++     r + ++s ski   G  v+f+ ss+++++     +         ++q 
  gi|70606794|ref|YP_255664.1| 194 ILEDDPYKPIAGVT----PMTI----KSLDRNGRVIYISSFSKIIAPGLRVGFIVSSSEEVSNKISLIEQMDFSTSTINQF 266
                                   *******9765432....2233....344455799*****************************999*99*********** PP

                                   HHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEESSS-HHHHHHHHHHCTEE---T CS
                Aminotran_MocR 291 rhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyfisldtldgvakrvvklaeeaGvsltaa 371
                                      ++lk+   ++  m++    +   ++  +++l + l  +++  ++ep+ G+f+ ld  +  + +v + a + G+s+ +a
  gi|70606794|ref|YP_255664.1| 267 VIARLLKKG-IVRERMKN----LHSYYKEKMKTLIDSLHDKGFKDFNEPQCGFFLLLDLKKD-SWKVFNEAVKLGLSFVPA 341
                                   ****99852.34555555....55556666677778888899****************8765.567899999999999999 PP

                                   TTTSSTT--SS CS
                Aminotran_MocR 372 GatypaGedpk 382
                                      y  G +  
  gi|70606794|ref|YP_255664.1| 342 KPFYLRGGETM 352
                                   99988876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2647.01
//
Query:       gi|70606795|ref|YP_255665.1|  [L=350]
Description: X-prodipeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-59  199.6   0.1    7.5e-59  198.9   0.1    1.3  1  Peptidase_M24  Metallopeptidase family M24
      4e-16   59.9   0.0    8.1e-16   58.9   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.9   0.1   8.4e-63   7.5e-59       2     208 ..     134     334 ..     133     335 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.9 bits;  conditional E-value: 8.4e-63
                                   HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEE CS
                 Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlidag 82 
                                    +r+  +ia++a+ ++++ i++g++e e+ +++ ++ ++++g  +++f+pi+ sg+n++++h ++++r++ +++++++d+g
  gi|70606795|ref|YP_255665.1| 134 ILREGVKIAEEAFLETINLIREGMKEVEISNLLIQK-FSERG-VKPSFEPIITSGPNTSMPHLRATNRKVARNEVIIFDFG 212
                                   58999*****************************88.66666.689*********************************** PP

                                   EEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSSSE CS
                 Peptidase_M24  83 aeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlevhd 163
                                   ++y+gya+D+tr+v++Gk++++  +++e+v+eaqe+a + v + v++se+d++ar+++ ++g++++f h++GHg+G++vh+
  gi|70606795|ref|YP_255665.1| 213 IRYKGYATDTTRVVSIGKPNEDVLKIHEIVREAQERAEEYVSEKVETSEVDKIARQTISKYGFGAYFIHRTGHGIGIDVHE 293
                                   **********************999*******************************************************9 PP

                                   EEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                 Peptidase_M24 164 egpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                   + p++s  s+ +r+++++m+ftiEpgiy  pg++g+ried+v v 
  gi|70606795|ref|YP_255665.1| 294 D-PYIS--SDYKRPIKNNMTFTIEPGIY-LPGKFGIRIEDMVFVN 334
                                   9.***9..6889****************.99***********996 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0     9e-20   8.1e-16       2     132 .]       5     126 ..       4     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 9e-20
                                   HHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHH CS
                  Creatinase_N   2 lerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpveala 82 
                                   ler++++++++++d l++ + +n+ YltGf++e  +r+l ++vt+++++++v++l++++  ++      +++y+d  e+ +
  gi|70606795|ref|YP_255665.1|   5 LERVKEELRARNIDYLILAPGSNMLYLTGFDEEQMERPLFYIVTQNEEFFVVPKLYEEQLSNHN-----LIVYTD-GENPF 79 
                                   89***************************************************66666665555.....*****9.77777 PP

                                   HHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                  Creatinase_N  83 dllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                   + +  +  +++ v+++++ ++ +f+ ++ + ++  +lv++se+++e+R++
  gi|70606795|ref|YP_255665.1|  80 KKIPIQ--KGRVVAIDDT-MWSSFTIDILNYFSPSQLVKSSEVLKEIRMI 126
                                   766666..45777****9.9************99***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2390.07
//
Query:       gi|70606796|ref|YP_255666.1|  [L=326]
Description: hypothetical protein Saci_1016 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-58  197.6   0.0    4.8e-58  197.1   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   0.0   2.7e-62   4.8e-58       1     293 [.      19     276 ..      19     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 2.7e-62
                                   SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldddt 81 
                                   h+enp+Rl+ +l++l+           +i+p+++++e+++ +H+++Y++l++ +s+   +              + ld dt
  gi|70606796|ref|YP_255666.1|  19 HVENPERLKIVLKALEGR-T-------IIKPKPVDEEDVKLIHNEDYVKLVKVASQMG-E--------------P-LDADT 75 
                                   89*************996.3.......4789******************998654332.2..............2.4679* PP

                                   HCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-.BTTB-B.....TTBSS-HHHHHHHHHHHCC-SS-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl  82 pvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHa.kaseas.....GFClvNnvaiaikylqakhelkrvai 156
                                   + ++ t++ alla g++  a +       + af+lvrPpgHHa  +++a+     GFC++Nnva+ i +l+     k+v+i
  gi|70606796|ref|YP_255666.1|  76 YTNEFTWSSALLALGGSYVAFQ-------NDAFALVRPPGHHAgISGRAMgaptlGFCIFNNVAYPIVKLKL----KKVLI 145
                                   ****************998775.......578************9999999999**************9977....8**** PP

                                   EE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 157 lDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleef 237
                                   +D+DvH+GnGt+e+f+++pdv++++iH+ ++++yPgtg  + +g g+++g+++n+ +++  gd+ y +++  i+++v+ ++
  gi|70606796|ref|YP_255666.1| 146 IDFDVHYGNGTQEIFWENPDVVHIDIHQDPRTLYPGTGFPDMIGGGEARGTKINLIIPPLGGDDLYEELI-PIIQSVIDDY 225
                                   ***************************************************************9999988.7999****** PP

                                   --SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 238 kPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnl 293
                                   kP++i++saGfD+ ++d l++l+ ++  y++l    +       k  ++leGGY+ 
  gi|70606796|ref|YP_255666.1| 226 KPSYIVYSAGFDGFEDDGLANLRATEWTYYNLGLLSRGY-----KRFAVLEGGYTV 276
                                   ***********************9986666655444444.....5589******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2340.62
//
Query:       gi|70606797|ref|YP_255667.1|  [L=432]
Description: hypothetical protein Saci_1017 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-38  131.9   0.2    5.3e-38  131.4   0.2    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.2     3e-42   5.3e-38      26     277 ..      10     279 ..       2     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 3e-42
                                   EEEEEEEEEEEEETTEEEEEE...ESS........HHHHHHHHHHHHHHCCS---TT-............GGS-HHHHHHH CS
                     PmbA_TldD  26 ssedsglgvrvikggrlgfastldtsd........ealeeaveraveiaklapedpea............eevsaeekiel 86 
                                    s ++g++ rv++++ l f s+++++d        ++ e+ v +          ++ +             ++++++k + 
  gi|70606797|ref|YP_255667.1|  10 KSVNEGYSARVFDENYLYFLSSDKPEDltasklkvKGWEKGVSE----------EKREggryevtqkinlLDIPVQDKMKE 80 
                                   567889*******99**998877777665443333233333332..........222234445567788889999999999 PP

                                   HHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE..STCS...ET.EEEEEEE CS
                     PmbA_TldD  87 leelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsviad.dggs...gd.gmgggsg 162
                                   l+el+k ++s d       + +i++ ++ + +  e+k i+  +G+++ ++ +rv+l++s++   +++s    +   gg +g
  gi|70606797|ref|YP_255667.1|  81 LSELAKSIYSLDL------RSKIVSSTIYYMEGIEDKEIVFEDGTEINSKIPRVRLFYSITLTyENRSatvFSeAVGGSGG 155
                                   9999988888777......56999999***********************************5475556796667788888 PP

                                   ESSHHHS..SSHHHHHHHHHHCTTT.-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTS CS
                     PmbA_TldD 163 yedleeedleeiaeeaaekalasle.akplppgkypVvlspeavgsllheavghaleadavl......egrSflkd.klGe 235
                                   ye ++e+d++  +e   + +   l   k++ pg+ +Vv+s+e  g + he+vgh++ead++l      +g S l + k+Ge
  gi|70606797|ref|YP_255667.1| 156 YELIKEKDPYGHLENKLKSVDNVLVkGKSVTPGRKDVVFSNELSGIMAHESVGHPFEADRILgresaqAGLSYLVGrKIGE 236
                                   87777777777777777777666654689*********************************9999999*****8878*** PP

                                   B-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE- CS
                     PmbA_TldD 236 kvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLk 277
                                   +++se ++++d+p+  gglg+y +DdEGv+++++ lI+nG+ +
  gi|70606797|ref|YP_255667.1| 237 RIGSEAVNVMDNPLVdGGLGYYRIDDEGVKARPKHLIKNGIIN 279
                                   **************99*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3228.06
//
Query:       gi|70606798|ref|YP_255668.1|  [L=419]
Description: hypothetical protein Saci_1018 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-32  112.0   1.9    6.5e-32  111.5   1.9    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   1.9   3.6e-36   6.5e-32       1     278 [.      17     283 ..      17     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 3.6e-36
                                   EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...... CS
                     PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...... 75 
                                   e+ev  ++ +++ ++f n+ev t++  +d  +g+ v kg+r  + s ++++ e+ ++  e   + a+l             
  gi|70606798|ref|YP_255668.1|  17 EVEVGENKVTRLLIKFVNSEVATIQKLIDVNYGIMVRKGNRYFMYSGTNLDVEEAKNGFE-VSSGAQLY-----Pilsrnd 91 
                                   589999*****************************99*9988884433444335555555.44444333.....1334446 PP

                                   GGS-HHHHHHHHHHHHHH.CHCSTTEEEEE..EEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE...STC CS
                     PmbA_TldD  76 eevsaeekielleelekalrsadpkiensk..garisgvsaslsaskeeklianSeGldveqtrtrvslslsvia.d.dgg 152
                                   +e  +++ +e l+e+ ++ ++ d +i+     ++ isgv   +s  ++++ +++S G++++++r+ ++ ++ +   + +  
  gi|70606798|ref|YP_255668.1|  92 REFVIDQNNENLREIVEK-ERIDGIISEIGkaELPISGV---ISIYETTTNLVTSYGFNGSERRYKIDGYVRAFNkEyS-- 166
                                   444444444444444433.23333333333223455655...5555567******************999999993322.. PP

                                   SETEEEEEEEE..SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--TTTT CS
                     PmbA_TldD 153 sgdgmgggsgy..edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavlegrSflkd 231
                                         g +++  e++  +d+++ +++a+e a      ++l  gky+Vv+sp +v++l+++ ++  ++a +v  g+Sfl++
  gi|70606798|ref|YP_255668.1| 167 ------GQWAFfsESP--NDIKDTIKKAVEFASITN-RVKLDDGKYNVVMSPLVVANLMGF-FADFASAFSVITGSSFLAK 237
                                   ......2233333333..558889999999998888.788********************5.66799************99 PP

                                   .-TTSB-S-TT--EEEETT-.....-SB-TTSBB---EEEEETTEE-- CS
                     PmbA_TldD 232 .klGekvaselltivddptsgglgsypfDdEGvptqrtvlIenGvLkn 278
                                    k+G+++as+llti+d p   + g ++fDdE   t+++++I+ G++++
  gi|70606798|ref|YP_255668.1| 238 fKVGDRIASDLLTISDIPI--KAGIRSFDDEAEFTRDKKIIDSGIFQS 283
                                   99****************5..5899********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2729.46
//
Query:       gi|70606799|ref|YP_255669.1|  [L=142]
Description: hypothetical protein Saci_1019 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-17   64.9   6.0    1.2e-17   64.6   6.0    1.1  1  Sm_multidrug_ex  Putative small multi-drug export protein
  ------ inclusion threshold ------
       0.03   14.3   0.4      0.058   13.4   0.2    1.6  1  Herpes_UL73      UL73 viral envelope glycoprotein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   6.0   1.4e-21   1.2e-17       1     121 []      19     129 ..      19     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.4e-21
               Sm_multidrug_ex   1 ElrgaiplgillgldpllallvsvlgnllpvplillflrkllellkkkkllkklfekleekaekksekiekygflGLllFv 81 
                                   El +a p+g+++gldpl a++++ ++nllp+p++l f++++++       + k+f+++++k++++++ i   + +G+++F 
  gi|70606799|ref|YP_255669.1|  19 ELLVAYPIGLAIGLDPLIAIITCSAFNLLPIPILLSFAEYISN------RFPKFFNWIASKGKTYEKYI---KSFGITIFL 90 
                                   8899************************************999......489************98888...899****** PP

               Sm_multidrug_ex  82 aiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                    +  p+ G++ +s+  +l+g+kk+ a+l+ +l+++i ++I
  gi|70606799|ref|YP_255669.1|  91 LL-TPIIGVYATSIFMFLIGFKKRIAFLVQALSICIYSVI 129
                                   **.*********************************9998 PP

>> Herpes_UL73  UL73 viral envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   6.4e-06     0.058      19      71 ..      61     115 ..      54     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-06
                   Herpes_UL73  19 eatndFYsv.sCsadtyslslsSF.ssiwallnvlvvivalliylrylCfkkFva 71 
                                   + +++F++  + + +ty+  ++SF  +i++ll+ ++ + a+ i++  + fkk +a
  gi|70606799|ref|YP_255669.1|  61 NRFPKFFNWiASKGKTYEKYIKSFgITIFLLLTPIIGVYATSIFMFLIGFKKRIA 115
                                   566778875256789********9559*******************999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 952.76
//
Query:       gi|70606800|ref|YP_255670.1|  [L=681]
Description: aldehyde oxidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.4e-106  357.2   0.0   1.2e-104  350.7   0.0    2.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.7e-11   42.8   0.0    1.7e-10   41.3   0.0    1.9  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.7   0.0  1.4e-108  1.2e-104       2     548 ..     133     623 ..     132     625 .. 0.94

  Alignments for each domain:
  == domain 1  score: 350.7 bits;  conditional E-value: 1.4e-108
                                   TTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT CS
                 Ald_Xan_dh_C2   2 heeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlg 80 
                                   h+    n++   +i  Gdve+ + +ad+v+e+e+   r   +++E+++ +a++  ++ +l++  s q  + v++ + e++g
  gi|70606800|ref|YP_255670.1| 133 HP--DGNIALdtEIAGGDVEQKL-NADVVIERELNQDRLVANPMEPKGLIAYY--DGSTLNLIGSFQSSFRVKSDLQEAIG 208
                                   55..455555677888*****99.8999*************************..689*********************** PP

                                   --GGGEEEE-.SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEE CS
                 Ald_Xan_dh_C2  81 lpenkvrviv.prvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvd 160
                                   l++++++v++ p+vGGGFG+K+ +++++vla +a+  +++pVk++++R++++++ ++++ +k+k+++  ++dG+i++++ +
  gi|70606800|ref|YP_255670.1| 209 LQPENIVVRSaPNVGGGFGNKVPAHAEYVLASIASIILKKPVKWIETRRDHLTNPTQGRGVKSKVRLYGKRDGTILGFEGE 289
                                   ********998********************************************************************** PP

                                   EEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHH CS
                 Ald_Xan_dh_C2 161 lladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelR 240
                                   +  d Gay  + ++++++ +++ + ++Y+ +  ++++ +vytN+pp++++RG+G+p+a++++E+l++e Ae++g d +e+R
  gi|70606800|ref|YP_255670.1| 290 IAVDLGAYaYSINTTTPSFIAGLIGNVYRTRFSKFRALAVYTNKPPTGPYRGAGRPEAVLITETLIEEFAEKIGKDSIEIR 370
                                   ********5599********************************************************************* PP

                                   HHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEEEEE CS
                 Ald_Xan_dh_C2 241 rrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqegalvr 321
                                   ++Nli+ + +tp g +  d+ +++el+ k+ke++++ +      ++    k +G++l+++   +      + +  ega+vr
  gi|70606800|ref|YP_255670.1| 371 EMNLIEGNYTTPLGYK-IDKAGYKELFLKGKETYNMVKN-----KY----KDKGVALVFFSTVV------RDSPGEGAKVR 435
                                   ******9999*****9.7**************9987322.....22....24789999888888......335568***** PP

                                   E-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 322 vntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrerllk 402
                                   v  +G+v++++g+ ++Gq ++t++  +a+e+Lg++++ ++v+ +dt + ++g+g+++Srs+  +g Av +A+++l   l+k
  gi|70606800|ref|YP_255670.1| 436 VG-KGKVEIFVGTGPHGQAHKTTFSILASETLGISPDVIEVKVNDTLSLKEGVGSFGSRSASAGGLAVIRACKELLSDLKK 515
                                   *8.8****************************************************************************9 PP

                                   HHHHHCTS-CCCEEEETTEEEETEEEECHHHHHHHHHHTTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT- CS
                 Ald_Xan_dh_C2 403 iaaellevspedleledgkvvvkeksvslaelaaaaylervslsatgfyktldeetgkgppfayfaygaavaeVevDtetg 483
                                                              sl++++++     ++ ++ + +          ++   ++ g+++a+V+ D+e +
  gi|70606800|ref|YP_255670.1| 516 RNM------------------------SLNDAINS-----EGYTEYEVF---------AKAEDIYSPGVHIAVVDFDREIC 558
                                   999........................89999994.....467777777.........566678999************** PP

                                   -EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGG CS
                 Ald_Xan_dh_C2 484 evkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaad 548
                                   + kvl++++++DvG++i p  vegQi GG+ qG+ +  +E   +de+G+++ +s a+  +Pt+ d
  gi|70606800|ref|YP_255670.1| 559 KPKVLEYYAIDDVGRAIIPSEVEGQIVGGILQGLSQIYLEGAPFDENGNPVYSSIAEAGVPTSLD 623
                                   **************************************************************987 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.8e-14   1.7e-10       1     109 [.      11     116 ..      11     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.8e-14
                                   TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCC....GTECCTTSSS-EEEESS-SSEE CS
                  Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpk....enkaigsiledeedallaedkv 77 
                                   +G+ +Y+dD+ + +++yl +vrSt+a++ i+ i      +  GV  ++t + +++    + +  ++++ +    +la+  v
  gi|70606800|ref|YP_255670.1|  11 SGNSRYIDDLVFNNMVYLGVVRSTYARGIIKGIT-----EPSGVELFLTQDRVKSfipaRPDRRAKNIVK--MPVLANGVV 84 
                                   5899*****************************6.....6889999999988765211133333344444..45******* PP

                                   SSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  78 rsvgqavaavvAedeetArkAaklvkveYeel 109
                                   ++vgq++ a v +d+++ ++ ++ v+++Y++l
  gi|70606800|ref|YP_255670.1|  85 NFVGQPIIAFVVKDRYEIEDKIEEVSIDYDPL 116
                                   *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 4137.29
//
Query:       gi|70606801|ref|YP_255671.1|  [L=269]
Description: hypothetical protein Saci_1021 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-23   82.7   0.1    4.1e-23   82.2   0.1    1.2  1  XdhC_C        XdhC Rossmann domain
     0.0025   18.3   0.3        1.9    9.1   0.1    2.4  2  Pyr_redox     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.17   11.2   0.0       0.26   10.6   0.0    1.2  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.1   6.8e-27   4.1e-23       1     125 []      84     224 ..      84     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 6.8e-27
                                   EEEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG-GGG-TT-SE................-EEEE--S-H.HHHHHHHHH CS
                        XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpre.efatkerfpeade................tavvvlthdh.klDaealea 63 
                                   ++i+G g +a++la+l++a+g+ v vv + +     +++f++ ++                ++v+v+ ++   +Da a   
  gi|70606801|ref|YP_255671.1|  84 VIIVGSGMIAKSLAKLGSAMGYYVAVVGNGDlP---EKEFESFTSfisnqietleqivdsnSMVIVANEGGkPYDAYATYI 161
                                   69*************************998843...33444333345566777777888976666666554379******* PP

                                   HSSS--SEEEESS-HHHHHHHCTTS.--.......T.TEESS-S--S---SHHHHHHHHHHHH CS
                        XdhC_C  64 alrkkaayigllGSrkkaarrlerlraaglseeela.rlhaPiGldigaktpeeIAvsilAei 125
                                   al+k a+y+g+l S+k+ a + +++ ++gl+ e+++ rl+aP+G+dig+kt eeIA+silAei
  gi|70606801|ref|YP_255671.1| 162 ALKKGAKYVGVLSSAKRGALIIAEIIKRGLKVEDFKdRLYAPVGIDIGSKTAEEIALSILAEI 224
                                   **999*************************9777644*************************8 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0014       8.3      18      61 ..      26      70 ..      21      78 .. 0.84
   2 !    9.1   0.1   0.00032       1.9       2      35 ..      84     117 ..      83     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                                  HHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSE CS
                     Pyr_redox 18 laelgkkVtvversdkllrllDeeaskilqeklekn.gievllnt 61
                                  +++ + + t+++ ++ ll +l+ e+s++  e+lek  +++v +n 
  gi|70606801|ref|YP_255671.1| 26 FKQDKVERTIFVDGKPLLGNLPTEISELANESLEKYvKVDVNTNY 70
                                  566667889999999999*****************9888888775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00032
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                   v++vG+G i+  lA+  +++g  V vv ++d + 
  gi|70606801|ref|YP_255671.1|  84 VIIVGSGMIAKSLAKLGSAMGYYVAVVGNGDLPE 117
                                   79*************************9999776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.3e-05      0.26      39      78 ..      84     123 ..      74     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.3e-05
                                   EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                  2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                   v i+G G I++++ak+ +a+g  v ++     +e+e+e+ 
  gi|70606801|ref|YP_255671.1|  84 VIIVGSGMIAKSLAKLGSAMGYYVAVVGNGDLPEKEFESF 123
                                   679*******************999998888877744433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1737.77
//
Query:       gi|70606802|ref|YP_255672.1|  [L=113]
Description: hypothetical protein Saci_1022 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.2   1.4      0.016   15.2   1.4    2.0  2  SapB_1    Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.11   1.9e+03       9      17 ..       5      13 ..       2      20 .. 0.53
   2 ?   15.2   1.4   9.2e-07     0.016      12      35 ..      83     104 ..      82     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
                                  HHHHHHHHH CS
                        SapB_1  9 vVkeveklL 17
                                  + +e+++ +
  gi|70606802|ref|YP_255672.1|  5 ILNEIKEKV 13
                                  334444444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.2e-07
                                   HHHHHH-SS--HHHHHHHHHHHHH CS
                        SapB_1  12 eveklLkdNkTeeeIieaLekvCs 35 
                                   e+ +++k+N  e+eIi+++ k+C+
  gi|70606802|ref|YP_255672.1|  83 EILDYVKNN--ETEIISYVQKLCK 104
                                   899******..************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 811.42
//
Query:       gi|70606803|ref|YP_255673.1|  [L=345]
Description: threonine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-57  194.5   0.0      3e-57  194.3   0.0    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
     0.0016   18.4   1.5      0.084   12.9   0.5    2.4  2  HypA           Hydrogenase/urease nickel incorporation, metal
  ------ inclusion threshold ------
      0.022   14.7   2.5        2.8    7.9   0.1    2.8  2  zinc_ribbon_4  zinc-ribbon domain
       0.09   12.6   0.2       0.18   11.6   0.2    1.4  1  DFP            DNA / pantothenate metabolism flavoprotein
       0.27   11.4   5.0       0.97    9.6   4.6    2.0  2  Zn-ribbon_8    Zinc ribbon domain
        0.8    9.2   4.2        2.5    7.6   4.2    1.8  1  zf-ribbon_3    zinc-ribbon domain
        3.3    7.2   5.1        8.5    5.9   0.4    2.5  2  Mu-like_Com    Mu-like prophage protein Com
        4.2    7.2   6.3         12    5.7   6.3    1.8  1  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   0.0   1.4e-60     3e-57       1     281 [.      60     329 ..      60     339 .. 0.89

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 1.4e-60
                                   GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                   +tlg+g+TPl+r  +        +++Kl++lnptgS+KdRg + l+++l+ + g k ++e ssGN+g+++Aa+++++G+ v
  gi|70606803|ref|YP_255673.1|  60 VTLGEGNTPLIRRGK--------VWFKLDFLNPTGSYKDRGSVTLISYLASN-GIKDIAEDSSGNAGASIAAYGKAAGMNV 131
                                   5899******88877........*****************************.**************************** PP

                                   EEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEE CS
                          PALP  82 tivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdav 161
                                   ti+vp++a   kv++++++Ga++++v g+ d+  +a    a++  g+y++s+ + p+  +g  ++++Ei+++l+ + p+ v
  gi|70606803|ref|YP_255673.1| 132 TIFVPETARGNKVKQIEAYGAKLMKVSGTRDDVTKA----AEK-SGYYYASHVFQPHFRDGIRSLAYEIVRDLNwKIPEKV 207
                                   **************************8887777777....777.9************************************ PP

                                   EEE-SSSHHHHHHHHHHHHHSTT......-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..CGTTCCHHHHS CS
                          PALP 162 vvpvGgGgliaGiaaglkerrpd......vrvigvepegsdalarslragrrvtvpvsdtiadglavg..spselafelld 234
                                   + pv+ G l++G++ g+k+   +      +++++v++++++++ + l + ++ +  + ++iad+l     +   +  ++l+
  gi|70606803|ref|YP_255673.1| 208 FIPVSAGTLLMGVYSGFKHLMESgviekiPTIVAVQTKQVMPVCAKLNNLSYAPPAKVTSIADALVSTnpALLQEMTDVLQ 288
                                   *******************4444556678******************99999999999*******9997544444455554 PP

                                   EEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHC CS
                          PALP 235 rlvdeivtvsdeealeamrllarregivvepssaaalaalklreage 281
                                   +  +e+  v+d+++ ea ++l  + g++ve ssa+++a l    +++
  gi|70606803|ref|YP_255673.1| 289 N-YGECRVVDDNQITEAWKELT-KIGLLVEYSSATVYASL----RKD 329
                                   4.455999**************.*****************....222 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   3.7e-05     0.084      68      95 ..       9      35 ..       4      45 .. 0.79
   2 ?    3.9   0.0     0.024        54      21      53 ..     278     310 ..     263     328 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                  --EEEETTTS-EEECHHHHHS-TTTSSS CS
                          HypA 68 pvkvrCreCgkefeleekalrCpkCgsa 95
                                   v+++C++Cgke e+  ++++C+kCg+ 
  gi|70606803|ref|YP_255673.1|  9 MVNIKCSRCGKERESL-HEIKCKKCGGV 35
                                  5789*******99955.3589****985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                   TT..EEEEEEEEEETTCT--HHHHHHHHHHHHC CS
                          HypA  21 aaarkvtkvkvevGelsgvepeaLefafellae 53 
                                   a  ++ t v  + Ge++ v+ ++++ a++ l++
  gi|70606803|ref|YP_255673.1| 278 ALLQEMTDVLQNYGECRVVDDNQITEAWKELTK 310
                                   33568999999*****************99986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2    0.0062        14      24      33 ..      10      19 ..       7      20 .. 0.83
   2 ?    7.9   0.1    0.0013       2.8      25      35 ..      26      36 ..      21      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0062
                 zinc_ribbon_4 24 vkvrCskCgh 33
                                  v+++Cs+Cg+
  gi|70606803|ref|YP_255673.1| 10 VNIKCSRCGK 19
                                  7899****85 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                 zinc_ribbon_4 25 kvrCskCghvF 35
                                  +++C+kCg vF
  gi|70606803|ref|YP_255673.1| 26 EIKCKKCGGVF 36
                                  68999999998 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     8e-05      0.18      20      66 ..     105     149 ..     102     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8e-05
                                   TEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE- CS
                           DFP  20 VRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkv 66 
                                   ++ i+  SSG  G+++A+   a+G++Vt+   +++    ++v+ ++ 
  gi|70606803|ref|YP_255673.1| 105 IKDIAEDSSGNAGASIAAYGKAAGMNVTIFVPETAR--GNKVKQIEA 149
                                   566999**********************97766432..222333333 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.6   0.00043      0.97       7      34 ..      13      34 ..      11      40 .. 0.85
   2 ?    9.2   0.3   0.00059       1.3       5      18 ..      26      39 ..      24      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00043
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                  +C +Cg+e e l+      +++C++Cg+
  gi|70606803|ref|YP_255673.1| 13 KCSRCGKERESLH------EIKCKKCGG 34
                                  7*********999......667****98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00059
                   Zn-ribbon_8  5 eYrCeeCghefevl 18
                                  e +C++Cg +fev 
  gi|70606803|ref|YP_255673.1| 26 EIKCKKCGGVFEVE 39
                                  779*********75 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.2    0.0011       2.5       3      25 ..      12      35 ..      10      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
                   zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtk 25
                                  ++C++CG+   s   ++C++CG++
  gi|70606803|ref|YP_255673.1| 12 IKCSRCGKeRESLHEIKCKKCGGV 35
                                  89******7756679*******97 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0038       8.5      23      31 ..      10      18 ..       6      20 .. 0.86
   2 ?    2.7   0.5     0.039        87      24      32 ..      26      34 ..      20      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0038
                   Mu-like_Com 23 ltiKCPRCG 31
                                  ++iKC RCG
  gi|70606803|ref|YP_255673.1| 10 VNIKCSRCG 18
                                  78******9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.039
                   Mu-like_Com 24 tiKCPRCGt 32
                                  +iKC +CG 
  gi|70606803|ref|YP_255673.1| 26 EIKCKKCGG 34
                                  69*****96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   6.3    0.0054        12       1      20 [.      13      33 ..      13      34 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0054
                 zinc_ribbon_2  1 fCpnCGaelqd.nakFCpyCG 20
                                  +C++CG+e +   +  C +CG
  gi|70606803|ref|YP_255673.1| 13 KCSRCGKERESlHEIKCKKCG 33
                                  8********977********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2159.91
//
Query:       gi|70606804|ref|YP_255674.1|  [L=297]
Description: protease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-25   88.4   1.7    1.2e-24   87.9   1.7    1.2  1  Trypsin_2      Trypsin-like peptidase domain
    4.8e-14   52.4   0.1    1.1e-13   51.3   0.1    1.6  1  PDZ_2          PDZ domain
    6.5e-11   41.9   0.2    1.2e-10   41.0   0.2    1.5  1  PDZ_6          PDZ domain
    2.1e-10   40.8   0.0    3.7e-10   40.0   0.0    1.4  1  Trypsin        Trypsin
    1.2e-06   28.8   0.1      3e-06   27.5   0.1    1.7  1  PDZ            PDZ domain
    0.00026   20.9   0.0    0.00059   19.8   0.0    1.6  1  Tricorn_PDZ    Tricorn protease PDZ domain
     0.0026   18.1   0.0     0.0053   17.1   0.0    1.5  1  GRASP55_65     GRASP55/65 PDZ-like domain
  ------ inclusion threshold ------
      0.036   12.7   0.5      0.058   12.0   0.5    1.2  1  Peptidase_S46  Peptidase S46
      0.036   13.9   2.8       0.19   11.5   0.4    2.3  2  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease
      0.054   12.7   0.1        0.7    9.0   0.0    2.2  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
        0.1   12.3   0.2       0.29   10.9   0.1    1.8  2  Peptidase_S29  Hepatitis C virus NS3 protease


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   1.7   7.4e-28   1.2e-24       1     150 []      37     167 ..      37     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 7.4e-28
                     Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpseal 81 
                                   GsGf +g+++ i+T +Hv+++a+++ +         +++dg + +a+++a++p  DlAl+k     + +l pl+l +  ++
  gi|70606804|ref|YP_255674.1|  37 GSGFSIGKGL-IVTSYHVIGQASSSMI---------VTRDGFRGEAEIIAVNPFNDLALIKT----DLDLKPLKLTD--DV 101
                                   9********9.****************.........****************777*******....99999999999..88 PP

                     Trypsin_2  82 kggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                   k+g+ v +vG plg +   s+++Givs+v+++ ++  g++ +++qtdaa++pG+SGGpl++++G+vvG+
  gi|70606804|ref|YP_255674.1| 102 KVGQGVLAVGSPLGLD---STTFGIVSSVDRTIQSPIGSSLYVIQTDAAVNPGNSGGPLVNTKGEVVGV 167
                                   99999*********99...69**********7777777777777************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   6.6e-17   1.1e-13       1      80 [.     203     291 ..     203     292 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 6.6e-17
                                   ....XX------............-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEE CS
                         PDZ_2   1 pylGvsvsdeed..........tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlR 71 
                                   py+Gv++ ++++          ++gv+v++V++ +Pa +ag++ gDvi+++++kkvks+ d+i  + +k   d+V+l v+R
  gi|70606804|ref|YP_255674.1| 203 PYIGVRIIKLNRamavyfnlpvDEGVIVIDVDPRSPAYQAGIRRGDVIYEINSKKVKSQLDIIAGIEEK-GLDQVELGVYR 282
                                   89*************************************************************999865.4589******* PP

                                   TTEEEEEEE CS
                         PDZ_2  72 dgkkktvev 80 
                                   +++k+++++
  gi|70606804|ref|YP_255674.1| 283 GKNKLKMSI 291
                                   ****99887 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.2   7.6e-14   1.2e-10       2      56 .]     230     282 ..     229     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.6e-14
                         PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvvrr 56 
                                   V  Vdp sPA++AG+r GD+i ++N + v  +s  d++a +++++  +v+l v r
  gi|70606804|ref|YP_255674.1| 230 VIDVDPRSPAYQAGIRRGDVIYEINSKKV--KSQLDIIAGIEEKGLDQVELGVYR 282
                                   889**************************..******999999998888888766 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.3e-13   3.7e-10      28     217 ..      38     187 ..      27     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.3e-13
                                   EEEEEETTEEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCB CS
                       Trypsin  28 gGslisenwvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpic 108
                                   +G+ i++  ++T  H++ +  + +       ++ ++g   +++ e +     +np +   D+al+k + +       +p++
  gi|70606804|ref|YP_255674.1|  38 SGFSIGKGLIVTSYHVIGQ-ASSS------MIVTRDG--FRGEAEIIA----VNPFN---DLALIKTDLD------LKPLK 96 
                                   799***************8.3333......3667788..455566643....69986...*******999......9**** PP

                                   BCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETT CS
                       Trypsin 109 lpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPlvcsd 189
                                   l +   +++vg+++l++G +   ++      + + v+ v+r t++s ++   +   ++++a     + ++G+SGGPlv+ +
  gi|70606804|ref|YP_255674.1|  97 LTD---DVKVGQGVLAVGSPLGLDST-----TFGIVSSVDR-TIQSPIGS--SLYVIQTDA-----AVNPGNSGGPLVNTK 161
                                   ***...789**********9942222.....3334444444.45554333..446788888.....9************** PP

                                   TEEEEEEEEESSSSCTTSEEEEEEGGGG CS
                       Trypsin 190 gelvGivswgkgcakgnrpgvytkvssy 217
                                   ge+vG++++    a+g  +g++++   +
  gi|70606804|ref|YP_255674.1| 162 GEVVGVITAMIPYAQG--IGFAIPSRLV 187
                                   *********9999999..8999887655 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   1.9e-09     3e-06      24      72 ..     224     270 ..     197     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.9e-09
                                   SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHT CS
                           PDZ  24 gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikg 72 
                                    d+g++v +v p ++a ++g++ GD+I ++N ++v++   +++++ i++
  gi|70606804|ref|YP_255674.1| 224 VDEGVIVIDVDPRSPAYQAGIRRGDVIYEINSKKVKSQ--LDIIAGIEE 270
                                   578*******************************9875..555555555 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.6e-07   0.00059      28      82 ..     234     286 ..     229     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.6e-07
                                   S-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT- CS
                   Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvkrkdgk 82 
                                   + rSP  + G++   Gd+i++++ ++v+++ +i   +++k+ ++veL v r+++k
  gi|70606804|ref|YP_255674.1| 234 DPRSPAYQAGIR--RGDVIYEINSKKVKSQLDIIAGIEEKGLDQVELGVYRGKNK 286
                                   679********9..9**********************************998765 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0053      41     103 ..     224     285 ..     210     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                                   TTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEETTT CS
                    GRASP55_65  41 aeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLlvYnses 103
                                   ++e + v+dv++ sPa +ag+    D i  ++++ +k++ d++  +e++   +++L vY  ++
  gi|70606804|ref|YP_255674.1| 224 VDEGVIVIDVDPRSPAYQAGIR-RGDVIYEINSKKVKSQLDIIAGIEEKGLDQVELGVYRGKN 285
                                   567788**************86.68**********************************7665 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   3.6e-05     0.058     631     651 ..     148     168 ..     136     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                   --TT-TT-EEE-TTS-EEEEE CS
                 Peptidase_S46 631 itGGNSGSPvlngkgelvGla 651
                                      GNSG P++n+kge+vG++
  gi|70606804|ref|YP_255674.1| 148 VNPGNSGGPLVNTKGEVVGVI 168
                                   456****************96 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.09   1.5e+02      82     107 ..      42      67 ..      20      68 .. 0.91
   2 ?   11.5   0.4   0.00012      0.19      82     115 ..     135     170 ..     118     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.09
                                   EE.EEEEEXXXXXTT-TTSEEE-TTS CS
                  Peptidase_S7  82 yGyglgitdlnlssGsSGSlvlnqnk 107
                                   +G+gl++t     +  S+S+++++++
  gi|70606804|ref|YP_255674.1|  42 IGKGLIVTSYHVIGQASSSMIVTRDG 67 
                                   69*********************985 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                                   EE.EEEEEXXX..XXTT-TTSEEE-TTSXEEEECEE CS
                  Peptidase_S7  82 yGyglgitdln..lssGsSGSlvlnqnkqivgiYfa 115
                                   +G +l +++++   ++G SG +++n ++++vg+  a
  gi|70606804|ref|YP_255674.1| 135 IGSSLYVIQTDaaVNPGNSGGPLVNTKGEVVGVITA 170
                                   5777777777633689****************8666 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.083   1.4e+02     111     140 ..      32      60 ..      27      85 .. 0.75
   2 ?    9.0   0.0   0.00043       0.7     205     227 ..     148     170 ..     131     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.083
                                   SSEEEEEEEECTTEEEEEEEHHHH-TSEEE CS
                 Peptidase_S32 111 sslGsGgvftidgevvvvtashvlgdnkar 140
                                   ++ G G+ f+i g+  +vt+ hv+g+ ++ 
  gi|70606804|ref|YP_255674.1|  32 VAQGLGSGFSI-GKGLIVTSYHVIGQASSS 60 
                                   57788999998.578899******965443 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00043
                                   --GGGTT-EEEETTE.EEEEEEE CS
                 Peptidase_S32 205 tkcGDsGspvvdedgelvGvhtG 227
                                    ++G+sG p+v+ +ge+vGv t 
  gi|70606804|ref|YP_255674.1| 148 VNPGNSGGPLVNTKGEVVGVITA 170
                                   479*****************985 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.2   3.6e+03     111     127 ..      43      59 ..      34      83 .. 0.61
   2 ?   10.9   0.1   0.00018      0.29     104     129 ..     147     172 ..     132     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                 Peptidase_S29 111 GsPilCdsGhvvGllva 127
                                   G  ++  s hv+G   +
  gi|70606804|ref|YP_255674.1|  43 GKGLIVTSYHVIGQASS 59 
                                   44555556666664433 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                 Peptidase_S29 104 selkGssGsPilCdsGhvvGllvaav 129
                                   ++  G sG+P++  +G vvG+++a +
  gi|70606804|ref|YP_255674.1| 147 AVNPGNSGGPLVNTKGEVVGVITAMI 172
                                   56679*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1943.51
//
Query:       gi|70606805|ref|YP_255675.1|  [L=206]
Description: hypothetical protein Saci_1025 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   76.9   3.5    1.2e-21   76.9   3.5    1.7  2  PAP2      PAP2 superfamily
    1.4e-09   37.9  13.6    1.6e-09   37.7   9.8    2.3  1  PAP2_3    PAP2 superfamily
  ------ inclusion threshold ------
      0.016   15.8   2.5      0.016   15.8   2.5    2.8  3  PAP2_C    PAP2 superfamily C-terminal


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.4       1.1   6.6e+03      86      91 ..      11      16 ..       4      25 .. 0.42
   2 !   76.9   3.5   2.1e-25   1.2e-21       4     130 ..      82     191 ..      79     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                          PAP2 86 llalil 91
                                  ll+lil
  gi|70606805|ref|YP_255675.1| 11 LLFLIL 16
                                  122222 PP

  == domain 2  score: 76.9 bits;  conditional E-value: 2.1e-25
                          PAP2   4 alllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkkigl 84 
                                    l+++ ++a++l +v+K+++ ++RPf   + t l + ++t          +s+PSgH++++ ++a++l l+ +++ +    
  gi|70606805|ref|YP_255675.1|  82 TLVISFVIAIVLGEVSKYVMAQLRPFNFVNPTYLLEPKPTD---------YSYPSGHALIVSTGAVTLLLTSPKWMWI--- 150
                                   68899999*****************************8886.........5***************************... PP

                          PAP2  85 vllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrl 130
                                        + ++ avlv++sR+y+gvH++ Dv+aG+l+G  + +l++++
  gi|70606805|ref|YP_255675.1| 151 -----LGIIEAVLVSYSRVYVGVHWPLDVIAGWLLGSWISFLSVQI 191
                                   .....78888**************************9999888765 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   9.8   2.7e-13   1.6e-09       3     184 ..      22     181 ..      20     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.7e-13
                        PAP2_3   3 lialdralgldweaalnklllahpalavilala..YaslhfqvtllvlvllflrrrerlreflttlllatllgllvyalfP 81 
                                   li  ++ +g+++e +     ++ + l+ ++ +   Y   +++++++ l+l+f r+r+ +  +++++++a +lg ++ +++ 
  gi|70606805|ref|YP_255675.1|  22 LIGGEQNIGFNVELFKLINYNQIATLNGLMVFLskYGREYVWIPVTALLLIFKRTRKIGITLVISFVIAIVLGEVSKYVMA 102
                                   6777888888888775534555555666666668899888889999999999***************************** PP

                        PAP2_3  82 aagPrlleeagfvdtvaaaslagalrdgasravllrgtienglaafPSlHvawallvalalwrlrrkrllrvlalllnvlm 162
                                    ++P+ +              ++        ++ll+ +     ++ PS H+ +    a++l  +++k+ +++l+++ +vl+
  gi|70606805|ref|YP_255675.1| 103 QLRPFNF--------------VN-------PTYLLEPK--PTDYSYPSGHALIVSTGAVTLLLTSPKW-MWILGIIEAVLV 159
                                   ****444..............22.......34445555..66789********999999999999888.9*********** PP

                        PAP2_3 163 ivatvatgnHYlvDviaGvala 184
                                    ++ v+ g H  +DviaG++l+
  gi|70606805|ref|YP_255675.1| 160 SYSRVYVGVHWPLDVIAGWLLG 181
                                   *******************997 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4      0.72   4.3e+03      35      48 ..       5      18 ..       1      22 [. 0.49
   2 ?    0.0   0.6      0.21   1.3e+03      22      22 ..      73      73 ..      44     100 .. 0.48
   3 ?   15.8   2.5   2.6e-06     0.016       8      68 ..     127     184 ..     121     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                        PAP2_C 35 illllallglflii 48
                                   +++l+ll+l+l i
  gi|70606805|ref|YP_255675.1|  5 YYWILLLLFLILSI 18
                                  44555444444433 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.21
                        PAP2_C 22 l 22
                                  +
  gi|70606805|ref|YP_255675.1| 73 F 73
                                  1 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.6e-06
                        PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlv 68 
                                   SGH++++++ ++++l +spk+++il +i ++l    +++ ++   H+ +DV+ g+++ + +
  gi|70606805|ref|YP_255675.1| 127 SGHALIVSTGAVTLLLTSPKWMWILGIIEAVL---VSYSRVYVGVHWPLDVIAGWLLGSWI 184
                                   9********************98888887665...5667788899**********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1327.33
//
Query:       gi|70606806|ref|YP_255676.1|  [L=149]
Description: hypothetical protein Saci_1026 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.51   10.9   3.4        1.5    9.3   0.1    2.4  2  DUF2542   Protein of unknown function (DUF2542)
        1.4    9.3  11.7         23    5.3  11.7    2.1  1  DUF4064   Protein of unknown function (DUF4064)
        3.4    6.3   5.2        6.3    5.4   5.2    1.5  1  DUF2207   Predicted membrane protein (DUF2207)
        5.8    7.1  15.0       0.21   11.7   6.0    2.1  2  DUF4870   Domain of unknown function (DUF4870)


Domain annotation for each model (and alignments):
>> DUF2542  Protein of unknown function (DUF2542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6     0.089     4e+02      61      76 ..       6      21 ..       1      23 [. 0.82
   2 ?    9.3   0.1   0.00034       1.5      33      73 ..      81     121 ..      75     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.089
                       DUF2542 61 ylglgvlslgmiiyll 76
                                   +g+g++ l+++ yll
  gi|70606806|ref|YP_255676.1|  6 VIGIGIIILAIVTYLL 21
                                  4799999999999998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00034
                       DUF2542  33 dkvvknarepvyvyraedpllyfsylvlylglgvlslgmii 73 
                                     +vk  +ep+  y +++      y  +y +++v++  +ii
  gi|70606806|ref|YP_255676.1|  81 IAIVKSGPEPIMFYNNNSVNATINYTLVYGSFTVVFAVAII 121
                                   569*******************************9988887 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  11.7    0.0052        23      10      82 ..       6     137 ..       2     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0052
                       DUF4064  10 lIGgilgillglllllflfllssgefsqeltee................................................ 42 
                                   +IG+ + il+++++ll+  ll s+ +++++++                                                 
  gi|70606806|ref|YP_255676.1|   6 VIGIGIIILAIVTYLLVPGLLFSSLTTTQQGKVvvlpgnefnltypqnlfvsvyysatppvkvtipsnateqsnviaivks 86 
                                   566666666666666666666666655555555666777777777777777777777777777777777777777777777 PP

                       DUF4064  43 ...........qalsgedasavleflstllivlgvialiaivlgivgalll 82 
                                              + +++ + + v++++++++ v+++++l+ i+lg++g++l+
  gi|70606806|ref|YP_255676.1|  87 gpepimfynnnSVNATINYTLVYGSFTVVFAVAIIGGLLPIALGVIGIVLI 137
                                   777777665556666666677789************************987 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.2    0.0014       6.3     383     431 ..       4     141 ..       1     149 [] 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0014
                       DUF2207 383 lsalglgliilglilillallllvll....................................................... 408
                                   + ++g+g+iil+++  ll+ +ll++                                                        
  gi|70606806|ref|YP_255676.1|   4 YTVIGIGIIILAIVTYLLVPGLLFSSltttqqgkvvvlpgnefnltypqnlfvsvyysatppvkvtipsnateqsnviaiv 84 
                                   455666666666666655555555447889999999999999999999999999999999999999999999999999999 PP

                       DUF2207 409 ..................................lvfllilllillliaiivlllfs 431
                                                                      ++ ++l ++l++i+i++++l  
  gi|70606806|ref|YP_255676.1|  85 ksgpepimfynnnsvnatinytlvygsftvvfavAIIGGLLPIALGVIGIVLIVLGV 141
                                   999999999999999999999999999888888866666666666666666655543 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.8       0.1   4.6e+02      68      85 ..       7      23 ..       2      56 .. 0.47
   2 ?   11.7   6.0   4.7e-05      0.21      45      94 ..      96     143 ..      52     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
                       DUF4870 68 vligflllllllllllnl 85
                                  ++ig+ ++l+++ +ll  
  gi|70606806|ref|YP_255676.1|  7 IGIGI-IILAIVTYLLVP 23
                                  22222.222222222222 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.7e-05
                       DUF4870  45 kealNFqislliysiilivlsllvligflllllllllllnlvlviiaaik 94 
                                    +++N +i++++++  ++v++ + +ig   ll ++l+++ +vl+++++i+
  gi|70606806|ref|YP_255676.1|  96 NNSVNATINYTLVYGSFTVVFAVAIIGG--LLPIALGVIGIVLIVLGVIR 143
                                   689********99888888888999998..99999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1034.73
//
Query:       gi|70606807|ref|YP_255677.1|  [L=303]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-25   89.4   0.0    5.9e-25   88.4   0.0    1.5  2  ABC_tran         ABC transporter
    3.9e-10   40.0   0.0    1.4e-05   25.1   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
  ------ inclusion threshold ------
      0.065   12.6   0.0       0.16   11.3   0.0    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
        0.1   12.8   0.0        0.2   11.9   0.0    1.5  1  Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich d


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   1.3e-28   5.9e-25       1     136 [.      18     161 ..      18     162 .. 0.95
   2 ?   -2.6   0.0       1.6   7.2e+03      79      87 ..     227     242 ..     187     261 .. 0.54

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1.3e-28
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l++vs++++ ge+v+ vG nGaGK+t +++++g  +p++G++++dg+++ + e+++++k++g++p+ p + ++ ++ +   
  gi|70606807|ref|YP_255677.1|  18 LQDVSFEVRDGEIVGYVGLNGAGKTTTIEIISGVRSPDQGDVEIDGHSIVK-EKRVASKNLGWVPELPIFEQDAKALDYfi 97 
                                   789***********************************************9.9999***********9999999988889* PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              +++++++++ s +gl++ +++++    +++S+G+k+r ala ++l++pk +l+DE  
  gi|70606807|ref|YP_255677.1|  98 ylagfygisteDARKKAQELFSMVGLEGREKDKL----KNYSQGMKKRFALAVSMLSDPKNFLFDEVL 161
                                   ********98767777************999999....****************************75 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
                                   H.......HHHTCHHH CS
                                   x.......xxxxxxxx RF
                      ABC_tran  79 n.......esdeeiek 87 
                                   +       + +e + k
  gi|70606807|ref|YP_255677.1| 227 StvrvvlqKPNETVIK 242
                                   0233333333344444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.5e-05     0.066       5      26 ..      34      56 ..      34      99 .. 0.75
   2 !   25.1   0.0     3e-09   1.4e-05     236     298 ..     133     192 ..      94     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                        AAA_21  5 iGpNgsGKSnLLdaldllarl.d 26
                                  +G Ng+GK++ +++++++++  +
  gi|70606807|ref|YP_255677.1| 34 VGLNGAGKTTTIEIISGVRSPdQ 56
                                  799**************986441 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3e-09
                        AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   + S+G+k+ +al++++l+++k    +l+DE+ ngL+P+ ++ + +l  + +++g  v++++H 
  gi|70606807|ref|YP_255677.1| 133 NYSQGMKKRFALAVSMLSDPKN---FLFDEVLNGLDPQGIAFFRDLAIRFKKEGKGVLFSSHI 192
                                   46******************88...************8888888777666666889******6 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.66     3e+03     309     323 ..      69      83 ..      59      87 .. 0.76
   2 ?   11.3   0.0   3.6e-05      0.16      69      99 ..     210     240 ..     206     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.66
                                   -THHHHHHH----SS CS
                 GDP_Man_Dehyd 309 daskakeeLgWkpkv 323
                                   + + a ++LgW p+ 
  gi|70606807|ref|YP_255677.1|  69 EKRVASKNLGWVPEL 83 
                                   5667899****9986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.6e-05
                                   HHHHHHT-SEEEE--S---HHHHTTSHHHHH CS
                 GDP_Man_Dehyd  69 rllaevqpdevynLAAqshVdvsfekPeyta 99 
                                   r+++e+++de+ n A+ s V+v ++kP +t+
  gi|70606807|ref|YP_255677.1| 210 RIMKEMRIDEIRNYAGSSTVRVVLQKPNETV 240
                                   89*************************9986 PP

>> Glyco_hydro_30C  Glycosyl hydrolase family 30 beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.5e-05       0.2      15      63 ..      16      67 ..       4      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
               Glyco_hydro_30C 15 snvetvAFlnpDGsiv.vvilNrsessvtitvs..dsskskgslsvparSiv 63
                                  + ++ v+F   DG iv  v lN +++ +ti++     s+++g +++ ++Siv
  gi|70606807|ref|YP_255677.1| 16 TALQDVSFEVRDGEIVgYVGLNGAGKTTTIEIIsgVRSPDQGDVEIDGHSIV 67
                                  689********************99*******85533457889999****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2166.47
//
Query:       gi|70606808|ref|YP_255678.1|  [L=429]
Description: 4-aminobutyrate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.5e-102  341.7   0.0   5.4e-102  341.5   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.053   12.7   0.0        3.7    6.6   0.0    2.1  2  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.5   0.0  6.1e-106  5.4e-102       9     406 .]      25     424 ..      18     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: 341.5 bits;  conditional E-value: 6.1e-106
                                   SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-B.T-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S CS
                   Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGh.ahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld 88 
                                    +lvi+++eGv+++d +g++ylD++s+i v+nlG+ +hP+v+k+++ q+  l h   + + n p+++la+ l++l p++++
  gi|70606808|ref|YP_255678.1|  25 QPLVIDRGEGVWVYDIEGNKYLDFTSGIGVNNLGWpSHPDVIKVAQIQMTRLAHAAANDFYNIPQMELAKRLVQLSPGNFS 105
                                   359*******************************978*******************************************9 PP

                                   .EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                   Aminotran_3  89 .kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                    kvf+ nsG+e+ve+++Kl +        t ++++iaf g+fHGrtlg+l++t+sk+  +   gpf+ +v +++yp +++ 
  gi|70606808|ref|YP_255678.1| 106 kKVFFSNSGTESVEASIKLVKG-------TGRKYLIAFLGSFHGRTLGSLALTASKPVQRYSAGPFSIGVFHVPYPNPFRN 179
                                   99******************99.......**************************9999*********************9 PP

                                   B-HHHHHHHHHHHHHHHH..........CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                   Aminotran_3 169 keneeeeaalleeleale..........kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                   + + +  +   e ++a++           +  +eva++i+EpiqgegG+vv++ +f+a+lr+l++k+++ li DEvq G+G
  gi|70606808|ref|YP_255678.1| 180 PWKINGYEKPDELINAVIeyidfwlfqhVVDPEEVAGIIFEPIQGEGGYVVPPHNFFAELRKLAQKYNIPLIDDEVQMGLG 260
                                   998855555555555554444577798667889************************************************ PP

                                   TTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHH CS
                   Aminotran_3 240 rTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqe 319
                                   rTGk+fA+eh++++pD++tlaKal+gG  p+ a++ + ++    ++g h++TfgGn l +++ l+v+e+i+e  l+ +++e
  gi|70606808|ref|YP_255678.1| 261 RTGKMFAIEHFNIEPDIITLAKALGGGlVPVGATIFRSDLDFK-KKGIHSNTFGGNALSMSIGLKVVELIKE--LMPHVNE 338
                                   **************************************98644.4777**********************85..899**** PP

                                   HHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHH CS
                   Aminotran_3 320 lgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGdnvirllppliitdeeid 396
                                   +g+++ e+L +++     + + Rg+Gl  +ie+++++++ +     +++++a ++G++++saG+++ir++ppl+i++ee++
  gi|70606808|ref|YP_255678.1| 339 IGKIFGEELCQMK-----VDDCRGLGLAWGIEFVKSDKTPDpkvrDRVVTEAFKEGLIVISAGKSSIRIIPPLVISEEEAK 414
                                   *********9999.....889***************99766999989********************************** PP

                                   HHHHHHHHHH CS
                   Aminotran_3 397 elleilkkal 406
                                    +l++lk a+
  gi|70606808|ref|YP_255678.1| 415 IGLSKLKTAI 424
                                   ******9986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0027        24      96     152 ..      52     109 ..      46     114 .. 0.73
   2 ?    6.6   0.0   0.00041       3.7     165     224 ..     231     285 ..     216     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0027
                                   EEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-.HHHHHHHHTTHHCTTETEEEE CS
                 Aminotran_1_2  96 ilvpdptyasyknilrlsggevvryplyseedfhld.lealeealkeapegnkktkvi 152
                                   i v ++ ++s+ ++++ +++++ r +   ++df +    +l + l ++++gn  +kv+
  gi|70606808|ref|YP_255678.1|  52 IGVNNLGWPSHPDVIKVAQIQMTRLAHAAANDFYNIpQMELAKRLVQLSPGNFSKKVF 109
                                   668899***************9999878788875540345666666666666655555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00041
                                   --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTS CS
                 Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafG 224
                                   ++++   +l +la+kyn+ l+ De+  g+  + + ++  ++n+e+++      +l+Ka+G
  gi|70606808|ref|YP_255678.1| 231 PPHNFFAELRKLAQKYNIPLIDDEVQMGLGRTGKMFAIEHFNIEPDII-----TLAKALG 285
                                   555556666667*******************98877555999999876.....7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2836.56
//
Query:       gi|70606809|ref|YP_255679.1|  [L=143]
Description: hypothetical protein Saci_1029 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 969.20
//
Query:       gi|70606810|ref|YP_255680.1|  [L=166]
Description: hypothetical protein Saci_1030 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-19   69.0   0.1    5.8e-19   68.5   0.1    1.2  1  Methyltransf_11  Methyltransferase domain
      7e-15   55.5   0.1    1.1e-14   54.9   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    9.5e-14   51.4   0.1    1.2e-13   51.2   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    4.2e-12   46.2   0.0      5e-12   46.0   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.1e-10   42.1   0.1    1.6e-10   41.6   0.1    1.2  1  Methyltransf_12  Methyltransferase domain
    1.9e-07   30.8   0.0    2.1e-07   30.6   0.0    1.1  1  MTS              Methyltransferase small domain
    6.3e-07   29.0   0.0    7.6e-07   28.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00015   21.3   0.0    0.00019   20.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00033   20.6   0.4    0.00053   19.9   0.4    1.3  1  Methyltransf_8   Hypothetical methyltransferase
    0.00055   19.6   0.1    0.00069   19.3   0.1    1.1  1  NodS             Nodulation protein S (NodS)
     0.0012   18.1   0.0     0.0016   17.8   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.014   15.0   0.1    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.038   13.5   0.2        1.5    8.3   0.0    2.1  2  CheR             CheR methyltransferase, SAM binding domain
      0.088   12.7   0.1       0.13   12.2   0.1    1.3  1  Methyltransf_18  Methyltransferase domain
       0.12   12.6   0.0       0.19   11.9   0.0    1.4  1  Plk4_PB1         Polo-like Kinase 4 Polo Box 1
       0.14   11.2   0.0       0.17   10.9   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.1   5.1e-22   5.8e-19       2      95 ..      26     116 ..      25     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 5.1e-22
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   ++GcG+G ++++l k +++v++vD++ e+l+ ak   +++ +   f++++a k+ ++d+ +D+v++ +++h +++ e++++
  gi|70606810|ref|YP_255680.1|  26 ELGCGSGFYCKKLVKLAKKVYCVDIDCEALEDAKLSLNTKAV---FLCESADKTSIPDAEIDVVLLANSFHDMDNKEEVVR 103
                                   79*************************************975...8*********************************** PP

                                   HHHHHEEEEEEEE CS
               Methyltransf_11  83 eiaRvLkpgGllv 95 
                                   ei+R+Lk +G+++
  gi|70606810|ref|YP_255680.1| 104 EIWRILKDDGRVL 116
                                   **********987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1   9.7e-18   1.1e-14       1      97 []      24     113 ..      24     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 9.7e-18
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   v +lGcG+G ++++l k    +kv++vDi+ e+le a+  +   + ++ f++ +a++ + +d+++D+v++++++h ++  +
  gi|70606810|ref|YP_255680.1|  24 VAELGCGSGFYCKKLVKLA--KKVYCVDIDCEALEDAKLSL---NTKAVFLCESADKTSIPDAEIDVVLLANSFHDMD--N 97 
                                   789*************996..9****************999...5799**********************99999887..5 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    e++++ei+r+Lk++G
  gi|70606810|ref|YP_255680.1|  98 KEEVVREIWRILKDDG 113
                                   669***********99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1     1e-16   1.2e-13       2     113 ..      19     121 ..      18     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1e-16
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq.gdieeleklledekfDlilsn 81 
                                   +++  v +lGCG+G+++++l ++    ++v+ +Di++ea+e A+     l+ + v +++ +d ++++    d+ +D++l  
  gi|70606810|ref|YP_255680.1|  19 SQNDIVAELGCGSGFYCKKLVKL---AKKVYCVDIDCEALEDAKLS---LNTKAVFLCEsADKTSIP----DAEIDVVLLA 89 
                                   5677899**************55...468***************95...555533333335555555....899******* PP

               Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr 113
                                   + ++++ +++++ +ei r lk++g++l+ d +
  gi|70606810|ref|YP_255680.1|  90 NSFHDMDNKEEVVREIWRILKDDGRVLVVDWK 121
                                   ***************************99987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   4.5e-15     5e-12      15     123 ..      13     123 ..       3     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 4.5e-15
               Methyltransf_23  15 rllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                   +l+++  ++  v ++GcG+G  ++ l +  ++v+ vD+++ea e a+     ka++ ++ +++ + p++ +d++ l ++++
  gi|70606810|ref|YP_255680.1|  13 FLPKYISQNDIVAELGCGSGFYCKKLVKLAKKVYCVDIDCEALEDAKlsLNTKAVFLCESADKTSIPDAEIDVVLLANSFH 93 
                                   5666778888999****************9**************9966655566666666666666*************** PP

               Methyltransf_23  94 hvpdppellrqiatllkpgGylllseplas 123
                                    +++ +e++r i+++lk++G++l+ ++ ++
  gi|70606810|ref|YP_255680.1|  94 DMDNKEEVVREIWRILKDDGRVLVVDWKKE 123
                                   *************************99765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   1.5e-13   1.6e-10       2      99 .]      26     115 ..      25     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1.5e-13
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdi 82 
                                   e+GcG+G + + l +    +++++vDi+ +a+edak  l+ +    + +   +++++ d       D+v+++n +h ++++
  gi|70606810|ref|YP_255680.1|  26 ELGCGSGFYCKKLVKL--AKKVYCVDIDCEALEDAKLSLNTKAV--FLCESADKTSIPDA----EIDVVLLANSFHDMDNK 98 
                                   89**************..**************999999888774..56666666666554....9**************** PP

               Methyltransf_12  83 revldnirklLkpgGrl 99 
                                   +ev+++i + Lk++Gr+
  gi|70606810|ref|YP_255680.1|  99 EEVVREIWRILKDDGRV 115
                                   ***************85 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.9e-10   2.1e-07      29     144 ..      20     124 ..      11     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.9e-10
                                   CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STT CS
                           MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfha 109
                                   +  ++ v+ lGcG G+   +l k  ++  v +vd+d +Ale ak  l+++++   + +s     ++++++d+++    fh+
  gi|70606810|ref|YP_255680.1|  20 Q--NDIVAELGCGSGFYCKKLVKLAKK--VYCVDIDCEALEDAKLSLNTKAV--FLCESADKTSIPDAEIDVVLLANSFHD 94 
                                   2..44599***************9988..9***************9999886..344444445567799***********9 PP

                                   TCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSC CS
                           MTS 110 gkatelavaeeliaeAkeaLkegGeLliVanrklg 144
                                     +      ee+++e  ++Lk++G+ l+V  +k +
  gi|70606810|ref|YP_255680.1|  95 MDN-----KEEVVREIWRILKDDGRVLVVDWKKEK 124
                                   988.....677777788999999999999766655 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   6.8e-10   7.6e-07      52     159 ..      25     125 ..      16     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.8e-10
                                   EEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-H CS
               Ubie_methyltran  52 lDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDk 132
                                    ++ +G+g +  kl + +    kv  +Di+ + L+ ++  l+ +++    fl+ +a +    d   Dvv ++  + ++ +k
  gi|70606810|ref|YP_255680.1|  25 AELGCGSGFYCKKLVKLA---KKVYCVDIDCEALEDAKLSLNTKAV----FLCESADKTSIPDAEIDVVLLANSFHDMDNK 98 
                                   578899997777766665...5899**********99999988775....9****************************** PP

                                   HHHHHHHHHHEEEEEEEEEEEE----S CS
               Ubie_methyltran 133 lkaLkeayrvlkpGGrlvvlefskvel 159
                                   +++++e++r+lk  Gr++v++  k ++
  gi|70606810|ref|YP_255680.1|  99 EEVVREIWRILKDDGRVLVVDWKKEKT 125
                                   ********************9887665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.7e-07   0.00019     155     257 ..      14     116 ..      12     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-07
                          PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvi.vaNI 234
                                   l k++ +++ v  +G+GSG      +kL akkv+ vDiD  A++ ak  ++   v      a + ++++ +++dv+ +aN 
  gi|70606810|ref|YP_255680.1|  14 LPKYISQNDIVAELGCGSGFYCKKLVKL-AKKVYCVDIDCEALEDAKLSLNTKAVFLCE-SADKTSIPD-AEIDVVlLANS 91 
                                   77899999**************999999.799*************99766555554433.234555666.88998735888 PP

                          PrmA 235 Laev..lielaedikklvkegglli 257
                                     ++    e + +i++++k++g+++
  gi|70606810|ref|YP_255680.1|  92 FHDMdnKEEVVREIWRILKDDGRVL 116
                                   8765224578888888888888765 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   4.7e-07   0.00053      72     158 ..      20     119 ..      13     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.7e-07
                                   TTS-EEEES-TT-HHH.HH--S-..EEEEESS..-SS........TTEEES-T.TS-S--TT-EEEEEEES---S.S-HHH CS
                Methyltransf_8  72 dnlvvadlGcGeakia.eavrekekvrsfdlv..avn........ervvacdl.akvPledesvdvavfclslmg.tnlad 139
                                   +n +va+lGcG      + v+  +kv ++d+   a++        + v  c+   k  + d  +dv+++  s+   +n ++
  gi|70606810|ref|YP_255680.1|  20 QNDIVAELGCGSGFYCkKLVKLAKKVYCVDIDceALEdaklslntKAVFLCESaDKTSIPDAEIDVVLLANSFHDmDNKEE 100
                                   6889*******987763445667788888764223321111111267899*986789999************986257788 PP

                                   HHHHHHHHEEEEEEEEEEE CS
                Methyltransf_8 140 flkeanrvlkvGGllkvae 158
                                    ++e+ r+lk  G + v +
  gi|70606810|ref|YP_255680.1| 101 VVREIWRILKDDGRVLVVD 119
                                   9**********99887765 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.2e-07   0.00069      47     143 ..      24     116 ..      15     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.2e-07
                          NodS  47 alevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelra 127
                                   + e+Gc +G + ++l  ++k++  vd+  ea++ a+  ++ ++      +d +    d++ d+++ a+ ++ +++++e   
  gi|70606810|ref|YP_255680.1|  24 VAELGCGSGFYCKKLVKLAKKVYCVDIDCEALEDAKLSLNTKAVFLCESADKT-SIPDAEIDVVLLANSFHDMDNKEE--- 100
                                   569************************************99665555555544.457999*******99877777766... PP

                          NodS 128 avrnlvsllapdgqlv 143
                                    vr++ ++l+ dg+++
  gi|70606810|ref|YP_255680.1| 101 VVREIWRILKDDGRVL 116
                                   5999999999999865 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0016      66     167 ..      24     120 ..      14     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                   EEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS-----..SEEEEESSGGGS-HHH CS
                Methyltransf_2  66 lvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslPea..DaillkrvlhDwsdek 144
                                   + ++G G+G   k+ v++  ++ ++  D  e  e+Ak      ++++  f   +  k s+P+a  D++ll++  hD ++++
  gi|70606810|ref|YP_255680.1|  24 VAELGCGSGFYCKKLVKLAKKVYCVDIDC-EALEDAKLS----LNTKAVFLCESADKTSIPDAeiDVVLLANSFHDMDNKE 99 
                                   66899999999999999988888888885.667888877....566666777777789***665599*********99875 PP

                                   HHHHHHHHHHH--TT-EEEEEE- CS
                Methyltransf_2 145 cvklLkrvkkalpagGkvivvea 167
                                     ++++++ + l+++G+v+vv+ 
  gi|70606810|ref|YP_255680.1| 100 --EVVREIWRILKDDGRVLVVDW 120
                                   ..899****************86 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.3e-05     0.014       9     103 ..      16     110 ..       9     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                          MetW   9 elikpgsrvldlGcGdGelle.llkeekqvdgrGleldeegvae..cvakGlsviqgdldkdlenfedksfdyvvlsqtlq 86 
                                   ++i ++  v +lGcG G   + l+k  k+v    ++ ++   a+    +k + + +     d +  +d + d+v+l+ ++ 
  gi|70606810|ref|YP_255680.1|  16 KYISQNDIVAELGCGSGFYCKkLVKLAKKVYCVDIDCEALEDAKlsLNTKAVFLCE---SADKTSIPDAEIDVVLLANSFH 93 
                                   678899999********887615556677766666555433333003344444443...3455789*************** PP

                          MetW  87 atrnpkevldellrigr 103
                                    + n +ev++e+ ri +
  gi|70606810|ref|YP_255680.1|  94 DMDNKEEVVREIWRILK 110
                                   **************965 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.048        54      61      83 ..      39      61 ..      33      69 .. 0.81
   2 ?    8.3   0.0    0.0013       1.5     133     173 ..      79     117 ..      63     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.048
                                  SSS-EEEEEEESSCHHHHHHHHT CS
                          CheR 61 aklkvkilAtDidlkvlekAkag 83
                                  +kl  k++ +Did ++le Ak  
  gi|70606810|ref|YP_255680.1| 39 VKLAKKVYCVDIDCEALEDAKLS 61
                                  556679**************965 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                   GG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                          CheR 133 vlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                                   +  ++Dv+++ n  ++ d +++e+v++++++ lk++g++l+
  gi|70606810|ref|YP_255680.1|  79 PDAEIDVVLLAN--SFHDMDNKEEVVREIWRILKDDGRVLV 117
                                   567899999999..6889999****************9876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.13      10      61 ..      16      65 ..      13      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
               Methyltransf_18 10 slvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakenieka 61
                                  ++++++++va  G+  g+   +lv  + akkv+ +Di  ++le ak +++++
  gi|70606810|ref|YP_255680.1| 16 KYISQNDIVAELGCGSGFYCKKLV--KLAKKVYCVDIDCEALEDAKLSLNTK 65
                                  68999*******************..68999**************9888765 PP

>> Plk4_PB1  Polo-like Kinase 4 Polo Box 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.19      33     104 ..      92     165 ..      74     166 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                      Plk4_PB1  33 llkkkngeekvvevlriSsdGqeiiiyqpesgkevplndrpse.saekskkvysldnLPekyw.kkYeyasrFv 104
                                   + +  n+ee v e+ ri +d  ++ ++  +++k+      +   s+e+  + ++  +L +k+   +Y+y   Fv
  gi|70606810|ref|YP_255680.1|  92 FHDMDNKEEVVREIWRILKDDGRVLVVDWKKEKTEIGPPVNIRfSEEDYVRYFKTFKLTDKFFpSRYHYGLVFV 165
                                   5556699***********99999999888877664333444444678888889999999998636899988887 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.17      28      63 ..      18      53 ..      14      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                  GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HH CS
                        RrnaAD 28 leekltvleigpGkGilTeeLakrakqvvvlElder 63
                                  +++++ v e+g G G+  ++L+k ak+v  + +d +
  gi|70606810|ref|YP_255680.1| 18 ISQNDIVAELGCGSGFYCKKLVKLAKKVYCVDIDCE 53
                                  778999**********************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 900.67
//
Query:       gi|70606811|ref|YP_255681.1|  [L=134]
Description: hypothetical protein Saci_1031 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.047   13.9   0.0    1.4  1  Polyketide_cyc  Polyketide cyclase / dehydrase and lipid tran


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.6e-06     0.047       7      35 ..      17      45 ..      13      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-06
                                  HHHHHHTTTGGCCSCCCCEEEEEE.SSSE CS
                Polyketide_cyc  7 qvyalvadvesypeflphcssvevleeae 35
                                  qv+++ +dv +++ef+ ++++  v+++ +
  gi|70606811|ref|YP_255681.1| 17 QVWQIASDVKRMTEFWRGIKELNVVKNGD 45
                                  9***********************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 745.30
//
Query:       gi|70606812|ref|YP_255682.1|  [L=141]
Description: HIT family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   80.5   0.0    1.4e-22   80.2   0.0    1.1  1  HIT       HIT domain
      2e-10   41.1   0.1    5.9e-10   39.6   0.0    1.6  2  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.014   14.3   0.0      0.018   13.9   0.0    1.1  1  FemAB     FemAB family
      0.015   15.2   0.1      0.025   14.4   0.0    1.4  2  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
      0.037   13.4   0.1       0.05   13.0   0.1    1.1  1  TniB      Bacterial TniB protein


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0     4e-26   1.4e-22       2      95 ..       3      96 ..       2      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 4e-26
                                  GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-S CS
                           HIT  2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqs 84
                                  +e++  +vy+d++++afld+ p apgh+L+++++h +++ d++e  l +l +++k++a+ +++ +k++g+rvv n g++a q 
  gi|70606812|ref|YP_255682.1|  3 GEEEGYIVYRDNYYTAFLDKYPIAPGHTLLVTNAHFENILDTSETHLNDLGKTIKMLANSIKRAVKADGIRVVSNAGRSAMQI 85
                                  6778889**************************************************************************** PP

                                  SSS-EEEEEEC CS
                           HIT 85 vahlHiHvipr 95
                                  v+h H+H+ip+
  gi|70606812|ref|YP_255682.1| 86 VFHFHVHIIPT 96
                                  *********97 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.6e-13   5.9e-10       9     101 ..       2      95 ..       1     100 [. 0.89
   2 ?   -1.3   0.0      0.83     3e+03      60      81 ..     116     134 ..     111     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.6e-13
                                   TTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEEEE--SCCC CS
                        DcpS_C   9 kgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdaeelrvgvhy 88 
                                   +g+e+  +vy+d+ ++++ D++p a+ h l + +++++++ d +++hl  l +  + + + i++  ++ + +   ++g  +
  gi|70606812|ref|YP_255682.1|   2 NGEEEGYIVYRDNYYTAFLDKYPIAPGHTLLVTNAHFENILDTSETHLNDLGKTIKMLANSIKRAVKAdGIRVVSNAGRSA 82 
                                   67888999****************************************99988888888888777755667788899**** PP

                                   T--S-S--EEEEE CS
                        DcpS_C  89 qPsvyhlHlHvis 101
                                    + v+h+H+H+i 
  gi|70606812|ref|YP_255682.1|  83 MQIVFHFHVHIIP 95 
                                   ***********95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.83
                                   HHHHHHHHHHHHHTT-T-EEEE CS
                        DcpS_C  60 kemrekakkvieekynevdaee 81 
                                   +e++eka+++i ++ n   +++
  gi|70606812|ref|YP_255682.1| 116 REYYEKARTLIYNEVN---RSN 134
                                   5778888888855554...443 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     5e-06     0.018     209     268 ..       5      66 ..       1      78 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-06
                         FemAB 209 rkgialrsldYYeklldtf..gdkaelmlAelnlaeylkelqekleklekklakleeklekn 268
                                    +g+ +  ++YY  +ld +  + + +l + ++++++ l++ +++l++l k+++ l ++++++
  gi|70606812|ref|YP_255682.1|   5 EEGYIVYRDNYYTAFLDKYpiAPGHTLLVTNAHFENILDTSETHLNDLGKTIKMLANSIKRA 66 
                                   5566677789*********76667*****************************999987765 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.1e-06     0.025      34     108 ..      14      95 ..       4     105 .. 0.72
   2 ?   -3.6   0.0       2.6   9.4e+03      74      87 ..     119     132 ..     117     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                                   SEEEE---.S-SSTT-EEEEESS--SSTTSS-H....HHHHHHHHHHHHHHHHHHHTT--EEEEEE-..SSS-----EEEE CS
                      CwfJ_C_1  34 kvYlalpk.gpLssgHvliipieHisallslde....evldeirkfrkalvkmykkqdkdavvfEis..sersvHlaiqvi 107
                                   + Y a     p++ gH l+++ +H ++ l ++e    ++ + i+   +++ +  k+ +  +v        +   H+++++i
  gi|70606812|ref|YP_255682.1|  14 NYYTAFLDkYPIAPGHTLLVTNAHFENILDTSEthlnDLGKTIKMLANSIKRAVKADGIRVVSNAGRsaMQIVFHFHVHII 94 
                                   5677755549*******************9999334344444555555555555555555555443355777889999999 PP

                                   E CS
                      CwfJ_C_1 108 p 108
                                   p
  gi|70606812|ref|YP_255682.1|  95 P 95 
                                   9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHTT- CS
                      CwfJ_C_1  74 frkalvkmykkqdk 87 
                                   ++ka + +y++ ++
  gi|70606812|ref|YP_255682.1| 119 YEKARTLIYNEVNR 132
                                   78888888887765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05      0.05     128     188 ..      38      98 ..      31      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                          TniB 128 ihnllagsarkqreflnalksLgnelkipivlvGteealralrtDpqlasRFepialprwk 188
                                   ++n+l  s ++ + +  ++k+L n +k ++ + G++ + +a r+  q+   F+ + +p+w+
  gi|70606812|ref|YP_255682.1|  38 FENILDTSETHLNDLGKTIKMLANSIKRAVKADGIRVVSNAGRSAMQIVFHFHVHIIPTWE 98 
                                   789999999999************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 884.76
//
Query:       gi|70606813|ref|YP_255683.1|  [L=399]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-36  124.0   0.2    8.5e-36  123.4   0.2    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.6e-28   98.1   0.0    1.2e-27   96.8   0.0    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.3e-21   74.9   0.1    8.9e-21   73.9   0.1    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.3e-16   59.8   0.0    5.8e-16   59.0   0.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.028   14.3   0.0    1.5  1  CBM39          Carbohydrate binding domain (family 32)


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.2   2.4e-39   8.5e-36       1     148 [.     240     389 ..     240     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 2.4e-39
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   g Gf++a e++++ R  v a+a+g+ ++a+e +++y+ +rkaf kp++++q+v++k+ e  a+l  +r l+y a +++++g
  gi|70606813|ref|YP_255683.1| 240 GMGFKYAVESFDYARTIVSAQAVGIGQSAFEKLVNYSLQRKAFDKPIAEFQIVQQKVSESFADLLTSRFLTYWAGSLYNKG 320
                                   57******************************************************************************* PP

                                   ---..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpd..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                   k d   ++as+aK++a+e+a++++ +am  +Gg+G++++ ++er++rd ++l  +eGt++iqr   ar+
  gi|70606813|ref|YP_255683.1| 321 KTDeyIVAASLAKFYATEAAEKIVMRAMTAHGGYGVSNSIGLERMLRDLQILKTYEGTNDIQRVSAARQ 389
                                   ***999*********************************************************988886 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.0   3.4e-31   1.2e-27       2     113 .]      17     127 ..      16     127 .. 0.97
   2 ?   -3.0   0.0       3.1   1.1e+04      36      44 ..     344     352 ..     325     364 .. 0.51

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 3.4e-31
                                   HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHH CS
                 Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalll 82 
                                   +++e lr+t+refae+e+  ++++ + e+ +p+ l ++++elGl+g  vp+e gG+g dyl+ +++ eel+r+++++++ll
  gi|70606813|ref|YP_255683.1|  17 QDHEILRQTIREFAEKEVSGYVDKGESERDVPKVLKERAKELGLYGPDVPTELGGQGSDYLSLLVISEELSRVWTSFSTLL 97 
                                   79***********************99999**999********************************************** PP

                                   HHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  83 gvhsslvapailrfGteeqkrryLpklasge 113
                                    vh +l+  ai+++G ee k++yLp  asge
  gi|70606813|ref|YP_255683.1|  98 LVHWMLN-RAIYKYGKEEVKKKYLPLTASGE 127
                                   ****999.79*******************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
                                   HHHHHHHTT CS
                 Acyl-CoA_dh_N  36 lwkklaelG 44 
                                   +++++ ++G
  gi|70606813|ref|YP_255683.1| 344 VMRAMTAHG 352
                                   244444433 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   2.5e-24   8.9e-21       1      97 []     131     228 ..     131     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.5e-24
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---...----EEEEEEE..GGGEEE--- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd...rarglslflvprdapgvsvrri 78 
                                   afa TEp+aG+dva++++ +a++ +++y++n +Ki+itn+ ia+++++ art  p+   r +g+++flv++ +   +v+ri
  gi|70606813|ref|YP_255683.1| 131 AFANTEPEAGTDVAGIRS-TAKKVNDHYIINARKIFITNGDIADYFVLTARTSPPSnnaRWKGITMFLVEKEWGVKTVSRI 210
                                   799***************.77777779************************6555567889*********98887777999 PP

                                   --BSS-TTS-EEEEEEE.. CS
                 Acyl-CoA_dh_M  79 eeklGlrglptgelvfedv 97 
                                   e ++Gl+  +t+e+ +edv
  gi|70606813|ref|YP_255683.1| 211 E-TTGLKASHTTEIILEDV 228
                                   5.7*************997 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   1.6e-19   5.8e-16       2     133 ..     256     379 ..     255     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.6e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   +++a+a+G+ ++a++++v +  +r+   + +++a+++++q+++ e+ a+l + r l++ a +  +++ ++++         
  gi|70606813|ref|YP_255683.1| 256 IVSAQAVGIGQSAFEKLVNYSLQRKA--FDKPIAEFQIVQQKVSESFADLLTSRFLTYWAGSL-YNKGKTDEY-----IVA 328
                                   689***********************..*********************************99.555666666.....599 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                   a++a+ +a+e a ++v +++ a+Gg+++ ++  l+R++RD++++++++++n
  gi|70606813|ref|YP_255683.1| 329 ASLAKFYATEAAEKIVMRAMTAHGGYGVSNSIGLERMLRDLQILKTYEGTN 379
                                   9**********************************************9987 PP

>> CBM39  Carbohydrate binding domain (family 32)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.7e-06     0.028      35      83 ..     134     181 ..     128     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.7e-06
                         CBM39  35 Nkefesleagqiacdv..ttevtyGkfiledeeavikkgDtlyywvivqkn 83 
                                   N e    eag+ ++ +  t +++++ +i++ +++ i +gD+  y v++ ++
  gi|70606813|ref|YP_255683.1| 134 NTEP---EAGTDVAGIrsTAKKVNDHYIINARKIFITNGDIADYFVLTART 181
                                   3333...7777778889999*************************998844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2700.56
//
Query:       gi|70606814|ref|YP_255684.1|  [L=419]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-30  106.9   0.0    8.7e-30  104.0   0.0    2.2  2  ABC_tran     ABC transporter
    1.5e-16   60.6   0.0    2.8e-16   59.8   0.0    1.4  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    4.9e-08   33.1   0.6    0.00031   20.7   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.1e-06   29.0   0.0     0.0058   16.9   0.0    2.4  2  AAA_22       AAA domain
    1.2e-06   28.2   0.1    9.1e-06   25.3   0.1    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    7.5e-06   25.5   0.1     0.0006   19.3   0.0    2.4  2  TniB         Bacterial TniB protein
    0.00038   20.6   0.0     0.0018   18.4   0.0    1.9  2  AAA_33       AAA domain
    0.00052   19.6   0.1        0.8    9.2   0.1    2.4  2  AAA_25       AAA domain
     0.0018   18.0   1.2     0.0064   16.2   0.0    2.0  3  AAA_15       AAA ATPase domain
     0.0062   15.3   0.1       0.57    8.8   0.0    2.3  2  AAA_13       AAA domain
     0.0075   16.8   0.1      0.028   15.0   0.0    2.1  2  AAA_18       AAA domain
     0.0084   15.8   0.1      0.015   15.0   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0087   16.5   0.2      0.022   15.2   0.2    1.7  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.011   14.9   0.3        0.1   11.8   0.2    2.2  2  NB-ARC       NB-ARC domain
      0.018   14.8   0.1       0.12   12.1   0.0    2.0  2  IstB_IS21    IstB-like ATP binding protein
      0.026   14.4   0.0      0.052   13.4   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.043   14.0   0.0       0.18   12.0   0.0    2.0  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.047   13.6   0.3       0.31   10.9   0.1    2.1  2  NACHT        NACHT domain
      0.053   13.5   0.0       0.11   12.5   0.0    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.066   12.9   0.1       0.24   11.1   0.1    1.7  1  AAA_24       AAA domain
       0.11   12.2   0.2        1.4    8.6   0.1    2.2  2  AAA_30       AAA domain
        0.2   11.4   0.9         18    5.0   0.0    2.9  3  DEAD         DEAD/DEAH box helicase
        0.2   12.1   0.9        4.3    7.8   0.9    2.6  1  AAA          ATPase family associated with various cellular a
       0.27   11.1   0.9        9.8    6.1   0.0    2.6  2  HTH_IclR     IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   1.2e-32   8.7e-30       2     137 .]      29     201 ..      28     201 .. 0.87
   2 ?    0.3   0.0       1.3   9.5e+02      34      72 ..     334     374 ..     326     411 .. 0.68

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.2e-32
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE.................EETTCEGGG.............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxx.............. RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei.................lldgkdlke.............. 51 
                                   ++v +k+ke e++a+vGe+G+GK+tL ++l gl++pt G+i                 +       +              
  gi|70606814|ref|YP_255684.1|  29 QDVYIKIKEEEVIALVGESGSGKTTLGRMLVGLESPTGGKIlfnvedkvleeyettdnQ-------Srkaeiesihdifkg 102
                                   68999************************************777777777766644441.......144455667778889 PP

                                   B-HHHCCHCEEEE-SS..--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHH CS
                                   xxxxxxxxxxxxxxxx..xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  52 qeleslrkeigvlpqe..pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqr 116
                                   +  +++r+++ +++q+  ++l+p+++v +               e+++++ ++l+ +gl++   + +++ p++LSgGq+qr
  gi|70606814|ref|YP_255684.1| 103 KIAKEFRRHVNMVFQDpyASLDPRMKVIDIikepmistgylrgeEANKRVRELLEAVGLPK---SFADRYPHELSGGQRQR 180
                                   99**************999******9999999********988888888888888888766...7777789********** PP

                                   HHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 117 valarallkkpkllllDEpta 137
                                   va+ara+ ++pk+++lDEpt+
  gi|70606814|ref|YP_255684.1| 181 VAVARAISTDPKFVVLDEPTS 201
                                   *******************96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                                   SS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS.--S-T CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      ABC_tran  34 llkpteGeilld.gkdlkeqeleslrkeigvlpqe.pqlfp 72 
                                    ++ teGei +d   d +++ + ++++++++++ + +++++
  gi|70606814|ref|YP_255684.1| 334 YYDLTEGEIVIDvLSDKEMKVRGISDEKLKMITSKeNEIKS 374
                                   46679999999966666667888899999998888333333 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   3.7e-19   2.8e-16       1      65 []     252     315 ..     252     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3.7e-19
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE+g+++++++ p+HPYT  Ll++vp++ ++      ++ge+p+l +l++GC F+pRCp+a   C
  gi|70606814|ref|YP_255684.1| 252 VETGTKEQIMKTPKHPYTVSLLSAVPKVGSKMN-RIVLRGEPPNLVDLPKGCNFHPRCPYAFGDC 315
                                   8***************************99999.8889***********************9999 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00046      0.34       2      76 ..      41      97 ..      40     124 .. 0.58
   2 !   20.7   0.0   4.1e-07   0.00031     231     300 ..     167     234 ..     134     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76
                                   +l+G  gsGK++L + l +l                    +   + l++ +++   e+e+++ +s++ +++ ++
  gi|70606814|ref|YP_255684.1| 41 IALVGESGSGKTTLGRMLVGLE------------------SPTGGKILFNVEDKVLEEYETTDNQSRKAEIESIH 97
                                  68****************9993..................33333333333333333333333444444444444 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4.1e-07
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                   ++ ++elS G+++  a++ a+  ++   +++++DEp + L+ + ++ +l ll++l+r  ++  +l TH+  
  gi|70606814|ref|YP_255684.1| 167 DRYPHELSGGQRQRVAVARAISTDP---KFVVLDEPTSALDVSTQAQILNLLRKLKReLKISMLLITHNIA 234
                                   567899*******989999999888...99**********************66666588999*****965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.8e-06    0.0058       4      28 ..      37      61 ..      33     131 .. 0.82
   2 !    9.9   0.0    0.0011      0.82      56     130 ..     151     231 ..     136     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleq 28
                                  ++ +++++GesG+GKTtl r+l+  
  gi|70606814|ref|YP_255684.1| 37 EEEVIALVGESGSGKTTLGRMLVGL 61
                                  67899***************99765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                        AAA_22  56 llrellralglelka...erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvql 125
                                     rell+a+gl+++    +    +el   + ++ + ara    ++++++DE    l+   ++++l+ Lr+l    + ++++
  gi|70606814|ref|YP_255684.1| 151 RVRELLEAVGLPKSFadrY---PHELSgGQRQRVAVARAIstdPKFVVLDEPTSaLDvstQAQILNLLRKLKR--ELKISM 226
                                   56899999**999995542...44444444444444444455778********99999655**********99..999999 PP

                        AAA_22 126 iLvGt 130
                                   +L+ +
  gi|70606814|ref|YP_255684.1| 227 LLITH 231
                                   99865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   1.2e-08   9.1e-06      23     203 ..      37     237 ..      24     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.2e-08
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE............. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............. RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk............. 89 
                                   ++++ a+vG+ GSGK+ l   +   L   +  k+  +  ++++ + + + +++ kae+e + d  + k             
  gi|70606814|ref|YP_255684.1|  37 EEEVIALVGESGSGKTTLGRML-VGLESPTGGKILFNVEDKVLEEyETTDNQSRKAEIESIHDIFKGKiakefrrhvnmvf 116
                                   4668899999999999999888.4455556667777777888887778888889999998874444444445555666555 PP

                                   ...SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--S CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  90 ...lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpap 160
                                          ++++++   +k+   s+ ++ g+e++k  v+elle +g+ k+       +LSgG+++ va+a  +++   +p  
  gi|70606814|ref|YP_255684.1| 117 qdpYASLDPRMKVIDIIKEPMISTGYLRGEEANK-RVRELLEAVGLPKSfadryphELSGGQRQRVAVARAIST---DP-K 192
                                   5444445566777777777777999999999875.79*********9999999999********9999976543...33.4 PP

                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn..aQfivislreemle 203
                                   +++lDe  +aLD +  +++ +ll++ + +    ++ i+++  + +
  gi|70606814|ref|YP_255684.1| 193 FVVLDEPTSALDVSTQAQILNLLRKLKRElkISMLLITHNIAVAS 237
                                   9***********************888773356778888766555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.046        34      16      51 ..      21      54 ..      17      65 .. 0.73
   2 !   19.3   0.0     8e-07    0.0006     108     166 ..     177     235 ..      98     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.046
                          TniB 16 akeilerLeeLleypkrkrmpnlllvGdsnnGKtmi 51
                                   k++++  ++++ + k+++   + lvG+s  GKt++
  gi|70606814|ref|YP_255684.1| 21 NKAVVKAVQDVYIKIKEEE--VIALVGESGSGKTTL 54
                                  5566666666665555555..799**********98 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 8e-07
                          TniB 108 eqqvlrllre..lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteeal 166
                                   ++q +++ r+  ++++ +++DE  ++l   +++q ++ln+l++L++elki++ l+  + a+
  gi|70606814|ref|YP_255684.1| 177 QRQRVAVARAisTDPKFVVLDEPTSAL--DVSTQAQILNLLRKLKRELKISMLLITHNIAV 235
                                   3444445554115789***********..889999*****************998666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.4e-06    0.0018       1      93 [.      40     134 ..      40     142 .. 0.82
   2 ?   -0.8   0.0       2.1   1.6e+03      61     100 ..     182     223 ..     166     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-06
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvild 76 
                                   ++ lvG +GsGK+tl + l+  +        +  +d++++ ++ td+qs +      +++++i ++ ++k  ++  n+++ 
  gi|70606814|ref|YP_255684.1|  40 VIALVGESGSGKTTLGRMLVGLESptggkILFNVEDKVLEEYETTDNQSRKA---EIESIHDIFKGKIAKEFRRHVNMVFQ 117
                                   7899*************99633334467555556788888888888887754...45699********************* PP

                        AAA_33  77 atnlsrrerarflklar 93 
                                    +++s + r++++ + +
  gi|70606814|ref|YP_255684.1| 118 DPYASLDPRMKVIDIIK 134
                                   *****999999988876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                        AAA_33  61 elarkalsagrnvildat..nlsrrerarflklarrlgvpvr 100
                                   ++ar   +  + v+ld +   l+ +++a++l+l+r+l+ + +
  gi|70606814|ref|YP_255684.1| 182 AVARAISTDPKFVVLDEPtsALDVSTQAQILNLLRKLKRELK 223
                                   556666677777888888666778888888888887776555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0011       0.8      30      49 ..      35      54 ..      22      70 .. 0.91
   2 !    7.8   0.0    0.0029       2.2     124     188 ..     177     231 ..     134     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                        AAA_25 30 lpagelallaGapgtGKttl 49
                                  + ++e+++l+G +g+GKttl
  gi|70606814|ref|YP_255684.1| 35 IKEEEVIALVGESGSGKTTL 54
                                  56899**************9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                        AAA_25 124 tlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                   +   ++  a+++ai    ++++vv+D  ++al+ + +     +++++ l++++r++++  ll+ H
  gi|70606814|ref|YP_255684.1| 177 Q---RQRVAVARAIST--DPKFVVLDEPTSALDVSTQ-----AQILNLLRKLKRELKISMLLITH 231
                                   2...223346777766..7*************99988.....89*******************99 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.6e-06    0.0064      12      78 ..      26      94 ..      26     114 .. 0.80
   2 ?   -2.1   0.0       3.3   2.5e+03     319     364 ..     186     231 ..     164     236 .. 0.78
   3 ?   -1.4   0.2         2   1.5e+03     153     180 ..     335     362 ..     319     405 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                        AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.kkvikiekedleifeniseskdik 78
                                  ++ +dv+i+++ee +  l+G+ +sGK+++ ++l  + + +  k  ++v ++  e++e+++n+s++ +i+
  gi|70606814|ref|YP_255684.1| 26 KAVQDVYIKIKEEeVIALVGESGSGKTTLGRMLVGLESPTGGKIlFNVEDKVLEEYETTDNQSRKAEIE 94
                                  6789********99*******************888887733336677788888888888888777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                        AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    +++++++++++EP   L  + q ++ +ll++l ++ k   ++ TH
  gi|70606814|ref|YP_255684.1| 186 AISTDPKFVVLDEPTSALDVSTQAQILNLLRKLKRELKISMLLITH 231
                                   5778899999999988888888888888888887776655566666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2
                        AAA_15 153 eklekekeelkidkedlkklikkleesl 180
                                   ++l++ +  +++ +++  k+     e+l
  gi|70606814|ref|YP_255684.1| 335 YDLTEGEIVIDVLSDKEMKVRGISDEKL 362
                                   3333333333333222222211111111 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.019        14      23      41 ..      45      63 ..      41     101 .. 0.83
   2 !    8.8   0.0   0.00077      0.57     526     579 ..     190     241 ..     181     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                        AAA_13 23 GwNGaGKTtLSrllrslel 41
                                  G  G+GKTtL r+l  le+
  gi|70606814|ref|YP_255684.1| 45 GESGSGKTTLGRMLVGLES 63
                                  788***********99975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00077
                        AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                     k vv+D P S LD   +  + +l+++   ++ k++ +++ THn+    ++++
  gi|70606814|ref|YP_255684.1| 190 DPKFVVLDEPTSALDVSTQAQILNLLRKLK-RELKIS-MLLITHNIAVASYLSD 241
                                   5789*************************8.556665.5566***988777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.7e-05     0.028       1      68 [.      41     104 ..      41     154 .. 0.75
   2 ?   -2.4   0.0       8.6   6.4e+03      25      44 ..     340     359 ..     325     406 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                   I+l G +G+GKttl++ L  ++ +  g ++ +++ ++ l+++++ +  ++s++++++    ++d++++ +
  gi|70606814|ref|YP_255684.1|  41 IALVGESGSGKTTLGRMLVGLE-SptGGKILFNVEDKVLEEYETTD--NQSRKAEIES---IHDIFKGKI 104
                                   899***************7764.44677777777777777777777..6666666665...444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.6
                        AAA_18  25 gvnlrdvakenglllevdpe 44 
                                   g++++dv++++++      +
  gi|70606814|ref|YP_255684.1| 340 GEIVIDVLSDKEMKVRGISD 359
                                   56666666666665554444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     2e-05     0.015      15      38 ..      31      54 ..      26      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                        AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                    i+i++++++ l+G+sGsGK+Tl
  gi|70606814|ref|YP_255684.1| 31 VYIKIKEEEVIALVGESGSGKTTL 54
                                  568899888**************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.9e-05     0.022      22     116 ..      36     148 ..      22     229 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-05
                        AAA_16  22 grpelvllsGesGvGKsslvrellralekd...........ggiflrgkcdqlesaipysalaqalareellrqlldeaes 91 
                                    ++e++ l+GesG+GK++l r+l   le             +++  ++++d  +++++   + +++ + + ++++ +++ +
  gi|70606814|ref|YP_255684.1|  36 KEEEVIALVGESGSGKTTLGRMLVG-LESPtggkilfnvedKVLEEYETTDNQSRKAEIESIHDIF-K-GKIAKEFRRHVN 113
                                   45589**************999984.4444343222222211111222222223334444455555.3.333334444344 PP

                        AAA_16  92 aeleawrekleeala..........avpelagaea 116
                                     +++  + l+ +++          +++ l+g+ea
  gi|70606814|ref|YP_255684.1| 114 MVFQDPYASLDPRMKvidiikepmiSTGYLRGEEA 148
                                   44444444455555556666666665555555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00013       0.1       3      38 ..      23      56 ..      21      66 .. 0.85
   2 ?    0.3   0.0      0.44   3.3e+02     111     150 ..     204     242 ..     167     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC  3 ksvekviekLlekdelqslvvalvGmgGvGKttlak 38
                                  + v++v++   + +e +  v+alvG  G+GKttl +
  gi|70606814|ref|YP_255684.1| 23 AVVKAVQDVYIKIKEEE--VIALVGESGSGKTTLGR 56
                                  56778888888888888..**************965 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.44
                                   EE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S- CS
                        NB-ARC 111 DVweeedwdkigvvlparenrlrvllTTRdeevanavsat 150
                                   DV ++ +  ++   l+ re ++++ll T + +va++ s++
  gi|70606814|ref|YP_255684.1| 204 DVSTQAQILNLLRKLK-RELKISMLLITHNIAVASYLSDR 242
                                   5555555446666677.99999999999999999999887 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.12      44      99 ..      35      90 ..      16      99 .. 0.81
   2 ?    0.1   0.0      0.79   5.9e+02     107     154 ..     189     238 ..     174     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgkl 99
                                  i+++e i+l+G sG GK+ l   l      +g ++lf   ++++ee ++ +++ + 
  gi|70606814|ref|YP_255684.1| 35 IKEEEVIALVGESGSGKTTLGRMLVGLESPTGGKILFNVEDKVLEEYETTDNQSRK 90
                                  678899**************999987778889999999999999998888877664 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.79
                     IstB_IS21 107 lkvdllilDd.lgllpld.qaeaellfeviekryerrsiiitsnlpfaew 154
                                   + ++ ++lD+  + l+++ qa+  +l++ +++  + + ++it n+ +a++
  gi|70606814|ref|YP_255684.1| 189 TDPKFVVLDEpTSALDVStQAQILNLLRKLKRELKISMLLITHNIAVASY 238
                                   45678888883234455413444567777777777778888999888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-05     0.052      88     121 ..      26      60 ..      16      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   ++++++  ++k+ ++++lvG+SG GK+tL  +l++
  gi|70606814|ref|YP_255684.1|  26 KAVQDVYIKIKEeEVIALVGESGSGKTTLGRMLVG 60 
                                   56667777777779***************999987 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.18      61      89 ..     188     216 ..     163     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                       SbcCD_C  61 epalrlvfLDEAFsklDeesiatllelle 89 
                                   ++++++v+LDE  s lD  ++a++l+ll+
  gi|70606814|ref|YP_255684.1| 188 STDPKFVVLDEPTSALDVSTQAQILNLLR 216
                                   45799**********************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00042      0.31       2      20 ..      40      58 ..      39      65 .. 0.87
   2 ?   -0.1   0.0         1   7.7e+02      90     126 ..     196     230 ..     193     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                                  CEEEEC-TTTCHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                  +++l Ge+GsGKTtL + l
  gi|70606814|ref|YP_255684.1| 40 VIALVGESGSGKTTLGRML 58
                                  799***********97665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                                   STT-SS-TCH.........HHHHHCTTTTT--EEEEE CS
                         NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeaslllt 126
                                   lDe  + l+ ++++++ +lL++l r+  l+ ++ll+t
  gi|70606814|ref|YP_255684.1| 196 LDEPTSALDVSTQAQILNLLRKLKRE--LKISMLLIT 230
                                   68888888888889999999999888..777777777 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.11      12      40 ..      33      59 ..      19      65 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                  HHHHHCH..TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE 12 kklakal..gdvilLeGdLGaGKTtlvrgla 40
                                   k    +  ++vi+L G+ G+GKTtl r l+
  gi|70606814|ref|YP_255684.1| 33 IK----IkeEEVIALVGESGSGKTTLGRMLV 59
                                  33....234789**************99875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00033      0.24       4      23 ..      40      65 ..      37      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                        AAA_24  4 kiliyGpsgiGKTtlakel......g 23
                                   i+++G+sg+GKTtl ++l      +
  gi|70606814|ref|YP_255684.1| 40 VIALVGESGSGKTTLGRMLvglespT 65
                                  699************99886655442 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0019       1.4      17      47 ..      37      67 ..      26      73 .. 0.79
   2 ?    1.2   0.0      0.35   2.6e+02      59     114 ..     152     217 ..     146     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaagg 47
                                  ++ v +l+G  G+GKtt+ + l+ +    gg
  gi|70606814|ref|YP_255684.1| 37 EEEVIALVGESGSGKTTLGRMLVGLESPTGG 67
                                  456999***********99988876665555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.35
                        AAA_30  59 AkvLaeelgieastiakllkrlk........grarlepg.tllivDE.agmvdtkqlaallkaaek 114
                                    ++L e++g++ s  +++ ++l          + +++++ + ++ DE ++ +d ++ a++l+ ++k
  gi|70606814|ref|YP_255684.1| 152 VRELLEAVGLPKSFADRYPHELSggqrqrvaVARAISTDpKFVVLDEpTSALDVSTQAQILNLLRK 217
                                   556667777777777777777778888888844556666699*****4455688877777777665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.089        67      11      30 ..      35      54 ..      26      70 .. 0.79
   2 ?   -0.2   0.0         1   7.5e+02     121     150 ..      72     101 ..      54     116 .. 0.80
   3 ?    5.0   0.0     0.024        18     121     152 ..     190     221 ..     117     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.089
                                  HHTTCEEEEEESTTSSHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                          DEAD 11 ilgggdvlvaaeTGsGKTla 30
                                  i +++ + + +e GsGKT+ 
  gi|70606814|ref|YP_255684.1| 35 IKEEEVIALVGESGSGKTTL 54
                                  4567778899********85 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                                   TEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlp 150
                                   +v+  Vl E  +  +q+++ +i++i+  ++
  gi|70606814|ref|YP_255684.1|  72 NVEDKVLEEYETTDNQSRKAEIESIHDIFK 101
                                   5666799*****************998775 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.024
                                   TEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                   + +f+VlDE    ld + + +i ++l++l++ 
  gi|70606814|ref|YP_255684.1| 190 DPKFVVLDEPTSALDVSTQAQILNLLRKLKRE 221
                                   5699******************9999999654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.9    0.0057       4.3       2      52 ..      42     118 ..      41     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0057
                                   EEESSTTSSHHHHHHHHHHH................H.........THEEEEEETTTCS.SSSTTHHHHHHHHHHHH CS
                           AAA   2 llyGppGtGKTllakavake................l.........gvefleisgsell.skyvgesekkirelfke 52 
                                    l+G  G GKT+l + ++                  l         +++    s ++++  k+ +e  ++++++f++
  gi|70606814|ref|YP_255684.1|  42 ALVGESGSGKTTLGRMLVGLesptggkilfnvedkvLeeyettdnqSRKAEIESIHDIFkGKIAKEFRRHVNMVFQD 118
                                   699************99887444333333222222102111111111222222334444444666666666666665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.013       9.8      20      38 ..     151     169 ..     142     174 .. 0.80
   2 ?    2.6   0.2      0.16   1.2e+02       6      24 ..     209     227 ..     208     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                                   BHHHHHHHHTS-HHHHHHH CS
                      HTH_IclR  20 tlselArrtglpkStvhRl 38 
                                   +++el ++ glpkS + R+
  gi|70606814|ref|YP_255684.1| 151 RVRELLEAVGLPKSFADRY 169
                                   799***********98887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                                   HHHHCT-CTTBSS-BHHHH CS
                      HTH_IclR   6 laiLdalaeapqeltlsel 24 
                                   ++iL++l++  +el++s l
  gi|70606814|ref|YP_255684.1| 209 AQILNLLRKLKRELKISML 227
                                   69*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 2654.92
//
Query:       gi|70606815|ref|YP_255685.1|  [L=452]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-24   87.4   0.1    3.9e-23   82.5   0.1    2.4  1  ABC_tran      ABC transporter
    1.6e-19   70.2   0.0    2.9e-19   69.4   0.0    1.5  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    3.2e-09   37.0   0.9    7.6e-08   32.5   0.9    2.3  1  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.4e-06   27.2   0.0    5.2e-05   22.8   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00067   19.3   0.0     0.0013   18.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0034   17.0   0.2       0.39   10.2   0.2    2.6  3  AAA_25        AAA domain
     0.0064   16.8   0.1        1.3    9.3   0.0    2.8  3  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.016   15.4   0.3       0.05   13.7   0.3    1.9  1  OSCP          ATP synthase delta (OSCP) subunit
      0.022   14.5   0.0      0.034   13.9   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.026   14.2   0.1        1.8    8.3   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
      0.038   13.3   0.7        3.1    7.1   0.1    2.6  2  ATPase        KaiC
      0.054   12.9   0.0       0.51    9.7   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.084   12.6   0.1        0.3   10.8   0.0    2.0  2  AAA_24        AAA domain
       0.12   12.7   0.3        0.3   11.4   0.3    1.8  1  AAA_16        AAA ATPase domain
       0.15   12.1   0.1       0.81    9.7   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
       0.21   10.3   1.7       0.72    8.6   0.1    2.5  2  ABC_ATPase    Predicted ATPase of the ABC class
       0.29   11.6   1.1        5.3    7.5   0.0    2.9  2  AAA           ATPase family associated with various cellular 
        0.7    9.9   2.3        2.3    8.3   2.2    2.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1   3.9e-26   3.9e-23       1     137 []      24     313 ..      24     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 3.9e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEE.................EETTCEGGG......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx.................xxxxxxxxx......... RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp....teGei.................lldgkdlke......... 51 
                                   l+ v+l++kege++++ Ge+G+GKStL+ ++ag l p    ++Ge+                                   
  gi|70606815|ref|YP_255685.1|  24 LNGVDLDVKEGEVLGVAGESGSGKSTLALTIAGVLPPnawiKKGEVrfkdidlvrelrevgdkG-------Fnkkknqraf 97 
                                   789**********************************99999****555555555555555551.......0444444455 PP

                                   .....B-HHHCCHCEEEE-SS..--S-TTSBHHHH.............................................. CS
                                   .....xxxxxxxxxxxxxxxx..xxxxxxxxxxxx.............................................. RF
                      ABC_tran  52 .....qeleslrkeigvlpqe..pqlfpeltvren.............................................. 79 
                                        +   +  ++i++++q+  ++l+p l+++ +                                              
  gi|70606815|ref|YP_255685.1|  98 kelnnRLQAFRGSKIAIVFQDpmTSLNPVLQIGYQigetiyyhnpallakrilarskvtkdelreiirlleqnketyvekl 178
                                   556635556667889999999886777777776668888****************************************** PP

                                   ..............................................................................HHH CS
                                   ..............................................................................xxx RF
                      ABC_tran  80 ..............................................................................esd 82 
                                                                                                                 e  
  gi|70606815|ref|YP_255685.1| 179 nefvkskglegledqilfiwerndihkakkqklilslegeklsgfvrnflenvaetnrvrnisripiisrrlkstlikEGY 259
                                   **************************9999999999999999999999999999988888888888888888777776666 PP

                                   TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   +++ ++l+ l+ ++ +++vv+  p++LSgG++qrva+a a++++p+l+++DEpt+
  gi|70606815|ref|YP_255685.1| 260 RKAVEILTMLNVPN-PEKVVYMYPHELSGGMRQRVAIAIAIVNNPELIIMDEPTS 313
                                   66888888888888.999999********************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   2.9e-22   2.9e-19       1      65 []     364     426 ..     364     426 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 2.9e-22
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE g++++++++plHPYT+ Llr+vp +d++      i+ge+p+ +  ++GC F+pRCpf++++C
  gi|70606815|ref|YP_255685.1| 364 VEVGNVEDVVTNPLHPYTQSLLRAVPTIDSQEV--SPIPGEVPDMRTPPSGCMFHPRCPFVMDKC 426
                                   8***************************99888..****************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.9   7.6e-11   7.6e-08       5     302 ..      40     348 ..      36     348 .. 0.56

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.6e-11
                        AAA_21   5 iGpNgsGKSnLLdaldllarl................drdvegltdelsggggirkipslldlydpeipfefeieeflsqg 69 
                                    G  gsGKS+L  ++ ++                    r+++  +d+  ++++++   ++l+++    ++    + f++ +
  gi|70606815|ref|YP_255685.1|  40 AGESGSGKSTLALTIAGVLPPnawikkgevrfkdidlVRELREVGDKGFNKKKNQRAFKELNNRLQAFRGSKIAIVFQDPM 120
                                   566677777777777555544777777777777777766666666666666666666666666655555555555566666 PP

                        AAA_21  70 vryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggv.svfslkelsvsepndlqfgkaltdits 149
                                   +  +  l++++++ e+  ++++ ll +++l +++++++e + + +  ++ +    ++ + +   +  + l+   ++++ ++
  gi|70606815|ref|YP_255685.1| 121 TSLNPVLQIGYQIGETIYYHNPALLAKRILARSKVTKDELREIIRLLEQNKETyVEKLNEFVKSKGLEGLEDQILFIWERN 201
                                   666666666666664444555555556666666666665555555444333320222333333333444444444444444 PP

                        AAA_21 150 rawsllllldglrke...rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvfleng 227
                                   +++++++ +  l +e    +g+ ++f +++ + ++ r ++r    +++  + l ++g+++      ++ ++   +    ++
  gi|70606815|ref|YP_255685.1| 202 DIHKAKKQKLILSLEgekLSGFVRNFLENVAETNRVRNISRIPIISRRLKSTLIKEGYRK------AVEILT-MLNVPNPE 275
                                   444444444444444444333333333333333333333322222222222222222211......111111.22222345 PP

                        AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                   +     ++elS G+++  a++ a+   +    l++ DEp + L+  +++ +lel+++l++  ++ +i+ +H+ ++l
  gi|70606815|ref|YP_255685.1| 276 KVVYMYPHELSGGMRQRVAIAIAIVNNP---ELIIMDEPTSALDVTVQAQVLELVRSLKKkYNSTFIFISHDLSVL 348
                                   56677899*********99999999999...9***********************88888899*********8875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   5.2e-08   5.2e-05     113     212 ..     150     358 ..      24     365 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 5.2e-08
                                   ETTEEE-HHHHHHHHHCTT-STT.......................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
                         SMC_N 113 ingkevtkkevsellesagiske.......................................................... 135
                                   + +++vtk e++e+++  + +ke                                                          
  gi|70606815|ref|YP_255685.1| 150 LARSKVTKDELREIIRLLEQNKEtyveklnefvkskglegledqilfiwerndihkakkqklilslegeklsgfvrnflen 230
                                   444455555555554444444447777777777777777778888888888888888888888888888888888888888 PP

                                   .....................................................CS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                   .....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 .....................................................lLSgGektLvalaLlfAiqkvkpaplyl 163
                                                                                        +LSgG ++ va+a+      v+   l +
  gi|70606815|ref|YP_255685.1| 231 vaetnrvrnisripiisrrlkstlikegyrkaveiltmlnvpnpekvvymyphELSGGMRQRVAIAIA----IVNNPELII 307
                                   88888888888888888888888888889999999999999999999999999*******99988754....4667779** PP

                                   ECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 164 lDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                   +De  +aLD +  ++v el+++ +k+  + fi is++  +l + +  + v+
  gi|70606815|ref|YP_255685.1| 308 MDEPTSALDVTVQAQVLELVRSLKKKynSTFIFISHDLSVLYEISDRIAVM 358
                                   *********************766654499******999887776555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0013      12      52 ..      24      64 ..      15      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkv 52
                                  ++g ++++++ ++  ++G+sGsGKSTl   i+ +L p+ ++
  gi|70606815|ref|YP_255685.1| 24 LNGVDLDVKEGEVLGVAGESGSGKSTLALTIAGVLPPNAWI 64
                                  566777777555889************99999999998865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0004      0.39      31      54 ..      32      55 ..      27      58 .. 0.89
   2 ?   -2.6   0.0       3.4   3.4e+03     105     153 ..      71     122 ..      62     125 .. 0.70
   3 ?    3.7   0.0     0.041        41      88     188 ..     248     343 ..     244     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0004
                        AAA_25 31 pagelallaGapgtGKttlaldla 54
                                   +ge+  +aG +g+GK+tlal +a
  gi|70606815|ref|YP_255685.1| 32 KEGEVLGVAGESGSGKSTLALTIA 55
                                  6899999*************9877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                        AAA_25 105 vldlagv.eslpLfakdrggtlltadvdaleaaieeveg..vrlvviDplsr 153
                                   + d++ v e + + +k+++ ++ ++++++l +++++  g  ++ v  Dp+++
  gi|70606815|ref|YP_255685.1|  71 FKDIDLVrELREVGDKGFNKKKNQRAFKELNNRLQAFRGskIAIVFQDPMTS 122
                                   5555555566666777777777888889999999988777777777777776 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.041
                        AAA_25  88 rRlravgealrddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvga 167
                                   rRl+ ++ +   ++ + +l+  +v  +  ++++  ++    +  ++++ ai  v++++l++ D  ++al+   +     ++
  gi|70606815|ref|YP_255685.1| 248 RRLKSTLIKEGYRKAVEILTMLNVpNPEKVVYMYPHELS-GGMRQRVAIAIAIVNNPELIIMDEPTSALDVTVQ-----AQ 322
                                   566665533344555666666666666666665544433.3444455556666678999999999999998888.....89 PP

                        AAA_25 168 lvealeriarrtgaavllvhH 188
                                   ++e +++++++++ +++++ H
  gi|70606815|ref|YP_255685.1| 323 VLELVRSLKKKYNSTFIFISH 343
                                   999999999999999999999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0013       1.3       7      26 ..      36      55 ..      30     106 .. 0.88
   2 ?   -1.3   0.0       2.4   2.4e+03      70      91 ..     159     187 ..     135     249 .. 0.66
   3 ?    4.2   0.0     0.047        47      70     128 ..     275     341 ..     224     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                        AAA_22  7 ilvvtGesGtGKTtllrrll 26
                                  +l v GesG+GK+tl+ +++
  gi|70606815|ref|YP_255685.1| 36 VLGVAGESGSGKSTLALTIA 55
                                  56689**********98765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                        AAA_22  70 a.......erlsseellealeqalrarav 91 
                                   +        ++++e ++e+l++ +++++ 
  gi|70606815|ref|YP_255685.1| 159 ElreiirlLEQNKETYVEKLNEFVKSKGL 187
                                   33334443344555555555555555444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.047
                        AAA_22  70 a.....erlsseell.ealeqalraravielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                   +     ++++++  + ++++ a+     +el+i DE    l+   ++++le +rsl +  +++ ++i++
  gi|70606815|ref|YP_255685.1| 275 EkvvymYPHELSGGMrQRVAIAIAIVNNPELIIMDEPTSaLDvtvQAQVLELVRSLKK--KYNSTFIFI 341
                                   455555333333333366666666666699******99999887669999999***99..999999987 PP

>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3     5e-05      0.05      43      88 ..     198     243 ..     167     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5e-05
                          OSCP  43 lsnpavsaeekkdlleelfkeklseavknflkllaenkRlalLpei 88 
                                    +   + +++k++l+ +l +ekls  v+nfl+ +ae +R+  ++ i
  gi|70606815|ref|YP_255685.1| 198 WERNDIHKAKKQKLILSLEGEKLSGFVRNFLENVAETNRVRNISRI 243
                                   566789999******************************9998876 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.4e-05     0.034       1      26 [.      36      61 ..      36     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                           PRK  1 vIgvagsSGaGkttvarklekifgre 26
                                  v+gvag+SG+Gk+t+a ++  ++  +
  gi|70606815|ref|YP_255685.1| 36 VLGVAGESGSGKSTLALTIAGVLPPN 61
                                  68*****************9998633 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0018       1.8      44     104 ..      31      94 ..      21     100 .. 0.72
   2 ?    3.6   0.0     0.049        48      98     151 ..     292     347 ..     280     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgv....eavraglsvlfvrvedLveelkrarrdgklaralk 104
                                   +++ e + + G sG GKs la +++     +a  +  +v+f  + dLv+el+   ++g  +++ +
  gi|70606815|ref|YP_255685.1|  31 VKEGEVLGVAGESGSGKSTLALTIAGvlppNAWIKKGEVRFKDI-DLVRELREVGDKGFNKKKNQ 94 
                                   5667788899***********99874222255556667888776.78888887777666655555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.049
                     IstB_IS21  98 klaralkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                   ++a a++ + +++l+i+D+   +l    qa+  +l + ++k+y+ + i i+ +l++
  gi|70606815|ref|YP_255685.1| 292 RVAIAIAIVNNPELIIMDEptSALDVTVQAQVLELVRSLKKKYNSTFIFISHDLSV 347
                                   566677888899******942244455566777788888999*9999999988765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0031       3.1      17      38 ..      32      53 ..      28      56 .. 0.89
   2 ?    3.9   0.1      0.03        30     138     163 ..     317     343 ..     289     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0031
                        ATPase 17 pegrvvlitGepGtGKtifalq 38
                                   eg+v  ++Ge+G+GK+++al+
  gi|70606815|ref|YP_255685.1| 32 KEGEVLGVAGESGSGKSTLALT 53
                                  5789999************975 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.03
                        ATPase 138 avaReilrqlvrvl.kklgvTailvse 163
                                    ++ +++ +lvr l kk++ T i++s 
  gi|70606815|ref|YP_255685.1| 317 VTVQAQVLELVRSLkKKYNSTFIFISH 343
                                   567899********9999*******96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00051      0.51      27      51 ..      39      63 ..      19      98 .. 0.85
   2 ?    0.4   0.0      0.35   3.5e+02     176     201 ..     276     301 ..     269     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                  Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplse 51
                                  ++G +GsGK+ la  ++++lpp   
  gi|70606815|ref|YP_255685.1| 39 VAGESGSGKSTLALTIAGVLPPNAW 63
                                  689******************9765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
                  Mg_chelatase 176 keierYlsklsgplldRidlqvevkk 201
                                   k +  Y + lsg +  R+ + +++ +
  gi|70606815|ref|YP_255685.1| 276 KVVYMYPHELSGGMRQRVAIAIAIVN 301
                                   55678999************999854 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003       0.3       5      29 ..      37      65 ..      33     118 .. 0.82
   2 ?   -1.8   0.0       2.1   2.1e+03     107     130 ..     319     343 ..     317     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                        AAA_24  5 iliyGpsgiGKTtlakel....gpkplfi 29
                                  + + G+sg+GK+tla+++    +p++ + 
  gi|70606815|ref|YP_255685.1| 37 LGVAGESGSGKSTLALTIagvlPPNAWIK 65
                                  6799*************987776666555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                        AAA_24 107 laeefrrllkklqelrk.nvifiah 130
                                   +++++ +l++ l++  + ++ifi+h
  gi|70606815|ref|YP_255685.1| 319 VQAQVLELVRSLKKKYNsTFIFISH 343
                                   677788888887766557*****99 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00031       0.3      24      50 ..      34      60 ..      21     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                        AAA_16 24 pelvllsGesGvGKsslvrellralek 50
                                  +e++ + GesG+GKs+l+ +++  l  
  gi|70606815|ref|YP_255685.1| 34 GEVLGVAGESGSGKSTLALTIAGVLPP 60
                                  377889***********9888755544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00081      0.81       5      46 ..      40      81 ..      37     118 .. 0.78
   2 ?   -0.8   0.1       1.4   1.4e+03      35      86 ..     154     212 ..     148     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00081
                                  E--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B- CS
                         AAA_5  5 vGppGtgKselaerlaaalnreveyvqltrdtteedlkgrre 46
                                   G++G+gKs+la  +a +l  + +++ +  + +  dl+ +++
  gi|70606815|ref|YP_255685.1| 40 AGESGSGKSTLALTIAGVLPPNAWIKKGEVRFKDIDLVRELR 81
                                  6******************99999988888777777777665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                                   T--HHHHH--B--.........--------.......G-SEEEEESGGG--HHHHHHHH CS
                         AAA_5  35 dtteedlkgrreikngttslvdsplvraar.......egeilvlDEveraesevlnsLl 86 
                                   + t+++l+  +++ +++++    +l + ++       e +il++ E + ++++  ++L+
  gi|70606815|ref|YP_255685.1| 154 KVTKDELREIIRLLEQNKETYVEKLNEFVKskgleglEDQILFIWERNDIHKAKKQKLI 212
                                   55666666666665333333333344444444455555556655555555555544444 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.43   4.3e+02     241     264 ..      30      54 ..      23      57 .. 0.85
   2 ?    8.6   0.1   0.00072      0.72     310     417 ..     272     364 ..     261     386 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.43
                                   EE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                    +++G v  ++G    GKsTL   +
  gi|70606815|ref|YP_255685.1|  30 DVKEGeVLGVAGESGSGKSTLALTI 54 
                                   578999999************7655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00072
                                   CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--E CS
                    ABC_ATPase 310 PegkdttkfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvs 390
                                   P+ ++   +  ++ SG + q ++i+ a+ ++ +l+++DE tsA    ++     + v          +++vr+l kk++ +
  gi|70606815|ref|YP_255685.1| 272 PNPEKVVYMYPHELSGGMRQRVAIAIAIVNNPELIIMDEPTSALDVTVQ-----AQV----------LELVRSLKKKYNST 337
                                   666666666667789****************************988773.....333..........45666666666666 PP

                                   EEEEESS-GCCTTT-SEEEEEETTEEE CS
                    ABC_ATPase 391 tilvvggsgdyldvAdtvilmeeykpk 417
                                    i ++  ++ + +++d++ +m + ++ 
  gi|70606815|ref|YP_255685.1| 338 FIFISHDLSVLYEISDRIAVMYAGRVV 364
                                   666666666666666666666555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0053       5.3       3      68 ..      39     121 ..      37     129 .. 0.58
   2 ?    1.3   0.6      0.42   4.2e+02      41      99 ..     284     333 ..     144     358 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                                   EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.........STTHHHHHHHHHHHHHHHTS..TSEEEE CS
                           AAA   3 lyGppGtGKTllakavakel.........gvefleisgsellsk.........yvgesekkirelfkeakeka..kpsilf 63 
                                   + G  G GK++la  +a  l         +v+f  i++ + l +           + + k++++ +++    +  k  i+f
  gi|70606815|ref|YP_255685.1|  39 VAGESGSGKSTLALTIAGVLppnawikkgEVRFKDIDLVRELREvgdkgfnkkKNQRAFKELNNRLQAF---RgsKIAIVF 116
                                   6799**************986666665544777777766666443443332222222223333333322...133356777 PP

                                   EETGG CS
                           AAA  64 iDEid 68 
                                    D + 
  gi|70606815|ref|YP_255685.1| 117 QDPMT 121
                                   66555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.42
                                   HHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                           AAA  41 esekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                   e +  +r+ ++ a +   +p  +++DE  +               v++q l+ +  +kkk
  gi|70606815|ref|YP_255685.1| 284 ELSGGMRQRVAIAIAIVnNPELIIMDEPTSALDVT----------VQAQVLELVRSLKKK 333
                                   33333333333322111235666666655554444..........566666666665554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2    0.0023       2.3       4      23 ..      39      58 ..      36     346 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0023
                                  EESSTTSSHHHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                          CbiA  4 astkGGvGKTtlaanLaral 23
                                  +++ +G+GK+tla+++a  l
  gi|70606815|ref|YP_255685.1| 39 VAGESGSGKSTLALTIAGVL 58
                                  6799************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 2871.00
//
Query:       gi|70606816|ref|YP_255686.1|  [L=292]
Description: peptide transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-30  104.3  14.2    6.4e-30  104.3  14.2    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
    5.4e-07   29.5   0.2    5.4e-07   29.5   0.2    3.3  4  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
       0.31   10.7   2.4       0.89    9.3   0.9    2.5  3  LRR_12        Leucine-rich repeat


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.059   3.5e+02      26      43 ..      14      31 ..       4     104 .. 0.76
   2 !  104.3  14.2   1.1e-33   6.4e-30       1     184 [.     106     289 ..     106     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.059
                  BPD_transp_1 26 vllslPsfvlaillvlvf 43
                                  +++s P+ v++++++l+ 
  gi|70606816|ref|YP_255686.1| 14 IFFSNPTAVIGLIIFLAY 31
                                  677778888888877554 PP

  == domain 2  score: 104.3 bits;  conditional E-value: 1.1e-33
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslp 80 
                                   g ++Gi+a+ +r++++d++l++++++++++P++vla+ +        +lg +  +  i+l+++ ++ y+r+ r++ l++  
  gi|70606816|ref|YP_255686.1| 106 GSVIGIIAG-YRGGIIDDILMRITDIFFAIPYLVLALAIG------FVLGRTTESmSIALIIVWWPLYARYARAQTLSIKR 179
                                   689******.****************************99......7899888887************************* PP

                  BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgydyseis.. 154
                                   + ++ aa++  ++  +i++k+vlPn+lppi+ ++ l +g+++  +++l+f+g  +      lg+l+   +++ ++   +  
  gi|70606816|ref|YP_255686.1| 180 MPFIDAAKVSNVGSLKIMFKHVLPNVLPPIFVQISLDLGSIMVIFSVLSFIGLITNpnlpeLGYLTSLGLQYIQT---Apw 257
                                   ****************************************************55555555555555555555444...255 PP

                  BPD_transp_1 155 ..nggvlalviavlllnlvadilqrlldprvr 184
                                     +++ la++i+ l++nl  d l +lldpr r
  gi|70606816|ref|YP_255686.1| 258 tvIFPGLAITIFALAVNLMGDGLRDLLDPRRR 289
                                   59****************************87 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   9.1e-11   5.4e-07       1      36 [.       6      41 ..       6      70 .. 0.73
   2 ?   -1.7   1.5      0.51   3.1e+03      15      29 ..      97     111 ..      88     145 .. 0.67
   3 ?   -2.2   0.0       0.7   4.2e+03      26      40 ..     156     170 ..     154     180 .. 0.73
   4 ?   -1.3   0.1      0.38   2.2e+03      24      35 ..     222     233 ..     218     255 .. 0.57

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 9.1e-11
                        OppC_N  1 slwqdawrrFkrNklAvvglvilllllliaifaPli 36
                                  s+++  ++ F++N++Av+gl+i+l+ ++ ai+ ++ 
  gi|70606816|ref|YP_255686.1|  6 SQLKLSLKIFFSNPTAVIGLIIFLAYVIDAIIVEVS 41
                                  799999**************************6544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.51
                        OppC_N  15 lAvvglvilllllli 29 
                                   + v+g +i+  ++ i
  gi|70606816|ref|YP_255686.1|  97 VIVIGGAIIGSVIGI 111
                                   557777777765554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.7
                        OppC_N  26 llliaifaPliaPyd 40 
                                   ++li ++ Pl a y 
  gi|70606816|ref|YP_255686.1| 156 IALIIVWWPLYARYA 170
                                   677888888888775 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.38
                        OppC_N  24 llllliaifaPl 35 
                                   +++ ++++++  
  gi|70606816|ref|YP_255686.1| 222 VIFSVLSFIGLI 233
                                   223333444322 PP

>> LRR_12  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.9   0.00015      0.89       5      12 ..      52      59 ..      52      60 .. 0.91
   2 ?   -2.2   0.0      0.57   3.4e+03       8      15 ..     180     187 ..     173     189 .. 0.72
   3 ?   -3.2   0.0       1.1   6.8e+03       1       7 [.     244     250 ..     244     256 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                        LRR_12  5 hLqmNFIn 12
                                  +LqmNFIn
  gi|70606816|ref|YP_255686.1| 52 QLQMNFIN 59
                                  59*****9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.57
                        LRR_12   8 mNFInqAq 15 
                                   m FI  A+
  gi|70606816|ref|YP_255686.1| 180 MPFIDAAK 187
                                   88999987 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                        LRR_12   1 LqtLhLq 7  
                                   L++L Lq
  gi|70606816|ref|YP_255686.1| 244 LTSLGLQ 250
                                   5666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1941.95
//
Query:       gi|70606817|ref|YP_255687.1|  [L=351]
Description: peptide transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-41  140.1  16.6    6.6e-41  140.1  16.6    2.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   2.4     0.083   1.5e+03      43      64 ..      80     119 ..      66     121 .. 0.46
   2 !  140.1  16.6   3.7e-45   6.6e-41       1     185 []     122     351 .]     122     351 .] 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.083
                  BPD_transp_1  43 f..................vilsilghlilpviillllsa 64 
                                   f                  +i   l ++il  ii+++l +
  gi|70606817|ref|YP_255687.1|  80 FsgdlgytntpiysgpvsgAIALFLPNTILLTIIASILIW 119
                                   2555554444444444444444445555555555555555 PP

  == domain 2  score: 140.1 bits;  conditional E-value: 3.7e-45
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...................................... 43 
                                   g+++G+ +a++r + +d+ +r+++++l+s+P++++a+ll+lvf                                      
  gi|70606817|ref|YP_255687.1| 122 GVPIGVRSAVKRDSAFDQSVRVVSFALYSMPIYLVAFLLILVFgvylkilpfafslsptlasnlswyvngvsypthiviid 202
                                   89******************************************************************************* PP

                  BPD_transp_1  44 ........vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglil 116
                                           ++ +++ h+ilp+++l+l ++a+++r++r+++l++l++d+v++ara+G++++ ++  ++ +nal+p++t+ ++
  gi|70606817|ref|YP_255687.1| 203 alihgnltAFANAILHAILPALTLALSTIAGIMRILRASMLEVLDQDYVRLARAKGVPEKVVINLHARRNALIPVLTLYGY 283
                                   ********************************************************************************* PP

                  BPD_transp_1 117 afggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                   ++++llggav++e ++s+pG+g+++++a+l++d+  i+ +++l+++i++++ +l++di+++l+dpr+r+
  gi|70606817|ref|YP_255687.1| 284 TVASLLGGAVVIEDIFSYPGMGYWTTQALLNNDVGGIM-ASTLIFGIVFVIASLLLDIIYALIDPRIRY 351
                                   **************************************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2552.28
//
Query:       gi|70606818|ref|YP_255688.1|  [L=867]
Description: hypothetical protein Saci_1038 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-54  185.2  10.4    1.7e-54  185.2  10.4    2.1  2  SBP_bac_5     Bacterial extracellular solute-binding proteins
    7.2e-09   35.4   6.7    3.9e-05   23.4   0.9    3.4  2  PKD           PKD domain
  ------ inclusion threshold ------
      0.026   14.9   0.9      0.065   13.7   0.9    1.6  1  COX4_pro      Prokaryotic Cytochrome C oxidase subunit IV
      0.043   14.0   0.0       0.31   11.2   0.0    2.2  2  U-box         U-box domain
       0.12   12.0   0.3        0.2   11.2   0.3    1.3  1  CD34_antigen  CD34/Podocalyxin family
        2.6    6.3   5.7        1.3    7.4   2.3    1.9  2  DUF515        Protein of unknown function (DUF515)
        3.8    8.5   5.8        3.1    8.8   3.6    2.1  2  Pilin_N       Archaeal Type IV pilin, N-terminal


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.2  10.4   6.8e-58   1.7e-54      12     375 ..     328     762 ..     312     764 .. 0.86
   2 ?   -0.9   0.4      0.25   6.3e+02     278     327 ..     773     818 ..     771     844 .. 0.82

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 6.8e-58
                                   EEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC.......................TCTEEE CS
                     SBP_bac_5  12 evsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee.......................dqdikk 69 
                                    ++++ +tytfk+R g++F+DG+p+tA Dv++s+ r+l   ++ + + ++                         +q+i +
  gi|70606818|ref|YP_255688.1| 328 GINTNYTTYTFKIRSGLYFADGSPITAYDVWYSMVRALLTVGGTPGTGTWILaqylipnstagvpvvsssdpnqgFQEIMN 408
                                   5899*****************************999999988888888776688*********************666666 PP

                                   EEEEE..TTEEEEEESSETTTTTTHCHHHHHHHGC........................CHTCTCTTTTTGTTTSE-BSSS CS
                     SBP_bac_5  70 veavd..dytvrftlkkpnalfltllaavpasiak........................kaaekeddkdkdtnekpvgtGP 124
                                   +++ +  + tv+f+l kp++++l+++a   +  a                         +++++e+ ++++  ++p  +GP
  gi|70606818|ref|YP_255688.1| 409 AVTYNntTDTVTFHLYKPTPPNLFFTAIADPLTAGilsakwlesvgdgitftpqgfltyENTANEGHYNTQVENDPLASGP 489
                                   6665511568********99888888887777777889999******************9999****************** PP

                                   EEEEEEETTTEEEEEE-TTSTTTSCS....SSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE..EE CS
                     SBP_bac_5 125 YklkefkpgqkivlernpdYwgggkp....kldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv..ly 199
                                   Y++k+++pgq++vl+ np++  +g p      d ++++ ++d++++ + + sG++d+v+++p+++ ++lk   +  +  +y
  gi|70606818|ref|YP_255688.1| 490 YMIKQYVPGQYVVLTPNPYF--PGVPgipkPNDTVVIEWVKDPQTAYNLFTSGQADIVTGLPTNYFASLKPLVAQGQasIY 568
                                   *******************9..6666666789********9999999999******************977777777889* PP

                                   EEEEEEEEEEEETTT................STGGGSHHHHHHHHHHS-HHHHHHHC......TTTSSEEESSSSTTTSTT CS
                     SBP_bac_5 200 espgggvtylafNtk................kppfddkrvRqAlsyAiDreeivkav......legyatpansllppsspg 258
                                   ++p+++ ++++fN +                 + f++  vR+A++yA++++ +++++          ++p ++++  ++p+
  gi|70606818|ref|YP_255688.1| 569 QFPTLSEFFFVFNLNistsglkqlgpnynipPNYFANLYVREAFAYAFNYTNYIENIlgnakyGFDFGEPYAGAIIKGLPY 649
                                   *****************************99889***********************333332234567777777777777 PP

                                   CCSCHCCCSHH....SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE.C CS
                     SBP_bac_5 259 adeeykpayka....ydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiGikvevktv.d 334
                                   + ++ +    +    ++++ Ak+lL + G  +    ++      + ++++sg++++ a++++++q++++i  +++++++ +
  gi|70606818|ref|YP_255688.1| 650 YTPPSEF---TgvptFNLTYAKQLLIKSGVYNES--VY------FPIIVPSGDTVDYAAVQMFAQTMQQIDPNIKIEPLyE 719
                                   7665554...15678**********999988875..34......***************************9999999955 PP

                                   HH.......HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCT CS
                     SBP_bac_5 335 wa.......atylervkdgdfdmillgwgadypdpdnflnpflsssga 375
                                   +                ++ ++m+ lgw adyp p++f+n++++++g 
  gi|70606818|ref|YP_255688.1| 720 PFstiiglqV-----PGQNPMPMYYLGWIADYPYPSDFVNAMYKENGT 762
                                   4478665322.....6699***********************998875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.25
                                   HHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEE CS
                     SBP_bac_5 278 lLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiGik 327
                                   +L + Gy++  + ++   +++ +l+++++s+++   a+l+ +q ++  i+
  gi|70606818|ref|YP_255688.1| 773 YLQQLGYTNEAQ-MY---QQLNNLIIQADSATNATQAALLYKQVEQQAIN 818
                                   789999999864.33...78999999999999998888888888875555 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.5   2.5e-05     0.064      15      58 ..      63     108 ..      49     111 .. 0.80
   2 !   23.4   0.9   1.5e-08   3.9e-05       6      64 ..     159     231 ..     155     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                   EEEEES.-SS-SEEEEE--SS...--EEEEETTEEEEEE-SSEEEEE CS
                           PKD  15 aftaavpdganvtysWdfgdg...svvqvlseptvthtYlspGeYeV 58 
                                   +ft +  +  n+  + +fgdg     ++++++ ++++tY  pG+Y+V
  gi|70606818|ref|YP_255688.1|  63 NFTVYN-TQPNAILTVNFGDGvikNFTATGTSTSFSYTYQYPGHYLV 108
                                   555555.5556666669*******9********************98 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.5e-08
                                   S--BSSEEEEEEEES....-SS-S...EEEEE--SS.........--EEEEETTEEEEEE-SSEEEEEEEEEE- CS
                           PKD   6 tvlvpgatvaftaav...pdganv...tysWdfgdg.........svvqvlseptvthtYlspGeYeVtvtasn 64 
                                    ++ +g+t+ f a+    p+g+n    +y+W+fg+g         s+ + +++p v+ tY+spG Y+V++t++ 
  gi|70606818|ref|YP_255688.1| 159 PFFRAGETAYFYAGFlqpPTGQNMrieSYTWNFGNGqtqtvkannSTLLPTVNP-VNTTYSSPGIYVVKLTLTT 231
                                   578889999999999988777776333688*******99998875555555554.899*************985 PP

>> COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   2.5e-05     0.065      26      69 ..      14      57 ..       5      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                      COX4_pro 26 laiiiilvlalvKavlillyFMHLkeekkglrllaliflvflil 69
                                   ++i+++v+ ++ ++ +++yF+ +++++++++ +al+++ f+il
  gi|70606818|ref|YP_255688.1| 14 RTVIAVIVVVVIIIAAVAAYFLLMNRSSSSIQAVALAPTSFVIL 57
                                  4566777799999**************99************996 PP

>> U-box  U-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.63   1.6e+03      20      49 ..     460     490 ..     458     499 .. 0.82
   2 ?   11.2   0.0   0.00012      0.31      15      43 ..     682     710 ..     676     719 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.63
                                   ETTT.EEEEHHHHHHHHTT.SSB-TTT-SB- CS
                         U-box  20 lpsg.vvvdrstiekhllsrdktdPftrepl 49 
                                   +p+g  +++ ++ e h + + ++dP+   p 
  gi|70606818|ref|YP_255688.1| 460 TPQGfLTYENTANEGHYNTQVENDPLASGPY 490
                                   799999*******************976655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                   SSEEEETTTEEEEHHHHHHHHTT.SSB-T CS
                         U-box  15 kdPvilpsgvvvdrstiekhllsrdktdP 43 
                                    +P+i+psg +vd ++++ +++  ++ dP
  gi|70606818|ref|YP_255688.1| 682 YFPIIVPSGDTVDYAAVQMFAQTMQQIDP 710
                                   58**************************9 PP

>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   7.7e-05       0.2      98     137 ..       7      43 ..       1      67 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
                  CD34_antigen  98 rseqdyskkllialvtsglllaiLlvagyYgclhrRlsks 137
                                   rs++  s+ ++ia+++  ++++i  va+y+  l++R s s
  gi|70606818|ref|YP_255688.1|   7 RSRKAISR-TVIAVIV-VVVIIIAAVAAYF-LLMNRSSSS 43 
                                   34455555.6666666.2666666777777.99***9986 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0005       1.3      29      60 ..      12      42 ..       2      48 .. 0.79
   2 ?   -0.6   0.1      0.13   3.4e+02     167     204 ..     786     825 ..     773     836 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0005
                        DUF515 29 rkrliiGasvlvvivillvfaiYsyienkele 60
                                    r +i a+++vv++i+ ++a+Y+ + n+  +
  gi|70606818|ref|YP_255688.1| 12 ISRTVI-AVIVVVVIIIAAVAAYFLLMNRSSS 42
                                  356789.999**************99998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.13
                        DUF515 167 vaeleeLlkqvdsaktiee..vleikvdkyllsldkkyYl 204
                                    ++l++L+ q dsa++  +  +l ++v++    l+ ++Yl
  gi|70606818|ref|YP_255688.1| 786 YQQLNNLIIQADSATNATQaaLLYKQVEQQAINLYMYIYL 825
                                   67899*******9997665337999***999999999994 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.6    0.0012       3.1       6      41 ..      16      49 ..      10      85 .. 0.62
   2 ?   -3.9   0.0         7   1.8e+04       3      12 ..     295     304 ..     295     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                       Pilin_N  6 ViGviLmvaitvIlaAviaafvlglasneekapqas 41
                                  Vi v  +v++++I+aAv a f l   s ++ ++ a 
  gi|70606818|ref|YP_255688.1| 16 VIAV--IVVVVIIIAAVAAYFLLMNRSSSSIQAVAL 49
                                  4443..466677777777777766655555555444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                       Pilin_N   3 VSpViGviLm 12 
                                   +S +iG +L+
  gi|70606818|ref|YP_255688.1| 295 ISNIIGTLLI 304
                                   699****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 5367.77
//
Query:       gi|70606819|ref|YP_255689.1|  [L=281]
Description: hypothetical protein Saci_1039 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.6   0.0      0.086   12.6   0.0    1.5  1  SKA2      Spindle and kinetochore-associated protein 2


Domain annotation for each model (and alignments):
>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.8e-06     0.086       3      60 ..     215     274 ..     214     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-06
                          SKA2   3 avdklealFqkaesdLd...yvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeq 60 
                                   ++++l++l+ ka+sdL    +v+ +L++++ q+ + n+ ++   ++++++v + +q+L+++
  gi|70606819|ref|YP_255689.1| 215 SIEGLVNLLGKAKSDLVlpgVVEGKLNQDVFQIRSVNE-ELSLPVKSVEEVSNFVQKLRKE 274
                                   589*************98889****************5.9999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1786.43
//
Query:       gi|70606820|ref|YP_255690.1|  [L=103]
Description: hypothetical protein Saci_1040 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.06   12.1   0.0       0.06   12.1   0.0    1.1  1  Neur          Neuraminidase
      0.086   12.9   0.2       0.19   11.8   0.0    1.6  2  Acyltransf_C  Acyltransferase C-terminus
       0.24   11.0   2.0         35    4.1   0.3    3.2  3  EF-hand_5     EF hand


Domain annotation for each model (and alignments):
>> Neur  Neuraminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     1e-05      0.06     237     286 ..       4      54 ..       1      92 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1e-05
                                   ----EEEEEE.EEEEEEEE-SSSSSSEEEEEEEEESS-TTT--S--EEEEE CS
                          Neur 237 vkGffvrqrl.kigvwvgrtisktsrsGlelivkkdgdtwtekdalslrvv 286
                                   +kG   r r    ++++     +  r+G+e+i+k+  d++ ek++l +++ 
  gi|70606820|ref|YP_255690.1|   4 IKGLHERVRSiLDDIYIESHEVRGVRNGFEIIQKYSRDNYVEKEELYINKK 54 
                                   7776555443377899999999**********************9766554 PP

>> Acyltransf_C  Acyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.2e-05      0.19      11      44 ..      17      50 ..      10      55 .. 0.93
   2 ?   -3.0   0.0       1.4   8.2e+03      14      25 ..      80      91 ..      74      96 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                  Acyltransf_C 11 hiyvrripleevPedeeelaeWlhelfeeKDkll 44
                                  +iy++ +++  v +  e ++++ ++ ++eK++l+
  gi|70606820|ref|YP_255690.1| 17 DIYIESHEVRGVRNGFEIIQKYSRDNYVEKEELY 50
                                  69*************88***************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                  Acyltransf_C 14 vrripleevPed 25
                                   r+i+ ee+ ++
  gi|70606820|ref|YP_255690.1| 80 ARKISSEELEKT 91
                                  566666666555 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.012        72      12      22 ..      40      50 ..      39      51 .. 0.91
   2 ?    1.3   0.0     0.044   2.6e+02      12      17 ..      74      79 ..      74      81 .. 0.83
   3 ?    4.1   0.3    0.0059        35      15      23 ..      82      90 ..      82      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.012
                                  -SSCE-HHHHH CS
                     EF-hand_5 12 gDGkIskeELk 22
                                  +D ++ keEL+
  gi|70606820|ref|YP_255690.1| 40 RDNYVEKEELY 50
                                  7999******7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.044
                                  -SSCE- CS
                     EF-hand_5 12 gDGkIs 17
                                  +DGkI 
  gi|70606820|ref|YP_255690.1| 74 KDGKIE 79
                                  7****7 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0059
                                  CE-HHHHHH CS
                     EF-hand_5 15 kIskeELkt 23
                                  kIs eEL++
  gi|70606820|ref|YP_255690.1| 82 KISSEELEK 90
                                  8******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 787.35
//
Query:       gi|70606821|ref|YP_255691.1|  [L=633]
Description: hypothetical protein Saci_1041 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-34  119.3   0.0    2.6e-34  118.8   0.0    1.2  1  Pkinase      Protein kinase domain
    4.3e-17   62.2   0.0      1e-16   61.0   0.0    1.6  1  Pkinase_Tyr  Protein tyrosine kinase
    0.00088   18.7   0.0     0.0014   18.0   0.0    1.2  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0074   15.9   0.1      0.031   13.9   0.0    1.9  2  FTA2         Kinetochore Sim4 complex subunit FTA2
     0.0075   16.6   0.1       0.99    9.8   0.0    3.3  2  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.097   12.0   0.0    1.8  1  Kinase-like  Kinase-like


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   0.0   8.8e-38   2.6e-34       1     260 [.     333     630 ..     333     632 .. 0.83

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 8.8e-38
                                   EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEE........... CS
                       Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfee........... 69 
                                   y+++  +G+G++G V+ka   +++k +A+K+++ e+ +k++ +++++E + lk+l+  ++iv +y+++ +           
  gi|70606821|ref|YP_255691.1| 333 YKVIDVVGQGGNGYVVKAE--RESKYYAIKILSPENLSKSSFDTLFKESENLKELSkNDKIVSIYGIYADsnyinsiikgn 411
                                   678899************9..799****************99**************99**********************8 PP

                                   .....SSEEEEEEE--TTEBHHHHHH..HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEET.......... CS
                       Pkinase  70 .....kdelylvleyveggeladlle..rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLide.......... 133
                                        +    +++e+++gg++adl++  r++ + +  +k i++++  +l+ylH++g +H D+Kp Ni+++           
  gi|70606821|ref|YP_255691.1| 412 aeayfNYPPAIIMEFMDGGTIADLINeiRSSPYFQYIVKAIIREVGLALKYLHKRGYVHLDVKPRNIFLSVippkdeklll 492
                                   7655544555****************7777779999**********************************66788777777 PP

                                   .....TTEEEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHH....TTSCBSHHHHHHHHHHHHHHHHHSS-.STTTSSHHH CS
                       Pkinase 134 .....kgelKitDFGlakelessskltsfvgtseYlAPEvl....keneyskkvDvWslGvilyelltgkp.pfsgekgke 204
                                        +g +K++D+G a ++ ++       +t+ Y +PE +    ++++ ++++D ++lGv+ y lltg+  p   +  + 
  gi|70606821|ref|YP_255691.1| 493 dqissRGIIKLGDLGSAVRVGEKI----TQATPAYSPPEQIeaviTGKGAQPSMDNYALGVTAYYLLTGNVsPIT-KYVER 568
                                   76655555************9976....789********99888888**********************862343.23222 PP

                                   HHHHHHHTHHHHHHHCTSHH...HHHTTS........-HHHHHHHHHHT-SSGCCSTTHHHHHT CS
                       Pkinase 205 kvekeldqlekilkilgetkeklpeasei........seeakdllkkllkkdpkkRltaeellq 260
                                    v   l++  k+ + l+e +++ +  + +         +e+ ++++  +  dp+kRlt ++++q
  gi|70606821|ref|YP_255691.1| 569 AVDLYLQN--KFNDALEEIDNSKKVLEGFkpslpintLPELNRVIQGTILSDPTKRLTSDDIVQ 630
                                   22222222..34444443333333333335555666699*******************999987 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   3.4e-20     1e-16       4     259 .]     336     632 ..     333     632 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.4e-20
                                   EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEE.STTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSS....... CS
                   Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtl.keeateeekeelleeakimkkl.khpnivkllgvctkeep....... 75 
                                    + +G+G  G Vv+++ +      +   a+K+l  e+ ++++ + l++e + +k+l k+++iv+++g++ +++        
  gi|70606821|ref|YP_255691.1| 336 IDVVGQGGNGYVVKAERE------SKYYAIKILsPENLSKSSFDTLFKESENLKELsKNDKIVSIYGIYADSNYinsiikg 410
                                   6789***********999......7788*****44667777899************99***********955555566666 PP

                                   .........EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE......... CS
                   Pkinase_Tyr  76 .........llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse......... 138
                                              i++e+++gG++ + +++ ++++     +  ++ +v  +++yL+++ +vH d+  rN++ls          
  gi|70606821|ref|YP_255691.1| 411 naeayfnypPAIIMEFMDGGTIADLINEIRSSPYFQYIVKAIIREVGLALKYLHKRGYVHLDVKPRNIFLSVippkdekll 491
                                   77788888899*****************9555555555666889***************************9999999988 PP

                                   ......TTEEEE-STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSE....EEHHHHHHHHHHHHHHHHTTSSGT.... CS
                   Pkinase_Tyr 139 ......nkvvkisDfGLardiekddeyvkkeeaklpvkWmapEslkekk....ftsksDvWsfGvllwEiftlgesp.... 205
                                         + ++k++D G a ++        ++ ++    + +pE +++       + + D ++ Gv+ + ++t   sp    
  gi|70606821|ref|YP_255691.1| 492 ldqissRGIIKLGDLGSAVRV-------GEKITQATPAYSPPEQIEAVItgkgAQPSMDNYALGVTAYYLLTGNVSPitky 565
                                   888887788888888888777.......344455566777777777666555578888**************888889999 PP

                                   .............TTTSHHHHHHHHHHTTEES-BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHHHH CS
                   Pkinase_Tyr 206 .............ypglkneevleklkegkrlekpekcpeelyelmkkcweedpeeRptfselvekl 259
                                                   l++ +  +k+ eg + + p ++ +el+++++    +dp++R t  ++v+ l
  gi|70606821|ref|YP_255691.1| 566 veravdlylqnkfNDALEEIDNSKKVLEGFKPSLPINTLPELNRVIQGTILSDPTKRLTSDDIVQIL 632
                                   9999999888884334477778889999999999***********************9999999865 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.6e-07    0.0014      88     153 ..     416     482 ..     368     494 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.6e-07
                           Kdo  88 leyrAlllterlegaqdLedllakwae..laeelkrallkavgrliaklhragvnHadlyaknillqq 153
                                   ++y  ++++e ++g   ++dl+++ ++  + +   +a++++vg + + lh++g  H d+ ++ni+l  
  gi|70606821|ref|YP_255691.1| 416 FNYPPAIIMEFMDGGT-IADLINEIRSspYFQYIVKAIIREVGLALKYLHKRGYVHLDVKPRNIFLSV 482
                                   4477889999999853.55555555555699999*******************************986 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     1e-05     0.031       7      63 ..     311     377 ..     305     405 .. 0.67
   2 ?   -1.0   0.0      0.39   1.2e+03     177     203 ..     452     478 ..     437     483 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                          FTA2   7 eidgPkLkpFdfsae..kdi...efleyLgkglhsiVlkvkirgkeYALKlFrfleaeele.....e 63 
                                   +++ P L+  d++    k+i   + ++++g+g +++V+k++ + k YA+K+    + ++ +     +
  gi|70606821|ref|YP_255691.1| 311 KVSLPSLNNWDPKIWinKEIygyKVIDVVGQGGNGYVVKAERESKYYAIKILSPENLSKSSfdtlfK 377
                                   55666666666666554443222678888*********************98776555544554442 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                          FTA2 177 qlpkllrdlkklhklgIvvrDlkeeny 203
                                   +++++   lk lhk g v+ D+k++n+
  gi|70606821|ref|YP_255691.1| 452 IIREVGLALKYLHKRGYVHLDVKPRNI 478
                                   556666678999999999999999997 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00033      0.99       8      26 ..     196     212 ..     193     249 .. 0.77
   2 ?    2.5   0.0     0.066     2e+02      10      24 ..     287     299 ..     286     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                                   EEESEEETTEEEEEECTCT CS
                   GTP_EFTU_D2   8 vysGtlkkGdevrilgndt 26 
                                   v+sG+++kG++v+i  + +
  gi|70606821|ref|YP_255691.1| 196 VVSGKIRKGQTVVI--KFK 212
                                   89************..543 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.066
                                   ESEEETTEEEEEECT CS
                   GTP_EFTU_D2  10 sGtlkkGdevrilgn 24 
                                   sG++k+G +v i  n
  gi|70606821|ref|YP_255691.1| 287 SGIVKRGSTVTI--N 299
                                   8*********99..4 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05     0.097     158     254 ..     461     566 ..     427     586 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                   Kinase-like 158 anLqakglvhgkftvdnlll............d...ekgglmlggftaLvragtkvvlsevekgfaPpEllgsrggytrkn 223
                                    +L+++g vh +++++n++l            d    +g ++lg++++ vr+g+k    +   +++PpE + +  +    +
  gi|70606821|ref|YP_255691.1| 461 KYLHKRGYVHLDVKPRNIFLsvippkdeklllDqisSRGIIKLGDLGSAVRVGEKIT--QATPAYSPPEQIEAVIT---GK 536
                                   5677777777777777776533333222222222225899***************99..77889*****9998555...23 PP

                   Kinase-like 224 ktkmthkldaWqlGlviyriwc.lklPltlat 254
                                         ++d ++lG+++y++    + P+t+  
  gi|70606821|ref|YP_255691.1| 537 G--AQPSMDNYALGVTAYYLLTgNVSPITKYV 566
                                   3..34579999999999986541455666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4391.44
//
Query:       gi|70606823|ref|YP_255692.1|  [L=367]
Description: NOL1/NOP2/sun family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-34  117.4   0.0      1e-33  116.7   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.6e-09   37.7   0.0    4.9e-09   36.2   0.0    1.8  2  Methyltransf_31  Methyltransferase domain
    3.5e-08   33.4   0.0    5.6e-08   32.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.4e-07   31.4   0.1    1.2e-05   26.0   0.0    2.9  3  Methyltransf_25  Methyltransferase domain
    6.8e-05   22.4   0.5    0.00086   18.8   0.1    2.1  2  Methyltransf_4   Putative methyltransferase
     0.0004   19.8   0.1    0.00091   18.6   0.1    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00046   20.8   0.0     0.0094   16.6   0.0    2.7  3  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.073   13.2   0.0    2.3  1  FtsJ             FtsJ-like methyltransferase
      0.019   14.8   0.0      0.035   13.9   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      0.034   13.4   0.0      0.063   12.6   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
       0.11   11.7   0.0       0.18   10.9   0.0    1.3  1  Fibrillarin      Fibrillarin
       0.11   12.1   0.0       0.18   11.3   0.0    1.3  1  MTS              Methyltransferase small domain
       0.11   13.0   0.0       0.22   12.0   0.0    1.6  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   7.4e-37     1e-33       2     199 ..     168     355 ..     167     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 7.4e-37
                                   HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
               Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                   ++L+p+++e+il++ +aPG KT++i ++ +nk+ v+ +d++++R+k  ++ +++Lgv+n+ ++  D+++++ +      D+
  gi|70606823|ref|YP_255692.1| 168 VFLDPKPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSKRIKIQQDLMNKLGVENVELVVSDGSNVPITK----ADK 244
                                   68*******************************************************************96554....59* PP

                                   EEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEEE CS
               Methyltr_RsmB-F  83 iLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelv 163
                                   +L+DaPC+  g+   dp++ lr ++kd+++l++lq+ +l ++ +  k     v+sTCs+ +eE e+  e+       + ++
  gi|70606823|ref|YP_255692.1| 245 VLIDAPCTNSGTFVADPSIFLRITKKDLMRLSRLQRSILRSIRK-FK--VPTVFSTCSLFPEEGEKIAEKYEAFLTPISID 322
                                   ***************************************99754.44..4579***********99877665555455555 PP

                                   SSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEE CS
               Methyltr_RsmB-F 164 etelsepkglklgeeagtlrllPhtenkdgffiakl 199
                                   +t   + k++k+ +    +r++P+ + ++gffiak+
  gi|70606823|ref|YP_255692.1| 323 TT-NYGYKRSKVWKR--VVRFYPNIHGTEGFFIAKF 355
                                   55.334355555555..59****************8 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.1     3e+03      71     101 ..      21      49 ..       5      67 .. 0.77
   2 !   36.2   0.0   3.5e-12   4.9e-09       2      95 ..     173     266 ..     172     325 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
               Methyltransf_31  71 edekfDlilsnevlnaladpdkileeiervl 101
                                    ++ fD+ +    ln+  +  k +++  rvl
  gi|70606823|ref|YP_255692.1|  21 PEKAFDIAVK--SLNHKVNRRKLFNKFLRVL 49 
                                   3478999777..4888888888888888887 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3.5e-12
               Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                   + + ++l++GC+ G +t  + +  + k+ v+GiDis + i+  +    klg++nve+ ++d  + +  ++  k D +l ++
  gi|70606823|ref|YP_255692.1| 173 KPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSKRIKIQQDLMNKLGVENVELVVSDGSNVP--IT--KADKVLIDA 249
                                   57899****************98899999***********************************99..55..799999997 PP

               Methyltransf_31  83 vl....naladpdkile 95 
                                   ++      +adp  +l+
  gi|70606823|ref|YP_255692.1| 250 PCtnsgTFVADPSIFLR 266
                                   77666433333333333 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   4.1e-11   5.6e-08      67     134 ..     168     235 ..     142     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.1e-11
                                   HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                          PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                    +l+ k+ +++Le+G+  G +t ++ ++ ++k +v++i+ + + ++  +  ++kl++env +vv+DG 
  gi|70606823|ref|YP_255692.1| 168 VFLDPKPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSKRIKIQQDLMNKLGVENVELVVSDGS 235
                                   46677899***********************************************************7 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.43   5.9e+02      60      93 ..      20      49 ..       9      51 .. 0.78
   2 ?   -0.7   0.0       1.7   2.3e+03      43      71 ..     101     129 ..      90     144 .. 0.71
   3 !   26.0   0.0   8.4e-09   1.2e-05       1      62 [.     178     241 ..     178     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.43
                                  SSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
               Methyltransf_25 60 fedgsfDlvvssgalhhlsdedlekalkeiarvL 93
                                   +++ fD+ v s  l+h  + +++k+++++ rvL
  gi|70606823|ref|YP_255692.1| 20 SPEKAFDIAVKS--LNH--KVNRRKLFNKFLRVL 49
                                  577899999996..667..335889*****9998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                   HTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
               Methyltransf_25  43 eeglnvefvqgdaedlpfedgsfDlvvss 71 
                                   ++ ++v+ +++d+ed+  + ++  +v+ +
  gi|70606823|ref|YP_255692.1| 101 QQWIRVNTLKADVEDVRRKLERKGVVLQR 129
                                   33348999999999988777766666654 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 8.4e-09
                                   EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfed 62 
                                   +L++Gc +G  t  +++   +k+ v+g+Dis++ +++ +  +++ g+ nve+v+ d +++p  +
  gi|70606823|ref|YP_255692.1| 178 ILEIGCAPGMKTSLIQQITnNKSLVIGIDISSKRIKIQQDLMNKLGVeNVELVVSDGSNVPITK 241
                                   8*********99999998855999*******************9999************99654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.11   1.5e+02      86     144 ..      98     156 ..      94     168 .. 0.74
   2 !   18.8   0.1   6.3e-07   0.00086       4      61 ..     177     235 ..     174     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                   SGGGGGGSTTS.HHHHHHHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEEESSCCCS CS
                Methyltransf_4  86 KkrhhKrRllq.pellkelarvLkkgGvlelaTDveeyaeemlkvleeeplferlskeee 144
                                   K+r++  R+ + ++ ++++ r+L+ +Gv+ l+ D +e+  +++k  ++  ++e  ++ e 
  gi|70606823|ref|YP_255692.1|  98 KTRQQWIRVNTlKADVEDVRRKLERKGVV-LQRDSFEFLFRVIKAKSRISDLEEFKNGEI 156
                                   56666666643266799999*******86.688999999999999988888887776655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.3e-07
                                   EEEEET-TTSHHHHHHHH.HSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CC CS
                Methyltransf_4   4 vvleiGcGkGeflvalAk.knPdknflGiEirvkvvakvlkkiealelkNlrilrgdal 61 
                                    +leiGc+ G  ++ + +  n + +++Gi+i++k+++   + +++l+++N++++ +d  
  gi|70606823|ref|YP_255692.1| 177 KILEIGCAPGMKTSLIQQiTNNKSLVIGIDISSKRIKIQQDLMNKLGVENVELVVSDGS 235
                                   589****988655444431566889*****************************99974 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   6.6e-07   0.00091      45     114 ..     172     241 ..     159     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.6e-07
                                   S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
               Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                   +k+ +k+l++ +  g  +  +++  ++k  v+++Di+++ +k+ ++ +++ g+ n+e++++++ ++p ++
  gi|70606823|ref|YP_255692.1| 172 PKPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSKRIKIQQDLMNKLGVENVELVVSDGSNVPITK 241
                                   57788**********999999999999**************************************99876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.86   1.2e+03      58      88 ..      21      49 ..       9      51 .. 0.78
   2 ?   -1.1   0.0       2.3   3.1e+03      40      74 ..     101     135 ..      90     146 .. 0.67
   3 !   16.6   0.0   6.8e-06    0.0094       1      59 [.     179     241 ..     179     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.86
                                  -TT-EEEEEEES-CCC-CCHHHHHHHHHHHE CS
               Methyltransf_11 58 ednsfDlvvssevlhhvedpekalkeiaRvL 88
                                  +++ fD+ v s  l+h  +++k+++++ RvL
  gi|70606823|ref|YP_255692.1| 21 PEKAFDIAVKS--LNHKVNRRKLFNKFLRVL 49
                                  67788877644..566668999999999998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                                   HHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
               Methyltransf_11  40 eeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                   ++ ++v+ ++ad+e++  + +   +v+ + +++++
  gi|70606823|ref|YP_255692.1| 101 QQWIRVNTLKADVEDVRRKLERKGVVLQRDSFEFL 135
                                   33336778888888877666666666666666655 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 6.8e-06
                                   EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-T CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaeklpfed 59 
                                   L++Gc  G  +  +++     + v+g+D+s + +k+ ++  ++ g+ +ve+vv+d +++p+ +
  gi|70606823|ref|YP_255692.1| 179 LEIGCAPGMKTSLIQQITnnkSLVIGIDISSKRIKIQQDLMNKLGVeNVELVVSDGSNVPITK 241
                                   89************94445579****************9999999999**********99765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.3e-05     0.073      20      99 ..     173     237 ..     149     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
                                   -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS CS
                          FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealserkvdlvvsDgapdv 99 
                                   kp+++++++g+aPG  +  + q +++k+ v+++D+ +         iq d +++   e+++         lvvsDg+ +v
  gi|70606823|ref|YP_255692.1| 173 KPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSK-----RIKIQQDLMNKLGVENVE---------LVVSDGS-NV 237
                                   47889******************9999********874.....234566666665555444.........4444444.33 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.035      20      61 ..     172     216 ..     152     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
               Methyltransf_23  20 lraggrvLdiGcGtGillevlre..ngfs.vtgvDlspeaveiae 61 
                                    +++ ++L+iGc+ G  ++++++  n +s v+g+D+s++ ++i +
  gi|70606823|ref|YP_255692.1| 172 PKPNEKILEIGCAPGMKTSLIQQitNNKSlVIGIDISSKRIKIQQ 216
                                   57899**********99999977334555266*****99888754 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-05     0.063      59     118 ..     171     231 ..     159     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                   T--TT-EEEEES-TTS..HHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEE CS
                          CMAS  59 elkpGmtlLdiGcGWG..slvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevkl 118
                                   + kp +++L+iGc  G  + +++ + +    v+g+ +S+++ k +++ +++l++e+ ve+ +
  gi|70606823|ref|YP_255692.1| 171 DPKPNEKILEIGCAPGmkTSLIQQITNNKSLVIGIDISSKRIKIQQDLMNKLGVEN-VELVV 231
                                   557899*******888324567788888999*********************9765.44444 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013      0.18      69     109 ..     173     213 ..     158     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                   -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
                   Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                                   k+++k+L +G a G   s +  i +++++v +++ s++ ++
  gi|70606823|ref|YP_255692.1| 173 KPNEKILEIGCAPGMKTSLIQQITNNKSLVIGIDISSKRIK 213
                                   899********************************987654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.18      17     108 ..     160     252 ..     155     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                   -HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTT CS
                           MTS  17 DkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleevee 95 
                                   Dk+s   +  l+ + ++k+l +Gc  G+ +  +++ +++ + v  +d++ + +++ +  +++ ++e ve+v sd+ +    
  gi|70606823|ref|YP_255692.1| 160 DKASVYSVVFLDPKPNEKILEIGCAPGMKTSLIQQITNNKSlVIGIDISSKRIKIQQDLMNKLGVEnVELVVSDGSNVPI- 239
                                   55666666678888999************9999999999887888*****************************977665. PP

                                   S-EEEEEE---ST CS
                           MTS  96 kkfdlivsNPPfh 108
                                    k d ++   P  
  gi|70606823|ref|YP_255692.1| 240 TKADKVLIDAPCT 252
                                   8888888777655 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.22      12      89 ..      83     163 ..      72     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                   HHGGGHHHHHHHH.H-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTTS-EE--TTT CS
               Methyltr_RsmF_N  12 llgeeaeaflaal.eeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaGlyYiQEpSa 89 
                                   + +e++++++  l  ++r++ +RvNtlK++ve++++  e  ++ l++  +     ++++++r +   ++++G + iQ+ ++
  gi|70606823|ref|YP_255692.1|  83 WAEERLQSIMGDLnVKTRQQWIRVNTLKADVEDVRRKLErkGVVLQRDSFEFLFRVIKAKSRISDLEEFKNGEIVIQDKAS 163
                                   556666666766756789999************998766567777777777777788888888999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2368.93
//
Query:       gi|70606822|ref|YP_255693.1|  [L=98]
Description: hypothetical protein Saci_1043 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 694.22
//
Query:       gi|70606824|ref|YP_255694.1|  [L=456]
Description: hypothetical protein Saci_1044 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-28   96.2   0.3    1.6e-27   95.4   0.3    1.4  1  Radical_SAM_C    Radical_SAM C-terminal domain
    6.3e-22   78.7   0.0    1.1e-21   77.9   0.0    1.4  1  Radical_SAM      Radical SAM superfamily
    2.6e-08   34.1   0.1    5.4e-08   33.1   0.1    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0045   16.9   0.0      0.057   13.4   0.0    2.3  2  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.4   0.3   3.5e-31   1.6e-27       1      81 [.     228     308 ..     228     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 3.5e-31
                 Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrlk 81 
                                   pd++K+yp+lv++  +Lael+k+g ykp+++e +v+l+ +i++l+pp++rv+R+++dip   +i g++++nlrel+e+r k
  gi|70606824|ref|YP_255694.1| 228 PDMLKIYPTLVVETAPLAELWKKGLYKPYDTETLVELISEIYKLIPPWVRVMRVQRDIPATIIIDGNKKGNLRELVENRAK 308
                                   8****************************************************************************9976 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   2.5e-25   1.1e-21       2     158 ..      12     211 ..      11     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.5e-25
                                   EEESEESS-.-TTTSCCTT................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHH CS
                                   xxxxxxxxx.xxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlr.CsfCarpet................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfve 65 
                                   ++ + C+++ C+fC+ +                     + ++ + +v++ l++ +++ +++ + e+i++gg+ l+ p  ++
  gi|70606824|ref|YP_255694.1|  12 THPHRCPHGkCIFCPGGVEygtpqsyygneptlmrAIENNYEPFYQVQSRLRQYEANGHNPSKIELIIMGGTFLATPLDYQ 92 
                                   5677899988*************************999*******************988888889999998999877777 PP

                                   HHHHHHHTC........................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                   xxxxxxxxx........................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  66 llerlakla........................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlk 119
                                   +++   +l+                         + ir++  t +t+pd   e +++ +l+lgv+ v+lg++++ d+  l 
  gi|70606824|ref|YP_255694.1|  93 DWFVTQALEamnrypsnqkpgfilledaqlrneTASIRCVGLTVETKPDwskEVHAKQMLRLGVTKVELGVQTVFDD-LLT 172
                                   777777777788999999999999999999999********************************************.999 PP

                                   HHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 120 lmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                   + nrght+++ +ea+++l+++g+k+v+++++glpG   +
  gi|70606824|ref|YP_255694.1| 173 KSNRGHTVKDSIEATKILKDNGFKVVYHMMLGLPGSDPD 211
                                   999********************************8765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   1.2e-11   5.4e-08      28     117 .]     346     444 ..     314     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.2e-11
                                   HHSTTCEEEEEEET.TEEEEEEEEEEEETTSTTEEEEEEEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.TES CS
                Acetyltransf_1  28 fsleaegllvaeed.geliGfisllkipdekggvayieslaV...........speyrgkGlGsaLlealeeraree.gik 95 
                                   +s  +e +l++e+d ++l+G+++l+k  + k +v+++++l++           + ++++kG+G +Ll ++e++  ee  +k
  gi|70606824|ref|YP_255694.1| 346 ASGGTEVFLSYEYDdDTLVGYLRLRKPSN-KDDVTIVRELHIygpetpvglwdDFSFQHKGYGGRLLSEAERISVEEfDAK 425
                                   33445555665555489************.99******999999999999999***************************9 PP

                                   EE.EEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  96 ki.vlaveedndaairlYeklGF 117
                                   ki vl    +  + +++Y+k G+
  gi|70606824|ref|YP_255694.1| 426 KIlVL----SGIGVREYYRKKGY 444
                                   99677....99999****88997 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   6.4e+02      32      52 ..     353     373 ..     342     388 .. 0.71
   2 !   13.4   0.0   1.3e-05     0.057      62     108 ..     400     446 ..     396     453 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
               Acetyltransf_10  32 lllvaeeggkivGvielrdgs 52 
                                   +l   ++++++vG+++lr+ s
  gi|70606824|ref|YP_255694.1| 353 FLSYEYDDDTLVGYLRLRKPS 373
                                   444457889********7765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.3e-05
               Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFka 108
                                   +++++G+g +Ll ++e+   ++  ++++ v +    +++Y+k G+++
  gi|70606824|ref|YP_255694.1| 400 SFQHKGYGGRLLSEAERISVEEFDAKKILVLSGIGVREYYRKKGYHN 446
                                   69****************76777777*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3215.62
//
Query:       gi|70606825|ref|YP_255695.1|  [L=443]
Description: hypothetical protein Saci_1045 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-50  170.9  28.2    6.4e-50  170.3  28.2    1.2  1  Sugar_tr  Sugar (and other) transporter
    2.2e-24   86.0  32.8    2.2e-24   86.0  32.8    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.3  28.2   7.1e-54   6.4e-50       3     448 ..       9     434 ..       7     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 170.3 bits;  conditional E-value: 7.1e-54
                                   HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                      Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                   l+a +g +  gY+++ ++ ++++++   nf   ++++        sgl+v+  ++Ga+i++l++gl++d+ GRk  + i +
  gi|70606825|ref|YP_255695.1|   9 LIAGMGVFTDGYNLYSLSLVIYSIS---NFIRLNNVT--------SGLLVAGSYFGAAISALIFGLISDFQGRKRMYGIDV 78 
                                   5666777888888888888887777...666666664........689********************************* PP

                                   HHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Sugar_tr  84 vlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklR.galvslyqlaitfGilvaaifglglnk 163
                                   +l+ iga+lqa+++   ++  l+++R+l+G+g+G+ +vl+P+ ++E+A k++R +a+v  + +++ +G +vaa+++ +   
  gi|70606825|ref|YP_255695.1|  79 TLMTIGAFLQAFSQ---NYGELFFSRLLLGMGIGADYVLSPVIVAENADKDKRgKAMVITFAVMWGLGAVVAAFVTQISYF 156
                                   **************...9***********************************7789********************9999 PP

                                   SS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTT CS
                      Sugar_tr 164 tsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswke 244
                                     ++ gwr+ lgl ++pal +++++  l E+  +l +++    + + l k     ++++  ++ k   +++      ++ +
  gi|70606825|ref|YP_255695.1| 157 LPASLGWRMVLGLGAIPALSVILARRKLSETLLFLSKVK---PDIKELNK-----LKSDG-VDLKVNVDES-----SFLIR 223
                                   999****************************77776666...55555555.....22222.2222223333.....13344 PP

                                   HHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTT.THHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHH CS
                      Sugar_tr 245 llssktvrqrlligvvlqifqqltGinaimyysp.tifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGa 324
                                   l++s  +  r++i++++ ++    +   + +y+p ti +nlgls+ + + +   +  +   ++ iflvdr+GRR+l +lG 
  gi|70606825|ref|YP_255695.1| 224 LIKS--M--RFIIIAAILWVLYDIYSSTFAIYGPiTIAHNLGLSPIMFTYVAQFFAGIPGQLICIFLVDRIGRRKLIVLGY 300
                                   4444..2..455555555555555555555555549**********9999999999************************* PP

                                   HHHHHHHHHHH......HHHHTTSS......CHHHHHHHHHHHHHH.HTTTTHHH..HHHHHHHSHTTTHHHHHHHHHHHH CS
                      Sugar_tr 325 agmaicfvilg....ivalllvaks...kaasivaivfialfialf.algwgpvp..wvlvsElfpqsvRskalaiavavn 395
                                   ag a+ +v+++    ++++++  k+   ++ + v+ + +++   lf a+g+++++   ++++El+ ++vR++ +ai+vav 
  gi|70606825|ref|YP_255695.1| 301 AGVALWLVMYSllliNPFIFGLPKTstlEGTGAVLGFSFYMLNYLFsAMGPASIIgsGMIAPELSFTKVRATSQAISVAVD 381
                                   *********99999977777776666778888888888877777774799**9983358********************** PP

                                   HHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCC CS
                      Sugar_tr 396 wlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleei 448
                                     a+  +  lfp +++ +g g++  ++a++a+++ ++v+ffvpet  r+l+ i
  gi|70606825|ref|YP_255695.1| 382 RAASATVISLFPSLVNIVGLGVMVGIYASVALISSLIVMFFVPETRTRELDFI 434
                                   *******************9999*************************99866 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0  32.8   2.5e-28   2.2e-24       5     337 ..      15     358 ..       8     362 .. 0.76
   2 !   14.6  25.2   1.3e-06     0.011      13     181 ..     246     432 ..     243     441 .. 0.80

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 2.5e-28
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfassl 85 
                                   +f  +++ + l++++   +++   ++  + gll+++ ++gaa+++l++G +sd  Gr+r++ + ++l+ +g++l +f++++
  gi|70606825|ref|YP_255695.1|  15 VFTDGYNLYSLSLVIY-SISNFIRLNNVTSGLLVAGSYFGAAISALIFGLISDFQGRKRMYGIDVTLMTIGAFLQAFSQNY 94 
                                   4444445555555555.888888899999******************************************5555585555 PP

                         MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigl.lsagfslGailgpllgg..lla.sslgWravfyilaivsl 162
                                     l+++r+l G+g ga + ++ +++a+ + k++rg+a+ + ++++++lGa++++ +    +++ +slgWr v  + ai +l
  gi|70606825|ref|YP_255695.1|  95 GELFFSRLLLGMGIGADYVLSPVIVAENADKDKRGKAMVItFAVMWGLGAVVAAFVTQisYFLpASLGWRMVLGLGAIPAL 175
                                   5*************************************662566*********99987776666***************** PP

                         MFS_1 163 lafv....lfllllpeepperkrkspkeee......kgtgpaplvp.......awkallkdpvlwillialllfffgfsg. 225
                                    +++    l   ll+ +++++  k+  +++      k                +++++++ +    ++i++++ ++ + + 
  gi|70606825|ref|YP_255695.1| 176 SVILarrkLSETLLFLSKVKPDIKELNKLKsdgvdlK--------VnvdessfLIRLIKSMR----FIIIAAILWVLYDIy 244
                                   **98888844444444444444444333322234321........12455667789999999....444444444577773 PP

                         MFS_1 226 ...lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavll 303
                                      + ++ p+ +   lgls  ++ +  + + +++g++++l++ +l+dr+grr+ ++l++++++l+++++ ll         
  gi|70606825|ref|YP_255695.1| 245 sstFAIYGPITIAHNLGLS-PIMFT--YVAQFFAGIPGQLICIFLVDRIGRRKLIVLGYAGVALWLVMYSLLLIN------ 316
                                   4556666666455555555.45555..999999999**********************************99999...... PP

                         MFS_1 304 llvlvl..........iGfglgfvfpsllalasdlappeeagta 337
                                     ++++           G  lgf f +l++l s + p++  g+ 
  gi|70606825|ref|YP_255695.1| 317 --PFIFglpktstlegTGAVLGFSFYMLNYLFSAMGPASIIGSG 358
                                   ..444445555555889999999999999999988887776665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-06
                         MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fass....... 84 
                                   s++++  p+++a++lg+sp    + +++ +++ + ++l+  +l+dr+Grr++++lg+++ al+l++ +  + ++       
  gi|70606825|ref|YP_255695.1| 246 STFAIYGPITIAHNLGLSPIM--FTYVAQFFAGIPGQLICIFLVDRIGRRKLIVLGYAGVALWLVMYSllL-INpfifglp 323
                                   455556666999999977776..5568999999******************************44444432.222333344 PP

                         MFS_1  85 .............lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                                + + ++  +++++g ++++ +g+++    f+k  r+   ++  a   ++++    l + l+  +g  +
  gi|70606825|ref|YP_255695.1| 324 ktstlegtgavlgFSFYMLNYLFSAMGPASIIGSGMIAPELSFTK-VRATSQAISVAVDRAASATVISLFPSLVNIVGLGV 403
                                   444566666666566677777899999999999999999999998.********************999999999****** PP

                         MFS_1 153 vfyilaivsllafvlfllllpeepperkr 181
                                   +  i a v+l++ +++++++pe+++++  
  gi|70606825|ref|YP_255695.1| 404 MVGIYASVALISSLIVMFFVPETRTRELD 432
                                   **************999999998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2742.64
//
Query:       gi|70606826|ref|YP_255696.1|  [L=218]
Description: hypothetical protein Saci_1046 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.8   0.2      0.042   13.8   0.2    2.0  2  AvrM_N    Flax-rust effector AvrM N-terminal domain
       0.13   12.5   0.0        1.3    9.3   0.0    2.3  1  Ndufs5    NADH:ubiquinone oxidoreductase, NDUFS5-15kDa


Domain annotation for each model (and alignments):
>> AvrM_N  Flax-rust effector AvrM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.55   4.9e+03      25      36 ..       2      14 ..       1      18 [. 0.72
   2 ?   13.8   0.2   4.7e-06     0.042      16      56 ..      85     125 ..      77     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.55
                        AvrM_N 25 ekLspde.liRYv 36
                                  +kLs +e l+RY+
  gi|70606826|ref|YP_255696.1|  2 RKLSLEEyLLRYL 14
                                  5777655489996 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.7e-06
                        AvrM_N  16 mkflkpaevekLspdeliRYvaerdtnvekmarkLykaake 56 
                                   m  l+p +++k s +++ RYv++ d +v  + +   ++ak+
  gi|70606826|ref|YP_255696.1|  85 MHVLNPINMKKASRNAVSRYVSNCDKEVDIEKIYYSELAKN 125
                                   899***********************999999999999987 PP

>> Ndufs5  NADH:ubiquinone oxidoreductase, NDUFS5-15kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00015       1.3       6      36 ..      34      64 ..      32     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00015
                                  X--S---SS-----SSS-S-SSS---TTHHH CS
                        Ndufs5  6 lqkklgvnldrwlliqsaeqprkraarchaf 36
                                  +++klgvn+d+ l    +++p k+ +   a+
  gi|70606826|ref|YP_255696.1| 34 IKEKLGVNIDKVLFRLKTKDPLKTVSILSAI 64
                                  789******************9998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1560.26
//
Query:       gi|70606827|ref|YP_255697.1|  [L=139]
Description: hypothetical protein Saci_1047 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 933.22
//
Query:       gi|70606828|ref|YP_255698.1|  [L=84]
Description: hypothetical protein Saci_1048 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-13   48.8   0.8    1.1e-12   48.6   0.8    1.0  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.8   5.9e-17   1.1e-12       4      76 .]      13      84 .]      11      84 .] 0.93

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.9e-17
                        MJ1316  4 aqdvlnRirWdkeldkskfvvgyldRfkgikevpleeiswied.flleeeegelaIPlHRiryikrkgevvWdR 76
                                  ++d +n+++W+++ + +kf++   dR+kg +evp+ +is++++ +++ +++  + IPlHR+ +i++ +e  W+R
  gi|70606828|ref|YP_255698.1| 13 IKDAINKVFWTESSSLDKFTLILRDRKKGSIEVPFPDISSVDNnYIYLKDD--TIIPLHRVIEIRKGNETWWRR 84
                                  8999*************************************9986666666..79***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 634.47
//
Query:       gi|70606829|ref|YP_255699.1|  [L=540]
Description: hypothetical protein Saci_1049 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-72  242.0  18.5      7e-72  242.0  18.5    2.5  3  Thermopsin  Thermopsin


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.0  18.5   3.9e-76     7e-72       9     260 .]      19     276 ..      11     276 .. 0.95
   2 ?   -1.7   0.4     0.091   1.6e+03     140     186 ..     332     380 ..     311     419 .. 0.52
   3 ?    1.3   1.9     0.011   1.9e+02     119     179 ..     412     471 ..     397     487 .. 0.75

  Alignments for each domain:
  == domain 1  score: 242.0 bits;  conditional E-value: 3.9e-76
                    Thermopsin   9 yssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvt.ggktysywvQnVvs 88 
                                   + s+  P+Gi++y          + ++ t svlG++nissl ay++ss++p++aslQLNv+l+v+t ++kty++w+QnV+s
  gi|70606829|ref|YP_255699.1|  19 HFSAV-PIGISSY----------QGTILTPSVLGYANISSLLAYSNSSQNPYGASLQLNVMLQVNTtTSKTYYFWLQNVAS 88 
                                   44444.9******..........679****************************************99************* PP

                    Thermopsin  89 fnttekqltfidNiWNftspsanlsnsaisGnGtvy...asskgefYyayatey.lelslPltlkLvinvsltsngvpevs 165
                                   f t++k ++f+dN+WN+t+p++++sn+  +GnG+vy   ++ +g+ +y+y+++y +++++P++++++in+s++ + v +v+
  gi|70606829|ref|YP_255699.1|  89 FLTNDKVAYFLDNVWNVTTPYTQISNV--KGNGQVYtisNGPYGQSFYGYTSNYpIRYNYPFSFYMFINTSYSGSLV-TVE 166
                                   ************************777..*******99999999*****************************8888.*** PP

                    Thermopsin 166 FgYsid.......ggvvtYDnvtinstgkasaeilvngssltps.........gllyDaeLvlgGpgngekttfnslnatl 230
                                   FgY+i        ++v tYD+v+++++g + a+i+vn+ s+tps         g+l D+eLv+gG +ngekt+f+++++ l
  gi|70606829|ref|YP_255699.1| 167 FGYVIVqnstvipPVVETYDEVQLRINGVQGASIIVND-SYTPSevienvpylGMLEDCELVWGGLSNGEKTSFENMSSLL 246
                                   ****999******99***********************.899999************************************ PP

                    Thermopsin 231 sLyYlngtnyqpvknaydfGsdTaEtaenv 260
                                   ++yYl++++++p+kn++d+G dTaE+a+n+
  gi|70606829|ref|YP_255699.1| 247 AMYYLSDQQWKPFKNIFDYGFDTAEGAYNL 276
                                   ****************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.091
                    Thermopsin 140 lelslPltlkLvinvsltsngvpevsFgYsid...ggvvtYDnvtinstg 186
                                   + ++ Pl+++++   s ++ ++ +++ + ++    +   ++ nvt+    
  gi|70606829|ref|YP_255699.1| 332 SYINSPLSITMFNDFSINKTAIAMLKTNNNTLtifP-SSWFKNVTLVPDY 380
                                   445566666666666666666555555555445531.3344444443333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.011
                    Thermopsin 119 GnGtvyasskgefYyayatey.lelslPltlkLvinvsltsngvpevsFgYsidggvvtYDn 179
                                   G  +v+   ++ +Yy+ +    + l++  +l+ +in+ l+ + + +v++  +i+g+  + Dn
  gi|70606829|ref|YP_255699.1| 412 GDTQVV--IQNLTYYESNDMRiVILKVQPSLNFTINSPLNVSVSTKVQYLVTINGISKWVDN 471
                                   445555..445556654443358889999999999999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3909.43
//
Query:       gi|70606830|ref|YP_255700.1|  [L=432]
Description: hypothetical protein Saci_1050 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-12   46.8   0.1    1.3e-11   44.7   0.0    2.1  2  AAA_31       AAA domain
    7.4e-12   45.4   0.0    1.9e-11   44.1   0.0    1.8  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    1.9e-06   27.5   3.2    2.8e-06   27.0   1.3    2.2  3  ParA         NUBPL iron-transfer P-loop NTPase
    3.2e-05   23.3   1.2    4.9e-05   22.7   0.4    1.7  2  ArsA_ATPase  Anion-transporting ATPase
    0.00012   21.7   0.0    0.00017   21.2   0.0    1.3  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0016   17.9   0.5     0.0056   16.2   0.1    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0042   16.4   0.6     0.0099   15.2   0.1    1.8  2  MipZ         ATPase MipZ
  ------ inclusion threshold ------
      0.087   12.1   0.1       0.19   11.0   0.1    1.4  1  VirC1        VirC1 protein
       0.11   12.1   0.1       0.21   11.2   0.1    1.4  1  AAA_25       AAA domain
       0.16   11.6   0.4       0.86    9.2   0.2    2.1  2  SRP54        SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   7.2e-15   1.3e-11       4     130 ..       5     133 ..       3     140 .. 0.81
   2 ?   -2.3   0.1       1.9   3.5e+03      80      80 ..     376     376 ..     305     422 .. 0.55

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 7.2e-15
                        AAA_31   4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenl..d 82 
                                   ++i   KGGvGK+T ++ l++ala +gkkvLl++ D+ + a++++gi+++ i  +l +    e++ +e  +k ++ +   +
  gi|70606830|ref|YP_255700.1|   5 VSILGVKGGVGKSTIALSLGKALALKGKKVLLIERDMVGYASFAFGIKRKGILAKLAD---GEEHFEESFKKLSFGDGelS 82 
                                   688899*****************************************88876555555...57777777777765443348 PP

                        AAA_31  83 lipssidLaeaeielvelekk...eeilkellekvkdeYDyiiiDcpPsLg 130
                                   l+  + d  ++ ++l ++++    +e l+ l +k+   Y y i D pP ++
  gi|70606830|ref|YP_255700.1|  83 LLKFYGDGERVYDDLKKVMSDislREKLSILASKFLYGYEYYITDNPPLIS 133
                                   999999999999999888877666666777778888889999999999776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                        AAA_31  80 n 80 
                                   +
  gi|70606830|ref|YP_255700.1| 376 T 376
                                   2 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.1e-14   1.9e-11       1     123 [.       5     235 ..       5     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.1e-14
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH....................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx....................... RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep....................... 54 
                                   ++i + kGGvGK+t+a++L++ala +g++Vll+  D  + +++           +                          
  gi|70606830|ref|YP_255700.1|   5 VSILGVKGGVGKSTIALSLGKALALKGKKVLLIERDMVGYASFAfgikR-----KGILakladgeehfeesfkklsfgdge 80 
                                   57999*************************************9555553.....44444555588889999********** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|70606830|ref|YP_255700.1|  81 lsllkfygdgervyddlkkvmsdislreklsilaskflygyeyyitdnpplisyndltlkveldlfysnvpnpkvlriyvs 161
                                   ********************************************************************************* PP

                                   .....CCHCCCHHHHHHCHCHHHH......EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                   .....xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....dlkrllellealgkkkall....lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                         + + +  l+++            +++ +++n+v + +e +++++ l+e++ ++gv     ip   +++e  +
  gi|70606830|ref|YP_255700.1| 162 sasrnIINSTIDYLKSFES----DvnyrGTPLAFIVNMVPSLDEVERIRQELREVITKLGVSYGIAIPLYREIMEKSQ 235
                                   9766533333333344443....3334489999**********************99997666446666666666555 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   1.3   1.5e-09   2.8e-06       6      46 ..       5      45 ..       2      61 .. 0.91
   2 ?   -2.3   0.0       1.3   2.4e+03     193     222 ..     208     237 ..     195     254 .. 0.83
   3 ?   -2.6   0.0       1.7   3.1e+03     142     203 ..     301     324 ..     284     339 .. 0.44

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.5e-09
                          ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGps 46
                                  + +l  KGGVGKSt+a +l  aLa kg+kv l+  D++G+ 
  gi|70606830|ref|YP_255700.1|  5 VSILGVKGGVGKSTIALSLGKALALKGKKVLLIERDMVGYA 45
                                  568889*********************************75 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                          ParA 193 ggeklaeelgvpllgeipldpeireasdeg 222
                                   + +++ ++lgv++  +ipl  ei+e+s+e 
  gi|70606830|ref|YP_255700.1| 208 ELREVITKLGVSYGIAIPLYREIMEKSQEN 237
                                   567788899999999999999999988765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.7
                          ParA 142 VttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgv 203
                                   V   + v                                       +++k++ +++ ++ g+
  gi|70606830|ref|YP_255700.1| 301 VEGSHVV--------------------------------------VVYTKEKITEILRSNGI 324
                                   2222222......................................22333333333333333 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.4   2.7e-08   4.9e-05       3      38 ..       5      40 ..       3      62 .. 0.86
   2 ?   -3.0   0.0       1.7   3.1e+03     223     232 ..     202     211 ..     192     263 .. 0.54

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.7e-08
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  v ++g KGGVGK+t++ +++  l+ kgkkvlli  D
  gi|70606830|ref|YP_255700.1|  5 VSILGVKGGVGKSTIALSLGKALALKGKKVLLIERD 40
                                  667899***************************988 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                   HHHHHHHHHH CS
                   ArsA_ATPase 223 teRaikeLkk 232
                                    eR  +eL +
  gi|70606830|ref|YP_255700.1| 202 VERIRQELRE 211
                                   4444444433 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   9.4e-08   0.00017       4      51 ..       5      52 ..       2     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 9.4e-08
                      CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvd 51
                                  + + Gv+GGvG+++++ +L++al   g++vl+i+        + F ++
  gi|70606830|ref|YP_255700.1|  5 VSILGVKGGVGKSTIALSLGKALALKGKKVLLIERDMVGYASFAFGIK 52
                                  5678*****************************877666666666655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   3.1e-06    0.0056       3      37 ..       5      40 ..       3      72 .. 0.81
   2 ?   -1.8   0.0      0.91   1.6e+03     167     200 ..     399     429 ..     393     431 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-06
                     Fer4_NifH  3 iaiyG.kGGiGksttsqnlsaalaemgkkvlivGCD 37
                                  ++i G kGG+Gkst +  l +ala +gkkvl++  D
  gi|70606830|ref|YP_255700.1|  5 VSILGvKGGVGKSTIALSLGKALALKGKKVLLIERD 40
                                  5566669************************99776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.91
                     Fer4_NifH 167 kyaksggvrlgGliinsrkvddereliekfaeel 200
                                    ++++ +v++  li++  k++de ++i+ +a+++
  gi|70606830|ref|YP_255700.1| 399 SMRNKRSVKIV-LICD--KIKDECDVIKSYADKI 429
                                   55566666664.7777..6899999999999886 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.5e-06    0.0099       8      39 ..      10      41 ..       3      54 .. 0.88
   2 ?   -2.5   0.0       1.3   2.4e+03     247     260 ..     205     218 ..     197     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                                  SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                          MipZ  8 ekGGsGksttavhvavaLlkkGarvaaidldl 39
                                   kGG Gkst+a+ +  aL+ kG++v  i+ d+
  gi|70606830|ref|YP_255700.1| 10 VKGGVGKSTIALSLGKALALKGKKVLLIERDM 41
                                  59***********************9998775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHTT- CS
                          MipZ 247 arqelrdLlaalkL 260
                                    rqelr+++++l++
  gi|70606830|ref|YP_255700.1| 205 IRQELREVITKLGV 218
                                   59*******99986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001      0.19       6      39 ..       7      40 ..       3      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                         VirC1  6 fcslkGGaGkttalmglcsalasdgkrvalfead 39
                                  +  +kGG Gk+t  ++l  ala +gk+v l e d
  gi|70606830|ref|YP_255700.1|  7 ILGVKGGVGKSTIALSLGKALALKGKKVLLIERD 40
                                  5678**************************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.21      35      64 ..       5      35 ..       3      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        AAA_25 35 lallaGapgtGKttlaldlalava.tGkpwl 64
                                  +++l   +g+GK+t+al+l+ a+a +Gk++l
  gi|70606830|ref|YP_255700.1|  5 VSILGVKGGVGKSTIALSLGKALAlKGKKVL 35
                                  7889999*****************8888765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2   0.00048      0.86       6      41 ..       7      43 ..       3      48 .. 0.86
   2 ?   -1.0   0.0      0.62   1.1e+03     170     186 ..      84     101 ..      80     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                                  EEESTT.SSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                         SRP54  6 lvGlqG.aGKTttlaKLaallkkegkkvllvaaDtfR 41
                                  ++G++G +GK t +  L + l  +gkkvll+  D+  
  gi|70606830|ref|YP_255700.1|  7 ILGVKGgVGKSTIALSLGKALALKGKKVLLIERDMVG 43
                                  67888659***********************999865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.62
                                   EEEEE-SSST.TGEEE-- CS
                         SRP54 170 ikfigvGeki.edleefd 186
                                   +kf g Ge++ +dl+++ 
  gi|70606830|ref|YP_255700.1|  84 LKFYGDGERVyDDLKKVM 101
                                   589******999**9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2745.11
//
Query:       gi|70606831|ref|YP_255701.1|  [L=500]
Description: hypothetical protein Saci_1051 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-26   91.1   0.0    8.1e-26   91.1   0.0    2.6  3  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.1e-25   90.0   0.0    2.7e-25   89.6   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.2e-17   61.4   0.1    1.3e-16   60.9   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-14   52.5   0.0    5.6e-14   52.0   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    2.9e-05   22.8  17.5     0.0037   15.8  12.5    2.8  2  Cellulose_synt   Cellulose synthase


Domain annotation for each model (and alignments):
>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.4   5.2         5   1.8e+04     166     196 ..      13      46 ..       6      55 .. 0.44
   2 !   91.1   0.0   2.3e-29   8.1e-26       2     188 ..     158     360 ..     157     376 .. 0.70
   3 ?   -1.8   2.3      0.69   2.5e+03     154     184 ..     432     460 ..     380     484 .. 0.49

  Alignments for each domain:
  == domain 1  score: -6.4 bits;  conditional E-value: 5
               Glyco_trans_2_3 166 alplhlallllfslla...lalvlllllllaall 196
                                   +l ++ ++++ +++ +   l+ + l+l+++ a++
  gi|70606831|ref|YP_255701.1|  13 PLIISAVITYFTWVKIetiLIDFGLWLAMVTAFY 46 
                                   4444445555555444555333333333333332 PP

  == domain 2  score: 91.1 bits;  conditional E-value: 2.3e-29
               Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrs 82 
                                   +++ DaD ++ +d++++++  +++p++a+vq p  + +   +      + + +     i++r ++gr ++s Gsg+++r++
  gi|70606831|ref|YP_255701.1| 158 VAIFDADQRPVRDFFKQVLPYFKDPKIAFVQVPQNYSET--FSGISTGAKYQQEPFLRIIMRGRSGRSAFSLGSGTVFRIQ 236
                                   7899*****************************999854..444444455777777889********************** PP

               Glyco_trans_2_3  83 alqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslv.kekspltlraalrQrkRwayGc.eleklil.......... 151
                                   al+evg+ +  e s++ED   +++l +kGy+ ++++ +l+ + + p +l a+l Q +Rwa+G+ +l k i+          
  gi|70606831|ref|YP_255701.1| 237 ALREVGYLP--ENSITEDAAVSIKLHSKGYNSVYIDVPLIwYGEPPQDLNAYLIQQSRWALGYfQLTKDIIkadlsflkyy 315
                                   *********..***************************774777888***************8633222223333333333 PP

               Glyco_trans_2_3 152 ........lvrllgylgsllwsalplhlallllfsllalalvlll 188
                                           +++   ++   + s+++++l+  ++  +++++++l++
  gi|70606831|ref|YP_255701.1| 316 dyfsgflyWIKEGPLAIVEFISPIVFLLTEIPILRINPILYLLVY 360
                                   322222221111111111111222233333344444443333322 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.69
               Glyco_trans_2_3 154 rllgylgsllwsalplhlallllfslla..........lal 184
                                    ++  l +l++s+            +            ++l
  gi|70606831|ref|YP_255701.1| 432 PHIVILLLLIVST------------VKGilwlisansnFLL 460
                                   2222222222222............1111111111222111 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.0   7.4e-29   2.7e-25       4     230 .]      74     296 ..      71     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 7.4e-29
               Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                   +a +V++fne++  ++++l s+        +v++ +d  d+   ++++e+   + ++++++v+++++  ++ k+ a+n+al
  gi|70606831|ref|YP_255701.1|  74 IAAFVTSFNEDPeIVERTLLSVKDAVSNQGDVFLLDDSTDENISRRLREF---CTRNDINYVHRKDR--RGYKAGAINDAL 149
                                   7899*******9667778888775445679*******************7...88889****99884..558********* PP

               Glyco_tranf_2_3  84 ravk.sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll.nrstlvsalgalefaerhlrflaarralgvltlnG 162
                                   r+++ +dlv+++D+D +   d++k++l++f++pk+++v++p++     s   +  ga + +e +lr+  + r+++ +++ G
  gi|70606831|ref|YP_255701.1| 150 RRIQgYDLVAIFDADQRPVRDFFKQVLPYFKDPKIAFVQVPQNYSeTFSGIST--GAKYQQEPFLRIIMRGRSGRSAFSLG 228
                                   ****99************************************66515665444..4422335666666666777799999* PP

               Glyco_tranf_2_3 163 sgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfp.sslkayikqrnRwvyg 230
                                   sg+++r + l+e + l + +++t+D+  +  l + g+ ++y   ++++  +p ++l ay  q  Rw+ g
  gi|70606831|ref|YP_255701.1| 229 SGTVFRIQALREVGYLPE-NSITEDAAVSIKLHSKGYNSVYIDVPLIWYGEPpQDLNAYLIQQSRWALG 296
                                   *************66666.***************************998755388***********975 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.1   3.6e-20   1.3e-16       3     169 ..      77     241 ..      75     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.6e-20
                                   EEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH--SS CS
               Glycos_transf_2   3 viptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglraatgd 81 
                                   +++++Ne ++ +++tl s+++       +++++DD+  ++    l+e++  + ++ +++r+ ++  kaga+n +lr+ +g 
  gi|70606831|ref|YP_255701.1|  77 FVTSFNEdPEIVERTLLSVKDA-VSNQGDVFLLDDSTDENISRRLREFCT-RNDINYVHRKDRRgYKAGAINDALRRIQGY 155
                                   89********************.999***********9999*******98.788888888888879**************9 PP

                                   .EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEE CS
               Glycos_transf_2  82 .yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaall 161
                                    +++++DaD  p +d++++++ ++++ ++ ++++q+p + +et+    +   ++++ ++ ++ +r + g ++f  gs +++
  gi|70606831|ref|YP_255701.1| 156 dLVAIFDADQRPVRDFFKQVLPYFKD-PK-IAFVQVPQNYSETFSGISTG-AKYQQEPFLRIIMRGRSGRSAFSLGSGTVF 233
                                   9*************************.55.78888888777777777654.4799999999999999************** PP

                                   EEHHHHHC CS
               Glycos_transf_2 162 rrealeel 169
                                   r  al+e+
  gi|70606831|ref|YP_255701.1| 234 RIQALREV 241
                                   ****9997 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   1.6e-17   5.6e-14      10     172 ..     133     294 ..     125     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.6e-17
               Glyco_transf_21  10 gdpvgvnpKvnnllqalea.akydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlag 89 
                                   + +    +K  +++ al++   ydl+ i D+d r  +d+++++l +++dpk+++V+ +  +s++ +  ++ ++ + +++ +
  gi|70606831|ref|YP_255701.1| 133 HRKDRRGYKAGAINDALRRiQGYDLVAIFDADQRPVRDFFKQVLPYFKDPKIAFVQVPQNYSETFSGISTGAKYQQEPFLR 213
                                   55666778999********999*********************************************************** PP

               Glyco_transf_21  90 vlqa.klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRql 169
                                   ++++ + ++  f +G+  ++r +aL+++G + +    + eD+a +  l+++G++ v  + p+ +   p  + l a+l +q 
  gi|70606831|ref|YP_255701.1| 214 IIMRgRSGRSAFSLGSGTVFRIQALREVGYLPE--NSITEDAAVSIKLHSKGYNSVYIDVPLIWYGEP-PQDLNAYLIQQS 291
                                   ****888899********************999..**************************9986555.6789******** PP

               Glyco_transf_21 170 rWa 172
                                   rWa
  gi|70606831|ref|YP_255701.1| 292 RWA 294
                                   **8 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00011      0.39     169     289 ..     130     239 ..     105     247 .. 0.73
   2 !   15.8  12.5     1e-06    0.0037     415     679 ..     241     483 ..     239     493 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                Cellulose_synt 169 vyvsrekrpGydhnkkaGamnalvrvsavlsnapfilnldcdhyinnskalreamcflldrelGkkvcyvqfpqr....fd 245
                                    yv r+ r Gy    kaGa+n  +r    +     +  +d d        +++ + ++ d++    +++vq pq     f 
  gi|70606831|ref|YP_255701.1| 130 NYVHRKDRRGY----KAGAINDALRR---IQGYDLVAIFDADQRPV-RDFFKQVLPYFKDPK----IAFVQVPQNysetFS 198
                                   57777777777....67777765554...23334445556665422.345666667777766....9******96444479 PP

                Cellulose_synt 246 GidksdryanrnvvffdinlraldGiqGpvyvGtGcvfrrqaly 289
                                   Gi +  +y ++   f+ i +r+  G +    +G+G+vfr qal 
  gi|70606831|ref|YP_255701.1| 199 GISTGAKYQQE--PFLRIIMRGRSG-RSAFSLGSGTVFRIQALR 239
                                   ********766..699********9.56789***********94 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1e-06
                Cellulose_synt 415 iGwi.yGsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklklle 494
                                   +G++   s+ted     k+h++G++svy       + G  p +l   l q  rwalG     f     ++ +    l +l+
  gi|70606831|ref|YP_255701.1| 241 VGYLpENSITEDAAVSIKLHSKGYNSVYID-VPLIWYGEPPQDLNAYLIQQSRWALGY----FQLTKDIIKA---DLSFLK 313
                                   66662369********************65.556789********************5....5556677777...8***** PP

                Cellulose_synt 495 rlaylnviiypftsifllvycil.palsllsgkfivkelsn.lasiyllllflslivlavlelkwsGvsleewwrneqfwv 573
                                      y+   +y +   +l +  ++ p + ll++  i++   + ++++yl  lf+s+       +  +G+  e  +  + f+ 
  gi|70606831|ref|YP_255701.1| 314 YYDYFSGFLYWIKEGPLAIVEFIsPIVFLLTEIPILRINPIlYLLVYLPYLFISIG------IFVAGIREETEYGLKGFFY 388
                                   *************9999766665166667777666554333134455555555543......3345665555555555555 PP

                Cellulose_synt 574 igGvs.ahlfavlqGllkvlaGvdisftvtskasddeddefadlyivkwttllippltllivnlvavvvgvsrainsayes 653
                                      v     +av   ++  l G +  f vt k+++        l       +l+p +++l++ +v+ v g+   i+ a+++
  gi|70606831|ref|YP_255701.1| 389 HQCVEfLEFTAVTASFISWLLGRKRPFRVTPKGGGR-------LN----LRILLPHIVILLLLIVSTVKGILWLIS-ANSN 457
                                   444441466788888999999999999999999982.......22....246788899999999999999887664.4555 PP

                Cellulose_synt 654 wgkllGklffafwvlvhlypflkGll 679
                                   +      +   fw + h+  fl G+l
  gi|70606831|ref|YP_255701.1| 458 FLLYYAIIVNVFWAIYHIPFFLGGIL 483
                                   66666677777888889888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3241.21
//
Query:       gi|70606832|ref|YP_255702.1|  [L=106]
Description: hypothetical protein Saci_1052 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   88.3   0.1    2.8e-25   88.1   0.1    1.0  1  GYD             GYD domain
    1.1e-05   25.3   0.1    1.9e-05   24.5   0.1    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.1   3.1e-29   2.8e-25       1      90 [.       7      95 ..       7      96 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3.1e-29
                           GYD  1 YivlvnytdegvkglkdsperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlraft 83
                                  +ivl+++td+g+k++  +per++e++e+l +++G+k++++y+++G+ D+v+ivE++  e++ ++ ++l+++Gtvrt+t+ a++
  gi|70606832|ref|YP_255702.1|  7 FIVLSSLTDDGAKTIVGKPERIKEVNEEL-AKIGAKVKEQYVVFGDMDFVNIVEVDNVESFLKALVELNSRGTVRTRTYLAMP 88
                                  8**************999***********.***************************************************** PP

                           GYD 84 eeefdea 90
                                  ++++ +a
  gi|70606832|ref|YP_255702.1| 89 VDDAIKA 95
                                  ***9886 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.2e-09   1.9e-05       9      73 ..      24      87 ..      17      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.2e-09
                                  GTTHHHHHHHHHHTS.TTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                AsnC_trans_reg  9 hpeqleefeealael.peVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                  +pe ++e+ e+la++   V+e y+v Gd+d++ +v v ++e++ + l+e l+s  g  rt+t++++
  gi|70606832|ref|YP_255702.1| 24 KPERIKEVNEELAKIgAKVKEQYVVFGDMDFVNIVEVDNVESFLKALVE-LNSR-GTVRTRTYLAM 87
                                  467799999999997368*******************************.8776.67799999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 802.47
//
Query:       gi|70606833|ref|YP_255703.1|  [L=216]
Description: hypothetical protein Saci_1053 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1515.85
//
Query:       gi|70606834|ref|YP_255704.1|  [L=552]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-88  295.8   0.0    5.2e-88  295.5   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    4.7e-21   75.6   0.0      1e-20   74.4   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.5   0.0   5.8e-92   5.2e-88       2     422 ..      24     445 ..      23     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 295.5 bits;  conditional E-value: 5.8e-92
                                   HHHHHHSTTSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                   AMP-binding   2 eeqaaktpdkvalvd....sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                   e++a+ + d  ++ d    +g  +++TYr+++ervnr+A++++ +l+v +gd V++l +n ++++ +++ + ++Gav+  l
  gi|70606834|ref|YP_255704.1|  24 EHAARVHGDTEVISDrrlqGGLRHRFTYRQVYERVNRIANAFErELNVAPGDIVGVLDWNDHRYYESYFSLPSIGAVTLEL 104
                                   667777778887766999989999*******************9************************************* PP

                                   ETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.....-TSCC CS
                   AMP-binding  78 nptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.....kpeee 153
                                   n +l + el yi++++++k l+  vd+ l  +l+e+ +k+++ + ++v++++++++ ++     + ee         ++++
  gi|70606834|ref|YP_255704.1| 105 NIRLHPTELGYIIKHTKPKGLL--VDDSL-LQLAEVLSKEHDFSFILVMSDKPVEEIKTNLRVLGYEE--LlrsnsPNRPS 180
                                   **********************..87776.66888888888888888888777666655444444443..13466734456 PP

                                   CS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE- CS
                   AMP-binding 154 eelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvll 234
                                    ++++ + a+  +TSGTTG PKGV +shr+++  + +++     +l+++dv l+i+p++h+ ++    +++ + G++++++
  gi|70606834|ref|YP_255704.1| 181 LTVDERSAATAAFTSGTTGLPKGVFYSHRSIILHAMAVA--IGNSLTPSDVGLQIVPMFHANAW-GTPFASTMMGMKMIYP 258
                                   689****************************98888864..3366889****************.***************7 PP

                                   TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEE CS
                   AMP-binding 235 pkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevleg 314
                                    + +   p++l+e i ++kvtv+agvP++l  +++  ++        + ++lr+  +gg+ ++++l+++f +l+g+ v++g
  gi|70606834|ref|YP_255704.1| 259 GRYT---PDTLVEHIVTHKVTVTAGVPTILLEIVRrLQQMG-----VKTPGLRI-TSGGSEPPSALAKAFMELGGR-VIQG 329
                                   7554...56899*********************99664444.....35789**9.59****************987.**** PP

                                   EEEGGGSSECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHH CS
                   AMP-binding 315 YGlTEttgvvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpea 384
                                   YG TEt++ v++         l + e+ +k  ++G p+ g+evk+vD+ t++++p dg++ Ge+++rgp+++k Y+++p +
  gi|70606834|ref|YP_255704.1| 330 YGATETSPLVSMalpkaelkeLSDIERFEKM-KQGLPIFGAEVKVVDPITNQELPwDGKSfGEIWLRGPWIAKEYYNDP-R 408
                                   **********777999999986656665554.69*********************88888*****************95.6 PP

                                   HHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 385 taeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                    +e+f+ +++w r+GD+g++d+ Gy+++v+R+kd+ik+
  gi|70606834|ref|YP_255704.1| 409 SSERFT-PDGWWRSGDVGVVDPLGYIRLVDRLKDVIKS 445
                                   7899*9.767**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.2e-24     1e-20       2      76 .]     455     534 ..     454     534 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.2e-24
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   +E+ l++hp V+ea VvGvp++++Ge+++a+V lk++   + +   +++eL++h+ k+++++  p++++fvde+pkt  GK
  gi|70606834|ref|YP_255704.1| 455 LENFLMAHPYVREASVVGVPHPKWGERPLAVVSLKPEyqsK-DkeeVKKELREHLLKRFAKWQLPDDFIFVDEIPKTSVGK 534
                                   7*********************************9875331.2567**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 3338.55
//
Query:       gi|70606835|ref|YP_255705.1|  [L=284]
Description: hypothetical protein Saci_1055 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   43.8   5.0    3.1e-10   39.7   4.5    2.9  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.019   14.7   0.0    2.9  3  DUF4184   Domain of unknown function (DUF4184)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   4.5   3.4e-14   3.1e-10       1     135 [.       1     113 [.       1     245 [. 0.76

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 3.4e-14
                          YdjM   1 MdgltHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflallal 81 
                                   M   +H+ll++alglal  +          +++ +gA++PD+D     l+r +    +       HR ++H ++f+++l  
  gi|70606835|ref|YP_255705.1|   1 MNLNSHILLALALGLALFHRVDL------AVLVGIGAAIPDLDREYTLLKRDIFRRMQ------LHRALFHNIFFIIALF- 68 
                                   77779***************974......46666789******555555555433333......39*****999998764. PP

                          YdjM  82 vlllllrlfgrsalrlglllllgvlsHlllDlltk...yGvpllwPfsk..kkvrlsll 135
                                          lf+++       + +g+l+H++ D++t+   +Gv+l++P++   k+++l+  
  gi|70606835|ref|YP_255705.1|  69 -------LFNKY-------IGIGALTHVIFDAFTSpsdRGVELFFPLTRliKEYKLNYE 113
                                   .......45666.......788*************************976655555544 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3     0.039   3.5e+02       6      53 ..       5      62 ..       3      74 .. 0.73
   2 ?   14.7   0.0   2.1e-06     0.019     110     139 ..      75     104 ..      65     112 .. 0.83
   3 ?   -0.2   2.6     0.076   6.8e+02     150     213 ..     198     269 ..     161     275 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.039
                       DUF4184  6 sHpaavlplkllkrkrlslsaLv.iGslaPDveyf.........lrlkakstltHtll 53
                                  sH  ++l l l   +r++l+ Lv iG+  PD+             r++  + l H++ 
  gi|70606835|ref|YP_255705.1|  5 SHILLALALGLALFHRVDLAVLVgIGAAIPDLDREytllkrdifRRMQLHRALFHNIF 62
                                  6777777777777788889999889999999965444777777667777777777764 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-06
                       DUF4184 110 liGaatHvlwDsfTHedgwfvrlipvlqss 139
                                    iGa+tHv++D+fT  ++  v+l+  l++ 
  gi|70606835|ref|YP_255705.1|  75 GIGALTHVIFDAFTSPSDRGVELFFPLTRL 104
                                   59*****************99998777665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.076
                       DUF4184 150 lqhgstllGlvviivvlvrllrraksksekeklavlaavivlali............aavgklvvgaisgllvgll 213
                                   + +++  +G+v+  ++  +++rr   +  ++++ v +a+ ++ ++                ++v  +i++l vg++
  gi|70606835|ref|YP_255705.1| 198 VKYIIISIGIVMFYAAGEVWRRR---NVGRRPIIVTMAIGFILILyqgsqlfsplsiG-SLEAVYLVIPSLAVGII 269
                                   34444444444444444444444...34567777777777777734444444443321.23344445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2015.48
//
Query:       gi|70606836|ref|YP_255706.1|  [L=64]
Description: hypothetical protein Saci_1056 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.2   0.1      0.039   14.2   0.1    1.1  1  DUF5442   Family of unknown function (DUF5442)


Domain annotation for each model (and alignments):
>> DUF5442  Family of unknown function (DUF5442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.2e-06     0.039      47      89 ..       5      47 ..       2      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-06
                       DUF5442 47 ylkdisirtvnciikrfeddpqaylvndtlnyyykkdliptdp 89
                                  y    +i+   c++kr++d+ +   ++dt+ y    + + + +
  gi|70606836|ref|YP_255706.1|  5 YTTLRVIKSTACMLKRIKDEKNLSSIDDTIRYLIVVERLNIRN 47
                                  55556789999*********************87766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 457.03
//
Query:       gi|70606837|ref|YP_255707.1|  [L=470]
Description: decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-18   67.1   0.0    1.9e-18   66.3   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    2.2e-10   40.1   0.0    7.2e-10   38.4   0.0    1.7  1  Aminotran_5      Aminotransferase class-V
    2.8e-08   33.3   0.0    1.5e-06   27.6   0.0    2.1  2  Aminotran_1_2    Aminotransferase class I and II
    3.1e-05   23.4   0.0    4.9e-05   22.8   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0014   17.2   0.0     0.0021   16.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.055   12.7   0.0       0.18   11.0   0.0    1.6  2  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   6.4e-22   1.9e-18      60     349 ..      54     321 ..      39     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 6.4e-22
                                   HHHHHT-BTSSTTTSHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HH CS
                 Pyridoxal_deC  60 LadainkngftweesPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkea 140
                                     + ink +++++ +P +   e+ ++ +   llg      e e +g ++ g++es+++a   ar  ++k+           
  gi|70606837|ref|YP_255707.1|  54 YNQFINKTMLDFTVYPSVLRFENDIIAMASSLLGGN----E-ETVGNFTFGGTESIMVATKSARDYFLKRHSSV------- 122
                                   5678*****************************998....3.37899*****************9999875544....... PP

                                   HHHCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHH CS
                 Pyridoxal_deC 141 eildklvlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelg 221
                                    i + l  +t   ah + +ka+ +lg+k+  +++d++    + +le +  + ke+  +  ++va +     g  dd+k l 
  gi|70606837|ref|YP_255707.1| 123 -IPEILLPVT---AHPAFNKASDYLGMKVTPVKIDPER--TTVDLEDLKSKLKEN--TA-MIVASAPNYPFGTIDDVKALS 194
                                   .455666665...7899******************954..888899988889999..55.6789999999*********** PP

                                   HHHHHCT-EEEEE-TTGGGGGGSGGGGG.......GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECC CS
                 Pyridoxal_deC 222 dicekydlwlHvDAAyaGsaficpeirh.......llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeY 295
                                   +i +  +lwlHvD   +G  f+ p+ r        ++  +e + Si++  hK++ ++ ++s++++++++  ++   +   +
  gi|70606837|ref|YP_255707.1| 195 EIAQDKKLWLHVDSCIGG--FLLPFLRDlgepippFDLSLEGVTSISADLHKYGYAPRGASVVLFRNSSYREGSIFVMSRW 273
                                   ******************..*******9999999999******************************98777666555555 PP

                                   CT.TTTTTSEECCCGSSSSSGHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Pyridoxal_deC 296 LehedsdvaadlgtkaiplsrrvrilklwfvlralGveglqnqirksvelakyl 349
                                    +   +   + ++t ++ +      +  w ++  lG  g+++  ++ ++   +l
  gi|70606837|ref|YP_255707.1| 274 PG---Y---PIVNTSVLSTRSAGPLAAAWGIIHGLGKDGYRKLANRILNTRIKL 321
                                   55...2...222333333333444555666666666666666666666555555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.4e-13   7.2e-10      66     177 ..      96     209 ..      83     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.4e-13
                                   EESSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHHH--TTEEEEE CS
                   Aminotran_5  66 ftsGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeeg.eldldelekllnektklva 144
                                   ft G+te+i ++ +s+++  lk+  +++   +    ++ + +++++  g+kv+ +++d+e  ++dl++l+++l+e+t+++ 
  gi|70606837|ref|YP_255707.1|  96 FTFGGTESIMVATKSARDYfLKRHSSVIPEILLPVTAHPAFNKASDYLGMKVTPVKIDPERtTVDLEDLKSKLKENTAMIV 176
                                   99**************999788777766665555555656789***************8762689**************** PP

                                   EESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 145 ithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                    ++ +   Gti++v+++ ++a++k+ +++vD++
  gi|70606837|ref|YP_255707.1| 177 ASAPNYPFGTIDDVKALSEIAQDKKLWLHVDSC 209
                                   *******************************97 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.2e-10   1.5e-06      95     189 ..     125     209 ..     114     219 .. 0.92
   2 ?    3.6   0.0      0.01        31     250     360 ..     283     393 ..     277     396 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.2e-10
                                   EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHH CS
                 Aminotran_1_2  95 eilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklld 175
                                   eil+p   ++ ++++  + g++v +++++ +e  ++dle+l+ +lke       t +i+   p+ P Gt+ + + l ++  
  gi|70606837|ref|YP_255707.1| 125 EILLPVTAHPAFNKASDYLGMKVTPVKID-PERTTVDLEDLKSKLKE------NTAMIVASAPNYPFGTIDDVKALSEI-- 196
                                   6999***********************77.7777*************......889**************999999999.. PP

                                   HHHHTTEEEEEEET CS
                 Aminotran_1_2 176 lakkynlllfvDea 189
                                    a+ ++l+l vD  
  gi|70606837|ref|YP_255707.1| 197 -AQDKKLWLHVDSC 209
                                   .***********86 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.01
                                   HTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHCHHHHHHH..HHHT CS
                 Aminotran_1_2 250 flsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaetakelskk..Llee 327
                                   +ls+ ++ +++aa+     l ++   + + r+ + r +l++eL + g  +l+++ +g++++t  +      l++   L + 
  gi|70606837|ref|YP_255707.1| 283 VLSTRSAGPLAAAWGIIHGLGKDGYRKLANRILNTRIKLTNELPKMGYRILGKPlGGIVSFTSEEFN----LAELptLMKG 359
                                   55533333333333333334456788999*************************9*****9654433....3443668888 PP

                                   CTEEEEEGGGGTS.TTEEEEECTTS-HHHHHHHH CS
                 Aminotran_1_2 328 vgvyvtpgtsftv.pgrlRitvAglteeeleelv 360
                                   + +  +pg+     p+++ +t+A + ++ ++e++
  gi|70606837|ref|YP_255707.1| 360 WFIQYQPGSRILGfPKSIHLTIAPGHDKVVDEFL 393
                                   8888888875555588888888777777777776 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.6e-08   4.9e-05      65     146 ..     125     209 ..      99     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                                   EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEE CS
               DegT_DnrJ_EryC1  65 eVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvi 142
                                   e++ p +   a  +a  +lg+k+ +v +dp+  ++d +++++++ e+t+ I++      +G + d++al +ia++++l++ 
  gi|70606837|ref|YP_255707.1| 125 EILLPVTAHPAFNKASDYLGMKVTPVKIDPERTTVDLEDLKSKLKENTAMIVASApnyPFGTIDDVKALSEIAQDKKLWLH 205
                                   67788888888899999*******************************999965422269********************* PP

                                   EE-T CS
               DegT_DnrJ_EryC1 143 eDaA 146
                                    D++
  gi|70606837|ref|YP_255707.1| 206 VDSC 209
                                   *998 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     7e-07    0.0021     111     176 ..     146     210 ..     101     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7e-07
                                   THHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
               Cys_Met_Meta_PP 111 vlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                    ++ ++i+ + + t dle+l++++kent ++   +p  p+  + D+++++++a+++++ + vD ++
  gi|70606837|ref|YP_255707.1| 146 KVTPVKIDPERT-TVDLEDLKSKLKENTAMIVASAPNYPFGTIDDVKALSEIAQDKKLWLHVDSCI 210
                                   333333333333.3589**********************************************986 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     6e-05      0.18      69     169 ..     117     209 ..      77     213 .. 0.70
   2 ?   -1.2   0.0      0.33   9.9e+02     191     216 ..     237     312 ..     222     351 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
                                   -TTEEEEEETT....-HHHHSSTTHHHHC.C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB- CS
               Beta_elim_lyase  69 qrgeevivtep....ahihfdetgaiael.agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqv 144
                                   +r+++vi ++     ah  f  +  +  l   v++++++ ++  ++dle+l++++ke      ++++i+   + n+     
  gi|70606837|ref|YP_255707.1| 117 KRHSSVIPEILlpvtAHPAFNKASDY--LgMKVTPVKIDPER-TTVDLEDLKSKLKE------NTAMIVA-SAPNY---PF 184
                                   55555555444443355555544333..22345566666666.9************9......6778865.56666...45 PP

                                   --HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase 145 vsleelrevaaiakkygiplhlDgA 169
                                    +++ ++++++ia+++++ lh+D++
  gi|70606837|ref|YP_255707.1| 185 GTIDDVKALSEIAQDKKLWLHVDSC 209
                                   5789*******************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.33
                                   EEEEESSSTT--SS-.EEEEE-HH.................................................... CS
               Beta_elim_lyase 191 svtmslkKdllanvG.gvlafrddel.................................................e 216
                                   s+++ l K + a+ G +v++fr++++                                                 +
  gi|70606837|ref|YP_255707.1| 237 SISADLHKYGYAPRGaSVVLFRNSSYregsifvmsrwpgypivntsvlstrsagplaaawgiihglgkdgyrklaN 312
                                   6778889999999998899999887777766666666666666655555555555555555555555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3615.41
//
Query:       gi|70606838|ref|YP_255708.1|  [L=504]
Description: sugar kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-38  130.9   0.0    9.5e-38  130.1   0.0    1.4  1  FGGY_N          FGGY family of carbohydrate kinases, N-termin
    1.4e-24   86.9   0.0    2.2e-24   86.3   0.0    1.2  1  FGGY_C          FGGY family of carbohydrate kinases, C-termin
     0.0035   16.2   0.2      0.033   13.0   0.1    2.1  2  MreB_Mbl        MreB/Mbl protein
  ------ inclusion threshold ------
      0.051   12.8   0.0       0.42    9.8   0.0    2.2  2  Hydantoinase_A  Hydantoinase/oxoprolinase
       0.19   11.4   0.0        2.6    7.7   0.0    2.3  2  Raco_middle     RACo middle region


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.0   2.7e-41   9.5e-38       1     245 []       6     258 ..       6     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 2.7e-41
                                   EEEEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS CS
                        FGGY_N   1 lilglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqre 80 
                                   +++++D+Gttstk  +++ ++ +v +  +++  +++pk+gwaeqd++++w+++ +  r +le     +  i+++ + + + 
  gi|70606838|ref|YP_255708.1|   6 YVIAFDVGTTSTKCGIISlKDFEVRKLVSTKSIVNYPKKGWAEQDANKLWETIVDLGRTALEDF---KFTISGLVFDAHMA 83 
                                   89**************************************************************...889*********** PP

                                   -EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHC.........CHHHHH.SS-SSTTSH.HHHHHHHHHHSCCHHCCH CS
                        FGGY_N  81 glvllDkndkpLynailwkdrrtaeiveklkeegnek.........klyekt.glvlstgft.lsklkWlkenepevfeki 150
                                   g++ +D  ++pL+nai+w d+r+++  e l + +++          k+  +t g + +tg   +sk+ W+++ne+++f k+
  gi|70606838|ref|YP_255708.1|  84 GVIPVDASGEPLRNAIIWLDERASGLPEDLWKGVIKLqgysilkllKFLRITgGAPSKTGKDvISKIIWIAQNERDIFSKT 164
                                   **************************999988444430111111112223331455566654259**************** PP

                                   CEEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTE..E-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-E CS
                        FGGY_N 151 ekflliddyLiwrLtgqfvtdvtnasesmlfnikkle..wdeellailgipeelLPklvesseiigelkpelaaklGlkeg 229
                                    k l i+ +Li + +g+fvt + +as s l + ++    w++e+l    i+++lLP++++s+ i+g++k e+a+ +G   +
  gi|70606838|ref|YP_255708.1| 165 YKLLDIKGFLISKASGVFVTSHDEASLSWLADTRTARaiWSDEILRDYKIDRNLLPEIKKSTDIAGYVKGEVAKLFG---E 242
                                   ********************************9986555**************************************...9 PP

                                   EEEEEEEEHHHHHHHH CS
                        FGGY_N 230 vpvvggggDqqaaalG 245
                                   +pv  g+gD  a+a+G
  gi|70606838|ref|YP_255708.1| 243 IPVFVGAGDLTASAVG 258
                                   *************998 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0     6e-28   2.2e-24       5     187 ..     271     438 ..     268     449 .. 0.86

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 6e-28
                        FGGY_C   5 lGTssflll.vgtkpv...isehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaae 81 
                                   +GTs  +   +++++v     + ++l+       ++ y++ + + vag++++w+++ lg+          e+ ++e +++ 
  gi|70606838|ref|YP_255708.1| 271 IGTSDWVAShISKRKVdvfHYVGSILS-----AIPGKYLYVAEQEVAGGAIEWVMRLLGM----------ERNYEEVEKLV 336
                                   688888888888888833222333333.....4669*********************999..........24455555777 PP

                        FGGY_C  82 avadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskn 162
                                   ++ d   ++f+p++ g+r+p+ dp +rg i+++s ++++a+i rA++e+val ++++    +kd    ++++ ++GGg+  
  gi|70606838|ref|YP_255708.1| 337 KSIDKTSLLFLPWLYGERSPIDDPTVRGGILNISLESSKAEILRAVMEGVALNIKWVFPLVAKD----VKEVNIVGGGALF 413
                                   8999999******************************************************777....************* PP

                        FGGY_C 163 dllmqllAdilgvpVerpktaeata 187
                                   d ++q+ Ad +g+pV+r+k  e t 
  gi|70606838|ref|YP_255708.1| 414 DSWCQIVADSIGLPVKRVKRPELTG 438
                                   *******************988775 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.052   1.9e+02     149     171 ..       9      31 ..       2      45 .. 0.81
   2 !   13.0   0.1   9.2e-06     0.033     245     318 ..     374     445 ..     365     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.052
                                   EEEE-SS-EEEEEEETTEEEEEE CS
                      MreB_Mbl 149 vvdiGggttevavislggivtsk 171
                                     d+G  +t++ +isl +  + k
  gi|70606838|ref|YP_255708.1|   9 AFDVGTTSTKCGIISLKDFEVRK 31 
                                   469*************9876655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.2e-06
                                   HHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHHT CS
                      MreB_Mbl 245 alkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgkv 318
                                   + +e ++a++e v+  ++ + p  a+d+ +  + ++GGgal+    +++ +++glpvk  ++p  +  +G g++
  gi|70606838|ref|YP_255708.1| 374 SKAEILRAVMEGVALNIKWVFPLVAKDVKE--VNIVGGGALFDSWCQIVADSIGLPVKRVKRPELTGLRGLGAI 445
                                   556788999999999999999999999966..6678****************************9999999876 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00012      0.42      78     104 ..       4      30 ..       1      42 [. 0.83
   2 ?   -0.1   0.0      0.12   4.4e+02     209     266 ..     370     427 ..     326     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevs 104
                                   +k vI fD+G Tst++  i+ + +ev+
  gi|70606838|ref|YP_255708.1|   4 DKYVIAFDVGTTSTKCGIISLKDFEVR 30 
                                   6779***************98888876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.12
                Hydantoinase_A 209 kveevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvk 266
                                   ++e   ++il+++ e +a +++ +     +d+ke+++v+ G   ++ ++ +a+++g++
  gi|70606838|ref|YP_255708.1| 370 SLESSKAEILRAVMEGVALNIKWVFPLVAKDVKEVNIVGGGALFDSWCQIVADSIGLP 427
                                   4666667899999999999999999999999999999888877899999999999865 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00074       2.6       1      32 [.       6      40 ..       6      45 .. 0.72
   2 ?    0.9   0.0     0.091   3.3e+02      36      53 ..     141     158 ..     138     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00074
                   Raco_middle  1 yGlavDiGtTtvvaaLvdlet...gkelaeasalN 32
                                  y +a+D+GtT+  + ++ l++   +k ++++s +N
  gi|70606838|ref|YP_255708.1|  6 YVIAFDVGTTSTKCGIISLKDfevRKLVSTKSIVN 40
                                  679********987666555422177788888877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.091
                   Raco_middle  36 kyGeDvlsRiayakeeee 53 
                                   k G+Dv+s i   +++e 
  gi|70606838|ref|YP_255708.1| 141 KTGKDVISKIIWIAQNER 158
                                   68********99888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3672.97
//
Query:       gi|70606839|ref|YP_255709.1|  [L=401]
Description: hypothetical protein Saci_1059 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-32  110.7  39.2    9.6e-32  110.3  39.2    1.3  1  MFS_1       Major Facilitator Superfamily
    3.8e-08   32.6  26.9    5.5e-05   22.2   7.0    2.9  3  Sugar_tr    Sugar (and other) transporter
     0.0084   14.6   8.7       0.39    9.0   8.7    2.3  1  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
      0.092   11.6  25.0        5.6    5.7  24.3    3.1  1  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3  39.2   2.1e-35   9.6e-32       3     351 ..      13     351 ..       7     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.1e-35
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa. 82 
                                   ++a++s l + +++++ ++++++ +++ +  igll ++  l ++ +s+p+G ++d+ G +  + lg+l++a+++++ +f+ 
  gi|70606839|ref|YP_255709.1|  13 FVAAISQLLWLNFASITTPIMTDLYNVPAEDIGLLSAIWPLIFIPLSIPAGIITDKKGFKYAVSLGALIMAVFSVARIFSg 93 
                                   455555555555666666699****************************************************88888987 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaiv 160
                                    +++lll++  l+G+g+ ++++++  ++ +wf ++erg+a+gl+ +g  lG + + ++ ++l+   +   ++ + ++  ++
  gi|70606839|ref|YP_255709.1|  94 ENFTLLLIFQSLAGVGQPFVYTSISKMVIEWFEDKERGLATGLAVIGQFLGLMSALIFTPMLVPDTNfseFQTMLIVYSAI 174
                                   8888***********************************************************66666699999******* PP

                         MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls 241
                                   s+l++++f ++  e+++++  ++          +++v+    +lk+  + il + ++++  +f+g+lt++ ++  e +g+s
  gi|70606839|ref|YP_255709.1| 175 SVLSLIIFTVVAKEKKVSSTESNM-------ISFGVVK---GVLKSTDFIILNVLFFIGIGFFTGILTWIESI-LEPRGIS 244
                                   ***988544444444444444444.......4445555...555555554345555555555555*******7.******* PP

                         MFS_1 242 glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsll 322
                                    +  +g++ +l+ ++g+++++++ +lsd+l+r+++ +l  l + ++a++l+++ v+++ ++l ++ +l+Gf+l  + p+ l
  gi|70606839|ref|YP_255709.1| 245 -VTDSGVIAGLILIGGIFGSIVIPFLSDKLQRKKMFFL--LDFGISAIMLYFITVSNDFIILSVSTFLLGFFLVSALPIGL 322
                                   .****************************999555555..5555555566666666558888889999***9999****** PP

                         MFS_1 323 alasdlappeeagtasglfntagslggal 351
                                    + ++l+ p+++gt++++  ++ + g++l
  gi|70606839|ref|YP_255709.1| 323 DYSAQLVEPNMTGTIQSILWLIAQGGAVL 351
                                   ******************99877777665 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.065   2.9e+02     386     414 ..      10      38 ..       6      61 .. 0.77
   2 !   19.3   7.1   9.7e-08   0.00043      63     190 ..      59     184 ..      40     189 .. 0.89
   3 !   22.2   7.0   1.2e-08   5.5e-05      44     153 ..     244     351 ..     186     395 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.065
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                      Sugar_tr 386 kalaiavavnwlanflisllfpiiteaig 414
                                   + + +a+ ++ l+  + s+++pi+t+ ++
  gi|70606839|ref|YP_255709.1|  10 SYMFVAAISQLLWLNFASITTPIMTDLYN 38 
                                   56889999*****************9998 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 9.7e-08
                                   HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHH CS
                      Sugar_tr  63 slfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvsly 143
                                   s+ ag+++d+ G k++   +a+++ + +v  +++   +++ +l++ + l+G+g  ++++ ++  + E   +k Rg  ++l 
  gi|70606839|ref|YP_255709.1|  59 SIPAGIITDKKGFKYAVSLGALIMAVFSVARIFSG--ENFTLLLIFQSLAGVGQPFVYTSISKMVIEWFEDKERGLATGLA 137
                                   7789*******************************..79****************************************** PP

                                   HHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                      Sugar_tr 144 qlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllf 190
                                     +  +G + a if+  l  +t+  ++++ +l + +++++l li++++
  gi|70606839|ref|YP_255709.1| 138 VIGQFLGLMSALIFTPMLvPDTNF-SEFQTMLIVYSAISVLSLIIFTV 184
                                   *************99998655555.79*****9999999998887765 PP

  == domain 3  score: 22.2 bits;  conditional E-value: 1.2e-08
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                   s ++sg+i+++ l+G+i+Gs+++ +l+d++ Rkk   ++ + f i+a++ ++++  n + +l v+ +l+G+++  a  +  
  gi|70606839|ref|YP_255709.1| 244 SVTDSGVIAGLILIGGIFGSIVIPFLSDKLQRKKM--FFLLDFGISAIMLYFITVSNDFIILSVSTFLLGFFLVSALPIGL 322
                                   67899*****************************5..56777899*********99***************9876666666 PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilv 153
                                    y + +  +++ g++ s+  l  + G ++
  gi|70606839|ref|YP_255709.1| 323 DYSAQLVEPNMTGTIQSILWLIAQGGAVL 351
                                   66666666666666666666666666555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   8.7   8.8e-05      0.39      36     355 ..      32     348 ..      12     359 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 8.8e-05
                         MFS_3  36 lmtdisaspl.mvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligi 115
                                   +mtd+   p+  + l+ a   L  + lsi+aG+++D+   +  +  + l++a+ sv   +++     +  lll++  l+g+
  gi|70606839|ref|YP_255709.1|  32 IMTDLYNVPAeDIGLLSAIWPLIFIPLSIPAGIITDKKGFKYAVSLGALIMAVFSVAR-IFSGE---NFTLLLIFQSLAGV 108
                                   5666666654246666666666666689999999998877777666766666666543.44444...45689999999999 PP

                         MFS_3 116 GaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlv..aavGaalaf..avnalsylalivallrwkre 192
                                   G+ +   + + +v e  + ++   A  L  +g  +        + +lv  + +    +      a+s l li+  + +k +
  gi|70606839|ref|YP_255709.1| 109 GQPFVYTSISKMVIEWFEDKERGLATGLAVIGQFLGLMSALIFTPMLVpdTNFSEFQTMliVYSAISVLSLIIFTVVAKEK 189
                                   999999999999999999888888888877777666555555555555222233332220033455655555544444433 PP

                         MFS_3 193 vrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvard.qldg.dalvyGillgalGvGAilga 271
                                    + ss  ++ +  ++  g+  +         ++  +lF++       +L  +    +  g   +  G++ g + +G i+g+
  gi|70606839|ref|YP_255709.1| 190 -KVSSTESNMISFGVVKGVLKST------DFIILNVLFFIGIGFFTGILTWIESIlEPRGiSVTDSGVIAGLILIGGIFGS 263
                                   .3344455556555555543222......223444455555554445554443320233314456799999999******* PP

                         MFS_3 272 lllsrLRerlsserlvllaavalAlvll.slalasslwvavlvlllgGaaWitals.tlnvavqlavPrWvvgRalavYlt 350
                                   ++ ++L ++l+ +++  l  +++ +++l  ++++++  ++ +   l+G   + al  +l+ ++ql+ P+   g   ++   
  gi|70606839|ref|YP_255709.1| 264 IVIPFLSDKLQRKKMFFLLDFGISAIMLyFITVSNDFIILSVSTFLLGFFLVSALPiGLDYSAQLVEPNM-TGTIQSILWL 343
                                   **************9988877776666516788888899999999**********648**********94.5555666666 PP

                         MFS_3 351 vlaGg 355
                                   + +Gg
  gi|70606839|ref|YP_255709.1| 344 IAQGG 348
                                   66655 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  24.3    0.0012       5.6      30     359 ..      38     346 ..      14     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0012
                    MFS_1_like  30 glkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaekt 110
                                   ++ a++ig++++i pl+ i  +   g + D+ g + +v + +l++++ +++ ++                       ++++
  gi|70606839|ref|YP_255709.1|  38 NVPAEDIGLLSAIWPLIFIPLSIPAGIITDKKGFKYAVSLGALIMAVFSVARIF-----------------------SGEN 95 
                                   567899999999999999988888999999999999998888888888888888.......................8999 PP

                    MFS_1_like 111 fwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllp.......ysally 184
                                   f +l+++ +la + ++ + + +  +++++ +++++         + G a++  ++G++   + + +l        ++++l+
  gi|70606839|ref|YP_255709.1|  96 FTLLLIFQSLAGVGQPFVYTSISKMVIEWFEDKERGL-------ATGLAVIGQFLGLMSALIFTPMLVpdtnfseFQTMLI 169
                                   9999999999999999999999999999997777664.......33444444444444443333322234444447789** PP

                    MFS_1_like 185 vlaallvisllvvlilnetekesklkvtksl.qvllnilknpeviifllvalilgmswgiienFlflYLkelgas....nt 260
                                   v+ a+ v+sl+++ ++ + +k s+++   +   v++ +lk    ii+ +  +i   ++  i ++++  L+  g s    + 
  gi|70606839|ref|YP_255709.1| 170 VYSAISVLSLIIFTVVAKEKKVSSTESNMISfGVVKGVLKSTDFIILNVLFFIGIGFFTGILTWIESILEPRGISvtdsGV 250
                                   ***********99988888887777666555588999**********99999976566666789*****999986222255 PP

                    MFS_1_like 261 llGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvski 341
                                   ++G +++ g +++i++ f++ kl +k  + +ll ++++a++l f+ +   +++ ++ +  +L g+ +     ++ +y++++
  gi|70606839|ref|YP_255709.1| 251 IAGLILIGGIFGSIVIPFLSDKLQRKK-MFFLLDFGISAIMLYFITV--SNDFIILSVSTFLLGFFLVSALPIGLDYSAQL 328
                                   677777778888888888888876664.6677777777777666655..5899999999********************** PP

                    MFS_1_like 342 apksleatgqgllsglyf 359
                                   + +++ +t+q++l  +  
  gi|70606839|ref|YP_255709.1| 329 VEPNMTGTIQSILWLIAQ 346
                                   ************977755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 2556.26
//
Query:       gi|70606840|ref|YP_255710.1|  [L=287]
Description: hypothetical protein Saci_1060 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-68  229.0  40.3    1.1e-66  225.0  40.3    2.0  1  DUF973      Protein of unknown function (DUF973)
  ------ inclusion threshold ------
       0.12   12.6   7.3       0.15   12.4   5.5    2.2  2  DUF4134     Domain of unknown function (DUF4134)
       0.28   11.4   4.1       0.75   10.0   1.2    2.6  2  Holin_SPP1  SPP1 phage holin
       0.29   11.4  20.7        2.3    8.5  13.4    2.7  2  DUF996      Protein of unknown function (DUF996)
       0.34   10.6  11.4       0.65    9.7  11.4    1.5  1  Yip1        Yip1 domain
        1.9    8.9  13.0       0.96    9.8   2.4    3.1  3  DUF3566     Transmembrane domain of unknown function (DUF3566
        3.1    7.7   4.7        2.2    8.2   2.6    1.9  2  TMEM154     TMEM154 protein family
          8    6.7  12.4          5    7.4   0.5    2.8  3  DUF2304     Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0  40.3   4.9e-70   1.1e-66       3     310 .]       6     286 ..       4     286 .. 0.94

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 4.9e-70
                        DUF973   3 egleklregslfliiasllaliliilvlvvlft....aissgl.......sqliqssasilssvlllliaaii..liiias 70 
                                   ++l +++ gslfl ++s+l++++ii+vl+++f+    +i++++       sql+q+++++l++ l+++i++i+  ++ii+s
  gi|70606840|ref|YP_255710.1|   6 SALGRIKIGSLFLELSSILFIVSIIVVLYTAFNtvakYINTSNgvsglnqSQLQQELLKQLNTPLIHAIPIIVtvIAIIGS 86 
                                   689******************************666644443377999*************************9999**** PP

                        DUF973  71 vllilgll..kirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilaliGqi 149
                                   +l+++g+l  ki++++s+L         G++g+++++iga++                     ++++++l+g i+++iGqi
  gi|70606840|ref|YP_255710.1|  87 ILILTGYLneKIKTNYSDL---------GKVGTIIMIIGAVV---------------------YALPVNLFGDIIFVIGQI 137
                                   *******9999********.........99999998888877.....................667899************ PP

                        DUF973 150 llglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsklrsttsqvpvlqvpstpqqvqisqvgqGtl 230
                                   +lg+sfy++Ge++n+g +k++Gil+++p++ i+++IGy+lsyig+++v+++l+s             +++v++s++g+G++
  gi|70606840|ref|YP_255710.1| 138 ILGISFYRTGETFNEGSLKNAGILVALPFL-ITQVIGYALSYIGVNKVIRELNS------------AKKTVKVSSLGSGII 205
                                   ****************************99.******************87766............446899********* PP

                        DUF973 231 rsnGtanltvysqvqvqIlsAsiegtnysttsinPntLkvGnNsitinFntv.lnLvpgstYtirLlLsngqtidvevtyq 310
                                   r+nG+ ++++ys+ +v I++A+i gtny++tsi+Pn+Lk+G+N+iti+Fn++ lnL+p+s Yt+rLlL+ng++id++vt q
  gi|70606840|ref|YP_255710.1| 206 RGNGILTISLYSDSDVYITQAQIVGTNYISTSITPNYLKHGFNNITIDFNNLsLNLIPNSLYTVRLLLANGDSIDIQVTAQ 286
                                   ***************************************************99*************************987 PP

>> DUF4134  Domain of unknown function (DUF4134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.5   6.5e-05      0.15       5      87 ..      30     119 ..      23     127 .. 0.77
   2 ?   -2.4   0.0       2.8   6.3e+03      74      86 ..     125     137 ..     119     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                       DUF4134   5 lllvlaalsafAqsk....Gaagise...atsevasyfdpvtkliyaiaavvglvgalkvYikwnsgdqdvkksiaawfga 78 
                                   ++++ +a +++A+      G +g+++   +++ +++  +p+ + i +i  v++++g++ +   + +++ +++ s  + +g 
  gi|70606840|ref|YP_255710.1|  30 IVVLYTAFNTVAKYIntsnGVSGLNQsqlQQELLKQLNTPLIHAIPIIVTVIAIIGSILILTGYLNEKIKTNYSDLGKVGT 110
                                   4444555555555445666999996522245668889999***************************************** PP

                       DUF4134  79 ciflvvaat 87 
                                   +i+++ a++
  gi|70606840|ref|YP_255710.1| 111 IIMIIGAVV 119
                                   *99997654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                       DUF4134  74 awfgaciflvvaa 86 
                                    +fg +if++   
  gi|70606840|ref|YP_255710.1| 125 NLFGDIIFVIGQI 137
                                   5677777777644 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.23   5.1e+02      40      72 ..      28      60 ..      12      66 .. 0.67
   2 ?   10.0   1.2   0.00033      0.75      10      53 ..      76     121 ..      72     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.23
                    Holin_SPP1 40 aitlvftvataivawyKNnyvTkkakkqkevlk 72
                                   i +v+ +a+ +va y N++ +  + +q ++ +
  gi|70606840|ref|YP_255710.1| 28 SIIVVLYTAFNTVAKYINTSNGVSGLNQSQLQQ 60
                                  455666677778888888888887755555444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                    Holin_SPP1  10 tillllallnqlltilGknplpidee..alytaitlvftvataiva 53 
                                    i+ ++a++ ++l+++G     i+ +   l +++t+++ ++++++a
  gi|70606840|ref|YP_255710.1|  76 IIVTVIAIIGSILILTGYLNEKIKTNysDLGKVGTIIMIIGAVVYA 121
                                   5999*************98777776666999999999999999987 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  13.4     0.001       2.3      32     135 .]      21     137 ..       3     137 .. 0.66
   2 ?    7.5  12.7     0.002       4.6      32     133 ..      75     180 ..      74     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                        DUF996  32 afilsiialvva.ilalllvlgalatalelpgleeaas.......lilllllvl.iiayvlliisavflkksyellgkrtg 103
                                   + il i++++v+ + a+ +v+  + t  +  gl++          l + l+ ++ ii++v++ii ++++   y + + +t+
  gi|70606840|ref|YP_255710.1|  21 SSILFIVSIIVVlYTAFNTVAKYINTSNGVSGLNQSQLqqellkqLNTPLIHAIpIIVTVIAIIGSILILTGYLNEKIKTN 101
                                   44555553333324444444555555555555555443567779744444444459999**************999***** PP

                        DUF996 104 vklFetagll.yfiGaiLtiv...lvGliilliaei 135
                                    + + ++g++ ++iGa+   +   l G ii +i++i
  gi|70606840|ref|YP_255710.1| 102 YSDLGKVGTIiMIIGAVVYALpvnLFGDIIFVIGQI 137
                                   ****9999862689**96544111679999999998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                        DUF996  32 afilsiialvvailalllvlgalatalelpgleeaas..lilllllvl...iiayvlliisavflkksyellgkrtgvklF 107
                                   ++i+++ia++  il+l + l + +    +   + ++   +i+ ++ +l   ++  ++++i  + l  s++++g+++++  +
  gi|70606840|ref|YP_255710.1|  75 PIIVTVIAIIGSILILTGYLNEKIKTNYSDLGKVGTIimIIGAVVYALpvnLFGDIIFVIGQIILGISFYRTGETFNEGSL 155
                                   5666667666666666666655554444443343333553333333335336677************************** PP

                        DUF996 108 etagllyfiGaiLtivlvGliillia 133
                                   + ag+l+ +  +L+  ++G  +++i+
  gi|70606840|ref|YP_255710.1| 156 KNAGILVALP-FLITQVIGYALSYIG 180
                                   ******9986.555567899999997 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.4   0.00029      0.65      28     151 ..      23     184 ..      13     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                          Yip1  28 llalltlllgllas...............lnlgqtlasg........eevqgltlssllgaiiggylglllgllllalllh 85 
                                   +l++++++++l+++               +                    q  t ++++  ii+++++++ ++l+l+++l+
  gi|70606840|ref|YP_255710.1|  23 ILFIVSIIVVLYTAfntvakyintsngvsG--------LnqsqlqqeLLKQLNTPLIHAIPIIVTVIAIIGSILILTGYLN 95 
                                   334444444444444446666655555542........1333333223444444455555599999999***********9 PP

                          Yip1  86 l....iakllggkgsfkqtlsvvgyallPlilgaliaillllllgt...................llllvgllaliWslvl 143
                                            lg  g++  ++ +v+yal ++++g +i+++  ++lg                    l++l +l+  + +++l
  gi|70606840|ref|YP_255710.1|  96 EkiktNYSDLGKVGTIIMIIGAVVYALPVNLFGDIIFVIGQIILGIsfyrtgetfnegslknagiLVALPFLITQVIGYAL 176
                                   955554455558888999********999999999999888888889999************9875555566666666666 PP

                          Yip1 144 lylglkaa 151
                                    y+g++++
  gi|70606840|ref|YP_255710.1| 177 SYIGVNKV 184
                                   66666654 PP

>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.4   0.00043      0.96      23      92 ..      20      87 ..       7      93 .. 0.79
   2 ?    2.9   0.7     0.059   1.3e+02      92     112 ..     110     130 ..     107     135 .. 0.87
   3 ?    2.1   0.1       0.1   2.3e+02      19      61 ..     158     198 ..     150     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                       DUF3566 23 lsvalfivlvvavavlylvldalgvfdkvnslvkdlvgeessldleevlslgrvlslaalvgvvnvvllt 92
                                  ls +lfiv    ++vly++ +++  + + ++ v+ l++++ +++l + l++  + ++ ++v v+ ++   
  gi|70606840|ref|YP_255710.1| 20 LSSILFIVS--IIVVLYTAFNTVAKYINTSNGVSGLNQSQLQQELLKQLNTPLIHAIPIIVTVIAIIGSI 87
                                  344444444..4579********9999999**********9999*9*****9999999998888887544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.059
                       DUF3566  92 talatlaallYNlvadlvGGl 112
                                   t++ +++a++Y l ++l+G +
  gi|70606840|ref|YP_255710.1| 110 TIIMIIGAVVYALPVNLFGDI 130
                                   88999************9965 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.1
                       DUF3566  19 lsfllsvalfivlvvavavlylvldalgvfdkvnslvkdlvge 61 
                                    ++l+++ ++i +v+ +a+ y+ +++  v+ ++ns+ k+++ +
  gi|70606840|ref|YP_255710.1| 158 AGILVALPFLITQVIGYALSYIGVNK--VIRELNSAKKTVKVS 198
                                   56788888999999999999988774..667777666665554 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.6   3.6e+03      71      81 ..      23      33 ..      20      50 .. 0.68
   2 ?    8.2   2.6   0.00097       2.2      36      91 ..      45     101 ..      29     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                       TMEM154 71 llllvviiliq 81
                                  +l++v ii++ 
  gi|70606840|ref|YP_255710.1| 23 ILFIVSIIVVL 33
                                  55555555553 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00097
                       TMEM154  36 kqeeakeslssaelsne.sdqlelvlmiiiPlvllillllvviiliqkkkrkrsKdd 91 
                                   ++++    l++ +l++e   ql+  l+ +iP +++++ ++  i++ + +  +++K +
  gi|70606840|ref|YP_255710.1|  45 NTSNGVSGLNQSQLQQElLKQLNTPLIHAIPIIVTVIAIIGSILILTGYLNEKIKTN 101
                                   4555555566666665524678889**********9999988888888999999987 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0022         5      64      98 ..      21      55 ..      17      57 .. 0.85
   2 ?    5.8   2.3    0.0068        15       3      48 ..      75     120 ..      73     145 .. 0.82
   3 ?   -3.1   0.1       4.1   9.2e+03       2      29 ..     169     196 ..     168     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0022
                       DUF2304 64 tnllfllgivfllvilfslslklskleekikeLaq 98
                                  +++lf+++i+++l+++f++ +k  + ++ ++ L q
  gi|70606840|ref|YP_255710.1| 21 SSILFIVSIIVVLYTAFNTVAKYINTSNGVSGLNQ 55
                                  57899************999999888888877776 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0068
                       DUF2304   3 qiiliivsvllllliirlvrkkklkleysllwlllalilivlslfp 48 
                                    ii+ +++++  +li+  + ++k+k +ys l  +  +i+i+ +++ 
  gi|70606840|ref|YP_255710.1|  75 PIIVTVIAIIGSILILTGYLNEKIKTNYSDLGKVGTIIMIIGAVVY 120
                                   5899999999999999999999999999988888888888777765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.1
                       DUF2304   2 lqiiliivsvllllliirlvrkkklkle 29 
                                    q+i  ++s + +  +ir ++++k +++
  gi|70606840|ref|YP_255710.1| 169 TQVIGYALSYIGVNKVIRELNSAKKTVK 196
                                   5788888888888888888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1883.96
//
Query:       gi|70606841|ref|YP_255711.1|  [L=424]
Description: hypothetical protein Saci_1061 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2752.75
//
Query:       gi|70606842|ref|YP_255712.1|  [L=193]
Description: hypothetical protein Saci_1062 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1374.69
//
Query:       gi|70606843|ref|YP_255713.1|  [L=178]
Description: hypothetical protein Saci_1063 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-10   38.5   0.0    1.2e-09   38.2   0.0    1.2  1  Cas_NE0113    CRISPR-associated protein NE0113 (Cas_NE0113)
     0.0014   17.5   0.0     0.0019   17.1   0.0    1.3  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
     0.0039   16.8   0.0     0.0054   16.3   0.0    1.2  1  LDcluster4    SLOG cluster4 family
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.18   11.6   0.0    2.4  2  ACT           ACT domain


Domain annotation for each model (and alignments):
>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.6e-13   1.2e-09       5     120 ..      15     117 ..      11     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.6e-13
                    Cas_NE0113   5 vTetldaLlqegepvdevvvittkdgkvrealelLleeflkdygakikldesaihviedvsgeelaDirteedneallqli 85 
                                   + et   L+++g  ++e+ vitt+d++v +a+++++  f       + l+e+  +v      + ++Di+te+d + + +++
  gi|70606843|ref|YP_255713.1|  15 ILETFLYLAKNGVDINEIRVITTRDPEVEKAWKIVKLMF------VCCLKERFSKVEIIQFPVSINDINTEQDLKDFKAFV 89 
                                   55777789999************************4444......45555555544334567889**************** PP

                    Cas_NE0113  86 vrlvrelrenegerlhlsiaGGRKtmsillalaaq 120
                                    +++ +   +     ++ i GGRK ms+ +alaa+
  gi|70606843|ref|YP_255713.1|  90 NNHISSE--D-----YVDITGGRKGMSVAAALAAK 117
                                   *999763..3.....789**************997 PP

>> Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.2e-07    0.0019      41      97 ..      68     123 ..      50     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-07
                                   EEEEE--TT-HHHHHHHHHHHHHHS.TTS-EEEE-SSS-HHHHHHHHHHHHHHTEEE CS
                  Cas_Cas02710  41 evlldedandllelykkikevlekaleeeevivDlTgGtkeMtaglalagillrvkl 97 
                                   ++++ ++  + ++  k +k  ++ +    e +vD+TgG k M++++ala+   ++k+
  gi|70606843|ref|YP_255713.1|  68 QFPVSINDINTEQDLKDFKAFVNNH-ISSEDYVDITGGRKGMSVAAALAAKSKGAKI 123
                                   5566666666666667888888888.667779*****************98877765 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0054      25      69 ..      89     133 ..      73     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                    LDcluster4  25 lGrliAkegavlltGgrtGvmeaaskGakeagGltv.Gilpassek 69 
                                   + + i +e++v +tGgr+G++ aa+ +ak++g   v  i+p++ e 
  gi|70606843|ref|YP_255713.1|  89 VNNHISSEDYVDITGGRKGMSVAAALAAKSKGAKIVtSIIPQD-EY 133
                                   567899************************9986652577774.43 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.1e-05      0.18      11      52 ..      12      57 ..       7      88 .. 0.83
   2 ?    1.0   0.0     0.084   3.8e+02      23      52 ..     105     132 ..     104     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                                  TTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEH CS
                           ACT 11 PGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvde 52
                                  PG + + f  la++g+ i  i + +++d      ++iv +++v + 
  gi|70606843|ref|YP_255713.1| 12 PGGILETFLYLAKNGVDINEIRVITTRDPevekAWKIVKLMFVCCL 57
                                  66666777779*******************9996666666655554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.084
                                   HTTSEEEEEEEEEESTTECEEEEEEEEEEH CS
                           ACT  23 drgiNidsieqrssedkvagivfvvivvde 52 
                                   + g +++ +  + s+   a+iv+++i  de
  gi|70606843|ref|YP_255713.1| 105 RKGMSVAAALAAKSKG--AKIVTSIIPQDE 132
                                   5688888888888888..778777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1196.55
//
Query:       gi|70606844|ref|YP_255714.1|  [L=269]
Description: hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-19   70.6   0.0    3.4e-19   70.3   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    8.7e-19   68.2   1.9      9e-10   38.6   0.0    3.0  3  Abhydrolase_1  alpha/beta hydrolase fold
    1.2e-09   37.8   0.0      2e-09   37.1   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00061   19.4   0.2     0.0013   18.3   0.2    1.5  1  LIDHydrolase   Lipid-droplet associated hydrolase
      0.001   19.2   0.0     0.0015   18.6   0.0    1.3  1  Abhydrolase_4  TAP-like protein
      0.002   16.9   0.0     0.0026   16.5   0.0    1.2  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.021   14.4   0.0    1.3  1  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.3e-22   3.4e-19       1     219 [.      23     262 ..      23     263 .. 0.61

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.3e-22
                                   EEEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH..CHHH.HHHHCCTT...TTSEEEEEETCHHH CS
                 Abhydrolase_6   1 vlllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldled..ladl.aalldelaa.gggpvvlvGHSlGGa 77 
                                   ++llHG ++   ++ +++ +  l++ + v  +D+ G+G+s+  ++d++d  ++ +  ++ ++l + + +++vl+GH+ G +
  gi|70606844|ref|YP_255714.1|  23 LVLLHGIPG--FCYDFRHNVDVLSKKFKVTRLDFKGFGHSEKGDYDVDDfrVEVQaKEIMEALNKlDIHDFVLLGHDIGSI 101
                                   79****666..555455666666999999******************77442222344444444478************** PP

                                   HHHHHHHCC..EE..EEES-..----TTTS----TTHHHHHH..............TT-CCCCHCCH........S-HSCC CS
                 Abhydrolase_6  78 lalaaaplalvvg..vlldppptalpagllaaalelllalla..............llrllawlsre........plprlf 134
                                   ++++ a  +   +  vl++p   a+    ++++    + ++               +lr       +        +  r f
  gi|70606844|ref|YP_255714.1| 102 VSQLIAQET--NCdlVLINP---AYKGMRGRWRDIANEYWYIffhqipiaekmitsNLR-------DyinyfldhLTVRKF 170
                                   999944444..334499999...444444333333333333322222122222222111.......011221222222344 PP

                                   CCHHH..C......CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEEC.TT-CHHH.HCHHCCCH.STTEEETCE... CS
                 Abhydrolase_6 135 laded..a......daawrarlarlaallaglgllpaaawadlpvpllvlg.geDplvp.rllerlla.qagarlpvvlpg 204
                                    ++e   +       +++ a +     ++a++  +++ +++ + + +lvl+ ++Dpl p  +++rl+   ++++l v + +
  gi|70606844|ref|YP_255714.1| 171 KEEEKeeYfkvyeePYSVKALVN---WYRAYVSHFRWNNIRKIKSKTLVLWaENDPLFPtSWVDRLWEeFEDYKL-VKIHD 247
                                   44333221222111222222222...444455566699*********9997699995554889999999999999.***** PP

                                   SSS-HHHHSHHHHHH CS
                 Abhydrolase_6 205 aGHlphleepdevae 219
                                   aGH+ph e+p+ev++
  gi|70606844|ref|YP_255714.1| 248 AGHWPHAENPEEVNN 262
                                   ************986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   3.5e-13     9e-10       3      93 ..      23     109 ..      21     119 .. 0.93
   2 ?    2.1   0.1     0.048   1.2e+02      52      75 ..     147     170 ..     108     171 .. 0.78
   3 !   25.9   0.1   2.6e-09   6.6e-06     196     257 .]     190     257 ..     177     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.5e-13
                                   EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                 Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                   lv+lhG+pg  + ++    ++ L+k +f v  lD  G+g+S+++   + dd++    a+ +  +l++l+++ ++l+Gh+ G
  gi|70606844|ref|YP_255714.1|  23 LVLLHGIPGFCYDFRH--NVDVLSK-KFKVTRLDFKGFGHSEKGDYDV-DDFRVEVQAKEIMEALNKLDIHDFVLLGHDIG 99 
                                   8********7777888..8889998.*******************998.8******************************* PP

                                   HHHHHHHHHH CS
                 Abhydrolase_1  84 Gmialayaae 93 
                                   + ++   a+e
  gi|70606844|ref|YP_255714.1| 100 SIVSQLIAQE 109
                                   *999988876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.048
                                   CHHSHHHHHHHHHHHHHHCTTSSE CS
                 Abhydrolase_1  52 ddygtasvaddldrildalgddkl 75 
                                   + + t +++d+++++ld+l ++k+
  gi|70606844|ref|YP_255714.1| 147 EKMITSNLRDYINYFLDHLTVRKF 170
                                   5678999************99986 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 2.6e-09
                                   CHHHHHHHHHC......THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                 Abhydrolase_1 196 dsaklllrlre......lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                   +  ++++ + +      +++++++tlv+++++Dpl+p +  ++l + + + +lv+i dagH+ + e+p
  gi|70606844|ref|YP_255714.1| 190 ALVNWYRAYVShfrwnnIRKIKSKTLVLWAENDPLFPTSWVDRLWEEFEDYKLVKIHDAGHWPHAENP 257
                                   33444444444555555778*******************99***99****************998876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   7.7e-13     2e-09       4     237 ..      20     255 ..      17     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 7.7e-13
                   Hydrolase_4   4 kavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhS 84 
                                   k  +vl+HG+   +  + + ++ L +  f+v  lD +G+G+se    +v++f   v+ +++++e++ +      ++llGh 
  gi|70606844|ref|YP_255714.1|  20 KRNLVLLHGIPGFCYDFRHNVDVLSK-KFKVTRLDFKGFGHSEKGDYDVDDFRVEVQ-AKEIMEALNKLD-IHDFVLLGHD 97 
                                   6789******************9987.6************************98887.667767777544.5569****** PP

                   Hydrolase_4  85 mGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqv............snnlkadslsrdpe 153
                                    G+++++l++++       l+l++Pa+k        ++  ++++    ++ ++++             n  + +   r+ +
  gi|70606844|ref|YP_255714.1|  98 IGSIVSQLIAQETNC---DLVLINPAYKGMRG----RWRDIANEYWYIFFHQIPIaekmitsnlrdyINYFLDHLTVRKFK 171
                                   ***********9999...9********99855....555555555555555555566666676677766777778888888 PP

                   Hydrolase_4 154 vvaayeadplvhgkitvrlllelldam..krleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                   + ++ e  + + +  +v+ l++ ++a    + +++  ki+  +l+l +e+D++ + +   +l e+    d +l  ++ + H
  gi|70606844|ref|YP_255714.1| 172 EEEKEEYFKVYEEPYSVKALVNWYRAYvsHFRWNNIRKIKSKTLVLWAENDPLFPTSWVDRLWEEFE--DYKLVKIHDAGH 250
                                   888888888888888888888888875115668999*******************999999999998..888888888888 PP

                   Hydrolase_4 233 ellnE 237
                                     + E
  gi|70606844|ref|YP_255714.1| 251 WPHAE 255
                                   87777 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   5.2e-07    0.0013       8     264 ..      26     254 ..      20     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-07
                  LIDHydrolase   8 ipGNPGlveFYetFlsllseklnpelevlgishaGfeleeeekeakenekvfsLedQiehkedflkellekaksekdvkli 88 
                                   + G PG+   +++ + +ls+k    ++v    + Gf  +e+    +   + f +e Q +   + l++l       +  +++
  gi|70606844|ref|YP_255714.1|  26 LHGIPGFCYDFRHNVDVLSKK----FKVTRLDFKGFGHSEKG---DYDVDDFRVEVQAKEIMEALNKL-------DIHDFV 92 
                                   555566655555556666555....99999999999999988...66778888888888888888885.......5689** PP

                  LIDHydrolase  89 lvGHSvGaYialevlkrlsersikkvvlLfPtiediakSpngkkltkllaylpflalvvglllrvl.kllPesvksllikl 168
                                   l+GH +G+ +++ ++++ +++    +vl+ P  + ++   ++    +  +++ ++ ++  ++ + l +++      +l +l
  gi|70606844|ref|YP_255714.1|  93 LLGHDIGSIVSQLIAQETNCD----LVLINPAYKGMRGRWRDIANEYWYIFFHQIPIAEKMITSNLrDYI----NYFLDHL 165
                                   ********************7....9**********9999999999888888888877777775555555....5555555 PP

                  LIDHydrolase 169 vlgkssspkeavettlkfvkspevvrqalhlakdEmeeikeddeeedvllkknkekalvfyfgkkDhWvpeetrdelkell 249
                                    ++k ++  e  e+ +k +++p +v+  ++  +     + +  ++    ++k k+k  +++++++D   p +  d l e++
  gi|70606844|ref|YP_255714.1| 166 TVRKFKE--EEKEEYFKVYEEPYSVKALVNWYRAY---VSHFRWN---NIRKIKSK-TLVLWAENDPLFPTSWVDRLWEEF 237
                                   5544444..35678899999999999888888765...5555566...57888888.788999999999999999999999 PP

                  LIDHydrolase 250 ge.eklevde.kgipHa 264
                                   ++ + +++    ++pHa
  gi|70606844|ref|YP_255714.1| 238 EDyKLVKIHDaGHWPHA 254
                                   99666667555888887 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     6e-07    0.0015      34      91 ..     211     268 ..     192     269 .] 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6e-07
                 Abhydrolase_4  34 aapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYL 91 
                                   ++++L+l +e+Dp  P+++  +l +++++ +lv  +++GH   a++ + v++a+ +++
  gi|70606844|ref|YP_255714.1| 211 KSKTLVLWAENDPLFPTSWVDRLWEEFEDYKLVKIHDAGHWPHAENPEEVNNAILTFF 268
                                   5899************************************998877788888888887 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-06    0.0026      85     276 ..      75     268 ..      40     269 .] 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                                   HHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES---S-..--HHHHHHHHHH...........TTTS CS
                           Ndr  85 ladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinitska..agwvewakeKls....skllkkvgltd 159
                                    a+++++ l++++++ ++ lG  +G  +  +     +e+   lvLin+  k     w + a e +     +  + ++ +t+
  gi|70606844|ref|YP_255714.1|  75 QAKEIMEALNKLDIHDFVLLGHDIGSIVSQL---IAQETNCDLVLINPAYKGmrGRWRDIANEYWYiffhQIPIAEKMITS 152
                                   5899*********************977554...45778899*****9766411569888887765111144466788899 PP

                                   -HHHHHHHHHS-HHHHHHT-HHHHHHHHHHHT-TTHHHHHHHHHHHHT-------TTSSSS-EEEEEETTSTTHHHHHHHH CS
                           Ndr 160 llkdlllahkFgkeeksensdlvreyrkllkerlnsknlelyleaynkRrdleierkklevkvllvvGdkspfvdevvevn 240
                                   +l d++ + +     ++ +++  +ey k  +e  + k l ++ +ay +    +  rk  + k+l++  ++ p   +    +
  gi|70606844|ref|YP_255714.1| 153 NLRDYINYFLDHLTVRKFKEEEKEEYFKVYEEPYSVKALVNWYRAYVSHFRWNNIRKI-KSKTLVLWAENDPLFPTSWVDR 232
                                   9999987655555555556777789**********************99888766555.5689999999999876654444 PP

                                   HHS-TTTEEEEEETT-TT-HHHH-HHHHHHHHHHHH CS
                           Ndr 241 skldkkkttllkvadsgglvleeqPdklaeslklfl 276
                                      + +  +l+k++d+g  + +e+P+ + +++  f+
  gi|70606844|ref|YP_255714.1| 233 LWEEFEDYKLVKIHDAGHWPHAENPEEVNNAILTFF 268
                                   444556788**********************99986 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   8.2e-06     0.021     120     188 ..     186     251 ..     178     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                           DLH 120 pevdaavafYG.lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188
                                     v+a v +Y     + + ++++kik   l+l +e+D+ +p + v++l e++++++    +k+++ agH 
  gi|70606844|ref|YP_255714.1| 186 YSVKALVNWYRaYVSHFRWNNIRKIKSKTLVLWAENDPLFPTSWVDRLWEEFEDYKL---VKIHD-AGHW 251
                                   5699******9444556899********************************77663...45555.7775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1788.83
//
Query:       gi|70606845|ref|YP_255715.1|  [L=265]
Description: hypothetical protein Saci_1065 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   27.7  27.2    1.6e-06   27.7  27.2    1.4  2  ABC2_membrane    ABC-2 type transporter
     0.0017   17.5  34.1     0.0023   17.1  34.1    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  27.2   1.8e-10   1.6e-06       6     201 ..       3     211 ..       1     213 [. 0.73
   2 ?   -3.2   0.4      0.52   4.7e+03      61      61 ..     238     238 ..     218     252 .. 0.45

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.8e-10
                 ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgn.lg.nsedglnr...pgllffsvlflafsaltsvapvferergv 81 
                                   llk+++++ +r+p+ + +w + +++++ ++  ++ ++ ++ + ++   +    +  ++++l  + + + s+ ++  ++ g 
  gi|70606845|ref|YP_255715.1|   3 LLKYTVKRLLRNPYVL-FWAIGFMIFWEVIGAYIQSKgVPaQYSQ---YyiaSWYAIIALLASS-AVAVSSTFMLNYQTGG 78 
                                   8999*********666.*******************754432222...2344555555555555.4555555999999999 PP

                 ABC2_membrane  82 lerelvsplyslsayvlakvlvelpvsllqalifllivyflv....gldls...rfflflllllltalaasslgl.lisal 154
                                   l +++++   s+  y+l+ + +  +v+++++ i+l+++y+l+    g+d+    +++ f ++++lt+l+ ++l++ l++  
  gi|70606845|ref|YP_255715.1|  79 LSHLFRFSRLSPLYYLLSIYSGITIVIMIVSGIMLATTYLLFgskfGYDIAlprNIIAFAPVFILTGLFYTALSIdLNILS 159
                                   999988888899999999999999999999999999*****94444555557765699**************998434444 PP

                 ABC2_membrane 155 ...apsfedasqlaslvllpllllsGffipidsm..pkwlqwiaylnPltya 201
                                      ++++ +++ + +l+++ l+ +s  + ++ ++   + +  ia l++++y+
  gi|70606845|ref|YP_255715.1| 160 lktTRKIGNVISFLPLIISYLFGFSYLYTNLGNIglGSPFVNIAMLSYYAYM 211
                                   1123455555555566666666666666666666764577778889988887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.52
                 ABC2_membrane  61 l 61 
                                    
  gi|70606845|ref|YP_255715.1| 238 S 238
                                   1 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  34.1   2.6e-07    0.0023     156     337 ..      42     247 ..      30     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.6e-07
               ABC2_membrane_3 156 lsnvasflvg..liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafgl 231
                                   ++ +++++++  +i+++l++  +++ ++++++  + ++ +l   s +spl y+ls + g+ +v ++++ ++l+   l+fg+
  gi|70606845|ref|YP_255715.1|  42 AQYSQYYIASwyAIIALLASSAVAVSSTFMLNYQTGGLSHLFRFSRLSPLYYLLSIYSGITIVIMIVSGIMLAttyLLFGS 122
                                   4555666777866666667777787899********************************************988679998 PP

               ABC2_membrane_3 232 ....gipfg.nlglllllfllfglayialgyllssl.fknsetaqilifivilllsgffgglfpledlpsalkwifsiiPf 306
                                        i    n++++  +f+l gl y+al+  l  l  k++++   +i+++ l++s +fg++++       l +i+   Pf
  gi|70606845|ref|YP_255715.1| 123 kfgyDIALPrNIIAFAPVFILTGLFYTALSIDLNILsLKTTRKIGNVISFLPLIISYLFGFSYLYT----NLGNIGLGSPF 199
                                   6655555556667777**************999999545555554456666666666666666544....45567777777 PP

               ABC2_membrane_3 307 fapglgllrlitgd.plwe................illsliilalfav 337
                                   + ++++ +  ++++ p+                  +l+s+i l+   +
  gi|70606845|ref|YP_255715.1| 200 VNIAMLSYYAYMNQdPPLYlignvnssispvlpliVLISWIGLLSVLA 247
                                   777777777765443444456666666666655543344444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1900.92
//
Query:       gi|70606846|ref|YP_255716.1|  [L=256]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-14   54.5   0.1    2.8e-14   53.8   0.1    1.3  1  ABC_tran  ABC transporter
    4.4e-12   46.4   0.1    2.1e-05   24.5   0.1    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    2.1e-07   31.6   0.1    2.1e-07   31.6   0.1    1.9  3  AAA_23    AAA domain
    7.3e-06   25.6   0.5    0.00092   18.7   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
    4.2e-05   23.2   0.0    8.1e-05   22.3   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
    5.7e-05   23.0   2.2    0.00017   21.4   0.1    2.0  2  AAA_15    AAA ATPase domain
      0.004   17.6   0.1     0.0072   16.7   0.1    1.7  1  AAA       ATPase family associated with various cellular acti
     0.0046   17.1   0.0      0.047   13.8   0.0    2.0  1  AAA_33    AAA domain
  ------ inclusion threshold ------
      0.019   12.5   0.4      0.025   12.1   0.4    1.1  1  DUF3584   Protein of unknown function (DUF3584)
       0.02   15.5   0.6      0.045   14.3   0.6    1.6  1  AAA_18    AAA domain
      0.026   14.2   0.0      0.034   13.9   0.0    1.3  1  AAA_30    AAA domain
      0.031   14.7   0.0      0.039   14.3   0.0    1.3  1  AAA_16    AAA ATPase domain
      0.035   14.0   0.5        0.1   12.5   0.5    1.9  1  ATPase_2  ATPase domain predominantly from Archaea
      0.042   14.2   0.2      0.089   13.1   0.2    1.8  1  AAA_19    AAA domain
      0.049   12.8   0.0      0.054   12.6   0.0    1.3  1  G-alpha   G-protein alpha subunit
      0.067   12.8   0.2       0.15   11.6   0.0    1.6  2  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.14   11.9   0.2       0.16   11.7   0.2    1.4  1  AAA_24    AAA domain
       0.14   11.2   0.1       0.26   10.3   0.1    1.4  1  T2SSE     Type II/IV secretion system protein
       0.17   11.5   0.0       0.26   10.9   0.0    1.2  1  AAA_27    AAA domain
       0.18   12.1   0.0        1.6    9.1   0.0    2.1  1  SbcCD_C   Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.1   3.1e-17   2.8e-14       6     136 ..      21     150 ..      19     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.1e-17
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS....--S-TTSBHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe....pqlfpeltvrenesd 82 
                                   ++l+ ++k+ ++G+nG+GK+t+l++++g  +   G+i++dg ++k+  ++++ k +  l++      +l ++l++ ++ +d
  gi|70606846|ref|YP_255716.1|  21 VTLSLSNKTLLLGPNGSGKTTILRAICGIRD-YDGSIKVDGMEVKR--ISRFTKLSCNLSEAyslgLKLIDKLELLKEIKD 98 
                                   5788999**********************87.79************..444444444444442224666666665555444 PP

                                   TC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  83 ee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +   ++++l+++g+++l+++      + LS Gq +    + al++ pk +++DEp+
  gi|70606846|ref|YP_255716.1|  99 LDislAKNMLKEVGISNLNQNY-----YDLSSGQVVLFNTVLALASYPKQIIIDEPF 150
                                   4445577777777777744444.....8****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.4e-08   2.1e-05       2      28 ..      29      55 ..      28      79 .. 0.74
   2 !   20.3   0.0   4.5e-07   0.00041     231     285 ..     117     168 ..      64     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-08
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrd 28
                                  ++l GpNgsGK+++L+a+ +++++d++
  gi|70606846|ref|YP_255716.1| 29 TLLLGPNGSGKTTILRAICGIRDYDGS 55
                                  89****************777765333 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.5e-07
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                   + ++++lS+G+  l+  ++al++ +k    ++iDEp  + +++  + ++ +lke 
  gi|70606846|ref|YP_255716.1| 117 NQNYYDLSSGQVVLFNTVLALASYPKQ---IIIDEPFENVDYAKRKVIINWLKEY 168
                                   5688*********************88...**********************764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   2.4e-10   2.1e-07       2      40 ..       2      47 ..       1      53 [. 0.77
   2 ?   -1.7   0.1       3.9   3.5e+03     164     164 ..      99      99 ..      62     171 .. 0.68
   3 ?   -2.6   0.0       7.3   6.6e+03     103     122 ..     225     244 ..     166     251 .. 0.62

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.4e-10
                        AAA_23  2 Lkienfrsf........rdqeidFskgltlItGpNGaGKTTildAik 40
                                  ++++n++ +        r++++ +s + tl+ GpNG+GKTTil+Ai+
  gi|70606846|ref|YP_255716.1|  2 IELKNVKVYgeknkeiiRGVTLSLS-NKTLLLGPNGSGKTTILRAIC 47
                                  7899999997743333344444445.889*****************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.9
                        AAA_23 164 e 164
                                    
  gi|70606846|ref|YP_255716.1|  99 L 99 
                                   1 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.3
                        AAA_23 103 ttkkaklelleideleqfis 122
                                   ++k++k++++  +++ ++i+
  gi|70606846|ref|YP_255716.1| 225 EIKGKKFSITIGKDRGDKIK 244
                                   33334444444444444444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1     1e-06   0.00092       5      45 ..       2      47 ..       1      62 [. 0.74
   2 ?    5.6   0.0      0.01       9.2     135     204 ..     104     184 ..      52     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1e-06
                                  EEEESETTEECEEEEE.....ETTSSEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  5 leienFksyagktvil.....pfsksftaivGpNGSGKsnlldAil 45
                                  +e++n+k y +k++++        ++ t ++GpNGSGK+ +l Ai+
  gi|70606846|ref|YP_255716.1|  2 IELKNVKVYGEKNKEIirgvtLSLSNKTLLLGPNGSGKTTILRAIC 47
                                  67888888876554331111123456899***************95 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                                   T.................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                   x.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e.................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                                      LS G+  L    L +A   + ++   ++De   + D +++k + + lke  +    ++++++
  gi|70606846|ref|YP_255716.1| 104 AknmlkevgisnlnqnyyDLSSGQVVLFNTVLALAS--YPKQ--IIIDEPFENVDYAKRKVIINWLKEYGE--EGLIVTHE 178
                                   233333334444455565799999888877666555..4443..589*********************995..46888898 PP

                                   HHHCCC CS
                                   xxxxxx RF
                         SMC_N 199 eemlek 204
                                    +ml+ 
  gi|70606846|ref|YP_255716.1| 179 LDMLSS 184
                                   888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   9.1e-08   8.1e-05      15      42 ..      21      46 ..       4      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.1e-08
                        AAA_29 15 htieidlkgatlltGpsGsGKSTllDAi 42
                                     +++l++ tll Gp+GsGK+T+l Ai
  gi|70606846|ref|YP_255716.1| 21 V--TLSLSNKTLLLGPNGSGKTTILRAI 46
                                  4..4555577***************887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1     2e-07   0.00017      15      43 ..      19      46 ..      13      51 .. 0.92
   2 ?    0.9   0.3      0.32   2.9e+02     268     332 ..      93     149 ..      63     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2e-07
                        AAA_15 15 kdveidlseeltvliGkNnsGKSsileal 43
                                  + v+++ls+  t+l G+N+sGK++il+a+
  gi|70606846|ref|YP_255716.1| 19 RGVTLSLSN-KTLLLGPNGSGKTTILRAI 46
                                  557899***.******************8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.32
                        AAA_15 268 idkikkfnykgkkneeieik.ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEP 332
                                   +++ik++ +  +kn ++e+  ++ ++++++ +sG+  l+  +l ++++ k+         ++i+EP
  gi|70606846|ref|YP_255716.1|  93 LKEIKDLDISLAKNMLKEVGiSNLNQNYYDLSSGQVVLFNTVLALASYPKQ---------IIIDEP 149
                                   334444444444444444447888888888888888888777777777777.........666666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   8.1e-06    0.0072       2      22 ..      30      50 ..      29     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.1e-06
                                  EEESSTTSSHHHHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavakel 22
                                  ll Gp G GKT++ +a++   
  gi|70606846|ref|YP_255716.1| 30 LLLGPNGSGKTTILRAICGIR 50
                                  89****************984 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.3e-05     0.047       3     105 ..      30     178 ..      29     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                        AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdt..........................................lrrrlfgt 40 
                                   ll G++GsGK+t ++ ++  ++    +  d                                           l +++ ++
  gi|70606846|ref|YP_255716.1|  30 LLLGPNGSGKTTILRAICGIRDyDGSIKVDGmevkrisrftklscnlseayslglklidklellkeikdldisLAKNMLKE 110
                                   678*************99777742335555566777777778888888888888888888887777777776644444433 PP

                        AAA_33  41 dqqskt...dytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarrlgvpvrivvve 105
                                      s     +y    ++    l++++   +s  +++i+d +  n++ ++r+ ++++++++g + +iv+ e
  gi|70606846|ref|YP_255716.1| 111 VGISNLnqnYYDL--SSGQVVLFNTVLALASYPKQIIIDEPfeNVDYAKRKVIINWLKEYGEEGLIVTHE 178
                                   3332221112222..2233356677777889999999999977788899999999999999777777766 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   2.8e-05     0.025       9      37 ..      20      46 ..      14      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                       DUF3584  9 GrvaeldldghtnieGtNaaGKTtLlrLi 37
                                  G++  l l+++t + G N++GKTt+lr i
  gi|70606846|ref|YP_255716.1| 20 GVT--LSLSNKTLLLGPNGSGKTTILRAI 46
                                  666..99********************76 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6     5e-05     0.045       2      92 ..      30     144 ..      30     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                        AAA_18   2 lltGtpGvGKttlakeL....skrlgf................gvnlrdvakenglllevdpe...aldeskrldedkldk 59 
                                   ll G+ G+GKtt+ +++         +                 ++l+++++e ++l     +    l+e k ld+   ++
  gi|70606846|ref|YP_255716.1|  30 LLLGPNGSGKTTILRAIcgirD----YdgsikvdgmevkrisrFTKLSCNLSEAYSLGLKLIDkleLLKEIKDLDISLAKN 106
                                   589**************65540....1444555666778888899999999999999999999888777777777777666 PP

                        AAA_18  60 lldaleenss.....aleegknlvidghlaeleseaak 92 
                                    l+++  ++      +l +g+++++  +la   +++++
  gi|70606846|ref|YP_255716.1| 107 MLKEVGISNLnqnyyDLSSGQVVLFNTVLALASYPKQI 144
                                   66655555556667799999999999999888777666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.7e-05     0.034       8      45 ..      16      53 ..      10     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                        AAA_30  8 aavealltsgdrvavltGpAGtGKttalkalreaweaa 45
                                  ++++ ++ s    ++l Gp G+GKtt+l+a+  + + +
  gi|70606846|ref|YP_255716.1| 16 EIIRGVTLSLSNKTLLLGPNGSGKTTILRAICGIRDYD 53
                                  566667777777799***************97665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.4e-05     0.039      27      48 ..      29      50 ..      17     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-05
                        AAA_16 27 vllsGesGvGKsslvrellral 48
                                  +ll G+ G+GK++++r++    
  gi|70606846|ref|YP_255716.1| 29 TLLLGPNGSGKTTILRAICGIR 50
                                  79**************998533 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   0.00011       0.1      23     150 ..      29     170 ..      15     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..........eeeekkklekal........... 82 
                                    ++ Gp gsGKt++l+ i   ++      i ++ ++ ++is++++             +          l           
  gi|70606846|ref|YP_255716.1|  29 TLLLGPNGSGKTTILRAICGIRDYD--GSIKVDGMEVKRISRFTKLSCnlseayslglK----------Lidklellkeik 97 
                                   5678**************9999443..57888888888888888863334433333330..........244455555556 PP

                      ATPase_2  83 .......giavpkaeleeilkeksklvfkaielllekikkkgkk.iiiiiDelqklidlglngaellvkeLlnlie 150
                                          ++ ++++ +   l+++  ++ +    l++ +   +     iiiDe ++ +d+   + +  +++L ++ e
  gi|70606846|ref|YP_255716.1|  98 dldislaKNMLKEVGIS-NLNQNYYDLSSGQVVLFNTVLALASYpKQIIIDEPFENVDYA--KRKVIINWLKEYGE 170
                                   66444433333333332.222222222222222222222222222347778888888555..45888888877765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   9.9e-05     0.089      10      41 ..      26      57 ..      16     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                        AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvk 41
                                  ++  l++++ G+GKT++l++i+ +    g++k
  gi|70606846|ref|YP_255716.1| 26 SNKTLLLGPNGSGKTTILRAICGIRDYDGSIK 57
                                  5567899**************98876666555 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.1e-05     0.054      25      44 ..      28      47 ..       5     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.1e-05
                                  EEEEEESTTSSHHHHHHHHH CS
                       G-alpha 25 kllllGqseSGKsTilkqlk 44
                                  k lllG ++SGK+Til+ + 
  gi|70606846|ref|YP_255716.1| 28 KTLLLGPNGSGKTTILRAIC 47
                                  89**************9875 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.15       3      22 ..      29      50 ..      27      59 .. 0.81
   2 ?   -3.1   0.0       5.7   5.1e+03      24      49 ..     153     178 ..     142     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                  EEEEESTTCCHHHHHHHHH..C CS
                          cobW  3 tvltGflGsGKTtLlnhll..e 22
                                  t+l G+ GsGKTt+l++++  +
  gi|70606846|ref|YP_255716.1| 29 TLLLGPNGSGKTTILRAICgiR 50
                                  7899*************99532 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                                   --SS-EEEEESS-SSCHCCCCCCHCC CS
                          cobW  24 raglklavivNefgevsiDaellret 49 
                                    +  k  vi+N ++e ++++ +++++
  gi|70606846|ref|YP_255716.1| 153 VDYAKRKVIINWLKEYGEEGLIVTHE 178
                                   55567789999888888888887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00017      0.16       3      47 ..      27      67 ..      25     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                        AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie 47
                                  +k l+ Gp+g+GKTt+++ +     + d +++  ++d+ ++++i+
  gi|70606846|ref|YP_255716.1| 27 NKTLLLGPNGSGKTTILRAI---CGIRDYDGSI-KVDGMEVKRIS 67
                                  7899************9988...4555555544.55555555555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00029      0.26     111     151 ..      10      48 ..       1      58 [. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                         T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                    ++ +++i + +  +++     l+ G+ gsGKtt+l a+  
  gi|70606846|ref|YP_255716.1|  10 YGEKNKEIIRGVTLSLS--NKTLLLGPNGSGKTTILRAICG 48 
                                   44555555555555533..345666***********99865 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00029      0.26      29      47 ..      29      47 ..       7      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                        AAA_27 29 hliyGpNEAGKstalrAis 47
                                  +l++GpN +GK+t+lrAi 
  gi|70606846|ref|YP_255716.1| 29 TLLLGPNGSGKTTILRAIC 47
                                  6899*************95 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0017       1.6      64      89 ..     141     166 ..      97     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                       SbcCD_C  64 lrlvfLDEAFsklDeesiatllelle 89 
                                   ++ +++DE F+++D  +++ +++ l+
  gi|70606846|ref|YP_255716.1| 141 PKQIIIDEPFENVDYAKRKVIINWLK 166
                                   5669**************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 1740.27
//
Query:       gi|70606847|ref|YP_255717.1|  [L=205]
Description: hypothetical protein Saci_1067 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1490.69
//
Query:       gi|70606848|ref|YP_255718.1|  [L=101]
Description: ArsR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-14   52.6   0.1    5.1e-14   52.2   0.1    1.1  1  HTH_34          Winged helix DNA-binding domain
    5.4e-08   32.6   0.2    1.6e-07   31.1   0.2    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
    1.4e-07   31.5   0.0      2e-07   31.0   0.0    1.3  1  HTH_20          Helix-turn-helix domain
    2.5e-05   24.0   0.1    3.6e-05   23.5   0.1    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    9.6e-05   22.2   0.2    0.00011   22.0   0.2    1.2  1  HxlR            HxlR-like helix-turn-helix
    0.00053   19.8   0.0     0.0014   18.5   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00054   20.1   0.0    0.00073   19.7   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0009   19.1   0.2     0.0015   18.4   0.2    1.3  1  MarR            MarR family
     0.0014   18.5   0.0     0.0019   18.1   0.0    1.2  1  PadR            Transcriptional regulator PadR-like family
     0.0023   17.4   0.1      0.007   15.9   0.0    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0091   15.9   0.0      0.021   14.8   0.0    1.7  1  HTH_12          Ribonuclease R winged-helix domain
     0.0094   15.8   0.0      0.012   15.5   0.0    1.2  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.088   13.2   0.1       0.14   12.5   0.1    1.4  1  Rrf2            Transcriptional regulator
      0.088   13.1   0.0       0.11   12.8   0.0    1.2  1  DUF2513         Hypothetical protein (DUF2513)
      0.098   13.2   0.0       0.15   12.6   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   4.3e-17   5.1e-14       2      78 ..      22      98 ..      21      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.3e-17
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78
                                  Rl++l +L+   + +f+el++++e+ ++ L  hl++Le++g ++v+k      prt+++iT++G e+ kky++ ++ 
  gi|70606848|ref|YP_255718.1| 22 RLGILISLYILGKTTFAELQKSTEIPKSSLHMHLQILEENGLVTVKKIPTLSGPRTIVQITEKGVEEIKKYINVIRD 98
                                  9***********************************************************************98875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   1.3e-10   1.6e-07       2      46 ..      20      65 ..      19      66 .. 0.96
   2 ?   -2.1   0.0       3.1   3.7e+03      13      23 ..      73      83 ..      72      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.3e-10
                                  HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  + Rl IL +L   g++++ el + +++++s + +HL +L+e GLV+
  gi|70606848|ref|YP_255718.1| 20 SSRLGILISLYIlGKTTFAELQKSTEIPKSSLHMHLQILEENGLVT 65
                                  78*******************************************7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                  TSSEEHHHHHH CS
                         HTH_5 13 egelcvcelae 23
                                  +g++++ +++e
  gi|70606848|ref|YP_255718.1| 73 SGPRTIVQITE 83
                                  58999999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.7e-10     2e-07       6      58 ..      16      68 ..       7      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                                  HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  +L++ +R++il  L   +  t++el +  +++k++l+ HL++Lee gLv+v +
  gi|70606848|ref|YP_255718.1| 16 VLSNSSRLGILISLYILGKTTFAELQKSTEIPKSSLHMHLQILEENGLVTVKK 68
                                  599***********************************************965 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1     3e-08   3.6e-05      20      49 ..      36      65 ..      23      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-08
                                  BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyve 49
                                  t++el + t +pkS+ h +Lq L+e G+v+
  gi|70606848|ref|YP_255718.1| 36 TFAELQKSTEIPKSSLHMHLQILEENGLVT 65
                                  899*************************97 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2     9e-08   0.00011      10      79 ..      25      96 ..       4     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9e-08
                                  HHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS.SS-EEEEEE-TCG.GGGHHHHHHH CS
                          HxlR 10 ilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevype.vPpkveYsltekG.rslepvlqel 79
                                  il++l   gk  f el++   +i+++ L  +L+ Le++gl+  + +p+  +p+   ++tekG +++++ ++ +
  gi|70606848|ref|YP_255718.1| 25 ILISLYIlGKTTFAELQKST-EIPKSSLHMHLQILEENGLVTVKKIPTlSGPRTIVQITEKGvEEIKKYINVI 96
                                  67777666*********998.*********************9999983589**********55677666655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0014      15      58 ..      27      70 ..      23      84 .. 0.87
   2 ?   -0.8   0.0       1.2   1.4e+03      18      34 ..      79      95 ..      72      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  + L  lg+ t  e+ + +++p+s+    L+ Le+ GlV+++k  
  gi|70606848|ref|YP_255718.1| 27 ISLYILGKTTFAELQKSTEIPKSSLHMHLQILEENGLVTVKKIP 70
                                  56778899*******************************99865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                  HHHCCCHHCHHCCCTTS CS
                          TrmB 18 lklgpatadeiaeelgv 34
                                  ++  ++ ++ei + ++v
  gi|70606848|ref|YP_255718.1| 79 VQITEKGVEEIKKYINV 95
                                  55556777888887776 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.1e-07   0.00073      22      55 ..      38      77 ..      35      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.1e-07
                B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsii......d 55
                                   +L k++++ ++sl+ +l+ Le++gL++ ++i+       
  gi|70606848|ref|YP_255718.1| 38 AELQKSTEIPKSSLHMHLQILEENGLVTVKKIPtlsgprT 77
                                  5899************************999985555440 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.2e-06    0.0015       5      53 ..      22      70 ..      19      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53
                                  ++ iL +ly  g  + +eL+k  ++ ks++   l  Le++Gl++ +k p
  gi|70606848|ref|YP_255718.1| 22 RLGILISLYILGKTTFAELQKSTEIPKSSLHMHLQILEENGLVTVKKIP 70
                                  6679****************************************99877 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0019      25      74 ..      42      90 ..      30      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                                  T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR 25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                    +e+ ++sl   L+ Le++glv+ ++ ++  ++pr + ++T++G +e++
  gi|70606848|ref|YP_255718.1| 42 KSTEIPKSSLHMHLQILEENGLVTVKKIPT-LSGPRTIVQITEKGVEEIK 90
                                  34789999******************9996.999***********99987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   1.5e+03      11      20 ..      10      19 ..       6      21 .. 0.60
   2 !   15.9   0.0   5.8e-06     0.007      16      48 .]      33      65 ..      18      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                        HTH_24 11 lLqknprisq 20
                                  +L  np +s+
  gi|70606848|ref|YP_255718.1| 10 ELLNNPVLSN 19
                                  4556676666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.8e-06
                        HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++++ +eL + + +++s ++ +l+ Lee+Gl++
  gi|70606848|ref|YP_255718.1| 33 GKTTFAELQKSTEIPKSSLHMHLQILEENGLVT 65
                                  6789***************************96 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.021      28      66 .]      44      89 ..      31      89 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                        HTH_12 28 ydigeravRyrLrkleergltrrvgya.......greltEkGleeL 66
                                   +i + ++  +L++lee+gl+  +            ++tEkG+ee+
  gi|70606848|ref|YP_255718.1| 44 TEIPKSSLHMHLQILEENGLVTVKKIPtlsgprtIVQITEKGVEEI 89
                                  4577889999*********7643333224555445689***99985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.012       9      54 ..      24      67 ..      17      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +L  L+  +    t +el + + ++ks+++ +l+ L++ GLv+ +
  gi|70606848|ref|YP_255718.1| 24 GILISLYILGK--TTFAELQKSTEIPKSSLHMHLQILEENGLVTVK 67
                                  56777777777..8*****************************876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012      0.14      22      58 ..      34      67 ..      17      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                  TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  +    + +e+ ++++i++s l   l+ L+++glv+++
  gi|70606848|ref|YP_255718.1| 34 K---TTFAELQKSTEIPKSSLHMHLQILEENGLVTVK 67
                                  3...6899**************************986 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-05      0.11      33      80 ..      42      87 ..      26     101 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                       DUF2513 33 aidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhd 80
                                  + ++ +k ++  hl++l+e+gL+ ++k  + s+    ++ ++t +G +
  gi|70606848|ref|YP_255718.1| 42 KSTEIPKSSLHMHLQILEENGLVTVKKIPTLSG--PRTIVQITEKGVE 87
                                  66777888999***************9999988..4455567777765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.15      17      68 .]      33      85 ..      21      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre.krvrlTdkG 68
                                  ++ + a+l + + + +s+ +  l  L+e+GLv+ ++ ++  ++ + v++T+kG
  gi|70606848|ref|YP_255718.1| 33 GKTTFAELQKSTEIPKSSLHMHLQILEENGLVTVKKIPTLSGPrTIVQITEKG 85
                                  555669**************************66666665555699******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 802.30
//
Query:       gi|70606849|ref|YP_255719.1|  [L=362]
Description: isovaleryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-25   89.3   0.0    4.5e-25   88.5   0.0    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.4e-20   73.3   0.0    2.2e-20   72.6   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.1e-13   50.2   0.1    7.8e-07   29.4   0.0    2.4  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
     0.0061   17.1   0.0      0.013   16.1   0.0    1.6  1  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0     1e-28   4.5e-25       3     113 .]       2     121 ..       1     121 [. 0.83

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1e-28
                                   HHHHHHHHHHHHHHHHTHHH.......HHHHHHHTSGH.....HHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHH CS
                 Acyl-CoA_dh_N   3 eqealrdtvrefaeeelaph.......aaewdeegefp.....relwkklaelGllgitvpeeygGagldyleaaivaeel 71 
                                   ++e++r ++++++e + +          + +    ef+     re+++kl  +G+lgit+p++ygG++l ++++ai++ee+
  gi|70606849|ref|YP_255719.1|   2 DEEEFRSALKKWIESNSPADlkgrrilFDTV----EFDdyqkiREWQRKLYSAGYLGITWPKQYGGQDLPPIYEAIAYEEF 78 
                                   5789999999999998855322222222222....33333234799*********************************** PP

                                   HHH-HHHHH.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  72 aradaglal.llgvhsslvapailrfGteeqkrryLpklasge 113
                                    +a+++++  l +++ +++apail++G+eeqk+ryLp+++s e
  gi|70606849|ref|YP_255719.1|  79 IKAGLPYGRsLGSIGLMVAAPAILKHGNEEQKKRYLPRILSAE 121
                                   *********99999**************************986 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0     5e-24   2.2e-20       1      85 [.     125     207 ..     125     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 5e-24
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----B CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieek 81 
                                   + +++Ep+aGsd+asvkt  ae +g+ + +nG+Kiw++ a+ a+++++lart++++ ++gl++f+v+ ++pg++v++i + 
  gi|70606849|ref|YP_255719.1| 125 CQGFSEPSAGSDLASVKT-RAEDKGDYFLVNGQKIWSSYAHLANYMILLARTGEDR-YGGLTMFVVDMKQPGIKVSPIYQI 203
                                   8899**************.77888888************************77777.********************9987 PP

                                   SS-T CS
                 Acyl-CoA_dh_M  82 lGlr 85 
                                   +G  
  gi|70606849|ref|YP_255719.1| 204 TGKS 207
                                   7765 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.7e-07    0.0017       1      33 [.     229     261 ..     229     264 .. 0.92
   2 !   29.4   0.0   1.7e-10   7.8e-07      57     150 .]     266     358 ..     263     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-07
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHH CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleea 33 
                                   g+G++vam+ lnheR+++++++l + ++a++++
  gi|70606849|ref|YP_255719.1| 229 GEGWKVAMTVLNHERFTLGITMLFTSKSAIDTL 261
                                   69***********************99999865 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.7e-10
                                   HHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS- CS
                 Acyl-CoA_dh_1  57 laemaaeleaarllvyraaealdagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGt 137
                                   l e++ ++e++ +  +r+  +l +g++   e +++Kl+ase++q+v++ a+  +  + ++ ++++   +  +r  +i++Gt
  gi|70606849|ref|YP_255719.1| 266 LEELRDDIEGLEAFYRRLLIKLRRGEDVDTEGAILKLVASEILQKVYEHAVSNYDLEFIM-SQKWYLGMLSSRGRTIAGGT 345
                                   6677889999****************************************9999777666.4445666789********** PP

                                   HHHHHHHHHHHH. CS
                 Acyl-CoA_dh_1 138 seiqrniiarrll 150
                                   sei+rn+i++r+l
  gi|70606849|ref|YP_255719.1| 346 SEILRNLIGERVL 358
                                   **********985 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-06     0.013      81     122 ..      74     120 ..      33     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                                   HHHHTHSS--TTH.....HHHHTHHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_ox_N  81 lgtglldeslplg.....lhfsMFlptlkgqgteeQqakWlpraenl 122
                                    ++ +++ +lp+g     + +++  p+++++g+eeQ++++lpr+ + 
  gi|70606849|ref|YP_255719.1|  74 AYEEFIKAGLPYGrslgsIGLMVAAPAILKHGNEEQKKRYLPRILSA 120
                                   4566666666666666677778899******************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2669.80
//
Query:       gi|70606850|ref|YP_255720.1|  [L=145]
Description: hypothetical protein Saci_1070 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-16   57.7   0.0    1.1e-15   57.2   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    2.5e-09   37.3   0.0    3.2e-09   37.0   0.0    1.1  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.025   14.9   0.1    1.5  1  S1               S1 RNA binding domain


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   1.9e-19   1.1e-15       6     117 ..       8     121 ..       5     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.9e-19
                                   TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHSTT...EGGGEEEEEE CS
               MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelgdn...vvarvgeikv 83 
                                   +g+k et k +tv ead+  + +++g +np+ +d+e+ kk++f+g+Ia G+lt++++ +l+++   d        +   ++
  gi|70606850|ref|YP_255720.1|   8 VGQKWET-KGRTVGEADVIVFSTMTGAYNPLFLDEEYGKKTRFKGRIAPGLLTASLAVGLTYQLPVDPfgeGFVALSRLEL 87 
                                   7999999.*********************************************************9998765566777888 PP

                                   EE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEE CS
               MaoC_dehydratas  84 rFtkpVlpgdtlkvelevvgkrdvrktkkvevtk 117
                                      k V +gdtlk  +ev +k++++k   v  ++
  gi|70606850|ref|YP_255720.1|  88 EAKKAVKIGDTLKCVVEVIDKKEREKNGRVFLNV 121
                                   889*****************99998776665555 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   5.4e-13   3.2e-09       3     131 ..       8     133 ..       7     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5.4e-13
               MaoC_dehydrat_N   3 iGaefepvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgid..lsrllhge.q 80 
                                   +G++ e++  +v++ +v  f   +g++np++ldee+ +++++++ iaP  ++  la      + +l++d  +++ + ++  
  gi|70606850|ref|YP_255720.1|   8 VGQKWETKGRTVGEADVIVFSTMTGAYNPLFLDEEYGKKTRFKGRIAPGLLTASLAVGL---TYQLPVDpfGEGFVALSrL 85 
                                   7999999999***************************************9999999877...8899999989******978 PP

               MaoC_dehydrat_N  81 efeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                   e+e ++ ++ GD+l ++ ++ d ++++      f+ v+t  +nq Ge v+ 
  gi|70606850|ref|YP_255720.1|  86 ELEAKKAVKIGDTLKCVVEVIDKKEREK-NGRVFLNVKT--INQLGEEVMN 133
                                   9999*********************984.5556776664..6799999985 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   4.1e-06     0.025      27      68 ..      75     111 ..      64     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-06
                                   TEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTT CS
                            S1  27 gvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrr 68 
                                     egfv +s l+ +      ++ +k+Gd++k +v+ +dk++r
  gi|70606850|ref|YP_255720.1|  75 FGEGFVALSRLELE-----AKKAVKIGDTLKCVVEVIDKKER 111
                                   569*********99.....9*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1060.70
//
Query:       gi|70606851|ref|YP_255721.1|  [L=267]
Description: hypothetical protein Saci_1071 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-08   34.5   0.0      2e-06   28.1   0.0    2.2  2  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.1e-10     2e-06      11      68 ..     149     206 ..     139     209 .. 0.81
   2 !    4.2   0.0    0.0025        45      97     127 ..     226     256 ..     222     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-10
                                   T--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  11 lnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaar 68 
                                   +n   ++  a+ +g   + + +++eya++r afgkp++++q++++++++  + le +r
  gi|70606851|ref|YP_255721.1| 149 FNRAVIMASAQIIGHGLATMKQIVEYAKNRVAFGKPIGSYQAIKHRVVDDVIGLELVR 206
                                   3444455567778999999****************************99877777766 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHHGGGTTSGGGHHHHHHHH CS
                 Acyl-CoA_dh_1  97 elaqevadlamqllGgaGyleeypverlyrd 127
                                   + a ++a + +q +Gg G++ +  ++ ++++
  gi|70606851|ref|YP_255721.1| 226 RKAFRAALDSIQFHGGIGFTSDLDLHLHLKR 256
                                   678999*************999887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1966.95
//
Query:       gi|70606852|ref|YP_255722.1|  [L=411]
Description: cytosine deaminase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-29  103.2   0.0    1.6e-25   90.5   0.0    2.2  2  Amidohydro_3  Amidohydrolase family
    3.2e-13   49.7   0.0    5.8e-13   48.9   0.0    1.4  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   2.4e-05      0.22       2      25 ..      35      58 ..      34      86 .. 0.80
   2 !   90.5   0.0   1.8e-29   1.6e-25     223     473 .]     129     392 ..      70     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.4e-05
                  Amidohydro_3  2 viDakGrlvlPGFvDsHtHlaggg 25
                                  v  a+G+lvlP+   +H Hl+++ 
  gi|70606852|ref|YP_255722.1| 35 VLEANGKLVLPPYLNMHFHLDSVF 58
                                  778******************987 PP

  == domain 2  score: 90.5 bits;  conditional E-value: 1.8e-29
                  Amidohydro_3 223 s....................pgseeltigavklfadgvlgsrtalltepyftgwpdfedea..laelvaaadergldvai 281
                                   +                     g+eel  +a+  +ad v+ +++ +lt++         d++  ++  +++ + +  d++ 
  gi|70606852|ref|YP_255722.1| 129 DvkelmdiqitafpqdgiftdKGNEELMYKALSEGADNVGLIPHNELTRE---------DGVrsIKFALELGKRYNRDIDG 200
                                   022333355555566678888999*************9999999999995.........7777899*************** PP

                  Amidohydro_3 282 haigdaavd.dvldafeaaaekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnf.edelldsrlg.perarg 356
                                   h++++++   ++l+ +++ + +ng+ +r+ + h +++   +++++ r+    + ag+++++n+  +  l++rl+ ++++rg
  gi|70606852|ref|YP_255722.1| 201 HIDETDDPNsRFLEVLAKETLENGWVGRVAAGHVTAMhswDNAYRYRILPHVANAGISVIPNPlINAVLQGRLDtYPKRRG 281
                                   ****************************************************************999************** PP

                  Amidohydro_3 357 stpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg.evlrpdeelsleealalyTrgpAkalgledrkGtLev 436
                                    +p+ke+ln gv+valg D   +++dpw+++g+ +m+++  ++ ++ +     +l+  + l+T ++Akal+     +++ v
  gi|70606852|ref|YP_255722.1| 282 MAPIKEMLNFGVNVALGYD---CMMDPWYPLGSGNMLQALFMAiHLDQLTGYEELRRSIYLITYNGAKALRIKN--YGICV 357
                                   *******************...****************************************************..9**** PP

                  Amidohydro_3 437 GadADlvvld....adpldvdppelaearvrltvvdGrvvy 473
                                   G++A+l+v       d++++ +p      +++++ +G++v+
  gi|70606852|ref|YP_255722.1| 358 GCEANLIVTAsnnvVDLIRFIDP------PSYVIRKGKIVA 392
                                   **********9999999999999......9*********95 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   6.5e-17   5.8e-13       2     344 .]      43     391 ..      42     391 .. 0.73

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 6.5e-17
                                   EEE-EEEEEEECETTECSSS.....GHHHHH.........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH...HHHH CS
                  Amidohydro_1   2 vlPGlIDaHvHleqsllrga.....tledwl.........vppetaaealesgiktalksGtttvadmgattst...giea 65 
                                   vlP   ++H Hl  s++  a     tl++ +         +++e+++  + +++k ++  Gt   + +   t++    ++a
  gi|70606852|ref|YP_255722.1|  43 VLPPYLNMHFHLD-SVFTKAenqsgTLWEGIkiwkklkqeLTEEQVYKNAVTAVKLMVAFGTLWLRTHVDITEKsfrLLRA 122
                                   888999******5.55555579999888888999999*********************************99999995555 PP

                                   HHHHHHT..SSSEEEEEEESSEGGS....GCCCSHHHHHHH.HHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH..HHHHH CS
                  Amidohydro_1  66 lleaaee..lplglrilggkvsldr....gsaetskasrek.lkagaaetikgkadgvvkvalapheapafsde..elkea 137
                                   ll+  e+    +++ i +           ++++  ++++ k l +ga+           +v+l ph   + +d    +k a
  gi|70606852|ref|YP_255722.1| 123 LLKVKEDvkELMDIQITAF-----PqdgiFTDKGNEELMYKaLSEGAD-----------NVGLIPHNELTREDGvrSIKFA 187
                                   5555555322345444443.....044675555555555440444442...........255555544444333558**** PP

                                   HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HH..HHHHHHHHHHHHC CS
                  Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt..pt..eaellkerlkeag 214
                                   l++ k+++  ++ H+ et+  ++  ++  ++++ +++ +            ++++ h + ++  ++   +++l+ ++ +ag
  gi|70606852|ref|YP_255722.1| 188 LELGKRYNRDIDGHIDETDDPNSRFLEVLAKETLENGWVG-----------RVAAGHVTAMHswDNayRYRILP-HVANAG 256
                                   **********************999999994444433333...........35566666666554455444443.457777 PP

                                   EE..HHHHHHHH.........SEHHHHHHHHHHHHTSCEEEEEECT........TSSCCGGHHHHHHHHHHHHHHCCTTTT CS
                  Amidohydro_1 215 va..hcpfsnsi.........lrsgrealrkaldeGvkvglgtDga........asgnslnlleelrlalklqrgllyede 276
                                   ++    p  n +          r g+++++++l+ Gv+v+lg D +        +sgn l   + l +a++l +       
  gi|70606852|ref|YP_255722.1| 257 ISviPNPLINAVlqgrldtypKRRGMAPIKEMLNFGVNVALGYD-CmmdpwyplGSGNML---QALFMAIHLDQ------L 327
                                   776655666666888899999***********************.667777665555555...55666664444......3 PP

                                   HCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CTCGGGTTTCTSEEEEEEEETTEEE CS
                  Amidohydro_1 277 egglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.dilaafvglkkdgnvkkvivkGklv 344
                                   +g  +l + +++ T+ngAkal++ ++ G i+vG +A+l+v +  +    + ++ +   +  vi kGk+v
  gi|70606852|ref|YP_255722.1| 328 TGYEELRRSIYLITYNGAKALRI-KNYG-ICVGCEANLIVTASnNVVDLIRFIDP---PSYVIRKGKIV 391
                                   66688999***************.5***.************77666888888888...88999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2842.76
//
Query:       gi|70606853|ref|YP_255723.1|  [L=317]
Description: hypothetical protein Saci_1073 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-06   26.5   1.5    7.6e-06   25.9   1.5    1.3  1  UPF0547         Uncharacterised protein family UPF0547
    9.9e-06   24.8   2.3    1.5e-05   24.2   2.3    1.3  1  zf-ribbon_3     zinc-ribbon domain
    1.1e-05   25.0   4.1    1.5e-05   24.5   4.1    1.2  1  zinc_ribbon_2   zinc-ribbon domain
    0.00024   21.1   1.3    0.00038   20.4   1.3    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.038   14.7   2.7      0.059   14.1   2.7    1.3  1  zinc_ribbon_15  zinc-ribbon family
        0.1   12.2   0.1       0.17   11.5   0.1    1.3  1  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   1.5   2.6e-09   7.6e-06       1      24 [.       3      26 ..       3      28 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.6e-09
                       UPF0547  1 KvCPeCeakvPvaaqfCphCGyvF 24
                                  K+CP+C   vP +a+ C  CGy F
  gi|70606853|ref|YP_255723.1|  3 KNCPRCGKSVPDDARYCYSCGYYF 26
                                  9****************77***98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   2.3   5.1e-09   1.5e-05       3      24 ..       3      24 ..       1      26 [. 0.92

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.1e-09
                   zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                                  ++CP+CG+ + +d++ C++CG+
  gi|70606853|ref|YP_255723.1|  3 KNCPRCGKSVPDDARYCYSCGY 24
                                  79******88***********7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   4.1   5.1e-09   1.5e-05       2      21 ..       5      24 ..       4      26 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5.1e-09
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                  Cp+CG+ ++d+a++C  CG+
  gi|70606853|ref|YP_255723.1|  5 CPRCGKSVPDDARYCYSCGY 24
                                  *******************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.3   1.3e-07   0.00038       1      19 [.       5      23 ..       3      34 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                           DZR  1 CpqCgeelppdarfCseCg 19
                                  Cp+Cg+ +p+dar+C+ Cg
  gi|70606853|ref|YP_255723.1|  5 CPRCGKSVPDDARYCYSCG 23
                                  8888888888888888888 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.7     2e-05     0.059      66      86 .]       3      23 ..       1      23 [. 0.95

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                  k C++Cgk+v ++ +yC +Cg
  gi|70606853|ref|YP_255723.1|  3 KNCPRCGKSVPDDARYCYSCG 23
                                  78******************9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.8e-05      0.17       4      16 ..       4      16 ..       2      18 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.8e-05
                        zf_UBZ  4 lCerCgkeipese 16
                                   C+rCgk++p+++
  gi|70606853|ref|YP_255723.1|  4 NCPRCGKSVPDDA 16
                                  6*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1323  (0.0737911); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 1969.40
//
Query:       gi|70606854|ref|YP_255724.1|  [L=107]
Description: hypothetical protein Saci_1074 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        4.8    7.5  19.9         65    3.9  19.3    2.4  2  DUF4064      Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  19.3    0.0036        65       4      80 ..       3      60 ..       1      95 [. 0.88
   2 ?   -0.9   3.4      0.11     2e+03       7      13 ..      86      92 ..      66     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0036
                       DUF4064  4 aeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgal 80
                                  +  iL++IGg+l ++++++ l++                   +   a++++++ s++l++lg+i++i +++ i g +
  gi|70606854|ref|YP_255724.1|  3 PSRILSIIGGVLALIIAITSLVI-------------------NKPLATYYVSIDSGVLTALGIISIIGGLADIYGGI 60
                                  678********************...................67899*********************999888776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                       DUF4064  7 iLglIGg 13
                                  +Lg+IGg
  gi|70606854|ref|YP_255724.1| 86 LLGFIGG 92
                                  1222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 761.86
//
Query:       gi|70606855|ref|YP_255725.1|  [L=135]
Description: hypothetical protein Saci_1075 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-05   24.8   0.0    3.4e-05   24.2   0.0    1.2  1  DrsE         DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.047   13.8   0.0      0.078   13.1   0.0    1.3  1  Root_cap     Root cap
      0.073   12.9   0.1       0.15   11.9   0.1    1.5  1  Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.7e-09   3.4e-05       1     117 []      28     135 .]      28     135 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.7e-09
                                   -EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT..-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHH CS
                          DrsE   1 kkvfilvtggpygseaarealelalaaaalg..hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgq 79 
                                   k++f++++    g+e+  +a+++a+  a+++  ++v+v+  g+  + l++    ++    +l+++++++ +++    +C+ 
  gi|70606855|ref|YP_255725.1|  28 KVLFLIMS----GDEKFELAMRMAYNSAKNKryEDVKVIYFGPSQKRLTQ---LQG----DLKDMFQEMLQNKLVDSACIG 97 
                                   45566666....77766777777766666668899999999999999999...445....8**********998889**** PP

                                   HHHHTT--GGGE-.T--EEEE-HH.HHHHHHHH-SEEEE- CS
                          DrsE  80 aakargldededl.gvgvevsglg.elaelqnegdrvitf 117
                                    a++++l +d  l  +gv ++ +g ++a+++n+g+ vitf
  gi|70606855|ref|YP_255725.1|  98 VAERMNLVPD--LkNMGVNLVPVGeRVAHYVNNGYEVITF 135
                                   ********64..54467777777769*************9 PP

>> Root_cap  Root cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.078      14      44 ..      12      42 ..       4      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                      Root_cap 14 VLGqTYrpdYvskvkvgvamPvmGGedkyat 44
                                  +LG+  r +Y+++  ++v   +m+G++k++ 
  gi|70606855|ref|YP_255725.1| 12 ILGRFKRWKYENRTMTKVLFLIMSGDEKFEL 42
                                  89***************************85 PP

>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.4e-05      0.15      50      95 ..      10      56 ..       2      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                  EEEEEEEEEECCSECCEEEEEEEEE--T.TS-HHHHHHHHHHHHHHH CS
                   Cofilin_ADF 50 rYavydveyehddeskrsklvfIswvPd.sapikqkmlyasskdalk 95
                                   +++ +++  + ++++ +k++f+  ++d +     +m y s k++  
  gi|70606855|ref|YP_255725.1| 10 SFILGRFKRWKYENRTMTKVLFLIMSGDeKFELAMRMAYNSAKNKRY 56
                                  5777777777777899************8899**********99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 957.79
//
Query:       gi|70606856|ref|YP_255726.1|  [L=114]
Description: hypothetical protein Saci_1076 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.28   10.5   3.2       0.36   10.2   3.2    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
       0.31   10.0  13.3       0.25   10.4   9.5    1.9  2  COX15-CtaA     Cytochrome oxidase assembly protein
        0.4   10.9   9.9       0.16   12.2   2.4    2.0  2  DUF2537        Protein of unknown function (DUF2537)
       0.86    9.5   1.8          1    9.3   1.8    1.2  1  Protocadherin  Protocadherin
        5.1    5.3  10.5        5.7    5.1  10.5    1.0  1  DUF2070        Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.2   9.9e-05      0.36     222     280 ..      19      77 ..       8      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 9.9e-05
                     OST3_OST6 222 ggsqnQfgaEtqivallygllallvilLiklvpriknakvqrvlvivllvlifllfsll 280
                                   g+s   +g+  +++++  ++ a+l+i++i ++ r+k++ ++r+lv  l++li+ ++  +
  gi|70606856|ref|YP_255726.1|  19 GNSMVFYGVSNILIGIHAIIAAVLLIIIIYGLARAKDSIKRRMLVGNLALLILTAVLGI 77 
                                   56666677778889999999999*******************99988888877665444 PP

>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.9   0.00088       3.2     281     323 ..       3      46 ..       1      47 [. 0.90
   2 ?   10.4   9.5   6.9e-05      0.25     258     321 ..      36     100 ..      31     103 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00088
                    COX15-CtaA 281 lavll.aallllQvalGistvllavplslavaHqlgaallllal 323
                                   + +l+ a++ +l +++G s v+++v   l  +H ++aa+ll+++
  gi|70606856|ref|YP_255726.1|   3 TLWLAgAGVSILEILIGNSMVFYGVSNILIGIHAIIAAVLLIII 46 
                                   567777999********************************986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.9e-05
                    COX15-CtaA 258 vllvllllailllrkars.pklarlavll.aallllQvalGistvllavplslavaHqlgaallll 321
                                    +++++ll+i+++  ar+   ++r +++  +all+l ++lGi+ +  +++++l ++H l+a+ ll+
  gi|70606856|ref|YP_255726.1|  36 AIIAAVLLIIIIYGLARAkDSIKRRMLVGnLALLILTAVLGIVYLQ-YFNIPLLIVHLLLALGLLS 100
                                   333333333334444444356666666666************9875.57799999*******9997 PP

>> DUF2537  Protein of unknown function (DUF2537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.4   4.6e-05      0.16       1      57 [.       3      60 ..       3      67 .. 0.85
   2 ?    3.3   1.5     0.026        94       7      39 ..      66      98 ..      62     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                       DUF2537  1 tpWatGltvavfvavvvavav.valslalaevhpllavvvnvvvvaGlaPtvwllrrv 57
                                  t W +G+ v+++  ++   +v + +s  l+ +h ++a v+ ++   Gla +  +++r+
  gi|70606856|ref|YP_255726.1|  3 TLWLAGAGVSILEILIGNSMVfYGVSNILIGIHAIIAAVLLIIIIYGLARAKDSIKRR 60
                                  78**********99998766626799999*******************9877666655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                       DUF2537  7 ltvavfvavvvavavvalslalaevhpllavvv 39
                                  l++ +++av+  v +  +   l  vh lla+++
  gi|70606856|ref|YP_255726.1| 66 LALLILTAVLGIVYLQYFNIPLLIVHLLLALGL 98
                                  56778999999999999******9**9999876 PP

>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.8   0.00029         1      38      65 ..      28      55 ..       8      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00029
                 Protocadherin 38 lkiliavlaGvvtvilvilivvlvRycr 65
                                  ++ili++ a +++v+l+i+i  l+R   
  gi|70606856|ref|YP_255726.1| 28 SNILIGIHAIIAAVLLIIIIYGLARAKD 55
                                  79***********************443 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  10.5    0.0016       5.7      90     169 ..      22      99 ..       2     111 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0016
                       DUF2070  90 illsallqalvllalvlslalvfalrllvlvavsdesllkav.....lpaliqpllailllvlyfspesfllllllslifa 165
                                   +++      + +  +++++ +++a +ll++++++ ++ + ++     +  l+ ++l ++l ++y  +++ ++ll+++l++a
  gi|70606856|ref|YP_255726.1|  22 MVF------YGVSNILIGIHAIIAAVLLIIIIYGLARAKDSIkrrmlVGNLALLILTAVLGIVY-LQYFNIPLLIVHLLLA 95 
                                   221......2233444455555555555555554444444444333344444444444555555.5666677777777777 PP

                       DUF2070 166 lavy 169
                                   l+++
  gi|70606856|ref|YP_255726.1|  96 LGLL 99 
                                   6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 874.68
//
Query:       gi|70606857|ref|YP_255727.1|  [L=167]
Description: hypothetical protein Saci_1077 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1231.79
//
Query:       gi|70606858|ref|YP_255728.1|  [L=396]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-64  215.9   0.3      5e-64  215.5   0.3    1.2  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
    6.2e-46  155.0   0.7    8.8e-22   77.5   0.2    2.9  3  3HCDH          3-hydroxyacyl-CoA dehydrogenase, C-terminal do
    0.00049   20.3   0.1    0.00097   19.3   0.1    1.5  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0064   17.1   0.1      0.018   15.6   0.1    1.9  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.3   1.1e-67     5e-64       2     179 ..       6     184 ..       5     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 1.1e-67
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-SE CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dadl 81 
                                    +v+GaG mG+gia++++ ag++V l d++e++l++a+e+i  sl++l ekg++k e+ e++l+r++ t + eea+ d+d+
  gi|70606858|ref|YP_255728.1|   6 FTVVGAGSMGHGIAELALIAGYDVWLNDVAENILKNAKERIGWSLKRLSEKGSIK-EDPEKILSRLHLTVSQEEAMkDTDF 85 
                                   59*****************************************************.99**************99999**** PP

                                   EEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHH CS
                       3HCDH_N  82 viEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvat 162
                                    iEav+E++++K+kvf++ +++a++dailasnTSsl+i+e+a+a+krperv+g+HFfnPp lm+LvE+++gekTseet+++
  gi|70606858|ref|YP_255728.1|  86 LIEAVIEDINVKKKVFEKADSLASKDAILASNTSSLPITEIATAVKRPERVVGMHFFNPPVLMQLVEIIKGEKTSEETMKR 166
                                   ********************************************************************************* PP

                                   HHHHHHHTT-EEEEE.CS CS
                       3HCDH_N 163 vvelakkigktpvvv.kd 179
                                   ++e+ kk+g+ p+ v kd
  gi|70606858|ref|YP_255728.1| 167 AYEMGKKLGRDPILVkKD 184
                                   ***************666 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.5   6.9e+03      43      66 ..      18      46 ..      11      59 .. 0.52
   2 !   77.5   0.2     2e-25   8.8e-22       1      97 []     187     281 ..     187     281 .. 0.97
   3 !   74.7   0.0   1.5e-24   6.6e-21       7      97 .]     305     395 ..     304     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHHH.....HHHHHHHHHHHT CS
                         3HCDH 43 pfelldlvgldv.....akkilevlaeel 66
                                  + el+  +g dv     a++il+  +e+ 
  gi|70606858|ref|YP_255728.1| 18 IAELALIAGYDVwlndvAENILKNAKERI 46
                                  55555555555410000455554444444 PP

  == domain 2  score: 77.5 bits;  conditional E-value: 2e-25
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GF vnR+l+++ +  + lve+g a++ ++Da + ++lG+pmG+f l d++g+dva+ + +++ e+ g +ay+ ++ +e+l+
  gi|70606858|ref|YP_255728.1| 187 GFLVNRILFRVNDISCLLVEKGKADVLEVDASAIYELGFPMGVFLLQDYAGVDVAYLVGKAMGER-GFKAYE-CKAFEQLY 265
                                   9***********************************************************99998.677798.******** PP

                                   HTT--BGGGTBSSSBC CS
                         3HCDH  82 eagrlgrktgkgfyky 97 
                                   +a+ lg ktgkgfy y
  gi|70606858|ref|YP_255728.1| 266 KAKNLGVKTGKGFYSY 281
                                   **************98 PP

  == domain 3  score: 74.7 bits;  conditional E-value: 1.5e-24
                                   HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--B CS
                         3HCDH   7 vlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlg 87 
                                   ++ap +ne   lv eg+++ ed D+ ++lgl++p G+fe +d++gld + k le l++e+g ++++p pll+k+v++grlg
  gi|70606858|ref|YP_255728.1| 305 LIAPAINEGAYLVREGIVTKEDTDKGCKLGLNWPKGVFEYADEYGLDNVVKTLEDLRKETGLDYFTPDPLLTKMVKEGRLG 385
                                   57899**************************************************************************** PP

                                   GGGTBSSSBC CS
                         3HCDH  88 rktgkgfyky 97 
                                   +k gkgfy+y
  gi|70606858|ref|YP_255728.1| 386 KKVGKGFYEY 395
                                   ********98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.2e-07   0.00097       2      98 ..       6     125 ..       5     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.2e-07
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHHCSEE CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvasldvv 59 
                                   + ++G G MG+ +a+  l agy+v + ++ ++ ++++ ++                        ++++ s ee++++ d+ 
  gi|70606858|ref|YP_255728.1|   6 FTVVGAGSMGHGIAELALIAGYDVWLNDVAENILKNAKERIgwslkrlsekgsikedpekilsrLHLTVSQEEAMKDTDFL 86 
                                   789***********************999987777777774799999****9********9999999999999******** PP

                                   EE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHH CS
                 NAD_binding_2  60 itmvkagkavdeviegllealkkgdilidgstsspedtr 98 
                                   i  v ++ +v++ +++ +++l++ d ++ + tss   t+
  gi|70606858|ref|YP_255728.1|  87 IEAVIEDINVKKKVFEKADSLASKDAILASNTSSLPITE 125
                                   **********99999988888777777776666655443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1     4e-06     0.018       2      69 ..       6      90 ..       5     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                                  EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....................-EEECECHHHHHHH-S CS
                 F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....................vkvtavdneeaaeead 63
                                  + ++GaG+mg+++a+ +l ag   ++++  n+  ++ ++ ++e++g                     +   +v++eea++++d
  gi|70606858|ref|YP_255728.1|  6 FTVVGAGSMGHGIAELALIAG---YDVW-LNDVAENILKNAKERIGwslkrlsekgsikedpekilsRLHLTVSQEEAMKDTD 84
                                  6799*****************...****.779999999999999999999999999999999999994455558999999999 PP

                                  EEEE-S CS
                 F420_oxidored 64 vvvlav 69
                                  +++ av
  gi|70606858|ref|YP_255728.1| 85 FLIEAV 90
                                  998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2762.32
//
Query:       gi|70606859|ref|YP_255729.1|  [L=364]
Description: glucose 1-dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-24   85.0   0.0    7.6e-24   84.4   0.0    1.2  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    1.1e-18   67.1   0.1    1.7e-18   66.5   0.1    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    9.5e-06   25.6   0.0    1.7e-05   24.8   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.029   13.7   0.0    1.7  2  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
       0.04   14.0   0.2       0.17   11.9   0.0    2.1  3  Shikimate_DH  Shikimate / quinate 5-dehydrogenase
      0.055   12.7   0.0      0.091   12.0   0.0    1.3  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   2.5e-27   7.6e-24       2     208 ..     142     359 ..     141     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.5e-27
                   Glu_dehyd_C   2 dvgvLvEPisiveKaielaeasrsafe.w.......epesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptid 74 
                                   d+g+L  P++ +eK+++ +  ++++   w       + ++ lv+G+G++GLL  +ll a++ g+e v+  +rrd ++ +  
  gi|70606859|ref|YP_255729.1| 142 DIGILAQPLADIEKSLQEIDDIQKRLPaWtcedgtiNCRKMLVIGTGPIGLLF-ILL-ARTLGYE-VWASNRRDPNETESV 219
                                   6899*************999988876546222222245789***********9.444.4589**8.**********99999 PP

                   Glu_dehyd_C  75 lveelGatYvdsretpvdeipeaseemdlvvEaTGsakhafea.iealapnGvaaLlGvpedsevevdggelhrelvleNk 154
                                   ++ee    Y +s  +  +++ +    +d++v+aTG+ +++++  i  l+ nG+  + G p+d  +++   +l+ +lv  Nk
  gi|70606859|ref|YP_255729.1| 220 IIEEGKINYYNS-SAGFEKLKDSVGGFDVIVDATGANAQLLDKvIPLLNRNGILGIFGFPSDGIFSISYKDLQ-TLVHGNK 298
                                   ****9999**98.7899******************99888876257889*********************996.57***** PP

                   Glu_dehyd_C 155 alvGsvNanrrhfeaavdtLaalpesl...ldelvtkvvdld...eleeAfe.dddetiKt 208
                                   +++G vN +  hf++a+ +La+ ++ +    + lvt+ + ++   e+ +A + ++ e+iK+
  gi|70606859|ref|YP_255729.1| 299 LILGLVNGQKPHFQQAIVHLASWKTMYpktSKLLVTRTISINdenEVMKALKeKQAEEIKV 359
                                   ***********************99987656679999886651115667774256688887 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   5.6e-22   1.7e-18       2     109 .]      25     136 ..      24     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 5.6e-22
                                   TEEEEEEEEEEE-HHHHHHHTTS....TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkgg....kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                   g+v ik  ++g+Cg+D ++++g+    k  + +  l+lGHE++G+vee   +v ++++Gd V+      cg+C +C  g++
  gi|70606859|ref|YP_255729.1|  25 GKVKIKSLYSGVCGTDRELVNGKlslgKAHKDRDYLVLGHEAIGVVEE---SVGEFSKGDLVMPVNRRGCGKCLNCLLGRP 102
                                   5899******************9877666666667***********99...67789************************* PP

                                   GG-TTBEETTTS...S-SSSBSEEEECGGGEEEE CS
                         ADH_N  79 nlCeeakllgvs...ldGgfaeyvvvpekklvkl 109
                                   ++Ce+++++ ++   +dG + e  + + k+lvk+
  gi|70606859|ref|YP_255729.1| 103 DFCETGGFVEAGiygMDGFMREEWYDDPKYLVKI 136
                                   *********999999*********9999999985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.8e-09   1.7e-05       1     125 [.     189     315 ..     189     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.8e-09
                                   HHHHHHHHHHHHTT-EEEEEESSHHHH..HHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC.SHHHHHHHHHC CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseekl..elakklGadevinykeadlverikeltggegvdvvfecvG.sgatleaalkl 78 
                                   ++Gl+ + lA+ lG ev a  + + +       + G   ++n++   + e++k+  g  g+dv+++++G + + l+  + l
  gi|70606859|ref|YP_255729.1| 189 PIGLLFILLARTLGYEVWASNRRDPNEteSVIIEEGKINYYNSSA-GF-EKLKDSVG--GFDVIVDATGaNAQLLDKVIPL 265
                                   79*****************77666532113344457777777744.44.56677773..9*********778899****** PP

                                   EEEEEEEEECSCTSSEEE....EEHHHHHHTT-EEEEE-SSCHHHHHHHHH CS
                    ADH_zinc_N  79 lkpgGrlvvvGggkgeee....fdlrnlllkeksilGsllgslreefkeal 125
                                   l+++G l ++G+++++       dl+ l+  +k ilG + g+ +  f++a+
  gi|70606859|ref|YP_255729.1| 266 LNRNGILGIFGFPSDGIFsisyKDLQTLVHGNKLILGLVNGQ-KPHFQQAI 315
                                   ************8888855666666669999******99999.88888865 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.8e-06     0.029      33      73 ..     176     216 ..     149     239 .. 0.82
   2 ?   -2.6   0.0         1     3e+03     131     146 ..     339     354 ..     333     357 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-06
                                   -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                  2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                   +++ +++ +iG+G IG  ++ +++ +g +v a +r+  +e+
  gi|70606859|ref|YP_255729.1| 176 TINCRKMLVIGTGPIGLLFILLARTLGYEVWASNRRDPNET 216
                                   578899****************************9977554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                                   GB-HHHHHHHHHTTSC CS
                  2-Hacid_dh_C 131 lvdeeaLleaLksgki 146
                                   + de+ +++aLk+++ 
  gi|70606859|ref|YP_255729.1| 339 INDENEVMKALKEKQA 354
                                   56999999***99875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   4.8e+03      60      77 ..     144     161 ..     135     164 .. 0.71
   2 ?   11.9   0.0   5.7e-05      0.17       9      92 ..     176     261 ..     171     263 .. 0.75
   3 ?   -3.6   0.1       3.5   1.1e+04      26      41 ..     344     359 ..     342     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                                   T-EEEEGCGHHHHHHT-S CS
                  Shikimate_DH  60 eiealkleelkellaead 77 
                                    i a++l ++++ l+e+d
  gi|70606859|ref|YP_255729.1| 144 GILAQPLADIEKSLQEID 161
                                   566788888888888877 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.7e-05
                                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS.HHHHHHHHHHHT.ET-..EEEEGCGHHHHHHT-SEEEE-SSSS CS
                  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRt.lerakelaeelkgeei..ealkleelkellaeadvvisatase 86 
                                   +++ +k+l+iG+G ++ l +    + g++ v   NR   +  +++  e ++ ++  +   +e+lk+ +  +dv++ at+++
  gi|70606859|ref|YP_255729.1| 176 TINCRKMLVIGTGPIGLLFILLARTLGYE-VWASNRRdPNETESVIIEEGKINYynSSAGFEKLKDSVGGFDVIVDATGAN 255
                                   57889**********99888666666666.9999976155556655554444331135679*******************9 PP

                                   S-SB-H CS
                  Shikimate_DH  87 epilek 92 
                                     +l+k
  gi|70606859|ref|YP_255729.1| 256 AQLLDK 261
                                   998865 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                                   HHHHHHHCCT-CEEEE CS
                  Shikimate_DH  26 lvakhLlakgvkkvvv 41 
                                   +v+k+L +k+++++ v
  gi|70606859|ref|YP_255729.1| 344 EVMKALKEKQAEEIKV 359
                                   6889999999988865 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05     0.091      21      98 ..     175     251 ..     161     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                   CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH..HHHHHHHHH-SEEEE- CS
                   AlaDh_PNT_C  21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqe..ellaeavkeadvvigt 98 
                                   G+++     k+lviG G  Gl  i  a+ lg +V + + r     +   +++  ++ ++s++  e+l+++v   dv++ +
  gi|70606859|ref|YP_255729.1| 175 GTIN---CRKMLVIGTGPIGLLFILLARTLGYEVWASNRRDPNETESVIIEEGKINYYNSSAgfEKLKDSVGGFDVIVDA 251
                                   6666...789***************************9997766665555554488876665447899999999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2409.33
//
Query:       gi|70606860|ref|YP_255730.1|  [L=352]
Description: hypothetical protein Saci_1080 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.7   0.4    2.8e-18   66.7   0.4    1.5  2  ATPase_2  ATPase domain predominantly from Archaea
    8.6e-12   45.2   0.4    4.2e-09   36.5   0.1    3.2  2  AAA_14    AAA domain
    3.9e-05   23.9   0.0    0.00011   22.5   0.0    1.7  2  AAA_22    AAA domain
    7.7e-05   23.1   0.1     0.0002   21.8   0.1    1.7  1  AAA_16    AAA ATPase domain
    0.00082   19.8   0.1      0.011   16.1   0.0    2.7  2  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.017   14.5   0.0        6.1    6.1   0.0    2.3  2  DUF3388   Protein of unknown function (DUF3388)


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.4   9.4e-22   2.8e-18       1     230 [.      14     240 ..      14     241 .. 0.78
   2 ?   -3.7   0.0         3   8.9e+03     122     134 ..     263     275 ..     258     282 .. 0.73

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 9.4e-22
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..........e 71 
                                   +fdReke++e+++ ++r   + + i G +++GKt+ l  ++++l+  d+ v  +i+ r+ ++++ ++ +            
  gi|70606860|ref|YP_255730.1|  14 LFDREKEIEEIKNNINR---PLLAISGIRRIGKTSTLLVALNELKT-DY-V--LIDCRRLKENYGRQDLYsifsasfssiI 87 
                                   59*************99...999*********************55.44.2..2333333333333332223333333444 PP

                      ATPase_2  72 eeekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesl 152
                                    ++++ l+ + g  +  +++e  +k k ++   ++++l++ ++kk  ++ii iDe+qkl+  g   +++  ++++ ++++ 
  gi|70606860|ref|YP_255730.1|  88 DKVRDILSGVRGVSIVGNSIE--FKWKGRQ-SLSLADLFDHLNKK--RLIIAIDEAQKLR--GPL-STEIKDAIAHAYDY- 159
                                   555666666667777777773..5545555.789999*****998..78***********..544.45666677777888. PP

                      ATPase_2 153 tkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfeeiyryvGGkPk 228
                                     +++l++++ +s+ gl+ +   + +++s+l+gr  y ++++ + +e +++fl +gf+e+    ++  +++++++++G+P+
  gi|70606860|ref|YP_255730.1| 160 --DENLTFIFTGSEIGLLYDflgVEDKNSPLYGRYYYsVTLERFSREMSKEFLTKGFQEVgLRANNSVVDKLVDLFDGIPG 238
                                   ..999************999887899**********************************655588889***********8 PP

                      ATPase_2 229 al 230
                                    l
  gi|70606860|ref|YP_255730.1| 239 WL 240
                                   65 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                      ATPase_2 122 iiiDelqklidlg 134
                                   + +Del klid +
  gi|70606860|ref|YP_255730.1| 263 VALDELEKLIDTK 275
                                   6678888888665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   1.4e-12   4.2e-09       2     106 ..      30     176 ..      29     202 .. 0.76
   2 ?    1.2   0.0      0.12   3.4e+02      68     103 ..     263     298 ..     245     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.4e-12
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd...................kkladpekllelileklke. 62 
                                   r++l+i+G+Rr+GKT  l   ++el     +++ i++ + ++                   +                 + 
  gi|70606860|ref|YP_255730.1|  30 RPLLAISGIRRIGKTSTLLVALNELK---TDYVLIDCRRLKEnygrqdlysifsasfssiiD-----------------Kv 90 
                                   67899************999997777...99******9988844444433332222222220.................13 PP

                        AAA_14  63 .....................................ekktylflDEiqev.....pewekalkslvdegknldvivtGSn 101
                                                                        +k+ ++ +DE+q++     +e+++a+ + +d ++nl +i+tGS 
  gi|70606860|ref|YP_255730.1|  91 rdilsgvrgvsivgnsiefkwkgrqslsladlfdhlnKKRLIIAIDEAQKLrgplsTEIKDAIAHAYDYDENLTFIFTGSE 171
                                   33444566677777788888888888888888888866777799*******9999999**********99**********9 PP

                        AAA_14 102 sklls 106
                                    +ll+
  gi|70606860|ref|YP_255730.1| 172 IGLLY 176
                                   99886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                        AAA_14  68 lflDEiqevpewekalkslvdegknldvivtGSnsk 103
                                   + lDE  ++ + ++ + ++  ++ ++ + + GS   
  gi|70606860|ref|YP_255730.1| 263 VALDELEKLIDTKRRVSEISARRYKYALKCLGSGMN 298
                                   789***********9999999998888888888665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.7e-08   0.00011       5     131 ..      30     171 ..      27     175 .. 0.81
   2 ?   -3.1   0.0         3   8.8e+03      96     112 ..     264     281 ..     257     304 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.7e-08
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka............ 70 
                                   + +l++ G   +GKT +l   l++l         + ++v++++  ++   +++dl++ +   + +  ++            
  gi|70606860|ref|YP_255730.1|  30 RPLLAISGIRRIGKTSTLLVALNEL---------KTDYVLIDCRRLKenyGRQDLYSIFSASFSSIIDKvrdilsgvrgvs 101
                                   56899********************.........999*****9999987766676666666666666669999******** PP

                        AAA_22  71 ........erlsseell.ealeqalraravielliiDEaqhlr...seealeeLrsllnlsrkgvqliLvGtp 131
                                           +++ ++ l  + l ++l++++   ++ iDEaq+lr   s e+   + + ++  + ++++i+ G +
  gi|70606860|ref|YP_255730.1| 102 ivgnsiefKWKGRQSLSlADLFDHLNKKRL--IIAIDEAQKLRgplSTEIKDAIAHAYD-YDENLTFIFTGSE 171
                                   ********9999999999**********99..**********66443444444444455.6778888888875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3
                        AAA_22  96 iiDEaqhlr.seealeeL 112
                                    +DE ++l+ +++ ++e+
  gi|70606860|ref|YP_255730.1| 264 ALDELEKLIdTKRRVSEI 281
                                   578888776545555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   6.6e-08    0.0002       2     148 ..      14     142 ..      13     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.6e-08
                        AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareell 82 
                                   l+ Re+e+e++++ ++r      +l+ +sG + +GK+s +  +l++l++d+   +  +c++l+++            ++ l
  gi|70606860|ref|YP_255730.1|  14 LFDREKEIEEIKNNINR------PLLAISGIRRIGKTSTLLVALNELKTDY---VLIDCRRLKEN---------Y-GRQDL 75 
                                   788*********99984......5899***********************5...99999999555.........3.33666 PP

                        AAA_16  83 rqlldeaesaeleawrekleealaavpelagaea....srllellkrllallsrderplvlvlDdlqwad 148
                                     + +++ s+  +  r+ l ++ + v+ +  +++     r    l++l++ l + +r l++ +D++q+++
  gi|70606860|ref|YP_255730.1|  76 YSIFSASFSSIIDKVRDILSGVRG-VSIVGNSIEfkwkGRQSLSLADLFDHLNK-KR-LIIAIDEAQKLR 142
                                   666666555555555554444333.22222222344446666666666666666.66.999999999876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.8e-06     0.011       4      72 ..      36     143 ..      33     177 .. 0.85
   2 ?   -1.1   0.0      0.77   2.3e+03      62      79 ..     263     280 ..     246     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-06
                                   ESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.........................................STTHHH CS
                           AAA   4 yGppGtGKTllakavakelgvefleisgsellsk.........................................yvgese 43 
                                   +G   +GKT++     +el+++++ i++ +l ++                                         + g ++
  gi|70606860|ref|YP_255730.1|  36 SGIRRIGKTSTLLVALNELKTDYVLIDCRRLKENygrqdlysifsasfssiidkvrdilsgvrgvsivgnsiefkWKGRQS 116
                                   677779**************9999999999997789999999999999999999*************************** PP

                                   HHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                           AAA  44 kkirelfkeakekakpsilfiDEidalak 72 
                                    ++++lf+++ +k+   i+ iDE+ +l +
  gi|70606860|ref|YP_255730.1| 117 LSLADLFDHLNKKR--LIIAIDEAQKLRG 143
                                   *********99987..********99854 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                                   EEEETGGGHHHHHTTCCC CS
                           AAA  62 lfiDEidalaksrsgses 79 
                                   + +DE+++l+ ++++ ++
  gi|70606860|ref|YP_255730.1| 263 VALDELEKLIDTKRRVSE 280
                                   568888888877744443 PP

>> DUF3388  Protein of unknown function (DUF3388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0021       6.3      48     113 ..      24      89 ..      10     102 .. 0.79
   2 ?    6.1   0.0     0.002       6.1      24      46 ..     158     180 ..     139     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0021
                       DUF3388  48 llkkeghkliGirGmPrvGktesivaasvcankrwlflsstllkqtvrsqliedeynednifiidg 113
                                   + ++ +  l+ i G+ r+Gkt +++ a    +  ++++    lk+    q +  +++++   iid 
  gi|70606860|ref|YP_255730.1|  24 IKNNINRPLLAISGIRRIGKTSTLLVALNELKTDYVLIDCRRLKENYGRQDLYSIFSASFSSIIDK 89 
                                   445557789***************999988888899998888887776666666666666666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.002
                       DUF3388  24 daddkktfrfvreelgllvdfla 46 
                                   d d++ tf+f+  e+gll dfl+
  gi|70606860|ref|YP_255730.1| 158 DYDENLTFIFTGSEIGLLYDFLG 180
                                   678899***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2355.98
//
Query:       gi|70606861|ref|YP_255731.1|  [L=140]
Description: hypothetical protein Saci_1081 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1052.13
//
Query:       gi|70606862|ref|YP_255732.1|  [L=505]
Description: acyl-CoA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-76  256.7   0.0    3.7e-76  256.4   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.6e-17   61.7   0.0    2.4e-16   60.4   0.0    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.077   13.1   0.0       0.24   11.5   0.0    1.8  1  Hormone_3      Pancreatic hormone peptide


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.4   0.0   6.1e-80   3.7e-76      12     422 ..      27     401 ..      16     402 .. 0.85

  Alignments for each domain:
  == domain 1  score: 256.4 bits;  conditional E-value: 6.1e-80
                                   EEEEE.CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHH CS
                   AMP-binding  12 valvd.sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayile 91 
                                     + + +++  ++TY+++ erv++lA++Lr +++  g++Va +++n+ +++ +++a+  +G+v+ ++n ++ + e++y+++
  gi|70606862|ref|YP_255732.1|  27 EIISRtHDSIVRYTYKDFSERVRKLANFLRTKNLA-GENVATIAWNTQRHLELYFAVPLLGGVLHTVNVRFHPSEMEYVIR 106
                                   444336678899******************85765.889****************************************** PP

                                   HHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SSS CS
                   AMP-binding  92 dseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTTG 172
                                   + e k+++  +d++      + ++     + v+vld+    +++++ ++     +    ++ + ++++  a+ ++TSGTTG
  gi|70606862|ref|YP_255732.1| 107 EMEDKAVF--IDRDI-----SYKG-----DNVTVLDE----RYDDEINSF----EP--LTDLPDIDEKVGAVACFTSGTTG 165
                                   ********..54433.....3343.....45777883....222222222....22..2234468999************* PP

                                   S-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT CS
                   AMP-binding 173 kPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklk 253
                                   kPKGV++shr++     sl  ++  +++++d+v+  +p++hi ++    +++l+ Ga++vl+ + ++  ++ ++ li++++
  gi|70606862|ref|YP_255732.1| 166 KPKGVIYSHRSIFIHSLSLLAKDVVGISSRDTVMPLVPMFHISAW-DLPFASLMTGAKLVLPGPRPK--AEDIVYLIKRYN 243
                                   *********99966655543555577889****************.9**************998888..455889****** PP

                                   -SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTC CS
                   AMP-binding 254 vtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedk 333
                                   v++ ag+P+v+  +l+  +++k      dls l++v++gg+ +++ l++++++l+ +  ++++G+TEt +++t ++++++ 
  gi|70606862|ref|YP_255732.1| 244 VSIGAGAPTVWIDVLNyVEREK-----MDLSPLKVVVTGGAEPPQGLMKKLKELGVR-TYHAWGMTETEAIAT-VNQSDSV 317
                                   ****************665444.....49*************************876.9**************.8889999 PP

                                   TSTTS-BEE-TTEEEEEE-TTTSCBEETTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEE CS
                   AMP-binding 334 kklgsvGkplpgvevkivDeetgepvpdgee.GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleiv 413
                                   + l+++G p+pg e+ ++De++ ++  dg++ Gel+ rg+ v+k Y+k+    ++ ++ + ++ rTGD++++ +dG++++v
  gi|70606862|ref|YP_255732.1| 318 EELSKQGYPMPGFEIGLMDENNRNLPWDGKSvGELVARGAFVTKKYYKQ----SDMMV-N-GFIRTGDVAKIYPDGNVKVV 392
                                   9999****************966666699889***************99....66666.4.799***************** PP

                                   EECCCEEEE CS
                   AMP-binding 414 gRkkdlikl 422
                                   +R+kdlik+
  gi|70606862|ref|YP_255732.1| 393 DRLKDLIKS 401
                                   *******97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   4.1e-20   2.4e-16       2      76 .]     411     487 ..     410     487 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 4.1e-20
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH..HT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk..elgpyavpkkvvfvdelpktrsGK 76 
                                   +E+a++s ++V ea+VvG++de++Ge+++a+Vv k++++  +ee++ ++++  +++ ++ p+k++fvd++pkt +GK
  gi|70606862|ref|YP_255732.1| 411 LENAIMSYEKVLEAVVVGIKDEKWGERPIALVVKKPDKDVNAEEIITYLKSlgRFPNWWMPEKIIFVDSIPKTSTGK 487
                                   7********************************876643357*******9999***********************9 PP

>> Hormone_3  Pancreatic hormone peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     4e-05      0.24       6      25 ..     445     464 ..     444     467 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
                                   XXXTTS-HHHHHHHHHHHHH CS
                     Hormone_3   6 rPgedaspEeLakYyaaLrh 25 
                                   +P  d ++Ee+++Y+++L++
  gi|70606862|ref|YP_255732.1| 445 KPDKDVNAEEIITYLKSLGR 464
                                   799***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3674.51
//
Query:       gi|70606863|ref|YP_255733.1|  [L=167]
Description: hypothetical protein Saci_1085 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-15   56.4   0.0    2.9e-15   55.9   0.0    1.2  1  MaoC_dehydratas  MaoC like domain
     0.0034   17.5   0.0     0.0046   17.1   0.0    1.5  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase


Domain annotation for each model (and alignments):
>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   3.2e-19   2.9e-15       6     108 ..      13     119 ..       9     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 3.2e-19
                                   TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHH....TTTS.SSB--HHHHHHHHHHHHHHHHSTTEGGGEEEE CS
               MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpefAkk....agfg.gpIahGmltlaivaklveeelgdnvvarvgei 81 
                                   +g+ ++ +  +++t  d+  ++l++ + n iH+++++ +k     +f+   +++G+ltlaiva+l++e   +n    +g++
  gi|70606863|ref|YP_255733.1|  13 VGQRFRSKVGRSLTDVDNIWFTLLTNNSNQIHFNRDYTEKyfsgEPFKgRLVVNGFLTLAIVAGLLVELTSQN-GFMLGIE 92 
                                   79999999***************************977652322468845599***************99995.467**** PP

                                   EEEE-S--BTTCEEEEEEEEEEEEEEE CS
               MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvr 108
                                   +v+F +pV++gdt++ e+ev + r+ +
  gi|70606863|ref|YP_255733.1|  93 NVKFMNPVFAGDTIYGEAEVIEARESK 119
                                   ********************9987766 PP

>> MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.1e-07    0.0046      75     131 ..      87     143 ..      13     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.1e-07
               MaoC_dehydrat_N  75 llhgeqefeyhepiraGDelttesriadvydkkgvGalefivvettvtnqrGepvat 131
                                    + g +++++ +p+ aGD+++ e+++ + ++ k+   + ++  +t  +nqrGe++++
  gi|70606863|ref|YP_255733.1|  87 FMLGIENVKFMNPVFAGDTIYGEAEVIEARESKSRPGFGIVKIRTWGYNQRGEKIVE 143
                                   55667899***********************99967788***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1238.13
//
Query:       gi|70606864|ref|YP_255734.1|  [L=382]
Description: CoA-transferase family III protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-90  303.7   0.0    2.3e-90  303.4   0.0    1.0  1  CoA_transf_3    CoA-transferase family III
  ------ inclusion threshold ------
       0.11   12.5   0.2       0.24   11.4   0.2    1.5  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.4   0.0   2.6e-94   2.3e-90       4     368 .]       6     353 ..       5     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 303.4 bits;  conditional E-value: 2.6e-94
                  CoA_transf_3   4 vrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkrLva 84 
                                   +rV++ls+++ +pl++++L++lGA+VIkvEpp kgD+ R v+p+ + g ++yf++vn++Krsv++Dlk++eg e++k+ va
  gi|70606864|ref|YP_255734.1|   6 MRVVELSNNISAPLVGQILSELGADVIKVEPP-KGDDRRGVKPEID-GVGVYFASVNKGKRSVSIDLKKPEGYEIFKKIVA 84 
                                   79******************************.********99997.********************************** PP

                  CoA_transf_3  85 kADVvieNfrpgvlerlglgyeelr.ainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvgvplg 164
                                   +AD++i+N+rp +l++l+++ye+++ + nP++iy+s++g+G++ ++a++p+yD+++ a sGlm++tge  ++Pvk  +++ 
  gi|70606864|ref|YP_255734.1|  85 TADIIITNYRPSALKKLRIDYESVKnQTNPKIIYCSITGFGNFTEEADKPAYDTTILALSGLMDMTGE--ENPVKFATSIS 163
                                   ***********************97367**************************************98..578******** PP

                  CoA_transf_3 165 DivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyrtkdgwvaiaa 245
                                   Di+t+l+  + il+ +    ++G    idv ++ + + l+ +++ +yl+tg  p+r+g++++ + py+++rtk+g++++a+
  gi|70606864|ref|YP_255734.1| 164 DITTALFSTILILWYY----NQGGPVFIDVPMIYTQFYLMLEDAYMYLNTGILPKRMGSAHRYLVPYQAFRTKNGYIYVAT 240
                                   *************999....78999******************************************************** PP

                  CoA_transf_3 246 atdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntleevlddpqlaa 326
                                   ++++q+++lckalgr++l     + t++sr++nr+ + +el++++++ t++ w + l++a+vp+ap+ +l+e++   q+  
  gi|70606864|ref|YP_255734.1| 241 FNNEQYTNLCKALGREDL---LIYDTQESRVRNREYIARELQKIFETNTREFWIKKLNEADVPVAPILNLAEAF---QIYG 315
                                   ****************97...689999********************************************994...4555 PP

                  CoA_transf_3 327 rglvvevddpdygevpvvglpvrlsetpa.rvkraaPklGedt 368
                                   ++lv   ++     +++v++p+++++ +   +  +aP+lGe+t
  gi|70606864|ref|YP_255734.1| 316 NKLVY--ERRS---LRYVRFPANVKDKREpGTGLPAPRLGEHT 353
                                   55555..4444...6799999999887775788899******8 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.7e-05      0.24      31      70 ..     254     296 ..     247     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                Sulfolobus_pRN  31 ekeellvylt...rlykrGlisrkWrkiaGkkvreyclkyrde 70 
                                    +e+ll+y t   r+ +r  i r+ +ki     re+ +k+ +e
  gi|70606864|ref|YP_255734.1| 254 GREDLLIYDTqesRVRNREYIARELQKIFETNTREFWIKKLNE 296
                                   699*****986669**********************9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 2304.06
//
Query:       gi|70606865|ref|YP_255735.1|  [L=328]
Description: dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-45  155.0   0.0    3.4e-45  154.4   0.0    1.2  1  Fe-ADH    Iron-containing alcohol dehydrogenase
      2e-08   34.3   0.0    2.6e-08   33.9   0.0    1.2  1  Fe-ADH_2  Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   3.8e-49   3.4e-45       2     363 ..       9     319 ..       8     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 3.8e-49
                                   SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.- CS
                        Fe-ADH   2 trivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareega 82 
                                   t++++gk+al+ l     +l+ +++ ivt++++l + ++l+ ++++l    ++ ++++g +++ ++++v+++ +  +  ++
  gi|70606865|ref|YP_255735.1|   9 TQVIYGKDALDWLV----NLKSSKVGIVTTRSLL-QGKTLS-LVTKL----VNADIIEGPRQHVPEDDVNALKE--KVGNY 77 
                                   78999999995554....55568*********99.555555.55555....688999*****************..55778 PP

                                   -EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS-- CS
                        Fe-ADH  83 dvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellP 163
                                   +++i++GGGs iD  K++    +                   + i+iPTt  +G+e t+    t ++ g k s       P
  gi|70606865|ref|YP_255735.1|  78 ETIIGLGGGSIIDGLKLVLEEKT-------------------KYIVIPTTL-SGAEHTKSGGYT-TQ-GLKRSKL--GKEP 134
                                   9************9998876666...................79*******.9*********99.44.4566555..367* PP

                                   SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Fe-ADH 164 dlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedleareqmllastlag 244
                                   d++i+Dp+ tl +Pk +++++++  + ha+Ea+ s+ ++p+ d la+e++  i+++l+++    ++l+ r ++ ++ +l+ 
  gi|70606865|ref|YP_255735.1| 135 DIVILDPRATLETPKWLLVSSAVRSIDHAVEALYSRDSTPFVDSLAKEGFHKIVNCLRDI----DSLDSRLECQIGVWLSS 211
                                   *********************************************************884....479************** PP

                                   HHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T--HHHHHHHHHHHHHTT- CS
                        Fe-ADH 245 lafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdeeaaeeliealrellkelgl 325
                                   l + +a++g++H++++ +g +f+iphg++ +i lpa+++fn+ a++e+l+ + ++          e l e l+++l+e+g+
  gi|70606865|ref|YP_255735.1| 212 LTMRYARMGMSHMFGYVFGPRFNIPHGYTSCISLPAAVKFNYGASKEKLKSIEKN----------EPLYEFLDNFLREIGV 282
                                   ******************************************9999**9999999..........89************** PP

                                   --SHHHHT-TT-HHHHHHHHHT-TSGGGGSSS---HHH CS
                        Fe-ADH 326 ptsLselgvdeedldklaeaalkdrslannpreltaed 363
                                    ++Lse+  + e++ k ae   + ++  +np +l+ +d
  gi|70606865|ref|YP_255735.1| 283 RKKLSEYT-SLEEALKYAEVFSQLSNNSGNPTKLSIDD 319
                                   ******95.33566777777766689999999998876 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.9e-12   2.6e-08      41     198 ..      44     196 ..      15     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.9e-12
                      Fe-ADH_2  41 slkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgasl 121
                                   sl ++ ++++++e  +++  +++v++l e++   +++ ++++GgG+iiD  k+v  +++ +y+++pT++S    + +g   
  gi|70606865|ref|YP_255735.1|  44 SLVTKLVNADIIEGPRQHVPEDDVNALKEKVG--NYETIIGLGGGSIIDGLKLV-LEEKTKYIVIPTTLSGAEHTKSGG-Y 120
                                   4555557778899889999999***9999998..*******************9.577889*********999998886.5 PP

                      Fe-ADH_2 122 vvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklanevseplaklsaamvqeaaeklve 198
                                   +++g kr+    + P  vi+D     e P+ ll s     +   +    ++ ++ + ++lak+ +++++++++ + +
  gi|70606865|ref|YP_255735.1| 121 TTQGLKRSK-LGKEPDIVILDPRATLETPKWLLVSSAVRSIDHAVEALYSRDSTPFVDSLAKEGFHKIVNCLRDIDS 196
                                   777888885.6889*******************99988888888888888888888888888888888888877755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 2032.66
//
Query:       gi|70606866|ref|YP_255736.1|  [L=107]
Description: hypothetical protein Saci_1088 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0019   17.9   4.2     0.0028   17.4   4.2    1.3  1  Fer4         4Fe-4S binding domain
     0.0026   17.9   3.6      0.004   17.2   3.6    1.5  1  Fer4_21      4Fe-4S dicluster domain
     0.0058   16.7   2.2     0.0062   16.6   2.2    1.3  1  Fer4_10      4Fe-4S dicluster domain
      0.006   17.1   1.8       0.01   16.3   1.8    1.4  1  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.028   14.9   0.2      0.036   14.6   0.2    1.2  1  Tox-REase-5  Restriction endonuclease fold toxin 5
       0.95   10.1   6.3        2.1    9.0   6.3    1.5  1  Fer4_4       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.2   9.5e-07    0.0028       4      23 ..       2      21 ..       1      22 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.5e-07
                                  ETTTSSS-THHHHHSTTTEE CS
                          Fer4  4 deekCigCGaCvevCPvgAI 23
                                  + + Ci+C+ C   CP +++
  gi|70606866|ref|YP_255736.1|  2 NFDTCIKCKSCWIHCPDECL 21
                                  7899************9987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.6   1.3e-06     0.004       6      28 ..       4      23 ..       1      54 [. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                       Fer4_21  6 dkCigCgkCliaCedtshqaiei 28
                                  d+Ci+C++C i C+d+   +++ 
  gi|70606866|ref|YP_255736.1|  4 DTCIKCKSCWIHCPDE---CLDE 23
                                  89************95...5544 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.2   2.1e-06    0.0062       5      24 ..       2      23 ..       1      89 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                       Fer4_10  5 dddtCirCgkCvkaCPadl..t 24
                                  + dtCi+C+ C   CP     +
  gi|70606866|ref|YP_255736.1|  2 NFDTCIKCKSCWIHCPDECldE 23
                                  569*************966662 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.8   3.5e-06      0.01       4      18 ..       4      18 ..       2      35 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                       Fer4_13  4 dtCiacgaCvelaPd 18
                                  dtCi c++C+  +Pd
  gi|70606866|ref|YP_255736.1|  4 DTCIKCKSCWIHCPD 18
                                  8*************8 PP

>> Tox-REase-5  Restriction endonuclease fold toxin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   1.2e-05     0.036      31      77 ..      60     104 ..      41     107 .] 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                   Tox-REase-5  31 fDGfksaeclllEaKagYdqffdkkepklkksfkgadklleqaerqa 77 
                                   f  ++ + ++ +E Ka+Y+ +++ +     k+ kg+++++ + +r +
  gi|70606866|ref|YP_255736.1|  60 FTDYRRPYEMWKENKAKYKDWLKSGR--ISKKRKGKHSMVGKMTRNS 104
                                   67799999***************995..5899999999998888765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.3   0.00071       2.1       2      16 ..       4      18 ..       3      22 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00071
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++Ci C+sC + CP+
  gi|70606866|ref|YP_255736.1|  4 DTCIKCKSCWIHCPD 18
                                  89************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 694.98
//
Query:       gi|70606867|ref|YP_255737.1|  [L=340]
Description: ATP-dependent helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-44  152.1   0.0    4.3e-44  150.4   0.0    1.8  2  DEAD             DEAD/DEAH box helicase
      6e-32  110.3   1.0      7e-31  106.9   0.1    2.4  3  Helicase_C       Helicase conserved C-terminal domain
      2e-10   40.9   0.0    4.2e-10   39.9   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
      0.008   16.5   0.1       0.18   12.1   0.0    2.9  2  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.026   13.9   0.0    1.6  1  CMS1             U3-containing 90S pre-ribosomal complex subu
      0.014   15.7   3.5       0.36   11.1   3.5    2.8  1  AAA_22           AAA domain
      0.028   14.1   0.0      0.083   12.6   0.0    1.8  1  AAA_30           AAA domain
      0.036   14.0   0.0       0.14   12.1   0.0    2.0  1  Flavi_DEAD       Flavivirus DEAD domain
      0.053   12.3   0.1       0.13   11.1   0.0    1.6  2  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   0.0   2.1e-47   4.3e-44       1     175 [.      14     167 ..      14     168 .. 0.94
   2 ?   -1.3   0.0      0.83   1.7e+03     134     168 ..     195     224 ..     177     231 .. 0.56

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 2.1e-47
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   t++Q+e+ip +lgg++v+v+a+TGsGKT+ +lip+l        ++g+ ali++PtreLa q+l++l+k++ky ++  +l+
  gi|70606867|ref|YP_255737.1|  14 TRVQQEVIPRLLGGKSVIVQAKTGSGKTASYLIPIL--------ESGKTALILSPTRELASQILDELRKLGKYKQVDFSLV 86 
                                   789*********************************........67889************************999***** PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                   iggv+++ q++     ++iv+gtpgrl+dl s++++++s+++++++DEadr+ld+gf d+i+ iln+ +      +  + v
  gi|70606867|ref|YP_255737.1|  87 IGGVKYEGQKQ-----ARIVIGTPGRLLDLWSKEEIDFSKFEVVIIDEADRMLDMGFIDDIRMILNNSK------P--EIV 154
                                   ******77755.....55**************************************************2......4..45* PP

                                   EEEESSBSHHHHH CS
                                   xxxxxxxxxxxxx RF
                          DEAD 163 ivlSATlpkdvkk 175
                                    ++SAT+p+++ +
  gi|70606867|ref|YP_255737.1| 155 GLFSATIPEKIAE 167
                                   ********88766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.83
                                   HHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 134 ldqgfsdfinrilnqlpqitcdgklqrqvivlSAT 168
                                       + d+ +++ + l++i+ + k    +iv++ T
  gi|70606867|ref|YP_255737.1| 195 IR-ARNDWTDKVTKLLDEINGKDK----IIVFTRT 224
                                   33.355666666666655544433....8888866 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.18   3.6e+02       5      44 ..      44      84 ..      40     100 .. 0.63
   2 ?   -3.9   0.0         9   1.8e+04      80      92 ..     117     129 ..     117     134 .. 0.79
   3 !  106.9   0.1   3.5e-34     7e-31       6     111 .]     205     310 ..     201     310 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                                  HHHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEE CS
                    Helicase_C  5 allellkleeeggkilifvntidrlek....vklllekkgikva 44
                                  +l+ +l   e+g+++li ++t++ +++    ++ l + k++ + 
  gi|70606867|ref|YP_255737.1| 44 YLIPIL---ESGKTALILSPTRELASQildeLRKLGKYKQVDFS 84
                                  566666...8999**********665332233444333345554 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9
                                   STSTTESEEEESS CS
                    Helicase_C  80 idipkvnlVinfd 92 
                                   id+ k ++Vi+ +
  gi|70606867|ref|YP_255737.1| 117 IDFSKFEVVIIDE 129
                                   7999999999855 PP

  == domain 3  score: 106.9 bits;  conditional E-value: 3.5e-34
                                   HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTES CS
                    Helicase_C   6 llellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvn 86 
                                   +++ll++ + ++ki++f++t++r++++++lle+kgi+   l g++pq+ r + +  f++g++++L+atd a+rGid+ +vn
  gi|70606867|ref|YP_255737.1| 205 VTKLLDEINGKDKIIVFTRTRERAKRLHYLLENKGIRNGLLSGDMPQSVRMKNFYGFKNGKYNILVATDLASRGIDVVDVN 285
                                   4556666699**************889****************************************************** PP

                                   EEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  87 lVinfdlprnvtsyiqriGRtgRag 111
                                    +infd+pr++++yi+r+GRtgR+g
  gi|70606867|ref|YP_255737.1| 286 IIINFDAPRDIETYIHRVGRTGRMG 310
                                   ***********************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   2.1e-13   4.2e-10      10     170 ..      19     162 ..      11     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.1e-13
                                   HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEES CS
                        ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvs 90 
                                   e+i +ll      + k +++++ TG+GKT  ++  i +  k      +l+l p+++l +q l+e++k+ + ++ + + ++ 
  gi|70606867|ref|YP_255737.1|  19 EVIPRLL------GGKSVIVQAKTGSGKTASYLIPILESGK-----TALILSPTRELASQILDELRKLGKYKQVDFSLVIG 88 
                                   5555554......568899**********999887777666.....79*********************999888888888 PP

                                   SS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---SEEEEEESS CS
                        ResIII  91 gdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfkeavllglTAT 168
                                   g k++     +++++i++ t  +l          +ee + ++f+v+iiDEa r+ ++   + +r il++ k+ ++  ++AT
  gi|70606867|ref|YP_255737.1|  89 GVKYEG----QKQARIVIGTPGRLLDLW-----SKEEIDFSKFEVVIIDEADRMLDMgfiDDIRMILNNSKPEIVGLFSAT 160
                                   888888....8889**********9999.....999********************9766688999999999888889*** PP

                                   -S CS
                        ResIII 169 pe 170
                                   ++
  gi|70606867|ref|YP_255737.1| 161 IP 162
                                   86 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   9.1e-05      0.18       1     124 [.      17     197 ..      17     221 .. 0.63
   2 ?   -0.9   0.0      0.97   1.9e+03      32      59 ..     207     232 ..     199     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                        AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae............ 68 
                                   q+e +   l  k ++v a  G+GKT      + +l++ +     + l++++t+  a+++ ++l++lg+             
  gi|70606867|ref|YP_255737.1|  17 QQEVIPrLLGGKSVIVQAKTGSGKTAS--YLIPILESGK-----TALILSPTRELASQILDELRKLGKYkqvdfslviggv 90 
                                   6667744788999***********985..4555555555.....679****************999888555555554444 PP

                        AAA_19  69 ...atTiHrlal.....................................................ldfddlltealelle. 92 
                                                                                                                  + 
  gi|70606867|ref|YP_255737.1|  91 kyeG-------QkqarivigtpgrlldlwskeeidfskfevviideadrmldmgfiddirmilnnS-------------Kp 151
                                   4440.......0444444444444446666666666666666666666666644444444333330.............13 PP

                        AAA_19  93 ..............eaeeekklqeeellivDEfqdvdelqyrLlka 124
                                                  +  +++  ++e ++ DE+  v+e+q ++++a
  gi|70606867|ref|YP_255737.1| 152 eivglfsatipekiAELATEFSPDAEKIVLDEYKPVEEVQHEFIRA 197
                                   3333334555554422233444455677777777777777777776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.97
                        AAA_19  32 allvelggvkpeeillvaftgrAakelr 59 
                                   +ll e++g   ++i++ + t+  ak+l+
  gi|70606867|ref|YP_255737.1| 207 KLLDEINGK--DKIIVFTRTRERAKRLH 232
                                   455555554..78999999998888886 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.026     175     210 ..      95     130 ..      86     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                          CMS1 175 ksrigiavGtpgRildLleeeslsvdeLkrivlDas 210
                                   +++  i +GtpgR+ldL  +e +  ++ + +++D +
  gi|70606867|ref|YP_255737.1|  95 QKQARIVIGTPGRLLDLWSKEEIDFSKFEVVIIDEA 130
                                   56677899*************************965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.5   0.00018      0.36       7     118 ..      29     148 ..      24     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdl.lrellralglelkaerlsseell.eal 82 
                                   +++v + +G+GKT ++     +  + a +     e +++++ +l ++++ k++ ++ +   ++ e+ +  ++       +l
  gi|70606867|ref|YP_255737.1|  29 SVIVQAKTGSGKTASYLIPILESGKTALILSptrELASQILDELRKLGKYKQVdFSLVIGGVKYEGQK-QARIVIGTpGRL 108
                                   66677777777777776666655433333335566666667777777777777677777777766666.445555555566 PP

                        AAA_22  83 eqalrarav....ielliiDEaqh.lrseealeeLrsllnl 118
                                    + +++        e++iiDEa++ l  +  + ++r++ln+
  gi|70606867|ref|YP_255737.1| 109 LDLWSKEEIdfskFEVVIIDEADRmL-DMGFIDDIRMILNN 148
                                   666666665667779*********77.9************6 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05     0.083       6      98 ..      17     131 ..      13     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                        AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa....................... 63 
                                   Q++++ +ll+++   +++++  G+GKt +   l  ++e +g++ ++l+pt + A ++                        
  gi|70606867|ref|YP_255737.1|  17 QQEVIPRLLGGKS--VIVQAKTGSGKTAS--YLIPILE-SGKTALILSPTRELASQILdelrklgkykqvdfslviggvky 92 
                                   8999999999885..9***********86..4556666.788999*******99995524444444443333333322222 PP

                        AAA_30  64 ...eelgieastiakllkrlk.........grarlepgtllivDEag 98 
                                      +++ i   t                  ++ ++++ +++i+DEa 
  gi|70606867|ref|YP_255737.1|  93 egqKQARIVIGT--------PgrlldlwskEEIDFSKFEVVIIDEAD 131
                                   222233344444........255555554765677777*******95 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.14       5      57 ..      28      76 ..      25     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                                  -EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS- CS
                    Flavi_DEAD  5 kltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkgle 57
                                  k  +++++ G+Gkt  +l  +++    + + +l+L+Ptr  ++ + + l++l 
  gi|70606867|ref|YP_255737.1| 28 KSVIVQAKTGSGKTASYLIPILE----SGKTALILSPTRELASQILDELRKLG 76
                                  5678999***********99975....57789********9999999888753 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.4e-05      0.13      47      84 ..      30      66 ..      14      83 .. 0.85
   2 ?   -2.9   0.0       1.1   2.1e+03      96     134 ..     252     290 ..     250     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
               T4SS-DNA_transf 47 vlvvAptrsgKgvgvviPnllkwkqsiVvlDpkgElae 84
                                  v+v A t+sgK++++ iP +l  ++++ +l p  Ela 
  gi|70606867|ref|YP_255737.1| 30 VIVQAKTGSGKTASYLIP-ILESGKTALILSPTRELAS 66
                                  899***************.7899999999999999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
               T4SS-DNA_transf  96 kVfvlePanlktsdrfNpldyidlkse.vetedilsvasl 134
                                    V++ ++  +k++ ++N l   dl s    ++d+ ++++ 
  gi|70606867|ref|YP_255737.1| 252 SVRMKNFYGFKNG-KYNILVATDLASRgIDVVDVNIIINF 290
                                   5788889999999.99999999999988999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2143.72
//
Query:       gi|70606868|ref|YP_255738.1|  [L=112]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-22   77.4   5.9    1.4e-21   76.7   1.2    2.0  2  DUF202           Domain of unknown function (DUF202)
     0.0088   16.2   4.7      0.014   15.5   0.6    2.1  2  SdpI             SdpI/YhfL protein family
  ------ inclusion threshold ------
      0.014   15.8   1.7      0.031   14.7   1.7    1.6  2  CopD             Copper resistance protein D
      0.019   14.4   2.6      0.043   13.3   2.6    1.6  1  SfLAP            Sap, sulfolipid-1-addressing protein
       0.22   11.5   0.0       0.32   10.9   0.0    1.3  1  GRIM-19          GRIM-19 protein
       0.47   10.1   4.3       0.19   11.4   0.4    1.8  1  Tetraspanin      Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   1.2   4.8e-25   1.4e-21       2      67 ..       7      78 ..       6      79 .. 0.90
   2 ?    3.5   0.2     0.033        99      40      57 ..      92     109 ..      81     112 .] 0.66

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 4.8e-25
                        DUF202  2 dglAnERTfLaWlRtslalialglallrffl.....tgepsalg.kilglilivlgiltllvglvrylrrqr 67
                                  d+lAnERTfLaW+Rt++ali++g++++rf l     +g++++++ +i g i+ivlg +++++g+++ylr++r
  gi|70606868|ref|YP_255738.1|  7 DHLANERTFLAWIRTGIALIGFGFVIARFALflevlRGGRTTGSsVIYGEIMIVLGGIMIAYGTYNYLRNER 78
                                  9***************************98888999666666543788*********************987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.033
                        DUF202  40 gkilglilivlgiltllv 57 
                                   + i++++ ++++i+++l+
  gi|70606868|ref|YP_255738.1|  92 NTIFATFVLLIAIILALI 109
                                   477788877777777765 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.044   1.3e+02      32      52 ..      17      37 ..       8      45 .. 0.67
   2 !   15.5   0.6   4.8e-06     0.014      28      65 ..      53     109 ..      46     112 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.044
                          SdpI 32 lwiiaGlillllalgavvlvl 52
                                   wi +G++l+ +++ ++ ++l
  gi|70606868|ref|YP_255738.1| 17 AWIRTGIALIGFGFVIARFAL 37
                                  699999999999832333333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.8e-06
                          SdpI  28 fagklwiiaGlilllla....................lgavvlvllvlvlllvivpii 65 
                                   + g ++i++G i+++ +                    ++++ ++++vl++ ++i+ +i
  gi|70606868|ref|YP_255738.1|  53 IYGEIMIVLGGIMIAYGtynylrnerdlknntftprtTENTIFATFVLLI-AIILALI 109
                                   5789********************************73333344444444.3333333 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.6   1.8e+03      83     100 ..      14      31 ..       5      39 .. 0.57
   2 ?   14.7   1.7     1e-05     0.031      45     101 ..      56     107 ..      13     112 .] 0.64

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.6
                          CopD  83 rlrrsaalelvlalvvll 100
                                   ++ +++++ ++l    ++
  gi|70606868|ref|YP_255738.1|  14 TFLAWIRTGIALIGFGFV 31 
                                   555555555555444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1e-05
                          CopD  45 laKlalllvllalaalnrfrlvprleaatgaggqalrhrlrrsaalelvlalvvlll 101
                                    ++++l+ +++a++ +n++r  + l    ++++ ++r +  +++ + +vl+++++l+
  gi|70606868|ref|YP_255738.1|  56 EIMIVLGGIMIAYGTYNYLRNERDL----KNNTFTPR-TTENTIFATFVLLIAIILA 107
                                   489**********************....45555555.6666666666666665553 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.6   1.4e-05     0.043      38      96 ..      27      79 ..      11     112 .] 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                         SfLAP 38 wlvvlvalglivlfvlrsllsgasaa.pssaikalqivlGvlllllaaveavrrpkassr 96
                                  ++ + +a ++++l     +l+g +++  s + +++ ivlG+++++++ ++++r    ++ 
  gi|70606868|ref|YP_255738.1| 27 GFGFVIARFALFLE----VLRGGRTTgSSVIYGEIMIVLGGIMIAYGTYNYLRN---ERD 79
                                  22223333333333....333333333778889********************9...222 PP

>> GRIM-19  GRIM-19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.32      19      69 ..      46      96 ..      40     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                  XXXXXXXSXSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GRIM-19 19 rklpktllsglsllalviavtavglyavlksnkerrrekiekrsarlailP 69
                                  r+   +++ g+ +++l+ +++a+g+y +l +++  +++ +  r+ +++i+ 
  gi|70606868|ref|YP_255738.1| 46 RTTGSSVIYGEIMIVLGGIMIAYGTYNYLRNERDLKNNTFTPRTTENTIFA 96
                                  6777889999****************************9999998887765 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   6.4e-05      0.19      11      63 ..      57     109 ..      50     112 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.4e-05
                                   XXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin  11 lfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfll 63 
                                   +++++g +++a+G +  l+++   ++++ +  +++++i a++++++ ++l+l+
  gi|70606868|ref|YP_255738.1|  57 IMIVLGGIMIAYGTYNYLRNERDLKNNTFTPRTTENTIFATFVLLIAIILALI 109
                                   799**********8887777767777777777888888888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 714.79
//
Query:       gi|70606869|ref|YP_255739.1|  [L=286]
Description: hypothetical protein Saci_1092 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-24   84.3  44.0    5.6e-18   65.4  15.4    2.3  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6  20.6   1.3e-09   2.3e-05       6     135 ..      21     141 ..      18     143 .. 0.90
   2 !   65.4  15.4   3.1e-22   5.6e-18       2     136 ..     148     280 ..     147     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-09
                          EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyal 86 
                                   +++  +l w+i+++l+k++  +vsp+ +++ r +++++++ ++   + + +           ++ +l+++++   l + ++
  gi|70606869|ref|YP_255739.1|  21 WIIPLSLAWGIAYPLTKVVTFSVSPILVSVARVIVGTLFFYFLGRGFSIGI---------KQFVNALFNVIILLALVNVGI 92 
                                   7788899*********************************99887777777.........459999999999999999999 PP

                          EamA  87 kktsas.naslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                     +++   ++ +++++P+f+l++  +l g k++l+ + g+v+++lGvl+ 
  gi|70606869|ref|YP_255739.1|  93 YLSPSPgLVATMIYTQPIFVLVIELIL-GSKISLRGMSGVVIGVLGVLIS 141
                                   99976449**************98766.*******************986 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 3.1e-22
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                   +g+l+ + ++l+wai++v+  + l+k + + l+++++li+  +l+ +++l    +  ++++++ ll++l+l++ v++f+++
  gi|70606869|ref|YP_255739.1| 148 IGLLFGIMGSLSWAIGTVYYYRNLSKDNVIKLNAFMSLISIPFLSSLTPLDYYFD--FNVTSVVLLIILALIAQVAGFYFW 226
                                   799***********************************************99999..************************ PP

                          EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   f a++++++  as  ++l+Pv++ + s+l+l+  +++ +++g++lil+Gv+l l
  gi|70606869|ref|YP_255739.1| 227 FNAVRDLGSVSASTGSLLVPVIAYLTSILILKVVPNVPEIIGLILILVGVYLSL 280
                                   ***************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1878.97
//
Query:       gi|70606870|ref|YP_255740.1|  [L=80]
Description: hypothetical protein Saci_1093 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 529.47
//
Query:       gi|70606871|ref|YP_255741.1|  [L=274]
Description: hypothetical protein Saci_1094 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.1   0.1    1.1e-07   31.7   0.1    2.8  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   6.4e-12   1.1e-07       6     128 ..      23     136 ..      20     138 .. 0.91
   2 !   16.0   0.0   4.7e-07    0.0084       9      77 ..     157     225 ..     153     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.4e-12
                                   SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEE CS
                           SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaI 86 
                                   +r yv+GaG sya+a+ +  k   ++g+  ++++ ++l ++     + + +++++s sg  k+ +++ae+ k +  ki ++
  gi|70606871|ref|YP_255741.1|  23 DRAYVTGAGDSYAVALTVEGK---TNGRFRAIDPYEALAYN-----RLEYPLVIVSVSGKPKSNIRLAEKFKGK-TKIYVV 94 
                                   699***********9988865...69999999999995555.....9999*********************985.79**** PP

                                   ESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                           SIS  87 Tdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                   T +++s+la+  d++++i++  +  v+ t s++ +l+a++ l
  gi|70606871|ref|YP_255741.1|  95 TANEESILAKLGDYVITIPYRSKQVVPGTLSFLMSLSAVYSL 136
                                   ************************************999877 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 4.7e-07
                                   EEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHH CS
                           SIS   9 yvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelak 77 
                                   +++G + +y ia +++lk+ ei g+ + +e  +++ h+++   + + +v+l s   ++  lv+++++ k
  gi|70606871|ref|YP_255741.1| 157 FFVGYRENYGIAYYGMLKFSEIFGYSANAERLEQFLHSPIFSTKGREIVLLSSGDSREDILVNLVNYTK 225
                                   89************************************8877776666666665555555555555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1963.79
//
Query:       gi|70606872|ref|YP_255742.1|  [L=81]
Description: hypothetical protein Saci_1095 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.4   0.2      0.058   13.3   0.2    1.1  1  DUF5412   Family of unknown function (DUF5412)


Domain annotation for each model (and alignments):
>> DUF5412  Family of unknown function (DUF5412)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.2e-06     0.058      51     113 ..      11      76 ..       1      78 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-06
                       DUF5412  51 naYlvnggattdyavrgelvnkktkkkkniYwnyreedakieWld...ektvvIngkkLnvkkdty 113
                                   +  ++++g+t    +r  l+   +k+ k i w+ r+e    +W++   +k v I +kk+n +k ty
  gi|70606872|ref|YP_255742.1|  11 EKGTCESGSTYMSLLRFWLEVGGNKEVKVIAWKGRQEGQVDNWVSqmaDKGVKIVDKKINSEKVTY 76 
                                   55578999*******************************99**87222578********9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 607.95
//
Query:       gi|70606873|ref|YP_255743.1|  [L=289]
Description: putative UV damage endonuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-63  213.2   0.2    4.7e-63  213.0   0.2    1.1  1  UvdE      UV-endonuclease UvdE


Domain annotation for each model (and alignments):
>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   0.2   2.6e-67   4.7e-63      31     273 ..      26     256 ..       3     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 2.6e-67
                          UvdE  31 erkeklkelakaNlkdllkllkynaaygirllRlSSslvPlashpevgykletalaeeleevGelakelglRltfHPeqft 111
                                     +e ++++ ++Nl  l ++l++n +++i ++R+SS+ +Plashp+   +    l++ l ++G ++ke  +R+++HP+q++
  gi|70606873|ref|YP_255743.1|  26 S-EERVLKVSSSNLLCLKNILEWNLKHEILFFRISSNTIPLASHPKFHVNWKDKLSHILGDIGDFIKENSIRISMHPGQYV 105
                                   2.6899*************************************************************************** PP

                          UvdE 112 llnSdrkevtesairdlayHdklldalklaeqqdavliiHvGGkfgdkeaalerfkenikrlpdsvkerlvLENDdksytv 192
                                   +lnS r+ev++s+i +l+yH+ lld ++++ +    + iHvG  +++ke++l+rf en+++lp ++ +rlv+ENDdk ++v
  gi|70606873|ref|YP_255743.1| 106 VLNSVREEVVRSSIMELKYHADLLDSMGIEGK----IQIHVGSSMNGKEESLNRFIENFRKLPSNISKRLVIENDDKVFSV 182
                                   ******************************99....********************************************* PP

                          UvdE 193 adlLpvceelniPlVlDyHHhnvldlreesldeslplveriveTWerkgikqkvHlSepldgkavrahkdrkhadrvldll 273
                                   +d L + e+++iP+++D  Hh +l ++ esl+ +l     ++ TW+++   + + +Se   g++   h+  ++++ +  + 
  gi|70606873|ref|YP_255743.1| 183 KDCLWISERTGIPVIFDNLHHSIL-NNGESLNDALS---LVRRTWKDR---PMIDYSEQEPGEKPGVHATTINEENFRRFV 256
                                   ************************.78888888887...7999****9...789999999998888888888888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1996.61
//
Query:       gi|70606874|ref|YP_255744.1|  [L=493]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.3e-154  512.7   0.0   8.5e-154  512.5   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.043   13.3   0.0      0.099   12.1   0.0    1.5  1  DUF1487   Protein of unknown function (DUF1487)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.5   0.0  9.5e-158  8.5e-154       9     461 ..      19     475 ..      11     476 .. 0.96

  Alignments for each domain:
  == domain 1  score: 512.5 bits;  conditional E-value: 9.5e-158
                                   EEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHH....HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                        Aldedh   9 ievinPa.tgeviakvpaataedvdaavaaAkeafk....awaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                   i   +P+  ++ ++k++ a+++dv++a++ A+e f+    +w + + + R ++L ++a+ ++ + + l++l++ e+G p++
  gi|70606874|ref|YP_255744.1|  19 IYRECPYnIDTSVTKINVAKESDVEEAIDVAREFFDkdknGWVS-NYKARDKVLFRIAEKIRGEIQTLSRLLVEEIGMPIR 98 
                                   66677886678899*******************99965544654.8999******************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTS CS
                        Aldedh  85 earaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeet 165
                                   +ar +v+ a+dv++yya+  +k+++++    ++ +  + +eP+Gvvg+ItPWNfPl  +a+klapa+ +G+t+v+KPa+ +
  gi|70606874|ref|YP_255744.1|  99 QARVQVNAAADVFEYYAGFGSKIYDTSKFLPSKDMVQIIKEPVGVVGLITPWNFPLTQSARKLAPAITVGCTIVWKPATYA 179
                                   **********************9986655555789999******************************************* PP

                                   HHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-T CS
                        Aldedh 166 plsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivle 246
                                   + +++ la+++   g+Pkg+lnv+  +g++vg+++v+++++dk+sftG+t++g+ i+++a+k+lkrv+lElGGk+p+i ++
  gi|70606874|ref|YP_255744.1| 180 AGISYQLAKIILSSGVPKGALNVIFDPGEKVGAQIVKSKKIDKISFTGETNTGKWIMSEASKDLKRVSLELGGKDPIILFS 260
                                   ********************************************************************************* PP

                                   TSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHH CS
                        Aldedh 247 daDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveea 327
                                   d Dl++a++++++ga++naGQ C a+srllv+esi++++  ++ +++kklk+g+pl+edtd+GP++s+ q +kv +y+e++
  gi|70606874|ref|YP_255744.1| 261 DSDLKNAIKGAIFGALRNAGQACGATSRLLVEESIAEKVEMAVSNEIKKLKLGNPLQEDTDIGPVVSKPQEDKVIDYIETG 341
                                   ********************************************************************************* PP

                                   HHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHH CS
                        Aldedh 328 keegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdle 407
                                   ++eg+kll+Gg+  ++ + ++gyf+ePtv+++v+++++iaqeEiFGPVl++i fkdeeeai++aNd  yGL+a+v+t+d +
  gi|70606874|ref|YP_255744.1| 342 IKEGYKLLVGGRkVTDGEFQRGYFIEPTVFSDVDNKSKIAQEEIFGPVLVIIYFKDEEEAISLANDVIYGLTASVWTNDYK 422
                                   ************98899**************************************************************** PP

                                   HHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEE CS
                        Aldedh 408 raervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevkt 461
                                   +a rv+++l++G+v+iNd  t+  e   +gG+kqSg+Gre g +g+e+++e+k 
  gi|70606874|ref|YP_255744.1| 423 KAIRVSRELRVGTVWINDVYTQPSEG-LWGGYKQSGIGRELGIQGIEDFLETKM 475
                                   *******************9999999.*************************96 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05     0.099       8      61 ..     256     311 ..     253     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                       DUF1487   8 mvifedgDlnsale.alveslkeP.faegavatvlveesirdefvervrsklkpls 61 
                                   +++f d+Dl++a++ a+  +l++   a+ga   +lveesi++++   v +++k+l+
  gi|70606874|ref|YP_255744.1| 256 IILFSDSDLKNAIKgAIFGALRNAgQACGATSRLLVEESIAEKVEMAVSNEIKKLK 311
                                   699********99857889999863789*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3316.36
//
Query:       gi|70606875|ref|YP_255745.1|  [L=604]
Description: phosphoenolpyruvate carboxykinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   7.2e-107  357.3   0.0   8.8e-107  357.0   0.0    1.1  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
    6.6e-59  199.1   0.0    9.1e-59  198.7   0.0    1.2  1  PEPCK_N    Phosphoenolpyruvate carboxykinase N-terminal domai


Domain annotation for each model (and alignments):
>> PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.0   0.0  9.8e-111  8.8e-107       1     358 []     233     585 ..     233     585 .. 0.96

  Alignments for each domain:
  == domain 1  score: 357.0 bits;  conditional E-value: 9.8e-111
                                   -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---SSTT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE-TT-S CS
                     PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamleptlegwkvetvgdDiawlkfgedgrlraiNpeaGfFgvapgtn 81 
                                   wL+Ehm i+g + ++g ++y++a+fps++GKt+++ml +        +++dD+a++k   dg +ra+Npe G+Fg+++g+n
  gi|70606875|ref|YP_255745.1| 233 WLSEHMAIVGFEGNRG-THYFTASFPSGSGKTSTSMLGS--------LISDDLAFIKEI-DGVCRAVNPEIGIFGIIQGIN 303
                                   9*************99.789******************6........8*********99.********************* PP

                                   TTT-HHHHHHTTBS..-EEES-EEETTS-EE-TT--------EE-TTSSEE-T..T-SSS-TT-EEEEEGGGSTTB-TTTT CS
                     PEPCK_GTP  82 ektnpnalktlkkn..tiftNvaltedgdvwWegleeeapaelidwkgkkwtke.kekaahpnsrftvpakqlpiiapewe 159
                                   e+++p ++++l+k   +if+Nv++t+dg v+Weg e e+p+++++++g  wtke +++a+hpn+rft p++++++++++++
  gi|70606875|ref|YP_255745.1| 304 ERDDPVIWDVLHKPgeVIFSNVLMTDDGGVYWEGSEVEKPEKGYNYEG-AWTKEsGKPASHPNARFTSPLTSFSNLDKDYD 383
                                   ***********55447********************************.999987899*********************** PP

                                   -TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHH.HHT-EEE--TTSSS-TT-EEE-GGG-GGG-SS-HHHHHHHHHHHT CS
                     PEPCK_GTP 160 dpeGvpisaiifggrrsetvplvleafdwehGvfl.gatlesetTaaaegkvgvvrrdPfamlpFlgynlgdYlehwlelg 239
                                   +p+Gv i+ iifg r+ +t+++v+eaf+wehGv++ ga++es +T+a+ gk++v++ +P+a+l+F++ +lg+Yl+++l++g
  gi|70606875|ref|YP_255745.1| 384 NPQGVVIDGIIFGVRDYSTLVPVTEAFSWEHGVITiGASMESSRTSAVIGKADVLEFNPMAILDFMPLSLGKYLNNYLTFG 464
                                   *********************************988********************************************* PP

                                   TSTT-B--EEEEEES--B-TTSSBSS--GGGHHHH.HHHHHHHHTT..S-EEETTEEEE-BTTC--TT-.........TT- CS
                     PEPCK_GTP 240 kklekklPkifsvNwfrkdeegkflWPGfgenlrv.lkWilkrvegeakavetpiGlvPkkedldlkgl.......dlske 312
                                   ++  k +Pkifs N+f+kde++kfl     e+ rv +kW++krve e++a+ tp+G++P++edl  ++l       +++ke
  gi|70606875|ref|YP_255745.1| 465 RN-LKYVPKIFSFNYFLKDENNKFLN--SKEDKRVwVKWAVKRVESETDAIYTPVGFIPYYEDL--SKLfnstlgkQYTKE 540
                                   99.9*********************8..788888879**************************5..5555667899***** PP

                                   -HHHHS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                     PEPCK_GTP 313 dleellsvdkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                   ++e +++++ ++++e++e+i+++++++ +++P e+++el+++++rl
  gi|70606875|ref|YP_255745.1| 541 AYELQFTLKLSKYLEKTERIMKIYSEI-ADTPIEVINELKAQKDRL 585
                                   **************************6.599***********9997 PP

>> PEPCK_N  Phosphoenolpyruvate carboxykinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.7   0.0     1e-62   9.1e-59       2     217 ..      31     228 ..      30     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 1e-62
                                   HHHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS--EE- CS
                       PEPCK_N   2 fveevaelcqPdkvvvcdgseeeneellkelvekgeliklekypnsylarsdpkDvARvesrTfictekeedagplnnwmd 82 
                                   f+++++el++Pd+v+v  g+e+++e+++k+++e++e+ikl k++++++++++p D+AR++++Tfi+t++  ++ p+ n++ 
  gi|70606875|ref|YP_255745.1|  31 FLSKTIELTTPDRVYVSFGEEKDREYVKKRALETKEEIKL-KMEGHTIHFDHPLDQARAREDTFILTDE--KI-PFVNTKP 107
                                   8999************************************.**************************54..44.99***** PP

                                   HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TSEEEEEE-S- CS
                       PEPCK_N  83 peemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeefvkclHsvga 163
                                   ++e  +e+ +l+kg+mkGr+myV ++s+Gp +s++s ++v+iTds+YV++s++i++r++ + +   +    f+k++Hs+g+
  gi|70606875|ref|YP_255745.1| 108 RDEGLREMLSLLKGSMKGREMYVGFYSLGPRNSKFSILAVQITDSPYVIHSENILYRNAFEDFYGDK---PFLKFIHSKGQ 185
                                   **********************************************************999998766...9*********7 PP

                                   -SS-SS-BTB---GG-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHH CS
                       PEPCK_N 164 plegqkdvkWpcnekkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasvia 217
                                    l    d      +k++i+++ +e++++sv+++Y+GN++++Kk +alR+++++a
  gi|70606875|ref|YP_255745.1| 186 -L----DI-----KKRRIMIDVKENTVYSVNTTYAGNSVGLKK-LALRLTVTKA 228
                                   .3....32.....489***************************.******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4416.22
//
Query:       gi|70606876|ref|YP_255746.1|  [L=298]
Description: bifunctional folate synthesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-30  104.5   1.0    5.9e-30  104.1   0.3    1.6  2  FolB       Dihydroneopterin aldolase
    1.7e-28   99.4   0.0    2.6e-28   98.8   0.0    1.3  1  HPPK       7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinas
  ------ inclusion threshold ------
      0.042   13.7   0.1       0.24   11.3   0.0    2.1  2  Prefoldin  Prefoldin subunit
        1.5    9.1   9.2       0.23   11.7   5.0    1.8  2  IF2_assoc  Bacterial translation initiation factor IF-2 assoc


Domain annotation for each model (and alignments):
>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.3   1.3e-33   5.9e-30       1     111 []       5     114 ..       5     114 .. 0.96
   2 ?   -3.1   0.0       2.5   1.1e+04      84      98 ..     149     164 ..     136     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 1.3e-33
                                   EEEEEEEEEEEESSSHHHHHC-EEEEEEEEEEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHH CS
                          FolB   1 ieikglrvpaiiGvnpeErelkQrvvvdleleldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaeall 81 
                                   ++i++lr+++iiGvnp+E+e++Q+v +d+  ++dl+k a+sd+l +tvdY+ l k++  +ve+ssf+llE+la r+++ +l
  gi|70606876|ref|YP_255746.1|   5 VSIEDLRLYTIIGVNPQEKETRQEVSIDVYYWADLRKGAKSDQLPETVDYKVLKKEIISYVENSSFNLLESLAYRLSKVVL 85 
                                   579***********************************************************99***************** PP

                                   CHSTESEEEEEEEETTSSSTCESEEEEEEE CS
                          FolB  82 eefpvekvevrveKpnapigaadavgveit 111
                                   ++ +++kv ++v Kp a+   a++v+ve++
  gi|70606876|ref|YP_255746.1|  86 QDNRIKKVVIKVGKPGAL-SRAKNVSVEVR 114
                                   *988*************6.449******85 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                   STESEE.EEEEEETTS CS
                          FolB  84 fpvekv.evrveKpna 98 
                                   ++++k+ +v ++Kp +
  gi|70606876|ref|YP_255746.1| 149 IKIKKIsTVYLTKPIP 164
                                   2366664577777766 PP

>> HPPK  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.0   5.9e-32   2.6e-28       1     111 [.     125     250 ..     125     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 5.9e-32
                                   EEEEEE-SSSHHHHHHHHHHHHHH..EEEEE---EEE--S..SS-GEEEEEEEEEESS-HHHHH.HHHHHHHHHTT--C.. CS
                          HPPK   1 ylalGsNlgdreanleealealee..kvvkvSslyetepv..dqpdFlNavvevetelspeell.ealkeiEkelgrer.. 74 
                                   y+++GsN+ ++e+n+++a+e l++  k+ k+S++y t+p+  dqpd++N+vve + ++sp++l  + l++iE+elgrer  
  gi|70606876|ref|YP_255746.1| 125 YISIGSNI-NPEDNVRRAIELLDKmiKIKKISTVYLTKPIppDQPDYFNCVVESRINISPKDLKyNILRRIESELGRERtk 204
                                   89******.899**********8877778***********999********************648899********9754 PP

                                   .STS-BS-EEEEEEET........EEES-TTGGG-HHHHHHHHHHC CS
                          HPPK  75 .rwgpRtlDlDillyg........ltlPhprlaeraFvlvplaela 111
                                    ++ pRt+DlD++lyg        +t+P p++++r+F   pl+el+
  gi|70606876|ref|YP_255746.1| 205 nKFLPRTIDLDLVLYGnqvineegVTVPDPEIEKREFLAIPLMELN 250
                                   4588***************************************996 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.38   1.7e+03      34      57 ..      15      41 ..       2      44 .. 0.75
   2 ?   11.3   0.0   5.4e-05      0.24      56      87 ..     119     150 ..     100     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.38
                                  T....-TT-EEEEEEETTEEEEEE--S CS
                     Prefoldin 34 k...edegkevlvplgaglyvkaevkd 57
                                      ++++ke+  +++ ++y +a++++
  gi|70606876|ref|YP_255746.1| 15 IigvNPQEKETRQEVSIDVYYWADLRK 41
                                  24477999999999999***9999865 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.4e-05
                                   -STTEEEEEEETTEEEEEEHHHHHHHHHHHHH CS
                     Prefoldin  56 kdtdkvlvdlGagyyveksleeAiellkkkle 87 
                                   ++  kv++++G+++  e ++  Aiell+k ++
  gi|70606876|ref|YP_255746.1| 119 DNLAKVYISIGSNINPEDNVRRAIELLDKMIK 150
                                   45568***********************9876 PP

>> IF2_assoc  Bacterial translation initiation factor IF-2 associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.0   5.2e-05      0.23       8      34 ..      91     117 ..      81     118 .. 0.76
   2 ?   -3.3   0.1       2.7   1.2e+04      11      24 ..     281     294 ..     281     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.2e-05
                     IF2_assoc   8 RksvselrqsfshGrsKtVsVEVRKKR 34 
                                   +k v  +  +++  r+K VsVEVR KR
  gi|70606876|ref|YP_255746.1|  91 KKVVIKVGKPGALSRAKNVSVEVRAKR 117
                                   55666677789999**********999 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.7
                     IF2_assoc  11 vselrqsfshGrsK 24 
                                   +selr   s+ r+K
  gi|70606876|ref|YP_255746.1| 281 TSELRSLISGSRKK 294
                                   68898777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2291.63
//
Query:       gi|70606877|ref|YP_255747.1|  [L=241]
Description: dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-27   96.6   0.0    1.8e-27   96.4   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.4e-21   75.6   0.0    4.5e-21   75.2   0.0    1.1  1  adh_short     short chain dehydrogenase
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.14   12.0   0.0    1.3  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0     3e-31   1.8e-27       1     233 [.      12     233 ..      12     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 3e-31
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHH.SSEEEEEE---- CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekf.gklDilvnnagi 79 
                                   G a+ IGr+iA  la+eG ++vl++   e+ + r+++  ee+g +   +  +  ++ +++ +++ + + g+lD+l+nna i
  gi|70606877|ref|YP_255747.1|  12 GSAKRIGRGIALGLAKEGVNIVLHYNTSEEsALRLKDEIEEIGVKCWLVKGELSKDYAKILDNAFKLTeGNLDFLINNASI 92 
                                   66788***********************9999999********99755555555678889998888888************ PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEE.EEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnl.ssvgaervvpnynaygaaKaalealtrylAvel 159
                                    p+      +++ e+++ ++ vn    +ll+  + + + + g+ivn+  s+ +   ++ y  y  +K  le +t +lA +l
  gi|70606877|ref|YP_255747.1|  93 FPA-----SKVTMENLNSIVTVNSWVPLLLSLDFSRKLSK-GKIVNIlDSIISGYNFERY-PYFLSKKLLEIITVSLALKL 166
                                   **9.....789***********************998876.6677764777665555554.899***************** PP

                                   GGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                  adh_short_C2 160 gpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                    p   +vN v+pg+i  +  ++     + le+l++  p++r g++eev +a++fL+   + +itGq+++vDgG 
  gi|70606877|ref|YP_255747.1| 167 SP-SFQVNGVAPGLILPPEGKDN----SYLENLKSFVPMKRYGNVEEVVNAVIFLLK--SDFITGQIIYVDGGE 233
                                   **.9************8887655....599999***********************8..56************6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   7.5e-25   4.5e-21       2     183 ..       7     181 ..       6     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 7.5e-25
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHH.SSESE CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkkl.gkldv 80 
                                   ++l+tG ++ IGr ia  lakeG+++v+ ++ see + ++++e++e g k + +++ ++  ++  +++++a k + g+ld 
  gi|70606877|ref|YP_255747.1|   7 TALITGSAKRIGRGIALGLAKEGVNIVLhYNTSEESALRLKDEIEEIGVKCWLVKGELS--KDYAKILDNAFKLTeGNLDF 85 
                                   89*******************************************************99..677889999999999***** PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                   L+nNA+i    p+s+++ e+ ++++ vN   ++ll+  + +++    +G+Ivn+   +    +++  +Y  sK  ++ +t 
  gi|70606877|ref|YP_255747.1|  86 LINNASI---FPASKVTMENLNSIVTVNSWVPLLLSLDFSRKLS---KGKIVNILDSIISGYNFERYPYFLSKKLLEIITV 160
                                   *******...8*******************************65...9******75555566677778************* PP

                                   HHHHHHGGGTEEEEEEEESSBS CS
                     adh_short 162 slakelaptgirvnavaPGlvd 183
                                   sla  l+p+  +vn+vaPGl+ 
  gi|70606877|ref|YP_255747.1| 161 SLALKLSPS-FQVNGVAPGLIL 181
                                   ********8.*********986 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.14       2      65 ..       7      67 ..       6     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                  EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-H CS
                            KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdk 65
                                  t litG +  +G+ +a  la++g + ++    s   +e++ +l +e+e+ g+++ +v+ ++s+ 
  gi|70606877|ref|YP_255747.1|  7 TALITGSAKRIGRGIALGLAKEGVNIVLHYNTS---EESALRLKDEIEEIGVKCWLVKGELSKD 67
                                  579********************8766665555...567777999*********9999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1632.58
//
Query:       gi|70606878|ref|YP_255748.1|  [L=463]
Description: hydroxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-84  281.9   0.4    8.3e-84  281.5   0.4    1.2  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
    1.7e-51  174.2   0.0    2.3e-51  173.8   0.0    1.2  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina
     0.0005   20.2   0.0     0.0012   19.0   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.5   0.4   1.4e-87   8.3e-84       1     272 []       3     261 ..       3     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 281.5 bits;  conditional E-value: 1.4e-87
                                   -HHHHHHHHHHS---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHHHH CS
                        HpaB_N   1 TgeeYlesLrdkgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDllk 81 
                                   T+ ++l+sLrd gr+v+++G+ Ved+t hp++  a+ ++++l++++ +        +++p+  +kv++ff+ p+s++Dll+
  gi|70606878|ref|YP_255748.1|   3 TKGDFLKSLRD-GRKVFYRGKPVEDITAHPILSIAAIHASKLFEYSDR-M------YEDPSL-GKVSKFFKKPTSTQDLLE 74 
                                   7789*******.********************************9555.4......456766.79**************** PP

                                   HHHHHHHHHHHTTT--S..--THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS-TTS-G CS
                        HpaB_N  82 krkairelarktggclg..Rcpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkgdRskrp 159
                                   ++k+i +++++++g+++  +++++da++al+++a++ d  +k+gt+ y+++++ky+eyv++ndl++++a+td+kgdRskrp
  gi|70606878|ref|YP_255748.1|  75 RHKLIYDTTMYCNGIFNisQAIGSDAIFALTITARQlD--RKYGTD-YTKRIQKYHEYVTKNDLTIATAQTDVKGDRSKRP 152
                                   ****************999*****************99..889999.********************************** PP

                                   GGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE-------S.. CS
                        HpaB_N 160 seqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfedklee 240
                                   seq+dpd+yvr+v+ ++dGivVrGak+++T++a++dei+v+ptram k++dkdyavafavp++apGlkl++r+  e   e 
  gi|70606878|ref|YP_255748.1| 153 SEQADPDMYVRIVDVKSDGIVVRGAKAHTTQSAVSDEIIVIPTRAM-KDSDKDYAVAFAVPANAPGLKLYVRPIDEI--E- 229
                                   **********************************************.**************************9776..3. PP

                                   -TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
                        HpaB_N 241 sefdyplssrfdendalvvfDdVfVPwerVfl 272
                                    ++ + ls++  e ++++vfD+VfVPw+rVfl
  gi|70606878|ref|YP_255748.1| 230 GNTSAVLSKKDYELETITVFDNVFVPWDRVFL 261
                                   5667888877779******************6 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.8   0.0   3.8e-55   2.3e-51       1     202 []     268     463 .]     268     463 .] 0.98

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 3.8e-55
                                   HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-E CS
                          HpaB   1 agklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdpsGvy 81 
                                   ag++++ fa++hr+++ +  ++ + +++++G a  +a+anGie+ +hv++++++li ++e+l++ +i+++ ++ +  +Gv 
  gi|70606878|ref|YP_255748.1| 268 AGNIAMLFATYHRFTALS--YRSALINLFLGSARVMAKANGIENEKHVRDDVVDLILYKEILRSTAITSAISPVML-EGVA 345
                                   578899************..********************************************************.**** PP

                                   E--HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHHHHHHTSHH CS
                          HpaB  82 lPdlllanaarvlvtrlypriveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllklawdltgsef 162
                                   +P++l+ n+++++ +++++++++ l d+aGG+++tlPs++df+++  g+ + kylrg+  v+ eeRvk+lkl+++l++s  
  gi|70606878|ref|YP_255748.1| 346 VPNPLYVNVGKLYSNMHFHDVIKDLVDVAGGIIATLPSQEDFDSE-EGKTIIKYLRGA--VDGEERVKILKLVKELAASPV 423
                                   ********************************************8.999999*****9..7******************** PP

                                   HHHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHHHHCH CS
                          HpaB 163 ggrhelyerhgaGspeaqriaiyrqydleekkelvkkllg 202
                                   +g+ ++ ++h++Gs ea +i+++r+yd++e++ l+kk++g
  gi|70606878|ref|YP_255748.1| 424 AGYLLTAMVHAEGSIEASKIELFRSYDYREAESLIKKIIG 463
                                   *************************************975 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.9e-07    0.0012      19      80 ..     163     227 ..     154     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-07
                                   EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE..----- CS
                 Acyl-CoA_dh_M  19 taaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsv..rriee 80 
                                   + ++ + +++v++G+K   t++a ++ ++v+   +++d  ++    f+vp++apg+++  r+i+e
  gi|70606878|ref|YP_255748.1| 163 RIVDVKSDGIVVRGAKAHTTQSAVSDEIIVIPTRAMKDsDKDYAVAFAVPANAPGLKLyvRPIDE 227
                                   557888899***************99998887734555445555599*******99875466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2989.62
//
Query:       gi|70606879|ref|YP_255749.1|  [L=252]
Description: 3-ketoacyl-ACP reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-52  176.3   0.9    8.8e-52  176.0   0.9    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.1e-50  171.8   2.1    1.5e-50  171.4   2.1    1.1  1  adh_short      short chain dehydrogenase
    4.8e-09   36.4   0.5    6.4e-09   36.0   0.5    1.1  1  KR             KR domain
  ------ inclusion threshold ------
      0.026   14.4   0.2      0.054   13.4   0.2    1.5  1  YjeF_N         YjeF-related protein N-terminus
      0.051   12.9   0.2      0.083   12.3   0.2    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.094   12.4   0.2       0.31   10.7   0.1    1.8  2  Wax2_C         WAX2 C-terminal domain
       0.16   11.4   0.6       0.28   10.6   0.6    1.6  1  Epimerase      NAD dependent epimerase/dehydratase family
       0.33   11.4   2.1       0.44   11.0   1.5    1.7  2  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   0.9   3.9e-55   8.8e-52       3     232 ..      15     244 ..      12     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 3.9e-55
                                   TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                  adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    +gIGraiA +la+eG ++v+   ++++  +++ e+++++g + v + +DV  +e +e+l + + +kfg +Dilvnnag  
  gi|70606879|ref|YP_255749.1|  15 GRGIGRAIALRLAQEGSKIVVNAKKRAEeVNETVEMVKKIGGDaVgVLADVGTKEGCETLLKSTLDKFGVVDILVNNAGLG 95 
                                   59********************999999866677777777766479*********************************** PP

                                   EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGG CS
                  adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvelgp 161
                                       + f++++++ +++ ++v+++s++++++a+++ m+egg ivn++s+++     + ++yga K+a+++lt+y+A el+p
  gi|70606879|ref|YP_255749.1|  96 LF--SLFMNADDKLIEKHISVDFKSVVYCSQAFAREMREGGEIVNIASIAGVLPAYGLSMYGAMKGAVISLTKYMALELAP 174
                                   *9..*********************************************9977777777********************** PP

                                   GTEEEEEEEE--BHCTGGGGSTT..HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTT CS
                  adh_short_C2 162 kgiRvNavspgpikTlaasgikg..fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgG 232
                                    +iRvNa++pg++kT++ +++ +  + + +e +e+ + +g++ +pe++ae +  ++  e  + tGq++vvD+G
  gi|70606879|ref|YP_255749.1| 175 -KIRVNAIAPGWVKTKLGESMYKllNMSEKEFVEKTTLMGKMLEPEDIAEFVTAILKIE--GLTGQVFVVDAG 244
                                   .9***************999998554555677899999******************855..***********9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   2.1   6.6e-54   1.5e-50       1     189 [.       7     193 ..       7     197 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 6.6e-54
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldv 80 
                                   kvv+vtG ++GIGraia +la+eG k+vv +++++e+++e+++ +k+ g +a+ + +Dv ++e +e+l++   +k+g +d+
  gi|70606879|ref|YP_255749.1|   7 KVVVVTGSGRGIGRAIALRLAQEGSKIVVnAKKRAEEVNETVEMVKKIGGDAVGVLADVGTKEGCETLLKSTLDKFGVVDI 87 
                                   89***************************9999************************************************ PP

                                   EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                     adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                   LvnNAG+  ++ f + +++ +e+ i+v +++v+ +++a++++m   ++G+Ivn++S+ag  p  g+++Y+A K+av++lt+
  gi|70606879|ref|YP_255749.1|  88 LVNNAGLGLFSLFMNADDKLIEKHISVDFKSVVYCSQAFAREMR--EGGEIVNIASIAGVLPAYGLSMYGAMKGAVISLTK 166
                                   ******************************************87..9********************************** PP

                                   HHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                     adh_short 162 slakelaptgirvnavaPGlvdTdmake 189
                                    +a elap+ irvna+aPG v+T++ ++
  gi|70606879|ref|YP_255749.1| 167 YMALELAPK-IRVNAIAPGWVKTKLGES 193
                                   ********8.*************99766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.5   2.9e-12   6.4e-09       3     163 ..       9     168 ..       7     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.9e-12
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                   +++tG   g+G+++a  la++g + +v   ++    e+ +++++ +++ g +   v aDv  k+  e+ll++  ++++ + 
  gi|70606879|ref|YP_255749.1|   9 VVVTGSGRGIGRAIALRLAQEGSKIVVNAKKR---AEEVNETVEMVKKIGGDAVGVLADVGTKEGCETLLKSTLDKFGVVD 86 
                                   79********************8766555555...56777799999999999999999*********************** PP

                                   EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHH CS
                            KR  84 GvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSiagllgsagqanYaaaNaflDalaey 162
                                     ++ Ag+   +l+++ +++ +e+ ++  +k +    +++++  ++   +v ++Siag+l + g + Y a    + +l +y
  gi|70606879|ref|YP_255749.1|  87 ILVNNAGLGLFSLFMNADDKLIEKHISVDFKSVVYCSQAFARemREGGEIVNIASIAGVLPAYGLSMYGAMKGAVISLTKY 167
                                   ****************************************997788889*******************9977766666666 PP

                                   H CS
                            KR 163 r 163
                                    
  gi|70606879|ref|YP_255749.1| 168 M 168
                                   5 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.4e-05     0.054      26      86 ..       5      59 ..       1      75 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                        YjeF_N 26 ekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvv 86
                                  + kv+v++Gsg+  g+++  A  Laqeg k+ v    + +k+ e++++ +e++kk+gg+ v
  gi|70606879|ref|YP_255749.1|  5 KDKVVVVTGSGRGIGRAI--ALRLAQEGSKIVV----NAKKRAEEVNETVEMVKKIGGDAV 59
                                  679*********777665..669********99....667999**************9876 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   3.7e-05     0.083      33      77 ..       3      48 ..       1      91 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                  -GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                  2-Hacid_dh_C 33 elsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeee 77
                                  +l++k v + G Gr IG+a+a rl++ g k+++  +++ +e +e  
  gi|70606879|ref|YP_255749.1|  3 SLKDKVVVVTGSGRgIGRAIALRLAQEGSKIVVNAKKRAEEVNETV 48
                                  7999*********88*****************99999776553333 PP

>> Wax2_C  WAX2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00014      0.31       1      41 [.       9      49 ..       9      55 .. 0.90
   2 ?   -1.4   0.0      0.77   1.7e+03      36      69 ..     186     220 ..     175     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                        Wax2_C  1 vlltgklskvaraialaLcergvkvlvlskeeyeklkkelp 41
                                  v++tg+   ++raial L+++g k++v+ k++ e+++++++
  gi|70606879|ref|YP_255749.1|  9 VVVTGSGRGIGRAIALRLAQEGSKIVVNAKKRAEEVNETVE 49
                                  78999999************************999998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.77
                        Wax2_C  36 lkkelpeelqknlvlskka.sskvWlvgdglteke 69 
                                   +k++l e++ k l +s+k+  +k+ l+g+ l+ ++
  gi|70606879|ref|YP_255749.1| 186 VKTKLGESMYKLLNMSEKEfVEKTTLMGKMLEPED 220
                                   56677778888888888866889999999988876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00013      0.28       1      44 [.       9      67 ..       9     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                  EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC..............E CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl..............e 44
                                  ++VtG    iG+a++ +l+++g + v++ +++ ++ n+  +  +              +
  gi|70606879|ref|YP_255749.1|  9 VVVTGSGRGIGRAIALRLAQEGSKiVVNAKKRAEEVNETVEMVKkiggdavgvladvgT 67
                                  68********************9978888888776666554444666666444444433 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5   0.00019      0.44       4      53 ..       3      53 ..       1     141 [. 0.74
   2 ?   -3.0   0.0       4.6     1e+04      46      55 ..     196     205 ..     168     232 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                 NAD_binding_7  4 dlkgkkvlvvGgGe.vAarkvrklleagakvtvvapevkeeleelvklaee 53
                                   lk+k v+v G G+ ++   + +l+++g k++v a++ +ee++e+v++ ++
  gi|70606879|ref|YP_255749.1|  3 SLKDKVVVVTGSGRgIGRAIALRLAQEGSKIVVNAKKRAEEVNETVEMVKK 53
                                  6899*********768999999***************98888888876554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                 NAD_binding_7  46 elvklaeeel 55 
                                   +l++++e+e+
  gi|70606879|ref|YP_255749.1| 196 KLLNMSEKEF 205
                                   4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1901.95
//
Query:       gi|70606880|ref|YP_255750.1|  [L=306]
Description: esterase/lipase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-62  210.3   0.0    3.5e-62  210.0   0.0    1.1  1  Abhydrolase_3  alpha/beta hydrolase fold
    2.3e-07   30.1   0.0      7e-07   28.5   0.0    1.7  1  COesterase     Carboxylesterase family
     0.0021   17.6   0.0     0.0036   16.8   0.0    1.5  1  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.0   5.8e-66   3.5e-62       1     210 [.      78     284 ..      78     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 5.8e-66
                                   EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                 Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                   +++fHGG+++lgs++t+da+ r l++ ++++v+svdYrlAPe++fP+av d+++a+ w++++a elg+d+++i+ +G SaG
  gi|70606880|ref|YP_255750.1|  78 VMHFHGGAWILGSIETEDAISRILSNSCECTVISVDYRLAPEYKFPTAVYDCFNAIVWARDNAGELGIDKDKIATFGISAG 158
                                   689***********************************************************99***************** PP

                                   HHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSC.HHHHHHHHHHHSS.GGGGGSTTTSGGGC CS
                 Abhydrolase_3  82 GnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgpllt.raaldlfwrlylp.eadrddplasplla 160
                                   Gnl+aa++l ard+ ++k+++qv + P + l +  s+s+   +++++g++l  +  +d+ +++y+  e+d+ +pl+spl a
  gi|70606880|ref|YP_255750.1| 159 GNLVAATSLLARDN-KLKLTAQVPVVPFVYL-DLASKSM---NRYRKGYFLDiNLPVDYGVKMYIRdEKDLYNPLFSPLIA 234
                                   *************8.89**********8878.8889999...89999***98355788999****66************** PP

                                   S-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                 Abhydrolase_3 161 edlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                   edls+lp+++vv+ae+Dplrd+geaya rl + gv++   +++g vH+f+
  gi|70606880|ref|YP_255750.1| 235 EDLSNLPQAIVVTAEYDPLRDQGEAYAYRLMESGVPTLSFRVNGNVHAFL 284
                                   ************************************************96 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.2e-10     7e-07      88     206 ..      62     169 ..      33     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-10
                                   -EEEEEEESSSSSTTSSEEEEEEE--STTTS-BGCG..S-THHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHH CS
                    COesterase  88 LyLnvytPkekkeakkklPVlVwihGggfqtgsase..ydgsaLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDq 166
                                   L + +y+P    +++++   ++ +hGg+   gs ++  +  + L ++ ++ v+++ YRl +         e +   +++D 
  gi|70606880|ref|YP_255750.1|  62 LPIRIYSPI---KRTNN-GLVMHFHGGAWILGSIETedAISRILSNSCECTVISVDYRLAP---------EYKFPTAVYDC 129
                                   667899995...33444.58999**********987668889999999***********97.........44445689*** PP

                                   HHHHHHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSG CS
                    COesterase 167 vlALrWVkenIasFGGdpervtlfGesAGaasvsllllsp 206
                                     A+ W ++n  + G d++++  fG sAG+ +v++ +l  
  gi|70606880|ref|YP_255750.1| 130 FNAIVWARDNAGELGIDKDKIATFGISAGGNLVAATSLLA 169
                                   *********************************9988764 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     6e-07    0.0036      49     110 ..     130     194 ..     124     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-07
                                   HHHHHHHHHTT...S--GGGEEEEEETHHHHHHHHHHH.H-GGG-SEEEEESE---CCCHHCSTTS CS
                  Peptidase_S9  49 iaaaealakeg...yvdserlaitGgSyGGyltgaaln.qrpdlFkaavaevpvvdvlrydsdtdl 110
                                   ++a+ ++ ++     +d++++a +G S+GG l++a+    r+++ k + a+vpvv  ++ d+ ++ 
  gi|70606880|ref|YP_255750.1| 130 FNAIVWARDNAgelGIDKDKIATFGISAGGNLVAATSLlARDNKLK-LTAQVPVVPFVYLDLASKS 194
                                   5544444333222389******************998844555444.6788888877777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2056.39
//
Query:       gi|70606881|ref|YP_255751.1|  [L=389]
Description: hypothetical protein Saci_1106 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-08   32.7   0.0    6.5e-08   32.1   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    1.2e-05   26.1   0.0    1.6e-05   25.7   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0031   17.2   0.0     0.0046   16.6   0.0    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.43   10.8   3.6        5.2    7.3   0.9    3.3  3  2C_adapt       2-cysteine adaptor domain


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.5e-11   6.5e-08      27     116 ..      84     181 ..      82     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.5e-11
                   Hydrolase_4  27 LaaqGfavyalDhrGhGrse.......gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdk 100
                                   +a++ ++vy +D+r h  s+       g  +++  ++++++D++++ve +ke ++ +++fl G+S GGl ++++++  p++
  gi|70606881|ref|YP_255751.1|  84 WANRCIDVYLMDYRTHFLSPekdpsefGFMVDW-GWEQWINDIKEVVEFIKEISSFKRVFLAGESFGGLATVNFATLFPED 163
                                   5667799************99999554444443.68********************************************* PP

                   Hydrolase_4 101 vaglils..aPalkikak 116
                                   ++ lil   +P l+ +++
  gi|70606881|ref|YP_255751.1| 164 LESLILLdgGPILRQPTN 181
                                   *****9755666665544 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   3.5e-09   1.6e-05       1     188 [.      50     291 ..      50     307 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.5e-09
                                   EEEE--GC..............G...CHHHH..HHHHCCT.CEEEEE--TTS.TS-GGCS--HHHCHHH..HHHHCCTT.. CS
                 Abhydrolase_6   1 vlllHGagss.........assW...lvapL..aallaag.vhvlapDlpGh.Grsdpppldledladl..aalldelaa. 62 
                                   +l l+G++ss          ++W       +    + a + + v+ +D++ h  +++ +p ++   +d+  ++ ++++++ 
  gi|70606881|ref|YP_255751.1|  50 LLILPGTWSSgeqlsantvDDDWkrnE--DIdePFFWANRcIDVYLMDYRTHfLSPEKDPSEFGFMVDWgwEQWINDIKEv 128
                                   678899998866666666666664321..3343335666776779********9899999777665555444444444444 PP

                                   .........TTSEEEEEETCHHHHHHHHHHCC.......EE.EEES-.........----TTT..........S----TTH CS
                 Abhydrolase_6  63 ........gggpvvlvGHSlGGalalaaapla.....lvvg.vlldppp.......talpagl..........laaalell 112
                                           + ++v+l G S+GG+        a     ++++ +lld+ p         +   +           ++a+e+ 
  gi|70606881|ref|YP_255751.1| 129 vefikeisSFKRVFLAGESFGGLATVN---FAtlfpeDLESlILLDGGPilrqptnSLD---FdgllekikntKSWAMEVG 203
                                   4445558899*************8888...444448877789*****776555443222...1223456555544444444 PP

                                   HHHHHTT-CCCCHCCH...S-HSCCCCHHH.C......CCCHCHCCCGHHHHCC.....HHCHTTCCHHTT-TTGCEEECT CS
                 Abhydrolase_6 113 lallallrllawlsre...plprlfladed.a......daawrarlarlaalla.....glgllpaaawadlpvpllvlgg 178
                                    + +al+ +  +  ++   p++ +  +++  +       + w+  l  +  +l      gl ++ +a + d +v+++++ +
  gi|70606881|ref|YP_255751.1| 204 GTKGALFLF-KYIDKNpnaPPTNPVTGEPLePrinpitGEKWNNILEWATFTLYsgwgpGLLTNVYAGYNDPRVLVHTMST 283
                                   444444444.33322233322222222222212311222444444444443333322223335567788888888776677 PP

                                   T-CHHHHCHH CS
                 Abhydrolase_6 179 eDplvprlle 188
                                    D+ +p  ++
  gi|70606881|ref|YP_255751.1| 284 FDRYWP--IR 291
                                   777776..54 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-06    0.0046      56     112 ..     123     184 ..      64     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                                   HHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE......CSSCCH CS
                 Abhydrolase_1  56 tasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga......idpaas 112
                                   + ++ +++++i++    +++ l G S+GG+   ++a ++pe   +l+ll++      ++++ +
  gi|70606881|ref|YP_255751.1| 123 N-DIKEVVEFIKEISSFKRVFLAGESFGGLATVNFATLFPEDLESLILLDGgpilrqPTNSLD 184
                                   3.5999*******************************************99666544444444 PP

>> 2C_adapt  2-cysteine adaptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.35   1.6e+03      25      34 ..      36      45 ..      36      46 .. 0.88
   2 ?    7.3   0.9    0.0012       5.2       9      21 ..     222     234 ..     216     235 .. 0.88
   3 ?    3.1   0.0     0.025   1.1e+02       9      18 ..     234     243 ..     232     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                      2C_adapt 25 tykklereCk 34
                                  +++ + +eCk
  gi|70606881|ref|YP_255751.1| 36 VHRLIKEECK 45
                                  6999*****8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0012
                      2C_adapt   9 ptvNPlTgRkikp 21 
                                   p+ NP+Tg ++ p
  gi|70606881|ref|YP_255751.1| 222 PPTNPVTGEPLEP 234
                                   789********98 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.025
                      2C_adapt   9 ptvNPlTgRk 18 
                                   p++NP Tg k
  gi|70606881|ref|YP_255751.1| 234 PRINPITGEK 243
                                   89******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2600.21
//
Query:       gi|70606882|ref|YP_255752.1|  [L=196]
Description: TetR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-15   55.2   0.1    6.9e-15   54.6   0.1    1.3  1  TetR_N    Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.048   13.3   0.0      0.065   12.9   0.0    1.2  1  Luteo_PO  Luteovirus P0 protein


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   7.7e-19   6.9e-15       1      47 []      18      64 ..      18      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 7.7e-19
                                  HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHHHH CS
                        TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLleal 47
                                  Ilda +el+a++G+ +t++++I ++AGv+ g++Y yF+sK ++l+++
  gi|70606882|ref|YP_255752.1| 18 ILDASVELIADKGFLSTSINDITSKAGVAYGLFYFYFKSKHDILDEI 64
                                  9*******************************************996 PP

>> Luteo_PO  Luteovirus P0 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-06     0.065     126     190 ..      58     122 ..      53     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                      Luteo_PO 126 qeilasgmeeFkrflsvwlrdierslpespkespvgdstvldlanlgtllvrlvlaeqllergll 190
                                    +il + +++F+r++ + l++  ++l +      vg + +l+ +n+ +  ++ +++ q++ ++ +
  gi|70606882|ref|YP_255752.1|  58 HDILDEIIRQFNRNMRYYLKTYTQNLDSRIDVEKVGMKKFLEWMNENKKYYKIFIETQVHRPDIY 122
                                   677888899***************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1276.69
//
Query:       gi|70606883|ref|YP_255753.1|  [L=373]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-23   83.7   0.1    2.4e-23   82.9   0.1    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
      5e-20   71.5   0.0    1.1e-19   70.4   0.0    1.6  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    6.1e-16   59.0   0.4    4.8e-14   52.8   0.4    2.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.9   0.0        0.2   12.2   0.0    1.4  1  Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.1   5.4e-27   2.4e-23       2     113 .]       6     118 ..       5     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 5.4e-27
                                   HHHHHHHHHHHHHHHHHTHHHHHHHH.HHT.SGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                 Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewd.eeg.efprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                   +e e++r +vre++++++++ ++e    +  e+ +++++k+ e+G+lg+++p+eygG g +++ ++iv ee+a+a++++a+
  gi|70606883|ref|YP_255753.1|   6 KELEEYRNKVREWIRKNVPEEIKEKGdMAPvEVLKSWQRKIYEAGYLGVSWPKEYGGWGDSPIKEIIVREEFAKAGVPYAT 86 
                                   5889**************7654444324445666888**********************99*****************987 PP

                                   HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasge 113
                                    +g++ s+ +pail+ G+eeqk++ ++++++ e
  gi|70606883|ref|YP_255753.1|  87 -IGLGVSVTGPAILNNGNEEQKKKHIRRILTAE 118
                                   .7778899999*****************99876 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   2.5e-23   1.1e-19       1      95 [.     122     214 ..     122     216 .. 0.92
   2 ?   -3.2   0.0       2.2     1e+04      57      74 ..     320     336 ..     291     343 .. 0.50

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.5e-23
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE----- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrriee 80 
                                   + +++Ep aGsd+as++t  +e +g++y +nG+Kiw++ a+ a+++l+l+rt++p+ r++gl++++v+ +++g++v++i++
  gi|70606883|ref|YP_255753.1| 122 CQGFSEPHAGSDLASIRT-KIEDKGDHYEVNGQKIWSSYAHLANYCLLLGRTGDPSeRHKGLTILIVDMRSEGIKVSPIKQ 201
                                   7899**************.88999999************************999999***********************9 PP

                                   BSS-TTS-EEEEEEE CS
                 Acyl-CoA_dh_M  81 klGlrglptgelvfe 95 
                                    +G+ + +   ++f+
  gi|70606883|ref|YP_255753.1| 202 ITGRSEFN--TVYFN 214
                                   99998655..56665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                                   ----EEEEEEE..GGGEE CS
                 Acyl-CoA_dh_M  57 rarglslflvprdapgvs 74 
                                   ++ g   ++v+ ++pg++
  gi|70606883|ref|YP_255753.1| 320 NTMGPEALVVE-RKPGFR 336
                                   34444455555.566666 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.4   1.1e-17   4.8e-14       1     149 [.     228     367 ..     228     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 1.1e-17
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   g+G+rvam+tln+eRl+++ + l   +r+++     + ++  +g          e l++ a ++ a+++   r+ e++++g
  gi|70606883|ref|YP_255753.1| 228 GEGWRVAMSTLNYERLNIG-TILFGVERIIR----DLVNTGYKG----------ESLINTAEDIIALKAFYKRILERMKKG 293
                                   69****************7.44555555555....455555556..........79************************* PP

                                   ---HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT....SGGGH.....HHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpdraeasmaKlfaselaqevadlamqllGgaGy....leeyp.....verlyrdarvlrigeGtseiqrniiarrl 149
                                     +++ea+m+Kl+ase +q+v+++a   +G +++        p     +   + ++r+ +i++Gtsei+rn++++++
  gi|70606883|ref|YP_255753.1| 294 YIAGPEAAMIKLVASESMQKVYESAFNTMGPEALvverK---PgfrpeIVYGLLASRSITIAGGTSEILRNLLGEVV 367
                                   **********************************65442...345555444569*******************9987 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05       0.2      93     121 ..      85     116 ..      38     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                                   H...HHHHTHHHHHHHHS-HHHHHHHHHHHHT CS
                 Acyl-CoA_ox_N  93 g...lhfsMFlptlkgqgteeQqakWlpraen 121
                                   +   l +s+  p+++++g+eeQ++k + r+ +
  gi|70606883|ref|YP_255753.1|  85 AtigLGVSVTGPAILNNGNEEQKKKHIRRILT 116
                                   4444889999***************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2514.90
//
Query:       gi|70606884|ref|YP_255754.1|  [L=663]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-69  232.9   0.0    5.1e-69  232.4   0.0    1.2  1  ECH_1            Enoyl-CoA hydratase/isomerase
    6.6e-65  218.4   0.2    1.2e-64  217.5   0.2    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    1.3e-43  147.5   0.1      2e-23   82.8   0.0    2.9  3  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    3.2e-40  138.6   0.2    5.5e-37  128.0   0.0    2.5  3  ECH_2            Enoyl-CoA hydratase/isomerase
    0.00053   20.2   0.0     0.0013   19.0   0.0    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0043   17.4   0.1      0.028   14.8   0.0    2.4  2  SeleniumBinding  Selenium binding protein
     0.0084   15.4   0.1      0.015   14.6   0.1    1.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.013   14.8   0.1      0.024   14.0   0.1    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.014   15.9   0.0      0.078   13.6   0.0    2.3  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.03   13.9   0.1      0.055   13.0   0.1    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.079   12.3   0.1       0.18   11.2   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.12   12.9   0.1       0.51   10.9   0.1    2.2  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.4   0.0   3.4e-72   5.1e-69       6     250 ..     419     662 ..     415     663 .] 0.96

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 3.4e-72
                                   EEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHH CS
                         ECH_1   6 vaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtklyt 86 
                                   +a i lnrPe +Nals+el+ El ++l +le ++ vr+v++tG ++aF+aGad++  +   + +   ++  +++   k++ 
  gi|70606884|ref|YP_255754.1| 419 LAWIVLNRPERLNALSQELMGELDKVLDELEFNNDVRVVIITGNGRAFSAGADVTSFTTLRPIDVVRYR-YMKNVIYKIQL 498
                                   57899******************************************************8654444443.46777899*** PP

                                   SSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHC CS
                         ECH_1  87 vpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkv 167
                                     kpviaa+nG+a+gGGlela+acDi+ia++ a+ g++e+++G+ipgaggtq+l+r +Gk +A+ ++++g+ i a+ea k+
  gi|70606884|ref|YP_255754.1| 499 YTKPVIAAINGFALGGGLELAMACDIRIASNLAQLGQPEINIGIIPGAGGTQRLPRLIGKGRAKLLIYTGDMIPAEEAYKM 579
                                   ********************************************************************************* PP

                                   TSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH--- CS
                         ECH_1 168 GlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrkpef 248
                                   Glvd+vvp+++++ee + +a k+aeksp++l ++k a++  +e +  ++ e+e+ lf  +f ++d+keG+ aflE+rkp+f
  gi|70606884|ref|YP_255754.1| 580 GLVDQVVPANKFEEEVRRVALKIAEKSPLSLLAAKLAVELGYEANIWTGQELESALFGLLFTTEDVKEGVRAFLERRKPQF 660
                                   ********************************************************************************* PP

                                   -- CS
                         ECH_1 249 ed 250
                                   ++
  gi|70606884|ref|YP_255754.1| 661 KG 662
                                   97 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.5   0.2   7.9e-68   1.2e-64       1     179 [.       8     187 ..       8     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 7.9e-68
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-S CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dad 80 
                                   k+ viGaGtmG+gia+++a ag++V l d+s+++l++a++k++ sl kl+e+g +k e+ve++l+ri++   l++ v dad
  gi|70606884|ref|YP_255754.1|   8 KILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDILNSAMDKVKWSLTKLKERGTIK-EDVETVLQRIRPVVGLDKTVsDAD 87 
                                   578*****************************************************.9*********************** PP

                                   EEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                       3HCDH_N  81 lviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetva 161
                                   + iEa++E++++Kr++fa+l+++++p+aila+nTSsl++s++aea+krp++v+g+H+fnPp lm+LvEv++g+kTs+et +
  gi|70606884|ref|YP_255754.1|  88 FSIEAITEKIDVKRQTFAKLDELLPPHAILATNTSSLPVSKIAEATKRPDKVVGMHYFNPPALMPLVEVMKGDKTSDETAK 168
                                   ********************************************************************************* PP

                                   HHHHHHHHTT-EEEEE.CS CS
                       3HCDH_N 162 tvvelakkigktpvvv.kd 179
                                    ++elakk+gk+p+ + kd
  gi|70606884|ref|YP_255754.1| 169 VTYELAKKLGKQPIMInKD 187
                                   ***************9666 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.1   1.4e+04      26      54 ..       3      32 ..       2      52 .. 0.69
   2 !   82.8   0.0   1.3e-26     2e-23       1      97 []     190     286 ..     190     286 .. 0.95
   3 !   61.5   0.0   5.8e-20   8.7e-17       7      97 .]     310     400 ..     309     400 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.1
                                  HHHHHHHHHHHHHHS.SCHHHHHHHHHHHH CS
                         3HCDH 26 pediDaamrlglGlp.mGpfelldlvgldv 54
                                  +edi +++  g+G    G+ el+  +g  v
  gi|70606884|ref|YP_255754.1|  3 VEDIKKILVIGAGTMgHGIAELAAIAGYQV 32
                                  677777777777765577777777777655 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 1.3e-26
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTH.GGHH-HHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelger.ayapspllekl 80 
                                   G+vvnR+l+ +    + +ve++ a+++++Da++r++lG+pmG+felld++g+dva++i++  +eelg + +   + l+ + 
  gi|70606884|ref|YP_255754.1| 190 GYVVNRILGGINIASCIVVEKKLADIKEVDAVARYKLGFPMGVFELLDYTGIDVAYYISK-SREELGVKdDIPICSLIVEK 269
                                   9**********************************************************9.6666666669999******* PP

                                   HHTT--BGGGTBSSSBC CS
                         3HCDH  81 veagrlgrktgkgfyky 97 
                                   +++++lg k+gkgfy+y
  gi|70606884|ref|YP_255754.1| 270 FKNNELGVKSGKGFYTY 286
                                   ***************98 PP

  == domain 3  score: 61.5 bits;  conditional E-value: 5.8e-20
                                   HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--B CS
                         3HCDH   7 vlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlg 87 
                                   ++ap +nea rlv e++as ed+D  + lglG+  G+++l+d+vg+d   + l+ l++ +g + + p pll+++v++g++g
  gi|70606884|ref|YP_255754.1| 310 IIAPAVNEAARLVRENIASKEDVDLGTVLGLGFQKGILKLADEVGIDNIVNSLSELKKLTGISSFDPDPLLTEMVSQGKVG 390
                                   6799***************************************************************************** PP

                                   GGGTBSSSBC CS
                         3HCDH  88 rktgkgfyky 97 
                                    k+g+gf++y
  gi|70606884|ref|YP_255754.1| 391 MKSGSGFFEY 400
                                   *******998 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.1   4.6e+03     175     211 ..      44      82 ..      26     109 .. 0.56
   2 !  128.0   0.0   3.7e-40   5.5e-37       2     179 ..     420     593 ..     419     599 .. 0.93
   3 !    9.0   0.0   0.00059      0.88     249     318 ..     595     661 ..     592     663 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                                   GGHHHHHHHHHTT..........--------......-- CS
                         ECH_2 175 eklealeeaLaelessd..eeaveevleelaeeaeeeee 211
                                   +++++++ +L++l+++   +e+ve+vl++++  +  +++
  gi|70606884|ref|YP_255754.1|  44 SAMDKVKWSLTKLKERGtiKEDVETVLQRIRPVVGLDKT 82 
                                   345666666666655556677777777776654444333 PP

  == domain 2  score: 128.0 bits;  conditional E-value: 3.7e-40
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   ++i Lnrp+ lNaLs+e++ +l++ l+e e +++v++v+++g+g +af+AG Dv ++++ +  +  +    +r   ++ y 
  gi|70606884|ref|YP_255754.1| 420 AWIVLNRPERLNALSQELMGELDKVLDELEFNNDVRVVIITGNG-RAFSAGADVTSFTTLRPIDVVR----YRYMKNVIYK 495
                                   5799**************************************88.*************998886544....56666899** PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgada 162
                                   i+ y+kpv+a ++G+++GgG+ l++ + +r++++ +++  PE++IG++P  Gg+  L+rl g   ++ l  TG+ + +++a
  gi|70606884|ref|YP_255754.1| 496 IQLYTKPVIAAINGFALGGGLELAMACDIRIASNLAQLGQPEINIGIIPGAGGTQRLPRLIGkGRAKLLIYTGDMIPAEEA 576
                                   ***********************************************************966488**************** PP

                                   HHTTS--EE--GGGHHH CS
                         ECH_2 163 laaglathyvpseklea 179
                                   +++gl +++vp++k+e+
  gi|70606884|ref|YP_255754.1| 577 YKMGLVDQVVPANKFEE 593
                                   *************9976 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00059
                                   HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                         ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                   +++++ +++++sP+sl ++  +++ g +++ + +  + E +l   l++++D+ eGvra l  +  kP++k
  gi|70606884|ref|YP_255754.1| 595 VRRVALKIAEKSPLSLLAAKLAVELGYEAN-IWTGQELESALFGLLFTTEDVKEGVRAFLERR--KPQFK 661
                                   567778999********************5.***************************99654..67765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.4e-07    0.0013       2      63 ..       9      77 ..       8     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.4e-07
                                  EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHC.SEEEE-S CS
                 NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasl.dvvitmv 63
                                  i +iG G+MG+ +a+  + agy+v++ +++++ +++++++                +i+e v+++ + +  +v
  gi|70606884|ref|YP_255754.1|  9 ILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDILNSAMDKVkwsltklkerG----TIKEDVETVlQRIRPVV 77
                                  779***********************************99878877744442....33333333333333333 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.6   6.8e+03      15      40 ..      27      51 ..      21      67 .. 0.65
   2 !   14.8   0.0   1.9e-05     0.028       6      60 ..     562     616 ..     560     624 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.6
               SeleniumBinding 15 iPGvelyylgivsavvesdnvdkilk 40
                                  i G ++y  + vs+ + ++ +dk+  
  gi|70606884|ref|YP_255754.1| 27 IAGYQVYLSD-VSQDILNSAMDKVKW 51
                                  6677776655.566677788888744 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.9e-05
               SeleniumBinding   6 kfiittaneiPGvelyylgivsavvesdnvdkilkaleekvkekkglaligfklt 60 
                                   k++i t + iP  e y +g+v +vv +++ ++ ++ +  k+ ek  l+l++ kl+
  gi|70606884|ref|YP_255754.1| 562 KLLIYTGDMIPAEEAYKMGLVDQVVPANKFEEEVRRVALKIAEKSPLSLLAAKLA 616
                                   689**********************************************998875 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.9e-06     0.015     143     185 ..       7      49 ..       1      99 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.9e-06
                                   SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TTS-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrll.raldkel 185
                                   k+i+v+G+G  G  +A  +a +g++v+l +  + +l +a+dk +
  gi|70606884|ref|YP_255754.1|   7 KKILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDILnSAMDK-V 49 
                                   79**********************************666664.3 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.024      30      73 ..       8      52 ..       2     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTC CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgak 73
                                  k+lviG+G+ G   ++ a+  g +V++ Dv+++ l+   + ++ +
  gi|70606884|ref|YP_255754.1|  8 KILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDILNSAMDkVKWS 52
                                  89******************************9998776644444 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.2e-05     0.078       1      52 [.       8      55 ..       8      75 .. 0.79
   2 ?   -3.1   0.0       8.4   1.3e+04      35      50 ..     426     441 ..     419     461 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEEC CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvta 52
                                  ki +iGaG mg+++a+ ++ ag   +++++  + +++ ++++ ++++ ++t+
  gi|70606884|ref|YP_255754.1|  8 KILVIGAGTMGHGIAELAAIAG---YQVYLS-DVSQDILNSAMDKVKWSLTK 55
                                  6889******************...999965.87888777777777655555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                                   SCCCHHHHHHHHC-EE CS
                 F420_oxidored  35 npekaeelaeelgvkv 50 
                                    pe++++l +el  ++
  gi|70606884|ref|YP_255754.1| 426 RPERLNALSQELMGEL 441
                                   6788888888876433 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.7e-05     0.055       6     183 ..      17     201 ..      13     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT...SE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----E CS
                  adh_short_C2   6 IGraiAkalaeeGaevvltdlneea.kkrveelaeelg...ae.vlecDVtdeeqvealveevvekfgklDilvnnagiap 81 
                                   +G++iA+++a +G++v l+d++++  ++++++++ +l    ++  ++ DV+   q  + v  + +++   D+ + ++    
  gi|70606884|ref|YP_255754.1|  17 MGHGIAELAAIAGYQVYLSDVSQDIlNSAMDKVKWSLTklkERgTIKEDVETVLQRIRPVVGLDKTVSDADFSIEAITEKI 97 
                                   89*********************9987777777665543325556999999999999999999999999999998887777 PP

                                   G.CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHH..HHHHHHHHHHHH CS
                  adh_short_C2  82 k.lkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaa..lealtrylAvel 159
                                   + +++ f+++++    +a+    +s + ++k  +++ k+  ++v + ++     +p  +++   K +    ++t  lA++l
  gi|70606884|ref|YP_255754.1|  98 DvKRQTFAKLDELLPPHAILATNTSSLPVSKI-AEATKRPDKVVGMHYFNPPALMPLVEVMKGDKTSdeTAKVTYELAKKL 177
                                   76777777775555444444444444455554.467788899***********************98334578999***** PP

                                   GGGTEEEEEEEE--BHCTGGGGST CS
                  adh_short_C2 160 gpkgiRvNavspgpikTlaasgik 183
                                   g++ i +N   pg++  ++  gi+
  gi|70606884|ref|YP_255754.1| 178 GKQPIMINKDIPGYVVNRILGGIN 201
                                   *********999999888877775 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.18      37      72 ..       7      42 ..       4      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72
                                  k++ +iG+G +G+ +a++++  g +v+  d+s++  
  gi|70606884|ref|YP_255754.1|  7 KKILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDIL 42
                                  7899**************************997743 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00034      0.51       1      54 [.       8      60 ..       8      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTT CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekng 54
                                  k++v+G+G+ g   A+ +a  g +V++ + s  +l +++D+   k+  +kl+++g
  gi|70606884|ref|YP_255754.1|  8 KILVIGAGTMGHGIAELAAIAGYQVYLSDVSQDILnSAMDKV--KWSLTKLKERG 60
                                  79*********************************9999887..88888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3979.05
//
Query:       gi|70606885|ref|YP_255755.1|  [L=306]
Description: hypothetical protein Saci_1110 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-25   90.0   1.7    1.2e-24   87.5   1.7    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0065   16.4   0.0      0.012   15.5   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.019   14.5   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   1.7   1.9e-28   1.2e-24       5     197 .]      15     215 ..      11     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.9e-28
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                    +nsy+i+++++++LiDtG++ e +  +  l+    k   +d+v++TH+H+DHiG ++ +++ +     ++       ++ 
  gi|70606885|ref|YP_255755.1|  15 HINSYVIRDGDDTLLIDTGLPIEDDAVV--LKEFIEKSGYPDYVLITHYHPDHIGQARLFKKSRILLNQEELQFITDVIEG 93 
                                   58**************************..7*******************************9876544444333333333 PP

                                   HHHHHHHHCCHH..................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEE CS
                   Lactamase_B  86 eaddaasrkgll..................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlft 148
                                    +++     +++                  + +    +++++e + dg+   +++ ++ ++ ++gh++g+ + + g  lf+
  gi|70606885|ref|YP_255755.1|  94 VHER---EMKDYllrngfpenflqrifsqrAFFKELLADIEFEGVKDGDKIVIGGNEAEVIWTPGHTVGHSCVKYGENLFC 171
                                   3333...22222334666679999*****9999999999999999************************************ PP

                                   CTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 149 GDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                   GD +l++ t+ ++l     +++++++ + yldsl+k+++l++ +++p+H
  gi|70606885|ref|YP_255755.1| 172 GDHILPNVTPNVSL-----HAPYDDPLGRYLDSLDKIEKLEINTIYPAH 215
                                   **************.....*****************************9 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-06     0.012       7      73 ..      16      86 ..      14     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                 Lactamase_B_3  7 hnsflletagarilvDPf........kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslev 73
                                   ns+++++++ ++l+D +           +++ ++   +D vli++ ++dH   ++l +   + ++l ++e+l++
  gi|70606885|ref|YP_255755.1| 16 INSYVIRDGDDTLLIDTGlpieddavV-LKEFIEKSGYPDYVLITHYHPDHIGQARLFK---KSRILLNQEELQF 86
                                  69**************88666664320.4566667799*************99988777...6666666666554 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.1e-06     0.019      30      61 ..      52      87 ..      27     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-06
                                  SEEEEE-SS--HHHHGGGGCCCC....C--EEEEEE CS
                 Lactamase_B_2 30 pidaVllthaHyDHlaglltlre....lrpkklply 61
                                    d Vl+th H DH+  +  +++    l +++l+++
  gi|70606885|ref|YP_255755.1| 52 YPDYVLITHYHPDHIGQARLFKKsrilLNQEELQFI 87
                                  579************777777767765444445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1939.50
//
Query:       gi|70606886|ref|YP_255756.1|  [L=550]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-74  249.4   0.0    6.2e-74  249.1   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    6.1e-21   75.2   0.0    1.7e-20   73.7   0.0    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.1   0.0   6.9e-78   6.2e-74      18     422 ..      42     444 ..      22     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 249.1 bits;  conditional E-value: 6.9e-78
                                   CSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESE CS
                   AMP-binding  18 gegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakv 97 
                                   g  + l Yr   +r++++ + L+ +l+ k gd ++il +n ++++ +++ + ++Gav+  ln +l +++l yil++++ak 
  gi|70606886|ref|YP_255756.1|  42 GVLHNLNYRKIFHRISSFTNSLEkELNTKAGDIIGILGWNDHRYFESFFTVPSLGAVLLELNIRLHPADLLYILKHTRAKG 122
                                   5567899****************9********************************************************* PP

                                   EEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.....-TSCCCS-BTTSEEEEEEE--SSSS CS
                   AMP-binding  98 liatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.....kpeeeeelkpddlayiiYTSGTTGk 173
                                   l+  vd+ ll+ l+ea +k+   + +i+++++++++ ++   ++  +e+        +++ ee++++++a+  +T GTTG 
  gi|70606886|ref|YP_255756.1| 123 LL--VDDSLLP-LAEALSKEYNFDYTIIMSDKPFEEIKTNIRNAFGYEE-LvksgsPNRKFEEVDEKSTAFAAFTTGTTGL 199
                                   **..8887755.4444544444555555555555555444444433333.1456775668889****************** PP

                                   -EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT- CS
                   AMP-binding 174 PKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkv 254
                                   PKGV +shr++v  + +++    ++lk++dv+l+ +p++h+ g+    ++  + G++ +++   ++ d   ++e i ++kv
  gi|70606886|ref|YP_255756.1| 200 PKGVFYSHRSVVLHALNIS----RDLKPSDVILQAVPFFHVHGW-GTQFAGAITGCKQIFPG-RPTVD--SMVEHILNHKV 272
                                   *************999984....56889****************.999999999****9966.44534..589******** PP

                                   SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE........ CS
                   AMP-binding 255 tviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv........ 326
                                   t +a+vP+v+  ll+   ++ +   + +l +lrl  +gg+ ++++l+ ++ ++++e   +gYG TEt++vv+         
  gi|70606886|ref|YP_255756.1| 273 TRTAAVPTVVLELLRR--IEtM-DPKPNLAGLRL-GIGGAEPPSALVSALAKHGIE-TGQGYGATETGPVVVAavakpefe 348
                                   ************9884..3322.23458999**9.57****************997.9*************666799***9 PP

                                   .CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEE CS
                   AMP-binding 327 .lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrl 404
                                    lp ee+ k+l ++G +l gvevk+vD+  ge++p dg++ Ge+++rgp++++ Y+++  + ae+f+ +++w ++ Dlg++
  gi|70606886|ref|YP_255756.1| 349 qLPVEEKFKRL-KQGLILFGVEVKVVDPVSGEELPwDGKSvGEIWFRGPWIARSYYND-PRSAESFT-SDGWWKSKDLGVI 426
                                   87766665555.6**********************877778****************9.57899**9.657********** PP

                                   ETTSEEEEEEECCCEEEE CS
                   AMP-binding 405 dedGyleivgRkkdlikl 422
                                   de Gy+++v+R+kd++k+
  gi|70606886|ref|YP_255756.1| 427 DELGYVKLVDRLKDVVKS 444
                                   ****************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   1.9e-24   1.7e-20       2      76 .]     454     533 ..     453     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.9e-24
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   +E+ l++hp V+ea VvGvp++++Ge+++a+V lk++   + +   +++ L +h+ k+++++  p+++vfvde+pkt  GK
  gi|70606886|ref|YP_255756.1| 454 LENFLMAHPYVREASVVGVPHPKWGERPLAVVSLKPEyqsK-DkeeVKKSLLDHLSKRFAKWQLPDDIVFVDEIPKTSVGK 533
                                   7*********************************9875331.2567**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3709.36
//
Query:       gi|70606887|ref|YP_255757.1|  [L=308]
Description: ribonucleotide-diphosphate reductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-19   68.6   0.0    7.4e-19   68.3   0.0    1.2  1  Ribonuc_red_sm   Ribonucleotide reductase, small chain
    6.6e-06   26.6   0.1      0.044   14.2   0.0    2.4  2  Rubrerythrin     Rubrerythrin
    0.00092   18.8   0.0       0.82    9.2   0.0    2.2  2  DUF455           Protein of unknown function (DUF455)
  ------ inclusion threshold ------
      0.016   14.9   0.1      0.025   14.3   0.1    1.3  1  Ald_deCOase      Long-chain fatty aldehyde decarbonylase
      0.026   13.4   0.1      0.066   12.1   0.0    1.6  2  FA_desaturase_2  Fatty acid desaturase
        0.1   12.4   0.0       0.16   11.7   0.0    1.4  1  Haem_oxygenas_2  Iron-containing redox enzyme


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   2.5e-22   7.4e-19      14     214 ..      29     234 ..      26     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.5e-22
                                   HHHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBS..SHHHHHHHHHHHHHH CS
                Ribonuc_red_sm  14 elykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevq..ipearafygfqaamE 92 
                                   +ly+   + fW p+ +dl++D +dw+ kL + +k ++ +v + + + +  v+  l + ++  v+    e+ +++  ++++E
  gi|70606887|ref|YP_255757.1|  29 KLYQLGKKLFWDPSTIDLTQDRADWD-KLRDIDKFLMVNVTSKFGAGEEAVALDLHPLIVTLVKegRVEEVMYLEQFIFEE 108
                                   6799999******************9.6**************************9999999999555688899******** PP

                                   HHHHHHHHHHHHHHT.-HHHHHHHHCHHH.H-HHHHHHHHHHHHHHCTTTSC..HHHHHHHHHHH.HHHHCCCHHHHHHHH CS
                Ribonuc_red_sm  93 niHaesYsllletlvkdekekdelfnaie.enpalqkkaewikkwyeskkde..ekfaerlvafa.llegilfysgFaail 169
                                   + H e++   l++++  +++  el + +  ++  +         w  +++ +  e+ +++ v +  ++eg+   +g++++ 
  gi|70606887|ref|YP_255757.1| 109 AKHVEAFRRFLDAVG-VKEDLVELTKDVSpNYAKIFYEELPKAMWNLNRD-PspENQVRAAVTYNlVVEGVAAEGGYNIFK 187
                                   ***************.5555555555444144445444444344444444.355666666555555**************9 PP

                                   HHH.HTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHHHH CS
                Ribonuc_red_sm 170 wlk.krgllpglaeiielilrDeglHtdfagllfkelkeen.elenk 214
                                   +++   +++pgla+++++i+ De+ H  f+ +l+ +l +e  e   k
  gi|70606887|ref|YP_255757.1| 188 YITrTFNIFPGLAKMVNYIATDESRHIAFGTYLIARLIKEGgESVYK 234
                                   999789*******************************8885544444 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00022      0.66      34      68 ..     100     135 ..      30     153 .. 0.85
   2 !   14.2   0.0   1.5e-05     0.044      12     108 ..     181     279 ..     175     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBB CS
                  Rubrerythrin  34 lFeelAeeEreHakilnklleklepele.levkekv 68 
                                   ++e+++ eE++H + ++++l+++  +++ +e  ++v
  gi|70606887|ref|YP_255757.1| 100 YLEQFIFEEAKHVEAFRRFLDAVGVKEDlVELTKDV 135
                                   678999999999999999999999999955555444 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHC..STTHH..B.SSBBS-------TTGGHHHHHHHHH CS
                  Rubrerythrin  12 sarrlYkelaekakegypqiaelFeelAeeEreHakilnkllekl..epele.levkekvreyaeakpkflttaknLeeai 89 
                                    +++++k++++ ++  +p +a++ +++A +E++H ++   l+  l  e+++   +   + ++y+ +++  ++ + n+ + +
  gi|70606887|ref|YP_255757.1| 181 GGYNIFKYITRTFN-IFPGLAKMVNYIATDESRHIAFGTYLIARLikEGGESvYKAAMEHINYLGPYAVGIFSEPNVPQGV 260
                                   68899999999999.********************9977777665222334435666778889999999999999999998 PP

                                   HHHHHHHHCHHHHHHHHHH CS
                  Rubrerythrin  90 egayaeeeemyrfyeelae 108
                                   e+  + + e+  +y++ + 
  gi|70606887|ref|YP_255757.1| 261 EIPLKLNPEVTVEYAKKLL 279
                                   8888888888888887765 PP

>> DUF455  Protein of unknown function (DUF455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00027      0.82     156     209 ..      76     128 ..      63     167 .. 0.80
   2 !    7.6   0.0   0.00083       2.5     179     209 ..     200     230 ..     193     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00027
                        DUF455 156 EArGLDvtpalieklraagdeesaeiLevIledEitHVaaGvrWfrylcekegl 209
                                   EA  LD +p ++  l + g  e +  Le  + +E +HV+a +r++  +  ke+l
  gi|70606887|ref|YP_255757.1|  76 EAVALDLHPLIV-TLVKEGRVEEVMYLEQFIFEEAKHVEAFRRFLDAVGVKEDL 128
                                   99******9766.57778999999***************999999888777666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00083
                        DUF455 179 aeiLevIledEitHVaaGvrWfrylcekegl 209
                                   a++++ I +dE +H+a+G+    +l ++ g+
  gi|70606887|ref|YP_255757.1| 200 AKMVNYIATDESRHIAFGTYLIARLIKEGGE 230
                                   7899***************999998877666 PP

>> Ald_deCOase  Long-chain fatty aldehyde decarbonylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   8.5e-06     0.025      66     162 ..     131     238 ..      73     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.5e-06
                                   ----H..HHHHHHHHHHHH...HHHHHHHTT-HHHHHHHHHTHHHHHHH.HHHHHHGGGS-HHH.....HHHHHHHHHHHH CS
                   Ald_deCOase  66 vkpdl..efakeffaelhe...nfqeaaaegkvvtclliqaliieafai.aayniyipvadefa.....rkitegvvkdey 135
                                   ++ d+  ++ak f++el +   n+++  + ++ v + +   l++e  a    yni+  ++  f      +k+++ +  de 
  gi|70606887|ref|YP_255757.1| 131 LTKDVspNYAKIFYEELPKamwNLNRDPSPENQVRAAVTYNLVVEGVAAeGGYNIFKYITRTFNifpglAKMVNYIATDES 211
                                   333333379*******987333556677789999999********9987268*******9999644455799********* PP

                                   HHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                   Ald_deCOase 136 lhlnfGeeWlkenfeevkeeleeanke 162
                                    h+ fG   ++  ++e  e + +a+ e
  gi|70606887|ref|YP_255757.1| 212 RHIAFGTYLIARLIKEGGESVYKAAME 238
                                   ******999888888888888777655 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.59   1.8e+03     194     207 ..     107     120 ..      99     131 .. 0.64
   2 ?   12.1   0.0   2.2e-05     0.066     184     222 ..     199     237 ..     192     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.59
               FA_desaturase_2 194 dEkrHeaaYtrvve 207
                                   +E++H  a++r+++
  gi|70606887|ref|YP_255757.1| 107 EEAKHVEAFRRFLD 120
                                   45555555555554 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.2e-05
               FA_desaturase_2 184 lakicgaiaadEkrHeaaYtrvvekllevdpdeavlala 222
                                   lak+++ ia+dE+rH a+ t ++++l++   +++ +a+ 
  gi|70606887|ref|YP_255757.1| 199 LAKMVNYIATDESRHIAFGTYLIARLIKEGGESVYKAAM 237
                                   89*************************999988887765 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05      0.16      48     109 ..     108     178 ..      54     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
               Haem_oxygenas_2  48 ernHvelyrrllkalGldeeplealpelpetlalinl.........feavalsrrll.....gallGallalEllv 109
                                   e++Hve +rr+l a+G++e+ +e ++ +    a i +         +     +r+        a++ ++l++E+++
  gi|70606887|ref|YP_255757.1| 108 EAKHVEAFRRFLDAVGVKEDLVELTKDVSPNYAKIFYeelpkamwnL-----NRDPSpenqvRAAVTYNLVVEGVA 178
                                   567*************9999999988883233333225555433332.....222212333244567777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2124.72
//
Query:       gi|70606888|ref|YP_255758.1|  [L=302]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-12   47.0   0.0    6.5e-12   45.9   0.0    1.5  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.22   11.8   0.0       0.34   11.2   0.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   7.2e-16   6.5e-12      17     137 ..     178     292 ..     171     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.2e-16
                                   ---..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  17 avaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlfase 97 
                                   + a ++lg  +++l+ a++y+++r afgkp++++q++++++++ a+++e +r+++++a           + + +aK +a +
  gi|70606888|ref|YP_255758.1| 178 LFASQMLGHGQEVLNMAVKYSKERIAFGKPIGSYQAIKHRVVNDAVDVELVRSIILEASDN-------IKYVWLAKELANK 251
                                   568999***************************************************9963.......4567888****** PP

                                   HHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHH.HHSSS- CS
                 Acyl-CoA_dh_1  98 laqevadlamqllGgaGyleeypverlyrdarvl.rigeGt 137
                                      +v+ + +q++Gg G+++++ ++ +++++++l  i+ G 
  gi|70606888|ref|YP_255758.1| 252 KIPKVILSGIQVHGGIGFTDDMDIHLHLKRSLTLsKIYNGK 292
                                   ***********************998887777651577775 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.34       2      66 ..     178     240 ..     177     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaarae 66 
                                   ++a ++lG  + +l+ +v++ +er+   +g+++   +a+++++ + a +++  r ++++a + ++
  gi|70606888|ref|YP_255758.1| 178 LFASQMLGHGQEVLNMAVKYSKERIA--FGKPIGSYQAIKHRVVNDAVDVELVRSIILEASDNIK 240
                                   7999**********************..*****************99999999999988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1909.73
//
Query:       gi|70606889|ref|YP_255759.1|  [L=395]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-66  224.3   0.0    2.2e-66  223.9   0.0    1.2  1  Thiolase_N     Thiolase, N-terminal domain
    2.7e-45  153.0   0.6    7.2e-45  151.6   0.4    1.9  2  Thiolase_C     Thiolase, C-terminal domain
    2.2e-06   27.4   0.4    2.6e-05   23.9   0.1    2.7  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.011   14.5   0.0       0.02   13.6   0.0    1.4  1  SpoVAD         Stage V sporulation protein AD (SpoVAD)


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.9   0.0     5e-70   2.2e-66       1     259 [.       5     264 ..       5     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 223.9 bits;  conditional E-value: 5e-70
                                   EEEEEEEEE--EET......TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-T CS
                    Thiolase_N   1 vvivsaartpigkf......ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagipe 74 
                                   v++v+ artp+++f      +  + +l+ eeL+ +++++l+ek+g++p e++e++ G+ lq ge +    r+ ++++ +p+
  gi|70606889|ref|YP_255759.1|   5 VYLVDFARTPFTRFtrkepqKDPFYNLRPEELAGIVINRLIEKNGINPREIEEIVTGCALQVGEQWSfGGRHEVFASRLPY 85 
                                   789********9972222223458899***********************************99999899*********** PP

                                   TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEH CS
                    Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehm 155
                                   ++p+++v+++c+S++++va +a ++a+g ad+v+agGvE+ms++p+ ++ ++  ++ + ++ +      +   d ++++ m
  gi|70606889|ref|YP_255759.1|  86 TIPSMAVDRQCASSITTVAIGAMEVATGMADIVLAGGVEKMSKTPMFDNPHIEPNMAFLTDPK----YAE--YDLTTGYVM 160
                                   ************************************************977666655554444....444..56889**** PP

                                   HHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTT CS
                    Thiolase_N 156 GltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkke 236
                                   Gltae+la++ kisRee d++ ++shq a +a+++g Fkdei+P++++++ +k t+++d+ +r+++++ekL++l paF+ +
  gi|70606889|ref|YP_255759.1| 161 GLTAERLAEEAKISREEMDRWSLRSHQMATKAIQEGYFKDEIIPFETEVEGKKITLTTDQSVRPDTSLEKLSQLPPAFRPN 241
                                   *************************************************8888**************************** PP

                                   SS-BTTSB--BEEEEEEEEEEEH CS
                    Thiolase_N 237 GtvtAgnasqisDGaaavllmse 259
                                   Gt+tAgn+ +++ G+a vllms+
  gi|70606889|ref|YP_255759.1| 242 GTITAGNSAPLNSGSAYVLLMSK 264
                                   *********************97 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.9     4e+03      27      43 ..      40      56 ..      38      66 .. 0.81
   2 !  151.6   0.4   1.6e-48   7.2e-45       2     123 .]     273     394 ..     272     394 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.9
                                  HHHHHHHHHT--GGGES CS
                    Thiolase_C 27 aikkvlkkagltvedid 43
                                  +i+++++k+g++ ++i+
  gi|70606889|ref|YP_255759.1| 40 VINRLIEKNGINPREIE 56
                                  68899999999998886 PP

  == domain 2  score: 151.6 bits;  conditional E-value: 1.6e-48
                                   --SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B-T CS
                    Thiolase_C   2 kplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHPl 82 
                                   +p+akirs+  +gv+p+ +g gP++ +kk+l+ka l+v+di l+EinEAFa+++L ++k+l+ld++ vN +GGaia+GHPl
  gi|70606889|ref|YP_255759.1| 273 TPMAKIRSFGFAGVPPAVMGKGPVPSSKKALEKANLNVKDISLWEINEAFAVVVLNAIKELGLDESTVNKRGGAIAIGHPL 353
                                   89******************************************************************************* PP

                                   TTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                    Thiolase_C  83 GasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                   Ga+GaRiv tl+++l  eg+ +gva+lC gggqg a+v+e+
  gi|70606889|ref|YP_255759.1| 354 GATGARIVGTLARQLLIEGKDYGVATLCVGGGQGGAIVVER 394
                                   **************************************986 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   5.8e-09   2.6e-05     167     206 ..      88     127 ..      72     133 .. 0.90
   2 ?   -0.8   0.0      0.21   9.3e+02      90     109 ..     257     276 ..     241     330 .. 0.74
   3 ?   -1.0   0.0      0.23     1e+03      94     175 ..     324     381 ..     296     393 .. 0.46

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.8e-09
                                   SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                 ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                   ps++vd  C+Ss + v+   +++ +g ad++laGGve + 
  gi|70606889|ref|YP_255759.1|  88 PSMAVDRQCASSITTVAIGAMEVATGMADIVLAGGVEKMS 127
                                   9***********99999999****************9875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHHHHTS-HHT CS
                 ketoacyl-synt  90 rllleaawealedagltpee 109
                                    ++l  +++al+++gltp +
  gi|70606889|ref|YP_255759.1| 257 AYVLLMSKNALKRYGLTPMA 276
                                   57788889999999998843 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHTS-HHTCTTGGEEEEEEESSTHHHHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHHHHT--SSEEEEESG CS
                 ketoacyl-synt  94 eaawealedagltpeeldgsrvgvfiGvgagdyaalaaldedgsevkaspkavgavlanviagrisyalglrGpsvtvdtA 174
                                   +++ +a+++ gl++ +++++  +  iG                       +++ga + + i g ++ +l ++G  + v t 
  gi|70606889|ref|YP_255759.1| 324 VVVLNAIKELGLDESTVNKRGGAIAIG-----------------------HPLGA-TGARIVGTLARQLLIEGKDYGVATL 380
                                   223333333333333333322222222.......................23333.5555555555555555555555555 PP

                                   G CS
                 ketoacyl-synt 175 C 175
                                   C
  gi|70606889|ref|YP_255759.1| 381 C 381
                                   5 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-06      0.02      54     131 ..      36     121 ..      19     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-06
                                   HHHHHHHHHHHHTT--GGG-SEEEEEESSGGGHHHHHHHHH........H---EEEB--GGGHHHHHHHHHHHHHHTTS-S CS
                        SpoVAD  54 lleeavkkalkkanlkkedidfllaGDLlnqlisssfaare........lkiPflglygaCstsaeslalaallvdggfak 126
                                   l    ++  ++k++++  +i+ +++G  l+     sf+ r+         +iP +++   C++s  ++a++a+ v +g+a+
  gi|70606889|ref|YP_255759.1|  36 LAGIVINRLIEKNGINPREIEEIVTGCALQVGEQWSFGGRHevfasrlpYTIPSMAVDRQCASSITTVAIGAMEVATGMAD 116
                                   5666789999999999999999999999988888888776533333333589999************************** PP

                                   EEEEE CS
                        SpoVAD 127 rvlaa 131
                                    vla+
  gi|70606889|ref|YP_255759.1| 117 IVLAG 121
                                   **997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2661.89
//
Query:       gi|70606890|ref|YP_255760.1|  [L=335]
Description: putative alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-27   95.6   0.1    1.4e-26   92.5   0.0    2.3  2  ADH_N          Alcohol dehydrogenase GroES-like domain
    2.3e-20   72.9   0.7    3.8e-20   72.2   0.7    1.3  1  ADH_zinc_N     Zinc-binding dehydrogenase
    9.9e-10   39.6   0.2    1.9e-09   38.7   0.0    1.5  2  ADH_zinc_N_2   Zinc-binding dehydrogenase
     0.0092   15.3   2.1      0.015   14.6   2.1    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.01   15.4   1.0      0.017   14.7   1.0    1.3  1  LDcluster4     SLOG cluster4 family
      0.018   15.0   0.4      0.033   14.2   0.4    1.5  1  SIS_2          SIS domain
      0.078   12.4   0.3       0.11   11.9   0.3    1.2  1  Epimerase      NAD dependent epimerase/dehydratase family
      0.081   13.1   0.1       0.16   12.2   0.1    1.5  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
       0.11   11.9   2.8       0.23   10.9   2.7    1.7  1  adh_short      short chain dehydrogenase
       0.12   11.7   0.2       0.17   11.1   0.2    1.2  1  CMAS           Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   7.9e-30   1.4e-26       2     109 .]      27     133 ..      26     133 .. 0.98
   2 ?    0.4   0.0      0.34     6e+02      90     104 ..     195     216 ..     152     221 .. 0.62

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 7.9e-30
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                    ev++k++ a++C  Dl  ++g   ++ k+plilGHE+vGe+eevg++v+++k+Gd V+    +++ +C++Ck gee +C+
  gi|70606890|ref|YP_255760.1|  27 SEVVVKLRKAALCYRDLLQIQG-FYPRSKYPLILGHEMVGEIEEVGEGVEGFKKGDIVTSLLYVPDWTCDNCKMGEEIYCN 106
                                   69********************.8********************************************************* PP

                                   TBEETTTSS-SSSBSEEEECGGGEEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvkl 109
                                   +++l+  +ldG fae+++v++++lvk+
  gi|70606890|ref|YP_255760.1| 107 NRQLYAQELDGFFAERILVKANSLVKV 133
                                   ***********************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                                   S.......S-SSSBSEEEECGG CS
                         ADH_N  90 s.......ldGgfaeyvvvpek 104
                                   +       + G f++yvvv +k
  gi|70606890|ref|YP_255760.1| 195 TseeskakIVGKFSDYVVVGNK 216
                                   2333334488888888888655 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.7   2.1e-23   3.8e-20       1     126 [.     175     295 ..     175     299 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.1e-23
                                   HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkp 81 
                                   gvG++a+q+AkalGa+v++v s e+k++++ k+  d+v+   + ++ e++++ +g   + +v++ vG g tl++++++lk 
  gi|70606890|ref|YP_255760.1| 175 GVGIHALQVAKALGAKVVGVTSEESKAKIVGKFS-DYVVVG-N-KFAEEVRKGFG--EPSIVVDNVG-GPTLDESMRSLKI 249
                                   9********************************7.666666.4.7*********4..9*********.************* PP

                                   EEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHH CS
                    ADH_zinc_N  82 gGrlvvvGg..gkgeeefdlrnlllkeksilGsllgslreefkeald 126
                                   gG++v vG   ++ + +++l++l+lk++ ++G  +++ ++++ + l+
  gi|70606890|ref|YP_255760.1| 250 GGKIVQVGNidPSVNFSLRLGYLVLKNVELIGHAGAT-KKDIVDTLE 295
                                   ********987777777******************99.777666655 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.4   1.7e+04      47      55 ..     164     172 ..     143     201 .. 0.51
   2 !   38.7   0.0     1e-12   1.9e-09       8     133 .]     214     333 ..     208     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.4
                                   EEEEE---- CS
                  ADH_zinc_N_2  47 Grlvsiggp 55 
                                   G++v ++g 
  gi|70606890|ref|YP_255760.1| 164 GDIVLVTGA 172
                                   444333322 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1e-12
                                   ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-... CS
                  ADH_zinc_N_2   8 dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkas... 84 
                                    ++ +e++++   ge  ++v+d+vgg++l ++s++ l+ gG++v++g+    +     +++ +   +k + l         
  gi|70606890|ref|YP_255760.1| 214 GNKfAEEVRKG-FGE-PSIVVDNVGGPTL-DESMRSLKIGGKIVQVGNI---DPSVNFSLRLGYLVLKNVEL-----Igha 283
                                   45556666433.354.89**********9.*******888*******61...11222222223333333333.....1224 PP

                                   ...-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                  ADH_zinc_N_2  85 ..aqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                      ++d + + ++++ ++k++pv++ + ++e+  +A++ l+ ++  GKi +
  gi|70606890|ref|YP_255760.1| 284 gaTKKD-IVDTLEMVRQNKITPVIGGEVSIEDFDKALDMLKDRKRHGKILI 333
                                   444677.*****************************************975 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.1   8.3e-06     0.015      31      89 ..     167     225 ..     149     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.3e-06
                                   EEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHH CS
                   AlaDh_PNT_C  31 vlviGg.GvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeav 89 
                                   vlv G+ G +G++A+++ak+lgakV+ +  ++++++ + ++    v v ++ +e++++  
  gi|70606890|ref|YP_255760.1| 167 VLVTGAgGGVGIHALQVAKALGAKVVGVTSEESKAKIVGKFSDY-VVVGNKFAEEVRKGF 225
                                   6788862579*******************999999999998888.666666666666555 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.0   9.3e-06     0.017      31      82 ..     163     214 ..     159     254 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.3e-06
                    LDcluster4  31 kegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyT 82 
                                   + ++vl+tG+ +Gv   a + ak  g  +vG++ ++s+ + + k+ d++++ 
  gi|70606890|ref|YP_255760.1| 163 QGDIVLVTGAGGGVGIHALQVAKALGAKVVGVTSEESKAKIVGKFSDYVVVG 214
                                   5579********************************9999999988888765 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.8e-05     0.033      96     138 .]     156     196 ..     119     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                                   HHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                         SIS_2  96 lrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                   l+++++k+gD+ lv  ++G   v ++a++ ak++g+kv+++ts
  gi|70606890|ref|YP_255760.1| 156 LKRANVKQGDIVLVTGAGGG--VGIHALQVAKALGAKVVGVTS 196
                                   4567899*******999995..88******************8 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   6.4e-05      0.11       1      36 [.     167     202 ..     167     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTT CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasn 36 
                                   +lVtGa G +G + ++  ++ g +v+g+++++s+ +
  gi|70606890|ref|YP_255760.1| 167 VLVTGAGGGVGIHALQVAKALGAKVVGVTSEESKAK 202
                                   79****************************977655 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.9e-05      0.16      54      86 ..     149     181 ..     121     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.9e-05
                                   HHHHHHHHHTTSS-TT-EEEEEEEETTTEEEEE CS
                 ACP_syn_III_C  54 plaLdeaveegklkpgdlvllvgfGaGltwgaa 86 
                                     ++ + +++ ++k+gd vl++g+G+G+ + a+
  gi|70606890|ref|YP_255760.1| 149 AAMIYRGLKRANVKQGDIVLVTGAGGGVGIHAL 181
                                   556777889999***************999886 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7   0.00013      0.23       2      38 ..     166     202 ..     165     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekle 38 
                                   +vlvtGa++G+G    +   + Gakvv v ++e+k++
  gi|70606890|ref|YP_255760.1| 166 IVLVTGAGGGVGIHALQVAKALGAKVVGVTSEESKAK 202
                                   79**************************999998874 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   9.7e-05      0.17      54     101 ..     155     204 ..     149     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.7e-05
                                   HHTTTT--TT-EEEEES-TTS..HHHHHHHHHH--EEEEEES-HHHHHHH CS
                          CMAS  54 ileklelkpGmtlLdiGcGWG..slvrraverydvkvvglTlSkeqakla 101
                                    l+++++k+G+ +L  G+G G    + + ++  ++kvvg+T  + +ak +
  gi|70606890|ref|YP_255760.1| 155 GLKRANVKQGDIVLVTGAGGGvgIHALQVAKALGAKVVGVTSEESKAKIV 204
                                   57899*********988876511566789999*********777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2217.33
//
Query:       gi|70606891|ref|YP_255761.1|  [L=305]
Description: acetyl esterase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-67  225.8   0.0    6.2e-67  225.5   0.0    1.1  1  Abhydrolase_3    alpha/beta hydrolase fold
    3.6e-09   36.0   0.5    1.2e-08   34.4   0.4    1.6  1  COesterase       Carboxylesterase family
      3e-06   26.4   0.0      4e-06   25.9   0.0    1.1  1  Say1_Mug180      Steryl acetyl hydrolase
    1.8e-05   23.8   0.0    2.7e-05   23.2   0.0    1.2  1  Chlorophyllase2  Chlorophyllase enzyme
     0.0063   15.6   0.0     0.0086   15.1   0.0    1.2  1  Chlorophyllase   Chlorophyllase


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.0   1.7e-70   6.2e-67       1     210 [.      74     277 ..      74     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 1.7e-70
                                   EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHH CS
                 Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaGdSaG 81 
                                   lvy+HGGGfv+g+++++d++cr +++++++vv s+dYrlAPe++fP av d+++a++w+ e+a++l+  ++ ++++GdSaG
  gi|70606891|ref|YP_255761.1|  74 LVYLHGGGFVIGDIESYDPVCRAITNACNCVVASIDYRLAPENKFPSAVVDSVDATKWIYENAESLEG-KQGVAVGGDSAG 153
                                   79************************************************************877665.567********* PP

                                   HHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS.GGGGGSTTTSGGGCS CS
                 Abhydrolase_3  82 GnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp.eadrddplaspllae 161
                                   Gnl+a+v++  + +  +++++qvliyP+t + + +s s+    e++dg++ltr+++++f ++yl    d+ d  +sp+l++
  gi|70606891|ref|YP_255761.1| 154 GNLSAVVSILTKGK--INLKHQVLIYPATGA-DYTSRSM---VEYYDGYFLTREQIEWFGSQYLRsYMDLLDIKFSPILNQ 228
                                   ********999986..9**********9988.8889999...799*******************669************** PP

                                   -SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                 Abhydrolase_3 162 dlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                   dl+glpp+l+++ae+Dplrd+geaya++l  ag +v+ +++++++Hgf+
  gi|70606891|ref|YP_255761.1| 229 DLTGLPPALIITAEYDPLRDQGEAYANKLLMAGIPVTSVRFNNVIHGFV 277
                                   ************************************************7 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.4   3.3e-12   1.2e-08      92     208 ..      62     166 ..      48     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.3e-12
                                   EEEESSSSSTTSSEEEEEEE--STTTS-BGCGS-T..HHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHH CS
                    COesterase  92 vytPkekkeakkklPVlVwihGggfqtgsaseydg..saLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlAL 170
                                   vy Pk    +k  + +lV++hGggf++g+ ++yd+  +a+++  n++v +i YRl +       ++++p   +++D v A 
  gi|70606891|ref|YP_255761.1|  62 VYYPK----TKGPYGILVYLHGGGFVIGDIESYDPvcRAITNACNCVVASIDYRLAP-------ENKFP--SAVVDSVDAT 129
                                   67774....345669*****************997336888888***********97.......33444..589******* PP

                                   HHHHHHGGGGTEEEEEEEEEEETHHHHHHHHHHHSGGG CS
                    COesterase 171 rWVkenIasFGGdpervtlfGesAGaasvsllllspls 208
                                   +W+ en +s  G ++ v + G+sAG+ + ++ ++ +  
  gi|70606891|ref|YP_255761.1| 130 KWIYENAESLEG-KQGVAVGGDSAGGNLSAVVSILTKG 166
                                   ************.588*********9876666555444 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.1e-09     4e-06     123     235 ..      72     180 ..      53     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
                   Say1_Mug180 123 pvllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvlesla....vydylvkskgfknvvv 199
                                    +l+ylHGGgf+++ i     +   + ++ + + +   DY +       +k+p  v +s+     +y+  +  +g + v v
  gi|70606891|ref|YP_255761.1|  72 GILVYLHGGGFVIGDIESYDPVCRAITNACNCV-VASIDYRLAP----ENKFPSAVVDSVDatkwIYENAESLEGKQGVAV 147
                                   59************9999999999999988744.4456***998....6778888777775344499999999******** PP

                   Say1_Mug180 200 lGdSaGGnl..vLslllklsklnkvvlPkkaiaiSPWl 235
                                    GdSaGGnl  v+s+l k    +k +  k+ ++i P  
  gi|70606891|ref|YP_255761.1| 148 GGDSAGGNLsaVVSILTK----GK-INLKHQVLIYPAT 180
                                   ********6336666655....33.3334445555544 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.6e-09   2.7e-05       5     131 ..      59     183 ..      55     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.6e-09
               Chlorophyllase2   5 pllvvaPteageYpvllflhGyl..l.lnslYsqlLkhiashgfivvapqlykvaeada..keiksaakvlnWlakgLesv 80 
                                   p  v++P+++g Y +l++lhG    +   + Y  + ++i+     vva   y++a ++   + +      ++W+ ++ e  
  gi|70606891|ref|YP_255761.1|  59 PARVYYPKTKGPYGILVYLHGGGfvIgDIESYDPVCRAITNACNCVVASIDYRLAPENKfpSAVVDSVDATKWIYENAE-- 137
                                   6679****************86542425689******************999976665558899999999****99976.. PP

               Chlorophyllase2  81 lpeevepdlsklalsgHSrGgktafal.algkaktslkfsaligvdPvagas 131
                                      ++e   + +a+ g S+Gg+ ++ + +l k k  ++++  + + P +ga+
  gi|70606891|ref|YP_255761.1| 138 ---SLEG-KQGVAVGGDSAGGNLSAVVsILTKGK--INLKHQVLIYPATGAD 183
                                   ...4444.4689**********877662455555..5556666666877755 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-06    0.0086      19     158 ..      41     181 ..      24     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                Chlorophyllase  19 itvdsssrsspapPk...pliivtPaeaGtypvvlflhG..tll.snkfyskllnhiashGfivvaPqlykllp....Psa 89 
                                   + v + +  + +  +   p ++  P+ +G y ++++lhG  +++   ++y  +   i+     vva   y+l+p    P  
  gi|70606891|ref|YP_255761.1|  41 MDVGNIEDIKIPGTEtmiPARVYYPKTKGPYGILVYLHGggFVIgDIESYDPVCRAITNACNCVVASIDYRLAPenkfP-- 119
                                   444444444444444111667999**************74445524589*************************63333.. PP

                Chlorophyllase  90 qdeidsaaevieWlseglkavlptsveanlsklalvGhsrGGktafalalgysseltfsaliGvdPvaG 158
                                      + ++ +  +W+ e+ +       e+  + +a+ G s GG+ +  +++    ++++   + + P  G
  gi|70606891|ref|YP_255761.1| 120 -SAVVDSVDATKWIYENAES-----LEG-KQGVAVGGDSAGGNLSAVVSILTKGKINLKHQVLIYPATG 181
                                   .4566666777888776543.....333.3567888888888877777765555555555555556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1633.07
//
Query:       gi|70606892|ref|YP_255762.1|  [L=498]
Description: glycerol kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-80  270.7   0.0    1.7e-80  270.2   0.0    1.3  1  FGGY_N         FGGY family of carbohydrate kinases, N-termina
    1.5e-57  194.5   0.0    2.7e-57  193.7   0.0    1.4  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
    0.00048   19.7   0.5       0.19   11.2   0.0    2.2  2  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.23   11.1   0.1         14    5.2   0.0    2.4  2  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.2   0.0   3.7e-84   1.7e-80       1     245 []       4     246 ..       4     246 .. 0.98

  Alignments for each domain:
  == domain 1  score: 270.2 bits;  conditional E-value: 3.7e-84
                                   EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                        FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                   +il++D Gtts +a+v+de+ +v++ aq+el++++p++g++eq+peei++++ + i+k++e+a+i+ +q++aIgi++qre+
  gi|70606892|ref|YP_255762.1|   4 YILAVDEGTTSARALVFDEDLNVISIAQTELTQYFPRPGYVEQNPEEIFEKQVSMIKKAVEKAKIEISQVSAIGIANQRET 84 
                                   89******************************************************************************* PP

                                   EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC....EEEEHH CS
                        FGGY_N  82 lvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie....kfllid 157
                                   ++++D +  +p+yna++w+drrt+ i + lk  ++ + +++ktgl+ +++f++sk+kW+++n+p+v+ek+e    kf+++d
  gi|70606892|ref|YP_255762.1|  85 TIMWDSRSgRPVYNAVVWQDRRTSDITDWLKS-NYLNLFKSKTGLIPDPYFSASKIKWILDNVPGVREKAErgeiKFGTVD 164
                                   ******999*****************998888.8999******************************************** PP

                                   HHHHHHHCT..--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEE CS
                        FGGY_N 158 dyLiwrLtg..qfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpvvggg 236
                                   +yLiw+Lt+  ++vtd++nas++mlfnikklewd+ +l+il ipe++LP++++sse++g+     a+ +G   ++p++g +
  gi|70606892|ref|YP_255762.1| 165 TYLIWKLTNgkVHVTDYSNASRTMLFNIKKLEWDRDILEILEIPEAILPEVRSSSEVYGY-----AEPVG---NIPISGDA 237
                                   ********999************************************************8.....66789...9******* PP

                                   EHHHHHHHH CS
                        FGGY_N 237 gDqqaaalG 245
                                   gDqqaa++G
  gi|70606892|ref|YP_255762.1| 238 GDQQAALFG 246
                                   ********9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   0.0   6.1e-61   2.7e-57       2     197 ..     256     444 ..     255     445 .. 0.95

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 6.1e-61
                        FGGY_C   2 kvslGTssflllvgtkpvisehglltpva.gedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaae 81 
                                   k+++GT+sf+l+++ + + + + llt++a    +   yalegsi+ +g++v+w++d lgl   +++++e+ esla     +
  gi|70606892|ref|YP_255762.1| 256 KCTYGTGSFILMNSGEEIYDSKDLLTTIAwKIGKDVKYALEGSIFTTGAAVQWVRDGLGL---VSSSDEI-ESLA-----S 327
                                   8***********7777776888888888844446789***********************...******9.****.....9 PP

                        FGGY_C  82 avadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkp.ldrlavdGGgsk 161
                                   +v+d+ggv+fvpafsgl +pywdp arg i+g+s++t+ +hiarA+le++a+q+r+++e ++kd gk+ ++ l vdGG sk
  gi|70606892|ref|YP_255762.1| 328 SVVDNGGVYFVPAFSGLGSPYWDPYARGLIIGISRGTSRGHIARAVLESIAYQVRDVIEVIKKDVGKEfVNVLKVDGGVSK 408
                                   ****************************************************************99999************ PP

                        FGGY_C 162 ndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                   n+llmq++Adilg+ ++rp+  e+t +Ga +lA++a
  gi|70606892|ref|YP_255762.1| 409 NNLLMQFQADILGIRIVRPRVIETTSMGASMLAGLA 444
                                   **********************************98 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   4.3e-05      0.19       3      53 ..       8      68 ..       6     100 .. 0.74
   2 !    6.7   0.2     0.001       4.5     186     267 .]     365     441 ..     359     441 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                                  EEE-SSEEEEEEEETTTEEEEEEEE--..........TTS-HHH.........HHHHHHHH CS
                   BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns..........anlesvrfeaaekvleealteale 53
                                  +D G+T+ +a ++de+ +v+  ++t            +++ ++ fe+ ++ +++a+++a  
  gi|70606892|ref|YP_255762.1|  8 VDEGTTSARALVFDEDLNVISIAQTELtqyfprpgyvEQNPEEIFEKQVSMIKKAVEKAKI 68
                                  8************************995566666555444445555555555555555543 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.001
                                   HTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.....EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHH CS
                   BcrAD_BadFG 186 sggekaedIlaglhraialrvialisrsggvtde....vtltGGvakneaavkelrklvkenygevkininpdsiytgalG 262
                                   s+g +a+++l+ ++ ++ + ++ + + +g    e    + + GGv+kn+ +++        ++++    + p  i t  +G
  gi|70606892|ref|YP_255762.1| 365 SRGHIARAVLESIAYQVRDVIEVIKKDVGK---EfvnvLKVDGGVSKNNLLMQFQ-----ADILGIR-IVRPRVIETTSMG 436
                                   455556666666666665555555555554...344467799******5555555.....5555543.2447777788888 PP

                                   HHHHH CS
                   BcrAD_BadFG 263 AalfA 267
                                   A+++A
  gi|70606892|ref|YP_255762.1| 437 ASMLA 441
                                   88876 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.014        61      34      58 ..      56      80 ..      51      81 .. 0.89
   2 ?    5.2   0.0    0.0032        14     195     258 ..     368     428 ..     301     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.014
                                  HHHHHHHHHHHTSTGGGEEEEEEEE CS
                 Peptidase_M22 34 lplieealaeaglsledldaIavtk 58
                                  +++i++a ++a++++++++aI +++
  gi|70606892|ref|YP_255762.1| 56 VSMIKKAVEKAKIEISQVSAIGIAN 80
                                  689******************9875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0032
                                   T.....HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHH.TTSEEEXXX CS
                 Peptidase_M22 195 e.....vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaee.lglkliiPp 258
                                          e++a+++ +     ++e+ ++ + ++ ++ l + GGv++n++L +     +++ lg+++++P+
  gi|70606892|ref|YP_255762.1| 368 HiaravLESIAYQVRD-----VIEVIKKDVGKEFVNVLKVDGGVSKNNLLMQ----FQADiLGIRIVRPR 428
                                   0444456777888777.....4666777778899***************876....23344677777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.38s 00:00:01.10 Elapsed: 00:00:00.57
# Mc/sec: 2610.75
//
Query:       gi|70606893|ref|YP_255763.1|  [L=428]
Description: glycerol-3-phosphate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-50  171.1   0.0    5.5e-50  170.9   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    1.3e-06   27.8   0.2      9e-05   21.7   0.1    2.1  2  FAD_binding_2   FAD binding domain
    1.8e-05   24.2   0.3    7.4e-05   22.2   0.5    1.8  2  FAD_binding_3   FAD binding domain
    3.3e-05   24.0   1.0    7.9e-05   22.8   0.5    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.6e-05   21.7   0.3    0.00026   20.3   0.1    1.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0001   21.2   1.5    0.00013   20.9   0.2    1.8  2  HI0933_like     HI0933-like protein
    0.00071   20.1   2.2     0.0085   16.6   0.5    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0057   16.0   1.4      0.033   13.6   1.4    2.0  1  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.015   14.6   0.8      0.028   13.7   0.2    1.7  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.02   14.5   0.1      0.038   13.6   0.1    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.056   13.9   0.1        1.7    9.2   0.1    2.7  2  NAD_binding_7   Putative NAD(P)-binding
       0.07   12.2   0.2        0.1   11.6   0.2    1.2  1  Lycopene_cycl   Lycopene cyclase protein
      0.088   11.9   1.4       0.15   11.2   0.6    1.7  2  GIDA            Glucose inhibited division protein A
        0.1   11.8   0.1       0.25   10.6   0.1    1.6  1  Thi4            Thi4 family
       0.33    9.7   0.5       0.56    9.0   0.5    1.3  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   4.6e-53   5.5e-50       2     352 .]       7     361 ..       6     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 4.6e-53
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTTS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgidid 80 
                                   v++iGGG +Gl+tA++L+ rg  Vtl+e+gdia+ g+Sg+  gllhsg ry+ +     + ++e+ +e + l++  ++++ 
  gi|70606893|ref|YP_255763.1|   7 VIVIGGGATGLFTALDLSLRGinVTLVERGDIAS-GTSGKFHGLLHSGARYAVNDP---ESAKECKQENEVLSKI-APEF- 81 
                                   9*****************************6655.**************9888863...5566777777777776.6655. PP

                                   EEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT CS
                           DAO  81 yrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaalaraaealG 160
                                   +r tG ++++ +e++ +++++ l +l+++g+ ++++d ee+ ++ep   ++ + a+++pd  +v  + l+a +a +a  +G
  gi|70606893|ref|YP_255763.1|  82 VRDTGGVFVGITEDDVNYSQRFLSALNSLGITNKVMDVEELIRREPFiNKKSKIAIWVPD-KVVYGYDLLATVALTASLNG 161
                                   6889999998888889***9*9999999***99*************9755999*******.******************** PP

                                   -EEEESECEEEEEEEETCEEEEE...EECT.EEEE..EEEEEEE--GGGHHHH.HTT..CTTTSEEEEEEEEEEEEEECCT CS
                           DAO 161 veilegtevtgleeedgkvwgve...rttp.gend..aadavVnaaGawsdll.gll..keldlpispvrgqvlvlkplse 232
                                   ++il++ ev+++ +e++ v +ve   +    ge++    d +Vn+aG+w+  + +++  +e+  p+ p+ g ++v+k++ +
  gi|70606893|ref|YP_255763.1| 162 AKILTYNEVKRVLREGNSVRRVEvkdN--IsGETKilNGDIIVNTAGPWAFRViEMAglGEI--PLLPTAGIMVVMKEKLN 238
                                   ***********9788889999987431..335543344477********9855677765655..************55444 PP

                                   HSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCGEE..EEEEEEEE CS
                           DAO 233 klvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgdvl..rkwaGlrp 311
                                   ++v ++        + +++g +++p+  ++ ++G+ta+   ++d++e+++edi+ l+e+ + ++P+l++v+  r++a +rp
  gi|70606893|ref|YP_255763.1| 239 SMVINR-------LRPPSDGDIIVPYG-DSSIIGTTATIIPDPDNFEISDEDINMLIEEGAYMIPRLKEVKpeRAYASVRP 311
                                   444443.......8999*********6.779******98889999*********************98877548******* PP

                                   ...E.TTS.....SEEEEEEE...TEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                           DAO 312 ...l.pdg.....lpligetp...gvkglylatGhsghGltlapatGkllael 352
                                      +  dg     +++i  ++     +gl+ + G     +t++ ++G+ ++++
  gi|70606893|ref|YP_255763.1| 312 likNaEDGrgatrDFMIIDHEkvdSLDGLISVIGG---KFTTSRLAGEKVSDM 361
                                   65424466888895555553445556688888776...999999999988875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   7.5e-08     9e-05       2      39 ..       7      44 ..       6      74 .. 0.88
   2 ?    4.3   0.0     0.015        17     135     201 ..     141     206 ..      84     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.5e-08
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  viViG+G+ GL  Al ++ +G +v++ve ++  +g++ 
  gi|70606893|ref|YP_255763.1|  7 VIVIGGGATGLFTALDLSLRGINVTLVERGDIASGTSG 44
                                  9*****************************99888775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                                   ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE---- CS
                 FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgG 201
                                   +++v g  lla+++ +a  +g ++++  e++++++e++ v+ ++v++  sg+ ++i +  +++ t G
  gi|70606893|ref|YP_255763.1| 141 DKVVYGYDLLATVALTASLNGAKILTYNEVKRVLREGNSVRRVEVKDNISGE-TKILNGDIIVNTAG 206
                                   457788999999999999999*************************665555.66777777777766 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   6.2e-08   7.4e-05       3      37 ..       6      40 ..       4      51 .. 0.87
   2 ?   -1.1   0.0      0.72   8.6e+02     116     151 ..     158     194 ..      98     246 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.2e-08
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSC CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttv 37
                                  +V+++G+G +Gl +al Ls +G++v+lve+ + ++
  gi|70606893|ref|YP_255763.1|  6 SVIVIGGGATGLFTALDLSLRGINVTLVERGDIAS 40
                                  79***************************976655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.72
                                   HHHTEEETCSEEEECCEECCCCCC.CEEEECCTTEEE CS
                 FAD_binding_3 116 eerglqvrfktevesleqdeegvt.aevrdketgeee 151
                                   +  g+++   +ev+ +++++++v+  ev+d+ +ge++
  gi|70606893|ref|YP_255763.1| 158 SLNGAKILTYNEVKRVLREGNSVRrVEVKDNISGETK 194
                                   4444555555555555555555431344444444444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.5   6.6e-08   7.9e-05       1      35 [.       9      43 ..       9      63 .. 0.89
   2 ?   -2.9   0.0       7.2   8.6e+03      31      43 ..     344     356 ..     342     363 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 6.6e-08
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                  ++G+G++Gl +A  L+ +g++v+l+e++d  +G +
  gi|70606893|ref|YP_255763.1|  9 VIGGGATGLFTALDLSLRGINVTLVERGDIASGTS 43
                                  8*****************************99965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.2
                                   SSGGG-EECETTC CS
                 NAD_binding_8  31 lGGraasyevpgv 43 
                                   +GG+ ++ ++ g 
  gi|70606893|ref|YP_255763.1| 344 IGGKFTTSRLAGE 356
                                   8999999998664 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.2e-07   0.00026       2      60 ..       6      74 ..       5     102 .. 0.76
   2 ?   -2.7   0.0       2.2   2.7e+03     196     232 ..     160     202 ..     145     209 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH......HHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias......evv 60
                                  +v+viGgG+ Gl +al+l+  g++vtlve    + gt   ++ ll++ ++ +  d+e a+      ev+
  gi|70606893|ref|YP_255763.1|  6 SVIVIGGGATGLFTALDLSLRGINVTLVErgdiASGTSGKFHGLLHSGARYAVNDPESAKeckqenEVL 74
                                  799999999999999999999999999987778777777777778888888888887777665554333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                                   TTEEEEESCEEEEEEETTEEEE.EEETTSCE.....EEESEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.....xxxxxxx RF
                   Pyr_redox_2 196 eGvevklgtsvkeidgngekle.vvledgee.....idadlvv 232
                                   +G ++ + ++vk++ ++g++++ v+ +d+ +     ++ d +v
  gi|70606893|ref|YP_255763.1| 160 NGAKILTYNEVKRVLREGNSVRrVEVKDNISgetkiLNGDIIV 202
                                   4666666667777766666333333333222223335555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   1.1e-07   0.00013       2      33 ..       6      37 ..       5      42 .. 0.93
   2 ?   -2.5   0.1       1.3   1.6e+03     251     373 ..     361     391 ..     356     399 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                  +viviGgGa Gl++A+ ++ rg +V+l+e+++
  gi|70606893|ref|YP_255763.1|  6 SVIVIGGGATGLFTALDLSLRGINVTLVERGD 37
                                  69***************************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                                   T-.......-TT--EEEECSTTS-...HHHHHHHHHHHTTTSBHHHHHTTTS-HHHHHHHHHC..TTT-TTBGGG--HHHH CS
                   HI0933_like 251 yvakale.kkeeetleidllPdldaeelkaalekekekeskkslknalaellpkrlvevlleealieeedkklaqlskkel 330
                                   +v+++l  +++++t +i+l+ +ld                                                         
  gi|70606893|ref|YP_255763.1| 361 MVSEKLGiREKSKTATIKLMSELD--------------------------------------------------------- 384
                                   555555545555555555555555......................................................... PP

                                   HHHHHHHHSEEE--SEE--TTT-SEEEEEE-GGGB-TTT-BBT CS
                   HI0933_like 331 kklaealkaltvkvngteglrkaevTaGGVdlkevssktmesk 373
                                                                       +k +e k
  gi|70606893|ref|YP_255763.1| 385 ------------------------------------EKLLEKK 391
                                   ....................................4444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   7.1e-06    0.0085       1      32 [.       6      37 ..       6      42 .. 0.95
   2 ?    1.8   0.0      0.31   3.7e+02      52      80 ..     159     187 ..     143     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.1e-06
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                  +v+v+GgG +gl  A  l+  g +Vt+ver+d
  gi|70606893|ref|YP_255763.1|  6 SVIVIGGGATGLFTALDLSLRGINVTLVERGD 37
                                  699***************************98 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                                   HTTEEEECSEEEEEEEEETTSEEEEEEET CS
                     Pyr_redox  52 kngievllntkveeiegsedgvesvklkd 80 
                                    ng ++l+ ++v+++  +++ v++v++kd
  gi|70606893|ref|YP_255763.1| 159 LNGAKILTYNEVKRVLREGNSVRRVEVKD 187
                                   58999***********9999999999985 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.4   2.7e-05     0.033       2     139 ..       7     201 ..       6     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig.......nkaee......qvvtgiareflerlrq 69 
                                   v+V+GGg+ G+  A+    +G +v Lve+ +   G++ +  +    g       +++++      +v ++ia ef++    
  gi|70606893|ref|YP_255763.1|   7 VIVIGGGATGLFTALDLSLRGINVTLVERGDIASGTSGKFHGLLHSGaryavndPESAKeckqenEVLSKIAPEFVRDTGG 87 
                                   9***************************99887665544333333332222222332226667778888888888887755 PP

                  FAD_oxidored  70 ......rgga..rlkkrskwn.........................................tfepevakavleemlaeag 101
                                         +     ++++    +                                         ++  + +++v+      +g
  gi|70606893|ref|YP_255763.1|  88 vfvgitE--DdvNYSQ----RflsalnslgitnkvmdveelirrepfinkkskiaiwvpdkvVYGYDLLATVALTASL-NG 161
                                   4332211..1122222....1223344566666777777777777777555555555444443444444444333333.47 PP

                  FAD_oxidored 102 vtvllntrlvevekegkriesvtveske.g.rktirAkvf 139
                                    ++l+  ++++v +eg+ ++ v+v+++  g +k ++++++
  gi|70606893|ref|YP_255763.1| 162 AKILTYNEVKRVLREGNSVRRVEVKDNIsGeTKILNGDII 201
                                   7777777777777777777777777766665666666665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.4e-05     0.028       1      33 [.       8      39 ..       4      44 .. 0.89
   2 ?   -3.4   0.0       3.6   4.3e+03      77     112 ..     143     178 ..     123     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                  i+iG+G+ Gl +a+ l   g+ +++ +E+g i 
  gi|70606893|ref|YP_255763.1|  8 IVIGGGATGLFTALDLSLRGI-NVTLVERGDIA 39
                                  799999999999999999999.79999999875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                   Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfeeVesvkkede 112
                                    + + ++l  ++  a+ +  +i +++eV++v +e++
  gi|70606893|ref|YP_255763.1| 143 VVYGYDLLATVALTASLNGAKILTYNEVKRVLREGN 178
                                   555555555556666667777888888888877654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.2e-05     0.038       1      37 [.       7      42 ..       7      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealk 37
                                  + ++G Ga G + a  L+  g +vtl+ r++ +++  
  gi|70606893|ref|YP_255763.1|  7 VIVIGGGATGLFTALDLSLRGINVTLVERGD-IASGT 42
                                  579**************************99.55444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0014       1.7       7      95 ..       4     120 ..       2     125 .. 0.46
   2 ?   -2.9   0.0       8.1   9.7e+03      84     103 ..     237     256 ..     231     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                 NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele.........................elvklaeeelekd.... 58 
                                   + +v+v+GgG  ++  +  l   g +vt+v       +                          +           +    
  gi|70606893|ref|YP_255763.1|   4 NSSVIVIGGGATGLFTALDLSLRGINVTLVERGD---IAsgtsgkfhgllhsgaryavndpesaK-----------Eckqe 70 
                                   5678888888888888888888888888876652...1112333333333333222222222111...........11111 PP

                 NAD_binding_7  59 ...........legad..lviaatddrelneriaeaakarrilvnvadkp 95 
                                              + ++   +v ++ dd + ++r   a  + +i   v+d +
  gi|70606893|ref|YP_255763.1|  71 nevlskiapefVRDTGgvFVGITEDDVNYSQRFLSALNSLGITNKVMDVE 120
                                   11111111111222222234444455555566666666666666666655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.1
                 NAD_binding_7  84 arrilvnvadkpelcdfifp 103
                                    + +++n+   p+++d+i+p
  gi|70606893|ref|YP_255763.1| 237 LNSMVINRLRPPSDGDIIVP 256
                                   46788999999999999999 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   8.8e-05       0.1       2      34 ..       7      37 ..       6      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-05
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                  v+viG+G+ gl  A  l  +  g++v+l+e ++
  gi|70606893|ref|YP_255763.1|  7 VIVIGGGATGLFTALDL--SLRGINVTLVERGD 37
                                  8****************..**********9886 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.6   0.00012      0.15       2      28 ..       7      33 ..       6      58 .. 0.87
   2 ?   -1.9   0.0       1.1   1.4e+03     116     152 ..     168     209 ..     157     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                  EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                  viViGgG  G+  Al ++ +G++v+L+
  gi|70606893|ref|YP_255763.1|  7 VIVIGGGATGLFTALDLSLRGINVTLV 33
                                  9*************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                   S-EEEEEECTTEEEEEEETTS.....-EEEECEEEE--TT-B CS
                          GIDA 116 eeveeliveekkvkgvvtedg.....etikakavviatGtfl 152
                                   +ev++++ e ++v+ v  +d+     ++++ +++v ++G++ 
  gi|70606893|ref|YP_255763.1| 168 NEVKRVLREGNSVRRVEVKDNisgetKILNGDIIVNTAGPWA 209
                                   566666666666666555544111114556668888888854 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00021      0.25      17      55 ..       4      42 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES.SSS--T CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer.svspGG 55
                                  +s v+++G+G++GL +a  l+ + +++v+++er  ++ G 
  gi|70606893|ref|YP_255763.1|  4 NSSVIVIGGGATGLFTALDLSLR-GINVTLVERgDIASGT 42
                                  578********************.********93466654 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   0.00047      0.56       2      38 ..       7      40 ..       6      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00047
                                  EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS-- CS
                Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigt 38
                                  ++++GGG  G  +A  l+  +   ++vtlve  +i  
  gi|70606893|ref|YP_255763.1|  7 VIVIGGGATGLFTALDLSLRG---INVTLVERGDIAS 40
                                  89**************99888...9******999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 2275.81
//
Query:       gi|70606894|ref|YP_255764.1|  [L=146]
Description: hypothetical protein Saci_1119 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-34  118.4   0.3    2.1e-34  118.3   0.3    1.0  1  COXG      Carbon monoxide dehydrogenase subunit G (CoxG)
     0.0075   16.5   0.3      0.011   16.0   0.3    1.3  1  DUF3211   Protein of unknown function (DUF3211)
  ------ inclusion threshold ------
      0.058   13.5   0.1      0.082   13.0   0.1    1.3  1  Tox-PL-2  Papain fold toxin 2


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.3   3.4e-38   2.1e-34       1     137 [.       5     145 ..       5     146 .] 0.96

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 3.4e-38
                                   EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEE....EEEEEEEEEETTTEEE..EEEEE CS
                          COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsf....karvelselekensttieikGkG 77 
                                   G+f v++++e+v+e+L+dp+ +++c+PG++++e  g+++k+++k++v+ +++++    +a++++    ++n+  i+ikG+G
  gi|70606894|ref|YP_255764.1|   5 GKFLVEKSEEKVKELLTDPKMFSQCLPGIQNYEISGESFKAVFKIDVSEMRIPHittlTASINATITTESNNQ-IHIKGNG 84 
                                   89****************************************************9999999999988888876.******* PP

                                   E-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHH CS
                          COXG  78 rgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfeciss 137
                                   r+agv+i++++v+    ++g t ++w+a  ++g+l + lG+++i+++a+++++ +++c+s+
  gi|70606894|ref|YP_255764.1|  85 RSAGVSIKMDIVLDLGSEEGkTAVKWTAILDMGMLTKLLGESNIRQIAESNVKSIISCLSR 145
                                   *************99888889*************************************986 PP

>> DUF3211  Protein of unknown function (DUF3211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.8e-06     0.011       1      76 [.       1      74 [.       1     115 [. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                                  -EEEEEEE-SS-HHHHHHHHT-HHHHHHHHSTTEEEEEEECTTEEEEEEETTEEEEE.EEEEEEETTEEEEEEEETT CS
                       DUF3211  1 mkieieiktkheieavlkiLSDpkFvlpkllpaikivkveeksFevegefllveiei.kgtvyvsntevkyvfevsk 76
                                  m+++ ++  ++  e v ++L Dpk ++ + lp i+  +++++sF++  ++ + e+ i + t      +++  ++ ++
  gi|70606894|ref|YP_255764.1|  1 MEMSGKFLVEKSEEKVKELLTDPK-MFSQCLPGIQNYEISGESFKAVFKIDVSEMRIpHITTLTA--SINATITTES 74
                                  78888999999999**********.6899*****************9998888887723344433..3333333333 PP

>> Tox-PL-2  Papain fold toxin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05     0.082      44      98 ..      61     111 ..      33     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                      Tox-PL-2  44 ksaedaasfilserlekqaaisenGrHegveveidgleivFDnlhpeGvsredwl 98 
                                   + +   ++ i+ e+ ++   i  nGr  gv++    ++iv D  ++eG +  +w 
  gi|70606894|ref|YP_255764.1|  61 TLTASINATITTESNNQI-HIKGNGRSAGVSI---KMDIVLDLGSEEGKTAVKWT 111
                                   344445677888877776.4************...889**********9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 981.69
//
Query:       gi|70606895|ref|YP_255765.1|  [L=175]
Description: hypothetical protein Saci_1120 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-14   52.6   0.1    5.2e-14   51.8   0.1    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    6.2e-13   48.5   0.2    9.9e-13   47.9   0.2    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
      0.036   14.2   2.4       0.09   13.0   2.4    1.7  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
      0.037   14.0   0.0      0.061   13.4   0.0    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.055   13.5   0.5        0.6   10.2   0.1    2.1  2  CxC5           CxC5 like cysteine cluster associated with KDZ
      0.076   13.5   0.0       0.11   13.0   0.0    1.4  1  Hepsin-SRCR    Hepsin, SRCR domain
       0.08   12.6   0.1       0.11   12.1   0.1    1.2  1  TackOD1        Thaumarchaeal output domain 1
       0.17   11.7   0.1       0.35   10.8   0.1    1.5  1  TrpBP          Tryptophan RNA-binding attenuator protein


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   2.3e-17   5.2e-14       1      37 []      62      98 ..      62      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2.3e-17
                       DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                  +++++eg+L++++C +CGt +fPP+  Cp+C++++le
  gi|70606895|ref|YP_255765.1| 62 FEGLKEGKLLATKCQKCGTIYFPPQDDCPKCRVSNLE 98
                                  69********************************998 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.2   4.4e-16   9.9e-13       1      64 [.      99     159 ..      99     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.4e-16
                                   EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                 OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                   w+e++++G+v +ftvv+ +p++f+ +  yvvg+V+  +gv +++++ g     v++G +V++++
  gi|70606895|ref|YP_255765.1|  99 WIEMPKEGEVIAFTVVNVKPTSFSHYSDYVVGIVRISNGVNVLGWIKGNN---VKVGSKVKLEV 159
                                   99**********************************************98...99******986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.4     4e-05      0.09      12      39 ..      69      92 ..      65      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                 Auto_anti-p27 12 tMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                  ++La+ C++Cg++ +    + +  C+ C
  gi|70606895|ref|YP_255765.1| 69 KLLATKCQKCGTIYFPP--QDD--CPKC 92
                                  89**************4..346..9999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-05     0.061      68     100 ..      70     100 ..      41     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
                                   --EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                          HypA  68 pvkvrCreCgkefeleekalrCpkCgsadveiv 100
                                    + ++C++Cg+ +   ++   CpkC  +++e +
  gi|70606895|ref|YP_255765.1|  70 LLATKCQKCGTIYFPPQD--DCPKCRVSNLEWI 100
                                   56789*****99997755..7*****9998865 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00027       0.6      40      60 ..      64      84 ..      46      86 .. 0.85
   2 ?    3.5   0.0     0.032        72       7      44 ..      83     119 ..      83     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                          CxC5 40 gvlpvwvlslyCpkCktrYyp 60
                                  g  + ++l ++C+kC+t+Y p
  gi|70606895|ref|YP_255765.1| 64 GLKEGKLLATKCQKCGTIYFP 84
                                  56778999***********87 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.032
                          CxC5   7 yPptkkClnceckrrsllqkesqrdvvlftldkgvlpv 44 
                                   +Pp+++C++c+ ++ + ++ +++ +v+ ft+  +v p+
  gi|70606895|ref|YP_255765.1|  83 FPPQDDCPKCRVSNLEWIEMPKEGEVIAFTVV-NVKPT 119
                                   69**********99999999999999999988.66664 PP

>> Hepsin-SRCR  Hepsin, SRCR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.8e-05      0.11      68     106 ..      41      80 ..       9      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                   Hepsin-SRCR  68 ffcvdeeeleyakklaevlavceC.ekgkvlavlCqdcgr 106
                                   +  v+e +l+y   +++v++  e  ++gk+la++Cq cg+
  gi|70606895|ref|YP_255765.1|  41 WVGVREITLRYQFPVKKVSKFFEGlKEGKLLATKCQKCGT 80 
                                   556777788888888888887775268************8 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     5e-05      0.11      74      99 ..      73      98 ..      53     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                       TackOD1 74 rlCpsCksghlnvrevCpkCkSidie 99
                                    C++C +  +  ++ CpkC+ +++e
  gi|70606895|ref|YP_255765.1| 73 TKCQKCGTIYFPPQDDCPKCRVSNLE 98
                                  57*******************99987 PP

>> TrpBP  Tryptophan RNA-binding attenuator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00015      0.35       3      34 ..     125     157 ..     123     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                   --EEE.EEESSTTEEEEEEESSSS--EEEEEEE CS
                         TrpBP   3 edyiv.ikalenGvtviGltrGkdtkfhhtekL 34 
                                   +dy+v i   +nGv+v+G  +G++ k+    kL
  gi|70606895|ref|YP_255765.1| 125 SDYVVgIVRISNGVNVLGWIKGNNVKVGSKVKL 157
                                   6899878889**************998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1061.81
//
Query:       gi|70606896|ref|YP_255766.1|  [L=395]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-30  105.7   0.0    4.7e-30  104.8   0.0    1.5  1  Thiolase_N      Thiolase, N-terminal domain
    2.8e-08   33.4   0.1    2.7e-06   27.1   0.1    2.6  2  Thiolase_C      Thiolase, C-terminal domain
    1.6e-07   31.2   7.1    4.8e-07   29.6   1.0    2.8  3  ketoacyl-synt   Beta-ketoacyl synthase, N-terminal domain
      9e-06   25.5   0.2    0.00034   20.4   0.1    2.4  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
      0.026   13.6   0.0      0.052   12.6   0.0    1.4  1  DUF2048         Abhydrolase domain containing 18
      0.035   13.4   0.0      0.064   12.5   0.0    1.4  1  FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protei


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.0   1.6e-33   4.7e-30       1     260 []       4     223 ..       4     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.6e-33
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+iv++  +++g      +d+s++eL+ ea+k++le+a+++++++++ +vGnv    +++ +a  +    ++  +  +++v
  gi|70606896|ref|YP_255766.1|   4 VAIVGTGHSKFGV----RNDVSMQELAWEAVKQALEEANLEQKDIQYFVVGNVGMWSAEELPAVVVGEYCDL-TPKGTMRV 79 
                                   6788888888887....9******************************************************.99999*** PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGltae 160
                                   + +c+ g +a+ +a q+i+age+dv++++GvE+ms++p  +  +++  +g  + + +  +l+ p            +l a 
  gi|70606896|ref|YP_255766.1|  80 EAACATGSAAIRDAYQAIKAGEIDVALVVGVEQMSQSPNPQVIELIgrAGNYFWEFENFGLTFPG---------YYALYAS 151
                                   ***************************************99999883344555555555666666.........789**** PP

                                   HHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BT CS
                    Thiolase_N 161 nlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtA 241
                                    + +ky++  e++ ++Avk+h  +a ++ a+ F++ei              + +e+++s+ +a +L+ l            
  gi|70606896|ref|YP_255766.1| 152 AYMAKYGMKEEDLGSVAVKNHYYGARNPYAQ-FQKEI--------------TMEEYLKSKPVAQPLKLL------------ 205
                                   *******************************.*****..............89****************............ PP

                                   TSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 242 gnasqisDGaaavllmses 260
                                    ++s+i+DGaaa++l+se+
  gi|70606896|ref|YP_255766.1| 206 -DSSPITDGAAALILASEE 223
                                   .***************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.018        54      19      45 ..      21      47 ..       7      53 .. 0.81
   2 !   27.1   0.1   8.9e-10   2.7e-06      26     114 ..     261     371 ..     244     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                                  GGGGHHHHHHHHHHHHHT--GGGESEE CS
                    Thiolase_C 19 ilglgPayaikkvlkkagltvedidlf 45
                                   ++     a+k++l++a l+ +di++f
  gi|70606896|ref|YP_255766.1| 21 SMQELAWEAVKQALEEANLEQKDIQYF 47
                                  556666789***************998 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 8.9e-10
                                   HHHHHHHHHHT--GGG....ESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                    Thiolase_C  26 yaikkvlkkagltved....idlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                    a+k++ k+a ++ +d     d+ ++++ F+   +++ ++l++++                    vNv GG  a GHP+Ga
  gi|70606896|ref|YP_255766.1| 261 VAAKEAYKRAKIDFSDawryFDVADVHDCFTIAEIMAYEDLGFAKrgeghlmarngetyiggkIPVNVDGGLKAKGHPIGA 341
                                   467777888888777744446999********************99***************87789*************** PP

                                   HHHHHHHHHHHHHHHCTTSEEEEEEEETTT CS
                    Thiolase_C  85 sGaRivvtllselkkeggklgvaalCiggg 114
                                   +G+ ++v+++++l  + +k + a + +g g
  gi|70606896|ref|YP_255766.1| 342 TGVSMAVSITRQLLYRAHKGTQADIRNGMG 371
                                   ***********9998877766666666665 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.1    0.0096        29      88     116 ..      22      50 ..      13      75 .. 0.83
   2 !   29.6   1.0   1.6e-10   4.8e-07     169     206 ..      77     114 ..      74     128 .. 0.91
   3 ?   -3.2   0.0       1.7   5.1e+03     114     126 ..     341     353 ..     328     377 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0096
                                   HHHHHHHHHHHHHHHHTS-HHTCTTGGEE CS
                 ketoacyl-synt  88 qqrllleaawealedagltpeeldgsrvg 116
                                   +q l+ ea+++ale+a+l++++++   vg
  gi|70606896|ref|YP_255766.1|  22 MQELAWEAVKQALEEANLEQKDIQYFVVG 50 
                                   799***************99988655444 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.6e-10
                                   EEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE--- CS
                 ketoacyl-synt 169 vtvdtACsSslvavhaavqslrsgeadvalaGGvelll 206
                                   + v++AC+++ +a+  a+q++++ge+dval+ Gve + 
  gi|70606896|ref|YP_255766.1|  77 MRVEAACATGSAAIRDAYQAIKAGEIDVALVVGVEQMS 114
                                   679*******************************9875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                                   GEEEEEEESSTHH CS
                 ketoacyl-synt 114 rvgvfiGvgagdy 126
                                   ++gv ++v++  +
  gi|70606896|ref|YP_255766.1| 341 ATGVSMAVSITRQ 353
                                   3666666666643 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.2e-07   0.00034       3      43 ..      79     119 ..      77     126 .. 0.92
   2 ?    2.4   0.0     0.047   1.4e+02      53      65 ..     211     223 ..     208     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-07
                                   EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-T CS
                   ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDw 43 
                                   ++aaC++  +a+  A ++i++g++  +Lv+g e++s+  ++
  gi|70606896|ref|YP_255766.1|  79 VEAACATGSAAIRDAYQAIKAGEIDVALVVGVEQMSQSPNP 119
                                   689*********************************97665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.047
                                   -EEEEEEEEEEES CS
                   ACP_syn_III  53 GDGAgAvvlease 65 
                                    DGA+A++l  +e
  gi|70606896|ref|YP_255766.1| 211 TDGAAALILASEE 223
                                   5********9874 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.052     114     146 ..     154     187 ..     145     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                       DUF2048 114 lakpllke.nigsiilenpfYglrkPkeQvrssl 146
                                   +ak  +ke ++gs+ ++n +Yg+r+P  Q+++++
  gi|70606896|ref|YP_255766.1| 154 MAKYGMKEeDLGSVAVKNHYYGARNPYAQFQKEI 187
                                   677777887********************99887 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05     0.064      83     177 ..      22     115 ..      11     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                FAE1_CUT1_RppA  83 aeevlfgavdellaktkvspkdidilvv.ncslfsptPslsamvvnryklredvksynLsgmGCsAglisidlaknllqvh 162
                                   ++e+  +av++ l++++++ kdi+ +vv n++++s++  l a+vv  y   +   ++ + +  C+ g  +i  a + +++ 
  gi|70606896|ref|YP_255766.1|  22 MQELAWEAVKQALEEANLEQKDIQYFVVgNVGMWSAE-ELPAVVVGEYCDLTPKGTMRVEA-ACATGSAAIRDAYQAIKAG 100
                                   7788899*****************8877589998865.89********7666666666665.7****************** PP

                FAE1_CUT1_RppA 163 kntlalvvstEnitl 177
                                   +  +alvv +E++++
  gi|70606896|ref|YP_255766.1| 101 EIDVALVVGVEQMSQ 115
                                   *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2500.01
//
Query:       gi|70606897|ref|YP_255767.1|  [L=537]
Description: acyl-CoA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-91  305.2   0.0    6.8e-91  305.0   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    1.3e-18   67.8   0.0    2.1e-18   67.0   0.0    1.4  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.0   0.0   7.6e-95   6.8e-91       6     422 ..      21     436 ..      16     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: 305.0 bits;  conditional E-value: 7.6e-95
                                   HHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHH CS
                   AMP-binding   6 aktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeel 86 
                                   +++pdk  +++  + +++T++ + + v+rl  gL++lGvkkg+r+++l + +  ++ +++++   Gav+ ++n +++ + +
  gi|70606897|ref|YP_255767.1|  21 RTFPDKEIVYR--DIRRYTFSSFSNSVKRLVTGLKKLGVKKGERIGVLDWDTDVYFHTYYGVPLSGAVLHTINLRYPLDLI 99 
                                   789****9988..9******************************************************************* PP

                                   HHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS..-TSCCCS-BTTSEEEEE CS
                   AMP-binding  87 ayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae..kpeeeeelkpddlayii 165
                                      + ++e k+l+  v +e ++ +++a+   +   +vi +++++ + +++  +++ +e   e  +p+ee  +k++d+ +i+
  gi|70606897|ref|YP_255767.1| 100 VKTILHAEDKYLV--VRDEFVPLIEKAKNIIPPGMKVITYSDNKEKVKSPISNADFWELI-EsnEPTEEFDVKENDMSTIF 177
                                   *************..877777767666665555555555555555555555555544433.14556667799********* PP

                                   EE--SSSS-EEEEEEHHHHHHHHHHHH.HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                   AMP-binding 166 YTSGTTGkPKGVmlshrnlvanvaslk.letr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpk 243
                                   YTSGTTG+PKGV  +hr l   + s++   tr  f+l+++dv++  +p++h+ ++  + ++++l+G + vl+ +    d +
  gi|70606897|ref|YP_255767.1| 178 YTSGTTGEPKGVWFTHRKLFMHAMSVAlTGTRspFNLSPEDVYMILVPMFHVHQW-GFPFVTFLAGTKYVLPGRY---DYG 254
                                   *******************99999999744446899999****************.***************8744...568 PP

                                   HHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC CS
                   AMP-binding 244 lllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvv 324
                                   ++l+l+ek++vt+ a vP++l+ ll +++    k+ + +++++++ +gg++l++ l+r++r+l+++ v  gYGl+Et++v+
  gi|70606897|ref|YP_255767.1| 255 FILKLMEKEGVTYSAMVPTILHLLLTHPDAP--KYTHVFKKWKIT-IGGSALPEGLARKARELGIT-VTTGYGLSETCPVL 331
                                   99************************87666..456689999995.7****************998.************** PP

                                   EE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEE CS
                   AMP-binding 325 tv.........lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwl 396
                                   ++         l+ e++ + + s+G p+p v++++vD++tg+  ++ge Ge++vr+p+++k Y+k+pe+ta+ +   g+wl
  gi|70606897|ref|YP_255767.1| 332 SMgyynnvaqkLDAEKKFSLQISTGVPIPLVQIRVVDPDTGKDKKPGEIGEIVVRSPWLTKEYYKNPEKTAQLWR--GGWL 410
                                   7777789999977788889999**************************************************997..57** PP

                                   EEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 397 rTGDlgrldedGyleivgRkkdlikl 422
                                   +TGDl+++de Gyl+iv+R kd ik+
  gi|70606897|ref|YP_255767.1| 411 HTGDLAYIDEYGYLHIVDRDKDAIKS 436
                                   ************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   2.4e-22   2.1e-18       2      76 .]     446     523 ..     445     523 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.4e-22
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHH.....HHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahv.....rkelgpyavpkkvvfvdelpktrsGK 76 
                                   +E a++ hp+Va++aVvGv+d+++Ge++vaf+v k+ +  +e+eL++++       ++ +++ p+k++fvd lp+t + K
  gi|70606897|ref|YP_255767.1| 446 LEDAISLHPKVAQVAVVGVKDQKWGERPVAFIVAKEKV--TEDELRQFMlgltdQGRIQKWWIPDKFIFVDTLPLTSTNK 523
                                   699*******************************8554..68*******9888778********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3601.54
//
Query:       gi|70606898|ref|YP_255768.1|  [L=400]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-41  141.0   4.5    5.9e-41  140.2   4.5    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.5e-33  115.1   1.9    4.1e-33  114.4   0.3    2.2  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.1e-27   94.2   0.0      9e-27   93.1   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      1e-18   67.9   2.1    2.2e-18   66.8   2.1    1.6  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.072   13.0   0.0    1.5  1  CBM39          Carbohydrate binding domain (family 32)


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   4.5   1.7e-44   5.9e-41       1     147 [.     241     389 ..     241     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 1.7e-44
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   g Gf++am+t++ +R++va +alg+a++ale + +y+ +r afg pl+ +q v+ek+ae  +e+ aarl +y aa ++++g
  gi|70606898|ref|YP_255768.1| 241 GMGFKYAMSTFDASRVGVAGQALGVAQAALEKMTNYSVQRSAFGSPLLGFQMVQEKIAETLTEVNAARLVTYWAATLYNKG 321
                                   57******************************************************************************* PP

                                   ---..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpd..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                     +    ++smaK+fa+e+a+++a +a+ ++Gg+G++++++verl+rd+ ++ i+eG+++iq+++i +
  gi|70606898|ref|YP_255768.1| 322 MTNeaIIASSMAKYFATEVAERAAIRAITVHGGYGVATSTGVERLLRDVEIMKIYEGANDIQKLVILK 389
                                   9998999*********************************************************9987 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.3   1.1e-36   4.1e-33       1     113 []      16     127 ..      16     127 .. 0.95
   2 ?   -1.7   0.1       1.2   4.5e+03      11      24 ..     332     345 ..     322     397 .. 0.60

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.1e-36
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                   +e++e +r++vref+e+ +ap++++ ++eg++p+e+++k++elGl+g++vpeeygG+g+d l ++i+ ee+ar++a+l++ 
  gi|70606898|ref|YP_255768.1|  16 SEKHELFRRAVREFMERDVAPYVEKGEKEGQIPKEVLEKAKELGLYGVSVPEEYGGQGGDSLMTVIAQEEMARVWAALSTR 96 
                                   689**************************************************************************9997 PP

                                   HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasge 113
                                   ++v+ +l + +il fG+eeq+++y+ ++a+g+
  gi|70606898|ref|YP_255768.1|  97 VAVG-GLFMTPILLFGSEEQRKKYVTPVAKGD 127
                                   7786.566789******************996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHTHHHHH CS
                 Acyl-CoA_dh_N  11 vrefaeeelaphaa 24 
                                   +++++++e+a++aa
  gi|70606898|ref|YP_255768.1| 332 MAKYFATEVAERAA 345
                                   45555555554433 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   2.5e-30     9e-27       1      97 []     131     229 ..     131     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 2.5e-30
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---...----EEEEEEE..GGGEEE.-- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd...rarglslflvprdapgvsv.rr 77 
                                   afa TEpqaGsdva++++ +a++ +g+y+ln +Ki+itn++ia++++v art  p+   r +g+s+f+v+r ++gv+v +r
  gi|70606898|ref|YP_255768.1| 131 AFANTEPQAGSDVAGMQS-TAKKVNGKYILNARKIFITNGGIADYYVVTARTSPPEpnaRWKGISMFVVEREWKGVKVlNR 210
                                   799***************.7777777*************************6555567899*****************888 PP

                                   ---BSS-TTS-EEEEEEE.. CS
                 Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                   i e++Gl+  +t+el fedv
  gi|70606898|ref|YP_255768.1| 211 I-ETMGLKASNTAELAFEDV 229
                                   8.68**************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   2.1   6.2e-22   2.2e-18       2     133 ..     257     380 ..     256     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.2e-22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   g+a +alG+A+aal++++ +  +r+   +g +l  ++++q ++ae  ++++AAr++++ aa+      ++g  +t e    
  gi|70606898|ref|YP_255768.1| 257 GVAGQALGVAQAALEKMTNYSVQRSA--FGSPLLGFQMVQEKIAETLTEVNAARLVTYWAATL----YNKG--MTNEAIIA 329
                                   6899**********************..********************************999....4444..4458889* PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                   +++a+ +a+e a +a+ +++ ++Gg++++++  ++Rl+RD++++++++++n
  gi|70606898|ref|YP_255768.1| 330 SSMAKYFATEVAERAAIRAITVHGGYGVATSTGVERLLRDVEIMKIYEGAN 380
                                   ***********************************************9876 PP

>> CBM39  Carbohydrate binding domain (family 32)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.072      35      81 ..     134     179 ..     122     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                         CBM39  35 Nkefesleagqiacdv..ttevtyGkfiledeeavikkgDtlyywvivq 81 
                                   N e    +ag+ ++ +  t ++++Gk+il+ +++ i +g +  y+v++ 
  gi|70606898|ref|YP_255768.1| 134 NTEP---QAGSDVAGMqsTAKKVNGKYILNARKIFITNGGIADYYVVTA 179
                                   3333...4555555558899************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3012.04
//
Query:       gi|70606899|ref|YP_255769.1|  [L=119]
Description: hypothetical protein Saci_1124 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.2   0.3      0.024   15.1   0.3    1.7  1  CcdA      Post-segregation antitoxin CcdA
      0.017   15.2   0.5      0.025   14.7   0.5    1.4  1  DUF2540   Protein of unknown function (DUF2540)
      0.089   12.8   1.0       0.17   11.8   0.6    1.7  2  RHH_1     Ribbon-helix-helix protein, copG family
       0.21   11.6   4.1       0.14   12.1   1.8    1.9  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   5.3e-06     0.024       1      32 [.      34      69 ..      34      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
                          CcdA  1 KkavnlsldsdllaqAralgiN....lSatleeaLa 32
                                  K++v+ls+ds++l++A++l +     lS+++e+a +
  gi|70606899|ref|YP_255769.1| 34 KVKVKLSIDSEVLKKAKELAVErkvtLSEIFEKAVS 69
                                  789***************976422227777776654 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   5.5e-06     0.025      15      62 ..      30      75 ..      15      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                                  HHHHHGGG-----HHHHHHHHHS---EEEEEE--HHHHHHHHHHGGGH CS
                       DUF2540 15 YllHklenlenvdvetlkkakeaekktkktltLsdeEkkIvkklGkaa 62
                                  Y+  k++   ++d e lkkake+   +++ +tLs++ +k v+ lG ++
  gi|70606899|ref|YP_255769.1| 30 YVYIKVKVKLSIDSEVLKKAKEL--AVERKVTLSEIFEKAVSELGNLS 75
                                  55556776779*********986..57899**************9875 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   3.9e-05      0.17       2      35 ..      37      70 ..      36      71 .. 0.94
   2 ?   -3.3   0.0       2.3     1e+04      25      31 ..      77      83 ..      75      84 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                                  EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlre 35
                                  v +++d+e+l++  ela +r+++ Se+++ A+ e
  gi|70606899|ref|YP_255769.1| 37 VKLSIDSEVLKKAKELAVERKVTLSEIFEKAVSE 70
                                  6799***************************987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                  HHHHHHH CS
                         RHH_1 25 rSelIRe 31
                                  +  ++Re
  gi|70606899|ref|YP_255769.1| 77 VNKIMRE 83
                                  5678998 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   5.7e+03      25      32 ..      24      31 ..      23      31 .. 0.83
   2 ?   12.1   1.8   3.2e-05      0.14       2      39 ..      34      71 ..      33      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                         RHH_3 25 rIprSkll 32
                                  ++++S ++
  gi|70606899|ref|YP_255769.1| 24 KVNISTYV 31
                                  79999997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.2e-05
                         RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAiell 39
                                  k+++  sid e ++k k+L  + ++ +S++ ++A+++l
  gi|70606899|ref|YP_255769.1| 34 KVKVKLSIDSEVLKKAKELAVERKVTLSEIFEKAVSEL 71
                                  788899*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 794.97
//
Query:       gi|70606900|ref|YP_255770.1|  [L=158]
Description: peroxiredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-36  125.2   0.1    1.6e-36  124.9   0.1    1.1  1  AhpC-TSA    AhpC/TSA family
    2.1e-25   89.2   0.0    2.5e-25   88.9   0.0    1.0  1  Redoxin     Redoxin
  ------ inclusion threshold ------
      0.047   13.8   0.0        2.1    8.5   0.0    2.3  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
       0.11   12.5   0.0        0.2   11.5   0.0    1.4  1  SCO1-SenC   SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.1   3.6e-40   1.6e-36       1     124 []       4     133 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 3.6e-40
                                   TTSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                      AhpC-TSA   1 vgdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                   vg+kap++el ++d ++ +  +d+kgk+vvl fyp++++ vCt+e++ +++ + +f e+++ v+g+svd+p+s k+f+e++
  gi|70606900|ref|YP_255770.1|   4 VGEKAPEIELVDTDLKKWKIpTDFKGKVVVLAFYPGAFTSVCTKEMCTFRDSLSKFNELNAVVLGISVDPPFSNKAFKEQN 84 
                                   79***************9999************************************************************ PP

                                   H.SSEEEE-TTSHHHHHTT-EETT.....TTECSCEEEEE-TTSBEEEE CS
                      AhpC-TSA  81 slnfpllsDeegkvakaygvlkee.....kglalratfvidkegkirya 124
                                   ++nfpllsD ++ ++kayg+  e      + +  r++f+idk+g+iry+
  gi|70606900|ref|YP_255770.1|  85 KINFPLLSDFNRVAVKAYGIAGELpilkdYVISKRSVFIIDKDGVIRYK 133
                                   *********************999***********************95 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   5.7e-29   2.5e-25       2     145 ..       4     147 ..       3     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 5.7e-29
                                   TTSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefw 80 
                                   +g+kaP+++l  ++td ++ ++   fkgk+vv+ f+pgaf+ +C++e++ + + l+++ +e +  v+++++d     k+f 
  gi|70606900|ref|YP_255770.1|   4 VGEKAPEIEL--VDTDLKKWKIPTdFKGKVVVLAFYPGAFTSVCTKEMCtFRDSLSKF-NELNAVVLGISVDPPFSNKAFK 81 
                                   89*******8..55********999************************877788888.9999999888777766688888 PP

                                   HHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
                       Redoxin  81 gkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepeteesnaea 145
                                   ++++++fp+lsD +   +ka+G++ e +  +   +  +++++id+dg+++y+ v ++p   e+n+e+
  gi|70606900|ref|YP_255770.1|  82 EQNKINFPLLSDFNRVAVKAYGIAGELPILKDyvISKRSVFIIDKDGVIRYKWVSDNPGI-EPNYEE 147
                                   88**********************99999999*999999***************999954.777776 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00048       2.1       4      53 ..      54     104 ..      51     111 .. 0.85
   2 ?    3.4   0.0     0.017        78      95     111 ..     120     136 ..      99     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00048
                    AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalgl 53 
                                   ++++++++ +  + +i+++ p s k+F ++++++f+l+ D ++ + +a g 
  gi|70606900|ref|YP_255770.1|  54 DSLSKFNELNAVVLGISVDPPfSNKAFKEQNKINFPLLSDFNRVAVKAYGI 104
                                   5567888899999*************************9998877777665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.017
                    AhpC-TSA_2  95 Gtflfdkqgelvyehrd 111
                                    +f++dk+g ++y++  
  gi|70606900|ref|YP_255770.1| 120 SVFIIDKDGVIRYKWVS 136
                                   58************976 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.6e-05       0.2       6      67 ..      13      73 ..       9      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                     SCO1-SenC  6 lvdqdgeavt.eedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDP 67
                                  lvd+d ++ +  +d++gk++++ f     ++vC++++ + ++ l++++e   +  +l i+vDP
  gi|70606900|ref|YP_255770.1| 13 LVDTDLKKWKiPTDFKGKVVVLAFYPGAFTSVCTKEMCTFRDSLSKFNEL--NAVVLGISVDP 73
                                  56666555542589**********************************99..788999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1218.48
//
Query:       gi|70606901|ref|YP_255771.1|  [L=550]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-70  236.0   0.0    7.1e-70  235.7   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    2.7e-22   79.5   0.0    5.5e-22   78.5   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   7.9e-74   7.1e-70      16     422 ..      36     444 ..      22     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 7.9e-74
                                   E....CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHH CS
                   AMP-binding  16 d....sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayile 91 
                                   d    +g+ + lTY+   erv+++ + ++ +l +++gd ++il +n ++++ +++ + ++Gav+  ln +l +++l yil+
  gi|70606901|ref|YP_255771.1|  36 DrrslGGKIHNLTYGKILERVSSFTNSIEsELKINPGDIIGILGWNDHRYFESFFTVPSLGAVLLELNIRLHPADLLYILK 116
                                   34444567899******************99************************************************** PP

                                   HHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.....-TSCCCS-BTTSEEEEEEE CS
                   AMP-binding  92 dseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.....kpeeeeelkpddlayiiYT 167
                                    +++k l+  vd+ ll+ l+ea +k+   + +i+++++++++ ++   ++  +e+        +++ +e+++++ a+  +T
  gi|70606901|ref|YP_255771.1| 117 LTKPKGLL--VDDSLLP-LAEALSKEYNFDYTIIMSDKPFEEIKTNIRNAFGYEE-LvksgsPNRKFDEVDEKSSALAAFT 193
                                   ********..8887755.4444544444555555555555555444444433333.1456775557889************ PP

                                   --SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHH CS
                   AMP-binding 168 SGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllel 248
                                    GTTG PKGV +shr++v  + +++    ++lk +dv+l ++p++h+ g+    ++  + G++ +++   ++ d   ++e 
  gi|70606901|ref|YP_255771.1| 194 TGTTGLPKGVFYSHRSIVLHALNAS----RRLKISDVLLPVVPFFHVHGW-GTQFAGAITGCKQIFPG-RPTVD--SMVEH 266
                                   *****************99988863....345559***************.999999999****9966.44534..589** PP

                                   HHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE.. CS
                   AMP-binding 249 ieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv.. 326
                                   i ++kvt + gvP+v+  ll+   ++ +   + dl++l +  +gg++ +p+l+ ++ + ++e   +gYG TEt++ v+   
  gi|70606901|ref|YP_255771.1| 267 ILNHKVTRTGGVPTVFFELLRR--IEnM-NPKPDLKGLVV-GIGGAAAPPALVSALAKYGIEVAGNGYGATETGPGVAGgi 343
                                   *****************99884..3312.23458888776.47*******************99*************7777 PP

                                   ......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEE CS
                   AMP-binding 327 ......lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpeataeafdsegrwlrTG 399
                                         lp+ee++ k+g +G p  gvev++vD+  ge++p dg++ Ge+++rgp+++k Y+++  + ae+f+ +++w ++ 
  gi|70606901|ref|YP_255771.1| 344 kpeleqLPPEERRIKAG-QGYPTFGVEVELVDPVSGEELPwDGKSvGEIWIRGPWIAKSYYND-PRSAESFT-SDGWWKSK 421
                                   89999867666655655.9*********************877778****************9.57899**9.657***** PP

                                   EEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 400 DlgrldedGyleivgRkkdlikl 422
                                   Dl+++de  +++iv+R+kd+ik+
  gi|70606901|ref|YP_255771.1| 422 DLAVIDELSHIKIVDRLKDVIKS 444
                                   ******99*************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   6.1e-26   5.5e-22       2      76 .]     454     533 ..     453     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 6.1e-26
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---....HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea....leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   +E+ l++hp V+ea VvGvp++++Ge+++a+Vvlk++  + +    +++eL++h+ k+++++  p+++vfvde+pkt  GK
  gi|70606901|ref|YP_255771.1| 454 LENFLMAHPYVREASVVGVPHPKWGERPLAIVVLKSDyeN-LpkdeVKRELREHLLKRFAKWQLPDDIVFVDEIPKTSVGK 533
                                   7*********************************977541.14457**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 3386.52
//
Query:       gi|70606902|ref|YP_255772.1|  [L=629]
Description: amino acid permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-40  137.8  56.1    4.4e-40  137.8  56.1    3.0  3  AA_permease_2  Amino acid permease
    5.8e-26   91.1  62.0    5.8e-26   91.1  62.0    2.3  2  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8  56.1   4.9e-44   4.4e-40       1     399 [.      29     460 ..      29     465 .. 0.80
   2 ?   -3.9  20.9       0.5   4.5e+03      80     205 ..     463     584 ..     457     589 .. 0.74
   3 !    4.6   4.0    0.0013        12      82     150 ..     563     626 ..     557     628 .. 0.75

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 4.9e-44
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   l+ + +++l++g vigsg ++     a+++g a il+++i+ +++ + v+lvyaEl+sa+p+sgGi+ y ++  g  v+f+
  gi|70606902|ref|YP_255772.1|  29 LGRFELLFLSLGGVIGSGWLFGAlyTAGYAGGAGILSWLIGGILV-IFVGLVYAELGSAIPKSGGIVRYPHYSHGGIVGFI 108
                                   577899************99999899999***************9.89********999********************** PP

                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgn.......twltyliaiaililvalinirgikesakiqnilgilkil 153
                                   + w+++++++ + a+ +s+ + yl +++++ l++n       t   +++a ++lil++++n+ g+++++k++   g++k++
  gi|70606902|ref|YP_255772.1| 109 MIWAYFLSAASAPAIEASATVTYLSYFIHS-LTTNgtftgqlTLEGIGLAYFLLILFFFLNYAGVNILGKVTHAAGWWKLI 188
                                   ******999998888799999999999975.4444446665677889999******************************9 PP

                 AA_permease_2 154 lpliiliilglitvdgggfsslstetdtffpn......gwpgv...llglli....vlwsfdGfesaanvsee..vkkkdv 219
                                   +p +++i l+l+++++  +    t+++ ffp+      g +g+   l++  i    v++s+ Gf  a+ +  e  +++kd+
  gi|70606902|ref|YP_255772.1| 189 IPSVTVI-LALAFLNHPANY---TAGGGFFPSstylsaGLSGFsavLFA--IptsgVVFSYLGFRQAVEYGGEgkNPRKDI 263
                                   9988777.555555443333...23334444433311133332211444..244779****************555559** PP

                 AA_permease_2 220 pkaifigllivlvlyllvniaflgvvpddei..........anlsnlgsvaalffeavg........gkvvaiivvilial 282
                                   p+a + +lli++vly+l+++af+g+v+++            ++++ +++++  +fe++g         +v a i+ i +++
  gi|70606902|ref|YP_255772.1| 264 PFAVIGSLLIAIVLYTLLQVAFTGGVNWSAAgvkvgnwtglTSSGMVNGPFLFMFENSGlvgpiaglFSVWALILLIDAVI 344
                                   ****************************99998999998866666688899999999999855432212444444455555 PP

                 AA_permease_2 283 sllgaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyl 363
                                   s +g +  +v +s+r+++ +a+ g+lP+ f k+ k+g p+ ++i ++++ +++ll f +       +l+   sl+ ++ ++
  gi|70606902|ref|YP_255772.1| 345 SPAGTGWIYVGTSTRTIYGFATNGYLPSLFLKIGKTGVPVFSLIASLLIGMLFLLPFPA-----WIALVGFISLATVFTCI 420
                                   777777788889*****************************************999986.....59*************** PP

                 AA_permease_2 364 lliigalilrkkrphlkr....pgkilvaiigalfllfll 399
                                   +  ig+  lr   p+l+r    p++ ++a i++l++ +++
  gi|70606902|ref|YP_255772.1| 421 MGGIGLHTLRNVAPDLPRrykvPAYKIIAPIATLVAGLIV 460
                                   ****************885444332344444454444444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.5
                 AA_permease_2  80 sawfnwfayvpvlasilsvaasyllnalgpdlqgntwltylia..iaililvalinirgikesakiqnilgilkillplii 158
                                   ++++++f  v +++++l+++++y+++ ++ +l+ ++ +++l a   +i +  a+   ++++++++++ni + l + +++++
  gi|70606902|ref|YP_255772.1| 463 AGFSTLFYVVTAIFLGLPIFFGYYAYKIF-KLD-KRMAAILGAidLGIALASAFSLDIATSGLSTANNIAFGLYMGIMIAL 541
                                   45555555555667789*********997.774.566777767233444444444445566779999********999999 PP

                 AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfe 205
                                   ++i  l+++d   ++      + + ++ w + l  + +++ +f+Gf 
  gi|70606902|ref|YP_255772.1| 542 VVINILVLWDSVSQDV----RKEIKASYWLIALIFIVMTISYFGGFG 584
                                   9999999998888874....678999999999999999999999995 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0013
                 AA_permease_2  82 wfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgil 150
                                    ++w+ ++++++ ++s+++++ l a+ p+  +++    ++a++i+++++++ +r+   +  i  i+ ++
  gi|70606902|ref|YP_255772.1| 563 ASYWLIALIFIVMTISYFGGFGLDAIIPF--PED---TIVAAIIILIFHFLAVRSGLRTEAIEEIISTT 626
                                   57999999999999999999999999886..444...36677777777777777777777777777665 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1  62.0   6.4e-30   5.8e-26       2     401 ..      34     449 ..      33     485 .. 0.75
   2 ?  -14.3  20.3         2   1.8e+04      28     155 ..     451     580 ..     447     615 .. 0.55

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 6.4e-30
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +l+ +lggviG g ++g  ++++ aG+ +++l++l++g+ +++v+l  +e+ +++pksgg+  y + ++g  +Gf + + y
  gi|70606902|ref|YP_255772.1|  34 LLFLSLGGVIGSGWLFGALYTAGYAGG-AGILSWLIGGILVIFVGLVYAELGSAIPKSGGIVRYPHYSHGGIVGFIMIWAY 113
                                   6899***********************.666************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvt............gavflvvlliinlvgvkvygeaefilalikiiaii 151
                                   ++s + + a+e  a + ++++   +++l  + +t            +  +l++++++n++gv   g++   + + k+i+  
  gi|70606902|ref|YP_255772.1| 114 FLSAASAPAIEASATVTYLSYF--IHSLT-TNGTftgqltlegiglAYFLLILFFFLNYAGVNILGKVTHAAGWWKLIIPS 191
                                   ***********55555555555..55555.8888899*******9766667778899*****9999988888888877777 PP

                   AA_permease 152 afiivgiillaggkpnkgagfrflgdngsifknnlppgfa.keeegafknfisvfvi..vvfaftGielvaiiagEvkdPe 229
                                    ++i+   +l   +        ++++ g+    ++p+++  + + + f+++++++++  vvf++ G+   +  +gE k+P+
  gi|70606902|ref|YP_255772.1| 192 VTVILALAFLNHPA--------NYTAGGG----FFPSSTYlSAGLSGFSAVLFAIPTsgVVFSYLGFRQAVEYGGEGKNPR 260
                                   77777733332222........3344466....8999988899999********98733789999**************** PP

                   AA_permease 230 ksiPkailqvviritifYvlsllligllvprndlgllndsasa.......aspfvifikesgvsv....laplinavilta 299
                                   k+iP a++  +++ +++Y+l+ ++ + +v++++ g+  +  ++        +pf  ++++sg+ +    l ++ ++++l+ 
  gi|70606902|ref|YP_255772.1| 261 KDIPFAVIGSLLIAIVLYTLLQVAFTGGVNWSAAGVKVGNWTGltssgmvNGPFLFMFENSGLVGpiagLFSVWALILLID 341
                                   *********************************999888888899999999**********97653111333333444443 PP

                   AA_permease 300 als..sanssly..sasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllal.....llaslnlaapivfnfllai 371
                                   a+   ++ + +y  +++R++y +a +g++P+ + k++k gvP+ ++++s++i++l+l      +a + ++  +  +++ +i
  gi|70606902|ref|YP_255772.1| 342 AVIspAGTGWIYvgTSTRTIYGFATNGYLPSLFLKIGKTGVPVFSLIASLLIGMLFLlpfpaWIALVGFI--SLATVFTCI 420
                                   33312344555522678****************************************5555534444444..444555555 PP

                   AA_permease 372 saliglivwlliilsylrfRkalkyqgrsi 401
                                    + igl ++  ++  ++  R +  ++++ +
  gi|70606902|ref|YP_255772.1| 421 MGGIGLHTLRNVAPDLP-RRYKVPAYKIIA 449
                                   55555555555554444.233333333322 PP

  == domain 2  score: -14.3 bits;  conditional E-value: 2
                   AA_permease  28 plgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln...ylfswitvlaleltaasiliqfwe 105
                                   +++++ ++++ ++ +    + + +i    p   g+y+y   +l+++++   G++     + +++ l +++ ++s   +++ 
  gi|70606902|ref|YP_255772.1| 451 IATLVAGLIVYWAGFSTLFYVVTAIFLGLPIFFGYYAYKIFKLDKRMAAILGAIdlgIALASAFSLDIATSGLSTANNIA- 530
                                   44555566666666666666666777777777788888888888888888888854433333333333333333333333. PP

                   AA_permease 106 lvtdlpkawvtgavflvvlliinlvg..vkvygeaefilalikiiaiiafii 155
                                    +  ++  +++++v++ +l++   v+  v+ + +a+++l+ +++i + + + 
  gi|70606902|ref|YP_255772.1| 531 -FGLYM-GIMIALVVINILVLWDSVSqdVRKEIKASYWLIALIFIVMTISYF 580
                                   .44444.344455555555555555423455555555533333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.82u 0.37s 00:00:01.19 Elapsed: 00:00:00.50
# Mc/sec: 3773.38
//
Query:       gi|70606903|ref|YP_255773.1|  [L=550]
Description: hypothetical protein Saci_1128 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-28  100.2   0.2    4.4e-28   98.9   0.0    1.7  2  DUF87            Helicase HerA, central domain
    1.1e-09   37.7   0.4    0.00021   20.4   0.0    2.3  2  AAA_10           AAA-like domain
    1.7e-08   34.9   0.9    1.7e-05   25.2   0.2    2.3  2  AAA              ATPase family associated with various cellul
    1.6e-07   30.6   0.0      3e-07   29.7   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    1.3e-06   27.3   0.2     0.0019   16.9   0.0    2.4  2  DUF853           Bacterial protein of unknown function (DUF85
    5.7e-06   26.7   0.1       0.09   13.1   0.0    2.5  2  AAA_22           AAA domain
    6.6e-05   22.4   0.0    0.00016   21.1   0.0    1.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
    0.00055   19.9   0.5      0.097   12.6   0.1    2.4  2  NACHT            NACHT domain
    0.00097   18.9   0.0      0.037   13.8   0.0    2.3  1  DEAD             DEAD/DEAH box helicase
     0.0011   18.8   0.1      0.095   12.5   0.0    2.4  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0014   18.3   0.4     0.0022   17.7   0.0    1.5  1  Zot              Zonular occludens toxin (Zot)
     0.0014   18.6   0.1       0.31   11.0   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.002   18.7   0.0     0.0042   17.6   0.0    1.6  1  ABC_tran         ABC transporter
     0.0023   17.5   0.0        1.2    8.7   0.0    2.2  2  AAA_25           AAA domain
     0.0024   17.9   2.1       0.58   10.2   0.1    3.0  3  AAA_14           AAA domain
     0.0027   17.5   4.8      0.011   15.5   4.8    1.9  1  AAA_15           AAA ATPase domain
     0.0039   16.3   0.2     0.0093   15.0   0.2    1.6  1  T2SSE            Type II/IV secretion system protein
     0.0041   16.3   0.1      0.007   15.6   0.1    1.3  1  G-alpha          G-protein alpha subunit
     0.0043   17.4   0.0       0.18   12.2   0.0    2.2  2  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.023   14.2   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.015   15.0   0.0       0.12   12.1   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.017   14.8   0.1       0.14   11.9   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain
      0.017   14.8   0.0      0.036   13.8   0.0    1.5  1  AAA_24           AAA domain
      0.019   14.7   0.0      0.048   13.4   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.032   13.5   0.1      0.055   12.7   0.1    1.3  1  Septin           Septin
      0.034   13.7   0.1      0.068   12.8   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.035   13.6   2.2      0.047   13.1   0.1    2.2  2  Pox_A32          Poxvirus A32 protein
      0.036   13.4   0.1       0.11   11.9   0.0    1.8  2  Gtr1_RagA        Gtr1/RagA G protein conserved region
       0.05   12.8   0.1        4.7    6.3   0.0    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.051   14.1   0.4      0.094   13.2   0.0    1.6  1  AAA_23           AAA domain
      0.054   13.9   0.0       0.15   12.5   0.0    1.7  1  AAA_16           AAA ATPase domain
      0.062   13.3   0.0       0.13   12.2   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.083   12.3   0.4          8    5.8   0.1    2.2  2  TniB             Bacterial TniB protein
       0.15   12.2   0.1       0.46   10.6   0.1    1.8  1  PFO_beta_C       Pyruvate ferredoxin oxidoreductase beta subu
       0.17   12.1   0.2       0.33   11.2   0.2    1.4  1  Roc              Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0   8.5e-31   4.4e-28       2     227 .]     156     408 ..     155     408 .. 0.86
   2 ?   -1.8   0.1       5.4   2.8e+03     211     223 ..     454     466 ..     410     500 .. 0.52

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 8.5e-31
                         DUF87   2 eiGrllsgse.vpvyldl.nklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal............ 68 
                                   e+G++++ s+ ++v+l+l +++++ H++ +g+TGsGK+++ + ++ + + k++ ++++lD++G+++++l            
  gi|70606903|ref|YP_255773.1| 156 EVGEVTTFSRqTDVRLRLeENILRSHVLLIGTTGSGKTTFLKTIFFSNY-KNKKSTIVLDRQGDFVRFLikqfkegtvivp 235
                                   89***97776366*****999****************************.*******************555555555555 PP

                         DUF87  69 ....ekllsekvkvitpspsa................................kdkelkinpwsldpeelldllee..ddk 111
                                       +                                                + + +++ p sl+++++++ l+    + 
  gi|70606903|ref|YP_255773.1| 236 ltvkA---------------MeeygsfenlvqdrycgentwqgddnsivcepeQGRLISFYPFSLRFKDIFRQLPDsfPYL 301
                                   55554...............0555555555555555****************9***********************77555 PP

                         DUF87 112 paaav.qrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdlia 191
                                   +++a+ ++s + +a++     ++ e  s+  +++k+le++     ++ ++++q+  +++++l+ l+++g+++   +++++ 
  gi|70606903|ref|YP_255773.1| 302 SDYARaSWSSVVRACE-----KLTEVSSTSPSFYKMLESCL----GRANINTQTSGNIQRSLSALIEYGILD--IPNTITG 371
                                   5555557777777777.....66699999999*********....***************************..9999999 PP

                         DUF87 192 llleklekegkitiidlsgvdelaqql.vvsvilrri 227
                                   + l +l k+++ ++idls v e+   +  +svi+ +i
  gi|70606903|ref|YP_255773.1| 372 SELIDLLKSSQNVVIDLSIVLETLFLVePISVISYNI 408
                                   9999999********************99*9999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.4
                         DUF87 211 vdelaqqlvvsvi 223
                                   v++ +++++++ i
  gi|70606903|ref|YP_255773.1| 454 VSKATVEKLINKI 466
                                   2222222222222 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.4e-05    0.0074      22      83 ..     180     239 ..     173     251 .. 0.81
   2 !   20.4   0.0     4e-07   0.00021     258     340 ..     459     531 ..     419     541 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                        AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl.peiakkinvvtLdse 83 
                                   s++l+iG +G GK  + k+++      ++  +++D++ +   f+++l +++++ + +v L+ +
  gi|70606903|ref|YP_255773.1| 180 SHVLLIGTTGSGKTTFLKTIFFSNYKNKKSTIVLDRQGD---FVRFLiKQFKEGTVIVPLTVK 239
                                   689******************9999999999*****999...777775667777777777644 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 4e-07
                        AAA_10 258 GkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFretdkeeikkvLeflgldvedednkkelrelesGqCL 338
                                    +kl+++++R GR+ n  v+l+t+s++D++   ++ +  +k++Fr     + + vL+ lgl          l+++ +G CL
  gi|70606903|ref|YP_255773.1| 459 VEKLINKILRFGRQRNLGVILATHSPKDLNSLVIQ-QTNTKFIFR-----NDRTVLRDLGLTE----FTDLLESAPAGYCL 529
                                   479*************************9876655.5689*****.....4467888888876....45678888888888 PP

                        AAA_10 339 mk 340
                                   +k
  gi|70606903|ref|YP_255773.1| 530 VK 531
                                   87 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0065       3.3       1      20 [.     182     201 ..     182     234 .. 0.84
   2 !   25.2   0.2   3.3e-08   1.7e-05      40     125 ..     417     496 ..     388     503 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0065
                                   EEEESSTTSSHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavak 20 
                                   vll+G+ G GKT++ k +  
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFF 201
                                   79*************99875 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 3.3e-08
                                   THHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                           AAA  40 gesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                    ++ k  ++ +++      p + l+iDE+++++++    ++e+++ +v++L++++ ++ ++ +++ vi+at++p++l++ +
  gi|70606903|ref|YP_255773.1| 417 DKMYKMRKKGVNDSNDI--PqTLLLIDEAHEMFPQI---SQEVSKATVEKLINKILRFGRQ-RNLGVILATHSPKDLNSLV 491
                                   44444444444443333..449**************...999****************996.66*************9988 PP

                                   HSTTSS CS
                           AAA 120 lrgRfd 125
                                   + +  +
  gi|70606903|ref|YP_255773.1| 492 I-QQTN 496
                                   8.5554 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   5.8e-10     3e-07      10      61 ..     174     225 ..     169     240 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.8e-10
                 TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairargdraivlDltGafvsrfyd 61 
                                   +++  ++h+l++GttGsGKt+ l+ +  +  + ++  ivlD +G+fv+   +
  gi|70606903|ref|YP_255773.1| 174 EENILRSHVLLIGTTGSGKTTFLKTIFFSNYKNKKSTIVLDRQGDFVRFLIK 225
                                   5666689***************************************986655 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0017      0.88       7      60 ..     165     218 ..     159     231 .. 0.78
   2 !   16.9   0.0   3.8e-06    0.0019     254     313 ..     431     495 ..     332     500 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                        DUF853   7 keaeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGd 60 
                                   ++++ +l+l+ ++   h l+ G tG Gkt  L+++  s  +   + ++ d +Gd
  gi|70606903|ref|YP_255773.1| 165 RQTDVRLRLEENILRSHVLLIGTTGSGKTTFLKTIFFSNYKNKKSTIVLDRQGD 218
                                   566677888899999******************987655555555555565555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.8e-06
                        DUF853 254 ldkPklvfffdeahLLf....ndapkallek.veqvvrLirskGvGvyfvtqnPldlPdtvLaqL 313
                                    d P+  ++ deah +f    ++ +ka +ek +++++r+ r +  Gv + t +P dl   v+ q 
  gi|70606903|ref|YP_255773.1| 431 NDIPQTLLLIDEAHEMFpqisQEVSKATVEKlINKILRFGRQRNLGVILATHSPKDLNSLVIQQT 495
                                   4789*************44444677888888568999*********************9999885 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00018      0.09       5      29 ..     179     203 ..     177     243 .. 0.80
   2 !   10.9   0.0   0.00079       0.4      90     128 ..     431     480 ..     411     490 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00018
                        AAA_22   5 agilvvtGesGtGKTtllrrlleql 29 
                                   +++++++G +G+GKTt l++++ ++
  gi|70606903|ref|YP_255773.1| 179 RSHVLLIGTTGSGKTTFLKTIFFSN 203
                                   5799***************987655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00079
                        AAA_22  90 av..ielliiDEaqhlr...s........eealeeLrsllnlsrkgvqliLv 128
                                    +  + ll+iDEa+ ++   s        e++++++ ++    + ++ +iL+
  gi|70606903|ref|YP_255773.1| 431 NDipQTLLLIDEAHEMFpqiSqevskatvEKLINKILRFGR--QRNLGVILA 480
                                   235668*********99987245665455555555555555..999999997 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.2e-07   0.00016      31      62 ..     171     202 ..     155     207 .. 0.78
   2 ?   -3.2   0.0       8.5   4.4e+03     212     241 ..     455     484 ..     436     486 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-07
                                   EEEEGGGS-.SEEEE--TTSSHHHHHHHHHHH CS
                  FtsK_SpoIIIE  31 lvldlkkmashllvaGatgsGKStalntLilS 62 
                                   l l+++   sh+l++G+tgsGK+t+l+t+  S
  gi|70606903|ref|YP_255773.1| 171 LRLEENILRSHVLLIGTTGSGKTTFLKTIFFS 202
                                   4455555559******************9776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                                   ....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                  FtsK_SpoIIIE 212 ssvlvedaivRlarkgraaglHlllatqrl 241
                                   s+  ve++i ++ r gr+  l  +lat ++
  gi|70606903|ref|YP_255773.1| 455 SKATVEKLINKILRFGRQRNLGVILATHSP 484
                                   366889999999999998777777777655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00019     0.097       3      22 ..     182     201 ..     180     211 .. 0.86
   2 ?    5.2   0.1     0.035        18      82     128 ..     435     482 ..     423     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                                   EEEEC-TTTCHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                   v+l G  GsGKTt+l+ + +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFF 201
                                   899*************9975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.035
                                   CEEEEEE-STT-SS-TCH..........HHHHHCTTTTT--EEEEEEE CS
                         NACHT  82 rlLlilDglDelvtdlgq.kekqpvrtlLselirkkllpeasllltvr 128
                                   ++Ll++D + e+  + +q   k+ v++l+++++r    ++  ++l+++
  gi|70606903|ref|YP_255773.1| 435 QTLLLIDEAHEMFPQISQeVSKATVEKLINKILRFGRQRNLGVILATH 482
                                   7899*********99999788899999999999875555555444443 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.3e-05     0.037      10     173 ..     176     487 ..     167     490 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-05
                                   HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS........................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                          DEAD  10 lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktg........................................... 47 
                                   +il   +vl+ + TGsGKT+      +++  +  +k++                                           
  gi|70606903|ref|YP_255773.1| 176 NIL-RSHVLLIGTTGSGKTTFLKTIFFSNYKN--KKSTivldrqgdfvrflikqfkegtvivpltvkameeygsfenlvqd 253
                                   556.45899999*******9866666655532..33337888899999999999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          DEAD  48 ................................................................................. 47 
                                                                                                                    
  gi|70606903|ref|YP_255773.1| 254 rycgentwqgddnsivcepeqgrlisfypfslrfkdifrqlpdsfpylsdyaraswssvvracekltevsstspsfykmle 334
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ...............................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT CS
                                   ...............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  48 ...............................pkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng 97 
                                                                  p ++  + +  L +   n +  +     l++l         + +s+++ +
  gi|70606903|ref|YP_255773.1| 335 sclgranintqtsgniqrslsalieygildiPNTITGSELIDLLKSSQNVVIDLSIV--LETL------FLVEPISVISYN 407
                                   999999999999999999988888555555555555555555555555555555443..2233......233445666644 PP

                                   .CSEEEEEHHHHHHHHHCTSSHCTTE..EEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHH CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                          DEAD  98 .vdivvgtpgrlddllstgklnlsqv..rflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kdv 173
                                    +di++   +++ ++ ++g  + +++  ++l +DEa+++  q  ++  ++ +++l ++  +   qr++ v+ AT + kd+
  gi|70606903|ref|YP_255773.1| 408 iLDIIYNYKDKMYKMRKKGVNDSNDIpqTLLLIDEAHEMFPQISQEVSKATVEKLINKILRFGRQRNLGVILATHSpKDL 487
                                   58999999999999886666556666667899999999999955555555555443333333345566666677665655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00019     0.095       3      22 ..     183     202 ..     182     258 .. 0.75
   2 ?    3.8   0.0     0.081        42     276     300 ..     460     485 ..     448     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                        AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                   +liG  gsGK+++L+++ + 
  gi|70606903|ref|YP_255773.1| 183 LLIGTTGSGKTTFLKTIFFS 202
                                   79***************553 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.081
                        AAA_21 276 rrll.ellkelsrngaQviltTHSpl 300
                                   ++l+ ++l+  ++++  vil+THSp 
  gi|70606903|ref|YP_255773.1| 460 EKLInKILRFGRQRNLGVILATHSPK 485
                                   6777788899999***********96 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.3e-06    0.0022      55     134 ..     406     491 ..     373     508 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-06
                           Zot  55 arlirid..npegaetlkefakwatid.kgallviDEcqeifpvrakegrkd..pevi.naftehRhlgwDivlltqdisk 129
                                    ++++i    +++  ++ +    +  d    ll+iDE++e+fp+ ++e+ k   ++ i + +   R+ +  ++l t  +  
  gi|70606903|ref|YP_255773.1| 406 YNILDIIynYKDKMYKMRKKGVNDSNDiPQTLLLIDEAHEMFPQISQEVSKAtvEKLInKILRFGRQRNLGVILATHSPKD 486
                                   5666666556777777888888888788899************9999876555467775566677999********99988 PP

                           Zot 130 ihkev 134
                                   +++ v
  gi|70606903|ref|YP_255773.1| 487 LNSLV 491
                                   87766 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0006      0.31      10      60 ..     168     213 ..     159     268 .. 0.74
   2 ?    5.2   0.0     0.037        19     123     148 ..     421     453 ..     368     473 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                                   HHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEE CS
                        ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflfl 60 
                                   ++  +l+e++    + ++l+  +TG+GKT  + + +  ++++k+    +++l
  gi|70606903|ref|YP_255773.1| 168 DVRLRLEENI---LRSHVLLIGTTGSGKTTFLkTIFFSNYKNKK---STIVL 213
                                   5555555555...37799***********999555566666652...34444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.037
                                   ....HHHTTT-S....EEEEETGGGTTS....T CS
                        ResIII 123 eeseellrdrfd....viiiDEaHrlgak...k 148
                                   +++++  +d++d    +++iDEaH +  +   +
  gi|70606903|ref|YP_255773.1| 421 KMRKKGVNDSNDipqtLLLIDEAHEMFPQisqE 453
                                   33333333444477889*******998754431 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.2e-06    0.0042      12      51 ..     180     221 ..     168     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.2e-06
                                   SEEEEEESTTSSHHHHHHHH.TTSS--SEEEEEET.TCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkll.agllkpteGeilld.gkdlke 51 
                                   + v ++G +G+GK+t+lk++   ++k+++ +i ld + d+ +
  gi|70606903|ref|YP_255773.1| 180 SHVLLIGTTGSGKTTFLKTIfFSNYKNKKSTIVLDrQGDFVR 221
                                   5689**************872578899999998885545554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.011       5.6      32      50 ..     178     196 ..     156     203 .. 0.79
   2 !    8.7   0.0    0.0023       1.2     144     192 ..     436     486 ..     424     488 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                        AAA_25  32 agelallaGapgtGKttla 50 
                                   + + +ll+G +g+GKtt++
  gi|70606903|ref|YP_255773.1| 178 LRSHVLLIGTTGSGKTTFL 196
                                   46789************97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0023
                        AAA_25 144 rlvviDplsralgg..densnsdvgalvealeriarrtgaavllvhHvgKe 192
                                    l+ iD   ++++   +e s++ v++l++++ r+ r+ +  v+l  H+ K+
  gi|70606903|ref|YP_255773.1| 436 TLLLIDEAHEMFPQisQEVSKATVEKLINKILRFGRQRNLGVILATHSPKD 486
                                   68899*******999777777888************************997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0011      0.58       5      36 ..     182     213 ..     179     238 .. 0.80
   2 ?   -0.0   0.0       1.6   8.5e+02      75     111 ..     346     383 ..     343     398 .. 0.76
   3 ?    5.6   0.1     0.029        15      55     106 ..     426     488 ..     388     517 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyi 36 
                                   +++ G   +GKTt+lk+++ +++ +k+s++ +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFFSNYKNKKSTIVL 213
                                   7899**************99999555555544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.6
                        AAA_14  75 evpewekalkslvdeg.knldvivtGSnskllskeiat 111
                                    + ++++ l  l++ g  ++   +tGS + +l+k  ++
  gi|70606903|ref|YP_255773.1| 346 TSGNIQRSLSALIEYGiLDIPNTITGSELIDLLKSSQN 383
                                   55677778888888776667779*********997665 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.029
                        AAA_14  55 lileklke...ekktylflDEiqev..........pewekalkslvd..egknldvivtGSnsklls 106
                                    +     +     +t+l++DE++e+           ++ek ++++++  +++nl vi++  + k+l 
  gi|70606903|ref|YP_255773.1| 426 GVN----DsndIPQTLLLIDEAHEMfpqisqevskATVEKLINKILRfgRQRNLGVILATHSPKDLN 488
                                   222....233335799*********999999999988888888888855446776666555555443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.8   2.1e-05     0.011      19     226 ..     171     467 ..     163     507 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                        AAA_15  19 idlsee....ltvliGkNnsGKSsilealdlFlnnkekkn...............................kkvikieked 64 
                                   + l+e+      +liG+ +sGK+++l+ + +F n k kk+                                         
  gi|70606903|ref|YP_255773.1| 171 LRLEENilrsHVLLIGTTGSGKTTFLKTI-FFSNYKNKKStivldrqgdfvrflikqfkegtvivpltvkaM--------- 241
                                   5566665555789****************.555555444466665554444333333333332222222220......... PP

                        AAA_15  65 leifeniseskdikIdvef.............................................................. 83 
                                                     +                                                              
  gi|70606903|ref|YP_255773.1| 242 ------------------Eeygsfenlvqdrycgentwqgddnsivcepeqgrlisfypfslrfkdifrqlpdsfpylsdy 304
                                   ..................244555555555555555555555555555566666666666666666777777777777777 PP

                        AAA_15  84 ....................aek.ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks 143
                                                         + ++ k  e++l + +++ ++    +++++l+ +i+  +l+++++ + +e i++ k  +
  gi|70606903|ref|YP_255773.1| 305 araswssvvracekltevssT-SpSFYKMLESCLGRANINTQT--SGNIQRSLSALIEYGILDIPNTITGSELIDLLKSSQ 382
                                   777777777777777765432.146666666777666666554..666666777777777777777777666666666655 PP

                        AAA_15 144 kkelpkekeeklekekeelkidkedlkklikkleeslkkee..elknvlksaiiklllisakRnvsdedsekkssllgklk 222
                                   ++ ++ +   +     e +++ + ++ ++i+ ++ ++ k     ++ +    +++ll+++a   + +   e+++ + +kl+
  gi|70606903|ref|YP_255773.1| 383 NVVIDLSIVLETLFLVEPISVISYNILDIIYNYKDKMYKMRkkGVNDSNDIPQTLLLIDEAHEMFPQISQEVSKATVEKLI 463
                                   443333333333333333333334444444434333322223333333333334444444455555555555555555555 PP

                        AAA_15 223 ekil 226
                                   +kil
  gi|70606903|ref|YP_255773.1| 464 NKIL 467
                                   5555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.8e-05    0.0093     128     150 ..     178     200 ..     155     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                         T2SSE 128 erglilvsGgTgsGKttllyall 150
                                    r  +l+ G+TgsGKtt+l ++ 
  gi|70606903|ref|YP_255773.1| 178 LRSHVLLIGTTGSGKTTFLKTIF 200
                                   46678999***********8875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-05     0.007       3      44 ..     163     200 ..     161     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                   XXXXXXXXXXXXXXXXXE..EEEEEEEESTTSSHHHHHHHHH CS
                       G-alpha   3 tssaidkslkaerkarkkkrevkllllGqseSGKsTilkqlk 44 
                                    s++ d  l+ e++  ++    ++ll+G+ +SGK+T+lk + 
  gi|70606903|ref|YP_255773.1| 163 FSRQTDVRLRLEENILRS----HVLLIGTTGSGKTTFLKTIF 200
                                   578888888999888899....9***************9975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00034      0.18       9      54 ..     178     240 ..     172     262 .. 0.73
   2 ?    3.1   0.0      0.22   1.1e+02      79     126 ..     414     459 ..     289     473 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp.................eeillvaftgrA 54 
                                    ++++l+++  G+GKT+ lk+i     ++++                    e  ++v +t +A
  gi|70606903|ref|YP_255773.1| 178 LRSHVLLIGTTGSGKTTFLKTIFFSNYKNKKSTIvldrqgdfvrflikqfkEGTVIVPLTVKA 240
                                   57899****************987766666544455555555555555555555555555555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.22
                        AAA_19  79 dfddlltealelleeaeeekklqeeellivDEfqdvd.elqyrLlkall 126
                                   +++d++ ++ +     ++++++  ++ll++DE+ ++  +  +++ ka +
  gi|70606903|ref|YP_255773.1| 414 NYKDKMYKMRKK--GVNDSNDI-PQTLLLIDEAHEMFpQISQEVSKATV 459
                                   444544333333..56788889.889******99887455555555544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.5e-05     0.023      33      62 ..     179     209 ..     167     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                         AAA_7  33 kkpvllvGptGtGKtviikd.llkkldkeky 62 
                                   + +vll+G+tG+GKt+ +k+ ++++++++k 
  gi|70606903|ref|YP_255773.1| 179 RSHVLLIGTTGSGKTTFLKTiFFSNYKNKKS 209
                                   579*****************88888886654 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.12      34      87 ..     180     232 ..     167     243 .. 0.76
   2 ?    0.0   0.0       1.2   6.3e+02      85     108 ..     435     458 ..     430     475 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt.nleekdv 87 
                                    hvll+G  G Gktt+ k i      +    s+ vl+++gd++ +l  +++e+ v
  gi|70606903|ref|YP_255773.1| 180 SHVLLIGTTGSGKTTFLKTIFFSNYKN--KKSTIVLDRQGDFVRFLIkQFKEGTV 232
                                   7**************888776544444..456789******99876514555555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                        RuvB_N  85 kdvlfideihrlsraveevlysam 108
                                   + +l+ide h + +++ + + +a 
  gi|70606903|ref|YP_255773.1| 435 QTLLLIDEAHEMFPQISQEVSKAT 458
                                   6789*******9988765555444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027      0.14      22      56 ..     179     213 ..     161     226 .. 0.83
   2 ?    0.1   0.1       1.1   5.6e+02      95     151 ..     436     493 ..     422     504 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                                   SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
               Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                   +++vl+ G +G+GK+++ ++i+ ++ +++k+ + +
  gi|70606903|ref|YP_255773.1| 179 RSHVLLIGTTGSGKTTFLKTIFFSNYKNKKSTIVL 213
                                   579******************98877777766655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                   SEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES..S-HHHHHHT CS
               Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn..edleeavee 151
                                     l++De +e+ +++ +++ ++  e+ ++++     ++ ++ +i at+  +dl++ v +
  gi|70606903|ref|YP_255773.1| 436 TLLLIDEAHEMFPQISQEVSKATVEKLINKILRF-GRQRNLGVILATHspKDLNSLVIQ 493
                                   6789999999999998888888888777776442.233445555665522566666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.1e-05     0.036       5      33 ..     182     217 ..     179     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-05
                        AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtek 33 
                                   +l++G  g+GKTt++k++       +++++++d  +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIffsnyknKKSTIVLDRQG 217
                                   89****************999999999999999765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.5e-05     0.048      24      39 ..     181     196 ..     156     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-05
                        AAA_29  24 atlltGpsGsGKSTll 39 
                                    +ll+G++GsGK+T+l
  gi|70606903|ref|YP_255773.1| 181 HVLLIGTTGSGKTTFL 196
                                   58************98 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011     0.055       7      34 ..     182     209 ..     178     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                   EEEEEBTTSSCCCCCCTTSSSS------ CS
                        Septin   7 lmvvGesglGkttlintlfetdlieeek 34 
                                   ++++G+ g Gktt+++t+f ++ +++++
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFFSNYKNKKS 209
                                   899****************999988854 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.068       3      36 ..     182     216 ..     180     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                   EEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS- CS
                          cobW   3 tvltGflGsGKTtLlnhll.enraglklavivNef 36 
                                   ++l G  GsGKTt+l+++  +n +++k  +++  +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFfSNYKNKKSTIVLDRQ 216
                                   57889*************99888888877776555 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.2e-05     0.047      16      35 ..     182     201 ..     170     213 .. 0.83
   2 ?   -1.3   0.2       2.3   1.2e+03     109     139 ..     456     485 ..     398     499 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                       Pox_A32  16 lalvGgsGsGktvyLlsLlr 35 
                                   + l+G +GsGkt++L+ ++ 
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFF 201
                                   679*************9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                       Pox_A32 109 dkqtksktLlellnvgRhlnvsiilLcqtyk 139
                                   +  t +k + ++l +gR  n+ +il  +  k
  gi|70606903|ref|YP_255773.1| 456 K-ATVEKLINKILRFGRQRNLGVILATHSPK 485
                                   2.33345566677788888888888777655 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.11       2      27 ..     182     208 ..     181     222 .. 0.79
   2 ?   -2.8   0.0       6.2   3.2e+03      96     121 ..     441     466 ..     429     471 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                     Gtr1_RagA   2 vLLmGksgsGKtsmrs.iiFdnylard 27 
                                   vLL+G  gsGKt+  + i F+ny  + 
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKtIFFSNYKNKK 208
                                   9***********975516679998765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.2
                     Gtr1_RagA  96 etlkeilealrqyspeakvfvlihKm 121
                                   ++ +e++ +++q   +a+v+ li+K+
  gi|70606903|ref|YP_255773.1| 441 DEAHEMFPQISQEVSKATVEKLINKI 466
                                   55677788888888889999999886 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0092       4.7       4      55 ..     182     231 ..     179     268 .. 0.77
   2 ?    4.5   0.0     0.034        17      78     120 ..     424     467 ..     408     480 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0092
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke 55 
                                   vl  G +G+GKt  l ++++     ++++++++l + +++v+ l +++++ +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFFSN--YKNKKSTIVLDRQGDFVRFLIKQFKEGT 231
                                   55669****************9..9999999999999999998888887766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
                       DUF2075  78 kkaeekkeepkedvvivDEAhrlltksdqaekqse.enqlkelm 120
                                   kk  ++ ++ + +++++DEAh +  + +q+ ++ + e+ +++++
  gi|70606903|ref|YP_255773.1| 424 KKGVNDSNDIPQTLLLIDEAHEMFPQISQEVSKATvEKLINKIL 467
                                   66667777778899**********98888777766344555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00018     0.094      22      47 ..     182     207 ..     162     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                        AAA_23  22 tlItGpNGaGKTTildAiklaLyget 47 
                                   +l++G +G+GKTT+l  i +  y  +
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFFSNYKNK 207
                                   6999**************99888644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00028      0.15      25      76 ..     180     227 ..     168     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                        AAA_16  25 elvllsGesGvGKsslvrellralekd.g.gif..lrgkcdqlesaipysalaqal 76 
                                   + vll+G  G+GK++ +++++ +  k+ +  i+   +g+++++        l++++
  gi|70606903|ref|YP_255773.1| 180 SHVLLIGTTGSGKTTFLKTIFFSNYKNkKsTIVldRQGDFVRF--------LIKQF 227
                                   689**************99885443333324443455555555........55555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.13      14      40 ..     173     200 ..     160     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                   HHHCH.TEEEEEEESTTSSHHHHHHHHH CS
                          TsaE  14 lakal.gdvilLeGdLGaGKTtlvrgla 40 
                                   l +++ ++ +lL G  G+GKTt+ + + 
  gi|70606903|ref|YP_255773.1| 173 LEENIlRSHVLLIGTTGSGKTTFLKTIF 200
                                   444344678***************9885 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.043        22      36      60 ..     180     205 ..     170     226 .. 0.79
   2 ?    5.8   0.1     0.016         8      98     152 ..     413     465 ..     407     480 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.043
                          TniB  36 pnlllvGdsnnGKtmivek.Farlhp 60 
                                   +++ll+G +  GKt+ ++  F ++++
  gi|70606903|ref|YP_255773.1| 180 SHVLLIGTTGSGKTTFLKTiFFSNYK 205
                                   689************99863444444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                          TniB  98 lkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgne 152
                                   ++ ++++ k++++ ++  +++   +L+iDE h++    + +q+   +++ +L n+
  gi|70606903|ref|YP_255773.1| 413 YNYKDKMYKMRKKGVNDSNDIPQTLLLIDEAHEMF--PQISQEVSKATVEKLINK 465
                                   6778899999999999999999***********98..666667777777766665 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0009      0.46       3      45 ..     405     448 ..     404     485 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0009
                                   TTXSSSXSXXXXX-EEEGGGS.T---EEHHHHHHHHT-----EE CS
                    PFO_beta_C   3 tFNkvnTfdwYkervykleed.gyDpsdlekAlekalewgdkip 45 
                                   ++N ++    Yk+++yk+ ++  +D +d+ + l ++ e+++ +p
  gi|70606903|ref|YP_255773.1| 405 SYNILDIIYNYKDKMYKMRKKgVNDSNDIPQTLLLIDEAHEMFP 448
                                   89999999************989999997777777777666655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00064      0.33       2      32 ..     182     211 ..     181     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00064
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTT CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfsekeksti 32 
                                   v+l+G +g+GKt++lk +  +++++k++ ti
  gi|70606903|ref|YP_255773.1| 182 VLLIGTTGSGKTTFLKTIFFSNYKNKKS-TI 211
                                   89****************9999987754.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.51
# Mc/sec: 3266.26
//
Query:       gi|70606904|ref|YP_255774.1|  [L=410]
Description: hypothetical protein Saci_1129 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   40.7   0.2    2.7e-10   40.4   0.2    1.2  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.065   13.4   0.0       0.17   12.1   0.0    1.6  1  SspH      Small acid-soluble spore protein H family


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.2     3e-14   2.7e-10      54     241 ..     145     369 ..      43     370 .. 0.70

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 3e-14
                                   E............HHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCH..................HHHHHHHHHHH CS
                          NurA  54 l............errirllmetlElklgallleekgedllllDGsligslv..................efdelheeley 104
                                   l            e+  ++ +       + +l++  + dll++DG++++++v                      + +  ++
  gi|70606904|ref|YP_255774.1| 145 LyedgnvntlydvEDMLDEARLYT----ENQLMKTIQDDLLIVDGPIYPTPVelmptffssfpkqkdeikHWGKATHRWSM 221
                                   033333444333344444444444....55599999***************************888866633344566677 PP

                                   HHHHHHHHHHTT-TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH.................---STTS-H CS
                          NurA 105 eeylyslsrlleaglnlvgvaKsfrskellnllletlligesisDiallgallrk.................pgytspllk 168
                                   +++++ + ++le+  + vgv+K+++++  ln+      +  +++Di++l+ l ++                    ++++++
  gi|70606904|ref|YP_255774.1| 222 AKLIKDRISVLEN-RKAVGVVKRLENSRKLNKI---FPDMGRLTDIEVLDLLSERqcsnviypeicvigpfkLTTKVSVTR 298
                                   7888888888885.*******************...777778999999999987777788888888877755555555555 PP

                                   HHHTT-HCCHHHHHH-EEEEEEES...STTTTEEEEEHHHHHHCCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHC CS
                          NurA 169 ilrekpllrealidkeiyfaYvrl...egggsilrleipaevstakdedvlsllasqrlsisGYprpLalAhelak 241
                                    +++   l+e + ++  y +Yv+l     ++s +r+e +   + +   d ++ +   + s+s  p++++ ++++ak
  gi|70606904|ref|YP_255774.1| 299 EDSGNVILSENELKD-RYAYYVILklyGFTRSFFRIESF---DLNVLNDSIPVVF-GNVSYSSLPVWIDEVDRRAK 369
                                   555544444444444.6666666666999********33...3366666666666.8999*************998 PP

>> SspH  Small acid-soluble spore protein H family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.8e-05      0.17      17      34 ..     351     368 ..     349     374 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                          SspH  17 eVtYngkpVwIehvdeen 34 
                                   +V+Y + pVwI++vd + 
  gi|70606904|ref|YP_255774.1| 351 NVSYSSLPVWIDEVDRRA 368
                                   79*************654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2743.75
//
Query:       gi|70606905|ref|YP_255775.1|  [L=86]
Description: hypothetical protein Saci_1130 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 623.53
//
Query:       gi|70606906|ref|YP_255776.1|  [L=518]
Description: phospholipase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-71  241.3   5.0    3.1e-71  240.4   5.0    1.4  1  Phosphoesterase  Phosphoesterase family


Domain annotation for each model (and alignments):
>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.4   5.0   1.7e-75   3.1e-71       1     356 []      31     370 ..      31     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 1.7e-75
               Phosphoesterase   1 ikhvViivqENrsfdhlfGtlk.gvrg.iddasp.laqqdGvkkqa..lnkaev......sapfsldtakg...lsaqvvv 67 
                                   ikh++ii+qEN+sfd+lfGt++ g+ + +++ +  +  ++G+++++  l++ ++      + p+      +   + +++ +
  gi|70606906|ref|YP_255776.1|  31 IKHIIIIIQENHSFDNLFGTYPfGYPPiVNNITLsVMFPQGLYTNYteLKQGTLdyisvpNVPWLSIFGYShpyYANSYST 111
                                   89*************************9999888877777*888887677777788877755654433222477889999* PP

               Phosphoesterase  68 edpehsfqaiqeq.wnggrndkfvaaaeselvmgyfkredipvlwelaqeftlcDryFssvlggtepNrlflisgtsdpsG 147
                                   edp++ + +++ + w+++  ++fv ++++ ++m+yf++e++  lw++a+e++l+D+yFs v+g t pNr+++++g      
  gi|70606906|ref|YP_255776.1| 112 EDPNEGWINYHGDyWFDT-FNGFVFYSGP-QSMAYFSYEQLAPLWDYAEEYVLADNYFSPVMGLTAPNRIAYLTGSP---- 186
                                   ***********9977877.99********.**********************************************9.... PP

               Phosphoesterase 148 teggpsladpkktvlkgftqktigerLsekgvswaiYqealdnlakskvapfnyyvrklkklearrkalkqlglaakqlek 228
                                       p ++d+  +v+ + +q++ + +Lse +++w+ Y        +++  p n +  + + +        ++      +++
  gi|70606906|ref|YP_255776.1| 187 ---PPFFTDEPGQVV-PIQQSI-FYQLSEYNLTWKYYVYGY--EGGVPY-PLNIFIGSDNYTS-------HYAN----ISQ 248
                                   ...556665555555.555555.555*********999988..223332.6677776655555.......3333....478 PP

               Phosphoesterase 229 fkkdvkngkLPqvsfikpng....andeHpgadvaagdklikevlealtsspqwaktllivtyDEngGfyDhVappvapvs 305
                                   f +d+k g+LP+vs+++  g    ++d+Hp  + ++g+kl+++v++a+++s++w+++++++t+DE gG++D+V+pp+++  
  gi|70606906|ref|YP_255776.1| 249 FYEDLKSGNLPSVSWVMFLGgstdQYDMHPPENLTSGEKLLVDVINAVMESKEWNSSAIFITFDEGGGYFDQVVPPSIN-- 327
                                   *****************9999999****************************************************777.. PP

               Phosphoesterase 306 dpdglkGdpyglgvrvPllviSpyakkgtvdhelfdhtSvlrfiekrfglp 356
                                            yglg+r+Pll+iSpyak+g+v++ + + +++l fi+++f+lp
  gi|70606906|ref|YP_255776.1| 328 --------YYGLGQRIPLLIISPYAKEGYVNNYTMSGYTILGFIDYNFNLP 370
                                   ........79***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3382.73
//
Query:       gi|70606907|ref|YP_255777.1|  [L=229]
Description: hypothetical protein Saci_1132 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-10   39.3   0.3    2.2e-09   38.1   0.3    1.6  1  Metallophos    Calcineurin-like phosphoesterase
    2.3e-09   37.7   0.0    4.1e-09   36.9   0.0    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.9e-05   23.5   0.1    6.2e-05   22.4   0.1    1.5  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
  ------ inclusion threshold ------
       0.13   12.1   0.1        1.7    8.5   0.0    2.5  3  WIYLD          Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3     5e-13   2.2e-09       1     200 [.       1     176 [.       1     180 [. 0.65

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5e-13
                                   EEEEEEESBTB...TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHH CS
                   Metallophos   1 lrilvigDlHl...algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfe 78 
                                   +r+l+++D+H     +++++ + ++++l +++++ kp +++ aGD+ d+  ++  +l+ ++++ k    + ++ GNHe   
  gi|70606907|ref|YP_255777.1|   1 MRFLLVSDVHKsfrIYRNYNESVAVEWLLNVIDRVKPEVLISAGDWDDGMTPND-FLNIMSKVKK----LLTVYGNHE--- 73 
                                   89********9988778888888888888888888***************9999.9999665555....8********... PP

                                   HHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHT CS
                   Metallophos  79 eellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepgdewlkdlekre 158
                                    + +  +gy     +++ ++++ + +  +++l++    k + +                 ++++      + +++   k++
  gi|70606907|ref|YP_255777.1|  74 -NFPLIEGYVM--HDGKVYEVGGLKIAGINGLIGEGsKKGIPMTSP--------------TRFR------NALYRI--KKA 129
                                   .4444444444..333333333333333333333322222222221..............1121......444444..667 PP

                                   TCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEES CS
                   Metallophos 159 kadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGH 200
                                    ++ +i++ H p+y        +   g+  +    ++ ++ l + GH
  gi|70606907|ref|YP_255777.1| 130 VDRLDILVMHQPPYlpevyPEMSEDEGSALVYQGIEELKPRLFFNGH 176
                                   88899999999999877775555555555555555555667777777 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   9.1e-13   4.1e-09       1     103 [.       1     151 [.       1     180 [. 0.63

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 9.1e-13
                 Metallophos_2   1 MklaiiSDlH.........snldaleavlealkevgvdaiihaGDl.eeeepe.vleellelapvlaVrGNnD........ 62 
                                   M+++++SD+H         ++  a+e +l+ +++v+++ +i aGD+  + +p+ +l+ + +++++l+V+GN++        
  gi|70606907|ref|YP_255777.1|   1 MRFLLVSDVHksfriyrnyNESVAVEWLLNVIDRVKPEVLISAGDWdDGMTPNdFLNIMSKVKKLLTVYGNHEnfpliegy 81 
                                   9*********666666555445555555******************98888877999999999**********88888877 PP

                 Metallophos_2  63 ......................eev.veedvlreaaelgtdlpeeaelelagekvlliHgdpl.......g 103
                                                         +e   +   + ++++++++l  + +  +++ ++l++H+ p+        
  gi|70606907|ref|YP_255777.1|  82 vmhdgkvyevgglkiagingliGEGsKKGIPMTSPTRFRNAL-YRIKKAVDRLDILVMHQPPYlpevypeM 151
                                   776655555555555544444422212223333444444444.2222223666688888876555555542 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.58   2.6e+03      21      41 ..      25      45 ..      15      55 .. 0.65
   2 !   22.4   0.1   1.4e-08   6.2e-05     110     221 ..      68     179 ..      60     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.58
                                  HHHHHHHHHHH--SEEEEES- CS
                 Metallophos_3 21 lerlveviedkdpDllvlvGd 41
                                  +e l++vi+  +p++l+  Gd
  gi|70606907|ref|YP_255777.1| 25 VEWLLNVIDRVKPEVLISAGD 45
                                  445555555555666655555 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.4e-08
                                   HHHTTTT-TTEE..E-SSEEEEETTTEEEEEE-SEEESS--BSSSS-EEEHHHHHHHGGGGGGS---EEEEEESS--S-SS CS
                 Metallophos_3 110 ayeaevvfpnlk..vvhesfaekeGevliaGmGGeivdgekeeefrLkYPaweveyrLkvlkelkdrrkvlllatpPigel 188
                                   +y+ +  fp +   v+h++ + + G + iaG+ G+i +g+k+    +  P++  + +L ++k++ dr  +l++++pP    
  gi|70606907|ref|YP_255777.1|  68 VYGNHENFPLIEgyVMHDGKVYEVGGLKIAGINGLIGEGSKKG-IPMTSPTRFRN-ALYRIKKAVDRLDILVMHQPPYLPE 146
                                   56667778888633589998888999*************9986.55667876554.677778888************8878 PP

                                   TBTTBS---S-HHHHHHHHHH--SEEEE-SS-- CS
                 Metallophos_3 189 vadkglkekgsevvaelvktlnPevvvvghavk 221
                                   v ++  +++gs+ v + + +l+P++ + gh ++
  gi|70606907|ref|YP_255777.1| 147 VYPEMSEDEGSALVYQGIEELKPRLFFNGHMTQ 179
                                   8999999***********************865 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00037       1.7      25      44 ..      58      79 ..      50      81 .. 0.87
   2 ?    0.1   0.0      0.16   7.1e+02       6      15 ..     124     133 ..     120     138 .. 0.83
   3 ?   -2.7   0.0       1.2   5.3e+03       7      36 ..     176     205 ..     174     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00037
                         WIYLD 25 vrpvlkkLLkvYgkn..WeliE 44
                                  +++ +kkLL vYg+    +liE
  gi|70606907|ref|YP_255777.1| 58 IMSKVKKLLTVYGNHenFPLIE 79
                                  7889*********877788888 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                         WIYLD   6 eRidaAidam 15 
                                    Ri++A+d++
  gi|70606907|ref|YP_255777.1| 124 YRIKKAVDRL 133
                                   69******98 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.2
                         WIYLD   7 RidaAidamkelGfskeqvrpvlkkLLkvY 36 
                                   ++ + + +++++ f+ +  r    +L k Y
  gi|70606907|ref|YP_255777.1| 176 HMTQGCYTFHNFQFQTKYLRVDSSQLHKCY 205
                                   566667778888888776665555566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1694.43
//
Query:       gi|70606908|ref|YP_255778.1|  [L=356]
Description: AAA ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-16   59.8   0.0    5.9e-16   59.1   0.0    1.4  1  ATPase_2    ATPase domain predominantly from Archaea
    6.4e-08   32.7   0.5    2.7e-06   27.4   0.0    2.8  3  AAA_14      AAA domain
    2.5e-06   27.8   0.1    5.9e-06   26.6   0.0    1.6  2  AAA_22      AAA domain
    5.1e-06   27.0   0.1    1.8e-05   25.2   0.1    1.9  1  AAA_16      AAA ATPase domain
     0.0099   16.2   0.0      0.036   14.4   0.0    1.8  1  AAA_19      AAA domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.038   13.9   0.0    1.5  1  NTPase_1    NTPase
      0.043   13.0   0.1      0.088   11.9   0.1    1.5  1  DUF815      Protein of unknown function (DUF815)
      0.058   13.1   0.0        0.1   12.3   0.0    1.3  1  DUF4423     Domain of unknown function (DUF4423)
      0.059   12.9   0.0       0.11   12.0   0.0    1.4  1  AAA_7       P-loop containing dynein motor region
       0.11   12.9   0.0       0.25   11.8   0.0    1.7  1  AAA         ATPase family associated with various cellular ac
       0.15   11.3   0.0       0.24   10.6   0.0    1.3  1  Zeta_toxin  Zeta toxin
       0.15   11.1   0.0       0.26   10.3   0.0    1.3  1  T2SSE       Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   3.9e-19   5.9e-16       4     230 ..      17     238 ..      14     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 3.9e-19
                      ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesi.skldefieeeeekkklekalg 83 
                                   R +e++++ + + +  ++ + i G +g+GKt+++k +i++l+  +     y +lr++++  +l + +  e +++kl + ++
  gi|70606908|ref|YP_255778.1|  17 RGTEVEYIIQQVIS--RNWVIISGQRGIGKTSVMKVSINELRRRNSTDGIYLNLRGVKTlRELLSLLISEINRNKLFNIFN 95 
                                   66666666555544..678899*******************7777755555666665541444444447777788999997 PP

                      ATPase_2  84 iavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvvi 162
                                    +v+ + +   ++  + +  v++ + +ll +i+++   ++i +De+q+l    +   + l++ L n++ s   + ++++++
  gi|70606908|ref|YP_255778.1|  96 VNVNLNFGPLGVElkRGRLTVQRGLLELLLSINRD---MVIGLDEVQELS--PVS--KPLLDVLGNVFMS---NPKVRFIF 166
                                   77777776444445366667888888899999888...99**********..555..99***********...66789*** PP

                      ATPase_2 163 clsSeglfiervy..neselegrhky.ilvddldketalnflkegfkel.eelskedfeeiyryvGGkPkal 230
                                    +s  gl+  +++  + s+l gr    + ++++dk t+ nflk+g  el  ++++++ ee+++ ++G+++ l
  gi|70606908|ref|YP_255778.1| 167 SGSYVGLVKALLSpkEGSPLLGRPPVeVRLRPFDKITSINFLKQGMMELgVDFENNEAEEVVNKLDGIVGWL 238
                                   **********76522669*******************************9999**************98766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.8e-09   2.7e-06       2     106 ..      31     175 ..      30     200 .. 0.72
   2 ?   -2.8   0.0       3.9   5.9e+03     105     125 ..     267     287 ..     249     292 .. 0.74
   3 ?   -3.4   0.0         6     9e+03      64      73 ..     323     332 ..     297     340 .. 0.54

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.8e-09
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderd..........................kkladpekllel 55 
                                   r+ ++i+G R +GKT ++k  i+el   ++ + +y+nl   ++                                      
  gi|70606908|ref|YP_255778.1|  31 RNWVIISGQRGIGKTSVMKVSINELRrRNSTDGIYLNLRGVKTlrellslliseinrnklfnifnvnvnL----------- 100
                                   5789******************999999999********9998666777766655544444443333330........... PP

                        AAA_14  56 ileklke..........................ekktylflDEiqev....pewekalkslvdegknldvivtGSnsklls 106
                                         +                          +++ ++ lDE+qe+    + + ++l +++ +++++++i++GS  +l +
  gi|70606908|ref|YP_255778.1| 101 ------NfgplgvelkrgrltvqrgllelllsiNRDMVIGLDEVQELspvsKPLLDVLGNVFMSNPKVRFIFSGSYVGLVK 175
                                   ......13344444444444444555555555689999*********6666667777878888889*********877654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                        AAA_14 105 lskeiatslagrvaeielypl 125
                                   +++e+++ l gr  e+ l  l
  gi|70606908|ref|YP_255778.1| 267 MLEELNHFLEGRNRELYLAIL 287
                                   446677778888777776655 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6
                        AAA_14  64 kktylflDEi 73 
                                     +y f+D i
  gi|70606908|ref|YP_255778.1| 323 LIKYNFIDKI 332
                                   2234444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   3.9e-09   5.9e-06       6     136 ..      32     176 ..      29     177 .. 0.80
   2 ?   -2.7   0.0       4.4   6.5e+03      83      90 ..     272     279 ..     248     309 .. 0.58

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.9e-09
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................ 70 
                                   + +++ G+ G+GKT +++   ++l ++     ++ + ++ +l + +++++ll+ l +++++++                  
  gi|70606908|ref|YP_255778.1|  32 NWVIISGQRGIGKTSVMKVSINELRRR-----NSTDGIYLNLRGVKTLRELLSLLISEINRNKLFnifnvnvnlnfgplgv 107
                                   5689*******************9654.....578888**********************99999*************888 PP

                        AAA_22  71 ..erlsseellealeqalraravielliiDEaqhlr..seealeeLrsllnl..srkgvqliLvGtp.elrkl 136
                                     +r+++   + +le  l+  ++  ++ +DE+q l+  s+ +l  L    n+  s  +v++i+ G + +l k 
  gi|70606908|ref|YP_255778.1| 108 elKRGRLTVQRGLLELLLSINRD-MVIGLDEVQELSpvSKPLLDVL---GNVfmSNPKVRFIFSGSYvGLVKA 176
                                   76555555555555555555555.8999*******54446666655...555556899******999888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.4
                        AAA_22  83 eqalrara 90 
                                   ++ l+ r 
  gi|70606908|ref|YP_255778.1| 272 NHFLEGRN 279
                                   22222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   1.2e-08   1.8e-05       1     158 [.      13     152 ..      13     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-08
                        AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslv....rellralekdggiflrgkcdqlesaipysa.laqal 76 
                                   +l+GR+ e+   + ++++v s   + v++sG++G+GK+s++    +el+r+ ++d gi+l+ + ++    ++++  l++ +
  gi|70606908|ref|YP_255778.1|  13 ELFGRGTEV---EYIIQQVISR--NWVIISGQRGIGKTSVMkvsiNELRRRNSTD-GIYLNLRGVKTL--RELLSlLISEI 85 
                                   589999999...4555566655..89**************954555555555555.566555555551..12222233333 PP

                        AAA_16  77 areellrqlldeaesaeleawrekleealaavpelagaea...srllellkrllallsrderplvlvlDdlqwadeaslql 154
                                    r++l++  + +               +++   +l  +++     + + l +ll  ls   r  v+ lD++q + + s  l
  gi|70606908|ref|YP_255778.1|  86 NRNKLFNIFNVN------------VNLNFG---PLGVELKrgrLTVQRGLLELL--LSI-NRDMVIGLDEVQELSPVSKPL 148
                                   344444433333............222222...222222211133444444444..444.5559********999999999 PP

                        AAA_16 155 laaL 158
                                   l+ L
  gi|70606908|ref|YP_255778.1| 149 LDVL 152
                                   9866 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.4e-05     0.036       6     125 ..      26     152 ..      22     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                        AAA_19   6 e.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal........ 77 
                                   +  ++++ +++ +  G GKT v+k  +++l ++++   + i+   ++ r +k lre l+ l  e++    + +        
  gi|70606908|ref|YP_255778.1|  26 QqVISRNWVIISGQRGIGKTSVMKVSINELRRRNST--DGIY---LNLRGVKTLRELLSLLISEINRNKLF-Nifnvnvnl 100
                                   43678889999999******************9966..5555...58899999999996666663333322.134455565 PP

                        AAA_19  78 .............ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkal 125
                                                l      t + +lle       +++  ++  DE+q+++++ + Ll+ l
  gi|70606908|ref|YP_255778.1| 101 nfgplgvelkrgrL------TVQRGLLE---LLLSINRDMVIGLDEVQELSPVSKPLLDVL 152
                                   66666644222222......33444444...123454555899999999999999888765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.038       2     128 ..      34     162 ..      33     183 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEE..EE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyte..evreggrrigFkivdlasgeegiLarveakreprvgkyvvdves 80 
                                   v+i+G+ G+GKt ++k  +++l+++  + +G+y +   v+   +     i ++  ++++ +   + + + ++g   v++++
  gi|70606908|ref|YP_255778.1|  34 VIISGQRGIGKTSVMKVSINELRRR-NSTDGIYLNlrGVKTLRELLSLLISEI--NRNKLFNIFNVNVNLNFGPLGVELKR 111
                                   79********************877.578***986114445555555555556..44444444445678888999998888 PP

                                   ....HHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEE CS
                      NTPase_1  81 ....feelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpv 128
                                       +++  le l  ++++  vi +DE+ ++   sk + + + +v+ s++ v
  gi|70606908|ref|YP_255778.1| 112 grltVQRGLLELLL-SINRDMVIGLDEVQELSPVSKPLLDVLGNVFMSNPKV 162
                                   65544444444443.3456668899999888888888888888887766655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.9e-05     0.088      54     102 ..      32      81 ..      19      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                        DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg.Lrlievekedlkelpklvell 102
                                   n v++ G+rG GK s++k  +ne+++++    i ++ + +k+l +l++ll
  gi|70606908|ref|YP_255778.1|  32 NWVIISGQRGIGKTSVMKVSINELRRRNsTDGIYLNLRGVKTLRELLSLL 81 
                                   56899******************998876555555555555555555554 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05       0.1      43      83 ..     304     344 ..     278     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                       DUF4423  43 akrlrpkisaeevekalefLlklgllkkdedgkyrqteksl 83 
                                   + +l+  i+ +e ++ale L k ++++k ++g+y+ t+  l
  gi|70606908|ref|YP_255778.1| 304 SVKLKRSIDDKEFSSALESLIKYNFIDKIKEGEYQITDPIL 344
                                   4578889****************************999766 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.11      21      87 ..      20      86 ..      17      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                         AAA_7 21 rysyllelllknkkpvllvGptGtGKtviikdllkkld.kekylsltinfsaqtsanqlqdiieskle 87
                                   ++y+++++++++  v++ G+ G GKt+++k  +++l  ++++  + +n+    + ++l +++ s+++
  gi|70606908|ref|YP_255778.1| 20 EVEYIIQQVISRN-WVIISGQRGIGKTSVMKVSINELRrRNSTDGIYLNLRGVKTLRELLSLLISEIN 86
                                  5678888888765.699***************999998345555666676666666666666666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.25       1      38 [.      34     104 ..      34     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                   EEEESSTTSSHHHHHHHHHHHHTHE.......................EEEEETTTCSSS...........S CS
                           AAA   1 vllyGppGtGKTllakavakelgve.......................fleisgsellsk...........y 38 
                                   v+++G  G+GKT+++k  ++el ++                       + ei+  +l+ +            
  gi|70606908|ref|YP_255778.1|  34 VIISGQRGIGKTSVMKVSINELRRRnstdgiylnlrgvktlrellsllISEINRNKLF-NifnvnvnlnfgP 104
                                   6899*****************9644455555444444444444333333333333333.1355555555552 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.24      17      43 ..      32      58 ..      19      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                    Zeta_toxin 17 klillgGqpGAGKselaellkdelerq 43
                                    ++++Gq G GK+++++ + +el+r+
  gi|70606908|ref|YP_255778.1| 32 NWVIISGQRGIGKTSVMKVSINELRRR 58
                                  679********************9744 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00017      0.26     118     156 ..      21      58 ..       8      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                         T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   ++ +++  v +r  +++sG  g GKt ++ + ++e+  +
  gi|70606908|ref|YP_255778.1|  21 VEYIIQ-QVISRNWVIISGQRGIGKTSVMKVSINELRRR 58 
                                   445555.56999********************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2747.40
//
Query:       gi|70606909|ref|YP_255779.1|  [L=662]
Description: hypothetical protein Saci_1134 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-69  231.6   0.0    1.3e-68  231.0   0.0    1.3  1  ECH_1           Enoyl-CoA hydratase/isomerase
    3.6e-63  212.7   0.3    6.6e-63  211.8   0.3    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    4.6e-45  152.2   0.1    4.6e-23   81.6   0.0    2.7  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    2.8e-41  142.1   0.1    9.6e-37  127.2   0.0    2.4  2  ECH_2           Enoyl-CoA hydratase/isomerase
     0.0034   17.6   0.0     0.0095   16.1   0.0    1.8  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0042   16.3   0.0     0.0075   15.5   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0084   16.1   0.1      0.038   14.0   0.0    2.2  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
       0.03   14.9   0.0       0.19   12.3   0.0    2.4  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.039   14.4   0.0       0.17   12.3   0.0    2.0  2  NAD_binding_7   Putative NAD(P)-binding
      0.066   12.7   0.0       0.15   11.5   0.0    1.6  1  adh_short       short chain dehydrogenase
       0.09   13.3   0.2       0.37   11.4   0.0    2.1  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.12   11.7   0.0        1.8    7.8   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.12   12.7   0.1       0.39   11.2   0.1    1.9  1  FlaC_arch       Flagella accessory protein C (FlaC)
       0.19   11.1   0.0       0.34   10.2   0.0    1.4  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0   0.0     1e-71   1.3e-68       2     250 ..     415     661 ..     414     662 .] 0.97

  Alignments for each domain:
  == domain 1  score: 231.0 bits;  conditional E-value: 1e-71
                                   EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHHHH CS
                         ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeevlelw 81 
                                   ie+ +a i lnrPe +Na++  +++E+++ l +l +d+ vr+v++tG++kaF+aGad++  ++ +  a  a++++   +l+
  gi|70606909|ref|YP_255779.1| 415 IEEPIATIILNRPERLNAINGRMSEEITNTLSTLAEDQRVRVVIITGSGKAFSAGADVTGFQQSGSpASRAIFRK---DLF 492
                                   67889*********************************************************9876677777776...789 PP

                                   HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                         ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                   + + + pkpviaa+nG+a+gGGlela+acDi+ia+ na+ g++e++l lipg ggtq+l+r vG+  A++i+ lg++isa 
  gi|70606909|ref|YP_255779.1| 493 STVAKFPKPVIAAINGFALGGGLELAMACDIRIASSNAELGQPEINLALIPGGGGTQRLTRLVGRGWAKYIVFLGERISAS 573
                                   99******************************************************************************* PP

                                   HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                         ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                    a ++Gl++ vvp e+l+eea  +a k+aeksp+al+++k a++ + e++  ++l +e++lf  +  ++d+keG+ af+Ek
  gi|70606909|ref|YP_255779.1| 574 LAREIGLIEFVVPPEKLEEEAKRIALKIAEKSPLALAAAKLAIDSTEEREISTGLSLESTLFGLLLTSEDSKEGVRAFMEK 654
                                   ********************************************************************************* PP

                                   SH----- CS
                         ECH_1 244 rkpefed 250
                                   rkp+f++
  gi|70606909|ref|YP_255779.1| 655 RKPQFKG 661
                                   *****96 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.8   0.3   5.2e-66   6.6e-63       1     179 [.       8     187 ..       8     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 5.2e-66
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-S CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dad 80 
                                   k+ v+GaGtmG+gia+vfa ag++V l d+se++l+k+l++i+ sl+kl+ek ++k e+v+++l+ri++   l+e v dad
  gi|70606909|ref|YP_255779.1|   8 KILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEDILNKSLNNIRWSLSKLKEKDRIK-ETVDEVLSRIRPVVGLNESVsDAD 87 
                                   578*****************************************************.9*********************** PP

                                   EEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                       3HCDH_N  81 lviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetva 161
                                   +v+Ea +E ++lKr++f +l+k+++p++ila+nTS+l+++ +aea+++perv+ +HFfnPp lm+LvEv++gekT++e+  
  gi|70606909|ref|YP_255779.1|  88 FVVEASPEIIDLKRQIFSTLDKLLSPNTILATNTSTLPVTSIAEATSKPERVVAMHFFNPPVLMELVEVMKGEKTNDEVAL 168
                                   ********************************************************************************* PP

                                   HHHHHHHHTT-EEEEE.CS CS
                       3HCDH_N 162 tvvelakkigktpvvv.kd 179
                                   t++elakkigk+p+ + kd
  gi|70606909|ref|YP_255779.1| 169 TTYELAKKIGKKPILIkKD 187
                                   ***************9666 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.0   3.6e-26   4.6e-23       1      97 []     190     286 ..     190     286 .. 0.94
   2 !   67.9   0.0   7.2e-22   9.2e-19       8      97 .]     311     400 ..     309     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 3.6e-26
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTH.GGHH-HHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelger.ayapspllekl 80 
                                   G+vvn +l+++   a+ lve+g a+++++Da+++++lG+pmG+f l+d+ gld+++++l+  +e+lg + +  p+ ++e+ 
  gi|70606909|ref|YP_255779.1| 190 GYVVNNILGAVSGTACLLVEKGLADIKEVDAVTMYKLGFPMGVFILADYSGLDIGYNALR-SREKLGLKtNRPPCSMVEEK 269
                                   9**********************************************************9.5555555558999******* PP

                                   HHTT--BGGGTBSSSBC CS
                         3HCDH  81 veagrlgrktgkgfyky 97 
                                   v+ g+lg k+gkg+y+y
  gi|70606909|ref|YP_255779.1| 270 VKRGELGVKSGKGYYQY 286
                                   ***************98 PP

  == domain 2  score: 67.9 bits;  conditional E-value: 7.2e-22
                                   HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BG CS
                         3HCDH   8 lapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlgr 88 
                                   l+  +n a r++ eg+++ e+iD a++lgl++p G+fe +d++g+d  ++++++l++  + + y p pll ++ + ++lg+
  gi|70606909|ref|YP_255779.1| 311 LCGAVNVASRMYREGIVTKEEIDLAVKLGLNYPKGIFEYADEIGIDEILSAMRTLKDISSSDFYDPDPLLLEMQKRNELGK 391
                                   6677899************************************************************************** PP

                                   GGTBSSSBC CS
                         3HCDH  89 ktgkgfyky 97 
                                   ktgkgfy+y
  gi|70606909|ref|YP_255779.1| 392 KTGKGFYEY 400
                                   *******98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   0.0   7.5e-40   9.6e-37       2     184 ..     420     597 ..     419     599 .. 0.95
   2 !   15.0   0.0     1e-05     0.013     246     317 ..     591     659 ..     588     661 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 7.5e-40
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   ++i+Lnrp+ lNa++  m ++++++l++ ++d++v++v+++g+g kaf+AG Dv  ++++ +  +++   +fr+  +l ++
  gi|70606909|ref|YP_255779.1| 420 ATIILNRPERLNAINGRMSEEITNTLSTLAEDQRVRVVIITGSG-KAFSAGADVTGFQQSGSPASRA---IFRK--DLFST 494
                                   689***************************************88.**************99997655...9998..5999* PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgada 162
                                   +a++pkpv+a ++G+++GgG+ l++ + +r+++ ++ +  PE+++ l+P  Gg+  L+rl g   ++y+   G+r++++ a
  gi|70606909|ref|YP_255779.1| 495 VAKFPKPVIAAINGFALGGGLELAMACDIRIASSNAELGQPEINLALIPGGGGTQRLTRLVGrGWAKYIVFLGERISASLA 575
                                   ***********************************************************977699**************** PP

                                   HHTTS--EE--GGGHHHHHHHH CS
                         ECH_2 163 laaglathyvpseklealeeaL 184
                                    ++gl +++vp ekle+ ++++
  gi|70606909|ref|YP_255779.1| 576 REIGLIEFVVPPEKLEEEAKRI 597
                                   **************99866665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-05
                                   SHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                         ECH_2 246 dewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                   +e ak+++ +++++sP++l+++  +++++++ + +++ l+ E +l   ll+++D  eGvra + +  +kP++
  gi|70606909|ref|YP_255779.1| 591 EEEAKRIALKIAEKSPLALAAAKLAIDSTEERE-ISTGLSLESTLFGLLLTSEDSKEGVRAFMEK--RKPQF 659
                                   567899999***********************5.***************************8744..57777 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.4e-06    0.0095       2      62 ..       9      92 ..       8     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
                                  EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHHCSEEEE CS
                 NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvasldvvit 61
                                  i ++G G+MG+ +a+ ++ agy+v++ +++++ +++ +++                        ++++  ++e v+++d+v+ 
  gi|70606909|ref|YP_255779.1|  9 ILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEDILNKSLNNIrwslsklkekdriketvdevlsrIRPVVGLNESVSDADFVVE 91
                                  779****************************9999999886678878444433333333333333333333333333344444 PP

                                  - CS
                 NAD_binding_2 62 m 62
                                   
  gi|70606909|ref|YP_255779.1| 92 A 92
                                  4 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.9e-06    0.0075     143     209 ..       7      73 ..       1      99 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                   SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkei 209
                                   k+i+vvG+G  G  +A ++a +g++v+l +  + +l++   +++  l +  ek+ ++  + ++  +i
  gi|70606909|ref|YP_255779.1|   7 KKILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEDILNKSLNNIRWSLSKLKEKDRIKETVDEVLSRI 73 
                                   79**********************************7666677777777777766665555555555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.9e-05     0.038       1     100 [.       8     118 ..       8     167 .. 0.77
   2 ?   -2.5   0.0       3.4   4.4e+03      72      99 ..     580     607 ..     572     614 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHHHHSSBTTTBTT-........---TTEEEES-HHHHHTT CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree....elieeineehenvkyLpgi........klpenlvattdlaealkg 69 
                                   ki v+GaG  G  +A v+a +g +v l   +e    +   ++n+ +     L++         ++ + ++ +  l+e++++
  gi|70606909|ref|YP_255779.1|   8 KILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEdilnK---SLNNIRWSLSKLKEKdriketvdEVLSRIRPVVGLNESVSD 85 
                                   799************************9999955551...3444444444444321111101135567888999******* PP

                                   --EEEE---H..HHHHHHHHHHCCC--TT-EEE CS
                NAD_Gly3P_dh_N  70 adiivlvvPs..qalrevlkklkgllkkkailv 100
                                   ad++v + P      r+++ +l++ll++++il+
  gi|70606909|ref|YP_255779.1|  86 ADFVVEASPEiiDLKRQIFSTLDKLLSPNTILA 118
                                   *******99832457888999999998888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                                   EEEE---HHHHHHHHHHHCCC--TT-EE CS
                NAD_Gly3P_dh_N  72 iivlvvPsqalrevlkklkgllkkkail 99 
                                   +i +vvP + l+e +k+++ ++++k +l
  gi|70606909|ref|YP_255779.1| 580 LIEFVVPPEKLEEEAKRIALKIAEKSPL 607
                                   6779999999999999999999777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.19       1      57 [.       8      60 ..       8      94 .. 0.80
   2 ?   -2.1   0.0       4.6   5.9e+03      35      65 ..     426     455 ..     419     466 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHH CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdnee 57
                                  ki ++GaG mg+++a+ ++ ag   +++++  + +++ +++  +++  ++++ + ++
  gi|70606909|ref|YP_255779.1|  8 KILVVGAGTMGHGIAEVFAIAG---YHVYLS-DVSEDILNKSLNNIRWSLSKLKEKD 60
                                  67899*****************...****66.8888888888777775555554444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                                   SCCCHHHHHHHHC-EEECECHHHHHHH-SEE CS
                 F420_oxidored  35 npekaeelaeelgvkvtavdneeaaeeadvv 65 
                                    pe+++++  +++ ++t  + +++ae++ v 
  gi|70606909|ref|YP_255779.1| 426 RPERLNAINGRMSEEITN-TLSTLAEDQRVR 455
                                   577777777777766666.666666655443 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.17       8      70 ..       7      94 ..       2     112 .. 0.72
   2 ?   -2.0   0.0       3.9     5e+03      36      76 ..     585     626 ..     540     646 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                 NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtv..vapevkeeleelvklaeeel.ekd......................legadlv 65
                                  kk+lvvG+G+++   ++ ++ ag +v +  v++++ +++ ++++++ ++l ekd                      +++ad+v
  gi|70606909|ref|YP_255779.1|  7 KKILVVGAGTMGHGIAEVFAIAGYHVYLsdVSEDILNKSLNNIRWSLSKLkEKDriketvdevlsrirpvvglnesVSDADFV 89
                                  89**************************9999998666566677766554222244444445555555555544448888888 PP

                 NAD_binding_7 66 iaatd 70
                                  + a +
  gi|70606909|ref|YP_255779.1| 90 VEASP 94
                                  87764 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                 NAD_binding_7  36 vapevkeeleelvkla.eeelekdlegadlviaatddrelne 76 
                                   v pe  ee  +++ l+  e+ +  l+ a+l+i  t++re+++
  gi|70606909|ref|YP_255779.1| 585 VPPEKLEEEAKRIALKiAEKSPLALAAAKLAIDSTEEREIST 626
                                   223322222233333212222333555666666666666665 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.15       1      78 [.       7      76 ..       7      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                  SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                     adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78
                                  k +lv+Ga+  +G+ ia+ +a +G++v++ d se+ l++ +++++            ++++++++++v+++ +++ ++
  gi|70606909|ref|YP_255779.1|  7 KKILVVGAG-TMGHGIAEVFAIAGYHVYLSDVSEDILNKSLNNIR-------WSLSKLKEKDRIKETVDEVLSRIRPV 76
                                  6799***98.9**********************998866666654.......44556666777777777777666666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.37       1      39 [.       8      47 ..       8      74 .. 0.87
   2 ?   -2.4   0.0       5.9   7.6e+03      27      51 ..     422     446 ..     420     460 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllD 39
                                  k++vvG+G+ g   A+++a  g +V++ + s+ +l + l+
  gi|70606909|ref|YP_255779.1|  8 KILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEDILnKSLN 47
                                  79***************************99999955554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                                   EEESSSSSSTTSSHHHHHHHHHHHH CS
                     Pyr_redox  27 vversdkllrllDeeaskilqekle 51 
                                   ++ ++++ l++++  +s+++++ l+
  gi|70606909|ref|YP_255779.1| 422 IILNRPERLNAINGRMSEEITNTLS 446
                                   5555555555555555555554443 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0014       1.8      30      67 ..       8      45 ..       2      91 .. 0.77
   2 ?    1.0   0.0      0.17   2.1e+02     144     175 ..     179     210 ..     172     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67
                                  k+lv+G+G+ G   +++ +  g +V++ Dv+++ l++ 
  gi|70606909|ref|YP_255779.1|  8 KILVVGAGTMGHGIAEVFAIAGYHVYLSDVSEDILNKS 45
                                  89*****************************9988654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
                                   TSEEEEETTEEEEEBSTGGGGSHHHHHHHHHH CS
                   AlaDh_PNT_C 144 gepvveekgvvhygvanlpgavprtasalltn 175
                                   ++p++ +k+v  y v+n+ gav+ ta  l  +
  gi|70606909|ref|YP_255779.1| 179 KKPILIKKDVPGYVVNNILGAVSGTACLLVEK 210
                                   5799999******************9887655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0003      0.39       5      49 ..      42      85 ..      40      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                     FlaC_arch  5 lEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVsn 49
                                  l + l+++  +l+ +k e + ++++v+e+  +++ +++L E Vs+
  gi|70606909|ref|YP_255779.1| 42 LNKSLNNIRWSLSKLK-EKDRIKETVDEVLSRIRPVVGLNESVSD 85
                                  6788999999999997.6799**********************97 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00026      0.34      19      42 ..       7      30 ..       2     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                                  SEEEEE--SHHHHHHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 19 skvllvGaGglGsellknLalsGv 42
                                  +k+l+vGaG+ G+ +++ +a +G 
  gi|70606909|ref|YP_255779.1|  7 KKILVVGAGTMGHGIAEVFAIAGY 30
                                  69******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3946.40
//
Query:       gi|70606910|ref|YP_255780.1|  [L=174]
Description: hypothetical protein Saci_1135 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       182  (0.0101512); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 1147.91
//
Query:       gi|70606911|ref|YP_255781.1|  [L=471]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-42  144.5  24.5    5.2e-42  144.2  24.5    1.0  1  Sugar_tr  Sugar (and other) transporter
    3.5e-29  101.8  46.9    2.3e-25   89.3  25.9    2.2  2  MFS_1     Major Facilitator Superfamily
    9.6e-07   28.4   7.9    9.6e-07   28.4   7.9    2.2  2  MFS_4     Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2  24.5   8.7e-46   5.2e-42      19     451 ..      34     461 ..      25     462 .. 0.86

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 8.7e-46
                                   GGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT CS
                      Sugar_tr  19 igafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk 99 
                                   ig+f+tl+++++n gl   + +  + +++ ++ivsi l+  iiGs+ +gl++dr+GR+++l++  vl+ ig++ +a++   
  gi|70606911|ref|YP_255781.1|  34 IGYFATLYDAVSNLGLALPYIPFIN-TTQASIIVSIGLAAYIIGSIGLGLVADRIGRRPALIALFVLLTIGSLGMALSV-- 111
                                   7999999999999999999999985.9****************************************************.. PP

                                   SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHH CS
                      Sugar_tr 100 nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvp 180
                                    ++ +l+v R++ G+g G+  +l+ +yisE++p ++Rg+ + +   +  +   +++ + +++ + +++ gwri +gl++v+
  gi|70606911|ref|YP_255781.1| 112 -NYPMLFVFRFIEGVGTGASLNLAMVYISEFSPSSKRGKYGNWIFISGWIAVGLGTLLVAFIVTANETIGWRIAFGLAAVL 191
                                   .9*****************************************9999999999999999999999999************* PP

                                   HHHHHHHG.GGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHH CS
                      Sugar_tr 181 allllill.lflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvv 260
                                    l+  +++ + +PES r l++kgk+++a+  ++ ++ ++ +  ++         + e+e++s  ++l++ + ++rl+   v
  gi|70606911|ref|YP_255781.1| 192 GLISTVVVsIKAPESVRVLIKKGKYQQAENLVEGIERVSMVRAKVSTLPPPKIVSYEQEQVSPLKILGESKFLKRLIGLTV 272
                                   *9988777699***************************9999999998877777777778999999999888888888888 PP

                                   HHHHHHHTTHHHHHHHTTTHHH.HSS-THH..HHHHHHHHHHHHHHHHHHH...HHHHHS-SHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 261 lqifqqltGinaimyysptife.nlglsks..llvtiivgvvnfvatfvai...flvdrfGRRtllllGaagmaicfvilg 335
                                    ++f  +  + + + ++pt+ +  +gl++   ++   ++g+v + at++++    +++r+ RR l  +Ga+g ++   + +
  gi|70606911|ref|YP_255781.1| 273 FWFFIYFIQYTS-TGLGPTFVKaVVGLTPGqyAEYIRLLGFVAVGATIISFamlGFIERTDRRILTQVGAIGFLVSSYVTT 352
                                   888888888655.5566665551679999987777788999999999999645579********999**999999999995 PP

                                   ..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT- CS
                      Sugar_tr 336 ivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaiggg 416
                                      +l+ +k    + +  + +++ + +    +    ++++sE fp+  Rs++ ai+  +  l  ++  ll   + + +g  
  gi|70606911|ref|YP_255781.1| 353 ---FLILNK----ALIPWFITYFLLEFVVNPPYLAGYLMSSESFPTTARSTGFAITDGIGHLGGVIGPLLLFPLISIVGPL 426
                                   ...777777....23333333333333333444466899*****************************9999999999966 PP

                                   HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGG CS
                      Sugar_tr 417 yvflvfaglavlfiifvfffvpetkgrtleeieel 451
                                   y  ++ a  + +++   +f+vp t+g+ lee++e+
  gi|70606911|ref|YP_255781.1| 427 YAWVILALPVPFAAALLWFTVPKTVGVRLEEVNEA 461
                                   666666666778889999**************985 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3  25.9   3.8e-29   2.3e-25      13     266 ..      45     327 ..      23     336 .. 0.75
   2 !   19.4  17.5   6.6e-08   0.00039      38     187 ..     310     460 ..     307     469 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 3.8e-29
                         MFS_1  13 silgpalplalaedlg........ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfassl 85 
                                   s+l            g        i+ +++++++++  ++++++s+ lG ++dr+Grr+ l++ ++l+ +g+l ++++ ++
  gi|70606911|ref|YP_255781.1|  45 SNL------------GlalpyipfINTTQASIIVSIGLAAYIIGSIGLGLVADRIGRRPALIALFVLLTIGSLGMALSVNY 113
                                   333............34444444467899******************************************7777777999 PP

                         MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsll 163
                                   ++l+v+r++ G+g+ga++ +++++i++ +p ++rg++  ++ ++  +++ lg ll ++++++     Wr +f ++a+++l+
  gi|70606911|ref|YP_255781.1| 114 PMLFVFRFIEGVGTGASLNLAMVYISEFSPSSKRGKYGNWIFISGWIAVGLGTLLVAFIVTANEtigWRIAFGLAAVLGLI 194
                                   9********************************************************9996544566************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeee...........................kgtgpaplvp.......awkallkdpvlw 210
                                   + v+  + + ++++ r   ++ +                             +        +       ++k+l  +++l 
  gi|70606911|ref|YP_255781.1| 195 STVV--VSIKAPESVRVLIKKGKYQqaenlvegiervsmvrakvstlpppkiV--------SyeqeqvsPLKILGESKFLK 265
                                   *997..66666666666666666658899999999988888887666666653........14444444466666666664 PP

                         MFS_1 211 illialllfffgfsg...lltllplylqevlgls.....glllaglllallalvgailallagr 266
                                    l+   +++ff++++    + l p++++ v gl+      ++ +++++a++a ++ ++  ++g+
  gi|70606911|ref|YP_255781.1| 266 RLIGLTVFWFFIYFIqytSTGLGPTFVKAVVGLTpgqyaEYIRLLGFVAVGATIISFA--MLGF 327
                                   2333333333333335559999**************8874444444455555555444..3333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.6e-08
                         MFS_1  38 ltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslw.lllvlrvlqGlgagalfpagaaliadwfp 115
                                   l+++a+ga + s+ +  +++r  rr +  +g+++f++++++ +f   +    ++++  +l  +     + ag+ + ++ fp
  gi|70606911|ref|YP_255781.1| 310 LGFVAVGATIISFAMLGFIERTDRRILTQVGAIGFLVSSYVTTFLilNKALiPWFITYFLLEFVVNPPYLAGYLMSSESFP 390
                                   5678999999999998888***9999************888887447555558**************************** PP

                         MFS_1 116 keergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                    + r+ ++++  +   lG ++gpll   l+s +g  ++++ila+   +a+ l  l+++++++   r +++ e
  gi|70606911|ref|YP_255781.1| 391 TTARSTGFAITDGIGHLGGVIGPLLLFPLISIVGPLYAWVILALPVPFAAAL--LWFTVPKTVGVRLEEVNE 460
                                   ***********************99999999***888888888888777666..999999888777766655 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   7.9   1.6e-10   9.6e-07      26     170 ..      58     204 ..      51     227 .. 0.77
   2 ?    0.6   0.4     0.046   2.7e+02      40      90 ..     311     373 ..     298     375 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.6e-10
                         MFS_4  26 slsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslv 106
                                   + +qa+++ ++ ++ Y++G++     + +   R  l a  ++ ++  l mal  +  ++++ Rf+ Gv+ ++ l ++   +
  gi|70606911|ref|YP_255781.1|  58 NTTQASIIVSIGLAAYIIGSIGLGLVADRIGRRPALIALFVLLTIGSLGMALSVNYPMLFVFRFIEGVGTGASLNLAMVYI 138
                                   579******************8877666666777788888999999*************************9999988888 PP

                         MFS_4 107 lahaaaarrervgallfaG....vGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp 170
                                    + +  ++r++ g ++f      vGlG ++ + +v++  + g+  +    ++avl ++ +++v + +p
  gi|70606911|ref|YP_255781.1| 139 SEFSPSSKRGKYGNWIFISgwiaVGLGTLLVAFIVTANETIGWRIA--FGLAAVLGLISTVVVSIKAP 204
                                   888889999999*999965133355555555555544444444443..66777777777777777766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.046
                         MFS_4  40 GYL.vGallaafalsagaeRlr...........llagllatvllllamaltesfaaflliRfl 90 
                                   G+  vGa + +fa+    eR+             l++  +t+ l+l  al+  f++++l+ f+
  gi|70606911|ref|YP_255781.1| 311 GFVaVGATIISFAMLGFIERTDrriltqvgaigFLVSSYVTTFLILNKALIPWFITYFLLEFV 373
                                   554368888888888777777666677887777788888999999999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2806.06
//
Query:       gi|70606912|ref|YP_255782.1|  [L=558]
Description: thiamine pyrophosphate enzyme [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-44  151.4   0.0    7.6e-44  149.3   0.0    2.0  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      1e-38  132.2   0.0    1.9e-38  131.3   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    9.2e-25   87.2   0.0      1e-23   83.9   0.0    2.6  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.032   14.0   0.0       0.11   12.2   0.0    1.8  2  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha
      0.062   12.9   0.7       0.14   11.8   0.7    1.6  1  CENP-B_N      CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.0   2.1e-47   7.6e-44       1     171 [.       1     168 [.       1     169 [. 0.97
   2 ?   -1.6   0.0      0.49   1.7e+03      31      87 ..     373     427 ..     350     432 .. 0.75

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 2.1e-47
                                   EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   m++++ l+++L +++v+hvfg++G+++ pl+da+++ ++i++v ar+E++a+++Ad+yar++ kpg+v v + +Ga  +l+
  gi|70606912|ref|YP_255782.1|   1 MKASKSLLELLDKYNVKHVFGLVGETSFPLYDAFNDYPNITHVFARDERNAVIMADAYARFSYKPGIVEVPN-VGAPYTLP 80 
                                   78999*****************************************************************88.7******* PP

                                   HHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkd 162
                                   +laeA+ ++iP+++++ d+pt+ +++++l  e d++ l +++ k++  v++p++lp+++rrA+r+a++gr+gPv++ +p++
  gi|70606912|ref|YP_255782.1|  81 GLAEANISGIPIIMFVSDIPTYVEKRNMLT-EHDNSYL-NKLSKEFLSVNDPSQLPRVVRRAFRVATTGRTGPVVVKIPMN 159
                                   ******************************.9998888.88**************************************** PP

                                   HCC-EEEHH CS
                  TPP_enzyme_N 163 vlleevded 171
                                   + + ev ++
  gi|70606912|ref|YP_255782.1| 160 IYDGEVSDE 168
                                   **9999865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.49
                                   HCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHH..TS-EEEEE-CHHHHHHCHHHHHHHH CS
                  TPP_enzyme_N  31 ldalseeqgirvvlarhEqgaafaAdgyarat..gkpgvvlvtsgpGatnaltalaeAk 87 
                                   l ++ +e   ++ l+++ ++ a++ ++y +++  g++ + + + g G+  al+al++A+
  gi|70606912|ref|YP_255782.1| 373 LSEFVDE---KTFLVVDPGTGAIFSSAYLKLKlaGRRIMYNYSMG-GLGYALPALIGAY 427
                                   5555555...46677777778888888888444377777777777.9999999999997 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.0   5.4e-42   1.9e-38       1     136 [.     191     325 ..     191     326 .. 0.91

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 5.4e-42
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGS.CHHHHHHHHH-SE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhg.skaanealeeaDl 80 
                                   i +a+++l +ak+pvi++G+gv  s+asee+++lae+l iPv+tt  gkg++pe+hpl++g++g  g ++  n++l+eaD+
  gi|70606912|ref|YP_255782.1| 191 ITEALKILYSAKNPVIVCGQGVLLSNASEEVVKLAEALSIPVATTITGKGSFPETHPLSIGVIGARGgTRFSNKILAEADV 271
                                   689************************************************************99876************* PP

                                   EEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                  TPP_enzyme_M  81 vlalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketlea 136
                                   v+++G++ d  +t   ++  ++ + +ii++d+++ e+g+ny+v ++++gd+k tl++
  gi|70606912|ref|YP_255782.1| 272 VFLIGTNTDSANT-WDWR-LPSSKsTIIQLDVSERELGNNYKV-IPLLGDAKLTLKE 325
                                   *******999544.3444.455555****************65.***********97 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.29   1.1e+03     126     152 ..     126     155 ..     118     156 .. 0.80
   2 !   83.9   0.0   2.8e-27     1e-23      12     153 .]     397     533 ..     386     533 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.29
                                   EESSH.HHHHHHHHHHHH.....CSSSEEEEE CS
                  TPP_enzyme_C 126 rvekadveeleealkeal.....ekkgpalie 152
                                   +  ++d+++l +++++a+      + gp+++ 
  gi|70606912|ref|YP_255782.1| 126 S--VNDPSQLPRVVRRAFrvattGRTGPVVVK 155
                                   4..45559999999999989889888999987 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 2.8e-27
                                   HHTTSS.SSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHH CS
                  TPP_enzyme_C  12 llkvkr.prsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggq 91 
                                   +lk+k   r+++ ++ +g +Gy+lpa iGa +a  + ++ +i+ DG ++++l el+t+ r n++ +++v+nN+++g ++  
  gi|70606912|ref|YP_255782.1| 397 YLKLKLaGRRIMYNYSMGGLGYALPALIGAYFAT-GGRILSITTDGNLFFNLGELETVKRLNVNAKIFVFNNKSFGWIRAA 476
                                   445555356777799*****************95.559******************************************* PP

                                   HHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  92 qepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   + +++g+  sg++     ++d+ kla ++G++ +r+ek+  ee+e + keal  + p +iev
  gi|70606912|ref|YP_255782.1| 477 MLSKYGRVLSGTE---ISEIDYSKLASSFGIDYLRIEKS--EEIESVTKEALVDDSPKFIEV 533
                                   ******9999998...99**************99*****..***********999*****97 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05      0.11      25      69 ..     191     235 ..     186     250 .. 0.88
   2 ?   -2.2   0.0      0.83     3e+03     104     130 ..     308     334 ..     302     359 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                                   SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEE CS
                         CO_dh  25 lkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvat 69 
                                   ++++ k++  ak+P+++ G  vl     e+ +k  +   ++v+ t
  gi|70606912|ref|YP_255782.1| 191 ITEALKILYSAKNPVIVCGQGVLLSNASEEVVKLAEALSIPVATT 235
                                   578999********************9**********99999887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.83
                                   ---SEEEEES--HHHHHHHHHHHHHH- CS
                         CO_dh 104 geydlvlfiGviyYyasqalsslkkft 130
                                   ++y+++ ++G     ++ +++++++  
  gi|70606912|ref|YP_255782.1| 308 NNYKVIPLLGDAKLTLKEMIRMIREVK 334
                                   788888888888888888888888765 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7     4e-05      0.14       7      31 ..     321     345 ..     319     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                                   --HHHHHHHHHHHHCTT-HHHHHHH CS
                      CENP-B_N   7 LTlreKievIqrleegeSkaelarr 31 
                                   LTl+e i++I+++ +++S  e+ r+
  gi|70606912|ref|YP_255782.1| 321 LTLKEMIRMIREVKRNQSISEIERE 345
                                   9*****************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3733.01
//
Query:       gi|70606913|ref|YP_255783.1|  [L=133]
Description: hypothetical protein Saci_1138 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-26   93.2  16.8    1.5e-26   93.0  16.8    1.0  1  VKOR        Vitamin K epoxide reductase family
  ------ inclusion threshold ------
        1.2    9.3   7.4       0.34   11.0   0.3    2.7  3  DUF4229     Protein of unknown function (DUF4229)
        1.4    9.3   8.5       0.58   10.6   2.9    2.9  2  HRG         Haem-transporter, endosomal/lysosomal, haem-respo
        8.5    6.4   8.2         14    5.8   3.7    2.4  2  OppC_N      N-terminal TM domain of oligopeptide transport pe


Domain annotation for each model (and alignments):
>> VKOR  Vitamin K epoxide reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0  16.8   3.4e-30   1.5e-26       2     121 ..       9     125 ..       8     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 3.4e-30
                                   HHHHHHHHHHHHHHHHHHHHH...HT---S.S-SSSS...HHHHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-.HHHHH CS
                          VKOR   2 lllvlalvGllvsiyltleklglktsssaa.lCdiss.vsCdkvlnSpyasilgvplsllGllayalvlllalapllwlll 80 
                                   ++++l+++G+++s ylt+e l+    + ++ +C+i+s v+C +v++Spy+ ++g+p+++lGl+++al+l l ++     ++
  gi|70606913|ref|YP_255783.1|   9 AFVLLSIIGIILSSYLTYETLT---ATFNTgYCNINSyVNCGTVASSPYSRFFGIPVAILGLAWFALMLGLWMIKK--EVT 84 
                                   6899*****************5...4444458***************************************99877..567 PP

                                   HHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHH CS
                          VKOR  81 llgslagvvfslyLiylslfvigalCpyClvsavlsllllv 121
                                   ++  ++gv+f++yLiy ++  i+a+C+yC++++++ l++ +
  gi|70606913|ref|YP_255783.1|  85 IYPWIIGVMFVGYLIYTEVELIHAICIYCTTAHIIALVMGY 125
                                   777889******************************99865 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.49   2.2e+03      31      45 ..      10      24 ..       4      31 .. 0.58
   2 ?    1.8   0.2     0.058   2.6e+02      23      42 ..      56      75 ..      47      81 .. 0.73
   3 ?   11.0   0.3   7.7e-05      0.34      18      54 ..      92     132 ..      87     133 .] 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.49
                       DUF4229 31 llvaallAlvvalpl 45
                                  ++++ +++++++  l
  gi|70606913|ref|YP_255783.1| 10 FVLLSIIGIILSSYL 24
                                  445555555555544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
                       DUF4229 23 rliglpvpllvaallAlvva 42
                                  r++g+pv +l +a +Al + 
  gi|70606913|ref|YP_255783.1| 56 RFFGIPVAILGLAWFALMLG 75
                                  56777777777777777665 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 7.7e-05
                       DUF4229  18 illvarliglp....vpllvaallAlvvalplSmvllkklR 54 
                                   +++v++li ++      + +  + A ++al+ ++++lk  R
  gi|70606913|ref|YP_255783.1|  92 VMFVGYLIYTEveliHAICIYCTTAHIIALVMGYFVLKVSR 132
                                   567777777774454556667789*************9776 PP

>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.16   7.3e+02       5      14 ..      11      20 ..       4      34 .. 0.63
   2 ?   10.6   2.9   0.00013      0.58       6      31 ..      57      82 ..      54     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.16
                           HRG  5 iaygifgsil 14
                                  ++ +i+g+il
  gi|70606913|ref|YP_255783.1| 11 VLLSIIGIIL 20
                                  3344444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                           HRG  6 aygifgsilglsaflvylvlaivnkq 31
                                  ++gi + ilgl++f+  l l+ ++k+
  gi|70606913|ref|YP_255783.1| 57 FFGIPVAILGLAWFALMLGLWMIKKE 82
                                  578999*****************998 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.025   1.1e+02      24      39 ..       8      23 ..       1      39 [. 0.71
   2 ?    5.8   3.7     0.003        14       9      36 ..      56      89 ..      52     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.025
                        OppC_N 24 llllliaifaPliaPy 39
                                  ++++l++i++  ++ y
  gi|70606913|ref|YP_255783.1|  8 IAFVLLSIIGIILSSY 23
                                  6677788887766543 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.003
                        OppC_N  9 rFkrNklAvvglvilllllli.......aifaPli 36
                                  rF+  ++A++gl++++l+l +        i+ P+i
  gi|70606913|ref|YP_255783.1| 56 RFFGIPVAILGLAWFALMLGLwmikkevTIY-PWI 89
                                  888889************9986666664343.666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 848.25
//
Query:       gi|70606914|ref|YP_255784.1|  [L=456]
Description: hypothetical protein Saci_1139 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3194.52
//
Query:       gi|70606915|ref|YP_255785.1|  [L=521]
Description: hypothetical protein Saci_1140 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-05   25.2  10.5    2.4e-05   24.4  10.5    1.4  1  RIFIN        Rifin
     0.0034   15.6   9.4     0.0049   15.1   9.4    1.1  1  Hid1         High-temperature-induced dauer-formation protein
     0.0093   15.5   8.9      0.017   14.6   8.9    1.5  1  Stevor       Subtelomeric Variable Open Reading frame
  ------ inclusion threshold ------
      0.021   14.0  29.3      0.029   13.6  29.3    1.1  1  SOG2         RAM signalling pathway protein
      0.028   14.7   1.8        0.2   12.0   1.8    2.3  1  Orf78        Orf78 (ac78)
       0.16   10.7   5.7       0.25   10.1   5.7    1.3  1  Amnionless   Amnionless
       0.28   10.0  20.3        0.4    9.5  20.3    1.1  1  VSP          Giardia variant-specific surface protein
       0.93    8.4  11.8        1.4    7.8  11.8    1.3  1  BPS1         Protein BYPASS1-related
        1.2    7.1  18.2        1.7    6.5  18.2    1.3  1  Dicty_REP    Dictyostelium (Slime Mold) REP protein
        1.8    5.6  14.8        2.3    5.2  14.8    1.0  1  GREB1        Gene regulated by oestrogen in breast cancer
        2.6    6.3   7.8        3.7    5.8   7.8    1.1  1  Menin        Menin
        3.9    7.7   6.1        5.8    7.1   6.1    1.2  1  GEMIN8       Gemini of Cajal bodies-associated protein 8
        4.4    7.7  14.4        9.1    6.7  14.4    1.5  1  DUF1180      Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4  10.5   1.7e-08   2.4e-05     181     299 ..     394     518 ..     345     521 .] 0.51

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                         RIFIN 181 tatnyknvtslvkaikeeyeescllklkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaeataea 261
                                    + +y++ t+ +++ ++++++s+++++++++++ t+++++++++++++++++++++++ ++  ++ +++++++++++++++
  gi|70606915|ref|YP_255785.1| 394 PTFSYSSSTTTTSTTSTTTSTSTTTSTSSTTTTSTTSSTTTQTTSQTTSTTSTTTSSTSSTSSSSVSSSTSTSTSSQSSTT 474
                                   334555555555555555444444433333333333333333333333333333333333333333333333333333333 PP

                         RIFIN 262 ekae......taaveattaslqtaiiasivaivvIvLimvIIYL 299
                                   ++++       ++ +++++ l+  iia++v++v+Iv ++vI  L
  gi|70606915|ref|YP_255785.1| 475 TTQSlsstvpSSTPASSSSGLSLGIIATVVVVVIIVAVLVILLL 518
                                   33331111113344555666777788888888888888877533 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   9.4   3.5e-06    0.0049     541     704 ..     328     488 ..     327     513 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                          Hid1 541 ealnnviqkqfkgnrnLvYsilrkrkvfealrnltlesaseeiersnesarldsideeeeenssessrieesrsesrspsl 621
                                    ++nnvi+ ++++n  Lv      + +++++++  ++ +  + ++   + +l++++++  +  +    +++ + +s++ ++
  gi|70606915|ref|YP_255785.1| 328 AVINNVIENKYSYNYILVN-YTNGNIIYNSTSSYAYPLQAFYSNGYLYQIQLTEANNAYISLINVL--TPTFSYSSSTTTT 405
                                   589***********99994.4567789999999999999988887777444444444444333333..3333334444444 PP

                          Hid1 622 sevpelksslaitddeskaereksatessssqavsqlremsekarakesaesteesrqesa....tskkspsgmsqsaeek 698
                                   s+ ++++s++ +t+  s ++ +++++++ ++  +s  +++s +++ ++s++st++s   s+    ts++s ++++qs +++
  gi|70606915|ref|YP_255785.1| 406 STTSTTTSTSTTTSTSSTTTTSTTSSTTTQT--TS--QTTSTTSTTTSSTSSTSSSSVSSStstsTSSQSSTTTTQSLSST 482
                                   4444444444444433333322222222221..12..22222222222222222222222200002222233333333333 PP

                          Hid1 699 ftptse 704
                                    + +++
  gi|70606915|ref|YP_255785.1| 483 VPSSTP 488
                                   333333 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   8.9   1.3e-05     0.017     156     261 ..     418     521 .]     379     521 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                        Stevor 156 csvgsvlltliglaaakaaavaakvalsaealkklasslsilnlfsesslesalk.aavsaaaasdlagtaasaassafep 235
                                   +s +s+ +t     ++++++   +++++++++++ +ss+s  ++ s++s +++ + ++++++ +s+++ + + a+ss   +
  gi|70606915|ref|YP_255785.1| 418 TSTSSTTTTSTTSSTTTQTTS--QTTSTTSTTTSSTSSTSSSSVSSSTSTSTSSQsSTTTTQSLSSTVPSSTPASSSSGLS 496
                                   233333333333333322222..3344444555555555556666666666555545556666666666667777788899 PP

                        Stevor 236 ygiaalvllilavvliiLYiwlyrRR 261
                                    gi a v++++++v +++ i l rRR
  gi|70606915|ref|YP_255785.1| 497 LGIIATVVVVVIIVAVLV-ILLLRRR 521
                                   9*9999988777666555.5555555 PP

>> SOG2  RAM signalling pathway protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  29.3   2.1e-05     0.029     254     362 ..     397     496 ..     346     519 .. 0.38

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                          SOG2 254 aspaangaqsetsersasssgvqssasstPlgegstsppgalsrqslsttgststltsssksrsssrsnt..nasastprs 332
                                   + +++++ +s+ts ++++s  ++s++s+t  +++s+++  ++++q+   t+ tst+tss +s+sss++++  ++s+s  +s
  gi|70606915|ref|YP_255785.1| 397 SYSSSTTTTSTTSTTTSTS-TTTSTSSTTTTSTTSSTT-TQTTSQT---TSTTSTTTSSTSSTSSSSVSSstSTSTSSQSS 472
                                   1222222222222211111.111111121111111111.2222222...22233334444444444443311222222233 PP

                          SOG2 333 lattpappasaesfastltasrintlaavD 362
                                    +tt++    +++ ++++t  + ++++++ 
  gi|70606915|ref|YP_255785.1| 473 TTTTQS---LSST-VPSST--PASSSSGLS 496
                                   333332...2222.22233..333333344 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8   0.00014       0.2      33      92 ..     462     521 .]     399     521 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                         Orf78  33 kaenkkekksaaeknditekesn.......aaekaqalnillisllavvcvlvllyviyYfvilrer 92 
                                   +++++++++s+++++       +       +++ a++ + l ++++a v+v+v++ +++ +++lr+r
  gi|70606915|ref|YP_255785.1| 462 STSTSTSSQSSTTTT-------QslsstvpSSTPASSSSGLSLGIIATVVVVVIIVAVLVILLLRRR 521
                                   122222222222222.......13455566789999999******************9999999975 PP

>> Amnionless  Amnionless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.7   0.00018      0.25     268     374 ..     413     520 ..     390     521 .] 0.52

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00018
                    Amnionless 268 evqlavskvaksqrevssdeeiqivildpekgsyaerlaqelladiaehgealgilsaeletsgasssdssaag....apg 344
                                   ++++++s+++ + ++++s++  q   + +++ s++++++   ++   +   +++  s ++ t ++s s++          +
  gi|70606915|ref|YP_255785.1| 413 STSTTTSTSSTTTTSTTSSTTTQTTSQTTSTTSTTTSSTSSTSSSSVSSSTSTSTSSQSSTTTTQSLSST---VpsstPAS 490
                                   3333333333333355566666665555333333333333333332333233333333333333333333...13333567 PP

                    Amnionless 345 esaglvlgivfglvlllllllillllllrr 374
                                   +s gl lgi++++v++++++++l++lllrr
  gi|70606915|ref|YP_255785.1| 491 SSSGLSLGIIATVVVVVIIVAVLVILLLRR 520
                                   8899999*9999999999999999888876 PP

>> VSP  Giardia variant-specific surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  20.3   0.00029       0.4     269     384 ..     400     514 ..     381     519 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00029
                           VSP 269 stvcttcldGyvkssdacakcdsscetctGaattcktcatGyyksatkevactssesdkgvtGvkdclscappssd.kGsv 348
                                   s++ tt +   + s+++ +   s+  t t ++tt +t +     ++t+ ++ tss s  +v   +   + +  s+  + s+
  gi|70606915|ref|YP_255785.1| 400 SSTTTTSTTSTTTSTSTTTSTSSTTTTSTTSSTTTQTTSQTTSTTSTT-TSSTSSTSSSSVSSSTSTSTSSQSSTTtTQSL 479
                                   333444455555666667777777777777777777666555444444.34455555556666655555555444404555 PP

                           VSP 349 lcylikdsgstnksGlstGaiaGisvavvvvvgGlv 384
                                      +   + ++  sGls G ia + v v++ v+ lv
  gi|70606915|ref|YP_255785.1| 480 SSTVPSSTPASSSSGLSLGIIATVVVVVII-VAVLV 514
                                   5555556678999*********99776555.56666 PP

>> BPS1  Protein BYPASS1-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.8     0.001       1.4     171     264 ..     418     514 ..     366     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                          BPS1 171 kdsgssggsernrsfgrsksfhrrsigssgggsigqlrslswsvsrsWsaakqlqalga.nL..atPrandvaatnglavp 248
                                    +++s+++++   s++ + ++++ s++s+ ++s++   s+s s s s s + q  + ++  L  ++P ++ +++++gl++ 
  gi|70606915|ref|YP_255785.1| 418 TSTSSTTTTSTTSSTTTQTTSQTTSTTSTTTSSTSSTSSSSVSSSTSTSTSSQSSTTTTqSLssTVPSSTPASSSSGLSLG 498
                                   344455555556666666666666666777788888888888888888888887765541453378999999999999998 PP

                          BPS1 249 vyimssvlllvmWvLv 264
                                   + +   v+++++ vLv
  gi|70606915|ref|YP_255785.1| 499 IIATVVVVVIIVAVLV 514
                                   8777777777777776 PP

>> Dicty_REP  Dictyostelium (Slime Mold) REP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  18.2    0.0013       1.7     209     299 ..     382     475 ..     333     504 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0013
                     Dicty_REP 209 dEeklselYsLyPfvdlekeesdieqesiesentqrensqpskeknktttttttttt..ttsq..artrkrkaidddklse 285
                                   ++  +s +  L P +    + ++++ ++ +++ t+ ++s  s+++++tt +ttt tt  tts+  ++t    +++  ++s+
  gi|70606915|ref|YP_255785.1| 382 NNAYISLINVLTPTFSYSSSTTTTS-TTSTTTSTSTTTSTSSTTTTSTTSSTTTQTTsqTTSTtsTTTSSTSSTSSSSVSS 461
                                   3555666666666666442222222.2222222222222222222222211111111001111001111111112222222 PP

                     Dicty_REP 286 nqakekkknskksd 299
                                   +++     +s+ ++
  gi|70606915|ref|YP_255785.1| 462 STSTSTSSQSSTTT 475
                                   11111111111111 PP

>> GREB1  Gene regulated by oestrogen in breast cancer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  14.8    0.0017       2.3    1163    1257 ..     401     483 ..     368     516 .. 0.36

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0017
                         GREB1 1163 kasakselseasaaaasaseeakspkasvtseeeeseeskekekeslsketesqlsle..aseqkealdakasskssss 1239
                                    +++++s++s+ +++++++++++++ ++s+t  +++++++++++++++s++t+s+ s++  +++++++++++++s+++++
  gi|70606915|ref|YP_255785.1|  401 STTTTSTTST-TTSTSTTTSTSSTTTTSTT--SSTTTQTTSQTTSTTSTTTSSTSSTSssSVSSSTSTSTSSQSSTTTT 476 
                                    1111111111.1111111111111111111..11111122222222111111111111001111111111111111111 PP

                         GREB1 1240 ssssssassPssscslak 1257
                                    +s+ss           + 
  gi|70606915|ref|YP_255785.1|  477 QSLSS-----------TV 483 
                                    11111...........11 PP

>> Menin  Menin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   7.8    0.0027       3.7     509     603 ..     391     489 ..     377     510 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0027
                         Menin 509 ilnpdfllqggdqplaeqkqkkageeserreannnnnsksnsek..eadkkasttsnggeass....tpsseseaavesps 583
                                   +l p f       + +++   +++++++++ +    ++ s++     +++ ++t+++++++ss    ++ss+++++ +s+ 
  gi|70606915|ref|YP_255785.1| 391 VLTPTFSYSSSTTTTSTTSTTTSTSTTTSTSSTTTTSTTSSTTTqtTSQTTSTTSTTTSSTSStsssSVSSSTSTSTSSQ- 470
                                   56666666666655555554444444444442222222222111002222222222222222210012222222222222. PP

                         Menin 584 ehkeakleeksqelasappa 603
                                       +  +  s ++ s++pa
  gi|70606915|ref|YP_255785.1| 471 -SSTTTTQSLSSTVPSSTPA 489
                                   .2222222223344444454 PP

>> GEMIN8  Gemini of Cajal bodies-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.1    0.0042       5.8      46     114 ..     381     468 ..     338     484 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                        GEMIN8  46 a....................elpsssyadeaseeqsrsdhhlasqdshskssekrrsgqsskdsskkqkseresvdqsiv 106
                                   a                    ++++s+ ++ +s +++++++ +++++s+++s++++++ q+++++s +++s++++ ++s++
  gi|70606915|ref|YP_255785.1| 381 AnnayislinvltptfsysssTTTTSTTSTTTS-TSTTTSTSSTTTTSTTSSTTTQTTSQTTSTTSTTTSSTSSTSSSSVS 460
                                   033333333332222221111222222211111.11222222222222222222222333333333333333333333333 PP

                        GEMIN8 107 seeeeese 114
                                   s+++++++
  gi|70606915|ref|YP_255785.1| 461 SSTSTSTS 468
                                   33332222 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  14.4    0.0066       9.1      29     120 ..     421     519 ..     384     521 .] 0.34

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0066
                       DUF1180  29 aasspeaepPlppgataaes.pgkataieaksaqaaeggngss.pragsaad.......aggslavvpelssntdkpmtlq 100
                                   + ++++++  +  ++t++++    +t+++++s++++ + + s+ + ++s++        ++++ +  p  ss+   +    
  gi|70606915|ref|YP_255785.1| 421 SSTTTTSTTSSTTTQTTSQTtSTTSTTTSSTSSTSSSSVSSSTsTSTSSQSSttttqslSSTVPSSTPASSSSGLSLGI-I 500
                                   1111111111111222222212222222333222222222222122222222222222233333333322222222222.2 PP

                       DUF1180 101 rallvlvvvsaavivylvvR 120
                                    a +v+vv+  av+v+l++R
  gi|70606915|ref|YP_255785.1| 501 -ATVVVVVIIVAVLVILLLR 519
                                   .2233333344455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3217  (0.17943); expected 358.6 (0.02)
Passed bias filter:                      904  (0.0504211); expected 358.6 (0.02)
Passed Vit filter:                       346  (0.0192983); expected 17.9 (0.001)
Passed Fwd filter:                        78  (0.00435049); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 1.25u 0.33s 00:00:01.58 Elapsed: 00:00:00.54
# Mc/sec: 2911.55
//
Query:       gi|70606916|ref|YP_255786.1|  [L=257]
Description: hypothetical protein Saci_1141 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-10   40.6   0.0    4.2e-10   40.2   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.026   14.7   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
       0.13   11.9   5.2        9.9    5.8   5.6    2.2  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   7.1e-14   4.2e-10       2     166 ..      25     191 ..      24     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 7.1e-14
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpgi 78 
                                   ++++ C++ C++C+  + v++ + + +  +++i++ +k+  ++k  ++v+ ++  ++ y + + l++  +k      + g+
  gi|70606916|ref|YP_255786.1|  25 NPYNNCRFSCIYCYAQRYVSDKWGEVITIKRNIVDVLKRE-VYKYRRGVVGVSTIVDPYQPVEGLYKLTRKSLevllSHGF 104
                                   67899*************9999999999999999999999.6776555555555455554444444444444468999*** PP

                                   EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmn.rghtfeevlealeklreagikrvvdrivglpGend 157
                                   r+++ t  +++  + l++l ++  d v +gl +++ + +v ++++   + ++++ e+++kl ++ ++  ++  ++++G+nd
  gi|70606916|ref|YP_255786.1| 105 RVSIQTKSPMV-VRDLDLLSRYS-DKVDVGLTITTLDkVVSRYIEpLAPPPKARAESIKKLSRS-VRTWIFLGPIIKGVND 182
                                   ***********.***********.777776666666656999999999****************.99889999******** PP

                                   HHHHHHHHH CS
                                   xxxxxxxxx RF
                   Radical_SAM 158 eeleellel 166
                                   + +ee+++l
  gi|70606916|ref|YP_255786.1| 183 SGFEEIVKL 191
                                   *****9987 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.3e-06     0.026       6      40 ..      28      63 ..      25     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                       Fer4_14  6 sgCnlsCkgCdnketwkselgkpqt.eelleqilkd 40
                                  + C++sC  C+ +   ++++g++ t ++ ++++lk 
  gi|70606916|ref|YP_255786.1| 28 NNCRFSCIYCYAQRYVSDKWGEVITiKRNIVDVLKR 63
                                  78*******************987724455566642 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.6    0.0017       9.9     253     265 .]      27      39 ..      22      39 .. 0.94
   2 ?    3.6   0.0    0.0079        47      63     109 ..     117     167 ..      73     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0017
                       DUF1848 253 yntClhgCvYCYA 265
                                   yn C+  C+YCYA
  gi|70606916|ref|YP_255786.1|  27 YNNCRFSCIYCYA 39 
                                   9***********9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0079
                       DUF1848  63 kkleelkergiklyfqfTltdyek...e.lepnvpsleerietfkelsekl 109
                                   + l+ l++ + k+ + +T+t+ +k     +ep  p+ + r e++k+ls+ +
  gi|70606916|ref|YP_255786.1| 117 RDLDLLSRYSDKVDVGLTITTLDKvvsRyIEPLAPPPKARAESIKKLSRSV 167
                                   4566666655566666666655441113599999*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1684.61
//
Query:       gi|70606917|ref|YP_255787.1|  [L=397]
Description: hypothetical protein Saci_1142 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-95  318.7   0.0    5.1e-95  318.4   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    2.4e-37  127.2   0.2    5.3e-37  126.1   0.1    1.6  2  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.4   0.0   5.7e-99   5.1e-95       1     270 []      15     278 ..      15     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.4 bits;  conditional E-value: 5.7e-99
                         Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklrl 81 
                                   Lcgl +cpi+ k  +++ ++ k    ++ GsspPs+fVGrygYPkVsv+p++ppv++d+s++++p++wl+++l+++++lrl
  gi|70606917|ref|YP_255787.1|  15 LCGLAYCPIVVKSITKKIVVPK----DMVGSSPPSIFVGRYGYPKVSVYPSAPPVVDDTSIYEDPKTWLNMDLNTFLSLRL 91 
                                   8*********998887776655....6****************************************************** PP

                         Nre_N  82 slvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkvekl 161
                                   slvrg ++++v++a+ ++++l+++q+l++s+ p ++e+e++k+  +k+ +de+l+P+Gpsa+++++k+   +  +r ve++
  gi|70606917|ref|YP_255787.1|  92 SLVRGGESFRVTDANnPQRFLHDVQTLSISSGPSEIEMEFAKE-PRKVVLDETLPPIGPSAPIREFKLGTLSAPQRIVERV 171
                                   **************9999*************************.699********************************** PP

                         Nre_N 162 veDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsgeyl 242
                                   +eD+dlk+++av++Ly+++v+v+ i+rlLSvG+LG+  kr+lVPTr sITAvd+ v+++l++e+k++++id++ev++++++
  gi|70606917|ref|YP_255787.1| 172 YEDKDLKSKDAVITLYSNKVEVNVISRLLSVGVLGV--KRKLVPTRRSITAVDKLVSDSLIEELKHFESIDKIEVYVRRHM 250
                                   ***********************************9..******************************************* PP

                         Nre_N 243 gNrflviLaPgkwsfelvEawapgslwn 270
                                   +N f+ iL+Pg+w+fe+ Eaw+pgs+wn
  gi|70606917|ref|YP_255787.1| 251 KNLFIGILIPGNWAFEWGEAWFPGSTWN 278
                                   ***************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.2   1.1e+04      63      85 ..     229     251 ..     223     252 .. 0.70
   2 !  126.1   0.1   5.9e-41   5.3e-37       1     102 [.     292     393 ..     292     396 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.2
                         Nre_C  63 lekkpkefesleealeevseklk 85 
                                   l ++ k+fes++++  +v++++k
  gi|70606917|ref|YP_255787.1| 229 LIEELKHFESIDKIEVYVRRHMK 251
                                   55677788888888777777765 PP

  == domain 2  score: 126.1 bits;  conditional E-value: 5.9e-41
                         Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevs 81 
                                   egy+gr++y++i+G+Yya+rl+v+e L+ +krqa vi++rei+p++++PvGvW+vRe++r+++++kp+ f++l++al+ v+
  gi|70606917|ref|YP_255787.1| 292 EGYRGRRTYPKIGGCYYASRLGVAESLRLRKRQAMVILWREIYPGFNLPVGVWFVRENIREMFKQKPEVFDTLDQALRRVK 372
                                   799****************************************************************************** PP

                         Nre_C  82 eklklplkkllkkskllkelk 102
                                    +lk++l+++lk s ++k ++
  gi|70606917|ref|YP_255787.1| 373 GELKVNLQEWLKISYVVKLFR 393
                                   ***************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2540.89
//
Query:       gi|70606918|ref|YP_255788.1|  [L=122]
Description: hypothetical protein Saci_1143 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   62.9   0.0    2.4e-17   62.9   0.0    1.0  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   1.4e-21   2.4e-17     150     263 ..       6     112 ..       1     122 [] 0.91

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.4e-21
                          LigB 150 sferlykLGeAlrkaveel...dknvlilgsGglsHqlegdeaakadaqtlllneefdeelldllkegrveelckmskeel 227
                                     +r+++LG+A++++v +    +++v+i+g+GglsH +  +  +       +++  fd+++l+ lk+g+ +el k+s ++l
  gi|70606918|ref|YP_255788.1|   6 PVRRCFELGRAIARIVAKKrpeNEKVAIIGTGGLSHFPGTPYYG-------KIDIDFDNFILETLKAGKGKELAKLSDDKL 79 
                                   679*************9999*****************9999988.......5888*************************9 PP

                          LigB 228 saaagheeeelvplvvalGalsgdkaelrkelvsye 263
                                   ++    +++el++++v  Ga+++++ae+ + +++y 
  gi|70606918|ref|YP_255788.1|  80 EET---GNIELRTWIVPVGAVGNKPAEILERQITYH 112
                                   999...8***************99999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 912.56
//
Query:       gi|70606919|ref|YP_255789.1|  [L=1275]
Description: hypothetical protein Saci_1147 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-11   44.1   0.1      2e-10   41.1   0.0    2.3  2  Pro-kuma_activ  Pro-kumamolisin, activation domain
      6e-07   29.0   0.1    1.8e-06   27.4   0.1    1.8  2  Peptidase_S8    Subtilase family
    8.2e-05   23.0   0.3        1.5    9.3   0.0    4.2  5  MG2             MG2 domain
  ------ inclusion threshold ------
      0.087   12.7   5.5        1.8    8.5   0.0    4.6  5  FlgD_ig         FlgD Ig-like domain
        2.7    7.5   4.8        4.7    6.7   4.8    1.4  1  Stevor          Subtelomeric Variable Open Reading frame


Domain annotation for each model (and alignments):
>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   5.7e-14     2e-10       5     117 ..      39     143 ..      35     152 .. 0.89
   2 ?   -0.4   0.0      0.36   1.3e+03      64      95 ..     540     572 ..     537     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 5.7e-14
                Pro-kuma_activ   5 krgraasstllpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtk 85 
                                   + + ++s+tll++++ ++++nl+ l+  +++v++ + +     lt++++ + f++ ++ ++++ n+Les+g+++ +   + 
  gi|70606919|ref|YP_255789.1|  39 NAKLLPSNTLLTLTFFIPPKNLNMLYYTAEEVANHQIS----PLTPQQIIKEFSQPNK-VTSLINFLESNGFTIYY--SSP 112
                                   5667899*************************984444....6**********99988.*****************..*** PP

                Pro-kuma_activ  86 gwiafsatvaqverllktsfeaYshkkgsssl 117
                                     ++++at++++ +++ t++  +s ++g+ ++
  gi|70606919|ref|YP_255789.1| 113 FAVVATATAGKIDNVFSTELGLFS-YNGHVYY 143
                                   ************************.8666665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                Pro-kuma_activ  64 idaVrnwLessgiaasr.hsdtkgwiafsatva 95 
                                   ++a++++L+ +++++s  ++ t  w+  + tv+
  gi|70606919|ref|YP_255789.1| 540 LNAIQQYLKTNNLEISVtTNGTIPWYMYNSTVS 572
                                   689***********9995555567777777776 PP

>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.1     5e-10   1.8e-06     104     265 ..     282     483 ..     250     499 .. 0.75
   2 ?   -3.8   0.0       1.7     6e+03      76     125 ..     759     808 ..     754     811 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5e-10
                                   HH..HHHHHHHHHHHH.CT-SEEEE-EE.............SCETTCHHCHHHHHH............HHHHHH.CCT-EE CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxx.............xxxxxxxxxxxxxxx............xxxxxxxxxxxxx RF
                  Peptidase_S8 104 metgteliraieeaae.dkvdvinmslg.............estslpktgrsieal............ainravnkkgvlv 158
                                   + +g++l++a+++++  +  dv++ms+g                           +             + ++   +g+ +
  gi|70606919|ref|YP_255789.1| 282 SDSGPTLYAAVDYVVTqKLGDVVSMSWGlsenlfaasgfyyF-------------IngqpfpnypyldYYFALGTAEGITF 349
                                   234589**********55568*******66654444444331.............2344566666667444444456**** PP

                                   EEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES................................TTSSB-TT--B-T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxx RF
                  Peptidase_S8 159 viSaGNngktgsslqagspvgtpstsknvitvgayt................................tegkiapfSsrGp 207
                                    +S+G  g +g+sl++    ++p+ts  v++vg++t                                +     p+ + G 
  gi|70606919|ref|YP_255789.1| 350 FASSGDTGAYGDSLTTYGGASFPATSPFVTAVGGTTlylssgkayetawsvlpqyfeyagtvssgggySTFFPRPWYQDGV 430
                                   ************9999988999*****************************************777774444555555554 PP

                                   T........-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHH CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 208 ssd.gklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsal 265
                                        ++ pd++a +      ++  + +  g+   + + GTS AsP+ ag++A ++s l
  gi|70606919|ref|YP_255789.1| 431 INSsFRAVPDVAADANP----YTGFNITVLGS--EEIIGGTSLASPLWAGMLADIISQL 483
                                   32248888999999998....88888444444..579****************999976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.7
                                   ..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8  76 apeegekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvi 125
                                   +p + ++ gv pg  i+ + +  t++g+ + ++++ + i+ ++ + v  +
  gi|70606919|ref|YP_255789.1| 759 TPINTGFPGVSPGQNITLFAFTLTPEGTGQLSSNVSAFIYNQNGQLVSTV 808
                                   477888999*****999999999999999875555444444444655555 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.43   1.5e+03      14      83 ..     568     635 ..     563     646 .. 0.74
   2 !    7.7   0.0    0.0014         5      25      92 ..     681     747 ..     673     750 .. 0.75
   3 !    9.3   0.0   0.00041       1.5      13      84 ..     770     851 ..     768     862 .. 0.84
   4 ?   -1.9   0.0       1.4   4.9e+03      65      80 ..     958     973 ..     924     992 .. 0.54
   5 ?   -3.9   0.0         5   1.8e+04      70      80 ..    1191    1201 ..    1172    1213 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.43
                                   T-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                           MG2  14 getVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsad 83 
                                   + tVs+ a++  ++++ + +  ++++i++++g +v + pl  + t    ++f+++ +     +s+ ++ +
  gi|70606919|ref|YP_255789.1| 568 NSTVSVIAYITYPNGTIVSQGTFSAYIQTTSG-TVTTIPLSFNGT-DWVGSFNIQPGMTPNIWSIIVNGS 635
                                   57899999999999999999999999987755.566788777766.357888888888888888777444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                                   STTCSB---EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEE CS
                           MG2  25 detlqglaklplkltirdpdgkevkelpl.atdetggaesefalpeaaklGeysvelsadsaeeslssg 92 
                                   +++++++ ++ + +++ +  gk+v++  l  t++ g + +++al + a++G+y +++ + s +++++  
  gi|70606919|ref|YP_255789.1| 681 NPDGTPAVNQTVNVYLLKN-GKVVESAVLtPTSQPGEYVGQLALITPAEQGTYILVV-NTSYGSAYTYV 747
                                   5788888888888888875.55555555537888888********************.55555555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00041
                                   TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEE..........EE-CTTEEEEEEE--TT--SEEEEEEEEEC CS
                           MG2  13 PgetVslkallrdetlqglaklplkltirdpdgkevkelpl..........atdetggaesefalpeaaklGeysvelsad 83 
                                   Pg+++ l a++++++++g  + ++++ i++++g+ v++  l          + + +g++  +f++p++   G ysv ++ +
  gi|70606919|ref|YP_255789.1| 770 PGQNITLFAFTLTPEGTGQLSSNVSAFIYNQNGQLVSTVNLtqapeitlfgVFNFFGLYYANFTIPSNFTPGFYSVIIQSQ 850
                                   9*********************************999999976776666666777888******************99433 PP

                                   S CS
                           MG2  84 s 84 
                                    
  gi|70606919|ref|YP_255789.1| 851 A 851
                                   3 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.4
                                   EE--TT--SEEEEEEE CS
                           MG2  65 falpeaaklGeysvel 80 
                                   +  p  +  G ++v++
  gi|70606919|ref|YP_255789.1| 958 LGYPPYTLSGPWTVYI 973
                                   3344455556666666 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 5
                                    T--SEEEEEEE CS
                           MG2   70 aaklGeysvel 80  
                                    a + G+y++++
  gi|70606919|ref|YP_255789.1| 1191 ALPSGQYTIVV 1201
                                    45789999998 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.097   3.5e+02      21      49 ..     686     716 ..     681     741 .. 0.75
   2 ?    8.5   0.0   0.00049       1.8      22      46 ..     790     814 ..     777     820 .. 0.87
   3 ?   -2.4   0.0       1.2   4.4e+03      48      70 ..     967     989 ..     966     992 .. 0.79
   4 ?   -1.3   0.1      0.58   2.1e+03      33      63 ..    1038    1068 ..    1031    1070 .. 0.81
   5 ?    0.7   0.0      0.14   4.9e+02      62      75 ..    1190    1203 ..    1187    1206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.097
                                   SSEEEEEEEE-S.S--EEEEEEEEESSS.EE CS
                       FlgD_ig  21 aadevtvtikDa.sGevVrtidlgaqsa.Gv 49 
                                   +a + tv+++   +G+vV++  l++ s+ G+
  gi|70606919|ref|YP_255789.1| 686 PAVNQTVNVYLLkNGKVVESAVLTPTSQpGE 716
                                   6677788888654********9999887444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00049
                                   SEEEEEEEE-SS--EEEEEEEEESS CS
                       FlgD_ig  22 adevtvtikDasGevVrtidlgaqs 46 
                                   +++v+  i++++G++V t++l++ +
  gi|70606919|ref|YP_255789.1| 790 SSNVSAFIYNQNGQLVSTVNLTQAP 814
                                   6788899**************9865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                   EEEEEEE-SB-TTS-B--SEEEE CS
                       FlgD_ig  48 GvvsftWdGtdndGnkladGaYt 70 
                                   G  ++   G  ++Gn+ ++G   
  gi|70606919|ref|YP_255789.1| 967 GPWTVYISGVSANGNPISSGPTY 989
                                   5667788999********99744 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.58
                                    S--EEEEEEEEESSSEEEEEEE-SB-TTS-B CS
                       FlgD_ig   33 sGevVrtidlgaqsaGvvsftWdGtdndGnk 63  
                                    ++ vV ++++ +++ Gv+s t++  +++ +k
  gi|70606919|ref|YP_255789.1| 1038 NNVVVGNLTVVNSQVGVSSSTLNSLTAKNSK 1068
                                    5668899***********9999988877766 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.14
                                    -B--SEEEEEEEEE CS
                       FlgD_ig   62 nkladGaYtvkvta 75  
                                    ++l++G+Yt+ v +
  gi|70606919|ref|YP_255789.1| 1190 SALPSGQYTIVVMT 1203
                                    579*******9865 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.8    0.0013       4.7     160     260 ..    1177    1275 .]    1138    1275 .] 0.60

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                        Stevor  160 svlltliglaaakaaavaakvalsaealkklas..slsilnlfsesslesalkaavsaaaasdlagtaasaas..safe 234 
                                    s   t+i++ ++++a  + + +++  +++ l    s +++n + + sl+s+l+     +a+++l+++++s as  + + 
  gi|70606919|ref|YP_255789.1| 1177 SQNSTTISIPFSSSALPSGQYTIVVMTYNGLPYnvSATVYNAYPQISLSSSLS-----NATTSLSSKISSNASdvAFYR 1250
                                    44556677777777777666666666666554400456677777777776553.....333344444444343003455 PP

                        Stevor  235 pygiaalvllilavvliiLYiwlyrR 260 
                                       ia l++ i++++l+i Y+ l+rR
  gi|70606919|ref|YP_255789.1| 1251 NITIASLIIAIISLILVI-YLLLRRR 1275
                                    677777777777766654.7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 8668.77
//
Query:       gi|70606920|ref|YP_255790.1|  [L=582]
Description: hypothetical protein Saci_1148 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-33  115.9   3.4    9.8e-32  110.4   3.4    2.1  1  PNGaseA   Peptide N-acetyl-beta-D-glucosaminyl asparaginase a


Domain annotation for each model (and alignments):
>> PNGaseA  Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   3.4   5.5e-36   9.8e-32      22     404 ..      76     430 ..      64     442 .. 0.80

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 5.5e-36
                       PNGaseA  22 FgnsygkPfvgkytpPecsfdrvvlnltvtssG.rqydRlallylgdvevwRTSTaepttagivwtylKdvseYlaLfkep 101
                                   F n+   P v++   P  +++ + ln+ ++  G +q+dR   ++ ++++++ +ST e ++    +t++ dv+ +  L++ +
  gi|70606920|ref|YP_255790.1|  76 FNNTGIIPKVVTLYIPPGNYSMILLNISIKEYGgAQFDRPVYIFANGIPIFWGSTQEIRN----STAQTDVTMFENLLQGN 152
                                   5555556877776666679**********98776***********************987....68899************ PP

                       PNGaseA 102 qklifdLgNliddt..ytgsfnvtltatfyaseelletaeaadlilpisarksasnsssafslpsd.katvtlslprntsr 179
                                    ++ + L     +     g +++++t+ +y  +   ++a  ++  +p+     + n s ++  p + ++t ++++p+ t r
  gi|70606920|ref|YP_255790.1| 153 VTFQLVLATYYAKSvgIVGLYSMNVTLLLYPGN---KPAGLPNYFIPLFM--NSLNYSRVVLNPLNdQVTQSVVMPNGTFR 228
                                   ***999999887652268***************...9************8..4445555554454438888888******* PP

                       PNGaseA 180 avlsisasgqaaeEfWysNvlssdteafedtvgelyghspfRevqvlidGqlagvvwPfpviftGGisPglwrPivgidaf 260
                                    vl ++  g + +EfWy+N+  +                  R++ v+ +  lagvv P+p+i+tGGi+   wrP+++i+++
  gi|70606920|ref|YP_255790.1| 229 SVLLLYYEGGGLDEFWYTNIPAT------------------RNILVYYNSLLAGVVNPYPIIYTGGINLFWWRPVTSINTL 291
                                   ********************876..................9*************************************98 PP

                       PNGaseA 261 Dlrele.iditpfLplLldgedheleikvagledeeegtatlsktvgsyWvvtgnlfvwldssskesegtivetdtkpeik 340
                                      +++ i++tp+L     +++ ++++ v++l      +a++  + + +W ++g l++w+++s+   +++++++d++   +
  gi|70606920|ref|YP_255790.1| 292 AFETPQyIELTPLLA---TSTKPNITVTVSNLLA----SAQELGSTALSWTISGVLMLWVNNSNPLISSKLISADARYVDS 365
                                   8887644****9765...688899********99....55556666789***************99999999999883333 PP

                       PNGaseA 341 akap.slkvtreleqnsatgtneslsytveaerslsvesttvtwsqklsfsntqllsqqglsqsv 404
                                   ++++  l+ +   +q +  ++n +   ++e+ ++++++ ++ +++   sf+ + +++q  l+q+ 
  gi|70606920|ref|YP_255790.1| 366 QPIFtGLSGSTYYQQGEYYSINYTSILKFENGQEFATTYEEGKVTAYQSFNPSFIYQQAILDQQF 430
                                   33333333344444444445555555556666777776666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3715.27
//
Query:       gi|70606921|ref|YP_255791.1|  [L=149]
Description: hypothetical protein Saci_1151 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-28   98.7   0.0    2.8e-28   98.5   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   1.6e-32   2.8e-28       2     121 ..      21     137 ..      20     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 1.6e-32
                     tRNA_edit   2 pgtktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvgPlg 82 
                                   p+++t++++   lgv++++iaKt+++  +++++++v+l+g+r++dl+kl+  l+++++r+a++ e+++++g+e+Gg++Pl 
  gi|70606921|ref|YP_255791.1|  21 PNARTVKDASMSLGVSEDRIAKTILVI-ADNKPYAVFLRGNRRVDLDKLKLYLNVREIRVAKASEVKKITGYEVGGLPPLI 100
                                   899************************.6888************************************************7 PP

                     tRNA_edit  83 lkaagvpvllDeslkeyp.tvvvgagengatlelspedlr 121
                                       gv++++De+l++ + +v++g+g ++++l++ p++l 
  gi|70606921|ref|YP_255791.1| 101 N---GVETIMDEELADDDkEVFCGGGNETTLLSIIPKELA 137
                                   5...7*************99***************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1008.76
//
Query:       gi|70606922|ref|YP_255792.1|  [L=61]
Description: hypothetical protein Saci_1152 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0065   16.4   0.6     0.0074   16.3   0.6    1.1  1  YscO          Type III secretion protein YscO
     0.0068   15.6   0.6     0.0068   15.6   0.6    1.0  1  Cas_St_Csn2   CRISPR-associated protein Csn2 subfamily St
  ------ inclusion threshold ------
      0.012   15.7   0.6       0.32   11.1   0.3    2.2  2  COMM_domain   COMM domain
      0.017   15.4   0.0      0.019   15.2   0.0    1.1  1  DUF948        Bacterial protein of unknown function (DUF948)
      0.025   15.1   0.4      0.038   14.5   0.4    1.5  1  YtxH          YtxH-like protein
      0.028   13.9   2.0      0.036   13.6   1.3    1.6  1  DegS          Sensor protein DegS
      0.039   14.2   2.0      0.052   13.9   2.0    1.2  1  Glu-tRNAGln   Glu-tRNAGln amidotransferase C subunit
      0.056   13.5   1.1      0.056   13.5   1.1    1.7  2  HisKA         His Kinase A (phospho-acceptor) domain
      0.061   13.4   1.6       0.12   12.4   1.6    1.8  1  YojJ          Bacterial membrane-spanning protein N-terminus
      0.064   13.2   1.6      0.068   13.1   1.6    1.1  1  RRF           Ribosome recycling factor
        0.1   12.6   0.1       0.11   12.5   0.1    1.1  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.11   13.0   0.0       0.13   12.8   0.0    1.1  1  DUF3391       Domain of unknown function (DUF3391)
       0.12   11.7   3.7       0.65    9.2   0.9    1.9  2  CorA          CorA-like Mg2+ transporter protein
       0.13   11.7   1.0       0.15   11.5   1.0    1.1  1  Golgin_A5     Golgin subfamily A member 5
       0.17   12.3   2.2       0.37   11.2   1.0    1.9  2  FlaC_arch     Flagella accessory protein C (FlaC)
        0.2   11.7   0.9       0.24   11.4   0.9    1.2  1  DUF1664       Protein of unknown function (DUF1664)
       0.77    9.1   5.1       0.85    8.9   5.1    1.0  1  TraF_2        F plasmid transfer operon, TraF, protein
          2    8.3   4.5        7.6    6.4   0.7    2.4  2  TnpW          Transposon-encoded protein TnpW


Domain annotation for each model (and alignments):
>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   7.4e-06    0.0074      33      87 ..       2      60 ..       1      61 [] 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-06
                                  HHHHHHHHHHHHHHHH...HHHHHHHHHH.HTTT--HHHHHHHHHHHHHHHHHHHHHHH CS
                          YscO 33 heqaresladyrawra...qeearlyaei.igklvllkelekvkqqvalLrekeaelek 87
                                  +e+a+e+l+d+r+ ++   ++ ++++ e+  gk ++ +el+++  +v++Lr+  ++l+ 
  gi|70606922|ref|YP_255792.1|  2 REEAKEELEDIRDKLErilDKINDMINELdSGKDIDYDELDRIIDEVGILRDDLKNLKR 60
                                  68899999999987762236899999999558********************9999875 PP

>> Cas_St_Csn2  CRISPR-associated protein Csn2 subfamily St
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   6.9e-06    0.0068     102     144 ..       5      45 ..       1      60 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                                   CHHHHHHHHHHHHHHHHHHHCC---EETTEE-------HHHHH CS
                   Cas_St_Csn2 102 ivvdlekiseqlerifeamneeikenigkveldleenslinll 144
                                    +++le i ++leri   +n+ i+e  +  ++d++e+  ++++
  gi|70606922|ref|YP_255792.1|   5 AKEELEDIRDKLERILDKINDMINELDSGKDIDYDEL--DRII 45 
                                   6789**********************99999999986..3333 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00032      0.32      50      70 ..       6      26 ..       3      32 .. 0.91
   2 ?    3.2   0.0     0.095        94      49      71 ..      37      59 ..      35      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                   COMM_domain 50 keqLqeLlneLeeiqkqlesl 70
                                  ke+L++ +++Le+i+++++++
  gi|70606922|ref|YP_255792.1|  6 KEELEDIRDKLERILDKINDM 26
                                  89**************99876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.095
                   COMM_domain 49 skeqLqeLlneLeeiqkqlesla 71
                                  + ++L+  ++e++  ++ l++l+
  gi|70606922|ref|YP_255792.1| 37 DYDELDRIIDEVGILRDDLKNLK 59
                                  789**********9999999886 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.9e-05     0.019      29      87 ..       3      58 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                        DUF948 29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87
                                  +ea++ +e+++++++ il++++d++++      +     +++d+++++v+ l + +++l
  gi|70606922|ref|YP_255792.1|  3 EEAKEELEDIRDKLERILDKINDMINELDS---GKDIDYDELDRIIDEVGILRDDLKNL 58
                                  578888899999999999999999988888...44447899999999999888888887 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   3.8e-05     0.038      26      53 ..       1      34 [.       1      60 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                          YtxH 26 tRkdlkekaddlkekakelleeakeka......k 53
                                  +R+++ke+++d+++k++++l+++++        k
  gi|70606922|ref|YP_255792.1|  1 MREEAKEELEDIRDKLERILDKINDMIneldsgK 34
                                  5899999999999999888766655555533330 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.3   3.6e-05     0.036      22      52 ..       2      32 ..       1      45 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                          DegS 22 aEsarkeverlkkeleelkeevsevikevdk 52
                                   E+a++e+e+++++le++ ++++++i+e d+
  gi|70606922|ref|YP_255792.1|  2 REEAKEELEDIRDKLERILDKINDMINELDS 32
                                  599*************************997 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   5.2e-05     0.052       4      42 ..       7      54 ..       5      61 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                                  HHHHHHHHHHHHHHHHH.TTCGCS-..-T.T----S.......-EB-S CS
                   Glu-tRNAGln  4 eEleklakelnsildyv.eqLqevd..tt.gveplthp.....vlReD 42
                                  eEle++  +l++ild + + ++e+d   + + + l ++      lR+D
  gi|70606922|ref|YP_255792.1|  7 EELEDIRDKLERILDKInDMINELDsgKDiDYDELDRIidevgILRDD 54
                                  99*************99567899**65455778888889999999999 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   5.6e-05     0.056      34      59 ..       2      27 ..       1      36 [. 0.85
   2 ?   -0.3   0.1       1.1   1.1e+03      50      58 ..      40      48 ..      29      59 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                  HSSCHHHHHHHHHHHHHHHHHHHHHH CS
                         HisKA 34 teelkeyletiesearrldhlvedlL 59
                                  +ee ke le+i++  +r+++ ++d+ 
  gi|70606922|ref|YP_255792.1|  2 REEAKEELEDIRDKLERILDKINDMI 27
                                  5999********************93 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                                  HHHHHHHHH CS
                         HisKA 50 rldhlvedl 58
                                   ld++++++
  gi|70606922|ref|YP_255792.1| 40 ELDRIIDEV 48
                                  556666554 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6   0.00012      0.12      12      35 ..      10      33 ..       1      58 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                          YojJ 12 eklkeeLeqiekeleevlkaldee 35
                                  e+++ +Le i  ++++++++ld+ 
  gi|70606922|ref|YP_255792.1| 10 EDIRDKLERILDKINDMINELDSG 33
                                  577777777777777777777765 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   6.8e-05     0.068      96     144 ..       3      53 ..       1      59 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.C.S-HHHHHHHHHHHHHHHH CS
                           RRF  96 keakkaaekakvairniRrdankklkklek.k.iseDdvkkaekeiqkltd 144
                                   +eak++ e++++++ +i  ++n+ +++l++ k i  D++ ++ +e+  l d
  gi|70606922|ref|YP_255792.1|   3 EEAKEELEDIRDKLERILDKINDMINELDSgKdIDYDELDRIIDEVGILRD 53 
                                   689***********************9999768999***999999876655 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011      0.11      39      90 ..       8      58 ..       2      61 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                  Baculo_PEP_C 39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnl 90
                                   l++i  +L+ + ++++++++eld+  d   ++L++ + ++   lr +L+nl
  gi|70606922|ref|YP_255792.1|  8 ELEDIRDKLERILDKINDMINELDSGKDIDYDELDRIIDEVG-ILRDDLKNL 58
                                  456666777777777777777777766666666666666665.666666665 PP

>> DUF3391  Domain of unknown function (DUF3391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.13      98     135 ..       3      40 ..       1      41 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                       DUF3391  98 eaereeleraeklyeeakqlvrslfsdvrlgkaidvep 135
                                   e+ +eele+++  +e+  + ++++++++ +gk id+++
  gi|70606922|ref|YP_255792.1|   3 EEAKEELEDIRDKLERILDKINDMINELDSGKDIDYDE 40 
                                   55677******************************986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.9   0.00066      0.65     188     217 ..       3      32 ..       1      37 [. 0.75
   2 ?    3.9   0.1     0.028        28     198     219 ..      38      59 ..      34      61 .] 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00066
                          CorA 188 dedkeylrdlldelerllemlealrerles 217
                                   +e+ke l+d++d+ler+l++++ + + l+s
  gi|70606922|ref|YP_255792.1|   3 EEAKEELEDIRDKLERILDKINDMINELDS 32 
                                   567777888888888888888888877776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.028
                          CorA 198 ldelerllemlealrerleslq 219
                                   +del+r+++++ +lr+ l +l+
  gi|70606922|ref|YP_255792.1|  38 YDELDRIIDEVGILRDDLKNLK 59 
                                   899**************99986 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   0.00015      0.15       3      66 ..       3      58 ..       2      61 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                     Golgin_A5  3 esakqeledYKqkAarILQsKekliasLkegsgeeglesstalsaeldelkqerdllreelqkl 66
                                  e+ak+eled + k +rIL + + +i++L +g+         +  +eld + +e  +lr++l++l
  gi|70606922|ref|YP_255792.1|  3 EEAKEELEDIRDKLERILDKINDMINELDSGK--------DIDYDELDRIIDEVGILRDDLKNL 58
                                  689*************************9775........234467777777777777777665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00037      0.37      18      41 ..       4      27 ..       1      32 [. 0.91
   2 ?    0.4   0.0      0.88   8.8e+02       9      26 ..      41      58 ..      34      61 .] 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                     FlaC_arch 18 tvkkeneelsksveelkenVkdll 41
                                   +k+e+e++++++e++ ++++d++
  gi|70606922|ref|YP_255792.1|  4 EAKEELEDIRDKLERILDKINDMI 27
                                  6899****************9998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.88
                     FlaC_arch  9 lsklsteletvkkeneel 26
                                  l+++  e++ +++++++l
  gi|70606922|ref|YP_255792.1| 41 LDRIIDEVGILRDDLKNL 58
                                  333333444444444444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   0.00024      0.24      47     102 ..       6      61 .]       1      61 [] 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                       DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                    ++le++ ++l++  +++++ i+++d+  d   +    i +ev  +r+dl+++++d
  gi|70606922|ref|YP_255792.1|   6 KEELEDIRDKLERILDKINDMINELDSGKDIDYDELDRIIDEVGILRDDLKNLKRD 61 
                                   56788888888888888888888888888888888899999999999999998865 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.1   0.00085      0.85      32      80 ..       5      60 ..       2      61 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00085
                        TraF_2 32 dvdnlvDkiDdlsdildgleaavnaasad......etq.vdeaaddlnalLedlgg 80
                                   +++l D  D+l+ ild++++ +n+++ +      e + + +++  l+++L++l++
  gi|70606922|ref|YP_255792.1|  5 AKEELEDIRDKLERILDKINDMINELDSGkdidydELDrIIDEVGILRDDLKNLKR 60
                                  6899*********************9999777655444677777777777777776 PP

>> TnpW  Transposon-encoded protein TnpW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7    0.0077       7.6      22      32 ..      10      20 ..       2      21 .. 0.90
   2 ?    5.6   0.6     0.014        14      24      32 ..      19      27 ..      17      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0077
                          TnpW 22 ETiaDKikRli 32
                                  E+i DK++R++
  gi|70606922|ref|YP_255792.1| 10 EDIRDKLERIL 20
                                  89*******97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
                          TnpW 24 iaDKikRli 32
                                  i DKi+++i
  gi|70606922|ref|YP_255792.1| 19 ILDKINDMI 27
                                  89******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1915  (0.10681); expected 358.6 (0.02)
Passed bias filter:                     1351  (0.0753528); expected 358.6 (0.02)
Passed Vit filter:                       224  (0.0124937); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 400.05
//
Query:       gi|70606923|ref|YP_255793.1|  [L=181]
Description: hypothetical protein Saci_1153 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-09   37.3   0.0    7.2e-09   35.5   0.0    1.7  2  Epimerase       NAD dependent epimerase/dehydratase family
    1.1e-07   31.9   0.0    1.4e-07   31.6   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
    2.7e-06   26.7   0.0    1.2e-05   24.6   0.0    1.9  1  RmlD_sub_bind   RmlD substrate binding domain
    1.6e-05   24.1   0.1    9.3e-05   21.6   0.1    2.1  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    6.3e-05   22.7   0.0    7.8e-05   22.3   0.0    1.2  1  NmrA            NmrA-like family
    0.00077   19.0   0.0    0.00089   18.7   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.015   14.8   0.0    1.2  1  adh_short       short chain dehydrogenase
      0.016   15.3   0.1      0.029   14.5   0.0    1.5  2  DapB_N          Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.2e-12   7.2e-09       1     111 [.       3     115 ..       3     123 .. 0.86
   2 ?   -0.6   0.0      0.33   7.4e+02     162     176 ..     141     155 ..     127     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.2e-12
                                   EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                   +lV+Ga+G +G++++  l ++gyev+g++r  ++    r    + v +++ d  +l ++++e +pd++i +    + ++ +
  gi|70606923|ref|YP_255793.1|   3 VLVVGASGVLGRNVIPLLVREGYEVTGITRSVEKVGILRSLGSHPVVCNVYDMPRLYNVVRESNPDVIISF--LTDLPDDM 81 
                                   79*****************************887777777777****************************..88888888 PP

                                   HSHHHHHH....HHTHHHHHHHHHHHHHTCTEEE CS
                     Epimerase  82 edpadfie....knlqgtlnlleaarkagvkrll 111
                                   +  ++f+     +  +gt nl+ ++++ gv r++
  gi|70606923|ref|YP_255793.1|  82 KLINEFAPlnnkIRREGTANLIRVSKDIGVSRIY 115
                                   8888887521124467999*******99997765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.33
                                   -EEEEEEESEEESTT CS
                     Epimerase 162 lnaiilrlfnlyGpr 176
                                    n ++lr+  lyG++
  gi|70606923|ref|YP_255793.1| 141 ANGVVLRYGRLYGEG 155
                                   46799********98 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   6.3e-11   1.4e-07       1      99 [.       7     120 ..       7     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.3e-11
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES-........... CS
                NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsal........... 68 
                                   GA+G  Gr ++  l+++ g+evt ++R+ ek+  l+ + g + v+ +v d   l ++++    d+++s l           
  gi|70606923|ref|YP_255793.1|   7 GASGVLGRNVIPLLVRE-GYEVTGITRSVEKVGILR-SLGSHPVVCNVYDMPRLYNVVRESnpDVIISFLtdlpddmklin 85 
                                   9****************.5**************775.79*******************86633788888866666655555 PP

                                   ..--TCC.....HHHHHHHHHHHHHHCT--EEEEEEET CS
                NAD_binding_10  69 ..ggggk.....deegaknivdaakeagvkRfvlvsai 99 
                                     +         ++eg++n++++ k  gv+R+ + s +
  gi|70606923|ref|YP_255793.1|  86 efA---PlnnkiRREGTANLIRVSKDIGVSRIYMESVA 120
                                   441...1333446677****************998865 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.2e-09   1.2e-05       1      98 [.       1     115 [.       1     162 [. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.2e-09
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...............T--TTSHHHHHHHHHHH--SEEEE----..--H CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...............eldltdaeavaellkeakpdvvvnaAAy..tav 64 
                                   mk+lv+Ga+G lG++++ +l +eg+ev+++tr+                +++ d  ++ ++++e +pdv+++       ++
  gi|70606923|ref|YP_255793.1|   1 MKVLVVGASGVLGRNVIPLLVREGYEVTGITRSvekvgilrslgshpvVCNVYDMPRLYNVVRESNPDVIISFLTDlpDDM 81 
                                   89**********************************************9*********************97532200222 PP

                                   HHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEE CS
                 RmlD_sub_bind  65 DkaEseeeaayavnaeavealAeaaaavgalLih 98 
                                       +   +++++  e++++l ++ + +g+  i+
  gi|70606923|ref|YP_255793.1|  82 KLINEFAPLNNKIRREGTANLIRVSKDIGVSRIY 115
                                   2333335556666666666666666666666555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   4.1e-08   9.3e-05       1     116 [.       4     118 ..       4     141 .. 0.80
   2 ?   -0.1   0.0      0.17   3.8e+02     153     172 ..     134     152 ..     128     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.1e-08
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag 81 
                                   +v+G++G lGr+++  Lvr++      v  +  s e+   l++++ +  + + v d ++l +++++++  + +  l+d+  
  gi|70606923|ref|YP_255793.1|   4 LVVGASGVLGRNVIPLLVREGY----EVTGITRSVEKVGILRSLGSH-PVVCNVYDMPRLYNVVRESNPDVIISFLTDLPD 79 
                                   69*******************5....67788888889899*****99.99****************987766666777765 PP

                     3Beta_HSD  82 .kltedei....mkvnvkGTrnvleacvkagvrvlvYtSs 116
                                    +   +e+     k+  +GT n++   ++ gv ++ Y+ s
  gi|70606923|ref|YP_255793.1|  80 dMKLINEFaplnNKIRREGTANLIRVSKDIGVSRI-YMES 118
                                   433334431111466778**************985.5444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                     3Beta_HSD 153 aEklvlkaNgrtlknggrly 172
                                    E +v++aNg +l+ g rly
  gi|70606923|ref|YP_255793.1| 134 MESIVKEANGVVLRYG-RLY 152
                                   5999******888877.666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.5e-08   7.8e-05       1      73 [.       3      75 ..       3     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.5e-08
                                  EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-..SEEEE--- CS
                          NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgv..dvvfsvtg 73
                                  +lv+Ga+G +G+ v+  l+++g++v  ++R +++  +  l + G   v  +++d   l ++++++  dv++s ++
  gi|70606923|ref|YP_255793.1|  3 VLVVGASGVLGRNVIPLLVREGYEVTGITRSVEKVGI--LRSLGSHPVVCNVYDMPRLYNVVRESnpDVIISFLT 75
                                  79*****************************987765..777888888888999999999998774356666655 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     4e-07   0.00089       1      82 [.       4      73 ..       4     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4e-07
                                  EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                 GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynL 82
                                  L+ G +G  G +++ lL+++gyev+gi+r  +  ++g +++l ++p          + +++ D  +l ++++e +pd ++ +
  gi|70606923|ref|YP_255793.1|  4 LVVGASGVLGRNVIPLLVREGYEVTGITRSVE--KVGILRSLGSHP----------VVCNVYDMPRLYNVVRESNPDVIISF 73
                                  89*************************87655..578888898765..........678999999999*****999999976 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   6.5e-06     0.015       3      68 ..       3      62 ..       1      68 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHH CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealv 68
                                  vlv+Gas+ +Gr++   l++eG++v+ + rs ek+  ++ +l++     +++ ++v d+ ++ ++v
  gi|70606923|ref|YP_255793.1|  3 VLVVGASGVLGRNVIPLLVREGYEVTGITRSVEKV-GILRSLGS-----HPVVCNVYDMPRLYNVV 62
                                  9*******************************998.77777775.....67777777666666665 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.3e-05     0.029       1      74 [.       1      73 [.       1      93 [. 0.76
   2 ?   -3.5   0.0       4.9   1.1e+04       7      26 ..     125     144 ..     123     147 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB..SSHHHHHHH..-SEEEE- CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt..ddleevlek..advliDF 74
                                  +kv+vvGasG +G++v+ ++ + e++e+++   + e    +  + + lg++++ ++v+   +l +v+++   dv+i F
  gi|70606923|ref|YP_255793.1|  1 MKVLVVGASGVLGRNVIPLLVR-EGYEVTGITRSVE----KVGILRSLGSHPVVCNVYdmPRLYNVVREsnPDVIISF 73
                                  89*****************999.9999999877766....34444555666666666633456666666677888877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.9
                                   TTTSHHHHHHHHHHHHSTTE CS
                        DapB_N   7 GasGrmGkevvkaveeaedl 26 
                                   G sGr   e+ + v+ea+++
  gi|70606923|ref|YP_255793.1| 125 GDSGRAVDEMESIVKEANGV 144
                                   66666666665556555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1270.94
//
Query:       gi|70606924|ref|YP_255794.1|  [L=209]
Description: hypothetical protein Saci_1154 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-18   67.3   0.0    2.1e-18   66.8   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    1.8e-06   27.9   0.1    8.2e-06   25.7   0.0    2.0  2  Peptidase_C26  Peptidase C26
     0.0014   18.5   0.0     0.0022   17.8   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
  ------ inclusion threshold ------
      0.038   13.6   0.0      0.057   13.0   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      0.083   11.8   0.0       0.14   11.1   0.0    1.3  1  HTS            Homoserine O-succinyltransferase


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   5.8e-22   2.1e-18      33     176 ..      29     169 ..       7     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 5.8e-22
                                   HHHHHHTHHSTSEEEEEEESSCTT.......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEE CS
                        GATase  33 aeeilellknpdgilvsgGpgspg.......vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmr 106
                                   aeei   ++ +d++++ gGp  ++        + ++++i++a ++k+ +LGICLG Ql+a+++g+kvvk + ++   g +r
  gi|70606924|ref|YP_255794.1|  29 AEEI-TGEERFDNVVIMGGPMGVYerekyrfLDLEMKLIRRAYSEKKRVLGICLGSQLIAEALGGKVVKGQ-FGVEIGVSR 107
                                   2333.24889***********999999999999**************************************.9*9999*** PP

                                   EEETTT.CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                        GATase 107 lgddet.allyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEstst 176
                                   ++  +  + + g+ +e+++ ++H++++     +p+g + +a se   ++  +++  + + g+QFH E+ s+
  gi|70606924|ref|YP_255794.1| 108 IRLVNDfKDYFGS-DELHVFQWHGDTFS----LPHGATLLAYSE---KYYQAFNIGR-ALGIQFHIEVDSE 169
                                   **98886666666.**************....7********994...4678888887.8********9886 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.3e-09   8.2e-06      93     127 ..      61      95 ..      32     103 .. 0.93
   2 ?   -0.7   0.0      0.27   9.7e+02     207     216 .]     156     165 ..     146     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.3e-09
                 Peptidase_C26  93 lelaLiraalergvPilgiCrGlqllnvalGGtly 127
                                   le++Lir+a+++++ +lgiC+G ql++ alGG+++
  gi|70606924|ref|YP_255794.1|  61 LEMKLIRRAYSEKKRVLGICLGSQLIAEALGGKVV 95 
                                   699*****************************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.27
                 Peptidase_C26 207 fvlgvQwHPE 216
                                    +lg+Q+H E
  gi|70606924|ref|YP_255794.1| 156 RALGIQFHIE 165
                                   589*****76 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.2e-07    0.0022      55     110 ..      30      89 ..      19     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-07
                                   GGCTCC.G-SEEEE--BHHHHHHHHTSHHH....HHHHHHHHHTT-EEEEETTTHHHHHHT CS
                     DJ-1_PfpI  55 ddvkaa.eyDalvlpGGragperlrenekv....velvkefaekgklvaaICagpqlLaaa 110
                                   ++++ + ++D +v+ GG     + re+ ++    ++l++++++++k+v  IC g ql a+a
  gi|70606924|ref|YP_255794.1|  30 EEITGEeRFDNVVIMGGPM-GVYEREKYRFldleMKLIRRAYSEKKRVLGICLGSQLIAEA 89 
                                   45555559*********87.44444444331222789*******************99986 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.6e-05     0.057      35      92 ..      36      90 ..      13     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                      GATase_3 35 eslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92
                                  e+++   ++vi++G   + ++ ++       + i++a++++++vlgiC G q+  e +
  gi|70606924|ref|YP_255794.1| 36 ERFD---NVVIMGGPMGVYEREKYRFLDLEMKLIRRAYSEKKRVLGICLGSQLIAEAL 90
                                  3442...48899998899999999888889999*******************998876 PP

>> HTS  Homoserine O-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.8e-05      0.14      92     147 ..      30      86 ..      17     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                                   GGT.TT--EEEEEE---S-TTS-GGGSTTHHHHHHHHHHHHHHEEEEEEETHHHHHH CS
                           HTS  92 eei.kdekfDgliiTGApveqlefeevkYWeelteildwakenvtstlfiCwaaqaa 147
                                   eei  +e+fD ++i G p+   e e+ ++ +  ++++  a ++ +  l iC+++q  
  gi|70606924|ref|YP_255794.1|  30 EEItGEERFDNVVIMGGPMGVYEREKYRFLDLEMKLIRRAYSEKKRVLGICLGSQLI 86 
                                   45535789***********************999*******************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1721.07
//
Query:       gi|70606925|ref|YP_255795.1|  [L=268]
Description: hypothetical protein Saci_1155 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-57  193.1   0.0    6.8e-57  192.7   0.0    1.0  1  ADC       Acetoacetate decarboxylase (ADC)


Domain annotation for each model (and alignments):
>> ADC  Acetoacetate decarboxylase (ADC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.7   0.0   3.8e-61   6.8e-57       2     234 ..       8     259 ..       7     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 192.7 bits;  conditional E-value: 3.8e-61
                                   SSTCTSSSCTTSSSE.E....EEEEEEEEEEE-HHHHHTTSBTTEEECSTSEEEEEEEEEEEECTTTC..........EEE CS
                           ADC   2 mPlaitpsgksalvp.y....naealtvsyrtdpeaaaallPepLelaerplvavyfaeypdssfggg..........qYn 67 
                                   +P+  t+sgksa+vp +    +++++++ ++++++++ ++lP  L     +++++y+ae+ ++s+  +          qY 
  gi|70606925|ref|YP_255795.1|   8 YPF--TRSGKSAIVPpPpwyyGVTYISAYVKFQKDTLYQFLPNFLDSK--GEGWIYIAEFISPSEETWdlmyqdpdltQYL 84 
                                   677..899*******735779************************999..8***************99************* PP

                                   EEEEEEEEEETTEEEEEEEEEEESSHHHHHHHHHHTT--EEE-EEEEEE............ETTEEEEEEEETTEEEEEEE CS
                           ADC  68 eagivvpvryggkegayilvlwvdkeaalaaGRElwGfPKklAditltr............egdtlggtverggkrlaelt 136
                                   e++i+++v y+gk+++y++++wvdk++al++G+ l G+PKk+A+i++t+            +g +lgg+v rgg+ l++l+
  gi|70606925|ref|YP_255795.1|  85 EGAIGLRVYYEGKSYLYFPFMWVDKDWALVRGW-LDGYPKKIAKISMTKlhpllpkynkpeNGLKLGGYVVRGGNFLFRLQ 164
                                   *********************************.*********************************************** PP

                                   EEEEEEE-HHHHHHHHHTS.EEEEEEEEE-TTSTSEEEEEEEEEEEEEEEEEEEEEEEEEEEE-SSTTCCGGGSCCSEEEE CS
                           ADC 137 velkerapddeealpslka.ptfllkiipsvdggkadvtelvryelsdtrvgeawtGpaslelepsaddpladlpvlevls 216
                                   vel+e++    ++ p +++   ++++i p++++++++v elv + ++++ +ge+w+G+a++el+++++d+l +l++++v++
  gi|70606925|ref|YP_255795.1| 165 VELREKV----DDVPLRSFgAPLNVRIYPARGESETSVFELVSRVRDENVLGEIWKGDAKIELGGYVNDELDKLKIEDVIA 241
                                   *******....77788888878*********************************************************** PP

                                   EEEEEEEEEEEEEEEEEE CS
                           ADC 217 ayyikadltvgggevled 234
                                   +yy++++++v+++++l++
  gi|70606925|ref|YP_255795.1| 242 GYYYTTYFKVRTTRLLAK 259
                                   ************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1814.22
//
Query:       gi|70606926|ref|YP_255796.1|  [L=561]
Description: hypothetical protein Saci_1156 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3810.80
//
Query:       gi|70606927|ref|YP_255797.1|  [L=368]
Description: hypothetical protein Saci_1157 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.5   0.0        7.3    6.6   0.0    2.8  3  SecA_SW   SecA Wing and Scaffold domain
       0.11   12.3   0.0       0.32   10.8   0.0    1.8  1  L27       L27 domain


Domain annotation for each model (and alignments):
>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.018   1.6e+02     102     138 ..       9      45 ..       2      58 .. 0.77
   2 ?    0.6   0.0     0.056     5e+02      69     124 ..     131     203 ..     106     221 .. 0.58
   3 ?    6.6   0.0   0.00081       7.3      36     131 ..     222     336 ..     206     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.018
                                   SSTHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH CS
                       SecA_SW 102 eleelaeellekaekayekkeeeiellrelervvlLe 138
                                   ++e+  +++ e+++k ye+ ++ ++l++++er v L+
  gi|70606927|ref|YP_255797.1|   9 DYETWDQYIQEDVMKVYETTSKVVNLYQQVERIVKLT 45 
                                   5557788999999999999999999999999998775 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.056
                                   HHHHHC.HHHHS.SS.C...SHHHHHHHHHCCCSSSTSST.............HHHHHHHHHHHHHHHHHHHH CS
                       SecA_SW  69 vveeiv.eesvpeeeke...ewdleglleelkeefsvele.............elaeellekaekayekkeee 124
                                   + ++i+ ++  +++e e     dl+g+++++ke ++  ++             +l+  +l+++ +ay+k +++
  gi|70606927|ref|YP_255797.1| 131 LSKRIIiSSGFRPREVErvsLSDLNGVFNTFKELLESLARfssvynprtffitSLTGDILKAFLEAYDKLNDK 203
                                   2233332333333333334456777888888876664444778888888888878888888888888765553 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00081
                                   HHHHHHHHHHHHHHHHCTHHCHHHHHHHHHHHHHHHHHCHHHHS.SS.CSHHHHHHHHHCCCSSSTSST............ CS
                       SecA_SW  36 mnkQRkviYkqRrevLegesedlrerildliedvveeiveesvpeeekeewdleglleelkeefsvele............ 104
                                   +n+ R +iY   ++ L+++ +dl+++ +d+++++ +e+++ + +     e d+e+ll+ + ++ +++              
  gi|70606927|ref|YP_255797.1| 222 LNDERYTIYGYTDNSLGRYITDLDKQAYDFLRNFRSEFIRLDGNI----EKDFESLLSYYITSSNLSEVldfafwtnpvrc 298
                                   799************************************444443....35666666666664444333566677788888 PP

                                   ..........HHHHHHHHHHHHHHHHHHHHC.HHHHHH CS
                       SecA_SW 105 ..........elaeellekaekayekkeeei.ellrel 131
                                             ++ ++  e+ +++y++++ ++ e+l+e+
  gi|70606927|ref|YP_255797.1| 299 hiplsnpskiTCDNSYSEAYKAKYRSRTYTLiEMLEEF 336
                                   89898888887777778888888888877665556665 PP

>> L27  L27 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.6e-05      0.32       5      46 ..     162     203 ..     159     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.6e-05
                           L27   5 lelLedLqslsdvnedlaeLqkvLqsphlqaLlevHDrVaet 46 
                                   +elLe+L + s+v +  ++  + L+ + l+a le++D++  +
  gi|70606927|ref|YP_255797.1| 162 KELLESLARFSSVYNPRTFFITSLTGDILKAFLEAYDKLNDK 203
                                   69999999999999999999999***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2546.28
//
Query:       gi|70606928|ref|YP_255798.1|  [L=195]
Description: hypothetical protein Saci_1158 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   44.7   0.0    3.1e-11   44.2   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
    1.5e-05   24.3   0.0    1.7e-05   24.1   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    3.3e-05   23.7   0.0    4.7e-05   23.2   0.0    1.2  1  CmcI             Cephalosporin hydroxylase
     0.0085   15.4   0.0       0.02   14.2   0.0    1.6  2  TylF             Macrocin-O-methyltransferase (TylF)
  ------ inclusion threshold ------
      0.084   13.2   0.0       0.16   12.3   0.0    1.5  1  Peptidase_U32_C  Peptidase family U32 C-terminal domain


Domain annotation for each model (and alignments):
>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   8.5e-15   3.1e-11       1     106 []      55     162 ..      55     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 8.5e-15
               Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg...aeeaaalareaglddrvrlikadseealasla..agsiDllfiD 76 
                                   +E Gv  Gvs+ ++l+al +     l+++d   +    +e++ ++ + +l++ +++  ++s+  l++      ++ +++ D
  gi|70606928|ref|YP_255798.1|  55 IETGVGPGVSSTIILSALPEDS--VLYSIDVRNRledGNEVGYIIPQ-KLRKKWKFFLGESRRFLPKILqeVNEVNFFLHD 132
                                   6999***************998..6******8877767779999998.*************999998776656899***** PP

               Methyltransf_24  77 gghaaeavledleallprlapggvvlfdDi 106
                                    +h++e v+++l +++ +l++ggv+l+d++
  gi|70606928|ref|YP_255798.1| 133 SDHSYENVMFELSTIWYKLSEGGVILVDNY 162
                                   ****************************97 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   4.9e-09   1.7e-05      38     158 ..      41     162 ..      16     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.9e-09
                                   HHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHH.HHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHT CS
                Methyltransf_3  38 fLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididrea.yeialkfiqkagvaekieliegdalkvLeelvk 117
                                    L  ++k +  k  +e Gv  G s   +  alPeD  + +id+ +         +i    + +k ++  g++++ L ++++
  gi|70606928|ref|YP_255798.1|  41 ILYAIIKETTPKIAIETGVGPGVSSTIILSALPEDSVLYSIDVRNRLeDGNEVGYIIPQKLRKKWKFFLGESRRFLPKILQ 121
                                   566788889999******************************85433022334567777799******************* PP

                                   SSS---EEEEEE-S-GGGHHHHHH..HHHHTEEEEEEEEEE-T CS
                Methyltransf_3 118 dkklpefDfifvDaDkssyvnyye..klleLvkvGgliaiDnt 158
                                   + +  e +f + D+D s     +e   +   +  Gg+i +Dn 
  gi|70606928|ref|YP_255798.1| 122 EVN--EVNFFLHDSDHSYENVMFElsTIWYKLSEGGVILVDNY 162
                                   995..9999999*998755555652123345788999999996 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-08   4.7e-05      24     146 ..      42     160 ..      33     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-08
                          CmcI  24 yQeliwelkPdliietGiahGGsalfsasllallkskrkvlaididireknrqaiea...hplasrieliegssvd..pei 99 
                                   +  +i e+ P++ ietG+  G s   s+ +l+ l ++  + +id++ r ++ +++     ++l+++ ++  g+s    p+i
  gi|70606928|ref|YP_255798.1|  42 LYAIIKETTPKIAIETGVGPGVS---STIILSALPEDSVLYSIDVRNRLEDGNEVGYiipQKLRKKWKFFLGESRRflPKI 119
                                   55799*************88855...7789999999999*********99987754322267899999**99997544788 PP

                          CmcI 100 veqvkslakekekvlvilDsdHthehvlaeLeayaplvsaGsYivve 146
                                   +++v++++      +   DsdH++e+v+ eL++    +s+G  i+v 
  gi|70606928|ref|YP_255798.1| 120 LQEVNEVN------FFLHDSDHSYENVMFELSTIWYKLSEGGVILVD 160
                                   88887765......8899**************999999999887775 PP

>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.52   1.9e+03      76     104 ..      44      72 ..      37      82 .. 0.74
   2 !   14.2   0.0   5.7e-06      0.02     192     232 ..     132     173 ..     101     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.52
                          TylF  76 dvleegvpGdliEtGvWRGGaailmrgvL 104
                                    +++e  p   iEtGv  G ++ ++ ++L
  gi|70606928|ref|YP_255798.1|  44 AIIKETTPKIAIETGVGPGVSSTIILSAL 72 
                                   57778888888999999887765555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.7e-06
                          TylF 192 Dgd.lyestldaleaLYdkvskGGfviiDDyaaveecreave 232
                                   D+d  ye  +  l++++ k+s+GG++++D+y   ++  ++v+
  gi|70606928|ref|YP_255798.1| 132 DSDhSYENVMFELSTIWYKLSEGGVILVDNYRFSNATIDFVS 173
                                   55525999***********************99666555554 PP

>> Peptidase_U32_C  Peptidase family U32 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.16      16      39 ..      77     100 ..      67     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
               Peptidase_U32_C  16 glaeveqRNkfsvGdelEvltPkg 39 
                                    l+ +++RN+++ G+e+ ++ P++
  gi|70606928|ref|YP_255798.1|  77 VLYSIDVRNRLEDGNEVGYIIPQK 100
                                   389*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1406.34
//
Query:       gi|70606929|ref|YP_255799.1|  [L=229]
Description: hypothetical protein Saci_1159 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1694.06
//
Query:       gi|70606930|ref|YP_255800.1|  [L=627]
Description: alpha-glucosidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-128  429.4   2.4   2.5e-128  429.0   2.4    1.1  1  Glyco_hydro_31   Glycosyl hydrolases family 31
    1.1e-21   76.9   0.2    2.9e-21   75.6   0.2    1.8  1  Gal_mutarotas_2  Galactose mutarotase-like
  ------ inclusion threshold ------
      0.033   14.2   0.1      0.062   13.2   0.1    1.4  1  GHL15            Hypothetical glycosyl hydrolase family 15
      0.081   13.2   0.1       0.19   12.0   0.1    1.6  1  Retrotrans_gag   Retrotransposon gag protein


Domain annotation for each model (and alignments):
>> Glyco_hydro_31  Glycosyl hydrolases family 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.0   2.4  5.5e-132  2.5e-128       1     440 []     145     574 ..     145     574 .. 0.93

  Alignments for each domain:
  == domain 1  score: 429.0 bits;  conditional E-value: 5.5e-132
                                   EEEE-SSHHHHHHHHHHHH-------GGGGSEEEE-TT--SHHHHHHHHHHHHHTT--EEEEEESCGGSBTTCCTB-.TTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31   1 yvflGptpkevvkqyteltGrpalpPrwalGfhqsrygykdeeeveevvdkfreagiPldvivlDidymdkrkdftwdker 81 
                                   +vf G++++ev++ y eltG+p  +P walG++ sry y  +e+veevv+++ e++iPl++i+lDidym+k++ ftwdk +
  gi|70606930|ref|YP_255800.1| 145 FVFEGDSVQEVIEHYVELTGKPFELPEWALGYQISRYSYYPQETVEEVVRRHLEEDIPLSAIYLDIDYMEKYRLFTWDKAK 225
                                   89************************************99***************************************** PP

                                   SS-HHHHHHHHHHTT-EEEEEE-SEE.E.-TTSHHHHHHHHTTSBECCCCCS.TCEC.TSSEEEEB-TTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31  82 Fpdpkemvdelhekgvklvvivdpaiskqeeeyeafdegkekgvflknkdgs.ykgk.wpgstafpDftnpearewwkkel 160
                                   Fp pke++++lh+ gvk+v+ivdp+++  +++y++f++g  +   ++n+dg+ y++  wpg ++fpDf+n+++reww + +
  gi|70606930|ref|YP_255800.1| 226 FPSPKELIEKLHSLGVKVVTIVDPCVRL-DQNYHVFKDGLGNY--VENEDGTiYADIlWPGLSVFPDFLNSKTREWWRNLV 303
                                   **************************65.88*******77555..5999999555559*********************99 PP

                                   HHHHCTCT--EEEE-STTTB.SCCCCHH.HHCCCTSCETTCCHHHHCCCHHHHHHHHHHHHHHHHTTTST-EEEESSEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 161 kkflldlgvdglwiDmnepsnfeegsds.eekeaketkaagshydvhnlygllmakatyeglkekkpkkrpfiltRstfaG 240
                                   +k++ + ++dg+w Dmneps  ++ + +    ++ +++++ +h++vhnly+l +a+at     +       f+l+R++++G
  gi|70606930|ref|YP_255800.1| 304 EKWVKENNIDGIWLDMNEPSPLNKKPFNpRAIHRLDDNSQVYHESVHNLYSLFQAMATKP---S-----VDFVLSRAGYSG 376
                                   9999999*************9998888866555655555555**************9433...3.....46********** PP

                                   GGGCTEEE--S-BSSHHHHHHHHHHHHHHHTTT--SEEEECT-SG..HCHHHHHHHHHHHHTTSSSEEE--STTSS--SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 241 sqryaahWsGdnassWeslresipallsfslsGvpfwgaDigGFe..ntteelyaRWvqlGafsPffrnHsskdakrqepw 319
                                    qryaa+W+Gdn++sW++l  +++ +l +s+sGvp++g+D+gGF   +t+  l+ R++q+++f+P+frnH++k+ ++qe++
  gi|70606930|ref|YP_255800.1| 377 IQRYAAIWTGDNTTSWSDLTLQLALTLGLSISGVPYVGCDLGGFIgrTTDYLLLYRYFQIALFFPIFRNHKDKGGSDQEIY 457
                                   ********************************************7645578****************************** PP

                                   HHCHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHH---SEE-HHHH-TT-CCCCC--S-EEETTTEEE----STT-SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 320 afgeeveeaarkaielRyrLlPylYtlfyeahetglpvvrplflefpedektfdiddqfmfGdsLLvaPvleeeatsvevy 400
                                   ++++  +e ++++i++Ry++lPyl  l++e+++tg p++rpl++++  de++f+i+dq+m+G+ LL aP +++ + ++ +y
  gi|70606930|ref|YP_255800.1| 458 SIPDYWKEKIKRVIKMRYQFLPYLNALARESSKTGHPIIRPLAYHYFRDENAFKINDQYMVGEYLLYAPQINK-EGKRLIY 537
                                   ***********************************************************************77.68***** PP

                                   E-SSEEEETTT--EEESSEEEEEE--TTSS-EEEETTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Glyco_hydro_31 401 LPggkWydfwtgekyeggqtveltapldeiplfvraGaIi 440
                                   LP+gkW ++wt+e+yeg++ +e +   ++ plf+r ++++
  gi|70606930|ref|YP_255800.1| 538 LPEGKWLNWWTDEEYEGKNWIESD---HDFPLFLRYNSVV 574
                                   **99*************8876665...56******99986 PP

>> Gal_mutarotas_2  Galactose mutarotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.2   6.5e-25   2.9e-21       2      66 .]      60     124 ..      59     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 6.5e-25
                                   -EEEEEES-SS-SS-TTEEEEE-----TS-HCC.CTS-SCEEEEEEEE.TCEEEEEE--SSSEEEE CS
               Gal_mutarotas_2   2 ehvyGlGEkagplnlrgtryrlwntdafgyeaessdplYgsiPfmisl.segyGvfvdnpaetwfD 66 
                                    hv+GlGEka +l++r+tr+++wntd++gy+++ sdplY+siPf+i + s+  G+f+++p++  fD
  gi|70606930|ref|YP_255800.1|  60 THVLGLGEKAFELDRRRTRVTMWNTDSYGYTWY-SDPLYVSIPFFILVdSSIKGYFFNSPSKLVFD 124
                                   69*******************************.9***********99*999***********999 PP

>> GHL15  Hypothetical glycosyl hydrolase family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.4e-05     0.062      66      96 ..     289     319 ..     267     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                         GHL15  66 dvsnpefrewWvksalnelrdsgiDGvfaDn 96 
                                   d+ n + rewW + + + +++++iDG+ +D 
  gi|70606930|ref|YP_255800.1| 289 DFLNSKTREWWRNLVEKWVKENNIDGIWLDM 319
                                   7899*************************95 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.2e-05      0.19       2      74 ..     286     360 ..     285     366 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                Retrotrans_gag   2 lastslegaAkswlkslvarsida...sesWkdlkkaflktflpserkdqleeelsslrQ.gtesvreYvtrfktla 74 
                                   +++ +l+++ ++w+++lv++++++     +W d+++    +  p     ++ ++l + +Q  +esv+  +  f+ +a
  gi|70606930|ref|YP_255800.1| 286 VFPDFLNSKTREWWRNLVEKWVKEnniDGIWLDMNEPSPLNKKP--FNPRAIHRLDDNSQvYHESVHNLYSLFQAMA 360
                                   67789******************999999*****9865555555..3345555577777777777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4429.36
//
Query:       gi|70606931|ref|YP_255801.1|  [L=349]
Description: HTH domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-67  226.7   1.6    2.7e-67  226.4   1.6    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.7e-12   47.0   0.1    4.1e-12   45.8   0.1    1.7  1  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.057   13.3   0.0    1.6  1  MarR            MarR family


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.4   1.6   4.4e-71   2.7e-67       2     232 ..     114     348 ..     113     349 .] 0.98

  Alignments for each domain:
  == domain 1  score: 226.4 bits;  conditional E-value: 4.4e-71
                                   EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS..----GGGSSSSEEEEEE-S--- CS
                Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp..dedleeldleevatevrvrrsg 80 
                                   +w++ks+e+v++++ ++I+sA+nel+v++p+++L++l +++i+ ae+gv+++l iyp  de+l ++ le++++ev+v+++g
  gi|70606931|ref|YP_255801.1| 114 MWMTKSTENVLNNCISVITSAKNELYVEIPNNYLQKLISYIIKVAESGVKTYLNIYPnvDEFLVNKLLESKVMEVKVHSLG 194
                                   8******************************************************************************** PP

                                   S.EEEEETTTEEEEE-SSS-.EEEE--HHHHHHHHHHHHHH........HHH-EEEEE..EES-TT-EEES-HHHHHHHHH CS
                Regulator_TrmB  81 apllvivDrkrgvvaprevl.rdkeeeyaiifkekelihvlshyFlttlWktsevikt..depvekpitfssirlavedik 158
                                   +++lv +D++++v++pr ++ +++++ y+++f++++++ +++hy+++  W+ts+++++   +++++p+ fs++r+a+++i+
  gi|70606931|ref|YP_255801.1| 195 HFFLVSADAEESVFMPRVMSlSTNPNIYSYVFRDSTMSLFFIHYYFEG-WRTSRTVYRkaVTQSDFPMIFSAHRFATWEIM 274
                                   ************************************************.*********999******************** PP

                                   HHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTT.EEEEEEEETTE.EEEEE-TT--SSSEEEEEEEEEE CS
                Regulator_TrmB 159 kllraglkveaeveGrdtetgeevtieGrvveatlnstpg.vaslvvetedg.evtVGGlgAvlEDieaeeitler 232
                                   k++++gl+++++v+G+ t+tge+v++ G + +  +n++++  ++ +ve ++g ++ +GG +A++ED+ ae+i++++
  gi|70606931|ref|YP_255801.1| 275 KAKEQGLRLKVKVDGVITRTGENVELFGYPNN--VNISSEvINFELVEERSGrSYLIGGDNALVEDVSAEKIEVYT 348
                                   ********************************..9999997888899999999********************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   6.8e-16   4.1e-12       1      65 [.      12      76 ..      12      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.8e-16
                                  HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                          TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                  L +lG+s+ Ea v+++L  +g ata+e  ++l + +++ Y++L sLe+kGl++++ ++pk+Y ++
  gi|70606931|ref|YP_255801.1| 12 LTVLGISKKEALVFAYLTYKGGATAKEMISDLYIHQPQLYNILLSLERKGLIYVQNSKPKFYIPA 76
                                  678***********************************************************886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-06     0.057      10      52 ..      26      68 ..      17      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-06
                                  HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  + l ++g+++ +e+ + l+++++ + ++l  Le+kGli+ + s
  gi|70606931|ref|YP_255801.1| 26 AYLTYKGGATAKEMISDLYIHQPQLYNILLSLERKGLIYVQNS 68
                                  567899********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2564.08
//
Query:       gi|70606932|ref|YP_255802.1|  [L=884]
Description: membrane bound alpha-amylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-41  142.7   1.1    3.7e-34  118.4   0.0    2.5  2  Glyco_hydro_57  Glycosyl hydrolase family 57
  ------ inclusion threshold ------
       0.12   12.5   0.5       0.37   10.9   0.2    2.0  2  DUF2057         Uncharacterized protein conserved in bacteria
        3.3    8.4  17.4        2.7    8.6   0.2    3.2  3  CBM53           Starch/carbohydrate-binding module (family 53


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.8   1.1e-08   6.6e-05       1      72 [.     332     411 ..     332     424 .. 0.78
   2 !  118.4   0.0   6.2e-38   3.7e-34     117     322 ..     425     642 ..     410     645 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.1e-08
                                   EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHH..........HHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHH CS
                Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYik..........lalilekfpkvhvtfeLsgsLiaqLeeylngekksyl 71 
                                   ++v+++Hqply +p+ g +++pwv +h  +d+++          +al+++k++ v+vt++++++L++q   +l+ ++  + 
  gi|70606932|ref|YP_255802.1| 332 VIVWNMHQPLYLSPQ-GVWEQPWVWVHTGQDFYWnsslvgayelQALLINKYN-VSVTIDFTPVLLYQWLTILSQTNPKFA 410
                                   58************9.***********88876652333333333567788877.9*************9999988877776 PP

                                   H CS
                Glyco_hydro_57  72 p 72 
                                    
  gi|70606932|ref|YP_255802.1| 411 S 411
                                   5 PP

  == domain 2  score: 118.4 bits;  conditional E-value: 6.2e-38
                                   T-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-...HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT CS
                Glyco_hydro_57 117 kevlelfrelqesgqvElltspyyHpllpllpd...sedieaqvkkarelyeeyfgqePrgfwlpElavspeileilaelG 194
                                   + +l l+r+l+++g+vE+lt+p+yHpl p++ d    +d  aq+ +++++ ++ f+++P g w pE+a++  ++ ++++ G
  gi|70606932|ref|YP_255802.1| 425 NYTLNLYRSLAQEGKVEVLTVPFYHPLQPIILDngwWSDDLAQILMGIQMTRQVFNVSPAGTWTPEQAFNMGLITLYNQTG 505
                                   6799***************************8878888889**************************************** PP

                                   --EEEE-C.....------------TTS-EE-TTS....-EEEE--CHH-TTTSGGG-............TTSB....... CS
                Glyco_hydro_57 195 feylftde.....laeiledkskespyrpyllkngg...iavffRdreLsddigFryseqypleavddfinwlkkvkka.k 266
                                   ++y++ d+     +  ++++    +py p+ + n+      v+fRd+ Ls++ +F++ +q p+ +++++i++l  ++++ +
  gi|70606932|ref|YP_255802.1| 506 IRYTILDQdaylpYVTVVSGN--TNPYQPFEVLNSLgqsTIVLFRDTALSNQFSFQFFSQPPQLTAQQLIQELAMIYMNnP 584
                                   ***********8844444444..366666665554445599***********************************9999* PP

                                   ....-TT---TT.T--BB-TT-S---HHHHHHHHHHH..HHHHHHHHHHHHHHSS-EEE CS
                Glyco_hydro_57 267 sevvtialdgEn.wghypetgkkeFleklyeeleeng..lielvtpsefikklkpkgli 322
                                   + vvt+a dgEn +   p tg +  l + y++l++ +  ++ + t s++i ++kp+ +i
  gi|70606932|ref|YP_255802.1| 585 GGVVTVAFDGENpLIFNPSTGPQ-DLNAIYQALSQYQgsWLITQTASQAIATHKPYSVI 642
                                   ************999******86.8***********9999***************9876 PP

>> DUF2057  Uncharacterized protein conserved in bacteria (DUF2057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   6.1e-05      0.37      13      69 ..     263     315 ..     252     324 .. 0.80
   2 ?   -3.4   0.0       1.5     9e+03      25      46 ..     795     816 ..     786     823 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.1e-05
                       DUF2057  13 vdgqkvksslfkgaksltLtpGkhqivvrykdlfkddsdsdsqdlvkSdplivtfda 69 
                                   v+ q  +   + + + +tL+pG++ i++ +++ f+++     +dl+ S+ l+ tf+ 
  gi|70606932|ref|YP_255802.1| 263 VNIQNNQ---L-SYNGITLNPGQNNITLPFTASFSQGVYYPVVDLYYSNSLQGTFNL 315
                                   4555555...3.2489************************************99996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.5
                       DUF2057  25 gaksltLtpGkhqivvrykdlf 46 
                                   ++ ++ L+pG + i v   + +
  gi|70606932|ref|YP_255802.1| 795 TSYNIVLNPGRNDISVNLPKSV 816
                                   5578899999999999887777 PP

>> CBM53  Starch/carbohydrate-binding module (family 53)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.2    0.0028        17       9      81 .]      46     120 ..      27     120 .. 0.82
   2 ?    8.6   0.2   0.00045       2.7      12      81 .]     149     220 ..     130     220 .. 0.70
   3 ?   -3.1   0.2       2.1   1.3e+04      12      24 ..     351     366 ..     339     373 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0028
                         CBM53   9 l.akevtlhygfn.....gWkssqdvamtksassgdseedwfeatvtvpkeaseldfvf.ds..egeenWDNNngqnYkvp 80 
                                     + +v+lh+g++     +W+++ d++mt+        ++ f+at+   ++ + + +vf d+  ++  n+DN    n++++
  gi|70606932|ref|YP_255802.1|  46 PsSDDVILHWGVQpgpqsSWTQVYDTPMTWN-------GNNFSATIGPFQNGTWIGWVFhDNttNTWINYDNHPFWNWNLE 119
                                   3344599****98899999************.......89*****998888788*****77777667799********987 PP

                         CBM53  81 v 81 
                                   v
  gi|70606932|ref|YP_255802.1| 120 V 120
                                   6 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00045
                         CBM53  12 evtlhygfn.......gWkssqdvamtksassgdseedwfeatvtvpkeaseldfvfdsegeenWDNNngqnYkvpv 81 
                                   ++ +hyg          W++ +dv+m + + +g    +  ++  + p+  + +++v ++ +e+++ +Nngqn+ ++v
  gi|70606932|ref|YP_255802.1| 149 DIVVHYGIAsgpqtglPWSNITDVTMVYNPLWG----NYTAVIGPFPN-GTWVQWVYHDLTENKYYSNNGQNFAIQV 220
                                   478888884366666669999999999994222....22233334555.344*****556899999*******9987 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.1
                         CBM53  12 e..vtlhygfn.gWks 24 
                                   +  v++h g +  W+s
  gi|70606932|ref|YP_255802.1| 351 QpwVWVHTGQDfYWNS 366
                                   1359999999757765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5838.93
//
Query:       gi|70606933|ref|YP_255803.1|  [L=285]
Description: sugar transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-14   54.4  22.6    1.3e-14   54.4  22.6    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   8.9      0.24   4.3e+03     101     171 ..      12      98 ..       3     103 .. 0.59
   2 !   54.4  22.6   7.2e-19   1.3e-14       5     179 ..      97     275 ..      93     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.24
                  BPD_transp_1 101 vvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgydyseis...........nggvlalviav 165
                                    ++++a+++++  ++  + ++   ++++  l + p      lg+ll + i+ + y  i+             +++ ++i+v
  gi|70606933|ref|YP_255803.1|  12 KIIRLAISYLVLVVMAIISIFPIYYIVITSLNNIPSlasvsLGSLLPSRISLNAYYDILfqepffvwlrnSLIMALGTIIV 92 
                                   566777777776666666666777777777777777555556666666666666665558888666665544444444444 PP

                  BPD_transp_1 166 lllnlv 171
                                    +l+++
  gi|70606933|ref|YP_255803.1|  93 SVLVAF 98 
                                   444433 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 7.2e-19
                  BPD_transp_1   5 Gilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                   ++l++    + n +++k+l ++ ++l  lPs++ +i+l+l+f+ l  l ++  ++i+++  ++ ++  ++++ +++++p +
  gi|70606933|ref|YP_255803.1|  97 AFLTGaalSRLNVPGKKALIVFLYILTFLPSVATVIPLYLMFASL-HLINTYYGLILAYSSGTSIFGAYLVKIFIDTIPPE 176
                                   55555567799****************************998666.56667788999************************ PP

                  BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.....nggv 158
                                   ++eaa ++G+sr++ + +++lP++ p ++  ++laf g+ ++++l+  ++++   g++++ ++ +y ++ ++     n+ +
  gi|70606933|ref|YP_255803.1| 177 YEEAAMVDGLSRFRAYIRILLPMTRPIVAFVMLLAFLGAYTDYALANAFITS---GNMWTLTLGMYYLAVTNhstlyNVFA 254
                                   ******************************************9999888854...55555555555555555669999*** PP

                  BPD_transp_1 159 lalviavlllnlvadilqrll 179
                                   ++ vi+ +++++++ ++q+++
  gi|70606933|ref|YP_255803.1| 255 AFSVIMGVPIMAIFIAFQKYI 275
                                   *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2082.95
//
Query:       gi|70606934|ref|YP_255804.1|  [L=294]
Description: transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-16   59.0  23.6      5e-16   59.0  23.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.03   14.4   2.8      0.067   13.3   2.8    1.5  1  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.7  14.5         2   1.8e+04      22      69 ..       6      91 ..       5      95 .. 0.65
   2 !   59.0  23.6   5.5e-20     5e-16       3     180 ..      86     291 ..      84     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: -8.7 bits;  conditional E-value: 2
                  BPD_transp_1 22 pliivllslPsfvlaillvlvf.....................................vilsilghlilp.viillllsaap 66
                                  ++++ ++ lP+++l+++l+l                                       ++   l++++++ +  l+ +++++
  gi|70606934|ref|YP_255804.1|  6 VIFNYFYLLPILALVLFLFLYPvayavyisftnfslfhffqysyigfknyiniltnpnfYFVELLKNTAIWtIGSLIPMMILG 88
                                  56777899999998888775435677777777777777777777777777777777777555666655554466666666666 PP

                  BPD_transp_1 67 yvr 69
                                  +++
  gi|70606934|ref|YP_255804.1| 89 FFL 91
                                  554 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 5.5e-20
                  BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfv...................laillvlvfvilsilghlilpviilll 61 
                                   +lG+++a   +++  k+++++   + +++++P ++                   ++++ ++ + +l+  ++++ ++i++ +
  gi|70606934|ref|YP_255804.1|  86 ILGFFLAlilNQSDLKFKNVFFSSFLIPWAFPAYIslliwsgmwdysygiinkiIGLIGIAPINWLNNTTYAWVALILTNV 166
                                   78999999999999*********************6555555555555555555555555555****************** PP

                  BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...... 136
                                   + ++py + i+ +al+s+p++l+e a+++Ga+  ++f +++lP+++++++   +  f++ ++++  + +l+++++      
  gi|70606934|ref|YP_255804.1| 167 WLSFPYYTSIFLSALQSIPRELYEIAEVDGAGMLTRFARITLPMMKSTLVFVGVSGFIFTWNNFYPVFILTGGGPgtstdi 247
                                   ***************************************************************987766655444376666 PP

                  BPD_transp_1 137 .lgtllleailgydyseisnggvlalviavlllnlvadilqrlld 180
                                    + +   ea ++++y+++s +++++ +i+++++ ++++   r+l+
  gi|70606934|ref|YP_255804.1| 248 lIVYSYQEAFSYNQYALAS-AYSIISTIILAIMAVIMFRYSRILE 291
                                   6666666666666666666.8888888888888888888888776 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.8   7.4e-06     0.067       2      23 ..      19      40 ..      18      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-06
                     TM_PBP2_N  2 lLlvfqvfpvlyTistafTNyG 23
                                  l+l++ ++pv+y ++++fTN++
  gi|70606934|ref|YP_255804.1| 19 LVLFLFLYPVAYAVYISFTNFS 40
                                  567788**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2172.78
//
Query:       gi|70606935|ref|YP_255805.1|  [L=480]
Description: sugar-binding periplasmic protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.3   2.0      0.026   14.5   2.0    1.4  1  DUF4083       Domain of unknown function (DUF4083)
      0.042   13.6   0.7      0.079   12.7   0.7    1.4  1  SP_C-Propep   Surfactant protein C, N terminal propeptide
      0.043   13.3   0.1      0.076   12.5   0.1    1.3  1  Zn_peptidase  Putative neutral zinc metallopeptidase
      0.099   13.6   0.0       0.24   12.4   0.0    1.5  1  DUF4834       Domain of unknown function (DUF4834)
       0.11   12.5   0.5       0.19   11.7   0.5    1.4  1  DUF2116       Uncharacterized protein containing a Zn-ribbon 
       0.71    9.7   4.8      0.072   12.9   0.4    1.5  2  SpoIIIAH      SpoIIIAH-like protein


Domain annotation for each model (and alignments):
>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.0   8.6e-06     0.026       4      39 ..      15      50 ..      14      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.6e-06
                       DUF4083  4 dliyliivivLilllvfsftlfiRrvvsrsaakkkk 39
                                  + i+ ++v+vLi+ + ++++l++ r +s+s++  ++
  gi|70606935|ref|YP_255805.1| 15 TQIIIVVVVVLIIVIGVGVYLLMGRSSSSSPSTTTN 50
                                  56899999999999999*******999999966655 PP

>> SP_C-Propep  Surfactant protein C, N terminal propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   2.7e-05     0.079      40      64 ..      17      42 ..      12      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                   SP_C-Propep 40 livvvvvvlvvvvvlga.llmglhms 64
                                  +i+vvvvvl++v+ +g  llmg   s
  gi|70606935|ref|YP_255805.1| 17 IIIVVVVVLIIVIGVGVyLLMGRSSS 42
                                  68999999999999997478887655 PP

>> Zn_peptidase  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.5e-05     0.076      33     114 ..      11      91 ..       4     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                  Zn_peptidase  33 lggktgllvlilvlvgllfGvdlsallglgqesstaeaaaqssegtaeeaedeqkefvsvvladtedtWtqifkekgktyq 113
                                   +  +t+++++++v++ +++Gv++  l+g +++ss++ +++ ss++++++++   ++ +++    t ++W  +  +++k ++
  gi|70606935|ref|YP_255805.1|  11 GVSNTQIIIVVVVVLIIVIGVGVYLLMGRSSSSSPSTTTNTSSSMSSSSSSGG-VSSTTSQTPVTITVWDTYSPSEDKAFN 90 
                                   4456788888888888889*********9999999988888877766664444.444444456677788877777777766 PP

                  Zn_peptidase 114 k 114
                                   +
  gi|70606935|ref|YP_255805.1|  91 Q 91 
                                   5 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.9e-05      0.24      10      69 ..      17      75 ..      14      93 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                       DUF4834 10 fiiailviglsilsv.ilrtvfglgsrkkssksaqkqfgnstnsnqqksq.srsetkeegei 69
                                  +ii+++v+ +++++v ++  + g  + ++ss s + ++++s +s++++   s++++++  +i
  gi|70606935|ref|YP_255805.1| 17 IIIVVVVVLIIVIGVgVYLLM-G--RSSSSSPSTTTNTSSSMSSSSSSGGvSSTTSQTPVTI 75
                                  577777777777777466555.5..4444443344444444444433333233333333333 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   6.5e-05      0.19      26      53 ..       3      30 ..       2      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                       DUF2116 26 eeyekkrkkvarsqqilfgililllavv 53
                                  + y++++k v ++q+i++++++l++++ 
  gi|70606935|ref|YP_255805.1|  3 KDYRRRKKGVSNTQIIIVVVVVLIIVIG 30
                                  6799999*********999988877764 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   2.4e-05     0.072       3      53 ..      19      68 ..      15     127 .. 0.62
   2 ?   -3.5   0.4       2.6   7.7e+03     139     149 ..     448     458 ..     441     467 .. 0.40

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                  XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      SpoIIIAH  3 qiiitaLalmiavagYlnftedsgkkaaetaeteqeesekaeigddkekde 53
                                  ++++++L+++i+v +Yl++  +s +++++t++t+++ s++++ g   ++++
  gi|70606935|ref|YP_255805.1| 19 IVVVVVLIIVIGVGVYLLMGRSSSSSPSTTTNTSSSMSSSSSSGG-VSSTT 68
                                  356677778888999999999887666666666666666666666.11122 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHH CS
                      SpoIIIAH 139 qqqllelteke 149
                                   qq  +e++ ++
  gi|70606935|ref|YP_255805.1| 448 QQAAQEMESTM 458
                                   22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1396  (0.0778627); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 3158.86
//
Query:       gi|70606936|ref|YP_255806.1|  [L=358]
Description: ABC transporter ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-33  115.4   0.0    5.4e-33  114.4   0.0    1.5  1  ABC_tran         ABC transporter
    1.1e-13   51.8   0.1    1.1e-12   48.6   0.1    2.6  2  OB_MalK          MalK OB fold domain
    1.1e-07   32.3   0.0    4.1e-07   30.5   0.0    2.0  2  CysA_C_terminal  CysA C-terminal regulatory domain
    1.3e-07   31.8   0.0      0.012   15.5   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.6e-07   31.4   0.0    3.8e-07   30.2   0.0    1.7  1  TOBE_2           TOBE domain
    9.5e-06   25.2   1.0    0.00022   20.7   1.0    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00055   19.9   0.1     0.0018   18.3   0.0    1.9  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00092   19.2   0.0     0.0016   18.4   0.0    1.4  1  Rad17            Rad17 P-loop domain
     0.0021   18.0   0.4      0.012   15.5   0.1    2.2  2  RsgA_GTPase      RsgA GTPase
     0.0082   16.7   3.7      0.014   15.9   0.1    2.4  2  AAA_23           AAA domain
     0.0083   15.0   0.5        4.8    5.9   0.0    2.9  2  ABC_ATPase       Predicted ATPase of the ABC class
     0.0094   15.9   0.0          4    7.3   0.0    2.5  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.094   12.7   0.0    2.5  2  AAA_14           AAA domain
      0.019   15.3   0.1      0.035   14.5   0.1    1.6  1  AAA_16           AAA ATPase domain
       0.02   14.6   0.1      0.045   13.5   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
       0.06   12.9   0.0        1.6    8.3   0.0    2.2  2  AAA_25           AAA domain
      0.063   13.2   0.2       0.18   11.7   0.0    1.8  2  NACHT            NACHT domain
      0.074   12.8   0.1       0.39   10.4   0.0    2.1  3  AAA_30           AAA domain
      0.077   13.3   0.2       0.22   11.8   0.2    1.8  1  AAA_22           AAA domain
      0.098   11.7   0.0       0.19   10.7   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
       0.14   11.0   0.1       0.22   10.3   0.1    1.2  1  DLIC             Dynein light intermediate chain (DLIC)
       0.17   12.1   0.0       0.45   10.7   0.0    1.7  2  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.0   6.6e-36   5.4e-33       1     136 [.      26     168 ..      26     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 6.6e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   lk vsl++++ge v+i+G++G GK+tLl++++gl+ +++Ge+ +dg+ +++  ++  ++++++++q+  + p ++v +n  
  gi|70606936|ref|YP_255806.1|  26 LKGVSLDVNKGEFVVILGPSGEGKTTLLRIISGLEVQDKGEVYIDGERVDN--IPPKDRNVAMVFQNYAIYPFMSVFDNia 104
                                   799***********************************************9..99999*********************** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              e  +++ ++++ l++++l d++     ++LSgGqkqrva+aral+k ++lll+DEp 
  gi|70606936|ref|YP_255806.1| 105 fplklkklpkqEIAKKVREVAELLQIEKLLDRKP----YQLSGGQKQRVAIARALVKGAQLLLMDEPL 168
                                   *****99876666666777777777777666666....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.1   1.3e-15   1.1e-12       1      53 []     242     290 ..     242     290 .. 0.94
   2 ?   -0.5   0.0         3   2.4e+03      11      32 ..     315     345 ..     311     355 .. 0.64

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.3e-15
                       OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                   G+P+MN+l+++v+e+   v+ ++ ++++p e   ++kl+   evi+GiRPE+i
  gi|70606936|ref|YP_255806.1| 242 GNPPMNLLKVKVDEGA--VLLDEYKIEIPSEI--SEKLKGRSEVIMGIRPEDI 290
                                   9************665..888999******99..******************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                       OB_MalK  11 tveedg.........vlvegggvtlplpeeq 32 
                                   +++ed+          +v+g+ ++l++++++
  gi|70606936|ref|YP_255806.1| 315 KIREDEirvvtnsssSYVKGDTIQLAISGNK 345
                                   5555555444444567788888888887766 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.5   6.9e+03       9      22 ..      64      78 ..      61      85 .. 0.76
   2 !   30.5   0.0     5e-10   4.1e-07       1      43 []     247     292 ..     247     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.5
               CysA_C_terminal  9 dGklriGglalp.vP 22
                                   G + i+g +++ +P
  gi|70606936|ref|YP_255806.1| 64 KGEVYIDGERVDnIP 78
                                  799999999998777 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 5e-10
               CysA_C_terminal   1 NlFhGrvedGklriGglalpvP.....elagadgqevvayVRPhDlei 43 
                                   Nl++ +v++G + ++++ +++P     +l+g+  +ev++++RP+D++i
  gi|70606936|ref|YP_255806.1| 247 NLLKVKVDEGAVLLDEYKIEIPseiseKLKGR--SEVIMGIRPEDIDI 292
                                   9*********************9986666666..************98 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-05     0.025       1      32 [.      38      66 ..      38      84 .. 0.72
   2 !   15.5   0.0   1.4e-05     0.012     223     299 ..     127     201 ..      85     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-05
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegl 32
                                  + v+ Gp g GK++LL+++++l       +g+
  gi|70606936|ref|YP_255806.1| 38 FVVILGPSGEGKTTLLRIISGL---EVQDKGE 66
                                  689*****************99...3333333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-05
                        AAA_21 223 flengdgqelparelSdGtkrllalltallralkkg.sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                   +l  ++  ++ +++lS G+k+     +a++ral kg  lll DEp ++L+ ++     e lkel+r  g  v+ +TH+ 
  gi|70606936|ref|YP_255806.1| 127 LLQIEKLLDRKPYQLSGGQKQR----VAIARALVKGaQLLLMDEPLANLDAQIRMIAREELKELQRkLGFTVVYVTHDQ 201
                                   4555566677789999999999....455555555559*************9999999********9**********94 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   4.6e-10   3.8e-07       1      76 []     283     349 ..     283     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 4.6e-10
                        TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                   ++iRPE++ +   gg   ++G Ve +e lG +++++v++ + ++ +v++++++    +  Gdt++l+++  +a+++
  gi|70606936|ref|YP_255806.1| 283 MGIRPEDIDI---GG--KIKGSVELTEPLGLFSVIHVKIREDEI-RVVTNSSS---SYVKGDTIQLAISGNKALFF 349
                                   58********...66..9***********************999.55555555...799*******9988777765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   1.0   2.7e-07   0.00022     112     210 ..     116     210 ..      16     220 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
                                   EETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 112 kingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                   +i +k    +ev+ell+      e        +LSgG+k+ va+a       vk a l l+De  a+LD++ + +  e lk
  gi|70606936|ref|YP_255806.1| 116 EIAKKV---REVAELLQI-----EklldrkpyQLSGGQKQRVAIARA----LVKGAQLLLMDEPLANLDAQIRMIAREELK 184
                                   233322...333333333.....0333334449*******9998754....6899************************** PP

                                   HHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 185 eksknaQfivislreemlekadklvg 210
                                   e + +  f v+ ++++++e      +
  gi|70606936|ref|YP_255806.1| 185 ELQRKLGFTVVYVTHDQTEALALADR 210
                                   ********999999888876654444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-06    0.0018      17      70 ..      33      85 ..      22     151 .. 0.71
   2 ?   -2.7   0.0       5.5   4.5e+03      43      67 ..     186     210 ..     178     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                      ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70
                                   ++ e+++i Gp g GKt+Ll+ ii+ le +dk  +y++  r ++i  +d+ ++
  gi|70606936|ref|YP_255806.1| 33 VNKGEFVVILGPSGEGKTTLLR-IISGLEVQDKGEVYIDGERVDNIPPKDRNVA 85
                                  567899**************97.89999999********999999999888754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                      ATPase_2  43 nledkdkyviyyialreesisklde 67 
                                    ++++++ v+y++  ++e+++ +d+
  gi|70606936|ref|YP_255806.1| 186 LQRKLGFTVVYVTHDQTEALALADR 210
                                   4467788888888877777666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0016      29     112 ..      20     103 ..      11     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                         Rad17  29 eevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrflsqies 108
                                   ++v e lk  +L+ +k + ++i GPsG gk+t ++++s   + +  e ++++  + + + +  ++  +++ +  + + + +
  gi|70606936|ref|YP_255806.1|  20 KQVIEVLKGVSLDVNKGEFVVILGPSGEGKTTLLRIISGLEVQDKGEvYIDGERVDNIPPKDRNVAMVFQ-NYAIYPFMSV 99 
                                   579999*******************************987776554426777776655555555544444.3346677777 PP

                         Rad17 109 fkel 112
                                   f ++
  gi|70606936|ref|YP_255806.1| 100 FDNI 103
                                   7664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.5e-05     0.012      98     130 ..      35      67 ..      10      73 .. 0.79
   2 ?   -0.5   0.0       1.3     1e+03      64      89 ..     179     204 ..     150     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                   TTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgev 130
                                   k++++v++G+SG GK+tL+  + + + +  gev
  gi|70606936|ref|YP_255806.1|  35 KGEFVVILGPSGEGKTTLLRIISGLEVQDKGEV 67 
                                   4599*****************999878777776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHTTSEEEE--TTTHTT CS
                   RsgA_GTPase  64 eleelkeelealgyevllvsaktkeg 89 
                                   + eelke  ++lg++v++v  +++e+
  gi|70606936|ref|YP_255806.1| 179 AREELKELQRKLGFTVVYVTHDQTEA 204
                                   56777888888888888886654443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-05     0.014      11      39 ..      19      56 ..      12      59 .. 0.69
   2 ?    1.4   0.3      0.47   3.8e+02     131     176 ..      93     174 ..      61     191 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                        AAA_23 11 rdqeidF........sk.gltlItGpNGaGKTTildAi 39
                                  ++q i+         +k  +++I Gp G GKTT+l+ i
  gi|70606936|ref|YP_255806.1| 19 KKQVIEVlkgvsldvNKgEFVVILGPSGEGKTTLLRII 56
                                  555555544444444552588**************987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.47
                        AAA_23 131 ilnlilflgqerfeefelkdkkerleelekeleeledekkllekl.................................... 175
                                   i ++ + ++   f  +++k +k+++++  +e  el +++kll+++                                    
  gi|70606936|ref|YP_255806.1|  93 IYPFMSVFDNIAFPLKLKKLPKQEIAKKVREVAELLQIEKLLDRKpyqlsggqkqrvaiaralvkgaqlllmdeplanlda 173
                                   455555555555555556677888888888888888888888888877777766666666666666544444433333332 PP

                        AAA_23 176 e 176
                                   +
  gi|70606936|ref|YP_255806.1| 174 Q 174
                                   1 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0067       5.5     241     264 ..      32      56 ..      15      62 .. 0.83
   2 !    5.9   0.0    0.0058       4.8     324     350 ..     142     168 ..     138     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0067
                                   EE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAl 264
                                    + kG  ++I G+  +GK+TLL+ +
  gi|70606936|ref|YP_255806.1|  32 DVNKGeFVVILGPSGEGKTTLLRII 56 
                                   467888899*************976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0058
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGG CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDt 350
                                   SG   q ++i++al  ga+llL+DE  
  gi|70606936|ref|YP_255806.1| 142 SGGQKQRVAIARALVKGAQLLLMDEPL 168
                                   899999999***************965 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0049         4       2      22 ..      39      59 ..      38      88 .. 0.68
   2 ?    6.0   0.0     0.012        10      25      65 ..     170     210 ..     150     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0049
                                  EEEE--TTSSHHHHHHHHHHH CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                  v+i Gp+G GKtTl++ ++ l
  gi|70606936|ref|YP_255806.1| 39 VVILGPSGEGKTTLLRIISGL 59
                                  6899**********9887643 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                   ..GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT- CS
                      NTPase_1  25 ssgvkvgGfyteevreggrrigFkivdlasgeegiLarvea 65 
                                   + + +++ +  ee +e +r+ gF++v ++ ++++ La  + 
  gi|70606936|ref|YP_255806.1| 170 NLDAQIRMIAREELKELQRKLGFTVVYVTHDQTEALALADR 210
                                   556667777789999******************99998774 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.094       3      73 ..      37     103 ..      35     125 .. 0.74
   2 ?   -0.8   0.0       1.8   1.5e+03      62      72 ..     338     351 ..     308     353 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEi 73 
                                   + +vi G+   GKTtll ++i+ l v+++  +yi+ ++ ++   +d  ++  ++++  ++     + ++D i
  gi|70606936|ref|YP_255806.1|  37 EFVVILGPSGEGKTTLL-RIISGLEVQDKGEVYIDGERVDNIPPKDR-NVAMVFQNYaIY---PFMSVFDNI 103
                                   689*************8.66667778***********9999776655.244444443333...355666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                        AAA_14  62 e...ekktylflDE 72 
                                   +   ++++ lf+DE
  gi|70606936|ref|YP_255806.1| 338 QlaiSGNKALFFDE 351
                                   12223555666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.2e-05     0.035      19      63 ..      33      76 ..      19     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                        AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                  v++g  e v++ G+sG GK++l+r +     +d g +++ g+ +++
  gi|70606936|ref|YP_255806.1| 33 VNKG--EFVVILGPSGEGKTTLLRIISGLEVQDkGEVYIDGERVDN 76
                                  5555..79***************98886444441344477777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.5e-05     0.045      14      39 ..      28      53 ..      24      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
                        AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                  g +++++  +++++ GpsG GK+Tll
  gi|70606936|ref|YP_255806.1| 28 GVSLDVNKGEFVVILGPSGEGKTTLL 53
                                  56778885559**************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.002       1.6      30      50 ..      33      53 ..       8      58 .. 0.88
   2 ?    2.2   0.0      0.14   1.2e+02     170     188 ..     181     199 ..     166     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  + +ge++++ G++g GKttl+
  gi|70606936|ref|YP_255806.1| 33 VNKGEFVVILGPSGEGKTTLL 53
                                  479****************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                        AAA_25 170 ealeriarrtgaavllvhH 188
                                   e l++++r++g +v+ v H
  gi|70606936|ref|YP_255806.1| 181 EELKELQRKLGFTVVYVTH 199
                                   6899**************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.18       3      20 ..      39      56 ..      37      66 .. 0.86
   2 ?   -1.5   0.0       2.6   2.1e+03      74      88 ..     151     165 ..     102     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                  EEEEC-TTTCHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkl 20
                                  v++ G++G GKTtLl+ +
  gi|70606936|ref|YP_255806.1| 39 VVILGPSGEGKTTLLRII 56
                                  89*************866 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.6
                                   HHHCCSCCCEEEEEE CS
                         NACHT  74 avllelperlLlilD 88 
                                   + ++ ++   Ll++D
  gi|70606936|ref|YP_255806.1| 151 IARALVKGAQLLLMD 165
                                   333333333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047      0.39      18      48 ..      36      66 ..      30      85 .. 0.83
   2 ?   -1.8   0.0       2.6   2.1e+03      81      96 ..     142     166 ..     110     201 .. 0.61
   3 ?   -1.7   0.0       2.4   1.9e+03      37      66 ..     182     211 ..     177     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggr 48
                                    ++v+ Gp G GKtt+l+ +  +  +++g+
  gi|70606936|ref|YP_255806.1| 36 GEFVVILGPSGEGKTTLLRIISGLEVQDKGE 66
                                  3589***************998776666544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                        AAA_30  81 k.........grarlepgtllivDE 96 
                                             +ra ++ ++ll+ DE
  gi|70606936|ref|YP_255806.1| 142 SggqkqrvaiARALVKGAQLLLMDE 166
                                   0444444444333333335555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.4
                        AAA_30  37 alreaweaaggrviglAptgkaAkvLaeel 66 
                                   +l+e+ ++ g++v+ +++ ++ A +La+ +
  gi|70606936|ref|YP_255806.1| 182 ELKELQRKLGFTVVYVTHDQTEALALADRV 211
                                   567778888999999999999998888765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00028      0.22       5      31 ..      36      62 ..      33     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                        AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                    ++v+ G+sG GKTtllr +    ++
  gi|70606936|ref|YP_255806.1| 36 GEFVVILGPSGEGKTTLLRIISGLEVQ 62
                                  6799**************977666544 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.19      99     151 ..       3      58 ..       1      72 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                         T2SSE  99 sakeltlddlgaeealkekiaevlrka...vrerglilvsGgTgsGKttllyallk 151
                                   s++ l+l+d+ ++ + k+++ evl+     v++   +++ G+ g GKttll ++  
  gi|70606936|ref|YP_255806.1|   3 SSAFLQLSDIWKSFKIKKQVIEVLKGVsldVNKGEFVVILGPSGEGKTTLLRIISG 58 
                                   67788999999999999999999875433388889999*************88765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00027      0.22      23      55 ..      34      66 ..      20      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                          DLIC 23 PsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                    g  v++lG +g Gkttl+  + G+e + kG 
  gi|70606936|ref|YP_255806.1| 34 NKGEFVVILGPSGEGKTTLLRIISGLEVQDKGE 66
                                  456779***********************9996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00055      0.45       2      20 ..      39      57 ..      38      77 .. 0.80
   2 ?   -2.7   0.0       7.6   6.2e+03     139     155 ..     181     197 ..     146     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  +vi+G+++ GKTtll+ ++
  gi|70606936|ref|YP_255806.1| 39 VVILGPSGEGKTTLLRIIS 57
                                  8**************9887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                        AAA_28 139 erlrealrelgipviiv 155
                                   e l+e+ r+lg+ v+ v
  gi|70606936|ref|YP_255806.1| 181 EELKELQRKLGFTVVYV 197
                                   45666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2221.60
//
Query:       gi|70606937|ref|YP_255807.1|  [L=160]
Description: hypothetical protein Saci_1167 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-28   98.0   4.7    1.6e-13   50.9   0.3    2.1  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.022   14.3   0.1      0.044   13.4   0.1    1.5  1  HAMP_N3   HAMP N-terminal domain 3
      0.042   14.0   0.0       0.11   12.7   0.0    1.7  2  YopE      Yersinia virulence determinant (YopE)
       0.11   12.1   0.1       0.17   11.5   0.1    1.5  1  DisA_N    DisA bacterial checkpoint controller nucleotide-bin


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.3   3.5e-17   1.6e-13       5      56 ..       9      60 ..       3      61 .. 0.92
   2 !   49.1   0.5   1.3e-16   5.8e-13       1      56 [.      68     122 ..      68     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 3.5e-17
                                  SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                   +++v++v+++++l  a ++mr++++++l VV+e++++vGi+t+rD+++a +
  gi|70606937|ref|YP_255807.1|  9 ISKPVLVVRENDSLLRATREMRNHNIGALVVVNENEEVVGIITERDVVKAFA 60
                                  799**************************889****************9976 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.3e-16
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   Vgd+m+r+v  v+  t++  al++m+++g+++lPVV e +k++Giv+ rDl++al+
  gi|70606937|ref|YP_255807.1|  68 VGDYMSREVKGVKIGTDIYTALKTMVDNGFRHLPVV-EGDKVHGIVSIRDLVKALV 122
                                   89**********************************.5667*************97 PP

>> HAMP_N3  HAMP N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.9e-06     0.044       7      20 ..      54      67 ..      53      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-06
                                  HHHHHHHTS----- CS
                       HAMP_N3  7 avvkayaeGdfsad 20
                                  +vvka+a+G+f+a 
  gi|70606937|ref|YP_255807.1| 54 DVVKAFADGNFDAT 67
                                  69**********96 PP

>> YopE  Yersinia virulence determinant (YopE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   6.3e+03      32      48 ..      39      55 ..      28      61 .. 0.64
   2 ?   12.7   0.0   2.4e-05      0.11      17      62 ..     114     156 ..     109     160 .] 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                  GHHHHHHHHHHHHCSEC CS
                          YopE 32 eveelraqasrllntsv 48
                                   v+e ++ ++ ++++ v
  gi|70606937|ref|YP_255807.1| 39 VVNENEEVVGIITERDV 55
                                  45555666677777766 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHHHHHHGGHHHHHHHHHHHHCSECTTCEGGGCC-SSSH CS
                          YopE  17 LRsliTalqglrkiseveelraqasrllntsvggialsQWGTiGGa 62 
                                   +R l+ al++l ++s+++   ++as l   +v+g  +  +G +G  
  gi|70606937|ref|YP_255807.1| 114 IRDLVKALVDLDNLSNMR---IEASDLNSCPVCGLEIDEFGYCGCG 156
                                   688888888888888765...**********************954 PP

>> DisA_N  DisA bacterial checkpoint controller nucleotide-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.17       2      30 ..      24      52 ..      23      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                  HHHHHHHHHT--EEEEEESSSCCCTTCCT CS
                        DisA_N  2 eaveelskkkiGaliviereeelkeiiet 30
                                  +a++e+ +++iGal+v++++ee+  ii++
  gi|70606937|ref|YP_255807.1| 24 RATREMRNHNIGALVVVNENEEVVGIITE 52
                                  58899*****************7555533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1099.66
//
Query:       gi|70606938|ref|YP_255808.1|  [L=147]
Description: alanyl-tRNA like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.004   17.2   0.0     0.0072   16.4   0.0    1.4  1  Sigma70_r3  Sigma-70 region 3


Domain annotation for each model (and alignments):
>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     4e-07    0.0072      12      39 ..      37      64 ..      35      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-07
                                  HHHHHHSSXXXHHHHHHHHTXXHHHHHH CS
                    Sigma70_r3 12 eLeqelgrePtpeEiAeeLglseekVre 39
                                  +L+ +++r P++eEiAe  +l  +kV+e
  gi|70606938|ref|YP_255808.1| 37 RLTVKFERKPSDEEIAEIFNLANKKVQE 64
                                  68899*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1008.98
//
Query:       gi|70606939|ref|YP_255809.1|  [L=327]
Description: thioredoxin reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-39  134.2   2.2    6.3e-39  133.9   2.2    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-19   69.7   2.4    9.7e-16   57.9   0.4    2.3  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.3e-08   33.6   5.4    3.4e-06   27.5   0.2    2.9  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    5.8e-08   32.7   1.8    8.3e-05   22.3   0.4    3.0  3  DAO            FAD dependent oxidoreductase
    1.2e-07   31.2   2.7    7.5e-06   25.3   0.3    3.0  3  FAD_binding_2  FAD binding domain
    2.6e-05   23.8   0.2    0.00011   21.6   0.0    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
    4.5e-05   22.8   0.4      0.013   14.8   0.1    2.3  2  Thi4           Thi4 family
    5.6e-05   23.3   0.1    0.00011   22.3   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    6.5e-05   22.2   0.1    6.5e-05   22.2   0.1    3.4  4  GIDA           Glucose inhibited division protein A
      0.001   17.9   0.9      0.026   13.2   0.0    2.6  3  HI0933_like    HI0933-like protein
     0.0029   16.7   0.3       0.18   10.8   0.1    2.2  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.061   12.6   0.0      0.092   12.0   0.0    1.3  1  FAD_binding_3  FAD binding domain
      0.075   11.4   0.1       0.68    8.3   0.0    2.2  3  FMO-like       Flavin-binding monooxygenase-like
      0.097   12.0   0.4       0.46    9.7   0.0    2.2  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
        0.1   12.9   0.0       0.19   12.0   0.0    1.7  1  FLgD_tudor     FlgD Tudor-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   2.2   5.3e-42   6.3e-39       1     294 []       7     291 ..       7     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 5.3e-42
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCHCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielllge 73 
                                   +d ++iGgG+AGl+aal+ a++++ ++++ +++  l+g+  l+  ++++++ ++i           + k++n+  e++lge
  gi|70606939|ref|YP_255809.1|   7 YDTIIIGGGIAGLSAALYSARQKLSTLVL-SKD--LGGQLTLTDLIENYPGIESIGGrglsqkiyTQAKRFNA--EFVLGE 82 
                                   5899*********************9999.555..89999999999999999988889999988866666665..599999 PP

                                   TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiG 154
                                   ev +i ++  ++ +   ++g ++ ++ +++vlA G +pr l++pG++e  gk+v++++ ++a   k +p  ++vvG G  G
  gi|70606939|ref|YP_255809.1|  83 EVKEISQEG-EIFI---VNGIHNVYQSKTIVLAFGKTPRELNVPGEQEFKGKGVSYCAICDAAFFKGKP--AMVVGEGEPG 157
                                   9****6666.6666...3577889*********************************************..********** PP

                                   HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE..EEETTSCE..EEESEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx..xxxxxx RF
                   Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle..vvledgee..idadlv 231
                                   +E    l+k +  +++v    +l        ++ +++ +  +++++++ ++v +i+gng+ +e  v+++ ge+  ++++ v
  gi|70606939|ref|YP_255809.1| 158 LEAIEILSKHANPAYYVTSSGQLS-----GDEELIKKIMSTSNIKIYTSSKVLQINGNGK-VEevVINKGGETlrLKVEGV 232
                                   *******************99996.....56889999**********************9.66645555555599****** PP

                                   EE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 232 vvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   ++  G+  +t++l  +  l+l+++g + vdef+rt+ +g++a+GDv+  ++ +++a+ A ++G
  gi|70606939|ref|YP_255809.1| 233 IIEMGYVLKTDFL--RGFLKLNDKGEVIVDEFGRTSREGVFAAGDVT--QTPYKQAVIAAAEG 291
                                   ************8..888999**************************..99999999999987 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   9.5e-05      0.11       1      30 [.      10      38 ..      10      56 .. 0.81
   2 !   57.9   0.4   8.1e-19   9.7e-16      91     305 .]      71     274 ..      56     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                  iIiG+G aGl+aa+   + +l + l+l k+
  gi|70606939|ref|YP_255809.1| 10 IIIGGGIAGLSAALYSARQKL-STLVLSKD 38
                                  8********************.68999986 PP

  == domain 2  score: 57.9 bits;  conditional E-value: 8.1e-19
                   Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvv 168
                                   ak+f+ +  l eeV+++++e+e f+v+  +++y++k++++A G+   P+ ln+pGe++   + + y  + +++ ++g+  +
  gi|70606939|ref|YP_255809.1|  71 AKRFNAEFVLGEEVKEISQEGEIFIVNGIHNVYQSKTIVLAFGK--TPRELNVPGEQEfkgKGVSYCAICDAAFFKGKPAM 149
                                   7889999999*********************************9..**********976456778888889999******* PP

                   Pyr_redox_3 169 ViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey.kvk 248
                                   V+G ++ + +a +e+ +k a+   ++ +s           +l+ d e+ +++++++++ik+++ ++v +i+ + +    v 
  gi|70606939|ref|YP_255809.1| 150 VVGEGEPGLEA-IEILSKHANPAYYVTSSG----------QLSGD-EELIKKIMSTSNIKIYTSSKVLQINGNGKVEeVVI 218
                                   *********95.777777777666666653..........34443.677888888888************97765441555 PP

                   Pyr_redox_3 249 tedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    + g++++ k + v++ +Gy  +++fl+   ++l+++g++ ++e    t  +g+f aG
  gi|70606939|ref|YP_255809.1| 219 NKGGETLRLKVEGVIIeMGYVLKTDFLR-GFLKLNDKGEVIVDEFG-RTSREGVFAAG 274
                                   77788888887777776**********9.99999999999998765.57799999998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   1.3    0.0093        11       3      70 ..      10      91 ..       8      98 .. 0.79
   2 !   27.5   0.2   2.8e-09   3.4e-06       3      79 ..     149     219 ..     147     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0093
                                  EEECSSHHHHHHHHHH...........HHTT...SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                     Pyr_redox  3 vvvGgGyiglElAgal...........aelg...kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70
                                  +++GgG  gl +A +            ++lg     + ++e+ + + +  ++ +s+ + ++ ++ + e++l+++v+ei +++
  gi|70606939|ref|YP_255809.1| 10 IIIGGGIAGLSAALYSarqklstlvlsKDLGgqlTLTDLIENYPGIESIGGRGLSQKIYTQAKRFNAEFVLGEEVKEISQEG 91
                                  89***********999888888888877788333334568888888888888888888888888899999999999988766 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.8e-09
                                   EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                   +vvG G  glE+ ++l+++++  + v  s +l        ++++++ ++  +i++++++kv +i+g+++ ve+v+++
  gi|70606939|ref|YP_255809.1| 149 MVVGEGEPGLEAIEILSKHANPAYYVTSSGQLS-----GDEELIKKIMSTSNIKIYTSSKVLQINGNGK-VEEVVIN 219
                                   7********************************.....2246778888999*****************9.9***987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   6.9e-08   8.3e-05       1      29 [.       8      38 ..       8      44 .. 0.85
   2 !    6.6   0.0    0.0043       5.2     150     201 ..      65     113 ..      57     141 .. 0.76
   3 ?    1.6   0.0      0.14   1.7e+02     152     198 ..     186     234 ..     151     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.9e-08
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                  d +iiGGGi+Gls+A++ ar++  +++l k+
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKlsTLVLSKD 38
                                  789****************998978888777 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                                   HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.E.EEEEEEE--G CS
                           DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttpgen.d.aadavVnaaG 201
                                   + ++ +a++  +e+++g+ev+++++ +g +  v +   g+  + + +++V+a G
  gi|70606939|ref|YP_255809.1|  65 QKIYTQAKRFNAEFVLGEEVKEISQ-EGEIFIV-N---GIHnVyQSKTIVLAFG 113
                                   678899999**************66.5677777.3...4432233377***988 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.14
                                   HHHH.HHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.E.EEEEEEE CS
                           DAO 152 lara.aealGveilegtevtgleeedgkvwgverttp.gen.d.aadavVn 198
                                   l ++ + +  ++i++ ++v  + + +gkv +v + ++ ge+ + +++ v++
  gi|70606939|ref|YP_255809.1| 186 LIKKiMSTSNIKIYTSSKVLQI-NGNGKVEEV-VINKgGETlRlKVEGVII 234
                                   4444477788************.667999999.555556653334444665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.3   6.3e-09   7.5e-06       1      31 [.       8      38 ..       8      45 .. 0.94
   2 ?    2.7   0.0     0.044        53     154     200 ..     193     237 ..     183     241 .. 0.84
   3 ?    1.1   0.0      0.14   1.7e+02     377     407 ..     258     282 ..     247     292 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.3e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                  D i+iG+G+AGL+AAl  a++ l+++v++k 
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVLSKD 38
                                  89***************************96 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                                   CT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 154 ag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                      ++++++ ++++++  +g+v  +v++  ++g++ r++  +v++  g
  gi|70606939|ref|YP_255809.1| 193 TSnIKIYTSSKVLQING-NGKVEEVVIN--KGGETLRLKVEGVIIEMG 237
                                   33499**********55.99********..**************9876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                                   EBETTSBESTTEEESSBTEEE-STCEESSSS CS
                 FAD_binding_2 377 etdengrvldadgqpipGLYAaGevaaggvh 407
                                    +de gr+        +G +AaG v+ + ++
  gi|70606939|ref|YP_255809.1| 258 IVDEFGRT------SREGVFAAGDVTQTPYK 282
                                   34555555......899********987776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   9.6e-08   0.00011       1      40 [.       8      45 ..       8     119 .. 0.76
   2 ?   -0.3   0.0      0.44   5.2e+02      91     130 ..     185     222 ..     172     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.6e-08
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                  D +++GGg+aG+ AA+ +ar+  ++l+++++  lGG+lt 
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVLSKD--LGGQLTL 45
                                  779*************************976..9***993 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                  FAD_oxidored  91 avleemlaeagvtvllntrlvevekegkriesvtveskeg 130
                                   ++++++++ +++++++ +++ +++ +g ++e+v++ +k g
  gi|70606939|ref|YP_255809.1| 185 ELIKKIMSTSNIKIYTSSKVLQINGNG-KVEEVVI-NKGG 222
                                   5678888999**************998.9******.5553 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   1.1e-05     0.013      16      51 ..       5      39 ..       1      45 [. 0.87
   2 !    6.1   0.0    0.0048       5.8      68     138 ..     150     219 ..     143     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                  TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                          Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersv 51
                                   + D +i+G+G +GL+aa y a++ +l +++l + +
  gi|70606939|ref|YP_255809.1|  5 KVYDTIIIGGGIAGLSAALYSARQ-KLSTLVLSKDL 39
                                  5689*******************9.99999998765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0048
                                   EEETTTHHHHHHTT---EEESSEEEESEHHHHHH..HHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEE CS
                          Thi4  68 vvrkpakelLdelgikyedegdyvvvkdaalfts..tllskvlqlanvkllnavaveDlivregegvaGvvin 138
                                   vv  +++  L+ ++i +++ +  ++v  + ++    +l+ k++  +n+k++++  v    +  + +v  vvin
  gi|70606939|ref|YP_255809.1| 150 VV-GEGEPGLEAIEILSKHANPAYYVTSSGQLSGdeELIKKIMSTSNIKIYTSSKVLQ--INGNGKVEEVVIN 219
                                   44.356667899999999999999999999887533799***********98765532..2222344444444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   9.5e-08   0.00011       1      38 [.      11      46 ..      11      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.5e-08
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  I+G+G++Gl+aA + a+++++ l+l k  +lGG+++  
  gi|70606939|ref|YP_255809.1| 11 IIGGGIAGLSAALYSARQKLSTLVLSK--DLGGQLTLT 46
                                  9************************77..699998755 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   5.4e-08   6.5e-05       1      48 [.       8      62 ..       8      87 .. 0.87
   2 ?   -1.1   0.0      0.62   7.5e+02     113     150 ..      79     114 ..      63     133 .. 0.73
   3 ?    0.2   0.2      0.26   3.1e+02     100     149 ..     185     237 ..     181     257 .. 0.64
   4 ?    2.8   0.2     0.042        51     354     390 ..     266     304 ..     253     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.4e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE.......ES-GGGTT--SSSSEEE-TT CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.......thkldtiaelsCnpsiggia 48
                                  d i+iGgG AG+ AAl +ar  +++l +          +d i + +  +sigg +
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVLskdlggqLTLTDLIENYPGIESIGGRG 62
                                  579***********************99999999888889999999999999985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.62
                                   EEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 113 iieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   ++ eev+e++  e+++  +v   ++++++k++v+a G 
  gi|70606939|ref|YP_255809.1|  79 VLGEEVKEISQ-EGEI-FIVNGIHNVYQSKTIVLAFGK 114
                                   56678888844.4444.4677788999999***99997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.26
                                   HHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEET.TS-EEEEC..EEEE--T CS
                          GIDA 100 evteklenepnleiiee.eveeliveekkvkgvvte.dgetikak..avviatG 149
                                   e+ +k+ ++ n++i +  +v +++  ++kv+ vv +  get++ k   v+i  G
  gi|70606939|ref|YP_255809.1| 185 ELIKKIMSTSNIKIYTSsKVLQING-NGKVEEVVINkGGETLRLKveGVIIEMG 237
                                   5567788889999976416777744.7888775554045555544445666655 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.042
                                   SSBTEEE-CGGGTB-SHHH...HHHHHHHHHHHHHHHHCT CS
                          GIDA 354 kvkgLflAGqinGteGYeE...aaaqGllAGinaarkakg 390
                                   +++g+f+AG+++ t  Y     aaa G+ A++ a +++++
  gi|70606939|ref|YP_255809.1| 266 SREGVFAAGDVTQTP-YKQaviAAAEGVKAALSAYNYLRS 304
                                   689*********998.766222678*******99988876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   2.2e-05     0.026       2      31 ..       8      37 ..       7      45 .. 0.92
   2 ?    2.0   0.0     0.056        67     117     163 ..      69     113 ..      62     116 .. 0.85
   3 ?   -1.4   0.0      0.61   7.3e+02     117     151 ..     189     223 ..     172     237 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                  d+i+iGgG AGl aA+  a+++ ++l+l k
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVLSK 37
                                  89**********************999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.056
                                   HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   +++k+ + ++ l +evk++++ e+++f v+   ++ ++++++vlA G
  gi|70606939|ref|YP_255809.1|  69 TQAKRFNAEFVLGEEVKEISQ-EGEIFIVNG-IHNVYQSKTIVLAFG 113
                                   67788899999********66.666699998.89***********98 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.61
                                   HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTE CS
                   HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktksee 151
                                   k ++ +++k++++++v +++ + + +  v  k++e
  gi|70606939|ref|YP_255809.1| 189 KIMSTSNIKIYTSSKVLQINGNGKVEEVVINKGGE 223
                                   55667888888888888886544433222223443 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00015      0.18       1      28 [.       8      35 ..       8      47 .. 0.77
   2 ?    3.9   0.0      0.02        23      80     132 ..     171     227 ..     162     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvv 28
                                  D ++iG+G Agls A  ++++k    v+
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVL 35
                                  88****************6655544443 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                 Lycopene_cycl  80 aYgrvsskrl..keellerlv..engvklleakvesveeeeageslvvleggrkira 132
                                   aY   ss +l   eel ++++  +n  +++++kv +++ + + e +v+ +gg+++r 
  gi|70606939|ref|YP_255809.1| 171 AYYVTSSGQLsgDEELIKKIMstSNIKIYTSSKVLQINGNGKVEEVVINKGGETLRL 227
                                   56666666663337788888765667789************99*********98874 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05     0.092       3      75 ..       8      78 ..       6     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEE CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgea 75
                                  d++I+G+G aGl++al  +++  +++++ k      +    + n   +e++  +Gl ++i+ ++  +  ++e+
  gi|70606939|ref|YP_255809.1|  8 DTIIIGGGIAGLSAALYSARQKLSTLVLSKDLGGQLTLTDLIENYPGIESIGGRGLSQKIYTQA--KRFNAEF 78
                                  899******************9999999999999888889999999999999999999999998..3333333 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   7.3e+02       6      44 ..      11      47 ..       9      58 .. 0.75
   2 ?   -0.1   0.0      0.19   2.3e+02     156     187 ..      49      80 ..      39      90 .. 0.86
   3 ?    8.3   0.0   0.00057      0.68     158     216 ..     120     178 ..     105     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                      FMO-like  6 viGaGvsGlasikccleegleptcfersddiGGlwrfke 44
                                  +iG+G++Gl++      + l    +  s+d+GG   +++
  gi|70606939|ref|YP_255809.1| 11 IIGGGIAGLSAALYSARQKLSTLVL--SKDLGGQLTLTD 47
                                  89*******9987777777765554..678888766666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                      FMO-like 156 lesfpGiekfkGqyfhsrdykepevfkgkrvl 187
                                   +e +pGie   G+ +  + y + + f+   vl
  gi|70606939|ref|YP_255809.1|  49 IENYPGIESIGGRGLSQKIYTQAKRFNAEFVL 80 
                                   589********************999987765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00057
                      FMO-like 158 sfpGiekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrsG 216
                                     pG ++fkG+ +      + + fkgk  +v+G G+ g +    ls+ a+  +  t sG
  gi|70606939|ref|YP_255809.1| 120 NVPGEQEFKGKGVSYCAICDAAFFKGKPAMVVGEGEPGLEAIEILSKHANPAYYVTSSG 178
                                   57*************************************999999**999888877777 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00039      0.46      31      51 ..       9      29 ..       4      51 .. 0.82
   2 ?   -3.4   0.0       4.1   4.9e+03      12      34 ..      88     110 ..      80     113 .. 0.77
   3 ?   -1.3   0.0      0.92   1.1e+03      31      47 ..     148     164 ..     125     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                                  EEEESTSHHHHHHHHHHHHTT CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglg 51
                                  +++iGgG+aGl+A+  +++ +
  gi|70606939|ref|YP_255809.1|  9 TIIIGGGIAGLSAALYSARQK 29
                                  68***********98877655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                                   GCTSEEETTCEETCB---EEEEE CS
                   AlaDh_PNT_C  12 ffggkgtlaGgvpgvepakvlvi 34 
                                    ++g++ ++ g++ v ++k++v+
  gi|70606939|ref|YP_255809.1|  88 SQEGEIFIVNGIHNVYQSKTIVL 110
                                   56788888889999999998887 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.92
                                   EEEESTSHHHHHHHHHH CS
                   AlaDh_PNT_C  31 vlviGgGvaGlqAiata 47 
                                    +v+G G  Gl+Ai++ 
  gi|70606939|ref|YP_255809.1| 148 AMVVGEGEPGLEAIEIL 164
                                   5899*********9875 PP

>> FLgD_tudor  FlgD Tudor-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.19      19      50 ..     201     232 ..      80     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                   EEEEE-EEEEEEEEEEEE.ETTEEEEEET.TEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                    FLgD_tudor  19 tsvaattlvygtVdsVslstggglmLnLg.lgg 50 
                                   +s  ++ + +g+V+ V++ ++gg +L+L   g 
  gi|70606939|ref|YP_255809.1| 201 SSKVLQINGNGKVEEVVI-NKGGETLRLKvEGV 232
                                   55668999**********.77777799986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2102.92
//
Query:       gi|70606940|ref|YP_255810.1|  [L=188]
Description: methionine sulfoxide reductase A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-65  218.8   0.6    4.4e-65  218.5   0.6    1.0  1  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.5   0.6   2.4e-69   4.4e-65       2     153 .]      16     166 ..      15     166 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.5 bits;  conditional E-value: 2.4e-69
                                   EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT-SSE CS
                          PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDptqlnr 82 
                                   a+l+gGCFW++e++f+++kGv+s++ GY gGk++nptYeevc+++tghaE+v++++dp++++++elle+ffeihDpt+ nr
  gi|70606940|ref|YP_255810.1|  16 ATLGGGCFWCTEAVFKRVKGVVSVKPGYSGGKVPNPTYEEVCTDETGHAEVVQITFDPSVITYRELLEIFFEIHDPTTPNR 96 
                                   79******************************************************************************* PP

                                   ETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS.--T CS
                          PMSR  83 qgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpeg.ych 153
                                   qgnDvG+qYrs+i y++eeqk++aee+++ +++k  l+kk+vte+ p++ fy+ae+yH ++++k+++  yc+
  gi|70606940|ref|YP_255810.1|  97 QGNDVGSQYRSIILYHSEEQKKIAEEMIKLYERK--LGKKVVTELVPFEAFYEAEDYHHDFYDKHKNYpYCK 166
                                   **********************************..******************************999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1301.57
//
Query:       gi|70606941|ref|YP_255811.1|  [L=269]
Description: hypothetical protein Saci_1171 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-10   39.6   8.0    1.3e-06   28.3   0.3    2.4  2  HTH_45           Winged helix-turn-helix
    6.1e-09   35.3   5.6    0.00015   21.2   0.6    3.1  3  HTH_24           Winged helix-turn-helix DNA-binding
    1.7e-07   31.0   0.3    3.8e-06   26.7   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.8e-06   27.7   0.1    6.1e-06   26.1   0.1    1.9  1  MarR             MarR family
    4.5e-06   26.5   0.0     0.0011   18.9   0.0    2.5  2  MarR_2           MarR family
    1.7e-05   24.6   5.3    0.00037   20.3   0.1    2.2  2  DUF4364          Domain of unknown function (DUF4364)
      2e-05   25.0   0.3    9.2e-05   22.9   0.0    2.0  2  HTH_27           Winged helix DNA-binding domain
    2.8e-05   24.1   0.0      0.045   13.8   0.0    2.5  2  HTH_20           Helix-turn-helix domain
      5e-05   23.2   4.3      0.014   15.3   0.3    2.9  2  HTH_11           HTH domain
    0.00021   21.6   0.6       0.01   16.2   0.0    2.5  2  Rrf2             Transcriptional regulator
    0.00029   20.6   1.7      0.021   14.7   0.1    2.5  2  HxlR             HxlR-like helix-turn-helix
     0.0019   17.9   0.0      0.028   14.2   0.0    2.3  2  HTH_23           Homeodomain-like domain
     0.0042   16.9   0.7      0.024   14.5   0.0    2.3  2  HTH_10           HTH DNA binding domain
     0.0044   17.0   6.3      0.019   15.0   0.8    2.9  2  HTH_Mga          M protein trans-acting positive regulator (M
     0.0067   16.1   0.9        1.6    8.5   0.1    2.7  2  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.096   12.7   0.0    2.3  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.022   14.4   0.0       0.15   11.7   0.0    2.2  2  GntR             Bacterial regulatory proteins, gntR family
      0.031   14.2   0.5       0.83    9.7   0.1    2.6  2  PadR             Transcriptional regulator PadR-like family
      0.049   13.5   4.2        3.2    7.7   0.4    2.7  2  RuvB_C           RuvB C-terminal winged helix domain
       0.05   13.3   0.0       0.11   12.3   0.0    1.5  1  HTH_psq          helix-turn-helix, Psq domain
      0.065   13.3   0.0       0.16   12.1   0.0    1.6  1  MerR_1           MerR HTH family regulatory protein
      0.067   13.2   0.0        4.1    7.5   0.0    2.3  2  HTH_29           Winged helix-turn helix
      0.073   13.2   0.1       0.28   11.3   0.1    2.0  1  Peptidase_C23    Carlavirus endopeptidase
      0.083   12.8   3.0        8.3    6.3   0.9    2.6  2  TFIIE_alpha      TFIIE alpha subunit
      0.097   12.9   0.2       0.51   10.6   0.0    2.1  2  HTH_17           Helix-turn-helix domain
       0.11   12.3   0.0       0.23   11.2   0.0    1.6  1  MerR             MerR family regulatory protein
       0.11   12.8   0.8       0.19   12.1   0.1    1.6  1  Penicillinase_R  Penicillinase repressor
       0.12   12.6   0.7       0.59   10.4   0.0    2.5  3  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.12   12.5   0.0       0.39   10.9   0.0    1.8  2  HTH_28           Helix-turn-helix domain
       0.67   10.3   7.1       0.58   10.5   0.2    3.4  3  NUMOD1           NUMOD1 domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.3   2.1e-09   1.3e-06       4      73 ..      23      94 ..      22      97 .. 0.90
   2 !   14.2   2.5   5.5e-05     0.033       9      75 ..     123     199 ..     118     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-09
                        HTH_45  4 kleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklkele 73
                                  + +   dIL ++  +g ++ T+i    n s k +   + +Lv+k+l++k +++ Y l ekG++lle+++ + 
  gi|70606941|ref|YP_255811.1| 23 RAKLQWDILIILAtKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKvKGDIYGLSEKGEKLLESFDSIM 94
                                  66777899999887999******************************776999**************99875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                        HTH_45   9 adILeais.egeakkTkimykanLsykllnkYLdmLvekgli.........kkskekYvlTekGlelleklkeleel 75 
                                   ++IL++   +++ +  k   +  +s ++l+ Y+++ +e++l+          ksk+ YvlT++ ++l+++l el +l
  gi|70606941|ref|YP_255811.1| 123 LEILKMALlNKQITIDKASHELGISKQTLKYYIETFTENKLLkvvnqesvlGKSKKIYVLTDESRKLVSRLPELTRL 199
                                   5677655446666677778888999999*************777888888899******************999887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.4   8.3e+02       1      13 [.       4      16 ..       4      17 .. 0.86
   2 !   21.2   0.6   2.6e-07   0.00015       3      48 .]      25      70 ..      23      70 .. 0.95
   3 !   15.1   0.1     2e-05     0.012       6      46 ..     123     163 ..     121     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                        HTH_24  1 ldetdrkILelLq 13
                                  +++  ++IL++L 
  gi|70606941|ref|YP_255811.1|  4 MNKRVFDILRELD 16
                                  788999****995 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.6e-07
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +++++IL +L  ++  s +e+++ ++ S+  +   +++L++++l++
  gi|70606941|ref|YP_255811.1| 25 KLQWDILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVT 70
                                  6789***************************************996 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2e-05
                        HTH_24   6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46 
                                   ++IL+    n  i++   + +lg+S++t++++++ ++e+ l
  gi|70606941|ref|YP_255811.1| 123 LEILKMALLNKQITIDKASHELGISKQTLKYYIETFTENKL 163
                                   689999999*************************9999866 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   6.3e-09   3.8e-06      12      58 ..      29      75 ..      24      83 .. 0.92
   2 ?    1.8   0.1      0.38   2.3e+02      17      62 ..     130     180 ..     124     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 6.3e-09
                                  CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  ++ + L ++gp++++ei++ ++ +r ++ +++r+L+dk lV+++kg 
  gi|70606941|ref|YP_255811.1| 29 DILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKGD 75
                                  5678999************************************9985 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.38
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEE CS
                          TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklY 62 
                                   Ll +++ t+d+ ++elg+++++   +++   +  l +++ ++      +k+Y
  gi|70606941|ref|YP_255811.1| 130 LL-NKQITIDKASHELGISKQTLKYYIETFTENKLLKVVNQEsvlgksKKIY 180
                                   44.888999999*******999888777777766666666555555555555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1     1e-08   6.1e-06       5      50 ..      27      72 ..      25      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1e-08
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  q++iL il+++gp s +e+   +++s+ ++  ++++L++k+l+++ 
  gi|70606941|ref|YP_255811.1| 27 QWDILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKV 72
                                  9******************************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.8e-06    0.0011       7      56 ..      27      74 ..      25      75 .. 0.96
   2 ?    4.9   0.0     0.039        24      28      53 ..     141     166 ..     125     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  q+++L  L+  ++   + +e+ ++ + s+ ++  ++++Lv++ Lv++++g
  gi|70606941|ref|YP_255811.1| 27 QWDILIILATKGP--SSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKG 74
                                  9***********9..8******************************9987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                                   HHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  28 arrlglsksavsrilkrLvaaGLver 53 
                                     +lg+sk+++ + ++ + +  L+  
  gi|70606941|ref|YP_255811.1| 141 SHELGISKQTLKYYIETFTENKLLKV 166
                                   569***************99999865 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   6.2e-07   0.00037      37      99 ..      57     116 ..      45     120 .. 0.91
   2 ?    6.1   1.5     0.014       8.5       7      72 ..     121     192 ..     119     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.2e-07
                       DUF4364  37 qqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylkenkeelkke 99 
                                    +a+ +Lv+++l+++    + ++y ++ekG++ le f++ ++ ++ +k d+++++n  +l + 
  gi|70606941|ref|YP_255811.1|  57 IDAIRKLVDKELVTK---VKGDIYGLSEKGEKLLESFDSIMSINVTDKPDSSIESNSISLTNI 116
                                   6899**********8...779***********************************9988775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                       DUF4364   7 Yllkkvkfpltnsqls.eiileneytnYfdlqqalseLvesglieeeek.....enktlykiTekGketlel 72 
                                   Y+l+ +k+ l n+q++ + +  +  ++  +l+ +++  +e++l+++ ++     ++k++y +T++ ++ ++ 
  gi|70606941|ref|YP_255811.1| 121 YMLEILKMALLNKQITiDKASHELGISKQTLKYYIETFTENKLLKVVNQesvlgKSKKIYVLTDESRKLVSR 192
                                   9*************98466777778999****************9995547777899********9998875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.5e-07   9.2e-05       4      68 .]      26      83 ..      25      83 .. 0.87
   2 ?   -0.7   0.0       3.6   2.2e+03      28      66 ..     144     184 ..     141     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.5e-07
                        HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +q+ +L  ++ + ++++ ++++++ n++  +i+ +++kL+ k+Lv++ + +       + l++kG
  gi|70606941|ref|YP_255811.1| 26 LQWDILIILA-TKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKGD------IYGLSEKG 83
                                  5888999999.9*********************************776654......66666666 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.6
                        HTH_27  28 lnvedshisyslkkLtekGLv..ertgdeadrrekrvrlTd 66 
                                   l +++++  y ++  te+ L+  + +++   +  k + lTd
  gi|70606941|ref|YP_255811.1| 144 LGISKQTLKYYIETFTENKLLkvVNQESVLGKSKKIYVLTD 184
                                   67888888899999999999866666666666667777777 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.5e-05     0.045      14      58 ..      29      73 ..       5      74 .. 0.80
   2 !    7.8   0.0    0.0059       3.5      22      59 ..     132     169 ..     123     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-05
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                  +il  La++++ + +e+ +++ +s++++ + +r+L++ +Lv+ v+
  gi|70606941|ref|YP_255811.1| 29 DILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVK 73
                                  455555***********************************9886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0059
                                   CTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20  22 aegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                   ++  t     ++l++sk+tl y +++  e  L++vv +
  gi|70606941|ref|YP_255811.1| 132 NKQITIDKASHELGISKQTLKYYIETFTENKLLKVVNQ 169
                                   666677778899**********************9975 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.4e-05     0.014       4      39 ..      29      63 ..      27      83 .. 0.86
   2 !    8.5   0.3    0.0033       1.9       4      39 ..     124     158 ..     122     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                  +il++L +++gp s  e+++ +n Sr+ +   I++L
  gi|70606941|ref|YP_255811.1| 29 DILIIL-ATKGPSSTTEISQTINTSRKSIIDAIRKL 63
                                  799999.***************************99 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                        HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39 
                                    il++ l +++ i++++ + eL++S++t   +I++ 
  gi|70606941|ref|YP_255811.1| 124 EILKMALLNKQ-ITIDKASHELGISKQTLKYYIETF 158
                                   79999766665.*****************9999875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-05      0.01      12      61 ..      29      75 ..      22      85 .. 0.87
   2 ?    3.2   0.1      0.19   1.1e+02      18      58 ..     127     167 ..     109     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                                  HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                   +l++La++      s++ei++  n+s++ +   ++kL  ++lv+ v+G 
  gi|70606941|ref|YP_255811.1| 29 DILIILATKGP---SSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKGD 75
                                  57888888777...67********************************96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                                   HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2  18 akeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58 
                                   ++   ++++++++ +++ +is++ l+  +++ ++++l+k+v
  gi|70606941|ref|YP_255811.1| 127 KMALLNKQITIDKASHELGISKQTLKYYIETFTENKLLKVV 167
                                   333334459********************999999999875 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.4e-05     0.021       5      80 ..      27      94 ..      25     101 .. 0.86
   2 ?    4.5   0.3      0.05        30      30      82 ..     145     199 ..     124     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                                  TTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                          HxlR  5 kWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                  +W +li+ + +kg+  ++e+++++ + s+k ++  +r+L  ++l+ ++          Y l+ekG++l + ++ ++
  gi|70606941|ref|YP_255811.1| 27 QWDILIILA-TKGPSSTTEISQTI-NTSRKSIIDAIRKLVDKELVTKVKG------DIYGLSEKGEKLLESFDSIM 94
                                  699999875.79************.99************99999987543......37999999999999888776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.05
                                   TS-HHHHHHHHHHHHHTTSEEEEEESSS..S-EEEEEE-TCGGGGHHHHHHHHHH CS
                          HxlR  30 kisqkmLaqrLreLeqdglierevypev..PpkveYsltekGrslepvlqelkkw 82 
                                   +is+++L   +    +++l++ +  ++v    k  Y lt++ r+l   l el+ +
  gi|70606941|ref|YP_255811.1| 145 GISKQTLKYYIETFTENKLLKVVNQESVlgKSKKIYVLTDESRKLVSRLPELTRL 199
                                   78999999999999999888877776662245779**********9999888765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.76   4.5e+02      19      40 ..      41      62 ..      32      74 .. 0.88
   2 !   14.2   0.0   4.6e-05     0.028       8      43 ..     123     160 ..     123     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.76
                        HTH_23 19 svreIAreLgvsrrTvyrwlkr 40
                                  s++eI++  + sr  +   +++
  gi|70606941|ref|YP_255811.1| 41 STTEISQTINTSRKSIIDAIRK 62
                                  789**********999877766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.6e-05
                        HTH_23   8 lrillllae..GlsvreIAreLgvsrrTvyrwlkryre 43 
                                   l+il++++    +++ +++ eLg+s++T+  +++++ e
  gi|70606941|ref|YP_255811.1| 123 LEILKMALLnkQITIDKASHELGISKQTLKYYIETFTE 160
                                   578888884459***********************976 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.5   8.7e+02      26      47 ..      42      63 ..      40      66 .. 0.79
   2 !   14.5   0.0   3.9e-05     0.024      22      46 ..     133     157 ..     131     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                        HTH_10 26 lkeLAkelGIskstlsehLrka 47
                                  + e++++++ s+ ++ + +rk 
  gi|70606941|ref|YP_255811.1| 42 TTEISQTINTSRKSIIDAIRKL 63
                                  6789999999999999988885 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.9e-05
                        HTH_10  22 RrvtlkeLAkelGIskstlsehLrk 46 
                                   +++t+++ + elGIsk+tl+++++ 
  gi|70606941|ref|YP_255811.1| 133 KQITIDKASHELGISKQTLKYYIET 157
                                   7999******************986 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.079        47       6      45 ..      26      64 ..      22      74 .. 0.82
   2 !   15.0   0.8   3.2e-05     0.019       9      45 ..     124     159 ..     123     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.079
                       HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                   + ++l +L + ++  +++e++   ++s++++ + i++L 
  gi|70606941|ref|YP_255811.1| 26 LQWDILIILAT-KGPSSTTEISQTINTSRKSIIDAIRKLV 64
                                  56777777888.8888999************999998886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.2e-05
                       HTH_Mga   9 kLlelLteneksltldelakeLglseltlqsdiseLn 45 
                                   ++l   +  +k +t+d++++eLg+s  tl+ +i+ ++
  gi|70606941|ref|YP_255811.1| 124 EILKMALL-NKQITIDKASHELGISKQTLKYYIETFT 159
                                   56666666.89**********************9876 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.023        13       5      49 ..      30      74 ..      27      81 .. 0.91
   2 !    8.5   0.1    0.0027       1.6       4      31 ..     124     151 ..     123     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                      HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthG 49
                                  il  l+ +g  s++e+++  ++S + i   +++L+ + l+t++ G
  gi|70606941|ref|YP_255811.1| 30 ILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKG 74
                                  7889999******************99999999999999999887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0027
                      HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTi 31 
                                   +il++      +++++++ +lg+S++T 
  gi|70606941|ref|YP_255811.1| 124 EILKMALLNKQITIDKASHELGISKQTL 151
                                   58888888899****************5 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016     0.096      21      54 ..      39      73 ..       7      83 .. 0.82
   2 ?    0.2   0.0       1.3   7.5e+02      22      52 ..     135     165 ..     116     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                  p + +e+++ ++++r ++  ++++L ++ l++  +
  gi|70606941|ref|YP_255811.1| 39 PSSTTEISQTINTSRKSIIDAIRKLVDKELVTkVK 73
                                  67889**************************9533 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                   HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis 52 
                                   +t +  ++ lG++ +t+   +  + + +l++
  gi|70606941|ref|YP_255811.1| 135 ITIDKASHELGISKQTLKYYIETFTENKLLK 165
                                   5555566789999999999999999988887 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00025      0.15      28      59 ..      43      74 ..      41      75 .. 0.91
   2 ?   -0.5   0.0       1.7   9.9e+02      32      61 ..     142     171 ..     131     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                          GntR 28 reLaaefgVsrttvReALrrLeaeglverrqg 59
                                   e+++ +++sr ++  A+r+L+ + lv+  +g
  gi|70606941|ref|YP_255811.1| 43 TEISQTINTSRKSIIDAIRKLVDKELVTKVKG 74
                                  5899***********************97766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                                   HHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                          GntR  32 aefgVsrttvReALrrLeaeglverrqgrG 61 
                                    e+g+s++t+   + + ++ +l+ + ++++
  gi|70606941|ref|YP_255811.1| 142 HELGISKQTLKYYIETFTENKLLKVVNQES 171
                                   689999999998888888888888888766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.27   1.6e+02      29      71 ..      51      85 ..      30      89 .. 0.64
   2 ?    9.7   0.1    0.0014      0.83      39      71 ..     156     188 ..     136     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.27
                                  TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                          PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                   s  s+ +a ++L +++lv++ + +        +Y l ++G++
  gi|70606941|ref|YP_255811.1| 51 TSRKSIIDAIRKLVDKELVTKVKGD--------IYGLSEKGEK 85
                                  4445666788888888888887766........5666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                                   HHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                          PadR  39 krLekeglveseweesgegpprkyYrlTdaGrr 71 
                                   +++ +++l++  ++es+ g+ +k+Y lTd+ r+
  gi|70606941|ref|YP_255811.1| 156 ETFTENKLLKVVNQESVLGKSKKIYVLTDESRK 188
                                   56788999999999***************9887 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.011       6.4      11      58 ..      30      73 ..      24      88 .. 0.80
   2 ?    7.7   0.4    0.0054       3.2      11      46 ..     122     157 ..     115     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.011
                                  HHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEET CS
                        RuvB_C 11 yLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIerts 58
                                  +L +l+    +gp + + ++++++++++ i+d i   L+ ++l+++ +
  gi|70606941|ref|YP_255811.1| 30 ILIILA---TKGPSSTTEISQTINTSRKSIIDAI-RKLVDKELVTKVK 73
                                  566666...689********************99.6799999998855 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0054
                                   HHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHH CS
                        RuvB_C  11 yLkllkekfkggpvglktlaailgeeketiedviEP 46 
                                   +L++lk +  ++++ ++  ++ lg++k+t+   iE 
  gi|70606941|ref|YP_255811.1| 122 MLEILKMALLNKQITIDKASHELGISKQTLKYYIET 157
                                   7999**9************************99995 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.11      13      39 ..     131     157 ..     126     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                       HTH_psq  13 vnGkmSirkAArkYgiPrsTLwrrkrg 39 
                                   +n++++i kA+ + gi++ TL +++++
  gi|70606941|ref|YP_255811.1| 131 LNKQITIDKASHELGISKQTLKYYIET 157
                                   699*******************99876 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00026      0.16       2      24 ..     136     158 ..     135     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                                   EHHHHHHHHTS-HHHHHHHHHHT CS
                        MerR_1   2 sigevakilgvtthtlrywekeg 24 
                                   +i++++ +lg+++ tl+y+ + +
  gi|70606941|ref|YP_255811.1| 136 TIDKASHELGISKQTLKYYIETF 158
                                   89*****************9987 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.14        83       7      37 ..      34      64 ..      28      73 .. 0.76
   2 ?    7.5   0.0    0.0068       4.1       7      38 ..     130     160 ..     125     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                        HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfe 37
                                  l+ +G s++ +i +  + sr+++ ++++  +
  gi|70606941|ref|YP_255811.1| 34 LATKGPSSTTEISQTINTSRKSIIDAIRKLV 64
                                  334444489**************99998765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0068
                        HTH_29   7 llaeGvstvsqiAkllglsrrtvyrwlkrfee 38 
                                   ll++   t+  + + lg+s++t   +++ f e
  gi|70606941|ref|YP_255811.1| 130 LLNKQI-TIDKASHELGISKQTLKYYIETFTE 160
                                   555666.9***************999999876 PP

>> Peptidase_C23  Carlavirus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00047      0.28       9      65 ..      45     101 ..      42     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
                 Peptidase_C23   9 vskAlkrrkadilAvlekvaseelveevseGrGlsiedvesvleildivgdvnvggk 65 
                                   +s+ ++++++ i+  ++k   +elv +v+    +  e+ e++le +d + ++nv +k
  gi|70606941|ref|YP_255811.1|  45 ISQTINTSRKSIIDAIRKLVDKELVTKVKGDIYGLSEKGEKLLESFDSIMSINVTDK 101
                                   89**************************87654445889***************998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021        12      17      58 ..      29      70 ..      18      75 .. 0.92
   2 ?    6.3   0.9     0.014       8.3      16      64 ..     123     171 ..     113     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                                  HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                   +l +L++kg  +  ++++ ++  ++ +  ++ +L ++ lv 
  gi|70606941|ref|YP_255811.1| 29 DILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVT 70
                                  6899***********************************996 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                                   HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
                   TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd 64 
                                    ++l++ l + ++t +  ++el+i ++ l+  +    e +l k++ +  
  gi|70606941|ref|YP_255811.1| 123 LEILKMALLNKQITIDKASHELGISKQTLKYYIETFTENKLLKVVNQES 171
                                   67888888899********************************988765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.3   1.4e+03       4      31 ..      42      71 ..      41      77 .. 0.71
   2 ?   10.6   0.0   0.00086      0.51       3      30 ..     136     167 ..     135     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.3
                        HTH_17  4 veEaAelLgvsrstvyrlir...rgelpaak 31
                                  + E+++  + sr+++ + ir   ++el ++k
  gi|70606941|ref|YP_255811.1| 42 TTEISQTINTSRKSIIDAIRklvDKEL-VTK 71
                                  677777888999999999986666666.665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00086
                        HTH_17   3 tveEaAelLgvsrstvyrli....rrgelpaa 30 
                                   t++ a+  Lg+s++t+  +i     ++ l+++
  gi|70606941|ref|YP_255811.1| 136 TIDKASHELGISKQTLKYYIetftENKLLKVV 167
                                   999*****************444436666666 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00039      0.23       1      21 [.     136     156 ..     136     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                                   EHHHHHHHHTTTHHHHHHHHH CS
                          MerR   1 tIgevAeltGvsprtLRyYEr 21 
                                   tI  +++ +G+s +tL yY +
  gi|70606941|ref|YP_255811.1| 136 TIDKASHELGISKQTLKYYIE 156
                                   7999***************75 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00032      0.19       3      55 ..      25      73 ..      24      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                                  -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
               Penicillinase_R  3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrek 55
                                  +l++ ++ il +kg+ +++e+ + ++      ++++   +r+Lv+K+l+++ k
  gi|70606941|ref|YP_255811.1| 25 KLQWDILIILATKGPSSTTEISQTINTS----RKSIIDAIRKLVDKELVTKVK 73
                                  689*******************999988....9****************9876 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00099      0.59      19      55 ..      36      72 ..      29      75 .. 0.88
   2 ?   -1.6   0.0       5.6   3.3e+03      27      53 ..     139     165 ..     128     172 .. 0.69
   3 ?   -2.2   0.0       8.5   5.1e+03      11      24 ..     177     191 ..     177     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00099
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                  +k++ +t+++++ +n s  s+   ++kL ++++v  +
  gi|70606941|ref|YP_255811.1| 36 TKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKV 72
                                  78899****************************9765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.6
                                   HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  27 dlaerLnvspssVsemlkkLekdGyve 53 
                                   + + +L++s+ +    ++   ++ +++
  gi|70606941|ref|YP_255811.1| 139 KASHELGISKQTLKYYIETFTENKLLK 165
                                   568889999888766666666665555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 8.5
                                   HHHHHHHH.HHSSB- CS
                Fe_dep_repress  11 etIYtlse.ekkvvk 24 
                                   + IY l + ++k v+
  gi|70606941|ref|YP_255811.1| 177 KKIYVLTDeSRKLVS 191
                                   579999987888876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.2   4.9e+03      14      35 ..      41      62 ..      32      63 .. 0.72
   2 ?   10.9   0.0   0.00066      0.39       3      31 ..     123     153 ..     123     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.2
                        HTH_28 14 svreaArelgisrrtvyrWikr 35
                                  s +e+++  ++sr ++ + i++
  gi|70606941|ref|YP_255811.1| 41 STTEISQTINTSRKSIIDAIRK 62
                                  6678888899999988666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00066
                        HTH_28   3 leiiklla.aGh.svreaArelgisrrtvyr 31 
                                   lei+k ++ +   +++ a++elgis +t++ 
  gi|70606941|ref|YP_255811.1| 123 LEILKMALlNKQiTIDKASHELGISKQTLKY 153
                                   6888886666666***************964 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.55   3.3e+02      17      37 .]      40      60 ..      40      60 .. 0.86
   2 ?   -0.9   0.0       3.7   2.2e+03      11      19 ..      85      93 ..      81      96 .. 0.80
   3 ?   10.5   0.2   0.00097      0.58      18      37 .]     136     155 ..     129     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.55
                        NUMOD1 17 sSireAakyLgishntInkyl 37
                                  sS +e ++ ++ s+++I  ++
  gi|70606941|ref|YP_255811.1| 40 SSTTEISQTINTSRKSIIDAI 60
                                  578999**********98765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.7
                        NUMOD1 11 ktigkFsSi 19
                                  k++ +F+Si
  gi|70606941|ref|YP_255811.1| 85 KLLESFDSI 93
                                  5689****9 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00097
                        NUMOD1  18 SireAakyLgishntInkyl 37 
                                   +i +A+  Lgis++t ++y+
  gi|70606941|ref|YP_255811.1| 136 TIDKASHELGISKQTLKYYI 155
                                   6889***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1933.73
//
Query:       gi|70606942|ref|YP_255812.1|  [L=478]
Description: flagella-like protein J [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-13   50.5   2.4    9.6e-09   35.3   0.1    3.0  2  T2SSF          Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.048   13.6   0.0      0.074   13.0   0.0    1.2  1  Auxin_canalis  Auxin canalisation
        9.4    6.6   9.0        4.8    7.5   1.5    2.8  2  Orf78          Orf78 (ac78)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   1.6e-12   9.6e-09       4     121 ..      23     145 ..      20     148 .. 0.90
   2 !   13.9   0.4   6.4e-06     0.038       1     102 [.     251     358 ..     251     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.6e-12
                                   HHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT-HH CS
                         T2SSF   4 qlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssef.pelvvqlirageeggnLa 78 
                                    +  l+saG+p++++L  +++ ++++p+ ++++ri++ ++     +s+ +     +++  +f +e++v+l++a+  g ++ 
  gi|70606942|ref|YP_255812.1|  23 FMMALFSAGLPPETVLLKVSNKDSFHPYLKVFRRIKNLVSGFRyKFSQGINyairNSKV-KFlSEFLVRLSQAVTFGDDMV 102
                                   6889**************************************98667666666625555.666****************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                         T2SSF  79 evLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                   ++Ler  ++  +e+ +   +  +++   l+++ +l  +l++l+
  gi|70606942|ref|YP_255812.1| 103 QFLEREIDFSLAEYSSHSARVIESMNNFLTVYATLNSSLAFLV 145
                                   ********************************99988888876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC...T-TT.TS.-HHHHHHHHHHHHHT-H CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale...rtpssef.pelvvqlirageeggnL 77 
                                   f+r++ +  s   +l e+L ++ + +  g  ++ ++r+++rl+ G + s+ ++   r   s++ ++l   l ++++ ggn+
  gi|70606942|ref|YP_255812.1| 251 FTRYFTRNYSVVNNLKESLMAVLRGD-LGSAKPMIRRALNRLNLGVNKSKIFSlmgRESKSVLvTMLSEILYETISNGGNM 330
                                   667777777777799***********.*******************99999998885445577799999999999999997 PP

                                   ...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         T2SSF  78 ...aevLerlaeyleeerelrrkllaal 102
                                      +e+L+++ + + + r+++ ++  a+
  gi|70606942|ref|YP_255812.1| 331 litGEILSKIGDVVLNIRARKEQNGRAF 358
                                   5558888888888888888887665555 PP

>> Auxin_canalis  Auxin canalisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.074     112     157 ..     335     381 ..     278     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                 Auxin_canalis 112 gksktvgrwlkdrkekkkeeaRaqnAqvhA.avSvAgvAAAvAAvaa 157
                                   +  + +g  + + + +k ++ Ra +A ++A  vS Agv+AA+ ++++
  gi|70606942|ref|YP_255812.1| 335 EILSKIGDVVLNIRARKEQNGRAFEASIYAlQVSSAGVSAALISITS 381
                                   4556688888899*****************55*********999876 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.1     0.032   1.9e+02      66      88 ..     162     184 ..     127     197 .. 0.77
   2 ?    7.5   1.5    0.0008       4.8      70      94 ..     436     460 ..     427     466 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.032
                         Orf78  66 llisllavvcvlvllyviyYfvi 88 
                                   ll  +    ++lv l vi+Y++ 
  gi|70606942|ref|YP_255812.1| 162 LLQIFFLSTVILVNLTVIMYYIY 184
                                   44444445566667777777764 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0008
                         Orf78  70 llavvcvlvllyviyYfvilrerqk 94 
                                    l ++ +l+++ +i+Y+vil+   +
  gi|70606942|ref|YP_255812.1| 436 SLYFIGLLMIMSAISYYVILTLTAQ 460
                                   578999**************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3301.31
//
Query:       gi|70606943|ref|YP_255813.1|  [L=513]
Description: hypothetical protein Saci_1173 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-47  160.0   0.0    8.4e-47  159.5   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.031   14.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.032   14.8   0.0      0.096   13.2   0.0    1.8  2  ABC_tran      ABC transporter
      0.047   13.0   0.0       0.08   12.3   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.067   13.7   0.4      0.067   13.7   0.4    1.8  2  AAA_23        AAA domain
       0.12   12.1   0.0        0.2   11.4   0.0    1.3  1  DEAD          DEAD/DEAH box helicase
       0.13   12.5   0.0       0.36   11.1   0.0    1.7  1  AAA_22        AAA domain
       0.15   11.5   0.0       0.26   10.8   0.0    1.3  1  DUF3300       Protein of unknown function (DUF3300)


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   0.0   3.7e-50   8.4e-47       5     258 ..     130     386 ..     126     396 .. 0.92

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 3.7e-50
                         T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvl 84 
                                   le+l++d+ + di +   ++ ++v++  +  +   +++ + ++l  li  +   + + +s++rp++da+lp +g r++ v 
  gi|70606943|ref|YP_255813.1| 130 LEPLIRDPYIEDISIPGLGHvYIVHKVFGP-MRTSIKFENYEELDNLIVSLSEKSYRPVSHNRPVVDASLP-DGSRVNFVY 208
                                   788999**************7777666666.9999************************************.999999887 PP

                         T2SSE  85 lPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtv 163
                                      +     +l++Rk s    ++ +l++ ++l+  +a+ + + + e +++ v G T sGKtt+l+a+ ++i+ +  +ivt+
  gi|70606943|ref|YP_255813.1| 209 GVDISRrgSNLTVRKFSRVPTSITQLIMFGTLSSMMAAYIWTMLDEGMNLFVCGETASGKTTTLNAITAFIPPN-LKIVTI 288
                                   5544443699***************************************************************9.****** PP

                         T2SSE 164 EDpvEiqleganqvqlnak....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagal 240
                                   ED+ E+ + + n v+ +++    ++++ + dll+aaLR+rP  i+vGEiRdke   + +A++TGH + ++T Ha + +  +
  gi|70606943|ref|YP_255813.1| 289 EDTPELTVPHSNWVAEVTRetggEGTIKLFDLLKAALRQRPNYILVGEIRDKEGNVAFQAMQTGHSV-MATFHAANITTLI 368
                                   **************99999899999******************************************.************* PP

                         T2SSE 241 erLeqlgaeveaaelkss 258
                                   +rL     ev++  +++ 
  gi|70606943|ref|YP_255813.1| 369 QRLTGYPIEVPKSYINNL 386
                                   ***998877777777665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05     0.031      20      49 ..     252     282 ..     243     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                        AAA_29  20 dlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                                     +g + ++ G++ sGK+T l Ai+a + p+
  gi|70606943|ref|YP_255813.1| 252 LDEGmNLFVCGETASGKTTTLNAITAFIPPN 282
                                   446778999****************988776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.096       8      48 ..     252     292 ..     248     313 .. 0.84
   2 ?   -3.2   0.0         5   1.1e+04      30      62 ..     332     365 ..     331     374 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkd 48 
                                   l eg  + + Ge+ +GK+t l++++    p+   +++++++
  gi|70606943|ref|YP_255813.1| 252 LDEGMNLFVCGETASGKTTTLNAITAFIPPNLKIVTIEDTP 292
                                   67899999*******************99998888888665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5
                                   HHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      ABC_tran  30 llagllkpteGeilldgkdlke.qeleslrkeig 62 
                                   +l g+ +++eG++ ++  ++ +    ++  ++i 
  gi|70606943|ref|YP_255813.1| 332 ILVGEIRDKEGNVAFQAMQTGHsVMATFHAANIT 365
                                   5788889999999887444433244444445555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.08      40      59 ..     256     275 ..     229     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                   .SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  40 shllvaGatgsGKStalntL 59 
                                    +l v+G t sGK+t+ln++
  gi|70606943|ref|YP_255813.1| 256 MNLFVCGETASGKTTTLNAI 275
                                   49****************96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.4   5.3e+03     173     195 ..      73      99 ..      24     105 .. 0.58
   2 ?   13.7   0.4     3e-05     0.067      19      41 ..     254     277 ..     250     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                        AAA_23 173 ekl....eqekekekeleeleeeleei 195
                                   e++    +  ke  +  +e+e+ + +i
  gi|70606943|ref|YP_255813.1|  73 EEKfalsIGDKEPPEDTKEKEKLIRSI 99 
                                   222222222333333333444444333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3e-05
                        AAA_23  19 kgltlI.tGpNGaGKTTildAikl 41 
                                    g++l+ +G++ +GKTT l+Ai+ 
  gi|70606943|ref|YP_255813.1| 254 EGMNLFvCGETASGKTTTLNAITA 277
                                   56665428**************95 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     9e-05       0.2       8      67 ..     249     302 ..     242     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                                   HHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   8 iplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnl 67 
                                   +  + +g +++v++eT+sGKT+   + ++ ++      ++ k++ +e t eL+  + n +
  gi|70606943|ref|YP_255813.1| 249 WTMLDEGMNLFVCGETASGKTTT--LNAITAF----IPPNLKIVTIEDTPELTVPHSNWV 302
                                   44445889*************98..5555445....356777777777777766665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.36       7      30 ..     257     280 ..     252     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                    l+v+Ge+ +GKTt+l+ ++   +
  gi|70606943|ref|YP_255813.1| 257 NLFVCGETASGKTTTLNAITAFIP 280
                                   689**************9988764 PP

>> DUF3300  Protein of unknown function (DUF3300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.26     122     150 ..     405     433 ..     392     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                       DUF3300 122 kvtveeeqiviepanpevvYvPyYdpavv 150
                                   +v++ +e i i+p++++vvY+P++  + v
  gi|70606943|ref|YP_255813.1| 405 RVVEVDEIIDIDPVTNDVVYIPAFTYDSV 433
                                   7889999***************9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3400.71
//
Query:       gi|70606944|ref|YP_255814.1|  [L=228]
Description: flagellar accessory protein FlaH [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-21   76.2   0.9    2.8e-21   75.9   0.9    1.0  1  ATPase           KaiC
      2e-07   30.5   2.1     0.0074   15.5   0.7    2.0  2  PAXNEB           PAXNEB protein
    0.00028   20.6   3.3    0.00033   20.4   2.5    1.4  1  DUF835           Protein of unknown function (DUF835)
     0.0022   17.5   0.6       0.11   12.0   0.0    2.4  3  RecA             recA bacterial DNA recombination protein
     0.0049   16.6   1.2      0.038   13.7   0.2    2.2  2  AAA_24           AAA domain
     0.0053   16.4   0.0      0.011   15.3   0.0    1.5  1  AAA_25           AAA domain
     0.0076   15.8   0.2     0.0087   15.6   0.2    1.1  1  Elong_Iki1       Elongator subunit Iki1
     0.0086   15.4   0.1      0.024   13.9   0.1    1.7  1  Rad51            Rad51
  ------ inclusion threshold ------
       0.03   13.3   0.1      0.038   12.9   0.1    1.2  1  AAA_10           AAA-like domain
      0.044   13.3   0.0        1.8    8.1   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
      0.071   12.5   0.3        3.4    7.0   0.1    2.1  2  TniB             Bacterial TniB protein
      0.088   12.7   1.9       0.27   11.1   1.9    1.9  1  NTPase_1         NTPase
        0.1   12.6   1.4       0.66   10.0   0.1    2.2  2  NOGCT            NOGCT (NUC087) domain
       0.13   12.0   0.1       0.26   11.0   0.0    1.5  2  Sigma54_activat  Sigma-54 interaction domain
       0.16   11.2   0.2       0.25   10.5   0.2    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.18   12.2   0.0       0.32   11.4   0.0    1.5  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.9   2.5e-24   2.8e-21       2     228 ..       4     222 ..       3     224 .. 0.92

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2.5e-24
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegk 82 
                                   +tg   lD+ l gGip  +++ i G+ GtGK+++++qF++  + + +++g  +t+e++ +d   ++k++ +dl  +  +gk
  gi|70606944|ref|YP_255814.1|   4 STGNDDLDRRL-GGIPYPASIMIEGDHGTGKSVLSAQFVLGFLLS-DKKGYVITTEQTTKDYLIKMKEIKIDLIPYFIRGK 82 
                                   799999****9.****************************99999.*********************************** PP

                        ATPase  83 laiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvse 163
                                   l i  + +++ +     +++ +e++++ + + i+++++  +viDs++ la  +ke+++ + + + +rvl ++g   +++  
  gi|70606944|ref|YP_255814.1|  83 LRIAPLNTKKFN----WNSSLAEKILDVIVNFIRSKNIDFIVIDSLSILAAFSKEKQLLQFM-KDIRVLVNTGKMILFTIH 158
                                   ********9987....558999***************************7777777766555.557899999999999999 PP

                        ATPase 164 kssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                    +++ ++  + ++   ivd  ++L   +i +++v++le vk  g    ++++ f++++  gikv++
  gi|70606944|ref|YP_255814.1| 159 -PDTFDEEMKSKITS-IVDVYLKLSAATIGGRRVKILERVKTTGGISGSDTISFDVDPaLGIKVVP 222
                                   .7777889999****.*****************************9************999*9987 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.4e-06     0.011      17      48 ..       1      31 [.       1      67 [. 0.78
   2 !   15.5   0.7   6.6e-06    0.0074     182     283 ..      98     182 ..      44     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.4e-06
                        PAXNEB 17 lltStGtpsLDklLgGGLplGsillieEdgtt 48
                                  +++StG+++LD+ L GG+p   +++ie d+ t
  gi|70606944|ref|YP_255814.1|  1 MIISTGNDDLDRRL-GGIPYPASIMIEGDHGT 31
                                  589***********.99**********98544 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.6e-06
                        PAXNEB 182 pryssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplslia 262
                                   +  +++l+ i +++++        kn+  ivi sL   +        sk+++ll+F++ +r l+ + +++++ t+  + + 
  gi|70606944|ref|YP_255814.1|  98 SLAEKILDVIVNFIRS--------KNIDFIVIDSLSILAA------FSKEKQLLQFMKDIRVLVNTGKMILF-TIHPDTF- 162
                                   2244555555555555........45889*****987776......789***************99988765.7777888. PP

                        PAXNEB 263 rssslvrkieqlvDtvieLes 283
                                    ++++ +ki+++vD  ++L++
  gi|70606944|ref|YP_255814.1| 163 -DEEMKSKITSIVDVYLKLSA 182
                                   .9***************9975 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.5     3e-07   0.00033      62     128 ..     101     166 ..      84     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                        DUF835  62 ekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeeke 128
                                   ek+++ iv+f+++++  +++iD+l  L + +  ++ l+f++ ++ ++++++++++++i +++++e+ 
  gi|70606944|ref|YP_255814.1| 101 EKILDVIVNFIRSKNIDFIVIDSLSILAAFSKEKQLLQFMKDIR-VLVNTGKMILFTIHPDTFDEEM 166
                                   699********************999998777777777777776.455668888899*******975 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        37      34      75 ..       3      42 ..       1      74 [. 0.83
   2 !   12.0   0.0   9.5e-05      0.11     116     144 ..     100     128 ..      95     158 .. 0.83
   3 ?   -2.6   0.0       2.7     3e+03      26      26 ..     197     197 ..     161     222 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                                  E--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHH CS
                          RecA 34 issGslaldialGiGGlpkGriieiyGpessGkttlalhaia 75
                                  is+G+  ld  lG  G+p    i i G   +Gk+ l+ + + 
  gi|70606944|ref|YP_255814.1|  3 ISTGNDDLDRRLG--GIPYPASIMIEGDHGTGKSVLSAQFVL 42
                                  8999999999987..99999999999********99988765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.5e-05
                                   HHHHHHHHHHHHTTT--SEEEEE-TTT-- CS
                          RecA 116 Geqaleiadalvrsgaidlivvdsvaalv 144
                                    e+ l+++  ++rs  id+iv+ds++ l 
  gi|70606944|ref|YP_255814.1| 100 AEKILDVIVNFIRSKNIDFIVIDSLSILA 128
                                   58899*******************87664 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.7
                                   - CS
                          RecA  26 k 26 
                                   k
  gi|70606944|ref|YP_255814.1| 197 K 197
                                   2 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   3.4e-05     0.038       3      78 ..      21     128 ..      20     136 .. 0.80
   2 ?    1.6   0.1      0.17   1.9e+02     124     172 ..     152     182 ..     131     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                        AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie...........................sw 49 
                                   ++i+i G+ g+GK+ l +++        +k  +i te+ +k  + +k+++i+                             
  gi|70606944|ref|YP_255814.1|  21 ASIMIEGDHGTGKSVLSAQFvlgfllsDKKGYVITTEQTTK-DYLIKMKEIKidlipyfirgklriaplntkkfnwnssLA 100
                                   689**********************9999999999**9665.445555555555666999999999999999997777555 PP

                        AAA_24  50 edfldevvelaaeladyktlviDtidele 78 
                                   e++ld +v + + ++ ++ +viD+++ l 
  gi|70606944|ref|YP_255814.1| 101 EKILDVIVNFIRSKN-IDFIVIDSLSILA 128
                                   667777777776666.********99775 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                        AAA_24 124 nvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlranl 172
                                   ++ f+ h +t   e                   + +++++vD+ l ++ 
  gi|70606944|ref|YP_255814.1| 152 MILFTIHPDTFDEE------------------MKSKITSIVDVYLKLSA 182
                                   55555554443333..................33445555555555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.011      33     188 ..      20     158 ..       9     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                        AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...rddarllvldlag 110
                                    + +++ G++gtGK++l  + +l  ++ +           k  ++ +E++ ++   +++++  +l     +++l++  l +
  gi|70606944|ref|YP_255814.1|  20 PASIMIEGDHGTGKSVLSAQFVLGFLLSD----------KKGYVITTEQTTKDYLIKMKEIKIDLipyFIRGKLRIAPLNT 90 
                                   5678999******************9655..........27899******************9996653356666665544 PP

                        AAA_25 111 veslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                   +        +++ +   ++  +d + + i++ ++++++viD+ls + + +++  ++  +++++++ +  +tg  +l++ H
  gi|70606944|ref|YP_255814.1|  91 K--------KFNWNSslAEKILDVIVNFIRS-KNIDFIVIDSLSILAAFSKE--KQLLQFMKDIRVL-VNTGKMILFTIH 158
                                   4........3333333145556666777777.99**********99888777..6778888888887.566666666666 PP

>> Elong_Iki1  Elongator subunit Iki1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   7.8e-06    0.0087      71     136 ..     100     164 ..      51     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.8e-06
                    Elong_Iki1  71 lkelakeiksalspkssekkkkalviiDslnplaslikeeslaaflssllssp..svslvavYHtdv..e 136
                                   ++++ + i + +++k     +   ++iDsl+ la++ ke++l +f++ +         ++ + H d+  e
  gi|70606944|ref|YP_255814.1| 100 AEKILDVIVNFIRSK-----NIDFIVIDSLSILAAFSKEKQLLQFMKDIRVLVntGKMILFTIHPDTfdE 164
                                   445555555555332.....4569***********99********9987532233778888888888763 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   2.1e-05     0.024      18     141 ..       2     124 ..       1     134 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                                   EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GG..GGHHHH...H CS
                         Rad51  18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrpe..rlveia...e 93 
                                    ++tG+ +lD+ L GGi+  +   i G++++Gk+ l+ ++ +   l       ++k   i te t +    ++ ei     
  gi|70606944|ref|YP_255814.1|   2 IISTGNDDLDRRL-GGIPYPASIMIEGDHGTGKSVLSAQFVLGFLLS------DKKGYVITTEQTTKDYliKMKEIKidlI 75 
                                   589********99.7899998889*************9998877775......5566667777776653113333333342 PP

                                   HT.T--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETT CS
                         Rad51  94 ry.kldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsv 141
                                    y    k ++   ++    +++   e++l+ + + + ++++ ++++Ds+
  gi|70606944|ref|YP_255814.1|  76 PYfIRGKLRIAPLNTKKFNWNSSLAEKILDVIVNFIRSKNIDFIVIDSL 124
                                   3303333333344444445566666777777777777777777777764 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.4e-05     0.038      24     120 ..      23     134 ..      11     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                        AAA_10  24 sliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe.........iakkinvvtLdseeene......gv 89 
                                    +i Gd G GKSvl+   vl  +l ++k  +i   + ++ +  +++e         i +k+++  L+ ++ n+        
  gi|70606944|ref|YP_255814.1|  23 IMIEGDHGTGKSVLSAQFVLGFLLSDKKGYVITTEQTTKDYLIKMKEikidlipyfIRGKLRIAPLNTKKFNWnsslaeKI 103
                                   5899****************************9999999997777663334444444445555555444333311111135 PP

                        AAA_10  90 LdPlvllkeekeaeslaedilelllgvkkke 120
                                   Ld +v + + k++  + +d l++l  ++k++
  gi|70606944|ref|YP_255814.1| 104 LDVIVNFIRSKNIDFIVIDSLSILAAFSKEK 134
                                   6666666666666666666666666655544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0016       1.8      35      56 ..      22      44 ..      17      72 .. 0.76
   2 ?    2.7   0.0     0.069        78     136     170 ..     162     197 ..     154     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                         AAA_7 35 pvllvGptGtGKtviikd.llkk 56
                                  ++++ G+ GtGK+v+  + +l  
  gi|70606944|ref|YP_255814.1| 22 SIMIEGDHGTGKSVLSAQfVLGF 44
                                  68999**********99944444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.069
                         AAA_7 136 Ydr.kklefkeikdvqlvaamgppgggrneitpRll 170
                                   +d   k ++++i+dv l  + ++ gg r +i +R++
  gi|70606944|ref|YP_255814.1| 162 FDEeMKSKITSIVDVYLKLSAATIGGRRVKILERVK 197
                                   67634568999********************99986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        37      36      56 ..      21      41 ..      17      65 .. 0.91
   2 ?    7.0   0.1     0.003       3.4     104     153 ..     100     150 ..      84     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                          TniB 36 pnlllvGdsnnGKtmivekFa 56
                                   ++++ Gd  +GK+++  +F 
  gi|70606944|ref|YP_255814.1| 21 ASIMIEGDHGTGKSVLSAQFV 41
                                  5799************99996 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.003
                          TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsarkq.reflnalksLgnel 153
                                   ++k+ + +++++r+ ++  ++iD +  l a s +kq  +f+  ++ L n+ 
  gi|70606944|ref|YP_255814.1| 100 AEKILDVIVNFIRSKNIDFIVIDSLSILAAFSKEKQlLQFMKDIRVLVNTG 150
                                   446677788999*******************99998459********9975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9   0.00024      0.27      81     149 ..      99     175 ..      22     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHHH..HHH-EEEE---STT.....GGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT CS
                      NTPase_1  81 feelalealrkal..seadviviDEiGkm.....ElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkd 149
                                   + e +l+++ + +  ++ d iviD    +     E +  +f + ++ +++++k++l++ih  + d+++  +i +  d
  gi|70606944|ref|YP_255814.1|  99 LAEKILDVIVNFIrsKNIDFIVIDSLSILaafskEKQLLQFMKDIRVLVNTGKMILFTIHPDTfDEEMKSKITSIVD 175
                                   44444555555543478899****9998844444556668********************99888888777776644 PP

>> NOGCT  NOGCT (NUC087) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00059      0.66      22      44 ..      60      82 ..      49      82 .. 0.92
   2 ?    1.1   0.2      0.35   3.9e+02      24      51 ..      94     120 ..      88     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                         NOGCT 22 kkkYllkndewkyDiiPEildGk 44
                                   k+Yl+k +e k D iP ++ Gk
  gi|70606944|ref|YP_255814.1| 60 TKDYLIKMKEIKIDLIPYFIRGK 82
                                  79*******************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.35
                         NOGCT  24 kYllkndewkyDiiPEildGkNvaDFid 51 
                                   ++     e+  D+i  ++  kN+ DFi 
  gi|70606944|ref|YP_255814.1|  94 NWNSSLAEKILDVIVNFIRSKNI-DFIV 120
                                   66666677888***********8.8885 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.26      20      41 ..      18      39 ..      10      67 .. 0.83
   2 ?   -3.5   0.0       6.3   7.1e+03     134     161 ..     142     169 ..     135     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                                  TSSS-EEEECSTTSSHHHHHHH CS
               Sigma54_activat 20 ktdlsvlitGesGtGKellara 41
                                  ++++s++i+G+ GtGK++l+ +
  gi|70606944|ref|YP_255814.1| 18 PYPASIMIEGDHGTGKSVLSAQ 39
                                  6789*************99765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.3
                                   -EEEEEEESS-HHHHHHTTSS-HHHHHH CS
               Sigma54_activat 134 dvriiaatnedleeaveegkfredLyyr 161
                                   d+r+++ t + +  +++ ++f e++  +
  gi|70606944|ref|YP_255814.1| 142 DIRVLVNTGKMILFTIHPDTFDEEMKSK 169
                                   6777777777777777777777666555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00023      0.25       3      26 ..      22      47 ..      20     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                       DUF2075  3 vvlVtGvaGtGKtvvllnllael..e 26
                                   ++++G+ GtGK+v+  +++     +
  gi|70606944|ref|YP_255814.1| 22 SIMIEGDHGTGKSVLSAQFVLGFllS 47
                                  589*************9998876541 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.32      24      60 ..      18      60 ..       7     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                        AAA_16 24 p..elvllsGesGvGKsslvrellr.alekd.ggif..lrgkc 60
                                  p   ++++ G+ G+GKs l  ++    l  d +g++  +++++
  gi|70606944|ref|YP_255814.1| 18 PypASIMIEGDHGTGKSVLSAQFVLgFLLSDkKGYVitTEQTT 60
                                  444899*************966653344444246663244444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1578.69
//
Query:       gi|70606945|ref|YP_255815.1|  [L=164]
Description: flagellar protein F [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.6   1.9    0.00025   21.1   1.9    1.2  1  DUF2393   Protein of unknown function (DUF2393)
  ------ inclusion threshold ------
      0.021   15.1   0.7      0.038   14.2   0.7    1.4  1  CARDB     CARDB
      0.043   14.2   3.9      0.079   13.3   3.9    1.3  1  FtsH_ext  FtsH Extracellular


Domain annotation for each model (and alignments):
>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.9   4.2e-08   0.00025      24     140 ..       8     148 ..       3     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-08
                       DUF2393  24 lsllilflapfvvhliidkylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnk........... 93 
                                   + +li+f++  +++++++ y+k  ++ +  q+ +   e   ++++it  ++  +++ +l++ l n+++ +           
  gi|70606945|ref|YP_255815.1|   8 AFILITFIGVSFGIVLLSAYFKSQQILNQAQELNHELELEQLETKIT-VSSVSLTGSTLNVVLENNGSTNlydfqgfsviv 87 
                                   56899*******************99999998888888888999999.899****************************** PP

                       DUF2393  94 ..............kskellkklkplvsksevikedlkpgeskeFrviidyfpyfknysvk 140
                                                 +  +++k  +p   + ++    l+pg+ ++ ++i +y+py +++++ 
  gi|70606945|ref|YP_255815.1|  88 qyyanisnistfnlSLYNYTKNSNPSPYYWTINTPLLAPGSQATLTIILPYPPYPNTQATV 148
                                   *************9999********9999977777789****************7776654 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   6.4e-06     0.038      17      84 ..      59     150 ..      43     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                                   TTSEEEEEEEEEE-SSS-EEEEE.....EEEEETTEEEEEEEE....................SEE-CTEEEEEEEEEE-S CS
                         CARDB  17 vgeentitvtvkNqGtaasgatk.....valyldgelvgtvtv....................psLaagesttvsftwtte 72 
                                     + +t++v ++N+G+ + ++++     v++y++ ++ +t+++                    p La+g+++t ++  +++
  gi|70606945|ref|YP_255815.1|  59 SLTGSTLNVVLENNGSTNLYDFQgfsviVQYYANISNISTFNLslynytknsnpspyywtintPLLAPGSQATLTIILPYP 139
                                   456789************99875444448999999999***99*************************************9 PP

                                   -S-CEEEEEEEE CS
                         CARDB  73 ategevtltvvv 84 
                                       +++ tvv+
  gi|70606945|ref|YP_255815.1| 140 -PYPNTQATVVI 150
                                   .66666666665 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.9   1.3e-05     0.079       1      85 [.      10     123 ..      10     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                      FtsH_ext   1 illwlllallllllllslfggsgtgstkeisy.seF.....ledle.qgnvekvvvqestis................... 55 
                                   il++++ + + ++ll+ +f++++          +e+     le+le + +v++v + +st +                   
  gi|70606945|ref|YP_255815.1|  10 ILITFIGVSFGIVLLSAYFKSQQILN-----QaQELnheleLEQLEtKITVSSVSLTGSTLNvvlenngstnlydfqgfsv 85 
                                   67888888888888888887333333.....33333444457***************88888888888889********** PP

                      FtsH_ext  56 ........alirrptgdgvsttkkgnstttystptlgs 85 
                                           ++i++ ++++ ++tk++n++++y+t ++++
  gi|70606945|ref|YP_255815.1|  86 ivqyyaniSNISTFNLSLYNYTKNSNPSPYYWTINTPL 123
                                   *********************************99654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1308.45
//
Query:       gi|70606946|ref|YP_255816.1|  [L=154]
Description: hypothetical protein Saci_1176 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-12   47.7   7.8    2.2e-12   47.4   7.8    1.0  1  Arch_flagellin  Archaebacterial flagellin
     0.0041   18.0   9.9       0.01   16.7   9.9    1.7  1  Pilin_N         Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.28   11.6   1.9       0.46   10.9   1.9    1.6  1  DUF1262         Protein of unknown function (DUF1262)


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   7.8   3.8e-16   2.2e-12      14     162 ..      11     149 ..       3     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.8e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEGGG-EEEEEES CS
                Arch_flagellin  14 mVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidlnkttisvtdd 94 
                                   m++V  +++gvl++t++ +++++++t+++ + q s+++ +t+  +d+atn++ n++  y++ n G ++i   + ++ ++++
  gi|70606946|ref|YP_255816.1|  11 MIIVSVTLIGVLAGTVFSVASSISTTMSSYSIQQSQKM-LTQLQIDYATNTSSNTVVAYLH-NVGETTISYLQNSVVYFGP 89 
                                   78888899999999999999999999999888888887.4455556788888899******.******************* PP

                                   S.--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEE CS
                Arch_flagellin  95 g.qetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGastti 162
                                   + q + +     g+++ s+  +++t+  + l++g +v++ + ++  +++  ++++++++v++nG + ++
  gi|70606946|ref|YP_255816.1|  90 NgQLQPV-----GYNSGSSPYWTVTS--NSLQPGSVVKIIIYLS--SPLSSNQYYTIQIVTPNGYTVSY 149
                                   *555544.....44555555555555..5**************5..9*****************98776 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   9.9   1.7e-06      0.01       3      67 ..       2      76 ..       1      90 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
                       Pilin_N  3 VSpViGviLmvaitvIlaAviaafvlgl.asneekapqasi........evkidssastgkna.vslehkgGdsi 67
                                  VS+Vi + +m+ + v l++v+a+ v+++ +s +++  + si        + +id+ ++t++n+ v   h+ G+++
  gi|70606946|ref|YP_255816.1|  2 VSEVISETIMIIVSVTLIGVLAGTVFSVaSSISTTMSSYSIqqsqkmltQLQIDYATNTSSNTvVAYLHNVGETT 76
                                  9***************************87888888999997666666644577777777777766777777764 PP

>> DUF1262  Protein of unknown function (DUF1262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9   7.6e-05      0.46      54      76 ..     116     138 ..      25     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.6e-05
                       DUF1262  54 sdevvfiPvldqplssnrYYvvk 76 
                                    + v +i  l  plssn+YY ++
  gi|70606946|ref|YP_255816.1| 116 GSVVKIIIYLSSPLSSNQYYTIQ 138
                                   36677788899*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1135.79
//
Query:       gi|70606947|ref|YP_255817.1|  [L=250]
Description: hypothetical protein Saci_1177 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0037   16.7   6.6      0.012   15.0   6.6    1.8  1  Not3            Not1 N-terminal domain, CCR4-Not complex comp
     0.0098   16.8   0.3      0.022   15.7   0.1    1.7  1  DUF4834         Domain of unknown function (DUF4834)
  ------ inclusion threshold ------
      0.011   14.2   2.6      0.015   13.7   2.6    1.2  1  Hemagglutinin   Haemagglutinin
      0.016   15.0   4.4      0.016   15.0   4.4    1.8  2  CdvA            CdvA-like coiled-coil domain
      0.021   14.9   5.0       0.14   12.2   1.7    2.5  3  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.038   14.3   2.9        2.7    8.3   0.0    2.3  2  Gp-FAR-1        Nematode fatty acid retinoid binding protein 
       0.04   12.3   7.4       0.14   10.6   7.4    1.7  1  Vitellogenin_N  Lipoprotein amino terminal region
      0.073   13.1   0.1       0.26   11.3   0.1    1.9  1  Phage_XkdX      Phage uncharacterised protein (Phage_XkdX)
       0.11   12.9   0.3        1.9    8.9   0.1    2.3  2  TAF6_C          TAF6 C-terminal HEAT repeat domain
       0.14   12.0   0.1       0.33   10.8   0.1    1.6  1  DUF1418         Protein of unknown function (DUF1418)
       0.14   12.0   1.2       0.33   10.8   1.2    1.6  1  HSBP1           Heat shock factor binding protein 1
        1.1    9.4  12.4      0.065   13.4   4.1    2.4  2  Fib_alpha       Fibrinogen alpha/beta chain family
        2.4    8.4   5.3          2    8.7   1.5    2.6  3  DASH_Dad1       DASH complex subunit Dad1


Domain annotation for each model (and alignments):
>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   6.6   8.9e-06     0.012      98     207 ..      66     173 ..      62     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
                          Not3  98 tKafSkeglakaaaekldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkkskekarveeleklierhkfh 178
                                   t ++S ++++ka ++ l + +k+++e+ + ++++ +e+++ +e+l++ +e+l+ + k ++++    + + ++++i++ + h
  gi|70606947|ref|YP_255817.1|  66 TSKYSSDSIEKALKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEELALSVKASESD----SSSPFNTIIQQEEEH 142
                                   789*******9999999************************************988777643....568899999999999 PP

                          Not3 179 iek.lelllrlleneelep.eevekikedie 207
                                   +++ ++++ +l+  ++ ++ +  + ik  + 
  gi|70606947|ref|YP_255817.1| 143 VSReISTVSQLVGSNNPNNvNLTWFIKSCVL 173
                                   8753666666665554444244455555555 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.6e-05     0.022       6      70 ..      10      75 ..       5      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                       DUF4834  6 filifiiailviglsilsvilrtvfglgsrkkssksaqkq.fgnstnsnqqksqsrsetkeegeii 70
                                   ++i++i + +  +++l  ++r ++ + +r + ++s q+  +++++ ++q+  +++++++++++i+
  gi|70606947|ref|YP_255817.1| 10 SLFIILIGVGIPIAAFLEILFRVILPKTKRVQTQQSPQNIsQEQRFPTQQKPANDETSKYSSDSIE 75
                                  579999999***************998888777655444303334444444444555555444443 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.6   1.1e-05     0.015     369     443 ..      70     143 ..      58     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHH.HHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Hemagglutinin 369 tqeainkitkkv.nsliekenkqleavgkelnelekrieeldkkvddgfldvityniellvllenerildfedsnv 443
                                   + ++i+k  k+v  ++ +ken  l+++++ +ne++k ie+l+  v+++ l v +++ +    +  + i++ e+++v
  gi|70606947|ref|YP_255817.1|  70 SSDSIEKALKDVlGKMDKKENELLTNITNSFNEMKKLIENLNSAVEELALSVKASESDSSSPF--NTIIQQEEEHV 143
                                   345566555554145667888999**************************9999887655433..34555555555 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.4   1.2e-05     0.016      14     104 ..      65     153 ..      62     156 .. 0.89
   2 ?   -2.6   0.1       3.4   4.7e+03      25      33 ..     223     231 ..     208     244 .. 0.42

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                          CdvA  14 dipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesa 94 
                                   + +k   ++i++ l++ l k+++k++el  +++++ +e ++ i++l++a+  l +s ++ E d ++     ++i+++ e++
  gi|70606947|ref|YP_255817.1|  65 ETSKYSSDSIEKALKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEELALSVKASESDSSS--PFNTIIQQEEEHV 143
                                   566777799***************************************************977665..6677899999999 PP

                          CdvA  95 leekeeikkl 104
                                   ++e++ +++l
  gi|70606947|ref|YP_255817.1| 144 SREISTVSQL 153
                                   9999988776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                          CdvA  25 ekleealkk 33 
                                    ++ e+++ 
  gi|70606947|ref|YP_255817.1| 223 ANIAESYSS 231
                                   222222222 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.7    0.0001      0.14      59     104 ..      72     117 ..      56     128 .. 0.55
   2 ?   -2.2   0.0       2.9   3.9e+03       2      20 ..     148     166 ..     146     173 .. 0.69
   3 ?    2.5   0.0       0.1   1.4e+02       8      57 ..     191     239 ..     182     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                  Baculo_PEP_C  59 aeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNi 104
                                    +++++l+++l +++++ n+l ++++n  + +++ + nL+s v  +
  gi|70606947|ref|YP_255817.1|  72 DSIEKALKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEEL 117
                                   3444455555555555555555444444444444444444444332 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                  Baculo_PEP_C   2 advqqLnggggnqfldLtn 20 
                                   + v qL g++  ++++Lt 
  gi|70606947|ref|YP_255817.1| 148 STVSQLVGSNNPNNVNLTW 166
                                   6799995555555688885 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.1
                  Baculo_PEP_C   8 nggggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksl 57 
                                   +  ++ + + +  +L+ i++ +++   +la++ ++i+++ ++l+ ++k+ 
  gi|70606947|ref|YP_255817.1| 191 GYVSSDDMFTILRILSFIKNRKITA-KELASIAANIAESYSSLTPEIKKY 239
                                   5556666777778888897777776.889999999999999999988875 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.0     0.013        18      36      78 ..      75     117 ..      39     149 .. 0.65
   2 ?    8.3   0.0    0.0019       2.7      94     126 ..     208     240 ..     200     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                      Gp-FAR-1  36 yknedellaalKkkspaLyekaeklqaklkekvdkLspeakeF 78 
                                    k  +++l  + kk ++L +++ +  +++k+ +++L+ +  e+
  gi|70606947|ref|YP_255817.1|  75 EKALKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEEL 117
                                   4555555555555555555555555555555555555444433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0019
                      Gp-FAR-1  94 lagekpdlselkkvaktifnkykslseeakael 126
                                   +++ k++ +el  +a++i+++y sl++e k+ +
  gi|70606947|ref|YP_255817.1| 208 IKNRKITAKELASIAANIAESYSSLTPEIKKYI 240
                                   67899***********************99865 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.4   9.9e-05      0.14     293     431 ..      50     240 ..      38     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.9e-05
                                   ........THHHHS-SS---TTS-HHHHHHHHHHHHHHH-SSS--TTHHHHHHHHHHHHTTS-HHHHHHHHHHHTT..... CS
                Vitellogenin_N 293 ekenfqsseqelssspsssssvenavklikeilkelvqnpsnevkedtlakfliLvrllrtaseeqleqlasqlya..... 368
                                    +e++ +++q+  +++ s++s ++++k++k++l ++  + +ne  +++ ++f+++ +l+ ++++  +e+la  ++a     
  gi|70606947|ref|YP_255817.1|  50 SQEQRFPTQQKPANDETSKYSSDSIEKALKDVLGKM-DKKENELLTNITNSFNEMKKLIENLNS-AVEELALSVKAsesds 128
                                   5678888999999999999*****************.888889*******************97.68999999999999** PP

                                   ....................................................SHHHHHH..HHHHHHHH-SHHHHHHHHHH CS
                Vitellogenin_N 369 ...................................................ekkkarkweifldavaqagTepAlkfikdk 398
                                                                                      +++k +++  +    ++  +  ++  i+++
  gi|70606947|ref|YP_255817.1| 129 sspfntiiqqeeehvsreistvsqlvgsnnpnnvnltwfikscvlleimeyDEEKIKQL--YELGYVSSDDMFTILRILSF 207
                                   ************************************************96666666666..999999************** PP

                                   HHTT-S-HHHHHHHHHHHHH.T----HHHHHHH CS
                Vitellogenin_N 399 ikskkitgeeaaqvlavlpktarypteeylkal 431
                                   ik++kit +e+a++ a ++++ ++ t+e+ k++
  gi|70606947|ref|YP_255817.1| 208 IKNRKITAKELASIAANIAESYSSLTPEIKKYI 240
                                   ********************9999999998776 PP

>> Phage_XkdX  Phage uncharacterised protein (Phage_XkdX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00019      0.26       2      31 ..     182     217 ..     182     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                    Phage_XkdX   2 ediKeyYdwglwtkeqvrdaVg......kgkITkee 31 
                                   e+iK+ Y++g+++ +++ +  +        kIT++e
  gi|70606947|ref|YP_255817.1| 182 EKIKQLYELGYVSSDDMFTILRilsfikNRKITAKE 217
                                   79**************98865544444355666666 PP

>> TAF6_C  TAF6 C-terminal HEAT repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.25   3.5e+02      29      54 ..      77     102 ..      75     136 .. 0.73
   2 ?    8.9   0.1    0.0014       1.9      23      51 ..     211     239 ..     199     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.25
                        TAF6_C  29 lLakilkkysssyktLkprvtrtllk 54 
                                    L+ +l k+ ++ ++L +++t+ + +
  gi|70606947|ref|YP_255817.1|  77 ALKDVLGKMDKKENELLTNITNSFNE 102
                                   57888888899999999999887765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                        TAF6_C  23 RdfAAslLakilkkysssyktLkprvtrt 51 
                                   R+  A+ La+i+ + ++sy++L+p++ + 
  gi|70606947|ref|YP_255817.1| 211 RKITAKELASIAANIAESYSSLTPEIKKY 239
                                   999*********************99876 PP

>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00024      0.33      45      91 ..      10      57 ..       5      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                       DUF1418 45 aivmiflGvllllPaavalvwrvaqalapll.rkrsPdkksrskrekk 91
                                   + +i +Gv++ + a + +++rv+   +  + +++sP++ s+++r ++
  gi|70606947|ref|YP_255817.1| 10 SLFIILIGVGIPIAAFLEILFRVILPKTKRVqTQQSPQNISQEQRFPT 57
                                  67899*****************99765555438899**9999998665 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2   0.00024      0.33       4      46 ..      75     117 ..      72     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                         HSBP1   4 tavVenlLqqlqdkFqtmsdqilsriDdMssriDdLEksiadl 46 
                                   +++  ++L ++++k +++ ++i++  ++M + i++L   +++l
  gi|70606947|ref|YP_255817.1|  75 EKALKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEEL 117
                                   5677899*****************************9999887 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.1    0.0022         3      52     128 ..      40     117 ..      33     124 .. 0.89
   2 ?   13.4   4.1   4.7e-05     0.065      22     104 ..      78     162 ..      77     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  52 keaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvlesneqkiqkLeqdidqk 128
                                    ++++  ++i++  r   ++k+ nd++ k ss+++e+   ++  ++d++e + + +++n +++ ++ i++L+++++++
  gi|70606947|ref|YP_255817.1|  40 VQTQQSPQNISQEQRFPTQQKPANDETSKYSSDSIEKALKDVLGKMDKKEnELLTNITNSFNEMKKLIENLNSAVEEL 117
                                   56778889999999999999999***************************888999***************9999876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.7e-05
                                   HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCH CS
                     Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqe 101
                                   l+d+l k++k+ ++ l++++n+++e+++  ++ ++ v+e+  s+++ ++ ++   +++i++ ++++ +ei+++ + + ++ 
  gi|70606947|ref|YP_255817.1|  78 LKDVLGKMDKKENELLTNITNSFNEMKKLIENLNSAVEELALSVKASESDSSSPfNTIIQQEEEHVSREISTVSQLVGSNN 158
                                   7999*************************************99999888777556**********************9998 PP

                                   .HHH CS
                     Fib_alpha 102 .sni 104
                                    +n+
  gi|70606947|ref|YP_255817.1| 159 pNNV 162
                                   4444 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.5    0.0015         2       5      34 ..      88     117 ..      84     124 .. 0.89
   2 ?   -0.5   0.0         1   1.4e+03      36      47 ..     142     153 ..     137     162 .. 0.81
   3 ?   -2.3   0.0       3.8   5.3e+03       5      18 ..     210     223 ..     207     236 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                     DASH_Dad1   5 qRdrliqeIaesmeevlnnlnaLNRsLEev 34 
                                   + ++l+++I++s++e+ + ++ LN   Ee+
  gi|70606947|ref|YP_255817.1|  88 KENELLTNITNSFNEMKKLIENLNSAVEEL 117
                                   55789*******************999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                     DASH_Dad1  36 avgkeFesVaaL 47 
                                    v++e+++V++L
  gi|70606947|ref|YP_255817.1| 142 HVSREISTVSQL 153
                                   578888888877 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.8
                     DASH_Dad1   5 qRdrliqeIaesme 18 
                                    R+   +e+a+   
  gi|70606947|ref|YP_255817.1| 210 NRKITAKELASIAA 223
                                   55555555444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2291  (0.127782); expected 358.6 (0.02)
Passed bias filter:                      952  (0.0530983); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 1506.01
//
Query:       gi|70606948|ref|YP_255818.1|  [L=304]
Description: flagellin protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-21   74.7   7.0    5.1e-20   72.3   7.0    2.1  1  Arch_flagellin  Archaebacterial flagellin


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   7.0   2.9e-24   5.1e-20       3     163 ..      13     290 ..      11     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.9e-24
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE...EEE-SSSSSEEEEEEE--TTS- CS
                Arch_flagellin   3 vgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg...dsatngtineitiyvklnaGss 80 
                                    g+ t+I++IA+++ AAv+a+v++n++ f++qka++t  ++ e +s++l+++g v    +++tn++  +++++v ++ G s
  gi|70606948|ref|YP_255818.1|  13 AGLDTAIILIAFIITAAVLAYVAVNMGLFVTQKAKTTINKGEETASTALSLSGNVLyavNYPTNTKSYWMYFTVSPSSGVS 93 
                                   6899***************************************************97777777777777************ PP

                                   -EEGGG-EEEEEESS--EE--E........................................................... CS
                Arch_flagellin  81 pidlnkttisvtddgqetlltad.......................................................... 103
                                   ++dl+ +t+ ++    ++ ++ +                                                          
  gi|70606948|ref|YP_255818.1|  94 SVDLSPSTTAISFTAASRGVSLSniyqfsllsvlpsqvnnkvqvklgtsiinltlafssnsagqtyvyysdpnyallalny 174
                                   ******999988887555555557899**************************************9999999999999999 PP

                                   .............................T-EE-TT-EEEEEEE--................................... CS
                Arch_flagellin 104 ............efgivvisdtdgsltngdevlekgekvelevnvn................................... 137
                                               ++ ++ is+t+  ++  ++ l+ +++++ ++ vn                                   
  gi|70606948|ref|YP_255818.1| 175 tlgqevkggqltSSPLYIISNTSIVAS--KPWLKNDNVFTFNISVNgteveyyayvnktfaftypvsgfplagsdiapags 253
                                   999999999997555555555443333..3688888888888888888888888888888888888888888888888888 PP

                                   ...........TTT---TT-EEEEEEE-SSS--EEEE CS
                Arch_flagellin 138 ...........eddgitagdevsvevvpenGasttie 163
                                              e +++ ++++v+++++p  G+++ti+
  gi|70606948|ref|YP_255818.1| 254 vigvmilfgpgEATNVFQYETVTIQITPNIGSPLTIS 290
                                   888888888**9999******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2373.76
//
Query:       gi|70606949|ref|YP_255819.1|  [L=125]
Description: hypothetical protein Saci_1179 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 890.44
//
Query:       gi|70606950|ref|YP_255820.1|  [L=269]
Description: hypothetical protein Saci_1180 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-08   34.6   0.6    0.00015   21.2   0.6    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
    4.2e-08   33.0   0.0    8.7e-06   25.5   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    5.3e-08   32.6   0.0     0.0021   17.9   0.0    2.3  2  MarR_2           MarR family
    1.6e-07   31.1   0.5    2.7e-06   27.2   0.2    2.4  2  MarR             MarR family
    3.4e-07   30.2   3.7    7.1e-06   25.9   0.2    2.4  2  HTH_45           Winged helix-turn-helix
    4.7e-07   29.7   1.5      0.012   15.6   0.3    2.5  2  HTH_11           HTH domain
    7.2e-06   26.0   0.0      0.045   13.8   0.0    2.3  2  HTH_20           Helix-turn-helix domain
    4.2e-05   24.0   0.0    8.4e-05   23.0   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
    8.1e-05   22.3   0.0    0.00091   19.0   0.0    2.1  2  HTH_23           Homeodomain-like domain
    0.00011   22.1   0.0     0.0064   16.5   0.0    2.3  2  HTH_29           Winged helix-turn helix
    0.00013   21.9   0.0       0.16   12.0   0.0    2.5  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00047   19.9   0.0    0.00091   19.0   0.0    1.4  1  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0017   18.1   0.0     0.0033   17.2   0.0    1.5  1  HTH_8            Bacterial regulatory protein, Fis family
      0.002   17.7   0.0       0.33   10.6   0.0    2.4  2  GntR             Bacterial regulatory proteins, gntR family
     0.0036   17.0   0.0      0.007   16.1   0.0    1.5  1  HTH_psq          helix-turn-helix, Psq domain
     0.0056   16.9   0.7       0.12   12.7   0.0    2.6  2  NUMOD1           NUMOD1 domain
     0.0059   16.7   0.1       0.18   11.9   0.0    2.3  2  HTH_7            Helix-turn-helix domain of resolvase
     0.0082   16.1   1.3       0.43   10.6   0.1    2.5  2  HTH_Mga          M protein trans-acting positive regulator (M
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.032   14.4   0.0    1.7  2  HTH_28           Helix-turn-helix domain
      0.011   15.6   0.1        0.5   10.3   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.021   15.0   0.6       0.08   13.1   0.1    2.1  2  HTH_17           Helix-turn-helix domain
      0.022   14.7   0.1       0.22   11.5   0.1    2.3  1  RWP-RK           RWP-RK domain
      0.023   14.4   0.3       0.18   11.5   0.0    2.4  2  Sigma70_r4_2     Sigma-70, region 4
      0.028   14.5   0.0      0.073   13.2   0.0    1.7  1  MerR_1           MerR HTH family regulatory protein
      0.033   14.0   0.3       0.23   11.3   0.0    2.1  2  HTH_10           HTH DNA binding domain
      0.033   14.4   0.2       0.71   10.1   0.1    2.4  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.052   13.9   0.3        0.2   12.0   0.1    1.9  2  Rrf2             Transcriptional regulator
      0.053   13.2   0.9        4.9    6.9   0.1    2.7  2  SelB-wing_3      Elongation factor SelB, winged helix
      0.056   13.5   0.0       0.16   12.1   0.0    1.8  1  HTH_3            Helix-turn-helix
      0.071   13.5   1.0       0.15   12.4   0.2    1.8  2  Penicillinase_R  Penicillinase repressor
      0.086   12.6   0.2        7.2    6.4   0.0    2.5  2  HTH_DeoR         DeoR-like helix-turn-helix domain
       0.09   12.7   0.0        1.3    9.0   0.0    2.4  2  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.091   12.4   0.0       0.22   11.1   0.0    1.6  1  SMC_ScpB         Segregation and condensation complex subunit
       0.13   12.1   0.0       0.33   10.8   0.0    1.6  1  MerR             MerR family regulatory protein
       0.14   12.6   0.4         16    6.0   0.1    2.4  2  Linker_histone   linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.6     3e-07   0.00015       3      48 .]      22      67 ..      20      67 .. 0.95
   2 !   11.0   0.0   0.00045      0.23      16      44 ..     134     162 ..     130     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-07
                        HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +++++IL +L  ++  s +e+++ ++ S+  +   +++L++++l++
  gi|70606950|ref|YP_255820.1| 22 KLQWDILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVT 67
                                  6789***************************************996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00045
                        HTH_24  16 prisqreLAerlglSpstvnrrlkrLeee 44 
                                    ++s    A++lg+S++t++++l+ +ee+
  gi|70606950|ref|YP_255820.1| 134 DGLSLDKAARELGVSRQTLKYYLELFEEK 162
                                   67888888***************999997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-08   8.7e-06      12      57 ..      26      71 ..      21      79 .. 0.91
   2 ?    5.1   0.0     0.041        21      20      65 ..     133     182 ..     127     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-08
                                  CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                          TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                  ++ + L ++gp++++ei++ ++ +r ++ +++r+L+dk lV+++k 
  gi|70606950|ref|YP_255820.1| 26 DILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKH 71
                                  5678999***********************************9975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.041
                                   HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE- CS
                          TrmB  20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYrav 65 
                                   ++ ++ d+ a+elgv+r++   +L+  e+k l +++ +r    +++Y++v
  gi|70606950|ref|YP_255820.1| 133 HDGLSLDKAARELGVSRQTLKYYLELFEEKKLFRVIGKRthfkKNIYKCV 182
                                   5667778889**********************999988889877799987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.2e-06    0.0021       7      55 ..      24      70 ..      22      72 .. 0.95
   2 !   12.3   0.0   0.00023      0.12      16      50 ..     132     164 ..     128     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  q+++L  L+  ++   + +e+ ++ + s+ ++  ++++Lv++ Lv++++
  gi|70606950|ref|YP_255820.1| 24 QWDILIILATKGP--SSTTEISQTINTSRKSIIDAIRKLVDKELVTKVK 70
                                  9***********9..8*****************************9986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                                   CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                        MarR_2  16 rrpgrdltvgelarrlglsksavsrilkrLvaaGL 50 
                                   +++g  l+    ar+lg+s++++ + l+ ++++ L
  gi|70606950|ref|YP_255820.1| 132 NHDG--LSLDKAARELGVSRQTLKYYLELFEEKKL 164
                                   6788..999999*******************9987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   5.4e-09   2.7e-06       5      52 ..      24      71 ..      22      72 .. 0.96
   2 ?    1.6   0.0      0.51   2.6e+02       3      34 ..     116     152 ..     115     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.4e-09
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  q++iL il+++gp s +e+   +++s+ ++  ++++L++k+l+++ k+
  gi|70606950|ref|YP_255820.1| 24 QWDILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKH 71
                                  9*******************************************9886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHHHSTTEEHH.....HHHHHHTS-HHHH CS
                          MarR   3 ltqfviLrilyeqgplsvs.....eLakklgvskstv 34 
                                   l+q+  L +l+ +  ++       + a+ lgvs+ t+
  gi|70606950|ref|YP_255820.1| 116 LSQYFYLINLSKMITINHDglsldKAARELGVSRQTL 152
                                   6677777777766666655443437788888888776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   1.4e-08   7.1e-06       4      74 ..      20      92 ..      19      95 .. 0.90
   2 ?    5.1   0.4     0.044        22      32      76 ..     148     201 ..     125     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.4e-08
                        HTH_45  4 kleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklkelee 74
                                  + +   dIL ++  +g ++ T+i    n s k +   + +Lv+k+l++k +++ Y l +kG+el +k++ + +
  gi|70606950|ref|YP_255820.1| 20 RAKLQWDILIILAtKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKvKHDIYGLSDKGKELWNKIDSVLN 92
                                  66777899999887999******************************776999***************98876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                        HTH_45  32 sykllnkYLdmLvekgli.........kkskekYvlTekGlelleklkeleela 76 
                                   s ++l+ YL+   ek+l          kk+  k vl ++G++ll +l e+ +++
  gi|70606950|ref|YP_255820.1| 148 SRQTLKYYLELFEEKKLFrvigkrthfKKNIYKCVLMNEGKRLLFRLPEFTKMK 201
                                   6678999**********44469998777777777999*********99999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   2.3e-05     0.012       4      40 ..      26      62 ..      24      80 .. 0.82
   2 !   12.7   0.0   0.00018     0.094      11      50 ..     131     171 ..     123     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.e 40
                                  +il++L +++gp s  e+++ +n Sr+ +   I++L  
  gi|70606950|ref|YP_255820.1| 26 DILIIL-ATKGPSSTTEISQTINTSRKSIIDAIRKLvD 62
                                  799999.***************************9953 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00018
                        HTH_11  11 eargpisgeeLAeeLnvSrrtvrrdIkaL.eelgvpIesep 50 
                                    +++ +s ++ A+eL+vSr+t   +++   e++++++++++
  gi|70606950|ref|YP_255820.1| 131 INHDGLSLDKAARELGVSRQTLKYYLELFeEKKLFRVIGKR 171
                                   45556999999****************99555669999887 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   8.7e-05     0.045      14      59 ..      26      71 ..       7      72 .. 0.91
   2 !    9.8   0.0    0.0016       0.8      23      53 ..     134     164 ..     127     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                  +il  La++++ + +e+ +++ +s++++ + +r+L++ +Lv+ v++
  gi|70606950|ref|YP_255820.1| 26 DILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKH 71
                                  788888************************************9985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                                   TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTT CS
                        HTH_20  23 egltaselaerldlskntlsyHLrvLeeagL 53 
                                   +gl++   a++l++s++tl y L+  ee  L
  gi|70606950|ref|YP_255820.1| 134 DGLSLDKAARELGVSRQTLKYYLELFEEKKL 164
                                   899********************99998766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.6e-07   8.4e-05       4      68 .]      23      80 ..      22      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-07
                        HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +q+ +L  ++ + ++++ ++++++ n++  +i+ +++kL+ k+Lv++ + +       + l+dkG
  gi|70606950|ref|YP_255820.1| 23 LQWDILIILA-TKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTKVKHD------IYGLSDKG 80
                                  5888999999.9*********************************777665......77777766 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.99   5.1e+02      19      40 ..      38      59 ..      29      64 .. 0.86
   2 !   19.0   0.0   1.8e-06   0.00091      16      44 ..     134     162 ..     126     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.99
                        HTH_23 19 svreIAreLgvsrrTvyrwlkr 40
                                  s++eI++  + sr  +   +++
  gi|70606950|ref|YP_255820.1| 38 STTEISQTINTSRKSIIDAIRK 59
                                  789**********998777765 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                        HTH_23  16 eGlsvreIAreLgvsrrTvyrwlkryree 44 
                                   +Gls  ++AreLgvsr+T+  +l+ ++e+
  gi|70606950|ref|YP_255820.1| 134 DGLSLDKAARELGVSRQTLKYYLELFEEK 162
                                   599**********************9765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.16        83       7      37 ..      31      61 ..      25      70 .. 0.76
   2 !   16.5   0.0   1.2e-05    0.0064      10      39 ..     134     162 ..     127     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                        HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfe 37
                                  l+ +G s++ +i +  + sr+++ ++++  +
  gi|70606950|ref|YP_255820.1| 31 LATKGPSSTTEISQTINTSRKSIIDAIRKLV 61
                                  334444489**************99998765 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                        HTH_29  10 eGvstvsqiAkllglsrrtvyrwlkrfeeg 39 
                                   +G+s    +A+ lg+sr+t   +l++fee+
  gi|70606950|ref|YP_255820.1| 134 DGLS-LDKAARELGVSRQTLKYYLELFEEK 162
                                   6887.9**********************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00031      0.16      21      54 ..      36      70 ..      15      78 .. 0.85
   2 !    7.3   0.0    0.0088       4.5      23      55 ..     137     170 ..     120     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg 54
                                  p + +e+++ ++++r ++  ++++L ++ l++  +
  gi|70606950|ref|YP_255820.1| 36 PSSTTEISQTINTSRKSIIDAIRKLVDKELVTkVK 70
                                  66889*************************99434 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0088
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                     HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglis.rgr 55 
                                   + +  A+ lG++r+t+   l  +++++l +  g+
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYLELFEEKKLFRvIGK 170
                                   55667999******************99986553 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06   0.00091      12      38 ..     135     161 ..     130     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                   TT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                        HTH_30  12 ggnisatAkaLhvHrnTlryRLrriee 38 
                                   g +++++A++L+v+r+Tl+y L+  ee
  gi|70606950|ref|YP_255820.1| 135 GLSLDKAARELGVSRQTLKYYLELFEE 161
                                   689*******************99887 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.4e-06    0.0033      20      37 ..     137     154 ..     128     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-06
                                   -HHHHHHHHTS-HHHHHH CS
                         HTH_8  20 nkskAArlLGisRrtLyr 37 
                                    + kAAr+LG+sR+tL +
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKY 154
                                   5789************87 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00064      0.33      28      55 ..      40      67 ..      38      71 .. 0.91
   2 ?    4.7   0.0     0.048        24      26      54 ..     137     165 ..     130     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00064
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          GntR 28 reLaaefgVsrttvReALrrLeaeglve 55
                                   e+++ +++sr ++  A+r+L+ + lv+
  gi|70606950|ref|YP_255820.1| 40 TEISQTINTSRKSIIDAIRKLVDKELVT 67
                                  5899**********************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.048
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          GntR  26 sereLaaefgVsrttvReALrrLeaeglv 54 
                                   s  + a e+gVsr+t+   L   e+++l 
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYLELFEEKKLF 165
                                   55666899*******98766655555554 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05     0.007      15      39 ..     135     158 ..     128     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                       HTH_psq  15 GkmSirkAArkYgiPrsTLwrrkrg 39 
                                   G +S+ kAAr+ g++r TL ++++ 
  gi|70606950|ref|YP_255820.1| 135 G-LSLDKAARELGVSRQTLKYYLEL 158
                                   4.9*****************99876 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.64   3.3e+02      17      37 .]      37      57 ..      37      57 .. 0.86
   2 !   12.7   0.0   0.00023      0.12      18      37 .]     137     156 ..     137     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.64
                        NUMOD1 17 sSireAakyLgishntInkyl 37
                                  sS +e ++ ++ s+++I  ++
  gi|70606950|ref|YP_255820.1| 37 SSTTEISQTINTSRKSIIDAI 57
                                  578999**********98765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00023
                        NUMOD1  18 SireAakyLgishntInkyl 37 
                                   S+ +Aa+ Lg+s++t ++yl
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYL 156
                                   6679***************8 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.37   1.9e+02      10      38 ..      24      53 ..      17      53 .. 0.87
   2 !   11.9   0.0   0.00036      0.18      19      42 ..     133     156 ..     123     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.37
                                  HHGGGGSSTTTT.--STTTSSSS---SSSS CS
                         HTH_7 10 dinrvvkLleeG.isiskIAkevnisRsTv 38
                                  +++ ++ L  +G +s ++I    n+sR ++
  gi|70606950|ref|YP_255820.1| 24 QWDILIILATKGpSSTTEISQTINTSRKSI 53
                                  6899999999*****************875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00036
                                   TTT--STTTSSSS---SSSS--SS CS
                         HTH_7  19 eeGisiskIAkevnisRsTvYRyl 42 
                                    +G s  k A+e+++sR+T++ yl
  gi|70606950|ref|YP_255820.1| 133 HDGLSLDKAARELGVSRQTLKYYL 156
                                   567788899***********9777 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.094        48       6      45 ..      23      61 ..      19      72 .. 0.82
   2 !   10.6   0.1   0.00084      0.43      17      56 ..     132     168 ..     123     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.094
                       HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                   + ++l +L + ++  +++e++   ++s++++ + i++L 
  gi|70606950|ref|YP_255820.1| 23 LQWDILIILAT-KGPSSTTEISQTINTSRKSIIDAIRKLV 61
                                  56777777878.8888999***********9999888886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00084
                       HTH_Mga  17 neksltldelakeLglseltlqsdiseLnelFpeelsivi 56 
                                   n + l+ld++a eLg s+ tl+ +++ +    +++l++vi
  gi|70606950|ref|YP_255820.1| 132 NHDGLSLDKAARELGVSRQTLKYYLELFE---EKKLFRVI 168
                                   567799******************98776...55665555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       9.6   4.9e+03      14      35 ..      38      59 ..      29      60 .. 0.72
   2 ?   14.4   0.0   6.2e-05     0.032      12      38 ..     135     161 ..     130     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.6
                        HTH_28 14 svreaArelgisrrtvyrWikr 35
                                  s +e+++  ++sr ++ + i++
  gi|70606950|ref|YP_255820.1| 38 STTEISQTINTSRKSIIDAIRK 59
                                  6678888899999988666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.2e-05
                        HTH_28  12 GhsvreaArelgisrrtvyrWikryee 38 
                                   G s + aArelg+sr+t++  +  +ee
  gi|70606950|ref|YP_255820.1| 135 GLSLDKAARELGVSRQTLKYYLELFEE 161
                                   559999************999999998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00097       0.5       8      41 ..      27      60 ..      23      61 .. 0.95
   2 ?    3.0   0.0      0.17        88      23      33 ..     141     151 ..     136     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00097
                 HTH_AsnC-type  8 ILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  IL +L   +  s +e+++ ++ S+  ++  +r+L
  gi|70606950|ref|YP_255820.1| 27 ILIILATKGPSSTTEISQTINTSRKSIIDAIRKL 60
                                  9999***************************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                 HTH_AsnC-type  23 LAervGlSest 33 
                                    A+++G+S++t
  gi|70606950|ref|YP_255820.1| 141 AARELGVSRQT 151
                                   59*******99 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.1   2.1e+03       4      26 ..      39      64 ..      38      74 .. 0.70
   2 ?   13.1   0.1   0.00016      0.08       2      40 ..     136     176 ..     136     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.1
                        HTH_17  4 veEaAelLgvsrstvyrlir...rge 26
                                  + E+++  + sr+++ + ir   ++e
  gi|70606950|ref|YP_255820.1| 39 TTEISQTINTSRKSIIDAIRklvDKE 64
                                  66777778889999998888444555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                        HTH_17   2 ltveEaAelLgvsrstvyrli...rrgelpaakiGrrwripr 40 
                                   l+ + aA+ Lgvsr+t+  ++    +++l +  iG+r  +++
  gi|70606950|ref|YP_255820.1| 136 LSLDKAARELGVSRQTLKYYLelfEEKKL-FRVIGKRTHFKK 176
                                   68899*************99955548888.555788777766 PP

>> RWP-RK  RWP-RK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00043      0.22      12      30 ..     135     153 ..     110     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                        RWP-RK  12 slplkeAAksLgvskttLK 30 
                                    l+l +AA++Lgvs  tLK
  gi|70606950|ref|YP_255820.1| 135 GLSLDKAARELGVSRQTLK 153
                                   6899**************9 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       2.1   1.1e+03      28      42 ..      38      52 ..      37      54 .. 0.86
   2 ?   11.5   0.0   0.00035      0.18      25      47 ..     134     156 ..     131     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                                  -HHHHHHHHT--HHH CS
                  Sigma70_r4_2 28 sykEIAellgisegt 42
                                  s+ EI++ +++s ++
  gi|70606950|ref|YP_255820.1| 38 STTEISQTINTSRKS 52
                                  889********9987 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00035
                                   S---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2  25 eglsykEIAellgisegtVksrl 47 
                                   +gls + +A++lg+s +t k++l
  gi|70606950|ref|YP_255820.1| 134 DGLSLDKAARELGVSRQTLKYYL 156
                                   79******************998 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014     0.073       2      24 ..     137     159 ..     136     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                   EHHHHHHHHTS-HHHHHHHHHHT CS
                        MerR_1   2 sigevakilgvtthtlrywekeg 24 
                                   s++++a++lgv+  tl+y+ + +
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYLELF 159
                                   6789***************9977 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.7   8.7e+02      26      47 ..      39      60 ..      37      63 .. 0.79
   2 ?   11.3   0.0   0.00045      0.23      25      50 ..     137     162 ..     135     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
                        HTH_10 26 lkeLAkelGIskstlsehLrka 47
                                  + e++++++ s+ ++ + +rk 
  gi|70606950|ref|YP_255820.1| 39 TTEISQTINTSRKSIIDAIRKL 60
                                  6789999999999999988885 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
                        HTH_10  25 tlkeLAkelGIskstlsehLrkaesk 50 
                                   +l++ A elG+s++tl+++L+  e+k
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYLELFEEK 162
                                   567789**************977765 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0014      0.71      35      85 ..      38      88 ..      30     101 .. 0.81
   2 ?    1.7   0.0      0.59     3e+02      32      52 ..     134     154 ..     125     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                       UPF0122 35 SlsEiAeefnvsrqavydnikrtekllekyEekLkllekykkreellekik 85
                                  S +Ei ++ n+sr+++ d i++  +  +    k  ++   +k +el +ki 
  gi|70606950|ref|YP_255820.1| 38 STTEISQTINTSRKSIIDAIRKLVDKELVTKVKHDIYGLSDKGKELWNKID 88
                                  779******************987766666667777777777777777775 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.59
                       UPF0122  32 dDlSlsEiAeefnvsrqavyd 52 
                                   d lSl   A e  vsrq++  
  gi|70606950|ref|YP_255820.1| 134 DGLSLDKAARELGVSRQTLKY 154
                                   568999999999999998654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00039       0.2      12      58 ..      26      69 ..      19      70 .. 0.86
   2 ?   -1.6   0.0       7.1   3.7e+03      24      50 ..     135     160 ..     122     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00039
                                  HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   +l++La++      s++ei++  n+s++ +   ++kL  ++lv+ v
  gi|70606950|ref|YP_255820.1| 26 DILIILATKGP---SSTTEISQTINTSRKSIIDAIRKLVDKELVTKV 69
                                  57888888777...67****************************865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 7.1
                                   C-B-HHHHHHHHTS-HHHHHHHHHHHH CS
                          Rrf2  24 epvsseeiaerqnispsylekilakLr 50 
                                   + +s+++ a++ ++s++ l+  l+  +
  gi|70606950|ref|YP_255820.1| 135 G-LSLDKAARELGVSRQTLKYYLELFE 160
                                   3.6777888888888888877666555 PP

>> SelB-wing_3  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.075        38       3      26 ..      31      54 ..      30      69 .. 0.88
   2 ?    6.9   0.1    0.0095       4.9      14      41 ..     141     168 ..     131     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.075
                                  HHTTS-BBHHHHHHHHT--HHHHH CS
                   SelB-wing_3  3 lkeegeitaaefRdllgtSRKyai 26
                                  l+++g+ ++ e  + ++tSRK +i
  gi|70606950|ref|YP_255820.1| 31 LATKGPSSTTEISQTINTSRKSII 54
                                  677888899999999******988 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0095
                                   HHHHHT--HHHHHHHHHHHHHCTSEEEE CS
                   SelB-wing_3  14 fRdllgtSRKyaiplLEyfDrigvTrRv 41 
                                   +   lg+SR  +  +LE f  +++ r +
  gi|70606950|ref|YP_255820.1| 141 AARELGVSRQTLKYYLELFEEKKLFRVI 168
                                   55689****************9998865 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00031      0.16       9      29 ..     135     155 ..     131     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00031
                                   THHHHHHHHHHTSSHHHHHHH CS
                         HTH_3   9 glsqeeLAeklGvsrstisri 29 
                                   gls+ ++A++lGvsr+t+  +
  gi|70606950|ref|YP_255820.1| 135 GLSLDKAARELGVSRQTLKYY 155
                                   9****************9766 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2    0.0003      0.15       3      56 ..      22      71 ..      21      74 .. 0.93
   2 ?   -1.3   0.0       5.5   2.8e+03      29      55 ..     143     169 ..     138     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                                  -S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE CS
               Penicillinase_R  3 elEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsreke 56
                                  +l++ ++ il +kg+ +++e+ + ++      ++++   +r+Lv+K+l+++ k+
  gi|70606950|ref|YP_255820.1| 22 KLQWDILIILATKGPSSTTEISQTINTS----RKSIIDAIRKLVDKELVTKVKH 71
                                  689*******************999988....9****************99875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.5
                                   GGG---HHHHHHHHHHHHHTTS-EEEE CS
               Penicillinase_R  29 eekelaysTVktllrrLvkKgllsrek 55 
                                   +e  ++++T k  l+  ++K+l++   
  gi|70606950|ref|YP_255820.1| 143 RELGVSRQTLKYYLELFEEKKLFRVIG 169
                                   566788899999999999998876543 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1       0.1        53       5      46 ..      27      68 ..      24      71 .. 0.83
   2 ?    6.4   0.0     0.014       7.2      11      31 ..     132     152 ..     125     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                      HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  il  l+ +g  s++e+++  ++S + i   +++L+ + l+t+
  gi|70606950|ref|YP_255820.1| 27 ILIILATKGPSSTTEISQTINTSRKSIIDAIRKLVDKELVTK 68
                                  78899999***************9988777777777777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                      HTH_DeoR  11 qqgklsveelvellgvSeaTi 31 
                                   +++ ls+++++ +lgvS +T 
  gi|70606950|ref|YP_255820.1| 132 NHDGLSLDKAARELGVSRQTL 152
                                   68889***************6 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0         1   5.2e+02      21      37 ..      44      60 ..      27      70 .. 0.86
   2 ?    9.0   0.0    0.0026       1.3      15      39 ..     137     161 ..     128     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                                  HHHTS-HHHHHHHHHHH CS
                         HTH_1 21 eeLglsqpavsrqikrL 37
                                  +  ++s +++ ++i++L
  gi|70606950|ref|YP_255820.1| 44 QTINTSRKSIIDAIRKL 60
                                  77899999**9999998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0026
                                   SHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_1  15 sftrAAeeLglsqpavsrqikrLEe 39 
                                   s+ +AA+eLg+s  ++   +   Ee
  gi|70606950|ref|YP_255820.1| 137 SLDKAARELGVSRQTLKYYLELFEE 161
                                   899***********99988877775 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00043      0.22      85     130 ..      24      72 ..       4      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                      SMC_ScpB  85 aletLaiIaykqpvtraeieeiRGvnsdsv...vrtLlerglieekgrk 130
                                   +  +L i a k p + +ei++    + +s+   +r+L++++l+++++++
  gi|70606950|ref|YP_255820.1|  24 QWDILIILATKGPSSTTEISQTINTSRKSIidaIRKLVDKELVTKVKHD 72 
                                   3469****************9988776654122799********99864 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00064      0.33       5      21 ..     141     157 ..     139     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                                   HHHHHTTTHHHHHHHHH CS
                          MerR   5 vAeltGvsprtLRyYEr 21 
                                   +A+ +Gvs +tL yY +
  gi|70606950|ref|YP_255820.1| 141 AARELGVSRQTLKYYLE 157
                                   89*************65 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.093        48      41      64 ..      48      71 ..      31      81 .. 0.75
   2 ?    6.0   0.1     0.031        16      19      54 ..     145     182 ..     137     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.093
                Linker_histone 41 kfksllkkalkkgvekgelvqpkg 64
                                    ++ +  a++k+v+k+ ++++k 
  gi|70606950|ref|YP_255820.1| 48 TSRKSIIDAIRKLVDKELVTKVKH 71
                                  345667889********9999995 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                Linker_histone  19 kGsSrqaIkkyikakykvv..dvskfksllkkalkkgv 54 
                                    G+Srq++k y++   + +   v   ++++kk + k+v
  gi|70606950|ref|YP_255820.1| 145 LGVSRQTLKYYLELFEEKKlfRVIGKRTHFKKNIYKCV 182
                                   59*********996555544577777999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1842.39
//
Query:       gi|70606951|ref|YP_255821.1|  [L=623]
Description: hypothetical protein Saci_1181 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-35  120.5   0.0    1.1e-34  120.0   0.0    1.2  1  Pkinase      Protein kinase domain
      2e-14   53.5   0.0    5.8e-14   52.0   0.0    1.8  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.057   12.8   0.0    1.6  2  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
      0.027   13.8   0.1       0.36   10.1   0.1    2.1  1  Kinase-like  Kinase-like
      0.037   14.1   0.0       0.12   12.5   0.0    1.8  1  GTF2I        GTF2I-like repeat
      0.044   13.4   0.1       0.36   10.4   0.0    2.0  2  FTA2         Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0   3.7e-38   1.1e-34       1     260 [.     317     619 ..     317     621 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 3.7e-38
                                   EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH..HHHHHHHHHHHHHS.CTTB--EEEEEEE......... CS
                       Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke..kkvlrEikilkklk.hpnivrlyevfee......... 69 
                                   y+++e +G G++G V+k+   ++g  +A+K+++++k +++ e  +++l+E + l+kl+  p++v +y++f +         
  gi|70606951|ref|YP_255821.1| 317 YRVIEVIGLGGNGYVMKVE--KNGLLYAMKVLSVNKFTNSLEhfDNLLKESENLEKLSkDPRLVSIYGSFVDknniqsala 395
                                   67899************99..7************9999888889**************9*************9******** PP

                                   .......SSEEEEEEE--TTEBHHHHHHHHSS--HH....HHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE... CS
                       Pkinase  70 .......kdelylvleyveggeladllerkgslsee....eakkiakqilegleylHskgiiHrDlKpeNiLidekge... 136
                                          k    +++e++egg+l+dl++r   ++++     +k ++k+i+++l +lH++g +H D+Kp+Ni+++ek +   
  gi|70606951|ref|YP_255821.1| 396 gdytsyyKYPPAIIMEFMEGGTLFDLISRVDLVQSKywqyIVKLVIKEIAKALTFLHKRGYVHLDVKPQNIFLKEKINgep 476
                                   *97755544455****************555555444444999*******************************8444455 PP

                                   .............EEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHH....TTSCBSHHHHHHHHHHHHHHHHHSS-STTTS CS
                       Pkinase 137 .............lKitDFGlakelessskltsfvgtseYlAPEvl....keneyskkvDvWslGvilyelltgkppfsge 200
                                                +K++D+G a ++ ++       +t+ Y +PE +    ++++ ++++D ++lGv+ly+llt k++ + +
  gi|70606951|ref|YP_255821.1| 477 evvykilsstpgiIKLGDLGSAVRVGEKI----TQATPAYSPPEQIeaviTGKGAQPSMDNYALGVTLYKLLTMKNLDYVN 553
                                   5666666666777************9976....789********99888888***********************998866 PP

                                   SHHHHHHHHHHT....HHHHHHHCT.....SHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHT CS
                       Pkinase 201 kgkekvekeldq....lekilkilg.....etkeklpeaseiseeakdllkkllkkdpkkRltaeellq 260
                                     ++ + + ++      +k +   +      +++k + +++  +e+ ++++  l +dpk+Rlt  ++++
  gi|70606951|ref|YP_255821.1| 554 YLDKAFDEYIKGdpsiAMKYI---NmakmsMVNFKPKLPHNTLPELANVVQGTLVVDPKRRLTSYDIVK 619
                                   666666666666443322222...234466778889999999*********************888765 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0     2e-17   5.8e-14       5     223 ..     321     568 ..     317     621 .. 0.70

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2e-17
                                   EEEEEESSEEEEEEEEETTTTSSEEEEEEEEE...STTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSS...... CS
                   Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtl...keeateeekeelleeakimkkl.khpnivkllgvctkeep...... 75 
                                   + +G G  G V++ + +       +  a+K+l   k +++ e+ ++ll+e + ++kl k p++v+++g  +++++      
  gi|70606951|ref|YP_255821.1| 321 EVIGLGGNGYVMKVEKN------GLLYAMKVLsvnKFTNSLEHFDNLLKESENLEKLsKDPRLVSIYGSFVDKNNiqsala 395
                                   66777777777766655......666677776322223444557899**********999*********996555567788 PP

                                   ..........EEEEEE--TTEBHHHHHHHTCTTTSBHHHHH..HHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE...... CS
                   Pkinase_Tyr  76 ..........llivteyvkgGdLlkfLrkkekekltlkdll..sfalqvAkGmeyLeskklvHrdlaarNvLlse...... 138
                                               i++e+++gG+L + + + +  + ++ + +   ++ ++Ak++ +L+++ +vH d+  +N++l+e      
  gi|70606951|ref|YP_255821.1| 396 gdytsyykypPAIIMEFMEGGTLFDLISRVDLVQSKYWQYIvkLVIKEIAKALTFLHKRGYVHLDVKPQNIFLKEkingep 476
                                   888888888899****************99665555555331146789********************************* PP

                                   ..........TTEEEE-STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSE....EEHHHHHHHHHHHHHHHHTTSSGT CS
                   Pkinase_Tyr 139 ..........nkvvkisDfGLardiekddeyvkkeeaklpvkWmapEslkekk....ftsksDvWsfGvllwEiftlgesp 205
                                               ++k++D G a ++        ++ ++    + +pE +++       + + D ++ Gv+l+ ++t+ +  
  gi|70606951|ref|YP_255821.1| 477 evvykilsstPGIIKLGDLGSAVRV-------GEKITQATPAYSPPEQIEAVItgkgAQPSMDNYALGVTLYKLLTMKNLD 550
                                   9999999988889999999988888.......344455556677777777665455578888**************99999 PP

                                   TTTSHHHHHHHHHHTTEE CS
                   Pkinase_Tyr 206 ypglkneevleklkegkr 223
                                   y ++ ++ + e++k +  
  gi|70606951|ref|YP_255821.1| 551 YVNYLDKAFDEYIKGDPS 568
                                   666655554444433322 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.74   2.2e+03     163     203 ..     226     266 ..     223     268 .. 0.83
   2 ?   12.8   0.0   1.9e-05     0.057      93     155 ..     407     472 ..     392     479 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.74
                           Kdo 163 liDldkarlrlradrwrekdLarLkrsflkielteadweal 203
                                   +i ++ a l+l+ ++  +  L++L+ ++++i +++ d e++
  gi|70606951|ref|YP_255821.1| 226 VIEINGASLKLKDRKFAKLSLEPLYWKVNEIRISREDEEEI 266
                                   67777788899999999999999999999999999997765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.9e-05
                           Kdo  93 lllterlegaq..dLedllakwae.laeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                   ++++e +eg    dL   +   ++ + +   +  +k+++++   lh++g  H d+ ++ni+l+++ 
  gi|70606951|ref|YP_255821.1| 407 AIIMEFMEGGTlfDLISRVDLVQSkYWQYIVKLVIKEIAKALTFLHKRGYVHLDVKPQNIFLKEKI 472
                                   56666666643113322222222247777778899***************************9975 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00012      0.36     147     243 ..     439     543 ..     399     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                   Kinase-like 147 lllTlqlirlaanLqakglvhgkftvdnllldek................gglmlggftaLvragtkvvlsevekgfaPpE 211
                                   l++  ++ +    L+++g vh +++++n++l+ek                g ++lg++++ vr+g+k    +   +++PpE
  gi|70606951|ref|YP_255821.1| 439 LVI-KEIAKALTFLHKRGYVHLDVKPQNIFLKEKingepevvykilsstpGIIKLGDLGSAVRVGEKIT--QATPAYSPPE 516
                                   555.44555566788888899999999888888644444444444444446789************999..77789***** PP

                   Kinase-like 212 llgsrggytrknktkmthkldaWqlGlviyri 243
                                    + +  +    +      ++d ++lG++ y +
  gi|70606951|ref|YP_255821.1| 517 QIEAVIT---GKG--AQPSMDNYALGVTLYKL 543
                                   9887444...223..33467888888888876 PP

>> GTF2I  GTF2I-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.9e-05      0.12      24      48 ..     201     225 ..     194     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                         GTF2I  24 kvpYekiekdpealvVeGLPegvpf 48 
                                    vpYek+++  + ++VeGLP + +f
  gi|70606951|ref|YP_255821.1| 201 GVPYEKFRNCFTVFEVEGLPPDTSF 225
                                   59******************99887 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00012      0.36      25      60 ..     318     353 ..     279     391 .. 0.76
   2 ?    0.5   0.0      0.13   3.9e+02     178     203 ..     441     466 ..     427     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                          FTA2  25 efleyLgkglhsiVlkvkirgkeYALKlFrfleaee 60 
                                   + +e++g g +++V+kv+ +g  YA+K+    + ++
  gi|70606951|ref|YP_255821.1| 318 RVIEVIGLGGNGYVMKVEKNGLLYAMKVLSVNKFTN 353
                                   56999**********************965543333 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                          FTA2 178 lpkllrdlkklhklgIvvrDlkeeny 203
                                   ++++ + l  lhk g v+ D+k++n+
  gi|70606951|ref|YP_255821.1| 441 IKEIAKALTFLHKRGYVHLDVKPQNI 466
                                   6899999****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4287.80
//
Query:       gi|70606952|ref|YP_255822.1|  [L=452]
Description: multidrug resistance protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-58  197.8  70.4    4.4e-47  160.7  47.6    2.8  2  MFS_1     Major Facilitator Superfamily
    1.7e-12   46.9  33.7    8.4e-11   41.4  13.7    3.1  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
      0.078   13.0   1.0        7.1    6.8   0.0    2.9  2  NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
        3.6    5.8  23.6       0.02   13.2   3.7    4.0  4  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7  47.6   9.9e-51   4.4e-47      14     353 .]       1     381 [.       1     381 [. 0.87
   2 !   51.0  14.8   2.2e-17   9.7e-14       6     186 ..     244     449 ..     239     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 9.9e-51
                         MFS_1  14 ilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvl 94 
                                   +++palp  + +++  s++++ +++++y ++ avas+++G l+dr+G ++++ll++++++l++l++ f++++++l+++r++
  gi|70606952|ref|YP_255822.1|   1 MVIPALP-KIEDQFSTSATTVAWITSAYLIVGAVASPVFGKLGDRYGKKKIYLLAIAFYSLAVLIAGFSTNIYMLIFARAI 80 
                                   5789***.******************************************************77777989999******** PP

                         MFS_1  95 qGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                   qGlg  a+fp+++a+i+d+fp+e+ + a ++lsa+ +lG++lg l+g+++++ lgW+++f  + i+s+++  +f+   +  
  gi|70606952|ref|YP_255822.1|  81 QGLGF-AVFPIAIAIITDLFPRERVAWAQSILSATLALGPALGLLIGAYIVQDLGWQYAFHTAFILSIIL--MFISIRFIQ 158
                                   ****7.****************************************************************..556888888 PP

                         MFS_1 176 pperkrkspkeee..............................................kgtgpaplvpawkallkdpvlw 210
                                   + ++k+k+ ++ +                                              ++++  pl + + +++ ++ + 
  gi|70606952|ref|YP_255822.1| 159 EIPSKTKERIDYLgavflmlavisllvyltegpsigwfsatqfsliltsiisfgvfifvERRVAEPLMK-LDLFRIRNIMV 238
                                   888888888888899*****************9999999999999999999999999999999999999.88888888664 PP

                         MFS_1 211 ....illialllfffgfsg..lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalllll 285
                                        l+++ ++f ++f g  +++ lp      lgls  + +gll+a +al ++++++++grl++ +g+++ l+++ ++++
  gi|70606952|ref|YP_255822.1| 239 anisGLIAGTAMF-LMFIGltYYAQLPK--PYGLGLS-IIDSGLLMAPVALTMMVVGPIVGRLINSTGPKPLLIFGSIVGI 315
                                   4553333333333.33333134444444..5566666.8****************************************** PP

                         MFS_1 286 laalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                   +++l+l  ++ t+ +vll  v++ +G+     +++l ++++ ++p++++g  +g +++++s+g+++gp
  gi|70606952|ref|YP_255822.1| 316 IGFLLLNAFNSTNIQVLLDTVVASVGI--ISLMIPLVNMVAVSLPEDQRGVGIGMNTLIRSIGSSVGP 381
                                   ************777776665555555..44456677777777789*********************8 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 2.2e-17
                         MFS_1   6 flsalarsilgpalplalaed.....lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                   +++++a+++ ++ l+ ++a+      lg+s    gll++ +al+++v  +++Grl++  G++++l++g ++ ++g +lll 
  gi|70606952|ref|YP_255822.1| 244 LIAGTAMFLMFIGLT-YYAQLpkpygLGLSIIDSGLLMAPVALTMMVVGPIVGRLINSTGPKPLLIFGSIVGIIG-FLLLn 322
                                   444444444444444.444436666699***********************************************.66665 PP

                         MFS_1  81 .fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.......... 149
                                    f +s    +l+  v++++g  +l+   + ++a   p+++rg +ig+ ++  s+G+ +gp+++ ++++ +           
  gi|70606952|ref|YP_255822.1| 323 aF-NSTNiQVLLDTVVASVGIISLMIPLVNMVAVSLPEDQRGVGIGMNTLIRSIGSSVGPVISTVFMDTYTawigylfnnq 402
                                   67.666668************99999999**************************************88888999****** PP

                         MFS_1 150 ............Wravfyilaivsllafvlfllllpeepperkrkspke 186
                                               +++++++   ++++ +++  +ll+ +++ +++++++e
  gi|70606952|ref|YP_255822.1| 403 ylpiasvpsseaFHYIYLVGICLMFINLLV--ALLTKNYVLKQKVKTTE 449
                                   ***************************776..99988888888887776 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4  13.7   1.9e-14   8.4e-11      43     188 ..      15     153 ..       6     162 .. 0.83
   2 !   11.9   9.9   1.7e-05     0.075      20     172 ..     249     396 ..     238     444 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.9e-14
                                   H...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                      Sugar_tr  43 essvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                   +s++++ +i+s++l+++++ s ++g+lgdr+G+kk++l a+++++ + ++ ++++   ++++li++R + G+g  ++ + +
  gi|70606952|ref|YP_255822.1|  15 TSATTVAWITSAYLIVGAVASPVFGKLGDRYGKKKIYLLAIAFYSLAVLIAGFST---NIYMLIFARAIQGLGFAVFPIAI 92 
                                   3667889************************************************...**************998776655 PP

                                   HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill 188
                                    + ++       R + v + q+ +++   ++  +gl + +++ ++ gw++ ++ +++++++l+++ 
  gi|70606952|ref|YP_255822.1|  93 AIITDL----FPRER-VAWAQSILSATLALGPALGLLIgAYIVQDLGWQYAFHTAFILSIILMFIS 153
                                   554444....44443.568888888888888888888889999999************98765543 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.7e-05
                                   GGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTS CS
                      Sugar_tr  20 gafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgkn 100
                                   + fl++++  +  +l k ++    s ++sgl+++ + +  ++ + ++g l++  G k+ l++++++ +ig +l  a +++ 
  gi|70606952|ref|YP_255822.1| 249 AMFLMFIGLTYYAQLPKPYG-LGLSIIDSGLLMAPVALTMMVVGPIVGRLINSTGPKPLLIFGSIVGIIGFLLLNAFNST- 327
                                   45556666666666666665.4458999*********************************************9999944. PP

                                   S-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS...-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHH CS
                      Sugar_tr 101 svevlivgRvlvGigvGlasvlvPmyisEiA...pkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwri 172
                                   +++vl+   v++  +vG++s ++P+ ++ +A   p++ Rg  ++++ l  ++G  v+ ++ +++ +++++   w  
  gi|70606952|ref|YP_255822.1| 328 NIQVLL-DTVVA--SVGIISLMIPL-VNMVAvslPEDQRGVGIGMNTLIRSIGSSVGPVISTVFmDTYTA---WIG 396
                                   454444.44554..79********8.56677778*************************99999677666...543 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.015        65      20      45 ..      74      98 ..      65     103 .. 0.75
   2 ?    6.8   0.0    0.0016       7.1      17      50 ..     232     264 ..     229     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.015
                      NDUF_B12 20 krfkraffpGfglavaafaaavgyEh 45
                                    f ra+ +G+g av  +a+a++ + 
  gi|70606952|ref|YP_255822.1| 74 LIFARAI-QGLGFAVFPIAIAIITDL 98
                                  3456666.*******99999998875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0016
                      NDUF_B12  17 skakrfkraffpGfglavaafaaavgyEhflgsk 50 
                                   + ++ ++  +  G+ +++a+f++ +g++++ + +
  gi|70606952|ref|YP_255822.1| 232 RIRNIMVANI-SGLIAGTAMFLMFIGLTYYAQLP 264
                                   5567777777.9*****************97655 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1    0.0039        17     321     351 ..       9      39 ..       2      68 .. 0.59
   2 ?   13.2   3.7   4.5e-06      0.02     131     239 ..      70     163 ..      65     189 .. 0.85
   3 ?   -1.6   1.3      0.14   6.1e+02     326     356 ..     270     300 ..     236     325 .. 0.62
   4 ?    2.1   0.6      0.01        45     471     523 ..     339     390 ..     327     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0039
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 321 lEtqFslsaseAnlltGvvvipgaalGillg 351
                                   +E qFs+sa++ + +t +++i+ga++  ++g
  gi|70606952|ref|YP_255822.1|   9 IEDQFSTSATTVAWITSAYLIVGAVASPVFG 39 
                                   5666666666666666666666666554444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.5e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyvdidseisltpkdprW 211
                                    ++++++a  ++G+G ++ ++++i+ i D   +++ +   +il+a+ +lGpalG l+G+++++              d  W
  gi|70606952|ref|YP_255822.1|  70 NIYMLIFARAIQGLGFAV-FPIAIAIITDLFPRERVAWAQSILSATLALGPALGLLIGAYIVQ--------------DLGW 135
                                   467999*********876.9***************************************8877..............4578 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 212 vgaWWlgflilgvllllaaiplffFPke 239
                                     a+   f+++ +l++++  ++   P +
  gi|70606952|ref|YP_255822.1| 136 QYAFHTAFILSIILMFISIRFIQEIPSK 163
                                   8888888888888887777666555554 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.14
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 326 slsaseAnlltGvvvipgaalGillgGllvk 356
                                   +ls   + ll+++v++ ++++G ++g l+ +
  gi|70606952|ref|YP_255822.1| 270 GLSIIDSGLLMAPVALTMMVVGPIVGRLINS 300
                                   4566677788888888888888888766544 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.01
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 471 sflgalgrvpallvilRcVkkedksfalGlqlllirllgliPgPiifGaiiDs 523
                                   s+ + +  +p + ++  + +++++ + +G+ +l+ ++ g   gP+i  +++D+
  gi|70606952|ref|YP_255822.1| 339 SVGIISLMIPLVNMVAVSLPEDQRGVGIGMNTLIRSI-GSSVGPVISTVFMDT 390
                                   44445556788888888999**********9887776.9999***99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 2906.18
//
Query:       gi|70606953|ref|YP_255823.1|  [L=967]
Description: hypothetical protein Saci_1183 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-16   61.0  21.7     0.0046   17.2   0.1    9.5 10  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi
    8.7e-05   22.7  41.5      0.064   13.5   2.6    8.1  9  CARDB        CARDB
     0.0032   17.7   2.0     0.0032   17.7   2.0    8.1  8  DUF11        Domain of unknown function DUF11
     0.0079   16.0   2.5        1.3    8.8   0.0    4.7  6  DUF5044      Domain of unknown function (DUF5044)
  ------ inclusion threshold ------
      0.028   13.2   0.0       0.18   10.6   0.0    2.3  4  Gryzun       Gryzun, putative trafficking through Golgi
        5.5    6.8   5.8        8.7    6.1   5.8    1.2  1  RIFIN        Rifin


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.8   1.1e+04      57      67 ..      86      96 ..      82     103 .. 0.64
   2 !   10.1   0.0   0.00026      0.77       3      78 ..     164     239 ..     162     240 .. 0.86
   3 ?    4.4   0.0     0.015        44       9      77 ..     283     350 ..     276     352 .. 0.84
   4 ?    1.7   0.1       0.1     3e+02       3      77 ..     388     462 ..     386     464 .. 0.69
   5 ?    3.4   0.0      0.03        91       8      77 ..     506     574 ..     498     576 .. 0.84
   6 !   11.1   0.2   0.00012      0.37       7      78 ..     617     688 ..     610     689 .. 0.72
   7 ?   -0.7   0.0      0.58   1.7e+03      58      74 ..     710     726 ..     709     730 .. 0.91
   8 !   17.2   0.1   1.5e-06    0.0046      10      78 ..     727     793 ..     717     794 .. 0.89
   9 !    5.7   0.1    0.0058        17       4      28 ..     826     850 ..     822     852 .. 0.86
  10 !   14.8   0.1   8.7e-06     0.026      42      78 ..     874     910 ..     865     911 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.8
                   NPCBM_assoc 57 vkVtppagaaa 67
                                   +Vt+p+++  
  gi|70606953|ref|YP_255823.1| 86 PTVTIPEWTPG 96
                                  57888888763 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00026
                   NPCBM_assoc   3 pGetvt.ltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                   pG+t+t lt+ + n g+a +tnv l+ s   P          a++++++pG + eatv  ++ ++a  G y +++k+++
  gi|70606953|ref|YP_255823.1| 164 PGQTNTpLTIILQNLGNALVTNVTLEFSSqfPVKFL---QNNATISAIEPGYYGEATVFASVYPNATEGVYYIKLKVNY 239
                                   677766589999**********98766533388887...8888899*****************************9986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.015
                   NPCBM_assoc   9 ltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                   lt++v n g+  ++nv l+l+   P +        a++  +++G++  atv  ++  +a +G y + ++++
  gi|70606953|ref|YP_255823.1| 283 LTIYVENLGENLLSNVTLTLKShyPIQFL---QNNATIGFVPAGQYNYATVIASVDRNATPGVYYIPVTVS 350
                                   67778888888888888877765677777...77888889************************9999887 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.1
                   NPCBM_assoc   3 pGetvt.ltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                   pG+t+t lt+ + n gta++tn  l+l+   P        s  s+  ++ G   e tv   + ++a +G y v ak++
  gi|70606953|ref|YP_255823.1| 388 PGQTNTpLTIILQNIGTATVTNATLQLESqyPVKFL---QSNLSIGNIPVGVPIELTVLSNVYPNATTGVYFVSAKIT 462
                                   677765588999999999999987776632255555...555555677777777777777777777777777777776 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.03
                   NPCBM_assoc   8 tltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                    lt++v n g+  ++nv l+l+   P +        a++  +++G++  atv   + ++a  G y + ++++
  gi|70606953|ref|YP_255823.1| 506 PLTVVVENLGENLLSNVTLTLKShyPIQFL---QNNATIGFVPAGQYNYATVIADIYPNASSGVYYIPVTVS 574
                                   578889999999999999988766688888...88888999***********99999999999999988887 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00012
                   NPCBM_assoc   7 vtltltvtndgtaaatnvslslslPeGWtvvevspasaa..slapGetveatvkVtppagaaaGdyevtakarl 78 
                                   v lt+ ++n+g+  + n  l+ s  ++    ++s ++a+   +++G++  atv+V++ ++a +G y + a++++
  gi|70606953|ref|YP_255823.1| 617 VPLTILLKNTGDVNVLNATLTFSN-SEYP-LKFSQTNAQvgIIPAGQENYATVTVSVYPNATPGVYYIPATLNY 688
                                   467777777777777777776665.2233.344555555449**************************999875 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 0.58
                   NPCBM_assoc  58 kVtppagaaaGdyevta 74 
                                    Vt p++ ++G y+v++
  gi|70606953|ref|YP_255823.1| 710 VVTLPPQVFPGYYDVRL 726
                                   59*************96 PP

  == domain 8  score: 17.2 bits;  conditional E-value: 1.5e-06
                   NPCBM_assoc  10 tltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                    + +tn g+  a+n s+s+s+P +  v ++   ++ +l+ G  v +t+ + +p+++++ +y+v +++++
  gi|70606953|ref|YP_255823.1| 727 LTILTNYGNGIAENASISVSTPFQ--VISSPEIKIGALPIGSPVNVTFLINIPNDTIPKTYTVNFTVTF 793
                                   56789*****************87..5566667888*****************************9986 PP

  == domain 9  score: 5.7 bits;  conditional E-value: 0.0058
                   NPCBM_assoc   4 Getvtltltvtndgtaaatnvslsl 28 
                                   ++ v +t+t++n+g+a+a+nv ++l
  gi|70606953|ref|YP_255823.1| 826 DSNVPITITLKNTGNATAKNVIVRL 850
                                   45689****************9886 PP

  == domain 10  score: 14.8 bits;  conditional E-value: 8.7e-06
                   NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                     + ++ p +t+ +t+ V ++ ga +G y++ + a++
  gi|70606953|ref|YP_255823.1| 874 VFVGDINPQQTANVTFVVDISGGASPGVYPLAIAATW 910
                                   455699**************************99987 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   3.7e+03      50      72 ..      86     108 ..      77     127 .. 0.63
   2 !    9.8   0.4    0.0003      0.91      15      87 ..     162     240 ..     152     246 .. 0.78
   3 ?    4.8   0.2     0.011        34      21      93 ..     281     358 ..     267     360 .. 0.86
   4 ?    0.9   0.3      0.18   5.3e+02      17      54 ..     388     429 ..     378     469 .. 0.65
   5 !    5.1   0.2    0.0092        28      18      93 ..     502     582 ..     491     584 .. 0.81
   6 !   10.1   1.3   0.00025      0.76      18      92 ..     614     694 ..     602     697 .. 0.82
   7 ?    2.2   0.3      0.07   2.1e+02      28      84 ..     731     791 ..     704     812 .. 0.68
   8 ?    1.9   0.4     0.089   2.7e+02      15      61 ..     779     826 ..     768     828 .. 0.74
   9 !   13.5   2.6   2.1e-05     0.064      17      84 ..     825     891 ..     809     907 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                   EEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB  50 gtvtvpsLaagesttvsftwtte 72 
                                    tvt+p+  +g+ ++v++ + ++
  gi|70606953|ref|YP_255823.1|  86 PTVTIPEWTPGQMVNVTYIFNVA 108
                                   45666666666666666655444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0003
                                   EETTSEEE.EEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CT..EEEEEEEEEE-S-S-CEEEEEEEESTT CS
                         CARDB  15 afvgeent.itvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaag..esttvsftwtteategevtltvvvDpd 87 
                                   + +g++nt +t+ ++N G+a  +++++++     ++   +++t++++++g  +++tv +++ ++ateg ++++++v  +
  gi|70606953|ref|YP_255823.1| 162 VGPGQTNTpLTIILQNLGNALVTNVTLEFSSQFPVKflqNNATISAIEPGyyGEATVFASVYPNATEGVYYIKLKVNYY 240
                                   55555544389999**************999887778999**********33345556666666**********99864 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.011
                                   EEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT-SS--S CS
                         CARDB  21 ntitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtltvvvDpdnevaEs 93 
                                   + +t+ v+N G+    +++++l      +   +++t+  + ag++ + ++   ++  at+g +++ v+v  +n  +E+
  gi|70606953|ref|YP_255823.1| 281 LPLTIYVENLGENLLSNVTLTLKSHYPIQflqNNATIGFVPAGQYNYATVIASVDrnATPGVYYIPVTVSMYNGYKET 358
                                   578999**************99998887788899******************99999999*******99999987776 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.18
                                   TTSEEE.EEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEE CS
                         CARDB  17 vgeent.itvtvkNqGtaasgatkvalyldgelv...gtvtv 54 
                                   +g++nt +t+ ++N Gta+ ++ +++l     ++   ++ ++
  gi|70606953|ref|YP_255823.1| 388 PGQTNTpLTIILQNIGTATVTNATLQLESQYPVKflqSNLSI 429
                                   554444389999******999999988665544455555555 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.0092
                                   TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT-SS--S CS
                         CARDB  18 geentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtltvvvDpdnevaEs 93 
                                   ++++ +tv v+N G+    +++++l      +   +++t+  + ag++ + ++   +   a++g +++ v+v  +n  +E+
  gi|70606953|ref|YP_255823.1| 502 ENNIPLTVVVENLGENLLSNVTLTLKSHYPIQflqNNATIGFVPAGQYNYATVIADIYpnASSGVYYIPVTVSMYNGYKET 582
                                   567899*****************9998887777889999999999999888876544447899999999999888877775 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.00025
                                   TSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT-SS-- CS
                         CARDB  18 geentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ategevtltvvvDpdnevaE 92 
                                   ++++ +t+ +kN+G+ +  + ++++  ++       ++++v  + ag++ + ++t+ +   at+g +++ ++   +n+ +E
  gi|70606953|ref|YP_255823.1| 614 ETQVPLTILLKNTGDVNVLNATLTFSNSEYPLkfsqTNAQVGIIPAGQENYATVTVSVYpnATPGVYYIPATLNYYNYKTE 694
                                   467899999********************99999998899999999887666655554445***********999998877 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.07
                                   EE-SSS-EEEEEEEEEETTEEE..EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEE CS
                         CARDB  28 kNqGtaasgatkvalyldgelv..gtvtvpsLaagesttvsftwtte..ategevtltvvv 84 
                                   +N G++ +++ ++++    ++    ++++ +L  g+ ++v+f + ++  + ++++t++++v
  gi|70606953|ref|YP_255823.1| 731 TNYGNGIAENASISVSTPFQVIssPEIKIGALPIGSPVNVTFLINIPndTIPKTYTVNFTV 791
                                   6777777777776666666666445566677777777777777777754444555554443 PP

  == domain 8  score: 1.9 bits;  conditional E-value: 0.089
                                   EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTE CS
                         CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaage 61 
                                    +  +++t+++tv+  G +a ++  +++y   +   ++v+ + +++g+
  gi|70606953|ref|YP_255823.1| 779 DTIPKTYTVNFTVTFDGGKANYQYALNVYPKANIIiTNVKYSTINPGD 826
                                   556788999999999999999999999997777666666667777765 PP

  == domain 9  score: 13.5 bits;  conditional E-value: 2.1e-05
                                   TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                         CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                     +++ it+t+kN+G+a+++++ v+l  ++       +    ++L+a + ++v + +  + ++ +  +t+vv
  gi|70606953|ref|YP_255823.1| 825 GDSNVPITITLKNTGNATAKNVIVRLGTSDVIYphvsS---SNPLQALTASEVFVGDINPQQTAN--VTFVV 891
                                   457899************************99974442...355555555555555554422222..33333 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.3       1.5   4.5e+03       4      17 ..      87     102 ..      36     117 .. 0.58
   2 ?   -3.3   5.6       3.8   1.1e+04       8      36 ..     160     189 ..     155     299 .. 0.60
   3 ?    0.4   0.4      0.27   8.2e+02      19      33 ..     284     298 ..     253     354 .. 0.48
   4 ?    0.2   3.4      0.31   9.1e+02       7      36 ..     383     413 ..     378     485 .. 0.79
   5 ?    1.1   1.3      0.17     5e+02      10      36 ..     498     525 ..     491     600 .. 0.69
   6 ?    3.9   2.8     0.022        65       9      85 ..     609     678 ..     602     699 .. 0.73
   7 ?   -4.0   0.2         6   1.8e+04      17      24 ..     786     793 ..     780     804 .. 0.58
   8 !   17.7   2.0   1.1e-06    0.0032       6      81 ..     818     896 ..     814     904 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                         DUF11   4 tvdksevrpGd..tvt 17 
                                   tv+ +e +pG+  +vt
  gi|70606953|ref|YP_255823.1|  87 TVTIPEWTPGQmvNVT 102
                                   2333344455533344 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                         DUF11   8 sevrpGd.tvtytltvtNtgpasangvvvt 36 
                                   + v pG+ ++  t++++N g+a  ++v+++
  gi|70606953|ref|YP_255823.1| 160 TVVGPGQtNTPLTIILQNLGNALVTNVTLE 189
                                   566777744567888888888888888875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.27
                         DUF11  19 tltvtNtgpasangv 33 
                                   t+ v N g + +++v
  gi|70606953|ref|YP_255823.1| 284 TIYVENLGENLLSNV 298
                                   222222222222222 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.31
                         DUF11   7 ksevrpGd.tvtytltvtNtgpasangvvvt 36 
                                   ++ v pG+ ++  t++++N g+a+ ++++++
  gi|70606953|ref|YP_255823.1| 383 PTVVGPGQtNTPLTIILQNIGTATVTNATLQ 413
                                   5678889855679************999986 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.17
                         DUF11  10 vrpGd.tvtytltvtNtgpasangvvvt 36 
                                   v+pG+ ++  t++v N g + +++v++t
  gi|70606953|ref|YP_255823.1| 498 VAPGEnNIPLTVVVENLGENLLSNVTLT 525
                                   6777767788999999999999999987 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.022
                         DUF11   9 evrpGd.tvtytltvtNtgpasangvvvtDtlPaglay.vsvsasqgtasaltsvgsLeagesatlsftvrvtrtaasg 85 
                                   +v pG+ +v  t+ ++Ntg ++  ++++t    ++ +y  ++s +      + +vg ++ag++ + ++tv+v + a+ g
  gi|70606953|ref|YP_255823.1| 609 TVSPGEtQVPLTILLKNTGDVNVLNATLTF---SNSEYpLKFSQT------NAQVGIIPAGQENYATVTVSVYPNATPG 678
                                   78999988999***********98888875...333321333333......3334567888888888888887777655 PP

  == domain 7  score: -4.0 bits;  conditional E-value: 6
                         DUF11  17 tytltvtN 24 
                                   t++ tvt 
  gi|70606953|ref|YP_255823.1| 786 TVNFTVTF 793
                                   44444443 PP

  == domain 8  score: 17.7 bits;  conditional E-value: 1.1e-06
                         DUF11   6 dksevrpGd.tvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsv....gsLeagesatlsftvrvtrt 81 
                                   + s+++pGd +v  t+t++Ntg+a+a++v v+ +  + + y  vs+s +  +alt +    g++++ ++a ++f v  +  
  gi|70606953|ref|YP_255823.1| 818 KYSTINPGDsNVPITITLKNTGNATAKNVIVR-LGTSDVIYPHVSSS-NPLQALTASevfvGDINPQQTANVTFVVDISGG 896
                                   55689****99******************998.34455666666666.333333333356699999999999999877665 PP

>> DUF5044  Domain of unknown function (DUF5044)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.14   4.1e+02      59      93 ..     152     188 ..     143     251 .. 0.80
   2 ?   -2.7   0.0       1.5   4.4e+03      66     150 ..     273     359 ..     252     371 .. 0.55
   3 ?    0.9   0.1      0.12   3.6e+02      58      87 ..     375     406 ..     362     419 .. 0.73
   4 ?   -0.7   0.0      0.38   1.1e+03      59      86 ..     489     517 ..     481     594 .. 0.76
   5 ?   -0.9   0.0      0.42   1.2e+03      59      85 ..     600     628 ..     588     642 .. 0.72
   6 !    8.8   0.0   0.00044       1.3      47      96 ..     801     851 ..     790     897 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.14
                       DUF5044  59 fW.eparlvaveP.ddelPltllaedaggaspklvvv 93 
                                    W  p+ +++v P + + Plt+++++ g a  + v +
  gi|70606953|ref|YP_255823.1| 152 VWgTPSNPTVVGPgQTNTPLTIILQNLGNALVTNVTL 188
                                   461459999999944689*****99998887666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                       DUF5044  66 vavePddelPltllaedaggas..pklvvvssdpdivtveldyvaksaeiessdvqqletarrealedslfflplsdafds 144
                                    a+  +  lPlt+ +e+ g          + s   i  ++ ++  ++    + ++  +  +        ++++p++ ++  
  gi|70606953|ref|YP_255823.1| 273 LAAAGSSFLPLTIYVENLGENLlsNVTLTLKSHYPIQFLQNNATIGFVPAGQYNYATVIASVDRNATPGVYYIPVTVSMYN 353
                                   456667789999998888654310222334555556556666666666666666655555554444445666665555555 PP

                       DUF5044 145 vsvedp 150
                                      e++
  gi|70606953|ref|YP_255823.1| 354 GYKETV 359
                                   555555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.12
                       DUF5044  58 lfWep.arlvaveP.ddelPltllaedaggas 87 
                                     W   + +++v P + + Plt+++++ g+a 
  gi|70606953|ref|YP_255823.1| 375 SVWGTpSNPTVVGPgQTNTPLTIILQNIGTAT 406
                                   456444999****944699*****99987664 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.38
                       DUF5044  59 fWeparlvaveP.ddelPltllaedagga 86 
                                      p+ +  v P ++++Plt+++e+ g  
  gi|70606953|ref|YP_255823.1| 489 WGSPSNPILVAPgENNIPLTVVVENLGEN 517
                                   44567777777735789****99988654 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.42
                       DUF5044  59 fWep.arlvaveP.ddelPltllaedagg 85 
                                    W     +  v P + ++Plt+l++++g 
  gi|70606953|ref|YP_255823.1| 600 LWGSiNSPITVSPgETQVPLTILLKNTGD 628
                                   455546666777735689*****999975 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.00044
                       DUF5044  47 wyalftleraglfWeparlvaveP.ddelPltllaedaggaspklvvvssd 96 
                                   +yal    +a++   ++++  ++P d ++P+t+ ++++g a +k v+v   
  gi|70606953|ref|YP_255823.1| 801 QYALNVYPKANIIITNVKYSTINPgDSNVPITITLKNTGNATAKNVIVRLG 851
                                   7999999999999999******996679************99999998644 PP

>> Gryzun  Gryzun, putative trafficking through Golgi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         1   3.1e+03     114     144 ..     163     192 ..     160     200 .. 0.83
   2 ?   -2.6   0.0      0.59   1.8e+03     114     144 ..     387     416 ..     383     420 .. 0.86
   3 ?   10.6   0.0   5.9e-05      0.18     105     156 ..     600     652 ..     593     663 .. 0.84
   4 ?   -3.1   0.0      0.83   2.5e+03     264     323 ..     874     933 ..     821     933 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                        Gryzun 114 kpgqtkvfelaiilreaGeakvasvtlsvee 144
                                    pgqt+   l+iil++ G+a v++vtl++++
  gi|70606953|ref|YP_255823.1| 163 GPGQTNT-PLTIILQNLGNALVTNVTLEFSS 192
                                   6777774.799***************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.59
                        Gryzun 114 kpgqtkvfelaiilreaGeakvasvtlsvee 144
                                    pgqt+   l+iil++ G a+v+++tl++e+
  gi|70606953|ref|YP_255823.1| 387 GPGQTNT-PLTIILQNIGTATVTNATLQLES 416
                                   6788775.79*****************9986 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 5.9e-05
                        Gryzun 105 lkgsad..LtlkpgqtkvfelaiilreaGeakvasvtlsveeekFdLeytisek 156
                                   l gs +  +t++pg+t+v  l+i l++ G+++v ++tl+++++++ L+ + ++ 
  gi|70606953|ref|YP_255823.1| 600 LWGSINspITVSPGETQV-PLTILLKNTGDVNVLNATLTFSNSEYPLKFSQTNA 652
                                   5554443389*******9.7***************************9987765 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 0.83
                        Gryzun 264 lpklgkless..astelsivltetedpleyeleikasYhlvsdletpiiktlsvklslvnpF 323
                                   +  +g ++ +  a++++ + ++  ++p  y l+i a+++  + +  p  ++ ++ +s+ +pF
  gi|70606953|ref|YP_255823.1| 874 V-FVGDINPQqtANVTFVVDISGGASPGVYPLAIAATWNQ-TGAIFPFEQSDTFYVSISQPF 933
                                   2.46777544004455566677777888888888887774.344456666666666666665 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.8    0.0029       8.7     277     307 ..     939     967 .]     930     967 .] 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                         RIFIN 277 qtaiiasivaivvIvLimvIIYLiLRYrRKk 307
                                   ++++i+ i+ai+++++i+v+  ++ R+rRKk
  gi|70606953|ref|YP_255823.1| 939 SSPLIYVIIAIIIVIIIIVV--VLSRFRRKK 967
                                   56677777777655554444..355****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (967 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 6102.92
//
Query:       gi|70606954|ref|YP_255824.1|  [L=654]
Description: acetyl-coenzyme A synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-83  279.6   0.0    4.4e-83  279.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.1e-21   77.6   0.2    2.2e-21   76.6   0.2    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.7e-18   65.2   1.6    7.3e-18   64.2   1.6    1.5  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.2   0.0   7.3e-87   4.4e-83       9     422 ..      88     525 ..      80     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 279.2 bits;  conditional E-value: 7.3e-87
                                   TTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHH CS
                   AMP-binding   9 pdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeel 86 
                                   + k a+++   ++e + lTY++l+ +vnr A++Lr++Gv+kgdrV i++p +pe v+++la+ ++Ga++ ++ ++++ ++l
  gi|70606954|ref|YP_255824.1|  88 KFKAAIIWesgKHERRVLTYQDLYYEVNRWANALREIGVRKGDRVTIYMPLTPEGVISMLAVTRLGAIHNVVFAGFGVQAL 168
                                   557888889999999****************************************************************** PP

                                   HHHHHHHTESEEE.......E..TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS....-TSCC CS
                   AMP-binding  87 ayiledseakvli.......a..tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae....kpeee 153
                                   a  ++d+++kv+i       +   v+ ++ ++++ +  +k   v++vi++++ +++    ++++ + + + e    kp ++
  gi|70606954|ref|YP_255824.1| 169 ADRISDAGSKVVItadayyrRgkLVELKKaVDESIRLLGKNSPVEKVIIYKRTGSEIP--FDDKRDVYFE-EiakyKPIDP 246
                                   **************99988725677788889999999999999999999997765433..3222222222.1344578899 PP

                                   CS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE CS
                   AMP-binding 154 eelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilelllallsGatvvl 233
                                   e++++ +++yi+YTSGTTGkPKG+++s++ ++   +s+  l  +   +e+d ++ + ++ +++g+++ ++++l+ G ++v+
  gi|70606954|ref|YP_255824.1| 247 EPVESTHPLYILYTSGTTGKPKGIVHSTAGYLVG-TSIMlLWSYGMSEENDILFNTSDIGWVVGHSYITYAPLVMGRSIVI 326
                                   99**************************777776.444445656444679******************************* PP

                                   -TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...E CS
                   AMP-binding 234 lpkdaald.pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge...e 310
                                   ++  ++ + ++ ++e ie+ +vtv+ +  ++l+ +++ g++   +k++dlsslr+++++gepl+ + +++  +++g+    
  gi|70606954|ref|YP_255824.1| 327 YEDAPDYPyADKWAEIIERNRVTVFGTSATALRSFMKYGDEV--VKKHDLSSLRVIVTAGEPLNYAPWKWGLEVVGNgrvY 405
                                   ***99955599**************************75554..6789******************************999 PP

                                   EEEEEEEGGGSSEC..EE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET...TS-SEBTT-H. CS
                   AMP-binding 311 vlegYGlTEttgvv..tv...lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp...gvmkgYlkkp. 382
                                   +++ +++TEt+     ++   ++   ++k+ +++G+plpg++++i+De+ g+  ++ + G l++  p   ++m g +++p 
  gi|70606954|ref|YP_255824.1| 406 MSHQWWQTETGSPNlgYMpglIY--LPMKSGPTCGFPLPGNKIEILDES-GNTTKPRNRGYLVMLPPyppSMMIGMWNDPg 483
                                   99********9998552276533..3344789****************9.99999*********9886678********87 PP

                                   .HHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 383 .eataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                    e+ +++++s+ ++ + +GD + +de+Gy++++gR++++ik+
  gi|70606954|ref|YP_255824.1| 484 nERLKKSYFSKfPGIYYSGDYAMIDEEGYIWVMGRADETIKV 525
                                   78888998876778***************************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.2   3.7e-25   2.2e-21       1      76 []     534     611 ..     534     611 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 3.7e-25
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evEs+ +shpaVaeaa++G pd+vkGe +  fVvlk+g  + +  l+ e++a++r ++g++ +p +++fv++lpktrsGK
  gi|70606954|ref|YP_255824.1| 534 EVESITTSHPAVAEAAAIGLPDPVKGENIHIFVVLKTGhvP-SqeLATEIQAYMRGHMGAIVTP-EIHFVEKLPKTRSGK 611
                                   8***********************************99642.235****************766.8*************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   1.6   1.2e-21   7.3e-18       1      55 []      23      78 ..      23      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.2e-21
                                  HHHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                        ACAS_N  1 ykelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                  yk++yk+Sie+p +FW+++a+  +dW++p++k++ +++g  +kWF+ GklN++yN+
  gi|70606954|ref|YP_255824.1| 23 YKNIYKQSIEEPSKFWDRIAESlIDWFEPWKKTFVQEEGLLTKWFVEGKLNASYNA 78
                                  999******************99*************9999***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4234.11
//
Query:       gi|70606955|ref|YP_255825.1|  [L=343]
Description: hypothetical protein Saci_1185 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   13.2  55.6      0.012   14.6  17.2    3.5  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  17.2   6.6e-07     0.012     212     345 ..       7     126 ..       1     133 [. 0.80
   2 ?    0.0  31.9     0.017   3.1e+02     132     324 ..     131     294 ..     120     329 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-07
                         MFS_1 212 llialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgla 292
                                   l ++++++++++++++ ++ +y  +++  +   l+ l++ ++ l+g+++all++++s+ lg +r+++l+++l  ++++ +a
  gi|70606955|ref|YP_255825.1|   7 LSTSWFIWGIAYYLYYPYTSIY-ASTFIKD--RLIPLIYIIYTLIGIPSALLSAKISKLLGLKRAIILFMALSGVGLMVVA 84 
                                   778999****************.8888888..788888******************************************* PP

                         MFS_1 293 llavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntag 345
                                   +++          +++++Gf+++  +++l+al + ++   ++    g+++ ++
  gi|70606955|ref|YP_255825.1|  85 IAPSL--------PVLILGFTMSS-SSLLIALPNYYY--YMNNLGKGVISKVW 126
                                   *****........88888887775.455555555555..44445555555555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.017
                         MFS_1 132 lGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwil 212
                                   l ai++p++gg++a++lg r+vf+ +++++ l+++    +l  e+ +++ +                 ++  +k +     
  gi|70606955|ref|YP_255825.1| 131 LPAIFTPVIGGAIAQLLGIRYVFLTAGLFMTLSGL---PVLGLEYDKESIV----------------FYENTRKLN----P 188
                                   44699*****************************9...4444444444444................233334455....6 PP

                         MFS_1 213 lialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                                   l +l+++ + +++ +++l +  ++ ++ls ++ +g+l  ++ ++g+++ +++++  ++     +++l+l++l+ ++++  l
  gi|70606955|ref|YP_255825.1| 189 LPGLVIIPISLASPFVFLIT--KDLYNLS-YVAVGVLATMSEVIGMVV-VFLSAGRNK---LLPIYLMLFSLVYLVFFNPL 262
                                   77888886666667777777..9999999.999998899999998666.333333466...44455555555555555555 PP

                         MFS_1 294 lavtssavllllvlvliGf.glgfvfpsllal 324
                                   ++++   + +l++l++  + g+++   s +  
  gi|70606955|ref|YP_255825.1| 263 FSLAFGLWEVLIPLAIEEVnGSSISAYSRMIS 294
                                   55555567777788886666666554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2218.95
//
Query:       gi|70606956|ref|YP_255826.1|  [L=94]
Description: MarR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-07   30.9   0.2    3.4e-07   30.1   0.2    1.3  1  MarR            MarR family
    2.8e-06   27.4   0.2    3.4e-06   27.1   0.2    1.1  1  HTH_34          Winged helix DNA-binding domain
    8.6e-06   26.2   0.2    1.3e-05   25.6   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
      1e-05   25.0   2.7    1.8e-05   24.2   2.7    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-05   24.0   0.3    4.9e-05   23.1   0.3    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    3.9e-05   23.5   0.2    7.3e-05   22.7   0.1    1.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.6e-05   23.0   0.0    7.8e-05   22.5   0.0    1.2  1  MarR_2          MarR family
    0.00061   19.6   0.4     0.0011   18.8   0.1    1.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0025   17.4   0.6       0.01   15.5   0.6    2.0  1  Crp             Bacterial regulatory proteins, crp family
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.016   15.5   0.1    1.3  1  Rrf2            Transcriptional regulator
      0.022   14.5   0.1      0.033   14.0   0.1    1.3  1  LexA_DNA_bind   LexA DNA binding domain
      0.026   14.2   0.3      0.044   13.4   0.2    1.5  2  GntR            Bacterial regulatory proteins, gntR family
      0.028   14.4   0.5      0.052   13.5   0.5    1.5  1  HTH_12          Ribonuclease R winged-helix domain
       0.03   14.3   0.6      0.047   13.6   0.6    1.4  1  HTH_11          HTH domain
      0.038   13.7   0.3      0.097   12.4   0.2    1.7  2  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.11   12.6   0.1       0.16   12.0   0.1    1.2  1  HTH_20          Helix-turn-helix domain
       0.11   11.5   0.0       0.11   11.5   0.0    1.0  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
       0.11   12.5   0.2       0.16   11.9   0.2    1.3  1  HTH_36          Helix-turn-helix domain
       0.16   11.8   0.6       0.23   11.3   0.6    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2   3.6e-10   3.4e-07       5      47 ..       5      47 ..       2      48 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.6e-10
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                  ++ iL++l++q++ls+ e+++ lgv +  ++r l++LekkGli
  gi|70606956|ref|YP_255826.1|  5 ELAILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  789***************************************9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.2   3.6e-09   3.4e-06       1      77 [.       4      78 ..       4      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3.6e-09
                        HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLk 77
                                  ++la+l++L++++e + +e+ + l++ + +Ls  lk Lek+g i  +k++ g+    ++ iT+eG ++  k    L+
  gi|70606956|ref|YP_255826.1|  4 LELAILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLIF-TKALIGN-GDMIIGITEEGVKELYKNYIVLR 78
                                  589***************************************885.5666666.58899******988766655555 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   1.4e-08   1.3e-05       5      68 .]       5      66 ..       3      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-08
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  + ++L l+   +++ +++++  +l v  +  s slk+L++kGL+ +++     +++ + +T++G
  gi|70606956|ref|YP_255826.1|  5 ELAILTLLS-DQEELSIREIGNYLGVRNIRLSRSLKELEKKGLIFTKAL-IGNGDMIIGITEEG 66
                                  668999999.9*********************************99988.79999999999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   2.7   1.9e-08   1.8e-05       1      47 [.       1      47 [.       1      47 [. 0.99

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.9e-08
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +d+++++IL lL ++  +s+re+   lg+    ++r lk+Le++GlI
  gi|70606956|ref|YP_255826.1|  1 MDILELAILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  799*******************************************9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   5.2e-08   4.9e-05       5      45 ..       6      47 ..       5      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.2e-08
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  l IL lL++ +el++ e+ ++lg+    +S+ Lk L++ GL+
  gi|70606956|ref|YP_255826.1|  6 LAILTLLSDqEELSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  67*******666*****************************8 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   7.8e-08   7.3e-05      21      52 ..      17      48 ..       4      65 .. 0.86
   2 ?   -2.0   0.0       3.9   3.7e+03      48      62 ..      65      80 ..      61      82 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.8e-08
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                   l+ +e++++lG++   +sr l+eL+++gli 
  gi|70606956|ref|YP_255826.1| 17 ELSIREIGNYLGVRNIRLSRSLKELEKKGLIF 48
                                  47889*************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                                  TTSEE..ETEEEEES-H CS
                     HTH_Crp_2 48 eglis..rgrririldl 62
                                  eg+ +  +++ i+++dl
  gi|70606956|ref|YP_255826.1| 65 EGVKElyKNY-IVLRDL 80
                                  6666642344.888886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   8.2e-08   7.8e-05       6      54 ..       4      50 ..       1      56 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.2e-08
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   ++ +L  L + ++  l+++e+  +lg+   ++sr lk+L+++GL+ ++
  gi|70606956|ref|YP_255826.1|  4 LELAILTLLSDQEE--LSIREIGNYLGVRNIRLSRSLKELEKKGLIFTK 50
                                  57889999999*99..******************************775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-06    0.0011      15      53 ..       9      48 ..       4      54 .. 0.90
   2 ?   -2.3   0.0       4.4   4.2e+03      40      47 ..      74      81 ..      60      83 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                  HHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB 15 laLl.klgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  l+Ll  +++++++ei + lgv   +  ++L++Le+kGl+ 
  gi|70606956|ref|YP_255826.1|  9 LTLLsDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLIF 48
                                  4677699*******************************96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.4
                                  HHHHHHHH CS
                          TrmB 40 YevLrsLe 47
                                  Y vLr L+
  gi|70606956|ref|YP_255826.1| 74 YIVLRDLV 81
                                  55666665 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   1.1e-05      0.01       3      32 .]      18      47 ..      17      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                  --HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           Crp  3 mSRqdIAdylGlTrETVSRlLtrLrekGLI 32
                                  +S  +I++ylG      SR L+ L++kGLI
  gi|70606956|ref|YP_255826.1| 18 LSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  56679************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   1.7e-05     0.016      14      57 ..       6      49 ..       3      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                                  HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  l++L++ +++e +s++ei +  ++    l++ l++L+k+gl+ +
  gi|70606956|ref|YP_255826.1|  6 LAILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLIFT 49
                                  566777777778*****************************965 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.5e-05     0.033      27      56 ..      19      47 ..       2      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyi 56
                                  sirei++ lg++        Lk Le+KG+i
  gi|70606956|ref|YP_255826.1| 19 SIREIGNYLGVR-NIRLSRSLKELEKKGLI 47
                                  9***********.7789999********99 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.7e-05     0.044      18      57 ..      12      50 ..       2      54 .. 0.87
   2 ?   -3.3   0.0       7.6   7.2e+03      28      32 ..      78      82 ..      68      87 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                                  S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                  l+  + L s re+   +gV    + ++L++Le +gl+  +
  gi|70606956|ref|YP_255826.1| 12 LSDQEEL-SIREIGNYLGVRNIRLSRSLKELEKKGLIFTK 50
                                  5566889.****************************9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                                  HHHHH CS
                          GntR 28 reLaa 32
                                  r+L++
  gi|70606956|ref|YP_255826.1| 78 RDLVK 82
                                  33333 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.6e-05     0.052      21      66 .]      18      70 ..       3      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                        HTH_12 21 eeLkkrgydigeravR..yrLrkleerg..ltrrvgyagre...ltEkGleeL 66
                                   +++++g  +g r +R  + L+ le++g  +t+    +g     +tE G++eL
  gi|70606956|ref|YP_255826.1| 18 LSIREIGNYLGVRNIRlsRSLKELEKKGliFTKALIGNGDMiigITEEGVKEL 70
                                  46778899999999997789********8888887777654233799999997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6     5e-05     0.047       3      44 ..       6      46 ..       4      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  l+il+lL + ++ +s+ e+  +L+v      r +k+Le++g+
  gi|70606956|ref|YP_255826.1|  6 LAILTLL-SDQEELSIREIGNYLGVRNIRLSRSLKELEKKGL 46
                                  6899999.66666************99999999999999994 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2    0.0001     0.097       4      44 ..       7      47 ..       5      53 .. 0.92
   2 ?   -2.0   0.0       3.4   3.2e+03      15      27 ..      75      87 ..      70      90 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                      HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                  +il ll +q  ls+ e+ ++lgv      R L+eLe++gl+
  gi|70606956|ref|YP_255826.1|  7 AILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  69*********************998888**********96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                      HTH_DeoR 15 lsveelvellgvS 27
                                  + + +lv + ++S
  gi|70606956|ref|YP_255826.1| 75 IVLRDLVKEMEYS 87
                                  5566677766666 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00017      0.16      13      54 ..       6      47 ..       4      49 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                  ++il +L++ e+l+  e+   l+++   ls+ L++Le+ gL+
  gi|70606956|ref|YP_255826.1|  6 LAILTLLSDQEELSIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  689*************************************98 PP

>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.11     139     185 ..      34      80 ..       8      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                   -SS-GGGS-TTSB--SS-EEETT-EEE---..B-----...------ CS
                RNA_pol_Rpb2_6 139 seealkkLdedGivrvgaevkegdilvgkvtkgeteltpeekllrai 185
                                    +++lk+L+++G++  +a + +gd+++g + +g +el ++  +lr  
  gi|70606956|ref|YP_255826.1|  34 LSRSLKELEKKGLIFTKALIGNGDMIIGITEEGVKELYKNYIVLRDL 80 
                                   56899***********************9768877777666666655 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00017      0.16      11      55 .]       6      47 ..       1      47 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                        HTH_36 11 lgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  l +l+ ++++++    s + + + lg+     sr +keLe++G+i
  gi|70606956|ref|YP_255826.1|  6 LAILTLLSDQEEL---SIREIGNYLGVRNIRLSRSLKELEKKGLI 47
                                  6678888888888...999999999999999************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00024      0.23       1      30 [.       1      30 [.       1      42 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlS 30
                                  +D + ++IL +L  +  +s +e++  +G+ 
  gi|70606956|ref|YP_255826.1|  1 MDILELAILTLLSDQEELSIREIGNYLGVR 30
                                  899999******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 671.53
//
Query:       gi|70606957|ref|YP_255827.1|  [L=311]
Description: inosine-uridine preferring nucleoside hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-74  250.4   0.0    3.2e-74  250.2   0.0    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.2   0.0   1.8e-78   3.2e-74       1     305 []       3     302 ..       3     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: 250.2 bits;  conditional E-value: 1.8e-78
                                   EEEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S-SHHH CS
                  IU_nuc_hydro   1 rkvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.kaaaei 80 
                                   r++i+D+D+  DD++ l ++l++  ++ + g+t+v Gn s +q ++nal  l +++g+++++vy+G++kpl+++ +  +e+
  gi|70606957|ref|YP_255827.1|   3 RHFIIDCDTAEDDIMSLFMLLRH--KVSVEGVTIVEGNISYQQEVNNALWAL-EYIGEENVKVYPGSDKPLVKDfRSVEEV 80 
                                   589**************999986..59*************************.5555777**************888888* PP

                                   HTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE---SSS--S CS
                  IU_nuc_hydro  81 hGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGGaftarGN 161
                                   hG+ G+gd+  ++++ k+e+++a+da++d++    +ypge+ ++a+ plTN+Ala+ +d+ l++k++++++MGG+  +rGN
  gi|70606957|ref|YP_255827.1|  81 HGKGGIGDKIAKPQKLKPENKKALDAIVDIA---DRYPGELEILAISPLTNLALAYLKDKTLTEKIRKVWVMGGTAWGRGN 158
                                   *******98766668899*******999999...999999***************************************** PP

                                   SSSSS-HHHHHSHHHHHHHHHT.S-E.EEEE-HHHHTTSC.HEECHHHHHHHHCSTCBHHHHHHHHHHHHHHHHHHHHHSS CS
                  IU_nuc_hydro 162 vtpvaEfNifvDPeAAkiVles.apvkitlvpldvthkvq.alltseeveelaalekglgafladllefyikaykeaegsd 240
                                   +tpvaE+Ni+vDP+AAkiV+++  +  it+vp+dv  +    + ++ee+++++   +++++f+ d+ ++y ++  ++e++ 
  gi|70606957|ref|YP_255827.1| 159 ITPVAEYNIWVDPDAAKIVFNAgFD--ITMVPWDVIVNYPvDNREWEEIKNMN---TKMSKFYVDIYTHYREYSMKNEKIG 234
                                   ********************87655..5********96663244446666643...4566699*********9999999** PP

                                   EEE-HHHHHHHHHH.-GGGEEE.EEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEEE-HHHHHH CS
                  IU_nuc_hydro 241 gaplhDplavaval.dpelvtt.krlavdveleggltrGrtvvdlrrl.kkaknvkvatevdverfle 305
                                   g+p  D ++++val ++++v++  +  vdve  + ltrG++v+d+ +  kk++n++v+ e+++e+fl+
  gi|70606957|ref|YP_255827.1| 235 GTPHPDLITTVVALnHENVVKRsDKHFVDVENCDCLTRGMVVIDYLSIwKKNPNTEVIYEIHKEEFLK 302
                                   **************4567777767888****************99999*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2059.53
//
Query:       gi|70606958|ref|YP_255828.1|  [L=453]
Description: alkyl-dihydroxyacetonephosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-37  128.6   0.0      2e-37  128.0   0.0    1.3  1  FAD_binding_4  FAD binding domain
    6.3e-25   88.2   0.0    8.8e-25   87.8   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
  ------ inclusion threshold ------
       0.05   13.3   0.1       0.14   11.9   0.1    1.6  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.0   3.3e-41     2e-37       1     138 [.      44     179 ..      44     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 3.3e-41
                                   EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                 FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                   p+av++p+s+ee+ ++++lan ++++v++++gGss++g+a+++++++ldls+ln++le++e++ t+tveaG++++dl+  l
  gi|70606958|ref|YP_255828.1|  44 PSAVIKPKSVEEITEVIKLANNYNACVVPYAGGSSVVGGAYHNSCTILDLSELNKVLELNEDDLTVTVEAGIKIKDLEDKL 124
                                   799****************************************************************************** PP

                                   HHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                 FAD_binding_4  82 aakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                   + kg++l  +p+s+  +t+GGaia  ++G++s+    i++ +l+ evvl++Ge+vr+
  gi|70606958|ref|YP_255828.1| 125 NSKGYTLDYHPQSFFLATIGGAIAHKGSGSHSSSN--IEELLLWIEVVLPNGEIVRI 179
                                   ***************************99777777..******************97 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   1.5e-28   8.8e-25       9     250 .]     225     451 ..     219     451 .. 0.86

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.5e-28
                                   EEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHHHHHTTT CS
                 FAD-oxidase_C   9 lvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelealveaile 89 
                                   ++ f+s+++a+k++ e + +  +p ++ + d+++ + ++++  +          + lv ++g d+e ++ e + l+ +i+ 
  gi|70606958|ref|YP_255828.1| 225 AFYFNSIDDAIKFAKEYTIRLPPPYRVVIHDSESANYMLGLPYF----------ISLVRVRGYDQELVDVEER-LIKSIAL 294
                                   56799999999999999999999999999999999999999999..........9*********777777777.9999999 PP

                                   -EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH...EEEEEEEEEE CS
                 FAD-oxidase_C  90 atgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyg...levvlfgHag 167
                                   + g+++     d+++++++ ++  + ++     l ++g + ++ D +  +s ++++++++++ l   +    + ++f+H +
  gi|70606958|ref|YP_255828.1| 295 KYGGKE----GDKETVRKWRDVFARNYEANFLSLVQSGYWTDTLDLAGSWSIIPKIYKELRENLYLINgvkSVLSRFTHLY 371
                                   999999....44444443333333333322334689**************************87766666699******** PP

                                   TTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT--BSTT CS
                 FAD-oxidase_C 168 dgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPkgiLNPg 248
                                    ++ +ly+++ l+  ++ e + k+++  ++++++ gGs s++HGvG+ kk+++ rek e+++ l++  K  lD kgi+NPg
  gi|70606958|ref|YP_255828.1| 372 INGTCLYVMVILR--QDPEVLLKVWETAAEVVIKWGGSTSHHHGVGFLKKPWILREK-EDEVRLYKMFKLSLDSKGIMNPG 449
                                   **********998..9999999**********************************9.66********************* PP

                                   -- CS
                 FAD-oxidase_C 249 kv 250
                                   k+
  gi|70606958|ref|YP_255828.1| 450 KL 451
                                   96 PP

>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.4e-05      0.14       4     114 ..      46     149 ..      43     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                   EEEE-SSHHHHHHHHHH..CTTSEEE..SS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHH CS
                 FAD_binding_5   4 eylrpasleealallaa..epdaklv..aGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaae 80 
                                   ++++p+s+ee++++++   + +a +v  aGg +++    ++     +++d+++++++ e++e++  +++ A++++++l  e
  gi|70606958|ref|YP_255828.1|  46 AVIKPKSVEEITEVIKLanNYNACVVpyAGGSSVVGGAYHNSC---TILDLSELNKVLELNEDDLTVTVEAGIKIKDL--E 121
                                   5789******9999876666666666559**999999999985...677888888888889*****************..5 PP

                                   HHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHH CS
                 FAD_binding_5  81 alvrerypalsealekiAspqiRnvaTiGGNlat 114
                                   + ++++  +l+++ + +       +aTiGG +a+
  gi|70606958|ref|YP_255828.1| 122 DKLNSKGYTLDYHPQSF------FLATIGGAIAH 149
                                   66665555555543333......46666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2839.46
//
Query:       gi|70606959|ref|YP_255829.1|  [L=286]
Description: hypothetical protein Saci_1189 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-07   30.2   0.0      6e-07   29.3   0.0    1.4  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   3.3e-11     6e-07       8     134 ..       4     120 ..       2     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.3e-11
                                   SSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTEC CS
                 FAD_binding_4   8 eseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvealaakglll 88 
                                   +seee+ +++r a   + ++ v+G G +   ++v ++   + ++++n   ei+  +g +++ aG+ + ++ ++++++glll
  gi|70606959|ref|YP_255829.1|   4 HSEEELFRIIRSAYLDNKKIQVLGYGRHGRISKV-DEY--VYTKNMNW-YEIK--DGKVQALAGADVTKIRKEASENGLLL 78 
                                   699*********************9988775554.333..34545998.7888..8************************* PP

                                   SSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSE CS
                 FAD_binding_4  89 glepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGe 134
                                   +    ++ +gt+GG++a n +++  + yG  +d+ l+ +++++ G 
  gi|70606959|ref|YP_255829.1|  79 P----TLYDGTIGGLLAINPISPLTTSYGRPSDFTLWTRFLTPYGG 120
                                   *....899**********************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1985.93
//
Query:       gi|70606960|ref|YP_255830.1|  [L=157]
Description: phosphoribosylaminoimidazole carboxylase catalytic subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-67  226.2   0.6    1.2e-67  226.1   0.6    1.0  1  AIRC          AIR carboxylase
    0.00075   19.3   0.0    0.00091   19.0   0.0    1.2  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
     0.0053   15.6   0.2     0.0088   14.9   0.1    1.3  2  Fe-ADH        Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.012   15.8   0.1      0.039   14.2   0.0    1.8  2  Glutaredoxin  Glutaredoxin
      0.013   15.1   0.0        0.1   12.2   0.0    1.9  2  DAGK_cat      Diacylglycerol kinase catalytic domain
       0.05   13.0   0.0      0.074   12.5   0.0    1.3  1  DUF4419       Domain of unknown function (DUF4419)
        0.2   12.0   0.0        5.3    7.4   0.0    2.2  2  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.1   0.6   4.8e-71   1.2e-67       1     147 [.       3     149 ..       3     150 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.1 bits;  conditional E-value: 4.8e-71
                                   EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EE CS
                          AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVi 81 
                                   kV++imGS+ D+e mk+a++ilke+gve+evrvvSahrtpe ++e+a++a+++g++viIagAGgaahLpg++aslt+lPVi
  gi|70606960|ref|YP_255830.1|   3 KVAVIMGSKNDWEYMKDAVDILKEFGVEVEVRVVSAHRTPEFMMEFAKTASQKGIEVIIAGAGGAAHLPGMTASLTHLPVI 83 
                                   69******************************************************************************* PP

                                   EEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                          AIRC  82 gvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                   gvPv sk+l+gldsllSivqmP gvpvatvaig++knAallA++il++k++e+ae++++++e++k+
  gi|70606960|ref|YP_255830.1|  84 GVPVPSKNLNGLDSLLSIVQMPYGVPVATVAIGNSKNAALLALRILGIKYSEIAERIKKFMEDMKS 149
                                   *************************************************************99975 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.6e-07   0.00091      21     107 ..       3      87 ..       1     114 [. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.6e-07
                      Fe-ADH_2  21 kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvp 101
                                   kv+++++++    + ++  + lke g++vev+  v+++++ e +++ ++ +++k++++++a G+G +  +  + ++ +++p
  gi|70606960|ref|YP_255830.1|   3 KVAVIMGSKNDWEYMKDAVDILKEFGVEVEVRV-VSAHRTPEFMMEFAKTASQKGIEVIIA-GAGGAAHLPGMTASLTHLP 81 
                                   7899999999999999999***********876.999***********************9.88888889999999***** PP

                      Fe-ADH_2 102 yvsvpT 107
                                   ++ vp 
  gi|70606960|ref|YP_255830.1|  82 VIGVPV 87 
                                   **9995 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.4e-06    0.0088      26      92 ..       4      67 ..       1      69 [. 0.84
   2 ?   -3.3   0.0       1.2     3e+03     308     321 ..     132     145 ..      99     150 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-06
                                  EEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHH CS
                        Fe-ADH 26 alivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGs 92
                                  + ++ +++  ++ ++++++++ l+e g+ev+v   v+ + t e ++e a+ a ++g++v+ia  GG 
  gi|70606960|ref|YP_255830.1|  4 VAVIMGSK--NDWEYMKDAVDILKEFGVEVEV-RVVSAHRTPEFMMEFAKTASQKGIEVIIAGAGGA 67
                                  44555444..34589****************6.789*************************976665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                                   --HHHHHHHHHHHH CS
                        Fe-ADH 308 aaeeliealrellk 321
                                   +  e++e+++++++
  gi|70606960|ref|YP_255830.1| 132 KYSEIAERIKKFME 145
                                   33344444444444 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.039       5      45 ..      10      52 ..       6      60 .. 0.79
   2 ?   -1.6   0.0       1.3   3.3e+03      19      29 ..     126     136 ..     120     151 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                  ESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH..HHHHHHHHHH CS
                  Glutaredoxin  5 tkptCpyCkkakrlLkelgvkfeeidvdkde..eireelkels 45
                                  +k+  +y k a+++Lke+gv++e++ v+++   e+  e  + +
  gi|70606960|ref|YP_255830.1| 10 SKNDWEYMKDAVDILKEFGVEVEVRVVSAHRtpEFMMEFAKTA 52
                                  6677778899*******************95557777766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                   HHHTTGGEEEE CS
                  Glutaredoxin  19 Lkelgvkfeei 29 
                                   L+ lg+k+ ei
  gi|70606960|ref|YP_255830.1| 126 LRILGIKYSEI 136
                                   55566666554 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     4e-05       0.1      11      64 ..       9      65 ..       6      83 .. 0.90
   2 ?    0.9   0.0      0.13   3.3e+02      77     113 ..     100     140 ..      89     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4e-05
                                  TTTTHHHHHHHCHHHHHHCTCEEEEEE--...STTHHHHHHHHHHHCC-SEEEEEES CS
                      DAGK_cat 11 Gkgkgekllrkvrelleeagveleliete...epgdakelakeakeegvdlivvaGG 64
                                  G+++ +++++ + ++l+e gve+e++ ++    p+   e+ak+a+++g+++i++  G
  gi|70606960|ref|YP_255830.1|  9 GSKNDWEYMKDAVDILKEFGVEVEVRVVSahrTPEFMMEFAKTASQKGIEVIIAGAG 65
                                  788999999**************99999865567779999**********9999766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                   T..HHCTTSEEEEEE-S.S--HHHHHCT--S.SHHHHHHCH CS
                      DAGK_cat  77 e..elatkpplgiiPlG.tgNdlaralgigk.dieealesi 113
                                      +    +p++++  G + N+   al+i + +  e +e+i
  gi|70606960|ref|YP_255830.1| 100 SivQMPYGVPVATVAIGnSKNAALLALRILGiKYSEIAERI 140
                                   25556778999999999888888888866555555555444 PP

>> DUF4419  Domain of unknown function (DUF4419)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05     0.074     129     158 ..       2      32 ..       1      58 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                       DUF4419 129 Psvt.LlGekeDWekllerlekLkefgeelk 158
                                   P+v  + G+k+DWe +++ ++ Lkefg e++
  gi|70606960|ref|YP_255830.1|   2 PKVAvIMGSKNDWEYMKDAVDILKEFGVEVE 32 
                                   6664279*******************86654 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0021       5.3     115     150 ..       3      36 ..       2      39 .. 0.87
   2 ?    3.9   0.0     0.024        62      24      67 ..      35      77 ..      32     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0021
                                   HHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 115 ekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                   + v  +m+ ++++e  ++a+++l+e g++ v +r+v
  gi|70606960|ref|YP_255830.1|   3 K-VAVIMGSKNDWEYMKDAVDILKEFGVE-VEVRVV 36 
                                   4.77899999******************9.777765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                                  HHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 24 grgrslsveeileevkelkaekgvkevilgggepllypdfvell 67
                                  ++++++++e  +e +k ++  kg++++i g g     p ++  l
  gi|70606960|ref|YP_255830.1| 35 VVSAHRTPEFMMEFAKTAS-QKGIEVIIAGAGGAAHLPGMTASL 77
                                  5677899999999999995.778999999988666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1068.29
//
Query:       gi|70606961|ref|YP_255831.1|  [L=364]
Description: phosphoribosylaminoimidazole carboxylase ATPase subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-48  164.5   0.0    2.4e-48  164.0   0.0    1.2  1  ATP-grasp    ATP-grasp domain
    8.3e-15   54.2   0.1    1.6e-14   53.3   0.1    1.5  1  PurK_C       Phosphoribosylaminoimidazole carboxylase C-termi
     0.0021   18.2   0.0     0.0039   17.3   0.0    1.5  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.077   12.7   0.0    1.4  1  Fungal_KA1   Fungal kinase associated-1 domain


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.0   5.2e-52   2.4e-48       2     171 .]     109     272 ..     108     272 .. 0.96

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 5.2e-52
                                   HTTT--B-EEEEECCHH.HHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEE CS
                     ATP-grasp   2 eklglpvprflaveske.eleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvl 81 
                                   ++++lp+prfl++e+ e +l+ + ee++   v+K++ +gydGkGq++++ + +  + l+   + k++vEefv+f++E s++
  gi|70606961|ref|YP_255831.1| 109 KEHNLPTPRFLVAEDGEeALKILKEEFNGIGVLKESLGGYDGKGQYFIKGDVNKYENLKSK-KVKFVVEEFVNFNYEASII 188
                                   789************99567778899******************************99998.9****************** PP

                                   EEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS--G CS
                     ATP-grasp  82 vvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpHn 162
                                   ++r+++G++++yp++ +++e+gil++++ p      + ++ eeiak+++++L++vG +++E+Fv  dge+l+nE+apR+Hn
  gi|70606961|ref|YP_255831.1| 189 AMRDKNGNFKAYPPTFNYNEKGILVYNYGPL-----HDNRFEEIAKRLADSLNYVGTMGIEFFVR-DGEILINEFAPRVHN 263
                                   ******************************9.....47899***********************9.*************** PP

                                   GGGGHHHHB CS
                     ATP-grasp 163 sGhvtldaa 171
                                   +Gh+tld+a
  gi|70606961|ref|YP_255831.1| 264 TGHYTLDSA 272
                                   ******985 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   3.7e-18   1.6e-14       3      56 .]     300     349 ..     298     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.7e-18
                        PurK_C   3 MvNlLGedaeekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeeleer 56 
                                   MvN+LG+d+   + e+l     ++++YgK ++++ RKmGH++v+g++ ee++++
  gi|70606961|ref|YP_255831.1| 300 MVNILGTDD--VPPEVLR--YGKVYWYGKPDVKKRRKMGHVNVIGKDLEEVKQK 349
                                   *********..7777777..5789***************************986 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.7e-07    0.0039      43     159 ..     149     262 ..     100     264 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-07
                                   -----B--SS--TTE..........EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHH CS
                   ATP-grasp_3  43 ggesvrvveekeeaeaaieeve...lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeev 120
                                   +g++  +++ + ++ + +++++   +v ef++  ++ +s+++   k+  +   +   + +ek  + + n  p +   ++++
  gi|70606961|ref|YP_255831.1| 149 DGKGQYFIKGDVNKYENLKSKKvkfVVEEFVNF-NYEASIIAMRDKNGNFKAYPPTFNYNEK-GILVYNYGPLH---DNRF 224
                                   555555555444444444444444566666653.3334444444444444444444433222.23333445554...899* PP

                                   HHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS-- CS
                   ATP-grasp_3 121 velaeevvekleglaGyvGvDlvlkdeepyviEvNPRlt 159
                                   +e+a+++  +l + +G +G+++ ++d+e+ + E  PR+ 
  gi|70606961|ref|YP_255831.1| 225 EEIAKRLADSL-NYVGTMGIEFFVRDGEILINEFAPRVH 262
                                   ***********.************************985 PP

>> Fungal_KA1  Fungal kinase associated-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05     0.077      52      99 ..     152     199 ..     147     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                    Fungal_KA1  52 esntitgkvsseNilslksvkFeieiisvsehklSlvrftkekGsass 99 
                                    ++ i+g v++   l+ k+vkF +e + + + + S++ ++ + G+ ++
  gi|70606961|ref|YP_255831.1| 152 GQYFIKGDVNKYENLKSKKVKFVVEEFVNFNYEASIIAMRDKNGNFKA 199
                                   5789*********************9999988**********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2627.13
//
Query:       gi|70606962|ref|YP_255832.1|  [L=114]
Description: HTH DNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-05   24.3   0.0    5.2e-05   23.1   0.0    1.5  2  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
  ------ inclusion threshold ------
      0.098   12.7   0.1       0.15   12.1   0.1    1.4  1  DUF2089   Protein of unknown function (DUF2089)
       0.11   12.3   0.9       0.11   12.3   0.9    1.5  2  Nsp1_C    Nsp1-like C-terminal region
       0.11   12.6   0.1       0.17   12.1   0.1    1.4  1  SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.2e-08   5.2e-05       5      42 ..      24      61 ..      22      63 .. 0.94
   2 ?   -2.9   0.0       1.5   6.8e+03      27      44 ..      92     109 ..      91     110 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.2e-08
                                  HHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHT CS
                         HTH_1  5 rlfvavaeegsftrAAeeLglsqpavsrqikrLEeelg 42
                                   l++++  +gs+++ A+ +++s++ ++  +k+ +e lg
  gi|70606962|ref|YP_255832.1| 24 NLLKEITLTGSISKSAKSMNVSYKFAWEYLKKVNEILG 61
                                  689999******************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHTS- CS
                         HTH_1  27 qpavsrqikrLEeelgvp 44 
                                   q+ v   + + E++l++ 
  gi|70606962|ref|YP_255832.1|  92 QKEVQNVLDKYEKRLNEI 109
                                   666777777778887765 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.5e-05      0.15      46      89 ..      29      89 ..      23     112 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                       DUF2089 46 ikarGnlkevekelgisYpTvrnrldeileaLgyeeeeeeeee.................e 89
                                  i   G++++ +k++++sY  + + l+++ e Lg  + ++  +                  e
  gi|70606962|ref|YP_255832.1| 29 ITLTGSISKSAKSMNVSYKFAWEYLKKVNEILGGIDMKKGGKGaggtilseklvdivnlyE 89
                                  5678***************************998877552221345566555666666663 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.83   3.7e+03      15      46 ..      26      57 ..      23      59 .. 0.64
   2 ?   12.3   0.9   2.4e-05      0.11      81     107 ..      86     112 ..      77     114 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                        Nsp1_C 15 lknktldelinkWtteLeeqekeFeeqakkvn 46
                                  lk  tl   i+k +++++ + k   e+ kkvn
  gi|70606962|ref|YP_255832.1| 26 LKEITLTGSISKSAKSMNVSYKFAWEYLKKVN 57
                                  56666777777777777666666666666666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.4e-05
                        Nsp1_C  81 eyiesqqdeLeslLdnyEkeleellsk 107
                                   ++ e+ q+e +++Ld+yEk+l+e+l+k
  gi|70606962|ref|YP_255832.1|  86 NLYEEAQKEVQNVLDKYEKRLNEILEK 112
                                   567899*****************9876 PP

>> SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.7e-05      0.17      51      83 ..      82     113 ..      65     114 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                      SpmSyn_N  51 ldlqsyeedekaqevdkllnkveerlkellegs 83 
                                   +d+  + e++++ ev+++l+k e+rl+e+le+s
  gi|70606962|ref|YP_255832.1|  82 VDIVNLYEEAQK-EVQNVLDKYEKRLNEILEKS 113
                                   566555555555.5***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 795.50
//
Query:       gi|70606963|ref|YP_255833.1|  [L=663]
Description: hypothetical protein Saci_1193 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-27   95.8   1.1    5.7e-27   94.7   0.0    2.0  3  Pkinase      Protein kinase domain
      2e-10   40.4   0.0    4.5e-10   39.3   0.0    1.7  1  Pkinase_Tyr  Protein tyrosine kinase
      1e-09   38.8   0.3      1e-05   26.0   0.1    2.9  3  TPR_19       Tetratricopeptide repeat
    3.6e-08   33.5   6.5    8.7e-07   29.1   0.8    2.5  2  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
    3.1e-07   30.6   1.8       0.21   11.9   0.0    3.9  4  TPR_12       Tetratricopeptide repeat
    5.9e-07   29.1   7.8      0.017   15.2   0.0    4.3  4  TPR_2        Tetratricopeptide repeat
    2.1e-06   27.3   7.9      0.052   13.4   0.1    4.3  4  TPR_1        Tetratricopeptide repeat
      6e-06   26.7   0.0        1.2   10.1   0.0    3.6  3  TPR_14       Tetratricopeptide repeat
    2.3e-05   24.9   0.0        3.3    8.5   0.0    3.3  2  TPR_16       Tetratricopeptide repeat
    2.8e-05   24.0   3.0      0.065   13.5   0.0    3.4  3  TPR_8        Tetratricopeptide repeat
    0.00037   20.9   1.3         11    6.9   0.0    4.9  4  TPR_6        Tetratricopeptide repeat
     0.0072   16.0   0.0       0.76    9.4   0.0    2.7  3  HrpB1_HrpK   Bacterial type III secretion protein (HrpB1_HrpK
  ------ inclusion threshold ------
      0.016   15.0   1.5      0.062   13.0   0.3    2.4  2  DUF1955      Domain of unknown function (DUF1955)
      0.016   15.3   1.5      0.065   13.4   0.4    2.3  2  GP3_package  DNA-packaging protein gp3
      0.031   14.3   2.7         12    6.2   0.0    3.9  4  TPR_7        Tetratricopeptide repeat
      0.044   13.7   4.6       0.39   10.7   0.1    3.0  3  TPR_10       Tetratricopeptide repeat
      0.046   14.0   3.9         47    4.5   0.0    5.0  5  PPR          PPR repeat
      0.048   13.1   0.2       0.19   11.1   0.0    1.9  2  Coatomer_E   Coatomer epsilon subunit
       0.13   12.2   0.0         15    5.4   0.0    2.3  2  APH          Phosphotransferase enzyme family
       0.16   11.9   0.0        2.5    8.0   0.0    2.1  2  Wzy_C_2      Virulence factor membrane-bound polymerase, C-te
       0.27   10.9   5.5       0.54   10.0   0.7    3.5  4  TPR_11       TPR repeat


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       6.4   5.5e+03      57     101 ..     153     200 ..     135     208 .. 0.58
   2 ?   -2.1   0.1       2.3   1.9e+03      53      91 ..     249     295 ..     245     316 .. 0.52
   3 !   94.7   0.0   6.7e-30   5.7e-27       1     242 [.     366     628 ..     366     634 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.4
                                   CTTB--EEEEEEE..SSEEEEEEE--TTEB.HHHHHHHHSS--HHHHH CS
                       Pkinase  57 hpnivrlyevfee..kdelylvleyvegge.ladllerkgslseeeak 101
                                   +++ ++ly+++e+  ++e + v e+ e+ e + ++l+  + +se++ +
  gi|70606963|ref|YP_255833.1| 153 CDEAITLYNSLEKkyPEESLAVAECYEKREeYLEALKIYSFFSEQKYR 200
                                   566667777776655344444555554443355555544556665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                                   HHHSCTTB--EEEEEEE.....SSEEEEEEE--TTEBHHHHHH...H CS
                       Pkinase  53 kklkhpnivrlyevfee.....kdelylvleyveggeladlle...r 91 
                                   +k +h++ v+++e   +     ++ l l + y+++++++++l    +
  gi|70606963|ref|YP_255833.1| 249 RKKNHKEAVKYFEEAVRrrrdfTNILSLANAYIQNQQFKEALDtiqE 295
                                   55566666666554333355544445577777777777766652222 PP

  == domain 3  score: 94.7 bits;  conditional E-value: 6.7e-30
                                   EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS..CTTB--EEEEEEE.......SSE CS
                       Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk..hpnivrlyevfee.......kde 72 
                                   y++++ +G+G++G V+ +   +  +++A+K++kke + ++    +l Ei+ l++++  +++ivr++ +f +       ++ 
  gi|70606963|ref|YP_255833.1| 366 YKVEKVIGSGGMGYVLLVE--KGMRKFAMKIVKKEFRYDE----MLYEIAKLQEISkgSKYIVRIFASFVDenftdyySSP 440
                                   78899***********998..799**********988874....689********999***********998876555555 PP

                                   EEEEEE--TTEBHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.T............ CS
                       Pkinase  73 lylvleyveggeladlle.......rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.e............ 133
                                     +v+ey+egg+l ++++       r++s  +e ++ ++++i+ ++ ++ ++g +H+D+Kp+NiL++ +            
  gi|70606963|ref|YP_255833.1| 441 PAIVMEYMEGGDLRQIITnneystlRHSSRWPEIVSIMFSKIADAIIHVNKNGYVHCDIKPSNILLNgKlpkygeqavqal 521
                                   56***************97765555555555558888999***************************55888888777777 PP

                                   ...TTEEEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHH CS
                       Pkinase 134 ...kgelKitDFGlakelessskltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeld 211
                                      k   Ki+D+G + ++ +      +  t++Y  P    + + + + Dv+sl + ly  lt++ pf++  ++e  e+ +d
  gi|70606963|ref|YP_255833.1| 522 leeKITPKISDLGSSVKVGTPV----IHYTPYYAHPLQRFGGRAEYNFDVYSLTISLYVALTNNFPFPEWLEREIEEAVID 598
                                   644444***********99966....99********7777788899**********************9999988888888 PP

                                   THHHHHHHCTSHH...HHHTTS-HHHHHHHH CS
                       Pkinase 212 qlekilkilgetkeklpeaseiseeakdllk 242
                                      k  +++++  +  p+ + +++e+ dl+ 
  gi|70606963|ref|YP_255833.1| 599 P-SKRENVIKDFYNMDPRLDYVPSEFHDLIL 628
                                   8.7788888899999*************996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   5.2e-13   4.5e-10       3     148 ..     368     534 ..     366     607 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 5.2e-13
                                   EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS..-BTTB--EEEEEE.......SSS CS
                   Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl..khpnivkllgvct.......kee 74 
                                   ++k +G+G  G V   +          k a+K++k+e + +   e+l e++ ++++    + iv++ +  +        ++
  gi|70606963|ref|YP_255833.1| 368 VEKVIGSGGMGYVLLVEKG------MRKFAMKIVKKEFRYD---EMLYEIAKLQEIskGSKYIVRIFASFVdenftdyYSS 439
                                   6788999999998876555......8899*****9988887...899999999999655789****999986655555566 PP

                                   SEEEEEE--TTEBHHHHHHHT....CTTTSBHHHHHHHH.HHHHHHHHHHHHTTEEEST-SGGGEEEEE............ CS
                   Pkinase_Tyr  75 pllivteyvkgGdLlkfLrkk....ekekltlkdllsfa.lqvAkGmeyLeskklvHrdlaarNvLlse............ 138
                                   p  iv+ey++gGdL++ ++++     +++ +  +++s++  ++A+++ +++++ +vH d+   N+Ll+             
  gi|70606963|ref|YP_255833.1| 440 PPAIVMEYMEGGDLRQIITNNeystLRHSSRWPEIVSIMfSKIADAIIHVNKNGYVHCDIKPSNILLNGklpkygeqavqa 520
                                   79*******************554434444455667655168*************************97666666666666 PP

                                   ....TTEEEE-STT CS
                   Pkinase_Tyr 139 ....nkvvkisDfG 148
                                       + + kisD G
  gi|70606963|ref|YP_255833.1| 521 lleeKITPKISDLG 534
                                   66544455666665 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0039       3.3      12      58 ..     124     170 ..     123     175 .. 0.92
   2 !    8.7   0.1    0.0029       2.5       2      47 ..     148     190 ..     147     192 .. 0.90
   3 !   26.0   0.1   1.2e-08     1e-05       4      59 ..     250     304 ..     247     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
                        TPR_19  12 alleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                   +l +++l+e pk++e+  + ++ l+ ++  deA+ l + l +++p +
  gi|70606963|ref|YP_255833.1| 124 ELVKYLLKEFPKYGEVVRRSIISLVGMNKCDEAITLYNSLEKKYPEE 170
                                   678999***********************************999985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                        TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                   + +++ +eA+ l+ ++   + k++e  l+ Ae++ +  ++ eA ++
  gi|70606963|ref|YP_255833.1| 148 VGMNKCDEAITLYNSL---EKKYPEESLAVAECYEKREEYLEALKI 190
                                   5677889********9...99**********************987 PP

  == domain 3  score: 26.0 bits;  conditional E-value: 1.2e-08
                        TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                    +++ eA++++e+a     +  +++  LA+a++++ q++eA ++++++ +  ++++
  gi|70606963|ref|YP_255833.1| 250 KKNHKEAVKYFEEAVRRRRDFTNILS-LANAYIQNQQFKEALDTIQEAEKIRRNSS 304
                                   5789**********************.*********************99999964 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.5    0.0085       7.2       6      47 ..     154     192 ..     149     203 .. 0.75
   2 !   29.1   0.8     1e-09   8.7e-07       2      75 ..     250     322 ..     249     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0085
                                   HHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHH CS
                        ANAPC3   6 knAiflaerllaaetespedayllAlclylngqykrAyellr 47 
                                   ++Ai l++ l    ++ pe +++ A+c+ ++++y +A+++++
  gi|70606963|ref|YP_255833.1| 154 DEAITLYNSLE---KKYPEESLAVAECYEKREEYLEALKIYS 192
                                   55555555555...7778888888999999999999999876 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1e-09
                                   TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHH CS
                        ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeA 75 
                                   ++n+k+A+ ++e ++ + +++  +++ lA ++ +n+q+k+A++ +++a++  ++   +yl++ +l  L+   eA
  gi|70606963|ref|YP_255833.1| 250 KKNHKEAVKYFEEAV-RRRRDFTNILSLANAYIQNQQFKEALDTIQEAEKIRRNSSTAYLKGIALEYLNAPMEA 322
                                   689************.********************************7778888899***9999988877776 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.8   4.1e+03      58      69 ..     150     161 ..     147     165 .. 0.69
   2 ?    6.0   0.1     0.017        15       8      27 ..     173     192 ..     169     213 .. 0.88
   3 !   11.9   0.0   0.00024      0.21      49      76 ..     241     268 ..     238     269 .. 0.90
   4 !    9.1   0.2    0.0019       1.6       6      36 ..     274     303 ..     270     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                        TPR_12  58 lgryeeAlelle 69 
                                   +++ +eA+ l++
  gi|70606963|ref|YP_255833.1| 150 MNKCDEAITLYN 161
                                   566777777765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                        TPR_12   8 nlaavlrrlgrydeAlelle 27 
                                    +a+++ ++++y eAl+++ 
  gi|70606963|ref|YP_255833.1| 173 AVAECYEKREEYLEALKIYS 192
                                   689**************996 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                        TPR_12  49 rnLgrlyralgryeeAlelleealaiae 76 
                                   + Lg+ + + ++++eA++++eea+++++
  gi|70606963|ref|YP_255833.1| 241 IKLGWHFIRKKNHKEAVKYFEEAVRRRR 268
                                   5799999999**************9987 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0019
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrl 36 
                                   l  la+++ + +++ eAl+  ++a  i+r++
  gi|70606963|ref|YP_255833.1| 274 L-SLANAYIQNQQFKEALDTIQEAEKIRRNS 303
                                   4.68888888888888888888888877765 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.9   6.7e+03      18      33 ..     154     169 ..     154     170 .. 0.81
   2 ?    3.1   0.7      0.15   1.3e+02       7      24 ..     174     191 ..     168     192 .. 0.86
   3 !   15.2   0.0     2e-05     0.017       6      30 ..     242     266 ..     240     270 .. 0.90
   4 !   12.5   0.1   0.00015      0.13       7      33 ..     276     302 ..     274     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.9
                         TPR_2  18 eeAleafekAleldPn 33 
                                   +eA+ +++   + +P+
  gi|70606963|ref|YP_255833.1| 154 DEAITLYNSLEKKYPE 169
                                   7999999988888775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.15
                         TPR_2   7 lGlayyklgdyeeAleaf 24 
                                    +++y+k+ +y eAl+ +
  gi|70606963|ref|YP_255833.1| 174 VAECYEKREEYLEALKIY 191
                                   689***********9977 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 2e-05
                         TPR_2   6 nlGlayyklgdyeeAleafekAlel 30 
                                    lG+  +++++++eA+++fe+A++ 
  gi|70606963|ref|YP_255833.1| 242 KLGWHFIRKKNHKEAVKYFEEAVRR 266
                                   699*******************986 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00015
                         TPR_2   7 lGlayyklgdyeeAleafekAleldPn 33 
                                   l++ay+++++++eAl+  ++A ++  n
  gi|70606963|ref|YP_255833.1| 276 LANAYIQNQQFKEALDTIQEAEKIRRN 302
                                   8********************988765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.14   1.2e+02       8      24 ..     175     191 ..     174     192 .. 0.89
   2 !   12.9   0.0   8.7e-05     0.074       7      33 ..     243     269 ..     241     270 .. 0.88
   3 !   13.4   0.1   6.1e-05     0.052       7      33 ..     276     302 ..     274     303 .. 0.92
   4 ?   -2.7   0.1       7.5   6.4e+03       5      20 ..     307     322 ..     307     324 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                   HHHHHHTT-HHHHHHHH CS
                         TPR_1   8 GnayfklgkydeAleyy 24 
                                   + +y k ++y eAl+ y
  gi|70606963|ref|YP_255833.1| 175 AECYEKREEYLEALKIY 191
                                   67************977 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.7e-05
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                   lG  + ++++++eA++y+e+A++ + +
  gi|70606963|ref|YP_255833.1| 243 LGWHFIRKKNHKEAVKYFEEAVRRRRD 269
                                   78888999*************998876 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6.1e-05
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                   l+nay ++++++eAl+  ++A +++ n
  gi|70606963|ref|YP_255833.1| 276 LANAYIQNQQFKEALDTIQEAEKIRRN 302
                                   9********************999876 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.5
                                   HHHHHHHHHTT-HHHH CS
                         TPR_1   5 ynlGnayfklgkydeA 20 
                                   y +G a+ +l+ + eA
  gi|70606963|ref|YP_255833.1| 307 YLKGIALEYLNAPMEA 322
                                   6788888888888777 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.21   1.8e+02      18      37 ..     154     173 ..     147     178 .. 0.88
   2 !    8.7   0.0     0.004       3.4       6      32 ..     242     268 ..     239     274 .. 0.87
   3 !   10.1   0.0    0.0014       1.2       6      39 ..     275     308 ..     272     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.21
                        TPR_14  18 deAiallrralalaPddaea 37 
                                   deAi+l++ + +++P++  a
  gi|70606963|ref|YP_255833.1| 154 DEAITLYNSLEKKYPEESLA 173
                                   8**************98776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.004
                        TPR_14   6 alaeallalGdpdeAiallrralalaP 32 
                                   +l++ + +  +++eA++++++a+++  
  gi|70606963|ref|YP_255833.1| 242 KLGWHFIRKKNHKEAVKYFEEAVRRRR 268
                                   6889999***************99865 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0014
                        TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawl 39 
                                    la a+ ++++++eA++  ++a +   ++ +a+l
  gi|70606963|ref|YP_255833.1| 275 SLANAYIQNQQFKEALDTIQEAEKIRRNSSTAYL 308
                                   69********************999888887775 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0038       3.3       6      55 ..     146     189 ..     144     192 .. 0.85
   2 ?    5.3   0.1     0.038        32       1      27 [.     274     300 ..     274     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                        TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                   +++  ++ d+A+ +++ + k++   P+    +l+ ++++ ++ ++ eA+ 
  gi|70606963|ref|YP_255833.1| 146 SLVGMNKCDEAITLYNSLEKKY---PE---ESLAVAECYEKREEYLEALK 189
                                   578899****************...65...56799999999999999985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.038
                        TPR_16   1 lalaraalragdyddAaaaleaalkrd 27 
                                   l la+a+++++++ +A+   ++a k +
  gi|70606963|ref|YP_255833.1| 274 LSLANAYIQNQQFKEALDTIQEAEKIR 300
                                   579999999999999999999987765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       6.5   5.6e+03      11      23 ..     178     190 ..     174     192 .. 0.53
   2 !   13.5   0.0   7.7e-05     0.065       7      33 ..     243     269 ..     241     270 .. 0.85
   3 !    9.2   0.2    0.0018       1.6       6      33 ..     275     302 ..     273     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                                   HHHTT-HHHHHHH CS
                         TPR_8  11 ylklgdyeeAkey 23 
                                   y+k ++y eA + 
  gi|70606963|ref|YP_255833.1| 178 YEKREEYLEALKI 190
                                   5555555555444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                   lg+  + +++++eA++y+e+a++ ++d
  gi|70606963|ref|YP_255833.1| 243 LGWHFIRKKNHKEAVKYFEEAVRRRRD 269
                                   56667899**************98876 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0018
                                   HHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekaleldpd 33 
                                    l+++y++ ++++eA  ++++a +++++
  gi|70606963|ref|YP_255833.1| 275 SLANAYIQNQQFKEALDTIQEAEKIRRN 302
                                   59*********************99986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.013        11      14      32 ..     151     169 ..     145     170 .. 0.87
   2 ?    1.7   0.1      0.57   4.8e+02       7      23 ..     175     191 ..     172     197 .. 0.86
   3 ?    4.2   0.0     0.094        81       6      29 ..     243     266 ..     241     269 .. 0.81
   4 ?    2.4   0.1      0.36   3.1e+02       6      25 ..     276     295 ..     273     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHH-TT CS
                         TPR_6  14 gdtdkAlealerlikeYPd 32 
                                   ++ d+A++++++l k+YP+
  gi|70606963|ref|YP_255833.1| 151 NKCDEAITLYNSLEKKYPE 169
                                   5679**************6 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAleal 23 
                                   a++y+k  ++ +Al+++
  gi|70606963|ref|YP_255833.1| 175 AECYEKREEYLEALKIY 191
                                   99****66*******99 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.094
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealerlike 29 
                                   l++ +++ +++ +A++++e+ +++
  gi|70606963|ref|YP_255833.1| 243 LGWHFIRKKNHKEAVKYFEEAVRR 266
                                   5555677779**********9987 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.36
                                   HHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAlealer 25 
                                   la +y++ ++  +Al++ ++
  gi|70606963|ref|YP_255833.1| 276 LANAYIQNQQFKEALDTIQE 295
                                   899***955*******9887 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.1   4.4e+03      56      81 ..     148     173 ..     144     175 .. 0.82
   2 !    9.4   0.0   0.00089      0.76      25      78 ..     218     270 ..     206     277 .. 0.89
   3 ?    3.4   0.0     0.067        57      53      82 ..     278     309 ..     272     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.1
                    HrpB1_HrpK  56 iergrweeAlrlLreveaeasgtpya 81 
                                   +  ++ +eA+ l +++e++ +++ +a
  gi|70606963|ref|YP_255833.1| 148 VGMNKCDEAITLYNSLEKKYPEESLA 173
                                   67789999***999999998888776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00089
                    HrpB1_HrpK  25 edtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgt 78 
                                   e+t++++ l +al +L P   + ++  g+  i++++ +eA+++++e   +++ +
  gi|70606963|ref|YP_255833.1| 218 ERTYNVKSLFEALSIL-PTYDAPAIKLGWHFIRKKNHKEAVKYFEEAVRRRRDF 270
                                   78999********999.*****************************98776655 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.067
                    HrpB1_HrpK  53 vlliergrweeAlrlLreve..aeasgtpyak 82 
                                   + +i++++++eAl +++e e   ++s+t+y k
  gi|70606963|ref|YP_255833.1| 278 NAYIQNQQFKEALDTIQEAEkiRRNSSTAYLK 309
                                   668*****************555555555555 PP

>> DUF1955  Domain of unknown function (DUF1955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   9.2e+02      64     135 ..     116     185 ..     107     198 .. 0.75
   2 ?   13.0   0.3   7.3e-05     0.062      88     157 ..     273     342 ..     249     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                   S-GGG-S-THHHHHHHHHTT---HHHHHHHHHHHHTT-HHHHHHHHHHH---S-HHHHHHHHHHHHHTT-HH CS
                       DUF1955  64 fdlskcqnlkrviecyvklnklseyvdlaldvlvkkgkkdqldkilkelkneikaelllkianalkklgder 135
                                   fdl k +n   v +      k+ e v  ++ +lv  +k d+   +++ l++   +e  l++a+ ++k ++  
  gi|70606963|ref|YP_255833.1| 116 FDLMK-GNYELVKYLLKEFPKYGEVVRRSIISLVGMNKCDEAITLYNSLEK-KYPEESLAVAECYEKREEYL 185
                                   55554.455555555566678889999999999999999999999999987.45666778999999876655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.3e-05
                                   HHHHHHHHHHHTT-HHHHHHHHHHH---S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHHH CS
                       DUF1955  88 yvdlaldvlvkkgkkdqldkilkelkneikaelllkianalkklgdereanellkkacekGikeacenin 157
                                    + la  ++ +++ k+ ld i++  k   +++  +  + al+ l++  ea++    ac +G+ +ac +i+
  gi|70606963|ref|YP_255833.1| 273 ILSLANAYIQNQQFKEALDTIQEAEKIRRNSSTAYLKGIALEYLNAPMEAQKEFFFACREGLVDACGKIK 342
                                   5667889999***********9877666677777777899999***********************9996 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.5   1.3e+03      48     106 ..     188     244 ..     151     246 .. 0.72
   2 ?   13.4   0.4   7.6e-05     0.065      57     101 ..     258     302 ..     255     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.5
                                   HHHHHT--HHHHHHHGG..S.HHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHH...T CS
                   GP3_package  48 LalyLgisrstlkeyekrkr.efsetierikqivenqqiegalagefnativalllsnfG 106
                                   L  y  +s+++ +e ekr r ++  +i+  + + + +++  al+  ++    a++l   G
  gi|70606963|ref|YP_255833.1| 188 LKIYSFFSEQKYRELEKRLRdKVNLLIDEFERTYNVKSLFEALSILPTYDAPAIKL---G 244
                                   55566688999999999999899999999888888887777776666665555555...5 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.6e-05
                                   HHHHHHGG..SHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHH CS
                   GP3_package  57 stlkeyekrkrefsetierikqivenqqiegalagefnativall 101
                                   ++++e+ +r r+f ++++++++ ++nqq++ al  + +a+ +++ 
  gi|70606963|ref|YP_255833.1| 258 KYFEEAVRRRRDFTNILSLANAYIQNQQFKEALDTIQEAEKIRRN 302
                                   78999999999**********************999999999884 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.7   2.3e+03      12      22 ..     150     160 ..     147     164 .. 0.87
   2 ?   -1.5   0.2         4   3.4e+03       6      22 ..     175     191 ..     172     191 .. 0.74
   3 ?    6.2   0.0     0.014        12       5      31 ..     243     267 ..     242     271 .. 0.81
   4 ?    4.9   0.1     0.036        31       3      24 ..     274     295 ..     273     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.7
                         TPR_7  12 lGdyeeAiely 22 
                                   +++ +eAi+ly
  gi|70606963|ref|YP_255833.1| 150 MNKCDEAITLY 160
                                   57889*****9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4
                         TPR_7   6 arlysrlGdyeeAiely 22 
                                   a++y+++ +y eA+++y
  gi|70606963|ref|YP_255833.1| 175 AECYEKREEYLEALKIY 191
                                   77888888888887776 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.014
                         TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                                   L+  + r  +++eA++++e+  a++++
  gi|70606963|ref|YP_255833.1| 243 LGWHFIRKKNHKEAVKYFEE--AVRRR 267
                                   66667788899*********..88865 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.036
                         TPR_7   3 lnLarlysrlGdyeeAielyeq 24 
                                   l La++y + ++++eA++  ++
  gi|70606963|ref|YP_255833.1| 274 LSLANAYIQNQQFKEALDTIQE 295
                                   68**************987766 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       8.1   6.9e+03      20      32 ..     179     191 ..     176     191 .. 0.70
   2 ?   10.7   0.1   0.00045      0.39      16      33 ..     251     268 ..     243     269 .. 0.90
   3 ?    3.8   0.1     0.064        55       7      23 ..     275     291 ..     273     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.1
                        TPR_10  20 eAealleealair 32 
                                   e ++ + eal i+
  gi|70606963|ref|YP_255833.1| 179 EKREEYLEALKIY 191
                                   5566778888776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00045
                        TPR_10  16 grydeAealleealairr 33 
                                   ++++eA++++eea+++rr
  gi|70606963|ref|YP_255833.1| 251 KNHKEAVKYFEEAVRRRR 268
                                   79**************98 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.064
                        TPR_10   7 NLanalrqrgrydeAea 23 
                                    Lana+ q ++++eA++
  gi|70606963|ref|YP_255833.1| 275 SLANAYIQNQQFKEALD 291
                                   59*************86 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.9   5.9e+03      13      24 ..     120     131 ..     114     137 .. 0.54
   2 ?    1.6   0.0      0.46     4e+02      10      29 ..     147     166 ..     144     167 .. 0.81
   3 ?   -0.6   0.1       2.5   2.1e+03       8      23 ..     176     191 ..     173     194 .. 0.87
   4 ?    4.0   0.1     0.084        71      11      29 ..     248     266 ..     246     267 .. 0.86
   5 ?    4.5   0.0     0.056        47       5      25 ..     275     295 ..     274     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.9
                           PPR  13 nGkleeAlelfk 24 
                                   +G++e ++ l+k
  gi|70606963|ref|YP_255833.1| 120 KGNYELVKYLLK 131
                                   355555555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                           PPR  10 ycknGkleeAlelfkeMkek 29 
                                   ++  +k++eA+ l++ +++k
  gi|70606963|ref|YP_255833.1| 147 LVGMNKCDEAITLYNSLEKK 166
                                   5557899*******998875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.5
                           PPR   8 sgycknGkleeAlelf 23 
                                    +y k  ++ eAl+++
  gi|70606963|ref|YP_255833.1| 176 ECYEKREEYLEALKIY 191
                                   5899999*******98 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.084
                           PPR  11 cknGkleeAlelfkeMkek 29 
                                    ++ +++eA+++f+e +++
  gi|70606963|ref|YP_255833.1| 248 IRKKNHKEAVKYFEEAVRR 266
                                   68899*********98776 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.056
                           PPR   5 slIsgycknGkleeAlelfke 25 
                                   sl ++y +n +++eAl+ ++e
  gi|70606963|ref|YP_255833.1| 275 SLANAYIQNQQFKEALDTIQE 295
                                   6889************99887 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.1e+03     177     202 ..     147     172 ..     134     209 .. 0.76
   2 ?   11.1   0.0   0.00023      0.19      67     131 ..     239     299 ..     225     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                                   HH-TTHHHHHHHHHHHHHHHS---HH CS
                    Coatomer_E 177 avggekiqdAyyifqelsekykstpl 202
                                    vg +k  +A  +++ l  ky++ +l
  gi|70606963|ref|YP_255833.1| 147 LVGMNKCDEAITLYNSLEKKYPEESL 172
                                   46777888888888888888876654 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00023
                                   HHHHHHHHHHH-STTHHHHHHHHHHHHHS----S-HHHHHHHHHHHHHTT-HHHHHHHHTT--SH CS
                    Coatomer_E  67 qAvrllaeylnspsrkeeilaelkeeladseiesnevlrllaaivflkegdfddalkllkksenL 131
                                    A++l  +++ + ++++e+++  +e + ++ + +n +l l+ a  ++++++f++al+++++ e++
  gi|70606963|ref|YP_255833.1| 239 PAIKLGWHFIRK-KNHKEAVKYFEEAVRRRRDFTN-ILSLANA--YIQNQQFKEALDTIQEAEKI 299
                                   577777677766.788999*************999.9999777..67799*********999876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.018        15      15      84 ..     382     455 ..     370     468 .. 0.85
   2 ?    4.3   0.0     0.038        32     167     181 ..     493     507 ..     480     517 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.018
                                   EEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTE....EEEEEE----EE-SS CS
                           APH  15 lvttpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigl....lfalieyvpgrsllr 84 
                                   lv+ + ++++++++ ++  + e+  e a l+ ++k  +++ +++a   d+++  +    ++ ++ey++g +l++
  gi|70606963|ref|YP_255833.1| 382 LVEKGMRKFAMKIVKKEFRYDEMLYEIAKLQEISKGSKYIVRIFASFVDENFTDYysspPAIVMEYMEGGDLRQ 455
                                   34444489*****9999889999999999****************999999998899************99988 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.038
                                   EEE-SS-SGGGEEEC CS
                           APH 167 vllHgDlhpgNllvd 181
                                   + +H+D++p N+l++
  gi|70606963|ref|YP_255833.1| 493 GYVHCDIKPSNILLN 507
                                   689**********99 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.003       2.5     124     177 ..     117     171 ..      92     181 .. 0.83
   2 ?    1.4   0.0      0.31   2.6e+02     142     171 ..     269     298 ..     239     306 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                       Wzy_C_2 124 enlaaklalarklihlsPe.pavierlilslallGdedeAeqilararalfpeed 177
                                   + ++  ++l + l++ +P+   v++r i+sl++  + deA + +  +++ +pee 
  gi|70606963|ref|YP_255833.1| 117 DLMKGNYELVKYLLKEFPKyGEVVRRSIISLVGMNKCDEAITLYNSLEKKYPEES 171
                                   55666788889999999962689*****************************996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                       Wzy_C_2 142 epavierlilslallGdedeAeqilarara 171
                                     + i  l+ ++ ++++ +eA++++++a++
  gi|70606963|ref|YP_255833.1| 269 DFTNILSLANAYIQNQQFKEALDTIQEAEK 298
                                   344455667777777777777777777764 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.56   4.8e+02       8      18 ..     151     161 ..     147     168 .. 0.86
   2 ?   -2.1   0.2       3.7   3.2e+03      15      23 ..     182     190 ..     181     191 .. 0.88
   3 ?   -2.3   0.0       4.3   3.6e+03       7      22 ..     250     265 ..     247     274 .. 0.75
   4 ?   10.0   0.7   0.00063      0.54       1      33 [.     277     309 ..     277     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.56
                        TPR_11   8 GkyeeAieaYk 18 
                                   +k +eAi+ Y+
  gi|70606963|ref|YP_255833.1| 151 NKCDEAITLYN 161
                                   7889******8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                        TPR_11  15 eaYkkAlkl 23 
                                   e+Y +Alk+
  gi|70606963|ref|YP_255833.1| 182 EEYLEALKI 190
                                   79****997 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.3
                        TPR_11   7 qGkyeeAieaYkkAlk 22 
                                   + + +eA++ +++A++
  gi|70606963|ref|YP_255833.1| 250 KKNHKEAVKYFEEAVR 265
                                   5678899999999987 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00063
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                                   ++ay + ++++eA+   ++A k++ ++ +ay++
  gi|70606963|ref|YP_255833.1| 277 ANAYIQNQQFKEALDTIQEAEKIRRNSSTAYLK 309
                                   59*************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (663 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 4550.69
//
Query:       gi|70606964|ref|YP_255834.1|  [L=58]
Description: hypothetical protein Saci_1194 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 398.31
//
Query:       gi|70606965|ref|YP_255835.1|  [L=125]
Description: endoribonuclease L-PSP [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-42  143.2   0.0    3.9e-42  143.1   0.0    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.1   0.0   2.2e-46   3.9e-42       2     119 ..       7     122 ..       6     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 2.2e-46
                                   TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHHH CS
                 Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladiedfaev 82 
                                   e+ap++++pYsqa+k+gn+++vsGq+p+dp+tgelv+g ++eqt++++enlka++++ag++l+dvV+ +v+l+d++ f+++
  gi|70606965|ref|YP_255835.1|   7 EKAPKPIGPYSQAIKVGNFLFVSGQIPIDPKTGELVKGGIKEQTKAVMENLKAIIESAGFTLQDVVMSNVYLKDLNMFNDF 87 
                                   79******************************************************************************* PP

                                   HHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEE CS
                 Ribonuc_L-PSP  83 nevyaeafdelkeaParsaveVaaLpkgakvEIeaia 119
                                   nevy  +f++    Par++v+Va+Lp++ ++EI +i 
  gi|70606965|ref|YP_255835.1|  88 NEVYSTYFPNRP--PARVTVQVAKLPRDSLIEISVIC 122
                                   **********95..*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 815.72
//
Query:       gi|70606966|ref|YP_255836.1|  [L=272]
Description: hypothetical protein Saci_1196 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-44  148.8  15.3    1.8e-14   53.9   0.1    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.4   3.5e-10   6.3e-06       2      56 ..       4      56 ..       3      57 .. 0.87
   2 !   41.4   0.4   7.8e-15   1.4e-10       2      52 ..      77     127 ..      75     131 .. 0.93
   3 !   53.9   0.1   9.8e-19   1.8e-14       1      54 [.     139     192 ..     139     195 .. 0.95
   4 !   36.0   0.3     4e-13   7.2e-09       1      56 [.     210     265 ..     210     266 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.5e-10
                                  HHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  2 gdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllrall 56
                                  + im  d++++   + l +a++++ +++ ++r+ +V  d+ l Giv+ rDl++ ++
  gi|70606966|ref|YP_255836.1|  4 KTIMLQDPPVLGLHDKLYDAFKRI-NTRgIGRVIIV--DKSLEGIVSTRDLISCIV 56
                                  67999*******************.6666****889..455***********9775 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 7.8e-15
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                   + +m++++ +v++d+++ +al +m+ +++++lPV+d ++k+ Givt+r  +
  gi|70606966|ref|YP_255836.1|  77 SKVMSPKPAYVYEDDDVVDALTIMVARNLGSLPVIDVEKKVKGIVTEREMM 127
                                   679**********************999*******9999********9865 PP

  == domain 3  score: 53.9 bits;  conditional E-value: 9.8e-19
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   V+ +mt++v t+++d+++ e ++lm+++g++rlPVVd +gklvG++t  D+l+ 
  gi|70606966|ref|YP_255836.1| 139 VSKFMTKRVTTIYEDMPVVEGAKLMVKRGFRRLPVVDTEGKLVGVITAADILKN 192
                                   7889************************************************85 PP

  == domain 4  score: 36.0 bits;  conditional E-value: 4e-13
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   ++di t++v+t++p+ ++ ea+ +m  +++++l VVd+d+ +  ivt+rDl+ al+
  gi|70606966|ref|YP_255836.1| 210 IKDIKTPNVHTIDPNKSINEAAAKMLLERIGSLIVVDNDNVPTAIVTERDLIIALH 265
                                   58999*******************97444****9999999999*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1871.06
//
Query:       gi|70606967|ref|YP_255837.1|  [L=610]
Description: hypothetical protein Saci_1197 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     7e-114  380.7   0.0     1e-113  380.2   0.0    1.2  1  GDE_C            Amylo-alpha-1,6-glucosidase
    3.4e-55  186.8   0.6    4.9e-55  186.3   0.6    1.2  1  GDE_N            Glycogen debranching enzyme N terminal
    0.00025   20.4   0.0    0.00038   19.8   0.0    1.2  1  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly
  ------ inclusion threshold ------
       0.14   11.9   0.1       0.28   10.9   0.1    1.5  1  DUF5507          Family of unknown function (DUF5507)


Domain annotation for each model (and alignments):
>> GDE_C  Amylo-alpha-1,6-glucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.2   0.0  2.3e-117    1e-113      12     383 .]     251     602 ..     240     602 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.2 bits;  conditional E-value: 2.3e-117
                         GDE_C  12 seslkeeekgvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqealyntvdaslwl 92 
                                    + l + ++g s++AG++wF++WGRDtfI+L+G+lL++g++++A+ei+++++++  +Gl+PN+++   e++y  vd slw 
  gi|70606967|ref|YP_255837.1| 251 LNFLVKGHQGYSIVAGYHWFDEWGRDTFISLEGILLLQGLYDQAKEIINRYLQYNNRGLLPNHITPSGEPIYLGVDVSLWA 331
                                   444577899************************************************************************ PP

                         GDE_C  93 ieaiekYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvkgepvtPRdGkaveina 173
                                   i++i+k ++y+ d++++ +iyp+lq+i+++y++G+     +   + l+++g+   ++TWmDa+++g+ vtPR+G+ave+na
  gi|70606967|ref|YP_255837.1| 332 INSIYKLYTYSRDTQFIGKIYPILQDIVESYMKGNGIVYTMG--EILFHRGA---PRTWMDASYNGRIVTPREGAAVEVNA 407
                                   ************************************666666..99*****9...************************** PP

                         GDE_C 174 LwyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlksseekdlslRpNflialslape 254
                                   Lwy+aL+il+ +++  lg+ ++s y+e+aek+k sf ++F          +  l+D+l +s + d  +RpN+++a+sl+++
  gi|70606967|ref|YP_255837.1| 408 LWYNALMILDYFSK-ILGD-SSSLYREVAEKVKRSFMERFVT--------NWGLYDYLTPSFTPDNTIRPNQIFAISLPFN 478
                                   *************9.9999.99******************44........4669*************************** PP

                         GDE_C 255 llseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyveallkfgeklgkskeale 335
                                   +l  ek+k v+ ++e+eLl+++Gl+tL+++dp+Yk+ Y+g++ +rd aYH+G vW+wl+g+yv+a+l+ ++++++sk  l+
  gi|70606967|ref|YP_255837.1| 479 ILPVEKGKSVILTIEKELLRSYGLSTLSSKDPKYKPVYRGERAKRDEAYHNGLVWPWLIGAYVDAKLRYETDIVRSKLLLD 559
                                   ********************************************************************************* PP

                         GDE_C 336 evkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                    +k+lLe     +++ + g ++Elf++ +++ + g+iaQAWSvae++r
  gi|70606967|ref|YP_255837.1| 560 TFKPLLE-----YAKLHNGFIPELFEDVPPYSNGGAIAQAWSVAEVYR 602
                                   *******.....888899***************************986 PP

>> GDE_N  Glycogen debranching enzyme N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   0.6   1.1e-58   4.9e-55       1     209 [.      10     216 ..      10     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 1.1e-58
                         GDE_N   1 REwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLesFel 81 
                                   +EwllT g+GGY+s+t++g+n+R+yhG+Lv++lnpp++R+l+lsk+++ l+++++ f+Lstn+y++ ++p+Gy+yL++F+ 
  gi|70606967|ref|YP_255837.1|  10 KEWLLTFGTGGYSSSTICGINSRTYHGYLVVPLNPPHKRYLILSKFEDFLVLNKEDFPLSTNHYSNAYYPDGYKYLKHFHW 90 
                                   7******************************************************************************** PP

                         GDE_N  82 e.pvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqe.eglveiqase 160
                                     ++++w+y v+++ +ek ++  +g+n v i+Y+  ++    ++++ pl++fR++h  +++++l+++++  ++lv++  ++
  gi|70606967|ref|YP_255837.1|  91 GrNYVKWIYDVNGIIVEKLLIANQGTNGVTIKYKATEG----SIKVYPLMTFRSHHLVSQPDNLIFTQKVkDNLVSLYRYD 167
                                   **********************************9994....5*****************99998888669999******* PP

                         GDE_N 161 aepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfev 209
                                   ++ +l++ ++++ +++++++ yy+++y  + e G +++e+ly+p  ++ 
  gi|70606967|ref|YP_255837.1| 168 GSLALNFVVENKFKLTNTGYSYYDFFYVIDYELGNNSKENLYNPFFLTS 216
                                   **********999*******************************88765 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.6e-08   0.00038     106     243 ..     334     485 ..     273     502 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.6e-08
                                   HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT.TB..--S-S--...STT......-SS----HHHH.HHHHHHHHHH CS
               Bac_rhamnosid6H 106 vpwelyetygDkeilkkqYesmkryldylkqrsddgle.elskfqlg...DWldpe.ardgaaktekalv.ataylvrslk 180
                                      +ly+++ D++++ k+Y+ ++  ++ + + +   +  + + f+ g    W+d + +  + ++ e+a v  +a  + +l+
  gi|70606967|ref|YP_255837.1| 334 SIYKLYTYSRDTQFIGKIYPILQDIVESYMKGNGIVYTmGEILFHRGaprTWMDASyNGRIVTPREGAAVeVNALWYNALM 414
                                   44689*******************999887777773444677777663336998887555666666777758********* PP

                                   HHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-TTS........-BTT--...HHHHHHHHHTT-S-GGGH CS
               Bac_rhamnosid6H 181 lvakiaellgkeedakkyaalaeelkaafnkkyldsetg........svandt...qtanalpLafglvpeaer 243
                                   +++ ++++lg  + ++ y++ ae++k+ f ++++ ++ g         + ++t    +  a++L f+++p ++ 
  gi|70606967|ref|YP_255837.1| 415 ILDYFSKILG--DSSSLYREVAEKVKRSFMERFV-TNWGlydyltpsFTPDNTirpNQIFAISLPFNILPVEKG 485
                                   **********..6799******************.999966666665222233222223345556666666655 PP

>> DUF5507  Family of unknown function (DUF5507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.2e-05      0.28      72     131 ..     110     167 ..      98     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.2e-05
                       DUF5507  72 vimgageqlkrikyevgennlkvfnvhfnnnhelvssgepdviclskqvwenlliklkle 131
                                   +i   g +   iky+  e  +kv+ +     h lvs  +pd + ++++v +nl+   + +
  gi|70606967|ref|YP_255837.1| 110 LIANQGTNGVTIKYKATEGSIKVYPLMTFRSHHLVS--QPDNLIFTQKVKDNLVSLYRYD 167
                                   56667778889****************99******9..69************98665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4133.94
//
Query:       gi|70606968|ref|YP_255838.1|  [L=617]
Description: glycosyl hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-18   64.9   0.6    4.8e-14   52.0   1.2    3.1  2  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   1.2   2.7e-18   4.8e-14      23     351 ..     275     558 ..     255     572 .. 0.78
   2 !    8.8   0.0   3.3e-05      0.59     403     446 ..     565     609 ..     558     611 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.7e-18
                                   TT-B-S-S-BSSS.....B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS-BTTB-TTS CS
                Glyco_hydro_15  23 tGlliASpstsdp.....DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagkvekfketqs 98 
                                    G +iAS++ s        Y+y+W RDs++++ a+  +gy  e   k y++  +l+   +g+l+  ++ +++        s
  gi|70606968|ref|YP_255838.1| 275 NGSIIASSDYSFMgiygdAYTYCWPRDSAISAYALDIAGYG-ELALKHYKFISKLIS-EEGYLYHKYNPDST------LAS 347
                                   699******9988999988****************989988.777777777777766.67788877777776......556 PP

                                   CGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHH....HCTT...HCHCCCCHHHHTHHHHHHHHHHHTTS-EE- CS
                Glyco_hydro_15  99 tkgLhakyftktgstvvGddewghlQlDatslyllalaqm....tasg...lqiistldevafvqnlvdYieaayktpdfg 172
                                   +   + +  +k g+          +Q D t+l + a+a         +   l  i+      +++ l+++ie    +p+f+
  gi|70606968|ref|YP_255838.1| 348 S---WHPWIYK-GKR------ILPIQEDETALEVWAIANHyriyK--DideLVEIYRSFIKPAIKFLMKFIEDGLPKPSFD 416
                                   6...7787777.444......4557*************9977541..23444444444444469999************** PP

                                   TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCECECSCH.....H CS
                Glyco_hydro_15 173 lWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntylildgsfaedke 253
                                   lWEe+ g++ +  +   +  Al+ea +++ ++g++  a+ + + ++ + + +       r +  ++  + +ld++      
  gi|70606968|ref|YP_255838.1| 417 LWEERYGIHIY--TVSTVYGALTEASKLVYDMGDEVMASDMVSVAEYMKSMM------LRKMTYNGRFIRRLDEN------ 483
                                   ***********..8888899*************8887777776666666555......44444555566666666...... PP

                                   HHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBTT--CGSSSBSCT CS
                Glyco_hydro_15 254 qvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRysedvkpdklglsG 334
                                      + +   das++     +++ + d          p +++++ +i++ l+  g          + Ry+ d++ ++ ++  
  gi|70606968|ref|YP_255838.1| 484 --GNIDTTIDASMYSPFFFGVIDPKD----------PIMVSTINAIESALKVNGG---------IIRYEGDTY-RRSKSRP 542
                                   ..56999******99999********..........****************999.........9********.6****** PP

                                   --BHHHHHHHHHHHHHH CS
                Glyco_hydro_15 335 rpyylctlwtvetllde 351
                                   +p++++tlw v++++ +
  gi|70606968|ref|YP_255838.1| 543 NPWLITTLW-VAEYYLR 558
                                   *********.4444433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHH.S-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                Glyco_hydro_15 403 adliveavee.dnslgvLteevdvylgeliraqpllfsealllri 446
                                   a+++++ v + +  +g+L e+vd +  ++++  pl +s+ +l+ +
  gi|70606968|ref|YP_255838.1| 565 ANEYISWVLDrAVPTGLLPEQVDPDNLQSTSVLPLVWSHSELVIA 609
                                   56677777777*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4237.56
//
Query:       gi|70606969|ref|YP_255839.1|  [L=417]
Description: glucose-1-phosphate adenylyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-41  141.8   0.0    3.4e-41  141.5   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    4.3e-06   26.2   8.1       0.06   13.1   0.2    4.7  5  Hexapep          Bacterial transferase hexapeptide (six repea
      5e-05   21.6   3.1     0.0002   19.7   3.1    1.8  1  DUF4954          Domain of unknown function (DUF4954)
    5.9e-05   23.5   0.0    0.00012   22.5   0.0    1.6  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.13   11.2   0.7          7    5.5   0.2    2.8  3  Fucokinase       L-fucokinase
       0.64    9.8   4.1        8.6    6.2   0.1    3.0  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.0   1.1e-44   3.4e-41       2     244 ..       9     256 ..       8     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 1.1e-44
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEE.EEETTTHHHHHHHHTTSGGGT......SEE CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiiv.vltqehsflveeqlkegskfg......vev 75 
                                    +I  GG+ tRL+PLt +++k  v  l+  +li++tl +la++gi+eii+ v  + +  ++ + ++eg  f+       +v
  gi|70606969|ref|YP_255839.1|   9 VIIPIGGEATRLRPLTIETSKATVRLLNR-PLIEYTLIELARQGIKEIIFgVRGYVNYRSLFDIYQEGIGFSaryhikPRV 88 
                                   57778************************.*****************9875777778888888888888888888855444 PP

                                   EEEEESS--..BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
               NTP_transferase  76 lialepegk..gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                    + ++p  +  g Ad+v+++ e+ + ++    vlv+ gD l+k +++++++ ++ek+a  ++t++i+p e+ +e+Gv+e +
  gi|70606969|ref|YP_255839.1|  89 HFKYQPRVDsiGNADSVRINMEYYNINDP---VLVVQGDNLFKLDVKKLLEYHEEKRA--MMTIVIKPMENVEEFGVAELE 164
                                   44444444488**************9996...**************************..********************* PP

                                   TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHH.CCHHHTT..SSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
               NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflak.dleelkr..gedeitdilpkaleegkvalaflfkdaeyWsD 231
                                   ++++++rfvEKP++++a s+l+++GiYv  +e+ ++  +  ++e+ +  + d+++di+p+++++g++ +a+ +++   W D
  gi|70606969|ref|YP_255839.1| 165 SDNKIRRFVEKPRREEApSNLVNTGIYVLSPEIRKIFESeEVKEMYEmgKMDFGKDIIPYLIRKGYPVYAYKMDG--LWFD 243
                                   ****************999**************9988777899887644689***********************..7*** PP

                                   XSSHHHHHHHHHH CS
               NTP_transferase 232 vGtldslleanek 244
                                   vGt+  +l+a   
  gi|70606969|ref|YP_255839.1| 244 VGTPGRYLDAVYT 256
                                   *****99999765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         4   1.2e+04       6      13 ..     165     172 ..     162     173 .. 0.52
   2 !   13.1   0.2     2e-05      0.06       4      28 ..     310     339 ..     307     345 .. 0.69
   3 !    8.6   0.5   0.00052       1.5       4      30 ..     333     358 ..     331     359 .. 0.71
   4 !   10.4   0.2   0.00014      0.41       5      29 ..     345     368 ..     341     370 .. 0.75
   5 !    6.4   0.9    0.0025       7.6       2      29 ..     359     395 ..     358     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4
                                   TTEEE-TT CS
                       Hexapep   6 snvlIgpf 13 
                                   s+++I+ f
  gi|70606969|ref|YP_255839.1| 165 SDNKIRRF 172
                                   55555554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2e-05
                                   EETTEEE-T.....TEEEETTEEE-TTEEE CS
                       Hexapep   4 IGsnvlIgp.....faviggnVkIGdnvkI 28 
                                   IG +++Ig+      + i + ++IG++vk+
  gi|70606969|ref|YP_255839.1| 310 IGRHCQIGKdtyieESSIDNFTIIGRRVKV 339
                                   777777777555558888888888888776 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00052
                                   EETTEEE-TTEEEETTEEE-TTEEEET CS
                       Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIga 30 
                                   IG  v++ +   +++ V IGdn+++++
  gi|70606969|ref|YP_255839.1| 333 IGRRVKVVKS-AVMDRVYIGDNAIVER 358
                                   5555555544.4559**********98 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00014
                                   ETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   5 GsnvlIgpfaviggnVkIGdnvkIg 29 
                                    + v+Ig +a++ +  ++G++v I 
  gi|70606969|ref|YP_255839.1| 345 MDRVYIGDNAIV-ERSIVGRHVEIR 368
                                   467888888888.777788888886 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.0025
                                   EEEETTEEE-T.........TEEEETTEEE-TTEEEE CS
                       Hexapep   2 tvIGsnvlIgp.........faviggnVkIGdnvkIg 29 
                                   +++G +v I++         ++vi++++++ +++ I 
  gi|70606969|ref|YP_255839.1| 359 SIVGRHVEIRSspkkptvvvNSVIADGTVVDEGTEIV 395
                                   57999999999999999999***********999985 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   3.1   6.6e-08    0.0002     169     243 ..     326     400 ..     190     414 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.6e-08
                       DUF4954 169 kksevGeigekvkilnaglikNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavi 243
                                      ++  ig++vk++++ ++  v+igd a +e +   +   i Ss ++p+ + ++Vi++ +++ +G++i ++ + 
  gi|70606969|ref|YP_255839.1| 326 SIDNFTIIGRRVKVVKSAVMDRVYIGDNAIVERSIVGRHVEIRSSPKKPTVVVNSVIADGTVVDEGTEIVNSKIY 400
                                   44567789999*********************99999999***************************99998765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     4e-08   0.00012       5     119 ..      13     146 ..       9     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                                   EESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH....CHHHH............HHTTCTS-EEE CS
                  NTP_transf_3   5 AGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd....eevla............alarlgvrvve 64 
                                    GG+++R+      + Ka ++l ++pl+e++l  l+++g++e++  ++     +++ +            +  +++v++ +
  gi|70606969|ref|YP_255839.1|  13 IGGEATRLRpltieTSKATVRLLNRPLIEYTLIELARQGIKEIIFGVRGyvnyRSLFDiyqegigfsaryH-IKPRVHFKY 92 
                                   69******7444425****************************9998773322333224444444444322.344788888 PP

                                   -TTSS.-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEE CS
                  NTP_transf_3  65 dedpg.kgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvv 119
                                   ++  +  g + s++  ++  + +d+vlv+ +D  +  +  v++ll+ +++++a ++
  gi|70606969|ref|YP_255839.1|  93 QPRVDsIGNADSVRINMEYYNINDPVLVVQGDNLF--KLDVKKLLEYHEEKRAMMT 146
                                   8777538************99************99..8899999999887766544 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.38   1.1e+03      52     123 ..     118     182 ..     109     200 .. 0.62
   2 ?    5.5   0.2    0.0024         7     271     306 ..     334     369 ..     303     372 .. 0.71
   3 ?    3.4   0.1      0.01        30     269     308 ..     370     409 ..     361     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                    Fucokinase  52 vlvtssDvlllfdsee.isfdka.gvtalavpstldigtnHGVfvlddqsseeeeleirsvkkflhKpseeelq 123
                                   vlv+ +D l   d ++ ++ +++  +++  v ++++  ++ GV  l+++         +++++f+ Kp +ee  
  gi|70606969|ref|YP_255839.1| 118 VLVVQGDNLFKLDVKKlLEYHEEkRAMMTIVIKPMENVEEFGVAELESD---------NKIRRFVEKPRREEAP 182
                                   6777777776553333033333323333334456667777788888888.........8888888888888865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0024
                    Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigs 306
                                    +++ v++S +  +v +g+++++e s ++ +v+i+s
  gi|70606969|ref|YP_255839.1| 334 GRRVKVVKSAVMDRVYIGDNAIVERSIVGRHVEIRS 369
                                   556778888888888888888888888888888876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.01
                    Fucokinase 269 kkkesavvinSvlessvsvgegsviehsslkgnvsigsns 308
                                   + k+  vv+nSv++ +  v+eg+ i +s++ ++  i + s
  gi|70606969|ref|YP_255839.1| 370 SPKKPTVVVNSVIADGTVVDEGTEIVNSKIYPHKVINADS 409
                                   447889***********************99888888776 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0029       8.6       2      26 ..     308     339 ..     307     340 .. 0.78
   2 ?    4.7   0.3    0.0085        25       3      27 ..     332     357 ..     331     361 .. 0.75
   3 ?   -1.4   0.2       0.7   2.1e+03      23      33 ..     379     389 ..     378     390 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0029
                                   EEE-TT-EE-TT-EE...S....EEE-TT-EE CS
                     Hexapep_2   2 viIGdnCliGanagi...G....vslGdncvv 26 
                                   + IG  C iG++ +i        +++G++++v
  gi|70606969|ref|YP_255839.1| 308 ILIGRHCQIGKDTYIeesSidnfTIIGRRVKV 339
                                   56************877525577888888776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0085
                                   EE-TT-EE-TT-EES.EEE-TT-EE- CS
                     Hexapep_2   3 iIGdnCliGanagiG.vslGdncvvg 27 
                                   iIG ++ + ++a++  v +Gdn++v+
  gi|70606969|ref|YP_255839.1| 332 IIGRRVKVVKSAVMDrVYIGDNAIVE 357
                                   66666666677777668999999997 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.7
                                   T-EE-TT-EE- CS
                     Hexapep_2  23 ncvvgaGvvit 33 
                                   n+v++ G v++
  gi|70606969|ref|YP_255839.1| 379 NSVIADGTVVD 389
                                   88999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2533.54
//
Query:       gi|70606970|ref|YP_255840.1|  [L=444]
Description: alpha-amylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-72  243.6   4.2      5e-72  242.8   4.2    1.3  1  Glyco_hydro_57  Glycosyl hydrolase family 57


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.8   4.2   2.8e-76     5e-72       1     316 [.       5     289 ..       5     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 242.8 bits;  conditional E-value: 2.8e-76
                                   EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHHHHHH CS
                Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateelleli 81 
                                   +++f++Hqp++ k +  ++++p +r +  e+Y++ +l+   f + +                    +k+y+pat+++l+ i
  gi|70606970|ref|YP_255840.1|   5 ILGFEVHQPFRIKGS--YFWNPQFRDNPIEKYFDNQLNRDVFLRAK--------------------QKCYIPATKIILDEI 63 
                                   689********7665..*****************************....................*************** PP

                                   HHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHH CS
                Glyco_hydro_57  82 eeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkare 162
                                   e+g++++++ k      ++++isg+++eq++kw  +ev++l+++l  + +vE+l+++yyH+++ l+ d +++++qvk++ e
  gi|70606970|ref|YP_255840.1|  64 ERGENEGYDVK------VFYSISGTFMEQAEKW-GREVIDLLQQLSYTRKVEFLSQTYYHSITGLWDDLDEWKEQVKQHSE 137
                                   ***********......****************.*********************************************** PP

                                   HHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--CHH-TTTSGGG CS
                Glyco_hydro_57 163 lyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdreLsddigFry 243
                                   l++eyf q+P++f ++El+v+p+il+ +++lGf+ ++ ++++++l+++   sp+++y++kn+++  ++R+++Lsddi+Fr+
  gi|70606970|ref|YP_255840.1| 138 LIKEYFDQTPTTFENTELLVTPRILKEVENLGFKSIIMEGKESVLNGR---SPNYVYRIKNSKLVGLLRNYRLSDDIAFRF 215
                                   ************************************************...****************************** PP

                                   -................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHH CS
                Glyco_hydro_57 244 s....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielvtpsefikkl 316
                                   s    +qypl +++++ +w+  +   +++v +i++d+E++g  h+pe+g+++Fl++l++el++++ i++ +p+e++++ 
  gi|70606970|ref|YP_255840.1| 216 SnrnwDQYPL-TAQKLSDWVLWS---EGDVGLIFVDYETFGehHWPESGILDFLRWLPRELSRRE-IKMKLPKEVYDRA 289
                                   **********.**********98...***************************************.*********9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3082.12
//
Query:       gi|70606971|ref|YP_255841.1|  [L=566]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-31  108.6   0.1    6.5e-31  107.9   0.1    1.3  1  Glyco_transf_5   Starch synthase catalytic domain
    3.7e-28   98.2   0.0      7e-28   97.3   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    3.3e-22   79.4   0.0    7.6e-22   78.2   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    5.4e-09   36.3   4.3    1.6e-07   31.5   3.7    2.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.9e-05   25.2   0.5     0.0003   21.3   0.5    2.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0031   17.9   0.0      0.023   15.1   0.0    2.2  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.079   13.0   0.1        4.3    7.4   0.0    2.6  2  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.1   2.6e-34   6.5e-31       1     226 [.      15     256 ..      15     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 2.6e-34
                Glyco_transf_5   1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPry.gaikeekkeleevaelskaaed.eveve.v...ekvk 75 
                                   +++++++E  ++a  GGL+ vv+ L k+L k+g +v+vi+P++ +++++ +++l ++ e+s  ae+  + +      +k++
  gi|70606971|ref|YP_255841.1|  15 HVWMISAELEKVASLGGLGPVVYNLGKELVKQGIKVTVIMPSHgRHLNDYYRSLLKLNEISLVAEGdRIGIDgKsyhYKLG 95 
                                   69*****************************************999999999999999999999998888876256899** PP

                Glyco_transf_5  76 vaklkkdgvdvyfldnpeffd.....reglYgdkgedyednaerfalfsraalellek.lgw.kpdvihahDWhtalvpal 149
                                   + + + dg++v++++  ++ +      +++Y       ++  e+ +l++ra+ ++++  +++ +p +ih+hDWh++++++ 
  gi|70606971|ref|YP_255841.1|  96 FEHGNLDGMNVVLIKGLDYNTgriidSWNIY-------DNAMEKSSLLARAVEKYAKFsIPNdIPSIIHVHDWHSVIAGVT 169
                                   ******************7754333344566.......67889999***********9555548***************** PP

                Glyco_transf_5 150 lkelykerglfkkiktvftiHNlayqgrfp.....kdelaalglpa........edfekldglefygkvnflkagivyada 217
                                   +k   + r ++  +++vft+H l  + + p     +d++  +++p+        + +++ +  +f +  +  k g ++ad 
  gi|70606971|ref|YP_255841.1| 170 AKFTFEARRVI--VPLVFTVH-LLNKVSAPwhyasEDWSGLMNYPHyiwriikhDLYTTREVWDFFSSGSIEKFGSYEADL 247
                                   **997677776..9*******.6667677744443334455777755666655433334444455559************* PP

                Glyco_transf_5 218 vttVSptya 226
                                   +t VS++y 
  gi|70606971|ref|YP_255841.1| 248 ITSVSKSYL 256
                                   ********6 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   2.7e-31     7e-28      13     159 ..     345     499 ..     336     507 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 2.7e-31
                                   TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.....STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
               Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG....ngeeekelkklaeelelsdnviflgevsredleel 89 
                                   e+ ++il+ gr++++Kg+d l+ af+++ k+  +n++l+i G    +   ++++ + +  ++   n++++  ++ ++l  l
  gi|70606971|ref|YP_255841.1| 345 ENGPLILFAGRMVYQKGIDSLLIAFDEVLKT-INNARLIILGlpssDYGLLQNVVSNISRHGG--NIRIILGKMSKELYRL 422
                                   7889*************************98.***********99988889999999999988..5555555554556555 PP

                                   HHC.ESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT-HHHHHHHHHHHHHSH CS
               Glycos_transf_1  90 lkn.adifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpnnaealaeairkllede 159
                                   + + a++fv+ps++E+fG+v++E+ma+g+pv+a+ +gg++e ++d        tGllv+p+n+ +l++a++++l+ +
  gi|70606971|ref|YP_255841.1| 423 FYYsASVFVIPSRWEPFGLVAVESMAVGTPVVAYSVGGLRESIVDIRvdqeqgTGLLVEPENVWELSKALISALSLS 499
                                   5555*****************************************999999********************999865 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0     3e-25   7.6e-22       2     132 ..     348     496 ..     347     497 .. 0.78

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 3e-25
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---.......HHHHHHHT..T-T.T.EEEE---.TH.HHHHH CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rp....eeleelaa..gleer.veftGfv.ed.laell 70 
                                   p ilf Gr+   +kg+d ll a+ +++k  + +rl+i G  p  +    +++ + ++  g   +  +++G++ ++  + ++
  gi|70606971|ref|YP_255841.1| 348 PLILFAGRM-VYQKGIDSLLIAFDEVLKTiNnARLIILG-LPsSDygllQNVVSNISrhG--GNiRIILGKMsKElYRLFY 424
                                   789******.456**********999988856*******.44333333323332332332..343788999975647778* PP

                                   HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--........TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv........gengllvppgdpealaeailrLl 132
                                    +a+vfv+Ps  e fgl+++E+ma+g+pvVa +vgg++e +        + +gllv+p+++ +l +a++  l
  gi|70606971|ref|YP_255841.1| 425 YSASVFVIPSrwEPFGLVAVESMAVGTPVVAYSVGGLRESIvdirvdqeQGTGLLVEPENVWELSKALISAL 496
                                   **********999**************************88877555322468**************99877 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   3.7   6.1e-11   1.6e-07       2     109 ..      30     201 ..      29     255 .. 0.77
   2 ?   -2.7   0.0       2.1   5.3e+03     121     143 ..     414     436 ..     404     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.1e-11
                Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev............................................. 37 
                                   GG + +v++L ++L ++G++Vtv+ p+++++l +                                               
  gi|70606971|ref|YP_255841.1|  30 GGLGPVVYNLGKELVKQGIKVTVIMPSHGRHLNDYYrsllklneislvaegdrigidgksyhyklgfehgnldgmnvvlik 110
                                   9***************************999999999**********************************9999998877 PP

                Glyco_transf_4  38 ....elvvrvprvplpllkrllrslaflrrlrrllkre....kpDvvHahspaalgaallalrr....rlgiplVltvHgl 106
                                        +++ + ++++  ++   +s   +r++ + +k       p ++H+h++++++a++ a       r  +plV+tvH l
  gi|70606971|ref|YP_255841.1| 111 gldyNTGRIIDSWNIYDNAME-KSSLLARAVEKYAKFSipndIPSIIHVHDWHSVIAGVTAKFTfearRVIVPLVFTVHLL 190
                                   766444444444443333333.33333444444444447777999**********999998888**999**********99 PP

                Glyco_transf_4 107 ye........k 109
                                             +
  gi|70606971|ref|YP_255841.1| 191 NKvsapwhyaS 201
                                   97755433320 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                Glyco_transf_4 121 rllralerrllrradrviavSea 143
                                   ++ ++l+r ++ +a  ++ +S++
  gi|70606971|ref|YP_255841.1| 414 KMSKELYRLFYYSASVFVIPSRW 436
                                   5678899999999*999999997 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.5   1.2e-07    0.0003       1     105 [.      30     200 ..      30     256 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapg..................................apeleedgvrvhrlpv 47 
                                   gG g +v++l ++L+++G  Vtv+ p+  +                                                   
  gi|70606971|ref|YP_255841.1|  30 GGLGPVVYNLGKELVKQGIKVTVIMPSHGRHlndyyrsllklneislvaegdrigidgksyhyklG--------------- 95 
                                   89***********************87777754444445554433332222222222222222111............... PP

               Glyco_trans_4_4  48 prrpspladlaal........................................ralrrll..rqrrerpdvvhahsptagl 86 
                                                                                        ra++ +   +     p ++h+h++++ +
  gi|70606971|ref|YP_255841.1|  96 -F----------EhgnldgmnvvlikgldyntgriidswniydnamekssllaRAVEKYAkfSIPNDIPSIIHVHDWHSVI 165
                                   .1..........0222222233345555555555556656666666665433344444445555699999********999 PP

               Glyco_trans_4_4  87 aarla.....rrrrgiplvvtlh...........g 105
                                   a++ a     +rr  +plv+t+h           +
  gi|70606971|ref|YP_255841.1| 166 AGVTAkftfeARRVIVPLVFTVHllnkvsapwhyA 200
                                   998886666534678********665554333330 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.8e-06     0.023       3      90 ..     431     547 ..     428     549 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.8e-06
               Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgk...........................evilfe..dleelae 54 
                                   + psr e + l+ +E +a G+++++ +  gl+e + + +                           ++ +++  +  ++++
  gi|70606971|ref|YP_255841.1| 431 VIPSRWEPFGLVAVESMAVGTPVVAYSVGGLRESIVDIRvdqeqgtgllvepenvwelskalisalSLSMASetNNGDFLK 511
                                   5699999*******************99999999999889999********************999666666678889999 PP

               Glyco_trans_1_2  55 kiryllanpeerraiaeaarervlaehtydhraeql 90 
                                     +   ++ +++++i+++  +rv +++++   a+ql
  gi|70606971|ref|YP_255841.1| 512 YTEVKTNDVKLWDKIRQNCVRRVNENFRWSASAKQL 547
                                   99988889999******************9999997 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0017       4.3      11      36 ..      34      59 ..      25      76 .. 0.79
   2 ?    2.9   0.1      0.04     1e+02      74     107 ..     152     188 ..     128     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
               Glyco_trans_4_2 11 vhtlrlakeLakrgyeVhvitpkkga 36
                                  +++++l keL k+g++V+vi p  g+
  gi|70606971|ref|YP_255841.1| 34 PVVYNLGKELVKQGIKVTVIMPSHGR 59
                                  578899***************95553 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
               Glyco_trans_4_2  74 kPDvvhahyakpygllgslaarls.....gvipvvlsvw 107
                                    P ++h+h   ++ ++g   a+++       +p+v++v+
  gi|70606971|ref|YP_255841.1| 152 IPSIIHVHDWHSV-IAG-VTAKFTfearrVIVPLVFTVH 188
                                   599******8886.334.444443101002356666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3911.71
//
Query:       gi|70606972|ref|YP_255842.1|  [L=200]
Description: hypothetical protein Saci_1202 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-37  129.3   0.0    1.3e-37  129.1   0.0    1.1  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.0   7.3e-42   1.3e-37       3     172 .]      22     167 ..      20     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 7.3e-42
                                   ----.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHH CS
                Oxidored_molyb   3 avpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLe 83 
                                    vp+v+ +++rl++ g+ve++++++++++ ++  v++t +++C++              +w   +v n+eW+G++++++ e
  gi|70606972|ref|YP_255842.1|  22 GVPQVNLNEYRLKIFGEVENKIEITYEEMLKMIDVKYTKDFHCVT--------------GW---SVENVEWEGIKMKTIAE 85 
                                   699999***************************************..............8*...9**************** PP

                                   HTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEE CS
                Oxidored_molyb  84 kagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievs 164
                                   ka+vk p a++v+f+++d      +y++ +ple+al++d ++A++mng+pL  + G+P R ++p+l+g++s+Kwl+ i++s
  gi|70606972|ref|YP_255842.1|  86 KAKVK-PGAKWVIFYSLD------GYTTVVPLEDALHEDSIIALKMNGRPLDIKSGFPARPFIPHLYGWKSAKWLTAIQFS 159
                                   ****7.***********9......5***********99******************************************* PP

                                   SS---SHH CS
                Oxidored_molyb 165 deesegyw 172
                                   +e  +g+w
  gi|70606972|ref|YP_255842.1| 160 REYIDGFW 167
                                   **999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1266.41
//
Query:       gi|70606973|ref|YP_255843.1|  [L=539]
Description: thermosome gamma subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.2e-159  531.2  21.7   2.6e-159  531.0  21.7    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.0  21.7  1.4e-163  2.6e-159       1     490 [.      28     521 ..      28     522 .. 0.98

  Alignments for each domain:
  == domain 1  score: 531.0 bits;  conditional E-value: 1.4e-163
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   la+++k++lGPkGmdKml++   +v++TnDG+ti+ke++i+hPaakl+veaa++qd +vGDGTt++v+L g L +ea kli
  gi|70606973|ref|YP_255843.1|  28 LAEMLKSSLGPKGMDKMLISGTSDVTITNDGVTIVKEMDIQHPAAKLVVEAAKAQDAQVGDGTTSAVVLSGFLADEADKLI 108
                                   79******************************************************************************* PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTS..SXXSTHHHHHHHHHHHH.HCHCCCS.. CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssk..ltskeaeelsklvvdAv.klieene.. 157
                                   ++++hp++iiegy+kal+ ale  k++   +s++ +dr++L++va t+lssk    s++ +++ +  +dA+ +++e+ +  
  gi|70606973|ref|YP_255843.1| 109 DQKIHPIVIIEGYKKALQIALETGKSV--GLSVNPQDRKSLKNVAFTALSSKffANSETLNRIIDVSIDAIlSVVEKVDna 187
                                   ************************999..9999999****************654566678999999****9999888899 PP

                                   EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHH CS
                    Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaee 238
                                   +++dl++ik +k++g+s+++++lv+G++ldk+v++++mp+++e+ak+++ld++Le ek+e+++++ ++d+++++  ++++ 
  gi|70606973|ref|YP_255843.1| 188 YKVDLSNIKFIKKKGESVDETTLVRGYILDKEVAHENMPRRVEKAKIAILDFPLEVEKPEISAKMSFNDPSQIKLALEEQA 268
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEECC CS
                    Cpn60_TCP1 239 kqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveeek 319
                                   k+++ +++ + k g++vv++qkg dd+alhflak+gi+++++v+++d+e++akatGa+++ssl+d+++e+lG+a+ vee+k
  gi|70606973|ref|YP_255843.1| 269 KYIRSMIDTLEKIGAKVVITQKGMDDIALHFLAKKGIMGIKNVSRSDVEKVAKATGAKIISSLKDVSSEDLGQAELVEERK 349
                                   ********************************************************************************* PP

                                   ETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHH CS
                    Cpn60_TCP1 320 igsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeql 400
                                   ig+ k+++ie++k+ k++t+l+rg+++ ++de+er+ +d+ln++kn+ie++++v GGG+ e+ela k++e++k+v g+eql
  gi|70606973|ref|YP_255843.1| 350 IGNSKVILIEDSKDTKAVTVLIRGSSEIIMDELERSFQDSLNAIKNVIESPYIVGGGGSYEVELAMKIREESKKVGGKEQL 430
                                   ********************************************************************************* PP

                                   HHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEE.ECCCCTXEEEHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1 401 aieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeii.dlveagvvDplkvkrqalksAteaasti 480
                                   aieafa+ALe+i  tLa  aG+d i+++ klr+ h++g k +gi+v +g+++ d+++++++Dpl vk+++lksAtea++ +
  gi|70606973|ref|YP_255843.1| 431 AIEAFANALEEITTTLAGTAGMDEIDTVVKLRNLHASGMKFAGINVLKGKVEeDVTKENIIDPLIVKESVLKSATEAVTAL 511
                                   **************************************************7516*************************** PP

                                   HCEEEEEXXX CS
                    Cpn60_TCP1 481 Lrideiikak 490
                                   L+id+ i a 
  gi|70606973|ref|YP_255843.1| 512 LKIDDYIAAS 521
                                   *****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3534.91
//
Query:       gi|70606974|ref|YP_255844.1|  [L=105]
Description: hypothetical protein Saci_1205 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.1   0.0       0.34   10.7   0.0    2.1  2  WIYLD     Ubiquitin-binding WIYLD domain
      0.091   12.6   0.1       0.16   11.8   0.1    1.3  1  SinI      Anti-repressor SinI


Domain annotation for each model (and alignments):
>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.1     9e+02      28      46 ..      22      42 ..      16      46 .. 0.69
   2 ?   10.7   0.0   3.8e-05      0.34       8      27 ..      67      86 ..      55      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                         WIYLD 28 vlkkLLkvYgkn..WeliEed 46
                                   l+++L +Y +   W  + ++
  gi|70606974|ref|YP_255844.1| 22 YLQDVLFIYKNGntWVTVSAE 42
                                  578888888755689776665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.8e-05
                         WIYLD  8 idaAidamkelGfskeqvrp 27
                                  id+A++ ++++G+s e+vr+
  gi|70606974|ref|YP_255844.1| 67 IDKAVNELRRMGISIEEVRN 86
                                  9**************99985 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.7e-05      0.16      13      24 ..      75      86 ..      73      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                                  HHHT--SHHHHH CS
                          SinI 13 kesGlskeEfRe 24
                                  + +G+s+eE+R+
  gi|70606974|ref|YP_255844.1| 75 RRMGISIEEVRN 86
                                  68*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 685.14
//
Query:       gi|70606975|ref|YP_255845.1|  [L=188]
Description: hypothetical protein Saci_1206 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-05   23.0   0.0     0.0036   17.9   0.0    2.4  2  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.039   13.3   0.0       0.06   12.7   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.067   13.9   0.0        0.6   10.9   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
        0.1   12.1   0.2          1    8.9   0.0    2.3  2  DNA_gyraseA_C    DNA gyrase C-terminal domain, beta-propeller


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.043   1.9e+02      48      71 ..      18      42 ..       1      52 [. 0.72
   2 !   17.9   0.0     8e-07    0.0036      51      93 ..     110     147 ..      84     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.043
                                  TTEECCC.TSS-TT-EEEEEEES-C CS
               Methyltransf_11 48 vvadaek.lpfednsfDlvvssevl 71
                                  +  +  k lp+ ++++D+++s + l
  gi|70606975|ref|YP_255845.1| 18 INLSYGKiLPLTEHTYDFIISPNLL 42
                                  444455526***********98776 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 8e-07
                                   ECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEE CS
               Methyltransf_11  51 daeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGl 93 
                                    +  lpf+d+ fD vv+sev+++     ++++e++Rv k gG+
  gi|70606975|ref|YP_255845.1| 110 AIIPLPFKDSVFDNVVISEVMDY-----DVVREAYRVTKRGGK 147
                                   44559**************9877.....59************7 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05      0.06     109     152 ..     113     151 ..      99     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                                   T-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
               Ubie_methyltran 109 eLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                    Lpf+d  fD v +s     v D++ +++eayrv k GG+ +++
  gi|70606975|ref|YP_255845.1| 113 PLPFKDSVFDNVVIS----EVMDYD-VVREAYRVTKRGGKGMII 151
                                   69**********998....799997.78***********97766 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22   9.7e+02      58      73 ..      26      41 ..       4      50 .. 0.79
   2 ?   10.9   0.0   0.00013       0.6      57      97 .]     113     146 ..      97     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                                  BSSSTTTEEEEEEEST CS
               Methyltransf_25 58 lpfedgsfDlvvssga 73
                                  lp+ ++++D+++s + 
  gi|70606975|ref|YP_255845.1| 26 LPLTEHTYDFIISPNL 41
                                  789999******9655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                                   GBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  57 dlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    lpf+d+ fD vv+s ++ +       ++++e++rv+k gG
  gi|70606975|ref|YP_255845.1| 113 PLPFKDSVFDNVVISEVMDY-------DVVREAYRVTKRGG 146
                                   589***********866666.......599**********9 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   4.7e+02      33      45 ..      99     111 ..      90     113 .. 0.80
   2 ?    8.9   0.0   0.00023         1      19      34 ..     138     153 ..     136     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                   SETTTTSSEEEEE CS
                 DNA_gyraseA_C  33 iklkegdklvsvl 45 
                                   +kl+ +d++v ++
  gi|70606975|ref|YP_255845.1|  99 YKLDSKDEIVRAI 111
                                   499999***9887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00023
                                   GS-BT-TTSCTEEGSE CS
                 DNA_gyraseA_C  19 elpeqgRgakGvkgik 34 
                                    +++++Rg+kG +++ 
  gi|70606975|ref|YP_255845.1| 138 AYRVTKRGGKGMIIVP 153
                                   79**********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1417.27
//
Query:       gi|70606976|ref|YP_255846.1|  [L=126]
Description: hypothetical protein Saci_1207 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-18   66.8   0.1    3.7e-09   36.9   0.0    2.1  2  CBS           CBS domain
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.024   14.1   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   4.1e-13   3.7e-09       1      55 [.       4      57 ..       4      59 .. 0.93
   2 !   28.1   0.1   2.3e-10   2.1e-06       8      56 ..      75     123 ..      67     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 4.1e-13
                                  HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                  V+ +m+++++ v  +t++ e  +lm ekgv+++ ++ e+g + Gi+t+rD ++a 
  gi|70606976|ref|YP_255846.1|  4 VKTYMSTPIFQVELNTSIQETCKLMLEKGVGSV-IITENGAPKGIFTDRDAVKAF 57
                                  6789*****************************.7779************99986 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-10
                                   SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   +++ + +dt+   a++lm+++++++lPV d+ g+++G++  +D+ ++l+
  gi|70606976|ref|YP_255846.1|  75 NLIIIEEDTDPFTAIDLMTKNKIRHLPVKDKKGNIIGMFAITDISKVLH 123
                                   578999************8888**********************99886 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-06     0.024     122     193 ..      32     107 ..      17     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-06
                                   HHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTT.EEEEEEHHHHHHH..TTTHHHHHHHHHGG.EEEEEE.EESS CS
                  AP_endonuc_2 122 kegvklalEtlagsgvelgdeelarlldavdspn.vgvclDtgHllia..eedvddalraladr.ikhvHikDakg 193
                                    +g  ++ E++a++g+++ ++ ++++ + +++   v+++   g+l+i    +d+ +a++ + +  i+h+ +kD kg
  gi|70606976|ref|YP_255846.1|  32 GVGSVIITENGAPKGIFTDRDAVKAFSSGLNPNDeVRLAATMGNLIIIeeDTDPFTAIDLMTKNkIRHLPVKDKKG 107
                                   456789*************9999999999998889*************8877888888888777799999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 962.79
//
Query:       gi|70606977|ref|YP_255847.1|  [L=235]
Description: hypothetical protein Saci_1208 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-22   78.1   0.9      4e-21   75.7   0.9    1.9  1  DSBA           DSBA-like thioredoxin domain
    6.5e-21   74.8   0.3    8.8e-21   74.4   0.3    1.2  1  Thioredoxin_5  Thioredoxin
      3e-08   34.0   1.4    8.6e-06   26.0   1.4    2.2  1  Thioredoxin_4  Thioredoxin
    0.00012   22.0   0.1     0.0042   17.1   0.0    2.4  2  Thioredoxin_3  Thioredoxin domain
    0.00065   20.1   1.7      0.021   15.2   1.7    2.3  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.9   1.1e-24     4e-21       1     190 [.      15     212 ..      15     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.1e-24
                                   EEEEEEBTTBHHHHHHHHHHHHHHHHCCT.EEEEEEE-SSSCHHHHCT.S.GGG...SHHHHHHHHHHHHHHHHHHT.... CS
                          DSBA   1 tvdeffDvlCPyCylgkerleklaarspd.vkvvlrpfelagakkasgnvgpse...lpeklkylledlkrlaeaegiplr 77 
                                   ++ +f Dv+CP+Cy+ ++rl+k+++  +d v v++++f +  +  +++     e    pe+ k l+ +  ++ +++  ++ 
  gi|70606977|ref|YP_255847.1|  15 KITFFHDVICPFCYVTSKRLRKVITEFKDqVVVKHKAFAIISSLEDLK-----EvafTPEEAKKLFFNEFQIVKKYFPDYD 90 
                                   589************************666*************66443.....34469999999887777777888999** PP

                                   GGSSHHH.HHHHHHHH..HHHHHHHH..GHHHHHHHHHH....HHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHH CS
                          DSBA  78 fpkdklk.nstraarl..llaagaeg..laekvvrelfe....alwsegqaitddqellevaekaGldaeeldealeseav 149
                                    +k+  k + t+++ +  l+a +a++  + ++  +e+++    +++ +g++itd+q+l ++a+++ ld ++++e++ s++ 
  gi|70606977|ref|YP_255847.1|  91 PDKIIEKsKFTYVWSIppLVACKAAEfqKGDEGHWEFYDkaqdRFFLQGEDITDEQVLISIAKELNLDLNKFREDIRSKKT 171
                                   ****88889999999854455555557788888888886222267789********************************* PP

                                   HHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHH CS
                          DSBA 150 keavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtlad 190
                                      v +++++a+++g+ GvP+++++++  v G+++ + ++d
  gi|70606977|ref|YP_255847.1| 172 RLSVIQDEEEAKAMGIKGVPAILINDEWLVRGVQSEEYYRD 212
                                   ***************************9999*999987766 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.3   2.4e-24   8.8e-21       3     165 ..      19     197 ..      17     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 2.4e-24
                 Thioredoxin_5   3 FidPlcseCweiEpelkklkveygekiklrfilllnlktlnksskkkkkas............asrtgmsidgdvl.leel 70 
                                   F d +c+ C+ + + l+k++ e ++++ +++  +  +++l++ ++   +++            ++++   +d d++  +++
  gi|70606977|ref|YP_255847.1|  19 FHDVICPFCYVTSKRLRKVITEFKDQVVVKHKAFAIISSLEDLKEVAFTPEeakklffnefqiVKKYFPDYDPDKIiEKSK 99 
                                   7899***********************999877666665555555544444556999***999888888888888844445 PP

                 Thioredoxin_5  71 lsssY..laslaiKAAelQgkkkgr.kFLrklqealflekkniskeellleiaekaglDveefkeDlesklakkafqcDlk 148
                                   ++  +  ++ +a+KAAe+Q   +g+ +F  k q+ +fl+ ++i++e++l++ia++ +lD+++f+eD+ sk +  +  +D +
  gi|70606977|ref|YP_255847.1| 100 FTYVWsiPPLVACKAAEFQKGDEGHwEFYDKAQDRFFLQGEDITDEQVLISIAKELNLDLNKFREDIRSKKTRLSVIQDEE 180
                                   55544225788********98888659****************************************************** PP

                 Thioredoxin_5 149 lakemgvtevPtlvffn 165
                                    ak mg++ vP++ + +
  gi|70606977|ref|YP_255847.1| 181 EAKAMGIKGVPAILIND 197
                                   ************99987 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.4   2.4e-09   8.6e-06      16     161 ..      15     211 ..      10     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.4e-09
                                   EEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---S.TTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHT CS
                 Thioredoxin_4  16 tvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkek.eslkaamaarcageespeaflaikallysqqeew 95 
                                   +++ ++d+ Cp C   ++ + k+++e+  +++v + ++ f++       ++ a   + a++   + f  +k+++ + +++ 
  gi|70606977|ref|YP_255847.1|  15 KITFFHDVICPFCYVTSKRLRKVITEF--KDQVVVKHKAFAIISSLeDLKEVAFTPEEAKKLFFNEFQIVKKYFPDYDPDK 93 
                                   677788888888888888888888888..7777777777754444412233334444444443456666677676666666 PP

                                   TS-.................HHHHH............................................HHHHHTS----- CS
                 Thioredoxin_4  96 aes.................lkelaae.......................................aldkdekfeacleee 120
                                     +                 +     +                                          +  kf ++++++
  gi|70606977|ref|YP_255847.1|  94 IIEkskftyvwsipplvackA-----AefqkgdeghwefydkaqdrfflqgeditdeqvlisiakeLNLDLNKFREDIRSK 169
                                   555333334444444333321.....03444556666666666677777777777777777776643444788999***** PP

                                   --HHHHHHHHHHHHHHT--SS-EEEETTEE.E-TT--HHHHH CS
                 Thioredoxin_4 121 kldalveaeskeakkagiestPtfiingek.veepqtyeelk 161
                                   k +  v ++ +eak++gi+++P ++in+e  v + q+ e ++
  gi|70606977|ref|YP_255847.1| 170 KTRLSVIQDEEEAKAMGIKGVPAILINDEWlVRGVQSEEYYR 211
                                   ****************************98566666666555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.033   1.2e+02       9      28 ..      23      42 ..      12      69 .. 0.72
   2 !   17.1   0.0   1.2e-06    0.0042      34      74 ..     174     213 ..     146     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.033
                                  SSTTCHHHHHHHHHHCHCCT CS
                 Thioredoxin_3  9 gCakCpklekavkeaaaekg 28
                                   C+ C+ ++k ++++++e +
  gi|70606977|ref|YP_255847.1| 23 ICPFCYVTSKRLRKVITEFK 42
                                  4*************999865 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-06
                                   ECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHHH CS
                 Thioredoxin_3  34 ekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirkl 74 
                                     ++d ee + +g+  vPa++i+++  v G v see  r +
  gi|70606977|ref|YP_255847.1| 174 SVIQDEEEAKAMGIKGVPAILINDEWLVRG-VQSEEYYRDV 213
                                   44588899999*******************.9999876655 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.7     6e-06     0.021       8     105 ..      15     210 ..      11     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                 Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkel.....ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd................. 65 
                                    +++f+d+ Cp+C    k l+++     d+v v++ +f+ +++  + k va+  ++ kk  f++                 
  gi|70606977|ref|YP_255847.1|  15 KITFFHDVICPFCYVTSKRLRKVitefkDQVVVKHKAFAiISSLEDLKEVAFTPEEAKKLFFNEfqivkkyfpdydpdkii 95 
                                   5899*********99998888888888999999999999999999999999999999986666677788888889999999 PP

                 Thioredoxin_2  66 ...............................................................................ie 67 
                                                                                                                  + 
  gi|70606977|ref|YP_255847.1|  96 ekskftyvwsipplvackaaefqkgdeghwefydkaqdrfflqgeditdeqvlisiakelnldlnkfredirskktrlsVI 176
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999966 PP

                 Thioredoxin_2  68 envelarkygvrgtPtivfldgkeivarlpGyvpaeel 105
                                   + +e a+++g++g+P+i++ d+      ++G  ++e +
  gi|70606977|ref|YP_255847.1| 177 QDEEEAKAMGIKGVPAILINDEW----LVRGVQSEEYY 210
                                   77777888899999999998888....66777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1697.15
//
Query:       gi|70606978|ref|YP_255848.1|  [L=360]
Description: hypothetical protein Saci_1209 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-24   84.2   3.7    5.1e-24   84.2   3.7    1.8  2  ArnB_C    Archaellum regulatory network B, C-terminal domain
    7.3e-15   55.7   0.1    1.6e-14   54.5   0.1    1.5  1  VWA       von Willebrand factor type A domain
    5.7e-09   36.1   0.0    1.7e-08   34.6   0.0    1.8  1  VWA_3     von Willebrand factor type A domain
    2.1e-07   31.5   0.0    5.8e-07   30.1   0.0    1.7  2  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.7e+03      51      72 ..     108     127 ..     102     131 .. 0.68
   2 !   84.2   3.7   1.1e-27   5.1e-24       1      78 []     290     360 .]     290     360 .] 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                   HTT--S-HHH.......HHHHH CS
                        ArnB_C  51 TrrLsrdlesteklskedlSEv 72 
                                   T +L +++++   l+k ++SE+
  gi|70606978|ref|YP_255848.1| 108 TTNLHKAITK--VLEKFKSSEI 127
                                   4555555555..7788888887 PP

  == domain 2  score: 84.2 bits;  conditional E-value: 1.1e-27
                                   HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHT-HHHHHHHTT--S-HHH.......HHHHHHHHHTG CS
                        ArnB_C   1 kdvinEyrYyellkkysealeagnlkeATrilqeleeiAeqTrrieliEaTrrLsrdlesteklskedlSEvtrklrs 78 
                                   ++vinE++Yy+ll+ y +++++g+ +eATr++qel ++Ae+T+r+eliE+T++L +d +        dlSEvt+++r+
  gi|70606978|ref|YP_255848.1| 290 RTVINEVSYYMLLRYYGNLISEGKSEEATRVVQELLTAAERTKRVELIERTKKLVNDPKV-------DLSEVTKTMRT 360
                                   68**********************************************************.......*********95 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   3.6e-18   1.6e-14       3     170 ..      42     194 ..      42     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 3.6e-18
                                   EEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HH CS
                           VWA   3 vfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntg 82 
                                   v+++D+S sm  e++++ +++ +++lv++++   +g  +++  fs++++t +   + +  +    +l+++  + g ttn+ 
  gi|70606978|ref|YP_255848.1|  42 VVMIDNSPSMkKENKINLALSSASRLVQDII---PGNFISIYLFSNDIETLYEGESGK--QI---ELKSI--KMGYTTNLH 112
                                   789*******7788899**************...*****************9999955..33...45554..4467777** PP

                                   HHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGC.TEEEEEEEESSSHHHHHHHHHSSSSCHHCEEE CS
                           VWA  83 kalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeq.gikvfavGvgnadekelLnkiasepgeghvft 162
                                   ka+ ++lek+ +s+       +  iill+dGk++d+ +++  ++++   +++++++G g++++++ ++ +a +++ g ++ 
  gi|70606978|ref|YP_255848.1| 113 KAITKVLEKFKSSEI------PVKIILLSDGKPTDKRYSRDYESLQVPkNVQLITIGLGEDYNEAIMKILADKGS-GVFYH 186
                                   ********8777755......5889***********99********888****************5555566555.***** PP

                                   ESSHHHHH CS
                           VWA 163 vtdfeele 170
                                    +d ++l 
  gi|70606978|ref|YP_255848.1| 187 INDPSQLP 194
                                   ***99987 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   3.7e-12   1.7e-08      77     152 ..     108     183 ..      40     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.7e-12
                         VWA_3  77 asnlegaLkealrqpakpgevrsvilltDgssaqgeervsdlis..rarekirfhalglgsslsaamlqaLAeasgGt 152
                                    +nl++a+ ++l+++++ +++ ++ill+Dg ++   +r s + +  + +++++++++glg++ ++a+++ LA  + G 
  gi|70606978|ref|YP_255848.1| 108 TTNLHKAITKVLEKFKSSEIPVKIILLSDGKPTD--KRYSRDYEslQVPKNVQLITIGLGEDYNEAIMKILADKGSGV 183
                                   589****************************744..3444444411677*************************9996 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   1.3e-10   5.8e-07       2     107 .]      42     138 ..      41     138 .. 0.91
   2 ?   -3.1   0.0       2.8   1.2e+04      22      42 ..     315     336 ..     297     342 .. 0.60

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.3e-10
                         VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaa 81 
                                   v+++D+S Sm  +    +++  a + +++l++++ pg+ +++  fs++ e+l   +++k+    +l++++  g  tnl++a
  gi|70606978|ref|YP_255848.1|  42 VVMIDNSPSMKKE----NKINLALSSASRLVQDIiPGNFISIYLFSNDIETLYEGESGKQI---ELKSIKM-GYTTNLHKA 114
                                   899********99....6**************8879*******************998774...4677775.588****** PP

                         VWA_2  82 LqlarkalkkrrkgekrvivlitDge 107
                                   + ++ + +k+     +  i+l++Dg+
  gi|70606978|ref|YP_255848.1| 115 ITKVLEKFKSSE--IPVKIILLSDGK 138
                                   *********885..**********95 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                         VWA_2  22 eaakdaveallkslp.gdrvgl 42 
                                   e a + v++ll +   + rv l
  gi|70606978|ref|YP_255848.1| 315 EEATRVVQELLTAAErTKRVEL 336
                                   4445555555554432445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.57
# Mc/sec: 1907.03
//
Query:       gi|70606979|ref|YP_255849.1|  [L=206]
Description: hypothetical protein Saci_1210 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   60.6   0.1    2.9e-16   59.6   0.1    1.6  1  FHA            FHA domain
    1.9e-09   37.7   0.0    3.3e-09   36.9   0.0    1.3  1  Yop-YscD_cpl   Inner membrane component of T3SS, cytoplasmic 
    1.8e-06   27.5   3.2      3e-06   26.8   3.2    1.4  1  zinc_ribbon_2  zinc-ribbon domain
     0.0014   17.9   1.6     0.0022   17.3   1.6    1.3  1  zf-RanBP       Zn-finger in Ran binding protein and others
     0.0021   18.0   1.5     0.0036   17.3   1.5    1.4  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.029   13.8   1.1      0.049   13.1   1.1    1.4  1  zf-ribbon_3    zinc-ribbon domain
       0.16   11.7   3.7        2.2    8.1   3.7    2.4  1  A2L_zn_ribbon  A2L zinc ribbon domain
        1.4    8.8  12.1        1.8    8.5  12.1    1.1  1  TFIIA          Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   1.3e-19   2.9e-16       1      69 []     128     196 ..     128     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.3e-19
                                   EEEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEE.TTEEEST.TSEEEE-TTEEEEET CS
                           FHA   1 vtiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfv.Ngqrigk.gepveLksgdvielG 69 
                                   v++GRs+++ ++++d+++SrkHa+i+ d++  ++y+eDl+S+nGt+v +g++ ++ + ++++  +++i+lG
  gi|70606979|ref|YP_255849.1| 128 VSMGRSPENIVIVPDSEVSRKHAVIYLDNS--ELYIEDLNSTNGTYVyDGKQFTPiKGKQKIEPNSIIKLG 196
                                   689***************************..***************855555544558888888888887 PP

>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   1.5e-12   3.3e-09      19      84 ..     128     198 ..     125     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.5e-12
                                   EEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EE.TTEE-S....ECC--TTSEEEETTE CS
                  Yop-YscD_cpl  19 vviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllv.ngerve....elelrpgdvlelGtt 84 
                                   v +G+++++ +++ D+evsrkh++++++++++ +edl+s+ng++v +g++++    +++++p++ ++lG+ 
  gi|70606979|ref|YP_255849.1| 128 VSMGRSPENIVIVPDSEVSRKHAVIYLDNSELYIEDLNSTNGTYVyDGKQFTpikgKQKIEPNSIIKLGNQ 198
                                   67899***99********************************98758899997655556**********75 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   3.2   1.3e-09     3e-06       1      21 [.       4      24 ..       4      26 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                 zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                  +C  CG+e++d+a FC +CG+
  gi|70606979|ref|YP_255849.1|  4 KCNLCGYENDDDALFCIKCGA 24
                                  7*******************8 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.6   9.9e-07    0.0022       5      29 ..       3      27 ..       2      28 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.9e-07
                                  EE-SSS--EEESSSSB-TTT--BTS CS
                      zf-RanBP  5 WdCskClvqNfawstkCvaCqapkp 29
                                  W+C+ C++ N   ++ C+ C+a k+
  gi|70606979|ref|YP_255849.1|  3 WKCNLCGYENDDDALFCIKCGAQKS 27
                                  **********************996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.5   1.6e-06    0.0036       1      26 [.       5      30 ..       5      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.6e-06
                           DZR  1 CpqCgeelppdarfCseCgtklkava 26
                                  C  Cg e+++da fC +Cg++ +++a
  gi|70606979|ref|YP_255849.1|  5 CNLCGYENDDDALFCIKCGAQKSSEA 30
                                  999****************9966544 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   2.2e-05     0.049       4      24 ..       4      24 ..       1      25 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                   zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGt 24
                                  +C+ CG  + ++d+ +C +CG+
  gi|70606979|ref|YP_255849.1|  4 KCNLCGYeN-DDDALFCIKCGA 24
                                  7********.***********8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.7     0.001       2.2      17      29 ..      12      24 ..       3      26 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                 A2L_zn_ribbon 17 seqgylvCieCga 29
                                   +++ l+Ci+Cga
  gi|70606979|ref|YP_255849.1| 12 NDDDALFCIKCGA 24
                                  4789********8 PP

>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  12.1   0.00079       1.8     154     228 ..      29      97 ..      14     135 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00079
                         TFIIA 154 iaaqplqqvvqq..sqgsaaqssvaalqaqsqqaqalaepqqqlekqqqqqqqqqqqqqqqqvqqqqqeesqqaqqa 228
                                    a+q  qq+ ++  +qg ++q++v    +     qa++ + qq  + qq++  q+++ q+q v+++    +qqa+q+
  gi|70606979|ref|YP_255849.1|  29 EAQQLPQQQPSEpqAQGVVTQQQVVTNPPV----QAQVATPQQ--PAQQPVLPQPEPAQPQPVSSTPA--PQQASQP 97 
                                   222222222111123444444333332222....112222222..11233333444433332222221..2222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1398.60
//
Query:       gi|70606980|ref|YP_255850.1|  [L=380]
Description: hypothetical protein Saci_1211 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-27   95.0  10.6    2.2e-27   95.0  10.6    1.8  2  ArnB_C    Archaellum regulatory network B, C-terminal domain
    1.6e-17   64.3   0.1    5.9e-17   62.5   0.0    1.8  2  VWA       von Willebrand factor type A domain
    4.2e-13   49.9   0.2    4.4e-12   46.6   0.0    2.4  2  VWA_2     von Willebrand factor type A domain
      5e-09   36.3   0.0    1.2e-08   35.1   0.0    1.6  2  VWA_3     von Willebrand factor type A domain
      3e-05   23.5   0.0    7.9e-05   22.2   0.0    1.6  2  VWA_CoxE  VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   6.2e+03       5      39 ..      88     122 ..      85     127 .. 0.48
   2 !   95.0  10.6   6.2e-31   2.2e-27       1      78 []     294     380 .]     294     380 .] 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                        ArnB_C   5 nEyrYyellkkysealeagnlkeATrilqeleeiA 39 
                                   +Ey     l +  +++ +g +    r l+++ eiA
  gi|70606980|ref|YP_255850.1|  88 SEYADAPSLVQQIKQIRSGGQTVLYRALERAIEIA 122
                                   55555555555556666664433334444444444 PP

  == domain 2  score: 95.0 bits;  conditional E-value: 6.2e-31
                                   HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHT-HHHHHHHTT--S-HHH................HHHHH CS
                        ArnB_C   1 kdvinEyrYyellkkysealeagnlkeATrilqeleeiAeqTrrieliEaTrrLsrdles.........teklskedlSEv 72 
                                   +d++nEyrYyel+ k++++l+++nl eATr++++++ iA+qTrr+eliE+Trr s+++e+         t+k ske++SEv
  gi|70606980|ref|YP_255850.1| 294 NDLVNEYRYYELMSKLANQLNSNNLSEATRTVEQMQMIAQQTRRMELIETTRRISESIETtrrigtveqTRKISKEITSEV 374
                                   69******************************************************************************* PP

                                   HHHHTG CS
                        ArnB_C  73 trklrs 78 
                                   t+klrs
  gi|70606980|ref|YP_255850.1| 375 TKKLRS 380
                                   ****96 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   1.6e-20   5.9e-17       3     172 ..      41     196 ..      41     199 .. 0.86
   2 ?   -1.1   0.1      0.53   1.9e+03      63      88 ..     308     331 ..     273     370 .. 0.62

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.6e-20
                                   EEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HHH CS
                           VWA   3 vfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntgk 83 
                                   +++lD+Sgsm + ++e++k+ + +l++++    eg ++++++fs++v +   + d     +l ++++++  ++gg+t +  
  gi|70606980|ref|YP_255850.1|  41 IILLDTSGSMYGVKIETAKQGAMELLSRIP---EGNKISFLTFSNNVNILSEYAD---APSLVQQIKQI--RSGGQTVLYR 113
                                   58****************************...****************855555...679*******8..777777799* PP

                                   HHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGC..TEEEEEEEESSSHHHHHHHHHSSSSCHHCEEE CS
                           VWA  84 alkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeq..gikvfavGvgnadekelLnkiasepgeghvft 162
                                   al+ a+e + k+        +  iilltdG+++d  p++ a e  ++   +kv+a+G+g+++++ lL+ i  +++ g  + 
  gi|70606980|ref|YP_255850.1| 114 ALERAIE-IAKKHDL-----PGYIILLTDGQPTD-VPETDAYEKLNYpeAYKVIAFGIGDDYNERLLKVITDKTA-GILYH 186
                                   *****99.6666666.....9*************.6665555555444699**************9999977777.***** PP

                                   ESSHHHHHHH CS
                           VWA 163 vtdfeeleel 172
                                   v+d +e+ e+
  gi|70606980|ref|YP_255850.1| 187 VEDAKEIAEM 196
                                   ***9987665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.53
                                   HHHHHHHTGSGGGGSSC-HHHHHHHH CS
                           VWA  63 ellsalnnlkysgggttntgkalkya 88 
                                   +l+++ln+ +  +  t+ t + ++  
  gi|70606980|ref|YP_255850.1| 308 KLANQLNS-NNLSEATR-TVEQMQMI 331
                                   33333333.23333333.33333333 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   1.2e-15   4.4e-12       2     107 .]      41     138 ..      40     138 .. 0.93
   2 ?    0.1   0.1      0.35   1.3e+03      59      94 ..     282     319 ..     267     347 .. 0.54

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.2e-15
                         VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaa 81 
                                   +++lDtSgSm +      ++e+ak+ + +ll+++p g++++ +tfs+++++l+   +   ++ + +++++  gg+t l  a
  gi|70606980|ref|YP_255850.1|  41 IILLDTSGSMYGV-----KIETAKQGAMELLSRIPeGNKISFLTFSNNVNILSEYAD-APSLVQQIKQIRS-GGQTVLYRA 114
                                   79**********9.....8***************9899****************988.5667777*****7.6******** PP

                         VWA_2  82 LqlarkalkkrrkgekrvivlitDge 107
                                   L+ a ++ kk     +  i+l+tDg+
  gi|70606980|ref|YP_255850.1| 115 LERAIEIAKKHD--LPGYIILLTDGQ 138
                                   ********9885..9*********96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.35
                         VWA_2  59 kakilnalrnleak.gggtnlaaaLqlarkalkkrr.k 94 
                                    ++++++l++++ +  ++ ++ + ++++ + l++++ +
  gi|70606980|ref|YP_255850.1| 282 ANDVKRFLDGINNDlVNEYRYYELMSKLANQLNSNNlS 319
                                   45555555555555544444444455555544444432 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.2e-12   1.2e-08       4     153 ..      41     184 ..      39     186 .. 0.92
   2 ?   -3.4   0.0       2.4   8.4e+03      61      73 ..     318     330 ..     307     352 .. 0.59

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.2e-12
                         VWA_3   4 vivvDvsssmsaen.klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgasnlega 83 
                                   +i++D+s sm + + +++k++   +l   p++ ki+ l f  ++  l+  ++a s      + q ik++    g++ l +a
  gi|70606980|ref|YP_255850.1|  41 IILLDTSGSMYGVKiETAKQGAMELLSRIPEGNKISFLTFSNNVNILSEYADAPS------LVQQIKQIRS-GGQTVLYRA 114
                                   79**********9998888888888889***************998888887777......999****998.9******** PP

                         VWA_3  84 LkealrqpakpgevrsvilltDgss.aqgeervsdlisrarekirfhalglgsslsaamlqaLAeasgGty 153
                                   L++a++  +k   +  +illtDg++ + +e+++ +++   +e+++++a+g+g++ ++++l+ +   + G++
  gi|70606980|ref|YP_255850.1| 115 LERAIEIAKKHDLPGYIILLTDGQPtDVPETDAYEKL-NYPEAYKVIAFGIGDDYNERLLKVITDKTAGIL 184
                                   ******88899**************888*********.889********************9999998875 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
                         VWA_3  61 lqealqkikelel 73 
                                   l+ea   +++++ 
  gi|70606980|ref|YP_255850.1| 318 LSEATRTVEQMQM 330
                                   4444444444333 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.2e-08   7.9e-05      59     164 ..      39     141 ..      20     152 .. 0.81
   2 ?   -2.4   0.4      0.71   2.5e+03     103     141 ..     321     356 ..     315     365 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                      VWA_CoxE  59 elvllvDvSgSmaaysaiflallhAllqqlp.....rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGgTriga 134
                                     ++l+D SgSm    +i  a   A+    +     ++++++F+ ++  l++  ++ ++++ +++++      gG T +++
  gi|70606980|ref|YP_255850.1|  39 HYIILLDTSGSMYG-VKIETAKQGAMELLSRipegnKISFLTFSNNVNILSEYADAPSLVQQIKQIR-----SGGQTVLYR 113
                                   5699********99.5555555555432222447999***********9999999888888888888.....89******* PP

                      VWA_CoxE 135 alaeflelvtrpaLsrravvvlvsDglerg 164
                                   al+ ++e  ++ +L    +++l++Dg  ++
  gi|70606980|ref|YP_255850.1| 114 ALERAIEIAKKHDL--PGYIILLTDGQPTD 141
                                   *************8..99*******86554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.71
                      VWA_CoxE 103 lTralrerDpaeaLarvsaavedlgGgTrigaalaefle 141
                                    Tr ++     + +a+  ++ e ++ + ri++++++ ++
  gi|70606980|ref|YP_255850.1| 321 ATRTVE---QMQMIAQQTRRMELIETTRRISESIETTRR 356
                                   444444...444555555566666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2522.61
//
Query:       gi|70606981|ref|YP_255851.1|  [L=54]
Description: hypothetical protein Saci_1212 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-08   32.6   0.9    5.9e-08   32.5   0.9    1.1  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0058   17.1   0.3     0.0072   16.8   0.3    1.0  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
     0.0062   16.3   1.5     0.0084   15.9   1.5    1.3  1  eIF-1a          Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.9   9.8e-12   5.9e-08       1      39 [.       6      44 ..       6      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 9.8e-12
                                  EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCC CS
                MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilr 39
                                  +kv+++ +++iP  +r++  i+eGd v ++ d+ +  +r
  gi|70606981|ref|YP_255851.1|  6 VKVSRNFQITIPVRIRKKFPIKEGDLVKVIYDEKDNTVR 44
                                  69******************************9855554 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.2e-06    0.0072       3      48 ..       7      52 ..       6      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytil.ddgkvvisraeeea 48
                                  ++ + +q tiP  +Rk   +k+  d ++   + +d++v i + +ee+
  gi|70606981|ref|YP_255851.1|  7 KVSRNFQITIPVRIRKKFPIKE-GDLVKVIYDeKDNTVRIVKITEEE 52
                                  68899****************9.667665554146789999988875 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.5   1.4e-06    0.0084      27      62 ..      12      46 ..       2      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                                  EEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEE CS
                        eIF-1a 27 vlaeipgkfRnkiwikrGdyVlVelspydltkGrIv 62
                                  +  +ip ++R+k  ik+Gd V V   ++ ++  rIv
  gi|70606981|ref|YP_255851.1| 12 FQITIPVRIRKKFPIKEGDLVKVIY-DEKDNTVRIV 46
                                  67789******************99.4545566776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 392.52
//
Query:       gi|70606982|ref|YP_255852.1|  [L=418]
Description: hypothetical protein Saci_1213 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-14   52.9   2.2    8.4e-14   51.5   1.8    2.0  1  DUF402     Protein of unknown function (DUF402)
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.024   14.1   0.0    1.4  1  RNase_E_G  Ribonuclease E/G family
      0.015   14.7   0.1       0.92    8.8   0.0    2.2  2  ATPase     KaiC


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   1.8   1.4e-17   8.4e-14       9      68 .]     329     387 ..     321     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.4e-17
                                   TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                        DUF402   9 lglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                      wy ++ ++d +++l+glYv+i+tppe+ ++++++ Dl++D+v   +++v+++D++EL
  gi|70606982|ref|YP_255852.1| 329 SRNWYQIHRYHDRNNNLKGLYVNISTPPELLKNRIRYLDLEVDVVK-VNNTVNIIDLEEL 387
                                   578**********99***************8899***********5.366*********8 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-06     0.024       4     102 ..     127     225 ..     125     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-06
                     RNase_E_G   4 GrylVllpegkkvgvSkkiedeeererlkelleelkpeevGlIvRtaaegaseeelekdleelkkkwe..eilekakkrka 82 
                                   G+++ +   + ++ +S+ i++ ++ +rl ++   ++++++ +  R++a+ a+++el+++le+l+ +++  + +e+ +    
  gi|70606982|ref|YP_255852.1| 127 GKFAMVWKGDGRTFFSEHIDE-RDSQRLLSVSIPFNKKGYNVKWRSNAAMATTAELKEELENLTMRYSynDFREQGE-DFL 205
                                   666666655555799****98.678999999989999*************************998775225555554.333 PP

                     RNase_E_G  83 psllyeeedlllrvlrdlln 102
                                     +l  e++l+l  +r l+ 
  gi|70606982|ref|YP_255852.1| 206 KVTLSLEDKLFLDDIRSLVI 225
                                   44455555555555554443 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0059        35      36     120 ..     189     274 ..     187     283 .. 0.83
   2 ?    8.8   0.0   0.00015      0.92      48      95 ..     344     391 ..     337     416 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0059
                        ATPase  36 alqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaeekdkedleeli.eelaeai 115
                                    +++ ++  ++ ge  + vt+  + + +  +++sl +++ k+ +  k+++ + +  +e++ + + ++ l +li +++ eai
  gi|70606982|ref|YP_255852.1| 189 TMRYSYNDFREQGEDFLKVTLSLEDKLFLDDIRSLVINTMKFHHMLKMTYSNEVDIEEGKVNPSPEKLLTSLIgDNMIEAI 269
                                   6899*****************************************999998888888887766777777776634677777 PP

                        ATPase 116 keika 120
                                   +++k 
  gi|70606982|ref|YP_255852.1| 270 EHVKP 274
                                   77776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00015
                        ATPase  48 gepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaees 95 
                                   + +g++v +  p+e l+++++ l+ +++ ++ ++ ++iid+ e ++++
  gi|70606982|ref|YP_255852.1| 344 NLKGLYVNISTPPELLKNRIRYLDLEVDVVKVNNTVNIIDLEELEANK 391
                                   779***************************9999******99877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3141.04
//
Query:       gi|70606983|ref|YP_255853.1|  [L=848]
Description: aconitate hydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.5e-163  543.2   0.0   7.4e-163  542.8   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    6.8e-36  123.5   0.0    1.6e-35  122.3   0.0    1.6  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.8   0.0  8.3e-167  7.4e-163      12     461 .]      62     525 ..      45     525 .. 0.94

  Alignments for each domain:
  == domain 1  score: 542.8 bits;  conditional E-value: 8.3e-167
                     Aconitase  12 egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknledefernkery 87 
                                   ++ +++p rv+lqd+tg + lvdlaa+r+++++ g+++ +i++ v++dl idhsv     g++++l  n ++efern ery
  gi|70606983|ref|YP_255853.1|  62 KEFSFLPTRVVLQDYTGIPLLVDLAAMRDEMSKRGEDPLKINPIVQSDLIIDHSVqvdyyGTASSLLLNKKKEFERNVERY 142
                                   337899******************************************************99******************* PP

                     Aconitase  88 efLksaakaf.girvvppgqGIvHqvnlEy...........g..lalpgktvvgtDSHTtmigglGvlaiGvGgieaeavl 154
                                   +fLk+a+++f ++rv+ppg+GI+Hq+nlEy           g  +a+p+ +v+gtDSHT+m +glGvl +GvGg eaeav+
  gi|70606983|ref|YP_255853.1| 143 KFLKWAQRSFkNLRVFPPGKGIIHQINLEYlskvvdvkefrGqlTAYPE-IVIGTDSHTPMTNGLGVLSWGVGGLEAEAVM 222
                                   ***********************************999998456999*9.******************************* PP

                     Aconitase 155 lgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfp 235
                                   lg+p+++ +p+vvgv+l G++kegvt++D+vl++++klrkkgvvgk+vEffG+ + +L++ draTiaNMa+E+GAt+++fp
  gi|70606983|ref|YP_255853.1| 223 LGEPYTMAVPEVVGVRLVGEIKEGVTPTDIVLYITEKLRKKGVVGKFVEFFGPSLGNLTVPDRATIANMAPEYGATASYFP 303
                                   ********************************************************************************* PP

                     Aconitase 236 vdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavplselvkkefkeele 316
                                   +d +tl+YL+at re++   ve+y+kaq++f    +++++y++v+++dls++ep +agpk+P+++vpl++l+k  f+e+  
  gi|70606983|ref|YP_255853.1| 304 IDYQTLNYLAATAREYKL--VEKYAKAQGIF---YESQPKYSEVVTIDLSEVEPAIAGPKNPDERVPLKDLKK-LFQEKK- 377
                                   **************9988..8********98...455789****************************66665.566654. PP

                     Aconitase 317 keaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsvaPGSevvkayleaeGl 396
                                             ++k+g  +kd +v++ ai+SCTN+sn+ v++ ag+la ka ++g + k++vkts+aPGS vv +yl+++Gl
  gi|70606983|ref|YP_255853.1| 378 ----------DKKKGSLVKDLDVVLTAITSCTNTSNPTVMIGAGILAkKAIQHGIRSKSYVKTSMAPGSPVVVEYLKESGL 448
                                   ..........57889999*************************************************************** PP

                     Aconitase 397 leiLekaGfevvgagCstCignsdrle.......ege.....aivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                   l++Le++Gf+vvg+gC+tCign+++l+       + +      +v s+NRN+egR++p     +LaSP lvva++laG
  gi|70606983|ref|YP_255853.1| 449 LPYLEALGFHVVGFGCTTCIGNAGPLPkkieedvK-SnklevYGVISGNRNYEGRINPYLSGvFLASPVLVVAFSLAG 525
                                   **************************977755552.057889******************999*************99 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3   0.0   1.8e-39   1.6e-35      12     129 ..     658     774 ..     651     776 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1.8e-39
                                   CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---TH CS
                   Aconitase_C  12 tedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSReh 92 
                                   ++d + ++++++ ++++++g +an +l+n lv+ ++ + t++++dg+ ++v++a ++ykkeg +lv++agk++G+GSSR++
  gi|70606983|ref|YP_255853.1| 658 EQDLNTYGARRGDHEVMLRGGFANSKLKNLLVD-VQGGFTKHFPDGKVMSVYEASQQYKKEGVPLVIVAGKQYGSGSSRDW 737
                                   678899**************************9.*********************************************** PP

                                   HHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                   Aconitase_C  93 AAkalrllGikaviaeSFerIfennliknglLplefk 129
                                   AAk ++llG+kav+aeSFerI+++nl+ +g++p+e++
  gi|70606983|ref|YP_255853.1| 738 AAKVTALLGVKAVLAESFERIHRSNLVAMGVVPIEIP 774
                                   ***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 5906.80
//
Query:       gi|70606984|ref|YP_255854.1|  [L=429]
Description: hypothetical protein Saci_1215 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-26   91.5   7.3    1.2e-25   90.9   7.3    1.3  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   7.3   6.8e-30   1.2e-25       1     359 []       4     390 ..       4     390 .. 0.77

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 6.8e-30
                     Cas_DxTHG   1 vlisflGtgnykevkYe.......lkeeeeeeketsfvqeallellaekedpdkvvilltdtlad.......keaeekeea 67 
                                   +lis++ + n +e kYe       ++e+e +e++ s++++++l+    +e++d++ +ll+  l+        ++++ +   
  gi|70606984|ref|YP_255854.1|   4 LLISIWTNLNNRENKYEiinergeETEREVVESKPSLAEVKFLRES--EEQVDML-VLLPSFLSAylktqdlPDSYVE--- 78 
                                   69*******************9887777888888888888887777..6665555.5555545555888777777777... PP

                     Cas_DxTHG  68 aklkeele.elle.iekvdveiipgggte.............eelwe........ifekllekleendeiilDiThGfryl 125
                                     lk++++ e+l+ ++ +dve+ip++gt              +   +        ++++l+++  + d+++lD++ ++ yl
  gi|70606984|ref|YP_255854.1|  79 --LKKRIQeEVLKrFQGIDVEVIPSSGTIdadgfmhihdnslG---NfnfsvyysVYNALTRY--NPDTVLLDLSETTSYL 152
                                   ..999998788889****************9999999964441...45566333355555555..55************** PP

                     Cas_DxTHG 126 Pvla......llalaylrnvk.nltikgiyYgafkeeeedPil...............dlteflelsdwltaverflktgd 184
                                     ++      ++  +y+++ k +                 P++               ++++ +++sd+lt+ e       
  gi|70606984|ref|YP_255854.1| 153 TYYTsdaaklAIQDYYITKRKaD----------------IPLIefstdfankiitlkkSTIRNVDISDYLTSQE------- 210
                                   66669999988888888888844................34443223222333455556666666666666665....... PP

                     Cas_DxTHG 185 aeklaellrekkekkkeklkklkklkeklkkeleefskalelirp..lell.ekaekleke...........iveklkeel 251
                                                     +k +k + ++ k+el ++ +al+l++p  l++l ++ e+l+k+           +v+k+++e+
  gi|70606984|ref|YP_255854.1| 211 ------------------IKLAKGMPTLSKSELFAIGRALQLGFPlaLLYLlNGIEELTKPedfmqkieesiTVSKKEQEK 273
                                   ..................556679999999***************88888888999**999**999888877777778999 PP

                     Cas_DxTHG 252 eei.esleeeesakplel..................lldeikkklekf..lkkqikwclekgliqqaltllreliisllle 311
                                   e + +s  +++++ p+++                   ld++ k+++ +  +         ++li+++l++l+ l+    l+
  gi|70606984|ref|YP_255854.1| 274 EYLvSSGVRAYNTAPYYFmgyhfieaykvksetgeyTLDDLLKLIDVYneP--------ARSLIKRELEILKRLA---GLK 343
                                   9999988888888888888*****999999999999999999999999443........699*************...566 PP

                     Cas_DxTHG 312 ..gedilnkkkrreeieeelknlskvekksseekeeklsniRNdiaHaGl 359
                                     ge+il++ +r    ++ +  + +   + ++++++++s++ ++i+HaG+
  gi|70606984|ref|YP_255854.1| 344 ddGEYILDYLIRLG--NSRVLDWLENVPIGESKIDCEISEY-EMISHAGM 390
                                   899999******33..4444478888888888888886666.99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2691.52
//
Query:       gi|70606985|ref|YP_255855.1|  [L=157]
Description: hypothetical protein Saci_1216 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   88.5   3.3    2.4e-25   88.5   3.3    2.0  2  DUF2258         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
       0.01   15.8  11.1      0.011   15.7   8.8    2.2  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.012   15.4   1.2      0.032   14.0   1.0    1.8  2  DASH_Duo1       DASH complex subunit Duo1
      0.022   15.2   1.9       0.05   14.0   0.5    2.1  2  LPP             Lipoprotein leucine-zipper
      0.046   14.2   0.7       0.11   12.9   0.7    1.8  1  DUF4140         N-terminal domain of unknown function (DUF414
      0.088   13.3   1.1      0.088   13.3   1.1    2.2  2  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.12   12.3   3.6       0.69    9.9   0.9    2.3  2  DASH_Dad4       DASH complex subunit Dad4
       0.12   12.7   0.4       0.25   11.7   0.4    1.5  1  DASH_Hsk3       DASH complex subunit Hsk3 like
       0.27   11.3   2.5       0.59   10.2   0.9    2.2  2  Bcr-Abl_Oligo   Bcr-Abl oncoprotein oligomerisation domain
       0.92    9.3   3.1        2.1    8.1   1.7    2.0  2  HDV_ag          Hepatitis delta virus delta antigen
        2.1    8.8  11.3        2.7    8.5  11.3    1.2  1  AAA_23          AAA domain
        2.3    8.4  10.1        1.6    8.9   3.1    2.5  2  MetOD2          Metanogen output domain 2
        3.7    8.0  10.0       0.63   10.5   2.8    2.5  2  DHHA1           DHHA1 domain
        6.6    6.8   8.5       0.94    9.4   0.8    3.2  3  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   3.3   1.9e-28   2.4e-25       1      77 [.      33     106 ..      33     107 .. 0.97
   2 ?   -0.1   0.3      0.82   1.1e+03      36      63 ..     121     147 ..     112     153 .. 0.56

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.9e-28
                                   EEEECEEGGGHHHHHHHHHHHHTCCCCHTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEE..EEEEETTEE CS
                       DUF2258   1 lsTGlviaaaYAdKlRrvlfaalsklvkkkkeekkeiaraiaeLNkklYevlveklkidKldvvrirv..eyeveekkl 77 
                                   lsTGl+iaa+YAdKlRrv+++a+s++++     k++i+r++aeLNkklY+++v+++k++Kl+v+ri v  ey+++e+kl
  gi|70606985|ref|YP_255855.1|  33 LSTGLIIAARYADKLRRVALVAFSRVAP-----KDVIVRDVAELNKKLYDIIVKEMKLNKLSVIRILVdaEYNERENKL 106
                                   89**************************.....9**********************************99999999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.82
                                   HHHHHHHHHHHHHHHHHHCCTT--TTSE CS
                       DUF2258  36 eiaraiaeLNkklYevlveklkidKldv 63 
                                   e  +++ +LN k+ + l ++l+  K+++
  gi|70606985|ref|YP_255855.1| 121 ECSNQLKQLNEKIKD-LEKELQTYKEKI 147
                                   555566666666533.334444444444 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.9   2.4e+03      15      23 ..      69      77 ..      59      89 .. 0.54
   2 ?   15.7   8.8   8.5e-06     0.011      27      65 ..     118     156 ..     117     157 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                    TMF_DNA_bd 15 aqLmeEGek 23
                                  a+L + + +
  gi|70606985|ref|YP_255855.1| 69 AELNKKLYD 77
                                  333333333 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.5e-06
                    TMF_DNA_bd  27 kelklnntikkLrkknkelekeikelkkkleklekelee 65 
                                   +e + +n++k+L++k+k+leke++++k+k++k e+ l++
  gi|70606985|ref|YP_255855.1| 118 TEEECSNQLKQLNEKIKDLEKELQTYKEKIKKIEQLLSS 156
                                   566779*****************************9987 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.5   3.2e+03      48      59 ..      91     102 ..      89     106 .. 0.63
   2 ?   14.0   1.0   2.5e-05     0.032       7      38 ..     124     155 ..     119     157 .] 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                     DASH_Duo1  48 irIlsqtehtqr 59 
                                   irIl  +e++ r
  gi|70606985|ref|YP_255855.1|  91 IRILVDAEYNER 102
                                   566666666554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.5e-05
                     DASH_Duo1   7 eqLrkinevienviesLkkaksniervketve 38 
                                   +qL+++ne i++++++L++ k++i+++++ ++
  gi|70606985|ref|YP_255855.1| 124 NQLKQLNEKIKDLEKELQTYKEKIKKIEQLLS 155
                                   79*************************98665 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.4e+03       5      17 ..      64      76 ..      62      89 .. 0.77
   2 ?   14.0   0.5   3.9e-05      0.05       4      34 ..     121     151 ..     119     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                           LPP  5 LssqVsqLkskvd 17
                                  +  +V +L++k  
  gi|70606985|ref|YP_255855.1| 64 IVRDVAELNKKLY 76
                                  5679999999865 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.9e-05
                           LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                   e s+q++qL++k++ l+++++  k+ ++++ 
  gi|70606985|ref|YP_255855.1| 121 ECSNQLKQLNEKIKDLEKELQTYKEKIKKIE 151
                                   679*********************9999875 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   8.9e-05      0.11      65      93 ..     110     152 ..      82     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.9e-05
                       DUF4140  65 e..............elkalraeleeledelaaledelaaaea 93 
                                   +              +lk+l+++++ le+el+ ++++++ +e+
  gi|70606985|ref|YP_255855.1| 110 NirvirylteeecsnQLKQLNEKIKDLEKELQTYKEKIKKIEQ 152
                                   2444444433444437*********************999887 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.33   4.3e+02      10      35 ..      65      76 ..      61      97 .. 0.58
   2 ?   13.3   1.1   6.8e-05     0.088      34      66 ..     123     155 ..     117     157 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                       NPV_P10 10 radikavddkVdalqqqvddvqenlp 35
                                    d++++++k+               
  gi|70606985|ref|YP_255855.1| 65 VRDVAELNKKL--------------Y 76
                                  44444444443..............2 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.8e-05
                       NPV_P10  34 lpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   ++++++lnek+ ++ ++L++ ++k+++I+++L+
  gi|70606985|ref|YP_255855.1| 123 SNQLKQLNEKIKDLEKELQTYKEKIKKIEQLLS 155
                                   466788************************998 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.11   1.4e+02      26      47 ..      67      88 ..      63      96 .. 0.84
   2 ?    9.9   0.9   0.00054      0.69      20      45 ..     126     151 ..     123     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                     DASH_Dad4 26 svvelnkeleeinkkNknvelv 47
                                   v+elnk+l +i  k ++++ +
  gi|70606985|ref|YP_255855.1| 67 DVAELNKKLYDIIVKEMKLNKL 88
                                  58999**999999999988765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00054
                     DASH_Dad4  20 vekLnesvvelnkeleeinkkNknve 45 
                                   +++Lne++++l+kel+++++k k++e
  gi|70606985|ref|YP_255855.1| 126 LKQLNEKIKDLEKELQTYKEKIKKIE 151
                                   689****************9999887 PP

>> DASH_Hsk3  DASH complex subunit Hsk3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4    0.0002      0.25       7      27 ..     122     142 ..     120     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                     DASH_Hsk3   7 LasqLaqLqaNLadteellev 27 
                                   +++qL+qL++ ++d+e++l +
  gi|70606985|ref|YP_255855.1| 122 CSNQLKQLNEKIKDLEKELQT 142
                                   689**************9987 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       0.3   3.8e+02      21      47 ..     106     133 ..      96     134 .. 0.67
   2 ?   10.2   0.9   0.00046      0.59      25      48 ..     132     155 ..     125     157 .] 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                 Bcr-Abl_Oligo  21 meLdsvedieq.eLerCkaslrrLekel 47 
                                   +e+d ++ i     e+C ++l++L++++
  gi|70606985|ref|YP_255855.1| 106 LEFDNIRVIRYlTEEECSNQLKQLNEKI 133
                                   5556666555412368999999998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00046
                 Bcr-Abl_Oligo  25 svedieqeLerCkaslrrLekeln 48 
                                    ++d+e+eL++ k++++++e+ l+
  gi|70606985|ref|YP_255855.1| 132 KIKDLEKELQTYKEKIKKIEQLLS 155
                                   689******************987 PP

>> HDV_ag  Hepatitis delta virus delta antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.43   5.5e+02     127     180 ..       4      56 ..       2      71 .. 0.66
   2 ?    8.1   1.7    0.0016       2.1      14      46 ..     120     152 ..     112     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.43
                        HDV_ag 127 eeelrrlteederrerriagpqvggvnpleggtrgapgggfvpsmqgvpespft 180
                                   ee  +r  e  e  e+  a   v g n +e  t       +   ++ v    f+
  gi|70606985|ref|YP_255855.1|   4 EE-EKRDLERAEEYEHITARATVIGKNKIELSTGLIIAARYADKLRRVALVAFS 56 
                                   33.344456667777778888888888888777666666666555555555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                        HDV_ag  14 eevleqwvsgrkkleelerdlrkvkkkikkled 46 
                                   ee  +q     +k+++le++l+  k+kikk+e+
  gi|70606985|ref|YP_255855.1| 120 EECSNQLKQLNEKIKDLEKELQTYKEKIKKIEQ 152
                                   777788888899******************996 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  11.3    0.0021       2.7      94     175 ..      73     153 ..       4     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                        AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllek 174
                                   ++l++   k+ k +kl+ ++i    ++ +++ + +++++++i +l +e+   ++lk+ +e++++lekel++ ++++k++e+
  gi|70606985|ref|YP_255855.1|  73 KKLYDIIVKEMKLNKLSVIRILVDAEYNERENKLEFDNIRVIRYLTEEEC-SNQLKQLNEKIKDLEKELQTYKEKIKKIEQ 152
                                   22333333444555666677766667777777777778888888888885.345566777777777777777777777776 PP

                        AAA_23 175 l 175
                                   l
  gi|70606985|ref|YP_255855.1| 153 L 153
                                   5 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7     0.065        83      32      76 ..      69     112 ..      65     118 .. 0.70
   2 ?    8.9   3.1    0.0012       1.6      57      86 ..     127     156 ..     111     157 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.065
                        MetOD2  32 vevnkrllslLsqtydidddkaevseeie.aalknlekkleaqeer 76 
                                   +e nk+l++++ +  ++++  + v + +  a+  + e+kle+++ r
  gi|70606985|ref|YP_255855.1|  69 AELNKKLYDIIVKEMKLNK--LSVIRILVdAEYNERENKLEFDNIR 112
                                   689********99999994..4444433326666667777776666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                        MetOD2  57 eeieaalknlekkleaqeerlkqikkeles 86 
                                   +++++ +k+lek+l++ +e++k+i++ l+s
  gi|70606985|ref|YP_255855.1| 127 KQLNEKIKDLEKELQTYKEKIKKIEQLLSS 156
                                   466778888888888888888888888876 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7       0.3   3.8e+02      74      74 ..      55      55 ..       3     105 .. 0.53
   2 ?   10.5   2.8   0.00049      0.63       1      27 [.     126     152 ..     126     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.3
                                  E CS
                         DHHA1 74 f 74
                                  f
  gi|70606985|ref|YP_255855.1| 55 F 55
                                  1 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00049
                                   HHHHCHHHHHHHHHHHCHHHHHHHHHH CS
                         DHHA1   1 leslneerkelekeleelkealaklka 27 
                                   l++lne++k+lekel+ +ke+++k+++
  gi|70606985|ref|YP_255855.1| 126 LKQLNEKIKDLEKELQTYKEKIKKIEQ 152
                                   789************888888877654 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3   1.7e+03      11      15 ..       8      12 ..       8      13 .. 0.89
   2 ?    9.4   0.8   0.00073      0.94       4      17 ..     127     140 ..     125     142 .. 0.87
   3 ?    3.1   0.8     0.074        95       2      18 ..     139     155 ..     138     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                Pox_A_type_inc 11 sDLEr 15
                                  +DLEr
  gi|70606985|ref|YP_255855.1|  8 RDLER 12
                                  7***9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00073
                Pox_A_type_inc   4 srlRsRIsDLErqL 17 
                                    +l ++I DLE++L
  gi|70606985|ref|YP_255855.1| 127 KQLNEKIKDLEKEL 140
                                   57889********9 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.074
                Pox_A_type_inc   2 EmsrlRsRIsDLErqLs 18 
                                   E++ ++++I  +E+ Ls
  gi|70606985|ref|YP_255855.1| 139 ELQTYKEKIKKIEQLLS 155
                                   999******99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2688  (0.149925); expected 358.6 (0.02)
Passed bias filter:                     1023  (0.0570584); expected 358.6 (0.02)
Passed Vit filter:                       198  (0.0110436); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1048.81
//
Query:       gi|70606986|ref|YP_255856.1|  [L=99]
Description: hypothetical protein Saci_1217 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        0.1   12.5   7.3       0.17   11.8   7.3    1.4  1  DUF1275          Protein of unknown function (DUF1275)
       0.17   10.9  15.4       0.51    9.3  14.9    1.8  1  MtrC             Tetrahydromethanopterin S-methyltransferase,
       0.53   11.0   7.7       0.43   11.3   6.8    1.4  1  PrgI             PrgI family protein
       0.79   10.2  11.1         15    6.1  11.1    2.1  1  FUN14            FUN14 family
       0.81    8.0   2.4       0.92    7.8   2.4    1.1  1  CBP_BcsG         Cellulose biosynthesis protein BcsG
       0.89    9.7  12.3       0.82    9.8   7.9    2.2  2  SPC12            Microsomal signal peptidase 12 kDa subunit (
        4.2    7.3  12.3          1    9.3   9.0    1.7  2  DUF3487          Protein of unknown function (DUF3487)
        4.2    7.4  11.5        2.5    8.1   7.2    2.5  2  DUF4389          Domain of unknown function (DUF4389)
        6.6    5.3   8.5        8.1    5.0   8.5    1.0  1  Clostridium_P47  Clostridium P-47 protein
        9.6    6.1  10.5        1.6    8.6   6.3    1.7  2  Fig1             Ca2+ regulator and membrane fusion protein F
         10    6.7  17.1    1.2e+03    0.1  17.1    2.3  1  FtsX             FtsX-like permease family


Domain annotation for each model (and alignments):
>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.3    0.0001      0.17      51     101 ..      12      70 ..       4      99 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                       DUF1275  51 lvsllaFvlGaalagllarrggrrrrlvllleallllaaallvpagsvsp..........l 101
                                   +++++aFvlG +++ l+++    +  +++l+ +++l+a++++ p++ vs           +
  gi|70606986|ref|YP_255856.1|  12 VMAIVAFVLGFLVGYLIKNVI--KIGIIVLAIIVILIAIGVVSPHTVVSGlqsmgvyatqA 70 
                                   689**************9774..66777777788899999887654433344433333330 PP

>> MtrC  Tetrahydromethanopterin S-methyltransferase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  14.9   0.00032      0.51     104     181 ..      10      91 ..       3      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
                          MtrC 104 piialvvaliiglvvgvlakkvikmkipileksttelaaaga...lsiiglsvaiagsfeikailskviat.Gliallfil 180
                                    i+  +va ++g++vg l k+vik++i +l   ++ +a+  +    ++ gl ++ + + ++++++s++i+   + ++lfi+
  gi|70606986|ref|YP_255856.1|  10 EIVMAIVAFVLGFLVGYLIKNVIKIGIIVLAIIVILIAIGVVsphTVVSGLQSMGVYATQAEQYVSRIINYlPYNSILFII 90 
                                   6999***********************999988777765322111456677777777778888899888753577778877 PP

                          MtrC 181 a 181
                                   +
  gi|70606986|ref|YP_255856.1|  91 G 91 
                                   6 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.8   0.00027      0.43      19      81 ..       8      80 ..       2      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                          PrgI 19 lRQliflvlallvaiglylllrafleelasvlvillavPvaalgfy........kkdglp........lekylkaiikf 81
                                    ++++ ++a+++++++ +l+++++     ++v++++v ++a+g++             +        +e+y+ +ii +
  gi|70606986|ref|YP_255856.1|  8 YTEIVMAIVAFVLGFLVGYLIKNVI--KIGIIVLAIIVILIAIGVVsphtvvsgL----QsmgvyatqAEQYVSRIINY 80
                                  5678899999999999999999999..4444444455556677777444333330....23333344488888887766 PP

>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  11.1    0.0091        15       3      35 ..      16      48 ..      14      99 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0091
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         FUN14  3 iGaviGlvtGfalkkvgKlaaiavGggllllqi 35
                                  + +v+G+++G+++k v K+ +i++++ ++l+ i
  gi|70606986|ref|YP_255856.1| 16 VAFVLGFLVGYLIKNVIKIGIIVLAIIVILIAI 48
                                  679**********************99999876 PP

>> CBP_BcsG  Cellulose biosynthesis protein BcsG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.4   0.00057      0.92      95     131 ..      14      52 ..       8      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00057
                      CBP_BcsG  95 mllalivllivylllsqwirvttlvllalialsvle..k 131
                                    ++a+++ ++v +l++++i++ ++vl+++++l ++   +
  gi|70606986|ref|YP_255856.1|  14 AIVAFVLGFLVGYLIKNVIKIGIIVLAIIVILIAIGvvS 52 
                                   467777778888999***********9999998877431 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.9   0.00051      0.82      15      51 ..      12      48 ..       8      56 .. 0.68
   2 ?    2.3   0.1      0.11   1.8e+02      18      30 ..      85      97 ..      66      99 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00051
                         SPC12 15 vilvlsaviafivGyitqdlkltlyillagvvltllv 51
                                  v+ +++ v++f+vGy+++++    +i+la +v+ +++
  gi|70606986|ref|YP_255856.1| 12 VMAIVAFVLGFLVGYLIKNVIKIGIIVLAIIVILIAI 48
                                  567888999******9999766666665555555444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
                         SPC12 18 vlsaviafivGyi 30
                                  ++  +i+f++G +
  gi|70606986|ref|YP_255856.1| 85 SILFIIGFVIGLV 97
                                  4666788888865 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   9.0   0.00062         1      19      72 ..       5      57 ..       3      80 .. 0.87
   2 ?   -1.1   0.1         1   1.7e+03      28      38 ..      87      97 ..      75      99 .] 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                       DUF3487 19 GltadEllvlaglglvvglvlglllallvgslaliptialllvllvvlvggkll 72
                                  G+  +E+++ a +++v+g+++g l+  +++  +++++i+++l++++v+   +++
  gi|70606986|ref|YP_255856.1|  5 GIPYTEIVM-AIVAFVLGFLVGYLIKNVIKIGIIVLAIIVILIAIGVVSPHTVV 57
                                  666778766.5689*******************************999877665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                       DUF3487 28 laglglvvglv 38
                                  l+ +g+v+glv
  gi|70606986|ref|YP_255856.1| 87 LFIIGFVIGLV 97
                                  44566666665 PP

>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.2    0.0015       2.5      12      72 ..      23      82 ..       8      85 .. 0.78
   2 ?    0.1   0.1      0.47   7.6e+02       7      28 ..      76      97 ..      75      99 .] 0.56

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                       DUF4389 12 llfaivlslaslvlwvvvvvqflivLvtgrpnepLrdfgksllrYiarilrfltlnseekP 72
                                  l+ + + ++ +++++v++++++li++    +++++++ ++s++ Y +++ ++++   +  P
  gi|70606986|ref|YP_255856.1| 23 LVGYLIKNVIKIGIIVLAIIVILIAIGV-VSPHTVVSGLQSMGVYATQAEQYVSRIINYLP 82
                                  5556677888888888888888888877.66777888899***********9986655555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                       DUF4389  7 Rlllmllfaivlslaslvlwvv 28
                                  R++  l++  +l + ++v+++v
  gi|70606986|ref|YP_255856.1| 76 RIINYLPYNSILFIIGFVIGLV 97
                                  5555566666666666665544 PP

>> Clostridium_P47  Clostridium P-47 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.5     0.005       8.1     365     426 ..       5      65 ..       3      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.005
               Clostridium_P47 365 wviitevilgvivavigsvagavggkvkslvd..kiiiaiivaiiagiivaiqeiiedviakgv 426
                                   ++  te+++ +++ v+g ++g +   +k++++   i++aiiv +ia ++v+ + ++  ++  gv
  gi|70606986|ref|YP_255856.1|   5 GIPYTEIVMAIVAFVLGFLVGYL---IKNVIKigIIVLAIIVILIAIGVVSPHTVVSGLQSMGV 65 
                                   67789******************...66665422688999999999999998888888887777 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.3   0.00097       1.6      80     147 ..       5      63 ..       1      75 [. 0.85
   2 ?   -0.4   0.1      0.58   9.4e+02      79      96 ..      79      95 ..      67      98 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00097
                          Fig1  80 yllmvaiiLtlllfllllyfplgseipllPfkskavskvalvlsflllllwlvgalwqhvassaastl 147
                                    ++++ i+++++ f+l   f       l+ +  k+v k+ +++ +++++l+++g++  h+++s  +++
  gi|70606986|ref|YP_255856.1|   5 GIPYTEIVMAIVAFVLG--F-------LVGYLIKNVIKIGIIVLAIIVILIAIGVVSPHTVVSGLQSM 63 
                                   67889999999999999..3.......356666779**************************988877 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.58
                          Fig1 79 pyllmvaiiLtlllflll 96
                                  +yl++   iL++++f++ 
  gi|70606986|ref|YP_255856.1| 79 NYLPYN-SILFIIGFVIG 95
                                  455554.57889999886 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1  17.1      0.71   1.2e+03      27      80 ..      12      97 ..       3      98 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.71
                          FtsX 27 litlvalviGlglgllaaqllsdvllss.......................vf.....s....selkisidlitvliiivlll 77
                                  + ++va+v+G+++g+l+ +++  ++                          ++     +    s++  ++++ ++l+ii++++
  gi|70606986|ref|YP_255856.1| 12 VMAIVAFVLGFLVGYLIKNVIKIGIIVLaiiviliaigvvsphtvvsglqsMGvyatqAeqyvSRIINYLPYNSILFIIGFVI 94
                                  45788888888888888887665555554444444444444444444333311444431455699999999999999999988 PP

                          FtsX 78 lla 80
                                   l+
  gi|70606986|ref|YP_255856.1| 95 GLV 97
                                  775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1566  (0.0873445); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 706.24
//
Query:       gi|70606987|ref|YP_255857.1|  [L=125]
Description: hypothetical protein Saci_1218 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.8   10.3  12.6        4.1    8.1   0.1    2.3  2  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1   0.00023       4.1       7      47 ..       3      43 ..       1      59 [. 0.84
   2 ?    3.7   9.3    0.0051        92      57      78 ..     100     122 ..      70     125 .] 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00023
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 Ribosomal_60s  7 ikkvlkaagveveaarvkllvkalegkdieellangaakla 47
                                  + k + +a+++ + + +++  ++ + k+i e+l+n+ ++l 
  gi|70606987|ref|YP_255857.1|  3 VVKYVLTAKIDYDGKEIEIKRSFRHRKNIFEFLKNADSNLK 43
                                  67788899****************************99865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0051
                                   XXXXXXXXXXXXXXXXXXX..XX CS
                 Ribosomal_60s  57 aaaaaaaaaaeekkkeeeee.Ee 78 
                                   a++++++ ++e+k++++ee+ Ee
  gi|70606987|ref|YP_255857.1| 100 AKKKKEESKQEKKEQKKEEKqEE 122
                                   33333333333333333333255 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3891  (0.217023); expected 358.6 (0.02)
Passed bias filter:                      869  (0.048469); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 834.19
//
Query:       gi|70606988|ref|YP_255858.1|  [L=127]
Description: transcriptional regulator Lrs14-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-10   40.3   0.4    3.3e-10   39.7   0.4    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    2.6e-09   36.9   1.6    3.1e-09   36.6   1.6    1.1  1  TFIIE_alpha      TFIIE alpha subunit
    6.6e-08   32.3   0.0    1.4e-07   31.3   0.0    1.6  1  MarR_2           MarR family
    3.3e-06   26.6   0.3    5.8e-06   25.8   0.3    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    5.9e-06   26.1   0.3    1.2e-05   25.1   0.1    1.6  2  MarR             MarR family
    5.1e-05   23.1   1.4    0.00011   22.0   0.3    1.9  2  HTH_11           HTH domain
    0.00011   22.1   0.1     0.0011   19.0   0.0    2.0  2  HTH_20           Helix-turn-helix domain
    0.00017   21.3   0.1    0.00034   20.4   0.1    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0002   21.0   0.7    0.00051   19.7   0.2    1.8  2  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00023   21.0   0.0    0.00038   20.4   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00029   20.4   1.1     0.0022   17.6   0.0    2.2  2  GntR             Bacterial regulatory proteins, gntR family
    0.00052   20.2   0.1     0.0012   18.9   0.1    1.7  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00076   19.9   0.1     0.0012   19.3   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
     0.0036   17.1   0.1     0.0074   16.1   0.1    1.6  1  CvfB_WH          CvfB-like winged helix domain
     0.0068   16.3   0.2      0.015   15.2   0.2    1.5  1  TBPIP            TBPIP/Hop2 winged helix domain
      0.007   16.7   0.1      0.012   15.9   0.1    1.4  1  Rrf2             Transcriptional regulator
     0.0076   16.3   0.1      0.016   15.2   0.1    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0096   15.9   0.4      0.017   15.1   0.1    1.6  1  HTH_6            Helix-turn-helix domain, rpiR family
  ------ inclusion threshold ------
      0.019   15.3   0.1      0.035   14.5   0.0    1.6  1  Penicillinase_R  Penicillinase repressor
      0.019   14.9   0.4      0.068   13.1   0.1    1.9  2  HTH_36           Helix-turn-helix domain
      0.021   14.5   1.1      0.027   14.2   0.1    1.6  2  DUF4423          Domain of unknown function (DUF4423)
      0.022   14.3   0.0      0.043   13.4   0.0    1.5  1  GerE             Bacterial regulatory proteins, luxR family
      0.025   14.6   0.1      0.048   13.7   0.1    1.4  1  FeoC             FeoC like transcriptional regulator
      0.031   14.1   0.2      0.072   13.0   0.1    1.6  2  RuvB_C           RuvB C-terminal winged helix domain
      0.035   14.7   0.8      0.045   14.4   0.8    1.3  1  RTP              Replication terminator protein
      0.036   13.9   0.0      0.068   13.0   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
      0.036   14.2   0.3      0.071   13.3   0.1    1.6  1  HTH_34           Winged helix DNA-binding domain
       0.04   14.0   0.1      0.085   13.0   0.1    1.6  1  Pigment_DH       Pigment-dispersing hormone (PDH)
      0.083   12.7   0.1       0.17   11.7   0.1    1.5  1  HTH_10           HTH DNA binding domain
        0.1   12.5   0.6        3.7    7.5   0.0    2.5  2  Nas2_N           Nas2 N_terminal domain
       0.17   11.6   1.5       0.22   11.3   0.9    1.5  1  HDV_ag           Hepatitis delta virus delta antigen
       0.41   10.7   2.5          1    9.4   0.5    2.2  2  Put_DNA-bind_N   Putative DNA-binding protein N-terminus


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.4   5.9e-13   3.3e-10       3      59 ..      24      85 ..      21     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 5.9e-13
                                  HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....T CS
                          TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....p 59
                                   +GL + +++v ++L+ ++ +++ deia  l+v++++++++L++L dkGl+ rek++    +
  gi|70606988|ref|YP_255858.1| 24 IYGLPKSDIDVLQVLIsQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKEEageeK 85
                                  69**************88999*********************************99866661 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   1.6   5.6e-12   3.1e-09      10     102 ..      24     122 ..      17     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.6e-12
                                   CS-..HHHHHHHHHHHC.TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE...TTTEEEEEEEEEECCCHCCC CS
                   TFIIE_alpha  10 fyg..eeavlvldvLle.kgevteedlakelkidlnelrklLnrLyearlvkykrrrd...eekswykyywrinyeklvdv 84 
                                   +yg  ++ + vl+vL++ k  ++ +++a  lk+ +  + k Ln+Ly+++l+   ++      +k+  +y + ++ e+l + 
  gi|70606988|ref|YP_255858.1|  24 IYGlpKSDIDVLQVLISqKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKEEAgeeKKKGRPSYIYWVDGERLYEK 104
                                   5666678899****99725689*****************************77666546546778889************* PP

                                   HHHHHHHHHHHHHHHHCC CS
                   TFIIE_alpha  85 vkrkleevvkkLeeklek 102
                                   + r le ++++++++le+
  gi|70606988|ref|YP_255858.1| 105 LERDLETLASQIKKELEE 122
                                   ***************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.4e-10   1.4e-07       2      56 ..      26      79 ..      25      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.4e-10
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  gl+ ++ +vL +L    +r ++  e+a+ l++sk+++++ l+ L ++GL+ r++ 
  gi|70606988|ref|YP_255858.1| 26 GLPKSDIDVLQVLISQKRR-MSSDEIADVLKVSKASINKSLNNLYDKGLILREKE 79
                                  7888999******999975.9*****************************88843 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.3     1e-08   5.8e-06       3      47 ..      29      74 ..      27      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1e-08
                        HTH_24  3 etdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  + d+++L++L   + r+s  e+A+ l +S++ +n+ l++L ++GlI
  gi|70606988|ref|YP_255858.1| 29 KSDIDVLQVLISqKRRMSSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  679999*999995666*****************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.2e-08   1.2e-05      11      52 ..      38      79 ..      29      81 .. 0.92
   2 ?   -2.5   0.0         9     5e+03      30      39 ..     108     117 ..     101     124 .. 0.52

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.2e-08
                                  HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                  +++++  +s  e+a+ l+vsk+++ + l  L++kGli R+k 
  gi|70606988|ref|YP_255858.1| 38 LISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKE 79
                                  6899999********************************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9
                                   -HHHHHHHHH CS
                          MarR  30 skstvtrvld 39 
                                   +  t+  +++
  gi|70606988|ref|YP_255858.1| 108 DLETLASQIK 117
                                   4444444444 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3     2e-07   0.00011       4      45 ..      33      74 ..      32      82 .. 0.90
   2 ?   -0.7   0.0       2.6   1.4e+03      18      37 ..      98     117 ..      96     122 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2e-07
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                  ++l+ L++++  +s++e+A+ L+vS++ + + +  L ++g+ 
  gi|70606988|ref|YP_255858.1| 33 DVLQVLISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  689***9***99*********************999888855 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.6
                        HTH_11  18 geeLAeeLnvSrrtvrrdIk 37 
                                   ge+L e+L++   t    Ik
  gi|70606988|ref|YP_255858.1|  98 GERLYEKLERDLETLASQIK 117
                                   66677777766555555554 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     2e-06    0.0011      14      60 ..      33      80 ..      30      81 .. 0.95
   2 ?    1.1   0.0      0.77   4.3e+02      17      40 ..     103     126 ..     100     127 .] 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-06
                                  HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  ++l+ L ++++ ++  e+a+ l +sk+++++ L+ L + gL+ +++e+
  gi|70606988|ref|YP_255858.1| 33 DVLQVLiSQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKEE 80
                                  79999999***********************************99985 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.77
                                   HHHSTCTTB-HHHHHHHHTS-HHH CS
                        HTH_20  17 raLaraegltaselaerldlsknt 40 
                                     L r+ +  as+++++l+ ++++
  gi|70606988|ref|YP_255858.1| 103 EKLERDLETLASQIKKELEERMQS 126
                                   556667788899999999988886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   6.1e-07   0.00034      10      45 ..      37      74 ..      31      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.1e-07
                                  HHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5 10 lLae..gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   L +  + +++ e+a+ l++s++ +   L+ L++ GL+
  gi|70606988|ref|YP_255858.1| 37 VLISqkRRMSSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  55554567999**************************8 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   9.1e-07   0.00051       8      46 ..      38      76 ..      32      79 .. 0.93
   2 ?   -1.1   0.0         3   1.7e+03      33      41 ..     107     115 ..     107     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.1e-07
                      HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  l+ q++ +s +e+++ l+vS+a i + Ln+L  +gl+ R
  gi|70606988|ref|YP_255858.1| 38 LISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILR 76
                                  799**********************************99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                      HTH_DeoR  33 RDLneLeeq 41 
                                   RDL++L+ q
  gi|70606988|ref|YP_255858.1| 107 RDLETLASQ 115
                                   9***99987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.8e-07   0.00038      19      53 ..      42      76 ..      20      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.8e-07
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisr 53
                                  + +++ +e+A+ l ++  ++++ l+ L ++gli r
  gi|70606988|ref|YP_255858.1| 42 KRRMSSDEIADVLKVSKASINKSLNNLYDKGLILR 76
                                  3589*****************************75 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.9e-06    0.0022      23      58 ..      44      78 ..      32      81 .. 0.87
   2 ?    1.3   0.2      0.49   2.8e+02       3      24 ..      99     120 ..      98     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                                  B---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 23 kLPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                  ++ s  e+a+ ++Vs+ +++++L++L  +gl+ r++
  gi|70606988|ref|YP_255858.1| 44 RM-SSDEIADVLKVSKASINKSLNNLYDKGLILREK 78
                                  56.7789*************************9987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.49
                                   HHHHHHHHHHHHTTSS-TTSB- CS
                          GntR   3 eqvyerLredIlsgelrpGdkL 24 
                                   e++ye+L++d+ +   +    L
  gi|70606988|ref|YP_255858.1|  99 ERLYEKLERDLETLASQIKKEL 120
                                   6889999999987666555555 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   2.2e-06    0.0012      22      56 ..      44      78 ..      34      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-06
                                  SB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 22 vvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                    +  ++a +L+vs++s+ ++l+ L ++G++  ek
  gi|70606988|ref|YP_255858.1| 44 RMSSDEIADVLKVSKASINKSLNNLYDKGLILREK 78
                                  567889***********************987666 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.1e-06    0.0012       9      53 ..      35      81 ..      27      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.1e-06
                        HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv..ertgd 53
                                  L ++  + rr++  +++++l+v++++i +sl+ L  kGL+  e+++ 
  gi|70606988|ref|YP_255858.1| 35 LQVLISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLIlrEKEEA 81
                                  55555699********************************6544333 PP

>> CvfB_WH  CvfB-like winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.3e-05    0.0074      21      54 ..      46      79 ..      35      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                       CvfB_WH 21 dPeeIkavfgmSKkaFKrAvGaLlkqgkIeieed 54
                                  +++eI +v+++SK++  +++ +L+ +g+I  e++
  gi|70606988|ref|YP_255858.1| 46 SSDEIADVLKVSKASINKSLNNLYDKGLILREKE 79
                                  789**************************88776 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.6e-05     0.015       6      49 ..      34      75 ..      31      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                         TBPIP  6 vleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkii 49
                                  vl+ l +q r +s+ ++++ l+  ++K+++ k L++L d+g+i 
  gi|70606988|ref|YP_255858.1| 34 VLQVLISQKRRMSSDEIADVLK--VSKASINKSLNNLYDKGLIL 75
                                  78999***************96..9****************995 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.2e-05     0.012      19      55 ..      40      74 ..      31      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglv 55
                                  ++++   +ss+eia+  ++s+  + k l++L  +gl+
  gi|70606988|ref|YP_255858.1| 40 SQKR--RMSSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  4444..49****************************9 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.8e-05     0.016       6      44 ..      30      68 ..      29      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-05
                       HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseL 44
                                  ++++ l  L++++++++ de+a  L  s  ++++ +++L
  gi|70606988|ref|YP_255858.1| 30 SDIDVLQVLISQKRRMSSDEIADVLKVSKASINKSLNNL 68
                                  67889999****************************998 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     3e-05     0.017      15      53 ..      28      63 ..      21      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
                                  -HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHH CS
                         HTH_6 15 tksekkiaeyilaspdkaielsikalAkaaavSeativr 53
                                  +ks+    ++++   ++ +++s++++A  ++vS+a+i++
  gi|70606988|ref|YP_255858.1| 28 PKSDI---DVLQVLISQKRRMSSDEIADVLKVSKASINK 63
                                  55554...5555555667899****************99 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   6.2e-05     0.035       5      57 ..      31      80 ..      27      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-05
                                  -SHHHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEET CS
               Penicillinase_R  5 Eaevmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekeg 57
                                  +  v+++l ++++ ++++e+ + l+      ++++   l++L++Kgl+ reke+
  gi|70606988|ref|YP_255858.1| 31 DIDVLQVLISQKRrMSSDEIADVLKVS----KASINKSLNNLYDKGLILREKEE 80
                                  567999999999989999999999866....9******************9985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00012     0.068      27      55 .]      46      74 ..      37      74 .. 0.90
   2 ?   -0.8   0.0       2.7   1.5e+03      32      48 ..     113     119 ..      95     123 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  s + +a  l++sk ++ + +++L ++G+i
  gi|70606988|ref|YP_255858.1| 46 SSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  6689***********************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.7
                        HTH_36  32 akrlglsknTvsraike 48 
                                   a          s ++ke
  gi|70606988|ref|YP_255858.1| 113 A----------SQIKKE 119
                                   3..........334444 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.8e-05     0.027      25      74 ..      34      80 ..      30      91 .. 0.86
   2 ?   -1.9   0.1       4.1   2.3e+03     131     150 ..     102     121 ..      98     125 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-05
                       DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedg 74
                                  v++ l++ k    + +e+a+ l+  +s++ ++k+l+ L + gl+ +++++
  gi|70606988|ref|YP_255858.1| 34 VLQVLISQKRR-MSSDEIADVLK--VSKASINKSLNNLYDKGLILREKEE 80
                                  56777788887.999********..*******************999874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                       DUF4423 131 yekikkeirefrkkilaiae 150
                                   yek+++ ++++ ++i + +e
  gi|70606988|ref|YP_255858.1| 102 YEKLERDLETLASQIKKELE 121
                                   55555555555555555444 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.6e-05     0.043      18      44 ..      45      71 ..      31      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                                  S-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE 18 ksnkeIAeelniSekTVkvhksnimkK 44
                                  +s+ eIA+ l +S+ +++  + n++ K
  gi|70606988|ref|YP_255858.1| 45 MSSDEIADVLKVSKASINKSLNNLYDK 71
                                  6899********************988 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   8.6e-05     0.048       8      53 ..      38      83 ..      33      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-05
                          FeoC  8 yleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaatacc 53
                                  ++ +++r s +e++  +k+s++ +++ L+ +  kG + +++++a+ 
  gi|70606988|ref|YP_255858.1| 38 LISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKEEAGE 83
                                  6889*********************************999998875 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00013     0.072       2      44 ..      25      65 ..      24      80 .. 0.85
   2 ?   -2.4   0.0       7.8   4.4e+03      23      34 ..     106     117 ..     100     123 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                  T---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                        RuvB_C  2 lGLdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                  +GL + di++L++l++  +++ ++ + +a +l+++k  i +  
  gi|70606988|ref|YP_255858.1| 25 YGLPKSDIDVLQVLIS--QKRRMSSDEIADVLKVSKASINKSL 65
                                  8**************8..799****************998765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.8
                                   -B-HHHHHHHTT CS
                        RuvB_C  23 pvglktlaailg 34 
                                   +  l+tla+ ++
  gi|70606988|ref|YP_255858.1| 106 ERDLETLASQIK 117
                                   445667776665 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   8.1e-05     0.045      44     105 ..      57     125 ..      31     127 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-05
                                   -HHHHHHHHHHHHHTTSEEEEEEEB..TSSSSSEEEEEEES.S..HHH....HHHHHHHHHHHHHHHHH CS
                           RTP  44 nhseiyralhelvedgilkrrkelk..ekaklqevviYslt.deGkek....aklykkqvkidldrckk 105
                                   +++ i ++l++l+++g++ r+ke    ek+k +  +iY ++ +  +ek    ++ +  q+k +l++ ++
  gi|70606988|ref|YP_255858.1|  57 SKASINKSLNNLYDKGLILREKEEAgeEKKKGRPSYIYWVDgERLYEKlerdLETLASQIKKELEERMQ 125
                                   67899*****************99876777888899998851333454111155677888888887766 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.068       7      48 ..      33      74 ..      32      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                  ++L+ l ++ ++++  e+A+ + ++k++    L+ L   G++
  gi|70606988|ref|YP_255858.1| 33 DVLQVLISQKRRMSSDEIADVLKVSKASINKSLNNLYDKGLI 74
                                  89***************************9999999888886 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00013     0.071       4      53 ..      33      83 ..      31      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                        HTH_34  4 avlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                   vl++L+s +++++  e+ + l+++++ + + l+ L ++g i ++ke  g 
  gi|70606988|ref|YP_255858.1| 33 DVLQVLISqKRRMSSDEIADVLKVSKASINKSLNNLYDKGLILREKEEAGE 83
                                  589999998999**********************************98776 PP

>> Pigment_DH  Pigment-dispersing hormone (PDH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00015     0.085       2      17 ..      18      33 ..      17      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                    Pigment_DH  2 sdLINfLLsLPKdMlD 17
                                  +dLI f  +LPK+  D
  gi|70606988|ref|YP_255858.1| 18 GDLISFIYGLPKSDID 33
                                  8***********9655 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0003      0.17      21      46 ..      42      67 ..      40      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                        HTH_10 21 PRrvtlkeLAkelGIskstlsehLrk 46
                                   Rr++++e+A+ l +sk+++ + L++
  gi|70606988|ref|YP_255858.1| 42 KRRMSSDEIADVLKVSKASINKSLNN 67
                                  7*********************9987 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0066       3.7      38      55 ..      26      43 ..      14      70 .. 0.76
   2 ?    2.9   0.1      0.18     1e+02      59      76 ..     105     122 ..     100     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                        Nas2_N 38 gFPrsDidvvavrtaRnr 55
                                  g P+sDidv++v +  +r
  gi|70606988|ref|YP_255858.1| 26 GLPKSDIDVLQVLISQKR 43
                                  77*******999876554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                        Nas2_N  59 lqNDlkelmkeieealae 76 
                                   l+ Dl++l ++i+++l+e
  gi|70606988|ref|YP_255858.1| 105 LERDLETLASQIKKELEE 122
                                   677888888888888776 PP

>> HDV_ag  Hepatitis delta virus delta antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.9   0.00039      0.22       8      47 ..      84     122 ..      75     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                        HDV_ag   8 knrggreevleqwvsgrkkleelerdlrkvkkkikklede 47 
                                   +++ gr      wv g +  e+lerdl  +  +ikk  +e
  gi|70606988|ref|YP_255858.1|  84 EKKKGRPSY-IYWVDGERLYEKLERDLETLASQIKKELEE 122
                                   455566554.47**********************995444 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5    0.0018         1      20      46 ..      38      63 ..      32      66 .. 0.80
   2 ?    0.5   0.1       1.1   6.3e+02      32      46 ..     104     118 ..     103     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                  HHHTT--EE-HHHHHHHCTS-HHHHHH CS
                Put_DNA-bind_N 20 lkeegveriSSteLaealgvtaaqvRK 46
                                  l ++ + r SS+e+a+ l+v+ a + K
  gi|70606988|ref|YP_255858.1| 38 LISQ-KRRMSSDEIADVLKVSKASINK 63
                                  4444.689**************99988 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                                   HHHHHCTS-HHHHHH CS
                Put_DNA-bind_N  32 eLaealgvtaaqvRK 46 
                                   +L ++l+  a+q+ K
  gi|70606988|ref|YP_255858.1| 104 KLERDLETLASQIKK 118
                                   7889999999***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1419  (0.0791455); expected 358.6 (0.02)
Passed bias filter:                      813  (0.0453455); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 906.38
//
Query:       gi|70606989|ref|YP_255859.1|  [L=331]
Description: periplasmic binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-19   70.1   0.4    3.2e-19   69.5   0.4    1.3  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.4   1.8e-23   3.2e-19       1     234 [.      49     277 ..      49     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.8e-23
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT......TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee....aivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                   i+sl+ps t+il+ lG+ + +vg d +++  l   ++ +    +++++ +  ++++  ++al+P++v+l +gl   + + +
  gi|70606989|ref|YP_255859.1|  49 IVSLAPSDTQILVSLGLGKDIVGMDIYSYQLLQTLNMTSmippNVTVITSVINLNITGIIALQPTVVVLEYGL-SGSYIPQ 128
                                   9*********************************99999**********************************.9999*** PP

                                   HHHHHS-EEE----TTS..HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE...EEEE- CS
                  Peripla_BP_2  78 llksgiptvivessntg..eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggade.ggyvvag 155
                                   l+ +g ++++ +s+ +   e++ ++i ++++ ++ +++a++l++++++ + +     ++  +  v++f + d+ g+ + +g
  gi|70606989|ref|YP_255859.1| 129 LENAGLKVLVTNSDYASnlENVINTISQIATFFNVTNQANQLIKWMNQSMVSY----PQT-NVSVAYFDWIDSdGTAYSIG 204
                                   ***************99********************************9875....444.5566777776666899**** PP

                                   TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE CS
                  Peripla_BP_2 156 snsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyal 234
                                   +n +i+dl+d +g+ n +++    +y+++ + q+l +dp vi+         +  +   + +  ++ + Avkn++Vy +
  gi|70606989|ref|YP_255859.1| 205 NNVFINDLIDRAGGFNSFSN--FTGYITVTPSQVLLADPHVIVAQEI----YNYSYTIYLIHKYFNYTYAVKNNQVYVI 277
                                   *****************999..7*********************999....8999999999999*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2611.75
//
Query:       gi|70606990|ref|YP_255860.1|  [L=332]
Description: hemin transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-66  224.3  39.1    2.2e-66  224.0  39.1    1.0  1  FecCD     FecCD transport family
    2.2e-06   27.3  26.7    3.7e-06   26.6  26.7    1.4  1  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
        9.9    6.3  11.7         14    5.8   0.0    4.1  3  DUF3180   Protein of unknown function (DUF3180)


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.0  39.1   3.6e-70   2.2e-66       4     312 .]      20     325 ..      13     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 224.0 bits;  conditional E-value: 3.6e-70
                         FecCD   4 lllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaa 84 
                                    +lllsl++g+v+i+p+e+++      +++ + i++e+rlp++++a+l+G++L+v+G ++Q ++rNpL dP+i G+ssg a
  gi|70606990|ref|YP_255860.1|  20 TSLLLSLMYGDVYIPPQEILHP-----SQIYRLILYEIRLPTIITAALIGIILSVSGSIMQHLLRNPLIDPYIAGTSSGGA 95 
                                   5899*****************8.....789*************************************************** PP

                         FecCD  85 lgavlallll....lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllll..neea 159
                                   +ga+l+++ll     +s  ++a pl+af++++la+++++l+    +g   + l++aG++vs+++s++ s+ll+ll     +
  gi|70606990|ref|YP_255860.1|  96 FGAILSYFLLgfslPLSVMIYAQPLIAFFFSFLATIITVLIG---RGRGIYGLVIAGVIVSYIFSSAYSILLVLLqeRYPQ 173
                                   *********9999989999********************999...99999**********************999555669 PP

                         FecCD 160 lesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvG 240
                                   +  i+fwl+G++  + ws +  l  l+l+ll+l++ ++r ldl++++de++ + G++++r+r++ l l++++++ +++++G
  gi|70606990|ref|YP_255860.1| 174 IPPIIFWLMGQITVVGWSLIPALTTLTLVLLILAYKMSRALDLVSISDEISYTHGIRPNRFRIFWLGLISFVVSFTISIAG 254
                                   9******************************************************************************** PP

                         FecCD 241 pigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylllr 312
                                   +igF+G++vPh++rl +g ++r+ll++s  +G++++ll++++a  +l  t +p+  ++a+i  pf+i++l+r
  gi|70606990|ref|YP_255860.1| 255 VIGFIGILVPHLIRLSIGGNMRTLLVYSSGIGITVMLLSNIIADGML-GTIIPITPILAVIASPFLILFLVR 325
                                   **********************************************9.6888****************9987 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6  26.7   6.3e-10   3.7e-06       7     233 ..      55     298 ..      49     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.3e-10
                         ABC-3   7 rallasilvslacallgsfv..vlrr...qsllgdalsHaalpGvalayllgvn.........lllgailvgliaavalel 73 
                                   + +++++l++++ ++ gs +  +lr      +++++ s  a++ +   +llg++           l a++++++a+++++l
  gi|70606990|ref|YP_255860.1|  55 PTIITAALIGIILSVSGSIMqhLLRNpliDPYIAGTSSGGAFGAILSYFLLGFSlplsvmiyaQPLIAFFFSFLATIITVL 135
                                   55555556665555555543223444222357888888888888877777777777777665533558999********** PP

                         ABC-3  74 lkrktklkedtaigivlsvflalg..lvlvslikk..skvdldsyLfGniltisqedliliaiieavvllllllfwkelll 150
                                   + r   ++  ++ g+++s +++ +  ++lv l ++      +  +L+G+i  +    +  ++ +++v+l+l+  + + l l
  gi|70606990|ref|YP_255860.1| 136 IGRGRGIYGLVIAGVIVSYIFSSAysILLVLLQERypQIPPIIFWLMGQITVVGWSLIPALTTLTLVLLILAYKMSRALDL 216
                                   *******************9975521666665555555667788889***999999999999999999999999******* PP

                         ABC-3 151 itfdeelAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlll 231
                                   ++++ e + ++g++++++++  l li+  v+ ++ ++Gvi  i +l+ P  + + ++ ++++ll++++ +g+  +++  ++
  gi|70606990|ref|YP_255860.1| 217 VSISDEISYTHGIRPNRFRIFWLGLISFVVSFTISIAGVIGFIGILV-PHLIRLSIGGNMRTLLVYSSGIGITVMLLSNII 296
                                   *********************************************96.***********************9998876666 PP

                         ABC-3 232 Sy 233
                                     
  gi|70606990|ref|YP_255860.1| 297 AD 298
                                   53 PP

>> DUF3180  Protein of unknown function (DUF3180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0024        14     105     134 ..      52      81 ..      43      81 .. 0.89
   2 ?   -0.3   1.5      0.19   1.1e+03      80     120 ..      89     133 ..      86     154 .. 0.55
   3 ?    2.6   2.8     0.024   1.4e+02      19      52 ..     181     214 ..     144     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0024
                       DUF3180 105 edllaavvavlaavalvvaglwlErlCrvP 134
                                    +l+++++a+l +++l v g ++++l r P
  gi|70606990|ref|YP_255860.1|  52 IRLPTIITAALIGIILSVSGSIMQHLLRNP 81 
                                   57899********************99987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.19
                       DUF3180  80 GAllaGvyaGllvyllragelp....aaaedllaavvavlaaval 120
                                   G+  +G+++++l y+l   +lp     +a+ l+a ++++la ++ 
  gi|70606990|ref|YP_255860.1|  89 GTSSGGAFGAILSYFLLGFSLPlsvmIYAQPLIAFFFSFLATIIT 133
                                   555666666666666643333300003344444444444444443 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.024
                       DUF3180  19 sygslpplpwlaavvllvlavvelvlAlqvrrri 52 
                                    +g+++ + w+++ +l  l +v+l+lA+++ r +
  gi|70606990|ref|YP_255860.1| 181 LMGQITVVGWSLIPALTTLTLVLLILAYKMSRAL 214
                                   678899999******************9998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2156.42
//
Query:       gi|70606991|ref|YP_255861.1|  [L=219]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-17   64.5   0.2    1.5e-16   61.2   0.2    2.1  1  ABC_tran       ABC transporter
    3.2e-13   49.6   2.7    1.2e-06   28.2   0.2    2.1  2  SMC_N          RecF/RecN/SMC N terminal domain
      2e-12   47.6   2.1      4e-05   23.6   0.6    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    2.9e-08   34.5   0.7    2.9e-08   34.5   0.7    1.9  2  AAA_23         AAA domain
    3.4e-08   33.6   3.2    0.00015   21.6   0.2    2.2  2  AAA_15         AAA ATPase domain
    1.7e-05   23.8   0.1    2.1e-05   23.5   0.1    1.2  1  Adeno_IVa2     Adenovirus IVa2 protein
    2.7e-05   23.8   0.0    5.5e-05   22.8   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
    8.8e-05   22.2   1.3    0.00026   20.6   1.3    2.0  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
    0.00037   20.5   0.9     0.0005   20.0   0.9    1.3  1  ATPase_2       ATPase domain predominantly from Archaea
    0.00098   19.4   0.0     0.0015   18.8   0.0    1.5  1  AAA_22         AAA domain
      0.001   18.2   0.1     0.0017   17.5   0.1    1.3  1  T2SSE          Type II/IV secretion system protein
     0.0012   19.2   0.1     0.0036   17.7   0.1    1.9  1  AAA_16         AAA ATPase domain
     0.0037   16.7   1.5     0.0053   16.2   0.5    1.7  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0053   17.1   0.6      0.012   15.9   0.5    1.8  1  AAA_19         AAA domain
     0.0059   16.6   1.7       0.05   13.6   1.7    2.5  1  AAA_14         AAA domain
     0.0071   16.9   2.4       0.75   10.3   2.4    2.4  1  AAA_18         AAA domain
     0.0071   16.1   0.1      0.012   15.3   0.1    1.5  1  AAA_30         AAA domain
      0.008   16.1   0.2      0.017   15.0   0.2    1.5  1  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
       0.01   15.8   0.6      0.021   14.8   0.2    1.7  2  NACHT          NACHT domain
      0.013   14.3   0.4      0.021   13.6   0.1    1.4  2  ABC_ATPase     Predicted ATPase of the ABC class
      0.018   15.0   0.7      0.081   12.8   0.1    2.0  2  Rad17          Rad17 P-loop domain
      0.019   15.2   0.0      0.044   13.9   0.0    1.7  1  AAA_33         AAA domain
      0.019   15.4   0.1      0.036   14.5   0.1    1.6  1  AAA            ATPase family associated with various cellular
      0.022   14.7   2.9       0.47   10.4   0.2    2.3  2  NTPase_1       NTPase
      0.032   13.9   0.2       0.15   11.8   0.0    2.0  2  AAA_24         AAA domain
      0.037   13.6   0.0      0.063   12.9   0.0    1.3  1  AAA_27         AAA domain
       0.07   13.4   0.1       0.53   10.5   0.1    2.1  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
      0.072   12.2   0.0      0.073   12.2   0.0    1.1  1  G-alpha        G-protein alpha subunit
      0.076   10.5   0.3        0.1   10.1   0.3    1.1  1  DUF3584        Protein of unknown function (DUF3584)
      0.096   11.6   0.0       0.15   11.0   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
        0.1   12.4   0.0       0.13   12.0   0.0    1.3  1  AAA_11         AAA domain
       0.13   12.4   0.3       0.24   11.5   0.3    1.6  1  MMR_HSR1       50S ribosome-binding GTPase
       0.13   11.6   0.0       0.23   10.8   0.0    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.14   12.5   0.5       0.39   11.1   0.1    2.0  2  RNA_helicase   RNA helicase
       0.17   11.8   0.7       0.48   10.3   0.2    1.9  2  MobB           Molybdopterin guanine dinucleotide synthesis p
        0.2   11.3   2.4       0.78    9.3   0.4    2.5  3  SRP54          SRP54-type protein, GTPase domain
       0.21   11.3   0.7        8.1    6.1   0.1    2.1  2  IstB_IS21      IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.2   3.1e-19   1.5e-16       1     137 []      16     136 ..      16     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.1e-19
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+nv+++l++g ++ i+G+nG+GK+tLlk+++g+ +p eG++ + +++l++ + e++  +++++                 
  gi|70606991|ref|YP_255861.1|  16 LDNVNIELRPG-ITLILGPNGSGKTTLLKTIIGMIEPIEGKV-IVNENLSYSPAEFYTVNMKTIDV------------Ila 82 
                                   799*******9.6779**************************.44455555444444444444432............233 PP

                                   .HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     ++ e +k+++ +++ +l ++      ++LS Gqk+ v +++al  + +l+++DEp+a
  gi|70606991|ref|YP_255861.1|  83 gRKKGEYQKYIELFNIADLMENDF----QNLSSGQKRLVLIVKAL-GEGDLVIMDEPFA 136
                                   3678999**********9888888....***********999997.6789*******85 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.9e-07   9.1e-05       3      44 ..       4      45 ..       2      64 .. 0.87
   2 !   28.2   0.2   2.4e-09   1.2e-06     116     213 ..      85     180 ..      66     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-07
                                  EEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  3 krleienFksyagktvilpfsksftaivGpNGSGKsnlldAi 44
                                  k l+++  k +  ++v +++ +++t i+GpNGSGK+ ll  i
  gi|70606991|ref|YP_255861.1|  4 KGLKVKLGKKIVLDNVNIELRPGITLILGPNGSGKTTLLKTI 45
                                  56666767777778999*********************9988 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2.4e-09
                                   EEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 116 kevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfi 193
                                   k+ +++++ el++ a++ ++   +LS G+k Lv     + +++     l+++De  a+LD kn+ +v + l + +++  fi
  gi|70606991|ref|YP_255861.1|  85 KKGEYQKYIELFNIADLMENdfqNLSSGQKRLV-----LIVKALGEGDLVIMDEPFANLDMKNRMIVLDSLLKLKSEKNFI 160
                                   556667777777777775544449******976.....4488999999*************************999***** PP

                                   EE-SSHHHCCC-SCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 194 vislreemlekadklvgvtk 213
                                   ++s++ e+++ ad+++ v+ 
  gi|70606991|ref|YP_255861.1| 161 ITSHELEVINYADEIILVKN 180
                                   **************998875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.6   8.4e-08     4e-05       1      22 [.      27      48 ..      27      75 .. 0.80
   2 !   23.5   0.0   8.7e-08   4.2e-05     234     303 .]     106     170 ..      83     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.4e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                  ++++ GpNgsGK++LL+++ ++
  gi|70606991|ref|YP_255861.1| 27 ITLILGPNGSGKTTLLKTIIGM 48
                                  79*****************444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 8.7e-08
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpllld 303
                                   + +lS+G+krl    +++  al++g+l++ DEp ++L+ k    +l+ l k++s+    +i+t+H  ++++
  gi|70606991|ref|YP_255861.1| 106 FQNLSSGQKRL----VLIVKALGEGDLVIMDEPFANLDMKNRMIVLDSLlKLKSE--KNFIITSHELEVIN 170
                                   6789*******....66666666779********************655588888..88******999886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.7   5.9e-11   2.9e-08      11      39 ..      17      45 ..      11      49 .. 0.91
   2 ?    0.3   0.1       1.8   8.7e+02     105     165 ..      89     154 ..      54     182 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.9e-11
                        AAA_23 11 rdqeidFskgltlItGpNGaGKTTildAi 39
                                  ++++i++ +g+tlI GpNG+GKTT+l  i
  gi|70606991|ref|YP_255861.1| 17 DNVNIELRPGITLILGPNGSGKTTLLKTI 45
                                  7899*********************9866 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.8
                        AAA_23 105 kkaklelleidel.eqfisellgskkiilnlilflgqer....feefelkdkkerleelekeleel 165
                                   +++  el++i++l e+ +++l + +k+   ++  lg+++     e+f++ d k+r+  l   l+ +
  gi|70606991|ref|YP_255861.1|  89 YQKYIELFNIADLmENDFQNLSSGQKRLVLIVKALGEGDlvimDEPFANLDMKNRMIVLDSLLKLK 154
                                   333334444422213334444444444445555566666666655555555555444443333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   3.2e-07   0.00015      14      48 ..      16      50 ..      15      65 .. 0.86
   2 !   12.6   0.7   0.00017     0.083     263     368 ..      72     168 ..      52     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.2e-07
                        AAA_15 14 lkdveidlseeltvliGkNnsGKSsilealdlFln 48
                                  l++v i+l + +t++ G+N+sGK+++l+ +  +++
  gi|70606991|ref|YP_255861.1| 16 LDNVNIELRPGITLILGPNGSGKTTLLKTIIGMIE 50
                                  57899***********************9976665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                        AAA_15 263 ilkkkidkikkfnykgkkneeieik...ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqa 340
                                   +  k id i  +  kg+ + +ie++   d +e ++ + +sG++rl+l++  +    ++       ++++++EP a+L  ++
  gi|70606991|ref|YP_255861.1|  72 VNMKTIDVILAGRKKGEYQKYIELFniaDLMENDFQNLSSGQKRLVLIVKAL---GEG-------DLVIMDEPFANLDMKN 142
                                   334445555555555555555555588899****************998543...344.......79************** PP

                        AAA_15 341 qkvlikllkelandnktQviitTHSphi 368
                                    +++ ++l++l ++++   iit+H   +
  gi|70606991|ref|YP_255861.1| 143 RMIVLDSLLKLKSEKN--FIITSHELEV 168
                                   ***********99997..******7665 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   4.4e-08   2.1e-05      78     215 ..      16     144 ..       6     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.4e-08
                    Adeno_IVa2  78 lsslnyglqPviGviyGPtGsGksqllrnlissklisPiPetvifitPekdmipPeelkaWelqlvegnyekredGtiiPk 158
                                   l  +n++l+P i +i GP GsGk+ ll+++i   +i+Pi   vi    e    +P e  + +++ ++   + r+ G     
  gi|70606991|ref|YP_255861.1|  16 LDNVNIELRPGITLILGPNGSGKTTLLKTIIG--MIEPIEGKVI--VNENLSYSPAEFYTVNMKTIDVILAGRKKGEYQKY 92 
                                   6789**************************96..9****99996..46677789999999999999999999999988877 PP

                    Adeno_IVa2 159 tstlr.pefvelayeeavapenldiddpknifvkaakrGpvaiildecmeklidkksv 215
                                      ++ ++++e +++++ + ++        + vka  +G++ +i+de   +l  k+ +
  gi|70606991|ref|YP_255861.1|  93 IELFNiADLMENDFQNLSSGQKRL-----VLIVKALGEGDL-VIMDEPFANLDMKNRM 144
                                   777763478888888777665433.....356777777776.4677777777666555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.1e-07   5.5e-05      14      45 ..      18      48 ..      12      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-07
                        AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqal 45
                                  +  ie++  g+tl+ Gp+GsGK+Tll  i+ +
  gi|70606991|ref|YP_255861.1| 18 NVNIELR-PGITLILGPNGSGKTTLLKTIIGM 48
                                  5566776.458**************9777655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.3   5.4e-07   0.00026       2      36 ..      27      61 ..      26     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.4e-07
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS- CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklavivNef 36
                                  +t++ G+ GsGKTtLl++++   +  +  vivNe 
  gi|70606991|ref|YP_255861.1| 27 ITLILGPNGSGKTTLLKTIIGMIEPIEGKVIVNEN 61
                                  58999***************999**********96 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.9     1e-06    0.0005      22     147 ..      27     152 ..      18     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                      ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..eeeekkklekalgiavpkaeleeilkeksk 100
                                   i +i Gp gsGKt+Llk ii   e  + +vi   +l+ +  + ++  ++  +   + + +   ++ ++ +++  ++++  +
  gi|70606991|ref|YP_255861.1|  27 ITLILGPNGSGKTTLLKTIIGMIEPIEGKVIVNENLSYSPAEFYTVNMKtiDVILAGRKKGEYQKYIELFNIADLMENDFQ 107
                                   889********************9999999988888887777777775544222222333333555555556666666667 PP

                      ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLln 147
                                   ++ +  ++l   +k  g    +i+De +   d++ +    ++++Ll+
  gi|70606991|ref|YP_255861.1| 108 NLSSGQKRLVLIVKALGEGDLVIMDEPFANLDMKNR--MIVLDSLLK 152
                                   777777777777888888888888888888866644..666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.1e-06    0.0015       5      96 ..      25     119 ..      21     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.1e-06
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..........erlss 75 
                                    gi+++ G+ G+GKTtll+++    +       +  + v v+ + s s++++++   + +++ l +          e  + 
  gi|70606991|ref|YP_255861.1|  25 PGITLILGPNGSGKTTLLKTIIGMIE-------PIEGKVIVNENLSYSPAEFYTVNMKTIDVILAGrkkgeyqkyiELFNI 98 
                                   699******************99985.......355666777777778888888877777777777777788888888888 PP

                        AAA_22  76 eell.ealeqalraravielli 96 
                                    +l+ + +++ ++ +++  +li
  gi|70606991|ref|YP_255861.1|  99 ADLMeNDFQNLSSGQKR-LVLI 119
                                   88887777777777777.5555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.4e-06    0.0017     130     164 ..      26      60 ..      13      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-06
                         T2SSE 130 glilvsGgTgsGKttllyallkeinksderivtvE 164
                                   g+ l+ G+ gsGKttll +++ +i+  + ++++ E
  gi|70606991|ref|YP_255861.1|  26 GITLILGPNGSGKTTLLKTIIGMIEPIEGKVIVNE 60 
                                   678999*******************9988887766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   7.3e-06    0.0036      23      62 ..      24      58 ..      15     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.3e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62
                                  rp+++l+ G+ G+GK++l++++   + +     ++gk   
  gi|70606991|ref|YP_255861.1| 24 RPGITLILGPNGSGKTTLLKTIIG-MIEP----IEGKVIV 58
                                  6899***************99874.3333....4444444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   1.1e-05    0.0053      18      60 ..       6      46 ..       3      49 .. 0.82
   2 ?   -1.7   0.0       3.1   1.5e+03     137     181 ..      88     131 ..      69     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                  TEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE 18 lpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLi 60
                                  l+v+lgk+i+ +++ ++l++    +l++G  gsGK+t l+t+i
  gi|70606991|ref|YP_255861.1|  6 LKVKLGKKIVLDNVNIELRPGI--TLILGPNGSGKTTLLKTII 46
                                  5677777777777777777766..9****************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                   HHHHHHHTT---B-TT-......................------ CS
                  FtsK_SpoIIIE 137 eiaedpldifgdvflvlDnyddlaaeneritsLsnqgpsygvhvl 181
                                   e +++++  f++ +l+  + ++l   ++r +++++   ++   ++
  gi|70606991|ref|YP_255861.1|  88 EYQKYIEL-FNIADLMENDFQNLSSGQKRLVLIVKALGEGDLVIM 131
                                   33333333.566666666666666666666655554444444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   2.5e-05     0.012       6      39 ..      20      54 ..      17     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-05
                        AAA_19  6 e.alkekvllvtaGpGtGKTrvlkhivallvelgg 39
                                  + +l+ ++ l++++ G+GKT++lk+i+ +++ ++g
  gi|70606991|ref|YP_255861.1| 20 NiELRPGITLILGPNGSGKTTLLKTIIGMIEPIEG 54
                                  447888999******************99877654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.7    0.0001      0.05       4      58 ..      27      82 ..      24     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                        AAA_14  4 ilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelile 58
                                  i +i G+  +GKTtllk++i     ++ + i+  nl   + + ++ + k +++il+
  gi|70606991|ref|YP_255861.1| 27 ITLILGPNGSGKTTLLKTIIGMIEpIEGKVIVNENLSYSPAEFYTVNMKTIDVILA 82
                                  889****************9766676666666666666555444433334444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   2.4    0.0015      0.75       2      90 ..      29     172 ..      29     185 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0015
                        AAA_18   2 lltGtpGvGKttlakeL.............skrlgf............................................. 24 
                                   l+ G+ G+GKttl k +             ++ l +                                             
  gi|70606991|ref|YP_255861.1|  29 LILGPNGSGKTTLLKTIigmiepiegkvivNENLSYspaefytvnmktidvilagrkkgeyqkyielfniadlmendfqnl 109
                                   58999********99996665555555554222233666666666666666666666555444444444444444444444 PP

                        AAA_18  25 ......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaelesea 90 
                                          v + + + e++l+++++p+       ld+++++ +ld l +  s    +kn +i +h  e + +a
  gi|70606991|ref|YP_255861.1| 110 ssgqkrLVLIVKALGEGDLVIMDEPF-----ANLDMKNRMIVLDSLLKLKS----EKNFIITSHELEVINYA 172
                                   44444333333444444444444444.....66777777777777777554....77777777766666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.5e-05     0.012      20      51 ..      27      58 ..      21     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.5e-05
                        AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvig 51
                                  ++++ Gp G+GKtt+lk++  ++e  +g+vi+
  gi|70606991|ref|YP_255861.1| 27 ITLILGPNGSGKTTLLKTIIGMIEPIEGKVIV 58
                                  7899******************9999777775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.6e-05     0.017      82     123 ..       8      49 ..       3      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                                   --TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  82 vsaktkegleelkellkdktsvlvGqSGvGKStLinallpel 123
                                   v+  +k  l++++ +l+  +++++G+ G GK+tL++++++  
  gi|70606991|ref|YP_255861.1|   8 VKLGKKIVLDNVNIELRPGITLILGPNGSGKTTLLKTIIGMI 49 
                                   55566777899999***********************98864 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   4.3e-05     0.021       3      21 ..      28      46 ..      27      51 .. 0.89
   2 ?   -2.1   0.0       6.6   3.2e+03      74      90 ..     107     123 ..      97     165 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-05
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   ++ G++GsGKTtLl+ ++
  gi|70606991|ref|YP_255861.1| 28 TLILGPNGSGKTTLLKTII 46
                                  5899************997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.6
                                   HHHCCSCCCEEEEEE-S CS
                         NACHT  74 avllelperlLlilDgl 90 
                                   ++l + ++rl+li+ +l
  gi|70606991|ref|YP_255861.1| 107 QNLSSGQKRLVLIVKAL 123
                                   55555666666554333 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.4e-05     0.021     242     264 ..      23      45 ..      17      54 .. 0.91
   2 ?   -3.6   0.0       7.6   3.7e+03     392     413 ..     159     180 ..     147     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                                   E-SSEEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 242 ipkGvtlIvGggfhGKsTLLeAl 264
                                   ++ G+tlI G++  GK+TLL+ +
  gi|70606991|ref|YP_255861.1|  23 LRPGITLILGPNGSGKTTLLKTI 45 
                                   688*****************988 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.6
                                   EEEESS-GCCTTT-SEEEEEET CS
                    ABC_ATPase 392 ilvvggsgdyldvAdtvilmee 413
                                   +++++   + ++ Ad++il+++
  gi|70606991|ref|YP_255861.1| 159 FIITSHELEVINYADEIILVKN 180
                                   6777777788888888888776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00017     0.081      46     133 ..      26     114 ..       6     124 .. 0.65
   2 ?    0.4   0.1       1.1   5.4e+02     113     169 ..     152     209 ..     128     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                         Rad17  46 riLLisGPsGCgkstvvkvLsk.elgi..k..lrewln..pvslkepdnqksdfkgltekesrflsqiesfkeleLkdaky 119
                                    i Li GP G gk+t +k +   +  i  k  ++e+l   p ++   + +  d+     k+ +++  ie f+   L++  +
  gi|70606991|ref|YP_255861.1|  26 GITLILGPNGSGKTTLLKTIIGmIEPIegKviVNENLSysPAEFYTVNMKTIDVILAGRKKGEYQKYIELFNIADLMENDF 106
                                   499**************9764413333112113333312366666666677777777778888888888888888888888 PP

                         Rad17 120 lklqklGddlrtdk 133
                                   + l+       ++k
  gi|70606991|ref|YP_255861.1| 107 QNLS------SGQK 114
                                   7777......3444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                         Rad17 113 eLkdakylklqklG.ddlrtdkklilvedlPnkfyrdsdalrevirkylrssealpli 169
                                   +Lk+ k+  +     + ++   ++ilv +   ++ ++ +++ ++i+  ++  +  +l+
  gi|70606991|ref|YP_255861.1| 152 KLKSEKNFIITSHElEVINYADEIILVKNGKVVYSGSKENVSDLILSQVYDVRIRSLV 209
                                   4555555555433313345567899999988999999999999999998887776666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.1e-05     0.044       3      81 ..      29     137 ..      27     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.1e-05
                        AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt..................lrrrlfgtdqqskt.........dytrvl 52 
                                   l+ G++GsGK+tl++ ++         v+++++                   l  r +g+ q+ ++         +  + l
  gi|70606991|ref|YP_255861.1|  29 LILGPNGSGKTTLLKTIIGMIEpiegKVIVNENLsyspaefytvnmktidviLAGRKKGEYQKYIElfniadlmeNDFQNL 109
                                   788************996554445556666666666666666666666665522233332222222444443333333333 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatnls 81 
                                   ++  ++l  l+ kal +g  vi d ++++
  gi|70606991|ref|YP_255861.1| 110 SSGQKRL-VLIVKALGEGDLVIMDEPFAN 137
                                   4444455.577777777777888888655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   7.4e-05     0.036       2      34 ..      29      77 ..      28     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-05
                                  EEESSTTSSHHHHHHHHHHHH.............T...HEEEEEETTTC CS
                           AAA  2 llyGppGtGKTllakavakel.............g...vefleisgsel 34
                                  l+ Gp G GKT+l k ++  +             +   +ef++++++++
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGMIepiegkvivnenlSyspAEFYTVNMKTI 77
                                  789***************9964443322222222122344544444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00097      0.47       4      24 ..      30      50 ..      27      61 .. 0.86
   2 ?    4.7   0.2     0.051        25      87     153 ..     117     184 ..      94     201 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00097
                                  EE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellk 24
                                  i Gp G+GKtTl+k ++ +++
  gi|70606991|ref|YP_255861.1| 30 ILGPNGSGKTTLLKTIIGMIE 50
                                  77**************99885 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                                   HHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT..TTSEEEEE--SS--SHHHHHHHT-TT-EEE CS
                      NTPase_1  87 ealrkalseadviviDE.iGkmElkskkfkeaveevLk..sekpvlavihrrkdlalveeirerkdvkvf 153
                                     + kal e d++++DE   ++ +k + +   ++ +Lk  sek+++++ h+ +  +  +ei   k++kv+
  gi|70606991|ref|YP_255861.1| 117 VLIVKALGEGDLVIMDEpFANLDMKNRMI--VLDSLLKlkSEKNFIITSHELEVINYADEIILVKNGKVV 184
                                   4566788999999***9444555555555..4555554449999****9999988899998877776654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.15       6      22 ..      29      45 ..      26     104 .. 0.90
   2 ?   -0.2   0.0       1.4   6.9e+02     114     132 ..     146     166 ..     136     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                        AAA_24  6 liyGpsgiGKTtlakel 22
                                  li Gp+g+GKTtl+k++
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTI 45
                                  89*************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                        AAA_24 114 llkklqelrk..nvifiahek 132
                                   +l+ l +l+   n+i+++he 
  gi|70606991|ref|YP_255861.1| 146 VLDSLLKLKSekNFIITSHEL 166
                                   567788888888999999986 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.063      25      47 ..      24      46 ..      11      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                        AAA_27 25 eadlhliyGpNEAGKstalrAis 47
                                  +++++li+GpN +GK+t+l+ i 
  gi|70606991|ref|YP_255861.1| 24 RPGITLILGPNGSGKTTLLKTII 46
                                  5899***************9885 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0011      0.53      65      86 ..     127     148 ..      97     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                       SbcCD_C  65 rlvfLDEAFsklDeesiatlle 86 
                                   +lv++DE F++lD +++  +l+
  gi|70606991|ref|YP_255861.1| 127 DLVIMDEPFANLDMKNRMIVLD 148
                                   79*************9987776 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015     0.073      27      80 ..      29      86 ..      11     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                  EEEESTTSSHHHHHHHHHHHCS--....--HHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                       G-alpha 27 lllGqseSGKsTilkqlkllykkg....fseeelatwraviqlnivrsiktileales 80
                                  l+lG ++SGK+T+lk +  + ++     + +e+l +  a  ++  ++ i+ il+  ++
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGMIEPIegkvIVNENLSYSPAEFYTVNMKTIDVILAGRKK 86
                                  89*************9986665655666666666666677777777778888877777 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00021       0.1      18      37 ..      26      45 ..      18      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                       DUF3584 18 ghtnieGtNaaGKTtLlrLi 37
                                  g t i G N++GKTtLl++i
  gi|70606991|ref|YP_255861.1| 26 GITLILGPNGSGKTTLLKTI 45
                                  7899*************987 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.15      18      61 ..      28      71 ..      19      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                 TrwB_AAD_bind 18 ilivGttGsGKtqalekllrairargdraivlDltGafvsrfyd 61
                                  +li+G  GsGKt+ l+ ++  i+  + ++iv        ++fy 
  gi|70606991|ref|YP_255861.1| 28 TLILGPNGSGKTTLLKTIIGMIEPIEGKVIVNENLSYSPAEFYT 71
                                  79**********************99999998877777777776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00027      0.13      17      41 ..      25      52 ..      14     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                        AAA_11 17 seitliqGPPGtgKT...ktivellsql 41
                                  ++itli GP G+gKT   kti+++++ +
  gi|70606991|ref|YP_255861.1| 25 PGITLILGPNGSGKTtllKTIIGMIEPI 52
                                  568************6666666666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00049      0.24       3      52 ..      29      97 ..      27     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00049
                                  EEEESTTSSHHHHHHHHHT............STEEESSSTTSSSSEEEEEEEETTEE.......EEEEE CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltg............ekaivsdkpgtTrdinegrvklkgke.......ielvD 52
                                  +i+G   +GK+tL+++++g            e+   s   + T +++++ v l g++       iel  
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGmiepiegkvivnENLSYSPAEFYTVNMKTIDVILAGRKkgeyqkyIELFN 97
                                  699***************866666655555345566667777777777777644433344444433333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00047      0.23      26      58 ..      29      61 ..      26      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                  Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplseeealeva 58
                                  l++Gp GsGKt l k + +++ p++ + +++ +
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGMIEPIEGKVIVNEN 61
                                  789*****************9999887666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0008      0.39       2      23 ..      29      50 ..      28     111 .. 0.71
   2 ?   -1.3   0.0       5.7   2.8e+03      53      90 ..     129     167 ..     125     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0008
                  RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                  ++ Gp+g GK+tl k+++  ++
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGMIE 50
                                  589*************887776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.7
                  RNA_helicase  53 vvidDfgqvkdeenps.dlaelirlvsstpyplnmasle 90 
                                   v++d+  ++ d +n +  l  l++l s +++++   +le
  gi|70606991|ref|YP_255861.1| 129 VIMDEPFANLDMKNRMiVLDSLLKLKSEKNFIITSHELE 167
                                   777777777777666667777777777777777666665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00099      0.48       3      24 ..      29      50 ..      27      58 .. 0.83
   2 ?   -1.4   0.0       4.1     2e+03      88     111 ..      74      97 ..      55     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00099
                          MobB  3 givgksgsGKTtLleklipelk 24
                                   i g +gsGKTtLl+ +i +++
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLLKTIIGMIE 50
                                  57899************98775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.1
                          MobB  88 lsevDlvlvEGfkkealpk.ievlr 111
                                   ++++D++l+ G kk +++k ie++ 
  gi|70606991|ref|YP_255861.1|  74 MKTIDVILA-GRKKGEYQKyIELFN 97 
                                   466888776.555555544377765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4    0.0016      0.78       3      20 ..      27      44 ..      25      59 .. 0.81
   2 ?    0.8   0.0      0.64   3.1e+02      80     115 ..      73     105 ..      58     137 .. 0.78
   3 ?   -1.2   0.0       2.8   1.3e+03      85     123 ..     143     181 ..     117     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                                  EEEEEESTTSSHHHHHHH CS
                         SRP54  3 villvGlqGaGKTttlaK 20
                                  ++l++G++G+GKTt l  
  gi|70606991|ref|YP_255861.1| 27 ITLILGPNGSGKTTLLKT 44
                                  789***********8865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.64
                                   HHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSS CS
                         SRP54  80 keekidvvlvDTaGrlqndkelmeelkkikkvvkpd 115
                                   + + idv+l   aGr + + +   el +i++ +++d
  gi|70606991|ref|YP_255861.1|  73 NMKTIDVIL---AGRKKGEYQKYIELFNIADLMEND 105
                                   556677777...8******99999999999999544 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.8
                                   SEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEET CS
                         SRP54  85 dvvlvDTaGrlqndkelmeelkkikkvvkpdevllvlda 123
                                    ++++D+  +l+++k+ +   ++++ +  +de++lv ++
  gi|70606991|ref|YP_255861.1| 143 RMIVLDSLLKLKSEKNFIITSHELEVINYADEIILVKNG 181
                                   456667777777777777777777777778888888766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.092        45      51      64 ..      29      42 ..      20      56 .. 0.84
   2 ?    6.1   0.1     0.017       8.1      82     148 ..      97     164 ..      81     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.092
                     IstB_IS21 51 vllGpsGvGKshla 64
                                  ++lGp G GK+ l 
  gi|70606991|ref|YP_255861.1| 29 LILGPNGSGKTTLL 42
                                  799*******9875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                     IstB_IS21  82 rvedLvee..lkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                    ++dL+e+   ++  ++ +l  ++k+l + dl+i+D+  + +ld +++  +++ + k    +  iits 
  gi|70606991|ref|YP_255861.1|  97 NIADLMENdfQNLSSGQKRLVLIVKALGEGDLVIMDEP-FANLDMKNRMIVLDSLLKLKSEKNFIITSH 164
                                   556665542223466788999999************95.788998888888877777666667777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 1381.74
//
Query:       gi|70606992|ref|YP_255862.1|  [L=123]
Description: transcriptional regulator Lrs14-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-11   42.0   1.1      1e-10   41.4   1.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.1e-08   34.8   0.0      2e-08   34.0   0.0    1.4  1  MarR_2           MarR family
      8e-08   31.9   0.2    7.6e-07   28.8   0.1    2.2  2  HTH_DeoR         DeoR-like helix-turn-helix domain
    3.6e-07   30.0   0.1    7.1e-07   29.1   0.1    1.5  1  MarR             MarR family
    4.2e-07   29.8   2.8    5.3e-07   29.5   2.8    1.2  1  TFIIE_alpha      TFIIE alpha subunit
    1.3e-06   28.0   0.7    2.2e-06   27.2   0.1    1.6  2  GntR             Bacterial regulatory proteins, gntR family
    1.9e-05   25.1   0.0      4e-05   24.0   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
    2.1e-05   24.6   0.5    0.00018   21.6   0.5    2.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    3.9e-05   23.9   0.2    7.1e-05   23.1   0.2    1.5  1  Rrf2             Transcriptional regulator
    4.2e-05   23.3   0.1    8.1e-05   22.4   0.1    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
    4.5e-05   22.9   0.3    7.6e-05   22.2   0.3    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00011   22.0   0.9    0.00027   20.8   0.3    1.9  2  HTH_11           HTH domain
     0.0002   21.5   0.3    0.00038   20.6   0.2    1.6  1  HTH_34           Winged helix DNA-binding domain
     0.0007   20.2   0.3      0.001   19.7   0.3    1.5  1  RTP              Replication terminator protein
      0.001   19.0   0.1     0.0021   18.0   0.0    1.7  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0013   18.7   2.6      0.029   14.4   0.1    2.9  3  Cullin_Nedd8     Cullin protein neddylation domain
     0.0016   18.7   3.4      0.017   15.4   3.4    2.1  1  UPF0122          Putative helix-turn-helix protein, YlxM / p1
     0.0023   17.8   0.2     0.0038   17.0   0.2    1.5  1  HxlR             HxlR-like helix-turn-helix
     0.0026   17.8   0.1     0.0057   16.7   0.0    1.6  1  HTH_20           Helix-turn-helix domain
     0.0095   16.0   0.1      0.071   13.2   0.0    2.1  2  FeoC             FeoC like transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.7   0.6      0.045   13.7   0.1    2.3  2  HTH_36           Helix-turn-helix domain
      0.016   14.7   0.3      0.053   13.1   0.1    2.1  3  Sigma70_r4       Sigma-70, region 4
      0.022   14.5   0.7       0.08   12.6   0.1    2.0  2  HTH_41           Helix-turn-helix domain
      0.023   14.4   1.1      0.035   13.8   0.5    1.6  1  DUF4423          Domain of unknown function (DUF4423)
      0.041   13.9   0.1      0.085   12.8   0.1    1.5  1  PadR             Transcriptional regulator PadR-like family
      0.041   13.9   0.0      0.066   13.2   0.0    1.4  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.046   13.9   0.0      0.077   13.2   0.0    1.5  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
       0.06   13.4   0.3       0.69   10.0   0.0    2.2  2  HemN_C           HemN C-terminal domain
      0.062   13.7   0.1       0.11   12.8   0.1    1.6  1  Penicillinase_R  Penicillinase repressor
      0.065   13.0   0.1       0.32   10.8   0.0    2.2  2  HTH_38           Helix-turn-helix domain
       0.07   13.7   1.2       0.07   13.7   1.2    2.0  2  Mga              Mga helix-turn-helix domain
      0.072   12.9   0.6       0.83    9.6   0.1    2.3  2  Homeodomain      Homeodomain
      0.083   13.0   0.1       0.11   12.7   0.1    1.2  1  MRP-L20          Mitochondrial ribosomal protein subunit L20
      0.085   13.0   0.1       0.24   11.5   0.0    1.8  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.089   13.0   0.9       0.16   12.2   0.2    1.6  2  DUF3920          Protein of unknown function (DUF3920)
      0.092   12.5   0.1       0.17   11.7   0.1    1.4  1  LexA_DNA_bind    LexA DNA binding domain
      0.093   12.7   1.4       0.67    9.9   0.1    2.6  3  TBPIP            TBPIP/Hop2 winged helix domain
      0.099   12.2   0.0       0.18   11.4   0.0    1.5  1  HTH_47           winged helix-turn-helix
        0.1   12.4   0.0        8.5    6.3   0.0    2.4  2  TetR_N           Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   1.1   2.2e-13     1e-10       1      61 [.      19      88 ..      19      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.2e-13
                                  HH.HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTE CS
                          TrmB  1 Lq.klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pkl 61
                                  L+  +GL+e E++  + Ll +  +++++e+aee +v+++ + ++L++L +kGl+erek +       p +
  gi|70606992|ref|YP_255862.1| 19 LEfMYGLNEKEVQLIFRLLySDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSnegrkgrPIY 88
                                  6778***************9999***********************************877888876433 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   4.4e-11     2e-08       2      61 ..      24      82 ..      23      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.4e-11
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  gl+  + ++++ L  ++ + l++ ela+++++sk+ +s+ l +L  +GL+er++ ++ +R
  gi|70606992|ref|YP_255862.1| 24 GLNEKEVQLIFRLLYSDTK-LNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGR 82
                                  77778999*********86.*********************************9999988 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   1.6e-09   7.6e-07       3      46 ..      31      74 ..      30      76 .. 0.95
   2 ?    0.6   0.0       1.1   4.9e+02      33      43 ..     103     113 ..     101     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.6e-09
                      HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  + i  ll +++kl++eel+e+++vS+a i + L+eL+++gl++R
  gi|70606992|ref|YP_255862.1| 31 QLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIER 74
                                  568899************************************99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                      HTH_DeoR  33 RDLneLeeqgl 43 
                                   RDL+eL+++ +
  gi|70606992|ref|YP_255862.1| 103 RDLEELVQASI 113
                                   9****998765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   1.6e-09   7.1e-07       8      57 ..      33      82 ..      25      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.6e-09
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                  i r+ly+   l++ eLa+ ++vsk+ +++ l +L  kGlieR+k  +  R
  gi|70606992|ref|YP_255862.1| 33 IFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGR 82
                                  3456666667*********************************9777666 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.8   1.1e-09   5.3e-07       7      95 ..      22     111 ..      13     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.1e-09
                                   HHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETT.TEEEEEEEEEECCCHCCCHH CS
                   TFIIE_alpha   7 vrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdee.kswykyywrinyeklvdvvk 86 
                                   + +  ++e+ l+   L ++ +++ e+la+e k+ +  + k L +L +++l++  +  +e+ k+   y ++++ e+l + ++
  gi|70606992|ref|YP_255862.1|  22 MYGLNEKEVQLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGrKGRPIYVYYVDREQLFKRIS 102
                                   45667799********************************************9998886515666788************* PP

                                   HHHHHHHHH CS
                   TFIIE_alpha  87 rkleevvkk 95 
                                   r lee+v+ 
  gi|70606992|ref|YP_255862.1| 103 RDLEELVQA 111
                                   *****9985 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   4.8e-09   2.2e-06      21      58 ..      40      76 ..      31      78 .. 0.91
   2 ?   -2.5   0.0       9.1   4.2e+03       7      15 ..      99     107 ..      94     117 .. 0.56

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.8e-09
                                  TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                   +kL   +eLa+ef+Vs+  + ++L++L+ +gl+er++
  gi|70606992|ref|YP_255862.1| 40 DTKL-NIEELAEEFKVSKALISKSLSELANKGLIEREK 76
                                  6899.9*****************************985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.1
                                   HHHHHHHHT CS
                          GntR   7 erLredIls 15 
                                    r+ +d+ +
  gi|70606992|ref|YP_255862.1|  99 KRISRDLEE 107
                                   555555443 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   8.7e-08     4e-05       2      59 ..      26      83 ..      25      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.7e-08
                        HTH_27  2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59
                                  ++ ++++++ +   + +  +++l++  +v+++ is+sl++L +kGL+er++   ++r 
  gi|70606992|ref|YP_255862.1| 26 NEKEVQLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGRK 83
                                  5667888666665999999****************************99998877776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.5   3.9e-07   0.00018      12      56 ..      32      76 ..      12      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.9e-07
                                  HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                   I++l  +  +    +lae+ +vs++ +s++l++L+++G++e ek
  gi|70606992|ref|YP_255862.1| 32 LIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREK 76
                                  578888888899999*************************99887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   1.6e-07   7.1e-05      21      58 ..      38      75 ..      29      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-07
                                  STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  ++++++++ee+ae++++s+  ++k l++L+++gl++ +
  gi|70606992|ref|YP_255862.1| 38 YSDTKLNIEELAEEFKVSKALISKSLSELANKGLIERE 75
                                  456679*****************************844 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.8e-07   8.1e-05      14      46 ..      41      73 ..      27      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-07
                                  SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +l + elaee+++s++ +S  L+ L + GL+e
  gi|70606992|ref|YP_255862.1| 41 TKLNIEELAEEFKVSKALISKSLSELANKGLIE 73
                                  67999**************************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   1.7e-07   7.6e-05       8      48 .]      33      73 ..      25      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-07
                        HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  I +lL+ + ++++ eLAe+  +S++ +++ l +L ++GlI+
  gi|70606992|ref|YP_255862.1| 33 IFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIE 73
                                  4599************************************7 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   5.9e-07   0.00027       4      43 ..      32      70 ..      29      84 .. 0.79
   2 ?   -1.6   0.0       5.9   2.7e+03      33      39 ..     110     116 ..     101     121 .. 0.51

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.9e-07
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   i +lL++ ++ +++eeLAee++vS++ + + + +L  +g
  gi|70606992|ref|YP_255862.1| 32 LIFRLLYSDTK-LNIEELAEEFKVSKALISKSLSELANKG 70
                                  46666655555.************************9988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.9
                        HTH_11  33 rrdIkaL 39 
                                   +  I++L
  gi|70606992|ref|YP_255862.1| 110 QASIAKL 116
                                   3334444 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   8.2e-07   0.00038       5      54 ..      33      82 ..      31     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.2e-07
                        HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkk 54
                                  ++ +L+s+ + + +el e+ +++++ +s+ l+ L ++g ie++k  ++++
  gi|70606992|ref|YP_255862.1| 33 IFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNEGR 82
                                  7889****************************************877653 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.3   2.2e-06     0.001      41      90 ..      52      99 ..      21     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.2e-06
                                  ----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHH CS
                           RTP 41 ykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekak 90
                                  +k +++ i ++l el ++g+++r+k  +e+ k + +++Y+++   ++ +k
  gi|70606992|ref|YP_255862.1| 52 FKVSKALISKSLSELANKGLIEREKVSNEGRKGRPIYVYYVDR--EQLFK 99
                                  6678999*********************************987..34344 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.5e-06    0.0021      19      55 ..      40      76 ..      16      97 .. 0.77
   2 ?   -2.1   0.0       8.4   3.9e+03      38      51 ..     101     114 ..      99     120 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-06
                                  EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                  + +l+ eelA+   ++   +s+ lseL ++gli+r++
  gi|70606992|ref|YP_255862.1| 40 DTKLNIEELAEEFKVSKALISKSLSELANKGLIEREK 76
                                  458899****************************764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.4
                                   HHHHHHHHHHTTSE CS
                     HTH_Crp_2  38 vsrilseLkregli 51 
                                   +sr l eL ++ + 
  gi|70606992|ref|YP_255862.1| 101 ISRDLEELVQASIA 114
                                   56777777666654 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.1   9.7e+02      45      54 ..      12      21 ..       8      24 .. 0.81
   2 !   14.4   0.1   6.4e-05     0.029      30      61 ..      45      76 ..      31      78 .. 0.92
   3 ?    2.9   0.1      0.25   1.2e+02      23      48 ..      95     120 ..      92     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.1
                  Cullin_Nedd8 45 kkrIesLiek 54
                                  k +Ie+L+e 
  gi|70606992|ref|YP_255862.1| 12 KTQIEKLLEF 21
                                  7899999985 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-05
                  Cullin_Nedd8 30 ieqlskrftpsiadikkrIesLiekeYleRde 61
                                  ie+l++ f++s+a+i k++ +L +k+ +eR++
  gi|70606992|ref|YP_255862.1| 45 IEELAEEFKVSKALISKSLSELANKGLIEREK 76
                                  89999*************************85 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.25
                  Cullin_Nedd8  23 neLvsevieqlskrftpsiadikkrI 48 
                                   ++L++++ ++l++ ++ sia  k+ I
  gi|70606992|ref|YP_255862.1|  95 EQLFKRISRDLEELVQASIAKLKEYI 120
                                   78999999999999999999999876 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.4   3.6e-05     0.017       2      57 ..      10      66 ..       9     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-05
                       UPF0122  2 ektlrlnaLfdiYqsLLTekqanyle.lyyadDlSlsEiAeefnvsrqavydnikrt 57
                                  +k++++++L+++   L  +  +  ++ ly +  l ++E+Aeef+vs+  ++ +++  
  gi|70606992|ref|YP_255862.1| 10 QKKTQIEKLLEFMYGLNEKEVQLIFRlLYSDTKLNIEELAEEFKVSKALISKSLSEL 66
                                  588899999999888765554445661566778*****************9998764 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   8.3e-06    0.0038       7      60 ..      30      83 ..      25     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.3e-06
                                  HHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-E CS
                          HxlR  7 kllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpk 60
                                    li++ l +  k   +el++++ k+s+ +++++L eL ++gliere +++ + k
  gi|70606992|ref|YP_255862.1| 30 VQLIFRLLYSdTKLNIEELAEEF-KVSKALISKSLSELANKGLIEREKVSNEGRK 83
                                  567888887746668999****9.***********************99988765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.2e-05    0.0057      15      60 ..      33      78 ..      31      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-05
                                  HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  i+r+L ++  l  +elae++ +sk+ +s+ L +L+  gL+e+++++
  gi|70606992|ref|YP_255862.1| 33 IFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVS 78
                                  8999**************************************9986 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.1   9.7e+02      28      39 ..      12      23 ..       9      25 .. 0.83
   2 !   13.2   0.0   0.00015     0.071      14      52 ..      42      80 ..      35      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.1
                          FeoC 28 pealeamLeqwv 39
                                  ++++e++Le++ 
  gi|70606992|ref|YP_255862.1| 12 KTQIEKLLEFMY 23
                                  6899*****985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00015
                          FeoC 14 rvslkeLsrhfkaspealeamLeqwvrkGrvekvaatac 52
                                  + +++eL+ +fk+s++ + + L  +  kG +e+++ +++
  gi|70606992|ref|YP_255862.1| 42 KLNIEELAEEFKVSKALISKSLSELANKGLIEREKVSNE 80
                                  6789*****************************999887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.9e-05     0.045      28      55 .]      45      72 ..      12      72 .. 0.93
   2 ?   -0.5   0.0       2.8   1.3e+03      41      53 ..     100     112 ..      96     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.9e-05
                        HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                   e la+ +++sk  +s+ + eL+ +G+i
  gi|70606992|ref|YP_255862.1| 45 IEELAEEFKVSKALISKSLSELANKGLI 72
                                  689***********************98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.8
                        HTH_36  41 TvsraikeLeqlG 53 
                                    +sr + eL+q+ 
  gi|70606992|ref|YP_255862.1| 100 RISRDLEELVQAS 112
                                   6888888888875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.053       5      38 ..      25      60 ..      21      69 .. 0.83
   2 ?   -1.7   0.0       4.6   2.1e+03      22      37 ..      62      77 ..      59      79 .. 0.69
   3 ?   -2.2   0.0       6.7   3.1e+03      16      28 ..     103     115 ..      93     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                  S-HHH.HHHHHHHH.TTT--HHHHHHHHTS-HHHHH CS
                    Sigma70_r4  5 Lpere.revlelrf.geglTleEIgerlgiSrerVr 38
                                  L+e+e + +++l + + +l+ eE++e++ +S+  ++
  gi|70606992|ref|YP_255862.1| 25 LNEKEvQLIFRLLYsDTKLNIEELAEEFKVSKALIS 60
                                  67777467899999*****************87665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.6
                                  -HHHHHHHHTS-HHHH CS
                    Sigma70_r4 22 TleEIgerlgiSrerV 37
                                  +l+E++++  i re V
  gi|70606992|ref|YP_255862.1| 62 SLSELANKGLIEREKV 77
                                  7888888766666666 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.7
                                   HHTTT--HHHHHH CS
                    Sigma70_r4  16 rfgeglTleEIge 28 
                                   r +e+l ++ I++
  gi|70606992|ref|YP_255862.1| 103 RDLEELVQASIAK 115
                                   4577777777775 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017      0.08       9      38 ..      45      74 ..      42      85 .. 0.84
   2 ?   -0.7   0.0       2.6   1.2e+03      22      31 ..     108     117 ..     107     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                        HTH_41  9 IeelakeleLSvGlvQkALklLeddkaisl 38
                                  Ieela+e+ +S  l+ k L  L +++ i+ 
  gi|70606992|ref|YP_255862.1| 45 IEELAEEFKVSKALISKSLSELANKGLIER 74
                                  9*************************9963 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.6
                        HTH_41  22 lvQkALklLe 31 
                                   lvQ+ + +L+
  gi|70606992|ref|YP_255862.1| 108 LVQASIAKLK 117
                                   79****9998 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   7.7e-05     0.035      28      72 ..      35      76 ..      10      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-05
                       DUF4423 28 ellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                   ll   ++  ++eela+ ++  +s++ ++k+l+ L + gl+++++
  gi|70606992|ref|YP_255862.1| 35 RLLYSDTK-LNIEELAEEFK--VSKALISKSLSELANKGLIEREK 76
                                  45555555.99*********..********************987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00019     0.085      19      63 ..      45      88 ..      41      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                                  HHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEE CS
                          PadR 19 leelsegllelseGslYpaLkrLekeglveseweesgegpprkyY 63
                                  +eel e+ +++s++ + + L++L ++gl+e+e++ ++ ++ r +Y
  gi|70606992|ref|YP_255862.1| 45 IEELAEE-FKVSKALISKSLSELANKGLIEREKVSNEGRKGRPIY 88
                                  6778655.9*************************99888888777 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00014     0.066      42      68 ..      59      85 ..      46      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHTTSEEEE.EEE-CC.C-E CS
                        Cdc6_C 42 vsdllseLemlgilele.ksskGrregr 68
                                  +s+ lseL+ +g++e+e +s++Gr+ gr
  gi|70606992|ref|YP_255862.1| 59 ISKSLSELANKGLIEREkVSNEGRK-GR 85
                                  7899*************44556885.76 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00017     0.077      22      59 ..      46      81 ..      43     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsiidsatk 59
                                   +La e+k ++  + + l  L +kgLI++ ++  s+++
  gi|70606992|ref|YP_255862.1| 46 EELAEEFKVSKALISKSLSELANKGLIEREKV--SNEG 81
                                  689****************************9..4443 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0015      0.69      18      54 ..      40      75 ..      30      82 .. 0.83
   2 ?    1.3   0.0      0.79   3.6e+02      28      47 ..      99     118 ..      91     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0015
                        HemN_C 18 reGldlaafeqrfgldleellaaaleklqeqGLLeld 54
                                  + +l++++++++f ++  +l  + l +l ++GL+e +
  gi|70606992|ref|YP_255862.1| 40 DTKLNIEELAEEFKVS-KALISKSLSELANKGLIERE 75
                                  56799**********9.6666888**********976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.79
                        HemN_C  28 qrfgldleellaaaleklqe 47 
                                    r+  dleel++a ++kl e
  gi|70606992|ref|YP_255862.1|  99 KRISRDLEELVQASIAKLKE 118
                                   56778888988888888876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00024      0.11      24      78 ..      45     104 ..      23     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00024
                                   HHT--GGG---HHHHHHHHHHHHHTTS-EEEEE...TTEE..EEE----XXXXXXXXXXX CS
               Penicillinase_R  24 veeleeekelaysTVktllrrLvkKgllsreke...graf..iYsplvseeeavasavkq 78 
                                   +eel+ee +++++ +   l+ L +Kgl++rek    gr+   iY   v++e++ ++ +++
  gi|70606992|ref|YP_255862.1|  45 IEELAEEFKVSKALISKSLSELANKGLIEREKVsneGRKGrpIYVYYVDREQLFKRISRD 104
                                   57888888899999***************9986333444322788888888887776655 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       7.5   3.5e+03       8      18 ..      10      20 ..       7      20 .. 0.79
   2 ?   10.8   0.0   0.00069      0.32       5      39 ..      25      61 ..      24      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.5
                        HTH_38  8 eeReeIerlla 18
                                  +   +Ie+ll+
  gi|70606992|ref|YP_255862.1| 10 QKKTQIEKLLE 20
                                  56789999985 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00069
                        HTH_38  5 LsleeReeIerl.l.aeGlslreIArrLgrspsTIsR 39
                                  L+  e + I rl + + +l++ e A + ++s+  Is+
  gi|70606992|ref|YP_255862.1| 25 LNEKEVQLIFRLlYsDTKLNIEELAEEFKVSKALISK 61
                                  78899*******554588*****************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   0.00015      0.07      14      55 ..      26      67 ..      11      75 .. 0.80
   2 ?   -1.2   0.0       6.8   3.1e+03      48      49 ..     110     111 ..      91     122 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                  HHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                           Mga 14 keslkyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                  +e +   + ++l+ + +++ieela+e+ +S++ + +++ el 
  gi|70606992|ref|YP_255862.1| 26 NEKEVQLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELA 67
                                  4444455778888***********************999984 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.8
                                   HH CS
                           Mga  48 kr 49 
                                   + 
  gi|70606992|ref|YP_255862.1| 110 QA 111
                                   22 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.71   3.3e+02      24      48 ..       9      34 ..       5      35 .. 0.73
   2 ?    9.6   0.1    0.0018      0.83       8      45 ..      41      78 ..      39      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.71
                                  S-SHHHHHHHHHHH.TS-HHHHHHHH CS
                   Homeodomain 24 ypsaeereeLAkkl.gLeerqVkvWF 48
                                  y ++ ++e+L + + gL+e+ V+  F
  gi|70606992|ref|YP_255862.1|  9 YQKKTQIEKLLEFMyGLNEKEVQLIF 34
                                  55667777777777899999999755 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                  -HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHH CS
                   Homeodomain  8 tkeqleeLeklFeenrypsaeereeLAkklgLeerqVk 45
                                  tk  +eeL ++F+ ++ + ++   eLA+k  +e ++V+
  gi|70606992|ref|YP_255862.1| 41 TKLNIEELAEEFKVSKALISKSLSELANKGLIEREKVS 78
                                  67789************************999988886 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00024      0.11      83     129 ..      22      67 ..       3      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                       MRP-L20  83 kyhltkedieeirrLraeDPekwsrkkLakkFgcsklfvsmvteapk 129
                                    y l++++++ i rL  +D +k ++++La++F++sk  +s  ++  +
  gi|70606992|ref|YP_255862.1|  22 MYGLNEKEVQLIFRLLYSD-TKLNIEELAEEFKVSKALISKSLSELA 67 
                                   499****************.7889*************9997765544 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00053      0.24      15      56 ..      30      71 ..      16      73 .. 0.90
   2 ?   -1.3   0.0       5.2   2.4e+03      22      37 ..      97     112 ..      95     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00053
                                  HHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTS CS
                         HTH_9 15 vakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrl 56
                                  v+ + ++L + ++l + el+++ k+s+ ++ ksL+ L + +l
  gi|70606992|ref|YP_255862.1| 30 VQLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGL 71
                                  7789999****************************9988776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.2
                                   HHHHSSBEHHHHHHHH CS
                         HTH_9  22 Llrkgrltlrelvkkt 37 
                                   L+++  + l elv+++
  gi|70606992|ref|YP_255862.1|  97 LFKRISRDLEELVQAS 112
                                   7788888888888765 PP

>> DUF3920  Protein of unknown function (DUF3920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00034      0.16      48      88 ..      16      56 ..       9      85 .. 0.79
   2 ?   -1.1   0.0       4.6   2.1e+03      59      89 ..      91     110 ..      82     122 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                       DUF3920 48 eeflfplsgvyhkekqlifvfkfedyeqvlktllhelrhal 88
                                  e+ l ++ g+  ke+qlif + + d +  ++ l  e++ + 
  gi|70606992|ref|YP_255862.1| 16 EKLLEFMYGLNEKEVQLIFRLLYSDTKLNIEELAEEFKVSK 56
                                  678999******************************98654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.6
                       DUF3920  59 hkekqlifvfkfedyeqvlktllhelrhalq 89 
                                   + ++           eq++k +  +l   +q
  gi|70606992|ref|YP_255862.1|  91 YVDR-----------EQLFKRISRDLEELVQ 110
                                   3333...........4444444433333333 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00036      0.17      29      59 ..      46      75 ..      44      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                  HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyierd 59
                                   e+a++++++  + + + L  L++KG+ier+
  gi|70606992|ref|YP_255862.1| 46 EELAEEFKVS-KALISKSLSELANKGLIERE 75
                                  6888888875.8899**************97 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       7.5   3.5e+03      31      40 ..      11      20 ..       6      24 .. 0.74
   2 ?    9.9   0.1    0.0015      0.67      28      49 ..      50      73 ..      29      77 .. 0.80
   3 ?    0.6   0.1       1.2   5.6e+02      35      53 ..     101     119 ..      98     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.5
                         TBPIP 31 gKtavqkaLd 40
                                  +Kt + k L+
  gi|70606992|ref|YP_255862.1| 11 KKTQIEKLLE 20
                                  5777777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                         TBPIP 28 k..klgKtavqkaLdeLvdegkii 49
                                  +  k++K+ + k L eL+++g+i 
  gi|70606992|ref|YP_255862.1| 50 EefKVSKALISKSLSELANKGLIE 73
                                  33589*****************96 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.2
                         TBPIP  35 vqkaLdeLvdegkiieKey 53 
                                   + + L+eLv++   + Key
  gi|70606992|ref|YP_255862.1| 101 ISRDLEELVQASIAKLKEY 119
                                   56779*****998888888 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.18      31      77 ..      27      73 ..      11      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                  --HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47 31 qaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                  ++e +l+  L ++D k ++ ++Ae+ +++ + + + + +La++gl++
  gi|70606992|ref|YP_255862.1| 27 EKEVQLIFRLLYSDTKLNIEELAEEFKVSKALISKSLSELANKGLIE 73
                                  56778899999**********************************97 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.019       8.5      17      33 ..      43      59 ..      41      62 .. 0.88
   2 ?    3.9   0.0       0.1        47      33      47 .]      87     101 ..      84     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                                  --HHHHHHHHTSSHHHH CS
                        TetR_N 17 ttvreIAkrAGvskgal 33
                                  + ++e+A++ +vsk+++
  gi|70606992|ref|YP_255862.1| 43 LNIEELAEEFKVSKALI 59
                                  6799***********98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                                   HHHHTSSHHHHHHHH CS
                        TetR_N  33 lYryFpsKeeLleal 47 
                                   +Y y+ ++e+L++++
  gi|70606992|ref|YP_255862.1|  87 IYVYYVDREQLFKRI 101
                                   8***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 786.70
//
Query:       gi|70606993|ref|YP_255863.1|  [L=79]
Description: hypothetical protein Saci_1224 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-24   83.5   0.9    7.3e-24   83.2   0.9    1.1  1  LSM       LSM domain
    0.00051   20.1   0.2    0.00063   19.8   0.2    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.9   8.2e-28   7.3e-24       2      67 .]      14      78 ..      13      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 8.2e-28
                                  HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                   l+++++++v+v+lk+++ +rGtLk++D +mNlvLe+ ee+++d+ ++rk+g+++iRG+n++l+s+
  gi|70606993|ref|YP_255863.1| 14 VLAESLGSTVLVKLKGEKIVRGTLKSYDMHMNLVLENSEEIMNDG-STRKVGTIVIRGDNVILVSP 78
                                  699******************************************.*****************986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2     7e-08   0.00063       7      56 ..      14      58 ..       9      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7e-08
                                  HHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS..... CS
                        SM-ATX  7 lltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansks 56
                                  +l+ + G++v v++k  ++ +G ++++++   +++vL++  ++ ++    
  gi|70606993|ref|YP_255863.1| 14 VLAESLGSTVLVKLKGEKIVRGTLKSYDM--HMNLVLENSEEIMND---G 58
                                  678999***********************..***********9992...2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 549.02
//
Query:       gi|70606994|ref|YP_255864.1|  [L=109]
Description: hypothetical protein Saci_1225 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 782.79
//
Query:       gi|70606995|ref|YP_255865.1|  [L=176]
Description: hypothetical protein Saci_1226 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   14.2   0.2       0.45   11.4   0.1    2.0  2  DUF469    Protein with unknown function (DUF469)


Domain annotation for each model (and alignments):
>> DUF469  Protein with unknown function (DUF469)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.055   9.8e+02      38      83 ..       9      56 ..       2      62 .. 0.73
   2 ?   11.4   0.1   2.5e-05      0.45      31      92 ..     103     164 ..      84     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.055
                        DUF469 38 afievieanglafggs.gkeeleglvclaklgsvte.edreaveawlk 83
                                  ++i++i + +l++g    ++el+ l+  +k   ++e e  +av+ +l+
  gi|70606995|ref|YP_255865.1|  9 RIIDIIFNSNLIYGKVvYEDELKRLIGNEKKLLCSErELIQAVKVYLR 56
                                  678999999999988766778888888886666666255777877776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.5e-05
                        DUF469  31 eidalvdafievieanglafggsgkeeleglvclaklgsvteedreaveawlkarsevkeve 92 
                                   +i    d+ +  + +n++ ++ +++e +++l++la+ +s+ +e  +++ ++l++++ v++++
  gi|70606995|ref|YP_255865.1| 103 RIVLYNDRTVVKVGENEMEYKINKNEVIKTLISLATQSSTRDEFITKLLKFLNDNNDVRTIQ 164
                                   55566788888999*********99******************************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1193.67
//
Query:       gi|70606996|ref|YP_255866.1|  [L=430]
Description: deoxyribodipyrimidine photolyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-66  221.7   2.1    1.1e-65  220.9   2.1    1.3  1  FAD_binding_7   FAD binding domain of DNA photolyase
    8.2e-27   94.2   0.0    8.2e-26   91.0   0.0    2.1  2  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.9   2.1   1.2e-69   1.1e-65       1     198 [.     240     423 ..     240     426 .. 0.95

  Alignments for each domain:
  == domain 1  score: 220.9 bits;  conditional E-value: 1.2e-69
                                   HHHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHH CS
                 FAD_binding_7   1 flreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmivasFl 81 
                                   f+r+L+wr+fy+ l++++p +  +++k+++d+i+we+se+  ++aWk+G+TG+P++DA+mr L++tG+++ r+Rm+va Fl
  gi|70606996|ref|YP_255866.1| 240 FTRQLYWRDFYTLLAYQNPYVFGHSFKTEYDKIKWENSER-YFNAWKDGMTGYPIIDAGMRALNTTGFINGRVRMLVAFFL 319
                                   899********************************88866.7*************************************** PP

                                   CTTT-B-HHHHHHHHHHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTTS-HHHHT- CS
                 FAD_binding_7  82 tkdLlidWregeevFeellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkklpakyihe 162
                                   tk L++dWr ge++F+++lvD+d+a+n+gnwqw+a+tg+d    fr+f+p+kq++k+Dpe+++i+ +v eL+++p ++ih+
  gi|70606996|ref|YP_255866.1| 320 TKVLFVDWRLGERYFATKLVDYDPAVNNGNWQWVASTGTDYI--FRVFDPWKQQEKYDPEAKFIKDYVRELRDYPPSVIHK 398
                                   ****************************************98..9***********************************8 PP

                                   GGGSGCHHHHHHT--TTTSS---SS-HHHHHHHHHH CS
                 FAD_binding_7 163 pwkapaeeqkkagvvlgkdYpkpivdhkearkrale 198
                                    +            ++ + Yp+piv+++e+ + +++
  gi|70606996|ref|YP_255866.1| 399 VY-----------LHKITGYPSPIVNWRERVEMVKQ 423
                                   66...........234579*********99887765 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   9.2e-30   8.2e-26       3     162 ..       5     152 ..       3     157 .. 0.89
   2 ?    0.7   0.1     0.052   4.6e+02     134     151 ..     354     371 ..     349     382 .. 0.78

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 9.2e-30
                                   EEESS---STT-HHHHHHHCTTSEEEEEEEE-HHHHTCG.S-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHH CS
                DNA_photolyase   3 vWfrrDlRlhDNpALaaAaasgepvipvfvldpekahkl.rvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpe 82 
                                   v frrDlRl DN+AL +A+ + ++++p+f++dp+++ +  +++   + fl+ sL +Ld+eL   +++L v++g p++++ +
  gi|70606996|ref|YP_255866.1|   5 VIFRRDLRLFDNTALVNAVYHCNKIYPIFIVDPRQMINNpYKSEFAATFLINSLVELDKEL---NGNLNVYYGYPENIVSK 82 
                                   569*******************************554447999*****************8...8************9988 PP

                                   HHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHHHHHCS-TTS CS
                DNA_photolyase  83 lakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwlkelkeplpa 162
                                   l     ++a+++n++y+p++ +rde++ke + ++gi++ s+ d +l +    + kk k+ + Ftpf+ ++++ l  ++p+
  gi|70606996|ref|YP_255866.1|  83 LD---MVNAIFINEDYTPFAIQRDEKMKENALNKGIKFFSYPDVLLSA----EEKKIKIGRSFTPFYTKARE-L--EVPK 152
                                   83...49************************************98866....556789**********9998.3..3333 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.052
                                   HHTTTSSSHSSHHHHHHC CS
                DNA_photolyase 134 vktkkgkpykvFtpfrkr 151
                                   + t+++++++vF p++++
  gi|70606996|ref|YP_255866.1| 354 ASTGTDYIFRVFDPWKQQ 371
                                   567778*********984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2983.28
//
Query:       gi|70606997|ref|YP_255867.1|  [L=451]
Description: hypothetical protein Saci_1228 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0003   21.1   0.2     0.0011   19.3   0.0    2.0  3  AAA_22    AAA domain
     0.0031   17.2   0.0     0.0068   16.1   0.0    1.5  1  AAA_30    AAA domain
     0.0038   17.6   0.0     0.0092   16.4   0.0    1.6  1  AAA_16    AAA ATPase domain
     0.0093   16.3   0.1      0.071   13.5   0.0    2.2  2  AAA_19    AAA domain
  ------ inclusion threshold ------
      0.012   16.2   0.5       0.12   12.9   0.1    2.3  2  ABC_tran  ABC transporter
      0.012   15.5   0.7      0.034   14.1   0.1    2.0  2  NTPase_1  NTPase
      0.016   14.4   0.0      0.029   13.5   0.0    1.4  1  MCM       MCM P-loop domain
      0.022   13.9   0.0      0.051   12.7   0.0    1.6  1  NB-ARC    NB-ARC domain
      0.041   13.8   0.1       0.18   11.7   0.0    2.0  2  NACHT     NACHT domain
      0.057   13.0   0.1       0.15   11.7   0.1    1.7  1  DUF4222   Domain of unknown function (DUF4222)
      0.064   12.8   0.3        0.2   11.1   0.0    2.0  2  AAA_7     P-loop containing dynein motor region
       0.11   12.5   0.1       0.41   10.6   0.0    2.0  2  AAA_5     AAA domain (dynein-related subfamily)
       0.12   12.9   0.2       0.54   10.7   0.0    2.2  3  AAA_17    AAA domain
       0.12   12.3   0.4       0.27   11.2   0.4    1.5  1  BORCS8    BLOC-1-related complex sub-unit 8
       0.15   12.6   0.2         19    5.8   0.0    2.5  2  MRFAP1    MORF4 family-associated protein1
        1.5    9.1   5.9        5.8    7.3   0.1    3.3  4  Img2      Mitochondrial large subunit ribosomal protein (Img2


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.6e-07    0.0011       4      64 ..      38      92 ..      34     125 .. 0.85
   2 ?   -2.9   0.0       6.8   7.6e+03      97     129 ..     166     193 ..     143     200 .. 0.63
   3 ?   -2.8   0.0       6.1   6.8e+03      43      64 ..     288     309 ..     254     326 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.6e-07
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellral 64
                                  ++ i  ++G++G+GKTt l+++ e   +       ++ ++f +l+s++   ++++ ++ r++
  gi|70606997|ref|YP_255867.1| 38 NKDIASIIGQPGMGKTTILKKVEEIISK-------EKFTLFLDLSSKGeIESEFWDKIDRFM 92
                                  788999******************9974.......888899999999966667777777665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.8
                        AAA_22  97 iDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                   +DE   + +e +l+++++l n s  +v++++++
  gi|70606997|ref|YP_255867.1| 166 VDE---I-REGHLSKIHRLIN-SGLNVPILMAI 193
                                   443...3.4556666666666.55555555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.1
                        AAA_22  43 vfvtlpsstsskdllrellral 64 
                                    ++tl++ ++ ++ l+++lr++
  gi|70606997|ref|YP_255867.1| 288 SSYTLKNVEENSTTLEKMLRET 309
                                   3444444443333344444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     6e-06    0.0068      14      49 ..      36      70 ..      31      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6e-06
                        AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                  ++++d +a + G +G GKtt+lk+++e++ ++++++
  gi|70606997|ref|YP_255867.1| 36 IKNKD-IASIIGQPGMGKTTILKKVEEIISKEKFTL 70
                                  55555.999********************9998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.2e-06    0.0092      26      76 ..      41      88 ..      30     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-06
                        AAA_16 26 lvllsGesGvGKsslvrellralekdg.gif..lrgkcdqlesaipysalaqal 76
                                  +  ++G++G+GK+++++++ + ++k++  +f  l+ k +        s +++ +
  gi|70606997|ref|YP_255867.1| 41 IASIIGQPGMGKTTILKKVEEIISKEKfTLFldLSSKGEIE------SEFWDKI 88
                                  56799********************9755555555555544......3455555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.3e-05     0.071       9      38 ..      38      67 ..      31      81 .. 0.85
   2 ?   -0.1   0.0      0.95   1.1e+03      91     122 ..     150     181 ..      90     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelg 38
                                  ++++  +++ pG+GKT++lk++ +++ +++
  gi|70606997|ref|YP_255867.1| 38 NKDIASIIGQPGMGKTTILKKVEEIISKEK 67
                                  567889*************99888877765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.95
                        AAA_19  91 leeaeeekklqeeellivDEfqdvd.elqyrLl 122
                                   l+  ++ k++    +++vDE+ +     + rL+
  gi|70606997|ref|YP_255867.1| 150 LKFVNDLKNV-MDITILVDEIREGHlSKIHRLI 181
                                   3333334444.45599****9887766666666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00011      0.12       8      42 ..      36      70 ..      31     116 .. 0.81
   2 ?    1.2   0.1      0.45     5e+02      39      92 ..     276     388 ..     251     409 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                  EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGei 42
                                  +k+  +  i+G+ G GK+t+lk + +  ++++ ++
  gi|70606997|ref|YP_255867.1| 36 IKNKDIASIIGQPGMGKTTILKKVEEIISKEKFTL 70
                                  56778899**************9888777765555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                   EEEEEETTCEGGG............B-HHHCCHCEEEE-SS--S-TTSBHHHH............................ CS
                                   xxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                      ABC_tran  39 eGeilldgkdlke............qeleslrkeigvlpqepqlfpeltvren............................ 79 
                                   eG++++ ++++++            + ++ lr+ i+ l++e                                        
  gi|70606997|ref|YP_255867.1| 276 EGNVECIKDSIQSsytlknveenstTLEKMLRETISSLSKE-----------Frvsyvhqrgkrvevkgknitvgifftkd 345
                                   33333333333333222222222222233333333333333...........02222222222344445555555555555 PP

                                   ..............................HHHTCHHHHHHHS CS
                                   ..............................xxxxxxxxxxxxx RF
                      ABC_tran  80 ..............................esdeeiekalskl 92 
                                                                 e d++i+k+++k+
  gi|70606997|ref|YP_255867.1| 346 dygylgivklsngneisgdeisllpyveqvENDKKIYKIRKKF 388
                                   5555555555555555555555555555555555555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     3e-05     0.034       4      28 ..      44      68 ..      42      71 .. 0.88
   2 ?   -2.9   0.0       4.9   5.5e+03     100     133 ..     165     194 ..     149     217 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                                  EE--TTSSHHHHHHHHHHHH...GG CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkssgv 28
                                  i G+pG+GKtT++kkv e ++++ +
  gi|70606997|ref|YP_255867.1| 44 IIGQPGMGKTTILKKVEEIISKEKF 68
                                  679***************9988765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                                   EE---STTGGG-HHHHHHHHHHHTTTSEEEEE-- CS
                      NTPase_1 100 viDEiGkmElkskkfkeaveevLksekpvlavih 133
                                   ++DEi   E    k+++ ++  L  ++p+l+ i+
  gi|70606997|ref|YP_255867.1| 165 LVDEIR--EGHLSKIHRLINSGL--NVPILMAIP 194
                                   455552..333333333333333..345555555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.029      61      93 ..      43      75 ..      11      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                  EEEESSTSTHHHHHHHHHHHSSSEEEEESSSSS CS
                           MCM 61 llvgdpgtaKsqlLkyveklapravytsgkgss 93
                                   ++g pg++K+++Lk+ve+++++  +t     s
  gi|70606997|ref|YP_255867.1| 43 SIIGQPGMGKTTILKKVEEIISKEKFTLFLDLS 75
                                  489********************9999765555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05     0.051      17      43 ..      38      62 ..      25     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                                  TSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 17 elqslvvalvGmgGvGKttlakqilnk 43
                                  +   ++ ++ G +G+GKtt++k++ + 
  gi|70606997|ref|YP_255867.1| 38 NK--DIASIIGQPGMGKTTILKKVEEI 62
                                  34..499***************98654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.18       5      28 ..      44      67 ..      40      78 .. 0.84
   2 ?   -1.2   0.0       1.5   1.7e+03     105     162 ..     173     233 ..     146     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                  EEC-TTTCHHHHHHHHHHHHCTS- CS
                         NACHT  5 lqGeaGsGKTtLlqklalawaegk 28
                                  + G++G+GKTt l+k+ + + ++k
  gi|70606997|ref|YP_255867.1| 44 IIGQPGMGKTTILKKVEEIISKEK 67
                                  89*************987777665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                   ....HHHHHCTTTTT--EEEEEEECCCHHH.....HCTTSSCE..EEEE--TCCHHHHHHHHC CS
                         NACHT 105 vrtlLselirkkllpeasllltvrpralrd.....leeqleeaivlevegfsesrrkqlvrky 162
                                       +++li+     ++++l+++ ++a ++     +++ l e+++    +++ +++k++v+ y
  gi|70606997|ref|YP_255867.1| 173 HLSKIHRLINS--GLNVPILMAIPTDAYNKvtdlaIRRRLDESRISLDSALTSDDIKEIVEAY 233
                                   45556667766..55788888888888877788888999999977777789999999988876 PP

>> DUF4222  Domain of unknown function (DUF4222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.15       8      43 ..     320     356 ..     315     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                       DUF4222   8 iYrDkrGvvVkvisvden.rVtFrRdGYehpcvaple 43 
                                    Y ++rG +V+v++   +  ++F  d+Y +  +++l+
  gi|70606997|ref|YP_255867.1| 320 SYVHQRGKRVEVKGKNITvGIFFTKDDYGYLGIVKLS 356
                                   6************987777***********9998875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018       0.2      29      70 ..      35      75 ..      23     106 .. 0.82
   2 ?   -2.3   0.1       2.3   2.6e+03      60     101 ..     288     328 ..     281     331 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                         AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  ++knk    ++G+ G GKt+i+k++ + ++kek++ l++ +s
  gi|70606997|ref|YP_255867.1| 35 VIKNKDIASIIGQPGMGKTTILKKVEEIISKEKFT-LFLDLS 75
                                  5788888999****************999988875.455555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                         AAA_7  60 ekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkk 101
                                   ++y+ ++++ +++t  ++l+++i  +l k  +  y+ + gk+
  gi|70606997|ref|YP_255867.1| 288 SSYTLKNVEENSTTLEKMLRETIS-SLSKEFRVSYVHQRGKR 328
                                   677888888888888888888885.47777777777777776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00037      0.41       4      30 ..      44      70 ..      43      79 .. 0.87
   2 ?   -2.9   0.0       5.7   6.4e+03      88     119 ..     420     450 ..     418     451 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                  EE--SSSSHHHHHHHGGGGBS--EEEE CS
                         AAA_5  4 LvGppGtgKselaerlaaalnreveyv 30
                                  ++G+pG gK+++ +++ + + +e ++ 
  gi|70606997|ref|YP_255867.1| 44 IIGQPGMGKTTILKKVEEIISKEKFTL 70
                                  69******************8777765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.7
                                   HHHSSEEE..-SSSEEE---.......-EEEEE CS
                         AAA_5  88 lleerrllleeggelvkakndd.llerfrviat 119
                                   +leer+++   ++elv+ ++++   ++f+ +at
  gi|70606997|ref|YP_255867.1| 420 ILEERTRS--ILKELVSDDQTTnVQNNFNAVAT 450
                                   67788887..66677777776655555888887 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00049      0.54       1      17 [.      45      61 ..      45      76 .. 0.83
   2 ?   -2.1   0.0       4.1   4.6e+03      72     105 ..     333     366 ..     289     387 .. 0.58
   3 ?   -2.5   0.0       5.7   6.3e+03      72     107 ..     386     421 ..     355     441 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00049
                                  EE-TTSSHHHHHHHHHH CS
                        AAA_17  1 lGgPGsGKgtqceklve 17
                                  +G PG+GK+t+++k+ e
  gi|70606997|ref|YP_255867.1| 45 IGQPGMGKTTILKKVEE 61
                                  59**********99976 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                   SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEE CS
                        AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdai 105
                                   ++ +  g + +k++ g+l  ++    +e++ d i
  gi|70606997|ref|YP_255867.1| 333 GKNITVGIFFTKDDYGYLGIVKLSNGNEISGDEI 366
                                   3333345555556666665555555555555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.7
                                   SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEE CS
                        AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiil 107
                                   k+++++    + +  + ++  + ev++ +  d +il
  gi|70606997|ref|YP_255867.1| 386 KKFIITNTKINVQGVDVVEIPTLEVIRIIRGDSLIL 421
                                   334443333322222223333334555555555554 PP

>> BORCS8  BLOC-1-related complex sub-unit 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00024      0.27      48      98 ..     265     315 ..     256     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                        BORCS8  48 kkevkeleeelqgacydveyaisavksikesessfeniqelLknsiflkqq 98 
                                   k ev+++e++ +g+++ ++++i+   ++k++e++ ++ +++L+++i+  ++
  gi|70606997|ref|YP_255867.1| 265 KSEVERIETDCEGNVECIKDSIQSSYTLKNVEENSTTLEKMLRETISSLSK 315
                                   89******************************************9987654 PP

>> MRFAP1  MORF4 family-associated protein1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017        19      44      71 ..     249     276 ..     245     299 .. 0.82
   2 ?    4.3   0.0      0.05        56      25      53 ..     304     332 ..     292     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                        MRFAP1  44 rarrklleidslldeikseveaseesal 71 
                                    + r l  + s+l+ ikseve  e    
  gi|70606997|ref|YP_255867.1| 249 WNGRELTTVSSILQFIKSEVERIETDCE 276
                                   4668899**************9887655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.05
                        MRFAP1  25 revrediaalereharaylrarrklleid 53 
                                   +  re i++l +e   +y+ +r k +e++
  gi|70606997|ref|YP_255867.1| 304 KMLRETISSLSKEFRVSYVHQRGKRVEVK 332
                                   678*********************99986 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.8   9.9e+03      24      34 ..      50      60 ..      43      70 .. 0.78
   2 ?    7.3   0.1    0.0052       5.8      29      66 ..     291     334 ..     280     340 .. 0.84
   3 ?   -1.6   0.0       3.1   3.5e+03      56      71 ..     386     405 ..     359     408 .. 0.56
   4 ?    3.2   0.1     0.099   1.1e+02      29      52 ..     410     433 ..     402     449 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.8
                          Img2 24 tkkltvirkie 34
                                    k+t+++k+e
  gi|70606997|ref|YP_255867.1| 50 MGKTTILKKVE 60
                                  56788888886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0052
                          Img2  29 virkieGDiaalredLrkalee......lvkvnevtgkieikGd 66 
                                   +++++e + + l++ Lr+++++       + v+++ +++e+kG+
  gi|70606997|ref|YP_255867.1| 291 TLKNVEENSTTLEKMLRETISSlskefrVSYVHQRGKRVEVKGK 334
                                   58999999************98665554499************6 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.1
                          Img2  56 e....vtgkieikGdrveev 71 
                                   +    ++ ki+++G  v+e+
  gi|70606997|ref|YP_255867.1| 386 KkfiiTNTKINVQGVDVVEI 405
                                   24444778888888777776 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.099
                          Img2  29 virkieGDiaalredLrkaleelv 52 
                                   vir i+GD   l+e  r+ l+elv
  gi|70606997|ref|YP_255867.1| 410 VIRIIRGDSLILEERTRSILKELV 433
                                   89******************9832 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 2924.48
//
Query:       gi|70606998|ref|YP_255868.1|  [L=167]
Description: hypothetical protein Saci_1229 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0079   16.1   0.0      0.018   15.0   0.0    1.5  1  MarR      MarR family
  ------ inclusion threshold ------
       0.03   14.7   0.0      0.048   14.0   0.0    1.3  1  Rrf2      Transcriptional regulator
      0.037   13.4   0.2      0.074   12.5   0.2    1.5  1  TehB      Tellurite resistance protein TehB
      0.048   13.6   0.0       0.11   12.4   0.0    1.6  1  HTH_15    Helix-turn-helix domain of alkylmercury lyase
        0.1   12.5   0.0       0.25   11.2   0.0    1.6  2  MarR_2    MarR family
       0.16   12.0   0.9       0.37   10.9   0.1    1.9  2  z-alpha   Adenosine deaminase z-alpha domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     6e-06     0.018       7      50 ..       9      52 ..       6      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6e-06
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                  ++L  ly+  p+  s++ ++++ ++  + +vl++Le +Gl++++
  gi|70606998|ref|YP_255868.1|  9 SVLQELYDGKPIAFSKIKRRIKEDPEDIEKVLTELESEGLVKKY 52
                                  79***************************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.6e-05     0.048      15      57 ..       9      51 ..       6      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                                  HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   +L++ ++++p++ ++i +r +  p+ +ek+l++L+ +glvk 
  gi|70606998|ref|YP_255868.1|  9 SVLQELYDGKPIAFSKIKRRIKEDPEDIEKVLTELESEGLVKK 51
                                  6788899999*******************************96 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.5e-05     0.074      52     103 ..      59     111 ..      53     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                                   T-EEEEEES-HHHHHHHHHHHH.HTT-TTEEEEE--GGG----S-EEEEEEES CS
                          TehB  52 gydvtawdknensiafleeike.kenlknistalydineaklderydfilstv 103
                                    y++  +d n   i+ l+eik+ +++l++i  + +++n  ++de yd +   +
  gi|70606998|ref|YP_255868.1|  59 SYELVKVDSNTIVIGLLREIKDeIKKLEEIVGEKWKLNVGSFDEVYDKVKDNL 111
                                   699999**************963799*********************886655 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.7e-05      0.11      21      60 ..       5      44 ..       2      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                        HTH_15 21 ellrpLlrlLakGepVtveeLAaatgrsveevrqaLaalp 60
                                   +++++l++L +G+p++  ++        e ++++L+ l 
  gi|70606998|ref|YP_255868.1|  5 DVVISVLQELYDGKPIAFSKIKRRIKEDPEDIEKVLTELE 44
                                  6789********************************8765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.4e-05      0.25       9      53 ..       9      51 ..       6      58 .. 0.93
   2 ?   -3.9   0.0       4.5   1.3e+04      27      35 ..     119     127 ..     115     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.4e-05
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   vL +L+++ +  ++ + + rr + ++  + ++l +L++ GLv +
  gi|70606998|ref|YP_255868.1|  9 SVLQELYDGKP--IAFSKIKRRIKEDPEDIEKVLTELESEGLVKK 51
                                  69*********..******************************86 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.5
                                   HHHHHTSSH CS
                        MarR_2  27 larrlglsk 35 
                                   +  +lgl+k
  gi|70606998|ref|YP_255868.1| 119 IRVELGLTK 127
                                   677888887 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00012      0.37       6      54 ..       4      52 ..       3      55 .. 0.92
   2 ?   -2.4   0.1       1.7     5e+03       5      18 ..      67      80 ..      63      85 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                  HHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEE CS
                       z-alpha  6 aekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyre 54
                                  ++ ++ +L+el ++k+    + +r ++ +  +i +vL +le +g v + 
  gi|70606998|ref|YP_255868.1|  4 KDVVISVLQELYDGKPIAFSKIKRRIKEDPEDIEKVLTELESEGLVKKY 52
                                  567999*************************************999876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                                  HHHHHHHHHHHC-T CS
                       z-alpha  5 qaekilelLeelge 18
                                   + +++ lL+e+ +
  gi|70606998|ref|YP_255868.1| 67 SNTIVIGLLREIKD 80
                                  55677777887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1060.32
//
Query:       gi|70606999|ref|YP_255869.1|  [L=218]
Description: TenA family transcription regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-38  133.1   1.0    1.3e-38  132.9   1.0    1.0  1  TENA_THI-4  TENA/THI-4/PQQC family
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.91    9.7   0.0    2.1  2  PTB         Phosphotyrosine-binding domain


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   1.0   1.5e-42   1.3e-38       4     209 ..      10     208 ..       7     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 1.5e-42
                                   CHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHHHH CS
                    TENA_THI-4   4 lrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrlae 84 
                                   +   +  + +HpF+  l +G+l+ e+f++y+iqdy+ylk+f ++la+  +k+++ e   +++ +  d ++ e +lh+ +  
  gi|70606999|ref|YP_255869.1|  10 ISDVYSAILSHPFITGLVSGKLEEERFKYYIIQDYHYLKDFSKALAVLSAKAESQEQSVLFATHVSDVIKVERDLHNYFFT 90 
                                   5566777888*********************************************************************** PP

                                   HTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHHCSHHHHH CS
                    TENA_THI-4  85 alGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkeyaseefra 165
                                    + + +e+   ++ sp +  y++yll+++ +  + e va +lpc++ y e+ ++l++k +   +p y++w+++y+ ee++ 
  gi|70606999|ref|YP_255869.1|  91 HWKINPED---FEQSPSNLMYTSYLLSTVYSRPFYEGVAVVLPCYWIYMEVGRELTKKGS--PNPLYKRWIDTYGGEEYEV 166
                                   ********...999******************************************9977..******************* PP

                                   HHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                    TENA_THI-4 166 aveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                    v+   ++++    +  d+q + + + f  a+ fe++f++ma++
  gi|70606999|ref|YP_255869.1| 167 GVKNVLNIINSFKLT--DSQEKMMFKHFRLASIFEYMFWDMAYR 208
                                   **********99888..55579999*****************98 PP

>> PTB  Phosphotyrosine-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0072        64      21      84 ..      47     110 ..      41     121 .. 0.71
   2 ?    9.7   0.0    0.0001      0.91      51      72 ..     178     199 ..     171     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0072
                           PTB  21 vedaiaklklldakgkvwaqevllkVssqgvtLtDnerKeel.esyplnsvseckavleerryes 84 
                                    +d  + l++l+ak +++ q+vl+  +   v  +  +  + +  ++++n  +  +  + + +y+s
  gi|70606999|ref|YP_255869.1|  47 LKDFSKALAVLSAKAESQEQSVLFATHVSDVIKVERDLHNYFfTHWKINPED-FEQSPSNLMYTS 110
                                   5777788999999999999999998887777777777666655777777643.344566666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0001
                           PTB  51 vtLtDnerKeelesyplnsvse 72 
                                    +LtD + K+ +++++l s+ e
  gi|70606999|ref|YP_255869.1| 178 FKLTDSQEKMMFKHFRLASIFE 199
                                   68****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1473.38
//
Query:       gi|70607000|ref|YP_255870.1|  [L=548]
Description: hypothetical protein Saci_1231 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.8   6.6     0.0021   17.8   6.6    3.3  3  GT87      Glycosyltransferase family 87


Domain annotation for each model (and alignments):
>> GT87  Glycosyltransferase family 87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   8.7      0.14   2.5e+03       9      94 ..      17     102 ..      13     118 .. 0.84
   2 !   17.8   6.6   1.1e-07    0.0021       3     142 ..     182     310 ..     180     337 .. 0.69
   3 ?    1.1   5.1     0.015   2.8e+02       1      49 [.     349     397 ..     349     444 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                          GT87   9 llfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqinllllllvlldll 89 
                                   llf+  +++   + l +w+++  ++++ ++ ++l +   +    +++ ++   lal p++  + +++i l+l++ v+l+l 
  gi|70607000|ref|YP_255870.1|  17 LLFLATSIMGANAYLNTWTVVADLVIVTLAGIVLFLDFKEVNERILTYIIYTELALIPIFYIILTQNIWLFLFTYVILGLG 97 
                                   7899999999999999*****99999999999988755555888888889999**************************99 PP

                          GT87  90 llrrr 94 
                                    ++r+
  gi|70607000|ref|YP_255870.1|  98 IYFRK 102
                                   99966 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.1e-07
                          GT87   3 YPPfaallfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqinllllll 83 
                                   YP ++ l+++p  ll   + ++ +++  l+ ++ + +l  +         +al+++  a+++++       G  +++ ++ 
  gi|70607000|ref|YP_255870.1| 182 YPSLSFLVLIPAVLLKISPNYVYLTFDLLIGIITFFYLSEKE--------YALFIS--AYLIPSYIFYSTGGVTDIVWVFF 252
                                   667777777777777777777777776677777777777443........344442..33334444445556678888888 PP

                          GT87  84 vlldllllrrrrpllaGlliGlaaaiKltPalfllylll..rrrwralaaaaatalvltal 142
                                   +ll+ll        + G++ Gl +a K+tP++ l ++l+  r++++ ++  a+ + +l+  
  gi|70607000|ref|YP_255870.1| 253 LLLSLLVKD---VKWKGVFYGLSIAYKQTPLAILPFYLIsyRKDLKKFLIPAVLVFFLFNG 310
                                   888866544...459********************9999999***9999986666555544 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.015
                          GT87   1 FtYPPfaallfaplallpyglalalwallnlaalllalrlllrrlgral 49 
                                   ++YP f++++ + + ++ + l +  w+++   a+l++ r+l++ l ++ 
  gi|70607000|ref|YP_255870.1| 349 YLYPLFFTVAPILIVVMGLLLFRNKWYGIAYFAFLFLYRVLWNYLIYWP 397
                                   7888888888888888888888888888888888888888877765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3889.28
//
Query:       gi|70607001|ref|YP_255871.1|  [L=255]
Description: short chain dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-62  210.9   0.7    2.1e-62  210.8   0.7    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.3e-54  183.8   1.0    2.9e-54  183.5   1.0    1.1  1  adh_short        short chain dehydrogenase
    2.3e-10   40.7   0.2    3.7e-10   40.0   0.2    1.4  1  KR               KR domain
  ------ inclusion threshold ------
      0.036   13.2   0.1      0.051   12.7   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.049   13.5   0.2      0.075   12.9   0.2    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.065   12.9   0.0      0.092   12.4   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.11   12.0   0.4       0.55    9.6   0.4    2.1  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.8   0.7   8.2e-66   2.1e-62       1     234 []      15     253 ..      15     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 8.2e-66
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                   Ga sgIGraiAk++a +   vv++ l e++ ++ v+el   +g+ev  +++DV+++++ve++v+++ e++ ++D+l+nnag
  gi|70607001|ref|YP_255871.1|  15 GAGSGIGRAIAKKFALNDSIVVAVELLEDRlNQIVQELRG-MGKEVlgVKADVSKKKDVEEFVRRTFETYSRIDVLCNNAG 94 
                                   889***********************99996777777766.6777559********************************* PP

                                   --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                   i++   +p++e+s+e ++r+l+vnlys+f+ ++a++p ++k+g g ivn++s+++ r+    + y++aK++l++ltr++A+
  gi|70607001|ref|YP_255871.1|  95 IMDG-VTPVAEVSDELWERVLAVNLYSAFYSSRAVIPiMLKQGkGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAA 174
                                   ***9.********************************555555999*********************************** PP

                                   HHGGGTEEEEEEEE--BHCTGGGGSTTHHH..HHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                  adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikgfde..lleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                   ++g++giR  av pg +kT++  g ++ +e  ++   + ++   rl++pe++a++++fLasdeas+++G  +vvDgGlt
  gi|70607001|ref|YP_255871.1| 175 HYGDQGIRAVAVLPGTVKTNIGLGSSKPSElgMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNGDAVVVDGGLT 253
                                   *********************88888866644778888899999*********************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.5   1.0   1.1e-57   2.9e-54       1     186 [.       9     195 ..       9     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.5 bits;  conditional E-value: 1.1e-57
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   kvv+vtGa+sGIGraiak++a ++  vv+v+  e++l+++++el+  g+++l +++Dv+++++ve++v++  + + ++dvL
  gi|70607001|ref|YP_255871.1|   9 KVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKADVSKKKDVEEFVRRTFETYSRIDVL 89 
                                   89******************************************************************************* PP

                                   EE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltr 161
                                    nNAGi  g++p++e+s+e werv++vNl ++f  +rav+p mlkq +G Ivn++S+ag  + + +a+Y+ +K++++gltr
  gi|70607001|ref|YP_255871.1|  90 CNNAGImDGVTPVAEVSDELWERVLAVNLYSAFYSSRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTR 170
                                   ******9999*********************************************************************** PP

                                   HHHHHHGGGTEEEEEEEESSBSSHH CS
                     adh_short 162 slakelaptgirvnavaPGlvdTdm 186
                                   s+a  + ++gir +av PG v+T++
  gi|70607001|ref|YP_255871.1| 171 SIAAHYGDQGIRAVAVLPGTVKTNI 195
                                   ***********************97 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.5e-13   3.7e-10       3     172 ..      11     185 ..       9     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.5e-13
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                            KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                   +++tG+  g+G+++a+  a +   ++v+       +++ ++ ++el+ +g ev  v+aDvs+k++ve+ +++  ++ ++i 
  gi|70607001|ref|YP_255871.1|  11 VIVTGAGSGIGRAIAKKFALN--DSIVVAVEL--LEDRLNQIVQELRGMGKEVLGVKADVSKKKDVEEFVRRTFETYSRID 87 
                                   79***************9865..567766666..6667778**************************************** PP

                                   EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHH... CS
                            KR  84 GvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNafl... 156
                                      + Ag+++  ++++e+++e +e+vla  +  a    +++ +    +   ++v ++Siag+ g +  a Y+ a + l   
  gi|70607001|ref|YP_255871.1|  88 VLCNNAGIMDgVTPVAEVSDELWERVLAVNLYSAFYSSRAVIPimlkQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLigl 168
                                   *********96799**************9988776666665553332777899********************98765111 PP

                                   .HHHHHHHHHHHHTEEE CS
                            KR 157 .Dalaeyrrsqglpavs 172
                                     ++a++  +qg +av+
  gi|70607001|ref|YP_255871.1| 169 tRSIAAHYGDQGIRAVA 185
                                   13445555566666665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     2e-05     0.051       1      74 [.      11      77 ..      11      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                  EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT CS
               Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekale 74
                                  v+vtGag  iG+++ ++++ ++ + ++ +e  E +l +i +el+  + k+ l      v +dv +k+ +e+ ++
  gi|70607001|ref|YP_255871.1| 11 VIVTGAGSGIGRAIAKKFALND-SIVVAVELLEDRLNQIVQELRG-MGKEVL-----GVKADVSKKKDVEEFVR 77
                                  79**************998665.668889*************954.444344.....45599999999998876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   2.9e-05     0.075       2     102 ..      11     115 ..      10     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                   EEEE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC..TTTTSS-HHHHCCCHHCE.EEES-HHHHHC CS
                       3HCDH_N   2 vaviGaGt.mGagiaavfasagleVvlvdiseealekalekiekslekl..vekgklkeeeveaalari.sfttdleeavd 78 
                                   v v GaG  +G+ ia+ fa ++  Vv v+  e++l++  ++++   +++  v++   k+++ve+ + r  ++ + ++ +++
  gi|70607001|ref|YP_255871.1|  11 VIVTGAGSgIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVlgVKADVSKKKDVEEFVRRTfETYSRIDVLCN 91 
                                   678999977********************************9985555422344444567777776654156666777777 PP

                                   -SEEEE-S-SSHHHHHHHHHHHHC CS
                       3HCDH_N  79 adlviEavvEnlelKrkvfaelek 102
                                      ++  v+   e+  ++++++ +
  gi|70607001|ref|YP_255871.1|  92 NAGIMDGVTPVAEVSDELWERVLA 115
                                   777777777777777777777655 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.6e-05     0.092      31      94 ..      30      95 ..       8     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                                  TTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.......EEEEEEEE--CCGGG CS
               Methyltr_RsmB-F 31 knkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.....elfDriLlDaPCsgtgv 94
                                   n + vvAv+  + Rl+++++ l+++g + +  ++aD++k ++v        e++ r  +D+ C   g+
  gi|70607001|ref|YP_255871.1| 30 LNDSIVVAVELLEDRLNQIVQELRGMGKE-VLGVKADVSKKKDVEEFvrrtfETYSR--IDVLCNNAGI 95
                                  47789**********************99.888899999986654324433333333..4666666665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00021      0.55       1      62 [.      11      78 ..      11     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00021
                                  EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHH CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfke 62
                                  ++VtGa   iG+a++k+++ ++  v+++  l+++ n+  +e          v++d+ +++++e+++++
  gi|70607001|ref|YP_255871.1| 11 VIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRgmgkevLGVKADVSKKKDVEEFVRR 78
                                  68*******************99999999996666655555449999988899999999988888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1831.25
//
Query:       gi|70607002|ref|YP_255872.1|  [L=177]
Description: hypothetical protein Saci_1233 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-33  116.0   0.0    1.8e-33  115.7   0.0    1.1  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.065   13.3   0.1       0.12   12.4   0.0    1.5  2  Daxx      Daxx N-terminal Rassf1C-interacting domain
      0.091   12.7   0.0       0.23   11.4   0.0    1.7  1  PELOTA_1  PELOTA RNA binding domain


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   3.1e-37   1.8e-33       2     122 .]      16     142 ..      15     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 3.1e-37
                        DUF488   2 lervydllkkdgvrvlvDVRlwPrSr.npgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.r...weefferYa 77 
                                   + ++++ll +++++vl+DVR+wPrS+  p+f+ke+l+ +l+++gi+Y+w+++lg+ r+  k++k+d      ++++f+++a
  gi|70607002|ref|YP_255872.1|  16 ISEFLNLLSAYKIEVLIDVRRWPRSKsFPHFNKENLSITLEDNGIQYIWFESLGGYRRFGKDIKDDGiGrcfKDDSFRAFA 96 
                                   789*************************************************************887536999******** PP

                        DUF488  78 aeleskeaakealeelkelakkg.vaLlcaekdperchrvvlaeyl 122
                                    +++++ +ak+ale+l +l++++ va++cae  p++chr++++++l
  gi|70607002|ref|YP_255872.1|  97 TYILKSVDAKKALEDLLHLCSTRtVAIMCAESLPWNCHRKIISDWL 142
                                   *****89999**********************************97 PP

>> Daxx  Daxx N-terminal Rassf1C-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.5   1.5e+04      56      63 ..      17      24 ..      12      29 .. 0.60
   2 ?   12.4   0.0   2.1e-05      0.12      13      68 ..     102     159 ..      91     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.5
                          Daxx 56 vefrnvlg 63
                                   ef n+l+
  gi|70607002|ref|YP_255872.1| 17 SEFLNLLS 24
                                  34555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                          Daxx  13 kleneklfeeflelCkketed..hPevvtflktrkqkaspeflasvefrnvlgrvlsr 68 
                                    ++ +k +e++l lC+++t    + e +++ ++rk  +   +  sve+  vlg+  + 
  gi|70607002|ref|YP_255872.1| 102 SVDAKKALEDLLHLCSTRTVAimCAESLPWNCHRKIISDWLYYKSVEVIHVLGKNKTI 159
                                   4788999**********9975449****************************997655 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.9e-05      0.23      40      76 ..      98     134 ..      92     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.9e-05
                      PELOTA_1  40 kvlvrdeeepdlahlllLakekgvpveevpdlpYsav 76 
                                    +l + ++++ l+ ll+L++ + v++  +++lp+++ 
  gi|70607002|ref|YP_255872.1|  98 YILKSVDAKKALEDLLHLCSTRTVAIMCAESLPWNCH 134
                                   45556678899************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1312.92
//
Query:       gi|70607003|ref|YP_255873.1|  [L=136]
Description: hypothetical protein Saci_1234 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-19   68.7   0.2    4.2e-19   68.0   0.2    1.3  1  Cupin_2          Cupin domain
    3.1e-08   33.7   0.1    3.5e-08   33.5   0.1    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    1.3e-07   31.4   0.1    3.8e-07   29.9   0.1    1.7  1  Auxin_BP         Auxin binding protein
    1.2e-06   28.4   0.0    1.5e-06   28.2   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
    2.4e-05   24.0   0.0    3.1e-05   23.7   0.0    1.1  1  DMSP_lyase       Dimethlysulfonioproprionate lyase
     0.0011   18.6   0.1     0.0046   16.6   0.1    1.9  2  Cupin_3          Protein of unknown function (DUF861)
     0.0024   18.0   0.0     0.0032   17.6   0.0    1.1  1  Ectoine_synth    Ectoine synthase
     0.0073   15.9   0.0      0.012   15.2   0.0    1.4  1  Cupin_1          Cupin
  ------ inclusion threshold ------
      0.024   15.0   0.1      0.042   14.3   0.1    1.4  1  JmjC             JmjC domain, hydroxylase
      0.039   13.9   0.0      0.064   13.2   0.0    1.5  1  Cupin_7          ChrR Cupin-like domain
        0.1   12.3   0.0       0.25   11.1   0.0    1.6  2  EutQ             Ethanolamine utilisation protein EutQ


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.2   2.6e-22   4.2e-19       1      70 [.      44     112 ..      44     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.6e-22
                                   EEEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   1 glvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                   g+ve++p+ s+p h H  e e++yVl+Geg+++++g ++e++a dsvy++ +tpHr+ Ntg++ +r++ v
  gi|70607003|ref|YP_255873.1|  44 GVVEVEPNNSTPLHKHNCE-EVYYVLDGEGVVEINGVKYEIKANDSVYIKENTPHRVFNTGKTTLRYVAV 112
                                   589****************.**********************************************9876 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   2.1e-11   3.5e-08      52     135 ..      25     112 ..       4     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.1e-11
               MannoseP_isomer  52 Gsyevldegeryqvkri.....tvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGk 127
                                    +++v+     + vk +     +v+P++   l+kh    e + v+ G   v+++  ++++k+n+s+yi++++ hr+ n Gk
  gi|70607003|ref|YP_255873.1|  25 KDWKVIYPETGFPVKSLvlgvvEVEPNNSTPLHKHNC-EEVYYVLDGEGVVEINGVKYEIKANDSVYIKENTPHRVFNTGK 104
                                   5566666666777775422211688998888887764.578899************************************* PP

               MannoseP_isomer 128 ipleliev 135
                                   ++l+ + v
  gi|70607003|ref|YP_255873.1| 105 TTLRYVAV 112
                                   ***99877 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   2.3e-10   3.8e-07      49     117 ..      46     105 ..      34     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.3e-10
                                   EEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSSS--S-EEEEE-TTEEEEE-TT--EEEE---SS CS
                      Auxin_BP  49 qtlapgsrtpihrhsceevfvvlkgkgtlylasssskypgkpqelpifanstlsipvndahqvkntgeh 117
                                     + p + tp+h+h ceev+ vl g+g + +            +++i an ++ i  n +h+v+ntg+ 
  gi|70607003|ref|YP_255873.1|  46 VEVEPNNSTPLHKHNCEEVYYVLDGEGVVEING---------VKYEIKANDSVYIKENTPHRVFNTGKT 105
                                   567899*********************987643.........345677899999999999999999954 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   9.1e-10   1.5e-06      12      65 ..      50     103 ..      44     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 9.1e-10
                                   TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
                  AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65 
                                   p+ s+p h h+  ++ yv++G+g +++ng  y+++++d + ++ ++pH+    +
  gi|70607003|ref|YP_255873.1|  50 PNNSTPLHKHNCEEVYYVLDGEGVVEINGVKYEIKANDSVYIKENTPHRVFNTG 103
                                   8899********************************************975555 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.9e-08   3.1e-05      86     154 ..      32      99 ..      26     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                    DMSP_lyase  86 prglekrddvalGlvllaPkvrYPdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikham 154
                                   p+  +  + ++lG+v   P+   P H+h+ ee+Y+vl g  ++  ++ +  + ++ ++++ + + +h++
  gi|70607003|ref|YP_255873.1|  32 PETGFPVKSLVLGVVEVEPNNSTPLHKHNCEEVYYVLDGEGVVEINGVK-YEIKANDSVYIKENTPHRV 99 
                                   56666778899***************************98899888888.5777888889999999986 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.26   4.2e+02      29      45 ..      37      55 ..      16      59 .. 0.65
   2 !   16.6   0.1   2.8e-06    0.0046      22      60 ..      57      95 ..      37     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.26
                                  E..EEEECEEEEEETTTEE CS
                       Cupin_3 29 c..yileGevkvtpegget 45
                                      ++ G v+v+p+++ +
  gi|70607003|ref|YP_255873.1| 37 PvkSLVLGVVEVEPNNSTP 55
                                  2556788999999988766 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.8e-06
                                  CESS.EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                       Cupin_3 22 tyee.dEfcyileGevkvtpeggetvelraGDlvvlpkgl 60
                                  +    +E  y+l Ge  v+  +g ++e++a D+v++++++
  gi|70607003|ref|YP_255873.1| 57 HKHNcEEVYYVLDGEGVVEI-NGVKYEIKANDSVYIKENT 95
                                  455558999***********.***************9988 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0032      42     106 ..      48     112 ..      34     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                   E-TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEE..EESS-EEEEEE CS
                 Ectoine_synth  42 ikagtetelkYknHleavycieGegeveeledgevyeikpgtlYlldkhdkHll..rakkelrlvcv 106
                                   ++ +++t l+ +n  e  y+++Geg ve   +g +yeik ++   + ++  H +  ++k+ lr v+v
  gi|70607003|ref|YP_255873.1|  48 VEPNNSTPLHKHNCEEVYYVLDGEGVVEI--NGVKYEIKANDSVYIKENTPHRVfnTGKTTLRYVAV 112
                                   6778889999999999999******9997..6*******8876666666677662234557877776 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.6e-06     0.012      37     105 ..      45     105 ..      36     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                                   EEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSS CS
                       Cupin_1  37 rvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgde 105
                                   +v +ep+   ++h h n +e+ yvl+Geg v++   +        ++++ d +++ ++ +h ++n+g++
  gi|70607003|ref|YP_255873.1|  45 VVEVEPNNSTPLHKH-NCEEVYYVLDGEGVVEINGVK-------YEIKANDSVYIKENTPHRVFNTGKT 105
                                   4556999999*****.**************7764433.......3566666666666666666666654 PP

>> JmjC  JmjC domain, hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.6e-05     0.042      25     108 ..      18     106 ..       2     112 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                                   EEEEES-EEEEEE-GGGHHHHHHHHHHH....HHCCSTTGCCTTTCEE-HHHHHHTT...---EEEEE-TT-EEEE-TT-E CS
                          JmjC  25 ylhfgapkvWyiipeekkeklekvlskk....nskeqpdllrhkstlispkqlekeg...ipvyrfvqkpgefVfvfpgay 98 
                                   + + ++ k W++i++e+   +++++        ++++p +    + +   ++l  eg   i   + + k+++ V++  +++
  gi|70607003|ref|YP_255873.1|  18 MEIKRGVKDWKVIYPETGFPVKSLVLGVvevePNNSTPLH--KHNCEEVYYVLDGEGvveINGVKYEIKANDSVYIKENTP 96 
                                   5566777888888888888887544444322222333333..22222222224443311167788999************* PP

                                   EEEEESSSEE CS
                          JmjC  99 Hsvfnlgfni 108
                                   H vfn+g + 
  gi|70607003|ref|YP_255873.1|  97 HRVFNTGKTT 106
                                   ******9876 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.9e-05     0.064      27      54 ..      44      71 ..      33     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                                  EEEEE-TTEE---EE-TT-EEEEEEEEE CS
                       Cupin_7 27 slvryapgsafsahkHpggeeilVLeGv 54
                                   +v+++p+++ + hkH   e  +VL+G+
  gi|70607003|ref|YP_255873.1| 44 GVVEVEPNNSTPLHKHNCEEVYYVLDGE 71
                                  5899**********************97 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   1.7e+03      82      98 ..      18      34 ..      14      47 .. 0.83
   2 ?   11.1   0.0   0.00016      0.25      76     144 ..      40     110 ..      34     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                          EutQ 82 memkettfdwtlnydei 98
                                  me+k  + dw + y e 
  gi|70607003|ref|YP_255873.1| 18 MEIKRGVKDWKVIYPET 34
                                  99999999999999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                          EutQ  76 rlgaGlmemk..ettfdwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvtdeakflyv 144
                                   +l  G++e++  ++t     n +e+ yv++G+  v i+G k   +a d ++i  ++  +   t+++ + yv
  gi|70607003|ref|YP_255873.1|  40 SLVLGVVEVEpnNSTPLHKHNCEEVYYVLDGEGVVEINGVKYEIKANDSVYIKENTPHRVFNTGKTTLRYV 110
                                   5666666654325666677899******************************9988766666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 975.84
//
Query:       gi|70607004|ref|YP_255874.1|  [L=81]
Description: hypothetical protein Saci_1235 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0097   16.7   6.8      0.043   14.6   6.8    2.0  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.016   15.1   0.0       0.03   14.2   0.0    1.4  1  Tail_P2_I     Phage tail protein (Tail_P2_I)
      0.031   14.5   0.4      0.034   14.3   0.4    1.2  1  Fib_alpha     Fibrinogen alpha/beta chain family
       0.04   14.3   1.8      0.042   14.3   0.3    1.8  2  SAPIS-gp6     Pathogenicity island protein gp6 in Staphylococ
      0.083   13.2   0.1       0.11   12.8   0.1    1.4  1  LAGLIDADG_3   LAGLIDADG-like domain


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   6.8   1.2e-05     0.043      12      63 ..      21      76 ..       4      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                  VAPB_antitox 12 kLkklKregeSFsdvIerLle.....kkkkgkkkellelfgilseeea.deiekaske 63
                                  +L++ K+e+ S +d+I+ L++     k+ k++ + ll l g++  + + +e+eka +e
  gi|70607004|ref|YP_255874.1| 21 ELQQNKGEKVSINDTIKFLIDfydksKEVKKDPQLLLSLLGSM--KGIrEELEKAREE 76
                                  78999*****************9988777888899******98..3444666666555 PP

>> Tail_P2_I  Phage tail protein (Tail_P2_I)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.5e-06      0.03      57      86 ..       8      37 ..       5      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.5e-06
                     Tail_P2_I 57 seeakRavikeaielhrlkGTpaavrrvle 86
                                  +ee+kR +i+ + el++ kG + ++ + ++
  gi|70607004|ref|YP_255874.1|  8 DEEVKRSLIRISSELQQNKGEKVSINDTIK 37
                                  699**********************99987 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   9.4e-06     0.034      25      76 ..       3      54 ..       1      78 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.4e-06
                                  CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdnd 76
                                  +l +++++vk++l ++ +el++++ ++ ++++++k + d + + ++ kkd +
  gi|70607004|ref|YP_255874.1|  3 TLVRVDEEVKRSLIRISSELQQNKGEKVSINDTIKFLIDFYDKSKEVKKDPQ 54
                                  78999**************************************999998744 PP

>> SAPIS-gp6  Pathogenicity island protein gp6 in Staphylococcus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   1.2e-05     0.042      31      53 ..       7      29 ..       3      42 .. 0.88
   2 ?   -0.5   0.1      0.47   1.7e+03      39      52 ..      63      76 ..      37      81 .] 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                     SAPIS-gp6 31 vdlDiKnnmqeiskElreneqek 53
                                  vd+++K+ +  is+El++n+ ek
  gi|70607004|ref|YP_255874.1|  7 VDEEVKRSLIRISSELQQNKGEK 29
                                  9*******************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                     SAPIS-gp6 39 mqeiskElreneqe 52
                                  m+ i +El +++ e
  gi|70607004|ref|YP_255874.1| 63 MKGIREELEKAREE 76
                                  55566666555554 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.1e-05      0.11      23      58 ..      36      72 ..       7      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                  TTTS..EEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EE CS
                   LAGLIDADG_3 23 kgvs..isltssskelledvqrlLlrlGIestiyek.kk 58
                                     +  i ++ +ske+ +d q lL+ lG    i+e+  k
  gi|70607004|ref|YP_255874.1| 36 I--KflIDFYDKSKEVKKDPQLLLSLLGSMKGIREElEK 72
                                  2..2459***************************99633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 599.46
//
Query:       gi|70607005|ref|YP_255875.1|  [L=130]
Description: hypothetical protein Saci_1236 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-12   47.7   0.1    2.5e-12   47.4   0.1    1.1  1  PIN           PIN domain
    3.5e-05   24.5   0.0    4.3e-05   24.3   0.0    1.3  1  PIN_3         PIN domain
  ------ inclusion threshold ------
       0.24   11.1   1.6         20    5.0   0.1    2.7  2  Fur_reg_FbpA  Fur-regulated basic protein A


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1   4.2e-16   2.5e-12       2     115 ..       4     116 ..       3     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 4.2e-16
                                   EE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                           PIN   2 vlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                   ++DT vl+++l+g++  e++ +l+ +   e ++++l+l El yv  r  +  +k+a++v ++ll    + i++ + + a++
  gi|70607005|ref|YP_255875.1|   4 IIDTGVLVEILEGSDIGEKITRLIIQNqIEPLITDLTLTELQYVTCR--KYGNKRANEVIQKLLkSGFFGIVN-SMRFARK 81 
                                   89*********99999999999887777*******************..778888888888888688888888.******* PP

                                   HHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH CS
                           PIN  81 aaeialkygllpnDaliaAtAkehgikliatfDed 115
                                   aaei+  +++++ Da+ +  A+e +i++i+ + ++
  gi|70607005|ref|YP_255875.1|  82 AAEIKCAHSVSIVDAFNIGAAQELKINAIFKKEKE 116
                                   ****************************9766665 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   7.1e-09   4.3e-05       2      67 ..       3      66 ..       2     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.1e-09
                         PIN_3  2 vvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaal 67
                                   ++Dt vl+++l  ++   +ki +++ +++i+++++  +l+El++v  r+ + ++ +++  +k+++
  gi|70607005|ref|YP_255875.1|  3 AIIDTGVLVEILEGSD-IGEKITRLIIQNQIEPLITDLTLTELQYVTCRK-YGNKRANEVIQKLLK 66
                                  689**********655.9*****************************999.666666666666443 PP

>> Fur_reg_FbpA  Fur-regulated basic protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3    0.0051        30      24      32 ..      38      46 ..      37      47 .. 0.86
   2 ?    5.0   0.1    0.0033        20       6      15 ..      61      70 ..      58      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0051
                  Fur_reg_FbpA 24 eLTleELer 32
                                  +LTl+EL++
  gi|70607005|ref|YP_255875.1| 38 DLTLTELQY 46
                                  69*****96 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0033
                  Fur_reg_FbpA  6 IekLIqsGiy 15
                                  I+kL++sG++
  gi|70607005|ref|YP_255875.1| 61 IQKLLKSGFF 70
                                  9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.57
# Mc/sec: 685.93
//
Query:       gi|70607006|ref|YP_255876.1|  [L=106]
Description: hypothetical protein Saci_1237 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.23   11.7   0.0    1.1  1  Chaperone_III  Type III secretion chaperone domain


Domain annotation for each model (and alignments):
>> Chaperone_III  Type III secretion chaperone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05      0.23      51     107 ..      21      78 ..      12      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                 Chaperone_III  51 edl.qailslnyaskvtlaadaeksvllalyrlpaeseeedilaglelyisrvkqlke 107
                                   ++l ++i+++  a++ ++    e++ ++a +r  ++++  ++l g++ y + + ++++
  gi|70607006|ref|YP_255876.1|  21 KELeKEIMRIGSADPPCVNWHLEQGHIVAWLRYIGNNTLAEMLKGVKDYREALARIRD 78 
                                   555246999999*************************************999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 819.91
//
Query:       gi|70607007|ref|YP_255877.1|  [L=207]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-44  149.9  15.9    2.1e-23   82.0   5.8    2.2  2  UPF0126   UPF0126 domain
  ------ inclusion threshold ------
      0.037   13.4   5.3      0.055   12.8   5.3    1.3  1  NnrS      NnrS protein


Domain annotation for each model (and alignments):
>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   2.4   9.2e-25   8.2e-21       2      77 ..      11      85 ..      10      86 .. 0.92
   2 !   82.0   5.8   2.4e-27   2.1e-23       2      76 ..      97     169 ..      96     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9.2e-25
                                  HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHHH CS
                       UPF0126  2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvlla 77
                                  i+++iG++afa+sGa++A+kkg+dllgv+vlG+ TA+gGG++ ++llg+++P  l+    y ++a+l++l++++++
  gi|70607007|ref|YP_255877.1| 11 IFNYIGIVAFAISGAIKAVKKGMDLLGVLVLGFSTALGGGIISNLLLGKTPPTNLIY-YPYPITAFLASLATFVFY 85
                                  799*********************************************855666665.699************997 PP

  == domain 2  score: 82.0 bits;  conditional E-value: 2.4e-27
                                   HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
                       UPF0126   2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76 
                                   ++daiGl+afa+sGa+ A +   ++++vv++G +TAvgGGv+RD+l + evP++l+re +yat+a++g++v++++
  gi|70607007|ref|YP_255877.1|  97 YADAIGLGAFASSGASLAYSVSNNVILVVIVGAITAVGGGVIRDILSN-EVPLILTRE-FYATTAVIGSFVYFIA 169
                                   68**********************************************.6*****998.**************96 PP

>> NnrS  NnrS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.3   6.1e-06     0.055     102     228 ..      73     189 ..       9     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-06
                          NnrS 102 lafllllalllarellaakqwrnlavlalllllalanllfhlallglatalasaglrlalllvlllillvggRvipfftan 182
                                   +afl+ la+++++++++ +  + l  + +++l+a+a+    la         s++ +++l++++  i+ vgg vi  + +n
  gi|70607007|ref|YP_255877.1|  73 TAFLASLATFVFYRIFT-NVGKPLLYADAIGLGAFASSGASLA--------YSVSNNVILVVIVGAITAVGGGVIRDILSN 144
                                   45666666666666655.3345555555555555555553333........3347889*********************** PP

                          NnrS 183 alelkarpsprldrlalallllalllelllllaaalalaaallqlv 228
                                    ++l  +++ +   +++++++ +++ +l +++ + ++++ +l++l+
  gi|70607007|ref|YP_255877.1| 145 EVPLILTREFYATTAVIGSFVYFIASDLSVPEDV-ALIVSFLITLI 189
                                   **77776666667788888888888888877777.33333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1489.71
//
Query:       gi|70607008|ref|YP_255878.1|  [L=250]
Description: hypothetical protein Saci_1239 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-23   78.9  20.5    1.3e-05   24.9   0.2    8.0  8  TPR_2         Tetratricopeptide repeat
    1.5e-20   71.6  16.9    5.5e-06   26.2   0.4    5.7  5  TPR_8         Tetratricopeptide repeat
    3.3e-20   71.0  24.9    1.1e-06   28.1   0.3    7.3  8  TPR_1         Tetratricopeptide repeat
    1.3e-17   64.1   0.8    0.00012   22.7   0.0    4.9  5  TPR_16        Tetratricopeptide repeat
    1.1e-16   60.0   5.1    0.00012   22.2   0.2    5.6  5  TPR_17        Tetratricopeptide repeat
    7.1e-16   57.6  22.6    1.8e-10   40.3   0.7    6.4  6  TPR_11        TPR repeat
    9.3e-13   48.5  11.2    8.3e-05   23.0   0.2    5.1  5  TPR_19        Tetratricopeptide repeat
    6.5e-10   38.3   2.5      0.099   12.7   0.2    5.5  5  TPR_7         Tetratricopeptide repeat
    6.5e-10   39.0   0.1      0.079   13.1   0.0    5.8  6  TPR_9         Tetratricopeptide repeat
    1.3e-09   38.2   9.0      0.038   14.3   0.0    5.6  6  TPR_12        Tetratricopeptide repeat
    2.9e-08   33.9   4.6        1.3   10.1   0.3    5.8  6  TPR_14        Tetratricopeptide repeat
    3.5e-07   29.5   5.8     0.0072   15.3   0.3    3.4  3  NARP1         NMDA receptor-regulated protein 1
    3.6e-07   30.3   5.1       0.36   11.1   1.3    3.5  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    7.4e-06   25.8   1.0       0.24   11.1   0.0    3.5  3  TPR_21        Tetratricopeptide repeat-like domain
    1.1e-05   24.9   0.6     0.0042   16.4   0.6    2.8  1  FAT           FAT domain
    5.5e-05   22.9   9.0       0.33   10.9   0.1    5.0  5  TPR_10        Tetratricopeptide repeat
    0.00027   20.4   0.5    0.00027   20.4   0.5    1.9  2  Coatomer_E    Coatomer epsilon subunit
     0.0004   20.8  15.3        4.2    8.2   0.2    6.3  6  TPR_6         Tetratricopeptide repeat
    0.00059   19.8   2.4    0.00059   19.8   2.4    2.7  2  SRP_TPR_like  Putative TPR-like repeat
     0.0013   18.7   0.1       0.77    9.6   0.0    2.2  2  Wzy_C_2       Virulence factor membrane-bound polymerase, C-t
     0.0015   18.0   0.1        4.1    6.7   0.0    3.5  4  TPR_MalT      MalT-like TPR region
  ------ inclusion threshold ------
      0.015   15.3   8.8       0.11   12.6   2.0    4.1  2  MIT           MIT (microtubule interacting and transport) dom
      0.016   15.5   1.7        7.1    7.0   0.2    4.1  5  TPR_20        Tetratricopeptide repeat
      0.018   15.1   2.8         27    4.8   0.0    3.8  4  DUF3856       Domain of Unknown Function (DUF3856)
      0.022   15.3   1.9        1.2    9.8   0.0    3.8  5  DUF4810       Domain of unknown function (DUF4810)
      0.022   14.6   8.9       0.02   14.8   4.3    2.5  2  Clathrin      Region in Clathrin and VPS
      0.024   14.3   0.0        8.2    6.1   0.0    3.5  4  HrpB1_HrpK    Bacterial type III secretion protein (HrpB1_Hrp
       0.11   12.3   0.0       0.21   11.5   0.0    1.4  1  DUF928        Domain of Unknown Function (DUF928)
       0.41   10.7   2.2         28    4.8   0.1    3.2  3  PTS_IIA       PTS system, Lactose/Cellobiose specific IIA sub
        3.8    7.2   8.1         11    5.7   0.1    4.2  3  HTH_Bact      Helix-turn-helix bacterial domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.14        81      11      33 ..       7      29 ..       5      30 .. 0.91
   2 !   20.5   0.2   5.5e-07   0.00033       2      27 ..      31      56 ..      30      58 .. 0.95
   3 ?    3.9   0.1      0.12        70       8      22 ..      63      77 ..      60      80 .. 0.87
   4 !    9.2   0.0    0.0024       1.5       6      22 ..      90     106 ..      86     109 .. 0.89
   5 ?    2.4   0.0      0.36   2.1e+02       4      32 ..     119     147 ..     116     149 .. 0.86
   6 ?    0.2   0.3       1.7     1e+03       1      15 [.     150     164 ..     150     164 .. 0.80
   7 !   24.9   0.2   2.2e-08   1.3e-05       1      33 [.     182     214 ..     182     215 .. 0.96
   8 !   21.9   0.1     2e-07   0.00012       2      32 ..     217     247 ..     216     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                         TPR_2 11 yyklgdyeeAleafekAleldPn 33
                                  +y+ g+++ Al+  ++ ++ +P 
  gi|70607008|ref|YP_255878.1|  7 AYQEGNLNYALRKINEIIKSNPS 29
                                  6999***************9995 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.5e-07
                         TPR_2  2 ealynlGlayyklgdyeeAleafekA 27
                                  ++++ lG+++++lg+ eeAleaf++A
  gi|70607008|ref|YP_255878.1| 31 DIYNLLGKILLELGKDEEALEAFRQA 56
                                  789**********************9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                         TPR_2  8 GlayyklgdyeeAle 22
                                  +++y+++g y++Al+
  gi|70607008|ref|YP_255878.1| 63 ARIYIQKGLYQDALN 77
                                  89***********97 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0024
                         TPR_2   6 nlGlayyklgdyeeAle 22 
                                    ++l+y+k+ ++++A+e
  gi|70607008|ref|YP_255878.1|  90 LRALIYIKMENFDKAKE 106
                                   69*************98 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.36
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                   +   G + y+  +y  Al+    Al+ +P
  gi|70607008|ref|YP_255878.1| 119 HKVKGIVEYHTANYYGALRSITIALREYP 147
                                   55679999999**************9999 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 1.7
                         TPR_2   1 aealynlGlayyklg 15 
                                   ae++y+++l+ ++lg
  gi|70607008|ref|YP_255878.1| 150 AELYYYRALVKAELG 164
                                   7999***99876665 PP

  == domain 7  score: 24.9 bits;  conditional E-value: 2.2e-08
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                   ae+++  G +++++g+++eA++++ kA+++ P+
  gi|70607008|ref|YP_255878.1| 182 AELYFSKGVILEQRGKLNEAVNYYSKAIKYKPE 214
                                   799***************************997 PP

  == domain 8  score: 21.9 bits;  conditional E-value: 2e-07
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                   +a+y+++++y+klg  +eA+++ ek+ el  
  gi|70607008|ref|YP_255878.1| 217 KAYYRRAKVYMKLGMDQEAEKDIEKVKELTD 247
                                   79***********************999865 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   7.6e-07   0.00045       2      27 ..      31      56 ..      30      59 .. 0.95
   2 ?    3.4   0.1      0.18   1.1e+02       8      21 ..      63      76 ..      58      80 .. 0.81
   3 !   10.3   0.1    0.0011      0.68       5      22 ..      89     106 ..      86     109 .. 0.87
   4 !   26.2   0.4   9.1e-09   5.5e-06       1      33 [.     182     214 ..     182     215 .. 0.96
   5 !   20.1   0.3   8.2e-07   0.00049       2      31 ..     217     246 ..     216     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.6e-07
                                  CHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyyeka 27
                                  ++y++lg+i+l+lg+ eeA e++++a
  gi|70607008|ref|YP_255878.1| 31 DIYNLLGKILLELGKDEEALEAFRQA 56
                                  68***********************9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.18
                                  HHHHHHTT-HHHHH CS
                         TPR_8  8 gsiylklgdyeeAk 21
                                  ++iy+++g y+ A 
  gi|70607008|ref|YP_255878.1| 63 ARIYIQKGLYQDAL 76
                                  89999999998875 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHTT-HHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAke 22 
                                    + ++iy+k++++++Ake
  gi|70607008|ref|YP_255878.1|  89 ILRALIYIKMENFDKAKE 106
                                   5789*************9 PP

  == domain 4  score: 26.2 bits;  conditional E-value: 9.1e-09
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   ae+y+ +g i+++ g+++eA+ yy ka++++p+
  gi|70607008|ref|YP_255878.1| 182 AELYFSKGVILEQRGKLNEAVNYYSKAIKYKPE 214
                                   799****************************96 PP

  == domain 5  score: 20.1 bits;  conditional E-value: 8.2e-07
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                   +ayy+ +++y+klg  +eA++ +ek+ el 
  gi|70607008|ref|YP_255878.1| 217 KAYYRRAKVYMKLGMDQEAEKDIEKVKELT 246
                                   89***********************99985 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.1     3e+03      12      29 ..       8      25 ..       7      29 .. 0.57
   2 !   20.2   0.0   5.9e-07   0.00035       1      27 [.      30      56 ..      30      56 .. 0.96
   3 ?    1.8   0.1      0.39   2.3e+02       9      21 ..      64      76 ..      62      77 .. 0.87
   4 !    9.8   0.0    0.0012      0.71       7      22 ..      91     106 ..      86     106 .. 0.90
   5 ?    0.3   0.3       1.2   7.1e+02      19      28 ..     149     158 ..     147     162 .. 0.77
   6 ?   -0.9   0.1       2.8   1.6e+03      22      33 ..     169     180 ..     168     181 .. 0.79
   7 !   28.1   0.3   1.9e-09   1.1e-06       1      33 [.     182     214 ..     182     215 .. 0.96
   8 !   23.0   0.1   7.9e-08   4.7e-05       1      30 [.     216     245 ..     216     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.1
                                  HHTT-HHHHHHHHHHHHH CS
                         TPR_1 12 fklgkydeAleyyekALe 29
                                  ++ g+++ Al   ++ ++
  gi|70607008|ref|YP_255878.1|  8 YQEGNLNYALRKINEIIK 25
                                  556666666665555555 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.9e-07
                                  HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         TPR_1  1 akalynlGnayfklgkydeAleyyekA 27
                                  +++++ lG ++++lgk +eAle++++A
  gi|70607008|ref|YP_255878.1| 30 PDIYNLLGKILLELGKDEEALEAFRQA 56
                                  589**********************98 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.39
                                  HHHHHTT-HHHHH CS
                         TPR_1  9 nayfklgkydeAl 21
                                   +y ++g y++Al
  gi|70607008|ref|YP_255878.1| 64 RIYIQKGLYQDAL 76
                                  5899********8 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0012
                                   HHHHHHHTT-HHHHHH CS
                         TPR_1   7 lGnayfklgkydeAle 22 
                                   ++++y k++++d+A e
  gi|70607008|ref|YP_255878.1|  91 RALIYIKMENFDKAKE 106
                                   89************76 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.2
                                   HHHHHHHHHH CS
                         TPR_1  19 eAleyyekAL 28 
                                   +A+ yy +AL
  gi|70607008|ref|YP_255878.1| 149 DAELYYYRAL 158
                                   5777888887 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.8
                                   HHHHHHHHHSTT CS
                         TPR_1  22 eyyekALelnPn 33 
                                   ++ + A+ lnP 
  gi|70607008|ref|YP_255878.1| 169 DDIDMAINLNPY 180
                                   67789999*996 PP

  == domain 7  score: 28.1 bits;  conditional E-value: 1.9e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                                   a+ ++ +G+++ + gk++eA+ yy+kA++  P+
  gi|70607008|ref|YP_255878.1| 182 AELYFSKGVILEQRGKLNEAVNYYSKAIKYKPE 214
                                   789**************************9996 PP

  == domain 8  score: 23.0 bits;  conditional E-value: 7.9e-08
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                   +ka+y+++ +y+klg+ +eA+++ ek+ el
  gi|70607008|ref|YP_255878.1| 216 VKAYYRRAKVYMKLGMDQEAEKDIEKVKEL 245
                                   58************************9876 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.5e-07   0.00051       7      60 ..       7      56 ..       2      58 .. 0.94
   2 ?    3.6   0.0      0.18   1.1e+02       2      18 ..      61      77 ..      59      81 .. 0.73
   3 ?    0.3   0.0         2   1.2e+03       3      18 ..      91     106 ..      89     111 .. 0.86
   4 !   10.4   0.3    0.0014      0.82      15      48 ..     134     164 ..     125     165 .. 0.88
   5 !   22.7   0.0     2e-07   0.00012       4      55 ..     189     237 ..     186     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.5e-07
                        TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraa 60
                                  a++ g+   A++  ++ +k++   P  ++ ++llg ++l++g  +eA++++r a
  gi|70607008|ref|YP_255878.1|  7 AYQEGNLNYALRKINEIIKSN---P-SPDIYNLLGKILLELGKDEEALEAFRQA 56
                                  899999999************...9.8************************986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.18
                        TPR_16  2 alaraalragdyddAaa 18
                                  + ar++++ g y+dA++
  gi|70607008|ref|YP_255878.1| 61 EVARIYIQKGLYQDALN 77
                                  45788888888888876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2
                        TPR_16   3 laraalragdyddAaa 18 
                                   +a+++++  ++d+A +
  gi|70607008|ref|YP_255878.1|  91 RALIYIKMENFDKAKE 106
                                   799***********86 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0014
                        TPR_16  15 dAaaaleaalkrdpssPdaaeAllllgdaalrqg 48 
                                    A++  ++al+ +   P +ae +++++++ +++g
  gi|70607008|ref|YP_255878.1| 134 GALRSITIALREY---PMDAELYYYRALVKAELG 164
                                   69***********...***********9866655 PP

  == domain 5  score: 22.7 bits;  conditional E-value: 2e-07
                        TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                   + ++ ++g+  +A++++  a+k+    P+ + A++ ++ ++ ++g  +eA+ 
  gi|70607008|ref|YP_255878.1| 189 GVILEQRGKLNEAVNYYSKAIKYK---PELVKAYYRRAKVYMKLGMDQEAEK 237
                                   667899******************...******************9999984 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00023      0.14      12      34 .]      29      51 ..      22      51 .. 0.91
   2 ?    2.4   0.0      0.42   2.5e+02       2      34 .]      72     106 ..      71     106 .. 0.80
   3 ?    4.4   0.1       0.1        60       5      27 ..     142     164 ..     141     174 .. 0.81
   4 !   16.0   0.0     2e-05     0.012       5      32 ..     174     201 ..     170     203 .. 0.94
   5 !   22.2   0.2   2.1e-07   0.00012       1      34 []     204     237 ..     204     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                        TPR_17 12 nadaynnLAelllknGdlmtArq 34
                                  ++d yn+L+++ll++G+ ++A++
  gi|70607008|ref|YP_255878.1| 29 SPDIYNLLGKILLELGKDEEALE 51
                                  589*****************985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.42
                        TPR_17   2 ylkalel..dPnnadaynnLAelllknGdlmtArq 34 
                                   y+ al    d +n ++  ++A ++ k  ++++A++
  gi|70607008|ref|YP_255878.1|  72 YQDALNEikDETNDESKILRALIYIKMENFDKAKE 106
                                   5555555557888899999************9986 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.1
                        TPR_17   5 aleldPnnadaynnLAelllknG 27 
                                   al+ +P +a++y+++A + +++G
  gi|70607008|ref|YP_255878.1| 142 ALREYPMDAELYYYRALVKAELG 164
                                   56778889********9877766 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 2e-05
                        TPR_17   5 aleldPnnadaynnLAelllknGdlmtA 32 
                                   a+ l+P +a++y+ ++++l+++G+l +A
  gi|70607008|ref|YP_255878.1| 174 AINLNPYYAELYFSKGVILEQRGKLNEA 201
                                   899**********************999 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 2.1e-07
                        TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                   +y ka+++ P  ++ay+ +A+++ k+G  ++A++
  gi|70607008|ref|YP_255878.1| 204 YYSKAIKYKPELVKAYYRRAKVYMKLGMDQEAEK 237
                                   699****************************985 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1     0.003       1.8      27      42 .]      29      44 ..       7      44 .. 0.76
   2 !   12.5   0.1   0.00014     0.086       1      20 [.      37      56 ..      37      58 .. 0.96
   3 ?    2.4   0.2      0.21   1.3e+02       2      15 ..      64      77 ..      63      78 .. 0.89
   4 ?    5.7   0.1     0.019        12      25      42 .]     147     164 ..     142     164 .. 0.89
   5 !    9.3   0.1    0.0015      0.89      20      39 ..     174     193 ..     173     194 .. 0.92
   6 !   40.3   0.7     3e-13   1.8e-10       6      42 .]     194     230 ..     189     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                        TPR_11 27 naeayynLGlayykqG 42
                                  ++++y+ LG++++++G
  gi|70607008|ref|YP_255878.1| 29 SPDIYNLLGKILLELG 44
                                  5***********9998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                        TPR_11  1 GdayyeqGkyeeAieaYkkA 20
                                  G+++ e+Gk eeA+ea+++A
  gi|70607008|ref|YP_255878.1| 37 GKILLELGKDEEALEAFRQA 56
                                  89*****************9 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                        TPR_11  2 dayyeqGkyeeAie 15
                                  ++y ++G y +A++
  gi|70607008|ref|YP_255878.1| 64 RIYIQKGLYQDALN 77
                                  79**********98 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.019
                        TPR_11  25 PdnaeayynLGlayykqG 42 
                                   P +ae+yy ++l+ +++G
  gi|70607008|ref|YP_255878.1| 147 PMDAELYYYRALVKAELG 164
                                   99***********99988 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0015
                        TPR_11  20 AlkldPdnaeayynLGlayy 39 
                                   A++l+P +ae+y+  G+++ 
  gi|70607008|ref|YP_255878.1| 174 AINLNPYYAELYFSKGVILE 193
                                   9***************9876 PP

  == domain 6  score: 40.3 bits;  conditional E-value: 3e-13
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++Gk++eA++ Y+kA+k++P+ + ayy ++++y+k+G
  gi|70607008|ref|YP_255878.1| 194 QRGKLNEAVNYYSKAIKYKPELVKAYYRRAKVYMKLG 230
                                   89*********************************99 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00027      0.16       2      51 ..       8      56 ..       7      59 .. 0.90
   2 ?    5.8   0.1     0.034        20      28      48 ..      59      79 ..      55      83 .. 0.84
   3 !   13.2   0.1   0.00016     0.098      14      53 ..      72     113 ..      70     122 .. 0.80
   4 ?   -0.2   0.1       2.4   1.5e+03      17      33 ..     142     158 ..     131     165 .. 0.70
   5 !   23.0   0.2   1.4e-07   8.3e-05       3      46 ..     194     237 ..     192     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00027
                        TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51
                                  ++eg++  Al+   ++++ +p ++++  lL ++ll+lg  +eA ++  ++
  gi|70607008|ref|YP_255878.1|  8 YQEGNLNYALRKINEIIKSNP-SPDIYNLLGKILLELGKDEEALEAFRQA 56
                                  789999999999999999999.**********************998765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.034
                        TPR_19 28 rllLAeallalgqldeAealL 48
                                  rl  A+++++ g +++A + +
  gi|70607008|ref|YP_255878.1| 59 RLEVARIYIQKGLYQDALNEI 79
                                  6778*************9866 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00016
                        TPR_19  14 leqalqe..dpknaearllLAeallalgqldeAealLdalpe 53 
                                   ++ al e  d  n+e ++l A +++++ ++d+A++ ++ +  
  gi|70607008|ref|YP_255878.1|  72 YQDALNEikDETNDESKILRALIYIKMENFDKAKEEIANINS 113
                                   56666553355699****9****************9987765 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.4
                        TPR_19  17 alqedpknaearllLAe 33 
                                   al e+p +ae+ ++ A 
  gi|70607008|ref|YP_255878.1| 142 ALREYPMDAELYYYRAL 158
                                   78999999999995443 PP

  == domain 5  score: 23.0 bits;  conditional E-value: 1.4e-07
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                   ++g++ eA++++++a++++p+   a ++ A+++++lg  +eAe+
  gi|70607008|ref|YP_255878.1| 194 QRGKLNEAVNYYSKAIKYKPELVKAYYRRAKVYMKLGMDQEAEK 237
                                   789***************************************98 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.2   0.00017     0.099       2      27 ..      33      56 ..      32      64 .. 0.91
   2 ?    3.2   0.1      0.18   1.1e+02       6      19 ..      63      76 ..      59      83 .. 0.90
   3 ?    0.4   0.0       1.4   8.6e+02       6      18 ..      92     104 ..      90     106 .. 0.88
   4 !    9.7   0.0    0.0015      0.88       2      33 ..     185     214 ..     184     217 .. 0.88
   5 ?    7.0   0.0     0.011       6.6       1      29 [.     218     246 ..     218     250 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                         TPR_7  2 LlnLarlysrlGdyeeAielyeqsLa 27
                                  ++ L+ +  +lG+ eeA+e ++q  a
  gi|70607008|ref|YP_255878.1| 33 YNLLGKILLELGKDEEALEAFRQ--A 56
                                  799*******************9..4 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                         TPR_7  6 arlysrlGdyeeAi 19
                                  ar+y + G y++A+
  gi|70607008|ref|YP_255878.1| 63 ARIYIQKGLYQDAL 76
                                  99***********8 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                         TPR_7   6 arlysrlGdyeeA 18 
                                   a +y ++ ++++A
  gi|70607008|ref|YP_255878.1|  92 ALIYIKMENFDKA 104
                                   779*********9 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0015
                         TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                                   ++  +++ +++G+  eA+ +y +  a+ + pe
  gi|70607008|ref|YP_255878.1| 185 YFSKGVILEQRGKLNEAVNYYSK--AIKYKPE 214
                                   566799*****************..9999886 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.011
                         TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                   a+++ a +y +lG  +eA++  e++ +lt
  gi|70607008|ref|YP_255878.1| 218 AYYRRAKVYMKLGMDQEAEKDIEKVKELT 246
                                   78899**************9999866666 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.92   5.5e+02      30      54 ..      31      55 ..       6      57 .. 0.65
   2 ?    4.3   0.1     0.074        44      28      51 ..      55      78 ..      50      81 .. 0.88
   3 ?    2.9   0.0       0.2   1.2e+02      35      51 ..      91     107 ..      89     116 .. 0.88
   4 ?    5.5   0.2     0.031        19      14      43 ..     135     164 ..     130     165 .. 0.91
   5 !   13.1   0.0   0.00013     0.079      17      61 ..     170     214 ..     166     219 .. 0.90
   6 ?    7.1   0.0      0.01       6.1      17      54 ..     204     241 ..     201     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.92
                         TPR_9 30 eerrdRGlllaqlGclsaAladLea 54
                                  + +   G +l +lG  ++Al+++ +
  gi|70607008|ref|YP_255878.1| 31 DIYNLLGKILLELGKDEEALEAFRQ 55
                                  5555568888999999999988865 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.074
                         TPR_9 28 dpeerrdRGlllaqlGclsaAlad 51
                                  ++  r++ ++++ q G ++ Al++
  gi|70607008|ref|YP_255878.1| 55 QANNRLEVARIYIQKGLYQDALNE 78
                                  67889****************986 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.2
                         TPR_9  35 RGlllaqlGclsaAlad 51 
                                   R+l++ +++++ +A ++
  gi|70607008|ref|YP_255878.1|  91 RALIYIKMENFDKAKEE 107
                                   9************9887 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.031
                         TPR_9  14 alavverllllaPddpeerrdRGlllaqlG 43 
                                   al+ +   l   P d+e+++ R+l+ a+lG
  gi|70607008|ref|YP_255878.1| 135 ALRSITIALREYPMDAELYYYRALVKAELG 164
                                   788888999999****************98 PP

  == domain 5  score: 13.1 bits;  conditional E-value: 0.00013
                         TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    +++ + l+P  +e+++  G++l+q+G l++A++    ++   p+
  gi|70607008|ref|YP_255878.1| 170 DIDMAINLNPYYAELYFSKGVILEQRGKLNEAVNYYSKAIKYKPE 214
                                   58999*****************************99999887775 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.01
                         TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                                   ++   +  +P+ +  ++ R+ ++++lG  ++A +d e 
  gi|70607008|ref|YP_255878.1| 204 YYSKAIKYKPELVKAYYRRAKVYMKLGMDQEAEKDIEK 241
                                   566677889***********************999886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   7.1e-05     0.042      47      71 ..      32      56 ..      29      61 .. 0.89
   2 ?    1.2   0.1      0.78   4.6e+02       9      23 ..      62      76 ..      56      80 .. 0.57
   3 ?    1.4   0.0      0.64   3.8e+02       9      23 ..      91     105 ..      85     108 .. 0.77
   4 ?   -1.3   0.1       4.7   2.8e+03      13      25 ..     126     138 ..     119     164 .. 0.60
   5 !   14.3   0.0   6.3e-05     0.038      41      74 ..     178     211 ..     171     214 .. 0.90
   6 !    8.0   0.0    0.0059       3.5       4      32 ..     217     245 ..     214     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-05
                        TPR_12 47 tlrnLgrlyralgryeeAlelleea 71
                                  +++ Lg ++++lg+ eeAle++++a
  gi|70607008|ref|YP_255878.1| 32 IYNLLGKILLELGKDEEALEAFRQA 56
                                  6999999999999999999999998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.78
                        TPR_12  9 laavlrrlgrydeAl 23
                                  +a ++ + g y++Al
  gi|70607008|ref|YP_255878.1| 62 VARIYIQKGLYQDAL 76
                                  455555555555554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.64
                        TPR_12   9 laavlrrlgrydeAl 23 
                                   +a+++ +++++d+A 
  gi|70607008|ref|YP_255878.1|  91 RALIYIKMENFDKAK 105
                                   788999999999985 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.7
                        TPR_12  13 lrrlgrydeAlel 25 
                                   +++  +y  Al+ 
  gi|70607008|ref|YP_255878.1| 126 EYHTANYYGALRS 138
                                   5555555555543 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 6.3e-05
                        TPR_12  41 hpltattlrnLgrlyralgryeeAlelleealai 74 
                                   +p++a+ ++  g +++++g++ eA++++ +a++ 
  gi|70607008|ref|YP_255878.1| 178 NPYYAELYFSKGVILEQRGKLNEAVNYYSKAIKY 211
                                   6889**************************9875 PP

  == domain 6  score: 8.0 bits;  conditional E-value: 0.0059
                        TPR_12   4 talnnlaavlrrlgrydeAlellekalei 32 
                                   +a++++a v+++lg  +eA++  ek+ e+
  gi|70607008|ref|YP_255878.1| 217 KAYYRRAKVYMKLGMDQEAEKDIEKVKEL 245
                                   68999*******************99887 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.3    0.0021       1.3       3      27 ..      32      56 ..      30      66 .. 0.87
   2 ?    1.2   0.0       1.5   9.1e+02       4      23 ..      59      78 ..      56      81 .. 0.83
   3 ?    0.1   0.0       3.4     2e+03       6      23 ..      90     107 ..      86     121 .. 0.82
   4 ?    3.2   0.1      0.35   2.1e+02       8      42 ..     123     157 ..     116     161 .. 0.83
   5 ?    6.5   0.0      0.03        18       6      29 ..     187     210 ..     182     215 .. 0.83
   6 !    8.7   0.0    0.0058       3.5       2      24 ..     217     239 ..     216     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0021
                        TPR_14  3 allalaeallalGdpdeAiallrra 27
                                   + +l+++ll+lG+ +eA++++r+a
  gi|70607008|ref|YP_255878.1| 32 IYNLLGKILLELGKDEEALEAFRQA 56
                                  66789******************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.5
                        TPR_14  4 llalaeallalGdpdeAial 23
                                  +l+ a+++ + G +++A++ 
  gi|70607008|ref|YP_255878.1| 59 RLEVARIYIQKGLYQDALNE 78
                                  67889***********9976 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.4
                        TPR_14   6 alaeallalGdpdeAial 23 
                                   ++a ++   +++d+A + 
  gi|70607008|ref|YP_255878.1|  90 LRALIYIKMENFDKAKEE 107
                                   578899999*****9875 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.35
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                                   + ++++  ++ +A++    al+ +P dae++++ a
  gi|70607008|ref|YP_255878.1| 123 GIVEYHTANYYGALRSITIALREYPMDAELYYYRA 157
                                   5678889999***************7777776654 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.03
                        TPR_14   6 alaeallalGdpdeAiallrrala 29 
                                     + +l+++G++ eA++++ +a++
  gi|70607008|ref|YP_255878.1| 187 SKGVILEQRGKLNEAVNYYSKAIK 210
                                   556789****************97 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0058
                        TPR_14   2 eallalaeallalGdpdeAiall 24 
                                   +a++++a++++ lG  +eA++  
  gi|70607008|ref|YP_255878.1| 217 KAYYRRAKVYMKLGMDQEAEKDI 239
                                   79*****************9855 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.5    0.0074       4.4      18      76 ..      11      68 ..       5     109 .. 0.55
   2 !   14.4   0.0   2.3e-05     0.014     213     248 ..     169     204 ..     127     207 .. 0.86
   3 !   15.3   0.3   1.2e-05    0.0072     209     255 ..     199     245 ..     197     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0074
                                  THHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHH CS
                         NARP1 18 gkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYye 76
                                  g+l+ Al +++e  k+      + +  +++ll+Lg+ eeA +++++  +r    + Y +
  gi|70607008|ref|YP_255878.1| 11 GNLNYALRKINEIIKS-NPSPDIYNLLGKILLELGKDEEALEAFRQANNRLEVARIYIQ 68
                                  4555555555554333.234445566667777777777777777766666555554433 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHH CS
                         NARP1 213 eyidkaiehtptlvelyltKarilkhaGdlkkAaev 248
                                   + id ai+ +p   ely  K+ il++ G l++A++ 
  gi|70607008|ref|YP_255878.1| 169 DDIDMAINLNPYYAELYFSKGVILEQRGKLNEAVNY 204
                                   359******************************986 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 209 ekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                   ++A++y +kai+ +p+lv  y+++a+++ + G  ++A + +e+ ++l
  gi|70607008|ref|YP_255878.1| 199 NEAVNYYSKAIKYKPELVKAYYRRAKVYMKLGMDQEAEKDIEKVKEL 245
                                   689****************************************9998 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0014      0.84      34      80 ..       8      54 ..       7      56 .. 0.89
   2 !    9.3   0.0    0.0022       1.3      23      75 ..      56     104 ..      54     111 .. 0.91
   3 ?    6.2   0.0      0.02        12      20      72 ..      82     132 ..      68     139 .. 0.71
   4 !   11.1   1.3   0.00061      0.36      26      81 ..     185     241 ..     148     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                                  HHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3 34 ylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                  y+ g+ + A++ +++  + + s+ +  l+++ ll+L+k eeA+ a+ 
  gi|70607008|ref|YP_255878.1|  8 YQEGNLNYALRKINEIIKSNPSPDIYNLLGKILLELGKDEEALEAFR 54
                                  788888899999999977789999*******************9986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
                                   HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHH CS
                        ANAPC3  23 pedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeA 75 
                                   +++++  A  + + g y+ A++ +++     ++ ++ +l A  ++k++++++A
  gi|70607008|ref|YP_255878.1|  56 ANNRLEVARIYIQKGLYQDALNEIKDE----TNDESKILRALIYIKMENFDKA 104
                                   6788889********************....999999************9998 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.02
                                   H--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-H CS
                        ANAPC3  20 tespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkky 72 
                                     ++e+  l Al + +++++++A e + +   ns+s+  + +++ + +   +y
  gi|70607008|ref|YP_255878.1|  82 ETNDESKILRALIYIKMENFDKAKEEIANI--NSNSPLFHKVKGIVEYHTANY 132
                                   456666677799999999999999988888..777777777766666555555 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00061
                                   HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  26 ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    + ++  l ++g+ ++A ++++ka k +++  ++ y  A+++ kL+  +eA++ +ek
  gi|70607008|ref|YP_255878.1| 185 YFSKGVILEQRGKLNEAVNYYSKAiKYKPELVKAYYRRAKVYMKLGMDQEAEKDIEK 241
                                   34458888899*************9**************************986665 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0004      0.24     125     178 ..       9      62 ..       5      69 .. 0.91
   2 !    6.9   0.1    0.0079       4.7     116     147 ..      59      90 ..      58     110 .. 0.74
   3 !    6.9   0.2    0.0077       4.6     149     188 ..     185     229 ..     174     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                        TPR_21 125 aekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaalee 178
                                   +e++++ Al+++++  +++ +  + +l G il++ gk +eA +a+++A ++le 
  gi|70607008|ref|YP_255878.1|   9 QEGNLNYALRKINEIIKSNPSPDIYNLLGKILLELGKDEEALEAFRQANNRLEV 62 
                                   7899999*****************************************999875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0079
                        TPR_21 116 rlRLarvllaekkydeAlktLeakkeeafaal 147
                                   rl +ar++++++ y++Al++++++++++ + l
  gi|70607008|ref|YP_255878.1|  59 RLEVARIYIQKGLYQDALNEIKDETNDESKIL 90 
                                   6889*****************99998865544 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0077
                        TPR_21 149 aelrGDilvaqgkldeAraaYqaAlaaleeka.....rellqlKl 188
                                      +G il ++gkl+eA + Y++A++ + e       r+ + +Kl
  gi|70607008|ref|YP_255878.1| 185 YFSKGVILEQRGKLNEAVNYYSKAIKYKPELVkayyrRAKVYMKL 229
                                   557999*******************98877666666666666666 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.6     7e-06    0.0042     184     300 ..      53     230 ..       6     248 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7e-06
                                   TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCC...........SS-SS---....................... CS
                           FAT 184 rappevvyaylKylwssgeqkealqkLreftsellekke...........elqsgleaq...................... 231
                                    ++ +  ++++++ +++g  ++al++++++t+  ++  +           +                              
  gi|70607008|ref|YP_255878.1|  53 FRQANNRLEVARIYIQKGLYQDALNEIKDETNDESKILRaliyikmenfdK-------Akeeianinsnsplfhkvkgive 126
                                   444466677777777777777777777777774444443444444443331.......02333444555566666666666 PP

                                   ....................................................HH.HHCCCTCCCCCCCCCCCT.S...-SS CS
                           FAT 232 .........................................keptnleeftkll.arcylkkGewqealqkldwseekiee 270
                                                                            ++   ++ + +   a++y+ kG  +e+ +k        +e
  gi|70607008|ref|YP_255878.1| 127 yhtanyygalrsitialreypmdaelyyyralvkaelgleyEDDIDMAINLNPYyAELYFSKGVILEQRGK-------LNE 200
                                   66777777777777777777555555555555555555554233333333333336667777777777777.......89* PP

                                   CCHHHHCCHHCTCCCHSTTCCCCHHHHHCC CS
                           FAT 271 ilqsysaateidpswykawhtwalfnfevv 300
                                   ++++ys+a ++ p++ ka+++ a+++ +  
  gi|70607008|ref|YP_255878.1| 201 AVNYYSKAIKYKPELVKAYYRRAKVYMKLG 230
                                   *******************99888776654 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.8   4.7e+03      25      34 ..       1      10 [.       1      10 [. 0.87
   2 !   10.9   0.1   0.00055      0.33       4      28 ..      32      56 ..      31      61 .. 0.95
   3 ?    1.7   0.0      0.42   2.5e+02       9      23 ..      63      77 ..      59      81 .. 0.87
   4 !   10.3   0.0   0.00084       0.5       9      29 ..     189     209 ..     188     212 .. 0.91
   5 ?    1.6   0.0      0.45   2.7e+02       9      28 ..     223     242 ..     217     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.8
                        TPR_10 25 leealairrr 34
                                  +ee+++++++
  gi|70607008|ref|YP_255878.1|  1 MEEVVRAYQE 10
                                  6999*99997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00055
                        TPR_10  4 slnNLanalrqrgrydeAealleea 28
                                  ++n L+ +l ++g+ +eA++ +++a
  gi|70607008|ref|YP_255878.1| 32 IYNLLGKILLELGKDEEALEAFRQA 56
                                  69*********************98 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.42
                        TPR_10  9 analrqrgrydeAea 23
                                  a+++ q g y++A++
  gi|70607008|ref|YP_255878.1| 63 ARIYIQKGLYQDALN 77
                                  899**********98 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00084
                        TPR_10   9 analrqrgrydeAealleeal 29 
                                   +++l qrg+++eA++++ +a+
  gi|70607008|ref|YP_255878.1| 189 GVILEQRGKLNEAVNYYSKAI 209
                                   78899************9998 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.45
                        TPR_10   9 analrqrgrydeAealleea 28 
                                   a ++ ++g  +eAe++ e++
  gi|70607008|ref|YP_255878.1| 223 AKVYMKLGMDQEAEKDIEKV 242
                                   6688899999*****99987 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.5   4.6e-07   0.00027     105     158 ..      59     112 ..      43     117 .. 0.90
   2 ?   -2.8   0.0       5.4   3.2e+03     140     160 ..     225     245 ..     195     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
                                   HHHHHHHHHHTT-HHHHHHHHTT--SHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    Coatomer_E 105 rllaaivflkegdfddalkllkksenLeavAlkvqillklhrvdlAekelkkmq 158
                                   rl  a +++++g ++dal+ +k  +n e+  l+  i++k++  d A++e+++++
  gi|70607008|ref|YP_255878.1|  59 RLEVARIYIQKGLYQDALNEIKDETNDESKILRALIYIKMENFDKAKEEIANIN 112
                                   566799*******************************************99876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                                   HHHHTT-HHHHHHHHHHHHHH CS
                    Coatomer_E 140 illklhrvdlAekelkkmqdi 160
                                   +++kl   + Aek + k++++
  gi|70607008|ref|YP_255878.1| 225 VYMKLGMDQEAEKDIEKVKEL 245
                                   333333334444444444444 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0         4   2.4e+03       8      31 ..       6      28 ..       5      29 .. 0.82
   2 !    8.1   0.1    0.0076       4.5       6      26 ..      36      56 ..      35      59 .. 0.89
   3 ?   -0.6   0.0       4.5   2.7e+03       4      20 ..      60      76 ..      57      78 .. 0.81
   4 ?    3.7   0.0      0.19   1.1e+02       6      21 ..      91     106 ..      89     116 .. 0.85
   5 ?    5.8   0.1     0.042        25       8      29 ..     183     211 ..     180     214 .. 0.72
   6 !    8.2   0.2    0.0071       4.2       2      26 ..     218     242 ..     217     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 4
                                  HHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6  8 lsyrklgdtdkAlealerlikeYP 31
                                  ++y+++ +   Al+  +++ik+ P
  gi|70607008|ref|YP_255878.1|  6 RAYQEG-NLNYALRKINEIIKSNP 28
                                  577777.99999999999999988 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0076
                                  HHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6  6 lalsyrklgdtdkAlealerl 26
                                  l++ +++lg+ ++Alea+++ 
  gi|70607008|ref|YP_255878.1| 36 LGKILLELGKDEEALEAFRQA 56
                                  89999**99*********996 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 4.5
                                  HHHHHHHHHHHHHHHHH CS
                         TPR_6  4 yklalsyrklgdtdkAl 20
                                  +  a+ y++ g +++Al
  gi|70607008|ref|YP_255878.1| 60 LEVARIYIQKGLYQDAL 76
                                  56799999988999986 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHHHHH CS
                         TPR_6   6 lalsyrklgdtdkAle 21 
                                   +al y+k+ + dkA+e
  gi|70607008|ref|YP_255878.1|  91 RALIYIKMENFDKAKE 106
                                   799****88*****98 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.042
                                   HHHHH.H......HHHHHHHHHHHHHHHH CS
                         TPR_6   8 lsyrk.l......gdtdkAlealerlike 29 
                                   ++y++ +      g+  +A+ ++ + ik 
  gi|70607008|ref|YP_255878.1| 183 ELYFSkGvileqrGKLNEAVNYYSKAIKY 211
                                   55554335555559***********9985 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0071
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerl 26 
                                   A+y++a+ y klg  ++A +  e++
  gi|70607008|ref|YP_255878.1| 218 AYYRRAKVYMKLGMDQEAEKDIEKV 242
                                   9**********99999998777766 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.4   9.8e-07   0.00059      23      98 ..      65     139 ..      21     179 .. 0.85
   2 ?   -0.2   2.9       1.6   9.8e+02      20      72 ..     188     243 ..     167     249 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.8e-07
                  SRP_TPR_like  23 aliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkveaee.kvkvlksqvlYrlgsyekAYklL 98 
                                    +i+ + y++aL+ +k++   +++ +  +a ++ k++++ ka + + ++++++   + +k  v Y+  +y  A + +
  gi|70607008|ref|YP_255878.1|  65 IYIQKGLYQDALNEIKDET--NDESKILRALIYIKMENFDKAKEEIANINSNSpLFHKVKGIVEYHTANYYGALRSI 139
                                   4677777********9998..999999***********************99988999************9997665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsalse...dvrfEkaYvlYklkkykkalkilkkve 72 
                                   k v l + +k +ea+++ +k+ +      +  + +a v+ kl   ++a k ++kv+
  gi|70607008|ref|YP_255878.1| 188 KGVILEQRGKLNEAVNYYSKAIKYKPelvKAYYRRAKVYMKLGMDQEAEKDIEKVK 243
                                   66666667777788777777764433111345777777777777777777776665 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0094       5.6     130     170 ..      17      57 ..       7      59 .. 0.86
   2 !    9.6   0.0    0.0013      0.77     117     170 ..     189     243 ..     176     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0094
                       Wzy_C_2 130 lalarklihlsPepavierlilslallGdedeAeqilarar 170
                                   l   +++i++ P p +++ l   l  lG+++eA+   ++a 
  gi|70607008|ref|YP_255878.1|  17 LRKINEIIKSNPSPDIYNLLGKILLELGKDEEALEAFRQAN 57 
                                   5556799****************************999986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                       Wzy_C_2 117 gllplspenlaaklalarklihlsPe.pavierlilslallGdedeAeqilarar 170
                                   g++  ++ +l + +  ++k+i+++Pe  + ++r +  ++ lG ++eAe+ +++++
  gi|70607008|ref|YP_255878.1| 189 GVILEQRGKLNEAVNYYSKAIKYKPElVKAYYRRAKVYMKLGMDQEAEKDIEKVK 243
                                   66677899999**************95689******************9877765 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.088        52     163     192 ..      32      61 ..      13      80 .. 0.66
   2 ?    3.5   0.0     0.065        39       2      22 ..      86     106 ..      85     111 .. 0.88
   3 !    6.6   0.0    0.0073       4.4      84     111 ..     186     213 ..     166     217 .. 0.81
   4 !    6.7   0.0    0.0068       4.1      86     111 ..     188     213 ..     179     250 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.088
                      TPR_MalT 163 ayvllarialaqGdleeAetllekaeelar 192
                                   +y ll +i l  G+ eeA++++++a + ++
  gi|70607008|ref|YP_255878.1|  32 IYNLLGKILLELGKDEEALEAFRQANNRLE 61 
                                   555666666666666666666666665544 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.065
                      TPR_MalT   2 eiaalrAllaiasgdaerale 22 
                                   e ++lrAl++i+++++++a+e
  gi|70607008|ref|YP_255878.1|  86 ESKILRALIYIKMENFDKAKE 106
                                   5689**************997 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0073
                      TPR_MalT  84 lqqaeilvaqGrLheAletyeqalqlat 111
                                    + + il ++G+L eA++ y +a+++ +
  gi|70607008|ref|YP_255878.1| 186 FSKGVILEQRGKLNEAVNYYSKAIKYKP 213
                                   467889******************9865 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0068
                      TPR_MalT  86 qaeilvaqGrLheAletyeqalqlat 111
                                    + il ++G+L eA++ y +a+++ +
  gi|70607008|ref|YP_255878.1| 188 KGVILEQRGKLNEAVNYYSKAIKYKP 213
                                   45677777888888888888777654 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6      0.28   1.6e+02      18      35 ..      44      61 ..      40     110 .. 0.80
   2 ?   12.6   2.0   0.00019      0.11       8      33 ..     186     211 ..     182     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.28
                           MIT 18 gnyeeAlelYkealelLl 35
                                  g+ eeAle++++a + L 
  gi|70607008|ref|YP_255878.1| 44 GKDEEALEAFRQANNRLE 61
                                  788888888888866655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00019
                           MIT   8 vkkAveeDnagnyeeAlelYkealel 33 
                                   ++k v ++++g+  eA+++Y++a+++
  gi|70607008|ref|YP_255878.1| 186 FSKGVILEQRGKLNEAVNYYSKAIKY 211
                                   678999******************99 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.7   4.2e+02       9      45 ..      18      53 ..      12      57 .. 0.74
   2 ?    7.0   0.2     0.012       7.1      23      44 ..      57      78 ..      42      81 .. 0.85
   3 ?   -0.4   0.0       2.5   1.5e+03      18      47 ..      81     110 ..      78     115 .. 0.81
   4 ?   -2.0   0.0       7.8   4.7e+03       9      34 ..     137     162 ..     133     177 .. 0.76
   5 ?    2.3   0.0      0.37   2.2e+02      11      41 ..     205     235 ..     193     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.7
                        TPR_20  9 aeleaalaanpddldarldlAlallaagryeeAleqL 45
                                  +++ + +++np+  d+   l + ll+ g+ eeAle++
  gi|70607008|ref|YP_255878.1| 18 RKINEIIKSNPSP-DIYNLLGKILLELGKDEEALEAF 53
                                  5666667777776.77777888888889999998865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                        TPR_20 23 darldlAlallaagryeeAleq 44
                                  + rl++A+ ++++g y++Al++
  gi|70607008|ref|YP_255878.1| 57 NNRLEVARIYIQKGLYQDALNE 78
                                  679*****************97 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                        TPR_20  18 npddldarldlAlallaagryeeAleqLle 47 
                                   + ++ + ++  Al +++ ++ ++A e++ +
  gi|70607008|ref|YP_255878.1|  81 DETNDESKILRALIYIKMENFDKAKEEIAN 110
                                   556779999999999999999999888765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 7.8
                        TPR_20   9 aeleaalaanpddldarldlAlalla 34 
                                   +++  al + p d ++ +  Al+ ++
  gi|70607008|ref|YP_255878.1| 137 RSITIALREYPMDAELYYYRALVKAE 162
                                   56666788889999999988887665 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.37
                        TPR_20  11 leaalaanpddldarldlAlallaagryeeA 41 
                                     +a++ +p+ ++a +  A+++++ g  +eA
  gi|70607008|ref|YP_255878.1| 205 YSKAIKYKPELVKAYYRRAKVYMKLGMDQEA 235
                                   56789999999*************9999998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.05        30     109     130 ..      39      60 ..      32      71 .. 0.85
   2 ?   -0.5   0.1       1.9   1.1e+03      41      41 ..      89      89 ..      49     153 .. 0.60
   3 ?    4.8   0.0     0.045        27     100     127 ..     182     209 ..     150     215 .. 0.78
   4 ?    3.6   0.1      0.11        64     100     133 ..     216     249 ..     212     250 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.05
                                   HHHHTT-HHHHHHHHHHHHHHH CS
                       DUF3856 109 aleelGrkdealkafrmagemi 130
                                    l elG+ +eal+afr+a++ +
  gi|70607008|ref|YP_255878.1|  39 ILLELGKDEEALEAFRQANNRL 60 
                                   57799***********998765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                                  T CS
                       DUF3856 41 t 41
                                   
  gi|70607008|ref|YP_255878.1| 89 I 89
                                  1 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 100 iaavfsravaleelGrkdealkafrmag 127
                                       fs++v le+ G+ +ea++++ +a 
  gi|70607008|ref|YP_255878.1| 182 AELYFSKGVILEQRGKLNEAVNYYSKAI 209
                                   55679*******************9986 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
                       DUF3856 100 iaavfsravaleelGrkdealkafrmagemiaer 133
                                   ++a ++ra+ + +lG  +ea k  ++++e+ +++
  gi|70607008|ref|YP_255878.1| 216 VKAYYRRAKVYMKLGMDQEAEKDIEKVKELTDNK 249
                                   678899**********************998765 PP

>> DUF4810  Domain of unknown function (DUF4810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     0.002       1.2      28      72 ..      12      57 ..       2      69 .. 0.77
   2 ?   -0.2   0.0       2.5   1.5e+03      51      73 ..      62      84 ..      58      91 .. 0.79
   3 ?   -1.8   0.0       8.1   4.9e+03      52      67 ..      92     107 ..      88     110 .. 0.83
   4 ?    1.2   0.0      0.92   5.5e+02      51      73 ..     188     210 ..     179     217 .. 0.80
   5 ?   -0.5   0.2       3.2   1.9e+03      52      70 ..     223     241 ..     193     247 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.002
                       DUF4810 28 klekiiekaeak.gkkvpPGlyAelGllylkegkkeeaieafekEk 72
                                  +l+ ++ k+++  ++++ P +y  lG ++l+ gk+eea eaf++ +
  gi|70607008|ref|YP_255878.1| 12 NLNYALRKINEIiKSNPSPDIYNLLGKILLELGKDEEALEAFRQAN 57
                                  566666666554156788************************9865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                       DUF4810 51 lGllylkegkkeeaieafekEke 73
                                  ++ +y+++g  ++a ++ + E++
  gi|70607008|ref|YP_255878.1| 62 VARIYIQKGLYQDALNEIKDETN 84
                                  66789999999999998888865 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 8.1
                       DUF4810  52 Gllylkegkkeeaiea 67 
                                   +l+y+k+ + ++a+e+
  gi|70607008|ref|YP_255878.1|  92 ALIYIKMENFDKAKEE 107
                                   6899999999999886 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.92
                       DUF4810  51 lGllylkegkkeeaieafekEke 73 
                                    G+++ ++gk +ea+++++k  +
  gi|70607008|ref|YP_255878.1| 188 KGVILEQRGKLNEAVNYYSKAIK 210
                                   599999**********9988655 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 3.2
                       DUF4810  52 Gllylkegkkeeaieafek 70 
                                   + +y+k g ++ea +  ek
  gi|70607008|ref|YP_255878.1| 223 AKVYMKLGMDQEAEKDIEK 241
                                   4456666666666665554 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.3   3.3e-05      0.02      11     125 ..       2     115 ..       1     128 [. 0.79
   2 ?    1.4   0.1      0.44   2.6e+02      17      56 ..     192     230 ..     189     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-05
                                   CCCHHHHHCTT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTSS---S-TTHHHHHHHT-SSHHHHHH CS
                      Clathrin  11 srvvklfeeaglleelleyLekvlkedskenpalqtallelyakyddpqeleeflkknnnydlekvaklcekadlyeeavi 91 
                                   ++vv++++e g+l+++l    +++k +   +p+++++l +++++ ++ +e++e +++ nn  + +va++  +++ly+ a+ 
  gi|70607008|ref|YP_255878.1|   2 EEVVRAYQE-GNLNYALRKINEIIKSN--PSPDIYNLLGKILLELGKDEEALEAFRQANN--RLEVARIYIQKGLYQDALN 77 
                                   799****99.9999999999****755..88**************876788888887777..999***********99998 PP

                                   HHHT.TXTHSSHSS.X.SSSSHCSCHHH.HTTTTTXXS CS
                      Clathrin  92 lykk.inefkkais.l.lkklkdfddai.eyaakvsnp 125
                                     k+  n+ +k +  l + k+++fd+a  e+a   sn+
  gi|70607008|ref|YP_255878.1|  78 EIKDeTNDESKILRaLiYIKMENFDKAKeEIANINSNS 115
                                   55554666666666766999999999985555554455 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.44
                                   HHCTT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT CS
                      Clathrin  17 feeaglleelleyLekvlkedskenpalqtallelyakyd 56 
                                   +e++g+l+e+  y  k++k + +e ++ + + ++ y k +
  gi|70607008|ref|YP_255878.1| 192 LEQRGKLNEAVNYYSKAIKYK-PELVKAYYRRAKVYMKLG 230
                                   566677777777766666543.555666666666666664 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   1.9e+03      57      81 ..       9      33 ..       2      48 .. 0.69
   2 ?    0.3   0.0      0.86   5.1e+02      52      69 ..      63      80 ..      48      88 .. 0.75
   3 ?    2.7   0.0      0.15        89      45      83 ..      85     123 ..      74     127 .. 0.82
   4 ?    6.1   0.0     0.014       8.2      39      73 ..     176     210 ..     157     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                    HrpB1_HrpK 57 ergrweeAlrlLreveaeasgtpya 81
                                  ++g+++ Alr ++e+ +++++ ++ 
  gi|70607008|ref|YP_255878.1|  9 QEGNLNYALRKINEIIKSNPSPDIY 33
                                  6788888999999998888776554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.86
                    HrpB1_HrpK 52 gvlliergrweeAlrlLr 69
                                  + ++i++g +++Al  ++
  gi|70607008|ref|YP_255878.1| 63 ARIYIQKGLYQDALNEIK 80
                                  7899********976554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.15
                    HrpB1_HrpK  45 aeldllegvlliergrweeAlrlLreveaeasgtpyaka 83 
                                    e ++l ++++i+ ++++ A   +++++ +++ +  +k 
  gi|70607008|ref|YP_255878.1|  85 DESKILRALIYIKMENFDKAKEEIANINSNSPLFHKVKG 123
                                   577899999999999999999999999988888877765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.014
                    HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlLrevea 73 
                                    L P  ael +  gv+l +rg+++eA+ + ++  +
  gi|70607008|ref|YP_255878.1| 176 NLNPYYAELYFSKGVILEQRGKLNEAVNYYSKAIK 210
                                   599************************98777664 PP

>> DUF928  Domain of Unknown Function (DUF928)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00035      0.21     123     154 ..      49      81 ..      19      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                        DUF928 123 laqqlaqatpl.ekaalYaengiWyDalttlae 154
                                     + ++qa+++ e a++Y ++g+++Dal+++ +
  gi|70607008|ref|YP_255878.1|  49 ALEAFRQANNRlEVARIYIQKGLYQDALNEIKD 81 
                                   445677899888*****************9877 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.1   6.7e+02      27      59 ..      44      77 ..      40      84 .. 0.67
   2 ?    4.8   0.1     0.047        28      15      40 ..      87     112 ..      84     125 .. 0.85
   3 ?    3.1   0.0      0.16        97      29      67 ..     191     229 ..     182     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                       PTS_IIA 27 gdfeeaeellkeAeeelkeAhk.aqteliqkeas 59
                                  g+ eea e +++A++ l+ A+  +q+ l q+  +
  gi|70607008|ref|YP_255878.1| 44 GKDEEALEAFRQANNRLEVARIyIQKGLYQDALN 77
                                  5667888888888888888874256666665555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.047
                       PTS_IIA  15 slameAlkaakegdfeeaeellkeAe 40 
                                   s+++ Al  +k ++f++a+e++++ +
  gi|70607008|ref|YP_255878.1|  87 SKILRALIYIKMENFDKAKEEIANIN 112
                                   7899****************998755 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                       PTS_IIA  29 feeaeellkeAeeelkeAhkaqteliqkeasgekvevsl 67 
                                   + e + +l+eA + +++A k++ el+++  +  kv ++l
  gi|70607008|ref|YP_255878.1| 191 ILEQRGKLNEAVNYYSKAIKYKPELVKAYYRRAKVYMKL 229
                                   56678899******************9999999998877 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.018        11      28      45 ..     152     169 ..     136     174 .. 0.87
   2 ?    0.7   0.1      0.67     4e+02      29      43 ..     185     199 ..     183     212 .. 0.50
   3 ?    2.7   0.2      0.15        92      29      44 ..     219     234 ..     217     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHTT--HHH CS
                      HTH_Bact  28 LyYqkgecleklgfseee 45 
                                   LyY+++  + +lg ++e+
  gi|70607008|ref|YP_255878.1| 152 LYYYRALVKAELGLEYED 169
                                   9************99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.67
                                   HHHHHHHHHHTT--H CS
                      HTH_Bact  29 yYqkgecleklgfse 43 
                                   y+ kg  le+ g  +
  gi|70607008|ref|YP_255878.1| 185 YFSKGVILEQRGKLN 199
                                   555555555443333 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHTT--HH CS
                      HTH_Bact  29 yYqkgecleklgfsee 44 
                                   yY +++   klg ++e
  gi|70607008|ref|YP_255878.1| 219 YYRRAKVYMKLGMDQE 234
                                   9**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1404.48
//
Query:       gi|70607009|ref|YP_255879.1|  [L=427]
Description: hypothetical protein Saci_1240 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-09   36.9   0.3    7.8e-09   35.6   0.3    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.3e-09   36.2   0.0    5.7e-05   22.6   0.0    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase
    1.1e-08   35.1   0.2    9.1e-08   32.1   0.2    2.1  1  DAO             FAD dependent oxidoreductase
    6.9e-08   32.9   4.4     0.0013   19.2   0.4    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.5e-07   30.2   4.4      9e-05   21.8   0.2    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-06   27.4   1.0     0.0011   17.5   0.0    2.2  2  GDI             GDP dissociation inhibitor
    2.1e-06   26.7   1.6     0.0022   16.8   0.4    2.2  2  HI0933_like     HI0933-like protein
    2.9e-05   23.3   1.7      0.025   13.7   0.7    2.1  2  FAD_binding_2   FAD binding domain
    0.00026   20.5   3.5     0.0015   18.0   0.5    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    0.00031   20.1   0.8    0.00048   19.5   0.8    1.2  1  FAD_binding_3   FAD binding domain
      0.002   17.4   3.4      0.043   13.1   0.3    2.2  2  Thi4            Thi4 family
     0.0024   17.0   1.8       0.11   11.6   0.4    2.4  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.038   13.5   0.1    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.07   13.6   0.2       0.24   11.8   0.0    2.0  2  NAD_binding_7   Putative NAD(P)-binding
        0.1   11.4   5.1       0.12   11.2   0.3    2.2  2  Trp_halogenase  Tryptophan halogenase
       0.13   12.0   0.1       0.28   10.9   0.1    1.6  1  CUE             CUE domain
       0.13   12.1   2.9        5.9    6.7   0.3    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.28   10.2   1.2       0.27   10.2   0.3    1.4  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.3   7.9e-12   7.8e-09       1      45 [.       8      52 ..       8      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 7.9e-12
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrv 45
                                  IvG+G  Gl + +lLa++g++v+lle++++lGG   ++e++gv++
  gi|70607009|ref|YP_255879.1|  8 IVGGGHNGLILSALLAEQGAKVTLLEANSKLGGMTDTIEIQGVKL 52
                                  9***************************************99654 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00024      0.24       3      37 ..      15      49 ..      15      59 .. 0.86
   2 !   22.6   0.0   5.7e-08   5.7e-05     113     262 ..     100     258 ..      69     277 .. 0.69
   3 ?   -2.2   0.0       1.9   1.9e+03     266     297 ..     340     370 ..     326     408 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                  HHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETT CS
                 Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvGGRirtvrsdG 37
                                  GL+    L+++G +Vt+lEa++ +GG   t++ +G
  gi|70607009|ref|YP_255879.1| 15 GLILSALLAEQGAKVTLLEANSKLGGMTDTIEIQG 49
                                  8888899*******************777776665 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.7e-08
                                   HHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCC CS
                 Amino_oxidase 113 leeklrlgleallqktldeldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllw 193
                                   +ee++++g ++ + +++d+l   +k l +++ ++++ +  d  +++      l+++++   + ++   se+ +   +    
  gi|70607009|ref|YP_255879.1| 100 REEMIKAGETRYP-EFEDKLLKFKKLLYDKFTFVEKPPTKD-SILEEAKKYGLEEFIQEPAKKVL---SEYISEDYHEFFI 175
                                   5777777777777.555555555555555555555555555.66666666555555555555555...5555555555555 PP

                                   HHHHHTSCCCEE...........TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTC.EEEEETTSTEEEESE.EEE- CS
                 Amino_oxidase 194 elegfggslllp...........rgGlsqlpealae..elrgldirlntrVkeikregdg.vtvtledgevveaDa.VvvT 259
                                      +++ s +++           +gG++++ + +ae    +g+++r+n++V e+   +d+ v+v++ +  vv++D  V+ T
  gi|70607009|ref|YP_255879.1| 176 YPGMERTSAYVIayffspewslvEGGMGTVSQKIAEyaIDKGVEVRVNSKVEELIVRDDKvVGVRMGNT-VVDGDVfVIAT 255
                                   55555555555578888999999**************99**************9996666599987544.44999945555 PP

                                   S-H CS
                 Amino_oxidase 260 vpl 262
                                   +pl
  gi|70607009|ref|YP_255879.1| 256 SPL 258
                                   554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                                   H.SSEEESCCSHHHHHHHHHSEEEEEEEEEEEE CS
                 Amino_oxidase 266 k.ailfsPplpdekaeairnlgfgsvnkvilef 297
                                   k +++++ +l  + ae i nl++g +n +   +
  gi|70607009|ref|YP_255879.1| 340 KsKVKYVDELNAFNAEKIYNLPYGDLNHL--PM 370
                                   44566777777788888888888888743..33 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.2   9.2e-11   9.1e-08       1     227 [.       5     276 ..       5     345 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.2e-11
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTH....................... CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeas....................... 55 
                                   ++vi+GGG  Gl     La++g  Vtlle+++ +g    +   +g+  s       as                       
  gi|70607009|ref|YP_255879.1|   5 RIVIVGGGHNGLILSALLAEQGakVTLLEANSKLGGmTDTIEIQGVKLS------RASyvlglmpgflinkfkipllyndi 79 
                                   59*****************************999932444444444333......222223346677889999999999** PP

                                   ........HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEE...SS........HHHHHHHHHHHHHHHHTTTTEEEEE CS
                           DAO  56 ........elarlslealeelreleeelgididyrrtGllsla...ad........eeelealdkllallleagldaelld 117
                                           ++ +++++++++++e+ +  +   +  +  ll      +d        +  +   d  l++++++gl+ e++ 
  gi|70607009|ref|YP_255879.1|  80 fqvfyvndKVIPFYRDSRKRREEMIKAGETRYPEFEDKLLKFKkllYDkftfvekpP-TK---DSILEEAKKYGLE-EFIQ 155
                                   *******7777**************98333233333555555422212233332221.12...2333444556665.4554 PP

                                   HHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHHH....................HHHHHHHTT-EEEESECEEEEEEEE CS
                           DAO 118 aeevrelepa..lpgllgalfypdtgqvdpakltaa....................laraaealGveilegtevtgleeed 176
                                   +  ++++ +   +++++  + yp+     + +++ a                    +a+ a ++Gve++ +++v++l  +d
  gi|70607009|ref|YP_255879.1| 156 EP-AKKVLSEyiSEDYHEFFIYPG--MERTSAYVIAyffspewslveggmgtvsqkIAEYAIDKGVEVRVNSKVEELIVRD 233
                                   43.444444443335555444555..335555555556777777777777777788********************98889 PP

                                   TCEEEEE.EECTEEE.EEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEE CS
                           DAO 177 gkvwgve.rttpgen.daadavVnaaGawsdllgllkeldlpispvrgqvlvl 227
                                   +kv+gv+      ++ +  d  V+a+ +   ++   +el +p +p rg++   
  gi|70607009|ref|YP_255879.1| 234 DKVVGVRmG----NTvVDGDVFVIATSPL--QF---PEL-VPNVPKRGYYPGW 276
                                   9*****553....33233488*****877..67...777.6779999998555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   1.3e-06    0.0013       1      39 [.       5      43 ..       5      52 .. 0.91
   2 !   14.7   0.3   3.4e-05     0.034      41      78 ..     204     241 ..     201     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllD 39
                                  ++v+vGgG  gl l + lae g+kVt++e+++kl  + D
  gi|70607009|ref|YP_255879.1|  5 RIVIVGGGHNGLILSALLAEQGAKVTLLEANSKLGGMTD 43
                                  79********************************95554 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesvkl 78 
                                   ++s+ ++e+  ++g+ev+ n+kvee+   +d+v +v++
  gi|70607009|ref|YP_255879.1| 204 TVSQKIAEYAIDKGVEVRVNSKVEELIVRDDKVVGVRM 241
                                   5789999*************************999987 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2     9e-08     9e-05     143     179 ..       4      40 ..       1      50 [. 0.88
   2 !    9.4   0.7   0.00055      0.55     185     235 ..     205     255 ..     198     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9e-08
                                   SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllr 179
                                   kriv+vGgG  G+ l+a la+ g++vtl+ea+++l  
  gi|70607009|ref|YP_255879.1|   4 KRIVIVGGGHNGLILSALLAEQGAKVTLLEANSKLGG 40 
                                   79*******************************9973 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvav 235
                                   +s+ ++e+  ++Gvev+++++v+e++ +++k+  v   ++++d d  v+a+
  gi|70607009|ref|YP_255879.1| 205 VSQKIAEYAIDKGVEVRVNSKVEELIVRDDKVVGVRMGNTVVDGDVFVIAT 255
                                   6888999999*******************9888899999999999999985 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2   0.00068      0.68       7      48 ..       6      47 ..       2      53 .. 0.91
   2 !   17.5   0.0   1.1e-06    0.0011     153     281 ..     127     252 ..     110     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00068
                                  EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-H CS
                           GDI  7 vivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltl 48
                                  ++++G G +  ils ll+ +g kv  l+ n+  Gg + ++++
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEANSKLGGMTDTIEI 47
                                  6899*******************************9988876 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.1e-06
                                   BGGGSTT--TTTSBHHHHHHHCT--HHHHHHHHHHTS--SSSGGGGSBCHHHHHHHHHHHHHHCCCSS-SEEEETT-TTHH CS
                           GDI 153 dpktyedldlkkatmkevykkfdlsedtkdfiGhalalyrdddylkqpaletleriklyaeslarygkspylyplyGlGel 233
                                   d+ t+ +  ++k+++ e  kk++l+e +++   + l+ y  +dy +   +  +er   y+  +a +    +     G+G +
  gi|70607009|ref|YP_255879.1| 127 DKFTFVEKPPTKDSILEEAKKYGLEEFIQEPAKKVLSEYISEDYHEFFIYPGMERTSAYV--IAYFFSPEWSLVEGGMGTV 205
                                   566888888999********************************************9996..566655557788899**** PP

                                   HHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEEETTEEEEECEEE CS
                           GDI 234 pqgfarlsaiyGGtymlnkpvdevvldedgkvvGvkseeevakakkvi 281
                                    q  a  +   G    +n +v+e+++  d+kvvGv+ ++ v+  +  +
  gi|70607009|ref|YP_255879.1| 206 SQKIAEYAIDKGVEVRVNSKVEELIV-RDDKVVGVRMGNTVVDGDVFV 252
                                   ******9888899999********99.7889********999887644 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   2.2e-06    0.0022       2      36 ..       5      39 ..       4      42 .. 0.95
   2 !    8.8   0.0   0.00059      0.59     119     169 ..     213     262 ..     202     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +++++GgG  Gl  ++ +a++g++V+lle+++klg
  gi|70607009|ref|YP_255879.1|  5 RIVIVGGGHNGLILSALLAEQGAKVTLLEANSKLG 39
                                  69******************************998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00059
                                   HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                   HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                   + ++gv++r++++v+++  ++d+++ v++ +++ +  d  v+At  l +P+
  gi|70607009|ref|YP_255879.1| 213 AIDKGVEVRVNSKVEELIVRDDKVVGVRM-GNTVVDGDVFVIATSPLQFPE 262
                                   5579*************************.*************98777776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.7   2.5e-05     0.025       2      38 ..       6      42 ..       5      45 .. 0.93
   2 !    8.6   0.0   0.00085      0.85     147     182 ..     209     244 ..     179     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                                  ++++G+G  GL  ++ +ae+G+kv+++e  ++ gg t
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEANSKLGGMT 42
                                  79****************************9999865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00085
                                   HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET CS
                 FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenp 182
                                    +e+a + gv+++ + +++eLiv+d++v+G+ + n 
  gi|70607009|ref|YP_255879.1| 209 IAEYAIDKGVEVRVNSKVEELIVRDDKVVGVRMGNT 244
                                   567788888**********************98866 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   1.5e-06    0.0015       2      38 ..       6      42 ..       5      47 .. 0.95
   2 ?    3.0   0.1     0.053        53      91     143 ..     208     255 ..     201     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                  +v+vGGg  G++     a++Gakv L+e +  lGG++
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEANSKLGGMT 42
                                  89*********999999******************97 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.053
                  FAD_oxidored  91 avleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDAT 143
                                   +++e  +++ gv+v  n++++e +++++++ +v++    g++++ ++vf+ AT
  gi|70607009|ref|YP_255879.1| 208 KIAEYAIDK-GVEVRVNSKVEELIVRDDKVVGVRM----GNTVVDGDVFVIAT 255
                                   445555555.***************999*******....58999**9999887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.8   4.8e-07   0.00048       4      34 ..       6      36 ..       3      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                                  EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  ++IVG+G  Gl+l+ lL+e+G +v+l+e  s
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEANS 36
                                  68**************************876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   4.3e-05     0.043      19      55 ..       5      40 ..       1      47 [. 0.92
   2 ?    4.9   0.2     0.013        13     101     142 ..     207     246 ..     193     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                  EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                   +vivG+G  GL  +  la++ + kv++le++  +GG
  gi|70607009|ref|YP_255879.1|  5 RIVIVGGGHNGLILSALLAEQ-GAKVTLLEANSKLGG 40
                                  59*******************.*********999998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.013
                                   HHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHH CS
                          Thi4 101 stllskvlqlanvkllnavaveDlivregegvaGvvinwtlv 142
                                    +++  +++  +v +     ve+livr+ ++v Gv +  t+v
  gi|70607009|ref|YP_255879.1| 207 QKIAEYAID-KGVEVRVNSKVEELIVRD-DKVVGVRMGNTVV 246
                                   567777888.8999999999********.9999998877777 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.4   0.00011      0.11       2      35 ..       6      38 ..       5      55 .. 0.83
   2 ?    4.3   0.0     0.018        17     114     150 ..     222     257 ..     203     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                  EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                  ++++GgGh G+  ++ +a+ Gakv+L+    +++
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEA-NSKL 38
                                  89************************943.3344 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                                   EES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 114 ieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   ++ +veeliv+++kv gv++  ++++  +++viat +
  gi|70607009|ref|YP_255879.1| 222 VNSKVEELIVRDDKVVGVRMG-NTVVDGDVFVIATSP 257
                                   36789************9875.6789999******87 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.9e-05     0.038       2      33 ..       5      36 ..       4      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDide 33
                                  +i+++G G+ Gl+ +a+lae+g +v+++  ++
  gi|70607009|ref|YP_255879.1|  5 RIVIVGGGHNGLILSALLAEQGAKVTLLEANS 36
                                  8*************************998886 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.24       6      39 ..       2      35 ..       1     105 [. 0.86
   2 ?   -1.4   0.1       3.3   3.3e+03      14      39 ..     201     226 ..     198     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                 NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvape 39
                                  ++k++++vGgG  ++     l+e+gakvt++  +
  gi|70607009|ref|YP_255879.1|  2 STKRIVIVGGGHNGLILSALLAEQGAKVTLLEAN 35
                                  789**************************98766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                 NAD_binding_7  14 GgGevAarkvrklleagakvtvvape 39 
                                   G G+v ++ ++  +++g +v v ++ 
  gi|70607009|ref|YP_255879.1| 201 GMGTVSQKIAEYAIDKGVEVRVNSKV 226
                                   66777777777777777777776654 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00012      0.12       1      34 [.       5      35 ..       5      39 .. 0.93
   2 ?    2.0   0.6     0.077        76     158     204 ..     207     252 ..     202     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  +ivivGGG  G +  a+la+++   ++vtl+e++
  gi|70607009|ref|YP_255879.1|  5 RIVIVGGGHNGLILSALLAEQG---AKVTLLEAN 35
                                  69********************...89****986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.077
                                   HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEE CS
                Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfi 204
                                   + + ++a ++Gv+++    ve  +  d++v ++r+   ++v++d f+
  gi|70607009|ref|YP_255879.1| 207 QKIAEYAIDKGVEVRVNSKVEELIVRDDKVVGVRM-GNTVVDGDVFV 252
                                   667899*******999988888889999*******.77889999998 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00029      0.28       2      17 ..     326     341 ..     325     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHHSTTS-H CS
                           CUE   2 eqmletLkemFPdlde 17 
                                   + +le+L++mFPdl +
  gi|70607009|ref|YP_255879.1| 326 MADLEDLYQMFPDLKS 341
                                   5789*********965 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0059       5.9       2      33 ..       6      37 ..       5      53 .. 0.90
   2 ?    5.2   0.2     0.018        18       6      38 ..     201     233 ..     200     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0059
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                  + ++G G  G  + a++a++g +V+l++ +++
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALLAEQGAKVTLLEANSK 37
                                  789************************98765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                                   --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                       3HCDH_N   6 GaGtmGagiaavfasagleVvlvdiseealeka 38 
                                   G Gt+ ++ia+ ++ +g+eV++    ee + + 
  gi|70607009|ref|YP_255879.1| 201 GMGTVSQKIAEYAIDKGVEVRVNSKVEELIVRD 233
                                   89*******************998877766655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00028      0.27       2      36 ..       6      38 ..       5      53 .. 0.93
   2 ?   -3.9   0.0       5.4   5.4e+03     219     234 ..     207     222 ..     204     255 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                 Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  +v++G+G  gl l a l  a++g kv+l+ea  +l
  gi|70607009|ref|YP_255879.1|  6 IVIVGGGHNGLILSALL--AEQGAKVTLLEANSKL 38
                                  79***************..9**********98775 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.4
                 Lycopene_cycl 219 krlaaylralglkvke 234
                                   +++a+y+ ++g++v+ 
  gi|70607009|ref|YP_255879.1| 207 QKIAEYAIDKGVEVRV 222
                                   4555555555555442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2862.17
//
Query:       gi|70607010|ref|YP_255880.1|  [L=140]
Description: thioesterase superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-15   56.7   0.1    3.3e-15   56.2   0.1    1.2  1  4HBT      Thioesterase superfamily
  ------ inclusion threshold ------
      0.025   14.8   0.0      0.029   14.6   0.0    1.1  1  4HBT_3    Thioesterase-like superfamily
      0.072   13.2   0.0      0.092   12.9   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.1   5.6e-19   3.3e-15       1      78 [.      53     128 ..      53     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 5.6e-19
                                   TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                          4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                   gG++hgGv+++ lD ++g+a ++ + +    v+ el+++fl +++ g ++ + ++v+r+g+t++vv+  ++d +++l+
  gi|70607010|ref|YP_255880.1|  53 GGILHGGVIMTVLDYTGGIATMTVNEG-FNQVTQELKVNFLEAMKDG-PFKCIGKVIRAGKTTVVVDLSLYDANNVLG 128
                                   69************************8.*******************.************************998876 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.9e-06     0.029      11      73 ..      55     124 ..      47     140 .] 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                                   ..-HHHHHHHHHHHHH...HT.-S.SS....EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEETT CS
                        4HBT_3  11 g.yGGyvlAlalraaq...rtvpdprl....hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsqgg 73 
                                   + +GG+++ ++         tv + ++      l v+Fl + + gp+ +  +++r G+++ ++  +l+   
  gi|70607010|ref|YP_255880.1|  55 IlHGGVIMTVLDYTGGiatMTVNE-GFnqvtQELKVNFLEAMKDGPFKCIGKVIRAGKTTVVVDLSLYDAN 124
                                   338888888876654432244544.34444689******************************99998754 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.092      19     130 ..      27     135 ..      20     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                   G--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-.--S-EEEEEE- CS
                       DUF4442  19 vgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak.atgdltavael 98 
                                   +g+++ ++++g+ae ++    +v    g +H++ i+++++ + G +a+ t+ ++   + +  +v++l+  ++g  +++ ++
  gi|70607010|ref|YP_255880.1|  27 IGLKVVKVSKGYAETTFDYSENVTRLGGILHGGVIMTVLDYTGG-IATMTVNEGFNQVTQELKVNFLEAmKDGPFKCIGKV 106
                                   78899*******************99999***********9876.67789****************9876899****9887 PP

                                   TTS-TT--EEEEEEEEEEETTE.EEEEEEEEE CS
                       DUF4442  99 epedvgekeelvvevevrdekgeevvraeitl 130
                                    ++    k+++vv+ +++d+++   ++a  t+
  gi|70607010|ref|YP_255880.1| 107 IRA---GKTTVVVDLSLYDANNVLGAKALGTW 135
                                   654...36789999999999987777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1070.19
//
Query:       gi|70607011|ref|YP_255881.1|  [L=115]
Description: Lrs14 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-11   41.9   0.1    9.2e-11   41.5   0.1    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
      2e-07   30.8   0.9    3.2e-07   30.2   0.9    1.4  1  MarR             MarR family
    4.8e-07   29.6   0.3    8.7e-07   28.8   0.3    1.4  1  HTH_11           HTH domain
    5.9e-07   29.9   0.1    8.6e-07   29.4   0.1    1.2  1  HTH_27           Winged helix DNA-binding domain
    6.9e-06   25.9   0.6    8.2e-06   25.6   0.6    1.3  1  TFIIE_alpha      TFIIE alpha subunit
    2.5e-05   24.1   0.1    3.8e-05   23.5   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    3.1e-05   23.6   0.1      4e-05   23.3   0.1    1.1  1  SMC_ScpB         Segregation and condensation complex subunit
    5.7e-05   22.9   0.0    7.7e-05   22.5   0.0    1.2  1  MarR_2           MarR family
    7.1e-05   22.7   0.0    0.00011   22.1   0.0    1.3  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    9.5e-05   22.0   0.0    0.00019   21.0   0.0    1.4  1  GntR             Bacterial regulatory proteins, gntR family
    0.00011   22.4   0.3     0.0002   21.5   0.2    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00058   19.6   0.1    0.00064   19.5   0.1    1.2  1  DUF4423          Domain of unknown function (DUF4423)
    0.00068   20.2   0.1     0.0018   18.8   0.1    1.7  1  Phage_rep_O      Bacteriophage replication protein O
    0.00072   19.1   0.2     0.0014   18.2   0.2    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00075   19.4   0.1     0.0012   18.8   0.1    1.3  1  PadR             Transcriptional regulator PadR-like family
      0.001   18.8   0.2     0.0018   18.0   0.2    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.005   17.2   0.0     0.0085   16.4   0.0    1.3  1  Rrf2             Transcriptional regulator
      0.006   15.6   0.1     0.0067   15.4   0.1    1.0  1  Tfb2             Transcription factor Tfb2
  ------ inclusion threshold ------
      0.012   15.2   0.2       0.02   14.5   0.2    1.4  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.012   15.6   0.0      0.019   15.0   0.0    1.2  1  HTH_20           Helix-turn-helix domain
      0.016   15.3   0.1      0.022   14.9   0.1    1.4  1  DUF2250          Uncharacterized protein conserved in archaea
      0.027   14.0   0.3      0.036   13.7   0.3    1.2  1  DDRGK            DDRGK domain
      0.032   14.1   0.5      0.056   13.3   0.5    1.4  1  RuvB_C           RuvB C-terminal winged helix domain
      0.034   13.8   0.0      0.044   13.4   0.0    1.3  1  RP-C             Replication protein C N-terminal domain
      0.044   13.7   0.0      0.086   12.8   0.0    1.5  1  HTH_36           Helix-turn-helix domain
      0.052   13.7   0.1      0.091   12.9   0.1    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.056   13.3   0.0       0.12   12.2   0.0    1.5  1  HTH_10           HTH DNA binding domain
       0.06   13.5   0.1      0.091   12.9   0.1    1.4  1  HTH_34           Winged helix DNA-binding domain
      0.066   13.6   0.4      0.096   13.0   0.4    1.5  1  Penicillinase_R  Penicillinase repressor
      0.068   13.2   0.0        0.1   12.7   0.0    1.4  1  FeoC             FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.1   1.5e-13   9.2e-11       3      63 ..      16      83 ..      13      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.5e-13
                                  HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEEE CS
                          TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklYr 63
                                  ++ +s++++++ l+L+  ++p t +e++ + +v+++++ ++L++L+d Gl++rek++      pk+Y 
  gi|70607011|ref|YP_255881.1| 16 CYKISDTDVDCLLKLIeLRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKKTdkrigrPKYYY 83
                                  6889************8899***********************************9999999877665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.9   5.3e-10   3.2e-07       8      57 ..      27      75 ..      19      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 5.3e-10
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTT CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrR 57
                                  +L +++ + p++  eL ++++vsk+t+ + l++L + Gli+R+k+  D+R
  gi|70607011|ref|YP_255881.1| 27 LLKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKK-TDKR 75
                                  45666777889999******************************9.7888 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3   1.5e-09   8.7e-07       7      43 ..      28      64 ..      25      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                        HTH_11  7 elLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                    L+e r+pi++eeL++ ++vS++t+ + +k+L ++g
  gi|70607011|ref|YP_255881.1| 28 LKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIG 64
                                  4566*****************************9988 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.4e-09   8.6e-07       7      61 ..      26      78 ..      22      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.4e-09
                        HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                  ++L li+  r + + ++l+++++v++++i +slkkL   GL++r+++ +d+r  r
  gi|70607011|ref|YP_255881.1| 26 CLLKLIE-LRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKK-TDKRIGR 78
                                  8899999.5555555***************************77777.8999765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.6   1.4e-08   8.2e-06       4      76 ..      10      85 ..       7     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-08
                                  HHHHHHCS-HHHHHH...HHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEE CS
                   TFIIE_alpha  4 kevvrkfygeeavlv...ldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywri 76
                                  kev+r  y ++   v   l+ +  +  +t e+l+  +k+ ++ + + L +L +++l+   ++ d  ++  kyy+ +
  gi|70607011|ref|YP_255881.1| 10 KEVIRCCYKISDTDVdclLKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKKTDKRIGRPKYYYTL 85
                                  6788877774444332226666678889**********************************************74 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   6.3e-08   3.8e-05       9      46 ..      28      67 ..      22      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.3e-08
                                  HHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  9 klLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                    L e  ++ ++ el++++++s+ t+   LkkL++ GL++
  gi|70607011|ref|YP_255881.1| 28 LKLIElrKPITSEELSDMMKVSKTTIENSLKKLMDIGLIT 67
                                  4555567899****************************96 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   6.7e-08     4e-05      89     141 ..      28      84 ..      17      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.7e-08
                      SMC_ScpB  89 LaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrkee.pgrpilYgt 141
                                   L +I +++p+t++e++++  v+    ++ +++L++ gli++++++++  grp  Y t
  gi|70607011|ref|YP_255881.1|  28 LKLIELRKPITSEELSDMMKVSkttIENSLKKLMDIGLITREKKTDKrIGRPKYYYT 84 
                                   789**************999874446789**********9988877769****9987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.3e-07   7.7e-05      12      61 ..      29      75 ..      20      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.3e-07
                                  HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                    +  r +  +t  el + +++sk ++ + lk+L + GL++r++  +DkR
  gi|70607011|ref|YP_255881.1| 29 KLIELRKP--ITSEELSDMMKVSKTTIENSLKKLMDIGLITREK-KTDKR 75
                                  55667777..9*******************************96.47999 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.8e-07   0.00011      18      55 ..      33      70 ..      14      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-07
                                  EEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilseLkreglisrgr 55
                                  ++ p+t eel++m+ ++  t+   l++L + gli+r++
  gi|70607011|ref|YP_255881.1| 33 LRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREK 70
                                  3459*******************************642 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.2e-07   0.00019      24      58 ..      37      70 ..      29      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-07
                                  ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrq 58
                                  + + +eL+++++Vs+tt+  +L++L   gl++r++
  gi|70607011|ref|YP_255881.1| 37 I-TSEELSDMMKVSKTTIENSLKKLMDIGLITREK 70
                                  5.779****************************97 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   3.3e-07    0.0002      14      57 ..      28      71 ..      24      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.3e-07
                                  HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57
                                  ++l e +k+++  +l+  ++vs+ ++  +lkkL + G++  ek+
  gi|70607011|ref|YP_255881.1| 28 LKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKK 71
                                  57888999******************************998886 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.1e-06   0.00064      25      79 ..      26      72 ..      17     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                       DUF4423 25 virellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqt 79
                                  ++++l++l++   + eel+++++  +s+  +e++l+ L+++gl++++++     t
  gi|70607011|ref|YP_255881.1| 26 CLLKLIELRKP-ITSEELSDMMK--VSKTTIENSLKKLMDIGLITREKK-----T 72
                                  67889999999.9**********..*********************997.....3 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1     3e-06    0.0018      48      89 ..      35      79 ..      32      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3e-06
                   Phage_rep_O 48 dwisnsqlveltgisrtkvskalkeLirekviikeg...rkvgvn 89
                                  ++i+ ++l++++++s+t +++ lk+L++ + i++e+   +++g+ 
  gi|70607011|ref|YP_255881.1| 35 KPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKktdKRIGRP 79
                                  6899******************************99777777765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.3e-06    0.0014       9      48 .]      28      67 ..      27      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                        HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  L+l++    i+  eL+++  +S++t+   lk+L++ GlI+
  gi|70607011|ref|YP_255881.1| 28 LKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLIT 67
                                  6666666789****************************96 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1     2e-06    0.0012      21      65 ..      40      85 ..      31      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
                                  CCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEE CS
                          PadR 21 elsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrl 65
                                  e ++ ++++s++++   Lk+L + gl+++e++++ + g+p+ yY+l
  gi|70607011|ref|YP_255881.1| 40 EELSDMMKVSKTTIENSLKKLMDIGLITREKKTDkRIGRPKYYYTL 85
                                  3446789*************************99788999999987 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     3e-06    0.0018       5      46 ..      27      68 ..      24      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                      HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  +l+l++ +  ++ eel++  +vS++Ti + L++L   gl+tR
  gi|70607011|ref|YP_255881.1| 27 LLKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITR 68
                                  79999999*********************************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-05    0.0085      15      56 ..      28      67 ..      20      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
                                  HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  l L +   ++p++see+++++++s++ +e  l+kL   gl++
  gi|70607011|ref|YP_255881.1| 28 LKLIEL--RKPITSEELSDMMKVSKTTIENSLKKLMDIGLIT 67
                                  444444..458*****************************97 PP

>> Tfb2  Transcription factor Tfb2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.1e-05    0.0067      35     106 ..      26     101 ..      10     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                          Tfb2  35 lvmrllylekpvplsdlekwvkkeskkekeealkkLkelhilkekk.....lkekk.qelklnptFkkslrkaltggg 106
                                   ++++l+ l+kp++ ++l++++k + k + e++lkkL ++ +++ +k        ++   ++l  +F++++r+ l++ +
  gi|70607011|ref|YP_255881.1|  26 CLLKLIELRKPITSEELSDMMKVS-KTTIENSLKKLMDIGLITREKktdkrI-GRPkYYYTLIINFEDKMRNDLLNCS 101
                                   6789999*************9987.7999*************9988555532.223368999999*****99998765 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.4e-05      0.02       4      54 ..      21      67 ..      18      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                  HrcA_DNA-bdg  4 svqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                  ++  + l +Liel    ++++ +ee+ +++k  + t+ N l+ L  +gL+ 
  gi|70607011|ref|YP_255881.1| 21 DTDVDCLLKLIEL----RKPITSEELSDMMKVSKTTIENSLKKLMDIGLIT 67
                                  5566777777777....579*****************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.1e-05     0.019      20      58 ..      32      70 ..      27      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                                  STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                        HTH_20 20 araegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                    +++ t +el + + +sk+t+ + L++L + gL+++++
  gi|70607011|ref|YP_255881.1| 32 ELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREK 70
                                  5599********************************987 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.6e-05     0.022      25      57 ..      39      71 ..      17      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                       DUF2250 25 aksiakeleipleevrellkkLeelGLlerveg 57
                                  +  ++++++++++ +++ lkkL+++GL++r ++
  gi|70607011|ref|YP_255881.1| 39 SEELSDMMKVSKTTIENSLKKLMDIGLITREKK 71
                                  56788999********************99875 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   6.1e-05     0.036      99     144 ..      22      67 ..       3      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                                   XHHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS- CS
                         DDRGK  99 klleefinyikekKvvlleelavkfklktqevierikeLeeqgslt 144
                                     ++++++ i+++K ++ eel+  +k++ + + + +k+L++ g +t
  gi|70607011|ref|YP_255881.1|  22 TDVDCLLKLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLIT 67 
                                   4799************************************999886 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   9.3e-05     0.056       5      59 ..      20      71 ..      17      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
                                  -HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETT CS
                        RuvB_C  5 deldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsr 59
                                  +++d+++L  l+e    +p+  + l+ +++++k+tie+     L+ +glI+r ++
  gi|70607011|ref|YP_255881.1| 20 SDTDVDCLLKLIE--LRKPITSEELSDMMKVSKTTIENSLK-KLMDIGLITREKK 71
                                  6899999999998..79********************9995.799*****99987 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.3e-05     0.044      75     113 ..      40      77 ..      14      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                          RP-C  75 aqLsralglsestlrrhlaaLveaGliirrDspngkRya 113
                                   ++Ls  +++s++t+++ l++L++ Gli+r    + kR +
  gi|70607011|ref|YP_255881.1|  40 EELSDMMKVSKTTIENSLKKLMDIGLITRE-KKTDKRIG 77 
                                   7899999*******************9864.56667765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.086      30      55 .]      41      66 ..      35      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                        HTH_36 30 tlakrlglsknTvsraikeLeqlGyi 55
                                   l+  +++sk T+ + +k+L++ G+i
  gi|70607011|ref|YP_255881.1| 41 ELSDMMKVSKTTIENSLKKLMDIGLI 66
                                  577779******************98 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.091      19      52 ..      37      70 ..      34      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqs 52
                                  it+ +L+  +k ++  +   lk+L+++gLI++ +
  gi|70607011|ref|YP_255881.1| 37 ITSEELSDMMKVSKTTIENSLKKLMDIGLITREK 70
                                  68999**************************986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.12      22      46 ..      35      59 ..      32      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                        HTH_10 22 RrvtlkeLAkelGIskstlsehLrk 46
                                  + +t++eL++ + +sk+t+++ L+k
  gi|70607011|ref|YP_255881.1| 35 KPITSEELSDMMKVSKTTIENSLKK 59
                                  56899******************98 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.091      14      55 ..      36      77 ..      24      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                        HTH_34 14 eadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkp 55
                                   ++ +el++ +++++  +   lkkL + g i+++k+ +++  
  gi|70607011|ref|YP_255881.1| 36 PITSEELSDMMKVSKTTIENSLKKLMDIGLITREKKTDKRIG 77
                                  567899******************************998864 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   0.00016     0.096      25      61 ..      40      76 ..      26     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                  HT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEE CS
               Penicillinase_R 25 eeleeekelaysTVktllrrLvkKgllsrekegrafi 61
                                  eel++ ++++++T+   l++L++ gl++rek+  + i
  gi|70607011|ref|YP_255881.1| 40 EELSDMMKVSKTTIENSLKKLMDIGLITREKKTDKRI 76
                                  57999999**********************9865543 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017       0.1       7      50 ..      29      72 ..      14      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                          FeoC  7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                  +++e r+ +  +eLs  +k+s++++e  L  ++  G ++++++t
  gi|70607011|ref|YP_255881.1| 29 KLIELRKPITSEELSDMMKVSKTTIENSLKKLMDIGLITREKKT 72
                                  56899*********************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 765.96
//
Query:       gi|70607012|ref|YP_255882.1|  [L=200]
Description: hypothetical protein Saci_1243 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.038   13.7   0.8        1.6    8.5   0.1    2.5  2  L27           L27 domain
       0.11   12.6   0.8       0.47   10.6   0.3    2.4  3  Fis1_TPR_C    Fis1 C-terminal tetratricopeptide repeat
       0.13   12.7   3.3       0.23   12.0   3.3    1.4  1  AAA_23        AAA domain
       0.63    9.1   4.0       0.18   10.9   0.6    1.7  2  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> L27  L27 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.015        69       3      31 ..      84     119 ..      84     133 .. 0.79
   2 ?    8.5   0.1   0.00036       1.6       4      29 ..     149     174 ..     146     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
                           L27   3 ralelLedLqsl.......sdvnedlaeLqkvLqsp 31 
                                   r++e L +L++         d +  ++eL+k+    
  gi|70607012|ref|YP_255882.1|  84 RLVEYLKELSKKkdeilkiEDKSKQAEELRKLIGRG 119
                                   6778888888888888886677799******97665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00036
                           L27   4 alelLedLqslsdvnedlaeLqkvLq 29 
                                   ++++Le+L + ++ ++ ++eL ++L+
  gi|70607012|ref|YP_255882.1| 149 LVDVLEKLAKMVEIPYSKEELDNILK 174
                                   79*********************995 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.89     4e+03      17      31 ..      65      79 ..      64      96 .. 0.58
   2 ?   10.6   0.3   0.00011      0.47      25      44 ..      97     116 ..      72     119 .. 0.88
   3 ?   -2.3   0.0       1.1   4.7e+03      16      27 ..     141     152 ..     139     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.89
                                  HHHHHHHHHHHHHHT CS
                    Fis1_TPR_C 17 YseArryvdalLeiE 31
                                  Y  ++   d lL +E
  gi|70607012|ref|YP_255882.1| 65 YIASKTVRDSLLTLE 79
                                  666666666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                                   HHHHHHTTS-HHHHHHHHHH CS
                    Fis1_TPR_C  25 dalLeiEPenrQaqsLkeli 44 
                                   d +L+iE + +Qa++L++li
  gi|70607012|ref|YP_255882.1|  97 DEILKIEDKSKQAEELRKLI 116
                                   789***************99 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.1
                                   -HHHHHHHHHHH CS
                    Fis1_TPR_C  16 eYseArryvdal 27 
                                   eY eA++ +  +
  gi|70607012|ref|YP_255882.1| 141 EYIEALQPLVDV 152
                                   899998865555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.3   5.1e-05      0.23      77     195 ..      47     179 ..       9     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                        AAA_23  77 ltfenkdgrytrsiererelskkkgkttkka.klelleideleqfisellgskkiilnlilflgqer.........feefe 147
                                     f  ++g+  +++    e+++  +kt++++  + ++++  l ++++el ++k++il++ +  +q +         f    
  gi|70607012|ref|YP_255882.1|  47 NLF--IKGDV-VIVNTGGEVRYIASKTVRDSlLTLEIQKVRLVEYLKELSKKKDEILKIEDKSKQAEelrkligrgF---- 120
                                   333..33331.445445555555555555553444566688899999999999999988888777774444444440.... PP

                        AAA_23 148 l...........kdkkerleelekeleeledekkllekleqekekekeleeleeeleei 195
                                               k+++  + e++++l+ l d+ ++l k  ++   ++el+++ + +e++
  gi|70607012|ref|YP_255882.1| 121 VliatgllslyeKRPETTIPEYIEALQPLVDVLEKLAKMVEIPYSKEELDNILKLIEKY 179
                                   044444445555777789***************99999988888888999998888887 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       0.3   1.4e+03     198     213 ..      96     111 ..      75     117 .. 0.58
   2 ?   10.9   0.6     4e-05      0.18     166     219 ..     137     190 ..     125     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.3
                                   HHHHHTHSSSS...HH CS
                  NAD_synthase 198 lDeiLklvekkkspee 213
                                    DeiLk+ +k k+ ee
  gi|70607012|ref|YP_255882.1|  96 KDEILKIEDKSKQAEE 111
                                   3555554444444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4e-05
                                   TT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT CS
                  NAD_synthase 166 lnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikeke 219
                                     +Pe +   +P  d  ++++   e++++ +elD+iLkl+ek + +++    k+
  gi|70607012|ref|YP_255882.1| 137 TTIPEYIEALQPLVDVLEKLAKMVEIPYSKEELDNILKLIEKYRGEKDYQIMKD 190
                                   5699999999*******************************9887776544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1438.20
//
Query:       gi|70607013|ref|YP_255883.1|  [L=322]
Description: GHMP kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-15   55.5   0.1    1.4e-14   54.0   0.1    1.8  1  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0005   20.4   0.1     0.0016   18.8   0.0    1.9  2  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.078   12.8   0.5       0.12   12.2   0.5    1.3  1  PCRF            PCRF domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.1   2.4e-18   1.4e-14      11      66 .]      96     154 ..      88     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.4e-18
                                   TSSSCHHHHHHHHHHHHHHHHTTEH..HHH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N  11 gaGLGSSAAlavalvaAllallgls..lee.aklaleaerlaqggngsggDvaasvyGg 66 
                                   ++GLGSS+A +val+a+l+al + +  l+e +k++++a  + q+g gsg+D+a++vyG+
  gi|70607013|ref|YP_255883.1|  96 KTGLGSSSASTVALTACLYALVNENvdLNEiHKISQVANYQRQRGIGSGFDIATAVYGS 154
                                   79********************766436557**************************95 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.6   1.6e+04       5      18 ..     200     213 ..     197     218 .. 0.77
   2 !   18.8   0.0   2.6e-07    0.0016      10      80 ..     238     302 ..     222     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.6
                GHMP_kinases_C   5 lergdlellgelln 18 
                                   +e++dle +++++ 
  gi|70607013|ref|YP_255883.1| 200 VEKRDLEQFKQMMK 213
                                   56788888888885 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.6e-07
                GHMP_kinases_C  10 lellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralr 80 
                                   l+l + +l +++  e++  v+i+++   el +++++++al a  +Ga gG +vfa++ d ++   v+++++
  gi|70607013|ref|YP_255883.1| 238 LKLSRLMLEQLA--ENVVGVKIENEKTIELRRIAEKYDALIAMSPGA-GGESVFAIGYDLSR---VIEEWK 302
                                   444444455444..5899*****************************.9********55555...888774 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   2.1e-05      0.12      41     134 ..     205     307 ..     180     319 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHTTTHHH...HT.......-S-..-GG......GTHHHHHHHHHH..HHHHHT-..SSSTTSEEEEEEEE-SSTH CS
                          PCRF  41 leeleealedleeakell.e..edeelaelaee......eleelekeleeleeelkklLlpkdendeknaileiraGaGGd 112
                                   le+++++++ +++ ++++ +  +d++l++ +e+       le+l++++  ++ e +k +  +  +++ +a++ +++GaGG+
  gi|70607013|ref|YP_255883.1| 205 LEQFKQMMKYIDAENSFAiKllKDNKLEQAVEHlklsrlMLEQLAENVVGVKIENEKTIELRRIAEKYDALIAMSPGAGGE 285
                                   44555555555544444333458888887766655544349999999999888888888888999999************* PP

                                   HHHHHHHHHHHHHHHHHHTTT- CS
                          PCRF 113 eaalfaedLlrmYtryaerkgw 134
                                          dL r+ +++ + kg 
  gi|70607013|ref|YP_255883.1| 286 SVFAIGYDLSRVIEEWKKIKGI 307
                                   9999999999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2178.19
//
Query:       gi|70607014|ref|YP_255884.1|  [L=325]
Description: diphosphomevalonate decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-33  115.2   0.1    1.6e-31  109.5   0.0    2.2  2  MDD_C            Mevalonate 5-diphosphate decarboxylase C-ter
    8.3e-08   32.4   1.4    1.8e-07   31.3   1.4    1.6  1  GHMP_kinases_N   GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.051   13.2   0.2        0.2   11.3   0.1    1.9  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> MDD_C  Mevalonate 5-diphosphate decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   2.6e-35   1.6e-31       3     132 ..     183     305 ..     181     307 .. 0.96
   2 !    4.0   0.0     0.006        36     171     187 .]     307     323 ..     304     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 2.6e-35
                         MDD_C   3 ilvvsdekkkvsStsGmqrsvetSeLlkhrakevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYlnd 83 
                                   i  ++ ++kkvsS +Gm++++ +S+L++ r+k  +++ +  + ++ik+kd ++f   tm+ Sn++hav ld++P+ fYlnd
  gi|70607014|ref|YP_255884.1| 183 IPLIQLKEKKVSSRKGMKNTALSSSLMECRLKF-IEDTLPLVIDSIKKKDEKEFYYWTMRHSNSMHAVILDSWPSFFYLND 262
                                   6678889************************87.9********************************************** PP

                         MDD_C  84 tSraiielvhelNeaagkikvAYtFDAGpNavlyleekdveellsllkk 132
                                   tS +i+e ++e+       ++AYtFDAGpN  +++++k+++e++++l++
  gi|70607014|ref|YP_255884.1| 263 TSFKIMEWIQEFG------NAAYTFDAGPNPHIFTTKKHLDEITQYLNS 305
                                   ************8......79***********************99986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.006
                         MDD_C 171 avkriiltkvgdGpkvl 187
                                    +k+ i+tkvg+Gp+v+
  gi|70607014|ref|YP_255884.1| 307 GIKDYIITKVGRGPRVI 323
                                   6999**********986 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   1.4     3e-11   1.8e-07       2      48 ..      93     142 ..      92     151 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3e-11
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHH CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerl 48 
                                   ++++ ++P + GL+SSAA ++alv+Al+++lgl l+     k+a  +   
  gi|70607014|ref|YP_255884.1|  93 VESYMNFPKSVGLASSAAGIAALVYALNDALGLGLSQrelSKIARIGSGS 142
                                   678889*************************9665221234444443333 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.19   1.1e+03     199     233 ..      65      99 ..      36     109 .. 0.61
   2 ?   11.3   0.1   3.4e-05       0.2      74     162 ..     228     308 ..     201     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.19
                                   GGG.CS-HHHHHHHHHHHHHH..HHTT-EEEEEEES CS
               MethyltransfD12 199 yetlafsdedevrlaevlksls.skfgvkvllsnsf 233
                                   + ++ f++    r ++++++l  +kf+vkv+ +++f
  gi|70607014|ref|YP_255884.1|  65 LREEEFEEYGG-RVINIFRELYgKKFSVKVESYMNF 99 
                                   33334444433.445555555456666666666555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.4e-05
                                   H.TCTTGGC.TSHHHHHHHHHHHH...HHH-HHHH..HHHHHHHHCCBGGG---B-TTS-B---B-S-SS-.....HHHHH CS
               MethyltransfD12  74 ekllekeelenereyfyelreefnkkidaireaee..aidflylnrllfsglervnkkgnfnvpygaykkp.kkvaekelk 151
                                   +       +++e+e++y + +  n    ++  ++     +f+yln + f+ +e +++ gn + +++a  +p  ++ +k l+
  gi|70607014|ref|YP_255884.1| 228 K-------KKDEKEFYYWTMRHSN----SMHAVILdsWPSFFYLNDTSFKIMEWIQEFGNAAYTFDAGPNPhIFTTKKHLD 297
                                   2.......2367777777777888....444444445567*******************************8888899999 PP

                                   HHHHHHHHCCE CS
               MethyltransfD12 152 lrseklknaki 162
                                   +++++l++  i
  gi|70607014|ref|YP_255884.1| 298 EITQYLNSIGI 308
                                   99999998555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2609.28
//
Query:       gi|70607015|ref|YP_255885.1|  [L=398]
Description: hypothetical protein Saci_1246 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   54.0   0.1    4.8e-14   52.6   0.0    1.8  2  HD        HD domain
     0.0023   17.4   0.0     0.0042   16.6   0.0    1.5  1  HDOD      HDOD domain
  ------ inclusion threshold ------
      0.074   12.8   0.0       0.15   11.7   0.0    1.5  1  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0     8e-18   4.8e-14       1      95 [.      50     152 ..      50     189 .. 0.74
   2 ?   -3.0   0.0       1.3   8.1e+03      83      96 ..     330     343 ..     316     375 .. 0.48

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 8e-18
                                   HHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHTTTTHHHHTS..HHH.........HHH...CTCCHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlge....eedrellllaaLlHDiGkgpfgdafekk.........eee...fekflaHekvgae 65 
                                   r+eHsl+V++la+++a+ ++     +  + l+++a+LlHDiG+  f+++fe +           +   +e+ + H+k+g++
  gi|70607015|ref|YP_255885.1|  50 RFEHSLGVMQLAGEFARFVKPpfftPGYERLVKIAGLLHDIGHLAFSHTFESAlqvaneiygV-KdvfYEGKKTHVKIGVK 129
                                   79***************887799**9999************************9887655541.1678999999******9 PP

                                   HHHHHHHHHHHHHHHHHHHHHTTCCHHHHH CS
                            HD  66 ilrevekrlgldledvaklirehheswegk 95 
                                   i++e++ +        +++i+  + s ++k
  gi|70607015|ref|YP_255885.1| 130 IIQENLSSI-------LEAIKDSTISDPIK 152
                                   999996555.......66666655555544 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                                   HHHHTTCCHHHHHH CS
                            HD  83 klirehheswegkk 96 
                                   k+i + +++ + k+
  gi|70607015|ref|YP_255885.1| 330 KIIYHEFFDVPYKE 343
                                   44444444444222 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     7e-07    0.0042      96     150 ..      51     110 ..      17     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7e-07
                                   HHHHHHHHHHHHHHHHHTT-S-.H....HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHH CS
                          HDOD  96 wehslavAlvarelaeelgled.p....eeaflaGLLhdiGklvllsllpeeleellekv 150
                                    ehsl v  +a e a+ ++ +  +      + +aGLLhdiG l++ ++++  l+  +e +
  gi|70607015|ref|YP_255885.1|  51 FEHSLGVMQLAGEFARFVKPPFfTpgyeRLVKIAGLLHDIGHLAFSHTFESALQVANEIY 110
                                   578888888888888888554421344346779******************999888765 PP

>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.5e-05      0.15       4      99 ..      51     147 ..      49     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT--S--HHHHHHCT-HHHHHCCCSSHH...HHHHHHHHHH CS
                      PDEase_I   4 frHAadVlqalfyllkkeklkeeltpleilalliaalcHDvdHpGtnNsFlvnskselailYndesvL...EnhHlalafq 81 
                                   f H++ V+q    + +  k    +tp  +  + ia+l HD++H  ++ +F+   +    ++Y  + v     + H+++ ++
  gi|70607015|ref|YP_255885.1|  51 FEHSLGVMQLAGEFARFVKPP-FFTPGYERLVKIAGLLHDIGHLAFSHTFESALQ-VANEIYGVKDVFyegKKTHVKIGVK 129
                                   567777777777777655543.58888899999******************9997.4567888888763334789****** PP

                                   HHTSGGG-TTTTS-HHHH CS
                      PDEase_I  82 llkkeecnifknlskeey 99 
                                   +++++ ++i++ +++++ 
  gi|70607015|ref|YP_255885.1| 130 IIQENLSSILEAIKDSTI 147
                                   **9999999999976663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2816.61
//
Query:       gi|70607016|ref|YP_255886.1|  [L=236]
Description: 5'-methylthioadenosine phosphorylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.4e-38  129.8   0.0    1.2e-37  129.4   0.0    1.1  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   0.0   6.6e-42   1.2e-37       2     213 ..      16     221 ..      15     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 6.6e-42
                                   EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEES CS
                     PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGgl 82 
                                   ++ii+g+pg+v+ +a+  l++++  +e+rgf ++tG++kg  ++++++GiG p++a +   +l++ +  k+++r+Gt G+l
  gi|70607016|ref|YP_255886.1|  16 RVIIAGDPGRVRYIAKF-LDDVRTVNENRGFLVYTGKYKGIDISVATHGIGGPSIA-IVLEELIMLG-GKTFVRFGTTGAL 93 
                                   79***************.**************************************.6666666644.7************ PP

                                   STTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHHH CS
                     PNP_UDP_1  83 npdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteaelr 163
                                    +d+++GD ++ + a +      + ++       ++ +++ +d el ++l ++ + +  k+h+G v ++d fyae ++ ++
  gi|70607016|ref|YP_255886.1|  94 ASDIEIGDYILVSGASYNPSSIVYQYF----KENVCISAT-PDFELSSALYNSFKNRKLKFHVGNVFSSDAFYAEDAEFAK 169
                                   **************8774444443333....334455555.566777777776777********************99999 PP

                                   HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTB..ETTCTCH.HC CS
                     PNP_UDP_1 164 llrrlgadaveMEtaavaqlArelgipfaairvvsdlaag..gadaeathee 213
                                    + + g  aveME++ +++l+r+++++ +a+ vvsd++++  + ++e+  + 
  gi|70607016|ref|YP_255886.1| 170 KWYERGNIAVEMECSTLFILSRLRKVRSGAVLVVSDNLVKggWISKEELENK 221
                                   9999999*****************************9998444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1804.05
//
Query:       gi|70607017|ref|YP_255887.1|  [L=65]
Description: hypothetical protein Saci_1248 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 457.20
//
Query:       gi|70607018|ref|YP_255888.1|  [L=444]
Description: gylcosyl transferase group 1 protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-37  128.0   0.2    4.9e-37  127.1   0.2    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    4.8e-24   85.3   0.1    7.6e-24   84.7   0.1    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-05   25.5   0.0    2.7e-05   24.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    6.8e-05   21.7   0.8      0.014   14.1   0.1    2.2  2  Glyco_transf_20  Glycosyltransferase family 20
     0.0082   16.3   0.2       0.14   12.3   0.1    2.7  3  RRM_2            RNA recognition motif 2


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.2   1.4e-40   4.9e-37       3     167 ..     238     412 ..     236     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 1.4e-40
                                   HHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..............STTHHHHHHHHHHHC CS
               Glycos_transf_1   3 ekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.............ngeeekelkklaeele 70 
                                   +k + k+++ +++k+i +v+r++++K +d++i a++++k   ++n+kl+++G              g++  +l++la +l+
  gi|70607018|ref|YP_255888.1| 238 DKVKSKYNIGKDEKVITVVARMDPMKSQDVAIMALKKIK---ESNAKLLLVGngsftsgalgtnkAGNWVRKLQSLASNLG 315
                                   6788999*******************************7...68************************************* PP

                                   TTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
               Glycos_transf_1  71 lsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaea 151
                                   + ++v f+g+vs+e+l ++++++d++vlps+ EgfG+v+ E   + +p+i+s   g++e+v dg +G+++k++n e+lae+
  gi|70607018|ref|YP_255888.1| 316 VDKKVVFTGHVSDEELNAIYEASDVIVLPSRIEGFGLVVCEGWFFEKPAIVSSGAGVSELVIDGSNGFVFKSGNYEELAEK 396
                                   ********************************************************************************* PP

                                   HHHHHHSHHHHHHHHH CS
               Glycos_transf_1 152 irklledeelrerlge 167
                                   i+ +l++++++ rl++
  gi|70607018|ref|YP_255888.1| 397 IDIVLKEPDKYSRLSR 412
                                   *********9999986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.1   2.1e-27   7.6e-24       2     132 ..     251     401 ..     250     403 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 2.1e-27
                                   EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...............HHHHHHHT..T-T.TEEEE---..TH CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rp............eeleelaa..gleerveftGfv..ed 65 
                                   +vi  v r+ ++ k +d+ + a++++++++++l++vG+g+  +            ++l++la+  g++++v+ftG+v  e+
  gi|70607018|ref|YP_255888.1| 251 KVITVVARM-DPMKSQDVAIMALKKIKESNAKLLLVGNGSfTSgalgtnkagnwvRKLQSLASnlGVDKKVVFTGHVsdEE 330
                                   7899*****.677**************999*******986644566666778777788877756999999*******8777 PP

                                   HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  66 laellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                   l+++++a+dv v+Ps  egfgl++ E   +++p ++++ +g++e+v  g ng+++++g+ e+lae+i  +l
  gi|70607018|ref|YP_255888.1| 331 LNAIYEASDVIVLPSriEGFGLVVCEGWFFEKPAIVSSGAGVSELVidGSNGFVFKSGNYEELAEKIDIVL 401
                                   ***************999********************99****999*******************98776 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   7.6e-09   2.7e-05       3      81 ..     342     422 ..     340     433 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.6e-09
               Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeh 81 
                                   + psr e++ l++ E   +  +a++++  g+ el+ +g  +++f+  + eelaeki+ +l++p++++++++   +++  e+
  gi|70607018|ref|YP_255888.1| 342 VLPSRIEGFGLVVCEGWFFEKPAIVSSGAGVSELVIDGSNGFVFKsgNYEELAEKIDIVLKEPDKYSRLSRDTVNKCNVEY 422
                                   5699**********************88*****************9************************98888876666 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1     4e-06     0.014     114     213 ..     115     209 ..     105     232 .. 0.83
   2 !    5.9   0.0    0.0012       4.3     267     391 ..     239     356 ..     212     379 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-06
                                   ----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHHHCCTTSEEEEEE-S----HHHHTTSTTHHHHHHH CS
               Glyco_transf_20 114 kefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLmllPellRkkledakigfflHiPFPsseifriLpvreeileg 194
                                    e + s++  Y + n + A+k++e  +d d+ +++D++L+l+  ++    + +    + HiPF ++++      r+ i+++
  gi|70607018|ref|YP_255888.1| 115 YEIKPSEYISYADYNWISAKKLLEFHNDSDVYFINDFQLLLVGGIIGPSAPAI---LWYHIPFVPENLSPR--IRDFIVRS 190
                                   5566778889************************************8877765...4779***99877543..59999999 PP

                                   HTTSSEEEESSHHHHHHHH CS
               Glyco_transf_20 195 llgadliGFhtedyarhFl 213
                                   + g+d + + t+++ +  l
  gi|70607018|ref|YP_255888.1| 191 FEGYDYVILSTKRDLEGLL 209
                                   9999999998888776655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0012
                                   HHHHHT...TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHHHHHHHHHHHH CS
               Glyco_transf_20 267 elkerf..enkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvvlvqiavpsredveeyqelekeveelvgrINge 345
                                   ++k+++  +++ k+i  v r+D +k  +  ++a++++    +e   k  lv   + +++        +++  + v+++ + 
  gi|70607018|ref|YP_255888.1| 239 KVKSKYniGKDEKVITVVARMDPMKSQDVAIMALKKI----KESNAKLLLVGNGSFTSGALG-----TNKAGNWVRKLQSL 310
                                   4444431167789999999999999999999997654....555566666665555555555.....67778888888888 PP

                                   H-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHH CS
               Glyco_transf_20 346 fgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvake 391
                                    ++l+    v ++ +++ eel a++ a+dv++  s  +G  lv  e
  gi|70607018|ref|YP_255888.1| 311 ASNLGVDKKVVFTGHVSDEELNAIYEASDVIVLPSRIEGFGLVVCE 356
                                   8888876666677789***************999999999888655 PP

>> RRM_2  RNA recognition motif 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.25   9.1e+02      29      71 ..      25      67 ..      17      82 .. 0.86
   2 ?   -3.2   0.0       2.8     1e+04      45      62 ..     123     140 ..     114     145 .. 0.74
   3 !   12.3   0.1     4e-05      0.14      17      52 ..     392     427 ..     386     440 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.25
                         RRM_2 29 tydflylpidfknkcnvgyafinlvepkkivafqkafngkkwe 71
                                  +y f+ lpi++ +     y f     pk+++++ + fn  +w 
  gi|70607018|ref|YP_255888.1| 25 KYGFFELPIELSQLDSSDYYFSVGGVPKMMLSLINKFNKVRWV 67
                                  6999999999999999999998888999999999999999996 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.8
                         RRM_2  45 vgyafinlvepkkivafq 62 
                                   + ya  n ++ kk++ f+
  gi|70607018|ref|YP_255888.1| 123 ISYADYNWISAKKLLEFH 140
                                   667888888888887776 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 4e-05
                         RRM_2  17 mllaaideknkgtydflylpidfknkcnvgyafinl 52 
                                    l ++id   k    +  l  d +nkcnv yaf +l
  gi|70607018|ref|YP_255888.1| 392 ELAEKIDIVLKEPDKYSRLSRDTVNKCNVEYAFNQL 427
                                   578899999999999999***************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3164.85
//
Query:       gi|70607019|ref|YP_255889.1|  [L=576]
Description: glycosyl hydrolase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-45  153.2   0.0    6.9e-44  150.4   0.1    1.9  2  Glyco_hydro_15   Glycosyl hydrolases family 15
     0.0041   16.1   0.1      0.054   12.4   0.0    2.5  2  Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
  ------ inclusion threshold ------
      0.018   15.5   0.0       0.15   12.5   0.0    2.3  2  TPR_19           Tetratricopeptide repeat
       0.19   11.0   0.0       0.34   10.2   0.0    1.4  1  Serpin           Serpin (serine protease inhibitor)


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   0.1   1.5e-47   6.9e-44       3     348 ..     206     515 ..     204     530 .. 0.90
   2 ?    0.6   0.0     0.043   1.9e+02     413     443 ..     535     565 ..     523     570 .. 0.83

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.5e-47
                                   HHHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHH CS
                Glyco_hydro_15   3 rldlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqslvk 74 
                                   + ++ +r++   + l+++p +G++iASp+ts p         DYry+WvRDs+y i+a++++     +r+    l + l  
  gi|70607019|ref|YP_255889.1| 206 YENAFYRSLSVILGLIYKP-SGGIIASPTTSIPeivgdernwDYRYVWVRDSSYAIEALVKANLLTHARRALDFLTNLLDP 285
                                   567788999999999****.****************************************8887789************** PP

                                   HHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTT...HCHCCCCHHH CS
                Glyco_hydro_15  75 lmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasg...lqiistldev 152
                                    ++ + +  ++ +g+  +  e +++   ++++f++++++++G+ ++ ++Q+D+ + y+ al+++++      +i+s  +  
  gi|70607019|ref|YP_255889.1| 286 SSKSFDHPFYSVDGT-PPPAEENLD---WLSGFMNSKPVRIGNAAYLQIQMDIEGAYMNALYEYYKRTldkDYISSIFWA- 361
                                   **************9.555556899...************************************7776332455555555. PP

                                   HTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GG CS
                Glyco_hydro_15 153 afvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrg 233
                                     v+ + d++ + ++  + ++WEe++ +++++++++++++Al++a ++a+++g ++  + +++ ++ei  ++      + g
  gi|70607019|ref|YP_255889.1| 362 --VEAISDWVSSSWRGESTDIWEERGISRHYTHTKLMSWVALDRASKLAKDLGYNKLFEEWKSRANEIKIDI-----LNNG 435
                                   ..69****************************************************************9999.....5555 PP

                                   GEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-S CS
                Glyco_hydro_15 234 fwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgel 314
                                    +++++ +++++g             ++ da+ll lp++ f+pa d            +++++++i+++l+ +        
  gi|70607019|ref|YP_255889.1| 436 -VKDNHHFVRYYGG------------DEIDAALLTLPIYDFIPATD----------TLFMNTLKKIDEELRVA-------- 485
                                   .566899999**99............9*******************..........9************9985........ PP

                                   TTS--SBTT--CGSSSBSCT--BHHHHHHHHHHH CS
                Glyco_hydro_15 315 dplvrRysedvkpdklglsGrpyylctlwtvetl 348
                                   d+l  Ry++d+    +gl+ +p+ l t+w+++ +
  gi|70607019|ref|YP_255889.1| 486 DGLYLRYKKDF----MGLAKNPFTLVTTWMARVY 515
                                   45699*****9....79************66543 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.043
                                   S-TTS---SEE-TTT--EESSTT-HHHHHHH CS
                Glyco_hydro_15 413 dnslgvLteevdvylgeliraqpllfseall 443
                                    ++lg++ e+vd ++ e +++ p lf +  +
  gi|70607019|ref|YP_255889.1| 535 NQDLGLIGEHVDPETCEARGNYPHLFPHSGM 565
                                   77899*********************99765 PP

>> Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.041   1.8e+02     120     165 ..     330     374 ..     247     397 .. 0.56
   2 !   12.4   0.0   1.2e-05     0.054     228     393 ..     393     547 ..     382     552 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
                                   --HHHHHHHHHHHHHHHHHH---TT--HHHHHHHHHHHHHHHHGG. CS
               Glyco_hydro_125 120 yelDSlaaflqlsseyyeatgdleffeekwvkaveaildvleeqqe 165
                                    ++D   a+++  +eyy++t d++ ++ + + aveai d +++  +
  gi|70607019|ref|YP_255889.1| 330 IQMDIEGAYMNALYEYYKRTLDKDYIS-SIFWAVEAISDWVSSSWR 374
                                   456777788888999999999999998.666677777665555443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHHHHHHHHHTS--.HHHHHHHHHHHHHHHHHHHSEEEETTTEEEE-SEE-SSS-EE----SSSS-STTHHHH CS
               Glyco_hydro_125 228 aNmmlaveLeklaeileklaekelakearklakeiregiekhavvehkkfgkiyAyEvDGyGsallmDDanvPsLLslpll 308
                                     +m  v+L+++++++++l  ++l +e ++ a+ei+  i +++v ++++f +        yG+  +  Da   +LL+lp++
  gi|70607019|ref|YP_255889.1| 393 TKLMSWVALDRASKLAKDLGYNKLFEEWKSRANEIKIDILNNGVKDNHHFVR-------YYGGDEI--DA---ALLTLPIY 461
                                   56788999**************************************999955.......4566554..44...59****** PP

                                   TSS-TT-HHHHHHHHHHTST...TSTTEEE.-SS-EEE--TTS-TTEEEHHHHHHHHHT---HHHHHHHHHHHHHTSTTSS CS
               Glyco_hydro_125 309 gyvkkddevYqnTrkfvlsk...anpYflk.GkalsgiGgphvglgkaWpmalivqaltsdddeeiaellklllkstaglg 385
                                   +++ ++d+++ nT k + ++   a+  +l+  k + g+     +l ++W ma +   l + d    + ll++l+k +++lg
  gi|70607019|ref|YP_255889.1| 462 DFIPATDTLFMNTLKKIDEElrvADGLYLRyKKDFMGLAKNPFTLVTTW-MARVYIRLKEFD--RARWLLETLIKCNQDLG 539
                                   ****************977766666666651566999999999999999.666555555544..55678999999999999 PP

                                   S--SEEET CS
               Glyco_hydro_125 386 lvhEsvnv 393
                                   l+ E v+ 
  gi|70607019|ref|YP_255889.1| 540 LIGEHVDP 547
                                   99998875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.38   1.7e+03      32      49 ..     260     277 ..     256     285 .. 0.86
   2 ?   12.5   0.0   3.5e-05      0.15      28      57 ..     508     537 ..     497     540 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                        TPR_19  32 AeallalgqldeAealLd 49 
                                   +eal++++ l+ A+++Ld
  gi|70607019|ref|YP_255889.1| 260 IEALVKANLLTHARRALD 277
                                   68999********99998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.5e-05
                        TPR_19  28 rllLAeallalgqldeAealLdalpeedpd 57 
                                     ++A++++ l+++d A+ lL++l + ++d
  gi|70607019|ref|YP_255889.1| 508 TTWMARVYIRLKEFDRARWLLETLIKCNQD 537
                                   5689********************999988 PP

>> Serpin  Serpin (serine protease inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   7.5e-05      0.34      81     152 ..     317     388 ..     267     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.5e-05
                                   SEEEEEEEEEEEETTSEB-HHHHHHHHHHHS-EEEEE-TTTHHHHHHHHHHHHHHHTTTSSSSSSSTTSS-T CS
                        Serpin  81 dkelkianglfvekglklkeeflklakklykaevesvdfkddeearkkINswvekqTngkIkdllsegsids 152
                                   +k ++i+n+ +++ ++ ++ ++ +++ ++yk ++ +   ++   a+++I++wv++  +g+ +d+ +e  i++
  gi|70607019|ref|YP_255889.1| 317 SKPVRIGNAAYLQIQMDIEGAYMNALYEYYKRTLDKDYISSIFWAVEAISDWVSSSWRGESTDIWEERGISR 388
                                   57799****************************99977777777****************999999987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3733.83
//
Query:       gi|70607020|ref|YP_255890.1|  [L=130]
Description: hypothetical protein Saci_1251 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        9.8    6.3   8.8        2.5    8.2   4.3    1.9  2  GWT1      GWT1


Domain annotation for each model (and alignments):
>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.3   0.00014       2.5      57      96 ..      31      69 ..      20      75 .. 0.67
   2 ?    0.4   0.1     0.037   6.6e+02      54      77 ..      93     116 ..      70     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00014
                          GWT1 57 llllsilllllllllelyvefvSRrlaNlpYvlwvvalnl 96
                                  l+++++ l+++l+++++ v  +SR  +N+++vl ++ + +
  gi|70607020|ref|YP_255890.1| 31 LSVATFTLVVVLFIMSYLV-RISRFAINVGFVLAILGILV 69
                                  4445555555555555555.56***********9987655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.037
                          GWT1  54 likllllsilllllllllelyvef 77 
                                   +  l++l + l+ +l+++++ ++f
  gi|70607020|ref|YP_255890.1|  93 VDILMILGFYLFPVLYIINWILDF 116
                                   333444444444444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 824.69
//
Query:       gi|70607021|ref|YP_255891.1|  [L=181]
Description: hypothetical protein Saci_1252 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-36  123.8   0.0    4.5e-36  123.5   0.0    1.1  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   2.5e-40   4.5e-36       1     118 []      29     142 ..      29     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 2.5e-40
                                   EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHHHH CS
                         Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeellaka 81 
                                   VnAaNs+l++gggva ai r +g  ++ee++e+ +++g++++Ge++vt+a++l+a+yvih+vgp++      e +++l++a
  gi|70607021|ref|YP_255891.1|  29 VNAANSYLSHGGGVALAIVRSGGYIIQEESDEYVRRNGPVPVGEVAVTTAGKLKARYVIHAVGPRYG----IEGDDKLESA 105
                                   9****************************************************************95....8999****** PP

                                   HHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                         Macro  82 yknalelaeekgiksvafPaistGifgvpweeaarva 118
                                   ++++le+a+e ++ s+a+PaistGi+g+p e +ar++
  gi|70607021|ref|YP_255891.1| 106 IRRSLEKADELKLSSIALPAISTGIYGYPYEICARIM 142
                                   **********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1321.00
//
Query:       gi|70607022|ref|YP_255892.1|  [L=264]
Description: hypothetical protein Saci_1253 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-07   29.4   1.5    2.2e-06   27.8   1.5    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.01   15.4   0.1      0.022   14.3   0.1    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   1.5   2.4e-10   2.2e-06      50     193 ..      40     174 ..      39     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.4e-10
                                   -SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTS CS
                   Lactamase_B  50 lTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpg 130
                                    TH+H+DHi+gl   ++    p+ +++ ++  +++   ++ +s          +++ d ++e l + +++ ++ +v  + +
  gi|70607022|ref|YP_255892.1|  40 ATHGHADHISGLLSNAKVKYLPKEEYWSITLQGRRMLTYGCTSLN------SEIFSYDYVKENLVDLTADYKDSEVESIKL 114
                                   6***********999999999999999999999998888888886......67899999999999999999999******* PP

                                   TSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEE CS
                   Lactamase_B 131 hghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevl 193
                                   +gh++g+ +y  ++vl++GD+++ ge+++  +   +++ +d ++a +++++++++ ++   v+
  gi|70607022|ref|YP_255892.1| 115 PGHTPGHTGYIVDNVLYAGDTFF-GERVLQNF--SVPFYIDFWSALDSIQKIKEISKSVENVV 174
                                   ***********************.66666666..67788888888888888887766655555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.4e-06     0.022      35     144 ..      39     136 ..      31     154 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-06
                                   E-SS--HHHHGGGGCCCC..C--EEEEEE.EEHHHHHHCCTTCGHHHCHTT..TTEEEEEE-TTSEEEECSTTEEEEEEEE CS
                 Lactamase_B_2  35 llthaHyDHlaglltlre..lrpkklply.apkgvlavleanfvylaleee..pavnvheldwgesfelgdggleitatpa 110
                                   l th+H+DH+ gll+ ++    pk  + +  +++ ++ l+ ++  l++e    + v+ + +d   + + +  + e++ + +
  gi|70607022|ref|YP_255892.1|  39 LATHGHADHISGLLSNAKvkYLPK-EEYWsITLQGRRMLTYGCTSLNSEIFsyDYVKENLVD--LTADYK--DSEVESIKL 114
                                   67*************999752233.3455566666666666655444444322122222222..223333..346888888 PP

                                   -EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                 Lactamase_B_2 111 rhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                   ++ ++           G++++    +v+y+gDt 
  gi|70607022|ref|YP_255892.1| 115 PGHTPG--------HTGYIVD----NVLYAGDTF 136
                                   888888........7888888....888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1613.58
//
Query:       gi|70607023|ref|YP_255893.1|  [L=159]
Description: hypothetical protein Saci_1254 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   11.5   0.7       0.33   10.8   0.1    1.6  2  FAD_syn   FAD synthetase


Domain annotation for each model (and alignments):
>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   1.8e-05      0.33      62     103 ..       6      49 ..       2      60 .. 0.81
   2 ?   -2.1   0.0      0.17     3e+03      63      72 ..     125     134 ..      96     152 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.8e-05
                       FAD_syn  62 Lttleeklelleelg..vdavlvvdFtkefaelsaeeFiekllv 103
                                   L++ ++ ++ + +++  +d ++++ F++++ e +++ F++++lv
  gi|70607023|ref|YP_255893.1|   6 LSQINDHIQSFPDYDipLDNLILLSFNETLEEKKYKFFVKTFLV 49 
                                   666777777887776336***********************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.17
                       FAD_syn  63 ttleeklell 72 
                                   ++l++++e +
  gi|70607023|ref|YP_255893.1| 125 NELDKQIEEF 134
                                   3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1200.64
//
Query:       gi|70607024|ref|YP_255894.1|  [L=191]
Description: NADPH-dependent FMN reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-39  133.0   0.0    9.5e-39  132.6   0.0    1.2  1  FMN_red       NADPH-dependent FMN reductase
    1.7e-07   31.1   0.0    2.3e-07   30.8   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold
      0.006   16.2   0.0     0.0098   15.6   0.0    1.3  1  DUF1987       Domain of unknown function (DUF1987)


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.6   0.0   1.6e-42   9.5e-39       2     154 ..       5     151 ..       4     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 1.6e-42
                                   EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEE.ETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEE CS
                       FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaeveli.dladlilpcalcdkdlesegqtsddvaellekiaaadaliivtP 81 
                                   kil+i GS rk+s+++ l+++ ++ l++ g+e+e++ d+++   p   +++d+e+  ++++ v++l++ki+++da++++tP
  gi|70607024|ref|YP_255894.1|   5 KILGIPGSIRKNSYNKLLLKATLNLLPQ-GVEMEIFeDISQ--IP--PFNQDEEN--NPPQVVKDLKRKIRESDAILFATP 78 
                                   9*************************99.9******66999..56..68888865..799999****************** PP

                                   ECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETSHH CS
                       FMN_red  82 eYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgkae 154
                                   eYn s++g+lKna+D++sr++ +++++gK++a+++++ g+ gg+ a+++l+q+l++l++ vv +++v v++a+
  gi|70607024|ref|YP_255894.1|  79 EYNRSIPGVLKNAIDWASRPYMDNSFNGKVAAIMSASIGMLGGALAHYHLKQILSFLNVNVVTGPEVFVSFAQ 151
                                   *******************************************************************999875 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   3.8e-11   2.3e-07       2     170 ..       5     140 ..       4     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.8e-11
                                   EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEE.EEHHCCT-----CCCCHCCHHHHTTC.HHHHHHHHHHHHCSSE CS
                  Flavodoxin_2   2 kiLiinahprpeksfssalaqafvealekagphevtv.rdLyadflpvlttrdlaaklayeekp.adveseqiekllaada 80 
                                   kiL i ++ r+ +s ++ l++a ++ l +    e ++  d+ +  +p +++       ++e+ p   v+  +  k++++da
  gi|70607024|ref|YP_255894.1|   5 KILGIPGSIRK-NSYNKLLLKATLNLLPQGV--EMEIfEDISQ--IPPFNQ-------DEENNPpQVVKDLK-RKIRESDA 72 
                                   78888888888.5887777777666665544..4544246666..688887.......44444536777778.******** PP

                                   EEEEEE-BTTB--HHHHHHHHHHS-TTTSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S-HHHHHHHHHHH CS
                  Flavodoxin_2  81 ivlqfPlwwfgvPailKgwiDrvltagfafyteeggegrgggLkgkkalvivttGgpeesyqerglegaamdellpplrgi 161
                                   i++++P ++ ++P +lK+ iD   ++ +           ++ + gk a +++++ g         l g a+ +++  l++i
  gi|70607024|ref|YP_255894.1|  73 ILFATPEYNRSIPGVLKNAIDWASRPYM-----------DNSFNGKVAAIMSASIGM--------LGG-ALAHYH--LKQI 131
                                   *********************9877755...........355789988887777777........334.788888..9999 PP

                                   HHHTT-EEE CS
                  Flavodoxin_2 162 lgfiGikdv 170
                                   l f+ +++v
  gi|70607024|ref|YP_255894.1| 132 LSFLNVNVV 140
                                   999998888 PP

>> DUF1987  Domain of unknown function (DUF1987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-06    0.0098       7      53 ..     142     188 ..     138     191 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                       DUF1987   7 tPevdfdaetgrleisGesypenaaeFYepvldwleayleeekkkki 53 
                                    Pev +++++++++ +G+ ++en+++F +++l+ l +y++  k+k++
  gi|70607024|ref|YP_255894.1| 142 GPEVFVSFAQQKFDENGNLVDENSKKFISQLLTNLVDYVKMVKSKQV 188
                                   59*************************************99886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1266.13
//
Query:       gi|70607025|ref|YP_255895.1|  [L=395]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-35  122.4  51.5    1.1e-20   73.9  29.2    2.0  2  MFS_1        Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9  29.2   6.1e-25   1.1e-20       2     242 ..      10     249 ..       9     258 .. 0.81
   2 !   54.1  16.1   6.2e-19   1.1e-14      38     180 ..     252     390 ..     246     394 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 6.1e-25
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll. 80 
                                   ++++f++  ++++l ++++ +l e l is+  +g l ++++ ++a+as+++ rl+dr      ++ lg+ll+++g l+l+ 
  gi|70607025|ref|YP_255895.1|  10 SISHFINDGNSWFLPVSFT-FLIEYLDISKFLVGVLSGIFFGVSALASPLVTRLVDRSNTHArIMGLGILLWGFG-LILFg 88 
                                   6899***************.9************************************997777************.55553 PP

                         MFS_1  81 ..fa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                     ++ +sl+l++++ +++G+ ++++ p+gaa+++  +++ + g a+g+ +++ slG ++ p l  ++   + +r +f+   
  gi|70607025|ref|YP_255895.1|  89 ssISiNSLPLMILAVAIAGFSSAFYHPLGAAILSITYKG-NAGTALGINGSMGSLGRAIYPTLMLAIFGFF-YRNMFLTSL 167
                                   443445566******************************.****************************555.9******** PP

                         MFS_1 159 ivsllafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqev 237
                                   i+++++++  l  ++   +     rk +        +++ ++  +++     ++ l i++ll +++++g++++lp++l+  
  gi|70607025|ref|YP_255895.1| 168 ILGVISILasLPSFFA--NIQLDTRKDDSAN----IKSNTSN--SSFSIVAIIL-LTISALLRSIFTQGISQFLPTLLVGS 239
                                   ******9955444444..3333333333333....2233333..3333333443.99999999****************** PP

                         MFS_1 238 lgls.....g 242
                                   +++s     g
  gi|70607025|ref|YP_255895.1| 240 FDYSysvnlG 249
                                   ****655442 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 6.2e-19
                         MFS_1  38 ltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfpke 117
                                   l++   +a+v++++lG lsdr+Grr+++ ++ ++ ++++ll+l + ++    +v+ ++ G+++ ++fp++++l+ d +p++
  gi|70607025|ref|YP_255895.1| 252 LSIALSAAVVGQPILGLLSDRVGRRSIYGISSVGAVISFLLFLrI-PN----IVFLCIFGFFTFSAFPLMLSLVGDFVPRN 327
                                   66777799******************************4444433.66....999************************** PP

                         MFS_1 118 ergraigl.lsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperk 180
                                     ++a+++ +++g+  G ++gp+l g l++  +   +  il iv++++++ ++ ++p +p+++k
  gi|70607025|ref|YP_255895.1| 328 STSFANSIvWGLGVTGGGVIGPILMGSLSQVSNLIFASEILSIVGVISAL-VVPFIPKPPKKSK 390
                                   ******653789*****************777755555566666666655.4477777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2573.38
//
Query:       gi|70607026|ref|YP_255896.1|  [L=140]
Description: hypothetical protein Saci_1257 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-06   27.5   0.0    4.6e-06   26.9   0.0    1.4  1  4HBT         Thioesterase superfamily
      2e-05   25.0   0.0    2.5e-05   24.8   0.0    1.1  1  4HBT_2       Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.079   12.2   0.1      0.099   11.9   0.1    1.2  1  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   7.7e-10   4.6e-06       1      76 [.      28     110 ..      28     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.7e-10
                                   TSSB-HHHHHHHHHHHHHHHHHHTTST.......TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETT CS
                          4HBT   1 gGvvhgGvylallDeaagaalrslggr.......gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrded 74 
                                   +G+ h + y++++  +   ++++  g        +  +v ve ++++++pv+lgd+lt+  ++  l++++++++ ++ +++
  gi|70607026|ref|YP_255896.1|  28 QGIAHYASYYRFFTNTIEKFIHEKVGIpypivndELWFVMVESHATYHKPVKLGDKLTILLTPKILSSKVIKFDLKIIRKG 108
                                   58899999999999999999999988899999989999***************************************9998 PP

                                   SC CS
                          4HBT  75 gr 76 
                                   + 
  gi|70607026|ref|YP_255896.1| 109 EL 110
                                   76 PP

>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.2e-09   2.5e-05       1     122 [.      20     138 ..      20     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.2e-09
                        4HBT_2   1 vrpndvDlnghlnnarylryleearvkfle.rtglksrsiarrgiglilssahvryrrplkfpdrltvefrvididaktli 80 
                                   vr  d+D+ g  + a+y r++   ++kf++ + g+ +  + ++    ++ ++h +y +p+k++d+lt+ ++    + k ++
  gi|70607026|ref|YP_255896.1|  20 VRIYDTDAQGIAHYASYYRFFTNTIEKFIHeKVGIPYPIVNDE-LWFVMVESHATYHKPVKLGDKLTILLTPKILSSKVIK 99 
                                   7889*************************85556688888877.67788899*****************999999999999 PP

                        4HBT_2  81 iehrflsnadgkkaarveerivvmdygkrskkapvPpellka 122
                                   ++ ++++  +g ++ ++  ++v ++ +   k +++P+e+l++
  gi|70607026|ref|YP_255896.1| 100 FDLKIIR--KGELTTEGNLTQVAINPKIW-KAVDIPNEILSK 138
                                   9999999..88888888888888888775.788888888776 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.7e-05     0.099      10     130 ..      20     138 ..      13     140 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                   Acyl-ACP_TE  10 vrvyevdvngtakleallnllqdvaanq.veelGlsddkflkklnlvWvvakyeieierlpefgdkveietwaesenklfc 89 
                                   vr+y+ d++g a+  +  + + ++ ++   e++G+     + + +l  v+ + + + ++++++gdk++i   ++  +   +
  gi|70607026|ref|YP_255896.1|  20 VRIYDTDAQGIAHYASYYRFFTNTIEKFiHEKVGIPYP--IVNDELWFVMVESHATYHKPVKLGDKLTILLTPKILSSKVI 98 
                                   78888888888888888888877665541456774443..46778888999999999999999999999999988888888 PP

                   Acyl-ACP_TE  90 yrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilae 130
                                   + d k+   kge   e + + v ++ +  +++++++eil++
  gi|70607026|ref|YP_255896.1|  99 KFDLKIIR-KGELTTEGNLTQVAINPKIWKAVDIPNEILSK 138
                                   88888876.89999999999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 939.08
//
Query:       gi|70607027|ref|YP_255897.1|  [L=231]
Description: nucleotidyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-33  115.4   0.0    3.6e-33  115.2   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    1.4e-09   38.5   0.0    1.9e-09   38.1   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0025   17.6   0.0     0.0038   17.0   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.2   0.0     6e-37   3.6e-33       1     245 [.       2     224 ..       2     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 6e-37
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   kavILaGG+G+RL+PLt + +k+lv ++gk ++++ ++  l + +i ++++   ++++ l++   k++++++v+++i+ e+
  gi|70607027|ref|YP_255897.1|   2 KAVILAGGYGKRLRPLTDEKPKPLVEIGGK-PILEWQILLLKRYKISSVYILAGYKKEVLLDWVSKNQERLEVKLAILSET 81 
                                   79****************************.*****************8888888888899999999999*********** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   e+ gt +A++  ++++++ +      vL+gD++++ ++ ++    i+++++ ++++++vp +  + yG+i+++++g++++f
  gi|70607027|ref|YP_255897.1|  82 EPLGTGGAIKRLEDFIKEPF-----YVLNGDIITNLDLDKL---KISEDSDDLASIALVPLK--SPYGIIRMKDGGKIIEF 152
                                   ****************9655.....8*********999876...344444447888888865..67*************** PP

                                   ECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 163 vEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   vEKP  ++  +++++GiY+ ++++++fl       + + d  + ++p + e+g    ++  +   yW+ + tl+++ ea +
  gi|70607027|ref|YP_255897.1| 153 VEKPIIKD--YWINAGIYYMKPQIFEFL-------PVKGDVEKTTFPLLAEKGILSGKTYDSV--YWRSIDTLKDYEEAGQ 222
                                   ******99..******************.......3466777888999999999999977777..8999999999999987 PP

                                   HH CS
               NTP_transferase 244 kl 245
                                   ++
  gi|70607027|ref|YP_255897.1| 223 EV 224
                                   76 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.1e-13   1.9e-09       1      96 [.       3     108 ..       3     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.1e-13
                                   EEEEEESS-TTTT....T.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH....TTCTS-E.EE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg....g.dKallplggkpllervldalraagvdevvvvggd..eevlaal....arlgvrv.vededpg 69 
                                   aviLAGG ++R+     + +K+l+++ggkp+le+++  l++ +++ v++ +g+  e +l+ +    +rl+v++ +  e + 
  gi|70607027|ref|YP_255897.1|   3 AVILAGGYGKRLRpltdEkPKPLVEIGGKPILEWQILLLKRYKISSVYILAGYkkEVLLDWVsknqERLEVKLaILSETEP 83 
                                   79**********6443325*********************************95222334333333444555422333345 PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT- CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDm 96 
                                    g++++++   + +  +++++vl +D+
  gi|70607027|ref|YP_255897.1|  84 LGTGGAIKRLEDFI--KEPFYVLNGDI 108
                                   78888888777776..57777777775 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.4e-07    0.0038       2      49 ..       2      51 ..       1      69 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.4e-07
                                  EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEE CS
                          IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivv 49
                                   +vi A G GkR++    ++pK ++e+ g+++le+ +  l  +k ++ + +
  gi|70607027|ref|YP_255897.1|  2 KAVILAGGYGKRLRpltDEKPKPLVEIGGKPILEWQILLLKRYK-ISSVYI 51
                                  69**********7533389*****************98877755.444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1901.59
//
Query:       gi|70607028|ref|YP_255898.1|  [L=155]
Description: methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-25   87.0   0.0    8.8e-25   86.6   0.0    1.1  1  DNA_binding_1    6-O-methylguanine DNA methyltransferase, DNA
     0.0061   16.2   0.0      0.011   15.4   0.0    1.4  1  Sigma70_r4_2     Sigma-70, region 4
  ------ inclusion threshold ------
      0.033   15.0   0.0       0.12   13.2   0.0    2.0  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   1.5e-28   8.8e-25       2      81 .]      71     147 ..      70     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.5e-28
                                   HHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTTS CS
                 DNA_binding_1   2 fqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEgv 81 
                                   f++rV + +r+I  Gkv tY+eiA+ l+  +++raVg al +np+ +++PcHR+++++g lgg++ g+e k++lLe Egv
  gi|70607028|ref|YP_255898.1|  71 FRRRVFNEVRRIGWGKVKTYKEIAETLK--TSPRAVGMALSKNPVLLIIPCHRIIAESG-LGGFSRGIELKKKLLELEGV 147
                                   9***************************..*****************************.******************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-06     0.011      28      48 ..      89     109 ..      88     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                                   -HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2  28 sykEIAellgisegtVksrls 48 
                                   +ykEIAe l++s+++V  +ls
  gi|70607028|ref|YP_255898.1|  89 TYKEIAETLKTSPRAVGMALS 109
                                   8***************98887 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05      0.12       2      34 ..       2      34 ..       1      66 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                  -EEEEEEETTEEEEEEEETTCEEEEEEEC-HHH CS
               Methyltransf_1N  2 lyytlidsplgrlllagdEkgllaidlldkdts 34
                                  + y ++ splg + +a +E+g+  +d+ d  ++
  gi|70607028|ref|YP_255898.1|  2 IVYGVYNSPLGTITVAKNERGIIMLDFCDCAER 34
                                  668899******************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1021.77
//
Query:       gi|70607029|ref|YP_255899.1|  [L=552]
Description: threonyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-41  142.3   0.0    4.4e-41  140.8   0.0    1.8  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    9.4e-18   64.2   2.7    1.1e-17   63.9   1.3    1.9  2  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.0   4.9e-45   4.4e-41       3     178 ..     223     434 ..     221     435 .. 0.94
   2 ?   -3.6   0.0       1.1   9.5e+03      14      35 ..     523     543 ..     516     545 .. 0.67

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 4.9e-45
                                   EEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   3 ledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                   +e +nd+e+ +kP+n+++++ +++ + +rs k+LP+++++++ +yR Ek+ +++GLlRvr+F+q+dg++f  e++++d+++
  gi|70607029|ref|YP_255899.1| 223 FEIDNDEELGIKPMNCPAHILIYKSK-VRSyKDLPIRFSEFGHVYRWEKKgELYGLLRVRGFTQDDGHIFLREDQIKDEIK 302
                                   7899********************99.***888****************999***************************** PP

                                   HHHHHHHHHHHHTT.SCEEEEEE..GTTSC...................................BTTSEEEEEEEEETTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxxx...................................xxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  82 dlikaisriferlglefraiiel..msaks...................................adykdkkefeavsesl 125
                                    l+k++ +++  +g++   ++    ++                                      a+y++k +f++ +  l
  gi|70607029|ref|YP_255899.1| 303 LLMKKTLDVLAIFGFKGDDVRVNlsTR--PdesigtdeqwnkatdalisalnelnikyevkekegAFYGPKIDFDIRDS-L 380
                                   ***************997666663322..244688899999**********************************9999.* PP

                                   SEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                  tRNA-synt_2b 126 tkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                   ++ ++++tiq + ++l+er++++++d+++++k+++m+++a  g + R+++++le+
  gi|70607029|ref|YP_255899.1| 381 SRWWQLSTIQVD-FNLPERFKLEYVDKDGSKKRPVMVHRAiYGsIDRFMAILLEH 434
                                   ************.***************************9899*********98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                                   -SSSHHHHHHHHHHHEEEBGGS CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  14 kPtneetfvelirdevlrskrL 35 
                                   +  n e fv++  +e +r+k+L
  gi|70607029|ref|YP_255899.1| 523 RGINVEKFVQALVEE-IRNKDL 543
                                   445666777777777.666665 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.92   8.3e+03      16      38 ..     342     364 ..     333     367 .. 0.72
   2 !   63.9   1.3   1.3e-21   1.1e-17       1      93 [.     447     536 ..     447     537 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHTTTSEEEEESSS CS
                HGTP_anticodon  16 eyakklaeeLraagirvelddsn 38 
                                   +  + l ++L++ +i+ e+++++
  gi|70607029|ref|YP_255899.1| 342 KATDALISALNELNIKYEVKEKE 364
                                   55667778888888888888766 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 1.3e-21
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   qv v+p+++   e+e+y ++l ++Lr++ irv++d  +e++ k+i++a   g+p+ ++vG ke ++g+vtvr r + e + 
  gi|70607029|ref|YP_255899.1| 447 QVRVLPITD---EIEDYGNSLMAKLRENKIRVDMDSGEETLSKRIKKAYDDGVPYLIIVGRKEKDEGKVTVRARGNIEIRG 524
                                   89*******...9******************************************************************** PP

                                   EETTHHHHHHHH CS
                HGTP_anticodon  82 vsldelveklke 93 
                                   + ++++v++l e
  gi|70607029|ref|YP_255899.1| 525 INVEKFVQALVE 536
                                   *******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3720.81
//
Query:       gi|70607030|ref|YP_255900.1|  [L=327]
Description: hypothetical protein Saci_1262 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-10   41.0   0.0    3.4e-10   40.2   0.0    1.5  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
  ------ inclusion threshold ------
      0.023   15.5   0.6      0.098   13.5   0.1    2.2  2  Ntox50           Bacterial toxin 50


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   3.7e-14   3.4e-10       2     102 ..     170     259 ..     169     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3.7e-14
                                   EEEEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-C CS
               Glyco_tran_28_C   2 ilVtGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRAGa 82 
                                   ilVt GS g+++L       ++ll+l+ +++++++qtGk + ++    + e++++ ++f+f+++++ +i++a+LvI++ G 
  gi|70607030|ref|YP_255900.1| 170 ILVTTGSMGFKKLF------DSLLNLR-GNYKFVIQTGKVDPTP----YIEKKPDWSFFSFDKDIERYIANAELVITHQGK 239
                                   89*********775......5677887.78********554433....444448889************************ PP

                                   HHHHHHHHTT--EEEE--TT CS
               Glyco_tran_28_C  83 gtiaEllalgkplIlvplpe 102
                                   ++   ++ +gkp+I+v +++
  gi|70607030|ref|YP_255900.1| 240 TAMESVVMYGKPTIIVYNKD 259
                                   ****************9876 PP

>> Ntox50  Bacterial toxin 50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.31   2.8e+03      22      54 ..     136     167 ..     102     178 .. 0.58
   2 ?   13.5   0.1   1.1e-05     0.098      34      86 ..     223     274 ..     205     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.31
                        Ntox50  22 yllidskeaqellkkyagtgevvkdrkgkwrnk 54 
                                   ++l + +e + l+++ +  g +v++ k k +nk
  gi|70607030|ref|YP_255900.1| 136 VFL-HWNEQKGLYDNGVVVGPIVEKPKYKSENK 167
                                   332.44455555555555566666655555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                        Ntox50  34 lkkyagtgevvkdrkgkwrnkevvdfgevigvvvdketgeeteTklgkIhysk 86 
                                   +++y +++e+v +++gk   + vv +g+   +v++ ++ +   Tk  +I ysk
  gi|70607030|ref|YP_255900.1| 223 IERYIANAELVITHQGKTAMESVVMYGKPTIIVYN-KDWKSATTKQDTILYSK 274
                                   789999****************************9.5556666*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2517.26
//
Query:       gi|70607031|ref|YP_255901.1|  [L=238]
Description: endonuclease III related protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-11   45.2   0.0    1.4e-11   44.8   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    2.5e-05   24.5   0.2    0.00013   22.2   0.3    2.0  2  DUF4332        Domain of unknown function (DUF4332)
     0.0023   18.5   1.7       0.87   10.2   0.4    2.8  2  HHH_5          Helix-hairpin-helix domain
     0.0049   16.7   0.3      0.021   14.7   0.0    2.1  2  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.14   12.5   1.1       0.24   11.8   1.1    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0     4e-15   1.4e-11       1      91 [.      56     176 ..      56     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 4e-15
                                   HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                   vs+il q t++e++ ++ ++l+er g    edla+++e++++eli+++ f r Kak++k+lA  +                
  gi|70607031|ref|YP_255901.1|  56 VSSILVQLTRWETVREVLKKLKER-GIRRIEDLASLEESEIEELIKKVNFRRAKAKRLKNLAMLVKeigihrlvvspells 135
                                   89**********************.789**********************************9999999999999999999 PP

                                   .................S-SSS--TTSHHHHHHHHHHTTSSS CS
                                   .................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 .................gkpdvlivvDvhvrrilkrlrsike 91 
                                                    g + +l++   + +r+l+rl +i+ 
  gi|70607031|ref|YP_255901.1| 136 niegigdetkeaillfaG-NIPLFPRSEYSKRVLSRLAGIRL 176
                                   999999999999999954.68999999999999999988865 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   3.7e-08   0.00013       5      62 ..      70     125 ..      67     136 .. 0.92
   2 ?   -0.8   0.0      0.49   1.8e+03      11      31 ..     198     218 ..     192     237 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.7e-08
                       DUF4332   5 keeaekLkkaGikttedLlelgktekgrkalaeklgisernvlklanlAdLarikgig 62 
                                   +e  +kLk+ Gi+  edL++l+++e+++  l++k ++   + ++l+nlA L+++ gi 
  gi|70607031|ref|YP_255901.1|  70 REVLKKLKERGIRRIEDLASLEESEIEE--LIKKVNFRRAKAKRLKNLAMLVKEIGIH 125
                                   67789***********************..**********************998886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                       DUF4332  11 LkkaGikttedLlelgktekg 31 
                                   L  aGi ++ +  ++++++k 
  gi|70607031|ref|YP_255901.1| 198 LFHAGIVSVGKSFCSNQNPKC 218
                                   555566555555555555555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.4   0.00024      0.87      15      40 ..      73      98 ..      70     116 .. 0.75
   2 !    6.9   0.1    0.0027       9.8      33      55 ..     130     152 ..     107     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00024
                                  HHHHHTTT--SHHHHHHS-HHHHHTS CS
                         HHH_5 15 AlallsaGiesvedlaaadveeLaki 40
                                   ++l + Gi+ +edla++++ e+ ++
  gi|70607031|ref|YP_255901.1| 73 LKKLKERGIRRIEDLASLEESEIEEL 98
                                  6899999**********987777663 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0027
                                   -HHHHHTSTTS-HHHHHHHHHHH CS
                         HHH_5  33 dveeLakipGiGkktAeriilel 55 
                                   ++e L+ i GiG +t e i+l +
  gi|70607031|ref|YP_255901.1| 130 SPELLSNIEGIGDETKEAILLFA 152
                                   67889999999999999998876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       0.7   2.5e+03       9      17 ..      83      91 ..      82      92 .. 0.80
   2 !   14.7   0.0   5.8e-06     0.021       9      30 .]     130     151 ..     127     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.7
                                  SHHHHHTST CS
                           HHH  9 sreeLlalP 17
                                   +e+L++l+
  gi|70607031|ref|YP_255901.1| 83 RIEDLASLE 91
                                  589999986 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.8e-06
                                   SHHHHHTSTT-SHHHHHHHHHH CS
                           HHH   9 sreeLlalPGVGpktAeaIlsy 30 
                                   s+e L  ++G+G +t eaIl +
  gi|70607031|ref|YP_255901.1| 130 SPELLSNIEGIGDETKEAILLF 151
                                   8899999************986 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.1   6.7e-05      0.24       4      17 .]     214     227 ..     214     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                 EndIII_4Fe-2S   4 RkPkCeaCPLaDlC 17 
                                   ++PkC  C   ++C
  gi|70607031|ref|YP_255901.1| 214 QNPKCNSCIFKEIC 227
                                   59************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1807.09
//
Query:       gi|70607032|ref|YP_255902.1|  [L=337]
Description: succinyl-CoA synthetase beta chain [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-28   97.7   3.7    5.9e-27   94.6   1.0    3.1  2  ATP-grasp_2     ATP-grasp domain
    1.3e-15   57.6   0.3    2.4e-15   56.6   0.3    1.4  1  Ligase_CoA      CoA-ligase
    1.7e-06   27.7   0.0      0.034   13.6   0.1    3.6  3  ATP-grasp_5     ATP-grasp domain
  ------ inclusion threshold ------
       0.03   14.2   0.1        0.7    9.8   0.0    2.2  2  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   1.0   1.3e-30   5.9e-27       1     201 [.       2     169 ..       2     170 .. 0.89
   2 ?   -1.1   0.0      0.26   1.2e+03     161     192 ..     253     284 ..     248     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.3e-30
                                   BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE CS
                   ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelv 81 
                                   +l+Ey++ke+++  g+++p+g v++s+ +        ++k+ vvKaQ l G+RGK g vk++++   +++++ e+  k+l 
  gi|70607032|ref|YP_255902.1|   2 KLYEYEGKELFKAVGIPIPKGVVTDSPIKW-------DGKA-VVKAQLLEGARGKRGLVKVTDN---VEQTIAEM--KKLG 69 
                                   69***********************99654.......4555.9**************9999955...55555555..4444 PP

                                   -TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHH CS
                   ATP-grasp_2  82 tkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqarei 162
                                             ++k lvee ++ ++ElY+s+++Dr++ ++++ aS+eGG+diE       ++++ ++i ++ g++++ + +i
  gi|70607032|ref|YP_255902.1|  70 ----------IQKFLVEEFIPHTRELYISALIDRDTAEPIIAASTEGGIDIES-----NSNVKIFHIPMERGIRSYDVYNI 135
                                   ..........88***************************************96.....456788899999*********** PP

                                   HHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                   ATP-grasp_2 163 akklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                    k lg+++     +  i+k ly+l++e da+l+EiNPL+
  gi|70607032|ref|YP_255902.1| 136 EKYLGVKG-----IEPILKGLYRLITEFDAELAEINPLA 169
                                   *****987.....789**********************8 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.26
                                   HHHHHCT--CHHHHHHHHHHHHHHHHHHHTTE CS
                   ATP-grasp_2 161 eiakklglekelvkkaakiikklyklfvelda 192
                                   e +k++ ++  + kk++ki++++y+ ++++d 
  gi|70607032|ref|YP_255902.1| 253 ERVKEAIINIASNKKVKKIVMNIYSGITRCDE 284
                                   55666677777888999999999988888875 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.3   5.5e-19   2.4e-15       3     142 ..     221     326 ..     219     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.5e-19
                                   SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEE CS
                    Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivl 83 
                                   nG++L++++md++k                g++++ + d+G++a            +++ ea+ ++a++++vk i+++i  
  gi|70607032|ref|YP_255902.1| 221 NGAGLTMATMDMVKIM--------------GGNPADFFDIGGGAG----------RERVKEAIINIASNKKVKKIVMNIYS 277
                                   8***************..............***************..........8************************* PP

                                   SSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE- CS
                    Ligase_CoA  84 GygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiass 142
                                   G+ +++++a ++++a+k +k     +p+ +r++Gt+++     e++++l+e g+ +++ 
  gi|70607032|ref|YP_255902.1| 278 GITRCDEVAMGIVEALKIVK-----IPIYVRLVGTNEE-----EGRRILRENGIPVYED 326
                                   *******************8.....*************.....***********99876 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00027       1.2      10      35 ..       3      28 ..       1      36 [. 0.91
   2 !   13.6   0.1   7.6e-06     0.034      86     222 .]      63     185 ..      37     185 .. 0.76
   3 ?   -2.0   0.0      0.45     2e+03      11      28 ..     308     325 ..     306     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00027
                   ATP-grasp_5 10 Lteaeakelleaygipvvetrlassa 35
                                  L+e+e kel++a+gip+++  + +s+
  gi|70607032|ref|YP_255902.1|  3 LYEYEGKELFKAVGIPIPKGVVTDSP 28
                                  99****************99988776 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.6e-06
                   ATP-grasp_5  86 ervkekspeariegvlVqemakrggrElivgvteDpv.FGpvilfGl.GGtavevlkdvavalpplnstlareliertkas 164
                                   +++    ++  i+++lV+e  + ++rEl +++  D     p+i+  + GG+ +e  ++v++ + p++     + i++  ++
  gi|70607032|ref|YP_255902.1|  63 AEM----KKLGIQKFLVEEFIP-HTRELYISALIDRDtAEPIIAASTeGGIDIESNSNVKIFHIPME-----RGIRSYDVY 133
                                   333....446799999999988.89999999999975155777765449999999999998888875.....557777777 PP

                   ATP-grasp_5 165 kllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarirl 222
                                   ++ k +     + ++ +e +l  l +L++++   +  +inPl v+++g ++alD ++ l
  gi|70607032|ref|YP_255902.1| 134 NIEK-Y-----LGVKGIEPILKGLYRLITEFDA-ELAEINPLAVTNDGkIIALDSKVIL 185
                                   7644.3.....3457999999999999999865.6779********998*****99975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.45
                   ATP-grasp_5  11 teaeakelleaygipvve 28 
                                   +e+e +++l+  gipv e
  gi|70607032|ref|YP_255902.1| 308 NEEEGRRILRENGIPVYE 325
                                   68999**********987 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.028   1.2e+02      70      99 ..      45      79 ..      31     104 .. 0.72
   2 ?    9.8   0.0   0.00016       0.7      52     104 ..     230     282 ..     200     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.028
                                  -TCC.....HHHHHHHHHHHHHHCT--EEEEEEET CS
                NAD_binding_10 70 gggk.....deegaknivdaakeagvkRfvlvsai 99
                                  ++gk      ++ ++++++ +k+ g+++f++   i
  gi|70607032|ref|YP_255902.1| 45 ARGKrglvkVTDNVEQTIAEMKKLGIQKFLVEEFI 79
                                  33333434444448889************986655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00016
                                   CHHHHHHTT-SEEEES---TCCHHHHHHHHHHHHHHCT--EEEEEEETTTTSG CS
                NAD_binding_10  52 edlaealkgadaVvsalggggkdeegaknivdaakeagvkRfvlvsaigvgde 104
                                    d+ + + g  a ++ +ggg+++e++ ++i++ a +++vk++v+  + g+++ 
  gi|70607032|ref|YP_255902.1| 230 MDMVKIMGGNPADFFDIGGGAGRERVKEAIINIASNKKVKKIVMNIYSGITRC 282
                                   56777888888889999***************************999998864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2357.90
//
Query:       gi|70607033|ref|YP_255903.1|  [L=256]
Description: succinyl-CoA ligase subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-23   83.8   2.1      1e-23   83.8   2.1    2.4  2  CoA_binding    CoA binding domain
    1.3e-12   47.8   1.3    2.3e-12   47.0   1.3    1.3  1  Ligase_CoA     CoA-ligase
    3.8e-08   33.2   0.1    6.6e-08   32.5   0.0    1.5  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.3e-07   32.1   0.0      3e-07   30.9   0.0    1.6  1  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
      0.022   15.6   0.1      0.061   14.2   0.0    1.7  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
      0.023   14.5   0.1        0.7    9.8   0.0    2.4  2  PDZ_6          PDZ domain


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   2.1   3.3e-27     1e-23      25      96 .]       1      72 [.       1      72 [. 0.98
   2 ?    1.1   0.8      0.22   6.4e+02       8      47 ..     123     166 ..     116     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 3.3e-27
                                  HHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESST CS
                   CoA_binding 25 klkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviiteg 96
                                  +lkyg+k+v+gv+p+k+gt+v+++pvy++v+++++++e+d+++i+vPa++a +av e++++gik+iv+ite+
  gi|70607033|ref|YP_255903.1|  1 MLKYGTKIVAGVTPGKGGTKVNNVPVYDTVADAVKEHEIDASIIFVPAKFATDAVYEAIDNGIKLIVVITEH 72
                                  789*******************************************************************95 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                                   EETTTSHHHHHH.HHHHHHHHECEEEEEEC-TT.TTTCEET.....T CS
                   CoA_binding   8 viGagglgiagl.yhfkeklkygikavfgvnpr.kvgtevl.....g 47 
                                   ++  +g+   ++   ++  +++g + v+g++++  +gt+ +      
  gi|70607033|ref|YP_255903.1| 123 IVSRSGT---LTyEISETIKHIGQSTVIGIGGDpIIGTTMDevvqmF 166
                                   4434444...4423333344566677777777766777776444440 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   1.3   7.6e-16   2.3e-12       1     150 [.     124     241 ..     124     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.6e-16
                                   EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEE CS
                    Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldi 81 
                                   ++++GtL+ye  + ik+                 +q+++i++G+d            +t++ e ++ + +dpe++ i++ +
  gi|70607033|ref|YP_255903.1| 124 VSRSGTLTYEISETIKHI----------------GQSTVIGIGGDPII---------GTTMDEVVQMFDQDPETEEIIVIG 179
                                   6899******99999999................9************7.........9*********************** PP

                                   EESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                    Ligase_CoA  82 vlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                   ++G g+ e+ +a+l k+ k        + ++a++aG +a+  +++++a+a+   g+ + +sk +a + a
  gi|70607033|ref|YP_255903.1| 180 EIG-GTMEERVAKLKKEGKIK------KKMIAYIAGMTAPREKRMGHAGAVVYMGMGTFDSKINAFKNA 241
                                   ***.****9999987665544......59*********************************9987766 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.6   1.1e+04      52      65 ..      60      73 ..      55      74 .. 0.70
   2 !   32.5   0.0   2.2e-11   6.6e-08       1     133 [.     118     254 ..     118     256 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.6
                  Succ_CoA_lig 52 dpetkvillylEsi 65
                                  d+ +k+i++  E+i
  gi|70607033|ref|YP_255903.1| 60 DNGIKLIVVITEHI 73
                                  67778888887776 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 2.2e-11
                  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaarra 78 
                                   +Gki+++s SG+l  ++ ++ ++  +g s+v+ +G    + +++ ++++++++dpet+ i++  E  +   ++ +++ ++ 
  gi|70607033|ref|YP_255903.1| 118 KGKIGIVSRSGTLTYEISETIKH--IGQSTVIGIGGdpIIGTTMDEVVQMFDQDPETEEIIVIGEIGGTmEERVAKLKKEG 196
                                   69***************999986..9*********9445788999******************998887467888888888 PP

                  Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgala....gsdavvdaafrqaGvlrvdsleelfd 133
                                   + kk+++++ +G ++   +  + h ga++    g  +    af++aG+ ++++  e+++
  gi|70607033|ref|YP_255903.1| 197 KIKKKMIAYIAGMTAPR-EKRMGHAGAVVymgmGTFDSKINAFKNAGIPVAKTPYEILE 254
                                   888*********87664.55578888876222244444456899999988888877766 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0     1e-10     3e-07      33     114 ..      12     101 ..       2     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1e-10
                                   ESSS-..SEETTEES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHTT-EE CS
                 CoA_binding_2  33 Vnpke..eeilgekvyaslaed..pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeeagirv 105
                                   V+p +  +++  ++vy ++a++  ++++d+  +f+p++ + + v ea++ g+k +++  +         + ++a+ +g r+
  gi|70607033|ref|YP_255903.1|  12 VTPGKggTKVNNVPVYDTVADAvkEHEIDASIIFVPAKFATDAVYEAIDNGIKLIVVITEhipvLDMLRISKYAKLKGTRI 92 
                                   777777799***********8458*********************************9999986667788888999***** PP

                                   E.ES-HHHH CS
                 CoA_binding_2 106 vgdrCilve 114
                                   +g++C++++
  gi|70607033|ref|YP_255903.1|  93 IGPNCPGLI 101
                                   ******986 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.061      46      93 ..      22      72 ..       7      91 .. 0.87
   2 ?   -2.0   0.0       2.1   6.3e+03      27      41 ..     161     175 ..     147     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                  TTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-...EEEEES CS
                  GFO_IDH_MocA 46 fgveaysdleelladpeidavivatpngtheelakaaleagk...hvllEK 93
                                   +v++y+ +++ +++ eida i+ +p++   + + +a+ +g+    v+ E+
  gi|70607033|ref|YP_255903.1| 22 NNVPVYDTVADAVKEHEIDASIIFVPAKFATDAVYEAIDNGIkliVVITEH 72
                                  6899**********99**************************665566665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                   EEEEEECSSHHHHHH CS
                  GFO_IDH_MocA  27 evvalldpdaeraea 41 
                                   evv  +d+d+e  e 
  gi|70607033|ref|YP_255903.1| 161 EVVQMFDQDPETEEI 175
                                   344444444444333 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.061   1.8e+02      23      43 ..      19      35 ..      19      39 .. 0.74
   2 ?    9.8   0.0   0.00023       0.7      21      50 ..     145     174 ..     144     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.061
                         PDZ_6 23 lsvNGqpveglsladvaallr 43
                                  ++vN++pv    ++ va++++
  gi|70607033|ref|YP_255903.1| 19 TKVNNVPV----YDTVADAVK 35
                                  68******....666666666 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00023
                         PDZ_6  21 iilsvNGqpveglsladvaallrgsagesv 50 
                                   +++ ++G p++g+++++v+++  ++++++ 
  gi|70607033|ref|YP_255903.1| 145 TVIGIGGDPIIGTTMDEVVQMFDQDPETEE 174
                                   5899******************97777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1826.73
//
Query:       gi|70607034|ref|YP_255904.1|  [L=346]
Description: hypothetical protein Saci_1267 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.83   10.2   6.4       0.84   10.2   0.9    3.3  3  DUF4369          Domain of unknown function (DUF4369)


Domain annotation for each model (and alignments):
>> DUF4369  Domain of unknown function (DUF4369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.06   1.1e+03      39      71 ..      71     103 ..      65     129 .. 0.72
   2 ?   -0.6   0.0      0.11   1.9e+03      59      85 ..     172     202 ..     148     205 .. 0.66
   3 ?   10.2   0.9   4.7e-05      0.84      51      89 ..     269     316 ..     245     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.06
                       DUF4369  39 tfkgkvdeprlaylliddkgg..alpfflengtit 71 
                                   tf+ + + p+l+y+++ ++ +  a   +l   ++t
  gi|70607034|ref|YP_255904.1|  71 TFHKNFQVPDLYYIFYHSNPStlA--YILLFNNVT 103
                                   677777888899999888888442..333333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.11
                       DUF4369  59 g...alpfflengtititiddgss.akvtGs 85 
                                   +   ++ f+ +++ ++ t+   s  ak++Gs
  gi|70607034|ref|YP_255904.1| 172 MytlNVSFMPNPSALSYTLYLVSPeAKISGS 202
                                   2444566666666666666666557999998 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 4.7e-05
                       DUF4369  51 ylliddkgg.....alpfflengtititiddgss....akvtGsptnd 89 
                                      +  + +      + ff   g+it+ +++g++    +kvtG   n+
  gi|70607034|ref|YP_255904.1| 269 NSTTPFTIDtigkyIVIFFPTGGNITVFLNNGNNplygVKVTGETGNK 316
                                   444444444556656778888889999999999999999999987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2477.49
//
Query:       gi|70607035|ref|YP_255905.1|  [L=199]
Description: hypothetical protein Saci_1269 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.9   0.0    0.00031   21.1   0.0    1.5  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.8e-08   0.00031      16     101 ..       8      90 ..       1     126 [. 0.59

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.8e-08
                                   HTTS-TTSEEEEEETTG---TT-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHS...HHCCSTTSSHHHHHHHHHHH CS
                        Pro_CA  16 itdagpGdlFvvrnvgnlvppadssvlaaleyAvevlkvkhivVlGHskCGavkaalk...aekseeeagaidkwlekire 93 
                                   ++  +  d  v+rn+g+ v   +s  +  ++y   +  ++++v l H++CGa+k +++   + k+++++   dk++++  +
  gi|70607035|ref|YP_255905.1|   8 YLAENFNDSIVIRNAGANV---NSLKTTLIKY---KNLIDEVVLLPHTDCGAMKVVYSnivEGKKATSTAVEDKLIKQFTK 82 
                                   5566778889999999999...5666778888...5569***************887755433323322222333343333 PP

                                   HHHHCHHH CS
                        Pro_CA  94 alekveee 101
                                   ++ +  +e
  gi|70607035|ref|YP_255905.1|  83 TKFSSLNE 90 
                                   33332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1500.01
//
Query:       gi|70607036|ref|YP_255906.1|  [L=297]
Description: hypothetical protein Saci_1270 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          8    6.8  13.0        2.7    8.3   0.4    3.4  3  DUF2104   Predicted membrane protein (DUF2104)


Domain annotation for each model (and alignments):
>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.7   0.00099        18       4      23 ..      49      68 ..      46      80 .. 0.87
   2 ?    8.3   0.4   0.00015       2.7      12      48 ..      84     120 ..      76     132 .. 0.87
   3 ?   -1.3   0.7      0.15   2.7e+03      13      24 ..     195     206 ..     183     250 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00099
                       DUF2104  4 llaviafivGsilGLlysYk 23
                                  ll ++ f++G i+GL+  Y 
  gi|70607036|ref|YP_255906.1| 49 LLFIVRFLIGIIFGLTITYA 68
                                  6789************9995 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00015
                       DUF2104  12 vGsilGLlysYkkysepyvekkidklalvlaviGwll 48 
                                    G  +G l+sY  ys ++  ++i++l+ ++ ++ +ll
  gi|70607036|ref|YP_255906.1|  84 AGRSIGWLLSYISYSLIHNWNEINILSGIIIIAASLL 120
                                   6899***********************9999988777 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.15
                       DUF2104  13 GsilGLlysYkk 24 
                                     ++G +  Yk 
  gi|70607036|ref|YP_255906.1| 195 LPLVGANIGYKL 206
                                   333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2112.11
//
Query:       gi|70607037|ref|YP_255907.1|  [L=214]
Description: hypothetical protein Saci_1271 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.4   1.7        3.5    7.7   0.1    2.2  2  DUF5392   Family of unknown function (DUF5392)


Domain annotation for each model (and alignments):
>> DUF5392  Family of unknown function (DUF5392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1    0.0059   1.1e+02      28      56 ..       2      30 ..       1      44 [. 0.82
   2 ?    7.7   0.1   0.00019       3.5      31      63 ..     110     142 ..     101     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0059
                       DUF5392 28 skysfislPLllvslinlillllkaelee 56
                                  +++++isl L+++ +i  ++l+++ ++++
  gi|70607037|ref|YP_255907.1|  2 NTWKIISLALIVIVVIESVFLFTTIQQSR 30
                                  5789************9999988877654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00019
                       DUF5392  31 sfislPLllvslinlillllkaeleedsliaii 63 
                                   sf+  PLl +slin  +++++ +   +++i++ 
  gi|70607037|ref|YP_255907.1| 110 SFLNNPLLNISLINATVFYMNGHEYLNITIKVY 142
                                   7999*****************999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1446.08
//
Query:       gi|70607038|ref|YP_255908.1|  [L=276]
Description: hypothetical protein Saci_1272 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.9    8.1   4.7        1.5    9.0   1.7    1.8  2  SSDP      Single-stranded DNA binding protein, SSDP


Domain annotation for each model (and alignments):
>> SSDP  Single-stranded DNA binding protein, SSDP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1     0.076   1.4e+03     200     217 ..      27      44 ..      20      49 .. 0.82
   2 ?    9.0   1.7   8.4e-05       1.5     122     231 ..     117     243 ..     107     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.076
                          SSDP 200 sgapgsgGpPgPtpimps 217
                                     + gs+G P Pt ++++
  gi|70607038|ref|YP_255908.1|  27 QITQGSTGDPIPTINTQN 44 
                                   556799********9987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 8.4e-05
                          SSDP 122 glggmnsRlnpprgnymeelsPteygv.gmrspppkstdgpgGinmPalqmggpggrkp..................rpqp 183
                                   ++    +  n p +  + e+sP++y   ++ +++ +st+     ++  ++ +g +  +                     +p
  gi|70607038|ref|YP_255908.1| 117 TMVQYINITNQPSNTFIYEVSPNNYWEyNVTGTTSQSTQLSL--SLNVMNEAGVSLTSGvsetfyiynivgqtylptGTNP 195
                                   56666666788888899999**99998899999999886654..677777776643333455899999999999988899* PP

                          SSDP 184 nasspldySsssPgsysgapgsgGpPgPtpimpsPedstnsgesvytl 231
                                   n     + + ++Pg++s+a +    P+ t i++   +stn   + y +
  gi|70607038|ref|YP_255908.1| 196 NYVEGWKWALNQPGTNSEAQTDWKWPTNTIILTPAMQSTNGYYNAYPI 243
                                   ********************9999****************98888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2060.80
//
Query:       gi|70607039|ref|YP_255909.1|  [L=754]
Description: hypothetical protein Saci_1274 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   63.3  40.2      2e-17   63.3  40.2    1.8  3  STT3      Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3  40.2   1.1e-21     2e-17      20     483 ..      33     511 ..      14     514 .. 0.72
   2 ?   -4.1   0.2      0.31   5.5e+03      47      82 ..     532     561 ..     528     572 .. 0.68
   3 ?   -3.3   0.4      0.17   3.1e+03     354     354 ..     707     707 ..     605     751 .. 0.53

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.1e-21
                                   CCCCCCT--S--SSCHHH.HHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCH..CCC.CHHHHHHCCHHCH CS
                          STT3  20 lFtdedglsylsefDpYY.nyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygpli..vlLamlasaiinhsldv 97 
                                   + +++ + + +  fD++Y +y+++ ++   G          +++ h+ ++P G  ++ +  i  + L  l+s   ++++  
  gi|70607039|ref|YP_255909.1|  33 IISITAFPQTINGFDSWYlFYNALLIVKAGGN-----WYAVPPDVHA-WFPWGYFIELENTIglPFLVALFSVPFYSIFGQ 107
                                   556778889999******77888888777777.....88899****9.*****9999887643377755666666666668 PP

                                   HHHHHHHCCHH.HHHHHHCHHHHHHH.HHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHC CS
                          STT3  98 sirevclwlpa.llgsLlaIpiyflv.relksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaikt 176
                                   +i  +  ++++ +l ++ ++++++ v   ++s ++G +AA++ a  P+++++ ++G+     +  v+ lf+++f+  aik+
  gi|70607039|ref|YP_255909.1| 108 NIVYTLTLVSPiVLDGIGVVAAFLAVeSITNSRVGGYIAAAITAFTPSLTYKNILGSLPKTSWGGVFVLFTIYFLSLAIKK 188
                                   9988888888836899999999999988889999*********************************************** PP

                                   CSTTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTT..S-CCHHHHHHHHHHHHHHH..CCCCCCCTTCHHH CS
                          STT3 177 ksnkislaviaaliiflivlaWggyailiyallllfilalLiigr..felklkiavtfsviiaflviaiivllflgfqvva 255
                                   k+    +   a+++ifl  ++Wggy    y+ + l i+a+Li+ +    ++     t+s i+a+++  +++ + +gf +  
  gi|70607039|ref|YP_255909.1| 189 KK--PLYGIPAGIMIFLANITWGGY---TYIDISLAIAAFLIVLFnkNDEISAKTLTISGITAAFL-TSLSPNTIGFMS-- 261
                                   **..99*******************...55555555555555554113333333447777777777.788899999987.. PP

                                   STTTCHHCCCCHHHHHHHHCCCHHC...CCCCCHHCC....CHHTT.HHHHTT--.GGGHHHHHHHHHHHHC......... CS
                          STT3 256 vseiigalgifgllqlvafgsvvvl.vaelkfyqfis....lfqpgilsevlgli.gevvtalavlglialw......... 321
                                      ++ al+i++l+  + ++   vl   +++++++      ++ ++ l+ +++++  + + ++ + ++i ++         
  gi|70607039|ref|YP_255909.1| 262 EVAHGLALLIIPLFLYLDLYLRRVLpKDIVDSKNIVIgaaiILLVS-LVVLGSVAfKVQLIPSRYYAIINPFfqftvpidr 341
                                   7788888888888877766555554023344444443444322222.3333333333334444444444444777777777 PP

                                   ..................CCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHC..TCH CS
                          STT3 322 ..................lgilyslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgiifvglllef..lav 382
                                                     +g+++s+++  y  l +k   ++ +wl+v ++a + g+    ++++  i+ v +l ++  + +
  gi|70607039|ref|YP_255909.1| 342 tvaeyipqsiaamiqdfgIGLFLSIIGI-YFLLTRK-QDMAGIWLVVLGAASIYGTSEQPYLFNYTIYIVAALAGVavAEL 420
                                   7777777777788888899999999974.3333333.34678899999999999998888888888866666655400344 PP

                                   HHHHHHHHHHHHCCC-SCHCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCT.TTTTHHH.TTHHHCHH CS
                          STT3 383 fvkiysvsqilfsgvvvillmltllpvlallaavkiskifstykdekeakikvaakavaptksnglkeslew.kantnrds 462
                                   f++     ++ ++ +++++lmltl+  +alla   i+   s+  ++  ++          t++  +  +l+w  +nt++++
  gi|70607039|ref|YP_255909.1| 421 FSR-----FMERKIRIAPILMLTLI-GVALLADAGIAVEASYAPQALINSSTS-----YLTTNYAWISALDWiNQNTPNNA 490
                                   444.....45588888998888886.457777777775555555554444444.....467999***************** PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
                          STT3 463 vvitwwdyghilaveadrpVt 483
                                    + +wwdyg+ + ++ +r V+
  gi|70607039|ref|YP_255909.1| 491 FILSWWDYGYWIHAVGNRTVI 511
                                   **********99999988885 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.31
                                   HT-C.....CCHHSSEETTSSTTT-EEESTTCCHCC CS
                          STT3  47 nnGfpGdvvikkknwfdhsqyyPpGsrvdygplivl 82 
                                   n++f    +++    + h   yP+G++ +  p++++
  gi|70607039|ref|YP_255909.1| 532 NESF----AVNVLENDFHL--YPYGNPNYTRPVYIV 561
                                   5555....56666666676..9***99888887765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.17
                                   H CS
                          STT3 354 a 354
                                   +
  gi|70607039|ref|YP_255909.1| 707 M 707
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (754 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4855.83
//
Query:       gi|297616207|ref|YP_003710347.1|  [L=56]
Description: H/ACA RNA-protein complex component Nop10p [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-23   80.7   2.6    6.2e-23   80.6   2.6    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.026   14.6   0.0    1.4  1  Elf1      Transcription elongation factor Elf1 like
      0.037   13.6   0.4      0.054   13.1   0.4    1.3  1  RecR      RecR protein
       0.53   10.1   3.5       0.45   10.3   1.3    1.9  2  Secapin   Honey bee peptides


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   2.6   1.4e-26   6.2e-23       1      50 [.       1      50 [.       1      52 [. 0.98

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.4e-26
                                      .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCHH CS
                            Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralKk 50
                                      mks++r+c+k+ +YT++++cp cg++t+ + P+RFSP Dky kyR++lKk
  gi|297616207|ref|YP_003710347.1|  1 MKSKIRRCNKDYTYTMSERCPTCGEKTFIPIPPRFSPVDKYVKYRIELKK 50
                                      9************************************************9 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.8e-06     0.026      46      72 ..      18      44 ..       2      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.8e-06
                              Elf1 46 vsCkvCgesfetkvnalsepvDvYskw 72
                                       +C +Cge++ + +++  +pvD Y k+
  gi|297616207|ref|YP_003710347.1| 18 ERCPTCGEKTFIPIPPRFSPVDKYVKY 44
                                      48**********************987 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.2e-05     0.054      12      35 ..       1      24 [.       1      27 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                      HHHH-EE-TTT--EESSSS-CCCC CS
                              RecR 12 akekvrhCsrCgnlteedlCaICs 35
                                      +k+k+r+C + +++t ++ C+ C 
  gi|297616207|ref|YP_003710347.1|  1 MKSKIRRCNKDYTYTMSERCPTCG 24
                                      589********************5 PP

>> Secapin  Honey bee peptides
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.19   8.5e+02      25      31 ..      16      22 ..      10      28 .. 0.70
   2 ?   10.3   1.3    0.0001      0.45      22      39 ..      28      45 ..      23      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                           Secapin 25 vPPrCPP 31
                                      +  rCP 
  gi|297616207|ref|YP_003710347.1| 16 MSERCPT 22
                                      5579995 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                           Secapin 22 iidvPPrCPPGskfvknr 39
                                       i +PPr  P  k+vk r
  gi|297616207|ref|YP_003710347.1| 28 FIPIPPRFSPVDKYVKYR 45
                                      589*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 383.76
//
Query:       gi|70607040|ref|YP_255910.1|  [L=263]
Description: translation initiation factor IF-2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-21   76.3   0.2    1.9e-21   76.3   0.2    2.1  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    4.4e-11   43.0   0.1    4.4e-11   43.0   0.1    2.4  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.031   14.0   2.0      0.042   13.6   2.0    1.2  1  N6_N4_Mtase  DNA methylase
       0.59   10.2   6.9       0.32   11.1   0.1    2.3  2  DUF848       Gammaherpesvirus protein of unknown function (DU


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.5      0.31   1.4e+03      72      84 ..      51      63 ..      44      94 .. 0.66
   2 !   76.3   0.2   4.3e-25   1.9e-21       2     115 ..     122     232 ..     121     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.31
                                  HHHHHHHHHHHST CS
                   EIF_2_alpha 72 veaIkeaLkagee 84
                                  v++I+++Lk+ ++
  gi|70607040|ref|YP_255910.1| 51 VKNIRDVLKEDRK 63
                                  7899999994433 PP

  == domain 2  score: 76.3 bits;  conditional E-value: 4.3e-25
                                   HHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHH CS
                   EIF_2_alpha   2 yeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLka 81 
                                   +++++ kl+ekyg+a+d + k+  +++++l+++++p+ +++ L+e+i k+++++kvk +  i+l+++++ Gve+Ik+++ +
  gi|70607040|ref|YP_255910.1| 122 WRDIAFKLEEKYGNAFDSLlKAYKEGDKILKDAGVPDIWIKPLMEEIGKHIEEKKVKASDVISLRTIDPGGVEKIKKVIDT 202
                                   67899**************9************************************************************5 PP

                                   HST.S..TTSSSEEEEEEEESSSSEEEEEEEES. CS
                   EIF_2_alpha  82 geeasneeeveeeeevkikliapPeYvltvetld 115
                                   + e    +  + ++evki++i++P+Y+++v  +d
  gi|70607040|ref|YP_255910.1| 203 AVE----KIDDLDVEVKIYTIGAPRYRIDVIGTD 232
                                   555....445689***************998776 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1   9.7e-15   4.4e-11       3      75 .]      10      83 ..       9      83 .. 0.97
   2 ?   -1.5   1.9      0.72   3.2e+03      34      65 ..     179     209 ..     171     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 9.7e-15
                                  TTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                            S1  3 ekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                    gev+ ++V+++ ++G +V+l+   + ++f+p se+s++  v+++ +vlk++ ++ vkv+++d++++ +++s+k
  gi|70607040|ref|YP_255910.1| 10 SDGEVLVATVKQIFDYGSYVYLDeySNLQAFLPWSEISSR-WVKNIRDVLKEDRKIVVKVIRIDRKKGTVDVSLK 83
                                  579*********************99**************.*****************************99986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.72
                                   GGGSSSSCEESCHHHCEETTEEEEEEEEEEET CS
                            S1  34 aselsrdarvedpdevlkvGdevkvkvlkvdk 65 
                                   as++ +  r+ dp+ v k+++ ++  v+k+d+
  gi|70607040|ref|YP_255910.1| 179 ASDVISL-RTIDPGGVEKIKKVIDTAVEKIDD 209
                                   6666666.889999999999999999999885 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.0   9.4e-06     0.042      22     116 ..      34     156 ..      20     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-06
                                   CCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.....HHHHHHHHHTT-EEEEEEEEEEES.......... CS
                   N6_N4_Mtase  22 yeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.....elkaladeifggffllnvivwkkp.......... 87 
                                   y   + +  ++e   +++k++r+vLk+d  i++ + ++  kk      lk++ +    + + ++++ wkk+          
  gi|70607040|ref|YP_255910.1|  34 YSNLQAFLPWSEISSRWVKNIRDVLKEDRKIVVKVIRIDRKKgtvdvSLKKVTE----DEKKKKMMLWKKTqrvdkileiv 110
                                   5566667779999**********************9999999766553333333....44558888888876665555555 PP

                                   .SSTTTSTCC...........S-B--EEEEEEEESSTT-....... CS
                   N6_N4_Mtase  88 .nsmpesnkd...........rltsthEyilvfsknkkyl.....l 116
                                    +++++ +++           ++ ++++ +l   k ++++      
  gi|70607040|ref|YP_255910.1| 111 sQKLGKKEDEawrdiafkleeKYGNAFDSLLKAYKEGDKIlkdagV 156
                                   3222222222445555555557777777777777777766554440 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   2.3     0.084   3.8e+02      57     110 ..      77     131 ..      54     142 .. 0.54
   2 ?   11.1   0.1   7.1e-05      0.32      58     119 ..     161     225 ..     157     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.084
                        DUF848  57 eikalveavdteieakkkelslLkk..lnrkkvarv.eeLtdkvlelkeevslelds 110
                                    +  ++++v++   +kkk++ l kk  +  k +++v ++L  k+ e+  +++++l++
  gi|70607040|ref|YP_255910.1|  77 TVDVSLKKVTED--EKKKKMMLWKKtqRVDKILEIVsQKLGKKEDEAWRDIAFKLEE 131
                                   333333333332..3333333333311223444544346777777777788888775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.1e-05
                        DUF848  58 ikalveavdteieakkk...elslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeeyq 119
                                   ik l+e ++++ie+kk    ++ +L+ +++  v+++ +  d   e  +++++e+   +   ++y 
  gi|70607040|ref|YP_255910.1| 161 IKPLMEEIGKHIEEKKVkasDVISLRTIDPGGVEKIKKVIDTAVEKIDDLDVEVKIYTIGAPRYR 225
                                   677889999999999861114568999**************************987776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1726  (0.0962686); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1628.28
//
Query:       gi|70607041|ref|YP_255911.1|  [L=66]
Description: 30S ribosomal protein S27e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-19   68.8   1.7    2.6e-19   68.7   1.7    1.1  1  Ribosomal_S27e  Ribosomal protein S27
     0.0051   16.5   2.1      0.014   15.0   2.1    1.8  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.011   15.8   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.011   15.6   1.7       0.33   10.9   0.0    2.2  2  DUF951          Bacterial protein of unknown function (DUF951
      0.015   15.2   1.8        2.9    7.9   0.0    2.1  2  DUF3797         Domain of unknown function (DUF3797)
      0.047   13.2   0.4      0.064   12.8   0.4    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.25   11.7   0.7       0.25   11.7   0.7    1.8  2  RNA_pol_N       RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   1.7     1e-22   2.6e-19       1      51 [.      12      62 ..      12      66 .] 0.94

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1e-22
                                  -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEE CS
                Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqil 51
                                  p+skF++vkC +C+ne+v+Fs a   v C+sCg  +v P+GGkak++ +++
  gi|70607041|ref|YP_255911.1| 12 PKSKFIRVKCRQCNNEQVIFSNATFPVRCLSCGAQIVIPKGGKAKIEGDTV 62
                                  89********************************************97765 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.1   5.5e-06     0.014       2      28 ..      20      48 ..      19      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-06
                                  B-SSS--B----SSS..----SSS----- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgd..piRCkeCGhRil 28
                                  +C +C++e  + +++  p+RC  CG  i+
  gi|70607041|ref|YP_255911.1| 20 KCRQCNNEQVIFSNAtfPVRCLSCGAQIV 48
                                  699*******98887679********997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   4.2e-06     0.011      68     104 ..      16      54 ..       3      61 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                   --EEEETTTS-EEECHHH...HHS-TTTSSS-EEEEESSS CS
                          HypA  68 pvkvrCreCgkefeleek...alrCpkCgsadveivsGee 104
                                    ++v+Cr+C++e  + ++    +rC +Cg++   i +G  
  gi|70607041|ref|YP_255911.1|  16 FIRVKCRQCNNEQVIFSNatfPVRCLSCGAQI-VIPKGGK 54 
                                   5799******9988554323566******964.4555544 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2    0.0053        14      29      39 ..      17      27 ..      15      37 .. 0.76
   2 ?   10.9   0.0   0.00013      0.33      22      44 ..      29      51 ..      25      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0053
                        DUF951 29 iklkClgcgre 39
                                  i++kC +c++e
  gi|70607041|ref|YP_255911.1| 17 IRVKCRQCNNE 27
                                  89******975 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                        DUF951 22 ilRvGadiklkClgcgrevmlpR 44
                                  ++   a + ++Cl+cg ++++p+
  gi|70607041|ref|YP_255911.1| 29 VIFSNATFPVRCLSCGAQIVIPK 51
                                  5666688999***********97 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.5    0.0018       4.5      14      30 ..      19      35 ..       9      39 .. 0.85
   2 ?    7.9   0.0    0.0011       2.9      14      39 ..      38      63 ..      37      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                       DUF3797 14 vqCPeCgNnkvlNsegk 30
                                  v+C +C N++v  s+++
  gi|70607041|ref|YP_255911.1| 19 VKCRQCNNEQVIFSNAT 35
                                  79*********998887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                       DUF3797 14 vqCPeCgNnkvlNsegkviieddtfy 39
                                  v C  Cg + v   +gk  ie dt +
  gi|70607041|ref|YP_255911.1| 38 VRCLSCGAQIVIPKGGKAKIEGDTVR 63
                                  6899*******************965 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.5e-05     0.064       2      29 ..      20      47 ..      19      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                  EETTTTCEECHEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                  kC  C+++++++ +++  ++C +CG+ +
  gi|70607041|ref|YP_255911.1| 20 KCRQCNNEQVIFSNATFPVRCLSCGAQI 47
                                  9************************865 PP

>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.96   2.5e+03       3      12 ..      17      26 ..      16      30 .. 0.74
   2 ?   11.7   0.7   9.7e-05      0.25       3      14 ..      36      47 ..      35      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                                  --SS-TTT-- CS
                     RNA_pol_N  3 iPVrCFtCGk 12
                                  i V+C  C++
  gi|70607041|ref|YP_255911.1| 17 IRVKCRQCNN 26
                                  5588888875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.7e-05
                                  --SS-TTT--B- CS
                     RNA_pol_N  3 iPVrCFtCGkvi 14
                                  +PVrC +CG  i
  gi|70607041|ref|YP_255911.1| 36 FPVRCLSCGAQI 47
                                  7********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 483.60
//
Query:       gi|70607042|ref|YP_255912.1|  [L=95]
Description: 50S ribosomal protein L44e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-28   97.0   9.2    6.5e-28   97.0   9.2    1.5  2  Ribosomal_L44   Ribosomal protein L44
  ------ inclusion threshold ------
      0.075   12.9   0.8        3.6    7.5   0.1    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.076   13.5   1.6      0.076   13.5   1.6    2.9  3  Ribosomal_L33   Ribosomal protein L33
       0.17   11.7   4.9       0.63    9.9   0.2    2.2  2  Cys_rich_KTR    Cysteine-rich KTR
       0.19   11.7   4.6        3.4    7.7   0.3    2.3  2  zinc_ribbon_4   zinc-ribbon domain
       0.33   11.1   6.8       0.44   10.6   1.0    2.1  2  CxC5            CxC5 like cysteine cluster associated with KD


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.1   3.3e+03      51      60 ..       6      15 ..       5      16 .. 0.78
   2 !   97.0   9.2   2.2e-31   6.5e-28       1      76 []      16      91 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                  -EEEEETTT- CS
                 Ribosomal_L44 51 vlrleCteCk 60
                                  v++  C +Ck
  gi|70607042|ref|YP_255912.1|  6 VIKTYCPKCK 15
                                  5678899998 PP

  == domain 2  score: 97.0 bits;  conditional E-value: 2.2e-31
                                  EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                 Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                  +Hteh+v+ yk gk+++la+g+Rry+rk+ gyg+++kp +k++aKttKK +l l+C++C ++++k+++R+kk+elv
  gi|70607042|ref|YP_255912.1| 16 THTEHSVSLYKGGKRRSLAEGQRRYERKNVGYGSKRKPEQKRFAKTTKKQTLVLKCQKCSYTIVKEGMRLKKLELV 91
                                  6*************************************************************************96 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.017        51       3       9 ..      10      16 ..       7      22 .. 0.76
   2 ?    7.5   0.1    0.0012       3.6      15      29 ..      62      76 ..      59      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.017
                                  BESTTTS CS
                RNA_POL_M_15KD  3 FCpkCgN 9 
                                   CpkC+ 
  gi|70607042|ref|YP_255912.1| 10 YCPKCKT 16
                                  5888874 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                                  ECSCCCEEEESSSS- CS
                RNA_POL_M_15KD 15 edkegknfeCrqCgY 29
                                  ++k + ++ C +C+Y
  gi|70607042|ref|YP_255912.1| 62 TKKQTLVLKCQKCSY 76
                                  445554599****** PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   2.5e-05     0.076      30      43 ..       7      20 ..       6      21 .. 0.90
   2 ?    0.3   0.5      0.32   9.6e+02      27      42 ..      52      67 ..      34      68 .. 0.71
   3 ?    1.9   1.0       0.1   3.1e+02       4      29 ..      68      89 ..      65      91 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                  EEEEETTTTEEEEE CS
                 Ribosomal_L33 30 lkKYcprcrkhtlh 43
                                  +k Ycp+c+ ht h
  gi|70607042|ref|YP_255912.1|  7 IKTYCPKCKTHTEH 20
                                  688*********99 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.32
                                  --EEEEEETTTTEEEE CS
                 Ribosomal_L33 27 rLelkKYcprcrkhtl 42
                                  + e k++ ++ +k tl
  gi|70607042|ref|YP_255912.1| 52 KPEQKRFAKTTKKQTL 67
                                  4467788888888876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                                  EEEET......EEEEETT..--S--E CS
                 Ribosomal_L33  4 tLeCtecksrnYtttknkkntperLe 29
                                   L+C++c    Yt+ k      ++Le
  gi|70607042|ref|YP_255912.1| 68 VLKCQKC---SYTIVKEG-MRLKKLE 89
                                  6899965...47777766.4455665 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00021      0.63      29      37 ..      10      18 ..       5      24 .. 0.85
   2 ?    3.8   0.8     0.016        48      16      38 ..      57      79 ..      51      95 .] 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                  Cys_rich_KTR 29 fCPKCkqet 37
                                  +CPKCk +t
  gi|70607042|ref|YP_255912.1| 10 YCPKCKTHT 18
                                  9*****865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                  Cys_rich_KTR 16 kiredTvLknfpLfCPKCkqetl 38
                                  +  + T  ++  L C KC +  +
  gi|70607042|ref|YP_255912.1| 57 RFAKTTKKQTLVLKCQKCSYTIV 79
                                  55667777888899999987655 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4    0.0047        14       3      10 ..       9      16 ..       6      19 .. 0.83
   2 ?    7.7   0.3    0.0011       3.4      20      35 ..      63      78 ..      59      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0047
                 zinc_ribbon_4  3 itCpsCka 10
                                  + Cp+Ck+
  gi|70607042|ref|YP_255912.1|  9 TYCPKCKT 16
                                  67999998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                 zinc_ribbon_4 20 pakgvkvrCskCghvF 35
                                  ++++  ++C kC+ ++
  gi|70607042|ref|YP_255912.1| 63 KKQTLVLKCQKCSYTI 78
                                  5677899*****9886 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.0   0.00015      0.44      46      71 ..       6      40 ..       2      49 .. 0.73
   2 ?    3.7   0.5      0.02        61      44      55 ..      64      75 ..      55      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                          CxC5 46 vlslyCpkCktrYypdyyvhdg.........vrtY 71
                                  v+ +yCpkCkt+  ++ + ++g         +r Y
  gi|70607042|ref|YP_255912.1|  6 VIKTYCPKCKTHTEHSVSLYKGgkrrslaegQRRY 40
                                  7899********99999999776544444445544 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                          CxC5 44 vwvlslyCpkCk 55
                                   ++l l+C+kC+
  gi|70607042|ref|YP_255912.1| 64 KQTLVLKCQKCS 75
                                  5899*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 692.10
//
Query:       gi|70607043|ref|YP_255913.1|  [L=153]
Description: hypothetical protein Saci_1278 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.1   0.0      0.082   12.5   0.0    1.4  1  3-HAO     3-hydroxyanthranilic acid dioxygenase


Domain annotation for each model (and alignments):
>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.6e-06     0.082      55      89 ..      95     129 ..      51     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-06
                                   EEEEEEES-EEEEEEETTCCCEEEE-TTEEEEE-T CS
                         3-HAO  55 effyqkkGdmvlkvldegkardivireGeifllPa 89 
                                     +y k+G+++ kv++  + ++i ++ G+  llP 
  gi|70607043|ref|YP_255913.1|  95 GNYYTKDGKILCKVVNPLTYNNITLNSGDFILLPL 129
                                   569******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 960.81
//
Query:       gi|70607044|ref|YP_255914.1|  [L=322]
Description: DNA primase small subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-10   40.9   0.7    1.1e-05   25.5   0.9    2.6  2  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.9   6.3e-10   1.1e-05      11      78 ..     130     197 ..      99     209 .. 0.85
   2 !   12.5   0.0   6.1e-06      0.11     144     171 ..     225     253 ..     214     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.3e-10
                                   .TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEE.ES-HHHHHHHHHH. CS
                 DNA_primase_S  11 cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdar.pltdeeraaivnyl 78 
                                   +++ +++  c + v + + vl+  l++dfg k   + fsg+rGfH+ v +++ + +l++e r++i++y+
  gi|70607044|ref|YP_255914.1| 130 REISEITVDCINRVFENALVLKDILIQDFGLK-PRIFFSGNRGFHIRVDCYNEWaNLDSEDRREIAEYI 197
                                   77788888999999999**************9.999**********999998888***********974 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.1e-06
                                   ..-----------------....---.-- CS
                 DNA_primase_S 144 prldeqvtkgikhllkapfcihgktg.nv 171
                                   +++deqvt + k+l ++p++++gk g +v
  gi|70607044|ref|YP_255914.1| 225 VKIDEQVTVDPKRLVRIPGSLNGKAGlKV 253
                                   79**********************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2134.99
//
Query:       gi|70607045|ref|YP_255915.1|  [L=245]
Description: DNA polymerase sliding clamp C [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-10   38.9   0.1    1.2e-09   37.9   0.1    1.5  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
      0.001   19.2   0.0      0.021   15.0   0.0    2.8  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
     0.0042   16.6   0.0     0.0047   16.4   0.0    1.2  1  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   2.1e-13   1.2e-09       8     101 ..       7      98 ..       1     108 [. 0.88
   2 ?   -2.4   0.0      0.59   3.5e+03      27      56 ..     154     183 ..     137     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-13
                                   SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEE CS
                        PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsv 88 
                                   +a  +  ++ ++ + v+ea++   ++G++++ +D s+v  + + + ++ fe+y  + ++ +gv+l+ ++ ++k + +ed++
  gi|70607045|ref|YP_255915.1|   7 DALGFSYIFKTLSQYVSEATLLFGNDGFKVKGMDPSKVVYIDIFVPKDYFEEYNLENEMKIGVSLKDVNEVIKNVSKEDIL 87 
                                   55556779999*********************************************************************9 PP

                                   EEEEETTSSEEEE CS
                        PCNA_N  89 tlkaedeadtlal 101
                                    l+ e   d++++
  gi|70607045|ref|YP_255915.1|  88 YLELEK--DKIMF 98 
                                   998765..44544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.59
                                   EEEEETTEEEEEEE-TTSSEEEEEEEEGGG CS
                        PCNA_N  27 nfdcddsGislqalDsshvaLvslelrseg 56 
                                    f++++  + l ++ +   ++v+l+l++ g
  gi|70607045|ref|YP_255915.1| 154 RFKAQNGKLYLSVMGDMGESIVELSLENGG 183
                                   455666666677777777777777776655 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   7.1e+03      15      40 ..       8      33 ..       5      38 .. 0.70
   2 ?    1.0   0.0     0.077   4.6e+02      57      89 ..      75     108 ..      59     130 .. 0.66
   3 !   15.0   0.0   3.6e-06     0.021      78     127 ..     193     242 ..     124     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                                  HHHHHHHHHHHTTT-SEEEEEEETTE CS
                        PCNA_C 15 ssefaricrdlsqlsdsvvisvtkeg 40
                                  +  f+ i + lsq   + ++    +g
  gi|70607045|ref|YP_255915.1|  8 ALGFSYIFKTLSQYVSEATLLFGNDG 33
                                  56789999999988776666666655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.077
                                   --BEESSSGGGCBEEEES.S-EEEEEEHHHHHHH CS
                        PCNA_C  57 kqvkdvdkeeeavklelk.epvtltfalkYlaef 89 
                                   ++v +   +e+   lel+ + + +t  ++Yl +f
  gi|70607045|ref|YP_255915.1|  75 NEVIKNVSKEDILYLELEkDKIMFTLDGEYLRTF 108
                                   3333333456666666641467777777777766 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3.6e-06
                                   EEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                        PCNA_C  78 tltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                   +  ++l+++ + tk    s++ ++ + s++Pl++ y++ ++g+  +++a+
  gi|70607045|ref|YP_255915.1| 193 ESLYGLEHVSNTTKMRRPSDTLEIAFGSQLPLKLRYNLPKGGYADFYIAP 242
                                   4568899999999***********************************98 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-07    0.0047       1      76 [.      11      84 ..      11     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-07
                          Rad9  1 laralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsak 76
                                  ++ ++++ls+   e  l  ++dg++++ ++ s+  y  +   k++F++y  + ++++++ +++K v +v++++s++
  gi|70607045|ref|YP_255915.1| 11 FSYIFKTLSQYVSEATLLFGNDGFKVKGMDPSKVVYIDIFVPKDYFEEY--NLENEMKIGVSLKDVNEVIKNVSKE 84
                                  567899999999999999*******************************..8999999************988733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1688.22
//
Query:       gi|70607046|ref|YP_255916.1|  [L=254]
Description: GTPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-57  195.1   0.1    1.8e-57  194.9   0.1    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    1.8e-06   27.9   0.0     0.0069   16.2   0.0    3.1  3  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    0.00012   22.6   0.0    0.00019   21.9   0.0    1.4  1  AAA_18           AAA domain
    0.00027   20.7   0.0      0.015   15.1   0.0    2.7  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
    0.00049   20.3   0.1     0.0013   18.9   0.0    1.6  1  DUF87            Helicase HerA, central domain
     0.0011   18.7   0.0      0.022   14.4   0.0    2.1  2  SRP54            SRP54-type protein, GTPase domain
     0.0012   18.5   0.0      0.093   12.3   0.0    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0018   18.7   0.1       0.43   10.9   0.0    2.5  2  AAA_19           AAA domain
     0.0022   18.3   0.0      0.011   16.0   0.0    2.1  2  AAA_22           AAA domain
     0.0026   18.2   0.0     0.0048   17.3   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0042   17.0   0.1       0.46   10.4   0.0    2.4  2  NTPase_1         NTPase
     0.0049   16.8   0.0        2.4    8.1   0.0    3.3  3  RsgA_GTPase      RsgA GTPase
     0.0051   16.9   0.1       0.05   13.7   0.1    2.2  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0051   16.8   0.0       0.01   15.8   0.0    1.5  1  NACHT            NACHT domain
     0.0054   16.8   0.0     0.0065   16.5   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0089   15.3   0.1       0.25   10.6   0.0    2.4  2  Septin           Septin
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.082   12.6   0.0    2.0  2  AAA_30           AAA domain
      0.011   15.4   0.0      0.018   14.8   0.0    1.3  1  AAA_24           AAA domain
      0.012   15.7   0.1        1.5    8.9   0.0    2.3  2  Dynamin_N        Dynamin family
      0.012   15.3   0.0      0.023   14.4   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.014   15.7   0.0       0.02   15.1   0.0    1.5  1  AAA_28           AAA domain
      0.015   14.5   0.0      0.022   14.0   0.0    1.4  1  ArsA_ATPase      Anion-transporting ATPase
      0.017   14.6   0.0      0.084   12.3   0.0    2.0  2  KTI12            Chromatin associated protein KTI12
      0.018   14.6   0.0       0.63    9.6   0.0    2.4  2  FeoB_N           Ferrous iron transport protein B
      0.029   13.4   0.0      0.046   12.7   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.03   14.1   0.0      0.068   12.9   0.0    1.6  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.033   13.3   0.0      0.049   12.7   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
      0.036   14.1   0.1        8.4    6.5   0.0    2.8  3  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
      0.046   13.7   0.2        0.2   11.7   0.1    2.2  2  AAA_14           AAA domain
      0.048   13.6   0.0        0.1   12.5   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.065   12.7   0.0       0.11   11.9   0.0    1.4  1  PhoH             PhoH-like protein
      0.065   13.7   0.2       0.12   12.9   0.2    1.5  1  ABC_tran         ABC transporter
      0.083   12.1   0.0       0.13   11.4   0.0    1.3  1  NB-ARC           NB-ARC domain
      0.092   13.1   0.0       0.33   11.4   0.0    2.0  1  RNA_helicase     RNA helicase
      0.094   11.9   0.0       0.16   11.2   0.0    1.4  1  KAP_NTPase       KAP family P-loop domain
       0.13   11.5   0.0       0.18   11.1   0.0    1.2  1  Zeta_toxin       Zeta toxin
       0.14   12.0   0.0       0.26   11.1   0.0    1.5  1  CPT              Chloramphenicol phosphotransferase-like prot
       0.14   12.0   0.0       0.28   11.1   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
       0.15   11.5   0.0         24    4.4   0.0    2.9  3  GTP_EFTU         Elongation factor Tu GTP binding domain
       0.22   11.7   0.0       0.37   11.0   0.0    1.4  1  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.1     4e-60   1.8e-57       1     239 [.       6     239 ..       6     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 4e-60
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldw 81 
                                   v+G+aGsGKtt+v+al+++l +++ + a++NLDPA+e lpY++++d re++++ dvm++++lgpn +lv+++++l ++  +
  gi|70607046|ref|YP_255916.1|   6 VLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPAVEVLPYKPDIDAREYVDVYDVMNKYELGPNSSLVISVDLLLTKAKE 86 
                                   89******************************************************************************* PP

                    ATP_bind_1  82 ldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvv 162
                                   l+e+l++ +++y+l+DtPGQielf +++ ++++   +++  + v+v+L+Ds  ++dp +f+s  l+++s+ +r+++P++ v
  gi|70607046|ref|YP_255916.1|  87 LKEDLNQLQANYVLVDTPGQIELFAYRDTGKILSSFISEGSKSVSVFLFDSYLSKDPKSFLSLFLLSSSIKFRIDMPQISV 167
                                   *****888***********************88888888****************************************** PP

                    ATP_bind_1 163 lnkfDllkek.lekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslideal 239
                                   l+k+Dll+++ le+   ++ed   +++l   + e+  +l ++i+e le f      +p+ss + +++++l++ +++ l
  gi|70607046|ref|YP_255916.1| 168 LSKVDLLSSSeLERMRSWIEDGSIIDELGSID-EYSFELVKTIVENLESFP-----IPVSSTNFSGLDQLYAEVQKVL 239
                                   ********888999999999988887777655.444556666666666555.....5599999999999999998865 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05    0.0069       1      32 [.       8      39 ..       8      44 .. 0.94
   2 ?    4.8   0.0     0.047        21      86     120 ..      79     113 ..      68     152 .. 0.76
   3 ?    3.5   0.0      0.12        54     100     131 ..     184     215 ..     164     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                        CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                  G   sGK+Tl++ L +y+l+++  +++++lD+
  gi|70607046|ref|YP_255916.1|  8 GTAGSGKTTLVKALQDYLLNNELDTAIINLDP 39
                                  7789***************************9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.047
                        CLP1_P  86 elareveekleenkkakasgliIntpGwvkglgae 120
                                    l+++++e  e  ++ +a+ ++++tpG ++ ++++
  gi|70607046|ref|YP_255916.1|  79 LLLTKAKELKEDLNQLQANYVLVDTPGQIELFAYR 113
                                   45555555555556789***********9988875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                        CLP1_P 100 kakasgliIntpGwvkglgaellleliealep 131
                                   +  ++g iI+  G ++++ +el + ++e le 
  gi|70607046|ref|YP_255916.1| 184 SWIEDGSIIDELGSIDEYSFELVKTIVENLES 215
                                   4567899******************9998875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   4.3e-07   0.00019       1      59 [.       4      69 ..       4     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.3e-07
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.....gvnlrdvakenglllevdpe..aldeskrldedkldk 59
                                  I++ Gt+G+GKttl k+L++ l ++      +nl   +    +  + d +   +d ++++++  l  
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLlNNeldtaIINLDPAVEVLPYKPDID-AreYVDVYDVMNKYELGP 69
                                  99****************999877777765222222222222222222.234455555555555444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-05     0.015       3      27 ..       3      27 ..       1      43 [. 0.81
   2 ?    3.0   0.0      0.17        76      82     117 ..     154     188 ..      83     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                     PduV-EutP  3 killiGkvgsGKttLtqalkgeelk 27
                                   i+++G+ gsGKttL +al++  l+
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKALQDYLLN 27
                                  5899****************97775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                     PduV-EutP  82 pgfasvfnkeviGiitkidlaedeenieaveelLks 117
                                    ++   +  + i ++ k+dl  +++++e  +++++ 
  gi|70607046|ref|YP_255916.1| 154 SSIKFRIDMPQISVLSKVDLL-SSSELERMRSWIED 188
                                   444445567789999999999.88889999998876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.8e-06    0.0013      28      83 ..       6      66 ..       4     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.8e-06
                         DUF87 28 ilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal....ekllsekvkvitpsp 83
                                  +lg++GsGK+++v+ L + ll+ + ++ i+ lDp  E  +++    ++++ + ++v+++ +
  gi|70607046|ref|YP_255916.1|  6 VLGTAGSGKTTLVKALQDYLLNnELDTAIINLDPAVEVLPYKpdidAREYVDVYDVMNKYE 66
                                  9********************999999*******999888887666555555555555533 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.8e-05     0.022       3      38 ..       3      38 ..       1      40 [. 0.92
   2 ?    2.1   0.0      0.29   1.3e+02      73      95 ..      85     107 ..      77     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                   i ++G+ G+GKTt +  L ++l +++ +++++ +D
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKALQDYLLNNELDTAIINLD 38
                                  57899*************************999988 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                                   HHHHHHHHHTTSSEEEEEE--SS CS
                         SRP54  73 keavekakeekidvvlvDTaGrl 95 
                                   ke  e  ++ ++++vlvDT G+ 
  gi|70607046|ref|YP_255916.1|  85 KELKEDLNQLQANYVLVDTPGQI 107
                                   5555667778899*******986 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00021     0.093       4      32 ..       5      35 ..       2      42 .. 0.83
   2 ?    3.5   0.0       0.1        46     139     167 ..     160     187 ..     151     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                                  EEEESTTCCHHHHHHHHH..CT--SS-EEEE CS
                          cobW  4 vltGflGsGKTtLlnhll..enraglklavi 32
                                   + G  GsGKTtL+++l     +++l++a+i
  gi|70607046|ref|YP_255916.1|  5 FVLGTAGSGKTTLVKALQdyLLNNELDTAII 35
                                  67899**********9988767788888888 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                                   HHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                          cobW 139 laaadllvlnKtDlldeeallekleerlr 167
                                   + +  + vl+K+Dll++++l e+++++++
  gi|70607046|ref|YP_255916.1| 160 IDMPQISVLSKVDLLSSSEL-ERMRSWIE 187
                                   66667789**********77.99987765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00096      0.43      13      38 ..       4      29 ..       2      40 .. 0.83
   2 ?    5.6   0.1     0.042        19     106     128 ..     190     212 ..      71     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00096
                        AAA_19 13 llvtaGpGtGKTrvlkhivallvelg 38
                                  ++v++ +G+GKT+++k+   +l++++
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNNE 29
                                  789************99888777655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.042
                        AAA_19 106 livDEfqdvdelqyrLlkallge 128
                                    i+DE   +de  ++L+k+++++
  gi|70607046|ref|YP_255916.1| 190 SIIDELGSIDEYSFELVKTIVEN 212
                                   58*****************9954 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.5e-05     0.011       7      38 ..       3      36 ..       1     106 [. 0.73
   2 ?   -0.4   0.0       2.8   1.3e+03      96     117 ..     191     211 ..     153     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-05
                        AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee..e 38
                                  +++v G +G+GKTtl++ l++ l + +  +   +
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKALQDYLLNNELDTAiiN 36
                                  899****************998876655444562 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.8
                        AAA_22  96 iiDEaqhlr..seealeeLrslln 117
                                   iiDE   ++  s   +e ++++++
  gi|70607046|ref|YP_255916.1| 191 IIDELGSIDeyS---FELVKTIVE 211
                                   777777774443...333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-05    0.0048      27      52 ..       4      29 ..       3     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                        AAA_16 27 vllsGesGvGKsslvrellralekdg 52
                                  +++ G +G+GK++lv++l+++l  ++
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNNE 29
                                  79*****************9998873 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0     0.001      0.46       2      26 ..       4      28 ..       3      33 .. 0.86
   2 ?    4.4   0.0      0.07        31      96     124 ..     187     215 ..     152     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                  EEEE--TTSSHHHHHHHHHHHH... CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                  +f+ G  G+GKtTlvk + + l ++
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNN 28
                                  7999************999988665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.07
                                   H-EEEE---STTGGG-HHHHHHHHHHHTT CS
                      NTPase_1  96 adviviDEiGkmElkskkfkeaveevLks 124
                                   +d  +iDE G++   s ++ +++ e L+s
  gi|70607046|ref|YP_255916.1| 187 EDGSIIDELGSIDEYSFELVKTIVENLES 215
                                   56789*******99999999999888876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0053       2.4     103     121 ..       5      23 ..       2      38 .. 0.82
   2 ?    2.2   0.0      0.33   1.5e+02     145     161 ..      90     106 ..      71     111 .. 0.85
   3 ?    2.6   0.0      0.25   1.1e+02      49      70 ..     164     184 ..     145     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0053
                                   EEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase 103 vlvGqSGvGKStLinallp 121
                                   +++G  G GK+tL++al+ 
  gi|70607046|ref|YP_255916.1|   5 FVLGTAGSGKTTLVKALQD 23 
                                   679*************987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.33
                                   EEEEETTTEEEESS-SS CS
                   RsgA_GTPase 145 ellelaegglliDtPGf 161
                                    l +l+++ +l+DtPG 
  gi|70607046|ref|YP_255916.1|  90 DLNQLQANYVLVDTPGQ 106
                                   5778899999*****95 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.25
                                   EEEEEE-GGG--HHHHHHHHHH CS
                   RsgA_GTPase  49 pvivlnKiDlleeeeeleelke 70 
                                    + vl+K+Dll+++e le++++
  gi|70607046|ref|YP_255916.1| 164 QISVLSKVDLLSSSE-LERMRS 184
                                   55699******9999.555444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   0.00011      0.05       2      85 ..       4     137 ..       3     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE.................................. CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke.................................. 47 
                                   + ++G   +GK+tL++al +       d++   +d+  + + +k  +                                  
  gi|70607046|ref|YP_255916.1|   4 IFVLGTAGSGKTTLVKALQDYlLNNELDTAIINLDPAVEVLPYK--Pdidareyvdvydvmnkyelgpnsslvisvdlllt 82 
                                   67899999**********87533444455555555555544422..11223345556666666777777777888888888 PP

                                   ...............EEEEECGGCSS.HHHHHH.HHHHHHHHHHCTSEEEEEEET CS
                      MMR_HSR1  48 ...............ielvDtpGlie.gaseek.glgkaflaleeadlillvvda 85 
                                                  ++lvDtpG ie  a ++  ++  +f +  + ++ ++++d+
  gi|70607046|ref|YP_255916.1|  83 kakelkedlnqlqanYVLVDTPGQIElFAYRDTgKILSSFISEGSKSVSVFLFDS 137
                                   888888888888888********87653333333567777765556777888773 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.2e-05      0.01       3      25 ..       4      26 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                                  EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                  +++ G aGsGKTtL++ l + + 
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLL 26
                                  799*************9988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-05    0.0065       4      55 ..       6      83 ..       3     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                                  EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..............................C CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................x RF
                          CbiA  4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..............................d 55
                                  + ++ G+GKTtl+ +L  +l +++l+++ + +Dp  + l +    ++di+                                
  gi|70607046|ref|YP_255916.1|  6 VLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPAVEVLPY----KPDIDAreyvdvydvmnkyelgpnsslvisvdllltK 83
                                  55788******************************999983....3333323345556666677777777777755555552 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00056      0.25       7      89 ..       4     123 ..       1     141 [. 0.69
   2 ?    2.3   0.0      0.19        86     145     168 ..     165     188 ..     156     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                   EEEEEBTTSSCCCCCCTTSSSS----..................................--------------S-E.EEE CS
                        Septin   7 lmvvGesglGkttlintlfetdliee..................................ekleeasekkkktveik.kkk 52 
                                   ++v G+ g Gkttl+++l    l +e                                  +    ++++   +v++  +k+
  gi|70607046|ref|YP_255916.1|   4 IFVLGTAGSGKTTLVKALQDYLLNNEldtaiinldpavevlpykpdidareyvdvydvmnKYELGPNSSLVISVDLLlTKA 84 
                                   7899*************9877777767777888888888888888888888888887775333445556666666654556 PP

                                   EEEEETTCEEEEE..EEE---BSSSSSHHCCCHHHHHHH CS
                        Septin  53 vvieedgvklnlt..viDtpgfGdavdnskswepiveyi 89 
                                   ++++ed  +l+ +  ++Dtpg  +    +++ +++ ++i
  gi|70607046|ref|YP_255916.1|  85 KELKEDLNQLQANyvLVDTPGQIELFAYRDTGKILSSFI 123
                                   667776444443322678888666666666655555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                                   EEEESSGGGS-HHHHHHHHHHHHH CS
                        Septin 145 iPviaKaDtltkeElkefKkkire 168
                                   i v++K D l ++El+++++ i +
  gi|70607046|ref|YP_255916.1| 165 ISVLSKVDLLSSSELERMRSWIED 188
                                   789***************998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018     0.082      22      42 ..       5      25 ..       2      43 .. 0.80
   2 ?    0.4   0.0         1   4.6e+02      83     109 ..     181     207 ..     160     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                        AAA_30 22 vltGpAGtGKttalkalreaw 42
                                  ++ G AG+GKtt++kal++ +
  gi|70607046|ref|YP_255916.1|  5 FVLGTAGSGKTTLVKALQDYL 25
                                  688*************98765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1
                        AAA_30  83 rarlepgtllivDEagmvdtkqlaall 109
                                   r+r + ++  i+DE g +d  +++ + 
  gi|70607046|ref|YP_255916.1| 181 RMRSWIEDGSIIDELGSIDEYSFELVK 207
                                   4455566788******99877666554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.9e-05     0.018       5      61 ..       4      89 ..       2     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-05
                        AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel..................... 59
                                  i++ G +g+GKTtl+k l       + ++++i+++  +  l  +   d++ + d++d +++                      
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALqdyllnnELDTAIINLDPAVEVLPYKPDIDAREYVDVYDVMNKYelgpnsslvisvdllltkake 86
                                  7899**************99999999999999999999998888888888666666666666333444444444444333333 PP

                        AAA_24 60 .aa 61
                                   ++
  gi|70607046|ref|YP_255916.1| 87 lKE 89
                                  333 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.061        27       1      18 [.       4      21 ..       4      28 .. 0.92
   2 ?    8.9   0.0    0.0032       1.5      92     146 ..      87     143 ..      48     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.061
                                  EEEEEBTTTTHHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                                  i v+G+  sGK++++ aL
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKAL 21
                                  789************998 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0032
                                   EEEEEETTS-SEEEEE---B-S.SSGTTS.HHHHHHHSTTEEEEEEEETTS-CCC-C CS
                     Dynamin_N  92 llkilsllvkgltlvDlPGlds.vnkrdq.elvkeyikkadiilavtsanhdlsnse 146
                                   l ++l+ l+ +++lvD+PG ++  + rd+ +++ ++i + +  + v  +++ ls+  
  gi|70607046|ref|YP_255916.1|  87 LKEDLNQLQANYVLVDTPGQIElFAYRDTgKILSSFISEGSKSVSVFLFDSYLSKDP 143
                                   5678889999*********98856666667777777765555555555555555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-05     0.023      26      50 ..       5      29 ..       2      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-05
                        AAA_29 26 lltGpsGsGKSTllDAiqalLvpak 50
                                  ++ G+ GsGK+Tl+ A+q  L+ ++
  gi|70607046|ref|YP_255916.1|  5 FVLGTAGSGKTTLVKALQDYLLNNE 29
                                  689**************98887765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.5e-05      0.02       2      22 ..       4      24 ..       3     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-05
                        AAA_28  2 ivitGgestGKTtlleaLaar 22
                                  i ++G+ ++GKTtl++aL++ 
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDY 24
                                  7899**************954 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.022       1      41 [.       1      41 [.       1     104 [. 0.94

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                                  -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTT CS
                   ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAh 41
                                  + +i+v G  G GKtt+  a+  +l +++ ++ +i +DPA 
  gi|70607046|ref|YP_255916.1|  1 MYFIFVLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPAV 41
                                  569************************************96 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019     0.084       1      38 [.       1      38 [.       1      55 [. 0.88
   2 ?   -0.7   0.0       1.7   7.6e+02     143     202 ..     157     238 ..     154     241 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                  E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                         KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                  M  + + G   sGK+t++k L+++l +++ +  +i+ +
  gi|70607046|ref|YP_255916.1|  1 MYFIFVLGTAGSGKTTLVKALQDYLLNNELDTAIINLD 38
                                  6678999*************************999854 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                   S-GGGS-SEEEE....TTS---HHHHHHHH.................HHHHTS--SSSTT-------HH..HHHHHHHHHH CS
                         KTI12 143 knrWDsPlftvls...aeeklpldeilkal.................iekkklkpnqatlskplaeanf..lqeLdketse 201
                                   k+r D P ++vls   +  + +l+++++++                    k   +n ++   p +++nf  l++L +e+++
  gi|70607046|ref|YP_255916.1| 157 KFRIDMPQISVLSkvdLLSSSELERMRSWIedgsiidelgsideysfELVKTIVENLESFPIPVSSTNFsgLDQLYAEVQK 237
                                   567788888887766555667777777777777777777777666653344455666666666666666334556556655 PP

                                   H CS
                         KTI12 202 i 202
                                   +
  gi|70607046|ref|YP_255916.1| 238 V 238
                                   5 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.18        82       3      22 ..       4      23 ..       2      35 .. 0.88
   2 ?    9.6   0.0    0.0014      0.63      44      90 ..      93     139 ..      81     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                                  EEEEESTTSSHHHHHHHHHT CS
                        FeoB_N  3 valvGnpnvGkttlfnaltg 22
                                  + ++G   +Gkttl+ al +
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQD 23
                                  67899**********99965 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                                   ETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGG CS
                        FeoB_N  44 lkgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatn 90 
                                   + + ++ +vD PG  +l ay    k+  +f+ e +  v v + d+  
  gi|70607046|ref|YP_255916.1|  93 QLQANYVLVDTPGQIELFAYRDTGKILSSFISEGSKSVSVFLFDSYL 139
                                   4568999*********************************9999864 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.046      34      69 ..       6      41 ..       2      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                  EEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                          MeaB 34 ltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                  + G+ G+Gk tlv+al   l ++    a++ +DP+ 
  gi|70607046|ref|YP_255916.1|  6 VLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPAV 41
                                  6799******************************85 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00015     0.068       1      21 [.       4      24 ..       4      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
               Viral_helicase1  1 ivvhGvpGcGKStlirkllrt 21
                                  i v G +G+GK+tl++ l + 
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDY 24
                                  5799*********98888765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.049     131     171 ..       3      45 ..       1      58 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                         T2SSE 131 lilvsGgTgsGKttllyallkeinks..derivtvEDpvEiql 171
                                    i v G+ gsGKttl+ al  ++ ++  d  i+ +  +vE+ +
  gi|70607046|ref|YP_255916.1|   3 FIFVLGTAGSGKTTLVKALQDYLLNNelDTAIINLDPAVEVLP 45 
                                   68999*************9998755547888999888888765 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       3.7   1.7e+03      52      67 ..      52      67 ..      46      90 .. 0.77
   2 ?    6.5   0.0     0.019       8.4      56      78 ..     162     184 ..     157     194 .. 0.87
   3 ?    3.9   0.0      0.12        52      65     102 ..     198     237 ..     194     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.7
                  MMR_HSR1_Xtn 52 nrvYipclyvlNKiDl 67
                                   r+Y+ +  v+NK  l
  gi|70607046|ref|YP_255916.1| 52 AREYVDVYDVMNKYEL 67
                                  5778888888888765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelar 78 
                                   +p + vl K+Dl+s +el+++++
  gi|70607046|ref|YP_255916.1| 162 MPQISVLSKVDLLSSSELERMRS 184
                                   7899***************9976 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.12
                  MMR_HSR1_Xtn  65 iDlisleeldelare..pnsvviSaekelnldeLkekiwe 102
                                   iD+ s e ++++ ++  +  +++S+ +  +ld+L  ++ +
  gi|70607046|ref|YP_255916.1| 198 IDEYSFELVKTIVENleSFPIPVSSTNFSGLDQLYAEVQK 237
                                   8999999999999973245677999999******988765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00045       0.2       5      41 ..       4      40 ..       2     140 .. 0.86
   2 ?   -1.0   0.0       3.6   1.6e+03      68      90 ..     190     213 ..     126     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                        AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldde 41
                                  +++ G   +GKTtl+k l + ll ++ ++  inld  
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPA 40
                                  6789999**********99888888889999999864 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                        AAA_14  68 lflDEiqevpew.ekalkslvdeg 90 
                                    ++DE   ++e  ++ +k +v++ 
  gi|70607046|ref|YP_255916.1| 190 SIIDELGSIDEYsFELVKTIVENL 213
                                   467777777664145566666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022       0.1       2      33 ..       4      35 ..       3      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
                          MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                  + + g+ gsGKTtL++ l   l +++l  ++i
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNNELDTAII 35
                                  5688******************9999998887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.11      21      61 ..       3      43 ..       1      65 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                  EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T CS
                          PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea 61
                                  ++f++G aG+GKt l  al   +l+++  + ii + pave+
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKALQDYLLNNELDTAIINLDPAVEV 43
                                  5899**********999988888888888899999999985 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00026      0.12      15      33 ..       5      23 ..       3      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00026
                                  EEEESTTSSHHHHHHHHTT CS
                                  xxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 15 aivGenGaGKStLlkllag 33
                                   ++G  G+GK+tL+k+l  
  gi|70607046|ref|YP_255916.1|  5 FVLGTAGSGKTTLVKALQD 23
                                  689*************975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.13      22      39 ..       3      20 ..       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                  EEEEEESTTSSHHHHHHH CS
                        NB-ARC 22 vvalvGmgGvGKttlakq 39
                                  ++++ G +G+GKttl+k 
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKA 20
                                  89*************985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00073      0.33       1      25 [.       4      28 ..       4      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00073
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                  i++ G +g GK+tl+k L + ll++
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLNN 28
                                  6899*************99999854 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00035      0.16      30      64 ..      11      83 ..       2     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                    KAP_NTPase 30 GsGKssllnkledelkefa......................................kpvrflfaefnawsfk 64
                                  GsGK++l++ l+d+l ++                                        p+++l+++++ +++k
  gi|70607046|ref|YP_255916.1| 11 GSGKTTLVKALQDYLLNNEldtaiinldpavevlpykpdidareyvdvydvmnkyelGPNSSLVISVDLLLTK 83
                                  ***************9997777777777777777777777777777777777777775555555555555544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.18      19      53 ..       4      39 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                    Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpDd 53
                                  i++ G  G+GK++l ++l+d+l  ++ +   ++ D 
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLnNELDTAIINLDP 39
                                  8999****************9975566666666665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00058      0.26       4      27 ..       4      27 ..       2      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                                  EEEEE-TTSSHHHHHHHHHHHSSS CS
                           CPT  4 ilLnGgsssGKsslaralqevlde 27
                                  i+  G++ sGK++l++alq+ l +
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQDYLLN 27
                                  7888***************98754 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00062      0.28       4      35 ..       3      34 ..       1      41 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                                  EEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                    APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvyl 35
                                   +++ G +gsGK+t+ +al+ +L ++   + +
  gi|70607046|ref|YP_255916.1|  3 FIFVLGTAGSGKTTLVKALQDYLLNNELDTAI 34
                                  58999******************998866654 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.054        24       6      25 ..       4      23 ..       1      39 [. 0.85
   2 ?    1.5   0.0      0.41   1.8e+02      68      82 ..      94     108 ..      66     116 .. 0.77
   3 ?    1.8   0.0      0.32   1.5e+02     122     186 ..     161     233 ..     152     240 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.054
                                  EEEEESTTSSHHHHHHHHHH CS
                      GTP_EFTU  6 igiighvDhGKtTLtdrLly 25
                                  i ++g   +GKtTL+ +L  
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKALQD 23
                                  6799999********99865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.41
                                   SSEEEEEEEESSSGG CS
                      GTP_EFTU  68 kkylinliDtPGHvd 82 
                                    + ++ l+DtPG ++
  gi|70607046|ref|YP_255916.1|  94 LQANYVLVDTPGQIE 108
                                   5667899*****875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.32
                                   TTEEEEEEESCGST.HHHHHHHHHHHHHHHHHH.........HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHH CS
                      GTP_EFTU 122 gvpiivfiNKmDrl.kaelkeiveevkqklsrk.........eeklekygekgekevpvvfgSalkgegvktlle 186
                                   ++p i ++ K+D l  +el+++ + +++    +          e ++ ++e+   e   +++S+ +  g+++l  
  gi|70607046|ref|YP_255916.1| 161 DMPQISVLSKVDLLsSSELERMRSWIEDGSIIDelgsideysFELVKTIVENL--ESFPIPVSSTNFSGLDQLYA 233
                                   6779999******9877777777766654322233333433322222222222..23345666666666666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00082      0.37       2      19 ..       4      21 ..       3      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00082
                        AAA_33  2 vllvGlpGsGKstlaerl 19
                                  +++ G +GsGK+tl++ l
  gi|70607046|ref|YP_255916.1|  4 IFVLGTAGSGKTTLVKAL 21
                                  6889***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 1617.40
//
Query:       gi|70607047|ref|YP_255917.1|  [L=291]
Description: ribose-phosphate pyrophosphokinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-28   97.7   0.0    1.9e-27   95.5   0.0    2.0  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    2.7e-17   62.7   0.2    6.5e-17   61.5   0.2    1.6  1  Pribosyltran    Phosphoribosyl transferase domain
    6.4e-13   49.1   4.2    6.6e-13   49.1   2.2    1.9  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
     0.0002   20.9   0.2    0.00051   19.5   0.1    1.7  2  UPRTase         Uracil phosphoribosyltransferase
     0.0064   16.0   0.1      0.014   14.9   0.1    1.6  1  PRTase_2        Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   5.2e-31   1.9e-27       1     116 []       1     117 [.       1     117 [. 0.98
   2 ?   -0.4   0.0      0.29     1e+03      14      59 ..     173     221 ..     166     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 5.2e-31
                Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakr 81 
                                   + i+ g++++ + e+++k l ++l+k++ + f+dgE +++i e + g+dv ++qsl +p +++l+el++++++l+  +a++
  gi|70607047|ref|YP_255917.1|   1 MIIIGGTATNWIDERLSKLLVSRLVKIEHKVFPDGESYIRIPERLMGEDVLVVQSLYPPQDKHLVELFFILETLNDMKANK 81 
                                   6799999999999******************************************************************** PP

                Pribosyltran_N  82 itaViPylgysrqdrk.ksrepisaklvaklLeaaG 116
                                   it++iPyl+ysrq+r+ k+ e++s k v++l+++ G
  gi|70607047|ref|YP_255917.1|  82 ITVIIPYLAYSRQNRRfKEGEAVSTKTVLNLIKKTG 117
                                   ****************9****************988 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.29
                Pribosyltran_N  14 ekiakrlgvelgkakvsr.fadgEikveieesvr..gkdvfiiqslskp 59 
                                   ++++++lg+     + +r  ++gE++v+   ++r  gk+v+++ ++ + 
  gi|70607047|ref|YP_255917.1| 173 KRLSQELGCDYSYLEKQRdLTTGEVRVTNLPDLRldGKEVILVDDIIST 221
                                   5556666666665544431577888887766555558888888877644 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.2   1.8e-20   6.5e-17      28     125 ..     156     250 ..     133     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.8e-20
                                   GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHH CS
                  Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaale 108
                                    +++ v+++++g++ +ak+l++eL++ + y++k++  + g   +++ +     +   ++gk V++VDDi++tGgT+  a +
  gi|70607047|ref|YP_255917.1| 156 VTNPFVLAPDKGALNRAKRLSQELGCDYSYLEKQRDLTTGEVRVTN-L-----PDLRLDGKEVILVDDIISTGGTMVQASQ 230
                                   5689******************************999999888874.3.....67889*********************** PP

                                   HHHCC-BSEEEEEEEE...E CS
                  Pribosyltran 109 lLkekgpeevriavlv...d 125
                                   +  +kg+++v++ +++    
  gi|70607047|ref|YP_255917.1| 231 IAYSKGAKKVIATAVHslfV 250
                                   ********999877764544 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.4   1.4e+03     104     142 ..      72     110 ..      64     125 .. 0.65
   2 !   49.1   2.2   1.8e-16   6.6e-13      82     168 ..     208     289 ..     197     291 .] 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.4
                                   HHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEE CS
                Pribosyl_synth 104 evlkerGaykiyvlathGllssdaprlleesaidevvvt 142
                                   e+l++  a ki v++ +  +s ++ r  e  a+    v 
  gi|70607047|ref|YP_255917.1|  72 ETLNDMKANKITVIIPYLAYSRQNRRFKEGEAVSTKTVL 110
                                   567777777777777777777666666665555444444 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.8e-16
                                   TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-TTEEEE-- CS
                Pribosyl_synth  82 gGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcskiktvdi 162
                                    G+  i+vdd+i    ++v+a+++   +Ga k+++ a h l+ ++a  +l ++ i+e++ tntip++      sk+  vd+
  gi|70607047|ref|YP_255917.1| 208 DGKEVILVDDIISTGGTMVQASQIAYSKGAKKVIATAVHSLFVENAYDRLINAGIKEIITTNTIPQDT-----SKVTIVDV 283
                                   69999*************************************************************98.....89999999 PP

                                   HHHHHH CS
                Pribosyl_synth 163 slllae 168
                                   s  +a 
  gi|70607047|ref|YP_255917.1| 284 SESIAR 289
                                   988876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.88   3.2e+03     109     129 ..      35      55 ..      15      56 .. 0.74
   2 !   19.5   0.1   1.4e-07   0.00051     100     158 ..     189     246 ..     181     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.88
                       UPRTase 109 veyynkLPkkiaertvlllDp 129
                                    e y ++P+++  + vl++ +
  gi|70607047|ref|YP_255917.1|  35 GESYIRIPERLMGEDVLVVQS 55 
                                   478999999998888988865 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.4e-07
                       UPRTase 100 qreeetlepveyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                                   qr+ +t e    +++LP+   + ++v+l+D +i+TGg++++a q+  ++g+++   + + 
  gi|70607047|ref|YP_255917.1| 189 QRDLTTGE--VRVTNLPDLRlDGKEVILVDDIISTGGTMVQASQIAYSKGAKKVIATAVH 246
                                   56665554..66789**98889**********************9999887644444444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     4e-06     0.014     118     152 ..     206     240 ..     193     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                      PRTase_2 118 laaakelvLvDDEistGktalnliralqeklprkr 152
                                     + ke++LvDD istG t+++  +   +k  +k 
  gi|70607047|ref|YP_255917.1| 206 RLDGKEVILVDDIISTGGTMVQASQIAYSKGAKKV 240
                                   456789**************998876666554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1960.00
//
Query:       gi|70607048|ref|YP_255918.1|  [L=301]
Description: RNA methylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-22   78.5   0.0    2.6e-21   76.2   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    1.1e-11   44.9   0.1    5.9e-10   39.3   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    1.8e-05   24.6   0.0    4.5e-05   23.3   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
    2.2e-05   25.1   0.0    6.6e-05   23.5   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    8.9e-05   22.2   0.0    0.00018   21.2   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0029   17.2   0.0      0.019   14.5   0.0    2.0  2  MTS              Methyltransferase small domain
     0.0058   16.4   0.0     0.0093   15.8   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase
     0.0064   16.2   0.9      0.053   13.2   0.0    2.4  3  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.027   14.1   0.0    1.7  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.015   14.6   0.0      0.039   13.2   0.0    1.7  1  N6_Mtase         N-6 DNA Methylase
      0.028   13.8   0.0      0.044   13.2   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.032   14.9   0.0      0.092   13.4   0.0    1.8  1  Methyltransf_11  Methyltransferase domain
      0.052   14.0   0.0       0.33   11.5   0.0    2.3  3  Eco57I           Eco57I restriction-modification methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   1.9e-24   2.6e-21       3     189 ..     136     286 ..     134     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.9e-24
                                   SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEE CS
                       UPF0020   3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsD 83 
                                   +R+++  ++L+ +LA+ +++l++ +  +  lDP+ G+GtilIEa +lg +++                          g+D
  gi|70607048|ref|YP_255918.1| 136 KRPYTRSGSLNVELARLMINLSRSR--SNVLDPFVGTGTILIEANWLGLKCI--------------------------GID 188
                                   79********************877..579**********************..........................*** PP

                                   S-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEE CS
                       UPF0020  84 ldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvl 164
                                   +d+++++ ++ N+ +   +   e+  ad   L+ ++   ++ivt+pPYG++ +  k l +LY++f  e+++v+++   l++
  gi|70607048|ref|YP_255918.1| 189 IDEQMIKNTKINLDYFHYE--CELIHADTNTLPITR--SEAIVTDPPYGRSFTP-KGLSELYQNFFAEASNVTKN---LIF 261
                                   **************98876..566677777778334..568*********9975.56899***********9999...888 PP

                                   EEESSHHHHHCC---ESEEEEEEET CS
                       UPF0020 165 ltsenkalekaleeralrkvkeknv 189
                                    t ++ +  + l++  ++++k   v
  gi|70607048|ref|YP_255918.1| 262 TTDSRFDWRDTLKSYGFKQIKIHTV 286
                                   8888888888888888888877766 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0   4.3e-13   5.9e-10     171     228 ..     138     196 ..      47     199 .. 0.73
   2 ?    3.8   0.0     0.029        41       3      17 ..     225     244 ..     224     296 .. 0.61

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 4.3e-13
                                   --..SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHH CS
                   N6_N4_Mtase 171 kH..paqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvel 228
                                    +    + +v+l++ +I+ls +  ++vlDpF G+Gt++++a+ lg k+iGi+i+e+ ++ 
  gi|70607048|ref|YP_255918.1| 138 PYtrSGSLNVELARLMINLS-RSRSNVLDPFVGTGTILIEANWLGLKCIGIDIDEQMIKN 196
                                   333367899********975.67899******************************9875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                                   EEEE--SSSSSCS....... CS
                   N6_N4_Mtase   3 livtdpPYntgkdy.....e 17 
                                    ivtdpPY+ +         
  gi|70607048|ref|YP_255918.1| 225 AIVTDPPYGRSFTPkglseL 244
                                   59*******99874444443 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         2   2.7e+03      72      93 ..     103     131 ..      85     153 .. 0.64
   2 !   23.3   0.0   3.3e-08   4.5e-05       3      70 ..     159     220 ..     157     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
               Methyltransf_31  72 d..ekfDlilsnevl.....naladpdki 93 
                                   +  +k D+i+s + +     +a +d ++i
  gi|70607048|ref|YP_255918.1| 103 KrcNKLDVIVSEGQIvvgerYAEKDTESI 131
                                   23478888888766655655555555555 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.3e-08
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekll 70 
                                   +  +vlD+  GtG++++e++  l  + + +GiDi+e++i+  + n++   ++ +e+ ++d ++l+  +
  gi|70607048|ref|YP_255918.1| 159 SRSNVLDPFVGTGTILIEAN-WL--GLKCIGIDIDEQMIKNTKINLDYFHYE-CELIHADTNTLP--I 220
                                   6789****************.44..478*******************99996.*******99999..4 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.5   6.2e+03      58      75 ..     101     118 ..      85     137 .. 0.64
   2 !   23.5   0.0   4.8e-08   6.6e-05       1      62 [.     163     222 ..     163     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.5
                                   BSSSTTTEEEEEEESTGG CS
               Methyltransf_25  58 lpfedgsfDlvvssgalh 75 
                                   l+   ++ D++vs g++ 
  gi|70607048|ref|YP_255918.1| 101 LSKRCNKLDVIVSEGQIV 118
                                   455567788888865543 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 4.8e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSST CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfed 62 
                                   vLd   GtG++++++    g  k +g+Di+e+m+++++ +++  ++++e++++d ++lp   
  gi|70607048|ref|YP_255918.1| 163 VLDPFVGTGTILIEANWL-G-LKCIGIDIDEQMIKNTKINLDYFHYECELIHADTNTLPITR 222
                                   89999*********9977.5.********************98888************9654 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.3e-07   0.00018      41     138 ..     159     246 ..     151     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                                   CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                    +++vLD f G+G++ +EA   g  k++ ++ d++++k  k nl+ ++ e    el++ +++ l+ +     + + +  DP
  gi|70607048|ref|YP_255918.1| 159 SRSNVLDPFVGTGTILIEANWLG-LKCIGIDIDEQMIKNTKINLDYFHYE---CELIHADTNTLPIT-----RSEAIVTDP 230
                                   5678****************999.789*********************76...46677777777766.....235799*** PP

                                   SSSTTCH.HHHHHHHHH CS
                 Cons_hypoth95 122 Pyakellieevlellee 138
                                   Py ++ +  + l++l +
  gi|70607048|ref|YP_255918.1| 231 PYGRSFT-PKGLSELYQ 246
                                   ***9976.777777764 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.27   3.7e+02      88     136 ..     100     146 ..      56     153 .. 0.77
   2 !   14.5   0.0   1.4e-05     0.019      24     128 ..     153     255 ..     148     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                                   STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                           MTS  88 dvleeveekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                   ++ +    +k+d+ivs   +  g+   ++ +e + +++k+  + +G+L 
  gi|70607048|ref|YP_255918.1| 100 NLSKRC--NKLDVIVSEGQIVVGERYAEKDTESIARHSKRPYTRSGSLN 146
                                   333333..59999999999999999999999999999999999999886 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                                   HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE- CS
                           MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsN 104
                                   + +l+   + +vlD   G+G + +++      ++   +d+d + ++ +k nl   + e+e+++ d        + ++iv+ 
  gi|70607048|ref|YP_255918.1| 153 MINLSR-SRSNVLDPFVGTGTILIEANWL--GLKCIGIDIDEQMIKNTKINLDYFHYECELIHADTNTLPI-TRSEAIVTD 229
                                   445666.4567999999999987776655..556899****************************876666.9******** PP

                                   --STTTC..HCHHHHHHHHHHHHHHH CS
                           MTS 105 PPfhagk..atelavaeeliaeAkea 128
                                   PP+ ++   +   ++ ++++aeA ++
  gi|70607048|ref|YP_255918.1| 230 PPYGRSFtpKGLSELYQNFFAEASNV 255
                                   **988763345578899999999876 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.7e-06    0.0093      56     146 ..     188     289 ..     167     298 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
               N6-adenineMlase  56 eiDkrFealyg.eekfvfYdlnnpeelpeel.kgkfdviviDPPF........lseeclkklaktaklllkklilctgevm 126
                                   +iD++  +  + + ++++Y+++  +  ++ l     + iv+DPP+        lse  ++ +a++ +   k+li++t ++ 
  gi|70607048|ref|YP_255918.1| 188 DIDEQMIKNTKiNLDYFHYECELIHADTNTLpITRSEAIVTDPPYgrsftpkgLSELYQNFFAEASNVT-KNLIFTTDSRF 267
                                   6666653222202348899988888666777788899************99998888888888866655.899**996665 PP

               N6-adenineMlase 127 ee..lekllgvkktkfepehen 146
                                         k +g+k++k +   e+
  gi|70607048|ref|YP_255918.1| 268 DWrdTLKSYGFKQIKIHTVYEH 289
                                   4435666667666665555444 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.5   6.2e+03     213     227 ..      93     108 ..      74     117 .. 0.56
   2 !   13.2   0.0   3.8e-05     0.053      20      59 ..     159     198 ..     148     218 .. 0.84
   3 ?    2.3   0.2     0.079   1.1e+02     153     219 ..     199     264 ..     190     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.5
                                   HHHHHHH..HHTT-EE CS
               MethyltransfD12 213 aevlksls.skfgvkv 227
                                    e++ks++ sk+++k 
  gi|70607048|ref|YP_255918.1|  93 EELIKSINlSKRCNKL 108
                                   2333444445555554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.8e-05
                                   --SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHH CS
               MethyltransfD12  20 kgktfvepFaGggaVffeakkqgkkvlinDinedlinlyk 59 
                                   + + + +pF+G+g + +ea   g k++  Di e+ i   k
  gi|70607048|ref|YP_255918.1| 159 SRSNVLDPFVGTGTILIEANWLGLKCIGIDIDEQMIKNTK 198
                                   556799*************88*************998877 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.079
                                   HHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH CS
               MethyltransfD12 153 rseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlksl 219
                                   ++ + + ++ e  ++d+++l    +++++  DPPY    +      ++++ f ++ +v    ++ + 
  gi|70607048|ref|YP_255918.1| 199 INLDYFHYECELIHADTNTLPI-TRSEAIVTDPPYGRSFTPKGLSELYQNFFAEASNVTKNLIFTTD 264
                                   5555556777888888888888.55558889****97666666777788888777775544444444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.027       3      61 ..     162     218 ..     160     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                    +lD+f G+G   i+    + k i+i+i+++ ++ ++ N   +  + +  l+++d ++l
  gi|70607048|ref|YP_255918.1| 162 NVLDPFVGTGTILIEANWLGLKCIGIDIDEQMIKNTKINLDYF--HYECELIHADTNTL 218
                                   58*************9999**********************99..77888889888762 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.039      33     145 ..     148     241 ..     146     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                      N6_Mtase  33 evsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgd 113
                                   e+ +l+++l  ++s+  v+Dp +G+g +l++a+            l+  G +++e+ ++ +k+Nl     e +     ++d
  gi|70607048|ref|YP_255918.1| 148 ELARLMINLSRSRSN--VLDPFVGTGTILIEANW---------LGLKCIGIDIDEQMIKNTKINLDYFHYECE---LIHAD 214
                                   567888888887777..9************9987.........379999***************976666666...78888 PP

                      N6_Mtase 114 tlekpkfekdkkfdvvvaNppfnqkewkektl 145
                                   t + p ++     +++v+ pp++ + ++ k l
  gi|70607048|ref|YP_255918.1| 215 TNTLPITR----SEAIVTDPPYGRS-FTPKGL 241
                                   88888776....789*******999.754444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05     0.044     158     217 ..     156     213 ..     148     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                          PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleval 217
                                   l +++++vlD   G+G + i a  Lg k  +++DiDe+ +k +k N+++ + e +l +++
  gi|70607048|ref|YP_255918.1| 156 LSRSRSNVLDPFVGTGTILIEANWLGLK-CIGIDIDEQMIKNTKINLDYFHYECEL-IHA 213
                                   5678899***999999999*******86.67****************999888766.444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.7e-05     0.092       5      58 ..     168     221 ..     164     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                                   -TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
               Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58 
                                   +GtG ++ +    g +++g+D++++m+k  k +    + ++e+++ad  +lp+ 
  gi|70607048|ref|YP_255918.1| 168 VGTGTILIEANWLGLKCIGIDIDEQMIKNTKINLDYFHYECELIHADTNTLPIT 221
                                   678888877777789************9998888888779999*******9975 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         7   9.7e+03      28      44 ..      88     103 ..      80     131 .. 0.60
   2 ?   -1.5   0.0       2.7   3.7e+03      50      77 ..     174     201 ..     167     214 .. 0.74
   3 ?   11.5   0.0   0.00024      0.33       5      71 ..     225     282 ..     222     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7
                        Eco57I  28 akdiyqkFvekalkled 44 
                                   ak++y++ + k+++l++
  gi|70607048|ref|YP_255918.1|  88 AKNVYEELI-KSINLSK 103
                                   455555544.2344443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                        Eco57I  50 iiparflasgkglkefrekllkdkklkk 77 
                                   +i a +l    ++ ++ e+++k++k++ 
  gi|70607048|ref|YP_255918.1| 174 LIEANWLGLKCIGIDIDEQMIKNTKINL 201
                                   5567777666677789999999999974 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00024
                        Eco57I   5 viiGNPPYqeseakkelkaleekakdiyqkFvekalkledkylaliiparflasgkglkefrekllk 71 
                                   +i+  PPY +s + k+l       +++yq+F+++a +++++ + + + +rf     +lk+++ k++k
  gi|70607048|ref|YP_255918.1| 225 AIVTDPPYGRSFTPKGL-------SELYQNFFAEASNVTKNLI-FTTDSRFD-WRDTLKSYGFKQIK 282
                                   79999***999944444.......58*************8877.99999996.44555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1982.90
//
Query:       gi|70607049|ref|YP_255919.1|  [L=292]
Description: metallo-beta-lactamase superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-17   63.8   0.0    4.3e-10   39.4   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.2e-05   25.4   0.1     0.0001   22.4   0.0    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.022   14.4   0.0    1.6  1  Lactamase_B_4  tRNase Z endonuclease
       0.06   13.2   0.0       0.35   10.7   0.0    2.0  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.6e-08   7.2e-05       3     131 ..      31     142 ..      30     150 .. 0.71
   2 !   39.4   0.0   9.6e-14   4.3e-10     133     201 .]     191     257 ..     185     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-08
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHH CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvyla 78 
                                   iL+D+g ++  q ++     e   ++ +++++ ++h H DH+ gl+ + +      r++kl l++p  ++++l+++++   
  gi|70607049|ref|YP_255919.1|  31 ILLDCGEGT--Q-NKMI---EHSISFMKLNLIGISHLHGDHVLGLPGIIQtmamySRQQKLLLMGPTTLQDYLKSSSKHTY 105
                                   99******5..4.3343...1255799*********************9999877666668899**********9977666 PP

                                   CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE CS
                 Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie 131
                                   +++       e +  +s e +  +l+it++   h+ +          +G++i+
  gi|70607049|ref|YP_255919.1| 106 FKPG-----FETEFIQSYEDQ--NLTITTFRTCHTIES---------YGFLIK 142
                                   5555.....444444444444..566777766665554.........555555 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 9.6e-14
                                   TTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 133 ggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                   +g +++y+gDt+ ++    + ++g+dll++d t+++++e   + gH++  +a+e+a ++++krl l Hi
  gi|70607049|ref|YP_255919.1| 191 KGLSIAYTGDTAPCDSV-LNAIKGVDLLIHDSTFLNEREAH-DYGHSNCTDAAEIASKADVKRLALYHI 257
                                   6889**********955.66*******************66.9*************************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.3e-08    0.0001      10      67 ..      23      75 ..      21      96 .. 0.94
   2 ?    0.6   0.0      0.11   4.9e+02     142     196 ..     192     255 ..     183     256 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-08
                                  EEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                   Lactamase_B 10 liegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                  li+ +g  iL D+G +t+++++      + +   ++  + ++HlH DH+ gl+g++++
  gi|70607049|ref|YP_255919.1| 23 LIRREGFEILLDCGEGTQNKMIE-----HSISFMKLNLIGISHLHGDHVLGLPGIIQT 75
                                  99********************8.....799999999999**************9875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                                   TCCEEEECTTTSSHHCCCCCC..........TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEES CS
                   Lactamase_B 142 ggkvlftGDallagetgridl.........tlrgaevrdpsdaekyldsllklaglkaevlvpg 196
                                   g ++++tGD+ +  + +   +         t  +    +++++++++d+++ + + ++++l++ 
  gi|70607049|ref|YP_255919.1| 192 GLSIAYTGDTAPCDSVLNAIKgvdllihdsTFLNEREAHDYGHSNCTDAAEIASKADVKRLALY 255
                                   6678889998885555555557777777777777777888888888888887777777777665 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     5e-06     0.022      13      56 ..      20      62 ..      12      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-06
                 Lactamase_B_4 13 PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                  P +l++ +    l+ ++gEgtQ  ++e+ +++ kl+ i +++ +
  gi|70607049|ref|YP_255919.1| 20 PGILIRREGFEILL-DCGEGTQNKMIEHSISFMKLNLIGISHLH 62
                                  67777777777788.9*******************998777766 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.8e-05      0.35      11     133 ..      23     218 ..      18     232 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.8e-05
                 Lactamase_B_3  11 lletagarilvDPfkanlgyeppa....eeaDlvlisqaledHahletlkql............................. 58 
                                   l++ +g +il+D ++++++  ++      + +l+ is+ + dH     l+++                             
  gi|70607049|ref|YP_255919.1|  23 LIRREGFEILLDCGEGTQNKMIEHsisfMKLNLIGISHLHGDHVL--GLPGIiqtmamysrqqklllmgpttlqdylksss 101
                                   788889999999887633333333456689999999999988863..4444444478888777777777766666666644 PP

                 Lactamase_B_3  59 ...............aenvkvleegeslevggleiravatsh...................................davg 89 
                                                              +e ++l i++++t h                                    ++g
  gi|70607049|ref|YP_255919.1| 102 khtyfkpgfetefiqS-----------YEDQNLTITTFRTCHtiesygflikekdktkvdaerlkkegitdwriirkLKEG 171
                                   4444444444444440...........444455555555555555555555555555555555555555555566542222 PP

                 Lactamase_B_3  90 gsergenngflleq.....dgltiyhlGhlahelsseelkelgrvDvvl 133
                                   ++++    +fl e+     +gl+i++ G++a    ++ l++++ vD+++
  gi|70607049|ref|YP_255919.1| 172 KRVEIDTKVFLPEDylyvkKGLSIAYTGDTAP--CDSVLNAIKGVDLLI 218
                                   33333344555444333338**********96..8999999*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1851.11
//
Query:       gi|70607050|ref|YP_255920.1|  [L=145]
Description: hypothetical protein Saci_1285 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-18   66.2   0.7    3.8e-18   65.9   0.7    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.7   2.1e-22   3.8e-18       1     118 [.       3     115 ..       3     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.1e-22
                                   EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HHH CS
                   RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....keL 76 
                                   ++ v+a+v+++Ed++kV++a++n+++ ++  i     e  +g   ++l ae ++   + +l kl++llre++i     k+L
  gi|70607050|ref|YP_255920.1|   3 RVIVEAVVKPSEDKDKVINAIRNFFDFDK--I----REEEHG-MEKLLIAESNS---LTSLLKLHRLLREQRIldaarKYL 73 
                                   589***********************884..2....233455.55677788888...99******************9*** PP

                                   HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.....EEEEEEE CS
                   RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegdd.....vIkvkik 118
                                   +k++ +     ++++++l+KQ a+ gkls+ ++++     +Ikv+i 
  gi|70607050|ref|YP_255920.1|  74 MKSIVG-----SRITFMLNKQVAAIGKLSFIDKEHesplgPIKVTID 115
                                   ****99.....9**********************999***9**9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 955.29
//
Query:       gi|70607051|ref|YP_255921.1|  [L=144]
Description: hypothetical protein Saci_1286 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-06   27.2   0.3    1.1e-05   26.0   0.2    1.7  2  AAA_18    AAA domain
  ------ inclusion threshold ------
       0.04   13.6   0.1      0.046   13.4   0.1    1.2  1  CoaE      Dephospho-CoA kinase


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.2   1.2e-09   1.1e-05      61     120 ..      35      96 ..       1     111 [. 0.72
   2 ?   -0.0   0.0      0.14   1.2e+03      16      44 ..      99     135 ..      95     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.2e-09
                        AAA_18  61 ldaleenssaleegknlvidghlaeleseaakdikk...vvLtaspeelleRlekRgyeeaki 120
                                   + +l      ++ ++++vidg++++ e e++ + +k   + ++as ++++ Rl +Rg+e++ +
  gi|70607051|ref|YP_255921.1|  35 VAKLCIEK-LNGTEDVVVIDGVRNWEEIEEFEKVGKviiIAVHASRSVRYSRLMNRGREDDST 96 
                                   33333322.367899*****************9999*********************998765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.14
                        AAA_18  16 keLskrlgf.........gvnlrdvakenglllevdpe 44 
                                   + L kr  f         ++ l d++  n++++e++++
  gi|70607051|ref|YP_255921.1|  99 QDLMKR-DFdelqmgigtVIALADYVITNDSSIEEFNK 135
                                   555555.3444455667788899999999999999888 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.1e-06     0.046     124     178 ..      71     131 ..      27     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-06
                                   EEEEEE--HHHHHHHHHHCC.TSTHHHHHHHHHH.....S--HHHHHHH-SEEEE-.SSHH CS
                          CoaE 124 rvlvvdvelelqveRlvard.gvseeevkaiiaa.....QlseeerlaladvvldNdssla 178
                                    ++ v+++ + + +Rl++r  + +++ +++ ++      Q+     +alad+v+ Ndss++
  gi|70607051|ref|YP_255921.1|  71 IIIAVHASRSVRYSRLMNRGrEDDSTSLQDLMKRdfdelQMGIGTVIALADYVITNDSSIE 131
                                   24456777777888****9645555566665543222339999999************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1066.15
//
Query:       gi|70607052|ref|YP_255922.1|  [L=195]
Description: 2',5' RNA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-28   97.8   0.0      1e-13   51.3   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    2.6e-15   56.6   0.0    3.5e-15   56.2   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    8.2e-10   38.9   0.0    1.5e-09   38.1   0.0    1.4  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.25   10.7   0.0    1.6  1  Corona_NS2A      Coronavirus NS2A protein


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   2.3e-17     1e-13       9      87 .]      14      88 ..       8      88 .. 0.93
   2 !   44.8   0.0   2.4e-15   1.1e-11       6      87 .]      93     174 ..      89     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.3e-17
                                  HHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
                    LigT_PEase  9 eelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                                  e++++l + +     ++++k+v+p n HiTL f+gev e k++ +++ l++i   +++f++++ g+g+fps  +prv++
  gi|70607052|ref|YP_255922.1| 14 EKINELMQAIS--RTGADIKLVEPWNIHITLVFIGEVHENKLELIKDGLKRI--SFNKFKVRLHGTGAFPSLGKPRVVW 88
                                  68999999999..8999***********************************..7779************988*****9 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 2.4e-15
                                   HHHHHHHHHHHHHHHHHCCTTEEET..SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.S CS
                    LigT_PEase   6 eiaeelarlaaeleralaklglkpv..rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl.r 82 
                                   e a el+ ++  + ++l  +g++p+  ++f pH+T+++++  +  +++ ++++++++ ++g     ++v++++l++s+l +
  gi|70607052|ref|YP_255922.1|  93 EGAIELRMIRGSIYKELVNRGIRPDeeKEFSPHLTIGRVRGPRnMQNLIQVINEYQGTDFGE----FTVEKFTLYKSTLtQ 169
                                   44679999********************************998899999*********9995....*************** PP

                                   CCEEE CS
                    LigT_PEase  83 prviy 87 
                                   +++iy
  gi|70607052|ref|YP_255922.1| 170 KGPIY 174
                                   ****9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   7.8e-19   3.5e-15      16     147 ..      28     164 ..      11     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 7.8e-19
               2_5_RNA_ligase2  16 lydkayprwppHitLlypfvededladlaellsrlak..etepfevrldgfgvFeh..kksvvylsv.sdsealqalraal 91 
                                   +  k+++ w  HitL++ ++  e      el+++++k  ++ +f+vrl g g F++  k +vv++ + ++  +l+ +r ++
  gi|70607052|ref|YP_255922.1|  28 ADIKLVEPWNIHITLVFIGEVHENK---LELIKDGLKriSFNKFKVRLHGTGAFPSlgKPRVVWVGIdEGAIELRMIRGSI 105
                                   55578999***********999864...455555555336899**************6666******999*********** PP

               2_5_RNA_ligase2  92 lealpeagdkeds.geftPHlTiaqsadstsaaellekl..aqalpplefevdevallr 147
                                   +++l   g + d+ +ef PHlTi++   ++ +++l++ +   q  +  ef+v++++l++
  gi|70607052|ref|YP_255922.1| 106 YKELVNRGIRPDEeKEFSPHLTIGRVRGPRNMQNLIQVIneYQGTDFGEFTVEKFTLYK 164
                                   ***99998888888*************************6666677788***9999987 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   3.2e-13   1.5e-09      16     202 ..      14     177 ..       8     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.2e-13
                                   HHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE..... CS
                     AKAP7_NLS  16 kklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpa 96 
                                   +k++++++ + + +   d +l ++p ++H+Tl+ +    +++++  k+ Lk+++         +++++rl+G + f  +  
  gi|70607052|ref|YP_255922.1|  14 EKINELMQAISRTGA--DIKL-VEPWNIHITLVFIGEVHENKLELIKDGLKRIS--------FNKFKVRLHGTGAF-PSLG 82 
                                   566777777776544..6667.89999999998887656666666665555553........399***********.7899 PP

                                   TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEE CS
                     AKAP7_NLS  97 karVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefg 177
                                   k rV++++++e     +L+ ++  i+k+++++g+  +++k+ + +H+T+  +r  ++ q+         +++++++ ++fg
  gi|70607052|ref|YP_255922.1|  83 KPRVVWVGIDEG--AIELRMIRGSIYKELVNRGIRPDEEKE-FSPHLTIGRVRGPRNMQN-------LIQVINEYQGTDFG 153
                                   9********965..699**********************99.*******99985444433.......3569********** PP

                                   EEE--EEEEEESSS---TTS--EEE CS
                     AKAP7_NLS 178 eekineihLsqlesddesdgyYkvi 202
                                   e +++++ L + + +++    Y+++
  gi|70607052|ref|YP_255922.1| 154 EFTVEKFTLYKSTLTQK-GPIYEPL 177
                                   *********99888877.6677665 PP

>> Corona_NS2A  Coronavirus NS2A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.5e-05      0.25      25     135 ..      17     135 ..       4     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.5e-05
                                   HHHHHHHHHCT-SEEE-SS-EEEEEEEE--CCCHHHHHHHHHHHHHCGGGG-CEEEEEEEE...EETTEEEEEE...ES.. CS
                   Corona_NS2A  25 lklqsqlveeGldgkkqkaphvsltlldlkeedvkkvefaiqeildelvlyetdividnph...mlGrylvlev...rG.. 97 
                                    +l   +   G d k+     + +tl+ + e + +k+e  i++ l  +   + ++ +        lG+  v+ v   +G  
  gi|70607052|ref|YP_255922.1|  17 NELMQAISRTGADIKLVEPWNIHITLVFIGEVHENKLE-LIKDGLKRISFNKFKVRLHGTGafpSLGKPRVVWVgidEGai 96 
                                   55555666677777777777777777777777777777.677777777776666666543211146766665543334422 PP

                                   .-HHHHHHHHHHHHHTT-EES-SS----EEEEEEESSS- CS
                   Corona_NS2A  98 .leelheevvevlrrrGiaadqsrmwkphltvaeideev 135
                                    l+ +   + + l +rGi  d+ + + phlt++++ + +
  gi|70607052|ref|YP_255922.1|  97 eLRMIRGSIYKELVNRGIRPDEEKEFSPHLTIGRVRGPR 135
                                   24455678888899*******************997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1367.02
//
Query:       gi|70607053|ref|YP_255923.1|  [L=416]
Description: tRNA CCA-pyrophosphorylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-42  143.4   0.0      8e-42  142.1   0.0    1.7  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    5.8e-16   58.6   0.2    1.5e-15   57.3   0.2    1.7  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0003   21.0   0.0    0.00069   19.8   0.0    1.6  1  SMODS            Second Messenger Oligonucleotide or Dinucleo
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.033   14.4   0.0    1.7  1  DNA_pol_B_palm   DNA polymerase beta palm
      0.079   13.1   0.0       0.23   11.6   0.0    1.8  1  Polbeta          Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.0   2.2e-45     8e-42       1     113 []     144     253 ..     144     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 2.2e-45
                                   HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEEE CS
               tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDpk 81 
                                   devrllK+f+kgigvYG+e+kvkGfsGY+aEll+++yg+f++vle+a++wkp+++++l e +   ++fdepl + DPvDpk
  gi|70607053|ref|YP_255923.1| 144 DEVRLLKQFMKGIGVYGAEIKVKGFSGYVAELLTIYYGNFRKVLESAKTWKPPIKLNLVEPK---RDFDEPLQIPDPVDPK 221
                                   89******************************************************866555...59************** PP

                                   EETTTTS-HHHHHHHHHHHHHHHHS--GGGGS CS
               tRNA_NucTransf2  82 RNvaaalsleklaefilaareflkkpseefff 113
                                   RN+a+a+sl+++a f+la++ f+++ps+efff
  gi|70607053|ref|YP_255923.1| 222 RNTASAVSLRNIAVFSLASKIFIERPSIEFFF 253
                                   *******************************6 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.2   4.2e-19   1.5e-15       2      94 ..      22     129 ..      21     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 4.2e-19
                                   HHHHHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH..............HHHEHHHHHHHHCCCEEECT CS
                  NTP_transf_2   2 kklleelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre..............kkeegleklaeiikfleell 67 
                                   +k++ee+ ++ ++ ++ + GS+++Gt+lkg  DiD++v++p+ev +e              +  +++ + ae+++ + +++
  gi|70607053|ref|YP_255923.1|  22 EKVAEEVLSRLKGFDAQIQGSFRKGTWLKGdTDIDIFVFYPKEVGKEylrekslkeliqlfQDLNYEIAFAEHPYLILKIN 102
                                   789999999999*************************************************999999************** PP

                                   TEEEEEECEEECCCCTEEEEEECEEEH CS
                  NTP_transf_2  68 glevdlvtrekledpllvksileerpl 94 
                                    +evd+v+  k+ + + v+++++++p+
  gi|70607053|ref|YP_255923.1| 103 NVEVDVVPALKIDSGEDVITAADRTPF 129
                                   **************9999999999987 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-07   0.00069      50     137 ..      38     118 ..       6     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-07
                         SMODS  50 llvGSyardTaikpvsdkdmlfeldvdllvvvnevegd..epsdlleklkkal.kktyksseirqdrqvvvvelneikidv 127
                                     +GS++++T +k+ +        d+d++v + +  g+    ++ l++l + + + +y+      +++ +++++n++++dv
  gi|70607053|ref|YP_255923.1|  38 QIQGSFRKGTWLKGDT--------DIDIFVFYPKEVGKeyLREKSLKELIQLFqDLNYEI--AFAEHPYLILKINNVEVDV 108
                                   468**********655........567777777666653357889999999997888888..99***************** PP

                         SMODS 128 vPavenkdgs 137
                                   vPa++ ++g+
  gi|70607053|ref|YP_255923.1| 109 VPALKIDSGE 118
                                   ****988753 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.1e-06     0.033      13      71 ..      23      83 ..      13      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.1e-06
                                  HHHHHHHHH-TT-EEEE-HHHHTT-SEESS..EEEEEEBTTBSTTSS--HHHHHHHHHHHH CS
                DNA_pol_B_palm 13 lvkkaakeldpevevivcGSYRRgaessGD..vDvlitkkdakseskklkklleklvkklk 71
                                   v +++ +  +++++++ GS+R+g    GD  +D+ +  +++  ++  ++k l++l++  +
  gi|70607053|ref|YP_255923.1| 23 KVAEEVLSRLKGFDAQIQGSFRKGTWLKGDtdIDIFVFYPKEVGKEYLREKSLKELIQLFQ 83
                                  34455555567899***********999963388888888888877778888888887655 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.4e-05      0.23      20      60 ..      41      83 ..      36     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                                  EEEE-S----.--EEEEEEEESS-..--HHHHHHHHHHHHHH.S CS
                       Polbeta 20 GSrakgkare.eSDiDlavllkek..ldleeelelaaeledikl 60
                                  GS+ kg+  + + DiD++v++ ++  +++ +e +l++ ++   +
  gi|70607053|ref|YP_255923.1| 41 GSFRKGTWLKgDTDIDIFVFYPKEvgKEYLREKSLKELIQLF-Q 83
                                  999999976559**********99874444444444333333.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2652.52
//
Query:       gi|70607054|ref|YP_255924.1|  [L=202]
Description: hypothetical protein Saci_1289 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0003   20.5   0.0    0.00042   19.9   0.0    1.3  1  RIO1      RIO1 family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.4e-08   0.00042      64     159 ..      83     171 ..      59     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.4e-08
                                   HHHHTT--S.--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-ST.T.SEEEET CS
                          RIO1  64 rleeagvpv.PkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSe.y.Nvlvde 141
                                   ++++   pv Pk++ + ++ ++me+i   g ++++ +++e         +++l + +++++  g+ H  LS  y Nvlv+e
  gi|70607054|ref|YP_255924.1|  83 KIQQLAYPVsPKVYLYGENFILMEYIR--GRHLTRQENIE-------TIRKILMK-ARMLELKGIEHKELSRpYkNVLVNE 153
                                   5666666766*****************..77776655555.......44555553.6888899********6567****** PP

                                   TEEEE--GTTEEETTSTT CS
                          RIO1 142 dkvviIDvsQaveldhpn 159
                                   ++ +iID   a+ + +p+
  gi|70607054|ref|YP_255924.1| 154 KDAYIIDYDSATIKPNPK 171
                                   *******97776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1357.06
//
Query:       gi|70607055|ref|YP_255925.1|  [L=69]
Description: hypothetical protein Saci_1290 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00075   19.1   3.6       0.14   12.0   0.5    2.2  2  zinc_ribbon_2   zinc-ribbon domain
     0.0051   16.9   1.8       0.58   10.3   0.1    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
     0.0076   16.3   1.2       0.66   10.1   0.1    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
     0.0083   15.6   0.2       0.52    9.8   0.0    2.2  2  DUF2688         Protein of unknown function (DUF2688)
  ------ inclusion threshold ------
      0.012   15.4   8.1       0.15   11.8   1.4    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.012   15.5   4.6          1    9.3   1.0    2.2  2  Nudix_N_2       Nudix N-terminal
      0.012   15.9   0.2       0.52   10.7   0.0    2.1  2  GFA             Glutathione-dependent formaldehyde-activating
      0.013   15.5   0.0      0.014   15.4   0.0    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.014   15.4   0.7      0.088   12.8   0.8    1.9  1  DZR             Double zinc ribbon
      0.019   15.3   0.6        5.4    7.5   0.1    2.2  2  zf-IS66         zinc-finger binding domain of transposase IS6
      0.027   14.3   1.0          1    9.3   0.1    2.1  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.028   13.8   5.7       0.54    9.7   0.9    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.058   13.0   1.3       0.88    9.2   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.075   13.2   4.3        1.8    8.7   4.3    2.2  1  Zn-ribbon_8     Zinc ribbon domain
      0.077   13.3   0.4       0.26   11.6   0.1    1.9  2  DUF2757         Protein of unknown function (DUF2757)
      0.085   12.8   0.3        7.5    6.6   0.1    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.15   11.7   3.8       0.44   10.2   0.4    2.2  2  zf_C2H2_13      Zinc finger domain
        0.3   11.6   3.8         11    6.7   0.1    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.41   10.2   5.9          3    7.4   0.2    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.42   10.5   4.3          3    7.8   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.47   10.5   4.3        2.9    8.0   4.3    2.0  1  ADK_lid         Adenylate kinase, active site lid
       0.54   10.3   3.5        6.7    6.8   0.1    2.2  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.54   10.2   7.3        4.8    7.1   0.8    2.1  2  zf-HIT          HIT zinc finger
       0.84    9.6   6.2        0.6   10.0   1.3    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        2.3    8.3   5.8         11    6.1   1.1    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0028         2       2       9 ..       7      14 ..       4      19 .. 0.76
   2 !   12.0   0.5   0.00019      0.14       1       9 [.      40      48 ..      40      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0028
                 zinc_ribbon_2  2 CpnCGael 9 
                                  C nCG++l
  gi|70607055|ref|YP_255925.1|  7 CRNCGYTL 14
                                  88888877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00019
                 zinc_ribbon_2  1 fCpnCGael 9 
                                  +Cp+CG++l
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPL 48
                                  799999998 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.3     0.019        14      21      26 .]       5      10 ..       4      16 .. 0.86
   2 !   10.3   0.1   0.00082      0.58       3      18 ..      40      55 ..      40      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                        zf-ACC 21 yVCPkC 26
                                  yVC++C
  gi|70607055|ref|YP_255925.1|  5 YVCRNC 10
                                  899999 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00082
                        zf-ACC  3 KCpsCgemlykkeLer 18
                                  KCp+Cg  l +  +e+
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLNAPAIED 55
                                  9*****9998877775 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00092      0.66      14      27 ..       2      15 ..       1      23 [. 0.89
   2 ?    5.6   0.1     0.025        18      18      26 ..      40      48 ..      34      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00092
                      zf-Mss51 14 hvdfeCpdCGipty 27
                                  +v++ C +CG+  y
  gi|70607055|ref|YP_255925.1|  2 PVKYVCRNCGYTLY 15
                                  699********998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                      zf-Mss51 18 eCpdCGipt 26
                                  +Cp+CG p 
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPL 48
                                  7*****996 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.046        33       9      19 ..       6      16 ..       3      29 .. 0.78
   2 !    9.8   0.0   0.00072      0.52       5      18 ..      36      49 ..      31      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.046
                       DUF2688  9 qCrRCGkslst 19
                                   Cr CG  l  
  gi|70607055|ref|YP_255925.1|  6 VCRNCGYTLYN 16
                                  5*****99865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                       DUF2688  5 iVtTqCrRCGksls 18
                                  i   +C RCGk+l 
  gi|70607055|ref|YP_255925.1| 36 IFGGKCPRCGKPLN 49
                                  55679*******96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4   0.00021      0.15       1       9 [.       5      13 ..       5      16 .. 0.93
   2 ?    7.6   0.7    0.0043       3.1      15      21 ..      39      45 ..      36      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  YvC++CG++
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGYT 13
                                  9*******7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0043
                  Rubredoxin_2 15 GrCpsCg 21
                                  G+Cp Cg
  gi|70607055|ref|YP_255925.1| 39 GKCPRCG 45
                                  9*****9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0    0.0014         1      23      33 ..       5      15 ..       3      16 .. 0.91
   2 ?    7.7   0.1    0.0047       3.4       3      11 ..      41      49 ..      41      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                                  EEETTTTEEE- CS
                     Nudix_N_2 23 lvCpaCgtihY 33
                                  +vC +Cg++ Y
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGYTLY 15
                                  7********99 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                                  -TTT--B-E CS
                     Nudix_N_2  3 CsqCGtpve 11
                                  C+ CG+p++
  gi|70607055|ref|YP_255925.1| 41 CPRCGKPLN 49
                                  *******87 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00072      0.52      49      74 ..       4      29 ..       2      32 .. 0.89
   2 ?    3.8   0.0       0.1        73      51      61 ..      40      50 ..      32      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00072
                           GFA 49 rsfCpeCgsplyseesaapevvivrv 74
                                  +++C++Cg +ly   +  ++++ vr+
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCGYTLYNFDKVGQDFYGVRT 29
                                  689*********88999999999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                           GFA 51 fCpeCgsplys 61
                                   Cp+Cg pl +
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLNA 50
                                  5******9975 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0     2e-05     0.014      68      95 ..       2      47 ..       1      65 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                                  --EEEETTTS-EEECHHHHH...................S-TTTSSS CS
                          HypA 68 pvkvrCreCgkefeleekal...................rCpkCgsa 95
                                  pvk+ Cr+Cg++    +k +                   +Cp+Cg+ 
  gi|70607055|ref|YP_255925.1|  2 PVKYVCRNCGYTLYNFDK-VgqdfygvrtpseirsifggKCPRCGKP 47
                                  8999******99874432.23346999*****************985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   0.00012     0.088      13      39 ..       5      49 ..       1      52 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                           DZR 13 rfCseCgtklkavaa..................edrCpsCgekvd 39
                                   +C +Cg +l +  +                    +Cp+Cg++++
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGYTLYNFDKvgqdfygvrtpseirsifGGKCPRCGKPLN 49
                                  579999999987666899999999999999999999****99965 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015        10      39      46 .]       4      11 ..       2      23 .. 0.91
   2 ?    7.5   0.1    0.0075       5.4       3      17 ..      40      55 ..      39      63 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
                       zf-IS66 39 kyaCpcCe 46
                                  ky C++C+
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCG 11
                                  89999997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0075
                       zf-IS66  3 tCpcCGg.llkpiged 17
                                  +Cp CG+ l  p+ ed
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKpLNAPAIED 55
                                  6*****9554444444 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.062        44      13      18 ..       6      11 ..       2      15 .. 0.64
   2 ?    9.3   0.1    0.0014         1       9      19 ..      36      46 ..      32      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.062
                       DUF35_N 13 rCpdCG 18
                                   C++CG
  gi|70607055|ref|YP_255925.1|  6 VCRNCG 11
                                  366666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                       DUF35_N  9 LvgqrCpdCGt 19
                                  + g++Cp CG+
  gi|70607055|ref|YP_255925.1| 36 IFGGKCPRCGK 46
                                  689******97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0069       4.9      18      24 ..       6      12 ..       5      14 .. 0.85
   2 ?    9.7   0.9   0.00075      0.54       4      12 ..      40      48 ..      39      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0069
                   zf-ribbon_3 18 vCpyCGt 24
                                  vC +CG+
  gi|70607055|ref|YP_255925.1|  6 VCRNCGY 12
                                  7*****8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00075
                   zf-ribbon_3  4 rCPnCGapl 12
                                  +CP+CG+pl
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPL 48
                                  599999875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11        77       2       9 ..       4      11 ..       3      19 .. 0.83
   2 ?    9.2   0.1    0.0012      0.88       4      14 ..      40      50 ..      39      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                        zf_UBZ  2 tylCerCg 9 
                                   y+C  Cg
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCG 11
                                  59*****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                        zf_UBZ  4 lCerCgkeipe 14
                                   C+rCgk++  
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLNA 50
                                  5******9866 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.3    0.0026       1.8       5      36 ..       4      48 ..       1      50 [. 0.69

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                   Zn-ribbon_8  5 eYrCeeCghefe................vlqsisdapltaCPeCgsev 36
                                   Y C++Cg +                  +++si+     +CP+Cg+++
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCGYTLYnfdkvgqdfygvrtpsEIRSIF---GGKCPRCGKPL 48
                                  599*****88775557666666655555555555...55699999865 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00036      0.26       1      18 [.       1      18 [.       1      27 [. 0.84
   2 ?   -0.2   0.0       1.8   1.3e+03       6      15 ..      40      49 ..      39      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                                  ---EEEETTT--BTT-SS CS
                       DUF2757  1 MaihYrCrhCgkkigtle 18
                                  M ++Y Cr Cg ++ + +
  gi|70607055|ref|YP_255925.1|  1 MPVKYVCRNCGYTLYNFD 18
                                  99*********9887665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                                  EETTT--BTT CS
                       DUF2757  6 rCrhCgkkig 15
                                  +C++Cgk ++
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLN 49
                                  5999988765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1      0.01       7.5      46      61 ..       4      20 ..       2      24 .. 0.74
   2 ?    4.7   0.0     0.039        28      30      38 ..      40      48 ..      31      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
                OrfB_Zn_ribbon 46 tfkCpnCgfe.adrDvn 61
                                  +++C+nCg++ ++ D +
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCGYTlYNFDKV 20
                                  57899999886666655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.039
                OrfB_Zn_ribbon 30 tCseCgskn 38
                                  +C++Cg+ +
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPL 48
                                  466666544 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.13        95      19      24 ..       6      11 ..       2      15 .. 0.87
   2 ?   10.2   0.4   0.00062      0.44      20      32 ..      41      53 ..      40      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                    zf_C2H2_13 19 vCnkCG 24
                                  vC +CG
  gi|70607055|ref|YP_255925.1|  6 VCRNCG 11
                                  9****9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00062
                    zf_C2H2_13 20 CnkCGkPisleai 32
                                  C  CGkP+   ai
  gi|70607055|ref|YP_255925.1| 41 CPRCGKPLNAPAI 53
                                  99******99988 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.7     0.028        20       1      10 [.       5      14 ..       5      19 .. 0.84
   2 ?    6.7   0.1     0.016        11       2      11 ..      40      49 ..      40      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                                  EEETTTTEEE CS
                       zf-C2H2  1 ykCpdCgksF 10
                                  y+C  Cg++ 
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGYTL 14
                                  9******875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                                  EETTTTEEES CS
                       zf-C2H2  2 kCpdCgksFk 11
                                  kCp Cgk+ +
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLN 49
                                  7******976 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0042         3      20      27 ..       5      12 ..       3      19 .. 0.58
   2 ?    5.0   1.4     0.025        18       2       9 ..      40      47 ..      39      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                                  EEESSSSB CS
                  TF_Zn_Ribbon 20 lvCtdCGl 27
                                  +vC +CG+
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGY 12
                                  55555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
                                  EETTTTCE CS
                  TF_Zn_Ribbon  2 kCPnCgst 9 
                                  kCP Cg +
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKP 47
                                  8****965 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0043         3      27      37 ..       3      13 ..       1      14 [. 0.83
   2 ?    4.4   0.6     0.048        34       2       8 ..      40      46 ..      39      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0043
                       TFIIS_C 27 vfykCtkCghr 37
                                  v y+C +Cg++
  gi|70607055|ref|YP_255925.1|  3 VKYVCRNCGYT 13
                                  78*******85 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.048
                       TFIIS_C  2 kCpkCgs 8 
                                  kCp+Cg+
  gi|70607055|ref|YP_255925.1| 40 KCPRCGK 46
                                  7999997 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.3     0.004       2.9       3      31 ..       6      48 ..       4      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                                  E-TTT--.EEETT........TB--S.....STTB-TTT--.- CS
                       ADK_lid  3 vCpkCGr.sYhvv........fnpPk.....veglCDkCGepL 31
                                  vC++CG   Y+           + P        g+C  CG pL
  gi|70607055|ref|YP_255925.1|  6 VCRNCGYtLYNFDkvgqdfygVRTPSeirsiFGGKCPRCGKPL 48
                                  999**9757996577777655233335666699********99 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.7     0.052        37      26      36 ..       5      13 ..       3      17 .. 0.89
   2 ?    6.8   0.1    0.0094       6.7       1      11 [.      40      50 ..      40      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.052
                     Ogr_Delta 26 yqCsnfeCgat 36
                                  y+C+n  Cg+t
  gi|70607055|ref|YP_255925.1|  5 YVCRN--CGYT 13
                                  99***..**98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0094
                     Ogr_Delta  1 rCPhCgapaaa 11
                                  +CP Cg+p  a
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKPLNA 50
                                  6*****99765 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8    0.0067       4.8      13      20 ..       4      11 ..       2      14 .. 0.85
   2 ?    6.6   0.9    0.0096       6.9      15      22 ..      40      47 ..      40      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0067
                                  SEE-TTT- CS
                        zf-HIT 13 kYkCpkCn 20
                                  kY C++C+
  gi|70607055|ref|YP_255925.1|  4 KYVCRNCG 11
                                  9******8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0096
                                  E-TTT--E CS
                        zf-HIT 15 kCpkCntr 22
                                  kCp+C+ +
  gi|70607055|ref|YP_255925.1| 40 KCPRCGKP 47
                                  8*****88 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.37   2.7e+02       3       8 ..       6      11 ..       4      13 .. 0.72
   2 ?   10.0   1.3   0.00084       0.6       1      10 [.      38      47 ..      38      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.37
                                  B-TTT- CS
                  zf-FPG_IleRS  3 pCpRCw 8 
                                  +C+ C+
  gi|70607055|ref|YP_255925.1|  6 VCRNCG 11
                                  477776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00084
                                  TSB-TTT--B CS
                  zf-FPG_IleRS  1 GepCpRCwry 10
                                  G +CpRC+ +
  gi|70607055|ref|YP_255925.1| 38 GGKCPRCGKP 47
                                  569*****87 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.031        22      19      27 ..       5      13 ..       2      29 .. 0.79
   2 ?    6.1   1.1     0.016        11      20      26 ..      40      46 ..      32      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.031
                 Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                   vC +Cg++
  gi|70607055|ref|YP_255925.1|  5 YVCRNCGYT 13
                                  589999865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                 Zn_Tnp_IS1595 20 vCPhCgs 26
                                   CP+Cg+
  gi|70607055|ref|YP_255925.1| 40 KCPRCGK 46
                                  6*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 498.99
//
Query:       gi|70607056|ref|YP_255926.1|  [L=716]
Description: hypothetical protein Saci_1292 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-24   84.0  30.4    3.8e-06   26.4   0.4    6.3  5  Kelch_1          Kelch motif
    1.9e-20   72.3  25.8    5.5e-06   26.5   0.3    6.2  6  Kelch_6          Kelch motif
    8.4e-17   61.3  16.1    1.5e-09   38.1   0.9    4.0  3  fn3              Fibronectin type III domain
    2.7e-15   55.6  16.2     0.0082   16.1   0.1    6.7  6  Kelch_2          Kelch motif
    3.9e-14   52.2  25.5    0.00015   21.6   0.3    5.9  5  Kelch_5          Kelch motif
    7.9e-12   45.0  21.0      0.012   15.6   0.0    6.0  6  Kelch_4          Galactose oxidase, central domain
    5.1e-11   42.6  17.3      0.014   15.6   0.6    5.8  5  Kelch_3          Galactose oxidase, central domain
  ------ inclusion threshold ------
       0.23   10.7   1.9       0.31   10.2   1.9    1.1  1  DUF5410          Family of unknown function (DUF5410)
       0.32   11.4   1.8         10    6.6   0.3    2.6  2  DUF2369          Uncharacterised conserved protein (DUF2369)
          1    9.8   7.3        7.7    7.0   1.3    2.8  3  DUF5104          Domain of unknown function (DUF5104)
        3.8    8.1  17.6        9.4    6.9   9.0    4.0  2  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08   1.9e-05       2      46 .]      42      85 ..      41      85 .. 0.93
   2 !   15.1   0.7   7.6e-06     0.012       3      38 ..      89     122 ..      87     130 .. 0.75
   3 !   25.3   0.1   5.2e-09   8.5e-06       3      41 ..     135     178 ..     133     180 .. 0.94
   4 !   26.4   0.4   2.3e-09   3.8e-06      11      45 ..     195     230 ..     193     231 .. 0.96
   5 !   12.7   0.1   4.5e-05     0.073       3      22 ..     284     303 ..     282     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                  BBSEEEEEETTEEEEEEEBCS.SSBEEEEEEEETTTTEEEEECCCS CS
                       Kelch_1  2 ragagavvvggkiYviGGsdg.gnalssvevyDpetntWrelpsMp 46
                                   +  +av+ +g iYviGG  +   ++ssv+v+   +++W   p++p
  gi|70607056|ref|YP_255926.1| 42 LSQSTAVYYNGSIYVIGGLTSgALFVSSVYVFQ--NGKWIDGPPLP 85
                                  57789****************************..*****999986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.6e-06
                                   BSEEEEEETTEEEEEEEBCSSSBEEEEEEEETTTTE CS
                       Kelch_1   3 agagavvvggkiYviGGsdggnalssvevyDpetnt 38 
                                   a ag vv+++ iYv+GG +++     + v++   n+
  gi|70607056|ref|YP_255926.1|  89 AEAGGVVLNNNIYVVGGLNESGIFGGILVFN--GNS 122
                                   66899**************966655555555..555 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 5.2e-09
                                   BSEEEEEETTEEEEEEEBCS.....SSBEEEEEEEETTTTEEEE CS
                       Kelch_1   3 agagavvvggkiYviGGsdg.....gnalssvevyDpetntWre 41 
                                   +ga++ + +++iYviGG++      + +++ + vy++ tn+Wr 
  gi|70607056|ref|YP_255926.1| 135 YGAVVFAYNNQIYVIGGMNTtgftlSPPSRLIQVYSLNTNSWRI 178
                                   6888999***********************************96 PP

  == domain 4  score: 26.4 bits;  conditional E-value: 2.3e-09
                                   TTEEEEEEEBCS.SSBEEEEEEEETTTTEEEEECCC CS
                       Kelch_1  11 ggkiYviGGsdg.gnalssvevyDpetntWrelpsM 45 
                                   g+ +Yv+GG+ g  + ++ v++y p +ntW  lp++
  gi|70607056|ref|YP_255926.1| 195 GNALYVVGGYIGyASGSNQVYMYFPSNNTWVSLPPL 230
                                   899*******************************98 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 4.5e-05
                                   BSEEEEEETTEEEEEEEBCS CS
                       Kelch_1   3 agagavvvggkiYviGGsdg 22 
                                    + + v vg+k+Y+iGG d 
  gi|70607056|ref|YP_255926.1| 284 VYSAYVQVGNKLYIIGGLDA 303
                                   5678899**********986 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   3.5e-07   0.00057       4      47 ..      44      85 ..      40      87 .. 0.86
   2 !   11.3   0.4    0.0002      0.33       8      49 ..      94     133 ..      91     136 .. 0.88
   3 !   26.5   0.3   3.4e-09   5.5e-06       7      49 ..     139     185 ..     133     189 .. 0.88
   4 !   19.0   0.5   7.5e-07    0.0012      11      48 ..     195     232 ..     184     235 .. 0.89
   5 ?   -2.0   0.2       3.2   5.2e+03      10      30 ..     242     257 ..     232     262 .. 0.65
   6 !   11.8   0.1   0.00014      0.23       4      24 ..     285     307 ..     281     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.5e-07
                       Kelch_6  4 ghslvsvggkiYifGGytdsspylnkvwvydpetksWeqlpplp 47
                                  + ++v ++g+iY++GG+t +  ++++v+v+  ++++W  +pplp
  gi|70607056|ref|YP_255926.1| 44 QSTAVYYNGSIYVIGGLTSGALFVSSVYVF--QNGKWIDGPPLP 85
                                  455688************998899999999..88*******998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0002
                       Kelch_6   8 vsvggkiYifGGytdsspylnkvwvydpetksWeqlp.plpvp 49 
                                   v+ ++ iY++GG++  s  +  ++v++   +sW +++ ++pvp
  gi|70607056|ref|YP_255926.1|  94 VVLNNNIYVVGGLNE-SGIFGGILVFNG--NSWYTIStSMPVP 133
                                   7899***********.7888999***97..9999997689988 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 3.4e-09
                       Kelch_6   7 lvsvggkiYifGGytds....spylnkvwvydpetksWeqlpplpvp 49 
                                   +++++++iY++GG +      sp+++ ++vy++ t+sW+ ++  p p
  gi|70607056|ref|YP_255926.1| 139 VFAYNNQIYVIGGMNTTgftlSPPSRLIQVYSLNTNSWRIIGYAPEP 185
                                   477************99*********************999877765 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 7.5e-07
                       Kelch_6  11 ggkiYifGGytdsspylnkvwvydpetksWeqlpplpv 48 
                                   g+ +Y++GGy ++ + +n+v+ y p++++W  lppl++
  gi|70607056|ref|YP_255926.1| 195 GNALYVVGGYIGYASGSNQVYMYFPSNNTWVSLPPLKT 232
                                   468*******999999*******************986 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3.2
                       Kelch_6  10 vggkiYifGGytdsspylnkv 30 
                                   +gg +Y +GGy+      n++
  gi|70607056|ref|YP_255926.1| 242 YGGILYGVGGYYY-----NSL 257
                                   4444788888876.....554 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00014
                       Kelch_6   4 ghslvsvggkiYifGGytds..s 24 
                                   + + v vg+k+Yi+GG+++s  +
  gi|70607056|ref|YP_255926.1| 285 YSAYVQVGNKLYIIGGLDASkgF 307
                                   555599***********996542 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   1.5   3.5e-10   5.8e-07       6      85 .]     327     399 ..     321     399 .. 0.90
   2 !   38.1   0.9   9.1e-13   1.5e-09       3      83 ..     410     487 ..     408     489 .. 0.90
   3 ?    1.7   1.0      0.21   3.4e+02      64      82 ..     550     568 ..     486     571 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.5e-10
                                   EEEEEESSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSEEEEEE CS
                           fn3   6 lsvsevtstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngggegpes 85 
                                   +++ + +++s+++sW        + +gY ++++++ +++ + +++v + + s+ + +L+ g +Y +r+  +n++g+g +s
  gi|70607056|ref|YP_255926.1| 327 IRFAQAGNNSISLSWYDT-----NTSGYYIQWWSSIDNN-KSTINVGNVS-SYLFINLTNGVTYYFRIIPYNQAGNGTSS 399
                                   4666779*********99.....79*************9.9999999999.************************99877 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 9.1e-13
                                   ECEEEEEEE.SSSEEEEEEE-CSSSSSTEEEEEEEEEETTSTSTEEEEEECSTSSEEEEESSSTTEEEEEEEEEEETSEEE CS
                           fn3   3 Psnlsvsev.tstsltvsWeppkdgggpitgYeveyrekgseeewneftvprtttsvtltgLkpgteYevrVqavngggeg 82 
                                   P  +sv+ + +++++tv W++p +gg pi gY +++++++s     +++v + +  +tlt+L+p   Yev V a+n+ g++
  gi|70607056|ref|YP_255926.1| 410 PDSPSVKVIvGDRNATVIWSKPYNGGFPILGYYLTVKTDNSSY---TINVGNVS-KYTLTNLTPEVLYEVMVVAYNKLGNS 486
                                   56677888889****************************8775...99999999.*********************99866 PP

                                   E CS
                           fn3  83 p 83 
                                    
  gi|70607056|ref|YP_255926.1| 487 S 487
                                   4 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.21
                                   STTEEEEEEEEEEETSEEE CS
                           fn3  64 kpgteYevrVqavngggeg 82 
                                    p+  Y+v+++a n++g+ 
  gi|70607056|ref|YP_255926.1| 550 IPYGIYNVTIRATNQVGTN 568
                                   578889******9999854 PP

>> Kelch_2  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.1e-06    0.0082       2      40 ..      42      78 ..      41      85 .. 0.86
   2 !   12.9   0.4   5.2e-05     0.084       8      44 ..      94     125 ..      94     129 .. 0.92
   3 !   12.3   0.0   7.9e-05      0.13       4      43 ..     136     177 ..     133     181 .. 0.87
   4 !    6.6   0.2    0.0051       8.3      11      47 ..     195     229 ..     186     231 .. 0.67
   5 !    6.1   0.5    0.0071        11       5      36 ..     237     269 ..     233     279 .. 0.70
   6 !    7.6   0.0    0.0023       3.8       4      20 ..     285     301 ..     282     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.1e-06
                       Kelch_2  2 rgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekh 40
                                  ++ +++++ +g iyv+GG     + l+ s+v+v+  +k+
  gi|70607056|ref|YP_255926.1| 42 LSQSTAVYYNGSIYVIGGL--TSGALFVSSVYVFQNGKW 78
                                  678899*************..999999999988877775 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.2e-05
                       Kelch_2   8 svpggkiyvvGGahtdnpnlsssdvhvldlekhvWee 44 
                                   +v+++ iyvvGG      n+s +   +l +++++W  
  gi|70607056|ref|YP_255926.1|  94 VVLNNNIYVVGGL-----NESGIFGGILVFNGNSWYT 125
                                   6899*********.....*****************76 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 7.9e-05
                       Kelch_2   4 ghsssvpggkiyvvGGa....htdnpnlsssdvhvldlekhvWe 43 
                                   g ++   +++iyv+GG     +t  p++  + v  + l++++W+
  gi|70607056|ref|YP_255926.1| 136 GAVVFAYNNQIYVIGGMnttgFTLSPPSRLIQV--YSLNTNSWR 177
                                   55555679************************9..999999997 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0051
                       Kelch_2  11 ggkiyvvGGa..htdnpnlsssdvhvldlekhvWeevtp 47 
                                   g+ +yvvGG+  +++++n + + +    ++ ++W  ++p
  gi|70607056|ref|YP_255926.1| 195 GNALYVVGGYigYASGSNQVYMYF----PSNNTWVSLPP 229
                                   789*******66655555544444....66666666555 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0071
                       Kelch_2   5 hsssvpggkiyvvGGa.htdnpnlsssdvhvld 36 
                                    ++ + gg +y vGG+ +++++   +  ++ ++
  gi|70607056|ref|YP_255926.1| 237 NAVGYYGGILYGVGGYyYNSLGQFIPGAIYYMN 269
                                   57889***********85555555555555554 PP

  == domain 6  score: 7.6 bits;  conditional E-value: 0.0023
                       Kelch_2   4 ghsssvpggkiyvvGGa 20 
                                    ++++ +g+k+y++GG 
  gi|70607056|ref|YP_255926.1| 285 YSAYVQVGNKLYIIGGL 301
                                   5667778*********9 PP

>> Kelch_5  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   1.1e-06    0.0017       1      37 [.      38      73 ..      38      74 .. 0.87
   2 !   12.3   0.3   7.9e-05      0.13       5      38 ..      88     119 ..      83     123 .. 0.86
   3 !   21.6   0.3   9.3e-08   0.00015       1      41 [.     130     173 ..     130     174 .. 0.73
   4 !    7.8   2.6     0.002       3.3      14      37 ..     195     217 ..     183     228 .. 0.79
   5 !    5.9   0.1    0.0081        13       9      28 ..     287     306 ..     282     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                       Kelch_5  1 iPppRaghcavtvsekiYvyGGkvgrdgsvs.ddvyvL 37
                                  +P p++++ av+++++iYv+GG ++  g ++ + vyv+
  gi|70607056|ref|YP_255926.1| 38 LPIPLSQSTAVYYNGSIYVIGGLTS--GALFvSSVYVF 73
                                  699*********************6..65555899986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.9e-05
                       Kelch_5   5 RaghcavtvsekiYvyGGkvgrdgsvsddvyvLd 38 
                                   +a +  v+++++iYv GG +  ++++++ ++v++
  gi|70607056|ref|YP_255926.1|  88 LAEAGGVVLNNNIYVVGGLN--ESGIFGGILVFN 119
                                   6678899*************..999999999986 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 9.3e-08
                       Kelch_5   1 iPppRaghcavtvsekiYvyGGkvg...rdgsvsddvyvLdlps 41 
                                   +P+p +g+ +++++++iYv+GG+++   + + +s  + v++l++
  gi|70607056|ref|YP_255926.1| 130 MPVPVYGAVVFAYNNQIYVIGGMNTtgfTLSPPSRLIQVYSLNT 173
                                   7***********************73222222245666666665 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.002
                       Kelch_5  14 sekiYvyGGkvgrdgsvsddvyvL 37 
                                   ++ +Yv GG++g   s+s+ vy +
  gi|70607056|ref|YP_255926.1| 195 GNALYVVGGYIG-YASGSNQVYMY 217
                                   3449*******8.99999999988 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0081
                       Kelch_5   9 cavtvsekiYvyGGkvgrdg 28 
                                   ++v v++k+Y++GG +++ g
  gi|70607056|ref|YP_255926.1| 287 AYVQVGNKLYIIGGLDASKG 306
                                   455579*********97443 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   4.2e-05     0.068       7      48 ..      45      85 ..      43      85 .. 0.83
   2 !   11.1   0.3   0.00019       0.3       6      44 ..      92     126 ..      89     132 .. 0.73
   3 !   15.6   0.0   7.3e-06     0.012       4      47 ..     135     182 ..     134     185 .. 0.81
   4 !   13.0   0.3   4.8e-05     0.079       5      47 ..     188     230 ..     186     232 .. 0.87
   5 ?   -3.4   0.3       6.2     1e+04      12      25 ..     243     256 ..     235     275 .. 0.73
   6 ?    3.9   0.1     0.033        55       8      24 ..     289     304 ..     283     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                       Kelch_4  7 atsi.pdgtiylfGGrgedgtllndlylldlstntWrrlgslP 48
                                  +t++ ++g+iy++GG ++ + +++ +y+  +++++W   ++lP
  gi|70607056|ref|YP_255926.1| 45 STAVyYNGSIYVIGGLTSGALFVSSVYV--FQNGKWIDGPPLP 85
                                  5666679***********8899999999..9999997766666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                       Kelch_4   6 satsipdgtiylfGGrgedgtllndlylldlstntWrrl 44 
                                   + +++ +++iy++GG +e g +++ + +  +  n+W ++
  gi|70607056|ref|YP_255926.1|  92 GGVVL-NNNIYVVGGLNESG-IFGGILV--FNGNSWYTI 126
                                   56777.79**********96.9999888..556666555 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 7.3e-06
                       Kelch_4   4 ghsatsipdgtiylfGGrgedg...tllndl.ylldlstntWrrlgsl 47 
                                   + +++  +++ iy++GG ++ g   ++ + l  +++l tn+Wr +g +
  gi|70607056|ref|YP_255926.1| 135 YGAVVFAYNNQIYVIGGMNTTGftlSPPSRLiQVYSLNTNSWRIIGYA 182
                                   666777799*************99977777744599*******98644 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 4.8e-05
                       Kelch_4   5 hsatsipdgtiylfGGrgedgtllndlylldlstntWrrlgsl 47 
                                   +s  + +++ +y++GG+ + ++ +n +y +  s+ntW  l++l
  gi|70607056|ref|YP_255926.1| 188 YSGYYFNGNALYVVGGYIGYASGSNQVYMYFPSNNTWVSLPPL 230
                                   5555667789*********99*****************99997 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 6.2
                       Kelch_4  12 dgtiylfGGrgedg 25 
                                   +g +y +GG++ + 
  gi|70607056|ref|YP_255926.1| 243 GGILYGVGGYYYNS 256
                                   56778889998774 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.033
                       Kelch_4   8 tsipdgtiylfGGrged 24 
                                   ++++ +++y++GG  + 
  gi|70607056|ref|YP_255926.1| 289 VQVG-NKLYIIGGLDAS 304
                                   7785.9*******9876 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.4   0.00011      0.18       2      25 ..      52      74 ..      51      78 .. 0.91
   2 ?    3.4   0.3     0.061     1e+02       2      16 ..      98     110 ..      97     137 .. 0.73
   3 !   13.0   0.1     6e-05     0.098       1      38 [.     143     185 ..     143     190 .. 0.82
   4 !   15.6   0.6   8.8e-06     0.014       1      37 [.     195     230 ..     195     235 .. 0.92
   5 !    6.6   0.0    0.0061       9.9       1      20 [.     292     312 ..     292     320 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                       Kelch_3  2 drlyifGGlgddgqdrlndvyvyd 25
                                  +++y++GGl+ +g  ++++vyv++
  gi|70607056|ref|YP_255926.1| 52 GSIYVIGGLT-SGALFVSSVYVFQ 74
                                  679*******.9**********96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                       Kelch_3   2 drlyifGGlgddgqd 16 
                                   + +y++GGl+ +   
  gi|70607056|ref|YP_255926.1|  98 NNIYVVGGLNES--G 110
                                   67*******953..3 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 6e-05
                       Kelch_3   1 gdrlyifGGlgddgqdrl..ndvy.vydldtntWaei..aslp 38 
                                   ++ +y++GG +++g + +  + +  vy+l+tn+W+ i  a+ p
  gi|70607056|ref|YP_255926.1| 143 NNQIYVIGGMNTTGFTLSppSRLIqVYSLNTNSWRIIgyAPEP 185
                                   689********99977778877777*********977555544 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 8.8e-06
                       Kelch_3   1 gdrlyifGGlgddg.qdrlndvyvydldtntWaeiasl 37 
                                   g+ ly++GG+   g   ++n+vy+y +++ntW ++++l
  gi|70607056|ref|YP_255926.1| 195 GNALYVVGGYI--GyASGSNQVYMYFPSNNTWVSLPPL 230
                                   799********..88******************99876 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0061
                       Kelch_3   1 gdrlyifGGlgd.dgqdrlnd 20 
                                   g++lyi+GGl++  g  ++++
  gi|70607056|ref|YP_255926.1| 292 GNKLYIIGGLDAsKGFVATSA 312
                                   89*********8444444444 PP

>> DUF5410  Family of unknown function (DUF5410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   0.00019      0.31     271     349 ..     461     540 ..     451     544 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                       DUF5410 271 dylltfkk.nelvdviyqgldksqtlkskvvdyigiksysiskenledvakiinselksshillkieaqeklkeiikele 349
                                   +y lt    + l +v+   ++k  +    +v+++ + + sis    ++v+++++s  k+ ++   +  ++k+ +ii ++ 
  gi|70607056|ref|YP_255926.1| 461 KYTLTNLTpEVLYEVMVVAYNKLGNSSPGIVNFVALTTASISVSVYKKVNGVLISWNKTENTTYNLLISDKKGKIIVNIT 540
                                   5555544304467899999999999999*******************************************999998876 PP

>> DUF2369  Uncharacterised conserved protein (DUF2369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.065   1.1e+02       3      32 ..     366     395 ..     365     405 .. 0.83
   2 ?    6.6   0.3    0.0063        10       3      40 ..     456     493 ..     455     546 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.065
                       DUF2369   3 vgkktkvtlseLkpdtqYyfdVFvvdqkrn 32 
                                   vg+ +++++ +L+ + +Yyf +   +q+ n
  gi|70607056|ref|YP_255926.1| 366 VGNVSSYLFINLTNGVTYYFRIIPYNQAGN 395
                                   677889999***********9998888766 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0063
                       DUF2369   3 vgkktkvtlseLkpdtqYyfdVFvvdqkrntssaytgt 40 
                                   vg+ +k+tl++L+p+  Y + V + ++  n+s   ++ 
  gi|70607056|ref|YP_255926.1| 456 VGNVSKYTLTNLTPEVLYEVMVVAYNKLGNSSPGIVNF 493
                                   68889**********************99988655544 PP

>> DUF5104  Domain of unknown function (DUF5104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       6.3     1e+04      79      99 ..     347     367 ..     343     388 .. 0.53
   2 ?    5.5   0.0     0.014        23      68      92 ..     439     463 ..     398     466 .. 0.84
   3 ?    7.0   1.3    0.0047       7.7      36      91 ..     505     556 ..     501     570 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.3
                       DUF5104  79 dkYviaievvlkdeknednvG 99 
                                   + Y+i+    ++++k+  nvG
  gi|70607056|ref|YP_255926.1| 347 SGYYIQWWSSIDNNKSTINVG 367
                                   445555555555555555554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.014
                       DUF5104  68 lsaiysiktdkdkYviaievvlkde 92 
                                   l +++++ktd+++Y+i++  v k++
  gi|70607056|ref|YP_255926.1| 439 LGYYLTVKTDNSSYTINVGNVSKYT 463
                                   67899************99998876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0047
                       DUF5104  36 lidfykGdivsyeeasssseessesgktktktlsaiysiktdkdkYviaievvlkd 91 
                                   ++++++G ++s++++++++ +   s+k+ +    +i++i+t++ +Y  +i + +++
  gi|70607056|ref|YP_255926.1| 505 VYKKVNGVLISWNKTENTTYNLLISDKKGK----IIVNITTTNTSYFAYIPYGIYN 556
                                   68999********99998888888888777....9***********9999876554 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.0    0.0058       9.4       3      84 ..     336     482 ..     322     492 .. 0.80
   2 ?    1.7   1.3      0.23   3.8e+02       4      66 ..     501     559 ..     498     571 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0058
               Pur_ac_phosph_N   3 qvhlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyet.............................. 53 
                                   +++ls+ +++++ + ++W ++ +++ks++ +g+ s+ l  + + + +ty                                
  gi|70607056|ref|YP_255926.1| 336 SISLSWYDTNTSGYYIQWWSSIDNNKSTINVGNVSSYLFINLT-NGVTYYFriipynqagngtssdiisltpgavpdspsv 415
                                   5777777777777888888887778888888888877544433.2233333677777788888888888************ PP

               Pur_ac_phosph_N  54 ....................................tnyksgyshkatltgLepgttYyYrvgddeg 84 
                                                                       ++ + g++ k+tlt+L+p   Y   v + ++
  gi|70607056|ref|YP_255926.1| 416 kvivgdrnatviwskpynggfpilgyyltvktdnssYTINVGNVSKYTLTNLTPEVLYEVMVVAYNK 482
                                   *********************************99999999*****************999877654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.23
               Pur_ac_phosph_N   4 vhlsltedtstsmtvsWitpektkksvvrygtssdalestaeatsstyettnyksgyshkatl 66 
                                   +++s+ + + + + +sW+ +e+ +++++ ++ ++++    ++ t++ +++  y  + ++++t+
  gi|70607056|ref|YP_255926.1| 501 ISVSVYK-KVNGVLISWNKTEN-TTYNLLISDKKGKII--VNITTTNTSYFAYIPYGIYNVTI 559
                                   5666777.778999*****999.888888888888754..44444444444555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.41
# Mc/sec: 5262.48
//
Query:       gi|70607057|ref|YP_255927.1|  [L=230]
Description: short chain dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-37  126.8   0.0    1.1e-36  126.2   0.0    1.3  1  adh_short     short chain dehydrogenase
    9.9e-31  107.1   0.0    1.3e-30  106.7   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.25   11.3   0.0    1.3  1  KR            KR domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   1.8e-40   1.1e-36      17     188 ..       2     161 ..       1     167 [. 0.91

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 1.8e-40
                                   HHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCS CS
                     adh_short  17 akelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfsels 97 
                                   ak+l  eG++vv ++rs +       e++      l+++vDvt+ree  ++++++ +k+gk+dvLvnNAG    g+f e+s
  gi|70607057|ref|YP_255927.1|   2 AKALKGEGYTVVSLSRSRS-------EIG-----DLIYEVDVTNREEDFRIINEVLSKFGKIDVLVNNAGFGIYGSFLETS 70 
                                   5555556666665555533.......445.....36899****************************************** PP

                                   HHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEE CS
                     adh_short  98 eeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnava 178
                                    +e e ++++ + +++  t+avlp+m+k++sG+Ivn+ S a+ v  + +  YsA+K a+a++t+ l  e+++++++v++++
  gi|70607057|ref|YP_255927.1|  71 LDEEEYMVKTLFLAPIYFTKAVLPHMVKRRSGSIVNIVSEAAYVTTPKLLIYSAAKSALASFTNGLWAEMRKYNVKVSGIY 151
                                   ********************************************************************************* PP

                                   ESSBSSHHHH CS
                     adh_short 179 PGlvdTdmak 188
                                   PG+v+T+++ 
  gi|70607057|ref|YP_255927.1| 152 PGPVKTNFTS 161
                                   ******9875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.0   2.1e-34   1.3e-30      25     211 ..      16     187 ..       1     189 [. 0.90

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 2.1e-34
                                   ESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHH CS
                  adh_short_C2  25 dlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlys 105
                                    ++           +e+g  ++e+DVt++e+  ++++ev +kfgk+D+lvnnag+     g+flets +e + ++++ + +
  gi|70607057|ref|YP_255927.1|  16 SRS----------RSEIGDLIYEVDVTNREEDFRIINEVLSKFGKIDVLVNNAGFGIY--GSFLETSLDEEEYMVKTLFLA 84 
                                   333..........34578889*************************************..********************* PP

                                   HHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                  adh_short_C2 106 lfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikg 184
                                    ++++ka+lp+m ++  gsivn+ s +a +++p+  +y+aaK al ++t  l +e+ +++++v  + pgp+kT+ +s+ + 
  gi|70607057|ref|YP_255927.1|  85 PIYFTKAVLPHMVKRrsGSIVNIVSEAAYVTTPKLLIYSAAKSALASFTNGLWAEMRKYNVKVSGIYPGPVKTNFTSHPS- 164
                                   **********7766668**********************************************************99876. PP

                                   HHHHHHHHHHHSTTSS-B-HHHHHHHH CS
                  adh_short_C2 185 fdelleelearaplgrlgtpeevaeaa 211
                                        ++  a++  + +++p+eva+a+
  gi|70607057|ref|YP_255927.1| 165 ----FSKNTASIFDKYAVEPQEVANAV 187
                                   ....5667788999999********98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05      0.25      58     160 ..      27     133 ..      11     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                                   ----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEE CS
                            KR  58 vaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlf 134
                                   +++Dv+++++  ++++e+ +++++i   ++ Ag+   + + e++ ++ e +++  + +     +++ +    ++   +v +
  gi|70607057|ref|YP_255927.1|  27 YEVDVTNREEDFRIINEVLSKFGKIDVLVNNAGFGIYGSFLETSLDEEEYMVKTLFLAPIYFTKAVLPhmvkRRSGSIVNI 107
                                   689*************************************99999887766554444444444433332333677788888 PP

                                   EEHHHHH--TT-HHHHHHHHHHHHHH CS
                            KR 135 SSiagllgsagqanYaaaNaflDala 160
                                    S a+ + +++   Y+aa + l ++ 
  gi|70607057|ref|YP_255927.1| 108 VSEAAYVTTPKLLIYSAAKSALASFT 133
                                   88999999999999999988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1621.37
//
Query:       gi|70607058|ref|YP_255928.1|  [L=229]
Description: deoxyribonuclease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-37  128.8   0.1    6.2e-37  127.4   0.1    1.6  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
       0.14   12.3   0.4         12    6.2   0.3    2.6  2  SSPI        Small, acid-soluble spore protein I


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.1   6.9e-41   6.2e-37       2     254 ..       4     226 ..       3     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 6.9e-41
                                   EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGG.GHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHH CS
                    TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtssk.dskavlelakkypnkvyavlGiHPnevdeasedlleelkela 81 
                                   DaHcH  s              + ++   ++   +s+  ds+   +++ k ++k+ + +GiHP++v++   + l+ + el 
  gi|70607058|ref|YP_255928.1|   4 DAHCHYIS-------------LRGKKYDEFIIAAVSMDyDSSLS-TVSLK-NEKILVGVGIHPWNVHN---ENLDRVLEL- 65 
                                   55555555.............22333444444444443233322.22223.44599***********5...556778888. PP

                                   HCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S-HH CS
                    TatD_DNase  82 nvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgsae 162
                                      ++k+  iGe+GLDy +  +++ke q + F+++++ A e ++ + +H+ +a++d  +il++ + +k + ++H+++g ++
  gi|70607058|ref|YP_255928.1|  66 ---TEKADFIGEVGLDY-RYAKADKESQIKYFQAFVDRAIEEDKLVNVHALDAWRDSFNILTRSG-VK-RAIFHWYTGPED 140
                                   ...556666********.5556*****************************************85.45.79********** PP

                                   HHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHH CS
                    TatD_DNase 163 eakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleela 243
                                    +k +   gyyi+++  + f  ++++ +++++ pl+ +L+E+D   + +  yrgk  ep  ++  ++ ++++ka+++eel+
  gi|70607058|ref|YP_255928.1| 141 LLKDIEGAGYYITINPSVSF--QQKHLRVLEKAPLEIILTESDG--GYE--YRGKMLEPTDIPIALKIISKVKAVEEEELK 215
                                   ******99************..77999****************7..555..88**************************** PP

                                   HHHHHHHHHHH CS
                    TatD_DNase 244 eitaeNakrlf 254
                                   +i++ N+k +f
  gi|70607058|ref|YP_255928.1| 216 RIIERNFKNAF 226
                                   *********99 PP

>> SSPI  Small, acid-soluble spore protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0087        78      26      40 ..      35      49 ..      29      62 .. 0.89
   2 ?    6.2   0.3    0.0013        12       6      25 ..     201     220 ..     196     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0087
                          SSPI 26 aiqskeEktLpGLGV 40
                                  +++ k+Ek+L G G+
  gi|70607058|ref|YP_255928.1| 35 TVSLKNEKILVGVGI 49
                                  68889*********8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0013
                          SSPI   6 aiiqnlkgsskeeleetIed 25 
                                    ii+++k  ++eel+++Ie 
  gi|70607058|ref|YP_255928.1| 201 KIISKVKAVEEEELKRIIER 220
                                   69****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1674.43
//
Query:       gi|70607059|ref|YP_255929.1|  [L=133]
Description: hypothetical protein Saci_1295 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0084   15.3   1.0      0.012   14.9   1.0    1.2  1  SPESP1      Sperm equatorial segment protein 1
  ------ inclusion threshold ------
      0.012   15.9   0.2      0.014   15.6   0.2    1.2  1  DUF3908     Protein of unknown function (DUF3908)
      0.096   12.7   4.0       0.32   11.0   2.8    2.0  2  Pox_C7_F8A  Poxvirus C7/F8A protein


Domain annotation for each model (and alignments):
>> SPESP1  Sperm equatorial segment protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.0   1.9e-06     0.012      65     120 ..      27      84 ..      19     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-06
                        SPESP1  65 stendvl.inpvseettafptsgftleiekkkrtes...tafWsikPnnvsvvLhteePy 120
                                   +t n+vl ++ v+ +t  +  ++ft+ ie++  t s   ++f   kP nv v+L++++P 
  gi|70607059|ref|YP_255929.1|  27 QT-NNVLvTTNVTTHTSVSEINNFTVTIESNS-TVSiytKSFSLSKPVNVTVILSSDKPL 84 
                                   34.55551567889999999*****9999988.443222788889*************95 PP

>> DUF3908  Protein of unknown function (DUF3908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   2.4e-06     0.014      19      82 ..      39     101 ..      25     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                       DUF3908  19 drkvveelkkvsiildendilliytkylfvdekklellfilkdnkfvkvgiekekrvvieklky 82 
                                   +   v e+++ ++ ++ n  + iytk  f   k +++  il  +k + + i ++ +vv+    +
  gi|70607059|ref|YP_255929.1|  39 THTSVSEINNFTVTIESNSTVSIYTKS-FSLSKPVNVTVILSSDKPLNITILNNGKVVLSEYLM 101
                                   4477889999****************7.8999*******************9999999875433 PP

>> Pox_C7_F8A  Poxvirus C7/F8A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.8   5.4e-05      0.32      63     103 ..      25      65 ..       8      95 .. 0.84
   2 ?    1.1   0.0     0.059   3.5e+02      46      77 ..     100     131 ..      83     133 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.4e-05
                                   EEEETTEEE---EEEE-SS-EEEEEEEEESS-EEEEEES-- CS
                    Pox_C7_F8A  63 rvklngkkvdvelvkeslveviYsavlniesksvielysdt 103
                                    +++n+  v +++ +++ v+ i + +++ies+s++++y+  
  gi|70607059|ref|YP_255929.1|  25 VIQTNNVLVTTNVTTHTSVSEINNFTVTIESNSTVSIYTKS 65 
                                   5789**********************************876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                                   EEEEE--GGG-SS----EEEETTEEE---EEE CS
                    Pox_C7_F8A  46 lvilkpdwseidevkplrvklngkkvdvelvk 77 
                                   l+ l+ ++s+i+ v +l++ + +++v++++++
  gi|70607059|ref|YP_255929.1| 100 LMKLNKSFSNISGVLTLNLYNFNSTVRLSVIS 131
                                   55577899999999999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 898.45
//
Query:       gi|70607060|ref|YP_255930.1|  [L=235]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-28   98.5   0.0    5.8e-28   98.1   0.0    1.2  1  ABC_tran      ABC transporter
    6.4e-14   52.5   0.9    3.7e-06   27.0   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      7e-06   25.6   0.2     0.0046   16.4   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    6.8e-05   22.7   0.1       0.32   10.7   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0022   18.3   0.2       0.01   16.1   0.2    1.9  1  AAA_22        AAA domain
     0.0048   16.6   0.0       0.02   14.6   0.0    1.9  2  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.014   15.9   0.0    1.3  1  AAA_23        AAA domain
      0.016   14.9   0.1       0.03   14.0   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.037   14.0   0.2       0.18   11.8   0.2    2.1  1  AAA_5         AAA domain (dynein-related subfamily)
      0.039   13.9   0.0      0.068   13.1   0.0    1.5  1  Rad17         Rad17 P-loop domain
      0.044   13.4   0.0       0.15   11.7   0.1    1.8  2  SRP54         SRP54-type protein, GTPase domain
      0.072   13.5   0.0       0.19   12.2   0.0    1.7  1  RNA_helicase  RNA helicase
      0.075   13.1   0.1       0.34   11.0   0.0    1.9  2  DUF87         Helicase HerA, central domain
        0.1   13.1   0.6       0.27   11.7   0.2    2.1  2  AAA           ATPase family associated with various cellular 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.0   4.5e-31   5.8e-28       1     137 []      19     159 ..      19     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 4.5e-31
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+n+s+++  g ++a++G+nGaGKSt +k+lagll++++Ge+ ++g + ++   + +++ +g+lp+e++  + l+vren  
  gi|70607060|ref|YP_255930.1|  19 LNNISFSVPCGGRYALLGPNGAGKSTTMKILAGLLSQDSGEVYIKGMKPTS---TDVKRILGYLPEESTPYRILSVRENle 96 
                                   79*******************************************777766...799999********************* PP

                                   .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            + +++ie++++ l+l   +   +     +LS G +q++ala +ll +p+++llDEp +
  gi|70607060|ref|YP_255930.1|  97 yiaslrglrDGQSRIENLIDILDLRPYERMQA----GKLSRGNQQKLALALVLLHNPEIILLDEPLN 159
                                   **999999888888999999999999666555....*****************************86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     2e-08   2.5e-05       3      83 ..      33     108 ..      32     125 .. 0.81
   2 !   27.0   0.1   2.9e-09   3.7e-06     233     298 ..     127     187 ..     123     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83 
                                   +l GpNg+GKS+ +++l +l    +  +++     g ++++ + +++ +y pe+++ ++i   + ++ +y  +lr  r++ 
  gi|70607060|ref|YP_255930.1|  33 ALLGPNGAGKSTTMKILAGLL---SQ-DSGEVYIKGMKPTSTDVKRILGYLPEESTPYRIL-SVRENLEYIASLRGLRDGQ 108
                                   799****************94...44.44444445899999*******************9.9999999999999888887 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.9e-09
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   +a +lS G ++ lal++ ll  +    ++l+DEp n L+   ++r+++ lk l +  a ++++TH 
  gi|70607060|ref|YP_255930.1| 127 QAGKLSRGNQQKLALALVLLHNP---EIILLDEPLNYLDIPTQERVIKYLKTLVN--ATFLISTHI 187
                                   57889***************999...9****************************..********5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0013       1.6      28      50 ..      33      55 ..      26      64 .. 0.82
   2 !   16.4   0.0   3.6e-06    0.0046     109     204 ..      58     193 ..      46     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                                  EEEESTTSSHHHHHHHHHHHCTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 28 aivGpNGSGKsnlldAilFvLGe 50
                                  a++GpNG+GKs  +  +  +L++
  gi|70607060|ref|YP_255930.1| 33 ALLGPNGAGKSTTMKILAGLLSQ 55
                                  789********999877666665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.6e-06
                                   EEEEETTEEE-HHHHHHHHHCTT-STT.............................................CS-HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxx RF
                         SMC_N 109 seykingkevtkkevsellesagiske.............................................lLSgGektL 144
                                    e++i+g + t+++v+++l     +++                                              LS+G+++ 
  gi|70607060|ref|YP_255930.1|  58 GEVYIKGMKPTSTDVKRILGYLPEESTpyrilsvrenleyiaslrglrdgqsrienlidildlrpyermqagKLSRGNQQK 138
                                   566666666666666666655444444566666666666666666666666666666666666666666666********* PP

                                   HHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 145 valaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                   +alaL++     +   + llDe    LD    ++v ++lk+   na f++ ++   + ++
  gi|70607060|ref|YP_255930.1| 139 LALALVL----LHNPEIILLDEPLNYLDIPTQERVIKYLKTLV-NATFLISTHIMSIATR 193
                                   *****95....33445899**********************99.8999999987666555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00025      0.32      28      50 ..      34      56 ..      22     118 .. 0.87
   2 !   10.6   0.1   0.00026      0.33     323     364 ..     148     186 ..     124     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                        AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                  l G+N++GKS+ +++l  +l+++
  gi|70607060|ref|YP_255930.1| 34 LLGPNGAGKSTTMKILAGLLSQD 56
                                  78**************9999977 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00026
                        AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   ++ i+l++EP ++L +  q+ +ik+lk l+n ++   +i+TH
  gi|70607060|ref|YP_255930.1| 148 NPEIILLDEPLNYLDIPTQERVIKYLKTLVNATF---LISTH 186
                                   4679*****************************6...99**9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   7.8e-06      0.01       9     119 ..      33     184 ..      29     199 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.8e-06
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsst......sskdllrellralglelka..... 70 
                                   ++ G+ G+GK+t+++ l+  l +++   +         +++ ++ +lp+++      s ++ l+ +++  gl   +     
  gi|70607060|ref|YP_255930.1|  33 ALLGPNGAGKSTTMKILAGLLSQDSGEVYikgmkptsTDVKRILGYLPEEStpyrilSVRENLEYIASLRGL---Rdgqsr 110
                                   789*****************9765443337788887733333333333333133233222222223222222...144466 PP

                        AAA_22  71 .............erlsseellealeqalrarav....ielliiDEaqh.lr...seealeeLrsllnl....s 119
                                                er +   l +  +q l  + v    +e++++DE  + l+   +e+++++L++l+n     s
  gi|70607060|ref|YP_255930.1| 111 ienlidildlrpyERMQAGKLSRGNQQKLALALVllhnPEIILLDEPLNyLDiptQERVIKYLKTLVNAtfliS 184
                                   77666666666553444444443333333333335667999999997776988766999999999999554433 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.6e-05      0.02      22      59 ..      33      72 ..      28     116 .. 0.83
   2 ?   -0.7   0.0       0.8     1e+03     116     133 ..     203     220 ..     185     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                        AAA_30 22 vltGpAGtGKttalkalreaweaaggrvi..glAptgkaA 59
                                  +l Gp G+GK+t++k l+ ++ ++ g+v   g+ pt++  
  gi|70607060|ref|YP_255930.1| 33 ALLGPNGAGKSTTMKILAGLLSQDSGEVYikGMKPTSTDV 72
                                  578*******************995555422666666555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.8
                        AAA_30 116 gakvilvGDerQlasVea 133
                                   + +v+ vG  +Ql+s ++
  gi|70607060|ref|YP_255930.1| 203 HGSVVWVGSIEQLKSLGR 220
                                   578999*******99875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   1.1e-05     0.014      18      47 ..      28      57 ..      10     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                        AAA_23 18 skgltlItGpNGaGKTTildAiklaLyget 47
                                    g +++ GpNGaGK+T +  +   L  ++
  gi|70607060|ref|YP_255930.1| 28 CGGRYALLGPNGAGKSTTMKILAGLLSQDS 57
                                  45678899***********99988887765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.4e-05      0.03      18      39 ..      25      46 ..      18      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                        AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                  ++   g + l Gp+G+GKST +
  gi|70607060|ref|YP_255930.1| 25 SVPCGGRYALLGPNGAGKSTTM 46
                                  555567899***********87 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00014      0.18       4      47 ..      34      78 ..      32     169 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                  EE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B-- CS
                         AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrrei 47
                                  L+Gp G gKs+ ++ la +l +++ e++    + t++d+k  + +
  gi|70607060|ref|YP_255930.1| 34 LLGPNGAGKSTTMKILAGLLsQDSGEVYIKGMKPTSTDVKRILGY 78
                                  99******************9777766666666677777766665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-05     0.068      50      85 ..      34      70 ..      31     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                         Rad17 50 isGPsGCgkstvvkvLskelgiklre.wlnpvslkep 85
                                  + GP G gkst++k+L+  l+ +  e ++ +++  ++
  gi|70607060|ref|YP_255930.1| 34 LLGPNGAGKSTTMKILAGLLSQDSGEvYIKGMKPTST 70
                                  57**************998877655424556553334 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011      0.15       5      34 ..      33      62 ..      30      75 .. 0.87
   2 ?   -1.5   0.0       1.3   1.6e+03      38      54 ..     205     221 ..     185     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvll 34
                                  +l+G++GaGK tt+  La ll+++  +v +
  gi|70607060|ref|YP_255930.1| 33 ALLGPNGAGKSTTMKILAGLLSQDSGEVYI 62
                                  799****************99998777766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                   STSSTTHHHHHHHHHHH CS
                         SRP54  38 DtfRaaAveQLktlaek 54 
                                    +  ++ +eQLk l+++
  gi|70607060|ref|YP_255930.1| 205 SVVWVGSIEQLKSLGRE 221
                                   45567889999998865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.19       3      39 ..      34      65 ..      32      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                  l Gp+g GKSt++k La  l++++     ++vy++++
  gi|70607060|ref|YP_255930.1| 34 LLGPNGAGKSTTMKILAGLLSQDS-----GEVYIKGM 65
                                  78*************888777444.....66666554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.34      26      53 ..      32      58 ..      25      62 .. 0.80
   2 ?   -0.4   0.0      0.77   9.9e+02      85     167 ..     124     168 ..      85     202 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                         DUF87 26 lAilgsTGsGKSntvavLleellekkga 53
                                   A lg  G+GKS+t+++L   l  ++++
  gi|70607060|ref|YP_255930.1| 32 YALLGPNGAGKSTTMKILAGLLS-QDSG 58
                                  699*************9876666.5555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.77
                         DUF87  85 a..........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelkkeke 155
                                   +          ++++l + + +l   e++ l e                                                
  gi|70607060|ref|YP_255930.1| 124 ErmqagklsrgNQQKLALALVLLHNPEIILLDEP----------------------------------------------- 157
                                   3444444444444444444444444444443333............................................... PP

                         DUF87 156 elrklknqaiar 167
                                    l++l+  +++r
  gi|70607060|ref|YP_255930.1| 158 -LNYLDIPTQER 168
                                   .23333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00021      0.27       3      26 ..      34      57 ..      32     178 .. 0.77
   2 ?   -2.1   0.0       3.7   4.7e+03      15      42 ..     187     212 ..     183     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                  EESSTTSSHHHHHHHHHHHHTHEE CS
                           AAA  3 lyGppGtGKTllakavakelgvef 26
                                  l Gp G GK++++k +a  l+++ 
  gi|70607060|ref|YP_255930.1| 34 LLGPNGAGKSTTMKILAGLLSQDS 57
                                  89***************9986443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                                   HHHHHHHHTHEEEEEETTTCSSSSTTHH CS
                           AAA  15 akavakelgvefleisgsellskyvges 42 
                                   + ++a+ l  +++ is  +++  +vg  
  gi|70607060|ref|YP_255930.1| 187 IMSIATRLTDHVIVISHGSVV--WVGSI 212
                                   567888888899999988888..88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1541.90
//
Query:       gi|70607061|ref|YP_255931.1|  [L=248]
Description: hypothetical protein Saci_1297 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.6   3.2       0.22   11.7   0.5    2.4  2  Sid-5     Sid-5 family


Domain annotation for each model (and alignments):
>> Sid-5  Sid-5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   1.3e-05      0.22      24      55 ..     151     182 ..     148     192 .. 0.92
   2 ?   -1.7   0.1      0.19   3.4e+03      24      36 ..     209     221 ..     185     224 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                         Sid-5  24 illlllNilqvvffnRakllklyRrrfqqlPe 55 
                                   il++llNi + ++f  a   ++y +r qq+P 
  gi|70607061|ref|YP_255931.1| 151 ILMVLLNIPSFIIFSMAINARFYPQRQQQIPT 182
                                   89*****************************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.19
                         Sid-5  24 illlllNilqvvf 36 
                                     l+ + i +v++
  gi|70607061|ref|YP_255931.1| 209 SSLITFTIASVIY 221
                                   2345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1591.88
//
Query:       gi|70607062|ref|YP_255932.1|  [L=180]
Description: hypothetical protein Saci_1298 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-18   67.4   0.0    1.3e-18   67.1   0.0    1.1  1  LDcluster4       SLOG cluster4 family
    5.9e-06   26.4   0.0    0.00025   21.1   0.0    2.1  2  Lysine_decarbox  Possible lysine decarboxylase
    7.7e-05   22.0   0.0    0.00042   19.6   0.0    1.9  2  LSDAT_prok       SLOG in TRPM, prokaryote
  ------ inclusion threshold ------
      0.011   15.3   0.0        0.6    9.6   0.0    2.3  2  LD_cluster2      SLOG cluster2
      0.022   14.8   0.0      0.037   14.0   0.0    1.5  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   3.6e-22   1.3e-18      19     156 ..      22     163 ..       4     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.6e-22
                    LDcluster4  19 lelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilvlssdv 99 
                                    +l+  l ++ A+++ v+l Gg  G+m+    +a ++   ++ +lp + e e+  +   + iyTG+++  R+++lv+ssdv
  gi|70607062|ref|YP_255932.1|  22 SQLMLLLRKYCAQKNPVVLVGGYWGLMKDIVDSAISNFLDVLVFLPVEREIENLPD-KVFKIYTGVEFRARSVMLVRSSDV 101
                                   55666677889**********************9999999999***9888777776.6899******************** PP

                    LDcluster4 100 viaiggrsGTlsEialaleegkpvivlkgt...dellseiiekkekder..kvivaespkel 156
                                   ++a+gg++GT  Ei +a+  gkpv vl+g+   +++l+e + +  ++ +  kv++++s++e+
  gi|70607062|ref|YP_255932.1| 102 LVALGGGVGTEIEILMAYAMGKPVYVLTGSglyTDKLKEAFPDFFDERKivKVFYSSSVEEI 163
                                   ********************************988999999998888888999999999875 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.022        80      82     106 ..      34      56 ..      22      62 .. 0.78
   2 !   21.1   0.0   7.1e-08   0.00025      33     111 ..      79     151 ..      64     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.022
                                   -S.EEEEEEGGGCCHHHHHHHHHHH CS
               Lysine_decarbox  82 qkvPiillnpkgyydkllefletlv 106
                                   qk P++l++  gy+  + +++++++
  gi|70607062|ref|YP_255932.1|  34 QKNPVVLVG--GYWGLMKDIVDSAI 56 
                                   777******..9**99999988766 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 7.1e-08
                                   -SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHHHHHTTSS-S.EE.EEEEGGGCCHHHHHHHHHHHHTTSS CS
               Lysine_decarbox  33 vnelvivedmeeRkealveladafvilPGGiGTleElleiltliqlgkhqkvPi.illnpkgyydkllefletlveegti 111
                                   v ++++  ++  R  +lv+ +d +v+l GG+GT  E+l +++   +g   k P+ +l++   y dkl e +    +e+ i
  gi|70607062|ref|YP_255932.1|  79 VFKIYTGVEFRARSVMLVRSSDVLVALGGGVGTEIEILMAYA---MG---K-PVyVLTGSGLYTDKLKEAFPDFFDERKI 151
                                   555566678999*********************988887777...43...4.4415566555888888877666666554 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.11   4.1e+02     116     144 ..      29      55 ..      20      66 .. 0.60
   2 !   19.6   0.0   1.2e-07   0.00042     124     169 ..      99     144 ..      84     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                    LSDAT_prok 116 atalaekkpsvtvlvnGgeitlkdiresv 144
                                    + +a+k+p  +vlv+G    +kdi++s 
  gi|70607062|ref|YP_255932.1|  29 RKYCAQKNP--VVLVGGYWGLMKDIVDSA 55 
                                   444444444..567777777777776654 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.2e-07
                    LSDAT_prok 124 psvtvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaalrg 169
                                   + v v ++Gg  t  +i ++ + g+p+ v++Gsg  +d++ +a   
  gi|70607062|ref|YP_255932.1|  99 SDVLVALGGGVGTEIEILMAYAMGKPVYVLTGSGLYTDKLKEAFPD 144
                                   568899*********************************9887743 PP

>> LD_cluster2  SLOG cluster2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.011        40     178     199 ..      33      54 ..      31      61 .. 0.89
   2 ?    9.6   0.0   0.00017       0.6     170     198 ..     112     140 ..      91     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                   LD_cluster2 178 kakkPlylvGGfGGaakevaka 199
                                   ++k+P+ lvGG+ G+ k+++++
  gi|70607062|ref|YP_255932.1|  33 AQKNPVVLVGGYWGLMKDIVDS 54 
                                   5789**************9985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                   LD_cluster2 170 lEEallalkakkPlylvGGfGGaakevak 198
                                     E+l+a++++kP+y++ G G ++ ++ +
  gi|70607062|ref|YP_255932.1| 112 EIEILMAYAMGKPVYVLTGSGLYTDKLKE 140
                                   5599***************9988887765 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     1e-05     0.037      50     103 ..      86     132 ..      47     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHHHHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S-G CS
               Nuc_deoxyrib_tr  50 raiyeadialirqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttda 103
                                    ++ ++ + l+r++D+++a   +        Gt +E+ +a+a+gkpv+++t   
  gi|70607062|ref|YP_255932.1|  86 VEFRARSVMLVRSSDVLVALGGG-------VGTEIEILMAYAMGKPVYVLTGSG 132
                                   56777888899999999998777.......8*****************997544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1087.27
//
Query:       gi|70607063|ref|YP_255933.1|  [L=220]
Description: ribose 5-phosphate isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-43  147.4   0.9    3.8e-43  147.1   0.9    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
     0.0037   16.4   0.0     0.0054   15.9   0.0    1.2  1  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   0.9   4.2e-47   3.8e-43       2     171 ..      47     213 ..      46     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 4.2e-47
                                   EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTT.S CS
                Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklg.k 81 
                                   ++++S +te ++++ g  +lsl +  + d++iD  D v++d+ ++KGgG+allrEKi+ + +k  ++i +++Klv+  + +
  gi|70607063|ref|YP_255933.1|  47 YIASSIDTELEISQRGGLILSLYSGIQPDIYIDSFDVVTKDKVMVKGGGAALLREKILTTFSKSSLFIGEYKKLVKIEQhS 127
                                   69********************8888*************************************************664445 PP

                                   S-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S- CS
                Rib_5-P_isom_A  82 fpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlgl 162
                                    +vPve++p++++++++++++ +g k+++Re++gk g +++dngn+i+Dv++  +i+++ e++k++ksipG++etG+F++ 
  gi|70607063|ref|YP_255933.1| 128 VKVPVEIVPVSIMYILKKINE-IGFKTSIREGTGKMGGIISDNGNMIIDVEV--RINQLCEFDKTIKSIPGIIETGVFCNK 205
                                   *******************96.6*****************************..5779**********************9 PP

                                   -SEEEEEET CS
                Rib_5-P_isom_A 163 adkvlvgke 171
                                    d vl ++e
  gi|70607063|ref|YP_255933.1| 206 YDVVL-ADE 213
                                   88776.444 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     6e-07    0.0054      42      74 ..       7      40 ..       4      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-07
                                  HHHHHHHH--TTEEEEE-SSHHHHHHHHHTHH.C CS
                    Sugar-bind 42 aaqllesllkdgdvvgvgwGrtlsavaealtp.k 74
                                   +q+++++l   +++g+g+Grt+++++e+l++  
  gi|70607063|ref|YP_255933.1|  7 LSQYVSKRLTGYSIIGLGTGRTVKKLIEHLDReG 40
                                  5799**************************9944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1521.51
//
Query:       gi|70607064|ref|YP_255934.1|  [L=433]
Description: hypothetical protein Saci_1302 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.5   0.0       0.99    9.7   0.0    2.3  2  FRD2      Bacteriophage FRD2 protein


Domain annotation for each model (and alignments):
>> FRD2  Bacteriophage FRD2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.012   2.1e+02       3      17 ..      55      69 ..      53      88 .. 0.76
   2 ?    9.7   0.0   5.5e-05      0.99       5      27 ..     108     130 ..     105     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.012
                          FRD2  3 vgiiqenggwfevks 17
                                  + i+q+ngg+f v +
  gi|70607064|ref|YP_255934.1| 55 LTIVQNNGGYFLVST 69
                                  579********8854 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 5.5e-05
                          FRD2   5 iiqenggwfevksissldgfdyv 27 
                                   +i + g wf+v +i+sldg d  
  gi|70607064|ref|YP_255934.1| 108 VITNMGTWFNVTNINSLDGGDLS 130
                                   68899**************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3343.93
//
Query:       gi|70607065|ref|YP_255935.1|  [L=468]
Description: 2-isopropylmalate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-72  242.1   2.9    9.9e-72  241.7   2.9    1.2  1  HMGL-like       HMGL-like
    8.9e-15   54.4   1.0    2.7e-13   49.7   0.4    3.1  3  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00015   22.3   3.2      0.016   15.8   0.2    4.2  4  ACT_4           ACT domain
     0.0018   17.7   0.3     0.0062   16.0   0.3    1.9  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
     0.0021   18.0   0.5      0.016   15.3   0.5    2.5  2  NapD            NapD protein
     0.0054   16.9   0.3      0.029   14.5   0.1    2.4  2  CinA_KH         Damage-inducible protein CinA KH domain
  ------ inclusion threshold ------
      0.038   14.6   2.1         31    5.3   0.0    3.8  3  FtsX_ECD        FtsX extracellular domain
      0.041   13.6   0.0      0.097   12.4   0.0    1.6  1  OmpA_membrane   OmpA-like transmembrane domain
      0.059   12.6   0.1      0.094   12.0   0.1    1.2  1  Glyco_hydro_97  Glycoside hydrolase 97
       0.15   12.3   0.3       0.45   10.7   0.1    1.9  2  ExbD            Biopolymer transport protein ExbD/TolR
       0.16   11.8   0.0       0.29   11.0   0.0    1.3  1  SurA_N_2        SurA N-terminal domain


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.7   2.9   6.1e-75   9.9e-72       2     264 .]      11     272 ..      10     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.7 bits;  conditional E-value: 6.1e-75
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B......--EE-SSHHHH CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar....ilalvrarekdi 78 
                                   v i+d+tLR+Geq++++ +++++ ++iakaL+++gv+ iE+g pa s+d  e +r i+k   +      i+a+ ra+++di
  gi|70607065|ref|YP_255935.1|  11 VGILDSTLREGEQTPGVVFTTDQRVEIAKALSDIGVQMIEAGHPAVSPDIYEGIRRIIKLKREGVikseIVAHSRAVKRDI 91 
                                   789*******************************************************98766533345************ PP

                                   HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT CS
                     HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaG 159
                                   ++ +e     +a+r+ +f  +s+ hlkak++ +r+e++++++e v +a+s+g +v++ +eda+r+d ++l+ev++++++aG
  gi|70607065|ref|YP_255935.1|  92 EVGAE----IEADRIAIFYGISDTHLKAKHHTTRDEALRSIAETVSYAKSHGVKVRFTAEDATRADYQYLLEVIKTVRDAG 168
                                   *****....************************************************************************ PP

                                   -SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHH CS
                     HMGL-like 160 atriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelv 240
                                   a+r++iaDtvGvl P+  +el++ l +r +  +++ +H+HndlG+Avan laA+e Ga+ + +t+nGlGer G a+l +++
  gi|70607065|ref|YP_255935.1| 169 ADRVSIADTVGVLYPSRTRELFKDLTSRFP-DIEFDIHAHNDLGMAVANVLAAAEGGATIIHTTLNGLGERVGIAPLQVVA 248
                                   ******************************.9************************************************* PP

                                   HHHHHTT-B----HHHHHHHHHHH CS
                     HMGL-like 241 aalealgvdtgldlqklrsiaalv 264
                                   aal+       +dl+kl ++a+lv
  gi|70607065|ref|YP_255935.1| 249 AALKYHFGIEVVDLKKLSEVASLV 272
                                   ****99988999*****9999987 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.8   9.4e+03      32      41 ..     286     295 ..     285     298 .. 0.82
   2 ?    1.5   0.0      0.19     3e+02       2      27 ..     343     365 ..     342     369 .. 0.83
   3 !   49.7   0.4   1.6e-16   2.7e-13       1      74 [.     396     466 ..     395     467 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.8
                                   ESSSSSEEEE CS
                AsnC_trans_reg  32 vtGdydyllk 41 
                                   +tGdy ++ k
  gi|70607065|ref|YP_255935.1| 286 ITGDYAFVHK 295
                                   89***99876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                                   EEEE-GGGTTHHHHHHHHHHTSTTEE CS
                AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVv 27 
                                   +v+l++++   ++++ ++++  p+V+
  gi|70607065|ref|YP_255935.1| 343 GVKLTDSE---IDQVLAKIKSNPNVR 365
                                   68888777...999999999999996 PP

  == domain 3  score: 49.7 bits;  conditional E-value: 1.6e-16
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                   + v+++++   +++++ +++  ++ V+e+  ++Gdyd+l+kv ++d  +l+++++  +++++gv++t ts++l+
  gi|70607065|ref|YP_255935.1| 396 ISVKCDSNV--YTTSVTRRIVLIEGVREVMEISGDYDILVKVEAKDSTELNQIIES-IRAVKGVKSTLTSLILK 466
                                   567777666..999****************************************99.***************98 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.43     7e+02      14      55 ..     119     159 ..     111     164 .. 0.79
   2 ?    1.8   0.0      0.23   3.7e+02      50      75 ..     253     278 ..     241     279 .. 0.87
   3 ?   -0.5   0.0       1.2   1.9e+03      61      75 ..     350     364 ..     341     365 .. 0.83
   4 !   15.8   0.2   9.6e-06     0.016      48      77 ..     429     458 ..     406     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.43
                         ACT_4  14 edrkglLaditqviseekanivsvnaktrkkdglaeikitve 55 
                                   + r+ +L++i++++s +k + v+v++++++    a+ +  +e
  gi|70607065|ref|YP_255935.1| 119 TTRDEALRSIAETVSYAKSHGVKVRFTAED-ATRADYQYLLE 159
                                   568999************999999999965.44666555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.23
                         ACT_4  50 ikitveVkdvehLsrviakLraipgV 75 
                                    ++ +eV d+++Ls+v   +++ +g+
  gi|70607065|ref|YP_255935.1| 253 YHFGIEVVDLKKLSEVASLVEKYSGI 278
                                   6899************9999988887 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.2
                         ACT_4  61 hLsrviakLraipgV 75 
                                   ++++v+ak+++ p+V
  gi|70607065|ref|YP_255935.1| 350 EIDQVLAKIKSNPNV 364
                                   5799********999 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 9.6e-06
                         ACT_4  48 aeikitveVkdvehLsrviakLraipgVis 77 
                                    +i ++ve kd+ +L+++i+++ra++gV+s
  gi|70607065|ref|YP_255935.1| 429 YDILVKVEAKDSTELNQIIESIRAVKGVKS 458
                                   6799************************86 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   3.8e-06    0.0062      69     130 ..      84     145 ..      30     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                   HHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE CS
                  AP_endonuc_2  69 vdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalE 130
                                    +a+kr ie  a++ a+ + ++ G+ + + k    ++++ + +s+ e + ya+ +gvk+ + 
  gi|70607065|ref|YP_255935.1|  84 SRAVKRDIEVGAEIEADRIAIFYGISDTHLKAKHHTTRDEALRSIAETVSYAKSHGVKVRFT 145
                                   5789****************************************************998664 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   4.3e+03      11      28 ..     347     364 ..     344     367 .. 0.72
   2 !   15.3   0.5   9.5e-06     0.016      15      67 ..     406     459 ..     394     464 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                          NapD  11 rperlaavkaalaalpgv 28 
                                      ++++v+a++++ p+v
  gi|70607065|ref|YP_255935.1| 347 TDSEIDQVLAKIKSNPNV 364
                                   566788888888887776 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9.5e-06
                          NapD  15 laavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVlsa 67 
                                   +++v++++  ++gv Ev   +++  + v +Ea+++ el ++ie+i+a++gV s+
  gi|70607065|ref|YP_255935.1| 406 TTSVTRRIVLIEGVrEVMEISGDYDILVKVEAKDSTELNQIIESIRAVKGVKST 459
                                   5678999999999989***********************************986 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.029      31      69 ..     133     170 ..     101     172 .. 0.88
   2 ?   -1.5   0.0       1.7   2.8e+03      38      57 ..     431     448 ..     426     457 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                   EEEETTEEEEEEE...EEHHHHHHHHH....HHHHHTTT CS
                       CinA_KH  31 iyakegevtvRltakaaneeeaealiapveeeirerlgd 69 
                                    yak ++v+vR ta+ a++++ + l++ v++ +r++ +d
  gi|70607065|ref|YP_255935.1| 133 SYAKSHGVKVRFTAEDATRADYQYLLE-VIKTVRDAGAD 170
                                   59*********************9999.99999987665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                   EEEEEE...EEHHHHHHHHH CS
                       CinA_KH  38 vtvRltakaaneeeaealia 57 
                                   + v++   a++ +e +++i+
  gi|70607065|ref|YP_255935.1| 431 ILVKVE--AKDSTELNQIIE 448
                                   444554..666777777776 PP

>> FtsX_ECD  FtsX extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16   2.6e+02      66      93 ..     251     278 ..     241     280 .. 0.87
   2 ?    5.3   0.0     0.019        31      10      33 ..     345     368 ..     335     422 .. 0.68
   3 ?    3.8   0.2     0.056        91      71      94 ..     434     457 ..     431     458 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                      FtsX_ECD  66 LpdsfevklkdpekleevaeelkklpgV 93 
                                   L+  f +++ d +kl+eva+ ++k+ g+
  gi|70607065|ref|YP_255935.1| 251 LKYHFGIEVVDLKKLSEVASLVEKYSGI 278
                                   788999******************9998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                      FtsX_ECD  10 dateeqiealeeklealpgVksvt 33 
                                   ++t+++i+++ +k++++p+V+ ++
  gi|70607065|ref|YP_255935.1| 345 KLTDSEIDQVLAKIKSNPNVRFYR 368
                                   58999*************997554 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.056
                      FtsX_ECD  71 evklkdpekleevaeelkklpgVe 94 
                                   +v++kd ++l+++ e++++++gV+
  gi|70607065|ref|YP_255935.1| 434 KVEAKDSTELNQIIESIRAVKGVK 457
                                   7999******************97 PP

>> OmpA_membrane  OmpA-like transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     6e-05     0.097     106     159 ..     109     165 ..      84     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                                   EEEESSSSB........EEEEEEEEEEEEEEEEEEEETTEEEEEEEEEESSSSSBTS CS
                 OmpA_membrane 106 adykvkedkkske...kknhdtkvslllavGveyaitpelalrleYqylnnvgdlrk 159
                                   +d+++k ++++++    ++  + vs+  + Gv+ + t e a+r++Yqyl +v ++  
  gi|70607065|ref|YP_255935.1| 109 SDTHLKAKHHTTRdeaLRSIAETVSYAKSHGVKVRFTAEDATRADYQYLLEVIKTVR 165
                                   56656666655555556778899**************************99977655 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.8e-05     0.094      34     129 ..      84     171 ..      68     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                Glyco_hydro_97  34 tetvkryiDfAaengleyvlvegwdegWeekkkkekefdftkpypdfdleelvaYakekgvgvelwlhsetsgnvanlekq 114
                                    + vkr i+  ae + + + +  +    +  ++ + + ++t++ +  +++e v+Yak+ gv+v++++++ t     + + q
  gi|70607065|ref|YP_255935.1|  84 SRAVKRDIEVGAEIEADRIAI--FYGISD--THLKAKHHTTRDEALRSIAETVSYAKSHGVKVRFTAEDAT-----RADYQ 155
                                   567888899999999999999..444454..4455678889999999*********************999.....33333 PP

                Glyco_hydro_97 115 .ldkafklyeklGvkg 129
                                    l +++k++++ G + 
  gi|70607065|ref|YP_255935.1| 156 yLLEVIKTVRDAGADR 171
                                   2455666666666655 PP

>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.45     100     126 ..     149     175 ..      84     178 .. 0.74
   2 ?   -1.9   0.0       2.1   3.5e+03      73     116 ..     414     454 ..     371     465 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                          ExbD 100 dkdvsygklvevldtlkkagiekvslv 126
                                     ++ y+ l+ev++t++ ag ++vs++
  gi|70607065|ref|YP_255935.1| 149 ATRADYQYLLEVIKTVRDAGADRVSIA 175
                                   45789********************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                          ExbD  73 vsveelaqklkerkakppdkltvaikadkdvsygklvevldtlk 116
                                   v++e +++ +++  + +     v ++a ++++ ++++e + ++k
  gi|70607065|ref|YP_255935.1| 414 VLIEGVREVMEISGDYD--I-LVKVEAKDSTELNQIIESIRAVK 454
                                   45555555444444332..2.55666666666666666655555 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.29      86     124 ..     322     363 ..     314     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                      SurA_N_2  86 reqvldqlvseklleqeaeklGltvsdeelqdaiqg...npa 124
                                   r+ v+d++  ++ +++ +++lG++ +d+e+++++ +   np+
  gi|70607065|ref|YP_255935.1| 322 RDYVIDKYTGKHAVKDRFDRLGVKLTDSEIDQVLAKiksNPN 363
                                   7889999999***********************998666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2891.80
//
Query:       gi|70607066|ref|YP_255936.1|  [L=91]
Description: hypothetical protein Saci_1305 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-41  141.1   5.9    1.2e-41  141.0   5.9    1.0  1  Ca_bind_SSO6904  Calcium binding protein SSO6904
     0.0074   16.1   0.2     0.0078   16.0   0.2    1.2  1  IL31             Interleukin 31
  ------ inclusion threshold ------
      0.013   15.8   0.2      0.015   15.6   0.2    1.2  1  DUF2513          Hypothetical protein (DUF2513)


Domain annotation for each model (and alignments):
>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.0   5.9     2e-45   1.2e-41       1      90 []       1      90 [.       1      90 [. 0.99

  Alignments for each domain:
  == domain 1  score: 141.0 bits;  conditional E-value: 2e-45
                                  --S-S-HHHHHHHHHT--S-HHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHTHHHHHHTHHHHHHHHHHHHHHHTTT-HHHHH CS
               Ca_bind_SSO6904  1 msildeeefvklrkfkgkvdveevekileeieedlrksnnikssiifvyanhveevkknkefydliskilekyakkiGvenvk 83
                                  msild+eef++l+k+kg++dv+++++ile+ie+d+rksnni ss+i++y++++++vk+nk+f+dl+ kil+kya+kiG+env+
  gi|70607066|ref|YP_255936.1|  1 MSILDQEEFQELNKYKGRLDVDVIRNILEMIEDDYRKSNNILSSAIYAYSENIQFVKQNKAFFDLLLKILQKYANKIGLENVS 83
                                  9********************************************************************************** PP

                                  HHHHHHH CS
               Ca_bind_SSO6904 84 elilnsl 90
                                  +li+++l
  gi|70607066|ref|YP_255936.1| 84 TLIITVL 90
                                  ****987 PP

>> IL31  Interleukin 31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.3e-06    0.0078      52      94 ..      33      75 ..       7      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                          IL31 52 sdreapnninssailaylkaikplldnksdideiieqLkklkl 94
                                   d + +nni ssai ay ++i+ + +nk+  d +++ L+k + 
  gi|70607066|ref|YP_255936.1| 33 DDYRKSNNILSSAIYAYSENIQFVKQNKAFFDLLLKILQKYAN 75
                                  5667899**************************9999998665 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   2.5e-06     0.015       1      47 [.      18      66 ..      18      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                       DUF2513  1 kldmdlvRdiLltleeletkeesldd.eeekls.aidgyskeeiiyhlk 47
                                  +ld+d++R+iL  +e+  +k +++   ++  +s +i+ +++++  + l 
  gi|70607066|ref|YP_255936.1| 18 RLDVDVIRNILEMIEDDYRKSNNILSsAIYAYSeNIQFVKQNKAFFDLL 66
                                  69*************7766666654404444446666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 638.92
//
Query:       gi|70607067|ref|YP_255937.1|  [L=227]
Description: uridylate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-27   97.2   0.3    3.5e-27   95.6   0.3    1.7  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.3   1.9e-31   3.5e-27       5     241 .]       5     203 ..       1     203 [. 0.93

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 1.9e-31
                                   EEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHHHHH CS
                     AA_kinase   5 vKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdalasl 85 
                                   +K+ G+ +++++ ++l  l + i +l+++g++++vV+Ggg++++++++  ++l+ +e+++               d l++l
  gi|70607067|ref|YP_255937.1|   5 LKVSGKFFDEENSENLSLLRDVIIDLVNNGHRVAVVTGGGGTARRYISMGRKLNLNESHL---------------DILGIL 70 
                                   7999*****666689**********************************88888888885...............****** PP

                                   HHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHH CS
                     AA_kinase  86 gerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaal 166
                                    +rl+a+ll   l+++ ++  +                    +e ++e  ++g+v++++gf+    +g+    s+  +aal
  gi|70607067|ref|YP_255937.1|  71 VSRLNAQLLLFSLDNIAYPKVPES------------------IEDFNERWASGKVVITGGFQ----PGQ----STAGVAAL 125
                                   ******************988766..................678899*************9....999....9999**** PP

                                   HHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH...CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                     AA_kinase 167 lAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee...saselatgGmkvkhpaalaaarrggipvvItn 241
                                   + e ++Ad+l+++t+V+GVy++dp k  da+llp+++v+e++     ++    g  + ++p a+++++r++i+v ++n
  gi|70607067|ref|YP_255937.1| 126 VSEIINADYLVLATNVNGVYTKDPQKFVDAKLLPKLTVSELKTileGSQSVNAGKYELLDPLAIKIVERSKIKVLVIN 203
                                   *********************************************7777777788888******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1500.13
//
Query:       gi|70607068|ref|YP_255938.1|  [L=59]
Description: hypothetical protein Saci_1307 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-30  103.3   2.3      5e-30  103.2   2.3    1.0  1  Cren7     Chromatin protein Cren7


Domain annotation for each model (and alignments):
>> Cren7  Chromatin protein Cren7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   2.3   2.8e-34     5e-30       2      58 .]       2      58 ..       1      58 [. 0.97

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2.8e-34
                                  SS-S-EEEE-TTS-EEEE--SEEEEESSTTS--EEEEEEE-TTT--EEEEEE-TTS- CS
                         Cren7  2 ackkpvkVktpeGkeleLvPvKvWqLaPkgkkGvkvgLFkdPetgkyfRakvpddyP 58
                                  + kk v+V+tp GkeleL P+K W+LaPkg+kGvk+gLFkdPe gkyfR+k+pddyP
  gi|70607068|ref|YP_255938.1|  2 SEKKRVRVRTPGGKELELTPEKTWVLAPKGRKGVKIGLFKDPESGKYFRHKLPDDYP 58
                                  5689****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 463.76
//
Query:       gi|70607069|ref|YP_255939.1|  [L=265]
Description: short chain dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-37  128.3   0.0      5e-37  127.7   0.0    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
      6e-36  123.7   0.0    7.1e-36  123.5   0.0    1.1  1  adh_short     short chain dehydrogenase
    1.3e-05   25.2   0.0      2e-05   24.6   0.0    1.3  1  KR            KR domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.026   14.6   0.0    1.3  1  Shikimate_DH  Shikimate / quinate 5-dehydrogenase


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.0   1.1e-40     5e-37       4     234 .]      17     262 ..      13     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 1.1e-40
                                   TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilvnnagiapk 82 
                                   +gIG +iA++l +eG+++v+t +ne++ k++v++l +  ++ + l+ D t+ +++++l++ + +k+g++D l+ n g  p+
  gi|70607069|ref|YP_255939.1|  17 EGIGLGIARTLSREGCKIVITSRNESKvKNAVNQLSRYNPEVYgLPSDLTNLDELDKLISFALDKLGGIDALIFNTGNPPN 97 
                                   8**************************99999999997666668************************************* PP

                                   CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGG CS
                  adh_short_C2  83 lkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgp 161
                                     + f+ t+ +++d  ++  l s+++l+k +lp ++k++ g+i+ lss   +   +      +++ +l++l++ + +++++
  gi|70607069|ref|YP_255939.1|  98 EPSTFEVTNMSDWDYSVKLYLLSAVKLTKLVLPeMIKNKwGRIIYLSSWTIKEPQSIFVLADVSRSSLVQLSKIISKDYAR 178
                                   77888889*************************8777667*********9988899999********************** PP

                                   GTEEEEEEEE--BHCTGGGGSTT.........HHH.HHHHHHHHSTTSS-B-H.HHHHHHHHHHCSGGGTT--SEEEEEST CS
                  adh_short_C2 162 kgiRvNavspgpikTlaasgikg.........fde.lleelearaplgrlgtp.eevaeaalfLasdeasyitGqtlvvDg 231
                                   ++++ N++  g  +T+ a++  +         f+e  ++e+ +r+plgr+g++ +e + ++++L+s+ +syitG+++ +Dg
  gi|70607069|ref|YP_255939.1| 179 YNVTSNVILMGSFETEGAKKSLRklaetkripFEElWYREVLQRSPLGRTGDIdKELGPLIVYLISEYSSYITGSVIQIDG 259
                                   ***************876543322443444443334788999*********87369************************* PP

                                   TGG CS
                  adh_short_C2 232 Glt 234
                                   G t
  gi|70607069|ref|YP_255939.1| 260 GTT 262
                                   *87 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   1.6e-39   7.1e-36       1     191 [.       8     200 ..       8     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.6e-39
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   k vl+t  ++GIG+ ia++l +eG+k+v+++r+e+k+++++++l + + +++ ++ D+t+ +e+++l++ a +klg++d+L
  gi|70607069|ref|YP_255939.1|   8 KRVLITASTEGIGLGIARTLSREGCKIVITSRNESKVKNAVNQLSRYNPEVYGLPSDLTNLDELDKLISFALDKLGGIDAL 88 
                                   679****************************************************************************** PP

                                   EE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                   + N+G   +++++f+ ++ ++w+ ++++ l ++++lt++vlp+m+k+++GrI+  sS + k+p   ++    s   +++l+
  gi|70607069|ref|YP_255939.1|  89 IFNTGNppNEPSTFEVTNMSDWDYSVKLYLLSAVKLTKLVLPEMIKNKWGRIIYLSSWTIKEPQSIFVLADVSRSSLVQLS 169
                                   ******9988999999999************************************************************** PP

                                   HHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                     adh_short 161 rslakelaptgirvnavaPGlvdTdmakelr 191
                                   + ++k++a+++++ n++  G ++T+ ak++ 
  gi|70607069|ref|YP_255939.1| 170 KIISKDYARYNVTSNVILMGSFETEGAKKSL 200
                                   *************************998875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.6e-09     2e-05       3      90 ..      10      93 ..       9     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.6e-09
                                  EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EE CS
                            KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGv 85
                                  +lit  + g+Gl +ar+l ++g  ++v++sR+   +++ k+ +++l++++ ev  ++ D+++ d++ +l++ + ++ + i   
  gi|70607069|ref|YP_255939.1| 10 VLITASTEGIGLGIARTLSREGC-KIVITSRN---ESKVKNAVNQLSRYNPEVYGLPSDLTNLDELDKLISFALDKLGGIDAL 88
                                  699*******************7.699*****...5677789****************************9998888888877 PP

                                  EE--- CS
                            KR 86 ihaAg 90
                                  i   g
  gi|70607069|ref|YP_255939.1| 89 IFNTG 93
                                  76555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.9e-06     0.026      23      81 ..      19      76 ..       2      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                                  HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                  Shikimate_DH 23 maelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                                  ++  +a+ L+++g+k +v++ R+ +++k+ +++l+ ++ e+  l +  + l+e d +is
  gi|70607069|ref|YP_255939.1| 19 IGLGIARTLSREGCK-IVITSRNESKVKNAVNQLSRYNPEVYGLPSDLTNLDELDKLIS 76
                                  455699*********.*********************9999999988889999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1909.43
//
Query:       gi|70607070|ref|YP_255940.1|  [L=358]
Description: putative pseudouridylate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-07   31.0   0.6    4.7e-07   30.0   0.1    1.8  2  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   2.6e-11   4.7e-07       2     137 ..      28     192 ..      27     194 .. 0.82
   2 ?   -1.9   0.0      0.18   3.2e+03      24      42 ..     315     327 ..     284     343 .. 0.49

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.6e-11
                                   HHHHHHHHTT.H-SEEEEETTEEEEECT...EEEEEETHHHHHHHHHTST....TECEEEEE.......EEEEESSHHHHH CS
                         THUMP   2 eieellkegkvnverveagkgrivvelk...gekpeedeellkealekar....giqrvipv.......cevceadledil 68 
                                   +++++l   + n+er++a k  ++++l    +e+++ d +++ke++        gi +++++       c++c++++++i+
  gi|70607070|ref|YP_255940.1|  28 RCFARLSYAHTNEERGKAIKLTLLLSLDyslKEHKIQDSNQVKEIMFNMGqisyGIFSLYFGddfqnrsCYICNNRIQEIK 108
                                   677777778888888888888888875322266777777777776665557777888888889999*************** PP

                                   HHHHHHHHHHHHHCT-.EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEE CS
                         THUMP  69 eaakeivkkkfeeeke.tFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivvrvei 133
                                   ++ ++     ++e++  tF  +v +++++                e  ++ei+revGk++  + + k d +nP++ ++ +i
  gi|70607070|ref|YP_255940.1| 109 RKFYQKALSLLREKGYkTFVLGVSLPRHMRdieqnfivengliyyESLKNEIKREVGKLLTGEES-KPDIDNPEVEIIYDI 188
                                   88776666666666666***********99***********************************.***********9988 PP

                                   ETTE CS
                         THUMP 134 ikdk 137
                                     d+
  gi|70607070|ref|YP_255940.1| 189 EYDT 192
                                   7766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.18
                                   EEEECTEEEEEETHHHHHH CS
                         THUMP  24 ivvelkgekpeedeellke 42 
                                   i++e k      d ++lk+
  gi|70607070|ref|YP_255940.1| 315 IFIEAK------DFNELKQ 327
                                   222222......3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2857.91
//
Query:       gi|70607071|ref|YP_255941.1|  [L=444]
Description: signal recognition 54 kDa protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-69  233.9   0.0    1.9e-69  233.3   0.0    1.3  1  SRP54       SRP54-type protein, GTPase domain
    1.3e-29  102.7   1.0      8e-29  100.2   0.5    2.4  2  SRP_SPB     Signal peptide binding domain
    4.4e-15   55.7   0.5    4.4e-15   55.7   0.5    2.6  3  SRP54_N     SRP54-type protein, helical bundle domain
    1.3e-05   25.3   0.0    0.00011   22.3   0.0    2.5  2  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0001   21.9   0.0    0.00017   21.1   0.0    1.3  1  ParA        NUBPL iron-transfer P-loop NTPase
    0.00017   21.2   0.1    0.00085   19.0   0.1    2.1  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
     0.0017   18.1   0.2     0.0067   16.2   0.1    2.0  2  AAA_30      AAA domain
     0.0021   18.3   0.0      0.007   16.6   0.0    1.9  1  AAA_22      AAA domain
     0.0032   17.7   0.1        1.7    9.0   0.0    3.4  3  PFOR_II     Pyruvate:ferredoxin oxidoreductase core domain II
     0.0034   17.3   0.2      0.013   15.5   0.2    2.1  1  AAA_31      AAA domain
     0.0047   17.4   0.9      0.022   15.2   0.1    2.4  2  AAA_17      AAA domain
      0.005   17.0   0.0      0.013   15.7   0.0    1.7  1  AAA_33      AAA domain
      0.007   15.4   0.0      0.017   14.2   0.0    1.5  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0075   16.2   0.3       0.02   14.8   0.3    1.7  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
     0.0084   15.3   0.0      0.025   13.7   0.0    1.5  1  G-alpha     G-protein alpha subunit
     0.0093   15.3   0.0      0.019   14.2   0.0    1.5  1  Zeta_toxin  Zeta toxin
     0.0098   16.4   0.5      0.032   14.8   0.0    2.1  2  AAA_18      AAA domain
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.053   13.8   0.1    1.6  1  TrbI_Ftype  Type-F conjugative transfer system protein (TrbI_
       0.03   14.3   1.9        0.1   12.6   0.2    2.5  2  ResIII      Type III restriction enzyme, res subunit
      0.034   13.9   0.1       0.15   11.8   0.0    2.1  2  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.13   12.5   0.0       0.24   11.6   0.0    1.5  1  AAA_28      AAA domain
       0.15   12.4   0.0       0.41   11.0   0.0    1.8  1  AAA_16      AAA ATPase domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0   2.3e-72   1.9e-69       2     196 .]      96     292 ..      95     292 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 2.3e-72
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                    +i+lvG+qG+GKTtt +KLa  +kk+g+kv lvaaD++R+aA+eQL ++++++++pv+++  +++p+++a +++ek+ +e
  gi|70607071|ref|YP_255941.1|  96 YIIMLVGVQGSGKTTTSGKLALFYKKKGYKVGLVAADIYRPAAYEQLIQIGQQINIPVYGEPGNKNPIEIATNGLEKFLKE 176
                                   68******************************************************************************* PP

                                   TSSEEEEEE--SSTT..HHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                         SRP54  83 kidvvlvDTaGrlqn..dkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                   k+++v++DTaGr+ +  +++l+ee+k++ + ++pdev+lv+da++gq+a+  a++F++a  i+++i++k+Dg+akgG+als
  gi|70607071|ref|YP_255941.1| 177 KMNIVIIDTAGRHGYgeEASLLEEMKSMYDKIHPDEVILVIDASIGQKAYDLASRFHQASPIGSLIVSKMDGTAKGGGALS 257
                                   ************97522778************************************************************* PP

                                   HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                         SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                   ++ +++  ikfig+Gek+++le+f+p+r+vsrllg
  gi|70607071|ref|YP_255941.1| 258 AVIATGAQIKFIGTGEKLDELEVFNPRRFVSRLLG 292
                                   *********************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.5   2.1e+03      13      34 ..     289     310 ..     284     322 .. 0.62
   2 !  100.2   0.5   9.9e-32     8e-29       2      97 ..     326     424 ..     325     426 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                                   HHHCCCCCCHHHHCCC.....H CS
                       SRP_SPB  13 qikkmGplskllsmiPgmsaea 34 
                                   ++  +G++++++++i  + + +
  gi|70607071|ref|YP_255941.1| 289 RLLGLGDIESIIEKIKSVEDYE 310
                                   5667888899988888744332 PP

  == domain 2  score: 100.2 bits;  conditional E-value: 9.9e-32
                                   SCTHHHHHHHHHHHCCCCCCHHHHCCC.........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHT CS
                       SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae....akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiArGs 78 
                                   +tlrd+++ql  ++kmGpl k+++m+Pg +      +++ + +e+k++ ++ai++SMT +E+d+p+ ++++ R+rRiA+G+
  gi|70607071|ref|YP_255941.1| 326 LTLRDIYKQLIALRKMGPLGKIFQMLPGAGILsqvpEEQLKLGEEKIRTFMAIMNSMTYKELDNPS-IIDKARMRRIAKGA 405
                                   79*************************95544666544448899**********************.999*********** PP

                                   TS-HHHHHHHHHHHHHHHH CS
                       SRP_SPB  79 Gtsvqevnellkqfeqmkk 97 
                                   G++v+ev+ellkq++++++
  gi|70607071|ref|YP_255941.1| 406 GVTVEEVKELLKQYQMTNN 424
                                   ***************9987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.5   5.4e-18   4.4e-15       3      75 .]       3      77 ..       1      77 [. 0.92
   2 ?   -2.1   0.1       5.8   4.7e+03       3       8 ..     314     319 ..     296     336 .. 0.55
   3 ?   -1.7   0.1       4.2   3.4e+03      17      29 ..     406     418 ..     392     433 .. 0.62

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 5.4e-18
                                  HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                       SRP54_N  3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                  ++l++a++k+ g+s   e++++e++kel+ +L++aDV+v++vk+l++++kk ++ e+k    + +++ +++iv+deL
  gi|70607071|ref|YP_255941.1|  3 DGLRDAVRKFLGSSD-YEKAVNEFIKELQIILIKADVNVRLVKDLTDRIKK-RITEEKppsaIEKREWFISIVYDEL 77
                                  6899*****999985.89*******************************88.6665778*****************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.8
                                   HHHHHH CS
                       SRP54_N   3 kklnsa 8  
                                   k+++++
  gi|70607071|ref|YP_255941.1| 314 KRMEDV 319
                                   333344 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.2
                                   CGHHHHHHHHHHH CS
                       SRP54_N  17 kideedleealke 29 
                                    ++ e ++e+lk+
  gi|70607071|ref|YP_255941.1| 406 GVTVEEVKELLKQ 418
                                   4555555555554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   2.5e+03      27      40 ..      28      41 ..      16      67 .. 0.72
   2 !   22.3   0.0   1.3e-07   0.00011       9      71 ..     105     311 ..      97     441 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                                  T--EEEEEEEESSC CS
                                  xxxxxxxxxxxxxx RF
                          CbiA 27 glrVllvDaDpqan 40
                                  +l+++l++aD+   
  gi|70607071|ref|YP_255941.1| 28 ELQIILIKADVNVR 41
                                  56677777777644 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.3e-07
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   G+GKTt++ +La   +++g++V lv aD  ++++   +  ++ ++                                    
  gi|70607071|ref|YP_255941.1| 105 GSGKTTTSGKLALFYKKKGYKVGLVAADIYRPAAY-EQLIQIGQQInipvygepgnknpieiatnglekflkekmniviid 184
                                   9********************************87.333333333378889999888889999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                          CbiA  55 ................................................................................. 54 
                                                                                                                    
  gi|70607071|ref|YP_255941.1| 185 tagrhgygeeaslleemksmydkihpdevilvidasigqkaydlasrfhqaspigslivskmdgtakgggalsaviatgaq 265
                                   999999999999999999999999999999999888888888888888888888888888888888888888888888888 PP

                                   .............................CCHCCCHHHHHHCHCHH CS
                                   .............................xxxxxxxxxxxxxxxxx RF
                          CbiA  55 .............................dlkrllellealgkkka 71 
                                                                d+++++e ++++    +
  gi|70607071|ref|YP_255941.1| 266 ikfigtgekldelevfnprrfvsrllglgDIESIIEKIKSVEDYEN 311
                                   8888888888888888888888888877755555555555554433 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.1e-07   0.00017       7      48 ..      98     139 ..      94     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
                          ParA   7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsip 48 
                                   ++l g  G GK+t++ +lAl  +kkg+kvgl+ aDiy p   
  gi|70607071|ref|YP_255941.1|  98 IMLVGVQGSGKTTTSGKLALFYKKKGYKVGLVAADIYRPAAY 139
                                   556677799****************************98754 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     1e-06   0.00085       2     158 ..      97     255 ..      96     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere 80 
                                   +++l+G  GsGKTt   +l    +++g+k+ ++  +++  +  ++l++  ++  + +       +  e +++ le++++++
  gi|70607071|ref|YP_255941.1|  97 IIMLVGVQGSGKTTTSGKLAlfYKKKGYKVGLVAADIYRPAAYEQLIQIGQQINIPVYGEPGNKNPIEIATNGLEKFLKEK 177
                                   5789************999989999*************9888888887664433333332333334467778888888887 PP

                                   TT-SEEEEEECT.TTTHHHH..HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC.. CS
                          cobW  81 erldviliEttG.laePapv..afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee.a 157
                                     +++++i t G      +   + + +++ +++  d v+ v+Da  + ++  + ++ +++       l+++K+D   +   
  gi|70607071|ref|YP_255941.1| 178 --MNIVIIDTAGrHGYGEEAslLEEMKSMYDKIHPDEVILVIDA-SIGQKAYDLASRFHQASPI-GSLIVSKMDGTAKGgG 254
                                   ..9********9866666664244499999**************.4445555555555554444.4567899998776654 PP

                                   . CS
                          cobW 158 l 158
                                    
  gi|70607071|ref|YP_255941.1| 255 A 255
                                   4 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   8.2e-06    0.0067      21     113 ..      98     202 ..      94     218 .. 0.65
   2 ?   -1.9   0.0       2.7   2.2e+03      61     110 ..     400     427 ..     375     444 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.2e-06
                        AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa....................eelgieastiakllkrlk 81 
                                    +l+G+ G+GKtt+ ++l+  ++++g++v ++A      ++ +                    + ++i+++ ++k+lk+  
  gi|70607071|ref|YP_255941.1|  98 IMLVGVQGSGKTTTSGKLALFYKKKGYKVGLVAADIYRPAAYEqliqigqqinipvygepgnkNPIEIATNGLEKFLKE-- 176
                                   5799*************************99997643333322112344333333333333322444555555555522.. PP

                        AAA_30  82 grarlepgtllivDEagmvdtkqlaallkaae 113
                                         + +++i+D ag  +  + a+ll++++
  gi|70607071|ref|YP_255941.1| 177 ------KMNIVIIDTAGRHGYGEEASLLEEMK 202
                                   ......23677777777777777777777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                        AAA_30  61 vLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallk 110
                                   ++a+++g++ + +++llk+++                      ++++llk
  gi|70607071|ref|YP_255941.1| 400 RIAKGAGVTVEEVKELLKQYQ----------------------MTNNLLK 427
                                   334444444444444444443......................3333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.6e-06     0.007       6     120 ..      96     208 ..      92     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.6e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...erlsseelleale 83 
                                   +i++++G  G+GKTt+  +l+  +++    +  ++++v  ++  +   ++l  ++ ++++ +  +   + +  e   + le
  gi|70607071|ref|YP_255941.1|  96 YIIMLVGVQGSGKTTTSGKLALFYKK----KGYKVGLVAADIYRPAAYEQL-IQIGQQINIPVYGepgNKNPIEIATNGLE 171
                                   79*********************953....346999997777777644443.66777777666665544566666779999 PP

                        AAA_22  84 qalraravielliiDEaqhlr...seealeeLrsllnlsr 120
                                   + l++++   ++iiD a +     ++ +lee +s+++ + 
  gi|70607071|ref|YP_255941.1| 172 KFLKEKMN--IVIIDTAGRHGygeEASLLEEMKSMYD-KI 208
                                   99999988..*****9999866544999999999999.44 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0021       1.7      22      52 ..     119     149 ..      98     155 .. 0.85
   2 ?    3.0   0.0      0.16   1.3e+02      45      87 ..     170     214 ..     167     239 .. 0.79
   3 ?    1.2   0.0      0.56   4.6e+02      66      86 ..     403     426 ..     361     435 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                                   HHHTT--EEEEEES--BS--HHHHHHHSTT- CS
                       PFOR_II  22 lReegikvGllrlrtlrPFPeeelkellkkv 52 
                                   ++++g+kvGl+   ++rP  +e+l ++ +++
  gi|70607071|ref|YP_255941.1| 119 YKKKGYKVGLVAADIYRPAAYEQLIQIGQQI 149
                                   799*******************999988776 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                                   HHHHSTT-SEEEEEE-S--TT-G..-HHHHHHHHHTGGGTSEEEE CS
                       PFOR_II  45 lkellkkvkkvvvldrnisfgse..Gqlveevkaalkkskvkvvn 87 
                                   l+++lk++ ++v +d +   g+     l+ee+k+   k +++ v 
  gi|70607071|ref|YP_255941.1| 170 LEKFLKEKMNIVIIDTAGRHGYGeeASLLEEMKSMYDKIHPDEVI 214
                                   7889999999*****9998887777999***99987665554443 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.56
                                   -G.-HHHHHHHHHTGGG..TSEEE CS
                       PFOR_II  66 se.Gqlveevkaalkks..kvkvv 86 
                                      G+ veevk+ lk++  + +++
  gi|70607071|ref|YP_255941.1| 403 KGaGVTVEEVKELLKQYqmTNNLL 426
                                   3359999****9999984333344 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.5e-05     0.013      12      45 ..     105     138 ..      97     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                        AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanat 45 
                                   G GKTTts +la +  k+g+kv lv +D    a+
  gi|70607071|ref|YP_255941.1| 105 GSGKTTTSGKLALFYKKKGYKVGLVAADIYRPAA 138
                                   89***********************999766555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       3.2   2.6e+03      48      68 ..      37      57 ..      10      65 .. 0.56
   2 !   15.2   0.1   2.6e-05     0.022       1     110 [.     101     219 ..     101     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.2
                                  TSHHHHHHHHHHHHHHHHHHH CS
                        AAA_17 48 klpleekkelqkeaaekiaee 68
                                  +++ +  k+l+++++++i ee
  gi|70607071|ref|YP_255941.1| 37 DVNVRLVKDLTDRIKKRITEE 57
                                  233344445555555555444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.6e-05
                                   EE-TTSSHHHHHHHHH...HHHTEEE.EEHHHHHHHHHHTTTSHSSHHHHC.....TSHHHHHHHHHHHHHHHHHHHHHSS CS
                        AAA_17   1 lGgPGsGKgtqceklv...ekygfth.lsaGdllreeakrgglakardemr.....klpleekkelqkeaaekiaeeakkk 72 
                                   +G+ GsGK+t + kl+   +k g+++ l a d+ r  a  ++l++  ++++     +  ++   e+  +  ek  +e k +
  gi|70607071|ref|YP_255941.1| 101 VGVQGSGKTTTSGKLAlfyKKKGYKVgLVAADIYRPAA-YEQLIQIGQQINipvygEPGNKNPIEIATNGLEKFLKE-KMN 179
                                   79*************95555668887678888888665.56677888888864443223333444444555555554.567 PP

                                   EEEEEE-SEE..EETTEEEESSHHHHHHHH..SEEEE.EE- CS
                        AAA_17  73 gvlvdghpri..keqagfldglpkevleelkpdaiil.lea 110
                                    v++d+  r    e+a +l++++  + +++ pd +il ++a
  gi|70607071|ref|YP_255941.1| 180 IVIIDTAGRHgyGEEASLLEEMK-SMYDKIHPDEVILvIDA 219
                                   89***987753245566667666.4789999*888873555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05     0.013       1      39 [.      97     140 ..      97     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                        AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfg 39 
                                   +++lvG++GsGK+t + +l   +kk g  + l++ d++r + ++
  gi|70607071|ref|YP_255941.1|  97 IIMLVGVQGSGKTTTSGKLalfYKKKGykVGLVAADIYRPAAYE 140
                                   589***************97777888866666888888877765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     2e-05     0.017      32      66 ..      98     132 ..      95     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB  32 vGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                   + l Gv G+Gk t+  +l+l ++++G++v+++a D
  gi|70607071|ref|YP_255941.1|  98 IMLVGVQGSGKTTTSGKLALFYKKKGYKVGLVAAD 132
                                   5689*****************************98 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   2.5e-05      0.02       1      33 [.      97     129 ..      97     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                   ++ +vg +gsGKTt   kl    k++g++vg++
  gi|70607071|ref|YP_255941.1|  97 IIMLVGVQGSGKTTTSGKLALFYKKKGYKVGLV 129
                                   6899***************************98 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.1e-05     0.025      22      74 ..      94     149 ..      84     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                                   .EEEEEEEESTTSSHHHHHHHHHHHCS--.--HHHH.HC.CHHHHHHHHHHHHHHH CS
                       G-alpha  22 revkllllGqseSGKsTilkqlkllykkg.fseeel.at.wraviqlnivrsikti 74 
                                    ++ ++l+G ++SGK+T+  +l l+ykk+ ++   + a  +r+  ++++++  ++i
  gi|70607071|ref|YP_255941.1|  94 LPYIIMLVGVQGSGKTTTSGKLALFYKKKgYKVGLVaADiYRPAAYEQLIQIGQQI 149
                                   56679*********************777655444334459999999999866666 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.3e-05     0.019      10      66 ..      89     144 ..      82     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.3e-05
                    Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRelhPeyeeilk 66 
                                   + +++ P +i+l+G +G+GK++++ +l+   +++g  v  + +D +R+    ye++++
  gi|70607071|ref|YP_255941.1|  89 VMPKKLPYIIMLVGVQGSGKTTTSGKLALFYKKKGYKVgLVAADIYRPAA--YEQLIQ 144
                                   566789******************99998888555555155677777765..666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       4.3   3.5e+03     105     120 ..      45      60 ..      19      68 .. 0.72
   2 !   14.8   0.0   3.9e-05     0.032       1      39 [.      98     145 ..      98     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.3
                        AAA_18 105 elleRlekRgyeeaki 120
                                    l +R++kR +ee+ +
  gi|70607071|ref|YP_255941.1|  45 DLTDRIKKRITEEKPP 60 
                                   4779999999887654 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.9e-05
                        AAA_18   1 IlltGtpGvGKttlakeL....skrlgf......gvnlrdvakenglll 39 
                                   I+l G++G+GKtt +  L    +k+ g+       +++r  a+e  + +
  gi|70607071|ref|YP_255941.1|  98 IMLVGVQGSGKTTTSGKLalfyKKK-GYkvglvaADIYRPAAYEQLIQI 145
                                   99****************8885555.44555565555555555544444 PP

>> TrbI_Ftype  Type-F conjugative transfer system protein (TrbI_Ftype)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.5e-05     0.053      59     104 ..       9      56 ..       4      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                    TrbI_Ftype  59 trrFn..kaleaslqelqkqkgaivLvaeaVvag.apDiTdevradiar 104
                                   +r+F+  +  e++++e+ k + +i+L++ +V    ++D+Td ++++i +
  gi|70607071|ref|YP_255941.1|   9 VRKFLgsSDYEKAVNEFIK-ELQIILIKADVNVRlVKDLTDRIKKRITE 56 
                                   56665214568999***99.9**********8888***********975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00013       0.1      25      79 ..      96     151 ..      19     218 .. 0.70
   2 ?    0.4   0.1      0.71   5.8e+02      35     117 ..     321     418 ..     297     434 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                   SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH...HHHHHHHHHGGGGTG CS
                        ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprk...slleqtleefkkfls 79 
                                     ++++   G+GKT ++ kl+  ++kkg+  k+ +++  +   + +eq+++  +++  
  gi|70607071|ref|YP_255941.1|  96 YIIMLVGVQGSGKTTTSGKLALFYKKKGY--KVGLVAADIyrpAAYEQLIQIGQQINI 151
                                   45678999*******************99..888887755444667776655555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.71
                                   STHHHHHHHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--............... CS
                        ResIII  35 tGKTlvaaklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkkvsgdkkka...........kekd 100
                                   +GKT + ++ i++ l + ++     k++ + p+  +l+q  ee  k+ +e+    + ++++ ++k+            ++ 
  gi|70607071|ref|YP_255941.1| 321 SGKTKLTLRDIYKQLIALRKMgplgKIFQMLPGAGILSQVPEEQLKLGEEKIRTFMAIMNSMTYKEldnpsiidkarMRRI 401
                                   699998877776655544444577788888888888888888877777777665444433333333333445555554445 PP

                                   ...-SEEEEEHHHHHHT CS
                        ResIII 101 stnkkilvttiqsldad 117
                                   ++ + ++v+++++l ++
  gi|70607071|ref|YP_255941.1| 402 AKGAGVTVEEVKELLKQ 418
                                   55555555555555555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.15       2      33 ..     101     132 ..     100     238 .. 0.79
   2 ?   -1.1   0.0       1.6   1.3e+03     198     231 ..     406     438 ..     367     440 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                    ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                   vG+ GsGKtt  g+l+ +++++g++v +v  D
  gi|70607071|ref|YP_255941.1| 101 VGVQGSGKTTTSGKLALFYKKKGYKVGLVAAD 132
                                   89************************999877 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                    ATP_bind_1 198 kklaeaiaelleefalvlrflplssekeesiedl 231
                                       e+++ell++++++ + l   +++++++ +l
  gi|70607071|ref|YP_255941.1| 406 GVTVEEVKELLKQYQMT-NNLLKMVKRRKGLAKL 438
                                   45678999999999999.6666666666666665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.24       2      45 ..      98     148 ..      97     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                        AAA_28   2 ivitGgestGKTtlleaLa....argyp...vvpEaareileeklakgeda 45 
                                   i+++G +++GKTt++ +La    ++gy+   v ++++r    e+l + +++
  gi|70607071|ref|YP_255941.1|  98 IMLVGVQGSGKTTTSGKLAlfykKKGYKvglVAADIYRPAAYEQLIQIGQQ 148
                                   789****************98865699855444888887777777555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00051      0.41      26     142 ..      97     218 ..      74     220 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                   +++l+G +G+GK++   +l+  ++k+g  +    +d + + ++y +l+q+  + ++   +  e+ ++++ + ++  +e + 
  gi|70607071|ref|YP_255941.1|  97 IIMLVGVQGSGKTTTSGKLALFYKKKGYKVGLVAADIY-RPAAYEQLIQIG-Q-QINIPVYGEPGNKNPIEIATNGLEKFL 174
                                   799*************9999888888444433333333.335564444444.3.333333333333333333333333333 PP

                        AAA_16 107 .........avpelagaea.srllellkrllallsrderplvlvlD 142
                                            +++  +g ++  +lle++k++ +++++ ++ ++lv+D
  gi|70607071|ref|YP_255941.1| 175 kekmniviiDTAGRHGYGEeASLLEEMKSMYDKIHP-DE-VILVID 218
                                   455556555434444443367888888888888887.55.788777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2939.88
//
Query:       gi|70607072|ref|YP_255942.1|  [L=131]
Description: translation initiation factor IF-5A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-09   35.4   0.1    1.5e-08   34.6   0.1    1.5  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    6.9e-07   29.2   0.0    2.8e-06   27.2   0.0    1.9  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.031   14.3   0.1      0.069   13.2   0.1    1.6  1  EFP       Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   2.6e-12   1.5e-08       1      69 []      69     131 .]      69     131 .] 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.6e-12
                                   --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                        eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                   ++++   q+++ ++D  l++md +++et++ l+ p    +++i +k  +g +  ++++s+mG+ ki++vK
  gi|70607072|ref|YP_255942.1|  69 IIEKHVGQILADKGD-NLTIMDlESYETFD-LEKP---TENEIVSKIRPGAE--IEYWSVMGRRKIVRVK 131
                                   589999*********.9************9.****...7788888888****..**************98 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.7e-10   2.8e-06       2      33 ..       8      39 ..       7      42 .. 0.93
   2 ?   -1.8   0.0      0.57   3.4e+03       3      13 ..     108     118 ..     107     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.7e-10
                                  GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                         EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                  + +lk G  ++idg++++V+e+   k Gk ++
  gi|70607072|ref|YP_255942.1|  8 VGDLKVGSYVMIDGEPCRVVEITKAKTGKHGS 39
                                  68**************************9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                                   GG--TT-EEEE CS
                         EFP_N   3 selkkGlviei 13 
                                   s +++G  ie+
  gi|70607072|ref|YP_255942.1| 108 SKIRPGAEIEY 118
                                   78999998886 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05     0.069       9      28 ..      81     100 ..      76     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                   ETTEEEEEETTT--EEEEEH CS
                           EFP   9 dgdeyvFMdnetYeqielpk 28 
                                    gd+++ Md e+Ye + l+k
  gi|70607072|ref|YP_255942.1|  81 KGDNLTIMDLESYETFDLEK 100
                                   69*************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 922.03
//
Query:       gi|70607073|ref|YP_255943.1|  [L=386]
Description: DNA topoisomerase VI subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-20   73.4   0.1    1.8e-20   72.7   0.1    1.4  1  TP6A_N       Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.074   13.0   0.1       0.14   12.1   0.1    1.4  1  GTP_EFTU_D4  Elongation factor Tu domain 4
       0.17   11.8   0.0       0.32   10.9   0.0    1.4  1  DUF2399      Protein of unknown function C-terminus (DUF2399)


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.1     3e-24   1.8e-20       1      62 []      76     152 ..      76     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 3e-24
                                   HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...............GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                        TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...............dvelFksQaesdrliddievllgvsReeLnv 62 
                                   ++f+q+++++++i+++l++++++T+Rd+YYr               +++++++Q+esd++i diev ++++Re++ +
  gi|70607073|ref|YP_255943.1|  76 KRFMQTTLMASIIYDALVNDEYPTIRDLYYRgkhsiilkdpngrayEENTWDEQKESDSVIVDIEVFTSLLREDMLI 152
                                   79*****************************************9999***************************986 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.3e-05      0.14      14      64 ..     130     180 ..     128     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                   ETCCCEEEEEEEEEEEEETT-E.EEETTE.EEEEEEEEEETTEEESEEETT- CS
                   GTP_EFTU_D4  14 rrsdpaivGvevlgGvikpgvk.likedGrevGeilqiqdkgkkleeakaGq 64 
                                   ++sd +iv +ev +  ++ ++  l ke+G+ vG  ++i++ ++ ++  k G+
  gi|70607073|ref|YP_255943.1| 130 KESDSVIVDIEVFTSLLREDMLiLSKEKGKVVGD-MRIRSGNDVIDLSKMGH 180
                                   5799**************9986266899*****9.589**999999999986 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.4e-05      0.32      19      78 ..     199     261 ..     186     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.4e-05
                       DUF2399  19 gravyVvENpavlaaaadr..lgakaaplvctsGqpsaaalelldklaaa.garlrYhGDfDw 78 
                                   ++ v VvE  av++ + ++    + +a lv  +Gqp +a+ +++++l ++    ++   D D+
  gi|70607073|ref|YP_255943.1| 199 AEFVLVVEKDAVFQQLHRAgfWKQYKAILVTSAGQPDRATRRFVRRLNEElKLPVYILTDADP 261
                                   45599**********999965555788899999**************6541445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2593.82
//
Query:       gi|70607074|ref|YP_255944.1|  [L=532]
Description: DNA topoisomerase VI subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-65  219.1   0.5    5.4e-65  218.1   0.5    1.6  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    8.7e-11   41.8   0.0    1.9e-10   40.7   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    9.5e-10   39.0   0.0    1.6e-09   38.2   0.0    1.4  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    2.5e-05   23.3   0.0    2.5e-05   23.3   0.0    2.0  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
    0.00056   20.3   0.0    0.00056   20.3   0.0    2.2  3  Ribosomal_S13   Ribosomal protein S13/S18
  ------ inclusion threshold ------
        1.6    8.7   3.3         44    4.1   0.0    2.9  3  OTCace_N        Aspartate/ornithine carbamoyltransferase, car


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.5   1.8e-68   5.4e-65       1     159 []     309     468 ..     309     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 1.8e-68
                Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvit 81 
                                   Ps+++ls ig++lie +l+k+++pefv+a+tr+pk+y+ghpfivE+g+ayGG ++  +++ +lR+aN++PL+yde++dvi+
  gi|70607074|ref|YP_255944.1| 309 PSAEALSVIGSDLIELSLQKVFNPEFVSAITRRPKAYQGHPFIVEAGVAYGGGIPAATEPLVLRYANKIPLIYDEKSDVIW 389
                                   999****************************************************************************** PP

                Topo-VIb_trans  82 kav.ksinwkrYkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeekek 159
                                   k++ ++i+wkrY++e+++ ++vv+vh++stkvP+ks+gKe+iadveeiekeikla+++var+Lkkyl++k+ke+e+k+k
  gi|70607074|ref|YP_255944.1| 390 KVIsEEIDWKRYGVETDQYQLVVMVHLCSTKVPYKSAGKESIADVEEIEKEIKLAIMDVARNLKKYLTEKRKEQEAKKK 468
                                   ***66*********************************************************************99976 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   6.3e-14   1.9e-10       5     105 ..      34     144 ..      30     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 6.3e-14
                   HATPase_c_3   5 kAlaelvdNsldAdaen.......vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGl 77 
                                   + + el++N+ldA   +       ++ie+ +++++  ++ +eD+G G+++  + na+ ++  ssk+    ++++G +G+G+
  gi|70607074|ref|YP_255944.1|  34 QTVRELIENALDATDVHnllpslkISIELVDQQKQIYKVNVEDNGIGIPPHVVPNAFgKVLYSSKYV--LRQTRGMYGLGV 112
                                   5689********965555****99********9999*******************8868*******5..79********** PP

                   HATPase_c_3  78 klAslslg....kkltvitkkegesstltldv 105
                                   k A+l +     k l+++t+  +++  +++++
  gi|70607074|ref|YP_255944.1| 113 KAAVLYSQmyqdKPLEIYTSPLNSKRIYFFRL 144
                                   ***98643122256777777666666544444 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.5e-13   1.6e-09       4      86 ..      30     120 ..      27     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.5e-13
                                   HHHHHHHHHHHHHHHHHHS...TTTEEEEEEEE..EE.TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTS.TSSSH CS
                     HATPase_c   4 krLrqiisnlvdNavkfat...kageieveika..se.ddlvisveDnGiGipkedlkklfe.kfsqddstkrgg.ggtGl 76 
                                   + L+q +++l++Na++++      ++++++i+   ++ + +++ veDnGiGip+  +++ f+  ++++++  r++ g  Gl
  gi|70607074|ref|YP_255944.1|  30 RALYQTVRELIENALDATDvhnLLPSLKISIELvdQQkQIYKVNVEDNGIGIPPHVVPNAFGkVLYSSKYVLRQTrGMYGL 110
                                   789*************933222333445555554322579999******************97444424444444366666 PP

                                   HHHHHHHHHH CS
                     HATPase_c  77 Glsivkklve 86 
                                   G++ +  +++
  gi|70607074|ref|YP_255944.1| 111 GVKAAVLYSQ 120
                                   6665544444 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.2e-09   2.5e-05     161     238 ..     225     303 ..     221     333 .. 0.85
   2 ?   -3.7   4.0       1.2   3.6e+03     407     454 ..     428     468 ..     423     469 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.2e-09
                                   SXXXSXBXTTSXXH.HHHHHHHHH..S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHH CS
                          FbpA 161 PpsqdklnPleaeeleefkellsk..kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqel 238
                                   Pp+  k+ P+ ++  e +k  + k  k  d++++Lvk+fq ++ ++a  +le  ++ k++++++l++e+++rl e ++++
  gi|70607074|ref|YP_255944.1| 225 PPEEVKPHPYGVDI-ELIKFMIAKidKPLDIRDFLVKEFQSVGDVTADKILELSKISKNKKITNLTDEEISRLVEVMKTF 303
                                   88889999**5555.55555555555669********************************************9887654 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHT-.-HHHHHHHHHHHHHTTS----TT------- CS
                          FbpA 407 keeleylesveaaleqaesledleeikeELieegylkkkkkkkkkkkk 454
                                   ke ++ +e++e++++ a     ++++++ L  ++yl +k+k+++ kkk
  gi|70607074|ref|YP_255944.1| 428 KESIADVEEIEKEIKLA-----IMDVARNL--KKYLTEKRKEQEAKKK 468
                                   67778888888888866.....99999999..7888888888777765 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.9e-07   0.00056      18      67 ..     260     309 ..     246     315 .. 0.89
   2 ?   -2.1   0.0       1.6   4.9e+03      51      89 ..     431     469 ..     410     483 .. 0.62
   3 ?   -3.0   0.3       2.9   8.7e+03      30      54 ..     508     532 .]     504     532 .] 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.9e-07
                 Ribosomal_S13  18 taikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykip 67 
                                   ++ + +G  +a +il+  +++++k+i +lt+eei++++e+++ + ++++p
  gi|70607074|ref|YP_255944.1| 260 KEFQSVGDVTADKILELSKISKNKKITNLTDEEISRLVEVMKTFDDFRPP 309
                                   56789************************************998887766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                 Ribosomal_S13  51 iekieeivenkaqykipnwi.nrqkdikdGkdshvvendl 89 
                                   i  +ee +e++++  i ++  n +k +++ +++++ +++l
  gi|70607074|ref|YP_255944.1| 431 IADVEE-IEKEIKLAIMDVArNLKKYLTEKRKEQEAKKKL 469
                                   444433.344455555555555555555555555555555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.9
                 Ribosomal_S13  30 iilkkadvdedkrigelteeeieki 54 
                                    i+++++++ +   +e++++++e++
  gi|70607074|ref|YP_255944.1| 508 LIIRRLEIEDKNLEEEIKKYKVEEV 532
                                   5889999999998999999888865 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.6   1.8e+03       5      25 ..     284     304 ..     261     314 .. 0.82
   2 ?    3.6   0.7     0.021        61       4      45 ..     432     473 ..     429     478 .. 0.84
   3 ?    4.1   0.0     0.015        44      79     117 ..     483     523 ..     474     531 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.6
                                   SGGGS-HHHHHHHHHHHHHHH CS
                      OTCace_N   5 sledlskeeieelldlaaelk 25 
                                   ++++l++eei +l+++++++ 
  gi|70607074|ref|YP_255944.1| 284 KITNLTDEEISRLVEVMKTFD 304
                                   467888888888888887775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                                   SSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEE CS
                      OTCace_N   4 lsledlskeeieelldlaaelkekvkkekkekllkgktlall 45 
                                    ++e+++ke   +++d+a++lk+  ++++ke+ +k+k ++ l
  gi|70607074|ref|YP_255944.1| 432 ADVEEIEKEIKLAIMDVARNLKKYLTEKRKEQEAKKKLITYL 473
                                   5678888777788************99999999999988765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.015
                                   TTTGGSTTSSCHHHHHHHHHHHT.SEEEEEES.SHHHHHHH CS
                      OTCace_N  79 lssvskgrkEsleDtarvlsryv.daiviRhp.gaeeleel 117
                                   ls +  g+kE++ Dt +vl +   d+i+ R + + ++lee 
  gi|70607074|ref|YP_255944.1| 483 LSMFVAGSKEKIPDTDKVLRSRLlDLIIRRLEiEDKNLEEE 523
                                   455667789**********76666******99866667643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3624.82
//
Query:       gi|70607075|ref|YP_255945.1|  [L=311]
Description: putative deoxyhypusine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   7.3e-101  337.2   0.0   8.9e-101  336.9   0.0    1.0  1  DS           Deoxyhypusine synthase
  ------ inclusion threshold ------
      0.054   13.7   0.1       0.81    9.9   0.0    2.3  2  Kindlin_2_N  Kindlin-2 N-terminal domain


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.9   0.0    1e-104  8.9e-101       9     286 ..      32     307 ..      27     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 336.9 bits;  conditional E-value: 1e-104
                            DS   9 i.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfe 88 
                                   + gf+a+++ +a++il++  k+     fl++t+nl+s+Glr+++adl+++++++v++tT+g+i++D+++++g k+y+g+fe
  gi|70607075|ref|YP_255945.1|  32 VyGFSAENVVKAVEILRDLIKE-ADLRFLSFTANLVSTGLRGLLADLIRREYFNVVITTGGTIDHDIARSFGGKYYKGSFE 111
                                   44*****************665.5699****************************************************** PP

                            DS  89 lddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSilywAykndipvfcpal 168
                                   +dd++L+e +i+R+gn+++p eny + +e++vr+ + ++ + +k ws+ el++e+Gk+ind++Sil+++y++++p  +p++
  gi|70607075|ref|YP_255945.1| 112 FDDTMLKELEIHRLGNIFIPFENYgKVIEEVVRKYIPEIVSVRKDWSVYELLWEFGKRINDQHSILKACYEKKVPLIVPGV 192
                                   ************************9999*************99************************************** PP

                            DS 169 tDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrngadyavyittaqefdGs 249
                                   +Dgs+G++l++++   + + lk+d+++D+r ++d++++++k+ga+i+GGG++Khh++++n++++g+dya+yittaqe+dGs
  gi|70607075|ref|YP_255945.1| 193 VDGSFGTNLFIVS---QFNGLKIDLFQDMRLIKDLIFSSEKSGALIIGGGISKHHTIWWNQFKDGLDYAIYITTAQEYDGS 270
                                   *******999999...5677************************************************************* PP

                            DS 250 lsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                   lsga+++Ea+Sw k++++a+sv++yaDaTi+lP+l a
  gi|70607075|ref|YP_255945.1| 271 LSGARPREAISWNKVRPSARSVTIYADATIILPILSA 307
                                   **********************************987 PP

>> Kindlin_2_N  Kindlin-2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   9.1e-05      0.81      35      62 ..     141     169 ..     116     182 .. 0.75
   2 ?    1.1   0.0     0.052   4.7e+02      52      64 ..     243     255 ..     234     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.1e-05
                   Kindlin_2_N  35 gvmlklvekl.dikkdwsDyalWWekkkk 62 
                                   +v+ k + ++  ++kdws y+l We  k+
  gi|70607075|ref|YP_255945.1| 141 EVVRKYIPEIvSVRKDWSVYELLWEFGKR 169
                                   444444433359************97766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.052
                   Kindlin_2_N  52 DyalWWekkkkWL 64 
                                    +++WW++ k  L
  gi|70607075|ref|YP_255945.1| 243 HHTIWWNQFKDGL 255
                                   489***9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1845.77
//
Query:       gi|70607076|ref|YP_255946.1|  [L=482]
Description: hypothetical protein Saci_1317 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.9e-162  539.3   0.3   7.9e-162  539.1   0.3    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.1   0.3  4.4e-166  7.9e-162       1     412 []      47     482 .]      47     482 .] 0.99

  Alignments for each domain:
  == domain 1  score: 539.1 bits;  conditional E-value: 4.4e-166
                                   HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-....-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk....gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelek 76 
                                   q++nv++l+g+++ v+++PD H+G+g+piG+++a      gv++P+++G+DI CGvrll+tnl+++++++klk+lv+e+ +
  gi|70607076|ref|YP_255946.1|  47 QATNVSCLQGVQESVYVLPDGHQGYGFPIGGIAASAideeGVVSPGGIGYDInCGVRLLRTNLDYKDVKDKLKDLVEEIYR 127
                                   899******************************99999******************************************* PP

                                   HS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB  77 avpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiE 157
                                   +vp+g+gs+++vkls ++l++vl+eg+kwav++g+g+++d+e+ie++g+++ ad++kvs  ak+r+++qlGtlG+GNHF+E
  gi|70607076|ref|YP_255946.1| 128 NVPSGVGSEGRVKLSYQQLDNVLSEGVKWAVDNGYGWNRDMEHIEQSGSWNLADPSKVSPIAKQRGHTQLGTLGAGNHFLE 208
                                   ********************************************************************************* PP

                                   EEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 158 vqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamq 237
                                   +q+v++i+de++aka+g+ +egq++vm+H+GSRglGhq+a+dyl+++++a+kk++ik+pdr+La++p++++e+q+Y++am+
  gi|70607076|ref|YP_255946.1| 209 IQVVDKIYDEKVAKAIGItHEGQITVMVHTGSRGLGHQVASDYLQVMERAMKKYNIKVPDRELAAIPFNTREAQDYIHAMS 289
                                   ******************889************************************************************ PP

                                   HHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-............ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx............ RF
                          RtcB 238 aaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA............ 302
                                    aan+A++NRq+it+++re++ +v++ + e+l+l++v+dvaHNiak Ee++ d   +kvlVhRKGAtrA            
  gi|70607076|ref|YP_255946.1| 290 SAANFAWTNRQMITHWARESFGRVYRIDPEKLDLNIVYDVAHNIAKIEEYDiDgkrKKVLVHRKGATRAfppgsteipadh 370
                                   ************************************************99996699************************* PP

                                   .TT--EEEE--STTS-EEEEE--HHHH.SSSEE---S-----------------TTTTTCCCT-EEEE------------- CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 303 .kvgqpviipGsmgtkSyivkGkgnae.sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEapea 381
                                    +vgq+v+ipGsmgt+Syi++G  + + ++ ++ HGAGR msR++a +++ +++v ++lee+gi+v+a++k++v+eEap+a
  gi|70607076|ref|YP_255946.1| 371 rNVGQIVLIPGSMGTASYIMAGIPEGRrTWFTAPHGAGRWMSREAAVRSYPVNSVVQNLEEKGIIVRAATKRVVAEEAPGA 451
                                   **********************9988889**************************************************** PP

                                   -----HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RtcB 382 YKdideVveaqaeaglvevvarlkpvlvvkg 412
                                   YKd+d+V+++++e ++++ varlkp++v kg
  gi|70607076|ref|YP_255946.1| 452 YKDVDRVAKVAHEVKIAKLVARLKPIGVTKG 482
                                   *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3198.48
//
Query:       gi|70607077|ref|YP_255947.1|  [L=71]
Description: hypothetical protein Saci_1319 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   17.1   0.5     0.0093   16.0   0.1    1.8  2  YHS       YHS domain
  ------ inclusion threshold ------
      0.015   15.4   3.2      0.089   13.0   2.3    2.0  2  YonK      YonK protein


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     1e-06    0.0093      19      40 ..      14      35 ..       6      37 .. 0.90
   2 ?   -2.8   0.0      0.79   7.1e+03      36      44 ..      48      56 ..      44      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                           YHS 19 seYkGkeYyFcSegCkdkFede 40
                                  ++ kG+ Y+F S++C  kF++e
  gi|70607077|ref|YP_255947.1| 14 ITVKGRDYLFHSKACAYKFLKE 35
                                  6669***************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.79
                           YHS 36 kFedePekY 44
                                  +F+  ++kY
  gi|70607077|ref|YP_255947.1| 48 AFKTIEKKY 56
                                  566666676 PP

>> YonK  YonK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.046   4.2e+02      42      55 ..       7      20 ..       6      23 .. 0.83
   2 ?   13.0   2.3   9.9e-06     0.089      11      46 ..      34      67 ..      31      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.046
                          YonK 42 ydekevSiTikeee 55
                                  y+++ + iT+k  +
  gi|70607077|ref|YP_255947.1|  7 YEGQGIKITVKGRD 20
                                  899999****9765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.9e-06
                          YonK 11 kkgildleemevteldkeeevvYdLseiLseydeke 46
                                  k++i d++  +v+e  k  e  Y  seiL++++ek+
  gi|70607077|ref|YP_255947.1| 34 KEAIYDMDADQVVEAFKTIEKKY--SEILEKFKEKK 67
                                  789**************999999..6********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1689  (0.0942049); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 471.90
//
Query:       gi|70607078|ref|YP_255948.1|  [L=934]
Description: putative ATP-dependent helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-30  104.0   0.0    4.1e-29  101.6   0.0    2.2  3  DEAD            DEAD/DEAH box helicase
    5.2e-16   59.0   0.1    1.3e-14   54.5   0.0    3.1  3  Helicase_C      Helicase conserved C-terminal domain
    2.2e-08   34.3   0.1    2.2e-07   31.0   0.0    2.3  2  ResIII          Type III restriction enzyme, res subunit
    3.9e-08   33.3   0.0    0.00011   22.0   0.0    2.5  2  DEAD_assoc      DEAD/H associated
     0.0025   16.6   0.0     0.0041   15.9   0.0    1.3  1  SNF2_N          SNF2 family N-terminal domain
     0.0042   16.9   0.2      0.017   15.0   0.0    2.2  2  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
       0.02   14.5   0.1      0.084   12.5   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.058   13.7   0.0       0.28   11.5   0.0    2.1  2  AAA_19          AAA domain
      0.097   12.9   0.1        8.5    6.7   0.1    2.6  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.11   12.3   0.0       0.28   11.1   0.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
       0.11   12.4   0.0        5.2    7.0   0.0    2.5  2  Glyco_transf_4  Glycosyltransferase Family 4
       0.15   12.2   0.0       0.54   10.4   0.0    2.0  1  HTH_28          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   2.8e-32   4.1e-29       1     171 [.      23     193 ..      23     199 .. 0.90
   2 ?   -1.7   0.0       1.4   2.1e+03      45     105 ..     244     305 ..     233     315 .. 0.74
   3 ?   -3.5   0.0         5   7.4e+03      57     102 ..     759     808 ..     748     824 .. 0.61

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.8e-32
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   t+iQ++++  il g++vl+ a+TG+GKT+a+l+p++++++++++ +    l+++P+++L+++  +++  + ++++  v+  
  gi|70607078|ref|YP_255948.1|  23 TSIQKKTLSPILLGKNVLIIAPTGYGKTEAALLPIFNSMLNDTSLSPVALLYITPLKALINDLTHRIDWWASKLGFIVSRK 103
                                   78***************************************999999999*************************999999 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH...HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddll...stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                    g+v+++++  +l++ ++i+v+tp+ l   l   ++ + n+++++++V+DE+++l  ++++ +++ +l++l++ +    ++
  gi|70607078|ref|YP_255948.1| 104 HGEVPQKEKSIRLKRVPHILVTTPEGLEVDLdwaTKFRENYKNIKWVVIDEVHELVHSKRGAQLSVLLERLKEYSG---ND 181
                                   *************777*********999877654333346*******************************65544...35 PP

                                   SEEEEEESSBSH CS
                                   xxxxxxxxxxxx RF
                          DEAD 160 rqvivlSATlpk 171
                                    q i lSAT+++
  gi|70607078|ref|YP_255948.1| 182 FQRIGLSATISN 193
                                   67********83 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                                   STS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtp 105
                                   k ++ +l+ + +r  +e  +++l+k+  +     ++ i+ +++++  ++l++g +++v+ t 
  gi|70607078|ref|YP_255948.1| 244 KIEKPTLLFTNSRFSTERLFEELEKYNIPSVFVHHSSISRDDKNKVEENLREGrANLVICTR 305
                                   55556677777888888888899998887555556788888888888999877799999885 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                                   HHHHHHHHHHHHHHTT...TST...SEEEEEETTSSHHHHHHHHHTTCSEEE CS
                                   xxxxxxxxxxxxxxxx...xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  57 reLaeqtlnnlkkfkk...yid...lrvlliiggvaardqlskldngvdivv 102
                                   r  + +   ++ + +k   y +   l+++l i++++ ++ l+k+ +++d  +
  gi|70607078|ref|YP_255948.1| 759 RPWITDLSIRIYQAMKggaY-TvseLSEMLGISEKSLESRLKKM-RKYDSKY 808
                                   55555555555555553322.12347777777778888877777.5555544 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.71   1.1e+03      35      62 ..      92     119 ..      71     130 .. 0.75
   2 !   54.5   0.0   8.7e-18   1.3e-14      13     108 ..     243     339 ..     232     341 .. 0.86
   3 ?   -2.3   0.0       3.6   5.4e+03      40      77 ..     582     616 ..     554     644 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.71
                                   HHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                    Helicase_C  35 llekkgikvavlhgelpqnereeileqf 62 
                                     +k g+ v + hge pq+e+   l++ 
  gi|70607078|ref|YP_255948.1|  92 WASKLGFIVSRKHGEVPQKEKSIRLKRV 119
                                   44556999999*********98877776 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 8.7e-18
                                   TTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                    Helicase_C  13 eeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                   +++++ +l+f+n++ + e  +l++e +     +v v+h++++ ++++++ e+ ++g+ +++i+t+ +e Gi + +v+ Vi+
  gi|70607078|ref|YP_255948.1| 243 NKIEKPTLLFTNSRFSTE--RLFEELEkynIPSVFVHHSSISRDDKNKVEENLREGRANLVICTRTLELGIHVGDVKKVIM 321
                                   688999*********998..6664444232456778899****************************************** PP

                                   SSSSSSHHHHHHHHTTSS CS
                    Helicase_C  91 fdlprnvtsyiqriGRtg 108
                                   + +p +v+s+ qr GR g
  gi|70607078|ref|YP_255948.1| 322 YRPPPSVSSFLQRLGRSG 339
                                   ****************87 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.6
                                   TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                    Helicase_C  40 gikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                    +++  +hg lp  +r+ i  +    +  ++ at ++e
  gi|70607078|ref|YP_255948.1| 582 FVNFYLVHG-LPLPNRKTIYVEKD--KNEIIYATLINE 616
                                   377777777.77777777766553..334666665554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.5e-10   2.2e-07      25     170 ..      37     192 ..      19     193 .. 0.73
   2 ?    0.0   0.2       0.5   7.4e+02      47      97 ..     240     291 ..     211     307 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.5e-10
                                   SEEEEEESTTSTHHHHH.HHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--... CS
                        ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee..kflflvprkslleqtleefkkflseayke...igkkvsgdkkkakek 99 
                                   k++li ++TG GKT  a + +  ++l+  + +    l + p k+l++ + +++  ++s+       + ++v +++k++  +
  gi|70607078|ref|YP_255948.1|  37 KNVLIIAPTGYGKTEAAlLPIFNSMLNDTSLSpvALLYITPLKALINDLTHRIDWWASKLGFIvsrKHGEVPQKEKSI--R 115
                                   7899*************666666667666666889999************9997777766444544444444444444..5 PP

                                   ....-SEEEEEHHHHHHTH........HHHTTT-S..EEEEETGGGTTS.T.......TTHHHHHT-.--SEEEEEESS-S CS
                        ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDEaHrlgakk.......swreilekf.keavllglTATpe 170
                                    +   +ilvtt + l  d+     + +++++++++   ++iDE+H l  +k         ++++e+  +++ ++gl+AT+ 
  gi|70607078|ref|YP_255948.1| 116 LKRVPHILVTTPEGLEVDL----DWATKFRENYKNikWVVIDEVHELVHSKrgaqlsvLLERLKEYSgNDFQRIGLSATIS 192
                                   88889**************....555555555554559***********875443444444445554444*********85 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.5
                                   HH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--... CS
                        ResIII  47 rllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka..k 97 
                                    + +k  e+ +l++ +++  +e++ ee++k+  + +  +  ++s d k++  +
  gi|70607078|ref|YP_255948.1| 240 TVINK-IEKPTLLFTNSRFSTERLFEELEKYNIPSVFVHHSSISRDDKNKveE 291
                                   33332.33466777777777777777777777766655555555544444332 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   7.4e-08   0.00011       1     107 [.     593     689 ..     593     699 .. 0.86
   2 !    8.8   0.0   0.00084       1.3     141     190 ..     701     748 ..     696     749 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.4e-08
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                   lP+++t+ vE+ ++     +++  ++   +v ++la ll +  ++ + ++v+v  + +g+ +   +++    +  + +  +
  gi|70607078|ref|YP_255948.1| 593 LPNRKTIYVEKDKN-----EIIYATLINEKVSNTLAHLLLYLATKDLSLNVSVRSSIYGFSIRGVENDL---M--SEIVNM 663
                                   79********9877.....67999**************************************5532222...2..346679 PP

                    DEAD_assoc  82 spdeleedleaalnaselfkrrFrev 107
                                   ++del++++ +++ +s+lf + + e+
  gi|70607078|ref|YP_255948.1| 664 NEDELRKLIIKSIMRSPLFYTVLKEI 689
                                   9******************8887776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00084
                    DEAD_assoc 141 eypdfpllleavrevledqlDlerlaellrriaageirvvevetprpSpf 190
                                    ++d +l++ea+++ + +++ ++++ ++++ i++++i++ +   + +Sp+
  gi|70607078|ref|YP_255948.1| 701 LHDDKLLIKEAIKQTVYKYFSIKNTLKYIKMIKNKDIDIIH--IEGISPL 748
                                   589**************************************..9999997 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06    0.0041      93     200 ..      66     169 ..      10     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                   ....S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT.......T CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                        SNF2_N  93 dtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelq.kkrs 171
                                       ++ L + P  +l++  ++ i+ ++s+    v   +g+    ++ ++ + +l +  ++++tt + l+ + ++  k r+
  gi|70607078|ref|YP_255948.1|  66 SLSPVALLYITPLkALINDLTHRIDWWASKLGFIVSRKHGEV---PQ-KEKSIRLKRVPHILVTTPEGLEVDLDWAtKFRE 142
                                   3445778999**999*************99988666666653...33.45588899999****************967788 PP

                                   TS-S-S-SEEEES-GGGT--TTSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 172 vlkqvewkrvvlDEghtlknstskaaeav 200
                                     k+++w  vv+DE h l  s++ a+  v
  gi|70607078|ref|YP_255948.1| 143 NYKNIKW--VVIDEVHELVHSKRGAQLSV 169
                                   8888887..9********99975555443 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       4.5   6.8e+03       1      16 [.     666     681 ..     666     683 .. 0.86
   2 !   15.0   0.0   1.1e-05     0.017       8      41 ..     770     803 ..     767     805 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.5
                                   SHHHHHHHHHHTTSSE CS
                         HTH_5   1 dptRlkILklLaegel 16 
                                   d+ R  I+k+ ++++l
  gi|70607078|ref|YP_255948.1| 666 DELRKLIIKSIMRSPL 681
                                   678999****999987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                                   HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_5   8 LklLaegelcvcelaeelglsqstvShHLkkLre 41 
                                    +++  g ++v+el+e+lg+s+  +   Lkk+r+
  gi|70607078|ref|YP_255948.1| 770 YQAMKGGAYTVSELSEMLGISEKSLESRLKKMRK 803
                                   56778899************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.5   8.3e+03       2      16 ..       4      18 ..       4      18 .. 0.81
   2 ?   12.5   0.0   5.6e-05     0.084      18      43 ..     778     803 ..     766     805 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.5
                        HTH_24  2 detdrkILelLqknp 16
                                  +++ +k+L+l+++++
  gi|70607078|ref|YP_255948.1|  4 NDLSYKLLSLIREKG 18
                                  5678999****9975 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.6e-05
                        HTH_24  18 isqreLAerlglSpstvnrrlkrLee 43 
                                    + +eL+e+lg+S   +  rlk++ +
  gi|70607078|ref|YP_255948.1| 778 YTVSELSEMLGISEKSLESRLKKMRK 803
                                   6899*******************987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00019      0.28       8     115 ..      34     159 ..      26     178 .. 0.72
   2 ?   -1.7   0.0       2.3   3.4e+03      43      85 ..     247     288 ..     231     314 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                        AAA_19   8 lkekvllvtaGpGtGKTr.vlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................... 68 
                                   l  k++l++a+ G GKT+  l  i + +++ ++++p  +l +++ +   + l+ r++    +                   
  gi|70607078|ref|YP_255948.1|  34 LLGKNVLIIAPTGYGKTEaALLPIFNSMLNDTSLSPVALLYITPLKALINDLTHRIDWWASKlgfivsrkhgevpqkeksi 114
                                   66799************8358899999*******************99********7777778888777777777777777 PP

                        AAA_19  69 .........atTiHrlalldfddlltealelleeaeeekklqeeellivDEfqdvd 115
                                             tT  +l ++d+d            ++ +++ ++ +++++DE+ ++ 
  gi|70607078|ref|YP_255948.1| 115 rlkrvphilVTTPEGL-EVDLDW----------ATKFRENYKNIKWVVIDEVHELV 159
                                   7644444433333333.222222..........34445555566799999998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                        AAA_19  43 eeillvaftgrAakelrerlaalgaeatTiHrlalldfddllt 85 
                                   ++ ll +  + ++++l e+l++++ +   +H+ + +  dd+++
  gi|70607078|ref|YP_255948.1| 247 KPTLLFTNSRFSTERLFEELEKYNIPSVFVHHSS-ISRDDKNK 288
                                   678899999999999*9*9999999999999774.44555542 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.075   1.1e+02      36      53 ..     325     342 ..     319     346 .. 0.88
   2 ?    6.7   0.1    0.0057       8.5      13      48 ..     769     803 ..     768     805 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.075
                                   HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress  36 pssVsemlkkLekdGyve 53 
                                   p+sVs  l++L + G ++
  gi|70607078|ref|YP_255948.1| 325 PPSVSSFLQRLGRSGHLI 342
                                   9************99765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0057
                                   HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                Fe_dep_repress  13 IYtlseekkvvktkdlaerLnvspssVsemlkkLek 48 
                                   IY++  +++  ++++l+e L++s  s    lkk++k
  gi|70607078|ref|YP_255948.1| 769 IYQAM-KGGAYTVSELSEMLGISEKSLESRLKKMRK 803
                                   78888.5566689********************997 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.28      18      42 .]     778     802 ..     771     802 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                 HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrrLe 42 
                                    +++eL+e++G+Se     R+++++
  gi|70607078|ref|YP_255948.1| 778 YTVSELSEMLGISEKSLESRLKKMR 802
                                   5899*******************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.094   1.4e+02      71     139 ..     245     303 ..     225     306 .. 0.66
   2 ?    7.0   0.0    0.0035       5.2      55      89 ..     719     753 ..     706     760 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.094
                Glyco_transf_4  71 e.kpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrvia 139
                                     kp ++ ++s ++       l  +++ip V+  H++         +  +++++++l r    ra+ vi+
  gi|70607078|ref|YP_255948.1| 245 IeKPTLLFTNSRFSTERLFEELE-KYNIPSVFVHHSSIS-------RDDKNKVEENL-R--EGRANLVIC 303
                                   34888888899888866655555.5************93.......33333333332.2..235555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0035
                Glyco_transf_4  55 lrslaflrrlrrllkrekpDvvHahspaalgaall 89 
                                   ++s+ + ++  +++k+ ++D++H+ +  +lg a+l
  gi|70607078|ref|YP_255948.1| 719 YFSIKNTLKYIKMIKNKDIDIIHIEGISPLGRAVL 753
                                   678889999*****************999999877 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036      0.54       8      38 ..     772     803 ..     767     805 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                        HTH_28   8 llaaGh.svreaArelgisrrtvyrWikryee 38 
                                   +++ G  +v+e+++ lgis+ ++ + +k+ ++
  gi|70607078|ref|YP_255948.1| 772 AMKGGAyTVSELSEMLGISEKSLESRLKKMRK 803
                                   4555558*********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 6578.18
//
Query:       gi|70607079|ref|YP_255949.1|  [L=90]
Description: DNA binding protein alba-1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-14   51.5   0.5    8.6e-14   51.1   0.5    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.066   13.1   0.1      0.066   13.1   0.1    1.1  1  DUF5077   Domain of unknown function (DUF5077)


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.5   9.6e-18   8.6e-14       1      66 [.       7      70 ..       7      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 9.6e-18
                                  CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                          Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                  nei ++++++i +yv+ ++ l+ n+++eeV + + G+ I+kA++v++ l +r+++g + +++++++
  gi|70607079|ref|YP_255949.1|  7 NEIVITKSKRIEDYVLDTIILF-NQGYEEVEIRGSGQEINKAIEVYNQLVDRLKEG-VRLEKVDIG 70
                                  89********************.******************************766.999999875 PP

>> DUF5077  Domain of unknown function (DUF5077)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.3e-06     0.066      67     115 ..       7      56 ..       1      81 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-06
                       DUF5077  67 kevtlk.sedskelsvgeitikkagYvkvdlqgvskkgksfakikslvis 115
                                    e++++ s++ +++ + +i + ++gY +v+++g  ++ ++  ++ + +++
  gi|70607079|ref|YP_255949.1|   7 NEIVITkSKRIEDYVLDTIILFNQGYEEVEIRGSGQEINKAIEVYNQLVD 56 
                                   45555549999**********************76666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 682.97
//
Query:       gi|70607080|ref|YP_255950.1|  [L=97]
Description: DNA/RNA-binding protein albA [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-22   79.6   0.6    1.4e-22   79.2   0.6    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.092   12.6   0.6       0.26   11.1   0.3    1.8  2  DUF3954   Protein of unknown function (DUF3954)


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.6   1.6e-26   1.4e-22       1      66 [.       9      72 ..       9      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.6e-26
                                  CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                          Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                  n++ V++ +p+m+yv++al+lL n++  e+++ka+GraIskAv+++ei+++rf++++++v+++ ++
  gi|70607080|ref|YP_255950.1|  9 NVVLVGK-KPVMNYVLAALTLL-NQGVSEITIKARGRAISKAVDTVEIVRNRFLPDKIEVKEIRIG 72
                                  7999***.**************.***************************************9876 PP

>> DUF3954  Protein of unknown function (DUF3954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.28   2.5e+03      19      26 ..      26      33 ..      21      39 .. 0.78
   2 ?   11.1   0.3   2.9e-05      0.26      30      46 ..      72      88 ..      69      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.28
                       DUF3954 19 vtLLnPPv 26
                                   tLLn  v
  gi|70607080|ref|YP_255950.1| 26 LTLLNQGV 33
                                  68999766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.9e-05
                       DUF3954 30 GeqvitWqGGkvDrvst 46
                                  G qv+t q G+  rvst
  gi|70607080|ref|YP_255950.1| 72 GSQVVTSQDGRQSRVST 88
                                  99**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 648.84
//
Query:       gi|70607081|ref|YP_255951.1|  [L=108]
Description: hypothetical protein Saci_1323 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 860.49
//
Query:       gi|70607082|ref|YP_255952.1|  [L=91]
Description: hypothetical protein Saci_1324 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 615.07
//
Query:       gi|70607083|ref|YP_255953.1|  [L=169]
Description: hypothetical protein Saci_1325 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1266.37
//
Query:       gi|70607084|ref|YP_255954.1|  [L=467]
Description: XPB/RAD25-related helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-24   87.1   3.9    1.4e-24   87.0   0.1    2.4  2  ResIII         Type III restriction enzyme, res subunit
    4.9e-24   84.9   0.5    1.1e-23   83.8   0.1    1.7  2  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.8e-18   66.9   1.2      3e-18   66.2   0.2    1.9  2  Helicase_C     Helicase conserved C-terminal domain
    6.7e-10   39.0   0.5    7.6e-09   35.6   0.0    2.6  3  DEAD           DEAD/DEAH box helicase
     0.0001   21.2   0.4    0.00097   17.9   0.3    2.1  2  SNF2_N         SNF2 family N-terminal domain
    0.00097   19.0   0.0     0.0021   17.9   0.0    1.6  1  Helicase_RecD  Helicase
     0.0012   19.2   0.6     0.0074   16.6   0.2    2.5  3  AAA_22         AAA domain
     0.0014   17.9   0.0     0.0029   16.9   0.0    1.5  1  DUF2075        Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.013   15.3   0.1        2.8    7.6   0.0    2.6  2  IstB_IS21      IstB-like ATP binding protein
       0.05   13.3   0.1       0.34   10.6   0.0    2.4  3  AAA_30         AAA domain
        0.1   12.4   1.3        3.4    7.4   0.0    2.8  3  AAA_11         AAA domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.1   8.5e-28   1.4e-24       3     171 .]      83     223 ..      81     223 .. 0.92
   2 ?    0.4   0.6      0.36   5.9e+02      56     114 ..     262     324 ..     238     351 .. 0.57

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 8.5e-28
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                   elreyQ+ea+ ++lek        g+i+++TG+GKTl+ ++++ ++++      +l++  +k+ + q++++f +f++ ++ 
  gi|70607084|ref|YP_255954.1|  83 ELREYQKEALSKWLEKG------SGVIALPTGAGKTLIGISAACAVKQ-----STLIVTYTKEQMLQWRDAFIRFTNIEKR 152
                                   89***********9665......6***********************9.....59**********************9998 PP

                                   .GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEEE CS
                        ResIII  84 eigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavllg 164
                                   +ig  +s++k+++         i+v+t+q++++++        + l+ +fdv++iDEaH+l a +++++i+ +  + ++lg
  gi|70607084|ref|YP_255954.1| 153 KIGLYYSEKKEIK--------PITVSTYQTAYRHI--------QELSYKFDVLVIDEAHHLPA-EKFKRIALNSIATKRLG 216
                                   7888888887777........**************........9999****************.*****9777677***** PP

                                   EESS-S- CS
                        ResIII 165 lTATper 171
                                   l+ATp+r
  gi|70607084|ref|YP_255954.1| 217 LSATPYR 223
                                   *****86 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.36
                                   -EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--.........-SEEEEEHHHH CS
                        ResIII  56 kflflvprkslleqtleefkkflseayke..igkkvsgdkkka..kekdstnkkilvttiqsl 114
                                   k+ + ++++ +++ +l++fkk++ + + +   +  ++gd++ +   ++ ++ +k++    q++
  gi|70607084|ref|YP_255954.1| 262 KVQLSIDERMMYNELLNKFKKYSRSRKVSelLMLAKKGDSDAIeaLKIYNDMRKLVNLAKQKI 324
                                   666667778888888899999888776545633334444444433333333333333333333 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.96   1.6e+03     185     221 ..     247     279 ..     242     313 .. 0.57
   2 !   83.8   0.1   6.5e-27   1.1e-23      36     184 ..     314     453 ..     304     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.96
                 ERCC3_RAD25_C 185 lvdqGY..afkviteleeleeeeelaystkeeqkellqk 221
                                   l+++GY   ++v++e  +l+  e+++y++        +k
  gi|70607084|ref|YP_255954.1| 247 LIEKGYlaPYEVVQEKVQLSIDERMMYNELL------NK 279
                                   6666663335666555555444444444333......22 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 6.5e-27
                 ERCC3_RAD25_C  36 kllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvg 116
                                   ++l+ +  +k+ a++ +++  +++g+ki++f+  v   +e+a++++  +i+G++s++er +il+ fk+  k  +++l  vg
  gi|70607084|ref|YP_255954.1| 314 RKLVNLAKQKIDAVKRIVE--KEKGNKILIFTQYVDQAEEIARTINGLLITGKISKSERERILNIFKSM-KSGVLVLTTVG 391
                                   5566667778888887765..689******************************************976.678999***** PP

                 ERCC3_RAD25_C 117 DtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqqf 184
                                   D+ +D+P+anv i + + +gsrrq  qrlGr+Lr+  +     ++a  Y ++ + t e + + kr++ 
  gi|70607084|ref|YP_255954.1| 392 DEGLDIPDANVGIIV-TGTGSRRQFIQRLGRLLRPGVD-----KKARLYEIMVRGTAEEYQALKRKET 453
                                   ***********9966.568****************988.....6899******************975 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.8   7.8e+03      17      47 ..     124     158 ..     117     186 .. 0.55
   2 !   66.2   0.2   1.8e-21     3e-18       2     110 ..     323     425 ..     322     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                                   SEEEEEESSHH.HHHH.HHHHHHHT..TSTEEEES CS
                    Helicase_C  17 gkilifvntid.rlek.vklllekk..gikvavlh 47 
                                   + +li++ t++ +l+    +++ ++  + k+  ++
  gi|70607084|ref|YP_255954.1| 124 QSTLIVTYTKEqMLQWrDAFIRFTNieKRKIGLYY 158
                                   55666666666333323222211112234444444 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 1.8e-21
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   k++a+++++ ++e+g+kilif++++d++e  ++    + i+ + ++g+++++ere+il+ f++ +s vL+ t+v+ +G+di
  gi|70607084|ref|YP_255954.1| 323 KIDAVKRIV-EKEKGNKILIFTQYVDQAE--EIA---RTINGLLITGKISKSERERILNIFKSMKSGVLVLTTVGDEGLDI 397
                                   889999998.99****************6..555...6699**********************9*99************** PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   p++n+ i++    + +++iqr GR  R 
  gi|70607084|ref|YP_255954.1| 398 PDANVGIIVTGTGSRRQFIQRLGRLLRP 425
                                   ************************9996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   4.6e-12   7.6e-09       2     170 ..      86     222 ..      85     228 .. 0.79
   2 ?    0.2   0.2      0.33   5.3e+02      59     103 ..     272     318 ..     265     346 .. 0.66
   3 ?   -1.5   0.1       1.1   1.8e+03      59      91 ..     319     349 ..     306     387 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.6e-12
                                   HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                   ++Q+ea+   l++g+ ++a +TG+GKTl+ + +++ +v       +  +liv+ t+e + q  + + +f++ i+ r    i
  gi|70607084|ref|YP_255954.1|  86 EYQKEALSKWLEKGSGVIALPTGAGKTLIGISAAC-AV-------KQSTLIVTYTKEQMLQWRDAFIRFTN-IEKRK---I 154
                                   68***************************777777.44.......4579*********************9.34233...3 PP

                                   TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvi 163
                                   g   + ++++++     i+v+t +   +++++      ++ +lV+DEa+ l  ++f++   + +++              +
  gi|70607084|ref|YP_255954.1| 155 G--LYYSEKKEI---KPITVSTYQTAYRHIQE-L--SYKFDVLVIDEAHHLPAEKFKRIALNSIATK------------RL 215
                                   3..222344445...789**********9963.3..468899************9988776644433............78 PP

                                   EEESSBS CS
                                   xxxxxxx RF
                          DEAD 164 vlSATlp 170
                                    lSAT+ 
  gi|70607084|ref|YP_255954.1| 216 GLSATPY 222
                                   8888876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
                                   HHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHH..TTCSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          DEAD  59 Laeqtlnnlkkfkkyidlrvlliiggvaardqlskld..ngvdivvg 103
                                   + ++ ln++kk+    ++++ll++ ++  +d +++l+  n+++ +v 
  gi|70607084|ref|YP_255954.1| 272 MYNELLNKFKKYSRSRKVSELLMLAKKGDSDAIEALKiyNDMRKLVN 318
                                   55677888888888777888888887777777777754344444444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHH CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          DEAD  59 Laeqtlnnlkkfkky.idlrvlliiggvaardql 91 
                                   La+q ++ +k++ ++  + ++l +++ v+   q 
  gi|70607084|ref|YP_255954.1| 319 LAKQKIDAVKRIVEKeKGNKILIFTQYVD---QA 349
                                   66677777776666522233332222222...22 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3     6e-07   0.00097      97     266 ..     124     279 ..      73     298 .. 0.64
   2 !    5.3   0.0    0.0041       6.7     256     344 ..     227     317 ..     223     324 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6e-07
                                   S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S- CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  97 gptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqv 176
                                   + tLiv  + + + qW + + r+++  + ++  y ++k              + + + + tY++  r+       ++l + 
  gi|70607084|ref|YP_255954.1| 124 QSTLIVTYTkEQMLQWRDAFIRFTNIEKRKIGLYYSEK-------------KEIKPITVSTYQTAYRHI------QEL-SY 184
                                   34666666656677777777777666655554444432.............245677777888777555......555.57 PP

                                   S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--.HH.HHHHHTHHHHH..... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx..... RF
                        SNF2_N 177 ewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledlygLlkfLreepfge.kq.tfdkllqrpie..... 250
                                   + + +v+DE+h l  ++ k   a++   + +r+ l++TP  ++ ++   L+kf++  ++ +  q   +k++  p+e     
  gi|70607084|ref|YP_255954.1| 185 KFDVLVIDEAHHLPAEKFKRI-ALN-SIATKRLGLSATPYRDDGKH-EELFKFMGGLIYFKsPQeLIEKGYLAPYEvvqek 262
                                   8999*********98876644.333.35679***********8776.4788888877766543347777777888766655 PP

                                   .HHHHHHHHHHHTT-ST CS
                                   .xxxxxxxxxxxxxxxx RF
                        SNF2_N 251 .aqaekgrsrLlqllqr 266
                                    + + + r   ++ll++
  gi|70607084|ref|YP_255954.1| 263 vQLSIDERMMYNELLNK 279
                                   54444444444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0041
                                   HHHHHHTT-STTEE---GGGT..--S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HH CS
                                   xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 256 grsrLlqllqrlmlrrakkdv..eknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekil 334
                                   + ++L + +  l+ +++ +++  + +l+p ++    ++ls  er +Yn+ll++  k  ++   ++  +  k++ ++  + l
  gi|70607084|ref|YP_255954.1| 227 KHEELFKFMGGLIYFKSPQELieKGYLAPYEVVQEKVQLSIDERMMYNELLNKFKKYSRSRKVSELLMLAKKGDSDAIEAL 307
                                   56789999999**********95557**********************777766665555544444444444443446666 PP

                                   HHHHHHHHHH CS
                                   xxxxxxxxxx RF
                        SNF2_N 335 elllelrqac 344
                                   ++    r+ +
  gi|70607084|ref|YP_255954.1| 308 KIYNDMRKLV 317
                                   6666666554 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0021       6     111 ..     107     206 ..     102     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                 Helicase_RecD   6 RGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke.....eekkkkaekaelrvrkqrieyiap 81 
                                    G GK+ ++G+ +a +++++   ++vt ++++ ++   +f+   +++++ ++     +ekk   e + ++v+  +  y + 
  gi|70607084|ref|YP_255954.1| 107 TGAGKT-LIGISAACAVKQST--LIVTYTKEQMLQWRDAFI--RFTNIEKRKiglyySEKK---EIKPITVSTYQTAYRHI 179
                                   588995.89********9965..888888877777544444..344444343443213333...33458888999999999 PP

                 Helicase_RecD  82 dellklkeqadllvvDEAAaiplpllkkll 111
                                   +el  +    d+lv+DEA  +p +  k++ 
  gi|70607084|ref|YP_255954.1| 180 QELSYKF---DVLVIDEAHHLPAEKFKRIA 206
                                   9999865...9***********99998884 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.5e-06    0.0074       5     112 ..      98     205 ..      96     218 .. 0.67
   2 ?   -2.3   0.0         3   4.9e+03     106     118 ..     307     319 ..     261     360 .. 0.62
   3 ?   -1.9   0.0       2.3   3.7e+03      45      70 ..     404     429 ..     394     452 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka..........erl 73 
                                   +g++v+  ++G+GKT+     +            + +++ vt +++    ++d + +   +++ e+ +             
  gi|70607084|ref|YP_255954.1|  98 KGSGVIALPTGAGKTLIGISAACAV---------KQSTLIVTYTKEQmlQWRDAFIR---FTNIEKRKiglyysekkeI-- 164
                                   6778888899999999999999988.........88888888888884555555555...4444444555788855441.. PP

                        AAA_22  74 sseell.ealeqalrarav....ielliiDEaqhlrseealeeL 112
                                     + +  ++ + a r+ +       +l+iDEa+hl ++e ++ +
  gi|70607084|ref|YP_255954.1| 165 --KPITvSTYQTAYRHIQElsykFDVLVIDEAHHL-PAEKFKRI 205
                                   ..444433333333333334446789*********.98888776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                        AAA_22 106 eealeeLrsllnl 118
                                    +++++ r+l+nl
  gi|70607084|ref|YP_255954.1| 307 LKIYNDMRKLVNL 319
                                   3444444444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.3
                        AAA_22  45 vtlpsstsskdllrellralglelka 70 
                                   + +++ +s++++ ++l r l  + ++
  gi|70607084|ref|YP_255954.1| 404 IIVTGTGSRRQFIQRLGRLLRPGVDK 429
                                   56677778888888888888765555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0029      10     102 ..     107     199 ..     103     233 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                       DUF2075  10 aGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke..ekkkkkeafeklssfinnlsef....kkaeekk 84 
                                   +G+GKt+++++++ ++     ++++ +++  ++++l  r a+ + +  ek+k++      ++ i++++       ++  ++
  gi|70607084|ref|YP_255954.1| 107 TGAGKTLIGISAACAV-----KQSTLIVTYTKEQMLQWRDAFIRFTniEKRKIGL-YYSEKKEIKPITVStyqtAYRHIQE 181
                                   6**************9.....5556666666677777776665555432333222.2222233333332233334556667 PP

                       DUF2075  85 eepkedvvivDEAhrllt 102
                                    + k+dv+++DEAh l  
  gi|70607084|ref|YP_255954.1| 182 LSYKFDVLVIDEAHHLPA 199
                                   889***********9866 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0017       2.8      36      84 ..      88     135 ..      69     141 .. 0.76
   2 ?    4.8   0.0     0.012        20      87     139 ..     164     216 ..     144     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                     IstB_IS21  36 keLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrve 84 
                                   ++ a  +++ek  +++ l p+G+GK+ + i+ + +  ++ l v++++ +
  gi|70607084|ref|YP_255954.1|  88 QKEALSKWLEKGSGVIAL-PTGAGKTLIGISAACAVKQSTLIVTYTKEQ 135
                                   444557899999998766.***********9998877788888887654 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                     IstB_IS21  87 veelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekrye 139
                                   ++ + +   +  + ++++   k+d+l++D+   lp ++ ++  l  +  kr +
  gi|70607084|ref|YP_255954.1| 164 IKPITVSTYQTAYRHIQELSYKFDVLVIDEAHHLPAEKFKRIALNSIATKRLG 216
                                   55566666677777777778899**************9999999998888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.34       2     108 ..      84     205 ..      83     214 .. 0.72
   2 ?   -2.7   0.0       2.5     4e+03     160     185 ..     287     314 ..     268     321 .. 0.67
   3 ?   -3.2   0.0       3.5   5.6e+03      36      65 ..     325     355 ..     323     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                        AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa................... 63 
                                   l++ Q++a+ + l++g    v+  p G+GKt +  +++ a++++    ++++ t+++  + +                   
  gi|70607084|ref|YP_255954.1|  84 LREYQKEALSKWLEKGS--GVIALPTGAGKTLIGISAACAVKQST---LIVTYTKEQMLQWRdafirftniekrkiglyys 159
                                   78899********9996..777779999***99888888888775...444445444444444445455554444445455 PP

                        AAA_30  64 eelgieastiakllkrlkgrarlepg.tllivDEagmvdtkqlaal 108
                                   e+ +i+  t+  + +++++ ++l+ + ++l++DEa  + +++++++
  gi|70607084|ref|YP_255954.1| 160 EKKEIKPITVSTYQTAYRHIQELSYKfDVLVIDEAHHLPAEKFKRI 205
                                   566677777777777777888999999********99988888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                        AAA_30 160 seeraaalalregdae..ealealadrg 185
                                    +  ++    ++gd +  eal+ ++d  
  gi|70607084|ref|YP_255954.1| 287 RKVSELLMLAKKGDSDaiEALKIYNDMR 314
                                   5566666677788887677777777765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                        AAA_30  36 kalreaweaa.ggrviglAptgkaAkvLaee 65 
                                    a+++++e++ g ++++++    +A+++a+ 
  gi|70607084|ref|YP_255954.1| 325 DAVKRIVEKEkGNKILIFTQYVDQAEEIART 355
                                   5778888888888998888888888887755 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.099   1.6e+02       2      32 ..      84     117 ..      83     154 .. 0.80
   2 ?    7.4   0.0    0.0021       3.4     198     226 ..     167     194 ..     159     196 .. 0.79
   3 ?    0.2   0.1      0.31   5.1e+02      79     136 ..     295     359 ..     260     459 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.099
                        AAA_11   2 lndsqreaiksalseseitliqGPPGtgKT....k 32 
                                   l + q+ea+++ l++ +  +i  P G gKT    +
  gi|70607084|ref|YP_255954.1|  84 LREYQKEALSKWLEKGS-GVIALPTGAGKTligiS 117
                                   6789************9.9***********54432 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                        AAA_11 198 ivltTlsgagsklleklakkfdvviIDEA 226
                                   i ++T ++a  + +++l  kfdv++IDEA
  gi|70607084|ref|YP_255954.1| 167 ITVSTYQTA-YRHIQELSYKFDVLVIDEA 194
                                   556777777.556777777*********9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.31
                        AAA_11  79 ldsegekykpkivRvgnee.eriseavksvsl.eekvekrlekee......kaqlakeiskelekl 136
                                   l ++g +  ++ ++++n+  + ++ a +++   +++vek++ + +      ++++a+ei+++++ l
  gi|70607084|ref|YP_255954.1| 295 LAKKGDSDAIEALKIYNDMrKLVNLAKQKIDAvKRIVEKEKGN-KiliftqYVDQAEEIARTINGL 359
                                   3455666666666666666422333333332202333333322.2355555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 3392.23
//
Query:       gi|70607085|ref|YP_255955.1|  [L=125]
Description: hypothetical protein Saci_1327 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 914.35
//
Query:       gi|70607086|ref|YP_255956.1|  [L=110]
Description: divalent cation tolerance protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-35  120.0   0.3    3.4e-35  119.9   0.3    1.0  1  CutA1     CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.016   15.2   0.8      0.035   14.1   0.8    1.6  1  HisK_N    Histidine kinase N terminal


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.3   3.8e-39   3.4e-35       1      98 [.       4     101 ..       4     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 3.8e-39
                                   EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                         CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81 
                                   +lvl+t++++e+a+k+a++lv+e++aACvni+p i+S+Y+W+gk   d+E+lllik++++  ++l +r+kelhpy++peii
  gi|70607086|ref|YP_255956.1|   4 ILVLTTTNTMESANKIAKTLVDERVAACVNIFPYIKSYYVWEGKTTVDDEILLLIKSHNSMTQKLIQRIKELHPYKIPEII 84 
                                   589****************************************************************************** PP

                                   EEEESEEEHHHHHHHHH CS
                         CutA1  82 alpieagseaYlkWiee 98 
                                    ++ ++g ++Yl+Wi+e
  gi|70607086|ref|YP_255956.1|  85 IINFNEGFDKYLDWIKE 101
                                   ***************98 PP

>> HisK_N  Histidine kinase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8   3.9e-06     0.035      49     115 ..       6      75 ..       2      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-06
                                   HHTTSS-GGGGHHHHHHHHHHHHHHT--THHHH..HHHHHHHHHHHHHHH.CC---HHHHHHHHHHHHHH CS
                        HisK_N  49 llkeeiseedlkelaekiakeRveanvnigdfv..yNvnvgrsivlkall.klnvsldelqllidkinef 115
                                   +l+ + + e+ +++a+ +  eRv a vni  ++  y v  g++ v + +l  ++ + +  q+li++i+e+
  gi|70607086|ref|YP_255956.1|   6 VLTTTNTMESANKIAKTLVDERVAACVNIFPYIksYYVWEGKTTVDDEILlLIKSHNSMTQKLIQRIKEL 75 
                                   5777888888999*******************96677889****98766515677777789999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 767.91
//
Query:       gi|70607087|ref|YP_255957.1|  [L=97]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit C [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-18   66.3   0.2      3e-18   65.9   0.2    1.2  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
    0.00078   20.0   1.0    0.00089   19.8   1.0    1.1  1  AF0941-like  AF0941-like


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.2   3.3e-22     3e-18       2      61 ..      22      90 ..      21      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3.3e-22
                                  -HHHHHHHHHHHHHHHHHHTTCGCS--TT----S......-EB-S--.....HHHHHTT-SSEETTEEE CS
                   Glu-tRNAGln  2 seeEleklakelnsildyveqLqevdttgveplthp....vlReDev.....reelLknApetedgyfv 61
                                  + eE++k+ ++l++i+d++e+++e+++ +vepl+hp     lR+De+     r+e+L+n++ +e+gy+v
  gi|70607087|ref|YP_255957.1| 22 KNEEKDKISNDLQRIIDFFEKINELELKDVEPLFHPissgKLRKDEPlkplnRDEALQNVKRKENGYIV 90
                                  679******************************************97789*9***************97 PP

>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.0   9.9e-08   0.00089       3      65 ..       5      72 ..       1      83 [. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.9e-08
                                  ---HHHHHHHHHHT.......TSS-GGGHHHHT-.HHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHH CS
                   AF0941-like  3 ykntyleklgellk....keviddiekvldelld.keeieelfrsdvedvleklkagdieeeeakknl 65
                                  +  +yl kl++l      +e  d+i++ l+ ++d  e+i+el  +dve +++ +++g++ ++e  k l
  gi|70607087|ref|YP_255957.1|  5 IDESYLSKLEQLALirlkNEEKDKISNDLQRIIDfFEKINELELKDVEPLFHPISSGKLRKDEPLKPL 72
                                  5679******98433355999*************88**************************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 692.50
//
Query:       gi|70607088|ref|YP_255958.1|  [L=476]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.7e-142  475.6   0.0   1.9e-142  475.4   0.0    1.0  1  Amidase    Amidase
  ------ inclusion threshold ------
       0.14   11.9   0.2        1.5    8.7   0.1    2.6  2  DASH_Duo1  DASH complex subunit Duo1


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.4   0.0  2.1e-146  1.9e-142       2     450 ..      19     456 ..      18     457 .. 0.97

  Alignments for each domain:
  == domain 1  score: 475.4 bits;  conditional E-value: 2.1e-146
                                   HHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS-- CS
                       Amidase   2 lveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDa 82 
                                    ve+ +++ie+v++ +++++t+ +++  ++ ++++k+++  ++ g L+Gv i++KDni++ g++tt++s++le+y++++Da
  gi|70607088|ref|YP_255958.1|  19 YVEKTYEKIERVEKLIHSFITIRNKQ--EIIDEVKKNIS--NKHGKLAGVLIAIKDNISTLGIRTTCASRILEDYIPPYDA 95 
                                   6999*************998888776..56677888886..899************************************* PP

                                   HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHC CS
                       Amidase  83 tvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfc 163
                                   tvve+Lk++Gavi+gkTnmdefamgs+te+s+fgpt+NPwd++rtpGGSSGGs+A++A g+v la+G+DtGGSiR PA+f+
  gi|70607088|ref|YP_255958.1|  96 TVVEKLKSEGAVIIGKTNMDEFAMGSTTETSYFGPTKNPWDLERTPGGSSGGSGAVLAGGIVELALGSDTGGSIRAPAAFN 176
                                   ********************************************************************************* PP

                                   TSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEG CS
                       Amidase 164 glvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvk 244
                                   g++GlKP+yg vSr+g++a+++sl+++Gp+a+++edl ll++vi+ged +d t+ +i + +++ + ++k +lk+++i+v+k
  gi|70607088|ref|YP_255958.1| 177 GVFGLKPSYGTVSRYGLIAYANSLEQIGPMAKNAEDLELLYDVIAGEDWRDATTISINKNEYKRDGSSKVDLKNIKIAVLK 257
                                   ********************************************************99888888999999*********** PP

                                   GGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCCCCHH CS
                       Amidase 245 edgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvry.erlsetkvlsellpks 324
                                   +   +  +++v+ a+++ l++L ++G+ +  +e++  e+al++yy+i+++eassnlar++gvry + +  + ++++++ k+
  gi|70607088|ref|YP_255958.1| 258 DIL-EASEKPVTSAFNEILDKLVSEGVSIDYIEFKLAEYALPAYYIIAMSEASSNLARFDGVRYgYSAHYDGIWKDTYGKN 337
                                   *99.799************************************************************************** PP

                                   HHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGC CS
                       Amidase 325 raellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynl 405
                                   r e++g evkrri+lg++ lsa+++++yy+ka kvrrl+++e++++++++D+++sPt+p+ +p+lge      +++ +y++
  gi|70607088|ref|YP_255958.1| 338 RGEGFGIEVKRRIMLGSFILSAGYYEQYYIKALKVRRLIKDEIDRILKQYDFIASPTMPIIPPKLGEVV---GDPLKMYAM 415
                                   *******************************************************************97...69******* PP

                                   CTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                       Amidase 406 ldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                   +  t   v++nlag pals p+g+++ +lP+G+q++g ++++ +l
  gi|70607088|ref|YP_255958.1| 416 DLNT---VIANLAGVPALSQPIGFYN-NLPIGLQLMGSYLSDYKL 456
                                   ****...*****************96.9**************877 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00016       1.5      15      59 ..       1      49 [.       1      62 [. 0.80
   2 ?    0.1   0.0     0.076   6.9e+02      19      48 ..      61      90 ..      52      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00016
                     DASH_Duo1 15 vienviesLkkak....sniervketvestntLLdkWirIlsqtehtqr 59
                                  +ie+v+esLk+ +    +++e+  e++e +++L++++i I +++e + +
  gi|70607088|ref|YP_255958.1|  1 MIEDVVESLKNGNltpeDYVEKTYEKIERVEKLIHSFITIRNKQEIIDE 49
                                  688888888874321247899*********************9997655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.076
                     DASH_Duo1 19 viesLkkaksniervketvestntLLdkWi 48
                                  + + L ++k+ni+++  +++ ++++L+ +i
  gi|70607088|ref|YP_255958.1| 61 LAGVLIAIKDNISTLGIRTTCASRILEDYI 90
                                  6677888999*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3026.40
//
Query:       gi|70607089|ref|YP_255959.1|  [L=358]
Description: tRNA-modifying protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-22   78.2   0.0      1e-21   77.0   0.0    1.6  1  Wyosine_form  Wyosine base formation
    2.2e-21   77.0   0.0    4.1e-21   76.1   0.0    1.4  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   1.1e-25     1e-21       2      63 .]     256     316 ..     255     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.1e-25
                                   HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                  Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                   ++p+++EvK+y++vG s++rLt++++P+h e+++f+k l+++++ Y++++eh +Sr+ ll+r
  gi|70607089|ref|YP_255959.1| 256 SQPTYIEVKSYMHVGPSTYRLTKDAMPKHNEIREFSKILANYTG-YKIISEHVPSRILLLSR 316
                                   69******************************************.**************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   4.6e-25   4.1e-21       4     165 ..      67     248 ..      64     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 4.6e-25
                                   ESEESS--TTTSCCTT............................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESST CS
                                   xxxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpet............................vrregrgrslsveeileevkelkaekgvkevilggge 56 
                                     +C +rC++C+r e                             ++r + g++      +++v  ++  +  ++ i++ ge
  gi|70607089|ref|YP_255959.1|  67 AAWCWFRCIHCWRLEPedigiewdetkipiedepeiiversieeHKRAVSGYFGRNGVPKNKVIDAA-TP-RHVAISLTGE 145
                                   679***********99**9999999998888888888888888888888888888888888887774.44.8888888*** PP

                                   GGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT...CTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                   Radical_SAM  57 pllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn...rghtfeevleal 134
                                   p+ly ++ el+++++++   g++++++t+g++p  ++l+ l e  ++++ ++++a++++  +k+mn    ++++e +le+l
  gi|70607089|ref|YP_255959.1| 146 PTLYNRIGELIKEYHRK---GLTTFLVTSGVRP--DILASLEEE-PTQLFVSIQAPNYK-KHKIMNrpiVPNSWELFLETL 219
                                   ****************9...************5..788888885.5*************.8888887888899******** PP

                                   HHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 135 eklreagikrvvdrivglpGendeeleelle 165
                                   ++l +   + +v+r+++++G+n++e e+  +
  gi|70607089|ref|YP_255959.1| 220 KILPSFSSP-TVIRMTMIKGYNMSE-EDAKD 248
                                   ******999.*************98.66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2320.79
//
Query:       gi|70607090|ref|YP_255960.1|  [L=159]
Description: hypothetical protein Saci_1332 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-40  136.0   0.0    8.2e-40  135.7   0.0    1.1  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.077   13.0   0.1      0.077   13.0   0.1    1.8  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.0   9.1e-44   8.2e-40       1     121 []      35     157 ..      35     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 9.1e-44
                                   EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCC.GHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEECCE CS
                CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldee.slelrkaleklkgieiegfedeertfgavkvypakieki 80 
                                   V+sGlgeG+++vsl++y+e+f++ lgf+pypGTLN  + ++ s+e+r  l+ ++gi i+++++++r +g+vk++pa+i+++
  gi|70607090|ref|YP_255960.1|  35 VTSGLGEGRIFVSLPYYMEAFNKFLGFQPYPGTLNAVIYDRiSMENRLLLDLSRGILIPEHKEPNRVLGSVKAFPASINSV 115
                                   89***************************************9*************************************77 PP

                                   .EEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                CTP-dep_RFKase  81 .kaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                    ++avv+p+rt+++++v+E+++p+kLReklel+dgde+e+ev
  gi|70607090|ref|YP_255960.1| 116 sPVAVVIPTRTTHPKSVVELLSPHKLREKLELEDGDEIEIEV 157
                                   69**************************************97 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.3       1.8   1.7e+04       8      12 ..     119     123 ..     119     123 .. 0.90
   2 ?   13.0   0.1   8.5e-06     0.077      12      31 ..     138     157 ..     138     158 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.8
                                   EEEE- CS
                MazE_antitoxin   8 avriP 12 
                                   av+iP
  gi|70607090|ref|YP_255960.1| 119 AVVIP 123
                                   899*9 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.5e-06
                                   -CCCHHHCCEECTCEEEEEE CS
                MazE_antitoxin  12 PkevrfelgireGdevelev 31 
                                   P+ +r++l+++ Gde+e+ev
  gi|70607090|ref|YP_255960.1| 138 PHKLREKLELEDGDEIEIEV 157
                                   999***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1131.44
//
Query:       gi|70607091|ref|YP_255961.1|  [L=228]
Description: hypothetical protein Saci_1333 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-17   61.8   0.7    9.3e-17   60.9   0.3    1.7  2  DUF357           Protein of unknown function (DUF357)
    2.3e-14   53.8   0.2    5.2e-14   52.6   0.0    1.6  2  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.076   12.6   0.0    1.7  2  Lambda_Kil       Bacteriophage lambda Kil protein
      0.052   13.2   0.3       0.36   10.4   0.1    2.0  2  DUF4085          Protein of unknown function (DUF4085)
      0.071   13.5   1.0       0.15   12.4   0.2    1.9  2  Urm1             Urm1 (Ubiquitin related modifier)
       0.13   12.1   0.1       0.71    9.7   0.1    2.2  1  FAD_syn          FAD synthetase
       0.15   12.0   1.9       0.17   11.8   0.1    1.9  2  Intron_maturas2  Type II intron maturase


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.3   3.6e-20   9.3e-17       1      72 [.      11      76 ..      11      77 .. 0.96
   2 ?   -2.3   0.0         2     5e+03      26      45 ..     141     160 ..     121     166 .. 0.53

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 3.6e-20
                                  HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                        DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                  +Yi+ +e+ l+k++       ++ +++e+++++a+ Y+eDaky+l+ +d v+Al+ ++YaeG+LDa + ++ 
  gi|70607091|ref|YP_255961.1| 11 KYIQGMEDRLSKIS------PEIIQKYEKIYNLAKLYVEDAKYYLSVNDKVTALVDVVYAEGLLDAIIEMEN 76
                                  7*************......89999*****************************************999875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHHH CS
                        DUF357  26 aaeevlemaesYleDakyfl 45 
                                   + ++v     ++l D k fl
  gi|70607091|ref|YP_255961.1| 141 VIKSVKYVYDAFLGDEKDFL 160
                                   44444445555555555555 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   3.8e+03     101     116 ..      29      44 ..       8      63 .. 0.67
   2 !   52.6   0.0     2e-17   5.2e-14       2     140 ..      89     216 ..      88     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHEEEE CS
               CTP_transf_like 101 keleeilgnvklvvvs 116
                                   +++e+i+   kl v++
  gi|70607091|ref|YP_255961.1|  29 QKYEKIYNLAKLYVED 44 
                                   3566666666666654 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 2e-17
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHT CS
               CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrevlkkl 80 
                                   + GtFD++H GH++ l++a k++   ++v+v+ d+++ k k  kp+ ++++Rle ++  k+v +++  d+ +  +  +++ 
  gi|70607091|ref|YP_255961.1|  89 VAGTFDILHPGHIAFLREASKYGR--VYVAVARDKNSEKIKgrKPINDENQRLEVIKSVKYVYDAFLGDEKDFLK-SVERV 166
                                   67********************99..7999*****99999669*******************************7.89999 PP

                                   TTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHH CS
               CTP_transf_like  81 kpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstki 140
                                   kp+  ++v+g d+  d   +++l + l+n++++v+++       +  + +++   S++ i
  gi|70607091|ref|YP_255961.1| 167 KPN--IIVLGPDQKVD---EQKLIDDLKNRGVIVEKIV-----RIPSRINNWAHSSTSSI 216
                                   9**..*******9999...7788778888888888544.....22333344445555555 PP

>> Lambda_Kil  Bacteriophage lambda Kil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   4.2e+03      20      30 ..      44      54 ..      41      58 .. 0.83
   2 ?   12.6   0.0     3e-05     0.076      11      37 ..     146     172 ..     136     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                    Lambda_Kil 20 DekMfleAvda 30
                                  D+k +l  +d 
  gi|70607091|ref|YP_255961.1| 44 DAKYYLSVNDK 54
                                  99999999986 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3e-05
                    Lambda_Kil  11 KavIArFlGDekMfleAvdayKkavli 37 
                                   K+v   FlGDek fl+ v+  K  + +
  gi|70607091|ref|YP_255961.1| 146 KYVYDAFLGDEKDFLKSVERVKPNIIV 172
                                   788889**************9988876 PP

>> DUF4085  Protein of unknown function (DUF4085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.054   1.4e+02      77     108 ..       3      34 ..       1      43 [. 0.82
   2 ?   10.4   0.1   0.00014      0.36      93     131 ..      36      74 ..      18     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.054
                       DUF4085  77 eevkkevdkwsreyekrfeqvldsyveyfnsi 108
                                   +e+ ++v+k+ + +e r+ +   +  +++++i
  gi|70607091|ref|YP_255961.1|   3 DEIADRVRKYIQGMEDRLSKISPEIIQKYEKI 34 
                                   57889999999999999999988888777776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                       DUF4085  93 rfeqvldsyveyfnsiakklpenvkelfkkslHDavikk 131
                                   +++++  +  +y+ s+++k+ + v  ++ + l Da+i+ 
  gi|70607091|ref|YP_255961.1|  36 NLAKLYVEDAKYYLSVNDKVTALVDVVYAEGLLDAIIEM 74 
                                   45677788899*************************974 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.1   2.7e+03      33      33 ..      68      68 ..      26     107 .. 0.58
   2 ?   12.4   0.2   5.9e-05      0.15      24      69 ..     132     177 ..     114     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.1
                                  H CS
                          Urm1 33 l 33
                                  l
  gi|70607091|ref|YP_255961.1| 68 L 68
                                  1 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.9e-05
                                   E-SSSSS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTC CS
                          Urm1  24 leieseevnleeliayikknlikerkevFlekdkvrPGilvLinda 69 
                                   ++ e++++++ + ++y+ + ++ ++k+   + ++v+P i+vL  d+
  gi|70607091|ref|YP_255961.1| 132 INDENQRLEVIKSVKYVYDAFLGDEKDFLKSVERVKPNIIVLGPDQ 177
                                   5578899999999***********9998888**********97665 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00028      0.71       6      33 ..      84     111 ..      79     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                       FAD_syn   6 egavvtlGnFDGvHlGHqallkkaveaa 33 
                                   ++ v + G FD +H GH a l++a +  
  gi|70607091|ref|YP_255961.1|  84 SKRVFVAGTFDILHPGHIAFLREASKYG 111
                                   6778999**************9998865 PP

>> Intron_maturas2  Type II intron maturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.98   2.5e+03      46      56 ..      27      37 ..      20      63 .. 0.47
   2 ?   11.8   0.1   6.7e-05      0.17      11      49 ..     182     219 ..     175     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
               Intron_maturas2 46 Illrykaiirg 56
                                  I+++y++i + 
  gi|70607091|ref|YP_255961.1| 27 IIQKYEKIYNL 37
                                  55555555442 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.7e-05
               Intron_maturas2  11 rkiikkLakagfvktkkekgkPrsvlrwidledrdIllr 49 
                                   +k+i  L+++g++ + k   +P ++  w ++++++I+++
  gi|70607091|ref|YP_255961.1| 182 QKLIDDLKNRGVIVE-KIVRIPSRINNWAHSSTSSIINE 219
                                   689*********999.5********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1634.73
//
Query:       gi|70607092|ref|YP_255962.1|  [L=251]
Description: diphthine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-23   83.0   0.0    3.3e-23   82.8   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.064   13.6   0.1          3    8.3   0.1    2.8  3  DUF1894       Domain of unknown function (DUF1894)


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   3.6e-27   3.3e-23       2     212 ..       4     219 ..       3     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 3.6e-27
                  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdV 82 
                                   l l+G+G+ + + +T  Al+ l+t+dvv++d+ +++    dl+ +   l++    +  + +   e++ +++ e+l++gk V
  gi|70607092|ref|YP_255962.1|   4 LKLIGLGL-SYKFITEIALNELRTSDVVYADT-YTSLTCGDLISR---LHQLGINPIPVGRDFIENNYKKILELLDQGKSV 79 
                                   56899999.66******************999.888888888887...4444444456666679999************** PP

                  TP_methylase  83 vllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeerelealla 159
                                    ++v+GDP++++t++ lv+++r   +g +v +iPGvs  + +++++ ++ +++g++++++    + ++++ +++ l++ l+
  gi|70607092|ref|YP_255962.1|  80 GIAVIGDPMIATTHISLVTEART--KGHQVSIIPGVSVHCYIISKSMLSSYKFGKSVTIIsstdYGKIDTTPYKVLKENLE 158
                                   ******************99999..8899********************************77733344444444444444 PP

                  TP_methylase 160 n.gdtlvllkapr.klaelaelL......kea.lyddttpvavveragtedervvrgtleel 212
                                   +  +t++ l  p   + +++ lL       e+ + +++  ++v++++g++de++v  +++e+
  gi|70607092|ref|YP_255962.1| 159 RnLHTIFYL-EPNmSARDAVSLLlqmekiEEQgIINEDSLIIVGQHLGCDDEEIVSLKIKEI 219
                                   435566555.44423334444433444437779999999****************9999987 PP

>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.016   1.4e+02      32      55 ..      35      58 ..      28      60 .. 0.84
   2 ?    8.3   0.1   0.00033         3      22      53 ..      59      90 ..      58      95 .. 0.93
   3 ?   -2.3   0.0      0.65   5.8e+03      21      42 ..     153     174 ..     145     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.016
                                  EEEES--EEESSS---SS----EE CS
                       DUF1894 32 vyevepgykilgvrliGvppipvg 55
                                  +  +  g+ i  ++ +G++pipvg
  gi|70607092|ref|YP_255962.1| 35 YTSLTCGDLISRLHQLGINPIPVG 58
                                  556778999999***********9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00033
                                  HHHHHHTTSEEEEES--EEESSS---SS---- CS
                       DUF1894 22 eeyikkkakevyevepgykilgvrliGvppip 53
                                  +++i++++k+++e+  + k +g+ +iG p i+
  gi|70607092|ref|YP_255962.1| 59 RDFIENNYKKILELLDQGKSVGIAVIGDPMIA 90
                                  69**************************9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.65
                                   HHHHHHHTTSEEEEES--EEES CS
                       DUF1894  21 ceeyikkkakevyevepgykil 42 
                                    +e ++ + + ++++ep+ +  
  gi|70607092|ref|YP_255962.1| 153 LKENLERNLHTIFYLEPNMSAR 174
                                   4555667777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1570.62
//
Query:       gi|70607093|ref|YP_255963.1|  [L=254]
Description: hypothetical protein Saci_1335 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-07   30.7   0.6    1.5e-06   28.8   0.5    1.8  1  Metallophos    Calcineurin-like phosphoesterase
    1.6e-06   28.4   0.0      2e-06   28.1   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
       0.05   13.3   0.9      0.075   12.7   0.9    1.3  1  Ribosomal_L4   Ribosomal protein L4/L1 family
       0.07   13.2   0.5        4.9    7.3   0.1    2.7  3  DpaA_N         Dipicolinate synthase subunit A N-terminal dom


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.5   3.4e-10   1.5e-06       4     139 ..      25     153 ..      22     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.4e-10
                                   EEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHHTSEEE CS
                   Metallophos   4 lvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalvkypipvy 68 
                                   ++++D+H+                q  ++l++++++l+  k + ++++GD+ ++      +   el e l++l +++i v 
  gi|70607093|ref|YP_255963.1|  25 VILSDVHIgfeqemankgiYIPKVQKKRFLTIYRKALNYFKTNKLIINGDFKHTFnkitkQERDELTEILTELNENKIEVK 105
                                   799********9999999966778888888999888888899********99998889985555577779999999***** PP

                                   EEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHH CS
                   Metallophos  69 lllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnl 139
                                   +++GNH+    +              +   +e+f+n+ l++ ++  +++ + hG+     + ++ ++++n+
  gi|70607093|ref|YP_255963.1| 106 IVKGNHD----N-------------YISAVTEKFSNVELVEDINV-NDISIFHGH-----KRINMQENENK 153
                                   *******....2.............22234777888888883333.478888888.....33333333333 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.6e-10     2e-06       3     130 ..      24     163 ..      22     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.6e-10
                 Metallophos_2   3 laiiSDlH....................snldaleavlealkevgvdaiihaGDl....eeeep..........evleell 49 
                                    +i+SD+H                    + l + +++l+ +k     ++i  GD+    +              e+l el 
  gi|70607093|ref|YP_255963.1|  24 AVILSDVHigfeqemankgiyipkvqkkRFLTIYRKALNYFKTN---KLIINGDFkhtfN---KitkqerdeltEILTELN 98 
                                   5799****999999998888888875444444455556665555...88889**643332...133345543434555555 PP

                 Metallophos_2  50 ela.pvlaVrGNnDeevveedvlreaaelgtdlpeeaele.lagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtH 128
                                   e + +v++V+GN+D         +    +++++ + + +e ++  ++ ++Hg+         ++++ +e++++v++ GH H
  gi|70607093|ref|YP_255963.1|  99 ENKiEVKIVKGNHD---------NYISAVTEKFSNVELVEdINVNDISIFHGH---------KRINMQENENKVYIIGHEH 161
                                   555***********.........56677777777555555477778******9.........34444445566******** PP

                 Metallophos_2 129 vp 130
                                    +
  gi|70607093|ref|YP_255963.1| 162 PR 163
                                   77 PP

>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   1.7e-05     0.075     103     179 ..      64     144 ..      41     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                   HHTT-EEEES---..-S...S--HHHHHHHHHHTT-TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSEE CS
                  Ribosomal_L4 103 akqglllvvdnle.ple...esktkelvellkklglksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadkv 179
                                   +k ++l++ ++++ +++   +++  el e+l +l+ ++ +v iv +++d+ +  +++ +++ve++e  ++n  ++ +++k 
  gi|70607093|ref|YP_255963.1|  64 FKTNKLIINGDFKhTFNkitKQERDELTEILTELNENKIEVKIVKGNHDNYISAVTEKFSNVELVEDINVNDISIFHGHKR 144
                                   6778899999777666666689999***********999**************************9999999999998884 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0011       4.9      63     115 ..      40      93 ..      36      94 .. 0.91
   2 ?    0.5   0.0      0.13     6e+02      14      56 ..      93     133 ..      90     161 .. 0.65
   3 ?    3.0   0.0     0.024   1.1e+02      19      67 ..     148     203 ..     145     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                   ETTTEE-BSS-SS-EE-.HHHHHTS-TT-EEEESS--HHHHHHHHHCT-EEEEG CS
                        DpaA_N  63 kdggeintpfseeklsl.eelleklkkgqllfgGiippelkelaeekgielvdl 115
                                   ++g++i    +++ l++ ++ l++ k ++l++ G +++++++++++++ el ++
  gi|70607093|ref|YP_255963.1|  40 NKGIYIPKVQKKRFLTIyRKALNYFKTNKLIINGDFKHTFNKITKQERDELTEI 93 
                                   7789999999***********************************999888775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.13
                                   HHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GGG-SEEE CS
                        DpaA_N  14 larkLaekgakvslygleleekiegvekaesleealedadvii 56 
                                   +  +L+e+  +v++++ ++++ i+ v+++ s  e +ed +  +
  gi|70607093|ref|YP_255963.1|  93 ILTELNENKIEVKIVKGNHDNYISAVTEKFSNVELVEDIN--V 133
                                   5678888888888887777777777777777777664443..3 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.024
                                   HHTT-EEEEES-.......TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTE CS
                        DpaA_N  19 aekgakvslygl.......eleekiegvekaesleealedadviilPvpgtkdgge 67 
                                   +e+++kv+++g        +   ++ +  ++       +++ vi+lP +gt + g+
  gi|70607093|ref|YP_255963.1| 148 QENENKVYIIGHehprlsiKDRLGFARKLQCFLKVPLRNNSTVIVLPATGTYQSGN 203
                                   566777777766665554444444444444444444558999******99976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1856.90
//
Query:       gi|70607094|ref|YP_255964.1|  [L=166]
Description: transcription factor [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-53  178.6   0.3    1.8e-29  101.5   0.1    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    7.8e-07   29.1   0.0       0.02   15.0   0.0    2.5  3  DUF3378   Domain of unknown function (DUF3378)
     0.0094   15.4   0.0      0.011   15.2   0.0    1.1  1  NMT1_3    NMT1-like family
  ------ inclusion threshold ------
      0.028   14.5   0.3        7.9    6.5   0.0    2.2  2  DUF155    Uncharacterised ACR, YagE family COG1723
       0.03   14.1   0.1        1.7    8.4   0.0    2.2  2  DRTGG     DRTGG domain


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   5.7e-25     2e-21      28      85 .]       5      62 ..       1      62 [. 0.95
   2 !  101.5   0.1     5e-33   1.8e-29       1      83 [.      71     151 ..      71     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 5.7e-25
                                  TTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHHC CS
                           TBP 28 krnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkkl 85
                                    n+eY+p++fpgl++rl++pk+t liF+sGk+v+tGaks++el +a+k+i++ lkk+
  gi|70607094|ref|YP_255964.1|  5 VPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTLKKY 62
                                  489*****************************************************96 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 5e-33
                                   EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                           TBP   1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                   +++iqN+vasanl++ ++L+k a+ +  +n  Yepe+fpgl+yr++ep+v++liFssGk+vitGak e+e+++a+kki+++
  gi|70607094|ref|YP_255964.1|  71 KIQIQNIVASANLHVIVNLDKAAFLL--ENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDK 149
                                   589*******************9998..***************************************************99 PP

                                   HH CS
                           TBP  82 lk 83 
                                   l 
  gi|70607094|ref|YP_255964.1| 150 LV 151
                                   86 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0     7e-05      0.25      25      56 ..      13      44 ..       8      48 .. 0.89
   2 ?   -1.5   0.0      0.77   2.8e+03       7      21 ..      52      66 ..      43      88 .. 0.57
   3 !   15.0   0.0   5.5e-06      0.02      23      61 ..     102     140 ..      76     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
                       DUF3378 25 kkppyavfaakkndttItaYtSgKVlFQGkna 56
                                   + p+ +f+ +++++t  +++SgK ++ G++ 
  gi|70607094|ref|YP_255964.1| 13 DQFPGLIFRLESPKITSLIFKSGKMVVTGAKS 44
                                  578************************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.77
                       DUF3378  7 skktikkmkeyyksk 21
                                   k  ik++k+y  + 
  gi|70607094|ref|YP_255964.1| 52 VKRIIKTLKKYGMQL 66
                                  455555555554333 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 5.5e-06
                       DUF3378  23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                   + ++ p+ +++ +++ ++  ++ SgK ++ G++ e e  
  gi|70607094|ref|YP_255964.1| 102 EPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVH 140
                                   56789****************************999875 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.9e-06     0.011     164     259 ..      63     158 ..      30     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-06
                        NMT1_3 164 aalvaGvPvsavtqlaasedikliplddeqldkllkeypvftkyvipagtypqded..ikTiavpnflvvradldeelvYe 242
                                     + +G P  ++++++as ++++i   d+  +++l e+++++++  p+ +y+ de+  +  i  +  +v +    e+ v++
  gi|70607094|ref|YP_255964.1|  63 GMQLTGKPKIQIQNIVASANLHVIVNLDK--AAFLLENNMYEPEQFPGLIYRMDEPrvVLLIFSSGKMVITGAKREDEVHK 141
                                   45678***************997654444..345556799***********976543344454445555566667888*** PP

                        NMT1_3 243 itkaifenldelnsihk 259
                                    +k if++l el  +++
  gi|70607094|ref|YP_255964.1| 142 AVKKIFDKLVELDCVKP 158
                                   *********99987766 PP

>> DUF155  Uncharacterised ACR, YagE family COG1723
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0027       9.6      94     138 ..      44      89 ..      30     106 .. 0.64
   2 ?    6.5   0.0    0.0022       7.9       2      49 ..     121     166 .]     120     166 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
                        DUF155  94 sldellestekipkelakkgklkl..srkellkktgellslrinlnl 138
                                   s+del++ +++i k+l+k g ++l  + k  ++++    +l   +nl
  gi|70607094|ref|YP_255964.1|  44 STDELIKAVKRIIKTLKKYG-MQLtgKPKIQIQNIVASANLHVIVNL 89 
                                   56778888888888888877.55522344455555555555555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0022
                        DUF155   2 fiFknGsvVfwgldeeeeknflnkllkflneeselpreeeqeteeley 49 
                                    iF++G +V+ g   ++e+++ + ++k +++ +el  ++  e+eele+
  gi|70607094|ref|YP_255964.1| 121 LIFSSGKMVITG--AKREDEVHKAVKKIFDKLVELDCVKPVEEEELEF 166
                                   79**********..8888888888888888777666666666777777 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.012        42      37      69 ..      31      68 ..      18      94 .. 0.70
   2 ?    8.4   0.0   0.00049       1.7      31      59 ..     116     144 ..      86     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.012
                                  HHHTSEEEEEETT-HHHHHHHTT-T.....EEEEEEET CS
                         DRTGG 37 rlkegdlvivpGDRediqlaaleag.....iaalilTg 69
                                   +k g++v++++  +d ++ a++         ++ lTg
  gi|70607094|ref|YP_255964.1| 31 IFKSGKMVVTGAKSTDELIKAVKRIiktlkKYGMQLTG 68
                                  477799****9999999999988775554444555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00049
                                   HHHHHHHHHTSEEEEEETT-HHHHHHHTT CS
                         DRTGG  31 venmlerlkegdlvivpGDRediqlaale 59 
                                   ++ +l  +  g++vi+++ Red +  a++
  gi|70607094|ref|YP_255964.1| 116 PRVVLLIFSSGKMVITGAKREDEVHKAVK 144
                                   5566778899************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      816  (0.0455129); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1200.37
//
Query:       gi|70607095|ref|YP_255965.1|  [L=75]
Description: hypothetical protein Saci_1337 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-27   93.0   4.8    1.1e-26   92.8   4.8    1.0  1  DUF5622   Domain of unknown function (DUF5622)


Domain annotation for each model (and alignments):
>> DUF5622  Domain of unknown function (DUF5622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   4.8   5.9e-31   1.1e-26       1      65 [.       2      67 ..       2      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 5.9e-31
                       DUF5622  1 lKHgKYvYVere.dgwYvKvRvLksreevndpekYivlgkkvkkpprkakvlkeddlPeevreklk 65
                                  lKH+KYvYV+++ +++++KvR+Lksr+e+n+pe+Y++l+k++ k pr+akv+k++dlP+ev++klk
  gi|70607095|ref|YP_255965.1|  2 LKHQKYVYVDIGdQKKFLKVRFLKSRSENNNPEAYVILDKISIKLPRNAKVIKYEDLPAEVKDKLK 67
                                  8**********95689************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 537.13
//
Query:       gi|70607096|ref|YP_255966.1|  [L=353]
Description: hypothetical protein Saci_1338 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-86  291.3  24.4    1.4e-86  291.0  24.4    1.0  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
        4.2    7.4   5.6        3.4    7.7   0.6    2.3  2  NPCC      Nuclear pore complex component


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.0  24.4   1.5e-90   1.4e-86       1     333 [.       3     332 ..       3     338 .. 0.93

  Alignments for each domain:
  == domain 1  score: 291.0 bits;  conditional E-value: 1.5e-90
                        DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvea 81 
                                   k++v++vD+DdDlg  +g++tPv+G+e+v +a+     + P+DSD+N+l+ a+++y+++++eg+dve+a+++G++k  +e+
  gi|70607096|ref|YP_255966.1|   3 KLIVIYVDIDDDLG-SIGISTPVIGQEEVAKAIRIAEEKIPTDSDLNTLLVAYNIYNKIRSEGSDVEIALISGSQKGSLES 82 
                                   589***********.69**************************************************************** PP

                        DUF373  82 drkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrktiL 158
                                   + +  e+ld v++++++++ai+V+D++eD++++pii+sr++v++++rV+V+q r++E+ty+ll    kkal++p+++k++L
  gi|70607096|ref|YP_255966.1|  83 QLAFTEKLDMVIKAVNPTKAIIVYDSPEDAKAIPIIESRLQVAGIERVLVEQYRSVEETYVLLgryiKKALSEPRFSKIFL 163
                                   ********************************************************************************* PP

                        DUF373 159 vplGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiisgy 239
                                   +++G++lli++ll++l+l+++a+ ++l+++G+++++rG++lde       +++e +++++i++v++++ ++++++gi++gy
  gi|70607096|ref|YP_255966.1| 164 GVPGVILLIIGLLSILNLTSYATPVVLIIIGAAFIIRGLRLDE-------TVEELWKSSSIMVVVSIIFIFSVILGIVYGY 237
                                   *******************************************.......899**************************** PP

                        DUF373 240 islesvssasvssglltlilafiygavewlalailtaslgkiideylkre...ekdiarllllpflvlaiglvlygasayl 317
                                   + +++++s    +  l  +l+ +++++++l+++i++++ g+++ ++l+r+   ++di+r+++++++++++ ++  ++ + l
  gi|70607096|ref|YP_255966.1| 238 SVFTTLKS----Y-NLLGVLQVLFSIMPFLIFGIVVLFGGRAVTKLLDRNirvWHDIYRIITTVVIYYMMVTIYKSIGSSL 313
                                   **998888....3.34557777999**********************999************************7777766 PP

                        DUF373 318 ls....lsilalslvvgivv 333
                                    +    + i+ ls+++++++
  gi|70607096|ref|YP_255966.1| 314 -QvlqlQIIYSLSITTIVLI 332
                                   .3354644455555555555 PP

>> NPCC  Nuclear pore complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4     0.029   2.6e+02      56      85 ..     200     233 ..     145     237 .. 0.69
   2 ?    7.7   0.6   0.00037       3.4       8      55 ..     275     322 ..     271     346 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.029
                          NPCC  56 s....eeslasalyaelveklirllfllnivial 85 
                                   +    +e++ + ++++ + +++ ++f++++++ +
  gi|70607096|ref|YP_255966.1| 200 RglrlDETVEELWKSSSIMVVVSIIFIFSVILGI 233
                                   1444477888889999999999999999999866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00037
                          NPCC   8 lkeilrRqvnkErevkriiaNvllllvfnlikklvklllklyelkkks 55 
                                   ++++l R+++   ++ rii+ v+++ ++ +i+k++   l++++l+   
  gi|70607096|ref|YP_255966.1| 275 VTKLLDRNIRVWHDIYRIITTVVIYYMMVTIYKSIGSSLQVLQLQIIY 322
                                   7899******************************99999888855433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2312.39
//
Query:       gi|70607097|ref|YP_255967.1|  [L=313]
Description: hypothetical protein Saci_1339 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.003   17.4  15.4      0.003   17.4  15.4    3.4  3  DUF724           Protein of unknown function (DUF724)
     0.0054   16.8   9.0     0.0054   16.8   9.0    5.0  5  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0056   16.9  52.7     0.0059   16.8  21.5    3.2  3  ATG16            Autophagy protein 16 (ATG16)
     0.0085   15.0  66.3      0.038   12.9  21.2    3.1  3  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.012   15.1   1.3      0.012   15.1   1.3    4.5  4  Trimer_CC        Trimerisation motif
       0.02   15.0  22.0       0.63   10.1   2.7    3.4  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.029   12.9   4.2       0.47    8.9   0.5    2.0  2  FUSC             Fusaric acid resistance protein family
      0.031   14.5  17.2        0.3   11.4   3.1    3.7  3  DUF948           Bacterial protein of unknown function (DUF94
      0.036   13.1  51.5      0.017   14.1  17.5    2.8  2  IFT57            Intra-flagellar transport protein 57
      0.041   14.5   2.6      0.041   14.5   2.6    5.4  2  SlyX             SlyX
      0.063   13.3  65.3      0.021   14.8  27.9    3.6  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.079   13.4   0.1      0.079   13.4   0.1    5.2  5  LPP              Lipoprotein leucine-zipper
       0.15   12.5  55.5       0.44   11.0  27.1    2.7  2  Fez1             Fez1
       0.17   12.3  10.5       0.13   12.7   3.4    3.3  3  HsbA             Hydrophobic surface binding protein A
       0.31   11.2  30.1      0.081   13.1   9.3    3.4  3  COG5             Golgi transport complex subunit 5
       0.48   10.8  46.9       0.08   13.3   5.7    5.0  4  Tup_N            Tup N-terminal
       0.77    9.6   6.6         15    5.5   0.2    3.8  4  DASH_Dam1        DASH complex subunit Dam1
        1.2    9.7  30.4       0.44   11.0   5.5    5.0  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.3    9.0  41.4       0.34   10.9   7.0    4.3  4  DUF1664          Protein of unknown function (DUF1664)
        1.6    7.8  63.7          1    8.4  20.4    3.5  3  Atg14            Vacuolar sorting 38 and autophagy-related su
        1.7    8.4  22.3        0.2   11.5   1.5    3.1  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        2.4    8.6   4.1        2.1    8.8   0.1    2.9  4  MtrB             Tetrahydromethanopterin S-methyltransferase 
        3.2    5.1  50.1       0.56    7.6  13.4    2.1  2  DUF3584          Protein of unknown function (DUF3584)
        3.5    7.9  65.0       0.81    9.9   7.9    5.2  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        4.4    7.1   9.4       0.59   10.0   1.2    3.0  3  RVT_3            Reverse transcriptase-like
        4.6    7.7  48.5       0.28   11.7  10.8    4.4  5  FlgN             FlgN protein
        7.9    5.6  41.9       0.12   11.6  12.7    3.0  2  TMPIT            TMPIT-like protein
        8.3    5.2  62.3        8.7    5.1  10.9    2.5  2  DUF812           Protein of unknown function (DUF812)
        9.4    6.0  55.4       0.36   10.6  28.0    2.9  2  ERM              Ezrin/radixin/moesin family
        9.4    6.5  13.8        3.9    7.7   0.4    4.7  5  DASH_Dad1        DASH complex subunit Dad1


Domain annotation for each model (and alignments):
>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  15.4     5e-06     0.003     100     185 ..      12      97 ..      11     100 .. 0.97
   2 ?    2.6  10.7      0.18   1.1e+02     129     183 ..     130     189 ..      96     192 .. 0.77
   3 ?    0.4  20.0      0.83   4.9e+02      97     178 ..     173     254 ..     165     295 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                        DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqe 180
                                   ++++++k+ ee++k++++  +  +e +kl+++ +e+ +k + +++ql++++e+ +++ +ei +lks+ ++l + + ++++e
  gi|70607097|ref|YP_255967.1|  12 IQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKE 92 
                                   899****************************************************************************** PP

                        DUF724 181 Feava 185
                                   Fe+++
  gi|70607097|ref|YP_255967.1|  93 FEELK 97 
                                   **975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                        DUF724 129 eeeidelekkilelerqlallk......ekkeaadkeiarlkseaekleeeledveqeFea 183
                                   e e +++  ki+eler+l+++k      ek+ ++ +e+ + ++e +++++++ +  q+ ++
  gi|70607097|ref|YP_255967.1| 130 E-EEKKIIIKIAELERKLEVAKkvaqikEKNTENRAELLAKRVELSTIRQKMLELSQQIKS 189
                                   3.33677789999***999999999998888899999999999999999999999998876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.83
                        DUF724  97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                   L  ++++  +l +++k  ++ +++ +se+  +++e+++l+ ki++l+++ + l +k +++ +ei r+k e +k +ee++++
  gi|70607097|ref|YP_255967.1| 173 LSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNM 253
                                   445555666666666665666666666666667777777777777777777777888888888888888888888887776 PP

                        DUF724 178 e 178
                                   +
  gi|70607097|ref|YP_255967.1| 254 N 254
                                   4 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2  17.5    0.0086       5.2       9      98 ..       8      97 ..       2     106 .. 0.74
   2 ?    3.2   0.8      0.15        89      49      92 ..      89     134 ..      86     138 .. 0.84
   3 ?    1.7   9.4      0.41   2.4e+02      70     118 ..     136     186 ..     128     188 .. 0.84
   4 !   16.8   9.0     9e-06    0.0054      58     120 ..     193     255 ..     188     265 .. 0.93
   5 ?   -0.3   1.0       1.7     1e+03      74      90 ..     270     286 ..     254     290 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0086
                    TPR_MLP1_2  9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleese 91
                                    ++++e+ ++a ++l+k +++  +  +++k+ +qk  + + k ++  ++lq++ree+++  +ei++lk++++++ + + e +
  gi|70607097|ref|YP_255967.1|  8 SEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIK 90
                                  45566777777777788888888888888888888888888888888888888888888888888888888887777766666 PP

                    TPR_MLP1_2 92 esweeqk 98
                                  ++ ee k
  gi|70607097|ref|YP_255967.1| 91 KEFEELK 97
                                  6666655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                    TPR_MLP1_2  49 lvkhaedvkelqalreel..nelkaeiaelkaeaesakaeleesee 92 
                                   + k  e++k++++++++l  + +  +i++l+ ++++ + +lee+++
  gi|70607097|ref|YP_255967.1|  89 IKKEFEELKNVTKVKDKLdpAAISRRIEQLEWRLQTSTLTLEEEKK 134
                                   5667789999999999997777889999999999999999999886 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.41
                    TPR_MLP1_2  70 kaeiaelkaeaesakaeleeseesweeqkeelek..elselekriedlneq 118
                                     +iael+ ++e ak+  + +e++ e++ e l k  els +++++ +l++q
  gi|70607097|ref|YP_255967.1| 136 IIKIAELERKLEVAKKVAQIKEKNTENRAELLAKrvELSTIRQKMLELSQQ 186
                                   56899***************************9844677888999999888 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 9e-06
                    TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNk 120
                                    lq+l++e + +++e+++l+++ +++++ ++e +++ +e+ +e+ + ++el+kr+e++ + N 
  gi|70607097|ref|YP_255967.1| 193 LLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMNV 255
                                   69********************************************************99994 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.7
                    TPR_MLP1_2  74 aelkaeaesakaelees 90 
                                   + l++++++++++l+++
  gi|70607097|ref|YP_255967.1| 270 EALENKRKQVEEKLKNN 286
                                   33444444444444433 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1  18.4    0.0047       2.8      60     158 ..       7     104 ..       1     138 [. 0.79
   2 !   16.8  21.5   9.9e-06    0.0059      68     166 ..     151     249 ..     109     258 .. 0.77
   3 ?    0.0   1.6       1.4   8.3e+02     121     143 ..     265     287 ..     249     292 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                         ATG16  60 ekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklk 140
                                   ++e++ +++ sk  +++ + +++ +ql +e+++l ++r e  ++l++  ++lq+ +e++k++ +++ +l+++r++l + + 
  gi|70607097|ref|YP_255967.1|   7 SSEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIG 87 
                                   3333333355778889999999******************************************************99888 PP

                         ATG16 141 dreeelrekeklvqdlqD 158
                                   + ++e++e++++  +++D
  gi|70607097|ref|YP_255967.1|  88 EIKKEFEELKNVT-KVKD 104
                                   8888888876653.3444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 9.9e-06
                         ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                   + ++ ++k ++  ++l++ r el++  ++  el+q++++++e lqkl+++    +++l++l++++++l++++++++++++e
  gi|70607097|ref|YP_255967.1| 151 KVAQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNE 231
                                   3344566777888888888************************************************************** PP

                         ATG16 149 keklvqdlqDElsaLqlq 166
                                   k + +  +++El   + +
  gi|70607097|ref|YP_255967.1| 232 KGNEIGRIKEELKKRREE 249
                                   ***********9876665 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.4
                         ATG16 121 deerlaeleaeraaletklkdre 143
                                    + + ++le++r+++e+klk+++
  gi|70607097|ref|YP_255967.1| 265 STINSEALENKRKQVEEKLKNNK 287
                                   44555566666666666666554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9  21.2   6.4e-05     0.038     153     251 ..       7     101 ..       2     119 .. 0.87
   2 !   11.0  23.2   0.00024      0.14     139     260 ..     117     232 ..     111     234 .. 0.69
   3 ?    1.4   8.9      0.19   1.2e+02     199     255 ..     234     288 ..     226     292 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.4e-05
                          Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleele 233
                                   + +++++++ +++ e l ++++ek +l +e++kl+++++e    + e+L+++r++l+++ +ei++k +e+++l++q+++l 
  gi|70607097|ref|YP_255967.1|   7 SSEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRRE----KVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLI 83 
                                   5567788888888888999999999999999999998887....899********************************** PP

                          Spc7 234 ekieelkeqkseleeeia 251
                                   + i e+k++ +el++ ++
  gi|70607097|ref|YP_255967.1|  84 QIIGEIKKEFEELKNVTK 101
                                   ******999999987655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                          Spc7 139 gLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeie 216
                                   +L+ +l+    +lee+k+ + k  e+  +   e+ ++ a+++e+ ++ +       +    ++ eL ++r+++ el+++i+
  gi|70607097|ref|YP_255967.1| 117 QLEWRLQTSTLTLEEEKKIIIKIAELERK--LEVAKKVAQIKEKNTENR-------AellAKRVELSTIRQKMLELSQQIK 188
                                   55555555555555555555554443222..234444444444444333.......233246999**************** PP

                          Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                   +kk+ l++l+++++ +++++e+l++++++l+++i e    ++e+
  gi|70607097|ref|YP_255967.1| 189 SKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEK 232
                                   **********************************9998777665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.19
                          Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                                   +e+  ++eel++  +e++  + ++++l eq  +++ + e+l+++++++ee++++ +r
  gi|70607097|ref|YP_255967.1| 234 NEIGRIKEELKKRREEVR--NMNVTDLYEQQLRSTINSEALENKRKQVEEKLKNNKR 288
                                   344555555555555555..4555555555555555555555555555555555554 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       3.3     2e+03      17      32 ..      12      27 ..       3      32 .. 0.69
   2 ?   -0.7   3.3       1.7     1e+03      26      40 ..      46      60 ..      33      71 .. 0.86
   3 ?   15.1   1.3     2e-05     0.012      27      52 .]     207     232 ..     202     232 .. 0.94
   4 ?   -0.8   1.0         2   1.2e+03      26      30 ..     248     252 ..     234     264 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                                  XXXX--HHHHHHHHHH CS
                     Trimer_CC 17 ssdavSRLEEelrkLq 32
                                   ++  S+  Eelrk +
  gi|70607097|ref|YP_255967.1| 12 IQERYSKAVEELRKFK 27
                                  4566677779999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                  HHHHHHHHHHHHHHH CS
                     Trimer_CC 26 EelrkLqatVQelQk 40
                                  E + kL+ + Q+lQ+
  gi|70607097|ref|YP_255967.1| 46 EKVEKLKSIRQQLQQ 60
                                  8899*********97 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Trimer_CC  27 elrkLqatVQelQkRLDrLEetvqaK 52 
                                   el  L++ +Q+l kR+D+L  +v++K
  gi|70607097|ref|YP_255967.1| 207 ELEDLNTKIQDLNKRIDELTAKVNEK 232
                                   8999*******************998 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2
                                   HHHHH CS
                     Trimer_CC  26 Eelrk 30 
                                   Ee+r+
  gi|70607097|ref|YP_255967.1| 248 EEVRN 252
                                   44555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.7    0.0011      0.63      69     119 ..      41      90 ..       5     100 .. 0.50
   2 ?    6.8   1.5     0.011       6.7      22      91 ..      75     143 ..      72     156 .. 0.81
   3 ?    9.1   8.8    0.0021       1.3      22     105 ..     173     254 ..     140     285 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                  Baculo_PEP_C  69 ltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnllqalnnld 119
                                    ++  +++ +l+ ++r++L+ +  ++ +  +++t ++s  +nl+q +  ++
  gi|70607097|ref|YP_255967.1|  41 KQKRREKVEKLK-SIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIK 90 
                                   333333444443.55555555555555555555555555555555555443 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
                  Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnln 91 
                                   L++ r  ++qi++++++ ++++++ +++++++l    a++++r+++l  +L+++  +l+  +++  ++  l+
  gi|70607097|ref|YP_255967.1|  75 LKSQRQNLIQIIGEIKKEFEELKN-VTKVKDKLDP--AAISRRIEQLEWRLQTSTLTLEeeKKIIIKIAELE 143
                                   55667778999**********999.9999999999..88999********9999999985555555555555 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0021
                  Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                                   L++ir +  +++ q+++ ++ +++ L++  + +++ l++l+t++++l +++++  ++++++  ne+  ++ +l     +v 
  gi|70607097|ref|YP_255967.1| 173 LSTIRQKMLELSQQIKSKKELLQK-LKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEK-GNEIGRIKEELKKRREEVR 251
                                   444544445554444444443333.444444444444444444444444444444444422.2333333333333333333 PP

                  Baculo_PEP_C 103 Nin 105
                                   N+n
  gi|70607097|ref|YP_255967.1| 252 NMN 254
                                   333 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0095       5.7     213     295 ..      15     102 ..      12     134 .. 0.77
   2 ?    8.9   0.5   0.00078      0.47     219     311 ..     171     259 ..     140     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0095
                          FUSC 213 rirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrral 293
                                   r + +++ lr + s+ l l+  + +l +  ++  ++ +  +++l+++ +e+++  + +   +l+ +++ l + + +++++ 
  gi|70607097|ref|YP_255967.1|  15 RYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKS--KINEITQLKSQRQNLIQIIGEIKKEF 93 
                                   56678899999999999999999999999999999999999999999999999..77889999999999999999999988 PP

                          FUSC 294 e.......a 295
                                   e        
  gi|70607097|ref|YP_255967.1|  94 EelknvtkV 102
                                   866666662 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00078
                          FUSC 219 ralrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadt 299
                                     l  ++++ml+l++++ s  +ll+ l++e++  ++el++l  ++++l   +  ++l+a++++   ++ +++++l+    +
  gi|70607097|ref|YP_255967.1| 171 VELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDL--NKRIDELTAKVNEKGNEIGRIKEELK--KRR 247
                                   568899****************************99999999999996..23444444444444444444444444..333 PP

                          FUSC 300 aalllarlaell 311
                                   +++   ++ +l 
  gi|70607097|ref|YP_255967.1| 248 EEVRNMNVTDLY 259
                                   333333333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00074      0.44      29      85 ..      10      66 ..       2      71 .. 0.88
   2 ?    5.7   1.5     0.029        17      29      75 ..      52     101 ..      51     160 .. 0.86
   3 ?   11.4   3.1    0.0005       0.3      28      85 ..     187     251 ..     173     256 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00074
                        DUF948 29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85
                                  de++++  +  +++++   e  +l+++v++l +  +ek+ek++++ ++++++ e ++
  gi|70607097|ref|YP_255967.1| 10 DEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIK 66
                                  7778888888899999999999******************************99986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                        DUF948  29 deaaatieelekqvdpilkevedllakvne...lledvneklekvdplte 75 
                                   ++++++++++++++++ ++e+++l ++ ++   +  +++++ e+++++t+
  gi|70607097|ref|YP_255967.1|  52 KSIRQQLQQIREEIKSKINEITQLKSQRQNliqIIGEIKKEFEELKNVTK 101
                                   67889999999999999999999988777744455667777777777664 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.0005
                        DUF948  28 ldeaaatieelekqvdpilkevedllakvne.......lledvneklekvdplteavadlgesvs 85 
                                   +++ ++ +++l+++ d i ke+edl +k+++       l++ vnek +++ ++ e++++  e v+
  gi|70607097|ref|YP_255967.1| 187 IKSKKELLQKLKSERDVIQKELEDLNTKIQDlnkrideLTAKVNEKGNEIGRIKEELKKRREEVR 251
                                   44444444444444444444444444444441111111555555555555555555555555554 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  17.5   2.9e-05     0.017     262     351 ..       6      96 ..       1     102 [. 0.90
   2 ?    3.5  26.3     0.046        28     186     328 ..     130     255 ..      98     288 .. 0.44

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                         IFT57 262 esrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg.splvkikkal 341
                                   +s E  +++++++ ++e+r+ + e  ++ +++k+l+++  e+ ++l++i ++l+++ +e++++ +++t   s+ +++ + +
  gi|70607097|ref|YP_255967.1|   6 SSSEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLkSQRQNLIQII 86 
                                   678999*************************************************************98536777888888 PP

                         IFT57 342 tklkkEikqm 351
                                    ++kkE +++
  gi|70607097|ref|YP_255967.1|  87 GEIKKEFEEL 96 
                                   8888887766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.046
                         IFT57 186 keeeiieskvdaaeWklEleRvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEk 266
                                   +ee+ i  k+ + e kl                  +  +++ q+k+ +++ +++l   + +l+ + +++ +  ++i+s+ +
  gi|70607097|ref|YP_255967.1| 130 EEEKKIIIKIAELERKL------------------EVAKKVAQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKE 192
                                   22222333333333333..................4444444444444444444444444444444444444444444444 PP

                         IFT57 267 ylns...qleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssm 328
                                    l++   + +   +e+++++++++++++++++l+++v+e+ +e  +i+eel+k  +e+  r+ ++
  gi|70607097|ref|YP_255967.1| 193 LLQKlksERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEV--RNMNV 255
                                   4432100111122234444444444444444444444444444444444444444433..22233 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.6   6.9e-05     0.041       2      52 ..     205     255 ..     204     266 .. 0.92
   2 ?   -1.9   0.0         9   5.4e+03      34      47 ..     270     283 ..     255     289 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                   ++ le+L +k+  + + i+eL + v e   +i r++++l++ +e++++++ 
  gi|70607097|ref|YP_255967.1| 205 QKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMNV 255
                                   6789******************************************99875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9
                                   HHHHHHHHHHHHT- CS
                          SlyX  34 drlqrqlrllaerl 47 
                                   ++l+ + ++++e+l
  gi|70607097|ref|YP_255967.1| 270 EALENKRKQVEEKL 283
                                   33444444444444 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  23.8     0.056        34       5      92 ..      16     103 ..      12     137 .. 0.81
   2 ?   14.8  27.9   3.6e-05     0.021      25     131 ..     138     250 ..     129     260 .. 0.84
   3 ?    2.1   1.0      0.31   1.8e+02       2      17 ..     273     288 ..     272     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.056
                CENP-F_leu_zip   5 klhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeL 85 
                                     ++ e+L++ ++++ +L d v++L++   +  e++ ++  +  + ++e+++  +ei +l++++++l + + ++++e eeL
  gi|70607097|ref|YP_255967.1|  16 YSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKEFEEL 96 
                                   56789************************************************************************9999 PP

                CENP-F_leu_zip  86 ekelqkk 92 
                                   ++  + k
  gi|70607097|ref|YP_255967.1|  97 KNVTKVK 103
                                   6543333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.6e-05
                CENP-F_leu_zip  25 kvenLerelemsee......nqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseL 99 
                                   k+ +Ler le +++      ++++   e   ++ e++t+++++ el+++ +  +  L++l+se++ ++kel++ + ++++L
  gi|70607097|ref|YP_255967.1| 138 KIAELERKLEVAKKvaqikeKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDL 218
                                   788888888876541111004444455555689999********************************************* PP

                CENP-F_leu_zip 100 eslnsslenlleekEqekvqmkeeskaaveeL 131
                                   +++  +l+  ++ek +e  ++kee k++ ee 
  gi|70607097|ref|YP_255967.1| 219 NKRIDELTAKVNEKGNEIGRIKEELKKRREEV 250
                                   **************************998876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.31
                CENP-F_leu_zip   2 ekkklhvlekLKeser 17 
                                   e+k+++v+ekLK+++r
  gi|70607097|ref|YP_255967.1| 273 ENKRKQVEEKLKNNKR 288
                                   7899********9998 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.9      0.04        24       4      36 ..      32      64 ..      30      67 .. 0.90
   2 ?    1.0   0.1      0.96   5.7e+02       2      24 ..      72      94 ..      68     107 .. 0.55
   3 ?   -1.9   0.1       7.5   4.5e+03      14      25 ..     150     161 ..     139     169 .. 0.71
   4 ?    3.3   2.2      0.18   1.1e+02       1      31 [.     179     209 ..     179     211 .. 0.89
   5 ?   13.4   0.1   0.00013     0.079       2      36 ..     208     242 ..     207     246 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                           LPP  4 eLssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                  +L ++V++Lk+k  +  ++++s+++++q+++eE
  gi|70607097|ref|YP_255967.1| 32 QLIDEVKKLKQKRREKVEKLKSIRQQLQQIREE 64
                                  6778999999999999999***********999 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.96
                           LPP  2 ldeLssqVsqLkskvdqlssdvn 24
                                  +++L sq ++L + + +++++ +
  gi|70607097|ref|YP_255967.1| 72 ITQLKSQRQNLIQIIGEIKKEFE 94
                                  34444444444444444444433 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.5
                           LPP  14 skvdqlssdvns 25 
                                   +kv+q++++ ++
  gi|70607097|ref|YP_255967.1| 150 KKVAQIKEKNTE 161
                                   677788776554 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.18
                           LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaq 31 
                                   k+ eLs+q+++ k+  ++l+s+ + ++++++
  gi|70607097|ref|YP_255967.1| 179 KMLELSQQIKSKKELLQKLKSERDVIQKELE 209
                                   7889******************999888765 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 0.00013
                           LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                   l+ L++ +++L++ +d+l+++vn+  +++  +keE
  gi|70607097|ref|YP_255967.1| 208 LEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEE 242
                                   6889*************************999999 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  21.6     0.055        33      62     146 ..      17     102 ..       2     151 .. 0.44
   2 ?   11.0  27.1   0.00073      0.44      13     149 ..     153     288 ..     147     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.055
                          Fez1  62 eektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqe.aeeleelkreverlr 141
                                   ++  +el + ++e  +  +e++ l++k ++  e+lk++r++l++  +e +++++e ++ k qrq+  + ++e k+e e+l+
  gi|70607097|ref|YP_255967.1|  17 SKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNlIQIIGEIKKEFEELK 97 
                                   555555555555555555555555555555555555555555555555555555555555555553222333333334333 PP

                          Fez1 142 aeLke 146
                                   +  k 
  gi|70607097|ref|YP_255967.1|  98 NVTKV 102
                                   32211 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00073
                          Fez1  13 slLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekle 93 
                                   + +K+   + +ae+ +k  e+ +++ ++ el++++++k e +++l+++++  ++ele ++ ++q  +++ + l  kv++  
  gi|70607097|ref|YP_255967.1| 153 AQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKG 233
                                   667777888999********************************************************************* PP

                          Fez1  94 eelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerq 149
                                   +e+ +++eel++  +e +++ + +d  ++q +++ ++e+l+++ ++++++Lk++++
  gi|70607097|ref|YP_255967.1| 234 NEIGRIKEELKKRREEVRNM-NVTDLYEQQLRSTINSEALENKRKQVEEKLKNNKR 288
                                   ***********976555544.44445556666678888888888888888887765 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.57   3.4e+02      18      84 ..      61      86 ..      48     108 .. 0.42
   2 ?   12.7   3.4   0.00022      0.13      33     116 ..     134     220 ..     109     224 .. 0.83
   3 ?   -1.3   0.0       4.8   2.9e+03      78     106 ..     237     265 ..     221     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.57
                                  HHHHHHH--SH..HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHHHHHHH CS
                          HsbA 18 ldtavnafnGgasalpilsasnalvsaikkattdaqasapltdeealalaqavqtLepdvkaaldal 84
                                  + + +++                                          ++++++L+ + +++++ +
  gi|70607097|ref|YP_255967.1| 61 IREEIKS-----------------------------------------KINEITQLKSQRQNLIQII 86
                                  3333333.........................................2223333333333333333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHH..HCHHHHHHHHHHHHHTHHHHHHH.T-HHHHHHHHHHHHHH CS
                          HsbA  33 pilsasnalvsaikkattdaqasapltdeealalaqavq..tLepdvkaaldaliaKkpafdka.gltslvlssLqdlkaa 110
                                   +i  + ++l+++++ a + aq  +  t++ a+ la  v+  t++ ++  + +++++Kk+ ++k+   ++++++ L+dl+++
  gi|70607097|ref|YP_255967.1| 134 KIIIKIAELERKLEVAKKVAQIKEKNTENRAELLAKRVElsTIRQKMLELSQQIKSKKELLQKLkSERDVIQKELEDLNTK 214
                                   666677889999999999999999999999999999777758**********************667************** PP

                                   HHHHHH CS
                          HsbA 111 sdaLsd 116
                                    ++L +
  gi|70607097|ref|YP_255967.1| 215 IQDLNK 220
                                   999986 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.8
                                   HHHHHHHHHTHHHHHHHT-HHHHHHHHHH CS
                          HsbA  78 kaaldaliaKkpafdkagltslvlssLqd 106
                                       + l+++++++ ++++t+l  ++L++
  gi|70607097|ref|YP_255967.1| 237 GRIKEELKKRREEVRNMNVTDLYEQQLRS 265
                                   55556788888999999999998888876 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.6     0.014       8.4      54     115 ..      27      85 ..       8      89 .. 0.75
   2 ?    0.2   0.3       1.3   7.7e+02      77     116 ..     115     156 ..      84     161 .. 0.60
   3 ?   13.1   9.3   0.00014     0.081      28     111 ..     166     245 ..     149     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHH CS
                          COG5  54 tsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqt 115
                                   +s++l+L+++++k k++     e  ++l+s+ + ++++++++  +++e+ +l+s+ ++l q+
  gi|70607097|ref|YP_255967.1|  27 KSEKLQLIDEVKKLKQK---RREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQI 85 
                                   44555555555555544...45555678899999999*********************9987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                   XXXXXXXXXXXXXXXX..-TTHHHHHHHHHHHHHHHHHHHHH CS
                          COG5  77 lksslesLsasyerlk..skvlepyeeaeklqsalkrlhqtl 116
                                   +++   +L+ s   l+  +k++ +++e+e + + +k++ q++
  gi|70607097|ref|YP_255967.1| 115 IEQLEWRLQTSTLTLEeeKKIIIKIAELERKLEVAKKVAQIK 156
                                   444444555565566422568888888888888888887775 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00014
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHH CS
                          COG5  28 eldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqs 107
                                    l   ++l+++ + + el +++     ++++eLl++l++++   +  l++l++++++L++ ++ l+ kv e+ +e+   ++
  gi|70607097|ref|YP_255967.1| 166 LLAKRVELSTIRQKMLELSQQI-----KSKKELLQKLKSERDVIQkELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKE 241
                                   3334455555555555555555.....3568899999998888877******************************99999 PP

                                   HHHH CS
                          COG5 108 alkr 111
                                   +lk+
  gi|70607097|ref|YP_255967.1| 242 ELKK 245
                                   9987 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   8.3      0.23   1.4e+02      23      71 ..       5      53 ..       1      62 [. 0.86
   2 ?    7.2   6.0     0.011       6.3      21      73 ..      52     106 ..      50     110 .. 0.82
   3 ?    6.0   4.3     0.024        14      16      60 ..     148     192 ..     141     200 .. 0.87
   4 ?   13.3   5.7   0.00013      0.08       7      65 ..     202     262 ..     196     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
                         Tup_N 23 lkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLka 71
                                  + +++de+  ++++ ++El +++++  +L  + +k+kq+  e +++Lk+
  gi|70607097|ref|YP_255967.1|  5 TSSSEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKS 53
                                  55688999999****************************9999999985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                         Tup_N  21 sslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEe..eiarLkaeL 73 
                                   +s+++q + +   i+s+i+E++q++++  +L +   +ik+++Ee  ++++ k +L
  gi|70607097|ref|YP_255967.1|  52 KSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKEFEElkNVTKVKDKL 106
                                   6788888888899999**************************9744566666665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.024
                         Tup_N  16 lsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikq 60 
                                   +++++ ++k+++ e  + + ++  El +irq++ eL ++ ++ k+
  gi|70607097|ref|YP_255967.1| 148 VAKKVAQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKE 192
                                   67888899999999999999999**************99988887 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00013
                         Tup_N   7 davkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkik..qqYEee 65 
                                   d++++E + l+++++ l+++ de+ +k++++ +E+ +i+++l+   e+ r++   + YE++
  gi|70607097|ref|YP_255967.1| 202 DVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMNvtDLYEQQ 262
                                   89**************************************998876666555311556665 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.024        15      10      34 ..      46      71 ..      32      73 .. 0.81
   2 ?   -2.0   0.0       5.2   3.1e+03      12      25 ..      86      99 ..      75     102 .. 0.66
   3 ?   -0.8   0.1       2.4   1.4e+03      19      23 ..     194     198 ..     171     215 .. 0.47
   4 ?    5.1   0.5     0.033        20       8      34 ..     204     231 ..     197     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                     DASH_Dam1 10 DsletLdknledLqqihesLsd.fNe 34
                                  +++e+L++  ++Lqqi+e++++  Ne
  gi|70607097|ref|YP_255967.1| 46 EKVEKLKSIRQQLQQIREEIKSkINE 71
                                  56888888889999999998887777 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                     DASH_Dam1 12 letLdknledLqqi 25
                                  + +++k +e+L+++
  gi|70607097|ref|YP_255967.1| 86 IGEIKKEFEELKNV 99
                                  45666677777665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.4
                     DASH_Dam1  19 ledLq 23 
                                   l++L+
  gi|70607097|ref|YP_255967.1| 194 LQKLK 198
                                   33332 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.033
                     DASH_Dam1   8 LaDsletLdknledLqqihesLsd.fNe 34 
                                   ++++le+L+++++dL++  ++L+  +Ne
  gi|70607097|ref|YP_255967.1| 204 IQKELEDLNTKIQDLNKRIDELTAkVNE 231
                                   5667777777777777766666555665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7  13.3       7.2   4.3e+03       6      60 ..      58      85 ..      19     157 .. 0.60
   2 ?    0.4   2.4       1.6   9.3e+02      13      58 ..     139     187 ..     133     199 .. 0.44
   3 ?   11.0   5.5   0.00074      0.44      15      63 ..     196     241 ..     166     253 .. 0.62
   4 ?   -1.7   0.0       7.2   4.3e+03      22      36 ..     271     285 ..     247     290 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                       NPV_P10  6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkven 60
                                  L +Ir++ik   + ++ l++q                            ++ ++ 
  gi|70607097|ref|YP_255967.1| 58 LQQIREEIKSKINEITQLKSQR---------------------------QNLIQI 85
                                  3333333333333333333332...........................222222 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                       NPV_P10  13 ikavddkVdalqqqvddvqe.nlpdvtelnek...LdaqsaqLaeletkv 58 
                                   i++++ k+  + ++v++++e n ++  el +k   L  + +++ el++++
  gi|70607097|ref|YP_255967.1| 139 IAELERKL-EVAKKVAQIKEkNTENRAELLAKrveLSTIRQKMLELSQQI 187
                                   56666666.55556655554133333333322222333333333333333 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00074
                       NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   ++++  d++q++++d++++++d   ln+++d+++a+++e  +++  I++
  gi|70607097|ref|YP_255967.1| 196 KLKSERDVIQKELEDLNTKIQD---LNKRIDELTAKVNEKGNEIGRIKE 241
                                   3344445566666666666555...666666666666666666666655 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 7.2
                       NPV_P10  22 alqqqvddvqenlpd 36 
                                   al+++ ++v+e+l++
  gi|70607097|ref|YP_255967.1| 271 ALENKRKQVEEKLKN 285
                                   444444555555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  10.6     0.014       8.1      48     121 ..      18      90 ..       1      92 [. 0.79
   2 ?    2.0   5.9      0.32   1.9e+02      36     105 ..      79     154 ..      77     166 .. 0.65
   3 ?    0.4   8.2         1   6.1e+02      50     119 ..     122     189 ..     109     201 .. 0.60
   4 ?   10.9   7.0   0.00057      0.34      49     107 ..     196     254 ..     190     282 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                       DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   k +e++  + ++ k +L ++++++ +k  e  e  k+i+++++++re++++  ++++++k+  ++l + + +i+
  gi|70607097|ref|YP_255967.1|  18 KAVEEL-RKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIK 90 
                                   444443.356778889999999999999999***************9999999999999998888888777775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                       DUF1664  36 krslsdavesvskqleqvseslaatkrhL.....ssridrvdkkldeqkeis...keikeevtevredlseigedves 105
                                   +++l + + ++ k+ e+++ +++++k++L     s+ri++++++l+ ++ +    k+i  +++e++++l+ + ++v +
  gi|70607097|ref|YP_255967.1|  79 RQNLIQIIGEIKKEFEELK-NVTKVKDKLdpaaiSRRIEQLEWRLQTSTLTLeeeKKIIIKIAELERKLE-VAKKVAQ 154
                                   7888888888899888875.57777776643333789999999999877555000445555666666654.3344444 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1
                       DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                   l++   +l++ k+ +  +i+++++kl+  k++ ++ike+ te r +l + + +++++++ + +l +++++
  gi|70607097|ref|YP_255967.1| 122 LQTSTLTLEEEKK-IIIKIAELERKLEVAKKV-AQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKS 189
                                   4444455555544.455677777777766655.4566666666666666666666666666666666654 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00057
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                   +l++  + +++  ++L+ +i+ ++k++de ++  +e  +e+ +++e+l++ +e+v++++
  gi|70607097|ref|YP_255967.1| 196 KLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMN 254
                                   44444555555556666666666666666666666666666666666666666665554 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  22.2    0.0077       4.6      21     113 ..      13     103 ..       3     118 .. 0.77
   2 ?    0.4  14.2      0.47   2.8e+02      54     128 ..     114     190 ..     100     192 .. 0.79
   3 ?    8.4  20.4    0.0017         1      47     122 ..     179     254 ..     176     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0077
                         Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekk 101
                                   +er+ +  e+l+k+ksek +l  +++k+ ++++   ++ +k+k+ +++l++++ +i ++ +++ +lk ++++l + i e k
  gi|70607097|ref|YP_255967.1|  13 QERYSKAVEELRKFKSEKLQLIDEVKKLKQKRR---EKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIK 90 
                                   578888889999999999999999986655555...888889999999999999999999999999999999999999999 PP

                         Atg14 102 kklaklsdklk.k 113
                                   k++++l++ +k k
  gi|70607097|ref|YP_255967.1|  91 KEFEELKNVTKvK 103
                                   9999999888841 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                         Atg14  54 eaeqledkiknkkakleelksliadlr..erlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleer 128
                                   + eqle+++++++  lee k+ i ++   er+ e+ +k+ q k+++ e +++l +++ +l++ r+++  l+++++++
  gi|70607097|ref|YP_255967.1| 114 RIEQLEWRLQTSTLTLEEEKKIIIKIAelERKLEVAKKVAQIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSK 190
                                   358999*******9999999877776522577889999***********************9888888888888876 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0017
                         Atg14  47 kalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslq 122
                                   k+le  ++ +++++ ++++k   + ++++ +dl+ ++q l++++++l+++++ek +++ + +++lkkRr++ + ++
  gi|70607097|ref|YP_255967.1| 179 KMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMN 254
                                   5666666666666666666666667777777777777777777777777777777777777777775555543333 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.7    0.0082       4.9      95     171 ..      20      99 ..       4     102 .. 0.66
   2 ?    6.9   4.6    0.0083         5      75     143 ..      35     105 ..      31     121 .. 0.64
   3 ?   -0.5   1.6       1.6   9.6e+02      92     140 ..     133     183 ..     109     201 .. 0.47
   4 ?   11.5   1.5   0.00033       0.2      98     151 ..     204     257 ..     186     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0082
                                   H.................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  95 iieiqkeinds...vesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevakv 171
                                   ++e+ k   +    ++ +++ +q+  e +e+ ++ +++l++i e++++  ++++++++  +++ + i e+ + +ee+++v
  gi|70607097|ref|YP_255967.1|  20 VEELRKFKSEKlqlIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKEFEELKNV 99 
                                   44444444444000444455556666666777777888888888888888888888888888888888888888887776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0083
                                   HHHHHHHHHHHHHH...HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH CS
                     MCPsignal  75 dEVrkLAersaqaa...keiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadl 143
                                   dEV+kL ++  ++    k i++ +++i +ei++ ++ +++ +++ ++  +++ e +++++e+  +v++v+d 
  gi|70607097|ref|YP_255967.1|  35 DEVKKLKQKRREKVeklKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKEFEELK-NVTKVKDK 105
                                   677777766554431115556666667777777777777777777777777777777777653.45555555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.6
                                   HHHH.................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH CS
                     MCPsignal  92 ealiiei...qkeindsvesleetrqrveegselveetgealkeiveavaev 140
                                   +++ii+i   +++ + + ++ +  ++++e+ +el ++ + +l++i +++ e+
  gi|70607097|ref|YP_255967.1| 133 KKIIIKIaelERKLEVAKKVAQIKEKNTENRAELLAK-RVELSTIRQKMLEL 183
                                   3333333000223332222222222223333222222.33344444444444 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00033
                                   ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                   iqke +d  + +++ ++r++e + +v+e g+++ +i e+ ++  ++v++++++ 
  gi|70607097|ref|YP_255967.1| 204 IQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMNVTD 257
                                   79************************************************9884 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.7     4e+03      46      46 ..      56      56 ..      32      85 .. 0.60
   2 ?   -1.8   0.0         7   4.2e+03      31      54 ..      86     108 ..      71     113 .. 0.61
   3 ?   -1.6   0.1       6.4   3.8e+03      15      45 ..     123     153 ..     116     162 .. 0.73
   4 ?    8.8   0.1    0.0035       2.1      22      55 ..     199     232 ..     182     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.7
                          MtrB 46 d 46
                                  +
  gi|70607097|ref|YP_255967.1| 56 Q 56
                                  2 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7
                          MtrB  31 ldpvleeidkLekiaddlvnsLdp 54 
                                   + ++++e ++L+++++ + ++Ldp
  gi|70607097|ref|YP_255967.1|  86 IGEIKKEFEELKNVTK-VKDKLDP 108
                                   5677777777776553.4555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.4
                          MtrB  15 etgvvaearedvvllsldpvleeidkLekia 45 
                                   +t+ ++ ++e  +++++++++ +++  +k+a
  gi|70607097|ref|YP_255967.1| 123 QTSTLTLEEEKKIIIKIAELERKLEVAKKVA 153
                                   5666666766678888888888887766666 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0035
                          MtrB  22 aredvvllsldpvleeidkLekiaddlvnsLdpe 55 
                                   +++dv+  +l++++++i++L+k  d+l  +++ +
  gi|70607097|ref|YP_255967.1| 199 SERDVIQKELEDLNTKIQDLNKRIDELTAKVNEK 232
                                   4789***********************9877655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  30.4      0.04        24     348     530 ..       4     195 ..       1     197 [. 0.81
   2 ?    7.6  13.4   0.00094      0.56     602     687 ..     195     284 ..     191     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.04
                       DUF3584 348 adldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrl......kaaieeale 422
                                   a  + +++i++ ++++ eel+ + ++  ++  + +++kqk+ e+  e+l+ ++++l++iree + +      ++ ++++l 
  gi|70607097|ref|YP_255967.1|   4 ATSSSEDEIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKV-EKLKSIRQQLQQIREEIKSKineitqLKSQRQNLI 83 
                                   55678999*******************************998765.67889999999999999987777777555555555 PP

                       DUF3584 423 al....esqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekaeaevealqaeee 499
                                   ++    ++++++ ++  k + + + + + +r+++l+ rl+  t t Ee ++i ++ ++le+  e ++k  + +e+ +++++
  gi|70607097|ref|YP_255967.1|  84 QIigeiKKEFEELKNVTKVKDKLDPAAISRRIEQLEWRLQTSTLTLEEEKKIIIKIAELERKLEVAKKVAQIKEKNTENRA 164
                                   55000044444444444555555667899**************************************************** PP

                       DUF3584 500 qlrkkrdeadealqkaerrleqlrqaleele 530
                                   +l +kr e ++++qk+ +  +q +++ e l+
  gi|70607097|ref|YP_255967.1| 165 ELLAKRVELSTIRQKMLELSQQIKSKKELLQ 195
                                   ******9999999999888888887766555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00094
                       DUF3584 602 eeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqne...kesekdkle.kaiaer 678
                                   ++L++++++++++l++ + k++ +++++++l a+++e+ +++ + +++lk++r++++ ++     +++++  ++ +a++++
  gi|70607097|ref|YP_255967.1| 195 QKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMNVTdlyEQQLRSTINsEALENK 275
                                   578888888888888888888888888888888888888888888888888888888877642223444444442677777 PP

                       DUF3584 679 kqqaeeqlq 687
                                   ++q+ee+l+
  gi|70607097|ref|YP_255967.1| 276 RKQVEEKLK 284
                                   777777765 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.9    0.0014      0.81      54     101 ..      15      62 ..       9      65 .. 0.89
   2 ?    4.8  13.2     0.052        31      39      96 ..      52     105 ..      49     142 .. 0.44
   3 ?   -1.4  15.4       4.4   2.6e+03      39      98 ..     133     202 ..     122     208 .. 0.56
   4 ?    8.9  18.5    0.0029       1.8      10      98 ..     159     251 ..     158     254 .. 0.82
   5 ?    2.5   8.0      0.28   1.7e+02      13      64 ..     238     288 ..     234     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                                   HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  54 elskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                   + sk+++++ k k ++ +li+evk+lk++  ++ ++lk ++++l+++ 
  gi|70607097|ref|YP_255967.1|  15 RYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIR 62 
                                   579999999999999999**************************9985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.052
                                   HHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                   ++++++l+++++e ++  +eI ++k +   ++ li+ + e+k+e+++l++ +++++++
  gi|70607097|ref|YP_255967.1|  52 KSIRQQLQQIREEIKSKINEITQLKSQ---RQNLIQIIGEIKKEFEELKN-VTKVKDK 105
                                   333333333333333333333333333...34444444444444444432.2222222 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.4
                                   HHHHHHHHHHHHHHHHHHHHCCCCCCTT...........S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  39 relqveleelqaerNelskeIgkakkkk...........edaeeliaevkelkeelkaleaelkeleaele 98 
                                   +++++++ el + + e++k+++++k+k+            + + +++++ el++++k +++ l++l++e +
  gi|70607097|ref|YP_255967.1| 133 KKIIIKIAELER-KLEVAKKVAQIKEKNtenraellakrVELSTIRQKMLELSQQIKSKKELLQKLKSERD 202
                                   555555555543.3466677777776666444444444445555556666666666666666666665544 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0029
                                   -HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHH CS
                  Seryl_tRNA_N  10 npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkal 86 
                                   n+e  +e l+kR e +   +++lel ++ ++ +  l++l++er  ++ke + +  k     + ++el a+v+e ++e+ ++
  gi|70607097|ref|YP_255967.1| 159 NTENRAELLAKRVELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIqdlnKRIDELTAKVNEKGNEIGRI 239
                                   7888899999999999999*******************************9998765566677777777777777777777 PP

                                   HHHHHHHHHHHH CS
                  Seryl_tRNA_N  87 eaelkeleaele 98 
                                   ++elk+ ++e+ 
  gi|70607097|ref|YP_255967.1| 240 KEELKKRREEVR 251
                                   777777777665 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.28
                                   HHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC CS
                  Seryl_tRNA_N  13 avkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakk 64 
                                    +ke lkkR+e+      + +l+e++ +  +  e+l ++r+++ ++ ++ k+
  gi|70607097|ref|YP_255967.1| 238 RIKEELKKRREE-VRNMNVTDLYEQQLRSTINSEALENKRKQVEEKLKNNKR 288
                                   699******855.55567999999999999*****************99987 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3         1   6.2e+02      65      99 ..      26      59 ..      18      70 .. 0.57
   2 ?    0.4   0.1      0.87   5.2e+02      74     104 ..      67      96 ..      60     100 .. 0.74
   3 ?   10.0   1.2   0.00098      0.59      33     104 ..     154     225 ..     134     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                         RVT_3 65 vegDsktvvqllngrekvksselanlldeirkllk 99
                                  +++ + ++++ +++ ++ +++++++ l++ir+ l+
  gi|70607097|ref|YP_255967.1| 26 FKSEKLQLIDEVKKLKQKRREKVEK-LKSIRQQLQ 59
                                  5566666777777777633333333.334443333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.87
                         RVT_3  74 qllngrekvksselanlldeirkllksfesv 104
                                   +++n+ ++  +s+ +nl++ i ++ k+fe+ 
  gi|70607097|ref|YP_255967.1|  67 SKINEITQ-LKSQRQNLIQIIGEIKKEFEEL 96 
                                   56777777.6778888888888888888875 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00098
                         RVT_3  33 klqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirkllksfesv 104
                                   ++++k++   AEl+A +  L ++ +  ++  +    +k++ q+l+++ +v ++el+ l ++i++l k+ ++ 
  gi|70607097|ref|YP_255967.1| 154 QIKEKNTENRAELLAKRVELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDEL 225
                                   478999***********************************************************9998876 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.6    0.0065       3.9      36     105 ..      19      91 ..       5     102 .. 0.75
   2 ?   -2.3  14.3       9.9   5.9e+03      38      80 ..      56      99 ..      54     164 .. 0.74
   3 ?    5.6   9.0     0.035        21      44     107 ..     129     191 ..     126     192 .. 0.93
   4 ?   11.7  10.8   0.00046      0.28      34     108 ..     177     255 ..     172     269 .. 0.93
   5 ?    0.3   0.2       1.6   9.3e+02      54      81 ..     269     295 ..     256     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0065
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT.....TCCHHHHHHHHHHHHHHHHHHH CS
                          FlgN  36 dieaLeelleekqellekleqleqkrakllaelglsaeeatlsellak.....eedeelkelwqelkelleelke 105
                                    +e+L +   ek +l++++++l+qkr++ +++l+    ++ l+++ ++     +e ++lk+++q l +++ e+k+
  gi|70607097|ref|YP_255967.1|  19 AVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSI--RQQLQQIREEikskiNEITQLKSQRQNLIQIIGEIKK 91 
                                   5778888889999*****************999999..4555555554554677777777777777777777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.9
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.SCHHHHHHH CS
                          FlgN 38 eaLeelleekqellekleqleqkrakllaelgls.aeeatlsel 80
                                  ++L+++ ee+++ +++++ql+ +r++l++ +g+  +e ++l+++
  gi|70607097|ref|YP_255967.1| 56 QQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIkKEFEELKNV 99
                                  5799999*******************999999985333333333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.035
                                   HHHHHHHHHHHHHHHHHHHHHHHHTT--.SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHH CS
                          FlgN  44 leekqellekleqleqkrakllaelgls.aeeatlsellakeedeelkelwqelkelleelkeln 107
                                   lee+++++ k+++le+k++ + + ++ + ++++   ella  ++ el +++q+  el +++k + 
  gi|70607097|ref|YP_255967.1| 129 LEEEKKIIIKIAELERKLEVAKKVAQIKeKNTENRAELLA--KRVELSTIRQKMLELSQQIKSKK 191
                                   799****************999999999889999999**9..*******************9876 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00046
                                   TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--..SCHHHHHHHHCT..TCCHHHHHHHHHHHHHHHHHHHHHH CS
                          FlgN  34 agdieaLeelleekqellekleqleqkrakllaelgls..aeeatlsellak..eedeelkelwqelkelleelkelne 108
                                   ++++ +L + ++ k+ell+kl+ + + ++k l++l+++  + ++ ++el ak  e+ +e+  + +elk++ ee++++n 
  gi|70607097|ref|YP_255967.1| 177 RQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKiqDLNKRIDELTAKvnEKGNEIGRIKEELKKRREEVRNMNV 255
                                   568999*********************************9999********************************9996 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHTT--SCHHHHHHHH CS
                          FlgN  54 leqleqkrakllaelglsaeeatlsell 81 
                                    e+le+kr ++ ++l+++ ++++ +ell
  gi|70607097|ref|YP_255967.1| 269 SEALENKRKQVEEKLKNN-KRLSFDELL 295
                                   578899999999999988.677777765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1  21.5       2.9   1.7e+03       3      83 ..      22     101 ..       3     172 .. 0.72
   2 ?   11.6  12.7   0.00019      0.12       3      88 ..     172     256 ..     169     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.9
                         TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                   e++++++e  +l ++ k++kqk +e  +  +++++++++ ++++k+  +++++lk++ +++  +++ e+k+e++e k+v k
  gi|70607097|ref|YP_255967.1|  22 ELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQ-RQNLIQIIGEIKKEFEELKNVTK 101
                                   455555555555555556666666666666666666666666666666666666655.34555555566666555555443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                         TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                   e++++++++ el+++ k+ k+ l++l++  + ++ke++  + ++++l++++++l+++v +e+ +e+ ++keelk+r++ ++
  gi|70607097|ref|YP_255967.1| 172 ELSTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELTAKV-NEKGNEIGRIKEELKKRREEVR 251
                                   56788899999999999999***********************************997.699999**************** PP

                         TMPIT  84 evesl 88 
                                   +++ +
  gi|70607097|ref|YP_255967.1| 252 NMNVT 256
                                   99765 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  45.0     0.022        13     296     480 ..      20     202 ..       2     206 .. 0.75
   2 ?    5.1  10.9     0.015       8.7     329     378 ..     205     254 ..     200     290 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                        DUF812 296 tkgsrfthaeklqftkeela..kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeen 374
                                    ++ r       +f++e+l+   ++++ ++ + ++ e+l+++++q+++++++i++  +ei +l+s+ + + + + e k+e 
  gi|70607097|ref|YP_255967.1|  20 VEELR-------KFKSEKLQliDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKKEF 93 
                                   22223.......4444433344558999999999999******************************************** PP

                        DUF812 375 eelekevklkkktlell..pdaeeniekLqalveasaqrlvelakqWe.khRvplieeyrelkesksekekeaerkleeik 452
                                   eel++ +k+k k+   +     e+   +Lq    + +++ + + k  e +++  + ++  + ke+++e ++e   k  e+ 
  gi|70607097|ref|YP_255967.1|  94 EELKNVTKVKDKLDPAAisRRIEQLEWRLQTSTLTLEEEKKIIIKIAElERKLEVAKKVAQIKEKNTENRAELLAKRVELS 174
                                   ************9655521334444445665443333333333333341566678899*********************** PP

                        DUF812 453 klrekmkevaeelrqkeellkqLvaele 480
                                    +r+km e+++++++k+ell++L++e +
  gi|70607097|ref|YP_255967.1| 175 TIRQKMLELSQQIKSKKELLQKLKSERD 202
                                   ************************9976 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                        DUF812 329 eeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneele 378
                                   ++ele+l+++i++l+++i+el++++++  ++i +++eel++++ee  + +
  gi|70607097|ref|YP_255967.1| 205 QKELEDLNTKIQDLNKRIDELTAKVNEKGNEIGRIKEELKKRREEVRNMN 254
                                   56677777777777777777777777777777777777766666544433 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8  22.4       7.5   4.5e+03       9      99 ..      11     101 ..       2     150 .. 0.35
   2 ?   10.6  28.0    0.0006      0.36      17     164 ..     146     292 ..     137     310 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.5
                           ERM   9 eleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreael 89 
                                   e++er  +  ee +k + +  +  +++++L++k+r+  e+ +   q+ ++++eei+    +  + ++++++l + + e + 
  gi|70607097|ref|YP_255967.1|  11 EIQERYSKAVEELRKFKSEKLQLIDEVKKLKQKRREKVEKLKSIRQQLQQIREEIKSKINEITQLKSQRQNLIQIIGEIKK 91 
                                   333333333333333333333333333333333333322222222222222222222222222222222222222222222 PP

                           ERM  90 eaarleeese 99 
                                   e+++l++  +
  gi|70607097|ref|YP_255967.1|  92 EFEELKNVTK 101
                                   2222222222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0006
                           ERM  17 lqeeaekaqeaLreseetaelLaekar..raeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarle 95 
                                   l+   + aq + ++ e++aelLa++ +    ++++ +L+q+ +  +e  q+lk ++   ++e e+l++k+++ + ++ +l+
  gi|70607097|ref|YP_255967.1| 146 LEVAKKVAQIKEKNTENRAELLAKRVElsTIRQKMLELSQQIKSKKELLQKLKSERDVIQKELEDLNTKIQDLNKRIDELT 226
                                   3445567888889999*******9765115677778888999999************************************ PP

                           ERM  96 eeserkeeeaerLkeeleeareaeeeakekllealstpskseseenveeseteeeeenseeesaeletd 164
                                    ++++k +e  r keel++ re+ ++++  + ++ +++ +s+ +++  e++++ + e++ ++++ l+ d
  gi|70607097|ref|YP_255967.1| 227 AKVNEKGNEIGRIKEELKKRREEVRNMN--VTDLYEQQLRSTINSEALENKRK-QVEEKLKNNKRLSFD 292
                                   *******************999997766..34444444333222222222222.223444455555544 PP

>> DASH_Dad1  DASH complex subunit Dad1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.2   1.9e+03       2      15 ..      26      39 ..      25      52 .. 0.81
   2 ?    1.0   2.9      0.81   4.8e+02      10      44 ..      58      96 ..      51      99 .. 0.55
   3 ?    2.0   0.2       0.4   2.4e+02       8      21 ..      84      97 ..      76     106 .. 0.71
   4 ?    1.0   0.0      0.85   5.1e+02      19      37 ..     134     152 ..     129     155 .. 0.81
   5 ?    7.7   0.4    0.0066       3.9      13      36 ..     204     227 ..     181     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.2
                     DASH_Dad1  2 FerqRdrliqeIae 15
                                  F+ ++ +li e+ +
  gi|70607097|ref|YP_255967.1| 26 FKSEKLQLIDEVKK 39
                                  999999***99987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.81
                     DASH_Dad1 10 iqeIaesmeevlnnlnaLN...RsLEevi.avgkeFesV 44
                                  +q+I+e++++ +n + +L    ++L ++i ++ keFe++
  gi|70607097|ref|YP_255967.1| 58 LQQIREEIKSKINEITQLKsqrQNLIQIIgEIKKEFEEL 96
                                  567777777777777776522133333331356666655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.4
                     DASH_Dad1  8 rliqeIaesmeevl 21
                                  ++i eI +++ee+ 
  gi|70607097|ref|YP_255967.1| 84 QIIGEIKKEFEELK 97
                                  35668999998864 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.85
                     DASH_Dad1  19 evlnnlnaLNRsLEeviav 37 
                                   +++ ++  L R+LE + +v
  gi|70607097|ref|YP_255967.1| 134 KIIIKIAELERKLEVAKKV 152
                                   67778999******88877 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0066
                     DASH_Dad1  13 IaesmeevlnnlnaLNRsLEevia 36 
                                   I +++e++ +++ +LN++++e++a
  gi|70607097|ref|YP_255967.1| 204 IQKELEDLNTKIQDLNKRIDELTA 227
                                   8899***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4415  (0.246249); expected 358.6 (0.02)
Passed bias filter:                      802  (0.044732); expected 358.6 (0.02)
Passed Vit filter:                       298  (0.0166211); expected 17.9 (0.001)
Passed Fwd filter:                       170  (0.00948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 2.35u 0.42s 00:00:02.77 Elapsed: 00:00:00.70
# Mc/sec: 1341.13
//
Query:       gi|70607098|ref|YP_255968.1|  [L=90]
Description: H/ACA RNA-protein complex component Gar1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   16.8   0.0     0.0049   16.7   0.0    1.1  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.7e-07    0.0049      44      75 ..      32      63 ..       2      73 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.7e-07
                                  -B--BTT-EEEETT--EEEE--EEES-SSS-E CS
                          Gar1 44 kkvldfnsilflenktqiGkVdEifGpvnepy 75
                                  +k  + + ++ +e+++ + k+ +++G+v+ py
  gi|70607098|ref|YP_255968.1| 32 SKQEYTGKVILDEKGNRVAKILDVIGNVKAPY 63
                                  4557999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 607.23
//
Query:       gi|70607099|ref|YP_255969.1|  [L=291]
Description: transcription initiation factor B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-23   80.3   0.3    4.7e-14   52.2   0.0    2.3  2  TFIIB           Transcription factor TFIIB repeat
    1.8e-14   53.0   0.5    2.9e-14   52.3   0.5    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0002   21.0   1.7    0.00046   19.8   1.7    1.6  1  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0018   17.8   1.1     0.0034   16.9   0.1    2.1  2  Sigma70_r4      Sigma-70, region 4
     0.0052   16.5   0.2     0.0097   15.6   0.2    1.5  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.015   15.0   0.2      0.046   13.4   0.2    1.8  1  Sigma70_r4_2    Sigma-70, region 4
      0.018   15.0   0.2       0.12   12.3   0.2    2.2  2  MA3             MA3 domain
      0.042   13.4   2.6      0.058   12.9   0.1    2.3  2  GerE            Bacterial regulatory proteins, luxR family
      0.071   13.1   0.2       0.21   11.5   0.2    1.9  1  HTH_11          HTH domain
      0.088   12.8   0.9       0.23   11.5   0.1    2.1  2  DUF2089         Protein of unknown function (DUF2089)
      0.096   12.5   0.0       0.29   11.0   0.0    1.8  1  HTH_23          Homeodomain-like domain
       0.56   10.1   2.3          5    7.1   0.0    2.9  3  Terminase_5     Putative ATPase subunit of terminase (gpP-lik


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   4.1e-09   6.1e-06       5      65 ..     112     172 ..     108     178 .. 0.92
   2 !   52.2   0.0   3.1e-17   4.7e-14       1      71 []     204     274 ..     204     274 .. 0.99

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.1e-09
                                   HHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS CS
                         TFIIB   5 adaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlq 65 
                                   a++l+Lpe V++ A  l+++  ee+  k   + +++AA++y  c+ ++  + + ei  +  
  gi|70607099|ref|YP_255969.1| 112 ASKLNLPEHVKETASILIRRLIEEGKAKRVEMYALIAAVIYYSCQVNRIPKLLNEIKTLYS 172
                                   89**************************9***************************87765 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 3.1e-17
                                   HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                         TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                   i+++ ++l+Lp +V  +A el++ ++++++++G+  +++aAA++y+ + +  vk+tqkei++ l ++e+ti
  gi|70607099|ref|YP_255969.1| 204 IPKITERLGLPAYVSTKASELVDIMYKNGLTSGKGYTALAAASVYLISTLMDVKKTQKEIADSLSITEVTI 274
                                   7899*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.5   1.9e-17   2.9e-14       1      42 [.       1      42 [.       1      43 [. 0.98

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.9e-17
                                  EEETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHH CS
                  TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVlednsidegpewre 42
                                  +kC++Cgs++l++D erg +vC +C +V ++  id gpewr+
  gi|70607099|ref|YP_255969.1|  1 MKCKICGSESLIFDRERGIYVCINCASVDDEPLIDQGPEWRA 42
                                  89***************************************8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.7   3.1e-07   0.00046       5      29 ..       2      27 ..       1      29 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                 A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCga 29
                                  +C+ Cg++ ++  +e+g++vCi+C +
  gi|70607099|ref|YP_255969.1|  2 KCKICGSESLIFdRERGIYVCINCAS 27
                                  8***********************65 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       5.8   8.7e+03      36      43 ..      93     100 ..      93     103 .. 0.59
   2 !   16.9   0.1   2.3e-06    0.0034      20      46 ..     257     283 ..     247     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.8
                                   HHHHHHHH CS
                    Sigma70_r4  36 rVrqiekr 43 
                                   rV+ +e++
  gi|70607099|ref|YP_255969.1|  93 RVSARERK 100
                                   56666665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.3e-06
                                   T--HHHHHHHHTS-HHHHHHHHHHHHH CS
                    Sigma70_r4  20 glTleEIgerlgiSrerVrqiekrAlr 46 
                                   + T++EI++ l i++ ++r + ++ ++
  gi|70607099|ref|YP_255969.1| 257 KKTQKEIADSLSITEVTIRNRYREIIK 283
                                   67*******************998875 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   6.5e-06    0.0097       9      36 ..       2      29 ..       1      33 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.5e-06
                                  E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                  kC+ C+ e  +F++   +  Ci C++v 
  gi|70607099|ref|YP_255969.1|  2 KCKICGSESLIFDRERGIYVCINCASVD 29
                                  9***********************9985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.1e-05     0.046      28      48 ..     259     279 ..     257     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                   -HHHHHHHHT--HHHHHHHHH CS
                  Sigma70_r4_2  28 sykEIAellgisegtVksrls 48 
                                   ++kEIA  l i+e+t+++r++
  gi|70607099|ref|YP_255969.1| 259 TQKEIADSLSITEVTIRNRYR 279
                                   89*****************97 PP

>> MA3  MA3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   8.2e-05      0.12      27      71 ..     114     157 ..     108     193 .. 0.80
   2 ?    0.6   0.0      0.36   5.4e+02      57      90 ..     161     194 ..     156     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.2e-05
                                   HTT--TTHHHHHHHHHHHHHHS..SS--HHHHHHHHHHHCC-HHHH CS
                           MA3  27 kLklpkqeheivkillecalee.sktyneyygllleklceknlilk 71 
                                   kL+lp+ ++e+++il+  ++ee +++  e+y+l+++ ++  ++   
  gi|70607099|ref|YP_255969.1| 114 KLNLPEHVKETASILIRRLIEEgKAKRVEMYALIAAVIY--YSCQV 157
                                   9*********************999999******99998..44444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.36
                                   HHHHHHHHCC-HHHHHHHHHHHHHHHHGGGGS-H CS
                           MA3  57 gllleklceknlilkkqfekgfwdvlesledlel 90 
                                    +ll+++ + ++++++++ k++++v e +   ++
  gi|70607099|ref|YP_255969.1| 161 PKLLNEIKTLYSLSQADLWKALEKVQEVAKSVKV 194
                                   5899999999999999999999988876665555 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3         1   1.5e+03      34      48 ..      80      95 ..      77     102 .. 0.73
   2 ?   12.9   0.1   3.9e-05     0.058      18      43 ..     258     283 ..     254     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                                  HHHHHHHHHH.HHT-S CS
                          GerE 34 Vkvhksnimk.KLnvk 48
                                  +kvhk ++m+ K++v 
  gi|70607099|ref|YP_255969.1| 80 IKVHKLRLMQnKIRVS 95
                                  7889888775366665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.9e-05
                                   S-HHHHHHHHTS-HHHHHHHHHHHHH CS
                          GerE  18 ksnkeIAeelniSekTVkvhksnimk 43 
                                   k+ keIA++l+i e T+++  ++i k
  gi|70607099|ref|YP_255969.1| 258 KTQKEIADSLSITEVTIRNRYREIIK 283
                                   789****************9999977 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00014      0.21      17      42 ..     259     284 ..     248     290 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                        HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaLeel 42 
                                   + +e+A+ L++++ t+r++ +++ ++
  gi|70607099|ref|YP_255969.1| 259 TQKEIADSLSITEVTIRNRYREIIKA 284
                                   889***************87776555 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.6   2.3e+03      21      21 ..      93      93 ..      64     144 .. 0.59
   2 ?   11.5   0.1   0.00016      0.23      31      81 ..     239     289 ..     226     291 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                       DUF2089 21 t 21
                                  +
  gi|70607099|ref|YP_255969.1| 93 R 93
                                  2 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00016
                       DUF2089  31 farLskeqlefvelfikarGnlkevekelgisYpTvrnrldeileaLgyee 81 
                                   ++ L + +  ++ +++ ++   ke++ +l i+  T+rnr  ei++a+++e 
  gi|70607099|ref|YP_255969.1| 239 YTALAAASVYLISTLMDVKKTQKEIADSLSITEVTIRNRYREIIKAFDIEV 289
                                   67888999999***********************************99886 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.29      12      37 ..     252     278 ..     247     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                        HTH_23  12 lllaeGlsvreIAreLgvsrrTvy.rw 37 
                                    l +++++++eIA+ L +++ T++ r+
  gi|70607099|ref|YP_255969.1| 252 TLMDVKKTQKEIADSLSITEVTIRnRY 278
                                   566779*****************9333 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.5   3.7e+03      38      50 ..      39      51 ..      38      53 .. 0.87
   2 ?    7.1   0.0    0.0034         5      27      52 ..     167     192 ..     148     195 .. 0.86
   3 ?    1.5   0.1      0.18   2.7e+02      16      31 ..     260     275 ..     258     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                   Terminase_5 38 ewddldplsrvee 50
                                  ew++++ +++ve+
  gi|70607099|ref|YP_255969.1| 39 EWRAYTTEDKVER 51
                                  7999999999986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0034
                   Terminase_5  27 eatVysWkkrdewddldplsrveeai 52 
                                    +t ys  ++d w++l +++ v +++
  gi|70607099|ref|YP_255969.1| 167 IKTLYSLSQADLWKALEKVQEVAKSV 192
                                   58********************9987 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.18
                   Terminase_5  16 vaeIAeelglkeatVy 31 
                                    +eIA  l + e t+ 
  gi|70607099|ref|YP_255969.1| 260 QKEIADSLSITEVTIR 275
                                   689*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2054.98
//
Query:       gi|70607100|ref|YP_255970.1|  [L=138]
Description: hypothetical protein Saci_1342 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-11   42.7   4.2    2.3e-08   33.8   1.6    2.0  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
    0.00011   22.3   0.3    0.00019   21.5   0.3    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0011   18.5   0.1     0.0021   17.6   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.067   12.9   3.1       0.13   12.0   3.1    1.4  1  DUF2963         Protein of unknown function (DUF2963)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   1.6   5.2e-12   2.3e-08      84     141 ..      19      75 ..      15      84 .. 0.89
   2 !   11.0   0.3   4.6e-05       0.2     272     333 ..      71     129 ..      68     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.2e-12
                                   SXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSS CS
                 RNA_pol_Rpc34  84 lsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkap 141
                                    s+ e+l+y+ I+e+G +GI +r++ + l+L   v + ++k L  +k ik+ ks+k  
  gi|70607100|ref|YP_255970.1|  19 SSSYEELIYQKIKEAGDKGIPQRDLIKNLGLDARVANTVIKKLIEQKKIKK-KSIKEN 75 
                                   577899*******************************************97.666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.6e-05
                                   EEEETTHHHHHCCTTTTS.XXXXXXXSSSSSTTXXSSXSSSSSXXTSSSSSSSSSSTTSSSS CS
                 RNA_pol_Rpc34 272 vqratkqnvlrltskrrkeakvvqpealasglveapcgecpvfdlceeggavspkncvYlke 333
                                   +++++++nv +l+ +++   + +   +  +++ve+pc +c  +++c +gg   p++c  l +
  gi|70607100|ref|YP_255970.1|  71 SIKENGKNVIKLFPNEE---ERIVIYVKLENIVEVPCFTCKNLSKCGNGGITTPSSCSILSK 129
                                   55666666666655444...344455566899*************************98876 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   4.3e-08   0.00019      12      60 ..      31      75 ..      25      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-08
                B-block_TFIIIC 12 assRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkk 60
                                    ++++Gi q+dL+k ++ d+r    ++k+L +++ I+k+si    +++
  gi|70607100|ref|YP_255970.1| 31 KEAGDKGIPQRDLIKNLGLDARVANTVIKKLIEQKKIKKKSI----KEN 75
                                  56789*************************************....333 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.7e-07    0.0021      15      48 .]      35      68 ..      26      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.7e-07
                        HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  + +i+qr+L + lgl     n+ +k+L+e+  Ik
  gi|70607100|ref|YP_255970.1| 35 DKGIPQRDLIKNLGLDARVANTVIKKLIEQKKIK 68
                                  789**************************98775 PP

>> DUF2963  Protein of unknown function (DUF2963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.1   2.8e-05      0.13      19      46 ..      64      89 ..      58      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                       DUF2963 19 gkkiKrtnYqedGktinsIeeyDdeeek 46
                                  +kkiK++ ++e+G   n I+ + +eee 
  gi|70607100|ref|YP_255970.1| 64 QKKIKKKSIKENG--KNVIKLFPNEEER 89
                                  9************..6678888866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 907.56
//
Query:       gi|70607101|ref|YP_255971.1|  [L=382]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-85  287.8   0.6    1.5e-85  287.7   0.6    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0057   16.4   0.0     0.0083   15.9   0.0    1.4  1  Met_10           Met-10+ like-protein
      0.006   16.1   0.2      0.016   14.8   0.0    1.7  2  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.01   15.7   0.6      0.022   14.7   0.6    1.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.015   15.0   0.0      0.029   14.1   0.0    1.4  1  Methyltransf_16  Lysine methyltransferase
      0.054   12.8   0.0       0.11   11.8   0.0    1.4  1  DNA_methylase    C-5 cytosine-specific DNA methylase
      0.091   12.7   1.7       0.19   11.7   1.7    1.4  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.096   12.1   0.3       0.14   11.5   0.3    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.096   12.7   0.1       0.19   11.8   0.1    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.26   10.7   2.4       0.28   10.6   0.7    1.9  2  zf_Rg            Reverse gyrase zinc finger
       0.77    9.9   4.7        1.8    8.7   4.7    1.6  1  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.7   0.6   9.2e-89   1.5e-85      15     375 ..      29     373 ..       9     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 287.7 bits;  conditional E-value: 9.2e-89
                                   -TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHH CS
                           TRM  15 skkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvk 95 
                                   ++ ++VFYNP +  nRDlsvl+    ++ k k     +++d+Lsa+G+R+iR+ lE++gv+e+++NDi + Avelik+Nvk
  gi|70607101|ref|YP_255971.1|  29 PSWAPVFYNPKMILNRDLSVLA---ANVVKPK-----SLIDGLSATGVRGIRYGLEINGVEEIILNDIDSDAVELIKKNVK 101
                                   56689*****************...9999999.....8******************************************* PP

                                   HTT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB-- CS
                           TRM  96 lneveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgaval 176
                                   +n+ e + +i +++ n ll+  + + d++D+DPfGspapfl s   ++k+k ++++TaTD+a+L  +s+ +  rkYg    
  gi|70607101|ref|YP_255971.1| 102 INDLESRAKIYNNNINSLLH--EIKVDYVDIDPFGSPAPFLLSSFSAAKSKQYVAITATDLAALMCSSKTSARRKYGLICN 180
                                   *****99999999******5..567899***************************************************** PP

                                   -STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--GGG- CS
                           TRM 177 kselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkglakf 257
                                   k+ +  E +lR l+++  +eaa  ekav+p++s+++d+Y+rv +kv++ga+kv++ l+kl++ ++C +C  + + + l++ 
  gi|70607101|ref|YP_255971.1| 181 KMSFSRELGLRGLISKAITEAAVVEKAVTPVFSFYNDYYYRVIFKVERGAKKVDRQLSKLVYYYECPKCGYRIESEYLQQ- 260
                                   *********************************************************************88666666666. PP

                                   -SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS--- CS
                           TRM 258 kaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyydlsqlasvlklsvppl 338
                                     +c++c+  ++ +GP + + l d ef+++++ e++k +  ++  ++k +L +ik+E+  +  yy ++ las  +++vp+ 
  gi|70607101|ref|YP_255971.1| 261 -MKCTNCNLVMQTYGPAYKESLVDYEFLNNMISELDKFSYFQTFSKLKSILLTIKDESKYSENYYRIDFLASLARVNVPRR 340
                                   .79**********************************88888899************************************ PP

                                   HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                           TRM 339 kkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                   ++v++ l      +srtH+ p ++kT  +l+++ e +
  gi|70607101|ref|YP_255971.1| 341 DNVINCL----VDASRTHLDPLGVKTSKNLDEIKECI 373
                                   *******....789****************9998865 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.1e-06    0.0083      74     191 ..      25     147 ..       2     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                                   EEEET..TTS---GGGHHHHH..HHHTT--TT-EEEETT-TTTCCHHHCCHHTTS.SEEEEEES-HHHHHHHHHHHHHTT- CS
                        Met_10  74 fklDv..skvyfsskleaEre..rlaklveegevVvdvfAGiGpfaipiakyska.krvlaidlnPesvkylkeniklNkv 149
                                    k+D   + v++++k +  r    la+ v + +  +d +   G   i  +   ++ ++++ +d++ ++v+++k+n+k N++
  gi|70607101|ref|YP_255971.1|  25 GKFDPswAPVFYNPKMILNRDlsVLAANVVKPKSLIDGLSATGVRGIRYGLEINGvEEIILNDIDSDAVELIKKNVKINDL 105
                                   5555411467777776665542156666666667777777777777777765554157999******************** PP

                                   TTCEEEEES-GGG---TT-EEEEEE--TTTGGGGHHHHHHHE CS
                        Met_10 150 ekvvkpileDgrevireqladrvvmnlpksaieFldkvlaal 191
                                   e++ k +++  + +++e ++d v ++   s   Fl + ++a+
  gi|70607101|ref|YP_255971.1| 106 ESRAKIYNNNINSLLHEIKVDYVDIDPFGSPAPFLLSSFSAA 147
                                   ********9999999888888766666666666655555544 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   9.9e-06     0.016      36     101 ..      60     128 ..      46     136 .. 0.81
   2 ?   -2.4   0.0       1.9   3.1e+03      49      78 ..     145     173 ..     140     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.9e-06
                                   EEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEE CS
                           MTS  36 lDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleeveekkfdli 101
                                   +D  + +Gv g+    e + +e + l d+d  A+e+ k+n++ n+le  ++++++++ + ++e k+d++
  gi|70607101|ref|YP_255971.1|  60 IDGLSATGVRGIRYGLEINGVEeIILNDIDSDAVELIKKNVKINDLEsrAKIYNNNINSLLHEIKVDYV 128
                                   5555566777777766666665599**********************99**********9999999998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                                   HHHHTTC.EEEEEESBHHHHHHHHHHHHHT CS
                           MTS  49 lakespeaevtlvdvdarAlesakenlean 78 
                                    a++s++  v ++  d +Al ++ ++ ++ 
  gi|70607101|ref|YP_255971.1| 145 SAAKSKQ-YVAITATDLAALMCSSKTSARR 173
                                   3443333.5777777888998888887665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   1.3e-05     0.022      30      56 ..     245     270 ..     219     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfea 56 
                                   +C++Cg++ +     +++kC+nC++++
  gi|70607101|ref|YP_255971.1| 245 ECPKCGYRIES-EYLQQMKCTNCNLVM 270
                                   8**********.999********9876 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.029      43     101 ..      52     110 ..      30     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
               Methyltransf_16  43 nelsklsvlELGsGtGlvGlavaell.peakviltDlee.llellkknielnknalkskvk 101
                                   n ++++s ++  s tG+ G+   + + +  ++il D++  ++el+kkn+++n+  l+s++k
  gi|70607101|ref|YP_255971.1|  52 NVVKPKSLIDGLSATGVRGIRYGLEInGVEEIILNDIDSdAVELIKKNVKIND--LESRAK 110
                                   55666667776699***********868899******977***********87..555444 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-05      0.11       9      59 ..      67     117 ..      64     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                                   TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS-GS- CS
                 DNA_methylase   9 GiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkkklp 59 
                                   G+ G+r+gle  g+e ++ ++id +a+++ ++n k  +++   ki ++++ 
  gi|70607101|ref|YP_255971.1|  67 GVRGIRYGLEINGVEEIILNDIDSDAVELIKKNVKINDLESRAKIYNNNIN 117
                                   999*******************************87777777777666443 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.7   0.00011      0.19      14      37 ..     246     269 ..     243     271 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                   -TTT-SB--SSSS-EEEETTT--E CS
                          C1_1  14 CkhCgeflwgkekqglkCswCkll 37 
                                   C +Cg  ++ + +q +kC++C+l+
  gi|70607101|ref|YP_255971.1| 246 CPKCGYRIESEYLQQMKCTNCNLV 269
                                   99******77***********986 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   8.8e-05      0.14     183     229 ..      79     127 ..      46     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                          PrmA 183 gakkvvavDiDevAvkvakeNaelNkveakleval..seellkeekadv 229
                                   g ++++  DiD+ Av+  k+N+++N++e++ ++++   ++ll+e k+d 
  gi|70607101|ref|YP_255971.1|  79 GVEEIILNDIDSDAVELIKKNVKINDLESRAKIYNnnINSLLHEIKVDY 127
                                   78899999*********************99996411355555666665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.19      64      93 ..     237     267 ..     198     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   EEEE--EEEETTTS-EEECHH.HHHS-TTTS CS
                          HypA  64 ieevpvkvrCreCgkefelee.kalrCpkCg 93 
                                   +++    ++C +Cg+++e+e  ++++C +C+
  gi|70607101|ref|YP_255971.1| 237 LSKLVYYYECPKCGYRIESEYlQQMKCTNCN 267
                                   555666789*********9985599*****7 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8     3e+03      19      30 ..     170     181 ..     168     181 .. 0.81
   2 ?   10.6   0.7   0.00017      0.28       2      31 ..     238     266 ..     237     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                         zf_Rg  19 deRlekGLpCkr 30 
                                   + R + GL C++
  gi|70607101|ref|YP_255971.1| 170 SARRKYGLICNK 181
                                   568899****85 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                         zf_Rg   2 ikavfeklCPNCgGdisdeRlekGLpCkrC 31 
                                   +k+v+   CP Cg  i++e l++ + C++C
  gi|70607101|ref|YP_255971.1| 238 SKLVYYYECPKCGYRIESEYLQQ-MKCTNC 266
                                   6899999*************998.899999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.7    0.0011       1.8       3      33 ..     241     267 ..     241     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                   Zn-ribbon_8   3 iYeYrCeeCghefe..vlqsisdapltaCPeCg 33 
                                   +Y Y+C +Cg + e   lq+++      C +C+
  gi|70607101|ref|YP_255971.1| 241 VYYYECPKCGYRIEseYLQQMK------CTNCN 267
                                   699**********977777665......88885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2825.04
//
Query:       gi|70607102|ref|YP_255972.1|  [L=305]
Description: HTH DNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.6   0.1    9.4e-10   38.4   0.1    1.7  1  HTH_3     Helix-turn-helix
    6.1e-07   29.4   0.4    1.7e-06   27.9   0.4    1.8  1  HTH_19    Helix-turn-helix domain
    8.7e-05   22.9   0.0    0.00022   21.6   0.0    1.7  1  HTH_26    Cro/C1-type HTH DNA-binding domain
    0.00064   20.0   0.0      0.001   19.4   0.0    1.3  1  HTH_31    Helix-turn-helix domain
     0.0026   17.6   0.6      0.011   15.6   0.6    2.1  1  Takusan   Takusan
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.059   13.3   0.0    2.1  1  HTH_11    HTH domain
      0.019   15.1   0.9      0.038   14.2   0.4    1.7  2  RTP1_C1   Required for nuclear transport of RNA pol II C-term
      0.021   14.7   0.0       0.04   13.8   0.0    1.5  1  HTH_25    Helix-turn-helix domain
      0.069   13.0   0.3       0.36   10.7   0.0    2.3  2  UvrB      Ultra-violet resistance protein B


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.1   4.7e-13   9.4e-10       1      49 [.     128     176 ..     128     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.7e-13
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49 
                                   l+e+R+++++s+ eL+++lGvsr +++++E+ ++  s+e+++kl + +g
  gi|70607102|ref|YP_255972.1| 128 LREKREEKNMSLGELSQRLGVSRISVYDYEKEDSYVSIEVAEKLIEIFG 176
                                   89********************************************998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.4   8.7e-10   1.7e-06       3      55 ..     127     178 ..     126     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.7e-10
                        HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                   +L+e Ree+++++ el++rlg+sr + + +E++ + + s+e+  k+ e++g +
  gi|70607102|ref|YP_255972.1| 127 KLREKREEKNMSLGELSQRLGVSRISVYDYEKEDS-YVSIEVAEKLIEIFGDE 178
                                   79********************************9.**************987 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.1e-07   0.00022       1      59 [.     127     185 ..     127     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                        HTH_26   1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgct.pgDLle 59 
                                   kLre   +++++  eL++++g+s+ +++ + k+  ++vs+++ +k+ +++g + +gD+++
  gi|70607102|ref|YP_255972.1| 127 KLREKREEKNMSLGELSQRLGVSRISVYDYEKED-SYVSIEVAEKLIEIFGDEvIGDIIK 185
                                   799******************************9.7************999887888875 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.2e-07     0.001       6      55 ..     128     176 ..     125     178 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                        HTH_31   6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                   Lr+ Re+ ++s+ e+ +rlgvs+  + ++E      +s +v e+l +++g
  gi|70607102|ref|YP_255972.1| 128 LREKREEKNMSLGELSQRLGVSRISVYDYEKEDSY-VSIEVAEKLIEIFG 176
                                   9999******************************8.********998876 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   5.7e-06     0.011      25      63 ..      29      67 ..      25      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.7e-06
                       Takusan 25 eLrkitreRdELrdiLalytegslndrpsvrlnpeyekL 63
                                   +  it+e ++ r+iL l +++s+ dr+++r+ ++++k+
  gi|70607102|ref|YP_255972.1| 29 SIDIITEEQNDKRRILVLKINNSTSDRRNFRILFDLKKI 67
                                  56779***************************9999987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.059      11      33 ..     132     154 ..     125     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                        HTH_11  11 eargpisgeeLAeeLnvSrrtvr 33 
                                   ++++++s  eL+++L+vSr  v+
  gi|70607102|ref|YP_255972.1| 132 REEKNMSLGELSQRLGVSRISVY 154
                                   34556**************9888 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.9e-05     0.038      41     108 ..     148     217 ..     124     220 .. 0.76
   2 ?   -3.2   0.0       4.7   9.5e+03      49      80 ..     235     254 ..     230     268 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                       RTP1_C1  41 ilkllleaLkdedsYvYLnaikgLvaLadvfpeevlklLleey.....eeenekeslderlkvGEaLlrvirr 108
                                   + ++ +   ++edsYv   +i++ ++L+++f +ev+  +++ y     ++++ +++ +e +k+ E L rv+ +
  gi|70607102|ref|YP_255972.1| 148 VSRISVYDYEKEDSYV---SIEVAEKLIEIFGDEVIGDIIKDYdsntkKKKELQSDYNEEVKILEKLDRVLSD 217
                                   5555555667899**9...88899999****************877655555666888999999999888765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.7
                       RTP1_C1  49 LkdedsYvYLnaikgLvaLadvfpeevlklLl 80 
                                   +k +++ ++   +++L++             l
  gi|70607102|ref|YP_255972.1| 235 IKGSEKLIFCTEVNTLAN------------SL 254
                                   344444444444444443............33 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-05      0.04       2      24 ..     128     150 ..     127     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                   HHHHHHTTT--HHHHHHHSS--H CS
                        HTH_25   2 LraaRearglsleevaketkIrk 24 
                                   Lr++Re++++sl e+++++ ++ 
  gi|70607102|ref|YP_255972.1| 128 LREKREEKNMSLGELSQRLGVSR 150
                                   9******************9985 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.36      16      33 ..     190     207 ..     182     210 .. 0.90
   2 ?   -1.8   0.1       1.5   2.9e+03      26      34 ..     256     264 ..     255     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                   HHHHHHHHHHHHHHHHT- CS
                          UvrB  16 eTerRReiQeaYNeehgI 33 
                                    T++++e+Q +YNee +I
  gi|70607102|ref|YP_255972.1| 190 NTKKKKELQSDYNEEVKI 207
                                   79*************887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                   HHHHHHT-- CS
                          UvrB  26 aYNeehgIt 34 
                                   ++Ne+++I 
  gi|70607102|ref|YP_255972.1| 256 KFNEANKIA 264
                                   89***9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1989.19
//
Query:       gi|70607103|ref|YP_255973.1|  [L=142]
Description: hypothetical protein Saci_1345 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-25   89.2   0.2    2.5e-25   89.0   0.2    1.0  1  DUF61     Protein of unknown function DUF61


Domain annotation for each model (and alignments):
>> DUF61  Protein of unknown function DUF61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.2   1.4e-29   2.5e-25       1     125 [.       3     123 ..       3     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.4e-29
                                   -S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE..EE CS
                         DUF61   1 drilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelgesvyl 81 
                                   d++++  +ks+ + +P+e +tLk++L+++ ++ ++ ++ +hrfdk e+ekl+++lp +lwd +kLP+++ ++ ++ge  y 
  gi|70607103|ref|YP_255973.1|   3 DKVFDLGFKSLLSYYPDEFVTLKDALNGKLSIRLKSKDLRHRFDKLEVEKLSQVLPIYLWDLVKLPFIVVKTLNTGE--YA 81 
                                   6899999*******************************************************************888..** PP

                                   EES-HH.HHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST...T CS
                         DUF61  82 vrgkae.vkvvskilgkereeedelviykpevrelrrklptatql 125
                                   v+g+++ v+ +s+il+ke    +++++++ +v++l++++++++ +
  gi|70607103|ref|YP_255973.1|  82 VSGSQWeVRSLSIILQKE---IKNTFLSTGDVEKLIKEYKSLIFI 123
                                   ******************...9*******************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 942.34
//
Query:       gi|70607104|ref|YP_255974.1|  [L=231]
Description: fibrillarin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   6.3e-101  336.2   0.2   7.3e-101  336.0   0.2    1.0  1  Fibrillarin  Fibrillarin
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.084   12.5   0.0    1.8  1  GCD14        tRNA methyltransferase complex GCD14 subunit
      0.044   13.5   0.0      0.082   12.7   0.0    1.4  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
       0.11   11.9   0.1       0.17   11.2   0.1    1.2  1  DUF1961      Domain of unknown function (DUF1961)
       0.11   13.0   0.1        1.2    9.7   0.0    2.3  2  Ntox33       Bacterial toxin 33


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.0   0.2    2e-104  7.3e-101       4     225 ..       9     231 .]       6     231 .] 0.99

  Alignments for each domain:
  == domain 1  score: 336.0 bits;  conditional E-value: 2e-104
                                   ECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSH CS
                   Fibrillarin   4 heklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGt 83 
                                   ++++++vy++  ++g++rl+tknl+pg++vYgE+lik+++ EyR+Wn+frsKla+ai+kglk  pi kgsk+LYlGaasGt
  gi|70607104|ref|YP_255974.1|   9 KTQFDNVYECIfNDGTTRLCTKNLSPGHNVYGERLIKYGGVEYREWNAFRSKLAGAIVKGLKYNPIVKGSKILYLGAASGT 89 
                                   679********9********************************************************************* PP

                                   HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHH CS
                   Fibrillarin  84 tvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklf 164
                                   t+sH+sDiv+ +g+vy+vefsprv+rel+ va+ R+n++Pil+DAr+P+ Y++lve+vD++++D+aqp++++i++ na++f
  gi|70607104|ref|YP_255974.1|  90 TPSHISDIVELQGKVYSVEFSPRVIRELLLVAQYRPNMFPILADARFPQYYKSLVENVDIVYVDIAQPNETEIAMYNARFF 170
                                   ********************************************************************************* PP

                                   EEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                   Fibrillarin 165 lkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                   lk++gy++i+ik+rsidvtk+p+e++++e +kl+++g+++ e+++l+py+kdha++v+kyk
  gi|70607104|ref|YP_255974.1| 171 LKKNGYMMIAIKSRSIDVTKDPREIYNAEAKKLEDAGFDIREVLELDPYDKDHAMIVVKYK 231
                                   **********************************************************996 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05     0.084      38     141 ..      74     177 ..      64     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                         GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDavf 118
                                   + +Gs+++  G+ sg+  + i+  v+ +G+++++ef  + +++    +   +   ++     D+    + + + ++vD v+
  gi|70607104|ref|YP_255974.1|  74 IVKGSKILYLGAASGTTPSHISDIVELQGKVYSVEFSPRVIREL---LLVAQYRPNMFPILADARFPQYYKSLVENVDIVY 151
                                   789*********************************86544332...2233333344444567777777788889999999 PP

                         GCD14 119 LDlPaPwe...aiphaakalkkeggr 141
                                   +D+ +P e   a+ +a   lkk+g +
  gi|70607104|ref|YP_255974.1| 152 VDIAQPNEteiAMYNARFFLKKNGYM 177
                                   99999987444556666666666655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.082      67     112 ..      70     115 ..      58     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                   HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHH CS
                          PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelve 112
                                   ++  + kg+++L +G+ sG     ++ +v+ +g+v s+e ++++++
  gi|70607104|ref|YP_255974.1|  70 KYNPIVKGSKILYLGAASGTTPSHISDIVELQGKVYSVEFSPRVIR 115
                                   4444999********************************9998765 PP

>> DUF1961  Domain of unknown function (DUF1961)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.8e-05      0.17      99     186 ..     134     223 ..     129     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                                   S-THHHHSSSEEEEEEEEEEESSHHHHTS-EEEEE...EETTTEEEEEEE-----GGG--S-EEEEEEEETTEEEEEETTE CS
                       DUF1961  99 Gsypqyhsgdinalhvsyfrrkweeerafhvanlr...kskGfhlvaqGadPlPdvedakgfyrielvkdkrevrfsindl 176
                                    ++pqy ++ ++ +++ y    +++e  + + n r   k +G+ ++a  +  +  ++d +++y+ e  k+ ++  f i ++
  gi|70607104|ref|YP_255974.1| 134 ARFPQYYKSLVENVDIVYVDIAQPNETEIAMYNARfflKKNGYMMIAIKSRSIDVTKDPREIYNAEA-KKLEDAGFDIREV 213
                                   579*************************999999877789************************996.6677889999888 PP

                                   EEEEEE--SS CS
                       DUF1961 177 pllewkdddk 186
                                   + l+  d+d+
  gi|70607104|ref|YP_255974.1| 214 LELDPYDKDH 223
                                   7777666655 PP

>> Ntox33  Bacterial toxin 33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.2   7.1e+02      15      35 ..     170     190 ..     166     192 .. 0.81
   2 ?    9.7   0.0   0.00034       1.2       5      25 ..     192     212 ..     188     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                        Ntox33  15 lLkkkGidahdlkgrgksisr 35 
                                   +Lkk+G+ +   k r+  + +
  gi|70607104|ref|YP_255974.1| 170 FLKKNGYMMIAIKSRSIDVTK 190
                                   8******99888888766655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                        Ntox33   5 dKslskgdiklLkkkGidahd 25 
                                   ++ + + + k+L+++G+d+++
  gi|70607104|ref|YP_255974.1| 192 PREIYNAEAKKLEDAGFDIRE 212
                                   7789999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1628.72
//
Query:       gi|70607105|ref|YP_255975.1|  [L=412]
Description: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-75  252.3   0.0    9.6e-75  251.0   0.0    1.6  2  Nop              snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
        0.1   12.2   1.3       0.17   11.5   0.3    1.8  2  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor
       0.54   10.3   6.0       0.91    9.6   6.0    1.4  1  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.35   2.1e+03      57     100 ..      67     111 ..      48     119 .. 0.63
   2 !  251.0   0.0   1.6e-78   9.6e-75       2     229 ..     146     371 ..     145     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.35
                                   .HHHHHHHHHHHHCHHHH.-SSS-S-HHHHHHHHHHHHHHHHHHH CS
                           Nop  57 deelakevimaakvtast.smgaelseedlknikelcdrvlelee 100
                                   d e+++ +++ +k +++  +mg+e+ +e+l n+   ++ v + +e
  gi|70607105|ref|YP_255975.1|  67 DAEVPALQKLGIKASSEIrNMGTEIFRENLVNVAIQTKIVNSEDE 111
                                   455666666666665554688999888888888776666666555 PP

  == domain 2  score: 251.0 bits;  conditional E-value: 1.6e-78
                                   HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HH..HHHHHHHHHHCHHHH-SSS-S CS
                           Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedee..lakevimaakvtastsmgael 80 
                                   +d+idk+in +++r+rewYs hFpEL++l++d++ Ya++++++g +r++l+++  + e  l+ke+i+ +  +a++s ga++
  gi|70607105|ref|YP_255975.1| 146 IDDIDKTINLFSERLREWYSIHFPELDKLIEDHWLYASIISKFG-HRDNLSDTGLE-EigLNKEKIEKIMNAAKNSIGADI 224
                                   79******************************************.89***888323.23699999999999999******* PP

                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCC CS
                           Nop  81 seedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfr 161
                                   ++ d+k++k l d +l+l+e r el++Y es m+++APN+++LvG++++arL+s aG+L+ LakmPastiq+lGaekalfr
  gi|70607105|ref|YP_255975.1| 225 TDVDIKSVKTLSDIILKLYEERLELTDYTESVMREVAPNVTSLVGPTLGARLLSLAGSLEDLAKMPASTIQVLGAEKALFR 305
                                   ********************************************************************************* PP

                                   CHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                           Nop 162 alk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                   al+ +++ pk+G+i++ + ++++ p+++++kiaR+laaK+a+aaR+D f  + + +G+kl ee++k+++
  gi|70607105|ref|YP_255975.1| 306 ALRkGGRPPKHGVIFQYPAIHNS-PRWQRGKIARALAAKLAIAARVDYF--SGKFIGNKLNEELKKRID 371
                                   ***6669**************77.************************9..57899***********97 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.87   5.2e+03      47      59 ..     207     219 ..     204     241 .. 0.66
   2 ?   11.5   0.3   2.8e-05      0.17      28      74 ..     352     399 ..     346     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.87
                                   HHHHHHHHHHHHH CS
                 Mt_ATP-synt_B  47 ekiqeelnqsrnl 59 
                                   eki++++n+++n+
  gi|70607105|ref|YP_255975.1| 207 EKIEKIMNAAKNS 219
                                   5677777776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHCC CS
                 Mt_ATP-synt_B  28 ilvakslgpsikefldkriekiqeelnqsr.nlkeealkerieqekkl 74 
                                   +++ k+ g++++e+l+kri++i+e+  q   +++e+++++  ++e+k 
  gi|70607105|ref|YP_255975.1| 352 YFSGKFIGNKLNEELKKRIDEIREKYAQPPpRKQEQKVEQKGKKERKN 399
                                   6999*******************9987765156688888877777765 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   6.0   0.00015      0.91      29      90 ..     345     407 ..     335     412 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
               Peptidase_S49_N  29 alaakkkkekgelevtkLneeykelkeeleealldeeelkaaekkekkeekeekkae.kkkak 90 
                                   a+aa+ +  +g++  +kLnee+k++ +e++e++ +   +k+++k e+k +ke+k+++ k++ k
  gi|70607105|ref|YP_255975.1| 345 AIAARVDYFSGKFIGNKLNEELKKRIDEIREKYAQPPPRKQEQKVEQKGKKERKNKKdKRRGK 407
                                   55555556667777789**************************99999888877666133333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1557  (0.0868425); expected 358.6 (0.02)
Passed bias filter:                      771  (0.043003); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 2781.96
//
Query:       gi|70607106|ref|YP_255976.1|  [L=54]
Description: 30S ribosomal protein S30e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-14   53.2   4.4      3e-14   52.9   4.4    1.1  1  Ribosomal_S30  Ribosomal protein S30
  ------ inclusion threshold ------
      0.035   14.6   5.9      0.061   13.8   5.4    1.6  2  Sas10          Sas10 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   4.4   3.4e-18     3e-14       3      44 ..       4      44 ..       3      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.4e-18
                                  BX-STTTTHHHHHS-------------THHHHHHHHHHHTTS CS
                 Ribosomal_S30  3 hGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvn 44
                                  hGsL++AGKVrn TPK++K+ek+K ++ R + Rl Y++R  +
  gi|70607106|ref|YP_255976.1|  4 HGSLTKAGKVRNATPKMQKKEKHK-EVPRVRNRLEYEKRVLK 44
                                  *********************999.899***********998 PP

>> Sas10  Sas10 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9    0.0027        24      17      38 ..       7      28 ..       3      29 .. 0.86
   2 ?   13.8   5.4   6.8e-06     0.061      19      50 ..      21      52 ..      14      54 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0027
                         Sas10 17 LtpkRkkenrnpRvkkrkkYek 38
                                  Lt+  k +n +p+++k++k+++
  gi|70607106|ref|YP_255976.1|  7 LTKAGKVRNATPKMQKKEKHKE 28
                                  8888899999*********986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.8e-06
                         Sas10 19 pkRkkenrnpRvkkrkkYekakkklksqvaev 50
                                  +k++k++  pRv++r  Yek + k  +q + v
  gi|70607106|ref|YP_255976.1| 21 QKKEKHKEVPRVRNRLEYEKRVLKSGQQSRAV 52
                                  688999****************9999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 394.67
//
Query:       gi|70607107|ref|YP_255977.1|  [L=446]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-59  201.0   0.0    1.7e-59  200.6   0.0    1.2  1  Asparaginase    Asparaginase, N-terminal
      9e-34  116.1   0.0    4.1e-32  110.8   0.0    2.3  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    5.8e-20   70.3   7.0    1.2e-19   69.4   7.0    1.5  1  GatD_N          GatD N-terminal domain
  ------ inclusion threshold ------
      0.026   14.5   0.2      0.078   13.0   0.2    1.8  1  DUF2187         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.0   3.9e-63   1.7e-59       2     185 ..      92     284 ..      91     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 3.9e-63
                                   EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEEE CS
                  Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfVv 81 
                                   v++++tGGTi s+ ++++ga++pal+ +e++e +pe+++ia++++e l++i S+nm+p+ w k+ae+ ++al++  +g+V+
  gi|70607107|ref|YP_255977.1|  92 VMIISTGGTIVSKIEYETGAVRPALTPDEIIEFMPEIKEIARIDAEILFSILSENMKPEYWIKIAEEAKKALDKgNKGVVI 172
                                   9***********************************************************************777****** PP

                                   E--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTT CS
                  Asparaginase  82 lhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranr 155
                                   +hGTDT+ayt++aLs+ +++++ p+vl+Gsqr++++++sD+ +Nll+++lva +  ++ +v+v ++g+       ++r+ +
  gi|70607107|ref|YP_255977.1| 173 AHGTDTMAYTSAALSFSFRKMTGPIVLVGSQRSSDRPSSDSSMNLLTSILVAKNA-PFGEVVVNMHGEssdtytlVHRGVK 252
                                   *****************************************************99.************************* PP

                                   EEE-BSSSSS-EEETTT--SEEE..ETTEEEE CS
                  Asparaginase 156 vtKvhtssldaFespnlgplaev..egskvkv 185
                                   v+K+hts++daF+s+n  pla+v   ++k+++
  gi|70607107|ref|YP_255977.1| 253 VRKMHTSRRDAFQSINDLPLAKVhyIDKKIEI 284
                                   *********************99444555555 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.023     1e+02      17      63 ..     160     206 ..     132     239 .. 0.77
   2 !  110.8   0.0   9.2e-36   4.1e-32       1     114 []     305     418 ..     305     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                                   HHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSB CS
                Asparaginase_C  17 kallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcps 63 
                                   k++l+kg kGvv++ +  + + ++    ++  k +g +v + sq +s
  gi|70607107|ref|YP_255977.1| 160 KKALDKGNKGVVIAHGTDTMAYTSAALSFSFRKMTGPIVLVGSQRSS 206
                                   67889*********999888887544444444445555555555444 PP

  == domain 2  score: 110.8 bits;  conditional E-value: 9.2e-36
                                   -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHT CS
                Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlg 81 
                                   rV++lk +pg++++++++l+++g++G+++egtG G+ +s+++e++k+a + g+ + +tsqc++g+v++++y +g+ l+++g
  gi|70607107|ref|YP_255977.1| 305 RVFLLKYYPGLSPDMVEHLISSGIRGIIIEGTGLGHTSSDFYEVFKKASKDGVFIGMTSQCLFGRVNMNVYTTGRLLQEAG 385
                                   8******************************************************************************** PP

                                   EEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                Asparaginase_C  82 visaddmtpeaarikLmlllgkgldpaevrklf 114
                                   v+  +dm pe+a +kLm+ l++++d +++++++
  gi|70607107|ref|YP_255977.1| 386 VVPLEDMLPETALVKLMWTLAHENDLDRIKEIM 418
                                   *******************************98 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   7.0   2.6e-23   1.2e-19       2      55 .]      19      71 ..      18      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 2.6e-23
                                  -TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                        GatD_N  2 evGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                  +vGD+i++ek+g++++Gi+mP + +++ddiivlKLdnGYNiGi++++i++++l+
  gi|70607107|ref|YP_255977.1| 19 DVGDIIELEKNGIQVKGIIMPTY-SNNDDIIVLKLDNGYNIGISVSNIQNVKLI 71
                                  89*********************.****************************97 PP

>> DUF2187  Uncharacterized protein conserved in bacteria (DUF2187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.8e-05     0.078       5      27 ..      20      43 ..      17      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                       DUF2187  5 vGdiieFkkgdlkltGiVekvn.e 27
                                  vGdiie +k++++++Gi+++ + +
  gi|70607107|ref|YP_255977.1| 20 VGDIIELEKNGIQVKGIIMPTYsN 43
                                  9******************98843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2777.87
//
Query:       gi|70607108|ref|YP_255978.1|  [L=642]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-72  242.4   0.1    7.5e-72  242.0   0.1    1.1  1  GatB_N     GatB/GatE catalytic domain
    6.4e-21   74.8   5.6    6.4e-21   74.8   5.6    2.3  2  GatB_Yqey  GatB domain
    4.9e-11   42.7   2.5    9.7e-11   41.8   0.1    2.6  3  GAD        GAD domain
     0.0051   16.9   0.7      0.013   15.6   0.7    1.7  1  YqeY       Yqey-like protein
  ------ inclusion threshold ------
        4.4    7.9   7.1       0.62   10.7   0.8    2.9  3  ATP-cone   ATP cone domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.0   0.1   2.1e-75   7.5e-72       2     272 ..      20     457 ..      19     458 .. 0.96

  Alignments for each domain:
  == domain 1  score: 242.0 bits;  conditional E-value: 2.1e-75
                                   EEEEEEEEEB--SB-SSSSSBSS..SSCE.........S.TTSS--TTTTTS..........................TT. CS
                                   xxxxxxxxxxxxxxxxxxxxxxx..xxxx.........x.xxxxxxxxxxxx..........................xxx RF
                        GatB_N   2 viGlEiHaqlktksKlFssaste..eege.........e.pnsevsevdlal..........................PGt 44 
                                   ++GlEiH+ql+t++KlF+++st+  e  +         + + se++e+d+a+                          P  
  gi|70607108|ref|YP_255978.1|  20 KVGLEIHQQLNTNKKLFCDCSTTldE--KhhgtlqrylRpSFSEIGEIDTAAlfewqkgkkylyqipfnsclveadeeP-- 96 
                                   89*******************88542..234678888854889********9***********************9999.. PP

                                   .--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---EEE CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                        GatB_N  45 lPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaaksv 123
                                    P+ ln+ea+ +++++a+ l+++i +e++++RK++++++ ++g+Q+t+    +a++G++ +  kk++i++i lEeDaa+++
  gi|70607108|ref|YP_255978.1|  97 -PHgLNREALAVVLAVAMSLESNIVDEIYVMRKIVIDGSDTTGFQRTS---IVAMGGQVIVeGKKIGIQTIALEEDAARKI 173
                                   .***********************************************...56699998876899**************** PP

                                   EEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 124 heekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvE 204
                                   +e+++e++++l+R+G+pLiEi+t+pd+++peea++v+ ++++llr +g++++++  G++R+D+NvS++        g ++E
  gi|70607108|ref|YP_255978.1| 174 SESANETMYSLDRLGIPLIEISTAPDITTPEEAEKVAFRIGQLLRLTGKVKRGI--GTIRQDLNVSIQG-------GVKTE 245
                                   **999*************************************************..************4.......59*** PP

                                   EEEE-SHHHHHHHHHHHHHHHHHHH........................................................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx........................................................ RF
                        GatB_N 205 iKnlnslksiekaieyeierqiell........................................................ 229
                                   iK++++l+ i ++i++e++rq ell                                                        
  gi|70607108|ref|YP_255978.1| 246 IKGVQRLELIPEIIKNEARRQYELLkikdelvnkrglsktiveneikelelthlfrntnskiikkelekggliygikfkgf 326
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                        GatB_N 230 ................................................................................. 229
                                                                                                                    
  gi|70607108|ref|YP_255978.1| 327 kgifgrelmpnrrfgteiadyvralaelggifhsdelpnygitseevesvkkelgigendgfvlvigdkeklkvaitkike 407
                                   ********************************************************************************* PP

                                   ..........-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 ..........qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseeli 272
                                             +eTr + +d g+t+ +R+++ +a   r++pe+d+ p++i+e+++
  gi|70607108|ref|YP_255978.1| 408 rvlyafvgvpKETRVALDD-GTTKFMRPQPgSA---RMYPETDIIPIKIDESIL 457
                                   *****************99.**********555...**************9986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.9      0.13   4.5e+02      56      97 ..     245     294 ..     232     311 .. 0.81
   2 !   74.8   5.6   1.8e-24   6.4e-21       1     146 [.     495     634 ..     495     636 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                                   SSGHHHHHHHHHHHHHHTXXH........HHHHHHCTXXXXXXSSXHHHH CS
                     GatB_Yqey  56 kIskkiakevleelleegksp........eeiieekgLkqisdeeelekl 97 
                                   +I + +  e+++e+++++           +e+++++gL +   e+e+++l
  gi|70607108|ref|YP_255978.1| 245 EIKGVQRLELIPEIIKNEARRqyellkikDELVNKRGLSKTIVENEIKEL 294
                                   56666667899999988666668899999999999999999988999876 PP

  == domain 2  score: 74.8 bits;  conditional E-value: 1.8e-24
                                   HHHHHHHHHSS...HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHH CS
                     GatB_Yqey   1 dffeevvkegad..aklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeei 79 
                                   d+fee+ k+++   ++++++ +l++ +++ +++g +i+   +t+e ++e+++ + ++kIsk++++e+l    +++k +++i
  gi|70607108|ref|YP_255978.1| 495 DLFEELSKKYSPkvSPIVIATTLENYIKYAKSKGGDISV--ITDEVIEEIINALYNDKISKDSIQEILVDYSTSKKPIRNI 573
                                   79********6667999**********************..9*************************************** PP

                                   HHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHH CS
                     GatB_Yqey  80 ieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellke 146
                                   ++ +   +i+d eel ++++++++en    + ++++ eka+++++G+vM+ +kG+a++k+v + lk 
  gi|70607108|ref|YP_255978.1| 574 VDNY--AKITD-EELNRIIDKILDEN---KDIINQKGEKAFNVIIGKVMNVVKGRAEGKKVVDTLKL 634
                                   9977..8****.**************...556678999***********************999985 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.8   1.7e+04      55      69 ..     280     294 ..     260     297 .. 0.64
   2 !   41.8   0.1   2.7e-14   9.7e-11       1      93 [.     308     400 ..     308     402 .. 0.95
   3 ?   -0.8   0.0      0.51   1.8e+03      55      81 ..     575     600 ..     563     602 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.8
                                   TTTCCCS-HHHHHHH CS
                           GAD  55 gpiakflteeevkkl 69 
                                    +++k + e+e+k+l
  gi|70607108|ref|YP_255978.1| 280 RGLSKTIVENEIKEL 294
                                   455555666655554 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 2.7e-14
                                   HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEE CS
                           GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDi 80 
                                   +++ l++gg + +++++g ++++ ++e+++ ++f++e +++ +a + ++g +++++++ + +t+eev+ +++ +g  e+D 
  gi|70607108|ref|YP_255978.1| 308 IKKELEKGGLIYGIKFKG-FKGIFGRELMPNRRFGTEIADYVRALAELGGIFHSDELPNYgITSEEVESVKKELGIGENDG 387
                                   67899*************.8************************************************************* PP

                                   EEEEEEEHHHHHH CS
                           GAD  81 llfvAdkkktvnk 93 
                                   +++v ++k++++ 
  gi|70607108|ref|YP_255978.1| 388 FVLVIGDKEKLKV 400
                                   ****999988765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.51
                                   TTTCCCS-HHHHHHHHHHCT--TTEEE CS
                           GAD  55 gpiakflteeevkklleavgaeegDil 81 
                                   ++ ak+ t ee++++++++  e+ Di+
  gi|70607108|ref|YP_255978.1| 575 DNYAKI-TDEELNRIIDKILDENKDII 600
                                   555666.77788888877777777775 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   3.5e-06     0.013      82     140 ..     573     633 ..     532     636 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                                   HHGGGS-----HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHH CS
                          YqeY  82 vleeYlPeqlseeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvk 140
                                   ++++Y  +++++ee++++++++++e     ++++ k++  +++++++ vkG+a+gkkv  ++k
  gi|70607108|ref|YP_255978.1| 573 IVDNY--AKITDEELNRIIDKILDENkdiiNQKGEKAFNVIIGKVMNVVKGRAEGKKVVDTLK 633
                                   55555..589*************9975555788************************998877 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.6   1.3e+04      47      75 ..     281     309 ..     259     312 .. 0.60
   2 ?   -2.9   0.0         3   1.1e+04      14      25 ..     394     405 ..     394     421 .. 0.67
   3 ?   10.7   0.8   0.00017      0.62      29      65 ..     527     564 ..     508     579 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.6
                                   HHIIT-BHHHHHHHHHHHHHHSS-HHHHH CS
                      ATP-cone  47 rlrdgisteeIqdlvektliehpdyavaa 75 
                                   +l ++i   eI +l    l ++++ ++++
  gi|70607108|ref|YP_255978.1| 281 GLSKTIVENEIKELELTHLFRNTNSKIIK 309
                                   35555666666666666666666666555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                                   -HHHHHHHHHHH CS
                      ATP-cone  14 dvekIkraiekA 25 
                                   d+ek+k ai+k 
  gi|70607108|ref|YP_255978.1| 394 DKEKLKVAITKI 405
                                   567777777765 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00017
                                   -HHHHHHHHHHHHHHHHHH.HIIT-BHHHHHHHHHHHH CS
                      ATP-cone  29 seeeideiaeeveaevrkr.lrdgisteeIqdlvektl 65 
                                   +  +i+ i++ev++e+ +  ++d+is + Iq++++++ 
  gi|70607108|ref|YP_255978.1| 527 KGGDISVITDEVIEEIINAlYNDKISKDSIQEILVDYS 564
                                   4667999*****999977736666**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3962.71
//
Query:       gi|70607109|ref|YP_255979.1|  [L=352]
Description: hypothetical protein Saci_1351 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2442.69
//
Query:       gi|70607110|ref|YP_255980.1|  [L=132]
Description: hypothetical protein Saci_1352 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00042   20.3   0.2     0.0006   19.8   0.1    1.4  2  DUF483    Protein of unknown function (DUF483)
      0.007   16.1   0.0      0.021   14.5   0.0    1.7  2  UPF0175   Uncharacterised protein family (UPF0175)
  ------ inclusion threshold ------
      0.016   15.2   0.5      0.026   14.6   0.5    1.3  1  HTH_3     Helix-turn-helix
      0.033   14.9   0.0       0.14   12.9   0.0    1.8  2  YukD      WXG100 protein secretion system (Wss), protein YukD
      0.035   14.1   0.0      0.088   12.9   0.0    1.7  1  Cro       Cro
       0.08   12.8   0.1       0.13   12.1   0.1    1.3  1  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> DUF483  Protein of unknown function (DUF483)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     2e-07    0.0006      12      71 ..      11      70 ..       1     106 [. 0.83
   2 ?   -2.1   0.0       1.2   3.7e+03      46      58 ..     114     126 ..      80     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-07
                        DUF483 12 kkkvrpaidplvseelgiyrrlddleiGkllgyPkCCvksfieekrfaidsehlkeieel 71
                                   k++ pai  +++e+l ++r++   +  +llg     ++ +i++kr +  ++ lk+  e 
  gi|70607110|ref|YP_255980.1| 11 VKELLPAIRAIIAEKLVVERKISIYKTSELLGVTPAAIENYIKKKRGTSIQQLLKNDREF 70
                                  47899*****************************************55545566665554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                        DUF483  46 kCCvksfieekrf 58 
                                   +C v+ f++   f
  gi|70607110|ref|YP_255980.1| 114 HCMVEDFLDGYNF 126
                                   5777777766655 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.9e-06     0.021      12      56 ..      10      54 ..       2      68 .. 0.87
   2 ?   -1.5   0.0      0.69   2.1e+03      52      70 ..     103     121 ..     100     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                       UPF0175 12 teeelerelrialAvklYeegrlSlgkAaelaglsrveflelLar 56
                                  + +el   +r  +A kl  e+++S+ k +el+g++    +++ ++
  gi|70607110|ref|YP_255980.1| 10 SVKELLPAIRAIIAEKLVVERKISIYKTSELLGVTPAAIENYIKK 54
                                  56899999**************************99888887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.69
                       UPF0175  52 elLarrgiplinydeeele 70 
                                   + L ++g +l +  +e++ 
  gi|70607110|ref|YP_255980.1| 103 KVLMKNGYSLTHCMVEDFL 121
                                   6799999999999999986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   8.7e-06     0.026       3      43 ..      24      65 ..      22      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.7e-06
                                  HHHH.HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHH CS
                         HTH_3  3 elRk.qlglsqeeLAeklGvsrstisriEnGernPsletlkk 43
                                  e++  ++++s+ + +e+lGv++++i ++++ +r  s++ l+k
  gi|70607110|ref|YP_255980.1| 24 EKLVvERKISIYKTSELLGVTPAAIENYIKKKRGTSIQQLLK 65
                                  566669*****************************9998876 PP

>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.5e-05      0.14      13      35 ..       1      23 [.       1      47 [. 0.84
   2 ?   -0.4   0.0      0.64   1.9e+03      33      70 ..      81     119 ..      67     119 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
                                  EEEEEETTSBTTHHHHHHHHHS- CS
                          YukD 13 vDlaLPadvpvaellpalvrllg 35
                                  +D+ LP ++ v+ellpa+ ++++
  gi|70607110|ref|YP_255980.1|  1 MDITLPCEYSVKELLPAIRAIIA 23
                                  69*****************9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.64
                                   HS-...--S---TT-EEEEGGG.EEEETTSBCGGGT--T CS
                          YukD  33 llgepddeagrpggwsLarvgg.apLsgdrtLaeagVrD 70 
                                   l+++   e+++   + L++ g+   ++   +L+++ V D
  gi|70607110|ref|YP_255980.1|  81 LVKDGKSEGVASYYCILCTEGKkVLMKNGYSLTHCMVED 119
                                   444555555555556688888866667777888877776 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.088      16      38 ..      35      57 ..      28      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                  HHHHHHHTS-HHHHHHHHHCT-E CS
                           Cro 16 aktAkdlgvkqsaIsKAlkakRn 38
                                   kt + lgv+++aI   +k+kR 
  gi|70607110|ref|YP_255980.1| 35 YKTSELLGVTPAAIENYIKKKRG 57
                                  69*******************95 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.3e-05      0.13       7      40 ..      19      54 ..      16      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                        HTH_23  7 Rlrillllae..GlsvreIAreLgvsrrTvyrwlkr 40
                                  R+ i+  l +  ++s+ + +++Lgv++  + +++k+
  gi|70607110|ref|YP_255980.1| 19 RAIIAEKLVVerKISIYKTSELLGVTPAAIENYIKK 54
                                  6666666665689********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 915.99
//
Query:       gi|70607111|ref|YP_255981.1|  [L=837]
Description: ribonucleotide reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.9e-183  608.4   0.0   1.5e-182  607.9   0.0    1.3  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    1.8e-28   98.4   0.2    4.2e-28   97.2   0.2    1.7  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    3.5e-06   27.5   0.3    1.4e-05   25.6   0.1    2.2  2  ATP-cone         ATP cone domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.9   0.0  2.4e-186  1.5e-182       1     524 []     198     777 ..     198     777 .. 0.91

  Alignments for each domain:
  == domain 1  score: 607.9 bits;  conditional E-value: 2.4e-186
                                   EEE.....BSS-.....EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC   1 ssCfvlsvedsl.....esIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkR 76 
                                   s+Cfv+ v+d +     ++I+++++++al++++ggG+G+++s+lR+kg++v++t+g asGpvsfm+++d ++dvvkqgGkR
  gi|70607111|ref|YP_255981.1| 198 SACFVIPVRDAMstpngDGIYDALRAMALVHQQGGGTGFDFSELRPKGDIVASTAGVASGPVSFMRIFDVSTDVVKQGGKR 278
                                   79**************9**************************************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
               Ribonuc_red_lgC  77 rGAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrt.................. 139
                                   rGA+m+++++wH+D+ +fi+aK+ +    + +l+n+nisvgv d Fm+av++++ ++L++Pr+                  
  gi|70607111|ref|YP_255981.1| 279 RGANMGVMHAWHADVQDFIRAKTGELR--DTHLQNFNISVGVYDYFMNAVERGEAVPLINPRKtripgkdwdyymtnargy 357
                                   **********************99888..9********************************8777777776666555555 PP

                                   ..........XXX...................................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   ..........xxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 140 ..........vvkleklygee..........feeeyeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrn 200
                                              ++le+  g +          ++e++  +e++++i  + v+a++Lf+ei++ aw++g+Pg+lf+D+iNrr+
  gi|70607111|ref|YP_255981.1| 358 mhdesvqeyiLKELEEKGG-SvyldesriitVDEALVIAEKENAIV-QWVNARQLFDEIVKGAWDSGDPGLLFIDEINRRH 436
                                   5544444443233333333.02444455665666666666665555.7********************************* PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 201 vlekakggkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpei 281
                                   ++++   gkI+atN+CgE+pll++es   CnL+si L+kfv  +++gk ++dwd l ++i++ vr+Ldnvid+n+ypl++i
  gi|70607111|ref|YP_255981.1| 437 PVWYI--GKINATNPCGEEPLLPWES---CNLGSISLEKFV-VEKDGKMSIDWDGLVEAIKYGVRFLDNVIDANRYPLKQI 511
                                   **776..7******************...************.777************************************ PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
               Ribonuc_red_lgC 282 ekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef. 361
                                   e++tkktR++GlGvmgla++l+klgipyds +al ++ +++++++y+a+k+S++lAke+g+fp ++   y++ +   + f 
  gi|70607111|ref|YP_255981.1| 512 EEATKKTRKVGLGVMGLARMLIKLGIPYDSVDALYISYQLAKFIYYHALKTSIDLAKEKGSFPAYDPYYYHDIWESARDFg 592
                                   *************************************************************************99999997 PP

                                   .....X.......................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   .....xxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 362 .....eeke.................kedweeLreeikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtvg 420
                                        +  +                 + d + L+ee  k Glrn++v+++aPTg+iS+iagtss+ieP+fal+++++v+vg
  gi|70607111|ref|YP_255981.1| 593 sllevS--NikdkpsdyvkkltevvdRLDFSLLKEERIKFGLRNSTVVSVAPTGTISIIAGTSSSIEPLFALAFVRNVAVG 671
                                   776651..1445667778888888889****************************************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 421 eflevnpvfeeeLkklglwseellkki..lesvqgleeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpn 499
                                   +f+e++p f+e L+k++l++ e+ +ki  +++v + + ip+++k++f+ta+++ +e h+ +qa +q+w d+++Sktinl++
  gi|70607111|ref|YP_255981.1| 672 KFIEIDPLFLEYLRKYELDDPEVVQKIaeTGTVAENPFIPRTMKKLFRTAHEVPPEYHVLHQAMWQQWNDSGTSKTINLKS 752
                                   ***************************66666************************************************* PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
               Ribonuc_red_lgC 500 eatvedvkelyllAwklGlKgvtyY 524
                                   e++ e+v+++y+lAwklG+Kgvt+Y
  gi|70607111|ref|YP_255981.1| 753 EEPPETVEKVYMLAWKLGIKGVTVY 777
                                   ************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.2     7e-32   4.2e-28       3      83 .]     113     195 ..     111     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 7e-32
               Ribonuc_red_lgN   3 ltynalkvledrYllkdeng.eivEspqqmfmRvAlalaiaealyd.kleedkdlaeefydlmssqkflpasPtlmnaGte 81 
                                    +ynalkvle+rYllkd n+ +++E+pq mf+RvA+++a  e+ly  +++++k++ +++y++ms++kf+p++P+lmn+Gt+
  gi|70607111|ref|YP_255981.1| 113 ISYNALKVLEARYLLKDPNTlRYIETPQMMFRRVARHIANVEKLYGkDEKQVKEIEDKLYEMMSNLKFIPNTPALMNSGTR 193
                                   68*****************************************88857778888888***********************9 PP

               Ribonuc_red_lgN  82 lg 83 
                                   lg
  gi|70607111|ref|YP_255981.1| 194 LG 195
                                   86 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   2.3e-09   1.4e-05       1      81 [.      13      92 ..      13      97 .. 0.81
   2 ?   -2.5   0.0       1.4   8.2e+03      44      61 ..     153     171 ..     142     178 .. 0.48

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.3e-09
                                  -EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH....HSS-H.HHHHHHH CS
                      ATP-cone  1 ikViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektli....ehpdy.avaaayi 78
                                  ikV KR+G +e f+ ek+ + +       e  +d i + v   +++++++ i+t  + d+ve++li    e+p+  ++a++y+
  gi|70607111|ref|YP_255981.1| 13 IKVLKRNGGYEQFKAEKVFSKLGSL---PEVVMDGILQDV---LQNSKENAIDTRALADIVERNLIehslEYPNLmDLAKRYV 89
                                  68***********************...355677775555...79999999***************66665555457777777 PP

                                  HHH CS
                      ATP-cone 79 lyr 81
                                  l r
  gi|70607111|ref|YP_255981.1| 90 LAR 92
                                  766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                                   HHHH.HIIT-BHHHHHHHH CS
                      ATP-cone  44 vrkr.lrdgisteeIqdlv 61 
                                   v+k  ++d+ +++eI d +
  gi|70607111|ref|YP_255981.1| 153 VEKLyGKDEKQVKEIEDKL 171
                                   3333333444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 4914.29
//
Query:       gi|70607112|ref|YP_255982.1|  [L=248]
Description: hypothetical protein Saci_1354 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1628.53
//
Query:       gi|70607113|ref|YP_255983.1|  [L=415]
Description: phosphoglycerate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-101  340.4   0.2   1.4e-101  340.2   0.2    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.2   0.2  7.8e-106  1.4e-101       1     377 [.      12     395 ..      12     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 340.2 bits;  conditional E-value: 7.8e-106
                                   GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHT CS
                           PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellg 80 
                                   ++dl+l++k+vl+R+D+N+p++k+ gk+ dd+ri+a+  Tik+ll+kg ++vl+sH+grp g+++ +slk++   Ls+++g
  gi|70607113|ref|YP_255983.1|  12 INDLELQNKKVLLRIDVNSPVDKNtGKLLDDSRIKAHSITIKELLKKGNSIVLISHQGRP-GDDDFISLKEHSLLLSKYVG 91 
                                   68*******************9999***********************************.89****************** PP

                                   T-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTT..TTT-H...H....HHHHHHHT-SEEEE--GGGTTS--TTTT CS
                           PGK  81 keVkfvedvvgeeveeaiaelkegevllLeNvrfykeE..eknde...e....lakklasladvyVnDAFgtahrahaStv 152
                                   +e++fved++g+ + e+i++l ++ v++LeN+r  +eE  e   +   +    l kkl+ l+d+yVnD+F++ahr++ S+v
  gi|70607113|ref|YP_255983.1|  92 TEIEFVEDIIGPYAVEKIKKLDNKGVIMLENIRLMSEEliE--APpqqHaksfLIKKLSPLFDAYVNDSFSAAHRSQPSLV 170
                                   **************************************542..3333313467**************************** PP

                                   HHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B-TTS CS
                           PGK 153 giakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqgleigks 231
                                   g++ vl++aaG++mekE++alsk+++ ++ p +++lGG kv+d +k+ienL+++   d++++gG++a  F  a+g+++gk+
  gi|70607113|ref|YP_255983.1| 171 GFPLVLPSAAGIVMEKEVSALSKIFNYEDSPKIFVLGGGKVNDTLKIIENLIKNRvaDRILTGGLVAELFAVAKGINLGKK 251
                                   ******99********************************************98668**********************99 PP

                                   S-...-GGG.....HHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHHCC- CS
                           PGK 232 lv...eedk.....lelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeaikea 304
                                    +   e+ k     +  a+++l +    g  i +pvD+v+++e++    ++ e+ + + +  + Dig++tie++++ ike+
  gi|70607113|ref|YP_255983.1| 252 NMqvlEN-KgllslVPRARKMLLS----GAPIEIPVDFVTEQENS----QTLEEPTSNLKGTIKDIGNTTIEMYSSFIKES 323
                                   9944333.1343336666666655....579**********8432....4445555566789******************* PP

                                   SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHH.HHTT-GGGSSEEESSSHHHHHHHCT CS
                           PGK 305 ktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaav.eklgladkvshvStGGgAsLelLeg 377
                                   k+vv+ GpmGv+e e+f++G+ka+++ + e     ++i+GGg+ ++++ ++++++++  hvStGGgA+L +L g
  gi|70607113|ref|YP_255983.1| 324 KVVVLRGPMGVIEDERFRRGSKALLTSAVEGPG--YVIIGGGHMISMIdKNIQINENKVHVSTGGGALLLFLAG 395
                                   ******************************865..*************456789999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2919.62
//
Query:       gi|70607114|ref|YP_255984.1|  [L=343]
Description: glyceraldehyde-3-phosphate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-17   63.0   0.2    3.5e-17   62.4   0.2    1.2  1  Gp_dh_C         Glyceraldehyde 3-phosphate dehydrogenase, C-t
    2.5e-12   47.0   0.2    5.9e-12   45.8   0.1    1.6  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
    2.4e-07   31.0   0.7    2.5e-05   24.6   0.1    3.0  3  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
     0.0013   18.2   0.1      0.046   13.1   0.1    2.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.035   14.5   0.0    1.8  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.017   15.9   0.0      0.042   14.7   0.0    1.7  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.028   14.0   0.2       0.31   10.6   0.1    2.5  3  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.035   14.7   0.4       0.16   12.6   0.1    2.2  2  PglD_N          PglD N-terminal domain
       0.16   12.6   0.0       0.64   10.7   0.0    2.1  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.2   1.8e-20   3.5e-17       3     155 ..     148     298 ..     146     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.8e-20
                                   HHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEEEEEESS CS
                       Gp_dh_C   3 plakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldglAvrVPt 81 
                                   +++  +n+  +i+k++ t+v++++++         k+++++++++   ++  +++++ak+v +Vl+   +++ ++A+  Pt
  gi|70607114|ref|YP_255984.1| 148 RVLCTINNFDKIEKVRGTIVRRAADP---------KEVKKGPINSivADPARIPSHHAKDVLTVLK--GIDIITSALVAPT 217
                                   66777888889***************.........9*********999******************..79*********** PP

                                   SSEEEEEEEEEESSTS-HHHHHHHHHHHHH.....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETTTEEEEE CS
                       Gp_dh_C  82 pnvsvvdlvvelekevtveevnaalkeaae.....galkgilsyteeelvssDlvgdph..ssifdaketivveenlvkvv 155
                                   + ++++ l ++++++v++e+  ++l+++++     ++  +  s++e +++++Dl + ++   +++  + +i +++n+++++
  gi|70607114|ref|YP_255984.1| 218 TLMHLHTLFITTRNKVSKEDLLNILSNTPRilllnTEKADAESTAEIMEIARDLGRYRNdvPETVIFEDSIYTNGNEIFLM 298
                                   **********************************99999****************999988999**************998 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   2.9e-15   5.9e-12       1      96 [.       4     108 ..       4     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.9e-15
                                   EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH........HHSSSS--S-BEBSSHHHHHHH-SEE CS
                        DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag........ellglgklgvavtddleevlekadvl 71 
                                   +kva++G+ G++Gk+v++a++ ++d+el ++ ++++  +++ ++  g        ++ +++++g++v  ++e++++++d++
  gi|70607114|ref|YP_255984.1|   4 VKVAINGY-GTIGKRVADAIRLQPDMELIGVAKTSPnyEAFTAMRKGyklyttkeNIQKFQNSGINVAGSIEDMIKDSDII 83 
                                   69******.************************9995545555555599999995555666******************** PP

                                   EE-S-HHHHHHHHHHHHHT.T-EEEE CS
                        DapB_N  72 iDFTtpeavlenlklalek.gvklVi 96 
                                   iD T p +v +n+k ++++ g+k+++
  gi|70607114|ref|YP_255984.1|  84 IDAT-PGGVGANYKKIYQEyGKKAIF 108
                                   ****.888887777776655999987 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.2e-08   2.5e-05       1      47 [.       4      50 ..       4      88 .. 0.70
   2 ?   -1.3   0.0       1.4   2.7e+03      20      54 ..     131     165 ..     125     202 .. 0.63
   3 ?    3.4   0.0     0.048        95      25      74 ..     246     299 ..     237     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.2e-08
                                  CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEET CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdletlayllkyDs 47
                                  vkvainG+G IG+ v+ a+  ++++e++ + ++  + ++   ++  +
  gi|70607114|ref|YP_255984.1|  4 VKVAINGYGTIGKRVADAIRLQPDMELIGVAKTSPNYEAFTAMRKGY 50
                                  69*****************************9544444444444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                   HHHTTCEEEEEE-TS-HHHHHHHHHEETTTEC-SS CS
                       Gp_dh_N  20 leekelevvaindltdletlayllkyDsvhgrfkg 54 
                                   ++++ ++vv  n+++ l+ l  + ++D + +   +
  gi|70607114|ref|YP_255984.1| 131 INKNYIRVVSCNTTGILRVLCTINNFDKIEKVRGT 165
                                   56667777777777777777777777766544443 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.048
                                   CEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEE...TTEEEETTEEEEEE- CS
                       Gp_dh_N  25 levvaind.ltdletlayllkyDsvhgrfkgeveae...eealvvngkkikvla 74 
                                    +++ +n+  +d+e+ a +++     gr++++v ++   e+++  ng++i ++ 
  gi|70607114|ref|YP_255984.1| 246 PRILLLNTeKADAESTAEIMEIARDLGRYRNDVPETvifEDSIYTNGNEIFLMY 299
                                   56778888789**********************999999*********997765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   2.3e-05     0.046      37      76 ..       4      46 ..       1      96 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                  SEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH..CHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlk.afgmkviaydrskkkee..eee 76
                                   +v+i G+G IG++va+ ++ + +m++i++ ++  + e  ++ 
  gi|70607114|ref|YP_255984.1|  4 VKVAINGYGTIGKRVADAIRlQPDMELIGVAKTSPNYEafTAM 46
                                  5899***************9999*****999887755533333 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.8e-05     0.035       1      94 [.       5     107 ..       5     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT..TTTSBHHHHSG......GGTTTECEBEEE..GGGGGCTT-SEEE CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssr..saGkklaeavk......aleegkdlkved..vdeeelkevdivf 71 
                                   kvai G  G +G++++  ++ +p++el+ ++ +s   +a +++++ +k      ++++ ++  ++     e+ +k+ di++
  gi|70607114|ref|YP_255984.1|   5 KVAING-YGTIGKRVADAIRLQPDMELIGVAKTSPnyEAFTAMRKGYKlyttkeNIQKFQNSGINVagSIEDMIKDSDIII 84 
                                   688888.8999***************999998888454444555555577777744444444444443677777******* PP

                                   E-SCHHHHHHHHHHHHHTTSEEE CS
                Semialdhyde_dh  72 lalpagvskelapklaeagvkvi 94 
                                    a+p+gv +++ + + e g k i
  gi|70607114|ref|YP_255984.1|  85 DATPGGVGANYKKIYQEYGKKAI 107
                                   ***********999999988765 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.1e-05     0.042       1      89 [.       4     107 ..       4     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.................HHHHHTCTTES CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.................leelladpeid 64 
                                   ++vai G+G ig++ + +++ + ++ e++++ +++++     a + g + y+                  +e++ +  + d
  gi|70607114|ref|YP_255984.1|   4 VKVAINGYGTIGKRVADAIRLQ-PDMELIGVAKTSPNYEAFTAMRKGYKLYTTkeniqkfqnsginvagsIEDMIK--DSD 81 
                                   589*************777666.*********99998888888888888888777888888899999888999999..669 PP

                                   EEEE-S-GGGHHHHHHHHHHTT-.EE CS
                  GFO_IDH_MocA  65 avivatpngtheelakaaleagk.hv 89 
                                   ++i atp g ++++ k   e gk ++
  gi|70607114|ref|YP_255984.1|  82 IIIDATPGGVGANYKKIYQEYGKkAI 107
                                   99999999888888777777666555 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00016      0.31       5      60 ..       4      61 ..       1      83 [. 0.81
   2 ?    3.3   0.0     0.027        54      37      73 ..      55      92 ..      52     112 .. 0.75
   3 ?   -2.0   0.0       1.1   2.2e+03     129     144 ..     290     305 ..     284     316 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                  S-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHH..HHHHTT-EEEEHHHHHHT CS
                          IlvN  5 kkiaviGyGsqGhaqalnlrdsgldvvvglregsksvk..kAkeegfevltvaeavkk 60
                                   k+a+ GyG+ G+  a  +r +     +g+ ++s +++  +A+++g++ +t++e ++k
  gi|70607114|ref|YP_255984.1|  4 VKVAINGYGTIGKRVADAIRLQPDMELIGVAKTSPNYEafTAMRKGYKLYTTKENIQK 61
                                  69************9999997766667888888865542279************9987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.027
                                  T-HHHHHHHHTT-EEE.EHHHHHHT-SEEEE-S-HHHH CS
                          IlvN 37 gsksvkkAkeegfevl.tvaeavkkadvvmiliPDelq 73
                                  ++++++k +++g++v+ ++++++k++d+++  +P  + 
  gi|70607114|ref|YP_255984.1| 55 TKENIQKFQNSGINVAgSIEDMIKDSDIIIDATPGGVG 92
                                  567889999999999647999********999997654 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                                   HTT----EEEEEEE-S CS
                          IlvN 129 eegkGvpaliaveqda 144
                                   ++g+ +  +++v+q++
  gi|70607114|ref|YP_255984.1| 290 TNGNEIFLMYGVHQES 305
                                   5555555555555543 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     8e-05      0.16       1      61 [.       5      69 ..       5      80 .. 0.74
   2 ?   -1.2   0.0       1.7   3.3e+03      13      45 ..     263     300 ..     261     317 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                        PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk.....tevegypvlgkaiellkslseeeyev 61
                                  k++I G G  gk vad i+ + + e+ig+   +++        +gy+ + +  e+++++++  ++v
  gi|70607114|ref|YP_255984.1|  5 KVAINGYGTIGKRVADAIRLQPDMELIGVAKTSPNyeaftAMRKGYKLYTT-KENIQKFQNSGINV 69
                                  799*************************99886543233223568888775.46666665555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                        PglD_N  13 vvadiieangeye....iigflDdnkkteveg.ypvlg 45 
                                   ++ +i+++ g+y+    + +++ d+  t+ ++ + ++g
  gi|70607114|ref|YP_255984.1| 263 EIMEIARDLGRYRndvpETVIFEDSIYTNGNEiFLMYG 300
                                   57788888887764444455555554333333133333 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.64       1      68 [.      10      88 ..      10     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                  --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT..................HHHHHT--CB---HHHHHHHHS-EEEEE CS
                 NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrdsllskd..................rkallasealtldlddliahldpdvvVE 65
                                  G+G+iG++v+++++ q++   +el +va+ +   +++                   k +     +  +++d+i+  d d++++
  gi|70607114|ref|YP_255984.1| 10 GYGTIGKRVADAIRLQPD---MELIGVAKTS--PNYEaftamrkgyklyttkeniQKFQNSGINVAGSIEDMIK--DSDIIID 85
                                  99***************6...8999999999..33333468888888888877744444445577888999999..9999999 PP

                                  -S- CS
                 NAD_binding_3 66 cas 68
                                  +++
  gi|70607114|ref|YP_255984.1| 86 ATP 88
                                  975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2218.24
//
Query:       gi|70607115|ref|YP_255985.1|  [L=135]
Description: hypothetical protein Saci_1357 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-21   76.6   0.3    1.1e-18   68.0   0.3    2.0  1  Usp             Universal stress protein family
      0.009   15.9   0.0      0.012   15.5   0.0    1.2  1  ETF             Electron transfer flavoprotein domain
  ------ inclusion threshold ------
      0.031   13.9   0.0      0.038   13.6   0.0    1.2  1  Peptidase_C71   Pseudomurein endo-isopeptidase Pei
        0.1   13.1   0.2       0.17   12.5   0.2    1.3  1  EF-G-binding_N  Elongation factor G-binding protein, N-termin


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.3   2.6e-22   1.1e-18       3     141 .]      13     135 .]      12     135 .] 0.90

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 2.6e-22
                                   SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEE CS
                           Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkve 83 
                                   +rIlV++Dgse+s +Al+ A+++a ++g+++++lhv++  ++++v +  ++    + ++                  ++ +
  gi|70607115|ref|YP_255985.1|  13 RRILVPIDGSENSLRALDLAVDFAMRYGSKVTVLHVCENCNDKEVEEHVKKRVNGRIVYD----------------FKVLK 77 
                                   8*************************************9998777655555555555544................56889 PP

                                   EEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  84 vvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                      +e +++ eil++ +e  +d +++G+rg+s  s+l +GSv+ +v+ +ap  V++Vr
  gi|70607115|ref|YP_255985.1|  78 YSSKESSVSNEILKHINESTYDAVIMGARGLSISSELNVGSVAVSVALNAPTTVILVR 135
                                   9*****************************999999*********************8 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-06     0.012      15      99 ..      23     107 ..      20     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                                   HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS-.-CCHHHHHHHHHHHHC--SEEE CS
                           ETF  15 pvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagy.daeatakalaalikkedpdlvl 94 
                                   +++l al  A+ ++ + g +vt++ v++++ ++ ++e ++ + +   i+ d   l+ +     +++ + + i++  +d v+
  gi|70607115|ref|YP_255985.1|  23 ENSLRALDLAVDFAMRYGSKVTVLHVCENCNDKEVEEHVK-KRVNGRIVYDFKVLKYSsKESSVSNEILKHINESTYDAVI 102
                                   689**********99999**********999999999999.88877777777777755356678899999999999***** PP

                                   EESSC CS
                           ETF  95 agata 99 
                                   +ga+ 
  gi|70607115|ref|YP_255985.1| 103 MGARG 107
                                   *9975 PP

>> Peptidase_C71  Pseudomurein endo-isopeptidase Pei
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.5e-06     0.038      66     112 ..      34      80 ..      18      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-06
                 Peptidase_C71  66 kvlealGyevkiehvrvrcndgkwyGhyllrvkgkeladgtvwdyvs 112
                                         G +v + hv   cnd +   h+  rv+g  + d  v +y s
  gi|70607115|ref|YP_255985.1|  34 DFAMRYGSKVTVLHVCENCNDKEVEEHVKKRVNGRIVYDFKVLKYSS 80 
                                   555667889**************************999999999976 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.7e-05      0.17      17      63 ..      45      97 ..      42     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                EF-G-binding_N 17 llnayrsvnDkkvveavkalaaekIlelfpelseeq......kelLeqiddik 63
                                  +l++++++nDk+v e vk  ++ +I   f+ l+  +      +e+L++i++ +
  gi|70607115|ref|YP_255985.1| 45 VLHVCENCNDKEVEEHVKKRVNGRIVYDFKVLKYSSkessvsNEILKHINEST 97
                                  799*********************99886665433322244578888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 982.72
//
Query:       gi|70607116|ref|YP_255986.1|  [L=433]
Description: serine hydroxymethyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-65  218.8   0.0    1.2e-64  218.4   0.0    1.1  1  SHMT             Serine hydroxymethyltransferase
      8e-09   35.1   0.0    3.7e-08   32.9   0.0    1.9  1  Aminotran_1_2    Aminotransferase class I and II
    2.7e-08   33.4   0.0    4.3e-08   32.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00081   18.5   0.0     0.0014   17.6   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
     0.0014   17.7   0.0     0.0036   16.4   0.0    1.8  2  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.026   13.8   0.0      0.064   12.6   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.028   13.0   0.0      0.038   12.5   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.046   13.5   1.1        1.7    8.5   0.0    2.9  3  XTBD             XRN-Two Binding Domain, XTBD
       0.11   12.6   0.3       0.54   10.4   0.0    2.2  2  CheD             CheD chemotactic sensory transduction
       0.31   11.3   3.4        3.4    7.9   0.6    2.8  3  MRPL52           Mitoribosomal protein mL52
        1.9    8.4   6.4          5    7.0   0.3    3.2  3  DUF919           Nucleopolyhedrovirus protein of unknown func


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.4   0.0   7.1e-68   1.2e-64       7     398 ..      10     384 ..       4     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 7.1e-68
                                   HHHHHHH.HHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTE CS
                          SHMT   7 evaeiik.kekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakw 86 
                                   ++ +i++ +++ r+ e+i+li+sen++s+ +  +  s +  +yaeG P kryy G+++ de+eela++   e+ + +    
  gi|70607116|ref|YP_255986.1|  10 KILQITReQNRWRRLETINLIPSENVMSPLAESVYMSDFMYRYAEGKPFKRYYQGTKYADEIEELAMKLVSEISSSK---- 86 
                                   4556654144558889********************************************************99999.... PP

                                   EEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHH CS
                          SHMT  87 gvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkake 167
                                   ++++++ sG+ an+ v+  l + gd+ +   + +G h++h        + a ++    ++y   +e   +d d+  k  +e
  gi|70607116|ref|YP_255986.1|  87 YADLRAVSGTIANAGVFRVLADSGDKAVIAPVQAGAHVSHTRFGT---LGALGIEQIEMPYD--QESMNVDVDKAIKLIEE 162
                                   ****************************************76555...58999988888886..56899************ PP

                                   H--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC-S CS
                          SHMT 168 fkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillrkg 247
                                   +kPk++  G s y      + l    + vga l+ d ah+ Gl++++   +P+e  advvt+ thkt+ Gp+ggli+++  
  gi|70607116|ref|YP_255986.1| 163 VKPKFVTLGGSLYLFPHPVKELAPHVHAVGAKLVYDSAHVYGLIVGKAWHNPLEEgADVVTASTHKTFPGPQGGLIVTN-- 241
                                   *****************************************************7549**********************.. PP

                                   EEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEGGGS. CS
                          SHMT 248 vksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyklvsgG. 327
                                              ++ l+kk+  ++fP      + h + ++a++  e ++   k+y++q++knakalaeal  +g+k++ +  
  gi|70607116|ref|YP_255986.1| 242 -----------DDSLYKKVSDTIFPWFVSNHHLHRLPSTAITALE-MKYFGKEYAQQIVKNAKALAEALAAEGFKVIGEHl 310
                                   ...........689************************9996433.44455**************************8633 PP

                                   ..-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT.-SEEEEESHHHHHTT--HHHHHHHHHH CS
                          SHMT 328 ..tdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalv.tsGlrlGtpaltsrgfkeedlekvakf 398
                                     t +h v +d+r+ g  G+++ k+ e++ni ankn +P+d  sa+  +sG+rlG   +t+ g+kee+++ +a++
  gi|70607116|ref|YP_255986.1| 311 gfTKSHQVAIDVRNLG-GGAKVAKLFEEANIIANKNLLPYDpPSAVKdPSGVRLGVQEMTRFGMKEEEMRIIARL 384
                                   349**********998.7999********************97777549**********************9987 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.3e-11   3.7e-08      40     306 ..      62     312 ..      51     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.3e-11
                                   T-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-E.EEEE..ESS-THHHHH..HHHTTS CS
                 Aminotran_1_2  40 ygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgde.ilvp..dptyasykni..lrlsgg 115
                                   y+ ++ ++e ee  +k+++   +++  + a +   sG+ a++ ++  l++   gd+ +++p  +  + s+++   l + g+
  gi|70607116|ref|YP_255986.1|  62 YQGTKYADEIEELAMKLVS---EISSSKYADLRAVSGTIANAGVFRVLAD--SGDKaVIAPvqAGAHVSHTRFgtLGALGI 137
                                   7899999************...88999999************99999996..66661554422457999998522677899 PP

                                   EEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSS CS
                 Aminotran_1_2 116 evvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfg 196
                                   e +++p y++e++++d+++ +++++e      k+k++ + +        + +  +++l+ ++++ ++ l+ D a+  +   
  gi|70607116|ref|YP_255986.1| 138 EQIEMP-YDQESMNVDVDKAIKLIEEV-----KPKFVTLGGS-----LYLFPHPVKELAPHVHAVGAKLVYDSAHVYGLIV 207
                                   99****.77****************95.....89****9863.....5666777*********************877766 PP

                                   SSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 197 sldavatranveeepnllivgslsKaf.GlaGeRvGyilg.naavvsqlrklsrpflsssllqaavaaalsdallkqsele 275
                                    + a+  +  +ee+ + +++ s  K f G  G   G i+  ++ + + + +   p+ +s++  + +   + +al+++ + +
  gi|70607116|ref|YP_255986.1| 208 GK-AW--HNPLEEGAD-VVTASTHKTFpGPQG---GLIVTnDDSLYKKVSDTIFPWFVSNHHLHRLPSTAITALEMKYFGK 281
                                   43.22..455666656.888888888889999...*****7779***********99966666666666666666667*** PP

                                   HHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                 Aminotran_1_2 276 emrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                   e +q++ k++k l ++La+ g+kv++++ g+
  gi|70607116|ref|YP_255986.1| 282 EYAQQIVKNAKALAEALAAEGFKVIGEHLGF 312
                                   *****************999*****987665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   2.6e-11   4.3e-08      49     267 ..      88     382 ..      45     423 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.6e-11
                                   EEEEES-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS- CS
               Beta_elim_lyase  49 aalfvpqGtaAnsillkillqrgeevivtep...ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgahee 126
                                   a l +++Gt An+  +++l+ +g++ ++      ah+  +  g + +l+  +    + +e  ++d++k  ++i+e      
  gi|70607116|ref|YP_255986.1|  88 ADLRAVSGTIANAGVFRVLADSGDKAVIAPVqagAHVSHTRFGTLGALGIEQIEMPYDQESMNVDVDKAIKLIEE-----V 163
                                   556689**************9998877654446666655555666666555555555556588999999999999.....6 PP

                                   EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EE CS
               Beta_elim_lyase 127 kiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgv 207
                                   k+k+++l           + +  ++e+a  +++ g +l++D+A ++      ++    + +++D+vt+s  K    + Gg+
  gi|70607116|ref|YP_255986.1| 164 KPKFVTLGGSLY------LFPHPVKELAPHVHAVGAKLVYDSAHVYGLI-VGKAWHNPLEEGADVVTASTHKTFPGPQGGL 237
                                   889998754444......3567799********************9877.344444455589******************* PP

                                   EEE-HH.......................................HHHHHHHHHHHHT---SSTHHHHH............ CS
               Beta_elim_lyase 208 lafrddel...................................edylaerveqrkylggglrqagvlaa............ 241
                                   ++++dd+l                                   ++y ++ v+ +k+l++ l   g+++             
  gi|70607116|ref|YP_255986.1| 238 IVTNDDSLykkvsdtifpwfvsnhhlhrlpstaitalemkyfgKEYAQQIVKNAKALAEALAAEGFKVIgehlgftkshqv 318
                                   ******99**********************************************************999888888888888 PP

                                   .........................................................HHHHHHHHSSTTHHHHHHHHHHHH CS
               Beta_elim_lyase 242 .......................................................leagiraleeglaslerdhktaeqla 267
                                                                                          +                  +  +  a
  gi|70607116|ref|YP_255986.1| 319 aidvrnlgggakvaklfeeaniianknllpydppsavkdpsgvrlgvqemtrfgmK-----------------EEEMRIIA 382
                                   88888888888888888777777777777777777777444444444444444333.................33333333 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.9e-07    0.0014      77     214 ..     102     242 ..      46     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.9e-07
                                   HHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB...ETTSCBEGGGHHHH--TTEEEEEEESBETTTTE CS
                   Aminotran_5  77 valslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl...deegeldldelekllnektklvaithvsnvtGt 154
                                   v + l    + gd++v+  +   a +    +      + ++ i++   +e  ++d+d++ kl+ e++k  ++t   +    
  gi|70607116|ref|YP_255986.1| 102 VFRVL---ADSGDKAVIAPVQAGAHV-SHTRFGTLGALGIEQIEMpydQESMNVDVDKAIKLI-EEVKPKFVTLGGSLYLF 177
                                   44444...455555555544433333.333333333333333333111555566677776666.55555555666666667 PP

                                   B--HHHHHHHHHHTT-EEEEE-TTT....TTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEE CS
                   Aminotran_5 155 iqpveeigklakkkgalvlvDaaqa....vghipidvkklgvDflafsghK.llgPtGiGvlyvr 214
                                    +pv+e++ +++++ga ++ D+a      vg++  +  + g+D++++s+hK + gP+G  ++   
  gi|70607116|ref|YP_255986.1| 178 PHPVKELAPHVHAVGAKLVYDSAHVygliVGKAWHNPLEEGADVVTASTHKtFPGPQGGLIVTND 242
                                   89*********************973333678899999*************999***95444444 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       3.5   5.7e+03     206     223 ..     105     123 ..      98     126 .. 0.72
   2 !   16.4   0.0   2.2e-06    0.0036     186     230 ..     201     245 ..     182     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.5
                                   EEEEETTS.TT-SSS-EEE CS
                          SelA 206 lvsfsGDk.llGgpqaGii 223
                                   +++ sGDk ++  +qaG  
  gi|70607116|ref|YP_255986.1| 105 VLADSGDKaVIAPVQAGAH 123
                                   7788999944566799965 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.2e-06
                                   GGGT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHH CS
                          SelA 186 seyglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkeli 230
                                   + ygl      ++ l+eG+d+v+ s  k + gpq G+iv + + +
  gi|70607116|ref|YP_255986.1| 201 HVYGLIVGKAWHNPLEEGADVVTASTHKTFPGPQGGLIVTNDDSL 245
                                   45889999999999*************************987654 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.9e-05     0.064      92     195 ..     144     250 ..      92     283 .. 0.84
   2 ?   -3.7   0.0       3.5   5.7e+03     100     120 ..     394     414 ..     391     422 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                                   B-TTTSSB-GGGCGGG--TTE.EEEEE.B-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCSSSEEEE CS
               DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitert.kaIlp.VhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGalgdaavf 167
                                    d++++n+d++++ ++i+e   k +++   ly  +  +++l    ++ g k++ D+Ah  G  +      ++ + +d+ + 
  gi|70607116|ref|YP_255986.1| 144 YDQESMNVDVDKAIKLIEEVKpKFVTLgGSLYLFPHPVKELAPHVHAVGAKLVYDSAHVYGLIVGKawhNPLEEGADVVTA 224
                                   6788999999999999998776777652567777889999999999**************988877666788888899999 PP

                                   E-BTTSSS-SSS-EEEEESTHHHHHHHH CS
               DegT_DnrJ_EryC1 168 SFyptKnlttGeGGavvtndeelaekar 195
                                   S +  K++    GG++vtnd+ l +k++
  gi|70607116|ref|YP_255986.1| 225 STH--KTFPGPQGGLIVTNDDSLYKKVS 250
                                   976..8999***************9986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.5
                                   -GGGCGGG--TTEEEEEEB-G CS
               DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhl 120
                                   d++++++++te +k  l V +
  gi|70607116|ref|YP_255986.1| 394 DVKEVKKKVTEFRKEFLEVKY 414
                                   788999999999987777765 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.038      62     223 ..      80     249 ..      34     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                   HHHHT-SEE.EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHH.THHHTT...CEEEEESTTSHHHHHHHCCT. CS
               Cys_Met_Meta_PP  62 aaLeggeaa.lavssGmaAiaaailallkaGdeivvsddlYggtqrllkk.vlkklg...ievkfvdtsdleelekaike. 136
                                   +++ +++ a l   sG+ A a +++ l+ +Gd+ v+     g   +  +  +l  lg   ie+ + + s   ++ kaik  
  gi|70607116|ref|YP_255986.1|  80 SEISSSKYAdLRAVSGTIANAGVFRVLADSGDKAVIAPVQAGAHVSHTRFgTLGALGieqIEMPYDQESMNVDVDKAIKLi 160
                                   555555544234558888888888888888888776543333322222221333344000445555556666777877744 PP

                                   .TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS.....-GGGGT-SEEEEETTTTTTCSSS--EEEE CS
               Cys_Met_Meta_PP 137 .ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllq.....rplklgaDivvhSaTKylgGhsdvvaGvi 211
                                    ++k  ++   ++  l  + ++++a  ++++g+ +v D + + +l++     +pl+ gaD+v+ S+ K   G +   +G+i
  gi|70607116|ref|YP_255986.1| 161 eEVKPKFVTLGGSLYLFPHPVKELAPHVHAVGAKLVYDSAHVYGLIVgkawhNPLEEGADVVTASTHKTFPGPQ---GGLI 238
                                   47777788777777777788999999************998877654333339***************999987...7999 PP

                                   EESSCHHHHHHH CS
               Cys_Met_Meta_PP 212 vvkgkeelkkel 223
                                   v+++ ++l k++
  gi|70607116|ref|YP_255986.1| 239 VTND-DSLYKKV 249
                                   9888.6666655 PP

>> XTBD  XRN-Two Binding Domain, XTBD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.085   1.4e+02      44      68 ..      61      85 ..      35      96 .. 0.79
   2 ?    8.5   0.0     0.001       1.7      29      67 ..     262     300 ..     240     305 .. 0.87
   3 ?   -1.9   0.1       1.7   2.9e+03      15      17 ..     404     406 ..     375     425 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.085
                                  HTT--B--HHHHHHHHHHHTTTTXX CS
                          XTBD 44 vflGcrYprevmekvkelaegiaae 68
                                   + G++Y  e+ e  ++l ++i  +
  gi|70607116|ref|YP_255986.1| 61 YYQGTKYADEIEELAMKLVSEISSS 85
                                  5789******777777777777443 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                                   -HHHHHHHHHHHHHHHTT--B--HHHHHHHHHHHTTTTX CS
                          XTBD  29 eedrLlsLsmvfanlvflGcrYprevmekvkelaegiaa 67 
                                   +++rL s + +   ++++G +Y ++++++ k lae +aa
  gi|70607116|ref|YP_255986.1| 262 HLHRLPSTAITALEMKYFGKEYAQQIVKNAKALAEALAA 300
                                   6799999999999**********************9866 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.7
                                   HHH CS
                          XTBD  15 elr 17 
                                   e+r
  gi|70607116|ref|YP_255986.1| 404 EFR 406
                                   333 PP

>> CheD  CheD chemotactic sensory transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00033      0.54      67     102 ..     289     324 ..     285     333 .. 0.93
   2 ?   -1.7   0.1       1.9   3.1e+03      27      43 ..     364     380 ..     359     414 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                                   HHHHHHHHHHHHTT--EEEEEE-SSS-EEEEEETTT CS
                          CheD  67 rNveavkelLkeegipivaedvggnygRtvlfdpat 102
                                   +N++a+ e+L++eg++++ e++g +++ +v +d+++
  gi|70607116|ref|YP_255986.1| 289 KNAKALAEALAAEGFKVIGEHLGFTKSHQVAIDVRN 324
                                   7*****************************999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                   HHHHHHTTT--GGG-EE CS
                          CheD  27 Linellklgakkerlea 43 
                                    ++e+++ g+k+e++++
  gi|70607116|ref|YP_255986.1| 364 GVQEMTRFGMKEEEMRI 380
                                   56777777777777765 PP

>> MRPL52  Mitoribosomal protein mL52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.086   1.4e+02      12      58 ..      31      82 ..      17      92 .. 0.71
   2 ?   -2.7   0.0       4.3     7e+03      47      64 ..     280     297 ..     270     300 .. 0.69
   3 ?    7.9   0.6    0.0021       3.4      36      85 ..     363     412 ..     355     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.086
                        MRPL52 12 rspneyGpLtd...lpD..fsfaDGRpapvtsgqlkrkkkqeelakkivkll 58
                                  +s n+ +pL +   ++D  + +a+G+p     +  k++ + eela k+v  +
  gi|70607116|ref|YP_255986.1| 31 PSENVMSPLAEsvyMSDfmYRYAEGKPFKRYYQGTKYADEIEELAMKLVSEI 82
                                  56666666655222356224689****9999999999999999998877543 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                        MRPL52  47 qeelakkivkllsEidea 64 
                                    +e+a++ivk  + + ea
  gi|70607116|ref|YP_255986.1| 280 GKEYAQQIVKNAKALAEA 297
                                   578888888877666655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0021
                        MRPL52  36 vtsgqlkrkkkqeelakkivkllsEideaeerykkkqeeeeeeeqkiies 85 
                                   ++ +++ r   +ee +++i +l+ E+  +++ +k+ +++  e +++++e 
  gi|70607116|ref|YP_255986.1| 363 LGVQEMTRFGMKEEEMRIIARLMREVAIENKDVKEVKKKVTEFRKEFLEV 412
                                   677889999999*****************************999998875 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.6      0.42   6.9e+02      27      44 ..       8      25 ..       5      27 .. 0.85
   2 ?    2.1   0.0      0.11   1.8e+02      34      48 ..      65      79 ..      58      81 .. 0.85
   3 ?    7.0   0.3    0.0031         5      37      57 ..     392     412 ..     385     416 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.42
                        DUF919 27 fErlkkitKnpkElqdle 44
                                  +E++ +it +++  ++le
  gi|70607116|ref|YP_255986.1|  8 LEKILQITREQNRWRRLE 25
                                  69******9998888776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                        DUF919 34 tKnpkElqdlekkln 48
                                  tK++ E+++l +kl 
  gi|70607116|ref|YP_255986.1| 65 TKYADEIEELAMKLV 79
                                  9**********9985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0031
                        DUF919  37 pkElqdlekklnklRqeFLnf 57 
                                   +k ++++ kk+ + R+eFL+ 
  gi|70607116|ref|YP_255986.1| 392 NKDVKEVKKKVTEFRKEFLEV 412
                                   5678999************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2788.22
//
Query:       gi|70607117|ref|YP_255987.1|  [L=411]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.6e-127  423.7   1.0   6.5e-127  423.5   1.0    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
       0.17   12.1   0.1        0.5   10.6   0.1    1.8  1  SAC3         Leucine permease transcriptional regulator helic


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.5   1.0  7.3e-131  6.5e-127       2     367 .]      32     407 ..      31     407 .. 0.98

  Alignments for each domain:
  == domain 1  score: 423.5 bits;  conditional E-value: 7.3e-131
                                   HHHHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHHHHH CS
                   HMG-CoA_red   2 veeRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsasrga 77 
                                   + +Rr ++e+lt+++l +++++ +d +e+ +k+ EnviG+vq+PlG+ gpl+i+g+    +++vP+At+Eg+l+As++rga
  gi|70607117|ref|YP_255987.1|  32 MVARRLAIEKLTGAKLPSIGSTIIDyAEIRNKNAENVIGAVQVPLGIIGPLKIDGEyakgDFYVPLATTEGALIASVNRGA 112
                                   5689***************************************************************************** PP

                                   HHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEEEEEEEE- CS
                   HMG-CoA_red  78 kainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvvlrlkvdt 158
                                   ka++ sgG +++++ dgmtra+++ l+s++d+ae+ +w+  +++ e+l++ a+st+++g+l++ie+ + g++v+lr+ ++t
  gi|70607117|ref|YP_255987.1| 113 KAVTLSGGTRVKIFYDGMTRAPIFKLDSIRDVAEFLEWV--DKNKEKLEQVANSTTSHGKLSKIEPLILGNNVWLRFVFST 191
                                   ***************************************..6666666666679*************************** PP

                                   TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HH CS
                   HMG-CoA_red 159 gDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdln 239
                                   gDAmG+Nm ++a e+++e+ie+efg++++l++++N+c+dkk s+ina++grgk+vvaea i++++v++ lk ++  ++++n
  gi|70607117|ref|YP_255987.1| 192 GDAMGMNMATIASEKLCEFIEKEFGKATCLAVSGNVCSDKKQSMINALHGRGKTVVAEALIPDSIVKSALKSDKHLIHEVN 272
                                   ********************************************************************************* PP

                                   HH....HHHHHHH........HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.----SBSHHHHH-HHH CS
                   HMG-CoA_red 240 ra.n.igtankGi.ggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsleVGtvGGgtklppqa 317
                                    + n +g a++G  +++nah+aN+iaA+flAtGqD+a+v+ess++++++e  e+g ly+s+tl sleVGtvGGgt+lp+q+
  gi|70607117|ref|YP_255987.1| 273 LRkNwLGGARAGNiFQYNAHFANIIAAIFLATGQDIAQVVESSMGYTWTEVRENG-LYISITLNSLEVGTVGGGTRLPTQR 352
                                   ************99**************************************999.************************* PP

                                   HHHHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                   HMG-CoA_red 318 ellkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                   e+l+++gv g++     na+++aei+a+++LA+el +l+ALa+++l k+H kl+r
  gi|70607117|ref|YP_255987.1| 353 EALSIMGVLGSGnppgsNARKFAEIVASAVLAGELNLLSALANKELGKAHAKLGR 407
                                   ****************************************************997 PP

>> SAC3  Leucine permease transcriptional regulator helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.6e-05       0.5       2      42 ..       2      43 ..       1      45 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                                  HHHHHHHHHHHHHHHHHHH.HHHHHHHHH...HHHHHHHHHH CS
                          SAC3  2 kqitdeiiqdvVdseleki.lknllkeenrknerkqiIdsLs 42
                                  ++++d+i+ +vV+ +++   + nll+++++ ++r++ I++L+
  gi|70607117|ref|YP_255987.1|  2 QETIDNIVDKVVKGQIQFHeIDNLLEANAAMVARRLAIEKLT 43
                                  689*************9766********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2739.25
//
Query:       gi|70607118|ref|YP_255988.1|  [L=137]
Description: hypothetical protein Saci_1360 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-17   61.7   0.1      7e-17   61.2   0.1    1.2  1  OB_aCoA_assoc    DUF35 OB-fold domain, acyl-CoA-associated
    3.4e-05   23.6   0.0    5.1e-05   23.0   0.0    1.2  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.014   15.0   0.2    1.1  1  TackOD1          Thaumarchaeal output domain 1
      0.018   15.4   0.3      0.028   14.7   0.3    1.2  1  DUF2039          Uncharacterized conserved protein (DUF2039)
      0.039   13.6   3.8        2.5    7.8   0.1    2.4  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.04   14.0   1.4       0.12   12.6   1.4    1.8  1  Zn-ribbon_8      Zinc ribbon domain
      0.088   12.5   1.2       0.85    9.4   0.1    2.6  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.14   11.7   2.4       0.48   10.0   2.5    1.8  2  RecR             RecR protein
        2.2    8.1   6.1          5    7.0   6.1    1.6  1  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   3.5e-20     7e-17       4      65 .]      50     111 ..      48     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3.5e-20
                                   E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                 OB_aCoA_assoc   4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                   ++g+G ++ +t+ +++ +gf+++ P +vg+V+Ldegv i+a +++++p  ++ G rV+avfr
  gi|70607118|ref|YP_255988.1|  50 SKGTGSLVDYTILYQPRDGFEKQSPMIVGLVRLDEGVNIVAPITDAEPSKLKEGVRVEAVFR 111
                                   589**********************************************************7 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.6e-08   5.1e-05       7      37 .]      16      46 ..      12      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.6e-08
                       DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddle 37
                                  +rL +++C++CG   fP + +C  Cgs d+e
  gi|70607118|ref|YP_255988.1| 16 YRLALGKCKKCGNIKFPYQKICEVCGSLDVE 46
                                  8**************************9886 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   7.2e-06     0.014      75     100 ..      22      47 ..      10      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.2e-06
                       TackOD1  75 lCpsCksghlnvrevCpkCkSidiee 100
                                    C++C   ++ ++++C  C+S d+e+
  gi|70607118|ref|YP_255988.1|  22 KCKKCGNIKFPYQKICEVCGSLDVEK 47 
                                   7**********************986 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   1.4e-05     0.028      40      78 ..       8      42 ..       3      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                       DUF2039 40 eWkvkykkYkaltkkkkCvkCeektvkkaYhkiCkkCak 78
                                  +W+ k   Y+   + +kC+kC   ++k  Y+kiC+ C +
  gi|70607118|ref|YP_255988.1|  8 SWRLKDTLYRL--ALGKCKKC--GNIKFPYQKICEVCGS 42
                                  58888777776..4689****..79************75 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7     0.004       7.9       8      15 ..      22      29 ..      18      30 .. 0.94
   2 ?    7.8   0.1    0.0013       2.5       9      27 ..      37      57 ..      34      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                  E-TTT--E CS
               Desulfoferrod_N  8 kCevCGni 15
                                  kC+ CGni
  gi|70607118|ref|YP_255988.1| 22 KCKKCGNI 29
                                  9******9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                                  -TTT-..-EEEECC--SS-EE CS
               Desulfoferrod_N  9 CevCG..niVeVleaGgGeLV 27
                                  CevCG  ++ ++  +G G LV
  gi|70607118|ref|YP_255988.1| 37 CEVCGslDVEKIFSKGTGSLV 57
                                  *****4446789*******99 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   5.8e-05      0.12       7      40 .]      22      49 ..      15      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrrvi 40
                                  +C++Cg+   + q+        C  Cgs +v++++
  gi|70607118|ref|YP_255988.1| 22 KCKKCGNIKFPYQK-------ICEVCGSlDVEKIF 49
                                  5*****88888874.......5**********986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.17   3.4e+02      24      30 ..      23      29 ..      23      31 .. 0.72
   2 ?    9.4   0.1   0.00043      0.85       3      14 ..      33      44 ..      31      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.17
                       zf-RRN7 24 CrrChtq 30
                                  C+ C+++
  gi|70607118|ref|YP_255988.1| 23 CKKCGNI 29
                                  7788875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00043
                       zf-RRN7  3 kgppCgvCgcrs 14
                                  + ++C+vCg+ +
  gi|70607118|ref|YP_255988.1| 33 YQKICEVCGSLD 44
                                  6799*****933 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.5   0.00024      0.48      16      35 ..      20      41 ..      14      44 .. 0.86
   2 ?    4.0   0.2     0.019        38      18      27 ..      36      45 ..      34      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                                  -EE-TTT--E..ESSSS-CCCC CS
                          RecR 16 vrhCsrCgnl..teedlCaICs 35
                                  ++ C++Cgn+    + +C++C 
  gi|70607118|ref|YP_255988.1| 20 LGKCKKCGNIkfPYQKICEVCG 41
                                  578*******777889*****5 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.019
                                  E-TTT--EES CS
                          RecR 18 hCsrCgnlte 27
                                   C++Cg l+ 
  gi|70607118|ref|YP_255988.1| 36 ICEVCGSLDV 45
                                  6999999875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.1    0.0025         5       1      21 [.      22      42 ..      22      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
                 zinc_ribbon_2  1 fCpnCGaelq.dnakFCpyCGt 21
                                  +C++CG+ ++ + +k C+ CG+
  gi|70607118|ref|YP_255988.1| 22 KCKKCGN-IKfPYQKICEVCGS 42
                                  8******.555*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 872.58
//
Query:       gi|70607119|ref|YP_255989.1|  [L=364]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-05   25.0   0.0    1.6e-05   24.4   0.0    1.3  1  Thiolase_N   Thiolase, N-terminal domain
     0.0001   22.1   0.0     0.0055   16.5   0.0    2.4  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.8e-09   1.6e-05       3     190 ..       4     178 ..       2     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-09
                                   EEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-.TTSEEEEEE CS
                    Thiolase_N   3 ivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagip.eevpavtvn 82 
                                   iv+   t++ +    + +ls ++L +ea k+l++k + ++++ d viv+     + g+ni     + +g+  +++ +++++
  gi|70607119|ref|YP_255989.1|   4 IVGCGLTKLDR----YYELSEKDLVSEAYKQLITKIK-EYDQPDIVIVSSGYIDVLGKNILSSYKISSGLGlQNTKVMRIE 79 
                                   66666666666....788999************9999.5566666777777777778876666666655542778889998 PP

                                   HGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHH CS
                    Thiolase_N  83 kvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenla 163
                                   +    g +++ +a   i++g a+ v+++G  + s+ p ++  +   +++l++++   + i+        +   +l  +++ 
  gi|70607119|ref|YP_255989.1|  80 N-GDNGGASILTAYSFIKSGVAKKVLLIGIDKFSDYPSKYV-NEYLSYNLDNDYTYHVGITP-------HAYSALLMKRYM 151
                                   7.5778899****************************9997.77788888888887777766.......56778889**** PP

                                   HHHT--HHHHHHHHHHHHHHHHHHHHT CS
                    Thiolase_N 164 kkykisReeqdefAvkshqkaaaaqka 190
                                   kky+++ e   ++ +k hq+a++++ a
  gi|70607119|ref|YP_255989.1| 152 KKYNVDYEYFTKWPIKMHQNASENPLA 178
                                   **********************99855 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.1e-07    0.0055      14      39 ..      88     113 ..      79     121 .. 0.91
   2 !    3.1   0.0    0.0097        87      53      74 ..     208     228 ..     189     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.1e-07
                                   HHHHHHHHHTTS-SEEEEEEEEEGGG CS
                   ACP_syn_III  14 lsvAdaliesgaakrvLvigaetlsk 39 
                                   + +A ++i+sg ak+vL+ig +++s+
  gi|70607119|ref|YP_255989.1|  88 ILTAYSFIKSGVAKKVLLIGIDKFSD 113
                                   5689********************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0097
                                   -EEEEEEEEEEESSSSCEEEEE CS
                   ACP_syn_III  53 GDGAgAvvleaseeegarilds 74 
                                   +DGA  v+++a+e  + r +ds
  gi|70607119|ref|YP_255989.1| 208 ADGASVVLVTADEVAK-RYFDS 228
                                   79*******9985333.56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 1874.00
//
Query:       gi|70607120|ref|YP_255990.1|  [L=348]
Description: hypothetical protein Saci_1362 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-11   43.5   0.0    2.6e-10   40.3   0.0    2.6  4  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.1e-05   25.4   0.1    1.6e-05   24.8   0.1    1.2  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
    0.00015   21.5   0.3    0.00036   20.3   0.2    1.8  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00047   19.9   0.1      0.034   13.8   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
  ------ inclusion threshold ------
       0.11   11.8   0.4       0.16   11.3   0.4    1.1  1  Thiolase_N      Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.69   2.5e+03      26      40 ..      30      45 ..      21      58 .. 0.73
   2 ?   -3.7   0.0       3.8   1.4e+04       1      15 [.      62      76 ..      59      77 .. 0.75
   3 ?   -2.9   0.0       2.3   8.1e+03      57      81 ..     135     159 ..     119     161 .. 0.68
   4 !   40.3   0.0   7.3e-14   2.6e-10       2      81 ..     220     299 ..     219     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.69
                                  H.HHHHHT--GGGB-- CS
                 ACP_syn_III_C 26 a.vakklglpeekvvv 40
                                  + v+k+lgl+e+ v+ 
  gi|70607120|ref|YP_255990.1| 30 SqVVKNLGLSEKAVPD 45
                                  44999***99877754 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                                  HHHTT--GGG-SEEE CS
                 ACP_syn_III_C  1 Lekagltpedidalv 15
                                  L++a+++p++i +++
  gi|70607120|ref|YP_255990.1| 62 LRRANIDPSQIGVVL 76
                                  567888888887765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.3
                                   HHHHHHTTSS-TT-EEEEEEEETTT CS
                 ACP_syn_III_C  57 LdeaveegklkpgdlvllvgfGaGl 81 
                                   L    ++ + +pgd + l+++ a +
  gi|70607120|ref|YP_255990.1| 135 LVIGSDTAQSNPGDVLELSSAAASV 159
                                   5555666777888888888877765 PP

  == domain 4  score: 40.3 bits;  conditional E-value: 7.3e-14
                                   HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETT CS
                 ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGaG 80 
                                   +++g++ +d+d++v+hq n ++  +va+kl+++++kv   l    +Gn   as +l L++ ++    kpg+++l++ fG G
  gi|70607120|ref|YP_255990.1| 220 RENGYKISDFDYFVFHQPNGKFPLQVARKLEISMDKVKDGLvsPYIGNPYNASALLGLAKVLD--IAKPGQRILVAPFGSG 298
                                   689**********************************999976789*****************..99*********99999 PP

                                   T CS
                 ACP_syn_III_C  81 l 81 
                                    
  gi|70607120|ref|YP_255990.1| 299 A 299
                                   6 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   4.5e-09   1.6e-05       6     172 ..       4     166 ..       1     168 [. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.5e-09
                HMG_CoA_synt_N   6 gilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtetii 86 
                                   gi++   y+p   ++  e+ +  g+e+ +    lg ++ +  ++ ed  +++    ++ l+r ++d  +ig +  g+e+ +
  gi|70607120|ref|YP_255990.1|   4 GIVGWGAYIPRYRINVNEIANLWGLES-QVVKNLGLSEKAVPDVDEDSTTMAWESSKNALRRANIDPSQIGVVLFGSESKV 83 
                                   999999****************99986.456688889999999************************************99 PP

                HMG_CoA_synt_N  87 dksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgnarpt.ggagava 166
                                      k   ++l++ ++     d  g d   ac g +aal      +e+s+   +y lv+  d a  + g+       a +v+
  gi|70607120|ref|YP_255990.1|  84 YAVKPTATILIDALGV--TNDSLGADMEFACRGASAALRLVGGMVEASKI--KYGLVIGSDTAQSNPGDVLELsSAAASVS 160
                                   9999999999988877..56889***************999999999975..8************9999876515667789 PP

                HMG_CoA_synt_N 167 lligpd 172
                                    ++gp+
  gi|70607120|ref|YP_255990.1| 161 YIVGPE 166
                                   999997 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2     1e-07   0.00036       2      37 ..     107     142 ..     106     177 .. 0.91
   2 ?   -3.4   0.0       2.5   9.1e+03      39      57 ..     279     300 ..     277     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                                   EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEG CS
                   ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetl 37 
                                   D++ aC g+ +al ++ +++e+ ++k+ Lvig++t 
  gi|70607120|ref|YP_255990.1| 107 DMEFACRGASAALRLVGGMVEASKIKYGLVIGSDTA 142
                                   9999******************************96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.5
                                   GCS-TTT...HHHHTTB-EEEE CS
                   ACP_syn_III  39 kilDwkd...rstavlfGDGAg 57 
                                   k+lD ++   r  +  fG GAg
  gi|70607120|ref|YP_255990.1| 279 KVLDIAKpgqRILVAPFGSGAG 300
                                   5666654322555556888887 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.1    0.0079        28      65      82 ..     224     241 ..     207     249 .. 0.84
   2 !   13.8   0.0   9.6e-06     0.034     143     208 ..     255     315 ..     243     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0079
                                   --GGG-SEEEE--SSHHH CS
                HMG_CoA_synt_C  65 ftlddfdyvifhsPfckl 82 
                                     + dfdy +fh P  k+
  gi|70607120|ref|YP_255990.1| 224 YKISDFDYFVFHQPNGKF 241
                                   5689**********9885 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9.6e-06
                                   HTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STT CS
                HMG_CoA_synt_C 143 kvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsed 208
                                   kvk  l v+  +Gn Y as+   la +l  ++     g+ri++  +GsG  +  fs+ v+++  e+
  gi|70607120|ref|YP_255990.1| 255 KVKDGL-VSPYIGNPYNASALLGLAKVLDIAK----PGQRILVAPFGSGAGSDAFSILVTDKILEK 315
                                   666655.56689****************4443....59*********************9987664 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   4.4e-05      0.16      25     114 ..      52     141 ..      41     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHS CS
                    Thiolase_N  25 eLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagead 105
                                    ++ e  k++l +a++dp+++  v +G   +  + +  a  +  ++g+ ++     ++ +c  + +a+ l+ +++ a +++
  gi|70607120|ref|YP_255990.1|  52 TMAWESSKNALRRANIDPSQIGVVLFGSESKVYAVKPTATILIDALGVTNDSLGADMEFACRGASAALRLVGGMVEASKIK 132
                                   566677899*********************9999999******************************************** PP

                                   EEEEEEEEE CS
                    Thiolase_N 106 vvvagGvEs 114
                                     +++G  +
  gi|70607120|ref|YP_255990.1| 133 YGLVIGSDT 141
                                   *****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2211.75
//
Query:       gi|70607121|ref|YP_255991.1|  [L=130]
Description: S-adenosylmethionine decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-31  107.3   0.0    4.9e-31  107.1   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   2.8e-35   4.9e-31       1     105 [.      20     127 ..      20     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.8e-35
                                   EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-..SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST CS
                     AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkf..epeGvsvvvliaeShlsiHtwpetgyaaiDvftcge 79 
                                   h++ +ly++d +ll d++lle ++ ea+++++++++++++++f  +++Gvsv++l++eSh+++Htw+e++ya++Dv+tcg 
  gi|70607121|ref|YP_255991.1|  20 HVFGNLYDIDDKLLMDKDLLEGLVLEAVKIAKMNLVEIKSWSFggKKGGVSVIALVEESHIALHTWNEYKYATLDVYTCGV 100
                                   999****************************************88778********************************* PP

                                   .HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                     AdoMet_dc  80 .ispekaleylieafkadrvtvdelkR 105
                                     +p++a+e++++++k++r+++  ++R
  gi|70607121|ref|YP_255991.1| 101 dSNPQAAFEFIVSNLKPKRHQMFFADR 127
                                   ********************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 893.82
//
Query:       gi|70607122|ref|YP_255992.1|  [L=280]
Description: hypothetical protein Saci_1364 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.0   0.1     0.0022   18.0   0.1    1.5  1  PapC_N    PapC N-terminal domain


Domain annotation for each model (and alignments):
>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.2e-07    0.0022      25      55 ..     212     242 ..     194     267 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-07
                                   SS-SEEEEEEEEETTEEEEEEEEEEEECCTC CS
                        PapC_N  25 avlpGeYrvdvyvNgkeigrqevefkaekkk 55 
                                   +++pGeY+v+vy N++ i+++++++++++ +
  gi|70607122|ref|YP_255992.1| 212 KIQPGEYTVKVYANNTLINQTQITLNPKQIS 242
                                   689*********************9987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1921.35
//
Query:       gi|70607123|ref|YP_255993.1|  [L=173]
Description: hypothetical protein Saci_1366 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.2   3.2      0.034   13.9   3.2    1.2  1  AAA_11    AAA domain


Domain annotation for each model (and alignments):
>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.2   1.9e-06     0.034      68     175 ..      50     170 ..      22     173 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-06
                        AAA_11  68 DellerllrglldsegekykpkivRvgneeeriseavksvsleekvekrlekee................kaqlakeiske 132
                                    +  +r+++gl+++    + +k++R+g ++ ++++++  +   + ++k +                    + +++k isk+
  gi|70607123|ref|YP_255993.1|  50 SNNGLRVVNGLKSKYALPEPLKLLRIGVPK-EVNSENITFEYVTFFDKDYVLIGfyttyefdkpfvvlefEKNQTKIISKS 129
                                   555667777666666667778*********.788888888888888888866559*********99999988888999999 PP

                        AAA_11 133 leklakelrafeeeeekeklkkskekskskleqerrklkkerk 175
                                   +++ a+ + ++  + +k+++kk+k+k+++k++ ++rk+k +++
  gi|70607123|ref|YP_255993.1| 130 ENDRAEVVTNQ--KVKKKTSKKKKRKKSAKKSSSKRKIKGKST 170
                                   99999888544..333455666666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2728  (0.152156); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1314.38
//
Query:       gi|70607124|ref|YP_255994.1|  [L=203]
Description: N-glycosylase/DNA lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   18.2   0.0      0.006   17.0   0.0    1.6  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.4e-07     0.006       3      99 ..      40     167 ..      38     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-07
                                   HHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTT..STTHHHHHHHHHHHHHHHH............... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx............... RF
                       HhH-GPD   3 ailsqqtsderanriierlferfgfptpedladadeekLrelire..lGfyrrKakyikelArilv............... 66 
                                   +il+++ s+ +a+++++ + ++        ++++de+++  l++e   +fy+ Kaky+   A+ l                
  gi|70607124|ref|YP_255994.1|  40 CILTSNSSFISAYKSMNYILDK--------ILYMDEKEISILLQEsgYRFYNLKAKYLYR-AKNLYgkvkktikeiadkdq 111
                                   6888888888888888888888........89*********99997789*********87.677777999*********** PP

                                   ..........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHH CS
                                   ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ..........................gkpdvlivvDvhvrrilkrlrsikekktkkkve 99 
                                                             g+ d l + D h+ r ++ l++  +   k+k e
  gi|70607124|ref|YP_255994.1| 112 mqarefiathiygigykeashflrnvGYLD-LAIIDRHILRFINNLGIPIKL--KSKRE 167
                                   **************************9999.5556*********99987665..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1505.62
//
Query:       gi|70607125|ref|YP_255995.1|  [L=310]
Description: D-isomer specific 2-hydroxyacid dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-53  179.1   0.2    9.7e-53  178.2   0.1    1.5  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    3.5e-34  117.4   0.7    3.9e-34  117.2   0.7    1.0  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.4e-07   31.8   0.8    1.4e-07   31.8   0.8    1.9  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
    3.8e-06   27.2   0.7    1.1e-05   25.7   0.2    1.9  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0001   21.7   1.2    0.00032   20.1   1.2    1.8  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0019   18.1   0.2     0.0053   16.7   0.1    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0027   17.3   0.2     0.0058   16.2   0.1    1.6  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0095   15.5   0.0        1.4    8.4   0.0    3.0  3  Peripla_BP_2    Periplasmic binding protein
  ------ inclusion threshold ------
      0.022   14.3   1.1       0.55    9.8   0.0    2.9  3  PrpR_N          Propionate catabolism activator
      0.059   13.4   1.1       0.31   11.1   0.1    2.3  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
        0.1   12.5   0.3       0.26   11.2   0.0    1.8  2  Rossmann-like   Rossmann-like domain
       0.13   13.0   6.8       0.66   10.7   0.8    3.4  3  PTS_IIB         PTS system, Lactose/Cellobiose specific IIB s
       0.13   11.8   3.3       0.21   11.1   0.4    2.6  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.18   12.4   1.7       0.45   11.1   0.3    2.5  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.6   3.3e+03      81      99 ..      33      51 ..      18      84 .. 0.69
   2 !  178.2   0.1   7.6e-56   9.7e-53       1     178 []     107     282 ..     107     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                                  EECSHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C 81 elvsleellaesDivslhl 99
                                  ++++l++++ + D++++  
  gi|70607125|ref|YP_255995.1| 33 SKEELQKIIYDYDVIVVRS 51
                                  5667777777777776644 PP

  == domain 2  score: 178.2 bits;  conditional E-value: 7.6e-56
                                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                   ++l++a++r+l +a +  ++g +   k++ g el+gkt+GiiG+GrIG++va +++a+gmkv+ayd    ke+ + ++g+e
  gi|70607125|ref|YP_255995.1| 107 IGLMIAAARNLYNAINLAKTGVF---KKIEGVELAGKTIGIIGFGRIGSKVATVANALGMKVLAYDILDIKER-ALKMGAE 183
                                   589********************...9*****************************************99877.8889*** PP

                                   ECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTC CS
                  2-Hacid_dh_C  82 lvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplped 162
                                    ++l+++l ++Di++lh+ + +et+ ++++e+++kmk+++i++Nt+R+++v+ + Lle +++gki ++a+Dvf++ep++e+
  gi|70607125|ref|YP_255995.1| 184 PCTLDDMLPRADIITLHVTVGKETKYILDREQFEKMKNNVIIVNTSRAAVVNGKILLEFIRKGKIFAYATDVFWNEPPKEE 264
                                   *******************************************************************************98 PP

                                   H..HHHHSTTEEE-SS-T CS
                  2-Hacid_dh_C 163 s..pllelpnviltPHia 178
                                      +ll++++vi+tPHi+
  gi|70607125|ref|YP_255995.1| 265 WeyELLRHERVIVTPHIG 282
                                   54488***********98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.7     3e-37   3.9e-34       1     126 [.       5     306 ..       5     310 .] 0.98

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 3e-37
                                   EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaak 81 
                                   +li++p++e  ++ l + +++++++ ++++eel + + d+d+++vrs+t+v++e++e+ +kLkviarag+GvDn+D + a+
  gi|70607125|ref|YP_255995.1|   5 ILITDPISEILINKLTKYNIKIDYRPDISKEELQKIIYDYDVIVVRSRTRVDKELIEKGKKLKVIARAGIGVDNIDTEEAE 85 
                                   799**************555899999******************************************************* PP

                                   HTT-EEEE-TTTTHHHHHHHH............................................................ CS
                                   xxxxxxxxxxxxxxxxxxxxx............................................................ RF
                    2-Hacid_dh  82 erGilVtnvpgystesvAElt............................................................ 102
                                   +r+i V+ +pg st+s+AElt                                                            
  gi|70607125|ref|YP_255995.1|  86 KRNIRVVYAPGTSTDSAAELTiglmiaaarnlynainlaktgvfkkiegvelagktigiigfgrigskvatvanalgmkvl 166
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                    2-Hacid_dh 103 ................................................................................. 102
                                                                                                                    
  gi|70607125|ref|YP_255995.1| 167 aydildikeralkmgaepctlddmlpradiitlhvtvgketkyildreqfekmknnviivntsraavvngkillefirkgk 247
                                   ********************************************************************************* PP

                                   ...................................T-BHHHHHHHHHHHHHHHHHHHTT CS
                                   ...................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                    2-Hacid_dh 103 ...................................aaTeeaqeniaeeaaenlvaflkg 126
                                                                      a T+eaq ++ae +a+nl++++k+
  gi|70607125|ref|YP_255995.1| 248 ifayatdvfwneppkeeweyellrhervivtphigAQTKEAQDRVAEVTAQNLINVMKE 306
                                   **********************************99*******************9987 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.4   1.7e+03     125     151 ..      45      71 ..      12      90 .. 0.67
   2 !   31.8   0.8   1.1e-10   1.4e-07      15     110 ..     131     229 ..     116     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                   T-EEEEEETTEEEEE-TTS-EEEEEGG CS
                 AdoHcyase_NAD 125 alkkeevkpqvdrvtlkdgkkiillae 151
                                   ++ +++ +++vd+  +++gkk+ ++a+
  gi|70607125|ref|YP_255995.1|  45 DVIVVRSRTRVDKELIEKGKKLKVIAR 71 
                                   333444455666666666666666654 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.1e-10
                                   HHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEE...EE-SS..SSS CS
                 AdoHcyase_NAD  15 ratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadiv...vtttG..nkd 90 
                                   +   v laGk++ ++G+G +G   a+  ++lG +v+  ++  i   +a+  G e  tl++++ +adi+   v t G  +k 
  gi|70607125|ref|YP_255995.1| 131 KIEGVELAGKTIGIIGFGRIGSKVATVANALGMKVLAYDILDIKE-RALKMGAEPCTLDDMLPRADIItlhV-TVGkeTKY 209
                                   5566889*********************************99986.5677799*************983323.34422577 PP

                                   SB-HHHHCCS-TTEEEEE-S CS
                 AdoHcyase_NAD  91 iitlehlkkmkddaivcniG 110
                                   i+ +e+++kmk+++i+ n  
  gi|70607125|ref|YP_255995.1| 210 ILDREQFEKMKNNVIIVNTS 229
                                   99**************9975 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6     2e+03     102     138 ..      82     117 ..      46     126 .. 0.62
   2 !   25.7   0.2   8.4e-09   1.1e-05       1      94 [.     141     233 ..     141     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                   HHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHH CS
                 NAD_binding_2 102 kelkekglkfldaPVSGGeegAekGtLsimvGGseea 138
                                   +e+++++++++ aP + ++  Ae  t+ +m+++ ++ 
  gi|70607125|ref|YP_255995.1|  82 EEAEKRNIRVVYAPGTSTDSAAEL-TIGLMIAAARNL 117
                                   455556666666664433333333.335555555555 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 8.4e-09
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                   +ig+iG G +Gs+ a+   + g+kv +y+   +  e++++ ga++++ + +++ ++d++ + v+ gk+++ ++++  +e++
  gi|70607125|ref|YP_255995.1| 141 TIGIIGFGRIGSKVATVANALGMKVLAYDIL-DIKERALKMGAEPCT-LDDMLPRADIITLHVTVGKETKYILDReQFEKM 219
                                   59***************************88.5667888899*9996.689***********************999**** PP

                                   -TT-EEEE-S---H CS
                 NAD_binding_2  81 kkgdilidgstssp 94 
                                   k++ i++++s +++
  gi|70607125|ref|YP_255995.1| 220 KNNVIIVNTSRAAV 233
                                   *******9997765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.2   2.5e-07   0.00032       6     126 ..     115     227 ..     110     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                                   HHHCSCGCTSEEETTCEETCB---..EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHH CS
                   AlaDh_PNT_C   6 akalekffggkgtlaGgvpgvepa..kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeel 84 
                                    + ++  + +k+ +  +++gve a  ++ +iG G  G + + +a++lg kV ++D+    +e+  ++ga+          +
  gi|70607125|ref|YP_255995.1| 115 RNLYNAINLAKTGVFKKIEGVELAgkTIGIIGFGRIGSKVATVANALGMKVLAYDILD-IKERALKMGAE--------PCT 186
                                   455666677777788899999866334669*************************965.55556668888........778 PP

                                   HHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEE CS
                   AlaDh_PNT_C  85 laeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivD 126
                                   l++ + +ad++   v   Gk++  ++++e  ++Mk++ +iv 
  gi|70607125|ref|YP_255995.1| 187 LDDMLPRADIITLHV-TVGKETKYILDREQFEKMKNNVIIVN 227
                                   999******865554.55999999*************99996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.6   4.6e+03      17      35 ..      68      86 ..      66      99 .. 0.81
   2 !   16.7   0.1   4.1e-06    0.0053       1      39 [.     141     182 ..     141     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.6
                                  HHHHTT-EEEEE-S-HHHH CS
                       3HCDH_N 17 vfasagleVvlvdiseeal 35
                                  v+a+ag+ V  +d++e+  
  gi|70607125|ref|YP_255995.1| 68 VIARAGIGVDNIDTEEAEK 86
                                  7899999999999988765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.1e-06
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S...-HHHHHHHH CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdi...seealekal 39 
                                   ++++iG G +G+++a+v+ + g++V  +di   +e+al+ ++
  gi|70607125|ref|YP_255995.1| 141 TIGIIGFGRIGSKVATVANALGMKVLAYDIldiKERALKMGA 182
                                   699***********************9988555677766655 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9     5e+03      78     113 ..      34      69 ..      28      90 .. 0.63
   2 !   16.2   0.1   4.6e-06    0.0058       2      91 ..     137     225 ..     136     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                   HHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEE CS
                          IlvN  78 eeeiepnlkegkalafahGfnihfglikppkdvdvv 113
                                   +ee+++ + + ++++  +   +  +li+  k+++v+
  gi|70607125|ref|YP_255995.1|  34 KEELQKIIYDYDVIVVRSRTRVDKELIEKGKKLKVI 69 
                                   555555555555555555555555556555555554 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.6e-06
                                   HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-.HHHHHHHHHHHT CS
                          IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP.Delqkevyeeei 81 
                                   l gk+i +iG+G  G   a+     g++v           ++A + g e  t++++  +ad++++ +   +  k ++++e 
  gi|70607125|ref|YP_255995.1| 137 LAGKTIGIIGFGRIGSKVATVANALGMKVLAYD--ILDIKERALKMGAEPCTLDDMLPRADIITLHVTvGKETKYILDREQ 215
                                   789************************997543..344689**********************976541555666666666 PP

                                   GGG--TT-EE CS
                          IlvN  82 epnlkegkal 91 
                                    +++k++ ++
  gi|70607125|ref|YP_255995.1| 216 FEKMKNNVII 225
                                   6666666555 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0011       1.4     178     213 ..      26      58 ..      13      68 .. 0.79
   2 ?    1.1   0.0      0.19   2.5e+02     178     203 ..      73     112 ..      64     136 .. 0.68
   3 ?    1.9   0.0      0.11   1.4e+02     178     203 ..     205     231 ..     151     250 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                                   STT-EEE-HHHHHH..H--SEEEEEEHHHHT-S--HHH CS
                  Peripla_BP_2 178 kseyeeisaEqila..sdpdvifvsgraeadnktglef 213
                                    +++ +is E++++  +d+dvi+v++r     + ++++
  gi|70607125|ref|YP_255995.1|  26 IDYRPDISKEELQKiiYDYDVIVVRSR-----TRVDKE 58 
                                   68999**********************.....333333 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                                   STT-EEE-HHHHHHH--SEEEEEEH..............H CS
                  Peripla_BP_2 178 kseyeeisaEqilasdpdvifvsgr..............a 203
                                   + + ++i+ E+  +++++v++  g+              a
  gi|70607125|ref|YP_255995.1|  73 GIGVDNIDTEEAEKRNIRVVYAPGTstdsaaeltiglmiA 112
                                   6677899*************99999555555555555555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.11
                                   STT-EEE-HHHHHHH--SEEEEEEH.H CS
                  Peripla_BP_2 178 kseyeeisaEqilasdpdvifvsgr.a 203
                                   k+    +++Eq+ +++  vi+v+++ a
  gi|70607125|ref|YP_255995.1| 205 KETKYILDREQFEKMKNNVIIVNTSrA 231
                                   55555689**************99943 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.18   2.3e+02     113     157 ..      82     124 ..      80     129 .. 0.75
   2 ?    9.8   0.0   0.00043      0.55      64     107 ..     132     175 ..     120     181 .. 0.84
   3 ?   -1.4   0.0       1.2   1.5e+03      66      89 ..     284     307 ..     281     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.18
                        PrpR_N 113 kelkaegvevvvGdgvvadlAekaGlksvlltsgkesvrqAieeA 157
                                   +e+ +++++vv  +g+++d A+++ +  ++      ++++Ai+ A
  gi|70607125|ref|YP_255995.1|  82 EEAEKRNIRVVYAPGTSTDSAAELTIGLMIAAA--RNLYNAINLA 124
                                   688999*************99998775444433..6666666655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
                        PrpR_N  64 lkqakklgekialvgfeniikglktlselldldieiytinseee 107
                                   ++ ++  g+ i+++gf++i ++++t++++l++++  y i + +e
  gi|70607125|ref|YP_255995.1| 132 IEGVELAGKTIGIIGFGRIGSKVATVANALGMKVLAYDILDIKE 175
                                   5666667889************************9999887776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                        PrpR_N  66 qakklgekialvgfeniikglktl 89 
                                   q k+ ++++a v+ +n+i+ +k++
  gi|70607125|ref|YP_255995.1| 284 QTKEAQDRVAEVTAQNLINVMKEM 307
                                   667788999999999999988875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.49   6.3e+02      67      83 ..      35      51 ..      16      92 .. 0.71
   2 ?   11.1   0.1   0.00024      0.31       8     101 ..     134     222 ..     128     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.49
                                  CGHHHHHHT-SEEEE-S CS
                  Shikimate_DH 67 eelkellaeadvvisat 83
                                  eel++++ ++dv+++  
  gi|70607125|ref|YP_255995.1| 35 EELQKIIYDYDVIVVRS 51
                                  78999999999988632 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
                                   S...TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS CS
                  Shikimate_DH   8 e.slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatasee 87 
                                   + +l++k++ +iG G+++++va+   a g+k   v+  ++   ke a ++++e    ++l+++  + + + + ++  + ++
  gi|70607125|ref|YP_255995.1| 134 GvELAGKTIGIIGFGRIGSKVATVANALGMK---VLAYDILDIKERALKMGAE---PCTLDDMLPRADIITLHVTVGKETK 208
                                   357999****************998888888...8999999999999999777...9999999877666666688889999 PP

                                   -SB-HHHHHCCHHH CS
                  Shikimate_DH  88 pilekeeveealkk 101
                                   +il++e++e+++++
  gi|70607125|ref|YP_255995.1| 209 YILDREQFEKMKNN 222
                                   *********99865 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.26      12     118 ..     141     245 ..     134     250 .. 0.84
   2 ?   -2.8   0.0       4.3   5.5e+03      42      68 ..     280     306 ..     270     310 .] 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                 Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaatg 92 
                                   ++Gii+ Gr+G+ +++  +  g +v +   +    +era ++  + +  +++d+  ra+++ l v   + ++ + +  + +
  gi|70607125|ref|YP_255995.1| 141 TIGIIGFGRIGSKVATVANALGMKVLAYDILD--IKERALKM--GAEPCTLDDMLPRADIITLHVTVGKETKYILDREQFE 217
                                   69**************9999999999977665..47888877..56677899***************************** PP

                 Rossmann-like  93 avraGtivahtsganGve..ilaPlteq 118
                                    +++  i++ ts a  v+  il   +++
  gi|70607125|ref|YP_255995.1| 218 KMKNNVIIVNTSRAAVVNgkILLEFIRK 245
                                   ************9987742255555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                 Rossmann-like  42 isaasreraerrlPdvpvlevedvaar 68 
                                   +  a  + a+ r+ +v+  ++ +v+++
  gi|70607125|ref|YP_255995.1| 280 HIGAQTKEAQDRVAEVTAQNLINVMKE 306
                                   445566667777777776666666655 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00051      0.66      24      81 ..      19      81 ..      12      90 .. 0.70
   2 ?    1.8   0.1      0.31   3.9e+02      48      77 ..     194     230 ..     152     242 .. 0.67
   3 ?    1.9   0.1      0.29   3.7e+02      51      82 ..     275     304 ..     272     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                                  HHHCTEEEEETTEE.GGGHHHHHHT-SEEEEEESSGG.CTHHHHTT....SEEEEECTTHHHCC CS
                       PTS_IIB 24 akelgieaegeagv.eleaeeiaddaDlvllapqvrv.kdlarfag....kpvavinikdalgi 81
                                  + + +i++     + + e ++i  d+D++++   +rv k+l ++ +    +  a i +++ +++
  gi|70607125|ref|YP_255995.1| 19 LTKYNIKIDYRPDIsKEELQKIIYDYDVIVVRSRTRVdKELIEKGKklkvIARAGIGVDN-IDT 81
                                  5677777777777788888999999************88888887733221233344444.444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                                   -SEEEEEE....SSGG.CTHHHHTT.S.EEEEECTTH CS
                       PTS_IIB  48 aDlvllap....qvrv.kdlarfag.k.pvavinikd 77 
                                   aD++ l+     ++++  d ++f++ k +v+++n++ 
  gi|70607125|ref|YP_255995.1| 194 ADIITLHVtvgkETKYiLDREQFEKmKnNVIIVNTSR 230
                                   5665554422226777866677777642688888776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.29
                                   EEEEESSGGCTHHHHTTSEEEEECTTHHHCCH CS
                       PTS_IIB  51 vllapqvrvkdlarfagkpvavinikdalgim 82 
                                   v+++p++   +++++++ +va ++ +++++ m
  gi|70607125|ref|YP_255995.1| 275 VIVTPHIG-AQTKEAQD-RVAEVTAQNLINVM 304
                                   89999999.48888888.89999999988655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.42   5.4e+02     105     125 ..      35      55 ..      19     103 .. 0.77
   2 ?   11.1   0.4   0.00017      0.21       2      44 ..     141     183 ..     140     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.42
                                   HHHHHHHHCEEEEEE-S---T CS
                UDPG_MGDP_dh_N 105 rsiaealkkgkvvvvkSTvpv 125
                                   +++++++ +++v+vv+S + v
  gi|70607125|ref|YP_255995.1|  35 EELQKIIYDYDVIVVRSRTRV 55 
                                   567788888888888886655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00017
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS- CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgki 44 
                                   +i +iG G +G   a+v +++g++v+  Di + k ++l+ g  
  gi|70607125|ref|YP_255995.1| 141 TIGIIGFGRIGSKVATVANALGMKVLAYDILDIKERALKMGAE 183
                                   799**************************98888777777665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.6   4.6e+03      53      73 ..      35      55 ..      18      71 .. 0.58
   2 ?   -1.7   0.1       3.4   4.4e+03      27      43 ..      45      61 ..      32      97 .. 0.58
   3 ?   11.1   0.3   0.00035      0.45       1      69 [.     141     201 ..     141     230 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                                  ECHHHHHHH-SEEEE-S-HHH CS
                 F420_oxidored 53 vdneeaaeeadvvvlavkped 73
                                   + ++ + + dv+v+  ++++
  gi|70607125|ref|YP_255995.1| 35 EELQKIIYDYDVIVVRSRTRV 55
                                  455555555555555444444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                                  CEEEEEESSCCCHHHHH CS
                 F420_oxidored 27 eivvansrnpekaeela 43
                                  +++v+ sr+    e ++
  gi|70607125|ref|YP_255995.1| 45 DVIVVRSRTRVDKELIE 61
                                  45544444433333222 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00035
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S CS
                 F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav 69 
                                   +igiiG+G++g+ +a  + a g    +++ a   +   ++e a ++g  +++ +  +++ +ad++ l v
  gi|70607125|ref|YP_255995.1| 141 TIGIIGFGRIGSKVATVANALG---MKVL-A--YDILDIKERALKMG--AEPCTLDDMLPRADIITLHV 201
                                   69***************99999...6666.4..34444444444444..33333666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2009.04
//
Query:       gi|70607126|ref|YP_255996.1|  [L=371]
Description: serine-glyoxylate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-27   96.4   0.0      2e-27   96.2   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    5.2e-07   29.2   0.0    7.8e-07   28.6   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    9.2e-06   24.4   0.0    1.4e-05   23.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00041   19.7   0.0    0.00055   19.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.017   14.2   0.1      0.038   13.0   0.0    1.6  2  DUF684           Protein of unknown function (DUF684)
      0.019   14.8   0.0       0.91    9.3   0.0    2.2  2  MCPVI            Minor capsid protein VI
      0.039   14.3   0.0         21    5.6   0.1    3.0  4  Fer2_BFD         BFD-like [2Fe-2S] binding domain
        0.2   10.4   0.0       0.28    9.8   0.0    1.2  1  DUF521           Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   8.8e-31     2e-27      13     338 ..      12     313 ..       1     336 [. 0.78

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 8.8e-31
                                   HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEE CS
                   Aminotran_5  13 qeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivv 93 
                                   ++Vl+a++             + h+g++++++v+  ++   + +  +     + t ++t a++++++s+    k+g++++ 
  gi|70607126|ref|YP_255996.1|  12 KSVLAATSLV-----------IDHRGNKFKDIVNRLEKLMIKHFSSK--RVALLTGSGTLAVEAMVYSF---TKRGEKVLA 76 
                                   5555555544...........77999999999999998876655544..34555666666*********...9******** PP

                                   ETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-E CS
                   Aminotran_5  94 teaehhanlvpwqelakrtgakvkvipldeegeldldelekll..nektklvaithvsnvtGt.iqpveeigklakkkgal 171
                                    + +  + +  ++ ++ r+ga+++ + +  + +  l+e+++ +  n+++  va+ h++++tG+ +  +eei + +k+kg  
  gi|70607126|ref|YP_255996.1|  77 LSYGEFGRR-LAESIK-RRGATLRLYDKPMGHSFSLEEVKQIIeeNKDVTTVALVHNETSTGIaLRNLEEISRFIKNKGLK 155
                                   *********.777776.88*********9**************66688999************9***************** PP

                                   EEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.S CS
                   Aminotran_5 172 vlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaG 251
                                   ++vD+++++  +++ v+++++D +a +++K l   +G+G++ v+++ l+++    l+++   +vsl+ +       k+e  
  gi|70607126|ref|YP_255996.1| 156 LIVDSVSGFAAYQLMVNEWKIDAVATGSQKaLASVPGLGFVAVSRDGLNEMVNEDLPTY--LDVSLHLKF----QDKYE-- 228
                                   ******************************88899****************88788777..666776555....45666.. PP

                                   S--HHHHHHHHH...HHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHH CS
                   Aminotran_5 252 Tpnvagiiglga...aleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLd 329
                                   Tp +++  +++a   a+e+le  g+e+ +k++++ ++y++++l+  +   l g   +++ +++v  +++    +d +  L+
  gi|70607126|ref|YP_255996.1| 229 TPFTPATGVFNAtlrAAELLELEGVERRWKRHEACTKYVRDALSYFGFSLL-GN--ENNFSNTVVAAIP--PIKDYRAKLK 304
                                   666666666666111667889999999****************98877766.53..2222222222222..2245555566 PP

                                   HTTEEEEEE CS
                   Aminotran_5 330 eegIavrsG 338
                                   e ++++ +G
  gi|70607126|ref|YP_255996.1| 305 EFNVEIAGG 313
                                   666666655 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   3.5e-10   7.8e-07      41     306 ..      30     285 ..       7     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.5e-10
                                   -BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THH....HHHHHHTTSEE CS
                 Aminotran_1_2  41 gpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasy....knilrlsggev 117
                                    +i     le+ ++k ++       kr  a+++gsG+ a+ +++  ++k  +g+++l+  ++y+++     + ++ +g+++
  gi|70607126|ref|YP_255996.1|  30 KDIV--NRLEKLMIKHFS------SKRV-ALLTGSGTLAVEAMVYSFTK--RGEKVLA--LSYGEFgrrlAESIKRRGATL 97 
                                   5555..789999999999......7888.*******************9..9999996..556655222278999****** PP

                                   EEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSS CS
                 Aminotran_1_2 118 vryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsl 198
                                   + y   ++ + +  le++++ ++e       + v  v+ +hN t t + l  le++ +++k ++l l+vD + +gf+    
  gi|70607126|ref|YP_255996.1|  98 RLYD--KPMGHSFSLEEVKQIIEE------NKDVTTVALVHNETSTGIALRNLEEISRFIKNKGLKLIVDSV-SGFAAY-- 167
                                   ****..99***************9......568999**********************************98.444444.. PP

                                   HTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEH...............HHHHHHHHHHHHHTS.SHHHHHHHHH CS
                 Aminotran_1_2 199 davatranveeepnllivgslsKaf.GlaGeRvGyilgna...............avvsqlrklsrpfls.ssllqaavaa 262
                                         + v+e   ++++++  Ka+ +++G  +G+++++                +v  +l+  +  +    +++  + +a
  gi|70607126|ref|YP_255996.1| 168 -----QLMVNEWKIDAVATGSQKALaSVPG--LGFVAVSRdglnemvnedlptylDVSLHLKF-QDKYETpFTPATGVFNA 240
                                   .....2334443336788888899966899..9*****7779999999999998877777654.44444448888888888 PP

                                   HHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
                 Aminotran_1_2 263 alsdallkqs.eleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                                    l++a+l +   +e + +r+++ +k++rd+L   g++ l++++++
  gi|70607126|ref|YP_255996.1| 241 TLRAAELLELeGVERRWKRHEACTKYVRDALSYFGFSLLGNENNF 285
                                   888888876657788889999999999999977799999999887 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   6.2e-09   1.4e-05      57     175 ..      36     161 ..      27     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6.2e-09
                                   HHHH.HHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHH CS
               Cys_Met_Meta_PP  57 leer.iaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleele 131
                                   le+  i +  +   al++ sG+ A++a++ ++ k G+++++ +  Yg   r l + +k+ g + + +d+      +lee++
  gi|70607126|ref|YP_255996.1|  36 LEKLmIKHFSSKRVALLTGSGTLAVEAMVYSFTKRGEKVLALS--YGEFGRRLAESIKRRGATLRLYDKpmghsFSLEEVK 114
                                   5554144566667899************************986..9**********************9777665788999 PP

                                   HHCCTT...EEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 132 kaiken...tklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                   + i+en   t + ++   t+  + +  +e+i++++k++g+ ++vD +
  gi|70607126|ref|YP_255996.1| 115 QIIEENkdvTTVALVHNETSTGIALRNLEEISRFIKNKGLKLIVDSV 161
                                   999885333555566666666677889******************86 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.4e-07   0.00055      34     169 ..      33     161 ..      23     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHHHTT.-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS
               Beta_elim_lyase  34 vnrLedavaelfg.keaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlek 113
                                   vnrLe+ + + f  k  al + +Gt A + ++  +++rge+v++ + + + ++ +  i    g++lr  +++    ++le+
  gi|70607126|ref|YP_255996.1|  33 VNRLEKLMIKHFSsKRVALLTGSGTLAVEAMVYSFTKRGEKVLALSYGEFGRRLAESI-KRRGATLRLYDKPMGHSFSLEE 112
                                   67888877666651558899**********************9998888777776666.55788899999999889***** PP

                                   HHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase 114 leaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                   ++++i+e+++    + + ++ + + t  G  + l +l+e++ + k++g++l++D+ 
  gi|70607126|ref|YP_255996.1| 113 VKQIIEENKD---VTTVALVHNETST--G--IALRNLEEISRFIKNKGLKLIVDSV 161
                                   *******555...4444444444443..4..6789*******************85 PP

>> DUF684  Protein of unknown function (DUF684)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.038     225     312 ..      80     167 ..      62     178 .. 0.87
   2 ?   -2.6   0.0      0.91     2e+03      61      75 ..     344     358 ..     342     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                        DUF684 225 anaedqliesfnrggcnvivyrSkkgktaseeeyeeikeevkklkneklkynknledilekqvvdiktlgencgfialvrk 305
                                    ++ ++l es++r+g +  +y    g++ s ee+++i ee k + +  l+ n+++  i+  ++++i ++ +n+g+ ++v++
  gi|70607126|ref|YP_255996.1|  80 GEFGRRLAESIKRRGATLRLYDKPMGHSFSLEEVKQIIEENKDVTTVALVHNETSTGIALRNLEEISRFIKNKGLKLIVDS 160
                                   46788999***********************************************************************99 PP

                        DUF684 306 dkkvevr 312
                                    + +++ 
  gi|70607126|ref|YP_255996.1| 161 VSGFAAY 167
                                   8877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.91
                        DUF684  61 enFkeayeknsPlel 75 
                                   ++F   yek++Ple 
  gi|70607126|ref|YP_255996.1| 344 RMFHSQYEKEPPLEC 358
                                   7899********985 PP

>> MCPVI  Minor capsid protein VI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00041      0.91      27      80 ..      76     129 ..      71     138 .. 0.87
   2 ?    3.2   0.0      0.03        66      40      99 ..     141     201 ..     130     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00041
                                   XXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         MCPVI  27 afsWgsLgssitsglkniGsfikntgskivnsstfqqlkqglkesnvlenvadl 80 
                                   a+s+g+ g ++  ++k  G +++ + + +++s + + +kq ++e+  +  va  
  gi|70607126|ref|YP_255996.1|  76 ALSYGEFGRRLAESIKRRGATLRLYDKPMGHSFSLEEVKQIIEENKDVTTVALV 129
                                   79****************************************998777666655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.03
                                   XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         MCPVI  40 glkniGsfikntgsk.ivnsstfqqlkqglkesnvlenvadlagetlsalvDigrlkvqkd 99 
                                    l++i +fikn g k iv+s ++  + q + ++  ++ va +  ++l+++  +g  +v +d
  gi|70607126|ref|YP_255996.1| 141 NLEEISRFIKNKGLKlIVDSVSGFAAYQLMVNEWKIDAVATGSQKALASVPGLGFVAVSRD 201
                                   577899*******9945789889999999999999999*****9***99999999998876 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0094        21       9      35 ..     109     136 ..     106     138 .. 0.88
   2 ?   -3.2   0.0       5.1   1.1e+04      23      34 ..     140     151 ..     139     154 .. 0.69
   3 ?   -3.3   0.0       5.5   1.2e+04       8      33 ..     198     222 ..     197     224 .. 0.73
   4 ?    5.2   0.0     0.013        28      17      40 ..     242     265 ..     237     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0094
                      Fer2_BFD   9 tegeIrdairrag.lttveevkrrtkag 35 
                                   + +e+++ i++++ +ttv+ v ++t +g
  gi|70607126|ref|YP_255996.1| 109 SLEEVKQIIEENKdVTTVALVHNETSTG 136
                                   6789*****99999***********988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                      Fer2_BFD  23 ttveevkrrtka 34 
                                   +++ee+ r+ k 
  gi|70607126|ref|YP_255996.1| 140 RNLEEISRFIKN 151
                                   677888877765 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.5
                      Fer2_BFD   8 vtegeIrdairraglttveevkrrtk 33 
                                   v+++ + + + ++ l t+ +v +++k
  gi|70607126|ref|YP_255996.1| 198 VSRDGLNEMV-NEDLPTYLDVSLHLK 222
                                   6677777788.666999988888876 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.013
                      Fer2_BFD  17 irraglttveevkrrtkagtgCgg 40 
                                    r+a+l ++e+v rr+k    C +
  gi|70607126|ref|YP_255996.1| 242 LRAAELLELEGVERRWKRHEACTK 265
                                   5567799***********999976 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00012      0.28     302     400 ..     109     207 ..     103     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00012
                        DUF521 302 sleElrelaellkgkkkkvkvelwvttsrevkeeaerlg.lveklekaGvkvlsdtCmvv...splikkkevkkvatnSgK 378
                                   sleE++++ e      k+v++  +v  ++++  ++++l+ + + ++++G k++ d+       + ++++++ ++vat S K
  gi|70607126|ref|YP_255996.1| 109 SLEEVKQIIEEN----KDVTTVALVHNETSTGIALRNLEeISRFIKNKGLKLIVDSVSGFaayQLMVNEWKIDAVATGSQK 185
                                   445555444433....4444444444444444444444306677***********9988888877888889********** PP

                        DUF521 379 aahYlpgltgvkvalgsleecv 400
                                   a+  +pgl+ v v    l+e+v
  gi|70607126|ref|YP_255996.1| 186 ALASVPGLGFVAVSRDGLNEMV 207
                                   ********99999888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2484.23
//
Query:       gi|70607127|ref|YP_255997.1|  [L=89]
Description: DNA-directed RNA polymerase subunit K [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   53.9   0.1    1.7e-14   53.5   0.1    1.2  1  RNA_pol_Rpb6    RNA polymerase Rpb6
    0.00071   19.6   0.5    0.00071   19.6   0.5    1.0  1  Pox_RNA_Pol_19  Poxvirus DNA-directed RNA polymerase 19 kDa s
     0.0099   14.2   0.0      0.011   14.1   0.0    1.0  1  DDE_Tnp_1_4     Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.1   2.8e-18   1.7e-14       4      49 .]      15      67 ..      12      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.8e-18
                                  TSS--HHHHHHHHHHHHHHH....HT..........S.S-SSSSTTCHHHHTT-S-- CS
                  RNA_pol_Rpb6  4 skvltrYelvriaakRArQieegesl..........e.tqkpvviAlrEiaegkipi 49
                                  +++lt+Ye++ri+++RA+Q+    s+          + +++ ++iA++E+  g +pi
  gi|70607127|ref|YP_255997.1| 15 KNKLTKYEIARIISARALQL----SMgalplidtsnLkSDDVISIAEEELKRGVLPI 67
                                  789*****************....9999999999984479***************97 PP

>> Pox_RNA_Pol_19  Poxvirus DNA-directed RNA polymerase 19 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   1.2e-07   0.00071      66     141 ..       4      83 ..       1      89 [] 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                Pox_RNA_Pol_19  66 ekisai.kkrytrrislfeitGilaesynllqrGrlPlvsdlsdetlkdnilkvvikeieegtcPiviek...nG..ells 140
                                   +ki++i k+++  +++ +ei+ i++     l  G lPl+   s+    d+++ +  +e++ g+ Pi i++   nG  el+s
  gi|70607127|ref|YP_255997.1|   4 DKINEIfKENWKNKLTKYEIARIISARALQLSMGALPLID-TSNL-KSDDVISIAEEELKRGVLPITIRRiypNGqvELIS 82 
                                   78888768899***************9999********95.4544.4589****************998644466334666 PP

                Pox_RNA_Pol_19 141 v 141
                                   v
  gi|70607127|ref|YP_255997.1|  83 V 83 
                                   5 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.8e-06     0.011      38      92 ..       4      58 ..       2      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-06
                   DDE_Tnp_1_4 38 rrlaaalkdkrkpslveHslekllrqrvyalalGyedlndadkLradpalklalg 92
                                  +++++++k++ k++l++++++ ++  r+++l +G   l d  +L++d ++++a +
  gi|70607127|ref|YP_255997.1|  4 DKINEIFKENWKNKLTKYEIARIISARALQLSMGALPLIDTSNLKSDDVISIAEE 58
                                  578999*******************************************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 584.54
//
Query:       gi|70607128|ref|YP_255998.1|  [L=668]
Description: DNA topoisomerase I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-106  357.1   0.2   1.8e-106  356.6   0.2    1.2  1  Topoisom_bac  DNA topoisomerase
    6.6e-17   61.6   2.3    9.5e-17   61.1   0.0    2.5  3  Toprim        Toprim domain
  ------ inclusion threshold ------
       0.13   11.4   2.8       0.21   10.7   2.8    1.3  1  Tmemb_cc2     Predicted transmembrane and coiled-coil 2 prote


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.6   0.2    3e-110  1.8e-106       3     412 ..     157     567 ..     155     568 .. 0.93

  Alignments for each domain:
  == domain 1  score: 356.6 bits;  conditional E-value: 3e-110
                  Topoisom_bac   3 nenlvdaaeaRrelDwliGinlsrlltk....klkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekk 78 
                                   + ++++a+ aR+++Dwl+Gin+sr+l+k      ++   +lsaGRVq+ptL  +++ + ++e Fvp +y+++++t++ ++k
  gi|70607128|ref|YP_255998.1| 157 DYDMIHAGIARHKVDWLWGINVSRALMKsvytL-TRkRVILSAGRVQSPTLIHVINNTVKRELFVPLPYYSINLTINLKNK 236
                                   6789************************76642.2247999**********************************987777 PP

                  Topoisom_bac  79 ekekkkkkkkerikdkeeaeaileklkk.keakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYeka 158
                                   e+   k    +++++k+ea+++le++kk +e++v+++e k    ++p pf++t+Lq ea r +g+s+  + ++a++LY + 
  gi|70607128|ref|YP_255998.1| 237 EF---KITIPKTFENKNEAKQYLEEIKKvGEVTVTNIELKDAVIYRPPPFNLTDLQLEAGRLFGYSPYLVERLAENLYLN- 313
                                   77...5899999**************99549*************7777*******************************7. PP

                  Topoisom_bac 159 glitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkks..vvknkkveaHeAIrPteelpklkelsddek 237
                                   gli+YpRT+s++++++ ++ +i+++l+k   k+y +  ++l + tk+k    +++k++ aH+AI+Pt+elp   +l+ +e 
  gi|70607128|ref|YP_255998.1| 314 GLISYPRTNSQKIPPSVNIYQIIDSLSKS--KRYGSLINTLSQITKGKYivRQGEKDDPAHPAIYPTGELP--YNLDTKEL 390
                                   ****************77*********96..78*************9998544455559************..58999999 PP

                  Topoisom_bac 238 klYelIvrrflaslmkdakyeettvklev..eeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkevele 316
                                   klYelI rrflas+++da++++++++l++   + e+k++ + ++ kG+  +y+++k ++ee  l ++k+g++ ++  ++ +
  gi|70607128|ref|YP_255998.1| 391 KLYELILRRFLASMSTDARVRKQEITLRIpkVDIELKLNIQSLIYKGWIILYPYTKFSDEE--LLDVKKGDKGRIVRANST 469
                                   ***************************77667899***********************997..****************** PP

                  Topoisom_bac 317 ekkTkpp.kryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvell.ekfkdlvspelTaele 395
                                    k Tkp  +r ++ +L+k+me++++Gt+aTr  iie+l++r+Y+ +k+k+ +pt+ G++++++l ++fkdl+++ lT+e+e
  gi|70607128|ref|YP_255998.1| 470 MKVTKPDtQRVSKIQLLKWMESNNLGTEATRGRIIETLFKRKYLMSKGKYAYPTPIGIVVTDVLsSYFKDLTDVRLTSEME 550
                                   ******879*************************************99****************6667************* PP

                  Topoisom_bac 396 ekLdeIaegkadakevl 412
                                   +kL+ I +gk +++ev+
  gi|70607128|ref|YP_255998.1| 551 KKLNGIISGKFSENEVV 567
                                   *************9998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   1.6e-20   9.5e-17       1     102 [.      10     140 ..      10     141 .. 0.96
   2 ?   -2.4   0.1      0.93   5.6e+03      38      58 ..     241     261 ..     203     266 .. 0.68
   3 ?   -1.8   0.3       0.6   3.6e+03      18      18 ..     578     578 ..     482     653 .. 0.65

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.6e-20
                                   EEEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS.........TTEEEEE...ECTTTH CS
                        Toprim   1 elvivEgpsdaktiakalg...................sgfqavtaslGhildlet.........efkpvye...eiedkk 50 
                                   +lvi+E+ ++a++ia+al+                   s+++++ +  Gh+++l           e+kp ++     +++k
  gi|70607128|ref|YP_255998.1|  10 TLVIAEKSKAARKIAEALSnnysyckkfyvnfwivnysSKYYIISPAAGHLFNLYGnssfpvyetEWKPLWQidpSARYTK 90 
                                   59*******************************************************999*999999999999999999** PP

                                   HHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                        Toprim  51 kvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                   k+ + +k+l+k+a+e i a+D D eG+ i+++++++l+++ ++  +r++fs 
  gi|70607128|ref|YP_255998.1|  91 KYYDLIKSLSKDAQEFINACDYDIEGSLIGYLIINFLGDIKRA--KRAKFSA 140
                                   **************************************88888..****986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.93
                                   TTEEEEEECTTTHHHHHHHHH CS
                        Toprim  38 efkpvyeeiedkkkvlkalke 58 
                                    +++ +e+++++k++l+++k+
  gi|70607128|ref|YP_255998.1| 241 TIPKTFENKNEAKQYLEEIKK 261
                                   445555678888888887776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.6
                                   H CS
                        Toprim  18 l 18 
                                    
  gi|70607128|ref|YP_255998.1| 578 I 578
                                   1 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.8   3.6e-05      0.21     227     299 ..     567     639 ..     539     651 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.6e-05
                     Tmemb_cc2 227 lqeikeeqerleeelerlkeqlkkelkllkqaLqeeryryerLEeqlndlteLhqnEienLKqelasmeekva 299
                                   ++e k+  e+  +e+e++k+++ + +  +   L+  +++y +LE   +dl   h n i+ LK++l+  +e+ +
  gi|70607128|ref|YP_255998.1| 567 VEETKKLIEKYINEFENSKNDIGTKIGKILGLLEYKKCKYCELEVYKDDLCKYHLNAIKLLKDNLKIWKERTD 639
                                   67888888999999***************************************************99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 4367.34
//
Query:       gi|70607129|ref|YP_255999.1|  [L=374]
Description: AAA ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  141.9   0.1    1.7e-40  138.5   0.0    2.2  2  AAA              ATPase family associated with various cellul
    5.8e-11   42.0   0.1    1.7e-10   40.6   0.1    1.8  1  AAA_lid_3        AAA+ lid domain
    1.8e-10   40.7   5.6      5e-10   39.3   5.6    1.8  1  MIT              MIT (microtubule interacting and transport) 
    3.6e-07   30.1   0.0    4.7e-06   26.4   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.8e-07   30.4   0.0    9.3e-07   29.1   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
      6e-07   30.0   0.0    0.00085   19.7   0.0    2.5  2  AAA_16           AAA ATPase domain
      6e-07   29.4   1.1    2.6e-06   27.3   0.2    2.5  2  Vps4_C           Vps4 C terminal oligomerisation domain
    6.9e-07   29.4   0.1    4.9e-06   26.6   0.0    2.4  2  AAA_14           AAA domain
      6e-06   26.6   0.0    0.00075   19.8   0.0    3.0  1  AAA_22           AAA domain
    8.4e-05   22.6   0.2     0.0027   17.7   0.1    3.0  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00017   21.4   0.0     0.0011   18.8   0.0    2.2  1  AAA_24           AAA domain
    0.00071   19.2   0.0      0.076   12.6   0.0    2.4  2  AAA_25           AAA domain
    0.00071   18.9   0.0     0.0012   18.2   0.0    1.4  1  TIP49            TIP49 P-loop domain
    0.00072   19.4   0.0     0.0028   17.4   0.0    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00083   19.3   9.2       0.26   11.2   0.1    3.8  4  ATPase_2         ATPase domain predominantly from Archaea
     0.0015   18.9   0.2      0.014   15.8   0.0    2.7  2  RNA_helicase     RNA helicase
     0.0031   18.1   0.1      0.021   15.4   0.0    2.6  1  AAA_18           AAA domain
     0.0039   16.8   0.2       0.01   15.5   0.2    1.7  1  TPR_11           TPR repeat
     0.0053   16.8   0.0      0.054   13.5   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
     0.0065   16.0   0.0      0.037   13.5   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
     0.0065   15.9   0.0      0.017   14.6   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0072   16.0   0.0       0.11   12.2   0.0    2.4  1  Sigma54_activat  Sigma-54 interaction domain
     0.0083   15.6   0.2        3.1    7.2   0.0    3.4  4  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.056   13.5   0.1    1.8  1  Fe_hyd_SSU       Iron hydrogenase small subunit
      0.025   13.9   0.0      0.092   12.0   0.0    2.0  1  Zeta_toxin       Zeta toxin
      0.028   13.5   0.0       0.07   12.2   0.0    1.6  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.031   14.2   0.0       0.37   10.6   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
      0.037   13.7   0.4       0.11   12.2   0.1    1.9  2  Casc1_N          Cancer susceptibility candidate 1 N-terminus
      0.038   13.7   0.0      0.084   12.6   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.039   13.2   0.0      0.083   12.1   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.047   13.6   0.0      0.095   12.6   0.0    1.5  1  NACHT            NACHT domain
      0.047   13.4   1.9        0.6    9.8   0.1    2.8  3  Use1             Membrane fusion protein Use1
      0.051   13.4   0.7      0.087   12.6   0.0    1.8  1  Bac_DnaA         Bacterial dnaA  protein
      0.059   13.5   0.1       0.17   12.0   0.0    1.8  1  SKI              Shikimate kinase
       0.06   12.5   0.0       0.12   11.5   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.061   13.7   0.1       0.34   11.4   0.0    2.3  2  AAA_17           AAA domain
       0.07   13.6   0.0       0.48   10.9   0.0    2.1  2  ABC_tran         ABC transporter
      0.072   13.2   2.7        0.9    9.7   0.3    3.1  2  DUF1912          Domain of unknown function (DUF1912)
      0.073   13.2   0.0       0.16   12.1   0.0    1.7  1  AAA_33           AAA domain
        0.1   12.2   0.0       0.21   11.2   0.0    1.5  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.14   12.4   0.5       0.98    9.8   0.3    2.6  1  TPR_8            Tetratricopeptide repeat
       0.15   12.0   0.5       0.47   10.4   0.2    2.0  1  TPR_1            Tetratricopeptide repeat
       0.24   11.6   2.9         17    5.7   0.1    2.6  2  T3SchapCesA      Type III secretion system filament chaperone
       0.25   11.7   6.3       0.53   10.6   0.4    3.5  4  Gp-FAR-1         Nematode fatty acid retinoid binding protein
        1.9    7.8   5.3        1.5    8.1   0.0    3.0  4  ATPase           KaiC


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.0   4.2e-43   1.7e-40       1     131 [.     140     274 ..     140     275 .. 0.96
   2 ?    0.9   0.1       1.4   5.6e+02      23      74 ..     291     352 ..     282     366 .. 0.64

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 4.2e-43
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgs 77 
                                   +l+yGppG+GKT++a ava+e++++f+++++++++sk++ge+ek+++++f++a+e +    kp+i+fiDEidal ++  +s
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSYFIQVDAASVMSKWLGEAEKNVAKIFNSARELSkkdgKPVIIFIDEIDALLGTY-NS 219
                                   69****************************************************999999999**************9.99 PP

                                   CCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
                           AAA  78 eseeeervvnqLlteldgvkkk..eskvivigatnrpdkldpallrgRfdrkieie 131
                                   e++ e rv nq+l+e+dg+++k  + kv vigatn+p++ld+++l +Rf+++i+i+
  gi|70607129|ref|YP_255999.1| 220 ENGGEVRVRNQFLKEMDGLQDKseNFKVYVIGATNKPWRLDEPFL-RRFQKRIYIR 274
                                   9*******************99666679*****************.7*******97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 1.4
                                   THEEEEEETTTCSSSSTTHHHHHHHHHHHHH.....HHTS.......TSEEEEEETGGGHHHHH CS
                           AAA  23 gvefleisgsellskyvgesekkirelfkea.....keka.......kpsilfiDEidalaksr 74 
                                   ++++ +++  el +++ g ++++i++++++a     k  +       +p  + ++++ ++ k r
  gi|70607129|ref|YP_255999.1| 291 KIKMDNVNIDELAKMTEGYTASDIKDIVQAAhirvvK--EmfdkkleQPRAVNMEDFKEILKIR 352
                                   5666678888888888899999999999887333331..0233334455666666666666655 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   4.2e-13   1.7e-10       1      45 []     296     347 ..     296     347 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.2e-13
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.......eitmedfee 45 
                                   +v+++eLA++TeGy+  D++ ++++A ++ +++ ++       +++medf+e
  gi|70607129|ref|YP_255999.1| 296 NVNIDELAKMTEGYTASDIKDIVQAAHIRVVKEMFDkkleqprAVNMEDFKE 347
                                   7********************************54444445656******97 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   5.6   1.3e-12     5e-10       4      65 .]      11      73 ..       9      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 1.3e-12
                           MIT  4 AlelvkkAveeDnagnyeeAlelYkealelLlqalk.ekneerrellrekieeYleRaeeLke 65
                                  A +++  Av++D++gn eeA+ +Yk+a+e+L q+++   + ++   +++ i+eY  R+e Lke
  gi|70607129|ref|YP_255999.1| 11 ARKYAINAVKADKEGNAEEAITNYKKAIEVLAQLVSlYRDGSTAAIYEQMINEYKRRIEVLKE 73
                                  6677889*****************************55898********************97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.2e-08   4.7e-06       5      96 ..     104     213 ..     100     220 .. 0.73
   2 ?    0.8   0.0      0.91   3.6e+02      19     153 ..     245     267 ..     227     273 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.2e-08
                        RuvB_N   5 sleeyigqekvkeklkifieaakkreeal.....dhvllyGpPGlGkttlakiiakelgvk.lkitsgPvlek.....agd 74 
                                   ++++ +g e+vke lk +i    +r +         +l+yGpPG Gkt +a+ +a+e+++  +++ ++ v++k     +++
  gi|70607129|ref|YP_255999.1| 104 NFNDIVGLEDVKEALKEAIVYPTRRPDLFplgwpRGILVYGPPGCGKTMIAAAVANEIDSYfIQVDAASVMSKwlgeaEKN 184
                                   5789999999999999999888888775422222579*********************98625666677765533332678 PP

                        RuvB_N  75 laallt...nleekd....vlfideihrl 96 
                                   +a +++   +l++kd    ++fidei  l
  gi|70607129|ref|YP_255999.1| 185 VAKIFNsarELSKKDgkpvIIFIDEIDAL 213
                                   88887622257777677778999999866 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.91
                        RuvB_N  19 lkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsra 99 
                                   +k++                                                                             
  gi|70607129|ref|YP_255999.1| 245 FKVY----------------------------------------------------------------------------- 248
                                   4444............................................................................. PP

                        RuvB_N 100 veevlysamedfrldivigkGpsarsikldlpkftlvgattragllssPlrdrf 153
                                                                      ++gat +   l +P+  rf
  gi|70607129|ref|YP_255999.1| 249 -----------------------------------VIGATNKPWRLDEPFLRRF 267
                                   ...................................5666666666666666666 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.3e-09   9.3e-07       6     104 ..     140     236 ..     138     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.3e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT.-HHHHTTSEEEEETGGG---- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappg.yvgaeegGivllDEidKihpk 83 
                                   il+ gp g+Gkt++a a+a+ ++    + +i +da +++     e+e+ v++   ++    ++  +  i+++DEid     
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEID----SYFIQVDAASVMSkwLGEAEKNVAKIFNSARElSKKDGKPVIIFIDEIDALLG- 215
                                   7999******************9....59***********8845566666665555555055555555********8887. PP

                                   ---------HHHHHHHHHHHH CS
                         AAA_2  84 essgadvSregVqrdLLqile 104
                                   + ++++  +  V + +L+ ++
  gi|70607129|ref|YP_255999.1| 216 TYNSENGGEVRVRNQFLKEMD 236
                                   444444444466677666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.1e-06   0.00085      24      49 ..     137     162 ..     107     179 .. 0.75
   2 !    8.0   0.0    0.0087       3.5     116     146 ..     182     212 ..     167     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellrale 49 
                                   p+ +l++G++G+GK+ ++ ++++++ 
  gi|70607129|ref|YP_255999.1| 137 PRGILVYGPPGCGKTMIAAAVANEID 162
                                   499******************99876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0087
                        AAA_16 116 asrllellkrllallsrderplvlvlDdlqw 146
                                   ++ ++  ++++ +l+++d++p+++++D+++ 
  gi|70607129|ref|YP_255999.1| 182 EKNVAKIFNSARELSKKDGKPVIIFIDEIDA 212
                                   46777888889999***************95 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.9   1.5e+03      42      50 ..     100     108 ..      88     121 .. 0.57
   2 !   27.3   0.2   6.5e-09   2.6e-06      20      59 ..     330     370 ..     318     371 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.9
                        Vps4_C  42 rptVskeDL 50 
                                   +p V+ +D+
  gi|70607129|ref|YP_255999.1| 100 KPKVNFNDI 108
                                   333333333 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 6.5e-09
                        Vps4_C  20 psdklleP.pvtlkDflkalkkarptVskeDLekheeFTke 59 
                                     +kl +P  v+++Df+++lk  +p+V++e ++ +e + ++
  gi|70607129|ref|YP_255999.1| 330 FDKKLEQPrAVNMEDFKEILKIRKPSVNSEVIKVYEAWHEK 370
                                   4689999999****************************876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.2e-08   4.9e-06       5     103 ..     140     255 ..     137     272 .. 0.77
   2 ?   -0.7   0.1       3.5   1.4e+03      34      80 ..     271     309 ..     259     350 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-08
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklke..ekktylflDEiqev... 76 
                                   +++ G+  +GKT+++  +++e     + ++ ++  +   k l + e    k+ +  +e+  +   k  ++f+DEi  +   
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEID---SYFIQVDAASVMSKWLGEAEknvaKIFNSARELS-KkdGKPVIIFIDEIDALlgt 216
                                   7899***********99996666...6666666666555444433321223444444442.23456778************ PP

                        AAA_14  77 ............pewekalkslvdegknldvivtGSnsk 103
                                               +++ k + +l d+++n++v+v G  +k
  gi|70607129|ref|YP_255999.1| 217 ynsenggevrvrNQFLKEMDGLQDKSENFKVYVIGATNK 255
                                   ***********************************8776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.5
                        AAA_14  34 lyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                   +yi l d +++k+      l++  +     k+  + +DE  +++e +
  gi|70607129|ref|YP_255999.1| 271 IYIRLPDIEQRKSLL----LHYTSKI----KMDNVNIDELAKMTEGY 309
                                   555555555544332....2333332....33447788877775533 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-06   0.00075       8     130 ..     140     252 ..     137     256 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-06
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalra 88 
                                   ++v+G++G+GKT+ ++ ++++          ++ ++ v+++s +      ++ l + +    +   +   +++  ++ +++
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEI---------DSYFIQVDAASVM------SKWLGEAE----K---NVAKIFNSARELSKK 198
                                   79*******************9.........7777788887777......22222222....2...566777888888888 PP

                        AAA_22  89 ravielliiDEaqhlr....s.........eealeeLrsllnlsrkgvqliLvGt 130
                                    ++++++ iDE++ l     s         ++ l+e   l++ ++ ++++ ++G 
  gi|70607129|ref|YP_255999.1| 199 DGKPVIIFIDEIDALLgtynSenggevrvrNQFLKEMDGLQD-KSENFKVYVIGA 252
                                   888777778888886555541344455444555555544444.666777666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   6.8e-06    0.0027       2     138 .]     140     267 ..     139     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.8e-06
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHH CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevl 82 
                                   +l+ GppG+gK+++a  +a  + +    +q  +    ++ +g+ e +  +   +  +l ++  ++ i+++DE++ +     
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSY--FIQVDAASVMSKWLGEAEKNVAKIFNSARELSKKDGKPVIIFIDEIDALLGTYN 218
                                   7899**************9999765..466666666677778887545555566777888888999*******94433333 PP

                                   HHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  83 nsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   ++       r   l e+++l+++++++   +++vi+++n++     +l++++++Rf
  gi|70607129|ref|YP_255999.1| 219 SENGGEVRVRNQFLKEMDGLQDKSENF---KVYVIGATNKPW----RLDEPFLRRF 267
                                   333333444444445555555444443...399999999999....8899999998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-06    0.0011       5      77 ..     140     213 ..     137     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-06
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                   il+yGp+g GKT++a+    + +  fi++++ +  +  + ++  ++++++ + + el++++ +  +++iD id l
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVanEIDSYFIQVDA-ASVMSKWLGEAEKNVAKIFNSARELSKKDGKPVIIFIDEIDAL 213
                                   89****************8888999*****9.5599999999888999999999999888888889999998877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00019     0.076      19      54 ..     125     158 ..     111     163 .. 0.79
   2 ?    4.2   0.0      0.07        28     131     178 ..     190     241 ..     164     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                        AAA_25  19 ppprrwlvk.gllpagelallaGapgtGKttlaldla 54 
                                   p++r +l++ g+ p+g  +l++G+pg+GKt++a  +a
  gi|70607129|ref|YP_255999.1| 125 PTRRPDLFPlGW-PRG--ILVYGPPGCGKTMIAAAVA 158
                                   667777777555.766..689************9877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.07
                        AAA_25 131 daleaaieevegvrlvviDplsralgg.densnsdv...galvealeriarr 178
                                   +  ++  ++  +++ + iD ++++lg  ++++  +v   +++++ ++ ++++
  gi|70607129|ref|YP_255999.1| 190 NSARELSKKDGKPVIIFIDEIDALLGTyNSENGGEVrvrNQFLKEMDGLQDK 241
                                   444455566566***************8777777755689999999998775 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.9e-06    0.0012      51      97 ..     138     182 ..      85     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                   r++L+ Gp+g Gkt +a a+++e+     f+++ ++ v s  +  +e
  gi|70607129|ref|YP_255999.1| 138 RGILVYGPPGCGKTMIAAAVANEID--SYFIQVDAASVMSKWLGEAE 182
                                   89**********************7..68999999999987666555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     7e-06    0.0028       1      72 [.     140     211 ..     140     219 .. 0.85
   2 ?   -1.2   0.0       3.5   1.4e+03      47      80 ..     278     311 ..     262     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-06
               Viral_helicase1   1 ivvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEyl 72 
                                   i+v G pGcGK+ +   ++++      + + +a + ++++ +++++  + ++s+ +  +k+ k  i+++DE+ 
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIdS-YFIQVDAASVMSKWLGEAEKNVAKIFNSARELSKKDGKPVIIFIDEID 211
                                   6899*********88888888754.44566669***********************999998889999***85 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
               Viral_helicase1  47 vrtvdsflmalvkstkgkililDEylllhaGyil 80 
                                   ++  +s+l + + + k + + +DE  +++ Gy  
  gi|70607129|ref|YP_255999.1| 278 IEQRKSLLLHYTSKIKMDNVNIDELAKMTEGYTA 311
                                   4455788888888888999999999999999865 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       3.3   1.3e+03      88     115 ..      13      40 ..       3      75 .. 0.71
   2 !   11.1   0.0    0.0007      0.28      23      45 ..     140     162 ..     135     169 .. 0.83
   3 !   11.2   0.1   0.00065      0.26      93     131 ..     176     214 ..     163     232 .. 0.81
   4 ?   -0.5   0.2       2.3   9.3e+02      77     218 ..     316     347 ..     277     370 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.3
                      ATPase_2  88 kaeleeilk.eksklvfkaielllekikk 115
                                   k +++++ k +k  ++++ai++++++i+ 
  gi|70607129|ref|YP_255999.1|  13 KYAINAV-KaDKEGNAEEAITNYKKAIEV 40 
                                   4444444.447888888888888888765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0007
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                   +++YGp g+GKt +   ++++ +
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEID 162
                                   68**********99988888765 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00065
                      ATPase_2  93 eilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                   + l e  k+v k ++++ e  kk+gk +ii+iDe+  l 
  gi|70607129|ref|YP_255999.1| 176 KWLGEAEKNVAKIFNSARELSKKDGKPVIIFIDEIDALL 214
                                   344488999999999999999999999*******98876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.3
                      ATPase_2  77 klekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekh 157
                                    + +a+ i+v k  +++ l++                                                            
  gi|70607129|ref|YP_255999.1| 316 DIVQAAHIRVVKEMFDKKLEQ------------------------------------------------------------ 336
                                   233333333333333333332............................................................ PP

                      ATPase_2 158 lcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleelskedfee 218
                                                                                      +  + edf+e
  gi|70607129|ref|YP_255999.1| 337 --------------------------------------------------PRAVNMEDFKE 347
                                   ..................................................22223333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-05     0.014       1      26 [.     140     165 ..     140     255 .. 0.78
   2 ?   -0.9   0.0       5.3   2.1e+03      51      78 ..     295     322 ..     280     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i++yGp+g+GK+++a  +a+++ + +
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSYF 165
                                   789***************99998766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.3
                  RNA_helicase  51 evvvidDfgqvkdeenpsdlaelirlvs 78 
                                   + v id++++++++++ sd++++++++ 
  gi|70607129|ref|YP_255999.1| 295 DNVNIDELAKMTEGYTASDIKDIVQAAH 322
                                   5677899999998888888888887765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.2e-05     0.021       1      31 [.     140     178 ..     140     304 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdv 31 
                                   Il+ G+pG+GKt +a +++++   +       +v ++ +
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIdSYfiqvdaaSVMSKWL 178
                                   99****************999733344443332222222 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.5e-05      0.01       7      29 ..      24      46 ..      23      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                        TPR_11  7 qGkyeeAieaYkkAlkldPdnae 29
                                   G+ eeAi++YkkA++   + ++
  gi|70607129|ref|YP_255999.1| 24 EGNAEEAITNYKKAIEVLAQLVS 46
                                  6999***********97665555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.4   5.6e+02      64      82 ..      54      72 ..      52     106 .. 0.74
   2 !   13.5   0.0   0.00013     0.054      26     116 ..     139     222 ..     108     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                                  HHHHHHHHHHGGGGTGG.. CS
                        ResIII 64 kslleqtleefkkflseay 82
                                   +++eq+++e+k+ ++  +
  gi|70607129|ref|YP_255999.1| 54 AAIYEQMINEYKRRIEVLK 72
                                  689********99887654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                                   EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SE CS
                        ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdstnkki 106
                                    +l+  + G+GKT++aa+++ ++ +       ++ v+  s+++++l e +k   + ++++ +  ++d+k    +++++++ 
  gi|70607129|ref|YP_255999.1| 139 GILVYGPPGCGKTMIAAAVANEIDS------YFIQVDAASVMSKWLGEAEKNVAKIFNSARELSKKDGKPV-IIFIDEIDA 212
                                   56678899***************98......46779**********9999999999998888888888877.678888888 PP

                                   EEEEHHHHHH CS
                        ResIII 107 lvttiqslda 116
                                   l+ t++s + 
  gi|70607129|ref|YP_255999.1| 213 LLGTYNSENG 222
                                   8888877554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.2   1.3e+03      98     116 ..      84     102 ..      80     125 .. 0.81
   2 !   13.5   0.0   9.4e-05     0.037      36     110 ..     140     211 ..     137     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                         AAA_7  98 ggkklvvFvDDlnmpakek 116
                                   +gk+  v vDDl m +k k
  gi|70607129|ref|YP_255999.1|  84 NGKHSQVSVDDLVMKEKPK 102
                                   68999999****9988765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.4e-05
                         AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr..rkgvygPpggkklvvFvDDln 110
                                   +l++Gp G+GKt+i+  + +++d     s +i++ a    ++     e+++ k   + + +  + gk +++F+D+++
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEID-----SYFIQVDAASVMSKWLGEAEKNVAKIfnSARELSKKDGKPVIIFIDEID 211
                                   89******************999.....6677777777777777777777777521446788889999999999875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.1e-05     0.017      25      43 ..     140     158 ..     136     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +l++GppG+GKtm+a++++
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVA 158
                                   799************9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00028      0.11      25      66 ..     140     178 ..     133     280 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                                   EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH CS
               Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeell 66 
                                   +l+ G  G+GK+++a a+ ++ +   + f++v+ a++ ++ l
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEID---SYFIQVDAASVMSKWL 178
                                   89***************987665...889***9998865544 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.7   1.1e+03       9      28 ..      30      49 ..      26      62 .. 0.81
   2 !    7.2   0.0    0.0077       3.1      36      56 ..     138     158 ..     113     174 .. 0.87
   3 ?   -0.5   0.0       1.7   6.7e+02     119     137 ..     201     218 ..     179     228 .. 0.76
   4 ?    3.4   0.0      0.11        43      64     136 ..     239     310 ..     217     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.7
                          TniB  9 rwigyprakeilerLeeLle 28
                                     +y++a e+l++L +L++
  gi|70607129|ref|YP_255999.1| 30 AITNYKKAIEVLAQLVSLYR 49
                                  5678999*****99999987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0077
                          TniB  36 pnlllvGdsnnGKtmivekFa 56 
                                   + +l++G++ +GKtmi+   a
  gi|70607129|ref|YP_255999.1| 138 RGILVYGPPGCGKTMIAAAVA 158
                                   689*************97655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.7
                          TniB 119 kvrvLiiDEihnllagsar 137
                                   k+ ++ iDEi+ ll g+++
  gi|70607129|ref|YP_255999.1| 201 KPVIIFIDEIDALL-GTYN 218
                                   4557889***9999.6655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.11
                          TniB  64 dedaekvpvlvvqappkpdekrlyaaiLealgaplkar.arvskleqqvlrllrelkvrvLiiDEihnllagsa 136
                                   + ++e+++v v+ a +kp   rl +  L+++++++  r  ++++ ++  l++ +++k+  + iDE+ ++ +g  
  gi|70607129|ref|YP_255999.1| 239 QDKSENFKVYVIGATNKP--WRLDEPFLRRFQKRIYIRlPDIEQRKSLLLHYTSKIKMDNVNIDELAKMTEGYT 310
                                   345678899999999999..789999999999998777357888889999*******************99954 PP

>> Fe_hyd_SSU  Iron hydrogenase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   0.00014     0.056      14      39 ..     343     370 ..     326     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                                   HH.HH.CCC-SGGG-HHHHHHHHCTTSS CS
                    Fe_hyd_SSU  14 iD.kk.kklrkSheNpevkklYkeflge 39 
                                   +D k+  k+rk+  N ev+k+Y+ ++++
  gi|70607129|ref|YP_255999.1| 343 EDfKEiLKIRKPSVNSEVIKVYEAWHEK 370
                                   4444449******************976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023     0.092      16      51 ..     137     170 ..     131     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                    Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                   P  il+ G pG+GK+ +a+++++e+  ++ ++++d+
  gi|70607129|ref|YP_255999.1| 137 PRGILVYGPPGCGKTMIAAAVANEI--DSYFIQVDA 170
                                   6779999*****************9..677777775 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.07     117     141 ..     140     164 ..     136     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                   +++yGp+ +Gkt++a+a a+ +++y
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSY 164
                                   799*****************99887 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0         1     4e+02      21      44 ..      59      82 ..      50     113 .. 0.79
   2 ?   10.6   0.0   0.00094      0.37       2      32 ..     140     170 ..     139     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1
                         AAA_3 21 kaldlefkriqftpdllPsdilGt 44
                                  ++++   +ri +  +l+P+d  G 
  gi|70607129|ref|YP_255999.1| 59 QMINEYKRRIEVLKELIPADGAGN 82
                                  667777899***********8876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00094
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqf 32 
                                   +l+ g PG +kt+++ a+a+ +d  f ++  
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSYFIQVDA 170
                                   7999*******************99977765 PP

>> Casc1_N  Cancer susceptibility candidate 1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.11      94     153 ..      16      75 ..      14      78 .. 0.94
   2 ?   -2.6   0.0         9   3.6e+03     103     110 ..     183     190 ..     153     243 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                       Casc1_N  94 lslwseeeeedieevmetctlvlklieeLeelledtaeeelsekeveeykevilelrell 153
                                   ++ ++ ++e ++ee++  ++++++++++L  l +d + +   e+ + eyk++i++l+el+
  gi|70607129|ref|YP_255999.1|  16 INAVKADKEGNAEEAITNYKKAIEVLAQLVSLYRDGSTAAIYEQMINEYKRRIEVLKELI 75 
                                   6888999999*******************99999***********************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9
                       Casc1_N 103 edieevme 110
                                   +++ ++++
  gi|70607129|ref|YP_255999.1| 183 KNVAKIFN 190
                                   22222222 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021     0.084      49      70 ..     139     160 ..     134     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                     IstB_IS21  49 nivllGpsGvGKshlaialgve 70 
                                   +i++ Gp+G GK+ +a+a++ e
  gi|70607129|ref|YP_255999.1| 139 GILVYGPPGCGKTMIAAAVANE 160
                                   6899**************9876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00021     0.083       4      26 ..     140     167 ..     137     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                       DUF2075   4 vlVtGvaGtGKtvvllnllael.....e 26 
                                   +lV G +G GKt+++ ++++e+     +
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIdsyfiQ 167
                                   89*******************9544432 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00024     0.095       3      24 ..     140     161 ..     138     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   +++ G++G+GKT+ ++ +a ++
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEI 161
                                   799**************99887 PP

>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.17        66      39      70 ..      16      47 ..       6      56 .. 0.80
   2 ?    9.8   0.1    0.0015       0.6      30      74 ..      36      81 ..      35     106 .. 0.73
   3 ?   -1.1   0.1       3.2   1.3e+03     191     200 ..     297     306 ..     252     365 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.17
                          Use1 39 leeLkkesskpskevlkeYsekveaLklllea 70
                                  +++ k++++  ++e++++Y++ +e L++l+  
  gi|70607129|ref|YP_255999.1| 16 INAVKADKEGNAEEAITNYKKAIEVLAQLVSL 47
                                  566677777799***************99875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                          Use1 30 kyvkaleemleeLkkessk.pskevlkeYsekveaLkllleaekls 74
                                  k++++l ++++   + s+  + +++++eY++++e Lk+l+ a+   
  gi|70607129|ref|YP_255999.1| 36 KAIEVLAQLVSLYRDGSTAaIYEQMINEYKRRIEVLKELIPADGAG 81
                                  55666665555554444445899****************9887665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.2
                          Use1 191 etlsksekaa 200
                                     +++ +k++
  gi|70607129|ref|YP_255999.1| 297 VNIDELAKMT 306
                                   2222222222 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022     0.087      37     205 ..     140     317 ..     137     334 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHHHHHHTT-SEEEEE-GGGGTT.... CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeefkeklrkvDvLliDDiqflag.... 111
                                   +++yg+ G Gkt +  a++ne+ + + +     + ++ +l e+ k + +  ++a+e+ +k  k  ++ iD+i  l g    
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSYFIQVDAASVMSK-WLGEAEKNVAKifNSARELSKKDGKPVIIFIDEIDALLGtyns 219
                                   699*******************999988887777664.4444445454445666777777777778888888877541111 PP

                                   ....-HHHHHHHHHHHHHHHTTT...-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHH...HHHHT CS
                      Bac_DnaA 112 ....kektqeelfhtfnalleeg...kqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkk...kieae 182
                                         ++++++++ ++ l +++   k  v+ +  +P++l   ++ +  rf+  + +    pd e r ++l +   ki+++
  gi|70607129|ref|YP_255999.1| 220 enggEVRVRNQFLKEMDGLQDKSenfKVYVIGATNKPWRL---DEPFLRRFQKRIYIR--LPDIEQRKSLLLHytsKIKMD 295
                                   1111446889999999999887622244589999999975...677888999876655..588999999886522256666 PP

                                   T----TTHHHHHHHH--S-HHHH CS
                      Bac_DnaA 183 klevpeevlefiaervtdnvRel 205
                                   ++++  e++++   +  ++++++
  gi|70607129|ref|YP_255999.1| 296 NVNID-ELAKMTEGYTASDIKDI 317
                                   66653.34444444444555554 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00042      0.17       1      40 [.     146     190 ..     146     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                                   TTSSHHHHHHHHHHHHTSEEEEHHH..HHHHHHT...S-HHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDe..liekrtg...ksiaeife 40 
                                   +G+GK+ ++ ++A++++  fi +D   +++k  g   k++a+if+
  gi|70607129|ref|YP_255999.1| 146 PGCGKTMIAAAVANEIDSYFIQVDAasVMSKWLGeaeKNVAKIFN 190
                                   6*********************99833444433322256666666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.12      23      46 ..     140     163 ..     137     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                   EEEEESTTSSHHHHHHHHCCSHCC CS
                        NB-ARC  23 valvGmgGvGKttlakqilnksde 46 
                                   + ++G +G+GKt +a+ + n+ d+
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDS 163
                                   569****************99665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       9.4   3.7e+03      42      86 ..      56     102 ..      39     123 .. 0.62
   2 ?   11.4   0.0   0.00084      0.34       1      31 [.     143     175 ..     143     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 9.4
                                   SHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE-SEEEETT CS
                        AAA_17  42 ardemrklpleekkelqkeaaekiaeea..kkkgvlvdghprikeqa 86 
                                     ++m ++++++ + l +++ ++ a +   k+++v vd   + ++++
  gi|70607129|ref|YP_255999.1|  56 IYEQMINEYKRRIEVLKELIPADGAGNGngKHSQVSVDDLVMKEKPK 102
                                   55666666666666666666555555443355567777776666555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00084
                                   EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHH CS
                        AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllr 31 
                                   +G+PG+GK+ +++ ++ ++   f  + a +++ 
  gi|70607129|ref|YP_255999.1| 143 YGPPGCGKTMIAAAVANEIdsYFIQVDAASVMS 175
                                   7***************99843455556666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       8.1   3.2e+03      50      85 ..      27      68 ..      11      98 .. 0.63
   2 ?   10.9   0.0    0.0012      0.48      16      68 ..     142     192 ..     138     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.1
                                  GGB-HHHCCHCEEEE-SS--S-TTSB...HHHH...HHHTCH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx...xxxxxx RF
                      ABC_tran 50 keqeleslrkeigvlpqepqlfpelt...vren...esdeei 85
                                   e+ ++ ++k i+vl q  +l ++ +   ++e+   e++++i
  gi|70607129|ref|YP_255999.1| 27 AEEAITNYKKAIEVLAQLVSLYRDGStaaIYEQminEYKRRI 68
                                  446677788888888888666554431223333554444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                                   EEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  16 ivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqep 68 
                                   + G+ G+GK+ +++++a++ +  +  i++d +++ ++ l +++k+++ ++  +
  gi|70607129|ref|YP_255999.1| 142 VYGPPGCGKTMIAAAVANEID--SYFIQVDAASVMSKWLGEAEKNVAKIFNSA 192
                                   78****************997..567778988998899999999999998774 PP

>> DUF1912  Domain of unknown function (DUF1912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0023       0.9      16      54 ..       2      40 ..       1      54 [. 0.87
   2 ?    2.0   0.0      0.57   2.3e+02      16      36 ..      87     107 ..      84     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0023
                                  HHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHH CS
                       DUF1912 16 ntqvkinelaleaskkvleedkderakdaliryesklda 54
                                  ++qv+++e+a + + + ++ dk+ +a++a+  y+  ++ 
  gi|70607129|ref|YP_255999.1|  2 SAQVMLEEMARKYAINAVKADKEGNAEEAITNYKKAIEV 40
                                  57******************************9876655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHHHHHH---- CS
                       DUF1912  16 ntqvkinelaleaskkvleed 36 
                                   ++qv++++l +++  kv  +d
  gi|70607129|ref|YP_255999.1|  87 HSQVSVDDLVMKEKPKVNFND 107
                                   58***********99987655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0004      0.16       2      33 ..     140     171 ..     140     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0004
                        AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtl 33 
                                   +l+ G+pG+GK+  a  ++++ + +++  d++
  gi|70607129|ref|YP_255999.1| 140 ILVYGPPGCGKTMIAAAVANEIDSYFIQVDAA 171
                                   5789***************9999888888873 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00053      0.21       8      65 ..     131     194 ..     130     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00053
                                   HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEE.EEEESEEHHHHHHHHHHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxx.xxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aii.yvgiGergnevaevleefpe 65 
                                   lfp++    +l+ g  g+Gkt+i+++++++ +s     d a++     Ge +++va+++++ +e
  gi|70607129|ref|YP_255999.1| 131 LFPLGWPRGILVYGPPGCGKTMIAAAVANEIDSYfiqvDaASVmSKWLGEAEKNVAKIFNSARE 194
                                   67888888899******************98776676633444145689999999998888777 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3    0.0025      0.98      13      29 ..      23      39 ..      21      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                                  HTT-HHHHHHHHHHHHH CS
                         TPR_8 13 klgdyeeAkeyyekale 29
                                  k g+ eeA+  y+ka+e
  gi|70607129|ref|YP_255999.1| 23 KEGNAEEAITNYKKAIE 39
                                  78**************8 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2    0.0012      0.47      13      30 ..      23      40 ..      18      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                                  HTT-HHHHHHHHHHHHHH CS
                         TPR_1 13 klgkydeAleyyekALel 30
                                  k g+ +eA+  y+kA+e+
  gi|70607129|ref|YP_255999.1| 23 KEGNAEEAITNYKKAIEV 40
                                  78999***********96 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6     0.061        24      34      86 ..      19      72 ..       8      78 .. 0.84
   2 ?    5.7   0.1     0.042        17      42      78 ..     289     325 ..     277     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.061
                   T3SchapCesA 34 vkesvnilsekaktd.pqaaeklnkliegytygeerklydsalskieklietlk 86
                                  vk + +  +e a t+  +a e l +l+  y  g    +y+  +   ++ ie lk
  gi|70607129|ref|YP_255999.1| 19 VKADKEGNAEEAITNyKKAIEVLAQLVSLYRDGSTAAIYEQMINEYKRRIEVLK 72
                                  56666666788888724688*************************999999987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.042
                   T3SchapCesA  42 sekaktdpqaaeklnkliegytygeerklydsalski 78 
                                   + k k d    ++l k+ egyt  + + + ++a  ++
  gi|70607129|ref|YP_255999.1| 289 TSKIKMDNVNIDELAKMTEGYTASDIKDIVQAAHIRV 325
                                   57899999999***********999988888876665 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.85   3.4e+02      25      72 ..      43      72 ..      10      76 .. 0.61
   2 ?   -1.7   0.0       8.1   3.2e+03     104     121 ..     181     198 ..     165     203 .. 0.74
   3 ?   -0.2   0.0       2.9   1.2e+03      59      84 ..     226     251 ..     207     295 .. 0.75
   4 ?   10.6   0.4    0.0013      0.53      25      71 ..     325     374 .]     311     374 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.85
                      Gp-FAR-1 25 qlkevvknykgyknedellaalKkkspaLyekaeklqaklkekvdkLs 72
                                  ql+ + ++ +++                    +e++ +++k++++ L+
  gi|70607129|ref|YP_255999.1| 43 QLVSLYRDGSTAAI------------------YEQMINEYKRRIEVLK 72
                                  34444444444444..................4555555555554444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 8.1
                      Gp-FAR-1 104 lkkvaktifnkykslsee 121
                                     k +++ifn++++ls++
  gi|70607129|ref|YP_255999.1| 181 AEKNVAKIFNSARELSKK 198
                                   456677888888888765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.9
                      Gp-FAR-1  59 klqaklkekvdkLspeakeFvkklia 84 
                                   ++++++ +++d+L++++ +F   +i+
  gi|70607129|ref|YP_255999.1| 226 RVRNQFLKEMDGLQDKSENFKVYVIG 251
                                   56778888999*****9999888883 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0013
                      Gp-FAR-1  25 qlkevvkn.ykg..yknedellaalKkkspaLyekaeklqaklkekvdkL 71 
                                    +ke++ +  ++  + n++++ ++lK ++p++ +++ k+++  +ek ++L
  gi|70607129|ref|YP_255999.1| 325 VVKEMFDKkLEQprAVNMEDFKEILKIRKPSVNSEVIKVYEAWHEKYKAL 374
                                   47888888666677889*************************99998776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       7.4     3e+03      85     116 ..      15      46 ..       6      65 .. 0.62
   2 ?    8.1   0.0    0.0039       1.5      21      37 ..     139     155 ..     130     164 .. 0.86
   3 ?   -1.0   0.0       2.2   8.8e+02      86     138 ..     168     219 ..     157     241 .. 0.59
   4 ?    0.2   0.2         1     4e+02     103     145 ..     277     319 ..     263     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.4
                        ATPase  85 iidasesaeesaeekdkedleelieelaeaik 116
                                    i+a++ ++e ++e+  ++ ++ ie la+ ++
  gi|70607129|ref|YP_255999.1|  15 AINAVKADKEGNAEEAITNYKKAIEVLAQLVS 46 
                                   44444444444555666666666666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0039
                        ATPase  21 vvlitGepGtGKtifal 37 
                                    +l++G pG+GKt++a+
  gi|70607129|ref|YP_255999.1| 139 GILVYGPPGCGKTMIAA 155
                                   589***********986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.2
                        ATPase  86 idasesaeesaeekdkedleelieelaeaikeika.krvviDsitgl..ayeekea 138
                                   +da++ +++    + ++++ ++ ++ +e  k+ +    + iD i++l  +y +  +
  gi|70607129|ref|YP_255999.1| 168 VDAASVMSKWLG-EAEKNVAKIFNSARELSKKDGKpVIIFIDEIDALlgTY-N--S 219
                                   555555544222.66777777777777777666553667799999994222.2..2 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1
                        ATPase 103 dleelieelaeaikeikakrvviDsitglayeekeavaReilr 145
                                   d+e+ ++ l ++ ++ik  +v iD ++ +++  +++ +++i++
  gi|70607129|ref|YP_255999.1| 277 DIEQRKSLLLHYTSKIKMDNVNIDELAKMTEGYTASDIKDIVQ 319
                                   56777778889999***********999966666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 2332.18
//
Query:       gi|70607130|ref|YP_256000.1|  [L=261]
Description: hypothetical protein Saci_1373 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-05   23.8   4.8    4.8e-05   23.0   4.6    1.6  1  Snf7             Snf7
    0.00071   19.4   0.0     0.0018   18.1   0.0    1.7  1  MarR_2           MarR family
     0.0011   18.8   0.1     0.0093   15.8   0.0    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0012   18.5   0.1     0.0023   17.6   0.1    1.5  1  DUF3231          Protein of unknown function (DUF3231)
     0.0014   18.5   0.0     0.0037   17.2   0.0    1.7  1  MarR             MarR family
     0.0016   19.1   0.0     0.0033   18.1   0.0    1.6  1  RPA_C            Replication protein A C terminal
     0.0019   18.1   0.0     0.0041   17.0   0.0    1.6  1  HTH_36           Helix-turn-helix domain
     0.0025   18.3   0.2       0.86   10.1   0.0    2.6  2  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.074   12.7   0.0    2.1  2  GntR             Bacterial regulatory proteins, gntR family
       0.04   13.7   0.2       0.04   13.7   0.2    2.3  3  Phage_GP20       Phage minor structural protein GP20
      0.042   13.8   0.2       0.18   11.8   0.0    2.2  2  HTH_11           HTH domain
      0.053   13.1   0.1       0.24   11.0   0.0    2.1  2  HTH_47           winged helix-turn-helix
      0.063   13.3   0.0       0.23   11.5   0.0    1.9  1  HTH_29           Winged helix-turn helix
      0.065   13.6   0.0       0.45   10.9   0.0    2.3  2  Rrf2             Transcriptional regulator
        0.1   12.8   0.6       0.38   10.9   0.0    2.3  3  DUF2250          Uncharacterized protein conserved in archaea
       0.15   11.6   3.6      0.082   12.5   0.7    1.9  2  DUF4795          Domain of unknown function (DUF4795)
       0.38   11.2   3.1       0.76   10.3   0.0    2.7  3  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   4.6   4.5e-08   4.8e-05       3     166 ..      27     190 ..      25     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.5e-08
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkev 83 
                                    ++L++++++ld  +++l+++ k+l +++ + + +g+ +ra +++ ++  ++k+++ +++ +  +e+v+l++++ +  + v
  gi|70607130|ref|YP_256000.1|  27 SLKLKEQQDRLDEAIRRLRERDKDLFEKVIRSQIEGDIARATIYAQEISDIRKMIKIIYTAYLAIEKVRLKLDTVQELQGV 107
                                   689***************************************************************************999 PP

                                   HHHHHHHHHHHHHHHHCTC..CHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-GGTTHHHHHHHHHHHHHHHHHCSH.HHH CS
                          Snf7  84 lnamkqgakamkamnkkvd..idkidklmdeiedqmekaeeisEalsrslddadeedEeeleaeLdaLeqelgdeelldes 162
                                      +  + +++ + +++v+   +++   +d i+ ++    +   als++  +++ + +e  ++++++ ++  + +   +  
  gi|70607130|ref|YP_256000.1| 108 SLVLFPVMRILGELKEQVRgiAPEVALALDSITSSVNSIAIETGALSEKT-FVPTVADEQAKQIMEEAQKMAEVKV-RELL 186
                                   99999999999988888875568888888888888888888888888887.6678888888887777666533333.2334 PP

                                   HHHH CS
                          Snf7 163 vklp 166
                                    +lp
  gi|70607130|ref|YP_256000.1| 187 PELP 190
                                   4444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.7e-06    0.0018       9      53 ..     216     259 ..     211     261 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHCTTTSEE.EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2   9 rvLaaLgrrpgrdl.tvgelarrlglsksavsrilkrLvaaGLver 53 
                                   ++L+++   +g  +  v  +a+ +++sk  v ++l+rL+++GL++ 
  gi|70607130|ref|YP_256000.1| 216 MILNYIKTTGG--FiDVDYIAKNFDVSKDEVFNVLRRLEEKGLIVL 259
                                   68999999999..669****************************86 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.3   1.3e+03      24      49 ..      22      47 ..      18      52 .. 0.87
   2 !   15.8   0.0   8.8e-06    0.0093      25      52 ..     230     257 ..     226     260 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                                  HHCHHCCCTTSSCHCHHHHHHHHHHC CS
                          TrmB 24 tadeiaeelgvprskvYevLrsLedk 49
                                   ++ei+ +l+  + +  e++r+L ++
  gi|70607130|ref|YP_256000.1| 22 AITEISLKLKEQQDRLDEAIRRLRER 47
                                  56899999999999999*****9987 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.8e-06
                                   HCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
                          TrmB  25 adeiaeelgvprskvYevLrsLedkGlV 52 
                                   +d ia++ +v++  v +vLr+Le+kGl+
  gi|70607130|ref|YP_256000.1| 230 VDYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   788***********************98 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.2e-06    0.0023      30     107 ..     150     226 ..     130     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                       DUF3231  30 lgialitgFlqvaedkeikelleralelsnkhikelkelLkeenlpiPsgfsesdvtdsaprlfsDklmlaylsilaa 107
                                   +g+   ++F+ ++ d+  k+++e+a ++++ +++el   L      +P+    ++v+ s+++  s++++l+y+++   
  gi|70607130|ref|YP_256000.1| 150 TGALSEKTFVPTVADEQAKQIMEEAQKMAEVKVRELLPELPHPPSELPKRV-AKQVQSSNKKSLSEDMILNYIKTTGG 226
                                   55667899*******************************************.9********************98765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.5e-06    0.0037       7      47 ..     216     257 ..     211     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-06
                                   HHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR   7 viLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47 
                                   +iL  +++ g+ + v  +ak + vsk  v +vl+rLe+kGli
  gi|70607130|ref|YP_256000.1| 216 MILNYIKTTGGfIDVDYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   67888888999899999************************9 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.1e-06    0.0033      41      97 ..     203     257 ..     155     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.1e-06
                                   XXXX...XSXHHHHHHHHHHHH.SXSTTT.EEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                         RPA_C  41 klan..kgltalaqqvlnlikqspeseeG.vhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                   ++ +  + ++  ++++ln+ik+    + G + vd+ia+++ +s+ +v ++++ L+++G+i
  gi|70607130|ref|YP_256000.1| 203 QV-QssNKKSLSEDMILNYIKT----TGGfIDVDYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   22.2344577789*********....44449***************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.9e-06    0.0041      14      55 .]     217     257 ..     216     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                        HTH_36  14 lasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55 
                                   ++ +  k++g f  ++++ak++ +sk+ v + ++ Le++G+i
  gi|70607130|ref|YP_256000.1| 217 ILNYI-KTTGGFIDVDYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   56666.55666999**************************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.022        23      19      49 ..      21      53 ..      16      58 .. 0.88
   2 !   10.1   0.0   0.00081      0.86      22      48 ..     231     257 ..     212     261 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.022
                        HTH_27 19 kkladlcgrlnvedshisyslkkLtek..GLve 49
                                  k++++++ +l+ ++    +++++L e+  +L+e
  gi|70607130|ref|YP_256000.1| 21 KAITEISLKLKEQQDRLDEAIRRLRERdkDLFE 53
                                  788***********************9666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00081
                        HTH_27  22 adlcgrlnvedshisyslkkLtekGLv 48 
                                     +++  +v++  + ++l++L+ekGL+
  gi|70607130|ref|YP_256000.1| 231 DYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   6689999*******************9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.7   3.9e+03      42      50 ..      38      46 ..      35      48 .. 0.74
   2 ?   12.7   0.0     7e-05     0.074      12      56 ..     216     259 ..     213     261 .] 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.7
                                  HHHHHHHHH CS
                          GntR 42 ReALrrLea 50
                                   eA+rrL +
  gi|70607130|ref|YP_256000.1| 38 DEAIRRLRE 46
                                  588888865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7e-05
                                   HHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          GntR  12 dIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglver 56 
                                   +Il+   + G  +  +  +a+ f+Vs+  v  +LrrLe++gl++ 
  gi|70607130|ref|YP_256000.1| 216 MILNYIKTTGGFI-DVDYIAKNFDVSKDEVFNVLRRLEEKGLIVL 259
                                   5556666667777.78889***********************975 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   3.8e-05      0.04     109     140 ..      26      57 ..      10      63 .. 0.76
   2 ?   -3.3   0.0       6.5   6.9e+03     101     119 ..      86     103 ..      78     105 .. 0.73
   3 ?   -1.5   0.1       1.8   1.9e+03       1      13 [.     165     176 ..     161     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                    Phage_GP20 109 lklkedgelkgLdeqikkLkesdkyLFeeeek 140
                                   ++lk  ++   Lde+i  L+e dk+LFe+   
  gi|70607130|ref|YP_256000.1|  26 ISLKLKEQQDRLDEAIRRLRERDKDLFEKVIR 57 
                                   44444456677****************97655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                    Phage_GP20 101 kalldkdklklkedgelkg 119
                                   +a l+++k++lk d +++ 
  gi|70607130|ref|YP_256000.1|  86 TAYLAIEKVRLKLD-TVQE 103
                                   67888888888877.6665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                    Phage_GP20   1 eqikkvmkaengk 13 
                                   eq+k++m +e +k
  gi|70607130|ref|YP_256000.1| 165 EQAKQIM-EEAQK 176
                                   6677777.33322 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       2.7   2.8e+03      36      46 ..      74      84 ..      64      95 .. 0.55
   2 ?   11.8   0.0   0.00017      0.18       5      46 ..     217     258 ..     214     261 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
                        HTH_11 36 IkaLeelgvpI 46
                                  I +++++   I
  gi|70607130|ref|YP_256000.1| 74 ISDIRKMIKII 84
                                  45555544333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                        HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46 
                                   il  ++ + g+i  +++A+ ++vS+  v + +++Lee+g+ +
  gi|70607130|ref|YP_256000.1| 217 ILNYIKTTGGFIDVDYIAKNFDVSKDEVFNVLRRLEEKGLIV 258
                                   67778777777****************************554 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   1.8e+03      50      73 ..      24      47 ..      20      49 .. 0.79
   2 ?   11.0   0.0   0.00023      0.24      26      77 ..     207     258 ..     199     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                                  HHHHHHHT--HHHHHHHHHHHHHT CS
                        HTH_47 50 ldiAeriglpfdrvaaiaraLaea 73
                                   +i+ +++ + dr+ +++r+L+e 
  gi|70607130|ref|YP_256000.1| 24 TEISLKLKEQQDRLDEAIRRLRER 47
                                  577778888899999999999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00023
                                   -------HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                        HTH_47  26 kntakqaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                    n+++  e+ +l+++    G  ++  iA++ +++ d+v +++r+L+e+gl++
  gi|70607130|ref|YP_256000.1| 207 SNKKSLSEDMILNYIKTTGGFIDVDYIAKNFDVSKDEVFNVLRRLEEKGLIV 258
                                   44445567888999999999999999************************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.23      18      42 ..     233     257 ..     228     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                        HTH_29  18 iAkllglsrrtvyrwlkrfeegGla 42 
                                   iAk+ ++s++ v+++l+r ee+Gl 
  gi|70607130|ref|YP_256000.1| 233 IAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   9**********************75 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.6   3.8e+03      16      51 ..      88     123 ..      81     124 .. 0.68
   2 ?   10.9   0.0   0.00043      0.45      20      55 ..     224     257 ..     215     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                                   HHHHSSTCC-B-HHHHHHHHTS-HHH..HHHHHHHHHH CS
                          Rrf2  16 yLakeeeeepvsseeiaerqnispsy..lekilakLrk 51 
                                   yLa e+ +  ++++++ e q++s +   + +il +L++
  gi|70607130|ref|YP_256000.1|  88 YLAIEKVR--LKLDTVQELQGVSLVLfpVMRILGELKE 123
                                   56666653..6888888888888776445677777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00043
                                   SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          Rrf2  20 eeeeepvsseeiaerqnispsylekilakLrkaglv 55 
                                     +   + ++ ia+++++s+  +  +l++L+++gl+
  gi|70607130|ref|YP_256000.1| 224 TGG--FIDVDYIAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   433..68999*************************9 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.5   4.7e+03      30      46 ..      28      44 ..      11      67 .. 0.62
   2 ?   -2.7   0.0       6.5   6.8e+03      25      42 ..     167     185 ..     160     190 .. 0.52
   3 ?   10.9   0.0   0.00036      0.38      22      52 ..     230     257 ..     205     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                       DUF2250 30 keleipleevrellkkL 46
                                   +l+ ++ + +e++++L
  gi|70607130|ref|YP_256000.1| 28 LKLKEQQDRLDEAIRRL 44
                                  34444444444555554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.5
                       DUF2250  25 aksiakelei.pleevrel 42 
                                   ak+i++e ++    +vrel
  gi|70607130|ref|YP_256000.1| 167 AKQIMEEAQKmAEVKVREL 185
                                   5666655443033355555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00036
                       DUF2250  22 vdYaksiakeleipleevrellkkLeelGLl 52 
                                   vdY   iak++++++ ev ++l++Lee GL+
  gi|70607130|ref|YP_256000.1| 230 VDY---IAKNFDVSKDEVFNVLRRLEEKGLI 257
                                   555...9***********************8 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   7.8e-05     0.082      90     140 ..      16      99 ..      13     110 .. 0.78
   2 ?   -0.9   0.2      0.98     1e+03     142     162 ..     167     177 ..      98     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                       DUF4795  90 kkeLekmleellekleeqeealkkaldtLq...eelkekld..............rlelepLkeqle.............. 139
                                   k  L+k ++e+  kl+eq+++l++a+  L+   ++l+ek+               ++e+++++++++              
  gi|70607130|ref|YP_256000.1|  16 KVHLSKAITEISLKLKEQQDRLDEAIRRLRerdKDLFEKVIrsqiegdiaratiyAQEISDIRKMIKiiytaylaiekvrl 96 
                                   557999************************999778877766777788999999999999999999877776654444443 PP

                       DUF4795 140 ..e 140
                                     +
  gi|70607130|ref|YP_256000.1|  97 klD 99 
                                   333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.98
                       DUF4795 142 lkelqkelqeamekedkedea 162
                                    k++ +e q+          +
  gi|70607130|ref|YP_256000.1| 167 AKQIMEEAQK----------M 177
                                   2222222222..........2 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.73   7.7e+02      43      58 ..      30      45 ..       6      61 .. 0.55
   2 ?   10.3   0.0   0.00072      0.76      24      58 ..      65     102 ..      62     146 .. 0.73
   3 ?   -3.0   0.1       9.9     1e+04      54      66 ..     167     179 ..     162     188 .. 0.44

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.73
                                  HHSSSS-HHHHHHHHH CS
               Acetyltransf_11 43 lyrsglsleealeele 58
                                  l +++ +l+ea+++l+
  gi|70607130|ref|YP_256000.1| 30 LKEQQDRLDEAIRRLR 45
                                  3333444444444443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00072
                                   HHTT--HHHHHHHHHHHHHHHSSSS-HHHHHHHH...H CS
               Acetyltransf_11  24 kRrgfseeeikalkkayrllyrsglsleealeel...e 58 
                                    R+ + ++ei++++k+ +++y   l +e+   +l   +
  gi|70607130|ref|YP_256000.1|  65 ARATIYAQEISDIRKMIKIIYTAYLAIEKVRLKLdtvQ 102
                                   5889999****************999999988773321 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.9
                                   HHHHHHHTTTSCC CS
               Acetyltransf_11  54 leeleeeaeespe 66 
                                   ++++ eea++ +e
  gi|70607130|ref|YP_256000.1| 167 AKQIMEEAQKMAE 179
                                   3444223333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1765  (0.0984439); expected 358.6 (0.02)
Passed bias filter:                      965  (0.0538234); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1651.67
//
Query:       gi|70607131|ref|YP_256001.1|  [L=238]
Description: hypothetical protein Saci_1374 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-39  133.2   9.4    5.7e-39  132.7   9.4    1.2  1  CdvA          CdvA-like coiled-coil domain
  ------ inclusion threshold ------
      0.054   14.1   2.6       0.17   12.4   1.2    2.2  2  Syntaxin-6_N  Syntaxin 6, N-terminal
       0.12   12.8   1.1         10    6.6   0.1    2.6  2  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.16   12.1   0.9         11    6.2   0.1    3.0  4  YojJ          Bacterial membrane-spanning protein N-terminus
       0.34   11.0   4.1       0.62   10.2   4.1    1.4  1  PRC           PRC-barrel domain
       0.75   10.1   5.0         18    5.7   0.1    2.5  2  BLOC1_2       Biogenesis of lysosome-related organelles compl
        1.1    9.9   3.4        0.7   10.5   1.6    1.6  2  DUF883        Bacterial protein of unknown function (DUF883)
        9.8    6.7   8.9        9.3    6.8   3.1    2.6  2  ZapB          Cell division protein ZapB


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.7   9.4   2.6e-42   5.7e-39       1     121 [.      86     206 ..      86     208 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 2.6e-42
                          CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYk 81 
                                   kr++ALeeL+s+++ipkstye++k+kl+++l k++++++ lk +lk rl+++edq++++++a+++lki+y+sGEi+E aYk
  gi|70607131|ref|YP_256001.1|  86 KRQRALEELYSRQEIPKSTYEDMKRKLDSELLKIRDEHSRLKGRLKDRLNSIEDQVAQIDRAMIALKINYISGEIPELAYK 166
                                   8******************************************************************************** PP

                          CdvA  82 saieairellesaleekeeikklleklskleleeeeveet 121
                                   +++e++r + +s+  e+++ikk+l+kl+ l++e +e +++
  gi|70607131|ref|YP_256001.1| 167 NSMEILRLSRDSYALERDDIKKTLDKLDGLDKEVIELKPS 206
                                   **********************************999876 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2   7.7e-05      0.17      17      83 ..      91     188 ..      76     204 .. 0.63
   2 ?    2.3   0.0      0.11   2.5e+02       1      39 [.     177     215 ..     177     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                  Syntaxin-6_N  17 aeslyrrwerlledtsss..............tseeldetrteLrkalrsiewdledLeetv................... 64 
                                   +e+ly+r e   ++   +               ++e ++++  L+  l+sie ++ ++++++                   
  gi|70607131|ref|YP_256001.1|  91 LEELYSRQEI-PKS---TyedmkrkldsellkIRDEHSRLKGRLKDRLNSIEDQVAQIDRAMialkinyisgeipelaykn 167
                                   4444444322.222...0222345566666669****************************95666655555555555555 PP

                  Syntaxin-6_N  65 ..riveknpskfkidekelsr 83 
                                     +i++ +++ + ++ +++++
  gi|70607131|ref|YP_256001.1| 168 smEILRLSRDSYALERDDIKK 188
                                   544555555556666666655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
                  Syntaxin-6_N   1 DPFfevkeeVqkslnkaeslyrrwerlledtssstseel 39 
                                   D +   +++++k+l+k+ +l ++  +l+ ++s +ts e 
  gi|70607131|ref|YP_256001.1| 177 DSYALERDDIKKTLDKLDGLDKEVIELKPSASLNTSTEQ 215
                                   678888999999999999999998776655544434333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.024        54      39      57 ..     129     147 ..     103     164 .. 0.63
   2 ?    6.6   0.1    0.0046        10      10      32 ..     183     205 ..     180     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.024
                       NPV_P10  39 elnekLdaqsaqLaeletk 57 
                                    l+++L+++ +q+a+++ +
  gi|70607131|ref|YP_256001.1| 129 RLKDRLNSIEDQVAQIDRA 147
                                   5677777777777777763 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0046
                       NPV_P10  10 radikavddkVdalqqqvddvqe 32 
                                   r+dik++ dk+d l+++v +++ 
  gi|70607131|ref|YP_256001.1| 183 RDDIKKTLDKLDGLDKEVIELKP 205
                                   89****************88864 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.052   1.2e+02      39      58 ..      77      96 ..      65      97 .. 0.85
   2 ?   -1.3   0.0       1.1   2.4e+03       8      23 ..     106     121 ..     102     124 .. 0.76
   3 ?    6.2   0.1    0.0049        11       6      32 ..     122     148 ..     118     152 .. 0.90
   4 ?   -3.2   0.0       4.1   9.2e+03      14      34 ..     186     192 ..     183     201 .. 0.46

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.052
                          YojJ 39 lLcelesirekfaeletlas 58
                                  +L+++e+ir+    le+l s
  gi|70607131|ref|YP_256001.1| 77 VLGQMEKIRKRQRALEELYS 96
                                  8*********9999998765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                          YojJ   8 eelkeklkeeLeqiek 23 
                                   e +k+kl  eL +i+ 
  gi|70607131|ref|YP_256001.1| 106 EDMKRKLDSELLKIRD 121
                                   6788888888888876 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0049
                          YojJ   6 leeelkeklkeeLeqiekeleevlkal 32 
                                   + + lk  lk  L+ ie ++ ++ +a+
  gi|70607131|ref|YP_256001.1| 122 EHSRLKGRLKDRLNSIEDQVAQIDRAM 148
                                   56789*****************99888 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.1
                          YojJ  14 lkeeLeqiekeleevlkalde 34 
                                   +               k+ld+
  gi|70607131|ref|YP_256001.1| 186 I--------------KKTLDK 192
                                   2..............222222 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.1   0.00028      0.62       7      77 ..       9      71 ..       5      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00028
                                  ---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEETTS-G CS
                           PRC  7 sdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriivdapke 77
                                  +++iG++V +  G+  G++  v+ ++ +g ++++++ +g+      +      +  vk+++d +++ ++++
  gi|70607131|ref|YP_256001.1|  9 TKFIGQKVKDVYGRDAGVIVHVYTEI-DGTITGIELFKGE------EIKTYSPN-SVKVDGDSVVILPDWK 71
                                  789*******************9999.*********9984......44444455.7999999999988875 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.2    0.0089        20      13      80 ..      79     147 ..      74     155 .. 0.74
   2 ?    5.7   0.1    0.0079        18      43      81 ..     169     207 ..     163     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0089
                       BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelq.pylqqidqiekqvteLeea 80 
                                   +++e  ++  + Le+l  +++     ++d+  +l ++l k++ ++  l+  ++++++ ie+qv+++  a
  gi|70607131|ref|YP_256001.1|  79 GQMEKIRKRQRALEELYSRQEIPKSTYEDMKRKLDSELLKIRDEHSRLKgRLKDRLNSIEDQVAQIDRA 147
                                   567777777777888877777777777777778888888888888877625667899999999988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0079
                       BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                   ++ l+ + + +  + + +++ l+++d ++k+v eL+  +
  gi|70607131|ref|YP_256001.1| 169 MEILRLSRDSYALERDDIKKTLDKLDGLDKEVIELKPSA 207
                                   555555666666677999****************98665 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   0.00031       0.7      10      66 ..      87     142 ..      79     147 .. 0.84
   2 ?   -3.6   0.0         8   1.8e+04       5      17 ..     184     196 ..     175     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                        DUF883  10 lladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                       leel +  ++  ++++e+++++l+++l + r++ ++++ ++++r +++ +++ 
  gi|70607131|ref|YP_256001.1|  87 RQRALEELYS-RQEIPKSTYEDMKRKLDSELLKIRDEHSRLKGRLKDRLNSIEDQVA 142
                                   5566788885.4557999*******************************99998875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8
                        DUF883   5 aeleslladleel 17 
                                   +++++ l++l+ l
  gi|70607131|ref|YP_256001.1| 184 DDIKKTLDKLDGL 196
                                   4555555555555 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.1    0.0041       9.3      18      70 ..      82     138 ..      75     139 .. 0.74
   2 ?    2.7   0.3     0.076   1.7e+02      13      34 ..     186     207 ..     168     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                          ZapB  18 dtitlLqmeieeLkeen....eelkeenreleeeneqlkeereawqerlkkLLgkle 70 
                                   ++i++ q  +eeL  ++    +++++ +r+l +e+ + ++e++ ++ rlk  L+ +e
  gi|70607131|ref|YP_256001.1|  82 EKIRKRQRALEELYSRQeipkSTYEDMKRKLDSELLKIRDEHSRLKGRLKDRLNSIE 138
                                   44555555555554444555588889999999******************9888776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.076
                          ZapB  13 iqkaidtitlLqmeieeLkeen 34 
                                   i+k++d+++ L +e+ eLk   
  gi|70607131|ref|YP_256001.1| 186 IKKTLDKLDGLDKEVIELKPSA 207
                                   7889999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1559.64
//
Query:       gi|70607132|ref|YP_256002.1|  [L=82]
Description: hypothetical protein Saci_1376 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0011   19.1   2.6     0.0012   18.9   2.6    1.2  1  Oxidored_q5_N   NADH-ubiquinone oxidoreductase chain 4, amino
     0.0037   15.8   1.2     0.0037   15.8   1.2    1.4  2  Phlebovirus_G2  Phlebovirus glycoprotein G2
  ------ inclusion threshold ------
      0.046   13.8   1.0      0.046   13.8   1.0    1.9  2  YrhC            YrhC-like protein
        0.6    8.4   2.4       0.66    8.3   2.4    1.1  1  Phlebovirus_G1  Phlebovirus glycoprotein G1
       0.69    9.8   5.9       0.76    9.7   5.9    1.1  1  Fig1            Ca2+ regulator and membrane fusion protein Fi
        2.2    8.6  11.8        2.3    8.5   0.9    2.2  2  DUF2929         Protein of unknown function (DUF2929)
        9.1    5.9   7.7         11    5.7   7.7    1.1  1  Tetraspanin     Tetraspanin family


Domain annotation for each model (and alignments):
>> Oxidored_q5_N  NADH-ubiquinone oxidoreductase chain 4, amino terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.6   4.9e-07    0.0012      56     109 ..      18      76 ..       1      77 [. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.9e-07
                 Oxidored_q5_N  56 llglDslSapLilLSlWllpLmilA.....SqkhlkkepknrqrlFllllilLlllLil 109
                                   +++   l + Li+L l +l++milA       k++k  p++  + F+++++++ ++L++
  gi|70607132|ref|YP_256002.1|  18 NFNGEPLATALIILGLAILSIMILAgliygAIKVVKAVPNMPFKQFIIVMLMIAVFLVI 76 
                                   34556667777777777777777763333379*************************97 PP

>> Phlebovirus_G2  Phlebovirus glycoprotein G2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.2   1.4e-06    0.0037     452     498 ..       9      55 ..       4      64 .. 0.87
   2 ?   -2.1   0.2      0.39   9.9e+02     469     484 ..      62      77 ..      58      81 .. 0.42

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-06
                Phlebovirus_G2 452 lsdwvsGlldwlGGplktilvilgyialaivllvllillvrtaveki 498
                                   + + +sG+ ++ G pl t+l+ilg  +l+i++l  li+ + + v+ +
  gi|70607132|ref|YP_256002.1|   9 IANQLSGIFNFNGEPLATALIILGLAILSIMILAGLIYGAIKVVKAV 55 
                                   67889****************************99999888887765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.39
                Phlebovirus_G2 469 tilvilgyialaivll 484
                                    ++++++ ia+ +v++
  gi|70607132|ref|YP_256002.1|  62 QFIIVMLMIAVFLVIV 77 
                                   4444444444433333 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.57   1.5e+03      48      48 ..      36      36 ..      22      55 .. 0.56
   2 ?   13.8   1.0   1.8e-05     0.046      10      31 ..      60      82 .]      57      82 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.57
                          YrhC 48 v 48
                                  +
  gi|70607132|ref|YP_256002.1| 36 L 36
                                  2 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.8e-05
                          YrhC 10 YkrFafvLLalsaFLyi.GlviP 31
                                  +k+F++v+L + +FL i G++iP
  gi|70607132|ref|YP_256002.1| 60 FKQFIIVMLMIAVFLVIvGVLIP 82
                                  9**************86699999 PP

>> Phlebovirus_G1  Phlebovirus glycoprotein G1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.4   0.00026      0.66     409     464 ..      14      69 ..       7      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00026
                Phlebovirus_G1 409 hGllnyqChtalsallvvtlvvlivlllllvlkrvlkllkllpkkllsPlsWlkvf 464
                                    G++n+    + +al++  l +l +++l  +++++ k++k +p++  + +  + ++
  gi|70607132|ref|YP_256002.1|  14 SGIFNFNGEPLATALIILGLAILSIMILAGLIYGAIKVVKAVPNMPFKQFIIVMLM 69 
                                   69****************************************98766665555544 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.9    0.0003      0.76      81     135 ..      28      80 ..      18      82 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                          Fig1  81 llmvaiiLtlllfllllyfpl.....gseipllPfkskavskvalvlsflllllwlvgal 135
                                   l++  +++  +++       l     g++  ++++++++ +++++v+ +++++l++vg+l
  gi|70607132|ref|YP_256002.1|  28 LIILGLAILSIMI-------LagliyGAIKVVKAVPNMPFKQFIIVMLMIAVFLVIVGVL 80 
                                   3333333333333.......23334356667889999999999**************997 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.9   0.00092       2.3      17      50 ..       6      42 ..       3      50 .. 0.76
   2 ?    4.7   5.1     0.015        38      31      53 ..      60      82 .]      41      82 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00092
                       DUF2929 17 vgYIgsaLtgv.tyd..fttalilavvfgvlviliia 50
                                    YI+++L+g  +++  ++ ++ + + +++l i+i a
  gi|70607132|ref|YP_256002.1|  6 FHYIANQLSGIfNFNgePLATALIILGLAILSIMILA 42
                                  57*************9966666666666666666654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                       DUF2929 31 fttalilavvfgvlviliialis 53
                                  f++ +i+++ ++v++++++ li+
  gi|70607132|ref|YP_256002.1| 60 FKQFIIVMLMIAVFLVIVGVLIP 82
                                  8999************9999986 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   7.7    0.0042        11      49      99 ..      24      80 ..       5      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0042
                                  ....XXXXXX.XXXXXXXXX.XXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXX CS
                                  xxxxxxxxxx.xxxxxxxxx.xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                   Tetraspanin 49 laillivvGv.llfllgflG.cigalkenk....cllltfsllllvlfllelaagil 99
                                  la++li++G  +l ++ ++G ++ga+k  k    +    f++++l++ ++++++g+l
  gi|70607132|ref|YP_256002.1| 24 LATALIILGLaILSIMILAGlIYGAIKVVKavpnMPFKQFIIVMLMIAVFLVIVGVL 80
                                  556799999966666666666667888777666677788999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1457  (0.081265); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 505.70
//
Query:       gi|70607133|ref|YP_256003.1|  [L=416]
Description: phosphopyruvate hydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.2e-94  314.6   0.1    8.3e-94  314.1   0.1    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    1.6e-34  118.9   0.2    2.8e-34  118.1   0.2    1.4  1  Enolase_N  Enolase, N-terminal domain
      1e-06   28.5   0.0    1.8e-06   27.7   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.1   0.1   1.4e-97   8.3e-94       3     282 ..     138     406 ..     136     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 314.1 bits;  conditional E-value: 1.4e-97
                                   EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHHH CS
                     Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkeal 83 
                                    +P+P+ln++nGG hagn+l++qef+i+P + ++f+ea++   evy++lk+++ ++ygk  t++GdeGGf+P l+++ +al
  gi|70607133|ref|YP_256003.1| 138 YIPMPLLNILNGGLHAGNNLKIQEFIIIPKNFDKFTEAIQASIEVYKRLKDLITERYGKIYTALGDEGGFSPPLEKTMDAL 218
                                   68******************************************************************************* PP

                                   HHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-HH CS
                     Enolase_C  84 dliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddwe 164
                                   dl+ ++i+  Gy++k+ +++d+a+s+f+  ++++y+ld+k          t+ +l d+yk+l++ yP++ iedp++e+d++
  gi|70607133|ref|YP_256003.1| 219 DLVYTSIKSLGYEDKIFMGMDAAASNFF--HESHYELDGKR--------YTAGELIDYYKQLADMYPLMYIEDPFEENDYD 289
                                   ****************************..667*****999........899***************************** PP

                                   HHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--HH CS
                     Enolase_C 165 awkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedtti 245
                                   ++++l+++l  k  + Gddl+vtn + lk++ie+ ++   ++k nqiG++te+l+ +  a++++  ++vshrsGeted++i
  gi|70607133|ref|YP_256003.1| 290 SFSQLQSKLK-KTIVTGDDLYVTNIEYLKKGIERMSSKGTIVKPNQIGTITETLDYIDFARRNAVKTIVSHRSGETEDSII 369
                                   *********9.8889****************************************************************** PP

                                   HHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHG CS
                     Enolase_C 246 adlavglsaGqiktGaparserlakynqllrieeelg 282
                                   adlavg+++  iktGap+r er +kyn+l+ ie + g
  gi|70607133|ref|YP_256003.1| 370 ADLAVGTQSEFIKTGAPSRGERTSKYNRLIEIELDYG 406
                                   ******************************9997665 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.2   4.8e-38   2.8e-34       1     131 []       7     131 ..       7     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 4.8e-38
                                   EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBT CS
                     Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldv 81 
                                   I+k+k++ei+dSr n T++v+v+t dg++g   +p+GaS+g++ea+el+D+      +  v +ave vn++++++l ++dv
  gi|70607133|ref|YP_256003.1|   7 IRKLKGYEIIDSRANRTIRVRVETYDGIVGFGDAPAGASKGANEAVELKDK------NGRVIDAVELVNTVLSDSLKDYDV 81 
                                   8999**********************************************8......456999****************** PP

                                   T-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  82 tdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                   ++q+ iD++li+lDgt+nks++G+N+++a+S+Av k a++a++++ ++y+
  gi|70607133|ref|YP_256003.1|  82 RRQRVIDTTLIRLDGTQNKSRIGGNTMIATSIAVLKTASRALGQEYFEYI 131
                                   *************************************************8 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     3e-10   1.8e-06      56     156 ..     257     359 ..     218     389 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3e-10
                                   TSBHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSS..SHHHHHHHHHHTSESEEEEBHHHH CS
                      MR_MLE_C  56 awdlatAirvarelee.ldllwlEEPvppeddleglaelrara.sipiaagEsly..sradfrelleagavdivqpdvsrv 132
                                   ++++ + i + ++l++ + l+++E+P+   +d+++  +l++ + +  i++g +ly  +++ +++ +e+       ++++++
  gi|70607133|ref|YP_256003.1| 257 RYTAGELIDYYKQLADmYPLMYIEDPFEE-NDYDSFSQLQS-KlKKTIVTGDDLYvtNIEYLKKGIERMSSKGTIVKPNQI 335
                                   68999***********999*********9.88********7.3356899999865327*********************** PP

                                   TSHHHHHHHHHHHHHTT-EEEEBS CS
                      MR_MLE_C 133 gGitearkvaalaeafgvpvapHs 156
                                   g ite+++ ++ a+ + v+ ++ +
  gi|70607133|ref|YP_256003.1| 336 GTITETLDYIDFARRNAVKTIVSH 359
                                   ***************999966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2766.40
//
Query:       gi|70607134|ref|YP_256004.1|  [L=103]
Description: hypothetical protein Saci_1378 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.8    4.9  10.6        7.6    4.7  10.6    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  10.6   0.00043       7.6      72     149 ..      34      96 ..       4     102 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.00043
                       DUF2070  72 lflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyf 149
                                   ++la +t+ ++                ++++++++ ++l ++++++ +++v +++++ +++p l+ ++++i +++++ 
  gi|70607134|ref|YP_256004.1|  34 FYLAWITAPFL--------------VGYFFYSTLVEVFLLLIFNIIGYIIVLKNKYK-YIFPLLLFSAVIIQIFYILT 96 
                                   33333333333..............44566778888999999999999999999876.56677777777777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 660.37
//
Query:       gi|70607135|ref|YP_256005.1|  [L=105]
Description: hypothetical protein Saci_1379 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-05   23.0   0.8       0.41   10.8   0.0    2.3  2  Zn-ribbon_8     Zinc ribbon domain
     0.0019   18.1   0.3     0.0038   17.2   0.3    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0044   17.0   0.1      0.009   16.0   0.1    1.5  1  DZR             Double zinc ribbon
     0.0059   16.6   0.1     0.0088   16.1   0.1    1.2  1  CpXC            CpXC protein
     0.0081   16.5   2.0      0.032   14.6   0.2    2.1  2  DUF4379         Probable Zinc-ribbon domain
      0.009   15.9   0.4        4.1    7.4   0.1    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.029   13.8   5.2       0.15   11.5   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
      0.041   13.7   4.8       0.19   11.6   0.5    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.044   13.5   0.4          7    6.4   0.0    2.3  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.047   14.4   0.8        1.9    9.2   0.1    2.4  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.054   13.2   7.5       0.31   10.8   0.9    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.063   13.1   1.0       0.48   10.2   0.0    2.2  2  zinc_ribbon_5   zinc-ribbon domain
      0.093   12.8   0.1        8.2    6.5   0.0    2.1  2  Zn_Tnp_IS91     Transposase zinc-binding domain
        0.1   12.5   1.1        9.1    6.3   0.1    2.6  2  Nudix_N_2       Nudix N-terminal
       0.16   11.7   1.8        1.9    8.2   0.2    2.4  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.18   11.9   4.5          3    8.0   0.6    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.21   11.6   2.4        4.1    7.5   0.2    2.2  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.28   11.6   4.1       0.34   11.3   1.5    2.4  2  zf-IS66         zinc-finger binding domain of transposase IS6
        0.3   11.0   6.1        1.8    8.6   0.2    2.7  3  zinc_ribbon_4   zinc-ribbon domain
       0.64    9.8   5.1        3.6    7.4   0.6    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.86   10.4   5.0       0.92   10.3   2.3    2.3  2  zf-3CxxC_2      Zinc-binding domain
        1.8    8.2   6.4        5.5    6.6   0.6    2.6  3  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00052      0.42      26      38 ..       8      21 ..       1      23 [. 0.71
   2 !   10.8   0.0    0.0005      0.41       6      20 ..      47      61 ..      46      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                   Zn-ribbon_8 26 lta.CPeCgsevrr 38
                                  + + CP+Cg+++++
  gi|70607135|ref|YP_256005.1|  8 EADvCPNCGKKAEK 21
                                  3344******9988 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
                   Zn-ribbon_8  6 YrCeeCghefevlqs 20
                                  Y+C +Cgh+  +++s
  gi|70607135|ref|YP_256005.1| 47 YECGNCGHKWKAVVS 61
                                  ********9997765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   4.7e-06    0.0038      20      45 ..      11      54 ..       7      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.7e-06
                 Zn_Tnp_IS1595 20 vCPhCgsr..kayrikt................rglfqCkeCrk 45
                                  vCP+Cg++  k+ ++++                 g ++C  C++
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKKaeKPVKTWQlvsplpdaygrititvMGSYECGNCGH 54
                                  8*******999999999*************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.1e-05     0.009      11      38 ..       8      56 ..       3      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                           DZR 11 darfCseCgtklkavaa.....................edrCpsCgekv 38
                                  +a +C++Cg+k +++ +                     ++ C +Cg+k 
  gi|70607135|ref|YP_256005.1|  8 EADVCPNCGKKAEKPVKtwqlvsplpdaygrititvmgSYECGNCGHKW 56
                                  7899*******9887778999*************************985 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05    0.0088       3      48 ..      12      57 ..      11      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                          CpXC  3 CpaCgkefeaeiwtsidadedpelkeklldgslfeatCpkCgatak 48
                                  Cp+Cgk+ e ++ t   ++  p++  ++    + +++C +Cg++ k
  gi|70607135|ref|YP_256005.1| 12 CPNCGKKAEKPVKTWQLVSPLPDAYGRITITVMGSYECGNCGHKWK 57
                                  *******99888888888888*********************9876 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.53   4.3e+02      32      37 ..      12      17 ..       2      27 .. 0.66
   2 !   14.6   0.2     4e-05     0.032      31      48 ..      48      65 ..      43      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.53
                       DUF4379 32 CakCgh 37
                                  C++Cg+
  gi|70607135|ref|YP_256005.1| 12 CPNCGK 17
                                  666665 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-05
                       DUF4379 31 kCakCgheWeasvsnrtk 48
                                   C +Cgh+W+a vs+  +
  gi|70607135|ref|YP_256005.1| 48 ECGNCGHKWKAVVSKIKA 65
                                  7************98764 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0051       4.1      30      45 ..      11      24 ..       4      30 .. 0.79
   2 !    6.7   0.0    0.0082       6.7      28      40 ..      46      58 ..      36      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0051
                OrfB_Zn_ribbon 30 tCseCgsknkealsgr 45
                                   C++Cg+k ++    +
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKKAEK--PVK 24
                                  69999999999..444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0082
                OrfB_Zn_ribbon 28 SktCseCgsknke 40
                                  S +C +Cg+k k 
  gi|70607135|ref|YP_256005.1| 46 SYECGNCGHKWKA 58
                                  6677777777554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00019      0.15      18      25 ..      11      18 ..       6      21 .. 0.64
   2 ?    3.9   1.1     0.046        37      19      25 ..      49      55 ..      47      56 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                   zf-ribbon_3 18 vCpyCGtk 25
                                  vCp+CG+k
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKK 18
                                  56666654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                   zf-ribbon_3 19 CpyCGtk 25
                                  C +CG+k
  gi|70607135|ref|YP_256005.1| 49 CGNCGHK 55
                                  7777765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.053        44       3       9 ..      12      18 ..      10      23 .. 0.80
   2 ?   11.6   0.5   0.00024      0.19      29      39 .]      47      57 ..      44      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.053
                       TFIIS_C  3 CpkCgsr 9 
                                  Cp+Cg++
  gi|70607135|ref|YP_256005.1| 12 CPNCGKK 18
                                  8888875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00024
                       TFIIS_C 29 ykCtkCghrWr 39
                                  y+C +Cgh+W+
  gi|70607135|ref|YP_256005.1| 47 YECGNCGHKWK 57
                                  9*********7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0086         7      23      28 ..      11      16 ..       1      29 [. 0.73
   2 ?    5.4   0.1     0.017        14       6      12 ..      49      55 ..      49      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0086
                 zf-NADH-PPase 23 vCpaCg 28
                                  vCp+Cg
  gi|70607135|ref|YP_256005.1| 11 VCPNCG 16
                                  555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                 zf-NADH-PPase  6 CgrCGap 12
                                  Cg CG++
  gi|70607135|ref|YP_256005.1| 49 CGNCGHK 55
                                  9999997 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0023       1.9       4      13 ..      11      20 ..       8      33 .. 0.78
   2 ?    3.8   0.1      0.12        95       5      15 ..      49      60 ..      47      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                       zf-ISL3  4 rCPnCgsktv 13
                                  +CPnCg+k  
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKKAE 20
                                  7******953 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                       zf-ISL3  5 CPnCgsk.tvvk 15
                                  C nCg k ++v+
  gi|70607135|ref|YP_256005.1| 49 CGNCGHKwKAVV 60
                                  *****9985543 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00038      0.31       2       9 ..      12      19 ..      11      24 .. 0.80
   2 ?    5.9   0.9     0.013        11      16      22 ..      49      55 ..      45      56 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                 zinc_ribbon_2  2 CpnCGael 9 
                                  CpnCG++ 
  gi|70607135|ref|YP_256005.1| 12 CPNCGKKA 19
                                  9****985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
                 zinc_ribbon_2 16 CpyCGtp 22
                                  C +CG++
  gi|70607135|ref|YP_256005.1| 49 CGNCGHK 55
                                  8888886 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.44   3.6e+02       5      10 ..      12      17 ..      11      19 .. 0.82
   2 ?   10.2   0.0   0.00059      0.48       4      26 ..      48      70 ..      47      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.44
                 zinc_ribbon_5  5 CpdCdt 10
                                  Cp+C+ 
  gi|70607135|ref|YP_256005.1| 12 CPNCGK 17
                                  9***85 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00059
                 zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkkV 26
                                   C +C+ k k v sk+K  g  V
  gi|70607135|ref|YP_256005.1| 48 ECGNCGHKWKAVVSKIKAGGSSV 70
                                  59***************988766 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       8.2      59      90 ..      11      42 ..       5      43 .. 0.77
   2 ?    4.3   0.1      0.05        41      39      52 ..      46      59 ..      44      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                   Zn_Tnp_IS91 59 hCpsCqkkateewlekqqeellpvpyrhvvfT 90
                                   Cp+C+kka++ +   q    lp  y  +++T
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKKAEKPVKTWQLVSPLPDAYGRITIT 42
                                  7*******999888777777777777777766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.05
                   Zn_Tnp_IS91 39 ryeCeeCghekivy 52
                                   yeC +Cgh+ +  
  gi|70607135|ref|YP_256005.1| 46 SYECGNCGHKWKAV 59
                                  599*****986654 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.011       9.1       3      11 ..      12      20 ..      10      25 .. 0.70
   2 ?    4.5   0.1      0.04        33       3      17 ..      49      66 ..      49      70 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                  -TTT--B-E CS
                     Nudix_N_2  3 CsqCGtpve 11
                                  C++CG++ e
  gi|70607135|ref|YP_256005.1| 12 CPNCGKKAE 20
                                  777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.04
                                  -TTT--B-E...EE--TT CS
                     Nudix_N_2  3 CsqCGtpve...lripdg 17
                                  C +CG++ +    +i +g
  gi|70607135|ref|YP_256005.1| 49 CGNCGHKWKavvSKIKAG 66
                                  999999855222566555 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.14   1.1e+02      20      25 ..      12      17 ..       5      21 .. 0.79
   2 ?    8.2   0.2    0.0023       1.9       1      10 [.      47      56 ..      47      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.14
                                  -SSS-- CS
                DNA_RNApol_7kD 20 CkeCGh 25
                                  C +CG 
  gi|70607135|ref|YP_256005.1| 12 CPNCGK 17
                                  777775 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                                  -B-SSS--B- CS
                DNA_RNApol_7kD  1 YiCgeCgaev 10
                                  Y Cg+Cg++ 
  gi|70607135|ref|YP_256005.1| 47 YECGNCGHKW 56
                                  9999999975 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.022        18      14      21 ..       9      16 ..       6      18 .. 0.73
   2 ?    8.0   0.6    0.0037         3      16      26 .]      48      58 ..      46      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                       UPF0547 14 aqfCphCG 21
                                  a +Cp CG
  gi|70607135|ref|YP_256005.1|  9 ADVCPNCG 16
                                  67788887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0037
                       UPF0547 16 fCphCGyvFqa 26
                                  +C  CG+ ++a
  gi|70607135|ref|YP_256005.1| 48 ECGNCGHKWKA 58
                                  7999*****96 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.005       4.1       2      10 ..      12      20 ..      11      25 .. 0.88
   2 ?    4.1   0.1     0.058        48      26      39 ..      47      58 ..      46      62 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                     Ogr_Delta  2 CPhCgapaa 10
                                  CP+Cg++a 
  gi|70607135|ref|YP_256005.1| 12 CPNCGKKAE 20
                                  ******996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.058
                     Ogr_Delta 26 yqCsnfeCgatfva 39
                                  y+C n  Cg++ +a
  gi|70607135|ref|YP_256005.1| 47 YECGN--CGHKWKA 58
                                  56666..7776655 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00042      0.34       3      46 .]      11      53 ..       9      53 .. 0.79
   2 ?   -2.0   0.1       6.3   5.1e+03      13      18 ..      80      85 ..      75      97 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                       zf-IS66  3 tCpcCGgllkpigedrvreeldipPakfrViehirpkyaCpcCe 46
                                  +Cp+CG++  +  ++ ++ +  +p a  r++ ++   y+C +C+
  gi|70607135|ref|YP_256005.1| 11 VCPNCGKKAEKPVKT-WQLVSPLPDAYGRITITVMGSYECGNCG 53
                                  8*****953444445.66677788999999999*********97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.3
                       zf-IS66 13 pigedr 18
                                   ige++
  gi|70607135|ref|YP_256005.1| 80 TIGEEK 85
                                  566653 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.034        28       5      11 ..      12      18 ..      11      20 .. 0.80
   2 ?    8.6   0.2    0.0022       1.8      27      36 .]      48      57 ..      45      57 .. 0.88
   3 ?   -1.8   0.0       3.8   3.1e+03      17      26 ..      61      70 ..      60      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.034
                 zinc_ribbon_4  5 CpsCkak 11
                                  Cp+C++k
  gi|70607135|ref|YP_256005.1| 12 CPNCGKK 18
                                  9999886 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0022
                 zinc_ribbon_4 27 rCskCghvFr 36
                                   C +Cgh+++
  gi|70607135|ref|YP_256005.1| 48 ECGNCGHKWK 57
                                  5********6 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.8
                 zinc_ribbon_4 17 eklpakgvkv 26
                                  +k++a+g++v
  gi|70607135|ref|YP_256005.1| 61 SKIKAGGSSV 70
                                  7999999988 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.038        31      17      21 ..      12      16 ..      11      21 .. 0.68
   2 ?    7.4   0.6    0.0044       3.6       1       9 [.      47      55 ..      47      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.038
                  Rubredoxin_2 17 CpsCg 21
                                  Cp+Cg
  gi|70607135|ref|YP_256005.1| 12 CPNCG 16
                                  77776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0044
                  Rubredoxin_2  1 YvCsqCGfe 9 
                                  Y+C +CG++
  gi|70607135|ref|YP_256005.1| 47 YECGNCGHK 55
                                  99*****95 PP

>> zf-3CxxC_2  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   1.2e+03      30      36 ..      12      18 ..       6      33 .. 0.58
   2 ?   10.3   2.3    0.0011      0.92       5      20 ..      44      59 ..      41      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                    zf-3CxxC_2 30 CkkCkek 36
                                  C +C++k
  gi|70607135|ref|YP_256005.1| 12 CPNCGKK 18
                                  3333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                    zf-3CxxC_2  5 fGefkCekCgkeWsSa 20
                                   G++ C +Cg++W   
  gi|70607135|ref|YP_256005.1| 44 MGSYECGNCGHKWKAV 59
                                  69***********875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6    0.0068       5.5       2       8 ..      11      17 ..      10      22 .. 0.77
   2 ?    4.5   0.1      0.03        25      19      29 ..      46      56 ..      44      62 .. 0.78
   3 ?   -3.5   0.1       9.8     8e+03      26      32 ..      91      97 ..      91     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0068
                                  EETTTTC CS
                  TF_Zn_Ribbon  2 kCPnCgs 8 
                                  +CPnCg 
  gi|70607135|ref|YP_256005.1| 11 VCPNCGK 17
                                  6888885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.03
                                  CEEESSSSBEE CS
                  TF_Zn_Ribbon 19 elvCtdCGlVl 29
                                   + C++CG  +
  gi|70607135|ref|YP_256005.1| 46 SYECGNCGHKW 56
                                  56699999876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 9.8
                                  SBEEEEC CS
                  TF_Zn_Ribbon 26 GlVledn 32
                                  G+V+e +
  gi|70607135|ref|YP_256005.1| 91 GEVIELD 97
                                  7888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 651.49
//
Query:       gi|70607136|ref|YP_256006.1|  [L=137]
Description: hypothetical protein Saci_1380 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00038   20.3   0.3    0.00055   19.8   0.3    1.2  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   3.1e-08   0.00055       2      57 ..      29      83 ..      28      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-08
                                  XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE. CS
                 Peptidase_S24  2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvlla 57
                                  ++G SM+p +++G l +    s++  G iv+ +   +  + i++vi  +g ++ ++
  gi|70607136|ref|YP_256006.1| 29 IEGVSMYPVFQNGFLTFYVSPSDISVGNIVIYKSTVGT-YVIHQVIHIDGNSYVTK 83
                                  89***********************************8.*********99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1059.79
//
Query:       gi|70607137|ref|YP_256007.1|  [L=505]
Description: glycine dehydrogenase subunit 2 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-12   45.7   0.0    1.1e-11   44.2   0.0    1.6  2  GDC-P            Glycine cleavage system P-protein
    4.3e-07   29.2   0.1      7e-07   28.5   0.1    1.4  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.025   13.8   0.1      0.038   13.3   0.1    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.9e-15   1.1e-11      23     285 ..      31     301 ..      25     313 .. 0.80
   2 ?   -2.0   0.0       0.2   1.2e+03     332     365 ..     338     371 ..     334     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.9e-15
                                   HHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SS. CS
                         GDC-P  23 lddliekavPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYq. 101
                                   l + i+ ++P+++k ++e +l+ + sE e++++  ++++      + f+  G   ++  + ++    + ++ ++   P q 
  gi|70607137|ref|YP_256007.1|  31 LRKEITLNIPENLKRRNEPNLP-SISELEAVRHYIRLSQMSFGvDTGFVPLGSCTMKYNPKVEE---KISDVVSGLHPLQd 107
                                   555566799****999998887.589**********99977653789*****999887777777...4578899999*996 PP

                                   GGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHH.HHHHHHHH-SSS--EEEEETTS-HHHHHHHH.HHHGGGT- CS
                         GDC-P 102 aEisqGrLeallnfqtlvadltGldianasllDegtAaaE.Avllaaraskkkakkvvvdkkvhpqtlevlk.trakglgi 180
                                   +E  qG Le + + q ++a++tG di +  l   +  a+E A +l+ ++ ++ ++++  d+ +  +t++  +   a   g 
  gi|70607137|ref|YP_256007.1| 108 SETVQGILEIIYEMQLMLAEITGTDICS--LQVPAGSAGElAGVLMIKKYHELKERFSRDEMLVADTAHGTNpASAAMAGY 186
                                   79************************75..544444444436666666666666888888888877776554256778889 PP

                                   EEEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEEEE-TT.GGGTB--HHHHT-SE CS
                         GDC-P 181 eivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslvvvaadll.aLtllkpPgelgaDi 252
                                   +++   + +e+  d       + +++ag ++  pnt G  e+ + e+++ +++ ++ +      +  +  +  Pg++g Di
  gi|70607137|ref|YP_256007.1| 187 KVIYIRSNKEGLVDidllrevVGEKTAGFMLTNPNTLGLFEEnIVEIAKLLHNVDAKLYYDGANMnGILGVVRPGDMGFDI 267
                                   999988888888888999998899**************9986599*********99988765555155556789******* PP

                                   E.EEE-TTTT---GGG----EEEEE-GGGGGG-- CS
                         GDC-P 253 v.vGsaqrfGvPlgyGGPhagffAvkeklkRkiP 285
                                   v +   + f vP g GGP ag + +k +++  +P
  gi|70607137|ref|YP_256007.1| 268 VhLNLHKTFAVPHGGGGPGAGAICAKGDMVDFLP 301
                                   94566889*************9988877766666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         GDC-P 332 aalyavyhGkeglkeiarrihkkteilakelkkk 365
                                   + +y+  +G+egl  i + +  +t+++  +l++ 
  gi|70607137|ref|YP_256007.1| 338 SYVYILGLGAEGLSMIGKLSTLATNYIIFKLRNV 371
                                   56899999*****************999888774 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   1.2e-10     7e-07      88     207 ..     164     281 ..     141     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-10
                                   TSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHHHHHH CS
                   Aminotran_5  88 gdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigklakk 167
                                   +de++v ++ h  n   + +++   g+kv +i+ ++eg++d+d l++ + ekt+  ++t + n++G   + + ei+kl+++
  gi|70607137|ref|YP_256007.1| 164 RDEMLVADTAHGTNP--ASAAM--AGYKVIYIRSNKEGLVDIDLLREVVGEKTAGFMLT-NPNTLGLfEENIVEIAKLLHN 239
                                   578888888887776..44443..69****************************99988.56889997899********** PP

                                   TT-EEEEE-TTTTTTS.---HHHHTESEEEEETTT.TTSSTT CS
                   Aminotran_5 168 kgalvlvDaaqavghi.pidvkklgvDflafsghK.llgPtG 207
                                   ++a +  D+a + g    +   ++g D++ +  hK +  P G
  gi|70607137|ref|YP_256007.1| 240 VDAKLYYDGANMNGILgVVRPGDMGFDIVHLNLHKtFAVPHG 281
                                   **********998865267899*************6555654 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.3e-06     0.038      35     169 ..     119     249 ..     106     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-06
                                   HHHHHHHHHHTT-S.EEEEES-HHHHHHHHHHHH--TTEEE...EEETT....-HHHHSSTTHHHHCC--EEEEE-EBTTT CS
               Beta_elim_lyase  35 nrLedavaelfgke.aalfvpqGtaAnsillkillqrgeev...ivtep....ahihfdetgaiaelagvklrdlknkeaG 107
                                   ++++  +ae++g++ + l vp G a++   + ++  +++e    + + +    a +   ++ a a++ag k++ ++++++G
  gi|70607137|ref|YP_256007.1| 119 YEMQLMLAEITGTDiCSLQVPAGSAGELAGVLMIK-KYHELkerFSR-DemlvADTAHGTNPASAAMAGYKVIYIRSNKEG 197
                                   6778889999999977889999*999987763333.22222010222.2466666666788899999*********9999* PP

                                   BE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase 108 kmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                    +d++ l++++ e      k++  +lt+ n    G  +  e++ e+a++ ++ + +l +DgA
  gi|70607137|ref|YP_256007.1| 198 LVDIDLLREVVGE------KTAGFMLTNPNTL--G--LFEENIVEIAKLLHNVDAKLYYDGA 249
                                   ********99998......5788899999997..4..789*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3641.14
//
Query:       gi|70607138|ref|YP_256008.1|  [L=447]
Description: glycine dehydrogenase subunit 1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.6e-111  371.7   0.0   6.1e-111  371.3   0.0    1.0  1  GDC-P     Glycine cleavage system P-protein


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.3   0.0  3.4e-115  6.1e-111      10     404 ..      12     420 ..       7     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 371.3 bits;  conditional E-value: 3.4e-115
                                   HHHHHHHHHT-SSHHHHHHHHS-GGGB--S-----..----HHHHHHHHHHHHTTB--..-EE--BTTB------HHHHHH CS
                         GDC-P  10 dqkemLetlGlkslddliekavPkeiklkkelkle..apksEeellaelekiasknkv..vksfiGaGyydtilPaviqrn 86 
                                    ++emL+ +G++++ +l+ ++vP+++ lk++l+++  +p sE+e+ ++l+++ +kn +  +  fiG G   +++P++++  
  gi|70607138|ref|YP_256008.1|  12 YTEEMLKEIGVNDIMNLF-SDVPQDLILKRKLNIPydKPLSEYEISQRLNELKKKNLElkYPPFIGGGLCPHYIPEAVKF- 90 
                                   5789**************.9*****99999998753378*****************9845667***************98. PP

                                   TTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETTS-HHH CS
                         GDC-P  87 ilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkkvhpqt 167
                                   i++++e+ytaYtPYq+EisqG L+a+ ++q+l+a+l  ++  nas++D ++A aEAvl+a+r++++k   v++ ++++p  
  gi|70607138|ref|YP_256008.1|  91 IMSRSEFYTAYTPYQPEISQGLLQAIYEYQSLMAELLEMEFVNASMYDWASAIAEAVLMAHRINRRK--SVLLPSNMNPYH 169
                                   ******************************************************************9..9*********** PP

                                   HHHHHHHHGGGT-EEEEE-GGG--S-............S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEEEE-TTG CS
                         GDC-P 168 levlktrakglgieivevdlteekvtd.........kekevagvlvqypnteGried.lkelvekakkkkslvvvaadlla 238
                                   +ev+kt   g gi i e ++ +++  +         ++++v+++ +q+pn+ G  e+ ++ +v+ akkk+++ ++ + +l+
  gi|70607138|ref|YP_256008.1| 170 REVVKTWVYGKGIRITELPTDSTSG-QidiekleqiNTDDVSAIYIQQPNFYGIFEEnIEYIVDFAKKKNIITIMGVSPLS 249
                                   ***************9987443322.134788999999***************99875899******************** PP

                                   GGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEEBTTS-EEEEEE-CCGSHHCCHHHC CS
                         GDC-P 239 LtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvskDaegkralrlalqtREqHirRdkA 317
                                   L+l+kpPge+g Di+vG++q++G+Pl yGGP  g fAv+ +  l+R++PGR+vG++kD++g+ra++l lqtREq  rR+kA
  gi|70607138|ref|YP_256008.1| 250 LGLIKPPGEYGIDIAVGDGQEIGLPLNYGGPLMGIFAVRWDsqLVRQMPGRIVGLTKDEKGNRAFTLILQTREQFTRREKA 330
                                   **************************************85555************************************** PP

                                   S-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..T-EE--SSBSSEEEEE--T.TTHHH.HHHHH CS
                         GDC-P 318 tsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk.leeelkkkkffdtllievee.kaaek.vlkka 395
                                   tsni t+ +L+A+ +a+y  ++Gk+gl+++a++i+ ++++++k+ ++  +++  +++ f +++++  ++ + ++  +l+k 
  gi|70607138|ref|YP_256008.1| 331 TSNITTNETLMAIGSAVYLSLLGKHGLRDLAEEIYVRSHYAKKKFEELgFKSPYSGEFFEEFVIQFPKNyNLIHSsLLNKR 411
                                   ***********************************************9555555555555555554444433433488888 PP

                                   HHTTEE-EE CS
                         GDC-P 396 ekeglnlrk 404
                                   ++ gl+l  
  gi|70607138|ref|YP_256008.1| 412 IHGGLQLND 420
                                   887765543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3193.35
//
Query:       gi|70607139|ref|YP_256009.1|  [L=351]
Description: glycine cleavage system aminomethyltransferase T [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-63  213.7   0.0    3.3e-63  213.5   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    6.1e-18   64.5   0.0    1.1e-17   63.7   0.0    1.3  1  GCV_T_C   Glycine cleavage T-protein C-terminal barrel domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   0.0   3.6e-67   3.3e-63       3     254 ..       8     242 ..       6     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 3.6e-67
                         GCV_T   3 drhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat.ytl 82 
                                   d   +l+a ++efa w+mP++Y  +s ++ehl vr++++ fD+Shmg+++vsG +    L+ l++++isk kp+++   t+
  gi|70607139|ref|YP_256009.1|   8 DIETKLNADIGEFANWKMPMKY--TSYQDEHLLVRTSVAFFDISHMGRLKVSGNQ--NELEFLVSKEISKNKPNSMIgPTA 84 
                                   667899****************..*****************************99..99**************88877*** PP

                         GCV_T  83 llnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlskllgadls 163
                                   +ln++Gg++dD+++++++e+efl+v+na n+ek+++w+ k     ++ + ved+t ++++la+qG +  + ++k     ++
  gi|70607139|ref|YP_256009.1|  85 FLNDKGGFEDDVMIYKVSENEFLIVTNAINREKIINWIGK-----NSGLNVEDLTFKYGMLAIQGRNVWNFIEKAE---VK 157
                                   ****************************************.....678*************************998...55 PP

                         GCV_T 164 elkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRlEaglrlyghdld 244
                                    l+f    ++++ g++ +l+sR+g+tGedG e++  a+  + ++++Ll    + g+kpaGl Ard+lR E+g+ lyg+d+d
  gi|70607139|ref|YP_256009.1| 158 PLEFIL--NTKFLGENVFLLSRSGWTGEDGLEVWADANTLTSIIQKLL----KLGIKPAGLIARDSLRQEMGYVLYGEDID 232
                                   544443..44555455699****************************6....6789************************* PP

                         GCV_T 245 eettPleagl 254
                                   +++tP+ea++
  gi|70607139|ref|YP_256009.1| 233 SNITPVEARY 242
                                   ********87 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.0   1.2e-21   1.1e-17       3      78 ..     269     347 ..     267     348 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.2e-21
                       GCV_T_C   3 lvglelddgapll.rggepilr..dgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                     g++l+++++ll r++++i    + + vG+vTS+++sp l++ i+++y+k+e+a +g e+ +++rgk+v+a++++ p+
  gi|70607139|ref|YP_256009.1| 269 RLGFKLKKDDRLLpRKDYKIKSplGSRDVGYVTSSTFSPYLNRVIGMGYIKPEYAYIGYELAIDIRGKQVKAKISDFPL 347
                                   579***95545555******7556999************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2189.69
//
Query:       gi|70607140|ref|YP_256010.1|  [L=138]
Description: glycine cleavage system protein H [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-42  144.5   0.5    1.5e-42  144.3   0.5    1.0  1  GCV_H          Glycine cleavage H-protein
    0.00082   19.2   0.3     0.0018   18.1   0.1    1.6  2  Biotin_lipoyl  Biotin-requiring enzyme
     0.0022   17.9   0.6      0.005   16.8   0.2    1.8  2  RnfC_N         RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.3   0.5   2.5e-46   1.5e-42       2     120 ..      16     133 ..      15     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 2.5e-46
                                   EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT-T CS
                         GCV_H   2 yytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekleeep 82 
                                   +yt+ +ew+  +++ +atvGitd+aq++l d+v +elp+vg +v  ge++a+vEsvKaa+++++p+sG v+evN++l+ +p
  gi|70607140|ref|YP_256010.1|  16 HYTETDEWILINGN-IATVGITDYAQKKLKDIVGIELPQVGREVTIGEQVAVVESVKAAADIFSPLSGSVLEVNKELQSSP 95 
                                   7************9.****************************************************************** PP

                                   THHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHH CS
                         GCV_H  83 eliNkdpyeegWliklklsnleeleeLlsaeeyekllk 120
                                   e iNkdpy+ gW++klk+++++e+++Ll+ e+y   +k
  gi|70607140|ref|YP_256010.1|  96 ETINKDPYGRGWIFKLKIKDEKEVSKLLNFEQYIISIK 133
                                   *******************************9976655 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     3e-07    0.0018      22      59 ..      53      90 ..      48      96 .. 0.93
   2 ?   -3.2   0.0       1.3   8.1e+03      51      65 ..     106     120 ..     105     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3e-07
                                  STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESST CS
                 Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeilvk 59
                                  +vG +V+ g+ +a+ve+ K+  +i +p +G v e+ ++
  gi|70607140|ref|YP_256010.1| 53 QVGREVTIGEQVAVVESVKAAADIFSPLSGSVLEVNKE 90
                                  689*****************************999876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                                   EEEEEESSTTTEEE- CS
                 Biotin_lipoyl  51 GvvkeilvkeGdtve 65 
                                   G + ++++k+ ++v+
  gi|70607140|ref|YP_256010.1| 106 GWIFKLKIKDEKEVS 120
                                   677788888777775 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   8.4e-07     0.005      47      90 ..      53      97 ..      33     100 .. 0.89
   2 ?   -1.4   0.0       0.4   2.4e+03      17      37 ..     115     135 ..     110     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.4e-07
                        RnfC_N 47 kvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgsg 90
                                  +vg +V+ G+++a  e+   +a ++++ sG V +++k l +++++
  gi|70607140|ref|YP_256010.1| 53 QVGREVTIGEQVAVVESvKAAADIFSPLSGSVLEVNKELQSSPET 97
                                  7999*********9999667899*************998887765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.4
                        RnfC_N  17 kekpieklplpkelvlplsqh 37 
                                   +ek+++kl   ++++++++q 
  gi|70607140|ref|YP_256010.1| 115 DEKEVSKLLNFEQYIISIKQR 135
                                   567777777778888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.36s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 726.94
//
Query:       gi|70607141|ref|YP_256011.1|  [L=248]
Description: hypothetical protein Saci_1385 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-36  126.4   0.0    1.8e-36  126.2   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   9.9e-41   1.8e-36       1     210 [.      20     226 ..      20     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 9.9e-41
                                   EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-HS CS
                          PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...repi 78 
                                   Li+G+p++G+Vg++a+++L+ +l++ ++++i+ +++lp     p+++v++g   +p ++y +    ++++v+++      +
  gi|70607141|ref|YP_256011.1|  20 LIVGLPDAGLVGTIATEFLVKKLGLSEFATIYAPDILP-----PIMHVRDGIAKSPLKFYHNG---KNMIVFHSyiaLPFS 92 
                                   89************************************.....********99*******665...89*******654444 PP

                                   CHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH....CT..-CEEEEHHHHHHHHH CS
                          PAC2  79 lqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele....es..eyggivgitglLlsa 153
                                   + + ++ak+l+d+a+++g++ ++ ++g++ ++r      +++  ++++++++  ee+e    ++   +g+i+g+ + +ls 
  gi|70607141|ref|YP_256011.1|  93 VIN-QIAKTLIDFAKKYGINNIISITGIPVENRLS---ATTLNSFVIGNNQQVTEEIEkmglSKkfGEGYIAGPYAPILSY 169
                                   444.5************************999952...334466788888888888853555116899************* PP

                                   HHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHH CS
                          PAC2 154 akergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqle 210
                                   +++++++ + +++e+   lpdP+a+a +l+ lsk++g+ +dte+L ++aee++e++ 
  gi|70607141|ref|YP_256011.1| 170 SQREKLNNIIIVVESFMDLPDPEASAIALSILSKYIGFPLDTEELLKEAEEVRERIR 226
                                   *****************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1621.10
//
Query:       gi|70607142|ref|YP_256012.1|  [L=124]
Description: hypothetical protein Saci_1386 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.03   14.7   0.0      0.054   13.9   0.0    1.6  2  PIH1_CS        PIH1 CS-like domain
      0.076   12.8   2.6       0.16   11.7   2.6    1.5  1  Orthopox_B11R  Orthopoxvirus B11R protein
       0.11   13.1   0.3       0.22   12.0   0.0    1.8  2  DUF1801        Domain of unknown function (DU1801)
       0.12   13.0   0.3       0.19   12.3   0.2    1.4  1  DUF883         Bacterial protein of unknown function (DUF883)


Domain annotation for each model (and alignments):
>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.86   3.9e+03      16      38 ..       7      30 ..       5      44 .. 0.67
   2 ?   13.9   0.0   1.2e-05     0.054      28      78 ..      52     104 ..      24     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.86
                       PIH1_CS 16 lqdftder.skkenvpkelaieie 38
                                  l+d+ +++  k+e++ k+++ eie
  gi|70607142|ref|YP_256012.1|  7 LEDLINNLiKKEEERLKKIRKEIE 30
                                  566666665557777777766664 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
                       PIH1_CS  28 nvpkelaieielPllksikevklrvger..rleleskk.akyfLslkLpYpvde 78 
                                   ++ +e+   i++P+   ++  k++v ++  r+e+ +k+  +yfL+++Lp  +d 
  gi|70607142|ref|YP_256012.1|  52 ELMDEYEYIIDIPKA-DLQSLKVDVVKDimRVECMTKSgGRYFLRIRLPPDIDP 104
                                   567888889999998.777777777665338899888899*********99875 PP

>> Orthopox_B11R  Orthopoxvirus B11R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.6   3.7e-05      0.16       6      46 ..       6      47 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                 Orthopox_B11R  6 nvediineidrekeeilknveiennkninknhps.Gyireal 46
                                  ++ed+in++ ++ ee lk +  e +k+i     s G+ re l
  gi|70607142|ref|YP_256012.1|  6 DLEDLINNLIKKEEERLKKIRKEIEKEIKEVEESiGFSREPL 47
                                  68**************************98665548888876 PP

>> DUF1801  Domain of unknown function (DU1801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.4   6.3e+03      65      77 ..       4      16 ..       3      17 .. 0.57
   2 ?   12.0   0.0     5e-05      0.22       3      32 ..      20      50 ..      18     111 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                                  EETTS---HHHHH CS
                       DUF1801 65 fkslddideelle 77
                                  fk+l+d+ ++l++
  gi|70607142|ref|YP_256012.1|  4 FKDLEDLINNLIK 16
                                  5666666665555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5e-05
                                  HHHHHHHHHHHHHSTTSEEEEET.TEEEEEE CS
                       DUF1801  3 eelerLrklilealpeveesikw.gmpfYty 32
                                  e+l+++rk i++++ eveesi++   p Yt 
  gi|70607142|ref|YP_256012.1| 20 ERLKKIRKEIEKEIKEVEESIGFsREPLYTM 50
                                  7899*******************77888887 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   4.3e-05      0.19      11      47 ..       4      40 ..       2      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                        DUF883 11 ladleellkeaadeageeaeelRerleerlerarerl 47
                                   +dle+l+++  ++ +e ++++R+++e++++++ e++
  gi|70607142|ref|YP_256012.1|  4 FKDLEDLINNLIKKEEERLKKIRKEIEKEIKEVEESI 40
                                  689*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2293  (0.127893); expected 358.6 (0.02)
Passed bias filter:                     1499  (0.0836076); expected 358.6 (0.02)
Passed Vit filter:                       232  (0.0129399); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 825.76
//
Query:       gi|70607143|ref|YP_256013.1|  [L=333]
Description: hypothetical protein Saci_1387 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-08   34.8   0.2    3.7e-08   33.1   0.2    2.0  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0021   17.9   0.0       0.17   11.6   0.0    2.3  2  RIF5_SNase_1    TbRIF5 SNase domain 1


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.2   4.2e-12   3.7e-08       3      38 ..      21      59 ..      19      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.2e-12
                                  ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT...CCCC CS
                MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd...kiil 38
                                  +++s+ +++Pk +  ++g+++Gd++++e+ +d   +++ 
  gi|70607143|ref|YP_256013.1| 21 GSSSLFITLPKKWINKWGVKPGDKIIIEISEDgglRLVA 59
                                  689*****************************8444444 PP

>> RIF5_SNase_1  TbRIF5 SNase domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   1.9e-05      0.17      77     138 ..      91     151 ..      78     169 .. 0.87
   2 !    3.9   0.0    0.0046        41      51      91 ..     272     312 ..     264     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                  RIF5_SNase_1  77 legyGDvlfstelkldapeeleWasLqEtLlrlGvarivRPiviRleaLldaEalaepvsss 138
                                   ++gy ++lf+t+++ld  e ++ + L  +L+ + va      +iRl+ Lld+E l++ +  +
  gi|70607143|ref|YP_256013.1|  91 ILGYDEMLFTTKKNLDPKEVENVITLSKNLVGIEVAEN-NNNLIRLDCLLDTEKLGSETLLR 151
                                   689********************************996.6789**********988776555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0046
                  RIF5_SNase_1  51 avakvlslvrdasrvyLRqDyysnfPlegyGDvlfstelkl 91 
                                   ++++  +l+++  ++y R+D   n+  + + D++f  e  l
  gi|70607143|ref|YP_256013.1| 272 RISNGYTLINQLKQKYERLDIKDNLIRNYFEDLIFNLEEAL 312
                                   67777899****************99999******988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2324.90
//
Query:       gi|70607144|ref|YP_256014.1|  [L=248]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-23   82.2   0.2    6.3e-23   81.8   0.2    1.2  1  ABC_tran     ABC transporter
    1.7e-07   31.4   0.5      0.012   15.4   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      5e-07   29.4   0.8    1.9e-06   27.5   0.8    1.8  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0029   17.4   0.1     0.0039   16.9   0.1    1.2  1  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.7   0.1       0.02   14.8   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
      0.012   15.3   0.2      0.029   14.1   0.2    1.6  1  AAA_29       P-loop containing region of AAA domain
      0.017   13.8   0.1      0.036   12.7   0.0    1.5  2  AAA_13       AAA domain
      0.017   15.5   0.2      0.043   14.2   0.2    1.9  1  AAA          ATPase family associated with various cellular a
      0.039   14.5   0.3      0.053   14.0   0.3    1.6  1  AAA_23       AAA domain
      0.064   13.0   0.0       0.12   12.1   0.0    1.4  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.071   12.7   0.0        0.1   12.2   0.0    1.4  1  AAA_25       AAA domain
       0.11   12.0   0.0       0.21   11.2   0.0    1.4  1  AAA_27       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.2   4.2e-26   6.3e-23       1     136 [.      19     171 ..      19     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.2e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                   lk +++++k ge+++++G+nG+GK++L  +l+g+ k   t+G+illd++d+++ ++ e++rk i   +q+p   +++++ +
  gi|70607144|ref|YP_256014.1|  19 LKGIDMEIKSGEIHVLMGPNGSGKTSLSLALMGHPKYkiTQGKILLDNEDITSlETFEKARKGIFLAFQNPIEISGVKLST 99 
                                   7899*****************************877777**************99***************99888887666 PP

                                   H.........HHHTCHHHHHHHSTTGG....TTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   x.........xxxxxxxxxxxxxxxxx....xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n.........esdeeiekalsklglke....lkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                              s+++++ ++++++ +     ++d+ ++++    +SgG+k+r ++ ++ll kpk+ +lDEp 
  gi|70607144|ref|YP_256014.1| 100 LliaeysrmhSSTAQPQMIIKQIKEVSksvgVNDSLLNRGIfDGFSGGEKKRTEILQMLLIKPKIAILDEPD 171
                                   699988999855555443333333333333356666655557****************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   8.4e-06     0.012       1      19 [.      31      49 ..      31      86 .. 0.83
   2 !   14.1   0.0     2e-05      0.03     248     300 ..     155     205 ..     140     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                  + vl GpNgsGK++L  al
  gi|70607144|ref|YP_256014.1| 31 IHVLMGPNGSGKTSLSLAL 49
                                  579************9998 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2e-05
                        AAA_21 248 ltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                   l +ll    k+++ ++DEp++g +   l+ + + + k++s+ ++ +++ TH   
  gi|70607144|ref|YP_256014.1| 155 LQMLLI---KPKIAILDEPDSGVDVDGLKAISDAIlKLKSESNTGFLIITHYRR 205
                                   444444...4499*******************99988888888********755 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.8   1.3e-09   1.9e-06       6     206 ..      12     211 ..       9     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.3e-09
                                   EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEE..EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx..xxxx RF
                         SMC_N   6 eienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkae..veit 82 
                                   e+e+ k ++g  ++++   ++ +++GpNGSGK++l  A+   +G+ ++   + ++ + l+ +    + +  +ka+  + + 
  gi|70607144|ref|YP_256014.1|  12 EVEGKKILKGIDMEIKSG-EIHVLMGPNGSGKTSLSLAL---MGHPKY---KITQGKILLDNedITSLETFEKARkgIFLA 85 
                                   566666665444444443.4899****************...**7666...555555666665533444555555225666 PP

                                   EEETTEESSSSSSCEEEE...EEEETTSEEEEEETT.EEE-H.HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS- CS
                                   xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  83 fdnedkklkiekeevsis...rrvkrkgeseyking.kevtk.kevsellesagiskelLSgGektLvalaLlfAiqkvkp 158
                                   f+n+ + + ++ + + i    r  +++ + ++ i++ kev+k   v++ l + gi    +SgGek+ + +     +  +kp
  gi|70607144|ref|YP_256014.1|  86 FQNPIEISGVKLSTLLIAeysRMHSSTAQPQMIIKQiKEVSKsVGVNDSLLNRGIFD-GFSGGEKKRTEIL---QMLLIKP 162
                                   788888766776665554111333334445566654245555467888888888875.69******98863...4445566 PP

                                   -SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 159 aplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekad 206
                                   + + +lDe d+  D    k++++ +   ++++n+ f++i++ +++le+ +
  gi|70607144|ref|YP_256014.1| 163 K-IAILDEPDSGVDVDGLKAISDAILklKSESNTGFLIITHYRRILEHLN 211
                                   5.89******************9886344556799********9999763 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.6e-06    0.0039      14      83 ..      19      86 ..       9     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                        AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83
                                  lk +++++++  + vl G+N+sGK+s+  al  +   k+k  + +i +++ed+    ++ e+ +  I + f
  gi|70607144|ref|YP_256014.1| 19 LKGIDMEIKSGeIHVLMGPNGSGKTSLSLAL--MGHPKYKITQGKILLDNEDITSL-ETFEKARKGIFLAF 86
                                  6667777777679**************9999..99999888888899999988877.44444444455555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.3e-05      0.02      80     127 ..       9      57 ..       2      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                   EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                   RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                   + v+++ k+ l+ +  ++k+ ++ vl+G+ G GK++L  al+++ + k+
  gi|70607144|ref|YP_256014.1|   9 IHVEVEGKKILKGIDMEIKSgEIHVLMGPNGSGKTSLSLALMGHPKYKI 57 
                                   566777778888999999988*****************99999876665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.9e-05     0.029      15      38 ..      22      45 ..      14      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                        AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                   ++ei+  ++++l+Gp+GsGK++l
  gi|70607144|ref|YP_256014.1| 22 IDMEIKSGEIHVLMGPNGSGKTSL 45
                                  568888666************998 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.4e-05     0.036      17      66 ..      30      75 ..      21      95 .. 0.81
   2 ?   -2.7   0.0       1.2   1.7e+03     526     569 ..     161     202 ..     156     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                        AAA_13 17 riNliYGwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVf 66
                                  +i ++ G NG+GKT+LS +l       ++ k ++g+i + n++   +  f
  gi|70607144|ref|YP_256014.1| 30 EIHVLMGPNGSGKTSLSLALMGH----PKYKITQGKILLDNEDITSLETF 75
                                  667889***********999985....67788899998888776655555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                        AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTH 569
                                   k ki ++D P S  D + l  ++  i +    +++   ++i TH
  gi|70607144|ref|YP_256014.1| 161 KPKIAILDEPDSGVDVDGLKAISDAILKLK--SESNTGFLIITH 202
                                   788999999999999999999998888886..566666777788 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.9e-05     0.043       2      74 ..      33     112 ..      32     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                   EEESSTTSSHHHHHHHHHHHHTHE....EEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH CS
                           AAA   2 llyGppGtGKTllakavakelgve....fleisgsell.skyvgesekkirelfkeakeka..kpsilfiDEidalaksr 74 
                                   +l+Gp G GKT+l  a++ + + +     + ++  +++  ++++++ k i   f++  e +  k s l+i E  ++++s 
  gi|70607144|ref|YP_256014.1|  33 VLMGPNGSGKTSLSLALMGHPKYKitqgKILLDNEDITsLETFEKARKGIFLAFQNPIEISgvKLSTLLIAEYSRMHSST 112
                                   599****************9654311223444445555333777777777777777444445777899999988888777 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   3.5e-05     0.053      18      45 ..      28      51 ..      10     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                        AAA_23 18 skgltlItGpNGaGKTTildAiklaLyg 45
                                  s  + ++ GpNG+GKT++     laL g
  gi|70607144|ref|YP_256014.1| 28 SGEIHVLMGPNGSGKTSL----SLALMG 51
                                  4468899*********97....455555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.12       5      33 ..      33      60 ..      30      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                     PduV-EutP  5 lliGkvgsGKttLtqalkgeelkYkktqa 33
                                  +l+G+ gsGKt+L+ al g+  kYk tq 
  gi|70607144|ref|YP_256014.1| 33 VLMGPNGSGKTSLSLALMGHP-KYKITQG 60
                                  69****************986.9999995 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05       0.1      31      55 ..      27      51 ..      16     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                        AAA_25 31 pagelallaGapgtGKttlaldlal 55
                                    ge+++l+G+ g+GKt l l l+ 
  gi|70607144|ref|YP_256014.1| 27 KSGEIHVLMGPNGSGKTSLSLALMG 51
                                  6799****************99975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.21      18      46 ..      21      49 ..       4      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAi 46
                                   +d++ ++ ++h+++GpN +GK+++  A+
  gi|70607144|ref|YP_256014.1| 21 GIDMEIKSGEIHVLMGPNGSGKTSLSLAL 49
                                  5777788999**************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1411.67
//
Query:       gi|70607145|ref|YP_256015.1|  [L=479]
Description: hypothetical protein Saci_1389 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-63  213.0   0.0    5.2e-63  212.6   0.0    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
      0.068   13.0   0.0       0.25   11.2   0.0    1.9  1  DUF4295   Domain of unknown function (DUF4295)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6   0.0   5.8e-67   5.2e-63       2     218 .]     222     448 ..     221     448 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 5.8e-67
                       UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakleltt 70 
                                   qfe+tl++++eg+ +++i   +gc            g+ve+++++nA +k++++qnws+d++n+++kra  ++++++e+++
  gi|70607145|ref|YP_256015.1| 222 QFEHTLLIADEGSYIHFI---EGCsapqlkkfsfhdGMVELYAKKNAYIKFTTIQNWSKDIINFNNKRAWADENSTVEWVE 299
                                   89****************...666666666666777*********************************9999******** PP

                       UPF0051  71 vslggkltrkepsvelkgegaeaelnglylakgk.qhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqk 150
                                   +slg++ +  +ps+ l+g+ga+++   +++++g+ +  d+++k++h++p t+s+++sk++   ++ +v+rg i+v+kga +
  gi|70607145|ref|YP_256015.1| 300 GSLGSRYSFVYPSTILRGKGASSTSLVVTFTSGEgEWKDSGSKMIHAAPYTKSKVVSKNIGFRGGLNVYRGLIRVNKGAVG 380
                                   ******************************9987589******************************************** PP

                       UPF0051 151 tdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                   ++a++++++L+l++k +a+t+P+ +++++d+ + H+A + +++e+qlfYLm+RG++e+eA +++v gf
  gi|70607145|ref|YP_256015.1| 381 SKAFVKCDSLMLDEKTKAYTFPHNQVFEEDADVAHEAHTFRMNEDQLFYLMTRGIDEKEAVSMLVLGF 448
                                   ******************************************************************99 PP

>> DUF4295  Domain of unknown function (DUF4295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.8e-05      0.25      10      39 ..     376     406 ..     373     412 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                       DUF4295  10 kga.sgkkytKvIkmvKspKTGaYtFkEeiV 39 
                                   kga ++k+++K+   + ++KT aYtF  + V
  gi|70607145|ref|YP_256015.1| 376 KGAvGSKAFVKCDSLMLDEKTKAYTFPHNQV 406
                                   667789********************76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3185.44
//
Query:       gi|70607146|ref|YP_256016.1|  [L=389]
Description: hypothetical protein Saci_1390 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-34  118.2   0.5    5.5e-34  117.8   0.5    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.5     3e-38   5.5e-34       8     218 .]     150     362 ..     142     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3e-38
                       UPF0051   8 ivveegaevtiieey.........agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltr 79 
                                   + + eg +v ++  y         ++ + + ++v +n++l+++ +   ++ ++ +++    +  + +++ + +s + klt 
  gi|70607146|ref|YP_256016.1| 150 LKIPEGENVDVV--YfsetddqnsMTSSLISFVVPQNSTLNLSIISLSAH-SFIYTK--GLV--KGTINANIFSSKTKLTH 223
                                   556666677777..3344466666667****************8885533.333332..222..56799************ PP

                       UPF0051  80 kepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnL 160
                                    ++ v+l+ e+a++++++ +++ +++++d+r+ v+h g +++s+ + +g+++d++ +++rg+  +++    +++++  ++ 
  gi|70607146|ref|YP_256016.1| 224 IDYYVDLD-EKAQSTFSSRAIGIEDNNVDIRVAVNHLGVQSRSEGTLRGISTDSSLVIVRGNAIISESGIDSSTSIIGKAY 303
                                   *******9.9*********************************************************************** PP

                       UPF0051 161 llsdkaradtiPeleidaddvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    ++++++a   P+le+++++v+ a+H A+++k+ e+ +fYL+sRG+s++eA++li++gf
  gi|70607146|ref|YP_256016.1| 304 TIGKDSKAIVAPMLEVKTGKVQmAKHSASISKVPEDLIFYLESRGFSRKEAESLIIKGF 362
                                   **********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2582.95
//
Query:       gi|70607147|ref|YP_256017.1|  [L=43]
Description: hypothetical protein Saci_1391 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-10   40.0   0.7    2.5e-10   39.9   0.7    1.0  1  RHH_1           Ribbon-helix-helix protein, copG family
    3.7e-05   23.6   1.1      7e-05   22.7   1.1    1.4  1  RHH_3           Ribbon-helix-helix domain
     0.0089   15.9   1.3      0.026   14.4   1.3    1.7  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.7   4.2e-14   2.5e-10       2      38 ..       4      40 ..       3      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 4.2e-14
                                  EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                  +++++de+ll +Ld  a+ +++SrSe+IReAl +yl+
  gi|70607147|ref|YP_256017.1|  4 ITFKVDEDLLQELDLYAINSKSSRSEIIREALIRYLK 40
                                  8**********************************97 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.1   1.2e-08     7e-05       5      42 ..       4      41 ..       2      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.2e-08
                         RHH_3  5 ttvsidpelaekLkaLSekTrIprSklldeAiellLek 42
                                  +t+ +d++l+++L+ +    +  rS++++eA+  +L++
  gi|70607147|ref|YP_256017.1|  4 ITFKVDEDLLQELDLYAINSKSSRSEIIREALIRYLKD 41
                                  699*********************************97 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.3   4.3e-06     0.026       4      40 ..       5      43 .]       1      43 [] 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                                  XXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXX------ CS
                VapB_antitoxin  4 nIeiDDeLlaeAirltglktK...rEaVnlALreLiqrrk 40
                                  +  +D++Ll+e + l+ ++ K   +E++++AL ++++ rk
  gi|70607147|ref|YP_256017.1|  5 TFKVDEDLLQE-LDLYAINSKssrSEIIREALIRYLKDRK 43
                                  6789******9.5666665542228***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 314.07
//
Query:       gi|70607148|ref|YP_256018.1|  [L=327]
Description: alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-27   95.8   0.9    2.1e-27   95.2   0.2    1.7  2  ADH_N          Alcohol dehydrogenase GroES-like domain
    3.1e-22   79.0   0.2    6.5e-22   77.9   0.2    1.5  1  ADH_zinc_N     Zinc-binding dehydrogenase
    5.5e-08   33.9   0.0    1.4e-07   32.6   0.0    1.6  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
     0.0071   16.2   0.1       0.01   15.7   0.1    1.2  1  YjeF_N         YjeF-related protein N-terminus
  ------ inclusion threshold ------
      0.018   15.1   0.1       0.14   12.2   0.1    2.4  3  SIS_2          SIS domain
      0.059   13.1   0.0      0.091   12.5   0.0    1.3  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
      0.068   13.3   0.7       0.96    9.6   0.7    2.4  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
        0.1   13.1   0.0        5.4    7.6   0.0    2.6  3  Rhodanese      Rhodanese-like domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.2   9.2e-31   2.1e-27       2     109 .]      27     132 ..      26     132 .. 0.98
   2 ?   -2.7   0.0       2.4   5.3e+03      61      78 ..     285     302 ..     276     313 .. 0.66

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 9.2e-31
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   ++vli+vk+ag++  D+ +++g   +  +lp i+G Ei Ge+++vg++vk++k Gd+Vvv+  + +geC+ C  g e lC+
  gi|70607148|ref|YP_256018.1|  27 HDVLIRVKMAGVNPIDYFVVEG--IPVKPLPHIPGAEIYGEIVKVGEHVKSVKPGDKVVVYNRVFDGECDFCLAGMEMLCR 105
                                   89*******************9..899****************************************************** PP

                                   TBEETTTSS-SSSBSEEEECGGGEEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvkl 109
                                   ++++++v ++Ggf+ey+ vpek+++k+
  gi|70607148|ref|YP_256018.1| 106 NGGIISVITNGGFSEYFAVPEKNVFKV 132
                                   ************************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                                   E-SEEE-SSSHHHHTT-G CS
                         ADH_N  61 vepliscgeCaaCkegee 78 
                                   ve ++ c++C+   ++ +
  gi|70607148|ref|YP_256018.1| 285 VELISLCKDCKVKVSKVY 302
                                   555666777776555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.2   2.9e-25   6.5e-22       3     128 ..     174     291 ..     173     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.9e-25
                                   HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEE CS
                    ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgG 83 
                                   G++a+qlA+ +Ga++iav++++     +k++ ad+v++y e + + +ik+ltgg+ +dvv++ vG  + ++ +lk+l  +G
  gi|70607148|ref|YP_256018.1| 174 GQFALQLARKMGATTIAVSRKQW----VKDF-ADYVVDY-E-NAENKIKDLTGGKLADVVINSVG-TSIWDLSLKVLGVNG 246
                                   9******************9997....****.9******.6.6**********************.*************** PP

                                   EEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                    ADH_zinc_N  84 rlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                   rlv++Gg  + + +++++ l  k+ +++G+++gs r+e+ e++ l+
  gi|70607148|ref|YP_256018.1| 247 RLVFFGGlTGSDGKINISALYGKHQKLIGTTGGS-RKEMVELISLC 291
                                   *******7444444********************.99999999886 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   6.3e-11   1.4e-07       3     125 ..     201     317 ..     201     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6.3e-11
                                   -SEEEETTSTTHH..HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG. CS
                  ADH_zinc_N_2   3 Adevidyrtedfe..aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsm 81 
                                   Ad v+dy++ + +  + tgg+  Dvv+++vg+  + + slkvl  +Grlv  gg   +  ++k +      + + +++ + 
  gi|70607148|ref|YP_256018.1| 201 ADYVVDYENAENKikDLTGGKLADVVINSVGTSIW-DLSLKVLGVNGRLVFFGGL--TGSDGKINI-SALYGKHQKLIGT- 276
                                   89******555556999*9************9999.*******888*******84..444444444.2234444444443. PP

                                   ..-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS CS
                  ADH_zinc_N_2  82 kasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesg 125
                                   + + +++ + el  l+++   ++ v++v+ le+ +eA++ +++ 
  gi|70607148|ref|YP_256018.1| 277 TGGSRKE-MVELISLCKDC--KVKVSKVYNLEDGKEALASIMKD 317
                                   3332555.88888888776..567999***********998765 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.7e-06      0.01      21     129 ..     153     291 ..     137     301 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
                        YjeF_N  21 g..nspaekkvlvlvG.sgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpeedleekl 98 
                                       ++++ +v+v+ G sgn+G  +l++Ar +  + + V       ++++ +d ++++  +++a++k+   +  + ++  +
  gi|70607148|ref|YP_256018.1| 153 LkeANVKPTDVVVVFGaSGNTGQFALQLARKMGATTIAVS------RKQWVKDFADYVVDYENAENKIKDLTGGKLADVVI 227
                                   13434666666666662679************44444444......47899999999999999999999888888777777 PP

                        YjeF_N  99 s............................apvdlviDAllGi.....glrgelreelaeliewl 129
                                   +                            ++ ++ i Al+G      g+ g  r+e+ eli+ +
  gi|70607148|ref|YP_256018.1| 228 NsvgtsiwdlslkvlgvngrlvffggltgSDGKINISALYGKhqkliGTTGGSRKEMVELISLC 291
                                   7778888888888888877777777777777777777777777777777777777777777655 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.9   4.2e+03     101     117 ..      24      40 ..      20      45 .. 0.85
   2 ?   12.2   0.1   6.2e-05      0.14      96     136 ..     153     191 ..     138     192 .. 0.91
   3 ?   -2.1   0.0       1.6   3.7e+03     111     133 ..     276     298 ..     273     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                   --TT-EEEEE-SS--SH CS
                         SIS_2 101 lkpgDvLlviSnsGnna 117
                                   + ++DvL+ +   G+n+
  gi|70607148|ref|YP_256018.1|  24 IGAHDVLIRVKMAGVNP 40 
                                   6689****999999997 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.2e-05
                                   HHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEE CS
                         SIS_2  96 lrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAl 136
                                   l+++++kp Dv +v+ +sGn      a++ a+++g+++iA+
  gi|70607148|ref|YP_256018.1| 153 LKEANVKPTDVVVVFGASGNTGQF--ALQLARKMGATTIAV 191
                                   677899***************997..8999**********8 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.6
                                   -SS--SHHHHHHHHHHHHHT-EE CS
                         SIS_2 111 SnsGnnavvveaaeaakergmkv 133
                                    ++G+ + +ve++  +k++ +kv
  gi|70607148|ref|YP_256018.1| 276 TTGGSRKEMVELISLCKDCKVKV 298
                                   678999999****9999999987 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     4e-05     0.091      20      63 ..     151     193 ..     136     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                                   HHHHHTTTS-STTEEEEEE--.SHHHHHHHHHHHHCT-EEEEEEE CS
                 ELFV_dehydrog  20 emlkklkldslegkrvaisGs.GnvgsyaallltelgakvvavsD 63 
                                   ++lk+++ +  ++  v++ G  Gn g++a +l+ ++ga+++avs 
  gi|70607148|ref|YP_256018.1| 151 HALKEANVK-PTD-VVVVFGAsGNTGQFALQLARKMGATTIAVSR 193
                                   455555555.333.46677777*********************95 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00043      0.96       3     118 ..     164     296 ..     163     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00043
                                   EEEETTTSHHHHHHHHHHHHS..............TTEEEEEEEETTCSTTTTTBHHHHSSSS..--S-BEBSSHHHHHHH CS
                        DapB_N   3 vavvGasGrmGkevvkaveea..............edlelvaavdrkeselegkdagellglg..klgvavtddleevlek 67 
                                   v+v+GasG  G+  ++++++               + +  v  +++ e+++++   g+l+++   ++g  + d   +vl  
  gi|70607148|ref|YP_256018.1| 164 VVVFGASGNTGQFALQLARKMgattiavsrkqwvkDFADYVVDYENAENKIKDLTGGKLADVVinSVGTSIWDLSLKVLGV 244
                                   778888888888888888886445555555555533334455555555555555555665543337788888888888888 PP

                                   -SEEEE-S-HHHHHHHHHHHHHT.T-EEEE--SS--HHHHHHHHHHTTTSEE CS
                        DapB_N  68 advliDFTtpeavlenlklalek.gvklViGTTGlseeelaeleelakkigv 118
                                   +  l+ F   +++  ++++ + + + +  iGTTG s++e+ el +l+k+ +v
  gi|70607148|ref|YP_256018.1| 245 NGRLVFFGGLTGSDGKINISALYgKHQKLIGTTGGSRKEMVELISLCKDCKV 296
                                   88999999999999999998888344579***********999999998655 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.086   1.9e+02      61     104 ..      72     121 ..      51     123 .. 0.61
   2 ?    7.6   0.0    0.0024       5.4      55      96 ..     150     191 ..     134     202 .. 0.81
   3 ?   -3.6   0.0       7.5   1.7e+04      89     101 ..     296     308 ..     273     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.086
                     Rhodanese  61 l..gidnkktvvvycdgggr.aaaa....aallkklGyknvsvldGGfkaw 104
                                   +   ++++++vvvy +  ++   +     ++l +  G     + +GGf+++
  gi|70607148|ref|YP_256018.1|  72 HvkSVKPGDKVVVYNRVFDGeCDFClagmEMLCRNGG-IISVITNGGFSEY 121
                                   14456999******99888844444544333444444.3466778888876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                     Rhodanese  55 peellelgidnkktvvvycdgggraaaaaallkklGyknvsv 96 
                                   +++l+e ++++ + vvv++++g+  ++a +l++k+G +++ v
  gi|70607148|ref|YP_256018.1| 150 YHALKEANVKPTDVVVVFGASGNTGQFALQLARKMGATTIAV 191
                                   44455558999*************************554665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 7.5
                     Rhodanese  89 lGyknvsvldGGf 101
                                     + +v++l+ G 
  gi|70607148|ref|YP_256018.1| 296 VKVSKVYNLEDGK 308
                                   5556688888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2420.74
//
Query:       gi|70607149|ref|YP_256019.1|  [L=618]
Description: arginyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-37  127.6   2.1    5.5e-35  120.9   2.1    2.2  1  tRNA-synt_1d    tRNA synthetases class I (R)
    5.5e-25   87.9   0.1    1.5e-24   86.4   0.0    1.8  2  DALR_1          DALR anticodon binding domain
     0.0004   19.8   0.3       0.37   10.1   0.1    2.8  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
     0.0049   15.7   0.3        0.1   11.3   0.1    2.7  3  tRNA-synt_1g    tRNA synthetases class I (M)
     0.0068   14.7   0.4      0.022   13.0   0.0    1.9  2  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.076   13.7   0.5       0.33   11.6   0.1    2.2  2  Cytochrom_B562  Cytochrome b562


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   2.1   1.8e-38   5.5e-35      13     315 ..      97     461 ..      85     488 .. 0.82

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.8e-38
                                   .---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTT...... CS
                  tRNA-synt_1d  13 qkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdek...... 87 
                                     k+++ k++vv+++s n   ++h+GhLr  i+Gd++sr+l + G+dv r  +v D G+q  +L  ++   ++ +      
  gi|70607149|ref|YP_256019.1|  97 VEKTENPKRIVVEHTSANPIHPLHIGHLRNSILGDTISRMLKIRGHDVNRRFYVNDAGRQVAILTLGYILLGEPEpspkvd 177
                                   4678899********************************************************987765444333000001 PP

                                   ......TTS-----SCCCHHHHHHHHCCCSHC.....................................CCHHHHHHHHHH CS
                  tRNA-synt_1d  88 ......llqeqelqdLeafykeakkdydeeei.....................................faerarnyvvkL 125
                                          +  + + ++ ++ +e kkd+d +                                       ++ + +++++  
  gi|70607149|ref|YP_256019.1| 178 hwfgliYSITNVIIEIRELKEELKKDLDPDTYkdkinrldelvataqslrernpeffdkladainsipdVESEIQKIIKSY 258
                                   111111223444556666666677777766659999*******************************99999********9 PP

                                   HCT-.HHHHHHHHHHHHHHHHHHHHHHHHCT---EC...--CCCCCCCHHHHHHHHHCTT-EEECTTCEEEEECCC..... CS
                  tRNA-synt_1d 126 qsgd.edirklwkllvditrtelqklydrldvtlie...rGeslykeslneivkelkkkglvkesdGalvvfldef..... 197
                                   ++gd ++i+++ +++v++    +++  d+l+++        e l+  +++ei+   k+ +++k+  G++ + l++      
  gi|70607149|ref|YP_256019.1| 259 EKGDdPKIKQIVRKIVNLNLDGFRESLDKLEISFDVydyESELLWSGMVDEILS--KAFQIAKDYKGTKALELEDInekik 337
                                   988615699999999999888777777777776633433455599999999997..5677999999999999999999999 PP

                                   .......TSSCCE.ECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE CS
                  tRNA-synt_1d 198 .......gkrlgv.vvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanf 270
                                          g +l+  v+ +sDG+ lytt+Dia   ++  + kad v+ vi ++qs+  +q+ + l  +gy+  +++l h ++
  gi|70607149|ref|YP_256019.1| 338 eilnipkGLKLPPlVLTRSDGTSLYTTRDIAYTVKKFSDFKADTVINVIAEQQSIPQMQLRASLYLLGYERLAQNLVHYSY 418
                                   9999999888876599*****************************************************999********* PP

                                   --EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS- CS
                  tRNA-synt_1d 271 GmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvl 315
                                   Gmv   ++ +++ r G  + L+d+++   e a+++i+ek  d + 
  gi|70607149|ref|YP_256019.1| 419 GMV-NLQGMRMSGRLGRFISLDDVIEKVSEVAKKKIEEKSGD-IT 461
                                   ***.88999******************************998.32 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.8   1.1e+04      42      57 ..     213     228 ..     194     249 .. 0.60
   2 !   86.4   0.0   5.2e-28   1.5e-24       1     119 []     502     618 .]     502     618 .] 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.8
                                   HHTHHHHHHHHHHHT- CS
                        DALR_1  42 laqfpevleeaaeele 57 
                                   + ++ e++++a + +e
  gi|70607149|ref|YP_256019.1| 213 INRLDELVATAQSLRE 228
                                   4445555555544444 PP

  == domain 2  score: 86.4 bits;  conditional E-value: 5.2e-28
                                   HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTS CS
                        DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkerv 81 
                                   +qy++aR+ +il k+++e + ++++ ++l    ++++Ll  +a+fpe+ ++a++el+p++l ++l   a+ f+++Yn erv
  gi|70607149|ref|YP_256019.1| 502 LQYTYARAYNILAKNQDEIKLTDADLSDL--IGDKRRLLLLIARFPETFNKAIDELRPEDLIDFLRRTADVFNRWYNFERV 580
                                   6*************999997777777777..7799999******************************************* PP

                                   TTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                        DALR_1  82 lkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                   l+e++  ++  RL +vk +++vL ngL+ LGi++++km
  gi|70607149|ref|YP_256019.1| 581 LQEPDYRKRITRLFIVKGIERVLYNGLNALGIKPLSKM 618
                                   *************************************9 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00013      0.37      23      49 ..     119     145 ..     105     155 .. 0.90
   2 !    6.7   0.0    0.0014         4     238     272 ..     410     446 ..     399     456 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                                   -BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                  tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvq 49 
                                    h+Gh R+ +  D + r+l+ +g+dv+
  gi|70607149|ref|YP_256019.1| 119 LHIGHLRNSILGDTISRMLKIRGHDVN 145
                                   7************************96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0014
                                   EEEEEE..E--EEETTBE--TTTT---BHHHHHTTS- CS
                  tRNA-synt_1e 238 vkyflh..nghlkiegekmsksLknfitikdvlkkfd 272
                                   ++  +h   g+++++g +ms  L+ fi++ dv++k++
  gi|70607149|ref|YP_256019.1| 410 AQNLVHysYGMVNLQGMRMSGRLGRFISLDDVIEKVS 446
                                   55555522599**********************9986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   3.5e-05       0.1      13      39 ..     118     144 ..     111     152 .. 0.92
   2 ?    0.4   0.0      0.07   2.1e+02      64      95 ..     271     302 ..     224     321 .. 0.81
   3 ?   -1.2   0.0      0.22   6.4e+02     316     345 ..     416     445 ..     398     448 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                                   ---HHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1g  13 klHlGhllevisaDifaRykrlrgeev 39 
                                   +lH+Ghl++ i +D ++R+ + rg++v
  gi|70607149|ref|YP_256019.1| 118 PLHIGHLRNSILGDTISRMLKIRGHDV 144
                                   78***********************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.07
                                   HHHHHHHHHHHHHHHHHTT---SEEEETTSHH CS
                  tRNA-synt_1g  64 eelvekvheeikelfkklnisfdkygrttsee 95 
                                   +++v+ + + ++e ++kl+isfd y+  ++  
  gi|70607149|ref|YP_256019.1| 271 RKIVNLNLDGFRESLDKLEISFDVYDYESELL 302
                                   56666677788999999999999998766655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.22
                                   EEE--EEE--------------HHHHHHHH CS
                  tRNA-synt_1g 316 vaheyltvegkKlSkSrgvvvkakealerl 345
                                   ++ ++++++g ++S   g+++  ++++e++
  gi|70607149|ref|YP_256019.1| 416 YSYGMVNLQGMRMSGRLGRFISLDDVIEKV 445
                                   466899******************999975 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   7.4e-06     0.022      38      73 ..     119     154 ..      94     160 .. 0.89
   2 ?   -1.5   0.1      0.18   5.5e+02     558     582 ..     422     446 ..     414     482 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.4e-06
                   tRNA-synt_1  38 lHiGhalaktlkdivirykrmkGkevlyvpGwDhaG 73 
                                   lHiGh  +++l d++ r+ +++G++v++++ +  aG
  gi|70607149|ref|YP_256019.1| 119 LHIGHLRNSILGDTISRMLKIRGHDVNRRFYVNDAG 154
                                   8***************************99887777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.18
                   tRNA-synt_1 558 deeGrKmSKslgNvidpldvikkyg 582
                                   + +G +mS +lg  i+ +dvi+k++
  gi|70607149|ref|YP_256019.1| 422 NLQGMRMSGRLGRFISLDDVIEKVS 446
                                   5699*****************9654 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00011      0.33      15      93 ..     199     276 ..     192     280 .. 0.85
   2 ?   -1.8   0.0       1.7   5.2e+03      20      39 ..     451     470 ..     437     483 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                Cytochrom_B562  15 qvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealakagkleeakaalkelkdl 93 
                                   +++k  d+++ k+++++l+++++ a++ + +++e    + +d  + + ++ ++++k+ ++ ++g+  ++k++++++ +l
  gi|70607149|ref|YP_256019.1| 199 ELKKDLDPDTYKDKINRLDELVATAQSLRERNPE-FFDKLADAINSIPDVESEIQKIIKSYEKGDDPKIKQIVRKIVNL 276
                                   56788899*****************999996666.55566666777788999**********************99765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                Cytochrom_B562  20 ddaeelkkalkelraaaeda 39 
                                   + +ee + ++++lr ++++a
  gi|70607149|ref|YP_256019.1| 451 KKIEEKSGDITNLRDIVNSA 470
                                   34555556666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4164.53
//
Query:       gi|70607150|ref|YP_256020.1|  [L=65]
Description: hypothetical protein Saci_1397 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 473.55
//
Query:       gi|70607151|ref|YP_256021.1|  [L=96]
Description: hypothetical protein Saci_1398 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 619.00
//
Query:       gi|70607152|ref|YP_256022.1|  [L=104]
Description: hypothetical protein Saci_1399 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.9   0.3      0.019   14.7   0.3    1.3  1  DUF4423   Domain of unknown function (DUF4423)
      0.018   15.0   0.1      0.033   14.1   0.1    1.5  1  TBPIP     TBPIP/Hop2 winged helix domain
      0.022   14.9   0.0      0.082   13.1   0.0    1.8  2  DpnI_C    Dam-replacing HTH domain
      0.036   14.1   0.0      0.054   13.6   0.0    1.2  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
        0.1   11.7   0.2       0.11   11.7   0.2    1.1  1  DUF763    Protein of unknown function (DUF763)


Domain annotation for each model (and alignments):
>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   5.2e-06     0.019      32      78 ..      56     102 ..      25     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.2e-06
                       DUF4423  32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78 
                                   lkd+  + +el  +l + +s+++++kal+ L + ++++  edgky +
  gi|70607152|ref|YP_256022.1|  56 LKDKPMNLKELHSALSGIASEDKIRKALSDLAEKNMVTLMEDGKYAK 102
                                   45666699*************************************75 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   9.1e-06     0.033       3      56 ..      49     100 ..      47     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.1e-06
                         TBPIP   3 eelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKq 56 
                                   +e++l++l++  +P++ ++  ++l +  +   + kaL  L++++ ++  e GK 
  gi|70607152|ref|YP_256022.1|  49 KEIILDLLKD--KPMNLKELHSALSGIASEDKIRKALSDLAEKNMVTLMEDGKY 100
                                   6788888875..9*******************************9998888885 PP

>> DpnI_C  Dam-replacing HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.31   1.1e+03      20      47 ..      25      52 ..      18      64 .. 0.63
   2 ?   13.1   0.0   2.3e-05     0.082      44      70 .]      76     102 ..      49     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                                  EEEHHHHHTTHHHHHHHSTT-S-HHHHH CS
                        DpnI_C 20 eFtlediykfeeeLkekhpkNnfikdKi 47
                                  e +l+ +y+ +e +    p+ + +k+ i
  gi|70607152|ref|YP_256022.1| 25 ERKLKVLYSDKEVVVMTAPNEEELKEII 52
                                  4556666777777767777777666655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHHHTTSEEE-STTEEEE CS
                        DpnI_C  44 kdKirqqLqvlRDkglieFlgrGkYkk 70 
                                   +dKir+ L  l +k+++  ++ GkY k
  gi|70607152|ref|YP_256022.1|  76 EDKIRKALSDLAEKNMVTLMEDGKYAK 102
                                   79***********************87 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.5e-05     0.054      17      59 ..      50      94 ..      48      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHSSBEHHHHHHHHS..STHHHHHHHHHHHHHTTSEEE CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktk..LsldqVkksLvvLiqhrlVqy 59
                                   ++  Ll+     l+el+++++   s d+++k+L+ L   ++V+ 
  gi|70607152|ref|YP_256022.1| 50 EIILDLLKDKPMNLKELHSALSgiASEDKIRKALSDLAEKNMVTL 94
                                  578899999999***********99******************85 PP

>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     3e-05      0.11     174     237 ..      17      80 ..       1     101 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                        DUF763 174 lesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekkl 237
                                    ++++++ ++ +    + +ev+ +++ + ee +++ildl+k+kp +l++  ++l+ +++++k  
  gi|70607152|ref|YP_256022.1|  17 DDKILTNVERKLKVLYSDKEVVVMTAPNEEELKEIILDLLKDKPMNLKELHSALSGIASEDKIR 80 
                                   345666666677776778889***********************99888877777665544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      744  (0.041497); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 710.88
//
Query:       gi|70607153|ref|YP_256023.1|  [L=114]
Description: hypothetical protein Saci_1400 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 813.06
//
Query:       gi|70607154|ref|YP_256024.1|  [L=558]
Description: thermosome alpha subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   2.5e-173  577.2  17.7   2.9e-173  577.0  17.7    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.011   15.6   0.1        2.2    8.2   0.0    3.3  3  Alba        Alba


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.0  17.7  3.2e-177  2.9e-173       1     489 [.      31     531 ..      31     533 .. 0.97

  Alignments for each domain:
  == domain 1  score: 577.0 bits;  conditional E-value: 3.2e-177
                                   HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                    Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                   la+++k++lGP+G+dKml++++g+v++TnDGati+ke+ei+hPaakllveaa++qd evGDGTt++v+Lag Ll++ae+l+
  gi|70607154|ref|YP_256024.1|  31 LAEMLKSSLGPRGLDKMLIDSFGDVTITNDGATIVKEMEIQHPAAKLLVEAAKAQDAEVGDGTTSAVVLAGLLLDKAEELL 111
                                   79******************************************************************************* PP

                                   HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSC....STT.HHHHHHHHHHCTTSSX...XSTHHHHHHHHHHHHHCHCC CS
                    Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisse....ekdreeLlkvartslssklt...skeaeelsklvvdAvkliee 155
                                   +++vhpt ii+gy+kal kale++++ + +i+++       + +L+k+++t++ssk++   ++e +++ +lv+dA++++ e
  gi|70607154|ref|YP_256024.1| 112 EQNVHPTIIIDGYKKALTKALEIIDQLSLKIDVNdlssPTAKAQLKKIVSTTMSSKFIaggAEEIDKIIDLVIDAITIVAE 192
                                   ***************************999999965555599**************662225788999********88888 PP

                                   CS....EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHH CS
                    Cpn60_TCP1 156 ne....keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeelek 232
                                   ++    +++ l+ ik+ k++ggs+eds lv+Glvldk+v+++ mp+++e+ak+++ld  Le ek+e+++++ ++++e++++
  gi|70607154|ref|YP_256024.1| 193 KRpdgtYNVPLDLIKIDKKKGGSIEDSILVHGLVLDKEVVHAGMPRRVEKAKIAVLDAALEVEKPEISAKISITSPEQIKS 273
                                   889*999999999******************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEE CS
                    Cpn60_TCP1 233 lekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtak 313
                                   ++++e ++l+e+++k+++ g+nvv+cqkgidd+a+hflak+gila+rrvk++d+e+l ka+Ga+++ss++d tpe+lG+a+
  gi|70607154|ref|YP_256024.1| 274 FLDEEARYLKEMVDKLASIGANVVICQKGIDDVAQHFLAKKGILAVRRVKRSDIEKLEKALGARIISSIKDATPEDLGYAE 354
                                   ********************************************************************************* PP

                                   EEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTS CS
                    Cpn60_TCP1 314 kveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksv 394
                                    vee++ig++k+++ie+ k+++++ illrg++d+ lde+er+++dAl++++n++ ++ +v+GGGa+e ela +l+eya+sv
  gi|70607154|ref|YP_256024.1| 355 LVEERRIGNDKMVFIEGAKNPRAVNILLRGSNDMALDEAERSLNDALHSLRNVLMKPMIVAGGGAVESELALRLREYARSV 435
                                   ********************************************************************************* PP

                                   XCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEE.CCCCTXEEEHHHHHHHHHHHH CS
                    Cpn60_TCP1 395 sgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiid.lveagvvDplkvkrqalksAt 474
                                    g+eqlaie+fa+ALe+ip++Lae aG++pi+ l +lra+h+kg ++ gid+ +g+i d +++ +v++p++vk+q+lksA+
  gi|70607154|ref|YP_256024.1| 436 GGKEQLAIEKFAEALEEIPMILAETAGMEPIQALMDLRARHAKGLVNSGIDAVNGKIADdMMKINVIEPVRVKSQVLKSAV 516
                                   ********************************************************8877********************* PP

                                   HHHHHHHCEEEEEXX CS
                    Cpn60_TCP1 475 eaastiLrideiika 489
                                   eaa+ iL+id+ + a
  gi|70607154|ref|YP_256024.1| 517 EAATAILKIDDLVAA 531
                                   ************987 PP

>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0092        82      37      54 ..      23      40 ..      20      46 .. 0.82
   2 ?    8.2   0.0   0.00025       2.2      16      48 ..     105     137 ..     103     149 .. 0.88
   3 ?   -2.3   0.0      0.46   4.1e+03       3      22 ..     505     523 ..     505     542 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0092
                                  THHHHHHHHHHHHHHHTC CS
                          Alba 37 raIskAvsvaeilkrrfg 54
                                  ++I  Av++ae+lk+ +g
  gi|70607154|ref|YP_256024.1| 23 NNILAAVTLAEMLKSSLG 40
                                  57778*********9886 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00025
                                   HHHHHHHTHTTESEEEEEEETTHHHHHHHHHHH CS
                          Alba  16 kralklLsnkkeeeVvlkatGraIskAvsvaei 48 
                                   ++a +lL+++ ++++++ ++ +a +kA+++   
  gi|70607154|ref|YP_256024.1| 105 DKAEELLEQNVHPTIIIDGYKKALTKALEIIDQ 137
                                   7899***9999*****************99765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.46
                                   EEE-STS-HHHHHHHHHHHH CS
                          Alba   3 iyVsskspimsyvkralklL 22 
                                   ++V+s   ++s+v++a  +L
  gi|70607154|ref|YP_256024.1| 505 VRVKS-QVLKSAVEAATAIL 523
                                   57777.77899999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4001.35
//
Query:       gi|70607155|ref|YP_256025.1|  [L=246]
Description: hypothetical protein Saci_1402 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00023   21.1   8.1     0.0013   18.7   1.1    2.5  2  DZR             Double zinc ribbon
     0.0019   18.7   8.2      0.061   13.9   0.6    3.4  3  Cript           Microtubule-associated protein CRIPT
     0.0036   17.0   4.8     0.0036   17.0   4.8    3.2  3  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.4   4.5        4.3    7.3   0.1    3.5  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.049   13.7   3.8       0.13   12.3   0.2    2.3  2  Zn_Tnp_IS91     Transposase zinc-binding domain
       0.39   10.9   7.0        0.4   10.8   1.0    2.4  2  DUF2318         Predicted membrane protein (DUF2318)
        0.8    9.7   5.4         32    4.6   3.3    3.2  3  zf-FCS          MYM-type Zinc finger with FCS sequence motif
       0.83   10.4  14.8       0.21   12.4   6.8    2.9  2  zinc_ribbon_15  zinc-ribbon family
        3.4    7.7   6.7        4.4    7.4   0.4    2.5  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
        8.7    6.3   9.1        2.3    8.2   0.7    2.6  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.9    0.0071        13      15      37 ..       4      28 ..       1      35 [. 0.62
   2 !   18.7   1.1   7.2e-07    0.0013       1      26 [.     216     241 ..     216     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0071
                           DZR 15 CseCgtk..lkavaaedrCpsCgek 37
                                  C++Cg++         + C+ Cg++
  gi|70607155|ref|YP_256025.1|  4 CQRCGKReyFTVIGGRKLCSMCGKD 28
                                  7777776553333446777777654 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 7.2e-07
                           DZR   1 CpqCgeelppdarfCseCgtklkava 26 
                                   C++Cg+ +++++++C++C+t l +++
  gi|70607155|ref|YP_256025.1| 216 CKNCGAYINSGQEYCERCKTYLASPS 241
                                   ********************998655 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.22     4e+02      70      79 ..       2      11 ..       1      16 [. 0.83
   2 !    6.2   0.3    0.0084        15      70      80 ..      20      30 ..      17      40 .. 0.76
   3 !   13.9   0.6   3.4e-05     0.061      23      65 ..     191     233 ..     171     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                         Cript 70 giCamCGkkl 79
                                  ++C+ CGk+ 
  gi|70607155|ref|YP_256025.1|  2 DLCQRCGKRE 11
                                  68*****975 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0084
                         Cript 70 giCamCGkkll 80
                                  ++C+mCGk  +
  gi|70607155|ref|YP_256025.1| 20 KLCSMCGKDEI 30
                                  68******874 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 3.4e-05
                         Cript  23 rkigenkllskk..krfnpyaaysskCkiCktkveqkgakYCqkC 65 
                                   +++ en  l ++  + +n + + + kCk+C + +++ g++YC++C
  gi|70607155|ref|YP_256025.1| 191 QQLRENYELFHTyfNTINLFRT-DNKCKNCGAYINS-GQEYCERC 233
                                   5666777775543334555555.67*********99.******** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3       0.1   1.8e+02       2       7 ..       4       9 ..       3      10 .. 0.73
   2 ?    3.0   0.1     0.051        91      14      21 ..      20      27 ..      18      28 .. 0.71
   3 !   17.0   4.8     2e-06    0.0036       1      21 [.     215     235 ..     215     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.1
                 zinc_ribbon_2 2 CpnCGa 7
                                 C +CG+
  gi|70607155|ref|YP_256025.1| 4 CQRCGK 9
                                 777876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.051
                 zinc_ribbon_2 14 kFCpyCGt 21
                                  k C+ CG 
  gi|70607155|ref|YP_256025.1| 20 KLCSMCGK 27
                                  67888885 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 2e-06
                 zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                   +C+nCGa +  ++ +C++C t
  gi|70607155|ref|YP_256025.1| 215 KCKNCGAYINSGQEYCERCKT 235
                                   8******************65 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.11   1.9e+02       4       8 ..       4       8 ..       2      11 .. 0.71
   2 ?    6.0   0.0    0.0062        11       3      11 ..     215     223 ..     213     225 .. 0.87
   3 ?    7.3   0.1    0.0024       4.3       4      13 ..     230     239 ..     227     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                 -TTT- CS
                  zf-FPG_IleRS 4 CpRCw 8
                                 C RC+
  gi|70607155|ref|YP_256025.1| 4 CQRCG 8
                                 77777 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0062
                                   B-TTT--BB CS
                  zf-FPG_IleRS   3 pCpRCwryi 11 
                                   +C  C+ yi
  gi|70607155|ref|YP_256025.1| 215 KCKNCGAYI 223
                                   9*******9 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0024
                                   -TTT--BBEE CS
                  zf-FPG_IleRS   4 CpRCwryier 13 
                                   C+RC++y+++
  gi|70607155|ref|YP_256025.1| 230 CERCKTYLAS 239
                                   *******986 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   7.4e-05      0.13      41      76 ..       3      38 ..       1      53 [. 0.82
   2 ?    2.3   0.4     0.099   1.8e+02      40      64 ..     214     234 ..     188     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
                   Zn_Tnp_IS91 41 eCeeCghekivyfsCksrhCpsCqkkateewlekqq 76
                                   C+ Cg+++++    +++ C+ C+k +  + ++k +
  gi|70607155|ref|YP_256025.1|  3 LCQRCGKREYFTVIGGRKLCSMCGKDEIVKRVRKEM 38
                                  5************************99888876654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.099
                   Zn_Tnp_IS91  40 yeCeeCghekivyfsCksrhCpsCq 64 
                                    +C++Cg     y   ++  C +C+
  gi|70607155|ref|YP_256025.1| 214 NKCKNCGA----YINSGQEYCERCK 234
                                   46777773....5666666666665 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0   0.00022       0.4      34      66 ..       1      34 [.       1      40 [. 0.82
   2 ?    3.0   0.6     0.062   1.1e+02      36      62 ..     215     238 ..     189     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                       DUF2318 34 ldaCevCekkgYv.qegeelvCknCgvrfaldsi 66
                                  +d C+ C+k++Y+   g +  C +Cg+   ++++
  gi|70607155|ref|YP_256025.1|  1 MDLCQRCGKREYFtVIGGRKLCSMCGKDEIVKRV 34
                                  699****99999977899999****987666555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.062
                       DUF2318  36 aCevCekkgYvqegeelvCknCgvrfa 62 
                                    C+ C   g +++  +  C++C++ +a
  gi|70607155|ref|YP_256025.1| 215 KCKNC---GAYINSGQEYCERCKTYLA 238
                                   45555...4444455558999998776 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.049        89       3      12 ..      19      28 ..      17      34 .. 0.86
   2 ?    4.6   3.3     0.018        32       3      18 ..     213     228 ..     212     237 .. 0.87
   3 ?    0.1   0.1      0.43   7.7e+02       5      14 ..     229     238 ..     225     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.049
                        zf-FCS  3 kkrCwfCkky 12
                                  +k C++C+k+
  gi|70607155|ref|YP_256025.1| 19 RKLCSMCGKD 28
                                  789*****97 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                        zf-FCS   3 kkrCwfCkkyikgkpe 18 
                                   +++C +C+ yi  ++e
  gi|70607155|ref|YP_256025.1| 213 DNKCKNCGAYINSGQE 228
                                   79*********99987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.43
                        zf-FCS   5 rCwfCkkyik 14 
                                    C+ Ck+y+ 
  gi|70607155|ref|YP_256025.1| 229 YCERCKTYLA 238
                                   6999**9985 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.0      0.18   3.3e+02       2      24 ..       3      25 ..       2      39 .. 0.81
   2 ?   12.4   6.8   0.00012      0.21      64      85 ..     192     233 ..     134     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                zinc_ribbon_15  2 lCpkCgklskaelvkkkkvlklf 24
                                  lC++Cgk++  +++  +k ++++
  gi|70607155|ref|YP_256025.1|  3 LCQRCGKREYFTVIGGRKLCSMC 25
                                  58888888888888888888777 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                zinc_ribbon_15  64 e....................kkeCknCgkeveeefkyCpkC 85 
                                   +                     ++CknCg+ +++  +yC +C
  gi|70607155|ref|YP_256025.1| 192 QlrenyelfhtyfntinlfrtDNKCKNCGAYINSGQEYCERC 233
                                   25555666777777777888899******************* PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.1     0.066   1.2e+02      19      49 ..       3      34 ..       1      39 [. 0.59
   2 ?    7.4   0.4    0.0025       4.4      13      47 ..     209     240 ..     206     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.066
                      zf-C2HC5 19 nClnCGki.iCakeglskpCsfCgspllssee 49
                                  +C  CGk    +  g  k Cs Cg++ + +  
  gi|70607155|ref|YP_256025.1|  3 LCQRCGKReYFTVIGGRKLCSMCGKDEIVKRV 34
                                  57778873223333444889999976555554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                      zf-C2HC5  13 LleaapnClnCGkiiCakeglskpCsfCgspllss 47 
                                   L+ +   C nCG  i + +++   C  C++ l s+
  gi|70607155|ref|YP_256025.1| 209 LFRTDNKCKNCGAYINSGQEY---CERCKTYLASP 240
                                   7777889******99888877...99999988776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.0      0.15   2.7e+02      31      54 ..       4      27 ..       2      29 .. 0.84
   2 ?    1.5   0.2      0.16   2.9e+02      29      47 ..      20      38 ..      18      49 .. 0.68
   3 ?    8.2   0.7    0.0013       2.3       4      55 ..     189     236 ..     186     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgf 54
                                  C +Cg++ + ++ g +  C+ Cg 
  gi|70607155|ref|YP_256025.1|  4 CQRCGKREYFTVIGGRKLCSMCGK 27
                                  999999999888899999999985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtf 47
                                  k Cs Cg+    ++ ++++
  gi|70607155|ref|YP_256025.1| 20 KLCSMCGKDEIVKRVRKEM 38
                                  67*****977665555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0013
                OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfe 55 
                                   + +ql++  + +   + ++n + T  +C +Cg+  +      + +C++C+++
  gi|70607155|ref|YP_256025.1| 189 VNQQLRENYELFHTYFNTINLFRTDNKCKNCGAYINS----GQEYCERCKTY 236
                                   56778888888888888999999**********9998....77789999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1535.81
//
Query:       gi|70607156|ref|YP_256026.1|  [L=273]
Description: hypothetical protein Saci_1403 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.61    9.1   3.1        1.2    8.1   0.0    2.2  3  DUF2009   Protein of unknown function (DUF2009)


Domain annotation for each model (and alignments):
>> DUF2009  Protein of unknown function (DUF2009)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.9     0.018   3.2e+02     163     206 ..       8      52 ..       3      56 .. 0.77
   2 ?    8.1   0.0   6.7e-05       1.2     139     207 ..      58     129 ..      52     156 .. 0.81
   3 ?   -3.1   0.0      0.17     3e+03     368     393 ..     189     214 ..     179     232 .. 0.47

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.018
                       DUF2009 163 aekksreeiqkeikekeeaieklakkysskk.lskeeieqvlysi 206
                                   +e+ks+e+ +ke k+k++  ++ ++ky +   l +e + +v++s+
  gi|70607156|ref|YP_256026.1|   8 EEEKSKENSTKEEKTKSTKKKSTKEKYVNPLeLLDEYLDEVINSL 52 
                                   567888888888888888888999999885448888888888887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 6.7e-05
                       DUF2009 139 vleekealelledklielataeisaekksreeiqkeikekeeaieklakkyss....kklskeeieqvlysie 207
                                    l++++++el++++  ++a+ e++++ ksr+ i++ + +ke+ +e la k  +    +kl+++++e v+  i+
  gi|70607156|ref|YP_256026.1|  58 NLDREGFKELIKEP-FSAAVGEVKSKPKSRTIINRLLANKEALMEFLAVKLLRvvnpEKLTNDQLEFVVFNIK 129
                                   57888999999998.788************************9998877765433336788888888877665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.17
                       DUF2009 368 tleeleklaedpelkeyieeefgsve 393
                                    + ++++l+e   + + +++ ++  +
  gi|70607156|ref|YP_256026.1| 189 SVISMKQLKEIIGVISVLQDYYEFDK 214
                                   33334444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2162  (0.120587); expected 358.6 (0.02)
Passed bias filter:                     1178  (0.0657036); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 1799.74
//
Query:       gi|70607157|ref|YP_256027.1|  [L=110]
Description: hypothetical protein Saci_1404 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2077  (0.115846); expected 358.6 (0.02)
Passed bias filter:                     1042  (0.0581181); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 770.97
//
Query:       gi|70607158|ref|YP_256028.1|  [L=239]
Description: hypothetical protein Saci_1405 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-05   23.8   0.4    0.00017   21.5   0.1    2.1  2  HTH_45     Winged helix-turn-helix
    0.00093   19.5   0.0      0.025   14.9   0.0    2.7  3  Rrf2       Transcriptional regulator
     0.0056   16.5   0.1      0.024   14.5   0.0    2.1  3  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0083   16.0   0.0       0.02   14.7   0.0    1.6  1  MarR_2     MarR family
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.026   14.4   0.0    1.6  1  HTH_5      Bacterial regulatory protein, arsR family
      0.014   15.3   0.8        4.7    7.2   0.0    2.7  3  MarR       MarR family
       0.05   13.4   0.0       0.14   12.0   0.0    1.8  1  HTH_23     Homeodomain-like domain
      0.073   13.2   0.1       0.27   11.4   0.0    1.9  2  AbiEi_4    Transcriptional regulator, AbiEi antitoxin
      0.079   13.1   1.2       0.15   12.1   1.2    1.5  1  PPO1_KFDV  Protein of unknown function (DUF_B2219)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   8.6e-08   0.00017      17      73 ..      36      92 ..      22      96 .. 0.84
   2 ?   -0.2   0.0       0.5     1e+03       8      45 ..     155     192 ..     153     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.6e-08
                        HTH_45 17 egeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkele 73
                                      + ++i  + nL+ k +++YL++  +kgl+ ++ + + l   G++l +++ e +
  gi|70607158|ref|YP_256028.1| 36 ARPLRTSEIATNLNLDTKYVSSYLSYWRKKGLVYQEAGRWHLSRVGEDLAKEILESK 92
                                  4667889******************************************99987765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.5
                        HTH_45   8 iadILeaisegeakkTkimykanLsykllnkYLdmLve 45 
                                   i ++Le+++ +e+   + ++k + ++  +  YLd+L+e
  gi|70607158|ref|YP_256028.1| 155 IEEVLEKLDADEKDLVSFLLKKYKEWGATYVYLDQLQE 192
                                   56788888888888888888888889999999999987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-05     0.025      24      61 ..      37      74 ..      27      85 .. 0.87
   2 ?   -0.7   0.0      0.94   1.9e+03      27      50 ..     139     163 ..     135     171 .. 0.70
   3 ?    0.5   0.0      0.39   7.7e+02      26      54 ..     185     213 ..     168     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                  C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                          Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                  +p++++eia++ n+  +y++  l+  rk+glv  + G+
  gi|70607158|ref|YP_256028.1| 37 RPLRTSEIATNLNLDTKYVSSYLSYWRKKGLVYQEAGR 74
                                  46899****************************99998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.94
                                   -HHHHHHHHTS-H.HHHHHHHHHHH CS
                          Rrf2  27 sseeiaerqnisp.sylekilakLr 50 
                                   +s+++ +rqn +p + +e +l+kL 
  gi|70607158|ref|YP_256028.1| 139 TSQDVNKRQNKEPeVCIEEVLEKLD 163
                                   7788888886554156788888886 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.39
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          Rrf2  26 vsseeiaerqnispsylekilakLrkagl 54 
                                   v ++++ e+++     l ++l+kL+ + +
  gi|70607158|ref|YP_256028.1| 185 VYLDQLQEEYGADSGWLFRVLRKLQTKRI 213
                                   6788999999999999********98876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.2e-05     0.024      16      58 ..      32      74 ..      27      87 .. 0.91
   2 ?   -3.2   0.0         4   7.9e+03      39      46 ..     155     162 ..     139     170 .. 0.71
   3 ?   -2.8   0.0       3.1   6.1e+03      28      48 ..     190     210 ..     187     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   Ll   p++++eia +l+++   v ++L+   +kGlV+ e gr
  gi|70607158|ref|YP_256028.1| 32 ILLLARPLRTSEIATNLNLDTKYVSSYLSYWRKKGLVYQEAGR 74
                                  688999*********************************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                                   HHHHHHHH CS
                          TrmB  39 vYevLrsL 46 
                                   + evL++L
  gi|70607158|ref|YP_256028.1| 155 IEEVLEKL 162
                                   55666666 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
                                   HCCCTTSSCHCHHHHHHHHHH CS
                          TrmB  28 iaeelgvprskvYevLrsLed 48 
                                   + ee g +     +vLr+L  
  gi|70607158|ref|YP_256028.1| 190 LQEEYGADSGWLFRVLRKLQT 210
                                   566666666667789999976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05      0.02      10      56 ..      30      73 ..      28      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  v+  L +rp   l+ +e+a  l+l+  +vs  l    ++GLv +++g
  gi|70607158|ref|YP_256028.1| 30 VMILLLARP---LRTSEIATNLNLDTKYVSSYLSYWRKKGLVYQEAG 73
                                  566788888...9*****************************99876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.026       9      46 ..      32      69 ..      23      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                  HHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  9 klLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   lL  ++l  +e+a  l+l    vS +L+  r+ GLV+
  gi|70607158|ref|YP_256028.1| 32 ILLLARPLRTSEIATNLNLDTKYVSSYLSYWRKKGLVY 69
                                  34555*******************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0063        13      12      48 ..      33      69 ..      27      72 .. 0.82
   2 ?   -4.4   0.9         9   1.8e+04      49      58 ..     121     130 ..     120     130 .. 0.81
   3 ?    7.2   0.0    0.0023       4.7      12      53 ..     177     220 ..     172     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0063
                                  HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 12 lyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  l    pl+ se+a  l++++ +v+  l    kkGl++
  gi|70607158|ref|YP_256028.1| 33 LLLARPLRTSEIATNLNLDTKYVSSYLSYWRKKGLVY 69
                                  5556799*****************9988888888876 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 9
                                   EEEETTSTTS CS
                          MarR  49 RskspeDrRe 58 
                                   ++k+ +Dr+e
  gi|70607158|ref|YP_256028.1| 121 KKKDNKDRKE 130
                                   6899999986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0023
                                   HHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                          MarR  12 lyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRsksp 53 
                                    +e+g+ +v   +L++  g +++ + rvl++L  k  ++ +++p
  gi|70607158|ref|YP_256028.1| 177 YKEWGATYVYldQLQEEYGADSGWLFRVLRKLQTKRILYLYHDP 220
                                   567888777777********************998777666665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.14       5      46 ..      26      67 ..      22      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                        HTH_23  5 reRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  ++ + ++llla+ l+++eIA+ L+     v+ +l+ +r++Gl
  gi|70607158|ref|YP_256028.1| 26 LMEAVMILLLARPLRTSEIATNLNLDTKYVSSYLSYWRKKGL 67
                                  55678999999999************************9*97 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.27      14      40 ..      39      70 ..      35      74 .. 0.92
   2 ?   -1.5   0.0       1.4   2.9e+03      34      41 ..     197     204 ..     194     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                       AbiEi_4 14 fttrelea.aGispsa....lrrLvrkGwLvr 40
                                  ++t+e++  +++++++    l+++++kG++ +
  gi|70607158|ref|YP_256028.1| 39 LRTSEIATnLNLDTKYvssyLSYWRKKGLVYQ 70
                                  699**9999*******************9987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                       AbiEi_4  34 rkGwLvrl 41 
                                   ++GwL r+
  gi|70607158|ref|YP_256028.1| 197 DSGWLFRV 204
                                   79***997 PP

>> PPO1_KFDV  Protein of unknown function (DUF_B2219)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   7.6e-05      0.15      50     108 ..     115     170 ..      83     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                     PPO1_KFDV  50 fvnvdedekavgpekaefaGSfvnvphkvhke.kkkaktslrlgitdlledLgaedddsv 108
                                    +n d+++k+ +++ +ef     ++ ++  ++ +k+++++ +++i+++le+L+a++ d v
  gi|70607158|ref|YP_256028.1| 115 TIN-DKTKKKDNKDRKEFL---LFIDQQTSQDvNKRQNKEPEVCIEEVLEKLDADEKDLV 170
                                   578.888888788888886...44444444444788*******************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1767  (0.0985554); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1683.93
//
Query:       gi|70607159|ref|YP_256029.1|  [L=360]
Description: hypothetical protein Saci_1406 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-52  178.1   0.0    2.3e-52  178.0   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
    0.00043   19.9   0.0     0.0026   17.3   0.0    2.1  2  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.085   12.0   0.1       0.19   10.8   0.0    1.6  2  Arb2        Arb2 domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.0   0.0   3.8e-56   2.3e-52      15     291 ..      33     355 ..       4     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.0 bits;  conditional E-value: 3.8e-56
                                   HHHHHHHHHHHCT-..EEEEECCGGCCSSSTT--HHHHTTTT--........EEECCC-TTTTTSSSEEEEEE-HHHHHHH CS
                    NAD_kinase  15 eraeevarwLldalsrvlevtveeklgeslaeaaefrsevisvlkkvkttd.dtrkaleafadagvdliivvGGDGTaldv 94 
                                   e+++++ r+L++   +v ++++ + +ge   ++ +f+++vi +  +  tt+ +t++a ++f + ++ +i+++GGDGTa+d+
  gi|70607159|ref|YP_256029.1|  33 EIHSKMERFLSTVPKQVKFIVPPGIMGEAFLKKHDFKFSVIDIHIDDPTTRqNTIEASRTFLELECTIIVFAGGDGTARDI 113
                                   6788999999999449*************************99877666666***************************** PP

                                   HHHHHHCT-EEEEEESSS--SS-SE..EGGGHHHHHHHHHHT-SEEEEEEEEE.........................EEE CS
                    NAD_kinase  95 arllqkaeiPvlgvnaGvkgfltef..epeaaaellekllegeirvekrevld.........................avi 148
                                   ++++++ +  +lg+++Gvk+++++f  +pe+a+ l+++l+++++++ ++e+ld                         +++
  gi|70607159|ref|YP_256029.1| 114 YSVVKD-KKLLLGIPTGVKMHSGIFanTPEDAGHLIRELINKRVEIVDAEILDideeqyrkgkydvklygyaktisfsTYL 193
                                   *****8.777********************************************************************888 PP

                                   EETTE..............EEEEEEESSE..EEEEESSSSS-EE..EEEEETTEEE.EEEEESEE................ CS
                    NAD_kinase 149 mrskgee........diadiviensvlne..vviirgpgstlie..lelyvdtell.eadqldgl................ 200
                                   ++sk e+        +i d++ +n   n+   v+i+gpgst ++  + l+++t++l ++++++++                
  gi|70607159|ref|YP_256029.1| 194 TPSKTEIyseqeelnEITDYLLDNVFQNHpdAVFIIGPGSTTKYiiKRLGYETNFLcTDVVIRNKligscvsyndllnltg 274
                                   88888778888888************997558*************99*******98355678999**************** PP

                                   ...EEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EE CS
                    NAD_kinase 201 ...ivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdev 278
                                      +++tP+G+++++l++G+++i Pgvl+         + ++++iV+ss++kl+     + e+l++++G++e++ ++ +++
  gi|70607159|ref|YP_256029.1| 275 elkLIVTPIGGQGFLLGRGNQEIGPGVLK--------RVNKDDIIVISSRRKLQ-----TFECLRIDTGDPEVDKKFLGIY 342
                                   *****************************........*****************.....77******************** PP

                                   EEEEESSEEEEEE CS
                    NAD_kinase 279 rvtasdkkfklir 291
                                   +v++++++f+ i+
  gi|70607159|ref|YP_256029.1| 343 KVIVGYNEFEPIK 355
                                   ********98776 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.14   8.1e+02       2      13 ..       5      16 ..       4      49 .. 0.81
   2 !   17.3   0.0   4.4e-07    0.0026      37      93 ..      79     131 ..      59     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.14
                                  EEEEE-TTCTTT CS
                      DAGK_cat  2 llvivNpksGkg 13
                                  ++++vNp +G+g
  gi|70607159|ref|YP_256029.1|  5 ICLLVNPVAGSG 16
                                  6799*****965 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.4e-07
                                   E--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS- CS
                      DAGK_cat  37 eteepgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtg 93 
                                   + + ++   e  ++  e +  +iv aGGDGt++ + +++ +   +k+ lg iP+G  
  gi|70607159|ref|YP_256029.1|  79 DPTTRQNTIEASRTFLELECTIIVFAGGDGTARDIYSVVKD---KKLLLG-IPTGVK 131
                                   333444455566666666889******************99...777777.476655 PP

>> Arb2  Arb2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.41   2.4e+03      93     110 ..      69      86 ..      66      93 .. 0.73
   2 ?   10.8   0.0   3.3e-05      0.19     113     163 ..     194     242 ..     174     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.41
                                   T-EEEEEEE----..... CS
                          Arb2  93 kygviDvnipkliteeee 110
                                   k+ viD+ i   +t++++
  gi|70607159|ref|YP_256029.1|  69 KFSVIDIHIDDPTTRQNT 86 
                                   799****99887666554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3.3e-05
                                   --SSSS-HHHHHHHHHHHHHHHHHTTTTSSS.SEEEEEEECCHHHHHHHHH CS
                          Arb2 113 skeeeeeesaasesqelllylwdnyielfesaekifllGvGdaysgvvkLl 163
                                   + +++e +s+++e +e+  yl dn  + +   + +f++G G+  + ++k l
  gi|70607159|ref|YP_256029.1| 194 TPSKTEIYSEQEELNEITDYLLDNVFQNHP--DAVFIIGPGSTTKYIIKRL 242
                                   556788999******************999..79*******9998887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2840.09
//
Query:       gi|70607160|ref|YP_256030.1|  [L=206]
Description: hypothetical protein Saci_1407 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00089   19.2   0.3     0.0018   18.2   0.3    1.5  1  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
      0.037   14.0   0.0       0.11   12.5   0.0    1.9  1  HTH_45          Winged helix-turn-helix
      0.045   13.4   0.0      0.087   12.5   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e
      0.049   13.6   0.2      0.096   12.6   0.2    1.4  1  MarR            MarR family
      0.052   13.8   0.0      0.094   12.9   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.088   12.9   0.1       0.12   12.5   0.1    1.2  1  Replic_Relax    Replication-relaxation
       0.13   12.2   1.0       0.59   10.1   0.1    2.4  2  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3     7e-07    0.0018       4      66 .]      30      86 ..      27      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-07
                        HTH_12  4 LkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgyagreltEkGleeL 66
                                  L+ ++++ +pig++ +   L + +  i  r++ +rLr le   +++  + ag  +t+kG ++L
  gi|70607160|ref|YP_256030.1| 30 LDTINKH-QPIGRQLLTRMLSLSEASI--RTMIRRLRELE---FVEVDRVAGIFITDKGKKLL 86
                                  5566665.5899999999999888888..77777777775...99**************9987 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.2e-05      0.11      30      71 ..      49      91 ..      30      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                        HTH_45 30 nLsykllnkYLdmLvekglikk.skekYvlTekGlelleklke 71
                                   Ls   ++ ++  L e ++++  +     +T+kG++lle l+e
  gi|70607160|ref|YP_256030.1| 49 SLSEASIRTMIRRLRELEFVEVdRVAGIFITDKGKKLLEYLHE 91
                                  68889999************652667799*********99876 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05     0.087      92     131 ..      51      90 ..      43      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                   HHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--X CS
                Ribosomal_S19e  92 sgsvirkilqqLeklglvkkekkkgrrltkkGqrlldria 131
                                   s++ ir++++ L +l++v+ ++  g  +t+kG++ll+ + 
  gi|70607160|ref|YP_256030.1|  51 SEASIRTMIRRLRELEFVEVDRVAGIFITDKGKKLLEYLH 90 
                                   7889**************988899***********98765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   3.7e-05     0.096       9      48 ..      30      69 ..      26      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                                  HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  L ++  ++p+  + L ++l++s +++ ++++rL + +++e
  gi|70607160|ref|YP_256030.1| 30 LDTINKHQPIGRQLLTRMLSLSEASIRTMIRRLRELEFVE 69
                                  899***********************************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.7e-05     0.094      19      56 ..      35      72 ..      28      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                  ++++++++ l + L  s +s+  m+++L++ ++ve+  
  gi|70607160|ref|YP_256030.1| 35 KHQPIGRQLLTRMLSLSEASIRTMIRRLRELEFVEVDR 72
                                  678899999*************************9865 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.6e-05      0.12       1      42 [.      30      70 ..      30     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                  Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsr 42
                                  L+++++h++  ++ ++r+l  s+ + +r+ ++rLrel++++ 
  gi|70607160|ref|YP_256030.1| 30 LDTINKHQPIGRQLLTRMLSLSEAS-IRTMIRRLRELEFVEV 70
                                  7899*********************.9999*****9999986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00023      0.59      11      44 ..      34      68 ..      27      76 .. 0.83
   2 ?   -0.7   0.1      0.56   1.4e+03      29      44 ..     110     125 ..     106     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                        HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdIkaLeelg.v 44
                                  ++++pi  + L + L++S++ +r  I++L+el  v
  gi|70607160|ref|YP_256030.1| 34 NKHQPIGRQLLTRMLSLSEASIRTMIRRLRELEfV 68
                                  6777799999********************98754 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.56
                        HTH_11  29 rrtvrrdIkaLeelgv 44 
                                     ++ + I +L+++g+
  gi|70607160|ref|YP_256030.1| 110 GVVILNGINILNKIGI 125
                                   567899999***9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1505.33
//
Query:       gi|70607161|ref|YP_256031.1|  [L=306]
Description: ornithine carbamoyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-56  191.2   0.1    1.8e-56  190.6   0.1    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    9.3e-45  152.3   0.1    2.4e-44  151.0   0.0    1.6  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.6   0.1     2e-60   1.8e-56       4     156 ..     152     304 ..     150     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.6 bits;  conditional E-value: 2e-60
                                   EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETT CS
                        OTCace   4 kiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmg 84 
                                   ++af+Gd+  nv+ sl+++++++g+++++++Pk+++p++ev+++++++ +ksg+ i++ ed+ eav g+ vvytdvwvsmg
  gi|70607161|ref|YP_256031.1| 152 NMAFIGDGTDNVLTSLMEFVSKMGLELRVASPKEFRPKQEVWRRIEEESEKSGAIIEFYEDPYEAVRGVKVVYTDVWVSMG 232
                                   79******************************************************************************* PP

                                   CCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                        OTCace  85 eekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                   +e+  ee+ kklkdy+vt++l++ a+kdai++HcLPa+rgeEv+d+V+d+++s+v++qaeNrl+t++A+l l
  gi|70607161|ref|YP_256031.1| 233 QESIAEEKKKKLKDYKVTRDLMRYASKDAIFMHCLPAVRGEEVEDDVIDGHQSAVWDQAENRLYTAMAVLSL 304
                                   *********************************************************************986 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   2.6e-48   2.4e-44       1     148 []       5     145 ..       5     145 .. 0.98
   2 ?   -1.7   0.0      0.29   2.6e+03      76     108 ..     230     266 ..     218     285 .. 0.66

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 2.6e-48
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   ++ll+l d+s+ eie++++l+ ++k+ v+ ++ +k+l++k +al+Fe+pStRTr+S+e+A+k lGg+ ++ls ++diql+ 
  gi|70607161|ref|YP_256031.1|   5 KSLLTLLDFSNYEIESIINLSFSMKSFVNLNSVPKTLENKKIALIFEKPSTRTRISTELAVKLLGGTSIVLS-KSDIQLG- 83 
                                   689***********************9999******************************************.77*****. PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       r+E++eDtarvl+ryvd+i +R+ ++++le l ky++ pviN + +d +HP+QaL+D++t++e
  gi|70607161|ref|YP_256031.1|  84 ----RGETVEDTARVLGRYVDGIGARVLNHNSLEILSKYSRKPVINLL-SDVSHPLQALTDFMTVKE 145
                                   ....78******************************************.***************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                                   TSCTTTGGSTTSSCHHH..HHHHHHHHT..SEEEEEE CS
                      OTCace_N  76 diqlssvskgrkEsleD..tarvlsryv..daiviRh 108
                                   ++ ++s+++++k +l+D  + r l ry+  dai+++ 
  gi|70607161|ref|YP_256031.1| 230 SMGQESIAEEKKKKLKDykVTRDLMRYAskDAIFMHC 266
                                   4445556666677888866666677777778887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1992.02
//
Query:       gi|70607162|ref|YP_256032.1|  [L=410]
Description: hypothetical protein Saci_1409 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-94  317.4   0.0    1.5e-94  316.8   0.0    1.3  1  Nre_N     Archaeal Nre, N-terminal
    2.9e-33  114.1   0.0    5.8e-33  113.1   0.0    1.5  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.8   0.0   1.7e-98   1.5e-94       1     270 []      18     290 ..      18     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 316.8 bits;  conditional E-value: 1.7e-98
                         Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg..dasvldspekwl.glsledii 77 
                                   Lcgl+ cpile++++v+++++ki  ++++eGs+pPs+++G+++YPkVs+++++pp +   +a+++++pe w+ ++sl+dii
  gi|70607162|ref|YP_256032.1|  18 LCGLSICPILERFKNVTSTVSKIvINNKIEGSTPPSILIGEKNYPKVSLVYNIPPGVIgeEAKDYENPEGWWgRKSLNDII 98 
                                   8*********************999******************************88778************9******** PP

                         Nre_N  78 klrlslvrgekk.vkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprk 157
                                   ++r+sl+++    ++v+++  + + +ei+ + +sekpv +e+  + k+ +klkfd++l P Gps +++++kv+enpkvpr+
  gi|70607162|ref|YP_256032.1|  99 SIRSSLISTILGgLNVRDPY-KLYEKEISLAGISEKPVVSETDSSGKIVPKLKFDGILIPRGPSLTVQSIKVSENPKVPRT 178
                                   *********9877******8.8889******************************************************** PP

                         Nre_N 158 veklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfs 238
                                   ++kl+ D dlkAee+v++Ly ++ ++y+i +++S+G+LG k++r+lVPTrWsITAvd+ivg++l+++i++l++id+ve+++
  gi|70607162|ref|YP_256032.1| 179 IQKLIFD-DLKAEESVIKLYLDNENYYRIISAFSLGFLGLKRNRKLVPTRWSITAVDQIVGNYLLDNIRTLDTIDNVEYYY 258
                                   *******.************************************************************************* PP

                         Nre_N 239 geylgNrflviLaPgkwsfelvEawapgslwn 270
                                   g+ylgN+f++iL+P+++s +++E+w+p slw+
  gi|70607162|ref|YP_256032.1| 259 GSYLGNHFHIILYPSSHSSTWIEIWHPLSLWT 290
                                   *******************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.0   6.5e-37   5.8e-33       8     110 .]     305     407 ..     300     407 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 6.5e-37
                         Nre_C   8 eyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevseklklpl 88 
                                   ey +++G+Y+aar++++e+L+k++rqa++i++reit++Y+aPvG+W++Re+v++ale+kpk+f+++ee l++v+++l+++ 
  gi|70607162|ref|YP_256032.1| 305 EYDSLDGGYIAARFSIIEKLYKRRRQAGIIIIREITKDYFAPVGNWHIRETVKRALENKPKTFNTIEESLKYVNTNLEAND 385
                                   688899*************************************************************************** PP

                         Nre_C  89 kkllkkskllkelkkqktLddF 110
                                   k  l   k +k++  q+++d+F
  gi|70607162|ref|YP_256032.1| 386 KINLLGLKSIKKIIGQRRIDEF 407
                                   ********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2730.14
//
Query:       gi|70607163|ref|YP_256033.1|  [L=223]
Description: hypothetical protein Saci_1410 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-14   50.9   0.0    1.6e-13   50.2   0.0    1.4  1  PHP_C     PHP-associated
    6.1e-06   26.6   0.0    5.4e-05   23.6   0.0    2.1  2  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   1.8e-17   1.6e-13       3      55 ..     129     182 ..     127     183 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-17
                         PHP_C   3 aNrrArrfAeklglpgtgGSDAHrleeVGrayTef.eepiatpdelleairegr 55 
                                   aN++A+ + + l+lpg+++SDAH+++ +G+ay+ f + ++ ++d +le ir+g+
  gi|70607163|ref|YP_256033.1| 129 ANDKALAVSKNLNLPGLANSDAHVIQALGSAYNYFkDISEFNIDNILEHIRKGK 182
                                   8**********************************9999999***********8 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     6e-09   5.4e-05       1      44 [.       4      45 ..       4      71 .. 0.89
   2 ?    0.9   0.0     0.056     5e+02      19      53 ..     132     166 ..     121     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6e-09
                                  EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHH CS
                                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyv 44
                                  d+HvH+ +s + +++l   +++k a + gl+aia+TDh+   gy+
  gi|70607163|ref|YP_256033.1|  4 DFHVHSFFSdGRESPL---NIIKYALRIGLDAIALTDHDTSKGYY 45
                                  79*******7775555...9*******************998876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.056
                                   HHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           PHP  19 elvkkakelglkaiaiTDhgnlfgyvefykaakkk 53 
                                   + ++  k+l+l+ +a +D  ++++   +y++ k+ 
  gi|70607163|ref|YP_256033.1| 132 KALAVSKNLNLPGLANSDAHVIQALGSAYNYFKDI 166
                                   56667789999999999999999777777776553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1463.12
//
Query:       gi|70607164|ref|YP_256034.1|  [L=350]
Description: aspartate-semialdehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-33  114.4   0.0      7e-33  113.6   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    3.3e-26   92.5   0.1    4.8e-26   92.0   0.1    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.025   14.7   0.1    1.6  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
      0.016   14.8   0.2      0.034   13.8   0.1    1.7  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
       0.03   14.4   0.0      0.054   13.6   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.031   15.0   0.1       0.19   12.5   0.0    2.3  3  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   0.0   2.3e-36     7e-33       1     119 [.       6     130 ..       6     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 2.3e-36
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivflalp 75 
                                   kv+++G tG+vGq+++++L++hp++elv +++s ++ Gk++++ vk      ++e++++l+v +++ e+ k+vd+v++alp
  gi|70607164|ref|YP_256034.1|   6 KVSLLGSTGMVGQKMVKILANHPYLELVKVSASPNKVGKRYQDSVKwietgdIPENIRNLPVVSTSYEDHKDVDVVLSALP 86 
                                   799****************************************************************************** PP

                                   HHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                   +++++  + +l+++g +vi+++s +R+++d++++ pevn e+++
  gi|70607164|ref|YP_256034.1|  87 NDIAEGAELELVKNGKIVISNASPYRMDPDVPLINPEVNWEHLE 130
                                   *****************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0   0.1   1.6e-29   4.8e-26       1     183 [.     160     330 ..     160     331 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 1.6e-29
                                   HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
               Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                   +kPLl+ ++  +++ ++t+q+vSGaG+                    +g + ++  gN+ipyi++eedk+  e  +  ++v
  gi|70607164|ref|YP_256034.1| 160 IKPLLE-IATKSKILITTLQSVSGAGY--------------------NGLSFMAMDGNVIPYIKGEEDKIAKELTKLNGKV 219
                                   589999.79999***************....................8*****************9999988888888888 PP

                                   HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSHCHHSSHHH CS
               Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvneeedrPtpaa 150
                                    ++k + ++ + v+at  rVP+  Gh+  +++ ++ ++v++ee++ +l++             p+  ++v+eeedrP+p  
  gi|70607164|ref|YP_256034.1| 220 INQKLEPANLD-VTATTIRVPIKVGHMGVINLITD-QKVSIEEIKYALKNFkslpqqkrlptaPKTPLIVREEEDRPQPMI 298
                                   88777777776.99********************6.999999999999999999*************************99 PP

                                   HTTC..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
               Semialdhyde_dhC 151 vagg..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                   ++    +++vsVGR+r  +   + l lv++gDNl+
  gi|70607164|ref|YP_256034.1| 299 DVIAenGMAVSVGRVRYEN---NVLRLVILGDNLI 330
                                   8865789**********99...5689********8 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   8.4e-06     0.025       2      74 ..       6      82 ..       5     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.4e-06
                                  EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH.....HHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEE CS
                       Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDiake.....kleGvaldlshistflsvkvkvsekeeealkdadvvv 74
                                  kv+++G++G++Gq++   lan+++ + +++   +++     + + + +++ +i  ++ ++  v ++ +e+ kd+dvv+
  gi|70607164|ref|YP_256034.1|  6 KVSLLGSTGMVGQKMVKILANHPYLELVKVSASPNKvgkryQDSVKWIETGDIPENI-RNLPVVSTSYEDHKDVDVVL 82
                                  9*********************99995555555544665323333445555555555.677778899********997 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.8   8.3e+03      50      71 ..      67      88 ..      63      91 .. 0.71
   2 ?   13.8   0.1   1.1e-05     0.034      65     110 ..     224     269 ..     197     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                  SEEEE-THHHHHHHHSGGGTTT CS
                       Gp_dh_C 50 iiptstgaakavglVlpelkgk 71
                                  ++ ts   +k+v  Vl  l ++
  gi|70607164|ref|YP_256034.1| 67 VVSTSYEDHKDVDVVLSALPND 88
                                  5666667788888888877655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                                   SGGGTTTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHH CS
                       Gp_dh_C  65 lpelkgkldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaa 110
                                   l   + +++++ +rVP++ +++  + + ++++v+ ee++ alk+  
  gi|70607164|ref|YP_256034.1| 224 LEPANLDVTATTIRVPIKVGHMGVINLITDQKVSIEEIKYALKNFK 269
                                   55567788999*******************************9866 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.054       2      42 ..       6      44 ..       5     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                  EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTT CS
                        DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegk 42
                                  kv ++G +G +G+++vk + +++ lelv++  +++   +gk
  gi|70607164|ref|YP_256034.1|  6 KVSLLGSTGMVGQKMVKILANHPYLELVKVSASPN--KVGK 44
                                  899***************************99987..2333 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.3e-05      0.19       1      33 [.       7      38 ..       7      53 .. 0.82
   2 ?   -1.7   0.0       1.5   4.6e+03      88     117 ..      75     104 ..      68     107 .. 0.78
   3 ?   -2.2   0.0       2.2   6.6e+03      66      91 ..     231     256 ..     209     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                                  EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEES CS
               DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaag 33
                                  v++LGsTG +G++ +++++++p   e+v ++a+
  gi|70607164|ref|YP_256034.1|  7 VSLLGSTGMVGQKMVKILANHP-YLELVKVSAS 38
                                  689******************9.6777777773 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   HTT-SEEEE--SSGGGHHHHHHHHHTTSEE CS
               DXP_reductoisom  88 eeeadvvvaaivGaaGLkptlaaikagkri 117
                                   ++++dvv++a+   +   + l+ +k+gk +
  gi|70607164|ref|YP_256034.1|  75 HKDVDVVLSALPNDIAEGAELELVKNGKIV 104
                                   689999999998888888888888888754 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                                   HHHTTSSSEEEESHHHHHHHHCHTT- CS
               DXP_reductoisom  66 lkekelktevlvGeealkelaeeeea 91 
                                   ++++ +++ + vG+ ++++l++ +++
  gi|70607164|ref|YP_256034.1| 231 VTATTIRVPIKVGHMGVINLITDQKV 256
                                   44456677788888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2561.82
//
Query:       gi|70607165|ref|YP_256035.1|  [L=447]
Description: aspartokinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-39  134.5   1.7    5.1e-39  134.3   0.2    1.8  2  AA_kinase  Amino acid kinase family
    0.00022   20.9   0.6      0.001   18.8   0.2    2.4  2  ACT_7      ACT domain
  ------ inclusion threshold ------
      0.046   13.5   4.7          2    8.3   0.4    3.4  4  ACT        ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.2   8.5e-43   5.1e-39       1     239 [.       1     277 [.       1     279 [. 0.89
   2 ?   -0.9   0.1      0.17     1e+03       2      30 ..     316     342 ..     315     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 8.5e-43
                                   TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH....TCCCCCHHHC........E..HH CS
                     AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal....ksglssgelaa....glrstlee 72 
                                   ++ V+K+GGs+ +d+++  ++ +a+ i+++ +++n+  +V+++ +++td+l +     ++ +++  ++     +l+s+l+ 
  gi|70607165|ref|YP_256035.1|   1 MIKVIKIGGSIQKDEKD--YELIADKISKY-SDENRTLIVTSAiKGVTDQLTSVinetDKAVDKVTEIYdkhiKLLSKLVD 78 
                                   689**************..***********.9999999999999**********665544444444433666644444444 PP

                                   HHHHHHH.............................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE....HHHTT CS
                     AA_kinase  73 agevatr.............................dalaslgerlvaallaaglpavglsaaaldateagr..degsdgn 122
                                     e ++                              d+++s+gerl   ll++ l++++ s++ l         ++ ++++
  gi|70607165|ref|YP_256035.1|  79 GIEFEKAfrdisrlvdelyriawsirvldeatprvkDYILSFGERLAVILLSSFLRTRKFSVNNLIEPPIVTdeNYSEANV 159
                                   4444444778889999999999999999999********************************99988777799******* PP

                                   TCEEECCHHHHHHHT..T-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCE CS
                     AA_kinase 123 vesvdaeaieellea..gvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarl 198
                                   + + ++e + + le+   +++vl+gfig + ++    +grg+sD++a+l++++++A+++ ++t+V+G+++adp+k+++ + 
  gi|70607165|ref|YP_256035.1| 160 LLEDSKELLSKKLEEsqQKIVVLPGFIGKSKNNRyttIGRGGSDYTATLIGKLVDAKEVRLVTEVPGIMTADPRKISNSVT 240
                                   *************65435************9999*********************************************** PP

                                   CCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                     AA_kinase 199 lpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvI 239
                                   + ++s +ea e    l++ G+k +hp++++++  ++++v+I
  gi|70607165|ref|YP_256035.1| 241 IQRLSLEEAIE----LSQLGAKKLHPRTFDPLFDANMKVII 277
                                   ***********....************************99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                                   EEEEEE-TT.CCCCTCCHHHHHHHHHHHHH CS
                     AA_kinase   2 rvVvKlGGs.sltdkeeaslrrlaeqiaal 30 
                                   r+V K+G++  +t++ +   ++ +++ia  
  gi|70607165|ref|YP_256035.1| 316 RIVGKIGSAsTITSEAK---NANVNIIALS 342
                                   79999999977775555...6777777655 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.7e-07     0.001       2      63 ..     303     366 ..     302     368 .. 0.92
   2 ?   -1.7   0.0      0.42   2.5e+03      46      65 .]     420     439 ..     417     439 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                                   EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHH CS
                         ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaL 63 
                                   +++g + ++++++++ +  +G +++++s   +a+++i ++S   +++t+ ++V+++d +k ve L
  gi|70607165|ref|YP_256035.1| 303 TKEGLSLITIESTRIVG-KIGSASTITSEAKNANVNIIALSqpaSETTIQFVVDQKDQKKFVERL 366
                                   5788999******9988.***************************************99877766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                                   -EEEEEEGGGHHHHHHHHHH CS
                         ACT_7  46 tdyiLVpeedlekAveaLhe 65 
                                   ++ ++V++++l+   + Lhe
  gi|70607165|ref|YP_256035.1| 420 SITFIVDKKELDSISKELHE 439
                                   78899999999999888885 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   1.3e+04      51      64 ..      14      27 ..      12      28 .. 0.84
   2 ?    0.5   0.0     0.092   5.5e+02      23      47 ..     304     328 ..     303     331 .. 0.84
   3 ?    8.3   0.4   0.00033         2      12      65 ..     322     369 ..     314     371 .. 0.79
   4 ?    4.9   0.1    0.0038        23      41      65 ..     416     440 ..     410     442 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                                  EHHHHHHHHHHHHT CS
                           ACT 51 deedleevlealkk 64
                                  de+d e + +++ k
  gi|70607165|ref|YP_256035.1| 14 DEKDYELIADKISK 27
                                  89999999999876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.092
                                   HTTSEEEEEEEEEESTTECEEEEEE CS
                           ACT  23 drgiNidsieqrssedkvagivfvv 47 
                                   + g++++ ie+++   k+++ ++++
  gi|70607165|ref|YP_256035.1| 304 KEGLSLITIESTRIVGKIGSASTIT 328
                                   6899**********99988877776 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00033
                                   THHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  12 GlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                   G ++ +++   ++++Ni+ ++q  s      ++++ +vvd++d ++ +e+l +l
  gi|70607165|ref|YP_256035.1| 322 GSASTITSEAKNANVNIIALSQPAS------ETTIQFVVDQKDQKKFVERLSQL 369
                                   6666666666788999999999999......88999999999999999988877 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0038
                                   CEEEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  41 agivfvvivvdeedleevlealkkl 65 
                                    + v ++++vd ++l+++ ++l+++
  gi|70607165|ref|YP_256035.1| 416 LKGVSITFIVDKKELDSISKELHEV 440
                                   67899*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3088.38
//
Query:       gi|70607166|ref|YP_256036.1|  [L=392]
Description: threonine synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-73  245.3   0.1      1e-72  245.1   0.1    1.1  1  PALP            Pyridoxal-phosphate dependent enzyme
     0.0059   16.7   0.1     0.0096   16.0   0.1    1.4  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
       0.02   14.8   0.5      0.033   14.1   0.5    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.034   14.3   0.1       0.09   13.0   0.1    1.8  1  zf-RING_7       C4-type zinc ribbon domain
      0.041   13.9   0.1       0.07   13.2   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.26   11.0   1.5       0.56    9.9   1.5    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   0.1   3.3e-76     1e-72       2     294 .]      63     359 ..      62     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 3.3e-76
                                   GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                          PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                   tl +g+TPl+++++       + ++K E+ nptgSfKdRg++ +++++      k vv+as+GN+++++Aa+++++Glk+ 
  gi|70607166|ref|YP_256036.1|  63 TLDEGNTPLIKSRKYD-----KTYFKFEGANPTGSFKDRGMTVAISSALSL-NYKIVVAASTGNTAASAAAYSSRAGLKSF 137
                                   7899*********987.....68****************************.***************************** PP

                                   EEEETTS-H.HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEE CS
                          PALP  83 ivvpadasp.ekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavv 162
                                   iv+p+++ + +k+a+  l+G  ++ev+g++d a++ +++l ++ +++++   ++np++ eg++ti++Ei+e++g +pd v+
  gi|70607166|ref|YP_256036.1| 138 IVLPKGKVAlGKLAQSILYGTVIIEVDGSFDIAMNSVMKLYRD-HKIVYPLNSFNPWRLEGQKTIAYEIVEDIG-VPDNVI 216
                                   ********88*********************************.8888888888*******************7.****** PP

                                   EE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTCS..CGTTCCHH CS
                          PALP 163 vpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarslragrrvtvpvs..dtiadglavg..spselafe 231
                                   vpvG++g+i +i++g+ e    +       +r+ig+++eg++++a++l++g +++  v   dtia+++++g  ++  +a++
  gi|70607166|ref|YP_256036.1| 217 VPVGNAGNIYAIWKGFNEllegG--LidkvPRMIGIQAEGAAPIAKALEKGLEQPEFVDspDTIASAIRIGkpVNWKKAIK 295
                                   ******************88662..14468******************9999888877777**********8888899*** PP

                                   HHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                          PALP 232 lldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                   +++ + + +v vsd+e++ a+++larreg+ +ep+saaa+a++ kl++ ++++e+++ vviltg
  gi|70607166|ref|YP_256036.1| 296 AMKSSKGFAVYVSDNEIITAQQELARREGVGAEPASAAAYAGYlKLLSSKKIEESEKSVVILTG 359
                                   **************************************************************98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.2e-06    0.0096       7      36 ..       2      27 ..       1      31 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.2e-06
                   Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                                  +C +Cg e  +l++    + ++CP+Cg+ +
  gi|70607166|ref|YP_256036.1|  2 KCLDCGYELSELRQ----DIITCPSCGGLL 27
                                  8*******999985....3677*****954 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   1.1e-05     0.033       6      27 ..       2      24 ..       1      26 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                   Prok-RING_1  6 kCpvCgkelkee.dDiVvCpeCg 27
                                  kC  Cg el+e  +Di++Cp Cg
  gi|70607166|ref|YP_256036.1|  2 KCLDCGYELSELrQDIITCPSCG 24
                                  8********98659********9 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     3e-05      0.09      13      30 ..       9      24 ..       9      27 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                  HHHHHCCSTB-EE-TTT- CS
                     zf-RING_7 13 vlselragdevvtCpeCG 30
                                  +lselr+   ++tCp+CG
  gi|70607166|ref|YP_256036.1|  9 ELSELRQD--IITCPSCG 24
                                  58999999..*******9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05      0.07      72     108 ..       2      40 ..       1      43 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                   EETTTS-EEE.CHHHHHS-TTTSSS.-EEEEESSSEEEE CS
                          HypA  72 rCreCgkefe.leekalrCpkCgsa.dveivsGeellvk 108
                                   +C +Cg+e + l+++ ++Cp+Cg+  +++i   +e+ ++
  gi|70607166|ref|YP_256036.1|   2 KCLDCGYELSeLRQDIITCPSCGGLlEIKIEFPSEFDLR 40 
                                   8********945545889*****9767777766676665 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5   0.00019      0.56       2      24 ..       2      24 ..       2      25 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                                  B-SSS--B----SSS----SSS- CS
                DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCG 24
                                  +C +Cg e s  ++d+i C  CG
  gi|70607166|ref|YP_256036.1|  2 KCLDCGYELSELRQDIITCPSCG 24
                                  699*******99999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2938.68
//
Query:       gi|70607167|ref|YP_256037.1|  [L=483]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.3e-128  428.5   0.0   2.7e-128  428.3   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.3   0.0  1.5e-132  2.7e-128       1     405 [.      10     420 ..      10     421 .. 0.94

  Alignments for each domain:
  == domain 1  score: 428.3 bits;  conditional E-value: 1.5e-132
                                   HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHH CS
                          UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklae 81 
                                   +e l++++++ +i++ev++elEia ++r+++ ++ pallF+nvk+  ++++v+tn+f++ + +  ++g ++leei  k+ +
  gi|70607167|ref|YP_256037.1|  10 IEFLRRNKNILEISDEVSTELEIAYLTREATYSKMPALLFTNVKNF-PEWKVITNIFNSLNVFYNIFGSNKLEEISGKFLD 89 
                                   6889**************************999**********866.89********************999999888766 PP

                                   HHHS..-..................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT CS
                          UbiD  82 llepkpp..................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetg 144
                                       + p                  ++p    ++k+p+  e     ++ +L+k+P+l++wp+D+G+y+t  ++it+dp+t+
  gi|70607167|ref|YP_256037.1|  90 EFLGQLPttffekirsfaemsklgkVFP----KSKKPVF-EL---HEEYSLDKFPALRTWPKDAGRYFTFSITITKDPDTE 162
                                   6655555677788877777765444444....4557888.44...579********************************* PP

                                   -EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--E CS
                          UbiD 145 krnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepve 225
                                   ++nl++yR+q+++++++++hwq+ k+g +  +k++kkg  ++pva++ GvdP++t++A+ p+P+gl++++faG+lr+e ve
  gi|70607167|ref|YP_256037.1| 163 VHNLSVYRIQLVNQKEAIVHWQAFKRGSITANKYLKKGITKVPVAIINGVDPITTFVAASPVPPGLDKYLFAGILRQEGVE 243
                                   *************999**********************99***************************************** PP

                                   EEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHH CS
                          UbiD 226 lvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgk 306
                                   +++ + +++ vpa+AE v+eG++d ++ + EGPfgdh+Gyy +++d +p++kV++i++R++pi+++t vgkpp eda++g 
  gi|70607167|ref|YP_256037.1| 244 VTRLD-NGILVPANAESVIEGYVDLNDVRLEGPFGDHLGYY-TPADFYPTLKVERIYVRDQPIFHATSVGKPPLEDAWIGR 322
                                   **995.69*********************************.88899******************999************* PP

                                   HHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHH CS
                          UbiD 307 alealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlw 387
                                   a+e+lflp+lk+ vpe++d++lpe g f+ + ++si+k+ypg+ k++m+alw+++q lsl K++ivvDedv+v+d++++l+
  gi|70607167|ref|YP_256037.1| 323 AVERLFLPFLKMIVPELVDMNLPEYGLFTGIGIFSIRKTYPGQGKRAMMALWGVGQ-LSLLKMIIVVDEDVNVHDINQILY 402
                                   ******************************************************88.************************ PP

                                   HHHHC--CCCCEEEECCC CS
                          UbiD 388 aiatrvdpdrDlviiegt 405
                                   ai+  vdp+rD++i++++
  gi|70607167|ref|YP_256037.1| 403 AISSTVDPKRDVLIVDNV 420
                                   ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2843.14
//
Query:       gi|70607168|ref|YP_256038.1|  [L=95]
Description: hypothetical protein Saci_1415 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 686.21
//
Query:       gi|70607169|ref|YP_256039.1|  [L=219]
Description: hypothetical protein Saci_1416 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   20.7   2.6    0.00037   20.1   2.6    1.5  1  Snf7      Snf7
  ------ inclusion threshold ------
       0.02   14.9   0.3      0.039   14.0   0.3    1.5  1  LOH1CR12  Tumour suppressor protein
       0.12   12.5   3.2        0.8    9.8   3.2    2.2  1  BLOC1S3   Biogenesis of lysosome-related organelles complex 1


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   2.6   6.2e-08   0.00037       3      87 ..      41     125 ..      39     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.2e-08
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkev 83 
                                   + +Lr+++ +ld ++++l+++   l +++ + + +++ +ra  +++++ +++k  +ql ++ + leqv+l +e+     ++
  gi|70607169|ref|YP_256039.1|  41 NYRLRTTISRLDVYISKLQERDRSLFEKVVESQISKDSARAAMYANEIAEIRKITKQLLTTEIALEQVQLRLETITEIGDI 121
                                   668**********************************************************************98776666 PP

                                   HHHH CS
                          Snf7  84 lnam 87 
                                   ++++
  gi|70607169|ref|YP_256039.1| 122 FTSL 125
                                   5555 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   6.6e-06     0.039      71     118 ..      73     120 ..      39     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-06
                      LOH1CR12  71 elrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelLd 118
                                   ++ +   + a ya+++++++++ +ql   +i le++   lEt+ e+ d
  gi|70607169|ref|YP_256039.1|  73 QISKDSARAAMYANEIAEIRKITKQLLTTEIALEQVQLRLETITEIGD 120
                                   22333456788**************************9****999855 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.2   0.00013       0.8      97     149 ..      57     116 ..       4     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00013
                       BLOC1S3  97 KLrEsNarLrkdvke.av......sqvysaaskelesvtsqLnksqsaiqnashsirlil 149
                                   KL+E++++L + v+e  +        +y +   e++++t+qL +++ a++++   + +i 
  gi|70607169|ref|YP_256039.1|  57 KLQERDRSLFEKVVEsQIskdsarAAMYANEIAEIRKITKQLLTTEIALEQVQLRLETIT 116
                                   899999999777765233221112579************************998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1478.98
//
Query:       gi|70607170|ref|YP_256040.1|  [L=792]
Description: phosphoenolpyruvate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   6.3e-114  380.6   1.6   9.9e-114  380.0   1.6    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.3e-82  276.4   0.0    4.3e-82  275.5   0.0    1.4  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.4e-29  101.6   0.3    4.9e-29   99.8   0.3    2.0  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.031   14.3   0.5       0.13   12.3   0.5    2.1  1  UPF0147          Uncharacterised protein family (UPF0147)
      0.067   13.4   0.9        2.1    8.5   0.0    3.1  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.0   1.6  2.8e-117  9.9e-114       2     322 ..      27     340 ..      26     345 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.0 bits;  conditional E-value: 2.8e-117
                        PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeele 82 
                                   e+vGGK+anL+ell+ +gi+vPpgf+it++afr+fl++ngl + i++++++      ++ +k+s+++++lil+ae+P++l+
  gi|70607170|ref|YP_256040.1|  27 EVVGGKAANLGELLS-LGIRVPPGFVITSNAFRYFLKYNGLYDVIKNIFEN-----DKDEKKVSEKVKSLILNAEIPPDLK 101
                                   68***********77.*******************************9998.....455689******************* PP

                        PPDK_N  83 eaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgldhe 163
                                   +ai++aye+l+k + ++e++vaVRSSat ED ++asfaGqqdt+Lnv+ +++++  ik+v+aSl nerAi+Yr++kg+dh 
  gi|70607170|ref|YP_256040.1| 102 KAISDAYEQLEK-ISNKEVLVAVRSSATVEDIEEASFAGQQDTFLNVS-KNDLFSYIKKVWASLHNERAISYRNAKGIDHL 180
                                   **********86.77777*****************************7.66699*************************** PP

                        PPDK_N 164 evalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigekeikivyd 244
                                   +  +avvvqkmvn++  a+GV+f+l+p+tG+ + v+i++ +GlGe+VV+G+vtpde+v++kst ki++k+i++k ik++yd
  gi|70607170|ref|YP_256040.1| 181 SAHMAVVVQKMVNAK--AAGVMFTLHPSTGDTNYVIIESNWGLGESVVGGKVTPDEIVIDKSTLKIVQKRISHKTIKVTYD 259
                                   ***************..**************************************************************** PP

                        PPDK_N 245 ekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaid...eeegklyllQaRpetrtsekkekkaae 322
                                   +++++++e +++e+e++++++++ee++eLa++a k+e+hy++pmdiE+aid   +  ++++llQaRpet +s+k++k ++e
  gi|70607170|ref|YP_256040.1| 260 KQMKKNVELKLDENEANSISITEEEAKELAKLALKVEQHYERPMDIEWAIDsdiKFPENIFLLQARPETYWSSKQVKPKEE 340
                                   ***99**********************************************99999*****************99987765 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.5   0.0   1.2e-85   4.3e-82       7     293 ..     475     777 ..     471     778 .. 0.94

  Alignments for each domain:
  == domain 1  score: 275.5 bits;  conditional E-value: 1.2e-85
                                   CCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTS.CC.HHHHHH..........HHHHHHHHHHHT CS
               PEP-utilizers_C   7 lktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmar.ee.lpteee..........qaeaykkvleam 75 
                                   +k++   +++++++k+++N+++p+ ++k+l+ +++GiGL+R+Ef+  ++ ++ + ++++          +ae +  v++a+
  gi|70607170|ref|YP_256040.1| 475 SKETILSLYPVTATKIYMNLGQPDVINKYLDLPFDGIGLMRIEFIVSEWiKYhPLYLIKngkpevfvdkLAEGISIVASAI 555
                                   6777788999**************************************9655577888899******************** PP

                                   TTSEEEEEXXXSSCC..GGSGGCHH.HH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCCC...EEEEEESSXXSH CS
               PEP-utilizers_C  76 ngrpvvvRtlDiggd..kelpelke.epeevNPmlGfRgirlglse..pelfetqlrAllrasaag...kleimlPmvasv 148
                                   ++rpvvvR+ D++++  k l  ++e ep e+NPmlG+Rg+++++s+  +  f+ +++A+ ++++++   ++++m+P+v++ 
  gi|70607170|ref|YP_256040.1| 556 YPRPVVVRFSDFKTNeyKRLYGGDEfEPDERNPMLGWRGVSRYISKqyEPAFRLEVKAIRKVREEMglkNVWVMFPFVRTS 636
                                   **************988999998652689**************9987799**************77788************ PP

                                   HHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHHH..SX CS
               PEP-utilizers_C 149 eeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevakl..yd 227
                                   +el++a +i+e +       g+++++++kv+iM Evps+++lad++ k vd+ SiG+NDL Q+tl+vdRd++ +a++  yd
  gi|70607170|ref|YP_256040.1| 637 WELKKAIEIMEDE-------GLRRNQEFKVWIMAEVPSVVILADEFSKIVDGYSIGSNDLAQLTLGVDRDSDLLARMgyYD 710
                                   **********998.......88889******************************************************** PP

                                   TTTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
               PEP-utilizers_C 228 plepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpaaraalaqve 293
                                   + +pavl++ik++i++a+++g++v+iCG++++ +p++ve+lv++G+d++S+++++v+ +r+++a+ve
  gi|70607170|ref|YP_256040.1| 711 ERDPAVLKGIKTLISVAHKYGKTVSICGQAPSvYPEVVEFLVRAGIDSISVNPDAVISVRRQVASVE 777
                                   ********************************9******************************9876 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.3   1.4e-32   4.9e-29       2      73 .]     378     449 ..     377     449 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.4e-32
                                   --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                 PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                   +++g+ILv+++t+p++++ ++ a+Givt++GGmtSHaAiv+relgiPaVvg+g+at ++k+g++it+D+++G
  gi|70607170|ref|YP_256040.1| 378 FNQGEILVTRMTDPDWVPLMKIASGIVTDEGGMTSHAAIVSRELGIPAVVGTGNATNSIKDGQQITIDAFRG 449
                                   6799*****************************************************************998 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   3.6e-05      0.13       5      58 ..      80     136 ..      76     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT...-TTS-HHHHHHHHHHHHHHHH CS
                       UPF0147   5 ikevielLeeiiedtsvPrniRraakeakekLk...dekeslavraataisiLdeis 58 
                                    k+v e  +++i + ++P   ++a+++a e+L+   +++  +avr++ +++ ++e s
  gi|70607170|ref|YP_256040.1|  80 EKKVSEKVKSLILNAEIPPDLKKAISDAYEQLEkisNKEVLVAVRSSATVEDIEEAS 136
                                   57899999******************9988876221566678999999999999976 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.095   3.4e+02      29      55 ..      92     121 ..      43     145 .. 0.66
   2 ?   -1.2   0.2      0.62   2.2e+03      62     112 ..     249     299 ..     234     301 .. 0.76
   3 ?    8.5   0.0   0.00059       2.1       1      16 [.     353     371 ..     353     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.095
                                   HHHHH.HHHHHHHHHHHHHHHHHHHHH..T CS
               PEP-utilisers_N  29 veael.erleeAlekvreelealaeka..l 55 
                                    +ae+   l++A+  + e+le++++k   +
  gi|70607170|ref|YP_256040.1|  92 LNAEIpPDLKKAISDAYEQLEKISNKEvlV 121
                                   55666347999*********9987554441 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.62
                                   HHHHHHHHHT-HHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHTT-HH CS
               PEP-utilisers_N  62 ifeahlmlleDpelleeveerIregglnaeaAveevveefaaqfealddey 112
                                   i + ++    D++++++ve +++e++ n  +  ee ++e+a+   +++++y
  gi|70607170|ref|YP_256040.1| 249 ISHKTIKVTYDKQMKKNVELKLDENEANSISITEEEAKELAKLALKVEQHY 299
                                   555666777899999999999999999988888888888888777766655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00059
                                   E-EEEE-SEEEEEEE...- CS
               PEP-utilisers_N   1 kGiaaspGiaiGkav...e 16 
                                   kG++aspGia+Gka    +
  gi|70607170|ref|YP_256040.1| 353 KGLPASPGIAYGKARvilD 371
                                   79************96551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 5194.40
//
Query:       gi|70607171|ref|YP_256041.1|  [L=93]
Description: hypothetical protein Saci_1418 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0041   17.3  31.7      0.011   15.9   6.6    4.0  4  zf-B_box     B-box zinc finger
  ------ inclusion threshold ------
      0.075   13.2  31.6        8.5    6.6  13.6    3.9  2  FYVE         FYVE zinc finger
       0.91    9.7  27.4       0.27   11.4   3.3    3.7  4  zf-AN1       AN1-like Zinc finger
        1.1    9.3  26.8    3.4e+02    1.3   8.0    3.8  2  DZR          Double zinc ribbon
        2.4    8.4  19.7      0.063   13.5   3.1    2.4  2  Prok-RING_2  Prokaryotic RING finger family 2
        9.2    6.5  28.2        9.3    6.5  13.0    2.4  2  FYVE_2       FYVE-type zinc finger


Domain annotation for each model (and alignments):
>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   3.2   0.00024      0.71       4      27 ..      12      35 ..       9      36 .. 0.91
   2 !   11.5   3.0   8.3e-05      0.25      16      29 ..      43      56 ..      40      64 .. 0.84
   3 !   15.9   6.6   3.7e-06     0.011       5      29 ..      52      76 ..      50      83 .. 0.90
   4 ?    1.4   0.7      0.12   3.5e+02      16      21 ..      85      90 ..      79      93 .] 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                      zf-B_box  4 tkCpeHknkpatlfCedCqqplCe 27
                                   kC++++++  t+ C+ C+  +C+
  gi|70607171|ref|YP_256041.1| 12 LKCEICEEEIGTFECKICGRNVCK 35
                                  69*****9999************7 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.3e-05
                      zf-B_box 16 lfCedCqqplCeeC 29
                                    C++C+  lCe C
  gi|70607171|ref|YP_256041.1| 43 NICKVCEMSLCEVC 56
                                  57************ PP

  == domain 3  score: 15.9 bits;  conditional E-value: 3.7e-06
                      zf-B_box  5 kCpeHknkpatlfCedCqqplCeeC 29
                                   C+ +++k  +  Ce+C++ +Ce+C
  gi|70607171|ref|YP_256041.1| 52 LCEVCGEKLSIGKCEKCGKIICEKC 76
                                  7*****99999************** PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.12
                      zf-B_box 16 lfCedC 21
                                   +C++C
  gi|70607171|ref|YP_256041.1| 85 RYCKNC 90
                                  578888 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  13.6    0.0051        15       9      65 ..      11      59 ..       8      64 .. 0.69
   2 ?    6.6  13.6    0.0028       8.5       9      42 ..      50      79 ..      49      93 .] 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0051
                                  -SB-TTT--B--SSS--EE-TTT--EE-STTS-EEE.EEGGGTEEEEEEE-HHHHHH CS
                          FYVE  9 vkkCeiCakkFsllrrrhhCrlCGkvvCekCssklvallekeaeeksvrvCkeClae 65
                                  + kCeiC+++  +      C++CG+ vC+   ++  +      ++ ++ +C+ C ++
  gi|70607171|ref|YP_256041.1| 11 SLKCEICEEEIGT----FECKICGRNVCKLDFNEEKNIC----KVCEMSLCEVCGEK 59
                                  5689999999955....4899999999976666655444....55666666666655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0028
                                  -SB-TTT--B--SSS--EE-TTT--EE-STTS-E CS
                          FYVE  9 vkkCeiCakkFsllrrrhhCrlCGkvvCekCssk 42
                                  ++ Ce C +k s+      C  CGk++CekC   
  gi|70607171|ref|YP_256041.1| 50 MSLCEVCGEKLSI----GKCEKCGKIICEKCVGY 79
                                  6789999999999....78************854 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3   9.1e-05      0.27       1      25 [.      14      35 ..      11      42 .. 0.90
   2 ?    1.3   1.9      0.14     4e+02      15      25 ..      44      54 ..      35      57 .. 0.79
   3 ?    6.4  10.7    0.0033       9.7       1      27 [.      53      76 ..      45      81 .. 0.87
   4 ?   -1.2   0.3      0.79   2.4e+03      23      26 ..      86      89 ..      83      92 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                        zf-AN1  1 CsfksCkkkdflpfkCryCgkvFCl 25
                                  C++  C +++   f+C+ Cg++ C+
  gi|70607171|ref|YP_256041.1| 14 CEI--CEEEIG-TFECKICGRNVCK 35
                                  664..999997.7***********7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.14
                        zf-AN1 15 kCryCgkvFCl 25
                                   C+ C+ + C+
  gi|70607171|ref|YP_256041.1| 44 ICKVCEMSLCE 54
                                  69999999996 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0033
                        zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkH 27
                                  C++  C++k++ ++kC++Cgk  C+k+
  gi|70607171|ref|YP_256041.1| 53 CEV--CGEKLS-IGKCEKCGKIICEKC 76
                                  664..999997.9***********997 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.79
                        zf-AN1 23 FClk 26
                                  +C++
  gi|70607171|ref|YP_256041.1| 86 YCKN 89
                                  4433 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   8.0      0.12   3.4e+02      15      48 ..      14      48 ..       8      51 .. 0.54
   2 ?   -1.2  23.3      0.72   2.2e+03       3      48 ..      28      90 ..      26      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                           DZR 15 CseCgtklkavaaedrCpsCgek.v....dpearfCpeC 48
                                  C+ C +++        C  Cg+  +    ++e+++C+ C
  gi|70607171|ref|YP_256041.1| 14 CEICEEEIG----TFECKICGRNvCkldfNEEKNICKVC 48
                                  666666665....45566666554411113344457777 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.72
                           DZR  3 qCgee.....lppdarfCseCgtklkavaa............edrCpsCgekvdpearfCpeC 48
                                   Cg++      +++++ C+ C  +l +v              ++ C +C   +d   r+C++C
  gi|70607171|ref|YP_256041.1| 28 ICGRNvckldFNEEKNICKVCEMSLCEVCGeklsigkcekcgKIICEKCVGYNDGVRRYCKNC 90
                                  555555555566777777777777766555677767789999999999999999999999999 PP

>> Prok-RING_2  Prokaryotic RING finger family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.1   2.1e-05     0.063      10      47 ..      14      48 ..       9      52 .. 0.81
   2 ?    1.1   8.4      0.15   4.5e+02      12      47 ..      52      90 ..      49      91 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                   Prok-RING_2 10 cdlcatahplaglrqcvlcGrWacdacWkdeyytcksc 47
                                  c++c+      g   c +cGr  c+  +++e  +ck c
  gi|70607171|ref|YP_256041.1| 14 CEICEEE---IGTFECKICGRNVCKLDFNEEKNICKVC 48
                                  6666543...35568*********************** PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                   Prok-RING_2 12 lcatahplaglrqcvlcGrWacdac..Wkdey.ytcksc 47
                                  lc+  +    + +c  cG+  c+ c  ++d     ck c
  gi|70607171|ref|YP_256041.1| 52 LCEVCGEKLSIGKCEKCGKIICEKCvgYNDGVrRYCKNC 90
                                  5555566666678999********943344431346666 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  13.0    0.0031       9.3      36      88 ..       8      59 ..       1      64 [. 0.74
   2 ?    6.4   7.4    0.0035        10      73     100 ..      64      90 ..      58      93 .] 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0031
                        FYVE_2 36 lekekskrellgnqaklgethCilCleef.kllvnsk.rqCldCklnvCkkCsve 88
                                  l + ++k+e+  +  ++g+ +C  C ++  kl  n++ + C+ C++ +C+ C+ +
  gi|70607171|ref|YP_256041.1|  8 L-ESSLKCEICEE--EIGTFECKICGRNVcKLDFNEEkNICKVCEMSLCEVCGEK 59
                                  4.45667887776..8999999999876526655554389************975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
                        FYVE_2  73 qCldCklnvCkkCsvenkkekvwlCkiC 100
                                   +C++C + +C+kC  +n   + + Ck+C
  gi|70607171|ref|YP_256041.1|  64 KCEKCGKIICEKCVGYNDGVRRY-CKNC 90 
                                   7***************9999987.8988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 563.93
//
Query:       gi|70607172|ref|YP_256042.1|  [L=358]
Description: inositol-1-phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-29  102.5   0.1    3.3e-29  101.3   0.0    1.6  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
     0.0085   15.5   0.0      0.075   12.4   0.0    2.3  2  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.73   6.6e+03      70      83 ..     100     113 ..      54     127 .. 0.54
   2 !  101.3   0.0   3.6e-33   3.3e-29       1     108 [.     191     300 ..     191     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.73
                                   EEEEE-GGGTTEEE CS
                Inos-1-P_synth  70 vvikYvpylgDsKv 83 
                                   ++i+ +++++D K+
  gi|70607172|ref|YP_256042.1| 100 HMIDVFNPVDDAKI 113
                                   34445555555554 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 3.6e-33
                                   SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GGG CS
                Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpyl 78 
                                   G+T+l+++L++l++ rg+kv+++++lN++Gn+D++n+++eer+++K+isK+++v+++++++ +l+ +  ++i   +Y+p+l
  gi|70607172|ref|YP_256042.1| 191 GATILHRTLTSLFRLRGVKVEETYQLNVGGNTDFLNMKTEERLYTKRISKTKAVTSTLEND-YLEREGRIRIgpsDYIPFL 270
                                   9*********************************************************985.55668999*********** PP

                                   TTEEEEEEEEEEEEGGGEEEEEEEEEEEEH CS
                Inos-1-P_synth  79 gDsKvaldeieseiflggkntielkleceD 108
                                   g++Kva++  ++++f g+++++e+ le++D
  gi|70607172|ref|YP_256042.1| 271 GNTKVAYIYTKGSGFAGMPVKVEAMLEVDD 300
                                   ***************************999 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.038   3.4e+02      64      98 ..      33      68 ..       9      86 .. 0.73
   2 !   12.4   0.0   8.4e-06     0.075     204     252 ..     138     194 ..     105     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.038
                                  xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5 64 vpikdllplvnpndl.vfgGwDisslnlaeamerak 98
                                    i  ++  ++++d+ v+ ++Dis+ ++ + +++a 
  gi|70607172|ref|YP_256042.1| 33 GLITPVIGKYKITDIeVVAAFDISKNKVGKDITEAI 68
                                  35677888999999988999****999998888775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.4e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.....x RF
                 NAD_binding_5 204 spstiyavAailegvpyingsPqntlvpg...lvelAekkgvfiaGdDfKt.....l 252
                                    +s  ya Aa++++v++in  P     +       l +kk++++aGdD+K      +
  gi|70607172|ref|YP_256042.1| 138 RASRTYARAALEANVAFINAIPVFIASDPkkeFPTLFQKKNLPLAGDDIKGqvgatI 194
                                   47999*****************9888554111556889************8444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2186.58
//
Query:       gi|70607173|ref|YP_256043.1|  [L=92]
Description: acylphosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-27   94.4   0.0    4.5e-27   94.3   0.0    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   2.5e-31   4.5e-27       2      84 ..       8      90 ..       7      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.5e-31
               Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFe 84
                                   ++v+G+VQgvg+R+f++ +A +lg+kGy++Nl+dgsVei+aeg ee++ k+l+++k+gpp ++v++v+v+  ++++ef +F+
  gi|70607173|ref|YP_256043.1|  8 YVIVYGIVQGVGYRRFIQIHAARLGIKGYAKNLPDGSVEILAEGYEEALYKLLDQIKRGPPLSKVEKVDVKFDDYTGEFASFD 90
                                  589******************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 649.84
//
Query:       gi|70607174|ref|YP_256044.1|  [L=424]
Description: tryptophan synthase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-41  141.4   0.0    4.9e-41  141.1   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   2.7e-45   4.9e-41       5     294 .]      73     405 ..      71     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.7e-45
                                   SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                    +pTPl+r++rl++ l++p  +++K+E+ +ptgS+K+++a    + ++++    + +e+++G++g a+A+aa+++ l++ti
  gi|70607174|ref|YP_256044.1|  73 GRPTPLIRARRLEEYLKTParIYFKYEGATPTGSHKINTAIPQAYFAANEGVSHVTTETGAGQWGTAVALAASMYDLESTI 153
                                   58********************************************666636667777777******************** PP

                                   E...EETTS-HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHH CS
                          PALP  84 v...vpadaspekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqfdnptviegy 143
                                   +   v+   +p ++  ++l+Ga+v+ +                  +g+   a++ a e+a e +++ ++  +    vi+ +
  gi|70607174|ref|YP_256044.1| 154 FmvrVSYEHKPMRRTIMELYGAKVHASptdltefgrkilkedsrhPGSLGIAMSEAIEYALE-NNYRYLVGSVLDVVILHQ 233
                                   *6665666669****************77777777777777777666688888888888888.55555555557888888* PP

                                   HTHHHHHH...HHTTTTEEEEEEE-SSSHHHHHHHHHHHH.HSTT-EEEEEEECTTCGGTTCCS..S.SS..B........ CS
                          PALP 144 gtiglEil...eqlggkpdavvvpvGgGgliaGiaaglke.rrpdvrvigvepegsdalarslragrrvtvpvs....... 213
                                   + ig+E +   e lg++pd+++ +vGgG++++G+  ++   +r++ + i+v +++++++ ++     ++   +        
  gi|70607174|ref|YP_256044.1| 234 SIIGMESInqlEALGEEPDTIIGCVGGGSNFGGFTYPFIGtKRGK-KYIAVGSSEVPKFSKGK----YEYDFPDsagllpl 309
                                   *******86668888************************955555.*****999999999999....33333335678999 PP

                                   .............SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH..HHHHH CS
                          PALP 214 .............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal..klrea 279
                                                +    gl+ + +++    l++++v e  + ++ee++  ++ + +++gi++ p sa+a+ a+  +++ea
  gi|70607174|ref|YP_256044.1| 310 vkmitlgkdfippPIYSGGLRYHGVAPTLSLLVKEKVVEWREYTEEEIYNSAKIFMKTQGIIPAPESAHAIKAAidEALEA 390
                                   9999****8888888888888887777777799**************************************9999****** PP

                                   HCCTTCEEEEEEE-B CS
                          PALP 280 gelkegdrvvviltg 294
                                   ++ +++++++v ++g
  gi|70607174|ref|YP_256044.1| 391 KKTNDKKVILVNVSG 405
                                   ******9**999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3086.27
//
Query:       gi|70607175|ref|YP_256045.1|  [L=245]
Description: tryptophan synthase subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-34  118.2   0.4    3.3e-34  117.9   0.4    1.0  1  Trp_syntA       Tryptophan synthase alpha chain
    1.6e-05   24.5   0.3      3e-05   23.6   0.3    1.4  1  His_biosynth    Histidine biosynthesis protein
      0.008   15.7   0.2      0.016   14.7   0.2    1.5  1  PcrB            PcrB family
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.023   14.0   0.0    1.4  1  TMP-TENI        Thiamine monophosphate synthase
      0.015   14.7   0.1      0.052   12.9   0.1    1.8  2  NMO             Nitronate monooxygenase
      0.017   14.1   0.1      0.025   13.6   0.1    1.2  1  FMN_dh          FMN-dependent dehydrogenase
      0.054   12.9   0.0      0.077   12.4   0.0    1.4  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.11   11.8   0.3       0.14   11.5   0.0    1.4  2  ThiG            Thiazole biosynthesis protein ThiG
       0.15   11.2   0.2       0.31   10.2   0.2    1.5  1  IGPS            Indole-3-glycerol phosphate synthase


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.4   1.6e-37   3.3e-34       9     238 ..       3     228 ..       1     242 [. 0.89

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 1.6e-37
                                   B-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS- CS
                     Trp_syntA   9 raafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevP 89 
                                   ++ +v+y+t+g+p+++++++ ++++e+ g+d++E+G+p      dGPvI+++ ++      ++++  e++ ev+ ++ ++P
  gi|70607175|ref|YP_256045.1|   3 KKYLVAYMTLGYPNVNDFYKFIDNIEDFGVDILEIGIPPKYAKYDGPVIRKTYKIV---SNNIKNYYEILYEVK-QRIKIP 79 
                                   789***********************************************999875...45789999******9.99**** PP

                                   EEEEE-CHH.HCCC-HHHHCHHHHHCTEEEEEETTSB...CCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S- CS
                     Trp_syntA  90 ivlltylnl.vlsygeerflaelkeagvdglivpDlP...leeaeelveaakkkglelvflvapttsderlkevveqaegf 166
                                   +v+ltyl+  v + g   fl +lke  vdg++ pDl    ++e e++v+++k++g+++v  +ap  +d+ + + ++ ++ f
  gi|70607175|ref|YP_256045.1|  80 VVILTYLEEyVDKLG--DFLLKLKESRVDGVLFPDLLidyVDEYEKYVNLIKNEGIKTVLFTAPLMPDDLIIKASKLTDLF 158
                                   *******86144555..8******************722256889999********************************* PP

                                   EEEESTTC-SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTT CS
                     Trp_syntA 167 vYvvsraGvTgaenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeae 238
                                    Y+  +  +Tg+   +  ++d+l++r++++ +  + vGFG+++ e++k+++  +adG+ vG  l+++++++  
  gi|70607175|ref|YP_256045.1| 159 LYYG-VRPTTGVV--IPISIDSLINRIRTMVQSKLVVGFGLNSIEDIKKAMsVGADGIAVGTSLIEEVDKNGV 228
                                   **85.55688885..6778*****************************999889**************98654 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.3   1.5e-08     3e-05      63     109 ..     177     223 ..     173     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-08
                                   HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                  His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                   +l+++i+  v+ ++ vG G +s+ed++++++ gad + +gt+ +++ 
  gi|70607175|ref|YP_256045.1| 177 SLINRIRTMVQSKLVVGFGLNSIEDIKKAMSVGADGIAVGTSLIEEV 223
                                   6899**************************************99876 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2     8e-06     0.016     162     216 ..     167     224 ..     147     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8e-06
                                   TTSSS-H..HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHH CS
                          PcrB 162 sGaledv..eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekde 216
                                    G+  ++  + +i+  + + +++l+vG G++s E+ k+ +   AD i vG+ + e+ +
  gi|70607175|ref|YP_256045.1| 167 TGVVIPIsiDSLINRIRTMVQSKLVVGFGLNSIEDIKKAMSVgADGIAVGTSLIEEVD 224
                                   566555544788888899999*******************999*******98877764 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.023      86     126 ..     179     219 ..     173     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                      TMP-TENI  86 vaearellgpdliiGlSvhsleeaeeaealgadYigvGpif 126
                                   ++++r +++++l++G   +s+e++++a + gad i+vG+  
  gi|70607175|ref|YP_256045.1| 179 INRIRTMVQSKLVVGFGLNSIEDIKKAMSVGADGIAVGTSL 219
                                   6889**********************************865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.5   9.9e+02      98     134 ..     117     153 ..     109     163 .. 0.81
   2 ?   12.9   0.1   2.6e-05     0.052     183     226 ..     177     220 ..     161     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.5
                           NMO  98 egvrfyrkvevvldekvevvsfgfglpteevvarlke 134
                                   + +++ + v+++ +e+ + v f++ l + +++++ ++
  gi|70607175|ref|YP_256045.1| 117 YVDEYEKYVNLIKNEGIKTVLFTAPLMPDDLIIKASK 153
                                   5566788899999999******999999999887665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.6e-05
                           NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                   +L+++++  v+  ++   G++  ++++ a+++GA g+++gt ++
  gi|70607175|ref|YP_256045.1| 177 SLINRIRTMVQSKLVVGFGLNSIEDIKKAMSVGADGIAVGTSLI 220
                                   688888888888888888***********************998 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.3e-05     0.025     258     323 ..     175     239 ..     170     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                   HHCH.HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHH CS
                        FMN_dh 258 idvL.peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilr 323
                                   id L  +i+  v+   +++v  G  + +D+ kA+ +GAd++++G  ++  +  +G +G+ ++++ lr
  gi|70607175|ref|YP_256045.1| 175 IDSLiNRIRTMVQ--SKLVVGFGLNSIEDIKKAMSVGADGIAVGTSLIEEVDKNGVNGALELIKKLR 239
                                   5555345566665..4455555888889999999999999999999999988888888888888876 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.8e-05     0.077      90     197 ..     117     219 ..      60     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                                   T-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHH.HHHHHHHHHHHHT---EE CS
                Ribul_P_3_epim  90 alehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevle.kikkvrklidekeldlki 169
                                    +++ ++ ++ ik+ G+k+ l   p +p + + +  +  dl l   v P  g    ip  ++  i+++r+++++     k+
  gi|70607175|ref|YP_256045.1| 117 YVDEYEKYVNLIKNEGIKTVLFTAPLMPDDLIIKASKLTDLFLYYGVRPTTGV--VIPISIDsLINRIRTMVQS-----KL 190
                                   56788999*****************************************9874..5665555157899999998.....88 PP

                                   EEESS--T.TTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 170 evDGGvkl.dnieqiaeagadvlVagsav 197
                                    v  G++  + i+++++ gad + +g+ +
  gi|70607175|ref|YP_256045.1| 191 VVGFGLNSiEDIKKAMSVGADGIAVGTSL 219
                                   89889975389999999999999999875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       3.6   7.2e+03     166     180 ..      68      82 ..      59      82 .. 0.72
   2 ?   11.5   0.0   6.9e-05      0.14     161     212 ..     173     224 ..      98     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.6
                                   HHHHHHHH-SS-BEE CS
                          ThiG 166 alkiiieeakvPviv 180
                                    l  + +++k+Pv++
  gi|70607175|ref|YP_256045.1|  68 ILYEVKQRIKIPVVI 82 
                                   456678889999996 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.9e-05
                                   -S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                          ThiG 161 llnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                   ++    ++ i+  ++  ++v  G+ s +d+ +am +Gad++ + t++ e  d
  gi|70607175|ref|YP_256045.1| 173 ISIDSLINRIRTMVQSKLVVGFGLNSIEDIKKAMSVGADGIAVGTSLIEEVD 224
                                   444456666777778889*************************999876655 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00015      0.31     203     247 ..     183     225 ..     173     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                   CHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTH CS
                          IGPS 203 aklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedv 247
                                   + +v+  + lv   G+++ ed++k  ++g++++ vG+sl+++ d+
  gi|70607175|ref|YP_256045.1| 183 RTMVQ--SKLVVGFGLNSIEDIKKAMSVGADGIAVGTSLIEEVDK 225
                                   44444..5677788**************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1797.92
//
Query:       gi|70607176|ref|YP_256046.1|  [L=342]
Description: anthranilate phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-74  249.6   0.0    4.6e-74  249.2   0.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    3.5e-16   58.8   0.4    7.2e-16   57.8   0.4    1.6  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.2   0.0   5.2e-78   4.6e-74       3     249 ..      68     314 ..      66     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 249.2 bits;  conditional E-value: 5.2e-78
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHS CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfape 83 
                                   +++D++gTGGdg  t+N+St +ai+++ +  +vakhgnrsvs ksGsaDvLealg+n++  pe ++kl++e++++flfa+ 
  gi|70607176|ref|YP_256046.1|  68 EALDTAGTGGDGLGTINVSTITAIILSQL-FPVAKHGNRSVSGKSGSADVLEALGYNINIAPELANKLIKENNFVFLFAQI 147
                                   689***********************987.9************************************************** PP

                                   SSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHHHH CS
               Glycos_transf_3  84 yhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakttv 163
                                   yh+amk+va+vr++lgirT+fnlLGPL+npa  ++ql+g +s +++  +a++++ l  +++++ hg  G de+s+ + ttv
  gi|70607176|ref|YP_256046.1| 148 YHPAMKNVANVRKTLGIRTIFNLLGPLTNPAGTRYQLIGLFSSKVMDIVAKAASLLDYKKVFIYHGePGIDEISPYGYTTV 228
                                   ********************************************************************************* PP

                                   HHHHTTEEEEEEEEEGSSTSSSEE.ESHHHHSSHHH.HHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHH CS
               Glycos_transf_3 164 aelkdgeiteytlepedfglkrae.lealeggepke.naeilkavlegkksaakrdlvllnagaalvlagkadslkegvak 242
                                   +e+++g+i++y l+ +dfglkr+   e++   +++e +++il++v+  +++ + rd + +n+++ l l gka++ ++g + 
  gi|70607176|ref|YP_256046.1| 229 YEITNGKIQQYRLHYSDFGLKRQIpIEKITATSANEsAIKILRGVMGIDSD-I-RDFIGINVAVGLKLIGKAEDARDGFEY 307
                                   *********************985279999999865167999999666655.5.9*************************9 PP

                                   HHHHHHT CS
               Glycos_transf_3 243 aeevids 249
                                   a ++++s
  gi|70607176|ref|YP_256046.1| 308 AMQLMES 314
                                   9998875 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.4   8.1e-20   7.2e-16       8      62 ..       6      60 ..       1      61 [. 0.92

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 8.1e-20
                                  HTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
               Glycos_trans_3N  8 rdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmres 62
                                   ++ +L+ e+ +++ ++++kge++++q++A+L++l +kGe+ eEi+++a+Amr+ 
  gi|70607176|ref|YP_256046.1|  6 FEKRDLSTEDSEAIANALMKGEIPEIQVSALLTSLAMKGESFEEIVGFARAMRNN 60
                                  4558*************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2296.30
//
Query:       gi|70607177|ref|YP_256047.1|  [L=199]
Description: anthranilate isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-28   97.3   0.0    1.1e-27   97.1   0.0    1.0  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   6.2e-32   1.1e-27       1     193 [.       4     190 ..       4     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 6.2e-32
                                   TCE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--EEEEEESSS-HHHHHHHHHHCTECEEEE-CGG CS
                          PRAI   1 akicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpaklVGVfvNqpieevlriaqelgldvvQLHGde 81 
                                   +k cg+++ +d++ a k gad++g++++ +s+r v++  + +++++v+  +V V v     +v++ +++ + d++Q+H+  
  gi|70607177|ref|YP_256047.1|   4 VKFCGIASLEDAILAEKLGADFIGFVTDTASPRFVKKDFIGFVRRYVEIPTVEVIVKG---NVSESIDKTKADLIQIHRVL 81 
                                   589*********************************************99*****976...56788999999********* PP

                                   .-HHHHHHHHHHS-TTSEEEEEEE-SSS--S-SSTT-.SEEEEESSS-SSSXXXXGGGGTTSXX.TTEEEESSXXTTTHHH CS
                          PRAI  82 deqeyeellktelpvikalkvaesvdevkearradhv.dllllDsgaGGtGelldwsliskllkslkviLAGGLtpeNvae 161
                                   + +e+ e      ++   l+v++s  +++++r    +   +l+Ds+   +G +++++l  ++ k+ ++ ++GG++p+N+ +
  gi|70607177|ref|YP_256047.1|  82 TRRELDEIHM--YRKKVILYVPSSDMYQEYFRSVISMgFNVLVDSEI--KGSKVNLDLARGWAKEYEIGIGGGISPDNLHD 158
                                   9999999999..777777888885569*********99*******65..5999999999****99**************** PP

                                   HHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                          PRAI 162 aiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                   ++   ++ ++DvssG+E++ G+kD  k+ k+++
  gi|70607177|ref|YP_256047.1| 159 FLS-INPKWIDVSSGIEKYkGKKDPSKMLKIIE 190
                                   ***.************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1353.30
//
Query:       gi|70607178|ref|YP_256048.1|  [L=432]
Description: anthranilate synthase component I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-93  310.6   0.0      1e-92  310.4   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme
    4.9e-23   81.9   0.0    2.4e-22   79.7   0.0    2.1  2  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.4   0.0   1.1e-96     1e-92       2     258 .]     169     422 ..     168     422 .. 0.99

  Alignments for each domain:
  == domain 1  score: 310.4 bits;  conditional E-value: 1.1e-96
                                   HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSE CS
               Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrr 82 
                                   +e+++  v+++ ++ir+g +++vvlsr +k+    + d +++y++lr+ np+py+f++++ d+e++g+SPE+l++v+gg  
  gi|70607178|ref|YP_256048.1| 169 KEEFEGIVKEALDYIRRGYIFQVVLSRFYKYI--YKGDLMRFYNNLRKVNPSPYMFYMKFMDREIIGSSPETLFSVQGG-V 246
                                   799*****************************..88999**************************************77.* PP

                                   EEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEE CS
               Chorismate_bind  83 ietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegel 163
                                   +et+piaG+r+rg+t eed +le++ll++eKeraEhlm+vdl+rnd+gkv+ +gsvkvpe+++ve+y+ v+h+vs++ g+l
  gi|70607178|ref|YP_256048.1| 247 VETYPIAGSRPRGRTLEEDLELERDLLSSEKERAEHLMLVDLARNDIGKVCYMGSVKVPEFMYVEKYAYVQHIVSKVVGTL 327
                                   ********************************************************************************* PP

                                   STT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEET CS
               Chorismate_bind 164 kedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIva 244
                                   +++++++d+lk++fP+g+v+GaPk  am++i+ +E+++Rg+YaG vg+++++g+ae+a++IR+a+v+++++r++aGaGIv 
  gi|70607178|ref|YP_256048.1| 328 RKNLTSFDVLKSTFPAGTVSGAPKPMAMNLIELFEHYKRGPYAGGVGFFSSNGDAEFAITIRSAFVNKDTIRIQAGAGIVY 408
                                   ******************************************************************9999*********** PP

                                   T--HHHHHHHHHHH CS
               Chorismate_bind 245 dSdpeaEyeEtlaK 258
                                   dS pe Ey Et++K
  gi|70607178|ref|YP_256048.1| 409 DSVPEMEYFETEHK 422
                                   ************99 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   2.7e-26   2.4e-22       4     142 .]      11     142 ..       9     142 .. 0.87
   2 ?   -1.8   0.0      0.36   3.2e+03      35      54 ..     231     250 ..     195     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 2.7e-26
                 Anth_synt_I_N   4 tplsvylklaeee.hkflLeSaeneggegrySfigldpflelkskngevevegpegeeleeeepldalrellerfrsaeds 83 
                                   +p +v+ +++++e  ++lLeS+++ + ++ryS+ig+  ++ +   +++++        +e ++p ++l e+l+++ s +++
  gi|70607178|ref|YP_256048.1|  11 QPNEVFSCIKKDEdVAVLLESGSGPQYKSRYSMIGWGRKGYISLYKNKSSGDI----VKEFYDPIEVLSEFLNKAPSLNVP 87 
                                   7899*******999********977777**********888775555555444....567778*************77554 PP

                 Anth_synt_I_N  84 eptelpfvgGlvGylgYDlvreieklpksakddlnlpdarlilydtlivfDhkerrlyl 142
                                        +f gG++Gy+gYD vr++e +++ +++  ++p a++++++++iv+Dh e+++yl
  gi|70607178|ref|YP_256048.1|  88 G----KFKGGIFGYMGYDGVRYWETIKDLKPEPEKWPYAEFFIPQNIIVYDHAEGKVYL 142
                                   3....5*********************99999888**********************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                 Anth_synt_I_N  35 figldpflelkskngeveve 54 
                                   +ig +p   + +++g ve++
  gi|70607178|ref|YP_256048.1| 231 IIGSSPETLFSVQGGVVETY 250
                                   45555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3315.25
//
Query:       gi|70607179|ref|YP_256049.1|  [L=189]
Description: anthranilate synthase component II [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-46  156.8   0.0    5.9e-46  156.6   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    1.3e-11   44.7   0.0    2.1e-11   44.0   0.0    1.4  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.049   13.5   0.0      0.065   13.1   0.0    1.5  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.6   0.0   9.9e-50   5.9e-46       2     189 ..       2     188 ..       1     189 [] 0.93

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 9.9e-50
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEET CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPiLGIC 78 
                                   +iDnyds+++n+++ + elg +  ++++d+  ++   ++ npd i++s+Gpgsp     ++   ++ik++   +iPi+G+C
  gi|70607179|ref|YP_256049.1|   2 IIDNYDSFVYNIAQLIGELGSYPIIIRNDEITLKGV-ERLNPDRIVISPGPGSPDkkedIGIVNDVIKYLGR-RIPIFGVC 80 
                                   79***************************7666555.589***************78878888888888666.******** PP

                                   HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTT.CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEE CS
                        GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddet.allyglknevierhrHryevnpkelepaglevtakseddeelmeii 158
                                   LG+Q+++  fg+ + ++k   +hg+ +++ + ++  l+ g +n+++++++H++++++   +++ l++ a se+d+e+m++ 
  gi|70607179|ref|YP_256049.1|  81 LGHQAIGFTFGAVIRRAK-TIYHGKISKIVHSSSsTLYDGIPNRFEATRYHSLVIDN---VKEPLVIDAYSEEDKEIMGVH 157
                                   ************999999.99********99888789999*****************...********************* PP

                                   EETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                        GATase 159 ekknpfvgvQFHPEststpegpellfnflik 189
                                   + +++++gvQFHPEs+ t  g +++ nfl k
  gi|70607179|ref|YP_256049.1| 158 HVEYRIYGVQFHPESVGTGYGRRIFYNFLNK 188
                                   ***************************9865 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   3.5e-15   2.1e-11      85     216 .]      53     171 ..      24     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.5e-15
                 Peptidase_C26  85 eadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgs 165
                                     d++ d+  +  + + l r++Pi+g+C+G+q +  ++G  +  +++    +  h      + s+ v+  +++l+  + + 
  gi|70607179|ref|YP_256049.1|  53 SPDKKEDIGIVNDVIKYLGRRIPIFGVCLGHQAIGFTFGAVIR-RAK----TIYH-----GKISKIVHSSSSTLYDGIPN- 122
                                   4555555555666667899***************555553332.222....3333.....34567777777777766665. PP

                 Peptidase_C26 166 eeievnslHhqaikelaeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                    ++e + +H+  i+++ e l + A +e D  i  +++ e  + ++gvQ+HPE
  gi|70607179|ref|YP_256049.1| 123 -RFEATRYHSLVIDNVKEPLVIDAYSEeDKEIMGVHHVE--YRIYGVQFHPE 171
                                   .*************************9898887777777..77********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.065     118     174 ..     117     175 ..      29     189 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                                   ETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEE.ET.TEEEESS-GGGSTT CS
                           SNO 118 fknliekftavfiraPvieeilddeavkvlyeldgeivvak.qk.kilatsfhPelaed 174
                                   + ++ + f a+   + vi+++ ++ +++  +e d ei++++  + +i ++ fhPe    
  gi|70607179|ref|YP_256049.1| 117 YDGIPNRFEATRYHSLVIDNVKEPLVIDAYSEEDKEIMGVHhVEyRIYGVQFHPESVGT 175
                                   4556699999999***************************9644699********7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1303.56
//
Query:       gi|70607180|ref|YP_256050.1|  [L=248]
Description: indole-3-glycerol-phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-75  251.6   0.5      7e-75  251.5   0.5    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
    0.00013   21.5   0.4     0.0059   16.1   0.0    2.2  2  His_biosynth  Histidine biosynthesis protein
      0.001   18.2   0.0          1    8.3   0.0    2.1  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.065   13.0   0.1       0.56   10.0   0.0    2.0  2  QRPTase_C     Quinolinate phosphoribosyl transferase, C-termi


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.5   0.5   1.6e-78     7e-75      30     247 ..      26     243 ..       1     247 [. 0.90

  Alignments for each domain:
  == domain 1  score: 251.5 bits;  conditional E-value: 1.6e-78
                                   -SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH- CS
                          IGPS  30 lakpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqav 108
                                   + +p  s+++++ ++  +    +iaE+K+ SPs   i+ d+++ e+ k +e+ gA+ iSVLteek+F+Gs++dL+ v+++v
  gi|70607180|ref|YP_256050.1|  26 RDRPIFSLKKSIISAknSGLNPIIAEYKRRSPSG--INVDINIIEYVKFMENNGATGISVLTEEKFFNGSYNDLELVAKNV 104
                                   46677788887766644556789**********9..********************************************* PP

                                   SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEET CS
                          IGPS 109 slpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnL 189
                                   +lp+l+KdF+++e+qi+ a+++gad+iLLi+k+l+++el +l+++aks+gle++vE++dee+l+ al+ + ++iGvN RnL
  gi|70607180|ref|YP_256050.1| 105 KLPILMKDFVVSEKQIDSAYNIGADVILLIAKILTERELVSLYKYAKSYGLEAIVEISDEEDLDVALRGNYDFIGVNARNL 185
                                   ********************************************************************************* PP

                                   TTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTH CS
                          IGPS 190 ktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedv 247
                                   ++lev+l++t++L +++pkd+l +aeSGi+tr+d+e+l+++g++afL+G+sl++++++
  gi|70607180|ref|YP_256050.1| 186 ESLEVSLDRTKKLLQMIPKDRLKIAESGISTRQDIEELRASGADAFLIGTSLLKDQNK 243
                                   ******************************************************9885 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.1    0.0081        36      32     141 ..      67     174 ..      59     205 .. 0.70
   2 !   16.1   0.0   1.3e-06    0.0059      79     115 ..     211     247 ..     194     248 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0081
                                   HHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHH CS
                  His_biosynth  32 velakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpeli 112
                                   +e++k  e++ga+ + v+  +  ++g+ ++l+l   +a++v++p+ +   + s ++++++ ++gad + +  + +++ el+
  gi|70607180|ref|YP_256050.1|  67 IEYVKFMENNGATGISVLTEEKFFNGSYNDLEL---VAKNVKLPILMKDFVVSEKQIDSAYNIGADVILLIAKILTERELV 144
                                   556666666667777666666666666666666...567777899999999999999999999999999999999988886 PP

                                   H..HHHHHHCGGGEEEEEEEEECEEEEETTT CS
                  His_biosynth 113 k..elaekfgsqkivvaiDarrgykvaikgw 141
                                   +  + a+ +g  + +v i  +++ +va +g 
  gi|70607180|ref|YP_256050.1| 145 SlyKYAKSYGL-EAIVEISDEEDLDVALRGN 174
                                   43378888888.4445554444446666665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.3e-06
                                   ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                  His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikel 115
                                    +GI++ +d+eel  +gad   igt+ +k+ + ikel
  gi|70607180|ref|YP_256050.1| 211 ESGISTRQDIEELRASGADAFLIGTSLLKDQNKIKEL 247
                                   5799999999999999999999999999999999986 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00022         1     203     242 ..      92     132 ..      36     134 .. 0.83
   2 !    8.0   0.0   0.00028       1.3     248     303 ..     182     237 ..     150     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00022
                                   --HHHHHHHHHHHSSEEEEEE.E-SHHHHHHHHHTTESEEE CS
                        FMN_dh 203 ltwddikwlreqtklplvvKG.vltaedakraveaGvdgiv 242
                                    +++d++ + +++klp+++K  v++++ ++ a+++G+d i+
  gi|70607180|ref|YP_256050.1|  92 GSYNDLELVAKNVKLPILMKDfVVSEKQIDSAYNIGADVIL 132
                                   3789****************9579999***********997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00028
                                   GTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                        FMN_dh 248 GRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                   +R+l++   ++d   ++ + ++++   ++ +Gi++ +D+    a GAda l+G  +
  gi|70607180|ref|YP_256050.1| 182 ARNLESLEVSLDRTKKLLQMIPKDRLKIAESGISTRQDIEELRASGADAFLIGTSL 237
                                   688999999999999998888875444689**********************9765 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   4.8e+02      88     106 ..     115     133 ..      98     141 .. 0.86
   2 ?   10.0   0.0   0.00012      0.56      82     156 ..     156     235 ..     141     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                   SSHHHHHHHHHHT-SEEEE CS
                     QRPTase_C  88 esleeleevleaeadiimL 106
                                    s+++++ +++ +ad+i+L
  gi|70607180|ref|YP_256050.1| 115 VSEKQIDSAYNIGADVILL 133
                                   578999***********98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                                   EEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTT.....SEEEEESS--TTTHHHHHCTT-SEEEECH CS
                     QRPTase_C  82 kievevesleeleevleaeadiimLDnfsveelkkaveelkeknkr.....vlievSGgvtlenveeyaksgvdvisvga 156
                                   +  ve++ +e+l+ +l  + d i +   + e l+  ++++k+  +      ++i  SG  t +++ee++ sg d++ +g+
  gi|70607180|ref|YP_256050.1| 156 EAIVEISDEEDLDVALRGNYDFIGVNARNLESLEVSLDRTKKLLQMipkdrLKIAESGISTRQDIEELRASGADAFLIGT 235
                                   45799************999999888776666655555443333223334599**********************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1649.03
//
Query:       gi|70607181|ref|YP_256051.1|  [L=400]
Description: aspartate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-77  259.7   0.0    5.2e-77  259.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.4e-09   37.0   0.0    5.9e-09   35.7   0.0    1.5  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      2e-07   30.3   0.0    5.4e-07   28.9   0.0    1.6  2  Aminotran_5      Aminotransferase class-V
    1.2e-05   24.1   0.0    2.2e-05   23.2   0.0    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00084   18.7   0.0     0.0014   17.9   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.074   11.8   0.0       0.18   10.5   0.0    1.6  2  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.5   0.0   1.7e-80   5.2e-77       2     362 ..      35     389 ..      34     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 1.7e-80
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalie 82 
                                   +++n+g++++++     t+++++ ++k+  +  g+++ y+   g +el+ ++a+fl++++++++  + +v+ ++Ga+  + 
  gi|70607181|ref|YP_256051.1|  35 KIVNFGIGQPDFP----TFQKIRDEAKK--ALDGGFTAYTSAYGIDELRAKIASFLSSKYNTNISSK-EVIITPGAKVSLY 108
                                   789*********9....***********..88899********************************.*********9999 PP

                                   HHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET..TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                 Aminotran_1_2  83 alifllklnpgdeilvpdptyasyknilrlsggevvryplyse..edfhldlealeealkeapegnkktkvilvesphNPt 161
                                   +++ l  +npgde++++dp+y sy +++++ gg+ v++++++    +f+l+l++le+++++      ktk++++++phNPt
  gi|70607181|ref|YP_256051.1| 109 LAFLLY-VNPGDEVIIFDPSYYSYPEVVKMLGGKPVYVKMKWRedTGFSLNLNDLENKITD------KTKMVVLNNPHNPT 182
                                   999999.9**************************9999988886688**************......************** PP

                                   --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT...EEEEEESSSTTSSGGG-EEEEEEEHHH CS
                 Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn...llivgslsKafGlaGeRvGyilgnaav 239
                                   G v++++e+ +l+++ak++nl++++De+Y  fv++ +     r+ +e+ ++    + v+++sK f+++G+R+Gy++++++v
  gi|70607181|ref|YP_256051.1| 183 GMVFDPKEIDQLIEIAKSKNLIVLSDEIYDYFVYEGKM----RSVLEDPDWknfSIYVNGFSKTFSMTGWRLGYVVAKENV 259
                                   ***********************************764....77777777789**************************** PP

                                   HHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH.. CS
                 Aminotran_1_2 240 vsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae.. 315
                                   ++ +  ++++++   +s +q+a++ a ++++    ++++m ++++krr+++++eL+++ g++v +sq++++++  l +   
  gi|70607181|ref|YP_256051.1| 260 IKKMSEIAANVYTcpTSFAQKAAVSAFDTFD----DVKKMIDTFKKRRDVMYSELKKIkGIQVNKSQGAFYMFPYLGEIlr 336
                                   **************999************99....89************************************99998899 PP

                                   ....CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHH CS
                 Aminotran_1_2 316 ....takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelvea 362
                                       + k++s  L++e+gv+ +pg+ f +   ++++R+++ +++e+ ++e v++
  gi|70607181|ref|YP_256051.1| 337 ksgmSTKDFSVNLIKEKGVVTIPGEVFPLdagKEFVRLSF-AVDENVIKEGVQR 389
                                   999999999999****************************.*******999987 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0     2e-12   5.9e-09       7     144 ..      53     208 ..      49     210 .. 0.76
   2 ?   -2.6   0.0      0.89   2.7e+03     234     304 ..     289     357 ..     280     365 .. 0.66

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                                   HHHHHHHHTSS..-SSSSHHHHHHHHHHHHHHT-SEEEEESS....HHHHHHHHHHH...TTTTTT-EEEEESSS-THHHH CS
               DegT_DnrJ_EryC1   7 leaveevlksg..wltsgpeveeFEkafaaylgvkhaiavss....GtaAlhlaLra...lgvgpgdeVIvpsltFvatan 78 
                                    ++++++l++g   +ts   ++e+ +++a +l +k+   +ss     t +  ++L     l v+pgdeVI+   ++ +  +
  gi|70607181|ref|YP_256051.1|  53 RDEAKKALDGGftAYTSAYGIDELRAKIASFLSSKYNTNISSkeviITPGAKVSLYLaflLYVNPGDEVIIFDPSYYSYPE 133
                                   56677777777433444667888888888888888888888744333555555555445799******************* PP

                                   HHHHTT-EEEEE-B-...TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB--...-HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1  79 avlelgakpvfvDvd...pdtynidpaaieaaitertkaIl...pVhlyGqva...dmdalkaiaakhglkvieD 144
                                   +v  lg kpv+v ++    + + ++ +++e++it +tk ++   p +  G v+   ++d+l +ia++++l+v++D
  gi|70607181|ref|YP_256051.1| 134 VVKMLGGKPVYVKMKwreDTGFSLNLNDLENKITDKTKMVVlnnPHNPTGMVFdpkEIDQLIEIAKSKNLIVLSD 208
                                   *************9733245599*****************944423345554423389***************99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.89
                                   HCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHC.CEE- CS
               DegT_DnrJ_EryC1 234 LerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkee.gigt 304
                                   ++ +++++++ ++  +++ +eL++++g+   +++k + +  ++ y+  + +++ ++ +++   l +e g+ t
  gi|70607181|ref|YP_256051.1| 289 FDDVKKMIDTFKKRRDVMYSELKKIKGI---QVNKSQGAFYMFPYLGEILRKSGMSTKDFSVNLIKEkGVVT 357
                                   5667777777777778888888888874...44444444677777777887777776666555544436655 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.8e-10   5.4e-07      45     175 ..      73     208 ..      64     214 .. 0.81
   2 ?   -2.3   0.0      0.53   1.6e+03      16      55 ..     260     299 ..     254     323 .. 0.52

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.8e-10
                                   HHHHHHHHHHHHT-S.....TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEE.EE CS
                   Aminotran_5  45 veearekvaelinae.....seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvk.vi 119
                                   ++e r+k+a ++  +     s++e+i t G+  ++ l+ l +   ++pgde+++ +  + +     ++l  +  + vk ++
  gi|70607181|ref|YP_256051.1|  73 IDELRAKIASFLSSKyntniSSKEVIITPGAKVSLYLAFLLY---VNPGDEVIIFDPSYYSYPEVVKMLGGK-PVYVKmKW 149
                                   677888888887554212223499******************...9*****************999999855.44444144 PP

                                   EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                   Aminotran_5 120 pldeegeldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                   + d + +l+l++le+++++ktk+v ++   n tG++++   +++++++ak k+ +vl D
  gi|70607181|ref|YP_256051.1| 150 REDTGFSLNLNDLENKITDKTKMVVLNNPHNPTGMVFDpkeIDQLIEIAKSKNLIVLSD 208
                                   666777899**************************876333777889999999999988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.53
                                   HHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHH CS
                   Aminotran_5  16 ldalqeyytdynanvhrsvhhlgkeatkaveearekvael 55 
                                   +++++e   + ++ +++ +++++  a + ++++++ + ++
  gi|70607181|ref|YP_256051.1| 260 IKKMSEIAANVYTCPTSFAQKAAVSAFDTFDDVKKMIDTF 299
                                   5555555555555554444444444444444444444333 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.2e-09   2.2e-05      79     174 ..     106     209 ..      83     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.2e-09
                                   HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST....TSHHHHHHHCCTTEEEEEEESS-TTTT--- CS
               Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt....sdleelekaikentklvylEtptnpllkvv 154
                                   ++ +a+l  ++ Gde+++ d  Y +  +++k +  k + +++k+ +      +l++le++i+++tk+v l  p np+  v 
  gi|70607181|ref|YP_256051.1| 106 SLYLAFLLYVNPGDEVIIFDPSYYSYPEVVKMLGGKpVYVKMKWREDtgfsLNLNDLENKITDKTKMVVLNNPHNPTGMVF 186
                                   555677888999***********9999999999877689999998774555689**************************9 PP

                                   -...HHHHHHHHHHTT-EEEEEG CS
               Cys_Met_Meta_PP 155 D...iekiaklakkagvlvvvDn 174
                                   D   i +++++ak+++++v+ D 
  gi|70607181|ref|YP_256051.1| 187 DpkeIDQLIEIAKSKNLIVLSDE 209
                                   96667788999****99998875 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   4.8e-07    0.0014      62     167 ..     109     208 ..      51     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.8e-07
                                   HHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT....TBE-HHHHHHHS--S-TTS-EEEEEEEESSBT CS
               Beta_elim_lyase  62 illkillqrgeevivtepahihfdetgaiaelagvklrdlknkea....GkmdlekleaaikevgaheekiklisltvTnn 138
                                   +++ + +++g+evi+ +p+ +   e    + + g k++ +k k        ++l++le++i++      k+k+++l + +n
  gi|70607181|ref|YP_256051.1| 109 LAFLLYVNPGDEVIIFDPSYYSYPEV---VKMLGGKPVYVKMKWRedtgFSLNLNDLENKITD------KTKMVVLNNPHN 180
                                   55566666666666666666655554...23334445544443333454579999****9999......699********* PP

                                   TTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 139 tagGqvvsleelrevaaiakkygiplhlD 167
                                      G v  ++e++++ +iak++++ ++ D
  gi|70607181|ref|YP_256051.1| 181 P-TGMVFDPKEIDQLIEIAKSKNLIVLSD 208
                                   5.9********************999887 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.1e-05      0.18      84     196 ..      96     198 ..      78     226 .. 0.76
   2 ?   -2.5   0.0      0.55   1.6e+03      53      85 ..     245     277 ..     229     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                                   EEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS-BE---GGGGSHHHHHHHHHHS CS
                      OKR_DC_1  84 syfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgiiggidlkefeeetlkekikev 163
                                     +++ G  +s        ++pgd v++      S  + + + g +Pvy++ + r+  g++ +++        l++ki+++
  gi|70607181|ref|YP_256051.1|  96 EVIITPGAKVSLYLAFLLYVNPGDEVIIFDPSYYSYPEVVKMLGGKPVYVKMKwREDTGFSLNLND-------LENKITDK 169
                                   55677888889999999999******99999*****************************988877.......77777765 PP

                                   TTTGSESEEEEESS-T.TSEEE-HHHHHHHHTTS CS
                      OKR_DC_1 164 pdakaprlavitnsTY.dGvlynakeivdklekl 196
                                   +  k+   +v+ n+    G++++ kei +++e  
  gi|70607181|ref|YP_256051.1| 170 T--KM---VVLNNPHNpTGMVFDPKEIDQLIEIA 198
                                   4..33...55666543258888888887776643 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.55
                                   TTTGGGBBTTTTBTHHHHHHHHHHHHCT-SEEE CS
                      OKR_DC_1  53 ievveLgdLldheGaikeaqkyaarvfgadksy 85 
                                   +   +Lg + ++e +ik+  + aa+v+    s+
  gi|70607181|ref|YP_256051.1| 245 MTGWRLGYVVAKENVIKKMSEIAANVYTCPTSF 277
                                   555567888888888999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2388.35
//
Query:       gi|70607182|ref|YP_256052.1|  [L=831]
Description: valyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.4e-126  421.0   0.1   1.2e-124  416.8   0.1    2.3  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    2.4e-31  108.8   1.8    4.7e-31  107.8   1.8    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.7e-21   75.8   0.1    1.2e-09   37.4   0.0    3.5  3  tRNA-synt_1g   tRNA synthetases class I (M)
    6.9e-06   25.7   0.0    0.00027   20.5   0.0    2.8  3  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.014   14.7   0.0       0.85    8.9   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
       0.14   12.3   0.8        6.3    7.0   0.2    2.4  2  Zn-ribbon_8    Zinc ribbon domain
       0.17   11.3   0.1        7.1    6.1   0.0    2.5  2  zf-TFIIB       Transcription factor zinc-finger
       0.41   10.1   1.8        1.5    8.4   0.2    2.2  2  zf-ribbon_3    zinc-ribbon domain
       0.67   10.4   2.4         25    5.4   0.1    2.8  2  zf-IS66        zinc-finger binding domain of transposase IS66


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.8   0.1    6e-128  1.2e-124       2     599 ..      44     600 ..      43     603 .. 0.93

  Alignments for each domain:
  == domain 1  score: 416.8 bits;  conditional E-value: 6e-128
                   tRNA-synt_1   2 lyekWeeedvfkkelekeke...kkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                   +++ W  +++++k ++ ++e    + f++  +PP+  G+lH+Gha+  t+ d++ r+kr++G++vl   GwD+ Gl++e k
  gi|70607182|ref|YP_256052.1|  44 WQNIWMTKEFWEKVFRFRDEdekSPVFVIDTPPPFTSGELHMGHAYWVTISDTIGRFKRLEGYNVLLPQGWDTQGLPTELK 124
                                   67788888888887665554312556******************************************************* PP

                   tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdr.eylTldkeleeavkevfvrladkgliyrg 159
                                   v+ kl   ++       re f +k+ ew + +++++r ++ rlG ++ ++r ey T ++++   +++ +  +++ gl+  +
  gi|70607182|ref|YP_256052.1| 125 VQYKLKVPKE------NRELFLKKCIEWTEDMIKSMRTAMIRLGYRAEWERfEYRTYESKYRRIIQKSLIDMHKMGLVEMR 199
                                   *****77766......899*******************************989**************************** PP

                   tRNA-synt_1 160 kklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeall 240
                                   + +v+w++k++tal++ Ev yk+++++l ++ fp+ d+e   + iaTT+Pe l + +avavnp+                 
  gi|70607182|ref|YP_256052.1| 200 EGPVYWCPKCETALAQSEVGYKEEDGVLAYILFPFVDGEG-GVTIATTRPELLGATQAVAVNPD----------------- 262
                                   ****************************************.9**********************................. PP

                   tRNA-synt_1 241 kslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedg 321
                                                 der+k+L+g++v+ pl +++i iiad+ v++ +GtG+V i+ + d++D +    y l+v  ++d++g
  gi|70607182|ref|YP_256052.1| 263 --------------DERYKSLVGRKVKIPLFDKEISIIADKAVEMTFGTGAVMISTYGDPQDIRWQLTYRLPVYEVVDDKG 329
                                   ..............9****************************************************************** PP

                   tRNA-synt_1 322 tlteeaaefeglkvfdarkkvveelkekglllkaekiehsv.pfcersk..kpiiyrateqWfvrvkeladaalkavekvq 399
                                   +++++ +  +gl+v++arkk++e lkekg l+k+eki+h+v  ++ers+   pi++ +++q +++v e ++++l+  +k++
  gi|70607182|ref|YP_256052.1| 330 KIKNTNGLLDGLTVKEARKKIIEILKEKGYLIKVEKITHNVlAHTERSDclSPIEFLIKKQIYIKVLEWRNKLLEDYKKMK 410
                                   ***************************************975899***95569**************************** PP

                   tRNA-synt_1 400 fvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekge 479
                                   f+p++     ++w++n + dW+iSRqr++G+++p+++ ++   ++      e v      ++ +  +ek  +  l     +
  gi|70607182|ref|YP_256052.1| 411 FTPQRMSYYLEEWIKNLEwDWNISRQRVYGTPLPFWYCDNGH-LIP---APEEVLP-IDPSKVNPPVEKCPHCGL-----D 481
                                   ****************977********************977.555...2333332.333333444455555566.....9 PP

                   tRNA-synt_1 480 lekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdee 560
                                   l+ ++dv DvW +S+ +     g+ +  ++ ++k+fp ++ l+G Diir W+      +lal g+ Pfkevl++g v+  +
  gi|70607182|ref|YP_256052.1| 482 LKPVKDVADVWVDSSVTVLYLTGFYDD-KSRFTKTFPSSLRLQGTDIIRTWLFYTYYRTLALAGNIPFKEVLINGQVLGPD 561
                                   ******************999998777.999************************************************** PP

                   tRNA-synt_1 561 GrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                   G +mSKs+gNv++pld +++ygada+Rltl+ ++ g d 
  gi|70607182|ref|YP_256052.1| 562 GTRMSKSKGNVVSPLDKVDEYGADAIRLTLLDAKIGDDF 600
                                   ********************************9999886 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.8   1.8   2.3e-34   4.7e-31       1     150 [.     643     785 ..     643     788 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 2.3e-34
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   d+wil+e  k+v++  eay++y+f+ ++ ++y+ fw++++d ylel+k+rl  e+++    a ++l  +++ ll+ll+P++
  gi|70607182|ref|YP_256052.1| 643 DKWILQEHKKFVQQSIEAYRNYDFYIVVESIYSYFWETIADEYLELIKHRLFMEDES----AIYTLSRIIKDLLILLYPIA 719
                                   9**************************************************988753....66****************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                   P+itEe++   e+++g+k si l++ p++++ + ++e+ ++  e++k++ +air l+ ++ ++  ++++v
  gi|70607182|ref|YP_256052.1| 720 PHITEEMY---ERLYGDKMSIALENLPDTSDLEdDGEA-QKLGEYIKKATSAIRTLKIQNRLAIPTPISV 785
                                   ********...4566************75555566666.89***************98888877777665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0     6e-13   1.2e-09       2     135 ..      71     218 ..      70     221 .. 0.79
   2 !   10.5   0.2     9e-05      0.18     180     238 ..     387     444 ..     355     454 .. 0.82
   3 !   23.5   0.0     1e-08   2.1e-05     247     373 ..     491     609 ..     483     620 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6e-13
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHH....HHHHHHHHHHHHH CS
                  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpee....lvekvheeikelf 78 
                                   ++ t+ p+++g+lH+Gh++ v ++D + R+krl+g++vl   g D+ G p+elk + +   p+e    + +k  e ++++ 
  gi|70607182|ref|YP_256052.1|  71 VIDTPPPFTSGELHMGHAYWVTISDTIGRFKRLEGYNVLLPQGWDTQGLPTELKVQYKLKVPKEnrelFLKKCIEWTEDMI 151
                                   689999************************************************998777776533333334333333343 PP

                                   HH.........TT---SEE.EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                  tRNA-synt_1g  79 kk.........lnisfdky.grttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                   k+         +  +++ + +rt +++ +++ q+ +  +++ gl++ +e  +++cpk+e+ l++++v
  gi|70607182|ref|YP_256052.1| 152 KSmrtamirlgYRAEWERFeYRTYESKYRRIIQKSLIDMHKMGLVEMREGPVYWCPKCETALAQSEV 218
                                   33111111111245678894599999************************************99887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9e-05
                                   .EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 180 etehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    +++++ k+ ++++kl e + ++ k ++++++ +++ew+k+   d++isr+  +G p+P
  gi|70607182|ref|YP_256052.1| 387 IKKQIYIKVLEWRNKLLEDY-KKMKFTPQRMSYYLEEWIKNLEWDWNISRQRVYGTPLP 444
                                   56889999999999888878.5555799*************667*************99 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 1e-08
                                   HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHH...HHHTHHHHHHHHTT----S-EEEE--EEE- CS
                  tRNA-synt_1g 247 VWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiik...FHtifwPaillgaelklpkkvvaheyltve 324
                                   VW+d  +  +  t+ +     +++++ + +      +   + g dii+   F   ++ ++ l+ ++ + + ++  + l  +
  gi|70607182|ref|YP_256052.1| 491 VWVDSSVTVLYLTGFYD----DKSRFTKTFP-----SSLRLQGTDIIRtwlFY-TYYRTLALAGNIPFKEVLINGQVLGPD 561
                                   88888888777777765....4557777772.....35778899999733233.467778888999**9************ PP

                                   -------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
                  tRNA-synt_1g 325 gkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfve 373
                                   g ++SkS+g+vv + + ++++ ad++R  l+  a+  +D+ f+w+++  
  gi|70607182|ref|YP_256052.1| 562 GTRMSKSKGNVVSPLDKVDEYGADAIRLTLLD-AKIGDDFPFKWDTVKS 609
                                   ***************************99986.56789******98865 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.079   1.6e+02      11      46 ..     229     264 ..     225     273 .. 0.86
   2 !   20.5   0.0   1.3e-07   0.00027      86     147 ..     271     332 ..     264     355 .. 0.87
   3 ?   -2.2   0.0       1.3   2.5e+03      15      39 ..     362     386 ..     352     409 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.079
                 tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfvalapehp 46 
                                    i f++ + e  +++ ttrp+ l   + va+ p+ +
  gi|70607182|ref|YP_256052.1| 229 YILFPFVDGEGGVTIATTRPELLGATQAVAVNPDDE 264
                                   578999999999***********9999999999876 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.3e-07
                 tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeek 147
                                   g k+  P+ +++i i   + v m++gtgavm     d +D ++  +y lp+ +v+  +++ k
  gi|70607182|ref|YP_256052.1| 271 GRKVKIPLFDKEISIIADKAVEMTFGTGAVMISTYGDPQDIRWQLTYRLPVYEVVDDKGKIK 332
                                   778999*************************************************9776543 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.3
                 tRNA-synt_1_2  15 kveeseeklevfttrpdtlfGvtfv 39 
                                   kve+ ++++  +t+r d l  ++f+
  gi|70607182|ref|YP_256052.1| 362 KVEKITHNVLAHTERSDCLSPIEFL 386
                                   566666789999*****99999997 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.026        51      22      49 ..      82     109 ..      77     119 .. 0.91
   2 ?    8.9   0.0   0.00043      0.85     246     294 ..     557     605 ..     538     611 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.026
                                   --BHHHHHHHHHHHHHHHHHHHTT-EEE CS
                  tRNA-synt_1e  22 ashlGhaRslvafDilrrilqalgYdvq 49 
                                   + h+Gha  + + D + r+ +  gY+v 
  gi|70607182|ref|YP_256052.1|  82 ELHMGHAYWVTISDTIGRFKRLEGYNVL 109
                                   68************************96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00043
                                   -EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HH CS
                  tRNA-synt_1e 246 hlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkee 294
                                   +l  +g +msks +n+++  d + ++ + ++Rl ll a+  + + fk +
  gi|70607182|ref|YP_256052.1| 557 VLGPDGTRMSKSKGNVVSPLDKVDEYGADAIRLTLLDAKIGDDFPFKWD 605
                                   4556899*****************************9988777777655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.049        98      19      35 ..     196     212 ..     192     215 .. 0.73
   2 ?    7.0   0.2    0.0032       6.3      20      36 ..     465     482 ..     458     485 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.049
                   Zn-ribbon_8  19 qsisdapltaCPeCgse 35 
                                   +++ + p   CP+C  +
  gi|70607182|ref|YP_256052.1| 196 VEMREGPVYWCPKCETA 212
                                   5677777556****875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0032
                   Zn-ribbon_8  20 sis.dapltaCPeCgsev 36 
                                   +++  +p ++CP+Cg ++
  gi|70607182|ref|YP_256052.1| 465 PSKvNPPVEKCPHCGLDL 482
                                   5564567677****9765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0035       7.1       2      15 ..     206     219 ..     205     229 .. 0.82
   2 ?    2.3   0.1     0.055   1.1e+02       1      11 [.     474     484 ..     471     494 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0035
                      zf-TFIIB   2 CPkCqdeleeserg 15 
                                   CPkC ++l +se+g
  gi|70607182|ref|YP_256052.1| 206 CPKCETALAQSEVG 219
                                   *********99983 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.055
                      zf-TFIIB   1 kCPkCqdelee 11 
                                   kCP C+ +l++
  gi|70607182|ref|YP_256052.1| 474 KCPHCGLDLKP 484
                                   57777766666 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.24   4.8e+02       5      23 ..     206     210 ..     204     217 .. 0.64
   2 ?    8.4   0.2   0.00074       1.5      17      26 .]     473     482 ..     467     482 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                   zf-ribbon_3   5 CPnCGaplssddnvCpyCG 23 
                                   CP+C               
  gi|70607182|ref|YP_256052.1| 206 CPKC--------------E 210
                                   5555..............4 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00074
                   zf-ribbon_3  17 nvCpyCGtkl 26 
                                    +Cp+CG +l
  gi|70607182|ref|YP_256052.1| 473 EKCPHCGLDL 482
                                   68*****987 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.036        72      38      46 .]     202     210 ..     196     210 .. 0.90
   2 ?    5.4   0.1     0.013        25       3      17 ..     474     488 ..     473     491 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.036
                       zf-IS66  38 pkyaCpcCe 46 
                                   p+y+Cp+Ce
  gi|70607182|ref|YP_256052.1| 202 PVYWCPKCE 210
                                   79******7 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                       zf-IS66   3 tCpcCGgllkpiged 17 
                                   +Cp+CG +lkp++++
  gi|70607182|ref|YP_256052.1| 474 KCPHCGLDLKPVKDV 488
                                   7*****988998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5152.21
//
Query:       gi|70607183|ref|YP_256053.1|  [L=329]
Description: hypothetical protein Saci_1431 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0011   19.1   0.0     0.0021   18.2   0.0    1.4  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.061   12.2   0.0       0.33    9.7   0.0    1.9  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.4e-07    0.0021       1      30 [.       6      36 ..       6      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-07
                                  EE--SHHHHHHHHHHHCC.TEEEEEE-SSSS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdr 30
                                  I+G+G+sG+++Ayl++k+ +  v +++  dr
  gi|70607183|ref|YP_256053.1|  6 ILGGGVSGSLLAYLIKKYtNNYVKIFDIKDR 36
                                  89***************98999*****9886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   3.7e-05      0.33       1      35 [.       3      37 ..       3      42 .. 0.85
   2 ?    0.0   0.0     0.033     3e+02     254     361 ..     152     259 ..     135     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.7e-05
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                  ki i+GGG +G+l A +++k++++ +++  ++   
  gi|70607183|ref|YP_256053.1|  3 KIAILGGGVSGSLLAYLIKKYTNNYVKIFDIKDRY 37
                                  799*******************8879987776655 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.033
                                   -SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHHCT--TTTS-EEEE---EEES-SEETTEEE-CCCTEE--CCCS CS
                Trp_halogenase 254 ekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellaeldgkleaeprkirfttGrrkqawvknvvalGlasgfvePles 333
                                   +  G  W  P ++ + n G+ + ++  ++d  l+ ++++++ + e++   ir      + + + n   +G+a g + Pl +
  gi|70607183|ref|YP_256053.1| 152 KYTGFYWIFPSEDGVYNiGAGFIEDKNSRDLTLKYIKEKFGDR-EYKIVDIRGAPISISPIHETNY-KIGEARGLLFPLSG 230
                                   5568888888888888888888888888888888888888744.4554555555555666666554.78888888888888 PP

                                   -HHHH.HHHHHHHHHHT--BTT--HHHHH CS
                Trp_halogenase 334 tsihl.iqaalrrLlallpdksdepaaia 361
                                    +i   + +a++   a+   k +++++ +
  gi|70607183|ref|YP_256053.1| 231 EGIRPsAISAVKAFEAIKNGKDFNKYLSE 259
                                   88874134455555555444445554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2378.16
//
Query:       gi|70607184|ref|YP_256054.1|  [L=130]
Description: hypothetical protein Saci_1432 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.12   12.7   0.1       0.36   11.1   0.0    1.8  2  TMEM131_like  Transmembrane protein 131-like


Domain annotation for each model (and alignments):
>> TMEM131_like  Transmembrane protein 131-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     2e-05      0.36      34      80 ..      30      78 ..       6      82 .. 0.80
   2 ?   -0.8   0.0       0.1   1.9e+03      30      57 ..      91     120 ..      85     129 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2e-05
                  TMEM131_like 34 lkllsvt..sdsiefqssffeevvlpPggntslkvvFLPrelGaseasl 80
                                  ++++++   s+ ++ +++  +++v+ P + t ++++F+    G ++++ 
  gi|70607184|ref|YP_256054.1| 30 VEVKEIKvkSKLNPVYKNGTRQLVIIPDKGTFIQLIFIKNVYGRVKGKA 78
                                  5555554004446699***************************999975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.1
                  TMEM131_like  30 kkeklkllsvtsdsie..fqssffeevvlp 57 
                                   + +klkl+ v+++ ++  +    fe++++p
  gi|70607184|ref|YP_256054.1|  91 NYRKLKLKIVSGNPAYadYVRKIFEKLKIP 120
                                   445566665555544333777778877774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 951.04
//
Query:       gi|70607185|ref|YP_256055.1|  [L=106]
Description: hypothetical protein Saci_1433 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.034   14.3   0.0    1.1  1  DUF2675         Protein of unknown function (DUF2675)
      0.064   12.9   0.1       0.17   11.5   0.1    1.6  2  TraT            Enterobacterial TraT complement resistance pr
      0.085   12.8   0.0       0.13   12.2   0.0    1.3  1  Arm-DNA-bind_2  Arm DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF2675  Protein of unknown function (DUF2675)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.6e-06     0.034      17      76 ..      17      77 ..      12      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-06
                       DUF2675 17 mssdvqailekdmlhlckqvgs.gaivpngkqkemivqflthgmeglmtfvvrtsfreaik 76
                                  ms+ v  ++ek+++ lc  v + g++v    +  +iv f        + + vr s  +a k
  gi|70607185|ref|YP_256055.1| 17 MSATVIDMIEKELVDLCSVVRTgGSLVCSPSDDSLIVVFTIFNQLRKLEIHVRFSSTNAKK 77
                                  9999***************976268999999*******99888777777778877776644 PP

>> TraT  Enterobacterial TraT complement resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.23   1.4e+03      58      80 ..      10      31 ..       6      43 .. 0.67
   2 ?   11.5   0.1   2.9e-05      0.17      23      55 ..      65      97 ..      53     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                          TraT 58 pkeAayiLqanvlyvdkktdkaa 80
                                  p + +y+++a+v+ +   ++ ++
  gi|70607185|ref|YP_256055.1| 10 PPNPEYVMSATVIDMIE-KELVD 31
                                  56678999999998866.45555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.9e-05
                          TraT 23 tiyvqirntSdkqeldleqkiiskLeakGYkvv 55
                                   i v++  t +k+ ++l ++++skL++kGY ++
  gi|70607185|ref|YP_256055.1| 65 EIHVRFSSTNAKKLAELINEVSSKLKSKGYLIT 97
                                  68999999999*999***************986 PP

>> Arm-DNA-bind_2  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05      0.13       9      50 ..      48      89 ..      39      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                Arm-DNA-bind_2  9 ggklridFrykGkrcreslglpdtpanrKkaerllaeIeeeI 50
                                  +++l++ F++ ++  + ++ ++   +n Kk+++l++e+ ++ 
  gi|70607185|ref|YP_256055.1| 48 DDSLIVVFTIFNQLRKLEIHVRFSSTNAKKLAELINEVSSKL 89
                                  6789*********************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 771.59
//
Query:       gi|70607186|ref|YP_256056.1|  [L=106]
Description: hypothetical protein Saci_1434 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.039   14.0   1.2      0.039   14.0   1.2    1.1  1  Methyltransf_21  Methyltransferase FkbM domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2   2.2e-06     0.039     110     150 ..      43      84 ..       5     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
               Methyltransf_21 110 kksridllkiDvEGaElevLeGaqkglkrcqpnl....ivvEvhk 150
                                   + ++i ++ +D+E  E+ +L   +  +++ ++n+    ++   ++
  gi|70607186|ref|YP_256056.1|  43 QYNKIAYIDMDIETTEFKIL---RLVVCKTRINIyvcnVIGKLKE 84 
                                   568*****************...6888******955553233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 704.88
//
Query:       gi|70607187|ref|YP_256057.1|  [L=72]
Description: hypothetical protein Saci_1435 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-05   24.0   2.4     0.0035   17.2   0.4    2.2  2  Prok-RING_1     Prokaryotic RING finger family 1
    0.00078   19.4   6.6       0.13   12.3   6.6    2.2  1  DZR             Double zinc ribbon
     0.0015   18.4   9.2        1.9    8.4   9.4    2.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.003   17.6   5.2     0.0045   17.1   3.3    1.9  2  Zn-ribbon_8     Zinc ribbon domain
     0.0052   17.0   4.0       0.43   10.9   0.7    2.3  2  zinc_ribbon_9   zinc-ribbon
  ------ inclusion threshold ------
      0.012   15.0  10.1      0.025   14.0   0.3    3.1  2  zf-ribbon_3     zinc-ribbon domain
      0.016   15.2   5.6      0.063   13.3   0.8    2.0  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.022   14.6   7.7        2.1    8.3   0.3    3.1  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.023   15.1   7.3       0.15   12.5   0.4    3.1  3  zf-H2C2_2       Zinc-finger double domain
      0.029   14.5   7.3       0.13   12.3   7.3    2.1  1  DUF1272         Protein of unknown function (DUF1272)
      0.032   14.2   1.6       0.74    9.9   0.2    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.039   14.0   5.7      0.049   13.6   0.1    2.3  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.047   14.1   3.0      0.047   14.1   3.0    1.6  1  DUF4379         Probable Zinc-ribbon domain
      0.049   13.4   2.3      0.063   13.0   2.3    1.2  1  Rep_fac-A_C     Replication factor-A C terminal domain
      0.051   13.2   0.3      0.051   13.2   0.3    2.4  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
      0.063   13.3   5.0       0.94    9.6   5.0    2.2  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
      0.065   13.0   0.8      0.065   13.0   0.8    3.4  3  zinc_ribbon_2   zinc-ribbon domain
       0.12   12.7   8.4      0.065   13.6   3.7    2.2  2  C1_2            C1 domain
       0.19   11.7   5.8        1.6    8.7   0.1    3.0  3  Cys_rich_CPXG   Cysteine-rich CPXCG
       0.28   10.8   8.0        2.8    7.6   0.5    3.1  3  Sgf11           Sgf11 (transcriptional regulation protein)
       0.33   11.1   0.2       0.33   11.1   0.2    2.9  3  UPF0547         Uncharacterised protein family UPF0547
       0.36   11.0   9.5       0.68   10.1   3.7    2.4  2  zf-AN1          AN1-like Zinc finger
        0.4   10.8  12.3        7.6    6.7   0.2    3.1  2  zf-BED          BED zinc finger
       0.42   10.4   9.3       0.52   10.1   3.4    2.1  2  zf-RING_4       RING/Ubox like zinc-binding domain
       0.56    9.7   9.9       0.26   10.7   0.8    2.3  2  Mu-like_Com     Mu-like prophage protein Com
       0.62   10.4   9.7        2.9    8.3   0.2    3.1  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.71    9.4   9.4        2.7    7.6   0.4    2.9  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.75   10.4  11.7        5.6    7.6   2.1    3.2  3  zf-C2H2         Zinc finger, C2H2 type
       0.91    9.5   6.4          2    8.4   1.4    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.1    8.7   6.6        4.2    6.8   0.1    2.4  3  zf-TFIIB        Transcription factor zinc-finger
        1.3   10.1  13.0        7.6    7.7   0.1    3.4  3  zf-C2H2_4       C2H2-type zinc finger
        1.5    8.9   8.3       0.57   10.2   4.4    2.2  2  ADK_lid         Adenylate kinase, active site lid
        1.7    8.6   8.4          1    9.3   0.5    2.7  3  TFIIS_C         Transcription factor S-II (TFIIS)
        1.7    8.8  10.5        6.5    7.0   6.2    2.8  2  zf-B_box        B-box zinc finger
          2    8.5   7.5        4.8    7.2   0.8    2.7  3  CpXC            CpXC protein
        2.3    8.2  11.6        2.9    7.9   7.5    2.7  2  zinc_ribbon_4   zinc-ribbon domain
        2.6    8.5   9.9        3.1    8.3   0.1    2.9  3  zf-IS66         zinc-finger binding domain of transposase IS6
        3.4    7.7  11.3          1    9.4   0.4    2.8  3  zf-RING_5       zinc-RING finger domain
        6.1    6.9  17.1        6.5    6.8   0.6    3.2  3  zf-C2HC_2       zinc-finger of a C2HC-type
        8.4    5.0   8.1        8.3    5.1   3.0    2.0  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta


Domain annotation for each model (and alignments):
>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   7.9e-06    0.0035       5      30 ..      19      45 ..      16      47 .. 0.86
   2 ?    6.9   0.1     0.014       6.1       4      14 ..      58      68 ..      55      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-06
                   Prok-RING_1  5 kkCpvCgkelkeedDiVv.CpeCgtpy 30
                                    C +C+++++ + D+V  Cp+C   y
  gi|70607187|ref|YP_256057.1| 19 VYCRICNRKIRIGTDLVYkCPKCEKKY 45
                                  57**************966****8655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                   Prok-RING_1  4 gkkCpvCgkel 14
                                  +kkCp Cg el
  gi|70607187|ref|YP_256057.1| 58 KKKCPYCGTEL 68
                                  68999999887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   6.6    0.0003      0.13       1      35 [.      38      65 ..      17      71 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                           DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCg 35
                                  Cp+C+++   +a fC++    lk     ++Cp Cg
  gi|70607187|ref|YP_256057.1| 38 CPKCEKK--YNAFFCEADARGLK-----KKCPYCG 65
                                  4444333..23334444444443.....5555555 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   9.4    0.0042       1.9       4      46 ..      20      67 ..      19      71 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                                  B-TTTSSSBS-..EEETTE......EEEEE-HHHHHHHHHTT-B-TTT--B CS
                    zf-C3HC4_3  4 eCviClerprn..vvllpC......gHlvlCeeCaekllkrkkkCpiCrrp 46
                                  +C iC+++ r    ++++C         ++Ce+ a+ l   kkkCp+C ++
  gi|70607187|ref|YP_256057.1| 20 YCRICNRKIRIgtDLVYKCpkcekkYNAFFCEADARGL---KKKCPYCGTE 67
                                  69999998554213555554335432455899999999...9******987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.9   8.6e+02      28      34 ..      19      26 ..      15      30 .. 0.61
   2 !   17.1   3.3     1e-05    0.0045       6      36 ..      36      68 ..      35      72 .] 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                   Zn-ribbon_8 28 a.CPeCgs 34
                                  + C  C+ 
  gi|70607187|ref|YP_256057.1| 19 VyCRICNR 26
                                  44666654 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1e-05
                   Zn-ribbon_8  6 YrCeeCghefe.vlqsisdaplta.CPeCgsev 36
                                  Y+C +C ++++  +++++ + l++ CP Cg e+
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKYNaFFCEADARGLKKkCPYCGTEL 68
                                  ***********55555554446666*****965 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.7   0.00096      0.43       3      29 ..      19      43 ..      18      45 .. 0.77
   2 ?    7.4   0.1     0.012       5.3      22      32 ..      60      69 ..      46      72 .] 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00096
                 zinc_ribbon_9  3 yWChqCdrfVsvspdedsdv.lCPhCgg 29
                                   +C  C+r +++    ++ v  CP C+ 
  gi|70607187|ref|YP_256057.1| 19 VYCRICNRKIRIG---TDLVyKCPKCEK 43
                                  57888*******6...456556****75 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                 zinc_ribbon_9 22 vlCPhCgggFV 32
                                  + CP+Cg   V
  gi|70607187|ref|YP_256057.1| 60 K-CPYCGTELV 69
                                  4.****98766 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   4.6      0.25   1.1e+02      17      23 ..      36      42 ..      17      44 .. 0.62
   2 ?   14.0   0.3   5.6e-05     0.025      17      26 .]      59      68 ..      49      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
                   zf-ribbon_3 17 nvCpyCG 23
                                   +Cp+C 
  gi|70607187|ref|YP_256057.1| 36 YKCPKCE 42
                                  4566665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.6e-05
                   zf-ribbon_3 17 nvCpyCGtkl 26
                                  ++CpyCGt+l
  gi|70607187|ref|YP_256057.1| 59 KKCPYCGTEL 68
                                  4566666654 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.8   0.00014     0.063      70      95 ..      18      44 ..      12      49 .. 0.87
   2 ?    5.0   0.3     0.053        24      79      97 ..      53      69 ..      44      72 .] 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                                  EEEETTTS-EEECHHH.HHS-TTTSSS CS
                          HypA 70 kvrCreCgkefeleek.alrCpkCgsa 95
                                  +v+Cr C++++++ ++  ++CpkC+++
  gi|70607187|ref|YP_256057.1| 18 TVYCRICNRKIRIGTDlVYKCPKCEKK 44
                                  689*********9987789*****985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.053
                                  EEE.CHHHHHS-TTTSSS-E CS
                          HypA 79 efe.leekalrCpkCgsadv 97
                                  + + l   + +Cp Cg++ v
  gi|70607187|ref|YP_256057.1| 53 DARgL---KKKCPYCGTELV 69
                                  33312...358****98765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3     0.053        24      25      35 ..      19      29 ..       4      31 .. 0.76
   2 ?    8.3   0.3    0.0046       2.1       4      15 ..      35      46 ..      35      48 .. 0.88
   3 ?    5.0   0.1      0.05        22      27      35 ..      61      69 ..      56      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.053
                Zn_ribbon_SprT 25 YrCrrCkgtLr 35
                                   +Cr+C  ++r
  gi|70607187|ref|YP_256057.1| 19 VYCRICNRKIR 29
                                  69****98765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0046
                Zn_ribbon_SprT  4 vYrCtgCgreyt 15
                                  vY+C+ C ++y+
  gi|70607187|ref|YP_256057.1| 35 VYKCPKCEKKYN 46
                                  7******99986 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.05
                Zn_ribbon_SprT 27 CrrCkgtLr 35
                                  C++C+ +L+
  gi|70607187|ref|YP_256057.1| 61 CPYCGTELV 69
                                  999998886 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       1.2   5.5e+02       9      22 ..      13      26 ..      10      28 .. 0.74
   2 ?   12.5   0.4   0.00034      0.15      15      25 ..      36      46 ..      30      47 .. 0.88
   3 ?    4.3   0.3      0.14        62      16      21 ..      60      65 ..      55      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.2
                     zf-H2C2_2  9 HtgekpyeCplCdk 22
                                  H g + + C  C+ 
  gi|70607187|ref|YP_256057.1| 13 HSGWFTVYCRICNR 26
                                  55556789*99*96 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00034
                     zf-H2C2_2 15 yeCplCdkaFk 25
                                  y+Cp+C k+++
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKYN 46
                                  9*******996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.14
                     zf-H2C2_2 16 eCplCd 21
                                  +Cp+C+
  gi|70607187|ref|YP_256057.1| 60 KCPYCG 65
                                  8****7 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   7.3    0.0003      0.13       8      53 ..      21      70 ..      17      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                       DUF1272  8 CecCdkdlppdseearic.....syEctFCaeCaeevlenvCPncgGelvk 53
                                  C  C+++++   +  + c      y   FC++ a  + ++ CP cg elv+
  gi|70607187|ref|YP_256057.1| 21 CRICNRKIRIGTDLVYKCpkcekKYNAFFCEADARGL-KKKCPYCGTELVS 70
                                  999****9999999988855555699*****999886.***********85 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.26   1.2e+02       1       6 [.      37      42 ..      32      44 .. 0.85
   2 ?    9.9   0.2    0.0017      0.74       1      10 [.      60      69 ..      60      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.26
                DNA_ligase_ZBD  1 hCPvCG 6 
                                  +CP C 
  gi|70607187|ref|YP_256057.1| 37 KCPKCE 42
                                  599995 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                DNA_ligase_ZBD  1 hCPvCGsavv 10
                                  +CP CG+++v
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTELV 69
                                  6*******98 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.5      0.36   1.6e+02      20      43 ..      21      44 ..      16      47 .. 0.68
   2 ?   13.6   0.1   0.00011     0.049      30      46 ..      54      70 ..      46      72 .] 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.36
                      zf-C2HC5 20 ClnCGkiiCakeglskpCsfCgsp 43
                                  C  C   i +   l+ +C+ C+++
  gi|70607187|ref|YP_256057.1| 21 CRICNRKIRIGTDLVYKCPKCEKK 44
                                  555655555555666999999875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                      zf-C2HC5 30 keglskpCsfCgsplls 46
                                  + gl+k+C++Cg++l+s
  gi|70607187|ref|YP_256057.1| 54 ARGLKKKCPYCGTELVS 70
                                  34677**********98 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.0    0.0001     0.047      28      56 .]      34      64 ..      26      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                       DUF4379 28 vwWkCakCgheWeasvsnrt.kgssk.CpkC 56
                                  +  kC+kC+++++a  ++   +g +k Cp+C
  gi|70607187|ref|YP_256057.1| 34 LVYKCPKCEKKYNAFFCEADaRGLKKkCPYC 64
                                  678***********9988863443335**** PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.3   0.00014     0.063      21      50 ..      21      48 ..      12      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                  --STT---B-EEETTTEEEETTTTEEESS- CS
                   Rep_fac-A_C 21 CpsedCnkKvveeedgewrCekCdkeveep 50
                                  C+   Cn+K+   +d  ++C kC+k+++ +
  gi|70607187|ref|YP_256057.1| 21 CR--ICNRKIRIGTDLVYKCPKCEKKYNAF 48
                                  66..8*********************9875 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   4.0      0.73   3.3e+02      10      16 ..      35      41 ..      23      44 .. 0.85
   2 ?   13.2   0.3   0.00011     0.051       8      19 ..      55      67 ..      52      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.73
                       zf-tcix 10 vrkCpkC 16
                                  v kCpkC
  gi|70607187|ref|YP_256057.1| 35 VYKCPKC 41
                                  569**** PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00011
                       zf-tcix  8 RGvr.kCpkCGty 19
                                  RG++ kCp CGt+
  gi|70607187|ref|YP_256057.1| 55 RGLKkKCPYCGTE 67
                                  888637*****96 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.0    0.0021      0.94      15      30 ..      56      71 ..      19      72 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                                  ESSSB-TTT-SB-B-S CS
                        Nop10p 15 TLkkvcpecggptksa 30
                                   Lkk+cp+cg++++sa
  gi|70607187|ref|YP_256057.1| 56 GLKKKCPYCGTELVSA 71
                                  69***********998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.31   1.4e+02       1      10 [.      20      29 ..      20      33 .. 0.85
   2 ?    5.6   1.5     0.031        14       1       8 [.      37      44 ..      37      47 .. 0.83
   3 ?   13.0   0.8   0.00014     0.065      15      23 .]      60      68 ..      58      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.31
                 zinc_ribbon_2  1 fCpnCGaelq 10
                                  +C  C +++ 
  gi|70607187|ref|YP_256057.1| 20 YCRICNRKIR 29
                                  7999999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                 zinc_ribbon_2  1 fCpnCGae 8 
                                  +Cp+C ++
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKK 44
                                  7****887 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00014
                 zinc_ribbon_2 15 FCpyCGtpl 23
                                   CpyCGt+l
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTEL 68
                                  599999987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7   0.00014     0.065      19      39 ..      19      42 ..       3      51 .. 0.77
   2 ?    1.6   0.7      0.78   3.5e+02      18      27 ..      58      67 ..      44      71 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                          C1_2 19 fnCsaCgrk...idgff..YsCseCd 39
                                    C++C rk   ++  +  Y+C++C+
  gi|70607187|ref|YP_256057.1| 19 VYCRICNRKiriGT--DlvYKCPKCE 42
                                  57*******87433..346******6 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.78
                          C1_2 18 sfnCsaCgrk 27
                                  +++C  Cg++
  gi|70607187|ref|YP_256057.1| 58 KKKCPYCGTE 67
                                  5778788765 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.33   1.5e+02      27      36 ..      21      30 ..      12      35 .. 0.77
   2 ?    2.2   0.6      0.37   1.6e+02       1      11 [.      36      46 ..      36      53 .. 0.83
   3 ?    8.7   0.1    0.0035       1.6       2      10 ..      60      68 ..      60      72 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.33
                 Cys_rich_CPXG 27 CqvCCrPivl 36
                                  C++C r i +
  gi|70607187|ref|YP_256057.1| 21 CRICNRKIRI 30
                                  8888887766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                 Cys_rich_CPXG  1 iqCPyCgeeie 11
                                  ++CP C ++ +
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKYN 46
                                  78****98765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0035
                 Cys_rich_CPXG  2 qCPyCgeei 10
                                  +CPyCg e+
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTEL 68
                                  6*****986 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5    0.0063       2.8       5      15 ..      19      29 ..      17      31 .. 0.86
   2 ?    4.6   0.1     0.054        24       5      13 ..      36      44 ..      33      47 .. 0.84
   3 ?    2.3   0.1      0.28   1.3e+02       6      11 ..      60      65 ..      58      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0063
                                  EE-TTTSSEEE CS
                         Sgf11  5 vtCpnCgRqia 15
                                  v C +C+R+i 
  gi|70607187|ref|YP_256057.1| 19 VYCRICNRKIR 29
                                  78*******96 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.054
                                  EE-TTTSSE CS
                         Sgf11  5 vtCpnCgRq 13
                                  ++Cp C+++
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKK 44
                                  79****986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.28
                                  E-TTTS CS
                         Sgf11  6 tCpnCg 11
                                  +Cp+Cg
  gi|70607187|ref|YP_256057.1| 60 KCPYCG 65
                                  6****8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       6.3   2.8e+03      14      17 ..      21      24 ..      19      28 .. 0.62
   2 ?    2.1   4.1      0.48   2.2e+02       2       9 ..      37      44 ..      37      52 .. 0.87
   3 ?   11.1   0.2   0.00074      0.33      15      23 ..      59      67 ..      58      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 6.3
                       UPF0547 14 aqfC 17
                                  +++C
  gi|70607187|ref|YP_256057.1| 21 CRIC 24
                                  4555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.48
                       UPF0547  2 vCPeCeak 9 
                                  +CP Ce k
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKK 44
                                  7****975 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00074
                       UPF0547 15 qfCphCGyv 23
                                  ++Cp+CG++
  gi|70607187|ref|YP_256057.1| 59 KKCPYCGTE 67
                                  689999986 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.7    0.0015      0.68       1      23 [.      21      45 ..      21      52 .. 0.83
   2 ?    3.5   1.1      0.18        82      13      21 ..      58      66 ..      48      68 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                        zf-AN1  1 CsfksCkkkd....flpfkCryCgkvF 23
                                  C +  C++k+     l++kC++C+k++
  gi|70607187|ref|YP_256057.1| 21 CRI--CNRKIrigtDLVYKCPKCEKKY 45
                                  664..****97765567********98 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.18
                        zf-AN1 13 pfkCryCgk 21
                                    kC+yCg 
  gi|70607187|ref|YP_256057.1| 58 KKKCPYCGT 66
                                  469****96 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   6.9       0.2        88      14      29 ..      16      31 ..      11      48 .. 0.86
   2 ?    6.7   0.2     0.017       7.6       6      27 ..      48      69 ..      47      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                                  SS--EETTTTEE---- CS
                        zf-BED 14 eqkavCryCgkilsrg 29
                                  +  ++Cr+C++++  g
  gi|70607187|ref|YP_256057.1| 16 WFTVYCRICNRKIRIG 31
                                  66799*****999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                                  SS----GGSS--EETTTTEE-- CS
                        zf-BED  6 yftpvslkeqkavCryCgkils 27
                                  +f +++++  k +C yCg +l 
  gi|70607187|ref|YP_256057.1| 48 FFCEADARGLKKKCPYCGTELV 69
                                  566777888899******9886 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.4    0.0012      0.52      25      48 .]      21      46 ..      18      46 .. 0.84
   2 ?    4.1   0.3      0.09        40      27      44 ..      49      65 ..      47      68 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                     zf-RING_4 25 ClfCyhrile..eeegrCPaCreeYk 48
                                  C+ C ++i+   +   +CP+C ++Y+
  gi|70607187|ref|YP_256057.1| 21 CRICNRKIRIgtDLVYKCPKCEKKYN 46
                                  9999998886547799*********6 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.09
                     zf-RING_4 27 fCyhrileeeegrCPaCr 44
                                  fC  +++   +++CP C 
  gi|70607187|ref|YP_256057.1| 49 FCEADAR-GLKKKCPYCG 65
                                  5655555.46899****5 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.5      0.09        40      10      30 ..      24      41 ..      18      46 .. 0.68
   2 ?   10.7   0.8   0.00059      0.26      14      32 ..      49      66 ..      44      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.09
                   Mu-like_Com 10 CaRLLaKaeAlDeltiKCPRC 30
                                  C R +  +   D l  KCP+C
  gi|70607187|ref|YP_256057.1| 24 CNRKIRIGT--D-LVYKCPKC 41
                                  555554443..5.789***** PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00059
                   Mu-like_Com 14 LaKaeAlDeltiKCPRCGt 32
                                   + a+A   l+ KCP CGt
  gi|70607187|ref|YP_256057.1| 49 FCEADARG-LKKKCPYCGT 66
                                  68999998.9********9 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.22        98      31      42 ..      18      29 ..      13      36 .. 0.74
   2 ?    3.5   1.7       0.2        90       3      13 ..      36      46 ..      34      51 .. 0.77
   3 ?    8.3   0.2    0.0065       2.9       4      12 ..      60      68 ..      58      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.22
                       zf-Di19 31 evvCPvCaekvt 42
                                   v C +C  k++
  gi|70607187|ref|YP_256057.1| 18 TVYCRICNRKIR 29
                                  689****98864 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.2
                       zf-Di19  3 ftCPyCgkelt 13
                                  ++CP C+k+++
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKYN 46
                                  78999988765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0065
                       zf-Di19  4 tCPyCgkel 12
                                  +CPyCg el
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTEL 68
                                  7****9875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       1.4   6.5e+02       2       8 ..      20      26 ..      19      30 .. 0.81
   2 ?    6.6   0.7     0.012       5.6       1      10 [.      36      45 ..      36      55 .. 0.83
   3 ?    7.6   0.4    0.0061       2.7       2       9 ..      60      67 ..      59      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.4
                                  EETTTTC CS
                  TF_Zn_Ribbon  2 kCPnCgs 8 
                                   C +C+ 
  gi|70607187|ref|YP_256057.1| 20 YCRICNR 26
                                  699**96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                  EEETTTTCEE CS
                  TF_Zn_Ribbon  1 ykCPnCgstn 10
                                  ykCP+C  ++
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKY 45
                                  89****9865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0061
                                  EETTTTCE CS
                  TF_Zn_Ribbon  2 kCPnCgst 9 
                                  kCP+Cg++
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTE 67
                                  8*****86 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.54   2.4e+02       2       9 ..      20      27 ..      19      29 .. 0.83
   2 ?    7.6   2.1     0.012       5.6       1      11 [.      36      46 ..      36      49 .. 0.90
   3 ?    6.1   0.1     0.038        17       2       8 ..      60      66 ..      59      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.54
                                  EETTTTEE CS
                       zf-C2H2  2 kCpdCgks 9 
                                  +C +C+++
  gi|70607187|ref|YP_256057.1| 20 YCRICNRK 27
                                  5****985 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                                  EEETTTTEEES CS
                       zf-C2H2  1 ykCpdCgksFk 11
                                  ykCp+C k+++
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKYN 46
                                  9*******996 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.038
                                  EETTTTE CS
                       zf-C2H2  2 kCpdCgk 8 
                                  kCp+Cg 
  gi|70607187|ref|YP_256057.1| 60 KCPYCGT 66
                                  8****97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4    0.0044         2      30      58 ..      20      47 ..      14      50 .. 0.91
   2 ?    4.0   0.4      0.11        49      29      38 ..      59      68 ..      50      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0044
                OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfeadr 58
                                   C  C +k +   ++ ++kCp+C  ++++
  gi|70607187|ref|YP_256057.1| 20 YCRICNRKIRI-GTDLVYKCPKCEKKYNA 47
                                  69999999999.9999*********9997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                OrfB_Zn_ribbon 29 ktCseCgskn 38
                                  k+C+ Cg ++
  gi|70607187|ref|YP_256057.1| 59 KKCPYCGTEL 68
                                  7899999765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.1      0.15        69      19      25 ..      35      41 ..      20      42 .. 0.77
   2 ?    3.7   1.4     0.086        39       1       6 [.      37      42 ..      37      46 .. 0.82
   3 ?    6.8   0.1    0.0093       4.2       1      10 [.      60      69 ..      60      72 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.15
                      zf-TFIIB 19 idyCpqC 25
                                  +++Cp+C
  gi|70607187|ref|YP_256057.1| 35 VYKCPKC 41
                                  6667777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.086
                      zf-TFIIB  1 kCPkCq 6 
                                  kCPkC 
  gi|70607187|ref|YP_256057.1| 37 KCPKCE 42
                                  799996 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0093
                      zf-TFIIB  1 kCPkCqdele 10
                                  kCP C++el+
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTELV 69
                                  8*******98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.42   1.9e+02       2       8 ..      20      26 ..      19      29 .. 0.84
   2 ?    5.1   3.1      0.11        49       1      10 [.      36      45 ..      36      51 .. 0.89
   3 ?    7.7   0.1     0.017       7.6       2      11 ..      60      69 ..      59      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.42
                     zf-C2H2_4  2 kCpiCgk 8 
                                  +C+iC++
  gi|70607187|ref|YP_256057.1| 20 YCRICNR 26
                                  7****87 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.11
                     zf-C2H2_4  1 fkCpiCgksF 10
                                  +kCp C k +
  gi|70607187|ref|YP_256057.1| 36 YKCPKCEKKY 45
                                  8*****9998 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.017
                     zf-C2H2_4  2 kCpiCgksFs 11
                                  kCp+Cg+   
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTELV 69
                                  8****98765 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.6   1.6e+03       4       9 ..      21      26 ..      19      28 .. 0.60
   2 ?   10.2   4.4    0.0013      0.57       4      32 ..      38      69 ..      36      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.6
                                  -TTT-- CS
                       ADK_lid  4 CpkCGr 9 
                                  C+ C+r
  gi|70607187|ref|YP_256057.1| 21 CRICNR 26
                                  555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                                  -TTT--EEETTT...B--SSTTB-TTT--.-B CS
                       ADK_lid  4 CpkCGrsYhvvf...npPkveglCDkCGepLv 32
                                  CpkC + Y+  f        + +C  CG +Lv
  gi|70607187|ref|YP_256057.1| 38 CPKCEKKYNAFFceaDARGLKKKCPYCGTELV 69
                                  *********5556533345899*********8 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       6.1   2.7e+03      31      36 ..      21      26 ..      18      29 .. 0.60
   2 ?    9.3   0.5    0.0023         1       2      11 ..      37      46 ..      31      55 .. 0.64
   3 ?    4.5   0.1     0.071        32       2       9 ..      60      67 ..      59      72 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.1
                       TFIIS_C 31 CtkCgh 36
                                  C  C+ 
  gi|70607187|ref|YP_256057.1| 21 CRICNR 26
                                  666654 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0023
                       TFIIS_C  2 kCpkCgsrea 11
                                  kCpkC ++  
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKKYN 46
                                  4555555544 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.071
                       TFIIS_C  2 kCpkCgsr 9 
                                  kCp Cg +
  gi|70607187|ref|YP_256057.1| 60 KCPYCGTE 67
                                  8****986 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.75   3.4e+02      15      23 ..      18      26 ..      16      28 .. 0.67
   2 ?    7.0   6.2     0.014       6.5       5      23 ..      37      55 ..      35      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.75
                      zf-B_box 15 tlfCedCqq 23
                                  t +C+ C+ 
  gi|70607187|ref|YP_256057.1| 18 TVYCRICNR 26
                                  567777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                      zf-B_box  5 kCpeHknkpatlfCedCqq 23
                                  kCp++++k   +fCe +  
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKKYNAFFCEADAR 55
                                  8*****99999****9986 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.12        56      36      57 ..      17      38 ..      14      40 .. 0.87
   2 ?    7.2   0.8     0.011       4.8      29      47 ..      27      45 ..      22      55 .. 0.79
   3 ?    4.9   0.3     0.058        26      37      47 ..      58      68 ..      52      72 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.12
                          CpXC 36 featCpkCgatakleapllyhd 57
                                  f++ C  C++++++  +l+y+ 
  gi|70607187|ref|YP_256057.1| 17 FTVYCRICNRKIRIGTDLVYKC 38
                                  7899**********99999975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                          CpXC 29 klldgslfeatCpkCgata 47
                                  k++ g+ + ++CpkC+++ 
  gi|70607187|ref|YP_256057.1| 27 KIRIGTDLVYKCPKCEKKY 45
                                  6777888888999998865 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.058
                          CpXC 37 eatCpkCgata 47
                                  + +Cp+Cg++ 
  gi|70607187|ref|YP_256057.1| 58 KKKCPYCGTEL 68
                                  56799999865 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.7   7.5e+02       4      12 ..      20      28 ..      18      35 .. 0.60
   2 ?    7.9   7.5    0.0065       2.9       4      33 ..      37      66 ..      36      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.7
                 zinc_ribbon_4  4 tCpsCkaky 12
                                   C  C+ k 
  gi|70607187|ref|YP_256057.1| 20 YCRICNRKI 28
                                  455555544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0065
                 zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCgh 33
                                   Cp+C++ky+       a+g k +C+ Cg+
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKKYNAFFCEADARGLKKKCPYCGT 66
                                  5*********9999999***********97 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       1.6   7.1e+02       4      17 ..      21      33 ..      18      36 .. 0.69
   2 ?    4.2   2.0      0.13        57      39      46 .]      35      42 ..      34      42 .. 0.88
   3 ?    8.3   0.1    0.0068       3.1       2      12 ..      59      69 ..      58      72 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.6
                       zf-IS66  4 CpcCGgllkpiged 17
                                  C  C+ +  +ig+d
  gi|70607187|ref|YP_256057.1| 21 CRICNRKI-RIGTD 33
                                  77788763.77776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.13
                       zf-IS66 39 kyaCpcCe 46
                                  +y+Cp+Ce
  gi|70607187|ref|YP_256057.1| 35 VYKCPKCE 42
                                  79*****7 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0068
                       zf-IS66  2 rtCpcCGgllk 12
                                  ++Cp CG++l+
  gi|70607187|ref|YP_256057.1| 59 KKCPYCGTELV 69
                                  68******654 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   4.9       1.2   5.4e+02      27      44 .]      26      43 ..      18      43 .. 0.59
   2 ?    3.5   0.9      0.16        72       1       9 [.      37      45 ..      37      48 .. 0.75
   3 ?    9.4   0.4    0.0022         1      23      43 ..      48      65 ..      46      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.2
                     zf-RING_5 27 kClkkll...ekeavCpiCrk 44
                                  + +          ++Cp C+k
  gi|70607187|ref|YP_256057.1| 26 RKI---RigtDLVYKCPKCEK 43
                                  333...333366789999986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
                     zf-RING_5  1 hCnkCfekl 9 
                                  +C+kC +k+
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKKY 45
                                  588888887 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0022
                     zf-RING_5 23 ifCekClkkllekeavCpiCr 43
                                  +fCe+ ++ l+   ++Cp C+
  gi|70607187|ref|YP_256057.1| 48 FFCEADARGLK---KKCPYCG 65
                                  79*********...******7 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9     0.025        11       5      11 ..      21      27 ..      18      27 .. 0.85
   2 ?    6.8   0.6     0.014       6.5       4      13 ..      37      46 ..      36      47 .. 0.89
   3 ?    3.7   2.6      0.13        60       4       9 ..      60      65 ..      59      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                     zf-C2HC_2  5 CpkCgRs 11
                                  C++C+R+
  gi|70607187|ref|YP_256057.1| 21 CRICNRK 27
                                  ******8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                     zf-C2HC_2  4 pCpkCgRsFn 13
                                  +CpkC  ++n
  gi|70607187|ref|YP_256057.1| 37 KCPKCEKKYN 46
                                  7*****9998 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                     zf-C2HC_2  4 pCpkCg 9 
                                  +Cp+Cg
  gi|70607187|ref|YP_256057.1| 60 KCPYCG 65
                                  8****9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.0     0.018       8.3     509     529 ..      20      45 ..      10      55 .. 0.68
   2 ?    3.9   0.4     0.042        19     515     527 ..      52      66 ..      46      72 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                                   EETT.--EESS.....SB-TTT--BE CS
                          NRDD 509 vCnecgykgei.....ekCpkCgsee 529
                                   +C+ c++k  i     +kCpkC+++ 
  gi|70607187|ref|YP_256057.1|  20 YCRICNRKIRIgtdlvYKCPKCEKKY 45 
                                   566666644444456799*****664 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.042
                                   -..EESSSB-TTT-- CS
                          NRDD 515 y..kgeiekCpkCgs 527
                                      +g+++kCp+Cg 
  gi|70607187|ref|YP_256057.1|  52 AdaRGLKKKCPYCGT 66 
                                   333889999*****4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 505.46
//
Query:       gi|70607188|ref|YP_256058.1|  [L=713]
Description: amylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-20   73.1   0.3    5.5e-19   68.3   0.0    3.0  3  CBM_48           Carbohydrate-binding module 48 (Isoamylase N
    2.6e-16   60.1   1.1    1.2e-08   35.0   0.2    3.4  2  Alpha-amylase    Alpha amylase, catalytic domain
     0.0032   17.2   0.1        0.1   12.4   0.1    2.4  1  GlgX_C           Glycogen debranching enzyme C-terminal domai
  ------ inclusion threshold ------
      0.058   14.0   0.0       0.19   12.3   0.0    1.8  1  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
        0.3   10.9   0.6          1    9.2   0.0    2.1  2  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin


Domain annotation for each model (and alignments):
>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   1.5e-22   5.5e-19       1      84 []      13     104 ..      13     104 .. 0.93
   2 ?   -0.6   0.1       0.5   1.8e+03      34      68 ..     478     513 ..     472     524 .. 0.68
   3 ?    0.5   0.0      0.23   8.2e+02      66      83 ..     663     680 ..     653     695 .. 0.69

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.5e-22
                                   TSEEEEESSCEEEEEEEE-TTSSEEEEEECGTT...TEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETT....S CS
                        CBM_48   1 plGahvsedekgvnfrvwapnAekVslvldfnn...wdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgps....g 74 
                                   plGa++ e+e+gvnf ++++nA+kV+l+ +++    +++e i+l+ +rtg+ W++f+pg  p g ++Y+yrv gp+    g
  gi|70607188|ref|YP_256058.1|  13 PLGATWIEEEDGVNFVLFSENATKVELLTYSQTrqdEPKEIIELR-QRTGDLWHVFVPGLRP-G-QLYGYRVYGPYkpeeG 90 
                                   79*****9889********************999999999*****.6***********8888.7.6**********99884 PP

                                   ....CEEEE--TT- CS
                        CBM_48  75 ....ekklllDPya 84 
                                       ++k+l+DPya
  gi|70607188|ref|YP_256058.1|  91 lrfnPNKVLIDPYA 104
                                   7777*********8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.5
                                   TEEECCB-EE...ECGGCEEEEEEETTSTTTT.EEEEE CS
                        CBM_48  34 wdaeeiplkr...rrtggvWelflpgdlphgslrYkyr 68 
                                   ++ e+++l +    ++++ W + ++g+   +s ++ y+
  gi|70607188|ref|YP_256058.1| 478 KHNEANKLNNedgMNENYSWNCGVEGETN-DS-NILYC 513
                                   4555555555445678999******7766.55.77776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.23
                                   EEEEEETTSCEEEE--TT CS
                        CBM_48  66 kyrvkgpsgekklllDPy 83 
                                     ++k+p+g+++l+l Py
  gi|70607188|ref|YP_256058.1| 663 NLKIKVPHGKWELVLHPY 680
                                   345555566666666555 PP

>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   3.2e-12   1.2e-08       9     104 ..     201     312 ..     191     321 .. 0.80
   2 !   19.7   0.1   1.4e-07    0.0005     123     333 ..     307     544 ..     294     548 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.2e-12
                                   TCCCCCCCT-SCEEE-B-CE..........-S-TTTTSS-SCECCE-CCC......--C.CCCCCHHHHHHCTT-EEEEEE CS
                 Alpha-amylase   9 kLdYlkeLGvtaiwlsPifk..........spqadhgYdiadytkidpef......Gtn.edlkeLiskahekgikvilDl 72 
                                    +dYlk+LG+t + + Pi +            +++ gY   +y + + ++      G++  ++k+L++ +h+ g+ vi+D+
  gi|70607188|ref|YP_256058.1| 201 MIDYLKDLGITTVEIMPIQQfvderfivdkGLKNYWGYNPINYFSPECRYsssgclGNQvIEFKKLVNSLHNAGLEVIIDV 281
                                   48*****************9********995568*********9988888444333443258******************* PP

                                   --SC--TTSCCCHCCHHSTTSGGGCCC-E... CS
                 Alpha-amylase  73 VvNHtsdehewfkeslkkkgepkrdyyiwkeg 104
                                   V NHt++ ++   + l+ kg +++ yy++ ++
  gi|70607188|ref|YP_256058.1| 282 VYNHTAEGNHL-GPTLSFKGIDNSSYYMLDPK 312
                                   ******98774.66666667677777776655 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.4e-07
                                   CEECTTTTCEEESSS-TTS-BB-TTTCCCCCCCCCCCCCCCTTT.-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHT CS
                 Alpha-amylase 123 weydekaqeyylhlflkklpdLnteneevrkelkdvvkfwlekg.idGfRlDvvkhvskvealesngeflheftqalnetv 202
                                   +  d k + yy+  f+ +   Ln  ++ v + + d +++w+ +  +dGfR D ++ ++    +  + ++l +f  a+++  
  gi|70607188|ref|YP_256058.1| 307 YMLDPKNKRYYI-DFTGTGNTLNLSHPRVLQLVLDSLRYWVLEMhVDGFRFDLASALAR---QLYSVNMLSTFFVAIQQDP 383
                                   444555555554.57778899*******************98777************99...4344455555555555443 PP

                                   CCGTT-EEEEE-TT-SCCCHCCCC-CGG-SICECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-C...CCTTC CS
                 Alpha-amylase 203 asrkevmtvgEvssdasedlrvyttearlelemvldfphldvaqkakikeqlksisakklkellkkwlkalee...aaeea 280
                                       +v +++E ++      +      + +++ +      + +  ++ ++++ ++  ++l+++l  + + +     +   +
  gi|70607188|ref|YP_256058.1| 384 -ILSQVKLIAEPWDVGPGGYQ------VGNFPYLWAEWNGKYRDTIRRFWRGDPVPYEELANRLLGSPDLYAGsnkTPFAS 457
                                   .45556666666654443222......222221122223333333344666666666666666644333332211244556 PP

                                   EEES--TTS--HHHHTTSSTTTT..................................HHHHHHHHHCCCTSSSEEEEETTC CS
                 Alpha-amylase 281 vtflgnHDqeRilsrlgddsaea..................................ekklklaaillltlrGvpviYyGe 327
                                    +++ +HD   +   ++++++++                                  ek+ ++++i l+ ++G+p+i  G+
  gi|70607188|ref|YP_256058.1| 458 INYITSHDGFTLQDLVSYNQKHNeanklnnedgmnenyswncgvegetndsnilycrEKQRRNFVITLFVSQGIPMILGGD 538
                                   6666666666555555555544455566666666666666666666677888888888889999999************** PP

                                   CCT--- CS
                 Alpha-amylase 328 Eigmtg 333
                                   Eig t 
  gi|70607188|ref|YP_256058.1| 539 EIGRTQ 544
                                   *99886 PP

>> GlgX_C  Glycogen debranching enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   2.9e-05       0.1      34      66 ..     650     683 ..     605     692 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                        GlgX_C  34 sdrwLitlnateevaelvLPeGeWrav.pPfage 66 
                                    d++Li+ln ++   ++++P+G+W++v  P+ +e
  gi|70607188|ref|YP_256058.1| 650 DDTFLIILNGASTNLKIKVPHGKWELVlHPYPHE 683
                                   478*********************9652677665 PP

>> Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05      0.19      19      80 ..      17      82 ..      11      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
               Pur_ac_phosph_N 19 sWitpektkksvvrygtssdalestaeatsstyet.....tnyksgyshkatltgLepgttYyYrvg 80
                                  +Wi  e+ + ++v ++++ +++e  ++ ++++ e        +++g  +++ + gL+pg+ Y Yrv 
  gi|70607188|ref|YP_256058.1| 17 TWIEEED-GVNFVLFSENATKVELLTYSQTRQDEPkeiieLRQRTGDLWHVFVPGLRPGQLYGYRVY 82
                                  6777777.677777777777755544444444333666668999*********************95 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.73   2.6e+03      18      24 ..     243     249 ..     242     249 .. 0.89
   2 ?    9.2   0.0   0.00029         1       4      20 ..     497     513 ..     496     515 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.73
                                   -B-TTT- CS
                    HscB_4_cys  18 fFCpqCR 24 
                                   +F p CR
  gi|70607188|ref|YP_256058.1| 243 YFSPECR 249
                                   799***9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00029
                                   SSS--B--SS-S---B- CS
                    HscB_4_cys   4 WnCGgpgapgrgdefFC 20 
                                   WnCG  g+  + ++++C
  gi|70607188|ref|YP_256058.1| 497 WNCGVEGETNDSNILYC 513
                                   ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 4559.88
//
Query:       gi|70607189|ref|YP_256059.1|  [L=556]
Description: maltooligosyl trehalose trehalohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-33  114.2   2.0    1.9e-22   80.3   0.1    3.3  3  Alpha-amylase  Alpha amylase, catalytic domain
    5.1e-32  109.5   1.6    1.4e-31  108.1   1.6    1.8  1  Alpha-amyl_C   Alpha-amylase, C terminal
     0.0003   21.1   0.0    0.00086   19.6   0.0    1.8  1  CBM_48         Carbohydrate-binding module 48 (Isoamylase N-t


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   3.2e-26   1.9e-22       1      83 [.     117     200 ..     117     217 .. 0.92
   2 !   21.7   0.2   2.1e-08   0.00012     150     209 ..     229     324 ..     224     348 .. 0.86
   3 !    9.8   0.0   8.5e-05      0.51     281     333 ..     369     422 ..     361     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 3.2e-26
                                   --CHHHHCTCCCCCCCT-SCEEE-B-CE-S.-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TT CS
                 Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifksp.qadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsde 80 
                                   G +kG+iekLdYlk+LG+t+i l P+ + p + d gYd    +++++++G   +l +L+++ah++gi vilD+V NH + e
  gi|70607189|ref|YP_256059.1| 117 GNFKGVIEKLDYLKDLGITGIELMPVAQFPgNRDWGYDGVFLYAVQNTYGGPWELAKLVNEAHKRGIAVILDVVYNHIGPE 197
                                   899*************************663689*********************************************99 PP

                                   SCC CS
                 Alpha-amylase  81 hew 83 
                                    ++
  gi|70607189|ref|YP_256059.1| 198 GNY 200
                                   887 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-08
                                   CCCCCCCCCCCCCCTTT.-SEEEETTCCCTTTCCCC...................................HCCHCCHHHH CS
                 Alpha-amylase 150 evrkelkdvvkfwlekg.idGfRlDvvkhvskveal...................................esngeflhef 194
                                   +vrk + + v++w++++ idG+RlD+v+ +  ++                                     + +++++ +f
  gi|70607189|ref|YP_256059.1| 229 QVRKFILENVEYWFKTFkIDGLRLDAVHAIFDNSPKhilqeiaekahqlgkfviaesdlndpkivkddcgyKIDAQWVDDF 309
                                   788999999*********************995544789999999999999999999999999999999998999999999 PP

                                   HHHHHHHTCCGTT-E CS
                 Alpha-amylase 195 tqalnetvasrkevm 209
                                   ++a++++++++k+ +
  gi|70607189|ref|YP_256059.1| 310 HHAVHAFITKEKDYY 324
                                   999999887666654 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 8.5e-05
                                   EEES--TTS--HHHHTTSSTTTT...HHHHHHHHHCCCTSSSEEEEETTCCCT--- CS
                 Alpha-amylase 281 vtflgnHDqeRilsrlgddsaea...ekklklaaillltlrGvpviYyGeEigmtg 333
                                   v+f++nHDq  +++r + ++ +    +    +aa+l ++++ +p i+ GeE + t+
  gi|70607189|ref|YP_256059.1| 369 VVFIQNHDQ--VGNRGNGERLSIltdKTTYLMAATLYILSPYIPLIFMGEEYYETN 422
                                   78******9..78888888865587777888999******************9998 PP

>> Alpha-amyl_C  Alpha-amylase, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   1.6   2.4e-35   1.4e-31       1      67 []     489     554 ..     489     554 .. 1.00

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 2.4e-35
                  Alpha-amyl_C   1 CkRkleVekednwltvklekilivvaFsdsvielkysGeLllssssFPkkikesklikvdkGvgvYk 67 
                                   CkR++eV++e+n++t+++eki+i+++F+d+vi++k++G+Ll+++ +FPkk+k+++likv++GvgvY+
  gi|70607189|ref|YP_256059.1| 489 CKRVKEVRREGNCITLIMEKIGIIASFDDIVINSKITGNLLIGI-GFPKKLKKDELIKVNRGVGVYQ 554
                                   ********************************************.*********************8 PP

>> CBM_48  Carbohydrate-binding module 48 (Isoamylase N-terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-07   0.00086       2      73 ..       4      65 ..       3      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-07
                                  SEEEEESSCEEEEEEEE-TTSSEEEEEECGTTTEEECCB-EEECGGCEEEEEEETTSTTTT.EEEEEEEETT CS
                        CBM_48  2 lGahvsedekgvnfrvwapnAekVslvldfnnwdaeeiplkrrrtggvWelflpgdlphgslrYkyrvkgps 73
                                  +G +++++  +  f++wap   +V+l l++     + ip++ ++++g++e+ ++ d++++ l Y y ++ + 
  gi|70607189|ref|YP_256059.1|  4 FGGNIEKN--KGIFKLWAPYVNSVKLKLSK-----KLIPME-KNDEGFFEVEID-DIEEN-LTYSYIIEDKR 65
                                  67777655..789***************85.....568***.69**********.99987.8*****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3682.11
//
Query:       gi|70607190|ref|YP_256060.1|  [L=174]
Description: hypothetical protein Saci_1442 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.1   0.2      0.053   13.6   0.1    1.8  2  DUF3726   Protein of unknown function (DUF3726)


Domain annotation for each model (and alignments):
>> DUF3726  Protein of unknown function (DUF3726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     3e-06     0.053      32      71 ..       9      48 ..       6      64 .. 0.84
   2 ?   -1.9   0.0      0.22   3.9e+03      38      53 ..      66      81 ..      59      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-06
                       DUF3726 32 rwLqmagLdGikelnnaleflfnekdvpldiksdssatad 71
                                   +L+   L+ ++ + n++ef+f e+++++d   + sa ++
  gi|70607190|ref|YP_256060.1|  9 KDLNYSKLEQTQVFGNVFEFVFLEREKEVDFFVRTSAQEE 48
                                  678899999*********************9666555544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.22
                       DUF3726 38 gLdGikelnnaleflf 53
                                  g+ G+  l++ ++f  
  gi|70607190|ref|YP_256060.1| 66 GFVGVLSLKKESDFYE 81
                                  7778888888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1378.78
//
Query:       gi|70607191|ref|YP_256061.1|  [L=208]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1417.96
//
Query:       gi|70607192|ref|YP_256062.1|  [L=342]
Description: hypothetical protein Saci_1445 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 2220.40
//
Query:       gi|70607193|ref|YP_256063.1|  [L=46]
Description: hypothetical protein Saci_1446 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   13.2   0.0      0.084   13.2   0.0    1.1  1  SF1-HH    Splicing factor 1 helix-hairpin domain


Domain annotation for each model (and alignments):
>> SF1-HH  Splicing factor 1 helix-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.7e-06     0.084      81     109 ..      15      43 ..       6      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-06
                        SF1-HH  81 evrvrkkLekerhelieeavkiipsfkpP 109
                                   e  + + Le+ r+ lie+  +++p+ +pP
  gi|70607193|ref|YP_256063.1|  15 ELETDEDLEEFRKMLIEAYYELNPDHRPP 43 
                                   5667899*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 334.59
//
Query:       gi|70607194|ref|YP_256064.1|  [L=514]
Description: hypothetical protein Saci_1447 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-29  101.5   0.1    8.7e-29  100.2   0.1    1.8  1  AAA_14        AAA domain
    1.5e-15   57.4   0.5    3.4e-15   56.3   0.3    1.9  2  DUF4143       Domain of unknown function (DUF4143)
    9.9e-05   22.4   0.2    0.00037   20.5   0.1    1.9  2  ATPase_2      ATPase domain predominantly from Archaea
    0.00013   22.4   0.0    0.00022   21.6   0.0    1.5  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.025   15.0   0.0    1.6  1  AAA           ATPase family associated with various cellular 
      0.013   15.9   0.2       0.38   11.1   0.0    2.3  2  AAA_19        AAA domain
      0.028   14.7   0.0      0.065   13.5   0.0    1.6  1  AAA_22        AAA domain
      0.029   14.7   0.0      0.092   13.1   0.0    1.9  2  RNA_helicase  RNA helicase
       0.06   13.9   0.2       0.33   11.5   0.0    2.4  3  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.1   4.4e-32   8.7e-29       3     130 ..      59     202 ..      57     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 4.4e-32
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevpe 78 
                                    i++++G+RrvGKTtl+k +i++l+    +++++i+yi ld e++k  + +  +lle+i e+  +++++y+flDE++++++
  gi|70607194|ref|YP_256064.1|  59 GIVTVRGPRRVGKTTLIKLIIRHLIkerqINPSNIFYIPLDYEQFKVDNISLiNLLEAIAES--NNEEKYVFLDEVSMYRG 137
                                   699********************99********************87664412555666664..4699************* PP

                        AAA_14  79 wekalkslvdeg....knldvivtGSnskllskeiatslagrva..........eielyplsfaEf 130
                                   w +alk+ +deg     ++++i+tGS+s++l  e+a++l++r+           ++ + pl f+E+
  gi|70607194|ref|YP_256064.1| 138 WAQALKNAYDEGliknYKVRIIATGSHSMDLA-EAASKLSDRQGemakminlggNLVMRPLRFSEV 202
                                   **********77662245799**********5.5899*****9999999999999********997 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.1   8.1e+03      76     104 ..      77     106 ..      76     110 .. 0.75
   2 !   56.3   0.3   1.7e-18   3.4e-15      18     122 .]     306     474 ..     208     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.1
                                   xxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       DUF4143  76 lVaqeLlkysekegaklyyyrdkn.gaEvD 104
                                   l++++L+k+++ +  +++y   ++ +  vD
  gi|70607194|ref|YP_256064.1|  77 LIIRHLIKERQINPSNIFYIPLDYeQFKVD 106
                                   689999999888888888876655566665 PP

  == domain 2  score: 56.3 bits;  conditional E-value: 1.7e-18
                                   x...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  18 k...............................................glverlppwsespnskkrlrkspKlyfvDtGLl 51 
                                   +                                               + ++  ++  es+++k +++++ K y++D++L+
  gi|70607194|ref|YP_256064.1| 306 RlleyltgpmtvsnlmnpinlevigedesgkpkrkinwkdyfnylittYSFFFGYR--ESEECKPNYEDMVKNYVLDPFLY 384
                                   35555555555555555555555666666666666777777776664444444444..4********************** PP

                                   xxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       DUF4143  52 vallgldkeelleds............enkGallEnlVaqeLlky.......sekegaklyyyrdkngaEvDfvielk... 110
                                   +++ +   ++   d+            ++kG l+E++Va++Ll++       +++e+ k+ +yr++++ E+Df++  +   
  gi|70607194|ref|YP_256064.1| 385 HSIRSYFHNS---DDpfeesrkmlkdnTFKGLLVESVVASHLLQSqylfehvTHVEYDKVLMYRKDDQGEIDFILCITknn 462
                                   **66544433...22355678999999**************************************99*******9544444 PP

                                   xxxxxxxxxxxx RF
                       DUF4143 111 ggkivpiEvKss 122
                                   ++  ++iE K+s
  gi|70607194|ref|YP_256064.1| 463 SKYKFYIESKYS 474
                                   88899*****96 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.8e-07   0.00037      17      60 ..      55     101 ..      47     153 .. 0.80
   2 ?   -1.9   0.0       1.3   2.6e+03     108     169 ..     112     166 ..     101     189 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                      ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienl.edkdk..yviyyialree 60 
                                   ++++ i+ + Gp+++GKt+L+k ii  l ++ +     i+yi+l  e
  gi|70607194|ref|YP_256064.1|  55 SGSYGIVTVRGPRRVGKTTLIKLIIRHLiKERQInpSNIFYIPLDYE 101
                                   56788999******************996444446799****99754 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                      ATPase_2 108 lllekikkkgkk.iiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSegl 169
                                   +lle+i ++  +   +++De+ + +  g        ++L n++++ + ++ ++ +i++ S ++
  gi|70607194|ref|YP_256064.1| 112 NLLEAIAESNNEeKYVFLDEVSMYR--GWA------QALKNAYDEGLIKNYKVRIIATGSHSM 166
                                   4555555555555667777777766..433......445555555444444444455555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.1e-07   0.00022      18      78 ..      52     119 ..      40     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                        AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd......ggiflrgkcdql.esaipysalaqalar 78 
                                   +  sg+ ++v ++G++ vGK++l++ + r+l k+      +++++  +++q+   +i+++ l++a+a+
  gi|70607194|ref|YP_256064.1|  52 NFVSGSYGIVTVRGPRRVGKTTLIKLIIRHLIKErqinpsNIFYIPLDYEQFkVDNISLINLLEAIAE 119
                                   5668888**********************999998898866666999988883334555556666643 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.3e-05     0.025       3     119 ..      63     172 ..      61     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHH CS
                           AAA   3 lyGppGtGKTllakavakel.........gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalaks 73 
                                   + Gp  +GKT+l+k ++++l         ++ ++ ++        ++  + ++ +l++++ e++ + + +f+DE+    + 
  gi|70607194|ref|YP_256064.1|  63 VRGPRRVGKTTLIKLIIRHLikerqinpsNIFYIPLDYE-----QFKVDNISLINLLEAIAESNnEEKYVFLDEVSMY-RG 137
                                   679****************86655332222223333333.....45577777777888866655467*******9766.33 PP

                                   HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                           AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                               +++L ++ d+   k+ kv +i+++ +  +l +a 
  gi|70607194|ref|YP_256064.1| 138 W-----------AQALKNAYDEGLIKNYKVRIIATGSHSMDLAEAA 172
                                   3...........6889999998888888899998888844444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00019      0.38      14      47 ..      62      95 ..      56     100 .. 0.84
   2 ?    2.4   0.0     0.091   1.8e+02      89     117 ..     112     139 ..      98     150 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                        AAA_19 14 lvtaGpGtGKTrvlkhivallvelggvkpeeill 47
                                   v ++   GKT+++k i+++l+++++++p +i  
  gi|70607194|ref|YP_256064.1| 62 TVRGPRRVGKTTLIKLIIRHLIKERQINPSNIFY 95
                                  56666668********************999876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.091
                        AAA_19  89 elleeaeeekklqeeellivDEfqdvd.el 117
                                   +lle  +e+   +ee++++ DE+++   + 
  gi|70607194|ref|YP_256064.1| 112 NLLEAIAES--NNEEKYVFLDEVSMYRgWA 139
                                   444433332..335679********98444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.065       5      87 ..      58     143 ..      54     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdl.lrellralglelka...erlsseell 79 
                                    gi++v G+  +GKTtl++ + + l +e ++   +p+ + ++ l  +  + +++ l +ll+a+ +++++     l++  ++
  gi|70607194|ref|YP_256064.1|  58 YGIVTVRGPRRVGKTTLIKLIIRHLIKERQI---NPSNIfYIPLDYEQfKVDNIsLINLLEAIAESNNEekyVFLDEVSMY 135
                                   58999*******************9555444...44444144444444656666666666666666655444244444444 PP

                        AAA_22  80 ealeqalr 87 
                                   +  +qal+
  gi|70607194|ref|YP_256064.1| 136 RGWAQALK 143
                                   44444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.6e-05     0.092       2      36 ..      62      96 ..      61     133 .. 0.85
   2 ?   -3.1   0.0       5.1     1e+04      27      50 ..     340     363 ..     318     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                   + Gp+++GK+tl+k ++++l k+ + + ++ +y+
  gi|70607194|ref|YP_256064.1| 62 TVRGPRRVGKTTLIKLIIRHLIKERQINPSNIFYI 96
                                  689*******************9997777666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                  RNA_helicase  27 klkkkdsvysrnpeddfwdgYtgq 50 
                                   k ++kd + +  ++ +f+ gY++ 
  gi|70607194|ref|YP_256064.1| 340 KINWKDYFNYLITTYSFFFGYRES 363
                                   455666666666777778888754 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.2   1.2e+04      59      76 ..      10      24 ..       3      48 .. 0.50
   2 ?   11.5   0.0   0.00017      0.33       1      80 [.      61     130 ..      61     144 .. 0.78
   3 ?   -2.5   0.0       3.5   6.9e+03      56      56 ..     408     408 ..     365     451 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                        AAA_18 59 klldaleenssaleegkn 76
                                  +ll++++++   +e+ ++
  gi|70607194|ref|YP_256064.1| 10 ELLKNFNRW---WENKDW 24
                                  333333333...222222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00017
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvid 80 
                                   + + G+ +vGKttl k + ++l   ++ r++ + n  +++ d e    + ++d   l +ll+a+ e+++   e+k + +d
  gi|70607194|ref|YP_256064.1|  61 VTVRGPRRVGKTTLIKLIIRHL---IKERQINPSNIFYIPLDYE----QFKVDNISLINLLEAIAESNN---EEKYVFLD 130
                                   5688**************9996...9999999999999999999....666666665666666666543...55555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.5
                        AAA_18  56 k 56 
                                   +
  gi|70607194|ref|YP_256064.1| 408 N 408
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 3033.75
//
Query:       gi|70607195|ref|YP_256065.1|  [L=118]
Description: hypothetical protein Saci_1448 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-05   24.2   0.9    4.4e-05   23.3   0.4    1.8  2  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
     0.0015   18.8   1.2     0.0024   18.2   1.2    1.3  1  CLZ              C-terminal leucine zipper domain of cyclic n
      0.002   17.8   0.9     0.0028   17.3   0.9    1.2  1  GrpE             GrpE
     0.0033   17.4   0.1     0.0073   16.3   0.0    1.6  2  MraZ             MraZ protein, putative antitoxin-like
  ------ inclusion threshold ------
      0.013   15.5   0.9      0.013   15.5   0.9    1.6  2  bZIP_1           bZIP transcription factor
      0.024   14.3   0.7      0.055   13.1   0.3    1.8  2  Nbl1_Borealin_N  Nbl1 / Borealin N terminal
      0.032   14.0   0.0      0.038   13.8   0.0    1.1  1  Corona_NS3b      ORF3b coronavirus protein
      0.097   12.2   1.2       0.13   11.9   1.2    1.2  1  Paralemmin       Paralemmin


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   3.3e+03      35      43 ..       6      14 ..       3      23 .. 0.68
   2 !   23.3   0.4     2e-08   4.4e-05       7      43 ..      32      69 ..      27      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                  CCCCCCCHH CS
                MazE_antitoxin 35 kiilrplks 43
                                  kiil++ ++
  gi|70607195|ref|YP_256065.1|  6 KIILAFTQN 14
                                  677776654 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2e-08
                                  EEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHH CS
                MazE_antitoxin  7 gavriPkevrfelgireGdevelevdgd.kiilrplks 43
                                  g++ iP  + +el++++G e+ l+  +d ki++++   
  gi|70607195|ref|YP_256065.1| 32 GRIKIPSSFIRELDLKPGEEIYLILTSDkKIVITKDGL 69
                                  5666************************9999998765 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.2   1.1e-06    0.0024      10      62 ..      65     115 ..      60     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                           CLZ  10 lKdglLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                   +Kdgl  ++  + ++  keleek erL ++L  L+  +ar l+ +++ ++k +
  gi|70607195|ref|YP_256065.1|  65 TKDGLPQNS--ELEERVKELEEKYERLAKELGRLEFDFARYLRRLSKDETKYQ 115
                                   677776655..678899**************************9999888865 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.9   1.2e-06    0.0028      12      58 ..      70     116 ..      62     118 .] 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                                   HHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHH CS
                          GrpE  12 deeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakk 58 
                                   +++ elee+++ele++++ l ++l rl+ +f  + +r+ k+  + ++
  gi|70607195|ref|YP_256065.1|  70 PQNSELEERVKELEEKYERLAKELGRLEFDFARYLRRLSKDETKYQQ 116
                                   57899*********************************999887765 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.2e-06    0.0073       4      30 ..      22      50 ..      20      67 .. 0.80
   2 ?   -2.3   0.0         2   4.5e+03      49      56 ..      86      93 ..      74     110 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-06
                                  TEEEEEB-TTSEEE--CHHHHHTTSC..S CS
                          MraZ  4 gatevelDakGRlllPaklreeakle..k 30
                                  ++ ++++D  GR+ +P+++++e+ l+  +
  gi|70607195|ref|YP_256065.1| 22 ETKKMTIDVRGRIKIPSSFIRELDLKpgE 50
                                  68899******************998663 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                  HHHHHHCH CS
                          MraZ 49 Wekyeeel 56
                                  +e++ +el
  gi|70607195|ref|YP_256065.1| 86 YERLAKEL 93
                                  44444444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.2   7.1e+03       4      10 ..      20      26 ..      13      28 .. 0.59
   2 ?   15.5   0.9     6e-06     0.013      29      53 ..      73      97 ..      71     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                                  XXXXXXX CS
                        bZIP_1  4 lKrekrk 10
                                  +K +k++
  gi|70607195|ref|YP_256065.1| 20 IKETKKM 26
                                  4444444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 29 eeLerrvkaLekeNksLkseleelk 53
                                  +eLe+rvk+Le++ + L++el++l+
  gi|70607195|ref|YP_256065.1| 73 SELEERVKELEEKYERLAKELGRLE 97
                                  69********************998 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   3.2e+03      31      31 ..      30      30 ..      21      45 .. 0.57
   2 ?   13.1   0.3   2.5e-05     0.055      11      31 ..      73      93 ..      72      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
               Nbl1_Borealin_N 31 l 31
                                  +
  gi|70607195|ref|YP_256065.1| 30 V 30
                                  2 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.5e-05
               Nbl1_Borealin_N 11 lEveeRirrlraelelllktl 31
                                   E+eeR+++l++++e l+k+l
  gi|70607195|ref|YP_256065.1| 73 SELEERVKELEEKYERLAKEL 93
                                  599***************986 PP

>> Corona_NS3b  ORF3b coronavirus protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05     0.038     159     207 ..      13      63 ..       5      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                   Corona_NS3b 159 lgdsivsfvstsdlylairGraeadlsllraveLldGellyvf..sqepvv 207
                                    ++ iv+  +t+++ + +rGr++   s +r+++L  Ge +y+   s++++v
  gi|70607195|ref|YP_256065.1|  13 QNNIIVEIKETKKMTIDVRGRIKIPSSFIRELDLKPGEEIYLIltSDKKIV 63 
                                   5788999999*******************************7532555555 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.2   5.6e-05      0.13       3      31 ..      71      99 ..      70     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.6e-05
                    Paralemmin  3 qleedeakvrkLEesiqrLekeieeLese 31
                                  q  e e++v++LEe+ +rL ke+ +Le +
  gi|70607195|ref|YP_256065.1| 71 QNSELEERVKELEEKYERLAKELGRLEFD 99
                                  567889********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1462  (0.0815439); expected 358.6 (0.02)
Passed bias filter:                      916  (0.0510904); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 908.29
//
Query:       gi|70607196|ref|YP_256066.1|  [L=381]
Description: hypothetical protein Saci_1449 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1531  (0.0853924); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2696.83
//
Query:       gi|70607197|ref|YP_256067.1|  [L=118]
Description: hypothetical protein Saci_1452 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.01   17.0   3.9      0.015   16.4   3.2    1.6  1  SOGA         Protein SOGA
      0.045   12.7   1.1      0.046   12.7   1.1    1.2  1  PL48         Filopodia upregulated, FAM65
      0.071   13.1   0.1      0.089   12.8   0.1    1.1  1  PilJ         Type IV pili methyl-accepting chemotaxis transdu
      0.083   13.2   9.5      0.092   13.1   1.1    3.0  2  TSC22        TSC-22/dip/bun family
       0.11   13.2   3.1       0.19   12.4   3.1    1.4  1  CaM_binding  Plant calmodulin-binding domain
       0.34   11.1   8.3        2.4    8.3   7.8    2.2  1  HR1          Hr1 repeat
       0.53   10.1   7.7       0.36   10.7   5.9    1.5  2  DUF1635      Protein of unknown function (DUF1635)


Domain annotation for each model (and alignments):
>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   3.2     6e-06     0.015       4      43 ..      42      81 ..      39      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                          SOGA  4 eLrrhLqfveeEaeLlrrslseleeenkqlteeLnkyksk 43
                                  eL + ++  +eE eLlr s+ el ++ kq  +eLn y+  
  gi|70607197|ref|YP_256067.1| 42 ELEKEIRNLKEEDELLRFSIPELVDQLKQTIKELNEYRKR 81
                                  899999999****************************975 PP

>> PL48  Filopodia upregulated, FAM65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   1.8e-05     0.046      79     125 ..      21      68 ..       5     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                          PL48  79 ldklssqqkdtkRnsRLaflydldkeiraleRyirrlefhisk.veel 125
                                    dkl +  kdt+++  L + y+l+keir l      l f+i   v+ l
  gi|70607197|ref|YP_256067.1|  21 ADKLLKLLKDTQKEDLLKLAYELEKEIRNLKEEDELLRFSIPElVDQL 68 
                                   699***************************999988988885424544 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-05     0.089      25      94 ..      16      81 ..      12      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                          PilJ 25 RlakeallaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkp 94
                                  +++  a  ++     +++++++l + + ++++ +++l++ d+  ++  p  +  +ql++ +++ +e++k 
  gi|70607197|ref|YP_256067.1| 16 KIVEAADKLLKLL--KDTQKEDLLKLAYELEKEIRNLKEEDELLRFSIP--ELVDQLKQTIKELNEYRKR 81
                                  5554444444444..899*************************999999..9***********9999985 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.7    0.0055        14      24      44 ..      41      61 ..      27      64 .. 0.85
   2 ?   13.1   1.1   3.6e-05     0.092       9      29 ..      58      78 ..      57     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0055
                         TSC22 24 keLeernseleeENslLkala 44
                                   eLe+++++l+eE +lL+  +
  gi|70607197|ref|YP_256067.1| 41 YELEKEIRNLKEEDELLRFSI 61
                                  69***************9665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.6e-05
                         TSC22  9 mfAVrEeVevLkekIkeLeer 29
                                   f + E V++Lk++IkeL e 
  gi|70607197|ref|YP_256067.1| 58 RFSIPELVDQLKQTIKELNEY 78
                                  578889************764 PP

>> CaM_binding  Plant calmodulin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.1   7.6e-05      0.19      51     109 ..      31      87 ..      10      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-05
                   CaM_binding  51 prkprelpeesekeaekVvLrhqdveekkkaeewllnnvieetaskLvearKsKVkaLV 109
                                   ++k++ l+   e e+e  +L+ +d   + + +e l+++ +++t+  L e rK+K+k+L+
  gi|70607197|ref|YP_256067.1|  31 TQKEDLLKLAYELEKEIRNLKEEDELLRFSIPE-LVDQ-LKQTIKELNEYRKRKIKLLI 87 
                                   455555566666677777788888888888888.8886.8******************8 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.8   0.00093       2.4      12      62 ..      14      76 ..      12      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00093
                           HR1 12 ElkireGAenllralesk.ktqnkkvrqeaeselsesns...........kielLreqLeelq 62
                                  E ki e+A +ll++l+   k++  k+  e e e++  +             +++L+++++el+
  gi|70607197|ref|YP_256067.1| 14 EEKIVEAADKLLKLLKDTqKEDLLKLAYELEKEIRNLKEedellrfsipeLVDQLKQTIKELN 76
                                  99*************966566666699999999999999666666666666666666666666 PP

>> DUF1635  Protein of unknown function (DUF1635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.35     9e+02      45      63 ..      12      31 ..       3      34 .. 0.49
   2 ?   10.7   5.9   0.00014      0.36       7      69 ..      33      95 ..      28     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                       DUF1635 45 tikEr.deAqeklqklllek 63
                                  + +E+  eA +kl kll ++
  gi|70607197|ref|YP_256067.1| 12 MNEEKiVEAADKLLKLLKDT 31
                                  44444235555555555443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                       DUF1635  7 rqsLlyttleLettklkaqeelrkrdeeviqLkdlLkktikErdeAqeklqkllleklllqqq 69
                                  +++Ll    eLe+   + +ee    +  + +L d Lk+tikE +e +++  kll++ l+++  
  gi|70607197|ref|YP_256067.1| 33 KEDLLKLAYELEKEIRNLKEEDELLRFSIPELVDQLKQTIKELNEYRKRKIKLLISILVIKLS 95
                                  678999999*********************************************999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1962  (0.109432); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 905.78
//
Query:       gi|70607198|ref|YP_256068.1|  [L=211]
Description: hypothetical protein Saci_1454 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   81.3   2.5    4.9e-23   80.6   2.5    1.4  1  DUF434    Protein of unknown function (DUF434)
    3.4e-23   82.5   0.3    5.4e-23   81.9   0.3    1.3  1  DUF5616   Domain of unknown function (DUF5616)


Domain annotation for each model (and alignments):
>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   2.5   5.4e-27   4.9e-23       1      56 []       7      62 ..       7      62 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 5.4e-27
                        DUF434  1 kLkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                  +L +A+eD++yLLnRGY++k al+l++ +Y+L+k+ Rl+L+Rc++sdeei++++sK
  gi|70607198|ref|YP_256068.1|  7 QLLMAYEDYKYLLNRGYNRKPALDLISSRYNLDKKSRLLLYRCIHSDEEIQHIRSK 62
                                  6899**************************************************98 PP

>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.3     6e-27   5.4e-23       8     139 ..      69     192 ..      62     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 6e-27
                       DUF5616   8 elliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDkpvSnSgelak 88 
                                    +++DG+N+ +tl s++ g+ ++lcdDg++RDl  + ++ +++ee+  +l l+ e+l++ k+k  +++lD+++S+Sgela+
  gi|70607198|ref|YP_256068.1|  69 YVILDGYNLALTLLSLIYGDEIFLCDDGFYRDLG-LGKRKNNSEEIFDMLVLLSEYLDQNKIK-FEIILDSQISRSGELAG 147
                                   589*****************************97.7777899999***************996.7999************* PP

                       DUF5616  89 lireileeaglegevelvknvDkeLkeseeivatsDsvildkvksvldlaa 139
                                   ++r         + +++v+++D eL+ s+++++t D  +l++++++++l a
  gi|70607198|ref|YP_256068.1| 148 KLRYRG------IYAKTVRKTDLELILSNNVICTNDFLVLNRARQIYNLLA 192
                                   *99764......579*********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1322.29
//
Query:       gi|70607199|ref|YP_256069.1|  [L=907]
Description: alanyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     8e-117  391.0   0.0   1.1e-116  390.5   0.0    1.2  1  tRNA-synt_2c    tRNA synthetases class II (A)
    2.6e-11   43.4   0.9    6.8e-11   42.1   0.9    1.8  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
    2.9e-05   24.5   1.5    9.2e-05   22.9   1.5    1.8  1  DHHA1           DHHA1 domain
  ------ inclusion threshold ------
        0.1   12.5   1.4       0.86    9.4   0.2    2.1  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
          2    8.6  10.9       0.54   10.4   5.6    2.5  2  Fib_alpha       Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.5   0.0  3.2e-120  1.1e-116       3     552 .]      67     598 ..      65     598 .. 0.92

  Alignments for each domain:
  == domain 1  score: 390.5 bits;  conditional E-value: 3.2e-120
                                   HHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTS.SS- CS
                  tRNA-synt_2c   3 rekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGkt.arH 82 
                                   rekFl fFek+gHt+v+ ++vv++++++l++++A++++f+p+++++ akp+++++v sQ+ciR++    D++nVG+t +rH
  gi|70607199|ref|YP_256069.1|  67 REKFLRFFEKRGHTIVPPKPVVAKWRDDLYLTIASIVDFQPFVTSGLAKPPANPLVVSQPCIRLE----DVDNVGITfGRH 143
                                   9****************************************************************....*******988** PP

                                   -SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHHE CS
                  tRNA-synt_2c  83 hTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdnf 156
                                   +T FeM+++++f+     +Y+k+e+++fa e++t+elg+++++l ++++++++  +a++++e +vg+ e ++l+f   +++
  gi|70607199|ref|YP_256069.1| 144 LTTFEMAAHHAFNypdkqIYWKDETVAFAKEFFTEELGIPEDQLNFKESWWEGggNAGPCFEVTVGGLELATLVF---MQY 221
                                   ****************************************************999********************...*** PP

                                   EESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHHTT CS
                  tRNA-synt_2c 157 wemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavLqe 237
                                   +  g+ +   + +++++++g e+ ++  + +++a  +++ +++    +++++  + + + L++ +i +G  +  + + +  
  gi|70607199|ref|YP_256069.1| 222 EIRGQDYVPLKLKIVDTGYGVERIAWFTQRTPTAFHAIYGNLVSSFYKKIGVG-EVNNELLKAAAIYAGRIDPDIKETITA 301
                                   ***************************************************99.89999********************** PP

                                   HSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT-S CS
                  tRNA-synt_2c 238 vrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrhakkLglk 318
                                    r++ +++l++ +    ee++            ++  + DH++++a +ladG+vpsn+g+gY+ R+l+Rra+r ++ Lg +
  gi|70607199|ref|YP_256069.1| 302 HREHLAKQLGLDLKYVNEELTR---------AARVFQVLDHTKTIALMLADGLVPSNSGEGYLGRLLIRRALRVLRLLGSD 373
                                   ********************99.........45666677****************************************** PP

                                   STHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHHCHXXXHH CS
                  tRNA-synt_2c 319 ekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLydtyGfPvd 399
                                    k l++l++ +++  ++ +p++ ++++++ +++ +Eee+++ T+++  ++l+ l k    k+++++++++++yd+ G+ +d
  gi|70607199|ref|YP_256069.1| 374 VK-LHELIKDQIDYWKEDFPQMLKNKDYIVDAVINEEEKYNDTISKIPSILSTLSK----KSKVDLDELINIYDSNGISPD 449
                                   **.******************************************98888877666....588****************** PP

                                   HHHHHHHCTTX..EEXHHHHHHHHHHHHHHHCCHHSXSS..XXXXXXXXTTSHCHH.CCTSTTTXXXXXXTSXXXXXXSEE CS
                  tRNA-synt_2c 400 ltkeiaeekgl..kvdiegfekameeqrerskkekkekk..likkdvealkelkkt.eeflgyeeleaeakvlallkdkef 475
                                   l+ + a+++++  +v+i+ ++++ +++++++    +++k    k+ ++++++ k + +  l+y++     + l     ++f
  gi|70607199|ref|YP_256069.1| 450 LILDEARKRNIniNVEIPHNFYSIVAKKHQNALVRENRKdkIPKEVIDEINNKKIEpTVPLYYKD-----QYL-----RTF 520
                                   *******998622578899*****99999997444433332445555666665555566677777.....444.....789 PP

                                   EEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESS..EEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                  tRNA-synt_2c 476 veeveegeevgvvLdrTpfYaesGGqigDeGliekeg..aefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                    ++v  + ++++vLd+T fY+e+GGqigD+G+i++ +  ++++v d+qk+kgv++h+ +     + +g++v +e+d++r
  gi|70607199|ref|YP_256069.1| 521 NAKVLLNYKNFLVLDQTTFYPEGGGQIGDTGIIRSIEgnKQAKVIDTQKYKGVIVHILDKD-SPFIQGEQVYGEIDWQR 598
                                   9******************************99875434899****************996.8999**********986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.9   1.9e-14   6.8e-11       1      44 []     697     740 ..     697     740 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.9e-14
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                   +r+++i+++++e CgGtH+ nTgeIg +ki++ e+ ++g+ R++
  gi|70607199|ref|YP_256069.1| 697 IRLIEIENWDIEGCGGTHLINTGEIGGVKIVNVEKLQDGVIRLE 740
                                   799***************************************86 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.5   2.6e-08   9.2e-05       2     116 ..     777     882 ..     770     903 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                                   HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC..TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEEC CS
                         DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevk..gvkvlvaevgeewdagalgiaadklksklkkpvivfvakeeg 80 
                                   +++ ee ++l++ l+ + +++    ++e+ e+   ++  g ++++ ++   +d   ++++  k+ s  ++  iv+ +  ++
  gi|70607199|ref|YP_256069.1| 777 KKHLEEYENLQNLLD-KYRKIVLDRIQEIAER---ISvnGITIYILRD--FIDEQLIKEVMRKITS--NNQNIVISIRGKD 849
                                   455555555555554.3333333333444333...3354777777777..99999***********..8888888887777 PP

                                   TEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEETC CS
                         DHHA1  81 dkvkvsarskkdgvdagelakeaaaklgggGGGHdl 116
                                    + +v ++++k ++++ +++ e  +k+gg+GGG+  
  gi|70607199|ref|YP_256069.1| 850 -TKNVEIATSK-DIKVDKIVDE-LRKIGGRGGGKGT 882
                                   .7788888888.**********.**********954 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.061   2.2e+02      72      99 ..     296     323 ..     290     335 .. 0.47
   2 ?    9.4   0.2   0.00024      0.86      43     101 ..     755     812 ..     739     843 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.061
                                   HHHCCHHHHHHHHHHHHCHHCCHHCHCC CS
                Apolipoprotein  72 rqrlapyteelrerlaadaeelqeqlav 99 
                                   +++++++ e l+++l +d++ + e l+ 
  gi|70607199|ref|YP_256069.1| 296 KETITAHREHLAKQLGLDLKYVNEELTR 323
                                   3333333333333333333333333333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHC CS
                Apolipoprotein  43 raeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavya 101
                                   +++l+e  + l + +++++ +l+++lee+ + l+++++++r+ ++ +++e+ e+++v++
  gi|70607199|ref|YP_256069.1| 755 DEKLNEISKLLNSPVSQINVRLKKHLEEYEN-LQNLLDKYRKIVLDRIQEIAERISVNG 812
                                   6889999999999999999999999999965.799999999999999999999999876 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2      0.28   9.9e+02      23      52 ..     402     431 ..     375     444 .. 0.65
   2 ?   10.4   5.6   0.00015      0.54      46     117 ..     757     828 ..     746     846 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.28
                                   HHCCCCCCCCCCHHHCCCCCCCCCCCCHHH CS
                     Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstk 52 
                                    d++ + e++++++++k+ + l+++s+++k
  gi|70607199|ref|YP_256069.1| 402 VDAVINEEEKYNDTISKIPSILSTLSKKSK 431
                                   345556666667777777777777666655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00015
                                   CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqk 117
                                   ++++ +k  ++ v++i+  l+++ +++++ +n++ k++k + ++i+++ e+i+ +  +i  L++ ++++  k
  gi|70607199|ref|YP_256069.1| 757 KLNEISKLLNSPVSQINVRLKKHLEEYENLQNLLDKYRKIVLDRIQEIAERISVNGITIYILRDFIDEQLIK 828
                                   5666677788899***************88**********999***********************988543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (907 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 6274.76
//
Query:       gi|70607200|ref|YP_256070.1|  [L=105]
Description: 50S ribosomal protein L12 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-21   74.4  11.1    9.4e-21   74.2  11.1    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
     0.0056   16.7   2.6        1.7    8.7   0.8    2.2  2  PepSY_2        Peptidase propeptide and YPEB domain
      0.006   16.9   0.3       0.01   16.1   0.0    1.5  2  EF-hand_14     EF-hand domain
  ------ inclusion threshold ------
       0.14   12.4   0.3       0.25   11.6   0.3    1.6  1  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2  11.1   2.1e-24   9.4e-21       1      87 [.      16     100 ..      16     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 2.1e-24
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S CS
                 Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd 81 
                                   e+++enik+vl+aag++v+++r+k++++al++++i+e+l++++a   ++aa+aa+a+++ ++aa+++e+kkeee++  +++
  gi|70607200|ref|YP_256070.1|  16 EISEENIKNVLSAAGITVDEVRLKAVAAALKEVNIDEILKTATAM--PVAAVAAPAGQQTQQAAEKKEEKKEEEKKGPSEE 94 
                                   69*****************************************99..999***********************99966666 PP

                                   S--STT CS
                 Ribosomal_60s  82 dmGfgL 87 
                                   + G+gL
  gi|70607200|ref|YP_256070.1|  95 EIGGGL 100
                                   666665 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00066       2.9      27      51 ..      14      38 ..      11      45 .. 0.90
   2 !    8.7   0.8   0.00038       1.7       4      33 ..      56      86 ..      53      95 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00066
                       PepSY_2 27 adwlpreklvakleaqGykvkkiev 51
                                  ++++++e+++  l a+G +v+++++
  gi|70607200|ref|YP_256070.1| 14 KKEISEENIKNVLSAAGITVDEVRL 38
                                  6889******************987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00038
                       PepSY_2  4 lalalallaaaAlA.grrdtdspkadwlpre 33
                                  +a+a+ ++a aA A +++++ ++k+++ ++e
  gi|70607200|ref|YP_256070.1| 56 TATAMPVAAVAAPAgQQTQQAAEKKEEKKEE 86
                                  6889999999999944444444455544444 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-06      0.01      10      52 ..      10      52 ..       2      65 .. 0.84
   2 ?   -2.4   0.3       1.4   6.5e+03      48      50 ..      80      82 ..      69      94 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-06
                    EF-hand_14 10 kdeetdklsvakllkaLaetGirkdDpRLkellkklkkvekek 52
                                   +  ++++s +++ ++L+++Gi+ d  RLk +  +lk+v+ ++
  gi|70607200|ref|YP_256070.1| 10 LHAAKKEISEENIKNVLSAAGITVDEVRLKAVAAALKEVNIDE 52
                                  3578899******************************998665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                    EF-hand_14 48 vek 50
                                   e+
  gi|70607200|ref|YP_256070.1| 80 KEE 82
                                  111 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   5.5e-05      0.25       8      56 ..       6      54 ..       3      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                     PhetRS_B1  8 keaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviy 56
                                  ++ L++a  ke++ee+++++l   G+ +De+  ++  ++ ++ + ++i+
  gi|70607200|ref|YP_256070.1|  6 ASLLLHAAKKEISEENIKNVLSAAGITVDEVRLKAVAAALKEVNIDEIL 54
                                  667889999**********************999885544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1702  (0.09493); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 763.27
//
Query:       gi|70607201|ref|YP_256071.1|  [L=335]
Description: acidic ribosomal protein P0 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-27   94.8   0.7    7.3e-27   93.4   0.7    1.7  1  Ribosomal_L10  Ribosomal protein L10
    7.1e-18   64.4   0.2    2.1e-17   62.9   0.2    1.9  2  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
  ------ inclusion threshold ------
      0.085   14.0   0.2       0.22   12.7   0.2    1.7  1  DUF3484        Membrane-attachment and polymerisation-promoti
        3.5    8.3  13.3         14    6.4  13.3    2.2  1  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.7   1.6e-30   7.3e-27       3      98 ..      13     108 ..      11     109 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.6e-30
                                   CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S.SCGCCSSSEEEE CS
                 Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek.lkellkgpvalv 82 
                                    ++K + v+el+e+lk++k+++++++eg+++ +l+e+Rkklr++ a +kv Kn+l+++Al+++g++ k ++++l+gp+a++
  gi|70607201|ref|YP_256071.1|  13 AKWKVDEVAELTEKLKTHKTIIIANIEGFPADKLHEIRKKLRGK-ADIKVTKNNLFNIALKNAGYDTKlFESYLTGPNAFI 92 
                                   68******************************************.********************976799********** PP

                                   EESS-TCHHHHCCCCC CS
                 Ribosomal_L10  83 ftnedpvalakvleef 98 
                                   ft+++p++l   l++f
  gi|70607201|ref|YP_256071.1|  93 FTDTNPFELQLFLSKF 108
                                   **********999999 PP

>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.2   4.7e-21   2.1e-17       3      71 .]     116     184 ..     114     184 .. 0.98
   2 ?   -2.5   0.0       1.2   5.2e+03      36      44 ..     195     203 ..     190     226 .. 0.54

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 4.7e-21
                  RL10P_insert   3 aGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                   +G++A+e+v++pag+++ a+g++ + + kl+++tk+++Gki++ +d++v+k G+++ ++ + +L++Lgi
  gi|70607201|ref|YP_256071.1| 116 PGDKADEEVVVPAGDTGIAAGPMLSVFGKLKIKTKVQDGKIHILQDTTVAKPGDEIPADIVPILQKLGI 184
                                   79******************************************************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                  RL10P_insert  36 tklkkGkiv 44 
                                   +  ++G+i+
  gi|70607201|ref|YP_256071.1| 195 IAYDNGVII 203
                                   444444443 PP

>> DUF3484  Membrane-attachment and polymerisation-promoting switch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   4.8e-05      0.22      24      63 ..     295     334 ..     261     335 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                       DUF3484  24 vqenpqvqeqaqeqPvpskeqeekepkkekltdrvkglFg 63 
                                    q +pqv eqa e+ +++ke+e+k p++e+++  + +lFg
  gi|70607201|ref|YP_256071.1| 295 IQAQPQVSEQAAEKKEEKKEEEKKGPSEEEIGGGLSSLFG 334
                                   3355666666655555567777777888899998888887 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  13.3     0.003        14      54      87 ..     296     329 ..     209     333 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.003
                                   XXXXXXXXXXXXXXXXXXXXXX.XX--SS--STT CS
                 Ribosomal_60s  54 aaaaaaaaaaaaaeekkkeeeeeEeedddmGfgL 87 
                                   +a+ + +++aa+++e+kkeee++  ++++ G+gL
  gi|70607201|ref|YP_256071.1| 296 QAQPQVSEQAAEKKEEKKEEEKKGPSEEEIGGGL 329
                                   4555556666666666667776655666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1342  (0.0748508); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2272.71
//
Query:       gi|162139946|ref|YP_256072.2|  [L=221]
Description: 50S ribosomal protein L1P [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-36  123.4   1.3    1.2e-35  123.2   1.3    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.2   1.3   6.5e-40   1.2e-35       5     203 ..      25     213 ..      17     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.2 bits;  conditional E-value: 6.5e-40
                                    S-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-H CS
                   Ribosomal_L1   5 akkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksf 84 
                                     k++f++svei+l+++++++kk d + ++++pLp+   k ++++++   +q eyak+a+     + vi+ ++l+k   ++
  gi|162139946|ref|YP_256072.2|  25 VKRNFTQSVEIILTFKGIDMKKGDLKLREIVPLPKQPSKAKRVLVVPSFEQLEYAKKAS----PNVVITREELQKLQGQK 100
                                    4899*************************************************776654....357************** PP

                                    HHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEET CS
                   Ribosomal_L1  85 eakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGkl 164
                                    +  +kl+ + ++fl  ++ m l +++LG+ +g+r+k+P+p    +  ++d+++ ++++++ +v v+++++  ++v +G+ 
  gi|162139946|ref|YP_256072.2| 101 RPVKKLARQNEWFLINQESMALAGRILGPALGPRGKFPTPL--PN--TADISEYINRFKR-SVLVKTKDQPQVQVFIGTE 175
                                    *****************************************..52..68***********.999999************* PP

                                    TSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                   Ribosomal_L1 165 sftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                    ++++e+laeN+ av++a+++k  k  +n+++iy+kttm+
  gi|162139946|ref|YP_256072.2| 176 DMKPEDLAENAIAVLNAIENK-AKVETNLRNIYVKTTMG 213
                                    *********************.7779************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1565.58
//
Query:       gi|70607203|ref|YP_256073.1|  [L=170]
Description: 50S ribosomal protein L11 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   76.4   0.7    1.1e-21   76.4   0.7    1.6  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    7.3e-19   68.0   0.6    1.5e-18   67.0   0.6    1.5  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
      0.077   13.2   1.3          8    6.7   0.0    2.8  3  Flagellin_IN     Flagellin hook IN motif
       0.52   10.5   4.0         15    5.8   0.2    2.5  2  FlaG             FlaG protein


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.7   2.4e-25   1.1e-21       5      62 ..       3      61 ..       2      64 .. 0.93
   2 ?   -3.7   0.0       2.5   1.1e+04      34      41 ..     142     149 ..     139     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 2.4e-25
               Ribosomal_L11_N  5 vkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqd 62
                                  +k++k++v++G A+p+PplGp+L++lGln+++++k++n+ T+++kg+ +pV+i++  ++
  gi|70607203|ref|YP_256073.1|  3 TKTIKIMVEGGSAKPGPPLGPTLSQLGLNVQEVVKKINDVTAQFKGMSVPVTIEIdSST 61
                                  699****************************************************5555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.5
               Ribosomal_L11_N  34 ikkfckef 41 
                                   +k+++ke+
  gi|70607203|ref|YP_256073.1| 142 PKDVIKEI 149
                                   78899987 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.6   3.4e-22   1.5e-18       2      70 .]      70     137 ..      69     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 3.4e-22
                                   --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                 Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                   +P+t++lL+ka+++++ sg p ++++G++ l+q+  IA  Kk++l+a+ +l aa+ks lgtArs+Gi+V
  gi|70607203|ref|YP_256073.1|  70 VPTTTSLLLKAINAQEPSGDPAHKKIGNLDLEQIADIAIKKKPQLSAK-TLTAAIKSLLGTARSIGITV 137
                                   6*********************************************99.******************99 PP

>> Flagellin_IN  Flagellin hook IN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0018         8      22      36 ..      31      45 ..      29      47 .. 0.87
   2 ?    4.3   0.1      0.01        46       1      33 [.      54      84 ..      54      88 .. 0.77
   3 ?   -3.2   0.0       2.2     1e+04       5      29 ..     138     148 ..     135     152 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0018
                                  BCHHHHHHHHHHCCT CS
                  Flagellin_IN 22 tlddiadaINavssk 36
                                  ++++++++IN+v+++
  gi|70607203|ref|YP_256073.1| 31 NVQEVVKKINDVTAQ 45
                                  6799********997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.01
                                  EEEEEETTECS-EEEEECTTTBCHHHHHHHHHH CS
                  Flagellin_IN  1 tltinggggketvtisvkagdtlddiadaINav 33
                                  t+ i   ++k++  i v   +t++ + +aINa+
  gi|70607203|ref|YP_256073.1| 54 TIEIDSSTKKYD--IKVGVPTTTSLLLKAINAQ 84
                                  566777778888..88888899999999**954 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.2
                                   EETTECS-EEEEECTTTBCHHHHHH CS
                  Flagellin_IN   5 nggggketvtisvkagdtlddiada 29 
                                    g++               +d+++ 
  gi|70607203|ref|YP_256073.1| 138 EGKD--------------PKDVIKE 148
                                   4444..............4444444 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.6    0.0036        16      32      67 ..      33      68 ..      25      85 .. 0.78
   2 ?    5.8   0.2    0.0033        15      62      90 ..     132     160 ..      79     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0036
                                  HHHHHHHHHHHHHHTTSS--EEEEEEEETTEEEEEE CS
                          FlaG 32 eeleeaveklnkklsslnteleFsvdedtkrvvVkv 67
                                  +e+ + ++++  +++ ++  +  ++d  tk++ +kv
  gi|70607203|ref|YP_256073.1| 33 QEVVKKINDVTAQFKGMSVPVTIEIDSSTKKYDIKV 68
                                  44555566666678888999************9999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0033
                                   EEEEEEEETTT-SEEEEE-HHHHHHHHHH CS
                          FlaG  62 rvvVkviDketgevIrqiPseevldlakk 90 
                                   ++ ++v  k+ ++vI++i + +  dl+ +
  gi|70607203|ref|YP_256073.1| 132 SIGITVEGKDPKDVIKEIDQGKYNDLLTN 160
                                   46799999**********99998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1361.38
//
Query:       gi|70607204|ref|YP_256074.1|  [L=152]
Description: transcription antitermination protein NusG [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-22   77.2   0.7    9.7e-21   73.5   0.1    2.0  2  Spt5-NGN         Early transcription elongation factor of RNA
    1.5e-07   31.1   0.1    3.2e-07   30.1   0.1    1.7  1  KOW              KOW motif
  ------ inclusion threshold ------
      0.098   12.5   1.4        1.1    9.2   0.2    2.0  2  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
       0.37   11.3   3.4        4.2    8.0   0.2    2.9  2  NusG             Transcription termination factor nusG


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.1   2.2e-24   9.7e-21       1      83 [.       8      87 ..       8      88 .. 0.96
   2 ?    2.5   0.0     0.029   1.3e+02      46      65 ..     117     136 ..      94     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 2.2e-24
                      Spt5-NGN  1 siwavkctagqErevalslmkkilelakken.leIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEved 82
                                  +++ +++t gqE +val l+++    +k++n +eI+Sv++p+++kGy+++EA+ +++v+ + +gi++v+gv++gl++ ++v++
  gi|70607204|ref|YP_256074.1|  8 NYYVLRVTGGQEINVALILEER----IKTNNiNEIFSVVVPPNIKGYVILEATGPHVVKLISSGIRHVKGVAHGLIQKEDVTK 86
                                  6899******************....9999966************************************************99 PP

                      Spt5-NGN 83 l 83
                                  +
  gi|70607204|ref|YP_256074.1| 87 F 87
                                  8 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.029
                      Spt5-NGN  46 yiyvEAdrkaaveralegip 65 
                                    + vE++++++v ++le+  
  gi|70607204|ref|YP_256074.1| 117 VVRVESTKNEVVLNILESSY 136
                                   67899999999999998755 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   7.1e-11   3.2e-07       1      30 [.      99     128 ..      99     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.1e-11
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEE CS
                           KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVf 30 
                                   +Gd V+V+sGp++G +++Vv+v+  k+ V+
  gi|70607204|ref|YP_256074.1|  99 EGDLVEVISGPFRGMQAQVVRVESTKNEVV 128
                                   59************************8876 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.025   1.1e+02      38      76 ..      12      52 ..       2      62 .. 0.75
   2 ?    9.2   0.2   0.00024       1.1      45     118 ..      69     145 ..      58     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.025
                                  ESS-TT-EEETT-EEEEEECTTCE..EEEEE--TT-EEEEE CS
               ATP-synt_ab_Xtn 38 pkvkvgdkvsggdilGtvqeteli..ehkimvppkvegkvk 76
                                   +v+ g++++ + il +   t+ i     ++vpp+++g v 
  gi|70607204|ref|YP_256074.1| 12 LRVTGGQEINVALILEERIKTNNIneIFSVVVPPNIKGYVI 52
                                  4788889999999998877777774346899******9874 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00024
                                   EEETT-EEEEEEC...TTCEEEEEE--TT-EEEEEEE--EEEE-.TTSECEEECETT.ECEEEESSEEEETTS---ES CS
               ATP-synt_ab_Xtn  45 kvsggdilGtvqe...teliehkimvppkvegkvkeiaeegeyt.vedtiaeveteegkekeltllqkwPvrkprpvk 118
                                   +  +g   G +q    t+++++ + +p   eg ++e+  +g ++ ++ ++++ve+++++ +   l  ++Pv+   p++
  gi|70607204|ref|YP_256074.1|  69 RHVKGVAHGLIQKedvTKFVSKSVALPAVKEGDLVEVI-SGPFRgMQAQVVRVESTKNEVVLNILESSYPVQVTVPLE 145
                                   555666677776522256789999*********99999.787652799******99976666667789***9887765 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00093       4.2       2      31 ..       8      44 ..       7      99 .. 0.79
   2 ?    2.9   0.4     0.034   1.5e+02       5      36 ..     117     148 ..     116     152 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00093
                                  EEEEEEE-TTTHHHHHHHH...HHHCT-....EEE-S CS
                                  xxxxxxxxxxxxxxxxxxx...xxxxxx....xxxxx RF
                          NusG  2 kWYvlqvepgkekkvkenL...leeegl....evivP 31
                                  ++Yvl+v  g+e +v+  L   ++ +++    +v+vP
  gi|70607204|ref|YP_256074.1|  8 NYYVLRVTGGQEINVALILeerIKTNNIneifSVVVP 44
                                  7999999999999999999777777777655555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.034
                                   EEEE-TTTHHHHHHHHHHHCT-EEE-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          NusG   5 vlqvepgkekkvkenLleeeglevivPaeekv 36 
                                   v++ve+ k + v + L  +  ++v vP+e+++
  gi|70607204|ref|YP_256074.1| 117 VVRVESTKNEVVLNILESSYPVQVTVPLEQVK 148
                                   7899999999888888333445******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1059.44
//
Query:       gi|70607205|ref|YP_256075.1|  [L=65]
Description: preprotein translocase subunit SecE [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0026   18.0   0.3     0.0032   17.7   0.3    1.0  1  M11L         Apoptosis regulator M11L like
  ------ inclusion threshold ------
      0.026   14.4   0.1      0.032   14.1   0.1    1.2  1  SecE         SecE/Sec61-gamma subunits of protein translocati
      0.036   14.1   0.4      0.058   13.5   0.4    1.3  1  Lambda_CIII  Lambda Phage CIII


Domain annotation for each model (and alignments):
>> M11L  Apoptosis regulator M11L like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   5.4e-07    0.0032     108     155 ..       9      55 ..       2      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.4e-07
                                   TTHHHHHHHTTHHHHHHHHTXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                          M11L 108 iddiidkIseeendiinfidrekkynvteyvkrsylkllgitaivvYk 155
                                   i+dii ++ e+ ++ii++ ++ +k+  +++ + ++l +++++++++Y 
  gi|70607205|ref|YP_256075.1|   9 ISDIIKRLREDWKRIISVAKKPDKDSFNYSIRLTLL-VMAVVGLIAYI 55 
                                   89********************99999999999988.9*******996 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.4e-06     0.032       7      48 ..      20      61 ..      15      65 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.4e-06
                                  HHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SecE  7 vkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfs 48
                                  +k+ +    +P+++ +  +   +l++++++gl+ ++v l  s
  gi|70607205|ref|YP_256075.1| 20 WKRIISVAKKPDKDSFNYSIRLTLLVMAVVGLIAYIVQLTTS 61
                                  5666666789**************************987665 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   9.8e-06     0.058      19      36 ..      10      27 ..       6      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                   Lambda_CIII 19 dRitrklRegwkrlidiL 36
                                  + i ++lRe wkr+i + 
  gi|70607205|ref|YP_256075.1| 10 SDIIKRLREDWKRIISVA 27
                                  56889**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 502.93
//
Query:       gi|70607206|ref|YP_256076.1|  [L=208]
Description: signal recognition particle protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-75  250.7   0.0    9.4e-75  250.6   0.0    1.0  1  SRP54            SRP54-type protein, GTPase domain
    2.9e-06   27.1   0.0    3.5e-06   26.9   0.0    1.2  1  AAA_30           AAA domain
    6.9e-06   25.8   0.1    8.9e-06   25.4   0.1    1.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    7.3e-06   26.0   1.6     0.0017   18.3   1.6    2.2  1  NTPase_1         NTPase
    7.7e-06   26.4   0.0    1.3e-05   25.6   0.0    1.5  1  AAA_17           AAA domain
    0.00019   20.8   0.0    0.00024   20.5   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00035   21.0   0.0    0.00058   20.3   0.0    1.4  1  AAA_16           AAA ATPase domain
    0.00036   20.8   0.1    0.00071   19.9   0.1    1.5  1  AAA_22           AAA domain
    0.00047   20.6   0.2     0.0009   19.7   0.2    1.8  1  AAA              ATPase family associated with various cellul
     0.0012   19.2   0.0     0.0013   19.1   0.0    1.2  1  AAA_19           AAA domain
     0.0018   18.5   0.0     0.0024   18.0   0.0    1.3  1  AAA_33           AAA domain
     0.0022   18.1   0.3     0.0057   16.7   0.3    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0076   15.5   0.0      0.016   14.5   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0077   16.3   0.0      0.013   15.6   0.0    1.3  1  AAA_14           AAA domain
      0.008   15.7   0.1      0.012   15.2   0.1    1.2  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.013   15.5   0.1    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.012   15.4   0.0      0.066   12.9   0.0    2.0  2  Thymidylate_kin  Thymidylate kinase
      0.012   15.7   0.7      0.064   13.3   0.7    2.0  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.012   15.5   0.0      0.024   14.5   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
      0.019   14.9   0.3      0.035   14.0   0.2    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.029   13.8   0.0      0.045   13.2   0.0    1.2  1  KTI12            Chromatin associated protein KTI12
      0.044   13.3   0.0       0.06   12.9   0.0    1.2  1  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.053   13.4   0.1       0.18   11.7   0.0    1.8  2  NACHT            NACHT domain
      0.059   13.1   1.1        0.2   11.4   1.1    2.0  1  AAA_24           AAA domain
      0.063   12.5   0.2      0.094   11.9   0.2    1.3  1  NB-ARC           NB-ARC domain
      0.063   12.7   0.1       0.13   11.7   0.1    1.5  1  Arf              ADP-ribosylation factor family
      0.073   12.6   0.0       0.27   10.7   0.0    1.8  2  PPK2             Polyphosphate kinase 2 (PPK2)
      0.075   12.8   0.0       0.13   12.0   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.081   12.4   0.0       0.11   11.9   0.0    1.3  1  KdpD             Osmosensitive K+ channel His kinase sensor d
      0.089   11.8   0.2       0.58    9.1   0.1    2.2  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
        0.1   11.7   0.1       0.15   11.1   0.1    1.3  1  T2SSE            Type II/IV secretion system protein
       0.15   12.0   0.2       0.54   10.2   0.0    2.0  2  RsgA_GTPase      RsgA GTPase
       0.21   12.1   0.3       0.39   11.3   0.3    1.6  1  AAA_18           AAA domain
       0.27   10.4   1.6        1.2    8.3   0.4    2.1  2  ArsA_ATPase      Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6   0.0   1.8e-77   9.4e-75       1     195 [.      12     206 ..      12     207 .. 0.99

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 1.8e-77
                                   SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                         SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                   p vi+++G++G+GKTtt+aK+ ++lkk++ +++++a DtfRaaA+eQL+ +a+kl+v++i+ k +adpa+va++a++ ak+
  gi|70607206|ref|YP_256076.1|  12 PFVIIFFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASDTFRAAAQEQLAYHASKLEVQLIRGKYGADPASVAFDAISFAKS 92 
                                   579****************************************************************************** PP

                                   TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHH CS
                         SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsi 162
                                   ++idvvl+DTaGr+++d++l+eelk++ +++kpd  +l+ld+++g++a++qa++F+++vg ++viltk+D+dakgG+als+
  gi|70607206|ref|YP_256076.1|  93 RNIDVVLIDTAGRMHIDSDLVEELKRVLRIAKPDFRILILDSLAGSDALEQARHFENNVGYDAVILTKVDADAKGGIALSL 173
                                   ********************************************************************************* PP

                                   HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                         SRP54 163 aaelklPikfigvGekiedleefdperlvsrll 195
                                   a+elk+P++++gvG++++dl +f+p+++v+r++
  gi|70607206|ref|YP_256076.1| 174 AYELKKPVVYMGVGQNYDDLIPFSPDWFVERIF 206
                                   *******************************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   6.7e-09   3.5e-06      19     113 ..      13     124 ..       1     150 [. 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.7e-09
                        AAA_30  19 rvavltGpAGtGKttalkalreaweaag.grviglAptgkaAkvLaeelgieastiakllkrlk.............grar 85 
                                    v +  G+ G GKtt+++++++++++++  ++i+++ t +aA+  +e+l  +as ++  l r k             + a+
  gi|70607206|ref|YP_256076.1|  13 FVIIFFGVNGVGKTTTIAKVVNMLKKNNlSTIIAASDTFRAAA--QEQLAYHASKLEVQLIRGKygadpasvafdaiSFAK 91 
                                   367778*********************7255555666667665..578999999999999888899999*****9985445 PP

                        AAA_30  86 lepgtllivDEagmv..dtkq...laallkaae 113
                                    ++ +++++D ag +  d++    l+++l++a+
  gi|70607206|ref|YP_256076.1|  92 SRNIDVVLIDTAGRMhiDSDLveeLKRVLRIAK 124
                                   5555*********98665554000444555554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.7e-08   8.9e-06       2     152 ..      14     163 ..      13     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-08
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
                          cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere 80 
                                   v+++ G  G GKTt + +++   ++++l++ +   +    +  ++l  ++++  v+l  G+        ++ +++a+   +
  gi|70607206|ref|YP_256076.1|  14 VIIFFGVNGVGKTTTIAKVVnmLKKNNLSTIIAASDTFRAAAQEQLAYHASKLEVQLIRGKYGAD---PASVAFDAISFAK 91 
                                   78899***************7666667777777788888999999999999999*******9988...6666666654333 PP

                                   .TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                          cobW  81 .erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                    +++dv+li t G +     ++ + +++ + ++ d+ + ++D+ +  ++  ++++ +e+ + + d ++l+K+D 
  gi|70607206|ref|YP_256076.1|  92 sRNIDVVLIDTAGrMHIDSDLVEELKRVLRIAKPDFRILILDSLAG-SDALEQARHFENNVGY-DAVILTKVDA 163
                                   357**********544444555568888899999*********776.7888999999999998.99******96 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.6   3.3e-06    0.0017       4     123 ..      17     121 ..      14     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                                   EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHHHH CS
                      NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarveakreprvgkyvvdvesfee 83 
                                     G  GvGKtT + kv+++lk+++++         r   +++ +++  +l    e +L           gky  d  s   
  gi|70607206|ref|YP_256076.1|  17 FFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASDTFRaAAQEQLAYHASKL----EVQLI---------RGKYGADPAS--- 81 
                                   56899******************998765555555544444555555555....33333.........3556666544... PP

                                   HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                      NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeaveevLk 123
                                   +a +a++ a  ++ dv++iD  G+m   s    e++++vL+
  gi|70607206|ref|YP_256076.1|  82 VAFDAISFAKsRNIDVVLIDTAGRMHIDSDL-VEELKRVLR 121
                                   4445554444466777777777777777654.345566655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.5e-08   1.3e-05       1     110 [.      18     133 ..      18     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.5e-08
                                   EE-TTSSHHHHHHHHHHHH...T.EEEEEHHHHHHHHHHTTTSHSSHHHHC.....TSHHHHHHHHHHHHHHHHHHHHHSS CS
                        AAA_17   1 lGgPGsGKgtqceklveky...g.fthlsaGdllreeakrgglakardemr.....klpleekkelqkeaaekiaeeakkk 72 
                                   +G+ G+GK+t ++k+v  +   +  t++ a+d +r+ a+++  a + ++++       +  +   +   a+   a+ ++ +
  gi|70607206|ref|YP_256076.1|  18 FGVNGVGKTTTIAKVVNMLkknNlSTIIAASDTFRAAAQEQL-AYHASKLEvqlirGKYGADPASVAFDAIS-FAKSRNID 96 
                                   69**************87744442567899*****9998773.33333332111112333334444444443.34444557 PP

                                   EEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE- CS
                        AAA_17  73 gvlvdghprikeqagfldglpkevleelkpdaiillea 110
                                    vl+d+  r+  +++++++l++ vl+ +kpd+ il+ +
  gi|70607206|ref|YP_256076.1|  97 VVLIDTAGRMHIDSDLVEELKR-VLRIAKPDFRILILD 133
                                   89**************999997.9********998754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.5e-07   0.00024       3     106 ..      14     112 ..      12     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.5e-07
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeek 83 
                                   v++  Gv G GKt    ++++ l   ++++ ++++  +  ++++ +e+la+++  +k + ++ + +    ++s   +a++ 
  gi|70607206|ref|YP_256076.1|  14 VIIFFGVNGVGKTTTIAKVVNML---KKNNLSTIIAASDTFRAAAQEQLAYHA--SKLEVQLIRGKYGADPASVAFDAISF 89 
                                   566679****************9...99999999*******************..666666666666666666559999** PP

                       DUF2075  84 keepkedvvivDEAhrlltksdq 106
                                   ++++++dvv++D A r+   sd 
  gi|70607206|ref|YP_256076.1|  90 AKSRNIDVVLIDTAGRMHIDSDL 112
                                   ****************9885554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-06   0.00058      25     148 ..      13     139 ..       1     151 [. 0.63

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-06
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql....esaipysalaqalareellrqllde.aesaeleawrek 100
                                    ++++ G  GvGK++ + ++ + l+k++  ++ +  d +    +++++y   a+ l + +l+r    + ++s +++a + +
  gi|70607206|ref|YP_256076.1|  13 FVIIFFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASDTFraaaQEQLAY--HASKL-EVQLIRGKYGAdPASVAFDAISFA 90 
                                   567889***************9999995555444445542224444555..66666.335555444442333333333333 PP

                        AAA_16 101 leealaavpelagaea....srllellkrllallsrderplvlvlDdlqwad 148
                                     +++  v  ++ a++    s+l e+lkr l+ +++d    +l+lD l   d
  gi|70607206|ref|YP_256076.1|  91 KSRNID-VVLIDTAGRmhidSDLVEELKRVLRIAKPDF--RILILDSLAGSD 139
                                   333333.4444444445667***********9999955..5*****886555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.3e-06   0.00071       7     118 ..      14     122 ..       8     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-06
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.......sskdllrellralglelkaerlsseelle 80 
                                   +++ +G  G+GKTt+++++++ l+        +  + ++ ++s+t        ++  +++l  +l +++  ++++   +  
  gi|70607206|ref|YP_256076.1|  14 VIIFFGVNGVGKTTTIAKVVNMLK--------KNNLSTIIAASDTfraaaqeQLAYHASKLEVQLIRGK--YGADPASVAF 84 
                                   58899******************6........3333355555555444210033333334444444333..4577777777 PP

                        AAA_22  81 aleqalraravielliiDEaqhlr.seealeeLrsllnl 118
                                        +++r    +++iD a ++    +++eeL++ l +
  gi|70607206|ref|YP_256076.1|  85 DAISFAKSRNI-DVVLIDTAGRMHiDSDLVEELKRVLRI 122
                                   77777777777.999999999995559999999877765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.7e-06    0.0009       1      74 [.      15     110 ..      15     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.7e-06
                                   EEEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS.....................STTHHHHHHHHHHHHHHHTST CS
                           AAA   1 vllyGppGtGKTllakavakelgve..fleisgsellsk.....................yvgesekkirelfkeakekak 58 
                                   ++++G  G+GKT+++  v++ l+ +     i +s+ +                       y  + ++   + ++ ak+ + 
  gi|70607206|ref|YP_256076.1|  15 IIFFGVNGVGKTTTIAKVVNMLKKNnlSTIIAASDTFRAaaqeqlayhasklevqlirgkYGADPASVAFDAISFAKSRN- 94 
                                   689******************97443313333333332234444444555555555555355555555556777777776. PP

                                   SEEEEEETGGGHHHHH CS
                           AAA  59 psilfiDEidalaksr 74 
                                     +++iD + +++ ++
  gi|70607206|ref|YP_256076.1|  95 IDVVLIDTAGRMHIDS 110
                                   8999999888886655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.5e-06    0.0013      12      59 ..      14      58 ..       3     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-06
                        AAA_19 12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelr 59
                                  v++  +  G GKT+++ ++v++l++++   + +i++++ t rAa + +
  gi|70607206|ref|YP_256076.1| 14 VIIFFGVNGVGKTTTIAKVVNMLKKNN---LSTIIAASDTFRAAAQEQ 58
                                  45556889****************999...589*******99997644 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.5e-06    0.0024       1      43 [.      14      61 ..      14     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-06
                        AAA_33  1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqq 43
                                  ++++ G++G+GK+t + ++++ l+     +++ +sdt+r +  ++   
  gi|70607206|ref|YP_256076.1| 14 VIIFFGVNGVGKTTTIAKVVNMLKknnlsTIIAASDTFRAAAQEQLAY 61
                                  89****************977777666878888888877776653333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   1.1e-05    0.0057       2      87 ..      15     138 ..      14     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                   EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEE............................ CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgke............................ 47 
                                   ++++G   vGK+t i + ++       ++ i+++  +     ++  ++ +  +                            
  gi|70607206|ref|YP_256076.1|  15 IIFFGVNGVGKTTTIAKVVNmlkknnlSTIIAASDTFRAAAQEQLAYHAS--Klevqlirgkygadpasvafdaisfaksr 93 
                                   7899**************98665543312233333333332222222211..12344455555566666666666666666 PP

                                   ...EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT..T CS
                      MMR_HSR1  48 ...ielvDtpGliegaseekglgkaflalee...adlillvvdas..e 87 
                                      ++l+Dt+G ++    + +l ++++++ +    d  +l++d+   +
  gi|70607206|ref|YP_256076.1|  94 nidVVLIDTAGRMH---IDSDLVEELKRVLRiakPDFRILILDSLagS 138
                                   666********554...5555555555444431169999999943442 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     3e-05     0.016      11      57 ..       7      54 ..       1      69 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                    Zeta_toxin 11 psqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57
                                   s+++P +i+  G  G GK+++++++ + l+ ++ + +    D++R+ 
  gi|70607206|ref|YP_256076.1|  7 SSGKKPFVIIFFGVNGVGKTTTIAKVVNMLKkNNLSTIIAASDTFRAA 54
                                  4669**************************966777888888999975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.4e-05     0.013       4     107 ..      14     141 ..      11     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-05
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe......kll.elileklkeekktylflDEiqev. 76 
                                   +++  G+  vGKTt + ++++ l   k++   i   +++++++a+++      kl+ +li+ k+   +   + +D i+ + 
  gi|70607206|ref|YP_256076.1|  14 VIIFFGVNGVGKTTTIAKVVNMLK--KNNLSTIIAASDTFRAAAQEQlayhasKLEvQLIRGKYG-ADPASVAFDAISFAk 91 
                                   67889**************97776..455544444444454444332223333333133333333.467778888888888 PP

                        AAA_14  77 ..................pewekalkslvd.egknldvivtGSnskllsk 107
                                                     +++ + lk++++  ++++++++  S+++    
  gi|70607206|ref|YP_256076.1|  92 srnidvvlidtagrmhidSDLVEELKRVLRiAKPDFRILILDSLAGSDAL 141
                                   88888888888888899888888888888844478899998888876555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.2e-05     0.012      36      70 ..      15      48 ..       4      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                         AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltinfs 70
                                  +++ G  G+GKt++i ++++ l+k+++++++   s
  gi|70607206|ref|YP_256076.1| 15 IIFFGVNGVGKTTTIAKVVNMLKKNNLSTII-AAS 48
                                  7899*******************66655544.333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   2.4e-05     0.013      11      70 ..       2      60 ..       1     136 [. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                      ATPase_2 11 leeilerepneiyfi.YGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70
                                  +e+i ++++++++ i +G  g+GKt+ + ++++ l++ +     +ia ++ + + ++e ++
  gi|70607206|ref|YP_256076.1|  2 IEKIRSSGKKPFVIIfFGVNGVGKTTTIAKVVNMLKKNNL--STIIAASDTFRAAAQEQLA 60
                                  67788888877777637******************77654..3344555555555555443 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.066       3      28 ..      19      44 ..      17      73 .. 0.87
   2 ?   -0.1   0.0       1.2   6.5e+02     101     125 ..     107     132 ..     101     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                  ESTTSSHHHHHHHHHHHHHHTTE.EE CS
               Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvv 28
                                  G++G+GKtt ++++++ lk++ ++++
  gi|70607206|ref|YP_256076.1| 19 GVNGVGKTTTIAKVVNMLKKNNLSTI 44
                                  9*******************998844 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                   TTTCHHHHHHGGGTTS.E-SEEEEEE CS
               Thymidylate_kin 101 gvdldlvlslnedvll.kPdltflld 125
                                   ++d dlv +l++ +   kPd+ +l+ 
  gi|70607206|ref|YP_256076.1| 107 HIDSDLVEELKRVLRIaKPDFRILIL 132
                                   57889999998887668999887764 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   0.00012     0.064       9      88 ..      22     165 ..      14     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   GvGKTt+ a+    l++++l ++    D+ + ++        +++                                    
  gi|70607206|ref|YP_256076.1|  22 GVGKTTTIAKVVNMLKKNNLSTIIAASDTFRAAAQE---QLAYHASklevqlirgkygadpasvafdaisfaksrnidvvl 99 
                                   9********************999999988777662...222222245556677888888899999999999999999999 PP

                                   .................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS.. CS
                                   .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .................................dlkrllellealgkkkalllkiagvvlnrvdgen 88 
                                                                    d   ++  le+ ++ +++++ +  v+l++vd ++
  gi|70607206|ref|YP_256076.1| 100 idtagrmhidsdlveelkrvlriakpdfrililDSLAGSDALEQARH-FENNVGYDAVILTKVDADA 165
                                   99998888888888888888888888888888855555555555554.3444666778888888764 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.5e-05     0.024       1      54 [.      11      64 ..      11      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-05
                                  S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHH CS
                    APS_kinase  1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfsee 54
                                  +++v+ + G+ g GK+t   ++ ++L++++ s+++   d+ R   +++L++++ 
  gi|70607206|ref|YP_256076.1| 11 KPFVIIFFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASDTFRAAAQEQLAYHAS 64
                                  5799***********998888999********************9999998765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   6.7e-05     0.035       1      29 [.      14      42 ..      14      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-05
                          MobB  1 vlgivgksgsGKTtLleklipelkarglr 29
                                  v+ + g +g GKTt + k++++lk+++l+
  gi|70607206|ref|YP_256076.1| 14 VIIFFGVNGVGKTTTIAKVVNMLKKNNLS 42
                                  67899********************9875 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.5e-05     0.045       4      54 ..      15      68 ..      12      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSS...S--GGGHH CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekds...ykdsakek 54
                                  ++++G+  +GK+t  +++ + l++++ s ++  +++++ + ++   y+ s+ e 
  gi|70607206|ref|YP_256076.1| 15 IIFFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASDTFRAAAQEqlaYHASKLEV 68
                                  899**********************************95444336788877664 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.06      10     107 ..      19     138 ..      11     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   ESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE....................TTCSSE CS
                      GTP_EFTU  10 ghvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle....................ketkky 70 
                                   g    GKtT++ +++  +++ + ++  a      Dt  +  + ++  +++  +++                    +++++ 
  gi|70607206|ref|YP_256076.1|  19 GVNGVGKTTTIAKVVNMLKKNNLSTIIAA----SDTFRAAAQEQLAYHASKLEVQlirgkygadpasvafdaisfAKSRNI 95 
                                   55567**********99999888777665....78888888888888888888888888888888888888887669**** PP

                                   EEEEEEESS..SGG..GHHHHHHH..HHT-SEEEEEEETTTBS CS
                      GTP_EFTU  71 linliDtPG..Hvd..Fskevirg..lrvlDgavlvvdaveGv 107
                                    + liDt G  H+d   ++e  r   +++ D+ +l++d+  G 
  gi|70607206|ref|YP_256076.1|  96 DVVLIDTAGrmHIDsdLVEELKRVlrIAKPDFRILILDSLAGS 138
                                   *********5543333888888884444569999999988875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00034      0.18       2      29 ..      14      41 ..      13      65 .. 0.92
   2 ?   -0.8   0.0       2.3   1.2e+03      77      92 ..     113     137 ..      97     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                                  CEEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawaegkl 29
                                  ++i  G +G+GKTt ++k++  +++++l
  gi|70607206|ref|YP_256076.1| 14 VIIFFGVNGVGKTTTIAKVVNMLKKNNL 41
                                  57889******************99986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                                   CCSCCCEE.........EEEE-STT CS
                         NACHT  77 lelperlL.........lilDglDe 92 
                                   +e  +r+L         lilD+l  
  gi|70607206|ref|YP_256076.1| 113 VEELKRVLriakpdfriLILDSLAG 137
                                   4445555555555556699998744 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00038       0.2       4      77 ..      14     106 ..      11     144 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                        AAA_24   4 kiliyGpsgiGKTtlakel.....gpkplfi.....dtekGlksldadkfpdieswedfldevvel............... 59 
                                    i+ +G +g+GKTt++++      + + l       dt++ +                    ++e                
  gi|70607206|ref|YP_256076.1|  14 VIIFFGVNGVGKTTTIAKVvnmlkK-NNLSTiiaasDTFRAA--------------------AQEQlayhasklevqlirg 73 
                                   68889*************9444431.1111112222333322....................2222222222223333355 PP

                        AAA_24  60 ...............aaeladyktlviDtidel 77 
                                                   a+ ++++++ iDt++ +
  gi|70607206|ref|YP_256076.1|  74 kygadpasvafdaisFAKSRNIDVVLIDTAGRM 106
                                   555557777777777666777888888887755 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00018     0.094      15      45 ..       7      37 ..       1      45 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                  TTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
                        NB-ARC 15 kdelqslvvalvGmgGvGKttlakqilnksd 45
                                  + + + +v+ + G  GvGKtt +++++n ++
  gi|70607206|ref|YP_256076.1|  7 SSGKKPFVIIFFGVNGVGKTTTIAKVVNMLK 37
                                  55666799****************9999754 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00024      0.13      10      73 ..       7      79 ..       1     133 [. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                  T..TTEEEEEEEESTTSSHHH....HHHHHHHSSCEECSS...SSS.EEEEEEEETTEEEEEEEE-SSGGGGG CS
                           Arf 10 lk.kkelrilllGLDnaGKtT....ilkklkleelvttvP...Tig.fnveeleiknlkftvwDvGGqeklRp 73
                                  ++ kk + i++ G  + GKtT    ++++lk+++l+t++    T      e+l+++  k++v  + G+  + p
  gi|70607206|ref|YP_256076.1|  7 SSgKKPFVIIFFGVNGVGKTTtiakVVNMLKKNNLSTIIAasdTFRaAAQEQLAYHASKLEVQLIRGKYGADP 79
                                  44378899************95555567888888888654111333134577777777777777766665555 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00051      0.27      22      61 ..       2      42 ..       1      66 [. 0.80
   2 ?   -0.8   0.0       1.7   9.2e+02     119     140 ..     140     161 ..     133     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                                  HHSGGGGG-E.EEEEEEESTTS-HHHHHHHHHTTS-GGG-E CS
                          PPK2 22 qekvkaegkk.lvvifegrDaAGKgGaikrvtealnprvar 61
                                  +ek++++gkk  v+if g ++ GK  +i++v++ l++ +  
  gi|70607206|ref|YP_256076.1|  2 IEKIRSSGKKpFVIIFFGVNGVGKTTTIAKVVNMLKKNNLS 42
                                  57788888877***********************9887654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHTTEEEEEE CS
                          PPK2 119 flreipefErmlvesgillvKf 140
                                   +l+++++fE+ +  ++++l K+
  gi|70607206|ref|YP_256076.1| 140 ALEQARHFENNVGYDAVILTKV 161
                                   7888999999998888888875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.13       2      43 ..      16      55 ..      15      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
               Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklp 43
                                  +  Gv G GK+t i k++++    + n +t++++++ +  + 
  gi|70607206|ref|YP_256076.1| 16 IFFGVNGVGKTTTIAKVVNM--LKKNNLSTIIAASDTFRAAA 55
                                  667*****************..55667777777777774433 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.11       7      94 ..      16     106 ..      11     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                          KdpD   7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveyk.gkeleeldldai...larkp 83 
                                   if+G+ +GvGkt ++ +  + lk+++   +i++ +t + +  e+l+ +   ++ + ++ k g+    +  dai    +r+ 
  gi|70607206|ref|YP_256076.1|  16 IFFGV-NGVGKTTTIAKVVNMLKKNNLSTIIAASDTFRAAAQEQLAYHASKLEVQLIRGKyGADPASVAFDAIsfaKSRNI 95 
                                   78885.8****************************9999888888866555555444332134444444444411156778 PP

                          KdpD  84 evvlvDelaht 94 
                                   +vvl+D  +  
  gi|70607206|ref|YP_256076.1|  96 DVVLIDTAGRM 106
                                   89999977655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0011      0.58      20      59 ..       3      42 ..       1      53 [. 0.77
   2 ?   -0.5   0.0       0.9   4.7e+02     110     139 ..      83     112 ..      71     125 .. 0.72
   3 ?   -2.7   0.0       4.4   2.3e+03     118     130 ..     149     161 ..     140     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0011
                                  HHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT-- CS
                          MeaB 20 erllakaGraqvvGltGvPGaGkstlvealglelrrrGkr 59
                                  e+++++  +  v+ + Gv G+Gk t++ +++  l+++   
  gi|70607206|ref|YP_256076.1|  3 EKIRSSGKKPFVIIFFGVNGVGKTTTIAKVVNMLKKNNLS 42
                                  5666666677889999**************9999877554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHTT-SEEEEEEESSTTHHHHH CS
                          MeaB 110 trevvllleaaGfDvvlietvGvGqsevdv 139
                                   + +++ +  +   Dvvli+t G    + d+
  gi|70607206|ref|YP_256076.1|  83 AFDAISFAKSRNIDVVLIDTAGRMHIDSDL 112
                                   567777788888999***999966555555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.4
                                   HHTT-SEEEEEEE CS
                          MeaB 118 eaaGfDvvlietv 130
                                   + +G+D v++  v
  gi|70607206|ref|YP_256076.1| 149 NNVGYDAVILTKV 161
                                   5689***999776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00029      0.15     127     168 ..      10      52 ..       1      74 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                         T2SSE 127 rerglilvsGgTgsGKttllyallkeinks.derivtvEDpvE 168
                                   ++  +i++ G  g GKtt++  ++++++k+    i+ + D+  
  gi|70607206|ref|YP_256076.1|  10 KKPFVIIFFGVNGVGKTTTIAKVVNMLKKNnLSTIIAASDTFR 52 
                                   566899**********************994567777777754 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001      0.54      91     123 ..       3      36 ..       1      76 [. 0.78
   2 ?   -0.3   0.0       1.7     9e+02      57      86 ..     133     162 ..      86     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                                   HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                   e++++  k+  ++++ G  GvGK+t i ++++ l
  gi|70607206|ref|YP_256076.1|   3 EKIRSSGKKpFVIIFFGVNGVGKTTTIAKVVNML 36 
                                   56666666657899***********988777643 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                                   GG--HHHHHHHHHHHHHHTTSEEEE--TTT CS
                   RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsakt 86 
                                   D l  +++le+ ++  +++gy+ +++ + +
  gi|70607206|ref|YP_256076.1| 133 DSLAGSDALEQARHFENNVGYDAVILTKVD 162
                                   333334445555555666666665555444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00074      0.39       1      56 [.      15      58 ..      15     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00074
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedk 56
                                  I+  G+ GvGKtt    + ++l          k+n+l++   +   d ++ + +++
  gi|70607206|ref|YP_256076.1| 15 IIFFGVNGVGKTTTIAKVVNML----------KKNNLSTIIAAS--DTFRAAAQEQ 58
                                  899**********998887775..........444444444444..4444444444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0022       1.2       3      38 ..      14      49 ..      13      55 .. 0.89
   2 ?    0.5   0.0       0.5   2.7e+02     114     133 ..      85     103 ..      76     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                   ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                  vi++ G  GVGKtt  a +   l +++ ++++ + D
  gi|70607206|ref|YP_256076.1| 14 VIIFFGVNGVGKTTTIAKVVNMLKKNNLSTIIAASD 49
                                  57888999***********999*****999998877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                                   HHHHHHHHCSSSSEEEEESB CS
                   ArsA_ATPase 114 eellkyvkeeeydvvvlDta 133
                                   ++ + + k+++ dvv++Dta
  gi|70607206|ref|YP_256076.1|  85 DA-ISFAKSRNIDVVLIDTA 103
                                   44.4578999*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 1322.92
//
Query:       gi|70607207|ref|YP_256077.1|  [L=146]
Description: prefoldin subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-27   93.6   4.2    1.2e-26   93.0   4.2    1.3  1  Prefoldin      Prefoldin subunit
     0.0039   17.3   0.0     0.0058   16.8   0.0    1.3  1  BppU_IgG       Baseplate upper protein immunoglobulin like do
  ------ inclusion threshold ------
      0.017   14.6   1.8        0.1   12.1   0.7    2.1  2  FAP206         Domain of unknown function
      0.032   14.7   1.8        1.7    9.2   0.1    2.3  2  NPV_P10        Nucleopolyhedrovirus P10 protein
      0.037   14.3   0.4        2.4    8.5   0.0    2.2  2  DUF948         Bacterial protein of unknown function (DUF948)
      0.044   14.0   0.1       0.12   12.6   0.1    1.9  1  HHH_6          Helix-hairpin-helix motif
      0.047   13.3   2.5      0.059   13.0   2.5    1.1  1  DUF4795        Domain of unknown function (DUF4795)
      0.072   14.2   2.6          8    7.6   0.8    2.2  2  DUF5320        Family of unknown function (DUF5320)
       0.09   12.6   1.2       0.17   11.7   1.2    1.6  1  SURF6          Surfeit locus protein 6
       0.18   11.7   0.6         11    5.9   0.1    2.2  2  Sec23_helical  Sec23/Sec24 helical domain
       0.23   11.6   6.8        1.5    8.9   0.9    2.2  2  DUF148         Domain of unknown function DUF148
       0.24   11.7   3.2        8.8    6.7   0.1    2.2  2  Muted          Organelle biogenesis, Muted-like protein
        0.4    9.9   5.2        0.7    9.2   0.8    2.0  2  CorA           CorA-like Mg2+ transporter protein
       0.41   10.7   4.5       0.18   11.9   0.7    2.1  2  DUF2205        Short coiled-coil protein
       0.47   10.4   6.1          2    8.4   0.6    2.3  2  Prefoldin_2    Prefoldin subunit
        1.1    9.6   4.2         16    6.1   0.0    3.3  3  KID            KID repeat


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   4.2   1.1e-29   1.2e-26       1     119 [.      24     142 ..      24     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.1e-29
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                     Prefoldin   1 lkeeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                   l++++++lq++la++ e++e +++++++++++ ke+++++++ + ++++ +k++ +d++kvl++lG +yy+e++ + A+++
  gi|70607207|ref|YP_256077.1|  24 LRQYIDTLQKNLAEVLESLEAVRASKSAVDEIGKENQEYLLFGDRKGNIVFKVNSVDKNKVLIHLGLNYYAEVDPQAAKKI 104
                                   5799***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   l++++++l + +++++ el k  d+++++ ++l+q++ 
  gi|70607207|ref|YP_256077.1| 105 LDDREQQLAEVSKNIQGELSKSIDAYNQIAEILSQVQG 142
                                   ***********************************996 PP

>> BppU_IgG  Baseplate upper protein immunoglobulin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.1e-06    0.0058      33      94 ..      55     120 ..      47     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                      BppU_IgG  33 lgtepkG..lFGgtntktipakveysdantvkvelprnyaltg...atveelkdgswylidgyktlk 94 
                                   +g+e +   lFG+ +   i  kv+++d+n v ++l+ ny+ +    a+++ l+d++ +l +  k+++
  gi|70607207|ref|YP_256077.1|  55 IGKENQEylLFGDRK-GNIVFKVNSVDKNKVLIHLGLNYYAEVdpqAAKKILDDREQQLAEVSKNIQ 120
                                   566554422466654.46779*******************987665566777888888888888886 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   9.1e-05       0.1      58     103 ..       8      53 ..       4      55 .. 0.94
   2 ?    1.4   0.0      0.16   1.8e+02       4      25 ..     110     131 ..      77     145 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                        FAP206  58 rqyeaylrilledveksaeeveellkrfeaeleklketvksktavp 103
                                   +q+  y+  l ++++ +++ +++l+k+++++le l+++  sk+av+
  gi|70607207|ref|YP_256077.1|   8 QQAAEYIAYLYDQASALRQYIDTLQKNLAEVLESLEAVRASKSAVD 53 
                                   69999*********************************99999996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                        FAP206   4 eaipatreaiekeleeaqelas 25 
                                   +++++++++i+ el++++++ +
  gi|70607207|ref|YP_256077.1| 110 QQLAEVSKNIQGELSKSIDAYN 131
                                   3344445555555555555555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0015       1.7      13      55 ..      14      53 ..       8      81 .. 0.73
   2 ?    5.0   0.1     0.031        34      24      65 ..     109     137 ..      92     143 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                       NPV_P10 13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55
                                  i+ + d+ +al q +d +q+nl +v    e L+a  a+  +++
  gi|70607207|ref|YP_256077.1| 14 IAYLYDQASALRQYIDTLQKNLAEVL---ESLEAVRASKSAVD 53
                                  66777889999999999999998855...55665555544444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.031
                       NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                   +qq+++v++n++   el++ +da            ++I +iL
  gi|70607207|ref|YP_256077.1| 109 EQQLAEVSKNIQG--ELSKSIDAY-----------NQIAEIL 137
                                   3455555555555..555555554...........3333333 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.044        50      51      82 ..      26      57 ..       7      62 .. 0.56
   2 ?    8.5   0.0    0.0021       2.4      24      67 ..     101     144 ..      83     146 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.044
                        DUF948 51 dllakvnelledvneklekvdplteavadlge 82
                                  + +++ ++ l++v e le+v +  +av ++g+
  gi|70607207|ref|YP_256077.1| 26 QYIDTLQKNLAEVLESLEAVRASKSAVDEIGK 57
                                  33333344444466666666666666666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                        DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvnekl 67 
                                   +kk+ld  +++++e+ k++++ l ++ d+ +++ e+l++v++k 
  gi|70607207|ref|YP_256077.1| 101 AKKILDDREQQLAEVSKNIQGELSKSIDAYNQIAEILSQVQGKK 144
                                   58999999999999999999999999999999999999999985 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011      0.12      22      50 ..      80     111 ..      26     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                         HHH_6  22 dga...irlGLaaikglgeaaaerivaeReke 50 
                                   d++   i lGL+   ++  +aa++i++ Re++
  gi|70607207|ref|YP_256077.1|  80 DKNkvlIHLGLNYYAEVDPQAAKKILDDREQQ 111
                                   222358***********************942 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   2.5   5.3e-05     0.059      33     140 ..      10     142 ..       1     145 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                       DUF4795  33 lekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq..................fDeakkeLek 95 
                                     + ++ + ++  al+++i+ l+k+ a+  ++e  +a+ a k+a++    ++q                  +D+ k +++ 
  gi|70607207|ref|YP_256077.1|  10 AAEYIAYLYDQASALRQYIDTLQKNLAE--VLESLEAVRASKSAVDEIGKENQeyllfgdrkgnivfkvnsVDKNKVLIHL 88 
                                   555556667788999********99999..*******************9999****999999999999998998888888 PP

                       DUF4795  96 ml........eellekleeqeealkkaldtLqeelkekld.rlelepLkeqlee 140
                                   +l        + + + l+  e++l ++ +++q el + +d  +++ ++ +q+++
  gi|70607207|ref|YP_256077.1|  89 GLnyyaevdpQAAKKILDDREQQLAEVSKNIQGELSKSIDaYNQIAEILSQVQG 142
                                   8899999999999999************************88888888888875 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8    0.0071         8      67      98 ..       6      37 ..       2      45 .. 0.65
   2 ?    6.5   0.0     0.015        17      63      97 ..      90     124 ..      52     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0071
                       DUF5320 67 aeaskeeekelLeeqaeaLeeeleaikkrlke 98
                                  +++++ e +++L +qa+aL++ +++++k+l+e
  gi|70607207|ref|YP_256077.1|  6 EQQQAAEYIAYLYDQASALRQYIDTLQKNLAE 37
                                  55566666667777777777777777776665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                       DUF5320  63 aaetaeaskeeekelLeeqaeaLeeeleaikkrlk 97 
                                    +++ae ++++ k++L ++++ L e  ++i+ +l+
  gi|70607207|ref|YP_256077.1|  90 LNYYAEVDPQAAKKILDDREQQLAEVSKNIQGELS 124
                                   6788999***********************99987 PP

>> SURF6  Surfeit locus protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   0.00015      0.17      90     138 ..      92     144 ..       6     146 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                         SURF6  90 gptkkdpkqaLkkleakkakleelke....ekrkeieekekWekalakaeGeK 138
                                     ++ dp++a+k l++++++l+e+++    e  k+i+  ++  ++l++++G+K
  gi|70607207|ref|YP_256077.1|  92 YYAEVDPQAAKKILDDREQQLAEVSKniqgELSKSIDAYNQIAEILSQVQGKK 144
                                   44567*********************99999999999**************99 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.027        31      19      47 ..      21      49 ..       8      86 .. 0.80
   2 ?    5.9   0.1    0.0097        11      13      45 ..     100     135 ..      98     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.027
                                  TS-HHHHHHHHHHHHHHHHHHHHHH---- CS
                 Sec23_helical 19 esgladarealdtslvdllsayrkvgasg 47
                                   s l++ ++ l++ l+++l ++  v as+
  gi|70607207|ref|YP_256077.1| 21 ASALRQYIDTLQKNLAEVLESLEAVRASK 49
                                  3678999999*********9999999886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0097
                                   HHHHTT...TS-HHHHHHHHHHHHHHHHHHHHHH-- CS
                 Sec23_helical  13 aidkal...esgladarealdtslvdllsayrkvga 45 
                                   a +k+l   e++la++ + ++  l++ + ay++  +
  gi|70607207|ref|YP_256077.1| 100 AAKKILddrEQQLAEVSKNIQGELSKSIDAYNQIAE 135
                                   56666666689********************99874 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9    0.0014       1.5      34      77 ..       7      50 ..       2      59 .. 0.91
   2 ?    5.9   0.6     0.012        13      38      74 ..     102     138 ..      95     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                        DUF148 34 tdeykefeakvkaqkeevkknvtavisnLssvqekleaIldnks 77
                                  +++ +e+ a + +q +++++ +++  +nL++v e+lea+ + ks
  gi|70607207|ref|YP_256077.1|  7 QQQAAEYIAYLYDQASALRQYIDTLQKNLAEVLESLEAVRASKS 50
                                  67889999999999************************999886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                        DUF148  38 kefeakvkaqkeevkknvtavisnLssvqekleaIld 74 
                                   k+   ++++q +ev+kn++  +s+  ++++++ +Il+
  gi|70607207|ref|YP_256077.1| 102 KKILDDREQQLAEVSKNIQGELSKSIDAYNQIAEILS 138
                                   4555567777777777777777777777777777775 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.014        15      54      91 ..      22      59 ..       1      64 [. 0.67
   2 ?    6.7   0.1    0.0079       8.8      48      81 ..      93     126 ..      79     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                         Muted 54 qllpkclesmkenLselnkkleaalekverllqkelee 91
                                  + l++ ++++++nL e+++ lea++ + + + +  +e+
  gi|70607207|ref|YP_256077.1| 22 SALRQYIDTLQKNLAEVLESLEAVRASKSAVDEIGKEN 59
                                  45667777788888888888777777766666554443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0079
                         Muted  48 vnelkeqllpkclesmkenLselnkkleaalekv 81 
                                     e++ q  +k+l+  +++L e++k+++  l+k+
  gi|70607207|ref|YP_256077.1|  93 YAEVDPQAAKKILDDREQQLAEVSKNIQGELSKS 126
                                   5688888999999999999999998887766554 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8   0.00062       0.7     185     226 ..       5      46 ..       2      52 .. 0.87
   2 ?    3.8   0.4     0.026        29     142     218 ..      65     140 ..      40     143 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00062
                          CorA 185 llddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                    + ++++ey+  l+d+++ l +++++l++ l  + +++ ++ 
  gi|70607207|ref|YP_256077.1|   5 AEQQQAAEYIAYLYDQASALRQYIDTLQKNLAEVLESLEAVR 46 
                                   45678889*************************999998875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                          CorA 142 edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerlesl 218
                                   + ++k +i+ ++  + ++ v ++  l++  ev  +  + +  +  +++ +e  ++++ el+++++  ++++e l+++
  gi|70607207|ref|YP_256077.1|  65 FGDRKGNIVFKVNSVDKNKVLIHLGLNYYAEVDPQAAK-KILDDREQQLAEVSKNIQGELSKSIDAYNQIAEILSQV 140
                                   55566666666666666666667777777777666665.44444444444444444444444555555555555444 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   0.00016      0.18      15      46 ..      18      49 ..       2      63 .. 0.80
   2 ?   -0.4   0.2         1   1.2e+03       8      28 ..     110     130 ..      98     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                       DUF2205 15 rearerLqqqakeLqssLqaLaervdeVkeeh 46
                                  +++  +L+q +++Lq+ L +++e  ++V+  +
  gi|70607207|ref|YP_256077.1| 18 YDQASALRQYIDTLQKNLAEVLESLEAVRASK 49
                                  566789**********************9765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                       DUF2205   8 edveklerearerLqqqakeL 28 
                                   +++ +++++++ +L++ +++ 
  gi|70607207|ref|YP_256077.1| 110 QQLAEVSKNIQGELSKSIDAY 130
                                   566667777777777766655 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6     0.018        21      83     103 ..      19      39 ..       3      67 .. 0.49
   2 ?    8.4   0.6    0.0018         2      57     105 ..      95     143 ..      77     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHCCT CS
                   Prefoldin_2  83 kqleklekeleelkeelqkkl 103
                                   +q + l++ ++ l+++l + l
  gi|70607207|ref|YP_256077.1|  19 DQASALRQYIDTLQKNLAEVL 39 
                                   333333333333333333222 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0018
                                   EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                                   ++d + +k+ L++r+ +l +++k+++ +l+k    ++++ e l + +++
  gi|70607207|ref|YP_256077.1|  95 EVDPQAAKKILDDREQQLAEVSKNIQGELSKSIDAYNQIAEILSQVQGK 143
                                   7788999***************************999999999998876 PP

>> KID  KID repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014        16       2       9 ..      28      35 ..      27      37 .. 0.91
   2 ?    1.8   1.4       0.4   4.5e+02       1       8 [.      75      82 ..      75      83 .. 0.93
   3 ?   -0.4   0.0       2.2   2.4e+03       5      10 ..     115     120 ..     114     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                           KID  2 IDsVEKNL 9 
                                  ID+  KNL
  gi|70607207|ref|YP_256077.1| 28 IDTLQKNL 35
                                  9******9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.4
                           KID  1 KIDsVEKN 8 
                                  K+ sV KN
  gi|70607207|ref|YP_256077.1| 75 KVNSVDKN 82
                                  899****9 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.2
                           KID   5 VEKNLn 10 
                                   V KN +
  gi|70607207|ref|YP_256077.1| 115 VSKNIQ 120
                                   78**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1617  (0.0901891); expected 358.6 (0.02)
Passed bias filter:                      803  (0.0447878); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 924.07
//
Query:       gi|70607208|ref|YP_256078.1|  [L=86]
Description: 50S ribosomal protein LX [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-12   45.2   0.7    1.8e-11   44.2   0.7    1.5  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.031   15.2   0.2      0.036   15.0   0.2    1.2  1  Ribosomal_S4    Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.7     2e-15   1.8e-11      78     121 .]      20      63 ..       3      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2e-15
                                   .TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                Ribosomal_L18A  78 rsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                     + ++f+k++r+l+e++a+e++Ys+lg+++++kr++I+I++++
  gi|70607208|ref|YP_256078.1|  20 FPTSQKFTKYVRALNEKQAIEYIYSQLGGKNKIKRYNIHIQEIK 63 
                                   56789************************************996 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2     4e-06     0.036      33      72 ..      23      64 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                                  -----CHCHHHHHHHHHHHHHT-S..HHHHHHHHHHHHHCCS CS
                  Ribosomal_S4 33 rkklseYgkqlrekqklkrrYgll..ekqfrryfkearrirG 72
                                  ++k ++Y   l+ekq + ++Y  l  ++ ++ry+   ++i+ 
  gi|70607208|ref|YP_256078.1| 23 SQKFTKYVRALNEKQAIEYIYSQLggKNKIKRYNIHIQEIKE 64
                                  7899*****************7777999******99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 588.30
//
Query:       gi|70607209|ref|YP_256079.1|  [L=223]
Description: translation initiation factor IF-6 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-62  210.7   9.3    1.6e-62  210.4   9.3    1.2  1  eIF-6     eIF-6 family
  ------ inclusion threshold ------
       0.53   10.0   2.0       0.44   10.2   0.3    1.7  2  PNK3P     Polynucleotide kinase 3 phosphatase


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.4   9.3   1.8e-66   1.6e-62       1     197 []       5     203 ..       5     219 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 1.8e-66
                                   .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHH CS
                         eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklke 81 
                                   +lsi+g+++iG+++++++ky+++p+  ++e++++i+  Lk+e+++tti++s lvG+lv+gN++ +l+p+t+  +e++ +ke
  gi|70607209|ref|YP_256079.1|   5 KLSIFGTDNIGIYIFTNDKYTIIPKIDDKEVIEKIQGILKTEIIQTTISKSVLVGILVTGNNDVILLPRTALADEIKVIKE 85 
                                   689*********************998999*************************************************** PP

                                   HHH.---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTS.EEEE--BTTBS-TTTSEEE-SSEEEE-TT--H CS
                         eIF-6  82 slk.leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgv.evvrgtiagiktvGsaavvtnkgllvhpkate 160
                                   ++k ++ve+++ + tAlGN+il N ++Al+++dls++++++++++L++   ++gtia+i tvGs+av+t+k +lvh +ate
  gi|70607209|ref|YP_256079.1|  86 QAKdVRVEVVDIRPTALGNIILSNTHGALIYQDLSEAEINKVKKALQIdTAIKGTIANIITVGSVAVITDKAGLVHIDATE 166
                                   *998999*****************************************6679***************************** PP

                                   HHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                         eIF-6 161 eeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                   eel++l+el+kv+++ gTvN+Gs +++sglvaN +g+
  gi|70607209|ref|YP_256079.1| 167 EELKKLSELFKVKLDSGTVNFGSVFIRSGLVANRNGV 203
                                   **********************************985 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   4.9e-05      0.44      34     112 ..       2      86 ..       1      98 [. 0.75
   2 ?   -2.4   0.1      0.39   3.5e+03      50      81 ..     106     132 ..     102     156 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.9e-05
                         PNK3P  34 vlekLkklkeegykivifsNqggvvekktkkslekfkekieallke.l.dvp......llvyaatkkdkyRKPetGmweel 106
                                   +l+kL+   +++  i if+N++ ++    k + ++++eki+ +lk+ + ++       + +++  ++d++  P+t +++e+
  gi|70607209|ref|YP_256079.1|   2 ILDKLSIFGTDNIGIYIFTNDKYTII--PKIDDKEVIEKIQGILKTeIiQTTisksvlVGILVTGNNDVILLPRTALADEI 80 
                                   67889999999**********99888..68888889999998887523422244556588899999999999999999998 PP

                         PNK3P 107 kkdlee 112
                                   k   e+
  gi|70607209|ref|YP_256079.1|  81 KVIKEQ 86 
                                   766555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                         PNK3P  50 ifsNqggvvekktkkslekfkekieallkeld 81 
                                   i+sN +g +  +           i+++ k+l+
  gi|70607209|ref|YP_256079.1| 106 ILSNTHGALIYQD-----LSEAEINKVKKALQ 132
                                   5566555544211.....11222333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1553.07
//
Query:       gi|70607210|ref|YP_256080.1|  [L=129]
Description: 50S ribosomal protein L31e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-07   29.9   2.8      1e-06   28.8   2.8    1.5  1  Ribosomal_L31e   Ribosomal protein L31e
  ------ inclusion threshold ------
       0.01   15.8   9.3      0.011   15.7   9.3    1.1  1  RPN2_C           26S proteasome regulatory subunit RPN2 C-ter
      0.013   15.6   1.3      0.016   15.4   1.3    1.1  1  DUF305           Domain of unknown function (DUF305)
      0.026   14.4   4.0      0.032   14.1   4.0    1.2  1  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
      0.039   12.4   3.8      0.042   12.3   3.8    1.1  1  ST7              ST7 protein
       0.15   11.9   1.9       0.26   11.2   1.9    1.5  1  NtA              Agrin NtA domain
        1.3    9.1   7.1        1.7    8.7   7.1    1.3  1  Peptidase_S49_N  Peptidase family S49 N-terminal
        3.4    6.3   5.5        3.4    6.3   5.5    1.1  1  Presenilin       Presenilin


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   2.8   4.6e-10     1e-06       6      73 ..      49     115 ..      47     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.6e-10
                Ribosomal_L31e   6 eytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsrk 73 
                                   e++In  + i g + + r +rA+k ++ ++++++g + v id+ L ka+  +g  ++ +r+r+ ++r 
  gi|70607210|ref|YP_256080.1|  49 EMVINFRRVIMG-RKTTRTKRAIKYVRYMVKRHFGAEKVIIDPLLAKAITMNGRDKIVRRVRIAVKRI 115
                                   788996666655.556778********************************************99985 PP

>> RPN2_C  26S proteasome regulatory subunit RPN2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   9.3   4.9e-06     0.011      68     122 ..       6      61 ..       1      88 [. 0.61

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-06
                                   ------------.---------------------SS----SSEEEEESSSB--TTC CS
                        RPN2_C  68 eekeedkmdvde.ekeekekkekekkekekeeekkkkekektfekleNpaRVlpaQ 122
                                   +++++++ +++e ++++ke+++ ++++++++eekk+k ++++fe++ N  RV+   
  gi|70607210|ref|YP_256080.1|   6 TATKQEEQKTSElQQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGR 61 
                                   22333333333314444444444444444455777777778999********9765 PP

>> DUF305  Domain of unknown function (DUF305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.3   7.1e-06     0.016      40     116 ..       9      85 ..       2     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                                   HHHHHHHHHHHHHHHHHT---........-----HHHHHHTT---HHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH CS
                        DUF305  40 aaQqaeiaemqgwleawgqpassagegeaaeaseaeeaampgmaseaelaalraasgadfdrlFlelMirhHqgave 116
                                   ++ ++   e+q+  ++ ++p++++++++++++++ e+++ ++  +  ++ + r+ + ++    +++ M+++H ga +
  gi|70607210|ref|YP_256080.1|   9 KQEEQKTSELQQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGRKTTRTKRAIKYVRYMVKRHFGAEK 85 
                                   34456678999999999999999998899999999999999999999999999*********************965 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.0   1.4e-05     0.032       9      78 ..       9      79 ..       2     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                          ACCA  9 aeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvqlaRhpeRpk.tldyiealfed 78
                                  ++ e+k +el+++++e++   +++ ++ e+k +k +ke ++ + ++ +v + R+++R k +  y++ +++ 
  gi|70607210|ref|YP_256080.1|  9 KQEEQKTSELQQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGRKTTRTKrAIKYVRYMVKR 79
                                  455788999*99999999999999999******************************86368999999875 PP

>> ST7  ST7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.8   1.9e-05     0.042     210     284 ..       5      79 ..       1      98 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                           ST7 210 etiseaekllkkalkvaealykrsqklqsksskeeavhrrdlnvlvyikrrlamcarklgrlkeavkmlrdlike 284
                                   +t ++ e+     l+ +++  ++ q+ ++++++e++++    n  + i+ r  +  rk  r+k a+k +r ++k 
  gi|70607210|ref|YP_256080.1|   5 TTATKQEEQKTSELQQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGRKTTRTKRAIKYVRYMVKR 79 
                                   56667777777788888888888888888888888887777788777776666668**************99885 PP

>> NtA  Agrin NtA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.9   0.00011      0.26       5      65 ..      19      89 ..      15     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                           NtA  5 tleereeeanviltgtveevkklkeesklykakvkvkRvlkGeslleseslse..........avnkvtid 65
                                  + +++ee+     t t +e kk+k+e++ ++  ++ +Rv+ G+++ ++++  +          + +kv+id
  gi|70607210|ref|YP_256080.1| 19 QQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGRKTTRTKRAIKyvrymvkrhfGAEKVIID 89
                                  566677777777788999999***********************988888777555555555555555555 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.1   0.00076       1.7      58     122 ..       9      73 ..       1      89 [. 0.61

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00076
               Peptidase_S49_N  58 eealldeeelkaaekkekkeekeekkaekkkakeeeekkrvfvldFkGdikAsevesLreeitav 122
                                   +++  +++el++++k+e+k +++++ ++ +k+++ e+++   v++F+  i  +++++ ++ i+ v
  gi|70607210|ref|YP_256080.1|   9 KQEEQKTSELQQQKKEEQKPQQATTTTKEEKKTKPEKENFEMVINFRRVIMGRKTTRTKRAIKYV 73 
                                   3333444445555555555555444444334444555666689***9999999998888888766 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.5    0.0015       3.4     272     306 ..       8      42 ..       1      86 [. 0.43

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
                    Presenilin 272 eeeseeesseaessaeesseekeseessesseeee 306
                                   ++++e+++se +++++e++++++++++++++++++
  gi|70607210|ref|YP_256080.1|   8 TKQEEQKTSELQQQKKEEQKPQQATTTTKEEKKTK 42 
                                   11111111111111111111111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3644  (0.203246); expected 358.6 (0.02)
Passed bias filter:                     1436  (0.0800937); expected 358.6 (0.02)
Passed Vit filter:                       259  (0.0144459); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 939.82
//
Query:       gi|70607211|ref|YP_256081.1|  [L=53]
Description: 50S ribosomal protein L39e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-19   69.7   7.6    1.4e-19   69.4   7.6    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   7.6   7.7e-24   1.4e-19       1      42 []      11      52 ..      11      52 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 7.7e-24
                 Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                  kKlrL+Kalk N+p+PaWv++kt+ ++r np rR+WRr++Lk
  gi|70607211|ref|YP_256081.1| 11 KKLRLGKALKRNSPIPAWVIIKTQAEIRFNPLRRNWRRNNLK 52
                                  7****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 351.81
//
Query:       gi|70607212|ref|YP_256082.1|  [L=96]
Description: hypothetical protein Saci_1468 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-26   92.9  12.9    1.6e-26   92.8  12.9    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
     0.0071   15.9   4.4     0.0077   15.8   4.4    1.0  1  4HB_MCP_1   Four helix bundle sensory module for signal trans
  ------ inclusion threshold ------
       0.56   10.5   8.5       0.42   10.9   2.7    2.0  2  DUF4355     Domain of unknown function (DUF4355)


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8  12.9   2.7e-30   1.6e-26      23     111 .]       4      93 ..       1      93 [. 0.91

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 2.7e-30
                                   .XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS-.--X CS
                    dsDNA_bind  23 seqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvae.kkk 102
                                   ++ +e+q++a+ e++k aiL++iL+peAr+RL++++lv+pe aea+en+Li laqsG+++ ++t+++Lk++L q+++ ++k
  gi|70607212|ref|YP_256082.1|   4 RQLEERQRKAEIEAQKDAILRTILTPEARQRLTNVKLVRPELAEAIENQLIALAQSGRIQAQITDDELKQILAQLNSqTRK 84 
                                   566777888889*****************************************************************6666 PP

                                   XXXX..XXX CS
                    dsDNA_bind 103 etkivisrr 111
                                   + ki+i+ r
  gi|70607212|ref|YP_256082.1|  85 DYKITIKER 93 
                                   69**99865 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   4.4   1.3e-06    0.0077      85     167 ..       9      90 ..       1      92 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                     4HB_MCP_1  85 eeleaeidkllekyektilteeEkelleefkeqlnaY.revrkkvlelakegkkdeAyqlyetegrparekliealeelvd 164
                                    +++aei+ +  ++ +tilt+e +++l+++k    +   ++++++++la++g  +   q++++e++++ ++l++   +  +
  gi|70607212|ref|YP_256082.1|   9 RQRKAEIEAQKDAILRTILTPEARQRLTNVKLVRPELaEAIENQLIALAQSGRIQ--AQITDDELKQILAQLNSQTRKDYK 87 
                                   68899********************************88999***********98..589**********99999888777 PP

                     4HB_MCP_1 165 lnl 167
                                   + +
  gi|70607212|ref|YP_256082.1|  88 ITI 90 
                                   665 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7     7e-05      0.42      46      91 ..       2      48 ..       1      53 [. 0.86
   2 ?    3.1   0.8     0.017     1e+02      26      52 ..      65      88 ..      46      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                       DUF4355 46 ekaeyeleklqkeleelkaelarkelkaearkvlaekkipi.ellnl 91
                                  ++++ e  ++++e+e++k++  r  l+ ear+ l+  k+   el++ 
  gi|70607212|ref|YP_256082.1|  2 QRRQLEERQRKAEIEAQKDAILRTILTPEARQRLTNVKLVRpELAEA 48
                                  89999999**************************9887755566665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.017
                       DUF4355 26 keledeikkeakklakmnaeekaeyel 52
                                  +  +de+   ++ la++n + +++y++
  gi|70607212|ref|YP_256082.1| 65 QITDDEL---KQILAQLNSQTRKDYKI 88
                                  4556777...88999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1667  (0.0929779); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 699.20
//
Query:       gi|70607213|ref|YP_256083.1|  [L=154]
Description: 30S ribosomal protein S19e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-48  163.2   0.0    2.9e-48  163.0   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0068   16.3   0.7      0.013   15.3   0.1    1.8  2  RuvB_C          RuvB C-terminal winged helix domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.038   13.9   0.0    1.8  2  HTH_12          Ribonuclease R winged-helix domain
      0.057   13.5   0.0       0.13   12.4   0.0    1.5  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.075   13.2   0.0       0.14   12.3   0.0    1.5  1  Mrr_N           Mrr N-terminal domain
      0.092   12.6   0.0        0.2   11.6   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.14   12.5   0.0       0.25   11.7   0.0    1.4  1  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.0   1.1e-51   2.9e-48       1     136 [.       3     140 ..       3     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 1.1e-51
                                   TSSSHHHHHHHHHS--S--.-S-SSS-SSSS-SS-S-SS-SSTTTH.HHHHHHHHHHTS--TTS.GGGGS----SS-SSS- CS
                Ribosomal_S19e   1 tvkdVpaeelikalaeeLk.ksgklevPewadlvKtgsakelaped.edWfyvRaAsilRkvyl.rgpvGverlrkvYGgk 78 
                                   tv+ Vpa+ li +lae+Lk + ++l++P+w+ ++Kt+s+ke+ p+d e+W+y+RaAs+lR++y+ ++p+G+++ rk Y+g+
  gi|70607213|ref|YP_256083.1|   3 TVQMVPADILIPKLAEYLKnNVKELNPPNWVYFAKTASFKERVPDDiENWWYIRAASLLRHLYIyKEPIGLQKTRKLYSGS 83 
                                   799****************77799**********************899**************9566************** PP

                                   ------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                Ribosomal_S19e  79 krrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                   krrg++p ++vka ++ ir+ilqqLek+glv+k++ +gr+l++kG++lld++a+e++k
  gi|70607213|ref|YP_256083.1|  84 KRRGTKPPRSVKAPTHSIRTILQQLEKAGLVTKTR-RGRILSPKGRSLLDKLAYEMFK 140
                                   *******************************8885.5******************987 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.7   4.5e+03      48      62 ..      60      74 ..      59      80 .. 0.58
   2 !   15.3   0.1   5.2e-06     0.013      50      71 ..     110     131 ..      98     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                  HHHTTSEEEETTEEE CS
                        RuvB_C 48 LlkeglIertsrGRi 62
                                  Ll++ +I + + G +
  gi|70607213|ref|YP_256083.1| 60 LLRHLYIYKEPIGLQ 74
                                  566666666655544 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.2e-06
                                   HTTSEEEETTEEEE-HHHHHHH CS
                        RuvB_C  50 keglIertsrGRilTkkglkyl 71 
                                   k gl+++t+rGRil++kg ++l
  gi|70607213|ref|YP_256083.1| 110 KAGLVTKTRRGRILSPKGRSLL 131
                                   789***************9877 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6     4e+03       4      17 ..      61      74 ..      59      80 .. 0.79
   2 ?   13.9   0.0   1.5e-05     0.038      32      66 .]      98     131 ..      91     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                        HTH_12  4 Lkilaesdkpigak 17
                                  L++l  +++pig +
  gi|70607213|ref|YP_256083.1| 61 LRHLYIYKEPIGLQ 74
                                  88888899999966 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.5e-05
                        HTH_12  32 eravRyrLrkleergltrrvgyagreltEkGleeL 66 
                                   + ++R  L+ le+ gl+ + +++ r l  kG ++L
  gi|70607213|ref|YP_256083.1|  98 THSIRTILQQLEKAGLVTKTRRG-RILSPKGRSLL 131
                                   689*****************998.****9998876 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     5e-05      0.13      31      60 ..      93     122 ..      90     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
                       DUF2250  31 eleipleevrellkkLeelGLlervegkti 60 
                                    +++p + +r +l++Le++GL+++  +  i
  gi|70607213|ref|YP_256083.1|  93 SVKAPTHSIRTILQQLEKAGLVTKTRRGRI 122
                                   5789999****************9886544 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.3e-05      0.14      54      86 ..     101     132 ..      82     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                         Mrr_N  54 vgWartyLkkagllespkrgvwkiTekGrevlk 86 
                                   ++  +++L kagl+++++rg + +++kGr++l 
  gi|70607213|ref|YP_256083.1| 101 IRTILQQLEKAGLVTKTRRGRI-LSPKGRSLLD 132
                                   6667899**********99985.9*****9985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.7e-05       0.2      32      58 ..      94     120 ..      91     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                                   TTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  32 lgvprskvYevLrsLedkGlVerekgr 58 
                                   ++ p  ++  +L++Le++GlV++ ++ 
  gi|70607213|ref|YP_256083.1|  94 VKAPTHSIRTILQQLEKAGLVTKTRRG 120
                                   67799999**************98754 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.25      34      60 ..      93     120 ..      91     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                                   HHTS-HHHHHHHHHHHHHTTSEE.EETT CS
                          Rrf2  34 rqnispsylekilakLrkaglvk.svrG 60 
                                   +++ + + ++ il++L+kaglv+ ++rG
  gi|70607213|ref|YP_256083.1|  93 SVKAPTHSIRTILQQLEKAGLVTkTRRG 120
                                   57788999**************625666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1151.27
//
Query:       gi|70607214|ref|YP_256084.1|  [L=390]
Description: nicotinate phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-22   78.2   0.0    7.9e-22   77.8   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    9.9e-06   25.9   0.0    7.5e-05   23.1   0.0    2.2  2  NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal d
    0.00017   21.6   0.0    0.00032   20.7   0.0    1.4  1  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
  ------ inclusion threshold ------
       0.17   12.3   0.0       0.77   10.2   0.0    1.9  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   1.8e-25   7.9e-22       1     167 [.     115     301 ..     115     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.8e-25
                                   HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHHHHHH CS
                     QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveavksvr 74 
                                   i t++ar+++ a +++v +++ R  +P+++++  +A++iGG+d       +  +g + + +++++ +  +g+ v+a+k+++
  gi|70607214|ref|YP_256084.1| 115 ISTKAARIKKLALDKTVLFFGLRALHPAIAPMVDRAAYIGGCDgvsgafnQETIGAEPTGTMPHALMLSVGDNVKAWKAFD 195
                                   789**********************************************9999**************************** PP

                                   HHHTTTSE.EEEEESSHHHHHHHHHHT......-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEESS--TTTH CS
                     QRPTase_C  75 eavdkevk.ievevesleeleevleae......adiimLDnfsv..eelkkaveel.keknkr....vlievSGgvtlenv 141
                                   ea++ +v+ i +   +++e +evl+a         +++LD++s+   +++k+v+e+ +  n++    ++i+vSGg+ +++v
  gi|70607214|ref|YP_256084.1| 196 EAMPSNVPrIILADTFEDERTEVLKAAellkdkLYGVRLDTPSSrrGNFRKIVQEIrWTLNIHgyghIKIFVSGGIDEDDV 276
                                   *******99666666777777777744465555889******997799*******989999989999************** PP

                                   HHHHCTT-SEEEECHHCHTB----EE CS
                     QRPTase_C 142 eeyaksgvdvisvgalthsvkalDis 167
                                    ++++ + d ++vg+ ++  +++D+s
  gi|70607214|ref|YP_256084.1| 277 VKLRDVV-DGFGVGTSISFPQSVDFS 301
                                   ***9987.*****************8 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.22     1e+03       2      26 ..     326     347 ..     325     352 .. 0.76
   2 !   23.1   0.0   1.7e-08   7.5e-05      51      87 ..     352     388 ..     346     389 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                    NAPRTase_C   2 KkvyRlydkdgkalaDlialadeke 26 
                                   K+vyR  d+   +  D+i+l d+ +
  gi|70607214|ref|YP_256084.1| 326 KQVYRCGDS---PDGDIITLLDDYP 347
                                   999998775...8899999888754 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1.7e-08
                    NAPRTase_C  51 rvekLlkkvfkdGklvyelpsleeireyvkeqlaelr 87 
                                   ++++Ll k++++Gk++ + p+ +eireyv +ql++l+
  gi|70607214|ref|YP_256084.1| 352 NCKPLLVKYIENGKIIRDIPTAKEIREYVISQLKKLP 388
                                   689*******************************997 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   7.1e-08   0.00032      26      89 .]      52     113 ..      37     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.1e-08
                                   SSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                     QRPTase_N  26 eegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                                   ++++++Gle++ +++e   +++v + +++G+ +++ + ++ ieGn+ ++   E   L +l ++S
  gi|70607214|ref|YP_256084.1|  52 SWAIFSGLEEVLKLLEGK-EVTVYA-MPEGTVFKEVEPVMIIEGNYLDFGVFETAFLGILRHYS 113
                                   678999999998888866.666655.5***********************************98 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.12   5.5e+02      18      53 ..      32      68 ..      16      72 .. 0.75
   2 ?   10.2   0.0   0.00017      0.77      79     124 ..      63     109 ..      59     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                    NAPRTase_N 18 gp.dvevvfelffRkkpfkgeyaivagleevieylen 53
                                  g  d +v++e+     p++++ ai+ gleev++ le 
  gi|70607214|ref|YP_256084.1| 32 GIkDLKVRMEVHSYGLPEGYSWAIFSGLEEVLKLLEG 68
                                  5557777888888888889999**********99975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                    NAPRTase_N  79 Lrtfrfkpse.vaveeeevvfpgepeirveGpwieaillEtplLaiv 124
                                   L+ ++ k+ + +a++e++v+++ ep + +eG  ++  ++Et++L i+
  gi|70607214|ref|YP_256084.1|  63 LKLLEGKEVTvYAMPEGTVFKEVEPVMIIEGNYLDFGVFETAFLGIL 109
                                   66666677772455556557777********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2543.27
//
Query:       gi|70607215|ref|YP_256085.1|  [L=350]
Description: hypothetical protein Saci_1471 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-08   32.8   0.1    2.9e-07   30.3   0.0    2.3  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0006   20.2   2.7     0.0006   20.2   2.7    3.0  3  PhoU            PhoU domain
  ------ inclusion threshold ------
      0.022   14.8   1.2        1.1    9.3   0.2    2.6  2  Tsi6            Tsi6
      0.072   13.2   1.3       0.21   11.7   1.3    1.8  1  DUF1542         Domain of Unknown Function (DUF1542)
      0.075   13.7   0.5       0.24   12.1   0.1    2.0  2  Cytochrom_B562  Cytochrome b562
       0.18   12.3   4.4        6.8    7.1   4.3    3.0  1  AbiJ_NTD4       AbiJ N-terminal domain 4
       0.47   10.0   5.9        3.9    7.0   5.8    1.9  1  Exonuc_VII_L    Exonuclease VII, large subunit


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-10   2.9e-07       5      41 ..      12      49 ..       9      52 .. 0.93
   2 ?   -1.3   0.1      0.85   2.2e+03       2      11 ..     304     313 ..     303     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-10
                                  TEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCC CS
                MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevdgd.kiilrpl 41
                                  +++++++P+e+++e g++ G +v levd+d ++ ++p+
  gi|70607215|ref|YP_256085.1| 12 STLMISLPAEWVKEVGLSSGESVYLEVDEDgSLKVYPP 49
                                  789***************************99999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.85
                                   EETTEEEEEE CS
                MazE_antitoxin   2 kvGnsgavri 11 
                                   k++++++v+i
  gi|70607215|ref|YP_256085.1| 304 KNTKNYRVSI 313
                                   99******98 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.8   7.2e+03      40      56 ..      93     110 ..      87     127 .. 0.59
   2 !   20.2   2.7   2.4e-07    0.0006       1      84 [.     142     228 ..     142     233 .. 0.82
   3 ?    2.8   1.8     0.062   1.6e+02       4      57 ..     254     305 ..     251     338 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHH.HG CS
                          PhoU  40 lekeiersllealak.rq 56 
                                    ek+++++ll+++++   
  gi|70607215|ref|YP_256085.1|  93 KEKAFSEDLLRKIKEaVR 110
                                   566666666666644233 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriardlER 77 
                                   l+r+a   ++ml+++   ++e  +  ++e +e+++eidrl+++  r+ll    +r+   +    +  +l++ + +++ +E 
  gi|70607215|ref|YP_256085.1| 142 LNRLATNLKQMLHYLNLGIKEASRTFLQETVELEKEIDRLYYLALRQLLLSQTNRSLAYMigvkR-IQLIGNRILIKAIEE 221
                                   78999******************************************887776555444475632.334778889999999 PP

                                   HHHHHHH CS
                          PhoU  78 igDhavn 84 
                                    +D + +
  gi|70607215|ref|YP_256085.1| 222 AADEVSE 228
                                   9998765 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.062
                                   HHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG CS
                          PhoU   4 maeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqp 57 
                                   + e +   +d a +al+++d ++++e +e+ + + r   +i++s  ++  ++++
  gi|70607215|ref|YP_256085.1| 254 LIEQAIVLIDHATRALSKEDMKIINETMEELRTLRRV--LITESTNFETTNSKN 305
                                   56667778999*********99999997655555544..555555555544333 PP

>> Tsi6  Tsi6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00043       1.1      46      81 ..     149     185 ..     115     187 .. 0.90
   2 ?    3.7   0.1     0.024        62       4      44 ..     253     295 ..     250     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00043
                                   -SCGGGG--HHHH.HHHHHTTT-HHHHHHHHHHHHHH CS
                          Tsi6  46 dkskLhkltlGal.AskeFeetdpelaeaLsdafyia 81 
                                    k+ Lh l+lG+  As+ F ++  el++++ + +y+a
  gi|70607215|ref|YP_256085.1| 149 LKQMLHYLNLGIKeASRTFLQETVELEKEIDRLYYLA 185
                                   5788*******855*********************98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHH..HHHHSTT-HHHHHHHHHHHHHHHHHH-TT CS
                          Tsi6   4 dyvdralalvqk..rekalpgfplYasieqqLeylkdvlegee 44 
                                   d +++a+ l+ +  r  + +++++ + + ++L+ l++vl  e+
  gi|70607215|ref|YP_256085.1| 253 DLIEQAIVLIDHatRALSKEDMKIINETMEELRTLRRVLITES 295
                                   78999999987522668889999**************997765 PP

>> DUF1542  Domain of Unknown Function (DUF1542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   8.2e-05      0.21       6      49 ..     216     259 ..     215     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.2e-05
                       DUF1542   6 kaaidkaaeekkaeInnnpnaTdeEKqaainkvnaalneaiknI 49 
                                   ++ai++aa+e  +++n+   +T +E ++ +++ n++++ + ++I
  gi|70607215|ref|YP_256085.1| 216 IKAIEEAADEVSEAVNDLLSLTPQELEEVKDNWNKTYDLIEQAI 259
                                   689*******************************9998777766 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.6   9.2e+03      69      90 ..      91     112 ..      84     120 .. 0.72
   2 ?   12.1   0.1   9.5e-05      0.24      23      95 ..     217     289 ..     206     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.6
                Cytochrom_B562  69 dkaealakagkleeakaalkel 90 
                                   ++ e++  ++ l ++k+a++ l
  gi|70607215|ref|YP_256085.1|  91 ESKEKAFSEDLLRKIKEAVRSL 112
                                   5556667777777888887776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 9.5e-05
                Cytochrom_B562  23 eelkkalkelraaaedakeatpsklek.dseeqkdYqeGldklidqldkaealakagkleeakaalkelkdlrk 95 
                                   +++++a++e  +a++d  + tp++le+ +++  k+Y+  +++ i+ +d a +++ +++++ + + ++el++lr+
  gi|70607215|ref|YP_256085.1| 217 KAIEEAADEVSEAVNDLLSLTPQELEEvKDNWNKTYD-LIEQAIVLIDHATRALSKEDMKIINETMEELRTLRR 289
                                   67889999999****************7667777775.79********************************97 PP

>> AbiJ_NTD4  AbiJ N-terminal domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.3    0.0026       6.8      75     127 ..     220     283 ..      48     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                     AbiJ_NTD4  75 teawkeienyffkc.........e....wyevyDfiEfvfrnredqeaeaneslereeelNerfee 127
                                   +ea +e+ + +++          e    w++ yD+iE ++ ++++  +   ++    + +Ne +ee
  gi|70607215|ref|YP_256085.1| 220 EEAADEVSEAVNDLlsltpqeleEvkdnWNKTYDLIEQAIVLIDHATRALSKEDM--KIINETMEE 283
                                   3333443333333112223333314445*************99888887777544..888888877 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.8    0.0015       3.9     107     226 ..     109     297 ..      97     336 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                  Exonuc_VII_L 107 visavGHEtDttiaDfvAdlrapTPtaaAelvvpdkaeleeql...................................... 149
                                   v s +G E+ t  +D+v   ++  Pt+     +   ++l+ +l                                      
  gi|70607215|ref|YP_256085.1| 109 VRSLIGYEITTQTIDYVQIQSFLDPTKYTMTSL--LNRLATNLkqmlhylnlgikeasrtflqetvelekeidrlyylalr 187
                                   556677777777788888888888887655444..3344333322224444455545555555555555555555555555 PP

                  Exonuc_VII_L 150 ................................eelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleer 198
                                                                   ee+++++++a++ ll+   q+le+++ + ++  +l+e++   +d++++ 
  gi|70607215|ref|YP_256085.1| 188 qlllsqtnrslaymigvkriqlignrilikaiEEAADEVSEAVNDLLSLTPQELEEVKDNWNKTYDLIEQAIVLIDHATRA 268
                                   555555555555555555555555555555557777788888888888888888888888888888888888888888888 PP

                  Exonuc_VII_L 199 leralkkqlkkkrerleelkerl.k..ekle 226
                                   l+++  k +++  e+l++l++ l +  +  +
  gi|70607215|ref|YP_256085.1| 269 LSKEDMKIINETMEELRTLRRVLiTesT--N 297
                                   8888777888888888888866644331..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2230.16
//
Query:       gi|70607216|ref|YP_256086.1|  [L=329]
Description: hypothetical protein Saci_1472 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-32  111.2   0.0    1.2e-31  110.0   0.0    1.5  2  DUF711    Uncharacterised ACR (DUF711)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0     0.096   1.7e+03       7      23 ..       1      17 [.       1      34 [. 0.69
   2 !  110.0   0.0     7e-36   1.2e-31     235     395 ..     155     310 ..     141     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.096
                        DUF711  7 ldiRtvTlgislldcas 23
                                  ++iR+ T++ s  d+ +
  gi|70607216|ref|YP_256086.1|  1 MKIRALTIFASNIDKDK 17
                                  79999999998775443 PP

  == domain 2  score: 110.0 bits;  conditional E-value: 7e-36
                        DUF711 235 tafkitrlgelvarevakrlgvefggiDlSlaPtpavgdSvaeileel..glesfGapGtlaalalltdavkkGGvmassk 313
                                    a+k   +++++a+++a++l++++ giD+Sl+P   +++Svaei+e+    l sfG+   + ++a +++ + +  +  +++
  gi|70607216|ref|YP_256086.1| 155 NAQKALSVADEYAKKIATQLKLKYLGIDVSLSPW--KEESVAEIIEKRsgKLFSFGN---MSTVAEINKEIFEIAWKLKIT 230
                                   67888999**************************..88********98444555555...555666677776656666799 PP

                        DUF711 314 vgGlsGlflpvsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavrlnKtlavRliPv 394
                                    +G+s ++lpv ED++l+e+++eg+lt++ L  +++VC  G+Dmv + +d   + i  ++ D +al ++ +++ +vRliP 
  gi|70607216|ref|YP_256086.1| 231 PIGFSEVMLPVAEDNVLIERVNEGTLTLQGLFLLTSVCVAGIDMVVVKKDY--DLIRKILKDSMALQIVKRRPYGVRLIPS 309
                                   9**********************************************9997..58*************************7 PP

                        DUF711 395 p 395
                                   +
  gi|70607216|ref|YP_256086.1| 310 T 310
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2048.79
//
Query:       gi|70607217|ref|YP_256087.1|  [L=131]
Description: hypothetical protein Saci_1473 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   57.1   0.2    2.3e-09   37.3   0.1    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
    1.8e-09   38.0   0.0    2.1e-09   37.7   0.0    1.1  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.6e-08   0.00068       4      59 ..       3      58 ..       1      64 [. 0.86
   2 !   37.3   0.1   2.5e-13   2.3e-09      81     150 ..      58     127 ..      40     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.6e-08
                                  EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--H CS
                        DrsE_2  4 klaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkksl 59
                                  kl+i++s++ ld  + al lA +A+al +ev++F     + ++ k++kk+ +  ++
  gi|70607217|ref|YP_256087.1|  3 KLTILVSNNSLDSLYHALALALSARALSWEVKVFVVSQAVTLFLKSSKKAFSLPFF 58
                                  899*******************************9888888888887777776665 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.5e-13
                                   HHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-EEE-HHHHHHHHHC-SE CS
                        DrsE_2  81 igtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgveiagaatylkeaeeadv 150
                                   ++   +++ mk  + +++e+++++a ++gv+++  ++ + +++ + e+l+dgv++ g  ++lk+a+e++v
  gi|70607217|ref|YP_256087.1|  58 FARFFVRRQMKRLNLPEIEKMINEAIKEGVEFYVDEIGIKMLNASPEDLYDGVKLSGSISFLKDAKESEV 127
                                   556678999***********************************************************98 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.4e-13   2.1e-09       2     116 ..       3     130 ..       2     131 .] 0.90

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.4e-13
                                   EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS................---TGGGTS---GGGGGG CS
                          DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllk................gqtanpadeknlaellka 66 
                                   k++ilv++   + ++ + al lal+a+al+ ev+vf+   +v+l+lk                  + +  + +++ +++++
  gi|70607217|ref|YP_256087.1|   3 KLTILVSNN--SLDSLYHALALALSARALSWEVKVFVVSQAVTLFLKsskkafslpffarffvRRQMKRLNLPEIEKMINE 81 
                                   677788755..6667899*********************************************55567778999******* PP

                                   CGGGT-EEEEEHHHHHHTT--GGGE-T--EEEE-HHHHHHHHHH-SEEEE CS
                          DrsE  67 lkeygvklyvCgqaakargldededlgvgvevsglgelaelqnegdrvit 116
                                   ++++gv++yv +   k  + + +edl  gv++sg  ++ + ++e++ vi+
  gi|70607217|ref|YP_256087.1|  82 AIKEGVEFYVDEIGIKMLNAS-PEDLYDGVKLSGSISFLKDAKESEVVIS 130
                                   *********************.567736************9999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 878.52
//
Query:       gi|70607218|ref|YP_256088.1|  [L=73]
Description: hypothetical protein Saci_1474 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-10   39.6   0.0    4.1e-10   39.4   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.032   13.9   0.0       0.04   13.6   0.0    1.1  1  FAS_I_H   Fatty acid synthase type I helical domain
       0.15   11.5   0.8       0.17   11.3   0.8    1.0  1  CAP_N     Adenylate cyclase associated (CAP) N terminal


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   6.8e-14   4.1e-10       8      69 ..       7      68 ..       2      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 6.8e-14
                                  -STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEE CS
                          TusA  8 lvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivir 69
                                   +CP+ llk+++a +++++ +++ v +  +a ++ + ++++++g+e++  ++++++y+++ir
  gi|70607218|ref|YP_256088.1|  7 DICPVILLKVLRAFKEAKDKDEIIVKSKWQAVVQELDKWCRETGNEYLGWNKDGEKYVVRIR 68
                                  69**********************************************************98 PP

>> FAS_I_H  Fatty acid synthase type I helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.6e-06      0.04      14      56 ..      12      54 ..      10      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-06
                       FAS_I_H 14 vlaryLgvdseasereaaessaevaelqaeLdlweaEhgdeyl 56
                                  +l + L   +ea+++ +   +++++++ +eLd w  E g+eyl
  gi|70607218|ref|YP_256088.1| 12 ILLKVLRAFKEAKDKDEIIVKSKWQAVVQELDKWCRETGNEYL 54
                                  57788888899999999999**********************7 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   2.8e-05      0.17     181     228 ..      15      63 ..      14      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                                   HHHHHHTT.T-HHHHHHHHHHHHHHHHHHHHHHHHSTTS----TTSBE. CS
                         CAP_N 181 rVlkeyke.kdkkhveWvksflqilkeLqaYvkeyhttGltWnkkGkda 228
                                   +Vl+ +ke kdk+++   +++ ++++eL ++ +e+ ++ l Wnk+G++ 
  gi|70607218|ref|YP_256088.1|  15 KVLRAFKEaKDKDEIIVKSKWQAVVQELDKWCRETGNEYLGWNKDGEKY 63 
                                   6777777734666677778999************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 529.01
//
Query:       gi|70607219|ref|YP_256089.1|  [L=295]
Description: cysteine synthase B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-50  171.6   0.1      7e-50  170.1   0.1    1.6  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.1   3.9e-54     7e-50       4     289 ..      18     278 ..      15     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 3.9e-54
                                   CSSS--EEEECCTCCCCCCEEEEEEGGGST.TSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   4 gigpTPlvrlprlskelgvplflKlEslnp.tgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                   g +pTPl+rl+      g +++ KlE+ np + S+KdR+a +l++++ ++ +++++vea+sGN+g+a+Aa ++ +++k+t+
  gi|70607219|ref|YP_256089.1|  18 GMWPTPLLRLNI-----GENVWGKLEFYNPfSRSIKDRTALFLFKQALRE-KTENIVEATSGNMGIAMAALSSIFNIKFTV 92 
                                   6789***88875.....899*********99***************9999.9***************************** PP

                                   EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT...TTEEE CS
                          PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg...gkpda 160
                                   +vp ++++  + +++llG ev+  g++++e + +++++ +  +++ +++qf n+ ++ + y+t++ E+  q +    k+  
  gi|70607219|ref|YP_256089.1|  93 FVPTTSPEVFKVMIKLLGSEVITAGTSTTEILPLVKKMSQL-GSYKHLDQFHNEVNVIAhYETTAKELDLQANaagIKIRR 172
                                   *****************************************.**********99999999********855555559**** PP

                                   EEEE-SSSHHHHHHHHHHHHHSTT.-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEE CS
                          PALP 161 vvvpvGgGgliaGiaaglkerrpd.vrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdei 240
                                   +++++G++g i Gi++++ke+ +d v+++gvep++ + + +                         ++ +f  + +++d +
  gi|70607219|ref|YP_256089.1| 173 IIASMGTAGHIVGISKYFKEKYGDeVEIVGVEPSEGERIPGIK-------------------RV-TEDNNFVKI-AKIDSV 232
                                   ********************88888*********777766666...................33.344444444.356778 PP

                                   EEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEE CS
                          PALP 241 vtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvv 289
                                   + v  ++ale+++++ar+ gi+v+ ss+a +aa+  ++ g+ k+  +++
  gi|70607219|ref|YP_256089.1| 233 IDVGFKDALEGVKEVARKSGILVGLSSGATVAAY--KKLGDTKGA-TIL 278
                                   88********************************..888888877.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1804.72
//
Query:       gi|70607220|ref|YP_256090.1|  [L=51]
Description: hypothetical protein Saci_1476 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 407.97
//
Query:       gi|70607221|ref|YP_256091.1|  [L=224]
Description: hypothetical protein Saci_1477 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.004   16.5   0.1     0.0075   15.7   0.1    1.7  1  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   4.2e-07    0.0075     106     142 ..     104     141 ..      19     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.2e-07
                                   HHHHHHHHHHHTTEE-SS-SGGGEEEETTTE.EEE-SG CS
                       Pkinase 106 qilegleylHskgiiHrDlKpeNiLidekge.lKitDF 142
                                   ++ ++l+y+Hskg+   D K eN+Li  +++ + ++D 
  gi|70607221|ref|YP_256091.1| 104 ELGHSLKYIHSKGFALGDTKVENFLIPPDNKiITVIDA 141
                                   57789*********************955554888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1631.19
//
Query:       gi|70607222|ref|YP_256092.1|  [L=54]
Description: hypothetical protein Saci_1478 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.032   13.7   0.0      0.049   13.1   0.0    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.035   14.0   0.2      0.055   13.4   0.2    1.3  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.051   13.7   0.1      0.067   13.3   0.1    1.2  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.2e-06     0.049      18      37 ..      19      38 ..      18      44 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-06
                                  TCEEESSSSBEEEECCCCCC CS
                  TF_Zn_Ribbon 18 gelvCtdCGlVlednsideg 37
                                    ++C++CG+ + d+ i   
  gi|70607222|ref|YP_256092.1| 19 YFYRCPACGTRINDELITVS 38
                                  5689*****99999999765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   9.1e-06     0.055       2      14 ..      18      30 ..      18      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-06
                Zn_ribbon_SprT  2 kyvYrCtgCgrey 14
                                  +y YrC+ Cg+++
  gi|70607222|ref|YP_256092.1| 18 RYFYRCPACGTRI 30
                                  688*******765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.067       4      18 ..      19      34 ..      18      45 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                   Zn-ribbon_8  4 YeYrCeeCghefe.vl 18
                                  Y YrC +Cg++ + +l
  gi|70607222|ref|YP_256092.1| 19 YFYRCPACGTRINdEL 34
                                  88*******9987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 380.48
//
Query:       gi|70607223|ref|YP_256093.1|  [L=313]
Description: molybdenum cofactor biosynthesis protein A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-25   87.6   0.1      1e-24   86.9   0.1    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    6.5e-25   88.4   0.1    1.9e-24   87.0   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.3e-07   31.9   0.1    5.5e-07   29.9   0.0    2.0  2  Fer4_12      4Fe-4S single cluster domain
    7.5e-05   22.9   0.0    0.00016   21.8   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.1   2.2e-28     1e-24       2     126 ..     178     303 ..     177     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 2.2e-28
                                   EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE- CS
                   Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnRlRlt 81 
                                   e+++IEl+pvg g+e +   +v  ++i  r++e  +l e++  +k++++ryk  +    +++++p+++p FC++CnR+Rlt
  gi|70607223|ref|YP_256093.1| 178 EIHLIELHPVGLGKE-AFYTHVDMSDIEGRLNEDCTLVEIR--NKHKRPRYKCGNLV--VEVVKPYANPiFCSGCNRIRLT 253
                                   699********9976.588999****************995..689*******6666..9********************* PP

                                   TTSEEESSSS-SS-.EEHHHHHHTT--HHH....HHHHHHHHHHT----H CS
                   Mob_synth_C  82 adGklktCLfaeee.idlrdllregaseee....Lkelikealarkkekh 126
                                   +dGklktCL+++++ id+ d+++++ s+ee    L+e+++ a+  +++++
  gi|70607223|ref|YP_256093.1| 254 VDGKLKTCLYRDDKiIDISDIIKSSYSTEEkeelLREAYRLAILIREPNF 303
                                   ************************99555547889999999998888876 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   4.1e-28   1.9e-24       1     152 [.      14     157 ..      14     170 .. 0.95
   2 ?   -1.6   0.0      0.67     3e+03      65      85 ..     286     310 ..     264     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 4.1e-28
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                   ++ t++Cn+ C fC+       ++    ls ++i   ++++  e g+++v l+ggep+l++d+ e++ +l++      +++
  gi|70607223|ref|YP_256093.1|  14 ITLTHACNFTCFFCHMEG---ENDGDSLLSADQISLVAQIG-MEFGIRTVKLTGGEPTLRRDLPEIISKLKEV--GIKEVS 88 
                                   57899************7...89999999*****9999999.8999**************************9..9***** PP

                                   EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                   ++tng+l+ +e + +l+++g+drv+++l+++d+  +++ + + + +++v+e++e ++++g+++ + ++v+ 
  gi|70607223|ref|YP_256093.1|  89 MTTNGYLL-KELAGKLKDAGLDRVNISLHSIDPVIFKEVT-GVNVLSKVVEGIEEAKKVGLRPLKLNYVVT 157
                                   ********.*************************99****.99*******************999998875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.67
                                   HHHHHHHHTC....CCTEEEEEEEC CS
                                   xxxxxxxxxx....xxxxxxxxxxx RF
                   Radical_SAM  65 ellerlakla....vpgiritvetn 85 
                                   ell+++ +la    +p++r+++et+
  gi|70607223|ref|YP_256093.1| 286 ELLREAYRLAilirEPNFRFRYETS 310
                                   3444444444555568888888887 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.2e-10   5.5e-07      11     105 ..      16     105 ..       9     119 .. 0.80
   2 ?   -1.8   0.0      0.75   3.4e+03     110     128 ..     249     267 ..     242     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.2e-10
                       Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90 
                                   +++ Cn+ C +C+ +   + +s    +   l ++i  ++    i+ + l+GGEP l   +++l e++ ++ke +++++ + 
  gi|70607223|ref|YP_256093.1|  16 LTHACNFTCFFCHMEGENDGDSLLSADqISLVAQIGMEF---GIRTVKLTGGEPTL---RRDLPEIISKLKEVGIKEVSMT 90 
                                   4789********977766666665555455666666666...88************...9***************99**** PP

                       Fer4_12  91 ytgytleelskkeke 105
                                   ++gy l+el  k k+
  gi|70607223|ref|YP_256093.1|  91 TNGYLLKELAGKLKD 105
                                   ********9876444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.75
                       Fer4_12 110 eidvlvdGkfeesledesl 128
                                    i  +vdGk++  l ++++
  gi|70607223|ref|YP_256093.1| 249 RIRLTVDGKLKTCLYRDDK 267
                                   5667888888777666665 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.6e-08   0.00016       6      96 ..      18     100 ..      14     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.6e-08
                       Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwle 86 
                                     Cn+ C +C  + + + ++    ++  l++++      e+ i+ + ltGGeP +    ++l +++++lke +  k++ + 
  gi|70607223|ref|YP_256093.1|  18 HACNFTCFFCHMEGENDGDSLLSADQISLVAQI----GMEFGIRTVKLTGGEPTLR---RDLPEIISKLKEVG-IKEVSMT 90 
                                   67*********9997777777777788887888....77888999********955...88999999999998.899**** PP

                       Fer4_14  87 tngtleiele 96 
                                   tng l +el 
  gi|70607223|ref|YP_256093.1|  91 TNGYLLKELA 100
                                   *998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1928.12
//
Query:       gi|70607224|ref|YP_256094.1|  [L=365]
Description: Xaa-Pro dipeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-63  214.6   0.9    1.5e-63  214.3   0.9    1.1  1  Peptidase_M24  Metallopeptidase family M24
    9.6e-18   65.1   0.0    1.7e-17   64.3   0.0    1.4  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.3   0.9   1.6e-67   1.5e-63       1     209 []     149     352 ..     149     352 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.3 bits;  conditional E-value: 1.6e-67
                                   HHHHHHHHHHHHHHHHHHHHHH.TTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEE CS
                 Peptidase_M24   1 elirkaariasaaleavleaik.pgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlid 80 
                                   eli+ka++i+s a++   e+i+ + v+e++la +i+ t ++++ga+++af+ iva+ en+a++h++p+drv+k+g+  +id
  gi|70607224|ref|YP_256094.1| 149 ELIKKAGDITSSAMKISSEKIHeEYVSEKQLAGLIDMT-MRNEGAEEYAFSSIVAFAENSAFPHHIPTDRVIKNGENAVID 228
                                   689************99888873679**********77.8999************************************** PP

                                   EEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSS CS
                 Peptidase_M24  81 agaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlev 161
                                   +ga+y++y+ D+trT++    ++e +++ye+vl+aqe+ai+av+ G+++seid++ar+v+e+ag++k+f h++GHgvG+e+
  gi|70607224|ref|YP_256094.1| 229 IGARYNNYCFDSTRTFVKS-NNDEVKKVYEIVLQAQEEAIDAVRDGTRASEIDRIARNVIEKAGYGKYFVHSTGHGVGIEI 308
                                   ****************874.5678999****************************************************** PP

                                   SEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                 Peptidase_M24 162 hdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                   h+  ps+s   +++  lee mv+t+Epgiy  +g++g+riedt++vt+
  gi|70607224|ref|YP_256094.1| 309 HEY-PSIS--LSSDAILEEDMVITVEPGIY-LKGKFGIRIEDTIIVTK 352
                                   *98.**99..567*****************.89*************96 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   1.9e-21   1.7e-17       1     131 [.       2     141 ..       2     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.9e-21
                                   HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS.....-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST.. CS
                  Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfa..tetgsrglalvvtadga.lllvdalryteaaeesatveevveydd.. 76 
                                   Rl++l +++ee+++  +++   +n++YltG++  ++ + + +al + +d+  +l+v+ l+ ++a+ +     evv y++  
  gi|70607224|ref|YP_256094.1|   2 RLQKLDRILEERDVKNAIIIGGANIFYLTGYDyiSTDFANAVAL-IYNDSVpILVVPVLEKNRAQSKVGDKIEVVAYSSyq 81 
                                   9********************************88889999999.9999999****************8888888888888 PP

                                   .....HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                  Creatinase_N  77 .....pvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRv 131
                                        +  +l+d++++++e+++r+++++ +    fy +l +++++++lvd+s  +  +R+
  gi|70607224|ref|YP_256094.1|  82 vsddvIRGSLVDIISKYIEANRRIAIDMLYSGSMFYLSLSKKISSENLVDVSKDFYIIRA 141
                                   899*************************************************99988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2397.63
//
Query:       gi|70607225|ref|YP_256095.1|  [L=209]
Description: GTP cyclohydrolase I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-63  213.5   0.1      2e-63  213.0   0.1    1.2  1  GTP_cyclohydroI  GTP cyclohydrolase I
  ------ inclusion threshold ------
      0.092   12.8   0.1        0.6   10.1   0.0    2.1  2  DUF3199          Protein of unknown function (DUF3199)
       0.15   12.2   0.7       0.44   10.7   0.3    2.0  2  KIP1             KIP1-like protein


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   0.1   3.4e-67     2e-63       1     178 [.      15     199 ..       7     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 3.4e-67
                                   HHHHHHHHHHHTT--TTSTTTTTHHHHHHHHHHHHTGGGGS-G..GGGG...SSEEETT--S-EEEEEEEEEEEETTT--E CS
               GTP_cyclohydroI   1 ieeavreiLealgedpereglketpkRvakayeelfkgleedp.kekvl...kkvfeeekdemvlvkdiefsSlCeHHllp 77 
                                   i+++v+eiL+ +ged+ereglketp+Rvaka+ e+++ l++ +   kv+   ++  ++ +d++vlvkdi+fsSlCeHHllp
  gi|70607225|ref|YP_256095.1|  15 IAKRVKEILQLIGEDTEREGLKETPERVAKALLEMTSALRSPQpYIKVFslaENENSSVEDQIVLVKDISFSSLCEHHLLP 95 
                                   5789**********************************9987756677733333333569********************* PP

                                   EEEEEEEEEE-..TTEEE-HHHHHHHHHHHHSSEE-HHHHHHHHHHHHHHH.H--SEEEEEEEEEEHHHHSSTT--TT-EE CS
               GTP_cyclohydroI  78 figkahvaYiP..kkkviGlSklaRivdvvarrlqvQErlteqiadaleev.lkpkgvavvieaehlCmtmrgvkkkeskt 155
                                   +igk+hvaY+   ++kv+GlSk++R+v+++a+r+q+QErl+eqia+a++++ ++pkgv+v+ +a h+C  +rgvk++e+++
  gi|70607225|ref|YP_256095.1|  96 IIGKVHVAYVVgkSGKVAGLSKIIRLVNYYASRPQIQERLVEQIAEAIMKSdIQPKGVMVIGDALHMCTYVRGVKDREASL 176
                                   **********75579*********************************9988***************************** PP

                                   EEEEEEEHHHH-HHHHHHHHHHH CS
               GTP_cyclohydroI 156 vtsalrGefkedaalreefleli 178
                                   ++ ++rG f ++++l++++++li
  gi|70607225|ref|YP_256095.1| 177 ISLSTRGIFSTKPSLKSQVFRLI 199
                                   ********************998 PP

>> DUF3199  Protein of unknown function (DUF3199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001       0.6      20      64 ..       7      51 ..       3      56 .. 0.93
   2 ?   -0.4   0.0      0.18   1.1e+03       9      33 ..     124     148 ..     119     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                                  -HHHHHHHHHHHHHHHHHHHT-----CCG----HHHHHHHHHHHH CS
                       DUF3199 20 pdelLkqDiieaeaeiiqivghkfsdeeYdplPekvklallklaq 64
                                   +e+L  +i++  +ei q +g++ + e  ++ Pe+v  all+++ 
  gi|70607225|ref|YP_256095.1|  7 NQERLVEEIAKRVKEILQLIGEDTEREGLKETPERVAKALLEMTS 51
                                  5899*************************************9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.18
                                   HH---HHHHHS-HHHHHHHHHHHHH CS
                       DUF3199   9 sYsvfekvkeRpdelLkqDiieaea 33 
                                    Y++  +++eR  e+++  i++++ 
  gi|70607225|ref|YP_256095.1| 124 YYASRPQIQERLVEQIAEAIMKSDI 148
                                   5677777777777777777776665 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   7.4e-05      0.44      20      43 ..      12      35 ..       2      52 .. 0.79
   2 ?   -2.0   0.0       0.7   4.2e+03      45      57 ..     121     133 ..     114     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.4e-05
                          KIP1 20 lseldekvkemlklieedadsfak 43
                                  ++e+ ++vke+l+li ed + +  
  gi|70607225|ref|YP_256095.1| 12 VEEIAKRVKEILQLIGEDTEREGL 35
                                  689************999887654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.7
                          KIP1  45 aemyykkrpeLie 57 
                                     +yy  rp++ e
  gi|70607225|ref|YP_256095.1| 121 LVNYYASRPQIQE 133
                                   5578888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1492.73
//
Query:       gi|70607226|ref|YP_256096.1|  [L=300]
Description: MarR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-10   38.7   0.1    1.8e-08   34.1   0.2    2.8  3  MarR            MarR family
    3.3e-08   32.9   1.6      9e-08   31.6   0.7    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
      1e-06   28.5   0.0    2.3e-06   27.4   0.0    1.5  1  MarR_2          MarR family
    8.5e-06   25.5   0.5    1.5e-05   24.8   0.5    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    4.7e-05   23.3   0.2    0.00013   21.9   0.2    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    5.5e-05   23.0   0.2     0.0012   18.7   0.2    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0009   19.4   0.2      0.024   14.8   0.2    2.3  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0025   17.8   0.1     0.0049   16.8   0.1    1.5  1  Cdc6_C          CDC6, C terminal winged helix domain
     0.0032   17.2   0.0     0.0055   16.5   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.004   17.0   0.6     0.0094   15.8   0.6    1.6  1  TFIIE_alpha     TFIIE alpha subunit
     0.0073   16.2   0.5      0.027   14.4   0.1    2.1  2  HTH_36          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.035   14.2   0.1    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.021   14.8   0.7      0.054   13.5   0.5    1.8  1  HTH_46          Winged helix-turn-helix DNA binding
      0.061   13.8   0.1       0.13   12.8   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
      0.063   13.4   0.0        0.1   12.7   0.0    1.3  1  DprA_WH         DprA winged helix domain
      0.074   13.1   0.0       0.17   12.0   0.0    1.5  1  HTH_54          ParA helix turn helix domain
      0.079   13.5   0.0       0.24   12.0   0.0    1.8  1  Phage_rep_O     Bacteriophage replication protein O
       0.16   12.4   0.1       0.86   10.0   0.2    2.0  2  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.2   1.8e-11   1.8e-08       7      51 ..       7      51 ..       1      52 [. 0.94
   2 ?   -0.6   0.0       1.3   1.3e+03      34      47 ..      80      93 ..      77      96 .. 0.87
   3 ?   -0.0   0.0      0.85   8.5e+02       1      20 [.     208     227 ..     208     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.8e-11
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                  +i+ il++ g+ls+s+L k +++sks v+++l +Lek+G ieR++
  gi|70607226|ref|YP_256096.1|  7 KIINILKNYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  68899**************************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                  HHHHHHHHHHTTSE CS
                          MarR 34 vtrvldrLekkGli 47
                                  v  +++ L +kG+i
  gi|70607226|ref|YP_256096.1| 80 VVPFVRSLKDKGFI 93
                                  667899*******9 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.85
                                   --HHHHHHHHHHHHSTTEEH CS
                          MarR   1 ltltqfviLrilyeqgplsv 20 
                                   lt++ ++iL+  +e++++++
  gi|70607226|ref|YP_256096.1| 208 LTRNGYKILHRFDEHNCCTL 227
                                   79999*********999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.7   9.1e-11     9e-08       2      48 .]       2      48 ..       1      48 [. 0.95
   2 ?   -1.7   0.0       2.3   2.3e+03      38      47 ..      84      93 ..      84      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 9.1e-11
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  ++ + kI+++L+  + +sq++L + + +S+s v++ l +Le++G+I+
  gi|70607226|ref|YP_256096.1|  2 SDSKNKIINILKNYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIE 48
                                  56778*****************************************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                        HTH_24 38 lkrLeeeGlI 47
                                  ++ L+++G+I
  gi|70607226|ref|YP_256096.1| 84 VRSLKDKGFI 93
                                  689******9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.3e-09   2.3e-06      12      55 ..      10      51 ..       2      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.3e-09
                                  HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  + L + ++  l++++l++  ++sks+vs il +L++ G +err+
  gi|70607226|ref|YP_256096.1| 10 NILKNYGE--LSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  55777787..********************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.5   1.5e-08   1.5e-05       3      46 ..       4      48 ..       2      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.5e-08
                                  HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   + kI+++L + gel+ ++l++  ++s+s vS+ L+ L++ G++e
  gi|70607226|ref|YP_256096.1|  4 SKNKIINILKNyGELSQSDLVKLSQMSKSRVSEILSELEKDGIIE 48
                                  5789***************************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   1.3e-07   0.00013      22      58 ..      18      53 ..       6      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                  HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEE CS
                     HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisrgrrir 58
                                  l+q +l  +  ++ + vs ilseL+++g+i+r+r ++
  gi|70607226|ref|YP_256096.1| 18 LSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR-LI 53
                                  89*****************************987.66 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   1.2e-06    0.0012      19      56 ..      14      51 ..       9      57 .. 0.92
   2 ?    1.6   0.0      0.26   2.6e+02      42      55 ..      83      96 ..      75     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                  ++g+++ +++ + +  ++s+v e+L++Le+ G++er++
  gi|70607226|ref|YP_256096.1| 14 NYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  799********************************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                                  HHHHHHHCTSEEEE CS
                          TrmB 42 vLrsLedkGlVere 55
                                   +rsL+dkG++  +
  gi|70607226|ref|YP_256096.1| 83 FVRSLKDKGFIVDV 96
                                  589*******9765 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   2.4e-05     0.024      20      54 ..      19      53 ..      13      73 .. 0.84
   2 ?    1.9   0.0      0.25   2.5e+02      37      57 ..      82     100 ..      79     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                B-block_TFIIIC 20 tqsdLakeskqdprslfyrlksLekkgLIvkqsii 54
                                   qsdL+k+s ++++ +  +l  Lek g I+++ +i
  gi|70607226|ref|YP_256096.1| 19 SQSDLVKLSQMSKSRVSEILSELEKDGIIERRRLI 53
                                  59*****************************9985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.25
                B-block_TFIIIC  37 yrlksLekkgLIvkqsiidsa 57 
                                    +++sL++kg+Iv ++i  ++
  gi|70607226|ref|YP_256096.1|  82 PFVRSLKDKGFIVDVKI--YN 100
                                   5789**********999..43 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     5e-06    0.0049      21      59 ..      11      51 ..       5      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5e-06
                                  HHHHHHHHHHHT..T-----HHHHHHHHHHHHHTTSEEEEE CS
                        Cdc6_C 21 vyevYkslCese..gvdpltqrevsdllseLemlgilelek 59
                                  + + Y +l +s    +++++ ++vs++lseLe+ gi+e+++
  gi|70607226|ref|YP_256096.1| 11 ILKNYGELSQSDlvKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  67788888888844568*********************986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.5e-06    0.0055       9      51 ..       9      50 ..       7      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                                  HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                      HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                  +++l   ++ l+ s+l + + ++kS v+ +L+ L++ G++e+ 
  gi|70607226|ref|YP_256096.1|  9 INILKNYGE-LSQSDLVKLSQMSKSRVSEILSELEKDGIIERR 50
                                  555666665.9****************************9985 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   9.4e-06    0.0094      14      61 ..       4      51 ..       1      59 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.4e-06
                                  HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                   TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykr 61
                                  +  +++++L   ge++  dl k+ ++ +  + ++L +L ++++++ +r
  gi|70607226|ref|YP_256096.1|  4 SKNKIINILKNYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  6779****************************************9887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.8   1.8e+03      36      48 ..       2      14 ..       1      18 [. 0.84
   2 !   14.4   0.1   2.8e-05     0.027      27      55 .]      19      47 ..      13      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.8
                        HTH_36 36 glsknTvsraike 48
                                    skn++++++k+
  gi|70607226|ref|YP_256096.1|  2 SDSKNKIINILKN 14
                                  5699999999986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-05
                        HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                  sq++l k++ +sk+ vs ++ eLe+ G+i
  gi|70607226|ref|YP_256096.1| 19 SQSDLVKLSQMSKSRVSEILSELEKDGII 47
                                  9************************9997 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.5e-05     0.035      17      51 ..       7      41 ..       5      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHH CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvL 51
                                  k++  L ++g l+ ++lvk++++s++ V  +L+ L
  gi|70607226|ref|YP_256096.1|  7 KIINILKNYGELSQSDLVKLSQMSKSRVSEILSEL 41
                                  89****************************99877 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.4e-05     0.054      34      57 ..      28      51 ..      23      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                        HTH_46 34 nLSrSsimkvLseLkkggyIeier 57
                                  ++S+S++ ++LseL k+g Ie +r
  gi|70607226|ref|YP_256096.1| 28 QMSKSRVSEILSELEKDGIIERRR 51
                                  79******************9776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013      0.13       9      51 ..       9      50 ..       5      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                        HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                  ++ ++ ++++ +++dl++  ++++s +s++l++L++ G +er 
  gi|70607226|ref|YP_256096.1|  9 INILK-NYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIERR 50
                                  55666.999*****************************99775 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001       0.1      30      58 ..      22      50 ..       2      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                       DprA_WH 30 qLvrrtglpaaevsaaLleLELaGlverl 58
                                  +Lv+ ++++ ++vs +L+eLE +G +er+
  gi|70607226|ref|YP_256096.1| 22 DLVKLSQMSKSRVSEILSELEKDGIIERR 50
                                  89***********************9995 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.17      19      61 ..       9      51 ..       2      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                        HTH_54 19 lkedeyyqtyskaalaklpklsrrkvdkavsemeaeGyefekk 61
                                  +++ + y + s++ l kl+++s+  v + +se+e++G+  +++
  gi|70607226|ref|YP_256096.1|  9 INILKNYGELSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  566778999****************************976666 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.24      49      89 ..      17      56 ..      12      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                   Phage_rep_O 49 wisnsqlveltgisrtkvskalkeLirekviikegrkvgvn 89
                                   +s+s+lv+l ++s+++vs+ l eL + ++i ++ r +g n
  gi|70607226|ref|YP_256096.1| 17 ELSQSDLVKLSQMSKSRVSEILSELEKDGIIERR-RLIGKN 56
                                  6899*************************99765.455555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00087      0.86      25      59 ..      17      51 ..       7      65 .. 0.83
   2 ?   -0.9   0.0       2.2   2.2e+03      40      72 ..      78     110 ..      73     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00087
                                  -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   +s +++ +  ++s+s ++ il++L+k g+++ +r
  gi|70607226|ref|YP_256096.1| 17 ELSQSDLVKLSQMSKSRVSEILSELEKDGIIERRR 51
                                  47888999999********************9887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHTTSEEEETTT-TCEEESSHCC CS
                          Rrf2  40 sylekilakLrkaglvksvrGkgGGyrLakppe 72 
                                   +++   ++ L+ +g++  v+  + G+ L+++++
  gi|70607226|ref|YP_256096.1|  78 PFVVPFVRSLKDKGFIVDVKIYNNGLDLTRDLA 110
                                   567778899******999988888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1948.53
//
Query:       gi|70607227|ref|YP_256097.1|  [L=473]
Description: glutamine synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.1e-135  449.7   0.0   7.7e-135  449.3   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    3.9e-25   87.4   0.0    8.8e-25   86.3   0.0    1.6  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.3   0.0  8.6e-139  7.7e-135       1     345 []     107     470 ..     107     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 449.3 bits;  conditional E-value: 8.6e-139
                                   TT-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCE...SSEEEEEEE.T.......B...B.TSS-TTBHCCCCCT CS
                    Gln-synt_C   1 erdPRsvlkralarlaeeGltvvvgpElEFflfdkeedke...asksllevdse.......ekgrpaekggyfsvapvdea 71 
                                   erdPR ++++a+++ +e+G+  ++gpElEFf+fdk+e ++   +s++ ++++s+        ++  + k+gy++ +pvd+ 
  gi|70607227|ref|YP_256097.1| 107 ERDPRGIAEEAEKYQSEQGYVSYFGPELEFFVFDKVEVDAslpQSGTGYKIHSReapwsknGGYVIRYKEGYYPASPVDQL 187
                                   58***********************************999898899999999999****99999***************** PP

                                   CCHHHHHHHHH.HHTT--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BE CS
                    Gln-synt_C  72 edlrreiveal.ealgieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgm 150
                                   +d+r ei+++l + +g+++ea+hhEvat+ Q Ei+++f+++ ++aD+v+++K+v+k++A+k+g+ atFmpKp++gdnGsgm
  gi|70607227|ref|YP_256097.1| 188 MDIRLEIISTLvDYFGFTIEAAHHEVATAgQGEIDFRFSTLADTADKVQVLKYVTKNIASKRGMIATFMPKPFFGDNGSGM 268
                                   ********9986889*************99*************************************************** PP

                                   EEEEEEEECTTEESSB-TTSGGG.B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE CS
                    Gln-synt_C 151 HvhlSlwdkdgknlfadeddeya.lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRip 230
                                   H+h+Slw+kdgknl++d++deya ls+++r++igGll+h +al+a++apt+nSY+RlvpgyeaPv+l+w+++NRsa++Rip
  gi|70607227|ref|YP_256097.1| 269 HTHFSLWTKDGKNLMYDPNDEYAeLSQIGRYIIGGLLEHGRALSAIVAPTTNSYRRLVPGYEAPVYLVWSKSNRSAAIRIP 349
                                   ********************************************************************************* PP

                                   -...TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHC CS
                    Gln-synt_C 231 a...skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealee 306
                                   a   + ekakr+E+R pd+s+NPYL+++a+l+AgldGi++kl+pg+pv++++y++s+e++  ++i+elP sl+eAl++le+
  gi|70607227|ref|YP_256097.1| 350 AyykGMEKAKRLEYRPPDPSSNPYLVFSAILMAGLDGIRRKLDPGDPVDENIYHMSEEKKrsLKIRELPGSLDEALNELES 430
                                   ***99****************************************************999999****************** PP

                                   S.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 307 d.ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                   d e+lk v+++++++ayl+lk++E + ++ +++++e+ +y
  gi|70607227|ref|YP_256097.1| 431 DnEFLKPVFNSSILQAYLDLKKEEAKMMQLYPHPMEIYQY 470
                                   ************************************9887 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   9.8e-29   8.8e-25       1      82 [.      19      99 ..      19     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 9.8e-29
                                  T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E.EEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE- CS
                    Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegv.sFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicdvyd 82
                                  ++k+vdlqFtD+ gkl+h+tip++e++e+ ++ g+ ++DGSsi+gf++i eSDm+L P ++t++++P+++   +arv+ +v++
  gi|70607227|ref|YP_256097.1| 19 NIKWVDLQFTDLLGKLQHITIPSNEFDESSFKVGFgKLDGSSIKGFTSIYESDMVLLPIPQTMTLIPWMQ-G-VARVLTKVFW 99
                                  69*******************************************************************6.4.8******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 3170.00
//
Query:       gi|70607228|ref|YP_256098.1|  [L=204]
Description: ABC transporter ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-21   76.8   0.0      3e-21   76.4   0.0    1.2  1  ABC_tran    ABC transporter
    5.3e-09   36.3   2.2    5.6e-05   23.1   0.2    2.3  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    5.8e-05   23.4   0.1    0.00014   22.2   0.1    1.6  1  AAA_22      AAA domain
    0.00011   22.0   0.1    0.00013   21.7   0.1    1.4  1  AAA_24      AAA domain
    0.00028   20.7   9.8     0.0014   18.4   9.8    2.0  1  AAA_15      AAA ATPase domain
    0.00065   20.2   9.1      0.012   16.1   9.0    2.5  1  AAA_23      AAA domain
    0.00074   18.9   0.0     0.0015   17.8   0.0    1.5  1  Zeta_toxin  Zeta toxin
    0.00075   18.8   1.6      0.001   18.3   0.1    1.8  2  NB-ARC      NB-ARC domain
    0.00099   17.9   0.2     0.0015   17.3   0.1    1.3  1  AAA_13      AAA domain
     0.0026   17.7   3.2      0.012   15.5   3.2    2.0  1  ATPase_2    ATPase domain predominantly from Archaea
      0.003   17.5   0.1     0.0052   16.7   0.1    1.4  1  NACHT       NACHT domain
     0.0041   17.7   0.7       0.01   16.4   0.7    1.8  1  AAA_18      AAA domain
     0.0051   16.5   0.1     0.0095   15.7   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
     0.0065   15.7   0.0     0.0085   15.4   0.0    1.3  1  DUF2075     Uncharacterized conserved protein (DUF2075)
     0.0073   15.5   0.3      0.013   14.6   0.1    1.5  2  PIF1        PIF1-like helicase
     0.0077   16.6   0.0     0.0099   16.3   0.0    1.5  1  AAA_16      AAA ATPase domain
     0.0081   16.6   0.2      0.025   15.0   0.2    2.0  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.035   14.3   0.0    1.8  1  AAA_33      AAA domain
      0.019   15.0   4.8        3.5    7.7   4.8    2.3  1  AAA_14      AAA domain
      0.021   13.9   0.0      0.036   13.1   0.0    1.4  1  T2SSE       Type II/IV secretion system protein
      0.027   14.5   0.1      0.061   13.3   0.0    1.5  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
      0.034   13.9   0.0      0.079   12.7   0.0    1.5  2  AAA_30      AAA domain
      0.042   13.8   0.2      0.073   13.0   0.1    1.6  1  Rad17       Rad17 P-loop domain
      0.043   13.3   0.2      0.086   12.3   0.2    1.5  1  SMC_N       RecF/RecN/SMC N terminal domain
       0.06   13.6   0.0        3.2    8.0   0.0    2.5  2  SbcCD_C     Putative exonuclease SbcCD, C subunit
      0.068   12.9   0.0       0.13   12.0   0.0    1.6  1  PduV-EutP   Ethanolamine utilisation - propanediol utilisatio
       0.12   12.0   0.0       0.16   11.6   0.0    1.1  1  Stk19       Serine-threonine protein kinase 19
       0.16   11.9   0.4       0.49   10.3   0.0    2.0  3  MobB        Molybdopterin guanine dinucleotide synthesis prot


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   4.7e-24     3e-21      10     136 ..      24     152 ..      17     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 4.7e-24
                                   TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..........H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........x RF
                      ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..........e 80 
                                    ++++ i G+nG+GK+tLlk+lagl++ +eG i++dg+++++  l+ +++ +  ++ + +  p+l+v ++          +
  gi|70607228|ref|YP_256098.1|  24 DSKIIFIHGKNGSGKTTLLKILAGLVDFDEGYIKIDGTEVSK--LPPWKRDLVLVTPD-SYIPNLSVMKHlyyglrksrnK 101
                                   467889************************************..99999999999999.8888888888899999955422 PP

                                   HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    ++ +++ ++ +++++ +++++    + LS G++++v+l+ all+ pk +l+DE++
  gi|70607228|ref|YP_256098.1| 102 NEKILDESMELIKDVD-ENKKL----RDLSLGMREKVSLVTALLSSPKYILIDEAF 152
                                   2222555556666555.55566....9***************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   8.8e-08   5.6e-05       3      28 ..      29      55 ..      27      83 .. 0.71
   2 !   13.1   0.1   9.9e-05     0.063     220     265 ..     108     150 ..      80     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.8e-08
                        AAA_21  3 vliGpNgsGKSnLLdaldllarl.drd 28
                                  ++ G+NgsGK++LL++l +l ++  ++
  gi|70607228|ref|YP_256098.1| 29 FIHGKNGSGKTTLLKILAGLVDFdEGY 55
                                  677***************996554222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.9e-05
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDE 265
                                    ++ l ++ + +  +r+lS G+++   l+tall+ +k    +liDE
  gi|70607228|ref|YP_256098.1| 108 ESMELIKDVDENKKLRDLSLGMREKVSLVTALLSSPK---YILIDE 150
                                   34445555556666899*****************995...5****9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.2e-07   0.00014       4     128 ..      24     179 ..      21     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-07
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsstsskdllrellralglelka... 70 
                                   + +i++++G  G+GKTtll+ l+   d ++   +            ++++v+vt+ s     +++++l   l  ++++   
  gi|70607228|ref|YP_256098.1|  24 DSKIIFIHGKNGSGKTTLLKILAGLVDFDEGYIKidgtevsklppWKRDLVLVTPDSYIPNLSVMKHLYYGLRKSRNKnek 104
                                   6789****************9988775443333367799999999777777888888888888888888888877777777 PP

                        AAA_22  71 .............erlsseellealeqalrarav....ielliiDEaqh.lr.seealeeLrsllnlsrkgvqliLv 128
                                                e++++++l   +++ ++   +    ++ ++iDEa   ++ ++  +++  sl++  ++++++i+v
  gi|70607228|ref|YP_256098.1| 105 ildesmelikdvdENKKLRDLSLGMREKVSLVTAllssPKYILIDEAFSnINnKDLFIQNYISLSK--KHDIRIIFV 179
                                   8888888888887555555555333333333333467999******98878765666677779999..999999998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.1e-07   0.00013       3      51 ..      26      71 ..      24     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.1e-07
                        AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswed 51
                                  + i+i G++g+GKTtl+k l   + ++d+++G+ ++d++++ +++ w+ 
  gi|70607228|ref|YP_256098.1| 26 KIIFIHGKNGSGKTTLLKIL---AGLVDFDEGYIKIDGTEVSKLPPWKR 71
                                  5699****************...999****************9998875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   9.8   2.3e-06    0.0014      16     116 ..      18     184 ..      11     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                        AAA_15  16 dveidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......................................... 54 
                                   ++ei+ ++++ ++ GkN+sGK+++l++l  + + +e +                                           
  gi|70607228|ref|YP_256098.1|  18 NAEINEDSKIIFIHGKNGSGKTTLLKILAGLVDFDEGYIkidgtevsklppwkrdlvlvtpdsyipnlsvmkhlyyglrks 98 
                                   56788777799999*******************88555588999************************************* PP

                        AAA_15  55 ...................................................kkvikiekedleifeniseskdikIdvefa 84 
                                                                                      + + +i+++dl i+++is sk+ +I++ f 
  gi|70607228|ref|YP_256098.1|  99 rnknekildesmelikdvdenkklrdlslgmrekvslvtallsspkyilidEAFSNINNKDLFIQNYISLSKKHDIRIIF- 178
                                   *9985555555555555555555555555555555555555555555555544555555555555555555555555555. PP

                        AAA_15  85 ekekakeyektlkskekkkadlllkkkesdlk 116
                                                              ++dl+
  gi|70607228|ref|YP_256098.1| 179 --------------------------VSQDLD 184
                                   ..........................222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   9.0   1.9e-05     0.012      12      39 ..      18      45 ..      10     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                        AAA_23 12 dqeidFskgltlItGpNGaGKTTildAi 39
                                  + ei+ ++++  I+G+NG+GKTT+l  +
  gi|70607228|ref|YP_256098.1| 18 NAEINEDSKIIFIHGKNGSGKTTLLKIL 45
                                  67788899****************9866 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0015      15      60 ..      24      69 ..      16      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                    Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                    k+i++ G  G+GK++l++ l+  ++ +++++++d++++ +l P 
  gi|70607228|ref|YP_256098.1| 24 DSKIIFIHGKNGSGKTTLLKILAGLVDFDEGYIKIDGTEVSKLPPW 69
                                  5689*********************************999888775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.6e-06     0.001       6      38 ..      10      43 ..       5      60 .. 0.82
   2 ?   -0.9   0.3       1.2   7.7e+02      91     115 ..     126     154 ..      96     201 .. 0.50

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                                  HHHHHHHHC.TTTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC  6 ekviekLle.kdelqslvvalvGmgGvGKttlak 38
                                  +k+ + Ll+ + + +s +++++G+ G+GKttl+k
  gi|70607228|ref|YP_256098.1| 10 KKLGNFLLNaEINEDSKIIFIHGKNGSGKTTLLK 43
                                  56667777655566778***************86 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                                   S....HHHHHHHHCCCT.TEEEEEEEE-SH CS
                        NB-ARC  91 s....lkrklvrlLltk.rfllvlDDVwee 115
                                   s     k  lv +Ll+  +++l +D  + +
  gi|70607228|ref|YP_256098.1| 126 SlgmrEKVSLVTALLSSpKYIL-IDEAFSN 154
                                   1344455666666666644443.4444433 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.4e-06    0.0015      10      39 ..      19      48 ..      11      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.4e-06
                        AAA_13 10 aeledfkriNliYGwNGaGKTtLSrllrsl 39
                                  ae+++ ++i +i G+NG+GKTtL ++l+ l
  gi|70607228|ref|YP_256098.1| 19 AEINEDSKIIFIHGKNGSGKTTLLKILAGL 48
                                  6677778999*****************987 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.2   1.9e-05     0.012      17      60 ..      22      64 ..      14     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                      ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialree 60
                                  +e ++i+fi G  gsGKt+Llk ++    d d+  i ++  + +
  gi|70607228|ref|YP_256098.1| 22 NEDSKIIFIHGKNGSGKTTLLKILAGLV-DFDEGYIKIDGTEVS 64
                                  56789****************9766555.555555555555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   8.2e-06    0.0052       2      21 ..      27      46 ..      26      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-06
                                  CEEEEC-TTTCHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                  +++++G++GsGKTtLl+ la
  gi|70607228|ref|YP_256098.1| 27 IIFIHGKNGSGKTTLLKILA 46
                                  689*************9876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7   1.6e-05      0.01       1      45 [.      28      94 ..      28     187 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgf........gvnlrdvakenglllevdpe..............a 45
                                  I++ G+ G+GKttl k L+ +  f        g++++++ + ++ l  v+p+               
  gi|70607228|ref|YP_256098.1| 28 IFIHGKNGSGKTTLLKILAGLVDFdegyikidGTEVSKLPPWKRDLVLVTPDsyipnlsvmkhlyyG 94
                                  89****************8885666655555644444333333333333333333444444444443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.5e-05    0.0095      18      39 ..      20      42 ..      15      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                        AAA_29 18 eidlkg.atlltGpsGsGKSTll 39
                                  ei++++ ++++ G++GsGK+Tll
  gi|70607228|ref|YP_256098.1| 20 EINEDSkIIFIHGKNGSGKTTLL 42
                                  5666667899************8 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05    0.0085       2      78 ..      26     126 ..      25     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                       DUF2075   2 avvlVtGvaGtGKtvvllnllael....................eddeeertavylsvNhplvlvlrealakkeekkkkke 62 
                                   ++++++G+ G+GKt +l  l+  +                    ++d    t    + N + +++l+  l+k++  +k ++
  gi|70607228|ref|YP_256098.1|  26 KIIFIHGKNGSGKTTLLKILAGLVdfdegyikidgtevsklppwKRDLVLVTPDSYIPNLSVMKHLYYGLRKSR--NKNEK 104
                                   79************98655555556676666666655555555444446677888899************9999..88899 PP

                       DUF2075  63 afeklssfinnlsef......k 78 
                                    + ++ ++i++++e       +
  gi|70607228|ref|YP_256098.1| 105 ILDESMELIKDVDENkklrdlS 126
                                   9999999999999764444440 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.1e-05     0.013      11      45 ..      14      48 ..       7      57 .. 0.86
   2 ?   -2.5   0.0       3.5   2.2e+03      95     111 ..     135     151 ..      99     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                  HHH......HCTS-EEEEESTTSSCHHHHHHHHHH CS
                          PIF1 11 daiieavlnekgklfFvtGsgGtgKtflwkallkk 45
                                  +  ++a +ne +k++F++G  G+gKt l+k l   
  gi|70607228|ref|YP_256098.1| 14 NFLLNAEINEDSKIIFIHGKNGSGKTTLLKILAGL 48
                                  66789999**********************98765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.5
                                   CCHHHHHC-SEEEEECG CS
                          PIF1  95 klaellkktsliiwDEa 111
                                    ++ ll+  + i++DEa
  gi|70607228|ref|YP_256098.1| 135 LVTALLSSPKYILIDEA 151
                                   34455666666666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-05    0.0099      16      45 ..      17      46 ..       7     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                        AAA_16 16 lervrsgrpelvllsGesGvGKsslvrell 45
                                  l++    ++ +++++G  G+GK++l++ l+
  gi|70607228|ref|YP_256098.1| 17 LNAEINEDSKIIFIHGKNGSGKTTLLKILA 46
                                  5544444559****************8766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   3.9e-05     0.025       2      38 ..      29      92 ..      28     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                                  EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS..........................S CS
                           AAA  2 llyGppGtGKTllakavakelgve..fleisgsellsk..........................y 38
                                   ++G  G GKT+l k +a  ++++  +++i+g+e+  k                          y
  gi|70607228|ref|YP_256098.1| 29 FIHGKNGSGKTTLLKILAGLVDFDegYIKIDGTEVS-KlppwkrdlvlvtpdsyipnlsvmkhlY 92
                                  689****************98644448999999887.4455555555555555555555555550 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.5e-05     0.035       2      20 ..      28      46 ..      27     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                        AAA_33  2 vllvGlpGsGKstlaerll 20
                                  ++++G +GsGK+tl++ l+
  gi|70607228|ref|YP_256098.1| 28 IFIHGKNGSGKTTLLKILA 46
                                  899***********99875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.8    0.0055       3.5       2      43 ..      25      65 ..      24     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                  +ki++i G   +GKTtllk l+      +e ++ i+  + ++
  gi|70607228|ref|YP_256098.1| 25 SKIIFIHGKNGSGKTTLLKILAGLVD-FDEGYIKIDGTEVSK 65
                                  68999************988873332.345555555555444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.6e-05     0.036     121     156 ..      16      52 ..       2      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                         T2SSE 121 vlrkavre.rglilvsGgTgsGKttllyallkeinks 156
                                   +l++ ++e  ++i + G  gsGKttll +l   ++ +
  gi|70607228|ref|YP_256098.1|  16 LLNAEINEdSKIIFIHGKNGSGKTTLLKILAGLVDFD 52 
                                   445556542577889************9998887765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.061       9      41 ..      11      47 ..       5      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                                  HHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE  9 algkklakal....gdvilLeGdLGaGKTtlvrglak 41
                                  +lg+ l +a     +++i+++G+ G+GKTtl + la 
  gi|70607228|ref|YP_256098.1| 11 KLGNFLLNAEinedSKIIFIHGKNGSGKTTLLKILAG 47
                                  44444444225655678***************99875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.079      16      43 ..      23      50 ..      16      82 .. 0.84
   2 ?   -1.5   0.0       2.8   1.8e+03      84      97 ..     138     151 ..      93     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                        AAA_30 16 sgdrvavltGpAGtGKttalkalreawe 43
                                  ++ ++ +++G  G+GKtt+lk l+ +++
  gi|70607228|ref|YP_256098.1| 23 EDSKIIFIHGKNGSGKTTLLKILAGLVD 50
                                  4556999**************9987765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                        AAA_30  84 arlepgtllivDEa 97 
                                   a l++ + +++DEa
  gi|70607228|ref|YP_256098.1| 138 ALLSSPKYILIDEA 151
                                   34445577788886 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.073      36      70 ..      18      50 ..       6     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                         Rad17 36 kadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                  +a++ e    +i+ i G  G gk+t +k+L+    
  gi|70607228|ref|YP_256098.1| 18 NAEINED--SKIIFIHGKNGSGKTTLLKILAGLVD 50
                                  3443333..58*******************97654 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00013     0.086      18      42 ..      19      43 ..       8      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                  EEEETTSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 18 vilpfsksftaivGpNGSGKsnlld 42
                                  ++++ ++++ +i G+NGSGK+ ll 
  gi|70607228|ref|YP_256098.1| 19 AEINEDSKIIFIHGKNGSGKTTLLK 43
                                  5667788999***********9975 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2   1.3e+02      65      82 ..      47      64 ..      33      66 .. 0.84
   2 ?    8.0   0.0     0.005       3.2      62      79 ..     141     158 ..     125     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                       SbcCD_C 65 rlvfLDEAFsklDeesia 82
                                  +lv +DE++ k+D++ ++
  gi|70607228|ref|YP_256098.1| 47 GLVDFDEGYIKIDGTEVS 64
                                  67889********98765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.005
                       SbcCD_C  62 palrlvfLDEAFsklDee 79 
                                   ++++ +++DEAFs++ ++
  gi|70607228|ref|YP_256098.1| 141 SSPKYILIDEAFSNINNK 158
                                   57899********99765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.13       2      23 ..      26      47 ..      24      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                     PduV-EutP  2 kkilliGkvgsGKttLtqalkg 23
                                  k i++ Gk gsGKttL + l g
  gi|70607228|ref|YP_256098.1| 26 KIIFIHGKNGSGKTTLLKILAG 47
                                  455566************9987 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.16      28     139 ..      80     200 ..      69     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                         Stk19  28 s.lPplvtvahlhsllaqsptkvereleeli.......rkgklrklvingrgkdisklgevlvltedyeklikesseleee 100
                                   s +P l +++hl+  l++s+ k e+ l e +       +++klr l +  r+k+  +l  +l  + +y    ++ s+++++
  gi|70607228|ref|YP_256098.1|  80 SyIPNLSVMKHLYYGLRKSRNKNEKILDESMelikdvdENKKLRDLSLGMREKV--SLVTALLSSPKYILIDEAFSNINNK 158
                                   44899999999999998888888886554331112222689***********99..8889********98889999***** PP

                         Stk19 101 ekvlekFlellkenptalsisasslse...eeisaLvraGfL 139
                                      ++++++l k++  ++ + +++l++   +e++ +++ G L
  gi|70607228|ref|YP_256098.1| 159 DLFIQNYISLSKKHDIRIIFVSQDLDDskySECMYIMENGIL 200
                                   *****************9998998866111555666666655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00077      0.49       1      20 [.      27      46 ..      27      59 .. 0.85
   2 ?   -2.9   0.0       9.3     6e+03      72      92 ..      97     117 ..      87     119 .. 0.69
   3 ?   -3.0   0.0       9.6   6.2e+03      12      34 ..     158     180 ..     146     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00077
                          MobB  1 vlgivgksgsGKTtLlekli 20
                                  ++ i gk+gsGKTtLl+ l 
  gi|70607228|ref|YP_256098.1| 27 IIFIHGKNGSGKTTLLKILA 46
                                  68899***********9775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.3
                          MobB  72 keleeaelsleellarlsevD 92 
                                   k+++++e  l+e ++ +++vD
  gi|70607228|ref|YP_256098.1|  97 KSRNKNEKILDESMELIKDVD 117
                                   445666777788888777777 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 9.6
                          MobB  12 KTtLleklipelkarglrvgtiK 34 
                                   K  ++++ i+  k++++r+  + 
  gi|70607228|ref|YP_256098.1| 158 KDLFIQNYISLSKKHDIRIIFVS 180
                                   45567777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1249.53
//
Query:       gi|70607229|ref|YP_256099.1|  [L=141]
Description: thioredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-22   79.4   0.0    2.5e-22   78.8   0.0    1.3  1  Thioredoxin    Thioredoxin
    2.2e-06   28.1   0.6    1.6e-05   25.3   0.6    2.4  1  Thioredoxin_2  Thioredoxin-like domain
    0.00094   18.6   0.0     0.0011   18.3   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0044   17.3   0.3      0.097   13.0   0.0    2.6  3  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.031   14.3   0.0    1.7  2  Thioredoxin_3  Thioredoxin domain
      0.053   13.7   0.0        0.1   12.8   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
      0.063   13.1   0.1      0.093   12.5   0.1    1.5  1  Thioredoxin_9  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   9.8e-26   2.5e-22       3     103 .]      38     137 ..      36     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 9.8e-26
                                   EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                   Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngk 83 
                                   +++++ n +e ++k ++ v+v+++ApwCg+C   +P+++++a ++k+k ++ +++vd+n++ a+k++v +iPt ++f  gk
  gi|70607229|ref|YP_256099.1|  38 VQINDGNIDEIISK-NNVVFVDCWAPWCGPCHLYEPVFKRVALKYKGKAVFGRLNVDDNANSADKFGVLNIPTTLIFVGGK 117
                                   67889999999999.****************************************************************** PP

                                   EEEEEESS-HHHHHHHHHHH CS
                   Thioredoxin  84 evkkyegarekeklaaflkk 103
                                    v++++ga e+e l++++kk
  gi|70607229|ref|YP_256099.1| 118 LVDQVVGAVEEEILEEYVKK 137
                                   **********9999999875 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.6   6.2e-09   1.6e-05       4     108 ..      51     134 ..       4     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 6.2e-09
                 Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt. 83 
                                   ++  v+v+ ++p+C+ C++ + ++k +     +     +k ++++   +++ +++              a+k+gv   Pt 
  gi|70607229|ref|YP_256099.1|  51 KNNVVFVDCWAPWCGPCHLYEPVFKRV---ALK-----YKGKAVFGRLNVDDNANS-------------ADKFGVLNIPTt 110
                                   5667899999*********99998888...555.....888888888888888887.............69*********7 PP

                 Thioredoxin_2  84 ivfldgkeivarlpGyvpaeeleal 108
                                   ++f  gk  v++++G+v +e le++
  gi|70607229|ref|YP_256099.1| 111 LIFVGGK-LVDQVVGAVEEEILEEY 134
                                   8899999.*********99999876 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.5e-07    0.0011      12     103 ..      36     114 ..      21     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.5e-07
                     OST3_OST6  12 gviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklg 92 
                                     +++nd n++e+++     + vv+ +  +p   C +C+  ep f+ va  ++ +        +F+++++d++ +   k+g
  gi|70607229|ref|YP_256099.1|  36 PTVQINDGNIDEIIS----KNNVVFVDCWAP--WCGPCHLYEPVFKRVALKYKGK-------AVFGRLNVDDNANSADKFG 103
                                   567777777777774....345677776655..5***************999888.......6****************** PP

                     OST3_OST6  93 lnsaPhlllfp 103
                                   + ++P  l+f 
  gi|70607229|ref|YP_256099.1| 104 VLNIPTTLIFV 114
                                   *******9996 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.58   1.5e+03      53      77 ..      26      51 ..       5      55 .. 0.56
   2 !   13.0   0.0   3.8e-05     0.097       1      35 [.      52      84 ..      51     102 .. 0.80
   3 ?    2.1   0.0     0.098   2.5e+02      69      88 ..      93     112 ..      86     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.58
                                  HGGGS.-TTSEE.EE-TT-HHHHTT- CS
                 Thioredoxin_8 53 ylkkn.kkpwlsvpfddkkrnklkkk 77
                                    k++ + +   v+ +d++++++++k
  gi|70607229|ref|YP_256099.1| 26 KAKNMiQTEDPTVQINDGNIDEIISK 51
                                  22222222455566677666666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.8e-05
                                  .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTS CS
                 Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklkkkkk 35
                                  + vv++ ++a wc pc  + p  k++  k+k   k
  gi|70607229|ref|YP_256099.1| 52 NNVVFVDCWAPWCGPCHLYEPVFKRVALKYK--GK 84
                                  579*********************9999998..33 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.098
                                   T-HHHHTT-S--TT-SEEEE CS
                 Thioredoxin_8  69 kkrnklkkkynvkaiPtlvv 88 
                                   +++   ++k++v +iPt+++
  gi|70607229|ref|YP_256099.1|  93 DDNANSADKFGVLNIPTTLI 112
                                   556778999********987 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.73   1.9e+03      36      47 ..      42      54 ..      10      61 .. 0.59
   2 ?   14.3   0.0   1.2e-05     0.031       8      75 ..      62     135 ..      53     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                                  CTTHHHH.HHCT- CS
                 Thioredoxin_3 36 vtdfeei.ekygV 47
                                    +++ei +k++V
  gi|70607229|ref|YP_256099.1| 42 DGNIDEIiSKNNV 54
                                  2344555555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.2e-05
                                   SSSTTCHHHHHHHHHHCHCCTCEC..EEECCTTHHHH.HHCT-SSSSEE..ECTTCEE..EESS---CCHHHHHH CS
                 Thioredoxin_3   8 pgCakCpklekavkeaaaekgika..evekvtdfeei.ekygVmsvPal..vidgkvv..vsGkvpseeeirkll 75 
                                   p C  C+  e ++k++a + + ka     +v d+ +  +k+gV  +P++  ++ gk+v  v+G + +ee +++ +
  gi|70607229|ref|YP_256099.1|  62 PWCGPCHLYEPVFKRVALKYKGKAvfGRLNVDDNANSaDKFGVLNIPTTliFVGGKLVdqVVG-AVEEEILEEYV 135
                                   66999***************999945445567777777**********977889999755888.67777777665 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05       0.1      17      80 ..      52     112 ..      40     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                   T--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---...SSEEEE CS
                 Thioredoxin_7  17 gkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg...vPvvaf 80 
                                   +  v+v+  a wc++C+ +e +f   ++  + +++k v+ r++v+ +  +    d+ g   +P+ ++
  gi|70607229|ref|YP_256099.1|  52 NNVVFVDCWAPWCGPCHLYEPVFK--RVALK-YKGKAVFGRLNVDDNANSA---DKFGvlnIPTTLI 112
                                   55699************9999994..45666.9********9998777644...4434345666655 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.6e-05     0.093      25     105 ..      37     114 ..       4     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                                   HHHHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE CS
                 Thioredoxin_9  25 kvelseeteekiksiekklkilvltedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliil 104
                                   +v++++  +++i s++ ++ ++   ++wCg +    Pv++++a +++ +  +  l  d+n +  d++   g  +iPt +i+
  gi|70607229|ref|YP_256099.1|  37 TVQINDGNIDEIISKN-NVVFVDCWAPWCGPCHLYEPVFKRVAlKYKGKAVFGRLNVDDNANSADKF---GVLNIPTTLIF 113
                                   5555555555553332.234444568****************9778888888888899999999988...88999988776 PP

                                   - CS
                 Thioredoxin_9 105 d 105
                                    
  gi|70607229|ref|YP_256099.1| 114 V 114
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1267  (0.0706676); expected 358.6 (0.02)
Passed bias filter:                      875  (0.0488036); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 990.84
//
Query:       gi|70607230|ref|YP_256100.1|  [L=292]
Description: hypothetical protein Saci_1486 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.019   15.3   0.0      0.034   14.5   0.0    1.3  1  GHMP_kinases_C  GHMP kinases C terminal
      0.045   14.0   0.1      0.076   13.3   0.1    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
      0.045   13.7   0.1       0.36   10.8   0.1    2.2  2  SAM_LFY         Floricaula / Leafy protein SAM domain
       0.16   11.0   0.0       0.23   10.5   0.0    1.1  1  ANF_receptor    Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.7e-06     0.034       3      77 ..     199     271 ..     197     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                GHMP_kinases_C   3 ealergdlellgellnlsqrs.elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                   +a+  +d+++  +++   q++  ++ +v   ++ +++l +++++ G + a++s    Gptv++++ +k e e++++
  gi|70607230|ref|YP_256100.1| 199 PAVIDHDISSALDAIAKIQNLgFKRIEVNMQTEQVRDLMKSMYNKG-FPAGISSF--GPTVYTFVNTKREGEELVS 271
                                   566667788888888888888888999*******************.77777666..***********99999875 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.7e-05     0.076       4      66 .]      63     121 ..      60     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                   EEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.HHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   4 ikseiPvgaGLGSSAAlavalvaAllallgls.leeaklaleaerlaqggngsggDvaasvyGg 66 
                                   i+ +   + GLG  + + +++++ +++++ l+ ++ ++la        +g +sg+ v+a+ yGg
  gi|70607230|ref|YP_256100.1|  63 IEEDYEAHVGLGHTTQFLLSAAKLAAEYN-LKnVDVVDLARIVK----RGGTSGVGVYAFKYGG 121
                                   667777889******************99.22123266666666....59*************8 PP

>> SAM_LFY  Floricaula / Leafy protein SAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   8.1e-05      0.36      19      49 ..     212     241 ..     206     246 .. 0.89
   2 ?   -0.1   0.0       0.2   9.1e+02      22      39 ..     248     265 ..     245     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.1e-05
                       SAM_LFY  19 tvakiaelGftvstlvnmkeeelddmmksls 49 
                                   ++aki +lGf     vnm+ e++ d+mks+ 
  gi|70607230|ref|YP_256100.1| 212 AIAKIQNLGFK-RIEVNMQTEQVRDLMKSMY 241
                                   68********7.5679*************96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                       SAM_LFY  22 kiaelGftvstlvnmkee 39 
                                    i+ +G tv t+vn k e
  gi|70607230|ref|YP_256100.1| 248 GISSFGPTVYTFVNTKRE 265
                                   5788999*******8754 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.2e-05      0.23     131     200 ..     171     244 ..     149     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                                   HHHHHHHHHHHHHHHTT..-EEEEEEEEST..CHHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTT CS
                  ANF_receptor 131 ygesglqaleeeleerg..icvalkekipe..ssnddevvrkllkeikskarvivlfcssedarellkaarrlg 200
                                    g + l+a+++e +  +  i+v++ e +p   + +++++++++ k ++   + i + +++e +r l+k ++  g
  gi|70607230|ref|YP_256100.1| 171 FGVEELNAFKKEVKGTSevIRVTFMELVPAviDHDISSALDAIAKIQNLGFKRIEVNMQTEQVRDLMKSMYNKG 244
                                   5666789999955555556**********8887778888888887777799*****************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2143.55
//
Query:       gi|70607231|ref|YP_256101.1|  [L=349]
Description: SUN family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-36  125.3   0.0      4e-34  118.0   0.0    2.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      8e-07   29.0   0.0    1.4e-06   28.1   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    0.00018   21.4   0.6    0.00041   20.3   0.6    1.6  1  PUA              PUA domain
  ------ inclusion threshold ------
       0.11   12.5   0.1        1.8    8.6   0.1    2.4  2  FliMN_C          Type III flagellar switch regulator (C-ring)
       0.12   11.3   1.2       0.98    8.3   1.2    2.0  1  FlgI             Flagellar P-ring protein


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   0.0   1.1e-37     4e-34       2     152 ..     174     319 ..     173     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 1.1e-37
                                   HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
               Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                   +l++p+++e+i+D+ a PGgK thi +l ++k++++  d+ k++++ + + ++rLg++ +    aD r+  ++   + +D+
  gi|70607231|ref|YP_256101.1| 174 YLIDPKPGEKIIDMTAHPGGKLTHIYQL-EPKARILGFDHTKRKVQDLRQLTQRLGMH-IETYLADSRYLYEDFRISDVDK 252
                                   7899************************.9***************************9.99*********99999999*** PP

                                   EEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHH CS
               Methyltr_RsmB-F  83 iLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneeviee 152
                                   +L+D PCs++g    +p++  +++++d+++l++ qk+ ++aa +llkk+G+l+YsTC+++  Ene  +e+
  gi|70607231|ref|YP_256101.1| 253 VLIDPPCSALGL---RPKIYDKKNKEDLINLSSYQKQFINAAYKLLKKDGILIYSTCTMTEIENERIVED 319
                                   **********98...577777899*****************************************99986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0     4e-10   1.4e-06       3     126 ..     180     320 ..     178     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4e-10
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.. 81 
                                    g +++D  +  G ++  ++ +l pka++ G+D +++ ++  r+ +q+lg   +e   +d   l +++  + +D +l +  
  gi|70607231|ref|YP_256101.1| 180 PGEKIIDMTAHPGGKLTHIY-QLEPKARILGFDHTKRKVQDLRQLTQRLGMH-IETYLADSRYLYEDFRISDVDKVLIDpp 258
                                   57788999999999999999.889***************************6.9999999999665544467999999988 PP

               Methyltransf_31  82 .................evlnaladpdkileeiervlkpggilliedprllaelp.akveees 126
                                                    +++n+ + ++++++ + ++lk++gil+ +++  ++e   + + e++
  gi|70607231|ref|YP_256101.1| 259 csalglrpkiydkknkeDLINLSSYQKQFINAAYKLLKKDGILIYSTCT-MTEIEnERIVEDE 320
                                   8777777777777777677799999999999*****************9.6666664444443 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.6   1.1e-07   0.00041       2      63 ..      84     142 ..      83     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                   EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHC CS
                           PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakik 63 
                                   +v+vd+  ++ ++ ga+++ pGv +v g+      V +v+e+g ++a G     ++ + ki+
  gi|70607231|ref|YP_256101.1|  84 KVIVDKRTAESVMMGANVYRPGVKRVIGN---SRFVNVVSENGIIIAEGELVNQGNLAVKIT 142
                                   79**************************5...669999999999999998777666666665 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0005       1.8      47      70 ..     121     143 ..     115     145 .. 0.87
   2 ?    0.9   0.0      0.13   4.5e+02      19      40 ..     149     169 ..     147     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0005
                                   ETTEEEEEEEEEEETTEEEEEEEE CS
                       FliMN_C  47 vngkpiarGelgvvggrlavrite 70 
                                    ng+ ia+Gel+   g+lav+it+
  gi|70607231|ref|YP_256101.1| 121 ENGIIIAEGELV-NQGNLAVKITK 143
                                   58*********9.6799*****97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
                                   EEHHHHHHHHTTSEEE--TTGG CS
                       FliMN_C  19 ltlrellnLkvGdvipLdkpad 40 
                                    +l++l +Lk G ++ L+ +a+
  gi|70607231|ref|YP_256101.1| 149 YPLSDLDELKTGEIL-LQGKAS 169
                                   6899*********99.666655 PP

>> FlgI  Flagellar P-ring protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2   0.00027      0.98     224     276 ..     100     151 ..      69     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                          FlgI 224 evepdakarvvinertgtvVigenvrise.vavshgnltvkikeepevsqpapl 276
                                   +v     +rv+ n+r   vV ++ + i e   v++gnl vki+++   s p  l
  gi|70607231|ref|YP_256101.1| 100 NVYRPGVKRVIGNSRFVNVVSENGIIIAEgELVNQGNLAVKITKSMYSSYP--L 151
                                   55566779*****************99872589*********997776665..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2362.26
//
Query:       gi|70607232|ref|YP_256102.1|  [L=169]
Description: hypothetical protein Saci_1488 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-19   66.7  15.3    2.8e-08   33.1   2.4    4.4  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
      1e-06   28.4   9.2      4e-05   23.3   3.2    3.7  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-08   0.00011       3      35 ..      12      44 ..      10      45 .. 0.93
   2 !    4.8   0.1    0.0028        25      19      35 ..      49      65 ..      47      66 .. 0.84
   3 !   13.8   1.0     4e-06     0.036      20      36 .]      72      88 ..      71      88 .. 0.74
   4 !   33.1   2.4   3.2e-12   2.8e-08       1      35 [.      88     122 ..      88     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-08
                                  EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                  ++ ++++I+p a+i g+V+I + + I+++vvi+
  gi|70607232|ref|YP_256102.1| 12 KVSNKAYIHPTAYIIGDVEIKELASIWHYVVIR 44
                                  6789****************************8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0028
                                  TEEE-TTEEEETTEEEE CS
                       Hexapep 19 nVkIGdnvkIgagvvig 35
                                   ++IG+ + I ++++++
  gi|70607232|ref|YP_256102.1| 49 SIVIGKETNIQENTTVH 65
                                  57899999999999986 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4e-06
                                  EEE-TTEEEETTEEEES CS
                       Hexapep 20 VkIGdnvkIgagvvigg 36
                                  ++IGd+v Ig+++vi+g
  gi|70607232|ref|YP_256102.1| 72 TIIGDRVSIGHNAVIHG 88
                                  57888888888888865 PP

  == domain 4  score: 33.1 bits;  conditional E-value: 3.2e-12
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   +++I snv+Ig++a+++++ k+G+++++gag+v+ 
  gi|70607232|ref|YP_256102.1|  88 GATIASNVIIGMGAILLNGSKVGEYSIVGAGSVVP 122
                                   589******************************95 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0     0.087   7.8e+02      10      20 ..      19      31 ..      16      33 .. 0.75
   2 ?   -1.3   0.0      0.22     2e+03       2      10 ..      50      58 ..      49      64 .. 0.74
   3 !   23.3   3.2   4.4e-09     4e-05       2      32 ..      72     103 ..      71     105 .. 0.94
   4 !    5.5   0.1    0.0016        14      19      32 ..     108     121 ..     106     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.087
                                  E-TT-EE.S.EEE CS
                     Hexapep_2 10 iGanagi.G.vsl 20
                                  i++ a+i G v++
  gi|70607232|ref|YP_256102.1| 19 IHPTAYIiGdVEI 31
                                  8999996565876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                                  EEE-TT-EE CS
                     Hexapep_2  2 viIGdnCli 10
                                  + IG+ ++i
  gi|70607232|ref|YP_256102.1| 50 IVIGKETNI 58
                                  568887776 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 4.4e-09
                                   EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                     Hexapep_2   2 viIGdnCliGanagi.GvslGdncvvgaGvvi 32 
                                   +iIGd++ iG na+i G ++  n+++g+G ++
  gi|70607232|ref|YP_256102.1|  72 TIIGDRVSIGHNAVIhGATIASNVIIGMGAIL 103
                                   79***************************876 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0016
                                   EE-TT-EE-TT-EE CS
                     Hexapep_2  19 slGdncvvgaGvvi 32 
                                   ++G+ ++vgaG+v+
  gi|70607232|ref|YP_256102.1| 108 KVGEYSIVGAGSVV 121
                                   57888999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1143.11
//
Query:       gi|70607233|ref|YP_256103.1|  [L=323]
Description: hypothetical protein Saci_1489 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.1e-14   52.5   0.1    4.7e-13   49.9   0.1    2.3  1  Radical_SAM  Radical SAM superfamily
    4.9e-10   39.8   0.0    1.7e-09   38.1   0.0    1.9  1  Fer4_12      4Fe-4S single cluster domain
    1.2e-08   35.1   0.0    4.8e-08   33.2   0.0    2.1  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   7.8e-17   4.7e-13       2     116 ..      29     151 ..      28     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 7.8e-17
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                    vt  Cnl CsfC+ ++    +g   + s+e++++ ++ ++ +  + ++ + ggep+ + d+ elle ++      + + +
  gi|70607233|ref|YP_256103.1|  29 KVTSRCNLHCSFCNPSY---YNGELGESSTEKVKKMIDNMR-DSSIVVLSFEGGEPTIRQDILELLEYAHDG---SFYVML 102
                                   6899************9...7*******************7.6669999999*****************996...9***** PP

                                   EECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHH...............H CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...............x RF
                   Radical_SAM  83 etngtlpd.eeklerllelgvdrvslgleaadde...............k 116
                                   +tng++++ e +l +l+++  d ++ +++ ++                 k
  gi|70607233|ref|YP_256103.1| 103 TTNGYRLNdESFLSKLADRI-DFLHYSIDEYHWNakaidnlqrfrdyglK 151
                                   ********999999999966.88888888777654444222333333331 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   2.8e-13   1.7e-09      12     114 ..      31     125 ..      23     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.8e-13
                       Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                                   +s+Cnl+C++C n++  + + g+  t++++ ++i+++ ++si  l++ GGEP     ++++lel+++     +  +++ ++
  gi|70607233|ref|YP_256103.1|  31 TSRCNLHCSFC-NPSYYNGELGESSTEKVK-KMIDNMRDSSIVVLSFEGGEPTI---RQDILELLEYAHDGSF-YVMLTTN 105
                                   799*******6.7************99886.6779*******************...9999******999999.69***** PP

                       Fer4_12  93 gytleelskkekeellkeidvl 114
                                   gy l++ s    ++l + id+l
  gi|70607233|ref|YP_256103.1| 106 GYRLNDES--FLSKLADRIDFL 125
                                   ****9987..356666666654 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     8e-12   4.8e-08       2     109 ..      28     126 ..      27     137 .. 0.79
   2 ?   -3.1   0.0       1.4   8.5e+03      65      79 ..     200     215 ..     197     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8e-12
                       Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                   f  +s+Cnl+C +C  +  ++ elg+ +te++  ++++++ +s i    l++ GGeP +    +++l+l+++ ++    + 
  gi|70607233|ref|YP_256103.1|  28 FKVTSRCNLHCSFCNPSY-YNGELGESSTEKVK-KMIDNMRDSSI--VVLSFEGGEPTIR---QDILELLEYAHDGS--FY 99 
                                   5569**********8777.*******9999887.88867777777..779*******966...99********9999..99 PP

                       Fer4_14  83 iwletngtleielektpdlkekleals 109
                                   + l tng    +     +l ++++ l+
  gi|70607233|ref|YP_256103.1| 100 VMLTTNGYRLNDESFLSKLADRIDFLH 126
                                   ***999765435444455666666555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                       Fer4_14  65 kellklvkrlkeey.p 79 
                                   +el+k++++lk++y p
  gi|70607233|ref|YP_256103.1| 200 NELYKVLSELKRKYgP 215
                                   5789999999999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2198.51
//
Query:       gi|70607234|ref|YP_256104.1|  [L=287]
Description: integrase/recombinase XerD [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-38  130.3   2.5    1.4e-37  129.2   0.8    2.0  2  Phage_integrase  Phage integrase family
    1.1e-13   51.4   0.5    4.1e-08   33.6   0.0    2.6  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
    3.2e-08   33.8   0.9     0.0039   17.5   0.0    2.8  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    0.00045   20.2   1.3     0.0041   17.0   1.3    2.3  1  Phage_integr_3   Archaeal phage integrase
  ------ inclusion threshold ------
      0.081   12.4   0.1       0.15   11.4   0.0    1.4  1  PMSI1            Protein missing in infertile sperm 1, putati


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.16   5.6e+02      98     128 ..      45      75 ..      25      89 .. 0.84
   2 !  129.2   0.8   3.8e-41   1.4e-37       3     169 ..     122     273 ..     120     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                                   SBETTSSB--HHHHHHHHHHHHHHCT-SSC- CS
               Phage_integrase  98 faskrgkplsrqtvrkafkraveeagiekpl 128
                                   f++k+ +++++++v++++ ++ + +  +k++
  gi|70607234|ref|YP_256104.1|  45 FVKKDPRQVTNSDVNAWLLKILKSSTRSKRV 75 
                                   8888999999999999999999988777655 PP

  == domain 2  score: 129.2 bits;  conditional E-value: 3.8e-41
                                   HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHH CS
               Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkel 83 
                                   lt +e+e+l a +++   +rd+ +l ll +tG+R++Ells++v+d+dle+++i++  r++K++ +r+v ++++   llk++
  gi|70607234|ref|YP_256104.1| 122 LTYEELEKLKASAKK---LRDAVILNLLIDTGIRAKELLSIKVQDIDLERRRIII--RNTKNGESRIVFFTSHTGALLKKY 197
                                   788999999999999...*************************************..************************ PP

                                   HHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHH CS
               Phage_integrase  84 lskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttq 164
                                   ++k+  ++e+++ l+       ++ q++++ ++r++++ gi+  l+pH lRh+fat+ +++g++l vvqk+lGH++i+ tq
  gi|70607234|ref|YP_256104.1| 198 IQKN--KKEPEDKLI------NMTYQALYRKLRRLGKKIGID--LRPHILRHTFATEAIRKGIPLPVVQKILGHKDIRVTQ 268
                                   ****..444444444......3579*****************..************************************* PP

                                   HHHCC CS
               Phage_integrase 165 iYthv 169
                                   +Yth+
  gi|70607234|ref|YP_256104.1| 269 VYTHL 273
                                   ****6 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.1e-11   4.1e-08       3      56 ..      16      68 ..      15      76 .. 0.90
   2 !   15.7   0.4   4.4e-06     0.016       3      40 ..      73     121 ..      72     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
               Phage_int_SAM_4  3 erfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLane 56
                                  ++f+ +l+lag se+Ti+ Y  aik+fl+f+k k p+++t+ d++a l + +++
  gi|70607234|ref|YP_256104.1| 16 NKFILTLNLAGASENTIRLYSIAIKDFLDFVK-KDPRQVTNSDVNAWLLKILKS 68
                                  78999***************************.***************998844 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.4e-06
               Phage_int_SAM_4   3 erfrealrlaglserTiksYlsaikrflrflkkk...........apee 40 
                                   +r+re+ + ++++ +T k Yl+a+ rfl++l k+           +++ 
  gi|70607234|ref|YP_256104.1|  73 KRVREENEKRRMKLTTAKIYLTAVLRFLKWLGKDvkptvpkarknEIRA 121
                                   578999999**********************944766444444444444 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0039      13      59 ..      26      68 ..      16      77 .. 0.84
   2 !   14.1   0.1   1.2e-05     0.042      11      65 ..      81     134 ..      75     145 .. 0.85
   3 ?   -2.9   0.0       2.4   8.7e+03      37      58 ..     202     223 ..     192     228 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                  -S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS---- CS
               Phage_int_SAM_1 13 glspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleee 59
                                  g+s+nT+r Y  ++++fl+f ++    + +q+t +dv a+l + +++
  gi|70607234|ref|YP_256104.1| 26 GASENTIRLYSIAIKDFLDFVKK----DPRQVTNSDVNAWLLKILKS 68
                                  45*********************....**************998885 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                                   TT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS---------- CS
               Phage_int_SAM_1  11 erglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsats 65 
                                    r++   T   Y+ ++ rflk+l ++ k+++ +++ +++ra   e +e+ l+a+ 
  gi|70607234|ref|YP_256104.1|  81 KRRMKLTTAKIYLTAVLRFLKWLGKDVKPTVPKARKNEIRALTYEELEK-LKASA 134
                                   6899999********************************9987777774.66654 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                                   TS--TTT--HHHHHHHHHS--- CS
               Phage_int_SAM_1  37 gkesleqlttedvraflaelee 58 
                                   +ke  ++l  +  +a  ++l++
  gi|70607234|ref|YP_256104.1| 202 KKEPEDKLINMTYQALYRKLRR 223
                                   4444444444444444444443 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.3   1.1e-06    0.0041      15     155 ..     129     283 ..     116     286 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                   HHHHH-H..HHHHHHHHHHHH---HHHHHHH.HHS..GGG-...EEETTEEEEEEEE-SSS-EEEEEEESS---......- CS
                Phage_integr_3  15 elkekse..evelvykllvfsGiRLkevlkl.LreyDpekl...iveddiarYpialekgeKkafyiylptelakele..r 87 
                                   +lk +++  + +++  ll+ +GiR ke l++ +++ D e+    i + +  +  i     +  a     +++ +ke e   
  gi|70607234|ref|YP_256104.1| 129 KLKASAKklRDAVILNLLIDTGIRAKELLSIkVQDIDLERRriiIRNTKNGESRIVFFTSHTGALLKKYIQKNKKEPEdkL 209
                                   333333300446899999999999999999834557766665443344444444443333333322222222222222224 PP

                                   -B--HHHHHHHHHT-T......--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHHHHH CS
                Phage_integr_3  88 lelseeavkefeakkk......vkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAdeaYk 155
                                   ++++++a+ ++ ++ +      ++ + +R+ +at  +++g+p+ v++ i G+k  +v + +   ++   ++aYk
  gi|70607234|ref|YP_256104.1| 210 INMTYQALYRKLRRLGkkigidLRPHILRHTFATEAIRKGIPLPVVQKILGHKDIRVTQVYTHLVIEDVEKAYK 283
                                   66777777766666557899999**********************************87665445555666676 PP

>> PMSI1  Protein missing in infertile sperm 1, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.15      23     129 ..     106     211 ..      86     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                         PMSI1  23 syrsta.rtdlprktrvtledeeDavaeadrLagPaaaeLLastvatgisksklsqi.eedgsleegvvinarkndteses 101
                                     + t+ + +  +    t e+ e + a+a +L      +LL     tgi+ ++l +i  +d  le   +i  + ++ es +
  gi|70607234|ref|YP_256104.1| 106 DVKPTVpKARKNEIRALTYEELEKLKASAKKLRDAVILNLLI---DTGIRAKELLSIkVQDIDLERRRIIIRNTKNGESRI 183
                                   5555553333444445899999**********9988877775...569988888887679999999998888888999999 PP

                         PMSI1 102 estssstagssssrfaanaqeaeirlts 129
                                      +s+t +     +++n++e+e +l  
  gi|70607234|ref|YP_256104.1| 184 VFFTSHTGALLKKYIQKNKKEPEDKLIN 211
                                   9******9***************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1945.25
//
Query:       gi|70607235|ref|YP_256105.1|  [L=291]
Description: hypothetical protein Saci_1491 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-06   25.8   0.0     0.0024   17.1   0.0    3.3  3  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.098   11.9   0.0    2.1  2  Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
      0.016   15.8   0.0        8.9    6.9   0.0    2.5  2  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     4e-07    0.0024       2     111 ..       2      91 ..       1     112 [. 0.76
   2 !    3.6   0.0    0.0056        33     151     200 ..     118     164 ..     117     170 .. 0.82
   3 ?   -0.8   0.0      0.12   7.3e+02     257     294 .]     183     216 ..     177     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgk 82 
                                   + +++G+G AGl+a  +l++   + +++++ + +     + ++ l+++  ++  +  v      +i +++  +v+++d + 
  gi|70607235|ref|YP_256105.1|   2 KTIIVGSGYAGLNAYYNLNE---EPIIISQHNKF-----VFYTSLTRSLLFKPLMDTV------NIPFVTVDKVIEFDLKG 68 
                                   789***************99...67777344444.....4445556666666655555......788888878*****999 PP

                                   EEEEETEEECTCEEEEEESEEEE---EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  83 kkvklekkkegdeekiaydklvlAtGssp 111
                                   k +k +      ++++ +d+l++AtG++ 
  gi|70607235|ref|YP_256105.1|  69 KWIKTQ------NHEYNADNLIIATGCNR 91 
                                   777773......347***********854 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0056
                                   SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 151 GyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvev 200
                                   Gy  v lA +l+klgk+v+  ++++ l + l++++++ l+++++++ ++ 
  gi|70607235|ref|YP_256105.1| 118 GYLVVQLAFYLKKLGKQVY--YHGSYL-SFLGDRVAQVLANKMNEKHIQY 164
                                   788899************9..555555.5779999999999999888765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.12
                                   EEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 257 givvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   +++v+e+l+   ++ + iGD +  ++ p+l   A+++G
  gi|70607235|ref|YP_256105.1| 183 FFKVNEYLQY--QNSFIIGDLI--ENMPKLGELAMRTG 216
                                   6789999965..999******9..88888877777665 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.049   2.9e+02       1      19 [.       4      22 ..       4      33 .. 0.84
   2 ?   11.9   0.0   1.6e-05     0.098     104     134 ..      58      89 ..      48     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.049
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkka 19
                                  iI+G G aGl+a ++l++ 
  gi|70607235|ref|YP_256105.1|  4 IIVGSGYAGLNAYYNLNEE 22
                                  8*********998887765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.6e-05
                   Pyr_redox_3 104 Vesvkk.edegfevetsketyeAkkviiAtGe 134
                                   V +v + + +g  ++t++++y+A+++iiAtG 
  gi|70607235|ref|YP_256105.1|  58 VDKVIEfDLKGKWIKTQNHEYNADNLIIATGC 89 
                                   5555553567889******************6 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0022        13       2      70 ..       3      68 ..       2      76 .. 0.77
   2 ?    6.9   0.0    0.0015       8.9       8      57 ..     118     164 ..     117     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEET CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegse 70
                                   ++vG+Gy gl +   + +l+ +  ++  ++k+   +   ++++l + l +  +i +++  kv e++ ++
  gi|70607235|ref|YP_256105.1|  3 TIIVGSGYAGLNA---YYNLNEEPIIISQHNKFV-FYTSLTRSLLFKPLMDTvNIPFVTVDKVIEFDLKG 68
                                  79********965...556666778888888888.88888888888888888888888888888877655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0015
                                   SHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE CS
                     Pyr_redox   8 GyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngiev 57 
                                   Gy+ + lA +l++lgk+V+    +   l+ l++ ++++l++k+ +++i+ 
  gi|70607235|ref|YP_256105.1| 118 GYLVVQLAFYLKKLGKQVYY---HGSYLSFLGDRVAQVLANKMNEKHIQY 164
                                   7888999********99875...555555779************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2126.93
//
Query:       gi|70607236|ref|YP_256106.1|  [L=219]
Description: hypothetical protein Saci_1492 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00012   21.7   0.0       0.68    9.4   0.0    2.9  3  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   3.8e-05      0.68      95     123 ..      83     112 ..      69     125 .. 0.78
   2 ?    0.9   0.0     0.015   2.6e+02     163     213 ..     129     179 ..     119     181 .. 0.79
   3 !    8.1   0.0   9.6e-05       1.7     240     265 ..     181     206 ..     177     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 3.8e-05
                                   SSS..T.EEEESTTTSHHHHHHHHHHCSTS CS
                VitK2_biosynth  95 egel.gkrvalpgestTsvlLlrlllaery 123
                                   ++++ + ++++pg++ T + L+r+++ + +
  gi|70607236|ref|YP_256106.1|  83 KKTEsKLKILVPGSNSTEYYLARMIYGHNV 112
                                   4444589*******************9985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.015
                                   TEEEEEHHHHHHHHH.SS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHH CS
                VitK2_biosynth 163 lkkvlDLgelWeelt.glPlvlglwvvrrdlaaeaakeleealreSveyala 213
                                    +  ++  + W+  + +lP+v  l+  ++ l++e++ +++ ++r S + a++
  gi|70607236|ref|YP_256106.1| 129 GTSEYSFKDFWNSNCgNLPFVIKLL-GSKILDEESLSRIKIVIRDSANLAYE 179
                                   5667788899999995599998765.45667899999999999999999886 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 9.6e-05
                                   HHCSHHHHS-CHHHHHHHHHHHHHHH CS
                VitK2_biosynth 240 lYvnelsydlgeegragleeflelaa 265
                                    Yvn +s +lg +gr++l+ f+++++
  gi|70607236|ref|YP_256106.1| 181 GYVNSFSKELGLKGREALDCFFKICR 206
                                   6**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1675.49
//
Query:       gi|70607237|ref|YP_256107.1|  [L=675]
Description: hypothetical protein Saci_1493 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4679.94
//
Query:       gi|70607238|ref|YP_256108.1|  [L=469]
Description: type II/IV secretion system protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-42  145.3   0.0    4.6e-42  144.0   0.0    1.6  2  T2SSE            Type II/IV secretion system protein
    2.4e-05   24.9   0.0    6.3e-05   23.5   0.0    1.7  1  ABC_tran         ABC transporter
    0.00018   21.2   0.0    0.00045   19.9   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
    0.00023   21.7   0.1    0.00023   21.7   0.1    2.9  3  AAA_23           AAA domain
    0.00026   21.3   0.0     0.0006   20.1   0.0    1.6  1  AAA_22           AAA domain
    0.00037   20.9   0.0    0.00087   19.7   0.0    1.7  1  AAA_16           AAA ATPase domain
    0.00086   18.9   0.1     0.0019   17.8   0.1    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0071   16.4   0.1       0.03   14.3   0.0    2.2  2  AAA_14           AAA domain
     0.0079   15.4   1.1      0.073   12.2   0.1    2.1  2  G-alpha          G-protein alpha subunit
     0.0095   15.9   0.0     0.0095   15.9   0.0    3.0  3  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.024   14.2   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.014   15.2   0.1      0.014   15.2   0.1    2.3  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.015   15.4   0.0      0.033   14.3   0.0    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.015   15.8   0.0      0.035   14.7   0.0    1.7  1  AAA_18           AAA domain
      0.016   14.7   0.0      0.035   13.6   0.0    1.5  1  Pox_A32          Poxvirus A32 protein
      0.016   14.6   0.0      0.035   13.5   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.02   14.3   0.0      0.041   13.3   0.0    1.5  1  SRPRB            Signal recognition particle receptor beta su
      0.021   14.7   0.0      0.042   13.7   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
      0.024   13.4   0.0      0.045   12.5   0.0    1.4  1  RNA12            RNA12 protein
      0.024   14.9   0.0      0.042   14.1   0.0    1.4  1  AAA_28           AAA domain
      0.034   14.1   0.0      0.075   13.0   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.039   13.9   0.0      0.086   12.8   0.0    1.5  1  NACHT            NACHT domain
       0.04   12.7   0.0      0.071   11.9   0.0    1.3  1  Adeno_IVa2       Adenovirus IVa2 protein
      0.056   13.9   0.0       0.13   12.7   0.0    1.7  1  AAA              ATPase family associated with various cellul
      0.096   12.1   0.0       0.18   11.2   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.099   12.4   1.4       0.67    9.8   0.2    2.5  2  SpoVIF           Stage VI sporulation protein F
        0.1   12.4   0.0       0.26   11.0   0.0    1.7  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   12.2   0.0       0.22   11.2   0.0    1.4  1  AAA_30           AAA domain
       0.12   11.8   0.0       0.26   10.7   0.0    1.6  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.13   12.5   0.0       0.32   11.2   0.0    1.6  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.15   11.8   0.0       0.28   10.9   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.16   10.9   0.0       0.24   10.3   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.16   11.9   0.0       0.35   10.8   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.6   1.4e+03     238     262 ..      59      81 ..      54      91 .. 0.76
   2 !  144.0   0.0   8.4e-45   4.6e-42       7     247 ..      92     340 ..      87     360 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                         T2SSE 238 galerLeqlgaeveaaelkssilav 262
                                   ++l rL++lg  v+++++++ + ++
  gi|70607238|ref|YP_256108.1|  59 KVLLRLKELG--VNDENVEKILYSI 81 
                                   5788899999..8888888877666 PP

  == domain 2  score: 144.0 bits;  conditional E-value: 8.4e-45
                         T2SSE   7 allddekvsdihvekper.vkv.rervdg..ielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvv 83 
                                   +ll d+++ +i    +++ + v + +  +    + +++  +++ + r+i+++a+ a+++++  rp ++ +lp +g+r+ + 
  gi|70607238|ref|YP_256108.1|  92 PLLLDPDIEEIECLGYGNpITVvHRKFPEciRFYTNIKLNDEETVVRIIEKLASKANKSVNIARPYVEFSLP-EGHRVAAT 171
                                   566778888888888888855414444445334567778889999***************************.99999887 PP

                         T2SSE  84 llPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                   +   +     ++ iRk   k l++ +++ + +l+e i + l   ++ r  i++ G+TgsGKttll+all+ +n +  +i+t
  gi|70607238|ref|YP_256108.1| 172 ISKEISLpgSTFDIRKFPLKPLNILEVINSSMLNELITAYLWLLLEYRPFIIILGPTGSGKTTLLNALLNLVNPH-YKILT 251
                                   77655444499****************************************************************.***** PP

                         T2SSE 163 vEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaag 238
                                   +ED+ Ei l ++n v+  a+     + ++ ++dl + aLR rPD +++GE+R+ke  ++++A+ +GH   ++T H   +++
  gi|70607238|ref|YP_256108.1| 252 IEDTSEISLLNKNWVRFIARstllsEFEISISDLAKLALRYRPDYMIIGEVRGKEIEALVHAAASGHGS-ITTFHGSRPID 331
                                   *******************99***999****************************************77.*********** PP

                         T2SSE 239 alerLeqlg 247
                                   a++r+ +l 
  gi|70607238|ref|YP_256108.1| 332 AVTRITDLL 340
                                   ******997 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.2e-07   6.3e-05      13      47 ..     221     255 ..     214     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-07
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgk 47 
                                    + i+G++G+GK+tLl++l++l++p    ++++++
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALLNLVNPHYKILTIEDT 255
                                   578**********************7776666633 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.4e-07   0.00045      25      50 ..     222     247 ..     213     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.4e-07
                        AAA_29  25 tlltGpsGsGKSTllDAiqalLvpak 50 
                                   +++ Gp+GsGK+Tll A+  l  p+ 
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVNPHY 247
                                   689******************99986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       2.3   1.2e+03      75     134 ..      13      76 ..       8     153 .. 0.66
   2 !   21.7   0.1   4.2e-07   0.00023      19      39 ..     219     239 ..     214     243 .. 0.92
   3 ?    1.0   0.6      0.96   5.2e+02      97     157 ..     378     420 ..     336     462 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                        AAA_23  75 veltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskki......ilnl 134
                                   v++++++ +g+   + e e +  ++ +++ k++ l++++ +++++f ++ l + k+      + + 
  gi|70607238|ref|YP_256108.1|  13 VKVRLTRSKGI--CNYEIEEPSFSDFEESLKEKVLSEIYYSKSTDFEDKVLLRLKElgvndeNVEK 76 
                                   56666666665..45555666666777777777777777777777766644444433333322233 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4.2e-07
                        AAA_23  19 kgltlItGpNGaGKTTildAi 39 
                                   +++ +I Gp+G+GKTT+l+A+
  gi|70607238|ref|YP_256108.1| 219 RPFIIILGPTGSGKTTLLNAL 239
                                   5889****************8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.96
                        AAA_23  97 skkkgkttkkaklelleidele...qfisellgskkiilnlilflgqerfeefelkdkkerlee 157
                                   + k +k++ ++k ++++ ++++   q++se+++++++                     ++r++e
  gi|70607238|ref|YP_256108.1| 378 INKGSKKITFKKIFEWSYQNNNfipQNVSEIIKRSYR---------------------LKRIKE 420
                                   2222223322222222222211122333333333333.....................222211 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.1e-06    0.0006       4      35 ..     218     249 ..     216     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.1e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeaka 35 
                                   ++ ++++ G++G+GKTtll+ ll+  + ++k+
  gi|70607238|ref|YP_256108.1| 218 YRPFIIILGPTGSGKTTLLNALLNLVNPHYKI 249
                                   6789*******************998655443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-06   0.00087      25      85 ..     220     278 ..     205     363 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                        AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrql 85 
                                   + +++ G+ G+GK++l+++ll+ ++ ++ +++++ + + +   +    +++ +ar++ll + 
  gi|70607238|ref|YP_256108.1| 220 PFIIILGPTGSGKTTLLNALLNLVNPHYkILTIEDTSEIS---LLNKNWVRFIARSTLLSEF 278
                                   6899*****************9998885455566655555...2223366666555554444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.4e-06    0.0019       1      30 [.     220     250 ..     220     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                                   EEEEEEESTTCCHHHHHHHHH.CT--SS-EE CS
                          cobW   1 pvtvltGflGsGKTtLlnhll.enraglkla 30 
                                   p +++ G+ GsGKTtLln+ll   + ++k+ 
  gi|70607238|ref|YP_256108.1| 220 PFIIILGPTGSGKTTLLNALLnLVNPHYKIL 250
                                   5789*****************5445555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.5e-05      0.03       3      49 ..     220     263 ..     218     350 .. 0.67
   2 ?   -2.0   0.1       6.3   3.4e+03      55      55 ..     408     408 ..     356     458 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                   + ++i G+  +GKTtll+ l+ +l   + ++  ++++d ++ +l ++
  gi|70607238|ref|YP_256108.1| 220 PFIIILGPTGSGKTTLLNALL-NLV--NPHYKILTIEDTSEISLLNK 263
                                   689**************9999.444..35555555555555443333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.3
                        AAA_14  55 l 55 
                                   +
  gi|70607238|ref|YP_256108.1| 408 I 408
                                   1 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.19     1e+02     103     174 ..      35     107 ..      18     199 .. 0.76
   2 !   12.2   0.1   0.00013     0.073      26     158 ..     222     433 ..     218     450 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.19
                                   -HCHHHH..........HHCCHHC-HCHHHHHHHHC.CSHHHHHHHCCG.CCTT--TTHHHHHC.THHHHCSTT- CS
                       G-alpha 103 kveasliaklssateeeqeiefnpraevgedikaLw.ndpgiqelyerr.nkiklednaeyFld.dleritspdY 174
                                   ++e+sl++k  s    ++++ f++  +v   +k+L  nd+++ +++++  ++i  ++ +  +ld d+e+i+   Y
  gi|70607238|ref|YP_256108.1|  35 DFEESLKEKVLSEIYYSKSTDFED--KVLLRLKELGvNDENVEKILYSIkKQILYNEITPLLLDpDIEEIECLGY 107
                                   456666666666666668888888..9999999998899999999997735666778888888878888877666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
                                   EEEEESTTSSHHHHHHHHHHHCS--........--HHHHHCCHH.........HHHHHHHHHHHHHHHHHHHTT....... CS
                       G-alpha  26 llllGqseSGKsTilkqlkllykkg........fseeelatwra.........viqlnivrsiktilealesleselsesf 89 
                                   +++lG  +SGK+T+l+ l  l +++         s        +         + ++++++ ++  +  l +l  +  +++
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVNPHykiltiedTS------EISllnknwvrfIARSTLLSEFEISISDLAKLALRYRPDY 296
                                   789****************9999995554433311......3341111111123444555555555555555544444444 PP

                                   ..................................................................HHHC-SS-SCCCS-H CS
                       G-alpha  90 ..................................................................elqelkerldplkkv 104
                                                                                                     e ++  +++ +++++
  gi|70607238|ref|YP_256108.1| 297 miigevrgkeiealvhaaasghgsittfhgsrpidavtritdllsgdlaklflqtiwnfiivgnrkEGNKTVRSVLDIYEI 377
                                   888888888888888888888888888888888888888888888888888888888888888777666666666666666 PP

                                   CHHHH.................HHCCHHC-HCHHHHHHHHCCSHHHHHHHCCGCCTT--TT CS
                       G-alpha 105 easliaklssateee.......qeiefnpraevgedikaLwndpgiqelyerrnkikledn 158
                                    ++ ++k++ +   +       +++++++  +v e ik+    + i+e+y+   +++l   
  gi|70607238|ref|YP_256108.1| 378 INKGSKKITFK---KifewsyqNNNFIPQ--NVSEIIKRSYRLKRIKEIYNVDVESELTRR 433
                                   66654443333...133477744444444..677777777777777777775545555544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       2.9   1.6e+03      63     116 ..      31      84 ..      25     101 .. 0.66
   2 !   15.9   0.0   1.8e-05    0.0095      14      56 ..     213     254 ..     205     291 .. 0.78
   3 ?   -0.9   0.3       2.3   1.2e+03      83      95 ..     379     391 ..     343     443 .. 0.51

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                      ATPase_2  63 skldefieeeeekkklekalgiavpkaeleeilk.eksklvfkaielllekikkk 116
                                    ++++f ee+ ++k l++   ++   +e + +l  ++    ++++e++l +ikk+
  gi|70607238|ref|YP_256108.1|  31 PSFSDF-EESLKEKVLSEIYYSKSTDFEDKVLLRlKELGVNDENVEKILYSIKKQ 84 
                                   556666.666666667777666666666666666655555577777777777765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.8e-05
                      ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56 
                                   +l  e ++++ i Gp gsGKt+Ll+ +++  +  +++++ + +
  gi|70607238|ref|YP_256108.1| 213 WLLLEYRPFIIILGPTGSGKTTLLNALLNLVNP-HYKILTIED 254
                                   566678999****************99998743.555555555 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.3
                      ATPase_2  83 giavpkaeleeil 95 
                                   ++  +k ++++i+
  gi|70607238|ref|YP_256108.1| 379 NKGSKKITFKKIF 391
                                   2333333333333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.4e-05     0.024      24      68 ..     210     253 ..     197     262 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                         AAA_7  24 yllelllknkkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                     l lll+ +  +++ GptG+GKt++++ ll+ ++  +y++lti+
  gi|70607238|ref|YP_256108.1| 210 AYLWLLLEYRPFIIILGPTGSGKTTLLNALLNLVN-PHYKILTIE 253
                                   55667888888999*****************9998.788888776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       9.6   5.2e+03      66     104 ..      44      85 ..      29      92 .. 0.58
   2 ?   15.2   0.1   2.5e-05     0.014       1      22 [.     221     242 ..     221     299 .. 0.82
   3 ?   -0.9   0.1       2.1   1.2e+03     137     161 ..     377     401 ..     322     456 .. 0.53

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.6
                        AAA_21  66 lsqgvryryglrlersqv...eeklssvetllesgllldkrs 104
                                   +++++ y+ + ++e++ +   +e   + e+++++ +  +k++
  gi|70607238|ref|YP_256108.1|  44 VLSEIYYSKSTDFEDKVLlrlKELGVNDENVEKILYSIKKQI 85 
                                   445555555555555555555555555555555555555555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.5e-05
                        AAA_21   1 lnvliGpNgsGKSnLLdaldll 22 
                                   + ++ Gp gsGK++LL al  l
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALLNL 242
                                   679****************665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.1
                        AAA_21 137 dlqfgkaltditsrawsllllldgl 161
                                   +  +g+  + +++ ++ ++++++++
  gi|70607238|ref|YP_256108.1| 377 IINKGSKKITFKKIFEWSYQNNNFI 401
                                   2223333333333333333333222 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-05     0.033       2      21 ..     222     241 ..     221     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                                   EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                   ++i+G + +GK+tL+nal++
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLN 241
                                   79****************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.4e-05     0.035       1      21 [.     222     242 ..     222     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                   I++ G+ G+GKttl ++L ++
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNL 242
                                   9****************9554 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.4e-05     0.035      13      44 ..     220     250 ..     213     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.4e-05
                       Pox_A32  13 pFrlalvGgsGsGktvyLlsLlrtlvkkykhi 44 
                                   pF ++++G +GsGkt+ L +Ll+ +  +yk +
  gi|70607238|ref|YP_256108.1| 220 PF-IIILGPTGSGKTTLLNALLNLVNPHYKIL 250
                                   44.6899**************99998899865 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.5e-05     0.035      41      60 ..     221     240 ..     199     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-05
                                   SEEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE  41 hllvaGatgsGKStalntLi 60 
                                    ++++G tgsGK+t ln+L+
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALL 240
                                   589***************97 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.5e-05     0.041       2      25 ..     218     241 ..     217     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-05
                                   ---EEEEE-STTSSHHHHHHHHHH CS
                         SRPRB   2 skpavllvGlsdsGKTslftrLtt 25 
                                   ++p ++++G++ sGKT+l++ L++
  gi|70607238|ref|YP_256108.1| 218 YRPFIIILGPTGSGKTTLLNALLN 241
                                   5789****************9975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-05     0.042     101     121 ..     221     241 ..     194     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
                                   EEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase 101 tsvlvGqSGvGKStLinallp 121
                                   +++++G++G GK+tL+nall+
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALLN 241
                                   6799**************987 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.3e-05     0.045      10      39 ..     212     240 ..     205     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-05
                         RNA12  10 ewleEnvntFivvkGPrGSGkkeLvldrvl 39 
                                    wl  +   Fi++ GP GSGk+ L+ +  l
  gi|70607238|ref|YP_256108.1| 212 LWLLLEYRPFIIILGPTGSGKTTLL-NALL 240
                                   588888999**************98.5444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.7e-05     0.042       2      21 ..     222     241 ..     221     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-05
                        AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                   i+i+G+ ++GKTtll+aL +
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLN 241
                                   89***************975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.075       2      35 ..     222     255 ..     221     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrd 35 
                                   ++++Gp+G+gK++l   l+ ++n  + +  + + 
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVNPHYKILTIEDT 255
                                   689*******************888887777654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016     0.086       3      22 ..     222     241 ..     220     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                                   EEEEC-TTTCHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                   +i+ G+ GsGKTtLl  l  
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLN 241
                                   89*************99875 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013     0.071      85     115 ..     218     245 ..     202     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                    Adeno_IVa2  85 lqPviGviyGPtGsGksqllrnlissklisP 115
                                    +P+i +i GPtGsGk+ ll +l+  +l++P
  gi|70607238|ref|YP_256108.1| 218 YRPFI-IILGPTGSGKTTLLNALL--NLVNP 245
                                   57888.899*************98..45555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00025      0.13       2      29 ..     223     250 ..     222     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00025
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                           AAA   2 llyGppGtGKTllakavakelgveflei 29 
                                   ++ Gp G GKT+l +a+ + ++ ++  +
  gi|70607238|ref|YP_256108.1| 223 IILGPTGSGKTTLLNALLNLVNPHYKIL 250
                                   789****************986432222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00032      0.18      25      66 ..     222     263 ..     220     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                  Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66 
                                   ++++Gp GsGKt l ++l +l+ p  +  ++e ++  s+ +k
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVNPHYKILTIEDTSEISLLNK 263
                                   6899******************99999888888887777764 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.1   5.9e+02       9      30 ..      68      89 ..      60      92 .. 0.64
   2 ?    9.8   0.2    0.0012      0.67      25      49 ..     128     152 ..     125     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                        SpoVIF  9 nvkkedilkLansvqkadlkde 30
                                  +v+ e++ k++ s++k+ l +e
  gi|70607238|ref|YP_256108.1| 68 GVNDENVEKILYSIKKQILYNE 89
                                  5666666666666666655555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                        SpoVIF  25 adlkdektlRqlikqvsklankpvs 49 
                                     l+de+t+ ++i+++++ ank+v+
  gi|70607238|ref|YP_256108.1| 128 IKLNDEETVVRIIEKLASKANKSVN 152
                                   579*******************996 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.26       4      24 ..     222     242 ..     220     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                     PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                   i+++G++gsGKttL +al + 
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNL 242
                                   899************999764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.22      20      43 ..     221     244 ..     210     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                        AAA_30  20 vavltGpAGtGKttalkalreawe 43 
                                   + ++ Gp G+GKtt+l+al ++++
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALLNLVN 244
                                   6799**************987765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.26      26      46 ..     221     241 ..     214     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                   EEEEEESTTSSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlldAilF 46 
                                   f +i+Gp GSGK+ ll+A+l 
  gi|70607238|ref|YP_256108.1| 221 FIIILGPTGSGKTTLLNALLN 241
                                   889***************954 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00059      0.32       2      24 ..     222     244 ..     222     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00059
                                   EEEESSTTSSHHHHHHCHCT-CC CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkf 24 
                                   ++++G +g+GKt+ll+ +++   
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVN 244
                                   79**************9986433 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00052      0.28       1      35 [.     222     251 ..     222     284 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
               Viral_helicase1   1 ivvhGvpGcGKStlirkllrtsliltvnrptaell 35 
                                   i++ G  G+GK+tl+  ll+      vn+   +l 
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNL-----VNPHYKILT 251
                                   689999*************99.....333333333 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00044      0.24      18      44 ..     222     248 ..     217     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                 TrwB_AAD_bind  18 ilivGttGsGKtqalekllrairargd 44 
                                   i+i+G tGsGKt+ l++ll+ ++   +
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLNLVNPHYK 248
                                   789****************99876655 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00064      0.35       2      33 ..     222     252 ..     221     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                          MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                   + i g  gsGKTtLl+ l++ l +  +++ ti
  gi|70607238|ref|YP_256108.1| 222 IIILGPTGSGKTTLLNALLN-LVNPHYKILTI 252
                                   678999************97.55666777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3004.43
//
Query:       gi|70607239|ref|YP_256109.1|  [L=488]
Description: hypothetical protein Saci_1495 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3257.34
//
Query:       gi|70607240|ref|YP_256110.1|  [L=143]
Description: hypothetical protein Saci_1496 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00013   22.8   1.8    0.00024   22.0   1.8    1.5  1  Pilin_N   Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.029   14.7   0.2       0.13   12.5   0.2    2.0  1  CBM_4_9   Carbohydrate binding domain
      0.071   12.9   0.6         12    5.8   0.0    2.4  2  fn3_3     Polysaccharide lyase family 4, domain II
       0.25   10.3   0.0        0.3   10.0   0.0    1.1  1  PL48      Filopodia upregulated, FAM65


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.8   5.3e-08   0.00024       1      63 [.       9      73 ..       9      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.3e-08
                       Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievkidssastgkna..vslehkg 63
                                  +A+S+V G ++ +ait+ l +++ a+  g+ sn ++ ++++++ ki  + st++    ++l ++g
  gi|70607240|ref|YP_256110.1|  9 KAISSVLGTVIVLAITIALGGLLYAYSQGMFSNLTQNTNINVQAKIIVNPSTNDSYlqLTLVNNG 73
                                  69****************************99999999999999976666666666234444444 PP

>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     3e-05      0.13      32      91 ..      68     129 ..      33     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                   C..SSSSEEEEEESCSSTTCEEEEEEECCS-TT-EE..EEEEEEEESSTSEEEEEEEEEESSTT CS
                       CBM_4_9  32 s..yngtyslkvsgrgetwdgqaiditirlekgktY..tvsfwvkassgksrtikvkigdtdad 91 
                                   +  +ng++ + +++ + + +g+ i i+ +l +g++Y  t+ ++ k  +g  +t +v++++++++
  gi|70607240|ref|YP_256110.1|  68 TlvNNGNLGINITKVTIDSNGISIPINVYLPPGQQYsnTFPLTSKMIAG--ETYTVTVYGNSNN 129
                                   2558********************************5556667777777..9999999999884 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0026        12      49      69 ..      31      52 ..      30      57 .. 0.91
   2 ?    5.1   0.1    0.0043        19      37      54 ..     109     126 ..     100     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                         fn3_3 49 ltvYadglfgdyk.qdsvtVta 69
                                  l++Y +g+f   + +++++V+a
  gi|70607240|ref|YP_256110.1| 31 LYAYSQGMFSNLTqNTNINVQA 52
                                  8********999999*****98 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0043
                         fn3_3  37 ftipnVkpGtYrltvYad 54 
                                    t++++   tY++tvY +
  gi|70607240|ref|YP_256110.1| 109 LTSKMIAGETYTVTVYGN 126
                                   577888888*******87 PP

>> PL48  Filopodia upregulated, FAM65
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.7e-05       0.3     255     307 ..      14      66 ..       3      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.7e-05
                          PL48 255 glatvlvgsvtceskdlfaarpqvvvvditelgtiklqlevtwnPFdseelks 307
                                    l tv+v ++t ++  l++a +q +  ++t+++ i +q +++ nP  +++  +
  gi|70607240|ref|YP_256110.1|  14 VLGTVIVLAITIALGGLLYAYSQGMFSNLTQNTNINVQAKIIVNPSTNDSYLQ 66 
                                   47789****************************************98887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 954.05
//
Query:       gi|70607241|ref|YP_256111.1|  [L=223]
Description: endonuclease III [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-16   60.6   0.0    2.8e-16   59.9   0.0    1.3  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
     0.0012   19.1   5.0     0.0022   18.3   5.0    1.5  1  EndIII_4Fe-2S   Iron-sulfur binding domain of endonuclease II
      0.004   17.7   0.7      0.032   14.8   0.4    2.3  2  HHH_5           Helix-hairpin-helix domain
     0.0051   16.6   0.0      0.013   15.3   0.0    1.7  1  HHH             Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.043   13.3   0.2      0.051   13.1   0.2    1.2  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
       0.11   12.9   0.0       0.27   11.6   0.0    1.7  1  HHH_8           Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   9.2e-20   2.8e-16       2     104 ..      40     176 ..      39     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 9.2e-20
                                   HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH................ CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv................ 66 
                                   ++ilsq+ +d++a  ++ +l e++g +tp+++  ad   + ++ir +G++++Ka+yik++A+ +                 
  gi|70607241|ref|YP_256111.1|  40 ATILSQNSTDKSALIAFSKLNETVGEITPDRIKHADINTIIDAIRVAGLGNSKARYIKNVAEVINdldlnieidcqklrdf 120
                                   79******************************************************************************* PP

                                   ......................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHH CS
                                   ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       HhH-GPD  67 ......................gkpdvlivvDvhvrrilkrlrsikekktkkkvekklee 104
                                                         +  + +++ D+h+rr+++rl+++   +++k + ++++ 
  gi|70607241|ref|YP_256111.1| 121 ltaiegigdktadvvlltcfrcR--E-FPI-DTHIRRVISRLGFLGSSPKYKDISEYFKT 176
                                   *******************8433..4.666.**********************9999865 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   5.0   7.4e-07    0.0022       1      17 []     198     214 ..     198     214 .. 0.99

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.4e-07
                 EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                   C+ RkP C+ C+++D+C
  gi|70607241|ref|YP_256111.1| 198 CKSRKPICDKCVIRDYC 214
                                   ***************** PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.02        59      24      51 ..      66      96 ..      57     100 .. 0.72
   2 !   14.8   0.4   1.1e-05     0.032       3      52 ..      81     136 ..      79     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.02
                                  -SHHHHHHS-HHHHHTS...TTS-HHHHHHH CS
                         HHH_5 24 esvedlaaadveeLaki...pGiGkktAeri 51
                                   +++ +++ad++++ ++    G+G+ +A+ i
  gi|70607241|ref|YP_256111.1| 66 ITPDRIKHADINTIIDAirvAGLGNSKARYI 96
                                  5899999**9999665434499999988755 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   HHHTSTT--HHHHHHHHTTT--SHHHH.......HHS-HHHHHTSTTS-HHHHHHHH CS
                         HHH_5   3 eLlsvsGiGpktAlallsaGiesvedl.......aaadveeLakipGiGkktAerii 52 
                                   + ++v G+G + A+ + +   e + dl       +++ ++ L++i GiG ktA+ ++
  gi|70607241|ref|YP_256111.1|  81 DAIRVAGLGNSKARYIKNV-AEVINDLdlnieidCQKLRDFLTAIEGIGDKTADVVL 136
                                   6789999999999999999.666676665534233333677************9776 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.4e-06     0.013      13      28 ..     121     136 ..     118     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
                                   HHTSTT-SHHHHHHHH CS
                           HHH  13 LlalPGVGpktAeaIl 28 
                                   L+a++G+G ktA+++l
  gi|70607241|ref|YP_256111.1| 121 LTAIEGIGDKTADVVL 136
                                   89************99 PP

>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.7e-05     0.051      68     195 ..       8     135 ..       4     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                                   TTTGGGGS-H.HHHHHHHHHHHHHHHHHHHHHHHHHH..T--GGGS-..--.S....SSS-HHHHHHHHHSSSHHHHHHHH CS
                vATP-synt_AC39  68 fnklreqapgpsrefldyllyrydidNvklllrgklsg.dldleeleeklhpl....gelsaldldklieaksveelyeal 143
                                   ++klre  + +++ef++ ++ +   +   ++l  +ls+ ++d + l+++  +l    ge++++ + k +  +++ + +++ 
  gi|70607241|ref|YP_256111.1|   8 YMKLREEYKIDQKEFISSYICGKTRNVFATILATILSQnSTDKSALIAFS-KLnetvGEITPDRI-KHADINTIIDAIRVA 86 
                                   7788886666778************************9888777776544.45466789999998.446666666666666 PP

                                   H.T-HHHHHHHHHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...H CS
                vATP-synt_AC39 144 l.gtpyakyleealdeleetgdleiienaLdkayledllkfckklggetaeil 195
                                     g   a+y++++ +++++     ++ +++d   l+d+l +++ +g++ta+++
  gi|70607241|ref|YP_256111.1|  87 GlGNSKARYIKNVAEVIND----LDLNIEIDCQKLRDFLTAIEGIGDKTADVV 135
                                   6999***************....***********************9998765 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.9e-05      0.27      22      63 ..      90     135 ..      73     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                                   CCCHHHHHHHHCCCCC-SS-HHHH.TT...HCTTSTT--HHHHHHH CS
                         HHH_8  22 pfrvraYrrAaraiealpeeitsl.ee...eltklpgiGkkiaaki 63 
                                   + ++r  +++a++i +l+  i+   ++    lt++ giG+k+a+++
  gi|70607241|ref|YP_256111.1|  90 NSKARYIKNVAEVINDLDLNIEIDcQKlrdFLTAIEGIGDKTADVV 135
                                   5688888999999999999766533444434599*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1413.42
//
Query:       gi|70607242|ref|YP_256112.1|  [L=199]
Description: hypothetical protein Saci_1498 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-07   32.2   0.0    1.8e-07   31.4   0.0    1.3  1  ParBc     ParB-like nuclease domain
    1.4e-06   27.4   0.5     0.0044   15.9   0.2    3.2  2  DUF1015   Protein of unknown function (DUF1015)
  ------ inclusion threshold ------
       0.07   13.4   0.0       0.15   12.3   0.0    1.6  1  B5        tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   2.9e-11   1.8e-07       3      80 ..       9      79 ..       5      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.9e-11
                         ParBc  3 vplseirpnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleiddee 80
                                  v ++++rp ++ +     + ++e ++ ++k+    Piiv+k+    + i++G++R+ A+  lgl ++p+i+++  +e+
  gi|70607242|ref|YP_256112.1|  9 VSPKQLRPHEDVI----LSIVNENIEILRKDNSMAPIIVDKNS---MVILDGHHRYYASLSLGLPKIPAIMIDYNSEQ 79
                                  4444444444433....344666677777788899*******9...*************************9988554 PP

>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.014        84     108     139 ..       5      36 ..       1      43 [. 0.82
   2 !   15.9   0.2   7.3e-07    0.0044     202     380 ..      45     181 ..      35     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.014
                       DUF1015 108 sledyeegvIlpHEkTlaekeedRlkllratk 139
                                   +le  + ++ +pHE+++ + +++ +++lr+ +
  gi|70607242|ref|YP_256112.1|   5 QLEWVSPKQLRPHEDVILSIVNENIEILRKDN 36 
                                   6777888999***************9999865 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.3e-07
                       DUF1015 202 dkklyIADGHHRyatalavreerkaeeeaatgeepanyflavlvnledpgLkilpihRvvkdlnglseeelleklaeafev 282
                                   +++++I DGHHRy ++l ++  +   +           + a +++ +++++++ + +R++  +         + ++++++v
  gi|70607242|ref|YP_256112.1|  45 KNSMVILDGHHRYYASLSLG--L--PK-----------IPAIMIDYNSEQVEVREWNRIIAPD---------SSIRDFLRV 101
                                   67889999999999999999..3..22...........4466677777779999999999776.........245555555 PP

                       DUF1015 283 apfglylkdgkwyklltlkdkavrsLdvsvlqelllepilgiedprkderidyvhgleeavekvdsgeagvafllnptsve 363
                                     f   + dg   ++++ k+      dv+  ++++ + +++ e+   ++ ++ ++   ++v+ +d   +++ ++++p++++
  gi|70607242|ref|YP_256112.1| 102 --FRSSV-DG--KYCVSYKS------DVVFCDDNIYSLYWKEEA--IEQLLSRMGY--NVVKTAD---QEATISIPPVPKN 164
                                   ..55555.44..34555567......777777777777777433..2444443333..6666664...4689999999999 PP

                       DUF1015 364 elfavadagevmPrKST 380
                                    +++ + +g + P+KST
  gi|70607242|ref|YP_256112.1| 165 VVIDFSYKGLRFPPKST 181
                                   99999999999999999 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.15      17      47 ..     131     161 ..     113     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                                   -HHHHHHHHHHTT-E.EESSTTCEEEE--TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5  17 seeeiikiLkrlgceriekdkdlllVtvPsw 47 
                                   +ee i+++L+r+g+++ ++ +++ ++ +P+ 
  gi|70607242|ref|YP_256112.1| 131 KEEAIEQLLSRMGYNVVKTADQEATISIPPV 161
                                   789**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1343.99
//
Query:       gi|70607243|ref|YP_256113.1|  [L=464]
Description: membrane glocosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-21   75.6   0.0    5.5e-21   75.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-17   64.0   0.2    1.7e-17   64.0   0.2    2.1  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.1e-11   43.9   0.1    2.9e-11   43.4   0.1    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.8e-11   43.3   0.0    6.3e-11   42.6   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.5e-08   34.3   0.0    3.3e-08   33.2   0.0    1.6  2  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.045   12.4   0.1      0.064   12.0   0.1    1.1  1  Osmo_MPGsynth    Mannosyl-3-phosphoglycerate synthase (osmo_M
        7.2    7.5  10.2         14    6.6   0.5    3.0  3  HKR_ArcB_TM      Histidine kinase receptor ArcB trans-membran


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.1e-24   5.5e-21       1     167 [.      49     220 ..      49     222 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.1e-24
                                   EEEEEESS-.TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-.HHHHHHHHHHHH CS
               Glycos_transf_2   1 svviptyNe.ektlletlesllaq.dpypdfeiivvDDgStDetveileelak.edprvrvirreenv.Gkagalnaglra 77 
                                   s+++p+ Ne  + ++ +l+ l +  ++++++eii+v D  +D+  +i+      +d  v ++rre++   k+gal  g+++
  gi|70607243|ref|YP_256113.1|  49 SIIVPIKNEeISVIQGLLDNLSNLiWDKKKLEIIIVSDDNEDYFTKIINTVKVpKDLTVYFYRREKKLgYKSGALQYGFEK 129
                                   8**************************************************77***************99*********** PP

                                   --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHCCCCCCSTTCST CS
               Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkrslkgnlsfeig 156
                                   atgd+il++D D+  +p+ l   +e+++ +  d+++ q+  ++++ +      ++  ++    +   + +++     + +g
  gi|70607243|ref|YP_256113.1| 130 ATGDLILTIDVDSRLPPNALINAYEKMQSNTCDAIVFQWNGYSSNQYSTLAK-GMvvSTLFASKALFEGKEKLKLKIYPVG 209
                                   *******************************************999988865.5559999999999999999999999999 PP

                                   CCCEEEEHHHH CS
               Glycos_transf_2 157 saallrreale 167
                                   s ++++real+
  gi|70607243|ref|YP_256113.1| 210 SGTMFSREALR 220
                                   99999999985 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.2   6.4e-21   1.7e-17       2     189 ..     135     343 ..     134     389 .. 0.70
   2 ?   -1.7   1.9      0.88   2.2e+03     173     191 ..     426     448 ..     395     461 .. 0.45

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 6.4e-21
               Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgp.vlvm.nvanwleelaalffaedhgkdilv..realgrvvpsvGsgaf 78 
                                   il +D D++lpp+ l  +++ ++s+ ++++ ++  ++  n  + l++  ++ +   +++  l+   e+l+  +  vGsg++
  gi|70607243|ref|YP_256113.1| 135 ILTIDVDSRLPPNALINAYEKMQSNTCDAIVFQwNGYSsNQYSTLAKGMVVST--LFASKALFegKEKLKLKIYPVGSGTM 213
                                   99***********************9**9987754454366666666666664..33443444115689999999****** PP

               Glyco_trans_2_3  79 lrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc......eleklil.. 151
                                   ++r+al+ v gwd   + v +D+++g rl  +G +v     + ++ ++p++++ ++ Q +Rwa+G             l  
  gi|70607243|ref|YP_256113.1| 214 FSREALRVVNGWD--YRLVQDDLEIGTRLIYNGKNVCASGIP-IYVEVPDNFYSFYVQQTRWAMGSaevlrnR-----Lky 286
                                   *************..99******************9999888.**********************76544330.....123 PP

               Glyco_trans_2_3 152 ..........lvrllgylgsl..lwsalplhlallllfslla.........lalvllll 189
                                             +++l+ yl ++  + ++++++ +l+l+ ++ +         l  +++l+
  gi|70607243|ref|YP_256113.1| 287 iikskisftqRMDLIIYLLQYtpVIVTFFISTLLSLMLPFRIghdplnspaL--LFWLV 343
                                   3344444444333333332221022222222223333333324455555331..22222 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.88
               Glyco_trans_2_3 173 llllfslla..........lalvllllll 191
                                   l+ll+s+l+          +      ll+
  gi|70607243|ref|YP_256113.1| 426 LYLLSSILYiyegyyvtgiW------LLY 448
                                   33334433333332222221......111 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.1   1.1e-14   2.9e-11       1     206 [.      49     247 ..      49     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.1e-14
               Glyco_tranf_2_2   1 svviplraseerhyieerv.lqkakyy.deeielivvddgSsekfleevssiidlnllv.ylkdeddk.ayslaaarNrGa 77 
                                   s+++p++++e    i+  +  + +  +  +++e+i+v d   + f + +++++  + l  y+   ++k  y  +a    G+
  gi|70607243|ref|YP_256113.1|  49 SIIVPIKNEEIS-VIQGLLdNLSNLIWdKKKLEIIIVSDDNEDYFTKIINTVKVPKDLTvYFYRREKKlGYKSGAL-QYGF 127
                                   789999998887.6777664233334434689********************987665548777777768887765.68** PP

               Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledl.laakstl 157
                                   +ka +dl+l +D+D    ++ + +  +     k++ n   a+v+ +  +  ++   l ++  +++s+++  ++ +  k+ l
  gi|70607243|ref|YP_256113.1| 128 EKATGDLILTIDVDSRLPPNALINAYE-----KMQSNTCDAIVFQWNGYSSNQYSTLAKG--MVVSTLFASKAlFEGKEKL 201
                                   ***************999999877777.....9****************98888888765..8888888876515678889 PP

               Glyco_tranf_2_2 158 vkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaiksl 206
                                      + p +s  +  r+a+  v G+D r+    ++D ++ +Rl    k++
  gi|70607243|ref|YP_256113.1| 202 KLKIYPVGSGTMFSREALRVVNGWDYRL---VQDDLEIGTRLIYNGKNV 247
                                   99**************************...899********9988887 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   2.5e-14   6.3e-11       4     230 .]      48     275 ..      46     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.5e-14
               Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqe..yprvevvvvvdesdaetlevaeelaaalp.dvrvrvvvnarnlgstgksraln 80 
                                   l+++Vp  nee  v+  +l++l++       +e+++v d +++   + +  +  + p d  v  ++++++lg   ks al+
  gi|70607243|ref|YP_256113.1|  48 LSIIVPIKNEEIsVIQGLLDNLSNLIwdKKKLEIIIVSDDNEDYFTKIINTV--KVPkDLTVYFYRREKKLG--YKSGALQ 124
                                   7899999888765666677777776421477*******99999988888764..444144455555566555..8****** PP

               Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar..ralgv.l 158
                                    +++ +++dl+l +D D+++ P++l  +   +++  ++a+  + + +  + + + +  + +   +++  ++   + l+  +
  gi|70607243|ref|YP_256113.1| 125 YGFEKATGDLILTIDVDSRLPPNALINAYEKMQSNTCDAIVFQWNGYSSNQYSTLAKGMVVSTLFASKALFEgkEKLKLkI 205
                                   ************************888888887777777765554444444433334444445555555555434445547 PP

               Glyco_tranf_2_3 159 tlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                   ++ Gsg+++ re l+   g+d   l+ dD+e+g rl  +g  ++ + g  ++ + p+++  ++ q +Rw++g
  gi|70607243|ref|YP_256113.1| 206 YPVGSGTMFSREALRVVNGWDY-RLVQDDLEIGTRLIYNGKNVC-ASGIPIYVEVPDNFYSFYVQQTRWAMG 275
                                   779*******************.*************99887776.66777*******************986 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         1   2.6e+03      25      40 ..      73      88 ..      68     107 .. 0.74
   2 !   33.2   0.0   1.3e-11   3.3e-08       6     172 ..     107     273 ..      99     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
               Glyco_transf_21 25 aleaakydllvisDsd 40
                                   +++ k +++++sD++
  gi|70607243|ref|YP_256113.1| 73 IWDKKKLEIIIVSDDN 88
                                  4788899999999997 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.3e-11
               Glyco_transf_21   6 llvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl.. 84 
                                   +++ + ++++ +K  +l +++e+a  dl+++ D d r++p++L +  ++++++++  ++    g+  +  +++l++ ++  
  gi|70607243|ref|YP_256113.1| 107 VYFYRREKKLGYKSGALQYGFEKATGDLILTIDVDSRLPPNALINAYEKMQSNTCDAIVFQWNGYSSN-QYSTLAKGMVvs 186
                                   56667889999****************************************98887655444433333.344444444433 PP

               Glyco_transf_21  85 ..ntlagvlqa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrssl 161
                                      +  +++    kl+     vG+  +++reaL+ + G     + + +D+++g++l  +G++v  s +pi  ++vp+   +
  gi|70607243|ref|YP_256113.1| 187 tlFASKALFEGkeKLKLKIYPVGSGTMFSREALRVVNGWDY--RLVQDDLEIGTRLIYNGKNVCASGIPIY-VEVPD--NF 262
                                   213334445547788888899*****************999..8888**********************87.79996..67 PP

               Glyco_transf_21 162 rallaRqlrWa 172
                                    +++ +q+rWa
  gi|70607243|ref|YP_256113.1| 263 YSFYVQQTRWA 273
                                   88********8 PP

>> Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.5e-05     0.064      41      75 ..      35      70 ..      26     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                 Osmo_MPGsynth 41 vseeele.evesklaivvpiknEelkvlegvlsgiP 75
                                  +++e+l+ + +  l+i+vpiknEe++v++g+l  + 
  gi|70607243|ref|YP_256113.1| 35 INQEALKySNLPVLSIIVPIKNEEISVIQGLLDNLS 70
                                  555555423455799****************98765 PP

>> HKR_ArcB_TM  Histidine kinase receptor ArcB trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.7   9.5e+03      45      57 ..      10      22 ..       3      43 .. 0.55
   2 ?    6.3   0.6    0.0064        16      25      60 ..     281     316 ..     272     323 .. 0.82
   3 ?    6.6   0.5    0.0054        14      14      60 ..     339     390 ..     334     395 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                   HKR_ArcB_TM 45 ilfgllsaPwvlY 57
                                  +l+ +  a++++Y
  gi|70607243|ref|YP_256113.1| 10 LLLFVYPAVFIIY 22
                                  3333334444444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0064
                   HKR_ArcB_TM  25 qillslllsgeveiedllrsilfgllsaPwvlYFls 60 
                                      l++++++++++++ ++ i+  l  +P+++ F+ 
  gi|70607243|ref|YP_256113.1| 281 RNRLKYIIKSKISFTQRMDLIIYLLQYTPVIVTFFI 316
                                   556899***********************9996653 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0054
                   HKR_ArcB_TM  14 vlllivlalliqillslllsgeveied....llrsilfgllsaPwvlY.Fls 60 
                                   ++ l++l l  + llsl+l+  ++ +d    + r  +f++ + P++++ F++
  gi|70607243|ref|YP_256113.1| 339 LFWLVSLGLYASLLLSLALKLGLNLKDslmgIGRLTAFTVSISPFIVFnFFK 390
                                   5566666666677777777777766662222567889**********95555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3359.53
//
Query:       gi|70607244|ref|YP_256114.1|  [L=876]
Description: ATP-dependent helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-55  187.5   0.0    3.6e-55  186.7   0.0    1.4  1  DEAD_assoc       DEAD/H associated
    1.9e-28   99.4   0.0    6.2e-27   94.5   0.0    2.8  3  DEAD             DEAD/DEAH box helicase
      1e-16   61.3   0.1    3.3e-16   59.6   0.1    1.9  1  Helicase_C       Helicase conserved C-terminal domain
    4.5e-08   33.3   0.0    1.6e-07   31.5   0.0    1.9  2  ResIII           Type III restriction enzyme, res subunit
     0.0038   17.1   0.0      0.012   15.5   0.0    1.8  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.012   15.9   0.0        5.3    7.4   0.0    2.8  2  AAA_19           AAA domain
       0.15   11.9   0.0        0.4   10.6   0.0    1.6  1  LapD_MoxY_N      LapD/MoxY periplasmic domain
       0.23   11.7   1.0        3.1    8.0   0.1    3.1  3  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.7   0.0   1.6e-58   3.6e-55       1     191 []     638     827 ..     638     827 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 1.6e-58
                    DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                   +Ptd+ ll+E ++d+ +++++++h ++Grr  +al++++a+ +s+ +++dv++a++D+g+++++p +++   ++ +++++l
  gi|70607244|ref|YP_256114.1| 638 VPTDKLLLIEVYDDDDQNRNFIFHGLYGRRTVDALSRAIAYIISKDLNMDVRIAITDNGFAITVPGKQEY--EISKVFDKL 716
                                   8***********99999***********************************************777775..4789***** PP

                    DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDl 162
                                   +pd++ e+l + + ++e++krrFr++A+r+++l++ry+g++++  + +++++ Ll v+r++++fp+l+e+vre+led++D+
  gi|70607244|ref|YP_256114.1| 717 EPDKMYEILSDVILRTEMIKRRFRHCAERSFMLLKRYKGRETSIDRRQINSEVLLGVVRQIEHFPVLKETVREILEDYMDI 797
                                   ********************************************************************************* PP

                    DEAD_assoc 163 erlaellrriaageirvveve.tprpSpfA 191
                                   +r+ e++++i++g+i+v+++   + pSpfA
  gi|70607244|ref|YP_256114.1| 798 KRAIEIVEKIRNGDIKVATIGpNQVPSPFA 827
                                   ********************98999****9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   2.8e-30   6.2e-27       1     170 [.      34     215 ..      34     223 .. 0.84
   2 ?    1.2   0.0      0.12   2.7e+02      43     103 ..     272     340 ..     244     373 .. 0.72
   3 ?   -1.3   0.0      0.74   1.6e+03      48      75 ..     836     863 ..     746     874 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.8e-30
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                          DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid.. 75 
                                   t+ Q+ aipli +g++vlv+ +TGsGKTla+++ +l+++++     + +++  a++++P+r+L +++ +nl + + +++  
  gi|70607244|ref|YP_256114.1|  34 TPPQKGAIPLIKKGKNVLVSSPTGSGKTLAAFLGILDTLIDLgyknELNKQIYAIYISPLRALNNDMRRNLIEPLTELRnl 114
                                   688************************************999999889999********************9999964445 PP

                                   ...SEEEEE...ETTSSHHHHHHHHHTTCSEEEEEHHHHHH.HH...HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                   ...xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  76 ...lrvlli...iggvaardqlskldngvdivvgtpgrldd.ll...stgklnlsqvrflVlDEadrlldqgfsdfinril 146
                                      l + +i   +++++  ++++ l++ ++i+++tp+ +   l+    ++k  ls+v+++++DE+++l +++++  +  +l
  gi|70607244|ref|YP_256114.1| 115 ypdLPEISIgvrTSDTSSYEKQKMLKKPPHILITTPESFGIsLVspkFREK--LSDVKWVIVDEIHELANSKRGAYLAGLL 193
                                   5555555443325566777777777666***********984556533444..**************************99 PP

                                   HHSHHHCTTSTTTSEEEEEESSBS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 147 nqlpqitcdgklqrqvivlSATlp 170
                                   +  ++  ++ +     i lSAT++
  gi|70607244|ref|YP_256114.1| 194 ELYKSFIAKNN--FVRIGLSATIS 215
                                   99988777766..459******97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                                   TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.......SEEEEEETTSSHHHHHHHHHTT.CSEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                          DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyid.......lrvlliiggvaardqlskldng.vdivvg 103
                                   + k+++ +li + tr  ae ++ +l+k+++  +          ++ ++ + + +  +kl++g +++vv+
  gi|70607244|ref|YP_256114.1| 272 EIKKHKTTLIFTNTRHAAERVAYKLRKMFEDQNifdsdlvAAHHSSLSRDVRLEVEEKLKRGeLKVVVS 340
                                   567777899999999999999999999999533334444222224455555556666665555666665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.74
                                   -EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  48 pkalivePtreLaeqtlnnlkkfkkyid 75 
                                   + +++ e  reL ++ +n++ +f+ + +
  gi|70607244|ref|YP_256114.1| 836 TDVVLAEDKRELLKELHNKVIEFLRNKG 863
                                   5677778889999999999999988633 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   1.5e-19   3.3e-16       6     108 ..     269     376 ..     262     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.5e-19
                                   HHHHHHHTTTTSEEEEEESSHHHHHH.....HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                    Helicase_C   6 llellkleeeggkilifvntidrlek.....vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                   l   +++ ++++++lif+nt+  +e+      k+++ ++   +  va++h++l+ + r+e+ e+ ++ge +v+++++ +e 
  gi|70607244|ref|YP_256114.1| 269 L---VDEIKKHKTTLIFTNTRHAAERvayklRKMFEDQNifdSDLVAAHHSSLSRDVRLEVEEKLKRGELKVVVSSTSLEL 346
                                   3...3566999***********6655555666777666688888899********************************** PP

                                   SSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                    Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtg 108
                                   Gidi  ++lV  ++ p++v+++ qr+GR+g
  gi|70607244|ref|YP_256114.1| 347 GIDIGYIDLVTLLSSPKSVSRLLQRVGRAG 376
                                   *****************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   7.1e-11   1.6e-07      22     169 ..      45     214 ..      17     216 .. 0.71
   2 ?   -3.0   0.0       2.9   6.4e+03     100     118 ..     274     292 ..     247     337 .. 0.57

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 7.1e-11
                                   .TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHHHGGGGTGG............... CS
                        ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtleefkkflseayke........... 84 
                                   k+ k++l+  +TG+GKTl a + + + l   g+++       ++ + p ++l + +++++ + l e ++            
  gi|70607244|ref|YP_256114.1|  45 KKGKNVLVSSPTGSGKTLAAfLGILDTLIDLGYKNelnkqiYAIYISPLRALNNDMRRNLIEPLTELRNLypdlpeisigv 125
                                   7889****************778888888887777999999999*************887444444433344444444333 PP

                                   GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-S..EEEEETGGGTTS.T..........TTH CS
                        ResIII  85 igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDEaHrlgakk..........swr 151
                                        ++d+ +   ++  ++  +il+tt +s+  ++      s +++++ +d   +i+DE H l+ +k           ++
  gi|70607244|ref|YP_256114.1| 126 R----TSDTSSYekQKMLKKPPHILITTPESFGISL-----VSPKFREKLSDvkWVIVDEIHELANSKrgaylaglleLYK 197
                                   1....22222223334557889**************.....55555555555559***********855655555554777 PP

                                   HHHHT---SEEEEEESS- CS
                        ResIII 152 eilekfkeavllglTATp 169
                                   + + k +++v++gl+AT+
  gi|70607244|ref|YP_256114.1| 198 SFIAK-NNFVRIGLSATI 214
                                   75555.45*********7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                                   ....-SEEEEEHHHHHHTH CS
                        ResIII 100 dstnkkilvttiqsldads 118
                                   +++++ +++t++  + ++ 
  gi|70607244|ref|YP_256114.1| 274 KKHKTTLIFTNTRHAAERV 292
                                   3444444444443333333 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.4e-06     0.012      15      86 ..     208     275 ..     202     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-06
                                   EEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHH CS
               Transketolase_C  15 vayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalae 86 
                                   ++ +++ +   e+a+ L   + + e++d+r+vkp D + ++      + lv  +e  ++ Gi s +++ + +
  gi|70607244|ref|YP_256114.1| 208 IGLSATISPLEEVAKFLVGGNGDYEIIDARFVKPTDIQVVS----PVKDLVHATEEEVNIGIYSYLVDEIKK 275
                                   678899999999************************99998....778888888888888988888777776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0024       5.3       2     115 ..      38     181 ..      37     200 .. 0.63
   2 ?    5.3   0.0      0.01        22      37      69 ..     272     311 ..     260     421 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                        AAA_19   2 reave.alkekvllvtaGpGtGKTr.vlkhivallvelggvkp..eeillv..aftgrAakelrerlaalgae........ 68 
                                   + a+    k k++lv  + G+GKT     +i+  l++lg  +   ++i+++  ++ +   + +r +l    ++        
  gi|70607244|ref|YP_256114.1|  38 KGAIPlIKKGKNVLVSSPTGSGKTLaAFLGILDTLIDLGYKNElnKQIYAIyiSPLRALNNDMRRNL---IEPltelrnly 115
                                   55665567889999**********6245677777777765544445665541155555556677777...33333366666 PP

                        AAA_19  69 .........atTiHrlalldfddlltealelle...........eaeeekklqeeellivDEfqdvd 115
                                             +T    +  + + l++ +  l             + + ++kl + +++ivDE+ ++ 
  gi|70607244|ref|YP_256114.1| 116 pdlpeisigVRTSDTSSYEKQKMLKKPPHIL-IttpesfgislvSPKFREKLSDVKWVIVDEIHELA 181
                                   6666666665555544333333333333333.24777888888866788899788899999998876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                        AAA_19  37 lggvkpeeillvaftgrAakelrerlaalgae........a 69 
                                   +   k ++ l+ + t++Aa++++ +l+++ ++         
  gi|70607244|ref|YP_256114.1| 272 EI-KKHKTTLIFTNTRHAAERVAYKLRKMFEDqnifdsdlV 311
                                   33.345899*****************999988566665542 PP

>> LapD_MoxY_N  LapD/MoxY periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018       0.4      62      92 ..     548     578 ..     542     584 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                   EETT--EEEEEE-------S-HHHHHHH--S CS
                   LapD_MoxY_N  62 tdldgkvlverenetkiegvPqWFirlvple 92 
                                      +g+ ++ +++e ++ +vP+WF +++pl 
  gi|70607244|ref|YP_256114.1| 548 IRSEGNSVIVKKSEGQRPTVPSWFSEMLPLA 578
                                   5568999999999999999*********986 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0014       3.1      32      91 ..     249     305 ..     236     306 .. 0.84
   2 ?   -3.0   0.0       3.9   8.8e+03      49      66 ..     323     340 ..     311     344 .. 0.74
   3 ?   -0.0   0.0      0.45     1e+03      42      63 ..     792     814 ..     773     832 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                                   -EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHHHHHHHHHHHTTS CS
                           MGS  32 pvtevvektgegerlggrveildaikngeidlvintlypfkatvakdgykirraaenidI 91 
                                   pv+++v+ t+e+ + g    ++d+ik+++  l+  ++ + +++va   yk+r++ e+ +I
  gi|70607244|ref|YP_256114.1| 249 PVKDLVHATEEEVNIGIYSYLVDEIKKHKTTLIFTNTRHAAERVA---YKLRKMFEDQNI 305
                                   577788888888555555599********************9996...********9998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.9
                                   CHHHHHHHHTTSCCEEEE CS
                           MGS  49 rveildaikngeidlvin 66 
                                   r e+++++k ge ++v+ 
  gi|70607244|ref|YP_256114.1| 323 RLEVEEKLKRGELKVVVS 340
                                   458999999999999985 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.45
                                   TGSGGTHCH.HHHHHHHTTSCCE CS
                           MGS  42 egerlggrv.eildaikngeidl 63 
                                   e+ +  +r  ei+++i+ng+i++
  gi|70607244|ref|YP_256114.1| 792 EDYMDIKRAiEIVEKIRNGDIKV 814
                                   33233333379*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 6070.81
//
Query:       gi|70607245|ref|YP_256115.1|  [L=108]
Description: hypothetical protein Saci_1501 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.15   12.2   0.0    1.2  1  F-112     F-112 protein


Domain annotation for each model (and alignments):
>> F-112  F-112 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.5e-06      0.15      30      58 ..      25      53 ..       5      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-06
                                  HH---HHHHHHHHHHHHHHHHH-TTTEEE CS
                         F-112 30 qfeisvssayaiqralkaicerhqdecev 58
                                  +fei +s  y++   +k i + h++ec+ 
  gi|70607245|ref|YP_256115.1| 25 MFEIDPSEFYKVAEKVKSILHTHEGECKP 53
                                  69*************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 791.47
//
Query:       gi|70607246|ref|YP_256116.1|  [L=300]
Description: hypothetical protein Saci_1502 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-36  121.6   0.3    1.6e-35  120.6   0.3    1.6  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor
      6e-25   87.5   1.0    4.2e-13   49.5   0.9    2.6  2  CBS           CBS domain
    7.9e-09   35.8   0.4    3.4e-08   33.7   0.0    2.3  2  Rrf2          Transcriptional regulator
    2.6e-05   23.9   0.3    0.00057   19.7   0.2    2.5  2  eIF-1a        Translation initiation factor 1A / IF-1
    3.4e-05   23.7   1.1    6.5e-05   22.8   0.1    2.0  2  HTH_11        HTH domain
  ------ inclusion threshold ------
      0.022   14.7   0.3      0.059   13.3   0.1    1.8  2  TrmB          Sugar-specific transcriptional regulator TrmB
      0.039   13.5   0.7       0.12   11.9   0.7    2.0  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.044   13.4   0.0       0.18   11.5   0.0    2.0  2  GntR          Bacterial regulatory proteins, gntR family
      0.049   13.4   0.0        0.1   12.4   0.0    1.6  1  HTH_IclR      IclR helix-turn-helix domain
      0.077   12.7   0.3       0.72    9.6   0.0    2.2  2  Sigma70_r4_2  Sigma-70, region 4
       0.13   12.1   0.2       0.37   10.6   0.0    1.9  2  HTH_38        Helix-turn-helix domain
       0.14   12.1   0.1       0.27   11.2   0.1    1.5  1  HTH_36        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   0.3   1.1e-38   1.6e-35       1      76 [.       3      78 ..       3      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 1.1e-38
                  HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiq 76
                                  +L+s+q+eil aLi++y+k+kr+vK++eiA++++++eGtvRN++ sLk+lgL+e++pGP+GGY+Ptlkayea+k+ 
  gi|70607246|ref|YP_256116.1|  3 NLSSTQREILLALIDIYNKNKRMVKSKEIADMIGKDEGTVRNVILSLKVLGLIESKPGPSGGYVPTLKAYEAIKNP 78
                                  69***********************************************************************976 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0     7e-12   1.1e-08       1      55 [.     174     228 ..     174     230 .. 0.96
   2 !   49.5   0.9   2.8e-16   4.2e-13       1      56 [.     237     292 ..     237     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7e-12
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+ im +++v ++p+ tl++a +++ ++g+++ PV+d++gk +Gi+t  D+++a 
  gi|70607246|ref|YP_256116.1| 174 VKNIMGKRLVALKPENTLRDASQILYKEGIRGAPVLDNEGKNLGILTTADIIKAF 228
                                   7899********************99999***********************986 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 2.8e-16
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+d+m ++v+++++d+++  a+++m  ++v+rl+V+++d +++Givt++D+l+ ++
  gi|70607246|ref|YP_256116.1| 237 VSDYMKTNVISISEDDDVLTAIKKMLIYNVGRLLVLNKDQRVIGIVTRTDILKTIA 292
                                   89**********************99788***********************9886 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.3e-11   3.4e-08       3      66 ..       4      66 ..       1      75 [. 0.91
   2 ?   -1.1   0.0       1.7   2.5e+03      35      47 ..     167     179 ..     150     227 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.3e-11
                                  --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                          Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                  lss  +  l al+++ +++++  v+s+eia++ +  +  ++ ++  L+  gl++s+ G++GGy+
  gi|70607246|ref|YP_256116.1|  4 LSSTQREILLALIDIYNKNKRM-VKSKEIADMIGKDEGTVRNVILSLKVLGLIESKPGPSGGYV 66
                                  56666677899*****999987.****************************************6 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                                   HTS-HHHHHHHHH CS
                          Rrf2  35 qnispsylekila 47 
                                   ++i+++ ++ i+ 
  gi|70607246|ref|YP_256116.1| 167 VSIPKVQVKNIMG 179
                                   5555555555553 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   3.8e-07   0.00057      18      62 ..     108     150 ..      98     151 .. 0.85
   2 ?    1.3   0.0       0.2   2.9e+02      25      50 ..     231     257 ..     210     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.8e-07
                                   EEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TT....EEEEE CS
                        eIF-1a  18 VelpdngkevlaeipgkfRnkiwikrGdyVlVelspydlt....kGrIv 62 
                                   ++ p ng++vl +++g +R   +ik Gd V + ++py  t     G I+
  gi|70607246|ref|YP_256116.1| 108 ITNP-NGNKVLLKVSGDLR---KIKVGDTVKIGPIPY--TrlviEGVII 150
                                   5677.9*************...***************..5446777776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                                   SBEEEEE-HHHH.CT----TT-EEEEE CS
                        eIF-1a  25 kevlaeipgkfR.nkiwikrGdyVlVe 50 
                                   +++ a+++  ++ n i i ++d Vl  
  gi|70607246|ref|YP_256116.1| 231 QRYDAKVSDYMKtNVISISEDDDVLTA 257
                                   5677899999************99865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   4.3e-08   6.5e-05       3      54 ..      13      65 ..      11      66 .. 0.92
   2 ?   -2.1   0.1       2.7     4e+03      27      41 ..     282     296 ..     281     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.3e-08
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54
                                  l+++ + ++++  + ++e+A+ ++  + tvr+ I +L+ lg  Ies+pg+  GY
  gi|70607246|ref|YP_256116.1| 13 LALIDIYNKNKRMVKSKEIADMIGKDEGTVRNVILSLKVLG-LIESKPGPsgGY 65
                                  5677888888888****************************.*********999 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                        HTH_11  27 vSrrtvrrdIkaLee 41 
                                   v+r+ + + I+ Lee
  gi|70607246|ref|YP_256116.1| 282 VTRTDILKTIAGLEE 296
                                   789999999999998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     4e-05     0.059       8      64 ..       6      74 ..       2      77 .. 0.73
   2 ?   -2.9   0.0       4.4   6.6e+03      27      43 ..     162     178 ..     159     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                  HHCCCHCHHHH.....HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.......TTEEEE CS
                          TrmB  8 eyEakvYlaLl.....klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.......pklYra 64
                                  ++  ++ laL+     ++   + +eia ++g ++ +v +v+ sL+  Gl+e ++g         k Y+a
  gi|70607246|ref|YP_256116.1|  6 STQREILLALIdiynkNKRMVKSKEIADMIGKDEGTVRNVILSLKVLGLIESKPGPsggyvptLKAYEA 74
                                  555566666666544334445779*****************************9996776644445655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.4
                                   HHCCCTTSSCHCHHHHH CS
                          TrmB  27 eiaeelgvprskvYevL 43 
                                   ++ +++ +p+ +v +++
  gi|70607246|ref|YP_256116.1| 162 DVTRMVSIPKVQVKNIM 178
                                   78899999999998876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   8.1e-05      0.12       3      48 .]       6      56 ..       4      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                        HTH_24  3 etdrkILelLqk....npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   t+r+IL +L +    n r    +e+A+++g   +tv+  +  L+  GlI+
  gi|70607246|ref|YP_256116.1|  6 STQREILLALIDiynkNKRmVKSKEIADMIGKDEGTVRNVILSLKVLGLIE 56
                                  6888888888888888**********************9998888888875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.18      27      59 ..      28      60 ..      18      66 .. 0.91
   2 ?   -2.3   0.0       2.5   3.7e+03      39      53 ..     189     203 ..     188     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                          GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   +e+a+++g +  tvR ++  L+  gl+e+++g
  gi|70607246|ref|YP_256116.1| 28 SKEIADMIGKDEGTVRNVILSLKVLGLIESKPG 60
                                  589****************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                   HHHHHHHHHHHHTTS CS
                          GntR  39 ttvReALrrLeaegl 53 
                                   +t+R A + L  eg+
  gi|70607246|ref|YP_256116.1| 189 NTLRDASQILYKEGI 203
                                   799***999999985 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.8e-05       0.1       6      50 ..      13      57 ..      10      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  la++d+ ++  + ++ +e+A+ +g    tv++ + +L  lG++e 
  gi|70607246|ref|YP_256116.1| 13 LALIDIYNKNKRMVKSKEIADMIGKDEGTVRNVILSLKVLGLIES 57
                                  6677777777888899**************************996 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.32   4.7e+02       9      20 ..       2      13 ..       1      15 [. 0.87
   2 ?    9.6   0.0   0.00048      0.72      29      45 ..      28      44 ..      26      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.32
                                  TTS-HHHHHHHH CS
                  Sigma70_r4_2  9 aeLperqreifl 20
                                  + L+  qrei+l
  gi|70607246|ref|YP_256116.1|  2 QNLSSTQREILL 13
                                  789*******98 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                                  HHHHHHHHT--HHHHHH CS
                  Sigma70_r4_2 29 ykEIAellgisegtVks 45
                                   kEIA ++g  egtV++
  gi|70607246|ref|YP_256116.1| 28 SKEIADMIGKDEGTVRN 44
                                  79*************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.37       5      41 ..       4      46 ..       1      47 [. 0.80
   2 ?   -3.5   0.0       6.4   9.5e+03      13      20 ..     195     202 ..     192     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                        HTH_38  5 LsleeReeIerl...laeGlslr...eIArrLgrspsTIsREl 41
                                  Ls ++Re + +l   +++++ +    eIA  +g++ +T+ + +
  gi|70607246|ref|YP_256116.1|  4 LSSTQREILLALidiYNKNKRMVkskEIADMIGKDEGTVRNVI 46
                                  77888888888754457888887899*************9987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.4
                        HTH_38  13 IerllaeG 20 
                                    ++l++eG
  gi|70607246|ref|YP_256116.1| 195 SQILYKEG 202
                                   58999998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.27       2      55 .]       3      55 ..       2      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                        HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  +Ls +++ +l+ l + +nkn     s + +a   g+++ Tv++ i +L  lG+i
  gi|70607246|ref|YP_256116.1|  3 NLSSTQREILLALIDIYNKNKRMVKS-KEIADMIGKDEGTVRNVILSLKVLGLI 55
                                  89999************999995555.67**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1970.88
//
Query:       gi|70607247|ref|YP_256117.1|  [L=228]
Description: hypothetical protein Saci_1503 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-79  264.7   6.4    7.1e-79  264.5   6.4    1.0  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.5   6.4     4e-83   7.1e-79       1     229 []       3     227 ..       3     227 .. 0.99

  Alignments for each domain:
  == domain 1  score: 264.5 bits;  conditional E-value: 4e-83
                       DUF2192   1 kelykkrievlvdllsklleee.kltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeelkelf 80 
                                   ke+y++r++vl++l+++l+e+  +ltRe lv+llk++Ye+++i+P+rG+++ ed+Y+kEl++lYvvgk+Glgl++++ke+f
  gi|70607247|ref|YP_256117.1|   3 KEIYRERVRVLTELWGSLVEKYtHLTREVLVDLLKESYETNDIKPIRGFKA-EDLYEKELISLYVVGKEGLGLFNDYKEVF 82 
                                   799******************99****************************.***************************** PP

                       DUF2192  81 dkifsvEekleealeiilskkkeeavekvkevlgkidenkvarvlrlvltkvvlgfadeeelikllrkl.eeafpelektv 160
                                   +k+++ E+ +++a+ei++++k  ea+e +++     d++++a+vlrl++++ +++f++ee+l+ ++r+l  ++++e+++t+
  gi|70607247|ref|YP_256117.1|  83 EKLLMPEIVIDRASEILIENKPIEAFELLQK-----DKGSLAKVLRLIFIQGIFSFKPEENLYIAMRNLdFTNIDEMKHTA 158
                                   ******************************9.....9********************************99********** PP

                       DUF2192 161 kkyarfyiAfkiaekiaegeirnrlekealkkalalrlgiekalPsdeyiaeiakevfkvpkkvlkkvl 229
                                    ++arfy+Afk+ae+iae++i+++++ ea+k+ala+++gi+++lP+ eyi+ i kevf++++k+lkkvl
  gi|70607247|ref|YP_256117.1| 159 VSFARFYTAFKVAEGIAEKTIKDKMNAEAFKRALAISIGIKYPLPKPEYISLIGKEVFNIDQKLLKKVL 227
                                   *******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1432.37
//
Query:       gi|70607248|ref|YP_256118.1|  [L=130]
Description: hypothetical protein Saci_1504 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   18.9   0.7     0.0015   18.5   0.7    1.2  1  Laminin_II     Laminin Domain II
     0.0071   16.5   0.0          3    8.1   0.0    2.1  2  T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, Ep
  ------ inclusion threshold ------
       0.02   15.2   2.4      0.043   14.2   2.4    1.5  1  FlaC_arch      Flagella accessory protein C (FlaC)
      0.029   14.5   0.2      0.075   13.2   0.2    1.6  1  DUF3896        Protein of unknown function (DUF3896)
      0.057   13.3   0.2      0.082   12.8   0.2    1.2  1  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
      0.062   13.3   0.2      0.084   12.9   0.2    1.1  1  DUF2532        Protein of unknown function (DUF2532)
      0.068   13.2   0.1       0.11   12.5   0.1    1.3  1  DBD_Tnp_Mut    MuDR family transposase
      0.071   13.6   0.2       0.11   12.9   0.2    1.3  1  DUF16          Protein of unknown function DUF16
      0.073   13.3   2.3       0.12   12.6   2.3    1.3  1  XhlA           Haemolysin XhlA
       0.12   12.5   2.6       0.26   11.4   2.6    1.6  1  bZIP_1         bZIP transcription factor
       0.13   12.1   0.3       0.24   11.3   0.3    1.4  1  Macscav_rec    Macrophage scavenger receptor
       0.56   10.0   3.0        2.5    7.9   3.0    1.9  1  DivIC          Septum formation initiator


Domain annotation for each model (and alignments):
>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.7     1e-06    0.0015      60     100 ..      17      58 ..      12      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                                   XXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHHHHHHHH CS
                    Laminin_II  60 svkkLeklapqLldklkelkqleeasss.lsdniseikelIa 100
                                   s ++Le+++ +L dk+++l + + a++  l+ +i++ik lI+
  gi|70607248|ref|YP_256118.1|  17 SASELEEEVKKLSDKVNNLVTDSRAQNEeLKTEINNIKSLIS 58 
                                   6789***************9999997779************7 PP

>> T3SS_needle_F  Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.1    0.0076        11       5      37 ..      25      57 ..      21      59 .. 0.88
   2 !    8.1   0.0     0.002         3      11      44 ..      70     101 ..      69     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0076
                                  HHHHHCCTHHHHHHHHHHHHHHHHSTTXHHHHH CS
                 T3SS_needle_F  5 asalsqkvskaekelqdalealkadpsdPaaLa 37
                                  +++ls+kv+++  + +++ e lk+++++ ++L+
  gi|70607248|ref|YP_256118.1| 25 VKKLSDKVNNLVTDSRAQNEELKTEINNIKSLI 57
                                  6899******************99***998887 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.002
                                   CTHHHHHHHHHHHHHHHHSTTXHHHHHHHHHHHH CS
                 T3SS_needle_F  11 kvskaekelqdalealkadpsdPaaLakvQfklq 44 
                                   k+++ + +++++ +a   ++sdP++L   Q  ++
  gi|70607248|ref|YP_256118.1|  70 KAKTCKHSVNEKCNAW--NISDPEKLGIPQEYVS 101
                                   57888999********..********88887665 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.4   2.9e-05     0.043       4      35 ..      20      55 ..      18      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                     FlaC_arch  4 elEnklsklsteletv....kkeneelsksveelke 35
                                  elE++++kls +++++    +++neel+++++++k 
  gi|70607248|ref|YP_256118.1| 20 ELEEEVKKLSDKVNNLvtdsRAQNEELKTEINNIKS 55
                                  9**********8777655559************996 PP

>> DUF3896  Protein of unknown function (DUF3896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     5e-05     0.075      13      46 ..      20      54 ..      11      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5e-05
                       DUF3896 13 yleekkqqlCkklssl.tlskkereqlkleidnye 46
                                   lee  ++l +k+++l t s+ + e lk ei+n  
  gi|70607248|ref|YP_256118.1| 20 ELEEEVKKLSDKVNNLvTDSRAQNEELKTEINNIK 54
                                  5899999********845689999********976 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.5e-05     0.082      85     124 ..      18      57 ..      10      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                                   TTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XX CS
                 Mt_ATP-synt_D  85 teevdaeekevkkeikefkeeskkrieelekeleklksll 124
                                   ++e+++e k+   ++++ +++s ++ eel+ e++++ksl+
  gi|70607248|ref|YP_256118.1|  18 ASELEEEVKKLSDKVNNLVTDSRAQNEELKTEINNIKSLI 57 
                                   5899**********************************98 PP

>> DUF2532  Protein of unknown function (DUF2532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.6e-05     0.084      66     125 ..      20      79 ..      14      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                       DUF2532  66 kihekykqfylqhnnklsdfsmqflekkseinsvetlisgflkfcednfqtskskshsln 125
                                   ++ e+ k++  + nn ++d   q  e k+ein +++lis +     + +  +k+  hs+n
  gi|70607248|ref|YP_256118.1|  20 ELEEEVKKLSDKVNNLVTDSRAQNEELKTEINNIKSLISWLSIARSQGIWKAKTCKHSVN 79 
                                   567889999999***************************887777788888888888887 PP

>> DBD_Tnp_Mut  MuDR family transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.3e-05      0.11      14      48 ..      51      85 ..      48      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-05
                   DBD_Tnp_Mut 14 eelrkalkkyaIahhrefrvvksdksrytvrCeke 48
                                  ++++  + + +Ia+ + ++ +k+ k+ +  +C+++
  gi|70607248|ref|YP_256118.1| 51 NNIKSLISWLSIARSQGIWKAKTCKHSVNEKCNAW 85
                                  678999**************************988 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   7.6e-05      0.11      50      89 ..      18      57 ..       9      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                         DUF16 50 inkleqkvekqgekikelkveqkaqgeelnkvdetlelil 89
                                   ++le++v+k+ +k+++l  +  aq+eel++  + +++++
  gi|70607248|ref|YP_256118.1| 18 ASELEEEVKKLSDKVNNLVTDSRAQNEELKTEINNIKSLI 57
                                  6789************************997666666655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.3   7.8e-05      0.12       8      46 ..      20      58 ..      15      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                          XhlA  8 rietkldnleervdkleekaaeaeekiknleedlkkles 46
                                  ++e+++++l+++v+ l  +++ + e++k   +++k+l s
  gi|70607248|ref|YP_256118.1| 20 ELEEEVKKLSDKVNNLVTDSRAQNEELKTEINNIKSLIS 58
                                  789*********999999999999998887777776644 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   0.00017      0.26      25      57 ..      22      58 ..      17      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                  HHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH CS
                        bZIP_1 25 qaeieeLerrvkaLe....keNksLkseleelkkeve 57
                                  ++e+++L+++v  L     ++N++Lk e++++k  ++
  gi|70607248|ref|YP_256118.1| 22 EEEVKKLSDKVNNLVtdsrAQNEELKTEINNIKSLIS 58
                                  58999*******9973333689999999999998876 PP

>> Macscav_rec  Macrophage scavenger receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00016      0.24       1      29 [.      21      49 ..      21      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                   Macscav_rec  1 lEkrIqkiSDleanLidsehFqNfSvttd 29
                                  lE++++k+SD   nL+   + qN  ++t+
  gi|70607248|ref|YP_256118.1| 21 LEEEVKKLSDKVNNLVTDSRAQNEELKTE 49
                                  7*******************9*9877775 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.0    0.0017       2.5      18      53 ..      17      55 ..      14      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                                  HHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHCC-XXX CS
                         DivIC 18 aykqlkqeiaalqaelakl....kaeneeLeaevkdLksd 53
                                  + ++l++e+++l +++++l    +a+neeL+ e+++ k +
  gi|70607248|ref|YP_256118.1| 17 SASELEEEVKKLSDKVNNLvtdsRAQNEELKTEINNIK-S 55
                                  56789999999999999886666899999999999985.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1851  (0.103241); expected 358.6 (0.02)
Passed bias filter:                     1263  (0.0704445); expected 358.6 (0.02)
Passed Vit filter:                       169  (0.00942607); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 860.87
//
Query:       gi|70607249|ref|YP_256119.1|  [L=108]
Description: hypothetical protein Saci_1505 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-08   33.0   0.5    9.8e-08   31.9   0.0    1.8  2  HTH_3           Helix-turn-helix
    0.00037   20.4   0.9    0.00092   19.1   0.1    2.1  2  HTH_11          HTH domain
     0.0017   18.2   0.0     0.0044   16.8   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
     0.0017   18.0   0.1      0.003   17.2   0.1    1.4  1  Sigma70_r4_2    Sigma-70, region 4
     0.0022   17.4   0.0     0.0039   16.6   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0051   16.9   2.1     0.0051   16.9   2.1    1.7  2  JIP_LZII        JNK-interacting protein  leucine zipper II
     0.0055   17.1   0.1       0.04   14.4   0.0    2.1  2  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0062   16.6   0.0      0.015   15.4   0.0    1.7  2  Trp_repressor   Trp repressor protein
     0.0066   16.3   4.2       0.63    9.9   1.2    3.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0092   16.2   0.0      0.021   15.0   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.015   15.6   0.0    1.2  1  HTH_31          Helix-turn-helix domain
      0.012   15.5   1.0      0.075   12.9   0.1    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
      0.013   15.4   0.0       0.02   14.8   0.0    1.4  1  MarR_2          MarR family
      0.019   14.5   0.1      0.019   14.5   0.1    3.7  4  HTH_24          Winged helix-turn-helix DNA-binding
      0.021   15.1   0.1      0.045   14.0   0.0    1.7  2  KORA            TrfB plasmid transcriptional repressor
      0.031   14.8   3.4       0.07   13.6   2.9    1.8  1  ParB            ParB family
      0.031   14.1   0.0      0.061   13.1   0.0    1.5  1  HTH_23          Homeodomain-like domain
      0.037   14.1   0.5       0.14   12.2   0.5    2.1  1  ENT             ENT domain
      0.041   13.7   0.2        3.6    7.5   0.0    2.7  3  LacI            Bacterial regulatory proteins, lacI family
      0.046   13.9   0.0      0.093   12.9   0.0    1.5  1  HTH_28          Helix-turn-helix domain
      0.094   12.3   0.1      0.099   12.2   0.1    1.1  1  FAD_binding_1   FAD binding domain
       0.11   12.8   0.2       0.16   12.3   0.2    1.4  1  Peptidase_Prp   Cysteine protease Prp


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.2e-10   9.8e-08       8      45 ..      21      58 ..      15      61 .. 0.91
   2 ?   -2.5   0.1       6.8   5.6e+03      38      46 ..      95     103 ..      93     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.2e-10
                                  TTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHH CS
                         HTH_3  8 lglsqeeLAeklGvsrstisriEnGernPsletlkkla 45
                                   + s++eLAe+l +s++++++  nG+++Ps +t++k  
  gi|70607249|ref|YP_256119.1| 21 ENRSKKELAEELEISPAAVTKFVNGITHPSDDTIEKAI 58
                                  689*******************************9965 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.8
                                   HHHHHHHHH CS
                         HTH_3  38 letlkklak 46 
                                   +e++kk+++
  gi|70607249|ref|YP_256119.1|  95 VEKIKKILN 103
                                   577888876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-06   0.00092       3      34 ..      13      41 ..      11      47 .. 0.90
   2 ?   -2.5   0.1       6.3   5.1e+03      34      45 ..      93     104 ..      91     106 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrr 34
                                   +i+e+Lle+r+    +eLAeeL++S ++v +
  gi|70607249|ref|YP_256119.1| 13 AKIIEILLENRS---KKELAEELEISPAAVTK 41
                                  69*********6...6*************976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.3
                        HTH_11  34 rdIkaLeelgvp 45 
                                   + ++++++++  
  gi|70607249|ref|YP_256119.1|  93 KKVEKIKKILNT 104
                                   556666666554 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-06    0.0044       9      34 ..      23      48 ..      14      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                YdaS_antitoxin  9 GgqkaLAealgvsqqaVsqWlkgkkq 34
                                  ++ k+LAe+l++s++aV ++++g + 
  gi|70607249|ref|YP_256119.1| 23 RSKKELAEELEISPAAVTKFVNGITH 48
                                  5899*****************98655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.6e-06     0.003       6      43 ..       2      39 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
                                  HHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                  Sigma70_r4_2  6 ealaeLperqreifllryleglsykEIAellgisegtV 43
                                  + +  L+++ r+ ++ + le+ s kE Ae+l+is+++V
  gi|70607249|ref|YP_256119.1|  2 RIIHNLSKDARAKIIEILLENRSKKELAEELEISPAAV 39
                                  67889*******************************99 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.8e-06    0.0039      11      44 ..       6      39 ..       5      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.8e-06
                  HTH_Tnp_ISL3 11 riTlrleayilelllesrsvkavArqlgvSwtTV 44
                                    +++++a+i+e lle+rs k+ A++l +S+  V
  gi|70607249|ref|YP_256119.1|  6 NLSKDARAKIIEILLENRSKKELAEELEISPAAV 39
                                  5799**************************9766 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.7     3e+03      17      20 ..      25      28 ..      12      41 .. 0.56
   2 !   16.9   2.1   6.3e-06    0.0051      19      58 ..      65     104 ..      61     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.7
                      JIP_LZII 17 Llet 20
                                   +e 
  gi|70607249|ref|YP_256119.1| 25 KKEL 28
                                  2222 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.3e-06
                      JIP_LZII  19 etknaLnvvkddLIarvdeLtsereiLreEleslqkaker 58 
                                   e ++ Ln+  dd++  v+eL +e++ + + +e+++k++++
  gi|70607249|ref|YP_256119.1|  65 EKREILNIIIDDIMISVEELVNEYKLVDKKVEKIKKILNT 104
                                   56889******************************99876 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   4.9e-05      0.04      12      45 ..      24      56 ..      20      58 .. 0.92
   2 ?    0.3   0.1       1.2     1e+03      11      20 ..      79      88 ..      68     104 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
                        HTH_26 12 tkseLargtgisaatlsrlvkgkpervsldtLdk 45
                                  +k+eLa+ ++is a ++++v+g ++ +s dt++k
  gi|70607249|ref|YP_256119.1| 24 SKKELAEELEISPAAVTKFVNG-ITHPSDDTIEK 56
                                  79********************.68999999987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                        HTH_26 11 itkseLargt 20
                                  i++ eL   +
  gi|70607249|ref|YP_256119.1| 79 ISVEELVNEY 88
                                  3555554444 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.015      37      79 ..      11      52 ..       7      62 .. 0.89
   2 ?   -1.1   0.0       2.6   2.1e+03      26      26 ..      77      77 ..      53     105 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                 Trp_repressor 37 qRlqvvkeLLkeelsqreIaeelgvSiAtItRvsrsLktgsde 79
                                  +R ++++ +L e++s +e+aeel++S A +t   + + + sd+
  gi|70607249|ref|YP_256119.1| 11 ARAKIIE-ILLENRSKKELAEELEISPAAVTKFVNGITHPSDD 52
                                  699****.999*********************99999987765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
                 Trp_repressor 26 l 26
                                  +
  gi|70607249|ref|YP_256119.1| 77 I 77
                                  2 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.2   0.00078      0.63       7      34 ..      14      39 ..       1      41 [. 0.73
   2 ?    1.8   0.1      0.26   2.1e+02       6      23 ..      67      84 ..      63      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                 HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestv 34
                                  kI+e+L e+  +s +eLAe++ +S+++v
  gi|70607249|ref|YP_256119.1| 14 KIIEILLEN--RSKKELAEELEISPAAV 39
                                  455555544..8899**********999 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                 HTH_AsnC-type  6 rkILeaLqedaRisyaeL 23
                                  r IL+++  d  is++eL
  gi|70607249|ref|YP_256119.1| 67 REILNIIIDDIMISVEEL 84
                                  89********99999997 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.021      24      44 ..      24      44 ..      17      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                  -HHHHHHHHTS-HHHHHHHHH CS
                Fe_dep_repress 24 ktkdlaerLnvspssVsemlk 44
                                  ++k+lae+L++sp+ V++ ++
  gi|70607249|ref|YP_256119.1| 24 SKKELAEELEISPAAVTKFVN 44
                                  679***************886 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.8e-05     0.015      15      52 ..      23      59 ..       9      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                        HTH_31 15 LsqeevAerlgvsestlsrlEqGrrgrpspavlealar 52
                                   s++e+Ae l +s++ +++  +G    ps +++e++ +
  gi|70607249|ref|YP_256119.1| 23 RSKKELAEELEISPAAVTKFVNGIT-HPSDDTIEKAIE 59
                                  699**********************.7*****998765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.1e-05     0.075       3      32 ..      11      39 ..       9      41 .. 0.85
   2 ?    1.1   0.1      0.47   3.8e+02       1      26 [.      63      89 ..      63      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHH CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstv 32
                                  +R kI+ +L e+ ++  elaeel++s+++v
  gi|70607249|ref|YP_256119.1| 11 ARAKIIEILLEN-RSKKELAEELEISPAAV 39
                                  799999999994.5558***********98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
                                  SHHHHHHHHHHTTSS.EEHHHHHHHHT CS
                         HTH_5  1 dptRlkILklLaege.lcvcelaeelg 26
                                  d+ +++IL++  +    +v el++e +
  gi|70607249|ref|YP_256119.1| 63 DEEKREILNIIIDDImISVEELVNEYK 89
                                  678899999988855357777777655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.5e-05      0.02      11      43 ..       4      44 ..       1      47 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                                  HHHHHCTTTS........EEEHHHHHHHHTSSHHHHHHHHH CS
                        MarR_2 11 LaaLgrrpgr........dltvgelarrlglsksavsrilk 43
                                  +++L    +         + + +ela++l +s++av++ ++
  gi|70607249|ref|YP_256119.1|  4 IHNLSKDARAkiieilleNRSKKELAEELEISPAAVTKFVN 44
                                  55555555446666555534899**************9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2       0.3   2.4e+02       7      23 ..       2      18 ..       1      21 [. 0.84
   2 ?   14.5   0.1   2.3e-05     0.019       7      38 ..      14      43 ..      10      44 .. 0.84
   3 ?    2.3   0.3      0.15   1.2e+02       5      15 ..      66      76 ..      62      87 .. 0.83
   4 ?   -0.4   0.1         1   8.4e+02       4      12 ..      97     105 ..      96     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.3
                        HTH_24  7 kILelLqknprisqreL 23
                                  +I+  L k++r  + e+
  gi|70607249|ref|YP_256119.1|  2 RIIHNLSKDARAKIIEI 18
                                  78889999999988887 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                        HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrl 38
                                  kI+e+L +  + s +eLAe+l +Sp++v++ +
  gi|70607249|ref|YP_256119.1| 14 KIIEILLE--NRSKKELAEELEISPAAVTKFV 43
                                  67777777..5599**************9876 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.15
                        HTH_24  5 drkILelLqkn 15
                                  +r+IL+++ ++
  gi|70607249|ref|YP_256119.1| 66 KREILNIIIDD 76
                                  699*****987 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1
                        HTH_24   4 tdrkILelL 12 
                                   + +kIL+++
  gi|70607249|ref|YP_256119.1|  97 KIKKILNTI 105
                                   579****98 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.5e-05     0.045      15      54 ..       6      45 ..       1      59 [. 0.87
   2 ?   -1.0   0.0       2.7   2.2e+03      29      29 ..      79      79 ..      46     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                          KORA 15 elaeqtveiargvLVegkkqadvatelgltkqavsqavkr 54
                                  +l ++ +  + ++L e+++++++a+el ++  av + v+ 
  gi|70607249|ref|YP_256119.1|  6 NLSKDARAKIIEILLENRSKKELAEELEISPAAVTKFVNG 45
                                  567888888999************************9985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                          KORA 29 V 29
                                  +
  gi|70607249|ref|YP_256119.1| 79 I 79
                                  2 PP

>> ParB  ParB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.9   8.6e-05      0.07      17      68 ..      27      79 ..      21     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                          ParB 17 kvaeklekkdvelseliekvkeei.ekvqsdtelaedeqkseilklikkeskr 68
                                  ++ae+le +  +++++++ +++   ++++++ e a+de+k eil++i  +   
  gi|70607249|ref|YP_256119.1| 27 ELAEELEISPAAVTKFVNGITHPSdDTIEKAIEIADDEEKREILNIIIDDIMI 79
                                  78999***************99761579999***************9766544 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.5e-05     0.061       3      36 ..       8      41 ..       6      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                        HTH_23  3 sereRlrillllaeGlsvreIAreLgvsrrTvyr 36
                                  s++ R++i+  l+e  s++e A+eL +s+  v +
  gi|70607249|ref|YP_256119.1|  8 SKDARAKIIEILLENRSKKELAEELEISPAAVTK 41
                                  6788*************************99875 PP

>> ENT  ENT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   0.00017      0.14       2      68 ..       2      86 ..       1     104 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                           ENT  2 rqLrrleleAYssvlsAfraqgdLseekkkllteLr......................keLsIsterHraelrrvksDerlkt 62
                                  r++++l ++A +++++ +       ++kk+l +eL                       k ++I++++ ++e+ ++  D+   +
  gi|70607249|ref|YP_256119.1|  2 RIIHNLSKDARAKIIEILLEN----RSKKELAEELEispaavtkfvngithpsddtieKAIEIADDEEKREILNIIIDDIMIS 80
                                  567777777777777766543....699************************************9999999999999998888 PP

                           ENT 63 iretis 68
                                  ++e+++
  gi|70607249|ref|YP_256119.1| 81 VEELVN 86
                                  887765 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.9   2.4e+03      26      38 ..       7      19 ..       4      22 .. 0.78
   2 ?    7.5   0.0    0.0044       3.6       3      38 ..      26      61 ..      26      65 .. 0.90
   3 ?    3.3   0.1     0.086        70      22      43 ..      86     107 ..      82     108 .] 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.9
                                  STHHHHHHHHHHH CS
                          LacI 26 VseetrerVeaam 38
                                   s++ r ++ +++
  gi|70607249|ref|YP_256119.1|  7 LSKDARAKIIEIL 19
                                  6888999999886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0044
                                  HHHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHHH CS
                          LacI  3 kDVArlAGVSkaTVSrvLnnkerVseetrerVeaam 38
                                  k++A++   S a+V++++n+  + s++t e+  +++
  gi|70607249|ref|YP_256119.1| 26 KELAEELEISPAAVTKFVNGITHPSDDTIEKAIEIA 61
                                  78999999********************99988877 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.086
                                   TSSSSTHHHHHHHHHHHHHTTB CS
                          LacI  22 nkerVseetrerVeaameelnY 43 
                                   n+++  ++  e++ ++++++ Y
  gi|70607249|ref|YP_256119.1|  86 NEYKLVDKKVEKIKKILNTITY 107
                                   7778889999*******99988 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.093       2      31 ..      12      41 ..      11      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                        HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyr 31
                                  R++ii+ l++ +s +e+A+el is+  v +
  gi|70607249|ref|YP_256119.1| 12 RAKIIEILLENRSKKELAEELEISPAAVTK 41
                                  99***********************99976 PP

>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012     0.099      87     148 ..      25      89 ..       2     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                   S--SSSSSEEHHHHHHHTB--SS---HHHHHHHGGG-SSHHHHHHHHHHHH-...HHHHHTTTTT CS
                 FAD_binding_1  87 ekeprleptTlrqalkyylditgppskqlleaLaefaseeeekqkLekLssd...egakeykelk 148
                                   +ke  +e     +a++++++ ++ ps   +e+ +e a +ee+++ L++++ d     ++ ++e k
  gi|70607249|ref|YP_256119.1|  25 KKELAEELEISPAAVTKFVNGITHPSDDTIEKAIEIADDEEKREILNIIIDDimiSVEELVNEYK 89 
                                   45555555556689999********************************9997653333333333 PP

>> Peptidase_Prp  Cysteine protease Prp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00019      0.16      34      86 ..      37      89 ..       6      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                  HHHHHHHHHHHHHHHHHS----....TTTTSHHHHHHHHHHHHHHHHHHHH-T CS
                 Peptidase_Prp 34 AavSalvittvnaleevlkekveleeseeekekaqllletlvlgLeeieeeyp 86
                                  Aav+  v ++ +  ++  ++++e+ ++ee++e ++++++ +++++ee+ +ey+
  gi|70607249|ref|YP_256119.1| 37 AAVTKFVNGITHPSDDTIEKAIEIADDEEKREILNIIIDDIMISVEELVNEYK 89
                                  55555555555555567777777777*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 768.60
//
Query:       gi|70607250|ref|YP_256120.1|  [L=293]
Description: hypothetical protein Saci_1506 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2270.12
//
Query:       gi|70607251|ref|YP_256121.1|  [L=399]
Description: aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-41  141.0   0.0    5.8e-41  140.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      1e-09   37.7   0.0    1.4e-09   37.3   0.0    1.1  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
     0.0015   18.0   0.0     0.0024   17.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.016   13.8   0.0      0.028   13.0   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.037   13.3   0.0      0.058   12.7   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
        0.1   12.7   0.8       0.33   11.1   0.8    1.8  1  Mst1_SARAH       C terminal SARAH domain of Mst1


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.0     2e-44   5.8e-41       2     361 ..      29     389 ..      28     391 .. 0.91

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2e-44
                                   EEEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                 Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                   +vi L+ + +  d  + +++e++k +++   ++ ++  +y+ + g  e++ +l  + + + +++  ++++v  + G+++++
  gi|70607251|ref|YP_256121.1|  29 NVISLAGGLPAPD--TFPVEEIKKITQDiLDNDPEKGLQYTATAGISEFRRELVNLSN-KRGITGINDRNVFATVGSQEAL 106
                                   6777777777666..669999999999977777888899*******************.6677777777************ PP

                                   HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEE.EEESS-TTT CS
                 Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvi.lvesphNPt 161
                                    +++ ll ++pgd+++v  p+y    nilr ++  ++ ++++   + +ldl++le+++k+  ++ kk+k++ ++ +++NP 
  gi|70607251|ref|YP_256121.1| 107 FMIFNLL-VDPGDVVIVEMPSYLAALNILRSRKPIFIGVNVK---ENGLDLDELETKIKKSISEGKKPKLLyVIPTAQNPA 183
                                   *******.9*******************************66...77***************9999999994579****** PP

                                   --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHH CS
                 Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsq 242
                                   Gt ++l + + ll++a+ y +l++ D+aY+ +vf+   + + +  +++   ++ ++++sK + ++G+R+G+i++n+++++ 
  gi|70607251|ref|YP_256121.1| 184 GTTMNLSDRKRLLEIAENYDILVVEDDAYGFLVFDGDNPPP-LKALDKSGRVIYTSTFSKIL-APGFRLGWIVANEEFIKN 262
                                   **********************************9766555.7777777789********98.6***************** PP

                                   HHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...TEEEECCSCSSEEEEEETHH.CH CS
                 Aminotran_1_2 243 lrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael...glkvlasqsgmflltdlsae.ta 317
                                   ++  ++++    +s +q ++++a++    +++++ + rq + ++r+++ d++++    +  + ++ +gmf++  l+++ + 
  gi|70607251|ref|YP_256121.1| 263 VEMYKQNVDLhtPSFTQMIAMEAIKRGV-IERQIPKIRQIYRHKRDVMLDAINKYfpkDARWSKPVGGMFVFAWLDKKiDT 342
                                   ******998899************9977.456********************999***********************877 PP

                                   HHHHHHHHHTCTEEEEEGGGGTS....TTEEEEECTTS-HHHHHHHHH CS
                 Aminotran_1_2 318 kelskkLleevgvyvtpgtsftv....pgrlRitvAglteeeleelve 361
                                   +++ ++ +++ gv+ +pg sf++    ++  R++++  te++le++++
  gi|70607251|ref|YP_256121.1| 343 TKMLEEAVKR-GVAYVPGASFYYdysgRNTMRLNFSYPTESDLEKAIQ 389
                                   7777778888.**************99999***************997 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   4.7e-13   1.4e-09     127     410 ..     120     396 ..     113     399 .] 0.80

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 4.7e-13
                                   EEEEES--HHHHHHHHHHT-EEEEEEEETTEE-HHHHH....HHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT--- CS
                Aminotran_MocR 127 llvtvpGydrhfllleelGielltvdlqddGpdvdave....klvaedasvkGilavpkysnptGetiseevarrlaalka 203
                                   ++v +p y   + +l++    ++ v+++++G d+d +e    k ++e    k ++++p+  np+G+t+     +rl  +  
  gi|70607251|ref|YP_256121.1| 120 VIVEMPSYLAALNILRSRKPIFIGVNVKENGLDLDELEtkikKSISEGKKPKLLYVIPTAQNPAGTTMNLSDRKRLLEIA- 199
                                   689999999999999999999*************9765111156667777899***********************9884. PP

                                   SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S-- CS
                Aminotran_MocR 204 aapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkylGlqsiGp 284
                                      d  +  dday    lv ++d+ + + al ++     r +  ++ ski   G  ++ + + e+ i+ ++ y     +  
  gi|70607251|ref|YP_256121.1| 200 ENYDILVVEDDAYGF--LVFDGDNPPPLKALDKS----GRVIYTSTFSKILAPGFRLGWIVANEEFIKNVEMYKQNVDLHT 274
                                   5689999******86..77799998888777654....466666666**************************99999988 PP

                                   -HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EE..EEESSS-HHHHHHHHHH CS
                Aminotran_MocR 285 dkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyfis..ldtldgvakrvvklaee 363
                                     + q+  +  +k    +e ++ + +++ + k + +l+++++ +   + a w++p GG f+   ld    +  ++++ a +
  gi|70607251|ref|YP_256121.1| 275 PSFTQMIAMEAIKR-GVIERQIPKIRQIYRHKRDVMLDAINKYFP--KDARWSKPVGGMFVFawLDKKIDT-TKMLEEAVK 351
                                   89999887776653.245777888888888888888888887764..679*********995224443332.356677888 PP

                                   CTEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHHHHHHH CS
                Aminotran_MocR 364 aGvsltaaGatypaGedpkdrnirlaptlppleevetamdvvatcvk 410
                                    Gv+  + Ga++ +    ++  +rl  + p+  ++e+a++ +++ +k
  gi|70607251|ref|YP_256121.1| 352 RGVAYVP-GASFYYDYSGRN-TMRLNFSYPTESDLEKAIQILSSVIK 396
                                   9***987.788887766665.49*****************9988876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     8e-07    0.0024      47     147 ..     102     212 ..      73     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8e-07
                                   HHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE.............EE CS
               DegT_DnrJ_EryC1  47 GtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert.............ka 114
                                     +Al ++ + l v+pgd VIv   +++a  n  +    kp+f+ v+ +   +d +++e +i +                a
  gi|70607251|ref|YP_256121.1| 102 SQEALFMIFN-LLVDPGDVVIVEMPSYLAALNILRS--RKPIFIGVNVKENGLDLDELETKIKKSIsegkkpkllyvipTA 179
                                   4455555554.5699***************998765..69*********************99988899999887666666 PP

                                   EEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT CS
               DegT_DnrJ_EryC1 115 IlpVhlyGqvadmdalkaiaakhglkvieDaAh 147
                                     p+ +  + +d ++l +ia+++++ v+eD A 
  gi|70607251|ref|YP_256121.1| 180 QNPAGTTMNLSDRKRLLEIAENYDILVVEDDAY 212
                                   666667777778889***************875 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.2e-06     0.028      70     175 ..      96     211 ..      87     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.2e-06
                                   EEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEE..EESTTSHH.HHHHHCCT..TEEEEEE. CS
               Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievk..fvdtsdle.elekaike..ntklvyl. 143
                                   ++a+   + A+++++  l+  Gd ++v+   Y  + ++l++  +  +g++vk    d ++le +++k i+e  + kl+y+ 
  gi|70607251|ref|YP_256121.1|  96 VFATVGSQEALFMIFNLLVDPGDVVIVEMPSYLAALNILRSRKPIfIGVNVKenGLDLDELEtKIKKSISEgkKPKLLYVi 176
                                   6677777889999999999********************998877444444411556655442677777778899****74 PP

                                   ESS-TT...TT----HHHHHHHHHHTT-EEEEEGT CS
               Cys_Met_Meta_PP 144 Etptnp...llkvvDiekiaklakkagvlvvvDnt 175
                                    t  np   ++++ D ++++++a + ++lvv D +
  gi|70607251|ref|YP_256121.1| 177 PTAQNPagtTMNLSDRKRLLEIAENYDILVVEDDA 211
                                   45556544489*******************99976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.058     100     169 ..     143     211 ..      93     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                   EE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
               Beta_elim_lyase 100 dlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                    ++ ke + +dl++le +ik+  +  +k+kl+++  T +  +G+ + l   +++ +ia++y+i ++ D A
  gi|70607251|ref|YP_256121.1| 143 GVNVKE-NGLDLDELETKIKKSISEGKKPKLLYVIPTAQNPAGTTMNLSDRKRLLEIAENYDILVVEDDA 211
                                   455666.789**********9544889*************************************998865 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.8   0.00011      0.33      23      46 ..     291     314 ..     286     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                    Mst1_SARAH  23 MEqEieelrkrYqaKRqPIlDAie 46 
                                   +E+ i ++r+ Y++KR  +lDAi+
  gi|70607251|ref|YP_256121.1| 291 IERQIPKIRQIYRHKRDVMLDAIN 314
                                   699********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3042.37
//
Query:       gi|70607252|ref|YP_256122.1|  [L=264]
Description: competence damage-inducible protein A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-27   96.4   0.0    1.8e-27   95.8   0.0    1.3  1  MoCF_biosynth    Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.014   15.4   1.0      0.057   13.5   0.1    2.3  3  DUF4261          Domain of unknown function (DUF4261)
      0.094   12.3   0.4       0.18   11.3   0.0    1.6  2  VirArc_Nuclease  Viral/Archaeal nuclease
        0.1   12.9   0.5         26    5.1   0.0    3.1  3  CotJB            CotJB protein


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0     4e-31   1.8e-27       1     142 [.       7     172 ..       7     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 4e-31
                                   EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHHHHHH CS
                 MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpealak 80 
                                   ++it+G+e+lsgk+ +tn++ +a+++ +lg+ v+++t+v Dd+eei+  +++a++++  +ii+tGG+Gpt dD t e la 
  gi|70607252|ref|YP_256122.1|   7 EIITIGNEILSGKTINTNASHIARRILSLGYVVRRITTVMDDIEEISLVFKEAINRKpKLIISTGGLGPTYDDKTSEGLAL 87 
                                   59************************************************99999999*********************** PP

                                   HHSEE-HHHHHHHHHHHHHHCC........................TTSHGGGGGGE.EETTE.EEEE-SSHHHHHHHHHH CS
                 MoCF_biosynth  81 lfekelegfeeafrrvslkpgk........................pvgvapgailsravgkt.iigLPGspkavkealee 136
                                   +++ + e ++ a +++  k++k                        + g+apg+++ ++ +   i++ PG+p++++ +le+
  gi|70607252|ref|YP_256122.1|  88 ALGVSFEINKDAYEMIVEKYKKrglplteervkmakmpagaapvrnDEGIAPGIYILHK-D-IeILATPGVPREMENVLEN 166
                                   ********************99***************8888888888888888877765.4.45***************** PP

                                   HHHGGH CS
                 MoCF_biosynth 137 illpal 142
                                   +++  l
  gi|70607252|ref|YP_256122.1| 167 FIKYHL 172
                                   *96555 PP

>> DUF4261  Domain of unknown function (DUF4261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.81   3.6e+03      37      50 ..       9      22 ..       8      30 .. 0.77
   2 ?   13.5   0.1   1.3e-05     0.057      10      43 ..     145     178 ..     143     182 .. 0.94
   3 ?   -1.5   0.0      0.65   2.9e+03       9      30 ..     220     243 ..     217     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.81
                       DUF4261 37 lengvelkdGdTig 50
                                  ++ g+e+ +G Ti 
  gi|70607252|ref|YP_256122.1|  9 ITIGNEILSGKTIN 22
                                  66689999999995 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                       DUF4261  10 lpdlevhfsglepeevvellyniasYilengvel 43 
                                   + d+e++++ + p e  ++l n+  Y l+n +++
  gi|70607252|ref|YP_256122.1| 145 HKDIEILATPGVPREMENVLENFIKYHLKNRPNI 178
                                   68****************************9998 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.65
                       DUF4261   9 glpdlevhf..sglepeevvelly 30 
                                   ++p+lev    s+ + ee+ ++ +
  gi|70607252|ref|YP_256122.1| 220 DKPELEVQVagSSTDKEEITRIVN 243
                                   566655543337788888877765 PP

>> VirArc_Nuclease  Viral/Archaeal nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.77   3.4e+03      62      75 ..      95     108 ..      90     110 .. 0.83
   2 ?   11.3   0.0   4.1e-05      0.18      61     112 ..     194     246 ..     169     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.77
               VirArc_Nuclease  62 inedyykdlldkyd 75 
                                   in+d y+ + +ky+
  gi|70607252|ref|YP_256122.1|  95 INKDAYEMIVEKYK 108
                                   89999999999995 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.1e-05
               VirArc_Nuclease  61 vinedyykdlldkydltlyvkak..dryypllyidvtGssfteeqskkrygeai 112
                                    i   y k+l +ky+l +  + +  +   p l + v+Gss  +e+ ++  +e i
  gi|70607252|ref|YP_256122.1| 194 TI-APYVKELVKKYNLYIKTHPRskEMDKPELEVQVAGSSTDKEEITRIVNECI 246
                                   44.3699*********7777654337778***********88888766666665 PP

>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.02        92      37      61 ..      96     120 ..      91     125 .. 0.83
   2 ?    0.1   0.0      0.21   9.6e+02      28      57 ..     161     190 ..     158     200 .. 0.84
   3 ?    5.1   0.0    0.0057        26      15      30 ..     204     219 ..     198     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.02
                         CotJB  37 yskkrkelkkeYeekygPLtldgvs 61 
                                    ++ +++++++Y+++  PLt + v+
  gi|70607252|ref|YP_256122.1|  96 NKDAYEMIVEKYKKRGLPLTEERVK 120
                                   5678999*************98765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.21
                         CotJB  28 kealelfnkyskkrkelkkeYeekygPLtl 57 
                                   +++le f ky+ k +  ++ Ye+++  L +
  gi|70607252|ref|YP_256122.1| 161 ENVLENFIKYHLKNRPNISYYENSFLLLGV 190
                                   68999999***9999999999999977755 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0057
                         CotJB  15 vdlnLYLDthPddkea 30 
                                   +  nLY+ thP  ke+
  gi|70607252|ref|YP_256122.1| 204 KKYNLYIKTHPRSKEM 219
                                   5689********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2028.88
//
Query:       gi|70607253|ref|YP_256123.1|  [L=542]
Description: phenylalanyl-tRNA synthetase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-33  114.1   0.0    1.3e-32  113.0   0.0    1.5  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    3.2e-19   69.0   0.4    2.1e-16   60.0   0.1    2.8  2  B5               tRNA synthetase B5 domain
    2.4e-14   53.4   0.2    7.7e-14   51.7   0.1    1.9  2  B3_4             B3/4 domain
     0.0035   17.5   0.3         11    6.3   0.0    3.9  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   4.8e+03     200     212 ..      74      86 ..      68      89 .. 0.90
   2 !  113.0   0.0   2.9e-36   1.3e-32      11     214 .]     352     536 ..     345     536 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
               tRNA_synthFbeta 200 afdlkqrvyvfEl 212
                                   ++d+kq vy fE+
  gi|70607253|ref|YP_256123.1|  74 KYDIKQSVYSFEV 86 
                                   79*******9996 PP

  == domain 2  score: 113.0 bits;  conditional E-value: 2.9e-36
               tRNA_synthFbeta  11 tegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNla 91 
                                   t g+l+ e +l r+lrdl +gaG++E++t+ + ++k+l++          v + nP++ +++++R sL+p+lL+ l++N++
  gi|70607253|ref|YP_256123.1| 352 T-GKLSAETELIRTLRDLSIGAGFSEIFTFILSNDKRLRNE--------YVSIVNPVTVEYNAVRNSLIPTLLNFLKYNQH 423
                                   4.459999*****************************9766........9******************************* PP

               tRNA_synthFbeta  92 rgnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpa 171
                                     ++ v +FEig+v++kd +++++++++ +   ++++++           v+++dl   v ++l sl i + ++++  + +
  gi|70607253|ref|YP_256123.1| 424 AIMP-VYVFEIGDVVIKDkRTDTGYKNSLRAVYGIMNSK-----------VNYEDLQSRVHQILMSLDI-EPTYKTYLDDM 491
                                   ****.**********************************...........*******************.999******** PP

               tRNA_synthFbeta 172 lhpgrsAeikv..dgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                   + pgr A+i    + +e+Gv+Ge++p +le+++++ +v++ E+ l
  gi|70607253|ref|YP_256123.1| 492 FIPGRGAKIIDtsKSVEIGVIGEINPVLLEELEIEFPVVISEIYL 536
                                   *********8733556**************************975 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0     0.003        13      14      51 ..      15      52 ..       8      59 .. 0.92
   2 !   60.0   0.1   4.6e-20   2.1e-16       1      67 []     274     339 ..     274     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                                  S---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5 14 idlseeeiikiLkrlgceriekdkdlllVtvPswRsDl 51
                                  +++s+++ +++L +l+ e++  d+d ++++v + R+Dl
  gi|70607253|ref|YP_256123.1| 15 LKISDNQLEELLFKLKSEVKPIDADHVEIEVNNDRPDL 52
                                  689**********************************8 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 4.6e-20
                                   EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5   1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                   vs+++++i+k lGi+ls +ei+k+L+   +++ +  +d+++VtvP++R+D++ ++Dl+EE+a+ +GY
  gi|70607253|ref|YP_256123.1| 274 VSVSANYISKNLGINLSLNEIEKYLRMARFDT-KVLNDVVEVTVPPYRVDILSQIDLVEEIAMTIGY 339
                                   6899**************************96.*********************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.1   1.7e-17   7.7e-14       2     133 ..      92     235 ..      91     241 .. 0.88
   2 ?   -2.0   0.0      0.54   2.4e+03      89     109 ..     434     461 ..     385     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.7e-17
                                   SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBT.EEEEEE--TTEEE CS
                          B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqg.divvrlakegekl 76 
                                   +p+++a +++++k + +s               +  ++  ++++++ +g+     +++++Dldki+  +i  +  + + k+
  gi|70607253|ref|YP_256123.1|  92 RPYAVAGIVKDIKLDDES---------------LRELIQFQEKLHITVGRkrkkvAIGIHDLDKITStKIYYKPLPLDYKF 157
                                   789999999999999999...............999******************************779998888889999 PP

                                   EBTTS-EEEE.-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHH CS
                          B3_4  77 vtldgkerel.de...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsir 133
                                   ++l++++    +e                     + i+ +++ v s+++++++++++++e+T+n+f+ +++ + +++ 
  gi|70607253|ref|YP_256123.1| 158 IPLNQSKLMTiKEvieqtpqgreygnisiydgLSPAIVEENGDVlSIPPIINSDKTRIDEKTRNIFIDVTGTSFEAVS 235
                                   99997755553559999999****999999988888888899999************************997766665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.54
                                   TSEEEETE......EEEE.EETTTEEBT CS
                          B3_4  89 edlviads......ekpv.slagvmgge 109
                                   +d+vi d+      ++ + +++g+m+++
  gi|70607253|ref|YP_256123.1| 434 GDVVIKDKrtdtgyKNSLrAVYGIMNSK 461
                                   7788888656666566677888888875 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0025        11       1      43 [.       1      41 [.       1      68 [. 0.75
   2 ?    2.7   0.0     0.032   1.5e+02       3      26 ..     273     296 ..     272     300 .. 0.91
   3 !    4.7   0.0    0.0079        36      35      79 ..     291     335 ..     284     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0025
                     PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeee 43
                                  MPti   k +L+++l  ++++++le+llf++  E+  i  ++ 
  gi|70607253|ref|YP_256123.1|  1 MPTIVSYKWTLINNL--KISDNQLEELLFKLKSEVKPIDADHV 41
                                  999999999999988..68999******998877766666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
                     PhetRS_B1   3 tisvkkeaLfkalgkelteeeled 26 
                                   t+sv+++++ k+lg +l+ +e+e+
  gi|70607253|ref|YP_256123.1| 273 TVSVSANYISKNLGINLSLNEIEK 296
                                   9****************9999886 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0079
                     PhetRS_B1  35 lDeiveeeekkkadkkseeviykidipAnryDLLcleglaralkv 79 
                                   l ei++    ++ d+k  + ++ + +p  r D+L+   l++ +++
  gi|70607253|ref|YP_256123.1| 291 LNEIEKYLRMARFDTKVLNDVVEVTVPPYRVDILSQIDLVEEIAM 335
                                   445554444566788889999**************9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4013.72
//
Query:       gi|70607254|ref|YP_256124.1|  [L=465]
Description: phenylalanyl-tRNA synthetase subunit alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-80  270.3   0.0      2e-80  269.8   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    9.8e-08   31.8   2.8    1.3e-06   28.1   0.6    2.7  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.9e-07   30.8   0.0    6.4e-06   25.8   0.0    2.3  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    4.3e-06   26.8   0.1    1.5e-05   25.1   0.1    1.9  1  HTH_34           Winged helix DNA-binding domain
    6.4e-06   25.6   0.2    2.1e-05   24.0   0.2    2.0  1  HTH_24           Winged helix-turn-helix DNA-binding
    0.00051   19.2   0.1       0.22   10.6   0.0    2.7  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    0.00055   19.7   0.0     0.0014   18.4   0.0    1.6  1  HTH_IclR         IclR helix-turn-helix domain
    0.00056   19.8   0.3     0.0073   16.2   0.1    2.7  2  MarR             MarR family
     0.0048   17.4   0.1      0.063   13.8   0.0    2.9  4  HTH_27           Winged helix DNA-binding domain
     0.0069   16.7   0.4       0.81   10.1   0.0    2.9  3  Penicillinase_R  Penicillinase repressor
     0.0078   16.1   2.2      0.024   14.5   0.0    2.9  3  MarR_2           MarR family
  ------ inclusion threshold ------
      0.014   15.5   0.9      0.014   15.5   0.9    2.2  2  DUF2250          Uncharacterized protein conserved in archaea


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.8   0.0   1.3e-83     2e-80       2     244 ..     199     460 ..     198     461 .. 0.98

  Alignments for each domain:
  == domain 1  score: 269.8 bits;  conditional E-value: 1.3e-83
                                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-...... CS
                  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka...... 76 
                                   ++v++  ++   +k+h +++++e++k+++ elgf+ev+  ++e e+ynfd L++ qdhpaR+++d+F ++   k+      
  gi|70607254|ref|YP_256124.1| 199 YNVEALPPYFPLAKKHFFRDFIEKLKDVMKELGFTEVNAGYIEMELYNFDLLFQAQDHPAREIHDSFRVDGLGKIdderll 279
                                   899999999999*********************************************************77777799**** PP

                                   ..................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--H CS
                  tRNA-synt_2d  77 ..................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsl 138
                                                     ++++l+LR++ttav++r l ++++ p+k +s+g+vfR d++Dathl+eFhq++g+++++++s+
  gi|70607254|ref|YP_256124.1| 280 keikemhekgwkyswdpqIAKRLVLRSQTTAVTARILsSRPSVPFKGFSLGKVFRPDSIDATHLIEFHQLDGVIIQKEFSF 360
                                   ******************999****************88999*************************************** PP

                                   HHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHH CS
                  tRNA-synt_2d 139 adlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGve 219
                                   +dl+g+l+e++ k+ g + +++f+p yfpftePs+ev   +  ++ +w+E+ gaG++rpe+l+a++i  + ++ a+G+G++
  gi|70607254|ref|YP_256124.1| 361 TDLLGILREIFYKI-GIK-EIKFKPGYFPFTEPSVEVYGKI--EGLGWVEMSGAGLLRPEILKAMDI--DANAGAWGIGID 435
                                   **************.***.********************99..************************..99********** PP

                                   HHHHHHHT-SSGHHHHTT.HHHHGG CS
                  tRNA-synt_2d 220 RlamlkygieDiRelvendlrflrq 244
                                   Rlaml +g++DiR l+ nd++flr+
  gi|70607254|ref|YP_256124.1| 436 RLAMLLFGLKDIRLLYANDIDFLRK 460
                                   ***********************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.6     9e-10   1.3e-06       6      60 ..       2      56 ..       2      63 .. 0.92
   2 ?    2.4   0.1     0.096   1.4e+02      35      59 ..     138     162 ..     127     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9e-10
                                  HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                          TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                  Lse+E+k+  +L  +++a+a+ei++elg+p s++ +  + Le+kG+V++ +++  
  gi|70607254|ref|YP_256124.1|  2 LSENEIKILSYLKLKKKANAEEISKELGLPLSSIFSLAKLLEEKGYVKIGERKII 56
                                  89**********************************************9887655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.096
                                   SCHCHHHHHHHHHHCTSEEEESSTT CS
                          TrmB  35 prskvYevLrsLedkGlVerekgrp 59 
                                   p+s   +vL++L+++ l++r+++++
  gi|70607254|ref|YP_256124.1| 138 PESADEKVLQELLSRKLITRKEESK 162
                                   5566679*************99875 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.058        87      16      37 ..     214     235 ..     204     260 .. 0.85
   2 !   25.8   0.0   4.3e-09   6.4e-06      96     207 ..     323     427 ..     303     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.058
               tRNA_synthFbeta  16 nkeqklrrklrdllagaGlnEv 37 
                                   +  +++ +kl+d++ ++G++Ev
  gi|70607254|ref|YP_256124.1| 214 HFFRDFIEKLKDVMKELGFTEV 235
                                   5568899**************8 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 4.3e-09
               tRNA_synthFbeta  96 dvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpalhpg 175
                                    ++ F +gkvf++d  + +   e ++l +v+ +k+           ++f dl gi+++++ ++gi++++f+p   p+ +p 
  gi|70607254|ref|YP_256124.1| 323 PFKGFSLGKVFRPDsIDATHLIEFHQLDGVIIQKE-----------FSFTDLLGILREIFYKIGIKEIKFKPGYFPFTEPS 392
                                   4889**********877899***************...........**********************************7 PP

               tRNA_synthFbeta 176 rsAeikvdgk...evGvlGelhpevleafdlkqrv 207
                                        k++g    e+  +G l pe+l+a+d+++++
  gi|70607254|ref|YP_256124.1| 393 VEVYGKIEGLgwvEMSGAGLLRPEILKAMDIDANA 427
                                   655555544344577778************99876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   9.7e-09   1.5e-05       3      71 ..       7      70 ..       6      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.7e-09
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71
                                  +++lsyL  +++a+++e++++l++  + + + +k Le++gY+++        + + +++T+eG+++ k+
  gi|70607254|ref|YP_256124.1|  7 IKILSYLKLKKKANAEEISKELGLPLSSIFSLAKLLEEKGYVKIGER-----KIIRFELTEEGKKRLKE 70
                                  689***************************************99654.....5666999****999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   1.4e-08   2.1e-05       1      48 []       2      49 ..       2      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  l+e+++kIL++L+ + + +  e++++lgl++s +    k Lee+G++k
  gi|70607254|ref|YP_256124.1|  2 LSENEIKILSYLKLKKKANAEEISKELGLPLSSIFSLAKLLEEKGYVK 49
                                  6799******************************************97 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.5   5.2e+03      29      45 ..     220     236 ..     216     239 .. 0.83
   2 !    5.5   0.0    0.0049       7.4      95     120 ..     327     351 ..     323     380 .. 0.75
   3 !   10.6   0.0   0.00014      0.22     283     307 ..     426     450 ..     416     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.5
                                   HHHHHHHHHHTT-EE-- CS
                                   xxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  29 tkavrkyleengfieie 45 
                                   ++ ++++++e gf+e++
  gi|70607254|ref|YP_256124.1| 220 IEKLKDVMKELGFTEVN 236
                                   67789999999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0049
                                   EEEEEEE--S--BTTB-S-CEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  95 fqiaraFRaEdsrtdrhlaEFtqiea 120
                                   f+++++FR  ++++++ + EF q++ 
  gi|70607254|ref|YP_256124.1| 327 FSLGKVFRPDSIDATHLI-EFHQLDG 351
                                   999**********99988.****994 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00014
                                   SEEEEEEEHHHHHHHHCT-SSGGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 283 phgGlglGldRlvmlllgsesIrdv 307
                                   + g +g+G+dRl mll g+++Ir +
  gi|70607254|ref|YP_256124.1| 426 NAGAWGIGIDRLAMLLFGLKDIRLL 450
                                   56779*****************965 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.2e-07    0.0014       8      49 ..       9      49 ..       6      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                  HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                  iL +l     + +  e+++++glp S+ + l + L+e Gyv+
  gi|70607254|ref|YP_256124.1|  9 ILSYLKLKKKA-NAEEISKELGLPLSSIFSLAKLLEEKGYVK 49
                                  67777777775.889*************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.9e-06    0.0073       1      47 [.       2      48 ..       2      49 .. 0.97
   2 ?    0.3   0.0      0.45   6.8e+02      21      41 ..     291     316 ..     277     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                  l++++++iL  l+ +  ++  e+ k lg+  s++  +++ Le+kG++
  gi|70607254|ref|YP_256124.1|  2 LSENEIKILSYLKLKKKANAEEISKELGLPLSSIFSLAKLLEEKGYV 48
                                  799******************************************98 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.45
                                   H.....HHHHHHTS-HHHHHHHHHHH CS
                          MarR  21 s.....eLakklgvskstvtrvldrL 41 
                                   +     ++ak+l + + t+  +++ L
  gi|70607254|ref|YP_256124.1| 291 KyswdpQIAKRLVLRSQTTAVTARIL 316
                                   35566699****99999998777766 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   4.2e-05     0.063       8      68 .]       9      64 ..       2      64 .. 0.82
   2 ?   -1.2   0.0         2     3e+03      20      59 ..     222     260 ..     220     268 .. 0.77
   3 ?   -1.9   0.0       3.4   5.1e+03      28      47 ..     271     290 ..     249     290 .. 0.79
   4 ?   -3.0   0.0       7.6   1.1e+04      40      52 ..     397     409 ..     389     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  +L  ++    ++ ++++++ l +  s+i +  k L+ekG+v    +  +r+  r++lT++G
  gi|70607254|ref|YP_256124.1|  9 ILSYLK-LKKKANAEEISKELGLPLSSIFSLAKLLEEKGYV----KIGERKIIRFELTEEG 64
                                  555566.5566777***************************....3345899*******99 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                        HTH_27  20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrre 59 
                                   kl+d+++ l ++  ++ y+  +L + +L+ + +d ++ re
  gi|70607254|ref|YP_256124.1| 222 KLKDVMKELGFTEVNAGYIEMELYNFDLLFQAQD-HPARE 260
                                   5688888888888888888888888888877777.56665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.4
                        HTH_27  28 lnvedshisyslkkLtekGL 47 
                                    +++d    + +k+++ekG+
  gi|70607254|ref|YP_256124.1| 271 GKIDDERLLKEIKEMHEKGW 290
                                   56777777888999999997 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 7.6
                        HTH_27  40 kkLtekGLvertg 52 
                                    k +  G+ve++g
  gi|70607254|ref|YP_256124.1| 397 GKIEGLGWVEMSG 409
                                   688999***9986 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00054      0.81       1      53 [.       2      50 ..       2      60 .. 0.93
   2 ?   -1.8   0.1       2.6   3.8e+03      41      57 ..     145     161 ..     134     187 .. 0.71
   3 ?    3.4   0.0     0.062        93      48      87 ..     280     319 ..     277     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                                  ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EE CS
               Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsr 53
                                  l+e E +++ +l  k++a+++e+ +el  +     s++ +l + L++Kg+++ 
  gi|70607254|ref|YP_256124.1|  2 LSENEIKILSYLKLKKKANAEEISKELGLP----LSSIFSLAKLLEEKGYVKI 50
                                  6899***********************999....99**************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                                   HHHHHHHTTS-EEEEET CS
               Penicillinase_R  41 llrrLvkKgllsrekeg 57 
                                   +l+ L+ ++l++r++e 
  gi|70607254|ref|YP_256124.1| 145 VLQELLSRKLITRKEES 161
                                   55566666666665554 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.062
                                   TTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R  48 KgllsrekegrafiYsplvseeeavasavkqlldklfegs 87 
                                   K++ + +++g ++ + p + ++ +++s++  ++ ++++++
  gi|70607254|ref|YP_256124.1| 280 KEIKEMHEKGWKYSWDPQIAKRLVLRSQTTAVTARILSSR 319
                                   566677899*************************999643 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.6e-05     0.024       8      52 ..       7      49 ..       2      67 .. 0.85
   2 ?   -1.2   0.1       1.3     2e+03      41      55 ..     145     159 ..     143     162 .. 0.83
   3 ?   -1.8   0.2         2   2.9e+03      26      46 ..     297     317 ..     296     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                    +L +L        ++ e+ ++lgl+ s++  + k L+++G+v 
  gi|70607254|ref|YP_256124.1|  7 IKILSYLKLKKK--ANAEEISKELGLPLSSIFSLAKLLEEKGYVK 49
                                  567788888887..89****************************4 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                   HHHHHHHTTSEEEEE CS
                        MarR_2  41 ilkrLvaaGLverrp 55 
                                   +l++L ++ L++r++
  gi|70607254|ref|YP_256124.1| 145 VLQELLSRKLITRKE 159
                                   6899*******9985 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2
                                   HHHHHHTSSHHHHHHHHHHHH CS
                        MarR_2  26 elarrlglsksavsrilkrLv 46 
                                   ++a+rl l  +++  + + L+
  gi|70607254|ref|YP_256124.1| 297 QIAKRLVLRSQTTAVTARILS 317
                                   799999999999877777666 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.9   9.1e-06     0.014       8      64 ..       4      60 ..       1      70 [. 0.89
   2 ?   -1.4   0.1       1.8   2.6e+03      37      61 ..     140     164 ..     123     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-06
                       DUF2250  8 elalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrte 64
                                  e+++k+l +lk  +   a  i+kel +pl+ + +l k Lee G ++  e+k+i+++ 
  gi|70607254|ref|YP_256124.1|  4 ENEIKILSYLKLKKKANAEEISKELGLPLSSIFSLAKLLEEKGYVKIGERKIIRFEL 60
                                  6789*************************************************9864 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                       DUF2250  37 eevrellkkLeelGLlervegktik 61 
                                   +  +++l++L +  L++r+e++ + 
  gi|70607254|ref|YP_256124.1| 140 SADEKVLQELLSRKLITRKEESKLE 164
                                   4446778999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3462.40
//
Query:       gi|70607255|ref|YP_256125.1|  [L=206]
Description: metal-dependent hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-18   65.0   0.0    7.7e-18   64.7   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.2e-11   42.7   0.0      8e-11   42.1   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.3e-05   25.3   1.1    2.9e-05   24.2   1.1    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.046   13.6   0.0       0.06   13.2   0.0    1.1  1  BDV_P24        Borna disease virus P24 protein


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.7e-21   7.7e-18      16     201 .]       9     171 ..       1     171 [. 0.87

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.7e-21
                                   TCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEE CS
                 Lactamase_B_2  16 lralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesf 96 
                                   +++ +Pv+l +  + +d++++th+HyDHl ++  l ++ pk + l+a+ ++  +l+++ + +        ++ + + g+ +
  gi|70607255|ref|YP_256125.1|   9 NPL-SPVKLDSFNNNVDLIVVTHDHYDHLGDAVELLKMNPK-ASLFATFDLEVYLSNEYKID------MSRFIPANVGGFI 81 
                                   555.48886666689**********************9885.89**************6543......3467899****** PP

                                   EECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH..HHHHHCT-SEEEEE-S-SSTTHHHHH CS
                 Lactamase_B_2  97 elgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee..igerlggadllllditayeddemirh 175
                                   +++  gl++ +t a h+s+       +d  G +i g++ +vy++gDtg ++++  ig ++ ++d +ll+i+         +
  gi|70607255|ref|YP_256125.1|  82 DFD--GLKLALTKAVHSSEH------SDPSGAIISGENITVYHAGDTGLFEDMklIG-EVFKPDYALLPIG---------G 144
                                   **8..89*************......9************************555366.66669********.........8 PP

                                   HT---STSHHHHCTTSS.SSEEEEESB CS
                 Lactamase_B_2 176 mgHltpeeaveaaadlg.akrlvliHi 201
                                    ++++p +a  a+++++ +k +++iH+
  gi|70607255|ref|YP_256125.1| 145 RFTMDPYQASLAVDMIKpKKYAIPIHF 171
                                   99***************666899***7 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   1.8e-14     8e-11      22     163 .]       3     170 ..       1     170 [. 0.72

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.8e-14
                 Lactamase_B_3  22 DPf.....kanlgyeppaeeaDlvlisqaledHahle.tlkqlaenvkvlee.......................geslev 73 
                                   DP+        ++++  + ++Dl+++++++ dH   + +l +++ ++ + ++                       g+ +++
  gi|70607255|ref|YP_256125.1|   3 DPMikdnpLSPVKLDSFNNNVDLIVVTHDHYDHLGDAvELLKMNPKASLFATfdlevylsneykidmsrfipanvGGFIDF 83 
                                   6654433322456667779**************743313444444444555555555555555555555555454555777 PP

                 Lactamase_B_3  74 ggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrL 154
                                   +gl++  +++ h +++  +     g +++ +++t+yh G+++   +++ + e  ++D  l+P+gg +t+++ +a+ ++ ++
  gi|70607255|ref|YP_256125.1|  84 DGLKLALTKAVHSSEHSDPS----GAIISGENITVYHAGDTGLFEDMKLIGEVFKPDYALLPIGGRFTMDPYQASLAVDMI 160
                                   77777777777766555555....5699***************99999999999*************************** PP

                 Lactamase_B_3 155 kpk.lvlPmh 163
                                   kpk + +P+h
  gi|70607255|ref|YP_256125.1| 161 KPKkYAIPIH 170
                                   **54899988 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   6.5e-09   2.9e-05      42     180 ..      20     158 ..       3     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.5e-09
                                   GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEE CS
                   Lactamase_B  42 pkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrra 122
                                    ++vd +++TH H+DH G++ +l +  + ++     ++++++ +e + + sr          + p ++    d++++   +
  gi|70607255|ref|YP_256125.1|  20 NNNVDLIVVTHDHYDHLGDAVELLKMNPKASLFATFDLEVYLSNEYKIDMSR----------FIPANVGGFIDFDGLKLAL 90 
                                   5789*********************999999999999998888888776555..........4566666677777777777 PP

                                   EEHECTTSTSCCEEEEEETTC.CEEEECTTTSSHHCCCCCC..........TTCEEE-SHCHHHHHHH CS
                   Lactamase_B 123 lyvtggpghghghgvveyggg.kvlftGDallagetgridl.........tlrgaevrdpsdaekyld 180
                                   +++++   h+  +g + +g+  +v  +GD++l ++  +i++         +++g +++dp++a+ + d
  gi|70607255|ref|YP_256125.1|  91 TKAVHSSEHSDPSGAIISGENiTVYHAGDTGLFEDMKLIGEvfkpdyallPIGGRFTMDPYQASLAVD 158
                                   78888888887777777765526777999999999999999999999888888888888888877774 PP

>> BDV_P24  Borna disease virus P24 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05      0.06     107     200 ..      79     177 ..      65     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                       BDV_P24 107 gfeslsalqvetiqtaqrcdhsd..sirilgenikildrsmktmmetmklmmekvdllyastavgtsapmlpshp..appr 183
                                   gf  +  l++   ++ +  +hsd     i geni +       ++e mkl+ e     ya   +g    m p +   a   
  gi|70607255|ref|YP_256125.1|  79 GFIDFDGLKLALTKAVHSSEHSDpsGAIISGENITVYHAGDTGLFEDMKLIGEVFKPDYALLPIGGRFTMDPYQAslAVDM 159
                                   677777777777788888888884224588***********************************9999998664226778 PP

                       BDV_P24 184 iypqlpsaptt.dewdii 200
                                   i p+  + p   + wd+i
  gi|70607255|ref|YP_256125.1| 160 IKPKKYAIPIHfNTWDLI 177
                                   899888888643678877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1444.14
//
Query:       gi|70607256|ref|YP_256126.1|  [L=299]
Description: methionine aminopeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-43  147.0   0.0    6.7e-43  146.8   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
      0.075   13.4   0.0         22    5.5   0.0    2.4  2  EntA_Immun     Enterocin A Immunity


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   0.0   7.5e-47   6.7e-43       1     207 [.       7     289 ..       7     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 7.5e-47
                                   HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..SSSB.--TTEEEE CS
                 Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..ndrv.lkegdlvl 78 
                                   el+r+a++ias+a++  +++ikpgv+  ++++ +e+   +++++ ++afp  + +++n +++hy+p  nd++ + e+ +v+
  gi|70607256|ref|YP_256126.1|   7 ELLRRAGKIASKARDFGAKMIKPGVKVIDVCDTVEKI--IEEEGAKPAFP--CNLSINVEAAHYSPiiNDTKiIPENAVVK 83 
                                   579********************************87..7778889****..6667777777**999965554899***** PP

                                   EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS CS
                 Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl 159
                                   +d+ga+++gy++D+++Tv++   +p++++l+ea +ea++aai+ ++ Gv+++ei+++++++++s+g+ k+++++ GH + +
  gi|70607256|ref|YP_256126.1|  84 LDIGAHINGYITDTAVTVSL---DPKYDKLVEASREALQAAIRTIRNGVDIGEIGRHIERTIKSYGF-KPIRNLGGHLIRR 160
                                   ********************...99******************************************.************9 PP

                                   .SSSEE..EEEESSSTTCSSB--TTBEEEEEE......EEEEETTT................................... CS
                 Peptidase_M24 160 .evhde..gpsvsresndgrkleeGmvftiEp......giyfapge................................... 196
                                    e+h +   p+v+  ++   k+ eG +++iEp      g++ ++g+                                   
  gi|70607256|ref|YP_256126.1| 161 yELHAGifIPNVY--GRGLGKIMEGSTYAIEPfatdgeGYV-IEGKevtiysiknlntksltedekkfltsiyekvnmvpf 238
                                   9***985555554..446899***********999998666.555566777777778888888999999999999999999 PP

                                   .......................................E.EEEEBEEEEE CS
                 Peptidase_M24 197 .......................................g.gvriedtvlv 207
                                                                          g ++++e+tvlv
  gi|70607256|ref|YP_256126.1| 239 serwlsnmdgnpdkvremlkiltrkgalrsypvlleakkGiVAQFEHTVLV 289
                                   99*************************************88*********9 PP

>> EntA_Immun  Enterocin A Immunity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0024        22      23      56 ..     114     147 ..     103     151 .. 0.87
   2 ?    5.4   0.0    0.0027        24       8      48 ..     210     247 ..     206     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0024
                    EntA_Immun  23 lrevLltaknklekgknvsvvasrLeqelrsyal 56 
                                    re+L +a+  + +g +  ++ +++e ++ sy +
  gi|70607256|ref|YP_256126.1| 114 SREALQAAIRTIRNGVDIGEIGRHIERTIKSYGF 147
                                   49***************************99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0027
                    EntA_Immun   8 lynlildpeikeneelrevLltaknklekgknvsv.vasrLe 48 
                                   ++nl +++++ e+e  ++ L++ ++k  +  ++s+ ++s+++
  gi|70607256|ref|YP_256126.1| 210 IKNL-NTKSLTEDE--KKFLTSIYEK-VNMVPFSErWLSNMD 247
                                   6666.9999*****..**********.777777777888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1905.99
//
Query:       gi|70607257|ref|YP_256127.1|  [L=378]
Description: hypothetical protein Saci_1514 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-144  481.7  11.9   1.4e-144  481.5  11.9    1.0  1  DUF1512   Protein of unknown function (DUF1512)


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.5  11.9  7.6e-149  1.4e-144       2     356 .]      23     377 ..      22     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: 481.5 bits;  conditional E-value: 7.6e-149
                       DUF1512   2 isliifllllill.llglnqklqlavllrdiekklakleklaeeakkkvvellkklgkedpkklverlleffviePvdleP 81 
                                   i++i+f++++il+ l+g++ +lq++++++die+ l++++++ +++ +k++++l+k+g++++++++++++++f+i+Pv++eP
  gi|70607257|ref|YP_256127.1|  23 ITYILFFAVIILTaLPGVQIRLQMYWASMDIERGLTRVKRVLDSTVSKTKQILEKNGASNSDEITRKFSDMFTIDPVNVEP 103
                                   899*********99******************************************************************* PP

                       DUF1512  82 tgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlqmllplll 162
                                   t+i++r++ llr++edk+k++++ ++p++d ++rs++++++ei++++n+iykv+rHylll++k +n++lllqlqm++p+l+
  gi|70607257|ref|YP_256127.1| 104 TDIISRMRLLLRSTEDKIKQVINVSIPTIDPMNRSKIQVSAEIVNTVNIIYKVIRHYLLLGRKLQNYYLLLQLQMIVPMLV 184
                                   ********************************************************************************* PP

                       DUF1512 163 klaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGpgstvGrlgeavekiv 243
                                   ++ae+yekal++fl+g+PvGD++Gplva+++l++ ++k +++++++++ ++ +egr+++++kaeGp++tvG++geave+++
  gi|70607257|ref|YP_256127.1| 185 RMAETYEKALDVFLQGVPVGDSLGPLVASRFLMNVSEK-WSPSREMIAGTTVYEGRRLVILKAEGPMATVGTPGEAVENVI 264
                                   *********************************99998.****************************************** PP

                       DUF1512 244 eklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviikmsleeAitaMtkeiaeavd 324
                                    kl+++v++iitvDAa+kLEGEetg++aeG+Gva+GdpG+eki+iErva+ky+ip+davi+kms+eeAitaM+++++ea+d
  gi|70607257|ref|YP_256127.1| 265 GKLNGSVSRIITVDAAAKLEGEETGEIAEGTGVAMGDPGPEKIAIERVAVKYNIPIDAVIVKMSMEEAITAMPQKVYEAAD 345
                                   ********************************************************************************* PP

                       DUF1512 325 kavervkeiikektkegetvivvGvGNtvGva 356
                                   k+ve++k++i e+tk+g+t+i+vGvGNtvGva
  gi|70607257|ref|YP_256127.1| 346 KVVEMIKRMIMERTKPGDTIILVGVGNTVGVA 377
                                   ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2485.84
//
Query:       gi|70607258|ref|YP_256128.1|  [L=66]
Description: hypothetical protein Saci_1515 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 479.11
//
Query:       gi|70607259|ref|YP_256129.1|  [L=400]
Description: hypothetical protein Saci_1517 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-10   39.8   0.4    2.4e-09   37.4   0.2    2.1  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   1.4e-13   2.4e-09       1     121 [.      50     168 ..      50     169 .. 0.78
   2 ?   -0.4   0.0     0.072   1.3e+03      62      92 ..     323     355 ..     300     387 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.4e-13
                                   HHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHH....HHH..CTCCHHHHHHHHHHHHHH CS
                            HD   1 rleHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekk....eee..fekflaHekvgaeilrev 70 
                                   r+ Hsl++ +la r +++l        ++  ll+la LlHDiG  pf+++ e +      +     +++ ++++ + ++e+
  gi|70607259|ref|YP_256129.1|  50 RFSHSLGTFHLATRVGNRLINeghinHDEALLLRLASLLHDIGQFPFSHSLEPIyisrD-KvsSSVIRDFIIYSDKEIEEA 129
                                   799**************99889***99999*******************9999987531.245666777777777666666 PP

                                   HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                            HD  71 ekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                   ++       d  +++   + s++            ++ ++ +++++D+l +
  gi|70607259|ref|YP_256129.1| 130 LGEYSI---DKKQIVDIYNTSSML---------GCIIDSDVDIDRMDYLLR 168
                                   665544...445555555555553.........49999*********9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.072
                                   HHHHHHHHHHHHHHHH....HHHHHHHHHTTCCHH CS
                            HD  62 vgaeilrevekrlgld....ledvaklirehhesw 92 
                                   + +++l+++++++  d    +e+++++i +   + 
  gi|70607259|ref|YP_256129.1| 323 EIVSKLQKYGIPE--DsvypFEEIIRIIDKSKLKV 355
                                   4556677777777..45688888888887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2776.65
//
Query:       gi|70607260|ref|YP_256130.1|  [L=227]
Description: hypothetical protein Saci_1518 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-27   95.2   0.4    9.1e-15   55.1   0.1    2.0  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
    1.4e-08   35.4   3.3     0.0065   16.9   0.0    3.1  3  HAD             haloacid dehalogenase-like hydrolase
    8.1e-07   29.5   2.0      0.029   14.7   0.0    3.2  3  Hydrolase       haloacid dehalogenase-like hydrolase
    8.9e-07   29.2   0.1     0.0028   17.7   0.0    2.6  3  HAD_2           Haloacid dehalogenase-like hydrolase
    5.3e-06   26.1   0.0     0.0009   18.8   0.0    2.1  2  S6PP            Sucrose-6F-phosphate phosphohydrolase
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.019   15.0   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
      0.027   14.6   0.1      0.074   13.2   0.0    1.8  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.4e-13   8.7e-10       1      72 [.       5      77 ..       5      97 .. 0.84
   2 !   55.1   0.1   3.6e-18   9.1e-15     170     255 .]     132     217 ..     102     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.4e-13
                                  EEEEIIIIIS-TTS-..--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTE CS
                   Hydrolase_3  1 ialDlDGTLlnsdkk..isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgk 72
                                  i +D+DGTL  +  +  i+  +++ ++k+++kgikv + +G+s+  ++ ++  +g++  ++a NG+++ +  +++
  gi|70607260|ref|YP_256130.1|  5 ILTDVDGTLTFDRDTynIDLDAVDLLRKVEKKGIKVGLVSGNSYPVLRALYTYFGFNGGIVAENGCIVyY--DNQ 77
                                  789******7755553699*************************************************43..333 PP

  == domain 2  score: 55.1 bits;  conditional E-value: 3.6e-18
                                   EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTH CS
                   Hydrolase_3 170 titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedG 250
                                    ++++s++ + i + +  K++++++l+k+ +++++ev+ +GD+  Die Le +g+ v +gna+e++k++ d+v+  ++  +
  gi|70607260|ref|YP_256130.1| 132 LYIKTSGYAVHISKSKRGKAEGVRELIKMHGLDKAEVVGIGDSSTDIEFLEEVGIRVVVGNADESLKSIGDFVMREKSGKA 212
                                   5789999***********************************************************************999 PP

                                   HHHHH CS
                   Hydrolase_3 251 Vakal 255
                                   V++++
  gi|70607260|ref|YP_256130.1| 213 VVEFI 217
                                   99987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.6      0.19   4.9e+02       1      15 [.       5      20 ..       5      26 .. 0.73
   2 !   16.1   0.0   4.5e-06     0.011      89     130 ..      25      62 ..      17      88 .. 0.81
   3 !   16.9   0.0   2.5e-06    0.0065     143     188 .]     141     182 ..     119     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                           HAD  1 alfDfDgTL.ldgdsl 15
                                  +l D+DgTL +d d++
  gi|70607260|ref|YP_256130.1|  5 ILTDVDGTLtFDRDTY 20
                                  689******4444765 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.5e-06
                           HAD  89 galellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                   +a++ll+++ ++G++v +vSg+  p++++l   +g     + 
  gi|70607260|ref|YP_256130.1|  25 DAVDLLRKVEKKGIKVGLVSGNSYPVLRALYTYFG----FNG 62 
                                   689***************************99999....444 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.5e-06
                           HAD 143 glegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                    ++ k+ rg  k+  +re    + +g+d +evv +GDs +D+++l+
  gi|70607260|ref|YP_256130.1| 141 VHISKSKRG--KAEGVRE--LIKMHGLDKAEVVGIGDSSTDIEFLE 182
                                   555555555..*******..77777788889***********9986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.9     0.034        86       1      14 [.       2      15 ..       2      21 .. 0.85
   2 !    8.9   0.0   0.00066       1.7     120     156 ..      23      59 ..      17      83 .. 0.82
   3 !   14.7   0.0   1.1e-05     0.029     168     210 .]     143     185 ..     125     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.034
                                  SSEEEEESBTTTBC CS
                                  xxxxxxxxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTLtt 14
                                  i++++ D+dGTLt 
  gi|70607260|ref|YP_256130.1|  2 IRLILTDVDGTLTF 15
                                  789*********94 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00066
                                   HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                     +a++++++  ++gi+v+l++g++    +++   +G
  gi|70607260|ref|YP_256130.1|  23 DLDAVDLLRKVEKKGIKVGLVSGNSYPVLRALYTYFG 59 
                                   568999********************99999988898 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   CESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 168 ietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   i++ +  + eg++++i+  + +++ev+ +GD+ +D+++l+++g
  gi|70607260|ref|YP_256130.1| 143 ISKSKRGKAEGVRELIKMHGLDKAEVVGIGDSSTDIEFLEEVG 185
                                   4444445789999999999********************9987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.1   2.8e+03       1      10 [.       5      14 ..       5      24 .. 0.75
   2 !    8.5   0.0   0.00075       1.9      83     119 ..      25      61 ..      14      65 .. 0.88
   3 !   17.7   0.0   1.1e-06    0.0028     135     176 ..     150     189 ..     137     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                         HAD_2  1 iiFDlDgTll 10
                                  i+ D+DgTl 
  gi|70607260|ref|YP_256130.1|  5 ILTDVDGTLT 14
                                  677*****95 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00075
                         HAD_2  83 gvkelLeeLkeagyklgivTsksreaveekleqlgie 119
                                   ++ +lL +++++g+k+g+v+ +s  +++   + +g++
  gi|70607260|ref|YP_256130.1|  25 DAVDLLRKVEKKGIKVGLVSGNSYPVLRALYTYFGFN 61 
                                   67899*******************9999988888875 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.1e-06
                         HAD_2 135 KPdpeviekaleklklkkeeviyvGDsptDieaakkagikvi 176
                                   K  +e ++++++  +l+k+ev+ +GDs+tDie   ++gi+v+
  gi|70607260|ref|YP_256130.1| 150 K--AEGVRELIKMHGLDKAEVVGIGDSSTDIEFLEEVGIRVV 189
                                   3..8999********************************997 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0039        10       3      54 ..       3      56 ..       1      89 [. 0.78
   2 !   18.8   0.0   3.5e-07    0.0009     156     212 ..     140     196 ..     120     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0039
                                  EEEEE-TBTTTB..S-HHHHH.HHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHH CS
                          S6PP  3 lllvsdLDntlv.dgdneala.rlnelleaeerkdvllvfaTGRsldsakellk 54
                                  +l+++d+D+tl+ d+d  +++ +  +ll++ e+k +++++++G s+   ++l++
  gi|70607260|ref|YP_256130.1|  3 RLILTDVDGTLTfDRDTYNIDlDAVDLLRKVEKKGIKVGLVSGNSYPVLRALYT 56
                                  689*********955554442234455555889999999999999887777765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.5e-07
                                   EEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HH CS
                          S6PP 156 dlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqee 212
                                   ++ +   + +k+e +r L k ++l+  +++  Gds  D+e l++    VvVgna+e 
  gi|70607260|ref|YP_256130.1| 140 AVHISKSKRGKAEGVRELIKMHGLDKAEVVGIGDSSTDIEFLEEVGIRVVVGNADES 196
                                   55566667899*******************************999999******998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   7.6e-06     0.019      12      46 ..     156     189 ..     146     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                                   HHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEE CS
                Hydrolase_like  12 falevlgsdpeevlmiGDrlatDiagAnnaGwksv 46 
                                   +  + +g+d++ev+ iGD+  tDi++  ++G++ v
  gi|70607260|ref|YP_256130.1| 156 ELIKMHGLDKAEVVGIGDS-STDIEFLEEVGIRVV 189
                                   55677899***********.******999999987 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.9e-05     0.074       1      41 [.       5      48 ..       5      67 .. 0.83
   2 ?   -2.6   0.0       2.4   6.1e+03      99      99 ..     162     162 ..     144     187 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                  EEEESTTTSE...ETTEE-TTHHHHHHHHHHTT-EEEEEE---S CS
                   Hydrolase_6  1 flfDidGvLw...rgdkaipgaaealnalraagkpvvllTNnss 41
                                  +l+D+dG+L    + +++   a+++l+ ++++g++v l++ ns 
  gi|70607260|ref|YP_256130.1|  5 ILTDVDGTLTfdrDTYNIDLDAVDLLRKVEKKGIKVGLVSGNSY 48
                                  689*******54334444569*******************9985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                   T CS
                   Hydrolase_6  99 g 99 
                                   g
  gi|70607260|ref|YP_256130.1| 162 G 162
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1624.49
//
Query:       gi|70607261|ref|YP_256131.1|  [L=567]
Description: glutamyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-81  273.1   0.1    1.5e-80  270.5   0.0    2.0  2  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
      8e-23   81.2   0.0    1.5e-22   80.3   0.0    1.5  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  270.5   0.0   1.7e-84   1.5e-80       3     313 ..     101     406 ..      99     407 .. 0.96
   2 ?    0.2   0.0     0.032   2.9e+02      49      90 ..     458     500 ..     456     503 .. 0.89

  Alignments for each domain:
  == domain 1  score: 270.5 bits;  conditional E-value: 1.7e-84
                                   EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCC..C--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHH CS
                  tRNA-synt_1c   3 rtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpe..rekeeaeesiledlkwlgikwdekptyqsdrfdel 81 
                                   +tRfaP+P G LH+G+a+aa++++ +A+ +nGkfilR++DTdp+  + ++ea + i+edlkwlgikwd   +++s r++++
  gi|70607261|ref|YP_256131.1| 101 VTRFAPNPDGPLHLGNARAAIISHEYARIYNGKFILRFDDTDPKtkKPIPEAYDWIKEDLKWLGIKWDL-EVRASARLETY 180
                                   7*****************************************96226678*****************64.789******** PP

                                   HHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSST CS
                  tRNA-synt_1c  82 kkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrDl 161
                                   +++a  L++kG+AY + c++ e +e r +  + ++++r+ + e+nl+lf e+m +g++e++kavvRlk d + +    rD 
  gi|70607261|ref|YP_256131.1| 181 YNFARILLSKGYAYIDLCKEAEFKERRSK--REACPHRETSPESNLELF-EKMIHGEFEEGKAVVRLKTDLKLPdPSQRDW 258
                                   ***************************99..88899*************.9***********************9****** PP

                                   EEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETTS CS
                  tRNA-synt_1c 162 vrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnlekk 242
                                   v  r+ + +++ h+  ++k+ + PtY+fa +idD++ ++th++r++e+  n +k+ w+++++g++  p+++e+ rl le+ 
  gi|70607261|ref|YP_256131.1| 259 VLLRVINVKKSPHPIEGDKYWVWPTYNFASAIDDYDLGVTHIFRGKEHAVNAEKQKWIYNYMGWK-YPYVREFGRLKLEGF 338
                                   ****99999999*****************************************************.9************** PP

                                   B-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
                  tRNA-synt_1c 243 klSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                                    +SK k+ ++  +++  + dd+r+++l +lrr+G+    ++e++ + +l + +  +++ ++l++ +rkkL+
  gi|70607261|ref|YP_256131.1| 339 MMSKSKIRTV--VEKGVGIDDPRLPTLAGLRRRGILSDTIKEIIITVGLKETD-ATISFDNLASTNRKKLD 406
                                   **********..666679*******************************9999.***************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.032
                                   -HHHHHHHHHHHHHTT---S.SEEEEGGGGHHHHHHHHHHHHH CS
                  tRNA-synt_1c  49 keeaeesiledlkwlgikwd.ekptyqsdrfdelkkyaeeLik 90 
                                   +++a++++l+ +++++++ + +k++y+s+  +  kk+  ++i+
  gi|70607261|ref|YP_256131.1| 458 ENDAKDKVLRLMELCNVTVNgDKLVYNSKGIEDAKKLGMKIIQ 500
                                   678999*************9999******99999998888875 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   1.7e-26   1.5e-22       1     174 []     409     552 ..     409     552 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.7e-26
                tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfsk..eiyiereDakrlkpgeevrLkelynikveevek 79 
                                   A+R+m+V +p +++i+ +p  +++ +++p+hp+np++ +r++ +++   i+i+++Dak    ++ +rL+el+n++v+    
  gi|70607261|ref|YP_256131.1| 409 AKRLMFVGSPKEFIID-IP--QPILAKIPYHPSNPNE-YREISVNPgdIILINENDAK----DKVLRLMELCNVTVNGD-- 479
                                   89**************.77..79**********9887.89999984449*******65....579***********887.. PP

                tRNA-synt_1c_C  80 desgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvl..eeglaepalanl 157
                                            kl y+++ +e+a+k  + ii+Wv+++e+v++                 +l pd +k +   +g++e++++nl
  gi|70607261|ref|YP_256131.1| 480 ---------KLVYNSKGIEDAKKLGMkIIQWVKKDESVPV----------------VVLSPDPEKGIetINGVGESEIRNL 535
                                   .........48999999****9*9999*************................999999999887789********** PP

                tRNA-synt_1c_C 158 kkgdivQfeRiGyfrvd 174
                                   +kg+ivQf R+G+++vd
  gi|70607261|ref|YP_256131.1| 536 NKGEIVQFIRYGFVKVD 552
                                   ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4213.50
//
Query:       gi|70607262|ref|YP_256132.1|  [L=126]
Description: 50S ribosomal protein L7Ae [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-33  114.2   1.9    2.1e-33  113.9   1.9    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    1.9e-06   27.6   0.1      3e-06   27.0   0.1    1.3  1  PELOTA_1        PELOTA RNA binding domain
    0.00051   20.1   0.1    0.00058   19.9   0.1    1.1  1  RNase_P_pop3    RNase P subunit Pop3
  ------ inclusion threshold ------
      0.042   13.8   1.7       0.26   11.3   0.2    2.7  3  DbpA            DbpA RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.9   1.9   4.7e-37   2.1e-33       1      95 []      17     111 ..      17     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 4.7e-37
                                   HHHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                Ribosomal_L7Ae   1 daieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81 
                                   d++ e++kkak++gk+++G++e+tka+er +aklv++Aedv+pee++++l+ lc+ek++pyv+v+skk LGe++g++++++
  gi|70607262|ref|YP_256132.1|  17 DKVLEAVKKAKDSGKIKKGTNETTKAVERSQAKLVVIAEDVQPEEIVAHLPLLCEEKKIPYVYVPSKKSLGEACGLQVAAA 97 
                                   57899**************************************************************************** PP

                                   EEEEEESTTTHHHH CS
                Ribosomal_L7Ae  82 alaikdegdskdlv 95 
                                   ++a  d+g++kdlv
  gi|70607262|ref|YP_256132.1|  98 SVALMDPGEAKDLV 111
                                   ***********985 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   6.6e-10     3e-06      15      71 ..      25      83 ..      14      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.6e-10
                      PELOTA_1 15 giedinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                  + +d   iK g  E+T+++ R + + v+++++ +  + +ahl lL++ek++p++ vp++
  gi|70607262|ref|YP_256132.1| 25 KAKDSGKIKKGTNETTKAVERSQAKLVVIAEDVQpeEIVAHLPLLCEEKKIPYVYVPSK 83
                                  5689999**********************9987733569**************999887 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.3e-07   0.00058      38     150 ..      15     120 ..       3     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                  RNase_P_pop3  38 vlkklvrlleskeneeseltvglneivelLecsesddvvllvcnkD.tPsvLlsqlpllvavanltvklvqlpksaqakld 117
                                   ++ k++++ + k +   ++  g ne  +  e     ++ l+v+ +D +P  ++ +lpll++ ++  ++ v +p +  + l 
  gi|70607262|ref|YP_256132.1|  15 LADKVLEAVK-KAKDSGKIKKGTNETTKAVE---RSQAKLVVIAEDvQPEEIVAHLPLLCEEKK--IPYVYVPSK--KSLG 87 
                                   4444455555.556677999********999...55566777888877***************9..777777755..4577 PP

                  RNase_P_pop3 118 eklGlskagmllvrkdasldkklaklvskkvee 150
                                   e+ Gl+ a + +   d    k+l++ + k+v+e
  gi|70607262|ref|YP_256132.1|  88 EACGLQVAAASVALMDPGEAKDLVDEIVKRVNE 120
                                   777777665544444444455777777777765 PP

>> DbpA  DbpA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   5.7e-05      0.26      43      66 ..       8      31 ..       3      34 .. 0.85
   2 ?    1.4   0.0     0.071   3.2e+02      30      55 ..      27      52 ..      25      54 .. 0.86
   3 ?   -0.6   0.0      0.29   1.3e+03      48      66 ..     108     124 ..     106     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                                  EEEE-TT-HHHHHHHHTT--SSS- CS
                          DbpA 43 fvevpkekaeevlkalkkkkikGr 66
                                   +evp+e a++vl+a+kk+k  G+
  gi|70607262|ref|YP_256132.1|  8 KFEVPQELADKVLEAVKKAKDSGK 31
                                  59***************9986665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.071
                                  GGEEEEEE-SS-EEEEE-TT-HHHHH CS
                          DbpA 30 kdIGkIdildkfSfvevpkekaeevl 55
                                  kd GkI+   + ++ +v++++a+ v+
  gi|70607262|ref|YP_256132.1| 27 KDSGKIKKGTNETTKAVERSQAKLVV 52
                                  5669999999***********99886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.29
                                   TT-HHHHHHHHTT--SSS- CS
                          DbpA  48 kekaeevlkalkkkkikGr 66 
                                   k+ ++e++k++++  ikG+
  gi|70607262|ref|YP_256132.1| 108 KDLVDEIVKRVNE--IKGK 124
                                   5677788888864..6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      760  (0.0423894); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 936.73
//
Query:       gi|70607263|ref|YP_256133.1|  [L=480]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-47  161.1  21.7    5.3e-47  160.7  21.7    1.0  1  Sugar_tr         Sugar (and other) transporter
    4.6e-31  108.0  43.8      2e-22   79.6  16.5    2.1  2  MFS_1            Major Facilitator Superfamily
    1.7e-06   26.9   1.8    1.7e-06   26.9   1.8    3.3  3  MFS_2            MFS/sugar transport protein
    0.00059   18.4  12.1      0.013   14.0   3.1    2.1  2  TRI12            Fungal trichothecene efflux pump (TRI12)
     0.0023   17.3  13.7     0.0037   16.6   3.4    3.4  4  MFS_4            Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
       0.17   12.2   4.5        0.3   11.4   2.1    2.3  2  Aim19            Altered inheritance of mitochondria protein 
       0.68   10.0   5.6       0.59   10.2   0.2    2.6  2  Phage_holin_3_7  Putative 3TM holin, Phage_holin_3


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.7  21.7   2.1e-50   5.3e-47      44     448 ..      58     463 ..      24     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 2.1e-50
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                   ++ + +++  ++++Ga+iG++++++l+d++GRkk ++++  ++v+g+vl+a++    ++  +++ R ++G+g+G+++  + 
  gi|70607263|ref|YP_256133.1|  58 TEFQASFLGTAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAGTVLSALSW---NFLSIALFRTITGLGIGGEYSAIN 135
                                   44566788899******************************************9...9*********************** PP

                                   HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-...TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT CS
                      Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsn...adgwrillglqlvpallllilllflPESPrylvekg 202
                                     i+E+ p+++Rg +    + ++ +G +v++ + l l + ++   + gwr+ +++ +++ + +++++  +PESPr+l+ +g
  gi|70607263|ref|YP_256133.1| 136 SAIDELIPARVRGWVDLAINGSWWIGTMVGSALSLYLLNPHEfpiDLGWRLSFAVGAILGVSIMLIRRYVPESPRWLLVHG 216
                                   ************************************97777779************************************* PP

                                   -HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTH CS
                      Sugar_tr 203 keeeakevlaklrgeedadrelaeekdsleaeqeee...kaswkellssktvrqrlligvvlqifqqltGinaimyyspti 280
                                   k eea+ev+++++ + ++++el e k+s+  +   +       k+++++  +++r+++g+ l+++q + ++++++ ys  +
  gi|70607263|ref|YP_256133.1| 217 KVEEAEEVVKQIEMKVQNSKELSEPKKSISITPIGNvgfRLVFKTVFGR--YKKRAILGLWLMAGQAFLYNAIFFTYSLIL 295
                                   ******************************9955555555555555555..99*****************999*****999 PP

                                   HHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHH CS
                      Sugar_tr 281 fenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialf 359
                                    +   +  +   l  + + + nf+  ++   l d +GRR++  l  ++   ++++ g+ ++l+       +    +f  + 
  gi|70607263|ref|YP_256133.1| 296 SKFYNVPSDeiGLYIFPFAIGNFTGPLILGRLFDSLGRRKMISLTYIISGSLLAFTGYLFYLGIL-----NAFTQTFAWVI 371
                                   99988888888899999*************************99999999999999955555554.....47899999999 PP

                                   HHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH..T-HHHH.HHHHHHHHHHHHHHHHS CS
                      Sugar_tr 360 ialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaig..ggyvfl.vfaglavlfiifvfffv 437
                                   i++fa   ++  +++vsE+fp+++R+ a+a+ +a+    +     +f +++++ +    ++++ + a l+++  i + f  
  gi|70607263|ref|YP_256133.1| 372 IFFFASAGASSAYLTVSEVFPLEIRAMAIAVFYAIGTGLSSYAPSFFGYLLGSKQpsDLFIGYlIGALLMIFPGILTIFLG 452
                                   999999999******************************************999977445544044555666667777777 PP

                                   --STT--CCCC CS
                      Sugar_tr 438 petkgrtleei 448
                                   +    ++lee+
  gi|70607263|ref|YP_256133.1| 453 VDAERKSLEEV 463
                                   78888888876 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6  16.5   7.9e-26     2e-22       8     229 ..      35     291 ..      28     294 .. 0.76
   2 !   33.0  25.2   1.1e-11   2.9e-08       8     179 ..     280     459 ..     271     477 .. 0.69

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 7.9e-26
                         MFS_1   8 salarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslw 86 
                                    +l  +i+g++ +  +  ++l++++ ++++l t+y lga+++++++++l+d++Gr+++++++l ++++g ++l+ ++ ++ 
  gi|70607263|ref|YP_256133.1|  35 DGLEVTIVGVISSVlTRPQTLNLTEFQASFLGTAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAG-TVLSaLSWNFL 114
                                   55666666666666667799*************************************************.55553568888 PP

                         MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wravfyilaivs 161
                                    ++++r ++Glg g+ ++a++++i ++ p + rg +   +++++ +G+++g +l+ +l+          Wr++f + ai++
  gi|70607263|ref|YP_256133.1| 115 SIALFRTITGLGIGGEYSAINSAIDELIPARVRGWVDLAINGSWWIGTMVGSALSLYLLNPHEfpidlgWRLSFAVGAILG 195
                                   9**********************************************************5444889999************ PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeee.......................kgtgpaplvp.........awkallkdpvl. 209
                                   +  ++   +  ++++++r+   + + e                       k        +         ++++++k  +  
  gi|70607263|ref|YP_256133.1| 196 VSIML---IRRYVPESPRWLLVHGKVEeaeevvkqiemkvqnskelsepkK--------SisitpignvGFRLVFKTVFGr 265
                                   **988...6777777777777777777779999999998877776543331........0233456667555555555222 PP

                         MFS_1 210 w......illialllfffgfsglltl 229
                                   +       l++++  +f+ +++++t+
  gi|70607263|ref|YP_256133.1| 266 YkkrailGLWLMAGQAFLYNAIFFTY 291
                                   13322213444444444333334444 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1.1e-11
                         MFS_1   8 salarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..f..a.s 83 
                                    a+ +++++++++l+l++ +++  +eigl +  +a+g + + l+lGrl d +Grr+++ l+++++++ l++    f  +  
  gi|70607263|ref|YP_256133.1| 280 QAFLYNAIFFTYSLILSKFYNVPSDEIGLYIFPFAIGNFTGPLILGRLFDSLGRRKMISLTYIISGSLLAFTGylFylGiL 360
                                   566677788888999**********************************************99999994444455455254 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav..fyilaivsl 162
                                   + ++  +++v+  ++a+a++++++  ++++fp e r++ai++++a     +  +p + g+l+ s   + +   y+++++++
  gi|70607263|ref|YP_256133.1| 361 NAFTQTFAWVIIFFFASAGASSAYLTVSEVFPLEIRAMAIAVFYAIGTGLSSYAPSFFGYLLGSKQPSDLfiGYLIGALLM 441
                                   444455566666666777789********************9999666666666666666663333332312333333333 PP

                         MFS_1 163 la.fvlfllllpeepper 179
                                   ++ ++l ++l ++ ++++
  gi|70607263|ref|YP_256133.1| 442 IFpGILTIFLGVDAERKS 459
                                   332444334433333333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   1.8   6.8e-10   1.7e-06     254     337 ..      54     136 ..      47     145 .. 0.90
   2 ?   -3.7   0.2       1.3   3.3e+03     144     183 ..     159     196 ..     155     201 .. 0.58
   3 ?  -11.2  20.2         7   1.8e+04     232     414 ..     274     449 ..     251     453 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.8e-10
                         MFS_2 254 vlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                   +l+ ++++as++ ++ +++a++g++++++l+ ++g+k+++++++ ++++++vl  l   +n l   ++ +i+g+g+g+ ++
  gi|70607263|ref|YP_256133.1|  54 TLNlTEFQASFLGTAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAGTVLSALS--WNFLSIALFRTITGLGIGGEYS 132
                                   5777899*******************************************9999888..****************998766 PP

                         MFS_2 334 lpws 337
                                   ++ s
  gi|70607263|ref|YP_256133.1| 133 AINS 136
                                   6655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.3
                         MFS_2 144 vlggvlaailafllvlilgglkserkgylifaliialLml 183
                                   ++g++++++l   l+   +       g+++  +++a+L +
  gi|70607263|ref|YP_256133.1| 159 WIGTMVGSALSLYLLNPHEF--PIDLGWRLSFAVGAILGV 196
                                   56666666666666655554..344466666666666655 PP

  == domain 3  score: -11.2 bits;  conditional E-value: 7
                         MFS_2 232 lfllaalalgvlnglllY..yltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll 309
                                   l l+a  a++ ++  + Y   l ++ +   +++ ++ + + i+++ g ++  +l   lg+++++ l +++  +ll+++  l
  gi|70607263|ref|YP_256133.1| 274 LWLMAGQAFLYNAIFFTYslILSKFYNvPSDEIGLYIFPFAIGNFTGPLILGRLFDSLGRRKMISLTYIISGSLLAFTGYL 354
                                   444444444444333333223455666577888888888899999999999999999999999988888887777765444 PP

                         MFS_2 310 ...qpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgyr 387
                                      +  n  + +++ vi++f++ + a+ ++ ++++v+           e+     ++++  +  +ig+g+s ++ s+fgy 
  gi|70607263|ref|YP_256133.1| 355 fylGILNAFTQTFAWVIIFFFASAGASSAYLTVSEVFPL---------EI-----RAMAIAVFYAIGTGLSSYAPSFFGYL 421
                                   345666666666666666666666666666666555533.........33.....33334444578888888888888884 PP

                         MFS_2 388 akasvqspqvv.lalrllyavlpavlll 414
                                    ++ + s+ ++   +  l++++p++l++
  gi|70607263|ref|YP_256133.1| 422 LGSKQPSDLFIgYLIGALLMIFPGILTI 449
                                   4444444433225566777777777765 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.1   5.1e-06     0.013      80     238 ..      62     226 ..      33     232 .. 0.74
   2 !    9.7   1.7   9.5e-05      0.24      77     172 ..     303     404 ..     281     450 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-06
                         TRI12  80 sslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagp.agasplfvgelm 159
                                    s++ t + +g  +  +v+  ltd++gr+ + ++   + + g+++ + + +f ++    t+ g+  g    a    + el+
  gi|70607263|ref|YP_256133.1|  62 ASFLGTAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAGTVLSALSWNFLSIALFRTITGLGIGGeYSAINSAIDELI 142
                                   4567899**********************99999888899999999999888877666777777665515666789***** PP

                         TRI12 160 snktk.flgllivs...ipvvvtsglspylg..qrlaiqgswrwifyiyiitsaiavllivvwyyppsfa..qlhgkkvrk 232
                                     + + ++ l i     i ++v s+ls yl     + i+  wr  f +  i+   +++l +  y p s +   +hgk v+ 
  gi|70607263|ref|YP_256133.1| 143 PARVRgWVDLAINGswwIGTMVGSALSLYLLnpHEFPIDLGWRLSFAVGAILGV-SIML-IRRYVPESPRwlLVHGK-VEE 220
                                   9998735555554334478999999****962257899*******999888753.4433.45677766551156886.556 PP

                         TRI12 233 reelak 238
                                    ee+ k
  gi|70607263|ref|YP_256133.1| 221 AEEVVK 226
                                   666554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.5e-05
                         TRI12  77 sensslfstlwttgqavsilvmgrltdrfgrrpfvilthil.glvgaivgc.....tatkfntllaamtllgvaagpagas 151
                                   s++ +l+   +++g+    l++grl d +grr ++ lt+i+ g + a  g        + f   +a + ++  a+  a ++
  gi|70607263|ref|YP_256133.1| 303 SDEIGLYIFPFAIGNFTGPLILGRLFDSLGRRKMISLTYIIsGSLLAFTGYlfylgILNAFTQTFAWVIIFFFASAGASSA 383
                                   5666788888899999999********************984444555553111114567777777777788888888888 PP

                         TRI12 152 plfvgelmsnktkflgllivs 172
                                    l v e++    + + + +  
  gi|70607263|ref|YP_256133.1| 384 YLTVSEVFPLEIRAMAIAVFY 404
                                   888888887777766665544 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   3.4   1.4e-06    0.0037      23     169 ..      55     202 ..      50     224 .. 0.83
   2 !    4.7   0.0    0.0062        16     312     360 ..     302     353 ..     269     357 .. 0.74
   3 ?    2.0   0.5      0.04     1e+02     323     360 ..     313     353 ..     312     417 .. 0.61
   4 ?    1.5   0.0     0.058   1.5e+02      38      50 ..     431     443 ..     426     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                         MFS_4  23 gqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgs 103
                                   ++l+  qa++l++a  lG  +Ga+++++   +   +   +++l   v+ ++ +al  +f+ ++l R ++G++ +    ++ 
  gi|70607263|ref|YP_256133.1|  55 LNLTEFQASFLGTAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAGTVLSALSWNFLSIALFRTITGLGIGGEYSAIN 135
                                   6778889*******************88776666555688999999999999********************999999999 PP

                         MFS_4 104 slvlahaaaarrervgallfaGvGlGiavsgllv.llllqlglsasslWlalavlsavllllvalll 169
                                   s + + + a  r+ v  ++ +   +G +v++ l  +ll+ ++      W +  ++ a+l + ++l++
  gi|70607263|ref|YP_256133.1| 136 SAIDELIPARVRGWVDLAINGSWWIGTMVGSALSlYLLNPHEFPIDLGWRLSFAVGAILGVSIMLIR 202
                                   9999999999999999999999999999987665155566777777779888777777777666654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0062
                         MFS_4 312 trrllglmTasfgigQilGpllasllaeatgs...lalallvaaaalvlaal 360
                                   +   +gl    f+ig   Gpl+ + l++ +g    ++l  ++++ +l++ + 
  gi|70607263|ref|YP_256133.1| 302 PSDEIGLYIFPFAIGNFTGPLILGRLFDSLGRrkmISLTYIISGSLLAFTGY 353
                                   45678888899******************99722234455677777777665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.04
                         MFS_4 323 fgigQilGpllasllaeatgs...lalallvaaaalvlaal 360
                                   f+ig   Gpl+ + l++ +g    ++l  ++++ +l++ + 
  gi|70607263|ref|YP_256133.1| 313 FAIGNFTGPLILGRLFDSLGRrkmISLTYIISGSLLAFTGY 353
                                   55666666666666655555411122233344444444333 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.058
                         MFS_4  38 ylGYLvGallaaf 50 
                                   ++GYL+Gall +f
  gi|70607263|ref|YP_256133.1| 431 FIGYLIGALLMIF 443
                                   89*******9865 PP

>> Aim19  Altered inheritance of mitochondria protein 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.38   9.6e+02      31      56 ..      48      74 ..      26      77 .. 0.69
   2 ?   11.4   2.1   0.00012       0.3      41     105 ..     338     401 ..     286     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.38
                         Aim19 31 l.sklallkpsklsvllfgaafalggy 56
                                  + +++++l+ +++++ ++g+a  lg+ 
  gi|70607263|ref|YP_256133.1| 48 VlTRPQTLNLTEFQASFLGTAYILGAV 74
                                  335666666677777777776666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00012
                         Aim19  41 klsvllfgaafalggymiydgDlenGsGfltAWSllYllvngkksikslrrgkvvPlaLsalala 105
                                    l+ ++ g++ a+ gy++y g + n+   ++AW +++ +  + +s   l++  v+Pl + a+a a
  gi|70607263|ref|YP_256133.1| 338 SLTYIISGSLLAFTGYLFYLG-ILNAFTQTFAWVIIFFFASAGASSAYLTVSEVFPLEIRAMAIA 401
                                   566777899999******998.7899999****************************99988875 PP

>> Phage_holin_3_7  Putative 3TM holin, Phage_holin_3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00023      0.59      30      71 ..      67     108 ..      56     109 .. 0.88
   2 ?    1.0   1.1      0.17   4.4e+02      29      58 ..     366     395 ..     361     407 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
               Phage_holin_3_7  30 lAyllivasgsvairillglyrevdlaevlinvvLlvlvlra 71 
                                    Ay+l ++ g++++ +l ++y + +l++v++ +  +  vl+a
  gi|70607263|ref|YP_256133.1|  67 TAYILGAVIGAIVFSYLTDKYGRKKLFMVMLGIYVAGTVLSA 108
                                   6******************************99999999876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.17
               Phage_holin_3_7  29 wlAyllivasgsvairillglyrevdlaev 58 
                                    +A+++i + +s+    ++ +  ev + e+
  gi|70607263|ref|YP_256133.1| 366 TFAWVIIFFFASAGASSAYLTVSEVFPLEI 395
                                   68*********9998888888777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.39
# Mc/sec: 3676.61
//
Query:       gi|70607264|ref|YP_256134.1|  [L=684]
Description: hypothetical protein Saci_1523 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00067   19.6   0.3      0.013   15.5   0.1    2.8  2  HTH_45       Winged helix-turn-helix
     0.0013   18.6   0.0     0.0037   17.1   0.0    1.8  1  TrmB         Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.078   13.5   0.0    2.0  1  HTH_27       Winged helix DNA-binding domain
      0.053   13.8   0.0        0.2   12.0   0.0    1.9  1  Sigma_reg_N  Sigma factor regulator N-terminal
      0.077   12.9   0.7       0.47   10.4   0.1    2.6  2  TFIIE_alpha  TFIIE alpha subunit
      0.085   12.2   0.0       0.18   11.1   0.0    1.6  1  AIG1         AIG1 family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.3e-06     0.013      24      71 ..     485     536 ..     464     540 .. 0.78
   2 ?    0.6   0.0      0.19   5.7e+02      55      75 ..     623     643 ..     620     645 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                        HTH_45  24 kimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklke 71 
                                    i  k +L+ +++ + L++L e+ l+    + +k  + +T+kG+++le+lk+
  gi|70607264|ref|YP_256134.1| 485 DIAIKLDLDKNTTASILEKLNENMLVgkefDGKKRYWWITDKGRDVLERLKT 536
                                   689999********************875444666678**********9985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                        HTH_45  55 kYvlTekGlelleklkeleel 75 
                                   +YvlT k  +++++l++++ l
  gi|70607264|ref|YP_256134.1| 623 SYVLTRKDIQTIKELDRVKCL 643
                                   8**************999865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0037       1      62 [.     456     520 ..     456     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                                   HHHCHHHHHCCCHCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                          TrmB   1 LqklGLseyEakvYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                   L+ +G+se E+k+  +L       p+t+ +ia +l++++++  ++L++L +  lV +e   +k+Y
  gi|70607264|ref|YP_256134.1| 456 LATYGISEREIKALEVLTstaPGSPMTTFDIAIKLDLDKNTTASILEKLNENMLVGKEFDGKKRY 520
                                   6789**************44334689*************************99999998888877 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.078       8      68 .]     471     527 ..     463     527 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                        HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   vL + + ++ +++  d++ +l++++ +++++l+kL e+ Lv   g+e d++ +   +TdkG
  gi|70607264|ref|YP_256134.1| 471 VLTSTA-PGSPMTTFDIAIKLDLDKNTTASILEKLNENMLV---GKEFDGKKRYWWITDKG 527
                                   566666.9999999***************************...999*************9 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.6e-05       0.2      46      86 ..      38      78 ..      29      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.6e-05
                   Sigma_reg_N 46 revlelaveitsPNvyvdsgsvsqsgffggeieyelskqvg 86
                                   + ++ + + ++PN+y+ ++s+++s  f  +++ +  +qv+
  gi|70607264|ref|YP_256134.1| 38 SSGVQKTAQTAQPNIYPGKRSLKNSQQFCKKVTSKDGRQVE 78
                                  66789999*************************99999885 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.65   1.9e+03      56      88 ..      83     108 ..      80     123 .. 0.54
   2 ?   10.4   0.1   0.00016      0.47       4      58 ..     452     511 ..     450     546 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                                   SEEEEEEEETTTEEEEEEEEEECCCHCCCHHHH CS
                   TFIIE_alpha  56 lvkykrrrdeekswykyywrinyeklvdvvkrk 88 
                                   +++y +r++++         i+y++l + +k+k
  gi|70607264|ref|YP_256134.1|  83 VINYEKRVENDS-------IIEYPNLKYLLKYK 108
                                   566666666443.......34444455555444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                   HHHHHHCS-.....HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha   4 kevvrkfyg.....eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58 
                                   ke++   yg     ++a +vl + +  + +t  d+a +l +d+n   ++L +L e  lv 
  gi|70607264|ref|YP_256134.1| 452 KEIILATYGisereIKALEVLTSTAPGSPMTTFDIAIKLDLDKNTTASILEKLNENMLVG 511
                                   67777777766222444455555555689**************************99984 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.1e-05      0.18       2      22 ..     221     241 ..     220     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                                   EEEEESSTTSSHHHHHHHHHT CS
                          AIG1   2 tivlvGktgnGkSaTgNsilg 22 
                                   + ++vGk g+GkS+ + s+lg
  gi|70607264|ref|YP_256134.1| 221 NFIVVGKYGAGKSSSVKSVLG 241
                                   679*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (684 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4555.72
//
Query:       gi|70607265|ref|YP_256135.1|  [L=117]
Description: hypothetical protein Saci_1524 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.048   13.8   0.4      0.057   13.5   0.4    1.1  1  MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase


Domain annotation for each model (and alignments):
>> MGDG_synth  Monogalactosyldiacylglycerol (MGDG) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   3.2e-06     0.057      16      86 ..      14      87 ..       5      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-06
                                  HGGGEEEEEEE----------------.-----------------------------------HH..HHHHHHH CS
                    MGDG_synth 16 fgdeyqvlvkdllkelnpfllkavlks.Ylflvkvsalyrllyygteekiqkksilaklatflak..elaalle 86
                                  ++++ +v+     k +  +++ ++++s Y ++v + +ly+++y+  e+k ++ + l  ++ +l+   e+++l++
  gi|70607265|ref|YP_256135.1| 14 NSEKKRVKYVYATKGAIFIVTGELKESkYSYAVEIRPLYGKFYDAKEKKTYNAEELREYKVYLNVrkEMEELVD 87
                                  5666666666666777778888888888*************************999999988753237777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 756.35
//
Query:       gi|70607266|ref|YP_256136.1|  [L=107]
Description: hypothetical protein Saci_1525 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-05   24.6   0.0    2.7e-05   23.6   0.0    1.6  1  Sigma70_r4      Sigma-70, region 4
    6.5e-05   22.9   0.0    0.00012   22.0   0.0    1.4  1  HTH_3           Helix-turn-helix
     0.0041   17.4   0.0     0.0059   16.9   0.0    1.2  1  HTH_31          Helix-turn-helix domain
     0.0066   16.4   0.3      0.018   15.0   0.2    1.8  2  HTH_37          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.5   0.1      0.082   12.6   0.1    2.2  1  Sigma70_r4_2    Sigma-70, region 4
      0.014   15.2   0.0      0.026   14.4   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.021   14.6   0.0      0.052   13.3   0.0    1.7  1  HTH_38          Helix-turn-helix domain
      0.022   14.5   0.0      0.038   13.8   0.0    1.4  1  LacI            Bacterial regulatory proteins, lacI family
      0.025   14.2   0.2       0.17   11.5   0.0    2.1  2  HTH_50          Helix-turn-helix domain
      0.031   13.9   0.5      0.051   13.2   0.1    1.5  1  Snf7            Snf7
      0.035   14.5   0.1      0.064   13.7   0.1    1.3  1  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.05   13.7   0.2      0.062   13.4   0.2    1.2  1  PARP_reg        Poly(ADP-ribose) polymerase, regulatory domai
       0.12   11.6   0.1       0.27   10.5   0.1    1.6  1  DUF3666         Ribose-5-phosphate isomerase


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   2.7e-05       1      41 [.       3      45 ..       3      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                  HHHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4  1 aLasLpererevlelrf..geglTleEIgerlgiSrerVrqie 41
                                  ++++L+++erev++       +l+++E ++ lg++ ++V+ + 
  gi|70607266|ref|YP_256136.1|  3 WIEHLTPKEREVVTDFVfsNVKLSMKEMAQALGVTAMAVSKLR 45
                                  789***********9988*********************9875 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     9e-08   0.00012       9      44 ..      24      59 ..      22      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9e-08
                                  THHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                         HTH_3  9 glsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                  +ls++e+A++lGv+  ++s++ + + +Ps etlk++
  gi|70607266|ref|YP_256136.1| 24 KLSMKEMAQALGVTAMAVSKLRRHQIRPSDETLKRM 59
                                  89*******************************987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.2e-06    0.0059      14      54 ..      24      63 ..      10      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                        HTH_31 14 GLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                   Ls +e+A++lgv++  +s+l + ++ rps ++l ++  +l
  gi|70607266|ref|YP_256136.1| 24 KLSMKEMAQALGVTAMAVSKLRRHQI-RPSDETLKRMYSIL 63
                                  6999**********************.9******9986655 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.3e-05     0.018      31      57 ..      24      50 ..      19      71 .. 0.80
   2 ?   -1.1   0.0       1.4   1.9e+03      49      71 ..      70      90 ..      66      92 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                  T--HHHHHHHHT--HHHHHHHHTT--T CS
                        HTH_37 31 elsqseaaqllgiaqPkvsrllrgkls 57
                                  +ls++e+aq+lg++   vs+l+r +++
  gi|70607266|ref|YP_256136.1| 24 KLSMKEMAQALGVTAMAVSKLRRHQIR 50
                                  79*********************8874 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                  HHHHTT--TT--HHHHHHHHHHT CS
                        HTH_37 49 srllrgklsrfsldkLlnlltal 71
                                    ll  +++r+++d L ++ + l
  gi|70607266|ref|YP_256136.1| 70 ELLL--NVRRMYEDILKEIDQEL 90
                                  4455..67777777777665555 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     6e-05     0.082       8      45 ..       4      43 ..       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                                  HTTS-HHHHHHHHHHHTS-..--HHHHHHHHT--HHHHHH CS
                  Sigma70_r4_2  8 laeLperqreifllryleg..lsykEIAellgisegtVks 45
                                  +++L++++re+++   + +  ls kE A+ lg++  +V +
  gi|70607266|ref|YP_256136.1|  4 IEHLTPKEREVVTDFVFSNvkLSMKEMAQALGVTAMAVSK 43
                                  89**********99888765589***********999865 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05     0.026      11      34 ..      27      48 ..      23      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkq 34
                                   k++A+algv+ +aVs++ +   q
  gi|70607266|ref|YP_256136.1| 27 MKEMAQALGVTAMAVSKLRR--HQ 48
                                  689**************974..44 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.052       4      34 ..       6      38 ..       4      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                        HTH_38  4 hLsleeReeIerll..aeGlslreIArrLgrsp 34
                                  hL++ eRe+  +    + +ls++e+A+ Lg+  
  gi|70607266|ref|YP_256136.1|  6 HLTPKEREVVTDFVfsNVKLSMKEMAQALGVTA 38
                                  9***********9445899***********876 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05     0.038       1      37 [.      26      62 ..      26      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                  -HHHHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHH CS
                          LacI  1 tikDVArlAGVSkaTVSrvLnnkerVseetrerVeaa 37
                                  ++k+ A++ GV++++VS+  +++ r s+et +r   +
  gi|70607266|ref|YP_256136.1| 26 SMKEMAQALGVTAMAVSKLRRHQIRPSDETLKRMYSI 62
                                  59****************9999999999999887666 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.17      25      49 ..      26      49 ..       4      50 .. 0.82
   2 ?    0.5   0.0      0.35   4.8e+02       3      15 ..      78      90 ..      76      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        HTH_50 25 StRklAkrLGvShtaianklrkYgI 49
                                  S+  +A++LGv+  a+  klr+ +I
  gi|70607266|ref|YP_256136.1| 26 SMKEMAQALGVTAMAV-SKLRRHQI 49
                                  8899********9997.79**9999 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.35
                        HTH_50  3 sLkeyveefErel 15
                                   ++++++e+++el
  gi|70607266|ref|YP_256136.1| 78 MYEDILKEIDQEL 90
                                  599******9987 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.7e-05     0.051      23      74 ..      48     100 ..      41     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                                   HHHHHHHHHHHHHCTT-.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Snf7  23 kikkleaelkklakkgn.kdralllLKqkkryekqldqldnqlanleqvslai 74 
                                   +i   ++ lk+++   + k+++ llL+ +++ye  l+++d+ l +l  ++ ++
  gi|70607266|ref|YP_256136.1|  48 QIRPSDETLKRMYSILDdKKKVELLLNVRRMYEDILKEIDQELGKLGYARGDL 100
                                   777788999999998655************************99998877665 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.6e-05     0.064      11      50 ..      25      63 ..      22      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-05
                        HTH_26 11 itkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                  ++ +e+a+++g++a  +s+l+  ++ r+s +tL +   +L
  gi|70607266|ref|YP_256136.1| 25 LSMKEMAQALGVTAMAVSKLRRHQI-RPSDETLKRMYSIL 63
                                  5899********************9.*******9987777 PP

>> PARP_reg  Poly(ADP-ribose) polymerase, regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.5e-05     0.062      19      66 ..      22      74 ..      10      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                      PARP_reg 19 lmkkamkele..iDlkkmPLGkLskeqikkgyevLkelselikkkekae...k 66
                                  ++k +mke+   + ++ m   kL ++qi+   e+Lk++++++++k+k e   +
  gi|70607266|ref|YP_256136.1| 22 NVKLSMKEMAqaLGVTAMAVSKLRRHQIRPSDETLKRMYSILDDKKKVElllN 74
                                  34445555543388999****************************99765551 PP

>> DUF3666  Ribose-5-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00019      0.27       6      17 ..      79      90 ..      75      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                  HHHHHHHS-HHH CS
                       DUF3666  6 lleiLkaiDqdL 17
                                  + +iLk+iDq+L
  gi|70607266|ref|YP_256136.1| 79 YEDILKEIDQEL 90
                                  669********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 753.75
//
Query:       gi|70607267|ref|YP_256137.1|  [L=104]
Description: hypothetical protein Saci_1526 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.4   0.1       0.13   11.4   0.1    1.2  1  TAP42     TAP42-like family


Domain annotation for each model (and alignments):
>> TAP42  TAP42-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     7e-06      0.13      97     121 ..      29      52 ..      10      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7e-06
                                   HHHHHHHHCCHHHTTS......... CS
                         TAP42  97 keyyeeFlkrlesyellseeekkll 121
                                   k++y+eFlk++++y++ +e  kk +
  gi|70607267|ref|YP_256137.1|  29 KKWYDEFLKWCDDYDV-TEYCKKDI 52 
                                   789*************.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 699.88
//
Query:       gi|70607268|ref|YP_256138.1|  [L=58]
Description: hypothetical protein Saci_1527 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.026   14.5   0.0    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-06     0.026      11      37 ..      20      48 ..      14      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-06
                                  E-CCCHHHCCEECTCEEEEEECTT..CCC CS
                MazE_antitoxin 11 iPkevrfelgireGdevelevdgd..kii 37
                                  iP+e++++lgi   de +l+v++   +i+
  gi|70607268|ref|YP_256138.1| 20 IPREIVRALGITSEDEFVLSVENRdgDIV 48
                                  9*********************9874444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 437.35
//
Query:       gi|70607269|ref|YP_256139.1|  [L=127]
Description: hypothetical protein Saci_1528 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.0   0.1       0.14   12.1   0.1    1.4  1  VWA_3_C   von Willebrand factor type A C-terminal domain


Domain annotation for each model (and alignments):
>> VWA_3_C  von Willebrand factor type A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.6e-06      0.14      13      33 ..      35      53 ..      27      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-06
                                  HHHHTTEEE.-TTT--EEE-S CS
                       VWA_3_C 13 klLrkVVdvvDpatGTVRLkk 33
                                   lLr+VV+   + tG VR+k+
  gi|70607269|ref|YP_256139.1| 35 ELLRRVVEL--DDTGLVRAKS 53
                                  69*******..569****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 860.01
//
Query:       gi|70607270|ref|YP_256140.1|  [L=63]
Description: hypothetical protein Saci_1529 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.8   0.1     0.0051   16.6   0.1    1.0  1  REC104    Meiotic recombination protein REC104
  ------ inclusion threshold ------
      0.045   13.7   0.1        0.5   10.4   0.0    2.1  2  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> REC104  Meiotic recombination protein REC104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-07    0.0051      33      88 ..       5      61 ..       2      63 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-07
                        REC104 33 lnnktvrrineeefdkaanciltet.sypepelkrtastyllkssfkkpttlslpfi 88
                                  ln     r+ eee++k  + + ++  +y  +++ r+a ++ l++  kk  +  +pf+
  gi|70607270|ref|YP_256140.1|  5 LNKTVATRVTEEEYNKLLEIVKAKGsQYQLSDVVREAIQFYLENYNKKGVLDKIPFL 61
                                  44444579***********9998751578899*******************99*996 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.035   3.2e+02       7      19 ..      11      23 ..       6      27 .. 0.73
   2 ?   10.4   0.0   5.6e-05       0.5      28      44 .]      34      50 ..      33      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.035
                         RHH_3  7 vsidpelaekLka 19
                                  +++++e ++kL +
  gi|70607270|ref|YP_256140.1| 11 TRVTEEEYNKLLE 23
                                  6788888888854 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.6e-05
                         RHH_3 28 rSklldeAiellLekYe 44
                                  +S+ ++eAi  +Le Y+
  gi|70607270|ref|YP_256140.1| 34 LSDVVREAIQFYLENYN 50
                                  6999************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      804  (0.0448435); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 403.53
//
Query:       gi|70607271|ref|YP_256141.1|  [L=640]
Description: thermopsin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-73  244.8  12.2    9.8e-73  244.8  12.2    2.6  2  Thermopsin     Thermopsin
  ------ inclusion threshold ------
      0.082   12.6   0.0       0.19   11.4   0.0    1.6  1  TAP_C          TAP C-terminal domain
       0.11   12.9   0.0        8.4    6.7   0.0    2.8  2  Chordopox_E11  Chordopoxvirus E11 protein
       0.41   11.0   0.1       0.41   11.0   0.1    3.1  2  DUF11          Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.8  12.2   2.2e-76   9.8e-73      16     259 ..      27     282 ..      14     283 .. 0.95
   2 ?   -3.9   5.0       1.7   7.6e+03     123     196 ..     341     397 ..     319     420 .. 0.52

  Alignments for each domain:
  == domain 1  score: 244.8 bits;  conditional E-value: 2.2e-76
                    Thermopsin  16 mGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvt.ggktysywvQnVvsfnttekq 95 
                                   +G+++           +  + t++vlG++ni+sl+aynss n p++aslQLNvvle+++ +g+ty++w+QnV++f t+e+ 
  gi|70607271|ref|YP_256141.1|  27 TGVSA----------HDGPIYTNAVLGYANITSLQAYNSSFNVPYGASLQLNVVLEATStNGNTYYFWLQNVAQFVTNESL 97 
                                   44444..........47899*************************************999********************* PP

                    Thermopsin  96 ltfidNiWNftspsanlsnsaisGnGtvy....asskgefYyayateylelslPltlkLvinvsltsngvpevsFgYsid. 171
                                   ++f+dN+WN+t+++a++sn+  +GnG+++      +++ ++y+y+te +++++Pl+l+L+in+sl+sngv +v+F+Y++  
  gi|70607271|ref|YP_256141.1|  98 MCFTDNVWNYTTATAEISNV--TGNGGIGftynILFGHPTFYGYSTEPMPYRFPLALYLLINESLSSNGV-IVNFIYVVLq 175
                                   *****************877..9******99988999********************************9.*******989 PP

                    Thermopsin 172 ......ggvvtYDnvtinstgkasaeilvngssltps..............gllyDaeLvlgGpgngekttfnslnatlsL 232
                                         ++ vtYD+v+i +++++sa+i+vn+ sltps              g+l+D+eLv+gG++nge+ttf++++++l L
  gi|70607271|ref|YP_256141.1| 176 ngslvpPHPVTYDSVFIPVPDPQSAYIIVND-SLTPSavvlnftlfyqealGNLMDTELVWGGYENGEFTTFTQMSSYLGL 255
                                   ******99***********************.899999******************************************* PP

                    Thermopsin 233 yYlngtnyqpvknaydfGsdTaEtaen 259
                                   +Yl+g++++p++++y++G+dTaE++ +
  gi|70607271|ref|YP_256141.1| 256 FYLSGNSFVPFSTVYTYGNDTAESTGD 282
                                   ***********************9865 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                    Thermopsin 123 vyasskgefYyayateylelslPltlkLvinvsltsngvpevsFgYsid...ggvvtYDnvtinstgkasaeilvng 196
                                   v+                    P+t++ + n +++s+ + ++++  + +   +  +t+ nv+i+ + +   +++vn+
  gi|70607271|ref|YP_256141.1| 341 VV-------------------HPVTITFYRNYTVNSSSYAVLDYPSQ-SltiTPSNTFKNVIITPQYTYYYKVIVNS 397
                                   33...................34444444444444444433333222.13443344445554444444444444443 PP

>> TAP_C  TAP C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.19      17      41 ..      96     120 ..      92     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                                   HHHHHSSTTT-HHHHHHHHHHHG.. CS
                         TAP_C  17 sqkcLeqnnWdyerAlqvFeelkak 41 
                                   s +c  +n W+y+ A++   +++ +
  gi|70607271|ref|YP_256141.1|  96 SLMCFTDNVWNYTTATAEISNVTGN 120
                                   89*************9977777655 PP

>> Chordopox_E11  Chordopoxvirus E11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.033   1.5e+02      68      90 ..     422     444 ..     416     472 .. 0.75
   2 ?    6.7   0.0    0.0019       8.4      67     123 ..     496     548 ..     489     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                 Chordopox_E11  68 Grvspvenefyvfdeellfvkdv 90 
                                    +vs+v+n++yv + e+ +v+++
  gi|70607271|ref|YP_256141.1| 422 TSVSLVNNTYYVSSGERFVVNNT 444
                                   589*********99998877765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0019
                 Chordopox_E11  67 kGrvspvenefyvfdeellfvkdvseeevtgveFvvtddmevsvkprksyavravsd 123
                                      v +v+n++yv + e+ +v+++  ++ t +e  v+  m++sv+  k+y+v+ vs+
  gi|70607271|ref|YP_256141.1| 496 GSAVELVNNTYYVSSGERYVVSSI--SPSTPIE--VSGPMNISVELVKEYKVEIVSS 548
                                   456899*************99999..7777776..8999*************98775 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.1e-05      0.41      55      91 .]      50      89 ..      19      89 .. 0.71
   2 ?   -2.5   5.0       1.4   6.4e+03      18      52 ..     345     384 ..     342     464 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                         DUF11 55 asaltsvgsLeagesatlsftvrvtrtaasga...ltnva 91
                                   +a  s+ ++++g+s++l++ +++t t+ ++    l+nva
  gi|70607271|ref|YP_256141.1| 50 LQAYNSSFNVPYGASLQLNVVLEATSTNGNTYyfwLQNVA 89
                                  233333389******************9998777777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                         DUF11  18 ytltvtNtgpasangvvvtDtlPaglayvsvsas.....q 52 
                                   +t+t+  +++++++ + v D + ++l++ ++ +      +
  gi|70607271|ref|YP_256141.1| 345 VTITFYRNYTVNSSSYAVLDYPSQSLTITPSNTFknviiT 384
                                   899999999*9999******99766666655554333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3928.18
//
Query:       gi|70607272|ref|YP_256142.1|  [L=460]
Description: hypothetical protein Saci_1535 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3159.12
//
Query:       gi|70607273|ref|YP_256143.1|  [L=239]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-33  116.4   0.0    2.3e-33  115.6   0.0    1.4  1  ABC_tran    ABC transporter
    2.5e-12   47.2   2.6    6.4e-06   26.2   0.4    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00024   20.6   0.1      0.062   12.7   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0008   19.2   0.6      0.013   15.3   0.0    2.1  2  AAA_15      AAA ATPase domain
     0.0019   18.6   0.1     0.0066   16.9   0.1    2.0  1  AAA         ATPase family associated with various cellular ac
     0.0094   15.6   0.2      0.023   14.3   0.0    1.6  2  SRP54       SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.019   14.9   0.1    1.8  1  NTPase_1    NTPase
      0.014   16.0   0.1      0.037   14.6   0.0    1.8  2  AAA_18      AAA domain
      0.031   14.5   0.1      0.063   13.5   0.1    1.5  1  AAA_28      AAA domain
      0.033   11.7   0.0      0.045   11.3   0.0    1.1  1  DUF3584     Protein of unknown function (DUF3584)
      0.035   14.6   1.8       0.07   13.6   1.8    1.9  1  AAA_23      AAA domain
      0.041   13.6   0.0      0.077   12.8   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
      0.053   13.9   0.0      0.063   13.7   0.0    1.5  1  AAA_16      AAA ATPase domain
      0.084   12.6   0.1        0.2   11.4   0.0    1.6  2  AAA_30      AAA domain
       0.09   13.0   0.1       0.18   12.0   0.1    1.6  1  AAA_22      AAA domain
        0.1   11.9   0.0       0.16   11.2   0.0    1.3  1  Zeta_toxin  Zeta toxin
       0.13   12.0   0.1       0.33   10.7   0.1    1.7  1  AAA_24      AAA domain
       0.15   12.1   1.2       0.82    9.7   0.2    2.1  2  AAA_5       AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   2.3e-36   2.3e-33       1     137 []      20     162 ..      20     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 2.3e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+ + + +k gekva++G+nGaGK+t l++lagll+p+eG ++++g d+++ + ++++++ig+lp+++  f +ltvren  
  gi|70607273|ref|YP_256143.1|  20 LDGLAFYIKCGEKVALLGPNGAGKTTTLRILAGLLRPNEGIVKIKGFDISK-NPREAKSNIGFLPEDAVPFLNLTVRENle 99 
                                   68899**********************************************.7778999********************** PP

                                   .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                            + +e+i+++l+ l+l e + ++v    ssLS G +q+vala+a++ +p +lllDEp +
  gi|70607273|ref|YP_256143.1| 100 yvgilrninNLKERINHLLDVLELWEYERKTV----SSLSRGNRQKVALAMAIIHEPAILLLDEPLN 162
                                   *********9*********************9....*****************************86 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.4   6.4e-09   6.4e-06       3      96 ..      34     123 ..      33     131 .. 0.85
   2 !   22.0   0.3   1.2e-07   0.00012     233     298 ..     130     189 ..     100     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.4e-09
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83 
                                   +l GpNg+GK++ L++l +l   +++    +++  ++++++  +++  +  pe ++ f    ++ ++ +y ++lr  ++  
  gi|70607273|ref|YP_256143.1|  34 ALLGPNGAGKTTTLRILAGLL--RPNEGIVKIKGFDISKNPREAKSNIGFLPEDAVPFLNL-TVRENLEYVGILRNINNLK 111
                                   799*****************9..79999999999999999999999999999999999999.9999999999999887766 PP

                        AAA_21  84 eeklssvetlles 96 
                                    e++ ++ ++le 
  gi|70607273|ref|YP_256143.1| 112 -ERINHLLDVLEL 123
                                   .555555555555 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.2e-07
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   ++++lS G ++  al+ a++  +   ++ll+DEp n L+   ++r++ ll++ ++     +++TH 
  gi|70607273|ref|YP_256143.1| 130 TVSSLSRGNRQKVALAMAIIHEP---AILLLDEPLNYLDIPTQERVINLLNSMNS---TMLVSTHI 189
                                   45678***************999...************************99955...99999996 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0063       6.3      19      40 ..      26      46 ..      14      54 .. 0.71
   2 !   12.7   0.0   6.2e-05     0.062     119     208 ..     116     200 ..      66     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0063
                                  EEETTSSEEEEEESTTSSHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 19 ilpfsksftaivGpNGSGKsnl 40
                                   ++  +   a++GpNG+GK+  
  gi|70607273|ref|YP_256143.1| 26 YIKCGE-KVALLGPNGAGKTTT 46
                                  555555.45899*******975 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.2e-05
                                   -HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 119 tkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                   +  +v el e ++ + ++LS+G+++ vala+   i  ++  ++ llDe    LD    ++v +ll++ +  + ++v ++  
  gi|70607273|ref|YP_256143.1| 116 HLLDVLELWEYERKTVSSLSRGNRQKVALAMA--I--IHEPAILLLDEPLNYLDIPTQERVINLLNSMN--STMLVSTHIM 190
                                   334555555566666679******98888765..4..4556799*********************9887..8889998877 PP

                                   HHCCC-.SCE CS
                                   xxxxxx.xxx RF
                         SMC_N 200 emleka.dkl 208
                                    + e+  +k+
  gi|70607273|ref|YP_256143.1| 191 SIAERLtNKI 200
                                   7777653444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.013      17      74 ..      25      77 ..      16      83 .. 0.84
   2 ?    2.5   0.1     0.098        98     319     364 ..     147     188 ..      99     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                        AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenises 74
                                  ++i+  e    l G+N++GK++ l++l  +l  +    +  +ki+  d++++  +++s
  gi|70607273|ref|YP_256143.1| 25 FYIKCGE-KVALLGPNGAGKTTTLRILAGLLRPN----EGIVKIKGFDISKNPREAKS 77
                                  6777778.899*********************99....89999999999998776665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.098
                        AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    +  +++ill++EP ++L +  q+ +i+ll ++ ++     +++TH
  gi|70607273|ref|YP_256143.1| 147 AIIHEPAILLLDEPLNYLDIPTQERVINLLNSMNSTM----LVSTH 188
                                   4566799********************9998875544....56665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.6e-06    0.0066       2      38 ..      34      89 ..      33     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-06
                                  EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS.................S CS
                           AAA  2 llyGppGtGKTllakavakel..gvefleisgsellsk.................y 38
                                   l Gp G GKT++ + +a  l  +  +++i+g ++ ++                 +
  gi|70607273|ref|YP_256143.1| 34 ALLGPNGAGKTTTLRILAGLLrpNEGIVKIKGFDISKNpreaksnigflpedavpF 89
                                  699*****************944466999999999833455555555555555550 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.3e-05     0.023       4      34 ..      33      63 ..      31      71 .. 0.81
   2 ?   -2.0   0.0       2.3   2.3e+03     159     177 ..     189     207 ..     171     231 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                  ++l+G++GaGKTttl  La ll+ ++  v +
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILAGLLRPNEGIVKI 63
                                  689****************999877665555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                                   HHHHHHHHTS-EEEEE-SS CS
                         SRP54 159 alsiaaelklPikfigvGe 177
                                   ++sia++l   i++i+ G+
  gi|70607273|ref|YP_256143.1| 189 IMSIAERLTNKIILITKGK 207
                                   4455555555555555554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.9e-05     0.019       2      48 ..      33      82 ..      32     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                  EEEE--TTSSHHHHHHHHHHHH...G..GGEEEE.EEEEE-------EEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg..vkvgGf.yteevreggrrigFk 48
                                  v++ Gp G GKtT ++ ++ ll+ ++  vk++Gf + ++ re ++ igF 
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILAGLLRPNEgiVKIKGFdISKNPREAKSNIGFL 82
                                  7899******************97643589****55677789999***95 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.7e-05     0.037       1      57 [.      33      98 ..      33     156 .. 0.73
   2 ?   -1.4   0.0       3.3   3.3e+03      51      77 ..     163     183 ..     146     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpe.aldeskrldedkl 57
                                  ++l G+ G+GKtt  + L+ +l  +       g+ ++++ +e  + +++ pe a++  +  ++++l
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILAGLLrPNegivkikGFDISKNPREAKSNIGFLPEdAVPFLNLTVRENL 98
                                  6899**************888766678899999999999999999999999873333333333332 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                        AAA_18  51 rldedkldklldaleenssaleegknl 77 
                                    ld++ +++++++l+  +s      + 
  gi|70607273|ref|YP_256143.1| 163 YLDIPTQERVINLLNSMNS------TM 183
                                   5677778888888888776......22 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   6.3e-05     0.063       1      20 [.      32      51 ..      32      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                        AAA_28  1 kivitGgestGKTtlleaLa 20
                                  k++++G+ ++GKTt+l+ La
  gi|70607273|ref|YP_256143.1| 32 KVALLGPNGAGKTTTLRILA 51
                                  799****************9 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.6e-05     0.045      12      37 ..      25      50 ..      14      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                       DUF3584 12 aeldldghtnieGtNaaGKTtLlrLi 37
                                    +++ +++ + G N+aGKTt+lr++
  gi|70607273|ref|YP_256143.1| 25 FYIKCGEKVALLGPNGAGKTTTLRIL 50
                                  568999******************86 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   7.1e-05      0.07      22      40 ..      33      51 ..      11     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
                        AAA_23 22 tlItGpNGaGKTTildAik 40
                                  +++ GpNGaGKTT l+ + 
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILA 51
                                  5789*********998776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.7e-05     0.077      17      49 ..      25      57 ..      16      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.7e-05
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  + i+  + + l Gp+G+GK+T l  ++ lL p+
  gi|70607273|ref|YP_256143.1| 25 FYIKCGEKVALLGPNGAGKTTTLRILAGLLRPN 57
                                  5566566899***********997777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.3e-05     0.063      26      61 ..      32      73 ..      13     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                        AAA_16 26 lvllsGesGvGKsslvrellralekdggif......lrgkcd 61
                                   v l G+ G GK++ +r l+  l+ ++gi+      ++ + +
  gi|70607273|ref|YP_256143.1| 32 KVALLGPNGAGKTTTLRILAGLLRPNEGIVkikgfdISKNPR 73
                                  5899****************9888887777533333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002       0.2      21      45 ..      33      57 ..      26      70 .. 0.82
   2 ?   -3.5   0.0       7.3   7.2e+03      46      60 ..     128     142 ..     119     160 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                        AAA_30 21 avltGpAGtGKttalkalreaweaa 45
                                  ++l Gp G+GKtt+l+ l+ +++ +
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILAGLLRPN 57
                                  5788************999887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.3
                        AAA_30  46 ggrviglAptgkaAk 60 
                                    ++v  l+  +++  
  gi|70607273|ref|YP_256143.1| 128 RKTVSSLSRGNRQKV 142
                                   333333333333222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018      0.18       9     104 ..      34     165 ..      31     198 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsstsskdllrellralglelk 69 
                                   ++ G+ G+GKTt+lr l+  l   + + +                    +++ v f +l++ ++++  +  +lr++++ ++
  gi|70607273|ref|YP_256143.1|  34 ALLGPNGAGKTTTLRILAGLLRPNEGIVKikgfdisknpreaksnigflPEDAVPFLNLTVRENLE--YVGILRNINNLKE 112
                                   688************999988544333337777777777766655555433333355555555222..2344444443333 PP

                        AAA_22  70 a.............erlsseellealeqalrarav....ielliiDEaqh.lr 104
                                   +             er++ + l +  +q +  +++    +++l++DE  + l+
  gi|70607273|ref|YP_256143.1| 113 RinhlldvlelweyERKTVSSLSRGNRQKVALAMAiihePAILLLDEPLNyLD 165
                                   34445666666664444444444333333333333566667777777544465 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.16      21      53 ..      35      67 ..      31     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                    Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                  l G  GAGK+++++ l+  l++++++v++++ d
  gi|70607273|ref|YP_256143.1| 35 LLGPNGAGKTTTLRILAGLLRPNEGIVKIKGFD 67
                                  55889***********************98755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00033      0.33       3      22 ..      31      50 ..      29      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                   k+++ Gp+g+GKTt+++ l
  gi|70607273|ref|YP_256143.1| 31 EKVALLGPNGAGKTTTLRIL 50
                                  589************99866 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00083      0.82       2      24 ..      33      55 ..      32      65 .. 0.84
   2 ?    1.1   0.0      0.36   3.6e+02      64     100 ..     147     187 ..     109     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00083
                                  EEEE--SSSSHHHHHHHGGGGBS CS
                         AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                  v L+Gp G gK++  + la +l+
  gi|70607273|ref|YP_256143.1| 33 VALLGPNGAGKTTTLRILAGLLR 55
                                  779****************9993 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.36
                                   -...G-SEEEEES.GGG--HHHHHHHHHHHHSSEEE..-SS CS
                         AAA_5  64 r...egeilvlDE.veraesevlnsLlslleerrllleegg 100
                                       e++il+lDE ++ ++  +++++++ll+     +  ++
  gi|70607273|ref|YP_256143.1| 147 AiihEPAILLLDEpLNYLDIPTQERVINLLNSMNSTMLVST 187
                                   13358888888885666667777777777776655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1607.34
//
Query:       gi|70607274|ref|YP_256144.1|  [L=876]
Description: DNA polymerase I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-55  187.1   6.5    7.6e-55  186.4   6.5    1.2  1  DNA_pol_B       DNA polymerase family B
    7.5e-31  107.5   0.9    7.5e-31  107.5   0.9    2.1  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    2.8e-06   27.4   0.9    3.9e-05   23.7   0.1    3.2  3  RNase_H_2       RNase_H superfamily
    1.5e-05   24.8   0.0    3.3e-05   23.7   0.0    1.5  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.4   6.5   1.7e-58   7.6e-55      42     427 ..     480     836 ..     445     853 .. 0.82

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 1.7e-58
                                   ...........-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EE CS
                     DNA_pol_B  42 e..........gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvef 112
                                   +          +Y+Ga V++P  g+y + v+vlDFaSLYPsii   N++y+t++ +e ++k   +++       +++++++
  gi|70607274|ref|YP_256144.1| 480 QvktaavikgkKYKGAVVIDPPAGVYFN-VVVLDFASLYPSIIKNWNISYETIDIDECTKKVWVEDE-------TGEKLHY 552
                                   123333555546**************75.889***********************999988544444.......2333333 PP

                                   E-..TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHH CS
                     DNA_pol_B 113 vk..ksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGR 191
                                   v   k+  + ++  l++d+  k  + k++  + ++e ++ l+d  Q a+Kv+ N++YG+ G++n +l++ a+A+svT+iGR
  gi|70607274|ref|YP_256144.1| 553 VCmdKPGITAVITGLIRDFRVKVYKKKAKYSNISEE-QRSLYDVVQRAMKVFINATYGVFGAENFPLYAPAVAESVTAIGR 632
                                   332467788899999999855554445555555555.******************************************** PP

                                   HHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEE CS
                     DNA_pol_B 192 emLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefekv 272
                                   +++++t++  ek                  +lkviYGDTDS+f+   +kd        +el + v++ +f  +l le++k 
  gi|70607274|ref|YP_256144.1| 633 YIITTTYKQAEKL-----------------NLKVIYGDTDSLFLYNPTKDKL------EELIKFVKQ-NF--NLDLEVDKS 687
                                   ***********87.................9*************99996643......456667777.44..479****** PP

                                   EEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHH CS
                     DNA_pol_B 273 ykkllLis.KKkYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvlee 352
                                   yk + +   KK Y g++ +     +k++iKG+   +r+  +++k+   +++++l +  +  ++++e+ ++l+  +kd++++
  gi|70607274|ref|YP_256144.1| 688 YKYVAFSGlKKNYFGVYPD-----GKTEIKGMLAKKRNTPEFIKKEFAEIKNMLASL-NSPNDIPEVKNKLEIKIKDIYNK 762
                                   ******965999*******.....999***************************999.8899******************* PP

                                   HHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEE CS
                     DNA_pol_B 353 leenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaserae 427
                                   l+++  +l+++ +  +lsk+ ++y++++  h+++  +l++  + ++ ++d+i++v v++k+ vk  +l + + + 
  gi|70607274|ref|YP_256144.1| 763 LRNKGYNLDDLAFRIMLSKPLDSYTKNTPQHVKAGLQLRAF-GVNVLPRDVIMFVKVKSKDGVKPIQLAKISEID 836
                                   *************************9999999998888777.789999***********9988655554444444 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.9   1.7e-34   7.5e-31       8     278 ..      78     329 ..      70     380 .. 0.75
   2 ?   -1.5   0.1      0.24   1.1e+03      76      99 ..     739     760 ..     654     813 .. 0.62

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.7e-34
                                   EEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHH CS
                DNA_pol_B_exo1   8 vcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirke 88 
                                   +++++ g+kpyf++++     + +  + ++++++++s +          l +++  y  k+++++k++v++p +++++r+ 
  gi|70607274|ref|YP_256144.1|  78 IMQDESGHKPYFLTDID----P-DKVNKITKVVRDPSFDHL-------ELINKVDPYTGKKIRLTKIVVKDPLAVRRMRSS 146
                                   678899**********9....3.556789999988865444.......455556666666677****************** PP

                                   HHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE............TEEEEGCC--C-.SEEE.EEETTTSCEETTTCC CS
                DNA_pol_B_exo1  89 lspleeivdvyeydvdylerflidnkivgfgwysvk............kylvraegkisncdvei.dcdvddliakpkese 156
                                   l       + ye+ ++y+ ++++dn++ ++  y+v+             ++++  +k+     e+ + +v d i++ ++ e
  gi|70607274|ref|YP_256144.1| 147 L------PKAYEAHIKYYNNYVYDNGLIPGLIYKVNkgkltqlnpelkGEEINEIKKAFADADEMtKETVNDWIPILET-E 220
                                   9......689**************************8777766666663333333333333333303334445554444.4 PP

                                   .S-EEEEEEEEEETEETTS.EETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEE CS
                DNA_pol_B_exo1 157 .pplrvlsFDIeckskkgk.fpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpeypgvkvle 234
                                    p+++  s DIe++  ++  +pd+e+ e pii ++++  dg +        ++ l+  + + ++       ++  gv+v +
  gi|70607274|ref|YP_256144.1| 221 vPDIKRVSLDIEVYTPNRGrIPDPERAEFPIISVALAGnDGSK-------IVLALKREDVNSDF-------SKKDGVQVEI 287
                                   6************9887666******************77777.......89999999955555.......555699**** PP

                                   ESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCC CS
                DNA_pol_B_exo1 235 fdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakely 278
                                   fdsEk+lL + +e+i++y    ++++N+d+FD+pYi  Ra  l+
  gi|70607274|ref|YP_256144.1| 288 FDSEKKLLARLFEIIREY--PMLLTFNGDDFDIPYIYFRALRLN 329
                                   ******************..*******************98333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.24
                                   ESSTCHHHHHHHHHHHCCCCCCCC CS
                DNA_pol_B_exo1  76 vsnpnelkkirkelspleeivdvy 99 
                                   +++pn++++++++l  + +i d+y
  gi|70607274|ref|YP_256144.1| 739 LNSPNDIPEVKNKL--EIKIKDIY 760
                                   22333333333333..23333333 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   8.7e-09   3.9e-05      42     117 ..     290     388 ..     276     421 .. 0.78
   2 ?   -4.1   0.0         3   1.3e+04      68      99 ..     570     601 ..     563     610 .. 0.73
   3 ?   -0.9   0.0      0.31   1.4e+03      20      78 ..     701     752 ..     694     780 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.7e-09
                     RNase_H_2  42 eeekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkel.rkkkl..... 102
                                   +e+k + +lf e++++++ l+tfng  FD+p++  ++ + ++++               +  hiDL+k + ++++      
  gi|70607274|ref|YP_256144.1| 290 SEKKLLARLF-EIIREYPMLLTFNGDDFDIPYIYFRALRLNFSPeevpldvvsgegkfLAGIHIDLYKFFfNRAVRiyafe 369
                                   4566666777.9**********************999666666655666668877555555******97753333356677 PP

                     RNase_H_2 103 ...esysLksveke.lgie 117
                                      + ysL +v+++ lgi 
  gi|70607274|ref|YP_256144.1| 370 gkySEYSLDAVATAlLGIS 388
                                   777889*******955554 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3
                     RNase_H_2  68 sFDvpflkrlfkkykldeeefrhiDLlkelrk 99 
                                    F v++ k+++k+ +++ee++  +D+ +++ k
  gi|70607274|ref|YP_256144.1| 570 DFRVKVYKKKAKYSNISEEQRSLYDVVQRAMK 601
                                   67788888888777788777777787776655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.31
                     RNase_H_2  20 iGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlf 78 
                                   +Gv+  d+k+ e ++ +la++++  ++i+++f    e k+ l + n  + D+p +k+++
  gi|70607274|ref|YP_256144.1| 701 FGVY-PDGKT-E-IKGMLAKKRNTPEFIKKEF---AEIKNMLASLNSPN-DIPEVKNKL 752
                                   6666.45543.3.5777888888888888877...55566666666666.666666666 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   7.4e-09   3.3e-05      35      77 ..     289     330 ..     264     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.4e-09
                DNA_pol_B_exo2  35 ssekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgv 77 
                                   +sek+l+++ fe+++++ p l +fng  fD+p +++ral+ + 
  gi|70607274|ref|YP_256144.1| 289 DSEKKLLARLFEIIREY-PMLLTFNGDDFDIPYIYFRALRLNF 330
                                   579**********9987.8********************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.43
# Mc/sec: 6082.31
//
Query:       gi|70607275|ref|YP_256145.1|  [L=147]
Description: hypothetical protein Saci_1538 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-52  175.7   3.6    4.7e-52  175.4   3.6    1.0  1  DUF2286    Uncharacterized protein conserved in archaea (DUF2
  ------ inclusion threshold ------
      0.028   14.4   0.1      0.056   13.4   0.1    1.5  1  PDDEXK_10  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> DUF2286  Uncharacterized protein conserved in archaea (DUF2286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   3.6   5.3e-56   4.7e-52       1     135 [.       2     135 ..       2     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 5.3e-56
                       DUF2286   1 kvlvikaeegkiaskeivegdleevvkevakealkeWnpeesDfivlrdklelelklplkpelydklkelslsregneaiv 81 
                                   k+lv+++eeg+i++ke+v+g l++++ ++a++al eW++++sDf++++d++e++++lplkp+ly+++k++ +sr+++eai+
  gi|70607275|ref|YP_256145.1|   2 KILVLRSEEGNISKKEVVDGGLRNILVKIANDALGEWDERSSDFTIIKDTQEVKIPLPLKPQLYEIIKDFLKSRTKTEAIA 82 
                                   89******************************************************************************* PP

                       DUF2286  82 klPvyvisfdnewidedtyvdkkvyvvapyiddeakkeleeeaaevtkeekeee 135
                                   ++Pvy+isfdn+w+ e++y+dkkvy+v+pyid++a+kele++a++vt+ e+ e 
  gi|70607275|ref|YP_256145.1|  83 EIPVYIISFDNQWV-ESDYRDKKVYIVSPYIDENAEKELEDYAKQVTSLERPEP 135
                                   **************.********************************9988665 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.2e-06     0.056      35      70 ..      93     126 ..      78     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-06
                     PDDEXK_10  35 kelYekakgvkvdrlivvtpfiddrnpervkavAer 70 
                                   +++ e   + k  ++++v+p+id++ ++ +   A++
  gi|70607275|ref|YP_256145.1|  93 NQWVESDYRDK--KVYIVSPYIDENAEKELEDYAKQ 126
                                   55666666666..9***********99999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 964.09
//
Query:       gi|70607276|ref|YP_256146.1|  [L=164]
Description: hypothetical protein Saci_1539 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-08   33.4   0.1    4.1e-07   29.7   0.1    2.0  1  DOT1             Histone methylation protein DOT1
      7e-06   25.9   0.1    1.2e-05   25.1   0.1    1.4  1  Methyltransf_31  Methyltransferase domain
    8.8e-06   26.3   0.0    1.6e-05   25.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.8e-05   24.7   0.1      2e-05   24.6   0.1    1.3  1  Methyltransf_18  Methyltransferase domain
    4.6e-05   22.9   0.0    5.8e-05   22.6   0.0    1.0  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00012   21.7   0.0    0.00016   21.3   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00019   21.0   0.0    0.00022   20.7   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0009   18.9   0.0    0.00095   18.8   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0013   18.1   0.0     0.0017   17.7   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0043   16.5   0.0     0.0057   16.1   0.0    1.1  1  TehB             Tellurite resistance protein TehB
     0.0053   17.5   0.1      0.014   16.1   0.1    1.8  1  Methyltransf_12  Methyltransferase domain
      0.006   15.9   0.0     0.0077   15.5   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
     0.0064   17.1   0.0      0.012   16.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.025   14.6   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
      0.045   13.3   0.1       0.16   11.5   0.1    1.8  1  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
       0.05   12.7   0.1      0.057   12.5   0.1    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.089   12.4   0.0        0.1   12.2   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.093   12.4   0.0       0.13   11.9   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   4.1e-10   4.1e-07      29     156 ..      18     130 ..      10     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.1e-10
                                   HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEE.SS CS
                          DOT1  29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefi.rk 108
                                   ++++++l+  + +ked+ +DLG G G+vv+ aa ++++k+sv +Ei d+     e+ ++++k+   + G       f+ ++
  gi|70607276|ref|YP_256146.1|  18 KVVKRMLEIAKAGKEDTVYDLGCGDGRVVITAAKDFEVKKSVCIEINDERL--KETLENINKSN--VVGR-----AFAvKG 89 
                                   568899999999**********************************99854..44444444432..2232.....233367 PP

                                   -STT-HHHHHHGGG-SEEEE--TT--HHHHHHHHHHHTT--TT-EEEE CS
                          DOT1 109 sFvenekveeiieeadvilvNNfaFdaelnkqlkellqdlkegtkiis 156
                                   +F e +  e  +   ++ l  N+  ++ l+ +l+   ++lk gt+i+s
  gi|70607276|ref|YP_256146.1|  90 NFFEADLSEATV--LTMFLLTNV--NEMLKPKLE---KELKPGTRIVS 130
                                   777666554442..222222222..223333333...35677777776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.2e-08   1.2e-05       3     122 ..      31     143 ..      29     159 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-08
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq.gdieeleklledekfDlilsne 82 
                                   k+ +v+DlGCG G+ ++ +a + ++ ++ v i+i+ e ++   en  k ++    F + g+++e++  l++    +++   
  gi|70607276|ref|YP_256146.1|  31 KEDTVYDLGCGDGRVVITAA-KDFEVKKSVCIEINDERLKETLENINKSNVVGRAFAVkGNFFEAD--LSE--ATVLTM-- 104
                                   6789****************.8888899*******************9999966666659999988..443..223222.. PP

               Methyltransf_31  83 vlnaladpdkile.eiervlkpggilliedprllaelpakv 122
                                      +l++ ++ l+ ++e+ lkpg+++++ ++ +  + p++v
  gi|70607276|ref|YP_256146.1| 105 --FLLTNVNEMLKpKLEKELKPGTRIVSHEFEIRGWIPKEV 143
                                   ..356777777777888999999999998888666666555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.6e-08   1.6e-05       1      70 [.      35     106 ..      35     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-08
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs 70 
                                   v dlGcG Gr+++ +ak ++ +k ++++i++e l+++ e+++++++  ++  v+g++ + ++ ++++  +++
  gi|70607276|ref|YP_256146.1|  35 VYDLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKSNVvgRAFAVKGNFFEADLSEATVLTMFL 106
                                   78*****************889********************999988777788888776666655555544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1     2e-08     2e-05       3      73 ..      21      90 ..      19     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2e-08
               Methyltransf_18  3 kRLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73
                                  kR+ +ia+  + +++v D G+  g + i ++k   +kk + ++in++ l++  eni+k+++  +  ++ ++
  gi|70607276|ref|YP_256146.1| 21 KRMLEIAKAGK-EDTVYDLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKSNVVGRAFAVKGN 90
                                  79999999877.889********************************************998777666666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.9e-08   5.8e-05     161     257 ..      31     129 ..      15     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.9e-08
                          PrmA 161 egeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk..eekadvivaNILae 237
                                   ++++v D+G+G G   i aa+ ++ kk v + i++  +k + eN+++ +v    + v  +++ ++   ++a v+    L +
  gi|70607276|ref|YP_256146.1|  31 KEDTVYDLGCGDGRVVItAAKDFEVKKSVCIEINDERLKETLENINKSNVVGrAFAV--KGNFFEadLSEATVLTMFLLTN 109
                                   3459*********777725566***********************876555527766..4555543345688999999999 PP

                          PrmA 238 vlielaedikklvkegglli 257
                                   v   l +++ k +k+g++++
  gi|70607276|ref|YP_256146.1| 110 VNEMLKPKLEKELKPGTRIV 129
                                   999999********999876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.6e-07   0.00016      23      86 ..      23      86 ..      14     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-07
                                  HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE CS
                           MTS 23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevva 86
                                  +le  ++ ++++v DlGcG G + +++ak  +  + ++++++ + l+ + en++++++ ++++a
  gi|70607276|ref|YP_256146.1| 23 MLEIAKAGKEDTVYDLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKSNVVGRAFA 86
                                  566666668899*****************************************99998754443 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.2e-07   0.00022       3      50 ..      33      80 ..      31     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-07
                                  EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT CS
                Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel 50
                                   +v ++GcG G+++++ Ak++  k+ + iEi+ +++++ l++i+++++
  gi|70607276|ref|YP_256146.1| 33 DTVYDLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKSNV 80
                                  5789***************************************99865 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   9.5e-07   0.00095       3      61 ..      34     106 ..      32     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.5e-07
               Methyltransf_15   3 vilDlfsGaGGnviqfalvf..ekviaieinleklacaqhNaevYgvsdkitlvlgdvfe............l 61 
                                   ++ Dl +G G  vi+ a+ f  +k ++iein e+l+ + +N +  +v  + + v+g++fe            l
  gi|70607276|ref|YP_256146.1|  34 TVYDLGCGDGRVVITAAKDFevKKSVCIEINDERLKETLENINKSNVVGRAFAVKGNFFEadlseatvltmfL 106
                                   577999************972257899********************************96666666544441 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0017      52     110 ..      21      80 ..      17     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS-S CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeldl 110
                                   +++le ++  + +t+ d+GcG G +v++a++ ++vk  v + + +e+ k + +++++ ++
  gi|70607276|ref|YP_256146.1|  21 KRMLEIAKAGKEDTVYDLGCGDGRVVITAAKDFEVKkSVCIEINDERLKETLENINKSNV 80 
                                   5667777777889**********************6379999999999999888888765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.7e-06    0.0057      23     123 ..      24     121 ..      12     131 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.7e-06
                                   HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEES CS
                          TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstv 103
                                   +e +k  k   v dlgcg+gr  +  +++ ++v+     e   + l+e+ e  n +n+  + + +    ++   d+  +tv
  gi|70607276|ref|YP_256146.1|  24 LEIAKAGKEDTVYDLGCGDGRVVI-TAAKDFEVKKSVCIEINDERLKETLENINKSNVVGRAFAVKGNFFE--ADLSEATV 101
                                   3444444555699********765.68899*9987666666666666666666666677777777665554..47888999 PP

                                   SGGGS-GGGHHHHHHHHHHT CS
                          TehB 104 vlmfleaeripsiienmqec 123
                                   + mfl ++    +   +++ 
  gi|70607276|ref|YP_256146.1| 102 LTMFLLTNVNEMLKPKLEKE 121
                                   99999876555444455555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-05     0.014       2      43 ..      37      78 ..      36     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
               Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakr 43
                                  ++GcG+G+++   +++++ ++ ++++i+ + ++ + e ++k 
  gi|70607276|ref|YP_256146.1| 37 DLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKS 78
                                  89******************************5555444443 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.7e-06    0.0077      30      71 ..      15      56 ..      12      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.7e-06
                      N6_Mtase 30 TPrevsklivellepksgesvyDpacGsggllvqaekvlkee 71
                                  TP +v+k + e+++  ++ +vyD  cG g + ++a+k ++ +
  gi|70607276|ref|YP_256146.1| 15 TPDKVVKRMLEIAKAGKEDTVYDLGCGDGRVVITAAKDFEVK 56
                                  9************9999999***************9987643 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05     0.012       2      64 ..      37      94 ..      36     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                  EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEE CS
               Methyltransf_11  2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDl 64
                                  d+GcG Gr++   ak +  ++ v++++++e lk   e++++++     vv++a    ++ n f +
  gi|70607276|ref|YP_256146.1| 37 DLGCGDGRVVITAAKDFevKKSVCIEINDERLKETLENINKSN-----VVGRAFA--VKGNFFEA 94
                                  9*************9999**************99999999998.....5555543..33333333 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.5e-05     0.025      12      85 ..      19      92 ..      15     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
               Methyltransf_32 12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraek...lgkkfnkrlsfa 85
                                  +v+++l+  ak+ ++ tv D+G+G g    + a    +    k v+i++++e+ +++ +  +k   +g++f+ + +f 
  gi|70607276|ref|YP_256146.1| 19 VVKRMLEI-AKAGKEDTVYDLGCGDGRVVITAAK---DfEVKKSVCIEINDERLKETLENINKsnvVGRAFAVKGNFF 92
                                  56666665.78899************98877777...42456789******999888765555122445555555544 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00016      0.16       1      58 [.      35      92 ..      35     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                          TrmK  1 laDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGl 58
                                  ++D+G+  ++  i + k  +v+  + +e+n+  l++  +n++ks+   +    +g+ +
  gi|70607276|ref|YP_256146.1| 35 VYDLGCGDGRVVITAAKDFEVKKSVCIEINDERLKETLENINKSNVVGRAFAVKGNFF 92
                                  58*******************************************9988777777766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.7e-05     0.057      17      73 ..      18      76 ..      15     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                  HHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S.-HHHHHHHHCHTT CS
                        RrnaAD 17 kvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlEl.derLakllqkkls 73
                                  kv+++ l+ ++  +++tv+++g G G      ak +  k+ v +E+ derL + l++ ++
  gi|70607276|ref|YP_256146.1| 18 KVVKRMLEIAKAGKEDTVYDLGCGDGRVVITAAKDFevKKSVCIEInDERLKETLEN-IN 76
                                  7889999999999*************999999999999*******747788777776.33 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001       0.1      14      54 ..      32      73 ..      15     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                          MetW 14 gsrvldlGcGdGellellkeekqvd.grGleldeegvaecva 54
                                  + +v dlGcGdG ++   +++ +v+ +  +e+++e ++e+++
  gi|70607276|ref|YP_256146.1| 32 EDTVYDLGCGDGRVVITAAKDFEVKkSVCIEINDERLKETLE 73
                                  468*********998877777777526789999988877654 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.13      23     102 ..      14      93 ..       6     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   SSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHT.T-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HH CS
                 Cons_hypoth95  23 PttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSR.gakkavlvekdkeavkilkenleelkleeetaelkedale 102
                                   Pt d+v + + +i + ++++ +v Dl +G G + + A+   ++kk+v++e ++e +k   en+++ ++ +++ ++k + +e
  gi|70607276|ref|YP_256146.1|  14 PTPDKVVKRMLEIAK-AGKEDTVYDLGCGDGRVVITAAKDfEVKKSVCIEINDERLKETLENINKSNVVGRAFAVKGNFFE 93 
                                   999**9999999866.788889*************99864389**********************9999877776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1123.70
//
Query:       gi|70607277|ref|YP_256147.1|  [L=106]
Description: hypothetical protein Saci_1540 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.57
# Mc/sec: 563.10
//
Query:       gi|70607278|ref|YP_256148.1|  [L=192]
Description: CDP-alcohol phosphatidyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-10   41.8   1.7    1.4e-10   41.8   1.7    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
        3.9    7.8   9.2       0.47   10.8   2.7    2.2  2  Orf78            Orf78 (ac78)


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   1.7   1.5e-14   1.4e-10       3      66 .]      27      90 ..      25      90 .. 0.94
   2 ?   -1.5   5.9      0.52   4.6e+03       8      39 ..     156     178 ..     108     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.5e-14
                                  HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
               CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                  +n+iT+++l+ls++ +++l++++  +l+++lll+++++Da+DG +AR  ++  + G +lDs +D
  gi|70607278|ref|YP_256148.1| 27 ANTITFVGLILSLIYLIVLVFFKNPILGLVLLLLSGFMDAIDGEVARLSGSAGSKGSFLDSSLD 90
                                  8************999999999999**************************778*******988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.52
                                   HHHHHHHHHHHHGGGS-H..HHHHHHHHHHHH CS
               CDP-OH_P_transf   8 llrlllsvlailllltyyplvlailllliasl 39 
                                   l+++++    + l+     l++a ++l+++++
  gi|70607278|ref|YP_256148.1| 156 LVSIFS----V-LI----SLYIAYIFLILSIV 178
                                   112222....2.22....24556666666655 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5     0.073   6.6e+02      65      80 ..      30      46 ..       6      50 .. 0.55
   2 ?   10.8   2.7   5.2e-05      0.47      63      89 ..     149     175 ..     126     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.073
                         Orf78 65 illisll.avvcvlvll 80
                                  i +++l+ +++ ++vl+
  gi|70607278|ref|YP_256148.1| 30 ITFVGLIlSLIYLIVLV 46
                                  22233220333333333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.2e-05
                         Orf78  63 lnillisllavvcvlvllyviyYfvil 89 
                                     +++i l+++++vl+ ly+ y f+il
  gi|70607278|ref|YP_256148.1| 149 IILFVILLVSIFSVLISLYIAYIFLIL 175
                                   456788999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1332.59
//
Query:       gi|70607279|ref|YP_256149.1|  [L=302]
Description: DNA primase large subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-06   25.2   3.0     0.0022   17.4   0.3    3.2  2  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
     0.0042   17.4   1.1        2.6    8.4   0.1    3.3  3  DUF1456          Protein of unknown function (DUF1456)
  ------ inclusion threshold ------
       0.29   11.5   4.4        4.2    7.8   0.3    2.9  3  SporV_AA         Stage V sporulation protein AA


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   3.7e-07    0.0022       3      55 ..     138     200 ..     136     209 .. 0.86
   2 !    5.2   0.2     0.002        12      98     140 ..     207     246 ..     203     296 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-07
                                   EEEEHHHHHHHTT..-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH........ CS
               DNA_primase_lrg   3 ykvpfedvldlvk..rr........rvllkkGyaylpkeeleslllekfrkrlekalestkes 55 
                                   +++p++d+l  ++  +r        ++++ +G++y++k +l +ll+ek+r ++ + ++s+k  
  gi|70607279|ref|YP_256149.1| 138 FSIPLTDYLFHIReiKRinenfklnKRIVTNGKVYINKADLTRLLREKIRLKIIELINSIKLP 200
                                   7899999997777676688899999******************************99999865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.002
                                   TGG.SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHC CS
               DNA_primase_lrg  98 kni.dklakesfPpCmrelleglkknghlkhegrlqltlFlkdi 140
                                   k+i d+l+ +  PpC+ el    +k+++l +e+ + l+++  ++
  gi|70607279|ref|YP_256149.1| 207 KKIaDELRGRKTPPCIVEL----RKKKELTDEEKRILVVYSVNV 246
                                   5677888888888888877....788888888887777776543 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00044       2.6      21      55 ..      30      64 ..      26      66 .. 0.93
   2 !    5.2   0.0    0.0046        28      17      44 ..     103     130 ..      97     136 .. 0.83
   3 ?   -0.0   0.0      0.19   1.1e+03      22      42 ..     165     185 ..     158     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00044
                       DUF1456 21 eifklggvevtkeelsalLkkedeegyeeckdqvL 55
                                  +i+++  +ev ke l++++k e+ e + +++++vL
  gi|70607279|ref|YP_256149.1| 30 DILESKYLEVAKERLEKIIKDEKVESFSNVRNSVL 64
                                  7999999*************************998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0046
                       DUF1456  17 edmveifklggvevtkeelsalLkkede 44 
                                   e+++ei kl gv+v+k+el+  +k +++
  gi|70607279|ref|YP_256149.1| 103 ENLLEIGKLLGVNVSKDELKFSIKDKGK 130
                                   6899***************877776655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.19
                       DUF1456  22 ifklggvevtkeelsalLkke 42 
                                   i+  g v ++k++l++lL+++
  gi|70607279|ref|YP_256149.1| 165 IVTNGKVYINKADLTRLLREK 185
                                   7788999999******99975 PP

>> SporV_AA  Stage V sporulation protein AA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0077        46      19      65 ..      26      76 ..      19      86 .. 0.78
   2 ?   -2.0   0.0      0.78   4.6e+03      59      59 ..     188     188 ..     155     201 .. 0.59
   3 ?    7.8   0.3   0.00071       4.2      21      74 ..     238     289 ..     223     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0077
                      SporV_AA 19 Vtlgdvae...vycsdkkvekklkaikvykikekkkkrvvi.svlkvieaI 65
                                  Vtl+d++e   ++  ++++ek +k+ kv ++++ ++++ v+ s + +++++
  gi|70607279|ref|YP_256149.1| 26 VTLNDILEskyLEVAKERLEKIIKDEKVESFSNVRNSVLVFySLILIVALL 76
                                  88999987666888999***************9988866651555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.78
                      SporV_AA  59 l 59 
                                   l
  gi|70607279|ref|YP_256149.1| 188 L 188
                                   2 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00071
                      SporV_AA  21 lgdvaevycsdkkvekklkaikvykikekkkkrvvisvlkvieaIkkeypnvev 74 
                                   +  v +v    ++v+++l +  v k++ ++++r+++  ++++++++  ++++ v
  gi|70607279|ref|YP_256149.1| 238 ILVVYSVNV--NEVTDELDKELVAKFRGNRRERYIVYSCEIMKKLNLCVAECGV 289
                                   444455554..5799***************************998776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1979.59
//
Query:       gi|70607280|ref|YP_256150.1|  [L=571]
Description: methionyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.3e-151  504.9   0.1   1.6e-151  504.6   0.1    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
    5.5e-11   41.4   0.6    2.9e-05   22.5   0.0    3.0  3  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    0.00017   21.6   0.0    0.00034   20.6   0.0    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
       0.27   11.3   3.7       0.54   10.3   3.7    1.5  1  DZR            Double zinc ribbon
        2.7    7.9   5.1         10    6.0   0.3    2.8  2  zinc_ribbon_2  zinc-ribbon domain
        5.5    6.6   9.2         12    5.4   0.7    2.8  2  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.6   0.1  5.2e-155  1.6e-151       1     391 []       3     397 ..       3     397 .. 0.98

  Alignments for each domain:
  == domain 1  score: 504.6 bits;  conditional E-value: 5.2e-155
                                   EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHT.T-E.EEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHH CS
                  tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlr.gee.vlfvcgtDehGtpielkAekegvtpeelvekvheeikelf 78 
                                   vlvt+a+pY+n+++HlG+l+ +++saD+faRy rl+ g+e v+fv+g+DehGtpie++A+k++++p++l++++h+  k+lf
  gi|70607280|ref|YP_256150.1|   3 VLVTSAWPYVNAVPHLGNLIgSILSADVFARYARLKyGKEnVVFVSGSDEHGTPIEIEARKRNIEPKKLTDQAHAYDKKLF 83 
                                   69*********************************995555**************************************99 PP

                                   .HHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB CS
                  tRNA-synt_1g  79 .kklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkk 158
                                    ++++isfd+y+rt+se hke+v++++ kl++  +i+ +e e  yc+kd+ flpdr+++g CP+c+ e+argdqc++cg+ 
  gi|70607280|ref|YP_256150.1|  84 iDTWKISFDNYSRTESEVHKEFVRNFLVKLEK--YIKVEEDEIPYCEKDKLFLPDRFIKGVCPYCGFEDARGDQCDNCGRL 162
                                   4569**************************98..9********************************************** PP

                                   -E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET. CS
                  tRNA-synt_1g 159 leptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP. 238
                                   l+p  l+n+k+a++g+ p++k t+h+ff+ls+f +k+++wi ++++++++nvk+++++w+kegL++++i+rd  wGip P 
  gi|70607280|ref|YP_256150.1| 163 LTPRSLVNAKCALCGNPPVFKVTKHWFFDLSEFGDKIRDWI-SSSSTMPDNVKSVALSWVKEGLRPRSITRDNMWGIPAPf 242
                                   *****************************************.77779********************************** PP

                                   .TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EE CS
                  tRNA-synt_1g 239 .gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvv 316
                                    gae+k++YVW++Al+gY+sat e++k+ g+ee wke+W   ++++ ++figkd+i+FH++++Pa+l++  ++++lp+ ++
  gi|70607280|ref|YP_256150.1| 243 aGAENKTIYVWFEALLGYLSATVEYFKNLGKEEMWKEFW-LYNDTKTYYFIGKDNIPFHAVILPAMLMAsnEKYNLPSVIA 322
                                   ***************************************.6689*************************9999******** PP

                                   EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                  tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                   a+eyl +eg+K+SkSr+++v+++ea + +d++++R+ l++ +pe+kD++f+w+++ + vN+eL+d++gn++nRvl
  gi|70607280|ref|YP_256150.1| 323 ATEYLLYEGQKFSKSRKIGVWIDEADKLMDVEYWRFILIRLRPEEKDTNFTWREALRIVNTELNDDIGNYANRVL 397
                                   *************************************************************************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   9.6e-09   2.9e-05      30     108 ..       8      90 ..       2     107 .. 0.73
   2 !   14.4   0.1   2.8e-06    0.0085     368     438 ..     176     247 ..     160     267 .. 0.87
   3 ?    1.9   0.0     0.017        52     518     601 ..     288     372 ..     244     373 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.6e-09
                   tRNA-synt_1  30 gPPyvtGslHiGhalaktlk.divirykrmk.Gk.evlyvpGwDhaGlaieakvekklgakek..kerkklgreefrekvr 105
                                     Pyv+  +H+G+ + ++l  d+  ry+r+k Gk +v +v G D +G +ie +  k+  + +k  ++ + + ++ f++  +
  gi|70607280|ref|YP_256150.1|   8 AWPYVNAVPHLGNLIGSILSaDVFARYARLKyGKeNVVFVSGSDEHGTPIEIEARKRNIEPKKltDQAHAYDKKLFIDT-W 87 
                                   56*****************5599******986652799**************998886555542144566666666654.4 PP

                   tRNA-synt_1 106 ewk 108
                                   ++ 
  gi|70607280|ref|YP_256150.1|  88 KIS 90 
                                   443 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-06
                   tRNA-synt_1 368 skkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhriplfvske 438
                                    ++p ++++t+ Wf  ++e+ d++ + +++ + +p+  ++   sw+++  +   i R+ +WG + p+  +++
  gi|70607280|ref|YP_256150.1| 176 CGNPPVFKVTKHWFFDLSEFGDKIRDWISSSSTMPDNVKSVALSWVKEgLRPRSITRDNMWGIPAPFAGAEN 247
                                   5677789***************************************8747999***********99765555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.017
                   tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgr 597
                                     +  G D i +    l  + +a +++    +v+     +  eG+K SKs +  +  ++  k + ++  R++li l +  +
  gi|70607280|ref|YP_256150.1| 288 TYYFIGKDNIPFHAVILPAMLMASNEKYNLPSVIAATEYLLYEGQKFSKSRKIGVWIDEADKLMDVEYWRFILIrLRPEEK 368
                                   345678888877665555555555555566688888888889********9988877777788899999999998888888 PP

                   tRNA-synt_1 598 dinl 601
                                   d+n+
  gi|70607280|ref|YP_256150.1| 369 DTNF 372
                                   8876 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00034      40     134 ..     457     563 ..     423     569 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                   Anticodon_1  40 cdwylelvkprlysesaedkra.aqevllevletllrllaPfmPfitEelwqr......eeeelgkkesimlaewpe.kae 112
                                    + yl+   p+   ++++++ + + ++    l+tl ++l+P+mP  +  l+q+      e+e+ ++  s+    +p  k  
  gi|70607280|ref|YP_256150.1| 457 GNLYLNNRAPWSLVKTNKEEANnVLYISVNSLRTLAIMLYPIMPTYSSNLYQQlglsnlESETWDSAGSL--KIMPGhKIG 535
                                   57788888888888777666444889999**********************8877665544333333333..223321221 PP

                   Anticodon_1 113 elekele............eeevellkeivkair 134
                                         e            ee ++ l+ei + ++
  gi|70607280|ref|YP_256150.1| 536 ------EirslfkkiemspEELMKKLDEIRREVE 563
                                   ......0222222344455666666666655555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.7   0.00018      0.54       1      35 [.     143     177 ..     125     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                           DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCg 35 
                                   Cp Cg e +++   C++Cg  l + +  + +C  Cg
  gi|70607280|ref|YP_256150.1| 143 CPYCGFE-DARGDQCDNCGRLLTPRSLvNAKCALCG 177
                                   6666666.5555566666666653333666666666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0035        10      16      22 ..     143     149 ..     136     149 .. 0.83
   2 ?    2.9   0.6     0.033        98       2      21 ..     156     178 ..     155     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0035
                 zinc_ribbon_2  16 CpyCGtp 22 
                                   CpyCG++
  gi|70607280|ref|YP_256150.1| 143 CPYCGFE 149
                                   9999975 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.033
                 zinc_ribbon_2   2 CpnCGaelqdnakF...CpyCGt 21 
                                   C nCG+ l +++     C  CG 
  gi|70607280|ref|YP_256150.1| 156 CDNCGRLLTPRSLVnakCALCGN 178
                                   88999988888777777777775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7    0.0041        12      18      24 ..     142     148 ..     142     149 .. 0.81
   2 ?    4.2   2.1    0.0099        30       4      23 ..     155     177 ..     153     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0041
                   zf-ribbon_3  18 vCpyCGt 24 
                                   vCpyCG 
  gi|70607280|ref|YP_256150.1| 142 VCPYCGF 148
                                   6999996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0099
                   zf-ribbon_3   4 rCPnCGaplssdd...nvCpyCG 23 
                                   +C nCG +l+++     +C+ CG
  gi|70607280|ref|YP_256150.1| 155 QCDNCGRLLTPRSlvnAKCALCG 177
                                   7******8788851113577776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3811.45
//
Query:       gi|70607281|ref|YP_256151.1|  [L=695]
Description: V-type ATP synthase subunit I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-30  105.8  12.9      6e-22   77.4   0.0    3.9  4  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.04   13.2   0.2      0.069   12.4   0.2    1.3  1  DUF3450     Protein of unknown function (DUF3450)
       0.12   12.8   3.4        0.3   11.6   2.0    2.2  2  ZapB        Cell division protein ZapB
       0.16   12.4   8.2      0.087   13.2   3.7    2.4  2  DUF4200     Domain of unknown function (DUF4200)


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.6    0.0021       9.2      36     119 ..      44     140 ..      33     175 .. 0.66
   2 !   77.4   0.0   1.3e-25     6e-22     245     423 ..     206     378 ..     185     406 .. 0.84
   3 ?    1.0   0.3     0.017        75     515     554 ..     459     498 ..     456     511 .. 0.91
   4 !   28.9   1.1   6.4e-11   2.9e-07     692     811 ..     570     688 ..     567     690 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0021
                    V_ATPase_I  36 erklrfleeeieklekavikeeea..............eesleapeekeldeleeelekleeelkelnenleklkkelnel 102
                                    r l  ++++i++     ++++e+                + ++  ++e +++ee+ ++l ee+++l+++ ++lk +l el
  gi|70607281|ref|YP_256151.1|  44 RRILGEINDKIAR-LILLMEASEIavepkgnlkqdkqdWIEIARIYTSEASKIEEKYRELLEEIQKLKSERDSLKLKLDEL 123
                                   5555555555554.3333333333344444444444333344555677888899999999999999999999999999999 PP

                    V_ATPase_I 103 velkavlekakefleee 119
                                   +  k v    k++++++
  gi|70607281|ref|YP_256151.1| 124 EPFKDVDIDLKKIYANT 140
                                   99999988887777655 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.3e-25
                    V_ATPase_I 245 eeklkeveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqk 325
                                   ++++k++++ri+ ++ vl +++++l+e  +e ++ +++   k+   +    +L +   + ++ ++  eg+v +++++++ +
  gi|70607281|ref|YP_256151.1| 206 SQQYKTIMDRINYIDGVLGAKRKELREKANEDKEWIQSTYGKLLTLRDSMLVLSKA--KISDYFIQIEGYVLEKSTKQLTN 284
                                   67788889999999999999888888888888888888877777777766666666..66789999*************** PP

                    V_ATPase_I 326 alkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlll 406
                                   +lk+        v +  ++  ++e+pPTy++  k  +   +i++ YG+++Y E+ p+lf iitFP +F++MF D+G +++l
  gi|70607281|ref|YP_256151.1| 285 SLKDSA----VVVYEYPKRFGEQEEPPTYVNLPKSIRPLESIIELYGTPSYWEISPTLFLIITFPLIFGLMFPDLGNAIIL 361
                                   ****66....556667777777899******************************************************** PP

                    V_ATPase_I 407 llfalllvlkekklkkk 423
                                   l+fa+++  + kk +++
  gi|70607281|ref|YP_256151.1| 362 LIFAVWFHNYGKKRNSE 378
                                   ******99888876655 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.017
                    V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllf 554
                                   +s +lG i ++++ +l ++N++ +k++  ++l  +P ll 
  gi|70607281|ref|YP_256151.1| 459 ISLLLGSILLFVSSILGVINTIKKKDYEYLVLDRLPLLLI 498
                                   699*********************************9875 PP

  == domain 4  score: 28.9 bits;  conditional E-value: 6.4e-11
                    V_ATPase_I 692 eeeefdfgevfihqvIh.tIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavl 771
                                   ++e+ ++g+ ++  +I+ + E  +  +Sn  S++R+    +AH     +l+   +    l+ +s  ++++++i  a  a++
  gi|70607281|ref|YP_256151.1| 570 KHEKVSIGNAIVTGFIEgAFEAGILLLSNVISFIRILIFAIAHY---YILFAFSFMG-YLAAGSPNSLLAVFINPASIAII 646
                                   577888888888888884578888899****************8...5899999998.55778888888899988888888 PP

                    V_ATPase_I 772 tvavLl..lmeglsafLHaLRLhWVEfqsKFykgdGykFepf 811
                                    v+ Ll   +egl  f+  +RLh  E+ sKFy+g G kF+p 
  gi|70607281|ref|YP_256151.1| 647 IVGNLLaiALEGLVVFIQDMRLHFYEMFSKFYEGRGRKFNPV 688
                                   8887752268******************************97 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.5e-05     0.069       7      71 ..      60     124 ..      54     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                       DUF3450   7 lllasgalaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqle 71 
                                   l+ as  + ++  ++++ ++ ++++a+   ++ +k++++ +ell+e+++lk+e +sl+++ ++le
  gi|70607281|ref|YP_256151.1|  60 LMEASEIAVEPKGNLKQDKQDWIEIARIYTSEASKIEEKYRELLEEIQKLKSERDSLKLKLDELE 124
                                   33344444677778999999***************************************999987 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.0   6.7e-05       0.3       8      37 ..      94     123 ..      89     128 .. 0.78
   2 ?   -1.9   0.0         1   4.6e+03      26      39 ..     226     239 ..     209     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                          ZapB   8 qLEskiqkaidtitlLqmeieeLkeeneel 37 
                                   + E+k+ +++++i++L+ e + Lk +  el
  gi|70607281|ref|YP_256151.1|  94 KIEEKYRELLEEIQKLKSERDSLKLKLDEL 123
                                   568888888888888888888888777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                          ZapB  26 eieeLkeeneelke 39 
                                   + +eL+e+ +e ke
  gi|70607281|ref|YP_256151.1| 226 KRKELREKANEDKE 239
                                   44455555555444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.7   1.9e-05     0.087      62     111 ..      79     128 ..      73     129 .. 0.87
   2 ?    0.5   0.1      0.17   7.7e+02      20      55 ..     207     242 ..     185     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                       DUF4200  62 aralkkaeeerklkkekeaeikklkaeietlkseiekleekleeykkYee 111
                                   ++ ++ a + + +  + e++ ++l +ei++lkse++ l+ kl+e++++++
  gi|70607281|ref|YP_256151.1|  79 QDWIEIARIYTSEASKIEEKYRELLEEIQKLKSERDSLKLKLDELEPFKD 128
                                   555677778888999999******************************97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                       DUF4200  20 eeiqrleealkqreeelekkeqeleedllkfdkflk 55 
                                   +++++++++++  +  l +k++el+e++++ ++ ++
  gi|70607281|ref|YP_256151.1| 207 QQYKTIMDRINYIDGVLGAKRKELREKANEDKEWIQ 242
                                   556666666666666666666666666655444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 3896.81
//
Query:       gi|70607282|ref|YP_256152.1|  [L=100]
Description: hypothetical protein Saci_1546 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-13   51.0   0.4    1.5e-13   50.9   0.4    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.013   15.5   0.2      0.016   15.3   0.2    1.1  1  MMR_HSR1    50S ribosome-binding GTPase
      0.026   14.3   0.1      0.037   13.8   0.1    1.3  1  DRTGG       DRTGG domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.4   2.5e-17   1.5e-13       1      79 [.       4      83 ..       4      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.5e-17
                                  EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSCCG CS
                    ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPskegp 79
                                  + vIGd+ tv  f+l+G +++  +d+ e+e++l ++ +red+ ++l+t++ +  ++e++d++  e ++P+i  IPs  ++
  gi|70607282|ref|YP_256152.1|  4 VIVIGDKYTVNLFKLIGTEGIILEDPLELENTLLKIRKREDVDLVLVTNDTYTPVKEKVDNLILEqKKPLITVIPSPFSE 83
                                  68***********************************************************99888**********8774 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   2.7e-06     0.016      47     112 ..      15      77 ..       3      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                                   EEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                      MMR_HSR1  47 eielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvl 112
                                    ++l+ t G+i   ++  +l++++l++++  d+ l++v  + ++++p++e++ +l+ e+kkpli v+
  gi|70607282|ref|YP_256152.1|  15 LFKLIGTEGIIL--EDPLELENTLLKIRKrEDVDLVLVT-N-DTYTPVKEKVDNLILEQKKPLITVI 77 
                                   578899999764..4566999999998886577666665.3.569*****************99886 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.1e-06     0.037      42     100 ..       3      59 ..       1      65 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
                                   EEEEEETT-HHHHHHHTT-TEEEEEEETT----HHHHHHHHHHT--EEE-SS-HHHHHH CS
                         DRTGG  42 dlvivpGDRediqlaaleagiaalilTgglepseevlklaeeaglpvlsveldtfttak 100
                                   +++++ GD++ + l  l    +++il   le+++++lk+ ++  + ++ v+ dt+t +k
  gi|70607282|ref|YP_256152.1|   3 KVIVI-GDKYTVNLFKLIGT-EGIILEDPLELENTLLKIRKREDVDLVLVTNDTYTPVK 59 
                                   66677.****9999887766.**********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 738.10
//
Query:       gi|70607283|ref|YP_256153.1|  [L=192]
Description: hypothetical protein Saci_1547 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-07   29.5  14.5      2e-06   27.4  14.5    2.0  1  vATP-synt_E      ATP synthase (E/31 kDa) subunit
     0.0073   16.7   4.9      0.013   15.9   4.9    1.4  1  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.089   12.5   0.7       0.52   10.1   0.1    2.3  4  Exotox-A_cataly  Exotoxin A catalytic
       0.24   11.2   0.0       0.24   11.2   0.0    2.4  3  ETC_C1_NDUFA5    ETC complex I subunit conserved region
       0.53   10.3   4.4       0.57   10.2   3.0    1.9  2  SPOUT_MTase      Predicted SPOUT methyltransferase
       0.63    9.7   7.7        1.4    8.6   7.7    1.7  1  UBN_AB           Ubinuclein conserved middle domain
        1.5    8.5  10.9        4.2    7.1  10.9    1.7  1  DUF445           Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  14.5   7.6e-10     2e-06      13     199 .]      22     190 ..       2     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.6e-10
                                   HHHHHHHHHHHHHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSH CS
                   vATP-synt_E  13 Ikakaeeefeiekaklveeee.ekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeaekkLaeveedk 92 
                                     +ka  e++ +++++ +e   e ++++ e   K++e+ +  +  +   +++++v k ++  +++vf+++  +L++++++k
  gi|70607283|ref|YP_256153.1|  22 ELKKAFTEANLIVDEAYNEILsEYSKRIQEIISKNIEALRG-EEAKLEVETKRAVNKEKDYWVQQVFQKTLDELEKIANTK 101
                                   23344455555555554443302233333444555555543.446778899****************************99 PP

                                   HCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSSSEEEECCSSSCE CS
                   vATP-synt_E  93 deYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledvlGGvvleaadgki 173
                                     Yk+ +++++   l     + +iv++ ++D++ +e +l+  ++ ++      +v v +d+     ++ GGv ++  d k 
  gi|70607283|ref|YP_256153.1| 102 -DYKNRIESILSRELT----EGAIVYCSNNDKKFIEGILT--TKRIN------NVSVEVDN-----SIKGGVKIYYPDKKL 164
                                   .9**999999987654....4689*************622..22222......25678888.....99************* PP

                                   EECCCHHHCHHHHHHHHHHCCCCCHC CS
                   vATP-synt_E 174 kvnnTlearLelvleqllpeirkaLF 199
                                     + Tl  +L++++e+l+  +++ LF
  gi|70607283|ref|YP_256153.1| 165 TRDFTLKTILNQIFEDLRDDVARILF 190
                                   ***********************999 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.9   5.1e-06     0.013      14      99 ..       5      91 ..       2      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHCS...HH CS
                  V-ATPase_G_2 14 EaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireear.araeaeaqavrkraear...lq 92
                                  E+ L++ +E  +k+  +e+++A  eA+ i+ eA +   ++ +ey+++++e +++  e  r ++a+ e+++ r+ ++++   +q
  gi|70607283|ref|YP_256153.1|  5 EELLSKTQEVEKKKIDEELKKAFTEANLIVDEAYN---EILSEYSKRIQEIISKNIEALRgEEAKLEVETKRAVNKEKdywVQ 84
                                  7779999***********************99976...567899999999987755555426788888877776666533356 PP

                                  HHHHHHH CS
                  V-ATPase_G_2 93 qAvelil 99
                                  q  ++ l
  gi|70607283|ref|YP_256153.1| 85 QVFQKTL 91
                                  6555555 PP

>> Exotox-A_cataly  Exotoxin A catalytic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.35   8.9e+02      83     120 ..       4      42 ..       2      60 .. 0.72
   2 ?   -0.7   0.1       0.4     1e+03      92     126 ..      31      66 ..      16      76 .. 0.67
   3 ?   10.1   0.1    0.0002      0.52     116     162 ..      93     137 ..      59     146 .. 0.74
   4 ?   -2.2   0.0       1.2   3.1e+03      74      94 ..     155     175 ..     141     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.35
                                   GGGEEE-SS-TTSHHHHHHHHHHHT.SSSS-S...S-EE CS
               Exotox-A_cataly  83 leklvrletpldkeeaakevkrllG.frlgedrsyleai 120
                                    e+l   ++ ++k+++++e+k+ +   +l  d++y e++
  gi|70607283|ref|YP_256153.1|   4 FEELLSKTQEVEKKKIDEELKKAFTeANLIVDEAYNEIL 42 
                                   567788888899999999999988624677777775554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.4
                                   -TTSHHHHHHHHHHHTSSSS-S....S-EEEEESST CS
               Exotox-A_cataly  92 pldkeeaakevkrllGfrlgedrsy.leairGpeed 126
                                    l  +ea +e+     +r+ e  s  +ea+rG+e +
  gi|70607283|ref|YP_256153.1|  31 NLIVDEAYNEILSEYSKRIQEIISKnIEALRGEEAK 66 
                                   455556667777777777777666558899997743 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0002
                                   .S-EEEEESSTTSSEEEEE-HHHHTTSEEEE-SS--BTTSTTSS--G CS
               Exotox-A_cataly 116 yleairGpeedkertetiLswklaeravaiPstikvdqrfgsgdldp 162
                                    le i  +++ k+r e iLs +l e a++  s    d++f  g l  
  gi|70607283|ref|YP_256153.1|  93 ELEKIANTKDYKNRIESILSRELTEGAIVYCSN--NDKKFIEGILTT 137
                                   27999**********************999884..677777776655 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                                   EEEEEEGGGGGGEEE-SS-TT CS
               Exotox-A_cataly  74 lrvyvPrqdleklvrletpld 94 
                                   +++y P ++l + + l+t l+
  gi|70607283|ref|YP_256153.1| 155 VKIYYPDKKLTRDFTLKTILN 175
                                   688999998888888887776 PP

>> ETC_C1_NDUFA5  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       2.3   5.9e+03      47      59 ..      14      26 ..       9      31 .. 0.60
   2 ?   -1.7   0.1      0.99   2.5e+03      22      35 ..      44      48 ..      34      72 .. 0.56
   3 ?   11.2   0.0   9.3e-05      0.24      15      42 ..      86     113 ..      83     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                 ETC_C1_NDUFA5 47 Veeeedvekiekk 59
                                  Ve+++  e+++k+
  gi|70607283|ref|YP_256153.1| 14 VEKKKIDEELKKA 26
                                  5566666666555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.99
                 ETC_C1_NDUFA5 22 kLkkiPessvYRqs 35
                                  +         Y + 
  gi|70607283|ref|YP_256153.1| 44 E---------YSKR 48
                                  3.........3333 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 9.3e-05
                 ETC_C1_NDUFA5  15 lytktLkkLkkiPessvYRqsvEaltkh 42 
                                   + +ktL++L+ki  +  Y+  +E++ + 
  gi|70607283|ref|YP_256153.1|  86 VFQKTLDELEKIANTKDYKNRIESILSR 113
                                   679********************99765 PP

>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.0   0.00022      0.57      13      72 ..      35      91 ..      23     123 .. 0.74
   2 ?    1.1   0.1      0.13   3.4e+02       8      35 ..      75     102 ..      74     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                  H.HHHHHHHHHHHHHTTT-EEEEEEE....--.-S-HHHHHHHHHHT--....TT-EEEEE CS
                   SPOUT_MTase 13 ekylkelieeYlkrlkkyakleiielkkekks.ekeeekakekegerilkklkkkayvill 72
                                  ++ ++e+++eY+kr++++++ +i  l+ e+++ e e+++a +ke++  ++    + +  +l
  gi|70607283|ref|YP_256153.1| 35 DEAYNEILSEYSKRIQEIISKNIEALRGEEAKlEVETKRAVNKEKDYWVQ----QVFQKTL 91
                                  56799*********************755555688888888888776554....3333344 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                   ES---H.HHHHHHHHHHHHHTTT-EEEE CS
                   SPOUT_MTase   8 vgklkekylkelieeYlkrlkkyaklei 35 
                                   v+k k+ ++++++++ l+ l+k+a+++ 
  gi|70607283|ref|YP_256153.1|  75 VNKEKDYWVQQVFQKTLDELEKIANTKD 102
                                   6666777777777777776666655543 PP

>> UBN_AB  Ubinuclein conserved middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.7   0.00053       1.4      72     172 ..       6      99 ..       2     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00053
                        UBN_AB  72 tLlkrlkklrlkkeeerlkellekLkeaidevmpeqlekYeeecqalkeakaakkaeeaekdteeeedeekkekkvkePrk 152
                                    Ll +++ ++ kk +e+lk+++ +    +de++ e+l++Y +  q++  ++ ++          ee++ e ++k++ + +k
  gi|70607283|ref|YP_256153.1|   6 ELLSKTQEVEKKKIDEELKKAFTEANLIVDEAYNEILSEYSKRIQEIISKNIEALR-------GEEAKLEVETKRAVNKEK 79 
                                   68899999***************************************999987665.......455566666677777777 PP

                        UBN_AB 153 kFkwneelRelLleivklke 172
                                    +   + + + L e+ k+ +
  gi|70607283|ref|YP_256153.1|  80 DYWVQQVFQKTLDELEKIAN 99 
                                   77777666666666665554 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  10.9    0.0016       4.2     158     284 ..      14     163 ..       3     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0016
                        DUF445 158 evkekikelidelieeesgklvlesivsmflreltsilekvksdpdhllreeedkkvreliadllndpelaakveklkkkk 238
                                    +k+ki+e +++ + e   +l+ ++  + +l+e ++ ++++ s++ + lr ee k  + + +++ n +e    v+++ +k+
  gi|70607283|ref|YP_256153.1|  14 VEKKKIDEELKKAFTEA--NLIVDEAYNEILSEYSKRIQEIISKNIEALRGEEAKL-EVETKRAVN-KEKDYWVQQVFQKT 90 
                                   34445555555555555..4557777788888888888888888888888777766.566666666.56666777788888 PP

                        DUF445 239 lsdlevqeyeealwealkdlllkdlneee....sllrerisklleklge..........................k 284
                                   l++le+ +++++  ++++++l+++l+e      s   ++ +k++e + +                          k
  gi|70607283|ref|YP_256153.1|  91 LDELEKIANTKDYKNRIESILSRELTEGAivycS---NNDKKFIEGILTtkrinnvsvevdnsikggvkiyypdkK 163
                                   8888888888888888888888887775563332...333333333333333444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2146  (0.119694); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1342.17
//
Query:       gi|70607284|ref|YP_256154.1|  [L=592]
Description: V-type ATP synthase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-86  288.1   0.0    5.5e-86  287.6   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      9e-46  154.7   0.1    1.6e-45  153.8   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.7e-12   47.7   1.8    1.7e-12   47.7   1.8    2.1  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
     0.0046   17.2   0.1      0.018   15.3   0.0    2.0  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.086   12.7   0.1       0.23   11.3   0.1    1.7  1  Biotin_lipoyl    Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.6   0.0   1.5e-89   5.5e-86       1     213 []     214     437 ..     214     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 287.6 bits;  conditional E-value: 1.5e-89
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtvl 74 
                                   G rv+D++fpi++G++ +ipg fg Gktv +qsl+k+s+++ ++iyvg+Gergne+++ l++fp+      g+ +++rt+l
  gi|70607284|ref|YP_256154.1| 214 GTRVVDTIFPIAKGGTAAIPGPFGSGKTVTLQSLAKWSEAK-VVIYVGCGERGNEMTDELRQFPKlkdpwtGKpLLQRTIL 293
                                   89***********************************9888.***********************988886337******* PP

                                   EEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  75 vantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka 155
                                   vantsn+pvaare siy+g+t+AEyfrdqg++vll+ads+srwaeAlre+++r++empa++g+p+yl ++la+ yERag++
  gi|70607284|ref|YP_256154.1| 294 VANTSNMPVAARESSIYVGVTMAEYFRDQGYDVLLVADSTSRWAEALRELGGRMEEMPAEEGFPSYLPSRLAEYYERAGRV 374
                                   ********************************************************************************* PP

                                   .....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 156 .....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        p+r Gsv+i  avsp+ggDf++pvt++tl+++ +f+ Ld +laq++h+Pain+ + +S
  gi|70607284|ref|YP_256154.1| 375 ialgkPERFGSVSIASAVSPPGGDFTEPVTSNTLRFVRVFWPLDVSLAQARHYPAINWIQGFS 437
                                   *****9****************************************************98766 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   0.1   4.6e-49   1.6e-45       1     121 []      85     205 ..      85     205 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 4.6e-49
                                   EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE-- CS
               ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiae 80 
                                   +DG+qrpL++iae+ +s f++rGvkvpal+r+kkw++ p +k+gdkvs+gdi+++v+et+lieh+i+vpp+v+g++kei++
  gi|70607284|ref|YP_256154.1|  85 FDGLQRPLDRIAESVKSpFVTRGVKVPALERNKKWHVIPVAKKGDKVSPGDIIAKVNETDLIEHRIIVPPNVHGTLKEISP 165
                                   9******************************************************************************** PP

                                   EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
               ATP-synt_ab_Xtn  81 egeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                   eg+ytved+ia+v+ e+ + kel+l+q+wPvr prp+kekl
  gi|70607284|ref|YP_256154.1| 166 EGDYTVEDVIARVDMEG-DVKELKLYQRWPVRIPRPFKEKL 205
                                   **************987.7********************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   1.8   4.7e-16   1.7e-12       1      69 []       7      69 ..       7      69 .. 0.98
   2 ?   -2.2   0.1       1.7   6.1e+03      53      68 ..     205     220 ..     205     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 4.7e-16
                                  EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                 ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                  +v+v+Gp+v +++++    ++ +++ev+  e    l+g++ ++++d++ ++v++ tdG+++G++ +rTG
  gi|70607284|ref|YP_256154.1|  7 VVRVNGPLVVADGMRN--AQMFEVVEVG--E--LRLVGEITRIEGDRAYIQVYEATDGIKPGEKAYRTG 69
                                  79*************9..**********..8..9999*******************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.7
                                   SS-STTBBTTSEEEEE CS
                 ATP-synt_ab_N  53 mgstdGlsrGteVkrT 68 
                                   +++t+ l  Gt+V++T
  gi|70607284|ref|YP_256154.1| 205 LEPTEPLLTGTRVVDT 220
                                   58999999******98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.9e-06     0.018       6      51 ..     228     265 ..     225     331 .. 0.83
   2 ?   -2.0   0.1       1.1   4.1e+03      58     118 ..     473     530 ..     468     553 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                                   g  ++ G+ G+GKT++l+ l+++          +++vv +v + + +
  gi|70607284|ref|YP_256154.1| 228 GTAAIPGPFGSGKTVTLQSLAKWS---------EAKVViYVGCGERG 265
                                   66799******************9.........44444488777766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                        AAA_22  58 rellralglelkaerlsseellealeqalraravielliiDEaqhlr.seealeeLrsllnl 118
                                   r+++r +g e  +   +++ l+    + +r+++  +    D+++ ++ ++++ +  r ++++
  gi|70607284|ref|YP_256154.1| 473 RQIVRLVGPESLS---DKDKLILEASKLIRDAFL-KQNAFDDIDAFSsPQKQAKIMRLIYDF 530
                                   5566666655555...566666666666666666.666688888885424444444444443 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.3e-05      0.23      20      65 ..     124     172 ..      98     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.3e-05
                                   SSSTTCEE-TTSEEEEE.ECTTEEEEE..EBSSSEEEEEESSTTTEEE- CS
                 Biotin_lipoyl  20 lvkvGdkVkagqvlaev.eamKmemei..eapkaGvvkeilvkeGdtve 65 
                                     k+GdkV+ g+++a v e++  e+ i  +  + G++kei  + + tve
  gi|70607284|ref|YP_256154.1| 124 VAKKGDKVSPGDIIAKVnETDLIEHRIivPPNVHGTLKEISPEGDYTVE 172
                                   4699*************88999998761155569******988555565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3783.45
//
Query:       gi|70607285|ref|YP_256155.1|  [L=452]
Description: V-type ATP synthase subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-63  212.9   0.0    5.4e-63  212.5   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    6.1e-11   42.7   0.5    1.2e-10   41.8   0.5    1.5  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.0   6.1e-67   5.4e-63       1     213 []     122     340 ..     122     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 6.1e-67
                                   SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlva 76 
                                   G++++D l+++ +Gq++ i++++g++ ++++++++kq++ +    + a+++++iG r +e+  + + f+e+++++r+ +++
  gi|70607285|ref|YP_256155.1| 122 GVSAIDGLTSLLRGQKLPIFSGSGLPANQLAAQIAKQATVRgeesNfAVVFAAIGIRYDEALFFRRFFEETGAINRVAMFV 202
                                   899**********************************9887999878********************************** PP

                                   EETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  77 ntsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkap 156
                                     +n+p+ ++++++ t++tlAEy+++ +++++l i+ ++++++eAlre+s++ +e+p++ gyp+y++++la  yERagk++
  gi|70607285|ref|YP_256155.1| 203 TLANDPPSLKILTPKTALTLAEYLAYeKDMHILAILIDMTNYCEALRELSASKEEVPGRGGYPGYMYTDLAVTYERAGKVR 283
                                   *************************9999**************************************************** PP

                                   SSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 157 drtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++Gs+t++++++++++D+++p+++ t +it+g+ivLd++l++++++P+invl+S+S
  gi|70607285|ref|YP_256155.1| 284 GKKGSITQMPILTMPNDDITHPIPDLTGYITEGQIVLDRSLFNKGIYPPINVLASLS 340
                                   *******************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.5   1.3e-14   1.2e-10       4      69 .]       2      65 ..       1      65 [. 0.94

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.3e-14
                                  EETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                 ATP-synt_ab_N  4 viGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                  + Gp++ +e++ +   ++++++eve+++ g++++g ++  + ++++v+v+++t+G+s+ +++V+++G
  gi|70607285|ref|YP_256155.1|  2 IKGPLMAIEGVTD--AAYNELIEVEMPD-GSKRRGIVVDSQSGVAIVQVFEGTTGVSPtQSKVRFLG 65
                                  79***********..888888888888*.************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3445.66
//
Query:       gi|70607286|ref|YP_256156.1|  [L=209]
Description: V-type ATP synthase subunit D [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-41  142.4   3.5    1.8e-41  142.2   3.5    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.055   12.8   0.2       0.15   11.4   0.0    1.7  2  DUF4763     Domain of unknown function (DUF4763)


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   3.5     2e-45   1.8e-41       1     196 []      12     203 ..      12     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 2e-45
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                    ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                   +Li+l+++++l++ +++lL++Kr++L+l +r++++e+++  +e+ ++l+++y+++ +  a++g ++i+ ++ + +   +++
  gi|70607286|ref|YP_256156.1|  12 NLINLRRQIRLIRTIKRLLENKREVLLLYLRQYADEYEKVYNEVSKVLSDVYSTYLQGVASEGLSTIQTYADSIP---SSL 89 
                                   79******************************************************************9998444...67* PP

                                   -SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D  82 kvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaLe 162
                                   +v+++ + ++GVk+pv++l+e+ + +++++g l+ ++++ + +e+++ ++++++ l ++e s++ L+ e++kt+r +Na++
  gi|70607286|ref|YP_256156.1|  90 NVNTSIKVLFGVKIPVVDLDES-TIQQQPFGNLEISPYILKSREQMSYAFKKILTLIEIESSIRALSGELRKTQRLINAID 169
                                   *******************885.455789**************************************************** PP

                                   TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_D 163 kvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                                     ++P +++  kyIks Ld++ reef+rlk+v+k
  gi|70607286|ref|YP_256156.1| 170 TSILPFYQSSSKYIKSVLDDRTREEFTRLKMVRK 203
                                   ********************************86 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.17   1.6e+03     233     233 ..      36      36 ..       4      64 .. 0.52
   2 ?   11.4   0.0   1.7e-05      0.15     181     230 ..     119     168 ..     111     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.17
                       DUF4763 233 e 233
                                    
  gi|70607286|ref|YP_256156.1|  36 V 36 
                                   1 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.7e-05
                       DUF4763 181 dkadfsnlirslrtkmeeslkklvplreykqdrrdaskelkelkkflkkl 230
                                      + s +i ++r++m++ +kk+++l e +   r +s el ++++ ++ +
  gi|70607286|ref|YP_256156.1| 119 GNLEISPYILKSREQMSYAFKKILTLIEIESSIRALSGELRKTQRLINAI 168
                                   5678999**************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1500.97
//
Query:       gi|70607287|ref|YP_256157.1|  [L=77]
Description: hypothetical protein Saci_1551 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-15   57.0   8.3    2.5e-15   56.5   8.3    1.2  1  ATP-synt_E_2   ATP synthase epsilon subunit
  ------ inclusion threshold ------
      0.012   15.2   4.9      0.057   13.0   0.2    2.4  2  VASP_tetra     VASP tetramerisation domain
      0.038   14.3   0.5      0.066   13.5   0.3    1.5  1  DUF3144        Protein of unknown function (DUF3144)
      0.047   13.8   0.6      0.051   13.7   0.6    1.2  1  KaiA           KaiA C-terminal domain
      0.071   12.9   0.4      0.079   12.8   0.4    1.0  1  Peptidase_M41  Peptidase family M41


Domain annotation for each model (and alignments):
>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   8.3   6.9e-19   2.5e-15      10      56 .]      27      73 ..      22      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 6.9e-19
                  ATP-synt_E_2 10 DKYlniLkskLdeKKsElLkkiNmEYEKlLKqRLdeLeklKrkvLKE 56
                                  + Y+n LkskLd +K E+L+++N EY+K+LK R ++Le +Kr++LKE
  gi|70607287|ref|YP_256157.1| 27 ETYINELKSKLDARKKEILSQLNEEYNKILKSRFEDLESVKRNILKE 73
                                  57********************************************9 PP

>> VASP_tetra  VASP tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.9     0.011        40       4      22 ..      37      55 ..      30      57 .. 0.86
   2 ?   13.0   0.2   1.6e-05     0.057       3      16 ..      62      75 ..      61      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                    VASP_tetra  4 lErlKqEILeEvrkELqKv 22
                                  l+  K+EIL+ +  E +K+
  gi|70607287|ref|YP_256157.1| 37 LDARKKEILSQLNEEYNKI 55
                                  788899***9999998886 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
                    VASP_tetra  3 DlErlKqEILeEvr 16
                                  DlE++K+ IL+Ev 
  gi|70607287|ref|YP_256157.1| 62 DLESVKRNILKEVQ 75
                                  9***********95 PP

>> DUF3144  Protein of unknown function (DUF3144)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.8e-05     0.066      47      75 ..      34      62 ..      26      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                       DUF3144 47 kedlaaekeealeyfveeyremLeenled 75
                                  k++l a+k+e+l+++ eey+++L++ +ed
  gi|70607287|ref|YP_256157.1| 34 KSKLDARKKEILSQLNEEYNKILKSRFED 62
                                  7899***********************99 PP

>> KaiA  KaiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   1.4e-05     0.051      16      59 ..      28      74 ..       9      77 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                  GSCCCSTH...HHHHHHHHHHHHHHHHHHHHCTSTTSSHHHHHHHHH CS
                          KaiA 16 kflrnlsk...eekkelleelkseyreivleyfkddsevnqkidefv 59
                                  +++ +l++   + kke+l++l++ey +i+ + f+d ++v+++i + v
  gi|70607287|ref|YP_256157.1| 28 TYINELKSkldARKKEILSQLNEEYNKILKSRFEDLESVKRNILKEV 74
                                  4555555311157999**********************999986655 PP

>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.2e-05     0.079     124     179 ..      17      72 ..       4      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                   ----.------SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH CS
                 Peptidase_M41 124 vflgkelkkekelseetaeeideevkelveeayerakeileekreelealaeaLle 179
                                    f++ + k ++++ +e+++++d+  ke++++  e+ ++il+++ e+le +  ++l+
  gi|70607287|ref|YP_256157.1|  17 YFKEGGNKMAETYINELKSKLDARKKEILSQLNEEYNKILKSRFEDLESVKRNILK 72 
                                   456666778899**************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1985  (0.110714); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 501.61
//
Query:       gi|70607288|ref|YP_256158.1|  [L=101]
Description: V-type ATP synthase subunit K [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-14   53.4  20.3    2.4e-14   53.4  20.3    1.8  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.7      0.25   4.5e+03      60      60 .]      11      11 ..       3      24 .. 0.53
   2 !   53.4  20.3   1.3e-18   2.4e-14       1      60 []      37      96 ..      37      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.25
                                  H CS
                    ATP-synt_C 60 l 60
                                  l
  gi|70607288|ref|YP_256158.1| 11 L 11
                                  2 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 1.3e-18
                                  HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                  +gaglavGl+a+g+G+++G+a++agi+ + ++ ++f+++li++a+ e ia+yg+i+a+++
  gi|70607288|ref|YP_256158.1| 37 IGAGLAVGLAAIGAGVAVGTAAAAGIGVLTEKREMFGTVLIFVAIGEGIAVYGIIFAVLM 96
                                  7********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 630.57
//
Query:       gi|70607289|ref|YP_256159.1|  [L=483]
Description: prolyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-25   90.7   0.1    1.7e-25   90.1   0.1    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      1e-18   67.2   0.5    2.4e-18   66.0   0.5    1.7  1  HGTP_anticodon  Anticodon binding domain
    1.1e-15   57.5   0.5    1.1e-15   57.5   0.5    2.1  3  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.033   14.3   0.0       0.12   12.5   0.0    2.0  1  ProRS-C_2       Prolyl-tRNA synthetase, C-terminal
       0.18   10.8   0.6       0.86    8.6   0.1    2.2  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.1   4.7e-29   1.7e-25       6     179 .]     100     274 ..      92     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 4.7e-29
                                   TT.SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEE.EEEEEEEEES.GGGHHHHHHH CS
                                   xx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxx RF
                  tRNA-synt_2b   6 rn.dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreF.hqkdgyvfha.easlddslrd 82 
                                   +n d +++L+Pt+e++++ +   + ++s k+LP k+yqi +++R+E++++r+++R+re  + k+++  h   ++++ ++++
  gi|70607289|ref|YP_256159.1| 100 ENlDIRLALRPTSETAITYMETYW-VQSyKQLPKKYYQIVSVFRYETKATRPMIRLREVsTFKEAHTLHEtYEDAERQVKE 179
                                   4447799*************9988.999788***************************93469*******8799******* PP

                                   HHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  83 likaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimi 162
                                    i+ ++++fe+lg+++    +  +++  a + ++  f+ +++  +++++igt++ lg+++ ++++++v ++++    ++ +
  gi|70607289|ref|YP_256159.1| 180 AIEIYKNFFEELGIPYIMSQRPeWDK-FAGAIYTIAFDTIMP-DSRVLQIGTVHHLGQHFTKAFDLKVQRKDGTLDYPHQT 258
                                   ***************76555546664.49999**********.999*********************************** PP

                                   EEEEEHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 163 caaigveRllsaileqn 179
                                    ++i+  R+++++++ n
  gi|70607289|ref|YP_256159.1| 259 SYGIS-DRVIAVAVSIN 274
                                   *****.******99865 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.5   6.8e-22   2.4e-18       1      93 [.     290     387 ..     290     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 6.8e-22
                                   SEEEEESSSS....HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                HGTP_anticodon   1 qvvviplnek....aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                   ++v+ip+  k    +e++ ey +++a+ L  +gi++++d+  ++++g+k+  ++ +g+p+++++G++el +++v +++rdt
  gi|70607289|ref|YP_256159.1| 290 KAVIIPIPAKdekeTEKIIEYSEDVAKILVSNGINTVIDKdTEKTPGEKYYIWEIKGVPLRIEIGPRELSSNSVFIKRRDT 370
                                   689****9999999999***********************9**************************************** PP

                                   CEEEEEETTHHHHHHHH CS
                HGTP_anticodon  77 reqervsldelveklke 93 
                                    + ++v+ ++lv+++ +
  gi|70607289|ref|YP_256159.1| 371 LQGISVKKENLVSEVVK 387
                                   *************9976 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.4   4.8e+03      19      32 ..     168     181 ..     163     209 .. 0.77
   2 ?   -3.0   0.0       2.5   8.9e+03      17      29 ..     297     309 ..     289     319 .. 0.55
   3 !   57.5   0.5   3.1e-19   1.1e-15       2      69 .]     415     483 .]     414     483 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.4
                                   SSGHHHHHHHHHHH CS
                     ProRS-C_1  19 cgeeecEekIkeet 32 
                                   +  e++E+++ke +
  gi|70607289|ref|YP_256159.1| 168 ETYEDAERQVKEAI 181
                                   55688999999976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                   EESSGHHHHHHHH CS
                     ProRS-C_1  17 pWcgeeecEekIk 29 
                                   p ++e+e+E+ I+
  gi|70607289|ref|YP_256159.1| 297 PAKDEKETEKIIE 309
                                   3345555555553 PP

  == domain 3  score: 57.5 bits;  conditional E-value: 3.1e-19
                                   HHHHHHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                     ProRS-C_1   2 eefkealekkg.fvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                   ee k+ l++k  +v +pWc+++ec  kI+e tga +l+ p d++   ++++C+vc+kpak++   +++Y
  gi|70607289|ref|YP_256159.1| 415 EEAKKMLDSKAgIVEVPWCESNECGLKIEETTGARVLGKPYDSPRDVSKSTCVVCKKPAKTTLRLAKTY 483
                                   89*******999******************************98899********************99 PP

>> ProRS-C_2  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05      0.12      13      51 ..     414     453 ..     407     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHCTTT-SEEEEE--GGG.-SHHHHHHHSS-EEEE CS
                     ProRS-C_2  13 lenikeklsekkGvvLvPfneei.YneefeeeidasvLGe 51 
                                   le+ k++l  k G+v vP+ e+      +ee ++a vLG+
  gi|70607289|ref|YP_256159.1| 414 LEEAKKMLDSKAGIVEVPWCESNeCGLKIEETTGARVLGK 453
                                   6899***************997414458***********7 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00024      0.86      22     107 ..      44     147 ..      42     154 .. 0.62
   2 ?   -3.7   0.0       1.4   4.9e+03     135     179 ..     379     416 ..     368     427 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHHHHHHHTT-EE----SEESS-.........-SSSS--EEEEETTT.T...EEE.......-E-S-SHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxx...xxx.......xxxxxxxxxx RF
                   tRNA-synt_2  22 lrlrstvtkavrkyleengfieietPiLsksd.........teegarlFkvksrekek...eff.......aLtqspqlyl 83 
                                   +++r+ +++++rk l+ +g  e+  P+L+ +d          + +++ F v++  +e+   ++        a+t     y 
  gi|70607289|ref|YP_256159.1|  44 FKIRQAAVDLIRKLLDAKGHEEVLFPLLVPEDllrregehiKGFESEVFWVTKGGEENldiRLAlrptsetAIT-----YM 119
                                   799**************************998766654443333455555544433334332222222233333.....44 PP

                                   HHHHHCT....HSEEEEEEEEE--S--B CS
                                   xxxxxxx....xxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2  84 ellivag....idrvfqiaraFRaEdsr 107
                                   e++ v       ++++qi  +FR E   
  gi|70607289|ref|YP_256159.1| 120 ETYWVQSykqlPKKYYQIVSVFRYETKA 147
                                   4444333111146888888888888765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2 135 eelikslvkevlessakdiefvirrnskdlkkpfkrltykeaiek 179
                                   e+l++++vk + e+ +kd++    +   ++ +  +++ y++ +e+
  gi|70607289|ref|YP_256159.1| 379 ENLVSEVVKLL-ETLRKDLK----ERAWNFLR--SKIRYTDNLEE 416
                                   66666666666.44433332....22222222..35555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2792.07
//
Query:       gi|70607290|ref|YP_256160.1|  [L=95]
Description: 30S ribosomal protein S26e [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-22   78.9   2.5      4e-22   78.7   2.5    1.1  1  Ribosomal_S26e  Ribosomal protein S26e
     0.0073   16.4   5.5       0.16   12.2   0.9    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.043   13.4   0.1      0.087   12.4   0.1    1.5  1  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.072   13.1   0.6      0.072   13.1   0.6    2.1  3  DUF2116         Uncharacterized protein containing a Zn-ribbo
       0.21   11.6   4.2        0.8    9.8   4.2    1.8  1  DZR             Double zinc ribbon
       0.36   10.8   5.9       0.37   10.8   0.5    2.4  2  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   2.5   1.3e-25     4e-22       1      97 [.       1      93 [.       1      95 [] 0.95

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.3e-25
                                  X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTTS CS
                Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihskv 83
                                  m+kKR n+gr k ++ghv  ++C++c+ ++p dKai  +  ++ v+ a +++l+++      ++ ++ ++++ycv+ca++  v
  gi|70607290|ref|YP_256160.1|  1 MPKKRENRGRRKGDKGHVGSIHCDQCGARIPEDKAICVTKPYSPVDPALAQELEKK----GAIIMRYPVTKCYCVNCAVYLGV 79
                                  9*****************************************************99....667778888999*********** PP

                                  S----TTTTS--S- CS
                Ribosomal_S26e 84 vrvRsredrknrep 97
                                  ++ R +++rk++++
  gi|70607290|ref|YP_256160.1| 80 IKIRPEQERKQKAK 93
                                  **********9975 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.3    0.0034        10      17      37 ..      22      38 ..      20      39 .. 0.81
   2 !   12.2   0.9   5.2e-05      0.16      22      39 ..      57      73 ..      57      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                 Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCv 37
                                  +C++Cg+ + +d+     +Cv
  gi|70607290|ref|YP_256160.1| 22 HCDQCGARIPEDK----AICV 38
                                  9******999964....5888 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.2e-05
                 Auto_anti-p27 22 gvPLmrdrkggkvyCvaC 39
                                  g+++mr++  +k+yCv+C
  gi|70607290|ref|YP_256160.1| 57 GAIIMRYPV-TKCYCVNC 73
                                  6799***93.69****** PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.9e-05     0.087       3      16 ..      21      34 ..      19      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                        zf_UBZ  3 ylCerCgkeipese 16
                                  + C++Cg++ipe++
  gi|70607290|ref|YP_256160.1| 21 IHCDQCGARIPEDK 34
                                  67*********985 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   2.4e-05     0.072       5      21 ..      22      38 ..      20      46 .. 0.92
   2 ?   -2.9   1.3       2.3   6.9e+03       6      11 ..      70      75 ..      68      79 .. 0.80
   3 ?   -3.3   0.2       3.1   9.2e+03      30      36 ..      86      92 ..      84      94 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                       DUF2116  5 HCivCGkaIpldesfCs 21
                                  HC  CG+ Ip+d  +C 
  gi|70607290|ref|YP_256160.1| 22 HCDQCGARIPEDKAICV 38
                                  ****************6 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                       DUF2116  6 CivCGk 11
                                  C++C +
  gi|70607290|ref|YP_256160.1| 70 CVNCAV 75
                                  999975 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.1
                       DUF2116 30 kkrkkva 36
                                  ++rk+ a
  gi|70607290|ref|YP_256160.1| 86 QERKQKA 92
                                  6666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.2   0.00027       0.8      11      34 ..      19      73 ..      13      77 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                           DZR 11 darfCseCgtklkavaa...............................edrCpsC 34
                                  +++ C++Cg+++++ +a                               +  C++C
  gi|70607290|ref|YP_256160.1| 19 GSIHCDQCGARIPEDKAicvtkpyspvdpalaqelekkgaiimrypvtKCYCVNC 73
                                  5677888888877655566666666666677777777777777777766667777 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   0.00012      0.37       4      17 ..      19      34 ..      16      38 .. 0.85
   2 ?    2.5   0.6     0.049   1.5e+02      26      31 ..      69      74 ..      60      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                  zf-dskA_traR  4 gs..CeeCGEpIpeaR 17
                                  gs  C+ CG  Ipe +
  gi|70607290|ref|YP_256160.1| 19 GSihCDQCGARIPEDK 34
                                  5568**********87 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.049
                  zf-dskA_traR 26 lCveCq 31
                                  +Cv+C+
  gi|70607290|ref|YP_256160.1| 69 YCVNCA 74
                                  9****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 706.51
//
Query:       gi|70607291|ref|YP_256161.1|  [L=336]
Description: pyridoxal biosynthesis lyase PdxS [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     5e-100  333.5   2.1   6.5e-100  333.1   2.1    1.1  1  SOR_SNZ         SOR/SNZ family
    7.1e-06   25.5   3.8    3.6e-05   23.2   0.0    2.4  3  ThiG            Thiazole biosynthesis protein ThiG
     0.0042   16.3   0.0       0.26   10.4   0.0    2.2  2  IGPS            Indole-3-glycerol phosphate synthase
     0.0047   16.3   2.3      0.024   14.1   0.0    2.3  2  NMO             Nitronate monooxygenase
     0.0079   15.3   0.2        1.2    8.1   0.0    2.4  2  Dus             Dihydrouridine synthase (Dus)
     0.0099   15.1   0.1       0.16   11.1   0.0    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
  ------ inclusion threshold ------
      0.013   15.1   0.1        2.9    7.4   0.0    2.5  3  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
      0.033   14.2   0.0      0.077   13.1   0.0    1.5  1  TetR_C_27       Tetracyclin repressor-like, C-terminal domain
      0.059   12.8   0.6        2.6    7.5   0.1    2.8  3  His_biosynth    Histidine biosynthesis protein
       0.11   13.1   0.0        0.3   11.6   0.0    1.7  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.1   2.1  3.6e-103  6.5e-100       3     207 .]      48     252 ..      46     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 333.1 bits;  conditional E-value: 3.6e-103
                                   HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HH CS
                       SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfv 83 
                                     k+ +  ++kgGvimdv+n+ qa+iae+aGavavm+l+++p d+rk+ggvarm+dpk+i+e++++++ipvmakvriGh+ 
  gi|70607291|ref|YP_256161.1|  48 MAKHAFPIFQKGGVIMDVTNVTQAEIAENAGAVAVMVLDKLPYDVRKSGGVARMADPKIIEEVMNSITIPVMAKVRIGHYY 128
                                   568889999************************************************************************ PP

                                   HHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHH CS
                       SOR_SNZ  84 eaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkike 164
                                   ea++lealgvd+iDesevltpadee+hi+k++fkvpfv+Garnlgealrri eGa+mirtkGeagtG+v+eav+h++ ++ 
  gi|70607291|ref|YP_256161.1| 129 EARVLEALGVDMIDESEVLTPADEEHHINKWEFKVPFVNGARNLGEALRRIYEGASMIRTKGEAGTGNVSEAVKHMKIMNY 209
                                   ********************************************************************************* PP

                                   HHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                       SOR_SNZ 165 eirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                   ei++l sl ee+  + a+e+++p++lv+ v +l+rlp+vnfaa
  gi|70607291|ref|YP_256161.1| 210 EISTLISLPEEDRLKKAREYQVPYQLVELVVKLKRLPIVNFAA 252
                                   *****************************************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.027        48     135     201 ..      69     141 ..      35     156 .. 0.76
   2 ?   -3.7   0.0       3.2   5.8e+03     182     195 ..     192     205 ..     183     208 .. 0.68
   3 !   23.2   0.0     2e-08   3.6e-05     167     224 ..     236     295 ..     225     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                                   HHHHHHHHTT-SEBEEBSS......STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEE CS
                          ThiG 135 vlarrleevGcaavmPlaa......piGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadav 201
                                     a+  e++G+ avm l          G    +++++ ++ +++++++Pv+    ig+  +a     lG+d +
  gi|70607291|ref|YP_256161.1|  69 TQAEIAENAGAVAVMVLDKlpydvrKSGGVARMADPKIIEEVMNSITIPVMAKVRIGHYYEARVLEALGVDMI 141
                                   55666788888888866432111113345555678899999999*********99999999988777888865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.2
                                   S---SHHHHHHHHH CS
                          ThiG 182 AGigspsdaaqame 195
                                   AG g+ s+a++ m+
  gi|70607291|ref|YP_256161.1| 192 AGTGNVSEAVKHMK 205
                                   56666666665554 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 2e-08
                                   HHHHHHH-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
                          ThiG 167 lkiiieeakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                                   ++++++  ++P++  A  Gi +p daa  m lG d++++ + + +++dp + A+a+ la 
  gi|70607291|ref|YP_256161.1| 236 VELVVKLKRLPIVNFAagGIATPADAALMMWLGSDGIFVGSGIFKSQDPDQRAKAVVLAA 295
                                   4555556699999654459************************************98875 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        28      60      89 ..      57      86 ..      39     141 .. 0.87
   2 !   10.4   0.0   0.00014      0.26     210     253 ..     247     290 ..     228     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                                  TTEESBSS--HHHHHHHHTTT.-SEEEEE- CS
                          IGPS 60 skgliredfdpaeiAkkyeeagAsaiSVLt 89
                                   kg + +d+  + +A+  e+agA a+ VL 
  gi|70607291|ref|YP_256161.1| 57 QKGGVIMDVTNVTQAEIAENAGAVAVMVLD 86
                                  4899999*******************9995 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                                   SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                          IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                   ++  a  Gi+t++d+  +   g +++ vG+ + +++d ++  ++
  gi|70607291|ref|YP_256161.1| 247 IVNFAAGGIATPADAALMMWLGSDGIFVGSGIFKSQDPDQRAKA 290
                                   6677999******************************9998775 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6      0.11   1.9e+02     139     198 ..      61     120 ..      36     126 .. 0.65
   2 !   14.1   0.0   1.3e-05     0.024     182     230 ..     233     283 ..     223     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                           NMO 139 liptissvkearkvearGaDaliv......qGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                   +i+ ++ v++a ++e++Ga a+ v      +  ++GG             +++++v++ + iPv+A
  gi|70607291|ref|YP_256161.1|  61 VIMDVTNVTQAEIAENAGAVAVMVldklpyDVRKSGGVAR------MADPKIIEEVMNSITIPVMA 120
                                   5777899999999999996665551111113445555554......23457888888888899988 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.3e-05
                           NMO 182 faLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                    +Lv+ v++   +P++  AaGGi +  + a ++ lG  g+ +g+     ++
  gi|70607291|ref|YP_256161.1| 233 YQLVELVVKLKRLPIVnfAAGGIATPADAALMMWLGSDGIFVGSGIFKSQD 283
                                   689************877*************************98777665 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.1     0.006        11     112     133 ..     105     126 ..      65     141 .. 0.79
   2 !    8.1   0.0   0.00067       1.2     180     224 ..     243     288 ..     222     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.006
                                   HHHHHHHCCSSS-EEEEEESES CS
                           Dus 112 qivkavvkaveiPvtvkirigi 133
                                   +i+++v + + iPv +k+rig 
  gi|70607291|ref|YP_256161.1| 105 KIIEEVMNSITIPVMAKVRIGH 126
                                   5788888899999999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00067
                                   HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHH CS
                           Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfa 224
                                   ++++i+ +a G+I ++ da  +++  G dg+ +g g    ++P   a
  gi|70607291|ref|YP_256161.1| 243 KRLPIVNFAAGGIATPADAALMMWL-GSDGIFVGSGIFksQDPDQRA 288
                                   46779999****************9.********9975114555554 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.081   1.5e+02     130     171 ..     100     142 ..      51     160 .. 0.67
   2 !   11.1   0.0   9.1e-05      0.16     134     179 ..     236     281 ..     223     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.081
                                   SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEE CS
                          NanE 130 aepDfalvkalsea.glkviaeGrintPekakkaieiGvdavv 171
                                      D +++++++++  + v+a  ri    +a+    +Gvd++ 
  gi|70607291|ref|YP_256161.1| 100 RMADPKIIEEVMNSiTIPVMAKVRIGHYYEARVLEALGVDMID 142
                                   4567777777665525678888888888888888888888775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.1e-05
                                   HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                          NanE 134 falvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                   ++lv +l+   +   a G i tP+ a+ ++ +G d + vGs i + 
  gi|70607291|ref|YP_256161.1| 236 VELVVKLKRLPIVNFAAGGIATPADAALMMWLGSDGIFVGSGIFKS 281
                                   456778888888899**************************99765 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   4.1e+03     175     207 ..      53      83 ..      41      84 .. 0.66
   2 ?    5.3   0.0    0.0074        13      81     151 ..     177     250 ..     172     262 .. 0.80
   3 ?    7.4   0.0    0.0016       2.9     197     224 ..     263     290 ..     247     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                   EHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEE CS
                     OMPdecase 175 tpgigleqggdgkgqqyntpekligiagadiii 207
                                    p  +  +gg+  ++ + t  ++++ aga  + 
  gi|70607291|ref|YP_256161.1|  53 FPIFQ--KGGVIMDVTNVTQAEIAENAGAVAVM 83 
                                   44455..57777777777777777777776655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0074
                                   HHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHH.SHHHHHHHHHHHHHHH...TT CS
                     OMPdecase  81 arikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqek.gytqacveaarehkae...df 151
                                    ri e+a ++   + aG++ v+++++ ++ ++   +  l  +  ++ l+ +++ ++ +++ve + + k+    +f
  gi|70607291|ref|YP_256161.1| 177 RRIYEGASMIRTKGEAGTGNVSEAVKHMKIMN-YEISTLISLPEEDRLKKAREyQVPYQLVELVVKLKRLpivNF 250
                                   6999************************9996.888888888888888887756999999999998885444444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0016
                                   HHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                     OMPdecase 197 ligiagadiiivGRgIlkagdpveeaer 224
                                   l+   g+d i vG gI+k++dp + a++
  gi|70607291|ref|YP_256161.1| 263 LMMWLGSDGIFVGSGIFKSQDPDQRAKA 290
                                   5555699*****************9987 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05     0.077      61      99 ..     275     313 ..     271     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                   HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGGG--H CS
                     TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsdpeie 99 
                                    +G Fk++dp++ a+av+ a a+  +P ++ e ++  +e
  gi|70607291|ref|YP_256161.1| 275 GSGIFKSQDPDQRAKAVVLAAANWEDPEIVLEAQKMISE 313
                                   589*************************99998876655 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.42   7.6e+02     196     205 ..      94     103 ..      52     141 .. 0.67
   2 ?    4.2   0.0     0.014        26     190     226 ..     245     281 ..     233     284 .. 0.75
   3 ?    7.5   0.1    0.0014       2.6      77     132 ..     273     324 ..     271     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.42
                                   EESS--SHHH CS
                  His_biosynth 196 asGGvgsled 205
                                    sGGv++++d
  gi|70607291|ref|YP_256161.1|  94 KSGGVARMAD 103
                                   4444444444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                                   HSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTT CS
                  His_biosynth 190 vkipviasGGvgsledlkelksegvdavivgsalyeg 226
                                   + i   a+GG+++++d + +   g d++ vgs +++ 
  gi|70607291|ref|YP_256161.1| 245 LPIVNFAAGGIATPADAALMMWLGSDGIFVGSGIFKS 281
                                   4445568999999999999999999999999877765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0014
                                   EEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                  His_biosynth  77 qvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr 132
                                    vG+GI + +d ++     a+ v+++ a  ++pe++ e+ + + ++k +++iD++ 
  gi|70607291|ref|YP_256161.1| 273 FVGSGIFKSQDPDQ----RAKAVVLAAANWEDPEIVLEAQKMISENKSMMGIDIKT 324
                                   67888877776544....4677*******************************986 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016       0.3      48     115 ..      66     132 ..      61     139 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   HHHCTSTTGGG--EEEEEE--..G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS--- CS
                Peptidase_S66C  48 tqlkeagvldkvkGivlGrftkpeek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspnlt 115
                                   t+  +a++ +++ ++++   +k +++   +  +++    +++eev+    +  +iPv++++ iGH ++  +
  gi|70607291|ref|YP_256161.1|  66 TNVTQAEIAENAGAVAVMVLDKLPYDvrkSGGVARMADPKIIEEVM----NSITIPVMAKVRIGHYYEARV 132
                                   5666777777777777776666633332344445555556666666....7999***********887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2366.48
//
Query:       gi|70607292|ref|YP_256162.1|  [L=200]
Description: glutamine amidotransferase subunit PdxT [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-48  163.3   0.1    6.1e-48  163.2   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
    5.8e-12   45.6   0.2    1.4e-10   41.1   0.2    2.7  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    9.2e-06   25.4   0.0    1.2e-05   25.1   0.0    1.2  1  Peptidase_S51  Peptidase family S51
    1.1e-05   25.3   0.4     0.0001   22.1   0.4    2.0  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.016   15.0   0.2      0.027   14.3   0.2    1.4  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.2   0.1   1.7e-51   6.1e-48       1     186 [.       5     198 ..       5     200 .] 0.91

  Alignments for each domain:
  == domain 1  score: 163.2 bits;  conditional E-value: 1.7e-51
                                   EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEET CS
                           SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtC 75 
                                   v+a qG++eeh  ++k+++ +         vk+++d++ +d+++iPGGest+++ ++e+ g++++++++++ + ++vlGtC
  gi|70607292|ref|YP_256162.1|   5 VIAYQGSFEEHAIQLKRAMSKLnltgevIAVKKPKDVDLIDGVVIPGGESTTIGIIAEKLGVLDEIKAKINAG-LPVLGTC 84 
                                   799***************988678889899****************************************988.******* PP

                                   HHHHHHCCEETTB.....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTC.SEEEEEESS--EEEEE-.TTTCEEEEEC CS
                           SNO  76 aGlillskelene.....lvktlellkvkvkrnafGrqvdsfekeldfknli.ekftavfiraPvieeilddeavkvlyel 150
                                   aG i+l+k+++         + ++ ++++v rn +Grq +sfe +ldf+ ++  k   vfiraP+i++  +d +  +  e+
  gi|70607292|ref|YP_256162.1|  85 AGAIMLAKDVSDAkvgkkSQPLIGTMDIQVVRNYYGRQRESFETDLDFRVIGgGKARVVFIRAPIIKRTWNDATALISFEN 165
                                   *********998745444456689***************************98999**************77766666655 PP

                                   TTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                           SNO 151 dgeivvakqkkilatsfhPelaeddirvhdyfveev 186
                                      iv a+qk++lat+fhPel+e+ + vh+yf+ ++
  gi|70607292|ref|YP_256162.1| 166 G--IVMAEQKNMLATTFHPELSES-TIVHEYFLSKI 198
                                   5..*********************.89*****9887 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.2   3.9e-14   1.4e-10      26     119 ..      31     118 ..      12     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.9e-14
                      GATase_3  26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageve 106
                                   +v+ v+ k ++++  +d v++pGg++t+  + +++  g+ ++ik++++ag pvlg C+G +mL + + d++     +++ +
  gi|70607292|ref|YP_256162.1|  31 EVIAVK-KPKDVDL-IDGVVIPGGESTTIGIIAEKL-GVLDEIKAKINAGLPVLGTCAGAIMLAKDVSDAKV---GKKSQP 105
                                   445555.5666644.9***************99999.******************************99864...57899* PP

                      GATase_3 107 glglLdietefek 119
                                    +g +di+++ + 
  gi|70607292|ref|YP_256162.1| 106 LIGTMDIQVVRNY 118
                                   *******998765 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.2e-09   1.2e-05      52     137 ..      19      98 ..       7     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.2e-09
                                   HHHHHHHTT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB CS
                 Peptidase_S51  52 vrkaleklglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivages 132
                                    ++a +kl+l  +++ ++  ++++++      d++++ GG+   +    ++ g+ + ++ ++++gl++ G+ AGai+ ++ 
  gi|70607292|ref|YP_256162.1|  19 LKRAMSKLNLTGEVIAVK--KPKDVDL----IDGVVIPGGESTTIGIIAEKLGVLDEIKAKINAGLPVLGTCAGAIMLAKD 93 
                                   456666666666666665..4455555....78*********************************************999 PP

                                   -GGGT CS
                 Peptidase_S51 133 ietts 137
                                   +   +
  gi|70607292|ref|YP_256162.1|  94 VSDAK 98 
                                   88777 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.4   2.9e-08    0.0001      13     182 ..      19     193 ..      11     200 .] 0.62

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.9e-08
                                   HHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCT...STS-EEEETHHHHHHHHHT CS
                        GATase  13 lvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikeare...nkiPiLGICLGmQllaief 88 
                                   l++a+ +l+++ ev+ ++++++        +dg++++gG  +    + +k+ ++ e+     +++P+LG C G  +la+++
  gi|70607292|ref|YP_256162.1|  19 LKRAMSKLNLTGEVIAVKKPKDVD-----LIDGVVIPGGESTTIgiIAEKLGVLDEIKAkinAGLPVLGTCAGAIMLAKDV 94 
                                   789999999999999999887777.....49********988878966666555555444449***************999 PP

                                   TT.EEEEEECEEEEEEEEEEEETTT......CGGTTTTSEEEEEEEEEEEEESG...........CHHHTTEEEEEEEETT CS
                        GATase  89 gr.kvvkekekehhggtmrlgddet......allyglknevierhrHryevnpk...........elepaglevtaksedd 151
                                      kv k++  + + gtm ++  ++      +          e+       + +            +  a ++   +++ +
  gi|70607292|ref|YP_256162.1|  95 SDaKVGKKS--QPLIGTMDIQVVRNyygrqrE--------SFET-------DLDfrvigggkarvVFIRAPIIKRTWNDAT 158
                                   873555555..677778988884444454431........2222.......211111111233332233322222222222 PP

                                   E...EEEEEEEETTT.EEEESSBTTSTTSTTHHHH CS
                        GATase 152 e...elmeiiekknp.fvgvQFHPEststpegpel 182
                                          +i+  +++ + ++ FHPE + ++  +e+
  gi|70607292|ref|YP_256162.1| 159 AlisFENGIVMAEQKnMLATTFHPELSESTIVHEY 193
                                   12222224444444449999999999988765555 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   7.5e-06     0.027      60     109 ..      42      92 ..      12     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-06
                                   CG-SEEEE--BHHHHHH.HHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHH CS
                     DJ-1_PfpI  60 aeyDalvlpGGragper.lrenekvvelvkefaekgklvaaICagpqlLaa 109
                                   +  D +v+pGG++     ++e+  v++ +k   ++g +v   Cag+++La+
  gi|70607292|ref|YP_256162.1|  42 DLIDGVVIPGGESTTIGiIAEKLGVLDEIKAKINAGLPVLGTCAGAIMLAK 92 
                                   4579*******996544156666999**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1458.23
//
Query:       gi|70607293|ref|YP_256163.1|  [L=510]
Description: ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-11   42.7   0.0    6.2e-11   41.9   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
    1.6e-05   25.3   0.0     0.0022   18.4   0.0    2.2  2  AAA_16           AAA ATPase domain
     0.0013   18.5   0.1      0.016   15.0   0.0    2.6  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.002   18.4   0.2      0.089   13.1   0.0    2.6  2  AAA_22           AAA domain
     0.0026   18.3   0.6      0.015   15.9   0.0    2.6  2  AAA_18           AAA domain
     0.0036   16.9   0.0     0.0086   15.7   0.0    1.6  1  AAA_25           AAA domain
     0.0042   16.4   0.0      0.012   14.9   0.0    1.7  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0043   17.0   0.1      0.021   14.8   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0047   16.7   0.0      0.012   15.4   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0053   16.9   0.0      0.014   15.5   0.0    1.7  1  Sigma54_activ_2  Sigma-54 interaction domain
     0.0061   17.0   0.0      0.024   15.1   0.0    2.0  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.012   15.1   0.1      0.034   13.7   0.0    1.8  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
      0.013   15.4   0.3      0.054   13.4   0.0    2.1  2  NACHT            NACHT domain
      0.017   15.1   0.0      0.037   14.0   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.024   14.8   0.0       0.27   11.5   0.0    2.5  2  DUF4279          Domain of unknown function (DUF4279)
      0.039   14.1   0.0       0.11   12.6   0.0    1.8  1  AAA_33           AAA domain
       0.04   13.8   0.1       0.21   11.5   0.0    2.3  2  NTPase_1         NTPase
      0.046   13.4   0.0       0.12   12.1   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      0.048   13.9   0.0       0.14   12.4   0.0    1.8  1  AAA_28           AAA domain
      0.049   12.9   0.0      0.099   11.9   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.055   13.2   0.7       0.13   12.0   0.1    1.9  2  AAA_24           AAA domain
      0.082   12.5   0.1       0.16   11.6   0.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
      0.095   13.0   0.2       0.36   11.2   0.0    1.9  2  AAA_19           AAA domain
       0.11   12.3   0.2       0.26   11.0   0.1    1.7  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.13   11.6   0.0       0.37   10.1   0.0    1.7  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.13   11.9   0.7         13    5.5   0.0    2.8  2  PNK3P            Polynucleotide kinase 3 phosphatase
       0.14   11.8   0.0       0.81    9.4   0.0    2.0  2  AAA_30           AAA domain
       0.14   12.5   0.0       0.43   11.0   0.0    1.9  1  RNA_helicase     RNA helicase
       0.15   11.4   0.0       0.28   10.5   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0     1e-13   6.2e-11      75     243 ..     204     361 ..     165     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1e-13
                         T2SSE  75 ekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                    +++r+ ++ +P++ g +++i ++ +k+ +l+++ ++e+    + + lr        il++G  g GKtt++ al ++   
  gi|70607293|ref|YP_256163.1| 204 LGNYRVVIIRPPLSDGWEVTITRPVVKK-KLEEYNMDEK----LLKRLRDK---AEGILIAGSPGMGKTTFAQALAEFYTR 276
                                   578999**********889988777777.8888887665....45556666...6899****************9999999 PP

                         T2SSE 156 sderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHans 235
                                    ++ + t+E p+ ++l  ++++q  ++    ++ +l   +L  rPD  +  E+R  e +++ +     G    ++ +Ha s
  gi|70607293|ref|YP_256163.1| 277 MNKVVKTIESPRDMHLP-PEVTQYSKN--YAEVGELHDILLLSRPDYTVYDEMRNDEDFKLyIDLRLAGIGM-IGVVHATS 353
                                   999999*********96.445555555..45666677777999******************99999999777.******** PP

                         T2SSE 236 aagalerL 243
                                   +++a++r 
  gi|70607293|ref|YP_256163.1| 354 PIDAIHRF 361
                                   ******96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.053        33      37     154 ..      10     115 ..      10     142 .. 0.57
   2 !   18.4   0.0   3.6e-06    0.0022      14      53 ..     241     279 ..     234     369 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.053
                        AAA_16  37 Ksslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaea. 116
                                   Ks+l+  l +++e +   +++g+   +    +++  ++  a+e+l++++ + +e + l + +e l                
  gi|70607293|ref|YP_256163.1|  10 KSALLHGLSKYIENR---TIYGNILIH---KRLLEDLEREAKEGLVTAEIALDEVKRLKEISENL--------------Lv 70 
                                   556666666555555...344444444...22222222222334444444444444444444444..............24 PP

                        AAA_16 117 .......srllellkrll.allsrderplvlvlDdlqwadeaslql 154
                                          + l+  l+  l +++ +++  ++++ D++q+  ++sl++
  gi|70607293|ref|YP_256163.1|  71 sfeivnsENLHGSLNGVLrDYCLSRKC-TIVTTDEIQKKLSESLNI 115
                                   444445589999999999888888455.*********777777765 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.6e-06
                        AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdgg 53 
                                    +l+r+r+   e +l+ G +G+GK++ +++l++ +++ + 
  gi|70607293|ref|YP_256163.1| 241 KLLKRLRDKA-EGILIAGSPGMGKTTFAQALAEFYTRMNK 279
                                   5788888777.89*******************98887743 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.3e+03      89     105 ..      54      70 ..      44      76 .. 0.85
   2 !   15.0   0.0   2.5e-05     0.016      30      56 ..     247     273 ..     224     301 .. 0.77
   3 ?   -1.7   0.0       3.5   2.1e+03      90     130 ..     355     393 ..     352     409 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                        RuvB_N  89 fideihrlsraveevly 105
                                    +de+ rl++  e++l 
  gi|70607293|ref|YP_256163.1|  54 ALDEVKRLKEISENLLV 70 
                                   58*******99999885 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.5e-05
                        RuvB_N  30 eealdhvllyGpPGlGkttlakiiake 56 
                                   +++ + +l++G+PG+Gktt+a+ +a+ 
  gi|70607293|ref|YP_256163.1| 247 RDKAEGILIAGSPGMGKTTFAQALAEF 273
                                   4566789****************9964 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.5
                        RuvB_N  90 ideihrlsraveevlysamedfrldivigkGpsarsikldl 130
                                   id ihr+ + ++    + + d    + i++G+ a+   ld+
  gi|70607293|ref|YP_256163.1| 355 IDAIHRFINRIDIGTIPNILDTV--VFINSGNVAKVYGLDI 393
                                   89999999888887777777765..4677777777776665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.32     2e+02      44     103 ..      52     109 ..      31     129 .. 0.52
   2 !   13.1   0.0   0.00014     0.089       5      31 ..     250     276 ..     246     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.32
                        AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseell.ealeqalraravielliiDEaqh.l 103
                                   ++ l + + +k++ ++ll  ++  +++   +++  l   l++++ +r+   ++  DE+q+ l
  gi|70607293|ref|YP_256163.1|  52 EIALDEVKRLKEISENLLVSFEIVNSE---NLHGSLnGVLRDYCLSRKC-TIVTTDEIQKkL 109
                                   333333334555555555555554444...4444443666666666666.666666666655 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqlde 31 
                                   a  +++ G +G+GKTt ++ l+e +++
  gi|70607293|ref|YP_256163.1| 250 AEGILIAGSPGMGKTTFAQALAEFYTR 276
                                   66689******************9965 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       7.1   4.4e+03      25      53 ..      85     116 ..      58     137 .. 0.67
   2 !   15.9   0.0   2.4e-05     0.015       1      33 [.     253     282 ..     253     334 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.1
                        AAA_18  25 gvnlrdvakenglllevdpe...aldeskrld 53 
                                     +lrd++  + + +  ++e   +l+es+ +d
  gi|70607293|ref|YP_256163.1|  85 NGVLRDYCLSRKCTIVTTDEiqkKLSESLNID 116
                                   66778888888888777777644444444444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.4e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvak 33 
                                   Il++G pG GKtt+a++L++     ++ ++v+k
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEF---YTRMNKVVK 282
                                   99****************885...444444443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.4e-05    0.0086      23      61 ..     240     278 ..     234     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                        AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalavatGk 61 
                                   ++l+k+l+ + e +l+aG pg GKtt+a  la  +++  
  gi|70607293|ref|YP_256163.1| 240 EKLLKRLRDKAEGILIAGSPGMGKTTFAQALAEFYTRMN 278
                                   6799999************************98877655 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.3   4.5e+03     162     187 ..     107     134 ..      97     146 .. 0.66
   2 !   14.9   0.0     2e-05     0.012      19      47 ..     250     278 ..     236     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.3
                                   HHHHHHCTSXEEEE..EEXSGGGCCSCC CS
                                   xxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                        DnaB_C 162 kalakelnvpvial..sqLsravesred 187
                                   k+l+  ln+ v+ l  sq + ++e+  d
  gi|70607293|ref|YP_256163.1| 107 KKLSESLNIDVVLLqpSQTELEIEKMFD 134
                                   7888888888888744455555555445 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                                   TXEEEEEEXTTSSHHHHHHHHHHHHHHCS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  19 gdliiiAarpsmGktalalniaenaavke 47 
                                   ++ i+iA+ p+mGkt++a  +ae  +  +
  gi|70607293|ref|YP_256163.1| 250 AEGILIAGSPGMGKTTFAQALAEFYTRMN 278
                                   56699*****************9876433 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.7   4.1e+03      58      77 ..      39      61 ..       9      81 .. 0.61
   2 !   14.8   0.0   3.4e-05     0.021       2      36 ..     253     290 ..     252     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.7
                                  -------G-SE...EEEESGGG- CS
                         AAA_5 58 plvraaregei...lvlDEvera 77
                                   l r+a+eg +   + lDEv+r+
  gi|70607293|ref|YP_256163.1| 39 DLEREAKEGLVtaeIALDEVKRL 61
                                  44455554444222456777665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.4e-05
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36 
                                   +l+ G pG gK+++a+ la+++   n+ v ++  +rd+
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEFYtrmNKVVKTIESPRDM 290
                                   7999******************9888888888888877 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-05     0.012      45      78 ..     248     281 ..     228     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                     IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsv 78 
                                   +k+e+i++ G +G+GK+ +a al+    r ++ v
  gi|70607293|ref|YP_256163.1| 248 DKAEGILIAGSPGMGKTTFAQALAEFYTRMNKVV 281
                                   789********************98777766555 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.2e-05     0.014      14      56 ..     243     285 ..     223     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                                   HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTH CS
               Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvver 56 
                                   L+ ++ +   ++++G +G gk+++A++L+++ ++  ++++ ++
  gi|70607293|ref|YP_256163.1| 243 LKRLRDKAEGILIAGSPGMGKTTFAQALAEFYTRMNKVVKTIE 285
                                   7889999999**********************99888776543 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-05     0.024       1      21 [.     253     273 ..     253     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-05
                                   EEEESSTTSSHHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavake 21 
                                   +l+ G pG+GKT++a+a+a+ 
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEF 273
                                   6899**************985 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.6e-05     0.034      51     108 ..      94     150 ..      82     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.6e-05
                                   SS-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE-S-B-GGG CS
                         Lon_C  51 pgkgklkltGklgdvmkesaqaalsyvrsraeelgidkevfekkdihihvPeGavPkd 108
                                   + k  + +t ++   + es ++ + +++  ++el+i+k +f+++ + +h+ eG +Pk 
  gi|70607293|ref|YP_256163.1|  94 SRKCTIVTTDEIQKKLSESLNIDVVLLQPSQTELEIEK-MFDETTMSVHLKEGVTPKA 150
                                   5677899999**************************95.9****************95 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.9   1.8e+03      99     142 ..      67     116 ..      30     139 .. 0.61
   2 ?   13.4   0.0   8.7e-05     0.054       3      22 ..     253     272 ..     251     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.9
                                   H................HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                         NACHT  99 q.......kekqpvrtlLselirkkllpeasllltvrpralrdleeqleea 142
                                   +        + ++++  L++ +r   l++ + ++t+     ++l e+l   
  gi|70607293|ref|YP_256163.1|  67 NllvsfeiVNSENLHGSLNGVLRDYCLSRKCTIVTTDE-IQKKLSESLNID 116
                                   45555555556677777888888866666666666543.333555555444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.7e-05
                                   EEEEC-TTTCHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                   +++ G +G+GKTt++q la+
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAE 272
                                   789*************9985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.1e-05     0.037      12      51 ..     240     287 ..     230     288 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.1e-05
                                   HHHHHCH...TEEEEEEESTTSSHHHHHHHHHHHTT--.....----T CS
                          TsaE  12 kklakal...gdvilLeGdLGaGKTtlvrglakalgve.....evkSP 51 
                                   +kl k l   ++ il+ G  G+GKTt++++la+ +        +++SP
  gi|70607293|ref|YP_256163.1| 240 EKLLKRLrdkAEGILIAGSPGMGKTTFAQALAEFYTRMnkvvkTIESP 287
                                   4444444433445******************99763322223456666 PP

>> DUF4279  Domain of unknown function (DUF4279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00043      0.27      28      84 ..     147     205 ..     127     212 .. 0.84
   2 ?    1.7   0.0      0.46   2.8e+02      23      71 ..     196     254 ..     193     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                       DUF4279  28 isdptkkrkegsWelstglee...sldleeqldklldrlepkaekikelakkygleiylq 84 
                                   +++  kk k gsW++++ l++   s d++ +++++l+++++ ++ + e+ +k +  + l+
  gi|70607293|ref|YP_256163.1| 147 TPKA-KKGKPGSWQFVELLSNpltSTDIKRVVNEILSSVNYVKDSFIEIERKGSTIVQLG 205
                                   3333.8999*******999999****************************9988877665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.46
                       DUF4279  23 vkGdrisdpt.......kkrkegsWels.tgleesldleeqldk..lldrlepkaekik 71 
                                   +kG++i +         +++  + We+  t   + + lee  ++  ll+rl +kae+i 
  gi|70607293|ref|YP_256163.1| 196 RKGSTIVQLGnyrvviiRPPLSDGWEVTiTRPVVKKKLEEYNMDekLLKRLRDKAEGIL 254
                                   56666665556667777888899999997777777777764333359****99999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018      0.11       2      21 ..     253     272 ..     253     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                        AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                   +l+ G pG+GK+t+a+ l++
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAE 272
                                   5789************9984 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00034      0.21       2      30 ..     253     281 ..     252     288 .. 0.84
   2 ?   -2.7   0.0       7.6   4.7e+03      98     110 ..     470     484 ..     439     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                   ++i G+pG+GKtT+ + ++e   + +  v
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEFYTRMNKVV 281
                                   789*************9999887777655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.6
                                   EEEE..---STTGGG CS
                      NTPase_1  98 vivi..DEiGkmElk 110
                                   +i i  DEiG +  k
  gi|70607293|ref|YP_256163.1| 470 IITIprDEIGMFNKK 484
                                   344444666655443 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.12      14      52 ..     242     280 ..     230     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                   HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
               Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekp 52 
                                    +k++ ++   +li G  G GK+++a+a+ e  +r +k 
  gi|70607293|ref|YP_256163.1| 242 LLKRLRDKAEGILIAGSPGMGKTTFAQALAEFYTRMNKV 280
                                   56777788889******************9988887765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00023      0.14       2      22 ..     253     273 ..     252     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                        AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                   i i G ++ GKTt ++aLa+ 
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEF 273
                                   789****************75 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016     0.099      16      47 ..     250     281 ..     235     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                    Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvv 47 
                                      il++G+pG GK++ a++l++  +r ++vv
  gi|70607293|ref|YP_256163.1| 250 AEGILIAGSPGMGKTTFAQALAEFYTRMNKVV 281
                                   5569****************999887666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.9   3.7e+03     149     167 ..     118     136 ..      95     152 .. 0.72
   2 ?   12.0   0.1   0.00021      0.13       5      22 ..     253     270 ..     249     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                        AAA_24 149 epklgkktanelkeevDlv 167
                                    + ++++t  e+++++D+ 
  gi|70607293|ref|YP_256163.1| 118 VLLQPSQTELEIEKMFDET 136
                                   4567788899999999975 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00021
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   ili G++g+GKTt+a  l
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQAL 270
                                   89*************987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00025      0.16       4      32 ..     253     281 ..     250     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkkegkkv 32 
                                   il++G  G+GKTt +  La+ +++++k v
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEFYTRMNKVV 281
                                   89********************9998765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.3   5.1e+03      94     122 ..      42      69 ..      19      79 .. 0.70
   2 ?   11.2   0.0   0.00058      0.36      11      40 ..     251     280 ..     244     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.3
                        AAA_19  94 aeeekklqeeellivDEfqdvdelqyrLl 122
                                   +e ++ l  ++ +  DE+  ++e   +Ll
  gi|70607293|ref|YP_256163.1|  42 REAKEGL-VTAEIALDEVKRLKEISENLL 69 
                                   3444445.456788899999988777776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00058
                        AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggv 40 
                                   + +l+ + pG+GKT+  ++  + + ++++v
  gi|70607293|ref|YP_256163.1| 251 EGILIAGSPGMGKTTFAQALAEFYTRMNKV 280
                                   568999************999999998876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00042      0.26       1      29 [.     255     283 ..     255     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvav 29 
                                   ++G +G GKttf +al+e+++  ++ v++
  gi|70607293|ref|YP_256163.1| 255 IAGSPGMGKTTFAQALAEFYTRMNKVVKT 283
                                   68*****************9998777666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0006      0.37      25      50 ..     253     278 ..     249     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0006
                  Mg_chelatase  25 lllvGppGsGKtmlakrlpsllppls 50 
                                   +l++G+pG GKt  a++l++  ++++
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEFYTRMN 278
                                   899***************99887776 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.021        13      31      92 ..     235     296 ..     220     339 .. 0.80
   2 ?    3.4   0.4     0.092        57      42      83 ..     419     459 ..     406     502 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                         PNK3P  31 sesvlekLkklkeegykivifsNqggvvekktkkslekfkekieallkeldvpllvyaatkk 92 
                                   + ++ ekL k  +++++ ++++   g+ +++ +++l++f +++++++k+++ p  + + ++ 
  gi|70607293|ref|YP_256163.1| 235 EYNMDEKLLKRLRDKAEGILIAGSPGMGKTTFAQALAEFYTRMNKVVKTIESPRDMHLPPEV 296
                                   45677899999888888889999999999999******************999666665554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.092
                         PNK3P  42 keegykivifsNqggvvekktkkslekfkekieallkeldvp 83 
                                   ++ +y+i +f  q  +v   ++ ++++ ++++e++++++  +
  gi|70607293|ref|YP_256163.1| 419 DKAEYEIYVFGEQTMIVP-VKNLQTNSTQRRLESMINNIIPS 459
                                   44569999*****99999.57888889999999999888433 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0013      0.81      20      47 ..     252     279 ..     240     287 .. 0.80
   2 ?   -0.8   0.0       1.7   1.1e+03      95     120 ..     476     501 ..     437     503 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                        AAA_30  20 vavltGpAGtGKttalkalreaweaagg 47 
                                     ++ G +G GKtt  +al+e +++ ++
  gi|70607293|ref|YP_256163.1| 252 GILIAGSPGMGKTTFAQALAEFYTRMNK 279
                                   56899*****************998754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                        AAA_30  95 DEagmvdtkqlaallkaaekagakvi 120
                                   DE+gm + k + +l k  +k+++k++
  gi|70607293|ref|YP_256163.1| 476 DEIGMFNKKVVSKLKKYEKKYKIKIR 501
                                   9**********999998888887776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0007      0.43       1      23 [.     253     275 ..     253     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                   i++ G++g GK+t+a+ La+  +
  gi|70607293|ref|YP_256163.1| 253 ILIAGSPGMGKTTFAQALAEFYT 275
                                   6899*************886544 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00045      0.28      27      59 ..     238     270 ..     225     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                                   TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  27 sgnplvldlkkmashllvaGatgsGKStalntL 59 
                                   ++++l   l+  a  +l+aG++g GK+t+ ++L
  gi|70607293|ref|YP_256163.1| 238 MDEKLLKRLRDKAEGILIAGSPGMGKTTFAQAL 270
                                   788888888888889**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 3653.19
//
Query:       gi|70607294|ref|YP_256164.1|  [L=143]
Description: holliday junction resolvase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-28   97.4   0.1    4.7e-28   97.0   0.1    1.2  1  Hjc        Archaeal holliday junction resolvase (hjc)
    0.00011   21.8   0.0    0.00016   21.2   0.0    1.3  1  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.1   5.2e-32   4.7e-28       2      91 ..      10     100 ..       9     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 5.2e-32
                                   HHHHHHHHHHHTT-EEEEBSCSSSSSS.SS-SEEEEETTEEEEEEEEEESSS.EEEEEHHHHHHHHHHHHHHTCEEEEEEE CS
                           Hjc   2 yERelvkiLrergfavvRsagSggatk.plpDviAirgdvvlviEvKsskke.riylkkeqvekllefarkaggelllavk 80 
                                    ER lv+ Lr++gfav+R+++Sg+ +k ++pDviA++ +v+++iE+Ks+k+  +iy++keq+e++ efa+k+ggel+l++k
  gi|70607294|ref|YP_256164.1|  10 LERYLVSRLRDKGFAVIRAPASGSNRKdHVPDVIAMKSGVIILIEMKSRKNGnKIYIQKEQAEGIKEFAKKSGGELFLGAK 90 
                                   7************************999*********************9766**************************** PP

                                   ETTTEEEEEEG CS
                           Hjc  81 lqgkewkllvv 91 
                                   +  k++k+l++
  gi|70607294|ref|YP_256164.1|  91 I-AKDLKFLRF 100
                                   8.788888876 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.7e-08   0.00016      16      66 ..      14      61 ..       2      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.7e-08
                     AHJR-like 16 laeqyrekGyevllhPnredlPdfLksYrpDliarkdeeaviiEvksrrss 66
                                  l + +r+kG+ v+ +P +       k++ pD+ia+k    + iE+ksr++ 
  gi|70607294|ref|YP_256164.1| 14 LVSRLRDKGFAVIRAPASGS---NRKDHVPDVIAMKSGVIILIEMKSRKNG 61
                                  67889***********9975...6789*********************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1050.84
//
Query:       gi|70607295|ref|YP_256165.1|  [L=332]
Description: ketol-acid reductoisomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-71  236.7   0.0    1.5e-70  236.0   0.0    1.3  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    1.5e-54  184.2   1.4    8.6e-54  181.7   2.7    1.5  2  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    2.4e-06   28.0   0.0    1.1e-05   25.9   0.0    2.0  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      3e-06   26.7   0.0    5.9e-06   25.7   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    2.9e-05   24.3   0.0    0.00012   22.3   0.0    2.0  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      5e-05   23.4   0.0    0.00025   21.1   0.0    2.0  2  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
  ------ inclusion threshold ------
      0.026   14.5   0.0        4.6    7.2   0.1    2.5  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.044   12.5   0.0       0.35    9.6   0.0    2.3  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
       0.12   12.0   0.1       0.25   11.0   0.1    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.0   0.0   7.7e-74   1.5e-70       1     165 []      14     178 ..      14     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.0 bits;  conditional E-value: 7.7e-74
                                   HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                          IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81 
                                   ++k+k++av+GyGsqG+a+alnlrdsg++v vgl+++++s+k+A+++gf+ l+++eav+++d++++l+PD++q++vy e++
  gi|70607295|ref|YP_256165.1|  14 VIKEKRVAVLGYGSQGRAWALNLRDSGIKVSVGLEREGNSWKQAENDGFKPLRTEEAVRNSDIIIFLLPDMIQRTVYLERV 94 
                                   589****************************************************************************** PP

                                   GGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTHH CS
                          IlvN  82 epnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGat 162
                                   +p+lkeg  l+fahGfnih++li+pp++vdv+++APk+pG +vre +++g+Gvpal+a +qd sgka ++ala+ak+iGat
  gi|70607295|ref|YP_256165.1|  95 KPYLKEGMDLVFAHGFNIHYRLIEPPSNVDVYMIAPKAPGPIVREYFAKGGGVPALVATYQDHSGKALQKALAVAKAIGAT 175
                                   ********************************************************************************* PP

                                   HH- CS
                          IlvN 163 raG 165
                                   raG
  gi|70607295|ref|YP_256165.1| 176 RAG 178
                                   **9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       4.1   8.2e+03      42      82 ..      90     131 ..      86     141 .. 0.71
   2 !  181.7   2.7   4.3e-57   8.6e-54       1     141 [.     184     324 ..     184     326 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.1
                                   HHHHTHHH.HHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHH CS
                          IlvC  42 yfeclhel.klivdliyegGiakmresiSdtaeygdltagpr 82 
                                   y+e ++   k+ +dl+  +G++  ++ i   +++  + ++p+
  gi|70607295|ref|YP_256165.1|  90 YLERVKPYlKEGMDLVFAHGFNIHYRLIEPPSNVDVYMIAPK 131
                                   566665555777888889998888888877777777776666 PP

  == domain 2  score: 181.7 bits;  conditional E-value: 4.3e-57
                                   HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHH CS
                          IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagp 81 
                                   FkeEtetDlfgEq+ L+Ggv++l++ +F+tlveaGy+pe+Ayfe+++e+klivdl+ye+G+++m+ ++Sdta+yg++t+g+
  gi|70607295|ref|YP_256165.1| 184 FKEETETDLFGEQVDLVGGVMQLMRYAFQTLVEAGYQPEVAYFETINEMKLIVDLVYEKGFSGMLTAVSDTAKYGGMTVGK 264
                                   9******************************************************************************** PP

                                   HHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHC CS
                          IlvC  82 rviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklral 141
                                    vi+e+vke+mk+ l++i+sG+fa++++ee+ +g++++k+ +ke +++  ekvg+ lr++
  gi|70607295|ref|YP_256165.1| 265 MVIDESVKERMKKALDNIRSGKFAEKWVEEYGKGANTIKEGMKEVDNSTEEKVGRSLRDI 324
                                   **********************************************************86 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.5e-09   1.1e-05       1      70 [.      19      82 ..      19      96 .. 0.85
   2 ?   -1.4   0.0       1.8   3.6e+03      34      52 ..     283     301 ..     261     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.5e-09
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk 70
                                  +++++G+G++g+a a++l  +g    ++ v+ +r+ ++ ++++++   + ++  +eea++++d++++ ++
  gi|70607295|ref|YP_256165.1| 19 RVAVLGYGSQGRAWALNLRDSG---IKVSVGLEREGNSWKQAEND---GFKPLRTEEAVRNSDIIIFLLP 82
                                  69********************...******88888876555444...4677779**********98765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                   SSCCCHHHHHHHHC-EEEC CS
                 F420_oxidored  34 rnpekaeelaeelgvkvta 52 
                                   r+ + ae++ ee+g ++ +
  gi|70607295|ref|YP_256165.1| 283 RSGKFAEKWVEEYGKGANT 301
                                   6677788888888866655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0     3e-09   5.9e-06      27     100 ..       8      82 ..       2      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3e-09
                                   CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EE.EEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S- CS
                  2-Hacid_dh_C  27 kallgkelsgktvGiiGlGrIGqavakrlkafgmkv.iaydrskkkeeeeeelgvelvsleellaesDivslhlp 100
                                   k+++   +++k+v+++G+G+ G+a a  l+  g+kv ++ +r  ++ +++e+ g++    ee++++sDi++  lp
  gi|70607295|ref|YP_256165.1|   8 KDVSLDVIKEKRVAVLGYGSQGRAWALNLRDSGIKVsVGLEREGNSWKQAENDGFKPLRTEEAVRNSDIIIFLLP 82 
                                   566777899**************************9446888888888999********************9998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   6.1e-08   0.00012       2      84 ..      20     102 ..      19     117 .. 0.87
   2 ?   -2.1   0.0       1.9   3.8e+03      79      88 ..     259     268 ..     203     287 .. 0.48
   3 ?   -1.9   0.0       1.6   3.2e+03      30      56 ..     283     309 ..     254     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.1e-08
                                   EEEE--SHHHHHHHHHHHHTT-EEEE.E-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC-- CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvav.ynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealk 81 
                                   ++++G G  G+  alnl ++g+kv+v  +r+ ++ +++ ++g+k++ + ee+v++ d++i+++++  +    +e+++++lk
  gi|70607295|ref|YP_256165.1|  20 VAVLGYGSQGRAWALNLRDSGIKVSVgLEREGNSWKQAENDGFKPLRT-EEAVRNSDIIIFLLPDMIQRTVYLERVKPYLK 99 
                                   89**********************98468999999999999*****98.7799************8887777777***999 PP

                                   TT- CS
                 NAD_binding_2  82 kgd 84 
                                   +g 
  gi|70607295|ref|YP_256165.1| 100 EGM 102
                                   985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                   C--TT-EEEE CS
                 NAD_binding_2  79 alkkgdilid 88 
                                    +  g+++id
  gi|70607295|ref|YP_256165.1| 259 GMTVGKMVID 268
                                   2333444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.6
                                   SSHHHHHHHHHTTEEE-SSHHHHHHHC CS
                 NAD_binding_2  30 rtkekveelvaegakaaesieelvasl 56 
                                   r+ + +e++v+e  k+a++i+e ++++
  gi|70607295|ref|YP_256165.1| 283 RSGKFAEKWVEEYGKGANTIKEGMKEV 309
                                   344445666666677777777666665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.3e-07   0.00025      20      83 ..      14      78 ..       6      92 .. 0.91
   2 ?   -1.1   0.0      0.86   1.7e+03       5      32 ..     267     296 ..     264     310 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                                  --TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE.-S-HHHHHHHHCTT-EE--HHHCTTT-SEEE CS
                 AdoHcyase_NAD 20 llaGkvavvaGyGdvGkGcaaslkglGarvivt.evdPicalqaameGfevvtleevvkkadivv 83
                                  ++  k + v GyG  G+  a  l+  G +v v  e +  +  qa  +Gf+  + ee+v+++di++
  gi|70607295|ref|YP_256165.1| 14 VIKEKRVAVLGYGSQGRAWALNLRDSGIKVSVGlEREGNSWKQAENDGFKPLRTEEAVRNSDIII 78
                                  4678999************************96488888899*********************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.86
                                   HCCCCCHHHHHHH-S--TTSEE..EEE--S CS
                 AdoHcyase_NAD   5 creslvdgikratdvllaGkva..vvaGyG 32 
                                   + es+ + +k+a d + +Gk a   v  yG
  gi|70607295|ref|YP_256165.1| 267 IDESVKERMKKALDNIRSGKFAekWVEEYG 296
                                   568999999999999999998722344454 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0023       4.6       2      27 ..      20      45 ..      19      60 .. 0.84
   2 ?    4.6   0.0     0.014        28      64     101 ..      68     106 ..      64     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0023
                                  EEEE--SHHHHHHHHHHHTTT--EEE CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrl 27
                                  +avlG Gs G a A  l + g +v++
  gi|70607295|ref|YP_256165.1| 20 VAVLGYGSQGRAWALNLRDSGIKVSV 45
                                  9********************98876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                                   HHHHTT--EEEE---HHHHHHH.HHHHCCC--TT-EEEE CS
                NAD_Gly3P_dh_N  64 aealkgadiivlvvPsqalrev.lkklkgllkkkailvs 101
                                   +ea++++dii++ +P  + r+v l+++k++lk+   lv 
  gi|70607295|ref|YP_256165.1|  68 EEAVRNSDIIIFLLPDMIQRTVyLERVKPYLKEGMDLVF 106
                                   79***************9999746889999998887775 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00017      0.35     268     351 ..      13     205 ..       2     220 .. 0.65
   2 ?   -1.6   0.0      0.44   8.7e+02     228     265 ..     243     284 ..     236     291 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                                   HHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHH.................................... CS
                Oxidored_nitro 268 eylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddee.................................... 312
                                   +++++krva+ g++++  a+a  l++ G++v + + +++ + +++                                    
  gi|70607295|ref|YP_256165.1|  13 DVIKEKRVAVLGYGSQGRAWALNLRDSGIKVSVGLEREG-NSWKQaendgfkplrteeavrnsdiiifllpdmiqrtvyle 92 
                                   56789*************************986555555.55554357777777777777777777777777777777777 PP

                                   ..........................................................................HHHHHS. CS
                Oxidored_nitro 313 ..........................................................................rlkaele 319
                                                                                                              + + ++
  gi|70607295|ref|YP_256165.1|  93 rvkpylkegmdlvfahgfnihyrlieppsnvdvymiapkapgpivreyfakgggvpalvatyqdhsgkalqkalAVAKAIG 173
                                   666666666666666666666666666666666666666666666666666666666666666666666664443333333 PP

                                   TT.SEEEES.CHHHHHHHHHHHT-SEEEE-CC CS
                Oxidored_nitro 320 egepeviddadleeleelikelkpdlllggsk 351
                                   ++   vi++   ee+e  +  +++dl+ g  +
  gi|70607295|ref|YP_256165.1| 174 ATRAGVIETTFKEETETDLFGEQVDLVGGVMQ 205
                                   33445666655566666666666666655555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
                                   SHHHHHHHHHHHHHHHT....CHHHHHHHHHHHHHHHHHHHH CS
                Oxidored_nitro 228 Gleatdaflrelakllg....kevaperiaeerarlldalad 265
                                   G+ ++ + + + ak+ g    k v +e+++e ++++ld+++ 
  gi|70607295|ref|YP_256165.1| 243 GFSGMLTAVSDTAKYGGmtvgKMVIDESVKERMKKALDNIRS 284
                                   666777777777777777776777777777777888887765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00012      0.25       1      38 [.      20      56 ..      20     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkk 38
                                  +a+lG G++G+ +a +L   g +v + l ++  +++k+
  gi|70607295|ref|YP_256165.1| 20 VAVLGYGSQGRAWALNLRDSGIKVSVGLERE-GNSWKQ 56
                                  69***************99****98877666.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2239.40
//
Query:       gi|70607296|ref|YP_256166.1|  [L=131]
Description: hypothetical protein Saci_1560 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-06   26.9   0.0    5.2e-06   26.2   0.0    1.3  1  ACT_5     ACT domain


Domain annotation for each model (and alignments):
>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.9e-10   5.2e-06       2      62 .]      15      75 ..      14      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.9e-10
                         ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVesersvelLsnQleKLidVlkV 62
                                  +p +LeR+++ +r+   ++ +++++++ d+g ++i   +    ++e  ++ l+K +dV+kV
  gi|70607296|ref|YP_256166.1| 15 DPSFLERIIGQFRKLLMDINWMQARKVSDNGLYEIYFGIPYTNNFEIAIANLSKTVDVEKV 75
                                  7999*******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 905.76
//
Query:       gi|70607297|ref|YP_256167.1|  [L=572]
Description: acetolactate synthase catalytic subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-55  185.1   0.0    3.3e-53  179.8   0.0    2.4  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.3e-47  159.7   0.0    3.6e-45  153.5   0.0    2.6  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.5e-38  130.1   0.0      1e-37  129.0   0.0    1.6  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    0.00023   21.0   0.0    0.00046   20.0   0.0    1.5  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   7.3e-57   3.3e-53       2     169 ..       3     172 ..       2     175 .. 0.98
   2 ?    2.7   0.0     0.019        83      75     160 ..     450     543 ..     427     549 .. 0.57

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 7.3e-57
                                   EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHC CS
                  TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatna 79 
                                   ++a+++v+ Lk++gv+++fg+pG +++p++da+ e     ++r+vl+rhEq+aa+aAd+yar++g pgv+ +tsgpG+tn+
  gi|70607297|ref|YP_256167.1|   3 SGARIVVDSLKREGVKVIFGIPGLSNMPIYDAFLEDLkngELRHVLMRHEQAAAHAADAYARVSGFPGVCTATSGPGVTNL 83 
                                   5899*****************************9988899***************************************** PP

                                   HHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEE CS
                  TPP_enzyme_N  80 ltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelp 160
                                   +t+l++A+ d++P+++++g++ + ++g+ ++q e d  ++f+++tky+ +v++ eelp++++ A+ +a +grpgPv++++p
  gi|70607297|ref|YP_256167.1|  84 VTGLISAYWDSSPVVAIAGQVVRPSIGKMAFQ-EADTIGIFEHITKYVIEVKKIEELPQMIKNAFYIAGTGRPGPVVVDIP 163
                                   ********************************.************************************************ PP

                                   HHHCC-EEE CS
                  TPP_enzyme_N 161 kdvlleevd 169
                                   +d+l+e+++
  gi|70607297|ref|YP_256167.1| 164 RDILNEKME 172
                                   *****9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.019
                                   HHHHCHHHHHHHHHHT--EEEEEEE--CCCHH............S..TC--T-CCHH.......HCCCSSEEEE-SSGGGH CS
                  TPP_enzyme_N  75 GatnaltalaeAkvdriPllvlsgdrptslrg............qgvlqqeldqlal.......frpvtkyaervtspeel 136
                                    ++ + t+la+A  ++iP++ +  d+ t                 g          +       f ++++ +  +   +++
  gi|70607297|ref|YP_256167.1| 450 SFLMTATNLATAVDENIPIISVIFDNRTLGLVrqvqdlffgrriVG----------VdygpspdFVKLAESFGALGFNATT 520
                                   567788999**********999999887666623333333322211..........1323333333334444445555555 PP

                                   HHHHHHHHHHHHSSS--EEEEEEE CS
                  TPP_enzyme_N 137 pealrrAirtalsgrpgPvylelp 160
                                    e+l++ i++a  +++ P ++ lp
  gi|70607297|ref|YP_256167.1| 521 YEELEKSIKIA-IKENIPSVIRLP 543
                                   55555555555.555566666666 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.011        51     125     153 .]     129     162 ..      99     162 .. 0.81
   2 !  153.5   0.0   8.1e-49   3.6e-45       1     151 [.     394     540 ..     394     542 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                                   EEESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
                  TPP_enzyme_C 125 arvekadveeleealkeal.....ekkgpaliev 153
                                   +++e++++eel + +k a+      + gp+++++
  gi|70607297|ref|YP_256167.1| 129 YVIEVKKIEELPQMIKNAFyiagtGRPGPVVVDI 162
                                   46778888**********999999999****996 PP

  == domain 2  score: 153.5 bits;  conditional E-value: 8.1e-49
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                   ++G++++wa  +++v +pr++l+s+g+gtmG+glpaAiGaklakpdr vv + GDG+flm+ + latav +n+pi+ v+++
  gi|70607297|ref|YP_256167.1| 394 GVGQHQMWAEVFWDVLEPRTFLSSTGMGTMGFGLPAAIGAKLAKPDRVVVDLDGDGSFLMTATNLATAVDENIPIISVIFD 474
                                   69******************************************************************************* PP

                                   -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                  TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpali 151
                                   N+++g++++ q+ f+g+r +g+++  ++++df+klae++Ga g+  +++  eele+ +k a++++ p++i
  gi|70607297|ref|YP_256167.1| 475 NRTLGLVRQVQDLFFGRRIVGVDY--GPSPDFVKLAESFGALGFNATTY--EELEKSIKIAIKENIPSVI 540
                                   *********************996..99****************98899..******************9 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.0   2.2e-41     1e-37       1     137 []     197     333 ..     197     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 2.2e-41
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlv 81 
                                   i+kaaell +a+rp+il+G g+ +s+a+ee+ elae l+ P+++t+ gk++ip+dhply+g +g+ g ++a++a+ e+D++
  gi|70607297|ref|YP_256167.1| 197 IKKAAELLINAERPIILAGTGATWSNATEEILELAELLHTPIISTFPGKSAIPHDHPLYFGPMGYYGRAEASMAALESDVM 277
                                   79******************************************************************************* PP

                                   EEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                  TPP_enzyme_M  82 lalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketleaL 137
                                   l++Gar++d rt  s++e+++ + k+i +++dp++  +  +vd+ +vg++k+ l++L
  gi|70607297|ref|YP_256167.1| 278 LVVGARLSD-RTITSYDEMKETKkKFIMVNVDPTDGERGLKVDINLVGNAKTLLREL 333
                                   *********.77766776667777******************************997 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     1e-07   0.00046      22     171 ..      31     180 ..      14     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-07
                                   HHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHH.HHHHCTT-E.EEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE-ST CS
                         POR_N  22 iaeelaellakgevgdvevvqmesEigaisav.iGAaaaGar.aaTaTSgqGllLmienlglaageelPvvivvvaRalps 100
                                   i++++ e l++ge+   + v m  E +a+ a+ + A ++G   + TaTSg+G+   +  l+ a  +  Pvv +  +   ps
  gi|70607297|ref|YP_256167.1|  31 IYDAFLEDLKNGEL---RHVLMRHEQAAAHAAdAYARVSGFPgVCTATSGPGVTNLVTGLISAYWDSSPVVAIAGQVVRPS 108
                                   56666677777776...7777888877776663789999986267************************************ PP

                                   TBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH.CTSEEEEEEEHHHH.HEEEEEEC-SGG CS
                         POR_N 101 tglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek.vrvPvivlfDgfllshevekvelpdee 171
                                    g   +++   +         v+ +++++e  +++ +Af +A +    Pv+v +   +l +++e+v+ p++ 
  gi|70607297|ref|YP_256167.1| 109 IGKMAFQEADTIGIFEHITKYVIEVKKIEELPQMIKNAFYIAGTgRPGPVVVDIPRDILNEKMEDVKWPEKP 180
                                   *8888888777777789999**********************996667898888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3897.84
//
Query:       gi|70607298|ref|YP_256168.1|  [L=177]
Description: hypothetical protein Saci_1562 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-12   45.8   0.1      9e-12   45.2   0.1    1.3  1  Acid_PPase  Acid Phosphatase
    1.8e-08   34.7   0.1    1.8e-08   34.7   0.1    2.0  3  HAD_2       Haloacid dehalogenase-like hydrolase
    7.2e-06   26.4   0.0     0.0041   17.4   0.0    2.2  2  Hydrolase   haloacid dehalogenase-like hydrolase
     0.0026   17.3   0.3      0.085   12.3   0.1    2.2  2  DUF2608     Protein of unknown function (DUF2608)
  ------ inclusion threshold ------
       0.34   11.2   4.4        1.9    8.9   0.4    2.8  3  PRD         PRD domain


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   2.5e-15     9e-12       3     135 ..       2     129 ..       1     146 [. 0.79

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.5e-15
                                   -SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHT CS
                    Acid_PPase   3 pklivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLkll 83 
                                    kl+vFD D+TLW+     +  +p++  +++ +v D+ g++l+l+++v+e l+e+++ +   a+a + + p+  + +L++l
  gi|70607298|ref|YP_256168.1|   2 IKLVVFDADKTLWTHSNISIFRPPIRLIDEN-SVEDSIGNKLRLFENVRETLSEIRQMGLFTAMA-TWNIPEKTELVLSTL 80 
                                   59***********9999999***********.************************888777776.35789********** PP

                                   T-G..........GGESEEEESS.S-HHHHHHHHHHHH---GGGEEEEES-HH CS
                    Acid_PPase  84 eindakekekklldvfddveiyk.gsktkhfeklkkktgieyedmlfFDdesr 135
                                   +++d  +  ++ ++ ++ + i +  +k + +    k+ +i+ ++++f Dd + 
  gi|70607298|ref|YP_256168.1|  81 KLKDYFDVIVSNEHPYKFLYIIEiINKLSRL----KNVKIKPDEIIFVDDRRS 129
                                   ***5555544444444444444412444443....356688899999999875 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.42   1.5e+03       1      15 [.       5      19 ..       5      23 .. 0.79
   2 !   34.7   0.1   4.9e-12   1.8e-08      76     161 ..      40     127 ..      24     131 .. 0.84
   3 ?   -3.2   0.1       2.1   7.5e+03      23      32 ..     156     165 ..     148     175 .. 0.42

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.42
                         HAD_2  1 iiFDlDgTlldteel 15
                                  ++FD D Tl   +++
  gi|70607298|ref|YP_256168.1|  5 VVFDADKTLWTHSNI 19
                                  79******9876655 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 4.9e-12
                         HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpevieka..leklklkkee 154
                                   ++++++++v+e+L e++++g+  + +T +  e++e  l+ l++++yFdviv+ e+  k     e+i+k+  l++ k+k++e
  gi|70607298|ref|YP_256168.1|  40 NKLRLFENVRETLSEIRQMGLFTAMATWNIPEKTELVLSTLKLKDYFDVIVSNEHPYKFLYIIEIINKLsrLKNVKIKPDE 120
                                   5899**************************************************98777556677776633445599**** PP

                         HAD_2 155 viyvGDs 161
                                   +i+v D 
  gi|70607298|ref|YP_256168.1| 121 IIFVDDR 127
                                   *****97 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.1
                         HAD_2  23 lleeyglsel 32 
                                   lle+ +    
  gi|70607298|ref|YP_256168.1| 156 LLEKIKTIYK 165
                                   3333333222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0019       6.8       1      16 [.       2      17 ..       2      24 .. 0.89
   2 !   17.4   0.0   1.1e-06    0.0041     115     199 ..      40     127 ..      23     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                                  SSEEEEESBTTTBCHH CS
                                  xxxxxxxxxxxxxxxx RF
                     Hydrolase  1 iktvvfDkdGTLttge 16
                                  ik+vvfD d TL+t +
  gi|70607298|ref|YP_256168.1|  2 IKLVVFDADKTLWTHS 17
                                  89***********876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                                   HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHT....... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLq....... 187
                                   ++l++++ ++e++ +++++g+ ++++t + pe  e +++ l  +dyf       ++ v+  +p  ++++i+ ++       
  gi|70607298|ref|YP_256168.1|  40 NKLRLFENVRETLSEIRQMGLFTAMATWNIPEKTELVLSTLKlKDYF-------DVIVSNEHPYKFLYIIEIINklsrlkn 113
                                   56679999**********************************99999.......555777777777777777766667777 PP

                                   ..STGGGEEEEESS CS
                                   ..xxxxxxxxxxxx RF
                     Hydrolase 188 ..gkpeevamVGDg 199
                                     +kp e+++V+D+
  gi|70607298|ref|YP_256168.1| 114 vkIKPDEIIFVDDR 127
                                   7799*******996 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.012        44      20      33 ..       4      17 ..       2      60 .. 0.89
   2 !   12.3   0.1   2.4e-05     0.085     173     197 ..     111     135 ..     104     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.012
                       DUF2608 20 LvvfDiDdtLltst 33
                                  LvvfD D tL t  
  gi|70607298|ref|YP_256168.1|  4 LVVFDADKTLWTHS 17
                                  9*********9865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.4e-05
                       DUF2608 173 LdkigrepksviFiDDkkknlasve 197
                                   L+ ++ +p+++iF+DD +++  ++ 
  gi|70607298|ref|YP_256168.1| 111 LKNVKIKPDEIIFVDDRRSHFGNIW 135
                                   88999**************998875 PP

>> PRD  PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.079   2.8e+02      22      69 ..      11      57 ..       7      60 .. 0.85
   2 ?    8.9   0.4   0.00052       1.9      43      83 ..      84     124 ..      73     126 .. 0.87
   3 ?    0.2   0.2      0.26   9.2e+02      35      53 ..     156     174 ..     149     177 .] 0.49

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.079
                                  HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                           PRD 22 erLitHlkfaieRlkegitienplleeikekypkefeiakeileelee 69
                                  + L tH ++ i R   +   en+  + i +k  ++fe ++e+l+e+ +
  gi|70607298|ref|YP_256168.1| 11 KTLWTHSNISIFRPPIRLIDENSVEDSIGNK-LRLFENVRETLSEIRQ 57
                                  5688999999999999989999999999987.8899999999999876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00052
                                   HHHHHHHHHHTHHHHHHHHHHHHHHHHHHTST--HHHHHHH CS
                           PRD  43 nplleeikekypkefeiakeileeleeeldielpedEiayl 83 
                                   + +   + +++p  f  + ei+++l +  ++++  dEi+++
  gi|70607298|ref|YP_256168.1|  84 DYFDVIVSNEHPYKFLYIIEIINKLSRLKNVKIKPDEIIFV 124
                                   5555678999*****************************97 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.26
                                   HHTT--HHHHHHHHHHHHT CS
                           PRD  35 lkegitienplleeikeky 53 
                                   l e+i++ ++l+ee k+ y
  gi|70607298|ref|YP_256168.1| 156 LLEKIKTIYKLKEESKKIY 174
                                   3444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1253.68
//
Query:       gi|70607299|ref|YP_256169.1|  [L=259]
Description: GTP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-15   57.4   0.4      5e-12   45.9   0.0    2.2  2  MMR_HSR1      50S ribosome-binding GTPase
    2.4e-12   47.1   0.0    4.1e-12   46.3   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
    3.2e-09   36.5   0.2    0.00015   21.3   0.2    2.2  2  FeoB_N        Ferrous iron transport protein B
    3.1e-05   24.1   0.5      0.023   14.8   0.0    2.7  2  Dynamin_N     Dynamin family
    0.00046   20.4   0.0      0.041   14.1   0.0    2.4  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.006   16.6   0.8       0.01   15.8   0.2    1.7  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.014   14.7   1.3         12    5.1   0.0    3.3  3  6PF2K         6-phosphofructo-2-kinase
      0.016   14.9   0.1       0.29   10.9   0.0    2.1  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.02   14.4   0.3       0.55    9.7   0.0    2.2  2  Arf           ADP-ribosylation factor family
      0.036   13.6   0.1        0.3   10.6   0.0    2.3  2  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.05   14.1   0.1       0.24   11.9   0.0    2.2  2  AAA_18        AAA domain
       0.23   11.1   0.4       0.55    9.8   0.1    1.7  2  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.3   0.00056      0.84      69     114 .]       4      49 ..       1      49 [. 0.79
   2 !   45.9   0.0   3.3e-15     5e-12       1      83 [.     100     187 ..     100     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00056
                                   HHHH.HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  69 afla.leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   ++la ++++dl++ v+da+e +l++  ++le++  e++k+l++vlnk
  gi|70607299|ref|YP_256169.1|   4 QILAyIRKSDLVVEVLDAREPDLTRS-KRLENYVMENQKKLLIVLNK 49 
                                   455524569********995567666.9999999999*********8 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 3.3e-15
                                   EEEEEESTTSSHHHHHHHHHTS.TEEESSST...TSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHH.HHHHHHHHHH CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkp...gtTrdinegrvklkgkeielvDtpGlie..gaseek.glgkaflale 74 
                                   +++++G+p +GKS++inal g+  a +s++p   g Tr i+ +r++   ++i  +DtpG+i   g++ e+   g ++ +le
  gi|70607299|ref|YP_256169.1| 100 KIIFIGYPKTGKSSIINALKGRhSATTSKHPmsyGYTRSIQLFRID---NRIFAWDTPGIIPpdGNELERiIRGANVDKLE 177
                                   589******************9678899999999***********8...69********9854455555523333333333 PP

                                   C.TSEEEEEE CS
                      MMR_HSR1  75 e.adlillvv 83 
                                   + +  + l++
  gi|70607299|ref|YP_256169.1| 178 DpVRGAKLLI 187
                                   3444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   2.8e-15   4.1e-12      21     161 ..      15     156 ..       3     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.8e-15
                                   EEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH.TTSEEEE--TTTHTTHHHHHHHCT.. CS
                   RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelea.lgyevllvsaktkegleelkellk.. 98 
                                   +v  l+  e +l + +r+   + e++ +++ivlnK Dl+  e  le++k+ +e+  g++++++sa+++ g++ l+e++k  
  gi|70607299|ref|YP_256169.1|  15 VVEVLDAREPDLTRSKRLENYVMENQKKLLIVLNKGDLIPVEV-LEKWKKFIEEnEGIPTIYISATRHLGTKVLREKIKel 94 
                                   4555555566666666777778889999**************9.99999988651689*******9988776655555411 PP

                                   ..T.SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                   RsgA_GTPase  99 ..d.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                     +   ++++G    GKS++inal++++++ t++   +   G   T++ +l+++++  +  DtPG+
  gi|70607299|ref|YP_256169.1|  95 ieGeGKIIFIGYPKTGKSSIINALKGRHSATTSKHPMS--YG--YTRSIQLFRIDNRIFAWDTPGI 156
                                   11556789******************977777655444..44..59*******************8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2     1e-07   0.00015      77     156 .]      10      91 ..       2      91 .. 0.92
   2 !   13.2   0.0   3.3e-05     0.049       2      27 ..     100     125 ..      99     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1e-07
                                   TSSSEEEEEEEGGG..HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                        FeoB_N  77 eepdvvvnvvdatn..lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                   ++ d+vv+v+da +  l r+  L   ++e +++++++ln+ d +  + +e  +k ++e+ g+p + +sa+++ g++ l+++
  gi|70607299|ref|YP_256169.1|  10 RKSDLVVEVLDAREpdLTRSKRLENYVMENQKKLLIVLNKGDLIPVEVLEKWKKFIEENEGIPTIYISATRHLGTKVLREK 90 
                                   678*********854499*********************************************************999987 PP

                                   H CS
                        FeoB_N 156 i 156
                                   i
  gi|70607299|ref|YP_256169.1|  91 I 91 
                                   6 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.3e-05
                                   EEEEEESTTSSHHHHHHHHHTTSEEE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkv 27 
                                   +++++G p +Gk++++nal g ++  
  gi|70607299|ref|YP_256169.1| 100 KIIFIGYPKTGKSSIINALKGRHSAT 125
                                   6889*****************98654 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0047         7     122     167 ..       5      49 ..       3      50 .. 0.88
   2 !   14.8   0.0   1.5e-05     0.023       1      31 [.     101     131 ..     101     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0047
                                   HHHHHSTTEEEEEEEETTS.-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                     Dynamin_N 122 vkeyikkadiilavtsanh.dlsnsealflarevdpkgkrtivvltk 167
                                   +  yi+k+d+++ v++a   dl+  ++++l++ v +++k+ ++vl+k
  gi|70607299|ref|YP_256169.1|   5 ILAYIRKSDLVVEVLDAREpDLT--RSKRLENYVMENQKKLLIVLNK 49 
                                   678**************995666..778899**************98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.5e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnpt 31 
                                   i+++G  + GKSS++naL g++   +++ p+
  gi|70607299|ref|YP_256169.1| 101 IIFIGYPKTGKSSIINALKGRHSATTSKHPM 131
                                   7899999***************998888876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.042        63      75     119 ..       7      51 ..       3      52 .. 0.71
   2 !   14.1   0.0   2.7e-05     0.041       1      65 [.     100     155 ..     100     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.042
                                   HHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                           Roc  75 lylreaalailvydsrssenlkeWlkelkkvagkspvilvgnkiD 119
                                    y+r+++l++ v+d+r+ +  ++   e   + +++++++v nk D
  gi|70607299|ref|YP_256169.1|   7 AYIRKSDLVVEVLDAREPDLTRSKRLENYVMENQKKLLIVLNKGD 51 
                                   599999****9**98876654433333333455678899999988 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.7e-05
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S CS
                           Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG 65 
                                   K++++G  ++GK+s+++ +  ++  +++k  +++ +++ ++ ++  +  d+     ++  WDt G
  gi|70607299|ref|YP_256169.1| 100 KIIFIGYPKTGKSSIINALKGRHSATTSKHPMSYGYTR-SI-QLFRI--DN-----RIFAWDTPG 155
                                   9******************9988887777777776643.33.34333..32.....366788866 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   6.9e-06      0.01      45     100 ..      32      91 ..       2      96 .. 0.82
   2 ?   -2.4   0.0       3.2   4.8e+03      41      59 ..     172     190 ..     167     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-06
                  MMR_HSR1_Xtn  45 lidviegnrvYipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLkeki 100
                                   l + +++n+  ++ l+vlNK Dli  e l++ ++         ++ iSa ++l+ + L eki
  gi|70607299|ref|YP_256169.1|  32 LENYVMENQ--KKLLIVLNKGDLIPVEVLEKWKKFieenegIPTIYISATRHLGTKVLREKI 91 
                                   556666666..489*****************999444554436888**********999998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                  MMR_HSR1_Xtn  41 tvDdlidviegnrvYipcl 59 
                                   +vD+l d + g +  i+ +
  gi|70607299|ref|YP_256169.1| 172 NVDKLEDPVRGAKLLIERI 190
                                   6777777777766555554 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0081        12      84     129 ..       1      46 [.       1      69 [. 0.91
   2 ?    4.5   0.1     0.012        18      15      33 ..     100     118 ..      88     129 .. 0.84
   3 ?    2.5   0.0     0.052        78     200     220 ..     236     256 ..     201     259 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0081
                                   HHHHHHHHHHTS--SEEEEES---SHHHHHHHHHHHHHTT-EEEEE CS
                         6PF2K  84 alkdllaylneeegqvaifDAtNttrerRklilefveennlkvlfl 129
                                   ++k++lay+ + +  v + DA      r k + + v en+ k l++
  gi|70607299|ref|YP_256169.1|   1 MIKQILAYIRKSDLVVEVLDAREPDLTRSKRLENYVMENQKKLLIV 46 
                                   6899***********************************9888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                   EEEEESSTTSSHHHHHHHH CS
                         6PF2K  15 vivlvGLpargKtyiskkl 33 
                                    i+++G p +gK+ i ++l
  gi|70607299|ref|YP_256169.1| 100 KIIFIGYPKTGKSSIINAL 118
                                   59***********998877 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.052
                                   EEE---SHHHHHHHHHHTT-- CS
                         6PF2K 200 vvnnvqgylqsrivyyllNih 220
                                    +  +++y +++i+yyll  +
  gi|70607299|ref|YP_256169.1| 236 AKAFIRDYHEGKIIYYLLPEN 256
                                   455699***********9655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.099   1.5e+02      59     142 ..       7      92 ..       1      93 [. 0.77
   2 ?   10.9   0.0    0.0002      0.29       2      45 ..      99     155 ..      98     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.099
                     PduV-EutP  59 vtsaeadvialvqdateeesvfppgfasvf...nkeviGiitkidlaedeenieaveelLk.saGaekifevsavekegie 135
                                   ++  ++d+++ v+da e++ + ++ + + +   +k+++ ++ k dl    e +e+ +++++ + G+ +i+ +sa+++ g +
  gi|70607299|ref|YP_256169.1|   7 AYIRKSDLVVEVLDAREPDLTRSKRLENYVmenQKKLLIVLNKGDLI-PVEVLEKWKKFIEeNEGIPTIY-ISATRHLGTK 85 
                                   55667899999999999999999887776533368899999999999.7788888888886257898887.8999999998 PP

                     PduV-EutP 136 ellkyle 142
                                    l++ ++
  gi|70607299|ref|YP_256169.1|  86 VLREKIK 92 
                                   8888776 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0002
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkg........eelkYkktqaief...sdev..iDtPG 45 
                                    ki++iG  ++GK ++ +alkg        + ++Y  t +i++    +++   DtPG
  gi|70607299|ref|YP_256169.1|  99 GKIIFIGYPKTGKSSIINALKGrhsattskHPMSYGYTRSIQLfriDNRIfaWDTPG 155
                                   59********************99999888889999998887522133332347777 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.033        49      78     144 ..       8      69 ..       5      96 .. 0.60
   2 ?    9.7   0.0   0.00037      0.55      12      42 ..      96     126 ..      83     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.033
                                   GCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGG CS
                           Arf  78 YfektdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellglee 144
                                   Y +k d v+ v+D+ + +  ++    L++ + e+   + +ll++ NK Dl      e+ ++ ++ +e
  gi|70607299|ref|YP_256169.1|   8 YIRKSDLVVEVLDAREPDLTRSK--RLENYVMEN---QKKLLIVLNKGDLIPVEVLEKWKKFIEENE 69 
                                   77777777777777766643332..344433333...3468999*****987777777777666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00037
                                   TTEEEEEEEESTTSSHHHHHHHHHHSSCEEC CS
                           Arf  12 kkelrilllGLDnaGKtTilkklkleelvtt 42 
                                   + e +i+++G  ++GK+ i++ lk  + +tt
  gi|70607299|ref|YP_256169.1|  96 EGEGKIIFIGYPKTGKSSIINALKGRHSATT 126
                                   6799********************9887775 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002       0.3      89     186 ..       7      89 ..       2      97 .. 0.67
   2 ?   -0.5   0.0      0.49   7.4e+02       6      32 ..     101     127 ..      99     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                   HHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEE CS
                      GTP_EFTU  89 rglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevp 169
                                   + +r+ D++v v+da+e   ++++++ + + +++ ++ +++NK D +  e+ e  ++                e++e  +p
  gi|70607299|ref|YP_256169.1|   7 AYIRKSDLVVEVLDAREPDLTRSKRLENYVMENQKKLLIVLNKGDLIPVEVLEKWKKFI--------------EENE-GIP 72 
                                   55788999999999999999999999999999999999999999999444333322222..............2222.456 PP

                                   EEEEBTTTTBTHHHHHH CS
                      GTP_EFTU 170 vvfgSalkgegvktlle 186
                                    +++Sa +  g k l e
  gi|70607299|ref|YP_256169.1|  73 TIYISATRHLGTKVLRE 89 
                                   66666666665555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.49
                                   EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                      GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaisk 32 
                                   i++ig   +GK++++ +L  +++a+++
  gi|70607299|ref|YP_256169.1| 101 IIFIGYPKTGKSSIINALKGRHSATTS 127
                                   778999999999999999766555544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   1.7e+03      32      68 ..       9      48 ..       4      72 .. 0.64
   2 ?   11.9   0.0   0.00016      0.24       1      33 [.     101     143 ..     101     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                        AAA_18 32 akenglllevdpe...aldeskrldedkldklldaleens 68
                                  +++++l+ ev ++   +l +skrl+  ++++  ++l   +
  gi|70607299|ref|YP_256169.1|  9 IRKSDLVVEVLDArepDLTRSKRLENYVMENQKKLLIVLN 48
                                  5666666666666666667777777666665555555444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00016
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvak 33 
                                   I+  G+p +GK+++ ++L+ r+             ++++++++
  gi|70607299|ref|YP_256169.1| 101 IIFIGYPKTGKSSIINALKGRHSAttskhpmsygYTRSIQLFR 143
                                   899***************7765223555555556444444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00037      0.55     111     166 ..      11      65 ..       3      74 .. 0.75
   2 ?   -1.8   0.1       1.3     2e+03       4      21 ..     102     119 ..     100     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00037
                                   CECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHH CS
                          cobW 111 tldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerl 166
                                   + d vv v+Da++ +  ++k  e++  + ++  l+vlnK Dl++ e l ek ++ +
  gi|70607299|ref|YP_256169.1|  11 KSDLVVEVLDAREPDLTRSKRLENYVMENQKKLLIVLNKGDLIPVEVL-EKWKKFI 65 
                                   5799*******9986666666666666677778***********9843.6655544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                   EEEESTTCCHHHHHHHHH CS
                          cobW   4 vltGflGsGKTtLlnhll 21 
                                   ++ G++ +GK++++n+l 
  gi|70607299|ref|YP_256169.1| 102 IFIGYPKTGKSSIINALK 119
                                   67899999*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2035.25
//
Query:       gi|70607300|ref|YP_256170.1|  [L=316]
Description: hypothetical protein Saci_1564 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.014   15.6   0.3       0.34   11.2   0.1    2.4  2  CARDB            CARDB
      0.078   12.3   0.0       0.11   11.8   0.0    1.2  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
       0.11   12.9   0.1       0.36   11.1   0.0    2.0  2  PilZ             PilZ domain


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.049   2.9e+02      53      91 ..      23      62 ..      13      63 .. 0.73
   2 ?   11.2   0.1   5.7e-05      0.34      20      82 ..     238     298 ..     227     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.049
                                  EESEE-CTEE.EEEEEEEE-S-S-CEEEEEEEESTT-SS- CS
                         CARDB 53 tvpsLaages.ttvsftwtteategevtltvvvDpdneva 91
                                   v++++ g+s ++v++++ ++ ++++v+l ++++ + ev+
  gi|70607300|ref|YP_256170.1| 23 LVSPVKLGSSdKEVTYSFSVDYKPQKVYLVINIERNKEVN 62
                                  5666665554256777777778899999999999998885 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.7e-05
                                   EEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                         CARDB  20 entitvtvkNqGtaasgatkvalyldgelvgtvtvpsLaagesttvsftwtteategevtltv 82 
                                   ++++tv++ N+G+ +  ++ v++ l+g + +  + ++++ ge +t ++  +++  +g++ ++v
  gi|70607300|ref|YP_256170.1| 238 NYSLTVKLLNEGDVDLDKVIVNVLLNGASISFKSFENVKKGELRTFTLPLQPK--KGTINVRV 298
                                   78999*************************************99999988886..66666665 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.11      69     161 ..     179     271 ..     167     314 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
               Phlebovirus_NSM  69 dkkyisneniisqikevktssdelklscGdedkslglvitadGlnnirGdaiidCdtndfirditvGe.qlgrvdyeklkk 148
                                   dkk+ s++++i ++ + k+    + +scG++ k+    +t+  ln +  + ++d +++     +tv   + g vd +k+  
  gi|70607300|ref|YP_256170.1| 179 DKKFDSRVDLIDLLVQ-KKGNIAVGFSCGNNVKASAHLLTFYNLNYVIPKIVLDVQAEVVNYSLTVKLlNEGDVDLDKVIV 258
                                   8888888888887754.56666899*********************99999999988888888888642678888888877 PP

               Phlebovirus_NSM 149 kaeekdktisrkt 161
                                   +     + is k+
  gi|70607300|ref|YP_256170.1| 259 NVLLNGASISFKS 271
                                   7766666666654 PP

>> PilZ  PilZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7     1e+04      16      33 ..      82      99 ..      77     100 .. 0.77
   2 ?   11.1   0.0   6.1e-05      0.36      10      74 ..     237     302 ..     220     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                  EEEEETTEEEEEEEEEEE CS
                          PilZ 16 vtleadegelkgrliDiS 33
                                  + +e++++++++++ D+S
  gi|70607300|ref|YP_256170.1| 82 IDVEDSNKRFSTVIFDVS 99
                                  567888899999999988 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.1e-05
                                   EEECEEEEEEETTEE.EEEEEEEEESSEEEEEES.T-SS-TTSEEEEEEECECEEEEEEEEEEEEEE CS
                          PilZ  10 vpvsipvtleadege.lkgrliDiSlgGlairlp.deelalgdrvelklpldkdqelslpgrVvrvk 74 
                                   v++s++v+l +++   l+ +++++ l+G++i+ +  e++++g+  +++lp ++ ++ ++ +rVv ++
  gi|70607300|ref|YP_256170.1| 237 VNYSLTVKLLNEGDVdLDKVIVNVLLNGASISFKsFENVKKGELRTFTLP-LQPKKGTINVRVVGIR 302
                                   788899999999888899********************************.6666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1990.30
//
Query:       gi|70607301|ref|YP_256171.1|  [L=275]
Description: (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-43  148.0  14.7    3.4e-43  147.8  14.7    1.0  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8  14.7   1.9e-47   3.4e-43       3     250 ..      20     260 ..      18     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 1.9e-47
                          UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglll 83 
                                   ++a++g+++a++  +++ l++l ll + l+aa+++++Nd++D+e D++  ++p+RPl+sGri ++ a++f+ivl+++gl++
  gi|70607301|ref|YP_256171.1|  20 VSAFMGYVIATTWKFTP-LFFLPLLVVSLIAAGGYVINDVYDIEVDKI--NKPERPLPSGRIAVNIARRFSIVLFAVGLII 97 
                                   7899*************.8888888999********************..******************************* PP

                          UbiA  84 lalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialand 164
                                   + + l++  ++++l++++l++ Y    lK+ +l+g+++++++ +l +  g  a  gsl   ++++++ +f++t++  +++ 
  gi|70607301|ref|YP_256171.1|  98 S-IPLGLIPFGFALITIVLLYEYA-RSLKKLGLVGNFIVALTSALSAYYGGLAS-GSLLGNFIIPTIYIFFFTLSREFVKG 175
                                   *.**********************.7**************************96.6789********************** PP

                          UbiA 165 lrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlvrrrdakkaak 244
                                   ++d+egD++ g++tl+v+lG+k + i+    +++++l++   l+++l   +++l+++l++ ++l++ + l+ + +++++a+
  gi|70607301|ref|YP_256171.1| 176 IEDIEGDKRNGVNTLAVKLGEKSTWIIaK--IILGILIFTSPLPYFLGFNVIYLIGILALDVLLVYILILHNTIESATKAR 254
                                   *************************9543..4444444555999999999******************************9 PP

                          UbiA 245 fflfls 250
                                   ++++++
  gi|70607301|ref|YP_256171.1| 255 SLMKIY 260
                                   999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1846.28
//
Query:       gi|70607302|ref|YP_256172.1|  [L=70]
Description: hypothetical protein Saci_1566 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 455.09
//
Query:       gi|70607303|ref|YP_256173.1|  [L=293]
Description: hypothetical protein Saci_1567 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.015   14.6   0.0       0.02   14.1   0.0    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.18   10.8   0.0       0.28   10.2   0.0    1.2  1  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.3e-06      0.02      57     111 ..      55     110 ..       6     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-06
                                   H........HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE CS
                                   x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  57 s........evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssp 111
                                   +        +  ++l q++++ l+    +i +++k+v       +++eki++dk+++A+G + 
  gi|70607303|ref|YP_256173.1|  55 AdlirlnryKLEQSLAQDLDVKLK--TDAIVKNEKEVIT-----NNNEKITADKVIIASGWKG 110
                                   144445444222355555555555..5555555566666.....6778999999999999654 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.1e-05      0.28      49     141 ..      26     108 ..      22     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.1e-05
                 Lycopene_cycl  49 edlgaleecvehsWsgtivylddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrk 129
                                   e l+   e+++   +  i++ +++k i++     r+++ +l++ l+++l       ++ k ++++++e+    v++++++k
  gi|70607303|ref|YP_256173.1|  26 EKLDISREFIDREFKSIILHYENKK-IQIRADLIRLNRYKLEQSLAQDLD------VKLKTDAIVKNEK---EVITNNNEK 96 
                                   4455458999999999999997665.5555599****************9......5667888888888...899****** PP

                 Lycopene_cycl 130 irarlvvdargl 141
                                   i a  v+ a+g 
  gi|70607303|ref|YP_256173.1|  97 ITADKVIIASGW 108
                                   **********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2200.86
//
Query:       gi|70607304|ref|YP_256174.1|  [L=122]
Description: S-adenosylmethionine decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-33  113.0   0.1    8.1e-33  112.9   0.1    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.1   4.5e-37   8.1e-33       3     105 ..      16     118 ..      14     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 4.5e-37
                                   EEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST.HHH CS
                     AdoMet_dc   3 lvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftcge.isp 82 
                                   +  ly+cd  +l +++ leqi+++aae+ ++t+l+v+ +k+  +Gvs+v+++ eSh++iHtwpe+++a++Dv++cg+ ++p
  gi|70607304|ref|YP_256174.1|  16 YGSLYECDTTVLGEQKVLEQIVRKAAEEGNMTLLDVKAWKIG-DGVSIVAIVLESHITIHTWPEYNFATVDVYSCGShTDP 95 
                                   6789*************************************8.8************************************* PP

                                   HHHHHHHHHHHT-SEEEEEEEEE CS
                     AdoMet_dc  83 ekaleylieafkadrvtvdelkR 105
                                   +ka+ y+++++ka+r+t++e++R
  gi|70607304|ref|YP_256174.1|  96 RKAFLYIVKELKARRYTMNEADR 118
                                   ********************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 858.13
//
Query:       gi|70607305|ref|YP_256175.1|  [L=104]
Description: hypothetical protein Saci_1569 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-36  123.9   5.2    2.4e-36  123.8   5.2    1.0  1  DUF211    Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   5.2   1.3e-40   2.4e-36       2      87 ..      14     100 ..      13     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 1.3e-40
                                   EEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEE CS
                        DUF211   2 irrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaG 81 
                                   irrlvLDvlkp +++sivela+k+++legvdgvni+v+++D+et++l+i+ieG+nid+ee+++++ee g++ihSiDevv G
  gi|70607305|ref|YP_256175.1|  14 IRRLVLDVLKPiRGISIVELANKISTLEGVDGVNISVIDMDVETMGLMIVIEGNNIDFEEVKKTLEEQGCAIHSIDEVVSG 94 
                                   9******************************************************************************** PP

                                   SS---- CS
                        DUF211  82 kkivee 87 
                                   +k+ve 
  gi|70607305|ref|YP_256175.1|  95 NKLVEG 100
                                   ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 771.61
//
Query:       gi|70607306|ref|YP_256176.1|  [L=320]
Description: ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-08   32.9   0.0    7.3e-08   32.4   0.0    1.3  1  ATP_bind_3    PP-loop family
     0.0047   16.1   0.0     0.0061   15.7   0.0    1.2  1  NAD_synthase  NAD synthase
  ------ inclusion threshold ------
       0.02   14.7   0.0       0.76    9.7   0.0    2.5  2  DUF2024       Domain of unknown function (DUF2024)


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.2e-11   7.3e-08       1     125 [.      49     186 ..      49     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.2e-11
                                   EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--H..........HH CS
                    ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvdv..........ak 70 
                                   k+++AvSgG DS +L   la+  ++   klva  +  g++  +  e+    k++ ++l+i+l+ ++++           a+
  gi|70607306|ref|YP_256176.1|  49 KIVLAVSGGKDSYVLADTLASFIDH--DKLVAYNIIEGISgYNRVEQVIQFKNFLNELGIELIEDSFEKsvgftldqmvAN 127
                                   589*******************774..4899999999999667888888899************999999999**999977 PP

                                   CTTSTCCCHHHH....HHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCH CS
                    ATP_bind_3  71 kkgknleeaARe....lRYevlkealkkegievlllAhhadDqaEtfllrlargsglag 125
                                   +k++nl+  A +    +R +++++a  k + ++++++h+ dD +  ++l+++rg  ++ 
  gi|70607306|ref|YP_256176.1| 128 SKKRNLNVSACTfcggFRRKLINTAGLKLNGDYVATGHNLDDEVQAIMLNVIRGDLIRL 186
                                   77888888887633337************************************987754 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     1e-06    0.0061       3      96 ..      29     128 ..      27     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-06
                                   HHHHHHHHHHHHHCT...TSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--...SSSTTHHHHHHHHHHHHHHTSEEE CS
                  NAD_synthase   3 eelvdflkeyvkkag...akgvvlGlSGGvDSslvaalavkalgkenvlalllP...ssvsseedvedalalaenlgievk 77 
                                   e++ d +k ++++ g   a+++vl +SGG DS + a    + +++++ +a  +    s ++  e+v + +++ ++lgie  
  gi|70607306|ref|YP_256176.1|  29 EDIRDRVKREIERLGlsrASKIVLAVSGGKDSYVLADTLASFIDHDKLVAYNIIegiSGYNRVEQVIQFKNFLNELGIELI 109
                                   56667777777765522279****************999999*99999997665235666777777788899999999999 PP

                                   E---HHHHHHHHHHHHHHH CS
                  NAD_synthase  78 tidikpivrafeqelkeak 96 
                                   + + ++ v    +++  ++
  gi|70607306|ref|YP_256176.1| 110 EDSFEKSVGFTLDQMVANS 128
                                   9988888877776665555 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00013      0.76      53      75 ..      21      43 ..       7      47 .. 0.87
   2 ?    2.3   0.0     0.026   1.5e+02      44      59 ..     127     142 ..     111     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00013
                                  TTEEEEEEEE--HHHHHHHHHHS CS
                       DUF2024 53 keCkfCHseeaeeeveeaikkqG 75
                                  + C++C +e ++++v+++i++ G
  gi|70607306|ref|YP_256176.1| 21 SLCRYCFIEDIRDRVKREIERLG 43
                                  56*****************9988 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.026
                                   T---S---TTTEEEEE CS
                       DUF2024  44 geeeakvtskeCkfCH 59 
                                   + ++++++ + C+fC 
  gi|70607306|ref|YP_256176.1| 127 NSKKRNLNVSACTFCG 142
                                   5678899********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2416.11
//
Query:       gi|70607307|ref|YP_256177.1|  [L=177]
Description: hypothetical protein Saci_1571 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-48  163.7   0.0    4.5e-48  163.5   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
      0.036   14.3   0.1        0.1   12.8   0.1    1.6  1  MIEAP            Mitochondria-eating protein
      0.043   14.3   0.4       0.52   10.8   0.1    2.3  2  Spectrin         Spectrin repeat
      0.075   12.6   0.6       0.12   12.0   0.1    1.5  2  HAUS-augmin3     HAUS augmin-like complex subunit 3


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.5   0.0     1e-51   4.5e-48       2     163 ..       2     159 ..       1     160 [. 0.94

  Alignments for each domain:
  == domain 1  score: 163.5 bits;  conditional E-value: 1e-51
                                   XXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S CS
               Cob_adeno_trans   2 yTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkk 82 
                                   +Tr+GD+G+Ts+v+ ++v Kd+p+ve++G++Delns+ig +++ l  ++e++ke+L++iq +Lf++g+++a++   ++kkk
  gi|70607307|ref|YP_256177.1|   2 FTRSGDDGKTSIVN-KKVGKDSPVVELLGDIDELNSHIGYTITRL--SWEDMKEDLQKIQVHLFEVGEDIASD---SKKKK 76 
                                   7************9.79*************************666..489********************954...67889 PP

                                   --HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS...HHHHHHHHHHHHHHHHHHH CS
               Cob_adeno_trans  83 iteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee..veeevlkylNRLSDlLfvla 161
                                   i+e+ v+++e++  ++++e  p+k f++pggs++a+ lh+ RtvcRr+ER++v+ ++e    +++ + ylNRLS+lLf++a
  gi|70607307|ref|YP_256177.1|  77 IDESYVKWIEERTIAYRKESGPVKLFVIPGGSEEASLLHITRTVCRRVERNMVRYSKELqeLNKQNIVYLNRLSSLLFAMA 157
                                   *******************************************************9955777899999************9 PP

                                   HH CS
               Cob_adeno_trans 162 rv 163
                                    v
  gi|70607307|ref|YP_256177.1| 158 LV 159
                                   76 PP

>> MIEAP  Mitochondria-eating protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.2e-05       0.1      33     143 ..      31     158 ..      24     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                         MIEAP  33 ddelvqkilfilvvlsfrvakealrslkervrkllstssadgsetke...............lssleeavsdylrkeadly 98 
                                    del+++i ++++ ls++  ke l++++ ++ ++ +   +d+++ k+               +++    v+  +    + +
  gi|70607307|ref|YP_256177.1|  31 IDELNSHIGYTITRLSWEDMKEDLQKIQVHLFEVGEDIASDSKK-KKidesyvkwieertiaYRKESGPVKLFVIPGGSEE 110
                                   58999****************************99996666655.446999*99999999987888888888877777766 PP

                         MIEAP  99 d.vksiveevisellktlkekpslkqe..kelesYirecvelaWamvv 143
                                   + + +i+++v++ +++++ ++ +  qe  k+   Y+++  +l +am+ 
  gi|70607307|ref|YP_256177.1| 111 AsLLHITRTVCRRVERNMVRYSKELQElnKQNIVYLNRLSSLLFAMAL 158
                                   6699*********************99999999*************86 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00012      0.52       7      40 ..      28      61 ..      24      78 .. 0.91
   2 ?    1.4   0.0       0.1   4.5e+02      42      64 ..     120     142 ..     108     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                  HHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHH CS
                      Spectrin  7 aqdadeleeWieekeellssedlgkdleevqall 40
                                    d+del++ i  + + ls+ed+ +dl+++q +l
  gi|70607307|ref|YP_256177.1| 28 LGDIDELNSHIGYTITRLSWEDMKEDLQKIQVHL 61
                                  6799***************************876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  42 khkaleaelaaqqervkalnela 64 
                                    ++++e+++  + +++++ln++ 
  gi|70607307|ref|YP_256177.1| 120 VCRRVERNMVRYSKELQELNKQN 142
                                   57888899999999999998764 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.65   2.9e+03      48      58 ..      49      63 ..      44      95 .. 0.49
   2 ?   12.0   0.1   2.6e-05      0.12      72     121 ..     120     169 ..     105     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                  HAUS-augmin3 48 aLeeaLktie....p 58
                                  +++e L++i+    +
  gi|70607307|ref|YP_256177.1| 49 DMKEDLQKIQvhlfE 63
                                  445555555543331 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.6e-05
                  HAUS-augmin3  72 ileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleee 121
                                    +   e +   + +elqeL k++   l+rl+ L  ++a  ++++++++e+
  gi|70607307|ref|YP_256177.1| 120 VCRRVERNMVRYSKELQELNKQNIVYLNRLSSLLFAMALVANKRKNVQEK 169
                                   55666778889***********************9999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1144.92
//
Query:       gi|70607308|ref|YP_256178.1|  [L=893]
Description: leucyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-54  183.3   0.0    3.4e-53  180.8   0.0    2.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.1e-20   72.7   0.3    6.8e-20   71.6   0.3    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.3e-16   60.4   0.2    4.9e-10   38.7   0.1    3.1  3  tRNA-synt_1g   tRNA synthetases class I (M)
    3.3e-12   46.3   0.1    7.3e-12   45.2   0.1    1.5  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    3.7e-10   39.7   0.0    2.3e-08   33.7   0.0    2.5  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.024   13.6   0.0      0.061   12.2   0.0    1.7  1  tRNA-synt_1f   tRNA synthetases class I (K)
      0.055   13.2   0.0       0.28   10.9   0.0    2.3  1  DUF4116        Domain of unknown function (DUF4116)
       0.17   11.9   0.5        3.1    7.9   0.0    3.2  4  SBDS_C         SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   0.0   1.5e-56   3.4e-53      50     602 .]       4     610 ..       2     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.5e-56
                   tRNA-synt_1  50 divirykrmkGkevlyvpGwDhaGlaieakvekkl.gakek....kerkklgreefrekvre..wkaeyaeeirkqvkrlG 123
                                   di  ry rm+G++vl+ + +   G +i a  +    g ke     k+ +++  + + + v    ++++++eei++++k++G
  gi|70607308|ref|YP_256178.1|   4 DIYARYMRMRGYNVLFPMAFHYTGTPIIAMADDVAkGDKELidifKSIYEIPDDVISKLVDPlfMANYFKEEIKQAMKEIG 84 
                                   8899********************99987776543022222111134444555555555543335678899********** PP

                   tRNA-synt_1 124 vsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevkl 202
                                    s+D+ re  T+d+e++  +++ f +l +kg i r +++v w++  + ++   ++  + + + + ++ + f+   +    l
  gi|70607308|ref|YP_256178.1|  85 LSIDWRREFTTIDPEFSSFIIWQFRKLQEKGFIVRDTHPVGWCPVHHIPVGMHDTkgDMEPEIGEFVLIYFDS--DMG-IL 162
                                   ********************************************99998877766335555667777777765..444.78 PP

                   tRNA-synt_1 203 viaTTtPeTllgdtavavnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiad 280
                                    +aT +PeT++g  av vnp + y+   i+++k+++ e+ +++l  + ++ k+   ++g+eL+++ + +p++++++pii  
  gi|70607308|ref|YP_256178.1| 163 PVATLRPETVFGAIAVWVNPHESYSiveIDGKKYVMSEKASSKLSFQIDNLKVITVVKGSELVKHSAVNPITGKEVPIIGA 243
                                   9***********************99999****************999999****************************** PP

                   tRNA-synt_1 281 dyvdkeaGtGvVkiaPahdedDyevgk..kynlevinildedgtlteea................................ 327
                                   ++vd  +GtGvV   Pah + Dy   k  k +l++i+++  +g+ ++ a                                
  gi|70607308|ref|YP_256178.1| 244 NFVDPLTGTGVVMSVPAHAPFDYFYLKktKSELSIISVIRVEGMGETLAkdlveksnpqndndlkklteqvyrieynkgvm 324
                                   **********************987661256899*******99877777888***************************** PP

                   tRNA-synt_1 328 ...............aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaa 391
                                                  +    l v +ar+k++e +++kgl  k+ +i+    +c  ++++++  +++qWf    +   +d a
  gi|70607308|ref|YP_256178.1| 325 iditklvkpeyveelKPLVNLPVPAARQKITEFITQKGLGRKIYEIMNRPVYCRCGNEVVVKILKDQWFLDYGNqeWKDLA 405
                                   ************999899999*************************999999999***************98654499999 PP

                   tRNA-synt_1 392 lkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkalekea 469
                                    k++e+++f+p   +k ++  +   q  +  R r  G+++p    ++ ++  + ++      +++ ++e++ + ++l+ e+
  gi|70607308|ref|YP_256178.1| 406 RKSIESIRFIPPEIKKDFEFVVDWLQKRACARTRGLGTPLPWdkkWIIESLSDSTIYMAFYTIAHRLKEHKLKPSQLTYEF 486
                                   9****************************************6445888877777775666666666666777788889999 PP

                   tRNA-synt_1 470 kdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePf.ke 549
                                    + +  ++g+   ++ +      Sg +p+ +++     ++e+   +p d+  +G D +   ++  i+   a++ ++ + k 
  gi|70607308|ref|YP_256178.1| 487 WEYIMLGNGNPDEISKI------SG-IPVEVIK---AMRDEFLYWYPLDVRHSGKDLVPNHLSFFIFNHAAIFPHQLWpKG 557
                                   99998999988888887......66.4666666...45899******************************9998855388 PP

                   tRNA-synt_1 550 vlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinls 602
                                   + v+g+v+  +G+KmSKsl N++   + i+ y+ d++R +l  ++d g+d+n+s
  gi|70607308|ref|YP_256178.1| 558 IAVNGFVL-YDGKKMSKSLRNIVPLRKAIRMYSPDVIRIALTtNADIGSDVNFS 610
                                   *******9.58*******************************9********986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.3     3e-23   6.8e-20       1     120 [.     643     777 ..     643     818 .. 0.76

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 3e-23
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   ++w+ s++++ v  vt+++++++++   +++ + f+  + + y+elv+++    ++       ++l  +l+ +++ll+Pf+
  gi|70607308|ref|YP_256178.1| 643 EKWLKSKFYQMVINVTQYMDSLDLRSSSNEILYNFSSYI-NEYFELVRSEGREPNG-------KLLSQILQIWIKLLSPFA 715
                                   69*****************************99999888.*******999866555.......8***************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpe.kaeel....ekele.......................e 120
                                   P+++Eelw    +++gk++ ++l++wp  + +      + + +                        
  gi|70607308|ref|YP_256178.1| 716 PHFAEELW----HKIGKNTLVSLESWPIiDQSNVdlfiDLT-HtyhrkllndiqailsvykdtpksI 777
                                   ********....9**************86654444443222.1333333333333333333333330 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.4e-07    0.0014      24      73 ..       2      51 ..       1      56 [. 0.91
   2 ?   -0.2   0.0      0.15   3.3e+02      61     125 ..      63     129 ..      54     133 .. 0.76
   3 !   38.7   0.1   2.2e-13   4.9e-10     289     372 ..     530     615 ..     512     631 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.4e-07
                                  HHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHH CS
                  tRNA-synt_1g 24 saDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvhee 73
                                   +Di+aRy r+rg++vlf  +    Gtpi   A++     +el++ ++++
  gi|70607308|ref|YP_256178.1|  2 TGDIYARYMRMRGYNVLFPMAFHYTGTPIIAMADDVAKGDKELIDIFKSI 51
                                  58********************************9999999999877665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                                   S-HHHHHHHHHHHHHHHHHHTT---SEEE..ETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETT CS
                  tRNA-synt_1g  61 vtpeelvekvheeikelfkklnisfdkyg..rttseehkelvqeifkklkekgliyekeieqlycpk 125
                                   v+p  +++ ++eeik+ +k++++s d     +t + e +++    f+kl+ekg+i + +  + +cp 
  gi|70607308|ref|YP_256178.1|  63 VDPLFMANYFKEEIKQAMKEIGLSIDWRRefTTIDPEFSSFIIWQFRKLQEKGFIVRDTHPVGWCPV 129
                                   56777888889999999999999988543113555666666667799*********99998888876 PP

  == domain 3  score: 38.7 bits;  conditional E-value: 2.2e-13
                                   EGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE- CS
                  tRNA-synt_1g 289 gkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfs 367
                                   gkd ++ H  f+     +   +   pk +++++++ ++gkK+SkS +++v  ++a+  +++d++R  l+++a+  +D++fs
  gi|70607308|ref|YP_256178.1| 530 GKDLVPNHLSFFIFNHAAifPHQLWPKGIAVNGFVLYDGKKMSKSLRNIVPLRKAIRMYSPDVIRIALTTNADIGSDVNFS 610
                                   9*******99997777777555568*******************************************************9 PP

                                   HHHHH CS
                  tRNA-synt_1g 368 wedfv 372
                                    + + 
  gi|70607308|ref|YP_256178.1| 611 DSYAK 615
                                   87654 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   3.3e-15   7.3e-12      22     150 ..     161     292 ..     148     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.3e-15
                 tRNA-synt_1_2  22 klevfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkksesereletkekeGv.ftglkaihPitgekipiw 101
                                    l v t rp+t+fG+  v + p+        + kk + +  ++ k + ++++ +  +  +G    +  a++Pitg+++pi 
  gi|70607308|ref|YP_256178.1| 161 ILPVATLRPETVFGAIAVWVNPHESYSIVEIDGKKYVMSEKASSKLSFQIDNLKVITVVKGSeLVKHSAVNPITGKEVPII 241
                                   5789999*************99888766655555555555555555555555444455566648999************** PP

                 tRNA-synt_1_2 102 vanyvlmeygtgavmavPahdqrDfeFakkyn..lpikqvikpedeekkle 150
                                    an+v    gtg+vm+vPah   D+ + kk +  l i+ vi+ e+  ++l+
  gi|70607308|ref|YP_256178.1| 242 GANFVDPLTGTGVVMSVPAHAPFDYFYLKKTKseLSIISVIRVEGMGETLA 292
                                   ***************************9987656*******9887654443 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.015        34      34      83 ..       3      52 ..       1     360 [. 0.91
   2 !   33.7   0.0     1e-11   2.3e-08     199     294 ..     514     612 ..     505     618 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.015
                                  HHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHH CS
                  tRNA-synt_1e 34 fDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieef 83
                                   Di +r+++++gY+v f   +      ii+ a +  k  kel + f + +
  gi|70607308|ref|YP_256178.1|  3 GDIYARYMRMRGYNVLFPMAFHYTGTPIIAMADDVAKGDKELIDIFKSIY 52
                                  69***************999999999999999998888777776665544 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1e-11
                                   HHHHHH-.SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHH CS
                  tRNA-synt_1e 199 maskllg.seidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlR 277
                                   m +++l    +d+   G+DL+  h    +  + a f  + + k    ng++  +g+kmsksL+n++ ++++++ ++p ++R
  gi|70607308|ref|YP_256178.1| 514 MRDEFLYwYPLDVRHSGKDLVPNHLSFFIFNHAAIFPhQLWPKGIAVNGFVLYDGKKMSKSLRNIVPLRKAIRMYSPDVIR 594
                                   55555543679**99******999999999*****99677899999*********************************** PP

                                   HHHHS.S-TTS-EEE-HH CS
                  tRNA-synt_1e 278 lllls.ahyrsqldfkee 294
                                   ++l++ a+  s ++f+++
  gi|70607308|ref|YP_256178.1| 595 IALTTnADIGSDVNFSDS 612
                                   *99862567788888776 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05     0.061     234     340 ..     525     632 ..     514     653 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                  tRNA-synt_1f 234 gVdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilr.rkP 313
                                   +V+   +GkD++ +  S+ + ++ a + +   P+++  + + l  g+kms+S  n++ l++++++++p+v+r  +   + +
  gi|70607308|ref|YP_256178.1| 525 DVR--HSGKDLVPNHLSFFIFNHAAIFPHQLWPKGIAVNGFVLYDGKKMSKSLRNIVPLRKAIRMYSPDVIRIALTTnADI 603
                                   443..578898888888888887776667778999999999999999*************************866650344 PP

                  tRNA-synt_1f 314 kkakkld..ldleilrlvdeYdklerkyf 340
                                    + ++++     +i++++ +Y++l +k+ 
  gi|70607308|ref|YP_256178.1| 604 GSDVNFSdsYAKSIIDTLKNYYDLLEKLK 632
                                   44444431123467777777777777765 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.28      10      31 ..     406     427 ..     382     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                       DUF4116  10 kkngsalkylseeLknDkeivl 31 
                                   +k  ++++++++e+k+D+e+v 
  gi|70607308|ref|YP_256178.1| 406 RKSIESIRFIPPEIKKDFEFVV 427
                                   455569**************96 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0014       3.1       7      40 ..      56      89 ..      47      94 .. 0.87
   2 ?   -1.9   0.0       1.5   3.3e+03       8      23 ..     224     239 ..     222     260 .. 0.77
   3 ?   -1.1   0.1      0.79   1.8e+03      99     115 ..     327     343 ..     294     427 .. 0.51
   4 ?   -1.8   0.0       1.3     3e+03      20      56 ..     586     622 ..     583     630 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                                  HHHHHHEEBTTTTB---HHHHHHHHHHTT----T CS
                        SBDS_C  7 eivaeklvnpqtkrpytttmIekalkelgtsvkt 40
                                  + v +klv+p   + y  + I++a+ke+g s++ 
  gi|70607308|ref|YP_256178.1| 56 DDVISKLVDPLFMANYFKEEIKQAMKEIGLSIDW 89
                                  45999**************************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                   HHHHHEEBTTTTB--- CS
                        SBDS_C   8 ivaeklvnpqtkrpyt 23 
                                   +v   +vnp t++  +
  gi|70607308|ref|YP_256178.1| 224 LVKHSAVNPITGKEVP 239
                                   6778888888887665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.79
                                   EEEEEEGGGHHHHHHHH CS
                        SBDS_C  99 vvvliePgaykeleefv 115
                                   ++ l++P+  +el+ +v
  gi|70607308|ref|YP_256178.1| 327 ITKLVKPEYVEELKPLV 343
                                   44444444443333332 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 1.3
                                   B---HHHHHHHHH...HTT----TTS-CCCCHHHHHHHHT CS
                        SBDS_C  20 rpytttmIekalk...elgtsvktnksaksQalevikaLi 56 
                                   r y++ +I  al+   ++g  v+ ++s    a  +i++L+
  gi|70607308|ref|YP_256178.1| 586 RMYSPDVIRIALTtnaDIGSDVNFSDS---YAKSIIDTLK 622
                                   789999999999652255555555555...4555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 4866.82
//
Query:       gi|70607309|ref|YP_256179.1|  [L=201]
Description: hypothetical protein Saci_1573 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   13.8   0.0       0.05   12.7   0.0    1.5  2  DUF2303          Uncharacterized conserved protein (DUF2303)
      0.026   14.9   0.2      0.053   13.9   0.1    1.6  2  Penicillinase_R  Penicillinase repressor
      0.028   13.1   0.1      0.033   12.9   0.1    1.1  1  DUF3723          Protein of unknown function (DUF3723)
      0.056   13.1   1.8      0.072   12.7   0.4    1.9  2  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
      0.058   13.7   0.5        0.3   11.4   0.1    2.3  2  DUF4777          Domain of unknown function (DUF4777)
       0.12   11.3   2.0       0.12   11.3   0.3    1.7  2  Phage_min_cap2   Phage minor capsid protein 2


Domain annotation for each model (and alignments):
>> DUF2303  Uncharacterized conserved protein (DUF2303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.6   4.8e+03      73      92 ..      11      30 ..       3      33 .. 0.77
   2 ?   12.7   0.0   1.7e-05      0.05     206     245 ..      69     108 ..      50     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.6
                       DUF2303 73 eesaifidadkmsavavfdl 92
                                  e s+if   +++++v++++l
  gi|70607309|ref|YP_256179.1| 11 EPSLIFSYYNNVKIVILLNL 30
                                  56788888899999988886 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.7e-05
                       DUF2303 206 ppyeggaerrielrlryrtddgelvlilrlvraeavleea 245
                                    +ye ++e+++++ +++++ +++l+l  r+++++++ e+ 
  gi|70607309|ref|YP_256179.1|  69 IVYEAEDEKEVPVKFTVIISSKKLKLGVRMIQIDKLGENL 108
                                   69********************************998875 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         4   1.2e+04      76      96 ..     101     121 ..      96     127 .. 0.73
   2 ?   13.9   0.1   1.8e-05     0.053       1      42 [.     134     175 ..     134     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4
                                   XXXXXXXXXXXXXXXXXXXXX CS
               Penicillinase_R  76 vkqlldklfegsvkelvaafv 96 
                                    ++l ++l+++++++ v+++ 
  gi|70607309|ref|YP_256179.1| 101 IDKLGENLYKMKINNNVLHLF 121
                                   566777888888888888765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.8e-05
                                   ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHH CS
               Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktll 42 
                                   +g+ E e++++l+e ++++++e+v+ ++++++ +++ V+  l
  gi|70607309|ref|YP_256179.1| 134 IGDVENEILKLLREYQQMSMREIVQIIAHKTNSSREEVRNKL 175
                                   79**************************99888877776655 PP

>> DUF3723  Protein of unknown function (DUF3723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.1e-05     0.033     381     457 ..      92     168 ..      65     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                       DUF3723 381 vklGFksseikklleqspdreiarelLlkarkpelyevdeekleslvrrivellaaaqpiseqeeeeelttevesek 457
                                    klG +  +i+kl e+  + +i +++L+  r  + y ++ee++ ++ ++i +ll+++q+ s  e  + ++++++s++
  gi|70607309|ref|YP_256179.1|  92 LKLGVRMIQIDKLGENLYKMKINNNVLHLFRVLNDYTIKEEQIGDVENEILKLLREYQQMSMREIVQIIAHKTNSSR 168
                                   58999******************************************************998887555554444443 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   4.2e+03      42      51 ..      29      38 ..      17      40 .. 0.74
   2 ?   12.7   0.4   2.4e-05     0.072       4      58 ..     136     189 ..     133     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                  HrcA_DNA-bdg 42 NqlqsLkalg 51
                                  N ++ L+++g
  gi|70607309|ref|YP_256179.1| 29 NLIKHLRSMG 38
                                  6677777775 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.4e-05
                  HrcA_DNA-bdg   4 svqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpG 58 
                                   +v +eil+ L e ++ + r +  + iA++ +     vRN l  Lk++g ve + G
  gi|70607309|ref|YP_256179.1| 136 DVENEILKLLREYQQMSMREI-VQIIAHKTNSSREEVRNKLYFLKTIGAVEIKEG 189
                                   678999998877777777776.578*************************98766 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.93   2.8e+03       8      18 ..     116     126 ..     112     131 .. 0.81
   2 ?   11.4   0.1    0.0001       0.3      19      42 ..     150     173 ..     136     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.93
                       DUF4777   8 lvlealkvlnr 18 
                                   +vl++++vln+
  gi|70607309|ref|YP_256179.1| 116 NVLHLFRVLND 126
                                   69999999985 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                       DUF4777  19 PaTldEivervaerydlseeelkk 42 
                                    ++++Eiv+ +a +++ s ee++ 
  gi|70607309|ref|YP_256179.1| 150 QMSMREIVQIIAHKTNSSREEVRN 173
                                   49********************97 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.25   7.6e+02       9      38 ..      11      40 ..       6      48 .. 0.81
   2 ?   11.3   0.3   3.9e-05      0.12      48     101 ..     130     183 ..     108     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.25
                Phage_min_cap2  9 lsdkivdlysaleqeiiediarrikktgel 38
                                   ++ i + y+++ + i+ +++++++ +g+ 
  gi|70607309|ref|YP_256179.1| 11 EPSLIFSYYNNVKIVILLNLIKHLRSMGKE 40
                                  56667889999*************999874 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.9e-05
                Phage_min_cap2  48 klaelgllnreilkliskltgksekelrkllkeagdkaiksddkelaiykeagl 101
                                   k +++g +++eilkl++++ + s +e+ ++++   +++ +++ ++l+  k  g+
  gi|70607309|ref|YP_256179.1| 130 KEEQIGDVENEILKLLREYQQMSMREIVQIIAHKTNSSREEVRNKLYFLKTIGA 183
                                   5689***************************************99999888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1333.33
//
Query:       gi|70607310|ref|YP_256180.1|  [L=360]
Description: histidinol-phosphate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-42  145.0   0.0    3.9e-42  144.7   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.018   14.5   0.1    1.3  1  Tax            HTLV Tax


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.0   4.3e-46   3.9e-42      11     363 .]      43     351 ..      33     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 4.3e-46
                                   TTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHT CS
                 Aminotran_1_2  11 ylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllkln 91 
                                    ++     ++ ++++a        +++ +yg+   +pel e+l +++   e++k+++e ++  ++G + +i  ++  l ++
  gi|70607310|ref|YP_256180.1|  43 SPYP----PPLHIIQAV-------EKYLIYGNRYQHPELTERLRRLAA--EYTKVEPE-NIYPTPGGDGAIRSVFYNL-VQ 108
                                   5554....555544444.......5699********************..********.*********9999999999.99 PP

                                   TT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--.B--HHHHH CS
                 Aminotran_1_2  92 pgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt.vatleele 171
                                   pgd+++   p+y++y+ ++  +g++  +++l   ed     e+ e++l+e +      +++++ +p+NPtG+ +++++ l+
  gi|70607310|ref|YP_256180.1| 109 PGDKVVFNYPSYSMYNIYASVRGLKKAKINLI--EDGDWWKEDNEKLLNESK----DARLVVIDNPNNPTGSpMLSEDVLK 183
                                   ******************************88..666666777777777733....3479***********9567888899 PP

                                   HHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS CS
                 Aminotran_1_2 172 klldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls 252
                                   +ll+++k    ++++DeaY +f+ +s        ++ ++pnl+iv++lsKaf+la +RvGy+++n++v++ l k s+pf +
  gi|70607310|ref|YP_256180.1| 184 ELLETVK---GFVMIDEAYFEFYGKSF-----SRLIYDYPNLMIVRTLSKAFSLASFRVGYLIANKDVIKVLMKPSTPFDI 256
                                   9*77776...8*************955.....56999******************************************** PP

                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEE CS
                 Aminotran_1_2 253 ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvt 333
                                   s ++  a  +al+d+     +++  ++++ k+r++l +eL++lglkv+ s ++++ + d +++       + l  + ++++
  gi|70607310|ref|YP_256180.1| 257 SLPGLIAGITALEDPS----YTKHVVAEVSKNREYLLSELRRLGLKVYNSFTNFVFVKDNRNL------LSFLMAKRIAIR 327
                                   ****************....99*****************************************......553333379999 PP

                                   EGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                 Aminotran_1_2 334 pgtsftvpgrlRitvAglteeeleelveal 363
                                   +     v+g  Ri+v  ++e+++e l++al
  gi|70607310|ref|YP_256180.1| 328 K----PVSGYYRISV--GSESDCEALIKAL 351
                                   9....889*******..*******999986 PP

>> Tax  HTLV Tax
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     2e-06     0.018      97     158 ..      44     107 ..      38     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-06
                                   XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                           Tax  97 pkvpp.aflqamrkyspyrngyleptlgdqlpslafpepglrpqnlytlwgk.svvclylyqls 158
                                   p  pp  ++qa+ ky  y n y  p l ++l  la     + p+n+y + g+   +   +y+l 
  gi|70607310|ref|YP_256180.1|  44 PYPPPlHIIQAVEKYLIYGNRYQHPELTERLRRLAAEYTKVEPENIYPTPGGdGAIRSVFYNLV 107
                                   555552578**************************************98775144555556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2321.20
//
Query:       gi|70607311|ref|YP_256181.1|  [L=285]
Description: ATP phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-48  162.6   0.1      1e-47  162.0   0.1    1.3  1  HisG      ATP phosphoribosyltransferase
    5.7e-19   68.0   2.6    9.9e-19   67.3   0.3    2.4  3  HisG_C    HisG, C-terminal domain
  ------ inclusion threshold ------
      0.069   13.0   1.4      0.096   12.5   1.4    1.1  1  DUF2100   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.1   1.7e-51     1e-47       1     159 [.      49     205 ..      49     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1.7e-51
                                   -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHHHHHH CS
                          HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnlakky 81 
                                   r +dip +Ve ga+d+GitG D v Es++  +v+el +L+fgk+k+v+avp + +++s ++  +++  riaT+y nlakky
  gi|70607311|ref|YP_256181.1|  49 RTEDIPSLVEAGAADIGITGYDYVLESGA--NVDELIRLDFGKAKIVLAVPLSWDYNSPDQI-KQE-IRIATKYYNLAKKY 125
                                   689***********************864..6*************************99987.443.6************* PP

                                   HHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHH.S.HHHHHHHHHHHH CS
                          HisG  82 feekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslk.k.kekieellerlr 159
                                   ++ekg+ ++++k+sG+ E+ p+lg aDaI+D+++tG+TL+ +gLk ++t+le++av+i n+  +k +  +ki+ +l+ ++
  gi|70607311|ref|YP_256181.1| 126 ITEKGIPAKVVKISGAAEVIPSLGAADAIIDVMSTGTTLKLHGLKPLDTVLETQAVVIGNRYWMKsDeADKINLMLTMMK 205
                                   *************************************************************9999544459999998887 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   1.3e+03      55      66 ..      53      64 ..      47      68 .. 0.86
   2 ?   -3.4   0.0       1.9   1.2e+04      47      62 ..     137     152 ..     135     154 .. 0.61
   3 !   67.3   0.3   1.7e-22   9.9e-19       1      73 []     210     282 ..     210     282 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                                  HHHHHCTT-EEE CS
                        HisG_C 55 ideLkaaGAsdI 66
                                  i+ L +aGA dI
  gi|70607311|ref|YP_256181.1| 53 IPSLVEAGAADI 64
                                  78999******9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                                   ECCCHHHHHHHHHCTT CS
                        HisG_C  47 eekevaevideLkaaG 62 
                                   + + +aevi+ L aa 
  gi|70607311|ref|YP_256181.1| 137 KISGAAEVIPSLGAAD 152
                                   5555667777776665 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 1.7e-22
                                   TTTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEEE-S- CS
                        HisG_C   1 ArkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvlpiek 73 
                                   Ar+++++ +nvp ++l++v++ lP++ sPT s+la+ + ++V +v++ +++ e+i ++ a GA+dI+v++iek
  gi|70607311|ref|YP_256181.1| 210 ARNKKMIFMNVPDSKLNNVIQSLPAMLSPTLSKLAKGDAWEVITVIDGDKLPEIIAKVVANGARDIVVVDIEK 282
                                   89*********************************************************************97 PP

>> DUF2100  Uncharacterized protein conserved in archaea (DUF2100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   1.6e-05     0.096      59     201 ..     123     267 ..     107     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                   THHHHHT.TTT-EE-HHHHHHHHHHHHHHHHHHHHHHHT.TT---X..X..XXXXSSSEEEESXHHHHHHHHHHXSSSXEE CS
                       DUF2100  59 deylykk.aPehelkkeeAeefckillkakkklekvLee.fgveee..edieeldkdalyivsnkkvlKaLkeinvdlnii 135
                                    +y+ +k +P + +k   A e+   l  a +++  v++    ++ +  + ++ + + + +++ n+  +K+ +  +++l   
  gi|70607311|ref|YP_256181.1| 123 KKYITEKgIPAKVVKISGAAEVIPSL-GAADAIIDVMSTgTTLKLHglKPLDTVLETQAVVIGNRYWMKSDEADKINLMLT 202
                                   567765438999999999*****999.55555555555414444446788888889999999********99999****** PP

                                   EXSSXSSSHHHHTT..XXXSTTTTTSHHHHHHHHHHHHHHHHHHXXSXEEEEXS..SHHHHHHHHH CS
                       DUF2100 136 steGvLeieDmkeiNPkipekalkgieKkveivkeeieklikklkpekvvvvveeddkadellakr 201
                                   + +G+L     k i  ++p++ l+++  ++  +      +++k ++ +v+ v + +dk  e++ak 
  gi|70607311|ref|YP_256181.1| 203 MMKGALYARNKKMIFMNVPDSKLNNVIQSLPAMLSPTLSKLAKGDAWEVITVID-GDKLPEIIAKV 267
                                   ******************************999998888999999999999999.69*99999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1873.95
//
Query:       gi|70607312|ref|YP_256182.1|  [L=226]
Description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-41  140.8   2.0    4.9e-41  140.7   2.0    1.0  1  His_biosynth  Histidine biosynthesis protein
    0.00046   19.7   0.9      0.011   15.3   0.1    2.1  2  PcrB          PcrB family


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.7   2.0   5.5e-45   4.9e-41       2     228 ..       3     220 ..       2     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 140.7 bits;  conditional E-value: 5.5e-45
                                   EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSS CS
                  His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGI 82 
                                   ++p++D+ +  +V++++G+   +  + gdp+++ak+  +eg+d +h+vDldaa eg + n+d++++i+   f   qvGGG+
  gi|70607312|ref|YP_256182.1|   3 VMPSIDISNKVAVKRIRGKG-GSGIILGDPLKIAKEIISEGYDAIHIVDLDAA-EGLGDNKDIIKQICTLGFSWTQVGGGV 81 
                                   89****************99.788899************************99.8************************** PP

                                   SSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.CEEEEETTTTEEEEEEHHHHHHHHHHTT-S CS
                  His_biosynth  83 rsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.gykvaikgwreetgldavelakkleelgag 162
                                   r+le ++++le  ++ ++++t  ++n +  +++++ +g +k++++iD  + g  v+ikgw+e+ ++++++l     +l+ g
  gi|70607312|ref|YP_256182.1|  82 RKLEIAKDILEY-CSSIVVSTLPITNRQEYDKIISGVGVDKVFLSIDYDDnG-YVLIKGWKEK-SVKVSDL----LDLESG 155
                                   ***********9.**********************************99956.**********.6666555....59999* PP

                                   EEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                  His_biosynth 163 eilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                    +++t i ++Gt+ G+d ++++ ++ +vk    ++GG+gsl+dl +lks g+d  i+g  +y+g+l
  gi|70607312|ref|YP_256182.1| 156 GVIFTYIPNEGTKGGIDNNVVEYVK-SVKKIKEYAGGIGSLDDLLKLKSFGFDYSIIGMSFYNGTL 220
                                   ********************97775.555555688***************************9986 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-06     0.011     151     222 ..      43     113 ..      28     117 .. 0.74
   2 !    3.2   0.1    0.0059        53     156     208 ..     159     212 ..     143     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                   HTT-SEEEEE-TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHHH CS
                          PcrB 151 llglrliYlEasGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekderkidai 222
                                   +  + ++ l+a+  l+d + +i+    l  +   vGGG+r+ E+Ak+++e+   ivv ++   +  + +d+i
  gi|70607312|ref|YP_256182.1|  43 YDAIHIVDLDAAEGLGDNKDIIKQICTLGFSWTQVGGGVRKLEIAKDILEYCSSIVVSTLPITNR-QEYDKI 113
                                   5566777777766667777777777788888889*****************99999999854444.345544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0059
                                   EEEEE-TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE- CS
                          PcrB 156 liYlEasGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvG 208
                                   + Y+   G+++ + ++v++ +k ++k++  + GGi s ++  +      D  ++G
  gi|70607312|ref|YP_256182.1| 159 FTYIPNEGTKGGIdNNVVEYVKSVKKIKE-YAGGIGSLDDLLKLKSFgFDYSIIG 212
                                   6799999******999******9999885.7778888776666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1659.25
//
Query:       gi|70607313|ref|YP_256183.1|  [L=193]
Description: imidazoleglycerol-phosphate dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-49  168.0   0.2    2.1e-49  167.5   0.2    1.2  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.2   1.2e-53   2.1e-49       1     144 []      32     175 ..      32     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 1.2e-53
                                   ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE--S CS
                          IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldlsg 81 
                                   T ++f++hmL +l  + +   kv+v    + ddHh+ved++i+lGqa+ke lgdk+gi+Rf+++++pmD+al+ va+d+sg
  gi|70607313|ref|YP_256183.1|  32 TPVNFFNHMLYTLLYYMNSTAKVNVVDRQNYDDHHVVEDTAITLGQAFKEVLGDKKGIRRFANTIIPMDDALVLVAVDISG 112
                                   899****************************************************************************** PP

                                   S-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                          IGPD  82 rpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                   r + ++e +lkr++ig+l++e++ +ff s++ ++g++lhv +lrg+n+hh++ea+fK+++ +L
  gi|70607313|ref|YP_256183.1| 113 RGVSNVEFKLKRNTIGDLAIENIYHFFSSFSYHSGVNLHVIQLRGKNTHHVLEASFKGLGMSL 175
                                   ************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1479.20
//
Query:       gi|70607314|ref|YP_256184.1|  [L=249]
Description: imidazole glycerol phosphate synthase subunit HisF [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-83  277.6   5.8    7.6e-83  277.5   5.8    1.0  1  His_biosynth  Histidine biosynthesis protein
    7.1e-07   28.9   2.8     0.0043   16.5   0.2    2.2  2  NMO           Nitronate monooxygenase
    8.3e-05   22.0   2.2    0.00049   19.5   0.3    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00024   20.5   0.4       0.18   11.1   0.1    2.2  2  TMP-TENI      Thiamine monophosphate synthase
    0.00071   19.0   1.0     0.0091   15.4   0.2    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.001   18.3   0.3       0.18   10.8   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.066   12.4   2.3        0.8    8.9   0.2    2.2  2  DHO_dh        Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.5   5.8     3e-86   7.6e-83       1     228 [.       5     231 ..       5     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 277.5 bits;  conditional E-value: 3e-86
                                   EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS CS
                  His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG 81 
                                   riip+lD+kdG+vV   kG++f +l+++gdpvela ryeeegade++++D++a+ egr+++ ++v+ +a+ ++ip++vGGG
  gi|70607314|ref|YP_256184.1|   5 RIIPCLDVKDGRVV---KGVNFLNLVDKGDPVELAARYEEEGADEIVFLDITATIEGRKTMMNVVKDTASVISIPLTVGGG 82 
                                   8*************...**************************************************************** PP

                                   SSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.C..EEEEETTTTEEEEEEHHHHHHHHHHT CS
                  His_biosynth  82 IrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.g..ykvaikgwreetgldavelakkleel 159
                                   Irsl+dv ++l +gadkv+i+taav+n++l++  + +fgsq+ivvaiD++r g  y v+++ ++ +tg++a+++ak++e+l
  gi|70607314|ref|YP_256184.1|  83 IRSLDDVSKILGNGADKVSINTAAVENKDLVSISSAEFGSQAIVVAIDVKRiGndYYVFTRSGKYNTGINAISWAKEVEKL 163
                                   ***************************************************8468************************** PP

                                   T-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                  His_biosynth 160 gageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                   gageillt+idrdGt++G+d+e+t+ ++++v+ip+iasGG+g+++d+  +  + +da++++ ++++g +
  gi|70607314|ref|YP_256184.1| 164 GAGEILLTSIDRDGTREGYDIEITELISKSVNIPIIASGGAGKIDDFLGIL-KVADAALAAGVFHDGVI 231
                                   *************************************************99.5558**********987 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   1.7e-06    0.0043     177     225 ..      57     106 ..      36     114 .. 0.88
   2 !   12.9   0.2   2.1e-05     0.054     142     207 ..     150     209 ..     118     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                           NMO 177 gd.kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                   ++ k  +++v+  +++++iP+   GGi    +v  +L  GA  v i t+ 
  gi|70607314|ref|YP_256184.1|  57 EGrKTMMNVVKDTASVISIPLTVGGGIRSLDDVSKILGNGADKVSINTAA 106
                                   34477899999999*********************************986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.1e-05
                           NMO 142 tissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrg 207
                                    i ++  a++ve++Ga  + ++  +  G +    +     +++ + + + v+iP+iA GG  +  +
  gi|70607314|ref|YP_256184.1| 150 GINAISWAKEVEKLGAGEILLTSIDRDGTRE--GY----DIEITELISKSVNIPIIASGGAGKIDD 209
                                   5788999999*****9999999999888776..34....356888899************876655 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   1.9e-07   0.00049     136     219 ..      35     118 ..      16     138 .. 0.74
   2 ?    2.4   0.1     0.032        83     164     194 ..     184     214 ..     151     226 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-07
                                   HHHHHHHTT-SEBEEB..SSSTTS----S-HHH.HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                          ThiG 136 larrleevGcaavmPl..aapiGsglGllnkea.lkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                   la r ee G+  ++ l  +a i   +G +++++ +k   + +++P+ v  Gi+s  d+ + +  Gad v +nta  e kd 
  gi|70607314|ref|YP_256184.1|  35 LAARYEEEGADEIVFLdiTATI---EGRKTMMNvVKDTASVISIPLTVGGGIRSLDDVSKILGNGADKVSINTAAVENKDL 112
                                   6777777777766544113444...454444441444555569************************************** PP

                                   HHHHHH CS
                          ThiG 214 vamAra 219
                                   v++ +a
  gi|70607314|ref|YP_256184.1| 113 VSISSA 118
                                   998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.032
                                   HHHHHHHHHH-SS-BEEES---SHHHHHHHH CS
                          ThiG 164 kealkiiieeakvPvivDAGigspsdaaqam 194
                                    e  ++i +++++P+i   G g+  d    +
  gi|70607314|ref|YP_256184.1| 184 IEITELISKSVNIPIIASGGAGKIDDFLGIL 214
                                   34567788899***********988866555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   7.1e-05      0.18     109     178 ..      36     103 ..      31     106 .. 0.81
   2 !    7.6   0.0   0.00084       2.1     116     159 ..     159     204 ..     128     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.1e-05
                      TMP-TENI 109 aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGit.lenvaevleagadgvavv 178
                                   a++ e++gad i++  i  T+t +++    ++ +k++a+ ++iP+ + GGi+ l++v ++l  gad v++ 
  gi|70607314|ref|YP_256184.1|  36 AARYEEEGADEIVFLDI--TATIEGR-KTMMNVVKDTASVISIPLTVGGGIRsLDDVSKILGNGADKVSIN 103
                                   77888888888888888..5555555.44578899****************73699***********9875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00084
                      TMP-TENI 116 gadYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi 159
                                    +  +g+G i  T+   d   e  ++e  + ++++++iP++a GG 
  gi|70607314|ref|YP_256184.1| 159 EVEKLGAGEILLTSIDRDGtrEGYDIEITELISKSVNIPIIASGGA 204
                                   5566788999988888777678889999*****************7 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   3.6e-06    0.0091     126     169 ..      61     104 ..      60     107 .. 0.92
   2 ?    2.0   0.0     0.047   1.2e+02     129     146 ..     185     202 ..     181     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                                   GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                  G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                   ++++v+k++ + ++ip+  GG i++ +dv ++l +Ga+ vs  +
  gi|70607314|ref|YP_256184.1|  61 TMMNVVKDTASVISIPLTVGGGIRSLDDVSKILGNGADKVSINT 104
                                   578999**********************************9865 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.047
                                   HHHCTSTTS...EEEEES CS
                  G3P_antiterm 129 kvikeikkelkipiiaGG 146
                                   ++++ i+k+++ipiia+G
  gi|70607314|ref|YP_256184.1| 185 EITELISKSVNIPIIASG 202
                                   67788999********99 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   7.2e-05      0.18     172     220 ..      63     110 ..      28     125 .. 0.74
   2 !    5.7   0.0    0.0026       6.6     127     209 ..     140     219 ..     122     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.2e-05
                                   CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCST CS
                           Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnP 220
                                    + +k+    +sip+ + G+I++++d+++il + Gad v i  +a +n 
  gi|70607314|ref|YP_256184.1|  63 MNVVKDTASVISIPLTVGGGIRSLDDVSKILGN-GADKVSINTAAVENK 110
                                   556777778899*******************99.*****9999998875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0026
                                   EEEESESSTTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH-- CS
                           Dus 127 vkirigiddeeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGa 207
                                   v +r g  ++  na+  ak ve+ Ga ++ +    r   +eg  d+e  + + ++v+ip+ia G+  +++d   il+   a
  gi|70607314|ref|YP_256184.1| 140 VFTRSGKYNTGINAISWAKEVEKLGAGEILLTSIDRDGTREG-YDIEITELISKSVNIPIIASGGAGKIDDFLGILKV--A 217
                                   566777777888899999999999999999977666655555.45555566889999*********999999999988..6 PP

                                   SE CS
                           Dus 208 dg 209
                                   d+
  gi|70607314|ref|YP_256184.1| 218 DA 219
                                   65 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00031       0.8     230     277 ..      62     107 ..      56     117 .. 0.84
   2 ?    3.3   0.2     0.015        40     238     263 ..     191     214 ..     183     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
                        DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                                    ++v+ + +++++  ip+   GGi s +D+   +  GA  v + ta v
  gi|70607314|ref|YP_256184.1|  62 MMNVVKDTASVIS--IPLTVGGGIRSLDDVSKILGNGADKVSINTAAV 107
                                   5677777777777..999999************************985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.015
                                   HHHTTT.S-EEEESS--SHHHHHHHH CS
                        DHO_dh 238 ykrlkkeipiIgvGGiesgeDaleki 263
                                   +k ++  ipiI++GG    +D l  +
  gi|70607314|ref|YP_256184.1| 191 SKSVN--IPIIASGGAGKIDDFLGIL 214
                                   34445..********98888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1860.42
//
Query:       gi|70607315|ref|YP_256185.1|  [L=393]
Description: histidinol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.4e-124  415.5   0.1   1.7e-123  412.7   0.1    1.8  1  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.7   0.1  9.3e-128  1.7e-123       6     408 ..      12     391 ..       8     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.7 bits;  conditional E-value: 9.3e-128
                                   ---HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC---- CS
                 Histidinol_dh   6 edseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkese 86 
                                   ++ ++v   v++il++v+e+Gd+alle++ek+Dk+k l+  ++ e++i+e ++k++ee k+a+++ ++++ +fh+++++  
  gi|70607315|ref|YP_256185.1|  12 NEFSKVLPLVEQILNQVKERGDKALLELEEKYDKAK-LD--SLVENRIDELASKIPEEYKAAIDRIYDQLVEFHKTTLPY- 88 
                                   566789999************************664.33..567789*******************************75. PP

                                   EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SSGG.--HHHHHHHHHCT-SEEEE CS
                 Histidinol_dh  87 eevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpqdgkvnpavlaaaklagvdeiyk 167
                                    +v    +g+ +g  +r+ie+vG+YvPgG ++ypSt+lm a+pA+vAgv+ei+v+tPp+  ++++ + ++ak+++++++y+
  gi|70607315|ref|YP_256185.1|  89 -MVGGGYNGIEFGILWRAIEKVGIYVPGGLKSYPSTLLMAAIPARVAGVSEIYVATPPN--RIDSVIAYIAKKLKINALYR 166
                                   .7889****************************************************95..8******************* PP

                                   --HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT-TT-E CS
                 Histidinol_dh 168 vGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEHdedaq 248
                                   +GGaqAiaalAyGtes++kvdkivGPGni+V+a K lvs++v+iD i GP+E++viaD++ad ++v +D+ +qaEH++++ 
  gi|70607315|ref|YP_256185.1| 167 IGGAQAIAALAYGTESVKKVDKIVGPGNIFVQASKFLVSKDVAIDGIEGPTELVVIADSSADYRHVILDMRAQAEHGSTSY 247
                                   ********************************************************************************* PP

                                   EEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SE CS
                 Histidinol_dh 249 avlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqvedpeellekiknaGa 329
                                   ++lvtts+ l+++v+ee++k+             +  + +i+ v++++eai++an++ApEHl+l v+dp+++l+kiknaGa
  gi|70607315|ref|YP_256185.1| 248 IILVTTSDFLIDKVREELDKEE------------F--TYYIVKVKSIDEAIDVANDIAPEHLSLFVNDPKSYLHKIKNAGA 314
                                   *****************96532............2..358999************************************** PP

                                   EEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                 Histidinol_dh 330 iflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHaeavkvR 408
                                   i lG+ +p +l DYaaG++h+LPT+ ++r+ +gl+v+dFlk is+ + s +  kel + ++ +Ae+Eg+  H++++ +R
  gi|70607315|ref|YP_256185.1| 315 ISLGK-TPPALIDYAAGPDHILPTNAWSRVRGGLTVYDFLKPISYAN-SVNPDKELVNMAKLIAEYEGFIYHSKSIGAR 391
                                   ****7.99*************************************99.6677799*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2776.61
//
Query:       gi|70607316|ref|YP_256186.1|  [L=95]
Description: phosphoribosyl-ATP pyrophosphatase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-13   51.0   0.2    1.7e-13   50.8   0.2    1.1  1  PRA-PH        Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
       0.08   12.8   0.1       0.24   11.3   0.1    1.8  2  Chordopox_L2  Chordopoxvirus L2 protein


Domain annotation for each model (and alignments):
>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.2   1.9e-17   1.7e-13       3      82 ..       8      92 ..       6      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.9e-17
                                  HHHHHCT----SS----.-HHHHHH....HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHHHHHH CS
                        PRA-PH  3 efhrligerkpetPeas.taelasl....raaligEEavElleaasegdlaeladelaDllYvtygllvllGidldavfeevh 80
                                  +++ +i +r +++ e+s t el ++    +a+++gEE++E ++a+  ++ +  ++e+ Dl+Y++++l++l ++++++v++e++
  gi|70607316|ref|YP_256186.1|  8 KLYSIILDRMKTMKEGSyTVELIKRgkhyVAQKVGEESTEAIIASLVESQQRFVEEVSDLIYHLLVLMALENVTPQDVYKELE 90
                                  56777888888888888888888878888****************************************************** PP

                                  HH CS
                        PRA-PH 81 ra 82
                                  r+
  gi|70607316|ref|YP_256186.1| 91 RR 92
                                  97 PP

>> Chordopox_L2  Chordopoxvirus L2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.18   1.6e+03       2      15 ..      12      25 ..      11      32 .. 0.76
   2 ?   11.3   0.1   2.7e-05      0.24      16      50 ..      41      75 ..      27      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                  Chordopox_L2  2 vlldklrsieeenk 15
                                  ++ld+++ ++e ++
  gi|70607316|ref|YP_256186.1| 12 IILDRMKTMKEGSY 25
                                  78999999887765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.7e-05
                  Chordopox_L2 16 anekfldaiitevesqqpailrpllrLlfDlLilv 50
                                  + e   +aii  ++++q++++  +  L++ lL+l+
  gi|70607316|ref|YP_256186.1| 41 VGEESTEAIIASLVESQQRFVEEVSDLIYHLLVLM 75
                                  5566679*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 646.97
//
Query:       gi|70607317|ref|YP_256187.1|  [L=199]
Description: imidazole glycerol phosphate synthase subunit HisH [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-20   72.9   0.0    3.6e-20   72.5   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.035   13.7   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.25   11.0   0.5       0.81    9.4   0.5    1.7  1  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   6.1e-24   3.6e-20       2     178 ..       5     186 ..       4     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 6.1e-24
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCT....STS-EEEE CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikeare....nkiPiLGI 77 
                                   +iD++ ++  ++   l+++g++ve+ +            k+ + ++v +G+gs + v + + a ke +e    n++ +LGI
  gi|70607317|ref|YP_256187.1|   5 IIDYGVGNLFSIYSGLRRVGFEVEISKEP----------KGSEDLIVFPGVGSFSaVSKYLVARKEKFEvlrsNGTGFLGI 75 
                                   79999999999999999999999999833..........467889**********866666666665555666******** PP

                                   THHHHHHHHHTTT...............EEE.EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTE CS
                        GATase  78 CLGmQllaiefgr...............kvv.kekekehhggtmrlgddetallyglknevierhrHryevnpkelepagl 142
                                   CLGmQ++++e ++               k+  ++ + +h g+      + ++l +g  ++ +++  H+y++ p    ++ +
  gi|70607317|ref|YP_256187.1|  76 CLGMQIMFEEGTEgglnkglgwlkgrvdKINhPRVKIPHIGWDKVNVIKYNELSEGI-DDQYVYYAHSYVAYP---TDKSV 152
                                   ***********99888888888887555333777779****9877666566777777.999************...55555 PP

                                   EEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTT CS
                        GATase 143 evtakseddeelmeiiekknpfvgvQFHPEststpe 178
                                   +   +++ +  + ++++  n +vg+QFHPE++s  +
  gi|70607317|ref|YP_256187.1| 153 IL-STTSYGIDYPAVVNIGN-IVGTQFHPEKSSLVG 186
                                   55.55558889********9.*********998665 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-06     0.035      28      93 ..      25      87 ..       8     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-06
                      GATase_3 28 rfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeie 93
                                  + v++++e  g+  dl+++pG  +  +  ++l +   +e+ + + ++g+  lgiC G+q++ ee +
  gi|70607317|ref|YP_256187.1| 25 FEVEISKEPKGS-EDLIVFPGVGSFSAVSKYLVA--RKEKFEVLRSNGTGFLGICLGMQIMFEEGT 87
                                  556767777765.8******99999998888888..55666666689*************988744 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5   0.00014      0.81     108     216 .]      72     180 ..      63     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00014
                 Peptidase_C26 108 ilgiCrGlqll.nvalGGtlyqdieeqsgltdhreheq....saashavkvekgsllaellgseeievnslHhqaikelae 183
                                    lgiC+G+q++    + G l++ +   +g++d  +h +         +v+v k   l+e +   +  v   H+       +
  gi|70607317|ref|YP_256187.1|  72 FLGICLGMQIMfEEGTEGGLNKGLGWLKGRVDKINHPRvkipHIGWDKVNVIKYNELSEGID--DQYVYYAHSYV-AYPTD 149
                                   69*******99234566899999999999999999997334444455777777777777766..56666666654.44445 PP

                 Peptidase_C26 184 elrveAvaeDgv.iEaieseeakafvlgvQwHPE 216
                                   +  + ++++ g+   a+  +     ++g Q+HPE
  gi|70607317|ref|YP_256187.1| 150 KSVILSTTSYGIdYPAVVNIG---NIVGTQFHPE 180
                                   555666666664133444333...6888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1370.68
//
Query:       gi|70607318|ref|YP_256188.1|  [L=124]
Description: phosphoribosyl-AMP cyclohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  105.0   0.2    2.2e-30  104.3   0.2    1.3  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.2   1.2e-34   2.2e-30       1      74 []      43     116 ..      43     116 .. 0.99

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 1.2e-34
                                   EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                        PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                   m++ mnk+a+ ktl+tg+++++S s+kklW KGetS n+q v+++++DcD+Dal++ v+++g++CHtg++sCFy
  gi|70607318|ref|YP_256188.1|  43 MVGSMNKDAVIKTLTTGYVHFWSISKKKLWLKGETSHNYQIVEDVKVDCDGDALVVLVNPQGSTCHTGNRSCFY 116
                                   999**********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 917.97
//
Query:       gi|70607319|ref|YP_256189.1|  [L=134]
Description: phenylacetic acid degradation protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-20   70.8   0.3      1e-19   70.4   0.3    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.061   12.3   0.0       0.13   11.2   0.0    1.5  2  YqhG            Bacterial protein YqhG of unknown function
       0.13   12.4   0.0       0.18   12.0   0.0    1.3  1  NifU            NifU-like domain
       0.17   12.1   0.0       0.31   11.2   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.3   2.3e-23     1e-19       1      73 [.      10      83 ..      10      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.3e-23
                                  HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT--EEEEE CS
                FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalr.alpgvevveVe 73
                                  k+++++aL +V+DPe++vd+v+lgl++e++i++ g++++ + lt p+c++++++   +e+ ++ ++p  ++veV+
  gi|70607319|ref|YP_256189.1| 10 KAKIMEALTQVYDPEIPVDIVNLGLIYELRINDdGEIYIRLGLTAPGCPVIDDLIYTVEQVVKeTVPA-KSVEVD 83
                                  689************************************************************99998.888886 PP

>> YqhG  Bacterial protein YqhG of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     3e-05      0.13     232     257 ..      11      36 ..       2      37 .. 0.81
   2 ?   -2.3   0.0      0.39   1.7e+03     167     196 ..      60      89 ..      58     110 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3e-05
                          YqhG 232 ekekealkeqYepkikvevinGGlfY 257
                                    k  eal++ Y+p+i v+++n Gl Y
  gi|70607319|ref|YP_256189.1|  11 AKIMEALTQVYDPEIPVDIVNLGLIY 36 
                                   345799******************99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.39
                          YqhG 167 ipdycftlsplikpksglkRlekliekaie 196
                                   i d ++t+ +++k +   k +e  i+   +
  gi|70607319|ref|YP_256189.1|  60 IDDLIYTVEQVVKETVPAKSVEVDIDFDTQ 89 
                                   557777777777776666666655554444 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05      0.18      25      63 ..      41      78 ..      13      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                                  EETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT- CS
                          NifU 25 vdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpev 63
                                   d+g++++rl     gCp  +  + + +e+ +ke vp  
  gi|70607319|ref|YP_256189.1| 41 NDDGEIYIRLGLTAPGCPVIDDLI-YTVEQVVKETVPAK 78
                                  4677****************9988.***********954 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.9e-05      0.31      44      71 ..      80     105 ..      74     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                        HTH_34  44 ievdkefkgkkprtllriTpeGreafkk 71 
                                   +evd++f+ +   t +++T eGre+fkk
  gi|70607319|ref|YP_256189.1|  80 VEVDIDFDTQ--WTPFKMTAEGRERFKK 105
                                   7888888888..799***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 978.35
//
Query:       gi|70607320|ref|YP_256190.1|  [L=458]
Description: seryl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-39  133.1   0.0      2e-38  132.1   0.0    1.5  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.5e-24   86.3  12.0    2.9e-24   85.4  12.0    1.5  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.03   12.9   1.5      0.051   12.2   1.5    1.3  1  FapA          Flagellar Assembly Protein A
        3.2    5.4   7.6        4.5    5.0   7.6    1.1  1  Nup88         Nuclear pore component
        6.3    7.3  12.6         24    5.5  12.6    2.0  1  APG6_N        Apg6 coiled-coil region
        6.7    6.3  15.4       0.22   11.2   9.0    1.7  2  YkyA          Putative cell-wall binding lipoprotein


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.0   6.8e-42     2e-38       7     178 ..     243     419 ..     236     420 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 6.8e-42
                                   TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                   ++++++L++t+e+ +++l+ +e + +++LPlkl+ +++ +R+E+     d++G++Rv++Fh+ ++++f+++++++   +++
  gi|70607320|ref|YP_256190.1| 243 EGEDLYLIATAEHSIAALYYKEEIPKEELPLKLVGVSPAFRKEAGaankDLKGIFRVHQFHKVEQFIFSSPEDSWKYHEEM 323
                                   4689******************998888****************7788999****************************** PP

                                   HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimica 164
                                   i+ +++if+ lgl++r+i    ++  a +++k+++e++++ + k++e+++++++ + ++ r++++++++nn++   ++++ 
  gi|70607320|ref|YP_256190.1| 324 IENAEEIFRGLGLPYRVINIASGDLGAPAAKKYDLEVWMPAQAKFREMVSCSNCLDWQAYRMRIRYVEKNNKKGYLHTLNS 404
                                   **************99888889999*******************************************************9 PP

                                   E.EEHHHHHHHHHHH CS
                                   x.xxxxxxxxxxxxx RF
                  tRNA-synt_2b 165 a.igveRllsaileq 178
                                   + i+ +R + aile+
  gi|70607320|ref|YP_256190.1| 405 TaIASTRAITAILEN 419
                                   99***********98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4  12.0   9.7e-28   2.9e-24       5     108 .]       7     108 ..       6     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 9.7e-28
                                   HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHH CS
                  Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelka 85 
                                    lir+npe +ke+lk+R+ d+++vd+ +eld+k+r++ +e+e l++e+N +s +I ka k+  +++eli+++kel + l++
  gi|70607320|ref|YP_256190.1|   7 ELIRNNPEVLKENLKRRFIDTSTVDKAVELDKKWRQTLQEVERLRHEHNLISSQIPKAPKE--QKSELINKAKELLKTLED 85 
                                   79********************************************************986..69**************** PP

                                   HHHHHHHHHHHHHHHHCTS---- CS
                  Seryl_tRNA_N  86 leaelkeleaeleklllaiPNip 108
                                   +e+el+++e+e e+lll++PN++
  gi|70607320|ref|YP_256190.1|  86 KEKELQKIEEERENLLLSLPNLV 108
                                   *********************85 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.5   1.7e-05     0.051     341     405 ..      35     101 ..      20     147 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                          FapA 341 eleeeleeleeeleklkkk...ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelk 405
                                   el+++ +++ +e+e+l+ +   i++  + ka+k+++se  ++ k+ll+t+e  ++el+++eee+++l 
  gi|70607320|ref|YP_256190.1|  35 ELDKKWRQTLQEVERLRHEhnlISSQIP-KAPKEQKSELINKAKELLKTLEDKEKELQKIEEERENLL 101
                                   5555555555555555555333222222.445566777888888888888888888888888888765 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   7.6    0.0015       4.5     531     634 ..       6     101 ..       3     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0015
                         Nup88 531 lqllsratqvlReeylkkqelvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkk 611
                                   l+l+ +  +vl+ e lk++ +  + ++k v+ l k+ +q l+e+++l++e + +s +  k        k++  +l++++k+
  gi|70607320|ref|YP_256190.1|   6 LELIRNNPEVLK-ENLKRRFIDTSTVDKAVE-LDKKWRQTLQEVERLRHEHNLISSQIPKA------PKEQKSELINKAKE 78 
                                   677778888886.569999999999999998.67778899****************99985......4788899******* PP

                         Nup88 612 vlkrlnsklpvlseaeremkkel 634
                                   +lk+l++k+  l ++e e ++ l
  gi|70607320|ref|YP_256190.1|  79 LLKTLEDKEKELQKIEEERENLL 101
                                   ***********999999866655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.6     0.008        24      14      81 ..      36     101 ..      27     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.008
                        APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereele 81 
                                   ldk+ +q+ +e + ++   + + ++ +++   +e+  el ++ ++l k+ e++++eL+++e+ere+l 
  gi|70607320|ref|YP_256190.1|  36 LDKKWRQTLQEVERLRHEHNLISSQIPKAP--KEQKSELINKAKELLKTLEDKEKELQKIEEERENLL 101
                                   555666666666666666666666655544..666677777777777777777777777777777764 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   9.0   7.4e-05      0.22       9      82 ..      29      98 ..      27     103 .. 0.92
   2 ?   -3.5   0.4       2.4   7.2e+03     165     183 ..     133     151 ..     129     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.4e-05
                          YkyA  9 aleeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeake 82
                                  ++++avel+k+ +++ ++ ++l  + + + ++i ++ +++++++ ++++e+l+++e++e++l+k    iee +e
  gi|70607320|ref|YP_256190.1| 29 TVDKAVELDKKWRQTLQEVERLRHEHNLISSQIPKAPKEQKSELINKAKELLKTLEDKEKELQK----IEEERE 98
                                  789***********************************************************99....555554 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                          YkyA 165 aneqFneatkkyneekkef 183
                                    +++ ne +k+ n  k ++
  gi|70607320|ref|YP_256190.1| 133 YKDDVNEFLKQTNGHKVDY 151
                                   6788899999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1527  (0.0851693); expected 358.6 (0.02)
Passed bias filter:                      832  (0.0464053); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 3141.15
//
Query:       gi|70607321|ref|YP_256191.1|  [L=489]
Description: hypothetical protein Saci_1585 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-16   61.7   0.0    5.8e-16   59.3   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.13   12.3   0.0        3.5    7.7   0.0    2.2  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.15   1.3e+03      55     100 ..     104     159 ..      57     169 .. 0.73
   2 !   59.3   0.0   6.4e-20   5.8e-16       1     167 []     207     393 ..     207     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                                   STGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..........HHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxx RF
                   Radical_SAM  55 gepllypdfvellerlaklavpgiritvetngtlpd..........eeklerllel 100
                                    ep+ y+ f+el++r   ++ +++ + +++ g+ +           + ++++l++ 
  gi|70607321|ref|YP_256191.1| 104 KEPINYKSFQELIRRPEIKKAKERGMKIIAGGPSVWqwlwredmiqDVQIDTLVDG 159
                                   57778888888887777777777777777777776566666555556666666555 PP

  == domain 2  score: 59.3 bits;  conditional E-value: 6.4e-20
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlaklavp 76 
                                   ++++rgC++ C+fC+++      ++ r+ ++++i++e+  + +++gv++ +++++++l+y      +  e l +l+kl v+
  gi|70607321|ref|YP_256191.1| 207 IEIMRGCARSCRFCSVT-----LRPTRYYPLDKIEKELLVN-VKNGVRHGVIHSDDVLFYgatgiFPRPEPLIKLHKL-VK 280
                                   689**************.....69*****************.999********************8888888888888.47 PP

                                   TEEEEEEECSSCHG...............HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHH........HHHHHHH CS
                                   xxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxx RF
                   Radical_SAM  77 giritvetngtlpd...............eeklerllelgvdrvslgleaaddekvlklmnrghtf........eevleal 134
                                   ++  t+  ++  +                 e++          v++g+e+++++   k +++ ++         e v +a+
  gi|70607321|ref|YP_256191.1| 281 KYYKTIAWSHASLAairyseekyglisklSEIIYDNESQKYLGVEVGIETGSSR-LAKEIMPAKSApfkieeypETVEQAF 360
                                   8888888888888888888667555555555555555555**************.6666666666678888888******* PP

                                   HHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 135 eklreagikrvvdrivglpGendeeleellell 167
                                   ++++e++i +  ++ivglp e+++++ +++el+
  gi|70607321|ref|YP_256191.1| 361 KIMHENRIIPAGTMIVGLPEETEDDVYKTIELV 393
                                   *****************************9986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.02   1.8e+02      13      43 ..      45      75 ..      41      90 .. 0.84
   2 ?    7.7   0.0   0.00039       3.5      65     102 ..     109     146 ..     106     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.02
                   B12-binding 13 hplGlavlaaalrdagfeVqllganvenedi 43
                                   p+Gl+ + a l dagf+  +++ +  n+ +
  gi|70607321|ref|YP_256191.1| 45 APYGLRKVEASLIDAGFKAAVIDPDHLNKYL 75
                                  589*******************998777554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00039
                   B12-binding  65 leavkelvel...lkrirprvkvvvGGahpsldpeetleak 102
                                   +  ++el+++   +k++ +++k+++GG  ps+ +++ ++++
  gi|70607321|ref|YP_256191.1| 109 YKSFQELIRRpeiKKAKERGMKIIAGG--PSVWQWL-WRED 146
                                   678999******9999999********..5565555.4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3571.84
//
Query:       gi|70607322|ref|YP_256192.1|  [L=80]
Description: hypothetical protein Saci_1586 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 612.02
//
Query:       gi|70607323|ref|YP_256193.1|  [L=99]
Description: protein, rpoM [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-08   34.6   2.2    2.2e-08   33.8   2.2    1.4  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
     0.0074   16.4   0.3      0.013   15.6   0.3    1.6  1  DUF2387         Probable metal-binding protein (DUF2387)
     0.0082   15.4   1.5      0.016   14.5   1.5    1.5  1  zf-TFIIB        Transcription factor zinc-finger
  ------ inclusion threshold ------
      0.012   15.8   1.2      0.024   14.9   1.2    1.5  1  IBR             IBR domain, a half RING-finger domain
      0.016   15.0   0.2      0.029   14.2   0.2    1.4  1  Cys_rich_CPCC   Cysteine-rich CPCC
       0.03   14.0   3.4      0.092   12.4   3.4    1.8  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.034   14.1   2.2       0.07   13.1   2.2    1.5  1  Nudix_N_2       Nudix N-terminal
      0.082   12.8   0.8       0.15   12.0   0.8    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.14   12.1   1.3       0.21   11.5   1.3    1.3  1  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.18   11.6   4.1       0.32   10.8   3.6    1.7  1  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.26   11.7   6.1      0.094   13.1   2.3    2.2  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.42   10.1   0.3       0.42   10.1   0.3    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.43   10.8   5.4        4.1    7.6   0.2    2.3  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
       0.68    9.7   5.6       0.94    9.3   1.3    2.4  2  zinc_ribbon_2   zinc-ribbon domain
        4.3    7.3   6.9         63    3.6   0.0    2.6  2  DUF1936         Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   2.2   1.8e-11   2.2e-08       1      35 [.       1      35 [.       1      36 [. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.8e-11
                                  EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                  ++FCpkCg l+ p++++ + ++ C +C+ e + ++
  gi|70607323|ref|YP_256193.1|  1 MQFCPKCGGLMVPAKKDNKDILRCTKCKFEREMTD 35
                                  9*****************************99875 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.1e-05     0.013      11      53 ..       4      44 ..       2      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                       DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvakel 53
                                  CP+C     ++  ++d++++  C++C+f  e+++k++++    
  gi|70607323|ref|YP_256193.1|  4 CPKCGGL--MVPAKKDNKDILRCTKCKFEREMTDKEKKQYSVK 44
                                  9999864..55668899**************999966554333 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.5   1.3e-05     0.016       2      26 ..       4      28 ..       3      28 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                      zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                  CPkC+  ++++++++  i +C++C+
  gi|70607323|ref|YP_256193.1|  4 CPKCGGLMVPAKKDNKDILRCTKCK 28
                                  ************************5 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.2     2e-05     0.024      19      47 ..       2      30 ..       1      31 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                           IBR 19 kwCprpdCeaiiekseg.cks..vtCskCgfe 47
                                  + Cp  +C++++ + ++ + +  ++C+kC+fe
  gi|70607323|ref|YP_256193.1|  2 QFCP--KCGGLMVPAKKdN-KdiLRCTKCKFE 30
                                  68**..******8888853.33488*****97 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.4e-05     0.029       2      44 ..       3      47 ..       2      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                 Cys_rich_CPCC  2 qCpcCgyltleeee..gsydiCpvCfWedDlvqlkapdleggaNk 44
                                   Cp Cg l+++ ++   ++  C  C  e ++++ +++++++ +Nk
  gi|70607323|ref|YP_256193.1|  3 FCPKCGGLMVPAKKdnKDILRCTKCKFEREMTDKEKKQYSVKENK 47
                                  5********966652356667*******************99997 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.4   7.7e-05     0.092       4      18 ..       2      16 ..       1      28 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                 zf-NADH-PPase  4 rFCgrCGaptepaeg 18
                                  +FC++CG+ ++pa+ 
  gi|70607323|ref|YP_256193.1|  2 QFCPKCGGLMVPAKK 16
                                  9********999975 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.2   5.9e-05      0.07       2      29 ..       3      28 ..       2      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                                  B-TTT--B-EEE--TT-SS-EEEETTTT CS
                     Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCg 29
                                  FC++CG+ +  +    Dn+  l+C++C 
  gi|70607323|ref|YP_256193.1|  3 FCPKCGGLMVPAK--KDNKDILRCTKCK 28
                                  *******977665..69999999****7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   0.00013      0.15      30      55 ..       3      30 ..       2      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgfe 55
                                   C++Cg  + +  +++++ ++C++C+fe
  gi|70607323|ref|YP_256193.1|  3 FCPKCGGLMVPakKDNKDILRCTKCKFE 30
                                  5********9999999**********97 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   0.00017      0.21      12      36 ..       2      29 ..       1      31 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                  -B-TTT-SB-...-SSSS-EEEETTT-- CS
                          C1_1 12 tfCkhCgefl...wgkekqglkCswCkl 36
                                  +fC +Cg ++   ++ +k +l+C+ Ck+
  gi|70607323|ref|YP_256193.1|  2 QFCPKCGGLMvpaKKDNKDILRCTKCKF 29
                                  79********996669**********97 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.6   0.00027      0.32       4      34 ..       4      31 ..       1      36 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                                  -SSS--EEEEEE-SSSEEEEESST.T----E CS
                zf-C4_Topoisom  4 CPkCggdLvlkrgkkGkFvGCsnYPeCkftk 34
                                  CPkCgg +v  ++ ++  + C+    Ckf +
  gi|70607323|ref|YP_256193.1|  4 CPKCGGLMVPAKKDNKDILRCTK---CKFER 31
                                  *********99998888888887...77766 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.3   7.9e-05     0.094       3      33 ..       3      32 ..       2      42 .. 0.76
   2 ?   -2.1   0.1       4.4   5.2e+03      12      24 ..      81      93 ..      74      93 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                       zf-IS66  3 tCpcCGgllkpigedrvreeldipPakfrVi 33
                                   Cp+CGgl++p+++d    +l     kf+  
  gi|70607323|ref|YP_256193.1|  3 FCPKCGGLMVPAKKD-NKDILRCTKCKFERE 32
                                  6*************9.677777776666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.4
                       zf-IS66 12 kpigedrvreeld 24
                                  k++g d  reel+
  gi|70607323|ref|YP_256193.1| 81 KEVGLDLLREELE 93
                                  5666677778876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00035      0.42      17      24 ..       2       9 ..       1      11 [. 0.62
   2 ?   -0.6   0.2       0.8   9.6e+02      19      23 ..      24      28 ..      23      30 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                   zf-ribbon_3 17 nvCpyCGt 24
                                  ++Cp+CG+
  gi|70607323|ref|YP_256193.1|  2 QFCPKCGG 9 
                                  56777775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.8
                   zf-ribbon_3 19 CpyCG 23
                                  C++C 
  gi|70607323|ref|YP_256193.1| 24 CTKCK 28
                                  77775 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0034       4.1      24      31 ..       2       9 ..       1      13 [. 0.86
   2 ?    5.4   1.1     0.017        20       8      32 ..      21      48 ..      14      81 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0034
                  NOB1_Zn_bind 24 kFCpkCGn 31
                                  +FCpkCG 
  gi|70607323|ref|YP_256193.1|  2 QFCPKCGG 9 
                                  8******6 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                  NOB1_Zn_bind  8 vlrChaCfk...vtkdmtkkFCpkCGnk 32
                                  +lrC+ C     +t + +k++  k  + 
  gi|70607323|ref|YP_256193.1| 21 ILRCTKCKFereMTDKEKKQYSVKENKG 48
                                  89*****865657788888887665554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.3   0.00079      0.94      14      20 ..       2       8 ..       1       9 [. 0.79
   2 ?    2.2   0.2      0.13   1.6e+02       1       5 [.      23      27 ..      23      36 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00079
                 zinc_ribbon_2 14 kFCpyCG 20
                                  +FCp+CG
  gi|70607323|ref|YP_256193.1|  2 QFCPKCG 8 
                                  5888887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                 zinc_ribbon_2  1 fCpnC 5 
                                  +C++C
  gi|70607323|ref|YP_256193.1| 23 RCTKC 27
                                  58888 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   5.2       0.1   1.2e+02       2      25 ..       4      24 ..       3      31 .. 0.72
   2 ?    3.6   0.0     0.053        63      16      22 ..      61      67 ..      58      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                                  -TTTSSSBEEEEE-TTS-EEEEEE CS
                       DUF1936  2 CPKCnvGkLEPVYNekGEIKvFRC 25
                                  CPKC+ G + P   ++ +I   RC
  gi|70607323|ref|YP_256193.1|  4 CPKCG-GLMVPAKKDNKDI--LRC 24
                                  ****9.7777877777665..455 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.053
                                  TTS-EEE CS
                       DUF1936 16 ekGEIKv 22
                                  +kGEIK+
  gi|70607323|ref|YP_256193.1| 61 DKGEIKL 67
                                  9*****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1678  (0.0935914); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 691.74
//
Query:       gi|70607324|ref|YP_256194.1|  [L=155]
Description: transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-19   68.4   0.3    5.8e-19   67.8   0.3    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.5e-13   50.0   3.1    8.7e-13   47.6   0.6    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
    9.9e-11   41.3   0.9    4.4e-10   39.2   1.5    1.7  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    3.7e-06   26.8   0.0    6.7e-06   26.0   0.0    1.5  1  HTH_11          HTH domain
     0.0008   19.0   0.1     0.0012   18.5   0.1    1.2  1  GntR            Bacterial regulatory proteins, gntR family
     0.0015   18.7   0.1     0.0029   17.8   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0017   18.2   0.1     0.0029   17.5   0.1    1.3  1  MarR_2          MarR family
     0.0021   17.8   0.0     0.0037   17.0   0.0    1.4  1  HTH_10          HTH DNA binding domain
     0.0042   16.9   0.1     0.0083   16.0   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0053   16.3   0.1      0.022   14.3   0.1    2.0  2  HTH_50          Helix-turn-helix domain
     0.0059   16.4   0.3       0.01   15.6   0.3    1.4  1  HTH_8           Bacterial regulatory protein, Fis family
     0.0064   16.4   0.1      0.013   15.4   0.1    1.5  1  MarR            MarR family
     0.0072   16.1   0.0      0.012   15.3   0.0    1.4  1  HTH_23          Homeodomain-like domain
     0.0078   15.9   0.1       0.02   14.6   0.1    1.7  1  HTH_DeoR        DeoR-like helix-turn-helix domain
     0.0099   16.2   0.1       0.02   15.3   0.1    1.5  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.017   14.5   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.012   16.1   0.2      0.037   14.5   0.1    1.8  2  PCI             PCI domain
      0.015   15.3   0.1       0.03   14.3   0.1    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.016   15.0   0.1      0.024   14.4   0.1    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.017   14.9   0.1      0.034   13.9   0.1    1.6  1  HTH_38          Helix-turn-helix domain
      0.035   14.2   0.0      0.059   13.5   0.0    1.4  1  HTH_28          Helix-turn-helix domain
      0.045   13.8   0.0      0.071   13.1   0.0    1.3  1  HTH_29          Winged helix-turn helix
      0.046   13.5   0.1      0.076   12.8   0.1    1.3  1  HTH_30          PucR C-terminal helix-turn-helix domain
      0.063   13.3   0.1      0.099   12.6   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.065   13.8   0.0       0.13   12.8   0.0    1.5  1  Mga             Mga helix-turn-helix domain
      0.083   12.7   0.0       0.17   11.7   0.0    1.4  1  LexA_DNA_bind   LexA DNA binding domain
       0.11   12.5   0.0       0.38   10.9   0.0    1.9  2  HTH_7           Helix-turn-helix domain of resolvase
       0.13   12.3   0.2       0.29   11.2   0.1    1.6  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.3     9e-22   5.8e-19       2      74 ..      76     144 ..      75     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 9e-22
                                   EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                   +++++++h   + efe+++ +l++Vv +y v G+yd +l++++r++e+l++f++  l ++p ++rt tsivl+
  gi|70607324|ref|YP_256194.1|  76 MIKVDGKH---ILEFEKEVSNLDNVVAVYDVVGEYDVMLIAKFRSIEDLDTFIKS-LLKNPKIERTYTSIVLN 144
                                   79***999...********************************************.***************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.6   1.4e-15   8.7e-13       2      48 .]      10      56 ..       9      56 .. 0.98
   2 ?    2.3   0.0      0.19   1.2e+02       8      19 ..     142     153 ..     140     155 .] 0.89

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.4e-15
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  d +d+k+L +L k++ris r LAe+ ++Sp+t++ rl rL++eG++k
  gi|70607324|ref|YP_256194.1| 10 DAIDKKLLIELLKDSRISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  89*******************************************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                        HTH_24   8 ILelLqknpris 19 
                                   +L++++++pri 
  gi|70607324|ref|YP_256194.1| 142 VLNVVKEDPRIK 153
                                   69********96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   1.5   6.9e-13   4.4e-10       1      41 [.       9      49 ..       9      50 .. 0.97
   2 ?   -1.8   0.0       4.5   2.9e+03       9      18 ..     143     152 ..     142     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 6.9e-13
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +D+iD+k+L +L +d+Ris ++LAe+ ++S++t ++R+ rL
  gi|70607324|ref|YP_256194.1|  9 IDAIDKKLLIELLKDSRISLRRLAEEMNVSPATLHNRLMRL 49
                                  6*************************************998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                 HTH_AsnC-type   9 LeaLqedaRi 18 
                                   L+   ed+Ri
  gi|70607324|ref|YP_256194.1| 143 LNVVKEDPRI 152
                                   788899***8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     1e-08   6.7e-06       4      43 ..      15      53 ..      13      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1e-08
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                  ++l+ L  +++ is  +LAee+nvS +t ++++ +L   g
  gi|70607324|ref|YP_256194.1| 15 KLLIEL-LKDSRISLRRLAEEMNVSPATLHNRLMRLVQEG 53
                                  555666.34555***********************97777 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.9e-06    0.0012      18      54 ..      20      55 ..       9      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                                  S-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          GntR 18 lrpGdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                  l   +++ s r La+e++Vs  t+   L rL++eg+v
  gi|70607324|ref|YP_256194.1| 20 LLKDSRI-SLRRLAEEMNVSPATLHNRLMRLVQEGVV 55
                                  5567889.9**************************99 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   4.5e-06    0.0029      23      53 ..      26      56 ..      18      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-06
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++  +lae++nvsp++    l +L ++G v+
  gi|70607324|ref|YP_256194.1| 26 ISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  67789**********************9885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.5e-06    0.0029      11      52 ..      17      56 ..      12      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                                  HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  L +L    +  ++ + la+++++s+++++++l rLv+ G v 
  gi|70607324|ref|YP_256194.1| 17 LIELLKDSR--ISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  666666665..999*************************985 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.8e-06    0.0037      23      46 ..      25      48 ..      22      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.8e-06
                        HTH_10 23 rvtlkeLAkelGIskstlsehLrk 46
                                  r++l+ LA+e+++s++tl+++L +
  gi|70607324|ref|YP_256194.1| 25 RISLRRLAEEMNVSPATLHNRLMR 48
                                  89*******************977 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.3e-05    0.0083       3      53 ..       6      56 ..       4      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  k+ +   + k  + Llk  + + + +aee +v+ ++  + L +L++ G+V+
  gi|70607324|ref|YP_256194.1|  6 KIEIDAIDKKLLIELLKDSRISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  77888999*****************************************97 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   3.5e-05     0.022       8      46 ..       9      48 ..       7      49 .. 0.88
   2 ?   -2.4   0.0       6.1   3.9e+03       6      19 ..     102     115 ..     100     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                        HTH_50  8 veefErelikkayek.YpStRklAkrLGvShtaianklrk 46
                                  +++++++l++++++    S R lA+ + vS ++  n+l +
  gi|70607324|ref|YP_256194.1|  9 IDAIDKKLLIELLKDsRISLRRLAEEMNVSPATLHNRLMR 48
                                  5899********986156*******************965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
                        HTH_50   6 eyveefErelikka 19 
                                   ++v+e++  li+k+
  gi|70607324|ref|YP_256194.1| 102 DVVGEYDVMLIAKF 115
                                   78999999999875 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.6e-05      0.01       3      41 ..      10      48 ..       8      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH CS
                         HTH_8  3 eevEkelIeaALertgGnkskAArlLGisRrtLyrKLkk 41
                                  ++++k+l+++ L+ ++  + + A++ ++s+ tL+++L +
  gi|70607324|ref|YP_256194.1| 10 DAIDKKLLIELLKDSRISLRRLAEEMNVSPATLHNRLMR 48
                                  6899********************************965 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.1e-05     0.013      11      47 ..      19      55 ..      15      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                                  HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                   l     +s+  La+ ++vs++t+ + l rL+++G +
  gi|70607324|ref|YP_256194.1| 19 ELLKDSRISLRRLAEEMNVSPATLHNRLMRLVQEGVV 55
                                  55555678999************************87 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.012       8      45 ..      15      53 ..       9      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                        HTH_23  8 lrillllae.GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                   + + ll++ ++s r+ A+e++vs+ T+ + l r ++eG
  gi|70607324|ref|YP_256194.1| 15 KLLIELLKDsRISLRRLAEEMNVSPATLHNRLMRLVQEG 53
                                  4567788888******************96554445666 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.1e-05      0.02       3      44 ..      14      55 ..      13      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                      HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                  +++l  l ++  +s+ +l+e+ +vS+aT  + L  L+++g++
  gi|70607324|ref|YP_256194.1| 14 KKLLIELLKDSRISLRRLAEEMNVSPATLHNRLMRLVQEGVV 55
                                  567777888889****************99999999888875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.1e-05      0.02      19      56 ..      20      56 ..       5      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-05
                                  HSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 19 keeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  + ++++ +s++ +ae++n+sp  l   l +L ++g+vk
  gi|70607324|ref|YP_256194.1| 20 LLKDSR-ISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  445555.9****************************98 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.7e-05     0.017      20      52 .]      17      50 ..      14      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                  HTH_Tnp_ISL3 20 ilellles.rsvkavArqlgvSwtTVwrildryv 52
                                   +ell++s +s +  A++++vS+ T++++l r+v
  gi|70607324|ref|YP_256194.1| 17 LIELLKDSrISLRRLAEEMNVSPATLHNRLMRLV 50
                                  589**************************99876 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.8e-05     0.037      49      92 ..      15      57 ..       6      59 .. 0.87
   2 ?   -1.1   0.0       4.3   2.8e+03      17      17 ..     120     120 ..      73     148 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-05
                                  HHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSSE CS
                           PCI 49 rllrqvskiyssislerlaklldlsvdevEkilvklIrdgeira 92
                                  +ll+++ k  s+isl rla+  ++s   +++ l++l+ +g +++
  gi|70607324|ref|YP_256194.1| 15 KLLIELLK-DSRISLRRLAEEMNVSPATLHNRLMRLVQEGVVKG 57
                                  55656665.89*****************************9987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
                                   H CS
                           PCI  17 g 17 
                                   +
  gi|70607324|ref|YP_256194.1| 120 D 120
                                   1 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.7e-05      0.03       6      44 ..      13      49 ..       8      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                       HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseL 44
                                  +k  L+elL +  ++++l  la+e++ s  tl +++  L
  gi|70607324|ref|YP_256194.1| 13 DKKLLIELLKD--SRISLRRLAEEMNVSPATLHNRLMRL 49
                                  66667776655..*******************9988665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.8e-05     0.024      17      49 ..      24      56 ..      17      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-05
                                  SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   + +l+ lA++  ++++t h+ L  Lv++G v+
  gi|70607324|ref|YP_256194.1| 24 SRISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  5679**************************997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.3e-05     0.034      10      43 ..      15      48 ..      11      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                        HTH_38 10 ReeIerllaeGlslreIArrLgrspsTIsRElkR 43
                                     Ie l +   slr+ A ++++sp T ++ l R
  gi|70607324|ref|YP_256194.1| 15 KLLIELLKDSRISLRRLAEEMNVSPATLHNRLMR 48
                                  567999999999***************9998776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.2e-05     0.059       5      41 ..      17      54 ..      13      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.2e-05
                        HTH_28  5 iikllaaGh.svreaArelgisrrtvyrWikryeegGi 41
                                   i+ll++ + s r +A+e+++s+ t+   + r+ ++G+
  gi|70607324|ref|YP_256194.1| 17 LIELLKDSRiSLRRLAEEMNVSPATLHNRLMRLVQEGV 54
                                  5778888899****************999999999886 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.071      10      42 ..      24      55 ..      14      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                        HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegGla 42
                                      + +++A+ +++s+ t  + l+r +++G+ 
  gi|70607324|ref|YP_256194.1| 24 SRI-SLRRLAEEMNVSPATLHNRLMRLVQEGVV 55
                                  344.599************************64 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00012     0.076      12      36 ..      25      49 ..      17      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                  TT-HHHHHHHHTS-HHHHHHHHHHH CS
                        HTH_30 12 ggnisatAkaLhvHrnTlryRLrri 36
                                    ++++ A++++v++ Tl++RL r+
  gi|70607324|ref|YP_256194.1| 25 RISLRRLAEEMNVSPATLHNRLMRL 49
                                  56899*****************996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00016     0.099      20      52 ..      24      56 ..       6      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis 52
                                   +++ + lA+ +++++ t+   l +L +eg+++
  gi|70607324|ref|YP_256194.1| 24 SRISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  4789999************************98 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00021      0.13      20      54 ..      15      49 ..       7      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00021
                                  HHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH CS
                           Mga 20 qllkflfeeeevsieelaqelyiSestlkrkikel 54
                                  +ll  l+++ ++s+ +la+e+ +S +tl + + +l
  gi|70607324|ref|YP_256194.1| 15 KLLIELLKDSRISLRRLAEEMNVSPATLHNRLMRL 49
                                  79999***********************9988776 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.17      27      57 ..      27      56 ..      26      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                  s r +a++++++ p++ +++L++L + G+++
  gi|70607324|ref|YP_256194.1| 27 SLRRLAEEMNVS-PATLHNRLMRLVQEGVVK 56
                                  7899******96.***************985 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00059      0.38      12      38 ..      15      42 ..       4      46 .. 0.89
   2 ?   -1.8   0.0       5.3   3.4e+03      12      21 ..      44      53 ..      43      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00059
                                  GGGGSSTTTT.--STTTSSSS---SSSS CS
                         HTH_7 12 nrvvkLleeG.isiskIAkevnisRsTv 38
                                    +++Ll++  is + +A+e n+s++T+
  gi|70607324|ref|YP_256194.1| 15 KLLIELLKDSrISLRRLAEEMNVSPATL 42
                                  57899999999****************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                                  GGGGSSTTTT CS
                         HTH_7 12 nrvvkLleeG 21
                                  nr+ +L++eG
  gi|70607324|ref|YP_256194.1| 44 NRLMRLVQEG 53
                                  8999****99 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00046      0.29      22      58 ..      20      56 ..      10      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                                  HHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                         HTH_9 22 LlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                  Ll+ +r +lr l+++ ++s+   ++ L+ L+q + V+
  gi|70607324|ref|YP_256194.1| 20 LLKDSRISLRRLAEEMNVSPATLHNRLMRLVQEGVVK 56
                                  999*****************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 993.00
//
Query:       gi|70607325|ref|YP_256195.1|  [L=203]
Description: multiple antibiotic resistance protein marC [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-30  105.7  14.4    2.6e-30  105.4  14.4    1.1  1  MarC             MarC family integral membrane protein
  ------ inclusion threshold ------
       0.22   12.0   0.1       0.22   12.0   0.1    1.9  2  Phage_holin_3_1  Phage holin family (Lysis protein S)
       0.77   10.1   9.6      0.074   13.4   1.0    2.3  2  DUF4233          Protein of unknown function (DUF4233)
        3.4    7.1   5.5        3.7    7.0   0.6    2.4  3  DUF3087          Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4  14.4   5.7e-34   2.6e-30       4     201 ..       9     199 ..       6     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 5.7e-34
                          MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkri.....alkasilallillvfllfGelilklfgisidalkiaGgil 79 
                                   i   +v L+aii+p++ +p +l++ ee + + ++++     + k +i  l++l++f l+G+ +l+++g+s++al+iaGg+l
  gi|70607325|ref|YP_256195.1|   9 IATIVVKLFAIIDPFSVLPFLLAIYEEANRDSQEKVswnymINKITIAILILLTLFSLIGRPLLDFLGLSAQALQIAGGVL 89 
                                   6678999**********************99999872222145666777788899************************** PP

                          MarC  80 lfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitlli 160
                                   l+  +id + + q+  +  +s         e +v+P+A+Pl+ GPg++t++++l+  ++     + +v++  +++l+++l+
  gi|70607325|ref|YP_256195.1|  90 LVYLGIDTMGGFQQL-RFIRSL-------REAIVTPIATPLLVGPGTMTALISLSVDYNP----LELVISSGIVTLLVYLS 158
                                   ***********9994.333333.......4579*************************99....5778888889999**** PP

                          MarC 161 lllsslilrllgktginaleRlmGllLvalavqlivdGike 201
                                   ll+ + +++ lg+tg  a  R ++++++a +vqli+ Gi++
  gi|70607325|ref|YP_256195.1| 159 LLSGPYLVKILGQTGTVAAGRFTAIIIAAFGVQLILSGISQ 199
                                   ***************************************87 PP

>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.9e-05      0.22      53      91 ..      62     101 ..      38     109 .. 0.83
   2 ?   -1.9   0.2         1   4.5e+03      73      86 ..     178     191 ..     145     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
               Phage_holin_3_1  53 gllalavrsllellglpaslavvigg.liGflGvekirel 91 
                                    l++l  r+ll++lgl+a++ +++gg l  +lG++++  +
  gi|70607325|ref|YP_256195.1|  62 TLFSLIGRPLLDFLGLSAQALQIAGGvLLVYLGIDTMGGF 101
                                   689999***********9998888761679*****98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
               Phage_holin_3_1  73 avviggliGflGve 86 
                                     +++++i  +Gv+
  gi|70607325|ref|YP_256195.1| 178 GRFTAIIIAAFGVQ 191
                                   34455555555555 PP

>> DUF4233  Protein of unknown function (DUF4233)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.0   1.6e-05     0.074      15      76 ..      28      92 ..       5     101 .. 0.79
   2 ?    1.1   2.0      0.11     5e+02      11      81 ..     112     189 ..     110     195 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                       DUF4233 15 vlLallvaiglrdtepatvlsvgg....vlavallllagllrrpwglalglvlQvlliaagfvvpa 76
                                  +lLa+  +   rd++ ++ +++++    +++++ll l  l++rp    lgl +Q+l ia g+++  
  gi|70607325|ref|YP_256195.1| 28 FLLAIYEE-ANRDSQEKVSWNYMInkitIAILILLTLFSLIGRPLLDFLGLSAQALQIAGGVLLVY 92
                                  45555555.667788999999999998778888888999*******************99988764 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                       DUF4233  11 EaivvlLallv.........aiglrdtepatvlsvgg.vlavallllagllrrpwglalglvlQvlliaagfvvp.amfvv 80 
                                   Eaiv   a++           i l +++ +  l +++   +v+ll+   ll+  + + ++++ Q  ++aag ++  ++++ 
  gi|70607325|ref|YP_256195.1| 112 EAIVTPIATPLlvgpgtmtaLISL-SVDYN-PLELVIsSGIVTLLVYLSLLS--GPYLVKILGQTGTVAAGRFTAiIIAAF 188
                                   677777777773333332221111.11122.222222344455555555554..557888888888888888777555444 PP

                       DUF4233  81 g 81 
                                   g
  gi|70607325|ref|YP_256195.1| 189 G 189
                                   4 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.5   6.7e+03      30      42 ..       6      18 ..       5      22 .. 0.77
   2 ?    2.5   0.1      0.02        91       8      42 ..      43      76 ..      39     110 .. 0.73
   3 ?    7.0   0.6   0.00083       3.7      19      70 ..     147     197 ..     138     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                       DUF3087 30 sllfstllialfg 42
                                  +++++t++++lf+
  gi|70607325|ref|YP_256195.1|  6 AITIATIVVKLFA 18
                                  6788888888886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.02
                       DUF3087  8 kerYrkklnrvivalvallavlsllfstllialfg 42
                                  k  +   +n++++a+++ll+++sl+ +  l+ ++g
  gi|70607325|ref|YP_256195.1| 43 KVSWNYMINKITIAILILLTLFSLI-GRPLLDFLG 76
                                  6666677899*********999985.555555555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.00083
                       DUF3087  19 ivalvallavlsllfstllialfgeeevsnfhlnllGvvlalvltaailrkl 70 
                                     ++v+ll+ lsll +  l++++g++++      ++ +++a++ + +il+ +
  gi|70607325|ref|YP_256195.1| 147 SSGIVTLLVYLSLLSGPYLVKILGQTGT-VAAGRFTAIIIAAFGVQLILSGI 197
                                   567999******************8777.44555666677777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1366.39
//
Query:       gi|70607326|ref|YP_256196.1|  [L=102]
Description: hypothetical protein Saci_1590 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00055   18.9   2.3     0.0006   18.8   2.3    1.1  1  Spc7          Spc7 kinetochore protein
    0.00075   17.9   4.5    0.00084   17.7   4.5    1.1  1  Cast          RIM-binding protein of the cytomatrix active zo
  ------ inclusion threshold ------
      0.011   16.4   1.5      0.019   15.7   1.2    1.5  1  Occludin_ELL  Occludin homology domain
       0.04   13.7   0.8      0.058   13.2   0.7    1.3  1  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
      0.089   12.5   0.0      0.089   12.5   0.0    1.1  1  YfiO          Outer membrane lipoprotein
       0.09   12.3   1.7       0.11   12.0   1.7    1.1  1  PP_M1         Phosphoprotein


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.3     2e-07    0.0006     170     238 ..       9      77 ..       4      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-07
                          Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                   p+ ee  +++++e+e++    e  e id+  L e+ ++l++l+ +i+e k+++++++ ++ ++ + +++
  gi|70607326|ref|YP_256196.1|   9 PKSEEDLDTIRREIEDEHHHDEHGEHIDQHMLDEILSALQQLQIKINETKDDTERCKGEISRIYSILSK 77 
                                   8899999****************************************************9999887766 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.5   2.8e-07   0.00084     540     608 ..      27      97 ..       2     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
                          Cast 540 lkkaqeaeeaeranpeitdriklLekevarkkeessksqaeveRLleiLre..venekndkdkkiaelesl 608
                                   ++  +    ++++ +ei + +++L+  ++ +k++++++++e+ R+  iL +  v +  +dkd++i+ l +l
  gi|70607326|ref|YP_256196.1|  27 HHDEHGEHIDQHMLDEILSALQQLQIKINETKDDTERCKGEISRIYSILSKlvVATFTEDKDQRIKILREL 97 
                                   234455566778999**********************************9833456789999999887655 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   1.2   6.5e-06     0.019      19      92 ..      29     101 ..      16     102 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.5e-06
                  Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshi 92 
                                   +e+ e  + +++l+e+ + +++L+ +++e k+++++ k  +++i++ ++kl   +   +k +r++ L+e Ls +
  gi|70607326|ref|YP_256196.1|  29 DEHGEHID-QHMLDEILSALQQLQIKINETKDDTERCKGEISRIYSILSKLVVATFTEDKDQRIKILRELLSQL 101
                                   55555554.4579**************************************88877788889******999876 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7     2e-05     0.058      93     154 ..      33      95 ..      25     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                  Bacillus_HBL  93 eavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklklak.dsknFktdvdeltsila 154
                                   e +d++  +e+l++l++Lq +i++ +  +++  +e+++  + l k  +++F++d+d+  +il 
  gi|70607326|ref|YP_256196.1|  33 EHIDQHMLDEILSALQQLQIKINETKDDTERCKGEISRIYSILSKlVVATFTEDKDQRIKILR 95 
                                   78999999******************************999998724799*******999995 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05     0.089      86     144 ..      43     102 .]      10     102 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                   HHHHHHHHSHSC.TTTS-THHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHHHHH CS
                          YfiO  86 glsalaqarell.rskrdpesarqafedfkklvekyPdseYaadakkrltelrerLArhE 144
                                    lsal+q +  + ++k d+e  +  +++++ +++k    ++++d  +r++ lre+L + E
  gi|70607326|ref|YP_256196.1|  43 ILSALQQLQIKInETKDDTERCKGEISRIYSILSKLVVATFTEDKDQRIKILRELLSQLE 102
                                   5677777776554778888999999*******************************9876 PP

>> PP_M1  Phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   3.6e-05      0.11      20      76 ..      10      67 ..       2      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                  XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         PP_M1 20 maeetvdlinrniednqahl.qGepievdslpedlsrlriedkkrkqkeeeaerkegk 76
                                   +ee  d i r+ied+  h   Ge i+ + l e ls l+  + k +++++++er +g+
  gi|70607326|ref|YP_256196.1| 10 KSEEDLDTIRREIEDEHHHDeHGEHIDQHMLDEILSALQQLQIKINETKDDTERCKGE 67
                                  689**************99637***********9999988888877777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1861  (0.103798); expected 358.6 (0.02)
Passed bias filter:                      873  (0.0486921); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 707.52
//
Query:       gi|70607327|ref|YP_256197.1|  [L=103]
Description: hypothetical protein Saci_1591 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 735.99
//
Query:       gi|70607328|ref|YP_256198.1|  [L=291]
Description: dihydroorotate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-45  154.7   0.5    3.9e-45  154.3   0.5    1.1  1  DHO_dh    Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
       0.15   11.0   0.1       0.27   10.2   0.1    1.4  1  IMPDH     IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.5   4.4e-49   3.9e-45       5     294 ..       3     273 ..       1     274 [. 0.86

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 4.4e-49
                                   EETTEEESSSEEE-TTSSTTSSSHHHHH..CTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHH CS
                        DHO_dh   5 kvlglkfknpiglAaGfdkegeeilkll..klgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlek 83 
                                   +v+g++f++pi++A+G+   ++e+ + +  k + +ai+ ++ t +p e +  P+ +++  +   lN++Gl n+G++ + + 
  gi|70607328|ref|YP_256198.1|   3 QVAGVNFEDPIVIASGIVPPTKEYMQNVceKYEPSAITSKTLTYSPLEPHRSPTFVKISDN-CYLNAIGLGNPGIQIL-RD 81 
                                   789******************9987654225559**********************99887.************9754.33 PP

                                   HHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHHHHHHHHHHSSE CS
                        DHO_dh  84 llkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkaillkvvkevskvp 164
                                   l     e    ++   ++s+ +++   v++y+  v ki+ +  ++elNvSsPn +g  +  ++    ++++k vk + k+p
  gi|70607328|ref|YP_256198.1|  82 LG----E----IKCKLIISIGGSN---VNEYIDAVSKINDIPVMIELNVSSPNRRGFGE--SNLTYVEEIVKNVKSIVKKP 149
                                   33....3....2356889999999...**************************996543..233455678999999***** PP

                                   EEEEE-SSSSHHHHHHHHHHHH.HHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTTT. CS
                        DHO_dh 165 vlvKlaPdltdeekkdiadvll.elkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlkke 244
                                   v+vKl P   ++++++  ++ + +++l+ i+    t++++ id++ +k++   +tGG+sGk +  +a++vi+++ k+ +  
  gi|70607328|ref|YP_256198.1| 150 VFVKLGP-WDNIVEIAGRALSAgADGLTLIN----TLKGMLIDVEDFKPILSYGTGGISGKCIHALAVRVIHDVFKEYE-- 223
                                   *******.55554444444444477777777....899999*************************************9.. PP

                                   S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHH CS
                        DHO_dh 245 ipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleel 294
                                     iIgvGG++  +Da+e i  GA lv ++t lv +g  ++++i +++   
  gi|70607328|ref|YP_256198.1| 224 PEIIGVGGVFDWRDAIELISVGAKLVGLGTVLVEKGFDVIREIREGIGTY 273
                                   568*****************************************999765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1     3e-05      0.27     194     264 ..     210     288 ..     202     291 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3e-05
                                   HHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTT........BTTSSSEEEEETTEEEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 194 tAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllag........teEspgeviliegrkyKeyrGmg 264
                                    Av  + ++ k+++ ++i  GG+   +d +  +++Ga+ v lG +l          ++E  g ++  +g k+ e rG+g
  gi|70607328|ref|YP_256198.1| 210 LAVRVIHDVFKEYEPEIIGVGGVFDWRDAIELISVGAKLVGLGTVLVEkgfdvireIREGIGTYLEEKGLKVEEIRGIG 288
                                   5788889999*********************************998632222222256788888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2077.65
//
Query:       gi|70607329|ref|YP_256199.1|  [L=389]
Description: dihydroorotase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-14   52.8   0.0    4.2e-08   32.9   0.0    2.1  2  Amidohydro_1  Amidohydrolase family
    0.00014   21.5   0.0     0.0018   17.8   0.0    2.0  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-07    0.0013       2      72 ..      43     102 ..      42     161 .. 0.80
   2 !   32.9   0.0   4.6e-12   4.2e-08     239     343 ..     246     367 ..     163     368 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-07
                                   EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..HHHHHHHHHHT CS
                  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..giealleaaee 72 
                                   +lP+ +D+HvH++               +  ++e++++++++a+ +G++ + dm++t ++    e+++e ++e
  gi|70607329|ref|YP_256199.1|  43 ILPASVDLHVHVR-------------GAQLSYKETVATATSEAVYGGVGVIVDMPNTVPYinTPERIKERLRE 102
                                   89**********9.............456689************************86667655555555544 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 4.6e-12
                                   TSC..EEEEEECT.................TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT- CS
                  Amidohydro_1 239 Gvk..vglgtDga.................asgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalgl 299
                                   G++    +++D+a                               ++  + +  y+   +g +s+ +a+++ + n+ ++l++
  gi|70607329|ref|YP_256199.1| 246 GLFevDCIASDHAphskeekrmnfdlcppgI------------AGVSFSTPYIYSlMFKGLISIDRAVSLLSGNPSRILNI 314
                                   5556667778877777775543333333333............444444555555555999******************** PP

                                   TTTSSSS-TTSB--EEEECC....CT.......CGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 300 ddkvGsievGkdADlvvvdl....di.......laafvglkkdgnvkkvivkGkl 343
                                      +G+i++G++A+++v++     +         +++ g + d +v++viv Gkl
  gi|70607329|ref|YP_256199.1| 315 --PTGKIKEGYRANFTVIKRenwrYTtkfskvtETPMDGFSLDAKVTNVIVEGKL 367
                                   ..8***************887665116789999********************97 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.019   1.7e+02       9      28 ..      42      61 ..      39      78 .. 0.75
   2 !   17.8   0.0     2e-07    0.0018     407     471 ..     294     367 ..     280     369 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.019
                  Amidohydro_3  9 lvlPGFvDsHtHlagggvnl 28
                                  l lP+ vD H H+ g+++ +
  gi|70607329|ref|YP_256199.1| 42 LILPASVDLHVHVRGAQLSY 61
                                  679999******88777544 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2e-07
                  Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear...........vrltvvdGrv 471
                                    +s+  a+ l++ +p ++l+ ++  G +++G++A+++v+ ++  + +++  + ++           v  ++v+G+ 
  gi|70607329|ref|YP_256199.1| 294 LISIDRAVSLLSGNPSRILNIPT--GKIKEGYRANFTVIKRENWRYTTKFSKVTEtpmdgfsldakVTNVIVEGKL 367
                                   68999******************..**************9555554443222222445556666668888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2677.72
//
Query:       gi|70607330|ref|YP_256200.1|  [L=207]
Description: hypothetical protein Saci_1594 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0063   16.3   3.9      0.013   15.3   3.9    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.9   7.4e-07     0.013       3      40 ..     169     198 ..     168     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-07
                                   --SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCC CS
               DHODB_Fe-S_bind   3 rMaCGvGaClgCvvktkggdggeykrvCkdGPvFdade 40 
                                    M C +G+C+ C  k         + +C++GP  + ++
  gi|70607330|ref|YP_256200.1| 169 KMNCTLGVCGECEYKG--------VIACVEGPFVQVSR 198
                                   5***********9999........789*****987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1364.93
//
Query:       gi|70607331|ref|YP_256201.1|  [L=164]
Description: aspartate carbamoyltransferase regulatory subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-33  114.1   4.6    5.4e-33  113.1   4.6    1.5  2  PyrI          Aspartate carbamoyltransferase regulatory chain
    9.2e-16   57.5   3.0    1.7e-15   56.7   3.0    1.4  1  PyrI_C        Aspartate carbamoyltransferase regulatory chain
  ------ inclusion threshold ------
       0.71    9.4   4.0        2.4    7.8   4.0    2.0  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   4.6     9e-37   5.4e-33       1      93 [.      10     101 ..      10     102 .. 0.97
   2 ?   -2.9   0.0       1.4   8.2e+03      52      68 ..     108     125 ..     105     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 9e-37
                                   X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEE CS
                          PyrI   1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatini 81 
                                   l v+ki+nG+ViDHI+ag+a+ vl++L++++ +++ ++a+++nv+skk+gkKdi+kie+ke+s++e++ ++liap+atini
  gi|70607331|ref|YP_256201.1|  10 LMVSKIKNGTVIDHIPAGRAFAVLNVLGIKG-HEGFRIALVINVDSKKMGKKDIVKIEDKEISDTEANLITLIAPTATINI 89 
                                   579***************************8.8888********************************************* PP

                                   EETTEEEEEE-- CS
                          PyrI  82 IkdgevveKkkv 93 
                                   ++++evv+K+k+
  gi|70607331|ref|YP_256201.1|  90 VREYEVVKKTKL 101
                                   *********998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                                   EEEEEEET---.-HHHHH CS
                          PyrI  52 Kdiikiegkel.seeeld 68 
                                   K+i+k ++ +  ++++++
  gi|70607331|ref|YP_256201.1| 108 KGILKCPNPYCiTSNDVE 125
                                   899998886654555555 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   3.0   2.8e-19   1.7e-15       2      48 .]     107     154 ..     106     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2.8e-19
                                   EESSS--S-TTBGGGTT.S-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                        PyrI_C   2 iegvlkCpNpnCItnne.pveskFkvedkekvklkCkYCekeiseeei 48 
                                   ++g+lkCpNp CIt+n  +  ++Fk+  ++++k++C+YCe++i+e+ei
  gi|70607331|ref|YP_256201.1| 107 VKGILKCPNPYCITSNDvEAIPTFKTLTEKPLKMRCEYCETIIDENEI 154
                                   89**************4466689***********************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.0   0.00039       2.4      18      37 ..     138     157 ..     111     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00039
                                   TCEEESSSSBEEEECCCCCC CS
                  TF_Zn_Ribbon  18 gelvCtdCGlVlednsideg 37 
                                     ++C+ C++++++n i++ 
  gi|70607331|ref|YP_256201.1| 138 LKMRCEYCETIIDENEIMSQ 157
                                   5689*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1152.69
//
Query:       gi|70607332|ref|YP_256202.1|  [L=299]
Description: aspartate carbamoyltransferase catalytic subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-41  140.8   0.0    6.4e-41  139.8   0.0    1.5  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    5.6e-25   88.3   0.0    9.7e-25   87.5   0.0    1.4  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.0   7.2e-45   6.4e-41       1     147 [.       2     141 ..       2     142 .. 0.92
   2 ?   -3.0   0.0      0.74   6.6e+03      18      49 ..     244     282 ..     235     284 .. 0.60

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 7.2e-45
                                   S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTT CS
                      OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlss 81 
                                   +h++s  ++s++e+e ++ l +++ ++ +  +++k+l+gkt+ + F+epStRT +Sf+ A+ +lGg+v+ +s +   +++s
  gi|70607332|ref|YP_256202.1|   2 KHIISAYNFSRDELEDIFALTDKYSKNLN--DTRKILSGKTISIAFFEPSTRTYLSFQKAIINLGGDVIGFSGE---ESTS 77 
                                   79***********************9986..999**************************************55...4677 PP

                                   GGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                      OTCace_N  82 vskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                   v+kg  E+l+Dt+r+l++y+d+iv+Rh+  ga   +   + +++pviNagdg++eHPtQa +D++ti 
  gi|70607332|ref|YP_256202.1|  78 VAKG--ENLADTIRMLNNYSDGIVMRHKydGA--SRFASEISDIPVINAGDGKHEHPTQAVIDIYTIN 141
                                   8999..**********************8666..34345668************************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.74
                                   HHHHHHHHHHHHT.......TT-STTTTT-EEEEEESS- CS
                      OTCace_N  18 ldlaaelkekvkk.......ekkekllkgktlallFeep 49 
                                   ldla+++k+++         ++ ++++++ t a  Fe+ 
  gi|70607332|ref|YP_256202.1| 244 LDLANKMKKDSIIlhplprvNEIDRKVDKTTKAKYFEQA 282
                                   567777776543355555555555555555556666555 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   1.1e-28   9.7e-25       2     155 ..     149     294 ..     148     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.1e-28
                                   C.EEEEESS.TTSHHHHHHHHHHHHCT-E.EEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                        OTCace   2 glkiafvGd.kknnvanslikllarlgmd.vvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                   gl +a++Gd k+ +++nsl+++l+r+  + v+l++P+ l+  ke+l+e++         ++  e++ e+++++Dv+y +++
  gi|70607332|ref|YP_256202.1| 149 GLVFALLGDlKYARTVNSLLRILTRFRPKlVYLISPQLLRARKEILDELNY-------PVKEVENPFEVINEVDVLYVTRI 222
                                   78899************************899999999********88866.......4667789999************* PP

                                   SETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                        OTCace  81 vsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                   +     ker+    +++k+k+ y v  +l +++kkd i+lH+LP  r +E++++V++  ++ +feqa++++ +++++l 
  gi|70607332|ref|YP_256202.1| 223 Q-----KERFvdeMEYEKIKGsYIVSLDLANKMKKDSIILHPLP--RVNEIDRKVDKTTKAKYFEQASYGVPVRMSILT 294
                                   *.....67766669999***99**********************..*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2356.32
//
Query:       gi|70607333|ref|YP_256203.1|  [L=197]
Description: orotate phosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-22   78.6   0.8    5.2e-22   78.1   0.8    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00032   20.2   0.0    0.00043   19.8   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.042   13.4   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.8   8.7e-26   5.2e-22      26     135 ..      54     153 ..      33     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 8.7e-26
                                   --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHH CS
                  Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaa 106
                                   ++ + d+++g+ +gGvpfa+ +a +L+ p+ y+r++k+ +++              ++d++gkkV++VDD+ +tGg++l+a
  gi|70607333|ref|YP_256203.1|  54 KGINFDMILGVVTGGVPFASFIACKLNKPMGYIRAEKKGHGTERLL----------EADVDGKKVIVVDDVATTGGSILKA 124
                                   5689**********************************99987765..........79*********************** PP

                                   HHHHHCC-BSEEEEEEEEE-HHHHHHHHH CS
                  Pribosyltran 107 lelLkekgpeevriavlvdkpateeevdk 135
                                   +e ++++g ++ ++ v+vd+ ++++e+  
  gi|70607333|ref|YP_256203.1| 125 VEEVRKAGGKVEHALVIVDREEGAFEKLE 153
                                   ***********************999865 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.2e-08   0.00043     115     157 ..      99     141 ..      77     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.2e-08
                       UPRTase 115 LPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvl 157
                                   L ++++ ++v+++D v  TGgs+ +a++ ++++g ++e+ lv+
  gi|70607333|ref|YP_256203.1|  99 LEADVDGKKVIVVDDVATTGGSILKAVEEVRKAGGKVEHALVI 141
                                   67888999*************************9999876654 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-06     0.042     120     158 ..     104     141 ..      87     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-06
                      PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr.kryvvvsl 158
                                   + k++++vDD ++tG ++l+ +++++++  + ++  v  +
  gi|70607333|ref|YP_256203.1| 104 DGKKVIVVDDVATTGGSILKAVEEVRKAGGKvEHALV--I 141
                                   34789********************998766333322..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1473.32
//
Query:       gi|70607334|ref|YP_256204.1|  [L=219]
Description: orotidine 5'-phosphate decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-20   71.9   0.0    7.7e-20   71.5   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   4.3e-24   7.7e-20      16     221 ..      16     199 ..       5     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 4.3e-24
                                   HHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT.SEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEEGT CS
                     OMPdecase  16 leladkvgpsivvlKthydlvegwgfegtgaklaalarkhg.flifeDrKfaDIGntvekqatagsarikewadivtvhav 95 
                                   + l+++++ +i  +K+ y  + + g        ++ +rk +  +i+ D+K+aDI +t+  +++    + ++ ad  + h +
  gi|70607334|ref|YP_256204.1|  16 INLLKDFTTHINKIKISYVTLLEGG-----LGYLKDIRKLDwDEIIFDLKLADIDSTMISIVK----NLEQFADSYISHSF 87 
                                   5678889999999999999999999.....99*********99*******************8....799*********** PP

                                   GH.HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCCHTH...HHHHH.TTCS CS
                     OMPdecase  96 aG.kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqetln...ateed.addf 171
                                    G ++++ +l++++++ + +gl+++  ms+kg+ ++   +y + +v+  +  k      G+v+++t++   ++ ++ +++ 
  gi|70607334|ref|YP_256204.1|  88 IGyEGALDKLKNYLDSRN-KGLYLVLSMSHKGWNDDYY-KYLKSIVNVTKP-K------GIVVGATKPlmlKLARSdFPNT 159
                                   **999*********9996.9*************99999.777777766544.5......8999999999774444469*** PP

                                   CEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHH CS
                     OMPdecase 172 ihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpvee 221
                                   i++ pg+g+         q  ++ ++i  +gad+ i+GR+I+ +g+p ++
  gi|70607334|ref|YP_256204.1| 160 IIISPGVGV---------QGAKIGEAIC-NGADYEIIGRSIYDSGEPLKT 199
                                   *******97.........4444566666.79**************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1491.37
//
Query:       gi|70607335|ref|YP_256205.1|  [L=218]
Description: hypothetical protein Saci_1599 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   12.9   0.4       0.13   12.3   0.4    1.5  1  Josephin  Josephin
       0.14   11.9   0.1       0.27   11.0   0.1    1.5  1  Prok-JAB  Prokaryotic homologs of the JAB domain


Domain annotation for each model (and alignments):
>> Josephin  Josephin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   1.5e-05      0.13      23     105 ..      15      95 ..      10     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                      Josephin  23 seLaeiAteldereralmtesesnsadettslskslkssqnvskqGnysieVlekaLerkglelvrvrnsenitkstssep 103
                                   +eLa i++ +d+ e+ + ++ e++++d ++  + s   +++v k Gny +  l +   +k ++ +r++ se  ++st++ +
  gi|70607335|ref|YP_256205.1|  15 EELARISEMIDKAEEIHEETGEVPTTDLVNLYTLSGYYESKVGK-GNYTYYHLYSVFAEKYVNFIRTTMSE-YARSTKETE 93 
                                   79************877777999**********99999988888.*******************9999766.466665544 PP

                      Josephin 104 ek 105
                                    +
  gi|70607335|ref|YP_256205.1|  94 IE 95 
                                   44 PP

>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     3e-05      0.27      70      95 ..     123     147 ..     119     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3e-05
                      Prok-JAB  70 vvgiwHSHpggsarPSetDrrdaaal 95 
                                    ++  H+Hpg   ++S +D+++a  l
  gi|70607335|ref|YP_256205.1| 123 ALASTHTHPGIC-FFSHKDLETADFL 147
                                   57889*******.*******999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1437.80
//
Query:       gi|70607336|ref|YP_256206.1|  [L=336]
Description: hypothetical protein Saci_1600 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-19   69.6   6.7    2.2e-16   60.1   0.4    2.7  3  PhoU            PhoU domain
    1.6e-10   40.7   0.1    5.5e-10   38.9   0.0    2.0  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.055   13.6   0.0    2.1  2  DUF192          Uncharacterized ACR, COG1430
      0.083   12.9   0.4       0.16   12.1   0.4    1.5  1  DUF600          Protein of unknown function, DUF600


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.7   1.2e+04      25      46 ..     104     129 ..      97     134 .. 0.51
   2 !   60.1   0.4   4.8e-20   2.2e-16       3      88 ..     146     234 ..     144     235 .. 0.91
   3 !   12.8   0.2   2.8e-05      0.13       8      88 ..     253     326 ..     249     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.7
                                   HHHHHHHHH....HHHHHHHHHHHHH CS
                          PhoU  25 elarevier....ddeidrlekeier 46 
                                   e ++e++++     + id+  ++i+ 
  gi|70607336|ref|YP_256206.1| 104 EKIKELVRNrllgAEVIDESSNNISI 129
                                   44444433334445666666555555 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 4.8e-20
                                   HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH...HHHHHHHHHHHHHHHHHHHH CS
                          PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae...dlrellsllriardlERigD 80 
                                   r ++i+++m++dal  l ++d+el +e+++rdd++dr+++  +r+l   +   + l+e   +l +l+++ +ia+++ER++D
  gi|70607336|ref|YP_256206.1| 146 RAFNISYNMFRDALNGLQKGDKELSKEIRNRDDDVDRFFFYTIRQLSLSVEYPDILDEekfNLTQLTDISSIAKSIERVSD 226
                                   7899*****************************************77777555556667899******************* PP

                                   HHHHHHHH CS
                          PhoU  81 havniaer 88 
                                   ha +iae 
  gi|70607336|ref|YP_256206.1| 227 HAIRIAEQ 234
                                   ******97 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   8 veemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaer 88 
                                   v e  + + +a++++d++ a +vi++  e  +   ++++ ++   +  +  +       s l +  ++ R+ +++ +iae 
  gi|70607336|ref|YP_256206.1| 253 VIELYKTSFSAFSNRDRKRAHDVINKGFETLDTNSKLSENVIMNFHSLKDDS-------STLIVLDSIRRVTRYSMDIAEA 326
                                   67788999****************9988888888888888666664444333.......368899999*******999997 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.2e-13   5.5e-10       2      43 ..      12      54 ..      11      57 .. 0.94
   2 ?   -1.6   0.0      0.64   2.9e+03      15      25 ..     155     166 ..     155     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.2e-13
                                  EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHH CS
                MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplks 43
                                  ++G+++++++Pk +++++ +++Gdeve+ +d   ++il+p + 
  gi|70607336|ref|YP_256206.1| 12 TGGSTYIISLPKGWVKQHSLKPGDEVEIAEDRQmRLILSPRAG 54
                                  89*************************************9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                                   CHHHC.CEECTC CS
                MazE_antitoxin  15 vrfel.gireGd 25 
                                   +r++l g+++Gd
  gi|70607336|ref|YP_256206.1| 155 FRDALnGLQKGD 166
                                   799999*****9 PP

>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.2e-05     0.055      71      96 .]      14      39 ..       2      39 .. 0.82
   2 ?   -1.5   0.0      0.64   2.8e+03      17      44 ..     295     323 ..     284     331 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                  -ECEEEEEETTHHHHHT--TT-EEE. CS
                        DUF192 71 svryvLElpaGaakklgikpGdrlei 96
                                     y++ lp+G++k++ +kpGd++ei
  gi|70607336|ref|YP_256206.1| 14 GSTYIISLPKGWVKQHSLKPGDEVEI 39
                                  4679*******************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.64
                                   TT-----TTEEEEEEECCEEE.EEE--TT CS
                        DUF192  17 mgreslpedegmlfvfdkere.hsfwMkn 44 
                                   m+ +sl++d+  l+v+d+ r+   + M  
  gi|70607336|ref|YP_256206.1| 295 MNFHSLKDDSSTLIVLDSIRRvTRYSMDI 323
                                   77788899999999888866424444444 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   3.5e-05      0.16      27     112 ..     117     199 ..      98     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                   EEE-TT.--EEEEEEEEETTT-EEEGGGGGGT--S-HHHHHHHHHHHHHHHHHHHHHHHHHHSS--SEEEEEEETTS-EEE CS
                        DUF600  27 aevled.sgevyFyylkkesekliysheipekynvseeeykkllkeLyelikeLreefkkeeqeaWtnltltlkksGklki 106
                                   aev+++ s+++   +l +e+ +l  +  + + +n+s + + + l+ L++  keL +e++++++++   +  t+++   l++
  gi|70607336|ref|YP_256206.1| 117 AEVIDEsSNNISIQFLVNEK-DLSITKSLGRAFNISYNMFRDALNGLQKGDKELSKEIRNRDDDVDRFFFYTIRQL-SLSV 195
                                   78888747777777777776.5666667889******************************999988887777777.6666 PP

                                   EEE--- CS
                        DUF600 107 eydydd 112
                                   ey   d
  gi|70607336|ref|YP_256206.1| 196 EY--PD 199
                                   65..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2151.22
//
Query:       gi|70607337|ref|YP_256207.1|  [L=169]
Description: hypothetical protein Saci_1601 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   17.4   0.1      0.004   16.7   0.1    1.3  1  DUF2106   Predicted membrane protein (DUF2106)


Domain annotation for each model (and alignments):
>> DUF2106  Predicted membrane protein (DUF2106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.2e-07     0.004      84     126 ..      85     125 ..      80     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-07
                       DUF2106  84 alGlvtayltPlsellaettlylGttivssPGGiideilyytr 126
                                   +lG v +yl+Pl e+l+e    lG++i  sP  iidei+   r
  gi|70607337|ref|YP_256207.1|  85 ILGNVVTYLSPLVEALNELKGQLGASIEFSP--IIDEIIETIR 125
                                   68***************************99..9****97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1357.08
//
Query:       gi|70607338|ref|YP_256208.1|  [L=134]
Description: hypothetical protein Saci_1602 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1024.02
//
Query:       gi|70607339|ref|YP_256209.1|  [L=210]
Description: hypothetical protein Saci_1603 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  106.3   0.0    2.5e-30  105.4   0.0    1.3  1  TYW3      Methyltransferase TYW3


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   1.4e-34   2.5e-30       3     209 ..       8     182 ..       6     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.4e-34
                                   HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEES CS
                          TYW3   3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlfvsH 83 
                                   Kak++e++    +++++ G++D++i ++++++ s+++ +T SSCsGR+s++            +ak  +++++++++f+ H
  gi|70607339|ref|YP_256209.1|   8 KAKAWERI----NRDKEIGYLDPDIYDILKAFFSRQKSYTQSSCSGRISII------------DAKLPWERRDSTVVFKDH 72 
                                   77778887....88899**********************************............899*************** PP

                                   S---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEEE CS
                          TYW3  84 dpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslkkkkviva 164
                                    +++ e+l++ l +                 r +++ ++ +I+Hv ++++e+A ++l++A++ Gf++SGi s + k ++v+
  gi|70607339|ref|YP_256209.1|  73 LKFSVEDLYDVLDKGI--------------VRRLWLIVQGPIIHVYTKDMEEALNVLKLARDVGFKHSGILSFNDKGILVE 139
                                   ************9997..............799************************************************ PP

                                   EE---EEEEEEE.STS---HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TYW3 165 irsglklevpig.kellvseeylkllvklanerfeenkkrierfee 209
                                   +r+g+k+  ++  +     ee  k lv+++ e +++ k++++++++
  gi|70607339|ref|YP_256209.1| 140 LRTGVKMVHLLKpN---LPEEEAKHLVEVSLEILNKGKEKLNNLRN 182
                                   ***********955...89999*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1602.53
//
Query:       gi|70607340|ref|YP_256210.1|  [L=211]
Description: hypothetical protein Saci_1604 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-14   52.0   0.1    1.2e-13   51.2   0.1    1.4  1  Fer4_14       4Fe-4S single cluster domain
    1.4e-12   48.3   0.0    2.8e-12   47.3   0.0    1.6  1  Radical_SAM   Radical SAM superfamily
    1.1e-09   38.6   0.0    1.7e-09   38.1   0.0    1.2  1  Fer4_12       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.071   13.0   0.0       0.11   12.4   0.0    1.3  1  SIR2          Sir2 family
       0.11   12.0   0.0       0.16   11.6   0.0    1.2  1  NTP_transf_5  Uncharacterised nucleotidyltransferase
       0.21   11.7   0.1       0.57   10.4   0.0    1.7  2  Staufen_C     Staufen C-terminal domain


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.1     4e-17   1.2e-13       2      96 ..      25     107 ..      24     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 4e-17
                       Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                   fvrl+gC++ C +Cd+k +w++    ++ +el  q++   +k +++ +  ++tGGePL     +++++l ++lk+     +
  gi|70607340|ref|YP_256210.1|  25 FVRLAGCHMRCIWCDTKYSWHK----YDGKELSIQEI--ISKINVSVKTTTITGGEPL----LQDIIPLAEELKKLE--QR 93 
                                   9****************96655....55555555555..45556666778********....67*********9977..9* PP

                       Fer4_14  83 iwletngtleiele 96 
                                   i +et+gt++ + +
  gi|70607340|ref|YP_256210.1|  94 IVVETSGTIKPNQK 107
                                   *********96655 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   9.4e-16   2.8e-12       2     118 ..      26     127 ..      25     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 9.4e-16
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   v + gC++rC++C+++++    ++g++ls++ei+ ++  ++    vk+ +++ggepll++ ++ l+e+l+kl   + ri+v
  gi|70607340|ref|YP_256210.1|  26 VRLAGCHMRCIWCDTKYS-WHKYDGKELSIQEIISKI-NVS----VKTTTITGGEPLLQD-IIPLAEELKKL---EQRIVV 96 
                                   5789************96.777888888888888888.333....*************66.99********9...9***** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvl 118
                                   et+gt       ++l el  d++s++ +  +   ++
  gi|70607340|ref|YP_256210.1|  97 ETSGTIK---PNQKLMELV-DVFSVSPKLSNAG-YR 127
                                   *****95...445555555.6666666666655.55 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   5.6e-13   1.7e-09       2     129 ..      13     131 ..      12     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.6e-13
                       Fer4_12   2 nGeGvrl.....slfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvk 77 
                                   +GeG ++     +++++gC ++C  C  k  w    gke +   ++eii ++ + s++  t++GGEPll    +++++l++
  gi|70607340|ref|YP_256210.1|  13 QGEGEVIgtpsnFVRLAGCHMRCIWCDTKYSWHKYDGKELS---IQEIISKI-NVSVKTTTITGGEPLL----QDIIPLAE 85 
                                   788866555666999*****************999999998...67777777.789999**********....99****** PP

                       Fer4_12  78 evkeekpekdiwlytgytleelskkekeellkeidv.lvdGkfeesledeslr 129
                                   e+k+      +++++g++  +      ++l++ +dv  v+ k++++  + + +
  gi|70607340|ref|YP_256210.1|  86 ELKKLEQ-RIVVETSGTIKPN------QKLMELVDVfSVSPKLSNAGYRLKYN 131
                                   ****998.5789999987443......36888888658888888777666555 PP

>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.7e-05      0.11     104     177 .]      32     104 ..      23     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                                   EEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-SHHHHHHHHHHHH-SEEEEES--STSTT CS
                          SIR2 104 kakcvkcekkldkeelqeeieaekvpecekcgkllkpdvvfFGealpdklkkliekveeadlllviGtSlkVap 177
                                   +++c+ c++k++++++  +  +  ++  +k +  +k++ +  Ge l + +  l+e++++ +  +v+ tS +++p
  gi|70607340|ref|YP_256210.1|  32 HMRCIWCDTKYSWHKYDGKELSI-QEIISKINVSVKTTTITGGEPLLQDIIPLAEELKKLEQRIVVETSGTIKP 104
                                   579**********9888766655.45677778899**9999****************************99987 PP

>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.16     112     185 ..     120     207 ..     108     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                  NTP_transf_5 112 lLeelGyelesd.gsekhevyyre...............kkgveielhwrllppesprlepdfddlleerarpveiggksi 176
                                    L+++Gy+l++  +++++++yy+                 ++ +i++   ll+p   r+++++++ l+e a++v   g ++
  gi|70607340|ref|YP_256210.1| 120 KLSNAGYRLKYNfKDDDWATYYKFvivnpktdipevikfVEENRIDHRKVLLQP-DGRRNDYVNA-LKELADSVMEFGVQF 198
                                   599********87788899999989************9999999**********.6777878776.5678*********** PP

                  NTP_transf_5 177 lvlspedll 185
                                   +vl + +++
  gi|70607340|ref|YP_256210.1| 199 RVLPQLHRI 207
                                   **9987765 PP

>> Staufen_C  Staufen C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00019      0.57       6      57 ..      67     118 ..      62     129 .. 0.80
   2 ?   -2.2   0.0       1.5   4.6e+03      47      65 ..     184     203 ..     166     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                                   HHHHHH.HHHHHHS--HHHHHHH--S-----------SHHHHHHHHHHHH--- CS
                     Staufen_C   6 staaia.kellsegtsptaeallkatsssgvvptslvrPkqqLeylarvqgfq 57 
                                   +t +i   e l + + p ae l k +++ +v ++++++P+q+L  l  v  ++
  gi|70607340|ref|YP_256210.1|  67 TT-TITgGEPLLQDIIPLAEELKKLEQRIVVETSGTIKPNQKLMELVDVFSVS 118
                                   44.4443789999********88888888887778********9999887665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                   HHHHH.HHH---EEEEEE-- CS
                     Staufen_C  47 Leyla.rvqgfqveysDfPk 65 
                                   L+ la  v  f v+++ +P+
  gi|70607340|ref|YP_256210.1| 184 LKELAdSVMEFGVQFRVLPQ 203
                                   44555247788888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1674.85
//
Query:       gi|70607341|ref|YP_256211.1|  [L=328]
Description: GTP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-31  107.0   1.2    9.2e-31  107.0   1.2    1.6  2  NOG1_N        NOG1 N-terminal helical domain
    4.7e-18   65.3   0.1    1.1e-17   64.2   0.1    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    2.6e-17   62.3   0.4    1.3e-16   60.1   0.1    2.2  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      7e-15   54.9   0.5      1e-14   54.4   0.5    1.2  1  FeoB_N        Ferrous iron transport protein B
    3.5e-06   27.2   1.4    0.00012   22.2   0.1    2.5  2  Dynamin_N     Dynamin family
    9.6e-06   25.4   0.3    2.5e-05   24.1   0.3    1.7  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    4.8e-05   23.3   1.7      0.044   13.7   0.2    2.6  2  RsgA_GTPase   RsgA GTPase
    5.9e-05   22.7   0.1     0.0052   16.3   0.1    2.9  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00069   19.6   0.3     0.0019   18.2   0.3    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0027   17.1   0.1      0.023   14.0   0.1    2.1  2  DnaB_C        DnaB-like helicase C terminal domain
     0.0054   16.1   0.1     0.0091   15.3   0.1    1.5  1  AIG1          AIG1 family
  ------ inclusion threshold ------
       0.02   15.5   0.0      0.056   14.0   0.0    1.9  1  AAA_18        AAA domain
      0.024   14.5   0.3        0.4   10.6   0.0    2.5  2  NTPase_1      NTPase
      0.025   14.2   0.1      0.079   12.5   0.1    1.8  1  Ras           Ras family
       0.03   14.1   0.1        6.8    6.4   0.0    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.037   14.4   0.0       0.14   12.5   0.0    2.0  2  AAA_16        AAA ATPase domain
       0.14   12.4   0.1        1.7    8.9   0.0    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
        2.7    8.8   9.2        5.2    7.9   0.1    3.8  4  RecG_N        RecG N-terminal helical domain


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   1.2   9.2e-34   9.2e-31       1     160 []       4     153 ..       4     153 .. 0.94
   2 ?   -2.6   0.0       4.6   4.6e+03      26      26 ..     292     292 ..     270     326 .. 0.46

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 9.2e-34
                        NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldvl 81 
                                   Feki ++ ++e +i+++l+r  +++ +t k+ +ei+r+        +++ +++  k++ +++ fP++++lhpFyrell+++
  gi|70607341|ref|YP_256211.1|   4 FEKISIPNDPETVIKTILNRIPKINGNTPKD-REIRRI--------KYVVEQV-RKYRVFLDTFPKISDLHPFYRELLEIT 74 
                                   9***************************876.788766........7778888.99************************9 PP

                        NOG1_N  82 vd.kdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    + + +++++L+++ ++  l++k++ ey++++k+  + ++ ++ +r+ +grv+svl+k ++++d +  + k+L+kL++iD
  gi|70607341|ref|YP_256211.1|  75 SGdIGHFQRCLSAIRKSVLLAEKLSDEYISLIKRDPQ-NRPNKYMRQYVGRVFSVLRKRKECIDLVIRISKELKKLQTID 153
                                   86268****************************9888.78***************************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                        NOG1_N  26 k 26 
                                    
  gi|70607341|ref|YP_256211.1| 292 I 292
                                   1 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.1   1.1e-20   1.1e-17       2     114 .]     159     276 ..     158     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.1e-20
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHC.TSEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflalee.adli 79 
                                   ++++G pNvGKS+L+++++ +k +++++p+tT++i  g+++ +   ++++DtpG+++  +++++  + ka+ a+++   +i
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAKPEIASYPFTTKEIHVGHITSGILTVQVIDTPGILDrpMKDRNVVELKAINAIKNlNGII 239
                                   899*************************************955599********98743333333777788888885589* PP

                                   EEEEETTTTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
                      MMR_HSR1  80 llvvdaseeklkpldeeleellee...akkplilvlnk 114
                                   l+++das++++   +e+l  ++ e    +k +i v+nk
  gi|70607341|ref|YP_256211.1| 240 LFLFDASNSSMYTYKEQLDLYR-EimgLGKVVIPVINK 276
                                   *****99554444444444443.334466677777776 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.1   1.3e-19   1.3e-16       2      58 .]     224     278 ..     223     278 .. 0.97
   2 ?   -0.5   0.0       1.1   1.1e+03      36      51 ..     283     298 ..     282     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.3e-19
                          NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                   +E++Ai+A+k+l++++lFl+D+s+++ y+ +eQl+L++ei  l   k vi v+nKiD
  gi|70607341|ref|YP_256211.1| 224 VELKAINAIKNLNGIILFLFDASNSSMYTYKEQLDLYREIMGL--GKVVIPVINKID 278
                                   79****************************************9..478********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                          NOG1  36 sLleeikelfankpvi 51 
                                   +L++ ik++++n++++
  gi|70607341|ref|YP_256211.1| 283 ELYNAIKNEIKNEQIF 298
                                   79*********98876 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.5     1e-17     1e-14       2     154 ..     158     313 ..     157     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1e-17
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHH.HHHHH..CTSS CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekva.rdfll..eeep 79 
                                   t++++G pnvGk++l+ +++ ak +++ +p +t e + g+++    +v+++D PGi +     ++ +v+  + +   ++  
  gi|70607341|ref|YP_256211.1| 158 TIIVAGPPNVGKSSLVSKISSAKPEIASYPFTTKEIHVGHITSGILTVQVIDTPGILD--RPMKDRNVVeLKAINaiKNLN 236
                                   6899**************************************888***********65..333444433033333225566 PP

                                   SEEEEEEEGGG.....HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
                        FeoB_N  80 dvvvnvvdatn.....lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                                    +++ + da+n      + +L L  +++ lg+ v+ ++n+id ++++ ++  +++++++   ++ ++sa+k++gi+ell+
  gi|70607341|ref|YP_256211.1| 237 GIILFLFDASNssmytYKEQLDLYREIMGLGKVVIPVINKIDDLNEELYNAIKNEIKNE---QIFEISAEKNTGINELLN 313
                                   889999***98443334789***************************999888888865...899************986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.05        50       1      22 [.     159     180 ..     159     201 .. 0.77
   2 !   22.2   0.1   1.2e-07   0.00012     100     168 .]     202     277 ..     177     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.05
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                   i+v G  + GKSS++ ++  ++
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAK 180
                                   7899***********9998877 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.2e-07
                                   S-SEEEEE---B-SSSGTTS.....HHHHHHH.STTEEEEEEEETTS..-CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
                     Dynamin_N 100 vkgltlvDlPGldsvnkrdq.....elvkeyi.kkadiilavtsanh..dlsnsealflarevdpkgkrtivvltkl 168
                                     ++ ++D+PG+ +++ +d      + + ++i + + iil++ +a++    + +e+l+l re+   gk +i v++k+
  gi|70607341|ref|YP_256211.1| 202 ILTVQVIDTPGILDRPMKDRnvvelKAI-NAIkNLNGIILFLFDASNssMYTYKEQLDLYREIMGLGKVVIPVINKI 277
                                   567999**************55544444.556599********99883224455********************995 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   2.5e-08   2.5e-05       4     140 ..     159     314 ..     157     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-08
                     PduV-EutP   4 illiGkvgsGKttLtqalkg............eelkYkktqaiefsdeviDtPGey...lenrkly..salivtsaeadvi 67 
                                   i++ G+ ++GK +L  +++             +e++     +  ++ +viDtPG     ++ r++   +a++++     +i
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSakpeiasypfttKEIHVGHITSGILTVQVIDTPGILdrpMKDRNVVelKAINAIKNLNGII 239
                                   8899999999999999999888877777777777776666666678899*****654448888876225777777777899 PP

                     PduV-EutP  68 alvqdateees.vfppg...fasv..fnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellky 140
                                    ++ da++++  ++ ++   ++++  + k vi +i kid   +ee  +a ++++k+   e+ife+sa +++gi+ell+y
  gi|70607341|ref|YP_256211.1| 240 LFLFDASNSSMyTYKEQldlYREImgLGKVVIPVINKIDDL-NEELYNAIKNEIKN---EQIFEISAEKNTGINELLNY 314
                                   9999988765414554422134442256999999****999.67777777888776...8****************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   4.4e-05     0.044      85     161 ..     144     213 ..      92     217 .. 0.68
   2 !    8.2   0.1    0.0021       2.1      51      96 ..     272     314 ..     238     325 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                   TTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-.----S-.-------------SEEEEEETTTEEEESS-SS CS
                   RsgA_GTPase  85 ktkegleelkellkdktsvlvGqSGvGKStLinallpel.elktge.vseklgrGkhTTtavellelaegglliDtPGf 161
                                   k+ ++l+++ ++l   t++++G+  vGKS+L+ ++ + + e++    + ++ + G  T   + +l ++    +iDtPG+
  gi|70607341|ref|YP_256211.1| 144 KELKKLQTIDPYLP--TIIVAGPPNVGKSSLVSKISSAKpEIASYPfTTKEIHVGHIT---SGILTVQ----VIDTPGI 213
                                   33566666666665..6999***************99621333322022223333222...2344444....8888887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0021
                                   EEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                   RsgA_GTPase  51 ivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                    v+nKiD l+ee  ++++k+e+++   +++ +sa++++g++el ++
  gi|70607341|ref|YP_256211.1| 272 PVINKIDDLNEEL-YNAIKNEIKNE--QIFEISAEKNTGINELLNY 314
                                   489**********.*******9988..99***********999765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   5.2e-06    0.0052      71     190 ..     204     317 ..     155     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                                   EEEEEEESSSGG...GHH.....HHHHHHHT-SEEEE.EEETTTBSTHHHHHHHHHHHH.TTTE..EEEEEESCGSTHHHH CS
                      GTP_EFTU  71 linliDtPGHvd...Fsk.....evirglrvlDgavl.vvdaveGvepqteevlrlalk.egvp..iivfiNKmDrlkael 139
                                   ++++iDtPG  d     +     + i++++ l+g +l ++da++  +   +e l l ++ +g+   +i +iNK+D l++el
  gi|70607341|ref|YP_256211.1| 204 TVQVIDTPGILDrpmKDRnvvelKAINAIKNLNGIILfLFDASNSSMYTYKEQLDLYREiMGLGkvVIPVINKIDDLNEEL 284
                                   5677888887664211111111134677888888876378999999999999988877633333559**********8887 PP

                                   HHHHH.HHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
                      GTP_EFTU 140 keive.evkqklsrkeeklekygekgekevpvvfgSalkgegvktllealve 190
                                    + ++ e+k++                   +++ +Sa k+ g+++ll++  +
  gi|70607341|ref|YP_256211.1| 285 YNAIKnEIKNE-------------------QIFEISAEKNTGINELLNYALK 317
                                   65544044322...................4666666666666666666555 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   1.9e-06    0.0019      59      99 ..     271     314 ..     267     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                  MMR_HSR1_Xtn  59 lyvlNKiDlisleeldelare...pnsvviSaekelnldeLkek 99 
                                   + v+NKiD +++e  +++++e   ++++ iSaek+++++eL++ 
  gi|70607341|ref|YP_256211.1| 271 IPVINKIDDLNEELYNAIKNEiknEQIFEISAEKNTGINELLNY 314
                                   679****************9666568888************875 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.3     3e+02      83     113 ..      31      61 ..      16      73 .. 0.83
   2 !   14.0   0.1   2.3e-05     0.023      22     159 ..     159     302 ..     140     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.3
                                   TSXHHHHHHHHHHHHHHHHSEEEEEEXSSXC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  83 klkeedweklteaieelseaklfiddtpalt 113
                                   + k++++++++  +e++++ ++f+d  p+++
  gi|70607341|ref|YP_256211.1|  31 TPKDREIRRIKYVVEQVRKYRVFLDTFPKIS 61 
                                   346899*******************999875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.3e-05
                                   EEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHH..HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                        DnaB_C  22 iiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklkeedweklte..aieels 100
                                   ii+A+ p +Gk++l+ +i ++  +   ++  +   e +  ++++ +l+  + id+  +    +k++++ +l++  ai++l+
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAKPE--IASYPFTTKEIHVGHITSGILTV-QVIDTPGILDRPMKDRNVVELKAinAIKNLN 236
                                   8*****************986543..34566778888888888888875.56999999999999999988776448999** PP

                                   HSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTS.CS......SSCCCHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx......xxxxxxxxxxxxx RF
                        DnaB_C 101 eaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegs.ee......kenreqevseisr 159
                                      lf+ d ++ ++ + ++++  +++  glg +vi  ++ +++  ee      +e +++++ eis 
  gi|70607341|ref|YP_256211.1| 237 GIILFLFDASNSSMYTYKEQLDLYREIMGLGKVVIPVINKIDDLnEElynaikNEIKNEQIFEISA 302
                                   *******************99988777*******99999999542224445545577778888886 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   9.1e-06    0.0091       2     101 ..     158     256 ..     157     313 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.1e-06
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTT.S---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHH.HHHHHHHHC CS
                          AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsa.qsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkisk.eivrcllls 80 
                                   ti++ G   +GkS+ +  i   k    ++++    tk+ +  + t    +++ViDTPg++d   ++ ++ + + ++    +
  gi|70607341|ref|YP_256211.1| 158 TIIVAGPPNVGKSSLVSKISSAKP---EIASyPFTTKEIHVGHITSGILTVQVIDTPGILDRPMKDRNVVElKAIN-AIKN 234
                                   799999999999999988855543...3333044556666666677779************987766554403333.3445 PP

                                   TT-ESEEEEEEETT.B-SHHHH CS
                          AIG1  81 eegihalllvlslg.rfteede 101
                                    +gi  +l++ s +  +t +++
  gi|70607341|ref|YP_256211.1| 235 LNGIILFLFDASNSsMYTYKEQ 256
                                   5666666666665555665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.6e-05     0.056       1      33 [.     159     200 ..     159     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........gvnlrdvak 33 
                                   I+++G+p vGK++l   +s+   ++         ++++++ +
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAKpEIasypfttkEIHVGHITS 200
                                   9*****************988666666666666444444433 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0004       0.4       2      22 ..     159     179 ..     158     229 .. 0.78
   2 ?    1.4   0.0      0.27   2.7e+02     119     160 ..     261     305 ..     252     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                                   EEEE--TTSSHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                   +++ Gpp vGK+ lv+k++++
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSA 179
                                   89****************976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.27
                                   HHHHTTTSEEEEE--SS-..-SHHHHHHHT-TT.-EEEE--TTTT CS
                      NTPase_1 119 eevLksekpvlavihrrk..dlalveeirerkd.vkvfevteenr 160
                                   +e++  +k+v+ vi + +  +++l++ i+++ +  ++fe+++e+ 
  gi|70607341|ref|YP_256211.1| 261 REIMGLGKVVIPVINKIDdlNEELYNAIKNEIKnEQIFEISAEKN 305
                                   678888999999999988888999999998855478999988765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     8e-05     0.079       2     158 ..     159     317 ..     158     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                                   EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT.......SGGGHHH.HHHHHTTESE CS
                           Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG.......qeefksl.relyyrdaeg 74 
                                   +++ G  +vGK+sl+ +  + k +  + +     + ++  ++ +  +++++ DT G         +  +l + + +++ +g
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAKPEIASYPFT--TKEIHVGHITSGILTVQVIDTPGildrpmkDRNVVELkAINAIKNLNG 237
                                   789999*********9998887665544433..2444444556888999******95444432122333313456778888 PP

                                   EEE.EEETTBHH..HHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHH CS
                           Ras  75 ill.vyditsre..sfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenvee 151
                                   i+l ++d ++++  ++++  ++++ei    +   +++ v nK+D  +++       +++ +e++  + +e+SA++n++++e
  gi|70607341|ref|YP_256211.1| 238 IILfLFDASNSSmyTYKEQLDLYREIMGLGK---VVIPVINKIDDLNEEL-----YNAIKNEIKnEQIFEISAEKNTGINE 310
                                   7762688887761134444467777777666...4556678887665333.....33444444446779***********9 PP

                                   HHHHHHH CS
                           Ras 152 afeellr 158
                                   +++ +l+
  gi|70607341|ref|YP_256211.1| 311 LLNYALK 317
                                   9988776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.012        12       1      22 [.     161     182 ..     161     187 .. 0.88
   2 ?    6.4   0.0    0.0068       6.8     175     237 ..     255     317 ..     205     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilel 22 
                                   v+Gp+ +GK+++v+++s+  ++
  gi|70607341|ref|YP_256211.1| 161 VAGPPNVGKSSLVSKISSAKPE 182
                                   89**************987766 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0068
                    ATP_bind_1 175 keleffedvealslllekee......ekykklaeaiaelleefalvlrflplssekeesiedllslide 237
                                   ++l+ + ++  l       +      +k  +l+e++ +++++   + +++ +s+ek+++i++ll++  +
  gi|70607341|ref|YP_256211.1| 255 EQLDLYREIMGLG------KvvipviNKIDDLNEELYNAIKNEIKNEQIFEISAEKNTGINELLNYALK 317
                                   3444444443333......133444589999**********999999****************998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         4     4e+03      58      93 ..      79     114 ..      68     127 .. 0.71
   2 ?   12.5   0.0   0.00015      0.14      23      51 ..     153     182 ..     137     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4
                        AAA_16  58 gkcdqlesaipysa.laqalareellrqlldeaesae 93 
                                   g+++++ sai+ s+ la+ l  +e++  ++++++++ 
  gi|70607341|ref|YP_256211.1|  79 GHFQRCLSAIRKSVlLAEKL-SDEYISLIKRDPQNRP 114
                                   67777766666677777777.5577777777766655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00015
                        AAA_16  23 rp..elvllsGesGvGKsslvrellralekd 51 
                                   +p  + +++ G++ vGKsslv ++  +++ +
  gi|70607341|ref|YP_256211.1| 153 DPylPTIIVAGPPNVGKSSLVSKIS-SAKPE 182
                                   455589****************999.67666 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0017       1.7       2      24 ..     159     181 ..     158     215 .. 0.76
   2 ?    0.9   0.0       0.5     5e+02      82     119 ..     238     278 ..     224     279 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                                   EEEESSTTSSHHHHHHCHCT-CC CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkf 24 
                                   +++ G  +vGK+sl++++ + k 
  gi|70607341|ref|YP_256211.1| 159 IIVAGPPNVGKSSLVSKISSAKP 181
                                   7899************9986654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.5
                                   EEEEEEEGHHHH..CHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                           Roc  82 lailvydsrsse..nlkeWlkelkkvagks.pvilvgnkiD 119
                                   ++++++d+++s+  + ke l+  ++ +g   +vi v+nkiD
  gi|70607341|ref|YP_256211.1| 238 IILFLFDASNSSmyTYKEQLDLYREIMGLGkVVIPVINKID 278
                                   566677755443125567777777777755156669***99 PP

>> RecG_N  RecG N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0052       5.2      64      86 ..      30      52 ..       9      54 .. 0.84
   2 ?    1.4   0.0      0.53   5.3e+02      30      53 ..      81     104 ..      68     125 .. 0.76
   3 ?   -1.1   0.1       3.2   3.2e+03      15      38 ..     127     150 ..     116     154 .. 0.79
   4 ?    2.1   1.0      0.33   3.3e+02      24      62 ..     282     318 ..     268     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0052
                                  SS-HHHHHHHHHHHHHHHHHHHH CS
                        RecG_N 64 sLpeeRkikRlknglemieklrd 86
                                  + p++R+i R+k ++e + k+r 
  gi|70607341|ref|YP_256211.1| 30 NTPKDREIRRIKYVVEQVRKYRV 52
                                  6799*****************95 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.53
                                   HHHHHHH---GGGG-HHHH.HHHH CS
                        RecG_N  30 ikkkleliddplleneevlkekls 53 
                                   +++ l++i +++l +e++++e++s
  gi|70607341|ref|YP_256211.1|  81 FQRCLSAIRKSVLLAEKLSDEYIS 104
                                   677788888888888888877665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.2
                                   S---TTT........HHHHHHH-- CS
                        RecG_N  15 kvlsgkleteelieeikkklelid 38 
                                   +vl++++e  +l+  i k+l++++
  gi|70607341|ref|YP_256211.1| 127 SVLRKRKECIDLVIRISKELKKLQ 150
                                   467788888899988988888875 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.33
                                   ......HHHHHHH---GGGG-HHHH.HHHHHHHHHHTTS CS
                        RecG_N  24 eelieeikkkleliddplleneevlkeklskfldYikpi 62 
                                   eel + ik+++++ +  ++++e+  +  ++++l+Y++++
  gi|70607341|ref|YP_256211.1| 282 EELYNAIKNEIKNEQIFEISAEK--NTGINELLNYALKL 318
                                   45556666644444444444444..44799999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2281.06
//
Query:       gi|70607342|ref|YP_256212.1|  [L=113]
Description: tRNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-29  102.1   0.2    1.6e-29  101.9   0.2    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.2   8.8e-34   1.6e-29       1      96 []      14     111 ..      14     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 8.8e-34
                                   EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEEC....C CS
                     tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaee....l 77 
                                   lrvG v eae++++  kLl+l+vd+G+e+ rqi+sg++++y+p+el++kkvvv++nlkp+k+rG+eS+GMil+a +    +
  gi|70607342|ref|YP_256212.1|  14 LRVGIVKEAERIEGT-KLLKLIVDLGTET-RQIISGIAEYYTPQELLGKKVVVIVNLKPRKIRGFESQGMILAAGCkedeA 92 
                                   79************9.9************.********************************************9988888 PP

                                   ESSCEEEEEESST--TTCE CS
                     tRNA_bind  78 dekevgilelpadveaGek 96 
                                   ++ + +il+++++++aG+k
  gi|70607342|ref|YP_256212.1|  93 KGIKPKILTVDGETPAGTK 111
                                   89999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 761.63
//
Query:       gi|70607343|ref|YP_256213.1|  [L=235]
Description: phosphoribosylaminoimidazole-succinocarboxamide synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-56  190.5   0.6    4.7e-56  190.2   0.6    1.0  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.6   2.6e-60   4.7e-56       2     237 ..       6     216 ..       5     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 2.6e-60
                                   EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSEEEEE CS
                   SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrsmlvk 80 
                                   ++eGK++ vYe  d++++ll +kD i+A d+++k+e+pgKG+++ q+sa++f++lek  i++h++       +++++m+v 
  gi|70607343|ref|YP_256213.1|   6 VAEGKTKIVYEF-DPEHYLLRFKDSITAGDGARKDELPGKGTLNAQTSALFFRLLEKndIRTHYVGM-----YDEKTMIVT 80 
                                   789********9.999****************************************667******66.....99******* PP

                                   -EEEESEEEEEEEE--HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHH CS
                   SAICAR_synt  81 klkmlpvEvvvRgyltGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvealg..teeea 159
                                   klkm+pvEvv R+++tGs+        k    rl   +kege +++pi+++++K++   hD+ +++++++  ++  t++ea
  gi|70607343|ref|YP_256213.1|  81 KLKMIPVEVVLRNIATGSI-------VK----RL--PIKEGEVFDPPIVEFFLKDDLR-HDPLLNYSHLQ-YFNllTRKEA 146
                                   *******************.......88....99..99******************97.8*********8.778899**** PP

                                   HHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT CS
                   SAICAR_synt 160 eeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdw 237
                                   e +ee+ ++v++ ++++++erg++l D KlEFG+d+ d++l+++De+ t Ds+R  d++t      ++ lDK+++R+ 
  gi|70607343|ref|YP_256213.1| 147 EIVEEVIVKVNAVMKNFLKERGLVLYDLKLEFGKDK-DNNLIVGDEI-TLDSMRVRDEKT------NKILDKDLYRKG 216
                                   ***********************************5.9*********.*********999......9*********64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1578.30
//
Query:       gi|70607344|ref|YP_256214.1|  [L=92]
Description: hypothetical protein Saci_1608 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-20   71.2   0.4    6.9e-20   71.0   0.4    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.4   3.9e-24   6.9e-20       2      76 ..       8      83 ..       7      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.9e-24
                                  EEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHT.TS-TTTEEEEEE CS
                          PurS  2 akveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemcekl.LaNpviedyeie 76
                                  +++++  K+g++Dp+G+++++ + +   ++v++ r gky+ + +e+++ eea+e+v++++e++ L+Np+++++ i+
  gi|70607344|ref|YP_256214.1|  8 VELIIISKDGIRDPEGETIQRYVVQKSTNNVRETRAGKYLLFRIESNSSEEAQETVKRIAEEMrLFNPIVHKIIIR 83
                                  788999*****************************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 689.94
//
Query:       gi|70607345|ref|YP_256215.1|  [L=710]
Description: phosphoribosylformylglycinamidine synthase II [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-39  134.7   0.6    5.1e-28   98.2   0.4    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    4.7e-38  129.7   0.1      2e-18   66.8   0.1    2.5  2  AIRS            AIR synthase related protein, N-terminal doma
    3.4e-09   37.1   0.3    6.9e-09   36.1   0.3    1.6  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.4   8.5e-32   5.1e-28       2     151 ..     191     334 ..     190     339 .. 0.91
   2 !   34.7   0.0   2.9e-12   1.7e-08       6     149 ..     548     680 ..     543     684 .. 0.73

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 8.5e-32
                                   TTEEEEEEET...SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHH CS
                        AIRS_C   2 pGdvliltgs...lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaem 79 
                                   +G +++l+g    +Glgga+ +++rk+  e++    avq++d+++ + +++v + +a    +v a++D++gGGL++ + em
  gi|70607345|ref|YP_256215.1| 191 AGLKIVLVGLtglDGLGGAS-FASRKLSGEDEIG--AVQIADPFAGKIVLDVTLQIAD---KVEAIKDLGGGGLVVGITEM 265
                                   7888999998889*******.7777777777644..9****************99999...6******************* PP

                                   HHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                        AIRS_C  80 apasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                   a++  +g+e++ldk+p++ +  +p e+l+se+++r+++av+pe+ ++v++++e ++ p +avIGe t++ + 
  gi|70607345|ref|YP_256215.1| 266 ANG--LGVEVELDKIPLRVKDLTPGEILVSETQERMVFAVKPERVKEVCEAFEYYEYP-CAVIGEFTNDTSI 334
                                   997..9**************************************************97.********99765 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 2.9e-12
                                   EEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHHHHHHHHHTTTE CS
                        AIRS_C   6 liltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlgalaemapasgv 85 
                                   +i++g     + g +l++  ++  +++         +l + l+   + + a+ +g++  a+D++ GGL+gal  ++  + +
  gi|70607345|ref|YP_256215.1| 548 IIMIGFTREEMGGSLLAKIFGNYGDVP-------KTRLNEELLSSELVIKAInDGKIIFAKDISKGGLVGALLPILVRG-F 620
                                   555555444444433333333333333.......33444445555555555567*********************9996.* PP

                                   EEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESS CS
                        AIRS_C  86 gaeidldkvpifdelesplemllsensGrllvavppeea.davlaileeeglpeaavIGevtake 149
                                   g+ id + +p      + +  l+sen Gr +v+ ++e++ +++ ++ +  g+  ++ IGevt ++
  gi|70607345|ref|YP_256215.1| 621 GVSIDTNLIPSDTD--DVISKLFSENGGRFIVLSEREDDiNWLESQSR--GIY-VSKIGEVTREQ 680
                                   *******7777665..58*********************888877777..795.********986 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   3.3e-22     2e-18       4      94 .]      67     178 ..      64     178 .. 0.92
   2 !   60.5   0.0   3.2e-20   1.9e-16       5      94 .]     428     533 ..     414     533 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 3.3e-22
                                   E.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHH CS
                          AIRS   4 a.........vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaa 66 
                                   +         vv++ +shn+p++++p+++ +a++++++++D+++ GArP+all+ + ++          l+++++g++ ++
  gi|70607345|ref|YP_256215.1|  67 GaldvgdgwaVVLKLESHNHPSAIDPFNG-AATGIGGIIRDIISKGARPIALLDMIRVGnlnnsrnrwLLKNIIAGIGFYG 146
                                   544444444489*****************.*************************************99************ PP

                                   HHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                          AIRS  67 eelgvplvgGdtsfsne....ptisvtavGlv 94 
                                   + +gvp+v G+++f++     p++ v+ +G+v
  gi|70607345|ref|YP_256215.1| 147 NSIGVPVVAGELAFDETyndnPLVDVAGLGVV 178
                                   **************9888999*********97 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 3.2e-20
                                   EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplvgG 76 
                                   ++++ d ++  ++ + ++  G+  va+++++la++GA+ +++++ l ++         ++ e+vrg+aea + +g+p+vgG
  gi|70607345|ref|YP_256215.1| 428 LAIKGDANPDLCAEDSYEC-GRYIVAEAYRNLATVGAKGIGVVDHLQFGdpkkpevyyQFVEAVRGIAEASKYFGTPIVGG 507
                                   4889999999999******.************************************************************* PP

                                   EEEEESS........EEEEEEEEEEE CS
                          AIRS  77 dtsfsne........ptisvtavGlv 94 
                                   ++sf+ne        pt+ v++ Glv
  gi|70607345|ref|YP_256215.1| 508 KVSFYNEnkegkpikPTPLVVMAGLV 533
                                   *****999*******9****999986 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.3   1.2e-12   6.9e-09       9      50 .]       2      40 ..       1      40 [. 0.97

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.2e-12
                FGAR-AT_linker  9 glaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                   l+Ls +E++ +++    lgr+P   E  ++ + wSEHC++K
  gi|70607345|ref|YP_256215.1|  2 RLSLSSQEMELVRKF---LGREPKEEEWLVVDALWSEHCSYK 40
                                  799************...9**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (710 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 5184.14
//
Query:       gi|70607346|ref|YP_256216.1|  [L=444]
Description: glutamine amidophosphoribosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-10   41.3   0.0      1e-09   38.4   0.0    2.1  1  GATase_7      Glutamine amidotransferase domain
    4.3e-10   39.9   0.0      1e-09   38.7   0.0    1.6  1  GATase_6      Glutamine amidotransferase domain
    1.4e-09   37.6   0.2    2.8e-09   36.7   0.2    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.14   11.6   0.1       0.25   10.8   0.1    1.3  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.2e-13     1e-09      10     122 ..      87     188 ..      76     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.2e-13
                      GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.....ewgeealerlnGmfAfaiwde 85 
                                     +aQP++   dg+++++fnG+i Ny +   +            Dte + ++l++     ++++++++  +G ++++++++
  gi|70607346|ref|YP_256216.1|  87 IDEAQPLS---DGKIALAFNGTIPNYINYNVR-----------IDTEFIYEVLKNqedirQGIRKLVDVADGGYSLVVLTN 153
                                   5689***9...699************876554...........689999999888889999******************99 PP

                      GATase_7  86 eekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   +  +l+  RD+ G++PL +g+  g+++++aSe +a++
  gi|70607346|ref|YP_256216.1| 154 KG-ELIGLRDPKGFRPLVLGKL-GSGYIIASEDSAIR 188
                                   88.9******************.89********9997 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   2.3e-13     1e-09      11     134 .]      69     183 ..      53     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.3e-13
                      GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.....eelG. 85 
                                   +++  ++HvR +++g  + ++aqP+  +dg+++l++NG+i ny     ++          r Dte +  +l      + G 
  gi|70607346|ref|YP_256216.1|  69 SSNFSIGHVRYSTTGRGVIDEAQPL--SDGKIALAFNGTIPNYI----NYN--------VRIDTEFIYEVLknqedIRQGi 135
                                   455889***********99999***..****************5....222........379*******996654433347 PP

                      GATase_6  86 eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                    ++++ ++G ++ ++ +  +++li +rd  g +pl+ +  +sg ++ase
  gi|70607346|ref|YP_256216.1| 136 RKLVDVADGGYSLVVLT-NKGELIGLRDPKGFRPLVLGKLGSGYIIASE 183
                                   88889999999997665.88999999**********************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   6.2e-13   2.8e-09      22     120 ..     253     359 ..     242     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.2e-13
                                   EEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE- CS
                  Pribosyltran  22 ilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVD 94 
                                   il e  + k d+vv+++  +vp+a   +++ ++pl y +++   +++s  ++ + + es          e +++kk++++D
  gi|70607346|ref|YP_256216.1| 253 ILAEnHPAKADIVVPVPESSVPIALGFSRKSGIPLEYGLVRTSVSKRSFIMPSQDKRESiveekfgVVGEVVRNKKIILID 333
                                   333337779**********************999998777777777777777666666678888***************** PP

                                   SEESSSHHHHHHHHHHHCC-BSEEEE CS
                  Pribosyltran  95 DildtGgTllaalelLkekgpeevri 120
                                   D +  G+T+++ ++l++e g+ e+++
  gi|70607346|ref|YP_256216.1| 334 DSIVRGTTMKKLVKLIRENGASEIHV 359
                                   **********************9975 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.5e-05      0.25     120     149 ..     325     354 ..     319     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                      PRTase_2 120 aakelvLvDDEistGktalnliralqeklp 149
                                   ++k+++L+DD i  G+t+ +l++ ++e+  
  gi|70607346|ref|YP_256216.1| 325 RNKKIILIDDSIVRGTTMKKLVKLIRENGA 354
                                   6789******************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3189.59
//
Query:       gi|70607347|ref|YP_256217.1|  [L=404]
Description: glutamine phosphoribosylpyrophosphate amidotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-08   32.5   0.4    2.2e-07   30.5   0.4    1.8  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0041   17.0   0.0       0.01   15.7   0.0    1.6  2  GATase_7      Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.051   13.1   0.0    1.4  2  PRTase_2      Phosphoribosyl transferase
       0.18   11.9   1.2        8.4    6.5   0.0    2.9  3  DUF3660       Receptor serine/threonine kinase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.4   4.9e-11   2.2e-07      19     120 ..     225     333 ..     209     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.9e-11
                                   TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE..-......EEEEEE-TTT--EE...............EE--- CS
                  Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeLevpla..y......vrkvkyrpdgseeaargssdes.......rlled 84 
                                    +++ ee + + dvv+g++  ++p a  ++++ ++p+   +      +r    ++d   +        +          + 
  gi|70607347|ref|YP_256217.1| 225 GEQLAEERKIEGDVVIGVPDTAIPYAIGYSRKSGIPFSlgFtrtgspIRTMLASDDFLKV--------IgvqlklnPIKSA 297
                                   5566677778899********************777441121111113333333333333........23333444699** PP

                                   -TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEE CS
                  Pribosyltran  85 pagkkVliVDDildtGgTllaalelLkekgpeevri 120
                                   ++gk+V+++DD + tG+Tl++++  L+  g++ev++
  gi|70607347|ref|YP_256217.1| 298 VKGKRVILIDDSMVTGRTLKNTIFNLRVLGAKEVHV 333
                                   *********************************987 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06      0.01      66     107 ..     106     146 ..      91     161 .. 0.78
   2 ?   -3.2   0.0       1.7   7.4e+03      27      36 ..     212     221 ..     210     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                      GATase_7  66 wgeealerlnGmfAfaiwdeeekrlllaRDrlGikPLyyged 107
                                     e al + +G f+++ + ++  r++  RD+lG+kPL +g  
  gi|70607347|ref|YP_256217.1| 106 DPETALMEADGVFSLVFLSKDG-RMIGYRDELGVKPLEIGGF 146
                                   46889999********999888.9*************88765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                      GATase_7  27 vfnGeiyNyk 36 
                                   vf+G iy+ +
  gi|70607347|ref|YP_256217.1| 212 VFDGNIYDIR 221
                                   8999999975 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       1.9   8.5e+03      39      65 ..     224     247 ..     219     255 .. 0.62
   2 ?   13.1   0.0   1.1e-05     0.051     120     150 ..     299     329 ..     287     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.9
                      PRTase_2  39 LaellaeakkeelpepvlvigfAEtAt 65 
                                   ++e+lae++     e  +vig+ +tA+
  gi|70607347|ref|YP_256217.1| 224 IGEQLAEER---KIEGDVVIGVPDTAI 247
                                   455555222...234456799999987 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.1e-05
                      PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr 150
                                   + k+++L+DD + tG+t+ n+i +l+    +
  gi|70607347|ref|YP_256217.1| 299 KGKRVILIDDSMVTGRTLKNTIFNLRVLGAK 329
                                   4578******************988765544 PP

>> DUF3660  Receptor serine/threonine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0019       8.4      26      38 ..      48      60 ..      40      61 .. 0.91
   2 ?   -2.9   0.0       1.6   7.3e+03      14      27 ..      87     100 ..      85     102 .. 0.72
   3 ?    3.0   0.1     0.024   1.1e+02       4      31 ..     202     233 ..     201     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0019
                       DUF3660 26 lsgEnktedLELP 38
                                  +sg+ ++edLELP
  gi|70607347|ref|YP_256217.1| 48 ISGDSAPEDLELP 60
                                  89**********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                       DUF3660  14 lmnevVissrryls 27 
                                   ++++vV ++   ls
  gi|70607347|ref|YP_256217.1|  87 SIDGVVKTDLNELS 100
                                   78999988766555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.024
                       DUF3660   4 iVdqvRsqdllmnevV....issrrylsgEnk 31 
                                   iV+q R+    +++ +    +  +  l +E+k
  gi|70607347|ref|YP_256217.1| 202 IVYQSRIDSYVFDGNIydirVRIGEQLAEERK 233
                                   9******999**99997766555667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2905.78
//
Query:       gi|70607348|ref|YP_256218.1|  [L=478]
Description: phosphoribosylamine--glycine ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-38  132.3   0.0    3.2e-38  131.5   0.0    1.4  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    2.7e-20   73.0   0.1    5.5e-20   72.0   0.1    1.6  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
      2e-06   28.0   0.0    5.7e-06   26.5   0.0    1.8  1  GARS_C           Phosphoribosylglycinamide synthetase, C doma
    0.00011   21.7   0.0    0.00025   20.6   0.0    1.5  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
     0.0003   20.1   0.0    0.00083   18.7   0.0    1.6  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
    0.00046   19.8   0.0     0.0029   17.2   0.0    2.2  2  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
       0.14   11.7   0.2       0.42   10.1   0.2    1.8  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   1.2e-41   3.2e-38       2     194 .]     110     313 ..     109     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.2e-41
                                   BHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE........SSHHHHHHHHHHHCTS CS
                        GARS_A   2 sKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva........kseeealkavkeilek 73 
                                   sK ++++l+ k++ip+  +++ f++++ea ++i e +  +  vK++   +g+gv+v+        +   e  +a+++ +e+
  gi|70607348|ref|YP_256218.1| 110 SKVWMRELMWKYEIPGRlRFRYFNNMQEAAKFILEYGGSV-AVKPAEQVGGRGVKVVadlqaylsE---EKRSALSKGVEN 186
                                   8***************99********************99.99*************9676664432...444444333333 PP

                                   .-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHHHHHH CS
                        GARS_A  74 .kkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellekikee 149
                                     +  +   k++iEe+++G E +l++l+dgk+  plplaqd+k ++e   gp TGGmG++s     +p++  e+ +k  e 
  gi|70607348|ref|YP_256218.1| 187 vASLVKGDVKILIEEKVDGPEYTLHVLTDGKSYLPLPLAQDYKNAYEDGIGPETGGMGSISgpdyLLPFINREEFDKSFE- 266
                                   123445689****************************************************999899**********999. PP

                                   THHHHHHHHHCTT.---EEEEEEEEEEE.TTEEEEEEEESS--TTCH CS
                        GARS_A 150 ileptveglkkeg.ipfkGvLyaglmlv.edgpkvlefnvRfgDpet 194
                                   i+++t+++++ke  + ++G+L +++ml+   gp ++e+  R gDpet
  gi|70607348|ref|YP_256218.1| 267 IVRKTADAIAKEVkQAYVGILSGQMMLTaIWGPTIIEYYSRLGDPET 313
                                   **********996267************6789**************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1   2.1e-23   5.5e-20       2      90 .]       3     108 ..       1     108 [. 0.94

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.1e-23
                                   EEEEEESSHHHHHHHHHHTTSTTESEEEEEE..--CGG................TTHHHHHHHHHHCTESEEEE-SHHHHH CS
                        GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvap..gNagt................edlealvefakeekidlvvvGpeapLv 64 
                                   kvL++G+G+Re+ la++l  s++  +v+++   +N+g+                +++e++ + +k+ + d+ v+Gpe+pL+
  gi|70607348|ref|YP_256218.1|   3 KVLLIGEGARENVLAEALGTSEEGYRVFALSsyKNPGIneivmktngeyligniNSVEEVRRAIKQVNPDFGVIGPEEPLF 83 
                                   8****************************99889****999999999999888877789********************** PP

                                   TTHHHHHHHHHT-EEES--CCCCHHH CS
                        GARS_N  65 aGvadaleeekgikvfGpskeaAqlE 90 
                                   +G+ad++++e gi+v+Gp++++A++E
  gi|70607348|ref|YP_256218.1|  84 HGIADEFRKE-GIPVVGPNADGAMIE 108
                                   *******777.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.2e-09   5.7e-06       3      79 ..     350     440 ..     348     441 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.2e-09
                                   EEEEEETTTT..SS--ST-EEBS.......TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-T CS
                        GARS_C   3 gvvlaskGYP..gsyekgkeitg.......egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfe 69 
                                      +a+ GYP  +++++g++i          g++v+  + +     l+t+G+R l ++ v ++ ++A +k  +  + i+ +
  gi|70607348|ref|YP_256218.1| 350 VKAVAPLGYPldKNMATGHTIWLdlprmreIGCNVYFGSISqeggkLITKGSRALEITVV-DDYDKAVEKLDRCFSLISSD 429
                                   567999****6666789****5588999996678888876677777***********987.579*************9998 PP

                                   T.EE--STTTH CS
                        GARS_C  70 g.lfyRkDIGa 79 
                                     l++R+DIG+
  gi|70607348|ref|YP_256218.1| 430 TkLIFRHDIGR 440
                                   7699******6 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.8e-08   0.00025      24     103 ..     132     216 ..     111     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.8e-08
                                   BSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESS.HHHHHHHHHHHHHH.....HHHHHSTS-EEEEE--SSSEEEEEE CS
                   CPSase_L_D2  24 vetleealaiakeigyPviikaafglGGkGmrvarn.eeelaelvkkalae.....akaafgnkqvlvekslkgpkeiEve 98 
                                    ++++ea ++  e+g  v +k+a  +GG+G +v+ + ++ l+e  ++al++     a+   g+ ++l+e+ ++gp e+ + 
  gi|70607348|ref|YP_256218.1| 132 FNNMQEAAKFILEYGGSVAVKPAEQVGGRGVKVVADlQAYLSEEKRSALSKgvenvASLVKGDVKILIEEKVDGP-EYTLH 211
                                   689******************************988333344444444433111114445689999*******99.67788 PP

                                   EEEET CS
                   CPSase_L_D2  99 vlrDa 103
                                   vl D 
  gi|70607348|ref|YP_256218.1| 212 VLTDG 216
                                   88886 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.2e-07   0.00083      47     127 ..     133     203 ..     106     208 .. 0.84
   2 ?   -2.4   0.0      0.85   2.2e+03     231     262 ..     275     304 ..     270     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.2e-07
                   ATPgrasp_ST  47 aeiseleafvkeleegvviKpakgsgGkGilviteredqdylkssgksalldelerhvsnilagLyslggkpdvalveeli 127
                                   ++++e+++f+ e+   v++Kpa++ gG+G+ v+++   q yl+++++sal + +e +v+       sl++ + ++l+ee +
  gi|70607348|ref|YP_256218.1| 133 NNMQEAAKFILEYGGSVAVKPAEQVGGRGVKVVAD--LQAYLSEEKRSALSKGVE-NVA-------SLVKGDVKILIEEKV 203
                                   6789999******555*****************66..999999999999999999.555.......999999999999987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.85
                   ATPgrasp_ST 231 laakaaeklpglgylGwDivldeekgplllEl 262
                                   +a+++ +   ++g+l+  + l++  gp ++E 
  gi|70607348|ref|YP_256218.1| 275 IAKEVKQ--AYVGILSGQMMLTAIWGPTIIEY 304
                                   6777777..89999999999999999999996 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0029       5      73 ..     149     215 ..     146     229 .. 0.80
   2 ?   -1.0   0.0      0.44   1.1e+03      23      50 ..     257     284 ..     254     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                   ATP-grasp_4   5 vviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfd 73 
                                   v +KP+ +++ +GV ++ + + + +  ++ ++ l++  e++++ v  + ++l+Ee ++G E+ + ++ d
  gi|70607348|ref|YP_256218.1| 149 VAVKPAEQVGGRGVKVVADLQAYLS--EEKRSALSKGVENVASLVKGDVKILIEEKVDGPEYTLHVLTD 215
                                   679***************9999866..44444555555666655556889*************999885 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                   ATP-grasp_4  23 neeewkaavaaieeeleqakeeykeevv 50 
                                   n+ee+++ ++ +++ ++ +++e+k+++v
  gi|70607348|ref|YP_256218.1| 257 NREEFDKSFEIVRKTADAIAKEVKQAYV 284
                                   7899999999999999999999998876 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00016      0.42      30      95 ..     140     217 ..     127     232 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                   HHHHHC-SSEEEEESSSSTTTTEEEESSGGGH.....HHH.......HHHHHTT-SCEEEEE--ESEEEEEEEEETSS CS
               Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeel.....kea.......ieeafkydekvlvEeaiegreievavlgnek 95 
                                   k + e g  v VKpa++    Gv+ v   + +     ++a       +++ +k d k+l+Ee ++g e +  vl ++k
  gi|70607348|ref|YP_256218.1| 140 KFILEYGGSVAVKPAEQVGGRGVKVVADLQAYlseekRSAlskgvenVASLVKGDVKILIEEKVDGPEYTLHVLTDGK 217
                                   555566667888888888788888776543221111123311111114456789********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3628.91
//
Query:       gi|70607349|ref|YP_256219.1|  [L=320]
Description: phosphoribosylaminoimidazole synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-26   91.7   0.0    7.8e-26   91.1   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.8e-17   63.8   1.4    3.1e-17   63.0   1.4    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   8.7e-30   7.8e-26       1     153 [.     160     310 ..     160     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 8.7e-30
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemap 81 
                                   +pGdv+++++s G++++g+sl+rk+++e +l       +++l++pt+iyvk  l  + +++ka++++Tg G  + l ++ +
  gi|70607349|ref|YP_256219.1| 160 RPGDVVLGLASNGVHSNGYSLIRKLIDEGKLR--LDDWAEELMKPTKIYVKSVLSVK-DKIKAVAHITG-GSFSKLRRITK 236
                                   79************************999966..67899*****************7.***********.79999****88 PP

                                   TTTEEEEEECGTHHHHHHHH....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                        AIRS_C  82 asgvgaeidldkvpifdele....splemllsensGrllvavppeea.davlaileeeglpeaavIGevtakeelsv 153
                                    + +++++ ++ + if+ +e    s++em++++n+G+++v+++ ++  d v+++l++++   ++++G vt++++ ++
  gi|70607349|ref|YP_256219.1| 237 FG-ISLKMPEP-LDIFKAIEsagvSHEEMYKVFNMGVGMVIFVDKKLkDDVIDTLAKRND-VVYELGVVTEGNGIKI 310
                                   85.66666666.88888888889********************99999**********98.7**********98775 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   1.4   3.5e-21   3.1e-17       2      93 ..      45     149 ..      35     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.5e-21
                                   SSEEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EE CS
                          AIRS   2 Daavvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvpl 73 
                                   D  +++++d++++++l++  ++     G  ++a+n++D++++GArP+a++++lal+      +++v++gl+++aee++v++
  gi|70607349|ref|YP_256219.1|  45 DKYLAMHVDGVGTKTLLALKTGiiepTGVDCIAMNVNDIVCVGARPIAIVDYLALEgemddVIQKVMKGLKAGAEEAEVNI 125
                                   44568899999999999877778999******************************************************* PP

                                   EEEEEEEESS....EEEEEEEEEE CS
                          AIRS  74 vgGdtsfsne....ptisvtavGl 93 
                                   +gG+t+ +++    + +s++a+G+
  gi|70607349|ref|YP_256219.1| 126 IGGETAIMPGvikgYDLSCSAIGI 149
                                   *******99999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2494.09
//
Query:       gi|70607350|ref|YP_256220.1|  [L=148]
Description: hypothetical protein Saci_1615 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.9   0.1     0.0059   17.1   0.1    1.4  1  OrsD      Orsellinic acid/F9775 biosynthesis cluster protein 
     0.0071   16.7   1.2       0.37   11.1   1.0    2.1  2  TCTP      Translationally controlled tumour protein
  ------ inclusion threshold ------
      0.049   13.2   0.2      0.081   12.5   0.2    1.4  1  zf_UBZ    Ubiquitin-Binding Zinc Finger
      0.074   13.1   0.0       0.16   12.0   0.0    1.6  1  PapB      Adhesin biosynthesis transcription regulatory prote
      0.097   13.0   0.1        0.2   12.0   0.1    1.5  1  DUF4120   Domain of unknown function (DUF4120)


Domain annotation for each model (and alignments):
>> OrsD  Orsellinic acid/F9775 biosynthesis cluster protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.6e-06    0.0059      12      57 ..      95     140 ..      87     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                          OrsD  12 liCreCkyavlpselerHLrkrhrqlkrektqelletvehemslrq 57 
                                     C+ C++++ +++ e+H rk h+++ + +++ +le +e+ ++ +q
  gi|70607350|ref|YP_256220.1|  95 YYCTLCNTSIPKEDTEEHVRKYHKEILTSTIKTMLERLEEYKKEKQ 140
                                   56***************************9**99999965544433 PP

>> TCTP  Translationally controlled tumour protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.014        52      87     128 ..      49      91 ..      39      98 .. 0.86
   2 !   11.1   1.0    0.0001      0.37      75     120 ..      98     143 ..      94     148 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHC.SCCHHHHHHHHHHHHHHHHCTCCT CS
                          TCTP  87 kaylkdYmkkvkkkleek.kpeevkeFkkgaqeavkkilanfk 128
                                   k  l++Y +++ +k  ++ + +++ ++ kg+ + vk i+++ +
  gi|70607350|ref|YP_256220.1|  49 KHQLRGYAQRIIEKSGSEgRAKKILPIIKGISKDVKPIVKRTD 91 
                                   67899*********977779******************98765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0001
                                   TEEEECCHHHHHHHHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH CS
                          TCTP  75 rLqetsfdkksykaylkdYmkkvkkkleekkpeevkeFkkgaqeav 120
                                    L +ts+ k++  +++++Y k++     ++  e+++e+kk+ q+++
  gi|70607350|ref|YP_256220.1|  98 TLCNTSIPKEDTEEHVRKYHKEILTSTIKTMLERLEEYKKEKQAVI 143
                                   58899************************************99987 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.3e-05     0.081       1      20 [.      93     112 ..      93     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                        zf_UBZ   1 dtylCerCgkeipeselqEH 20 
                                   d y C  C+++ip ++ +EH
  gi|70607350|ref|YP_256220.1|  93 DLYYCTLCNTSIPKEDTEEH 112
                                   5799**************** PP

>> PapB  Adhesin biosynthesis transcription regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.4e-05      0.16      39      77 ..      21      59 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                          PapB 39 SekvinalrdylVkGvsrkevCeryevnqgYlsislkrl 77
                                  S+ +++al+ ylVkG     v  +y++++  l    +r+
  gi|70607350|ref|YP_256220.1| 21 SDYILEALEKYLVKGEGPATVAYEYQISKHQLRGYAQRI 59
                                  77899**********************997776666665 PP

>> DUF4120  Domain of unknown function (DUF4120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.6e-05       0.2       6      38 ..     108     140 ..     103     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                       DUF4120   6 ehydkvvqyaesikdtslqeclerlkaweknpd 38 
                                   +  ++v++y + i  ++++  lerl++++k+++
  gi|70607350|ref|YP_256220.1| 108 DTEEHVRKYHKEILTSTIKTMLERLEEYKKEKQ 140
                                   55689*********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 972.71
//
Query:       gi|70607351|ref|YP_256221.1|  [L=52]
Description: hypothetical protein Saci_1616 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00042   20.1   0.0    0.00052   19.9   0.0    1.1  1  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.026   14.6   0.0      0.034   14.3   0.0    1.2  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.8e-08   0.00052       2      39 .]       5      43 ..       4      43 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.8e-08
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                  vs+rl e+++ ++d  + ++g  Sr +++++Al  y++r
  gi|70607351|ref|YP_256221.1|  5 VSVRLREDVVNKIDYFVSEMGlESRTDFLKQALDYYVKR 43
                                  9***********************************987 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.8e-06     0.034      92     122 ..       5      36 ..       1      37 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-06
               HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgflaka 122
                                   + + l e+v+++iD +v++ g esR  fl +a
  gi|70607351|ref|YP_256221.1|   5 VSVRLREDVVNKIDYFVSEMGlESRTDFLKQA 36 
                                   678999***************99******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 395.44
//
Query:       gi|70607352|ref|YP_256222.1|  [L=391]
Description: argininosuccinate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-139  466.1   0.1   1.2e-139  465.9   0.1    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    0.00023   20.7   0.2    0.00048   19.7   0.2    1.7  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.014   15.4   0.3       0.58   10.1   0.1    2.4  2  Phage_30_8       Phage GP30.8 protein
      0.029   14.4   0.0      0.083   12.9   0.0    1.8  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.9   0.1  2.8e-143  1.2e-139       1     385 [.       4     383 ..       4     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 465.9 bits;  conditional E-value: 2.8e-143
               Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedr 81 
                                   vLaysGGlDt+v+i +l+e  +++v +v+vdvGq+ +d+ +++++a  +ga+k++++Dak++f+e yi  aik n+lYed 
  gi|70607352|ref|YP_256222.1|   4 VLAYSGGLDTTVAIRWLRETFNADVTTVTVDVGQK-DDFYQIEKRAYIAGAIKHYTIDAKKDFAERYISYAIKMNGLYEDI 83 
                                   8**********************************.********************************************* PP

               Arginosuc_synth  82 YllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipve 162
                                   Y+l+talaRPli++k+ve+akk gaea+ahG+t kGnDqvRf++++++l P+ k+iaP+R +++tR++eieyak+kgip++
  gi|70607352|ref|YP_256222.1|  84 YPLSTALARPLIVEKVVEIAKKIGAEAIAHGSTSKGNDQVRFDLAVKALYPEAKIIAPARIWNMTRDKEIEYAKSKGIPIK 164
                                   ********************************************************************************9 PP

               Arginosuc_synth 163 vtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneia 243
                                   ++++k ysiDenl+grsie++i+ dp+++ ped++e+tk+ ++++    ++++ f+kG+Pv+++ge+++ l++i+ lne+ 
  gi|70607352|ref|YP_256222.1| 165 TESSK-YSIDENLWGRSIEGDIISDPSKEVPEDAFEWTKKTKDDK---LKISLTFDKGLPVEVNGEKMDLLKVIQVLNELV 241
                                   99655.********************************9776555...89******************************* PP

               Arginosuc_synth 244 gkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkGlwfsPlkealdafie 324
                                   g +G GR++++e+R+vg+ksRe+Ye paalvLi++hkdlek t +  + +fk++++ ++++lvY+Glwf+Pl+e+++ + +
  gi|70607352|ref|YP_256222.1| 242 GSRGFGRVEHLENRVVGFKSREVYEVPAALVLINSHKDLEKSTYTPLEFRFKRSLDGQWSDLVYQGLWFEPLRETIQIAGD 322
                                   ********************************************************************************* PP

               Arginosuc_synth 325 ktqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqak 385
                                   + ++ ++G+v +++ +G++++lgR+ + s ++ee+asy++     ++ a+Gfi+i+g+++ 
  gi|70607352|ref|YP_256222.1| 323 NLNKWISGEVFIEVENGNMKILGRKGKFSPFSEEIASYNKGWYPSDEMARGFIEIFGMHSL 383
                                   ***************************************999999999*********9875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.1e-07   0.00048       2     120 ..       3     114 ..       2     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                                   EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-------- CS
                          QueC   2 avvllSGGlDSttvlalakkeg.kevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaLtdeeievp 80 
                                   +v+  SGGlD t+++ + ++++ + v+++t+d gq+    ++e+++ ia +  + +h ++d +  k++++  +  +   ++
  gi|70607352|ref|YP_256222.1|   3 IVLAYSGGLDTTVAIRWLRETFnADVTTVTVDVGQKdDFYQIEKRAYIAGA--I-KHYTIDAK--KDFAERYISYA---IK 75 
                                   68889****************9568***********666677777777654..3.56666666..55555443222...33 PP

                                   ---...--------TTHHHHHHHHHHHHHHHHT-SEEEE- CS
                          QueC  81 keeleeeelpntfVpaRNliflslaasyaealgaeaiiiG 120
                                    + l e+  p +   aR li+  + +  a+++gaeai+ G
  gi|70607352|ref|YP_256222.1|  76 MNGLYEDIYPLSTALARPLIVEKV-VEIAKKIGAEAIAHG 114
                                   333555666666666665554443.345666666666655 PP

>> Phage_30_8  Phage GP30.8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00013      0.58      26     112 ..      17     107 ..       6     117 .. 0.77
   2 ?    2.7   0.0     0.025   1.1e+02      22      53 ..     171     201 ..     160     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                    Phage_30_8  26 lqwllravegdvvevettdgmsddftytievenfftgei..yrlnsvvvgkirsktyedeelgesedvvwyetarnr...a 101
                                   ++wl  + + dv  v+   g  ddf y+ie + +++g i  y +++      r  +y  +  g  ed+    ta  r    
  gi|70607352|ref|YP_256222.1|  17 IRWLRETFNADVTTVTVDVGQKDDF-YQIEKRAYIAGAIkhYTIDAKKDFAERYISYAIKMNGLYEDIYPLSTALARpliV 96 
                                   78**********************9.9**********99556666666566667777777788888887777776663334 PP

                    Phage_30_8 102 esliekikkkg 112
                                   e+++e  kk g
  gi|70607352|ref|YP_256222.1|  97 EKVVEIAKKIG 107
                                   67777667666 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                    Phage_30_8  22 kvdelqwllravegdvvevettdgmsddftyt 53 
                                    +de  w  r++egd++   + + + d f +t
  gi|70607352|ref|YP_256222.1| 171 SIDENLW-GRSIEGDIISDPSKEVPEDAFEWT 201
                                   5688888.59********99999999999887 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.083       1     107 [.       2     115 ..       2     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                   CEEEE--SSCTCHHHHHHHHHHCTT.HEEEEEE-STB..-H..HHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
                   PAPS_reduct   1 elvvsvsgGkdslVllhLalkafkp.vpvvfvdtghe..fp..etiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                                   ++v+++sgG d +V +  ++++f+  v++v vd g++  f   e  +++    ++y ++ k    e+ ++ +i++++    
  gi|70607352|ref|YP_256222.1|   2 KIVLAYSGGLDTTVAIRWLRETFNAdVTTVTVDVGQKddFYqiEKRAYIAGAIKHYTIDAKKDFAERYISYAIKMNG---- 78 
                                   589********************996799999998763344223446778888888888777777777788888887.... PP

                                   HHHC......HHHHHHTHHHHHHHHHCTTECEEE--- CS
                   PAPS_reduct  77 lyee......aaeriaKveplkkaLekldedalltGa 107
                                   lye+      a+ r   ve++ +  +k++++a+  G+
  gi|70607352|ref|YP_256222.1|  79 LYEDiyplstALARPLIVEKVVEIAKKIGAEAIAHGS 115
                                   6777666677666666666666666677777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2807.27
//
Query:       gi|70607353|ref|YP_256223.1|  [L=447]
Description: argininosuccinate lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-40  138.2   0.0    8.1e-40  137.1   0.0    1.6  2  Lyase_1   Lyase
     0.0024   18.6   0.0     0.0073   17.0   0.0    1.8  1  ASL_C2    Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   0.0     9e-44   8.1e-40      75     310 ..      69     288 ..       9     290 .. 0.85
   2 ?   -2.9   0.0      0.38   3.4e+03     165     194 ..     402     430 ..     401     436 .. 0.77

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 9e-44
                                   SSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEE CS
                       Lyase_1  75 iqegsgtavnmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvki 155
                                     e+ + a++  + + ig       e  ++v  g+S+nD v+Talrl +++ + + ++++l  L+++l e+ak++ +++++
  gi|70607353|ref|YP_256223.1|  69 GYEDVHEALEDYIIKNIG-------EEGGWVGLGRSRNDHVATALRLRTREYIFD-IMEELYLLRKSLIEQAKKNLNTIMP 141
                                   456777777776666666.......99**************************66.************************* PP

                                   EEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHH CS
                       Lyase_1 156 GrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsf 236
                                   ++Th q+A+P+tl++ ++   e+l+   e l ++lk ++ ++lg+g++vg  +++d++   + a+ l+ ++    +  n++
  gi|70607353|ref|YP_256223.1| 142 SYTHFQPAQPTTLAHYFMYLEEELNTPWEALFNSLKLINRSPLGSGAIVGSNVKIDRK---REAELLG-FDD---VLYNTI 215
                                   **********************************************************...9999999.999...999*** PP

                                   HHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHH CS
                       Lyase_1 237 eavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrv 310
                                    ++s+r + +++++ l+ll++ Ls+faeD++llss  +++++l +   +  SS+MP+K+N v++E l+ + g  
  gi|70607353|ref|YP_256223.1| 216 SSTSSRIDFINAISSLTLLMLVLSRFAEDMILLSSMFVNIIKLPDSHVS-TSSLMPQKRNSVTMEILRTKVGEC 288
                                   ***********************************88999999999888.8*****************998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.38
                                   EEEHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                       Lyase_1 165 Pvtlgqelsayaealerdrerlkellkrll 194
                                   P+ l qe++   + l++++e++k+ ++  +
  gi|70607353|ref|YP_256223.1| 402 PSLLTQEIEIKEKRLNNQHEKFKQYKE-SV 430
                                   777889999999999999999999884.33 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.1e-07    0.0073       3      26 ..     350     373 ..     349     396 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.1e-07
                                   THHHHHHHHHHCTS-HHHHHHHHH CS
                        ASL_C2   3 tATdlADyLvrkGlpFReAHeivg 26 
                                   tATdlA+ ++ +G+p+R+A+  v+
  gi|70607353|ref|YP_256223.1| 350 TATDLAEEMAISGIPYRKAYIDVA 373
                                   9******************97666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2757.02
//
Query:       gi|70607354|ref|YP_256224.1|  [L=371]
Description: carbamoyl phosphate synthase small subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-46  156.6   0.0      4e-46  156.0   0.0    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    6.7e-40  136.9   0.0      1e-39  136.3   0.0    1.3  1  GATase           Glutamine amidotransferase class-I
    1.9e-06   27.8   1.1      0.001   18.9   0.1    2.2  2  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.0   0.0   6.7e-50     4e-46       3     128 .]      11     144 ..       9     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.0 bits;  conditional E-value: 6.7e-50
               CPSase_sm_chain   3 vLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGv........needvesekikva 74 
                                   +++LedGt ++G +fg ++  vGE+vf+T+m GY+e+ltDpsY+gqilv+t+pliGnyGv          +++ese+i+++
  gi|70607354|ref|YP_256224.1|  11 YVYLEDGTLMKGIGFGaKGIRVGEIVFTTSMNGYPESLTDPSYKGQILVITHPLIGNYGVpeknyvngILTNFESERIQAE 91 
                                   799*************66888***************************************655555443345566****** PP

               CPSase_sm_chain  75 glvvrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                                   glv++el+ ep +w+++++L+ewl +e+ipg++g+DTRa++k++r++g+m+g+i
  gi|70607354|ref|YP_256224.1|  92 GLVISELT-EPFKWNSKQTLHEWLLSEGIPGVYGIDTRAVVKRVRSRGVMMGII 144
                                   ******98.6789***************************************98 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   1.7e-43     1e-39       2     189 ..     188     365 ..     187     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.7e-43
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGm 81 
                                   ++D++  +++ ++ +l+ +g++v  vp+++sa++i+     p+g+l+s+Gpg+p+  +  +++ +e++e ++P LGICLG+
  gi|70607354|ref|YP_256224.1| 188 VVDCG--IKHGILYQLYLRGFTVVRVPCNYSADKIM--DFYPKGLLFSNGPGNPNlLTDLVKNFREIIEYNLPTLGICLGH 264
                                   89***..****************************7..678**************************************** PP

                                   HHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETT CS
                        GATase  82 QllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekkn 162
                                   Q+++ ++g+kv k+k ++h+  + ++ d      + +++++i++h+H+y++  k+ +p   +v + + dd+++++ i++k+
  gi|70607354|ref|YP_256224.1| 265 QIATMALGGKVKKMK-FGHRAINKPVID------TTTGKSYITTHNHGYAILSKQDVPIHTRVWFYNPDDGTVEGWIHEKY 338
                                   ***************.************......89999****************************************** PP

                                   TEEEESSBTTSTTSTTHHHHHHHHHHH CS
                        GATase 163 pfvgvQFHPEststpegpellfnflik 189
                                   +++ +QFHPE++++p + +++f+++ k
  gi|70607354|ref|YP_256224.1| 339 NIITTQFHPEARPGPWDVTWVFDKFKK 365
                                   ************************987 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.7e-07     0.001      99     127 ..     248     276 ..     243     302 .. 0.90
   2 !    7.7   0.1   0.00045       2.7     181     216 .]     314     348 ..     285     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
                 Peptidase_C26  99 raalergvPilgiCrGlqllnvalGGtly 127
                                   r+++e ++P lgiC+G+q+  +alGG++ 
  gi|70607354|ref|YP_256224.1| 248 REIIEYNLPTLGICLGHQIATMALGGKVK 276
                                   7899**********************975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00045
                 Peptidase_C26 181 laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                   +  + rv    + Dg++E   +e+  + ++  Q+HPE
  gi|70607354|ref|YP_256224.1| 314 VPIHTRVWFYNPdDGTVEGWIHEK--YNIITTQFHPE 348
                                   56666777777779*****99888..66********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2517.77
//
Query:       gi|70607355|ref|YP_256225.1|  [L=1052]
Description: carbamoyl phosphate synthase large subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-97  325.4   0.0    6.8e-66  221.8   0.0    2.3  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.1e-34  117.9   0.2    1.1e-33  116.2   0.2    2.0  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    2.5e-20   72.7   0.0      2e-09   37.2   0.0    2.3  2  ATP-grasp        ATP-grasp domain
    1.2e-14   54.3   0.1    1.2e-07   31.5   0.1    2.6  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      5e-13   48.9   0.0    2.3e-06   27.4   0.0    2.6  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    1.2e-08   35.1   0.2    0.00039   20.5   0.1    3.2  2  ATP-grasp_3      ATP-grasp domain
    3.4e-06   26.7   0.1     0.0083   15.6   0.0    3.1  2  ATP-grasp_5      ATP-grasp domain
    9.7e-05   22.0   0.0     0.0046   16.6   0.0    2.9  3  RimK             RimK-like ATP-grasp domain
     0.0002   21.2   0.1       0.01   15.6   0.1    2.8  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
     0.0079   15.8   0.0       0.26   10.8   0.0    3.2  4  ATP-grasp_2      ATP-grasp domain
  ------ inclusion threshold ------
       0.06   12.8   0.0        3.3    7.1   0.0    2.4  2  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.8   0.0   4.2e-69   6.8e-66       2     210 ..     127     331 ..     126     332 .. 0.98
   2 !  101.3   0.0     3e-32   4.9e-29       1     199 [.     669     859 ..     669     868 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.8 bits;  conditional E-value: 4.2e-69
                                   HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS- CS
                   CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkq 82 
                                   +e+++e++ ++n pv ps +a  +++eeal+ a++igyPv+++ +f lGG+G+ va++ee+l+  + +al+++      ++
  gi|70607355|ref|YP_256225.1| 127 REKFRETMINVNLPVPPSLSA--RSEEEALEKARQIGYPVMVRVSFNLGGRGSTVAWSEEDLKRDIGRALSQSY----IHE 201
                                   899******************..**************************************************5....9** PP

                                   EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEE CS
                   CPSase_L_D2  83 vlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtve 161
                                   vl+ek+l+++ e+E+ev+rD++gn  +++ +en++++  +t+++ ++AP qtL+++e+q +r+ ++ v++++++vg+++v+
  gi|70607355|ref|YP_256225.1| 202 VLIEKYLHHWIELEYEVMRDKHGNSAVIACIENLDPMgvHTGESTVIAPCQTLDNKEFQDMRSMSIDVAKSIDLVGECNVQ 282
                                   ********************************************************************************* PP

                                   EEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                   CPSase_L_D2 162 flldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                   f+l+p   eyy+iE N+R+s++sala+kaTG++l++++ak+alg++L e
  gi|70607355|ref|YP_256225.1| 283 FALNPLAYEYYIIETNPRMSRSSALASKATGYPLAYVSAKLALGYELYE 331
                                   **********************************************976 PP

  == domain 2  score: 101.3 bits;  conditional E-value: 3e-32
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   D+e+++++l+k++++  +  +a  +++ee+ ++++ +gyPv++++++ l G+ mr+++n+ el+  +kka++ +    +++
  gi|70607355|ref|YP_256225.1| 669 DREKFSRLLDKLGIKQPDWISA--RSIEEVRKFVEMVGYPVLVRPSYVLSGSAMRIVYNDTELVSYIKKATEIS----SEH 743
                                   9**************9999998..**************************************************....69* PP

                                   -EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEE CS
                   CPSase_L_D2  82 qvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtvef 162
                                    v v k++++  e E++  +D +g   +v e      ++ ++     P + L++e+ ++++e+   + re++++g  +v+f
  gi|70607355|ref|YP_256225.1| 744 PVVVSKYIDNAIEAEIDGASDGRGVYGVVLEHVEEAGVHSGDATISIPFKKLSPETVHKMKESIHSISRELNIKGPFNVQF 824
                                   ***********************999888888888899******************************************* PP

                                   EEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHH CS
                   CPSase_L_D2 163 lldpkskeyyviEvNtRlsvesalaekaTGldlvkea 199
                                   +++  ++  y+iE+N R s++ + ++k+ G +++  a
  gi|70607355|ref|YP_256225.1| 825 VVK--NGTPYIIEMNLRASRSMPFSSKVVGKNIIDLA 859
                                   **9..5999*********************9999776 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.2   6.5e-37   1.1e-33       3     122 .]     424     541 ..     422     541 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 6.5e-37
                   CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaelleee 83 
                                   lke ++  +++  +a+++g++++e++e+t i+++FL+k+++lv++ +++k++k  ld+++l  ak+lGfsD qia+ ++  
  gi|70607355|ref|YP_256225.1| 424 LKERRPYWFLYASKAFKEGATIDEVYEVTGINKFFLNKIKNLVDFYESIKNNK-GLDQKTLSIAKRLGFSDYQIASAVG-L 502
                                   6777778889999*************************************998.7********************9976.7 PP

                   CPSase_L_D3  84 eeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                   +e+++relr+k+gi+p++k++Dt+A+e++a t+YlY tY
  gi|70607355|ref|YP_256225.1| 503 SEKDIRELRQKYGIEPKVKQIDTLAGEWPAVTNYLYVTY 541
                                   8899**********************************9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.3e-12     2e-09       3     143 ..     136     283 ..     134     304 .. 0.85
   2 !   33.2   0.0   2.2e-11   3.6e-08       2     159 ..     678     839 ..     677     843 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.3e-12
                                   TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEE CS
                     ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEls 79 
                                   +++lpvp+ l ++s+ee+ e a+++g+pv+v+       G+G++v  seedl++ +  +      ++v++E++ +   El 
  gi|70607355|ref|YP_256225.1| 136 NVNLPVPPSLSARSEEEALEKARQIGYPVMVR-VSFNLGGRGSTVAWSEEDLKRDIGRAlsqsYIHEVLIEKYLHHWIELE 215
                                   5789****************************.99999************99876655555557789************** PP

                                   EEEEEETTC-EEE--EEEEEEETTEEE...EEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEE CS
                     ATP-grasp  80 vlvvrsaeGetafypvvetvqedgilr...lsvapaevsek.aqkkaeeiakkiveeLggvGvfavEl 143
                                     v+r+++G+ a+++ +e++   g+     +++ap++  ++ + +  +++  +++++++ vG   v +
  gi|70607355|ref|YP_256225.1| 216 YEVMRDKHGNSAVIACIENLDPMGVHTgesTVIAPCQTLDNkEFQDMRSMSIDVAKSIDLVGECNVQF 283
                                   ************************98533378999887655255677777779********9877765 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 2.2e-11
                                   HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEE CS
                     ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekEl 78 
                                   +klg++ p+++ ++s ee+++++e +g+pv+v+ +    +G    +v ++ +l + ++ +    +e++v+v ++++   E 
  gi|70607355|ref|YP_256225.1| 678 DKLGIKQPDWISARSIEEVRKFVEMVGYPVLVR-PSYVLSGSAMRIVYNDTELVSYIKKAteisSEHPVVVSKYIDNAIEA 757
                                   799******************************.99999***********9998888877788899*************** PP

                                   EEEEEEETTC-.EEE--EEEEE.EETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
                     ATP-grasp  79 svlvvrsaeGe.tafypvvetv.qedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEla 157
                                    + ++ + +G   ++++ ve+   ++g+  +s+  +++s +  +k +e ++ i +eL++ G f v + v+ +g+ ++ E+ 
  gi|70607355|ref|YP_256225.1| 758 EIDGASDGRGVyGVVLEHVEEAgVHSGDATISIPFKKLSPETVHKMKESIHSISRELNIKGPFNVQFVVK-NGTPYIIEMN 837
                                   ******99995323344444331467888999999999***************************86555.8886666666 PP

                                   SS CS
                     ATP-grasp 158 pR 159
                                    R
  gi|70607355|ref|YP_256225.1| 838 LR 839
                                   55 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.6e-07   0.00042      26     174 ..     151     299 ..     136     316 .. 0.76
   2 !   31.5   0.1   7.1e-11   1.2e-07       4     173 ..     679     837 ..     676     840 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                                   HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHT..T-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEE CS
               Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafk..ydekvlvEeai.egreievavlgneklevsevge 103
                                   e   +   ++gypv+V+ + +    G + + see+lk+ i +a++  y ++vl+E+++ +  e+e  v+ + +   s v++
  gi|70607355|ref|YP_256225.1| 151 EEALEKARQIGYPVMVRVSFNLGGRGSTVAWSEEDLKRDIGRALSqsYIHEVLIEKYLhHWIELEYEVMRDKH-GNSAVIA 230
                                   334455789********997777789999999******999987522789********999********9443.3344444 PP

                                   EE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEES CS
               Dala_Dala_lig_C 104 ivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNt 174
                                    + + +       ++++++ +    +l++++ + ++ +++++ k +dl G + v f l     e ++ E N+
  gi|70607355|ref|YP_256225.1| 231 CIENLDPMGV---HTGESTVIAPCQTLDNKEFQDMRSMSIDVAKSIDLVGECNVQFALnPLAYEYYIIETNP 299
                                   4443333333...3455666666677999999**************************55678899988774 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.1e-11
                                   HTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--. CS
               Dala_Dala_lig_C   4 aaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai. 81 
                                   ++G+++++++  ++        e ++k +e +gypv+V+p+   S   +  v +  el ++i++a +   ++ v+v ++i 
  gi|70607355|ref|YP_256225.1| 679 KLGIKQPDWISARSI-------EEVRKFVEMVGYPVLVRPSYVLSGSAMRIVYNDTELVSYIKKATEIssEHPVVVSKYId 752
                                   555666655544332.......446688*************99999999****************87522678*******9 PP

                                   ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS.----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE CS
               Dala_Dala_lig_C  82 egreievavlgneklevsevgeivvkkgfydyeakysddkaqlevp.aklekeveekiqelalkaykaldlrGlaRvDffl 161
                                   ++ e e+    +++    +v e+v + g+          +a++ +p  kl++e+ +k++e    + + l+++G   v f++
  gi|70607355|ref|YP_256225.1| 753 NAIEAEIDGASDGRGVYGVVLEHVEEAGVHS-------GDATISIPfKKLSPETVHKMKESIHSISRELNIKGPFNVQFVV 826
                                   999999999999999999999**99999865.......444555662579*****************************99 PP

                                   ETTTEEEEEEEE CS
               Dala_Dala_lig_C 162 teegeivlnEvN 173
                                   + +g++++ E+N
  gi|70607355|ref|YP_256225.1| 827 K-NGTPYIIEMN 837
                                   8.9********9 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.6e-07    0.0011      48     120 ..     261     336 ..     250     345 .. 0.81
   2 !   27.4   0.0   1.4e-09   2.3e-06      48     111 ..     802     866 ..     745     886 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.6e-07
                  ATPgrasp_Ter  48 elielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepe 120
                                   ++ +++ ++a+++ l g  nvQ+  +     ++++E NpR+s      s ++G  l+y+++kl+lg e  ev ++ 
  gi|70607355|ref|YP_256225.1| 261 DMRSMSIDVAKSIDLVGECNVQFALNPLAyeYYIIETNPRMSRSSAlASKATGYPLAYVSAKLALGYELYEVLNKV 336
                                   66788999***************998655469*********96655156777**************9877776655 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.4e-09
                  ATPgrasp_Ter  48 elielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysala.Gvnlpylalklllgl 111
                                   ++ e  +++ +e++++g +nvQ+  ++++p+++E+N Ras  +  s    G n+++lal+ + + 
  gi|70607355|ref|YP_256225.1| 802 KMKESIHSISRELNIKGPFNVQFVVKNGTPYIIEMNLRASRSMPFSSKVvGKNIIDLALTGVIKG 866
                                   5567788999**********************************987655********9987664 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00023      0.37     115     159 ..     257     302 ..     126     304 .. 0.66
   2 !   20.5   0.1   2.4e-07   0.00039       2     158 ..     668     840 ..     667     843 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                                   -HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS-- CS
                   ATP-grasp_3 115 elkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRlt 159
                                   ++ ++++++  +v +++ +l+G   v + l+   +e y+iE NPR+ 
  gi|70607355|ref|YP_256225.1| 257 KEFQDMRSMSIDVAKSI-DLVGECNVQFALNPlaYEYYIIETNPRMS 302
                                   33456778889999999.************99999**********85 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.4e-07
                                   TSHHHHHHHHTTT.S---....-EESS--.......SSSEEEEESS-------B--SS--TTE...............EEE CS
                   ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve........lvq 67 
                                   +d  k+ + L++ g+k P+ ++a ++ee+        +++ v p++   g+++r+v ++ e+ + i++ +        +v+
  gi|70607355|ref|YP_256225.1| 668 EDREKFSRLLDKLGIKQPDWISARSIEEVrkfvemvGYPVLVRPSYVLSGSAMRIVYNDTELVSYIKKATeissehpvVVS 748
                                   6788899999********6666666666666678889**********************999999998889999******* PP

                                   E---.SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEE...S----HHHHHHHHHHHHHTTST...T--EEEEEE CS
                   ATP-grasp_3  68 efie.GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvt...pietelkeevvelaeevvekle...glaGyvGvD 141
                                   ++i+   ++ ++  sdg  v+ +++  +++e   +  v +G  t   p++ +l+ e+v+ ++e ++++    +++G + v 
  gi|70607355|ref|YP_256225.1| 749 KYIDnAIEAEIDGASDGRGVYGVVL--EHVE---EAGVHSGDATisiPFK-KLSPETVHKMKESIHSISrelNIKGPFNVQ 823
                                   ***7368999******998887765..3444...4577888765211444.55888888888888888777799******* PP

                                   EEESS.SEEEEEEESS- CS
                   ATP-grasp_3 142 lvlkdeepyviEvNPRl 158
                                   +v+k++ py+iE N R 
  gi|70607355|ref|YP_256225.1| 824 FVVKNGTPYIIEMNLRA 840
                                   **************885 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.1e-06    0.0083       8      53 ..     123     168 ..     118     172 .. 0.89
   2 !    7.4   0.0    0.0017       2.7      16      52 ..     674     710 ..     666     762 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                   ATP-grasp_5   8 tlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKi 53 
                                   + L+ ++ +e +  +++pv+++  a+s+eea+e a++igypv +++
  gi|70607355|ref|YP_256225.1| 123 RALSREKFRETMINVNLPVPPSLSARSEEEALEKARQIGYPVMVRV 168
                                   567888888899999***************************9987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0017
                   ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                                    +ll+ +gi+ ++ + a+s ee+ + +e +gypv ++
  gi|70607355|ref|YP_256225.1| 674 SRLLDKLGIKQPDWISARSIEEVRKFVEMVGYPVLVR 710
                                   689******************************9875 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.72   1.2e+03     136     174 ..      16      56 ..      15      61 .. 0.81
   2 ?    1.2   0.0      0.15   2.5e+02      15      74 ..     138     196 ..     126     215 .. 0.73
   3 !   16.6   0.0   2.8e-06    0.0046       1      88 [.     667     757 ..     667     761 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.72
                                   HHHHHHCT-SEEEEEEEEE..TTEEEEEEEESS--SHHHHH CS
                          RimK 136 ikaakamelvvaGvDllra..krgllvlEvnsspglekiek 174
                                   ik+a+a e ++ G   l+a  ++g+  + vns++ + + ++
  gi|70607355|ref|YP_256225.1|  16 IKIAEAAEFDYSGSQALKAlkEEGIETILVNSNVATVQTSR 56 
                                   8999*********99887532567888999**999887776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                                   T-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG CS
                          RimK  15 kikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lke 74 
                                   +++vp +  ar+ee+a +   +i  + Pv+v+ ++   G +  +a  e++lk  +   l +
  gi|70607355|ref|YP_256225.1| 138 NLPVPPSLSARSEEEALEKARQI--GYPVMVRVSFNLGGRGSTVAWSEEDLKRDIGRaLSQ 196
                                   56777788888999998888888..69********99999999999888887654322333 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 2.8e-06
                                   HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....GGG-- CS
                          RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....lkeai 76 
                                   a+d+ k  +lL k +ik p    ar+ e+++k++e++  + Pv+v+ ++   G  + +  +  +l++ ++       ++ +
  gi|70607355|ref|YP_256225.1| 667 AEDREKFSRLLDKLGIKQPDWISARSIEEVRKFVEMV--GYPVLVRPSYVLSGSAMRIVYNDTELVSYIKKateisSEHPV 745
                                   67888999*****************************..69************************9999875454334446 PP

                                   EEEEE--SS-SE CS
                          RimK  77 lvqeyieeaene 88 
                                   +v +yi++a ++
  gi|70607355|ref|YP_256225.1| 746 VVSKYIDNAIEA 757
                                   9999*9988665 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.087   1.4e+02       7     100 ..     131     220 ..     126     270 .. 0.81
   2 !   15.6   0.1   6.4e-06      0.01       8     188 ..     675     839 ..     669     842 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.087
                                   HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE CS
                        GARS_A   7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEe 87 
                                   ++ + ++++p +   +  + eea e  ++ + ++  v+ +   +g+g +va see+  + +   l++       ++v+iE+
  gi|70607355|ref|YP_256225.1| 131 RETMINVNLPVPPSLSARSEEEALEKARQIGYPV-MVRVSFNLGGRGSTVAWSEEDLKRDIGRALSQSY----IHEVLIEK 206
                                   6778889999999999999999***********9.778787789************9999999998543....47999999 PP

                                   ---S.EEEEEEEEE CS
                        GARS_A  88 lleG.eEvsllalv 100
                                   +l+  +E+   ++ 
  gi|70607355|ref|YP_256225.1| 207 YLHHwIELEYEVMR 220
                                   99632566555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.4e-06
                                   HHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE- CS
                        GARS_A   8 dllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEel 88 
                                   +ll+k gi+ +++ +  + ee+++++e ++ ++  v+++ + +g  + ++ + +e ++++k+  e     ++++ vv+ ++
  gi|70607355|ref|YP_256225.1| 675 RLLDKLGIKQPDWISARSIEEVRKFVEMVGYPV-LVRPSYVLSGSAMRIVYNDTELVSYIKKATE----ISSEHPVVVSKY 750
                                   5899*****************************.99************************99987....46899******* PP

                                   --.SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEE CS
                        GARS_A  89 le.GeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglkkegipfkGv 168
                                   ++  +E  +   +dg+ v+ + l  +  +v   + g+  G      p   +++e+++k+ke      ++ +++e  + kG 
  gi|70607355|ref|YP_256225.1| 751 IDnAIEAEIDGASDGRGVYGVVL--E--HVE--EAGVHSGDATISIPFKKLSPETVHKMKE-----SIHSISRE-LNIKGP 819
                                   97357999999999999987654..3..344..3577777777777999999999998888.....55667776.788898 PP

                                   EEEEEEEETTEEEEEEEESS CS
                        GARS_A 169 LyaglmlvedgpkvlefnvR 188
                                     +++++ +  p+++e+n R
  gi|70607355|ref|YP_256225.1| 820 FNVQFVVKNGTPYIIEMNLR 839
                                   88898887777999999998 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   3.5e+03       8      18 ..     103     113 ..     101     118 .. 0.88
   2 !   10.8   0.0   0.00016      0.26      10      55 ..     133     177 ..     126     200 .. 0.89
   3 ?   -2.1   0.0       1.4   2.3e+03     146     172 ..     494     520 ..     473     527 .. 0.79
   4 ?    0.0   0.0      0.32   5.3e+02       9      51 ..     675     717 ..     672     738 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                                   HHHHHCTT--- CS
                   ATP-grasp_2   8 keilakygvkv 18 
                                   keil+kygvkv
  gi|70607355|ref|YP_256225.1| 103 KEILKKYGVKV 113
                                   89*******98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                                   HHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCC CS
                   ATP-grasp_2  10 ilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGK 55 
                                    + + +++vp +  a+s+eea e+a+++g  + +v+     GGRG 
  gi|70607355|ref|YP_256225.1| 133 TMINVNLPVPPSLSARSEEEALEKARQIGYPV-MVRVSFNLGGRGS 177
                                   5667899***********************99.9**********96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                                   EEEBTTTB--HHHHHHHHHHCT--CHH CS
                   ATP-grasp_2 146 vaidpakglkeeqareiakklglekel 172
                                   ++i  a+gl+e+ +re+ +k g+e ++
  gi|70607355|ref|YP_256225.1| 494 YQIASAVGLSEKDIRELRQKYGIEPKV 520
                                   567778888888888888888888764 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.32
                                   HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSS CS
                   ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaG 51 
                                    +l k g+k p    a+s ee+++ ++ +g  +lv  + vl G
  gi|70607355|ref|YP_256225.1| 675 RLLDKLGIKQPDWISARSIEEVRKFVEMVGYPVLVRPSYVLSG 717
                                   6899***********************9999998877777776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.002       3.3      10      69 ..      27      85 ..      26      99 .. 0.91
   2 ?    2.9   0.0     0.038        62       7      37 ..     638     668 ..     635     702 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.002
                                  HHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEE CS
                     Epimerase 10 iGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavi 69
                                   Gs+ +kal+e+g+e i ++++  + +t+r+   +l+ + +t  + +er++++e+pda++
  gi|70607355|ref|YP_256225.1| 27 SGSQALKALKEEGIETILVNSNVATVQTSRKFADKLYMIPVTWWT-VERVIEKERPDAIM 85
                                  59********************99***999999999999999776.************98 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.038
                                   TSHHHHHHHHHHHHCTSEEEEEES-STTTTC CS
                     Epimerase   7 tGfiGsalvkallekgyevigldrlssasnt 37 
                                    G+iG+ + k+l+e+g++++g +  s + ++
  gi|70607355|ref|YP_256225.1| 638 GGQIGNTISKKLEENGVKLLGTSGHSVDIAE 668
                                   69****************9998877555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1052 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.43
# Mc/sec: 7272.76
//
Query:       gi|70607356|ref|YP_256226.1|  [L=282]
Description: 30S ribosomal protein S6 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-26   91.0   0.0    1.1e-25   90.3   0.0    1.3  1  RimK             RimK-like ATP-grasp domain
    8.6e-08   31.8   0.0    1.5e-07   31.0   0.0    1.3  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
      9e-07   29.1   0.0    1.8e-06   28.1   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.015   14.6   0.0       0.14   11.4   0.0    2.1  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.025   14.1   0.1      0.084   12.4   0.1    1.9  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   3.2e-29   1.1e-25       3     187 ..      86     275 ..      84     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 3.2e-29
                                   -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH....GGG--... CS
                          RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea....lkeai... 76 
                                   dK+++   L +++i++p + +a + + a k  e+   +fP++ K   gs G  v l ++  + k ++e      + a+   
  gi|70607356|ref|YP_256226.1|  86 DKILTYSKLYREGIPIPDSIIAMSSDAALKAYEQK--GFPLIDKPPIGSWGRLVSLIRDIFEGKTIIEHrelmGNSALkvh 164
                                   89999999**************************9..6*****************************99887634444667 PP

                                   EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEE.ETT CS
                          RimK  77 lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllr.akr 156
                                   +vqeyi+ + ++diR++v++ e  + + r     ++R+n+ +Gg  +++++++++ke  +ka+ +++  ++ +D+++ + +
  gi|70607356|ref|YP_256226.1| 165 IVQEYINYK-SRDIRCIVIGSELLGCYARNIPSNEWRANIALGGYPSQIEVDHKLKETVLKATSIIGGEFVSIDVMEhQSK 244
                                   9*****976.89*****************999999***************************************8862678 PP

                                   EEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                          RimK 157 gllvlEvnsspglekiektlgidiakkliea 187
                                   ++++ E n  p+ +++   ++id+a++l+++
  gi|70607356|ref|YP_256226.1| 245 NYVINEFNDVPEFKGFMLATNIDVAEELVSY 275
                                   88889***********************987 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   4.1e-11   1.5e-07      12     154 ..     101     241 ..      91     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.1e-11
                                   S--EEEES-H.HHHHHHHHHHSSEEEEESS--TTTT-EEE-TT..-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EEEEE CS
                     GSH-S_ATP  12 ipktlvskdk.eeirafleeqgdvilKPldgkgGegvfrvkks..dpnlksilellteegkepviaqrylpeikeGDkRil 89 
                                   ip+++++ ++ ++++a+ ++   +i KP  g+ G+ v  +++    + +    el+ ++  +  i+q+y++  k+ D R +
  gi|70607356|ref|YP_256226.1| 101 IPDSIIAMSSdAALKAYEQKGFPLIDKPPIGSWGRLVSLIRDIfeGKTIIEHRELMGNSALKVHIVQEYINY-KSRDIRCI 180
                                   5677777655145677777777799999999999988777664224445555677888888999******86.556***** PP

                                   EETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                     GSH-S_ATP  90 lvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                   ++  e +g + aR   ++e R+n+a gg  ++ e++   +++ e++ ++ +  G  fv +Dv+++
  gi|70607356|ref|YP_256226.1| 181 VIGSELLG-CYARNIPSNEWRANIALGGYPSQIEVD---HKLKETVLKATSIIGGEFVSIDVMEH 241
                                   ********.999988899************999885...56677777777888999999999875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.9e-10   1.8e-06       1     152 [.      84     248 ..      84     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.9e-10
                                   HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE................. CS
                   ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.......... 64 
                                   + dK+ ty kL ++g+++P       + +  +  e++  +l+ Kp  G+ g  v+++++  e +++ie+ e          
  gi|70607356|ref|YP_256226.1|  84 CGDKILTYSKLYREGIPIPdsiiamsSDAALKAYEQKGFPLIDKPPIGSWGRLVSLIRDIFEGKTIIEHRElmgnsalkvh 164
                                   78*****************888877666666677777999****************************999********** PP

                                   EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEES CS
                   ATP-grasp_3  65 lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlk 145
                                   +vqe+i+ k+  + +++ g++ l+ +  r++  ++++ ++  G+  p++ e ++++ e++ ++++ +     +v +D++ +
  gi|70607356|ref|YP_256226.1| 165 IVQEYINYKSRDIRCIVIGSE-LLGCYARNIPSNEWRANIALGG-YPSQIEVDHKLKETVLKATSII--GGEFVSIDVMEH 241
                                   *****************6643.3345566666777777777776.4788888889999999998888..234788999999 PP

                                   S.SEEEE CS
                   ATP-grasp_3 146 deepyvi 152
                                   +++ yvi
  gi|70607356|ref|YP_256226.1| 242 QSKNYVI 248
                                   8888888 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     4e-05      0.14       9      96 ..      74     157 ..      70     185 .. 0.79
   2 ?    0.8   0.0     0.066   2.4e+02     226     272 ..     216     261 ..     209     274 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4e-05
                   ATPgrasp_ST   9 kyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdylk 89 
                                    +N+   + l  dK+++++ + r+g+++p+ ++ ++  a +++ e+  k++ + ++ Kp  gs+G+ ++ i ++ + + + 
  gi|70607356|ref|YP_256226.1|  74 TINSSDTISLCGDKILTYSKLYREGIPIPDSIIAMSSDAALKAYEQ--KGF-P-LIDKPPIGSWGRLVSLIRDIFEGKTII 150
                                   68999999**********************8888887777666654..444.5.789999999999998888777666655 PP

                   ATPgrasp_ST  90 ssgksal 96 
                                   +  + + 
  gi|70607356|ref|YP_256226.1| 151 EHRELMG 157
                                   5555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.066
                   ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpglaivq 272
                                   +++ e++ ka   + g   +++D+   ++k+ ++ E N+ p  + + 
  gi|70607356|ref|YP_256226.1| 216 HKLKETVLKATS-IIGGEFVSIDVMEHQSKNYVINEFNDVPEFKGFM 261
                                   577888899988.999999*****99999999999***999887665 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.4e-05     0.084     133     179 ..     213     258 ..     154     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                   HHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS---S CS
               Dala_Dala_lig_C 133 eveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPGfT 179
                                   ev +k++e++lka ++++++ ++ +D++ +++ + v+nE N +P f 
  gi|70607356|ref|YP_256226.1| 213 EVDHKLKETVLKATSIIGGE-FVSIDVMEHQSKNYVINEFNDVPEFK 258
                                   78899*********999986.778********************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2114.94
//
Query:       gi|70607357|ref|YP_256227.1|  [L=195]
Description: haloacid dehalogenase superfamily protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-09   38.0   2.2    2.8e-07   30.7   2.2    2.1  1  Translin  Translin family
     0.0087   16.3   1.0        1.6    9.1   0.3    2.4  2  Coat_F    Coat F domain
  ------ inclusion threshold ------
        1.2    9.5   5.8        5.2    7.4   0.4    3.1  2  TPR_2     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   2.2   4.7e-11   2.8e-07       1     192 [.      22     183 ..      22     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 4.7e-11
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.HHHHHHHHHHHTTSS..........GHHHHGGGTH.HHHH CS
                      Translin   1 drreriikasrditaaskkiifllhrvrsekteaqdkkakikkeakeklkeiakllasvaeelqgsnayrYqrqisgglqe 81 
                                   d re+   +sr+i +++ ++i l hr+r+    ++ +k k++ e  ++lk++ +++          +   Y  +i  + qe
  gi|70607357|ref|YP_256227.1|  22 DAREKAFSISREIIRYAGEAISLSHRFRK---DEALNKYKLALEKLDNLKKLIEKY----------PELLY-GEIATAFQE 88 
                                   789*************************4...445666665555555555555555..........33335.466669999 PP

                                   HHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHH CS
                      Translin  82 liealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflre 162
                                   + ea   ++   +q+L+     ++           ++ ++   Y+lG++d +gEL R    ++ +++ e ++ +++++++e
  gi|70607357|ref|YP_256227.1|  89 VAEATIVISIYFNQNLLI----AT-----------DLGIPDAFYILGIADAIGELRRKTLEHLRKKELE-EAEKTYQMMEE 153
                                   999987766666666653....23...........34567788*********************99977.9********** PP

                                   HHHHHHTS----HH...HHHHHTTHHHHHH CS
                      Translin 163 lragfellnlkndsakdlrkKldvlkqsvk 192
                                   l++ +  l+ +     +lr+K+d+++  ++
  gi|70607357|ref|YP_256227.1| 154 LYELLWELEYPKALVPNLRQKIDAMRRVLE 183
                                   ***99999999655679********98765 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3   0.00026       1.6      33      55 ..     130     152 ..     127     154 .. 0.94
   2 !    5.3   0.0    0.0037        22      30      51 ..     169     190 ..     168     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00026
                        Coat_F  33 Rqtlkqilneeiemqeelfnlmn 55 
                                   R+tl +++++e+e +e+ +++m 
  gi|70607357|ref|YP_256227.1| 130 RKTLEHLRKKELEEAEKTYQMME 152
                                   89********************7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0037
                        Coat_F  30 pelRqtlkqilneeiemqeelf 51 
                                   p+lRq + +++   +e + ++f
  gi|70607357|ref|YP_256227.1| 169 PNLRQKIDAMRRVLEETHHDIF 190
                                   9********************9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4   0.00088       5.2       7      30 ..      40      63 ..      35      67 .. 0.85
   2 ?    3.5   0.5     0.016        95      11      25 ..     135     149 ..     133     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00088
                         TPR_2  7 lGlayyklgdyeeAleafekAlel 30
                                   + ++ ++ + +eAl+ ++ Ale 
  gi|70607357|ref|YP_256227.1| 40 EAISLSHRFRKDEALNKYKLALEK 63
                                  678888999*************96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                         TPR_2  11 yyklgdyeeAleafe 25 
                                   +++++++eeA++ ++
  gi|70607357|ref|YP_256227.1| 135 HLRKKELEEAEKTYQ 149
                                   7899********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1308.06
//
Query:       gi|70607358|ref|YP_256228.1|  [L=320]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-49  168.2   0.0    2.6e-49  167.5   0.0    1.3  1  3HCDH_N   3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
      2e-17   63.6   0.1    4.3e-17   62.5   0.1    1.5  1  3HCDH     3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.18   11.5   0.0       0.39   10.4   0.0    1.6  1  ApbA      Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.0   4.3e-53   2.6e-49       2     178 ..       7     184 ..       6     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 4.3e-53
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEE CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlv 82 
                                   v ++GaG++Gag+ +++a +g++   +  ++e+l+k+  ki+  l+ ++e  kl +++ e++++ i++ttd++++ + d++
  gi|70607358|ref|YP_256228.1|   7 VSIVGAGIIGAGWSTLLAVHGYRNIFYTEKKETLDKGILKIKGYLQVMHE-YKLADKSPEEYMKLITPTTDFNDVLKGDFI 86 
                                   89****************************************98887755.556669************************ PP

                                   EE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCS.SSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHH CS
                       3HCDH_N  83 iEavvEnlelKrkvfaelekiakpdailasnTSslsiselaeal.krperviglHFfnPpplmkLvEvvrgekTseetvat 162
                                   iEav+E++ +K+kvf el++ +++d+i+as+TS+l ise+++++ ++per i++H++nPp+l++LvE+v+gekTsee+++ 
  gi|70607358|ref|YP_256228.1|  87 IEAVIEDYGVKKKVFGELDERLDKDVIIASSTSGLLISEIQKSMsRHPERAIIAHPWNPPHLLPLVEIVPGEKTSEEVIQS 167
                                   *******************************************9459********************************** PP

                                   HHHHHHHTT-EEEEE.C CS
                       3HCDH_N 163 vvelakkigktpvvv.k 178
                                   ++e++++  k +vvv k
  gi|70607358|ref|YP_256228.1| 168 TREFMEDKLKRVVVVlK 184
                                   *****988555555534 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.1   7.1e-21   4.3e-17       1      87 [.     189     273 ..     189     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 7.1e-21
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GF+ nR++++l++eav+l++egva++ediD+++++++Gl++ +++++ +++l++++  le+++++     ++  +++ +l+
  gi|70607358|ref|YP_256228.1| 189 GFIGNRLAFALFREAVHLIDEGVATVEDIDKVVTAAIGLRWVFMGPFLTYHLGGGEGGLEYFFSRGFGYGAN--EWMYTLA 267
                                   9***********************************************************999886655444..7999999 PP

                                   HTT--B CS
                         3HCDH  82 eagrlg 87 
                                   +++++ 
  gi|70607358|ref|YP_256228.1| 268 KYDKFP 273
                                   888875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.5e-05      0.39       2      45 ..       8      49 ..       7      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.5e-05
                                  EEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEE CS
                          ApbA  2 ailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrlts 45
                                   i+GaG iG  +   La +g+  ++++ ++  e+l k  l++++
  gi|70607358|ref|YP_256228.1|  8 SIVGAGIIGAGWSTLLAVHGYRNIFYTEKK--ETLDKGILKIKG 49
                                  79**************99********9999..555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2386.81
//
Query:       gi|70607359|ref|YP_256229.1|  [L=188]
Description: hypothetical protein Saci_1624 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-15   56.5   0.1    2.4e-15   56.0   0.1    1.3  1  Cupin_2         Cupin domain
      3e-10   39.9   0.0    5.1e-10   39.2   0.0    1.3  1  Cupin_1         Cupin
    1.8e-07   31.1   0.0    3.5e-07   30.2   0.0    1.4  1  AraC_binding    AraC-like ligand binding domain
    1.5e-05   25.1   0.0    2.4e-05   24.5   0.0    1.3  1  CENP-C_C        Mif2/CENP-C like
    0.00011   22.5   1.1    0.00052   20.2   0.0    2.1  2  ARD             ARD/ARD' family
     0.0011   18.8   0.0     0.0021   17.9   0.0    1.5  1  Asp_Arg_Hydrox  Aspartyl/Asparaginyl beta-hydroxylase
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.02   14.7   0.0    1.3  1  EutQ            Ethanolamine utilisation protein EutQ
      0.026   14.2   0.0      0.064   12.9   0.0    1.6  1  Auxin_BP        Auxin binding protein
      0.031   14.2   0.4        5.2    7.1   0.0    2.2  2  Prefoldin_2     Prefoldin subunit
       0.13   11.9   0.1       0.24   11.0   0.1    1.4  2  DMSP_lyase      Dimethlysulfonioproprionate lyase
       0.14   11.8   0.0       0.27   10.9   0.0    1.4  1  AraC_N          AraC-type transcriptional regulator N-terminu


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   1.5e-18   2.4e-15       2      70 ..      99     166 ..      98     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.5e-18
                                   EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                   ++ l+pG ++++h+H  +  ++ V++G+g  +++g++ve e Gd++++pa+ pH+++Nt+d++  l++v
  gi|70607359|ref|YP_256229.1|  99 FQYLKPGSKTQPHSHNMA-SIYLVVRGKGYSIIGGKKVEWENGDVFVVPANLPHYHVNTSDTESILFDV 166
                                   6789**************.******************************************99888877 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   3.1e-13   5.1e-10      36     114 ..      97     168 ..      89     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.1e-13
                                   EEEEE..TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEE.EETTEEEEE-TT-EEEEEEESSSSEEEEEEEE CS
                       Cupin_1  36 arvdl.epgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkk.lreGdvfvvPaglvhfqynsgdepavaivvfd 114
                                   a + + +pg+  +Ph h n ++i  v+ G+g+  ++  +       k+  + GdvfvvPa+l+h+++n+ d++   + v d
  gi|70607359|ref|YP_256229.1|  97 AGFQYlKPGSKTQPHSH-NMASIYLVVRGKGY-SIIGGK-------KVeWENGDVFVVPANLPHYHVNTSDTESILFDVTD 168
                                   4455669**********.**************.555444.......3459*******************988887775555 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.1e-10   3.5e-07      12      61 ..     104     153 ..      96     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.1e-10
                                   TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEE CS
                  AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdy 61 
                                   p+  ++ph h+ + i +v++G+g+  ++g+ ++ + Gd+f +p + pH+ 
  gi|70607359|ref|YP_256229.1| 104 PGSKTQPHSHNMASIYLVVRGKGYSIIGGKKVEWENGDVFVVPANLPHYH 153
                                   78899*******************************************85 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.4e-08   2.4e-05      10      82 ..      93     164 ..      88     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                                   TS-EEEEEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-EEEE CS
                      CENP-C_C  10 kflasGilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkeaklf 82 
                                   + + +G+ +L+pg +K++ +s+++  ++ V++G+    + +++    +g+vF vPa       N++++e+ lf
  gi|70607359|ref|YP_256229.1|  93 PTMMAGFQYLKPG-SKTQPHSHNMASIYLVVRGKGYSIIGGKKVEWENGDVFVVPANLPHYHVNTSDTESILF 164
                                   57889******97.689999*************************************999999******9998 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       0.4   6.6e+02      70      98 ..       8      36 ..       2      49 .. 0.65
   2 !   20.2   0.0   3.2e-07   0.00052      86     140 ..     109     158 ..     105     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.4
                           ARD 70 lkestpnfdeklekFfeEhlhedeeirli 98
                                  + ++ +   +k+++  +E  ++de+++++
  gi|70607359|ref|YP_256229.1|  8 IDKQSEIITDKIKNVIREIEQSDEDLKVV 36
                                  44444555667777777777777766654 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.2e-07
                           ARD  86 eEhlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhrFtlted 140
                                   ++h+h+ + i l+v G+gy  +  k  +w      +GD  v+Pa++ h+   t+d
  gi|70607359|ref|YP_256229.1| 109 QPHSHNMASIYLVVRGKGYSIIGGKKVEWE-----NGDVFVVPANLPHYHVNTSD 158
                                   79***********************99996.....*************9866655 PP

>> Asp_Arg_Hydrox  Aspartyl/Asparaginyl beta-hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0021      75     147 ..      94     161 ..      76     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                   EEEEEEEEE-TTEEEEEE-S..-TTSEEEEEEE--TTEEEEETTEEE---TTEEEEE-TTS-EEEEE-SSS-E CS
                Asp_Arg_Hydrox  75 lgealfsvlepgshikpHrgptngrlrlhLgLvvPeeceirvggetrtweeGevllfDdsfeHevwnetdeeR 147
                                     +a f  l+pgs+ +pH+ +++      + Lvv  + +  +gg++ +we+G+v+++ +  +H+ +n++d+e 
  gi|70607359|ref|YP_256229.1|  94 TMMAGFQYLKPGSKTQPHSHNMA-----SIYLVVRGKGYSIIGGKKVEWENGDVFVVPANLPHYHVNTSDTES 161
                                   56899**************9333.....4457788888999****************************9875 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.2e-05      0.02       3     128 ..      12     148 ..      10     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                          EutQ   3 kelleqlvrkvikeklglekaeqsesfkkkvdksGilsvklid.vkvkkedrl.dtgnPkdvvltkdlv...tlee....s 74 
                                    e++ + +++vi+e    +++ + + f++++ +   +  k+i+  kv +  rl    nP + +++k ++   t       +
  gi|70607359|ref|YP_256229.1|  12 SEIITDKIKNVIREIEQSDEDLKVVAFMEHTSPPETIKPKIIKfHKVLELLRLlADDNPIEKGVAKVMFqspTTGRakglT 92 
                                   578899999999998888888999999999988877777776525677777762567999999999888333222212224 PP

                          EutQ  75 krlgaGlmemk..ettfdwtlnydeidyvieGrldvlidGrkvvaeaGdviliPkg 128
                                   + + aG+  +k    t +   n   i +v+ G+   +i G+kv  e Gdv ++P +
  gi|70607359|ref|YP_256229.1|  93 PTMMAGFQYLKpgSKTQPHSHNMASIYLVVRGKGYSIIGGKKVEWENGDVFVVPAN 148
                                   67888988777335799*************************************87 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05     0.064      48      86 ..      99     137 ..      88     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                                   EEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSSS CS
                      Auxin_BP  48 lqtlapgsrtpihrhsceevfvvlkgkgtlylassssky 86 
                                   +q l pgs+t  h h    ++ v++gkg  +++  + ++
  gi|70607359|ref|YP_256229.1|  99 FQYLKPGSKTQPHSHNMASIYLVVRGKGYSIIGGKKVEW 137
                                   68899***********************99888666555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.013        21      29      47 ..      17      35 ..       3      39 .. 0.72
   2 ?    7.1   0.0    0.0032       5.2      27      59 ..      51      83 ..      46      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                  HHHHHHHHHHHHS-TT--E CS
                   Prefoldin_2 29 kelelvleelelldedtkv 47
                                  ++++ v+ e+e+ ded kv
  gi|70607359|ref|YP_256229.1| 17 DKIKNVIREIEQSDEDLKV 35
                                  5678888888888888776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0032
                                  HHHHHHHHHHHHHHS-TT--EEEEETTEEEEE- CS
                   Prefoldin_2 27 qlkelelvleelelldedtkvyklvGdvlvkqd 59
                                  ++ + ++vle l ll++d+++ k v +v+++ +
  gi|70607359|ref|YP_256229.1| 51 KIIKFHKVLELLRLLADDNPIEKGVAKVMFQSP 83
                                  5567899*********************99875 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.6   5.9e+03      44      60 ..      18      34 ..       8      49 .. 0.57
   2 ?   11.0   0.1   0.00015      0.24      93     154 ..      93     153 ..      84     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.6
                    DMSP_lyase 44 alralvralkalepaLe 60
                                  ++++++r +++  ++L+
  gi|70607359|ref|YP_256229.1| 18 KIKNVIREIEQSDEDLK 34
                                  34455555554444443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                    DMSP_lyase  93 ddvalGlvllaPkvrYPdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikham 154
                                   +++++G+  l P  +   H+h+ + +Ylv+ g   ++  +++ ++ + G+v+  + +++h+ 
  gi|70607359|ref|YP_256229.1|  93 PTMMAGFQYLKPGSKTQPHSHNMASIYLVVRGK-GYSIIGGKKVEWENGDVFVVPANLPHYH 153
                                   67999**********99*************986.677777777999***********99975 PP

>> AraC_N  AraC-type transcriptional regulator N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.27      16      57 ..     109     150 ..     102     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                        AraC_N  16 valvvyepslcivlqGkKrvhlgdeafeydpgeylvvsvdlp 57 
                                    +++ +  s+ +v++Gk   ++g++++e ++g+++vv+++lp
  gi|70607359|ref|YP_256229.1| 109 QPHSHNMASIYLVVRGKGYSIIGGKKVEWENGDVFVVPANLP 150
                                   566777889********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1288.70
//
Query:       gi|70607360|ref|YP_256230.1|  [L=61]
Description: hypothetical protein Saci_1625 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.28   11.2   7.1        2.8    8.0   0.1    2.7  2  DUF326      Domain of Unknown Function (DUF326)
       0.97    7.6   5.7        1.1    7.5   5.7    1.0  1  Fusion_gly  Fusion glycoprotein F0


Domain annotation for each model (and alignments):
>> DUF326  Domain of Unknown Function (DUF326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00031       2.8      12      20 ..      10      18 ..      10      19 .. 0.93
   2 ?    4.7   2.9    0.0034        31       3       9 ..      32      42 ..      31      46 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00031
                                  HHHHHHHHH CS
                        DUF326 12 rkCAkaCrk 20
                                  rkC+++C k
  gi|70607360|ref|YP_256230.1| 10 RKCVEICGK 18
                                  8******98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0034
                                  HHHHHH....H CS
                        DUF326  3 hckkCA....k 9 
                                  +c+kCA    k
  gi|70607360|ref|YP_256230.1| 32 ICEKCAngdkK 42
                                  46666655555 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.7   0.00012       1.1     302     342 ..       5      45 ..       2      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00012
                                   EEE-GGGCEEETTEEEESS--EE---HHHHHHHTT-GGGSE CS
                    Fusion_gly 302 sevdasdCkvtsesviCkqdaaltlskeveeClsgstsaCk 342
                                    +++  +C++   +v+C+++ +    +  e+C +g++++C 
  gi|70607360|ref|YP_256230.1|   5 VYYENRKCVEICGKVVCDKATVEDYGSICEKCANGDKKSCI 45 
                                   578899**********************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 381.60
//
Query:       gi|70607361|ref|YP_256231.1|  [L=190]
Description: hypothetical protein Saci_1626 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0036   16.2   6.2     0.0041   16.0   6.2    1.1  1  DUF2142      Predicted membrane protein (DUF2142)
  ------ inclusion threshold ------
      0.028   14.2  16.7      0.028   14.2   6.2    2.1  2  7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
       0.13   12.1  16.2       0.28   11.0   4.0    2.1  2  VIT1         VIT family
        0.2   11.7   1.3         17    5.5   0.1    2.9  3  NDUF_B12     NADH-ubiquinone oxidoreductase B12 subunit famil
       0.27    9.5  10.5       0.32    9.2  10.5    1.1  1  DUF2070      Predicted membrane protein (DUF2070)
       0.76   10.0   8.8         15    5.8   8.8    2.1  1  EI24         Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> DUF2142  Predicted membrane protein (DUF2142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   6.2   1.4e-06    0.0041     237     376 ..      52     188 ..      18     190 .] 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                       DUF2142 237 sallllaliiiaialalrivqkipairgels.senvdvsaqlklllshplaivr...vfirsvetnlsvfvgqfigdlgwl 313
                                     ll+++++ i+ a+++  ++ +  i+ ++   +n    + lk l + ++ + +   +f++++++ ls f+g  i  + ++
  gi|70607361|ref|YP_256231.1|  52 TILLGIMSGLIGVAMSSLCNTLVVEIKEKELeLRNL-ERQILKSLKGTIIDYSQkigIFLNTLVHGLSPFIGIVIIVFYYF 131
                                   246777777777777777777777666666432222.23334444444444444555************************ PP

                       DUF2142 314 dvplPswlifawivllllllfaalvlgelrlkekllvllvvlaivilivlalylswtpvgaev 376
                                   + ++    i +++  l+l  + + + ge++    ++ ++++++i +l+ +al ++ t + +++
  gi|70607361|ref|YP_256231.1| 132 SENM---WITIFLSSLILSILGSIYSGEIK---ERINTAIIMLIAGLVTAALSIVLTKTLGSP 188
                                   ****...55555556666666668888888...889999999999************999887 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.8    0.0038        11      89     123 ..      35      70 ..      26      72 .. 0.83
   2 ?   14.2   6.2   9.2e-06     0.028      82     147 ..     116     181 ..     105     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0038
                   7TM-7TMR_HD  89 vllsllisil.fgnnlellllalvsglvgallvrkl 123
                                   v ls+l+s + ++ n++ +ll+++sgl+g+ + + +
  gi|70607361|ref|YP_256231.1|  35 VGLSILVSTViVEANFNTILLGIMSGLIGVAMSSLC 70 
                                   456777777769*****************9887655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.2e-06
                   7TM-7TMR_HD  82 rlalvvsvllsllisilfgnnlellllalvsglvgallvrklrsRsdllragllvalvnvlvilal 147
                                    l+ +++++++++  +  + +++++l +l+ +++g+++ +++++R++ + + l ++lv +++ ++l
  gi|70607361|ref|YP_256231.1| 116 GLSPFIGIVIIVFYYFSENMWITIFLSSLILSILGSIYSGEIKERINTAIIMLIAGLVTAALSIVL 181
                                   466788888888888888***************************************999554433 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.7   0.00074       2.2       2      47 ..      23      67 ..      22      94 .. 0.89
   2 ?   11.0   4.0   9.4e-05      0.28     141     214 ..     108     182 ..      78     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00074
                          VIT1  2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiS 47
                                  r ++lGa DG+++ +++ +  + +++ + +t+ll+ +++l+  a+S
  gi|70607361|ref|YP_256231.1| 23 RYLILGAFDGILVGLSILVSTVIVEA-NFNTILLGIMSGLIGVAMS 67
                                  5689*************999998885.9999**9999****99998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.4e-05
                          VIT1 141 salsfliGgliPllpylfve..svglalvvsiavtllalllfGavkalltgssk.lvsalrmlliGalAaaaaylig 214
                                   ++l  l+ gl P + ++++     ++ +++ i +++l+l ++G + +  ++ +  +  a+ ml+ G+++aa++++++
  gi|70607361|ref|YP_256231.1| 108 IFLNTLVHGLSPFIGIVIIVfyYFSENMWITIFLSSLILSILGSIYS--GEIKErINTAIIMLIAGLVTAALSIVLT 182
                                   788899999999999987665679999999999**********9865..666666999**************99876 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.032        95      24      46 ..      28      49 ..      20      54 .. 0.84
   2 ?    5.5   0.1    0.0058        17      19      47 ..     106     136 ..     102     142 .. 0.87
   3 ?    0.0   0.0       0.3   9.1e+02      23      46 ..     165     184 ..     153     190 .] 0.57

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.032
                      NDUF_B12 24 raffpGfglavaafaaavgyEhf 46
                                  +af  G  +++++ + +v++E  
  gi|70607361|ref|YP_256231.1| 28 GAF-DGILVGLSILVSTVIVEAN 49
                                  567.9***************976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0058
                      NDUF_B12  19 akrfkraffpGf..glavaafaaavgyEhfl 47 
                                      f +++++G+   +++++++ +   E+++
  gi|70607361|ref|YP_256231.1| 106 IGIFLNTLVHGLspFIGIVIIVFYYFSENMW 136
                                   567899999***989*************998 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.3
                      NDUF_B12  23 kraffpGfglavaafaaavgyEhf 46 
                                   + ++  G+ +a+  ++++    + 
  gi|70607361|ref|YP_256231.1| 165 IIMLIAGLVTAALSIVLT----KT 184
                                   455555665555555554....44 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  10.5   0.00011      0.32      21     175 ..      34     185 ..      14     190 .] 0.60

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00011
                       DUF2070  21 iillalligllaflssk...lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall.q 97 
                                   ++ l++l++ + +++++   l gi+  ++   ++ l  + v++i ++       l l  l   i  + sl ++++ +    
  gi|70607361|ref|YP_256231.1|  34 LVGLSILVSTVIVEANFntiLLGIMSGLIGVAMSSLCNTLVVEIKEKE------LELRNLERQI--LKSLKGTIIDYSQkI 106
                                   344444444444444411113333333333444444444444443333......2222222222..223455555555556 PP

                       DUF2070  98 alvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.fspesfllllllslifalavylfivvv 175
                                    ++l+ lv +l+  ++++++v++ +s++ ++++ l +li ++l+ +++  +  + ++++++l++ l+ a++++++ + +
  gi|70607361|ref|YP_256231.1| 107 GIFLNTLVHGLSPFIGIVIIVFYYFSENMWITIFLSSLILSILGSIYSGEIkERINTAIIMLIAGLVTAALSIVLTKTL 185
                                   66778999***********************999999999999999999995444566666666666666666665555 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.8    0.0051        15      58     129 ..      58     137 ..       6     189 .. 0.41

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0051
                                   HHHHHHHHHHHHHHHHHHHHHH.HH.......CCTTSHHHHHHHHHHHHHHHHHHHHHHH.TTHHH....HHHHHHHHHH CS
                          EI24  58 fplvalllaapfygllaekvekrhl.......glvkslaeslkslllllllllvllplli.Pvvglilsplllswltayf 129
                                   ++++  + ++ ++++l+ ++++++l       +++ksl  ++      + ++l +l+ ++ P++g++++++  +  + ++
  gi|70607361|ref|YP_256231.1|  58 MSGLIGVAMSSLCNTLVVEIKEKELelrnlerQILKSLKGTIIDYSQKIGIFLNTLVHGLsPFIGIVIIVFYYFSENMWI 137
                                   22333333333333333333222322333333444444433333333333333333332224444444444333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1316.22
//
Query:       gi|70607362|ref|YP_256232.1|  [L=129]
Description: hypothetical protein Saci_1627 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.027   14.0   0.1    1.5  1  GSHPx     Glutathione peroxidase
       0.07   13.2   0.0       0.15   12.1   0.0    1.5  1  BiPBP_C   Penicillin-Binding Protein C-terminus Family
      0.071   13.4   0.6      0.088   13.1   0.6    1.1  1  DUF4293   Domain of unknown function (DUF4293)


Domain annotation for each model (and alignments):
>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-06     0.027      63     108 .]      77     128 ..      70     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                                   TTTT---S-GGG..HHHTSSHTTT-...SSEEB--BBSSSTTB-HH.HHHHH CS
                         GSHPx  63 qfgkqepgsdee..ikkfrqgkyev...tfellekievnGekedpl.ykflk 108
                                   ++ +q  ++++   i ++++g+y+v   tf+l + i+vnG+ e  l y++lk
  gi|70607362|ref|YP_256232.1|  77 KYLNQTSTNNQGiaIFYVQPGNYTVfftTFKLTKSITVNGNTEVTLnYAYLK 128
                                   57788888888855678889998874446778899******99887688886 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.5e-05      0.15      43      75 ..      67     101 ..      59     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.5e-05
                       BiPBP_C  43 eaplrWlldgepl.aetkrgrelawqp.epGrhrL 75 
                                    ap++++ +g++l ++ ++++ +a+   +pG++++
  gi|70607362|ref|YP_256232.1|  67 SAPIWLYYNGKYLnQTSTNNQGIAIFYvQPGNYTV 101
                                   459**********666677778888889****997 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   1.5e-05     0.088       7     117 ..       5     117 ..       4     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                       DUF4293   7 lyLllaailmaaflflplasivtedellsfyalgvstaeaetsvnvsvwvlvilllliailaliaIflyknRk..lQlrlc 85 
                                   lyL+la+i+++++ +  +as  + ++++++++lg st +++ + +v+v+v       +  la + I ly n k   Q    
  gi|70607362|ref|YP_256232.1|   5 LYLVLAIIVILITAVGVYASESSYKTTIQVNNLGGSTVDGKYVLEVQVIVNYGPFGGSQPLASAPIWLYYNGKylNQTSTN 85 
                                   8*************8888887777878****************************************99998744577777 PP

                       DUF4293  86 linllllvllyvllallllvnkanaaaeslge 117
                                      + ++ +  + + ++++++k +++ + +g+
  gi|70607362|ref|YP_256232.1|  86 NQGIAIFYVQPGNYTVFFTTFKLTKSITVNGN 117
                                   76666666666666666666666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 951.03
//
Query:       gi|70607363|ref|YP_256233.1|  [L=162]
Description: hypothetical protein Saci_1629 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-78  260.4   0.1      5e-78  260.2   0.1    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.2   0.1   2.8e-82     5e-78       1     154 []       8     161 ..       8     161 .. 1.00

  Alignments for each domain:
  == domain 1  score: 260.2 bits;  conditional E-value: 2.8e-82
                                   EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEEE CS
                 Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvill 81 
                                   v++e+pe++nvi+gqshfiktvedlyeal++s+++ikfg+afcEasgkrLvr++gndeel+++a+k+alaigagh+f+++l
  gi|70607363|ref|YP_256233.1|   8 VRVEIPEGTNVIIGQSHFIKTVEDLYEALASSSTSIKFGIAFCEASGKRLVRWDGNDEELIKIAQKTALAIGAGHTFIVYL 88 
                                   789****************************************************************************** PP

                                   EST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                 Adenosine_kin  82 knafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                   kn+fPinvln+iksv+evv+ifaAtanpl+v+va+t+qgrg++gvvDGf+p+gve ++++kerke+lrkigYk
  gi|70607363|ref|YP_256233.1|  89 KNGFPINVLNRIKSVEEVVRIFAATANPLQVLVAQTDQGRGIIGVVDGFTPLGVEGDAEIKERKEFLRKIGYK 161
                                   ************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1178.71
//
Query:       gi|70607364|ref|YP_256234.1|  [L=122]
Description: hypothetical protein Saci_1630 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   50.5   0.0    1.5e-13   50.2   0.0    1.1  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   8.1e-18   1.5e-13       4      54 ..      39      90 ..      37      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 8.1e-18
                        DUF309  4 aielfnegeffeaHEvlEelWkeagep.erkllqglIqlAvAlyhlrrgnvr 54
                                  +++lf + +f+e HE lE+lW+ + +p ++k+lq+lI ++++++++ +g+ +
  gi|70607364|ref|YP_256234.1| 39 FQDLFYDFKFWETHESLEKLWRVETDPqRKKYLQALILICASMVKYCKGQIQ 90
                                  899******************6666666********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 973.47
//
Query:       gi|70607365|ref|YP_256235.1|  [L=115]
Description: hypothetical protein Saci_1631 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 741.55
//
Query:       gi|70607366|ref|YP_256236.1|  [L=351]
Description: hypothetical protein Saci_1632 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-19   68.9   0.3    3.5e-18   66.5   0.0    2.1  2  Radical_SAM     Radical SAM superfamily
      0.004   16.5   6.7       0.12   11.8   0.1    2.9  3  zf-ribbon_3     zinc-ribbon domain
     0.0072   16.3   5.4      0.017   15.1   0.1    3.0  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.046   14.0   0.1       0.17   12.2   0.0    1.9  2  Fer4_12         4Fe-4S single cluster domain
       0.47   10.0   6.0       0.87    9.1   1.4    3.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.58    9.9   0.0       0.58    9.9   0.0    3.9  5  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        1.1    9.8   6.3         15    6.3   0.1    3.2  3  zf-C2H2         Zinc finger, C2H2 type
        1.3    8.8  11.4       0.69    9.7   0.4    3.1  3  zinc_ribbon_2   zinc-ribbon domain
        1.8    8.6   5.9       0.47   10.5   0.3    2.6  2  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   1.8e-21   3.5e-18       4     154 ..      79     221 ..      77     234 .. 0.91
   2 ?   -0.6   0.0      0.76   1.5e+03       9      17 ..     322     330 ..     321     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.8e-21
                                   ESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   4 trgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                   t gCn +C +C+++   +rr+  g ++s+eei+e + ++      ++++ +  ep   ++f+ ++  +a++   g+ +t++
  gi|70607366|ref|YP_256236.1|  79 TFGCNWMCMYCQNYDIsQRRRAEGTEISPEEIVEMALAYE----SEGITYTYNEPAIFAEFAHDTGVIARK--HGLFNTMV 153
                                   67************99***********************8....9**************************..7******* PP

                                   ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                   Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpG 154
                                   tng++   e ++  ++   + v+++ +   +ek+ k+  +  ++e +le+++ l ++gi++ ++d   ++p 
  gi|70607366|ref|YP_256236.1| 154 TNGYWS-IELVDYVKDFL-NAVTVDFKGNGEEKFMKRYTGATGPEPILETIRELSKRGIHVeITDL--IIPE 221
                                   *****8.*********77.*************999999899*******************555554..4443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.76
                                   S--TTTSCC CS
                                   xxxxxxxxx RF
                   Radical_SAM   9 lrCsfCarp 17 
                                   +rC++C  +
  gi|70607366|ref|YP_256236.1| 322 MRCKYCGYK 330
                                   79****876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       2.6   5.1e+03      18      23 ..      85      90 ..      85      91 .. 0.79
   2 !   11.8   0.1   6.2e-05      0.12       2      12 ..     295     306 ..     294     308 .. 0.81
   3 !    8.1   0.1   0.00091       1.8      16      26 .]     321     331 ..     317     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                   zf-ribbon_3 18 vCpyCG 23
                                  +C yC+
  gi|70607366|ref|YP_256236.1| 85 MCMYCQ 90
                                  599996 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.2e-05
                   zf-ribbon_3   2 tvrCPnCGa.pl 12 
                                    ++CPnCG+ ++
  gi|70607366|ref|YP_256236.1| 295 NTYCPNCGKmVI 306
                                   689*****9886 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00091
                   zf-ribbon_3  16 dnvCpyCGtkl 26 
                                   d+ C+yCG+kl
  gi|70607366|ref|YP_256236.1| 321 DMRCKYCGYKL 331
                                   667******97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.13   2.7e+02      28      49 .]      14      35 ..       3      35 .. 0.74
   2 ?   -0.2   0.1      0.53   1.1e+03      30      36 ..      85      91 ..      60      99 .. 0.80
   3 !   15.1   0.1   8.5e-06     0.017      10      41 ..     293     334 ..     288     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                           DZR 28 edrCpsCgekvdpearfCpeCG 49
                                   +rC +C +k+  +++  + CG
  gi|70607366|ref|YP_256236.1| 14 RIRCLACARKCLIGENQVGFCG 35
                                  68999**999877777666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.53
                           DZR 30 rCpsCge 36
                                  +C+ C+ 
  gi|70607366|ref|YP_256236.1| 85 MCMYCQN 91
                                  6888875 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 8.5e-06
                           DZR  10 pdarfCseCgtklkavaa..........edrCpsCgekvdpe 41 
                                    ++ +C++Cg+ + +               rC  Cg+k++ e
  gi|70607366|ref|YP_256236.1| 293 YENTYCPNCGKMVIRRYGfrilewhlkeDMRCKYCGYKLPIE 334
                                   5788********98666699******99999******98876 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.3e-05      0.17       7     113 ..      73     175 ..      69     193 .. 0.68
   2 ?   -1.6   0.0       1.5   3.1e+03       5      23 ..     310     328 ..     306     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-05
                       Fer4_12   7 rlslf.vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpek 86 
                                    ++ f + gCn  C +C n ++ + ++ +  t+   eei+e +  ++ eg+t++  EP   ++    + ++ +    +   
  gi|70607366|ref|YP_256236.1|  73 KVFSFsTFGCNWMCMYCQNYDISQRRRAEG-TEISPEEIVEMALAYESEGITYTYNEPAIFAEFAHDTGVIARKHGLF--- 149
                                   44455578***********99987665544.44455677777778999999999999998666655555555444433... PP

                       Fer4_12  87 diwlytgytleelskkekeellkeidv 113
                                   + ++++gy   el + +++++l+ + v
  gi|70607366|ref|YP_256236.1| 150 NTMVTNGYWSIELVD-YVKDFLNAVTV 175
                                   467788887777764.56677766655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                       Fer4_12   5 GvrlslfvsgCnlsCkgCf 23 
                                   G+r++ +    +++Ck+C 
  gi|70607366|ref|YP_256236.1| 310 GFRILEWHLKEDMRCKYCG 328
                                   6666666666689999996 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   3.4e+03      15      25 ..      10      20 ..       7      23 .. 0.80
   2 ?   -2.8   0.0       2.4   4.8e+03       2      10 ..      85      93 ..      85     101 .. 0.79
   3 ?    9.1   1.4   0.00044      0.87       2      29 ..     297     331 ..     296     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                                  TSTTCEEESSS CS
                  TF_Zn_Ribbon 15 pergelvCtdC 25
                                  +e+g ++C +C
  gi|70607366|ref|YP_256236.1| 10 FESGRIRCLAC 20
                                  68899999999 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  +C +C +++
  gi|70607366|ref|YP_256236.1| 85 MCMYCQNYD 93
                                  799998876 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00044
                                   EETTTTCEE.C.......HEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon   2 kCPnCgstn.l.......veDpergelvCtdCGlVl 29 
                                    CPnCg  + +       +e +   +++C+ CG+ l
  gi|70607366|ref|YP_256236.1| 297 YCPNCGK-MvIrrygfriLEWHLKEDMRCKYCGYKL 331
                                   6*****5.535788888544489999*******987 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.5      0.66   1.3e+03      17      26 ..      14      23 ..      10      26 .. 0.78
   2 ?   -2.8   0.1       2.7   5.4e+03      23      28 ..      34      39 ..      33      39 .. 0.84
   3 ?   -3.9   0.3         6   1.2e+04       3       7 ..      86      90 ..      85      91 .. 0.73
   4 ?    0.4   0.1      0.27   5.4e+02      20      25 ..     298     303 ..     292     306 .. 0.78
   5 ?    9.9   0.0   0.00029      0.58      15      26 ..     319     330 ..     315     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.66
                                  ----SSS--- CS
                DNA_RNApol_7kD 17 piRCkeCGhR 26
                                   iRC  C  +
  gi|70607366|ref|YP_256236.1| 14 RIRCLACARK 23
                                  59**999765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                                  S----- CS
                DNA_RNApol_7kD 23 CGhRil 28
                                  CG R++
  gi|70607366|ref|YP_256236.1| 34 CGIRSV 39
                                  999986 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6
                                  -SSS- CS
                DNA_RNApol_7kD  3 CgeCg 7 
                                  C+ C+
  gi|70607366|ref|YP_256236.1| 86 CMYCQ 90
                                  88886 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.27
                                   -SSS-- CS
                DNA_RNApol_7kD  20 CkeCGh 25 
                                   C +CG 
  gi|70607366|ref|YP_256236.1| 298 CPNCGK 303
                                   888985 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00029
                                   SS----SSS--- CS
                DNA_RNApol_7kD  15 gdpiRCkeCGhR 26 
                                   ++  RCk+CG++
  gi|70607366|ref|YP_256236.1| 319 KEDMRCKYCGYK 330
                                   5678******98 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       8.3   1.7e+04       3       6 ..      86      89 ..      84      90 .. 0.80
   2 ?    6.3   0.1    0.0074        15       2      16 ..     297     311 ..     296     313 .. 0.86
   3 ?    6.1   0.1    0.0085        17       2      19 ..     323     340 ..     322     342 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.3
                                  ETTT CS
                       zf-C2H2  3 CpdC 6 
                                  C +C
  gi|70607366|ref|YP_256236.1| 86 CMYC 89
                                  9999 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0074
                                   EETTTTEEESSHHHH CS
                       zf-C2H2   2 kCpdCgksFkrksnL 16 
                                   +Cp Cgk+  r++ +
  gi|70607366|ref|YP_256236.1| 297 YCPNCGKMVIRRYGF 311
                                   6*******9999876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0085
                                   EETTTTEEESSHHHHHHH CS
                       zf-C2H2   2 kCpdCgksFkrksnLkrH 19 
                                   +C++Cg++ +    L +H
  gi|70607366|ref|YP_256236.1| 323 RCKYCGYKLPIEGKLSKH 340
                                   8******99999999888 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.7       8.8   1.8e+04      16      19 ..      86      89 ..      86      89 .. 0.91
   2 ?    9.7   0.4   0.00035      0.69      14      21 ..     296     303 ..     294     305 .. 0.63
   3 ?    6.4   0.1    0.0039       7.8      16      23 .]     324     331 ..     318     334 .. 0.66

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 8.8
                 zinc_ribbon_2 16 CpyC 19
                                  C yC
  gi|70607366|ref|YP_256236.1| 86 CMYC 89
                                  9999 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00035
                 zinc_ribbon_2  14 kFCpyCGt 21 
                                   ++Cp+CG 
  gi|70607366|ref|YP_256236.1| 296 TYCPNCGK 303
                                   66666664 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0039
                 zinc_ribbon_2  16 CpyCGtpl 23 
                                   C yCG++l
  gi|70607366|ref|YP_256236.1| 324 CKYCGYKL 331
                                   66666654 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.9       0.7   1.4e+03       1       4 [.     298     301 ..     298     303 .. 0.89
   2 ?   10.5   0.3   0.00023      0.47      15      27 .]     320     332 ..     314     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.7
                      PriA_CRR   1 CpnC 4  
                                   CpnC
  gi|70607366|ref|YP_256236.1| 298 CPNC 301
                                   **** PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                      PriA_CRR  15 nrLrCHyCgyteP 27 
                                   + +rC yCgy+ P
  gi|70607366|ref|YP_256236.1| 320 EDMRCKYCGYKLP 332
                                   679*******977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2404.08
//
Query:       gi|70607367|ref|YP_256237.1|  [L=257]
Description: 3-hydroxybutyryl-CoA dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-72  242.0   0.0    7.2e-72  241.7   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.3e-41  143.3   0.0    1.9e-39  136.1   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.028   13.4   0.0       0.19   10.7   0.0    1.9  2  SDH_sah   Serine dehydrogenase proteinase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.7   0.0   1.2e-75   7.2e-72       8     250 ..      14     256 ..       9     257 .] 0.99

  Alignments for each domain:
  == domain 1  score: 241.7 bits;  conditional E-value: 1.2e-75
                                   EEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHHSS CS
                         ECH_1   8 viklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtklytvp 88 
                                    i+lnrP+ +Na+++++++E+  +le+  +d++vr+++ tG ++aF+aGad+ +  e e   + ++  +  el++ + + p
  gi|70607367|ref|YP_256237.1|  14 RITLNRPDRLNAINKKMIEEIRTVLEETVKDEKVRVIIFTGNGRAFSAGADISQFKELEGLTAWQFAMKGRELMDYIENYP 94 
                                   79*******************************************************99899999**************** PP

                                   SEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTS CS
                         ECH_1  89 kpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkvGl 169
                                   kp+ia++nG+a+gGGlelalacDi+ia+d+a+ gl+e+ lG++pg+ggtq+l + vGks+  e+++lg++isa++a+++Gl
  gi|70607367|ref|YP_256237.1|  95 KPTIAMINGYALGGGLELALACDIRIASDEAQLGLPEITLGIYPGFGGTQRLLKLVGKSRTLEMIMLGERISAKDAERIGL 175
                                   ********************************************************************************* PP

                                   SSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH----- CS
                         ECH_1 170 vdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrkpefed 250
                                   v++vvp ++l++e+l+la klae +p+a++  k ++n+ +++  + +l++e+     +f ++d+keG++aflEkrkp+f++
  gi|70607367|ref|YP_256237.1| 176 VNRVVPSNDLEKETLNLASKLAERPPLAIQLSKLIVNQGMNSPITVGLNMESLGWGVIFTTKDSKEGVNAFLEKRKPNFKG 256
                                   *******************************************************************************97 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.1   0.0   3.2e-43   1.9e-39       3     185 ..      14     193 ..      12     198 .. 0.93
   2 !    6.9   0.0   0.00065       3.9     252     317 ..     192     254 ..     186     257 .] 0.88

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 3.2e-43
                                   EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHH CS
                         ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyli 83 
                                   +itLnrp+ lNa++ +m+++++  l+e  kd++v++++ +g+g +af+AG D+ ++ e +  ++++   f  +  +l  +i
  gi|70607367|ref|YP_256237.1|  14 RITLNRPDRLNAINKKMIEEIRTVLEETVKDEKVRVIIFTGNG-RAFSAGADISQFKELEGLTAWQ---FAMKGRELMDYI 90 
                                   79***************************************88.*************999887776...9*********** PP

                                   HC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHHH CS
                         ECH_2  84 atypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgadal 163
                                   ++ypkp++a+++G+++GgG+ l++ + +r++++++++  PE+++G++P  Gg+  L +l g +  l + + G+r++++da 
  gi|70607367|ref|YP_256237.1|  91 ENYPKPTIAMINGYALGGGLELALACDIRIASDEAQLGLPEITLGIYPGFGGTQRLLKLVGkSRTLEMIMLGERISAKDAE 171
                                   ******************************************************99999773567789999********** PP

                                   HTTS--EE--GGGHHHHHHHHH CS
                         ECH_2 164 aaglathyvpseklealeeaLa 185
                                    +gl + +vps++le+ + +La
  gi|70607367|ref|YP_256237.1| 172 RIGLVNRVVPSNDLEKETLNLA 193
                                   *************987655554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00065
                                   HHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                         ECH_2 252 tletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                    +++l++r P++++++   +++g +   ++  l+mE      ++++kD  eGv+a l ++  kP++
  gi|70607367|ref|YP_256237.1| 192 LASKLAERPPLAIQLSKLIVNQGMNSP-ITVGLNMESLGWGVIFTTKDSKEGVNAFLEKR--KPNF 254
                                   67899*********************7.*********99999999**********99554..6666 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.044   2.6e+02      79     108 ..      32      61 ..      22      86 .. 0.75
   2 ?   10.7   0.0   3.2e-05      0.19     113     164 ..      88     139 ..      74     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.044
                       SDH_sah  79 eevlrairltpkdkpidliihtpGGlvlaa 108
                                   ee+   +  t kd  + +ii t  G +++a
  gi|70607367|ref|YP_256237.1|  32 EEIRTVLEETVKDEKVRVIIFTGNGRAFSA 61 
                                   666666777888888888888888877765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.2e-05
                       SDH_sah 113 kalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqypa 164
                                     +++++ +t  ++  ya+ GG  +ala d  i  ++a lG  +  lg yp 
  gi|70607367|ref|YP_256237.1|  88 DYIENYPKPTIAMINGYALGGGLELALACDIRIASDEAQLGLPEITLGIYPG 139
                                   567788999999*****************************99999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1692.43
//
Query:       gi|70607368|ref|YP_256238.1|  [L=92]
Description: hypothetical protein Saci_1634 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 676.07
//
Query:       gi|70607369|ref|YP_256239.1|  [L=285]
Description: protoheme IX farnesyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-48  163.2  21.0    9.2e-48  162.7  21.0    1.1  1  UbiA             UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7  21.0   5.2e-52   9.2e-48       5     247 ..      28     266 ..      26     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 5.2e-52
                          UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilglllla 85 
                                   a++++ la +g  ++ +l+ +l+g+  aa++++++N  +++e+D+ m+rt +RP v+G++ +kea++++ + ++lg l++ 
  gi|70607369|ref|YP_256239.1|  28 AIASYILAFKG--NWYNLIPVLIGGSIAAGGSMIINGGLEIEKDKVMKRTSWRPTVKGEVGRKEAYMVGGIACALGSLIG- 105
                                   67779999888..8999***************************************************************. PP

                          UbiA  86 lllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandl 165
                                   ll+nplta+++ll+ l+y +vY+ ++lK rt+l++v+gg+a+  ++++g+aa+++s++l+ lll+l+vf++t ++++a +l
  gi|70607369|ref|YP_256239.1| 106 LLANPLTAFFILLGSLVYvFVYS-YYLKPRTWLNIVIGGFAGSAAAWAGYAAASNSFNLESLLLGLLVFAWTPGHFWALAL 185
                                   ***********************.8******************************************************** PP

                          UbiA 166 rdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaalallraarlvrrrdakkaakf 245
                                   r ++++++a i++lp++  +k+a++  a+++  +l++ ++l l+++l+l+y++++l++ a++l++ +rl+r+ ++++ + +
  gi|70607369|ref|YP_256239.1| 186 RYKRDYANAEIPMLPAIVDDKTAAR--AIAISNILMIpFALGLMLYLNLIYVIITLAATAVLLYFNVRLMRNPTPEESWIS 264
                                   ******************9999999..44444444444677999999999***************************9999 PP

                          UbiA 246 fl 247
                                   + 
  gi|70607369|ref|YP_256239.1| 265 YK 266
                                   83 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2019.23
//
Query:       gi|70607370|ref|YP_256240.1|  [L=261]
Description: homoserine dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-48  162.4   0.0    1.2e-47  162.1   0.0    1.1  1  Homoserine_dh  Homoserine dehydrogenase


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.0   6.5e-52   1.2e-47       8     173 .]      94     254 ..      88     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 6.5e-52
                                   HTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT--GGGSE CS
                 Homoserine_dh   8 eilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgleveledve 88 
                                   ++l g++++ri+Gilngt+nyilt+m + g sf+e+lk+aq lGyae+Dpt+D++G+Da +Kl+ila+l+++l+++++dv+
  gi|70607370|ref|YP_256240.1|  94 RVLPGSEVKRIRGILNGTTNYILTKMYN-GLSFTEALKDAQTLGYAESDPTNDISGFDAGAKLTILANLMLNLDITIRDVK 173
                                   57899**********************6.999************************************************* PP

                                   E--STTS-HHHHHHHHCTTEEEEEEEEE..CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-SSHHHHHHH CS
                 Homoserine_dh  89 vegiskltaedikeakeegkvlklvasa..vearVkpelvpkshplasvkgsenavlvetdrlgelviqGpgaGaepTAsa 167
                                   +egi++l+      ak+++k++kl+a a   +++V+p  + +++pl+sv+g+en++ ++td ++++vi+GpgaG++  A +
  gi|70607370|ref|YP_256240.1| 174 IEGIQNLD-----SAKRDNKKIKLIAYAdeKTVQVRPVPLLPEDPLFSVDGVENGLEISTD-IQTIVIRGPGAGPKNAAYG 248
                                   ****9875.....578999********987589***************************9.589**************** PP

                                   HHHHHH CS
                 Homoserine_dh 168 vlsDll 173
                                   +lsDl+
  gi|70607370|ref|YP_256240.1| 249 LLSDLI 254
                                   ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1919.71
//
Query:       gi|70607371|ref|YP_256241.1|  [L=222]
Description: hypothetical protein Saci_1637 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-29  102.0   0.0    4.2e-29  101.4   0.0    1.3  1  B3_4      B3/4 domain


Domain annotation for each model (and alignments):
>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   2.4e-33   4.2e-29       2     173 ..      60     211 ..      59     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 2.4e-33
                                   SSEEEEEEEES--.-----HHHHHHHHHTT---.--HHHHHHHHHHHHHT--EEEEEGGGTBTEEEEEE--TTEEEEBTTS CS
                          B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirp.innvVDitNyvmlelgqPlhafDldkiqgdivvrlakegeklvtldg 81 
                                   ++ ++++++ +++kt+ps e+l+rr+ r+g  p inn+VDi N+v+ ++ +P++++D +++q +i ++l+ +ge + +++ 
  gi|70607371|ref|YP_256241.1|  60 YRDFYWKIGIDPTKTRPSGEALRRRISRNGSIPrINNIVDIGNLVSADTLVPIGIYDKARFQYPIYLKLSSGGELFYAIGR 140
                                   789****************************************************************************** PP

                                   -EEEE.-TTSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHHTT---HHHHHHHH---TTTHHH CS
                          B3_4  82 kerel.deedlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirktarrlglrseaskrfergvdpeklea 160
                                   +e e  d+++++ +ds+++v ++++++++  + v e+Tk+v++ +a++                       +gv+++++  
  gi|70607371|ref|YP_256241.1| 141 SEPEKiDPNIPILVDSKGVVmHIYPHRDSTLTNVIETTKDVLIVSAGV-----------------------KGVNEDLVIL 198
                                   *99988*****************************************4.......................569******* PP

                                   HHHHHHHHHHHHH CS
                          B3_4 161 aldravallselc 173
                                   a +r+++ll++++
  gi|70607371|ref|YP_256241.1| 199 ASKRTAELLVKYA 211
                                   *******999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1479.60
//
Query:       gi|70607372|ref|YP_256242.1|  [L=448]
Description: hypothetical protein Saci_1638 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-43  147.1   0.2    1.4e-42  146.5   0.2    1.3  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.052   13.9   1.3       0.12   12.7   1.3    1.6  1  Tup_N      Tup N-terminal


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.2   1.6e-46   1.4e-42       1     277 [.      14     299 ..      14     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 1.6e-46
                                   EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEE.EE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                     PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgf.astldtsdealeeaveraveiaklapedpea..... 75 
                                   +a++r+ +s+++s+ + +++ + +s+ +++g+++rv++ + +g+ +s++++++e++++a++ av +      +  +     
  gi|70607372|ref|YP_256242.1|  14 FADLRYFKSKGLSLVVTEDREQVSSYGTERGYSLRVLYRNNWGYfSSSKEIEEENVKQAINSAVGNE-----NV-Niillp 88 
                                   699*****************************************87777999778888888766665.....22.246788 PP

                                   .............GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEE CS
                     PmbA_TldD  76 .............eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvsls 143
                                                 + s+ ek e l++l ++l++ d         ri++v++++ +++ +k + ++eG +++q+++  ++s
  gi|70607372|ref|YP_256242.1|  89 skhdeimlkpryeVSKSVHEKMEDLKRLRQKLFDLDS--------RIKSVTIRYAEEEIRKEYYSTEGREIKQSYYLSGIS 161
                                   8898899888877777777777789999999999999........************************************ PP

                                   EEEEE...S.TCS.ETEEEEEEEE..SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTB CS
                     PmbA_TldD 144 lsvia.d.d.ggs.gdgmgggsgy..edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghale 218
                                   ++via + d   s ++  ++ ++y    +e ++ eei++ ++ ++  +     +++g y+V+lsp++ g++ hea+gh +e
  gi|70607372|ref|YP_256242.1| 162 INVIArEgDtI-SsAY--HRHFSYqgYPFEVFNEEEILDTVKMRINNQFIGLTPKAGLYTVILSPDVSGVFAHEAIGHLAE 239
                                   *****665542.2322..2233334333444557999999999999999888899************************** PP

                                   HHHHHTT--TTTT-TTSB-S-TT--EEEETT..-......-SB-TTSBB---EEEEETTEE- CS
                     PmbA_TldD 219 adavlegrSflkdklGekvaselltivddpt..s.gglgsypfDdEGvptqrtvlIenGvLk 277
                                   ad    g  f     G+k+a++ +ti+d p+    +g+g + +DdEGv  +++++I++Gv+k
  gi|70607372|ref|YP_256242.1| 240 ADLSTNGILFP--LRGKKIAPDSVTIMDSPLvqYpEGIGVTLYDDEGVEGRDVKIIDKGVVK 299
                                   *****877777..89****************98579************************99 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   1.4e-05      0.12      27      66 ..      99     139 ..      89     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                         Tup_N  27 kdeyelkiqsqiqElqqirqtlyeLeeahrkikqqY.Eeei 66 
                                   + e+ +++++++++l+++rq+l++L+++ +++  +Y Eeei
  gi|70607372|ref|YP_256242.1|  99 RYEVSKSVHEKMEDLKRLRQKLFDLDSRIKSVTIRYaEEEI 139
                                   5566777*****************************55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3136.58
//
Query:       gi|70607373|ref|YP_256243.1|  [L=415]
Description: hypothetical protein Saci_1639 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-36  126.9   0.1    2.1e-36  126.2   0.1    1.3  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.077   12.9   0.0       0.24   11.3   0.0    1.8  1  DUF3658    Protein of unknown function
       0.24   11.3   4.2        5.5    6.9   4.3    2.8  2  LMP        LMP repeated region


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.1   3.6e-40   2.1e-36       9     279 .]      24     295 ..      18     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 3.6e-40
                                   EEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.............G CS
                     PmbA_TldD   9 sestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.............e 76 
                                    e  s+++ +++     + +d+g+g+rvik+g++gfa+++ ++    ++++e a+e +kl++ed+++             +
  gi|70607373|ref|YP_256243.1|  24 VEVSSIQYKKDRQAHFFNLRDTGYGLRVIKDGKVGFAHSNLLD----DSLLEMAIETMKLSKEDKFNvlpyskpvnkinlK 100
                                   45667778888888888889****************9988777....69*******************9887777777765 PP

                                   GS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE..STCSETE CS
                     PmbA_TldD  77 evsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsviad.dggsgdg 156
                                     ++ee +e l+e++k +++a++      +  ++ v+  ++a+++++ i+++eG+dve++r+ v++s+    + + +    
  gi|70607373|ref|YP_256243.1| 101 FFDIEEVREKLLEFSKQTEEAKD------Y--ANVVNEYYEAVNSKIKIISTEGMDVEEERSLVGMSIVYNFKiG-D---- 168
                                   55555555545555544333333......3..334455899999********************87777777322.2.... PP

                                   EEEEEEE...SSHHHS..SSHHHHH.....HHHHHCTTT.-B---SEE...EEEEE-HHHHHHHHHGHHHHHTBHHHHHTT CS
                     PmbA_TldD 157 mgggsgy...edleeedleeiaeea.....aekalasle.akplppgk...ypVvlspeavgsllheavghaleadavleg 225
                                         y   e +e+++ ++i++        +k++ + +  k+    +     V+l+p+av sl+  ++ h+l++++  +g
  gi|70607373|ref|YP_256243.1| 169 ------YvspEIYEGISSRDIGKLDvqrgiMDKIVTKRNlYKNMNKERlkfNSVILTPKAVSSLFIPLLMHSLSLENKFRG 243
                                   ......21232222233333444441111155555555555555555588899**************************** PP

                                   --TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 226 rSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   +S+l     e++++e lt++d+p   +++gs++fD+EG+p++ ++lIe+G+++n+
  gi|70607373|ref|YP_256243.1| 244 KSIL---KDEEILNESLTLIDNPSLsHAPGSRSFDGEGLPSKIVQLIERGKVRNF 295
                                   ****...58***************99***************************98 PP

>> DUF3658  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     4e-05      0.24      17      57 ..      36      76 ..      25      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                       DUF3658 17 akeWqelkrenaeLRiwkdgklvsveedyfDdlileaakke 57
                                  ++ + +l+++   LR++kdgk+  ++ + +Dd +le+a + 
  gi|70607373|ref|YP_256243.1| 36 QAHFFNLRDTGYGLRVIKDGKVGFAHSNLLDDSLLEMAIET 76
                                  556668999999************************99776 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.077   4.6e+02      49      77 ..      17      45 ..       2      52 .. 0.81
   2 ?    6.9   4.3   0.00092       5.5      68     111 ..      98     141 ..      60     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.077
                           LMP 49 LdakvteitkkLekFnkdkeakFkeLeqt 77
                                  ++a +  ++   ++++kd++a+F +L+ t
  gi|70607373|ref|YP_256243.1| 17 VTAEIYSVEVSSIQYKKDRQAHFFNLRDT 45
                                  67788888888999*********999988 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00092
                           LMP  68 eakFkeLeqtRkdieeFlkdvknnpnYaelvkdLtskkdsknsv 111
                                   + kF ++e+ R+++ eF k+ ++   Ya++v++  ++++sk  +
  gi|70607373|ref|YP_256243.1|  98 NLKFFDIEEVREKLLEFSKQTEEAKDYANVVNEYYEAVNSKIKI 141
                                   5799*******************************999999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2757.66
//
Query:       gi|70607374|ref|YP_256244.1|  [L=142]
Description: universal stress protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-37  129.1   0.2    1.9e-37  128.9   0.2    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.2     1e-41   1.9e-37       1     141 []       1     142 []       1     142 [] 0.98

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1e-41
                                   S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH.HHHHHHCTTC CS
                           Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada.akaaaeaggv 80 
                                   m+k+I+Va+Dgs+++ +Al+ A++lak+++a+l ++ v+d++a    + a+ +    ++++++a+++ ++ + +a+++g++
  gi|70607374|ref|YP_256244.1|   1 MFKKIVVAYDGSDNANRALDVAIDLAKKYDAKLDVVQVVDTSALLGMGLAPVPNDLIQQVYSKAKSDVENaKSKATNQGIK 81 
                                   9***************************************************9999999999999998888********** PP

                                   EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                           Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                   +v+ +v+egdpa +i+e+  + +a+liV+Gsrg+s+++rlllGSvs ++++++ +pVl+V+
  gi|70607374|ref|YP_256244.1|  82 EVDGIVLEGDPASSIVEYSSKSGANLIVTGSRGLSTFKRLLLGSVSTKIAQESRIPVLIVK 142
                                   ************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 918.67
//
Query:       gi|70607375|ref|YP_256245.1|  [L=230]
Description: biotin operon repressor/acetyl-CoA carboxylase ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-13   50.8   0.1    3.1e-13   49.8   0.0    1.5  2  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
  ------ inclusion threshold ------
      0.041   14.0   0.1      0.075   13.2   0.1    1.4  1  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   3.5e-17   3.1e-13       3     131 .]       7     126 ..       5     126 .. 0.88
   2 ?   -2.7   0.0      0.59   5.3e+03      42      63 ..     133     153 ..     132     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.5e-17
                                   EEES-HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH CS
                 BPL_LplA_LipB   3 evikstntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavleal 79 
                                   ++++st++l++  + +     +++v +++qt  r    + w spkg+l+++ +++    +++ + ++++++ ++l + +al
  gi|70607375|ref|YP_256245.1|   7 PSVTSTQDLAE-AIYYMINAEEFVVTAEEQTNARgryrREWYSPKGGLWITYVVK----NYDVDKVPFLTLKVSLGIRNAL 82 
                                   56778877666.8888888999********985555******************9....67888***************** PP

                                   ......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  80 gyrdskpgiegipvfikwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                            + +++ i+wpnD++v+++K+aG++++ + ++ +  + ig+g++
  gi|70607375|ref|YP_256245.1|  83 --------AKYVNAGIRWPNDIVVGNKKIAGVLIEGIAEGSSGTVFIGAGID 126
                                   ........566677777*******************************9997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.59
                                   -TTSEEEEEEEEESS...-CCG CS
                 BPL_LplA_LipB  42 pkgeltyslllspeqktfqnrv 63 
                                   p+ ++++s+ll+ + k+++n++
  gi|70607375|ref|YP_256245.1| 133 PEDIIATSILLE-TGKEVDNDE 153
                                   566788899888.446777655 PP

>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.3e-06     0.075      75     122 ..     147     199 ..     131     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-06
                 Mad3_BUB1_I_2  75 nkvydkeilkeelksikkl...ekklseeeakkl..lkpkkirlfGkeWveie 122
                                   ++v ++e+l+e ++sik++    +++++++++++  +k kkir++G+ W +i 
  gi|70607375|ref|YP_256245.1| 147 KEVDNDELLNEIINSIKNImnlDDRTTIDKINEVlqIKDKKIRIMGQDWEKIC 199
                                   4556666666666666555443788888888887225789*********9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1533.72
//
Query:       gi|70607376|ref|YP_256246.1|  [L=352]
Description: hypothetical protein Saci_1642 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-56  190.0   0.0    3.9e-56  189.4   0.0    1.3  1  Sua5_yciO_yrdC  Telomere recombination
    3.7e-24   85.8   0.0    5.3e-24   85.3   0.0    1.2  1  SUA5            Putative GTP-binding controlling metal-bindin
  ------ inclusion threshold ------
       0.15   12.7   0.2       0.94   10.1   0.0    2.3  3  Fe-S_assembly   Iron-sulphur cluster assembly


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4   0.0   6.5e-60   3.9e-56       1     179 []      22     198 ..      22     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 6.5e-60
                                   HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                   e++++Gg+v +ptetvYgL+++a++ +a+ +++++K+rp d+pl+v++a+l++l ++a  +++e++l++++ +wPGp+tl+
  gi|70607376|ref|YP_256246.1|  22 EVIKRGGLVSFPTETVYGLGANAYDGNACLKIFQAKNRPPDNPLIVHIAELDQLFDVAV-DINEKVLEIVQVIWPGPLTLI 101
                                   689*******************************************************9.********************* PP

                                   EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS-- CS
                Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvd 162
                                   lk+s++ +pkev++gl+tv+vr+P++p+a++L+++ g p++a+Sanl ++ps+t+ae+v ++l+++vd+i+dgg +  gv+
  gi|70607376|ref|YP_256246.1| 102 LKKSSK-IPKEVSAGLDTVAVRMPAHPIALQLIRESGVPIAAPSANLATRPSPTRAEDVLNDLNGRVDIIIDGGHTFFGVE 181
                                   **8665.************************************************************************** PP

                                   -EEEETTSSTSSECEXX CS
                Sua5_yciO_yrdC 163 stVvdltegkpkilRrG 179
                                   st+v++t+++p++lR+G
  gi|70607376|ref|YP_256246.1| 182 STIVNVTSNPPTLLRPG 198
                                   ***************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   8.8e-28   5.3e-24       2     134 .]     201     336 ..     200     336 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 8.8e-28
                                   -HHHHHHHS.-.--..........-------------S-SSEEEEE--GGGHHHH.....HHHHHTTS-EEEEEEGGGTGG CS
                          SUA5   2 tleeleevl.d.avek......keekpraPGmkyrHYaPkapvvlveaeeeeeaakeekleekkksgkkvgvlatseskea 74 
                                   t+eel++ + d +v +      + +   aPGmkyrHYaP+ +++l+e+ + +++       +  +++ kv vl t+e  ++
  gi|70607376|ref|YP_256246.1| 201 TVEELRSFFpDiQVPEfarglgEADIALAPGMKYRHYAPSKKIILIENRSLMRKV-----VDLLSAKYKVTVLITKELVNE 276
                                   6788888874232222333555566679**********************99986.....699999********9999999 PP

                                   .TSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHTT CS
                          SUA5  75 .assvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAAg 134
                                    +++ +++ lgs+++l e+arnLF+ +r l++++ +l ++ g+pe+g+glA+mnR rkA+g
  gi|70607376|ref|YP_256246.1| 277 fKDKDMIV-LGSDENLYEVARNLFESFRLLENRDTELGVMVGFPERGVGLAIMNRARKASG 336
                                   66666666.9*********************9999999999******************96 PP

>> Fe-S_assembly  Iron-sulphur cluster assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.94      31      59 ..      66      94 ..      62      96 .. 0.91
   2 ?   -1.3   0.0      0.59   3.5e+03       9      23 ..     269     283 ..     266     303 .. 0.66
   3 ?   -2.4   0.0       1.3   7.5e+03       5      18 ..     290     303 ..     287     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                 Fe-S_assembly 31 hewvleLpefdddpeksnEkiLEaIqmaW 59
                                     + eL++  d   + nEk+LE +q  W
  gi|70607376|ref|YP_256246.1| 66 IVHIAELDQLFDVAVDINEKVLEIVQVIW 94
                                  567999*********************** PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.59
                 Fe-S_assembly   9 IAiaLyekypdvdpl 23 
                                   I  +L ++++d d +
  gi|70607376|ref|YP_256246.1| 269 ITKELVNEFKDKDMI 283
                                   566777777777654 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.3
                 Fe-S_assembly   5 dseeIAiaLyekyp 18 
                                   + +e+A +L+e+++
  gi|70607376|ref|YP_256246.1| 290 NLYEVARNLFESFR 303
                                   66899999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2674.70
//
Query:       gi|70607377|ref|YP_256247.1|  [L=171]
Description: NADH:ubiquinone oxidoreductase subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-21   75.1   0.0    5.7e-21   74.7   0.0    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   3.2e-25   5.7e-21       5     129 ..      51     156 ..      48     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 3.2e-25
                                   HHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH CS
                   Oxidored_q6   5 sisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAaf 85 
                                     ++ a     +d+     +ry+    ++++         + ++lv+eG++trk+  a ++++++++++k+via+G+CA  
  gi|70607377|ref|YP_256247.1|  51 GTEFGAFAAARFDA-----ERYGVLPFSSAR---------QTNLLVIEGTLTRKMGRAAKIVYDQMPEPKFVIAMGACALE 117
                                   55555555555555.....666665555555.........899************************************** PP

                                   -TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                   Oxidored_q6  86 GGipaaannpsvgeevgellevvpvdinipGCPphpeailetll 129
                                   GGi+  +n+++    v + +  +pvdi+ pGCP++pea+++++l
  gi|70607377|ref|YP_256247.1| 118 GGIF--WNSYN---TVLPSDLGIPVDIYAPGCPTRPEALARAVL 156
                                   ****..77443...35688888*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1248.38
//
Query:       gi|70607378|ref|YP_256248.1|  [L=382]
Description: succinyl-diaminopimelate desuccinylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-38  131.1   0.0    5.6e-38  130.7   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.1e-18   66.2   0.0    3.9e-18   65.3   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
    2.3e-09   37.2   0.0    1.9e-07   31.0   0.0    2.1  2  Peptidase_M28  Peptidase family M28
     0.0029   16.7   0.0       0.28   10.2   0.0    2.8  3  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   0.0   1.2e-41   5.6e-38       1     206 [.      68     380 ..      68     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 1.2e-41
                                   EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THHH CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGak 79 
                                   +l++H+DvVp+++ ++w++ pfs+ + ++k+yGrG++dmk g++  ++++ +l+d+    ++++v++++pdEE+g+  Gak
  gi|70607378|ref|YP_256248.1|  68 MLNGHYDVVPTGDLKSWSHdPFSALILEDKIYGRGSSDMKSGLAVQMKVFVELADKL---DYNLVFTAVPDEESGGfHGAK 145
                                   79********99999**********999****************************8...9************9889**** PP

                                   HHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                 Peptidase_M20  80 allegleerekvdavfelhieepgileagklaigvv............................................. 115
                                   +l+e    ++k+  v+   ++ep+++e     i+++                                             
  gi|70607378|ref|YP_256248.1| 146 HLAE----KYKPNLVL---VSEPSGSE--W--INIGekgllqvklkskgkvahgslpslgdnaimkivrdlvnlekirdvk 215
                                   ****....89999966...99999999..4..555577999999************************************* PP

                                   ........................................................................EEEEEEEEE CS
                                   ........................................................................xxxxxxxxx RF
                 Peptidase_M20 116 ........................................................................kvevelleg 124
                                                                                                           + eve++  
  gi|70607378|ref|YP_256248.1| 216 ipipselkeaisarassevekdyvsisfnpgvikggvkvnvvpdyaeaevdmrippgiknsealslvkklvsESEVEPIDL 296
                                   ***********************************************************************879***9999 PP

                                   ESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHH CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 125 gapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgikvl 201
                                   ++p  +n +++ vk+l+e++++++g ++++++   g+td r+f  +gip++ ++gpg+ g aH+ nE+v+ +++ +++kv+
  gi|70607378|ref|YP_256248.1| 297 SEPNYTNpENHYVKKLEETISKTLGIRPKNYIIT-GATDGRYFrnKGIPAI-VYGPGElGVAHTYNEFVSFKEVINAYKVI 375
                                   9999999999************99*999999999.9*******99999877.7****88********************** PP

                                   HHHHH CS
                                   xxxxx RF
                 Peptidase_M20 202 arlle 206
                                    ++l+
  gi|70607378|ref|YP_256248.1| 376 REYLL 380
                                   99985 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   8.8e-22   3.9e-18       1     103 [.     169     288 ..     169     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 8.8e-22
                                   SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......................TCCTCCCCCEECC CS
                     M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.................eerslprttlnvtgie 64 
                                   ig+kGl+++k++ kgk +H++ p  g+NAi+k +r l  le+ ++ +                   e++    ++n+++i+
  gi|70607378|ref|YP_256248.1| 169 IGEKGLLQVKLKSKGKVAHGSLPSLGDNAIMKIVRDLVNLEKIRDVKIpipselkeaisarasseVEKDYVSISFNPGVIK 249
                                   699****************************99999999999976666********************************* PP

                                   E-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                     M20_dimer  65 gGsaknvipdeaeakidiRllpgedpeevleeieeilek 103
                                   gG + nv+pd+aea++d+R++pg +  e+l  +++++++
  gi|70607378|ref|YP_256248.1| 250 GGVKVNVVPDYAEAEVDMRIPPGIKNSEALSLVKKLVSE 288
                                   ********************************9999886 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   4.2e-11   1.9e-07       1      84 [.      54     151 ..      54     177 .. 0.86
   2 !    4.2   0.0    0.0067        30     114     163 ..     300     348 ..     274     369 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.2e-11
                                   EEEEEESTTCESEEEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEE CS
                 Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrf 65 
                                   N+i+   +k+ d+ ++l++HyD v++g               +++    G  D  sg a+ +++   la+   +++++++f
  gi|70607378|ref|YP_256248.1|  54 NIIVNNGKKS-DKSIMLNGHYDVVPTGdlkswshdpfsalilEDKiYGRGSSDMKSGLAVQMKVFVELAD---KLDYNLVF 130
                                   6777665555.9********************99988888863334567********************9...99****** PP

                                   EEESSCSG.SSHHHHHHHH.H CS
                 Peptidase_M28  66 lffdaEEa.gllGSkafak.a 84 
                                    ++  EE  g+ G+k++a+  
  gi|70607378|ref|YP_256248.1| 131 TAVPDEESgGFHGAKHLAEkY 151
                                   ********99********643 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0067
                                   HHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE CS
                 Peptidase_M28 114 kssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl 163
                                   +  +  ++++k+l ++++++    p  +  ++g +D + f+++g+p++ +
  gi|70607378|ref|YP_256248.1| 300 NYTNPENHYVKKLEETISKTLGIRPK-NYIITGATDGRYFRNKGIPAIVY 348
                                   55555567777777777777644553.3349999************9977 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.013        60       4      25 ..      55      76 ..      53      79 .. 0.84
   2 !   10.2   0.0   6.2e-05      0.28     128     187 ..      98     158 ..      76     164 .. 0.83
   3 ?    0.1   0.0     0.071   3.2e+02     227     290 ..     310     372 ..     300     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.013
                                  EEEEESSTTSSEEEEEEE--B- CS
                 Peptidase_M42  4 iakkkgkekepkvmiaAHmDei 25
                                  i++ +gk++++++m+ +H D +
  gi|70607378|ref|YP_256248.1| 55 IIVNNGKKSDKSIMLNGHYDVV 76
                                  45577889************76 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.2e-05
                                   EEET.THHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTT.TSHHHHHHHHHH--SEEEE CS
                 Peptidase_M42 128 ivsk.alDdragvavllellkelkeeeleatvylvatvqEEv.GlrGaktsaekikpdiaia 187
                                   i ++   D + g+av ++++ el+++ l++++++ a   EE  G  Gak +aek+kp+++++
  gi|70607378|ref|YP_256248.1|  98 IYGRgSSDMKSGLAVQMKVFVELADK-LDYNLVFTAVPDEESgGFHGAKHLAEKYKPNLVLV 158
                                   5555246889*************996.8999999999999983589***********99886 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.071
                                   HHHHH.HHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEE.EBSTTSTTEEEEHHHHHHHH CS
                 Peptidase_M42 227 kklle.lAkknnipyqlevlsgggtDAgaihltgegvptalisip.tryiHspvevahlddleatv 290
                                   kkl+e + k+ +i+ +  ++ +g tD+  +  +  g+p+++ +++ +   H+ +e ++ + + ++ 
  gi|70607378|ref|YP_256248.1| 310 KKLEEtISKTLGIRPKN-YIITGATDGRYFRNK--GIPAIVYGPGeLGVAHTYNEFVSFKEVINAY 372
                                   55544156777888877.777899999987655..********98346789999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2629.55
//
Query:       gi|70607379|ref|YP_256249.1|  [L=354]
Description: hypothetical protein Saci_1646 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-39  136.3   4.9    1.3e-39  136.3   4.9    1.9  3  VIT1          VIT family
    2.6e-09   37.6   7.2    5.9e-09   36.5   7.2    1.5  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
       0.12   12.1   0.1       0.36   10.6   0.1    1.9  2  DUF2299       Uncharacterized conserved protein (DUF2299)
       0.19   12.5   3.3        2.2    9.1   1.2    2.6  2  DUF5409       Family of unknown function (DUF5409)
        0.6   10.4   4.6        1.4    9.2   0.5    2.3  2  DRY_EERY      Alternative splicing regulator
        1.7    7.5   4.7        1.7    7.5   1.6    2.1  2  tRNA-synt_1d  tRNA synthetases class I (R)
        2.9    8.0   5.5        8.9    6.4   0.7    2.7  2  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.9   7.5e+03      64      81 ..      20      38 ..      14      72 .. 0.49
   2 ?   -2.3   0.1       1.3   3.4e+03      52      75 ..     100     122 ..      92     137 .. 0.66
   3 !  136.3   4.9   5.2e-43   1.3e-39       3     214 ..     142     340 ..     140     341 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.9
                          VIT1 64 kaerkreeeeleedpe.eg 81
                                  ++  k+e++++++++  + 
  gi|70607379|ref|YP_256249.1| 20 RELAKDEKDNYARECLlKL 38
                                  4444444444444442211 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                          VIT1  52 eYlsvkserdlekaerkreeeele 75 
                                   +Yls    ++++++er++  +e++
  gi|70607379|ref|YP_256249.1| 100 KYLSLARTEEFTQQERQKI-REIA 122
                                   6888888888888777763.3343 PP

  == domain 3  score: 136.3 bits;  conditional E-value: 5.2e-43
                          VIT1   3 davlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleedpeegea 83 
                                   d+++G++DGLv ++a + G+++a  g++  v ++Gl    +G +SM iG+Yls+ks++++ + +rkr ee+ + d++e+  
  gi|70607379|ref|YP_256249.1| 142 DFIYGISDGLVEVLAATSGIAGAI-GNPLFVAVSGLIVGASGTLSMSIGAYLSTKSSKEINQIKRKRIEEAKAIDKNEV-M 220
                                   9********************866.9*****************************************888888887555.5 PP

                          VIT1  84 eelaeilearglseelaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliGgliPllpylfvesvgl 164
                                   + l+e+l ++g++ee a+++  +l++  + + +        p+   + +sp k+Al+++ls+++G++iP++ yl+  s+ +
  gi|70607379|ref|YP_256249.1| 221 DRLSEVLVDMGVKEEVAEKLSPRLVDVAEDIIS--------PE---TDESPRKSALITGLSYIVGAIIPVITYLIGLSGLT 290
                                   9****************9999999987666433........22...2248999**********************778*** PP

                          VIT1 165 alvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaaylig 214
                                   +l+ s +v++la++ +G + +l++++++++++ +ml++G++Aa+a+ l+g
  gi|70607379|ref|YP_256249.1| 291 GLISSYLVSGLAIFTVGSLIGLISEVNPVKKGAEMLVLGIGAAIATHLLG 340
                                   **********************************************9997 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   7.2   2.3e-12   5.9e-09       6     136 ..       8     135 ..       6     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.3e-12
                                   HHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG.GHHHHH CS
                  Rubrerythrin   6 AiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl.ttaknL 85 
                                   +++ E  +r++Y+ela+  k++y   +e++++lAe+E++Ha++ +k+ +   ++le +  +  r   +++++f  ++  +L
  gi|70607379|ref|YP_256249.1|   8 NYKDELFDREVYRELAKDEKDNYA--RECLLKLAEMEEKHAEVWRKIADRKGLGLE-QLGKIDRLRIKFYKTFRkIFGLQL 85 
                                   6788999*************7777..******************************.444445555555555531344455 PP

                                   HHHHHHHHHHHHCHHHHHHHHHHHT.TSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  86 eeaiegayaeeeemyrfyeelaeke.gneeakklfkklaeaEkkHeerlrkl 136
                                   +  i++ + +e e++ +y  la+ e + +++++ ++++a +E  Hee+l +l
  gi|70607379|ref|YP_256249.1|  86 T--IKLLESRENESINKYLSLARTEeFTQQERQKIREIAIDEAVHEELLGRL 135
                                   5..999999999999999988875515677899**************99887 PP

>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.5   6.5e+03      60      80 ..     127     147 ..     113     154 .. 0.69
   2 ?   10.6   0.1   0.00014      0.36      56     130 ..     199     275 ..     195     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
                                   HHHHHHHHS-HHHHHHHHHHH CS
                       DUF2299  60 ehkkalsslkeeerkeflsel 80 
                                    h++ l  lk ++  +f+  +
  gi|70607379|ref|YP_256249.1| 127 VHEELLGRLKAKDVGDFIYGI 147
                                   477788888888877777655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                                   E--HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT-EEEEE-TTS--.-EEEEEEEEEGGG-....-HHHHHHHHHHHHHH CS
                       DUF2299  56 kvseehkkalsslkeeerkeflselkrdLlrlcvdfqlipqdeelpqsiqvskeiykdgl....tknelldavkrvrna 130
                                   ++++ ++k++++ k  +++e++ +l++ L++++v+ ++  + +  p+ + v++ i + +      k++l+  + +++ a
  gi|70607379|ref|YP_256249.1| 199 EINQIKRKRIEEAKAIDKNEVMDRLSEVLVDMGVKEEVAEKLS--PRLVDVAEDIISPETdespRKSALITGLSYIVGA 275
                                   5788999********************************9999..9******999876554445666666666666555 PP

>> DUF5409  Family of unknown function (DUF5409)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.095   2.4e+02      40      67 ..      94     121 ..      72     130 .. 0.78
   2 ?    9.1   1.2   0.00085       2.2       2      37 ..     269     307 ..     268     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.095
                       DUF5409  40 nPyslskylsldslnpfkkeekkeegfl 67 
                                   +  s++kylsl     f ++e+++++ +
  gi|70607379|ref|YP_256249.1|  94 ENESINKYLSLARTEEFTQQERQKIREI 121
                                   444889***************9887755 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                       DUF5409   2 lsyiinpilsivyfii..gkiskll.syllvklilfllk 37 
                                   lsyi++ i+ ++ ++i  + +++l+ syl++ l +f + 
  gi|70607379|ref|YP_256249.1| 269 LSYIVGAIIPVITYLIglSGLTGLIsSYLVSGLAIFTVG 307
                                   8*****9998887776225799998469********987 PP

>> DRY_EERY  Alternative splicing regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5   0.00056       1.4      68     108 ..       6      46 ..       1      68 [. 0.73
   2 ?    2.6   0.3      0.06   1.5e+02      78     110 ..      98     130 ..      83     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00056
                      DRY_EERY  68 eeeeeeeelnyERYrdLiknefeevseeeelkqiaeeesfs 108
                                   +++ ++e  ++E Yr+L+k+e+++ ++e  lk  + ee+++
  gi|70607379|ref|YP_256249.1|   6 SKNYKDELFDREVYRELAKDEKDNYARECLLKLAEMEEKHA 46 
                                   556678899********999999877776666666666533 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.06
                      DRY_EERY  78 yERYrdLiknefeevseeeelkqiaeeesfsae 110
                                     +Y++L+++e+   +e++++++ia +e++++e
  gi|70607379|ref|YP_256249.1|  98 INKYLSLARTEEFTQQERQKIREIAIDEAVHEE 130
                                   468****999999999*********99998765 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.6   0.00065       1.7     100     215 ..      14     146 ..       6     152 .. 0.61
   2 ?    0.1   0.1      0.12   3.1e+02      90     144 ..     196     249 ..     183     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00065
                                   HHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHH..HHHCT---EC.............--CCC CS
                  tRNA-synt_1d 100 fykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqkl..ydrldvtlie.............rGesl 165
                                   f +e+ ++++++e   + ar+++ kL + +e+  ++w+++ d     l++l   drl +   +               es 
  gi|70607379|ref|YP_256249.1|  14 FDREVYRELAKDEK-DNYARECLLKLAEMEEKHAEVWRKIADRKGLGLEQLgkIDRLRIKFYKtfrkifglqltikLLESR 93 
                                   56788889999987.789**********************99754433332112344443333333344444444455666 PP

                                   CCCCHHHHHHHHHCTT-EEEC.TTCEEEEECCC..TSSCCEECC-TTS-B-HH CS
                  tRNA-synt_1d 166 ykeslneivkelkkkglvkes.dGalvvfldef..gkrlgvvvqksDGgylyt 215
                                    +es+n+ +   + +++ +++ +  + + +de    + lg++  k  G ++y 
  gi|70607379|ref|YP_256249.1|  94 ENESINKYLSLARTEEFTQQErQKIREIAIDEAvhEELLGRLKAKDVGDFIYG 146
                                   66666666666666666554303333455555433555666666666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                                   S-----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHH CS
                  tRNA-synt_1d  90 qeqelqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditr 144
                                   +++e+++++    e  k  d++e++ +r  +++v +  ++e  +kl  +lvd+++
  gi|70607379|ref|YP_256249.1| 196 SSKEINQIKRKRIEEAKAIDKNEVM-DRLSEVLVDMGVKEEVAEKLSPRLVDVAE 249
                                   4667777777777788888888876.56677888888888888888888888765 PP

>> CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.046   1.2e+02      24      36 ..     272     284 ..     269     285 .. 0.91
   2 ?    6.4   0.7    0.0035       8.9      15      39 .]     326     350 ..     324     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.046
                  CytB6-F_Fe-S  24 aaaaLyPvvkFFi 36 
                                   +++a+ Pv++++i
  gi|70607379|ref|YP_256249.1| 272 IVGAIIPVITYLI 284
                                   689********98 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0035
                  CytB6-F_Fe-S  15 llvGaialtaaaaLyPvvkFFiPPs 39 
                                   l++G++a+ a+ +L   ++ F+PP+
  gi|70607379|ref|YP_256249.1| 326 LVLGIGAAIATHLLGVLAAHFLPPG 350
                                   89999999999999999*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2594.46
//
Query:       gi|70607380|ref|YP_256250.1|  [L=470]
Description: hypothetical protein Saci_1647 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-56  191.8  46.3    1.5e-56  191.8  46.3    2.0  2  MFS_1     Major Facilitator Superfamily
    7.3e-07   27.9  16.7      1e-06   27.5  11.3    2.3  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8  46.3   1.7e-60   1.5e-56       1     352 [.      10     400 ..      10     401 .. 0.91
   2 ?    0.4   0.4     0.028   2.5e+02     138     172 ..     429     459 ..     419     469 .. 0.66

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 1.7e-60
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                   l+l+++++a + +i+++alp ++++dl+ +  +  ++l +y l+ a++s  +Gr++d +Gr r++ +g+llf l+ +l+++
  gi|70607380|ref|YP_256250.1|  10 LMLGTLMAAVDTTIVLLALP-TITTDLHTDLYTSIWVLLAYLLVLAILSTQAGRIGDIVGRSRIYNMGFLLFTLAsGLCGI 89 
                                   6899****************.******************************************************666666 PP

                         MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    ++++ +l+ +r+lq++g+++l+++++a++ad+ p+++rg a+gl s+g+++Ga+lg +lgg+l++ lgWr++fyi+ +++
  gi|70607380|ref|YP_256250.1|  90 -SPNIEFLIGFRILQAAGGAMLASNSGAIVADILPPNRRGGAYGLTSLGWNVGALLGIILGGVLTTFLGWRYIFYINVPIG 169
                                   .67777*************************************************************************** PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeee............................................kgtgpaplvp 198
                                   ++a++l   +   +++++ +++    +                                            ++++ ap+v+
  gi|70607380|ref|YP_256250.1| 170 IIAVIL--GFREIKDVNKTKNKLDIAGslvlglllflisfgavliagegasissilmiivgvllipafilvERKVSAPIVN 248
                                   ***886..555444444444443333388**************************************************** PP

                         MFS_1 199 awkallkdpvlwillialllf...ffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrr 276
                                     + ++ ++    l ++++ +   ++g  ++++ll +ylq v+g+s  ++++++l+ +++v+ ila++ gr++dr ++ ++
  gi|70607380|ref|YP_256250.1| 249 -MRVFREKK----LSYSVFANflqGLGALAVSFLLIMYLQGVRGYS-PFYSSIILSPGYIVASILAPIMGRVADRGKPGII 323
                                   .99999999....44444444111346666****************.8***************************999*** PP

                         MFS_1 277 lllallllllaalglallavtssavllllvlvl.iGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                     ++l++++l++++++l+ ++++++ ++l++ +  G+g+g+++ps +++++ +ap+e+ g++sg+  t+g++g++l+
  gi|70607380|ref|YP_256250.1| 324 AGIGLIFTFLSLIAYYLFLTPTTPIEIILMITFiTGVGSGMFWPSNQTAIMFNAPREYYGAVSGVSRTLGNIGTILS 400
                                   ***************************9966553777*************************************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.028
                         MFS_1 138 pllggllasslgWravfyilaivsllafvlfllll 172
                                    +++++++   g +++f+i  ++ ++a++l    l
  gi|70607380|ref|YP_256250.1| 429 GGVSSVFV--DGLHLAFLISSVIVVVAAIL--SIL 459
                                   45555565..35678899999999999886..444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5  11.3   1.1e-10     1e-06      15     191 ..      10     182 ..       4     231 .. 0.88
   2 !    3.2   0.2    0.0026        23      63     128 ..     306     373 ..     294     386 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.1e-10
                         MFS_3  15 iWiaslvsnlGtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvl 95 
                                   + + +l++ + t i   a   + td+++  ++   v  a  L + +ls  aG + D++ r ++  ++ ll  l+s l  ++
  gi|70607380|ref|YP_256250.1|  10 LMLGTLMAAVDTTIVLLALPTITTDLHTDLYTSIWVLLAYLLVLAILSTQAGRIGDIVGRSRIYNMGFLLFTLASGLCGIS 90 
                                   5566777777777778888888999999999999999**************************************999988 PP

                         MFS_3  96 aalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna 176
                                     +++     l+++ +l + G a+ +    A+v ++++ +    A  L+s+g+n+    G  lgGvl +++G  + f +n+
  gi|70607380|ref|YP_256250.1|  91 PNIEF-----LIGFRILQAAGGAMLASNSGAIVADILPPNRRGGAYGLTSLGWNVGALLGIILGGVLTTFLGWRYIFYINV 166
                                   87765.....8*******************************************************************998 PP

                         MFS_3 177 .lsylalivallrwkr 191
                                    +  +a+i+ + ++k 
  gi|70607380|ref|YP_256250.1| 167 pIGIIAVILGFREIKD 182
                                   4566666666555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0026
                         MFS_3  63 ilaGalaDnfdrRk.vllavqlllal.vsvlltvlaalgllspwlllaltlligiGaalndPaWqAsv 128
                                   ila ++    dr k  ++a+  l+ +  s+++  l ++  +   ++l++t+++g+G+ +  P+ q ++
  gi|70607380|ref|YP_256250.1| 306 ILAPIMGRVADRGKpGIIAGIGLIFTfLSLIAYYLFLTPTTPIEIILMITFITGVGSGMFWPSNQTAI 373
                                   4454444555554422344444443303444444444444445578999*************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 2636.58
//
Query:       gi|70607381|ref|YP_256251.1|  [L=441]
Description: pyruvate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-81  273.1   2.2    4.6e-81  272.4   2.2    1.3  1  PK         Pyruvate kinase, barrel domain
    2.8e-21   75.9   0.0    9.2e-21   74.3   0.0    1.9  1  PK_C       Pyruvate kinase, alpha/beta domain
  ------ inclusion threshold ------
        0.1   11.7   0.0       0.21   10.7   0.0    1.5  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.4   2.2   7.6e-85   4.6e-81       2     343 ..       4     316 ..       3     321 .. 0.94

  Alignments for each domain:
  == domain 1  score: 272.4 bits;  conditional E-value: 7.6e-85
                                   --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCSS CS
                            PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgkk 82 
                                   r+tki++t+GP+se+   +++l++a ++++r+n +hG+ e+h++  ++vr        kv il D+ Gp++r+g lk+   
  gi|70607381|ref|YP_256251.1|   4 RKTKIIATMGPNSEK--IIDELAKA-VDIIRINLAHGDEEQHRRYFDMVRD-------KVPILADLPGPKLRIGDLKN--- 71 
                                   89*********9976..58888876.89********************996.......799****************9... PP

                                   SEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BEE CS
                            PK  83 dielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkgvn 163
                                    i+lk gdk+++  d           i +d +  +k ++  + +l++DG+++lk++ev e k  + +v  +g+++s+kg+n
  gi|70607381|ref|YP_256251.1|  72 PIDLKPGDKVTFGQD-----------IPVDNEIFFKLIKKDSNVLIADGRIKLKIEEVGEGK-AVATVIEGGTITSRKGIN 140
                                   79*******996544...........667777788999999********************9.55668889********** PP

                                   -TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHHSSEEE CS
                            PK 164 lpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeileasDgim 244
                                   lp+++ ++ +l+ +D + l+++++ g  +i +sfv +a+Dvk+vre+++   +++ +i+kie++++++nl ei +asDg+m
  gi|70607381|ref|YP_256251.1| 141 LPDADTPV-GLTKRDYELLKLAIDLGATFIGLSFVINADDVKKVREIVG---NRVWLISKIEKKKALSNLKEICKASDGVM 217
                                   ****9987.8*************************************97...579************************** PP

                                   EEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-HH CS
                            PK 245 varGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyPv 325
                                   varGDlG+e++ ++++ +q++++k +++ gkpvi atq+lesm+++P ptraev+Dvan++  G Da+mLs eta G yP 
  gi|70607381|ref|YP_256251.1| 218 VARGDLGVEVGLPSLPQIQRRIVKIARNYGKPVILATQVLESMVESPLPTRAEVTDVANSISQGVDAIMLSDETAIGLYPL 298
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHTS- CS
                            PK 326 eavkamaevaleaekalk 343
                                   + vk++ ++ ++ ek++k
  gi|70607381|ref|YP_256251.1| 299 DVVKTLDSLIISVEKTFK 316
                                   ********9999999876 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   1.5e-24   9.2e-21       1     116 [.     328     437 ..     328     438 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.5e-24
                                   HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHH CS
                          PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellrea 81 
                                   eaia++av  +   +  aI v+t+sG+tA++is++rp++pii +t ++++a++l+++ G+ypvl +k    e++d++ r+a
  gi|70607381|ref|YP_256251.1| 328 EAIAYSAVVSSILSNSPAIFVYTRSGSTALRISRLRPTCPIITLTFDKSVAKRLSMCYGIYPVLTDK---LETLDDITRKA 405
                                   79**********9**************************************************9886...788******** PP

                                   HHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEE CS
                          PK_C  82 vkvakeaglvkkgdevvvtaGtpkgesgttNtlrV 116
                                    ++a++ gl  +g ++vv++  +  ++gtt ++r+
  gi|70607381|ref|YP_256251.1| 406 KETALNLGL--NG-NIVVVGAARPDQKGTTRFVRI 437
                                   ********9..45.566666666667****99998 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.6e-05      0.21     105     162 ..     186     231 ..     133     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.6e-05
                                   HTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HHHHHHHTT-TT CS
                     HpcH_HpaI 105 alrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGaeDlsadlgtkr 162
                                   +            +++ l+  iE +++++n++eI  a++g   v+++  Dl +++g+ +
  gi|70607381|ref|YP_256251.1| 186 I----------VGNRVWLISKIEKKKALSNLKEICkASDG---VMVARGDLGVEVGLPS 231
                                   3..........34567999***************977665...5566777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2976.30
//
Query:       gi|70607382|ref|YP_256252.1|  [L=159]
Description: hypothetical protein Saci_1649 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-48  164.4   0.0    1.4e-48  164.2   0.0    1.0  1  DUF2299   Uncharacterized conserved protein (DUF2299)


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.0   7.7e-53   1.4e-48       1     137 [.       5     140 ..       5     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 7.7e-53
                                   HHHHHHHHTT-EEEE---TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHH CS
                       DUF2299   1 eikeWLkeeGlkveevpdanaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselk 81 
                                   ei++++ke+Gl+v+++p+a+++fhi+++ppq g +vvd+i++++ks++++++mgv++++ hkka+ +lk eerkefl++l 
  gi|70607382|ref|YP_256252.1|   5 EIEDVMKELGLNVSRPPQAQEKFHIVTTPPQ-GFPVVDIIRLTDKSRFYLITMGVAIHPVHKKAIGGLKLEERKEFLNNLA 84 
                                   69*****************************.8************************************************ PP

                                   HHHTTTT-EEEEE-TTS--.-EEEEEEEEEGGG--HHHHHHHHHHHHHHHHHHHHH CS
                       DUF2299  82 rdLlrlcvdfqlipqdeelpqsiqvskeiykdgltknelldavkrvrnakllviwl 137
                                   +dLl+++vdf+++p+++++p+ iq++++i+ dg+t+nell+a++ vrna++lvi++
  gi|70607382|ref|YP_256252.1|  85 EDLLKMGVDFAFLPPGTDVPDAIQIIRIIFADGMTPNELLSAYYVVRNAGMLVINR 140
                                   ******************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1104.12
//
Query:       gi|70607383|ref|YP_256253.1|  [L=107]
Description: hypothetical protein Saci_1650 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.3    7.2  18.0        1.6    6.9  18.0    1.1  1  DUF2070     Predicted membrane protein (DUF2070)
        9.9    5.8   8.1         11    5.6   8.1    1.2  1  DUF2981     Protein of unknown function (DUF2981)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  18.0   0.00018       1.6      45     125 ..      11      90 ..       2     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00018
                       DUF2070  45 glp.alvaflltlpvlrilggrltykrslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsd 124
                                   +++ +l++fl+++    ++++rl++k+sl+ +l+++l+++++s+l +++ +++   +l  +  + ++++ +r l+l++v  
  gi|70607383|ref|YP_256253.1|  11 YVTlFLLSFLVLTISYGVISKRLDLKKSLIASLFSLLFMSLFSTLDYIFLLVI--PLLVLVYRGAFSITWMRSLILTIVYL 89 
                                   3334899999999999999999*************************988665..34444444456666777777666654 PP

                       DUF2070 125 e 125
                                   +
  gi|70607383|ref|YP_256253.1|  90 S 90 
                                   3 PP

>> DUF2981  Protein of unknown function (DUF2981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.1    0.0013        11      35      77 ..      59     103 ..      12     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0013
                       DUF2981  35 lllgvnaisavlG..flGalkRslvveavYlvfylislvlvvltv 77 
                                   +ll++  ++ v    f   + Rsl++  vYl fy+i + ++++ +
  gi|70607383|ref|YP_256253.1|  59 FLLVIPLLVLVYRgaFSITWMRSLILTIVYLSFYAIFMNYIFFHI 103
                                   233333333332134566799*******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 756.80
//
Query:       gi|70607384|ref|YP_256254.1|  [L=193]
Description: hypothetical protein Saci_1651 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-15   57.3   0.0    3.4e-15   56.5   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    9.4e-12   45.5   0.0    1.4e-11   45.0   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    1.7e-08   34.4   0.0    2.3e-08   34.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.3e-07   30.9   0.0    3.6e-07   30.3   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
    5.6e-07   30.2   0.0    9.6e-07   29.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.3e-05   25.1   0.0    1.9e-05   24.5   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00011   21.6   0.0     0.0006   19.2   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0022   17.0   0.0     0.0034   16.3   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0084   15.7   0.0      0.011   15.3   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.048   12.9   0.0    1.6  1  CMAS             Mycolic acid cyclopropane synthetase
       0.12   11.6   0.1       0.25   10.5   0.0    1.5  2  Methyltransf_7   SAM dependent carboxyl methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   2.1e-18   3.4e-15       2      95 ..      34     120 ..      33     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.1e-18
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   d+GcG+G+++  l+  ++  +++D+s ++l  a++k+ e       ++ad+e lp++d+  D  v   ++hh+e p+  lk
  gi|70607384|ref|YP_256254.1|  34 DIGCGSGQNCMILK--AKVRLCIDFSRKQLYEARKKGCEHL-----LEADMEYLPLRDSCLDGAVFIASIHHLETPDNSLK 107
                                   9*************..44479************99998876.....9********************************** PP

                                   HHHHHEEEEEEEE CS
               Methyltransf_11  83 eiaRvLkpgGllv 95 
                                   e++RvLk+ G ++
  gi|70607384|ref|YP_256254.1| 108 EAYRVLKKHGNIL 120
                                   **********876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   8.3e-15   1.4e-11       1      97 []      32     117 ..      32     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 8.3e-15
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   + d+GcG+G++++ l +++     +++D+s ++l +ar++        +++++d+e lp+ d+  D  v + ++hhl+ +d
  gi|70607384|ref|YP_256254.1|  32 IADIGCGSGQNCMILKAKV----RLCIDFSRKQLYEARKKG-----CEHLLEADMEYLPLRDSCLDGAVFIASIHHLETPD 103
                                   78*************9987....59***************9.....4479********************878****9988 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                     + lke++rvLk+ G
  gi|70607384|ref|YP_256254.1| 104 --NSLKEAYRVLKKHG 117
                                   ..77*********998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.4e-11   2.3e-08       6     110 ..      31     122 ..      28     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.4e-11
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                   ++ D+GCG+G+ +  l  ++        iD+s + +  Ar+    +g +  ++ ++d+e l+  l d++ D  +  + +++
  gi|70607384|ref|YP_256254.1|  31 VIADIGCGSGQNCMILKAKV-----RLCIDFSRKQLYEARK----KGCE--HLLEADMEYLP--LRDSCLDGAVFIASIHH 98 
                                   689**************665.....489************9....5777..7778*******..99*************** PP

               Methyltransf_31  87 ladpdkileeiervlkpggillie 110
                                   l  pd+ l+e+ rvlk++g +l++
  gi|70607384|ref|YP_256254.1|  99 LETPDNSLKEAYRVLKKHGNILLT 122
                                   *******************99965 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.2e-10   3.6e-07      73     163 ..      29     130 ..      11     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.2e-10
                                   TS-EEEES-TT-HHHHH--S-..EEEEESS-SS.........TTEEES-TTS-S--TT-EEEEEEES---SS-H.HHHHHH CS
                Methyltransf_8  73 nlvvadlGcGeakiaeavrekekvrsfdlvavn.........ervvacdlakvPledesvdvavfclslmgtnl.adflke 143
                                     v+ad+GcG  +  +  + k +  ++d+   +         e++   d+  +Pl d+  d avf  s+   +   + lke
  gi|70607384|ref|YP_256254.1|  29 GRVIADIGCGSGQNCMILKAKVR-LCIDFSRKQlyearkkgcEHLLEADMEYLPLRDSCLDGAVFIASIHHLETpDNSLKE 108
                                   579*******8776633333322.244543221111112223678899*********************987662568*** PP

                                   HHHHEEEEE..EEEEEEEGGG- CS
                Methyltransf_8 144 anrvlkvGG..llkvaevksrf 163
                                   a+rvlk+ G  ll v  v+ rf
  gi|70607384|ref|YP_256254.1| 109 AYRVLKKHGniLLTVWLVQPRF 130
                                   *****99883345666677776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.9e-10   9.6e-07       2      98 ..      34     118 ..      33     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.9e-10
               Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdi 82 
                                   +iGcG+G++ + l +k      +++D+s++++   +++ +  e +  + +e+  l ++        D  v +  +hhl+++
  gi|70607384|ref|YP_256254.1|  34 DIGCGSGQNCMILKAK----VRLCIDFSRKQL--YEARKKGCEHLLEADMEYLPLRDS------CLDGAVFIASIHHLETP 102
                                   9************999....667*********..555556666656666666666665......899************** PP

               Methyltransf_12  83 revldnirklLkpgGr 98 
                                   + +l++++++Lk+ G 
  gi|70607384|ref|YP_256254.1| 103 DNSLKEAYRVLKKHGN 118
                                   ************9986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.2e-08   1.9e-05      21     124 ..      27     128 ..       3     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.2e-08
               Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppel 101
                                    +g  + diGcG+G ++ +l+++      +D s+++  +a+k+ + +   +d +  +  +   d +v + +++h++ p   
  gi|70607384|ref|YP_256254.1|  27 IEGRVIADIGCGSGQNCMILKAK--VRLCIDFSRKQLYEARKKGCEHLLEADMEYLPLRDSCLDGAVFIASIHHLETPDNS 105
                                   4455677*************777..55789*****9999999999999999777777788899****************** PP

               Methyltransf_23 102 lrqiatllkpgGylllseplasl 124
                                   l+ +++ lk  G++ll+++l+  
  gi|70607384|ref|YP_256254.1| 106 LKEAYRVLKKHGNILLTVWLVQP 128
                                   ******************98743 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.7e-07    0.0006      37     150 ..      18     120 ..      11     132 .. 0.86
   2 ?   -0.2   0.0      0.32   5.2e+02     203     222 ..     158     177 ..     155     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.7e-07
                                   HHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
               Ubie_methyltran  37 kfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                   ++  k v   +g+ + D+ +G+g   + l  +v+       +D++ + L +++kk  e      ++l a+ e Lp  d   
  gi|70607384|ref|YP_256254.1|  18 RKPLKFVQLIEGRVIADIGCGSGQNCMILKAKVR-----LCIDFSRKQLYEARKKGCE------HLLEADMEYLPLRDSCL 87 
                                   5556677778899999*******99999887776.....468********99998766......4799999********** PP

                                   EEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 118 DvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                   D       +  +   +++Lkeayrvlk  G+++
  gi|70607384|ref|YP_256254.1|  88 DGAVFIASIHHLETPDNSLKEAYRVLKKHGNIL 120
                                   *9999999*******************988765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                                   HHHHHHHHTTEEEEEEEEEG CS
               Ubie_methyltran 203 tlkeliedaGfksveyeslt 222
                                   ++k+++e+ Gf++ +y ++ 
  gi|70607384|ref|YP_256254.1| 158 EIKKVVEKEGFRTLKYINFR 177
                                   578999**********9985 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0034     110     220 ..      23     124 ..      15     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                                   GS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEE CS
                Methyltransf_9 110 hlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsm 189
                                    +  ++gr+i+d+Gcg+G   +  +  +ak+ + id s+  l+  ea +k       +hll   +e lp   +++d    +
  gi|70607384|ref|YP_256254.1|  23 FVQLIEGRVIADIGCGSGQNCM--I-LKAKVRLCIDFSRKQLY--EARKKGC-----EHLLEADMEYLPLrDSCLDGAVFI 93 
                                   566689************8764..3.35677777777777664..5555543.....677777788888845568988888 PP

                                   S-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE CS
                Methyltransf_9 190 GvlyhrrsPldhllqlkdqlvkgGelvletl 220
                                     ++h ++P + l +    l+k G+++l   
  gi|70607384|ref|YP_256254.1|  94 ASIHHLETPDNSLKEAYRVLKKHGNILLTVW 124
                                   8899********************9998765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.9e-06     0.011      14     104 ..      29     115 ..      18     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.9e-06
                          MetW  14 gsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkev 94 
                                   g  + d+GcG G+   +lk   +v+   ++ +++ + e+ +kG + +  ++d +    +d+ +d +v+  ++  +  p++ 
  gi|70607384|ref|YP_256254.1|  29 GRVIADIGCGSGQNCMILKA--KVR-LCIDFSRKQLYEARKKGCEHL-LEADMEYLPLRDSCLDGAVFIASIHHLETPDNS 105
                                   34567*************77..444.58***************9754.46677777889********************** PP

                          MetW  95 ldellrigrr 104
                                   l+e  r+ ++
  gi|70607384|ref|YP_256254.1| 106 LKEAYRVLKK 115
                                   ******9776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     3e-05     0.048      55     220 ..      21     178 ..       9     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEEE CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.kvdrvvsv 134
                                   l+ ++l +G  + diGcG G+ ++   ++  v+ + + +S++q   a+k+    + e+  e ++ +y  l++  +d  v +
  gi|70607384|ref|YP_256254.1|  21 LKFVQLIEGRVIADIGCGSGQNCMILKAK--VR-LCIDFSRKQLYEARKK----GCEHLLEADM-EYLPLRDsCLDGAVFI 93 
                                   6778999**************99877777..54.5799999998887765....3444444443.4666666478999999 PP

                                   S-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCC.HHHH.HHTSTTS---BHHHHHHHHHHTT-EEE CS
                          CMAS 135 gafehvgkenydtffkklkkllkedGllllhtitslhkkelaerglkl.kfid.keiFPgGelpsieeieeeiseagftvv 213
                                     + h+ +   d+  k+++++lk+ G +ll      +++ l  r++++ + i+ ke++   +l    ei++ +++ gf+ +
  gi|70607384|ref|YP_256254.1|  94 ASIHHLET--PDNSLKEAYRVLKKHGNILLTVW-LVQPRFLFRRRVTIrSVINgKEVYRFYRLYLPGEIKKVVEKEGFRTL 171
                                   99999855..46778999999999999988544.44555555455554344433778777777777888888888888888 PP

                                   EEEE-HH CS
                          CMAS 214 dveslra 220
                                   ++ ++r+
  gi|70607384|ref|YP_256254.1| 172 KYINFRQ 178
                                   8888776 PP

>> Methyltransf_7  SAM dependent carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.25      17      36 ..      31      50 ..      21      72 .. 0.79
   2 ?   -2.7   0.0       1.5   2.5e+03     237     254 ..     157     174 ..     148     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                  EEEEET--SSCHHHHHHHHH CS
                Methyltransf_7 17 kiaDLGCSsGpNtllvvsei 36
                                  +iaD+GC sG+N +++  ++
  gi|70607384|ref|YP_256254.1| 31 VIADIGCGSGQNCMILKAKV 50
                                  7***********99875555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                   HHHHHHHHHH-SEEEEEE CS
                Methyltransf_7 237 eevkeviekegsFkiekl 254
                                    e+k+v+ekeg  +++ +
  gi|70607384|ref|YP_256254.1| 157 GEIKKVVEKEGFRTLKYI 174
                                   699999999997666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1293.99
//
Query:       gi|70607385|ref|YP_256255.1|  [L=68]
Description: hypothetical protein Saci_1652 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-06   28.9   0.2    1.5e-06   28.7   0.2    1.1  1  ThiS         ThiS family
     0.0065   16.5   0.0     0.0085   16.1   0.0    1.3  1  ThiS-like    ThiS-like ubiquitin
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.015   15.4   0.0    1.3  1  CRISPR_Cas2  CRISPR associated protein Cas2
      0.021   14.7   0.4      0.061   13.2   0.2    1.7  2  TOBE_3       TOBE-like domain
      0.028   15.1   0.5      0.057   14.1   0.4    1.6  1  YukD         WXG100 protein secretion system (Wss), protein Y
       0.11   12.8   0.1       0.13   12.6   0.1    1.1  1  DUF3247      Protein of unknown function (DUF3247)


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2     5e-10   1.5e-06      15      77 .]      15      68 .]       3      68 .] 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5e-10
                                  EEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                          ThiS 15 elelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                  e+el+e + v++ll+++g+r       ++ +v  N   + +   d+elkdgD++ ++ + +GG
  gi|70607385|ref|YP_256255.1| 15 EVELPERARVRDLLKKIGYRV------QGSVVVKNSLPIIE---DEELKDGDKLRVFLAASGG 68
                                  6899*****************......**************...******************9 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.9e-06    0.0085      28      52 ..      36      60 ..      14      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                     ThiS-like 28 daDvvIlNGFpikeDteLkegDevf 52
                                  +  vv+ N  pi eD eLk+gD++ 
  gi|70607385|ref|YP_256255.1| 36 QGSVVVKNSLPIIEDEELKDGDKLR 60
                                  445*******************985 PP

>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   5.2e-06     0.015      15      38 ..      20      42 ..      15      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.2e-06
                                  HHHHHHHHHHHTTEEEEETTEEEE CS
                   CRISPR_Cas2 15 rrrkvakilkkyGfqrvQySVFeg 38
                                  +r++v+++lkk  ++rvQ+SV ++
  gi|70607385|ref|YP_256255.1| 20 ERARVRDLLKKI-GYRVQGSVVVK 42
                                  589*********.********877 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     2e-05     0.061      21      55 ..       3      35 ..       1      36 [. 0.82
   2 ?   -1.0   0.0      0.56   1.7e+03      46      57 ..      50      61 ..      48      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                        TOBE_3 21 vRlELerlgdtgeliEvelprdrfeelglae.Getv 55
                                  v +EL r+     +iEvelp+ ++ +  l++ G +v
  gi|70607385|ref|YP_256255.1|  3 VTVELVRE---NKIIEVELPERARVRDLLKKiGYRV 35
                                  56777666...77**********9999999989877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.56
                        TOBE_3 46 elglaeGetvyl 57
                                  +++l+ G+++++
  gi|70607385|ref|YP_256255.1| 50 DEELKDGDKLRV 61
                                  568888999886 PP

>> YukD  WXG100 protein secretion system (Wss), protein YukD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.9e-05     0.057       2      30 ..       3      31 ..       1      60 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                                  EEEEEE-TTTEEEEEEETTSBTTHHHHHH CS
                          YukD  2 vrVtvlagnrrvDlaLPadvpvaellpal 30
                                  v+V  + +n+ ++++LP+   v++ll  +
  gi|70607385|ref|YP_256255.1|  3 VTVELVRENKIIEVELPERARVRDLLKKI 31
                                  4566669*******************987 PP

>> DUF3247  Protein of unknown function (DUF3247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.3e-05      0.13      24      63 ..      17      57 ..       4      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                  CTTTT-EEEEEETT.S-EEEEEECC---EEEEE-TT--EEE CS
                       DUF3247 24 lldseervaleled.GrqlaGtvavrptvqiyrdeqereGv 63
                                   l+ ++rv+ +l+  G +++G+v v+ ++ i  de+ ++G 
  gi|70607385|ref|YP_256255.1| 17 ELPERARVRDLLKKiGYRVQGSVVVKNSLPIIEDEELKDGD 57
                                  5999****9777644********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 505.38
//
Query:       gi|70607386|ref|YP_256256.1|  [L=223]
Description: hypothetical protein Saci_1653 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1588.75
//
Query:       gi|70607387|ref|YP_256257.1|  [L=367]
Description: hypothetical protein Saci_1654 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-39  133.9   0.0    1.2e-38  133.6   0.0    1.1  1  DAO              FAD dependent oxidoreductase
    1.3e-07   31.7   0.1    3.1e-07   30.5   0.1    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    5.8e-05   22.5   0.0    7.2e-05   22.2   0.0    1.2  1  FAD_binding_3    FAD binding domain
    0.00018   21.2   0.3    0.00034   20.3   0.3    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
    0.00024   20.5   0.0      0.001   18.4   0.0    1.9  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00032   21.2   3.0     0.0051   17.3   0.2    3.3  4  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0011   18.9   0.1     0.0017   18.3   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0021   18.1   1.7     0.0064   16.6   0.1    2.6  2  PMBR             Pseudomurein-binding repeat
  ------ inclusion threshold ------
      0.035   12.9   0.4      0.051   12.4   0.4    1.2  1  Trp_halogenase   Tryptophan halogenase
      0.064   12.5   0.3       0.11   11.7   0.3    1.4  1  Thi4             Thi4 family
      0.072   13.1   0.3       0.27   11.2   0.3    1.9  2  NAD_binding_9    FAD-NAD(P)-binding
      0.083   11.9   0.1       0.13   11.3   0.1    1.2  1  FAD_binding_2    FAD binding domain
      0.098   12.6   0.0       0.18   11.8   0.0    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.16   12.2   0.1       0.34   11.2   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.17   10.5   0.4       0.27    9.9   0.4    1.3  1  HI0933_like      HI0933-like protein
       0.19   10.8   0.1       0.35    9.9   0.1    1.4  1  GIDA             Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.0   1.1e-41   1.2e-38       1     352 []       2     342 ..       2     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1.1e-41
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH........................ CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas........................ 55 
                                   +v+iiGGGi+G+++Ay+L+r+g  Vt++ek+  +g   S +++gl+ ++  ++  ++                        
  gi|70607387|ref|YP_256257.1|   2 KVAIIGGGIVGSFIAYYLSREGvdVTIYEKS-SLG-SGSVHAAGLIEPYRFDKI-NTtgmikkmlsyvgkkvtivkqlnpe 79 
                                   59*****************************.9**.9***********554333.44699999****************** PP

                                   ...................HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEE CS
                           DAO  56 ...................elarlslealeelreleeelgididyrrtGllslaadeeelealdkllallleagldaelld 117
                                                       + r++  +l+e+++++ee + d+dy+++Gll +++d     +l       le+g+++e  +
  gi|70607387|ref|YP_256257.1|  80 wiksllsilnkeppqeawdIIRRMATFSLKEYKRMAEEVN-DFDYEENGLLEIYQD-----RLN------LEHGVEEEKRN 148
                                   ******************64449***************77.9***********854.....552......23444443333 PP

                                   H....HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEE CS
                           DAO 118 a....eevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaad 194
                                   +     ev +++    g+ ga+++p+   ++++k++  + r+++  Gv+i  + e+++l+e    +++      g    +d
  gi|70607387|ref|YP_256257.1| 149 PfnpkFEVIDVK----GFSGAIYFPELSKLNTYKFMERMKRELK--GVKIEIR-EIVNLDE----ISK------G----YD 208
                                   310012333333....89*************************7..9999888.8888843....222......4....79 PP

                                   EEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEE.EESSEEETT CS
                           DAO 195 avVnaaGawsdllgllkeldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlv.Ggtadeesg 274
                                   +vV++aG+w        +l  pi+ ++g+ ++++   +          +p ++  + gv v+    +++++ Gg +     
  gi|70607387|ref|YP_256257.1| 209 TVVLSAGVWL------SKLGMPITSFKGYGYRVSGEML---V---K--YP-SVISELGVAVVKNS-DHIKItGGFD----- 268
                                   *********4......445579***********54322...2...2..34.9999********97.77***66643..... PP

                                   CSSTSCSHHHHHHHHHHHHHHSGGGCGEEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                           DAO 275 dddpevdeedidellealrklfPqlgdvlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                     d+++d e++  +l+a   l  ++++v     G+rp+ pdg+p+ig+   v  +++ tG+++ G++++p +Gk +a+l
  gi|70607387|ref|YP_256257.1| 269 -ADFSADVERAKIFLDAGGCLA-KIDKVYDLSMGYRPCsPDGFPIIGR---VGQFVISTGACRLGWSFGPSMGKFTADL 342
                                   .334667777777777666555.4456666667****669********...589***********************97 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   2.8e-10   3.1e-07       1      33 [.       5      37 ..       5      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.8e-10
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                  I+G+G+ G+ +Ay+L+++g+dv+++ek++  +G
  gi|70607387|ref|YP_256257.1|  5 IIGGGIVGSFIAYYLSREGVDVTIYEKSSLGSG 37
                                  9**************************865545 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.5e-08   7.2e-05       3      66 ..       2      66 ..       1     125 [. 0.82

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.5e-08
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaeg 66
                                  +V+I+G+G +G   a  Ls+ Gv+v++ ek s  +     a+ +++  ++ +++ G+ +++l+  
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEKSSLGSGSVhAAGLIEPYRFDKINTTGMIKKMLSYV 66
                                  79******************************999999344556888888888888888888765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   3.1e-07   0.00034       1      31 [.       3      33 ..       3      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.1e-07
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  +ai+G G +Gs++a++L++ g dvt++ +s 
  gi|70607387|ref|YP_256257.1|  3 VAIIGGGIVGSFIAYYLSREGVDVTIYEKSS 33
                                  69***********************998776 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   9.2e-07     0.001       2      89 ..       2     110 ..       1     238 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH...............HHHHCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias...............evvkkl 63 
                                   +v++iGgG+ G   a +l++ g++vt++e            g + +  l +  ++ +i +                 vk+l
  gi|70607387|ref|YP_256257.1|   2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEksslG------SGSVHAAGLIEPYRFDKINTtgmikkmlsyvgkkvTIVKQL 76 
                                   89**************************555543......44444444444444444333444444777888777666666 PP

                                   HHH.CCCCHC.......CTCEEEEESCEEEEETE CS
                                   xxx.xxxxxx.......xxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  64 nqg.ielllg.......eevvkidpgkkkvklek 89 
                                   n + i+ ll        +e+ +i++  +++ l++
  gi|70607387|ref|YP_256257.1|  77 NPEwIKSLLSilnkeppQEAWDIIRRMATFSLKE 110
                                   6665555555555555555555555555555554 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   4.6e-06    0.0051       1      31 [.       2      32 ..       2      34 .. 0.94
   2 ?   -1.1   0.0       2.7     3e+03      18      30 ..      63      75 ..      61      78 .. 0.79
   3 ?   -2.0   0.1         5   5.6e+03      44      69 ..     181     206 ..     175     213 .. 0.59
   4 ?    1.6   0.0      0.38   4.2e+02      21      46 ..     250     275 ..     243     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-06
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                  kv+++GgG +g   A +l++ g +Vt+ e s
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEKS 32
                                  79*************************8876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                                  HHHTTSEEEEEES CS
                     Pyr_redox 18 laelgkkVtvver 30
                                  l+  gkkVt+v  
  gi|70607387|ref|YP_256257.1| 63 LSYVGKKVTIVKQ 75
                                  66789*****975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5
                                   HHHHHHHHHTTEEEECSEEEEEEEEE CS
                     Pyr_redox  44 kilqeklekngievllntkveeiegs 69 
                                   ++++++l+  +ie++   ++ ei + 
  gi|70607387|ref|YP_256257.1| 181 ERMKRELKGVKIEIREIVNLDEISKG 206
                                   44555555556666666666666554 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.38
                                   TTSEEEEEESSSSSS..TTSSHHHHHHH CS
                     Pyr_redox  21 lgkkVtvversdkll..rllDeeaskil 46 
                                   lg  V vv +sd++    ++D+++s+ +
  gi|70607387|ref|YP_256257.1| 250 LG--VAVVKNSDHIKitGGFDADFSADV 275
                                   44..889999999999999999988766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.5e-06    0.0017       1      32 [.       2      33 ..       2      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdise 32
                                  kva+iG G++G+ ia+ + ++g++V++++ s+
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEKSS 33
                                  79**************************9865 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.7e-06    0.0064       3      25 ..     104     127 ..     102     129 .. 0.93
   2 ?   -0.8   0.3       1.8     2e+03      18      27 ..     177     186 ..     175     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                          PMBR   3 gkisyeeyldmasrvlaf.iesng 25 
                                    ++s+ ey++ma +v++f +e+ng
  gi|70607387|ref|YP_256257.1| 104 ATFSLKEYKRMAEEVNDFdYEENG 127
                                   699********************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                          PMBR  18 lafiesngrl 27 
                                   ++f+e+ +r+
  gi|70607387|ref|YP_256257.1| 177 YKFMERMKRE 186
                                   79******95 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   4.5e-05     0.051       1      40 [.       2      38 ..       2      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvg 40
                                  k+ i+GGG+ G+  A +l++ +   ++vt+ e++ +g   
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREG---VDVTIYEKSSLGSGS 38
                                  799******************9...9******99998755 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3    0.0001      0.11      19      57 ..       2      38 ..       1      69 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                  EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                          Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                   v+i+G+G  G   ayyl+++ ++ v+i e+s s+G G+
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSRE-GVDVTIYEKS-SLGSGS 38
                                  699******************.********87.566554 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00024      0.27       1      43 [.       4      41 ..       4      46 .. 0.93
   2 ?   -2.1   0.0         3   3.4e+03     116     141 ..     189     215 ..     177     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43
                                  ai+G+G+ G  ++  L ++      +++t++++s++g+g+v+ 
  gi|70607387|ref|YP_256257.1|  4 AIIGGGIVGSFIAYYLSRE-----GVDVTIYEKSSLGSGSVHA 41
                                  8****************99.....6************999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                 NAD_binding_9 116 tvevhraevvdleeradgq.avlladg 141
                                    v++   e+v+l+e  +g+ +v+l+ g
  gi|70607387|ref|YP_256257.1| 189 GVKIEIREIVNLDEISKGYdTVVLSAG 215
                                   345555788888888888766766655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00011      0.13       2      45 ..       3      45 ..       2      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                                  v +iG+G+ G   A+ ++++G +v++ ek +  g+ ++ + G i
  gi|70607387|ref|YP_256257.1|  3 VAIIGGGIVGSFIAYYLSREGVDVTIYEKSSL-GSGSVHAAGLI 45
                                  89****************************97.77777777766 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.18       1      33 [.       2      43 ..       2      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                  -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.........H CS
                NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvree.........e 33
                                  k+a++G+G  G+ +A  l+++g +v+++ +++          
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEKSSlgsgsvhaaG 43
                                  79*************************998775555555550 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0003      0.34       1      40 [.       3      39 ..       3      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHH CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskekleal 40
                                  v iiG+G vG+++a +l+r++    ++t+ ++s  +   +
  gi|70607387|ref|YP_256257.1|  3 VAIIGGGIVGSFIAYYLSREGV---DVTIYEKSSLGSGSV 39
                                  689****************985...699998887664444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00024      0.27       2      32 ..       2      32 ..       1      43 [. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                  +v++iGgG  G + A  ++++g +V+++ek 
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEKS 32
                                  79***************************97 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00031      0.35       1      30 [.       2      31 ..       2      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                  +v +iGgG  G+  A+ ++r G++v+++ +
  gi|70607387|ref|YP_256257.1|  2 KVAIIGGGIVGSFIAYYLSREGVDVTIYEK 31
                                  699***********************9943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2684.33
//
Query:       gi|70607388|ref|YP_256258.1|  [L=173]
Description: hypothetical protein Saci_1655 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-72  240.5   7.8    7.4e-72  240.3   7.8    1.0  1  DUF1955   Domain of unknown function (DUF1955)
  ------ inclusion threshold ------
      0.021   14.4   1.6      0.024   14.2   1.6    1.1  1  RexA      Intracellular sensor of Lambda phage, Abi component


Domain annotation for each model (and alignments):
>> DUF1955  Domain of unknown function (DUF1955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.3   7.8   8.3e-76   7.4e-72       1     156 [.       7     165 ..       7     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.3 bits;  conditional E-value: 8.3e-76
                                   -HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHH CS
                       DUF1955   1 ellkklmeakkllldGyveeGveiieklvkssnikeanWvicniidaidcdylvevldsiGkifdlskcqnlkrviecyvk 81 
                                   ++lkklm+akkll+dG++eeG++ii++l+kss+++e+nW+icni+d+i+cd+l+ vl++iG++fdlskcqnl+++i+c++k
  gi|70607388|ref|YP_256258.1|   7 DTLKKLMDAKKLLSDGIIEEGDKIIKELAKSSPRDEYNWFICNIVDTISCDTLFVVLEDIGSNFDLSKCQNLRTIINCGIK 87 
                                   689****************************************************************************** PP

                                   TT---HHHHHHHHHHHHTT-HHHHHHHHHHH..---.S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHH CS
                       DUF1955  82 lnklseyvdlaldvlvkkgkkdqldkilkel..kne.ikaelllkianalkklgdereanellkkacekGikeaceni 156
                                   ln++s+y+d+ald+l+++gkk+ql++i+k+l   ne +k+e+++kianalkk+g++rean+l+++ac++Gik+ac+++
  gi|70607388|ref|YP_256258.1|  88 LNINSKYFDMALDYLTAQGKKEQLEDISKNLfkLNEqPKPEIVIKIANALKKIGSTREANDLMNEACKRGIKDACASV 165
                                   *******************************996777**************************************998 PP

>> RexA  Intracellular sensor of Lambda phage, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.6   2.6e-06     0.024     115     218 ..      38     142 ..       2     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                          RexA 115 aPkaealkdylnevlsllglsdlefklealmesvtKkdvlklpfigrtaievnkssellkelvevLlgnsvda..ellesl 193
                                   +P+ +++++++ +++ +++   l + le +  + + +   +l  i    i++n +s+ +   +++L +++ ++  e++   
  gi|70607388|ref|YP_256258.1|  38 SPR-DEYNWFICNIVDTISCDTLFVVLEDIGSNFDLSKCQNLRTIINCGIKLNINSKYFDMALDYLTAQGKKEqlEDISKN 117
                                   555.5799***********9999999*****************************************99876646777777 PP

                          RexA 194 eitlKPklkknikkaakniiknipd 218
                                     +l  ++k +i  ++ n++k+i +
  gi|70607388|ref|YP_256258.1| 118 LFKLNEQPKPEIVIKIANALKKIGS 142
                                   7788888888988888888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1358.30
//
Query:       gi|70607389|ref|YP_256259.1|  [L=478]
Description: hypothetical protein Saci_1656 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     4e-113  378.1   4.9   4.7e-113  377.8   4.9    1.1  1  DUF790    Protein of unknown function (DUF790)


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.8   4.9  2.6e-117  4.7e-113       1     387 []       1     367 [.       1     367 [. 0.97

  Alignments for each domain:
  == domain 1  score: 377.8 bits;  conditional E-value: 2.6e-117
                        DUF790   1 MLpsdllrvrrrggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaefetes 81 
                                   MLp +l+r++++g +i+p f++  n e+a+e+++lf++  Ge+ g++ e+ k le+  +dyklvrGL +l+ r + +e++s
  gi|70607389|ref|YP_256259.1|   1 MLPWELARFKIQGSRIIPLFID--NSEIAQEVLDLFQK--GERLGNVIEQAKYLEK-IYDYKLVRGLIRLIIRVTSLEEDS 76 
                                   *********************8..999***********..****************.89********************** PP

                        DUF790  82 pldpeelReevFeaaaeavvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLlkrYNlslvqtlL 162
                                   p+dp+ lR+e+F++++  v +++ +e+v+ee+++++++   e  +++++dl+e+k++ e ++i+++eL+k YNlsl+qtlL
  gi|70607389|ref|YP_256259.1|  77 PIDPSILRRELFSRGP--VFDKKVKEDVIEEIKKKYNI---EPIRYMFSDLDEEKRIIEKPNISADELIKWYNLSLLQTLL 152
                                   ****************..********************...999************************************* PP

                        DUF790 163 fkatelrirvsdaeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpallkvekWeleAeikd 243
                                   fk ++l+irvs+ ++ke++++ kllgLmy++++++   le+++ GPa+l+k++e+YG+++A llp+++++ +W+++Aei  
  gi|70607389|ref|YP_256259.1| 153 FKGYRLSIRVSS-NWKEIIWRAKLLGLMYYAYKEP---LELEFIGPATLVKMNEKYGRNFAVLLPYVVSSPDWSIRAEIVL 229
                                   ************.9*********************...9****************************************** PP

                        DUF790 244 rdkkkrelrfeldsedsglvshyeeekefdssveeefaerfeklktdwelerepellkiggsvmiPDFaleekdgrrvyle 324
                                   ++ kkr++++e+++ + +l   + +ek+fdss+ee+f+++f+++ +dw+++repe+l++++++++PDF   ek++ +vy+e
  gi|70607389|ref|YP_256259.1| 230 GKLKKRIYKLEASNLK-NLREIKIDEKKFDSSIEEKFYNDFTSILKDWKITREPEPLVVKDKIFLPDFVA-EKGKLKVYIE 308
                                   **************76.66565666777******************************************.9********* PP

                        DUF790 325 IvGfwtpeylkkKleklrkaerkelivavserlklekagvkakdlrvilfkdklrvkdVlevl 387
                                   IvGfwt++yl++Klek++++e ++l+++v+e+l+++ + +  +  ++il+k+k++v +V+++l
  gi|70607389|ref|YP_256259.1| 309 IVGFWTKKYLQNKLEKVSDVE-NPLLLLVNEELSIDGK-I--DLPNIILYKKKIDVMKVYKWL 367
                                   ********************9.**************74.4..4567**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2849.16
//
Query:       gi|70607390|ref|YP_256260.1|  [L=443]
Description: hypothetical protein Saci_1657 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-26   91.5   0.0    4.8e-25   88.5   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
    3.3e-17   62.8   0.2    1.4e-16   60.8   0.1    2.0  2  Helicase_C     Helicase conserved C-terminal domain
      2e-16   59.9   0.4    4.2e-16   58.9   0.4    1.5  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    9.1e-11   41.5   0.1    2.2e-10   40.3   0.1    1.7  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    3.1e-08   33.6   0.0    1.2e-07   31.6   0.0    2.0  1  DEAD           DEAD/DEAH box helicase
    2.4e-07   29.8   0.1    1.5e-06   27.2   0.0    2.2  3  SNF2_N         SNF2 family N-terminal domain
     0.0026   18.0   0.8       0.87    9.9   0.0    3.1  3  AAA_22         AAA domain
     0.0033   17.1   0.3        0.1   12.3   0.0    2.8  2  SWI2_SNF2      SWI2/SNF2 ATPase
  ------ inclusion threshold ------
      0.019   13.9   0.2       0.64    8.9   0.0    2.3  2  ORC2           Origin recognition complex subunit 2
       0.14   12.4   2.0          1    9.5   0.0    3.0  4  Helicase_C_2   Helicase C-terminal domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   2.7e-28   4.8e-25       2     171 .]      68     207 ..      67     207 .. 0.93
   2 ?    0.0   0.1      0.42   7.5e+02      46      89 ..     318     361 ..     310     383 .. 0.67

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 2.7e-28
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   lelr+yQ+ea++++l     k+ krg++  +TG+GKT+v +k+i+ l+       +l++vp+++l++q+ + +++ l+++ 
  gi|70607390|ref|YP_256260.1|  68 LELRDYQMEAVKSWL-----KNGKRGIVIFPTGAGKTMVGVKAIALLKV-----STLVVVPTIDLMNQWVSIIERHLDTE- 137
                                   79************9.....7889***********************99.....5**********************998. PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEE CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavll 163
                                     + +++ g k++        k i+v+t++s++ +         e l ++f++ii+DE+H+l + + +   +++f + ++l
  gi|70607390|ref|YP_256260.1| 138 --V-GSIGGGKDDL-------KGITVITYDSAYTRA--------EELGNKFLLIIFDEVHHLPS-EGYSLMAKMFASPYRL 199
                                   ..3.5555656665.......69*************........99******************.**************** PP

                                   EEESS-S- CS
                        ResIII 164 glTATper 171
                                   glTATper
  gi|70607390|ref|YP_256260.1| 200 GLTATPER 207
                                   ******86 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.42
                                   HHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEE CS
                        ResIII  46 erllkkgkeekflflvprkslleqtleefkkflseaykeigkkv 89 
                                   ++ll++++ +k++++   ++l     +ef     ++++++ + +
  gi|70607390|ref|YP_256260.1| 318 RELLREFHDRKIIVFTRDTELAYDISKEFLIPVVTYKTSKDERF 361
                                   56778888899999999999999999999666665554433332 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7     3e+03      18      36 ..     112     131 ..     105     165 .. 0.65
   2 !   60.8   0.1   7.9e-20   1.4e-16       2     110 ..     313     415 ..     312     416 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                                   EEEEEESSHHHHHH.HHHHH CS
                    Helicase_C  18 kilifvntidrlek.vklll 36 
                                    +l++v+tid +++ v++++
  gi|70607390|ref|YP_256260.1| 112 STLVVVPTIDLMNQwVSIIE 131
                                   68999999997766555552 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 7.9e-20
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                   k+e+l ell +e +++ki++f++ ++ ++  ++    k++ + v++ +++++er eil++f++g+++v++a++v  +G+di
  gi|70607390|ref|YP_256260.1| 313 KIEKLRELL-REFHDRKIIVFTRDTELAY--DIS---KEFLIPVVTYKTSKDERFEILSKFKEGNYRVIVASTVFDEGVDI 387
                                   899999999.8999************997..666...447788889999******************************** PP

                                   TTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   p+++  i+++   + +++iqr GR+ R+
  gi|70607390|ref|YP_256260.1| 388 PDAEIAIIMGGYGTKRQFIQRLGRILRG 415
                                   *************************997 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.4   2.3e-19   4.2e-16      44     181 ..     312     439 ..     283     442 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.3e-19
                 ERCC3_RAD25_C  44 nkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPe 124
                                    k++ +  L++  e ++ kiivf+ +     +++k++  p ++ +ts+ er +il+kfk+  ++++i+ s v D+ +D+P+
  gi|70607390|ref|YP_256260.1| 312 AKIEKLRELLR--EFHDRKIIVFTRDTELAYDISKEFLIPVVTYKTSKDERFEILSKFKEG-NYRVIVASTVFDEGVDIPD 389
                                   55555544443..334559*****99999999**************************987.79***************** PP

                 ERCC3_RAD25_C 125 anvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkr 181
                                   a++ i i   +g++rq  qrlGriLr + k      +a    +v k t +   s++r
  gi|70607390|ref|YP_256260.1| 390 AEIAI-IMGGYGTKRQFIQRLGRILRGRGK------KALLIEIVTKGTADYRLSKRR 439
                                   **999.7789****************9887......688888888888888777766 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   1.2e-13   2.2e-10       1      57 []       4      54 ..       4      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.2e-13
                                  EEEETTEEEECSSSTT...-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                       XPB_DRD  1 LrYdrGTllidgdprgkaslpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                  LrY++G l++d++++g   l+   wDe+ ++y   A++Yrd+ +++ ++gie+ ++v
  gi|70607390|ref|YP_256260.1|  4 LRYYKGLLISDAYAPG---LK---WDEKLQGYINFAYKYRDVKKYFLTEGIEVVENV 54
                                  9*************98...66...*****************************9887 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   6.9e-11   1.2e-07       2     142 ..      72     190 ..      71     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.9e-11
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   d+Q ea++  l +g+  +v  +TG+GKT++ + ++   +       +  +l+v+Pt  L++q ++ +++ ++    +v +i
  gi|70607390|ref|YP_256260.1|  72 DYQMEAVKSWLkNGKRGIVIFPTGAGKTMVGVKAIA--L------LKVSTLVVVPTIDLMNQWVSIIERHLD---TEVGSI 141
                                   89*********77789**************887777..3......36789*****************99999...466677 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfi 142
                                    gg++  + ++++  ++d  ++  + l +          ++ ++++DE++ l ++g+s   
  gi|70607390|ref|YP_256260.1| 142 GGGKDDLKGITVI--TYDSAYTRAEELGN----------KFLLIIFDEVHHLPSEGYSLMA 190
                                   6776664444444..55555555555544..........56799**********9998554 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   8.3e-10   1.5e-06      64     224 ..      94     214 ..      62     273 .. 0.70
   2 ?   -0.7   0.0      0.25   4.5e+02     263     308 ..     218     263 ..     206     299 .. 0.70
   3 ?   -1.9   0.0      0.59   1.1e+03     218     270 ..     275     327 ..     273     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.3e-10
                                   TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH--------- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  64 mGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkva 143
                                   +G+GKT+  +  i+                 l++ tL+vvP+ +l++qW++ ierh+      v   gg+k          
  gi|70607390|ref|YP_256260.1|  94 TGAGKTMVGVKAIA----------------LLKVSTLVVVPTiDLMNQWVSIIERHLDTE---VGSIGGGK---------- 145
                                   55555544444444................34578**********************998...34444432.......... PP

                                   --------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SSS-HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 144 pklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiqnsledly 224
                                         +++ ++tYd   ++a      ++l   +   ++ DE h l ++    + +++ +++ +r+ lt+TP   + +++ 
  gi|70607390|ref|YP_256260.1| 146 ---DDLKGITVITYDSAYTRA------EELG-NKFLLIIFDEVHHLPSEG--YSLMAKMFASPYRLGLTATPERGDGKEVL 214
                                   ...2358***********888......7775.57889*********9984..4456666779**********887777764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.25
                                   T-STTEE---GGGT.--S---EEEEEEEEE--HHHHHHHH....... CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 263 llqrlmlrrakkdv.eknlPpkteeiiflklskverksYnrllevlr 308
                                   l+ +++ +++ k++  k++++ +    +++++++e++ Y+  l  + 
  gi|70607390|ref|YP_256260.1| 218 LVGPIVYKKSLKELsGKYIADFEIIKEYVEMTSEEKERYK-ELRGKL 263
                                   5667777777788845568888888889999999999999.333332 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.59
                                   S-HHHHHHHHHHH-TTTT--HH..HHHHHTHHHHHHHHHHHHHHHHTT-STTEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 218 nsledlygLlkfLreepfgekq..tfdkllqrpieaqaekgrsrLlqllqrlmlr 270
                                   nsl+d+y L+ +   ++        +++ l   ++  +++++++L++ll+++  r
  gi|70607390|ref|YP_256260.1| 275 NSLNDFYKLIRLASKDKKAREAllAWHESLRLAVN--SRAKIEKLRELLREFHDR 327
                                   78888888888888777665444588888887777..788888888888866544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00048      0.87       8     107 ..      88     184 ..      82     199 .. 0.73
   2 ?    4.7   0.2     0.019        35      38     117 ..     237     322 ..     206     339 .. 0.74
   3 ?   -1.0   0.0       1.1     2e+03      70      97 ..     391     423 ..     345     426 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00048
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdl.lrellralglelkaerlsseellealeqa 85 
                                   ++v+ ++G+GKT++  +    l         +++++  v    ++  + ++  r+l  ++g+ + +  ++++ +    ++ 
  gi|70607390|ref|YP_256260.1|  88 GIVIFPTGAGKTMVGVKAIALL---------KVSTLvVVPTIDLMnQWVSIiERHLDTEVGSIGGG-KDDLKGITVITYDS 158
                                   667779*********9999999.........66666333333333577777578888999988888.77777777777777 PP

                        AAA_22  86 lrarav.....ielliiDEaqhlrsee 107
                                   + +ra        l+i DE++hl + e
  gi|70607390|ref|YP_256260.1| 159 AYTRAEelgnkFLLIIFDEVHHL-PSE 184
                                   77777788888999*********.644 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.019
                        AAA_22  38 erpevv..fvtlpsst..sskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqhlr..seealee 111
                                   ++ e++  +v+++s++    k+l+ +l ++l +++ +  +s+ +++++++ a++++++  +ll   E  +l   s + +e+
  gi|70607390|ref|YP_256260.1| 237 ADFEIIkeYVEMTSEEkeRYKELRGKLKEFLSSRGMR-LNSLNDFYKLIRLASKDKKArEALLAWHESLRLAvnSRAKIEK 316
                                   5666667778888888779999999999999999999.8889999999999999999888888888888887765555555 PP

                        AAA_22 112 Lrslln 117
                                   Lr+ll 
  gi|70607390|ref|YP_256260.1| 317 LRELLR 322
                                   555554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                        AAA_22  70 a......erlsseellealeqalraraviellii 97 
                                   +        +++++++++l + lr r++ ++l+i
  gi|70607390|ref|YP_256260.1| 391 EiaiimgGYGTKRQFIQRLGRILRGRGK-KALLI 423
                                   0445554456777788888888888888.66655 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   5.6e-05       0.1       7     160 ..      79     208 ..      71     247 .. 0.73
   2 ?    0.8   0.0      0.19   3.3e+02      41      98 ..     319     375 ..     307     382 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                     SWI2_SNF2   7 ekavervke..gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekpkqaesrke 85 
                                   +       +  ++ k G++   +G+GK++  v++ + l+         +vv+   dL +Q  + +++  +++   + s   
  gi|70607390|ref|YP_256260.1|  79 K-------SwlKNGKRGIVIFPTGAGKTMVGVKAIALLKV------STLVVVPTIDLMNQWVSIIERHLDTE---VGSIGG 143
                                   2.......233457889999*******9999888777766......456777889*******9999887776...456666 PP

                     SWI2_SNF2  86 LkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpnaafigFTGTPilk 160
                                    k+ l   ++  ++t    ++     + e+l ++  +++++DE H   +++++  + k++    ++g+T TP   
  gi|70607390|ref|YP_256260.1| 144 GKDDL---KGITVITYDSAYT-----RAEELGNKF-LLIIFDEVHHLPSEGYS-LMAKMFASPYRLGLTATPERG 208
                                   67777...2333333333332.....345677776.99*******99998875.799***************654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                     SWI2_SNF2  41 klleeelknpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeLkellekesekii 98 
                                   +ll+ e+++ k++v t  ++L   +sk+f     + ++++++r e+ +++++ + ++i
  gi|70607390|ref|YP_256260.1| 319 ELLR-EFHDRKIIVFTRDTELAYDISKEFLIPVVTYKTSKDERFEILSKFKEGNYRVI 375
                                   3344.78999999999999*******99986544444456666666666655544444 PP

>> ORC2  Origin recognition complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00035      0.64     298     318 ..     316     336 ..     305     341 .. 0.90
   2 ?    2.5   0.0      0.03        54      54      73 ..     393     412 ..     389     430 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                                   GHHHHHHHHTTTTSS-B---- CS
                          ORC2 298 alrtlLkEFkDHklikskkda 318
                                   +lr+lL+EF+D k+i+ ++d+
  gi|70607390|ref|YP_256260.1| 316 KLRELLREFHDRKIIVFTRDT 336
                                   79**************99886 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.03
                                   EEEE--SS--HHHHHHHHSS CS
                          ORC2  54 slllyGvGSKrklleeFaee 73 
                                    +++ G+G Kr++++++ + 
  gi|70607390|ref|YP_256260.1| 393 AIIMGGYGTKRQFIQRLGRI 412
                                   6999**********998665 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   4.7e+03      94     112 ..      59      77 ..      44     127 .. 0.59
   2 ?   -1.6   0.0       1.5   2.7e+03       8      34 ..     109     135 ..     102     149 .. 0.82
   3 ?    9.5   0.0   0.00058         1      35      87 ..     343     394 ..     294     399 .. 0.63
   4 ?   -0.2   0.4      0.53   9.5e+02     129     146 ..     403     420 ..     399     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                  Helicase_C_2  94 Pfpnpkdpeveakreylde 112
                                   Pfp + +  +e++   +++
  gi|70607390|ref|YP_256260.1|  59 PFPLIREKSLELRDYQMEA 77 
                                   5555544444444332222 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                  Helicase_C_2   8 vpggvlvffpSyklleevverlkeele 34 
                                    +  +lv++p  +l+++ v+ ++++l+
  gi|70607390|ref|YP_256260.1| 109 LKVSTLVVVPTIDLMNQWVSIIERHLD 135
                                   5567999**********9999988874 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00058
                  Helicase_C_2  35 skkieifvee.........keesrekvleeykekkkkgaillavcrGklsEGidfsddllra 87 
                                   sk+                ++ +r ++l+++ke  ++  +++a+    + EG+d++d+++ +
  gi|70607390|ref|YP_256260.1| 343 SKE------FlipvvtyktSKDERFEILSKFKE--GNYRVIVAST--VFDEGVDIPDAEIAI 394
                                   233......03333334447778999*******..8888888888..8********988755 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.53
                  Helicase_C_2 129 ravnQaiGRliRhkdDyg 146
                                   r++ Q +GR++R +  ++
  gi|70607390|ref|YP_256260.1| 403 RQFIQRLGRILRGRGKKA 420
                                   8899********887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2830.27
//
Query:       gi|70607391|ref|YP_256261.1|  [L=276]
Description: hypothetical protein Saci_1658 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-26   91.7   6.4    7.1e-16   57.5   0.3    2.3  2  HTH_24          Winged helix-turn-helix DNA-binding
      5e-18   64.7   0.0    1.5e-10   40.8   0.0    2.3  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.1e-07   31.6   0.7      0.014   15.3   0.0    2.8  3  TrmB            Sugar-specific transcriptional regulator TrmB
    1.5e-06   28.0   0.0      0.035   14.0   0.0    2.3  2  MarR_2          MarR family
      3e-06   27.0   0.1      0.016   15.1   0.0    2.4  2  MarR            MarR family
    8.1e-05   22.6   0.3      0.018   15.0   0.0    2.7  2  HTH_Mga         M protein trans-acting positive regulator (MG
    0.00016   21.6   0.0      0.077   13.0   0.0    2.5  2  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00021   21.1   0.0       0.59   10.0   0.0    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
    0.00033   20.7   0.3       0.86    9.7   0.1    2.3  2  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
    0.00039   20.7   0.2       0.35   11.2   0.0    2.3  2  Rrf2            Transcriptional regulator
    0.00058   19.9   0.0       0.57   10.3   0.0    2.4  2  HTH_20          Helix-turn-helix domain
     0.0013   19.3   0.1        1.8    9.2   0.1    2.5  2  Mga             Mga helix-turn-helix domain
     0.0016   18.3   1.1       0.56   10.2   0.2    2.4  2  HTH_11          HTH domain
     0.0018   18.1   1.2       0.15   11.9   0.1    2.5  2  TFIIE_alpha     TFIIE alpha subunit
     0.0052   17.3   0.1          3    8.5   0.0    2.4  2  Phage_rep_O     Bacteriophage replication protein O
  ------ inclusion threshold ------
      0.012   15.8   0.3       0.45   10.7   0.0    2.3  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.016   15.0   0.1       0.83    9.5   0.0    2.4  2  LexA_DNA_bind   LexA DNA binding domain
       0.07   13.1   1.5        2.7    8.0   0.1    2.5  2  HTH_45          Winged helix-turn-helix
      0.078   12.8   0.0        6.2    6.7   0.0    2.3  2  HTH_23          Homeodomain-like domain
       0.11   12.2   0.0        2.5    7.9   0.0    2.3  2  Sigma70_r4_2    Sigma-70, region 4
       0.12   12.0   0.0       0.38   10.5   0.0    1.7  2  UPF0175         Uncharacterised protein family (UPF0175)
       0.17   12.1   0.0        4.7    7.4   0.0    2.2  2  HTH_28          Helix-turn-helix domain
       0.21   12.1   1.2        8.2    7.0   0.1    2.5  2  PCI             PCI domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.3   9.1e-19   7.1e-16       1      48 []       2      49 ..       2      49 .. 0.98
   2 !   36.8   1.2   2.6e-12     2e-09       4      48 .]     133     177 ..     131     177 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 9.1e-19
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +d +d+kIL +L +++risqr +Ae++ lS + +n+r ++L+e+G+Ik
  gi|70607391|ref|YP_256261.1|  2 MDSIDKKILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIK 49
                                  799********************************************8 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2.6e-12
                        HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   +d+kI + + knpri ++e+A+ l+l++  vnrr++ L+++  I+
  gi|70607391|ref|YP_256261.1| 133 IDIKIVKSVIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   8****************************************9996 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.9e-13   1.5e-10       1      41 [.       2      42 ..       2      43 .. 0.98
   2 !   21.8   0.0   1.5e-07   0.00012       4      39 ..     133     168 ..     131     171 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.9e-13
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +D iD+kIL  L +d+Ris +++Ae+v lS++    R ++L
  gi|70607391|ref|YP_256261.1|  2 MDSIDKKILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKL 42
                                  9*************************************998 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                 HTH_AsnC-type   4 iDrkILeaLqedaRisyaeLAervGlSestvlrRvr 39 
                                   iD+kI++   +++Ri  +e+A+ ++l    v rR++
  gi|70607391|ref|YP_256261.1| 133 IDIKIVKSVIKNPRIEISEIAKDLNLPSKSVNRRIN 168
                                   9*********************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.4e-05     0.042       9      62 ..       5      60 ..       2      66 .. 0.90
   2 !   15.3   0.0   1.8e-05     0.014      10      54 ..     134     178 ..     131     181 .. 0.89
   3 ?   -2.5   0.0       6.1   4.8e+03      24      42 ..     237     255 ..     234     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                                  HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEE CS
                          TrmB  9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklY 62
                                   + k+ ++L + g+ + ++iaee++++ ++ +   ++L++ G+++  k +  p+lY
  gi|70607391|ref|YP_256261.1|  5 IDKKILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKSFKVQvnPNLY 60
                                  5889999*************************************988766557777 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
                                   CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                          TrmB  10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54 
                                   ++k+ + ++k+ + +++eia++l++p  +v++ ++ L +k ++++
  gi|70607391|ref|YP_256261.1| 134 DIKIVKSVIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIRI 178
                                   66777788899999****************************986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.1
                                   HHCHHCCCTTSSCHCHHHH CS
                          TrmB  24 tadeiaeelgvprskvYev 42 
                                   ++++i +e+++  ++ Y++
  gi|70607391|ref|YP_256261.1| 237 NVRDIDREAEIMVTTSYDI 255
                                   7899999999988888875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.5e-05     0.035      10      52 ..       9      49 ..       6      57 .. 0.90
   2 !   11.6   0.0   0.00026       0.2      18      52 ..     145     177 ..     137     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  +L +L r ++  ++++ +a++ +ls  +++++ ++L + G + 
  gi|70607391|ref|YP_256261.1|  9 ILIYLFRDGR--ISQRKIAEEVKLSATSLNYRFNKLIEDGIIK 49
                                  5777777776..****************************985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                                   TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2  18 pgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                   p+  + ++e+a+ l+l+  +v+r+++ L  + +++
  gi|70607391|ref|YP_256261.1| 145 PR--IEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   54..889***********************99997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.016       8      49 ..       9      50 ..       7      54 .. 0.93
   2 !    9.6   0.0    0.0011      0.82      10      48 ..     139     177 ..     134     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                  iL  l + g +s+ ++a+ +++s +++     +L+++G i++
  gi|70607391|ref|YP_256261.1|  9 ILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKS 50
                                  88899999********************************87 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                                   HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                    ++  ++ + +se+ak l++ + +v r +  L  k++i+
  gi|70607391|ref|YP_256261.1| 139 KSVIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   55667899****************************998 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.039        30       8      38 ..       7      36 ..       3      44 .. 0.87
   2 !   15.0   0.0   2.3e-05     0.018       7      44 ..     134     170 ..     133     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.039
                       HTH_Mga  8 lkLlelLteneksltldelakeLglseltlq 38
                                   k+l +L+  +++++  ++a+e  ls  +l+
  gi|70607391|ref|YP_256261.1|  7 KKILIYLFR-DGRISQRKIAEEVKLSATSLN 36
                                  689999999.9***************98886 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-05
                       HTH_Mga   7 klkLlelLteneksltldelakeLglseltlqsdiseL 44 
                                   ++k++  +++ +++++++e+ak L+l +++++ +i+ L
  gi|70607391|ref|YP_256261.1| 134 DIKIVKSVIK-NPRIEISEIAKDLNLPSKSVNRRINVL 170
                                   689999****.*********************999877 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   9.8e-05     0.077      21      52 ..      18      49 ..       7      56 .. 0.88
   2 ?    5.8   0.0     0.017        13      25      53 ..     150     178 ..     138     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-05
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                  +++q+ +A+ + l+  +++  +++L ++g+i+
  gi|70607391|ref|YP_256261.1| 18 RISQRKIAEEVKLSATSLNYRFNKLIEDGIIK 49
                                  79*****************************8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.017
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglisr 53 
                                    e+A  l+l   +v+r ++ L ++++i+ 
  gi|70607391|ref|YP_256261.1| 150 SEIAKDLNLPSKSVNRRINVLTNKNMIRI 178
                                   79************************985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00076      0.59       8      47 .]      11      50 ..       6      50 .. 0.84
   2 !    8.8   0.0    0.0019       1.5       6      45 ..     136     176 ..     135     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00076
                                  HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  ++l ++g  +   +aee++ls   + + ++kL e G++++
  gi|70607391|ref|YP_256261.1| 11 IYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKS 50
                                  4455558888899************************985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                                   HHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5   6 kILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45 
                                   kI+k++ +++   ++e+a++l+l+   v +  ++L + +++
  gi|70607391|ref|YP_256261.1| 136 KIVKSVIKNPrIEISEIAKDLNLPSKSVNRRINVLTNKNMI 176
                                   8*********889***********99999999988877765 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0026         2      16      43 ..       7      34 ..       3      38 .. 0.90
   2 !    9.7   0.1    0.0011      0.86      17      57 ..     136     176 ..     135     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0026
                                  HHHHHHHHHHSSBEHHHHHHHHSSTHHH CS
                         HTH_9 16 akVvetLlrkgrltlrelvkktkLsldq 43
                                  +k+  +L+r gr + r++++++kLs ++
  gi|70607391|ref|YP_256261.1|  7 KKILIYLFRDGRISQRKIAEEVKLSATS 34
                                  68999*******************9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9  17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57 
                                   k+v+  +++ r  ++e++k+++L+ ++V +   vL++ +++
  gi|70607391|ref|YP_256261.1| 136 KIVKSVIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMI 176
                                   68888899999999*************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00046      0.35      15      58 ..      11      51 ..       7      52 .. 0.84
   2 !    7.3   0.1    0.0079       6.2      25      56 ..     146     177 ..     137     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                                  HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                  +yL +  +++ +s ++iae++++s++ l   ++kL + g++ks 
  gi|70607391|ref|YP_256261.1| 11 IYLFR--DGR-ISQRKIAEEVKLSATSLNYRFNKLIEDGIIKSF 51
                                  44443..444.99*****************************96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0079
                                   -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2  25 pvsseeiaerqnispsylekilakLrkaglvk 56 
                                    ++++eia+  n++ + + + ++ L+++++++
  gi|70607391|ref|YP_256261.1| 146 RIEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   4899************************9997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00073      0.57      24      55 ..      18      49 ..       3      53 .. 0.83
   2 !    7.0   0.0    0.0076         6      28      49 ..     150     171 ..     147     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00073
                                  TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                        HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLve 55
                                    +   +ae++ ls ++l+y++++L e g+++
  gi|70607391|ref|YP_256261.1| 18 RISQRKIAEEVKLSATSLNYRFNKLIEDGIIK 49
                                  5555679***********************97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0076
                                   HHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_20  28 selaerldlskntlsyHLrvLe 49 
                                   se+a+ l l+ ++++++++vL 
  gi|70607391|ref|YP_256261.1| 150 SEIAKDLNLPSKSVNRRINVLT 171
                                   8********************7 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1    0.0022       1.8      15      56 ..       3      44 ..       1      62 [. 0.81
   2 !    7.5   0.0    0.0079       6.1      15      54 ..     131     170 ..     125     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                                  HSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
                           Mga 15 eslkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56
                                  +s++ ++l +lf + ++s  ++a+e+ +S ++l+   ++l +
  gi|70607391|ref|YP_256261.1|  3 DSIDKKILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIE 44
                                  578889***************************988888765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0079
                                   HSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH CS
                           Mga  15 eslkyqllkflfeeeevsieelaqelyiSestlkrkikel 54 
                                   + ++++++k ++++ +++i e+a+ l + + +++r i+ l
  gi|70607391|ref|YP_256261.1| 131 SGIDIKIVKSVIKNPRIEISEIAKDLNLPSKSVNRRINVL 170
                                   668999*****************************99866 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       7.8       3      44 ..       7      51 ..       6      61 .. 0.79
   2 !   10.2   0.2   0.00071      0.56       9      47 ..     141     179 ..     135     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                  ++il+ L++    is  ++Aee ++S +    +  +L e g    +
  gi|70607391|ref|YP_256261.1|  7 KKILIYLFRDG-RISQRKIAEEVKLSATSLNYRFNKLIEDGiiksF 51
                                  58999996655.5*************99999888888888854444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00071
                        HTH_11   9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIe 47 
                                   ++++   i ++e+A+ Ln+  + v r+I  L+ +  ++I+
  gi|70607391|ref|YP_256261.1| 141 VIKNP-RIEISEIAKDLNLPSKSVNRRINVLTNKNmIRIY 179
                                   54444.4************************666555554 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1    0.0002      0.15      16      67 ..       7      58 ..       1      75 [. 0.82
   2 ?    4.7   0.1     0.035        28      16      60 ..     135     179 ..     131     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                  HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTT CS
                   TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeek 67
                                  +++l  L ++g ++   +a+e+k+  + l    n+L e++++k  + + +  
  gi|70607391|ref|YP_256261.1|  7 KKILIYLFRDGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKSFKVQVNPN 58
                                  6899**************************************9766554443 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.035
                                   HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                   TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60 
                                   ++++++++++  +   ++ak+l++  + + + +n L ++ ++ + 
  gi|70607391|ref|YP_256261.1| 135 IKIVKSVIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIRIY 179
                                   5788889999999999**********************9999875 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0039         3      47      89 ..      16      58 ..       8      63 .. 0.91
   2 ?    6.3   0.0     0.019        15      47      81 ..     144     178 ..     141     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0039
                   Phage_rep_O 47 sdwisnsqlveltgisrtkvskalkeLirekviikegrkvgvn 89
                                  + +is+ +++e +++s t+++   ++Li+ ++i+  + +v +n
  gi|70607391|ref|YP_256261.1| 16 DGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKSFKVQVNPN 58
                                  5689*****************************9988888777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                   Phage_rep_O  47 sdwisnsqlveltgisrtkvskalkeLirekviik 81 
                                   + +i+ s++++  ++++++v++ ++ L+++++i +
  gi|70607391|ref|YP_256261.1| 144 NPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIRI 178
                                   56889999999**********************75 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00058      0.45      19      57 ..      19      56 ..      15      74 .. 0.89
   2 ?    2.8   0.0      0.17   1.3e+02      23      54 ..     151     182 ..     148     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                B-block_TFIIIC 19 itqsdLakeskqdprslfyrlksLekkgLIvkqsiidsa 57
                                  i q+ +a e+k ++ sl yr ++L + g I+  ++ +++
  gi|70607391|ref|YP_256261.1| 19 ISQRKIAEEVKLSATSLNYRFNKLIEDGIIKSFKV-QVN 56
                                  5689999***********************99888.555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.17
                B-block_TFIIIC  23 dLakeskqdprslfyrlksLekkgLIvkqsii 54 
                                   ++ak ++  ++s+  r+++L++k+ I   +i+
  gi|70607391|ref|YP_256261.1| 151 EIAKDLNLPSKSVNRRINVLTNKNMIRIYPIV 182
                                   566777777899************99877774 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.12        93      27      57 ..      20      49 ..      19      53 .. 0.87
   2 ?    9.5   0.0    0.0011      0.83      28      60 ..     149     180 ..     141     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.12
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyie 57
                                  s r ia++++l+ + + + + ++L   G+i+
  gi|70607391|ref|YP_256261.1| 20 SQRKIAEEVKLS-ATSLNYRFNKLIEDGIIK 49
                                  679********7.888999999999998886 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                   HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind  28 ireiaralglkSpsaveehLkaLerKGyierdp 60 
                                   i eia+ l+l  +++v+ + + L +K +i++ p
  gi|70607391|ref|YP_256261.1| 149 ISEIAKDLNLP-SKSVNRRINVLTNKNMIRIYP 180
                                   67*********.689***************976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.073        57      17      51 ..      16      50 ..       4      60 .. 0.83
   2 ?    8.0   0.1    0.0035       2.7      14      50 ..     141     177 ..     133     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.073
                        HTH_45 17 egeakkTkimykanLsykllnkYLdmLvekglikk 51
                                  +g+ ++ ki  ++ Ls   ln   ++L+e g+ik 
  gi|70607391|ref|YP_256261.1| 16 DGRISQRKIAEEVKLSATSLNYRFNKLIEDGIIKS 50
                                  56667789999**********************76 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0035
                        HTH_45  14 aisegeakkTkimykanLsykllnkYLdmLvekglik 50 
                                   +i++ + + ++i ++ nL  k +n+ ++ L++k++i+
  gi|70607391|ref|YP_256261.1| 141 VIKNPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   4567788899************************994 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.008       6.2      10      34 ..      10      35 ..       3      48 .. 0.83
   2 ?    3.6   0.0     0.076        59      15      37 ..     142     166 ..     135     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.008
                        HTH_23 10 illllae.GlsvreIAreLgvsrrTv 34
                                   ++l+++ ++s+r+IA+e   s   +
  gi|70607391|ref|YP_256261.1| 10 LIYLFRDgRISQRKIAEEVKLSATSL 35
                                  58999999***********9998765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                        HTH_23  15 ae..GlsvreIAreLgvsrrTvyrw 37 
                                    +  ++ ++eIA+ L+ +   v r 
  gi|70607391|ref|YP_256261.1| 142 IKnpRIEISEIAKDLNLPSKSVNRR 166
                                   44567889*********99999875 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.26     2e+02      24      46 ..      16      38 ..       2      41 .. 0.74
   2 ?    7.9   0.0    0.0032       2.5      30      47 ..     150     167 ..     148     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.26
                                  TS---HHHHHHHHT--HHHHHHH CS
                  Sigma70_r4_2 24 leglsykEIAellgisegtVksr 46
                                      s++ IAe+ ++s ++ ++r
  gi|70607391|ref|YP_256261.1| 16 DGRISQRKIAEEVKLSATSLNYR 38
                                  45569999********9987765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0032
                                   HHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2  30 kEIAellgisegtVksrl 47 
                                    EIA+ l++++++V++r+
  gi|70607391|ref|YP_256261.1| 150 SEIAKDLNLPSKSVNRRI 167
                                   7**************998 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00049      0.38      22      43 ..       7      28 ..       3      37 .. 0.83
   2 ?   -2.9   0.0       7.3   5.7e+03       4      20 ..     151     167 ..     150     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                       UPF0175 22 ialAvklYeegrlSlgkAaela 43
                                  + + ++l+++gr+S+ k ae +
  gi|70607391|ref|YP_256261.1|  7 KKILIYLFRDGRISQRKIAEEV 28
                                  5689**************9955 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.3
                       UPF0175   4 ellqalklteeelerel 20 
                                   e+++ l+l+ ++++r++
  gi|70607391|ref|YP_256261.1| 151 EIAKDLNLPSKSVNRRI 167
                                   78999999999999886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.006       4.7       4      30 ..       8      37 ..       7      47 .. 0.83
   2 ?    2.4   0.0      0.22   1.7e+02       4      33 ..     136     167 ..     135     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.006
                        HTH_28  4 eiiklla.aGh.svreaArelgisrrtv.y 30
                                  +i+ +l  +G+ s+r +A+e+ +s +++ y
  gi|70607391|ref|YP_256261.1|  8 KILIYLFrDGRiSQRKIAEEVKLSATSLnY 37
                                  68888886799*************998855 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.22
                        HTH_28   4 eiikllaaG.h.svreaArelgisrrtvyrWi 33 
                                   +i+k +++  +  ++e+A+ l++ + +v r i
  gi|70607391|ref|YP_256261.1| 136 KIVKSVIKNpRiEISEIAKDLNLPSKSVNRRI 167
                                   567776755456899********999997766 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.14   1.1e+02      60      91 ..      18      49 ..       5      54 .. 0.90
   2 ?    7.0   0.1     0.011       8.2      58      91 ..     144     177 ..     135     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                                  EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSS CS
                           PCI 60 sislerlaklldlsvdevEkilvklIrdgeir 91
                                  +is  ++a+ ++ls   + +   klI+dg i+
  gi|70607391|ref|YP_256261.1| 18 RISQRKIAEEVKLSATSLNYRFNKLIEDGIIK 49
                                  89999************************997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                   ESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSS CS
                           PCI  58 yssislerlaklldlsvdevEkilvklIrdgeir 91 
                                     +i+++++ak l+l+++ v + +  l +++ ir
  gi|70607391|ref|YP_256261.1| 144 NPRIEISEIAKDLNLPSKSVNRRINVLTNKNMIR 177
                                   779***************9999887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2055.11
//
Query:       gi|70607392|ref|YP_256262.1|  [L=171]
Description: hypothetical protein Saci_1659 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.66   10.0   4.4          1    9.4   3.6    1.7  1  NPCC      Nuclear pore complex component


Domain annotation for each model (and alignments):
>> NPCC  Nuclear pore complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.6   5.8e-05         1      58      93 ..      51      86 ..       3      93 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 5.8e-05
                          NPCC 58 eslasalyaelveklirllfllniviallkLlrkqd 93
                                  + +  a  ++++ +++r+++++niv al+ ++rk+ 
  gi|70607392|ref|YP_256262.1| 51 SYVIIANIVNILLTAFRIYVIVNIVYALIYIFRKKQ 86
                                  344555678889999*****************9955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1234.84
//
Query:       gi|70607393|ref|YP_256263.1|  [L=134]
Description: hypothetical protein Saci_1660 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.1   3.6      0.021   14.8   1.2    2.0  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.2   1.2e-06     0.021      10      47 ..       7      43 ..       5      54 .. 0.85
   2 ?    0.8   0.1     0.024   4.3e+02     114     129 ..      66      81 ..      44     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                                  HHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHH CS
               ECF-ribofla_trS 10 tailaAlvvvltlfisIplpantegsinlgdavlalaa 47
                                   +++aA+++++t+f++I     ++g  ++++   +l++
  gi|70607393|ref|YP_256263.1|  7 AGLIAAVIFIITMFFQIQGS-INNGVAQIQEYRSMLSS 43
                                  79****************98.55699999988777766 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHH CS
               ECF-ribofla_trS 114 faivmvigyviaegll 129
                                   f++ m+i++v ++ + 
  gi|70607393|ref|YP_256263.1|  66 FNLTMIIQNVTGQYMK 81 
                                   6677777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1007.40
//
Query:       gi|70607394|ref|YP_256264.1|  [L=490]
Description: thermostable carboxypeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-152  508.6   0.0   2.1e-152  508.3   0.0    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
        1.1    8.7   3.3       0.91    9.0   0.4    2.3  3  4HB_MCP_1      Four helix bundle sensory module for signal tr


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.3   0.0  2.3e-156  2.1e-152       2     488 .]      10     487 ..       9     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 508.3 bits;  conditional E-value: 2.3e-156
                 Peptidase_M32   2 lkellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavveelkr 82 
                                   l + +kk+++l+ a++l+ wD et+mp++ a  r+e ++t+se+++e++  +++++++e+ e ++    ++e+ +++ l r
  gi|70607394|ref|YP_256264.1|  10 LLAEYKKLWSLQYAESLMGWDIETYMPEDDAMTRGEVISTFSEIKREIY--QKLGKIIERYEGKEGLN-DEERGILRVLGR 87 
                                   567789*****************************************97..689*******9888755.56********** PP

                 Peptidase_M32  83 eykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeyepgltveki 163
                                   +yk+++k+p e+ +++++  ++a+ +Wr+a++++d+++f+p+Le++ +l+ +iae++ +++++pY+aLld  e+g+++ + 
  gi|70607394|ref|YP_256264.1|  88 DYKYYSKIPLEIIQQIERVRSEATVVWRQAKAKSDYSMFKPYLEKIKDLQIKIAEYW-GYEDHPYNALLDLNEEGFSIRDG 167
                                   *********************************************************.*********************** PP

                 Peptidase_M32 164 dalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdfdrgrldeseHPFttsfsrkDvRitt 244
                                   d++F++l  +l +++kk++e+    k+ +++ e ++++ +++ +++e++k l +   + rld s+HPFt  +s++DvRitt
  gi|70607394|ref|YP_256264.1| 168 DRIFSRLLPELSDIMKKVSEKGYFPKS-HELEEVSYDIGRMKVVNEEVIKILEMPKGKFRLDISAHPFTVRISADDVRITT 247
                                   **********************97655.5599************************************************* PP

                 Peptidase_M32 245 ryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwevllpklkeafpeqlddv 325
                                   rye +++ s+lfsv+HE+GHa+Ye+++++el++tp+gggvs+gihE+qSr++Eniigrs+eF++ ++pklk++  ++l+++
  gi|70607394|ref|YP_256264.1| 248 RYEGKDFRSTLFSVVHECGHAIYELGIDRELEGTPIGGGVSMGIHEAQSRFWENIIGRSREFVSLIYPKLKQN-LDFLSKY 327
                                   ************************************************************************8.566888* PP

                 Peptidase_M32 326 sleefyeavnkvepsliRveADEltYslHillRyelEkeliegklsvkdlpeaWnekykeyLgidppddaeGvLQDvHWss 406
                                   +++++y+++n v+ps+iRv+ADE+tY++Hi +Rye+Ek li g+++v+++p++W e +++yLgi+p++daeG LQD+HW +
  gi|70607394|ref|YP_256264.1| 328 NEDDIYRYFNIVRPSFIRVDADEVTYNFHIAVRYEIEKRLIGGEIKVDEIPSLWSELMEKYLGITPKNDAEGALQDIHWTG 408
                                   *******************************************************************************98 PP

                 Peptidase_M32 407 gafGYFPtYalGniyaaqlfeamekdlpeleiakgefseikkWLkenihqkGslysseellkkatgeslnaeyyidyLkek 487
                                   g+ GYFP Y+lGn++++ ++++  + + +l +++g+++eik+ ++e+i+++G++ys+++ll+k+ ge+ n+e +i yL++k
  gi|70607394|ref|YP_256264.1| 409 GF-GYFPAYTLGNVVSGIVYSKTPNLY-NL-LREGKIGEIKTIMTEKIYKYGATYSPKDLLRKTFGEEYNPEGLILYLRHK 486
                                   86.*******************98877.55.6************************************************* PP

                 Peptidase_M32 488 y 488
                                   y
  gi|70607394|ref|YP_256264.1| 487 Y 487
                                   9 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.32   2.9e+03     110     124 ..       3      17 ..       2      25 .. 0.78
   2 ?    9.0   0.4    0.0001      0.91      64     171 ..      30     142 ..      26     145 .. 0.85
   3 ?   -2.3   0.0      0.31   2.8e+03      82     102 ..     440     460 ..     425     464 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.32
                     4HB_MCP_1 110 lleefkeqlnaYrev 124
                                   ++e++ke l++Y+++
  gi|70607394|ref|YP_256264.1|   3 RFENLKELLAEYKKL 17 
                                   688888888888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0001
                     4HB_MCP_1  64 dlleliltkdkaekdellkdieeleaeidk....llekye.ktilteeEkelleefkeqlnaYrevrkkvlelakegkkde 139
                                   d+++++ ++d   + e++++  e+++ei +    ++e+ye k  l++eE+ +l  + +  + Y+++  ++++ +++   + 
  gi|70607394|ref|YP_256264.1|  30 DIETYMPEDDAMTRGEVISTFSEIKREIYQklgkIIERYEgKEGLNDEERGILRVLGRDYKYYSKIPLEIIQQIERVRSEA 110
                                   5778888888888999998888888887651111567787455699999*****************************999 PP

                     4HB_MCP_1 140 AyqlyetegrparekliealeelvdlnlkvAe 171
                                        ++++++ ++ ++  le++ dl++k Ae
  gi|70607394|ref|YP_256264.1| 111 TVVWRQAKAKSDYSMFKPYLEKIKDLQIKIAE 142
                                   9999999999*******************998 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.31
                     4HB_MCP_1  82 kdieeleaeidkllekyekti 102
                                    +i e+++ + +++ ky  t+
  gi|70607394|ref|YP_256264.1| 440 GKIGEIKTIMTEKIYKYGATY 460
                                   356666666777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3232.43
//
Query:       gi|70607395|ref|YP_256265.1|  [L=1152]
Description: hypothetical protein Saci_1662 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-68  229.4  17.9    1.2e-34  119.8   6.6    2.4  2  MMPL            MMPL family
     0.0026   17.6   4.0     0.0026   17.6   4.0    3.0  2  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
  ------ inclusion threshold ------
       0.12   12.1   0.9       0.47   10.2   0.9    2.1  1  Lectin_N        Hepatic lectin, N-terminal domain
       0.56    9.5   2.0       0.74    9.1   1.0    1.6  2  EPOP            Elongin BC and Polycomb repressive complex 2-


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   3.4   8.1e-37   3.6e-33     121     312 ..     598     789 ..     573     804 .. 0.93
   2 !  119.8   6.6   2.7e-38   1.2e-34      89     305 ..     932    1143 ..     916    1151 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 8.1e-37
                          MMPL 121 eglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglels 200
                                   + l+  +tG  ++ + l+ +++    +++ v++++++++  + +rS++aa++pl   +  +l+a  l  l+  +llgl+ls
  gi|70607395|ref|YP_256265.1| 598 THLNTVLTGGEPISHQLSGIASTAYSVAIPVGIALAIILAGVYFRSVIAAFMPLTIFLSAYLVASVLlYLVAIKLLGLQLS 678
                                   4678889************************************************99999***99998899999******* PP

                          MMPL 201 tfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaia 281
                                     +++ + +l+++ GtDY +++ sRy ee+++g+d+++av++av+  g++vt+ +++v++++l   + r+p+++ +++   
  gi|70607395|ref|YP_256265.1| 679 FLTPSEVLLLALGLGTDYVVFISSRYVEERKNGRDQRDAVYDAVRWGGRAVTITAFIVILSFLFIYIYRIPFFSDTAISNM 759
                                   ********************************************************************************* PP

                          MMPL 282 lGvlvdvlivlTllPAllvllGraalakprr 312
                                   +Gv+++ l+++Tl P++l ++G + l+ pr+
  gi|70607395|ref|YP_256265.1| 760 VGVVIVWLVSITLYPSILRVAGDR-LFYPRK 789
                                   ************************.888876 PP

  == domain 2  score: 119.8 bits;  conditional E-value: 2.7e-38
                          MMPL   89 ralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSl 167 
                                     + ++ + dp+st+a + v+++ ++v +         +v+G ++    +   ++ + +li+v + v  +viL i++rSl
  gi|70607395|ref|YP_256265.1|  932 LFEINQKYDPFSTQAFNVVKQVDKIVGNSG-------YVGGGPVDDYNIYSFVEGNFGLIVVEISVTMFVILWIITRSL 1003
                                    577888888888999888888888888888.......*******9999******************************* PP

                          MMPL  168 vaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeavirava 245 
                                       + ++ +++  ++++l++  li++ +lg+ +  +v+ +lv+++i++G DY+++Lv+R++eel++g d  +av  av+
  gi|70607395|ref|YP_256265.1| 1004 SVSATIIFVILSAVAITLAIqRLIFSSILGFSIFAVVPLFLVAIIIGIGMDYNIFLVARIHEELEKGNDMGSAVEVAVR 1082
                                    ******************************************************************************* PP

                          MMPL  246 stgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGra 305 
                                    + + ++++ Gl++a+++ +L++++ p+l+++G+a a++ ++ + +  +ll P+ll ll r+
  gi|70607395|ref|YP_256265.1| 1083 RLWLTIAFLGLIFAGTLGSLMLVNAPILQELGFAFAIAAILETTLLWSLLaPSLLLLLYRK 1143
                                    ********************************************************99777 PP

>> Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   4.0   5.8e-07    0.0026       8     139 ..     651     783 ..     642     790 .. 0.86
   2 ?   -0.8   9.9      0.27   1.2e+03       7     110 ..    1004    1113 ..     986    1144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-07
                                   HHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCHHCCHHCHHHHHHHHTTTCH.HHHHHHHHHHHCCCCHH CS
                Sterol-sensing   8 LglagviivllsvasslgllaylgltltliilevlPflvlavgvdnifvlvkavqrtsrslde.seriaealgevgpsill 87 
                                   L+++  + +++sv+  l  + +lgl+l+ ++   +  l+l  g+d +  +   +++  ++ ++  + +  a++  g ++++
  gi|70607395|ref|YP_256265.1| 651 LTIFLSAYLVASVLLYLVAIKLLGLQLSFLTPSEVLLLALGLGTDYVVFISSRYVEERKNGRDqRDAVYDAVRWGGRAVTI 731
                                   5666667777888888888899999999888777789********998888877777666555599*************** PP

                                   CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH CS
                Sterol-sensing  88 tsltellalllgaltdvpavqeFclfaavavlvdFllqitfFvavLsldirr 139
                                   t++  +l++l+ ++ ++p  +  ++  +v+v++ +l+ it++ ++L +   r
  gi|70607395|ref|YP_256265.1| 732 TAFIVILSFLFIYIYRIPFFSDTAISNMVGVVIVWLVSITLYPSILRVAGDR 783
                                   **********************************************887655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHCCHHHHCCHHHH.HHHHHHHHHHHHHH.H...HHHHHCHH.CCHHCHHHHHHHHTTTCHHHHHHHHHH CS
                Sterol-sensing    7 gLglagviivllsvasslgllay.lgltltliilevlP.f...lvlavgvd.nifvlvkavqrtsrsldeseriaealg 79  
                                     +++++++++l++va +l +  + +   l   i+ v+P f   +++ +g+d nif++ + ++++++ +d  + +  a++
  gi|70607395|ref|YP_256265.1| 1004 SVSATIIFVILSAVAITLAIQRLiFSSILGFSIFAVVPlFlvaIIIGIGMDyNIFLVARIHEELEKGNDMGSAVEVAVR 1082
                                    5778999999999999999976514555566677788844333467899999999999988888888887777666666 PP

                                    HHCCCCHHCCCHHHHHHHHHHHCCHHHHHHH CS
                Sterol-sensing   80 evgpsilltsltellalllgaltdvpavqeF 110 
                                    +    i    l  + +l   +l++ p +qe 
  gi|70607395|ref|YP_256265.1| 1083 RLWLTIAFLGLIFAGTLGSLMLVNAPILQEL 1113
                                    6555544444433333332234555666664 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00011      0.47      58     112 ..     102     157 ..      98     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                      Lectin_N  58 etLketfsnfssstla.eiqalssqggslsekvtsleaklekkqqdlkadhselll 112
                                    t+++++ n++ s l+  + +l+   +++s   tsle+kl+ ++q+++ d  +l+l
  gi|70607395|ref|YP_256265.1| 102 YTIEKDLLNTTFSQLSpRVDNLTKILQNISSSETSLESKLQTQRQNITGDINKLML 157
                                   678888888886655438999*****************************999876 PP

>> EPOP  Elongin BC and Polycomb repressive complex 2-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.0   0.00017      0.74     132     249 ..      92     208 ..      87     215 .. 0.76
   2 ?   -2.3   0.0      0.49   2.2e+03     161     196 ..     271     306 ..     239     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00017
                          EPOP 132 hkaeneviaapklkdaalnskkeskiskqsklatplkkikseseetsvtakskaentktaktlpfelhnvKikvedssdee 212
                                   + ++ +vi    +++  ln++    +++  +l++ l++i s       + + + +n +++ +  + l n  ik+e+s+ + 
  gi|70607395|ref|YP_256265.1|  92 SYKNISVISFYTIEKDLLNTTFSQLSPRVDNLTKILQNISSSETSLESKLQTQRQNITGDINKLMLLRNATIKIENSFINI 172
                                   556677777778888899999999999999*********8766655555555555556655555558************** PP

                          EPOP 213 eYeselikeklkvkckvdeeelankteakeeesdaik 249
                                    Y  +  kekl   ++   e+ ++  e+ ++e+ +  
  gi|70607395|ref|YP_256265.1| 173 SYTLNSTKEKLALLHRSMVENYTTF-ENLRKEELNVN 208
                                   ******99**999999888877555.77777666654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.49
                          EPOP 161 sklatplkkikseseetsvtakskaentktaktlpf 196
                                   s++++pl++++ +++    +a++k+ n+++++ + f
  gi|70607395|ref|YP_256265.1| 271 SSIPNPLPNLQYNAQKSIENASAKIFNSTEYQFISF 306
                                   6789999******99999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1422  (0.0793128); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.90u 0.32s 00:00:01.22 Elapsed: 00:00:00.51
# Mc/sec: 6736.62
//
Query:       gi|70607396|ref|YP_256266.1|  [L=201]
Description: hypothetical protein Saci_1663 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   45.3   0.0    1.8e-11   44.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      8e-06   26.5   0.0    1.4e-05   25.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    0.00015   21.7   0.0    0.00017   21.5   0.0    1.1  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.02   14.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.025   13.9   0.0      0.044   13.1   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   4.9e-15   1.8e-11       2      90 ..      40     118 ..      39     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 4.9e-15
                                   EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHH CS
               Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalk 82 
                                   d+G+G G + e +    +r + +D+s  ml+ +    + e+ +   + ad++++p++dn  D+v++s ++++v+d++k+++
  gi|70607396|ref|YP_256266.1|  40 DLGSGPGTFHEVIN---GRKISIDISLLMLNEV---DKSED-R---ILADVSDIPLRDNATDCVFISLTICFVDDVRKFID 110
                                   9*************...899**********444...33332.2...9********************************** PP

                                   HHHHHEEE CS
               Methyltransf_11  83 eiaRvLkp 90 
                                   e++Rv k 
  gi|70607396|ref|YP_256266.1| 111 EAMRVTKE 118
                                   *****995 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   3.9e-09   1.4e-05       2      95 ..      39     118 ..      38     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.9e-09
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedl 82 
                                   +dlG G+G++ + +      ++ + +Dis  ml+++ +         + + +d++d+p+ d+  D+v++s ++++++  d+
  gi|70607396|ref|YP_256266.1|  39 IDLGSGPGTFHEVIN-----GRKISIDISLLMLNEVDKSE-------DRILADVSDIPLRDNATDCVFISLTICFVD--DV 105
                                   599*****9988886.....4669************9998.......5699******************97788776..99 PP

                                   HHHHHHHHHHEEE CS
               Methyltransf_25  83 ekalkeiarvLkp 95 
                                   +k+++e+ rv+k+
  gi|70607396|ref|YP_256266.1| 106 RKFIDEAMRVTKE 118
                                   **********996 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.7e-08   0.00017      74     150 ..      36     118 ..      11     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.7e-08
                                   S-EEEES-TT-HHHHH--S...-..EEEEESS-SS..TTEEES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHE CS
                Methyltransf_8  74 lvvadlGcGeakiaeavre...kekvrsfdlvavn..ervvacdlakvPledesvdvavfclsl.mgtnladflkeanrvl 148
                                   +  +dlG G     e ++    + ++  + l  v+  e+ +  d++ +Pl d++ d + + l++  ++++++f+ ea rv 
  gi|70607396|ref|YP_256266.1|  36 KNCIDLGSGPGTFHEVINGrkiSIDISLLMLNEVDksEDRILADVSDIPLRDNATDCVFISLTIcFVDDVRKFIDEAMRVT 116
                                   5567888887776644432001334445555555522567899*******************984689************9 PP

                                   EE CS
                Methyltransf_8 149 kv 150
                                   k 
  gi|70607396|ref|YP_256266.1| 117 KE 118
                                   96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   5.6e-06      0.02      20     111 ..      32     118 ..      18     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-06
               Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppe 100
                                    ++ ++++d+G G G++ ev+  +      +D+s  + +++  +k      +d ++++  ++ +d++  + +++ v+d+ +
  gi|70607396|ref|YP_256266.1|  32 SFKLKNCIDLGSGPGTFHEVINGRKI---SIDISLLMLNEV--DKSEDRILADVSDIPLRDNATDCVFISLTICFVDDVRK 107
                                   7899*****************66543...456666555554..3333334444445666889******************9 PP

               Methyltransf_23 101 llrqiatllkp 111
                                    ++ + + +k+
  gi|70607396|ref|YP_256266.1| 108 FIDEAMRVTKE 118
                                   99999887775 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.044     103     144 ..      76     117 ..      23     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                   EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEE CS
               Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlk 144
                                   + a+  ++p  d++ D+v +s  +  v D  k + ea+rv k
  gi|70607396|ref|YP_256266.1|  76 ILADVSDIPLRDNATDCVFISLTICFVDDVRKFIDEAMRVTK 117
                                   56788899********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1324.93
//
Query:       gi|70607397|ref|YP_256267.1|  [L=492]
Description: hypothetical protein Saci_1664 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-24   86.2   0.0    3.7e-24   85.2   0.0    1.6  1  ABC1      ABC1 family
    2.7e-06   27.1   0.2    1.1e-05   25.1   0.0    2.0  2  RIO1      RIO1 family
    2.5e-05   23.8   0.4    0.00035   20.0   0.4    2.3  1  Pkinase   Protein kinase domain
  ------ inclusion threshold ------
        0.2   11.6   0.1        0.7    9.8   0.1    1.8  2  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   8.2e-28   3.7e-24      12     119 .]     106     215 ..      97     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 8.2e-28
                          ABC1  12 aefdeePiAaASiaqVhrAklk.sgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldleelvdefskslleE 90 
                                    e+d++Pi +ASi+ V+ Ak k +g+ V++Kv rp++k+  ++D+++lk la l+k ++ e + ++++ lvd+f k+++eE
  gi|70607397|ref|YP_256267.1| 106 YEIDPTPISSASIGVVYIAKRKkDGKLVVIKVNRPNIKEMADQDISVLKSLAPLTKYVFDESFyESFKVLVDNFGKKIYEE 186
                                   489******************989***********************************9999899*************** PP

                          ABC1  91 ldferEAknaekfrenfaklkevkvPkvy 119
                                   ++f+ E  +++k+re++++++++++P+ y
  gi|70607397|ref|YP_256267.1| 187 MEFTIEEFHMKKIREEMSDYPWIRIPEPY 215
                                   **************************976 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.29   1.3e+03       2      27 ..     121     147 ..     120     155 .. 0.78
   2 !   25.1   0.0   2.6e-09   1.1e-05      70     152 ..     209     289 ..     178     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                                   EEEEEE.TTTEEEEEEEE-S---SS-H CS
                          RIO1   2 Vyhavs.edgkevaiKiyktstteFkk 27 
                                   Vy a   +dgk v+iK+ + +++e  +
  gi|70607397|ref|YP_256267.1| 121 VYIAKRkKDGKLVVIKVNRPNIKEMAD 147
                                   888877578889999999998887765 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.6e-09
                                   --S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                          RIO1  70 vpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                   +++P+p+   + vl+me+++  +v   + k +     a +l ++v ++  +++ + ++ HaD    N+ +de+ ++++ D+
  gi|70607397|ref|YP_256267.1| 209 IRIPEPYLATKRVLIMEYVKGYKVTSEEAKRIM---RAPDLSYMVFRTFMVMLLTKEYFHADPHPGNIALDEKgNLILYDF 286
                                   89******************7777777777777...899999**************************9999989999999 PP

                                   TTE CS
                          RIO1 150 sQa 152
                                   +  
  gi|70607397|ref|YP_256267.1| 287 GIV 289
                                   755 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   7.9e-08   0.00035      11     152 ..     117     296 ..     111     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.9e-08
                                   SSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS..CTTB-..-EEEEEEE.................. CS
                       Pkinase  11 sfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk..hpniv..rlyevfee.................. 69 
                                   s G+Vy a++k++gk v++K+ + + +k++ +    + i++lk+l    +++    +ye+f+                   
  gi|70607397|ref|YP_256267.1| 117 SIGVVYIAKRKKDGKLVVIKVNRPN-IKEMAD----QDISVLKSLAplTKYVFdeSFYESFKVlvdnfgkkiyeemeftie 192
                                   5788999999999999999865444.444443....577888887774455442224444444788888888888888888 PP

                                   ........................SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-S CS
                       Pkinase  70 ........................kdelylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlK 125
                                                            ++++l++eyv+g ++++           +a ++ + +++ +  +   k+ +H D  
  gi|70607397|ref|YP_256267.1| 193 efhmkkireemsdypwiripepylATKRVLIMEYVKGYKVTSEEA----KRIMRAPDLSYMVFRTFMVMLlTKEYFHADPH 269
                                   99999999999999999999999999999*******885544443....3444556666777777655443999******* PP

                                   GGGEEEETTTEEEE-SGTTSEESSSSC CS
                       Pkinase 126 peNiLidekgelKitDFGlakelesss 152
                                   p Ni +dekg+l + DFG++ ++++++
  gi|70607397|ref|YP_256267.1| 270 PGNIALDEKGNLILYDFGIVGRMDRDT 296
                                   ********************9999876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00016       0.7     168     200 ..     263     293 ..     224     296 .. 0.86
   2 ?   -1.8   0.0      0.55   2.5e+03      71     124 ..     316     364 ..     298     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                   EE-SS-SGGGEEEC..TTEEEEE---TT-EEEE CS
                           APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglgp 200
                                     H D+hpgN+ +d+ ++ +  + Df+ +g ++
  gi|70607397|ref|YP_256267.1| 263 YFHADPHPGNIALDEKGNLI--LYDFGIVGRMD 293
                                   57************888888..99999988776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.55
                                   EEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHCHTCC CS
                           APH  71 falieyvpgrsllrklsaaqlpellealgeflaalhqvdpaalpladflaqdle 124
                                   + ++e +++ +++      +++ l+  +g fl +++ + p++l ++ fl+ + e
  gi|70607397|ref|YP_256267.1| 316 VKVLEELGAIQPEA-----DREILAKGIGLFLEQFQGITPETLEVEQFLEATNE 364
                                   55666666666666.....88888999999999999999988888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3417.22
//
Query:       gi|70607398|ref|YP_256268.1|  [L=126]
Description: Hsp20/alpha crystallin family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.7e-09   36.0   0.0    6.9e-09   35.8   0.0    1.1  1  HSP20       Hsp20/alpha crystallin family
    5.3e-08   32.3   0.0    7.9e-08   31.8   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   7.7e-13   6.9e-09       9      87 ..      39     117 ..      31     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.7e-13
                                   EEEEEE-TT--CCCEEEEEETTE.EEEEEE--..---TT----SS---EEEEEE--STTB-TT.T-EEEEETTEEEEEEEB CS
                         HSP20   9 fevkldvpglkkeelkvkvednr.vlvkgeheeeeedekglikerssrkFsrkftLPenvdad.kvkaslkdGvLtvtvpk 87 
                                     v +d++g++k+ +k  + +++ +++++e+e  e + k+l +  + +  +r+++LP nv +d +v++++++GvLt+ +p 
  gi|70607398|ref|YP_256268.1|  39 LIVVADLAGFNKDKIKARISGQNeLIIEAEREISEPGIKYLTQ--RPKYIRRTIKLPINVAKDaEVAGKYENGVLTIRIPI 117
                                   46889**************97655********88888888888..555567899****9866538*************995 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   8.8e-12   7.9e-08       4      62 ..      39     114 ..      36     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 8.8e-12
                    ArsA_HSP20   4 yvlkldLPfvdkeeidlsrs.gdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                    ++++dL +++k++i+ ++s  +eL+I+++                  rR+i LP  +a++  +  k+e+gvL+Ir
  gi|70607398|ref|YP_256268.1|  39 LIVVADLAGFNKDKIKARISgQNELIIEAEreisepgikyltqrpkYIRRTIKLPINVAKDAEVAGKYENGVLTIR 114
                                   6899****************5579*********************999***********9988899*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 843.70
//
Query:       gi|70607399|ref|YP_256269.1|  [L=286]
Description: hypothetical protein Saci_1666 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-10   41.3   0.0    4.6e-08   33.2   0.1    2.6  3  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.88   1.6e+04      28      43 ..      11      27 ..       7      29 .. 0.73
   2 !    5.4   0.0    0.0012        21      17      84 ..      87     155 ..      74     156 .. 0.82
   3 !   33.2   0.1   2.6e-12   4.6e-08       2      84 ..     187     271 ..     186     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.88
                           CCG 28 lgveleel.ekesCCGa 43
                                  +  +++++ +k+ C G+
  gi|70607399|ref|YP_256269.1| 11 EKYDFPYNiDKKICSGW 27
                                  55677888888999886 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0012
                           CCG  17 vrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgCllql 84 
                                   v +++  ll+++gv++ +l e+e   Ga     g+ +++   a+r  + ++e+g++ i+t +p+ ++ l
  gi|70607399|ref|YP_256269.1|  87 VLRNIVSLLKKNGVNFGYLyEEEPYSGAILLELGYLNEFGIHAERVTKFLKEKGVKRIITVDPHTHNAL 155
                                   55667788899999999999999999999999999888888888888888999*********9977665 PP

  == domain 3  score: 33.2 bits;  conditional E-value: 2.6e-12
                           CCG   2 ayfdgChllraa......ypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivta 76 
                                   +++d+C + r        ++ +++a  k++e l v+ +e   ++CCG+++   ++e l e++ak +ve+++++  d i++ 
  gi|70607399|ref|YP_256269.1| 187 VIHDSCLYSRFLglrdvyRQILTNAGGKIVEDLMVTSKEV--SYCCGSPIKPVNHE-LGEKVAKSRVEQLKKL-SDNILVV 263
                                   5799995555559988866667778888989888888877..*******9966666.9**************9.777**** PP

                           CCG  77 cpgCllql 84 
                                   cp C+++l
  gi|70607399|ref|YP_256269.1| 264 CPMCYANL 271
                                   *****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2025.81
//
Query:       gi|70607400|ref|YP_256270.1|  [L=388]
Description: 4Fe-4S binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-53  181.3   0.8    2.9e-53  180.4   0.8    1.4  1  LUD_dom   LUD domain
    6.5e-11   42.5   3.0    1.1e-10   41.8   3.0    1.4  1  Fer4_8    4Fe-4S dicluster domain
    3.8e-08   33.3   2.0      0.005   16.9   0.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
    1.2e-06   29.0   5.4    2.1e-06   28.2   5.4    1.4  1  Fer4_7    4Fe-4S dicluster domain
    7.1e-06   26.5   5.7    2.3e-05   24.8   5.9    1.8  2  Fer4_17   4Fe-4S dicluster domain
    0.00042   20.0   8.6     0.0019   18.0   1.8    2.3  2  Fer4      4Fe-4S binding domain
    0.00067   19.4   1.9       0.11   12.2   0.1    2.5  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
     0.0012   19.0   5.8      0.066   13.4   7.9    2.2  3  Fer4_9    4Fe-4S dicluster domain
     0.0019   18.3   4.0     0.0073   16.4   4.0    1.9  1  Fer4_21   4Fe-4S dicluster domain
     0.0089   16.1  10.1      0.021   14.9   2.6    2.3  2  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   15.7   6.1      0.062   13.4   1.1    2.4  2  Fer4_2    4Fe-4S binding domain
      0.016   16.0   4.1       0.36   11.7   0.7    2.4  2  Fer4_22   4Fe-4S dicluster domain
      0.017   16.0   8.0       0.11   13.5   8.0    2.2  1  Fer4_16   4Fe-4S double cluster binding domain
       0.03   14.5   1.6          1    9.6   0.0    2.3  2  Fer4_18   4Fe-4S dicluster domain
      0.034   14.7   1.4      0.034   14.7   1.4    2.2  2  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   0.8   2.4e-56   2.9e-53       1     189 []      51     282 ..      51     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 2.4e-56
                       LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl......... 51 
                                   +ee+i+++++ g+++y++++a+ea+e i +++ +++                      + e+++tdlge+ +         
  gi|70607400|ref|YP_256270.1|  51 IEETINSVKRIGGNAYFVRDANEAREVISKIVGSGKKvvmgksmvayeiglrkhlqsiGNEVWETDLGEFLIqladeppsh 131
                                   799********************************8889****************************************** PP

                       LUD_dom  52 ..apalhsgreevldlfeekl.............treareelrekfltadvgitganfaiAetGtlvlvdnegnrraltfl 117
                                     apa+h+++e +++l +ekl             +++ re lrekf +advgitgan++ A+tG+++lv+negn r+ ++l
  gi|70607400|ref|YP_256270.1| 132 ilAPAVHMTKERIAKLIREKLhvdvdvnssheelVAKVREFLREKFVKADVGITGANAVAADTGSVILVENEGNIRMSSVL 212
                                   ********************************************************************************* PP

                       LUD_dom 118 pkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                   p vhi+v+g++kivp+++da++ ++   + a    + ++y+++ sgps+t+die++ v+ +hgpk++h+++v
  gi|70607400|ref|YP_256270.1| 213 PTVHIAVAGVEKIVPTFYDALTEATV--QAAFAGLYPPTYINVSSGPSSTGDIEMKRVSPAHGPKEFHLVIV 282
                                   **************************..66777789**********************************98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   3.0   9.1e-14   1.1e-10       5      65 .]     301     362 ..     297     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 9.1e-14
                        Fer4_8   5 CieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                   Ci+Cg+C  +Cpv+r ++ ++   ++ + ++ +++  v+ + + + +C++ g+C+evCp++i
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCPVYRVEGvDWGDPPYTGPMGAMWSYAVYRDTKPAMYCMHSGNCKEVCPMKI 362
                                   ******************9************888888888899****************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   4.2e-06     0.005       5      27 ..     297     315 ..     293     334 .. 0.78
   2 !   15.7   0.1     1e-05     0.012       6      24 ..     345     369 ..     340     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                       Fer4_10   5 dddtCirCgkCvkaCPadltsvg 27 
                                   ++  CirCg+C   CP++    +
  gi|70607400|ref|YP_256270.1| 297 ETLLCIRCGRCHMHCPVY----R 315
                                   5567************93....3 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                       Fer4_10   6 ddtCirCgkCvkaCPadl......t 24 
                                   +  C++ g+C+++CP+++      +
  gi|70607400|ref|YP_256270.1| 345 AMYCMHSGNCKEVCPMKIniprvlE 369
                                   567*************775443331 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   5.4   1.8e-09   2.1e-06       2      51 ..     301     361 ..     300     362 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekv...........eidpekClgCgaCvavCPtg 51 
                                   Ci Cg+C   Cpv+ +e  +  +++ t  +           +  +++C++ g+C +vCP +
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCPVYRVEGVDWGDPPYTGPMgamwsyavyrdTKPAMYCMHSGNCKEVCPMK 361
                                   ************99999998777774422222344455554455789************76 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   2.0   0.00014      0.17      41      57 ..     296     312 ..     284     316 .. 0.78
   2 !   24.8   5.9     2e-08   2.3e-05       2      61 .]     301     363 ..     300     363 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                       Fer4_17  41 ekaslCieCgeCerkCP 57 
                                   ++  lCi Cg+C + CP
  gi|70607400|ref|YP_256270.1| 296 KETLLCIRCGRCHMHCP 312
                                   56779999999999999 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2e-08
                       Fer4_17   2 CiqCgyClpeCpsyea....ydnepkk.llraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                   Ci+Cg C  +Cp y+      ++ p + ++ a ++ +     + + a  C++ g+C+++CP++++
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCPVYRVegvdWGDPPYTgPMGA-MW-SYAVYRDTKPAMYCMHSGNCKEVCPMKIN 363
                                   ***************95533333455436666.33.233334558999**************985 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.8   1.6e-06    0.0019       7      20 ..     300     313 ..     296     314 .. 0.92
   2 ?    5.8   0.7      0.01        13      12      20 ..     352     360 ..     346     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                   TSSS-THHHHHSTT CS
                          Fer4   7 kCigCGaCvevCPv 20 
                                   +Ci+CG+C + CPv
  gi|70607400|ref|YP_256270.1| 300 LCIRCGRCHMHCPV 313
                                   7************8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.01
                                   THHHHHSTT CS
                          Fer4  12 GaCvevCPv 20 
                                   G+C evCP 
  gi|70607400|ref|YP_256270.1| 352 GNCKEVCPM 360
                                   99******6 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.3    0.0086        10      11      38 ..     288     313 ..     282     317 .. 0.86
   2 !   12.2   0.1   9.6e-05      0.11      25      50 ..     346     372 ..     334     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0086
                                   ---HHHHHHHHTT----TT-HHHHCSTT CS
                       Fer4_20  11 glteeealeeAsRClqCkkapcvkgCPv 38 
                                   +++++e+l+e   C++C    c+ +CPv
  gi|70607400|ref|YP_256270.1| 288 QISKDEILKETLLCIRC--GRCHMHCPV 313
                                   56788999*********..78******9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.6e-05
                                   ---T.T-HHHHCSTT---HHHHHHHHH CS
                       Fer4_20  25 lqCk.kapcvkgCPveidipefikkia 50 
                                   ++C  + +c++ CP++i+ip+ +++i+
  gi|70607400|ref|YP_256270.1| 346 MYCMhSGNCKEVCPMKINIPRVLERIK 372
                                   56762468*************999987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.8   0.00015      0.17      34      48 ..     299     313 ..     274     317 .. 0.71
   2 !   13.4   7.9   5.5e-05     0.066       2      49 ..     301     361 ..     300     364 .. 0.74
   3 !    7.2   0.7    0.0048       5.7       2      24 ..     348     370 ..     347     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                        Fer4_9  34 eaCigCgaCveaCpk 48 
                                     Ci Cg+C  +Cp 
  gi|70607400|ref|YP_256270.1| 299 LLCIRCGRCHMHCPV 313
                                   579999999999985 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.5e-05
                        Fer4_9   2 CtgCgaCveaC.................pagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C++Cg+C+  C                 p+g++   a+ r  +  +     C++ g C e+Cp +
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCpvyrvegvdwgdppytgPMGAMWSYAVYRDTKPAM----YCMHSGNCKEVCPMK 361
                                   ***********66666666666666666666665555555555555....5************97 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0048
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaer 24 
                                   C+  g+C e+Cp+++++++  er
  gi|70607400|ref|YP_256270.1| 348 CMHSGNCKEVCPMKINIPRVLER 370
                                   77778999999999988877666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   4.0   6.1e-06    0.0073       7      54 ..     300     361 ..     294     365 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.1e-06
                       Fer4_21   7 kCigCgkCliaCedtshqai..........eidaktvl..........kvvedeCvGCnlCssvCPve 54 
                                    Ci Cg+C++ C+   ++ +                            +  +  C+    C +vCP++
  gi|70607400|ref|YP_256270.1| 300 LCIRCGRCHMHCPVYRVEGVdwgdppytgpM------GamwsyavyrdTKPAMYCMHSGNCKEVCPMK 361
                                   5*******************55555544331......03334433332333678************84 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.6   1.8e-05     0.021       8      22 ..     300     314 ..     299     318 .. 0.90
   2 ?    5.3   0.9     0.018        22       9      22 ..     348     361 ..     347     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                        Fer4_6   8 kCigCgdCvrvCPeg 22 
                                   +Ci Cg+C ++CP +
  gi|70607400|ref|YP_256270.1| 300 LCIRCGRCHMHCPVY 314
                                   7************75 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                        Fer4_6   9 CigCgdCvrvCPeg 22 
                                   C + g+C  vCP++
  gi|70607400|ref|YP_256270.1| 348 CMHSGNCKEVCPMK 361
                                   777799******86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   5.2e-05     0.062       6      21 ..     297     312 ..     292     313 .. 0.86
   2 ?    4.5   0.3     0.035        42      10      21 ..     348     359 ..     339     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                        Fer4_2   6 dtdrCigCgaCvsaCP 21 
                                   +t  Ci+Cg C   CP
  gi|70607400|ref|YP_256270.1| 297 ETLLCIRCGRCHMHCP 312
                                   6779*******999** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.035
                        Fer4_2  10 CigCgaCvsaCP 21 
                                   C++ g C  +CP
  gi|70607400|ref|YP_256270.1| 348 CMHSGNCKEVCP 359
                                   9999******** PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7    0.0003      0.36      78      94 ..     297     313 ..     284     315 .. 0.80
   2 ?    5.0   0.1     0.037        45      78      95 ..     344     361 ..     332     362 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   ++  C+ CgRC+++cpv
  gi|70607400|ref|YP_256270.1| 297 ETLLCIRCGRCHMHCPV 313
                                   67789999999999997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.037
                       Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                    ++ C+  g C+e+cp+k
  gi|70607400|ref|YP_256270.1| 344 PAMYCMHSGNCKEVCPMK 361
                                   556677777777777766 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   8.0   8.9e-05      0.11       2      66 ..     301     360 ..     300     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekck.kqeaitgCdiCqdvCPa 66 
                                   C++Cg+C + CP+  +++     +  +    y+ ++   ++    +++  ++ ++  ++C++vCP+
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCPVYRVEGV---DWGDP---PYTGPMGAMWSYAVYRDTkPAMYCMHSGNCKEVCPM 360
                                   *****************99...44422...345667777776666655356779999********8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3      0.06        71      57      73 ..     297     313 ..     282     320 .. 0.77
   2 ?    9.6   0.0   0.00085         1      54      79 ..     341     366 ..     332     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.06
                       Fer4_18  57 gagdcidcescvkvcPt 73 
                                   ++  ci c+ c   cP+
  gi|70607400|ref|YP_256270.1| 297 ETLLCIRCGRCHMHCPV 313
                                   55569999999999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00085
                       Fer4_18  54 kekgagdcidcescvkvcPtgidirk 79 
                                    +k+a  c++ + c +vcP++i+i  
  gi|70607400|ref|YP_256270.1| 341 DTKPAMYCMHSGNCKEVCPMKINIPR 366
                                   5677888****************965 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.4   2.8e-05     0.034       4      16 ..     301     313 ..     296     320 .. 0.91
   2 ?    2.2   0.7      0.27   3.2e+02       4      16 ..     348     360 ..     345     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-05
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   Ci+Cg+C+  CP+
  gi|70607400|ref|YP_256270.1| 301 CIRCGRCHMHCPV 313
                                   ************5 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.27
                        Fer4_4   4 CigCgsCvaaCPq 16 
                                   C + g C  +CP+
  gi|70607400|ref|YP_256270.1| 348 CMHSGNCKEVCPM 360
                                   666678******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3111.10
//
Query:       gi|70607401|ref|YP_256271.1|  [L=584]
Description: hypothetical protein Saci_1668 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.6   0.8     0.0044   16.8   0.6    2.2  1  DUF4448         Protein of unknown function (DUF4448)
  ------ inclusion threshold ------
      0.011   15.6   3.4      0.011   15.6   3.4    2.5  2  TMEM154         TMEM154 protein family
      0.014   15.8   4.4       0.03   14.7   4.4    1.5  1  DUF1180         Protein of unknown function (DUF1180)
      0.036   13.5   3.4      0.076   12.4   3.4    1.5  1  Plasmodium_Vir  Plasmodium vivax Vir protein
       0.27   11.5   5.4       0.35   11.2   0.1    3.1  2  DUF4064         Protein of unknown function (DUF4064)
       0.85    9.3   4.8        2.3    7.9   4.8    1.7  1  DUF3149         Protein of unknown function (DUF3149)


Domain annotation for each model (and alignments):
>> DUF4448  Protein of unknown function (DUF4448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   1.5e-06    0.0044     123     180 ..     504     581 ..     409     584 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                       DUF4448 123 d......eveikkGpkVsltkkedlk..........................kledkeseegkkaekyalaialPvvvvvl 171
                                   +      +            ++ ++                           + +++++++++++++++ +i+l v+v+++
  gi|70607401|ref|YP_256271.1| 504 TgtttqsN------------TQTSSSstsqtnssssstqstpsgtgvplnsgSSSTTPPQSSSQSSNNTFYIVLAVIVIII 572
                                   23222221............1111112222223333344555555555555544567899999999*************** PP

                       DUF4448 172 vlgligfvl 180
                                   v+g+++++l
  gi|70607401|ref|YP_256271.1| 573 VIGVVALLL 581
                                   ****99886 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.1     0.068     2e+02       7      71 ..      63     128 ..      55     131 .. 0.81
   2 ?   15.6   3.4   3.7e-06     0.011       5      80 ..     499     580 ..     487     584 .] 0.61

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.068
                       TMEM154   7 sgdtaletatleeesadatsaasteseslkqeeakeslssaelsnesd.qlelvlmiiiPlvllil 71 
                                   ++++al ++tl++++  at ++  e++ l +  +  ++ s+++s ++  ++el++   iP  + ++
  gi|70607401|ref|YP_256271.1|  63 IATSALYNTTLSNQTNGATRITYNETSYLLEFSDTYKTYSGNISITAKpDMELIINSQIPYLIRVI 128
                                   7899******************99888888777888888899887654378888888888777665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.7e-06
                       TMEM154   5 eksgdtaletatleeesadatsaasteseslk......qeeakeslssaelsnesdqlelvlmiiiPlvllillllvviil 79 
                                   +++++t + t+  +++s+ +ts +++ s+s +      +   +   ss+   + s+q ++   +i+ +v++i++++ v+ l
  gi|70607401|ref|YP_256271.1| 499 PQQTSTGTTTQSNTQTSSSSTSQTNSSSSSTQstpsgtGVPLNSGSSSTTPPQSSSQSSNNTFYIVLAVIVIIIVIGVVAL 579
                                   566777777777777777777777776666666667632223333344444444555566667777777777776666555 PP

                       TMEM154  80 i 80 
                                    
  gi|70607401|ref|YP_256271.1| 580 L 580
                                   4 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   4.4     1e-05      0.03      40     120 ..     498     582 ..     488     584 .] 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                       DUF1180  40 ppgataaespgkataieaksaqaaeggngsspragsaad....aggslavvpelssntdkpmtlqrallvlvvvsaavivy 116
                                   +p++t++++  ++++  ++s++++ +++ ss+++++++     ++gs +  p  ss+++  +t+  +l v+v++  + +v 
  gi|70607401|ref|YP_256271.1| 498 QPQQTSTGTTTQSNTQTSSSSTSQTNSSSSSTQSTPSGTgvplNSGSSSTTPPQSSSQSSNNTFYIVLAVIVIIIVIGVVA 578
                                   588999998888888777777787777777777777766778888888888878888888899888888888887777777 PP

                       DUF1180 117 lvvR 120
                                   l++R
  gi|70607401|ref|YP_256271.1| 579 LLLR 582
                                   7777 PP

>> Plasmodium_Vir  Plasmodium vivax Vir protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.4   2.5e-05     0.076     232     323 ..     499     580 ..     488     584 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                Plasmodium_Vir 232 kekaeqgksekslgseslssekpearkgveeqlvhaltsassgtgndaspesiansssslesvseelssnfirniimaaai 312
                                   +++++ g++++s+++ s+ss+ +         + + ++s++s+++++++p + ++ss++   +s+++s+n++     + +i
  gi|70607401|ref|YP_256271.1| 499 PQQTSTGTTTQSNTQTSSSSTSQ---------TNSSSSSTQSTPSGTGVPLNSGSSSTTPPQSSSQSSNNTFYIVLAVIVI 570
                                   45555555666666555555444.........446889999*******************************999955555 PP

                Plasmodium_Vir 313 lgtgiflfsyl 323
                                   ++ +i +++ l
  gi|70607401|ref|YP_256271.1| 571 II-VIGVVALL 580
                                   55.55444444 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.4      0.22   6.7e+02      15      60 ..       8      57 ..       4     107 .. 0.70
   2 ?   11.2   0.1   0.00012      0.35      42      81 ..     524     581 ..     494     584 .] 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                       DUF4064 15 lgillglllllflfllssgefsqeltee....qalsgedasavleflstl 60
                                  l +l++ l++++++ + ++++s++ t +       s + ++++ + l++ 
  gi|70607401|ref|YP_256271.1|  8 LTLLFFSLAGIIALSVDATPSSNNTTLNimyqRYGSIYINTNYTGLLTNA 57
                                  56777777777777777777777776665555444444444444444333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                       DUF4064  42 e..................qalsgedasavleflstllivlgvialiaivlgivgall 81 
                                   +                  ++ s++ +++++ + ++++++ + + +i+iv+g+v++ll
  gi|70607401|ref|YP_256271.1| 524 SsssstqstpsgtgvplnsGSSSTTPPQSSSQSSNNTFYIVLAVIVIIIVIGVVALLL 581
                                   144556666778888888777777778888888999999999999999999*999987 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.8   0.00076       2.3       7      28 ..     560     581 ..     559     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00076
                       DUF3149   7 sdvGLlSliVIvftigmgaffi 28 
                                   + +++l +iVI+++ig++a  +
  gi|70607401|ref|YP_256271.1| 560 TFYIVLAVIVIIIVIGVVALLL 581
                                   7899*************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1841  (0.102683); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 3867.84
//
Query:       gi|70607402|ref|YP_256272.1|  [L=555]
Description: multidrug efflux protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-36  126.2  50.9    9.2e-28   97.2  19.8    3.2  3  MFS_1     Major Facilitator Superfamily
    7.4e-09   35.0  36.6    2.4e-05   23.4  15.0    3.8  4  Sugar_tr  Sugar (and other) transporter
     0.0003   19.3   3.7     0.0003   19.3   3.7    2.2  2  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
        5.1    5.3   9.0        4.9    5.3   2.5    3.2  3  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2  19.8   2.1e-31   9.2e-28       2     173 ..      12     189 ..      11     204 .. 0.89
   2 !   43.2  23.2   5.1e-15   2.3e-11     135     352 ..     220     426 ..     204     427 .. 0.74
   3 ?   -4.3   5.0       1.4   6.3e+03     261     285 ..     496     520 ..     427     543 .. 0.48

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 2.1e-31
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg. 75 
                                   ++++fl++++++++++alp ++ ++l+++p++      + +++ +y+++++ +++ +Gr+sd  Gr r++++g+l+f+++ 
  gi|70607402|ref|YP_256272.1|  12 SIGIFLAFANYNMIILALP-TIFSSLNFNPTSpgaldyLLWVILGYMIVTSSLVVTMGRISDMKGRARLYMIGFLIFSISs 91 
                                   689****************.9999999999998788888889999***********************************7 PP

                         MFS_1  76 lllllfa....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                   +ll++++     ++  +++lr++qG+g+g+l+ ++aa+++d+fpk+e g+a+gl +++  +G ++g +lgg+la  ++Wr+
  gi|70607402|ref|YP_256272.1|  92 GLLASVVspgaEGIMEIILLRIVQGIGGGFLMVNSAAVLTDYFPKSELGKALGLNQVSGLVGNVVGLILGGILA-TVNWRY 171
                                   7777753455566778**********************************************************.999*** PP

                         MFS_1 153 vfyilaivsllafvlfllllp 173
                                   +f++  +v++ + +   + ++
  gi|70607402|ref|YP_256272.1| 172 IFIFDLVVGIAGTL---WSYR 189
                                   ***********988...5443 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 5.1e-15
                         MFS_1 135 ilgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw...il 212
                                    +++++ ++  + lgW  +f+i++ivs l+++ +++l+ e++ +++ +            +l++ ++ +   ++     +l
  gi|70607402|ref|YP_256272.1| 220 SVTYGITPYGNQELGWGNPFVIAGIVSSLVLI-GVFLFIESRIKNPMFDL----------SLFK-IRDFSIGNFTNfvvSL 288
                                   444555666667777**************977.55777666666666633..........4444.5555555533112334 PP

                         MFS_1 213 lialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglal 293
                                       +l  + + +  ++lpl     +  +  + ag++l    l++a++++++g lsd++g++ ++ l+l+l ++++++l  
  gi|70607402|ref|YP_256272.1| 289 TRQGILLVLLVLLQGIWLPLH-GVAYADT-PFWAGIYLIPNVLGFAVFGPISGILSDKYGSKLFTSLGLFLSAIGFFLLSE 367
                                   444444444555688999996.5555555.599999999999999999************988888888888888888887 PP

                         MFS_1 294 lavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                   l+   +++ + ++ +++G g+g+++++ +a ++ +ap e++g asg   ++++ g+al+
  gi|70607402|ref|YP_256272.1| 368 LPYNFDPWEFFVITFIMGAGMGLFSSPNMADIMASAPVEKRGIASGMRASLQNTGSALS 426
                                   7888**************************************************99986 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 1.4
                         MFS_1 261 allagrlsdrlgrrrrlllalllll 285
                                   ++++++++  + + +rl+l ++ +l
  gi|70607402|ref|YP_256272.1| 496 QFFVSAIAPSFMSAFRLMLYISTAL 520
                                   3333333322222222222222222 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.6     0.033   1.5e+02     255     307 ..       7      65 ..       2      67 .. 0.81
   2 !   23.4  15.0   5.3e-09   2.4e-05      50     187 ..      51     186 ..      20     189 .. 0.82
   3 !    3.8   0.5    0.0047        21     152     194 ..     217     259 ..     201     261 .. 0.76
   4 !   17.9   5.1   2.5e-07    0.0011      58     164 ..     330     436 ..     311     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.033
                                   HHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH......HHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 255 lligvvlqifqqltGinaimyysptifenlglsks......llvtiivgvvnfvatfva 307
                                   +l+   + if  +  +n+i+   ptif++l ++++      +l  +i+g + +++++v+
  gi|70607402|ref|YP_256272.1|   7 ALTNTSIGIFLAFANYNMIILALPTIFSSLNFNPTspgaldYLLWVILGYMIVTSSLVV 65 
                                   5667788999999********************99888888777777777777777665 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.3e-09
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH..HH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavl..qaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                   ++   ++++     +++g ++d+ GR   ++i+ ++f+i++ l  +++++g++ +  +i+ R++ Gig G+  v +   + 
  gi|70607402|ref|YP_256272.1|  51 WVILGYMIVTSSLVVTMGRISDMKGRARLYMIGFLIFSISSGLlaSVVSPGAEGIMEIILLRIVQGIGGGFLMVNSAAVLT 131
                                   44444555555556889**********************9876225789999***************************** PP

                                   TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                      Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                    + pk+  g+  +l+q++  +G +v+ i+g +l+++ n   wr+ + + lv  ++  ++
  gi|70607402|ref|YP_256272.1| 132 DYFPKSELGKALGLNQVSGLVGNVVGLILGGILATV-N---WRYIFIFDLVVGIAGTLW 186
                                   **********************99999999888764.5...999999999999887766 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0047
                                   HHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                      Sugar_tr 152 lvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                   l+ ++++ ++ + +++ gw  ++ ++ + + l+li+++++ ES
  gi|70607402|ref|YP_256272.1| 217 LLVSVTYGITPYGNQELGWGNPFVIAGIVSSLVLIGVFLFIES 259
                                   4555555555666669*********************998888 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHH CS
                      Sugar_tr  58 GaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRga 138
                                   G ++ + ++g+l+d++G k     + +l+ ig +l    + ++  + ++v  +++G g+Gl+s      i   Ap ++Rg+
  gi|70607402|ref|YP_256272.1| 330 GFAVFGPISGILSDKYGSKLFTSLGLFLSAIGFFLLSELPYNFDPWEFFVITFIMGAGMGLFSSPNMADIMASAPVEKRGI 410
                                   44555568899**************************99999*********************99999999999******* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHTS CS
                      Sugar_tr 139 lvslyqlaitfGilvaaifglglnkt 164
                                     ++  +   +G  ++ ++++ +  t
  gi|70607402|ref|YP_256272.1| 411 ASGMRASLQNTGSALSVGVYFSVIIT 436
                                   ************99999998888554 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.7   6.7e-08    0.0003      61     175 ..      63     176 ..      57     202 .. 0.89
   2 !    2.4   0.3     0.009        40      61     123 ..     334     394 ..     325     450 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.7e-08
                         MFS_3  61 lsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAv 141
                                   l +  G ++D   r ++ +++ l+  ++s ll++++  g    + ++ l ++ giG  + +    A++ +  +++++ +A 
  gi|70607402|ref|YP_256272.1|  63 LVVTMGRISDMKGRARLYMIGFLIFSISSGLLASVVSPGAEGIMEIILLRIVQGIGGGFLMVNSAAVLTDYFPKSELGKAL 143
                                   56789**************************************************************************** PP

                         MFS_3 142 aLnsvginiaRsvGPAlgGvlvaavGaalafavn 175
                                    Ln v   +   vG  lgG+l a+v   + f ++
  gi|70607402|ref|YP_256272.1| 144 GLNQVSGLVGNVVGLILGGIL-ATVNWRYIFIFD 176
                                   *******************86.556666666655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.009
                         MFS_3  61 lsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPa 123
                                   +  ++G+l+D++  + +   +  l a++  ll  l     ++pw   ++t+++g G+ l +  
  gi|70607402|ref|YP_256272.1| 334 FGPISGILSDKYGSKLFTSLGLFLSAIGFFLLSEL--PYNFDPWEFFVITFIMGAGMGLFSSP 394
                                   55579999999998755555544444444443333..33579**************9986533 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.5    0.0011       4.9     135     193 ..     108     166 ..      12     178 .. 0.89
   2 ?    0.8   0.0     0.026   1.2e+02     474     510 ..     176     212 ..     169     220 .. 0.87
   3 ?    0.8   0.4     0.025   1.1e+02     463     521 ..     377     435 ..     373     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0011
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 135 fflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                   ++l  +++GiG+  ++    + + D+  k++    lg+ ++  ++G ++G +lG++l+ 
  gi|70607402|ref|YP_256272.1| 108 IILLRIVQGIGGGFLMVNSAAVLTDYFPKSELGKALGLNQVSGLVGNVVGLILGGILAT 166
                                   5666899************************************************9876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.026
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 474 galgrvpallvilRcVkkedksfalGlqlllirllgl 510
                                     +  ++++l  +R+ k+ +k ++++l ++ + l+g+
  gi|70607402|ref|YP_256272.1| 176 DLVVGIAGTLWSYRSLKDAQKPISQSLDVIGTTLFGV 212
                                   55667889999*******************9999985 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.025
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 463 flillflvsflgalgrvpallvilRcVkkedksfalGlqlllirllgliPgPiifGaii 521
                                   f+++ f++ + + l + p++  i+ + + e++ +a G+   l ++ +++   ++f +ii
  gi|70607402|ref|YP_256272.1| 377 FFVITFIMGAGMGLFSSPNMADIMASAPVEKRGIASGMRASLQNTGSALSVGVYFSVII 435
                                   899999999999999******999***************99999988888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3752.38
//
Query:       gi|70607403|ref|YP_256273.1|  [L=140]
Description: MarR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-14   52.0   0.3    1.1e-13   50.8   0.0    1.8  2  MarR            MarR family
    5.6e-14   52.4   0.2    9.6e-14   51.6   0.2    1.4  1  HTH_27          Winged helix DNA-binding domain
    2.9e-09   36.7   0.0    4.5e-09   36.1   0.0    1.3  1  MarR_2          MarR family
    1.2e-08   34.7   1.2    1.9e-08   34.1   1.2    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      1e-07   31.7   0.7      2e-07   30.8   0.1    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
    3.3e-07   30.4   0.3    5.1e-07   29.8   0.3    1.3  1  HTH_34          Winged helix DNA-binding domain
    1.9e-05   24.8   1.1    3.7e-05   23.8   1.1    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00012   21.8   0.6    0.00019   21.2   0.5    1.3  1  DUF4423         Domain of unknown function (DUF4423)
    0.00059   19.7   0.0     0.0012   18.7   0.0    1.5  1  HTH_36          Helix-turn-helix domain
     0.0011   18.9   1.9     0.0025   17.7   1.9    1.7  1  HTH_45          Winged helix-turn-helix
     0.0021   18.3   1.1     0.0038   17.5   1.1    1.5  1  DUF4362         Domain of unknown function (DUF4362)
     0.0023   17.8   0.5      0.004   17.0   0.5    1.4  1  HxlR            HxlR-like helix-turn-helix
     0.0067   17.1   0.3       0.12   13.1   0.0    2.1  2  Ead_Ea22        Ead/Ea22-like protein
     0.0077   16.1   1.7     0.0095   15.8   1.7    1.1  1  DUF3877         Domain of unknown function, E. rectale Gene d
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.026   14.8   0.1    1.6  1  Rrf2            Transcriptional regulator
      0.012   15.4   0.0       0.03   14.1   0.0    1.8  1  HTH_IclR        IclR helix-turn-helix domain
      0.012   15.5   0.1      0.026   14.5   0.1    1.6  1  PadR            Transcriptional regulator PadR-like family
      0.023   14.8   1.6      0.039   14.0   1.0    1.7  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.024   14.5   0.3       0.05   13.5   0.2    1.6  1  GFRP            GTP cyclohydrolase I feedback regulatory prot
      0.034   13.9   0.3      0.043   13.5   0.3    1.2  1  Ribosomal_S19e  Ribosomal protein S19e
      0.043   13.8   0.5       0.05   13.6   0.5    1.1  1  DUF5033         Domain of unknown function (DUF5033)
      0.047   13.3   0.0       0.15   11.6   0.0    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.084   13.0   0.2       0.11   12.7   0.2    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.095   12.7   0.0       0.21   11.6   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.099   13.3   2.2       0.14   12.8   1.7    1.5  2  RTP             Replication terminator protein


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.6e-16   1.1e-13       1      59 []      27      84 ..      27      84 .. 0.96
   2 ?   -2.7   0.0       8.3     6e+03      11      24 ..     127     140 .]     126     140 .] 0.78

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-16
                                  --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                          MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                  lt+t + +L++l+ +g+ +vs Lak + v+kst+ +vld+Lek G+i++sk+++D+R+v
  gi|70607403|ref|YP_256273.1| 27 LTYTDVQVLYSLS-SGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNEQDKRVV 84
                                  7999999999996.799****************************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.3
                                   HHHHSTTEEHHHHH CS
                          MarR  11 ilyeqgplsvseLa 24 
                                   i+++ + +s+s La
  gi|70607403|ref|YP_256273.1| 127 IIDQAEKQSLSTLA 140
                                   68888888888887 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.2   1.3e-16   9.6e-14       1      68 []      27      92 ..      27      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.3e-16
                        HTH_27  1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  lt+ +++vL ++    ++k  + l++ ++v++s+++++l+kL+++G++++++ e+d+r + +++T++G
  gi|70607403|ref|YP_256273.1| 27 LTYTDVQVLYSLS--SGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNEQDKRVVIIKVTEEG 92
                                  7999*********..****************************************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   6.2e-12   4.5e-09       1      61 [.      25      82 ..      25      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.2e-12
                                  TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  lglt ++ +vL+ L  ++    +v+ la+  ++ ks++  +l++L++ G++ +++++ DkR
  gi|70607403|ref|YP_256273.1| 25 LGLTYTDVQVLYSLSSGEK---NVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNEQDKR 82
                                  69****************8...**************************************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   1.2   2.6e-11   1.9e-08       3      58 ..      24      78 ..      22      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.6e-11
                                  HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  klGL+ ++++v   L ++g+++++++a+ ++v +s+  evL +Le++G+++++k +
  gi|70607403|ref|YP_256273.1| 24 KLGLTYTDVQVLYSL-SSGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNE 78
                                  8**********9997.6***********************************9976 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   2.7e-10     2e-07       5      47 .]      32      74 ..      30      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.7e-10
                                  HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  +++L++L++ge+ v+ la+ +++++st  + L kL+++G+++k
  gi|70607403|ref|YP_256273.1| 32 VQVLYSLSSGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKK 74
                                  79***************************************86 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   7.1e-10   5.1e-07       8      72 ..      37      99 ..      31     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 7.1e-10
                        HTH_34  8 yLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkky 72
                                  +L+   e + ++l + + ++++ +   l+kLek gYi+ +k+ ++k +  ++++T+eG++   ++
  gi|70607403|ref|YP_256273.1| 37 SLS-SGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNEQDK-RVVIIKVTEEGLNILTQV 99
                                  333.455678999*****************************9999.9**********9977665 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   1.1   5.2e-08   3.7e-05      12      56 ..      34      76 ..      32      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.2e-08
                                  HHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                Fe_dep_repress 12 tIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                  ++Y+ls ++k   ++ la+  +v +s+  e l kLek+Gy++ +k
  gi|70607403|ref|YP_256273.1| 34 VLYSLSSGEKN--VSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSK 76
                                  67888865554..467*************************9877 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.5   2.7e-07   0.00019      23      86 ..      29      89 ..       9      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.7e-07
                       DUF4423 23 ypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksltts 86
                                  y+ ++ l +l  +++++++lak +   ++++   + l+ L+k+g +kk+++ +  + +  ++++
  gi|70607403|ref|YP_256273.1| 29 YTDVQVLYSLSSGEKNVSTLAKLVD--VNKSTMVEVLDKLEKMGYIKKSKN-EQDKRVVIIKVT 89
                                  45678899*****************..***********************9.544444455555 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0012      21      55 .]      41      72 ..      34      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                        HTH_36 21 nggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                  ++     ++tlak+  ++k+T +  +++Le+ Gyi
  gi|70607403|ref|YP_256273.1| 41 GEK---NVSTLAKLVDVNKSTMVEVLDKLEKMGYI 72
                                  444...699*************************9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.9   3.6e-06    0.0025      10      71 ..      33     101 ..      31     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-06
                        HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli.....kkskek....YvlTekGlelleklke 71 
                                   ++L ++s+ge++ + + + ++ + +++ + Ld+L + g+i     +  ++k     ++Te+Gl++l ++++
  gi|70607403|ref|YP_256273.1|  33 QVLYSLSSGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIkksknE--QDKrvviIKVTEEGLNILTQVRT 101
                                   78999***********************************666431..2222222568********99885 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.1   5.3e-06    0.0038       5      58 ..      54     109 ..      50     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.3e-06
                       DUF4362   5 vvkhveisNvdklek..FienveqkkkdkirivsyTeeGdpiledleydgkklkyi 58 
                                   v+k++ +  +dklek  +i++ +++++ ++ i++ TeeG  il+++ +  k+l ++
  gi|70607403|ref|YP_256273.1|  54 VNKSTMVEVLDKLEKmgYIKKSKNEQDKRVVIIKVTEEGLNILTQVRTRYKDLILT 109
                                   4666777889***98668****************************9988887654 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   5.5e-06     0.004       9      74 ..      33      97 ..      30     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.5e-06
                                  HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                          HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslep 74
                                   +l++l +g+k  s l++ + ++ ++++++ L +Le+ g i+++  ++    v  ++te+G ++  
  gi|70607403|ref|YP_256273.1| 33 QVLYSLSSGEKNVSTLAKLV-DVNKSTMVEVLDKLEKMGYIKKSKNEQDKRVVIIKVTEEGLNILT 97
                                  69***************999.9*****************************9*********87754 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00016      0.12      46      89 ..      23      78 ..       5      95 .. 0.80
   2 ?    2.4   0.1      0.31   2.2e+02      68      89 ..     106     127 ..      84     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                      Ead_Ea22 46 fklgrtvakeh..............daefiaaanpatvlaLLDelekkqqrikeleee 89
                                  +klg t+ + +               a+ +++ n +t+ + LD+le k ++ik  + e
  gi|70607403|ref|YP_256273.1| 23 EKLGLTYTDVQvlyslssgeknvstLAKLVDV-NKSTMVEVLDKLE-KMGYIKKSKNE 78
                                  66777777777777888888888889999999.9************.69999998855 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.31
                      Ead_Ea22  68 tvlaLLDelekkqqrikeleee 89 
                                    +l LLD+ e k++  + ++++
  gi|70607403|ref|YP_256273.1| 106 LILTLLDKVENKECVLAFFNAI 127
                                   5899*******99987777665 PP

>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.7   1.3e-05    0.0095       6     123 ..      12     129 ..       9     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                       DUF3877   6 knlidvikEeqlKlGyrkekirlyyPlssLnhlleaeedaeelkealeefaeeakeklGevevt...ekkdrfcveipeeg 83 
                                   k+l  +++ e  KlG +  ++++ y lss ++ +++ ++  ++++        + ek+G ++ +   + k  + +++ eeg
  gi|70607403|ref|YP_256273.1|  12 KKLRKLLQNEAEKLGLTYTDVQVLYSLSSGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSkneQDKRVVIIKVTEEG 92 
                                   677788899999*****************9999998885555555544444445667777776622133334567899999 PP

                       DUF3877  84 aeyvhe.eikeneFlkeliellkkhectledilelFkkysk 123
                                    +   + +++ ++++ +l++ ++++ec l    ++F++  +
  gi|70607403|ref|YP_256273.1|  93 LNILTQvRTRYKDLILTLLDKVENKECVL----AFFNAIID 129
                                   98876624556777777777777776654....44444443 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   3.7e-05     0.026      20      57 ..      41      74 ..      29      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-05
                                  SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 20 eeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   e     +++++a+ +++++s +  +l kL+k g++k 
  gi|70607403|ref|YP_256273.1| 41 GE----KNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKK 74
                                  33....4789**************************85 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.2e-05      0.03      11      50 ..      37      74 ..      32      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-05
                                  T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   l+++    ++s lA+  +++kSt    L  L+++Gy+++
  gi|70607403|ref|YP_256273.1| 37 SLSSGEK--NVSTLAKLVDVNKSTMVEVLDKLEKMGYIKK 74
                                  5555555..499*************************997 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.6e-05     0.026      25      70 ..      50      93 ..      42     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                                  T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                          PadR 25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70
                                   l+++++++   +L++Lek g+++++++e  ++++  + ++T++G 
  gi|70607403|ref|YP_256273.1| 50 KLVDVNKSTMVEVLDKLEKMGYIKKSKNE--QDKRVVIIKVTEEGL 93
                                  46789999999***************998..578888888888885 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   5.5e-05     0.039       7      59 ..      28      79 ..      22     104 .. 0.80
   2 ?   -1.9   0.0       5.3   3.8e+03      37      57 ..      97     116 ..      89     119 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                       DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegkt 59
                                  ++ +++vl+ l   + + + ++ak ++++++ + e+l+kLe++G +++ +++ 
  gi|70607403|ref|YP_256273.1| 28 TYTDVQVLYSLSSGEKNVS-TLAKLVDVNKSTMVEVLDKLEKMGYIKKSKNEQ 79
                                  5667788888888877765.789************************999864 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                       DUF2250  37 eevrellkkLeelGLlerveg 57 
                                   ++vr  +k+L  l Ll++ve+
  gi|70607403|ref|YP_256273.1|  97 TQVRTRYKDLI-LTLLDKVEN 116
                                   45566666654.346666655 PP

>> GFRP  GTP cyclohydrolase I feedback regulatory protein (GFRP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2     7e-05      0.05      18      72 ..      25      79 ..      17      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                          GFRP 18 vGdessdpeLmkeLgaklrkvlgnkfkeylved.pprvvLnkLekkGykvvamtgv 72
                                  +G  + d +++ +L +  ++v+ +  k + v++ +  +vL+kLek+Gy   ++ + 
  gi|70607403|ref|YP_256273.1| 25 LGLTYTDVQVLYSLSSGEKNVS-TLAKLVDVNKsTMVEVLDKLEKMGYIKKSKNEQ 79
                                  6677889999999988777777.445555555515678**********65555555 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3     6e-05     0.043      76     130 ..      40      99 ..       9     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                   SS-------THHHHHHHHHTTSSS--SSS---SS.-.HHHHHTH....HHHH--SS--S-- CS
                Ribosomal_S19e  76 GgkkrrgvrpshfvkasgsvirkilqqLeklglv.k.kekkkgr....rltkkGqrlldri 130
                                   +g +++ ++  + v+ ++s + ++l +Lek+g++ k k+++++r    ++t++G ++l ++
  gi|70607403|ref|YP_256273.1|  40 SG-EKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIkKsKNEQDKRvviiKVTEEGLNILTQV 99 
                                   33.3457788999999******************532333344422223577777777666 PP

>> DUF5033  Domain of unknown function (DUF5033)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     7e-05      0.05       9      72 ..      28      90 ..      20     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                       DUF5033  9 tfellestYGaesvtynnsdlkdvPavsleemdevLeaLrkntnakeecesesvegykkvkmta 72
                                  t+  ++ +Y   s   n+s l ++  v  + m evL+ L k + +k+  ++e+++    +k+t+
  gi|70607403|ref|YP_256273.1| 28 TYTDVQVLYSLSSGEKNVSTLAKLVDVNKSTMVEVLDKLEKMGYIKKS-KNEQDKRVVIIKVTE 90
                                  899999**************************************9998.777777765555554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.6   3.3e+03      24      30 ..      22      28 ..      22      32 .. 0.84
   2 ?   11.6   0.0   0.00021      0.15      19      48 .]      44      73 ..      27      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.6
                        HTH_24 24 AerlglS 30
                                  Ae+lgl+
  gi|70607403|ref|YP_256273.1| 22 AEKLGLT 28
                                  8999997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
                        HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  + + LA+ +++ +st  + l++Le++G+Ik
  gi|70607403|ref|YP_256273.1| 44 NVSTLAKLVDVNKSTMVEVLDKLEKMGYIK 73
                                  66779************************8 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00015      0.11      21      53 ..      45      77 ..      39     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                B-block_TFIIIC 21 qsdLakeskqdprslfyrlksLekkgLIvkqsi 53
                                   s Lak+++  ++ +  +l++Lek g+I+k + 
  gi|70607403|ref|YP_256273.1| 45 VSTLAKLVDVNKSTMVEVLDKLEKMGYIKKSKN 77
                                  5789*************************9865 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.21      26      59 ..      47      85 ..      44      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                  HHHHHTTSSHHHHHHHHHHHHHTTSEE..ET...EEEEE CS
                     HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis..rg...rriri 59
                                   lA ++ ++ +t+  +l +L++ g+i+  ++   +r++i
  gi|70607403|ref|YP_256273.1| 47 TLAKLVDVNKSTMVEVLDKLEKMGYIKksKNeqdKRVVI 85
                                  69*************************653322234554 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.82   5.9e+02      75     110 ..      32      66 ..       9      68 .. 0.71
   2 ?   12.8   1.7   0.00019      0.14      44      99 ..      55     106 ..      28     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.82
                                   EEEEEEESS..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                           RTP  75 evviYsltdeGkekaklykkqvkidldrckklleka 110
                                   + v+Ysl+  G+ ++  + k+v ++     ++l+k 
  gi|70607403|ref|YP_256273.1|  32 VQVLYSLSS-GEKNVSTLAKLVDVNKSTMVEVLDKL 66 
                                   336788888.89999999999888877777777775 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
                                   -HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHHHHHHHHHHH CS
                           RTP  44 nhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekaklykkqvkid 99 
                                   n+s++ + l+ l + g++k+ k+ +     + vvi ++t+eG + ++  + ++k  
  gi|70607403|ref|YP_256273.1|  55 NKSTMVEVLDKLEKMGYIKKSKNEQ----DKRVVIIKVTEEGLNILTQVRTRYKDL 106
                                   789999*************999877....6789999******99988877777743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1248  (0.0696079); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 897.15
//
Query:       gi|70607404|ref|YP_256274.1|  [L=359]
Description: hypothetical protein Saci_1671 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2325.05
//
Query:       gi|70607405|ref|YP_256275.1|  [L=158]
Description: hypothetical protein Saci_1672 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   31.4   0.0      2e-07   30.7   0.0    1.3  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.1e-11     2e-07      26     111 ..      64     147 ..      56     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.1e-11
                                   EETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBEC CS
                       dUTPase  26 vkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifarilt 106
                                   +kp +t+l  +   +++p +la li+ +S +a++g++ +p+vid+ y+G++++ l+   +   k+kkg    +Lif r+++
  gi|70607405|ref|YP_256275.1|  64 LKPLKTYLFESCEEFDMPSDLAVLITLKSTMARNGFLAPPTVIDAGYKGKIAIALTPVYS--TKLKKGMSTHHLIFLRLDE 142
                                   678888899999999**********************************88888886665..799***********99998 PP

                                   GEEEE CS
                       dUTPase 107 aelee 111
                                   ++ ++
  gi|70607405|ref|YP_256275.1| 143 PSSKT 147
                                   55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1136.69
//
Query:       gi|70607406|ref|YP_256276.1|  [L=179]
Description: hypothetical protein Saci_1673 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   16.5   4.8     0.0025   16.2   4.8    1.1  1  DUF2070   Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
       0.11   12.7   8.9       0.15   12.2   8.9    1.1  1  DUF5518   Family of unknown function (DUF5518)
       0.15   11.9   0.3       0.48   10.3   0.1    1.8  2  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   4.8   4.2e-07    0.0025     133     217 ..      42     133 ..       8     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-07
                       DUF2070 133 paliqpllailllvly.......fspesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skel 205
                                   +a+   ++++++l l+       f++ ++ll+++++++ +++++l +++++ ++   + +s+  +   F a+ l++ ++++
  gi|70607406|ref|YP_256276.1|  42 LAICDVVSSVVYLSLVyflrisfFGNIFTLLIIVFTIAGVAVSVLSLMFFTNNITT-TTISGNTINTEFYASSLNEvEEKV 121
                                   222222222222222245677789999***************************87.66********************** PP

                       DUF2070 206 Eeffeeigeead 217
                                   ++f+++ig +++
  gi|70607406|ref|YP_256276.1| 122 DKFLSNIGINRE 133
                                   ********8876 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   8.9   2.5e-05      0.15      23     102 ..      13      89 ..       6     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                       DUF5518  23 psvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaaigglagfvallvalllvvllllvv 102
                                     ++ llg+++ G+v++ l+++  ++g++  a++ ++ ++++l l+ +l +++++ i +l+ +v++++++++   +l+++
  gi|70607406|ref|YP_256276.1|  13 VWWIPLLGPFILGFVTAMLERE-FRRGLISLAICDVVSSVVYLSLVYFLRISFFGNIFTLLIIVFTIAGVAVS--VLSLM 89 
                                   456778************9977.89*****************8888888777888777777777777777776..33332 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1     8e-05      0.48       4      50 ..      71     118 ..      70     125 .. 0.85
   2 ?   -1.8   0.0      0.46   2.7e+03      45      59 ..     154     168 ..     139     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8e-05
                       DUF4307   4 llvillvvlvvvalalvawigysq.gsadvsaevvgfevvddstvevt 50 
                                   ll+i++++++v++ +l  ++++++ +++++s+++++ e    s  ev+
  gi|70607406|ref|YP_256276.1|  71 LLIIVFTIAGVAVSVLSLMFFTNNiTTTTISGNTINTEFYASSLNEVE 118
                                   68999*****************************99887766666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                       DUF4307  45 stvevtfeVtrddgs 59 
                                   ++v+v++e+t++  +
  gi|70607406|ref|YP_256276.1| 154 NNVKVEYEITKPGRK 168
                                   567788888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1262.37
//
Query:       gi|70607407|ref|YP_256277.1|  [L=275]
Description: gluconolactonase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-76  254.6   0.0    1.1e-75  254.4   0.0    1.0  1  SGL           SMP-30/Gluconolactonase/LRE-like region
    0.00034   20.5   0.2        1.5    9.3   0.0    4.0  3  Reg_prop      Two component regulator propeller
      0.008   16.3   0.0      0.024   14.8   0.0    1.8  1  Str_synth     Strictosidine synthase
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.36   11.0   0.0    1.7  1  Arylesterase  Arylesterase


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.4   0.0   2.5e-79   1.1e-75       3     246 .]      13     250 ..      11     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 254.4 bits;  conditional E-value: 2.5e-79
                           SGL   3 EGpvwdeeegaLlwvDilgqrihrldpatgketvldtpesvGaiaprkdgrlvvasksglalldlasgeletladeeedek 83 
                                   EGp+w    ++L++vDi+++++h+l++++++   +++p  v+++ p+k+g+++v++ +g++l++ ++ +++ l++  + + 
  gi|70607407|ref|YP_256277.1|  13 EGPIWA--YNSLYFVDIPKGELHNLKEDGTHWA-VKFPTYVSSLQPTKRGGIIVTAGNGFYLVK-DKDQISLLYEVKDWD- 88 
                                   9*****..7****************87776665.7***********999**************7.5679******97777. PP

                           SGL  84 pllrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldpdgklervlddltipNGlawspdgktlYlaDsltrkiwaydvd 164
                                    ++rfNDg++d+ Gr+w+Gtm+ ee+ ++  g+l++ld d k +rvl+d+ti+NGlaws d+k lY++Ds+trki+++++d
  gi|70607407|ref|YP_256277.1|  89 SRNRFNDGKCDQMGRYWIGTMNLEEKYPT--GGLFVLDLDMKFRRVLTDVTISNGLAWSLDNKYLYYIDSPTRKIFKFKFD 167
                                   9****************************..************************************************** PP

                           SGL 165 aeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpd.GklieeiklpakrvtscaFgGpdlrtLyits 244
                                    e g++s+r+v++dlk++eg+pDG+++D+eGn+wvA++ggg v r+d +  k+i+e +lpa rvts++FgG++++tL+it+
  gi|70607407|ref|YP_256277.1| 168 LERGDISQREVLIDLKEYEGVPDGMTIDSEGNLWVALYGGGAVLRIDVEkRKVIQELRLPAPRVTSVIFGGSNMDTLFITT 248
                                   ************************************************999*********99******************* PP

                           SGL 245 ak 246
                                   a+
  gi|70607407|ref|YP_256277.1| 249 AN 250
                                   96 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.4   1.8e+03       5      20 ..      48      63 ..      46      67 .. 0.81
   2 !    5.7   0.0     0.005        23      13      24 .]      99     110 ..      97     110 .. 0.84
   3 !    9.3   0.0   0.00033       1.5      10      22 ..     192     204 ..     186     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.4
                                  SCEEEEEE-TTSCEEE CS
                      Reg_prop  5 nnvtaileDsdGrlWv 20
                                  ++v++++ +++G + v
  gi|70607407|ref|YP_256277.1| 48 TYVSSLQPTKRGGIIV 63
                                  5789*******98855 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.005
                                   -TTSCEEEEESS CS
                      Reg_prop  13 DsdGrlWvGteg 24 
                                   D+ Gr W+Gt +
  gi|70607407|ref|YP_256277.1|  99 DQMGRYWIGTMN 110
                                   7779******76 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00033
                                   EEE-TTSCEEEEE CS
                      Reg_prop  10 ileDsdGrlWvGt 22 
                                   +  Ds+G+lWv+ 
  gi|70607407|ref|YP_256277.1| 192 MTIDSEGNLWVAL 204
                                   678********85 PP

>> Str_synth  Strictosidine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.3e-06     0.024      29      83 ..     110     163 ..      99     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                     Str_synth  29 allegdktGrllkydkstkvvkvlldkLyfanGialsedgsfvlvcetamkrisr 83 
                                   +l e+ +tG l+ +d   k  +vl  +   +nG+a s d++++ + + ++++i +
  gi|70607407|ref|YP_256277.1| 110 NLEEKYPTGGLFVLDLDMKFRRVLT-DVTISNGLAWSLDNKYLYYIDSPTRKIFK 163
                                   5678899************999876.6899********************99987 PP

>> Arylesterase  Arylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.1e-05      0.36      46      82 ..     129     165 ..     109     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                  Arylesterase  46 vkvvasglssanGInidadkkyiyvadilresihvmk 82 
                                    + v   ++ +nG+  + d+ky+y  d+  ++i+ +k
  gi|70607407|ref|YP_256277.1| 129 FRRVLTDVTISNGLAWSLDNKYLYYIDSPTRKIFKFK 165
                                   5678889999************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1975.25
//
Query:       gi|70607408|ref|YP_256278.1|  [L=262]
Description: hypothetical protein Saci_1675 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-21   75.4   0.0    1.4e-20   73.9   0.0    1.7  1  Peptidase_M48  Peptidase family M48
      1e-07   31.5   4.3      1e-07   31.5   4.3    1.4  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
        0.3   10.8   2.4        2.6    7.8   0.4    2.3  2  ISK_Channel    Slow voltage-gated potassium channel
       0.62   10.5   2.9        1.4    9.3   2.9    1.7  1  DUF5313        Family of unknown function (DUF5313)
        1.2    8.1   7.9        2.5    7.0   7.6    1.6  2  Pex24p         Integral peroxisomal membrane peroxin


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   3.9e-24   1.4e-20       4     194 ..      63     257 ..      60     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 3.9e-24
                                   SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvsl 84 
                                   ++++ +++e +++ +++  +++k+ ++ns+k NAF+lg++ +  +++t+gLl + l+++el  Vl HEl Hik+r+  ++l
  gi|70607408|ref|YP_256278.1|  63 NEDVLRKFEYALALVQM--KKIKLHEINSSKPNAFVLGNFLSYNVIVTRGLL-ESLNDRELISVLLHELHHIKNRDIEIQL 140
                                   67777888888888888..*********************999*********.************************9996 PP

                                   HHHHHHH.HHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT..HHHHHHHHHHHHH CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                 Peptidase_M48  85 ivsllas.illllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkr.akdlvraliklak 163
                                   i  l+ + ++++++             +  l+    +ig++ ++   ++ R  E +AD  + ++++  + +l++al+k+ +
  gi|70607408|ref|YP_256278.1| 141 IYVLIVNtFYIYIANY-----------NPLLGLSELVIGVVLLF---PVHRLLEKNADIKACRTTNWiPLNLANALVKIGY 207
                                   6666555055555543...........33333344455555556...******************9536789999999999 PP

                                   HTT-.......-S---HHHH...................HHS-SS--HHHHHHHHHH CS
                                   xxxx.......xxxxxxxxx...................xxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 164 dler.......qdvsaslrs...................ellstHPplleRiqalke 194
                                     +        +                            ++stHP l+eR++ +++
  gi|70607408|ref|YP_256278.1| 208 LSRFlpheiirD-------YsevdltlaketilrddkkgFIFSTHPALSERLKYISK 257
                                   888855555540.......245555566677777788889************99876 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   4.3   2.8e-11     1e-07     111     233 ..      37     162 ..      25     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.8e-11
                 Peptidase_M56 111 vgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgll.kprIvlPadflkk 190
                                   v+++++l y+i    +l+   v k++k+++e   ++ + a   +q+k+     ++ss  + +vlg +  + +++   +l++
  gi|70607408|ref|YP_256278.1|  37 VIFILFLWYIISPGILLR---VIKSKKVENEDVLRKFEYALALVQMKKIKLHEINSSKPNAFVLGNFlSYNVIVTRGLLES 114
                                   344555566776666677...9999********************877555567777778899997525668888899*** PP

                 Peptidase_M56 191 lsdeeleyillHElaHlkrkDllvnllvavlq.....clfwfNPlvhl 233
                                   l+d+el  +llHEl H+k++D+ ++l+++++       +  +NPl+ l
  gi|70607408|ref|YP_256278.1| 115 LNDRELISVLLHELHHIKNRDIEIQLIYVLIVntfyiYIANYNPLLGL 162
                                   *********************988887765431111257789999866 PP

>> ISK_Channel  Slow voltage-gated potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4   0.00071       2.6      38      70 ..      32      64 ..      30      71 .. 0.91
   2 ?    2.5   0.1     0.032   1.1e+02      32      53 ..     132     153 ..      97     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00071
                   ISK_Channel 38 levlyillllgffgfftlGimlsyirskklehs 70
                                  +e++ ++++l ++  +  Gi+l  i+skk e+ 
  gi|70607408|ref|YP_256278.1| 32 IEIIGVIFILFLWYIISPGILLRVIKSKKVENE 64
                                  689999999999999***************975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.032
                   ISK_Channel  32 rseddklevlyillllgffgff 53 
                                   ++ d +++++y+l++ +f+ ++
  gi|70607408|ref|YP_256278.1| 132 KNRDIEIQLIYVLIVNTFYIYI 153
                                   555888999******9999765 PP

>> DUF5313  Family of unknown function (DUF5313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.9    0.0004       1.4      34      78 ..       4      48 ..       1      86 [. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                       DUF5313 34 aaaRhviraavplvlilavllLlpgslyvrlemtllillvavlys 78
                                  + + h++ +++  ++il++++L+p  +y+ +  ++ il   ++ s
  gi|70607408|ref|YP_256278.1|  4 WWRYHLATIIILFAMILTIYFLVPPLFYIEIIGVIFILFLWYIIS 48
                                  778899************************998887765544444 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.6   0.00069       2.5      45     170 ..      14     156 ..       3     176 .. 0.61
   2 ?   -3.4   0.0         1   3.7e+03       8      21 ..     241     254 ..     223     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00069
                        Pex24p  45 lsfllvytficlvpyl...elvvlplllllfvvmvpaylyrhplrksslik...............keesknestsegptl 107
                                   + f ++ t++ lvp l   e++ ++++l+l  ++ p++l r    k++ +                k+ + +e +s++p+ 
  gi|70607408|ref|YP_256278.1|  14 ILFAMILTIYFLVPPLfyiEIIGVIFILFLWYIISPGILLRVIKSKKVENEdvlrkfeyalalvqmKKIKLHEINSSKPNA 94 
                                   344455555555554455577777777777777788888886444444444788888888777664444443444444443 PP

                        Pex24p 108 deaskeivlnLr....dlqnkmedllnpidalekflkelagfkdenlstllfltllltpililllsr 170
                                         ++ n+      ++  +   ln  + ++ +l el ++k++++ + l+++l++ +++i +  +
  gi|70607408|ref|YP_256278.1|  95 F-----VLGNFLsynvIVTRGLLESLNDRELISVLLHELHHIKNRDIEIQLIYVLIVNTFYIYIANY 156
                                   3.....33343322224455555566666778888999999*********************99843 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                        Pex24p   8 lssnppqlssrLak 21 
                                   + s+ p+ls rL +
  gi|70607408|ref|YP_256278.1| 241 IFSTHPALSERLKY 254
                                   33444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1907.95
//
Query:       gi|70607409|ref|YP_256279.1|  [L=214]
Description: hypothetical protein Saci_1676 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1610.86
//
Query:       gi|70607410|ref|YP_256280.1|  [L=292]
Description: hypothetical protein Saci_1677 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1979.79
//
Query:       gi|70607411|ref|YP_256281.1|  [L=211]
Description: hypothetical protein Saci_1678 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1653.68
//
Query:       gi|70607412|ref|YP_256282.1|  [L=585]
Description: hypothetical protein Saci_1679 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-49  167.7   0.1    3.3e-49  167.3   0.1    1.2  1  Peptidase_S9     Prolyl oligopeptidase family
    2.8e-09   37.0   0.9    1.2e-06   28.4   0.5    2.2  2  Abhydrolase_1    alpha/beta hydrolase fold
    3.5e-08   33.4   0.2    4.6e-05   23.1   0.2    2.4  2  Peptidase_S15    X-Pro dipeptidyl-peptidase (S15 family)
    3.7e-07   29.7   0.1     0.0063   15.8   0.0    2.2  2  Hydrolase_4      Serine aminopeptidase, S33
    8.4e-06   25.5   0.0      2e-05   24.2   0.0    1.6  1  DLH              Dienelactone hydrolase family
     0.0012   17.7   0.0      0.033   13.0   0.0    2.4  2  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
     0.0065   17.1   0.0     0.0091   16.6   0.0    1.3  1  Abhydrolase_6    Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.033   13.9   0.0    1.4  1  FSH1             Serine hydrolase (FSH1)
      0.084   12.7   0.1       0.27   11.0   0.0    1.8  2  Abhydrolase_2    Phospholipase/Carboxylesterase
       0.41   10.5   1.7          3    7.8   0.3    2.4  2  Op_neuropeptide  Opioids neuropeptide


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.3   0.1   1.8e-52   3.3e-49       5     210 ..     375     584 ..     371     585 .] 0.93

  Alignments for each domain:
  == domain 1  score: 167.3 bits;  conditional E-value: 1.8e-52
                                   HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH- CS
                  Peptidase_S9   5 selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqr 85 
                                    e+q++a +Gy v++ n+rGs+gyGe+f++a+ +++g ++++D++  +e++ k++y  + ++++tGgSyGG++t+++++ +
  gi|70607412|ref|YP_256282.1| 375 IEFQYFARNGYNVIYSNPRGSQGYGEEFAKACVGDWGGKDMNDLLLFVEEV-KRKYNLKGKIGVTGGSYGGFMTNWLVT-Q 453
                                   589***********************************************9.888888*********************.* PP

                                   GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTT..CHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THH CS
                  Peptidase_S9  86 pdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpee..neegykelspyspldnvkaypplLlihGlaDdrvppae 161
                                   +++F+aa++e+++++++++  ++d+   +++   + ++p+   ++ + +++sp+ +++n  +++p++lihG++D+r+p+++
  gi|70607412|ref|YP_256282.1| 454 TNVFSAAISERGISNLVSMCGTSDIgfwFNAVESGVTDPWTeeSQMKLMRMSPIYYVKN--VKTPTMLIHGEEDYRCPIEQ 532
                                   **************************977777777888888334444568999999999..99****************** PP

                                   HHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHCT CS
                  Peptidase_S9 162 alklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkealg 210
                                   +++++ aL+ +g+++ l+ + +  H   + gkp++ +++l+r l++++++l+
  gi|70607412|ref|YP_256282.1| 533 SEQFFIALKMNGVDTILVRYQQDSHehaRRGKPKNMRDRLERKLEWFDKYLK 584
                                   **************99999999999999999*******************98 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.5   6.8e-10   1.2e-06       1     104 [.     356     472 ..     356     485 .. 0.74
   2 !    6.9   0.0    0.0024       4.3     187     231 ..     486     534 ..     477     543 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.8e-10
                                   SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTST.T.SSSTTTGB.CHHSHHHHHHHHHHH...HHHCTTSSEE CS
                 Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvg.y.Sspapacinddygtasvaddldri...ldalgddklt 76 
                                   p+++++hG+p +++ +a +  ++++a++g+ vi  ++rG+  y  ++a+ac+  d+g  +++d l ++   + +++++  +
  gi|70607412|ref|YP_256282.1| 356 PTILFIHGGPHTAYGYAYFIEFQYFARNGYNVIYSNPRGSQgYgEEFAKACVG-DWGGKDMNDLLLFVeevKRKYNLKGKI 435
                                   789********9999999999******************85242568999985.555555666555444446666666666 PP

                                   .EEEETHHHHHHHHHHHHH........GGGEEEEEEE CS
                 Abhydrolase_1  77 .lvGhSmGGmialayaaey........perVkalvll 104
                                    + G+S+GG++  ++  +            +++lv++
  gi|70607412|ref|YP_256282.1| 436 gVTGGSYGGFMTNWLVTQTnvfsaaisERGISNLVSM 472
                                   6*********998887665555555555555555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0024
                                   HHHHHHHHCCHHHHHHHHHC....THHHHSEEEEEEETTCSSSCHHHHH CS
                 Abhydrolase_1 187 ksieqwpttdsaklllrlre....lknvlaptlvisgtsDplvppkale 231
                                   +s  + p+t +++  l++ +    +knv+ pt++i+g++D   p++++e
  gi|70607412|ref|YP_256282.1| 486 ESGVTDPWTEESQMKLMRMSpiyyVKNVKTPTMLIHGEEDYRCPIEQSE 534
                                   555555666666666665558999****************888886665 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.2   2.6e-08   4.6e-05      52     139 ..     371     470 ..     318     480 .. 0.80
   2 !    7.3   0.0    0.0018       3.2     223     259 ..     509     547 ..     478     557 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.6e-08
                                   H........HHHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHC CS
                 Peptidase_S15  52 v........fvarGYavVvqdvrGtggSeGeftvg.....dsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaa 119
                                            f+++GY v++++ rG+ g   ef  +     + ++ +d    ++ + ++   +Gk+g+tG SY+G++ + + 
  gi|70607412|ref|YP_256282.1| 371 YayfiefqyFARNGYNVIYSNPRGSQGYGEEFAKAcvgdwGGKDMNDLLLFVEEVKRKYNLKGKIGVTGGSYGGFMTNWLV 451
                                   055555555***************8877666666678777888888888888888999******************99998 PP

                                   TT--TTEEEEEEECE-S-TC CS
                 Peptidase_S15 120 atgvpalkaivpeaaisdly 139
                                   + ++    a+++e +is+l+
  gi|70607412|ref|YP_256282.1| 452 T-QTNVFSAAISERGISNLV 470
                                   8.999999999999999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
                                   HHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-.E CS
                 Peptidase_S15 223 dadkvkapvllvgGwnDwnvk.ngaiklyealkapgv.k 259
                                    +++vk+p++l++G  D     +++ +++ alk +gv  
  gi|70607412|ref|YP_256282.1| 509 YVKNVKTPTMLIHGEEDYRCPiEQSEQFFIALKMNGVdT 547
                                   569**************99999***********999853 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.5e-06    0.0063       3      95 ..     354     452 ..     352     463 .. 0.76
   2 !   11.7   0.0   6.2e-05      0.11     188     232 ..     511     557 ..     507     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.5e-06
                   Hydrolase_4   3 pkavvvlvHGlaehsgryael..aeaLaaqGfavyalDhrG.hGrse..gkrghvpsf.ddyvdDlaafvekvkeehpel. 76 
                                   +  +++++HG   ++  ya +  ++++a++G++v+  + rG +G  e   k + v ++  + ++Dl  fve+vk++++ + 
  gi|70607412|ref|YP_256282.1| 354 NNPTILFIHGGPHTAYGYAYFieFQYFARNGYNVIYSNPRGsQGYGEefAKAC-VGDWgGKDMNDLLLFVEEVKRKYNLKg 433
                                   56799***********9999733579************998545544534444.555525779***********8887778 PP

                   Hydrolase_4  77 plfllGhSmGGliallyll 95 
                                   ++ + G S GG+++  +++
  gi|70607412|ref|YP_256282.1| 434 KIGVTGGSYGGFMTNWLVT 452
                                   ***********98644443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.2e-05
                   Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyH 232
                                   +++++P++l+hGe+D  ++ e+s++++ +l+ +  d  l  y++  H
  gi|70607412|ref|YP_256282.1| 511 KNVKTPTMLIHGEEDYRCPIEQSEQFFIALKMNgvDTILVRYQQDSH 557
                                   6799***********************99988755555556666555 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.1e-08     2e-05      86     216 ..     422     582 ..     369     584 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.1e-08
                           DLH  86 vaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG...................................l 131
                                   v+ +k +    ++k+gv+G   GG ++  l ++ + + aa++  G                                   l
  gi|70607412|ref|YP_256282.1| 422 VEEVKRKY-NLKGKIGVTGGSYGGFMTNWLVTQTNVFSAAISERGisnlvsmcgtsdigfwfnavesgvtdpwteesqmkL 501
                                   44444443.45699**********9999999999899*****999*****************************9999998 PP

                           DLH 132 spekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervlel 212
                                   +  +++ +++++k+p + ++geeD   p ++ e++  alk ++vd  l+ Y++  H  a++ ++    +  +d  er le+
  gi|70607412|ref|YP_256282.1| 502 MRMSPIYYVKNVKTPTMLIHGEEDYRCPIEQSEQFFIALKMNGVDTILVRYQQDSHEHARRGKP----KNMRDRLERKLEW 578
                                   9999****************************************************99988876....5566777777777 PP

                           DLH 213 fkqv 216
                                   f ++
  gi|70607412|ref|YP_256282.1| 579 FDKY 582
                                   7766 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.8e-05     0.033     264     354 .]     135     222 ..     114     222 .. 0.85
   2 ?    2.0   0.0     0.038        69     256     305 ..     271     315 ..     257     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                   EEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEESS..SETTEBEEEEEESSCTTEEEESSTTTSEEEEEEE-TTSSE CS
                       DPPIV_N 264 lfdldgkseikqlTsGeweVtsilavdekrdlvyFtatk..dsPlerhlYsvslesggeltrltdeegdhysasfspsgky 342
                                   l+  + ++  +++ sG+++V   + v+ + ++++ +atk  d+ +   lY v++e +gel+r+t+ eg+   ++++++g++
  gi|70607412|ref|YP_256282.1| 135 LYLFSHGE-LRKVVSGDFDV---TDVATNGKRIIISATKegDDYGLGDLYEVDVE-TGELKRITKGEGTVVAVAMNEKGEV 210
                                   55555555.7899*******...678889999*******444478899*******.**********99999*******999 PP

                                   EEEEEESSSSSE CS
                       DPPIV_N 343 yvlkysgpdtpp 354
                                   + l +++ +tp+
  gi|70607412|ref|YP_256282.1| 211 AYLGHREGKTPW 222
                                   999999888887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.038
                                   TTSSEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEE.ESSSET CS
                       DPPIV_N 256 kdGfkHLylfdldgkseikqlTsGeweVtsilavdekrdlvyFt.atkdsP 305
                                   + G  HLyl++  +++   ++T G+  V    ++d k++++ +t +t ++P
  gi|70607412|ref|YP_256282.1| 271 EGGEAHLYLLSDGKSQ---KMTDGKIVV---RSFDYKEGKLVYTySTPEKP 315
                                   456889*999866655...9********...44565555555542555555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.1e-06    0.0091       1      81 [.     358     453 ..     358     562 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                                   EEEE--GC.....G.CHHHHHHHHCCTCEEEEE--T....TSTS-GGCS...--HHH..CHHHHHHHCCTT.....TTSEE CS
                 Abhydrolase_6   1 vlllHGagssassW.lvapLaallaagvhvlapDlp....GhGrsdppp...ldled..ladlaalldelaa...gggpvv 68 
                                   +l++HG++++a+++ ++ +++++++ g+ v+ ++ p    G+G  + +     d+      dl+ +++e++      g++ 
  gi|70607412|ref|YP_256282.1| 358 ILFIHGGPHTAYGYaYFIEFQYFARNGYNVI-YSNPrgsqGYG-EEFAKacvGDWGGkdMNDLLLFVEEVKRkynLKGKIG 436
                                   89********999954778899999997778.88877777778.333333445555533455577888887799999999* PP

                                   EEEETCHHH....HHHH CS
                 Abhydrolase_6  69 lvGHSlGGa....lala 81 
                                   + G S+GG+    l+++
  gi|70607412|ref|YP_256282.1| 437 VTGGSYGGFmtnwLVTQ 453
                                   ********955553333 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.033     104     188 ..     435     541 ..     407     557 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                          FSH1 104 dGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepk......................yeeyyeedkiqt 162
                                    G+ G S G+++++ l+++++      s+  +  ++ ++G +  +                        +++ y  ++++t
  gi|70607412|ref|YP_256282.1| 435 IGVTGGSYGGFMTNWLVTQTNVFSAAISERGISNLVSMCGTSDIGFWfnavesgvtdpwteesqmklmrMSPIYYVKNVKT 515
                                   599999************9999888777777777777777655222244444566666666666666554445548889** PP

                          FSH1 163 ptLhvlGelDtvvdeerseaLaeafk 188
                                   pt+ ++Ge+D   + e+se++  a k
  gi|70607412|ref|YP_256282.1| 516 PTMLIHGEEDYRCPIEQSEQFFIALK 541
                                   ************99999999876666 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.5   4.5e+03      12      22 ..     353     363 ..     349     383 .. 0.79
   2 ?   11.0   0.0   0.00015      0.27     154     202 ..     512     560 ..     500     568 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.5
                                   ---EEEEEE-- CS
                 Abhydrolase_2  12 kaqavviflHG 22 
                                   +++++++f+HG
  gi|70607412|ref|YP_256282.1| 353 ENNPTILFIHG 363
                                   56789*****9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00015
                                   GGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS-- CS
                 Abhydrolase_2 154 tkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsid 202
                                   ++k+p ++iHgeeD+  p+  ++++  +lk +  +  l+ y++ +H+  
  gi|70607412|ref|YP_256282.1| 512 NVKTPTMLIHGEEDYRCPIEQSEQFFIALKMNGVDTILVRYQQDSHEHA 560
                                   589**************************99999999*********976 PP

>> Op_neuropeptide  Opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0016         3       1       8 [.     442     449 ..     442     451 .. 0.93
   2 ?    1.3   0.1      0.17   3.1e+02       7      17 ..     492     502 ..     488     503 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
               Op_neuropeptide   1 YGGFMksW 8  
                                   YGGFM+ W
  gi|70607412|ref|YP_256282.1| 442 YGGFMTNW 449
                                   ******99 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.17
               Op_neuropeptide   7 sWdErsqkPLi 17 
                                   +W E+sq+ L+
  gi|70607412|ref|YP_256282.1| 492 PWTEESQMKLM 502
                                   9******9666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4066.76
//
Query:       gi|70607413|ref|YP_256283.1|  [L=176]
Description: hypothetical protein Saci_1680 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.14   12.1   0.0    1.2  1  TraI_2_C  Putative conjugal transfer nickase/helicase TraI C-


Domain annotation for each model (and alignments):
>> TraI_2_C  Putative conjugal transfer nickase/helicase TraI C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     8e-06      0.14      41     109 ..      23      93 ..       7     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-06
                                   THHHHHHHHHHHHHHHTT-TT-TTEEEEEEB--..HHHHHHHSS..TT---------EEEEEES-GGGT-- CS
                      TraI_2_C  41 giFkrYaqealakeedkekwkkvqkrfeklklh..rkkksglniwtcevtgarkssklkGyLledpsllfe 109
                                   g+F  Y+  ++++ ++ ++++++ ++f+   ++    ++++++i+   + + + +  ++G+L+ ++ +  +
  gi|70607413|ref|YP_256283.1|  23 GLFSAYYGINATQINQVKNIQQIASEFQVRLIEsqISNSETSFIVIPYIPNYKGTLYVSGFLISSQYVNSQ 93 
                                   5788888889******************98777556777788888888888899999******87766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1283.09
//
Query:       gi|70607414|ref|YP_256284.1|  [L=598]
Description: hypothetical protein Saci_1681 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4296.44
//
Query:       gi|70607415|ref|YP_256285.1|  [L=188]
Description: hypothetical protein Saci_1682 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1478.87
//
Query:       gi|70607416|ref|YP_256286.1|  [L=460]
Description: hypothetical protein Saci_1683 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.83    9.4   4.8         23    4.8   0.0    2.8  2  UPF0730   UPF0730 unknown protein family


Domain annotation for each model (and alignments):
>> UPF0730  UPF0730 unknown protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0013        23      20      38 ..     267     285 ..     260     297 .. 0.85
   2 ?    3.5   2.7    0.0032        58      19      31 ..     406     418 ..     393     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0013
                       UPF0730  20 YesenalYGvGYssshleq 38 
                                   Y  ++ lY v Ysss +++
  gi|70607416|ref|YP_256286.1| 267 YVKNSNLYVVSYSSSEPQK 285
                                   788999********99985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0032
                       UPF0730  19 PYesenalYGvGY 31 
                                    Y+sen lY +GY
  gi|70607416|ref|YP_256286.1| 406 IYNSENELYAIGY 418
                                   4************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3197.54
//
Query:       gi|70607417|ref|YP_256287.1|  [L=468]
Description: hypothetical protein Saci_1686 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.015   15.0   1.1      0.027   14.1   1.1    1.4  1  ITI_HC_C        Inter-alpha-trypsin inhibitor heavy chain C-t
       0.64    8.9   2.8       0.95    8.3   2.8    1.1  1  Phage_min_cap2  Phage minor capsid protein 2


Domain annotation for each model (and alignments):
>> ITI_HC_C  Inter-alpha-trypsin inhibitor heavy chain C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.1     3e-06     0.027      44     134 ..     240     329 ..     227     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-06
                      ITI_HC_C  44 ttekitlkdgekrlvlswsdtaslkkkglevsvskesnvtvtlkdsvkfvvllHrvkkkhplqvdyLgfYildskglSksv 124
                                   tt+ it++ ++k ++l  + +  +++ +l+++ +++ +++v++ ++v+ +v  H  ++  p       +Y+l+++  S+ +
  gi|70607417|ref|YP_256287.1| 240 TTQGITVTLQGKPVILIANYSQLVQSVNLSIKTNANFSIVVNI-NGVNYTVNNHALSATVPAGYVNFTVYTLQGNDTSSMS 319
                                   8999***999999999999999999988888888888888888.58********999998887777778************ PP

                      ITI_HC_C 125 hGllGqFlhe 134
                                   +G++ ++  +
  gi|70607417|ref|YP_256287.1| 320 SGIIKHYKFN 329
                                   ***9877554 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.8   0.00011      0.95     107     178 ..     166     245 ..     156     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00011
                Phage_min_cap2 107 ekseelqqlveaylkqtegelkNltnttal.......tslekaYerildeavakvvsGafsyqqAird.tvkklaekGvr 178
                                    +s++++ +  +++++++g+++N+t  + +       +  ++ Y  ++++ + kv++G+fs  q + + tv+  + +G++
  gi|70607417|ref|YP_256287.1| 166 YTSSQIYSTSINITTNINGKFSNYTTPITFpnqtgtfQVKAREYIYYINSKTGKVITGVFSNWQILGSaTVNSTTTQGIT 245
                                   567778888888999**********999999999996555678**********************976379999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2916.16
//
Query:       gi|70607418|ref|YP_256288.1|  [L=160]
Description: hypothetical protein Saci_1687 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1161.40
//
Query:       gi|70607419|ref|YP_256289.1|  [L=177]
Description: hypothetical protein Saci_1688 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-20   71.6  15.2      7e-20   71.4  15.2    1.0  1  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
        0.2   11.6   3.0        5.7    7.1   0.9    3.0  2  Melittin  Melittin
        2.7    7.8   7.3        3.5    7.4   7.3    1.2  1  VIT1      VIT family


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4  15.2   1.2e-23     7e-20       2     183 ..      13     170 ..      12     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.2e-23
                        DUF998   2 aaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavaglg 82 
                                   ++   +l+++++a +l+pgy++  ++iS+Lg   g ++ +fn+ + llg+lv++ ++++     +++   ++ l+ + g+g
  gi|70607419|ref|YP_256289.1|  13 IGTSQFLILMIVAEALYPGYSVKNNYISDLGV--GRTAVIFNVSVALLGVLVIVASILM-----RKVFSYASYLVLLNGIG 86 
                                   6677799*************************..**********************966.....899999999999***** PP

                        DUF998  83 lvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvalll.lvaalvwllaaaldgsl 162
                                   ++ +g+fp+++g         +H + ++ afl   +a++l +         + r + +++l +  +++l++ l + ++g+l
  gi|70607419|ref|YP_256289.1|  87 ALIVGLFPETTGL--------PHLIGALSAFLFGGLAAILTS---------IKRNYFWTVLGAiTLISLFLYLGK-MYGPL 149
                                   **********996........*********************.........333333333333033344444444.7888* PP

                        DUF998 163 llGlaerllvlaitawllala 183
                                   + G +erl+v+ +++w + l+
  gi|70607419|ref|YP_256289.1| 150 GNGGLERLIVYPELVWGISLG 170
                                   ****************98876 PP

>> Melittin  Melittin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.9   0.00095       5.7       1      17 [.      84     103 ..      84     107 .. 0.81
   2 ?    5.3   0.1    0.0036        21       2      22 ..     103     123 ..     103     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00095
                                   -HHHHHHHH...HTHHHHHH CS
                      Melittin   1 GiGAvLKvL...ttGLPALi 17 
                                   GiGA +  L   ttGLP Li
  gi|70607419|ref|YP_256289.1|  84 GIGALIVGLfpeTTGLPHLI 103
                                   788887776677*******9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHTHHHHHHHHHHH CS
                      Melittin   2 iGAvLKvLttGLPALisWiKR 22 
                                   iGA    L  GL A++  iKR
  gi|70607419|ref|YP_256289.1| 103 IGALSAFLFGGLAAILTSIKR 123
                                   89999999************9 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.3   0.00059       3.5     137     211 ..      47     120 ..      12     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00059
                          VIT1 137 aAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaay 211
                                    A++  +s ++ g++ +++ +++ +v     + +++ ++  l++G++    tg++ l++al+  l+G+lAa+++ 
  gi|70607419|ref|YP_256289.1|  47 TAVIFNVSVALLGVLVIVASILMRKVFSYASYLVLLNGIGALIVGLFPET-TGLPHLIGALSAFLFGGLAAILTS 120
                                   46666677777777777777777777777777777788888888888774.57*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1198.86
//
Query:       gi|70607420|ref|YP_256290.1|  [L=255]
Description: hypothetical protein Saci_1689 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1853.05
//
Query:       gi|70607421|ref|YP_256291.1|  [L=331]
Description: alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-25   88.0   1.8    4.7e-25   87.6   0.2    2.0  2  ADH_N          Alcohol dehydrogenase GroES-like domain
    3.9e-25   88.3   4.1    4.4e-25   88.2   0.2    2.6  3  ADH_zinc_N     Zinc-binding dehydrogenase
    4.5e-08   34.2   0.0    8.3e-08   33.4   0.0    1.5  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
     0.0077   16.0   0.1      0.011   15.5   0.1    1.3  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.077   13.0   0.1    2.1  3  SIS_2          SIS domain
      0.017   14.7   0.1      0.025   14.1   0.1    1.3  1  NmrA           NmrA-like family
      0.018   14.4   0.0      0.027   13.9   0.0    1.3  1  PALP           Pyridoxal-phosphate dependent enzyme
      0.073   12.4   0.1       0.13   11.6   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
        0.1   12.4   0.0       0.18   11.6   0.0    1.3  1  DFP            DNA / pantothenate metabolism flavoprotein
       0.13   12.4   0.1        2.6    8.2   0.0    2.3  2  Arteri_nsp7a   Arterivirus nonstructural protein 7 alpha


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.2   2.6e-28   4.7e-25       2     108 ..      27     131 ..      26     132 .. 0.97
   2 ?   -1.7   0.1       1.5   2.6e+03      44      59 ..     211     226 ..     201     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 2.6e-28
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-T CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCe 82 
                                   ++vlikvk ag++  D+ +++      ++ p i+G E++Gev++vg++v++++ GdrV+++  i +g+C+ C +g+e++C+
  gi|70607421|ref|YP_256291.1|  27 HDVLIKVKLAGVNPVDYYTIEA--LKVNPIPHIPGVEFAGEVVKVGEHVRSVRPGDRVTIYGRIFDGTCDMCMSGYETVCR 105
                                   89***************99997..8999***************************************************** PP

                                   TBEETTTSS-SSSBSEEEECGGGEEE CS
                         ADH_N  83 eakllgvsldGgfaeyvvvpekklvk 108
                                   +++ +gv+ +Ggfaey+ ++ek++++
  gi|70607421|ref|YP_256291.1| 106 SGGRVGVDANGGFAEYISLEEKYVFR 131
                                   *********************99976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                   EEESTT-CS--TT-EE CS
                         ADH_N  44 eevgpevkklkvGdrV 59 
                                    ev+++vk+++ G++ 
  gi|70607421|ref|YP_256291.1| 211 NEVEEKVKEVTNGKMA 226
                                   5778888888888753 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.38   6.8e+02      64      95 ..      61      92 ..      59     112 .. 0.78
   2 ?   -1.1   0.0      0.96   1.7e+03      79      92 ..     160     173 ..     157     175 .. 0.83
   3 !   88.2   0.2   2.4e-28   4.4e-25       3     129 ..     176     295 ..     174     296 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.38
                                  ESSCSHHHHHHHHHCEEEEEEEEECSCTSSEE CS
                    ADH_zinc_N 64 ecvGsgatleaalkllkpgGrlvvvGggkgee 95
                                  e++G    + + +++++pg r++++G  ++++
  gi|70607421|ref|YP_256291.1| 61 EFAGEVVKVGEHVRSVRPGDRVTIYGRIFDGT 92
                                  56666677778899999999999999866655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.96
                                   EEEEEEEEECSCTS CS
                    ADH_zinc_N  79 lkpgGrlvvvGggk 92 
                                   l+pg ++vv+G+++
  gi|70607421|ref|YP_256291.1| 160 LRPGETVVVFGASG 173
                                   89*********854 PP

  == domain 3  score: 88.2 bits;  conditional E-value: 2.4e-28
                                   HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEE CS
                    ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgG 83 
                                   G++ vqlAk +Ga+v+av++++     +k++Gad v++y + +++e++ke t+g+ +dvv++ +G ++ +e +++++  +G
  gi|70607421|ref|YP_256291.1| 176 GIFIVQLAKKFGAKVVAVSRKKW----LKDFGADLVVDY-N-EVEEKVKEVTNGKMADVVVNSLG-EKFWEKSFSVVGIRG 249
                                   9*******************997....************.5.5**********************.*************** PP

                                   EEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                    ADH_zinc_N  84 rlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                   +lv++G+ ++ e +++l++l  k++silG+++g+ r++f e+l+l++
  gi|70607421|ref|YP_256291.1| 250 KLVTFGTlLGAEVKVNLSQLYSKHISILGVNRGN-RKDFVELLELCK 295
                                   *******8777788********************.*******99975 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   4.6e-11   8.3e-08       2     129 ..     203     324 ..     202     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4.6e-11
                                   T-SEEEETT.STTHH.HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG CS
                  ADH_zinc_N_2   2 GAdevidyr.tedfe.aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfs 80 
                                   GAd v+dy   e+ + ++t+g+  Dvv++++g + + e+s++v+  +G+lv+ g   l  a  k+++     s +++ l  
  gi|70607421|ref|YP_256291.1| 203 GADLVVDYNeVEEKVkEVTNGKMADVVVNSLGEKFW-EKSFSVVGIRGKLVTFGT--LLGAEVKVNL-SQLYSKHISILG- 278
                                   9*******97444446****************7755.*******555*****996..3444444444.556888888888. PP

                                   ...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SS CS
                  ADH_zinc_N_2  81 mkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarG 129
                                   +++++++d + el++l+++ k+++   + f+l++ +eA++ l +    G
  gi|70607421|ref|YP_256291.1| 279 VNRGNRKD-FVELLELCKDCKVKTW--KIFDLKDGVEAVKSLFNEDRDG 324
                                   77776888.**********999876..5799999999998886666655 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.2e-06     0.011      22      64 ..     155     196 ..     140     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.2e-06
                                   HHHTTTS-STTEEEEEE--.SHHHHHHHHHHHHCT-EEEEEEES CS
                 ELFV_dehydrog  22 lkklkldslegkrvaisGs.GnvgsyaallltelgakvvavsDs 64 
                                   lk+++l+   g++v++ G  Gn g + ++l+++ gakvvavs +
  gi|70607421|ref|YP_256291.1| 155 LKEANLR--PGETVVVFGAsGNTGIFIVQLAKKFGAKVVAVSRK 196
                                   3333333..58899999999*********************965 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.5   2.6e+03     102     118 ..      25      41 ..      19      50 .. 0.80
   2 ?   13.0   0.1   4.3e-05     0.077      96     136 ..     155     193 ..     142     194 .. 0.89
   3 ?   -3.4   0.0       4.9   8.8e+03     108     132 ..     276     300 ..     264     301 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.5
                                   -TT-EEEEE-SS--SHH CS
                         SIS_2 102 kpgDvLlviSnsGnnav 118
                                    ++DvL+ +   G+n+v
  gi|70607421|ref|YP_256291.1|  25 GQHDVLIKVKLAGVNPV 41 
                                   689**********9987 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.3e-05
                                   HHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEE CS
                         SIS_2  96 lrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAl 136
                                   l++++l+pg++ +v+ +sGn  + +  ++ ak+ g+kv+A+
  gi|70607421|ref|YP_256291.1| 155 LKEANLRPGETVVVFGASGNTGIFI--VQLAKKFGAKVVAV 193
                                   677899**************99776..899**********8 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.9
                                   EEE-SS--SHHHHHHHHHHHHHT-E CS
                         SIS_2 108 lviSnsGnnavvveaaeaakergmk 132
                                   +   n Gn +  ve++e +k++ +k
  gi|70607421|ref|YP_256291.1| 276 ILGVNRGNRKDFVELLELCKDCKVK 300
                                   5556778888888888888887666 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.4e-05     0.025       1      48 [.     166     207 ..     166     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE CS
                          NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv 48 
                                   ++v+Ga+G+ G ++v+ + k g kv a+ R+        lk+ G+ lv
  gi|70607421|ref|YP_256291.1| 166 VVVFGASGNTGIFIVQLAKKFGAKVVAVSRKK------WLKDFGADLV 207
                                   78**************************9986......3444444444 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.027      42     121 ..     151     220 ..     140     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHH CS
                          PALP  42 aeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvevggdydeavaaaael 121
                                   a++ l+++    g ++vv + sGN+g+ +   a+++G kv+ v         ++ l+ +Ga++v+    y+e +++++e+
  gi|70607421|ref|YP_256291.1| 151 AYHSLKEANLRPGETVVVFGASGNTGIFIVQLAKKFGAKVVAVSR-------KKWLKDFGADLVVD---YNEVEEKVKEV 220
                                   5566666333333555555666***************99998744.......44456666666665...55555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.1e-05      0.13      36      90 ..     163     218 ..     150     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                                   TSEEEEES-.SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHH CS
                  2-Hacid_dh_C  36 gktvGiiGl.GrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleella 90 
                                   g+tv ++G+ G+ G  + +++k+fg+kv+a++r+k  ++  ++l v++ ++ee ++
  gi|70607421|ref|YP_256291.1| 163 GETVVVFGAsGNTGIFIVQLAKKFGAKVVAVSRKKWLKDFGADLVVDYNEVEEKVK 218
                                   78999999669***********************8876655555666666666554 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.18      27      87 ..     171     230 ..     169     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   ---HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-E.EEE--SHHHHHHHHHHHHTT-SEEE CS
                           DFP  27 SSGkmGyalAeaaaarGaeVtlvsgpvsletpegve.vvkvesaeemleaveealkeadivi 87 
                                   +SG +G+ + + a + Ga+V  vs +  l++  g++ vv+++++ee  ++v++  k ad+v+
  gi|70607421|ref|YP_256291.1| 171 ASGNTGIFIVQLAKKFGAKVVAVSRKKWLKDF-GADlVVDYNEVEEKVKEVTNG-KMADVVV 230
                                   69************************888865.443266677777766666655.5568887 PP

>> Arteri_nsp7a  Arterivirus nonstructural protein 7 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.17   3.1e+02      76      95 ..      73      92 ..      68     106 .. 0.75
   2 ?    8.2   0.0    0.0015       2.6      64     100 ..     145     181 ..     139     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                  Arteri_nsp7a 76 skelkpGDvvvllGkkpvge 95
                                  +++++pGD+v + G+   g+
  gi|70607421|ref|YP_256291.1| 73 VRSVRPGDRVTIYGRIFDGT 92
                                  789*******9999865554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                  Arteri_nsp7a  64 alAkLedFaegvskelkpGDvvvllGkkpvgelvdik 100
                                   ++A L ++ + ++ +l+pG++vv++G++  + ++ ++
  gi|70607421|ref|YP_256291.1| 145 TVAGLTAYHSLKEANLRPGETVVVFGASGNTGIFIVQ 181
                                   67999999999***************98777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2207.18
//
Query:       gi|70607422|ref|YP_256292.1|  [L=312]
Description: microsomal dipeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-74  249.7   0.0    4.3e-74  249.5   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
    0.00033   20.5   0.1     0.0007   19.5   0.1    1.5  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity


Domain annotation for each model (and alignments):
>> Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   0.0   4.8e-78   4.3e-74       7     317 ..       2     306 ..       1     308 [. 0.95

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 4.8e-78
                                   .EEEEEE-HHHHHHHCTTTTT-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C.................CCCCCCHHHHHH CS
                 Peptidase_M19   7 iviDghndlplklrqekkeslllekdselqtdlerlraggvsavlfaifvpe.................dasyeeavkatl 70 
                                   +++D h+dl+++ +  ++ ++     +e++++  ++ ++  s+ + +if++                  ++ ++ +++  l
  gi|70607422|ref|YP_256292.1|   2 KIVDLHQDLAYSNQMGRDVIE-----EEQKQSSIKMLRNFDSLIFGSIFPHIdtlndkshklsnlygrpTRGTSFSFSLFL 77 
                                   79**********766666655.....777888889999***********55589***************999********* PP

                                   HHHHHHHHHHHHGTTTEEE-SSHHHHHHHHHTT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEES-SSS-BSSB-BCCG CS
                 Peptidase_M19  71 eqidlirrlvrknpeqlklvrtaddierakkegkiavllgiegaealgddlallrafyalGvrvlgltynrnnkfAdgale 151
                                   +q++ ++ l r  ++ ++lvr+ +d+e    +  i+vll++ega++l +d++ ++ +++l+v  lglt+n++nkfA+++++
  gi|70607422|ref|YP_256292.1|  78 DQVKFYYYLDR--RGYITLVRRKEDLE----KPGIKVLLSLEGADVL-RDYEDIYLLKELHVYNLGLTWNYDNKFASSCMS 151
                                   *****999998..4459**********....99**************.********************************* PP

                                   TT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TTSB-HHHHHHHHHTT-EEEE CS
                 Peptidase_M19 152 ekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpRNltDeqlkaiaesgGvvgv 232
                                   +  +d GL++ G+elV+ +N+lgi+iDl+h++++t+ldv+++Sk+P+++SH nar+l+dh+RNl+De+++ai++++Gv+gv
  gi|70607422|ref|YP_256292.1| 152 N--KDYGLTDEGEELVKTANSLGIIIDLAHAGKRTLLDVASISKRPIIVSHGNARKLKDHRRNLDDEEIEAIVKTNGVIGV 230
                                   9..****************************************************************************** PP

                                   -SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---TTTTSS-BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHHTHHH CS
                 Peptidase_M19 233 tfvpaflkekaeatledvvdhidyivelaGidhVGlGsDfdgggelpegledvsklpnltaeLlrrgyseadiekilggNf 313
                                   t++ ++l+   e+t++ +v+ i+yi e +G+++V++G+Df g++++peg+e+v kl++l + L      + + e++l++N+
  gi|70607422|ref|YP_256292.1| 231 TAIVETLR---EPTINGLVENIKYIGESFGWEYVAIGTDFLGIQKVPEGFENVMKLRELSDML------DGHSEEVLWKNA 302
                                   ***99996...5***************************************************......5677889***** PP

                                   HHHH CS
                 Peptidase_M19 314 lrvl 317
                                   +rv+
  gi|70607422|ref|YP_256292.1| 303 MRVI 306
                                   **97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   7.8e-08    0.0007      15      60 ..     178     221 ..     178     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.8e-08
                         RMMBL  15 gHadknellelirklkprnvilvHGeeeatsalarllkeeegidvf 60 
                                   +Ha+k+ ll++ +++++r++i+ HG  +++++++r l ++e+i+++
  gi|70607422|ref|YP_256292.1| 178 AHAGKRTLLDV-ASISKRPIIVSHGNARKLKDHRRNL-DDEEIEAI 221
                                   89999999997.56889********************.99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1916.60
//
Query:       gi|70607423|ref|YP_256293.1|  [L=93]
Description: hypothetical protein Saci_1692 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   50.5   0.0    2.8e-13   50.1   0.0    1.2  1  HMA       Heavy-metal-associated domain
  ------ inclusion threshold ------
       0.14   11.2   0.9       0.75    8.8   0.1    1.9  2  EcoRI     Restriction endonuclease EcoRI


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   3.1e-17   2.8e-13       1      58 [.      17      80 ..      17      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3.1e-17
                           HMA  1 tvrvsgmhCagCaakvekvLselpgV..esvkvdlatktvtVeg....daestklrkiieaiek 58
                                  +++v++++C++C+ k++++L++lp+V   +++ d+++++++V +    + ++ ++++i+++i++
  gi|70607423|ref|YP_256293.1| 17 RFQVFDVECGNCVYKIKRALATLPDVvdINITPDFDNSKAVVILrykgNLDKREIEEILKEISE 80
                                  599***********************999999***********999998898666777777776 PP

>> EcoRI  Restriction endonuclease EcoRI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1    0.0085        76      44      66 ..       3      30 ..       1      59 [. 0.61
   2 ?    8.8   0.1   8.3e-05      0.75      33      59 ..      54      80 ..      37      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.0085
                         EcoRI 44 eiskkeinealkki.....dkelGqtlf 66
                                  e +kkein++l+ +     d e G+ ++
  gi|70607423|ref|YP_256293.1|  3 EFNKKEINNELRVMrfqvfDVECGNCVY 30
                                  6789****99975421222555566555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 8.3e-05
                         EcoRI 33 efpqltfryrkeiskkeinealkkidk 59
                                    + + +ry+ +++k+ei+e lk+i +
  gi|70607423|ref|YP_256293.1| 54 SKAVVILRYKGNLDKREIEEILKEISE 80
                                  4556779****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 606.28
//
Query:       gi|70607424|ref|YP_256294.1|  [L=308]
Description: sodium/calcium exchanger protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-29  100.9  34.0      4e-16   59.3  13.7    2.1  2  Na_Ca_ex       Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3  13.7   2.2e-20     4e-16       3     149 ..       5     146 ..       3     148 .. 0.81
   2 !   47.7  12.4   8.3e-17   1.5e-12       5     149 ..     169     305 ..     166     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.2e-20
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHH CS
                      Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllvi 83 
                                   +v fi  ++++ ++a+++ + a+e+ +   + + + G +ll + + lpE+i  iia l+g+ d+a g+++G+ni+ ++++ 
  gi|70607424|ref|YP_256294.1|   5 WVEFIGTFIGLFISAELIAKGADELEE--VLGQGITGGILLGFITALPETIFVIIASLGGSLDVAFGSAIGGNILLFTVGA 83 
                                   6779999*******************9..9999************************************************ PP

                                   HHHHHHHH......BTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  84 Glialigs......lkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                   Gl++++        l        +d ++ +   +l++++v+l+l+ l    +l+v  g++l+l+Y+ y+++ 
  gi|70607424|ref|YP_256294.1|  84 GLVGIVYFwkwknnL-------VMDQEYQVENKFLIISTVALVLITLY--SKLNVIAGVCLILIYVYYVIYR 146
                                   ******664444332.......33333333333333333333332222..9******************986 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 8.3e-17
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTT..HHHHHHHHHHHHHHHHHTHH CS
                      Na_Ca_ex   5 lfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltge..vdlaignvlGsnifnlllvi 83 
                                   +++++ +l+++l++++v+ +++i+ s+gi+   ++l+l ++++ l E is++  +   +  ++l++ + +Gs i n ++ +
  gi|70607424|ref|YP_256294.1| 169 FMVVGAILLIILSHYFVEQLDQISLSFGIPAVWISLVLSPIAGELEEKISAFRLITLSKkgGSLSLLSFVGSKIENNTVLL 249
                                   689999*********************************************9887743335******************** PP

                                   HHHHHHHHBTTSSCECCHHH.HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  84 Glialigslkvdseslkldl.gllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                                   G+i+l+g          ++l +++  ++ l+l+ v++l +++  +++ltvle+ +l+++Ya++++ +
  gi|70607424|ref|YP_256294.1| 250 GIIGLFGD---------YSLrPVIPEMVSLILVNVSVLRVLF--DRKLTVLESSLLIIAYAVIIIAL 305
                                   ******44.........4554555555555556566655443..6*****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2367.47
//
Query:       gi|70607425|ref|YP_256295.1|  [L=413]
Description: kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-39  135.7   0.1    2.6e-39  135.2   0.1    1.1  1  Pkinase      Protein kinase domain
    6.5e-20   71.5   0.0    4.8e-19   68.7   0.0    2.3  1  Pkinase_Tyr  Protein tyrosine kinase
    4.4e-06   26.2   0.0    6.3e-05   22.4   0.0    2.0  2  Kinase-like  Kinase-like
  ------ inclusion threshold ------
      0.012   15.0   0.0       0.02   14.3   0.0    1.3  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   0.1   5.8e-43   2.6e-39       1     259 [.     109     400 ..     109     402 .. 0.85

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 5.8e-43
                                   EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.......HHHHHHHHHHHHHSCTTB--EEEEEEE..... CS
                       Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.......kkvlrEikilkklkhpnivrlyevfee..... 69 
                                   y+  + lG+G+ G V+ a  +++ ++ AvK+ + e++++ ++        ++++ i+ + kl+hp+++++y+v  +     
  gi|70607425|ref|YP_256295.1| 109 YKISKILGSGGAGYVMLAE-DKQANKLAVKIYRLESENQGETalfrdsmIELANNINKISKLDHPKLIKFYDVNVNlevik 188
                                   678999************9.5788899*********99999999998888899999************************* PP

                                   ...........SSEEEEEEE--TTEBHHHHHHHHSS--HH....HHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TT CS
                       Pkinase  70 ...........kdelylvleyveggeladllerkgslsee....eakkiakqilegleylHskgiiHrDlKpeNiLid.ek 134
                                              kd  y+ +ey+ +g+++dll r+  + +      + +i+ q+++gl ylHs+g +H D+Kp+Ni+i+  k
  gi|70607425|ref|YP_256295.1| 189 syfkgitylylKDPPYVAMEYMGNGTVKDLLLRDEYFYSVrwkkLVYRIIFQVARGLLYLHSEGYVHLDVKPSNIFIEsVK 269
                                   *******************************9877766651222444677899*************************666 PP

                                   TE...EEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHH....TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHH CS
                       Pkinase 135 ge...lKitDFGlakelessskltsfvgtseYlAPEvl....keneyskkvDvWslGvilyelltgkppfsgekgkekvek 208
                                   g+   +K++D++  k++ +s       +t+eY +PE l    ++++  +++D++slG+++yellt+k   ++   +   + 
  gi|70607425|ref|YP_256295.1| 270 GDdirVKLGDLDSMKRVGQSI----LEITPEYAPPEQLqahyTKEGARPTMDIFSLGITFYELLTRKKRQPNYLVSALEAL 346
                                   66899*************977....99***********776555777899***************9988775555554444 PP

                                   HHHTHHHHHHHCT...SHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHH CS
                       Pkinase 209 eldqlekilkilg...etkeklpeaseiseeakdllkkllkkdpkkRltaeell 259
                                      ++ +  k+++    +  +++ +s  ++++kdl++++++ dpk+R+ta+e++
  gi|70607425|ref|YP_256295.1| 347 SKGNHDEAKKLINddiIYLSTWNIDSIDDDKIKDLIQRMVSPDPKSRPTAKEIV 400
                                   44445566666665544455666666669**********************997 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   1.1e-22   4.8e-19       2     259 .]     110     403 ..     109     403 .. 0.74

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.1e-22
                                   EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH........HHHHHHHHHHHHTS-BTTB--EEEEEE... CS
                   Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee........keelleeakimkklkhpnivkllgvct... 71 
                                   +++k lG+G  G V+ ++ k     +  k avK+ + e++++         + el ++++ ++kl+hp+++k++ v +   
  gi|70607425|ref|YP_256295.1| 110 KISKILGSGGAGYVMLAEDK-----QANKLAVKIYRLESENQGetalfrdsMIELANNINKISKLDHPKLIKFYDVNVnle 185
                                   57899**********99988.....6677777777544444331123311144555678889999*********9987555 PP

                                   .............SSSSEEEEEE--TTEBHHHHHHHT.CTTTSBHHHHH.HHHHHHHHHHHHHHHTTEEEST-SGGGEEEE CS
                   Pkinase_Tyr  72 .............keepllivteyvkgGdLlkfLrkk.ekekltlkdll.sfalqvAkGmeyLeskklvHrdlaarNvLls 137
                                                 ++p ++ +ey+ +G++++ L ++    +++ k+l+ ++++qvA+G+ yL+s+ +vH d+   N++++
  gi|70607425|ref|YP_256295.1| 186 viksyfkgitylyLKDPPYVAMEYMGNGTVKDLLLRDeYFYSVRWKKLVyRIIFQVARGLLYLHSEGYVHLDVKPSNIFIE 266
                                   554444444444445559**************876651556777777653799**************************** PP

                                   E....TTEEEE-STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSE....EEHHHHHHHHHHHHHHHHTTSSGT..... CS
                   Pkinase_Tyr 138 e....nkvvkisDfGLardiekddeyvkkeeaklpvkWmapEslkekk....ftsksDvWsfGvllwEiftlgesp..... 205
                                   +    +  vk++D   ++++        ++  ++  ++ +pE l+++          D++s G++ +E++t  ++      
  gi|70607425|ref|YP_256295.1| 267 SvkgdDIRVKLGDLDSMKRV-------GQSILEITPEYAPPEQLQAHYtkegARPTMDIFSLGITFYELLTRKKRQpnylv 340
                                   87776779999998777766.......667788999********9988445556678**************8875558888 PP

                                   .....TTTSHHHHHHHHHHTT....EES-BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHHHH CS
                   Pkinase_Tyr 206 .....ypglkneevleklkeg....krlekpekcpeelyelmkkcweedpeeRptfselvekl 259
                                        +++ ++ e+ + ++++       +  +   +++++l+++  + dp++Rpt +e+v +l
  gi|70607425|ref|YP_256295.1| 341 saleaLSKGNHDEAKKLINDDiiylSTWNIDSIDDDKIKDLIQRMVSPDPKSRPTAKEIVYEL 403
                                   8887744444444555554441111445566667899*********************98765 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.033   1.5e+02      14      54 ..     109     148 ..     102     183 .. 0.81
   2 !   22.4   0.0   1.4e-08   6.3e-05     151     244 ..     239     329 ..     212     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.033
                   Kinase-like  14 lvrgellkkgdrsvvfevkdqetgeplavkvfllpseaskk 54 
                                   ++  ++l+ g+ + v++++d++  ++lavk+  l+se+  +
  gi|70607425|ref|YP_256295.1| 109 YKISKILGSGGAGYVMLAEDKQ-ANKLAVKIYRLESENQGE 148
                                   567899**************99.899*****9999987654 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.4e-08
                   Kinase-like 151 lqlirlaanLqakglvhgkftvdnlllde....kgglmlggftaLvragtkvvlsevekgfaPpEllgsrggytrknktkm 227
                                    q+ r   +L+++g vh ++++ n++ +     + +++lg+++++ r+g++    e+   +aPpE l +   yt+ + ++ 
  gi|70607425|ref|YP_256295.1| 239 FQVARGLLYLHSEGYVHLDVKPSNIFIESvkgdDIRVKLGDLDSMKRVGQSIL--EITPEYAPPEQLQA--HYTK-EGARP 314
                                   577888889*****************9853222678***************99..9999******9988..5655.55555 PP

                   Kinase-like 228 thkldaWqlGlviyriw 244
                                   t  +d   lG++ y + 
  gi|70607425|ref|YP_256295.1| 315 T--MDIFSLGITFYELL 329
                                   5..89999**9999875 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.4e-06      0.02     122     168 ..     236     282 ..     217     288 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-06
                           Kdo 122 allkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldk 168
                                   +++ +v+r    lh+ g  H d+ + ni+++  +++++++ l Dld 
  gi|70607425|ref|YP_256295.1| 236 RIIFQVARGLLYLHSEGYVHLDVKPSNIFIESVKGDDIRVKLGDLDS 282
                                   677899***************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2577.71
//
Query:       gi|70607426|ref|YP_256296.1|  [L=376]
Description: hypothetical protein Saci_1697 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-29  102.1  47.8    1.2e-20   73.8  19.6    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8  19.6   6.5e-25   1.2e-20      14     224 ..      19     211 ..       6     222 .. 0.80
   2 !   30.8  25.9   7.5e-12   1.4e-07       3     165 ..     198     361 ..     196     375 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 6.5e-25
                         MFS_1  14 i...lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllv 90 
                                   +    + al ++l + l+ s  +++l +tl++++++ +++++G+++d+ G+r++ +++++l+alg +l++ f++++++++v
  gi|70607426|ref|YP_256296.1|  19 LyqySWNALEPLLEKGLTQSIIQLSLGFTLFSFFSSMFQPLGGHFADKQGPRKIGVISAILSALG-FLGTyFSPNIYVFYV 98 
                                   2233455555588888999999*******************************************.66665989999**** PP

                         MFS_1  91 lrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv.lfll 170
                                   ++ l ++g+g+l+ ++a l+ +wf++ + ++a+g++s+gf++G++++ ++ +l+    ++  v + +++v ++++  l  l
  gi|70607426|ref|YP_256296.1|  99 FWTLGSIGEGILYGIAANLAMKWFTD-KMAFATGIVSMGFGIGSAVANPFISLVG---NYKTVTLTIGLVEIVLLPiL--L 173
                                   **************************.***********************99999...9999*999999999996623..8 PP

                         MFS_1 171 llpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfs 224
                                   ++ e p++ k ++p+e                +   + +w++ i+++++++++s
  gi|70607426|ref|YP_256296.1| 174 WISEYPKTLKGQPPRET---------------IIDMR-FWLIYISFIGATAVLS 211
                                   88888888888888777...............33333.5644455554444444 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 7.5e-12
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                   l+++  + a ++l+++ +++     g+ ++e+ +l+++  l+++ + +++G+++dr+G  r+ ll  +++ +g+++llf +
  gi|70607426|ref|YP_256296.1| 198 LIYISFIGATAVLSVLSSQLSVLGKGLPKQELITLVSILPLLSGGLRPIFGYVGDRIGLVRTALLLNVVLTFGAFMLLF-N 277
                                   4555555555555555555444555799*********************************999999999999788887.7 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wravfyila 158
                                   +   l+++ +l G+++g+++++   +  ++f  +  +   g+l++g ++G +lg  + +l++  +g      +  +  +++
  gi|70607426|ref|YP_256296.1| 278 Q---LALSTILVGFAGGSIITLYFNISGEIFGTKFSTVNSGILYTGKAIGGVLGSSVFALVY-TIGliaseiYVIILGLVG 354
                                   8...**************************************************99999999.555343222222222233 PP

                         MFS_1 159 ivsllaf 165
                                   ++sll++
  gi|70607426|ref|YP_256296.1| 355 VFSLLSV 361
                                   3333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2346.95
//
Query:       gi|70607427|ref|YP_256297.1|  [L=238]
Description: hypothetical protein Saci_1698 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   50.8  36.8    1.4e-13   50.8  36.8    1.8  2  ABC2_membrane    ABC-2 type transporter
    8.3e-06   25.1  37.2    8.3e-06   25.1  37.2    2.2  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        2.2    8.1   6.1          1    9.2   1.3    2.7  2  Phage_holin_2_3  Bacteriophage holin family HP1


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8  36.8   2.3e-17   1.4e-13      10     202 ..      12     199 ..       3     207 .. 0.89
   2 ?   -2.1   3.2      0.34   2.1e+03     115     147 ..     204     233 ..     197     235 .. 0.53

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.3e-17
                 ABC2_membrane  10 eflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvspl 90 
                                   +f+ ++     ++++++++pl +++ fgt++ +   + + + + g + f++  ++++++++  +  er  g +  + +s++
  gi|70607427|ref|YP_256297.1|  12 QFKMIKAYLPVFIFFSILFPLGFIFSFGTIIQR---TLSTYLISGSITFFISINSIISVAQN-LALERSSGRFSLMIASGI 88 
                                   555555555566789999*************95...33444569999999999998888888.9***************** PP

                 ABC2_membrane  91 yslsayvlakvlvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllisalapsfedasqlaslvllp 171
                                    +   y+++ ++++ + +l+++ +fl++ yfl+g+++s+ ++f+l ++ ++ +as +glli++  ++++ ++q +s++ ++
  gi|70607427|ref|YP_256297.1|  89 -PIQLYAISITISNGIQTLMLIPVFLVLGYFLLGVRISSALFFVLSIIGSIYMASMVGLLIGTAIRNLHAVNQWSSIIGFI 168
                                   .************************************977999************************************** PP

                 ABC2_membrane 172 llllsGffipidsmpkwlqwiaylnPltyav 202
                                   l +++++++p++++p  ++++ayl P ty+ 
  gi|70607427|ref|YP_256297.1| 169 LSFFAPVYFPLTQIPLPFRYLAYLEPTTYVS 199
                                   **************999************85 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.34
                 ABC2_membrane 115 fllivyflvgldlsrfflflllllltalaassl 147
                                   f l+  ++ +l +  f+  +++ +l+++++s l
  gi|70607427|ref|YP_256297.1| 204 FALVGNPI-SLAW--FGGTVVIGFLFSFLSSLL 233
                                   33333333.5555..666666666666666554 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   5.3      0.13   7.9e+02       2      23 ..      22      43 ..      21      48 .. 0.86
   2 !   25.1  37.2   1.4e-09   8.3e-06     160     343 ..      48     227 ..      43     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.13
               ABC2_membrane_3  2 sfliitlllPiilvlllglifs 23
                                   f+++++l+P+ +++ +g+i++
  gi|70607427|ref|YP_256297.1| 22 VFIFFSILFPLGFIFSFGTIIQ 43
                                  5999**************9986 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.4e-09
               ABC2_membrane_3 160 asflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyl..lqlllill.lafglgipfgn 237
                                   ++ + g i +++++ +++++a++++ E++s+   l++ sg+    y +s  ++ ++  l  ++++l+l+ +++g  + +++
  gi|70607427|ref|YP_256297.1|  48 TYLISGSITFFISINSIISVAQNLALERSSGRFSLMIASGIPIQLYAISITISNGIQTLmlIPVFLVLGyFLLG--VRISS 126
                                   455666999999*****************************999999999998887655116666655546999..99999 PP

               ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlit 318
                                    ++++l ++  + +++++g+l++++++n  ++++  +i+ ++ls+f  + fpl ++p ++++++++ P+++++++ +  + 
  gi|70607427|ref|YP_256297.1| 127 ALFFVLSIIGSIYMASMVGLLIGTAIRNLHAVNQWSSIIGFILSFFAPVYFPLTQIPLPFRYLAYLEPTTYVSQSTYFALV 207
                                   99999999999******************************99998888899***************************** PP

               ABC2_membrane_3 319 gdplweillsliilalfavvyllla 343
                                   g+p+     sl++  +++v+ +l++
  gi|70607427|ref|YP_256297.1| 208 GNPI-----SLAWFGGTVVIGFLFS 227
                                   9944.....4444444444444443 PP

>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3   0.00017         1       9      37 ..     139     172 ..     135     176 .. 0.83
   2 ?   -0.6   0.2       0.2   1.2e+03      15      37 ..     219     229 ..     200     234 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
               Phage_holin_2_3   9 YisSavavvlG.....llsLseWAiviGIicgvv 37 
                                   Y++S v +++G     l   ++W ++iG i++++
  gi|70607427|ref|YP_256297.1| 139 YMASMVGLLIGtairnLHAVNQWSSIIGFILSFF 172
                                   99999999999876654489**********9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
               Phage_holin_2_3  15 avvlGllsLseWAiviGIicgvv 37 
                                   +vv+G             +++++
  gi|70607427|ref|YP_256297.1| 219 TVVIG------------FLFSFL 229
                                   45555............444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1500.52
//
Query:       gi|70607428|ref|YP_256298.1|  [L=283]
Description: ABC transporter ATP binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-31  109.7   0.0    2.7e-31  108.9   0.0    1.4  1  ABC_tran      ABC transporter
    3.8e-15   56.5   0.3    1.5e-10   41.4   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.1e-07   31.0   0.0     0.0016   18.3   0.0    2.3  2  AAA_15        AAA ATPase domain
    5.7e-05   23.6   0.0    0.00015   22.2   0.0    1.7  2  AAA_16        AAA ATPase domain
    5.8e-05   22.6   0.1       0.24   10.8   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00028   20.9   0.2    0.00083   19.3   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
    0.00092   19.5   0.4     0.0048   17.2   0.3    2.2  1  AAA_22        AAA domain
     0.0012   19.3   0.2     0.0093   16.5   0.1    2.4  2  AAA_18        AAA domain
     0.0013   18.5   0.2      0.075   12.8   0.0    2.2  2  AAA_24        AAA domain
     0.0015   18.5   0.1     0.0068   16.4   0.1    2.3  1  AAA_14        AAA domain
     0.0017   18.1   0.1        1.6    8.5   0.0    2.9  2  IstB_IS21     IstB-like ATP binding protein
     0.0017   18.7   0.1      0.005   17.3   0.1    2.1  1  AAA           ATPase family associated with various cellular 
     0.0021   18.2   0.0     0.0048   17.1   0.0    1.8  1  AAA_33        AAA domain
     0.0023   17.9   0.0     0.0067   16.4   0.0    1.7  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
     0.0031   18.2   0.0      0.011   16.4   0.0    2.0  1  DUF4162       Domain of unknown function (DUF4162)
     0.0031   17.2   0.0     0.0076   16.0   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0039   17.7   1.5     0.0085   16.6   1.5    1.9  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.011   15.0   0.1      0.054   12.7   0.0    2.1  2  NB-ARC        NB-ARC domain
      0.021   14.8   0.1      0.052   13.5   0.0    1.7  2  NACHT         NACHT domain
      0.022   14.5   0.0      0.035   13.8   0.0    1.5  1  AAA_30        AAA domain
      0.024   14.2   0.0       0.14   11.8   0.0    2.1  2  AAA_25        AAA domain
      0.027   14.7   0.0       0.13   12.5   0.0    2.1  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.028   14.3   0.6       0.36   10.7   0.1    2.5  3  NTPase_1      NTPase
      0.032   13.7   0.0      0.055   13.0   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
      0.044   13.7   1.0       0.16   11.9   0.0    2.2  2  ATPase_2      ATPase domain predominantly from Archaea
      0.067   13.1   0.0       0.16   11.9   0.0    1.6  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.069   12.7   0.0       0.15   11.6   0.0    1.5  1  AAA_27        AAA domain
      0.071   13.1   0.2       0.13   12.2   0.2    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
      0.073   11.9   0.0       0.11   11.4   0.0    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
      0.077   13.2   0.0       0.18   12.1   0.0    1.6  1  AAA_28        AAA domain
      0.097   12.3   0.0        0.2   11.2   0.0    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.15   11.5   0.0       0.25   10.8   0.0    1.4  1  PhoH          PhoH-like protein
       0.17   12.3   0.0       0.42   11.0   0.0    1.7  1  RNA_helicase  RNA helicase
       0.19   11.3   0.1       0.31   10.6   0.1    1.3  1  SRP54         SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0     5e-34   2.7e-31       2     136 ..      25     165 ..      24     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 5e-34
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   +n+s++++ege+va++G+nGaGK+tL+k l+g+l+p++Gei++ g + ++   +  +k++gv+pqe +   +ltv +n   
  gi|70607428|ref|YP_256298.1|  25 ENISMNIEEGEIVALLGPNGAGKTTLVKQLYGELNPNKGEIRVLGSKPTD---RGIKKHMGVVPQECEPYGDLTVWDNiyy 102
                                   69******************************************988888...899************************* PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              ++e+ +++l++l+l+++ +t     ++ LSgG k+r+ + +al+++pkl++lDEpt
  gi|70607428|ref|YP_256298.1| 103 marikgvdkeRAKERTKELLEQLELSDKGKTL----GRDLSGGLKRRLLISMALVNDPKLIILDEPT 165
                                   ******999888888************55555....5*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00011     0.055       1      19 [.      36      54 ..      36      76 .. 0.85
   2 !   41.4   0.0   2.9e-13   1.5e-10     201     298 ..     103     196 ..      98     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                        AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                  + +l GpNg+GK++L + l
  gi|70607428|ref|YP_256298.1| 36 IVALLGPNGAGKTTLVKQL 54
                                  5789***********8866 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 2.9e-13
                        AAA_21 201 dlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllel 281
                                   + +++ ++ ++++er +e  + +le +d +++  r+lS G kr l +  al  ++   +l+++DEp +gL+P++ r+++++
  gi|70607428|ref|YP_256298.1| 103 MARIKGVDKERAKERTKE-LLEQLELSDKGKTLGRDLSGGLKRRLLISMALVNDP---KLIILDEPTTGLDPQARREVWDI 179
                                   566666777777777777.999999999999999**********66666666655...8********************** PP

                        AAA_21 282 lkelsrngaQviltTHS 298
                                   l +l+++g  ++ltTH 
  gi|70607428|ref|YP_256298.1| 180 LLKLKKEGKSILLTTHY 196
                                   *777777*********6 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00093      0.49      16      44 ..      26      55 ..      21      62 .. 0.86
   2 !   18.3   0.0     3e-06    0.0016     280     364 ..     121     195 ..      98     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00093
                        AAA_15 16 dveidlsee.ltvliGkNnsGKSsileald 44
                                  +++++++e  +  l G+N++GK+++++ l+
  gi|70607428|ref|YP_256298.1| 26 NISMNIEEGeIVALLGPNGAGKTTLVKQLY 55
                                  677888887899*************99886 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3e-06
                        AAA_15 280 kneeieikddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360
                                     e+ e++d+ ++   + + G++r ll+++ +++         ++++++++EP + L pqa +++++ l++l +++k  ++
  gi|70607428|ref|YP_256298.1| 121 LLEQLELSDKGKTLGRDLSGGLKRRLLISMALVN---------DPKLIILDEPTTGLDPQARREVWDILLKLKKEGK-SIL 191
                                   3444444477788888888899999999887764.........4677*****************************9.9** PP

                        AAA_15 361 itTH 364
                                   +tTH
  gi|70607428|ref|YP_256298.1| 192 LTTH 195
                                   **** PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.8e-07   0.00015      23     142 ..      33     162 ..      25     193 .. 0.56
   2 ?   -2.3   0.0       9.5     5e+03      36      59 ..     187     213 ..     186     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.8e-07
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekd..................ggiflrgkcdqlesaipy..salaqalareellr 83 
                                   ++e+v l G+ G GK++lv++l+ +l+ +                  ++ ++ ++c+       y  +++++ +    +++
  gi|70607428|ref|YP_256298.1|  33 EGEIVALLGPNGAGKTTLVKQLYGELNPNkgeirvlgskptdrgikkHMGVVPQECEP------YgdLTVWDNIY---YMA 104
                                   559************************9987555555555555444444444444444......33223455552...333 PP

                        AAA_16  84 qlldeaesaeleawrekleealaavpelagaea...srllellkrll.allsrderplvlvlD 142
                                    ++  +++  + +  ++l+e+l+    l+++++   ++l   lkr l   ++   +p +++lD
  gi|70607428|ref|YP_256298.1| 105 RIKGVDKE-RAKERTKELLEQLE----LSDKGKtlgRDLSGGLKRRLlISMALVNDPKLIILD 162
                                   33333222.33333333444444....333333344555555555555444444555556665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.5
                        AAA_16  36 GKsslv.rellralekd..ggiflrgk 59 
                                   GKs l+ ++ l+++e+   +++f++ k
  gi|70607428|ref|YP_256298.1| 187 GKSILLtTHYLEEAERLanRIYFIYRK 213
                                   888888666666555545557777665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00097      0.51      15      43 ..      24      53 ..      17      67 .. 0.80
   2 !   10.8   0.0   0.00045      0.24     119     205 ..     114     200 ..      99     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00097
                                  CEEEEEETTS.SEEEEEESTTSSHHHHHHH CS
                                  xxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                         SMC_N 15 gktvilpfsk.sftaivGpNGSGKsnlldA 43
                                  ++++++++++ ++ a++GpNG+GK+ l+  
  gi|70607428|ref|YP_256298.1| 24 NENISMNIEEgEIVALLGPNGAGKTTLVKQ 53
                                  566666666525889**********99875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00045
                                   -HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE CS
                                   xxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 119 tkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfi 193
                                    k+  +elle+ ++s +       LSgG k      Ll+++  v+   l +lDe    LD + +++v ++l + +k+   i
  gi|70607428|ref|YP_256298.1| 114 AKERTKELLEQLELSDKgktlgrDLSGGLKR----RLLISMALVNDPKLIILDEPTTGLDPQARREVWDILLKLKKEGKSI 190
                                   4556677777777777677777789999776....45555555688889********************999988886555 PP

                                   E.E-SSHHHCCC- CS
                                   x.xxxxxxxxxxx RF
                         SMC_N 194 v.islreemleka 205
                                     +++  e   +a
  gi|70607428|ref|YP_256298.1| 191 LlTTHYLE---EA 200
                                   40444433...33 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.6e-06   0.00083      91     131 ..      25      66 ..      17      76 .. 0.87
   2 ?   -1.7   0.0       4.5   2.4e+03      64     100 ..     223     260 ..     179     263 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.6e-06
                                   HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                   RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                   e+++ ++++ ++++l+G+ G+GK+tL+++l +el+ + ge++
  gi|70607428|ref|YP_256298.1|  25 ENISMNIEEgEIVALLGPNGAGKTTLVKQLYGELNPNKGEIR 66 
                                   56677777779**********************999999987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                                   HHHHHHHHHHHTTSEEE.E--TTTHTTHHHHHHHCTTS CS
                   RsgA_GTPase  64 eleelkeelealgyevl.lvsaktkegleelkellkdk 100
                                     +++++ +e ++y++  + ++k +++++++ ++l++k
  gi|70607428|ref|YP_256298.1| 223 VKDKFANWYEVIDYSTGnVYRVKGEDEVKRIIQQLNGK 260
                                   24455666666666654133445556677777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3     9e-06    0.0048       4      83 ..      33     126 ..      29     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............erpevvfvtlpsst..sskdllrellralglelka 70 
                                   +  i+++ G+ G+GKTtl+++l  +l+  +   +            ++ +vv  ++   +  +  d    ++r+ g+++++
  gi|70607428|ref|YP_256298.1|  33 EGEIVALLGPNGAGKTTLVKQLYGELNPNKGEIRvlgskptdrgikKHMGVVPQECEPYGdlTVWDNIYYMARIKGVDKER 113
                                   567999***************999996444444489999999999966666655555555443333334444444444444 PP

                        AAA_22  71 erlsseelleale 83 
                                   +  +++elle+le
  gi|70607428|ref|YP_256298.1| 114 AKERTKELLEQLE 126
                                   3444444444443 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.8e-05    0.0093       1     115 [.      37     208 ..      37     223 .. 0.72
   2 ?   -1.3   0.0       5.6   2.9e+03      51      70 ..     214     245 ..     206     275 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.....................gvnlrdvakenglllevdpe.aldeskrldedkld 58 
                                   ++l G+ G+GKttl k L  +l  +                     +  + + +   g l+ +d+     + k +d+++ +
  gi|70607428|ref|YP_256298.1|  37 VALLGPNGAGKTTLVKQLYGELnPNkgeirvlgskptdrgikkhmgV--VPQECEPYGDLTVWDNIyYMARIKGVDKERAK 115
                                   6899**************66653337777888888888888888532..44444444444444444457777777777766 PP

                        AAA_18  59 klldaleenss.........................aleegknlvidghlaeleseaakdikk...........vvLtasp 103
                                   +  ++l e+ +                            ++k +++d     l + a+++              + Lt+++
  gi|70607428|ref|YP_256298.1| 116 ERTKELLEQLElsdkgktlgrdlsgglkrrllismaLVNDPKLIILDEPTTGLDPQARREVWDillklkkegksILLTTHY 196
                                   666666666556667888888888999999999998777788888887777666666655444777899999999999999 PP

                        AAA_18 104 eelleRlekRgy 115
                                    e +eRl++R y
  gi|70607428|ref|YP_256298.1| 197 LEEAERLANRIY 208
                                   999999998865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.6
                        AAA_18  51 rldedkldklldaleenss............a 70 
                                   +++e+  +++ d++ ++++            +
  gi|70607428|ref|YP_256298.1| 214 IIVEGTPNEVKDKFANWYEvidystgnvyrvK 245
                                   55555666677777777665544444443322 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00014     0.075       5      23 ..      37      59 ..      33     103 .. 0.81
   2 ?    3.9   0.1     0.072        38     107     164 ..     172     227 ..     170     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                        AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                  +++ Gp+g+GKTtl+k+l     
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLygelN 59
                                  799**************966552 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.072
                        AAA_24 107 laeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeev 164
                                   +++e++++l kl++ +k + ++ h  ++     ++   y  ++  + ++t ne+k ++
  gi|70607428|ref|YP_256298.1| 172 ARREVWDILLKLKKEGKSILLTTHYLEEAERLANRI--YFIYRKIIVEGTPNEVKDKF 227
                                   6789***********************999999777..99999999999999999887 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.3e-05    0.0068       2      42 ..      34      73 ..      33     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldder 42
                                  ++i+++ G+  +GKTtl+kql+ el  +++  + +   +++
  gi|70607428|ref|YP_256298.1| 34 GEIVALLGPNGAGKTTLVKQLYGELN-PNKGEIRVLGSKPT 73
                                  5799******************9988.55555555555555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0     0.003       1.6      44      64 ..      31      51 ..      22      59 .. 0.88
   2 ?    6.0   0.0     0.016       8.7     105     148 ..     152     195 ..     115     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.003
                     IstB_IS21 44 iekkenivllGpsGvGKshla 64
                                  ie+ e ++llGp G+GK+ l 
  gi|70607428|ref|YP_256298.1| 31 IEEGEIVALLGPNGAGKTTLV 51
                                  788999************986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                     IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviek.ryerrsiiitsn 148
                                    +  ++l+ilD+   + ld ++++++++++ k + e +si++t+ 
  gi|70607428|ref|YP_256298.1| 152 LVNDPKLIILDEPT-TGLDPQARREVWDILLKlKKEGKSILLTTH 195
                                   44567899999975.679999999999987652678899999985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   9.5e-06     0.005       2      93 ..      38     125 ..      37     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.5e-06
                                   EEESSTTSSHHHHHHHHHHHHTHEE..EEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                           AAA   2 llyGppGtGKTllakavakelgvef..leisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    l Gp G GKT+l+k++  el+ +   +++ gs+ ++  +++   ++  + +e++        + D+i+ +a+ + g ++e
  gi|70607428|ref|YP_256298.1|  38 ALLGPNGAGKTTLVKQLYGELNPNKgeIRVLGSKPTDRGIKK---HMGVVPQECEPYG--DLTVWDNIYYMARIK-GVDKE 112
                                   699*****************9855411444444444332222...2222222222222..455556666666655.55555 PP

                                   HHHHHHHHHHHHH CS
                           AAA  81 eeervvnqLltel 93 
                                    +++  ++Ll++l
  gi|70607428|ref|YP_256298.1| 113 RAKERTKELLEQL 125
                                   5555555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   9.2e-06    0.0048       2      33 ..      37     102 ..      36     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.2e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg......avllssdt............................l 33 
                                   v l G++G+GK+tl+++l+ +l        vl s++t                            +
  gi|70607428|ref|YP_256298.1|  37 VALLGPNGAGKTTLVKQLYGELNpnkgeiRVLGSKPTdrgikkhmgvvpqecepygdltvwdniyY 102
                                   7789**************999887777533333444466655555555555555555555555543 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0067      12      44 ..      29      59 ..      14      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                                  HHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                          TsaE 12 kklakalgdvilLeGdLGaGKTtlvrglakalg 44
                                   ++ +  g++++L G+ GaGKTtlv++l  +l+
  gi|70607428|ref|YP_256298.1| 29 MNIEE--GEIVALLGPNGAGKTTLVKQLYGELN 59
                                  33333..889*****************988775 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.1e-05     0.011      14      80 ..     213     275 ..     202     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                                   EEEEE-------..--.-EEEE-TTS-EEEEE-----------------EEEEEEEE---HHHHHHHH CS
                       DUF4162  14 rieveadaeelleepg.veeveeeggelelkledeeaanellkaltsgveirsFeeeePsLndIFiek 80 
                                   +i ve+ + e+++  + + ev +  ++ + ++++e+  ++++++l+      +Fe++ PsL+d+++e+
  gi|70607428|ref|YP_256298.1| 213 KIIVEGTPNEVKDKFAnWYEVIDYSTGNVYRVKGEDEVKRIIQQLN-----GKFEVRAPSLEDVYLEV 275
                                   4556655666665544488886666666788888889********4.....58*************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-05    0.0076      16      39 ..      28      51 ..      15      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                        AAA_29 16 tieidlkg..atlltGpsGsGKSTll 39
                                  +++i+  +  ++ l Gp+G+GK+Tl+
  gi|70607428|ref|YP_256298.1| 28 SMNIE--EgeIVALLGPNGAGKTTLV 51
                                  34455..3369**************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.5   1.6e-05    0.0085       9      37 ..      20      52 ..      15     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
                        AAA_23  9 sf.rdqeidF...skgltlItGpNGaGKTTild 37
                                  +f  +++i     +  ++++ GpNGaGKTT++ 
  gi|70607428|ref|YP_256298.1| 20 KFvANENISMnieEGEIVALLGPNGAGKTTLVK 52
                                  555566665555666799*************86 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.054      18      43 ..      34      57 ..      15      65 .. 0.83
   2 ?   -0.7   0.0       1.3   6.6e+02     116     142 ..     175     198 ..     109     216 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                  SCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 18 lqslvvalvGmgGvGKttlakqilnk 43
                                      +val G  G GKttl+kq + +
  gi|70607428|ref|YP_256298.1| 34 G--EIVALLGPNGAGKTTLVKQLYGE 57
                                  3..59*****************9866 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                   HHH.....HHHHCHTTSEEEEEESBCC CS
                        NB-ARC 116 edwdkigvvlparenrlrvllTTRdee 142
                                   e+w    + l+ ++++ ++llTT   e
  gi|70607428|ref|YP_256298.1| 175 EVW---DILLKLKKEGKSILLTTHYLE 198
                                   336...455555688888888886555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.9e-05     0.052       2      25 ..      36      59 ..      35      66 .. 0.86
   2 ?   -2.5   0.0       8.1   4.3e+03      71      79 ..     175     183 ..     142     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.9e-05
                                  CEEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                  +v+l G++G GKTtL+++l  ++ 
  gi|70607428|ref|YP_256298.1| 36 IVALLGPNGAGKTTLVKQLYGELN 59
                                  689***************987765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.1
                                   CCHHHHCCS CS
                         NACHT  71 evwavllel 79 
                                   evw +ll+l
  gi|70607428|ref|YP_256298.1| 175 EVWDILLKL 183
                                   233333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.7e-05     0.035      18      57 ..      34      75 ..      27     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                        AAA_30 18 drvavltGpAGtGKttalkal.reaweaag.grviglAptgk 57
                                    +++l Gp G+GKtt++k+l  e+  ++g  rv+g  pt +
  gi|70607428|ref|YP_256298.1| 34 GEIVALLGPNGAGKTTLVKQLyGELNPNKGeIRVLGSKPTDR 75
                                  358999**************9555555553367777666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.14      30      53 ..      31      54 ..      23      61 .. 0.88
   2 ?   -0.7   0.0       1.7   9.2e+02     136     150 ..     149     163 ..     104     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                        AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                  + +ge+++l G+ g+GKttl+ +l
  gi|70607428|ref|YP_256298.1| 31 IEEGEIVALLGPNGAGKTTLVKQL 54
                                  689*****************9776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                        AAA_25 136 aieevegvrlvviDp 150
                                    +  v++++l+++D 
  gi|70607428|ref|YP_256298.1| 149 SMALVNDPKLIILDE 163
                                   455567788888884 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00025      0.13       2      62 ..      37      98 ..      36      99 .. 0.64
   2 ?   -1.0   0.0       3.7   1.9e+03      72     103 ..     204     235 ..     181     243 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                                  EEEESSTTSSHHHHHHCHCT-CC.C-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEE CS
                           Roc  2 vvlvGdsgvGKtsllkrfvedkf.sekekstigvdfltkevtkikgvendkkvkkvklniWD 62
                                  v l+G +g+GKt+l+k++  +   ++ e   +g + +++ ++k  gv  ++      l +WD
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLYGELNpNKGEIRVLGSKPTDRGIKKHMGVVPQECEPYGDLTVWD 98
                                  679**************986533144566666766666666555555444444445566666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.7
                                   T-HHHHCTSCEEEEEEEGHHHHCHHHHHHHHH CS
                           Roc  72 lhplylreaalailvydsrssenlkeWlkelk 103
                                    +++y+  +++++  + ++ ++++ +W++ ++
  gi|70607428|ref|YP_256298.1| 204 ANRIYFIYRKIIVEGTPNEVKDKFANWYEVID 235
                                   34556666666655555666667777776665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00068      0.36       2      25 ..      37      60 ..      36      71 .. 0.84
   2 ?   -2.7   0.0       9.4     5e+03     121     135 ..     183     197 ..     149     209 .. 0.55
   3 ?    1.2   0.0      0.56     3e+02      47      91 ..     231     278 ..     212     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                                  EEEE--TTSSHHHHHHHHHHHH.. CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellks 25
                                  v++ Gp G GKtTlvk+++ +l+ 
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLYGELNP 60
                                  5688**************999964 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.4
                                   HHTTTSEEEEE--SS CS
                      NTPase_1 121 vLksekpvlavihrr 135
                                   + k++k +l + h  
  gi|70607428|ref|YP_256298.1| 183 LKKEGKSILLTTHYL 197
                                   223555566665554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.56
                                   EEEEET.T--EEEEEETT---SS...EETTEEE-HHHHHHHHHHHHHH CS
                      NTPase_1  47 FkivdlasgeegiLarveakrep...rvgkyvvdvesfeelalealrk 91 
                                   ++++d ++g+      +++ +++    +gk+ v+  s+e++ le+++ 
  gi|70607428|ref|YP_256298.1| 231 YEVIDYSTGNVYRVKGEDEVKRIiqqLNGKFEVRAPSLEDVYLEVIKS 278
                                   56666666666666666533332232689*************999986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.055      27      61 ..      28      62 ..      21      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                         AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkek 61
                                  ++ ++++  v l Gp G GKt+++k+l  +l+++k
  gi|70607428|ref|YP_256298.1| 28 SMNIEEGEIVALLGPNGAGKTTLVKQLYGELNPNK 62
                                  5678889999****************999999876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.16      18      44 ..      32      58 ..      26      74 .. 0.84
   2 ?   -1.0   0.1       2.6   1.4e+03     225     225 ..     141     141 ..      98     200 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                      ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienl 44
                                  e+ ei+ + Gp g GKt+L+k+++ +l
  gi|70607428|ref|YP_256298.1| 32 EEGEIVALLGPNGAGKTTLVKQLYGEL 58
                                  6689999***************99877 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.6
                      ATPase_2 225 G 225
                                   G
  gi|70607428|ref|YP_256298.1| 141 G 141
                                   1 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.16       1      32 [.      36      67 ..      36      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrvgt 32
                                  ++++ g +g+GKTtL+++l  el+ ++ ++ +
  gi|70607428|ref|YP_256298.1| 36 IVALLGPNGAGKTTLVKQLYGELNPNKGEIRV 67
                                  68899*****************9988776665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00029      0.15      10      44 ..      17      52 ..      14      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                        AAA_27 10 ryGkf.tdrsldfsaeeadlhliyGpNEAGKstalr 44
                                   yGkf ++++++++ ee ++  ++GpN AGK+t+++
  gi|70607428|ref|YP_256298.1| 17 LYGKFvANENISMNIEEGEIVALLGPNGAGKTTLVK 52
                                  599995578999*999*****************986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00025      0.13       2      37 ..      37      73 ..      36     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                  EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                  v L+Gp G gK++l+++l   l  ++ e+  l ++ t
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLYGELnPNKGEIRVLGSKPT 73
                                  679**************99888655555555555555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.11      22      55 ..      31      64 ..      10      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                          DLIC 22 lPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                  +  g  v +lG +g+Gkttl+ +l G  +++kG 
  gi|70607428|ref|YP_256298.1| 31 IEEGEIVALLGPNGAGKTTLVKQLYGELNPNKGE 64
                                  55677899******************99999995 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00034      0.18       2      20 ..      37      55 ..      36      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                        AAA_28  2 ivitGgestGKTtlleaLa 20
                                  ++++G+ ++GKTtl+++L 
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLY 55
                                  799*************995 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038       0.2       3      24 ..      37      60 ..      35      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                  EEEEESTTCCHHHHHHHHH..CT- CS
                          cobW  3 tvltGflGsGKTtLlnhll..enr 24
                                  + l G+ G+GKTtL+++l    n 
  gi|70607428|ref|YP_256298.1| 37 VALLGPNGAGKTTLVKQLYgeLNP 60
                                  6789************99865444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00047      0.25      11      91 ..      26     104 ..      18     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                                   HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T.T----SS---------TTTH.HHHHHHTT CS
                          PhoH  11 eylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea.geelGflpgdleekvdpylr.plydaLkd 89 
                                   ++  ++++ +iv  +Gp G+GKt l  +l  e+  +k   r++ ++p+    ++++G++p + e    py   +++d+++ 
  gi|70607428|ref|YP_256298.1|  26 NISMNIEEGEIVALLGPNGAGKTTLVKQLYGELNPNKGEIRVLGSKPTDRGiKKHMGVVPQECE----PYGDlTVWDNIYY 102
                                   566778999***************9988877777777777888888887544777887777544....4432145666666 PP

                                   TS CS
                          PhoH  90 ll 91 
                                   + 
  gi|70607428|ref|YP_256298.1| 103 MA 104
                                   65 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00079      0.42       2      23 ..      38      59 ..      37     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00079
                  RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                   l Gp+g GK+tl+k+L  +l 
  gi|70607428|ref|YP_256298.1| 38 ALLGPNGAGKTTLVKQLYGELN 59
                                  589*************998887 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00059      0.31       3      25 ..      36      58 ..      34      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                                  EEEEEESTTSSHHHHHHHHHHHH CS
                         SRP54  3 villvGlqGaGKTttlaKLaall 25
                                  +++l+G++GaGKTt + +L   l
  gi|70607428|ref|YP_256298.1| 36 IVALLGPNGAGKTTLVKQLYGEL 58
                                  789************99886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1718.51
//
Query:       gi|70607429|ref|YP_256299.1|  [L=481]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-165  551.8   0.0   1.1e-165  551.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.6   0.0  6.4e-170  1.1e-165       6     462 .]      15     477 ..      10     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 551.6 bits;  conditional E-value: 6.4e-170
                                   SSE.EEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                        Aldedh   6 set.ievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                   +++ +ev nPa  +e++ k+p+  ++dv +a++ Ake +++w++ +a+eRa+iL k+ad+le+r +e+a+++t+e Gk+l 
  gi|70607429|ref|YP_256299.1|  15 DREwYEVRNPAdYREIVSKFPRLHRKDVVDAIKIAKESYEKWREYTAYERAKILFKTADILESRMQEIAKTLTMEEGKTLG 95 
                                   44559******7789999*************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TT CS
                        Aldedh  85 earaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaee 164
                                   e++ eve++ + lryy +l  + +g++l+s  ++++ l++reP+Gvvg+ItPWNfP+l++ wk+apala+GNtvv+KPa++
  gi|70607429|ref|YP_256299.1|  96 ESAYEVERVTSLLRYYGGLTLNSHGKTLQSsMKNSMHLTVREPIGVVGIITPWNFPFLIPGWKIAPALATGNTVVFKPASN 176
                                   ******************************55************************************************* PP

                                   SHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE- CS
                        Aldedh 165 tplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivl 245
                                   tp +a  l++++ eaglP+gv+n+vtgsg+evg+++v+++e+++vsftGs evgr++ ++ +++++r++lElGGkn+++ +
  gi|70607429|ref|YP_256299.1| 177 TPTVAFELVNALYEAGLPEGVVNLVTGSGREVGDEIVTNKEIKAVSFTGSLEVGREVNSKIGNRFTRLQLELGGKNATVLT 257
                                   ********************************************************************************* PP

                                   TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHH CS
                        Aldedh 246 edaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyvee 326
                                   ++ D++ a+e + +++++n+GQvC a+sr+lv+++++d+ v++++e +k+l vg++l++ +++GPl s++q+ekv +yve 
  gi|70607429|ref|YP_256299.1| 258 KNGDFNLAIEHVTWSVMVNTGQVCLATSRFLVPKELHDKAVNAMTESFKSLVVGNALKQPVHMGPLSSRDQYEKVLGYVEI 338
                                   ********************************************************************************* PP

                                   HHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBH CS
                        Aldedh 327 akeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdl 406
                                   +k+egakl++Gge  + ++++ gyfv+Pt+++nvt+dmria+eEiFGPVl+++++++++eaiei+N+t+yGL+a ++t++l
  gi|70607429|ref|YP_256299.1| 339 GKDEGAKLVYGGEpIKGEDYDYGYFVKPTIFDNVTKDMRIAKEEIFGPVLAIMTYESLDEAIEIVNSTDYGLTAEIVTNNL 419
                                   *************9889**************************************************************** PP

                                   HHHHHHHHHS-SSEEEESSSST--TTT.SEB--CGGGEES..-BSHHHHHHHTEEEEEE CS
                        Aldedh 407 eraervaerleaGnvyiNdsttgaaea.lpfgGvkqSglG..reggkegleeytevktv 462
                                   ++a++++e +eaG v +N++ t++ ++ +p+gG+k Sg+   +e g+e+l++yt++k+v
  gi|70607429|ref|YP_256299.1| 420 NEAMKFSEGVEAGVVKVNRP-TVELDQwVPYGGFKGSGNDvyKELGEEALDFYTKIKAV 477
                                   ********************.6666666************99***************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3383.28
//
Query:       gi|70607430|ref|YP_256300.1|  [L=483]
Description: hypothetical protein Saci_1701 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-20   70.7  51.8    2.5e-18   66.0  51.8    2.1  1  Xan_ur_permease  Permease family
  ------ inclusion threshold ------
      0.038   14.2   0.6      0.038   14.2   0.6    3.5  3  UPF0114          Uncharacterized protein family, UPF0114
       0.16   11.9   4.0        1.4    8.8   0.1    2.8  2  DUF5453          Family of unknown function (DUF5453)


Domain annotation for each model (and alignments):
>> Xan_ur_permease  Permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0  51.8   4.2e-22   2.5e-18      32     387 ..      69     441 ..      17     443 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 4.2e-22
                                   .......H.HHHHHHHHHHHHHHHHHTTT-----EEE-GGGHHHHHGGG-................HHHHHHHHHHHHHHH CS
               Xan_ur_permease  32 aeelr.qlisatllasGiatllqllifgirlpillgssfafvtalmialGsa............edieialagllgallva 99 
                                   ++ +r   + at  a+++atl+++l+ +++  ++ g++ +++ a+++   ++            +    a+   l +++  
  gi|70607430|ref|YP_256300.1|  69 DNVIRiGFTVATATAAAVATLIMALFGKMPFGLAPGMGENAFIAYTVIPSFTnvlitshymqgeSAAVFAVYLSLISVFFN 149
                                   3444444556677789*********9999999999999777663333333234668888876655555566667789999* PP

                                   HHHHHHHHTT-SH.HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSS-..BTT.B---HHHHHHHHHHHHHHHHHHHS... CS
               Xan_ur_permease 100 gvlfilisltglrgrlarlipPvvtgpvvlliGlslaqiavkkvgggwaavegltvvslkllllavvvllvilllsvf... 177
                                   g+lf+++s+ g+r+ ++   p +   ++ ++iGl++  i++ ++g+++   +g t ++l++ ll++    ++l+       
  gi|70607430|ref|YP_256300.1| 150 GILFLIFSVGGIREFIINSVPETLRIGIGIGIGLFISLIGLADIGIVEPG-QG-TPIQLNTALLSQGAFYLGLVSFFIaaa 228
                                   ***********************************************855.55.557777777777766666665555221 PP

                                   SSTTTTTHHHHHHHHHHHHHHHHHHHTTSSHH......HHS-SS-----------HH....H.HHHHTHHH.HHHHHHHHH CS
               Xan_ur_permease 178 lkglfsqlpiLigiiagwllalfmgivnlspe......vseapwfqlpsplkfgtpl..fnlgliltvlavalvavvesvG 250
                                   l    + ++  i+iia++++  +mg v+l ++      +  a  + +   ++f  ++  f lg ++++++++lv +++ vG
  gi|70607430|ref|YP_256300.1| 229 LLIARVIGGFIIAIIATTVVGGVMGYVSLPSAiltvpdF--ATSIVPNLSTSFYLYFvlFGLG-FPIAFSLFLVDFFDGVG 306
                                   3333356899*******************9997776433..3333333334444444436665.56666677********* PP

                                   HHHHHHHHHTS-TII..IIIHHHHHHHHHHHHHHHHHHT---EEE-HHHHHHHHHHTB--HHHHHHHHHHHHHHT--HHHH CS
               Xan_ur_permease 251 diravakvvgrslkp..kpdlrralladGlatllsgllGalpvttyaeniGvvaltkvasrrvmvtagvilillglipkla 329
                                   +i ++a  +g+ +++   ++++r+l+ d la++l+ ++G++ +  y+e++ +++++    ++ ++ta vi +l+  +  la
  gi|70607430|ref|YP_256300.1| 307 TISGLATKAGLIDEKgkIKNINRTLISDALASILAPFFGTSTTVIYVESATGIEQG----GKSGLTALVISLLFFASIPLA 383
                                   *******99998888899**************************************....********************* PP

                                   HHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHTTS-SHHHHHHHHHHHHHHHH----- CS
               Xan_ur_permease 330 allssIPepvlgGvllvvfgmiaasgvsnlqtvdldsarnllivavslvlGlgvatvp 387
                                   +l+s++P+++ gGvl++v  + ++ + + +  +d++++  ++++ +s+ ++ ++++++
  gi|70607430|ref|YP_256300.1| 384 PLFSVVPGFATGGVLVLVGLLFLSLAGKLVTNNDMTDTIPAFVTMISIPFTYSITAGI 441
                                   ***************999999999****************************999875 PP

>> UPF0114  Uncharacterized protein family, UPF0114
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   6.4e-06     0.038      31      77 ..     122     167 ..     103     175 .. 0.75
   2 ?   -1.9   0.8      0.63   3.7e+03      53      71 ..     220     238 ..     210     258 .. 0.58
   3 ?   -1.4   1.8      0.45   2.7e+03     100     113 ..     461     474 ..     392     481 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                       UPF0114  31 lelvveafkaklteelilavleliDlvLigtvllivglGlYelFvsk 77 
                                   + +  ++++   +  +  + l+li +++ g+++li+++G+   F+ +
  gi|70607430|ref|YP_256300.1| 122 VLITSHYMQ-GESAAVFAVYLSLISVFFNGILFLIFSVGGIREFIIN 167
                                   333445553.455599999*************************976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
                       UPF0114  53 liDlvLigtvllivglGlY 71 
                                   l+ +++ + +l+  ++G++
  gi|70607430|ref|YP_256300.1| 220 LVSFFIAAALLIARVIGGF 238
                                   4444444444444444443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.45
                       UPF0114 100 tklakvivailsvh 113
                                    kl+++i++il + 
  gi|70607430|ref|YP_256300.1| 461 LKLGSIIITILFII 474
                                   36777777777665 PP

>> DUF5453  Family of unknown function (DUF5453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.0     0.017     1e+02      82     142 ..     138     188 ..     125     197 .. 0.69
   2 ?    8.8   0.1   0.00024       1.4      95     151 ..     399     455 ..     390     463 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.017
                       DUF5453  82 rvylsGvivfllnillgvlllvllvnfltnqileekysllltnalpllyssvGvsivlsli 142
                                    vyls ++vf+     g+l+l+++v  +++ i+++  ++l       + + +G+  ++sli
  gi|70607430|ref|YP_256300.1| 138 AVYLSLISVFFN----GILFLIFSVGGIREFIINSVPETL------RIGIGIGIGLFISLI 188
                                   589999999986....556888888888888887766655......233444444444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                       DUF5453  95 illgvlllvllvnfltnqileekysll.ltnalpllyssvGvsivlslisiglsklar 151
                                   +l+g+l+l l  + +tn+++++        ++ p+ ys +   i l +is+++ kla 
  gi|70607430|ref|YP_256300.1| 399 VLVGLLFLSLAGKLVTNNDMTDTIPAFvTMISIPFTYS-ITAGIGLGFISYVVLKLAS 455
                                   89********************9988725578899885.667888999***9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 2639.11
//
Query:       gi|70607431|ref|YP_256301.1|  [L=321]
Description: pyridine nucleotide-disulfide oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-45  154.0   0.3    7.7e-45  153.4   0.3    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      3e-18   66.1   3.9    1.3e-16   61.0   0.3    2.7  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    8.9e-06   25.2   0.0    2.1e-05   23.9   0.0    1.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.3e-05   23.8   0.6       0.07   12.4   0.1    2.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00088   18.1   0.0     0.0013   17.5   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
     0.0034   17.6   0.0        1.8    8.8   0.0    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.026   14.1   7.3       0.48    9.9   0.0    3.4  4  DAO             FAD dependent oxidoreductase
       0.11   11.2   3.9        5.8    5.5   0.1    3.8  4  HI0933_like     HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4   0.3   3.5e-48   7.7e-45       2     294 .]       2     262 ..       1     262 [. 0.88

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 3.5e-48
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.evvkklnqgielllgeevvkidpg 81 
                                   +vv++GgG+AGl+a +t ++     +l++++++++     l++ l+ v + ++ +  +        ++++l+++v ++d++
  gi|70607431|ref|YP_256301.1|   2 RVVILGGGFAGLSALKTYRN----SILIDEKDYFV-----LTHRLVDVVRTGNPEIaKL------PYRKVLRATVKSVDFK 67 
                                   8*************999999....57885666554.....4555666666655333222......489999999******* PP

                                   CEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  82 kkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiGvElAaal 161
                                   +kkv  +      e +i ydkl++  G s+r++  pG      kl +++++a ++++kl++ k+++v GgG+ +vElA+++
  gi|70607431|ref|YP_256301.1|  68 EKKVITT------EGTIPYDKLIITLGYSQRLI--PGS----EKL-ENIEDALRIREKLRKaKKVAVLGGGALSVELAGYA 135
                                   *9**994......348***********888885..999....233.89************99******************* PP

                                   HHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 162 aklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpste 242
                                   ++lgkev+lve rd+ll  + k+ s++++++le++Gv+++l+t+v+ id ng+   +v+++g+ ++adlv+ +vG++    
  gi|70607431|ref|YP_256301.1| 136 RELGKEVYLVEERDKLLGFMSKDSSEYAKRRLEEMGVNLYLKTKVEGID-NGT---LVTTNGN-LKADLVISGVGFKGPEI 211
                                   *********************************************7777.776...8999999.8************9965 PP

                                   HCSHCCT-EEEETTEEE--TTSBES.STTEEE-GGGC.TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 243 lleeklglelderggivvdeflrtn.vpgiyaiGDva.ggkggpelaqaAvqqG 294
                                   +   +lgl+ + + +++v+e+lr++  +++y +GD+a  +  +p++aq+Avq+G
  gi|70607431|ref|YP_256301.1| 212 I--SRLGLT-NVNSRMLVNEYLRSEdFEDVYGAGDCAtTKSFIPMSAQVAVQAG 262
                                   5..89**96.59************99***********9999***********98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0081        18       1      18 [.       2      19 ..       2      50 .. 0.88
   2 ?   -3.7   0.1         8   1.8e+04      59      72 ..      57      70 ..      55      75 .. 0.67
   3 !   61.0   0.3   5.6e-20   1.3e-16       1      68 [.     118     185 ..     118     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0081
                                  EEEEECSSHHHHHHHHHH CS
                     Pyr_redox  1 kvvvvGgGyiglElAgal 18
                                  +vv++GgG+ gl + +++
  gi|70607431|ref|YP_256301.1|  2 RVVILGGGFAGLSALKTY 19
                                  79*********9876665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                                  CSEEEEEEEEETTS CS
                     Pyr_redox 59 lntkveeiegsedg 72
                                  l ++v++++ +e++
  gi|70607431|ref|YP_256301.1| 57 LRATVKSVDFKEKK 70
                                  56788888877776 PP

  == domain 3  score: 61.0 bits;  conditional E-value: 5.6e-20
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeieg 68 
                                   kv+v+GgG + +ElAg+++elgk+V++ve +dkll  + ++ s++ +++le++g++++l+tkve i+ 
  gi|70607431|ref|YP_256301.1| 118 KVAVLGGGALSVELAGYARELGKEVYLVEERDKLLGFMSKDSSEYAKRRLEEMGVNLYLKTKVEGIDN 185
                                   79***************************************************************994 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.91     2e+03       1      12 [.       4      15 ..       4      33 .. 0.76
   2 !   23.9   0.0   9.4e-09   2.1e-05     103     305 .]      60     242 ..      52     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.91
                   Pyr_redox_3  1 iIiGaGPaGlaa 12
                                  +I G+G aGl+a
  gi|70607431|ref|YP_256301.1|  4 VILGGGFAGLSA 15
                                  799******986 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 9.4e-09
                   Pyr_redox_3 103 eVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya.gqkvvViGgknSavDaAle 182
                                   +V+sv+ +  + +v t+++t+  +k+ii  G+     +  ipG+ekl       +  +k++  +kv+V Gg+  +v+ A  
  gi|70607431|ref|YP_256301.1|  60 TVKSVDFK--EKKVITTEGTIPYDKLIITLGY----SQRLIPGSEKLENIEDALRIREKLRkAKKVAVLGGGALSVELAGY 134
                                   45555554..4689******************....5556999998777777776555555389***************** PP

                   Pyr_redox_3 183 lvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvl 263
                                     + g+eV +v +++++       s   + + + rlee+   + ++++ +++v+ i++      v+t+   ++ + d v+ 
  gi|70607431|ref|YP_256301.1| 135 ARELGKEVYLVEERDKLLGFM---SKDSSEYAKRRLEEM---G-VNLYLKTKVEGIDNG---TLVTTNG--NL-KADLVIS 202
                                   ***********9998877764...444478999999996...3.899*********964...3454444..22.3355555 PP

                   Pyr_redox_3 264 atGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    +G+k   +++++ +++ + ++r++++e   +  +++++ aG
  gi|70607431|ref|YP_256301.1| 203 GVGFKGP-EIISRLGLT-NVNSRMLVNEYLRSEDFEDVYGAG 242
                                   5999876.455543333.367777888877777777777766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0003      0.68      30      46 ..       2      18 ..       1      22 [. 0.90
   2 !   12.4   0.1   3.1e-05      0.07      28      98 ..     116     203 ..     111     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0003
                                  EEEEESTSHHHHHHHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiat 46
                                  +v+++GgG aGl+A++t
  gi|70607431|ref|YP_256301.1|  2 RVVILGGGFAGLSALKT 18
                                  79************998 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.1e-05
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH....TTTCECEE.............HCHHHHHHHHHHHH CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles....lgakfvev.............lksqeellaeavke 91 
                                   + kv v+GgG   ++ +  a++lg +V++++ r + l  +++    + ++ +e              + +     ++   +
  gi|70607431|ref|YP_256301.1| 116 AKKVAVLGGGALSVELAGYARELGKEVYLVEERDKLLGFMSKdsseYAKRRLEEmgvnlylktkvegIDNGTLVTTNGNLK 196
                                   569****************************99988766655333333333333555556555555444444444444555 PP

                                   -SEEEE- CS
                   AlaDh_PNT_C  92 advvigt 98 
                                   ad+vi+ 
  gi|70607431|ref|YP_256301.1| 197 ADLVISG 203
                                   6666655 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     6e-07    0.0013     257     351 ..     101     205 ..      88     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6e-07
                                   HHHHHHHHHHHHHHTT.-EEEEECSSHHHHHHHHHHHHHT-EEEEE.....EESSS-HHHHHHHHHHS.TT.......SEE CS
                Oxidored_nitro 257 arlldaladyheylag.krvaiygdpdrvvalarllkelGmevvaa.....gtetahrddeerlkaeleeg......epev 325
                                   ++++dal+  +e+l++ k+va+ g++ ++v la + +elG ev ++     + ++ ++d  e +k +lee       +   
  gi|70607431|ref|YP_256301.1| 101 ENIEDALRI-REKLRKaKKVAVLGGGALSVELAGYARELGKEVYLVeerdkLLGFMSKDSSEYAKRRLEEMgvnlylK-TK 179
                                   677777776.8888866***************************9955555566777777788888888888889953.77 PP

                                   EES.CHHHHHHHHHHHT-SEEEE-CC CS
                Oxidored_nitro 326 iddadleeleelikelkpdlllggsk 351
                                   +++ d+ +l     +lk+dl+++g+ 
  gi|70607431|ref|YP_256301.1| 180 VEGIDNGTLVTTNGNLKADLVISGVG 205
                                   889999****************9874 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0044       9.9       1      17 [.       5      21 ..       5      33 .. 0.84
   2 !    8.8   0.0   0.00082       1.8       1      38 [.     121     159 ..     121     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0044
                                  EE--SHHHHHHHHHHHC CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLak 17
                                  I+G+G++Gl+a  ++++
  gi|70607431|ref|YP_256301.1|  5 ILGGGFAGLSALKTYRN 21
                                  89********9988875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00082
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS.SSGGG-EE CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr.lGGraasy 38 
                                   ++G+G+ +  +A ++++ g++v l+e rd+ lG  +++ 
  gi|70607431|ref|YP_256301.1| 121 VLGGGALSVELAGYARELGKEVYLVEERDKlLGFMSKDS 159
                                   79****************************555554433 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.9     0.016        35       1      14 [.       2      15 ..       2      31 .. 0.85
   2 ?   -1.7   0.0      0.73   1.6e+03     165     207 ..      57      94 ..      31     112 .. 0.70
   3 ?    1.9   0.2      0.06   1.3e+02       1      30 [.     118     149 ..     118     161 .. 0.88
   4 ?    9.9   0.0   0.00021      0.48     154     203 ..     165     207 ..     159     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                  EEEEECTSHHHHHH CS
                           DAO  1 dvviiGGGiiGlst 14
                                  +vvi GGG +Gls+
  gi|70607431|ref|YP_256301.1|  2 RVVILGGGFAGLSA 15
                                  59**********97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.73
                                   ESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH CS
                           DAO 165 egtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll 207
                                   ++++v++++ +++k   v  tt+g++  +d+++++ G +s+ l+
  gi|70607431|ref|YP_256301.1|  57 LRATVKSVDFKEKK---V-ITTEGTI-PYDKLIITLG-YSQrLI 94 
                                   44577777555434...3.2444765.6789999998.555355 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.06
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                   +v++ GGG   +  A ++ + g  V l+e +d
  gi|70607431|ref|YP_256301.1| 118 KVAVLGGGALSVELAGYARELGkeVYLVEERD 149
                                   59****************77789******996 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.00021
                                   HHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGG CS
                           DAO 154 raaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGaw 203
                                   r++e+ Gv+++++t+v+g+++    ++ v  tt+g+  +ad v+   G  
  gi|70607431|ref|YP_256301.1| 165 RRLEEMGVNLYLKTKVEGIDN----GTLV--TTNGNL-KADLVISGVGFK 207
                                   569****************65....5667..887654.458899877755 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.036        81       2      15 ..       2      15 ..       1      32 [. 0.76
   2 ?    0.4   0.0     0.094   2.1e+02     110     163 ..      39      88 ..      26      97 .. 0.77
   3 ?    5.5   0.1    0.0026       5.8       2      35 ..     118     151 ..     117     156 .. 0.93
   4 ?    1.5   0.0     0.043        97     116     160 ..     164     202 ..     154     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.036
                                  SEEEE--SHHHHHH CS
                   HI0933_like  2 dviviGgGaAGlma 15
                                  +v+++GgG AGl a
  gi|70607431|ref|YP_256301.1|  2 RVVILGGGFAGLSA 15
                                  69*********966 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.094
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   d+v++   e+ +   +  l+ +vksv+ +e++   v t +e+++  dkl++++G
  gi|70607431|ref|YP_256301.1|  39 DVVRTGNPEIAKLPYRKVLRATVKSVDFKEKK---VIT-TEGTIPYDKLIITLG 88 
                                   66677777777777788888999999665555...555.58999******9998 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0026
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   +v+v+GgGa  +  A  a++ gk+V l+e+ +kl
  gi|70607431|ref|YP_256301.1| 118 KVAVLGGGALSVELAGYARELGKEVYLVEERDKL 151
                                   79***************************99886 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.043
                                   HHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE CS
                   HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvktkseeeleadklvl 160
                                   +++l+e gv+l+l+t+v+++   ++g   v+t  +++l+ad ++ 
  gi|70607431|ref|YP_256301.1| 164 KRRLEEMGVNLYLKTKVEGI---DNG-TLVTT--NGNLKADLVIS 202
                                   689999*************9...334.45555..67777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2251.73
//
Query:       gi|70607432|ref|YP_256302.1|  [L=364]
Description: nucleotidyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-53  180.3   0.0    5.9e-53  180.0   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    8.7e-07   29.4   0.0    1.3e-06   28.9   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.3e-06   27.6   0.1    1.8e-06   27.1   0.1    1.2  1  Fucokinase       L-fucokinase
    1.1e-05   24.9  10.4    2.8e-05   23.6   0.3    5.2  6  Hexapep          Bacterial transferase hexapeptide (six repea


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.0   0.0   1.3e-56   5.9e-53       1     246 [.      17     247 ..      17     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 1.3e-56
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   ka+IL+GG+GtRL+PLt+t +k+l+ ++gk ++    +  l + gi++  ++l ++h + v e++++gskfg++v+++++ 
  gi|70607432|ref|YP_256302.1|  17 KAIILHGGQGTRLRPLTHTGPKQLIKIAGK-PISLWGVLSLRDIGIRDFGIILGNNHPEKVIEYYGDGSKFGIKVTYIYQG 96 
                                   79****************************.************************************************** PP

                                   S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEE CS
               NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverf 162
                                   e +g+AdA+++++++++d++    +++Lg++++ +  + ++v +     +   +++++ +v++++++Gv+ ++++++v r+
  gi|70607432|ref|YP_256302.1|  97 EARGLADAIYKVKDFVKDDNF---IVYLGDNVVLE-GLDKLVSFN----S--SASILLARVDNPNRFGVAVINNDNKVVRL 167
                                   ******************996...99999999998.888888764....3..456899*********************** PP

                                   ECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHH CS
               NTP_transferase 163 vEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleane 243
                                   vEKPke   s+la  G+Y+f++e+++ + +++++++rge eitd+++++++egk+  + + k++  W+D+Gt+d+llean+
  gi|70607432|ref|YP_256302.1| 168 VEKPKERI-SDLALVGVYTFTPEIFHAI-EKIKPSWRGELEITDAIQELINEGKEVSYSIIKGW--WKDTGTPDDLLEANM 244
                                   ******88.*******************.67********************************6..**************9 PP

                                   HHH CS
               NTP_transferase 244 kla 246
                                    l+
  gi|70607432|ref|YP_256302.1| 245 ILL 247
                                   765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.8e-10   1.3e-06       1     100 [.      18     128 ..      18     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.8e-10
                                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTC...T..S-EEE-TTS CS
                  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd...eevlaalarl...g..vrvvededp 68 
                                   a+iL GG+++R+      g+K+l++++gkp+  + + +lr+ g+++  ++ g+   e+v +++ +    g  v+++++  +
  gi|70607432|ref|YP_256302.1|  18 AIILHGGQGTRLRplthtGPKQLIKIAGKPISLWGVLSLRDIGIRDFGIILGNnhpEKVIEYYGDGskfGikVTYIYQG-E 97 
                                   79**********6554447*************************99988866623333444433223334225555554.4 PP

                                   S-SHHHHHHHHHHHH.SSSCEEEEETT-TT-- CS
                  NTP_transf_3  69 gkgplaslaaalraaadadavlvlacDmPllt 100
                                    +g + +++   + + ++d ++v ++D + l+
  gi|70607432|ref|YP_256302.1|  98 ARGLADAIYKVKDFV-KDDNFIVYLGDNVVLE 128
                                   677777777777777.99*******9988774 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   4.1e-10   1.8e-06     271     337 ..     254     317 ..     195     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.1e-10
                    Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlslkl 337
                                    +++ v++S +e++v ++egsv+e+s ++g+v +g+n+ + g ++   ++   + d++++   ++++
  gi|70607432|ref|YP_256302.1| 254 VNKGKVVDSRVEGRVVIDEGSVVEKSVIRGPVYVGKNCKIRGSHILPFTS---IGDNVVIEDSEVSN 317
                                   567889****************************************9877...88888888777765 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.15   6.5e+02      20      29 ..     119     128 ..     119     129 .. 0.67
   2 !   12.7   1.8   1.8e-05     0.081       3      29 ..     269     294 ..     261     296 .. 0.83
   3 !   23.6   0.3   6.3e-09   2.8e-05       2      29 ..     285     311 ..     284     313 .. 0.94
   4 ?   -1.0   0.0      0.37   1.7e+03       6      16 ..     316     326 ..     316     328 .. 0.64
   5 ?   -2.1   0.0      0.82   3.7e+03      28      34 ..     336     342 ..     334     344 .. 0.53
   6 ?   -1.5   0.0      0.56   2.5e+03      22      27 ..     356     361 ..     355     363 .. 0.42

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                                   EEE-TTEEEE CS
                       Hexapep  20 VkIGdnvkIg 29 
                                   V +Gdnv+++
  gi|70607432|ref|YP_256302.1| 119 VYLGDNVVLE 128
                                   5678888765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.8e-05
                                   EEETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                   vI +++++   +vi+g+V +G+n+kI 
  gi|70607432|ref|YP_256302.1| 269 VIDEGSVVE-KSVIRGPVYVGKNCKIR 294
                                   566666666.89**************7 PP

  == domain 3  score: 23.6 bits;  conditional E-value: 6.3e-09
                                   EEEETTEEE-TTEEEETTEEE-TTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIg 29 
                                   + +G+n++I+ +++i++ + IGdnv+I+
  gi|70607432|ref|YP_256302.1| 285 VYVGKNCKIR-GSHILPFTSIGDNVVIE 311
                                   689*******.****************8 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.37
                                   TTEEE-TTEEE CS
                       Hexapep   6 snvlIgpfavi 16 
                                   sn+lI+  ++i
  gi|70607432|ref|YP_256302.1| 316 SNSLIMDDVQI 326
                                   56777777776 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 0.82
                                   EETTEEE CS
                       Hexapep  28 Igagvvi 34 
                                   Ig+g+++
  gi|70607432|ref|YP_256302.1| 336 IGSGARV 342
                                   5555554 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 0.56
                                   E-TTEE CS
                       Hexapep  22 IGdnvk 27 
                                   IG+n+ 
  gi|70607432|ref|YP_256302.1| 356 IGENSL 361
                                   444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2523.52
//
Query:       gi|70607433|ref|YP_256303.1|  [L=309]
Description: NAD-dependent epimerase/dehydratase protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-62  210.2   0.0    6.9e-62  209.8   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.1e-55  187.3   0.0    3.7e-55  187.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    7.9e-19   67.8   0.0    9.6e-19   67.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.2e-15   57.3   0.0    1.6e-15   56.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.9e-14   53.5   0.4    2.3e-13   50.0   0.4    2.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.1e-10   39.3   1.8    4.3e-09   35.9   0.2    2.7  2  NAD_binding_4    Male sterility protein
      4e-05   23.6   0.0    5.6e-05   23.1   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.024   14.1   0.7       0.33   10.4   0.7    2.5  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.8   0.0   3.1e-65   6.9e-62       1     314 [.       1     270 [.       1     274 [. 0.90

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 3.1e-65
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   ++TG+aGfiGs + +   +        v  + ++++gr+e+l   ++        ++kgD+++ s+le+ +++++++ ++n
  gi|70607433|ref|YP_256303.1|   1 MVTGGAGFIGSSFSREVKKP-------VIFDLLTYAGRLENLIGVDH-------IFVKGDIRNYSQLEDTVKKYDIKIIVN 67 
                                   69**********98865443.......33578999*******97653.......6************************** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadw 162
                                   + A+ hVd+s+++++ ++++nv G+++LLe++r++     +r++q+St+EvYG+++    tE+ p++P sPY+a+K++ad+
  gi|70607433|ref|YP_256303.1|  68 FSAETHVDRSINNAHIFLDTNVYGVVNLLEICRRYD----TRLVQISTDEVYGEQE--NATEDFPLRPSSPYSASKASADM 142
                                   **********************************95....8*************97..679******************** PP

                                   HHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS-- CS
                 GDP_Man_Dehyd 163 ivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpe 243
                                   ++ +y ++yg+ a++ + +n+++pr+    ++++i+++++r++lg+ e++++G++d+ Rdw +v+D+++++ ++++ +k  
  gi|70607433|ref|YP_256303.1| 143 FILAYVRTYGVDAIIIRPSNNYGPRQ---HIEKLIPKTIVRTLLGL-EIPIYGKGDQERDWIYVEDTAKVIAQLVETGK-- 217
                                   *************************7...689*************9.7888*************************998.. PP

                                   -EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHH CS
                 GDP_Man_Dehyd 244 dyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskak 314
                                        +ge ++v +  + ++++l++ i         +         + +++++++rpg+++++ +  +k+ 
  gi|70607433|ref|YP_256303.1| 218 -----KGEIYNVPGGQRTTNIKLVEMIGEL------M-------GREPKIKFVKDRPGHDKKYSMVSTKLS 270
                                   .....7999999999999999998765432......1.......235678889999999999988888875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.0   1.7e-58   3.7e-55       2     240 ..       1     224 [.       1     225 [. 0.96

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 1.7e-58
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHH CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAavggvaas 80 
                                   +VtG++GfiGs + +++++     + +d l++a++ ++l  +   +v++d+++ s+le+ +k++++ +++++ a+ +v++s
  gi|70607433|ref|YP_256303.1|   1 MVTGGAGFIGSSFSREVKKP----VIFDLLTYAGRLENLIGVdhIFVKGDIRNYSQLEDTVKKYDIKIIVNFSAETHVDRS 77 
                                   59****************86....67777777777777777788************************************* PP

                                   HHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT CS
                     Epimerase  81 sedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyg 161
                                   ++++  f+++n+ g++nlle +r+++  rl+++s++evYG++++   +e+    pl+p+spY+a+K+ ++  + ay ++yg
  gi|70607433|ref|YP_256303.1|  78 INNAHIFLDTNVYGVVNLLEICRRYDT-RLVQISTDEVYGEQEN--ATEDF---PLRPSSPYSASKASADMFILAYVRTYG 152
                                   ***************************.************9888..89999...*************************** PP

                                   -EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
                     Epimerase 162 lnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                                   ++aii+r++n+yGpr   ++ +++ip+ i + l+g  e+ ++g+g++ Rd++yveD a++i  ++e    g+kgeiyn+
  gi|70607433|ref|YP_256303.1| 153 VDAIIIRPSNNYGPR---QHIEKLIPKTIVRTLLGL-EIPIYGKGDQERDWIYVEDTAKVIAQLVET---GKKGEIYNV 224
                                   ***************...99****************.******************************...999*****8 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   4.3e-22   9.6e-19       4     235 ..       1     247 [.       1     269 [. 0.87

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.3e-22
                                   EEESTTSHHHHHHHHHCTTTS.EEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSH CS
                 RmlD_sub_bind   4 lvtGanGqlGseLakqlaeeg.levlaltre............eldltdaeavaellkeakpdvvvnaAAytavDkaEsee 71 
                                   +vtG+ G +Gs   +++++   +++l+   +            + d+++ +++++++k+ + +++vn  A t vD+  ++ 
  gi|70607433|ref|YP_256303.1|   1 MVTGGAGFIGSSFSREVKKPViFDLLTYAGRlenligvdhifvKGDIRNYSQLEDTVKKYDIKIIVNFSAETHVDRSINNA 81 
                                   69***************98541455555333679*********************************************** PP

                                   HHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEEE CS
                 RmlD_sub_bind  72 eaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkkalivRt 148
                                   +     n+ +v +l e +++++  L+++StD V+  +++   +ed +  P + Y ++K+     +la    +g +a+i+R 
  gi|70607433|ref|YP_256303.1|  82 HIFLDTNVYGVVNLLEICRRYDTRLVQISTDEVYGEQENA--TEDFPLRPSSPYSASKASADMFILAyvrtYGVDAIIIRP 160
                                   **********************************877655..9999****************99888555577899***** PP

                                   -SEESS...SSS-HHHHHHHHH.HH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHH CS
                 RmlD_sub_bind 149 swvyge...kgknfvktmlrla.kereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefAr 225
                                   s  yg     +k   kt++r +   + ++    Dq +   +++d A+v++ql+e+ ++     ++y + + + t+  ++ +
  gi|70607433|ref|YP_256303.1| 161 SNNYGPrqhIEKLIPKTIVRTLlGLEIPIYGKGDQERDWIYVEDTAKVIAQLVETGKK----GEIYNVPGGQRTTNIKLVE 237
                                   ****98554567788999987746677899999**********************998....8999999999999999988 PP

                                   HHHHHHCHTT CS
                 RmlD_sub_bind 226 ailkeagads 235
                                    i + +g ++
  gi|70607433|ref|YP_256303.1| 238 MIGELMGREP 247
                                   8877776655 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   7.3e-19   1.6e-15       1     224 [.       1     208 [.       1     218 [. 0.81

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 7.3e-19
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvd..vvihlaslvdv 79 
                                   +vtGgaGF+G++  +e+      k+  ++Dl +    le+l  v+ + +++gD+++ ++le+ +++ d  +++   + + v
  gi|70607433|ref|YP_256303.1|   1 MVTGGAGFIGSSFSREV------KKPVIFDLLTYAGRLENLIGVDHI-FVKGDIRNYSQLEDTVKKYDikIIVNFSAETHV 74 
                                   59*********976653......44459*********9*99999999.****************97651156666777788 PP

                     3Beta_HSD  80 agklte.deimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                      +++   + + nv+G  n+le c++ +  +lv  S+ ev g+   +    n+   +  +  ++++y+ sKa a+ ++l+
  gi|70607433|ref|YP_256303.1|  75 DRSINNaHIFLDTNVYGVVNLLEICRRYDT-RLVQISTDEVYGE---Q---ENAT--EDFPLRPSSPYSASKASADMFILA 146
                                   77665515668****************995.699*********9...2...2344..45677899**************98 PP

                     3Beta_HSD 160 aNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak..lglalfkigdeevlsdrvYvgNvawa 224
                                           g  +  + +Rp+  yG++++  +   k++++  lgl++  +g+ ++  d++Yv+  a++
  gi|70607433|ref|YP_256303.1| 147 YVR---TYG--VDAIIIRPSNNYGPRQHIEKLIPKTIVRtlLGLEIPIYGKGDQERDWIYVEDTAKV 208
                                   766...333..67899*********99765544444444227999*****************98865 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.4     1e-16   2.3e-13       2     276 ..       1     266 [.       1     281 [. 0.80

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1e-16
                                   EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEE CS
               Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvf 82 
                                   +vtG++G iGs++ r++ k  +  ++ +     +l  +++          +      v gd+r+ ++le++++++++++++
  gi|70607433|ref|YP_256303.1|   1 MVTGGAGFIGSSFSREVKKPVIFDLLTYAGRLENLIGVDH----------I-----FVKGDIRNYSQLEDTVKKYDIKIIV 66 
                                   7999999999999887765544444444333333333332..........3.....345********************** PP

                                   E------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG............SS--SHHHHHHHHHHHHHHH CS
               Polysacc_synt_2  83 haAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA............vnPtnvmGatKrlaekllqa 151
                                   +  A  hV    +n++  ++tNv+g  n++e++ +++  ++v iStD               +P + + a+K+ a++++ a
  gi|70607433|ref|YP_256303.1|  67 NFSAETHVDRSINNAHIFLDTNVYGVVNLLEICRRYDT-RLVQISTDEVygeqenatedfpLRPSSPYSASKASADMFILA 146
                                   ************************************96.79*****98533333333333358****************** PP

                                   GGG--SSS--EEEEEEE-EETTGTTSSHHHHHHHHHT...TSSEEES.-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE CS
               Polysacc_synt_2 152 lakeseekktkfvvvRfGNVlgSrGSviplFkkqike...ggpvtvT.dpemtRyfmtieeavqLvlqalalakggeifvl 228
                                   + ++        +++R  N  g r  +  l  k i +   g ++++    +  R ++ +e++++++ q ++++k+gei+ +
  gi|70607433|ref|YP_256303.1| 147 YVRTY---GVDAIIIRPSNNYGPRQHIEKLIPKTIVRtllGLEIPIYgKGDQERDWIYVEDTAKVIAQLVETGKKGEIYNV 224
                                   *9999...8999************9886666666654222799**97256899**************************** PP

                                   --.-EEEHHHHHHHH..........SSSS-EEE----TT--SS-EEE- CS
               Polysacc_synt_2 229 dmGepvkivdlakalielsgleekkeedieikitGlRpGEklyEeLli 276
                                     G+ ++ ++l++ + el+g       + +ik++  RpG     ++++
  gi|70607433|ref|YP_256303.1| 225 PGGQRTTNIKLVEMIGELMGR------EPKIKFVKDRPGHDKKYSMVS 266
                                   ************999999985......456889999999655555555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.11   2.6e+02       1      11 [.       2      12 ..       2      17 .. 0.85
   2 !   35.9   0.2   1.9e-12   4.3e-09      87     209 ..      61     174 ..      49     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                  EE-TTSHHHHH CS
                 NAD_binding_4  1 lTGaTGFLGkv 11
                                  +TG+ GF+G+ 
  gi|70607433|ref|YP_256303.1|  2 VTGGAGFIGSS 12
                                  7********86 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.9e-12
                                   H--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH-- CS
                 NAD_binding_4  87 evdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeeklded 164
                                    +++i++  A +++d+++++   +l++Nv G++++le++++      l+++ST  v+ge+e++                  
  gi|70607433|ref|YP_256303.1|  61 DIKIIVNFSAETHVDRSINNahiFLDTNVYGVVNLLEICRRYDTR--LVQISTDEVYGEQENA------------------ 121
                                   5889************887755589***************88666..******9999999964.................. PP

                                   EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-........- CS
                 NAD_binding_4 165 eraklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg........e 209
                                   +++     +  Y+ sKa a++ + ++ r  g+ ++i+Rps+ +g         
  gi|70607433|ref|YP_256303.1| 122 TEDFPLRPSSPYSASKASADMFILAYVRTYGVDAIIIRPSNNYGprqhieklI 174
                                   34455667789*****************************8776555555550 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.5e-08   5.6e-05      43     145 ..      42     162 ..       4     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.5e-08
                                   EEE--TT-CCHHHHHHTT-SE.EEES---TCC.HHHH..............HHHHHHHHHHCT--EEEEEEETTTTSGCGC CS
                NAD_binding_10  43 vvegdvtdvedlaealkgada.Vvsalggggk.deeg..............aknivdaakeagvkRfvlvsaigvgdevpg 107
                                    v+gd+ + ++l++++k +d+ ++++++++   d ++              ++n+++ +++ ++ R+v +s+  v+ e+++
  gi|70607433|ref|YP_256303.1|  42 FVKGDIRNYSQLEDTVKKYDIkIIVNFSAETHvD-RSinnahifldtnvygVVNLLEICRRYDT-RLVQISTDEVYGEQEN 120
                                   599*****************76888887777752.2335556677777899**********999.**************** PP

                                   HHHHHHHHCCHHHHHHHHHHHHH....HHHSSSEEEEEEE-C CS
                NAD_binding_10 108 efgewnkellkaylaakraaeel....lrasgldwTivrpgg 145
                                   +++++  +  ++y a k+ a+      +r+ g+d  i+rp+ 
  gi|70607433|ref|YP_256303.1| 121 ATEDFPLRPSSPYSASKASADMFilayVRTYGVDAIIIRPSN 162
                                   *9999999999**999999998633336889*********86 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00015      0.33      40     169 ..      28     153 ..       1     161 [. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                                   HHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHH CS
                     adh_short  40 vakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltrav 119
                                    a  l+++ g + +++++D+++++++e++v+k       + ++vn  + t      + s ++    +++N+ gv++l + +
  gi|70607433|ref|YP_256303.1|  28 YAGRLENLiGVDHIFVKGDIRNYSQLEDTVKKY-----DIKIIVNFSAET----HVDRSINNAHIFLDTNVYGVVNLLEIC 99 
                                   455677777889999999***999999999998.....888888877762....334444555568999999999999988 PP

                                   HHHHHHCTTEEEEEEEE..GGGTSB-TT.......BHHHHHHHHHHHHHHHHHHHHHGG CS
                     adh_short 120 lpamlkqssGrIvnvsS..vagkvpvag.......vaaYsAsKaavagltrslakelap 169
                                    ++       r v++s   v g++++a         ++YsAsKa  ++++ +  + +  
  gi|70607433|ref|YP_256303.1| 100 RRY-----DTRLVQISTdeVYGEQENATedfplrpSSPYSASKASADMFILAYVRTYGV 153
                                   888.....567777776334454443331111122689*********999887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1988.89
//
Query:       gi|70607434|ref|YP_256304.1|  [L=282]
Description: dTDP-4-dehydrorhamnose reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-60  202.1   0.0    1.1e-59  202.0   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    5.1e-12   45.8   0.0    7.6e-12   45.2   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.5e-07   30.4   0.1    2.5e-07   30.4   0.1    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      9e-07   28.3   1.7    3.5e-06   26.4   0.3    2.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.0   2.4e-63   1.1e-59       1     286 [.       1     280 [.       1     281 [. 0.94

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 2.4e-63
                                   EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHH CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre......eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaay 75 
                                   m  l++G++GqlG+eL k+++ +    l+++++       ld +d  +v++l+ ++kp+v++n+ A t+vDk+E ++ +a+
  gi|70607434|ref|YP_256304.1|   1 MVTLIIGGSGQLGQELGKLIKDSI---LTFSSRpieggiYLDTRDYIRVEDLIMKTKPEVIINTSAITDVDKCEVDRINAH 78 
                                   5679****************9664...4443334678899***************************************** PP

                                   HHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSS CS
                 RmlD_sub_bind  76 avnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekg 156
                                    vn+ av+++ +aa+ +++ ++++StDyVFdG++ + Y+edd ++Pln+YG tKl+GE   l + +  l++Rts +yg+++
  gi|70607434|ref|YP_256304.1|  79 SVNSLAVKHMVRAASITKSYFVQISTDYVFDGNRGN-YNEDDLPNPLNYYGLTKLLGETYSL-SYDYSLVIRTSGIYGSNK 157
                                   *********************************766.**********************988.667899************ PP

                                   S-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSE CS
                 RmlD_sub_bind 157 knfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadsee 237
                                   +nf   +l+ +++  +++ v D + sP  +++lAe+++qll  ++      g++ +a+++ +s++++A +i+k++  +++ 
  gi|70607434|ref|YP_256304.1| 158 ENFPLYVLKSLEKGSKVRAVWDMYYSPINVKQLAEAIVQLLPLRKT-----GILNIAGDR-ISRYDLALKIAKMSSLNENL 232
                                   *****************************************99996.....*******99.******************** PP

                                   EEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHHT CS
                 RmlD_sub_bind 238 vkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkell 286
                                   +++ s +e+  +AkRP++S+Ld++ +++ + ++l + +e+l++++++++
  gi|70607434|ref|YP_256304.1| 233 IEAASYEEMSWRAKRPKDSSLDSSTVKKYVSVNL-SLEEGLRRLINDVQ 280
                                   ****************************988877.99999999999875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   1.7e-15   7.6e-12       2     185 ..       4     160 ..       3     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.7e-15
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHH CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaasse 82 
                                   l++G++G++G+ l k +++    ++++++++ +           ++ld +d  ++e+l+ +++p+++i+  a+ +v+    
  gi|70607434|ref|YP_256304.1|   4 LIIGGSGQLGQELGKLIKDS---ILTFSSRPIE---------GGIYLDTRDYIRVEDLIMKTKPEVIINTSAITDVDKCEV 72 
                                   89***************995...8888888333.........458************************************ PP

                                   SHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-E CS
                     Epimerase  83 dpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqygln 163
                                   d+      n   + +++ aa+ ++   ++++s++ v+  +     +e+      +p + Y+++Kl+ge +  +y  +y   
  gi|70607434|ref|YP_256304.1|  73 DRINAHSVNSLAVKHMVRAASITKS-YFVQISTDYVFDGNRGN-YNEDD---LPNPLNYYGLTKLLGETYSLSY--DY--- 143
                                   *********************9999.***********988885.55665...469**************99998..44... PP

                                   EEEEEESEEESTTS-TTSTTSH CS
                     Epimerase 164 aiilrlfnlyGprngegevsrv 185
                                    +++r + +yG +      +++
  gi|70607434|ref|YP_256304.1| 144 SLVIRTSGIYGSN-----KENF 160
                                   3578888888888.....3333 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2      0.49   2.2e+03       1      13 [.       4      16 ..       4      22 .. 0.85
   2 !   30.4   0.1   5.6e-11   2.5e-07      57     176 ..      36     150 ..      32     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.49
                                  EEETTTSHHHHHH CS
                 GDP_Man_Dehyd  1 LiTGiaGfiGsyl 13
                                  Li G++G+ G+ l
  gi|70607434|ref|YP_256304.1|  4 LIIGGSGQLGQEL 16
                                  89********877 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5.6e-11
                                   EE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S CS
                 GDP_Man_Dehyd  57 hkgDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq 137
                                   ++ D +D  ++e+l+ +++p+ ++n  A   Vd+   +      vn l++ +++ a+ +++      f+q+St+ v+    
  gi|70607434|ref|YP_256304.1|  36 IYLDTRDYIRVEDLIMKTKPEVIINTSAITDVDKCEVDRINAHSVNSLAVKHMVRAASITK----SYFVQISTDYVFDGN- 111
                                   589********************************9999*****************98865....57**********444. PP

                                   SSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EE CS
                 GDP_Man_Dehyd 138 evpqtEttpfyPrsPYaaaKlyadwivvnyreayglfav 176
                                   +  ++E+   +P + Y+ +Kl  ++   +y  +  + ++
  gi|70607434|ref|YP_256304.1| 112 RGNYNEDDLPNPLNYYGLTKLLGETYSLSYDYSLVIRTS 150
                                   47899*******************999999877655554 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.18   8.1e+02       2      18 ..       4      20 ..       3      32 .. 0.84
   2 !   26.4   0.3   7.8e-10   3.5e-06      61     153 ..      38     142 ..      11     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.18
                                  EEETTTSHHHHHHHHHH CS
               Polysacc_synt_2  2 lvtGagGsiGselvrqi 18
                                  l+ G++G +G+el + i
  gi|70607434|ref|YP_256304.1|  4 LIIGGSGQLGQELGKLI 20
                                  899********997655 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 7.8e-10
                                   --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGS......... CS
               Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAv......... 132
                                    d rd  r+e+++ ++k++v++++ A+  V  +e   ++a + N l+ +++++aa  ++ + +v iStD            
  gi|70607434|ref|YP_256304.1|  38 LDTRDYIRVEDLIMKTKPEVIINTSAITDVDKCEVDRINAHSVNSLAVKHMVRAASITK-SYFVQISTDYVFdgnrgnyne 117
                                   5899*************************************************998766.89******9765333333333 PP

                                   ....S--SHHHHHHHHHHHHHHHGG CS
               Polysacc_synt_2 133 ....nPtnvmGatKrlaekllqala 153
                                       nP n +G+tK+l e +  +++
  gi|70607434|ref|YP_256304.1| 118 ddlpNPLNYYGLTKLLGETYSLSYD 142
                                   4444799999999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1840.06
//
Query:       gi|70607435|ref|YP_256305.1|  [L=184]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-56  188.1   0.0      1e-55  188.0   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    6.5e-05   22.6   0.0    8.5e-05   22.2   0.0    1.1  1  Cupin_1          Cupin
  ------ inclusion threshold ------
      0.095   12.1   0.0       0.14   11.6   0.0    1.1  1  Cupin_4          Cupin superfamily protein


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   0.0   1.8e-59     1e-55       2     169 .]       7     171 ..       6     171 .. 0.95

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 1.8e-59
                                   -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEEE CS
               dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaVD 82 
                                    +i++vl+ie+++++DeRG+ +e f++++f       ++vq n+s+skkgv+RGlH+q +pk+q+klv+v+ G+++dvaVD
  gi|70607435|ref|YP_256305.1|   7 KDIPDVLVIETDKYEDERGLLMELFKRSNFIFI---DSIVQVNYSYSKKGVIRGLHYQLKPKEQGKLVTVIDGKIYDVAVD 84 
                                   589**************************9854...379****************************************** PP

                                   -BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEES.S---GGGEEEE-TT-TTTT---..SS.B--HH CS
               dTDP_sugar_isom  83 lRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvt.eyyapesergirwnDpelgidw..eelilSek 160
                                   +R+gSp +gk v+  L     ++l+ip+gfahGf++l++ ++v+Y ++ + ++p se+gir++Dp++g++w  +++i+S+k
  gi|70607435|ref|YP_256305.1|  85 IRRGSPWYGKFVSEILV--PGKMLWIPPGFAHGFQALEN-SHVVYFISgNDFSPPSEAGIRYDDPDIGVNWpiQNPIVSQK 162
                                   ****************9..99****************97.66666666699**********************99****** PP

                                   HHT-B-HHH CS
               dTDP_sugar_isom 161 Dkaapslae 169
                                   D ++psl+e
  gi|70607435|ref|YP_256305.1| 163 DLRWPSLKE 171
                                   ******986 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.4e-08   8.5e-05      29     115 ..      38     132 ..      15     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.4e-08
                                   HSSTEEEEEEEE..TTEEEEEEEE...SSS-EEEEEEESEEEEEEEETTSS....EEEEEE.EETTEEEEE-TT-EEEEEE CS
                       Cupin_1  29 ntlgisaarvdl.epgglllPhyh...pnateiayvlqGegrvgfvvpgng...nrdfhkk.lreGdvfvvPaglvhfqyn 101
                                   +   i+ +   + ++g ++ +hy        +++ v++G+ + + v   +g   + +f ++ l +G ++++P+g++h +++
  gi|70607435|ref|YP_256305.1|  38 FIDSIVQVNYSYsKKGVIRGLHYQlkpKEQGKLVTVIDGKIYDVAVDIRRGspwYGKFVSEiLVPGKMLWIPPGFAHGFQA 118
                                   556677777788788889999999332234579*********88888888899*9999999******************** PP

                                   ESSSSEEEEEEEES CS
                       Cupin_1 102 sgdepavaivvfdt 115
                                    +++ +v +++ ++
  gi|70607435|ref|YP_256305.1| 119 LENSHVVYFISGND 132
                                   *9888888887665 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.14     178     202 ..      98     122 ..      90     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                   EEE-TT-EEEE-TT-EEEEEBBT-C CS
                       Cupin_4 178 fvLepGDlLYlPrgviHqgvaedes 202
                                   ++L pG +L +P+g++H  +a+++s
  gi|70607435|ref|YP_256305.1|  98 EILVPGKMLWIPPGFAHGFQALENS 122
                                   689**************99888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1361.80
//
Query:       gi|70607436|ref|YP_256306.1|  [L=377]
Description: hypothetical protein Saci_1707 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-26   92.3   0.2    5.1e-26   91.8   0.2    1.2  1  SBP_bac_11     Bacterial extracellular solute-binding protein
    1.1e-10   41.9   6.9    1.8e-10   41.3   6.9    1.2  1  SBP_bac_1      Bacterial extracellular solute-binding protein
     0.0061   17.5   1.6      0.014   16.3   1.6    1.6  1  Pilin_N        Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.022   14.9   0.3    1.5  1  DUF2371        Uncharacterised conserved protein (DUF2371)
      0.021   15.1   7.7      0.021   15.1   7.7    2.2  2  DUF3446        Early growth response N-terminal domain
      0.071   12.9   0.2       0.17   11.7   0.2    1.6  1  DUF4307        Domain of unknown function (DUF4307)
       0.32   11.2   2.9       0.66   10.2   2.9    1.5  1  DUF2749        Protein of unknown function (DUF2749)
       0.47   10.5   2.5        9.2    6.3   0.3    2.5  2  NVEALA         NVEALA protein
       0.88    8.2   5.7       0.25   10.0   2.6    1.5  2  Prog_receptor  Progesterone receptor


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.2   2.6e-29   5.1e-26       1     219 [.      62     331 ..      62     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.6e-29
                                   .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEE CS
                    SBP_bac_11   1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplasspl 81 
                                   l ++ ag++aa+l+ la +F+++tg++ +v  ggs +la+qi +g+++Dv++p     ++++  +g  ++++  ++ s ++
  gi|70607436|ref|YP_256306.1|  62 LVIYGAGAYAAILNYLASQFQNQTGIQTHVNPGGSFALASQISQGSPVDVFVPVA--FIQAIPLEGSENPGWTIAFLSDQM 140
                                   6799**************************************************5..78888778888889********** PP

                                   EEEESTT-...T...............T---SHHH...HHHSS--EEEE--T-TTTTHH.HHHHGGG--.......HHHHH CS
                    SBP_bac_11  82 viavpkgn...p...............kkikgwad...LlkpglklavadPttspsGlaalalleaaga.......qellk 134
                                    i++   +   p               ++ + w +   Ll  +++l++a+P+t+p Gl+a+ +l+ ag        +++ +
  gi|70607436|ref|YP_256306.1| 141 TIVYSNYTesaPywnqlysnytmamktNQTQYWYNffyLLSTKFSLGIANPNTDPEGLYAYLILNMAGYlyanhnsSYFTD 221
                                   ****99985552444444444444432222223334557778***********************9999998888644444 PP

                                   HHHHT.EEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--......................... CS
                    SBP_bac_11 135 alekk.vvklgessrqlltaveageadagivyeseakaaengdkleavylpeglnld........................ 190
                                    ++ +  vk+++++   ++ ++age d  ++y s a     ++kl+++ lp+ l +                         
  gi|70607436|ref|YP_256306.1| 222 LVKANpNVKSATTTAAFVSPLKAGELDFTFSYVSYAV----SQKLDYLKLPPWLSFGyypnetqwysqfsynitvsgktlt 298
                                   44444233455555666666****************9....89999999999888635888999999************** PP

                                   ......EEEEEEEE-TT--HHHHHHHHHTTSHH CS
                    SBP_bac_11 191 ....pldypaavlkkaakreaAraFlafLrspe 219
                                       p++++++v+ ++++++aA  F++f++s+e
  gi|70607436|ref|YP_256306.1| 299 ihgnPVYLYITVPLTSTNPNAAYQFIQFILSHE 331
                                   *******************************87 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   6.9   8.8e-14   1.8e-10       8     313 ..      72     332 ..      65     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.8e-14
                                   HHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                     SBP_bac_1   8 aalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkd 88 
                                   a+l++l+  +f+   +gi+  ++++gs +la     +i++G+ p Dv+              +++   p+ + +++ ++  
  gi|70607436|ref|YP_256306.1|  72 AILNYLA-SQFQN-QTGIQTHVNPGGSFALAS----QISQGS-PVDVFVP-----------VAFIQAIPLEGSENPGWTIA 134
                                   4677777.99988.7**********9999999....******.66*****...........999999999*****999988 PP

                                   TEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHH CS
                     SBP_bac_1  89 aadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyfa 169
                                   + ++                     ++ ++Y   + e a+      W++l+     +++ + +        ++ +  y++ 
  gi|70607436|ref|YP_256306.1| 135 FLSD---------------------QMTIVY-SNYTESAP-----YWNQLYSNYTMAMKTNQTQ-------YWYNFFYLLS 181
                                   7777.....................677777.66667777.....*******************.......9999999999 PP

                                   HHHHHHHTGGGEECCCT......HHCSHHHHS.HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHH CS
                     SBP_bac_1 170 lalakslggkvfdkdgg......gldnpegvt.aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglw 243
                                   + ++++ +++  d +g       +++ + + + +  y+++l+       +  +++++ ++ aa ++ ++aGe ++++++ +
  gi|70607436|ref|YP_256306.1| 182 TKFSLGIANPNTDPEGLyaylilNMAGYLYANhNSSYFTDLV-------KANPNVKSATTTAAFVSPLKAGELDFTFSYVS 255
                                   99999999999999999****999999999999999*****9.......55555556666666679999************ PP

                                   HHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.......EEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                     SBP_bac_1 244 aalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.......lgayglaipkgsknpeaAkkFldfllspea 313
                                   +a ++++ ++k + + +  ++++e+ +           g        +++ ++++p +s np aA +F++f+ls+e 
  gi|70607436|ref|YP_256306.1| 256 YAVSQKLDYLKLPPWLSFGYYPNETQWYSQFSYNITVSGKtltihgnPVYLYITVPLTSTNPNAAYQFIQFILSHES 332
                                   ****************************987776666666999*******************************985 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.6     7e-06     0.014      12      54 ..      13      55 ..      10      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7e-06
                       Pilin_N 12 mvaitvIlaAviaafvlglasneekapqasievkidssastgk 54
                                  +v +++I++Av+++ v  l+++++++p  s +++++ss+s+++
  gi|70607436|ref|YP_256306.1| 13 IVIVVIIVIAVVGVAVYFLSQKPSSSPTSSSSTSSSSSNSASS 55
                                  6889999**********99999999999988666444443322 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   1.1e-05     0.022      38      92 ..       9      63 ..       4      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                       DUF2371 38 svsglvlllGllvllvGiamavlgywpkkaklaseekssssstaessseklglla 92
                                   v+++v+++ +++ +vG+a+  l+  p+++ ++s+++sssss++ ss++++g l+
  gi|70607436|ref|YP_256306.1|  9 RVQAIVIVVIIVIAVVGVAVYFLSQKPSSSPTSSSSTSSSSSNSASSTSQSGNLV 63
                                  57889999*********************88888888888887777777777664 PP

>> DUF3446  Early growth response N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   7.7     1e-05     0.021      23      66 ..      19      59 ..       7      74 .. 0.52
   2 ?   -2.0   0.0       2.2   4.5e+03      32      32 ..     215     215 ..     168     245 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                       DUF3446 23 lvsglvgvan......ppsspsssssssssssssssspslscsvaaqqss 66
                                  +v  +vgva       p+ssp+ssss+sssss s+ss s          s
  gi|70607436|ref|YP_256306.1| 19 IVIAVVGVAVyflsqkPSSSPTSSSSTSSSSSNSASSTSQ---------S 59
                                  4447777766544432333333333333333333333322.........2 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                       DUF3446  32 n 32 
                                   n
  gi|70607436|ref|YP_256306.1| 215 N 215
                                   2 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   8.4e-05      0.17       3      38 ..       9      46 ..       8      59 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                       DUF4307  3 rllvillvvlvvvalalvawigysq..gsadvsaevvg 38
                                  r+ +i++vv++v+a+++va++++sq  +s++ s++ ++
  gi|70607436|ref|YP_256306.1|  9 RVQAIVIVVIIVIAVVGVAVYFLSQkpSSSPTSSSSTS 46
                                  67789999999999999999998886644444444433 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.9   0.00033      0.66       4      35 ..      12      44 ..      10      58 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00033
                       DUF2749  4 rilIvlviavaagagtilwlvvqpr.agtsgsg 35
                                  +i+Iv++i++a+++  +  l  +p  ++ts+s 
  gi|70607436|ref|YP_256306.1| 12 AIVIVVIIVIAVVGVAVYFLSQKPSsSPTSSSS 44
                                  7999*********99999997777763333332 PP

>> NVEALA  NVEALA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3    0.0046       9.2       3      30 ..      10      37 ..       8      39 .. 0.58
   2 ?    3.4   0.1     0.037        73      14      37 ..     203     226 ..     197     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0046
                        NVEALA  3 ifkilfvlvfavlagtgiyksnkkevsl 30
                                  +++i++v+++++++  + +++  +++s+
  gi|70607436|ref|YP_256306.1| 10 VQAIVIVVIIVIAVVGVAVYFLSQKPSS 37
                                  5666666666655555556666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.037
                        NVEALA  14 vlagtgiyksnkkevslsdLalaN 37 
                                   +l + g+++ n+++  ++dL+ aN
  gi|70607436|ref|YP_256306.1| 203 ILNMAGYLYANHNSSYFTDLVKAN 226
                                   44455559**************99 PP

>> Prog_receptor  Progesterone receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.6   0.00013      0.25     430     544 ..      33     148 ..      21     153 .. 0.84
   2 ?   -2.6   0.1      0.81   1.6e+03     405     426 ..     209     230 ..     206     260 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                 Prog_receptor 430 raPssrpGeaavaaaaasasvssasssGsalecilykaeGappqqGpfaplpckaPgagacllprdglastsas....aaa 506
                                   + Pss p  ++ +++++s s+ss+s sG   + ++y a    +    +a++  ++ g+ + + p  ++a +s+      + 
  gi|70607436|ref|YP_256306.1|  33 QKPSSSPTSSSSTSSSSSNSASSTSQSG---NLVIYGAGAYAAILNYLASQFQNQTGIQTHVNPGGSFALASQIsqgsPVD 110
                                   5699999999999999999999999999...789**99887888899999999999******9999988887762221233 PP

                 Prog_receptor 507 agaaPalyeplglnglpqlGyqaavlkeglpqvyqpyl 544
                                      + a+++++ l+g  + G+  a l++ +  vy+ y 
  gi|70607436|ref|YP_256306.1| 111 VFVPVAFIQAIPLEGSENPGWTIAFLSDQMTIVYSNYT 148
                                   3456799***************************9995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.81
                 Prog_receptor 405 ylvaganaavfpdfplapppea 426
                                   yl a+ n++ f+d+  a p+ +
  gi|70607436|ref|YP_256306.1| 209 YLYANHNSSYFTDLVKANPNVK 230
                                   8999999999999988876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1483  (0.0827152); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 2521.00
//
Query:       gi|70607437|ref|YP_256307.1|  [L=454]
Description: mercuric reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-55  187.6   0.2      4e-55  187.1   0.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.9e-30  104.3   0.1    8.7e-30  103.2   0.1    1.6  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
      5e-17   62.1   0.3    8.1e-17   61.4   0.3    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-10   41.3   1.8    2.3e-10   40.9   0.0    2.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.2e-07   31.2   9.8    0.00029   20.0   2.1    4.4  4  GIDA           Glucose inhibited division protein A
    0.00021   20.1   1.4        0.4    9.3   0.0    3.1  3  HI0933_like    HI0933-like protein
     0.0018   17.5   2.3       0.29   10.2   0.0    2.3  2  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.095   11.8   0.6       0.68    9.0   0.0    2.4  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.1   0.2   1.8e-58     4e-55       1     294 []       2     310 ..       2     310 .. 0.95

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 1.8e-58
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH...................HH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx...................xx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias...................ev 59 
                                   +d+++iG G+AG++a +++++ g+k ++++    +gtc+n+gc++sk ll+++e ++ as                   e 
  gi|70607437|ref|YP_256307.1|   2 YDLAIIGYGAAGFSALIRANELGIKPVIIGygeIGGTCVNVGCVPSKRLLSIGETYKYASialnqkttpnfeksfedksEI 82 
                                   689**************************8888**********************************************99 PP

                                   HHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCS CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  60 vkklnqg.ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklk 139
                                   v++l+++ +e +l++   k+++g++++   +  + ++e ++++k ++AtGssp +++i+G+ e +     +++++eal+  
  gi|70607437|ref|YP_256307.1|  83 VSSLRKEkYEDVLNSYDAKVIKGRAHFISPNAIKVNGEIVEAKKFIIATGSSPSIPDIKGLREAG-----YWTNVEALSPT 158
                                   99999999******9999*******************************************5555.....79********* PP

                                   S-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgngeklevv 219
                                    +  +++++Gg + ++E+++++++lg++++++++ +r+l++ ++e+s  ++ +le++  + v ++ +vke++ +++  +v+
  gi|70607437|ref|YP_256307.1| 159 RRISSLAIIGGRALALEFSQMYKRLGVDTVILQRSNRILPNWEPEISLSVKSYLENMeEIPVFTQVKVKEVETKND-QKVI 238
                                   *********************************************************9**************9998.78** PP

                                   ETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    +d  e+++d ++va+G+rp+ +l + + +g+ l+e+gg++vde lrt+ p+i+a+GDv+   g  +l  +A ++G
  gi|70607437|ref|YP_256307.1| 239 ITDMGEVEVDEILVATGRRPNVDL-NlNVAGVSLNEKGGVKVDEELRTTNPNIFAAGDVI---GEQMLESVAGKEG 310
                                   *********************999.77*********************************...6667767776665 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.1   3.9e-33   8.7e-30       1     109 [.     330     438 ..     330     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.9e-33
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   ip+vvf dp+v+ vGlt+ eA+  g+ +++  ++++++ +a++ +e++g++K+v+++++ ++lGa i+G++ +e+i+e+a+
  gi|70607437|ref|YP_256307.1| 330 IPQVVFIDPNVSRVGLTQVEAESSGYTVDYRVVNMESVPKARILRESHGLIKMVVNREDMRILGAEIFGKNSAEIINEAAL 410
                                   79******************************************************************************* PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                   aik+++t+ d++dtih+ Pt+se+lk a
  gi|70607437|ref|YP_256307.1| 411 AIKFRATIYDIIDTIHVFPTMSESLKIA 438
                                   ***********************99865 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.3   3.6e-20   8.1e-17       2     305 .]       6     294 ..       5     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.6e-20
                   Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgnignsiyry..pkemtfispsftsekleipdlnaiseetspafslkeeklsr 80 
                                   IiG G+aG +a i ++++g+ + +i+  g+ig +  +     +++++s     e  +   + a+ ++t p+  +++    +
  gi|70607437|ref|YP_256307.1|   6 IIGYGAAGFSALIRANELGI-KPVIIGYGEIGGTCVNVgcVPSKRLLSIG---ETYKYASI-ALNQKTTPN--FEKSFEDK 79 
                                   9*******************.578**********9996225689999*75...55555554.566777785..56777777 PP

                   Pyr_redox_3  81 kealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhk 161
                                    e+++ lr+   +  l+    + ++  ++  +   ++ + e +eAkk iiAtG    P  ++i+G    +    +v+++++
  gi|70607437|ref|YP_256307.1|  80 SEIVSSLRKEKYEDVLNSYDAKVIKGRAHFISPNAIKVNGEIVEAKKFIIATGS--SPSIPDIKGLR-EAGYWTNVEALSP 157
                                   78888887776665554444444444444455668******************9..**********9.7888889999999 PP

                   Pyr_redox_3 162 ya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikek 241
                                   ++    +++iGg   a +      r g +  ++ r++ i  +    + +++  +++ le++   e+i v ++ +vke+++k
  gi|70607437|ref|YP_256307.1| 158 TRrISSLAIIGGRALALEFSQMYKRLGVDTVILQRSNRILPNW---EPEISLSVKSYLENM---EEIPVFTQVKVKEVETK 232
                                   8857899****************************99887752...223333445555554...5699***********99 PP

                   Pyr_redox_3 242 eeeykvktedgkkvevkddvvlatGykpdlsflkk.slfeldedgrpvlteeteetnvpglflaG 305
                                   + +  + t+ g +vev d++++atG +p++++  + ++++l+e+g ++++ee   t  p++f aG
  gi|70607437|ref|YP_256307.1| 233 NDQKVIITDMG-EVEV-DEILVATGRRPNVDLNLNvAGVSLNEKGGVKVDEELRTT-NPNIFAAG 294
                                   88866666665.7787.88899**********5555***************99887.59***998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.6       5.6   1.3e+04       3      28 ..       5      30 ..       4      36 .. 0.62
   2 !   40.9   0.0     1e-13   2.3e-10       2      77 ..     164     238 ..     163     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.6
                                  EEECSSHHHHHHHHHHHHTTSEEEEE CS
                     Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvv 28
                                  +++G G  g  +   ++elg k  ++
  gi|70607437|ref|YP_256307.1|  5 AIIGYGAAGFSALIRANELGIKPVII 30
                                  67777777766666666666554444 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1e-13
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                   ++++Gg  ++lE+ +++++lg ++ +++rs+++l++ ++e+s  ++ +le++  i v ++ kv+e+e+++d+  +v 
  gi|70607437|ref|YP_256307.1| 164 LAIIGGRALALEFSQMYKRLGVDTVILQRSNRILPNWEPEISLSVKSYLENMeEIPVFTQVKVKEVETKNDQ--KVI 238
                                   79**************************************************9**************99996..354 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.1   1.3e-07   0.00029       1     150 [.       3     133 ..       3     156 .. 0.83
   2 ?    2.9   0.2      0.02        45      98     149 ..     205     255 ..     201     268 .. 0.76
   3 !    8.4   0.0   0.00045         1     347     390 ..     280     323 ..     275     325 .. 0.86
   4 ?   -1.5   0.0      0.47     1e+03     323     346 ..     344     367 ..     340     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEEST CS
                          GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilNr 79 
                                   d+ +iG G AG+ A + a +lG+k ++i   +  +t+++++C ps + ++ g+  +               a  q+ + N 
  gi|70607437|ref|YP_256307.1|   3 DLAIIGYGAAGFSALIRANELGIKPVIIgyGEIGGTCVNVGCVPSKRLLSIGETYKYASI-----------ALNQKTTPNF 72 
                                   5789*********************999989999***************99977654332...........2223335677 PP

                                   TS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA  80 skGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   +k +  ++    +  +l +++++++l++  + ++i+++++ +++        ++ +ge+++ak+++iatG+
  gi|70607437|ref|YP_256307.1|  73 EKSFEDKSE---IVSSLRKEKYEDVLNS-YDAKVIKGRAHFISP------NAIKVNGEIVEAKKFIIATGS 133
                                   777777666...7778888888888888.889**********99......788899**************9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.02
                                   HHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                          GIDA  98 skevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavviatG 149
                                   s +v+ +len +++ ++++ +v+e+++ ++  k+++t++g +++ + + +atG
  gi|70607437|ref|YP_256307.1| 205 SLSVKSYLENMEEIPVFTQvKVKEVET-KNDQKVIITDMG-EVEVDEILVATG 255
                                   668999**********97647999966.555555555555.567778888998 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00045
                                   -TTSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHHHHHCT CS
                          GIDA 347 lntLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaarkakg 390
                                    ++L+t  ++++f+AG++ G +  +E++a   G++A  na +++++
  gi|70607437|ref|YP_256307.1| 280 DEELRTT-NPNIFAAGDVIGEQ-MLESVAgkEGFIAVDNAILNSHK 323
                                   4578887.9************9.999999999****9999887765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.47
                                   T-TT--EEE--EEEEEEEE-GGGB CS
                          GIDA 323 GLenaeivrpGyaieydyvdprql 346
                                   GL ++e    Gy ++y++v+ + +
  gi|70607437|ref|YP_256307.1| 344 GLTQVEAESSGYTVDYRVVNMESV 367
                                   9999**9************97765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.4    0.0037       8.2       2      29 ..       3      30 ..       2      39 .. 0.86
   2 ?    3.0   0.0     0.015        34     143     169 ..     113     139 ..      74     150 .. 0.71
   3 !    9.3   0.0   0.00018       0.4     122     187 ..     216     279 ..     174     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0037
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlll 29
                                  d+++iG GaAG+ a i+a++ g + +++
  gi|70607437|ref|YP_256307.1|  3 DLAIIGYGAAGFSALIRANELGIKPVII 30
                                  899***************9999887766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
                                   EEEEE.TTEEEEESEEEE----S.S-GG CS
                   HI0933_like 143 frvktkseeeleadklvlAtGGl.SiPk 169
                                     +k+ ++e +ea+k ++AtG+  SiP 
  gi|70607437|ref|YP_256307.1| 113 NAIKV-NGEIVEAKKFIIATGSSpSIPD 139
                                   56788.99*************7437776 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00018
                                   HT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT--SHHHHHHHHTT--E CS
                   HI0933_like 122 agvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGstgkgyklaeqfghti 187
                                   +++ + ++ +vk+ve+++d+   + t + +e+e d++++AtG      l  + +g++l e+ g+++
  gi|70607437|ref|YP_256307.1| 216 EEIPVFTQVKVKEVETKNDQ-KVIIT-DMGEVEVDEILVATGRRPNVDLNLNVAGVSLNEKGGVKV 279
                                   5788999*******999999.44555.79*************988888877788888877777777 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   1.2     0.002       4.5       1      28 [.       3      30 ..       3      40 .. 0.86
   2 !   10.2   0.0   0.00013      0.29     372     406 ..     273     301 ..     224     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEE CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavv 28
                                  D+ +iG G+AG +A ++a+e G k +++
  gi|70607437|ref|YP_256307.1|  3 DLAIIGYGAAGFSALIRANELGIKPVII 30
                                  899*******************976666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
                                   ES-EEEBETTSBESTTEEESSBTEEE-STCEESSS CS
                 FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGevaaggv 406
                                     gGv++de++r+      + p+ +AaG v++ ++
  gi|70607437|ref|YP_256307.1| 273 EKGGVKVDEELRT------TNPNIFAAGDVIGEQM 301
                                   579**********......***********97665 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.19   4.2e+02       2      24 ..       1      23 [.       1      30 [. 0.84
   2 ?    9.0   0.0    0.0003      0.68     142     199 ..     117     169 ..      74     199 .. 0.76
   3 ?   -1.8   0.0       0.6   1.3e+03     295     339 ..     218     255 ..     177     258 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                   K_oxygenase  2 ilDligiGiGpsnLsLailleev 24
                                  ++Dl++iG G++  s  i+++e 
  gi|70607437|ref|YP_256307.1|  1 MYDLAIIGYGAAGFSALIRANEL 23
                                  59**********99988887765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                   K_oxygenase 142 geeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGs 199
                                    + e +ea++ ++++G++p+iP++   l+ ++  + + e+l+ +   ++  ++a++G+
  gi|70607437|ref|YP_256307.1| 117 VNGEIVEAKKFIIATGSSPSIPDIK-GLR-EAGYWTNVEALSPT---RRISSLAIIGG 169
                                   456789****************974.455.36667776666665...45666777775 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.6
                   K_oxygenase 295 lrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                   + + ++++v+++e +++++v +  ++       ++evd +++ATG
  gi|70607437|ref|YP_256307.1| 218 IPVFTQVKVKEVETKNDQKVII--TD-----MGEVEVDEILVATG 255
                                   4445555555555555422222..22.....34567777778877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2939.33
//
Query:       gi|70607438|ref|YP_256308.1|  [L=52]
Description: hypothetical protein Saci_1709 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-05   25.2   2.0    1.8e-05   24.7   2.0    1.2  1  YHS              YHS domain
    4.2e-05   23.8   4.5    5.7e-05   23.4   4.5    1.2  1  Arc_trans_TRASH  Archaeal TRASH domain
    7.3e-05   22.6   4.2    9.6e-05   22.2   4.2    1.2  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
    0.00047   20.8   4.9    0.00055   20.6   4.9    1.1  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
  ------ inclusion threshold ------
       0.01   16.1   0.9      0.011   16.0   0.9    1.1  1  Ta0938           Ta0938
       0.02   15.6   4.3      0.025   15.3   4.3    1.2  1  zinc_ribbon_15   zinc-ribbon family
      0.049   13.9   3.0      0.057   13.7   3.0    1.2  1  DUF2175          Uncharacterized protein conserved in archaea
      0.093   13.0   7.1        2.8    8.3   7.0    2.1  1  LIM              LIM domain
       0.14   12.6   3.7        1.3    9.4   0.5    2.1  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.18   11.9   5.0        1.7    8.7   5.0    1.9  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.32   11.0   7.8        4.4    7.3   7.8    2.1  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.61   10.2   8.5        3.1    8.0   0.3    2.2  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   2.0   1.2e-08   1.8e-05       6      39 ..      16      48 ..      15      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdkFed 39
                                  cgm +  e+  ++   kGke yFc++ C ++Fe+
  gi|70607438|ref|YP_256308.1| 16 CGMEL-TEEHIYTRMIKGKEHYFCCADCSNEFER 48
                                  *****.5558888889****************96 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   4.5   3.8e-08   5.7e-05       1      36 [.      13      49 ..      13      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.8e-08
               Arc_trans_TRASH  1 CDYCGkeivgePivyk.lknkvYyvCCktCkselkkk 36
                                  C  CG e+++e i  + +k k  y+CC  C +e+ +k
  gi|70607438|ref|YP_256308.1| 13 CENCGMELTEEHIYTRmIKGKEHYFCCADCSNEFERK 49
                                  899*******9986662688**************987 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   4.2   6.4e-08   9.6e-05       4      41 .]      11      46 ..       8      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-08
                        zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41
                                   +C++C+ +++  +   y + ++g++++FC+ +C +++
  gi|70607438|ref|YP_256308.1| 11 LKCENCGMELTEEHI--YTRMIKGKEHYFCCADCSNEF 46
                                  58*****99988887..8****************9998 PP

>> ATPase-cat_bd  Putative metal-binding domain of cation transport ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   4.9   3.7e-07   0.00055       1      33 [.      12      44 ..      12      48 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-07
                 ATPase-cat_bd  1 aCyHCglpveesaklkaeiegeerefCCkGCqa 33
                                  +C  Cg +++e++ +++ i+g+e++fCC+ C +
  gi|70607438|ref|YP_256308.1| 12 KCENCGMELTEEHIYTRMIKGKEHYFCCADCSN 44
                                  69*****************************85 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.9   7.5e-06     0.011      14      48 ..      10      47 ..       2      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.5e-06
                                  GGS-SS---S---...SS-B-TT--BSSS--SSSS-TT CS
                        Ta0938 14 ekgcalcgatwgd...yyeevdgeklffccdicakefv 48
                                  e  c  cg    +   y   ++g++ +fcc  c++ef 
  gi|70607438|ref|YP_256308.1| 10 ELKCENCGMELTEehiYTRMIKGKEHYFCCADCSNEFE 47
                                  556888887665534477889***************96 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   4.3   1.7e-05     0.025      29      81 ..       2      52 .]       1      52 [] 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                zinc_ribbon_15 29 fkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveeefky 81
                                  +k++ +k  l+c++C++ l++++ +++ i+ k  +++  C++C++e e +f++
  gi|70607438|ref|YP_256308.1|  2 VKIRMNKNELKCENCGMELTEEHIYTRMIKGK--EHYFCCADCSNEFERKFNF 52
                                  567778899************99777777644..45889************98 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   3.8e-05     0.057       2      33 ..      10      41 ..       9      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                       DUF2175  2 kwkCyiCgkeivegekFTftkkgvvHyeClve 33
                                  + kC  Cg e++e++ +T + kg  Hy C ++
  gi|70607438|ref|YP_256308.1| 10 ELKCENCGMELTEEHIYTRMIKGKEHYFCCAD 41
                                  569**************************765 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.0    0.0018       2.8       1      39 [.      13      49 ..      13      52 .] 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                                  -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT CS
                           LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkeg 39
                                  C++C+ + +++++ +++   +  e+ F+C+dC++e++++
  gi|70607438|ref|YP_256308.1| 13 CENCGMELTEEHIYTRMIKGK--EHYFCCADCSNEFERK 49
                                  999999999888776665555..45799*****999876 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.029        43      21      37 ..       4      17 ..       1      19 [. 0.60
   2 ?    9.4   0.5    0.0009       1.3      18      38 ..      27      44 ..      24      45 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.029
               FeoB_associated 21 ikkkkkG.sCgggCsgCs 37
                                  i+  k++ +C     +C+
  gi|70607438|ref|YP_256308.1|  4 IRMNKNElKC----ENCG 17
                                  4556777455....5553 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0009
               FeoB_associated 18 rrlikkkkkGsCgggCsgCss 38
                                   r+ik k++  C   C++Cs+
  gi|70607438|ref|YP_256308.1| 27 TRMIKGKEHYFC---CADCSN 44
                                  589998777777...777775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.0    0.0011       1.7      63      94 ..       3      44 ..       1      48 [. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                                  EEEEE--EEEETTTS-EEECHH.HHH..........S-TTTSS CS
                          HypA 63 eieevpvkvrCreCgkefelee.kal..........rCpkCgs 94
                                  +i+  + +++C++Cg e ++e+ + +           C +C++
  gi|70607438|ref|YP_256308.1|  3 KIRMNKNELKCENCGMELTEEHiY-TrmikgkehyfCCADCSN 44
                                  678889999******999977642.135788889999999986 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.8     0.003       4.4       4      30 .]      12      47 ..      11      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.003
                PhnA_Zn_Ribbon  4 kCplCaSeytY.........edgallvCpeCahEwe 30
                                  kC++C++e t               + C +C++E+e
  gi|70607438|ref|YP_256308.1| 12 KCENCGMELTEehiytrmikGKEHYFCCADCSNEFE 47
                                  9******98867777****666667899******97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3     0.002       3.1       5      14 ..      10      19 ..       1      25 [. 0.59
   2 ?    4.1   8.8     0.034        51       5      39 ..      10      49 ..      10      51 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.002
                   Zn-ribbon_8  5 eYrCeeCghe 14
                                  e +Ce+Cg e
  gi|70607438|ref|YP_256308.1| 10 ELKCENCGME 19
                                  3455555543 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.034
                   Zn-ribbon_8  5 eYrCeeCghefe...vlqsisdaplta..CPeCgsevrrv 39
                                  e +Ce+Cg e +   +  ++ + ++    C +C  e +r 
  gi|70607438|ref|YP_256308.1| 10 ELKCENCGMELTeehIYTRMIKGKEHYfcCADCSNEFERK 49
                                  6789999988888874444443333333688997788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 371.48
//
Query:       gi|70607439|ref|YP_256309.1|  [L=132]
Description: hypothetical protein Saci_1710 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-16   57.6   0.8    1.4e-15   56.9   0.8    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
    3.8e-10   39.7   0.0    5.5e-10   39.2   0.0    1.3  1  HTH_20         Helix-turn-helix domain
    2.1e-06   27.5   0.0    3.7e-06   26.7   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
    1.4e-05   25.2   0.1    2.4e-05   24.4   0.1    1.3  1  HTH_34         Winged helix DNA-binding domain
      4e-05   23.1   0.1    8.5e-05   22.0   0.1    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    0.00061   20.1   0.0     0.0009   19.5   0.0    1.3  1  Rrf2           Transcriptional regulator
     0.0008   19.2   1.1      0.002   18.0   1.1    1.6  1  TFIIE_alpha    TFIIE alpha subunit
     0.0014   18.4   0.1     0.0022   17.9   0.1    1.3  1  MarR_2         MarR family
      0.003   17.0   0.0      0.056   13.0   0.0    2.2  2  Sigma70_r4     Sigma-70, region 4
     0.0048   16.8   0.0     0.0088   16.0   0.0    1.5  1  HTH_11         HTH domain
     0.0059   16.8   0.3      0.014   15.6   0.3    1.6  1  DUF2551        Protein of unknown function (DUF2551)
     0.0097   15.6   0.1       0.02   14.7   0.1    1.5  1  HTH_38         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.019   14.8   0.0    1.3  1  HTH_23         Homeodomain-like domain
      0.029   14.8   0.1      0.044   14.2   0.1    1.3  1  HTH_40         Helix-turn-helix domain
      0.045   13.6   0.4        0.1   12.5   0.4    1.6  1  HTH_Tnp_Tc3_1  Tc3 transposase
      0.066   13.3   0.1        0.1   12.7   0.1    1.3  1  Phage_RpbA     Phage RNA polymerase binding, RpbA
       0.11   12.7   0.6        0.2   11.8   0.6    1.4  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
       0.13   12.1   0.0        0.2   11.5   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
       0.13   12.0   0.0       0.25   11.2   0.0    1.4  1  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.8   1.4e-18   1.4e-15       1      46 [.      17      63 ..      17      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 1.4e-18
                                  SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  d+tRl I+ +L e +e +v e+++ l++sqs +ShHL++Lr++G+V+
  gi|70607439|ref|YP_256309.1| 17 DKTRLSIVLFLLEkEEVTVDEISRTLNKSQSLISHHLACLRNCGIVK 63
                                  89*******9999788******************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   5.9e-13   5.5e-10       3      61 .]      11      69 ..       9      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 5.9e-13
                                  HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                   ++AL++++R+ i   L ++e++t+ e+ ++l  s++ +s+HL+ L+  g+v+v+reg+
  gi|70607439|ref|YP_256309.1| 11 FFSALSDKTRLSIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVKVRREGK 69
                                  699******************************************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     4e-09   3.7e-06      16      62 ..      26      72 ..      22      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4e-09
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62
                                   Ll++++ t+dei++ l+ ++s +   L  L ++G+V+++++ +  Y
  gi|70607439|ref|YP_256309.1| 26 FLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVKVRREGKFSY 72
                                  599*************************************9887644 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   2.5e-08   2.4e-05       2      49 ..      20      67 ..      19      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.5e-08
                        HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdke 49
                                  Rl+++ +L++++e++  e++ +l+ +++ +s hl  L + g ++v+ e
  gi|70607439|ref|YP_256309.1| 20 RLSIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVKVRRE 67
                                  9*****************************************999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1     9e-08   8.5e-05       2      48 .]      17      63 ..      16      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9e-08
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  d+t++ I   L ++   +  e+++ l+ S+s ++ +l  L + G++k
  gi|70607439|ref|YP_256309.1| 17 DKTRLSIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVK 63
                                  89*******************************************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.6e-07    0.0009      16      69 ..      24      77 ..      14      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.6e-07
                                  HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET.TT-TCEEESS CS
                          Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr.GkgGGyrLak 69
                                  +L + e+ee v+++ei++  n s+s +++ la Lr+ g+vk++r Gk   y+La 
  gi|70607439|ref|YP_256309.1| 24 VLFLLEKEE-VTVDEISRTLNKSQSLISHHLACLRNCGIVKVRReGKFSYYSLAD 77
                                  444555655.*******************************98657777777765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   2.1e-06     0.002      17      95 ..      22      94 ..      11     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                                  HHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHH CS
                   TFIIE_alpha 17 lvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkk 95
                                   ++  Llek evt +++++ l+  +  + + L+ L++ ++vk++r+       +  y+ + +e + + vk+ +e+v+k 
  gi|70607439|ref|YP_256309.1| 22 SIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVKVRREG------KFSYYSLADEDIKNLVKNAIEHVRKY 94
                                  56677899***********************************9853......456999****************9985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.3e-06    0.0022      10      55 ..      24      66 ..      15      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                  vL+ L  ++   +tv e+ r+l+ s+s +s +l+ L   G v  r+
  gi|70607439|ref|YP_256309.1| 24 VLFLLEKEE---VTVDEISRTLNKSQSLISHHLACLRNCGIVKVRR 66
                                  566666665...******************************8875 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     6e-05     0.056       3      39 ..      13      51 ..      11      55 .. 0.91
   2 ?    1.9   0.0      0.17   1.6e+02      35      50 .]      78      93 ..      72      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-05
                                  HHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHH CS
                    Sigma70_r4  3 asLpererevlelrf..geglTleEIgerlgiSrerVrq 39
                                  + L+++ r  ++l     e+ T  EI+++l+ S++ ++ 
  gi|70607439|ref|YP_256309.1| 13 SALSDKTRLSIVLFLleKEEVTVDEISRTLNKSQSLISH 51
                                  6899*********99999****************98875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                                  HHHHHHHHHHHHHHHH CS
                    Sigma70_r4 35 erVrqiekrAlrkLRk 50
                                  e ++ + k+A++++Rk
  gi|70607439|ref|YP_256309.1| 78 EDIKNLVKNAIEHVRK 93
                                  789***********97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.3e-06    0.0088       2      49 ..      20      64 ..      19      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-06
                        HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIese 49
                                  +l+i+ +Lle+++ ++ +e+++ Ln S + +  +++ L+  g v+   +
  gi|70607439|ref|YP_256309.1| 20 RLSIVLFLLEKEE-VTVDEISRTLNKSQSLISHHLACLRNCGiVK---V 64
                                  6789999988888.***************************9433...3 PP

>> DUF2551  Protein of unknown function (DUF2551)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.4e-05     0.014       1      79 [.       8      79 ..       8      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                       DUF2551  1 LkkylerDksGiRrevLklfleakkltveeiyeklkekfdvsykgvasmvGliasrlGIlkvkkeskgeknvYsLkeey 79
                                  L+++ +  ++  R ++  ++le++++tv+ei ++l+++ ++  +  a +        GI+kv  +++g+ + YsL +e+
  gi|70607439|ref|YP_256309.1|  8 LESFFSALSDKTRLSIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACL-----RNCGIVKV--RREGKFSYYSLADED 79
                                  677888889999*************************988888888776.....45788888..555666677777665 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.1e-05      0.02      17      41 ..      28      53 ..      13      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                        HTH_38 17 l.aeGlslreIArrLgrspsTIsREl 41
                                  l +e  ++ eI r L++s s Is +l
  gi|70607439|ref|YP_256309.1| 28 LeKEEVTVDEISRTLNKSQSLISHHL 53
                                  32577999***************987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     2e-05     0.019       3      36 ..      16      51 ..      14      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                        HTH_23  3 sereRlrillllae..GlsvreIAreLgvsrrTvyr 36
                                  s + Rl+i+l l+e    +v eI+r L+ s++ +++
  gi|70607439|ref|YP_256309.1| 16 SDKTRLSIVLFLLEkeEVTVDEISRTLNKSQSLISH 51
                                  7899*********999**************997765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.6e-05     0.044       9      66 ..      28      93 ..      21     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                        HTH_40  9 l.eeglsieeIAkerglkesTIegHLaelieeg.......eeidlerlvseeeekeIeeaiekvgs 66
                                  l +e  +++eI++  + ++s I  HLa l + g        ++++  l +e++++ +++aie+v++
  gi|70607439|ref|YP_256309.1| 28 LeKEEVTVDEISRTLNKSQSLISHHLACLRNCGivkvrreGKFSYYSLADEDIKNLVKNAIEHVRK 93
                                  458999*********************9888865555554349999999*************9873 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00011       0.1       3      41 ..      13      53 ..      12      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                  ----HHHH.HHHH.HHHHTT--HHHHHHHHT--HHHHHHHH CS
                 HTH_Tnp_Tc3_1  3 saLSDtEr.aill.vmkllnvklsEiarklsRsRnCIrryL 41
                                  saLSD  r +i+l  + +  v + Ei+r l++s   I+ +L
  gi|70607439|ref|YP_256309.1| 13 SALSDKTRlSIVLfLLEKEEVTVDEISRTLNKSQSLISHHL 53
                                  79999988334441456678****************99987 PP

>> Phage_RpbA  Phage RNA polymerase binding, RpbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011       0.1      38      78 ..      64     105 ..      55     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                    Phage_RpbA  38 leqevrfelYkeiDkeVsd...kwielmrkhredslaagakvvk 78 
                                   + +e +f +Y   D+++++   ++ie +rk+ +++la+   vv 
  gi|70607439|ref|YP_256309.1|  64 VRREGKFSYYSLADEDIKNlvkNAIEHVRKYSKSILACE--VVS 105
                                   57899*********9998633368************995..444 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   0.00021       0.2      17      58 ..      22      63 ..      15      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                  HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                         HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                   +v +Ll+k   t++e++++++ s +++ + L+ L + ++V+
  gi|70607439|ref|YP_256309.1| 22 SIVLFLLEKEEVTVDEISRTLNKSQSLISHHLACLRNCGIVK 63
                                  5899*******************************9988885 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021       0.2      16      49 ..      30      63 ..      21      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                  BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   +e+t+ e++r +  + S  +++L+ L ++G+v+
  gi|70607439|ref|YP_256309.1| 30 KEEVTVDEISRTLNKSQSLISHHLACLRNCGIVK 63
                                  5679****************************98 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.25      27      58 ..      34      64 ..      33      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                  ++ ei+r l+ kS s + +hL+ L++ G++++
  gi|70607439|ref|YP_256309.1| 34 TVDEISRTLN-KSQSLISHHLACLRNCGIVKV 64
                                  6889****99.89***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1198  (0.0668191); expected 358.6 (0.02)
Passed bias filter:                      831  (0.0463495); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 914.42
//
Query:       gi|70607440|ref|YP_256310.1|  [L=587]
Description: voltage-gated chloride channel [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-94  317.1  36.3    7.6e-94  314.9  29.2    2.1  2  Voltage_CLC  Voltage gated chloride channel
    4.2e-17   62.3   0.7      4e-08   33.6   0.2    2.5  2  CBS          CBS domain
     0.0072   16.7   0.0      0.012   16.0   0.0    1.2  1  DUF2589      Protein of unknown function (DUF2589)


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.6    0.0006       3.6     162     193 ..      11      42 ..       3      69 .. 0.83
   2 !  314.9  29.2   1.3e-97   7.6e-94       1     353 [.      78     429 ..      78     430 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0006
                                   GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Voltage_CLC 162 lelilfvllGilgGllgalfvrlllkverlfr 193
                                   +++il v+lGi++Gl++ +f  ll+++e lf 
  gi|70607440|ref|YP_256310.1|  11 KWFILGVILGIIAGLAATAFYLLLHVFEGLFL 42 
                                   579999*****************999998764 PP

  == domain 2  score: 314.9 bits;  conditional E-value: 1.3e-97
                                   HHHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT. CS
                   Voltage_CLC   1 lggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllkl 81 
                                   lggll+gl+v+ +apea+g+G++  ++a++  +g++++ v++vk++as++t+gsG+s+GreGp+ q +A vgs++++llkl
  gi|70607440|ref|YP_256310.1|  78 LGGLLSGLIVYTFAPEAEGHGTDAAIKAYHYYQGKIKWIVVPVKIIASAITIGSGGSAGREGPTAQFSAGVGSIIADLLKL 158
                                   589****************************************************************************** PP

                                   --SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T---...--G CS
                   Voltage_CLC  82 srndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafgeveslfalsl 161
                                   s++d +r  va+G++AGi+ +F++P+gG+++a E+ + r+++++++ p+++as++++ ++ +++g ep fg  +   ++++
  gi|70607440|ref|YP_256310.1| 159 SPED-RRKAVAVGIGAGIGTIFKTPIGGAILAAEIlYKRDIEPEVIYPTLIASAIGYTIFGSIFGFEPVFGYYTG--SFNP 236
                                   9888.888***************************888*********************************7444..7*** PP

                                   GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCCHHHHHCTT-S-. CS
                   Voltage_CLC 162 lelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggyeliasllegstl. 241
                                   l l+++++lG+++Gll++l+v++++ ++++f+kl   k+k++++p+++gl+ g+++ll+p+ v+g gy++i+ + +++ + 
  gi|70607440|ref|YP_256310.1| 237 LRLPMYAILGVISGLLAILYVKTFYGINSFFKKL---KTKNYIKPLIGGLVSGAIALLVPE-VMGVGYGWINLVEYEKFSs 313
                                   *********************************9...888999******************.*********9888776667 PP

                                   .....HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC...HHHHHHCCTHHHHHC CS
                   Voltage_CLC 242 .....llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassdpgafalvGmaaflagv 317
                                        l  +++l+l+ +lk+lat++++gsg++gG+faP L+iGA +G+ vglv++ll+p  ++ d++ f+++Gm++f++++
  gi|70607440|ref|YP_256310.1| 314 fyspiLPFFVILALIPFLKILATSFSIGSGASGGVFAPGLFIGAFMGADVGLVFHLLFPTIVP-DISPFVIIGMMSFFSAA 393
                                   888988999999***********************************************6655.889************** PP

                                   CS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                   Voltage_CLC 318 trapltaiviviEltgdlelllplmlavliAkavad 353
                                    +apl++i++v+E+tg+l+ll+  m+av+i++++++
  gi|70607440|ref|YP_256310.1| 394 GKAPLSVIIMVTEMTGSLQLLPGAMIAVAISYLISG 429
                                   ********************************9985 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   6.7e-12     4e-08      10      51 ..     469     510 ..     460     511 .. 0.91
   2 !   26.6   0.0     1e-09   6.1e-06      10      55 ..     528     572 ..     515     574 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 6.7e-12
                                   EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                   v v+  t+++eal++mr+k++ +lPVVd++ +++Giv ++D+
  gi|70607440|ref|YP_256310.1| 469 VKVKVYTSVKEALKIMRDKDLLSLPVVDDNSNFIGIVYMKDI 510
                                   589999**************66*****9999**********8 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1e-09
                                   EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   ++v+ +++leea e++ + + + +PVV+  + ++Gi+t  Dll+a 
  gi|70607440|ref|YP_256310.1| 528 PYVTLNSSLEEAWEILSRLKSRWVPVVN-HNVFLGIITIDDLLNAY 572
                                   48899999********765589*****5.888***********986 PP

>> DUF2589  Protein of unknown function (DUF2589)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-06     0.012      49      91 ..     436     479 ..     431     488 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
                       DUF2589  49 rkvpdedek.eeekevkvPLlalvpipsLaIeevtvdfdlevks 91 
                                    +vp+  +  +  +e+++PLl+l++++s +Ie+v+v+    vk+
  gi|70607440|ref|YP_256310.1| 436 AQVPTRRDSpAHLQEYETPLLTLIKVSSCRIEDVKVKVYTSVKE 479
                                   556666666556677*********************98777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3899.57
//
Query:       gi|70607441|ref|YP_256311.1|  [L=199]
Description: hypothetical protein Saci_1712 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1388.64
//
Query:       gi|70607442|ref|YP_256312.1|  [L=390]
Description: multicopy acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-31  108.2   0.0    5.8e-31  107.7   0.0    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      2e-17   63.2   0.0    3.3e-17   62.5   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.8e-10   41.2   0.0    2.8e-10   40.6   0.0    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    6.2e-07   30.1   0.0    1.1e-06   29.3   0.0    1.4  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   1.3e-34   5.8e-31       1     134 [.     232     368 ..     232     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.3e-34
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   ++Gf++ +  ln eR+++a  ++g a+  ++ a+eyar+r  fgkp++++q v++ +a+++aelea++++  + +e++d++
  gi|70607442|ref|YP_256312.1| 232 NRGFYYLLDLLNAERFMIASEMIGNAEWFINKAVEYARNRVVFGKPIGSYQGVQFPIAKVYAELEAVKSYFNDGIEHFDKD 312
                                   79******************************************************************************* PP

                                   ---...HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHS CS
                 Acyl-CoA_dh_1  82 kpd...raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrig 134
                                   k++   +  a++ K++a+e+a+e+ + am+ +Gg+Gy+ ++++er +r++r++ ++
  gi|70607442|ref|YP_256312.1| 313 KDSkliGSYANISKYLATEIAWEAGNIAMDTYGGYGYAVDTGIERKLRETRLYKVA 368
                                   ****************************************************9876 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   7.3e-21   3.3e-17       1      96 [.     121     219 ..     121     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 7.3e-21
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---....----EEEEEEE....GGG CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd....rarglslflvp..rdapg 72 
                                   ++alTEp++Gsd +++kt a ++d+  yv+nG+Ki+i++ +++++++v+ar       d    +++g++lflv+   ++ +
  gi|70607442|ref|YP_256312.1| 121 SLALTEPDVGSDSTRIKTLARKKDDRTYVINGHKIFISRLKYSDFMIVVARtipY---DvverKTDGITLFLVDlrVSRDN 198
                                   589***************889999999************************7551...23557799********6545559 PP

                                   EEE-----BSS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  73 vsvrrieeklGlrglptgelvfed 96 
                                   + +++i++   + ++++ e+++++
  gi|70607442|ref|YP_256312.1| 199 IDMKEIKT---MSNTSAFEVFLNN 219
                                   99999976...6666777777665 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   6.2e-14   2.8e-10       2     124 ..     248     363 ..     247     367 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 6.2e-14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   +ia  ++G+A+  ++++ve+ar+rv   +g+++   + +q+ +a++ a+l+A +  + + ++   ++ +++k +       
  gi|70607442|ref|YP_256312.1| 248 MIASEMIGNAEWFINKAVEYARNRVV--FGKPIGSYQGVQFPIAKVYAELEAVKSYFNDGIEH-FDKDKDSKLI----GSY 321
                                   68999*********************..******************************99999.5556666665....99* PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHH CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDah 124
                                   a +++ la+e+a +a + ++++ Gg++++ +  ++R +R+ +
  gi|70607442|ref|YP_256312.1| 322 ANISKYLATEIAWEAGNIAMDTYGGYGYAVDTGIERKLRETR 363
                                   ***************************************976 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   2.4e-10   1.1e-06       2     112 ..       8     116 ..       7     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.4e-10
                                   HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHH CS
                 Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalll 82 
                                   ee++ +  tv+e++++  + +  + d ++efp ++++++ elGl  + +p+e gGag       +++e l ++++ ++ ++
  gi|70607442|ref|YP_256312.1|   8 EEEKLILSTVNELMKKYDERYWLDKDLKREFPLDFLQEFSELGLGSVLIPKENGGAGK---GLRLACEILYHVNVNGGNSY 85 
                                   89**************99999999998899***************************5...57889999999999877877 PP

                                   HHHHHTTH.HHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  83 gvhsslva.pailrfGteeqkrryLpklasg 112
                                    +h        +++++ +  +++y   +++g
  gi|70607442|ref|YP_256312.1|  86 FIHGHYYNtTLLVKHAGKLIREKYFEGIVKG 116
                                   777666644899*************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3019.54
//
Query:       gi|70607443|ref|YP_256313.1|  [L=330]
Description: thermopsin precursor [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-89  298.2  25.5    6.2e-89  297.9  25.5    1.1  1  Thermopsin  Thermopsin


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.9  25.5   3.5e-93   6.2e-89       2     260 .]      32     300 ..      31     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 297.9 bits;  conditional E-value: 3.5e-93
                    Thermopsin   2 lvnvlslyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssn....spesaslQLNvvlevvtggkt 78 
                                   +vn++ +y+s+paP+Gia++G++n+sg++tpy+++t+++lG+vni+sl ayn ++     +p+sa+lQ+N+vl+v+t+++ 
  gi|70607443|ref|YP_256313.1|  32 YVNPYLYYTSPPAPAGIASFGLYNYSGNVTPYVITTNEMLGYVNITSLLAYNREALrygvDPYSATLQFNIVLSVNTSNGV 112
                                   79***************************************************9988999********************* PP

                    Thermopsin  79 ysywvQnVvsfnttekqltfidNiWNftspsanlsnsaisGnGtvy.asskgefYyayateylelslPltlkLvinvslts 158
                                   y+yw+Q+V +f+t++++ltfidN+WN+t++ ++ls+sai+GnG+v+ a+++++fYy+++++ +++s+Pl++ ++in+s+ts
  gi|70607443|ref|YP_256313.1| 113 YAYWLQDVGQFQTNKNSLTFIDNVWNLTGSLSTLSSSAITGNGQVAsAGGGQTFYYDVGPS-YTYSFPLSYIYIINMSYTS 192
                                   **********************************************8899999********.9****************** PP

                    Thermopsin 159 ngvpevsFgYsid.......ggvvtYDnvtinstgkasaeilvngssltpsgllyDaeLvlgGpgngekttfnslnatlsL 232
                                   n+v +v++gY i        g+v++YD++ti +++ +sa++++ng+++tp+gl+yDaeLv+gG gng+ t+fnsln+tl L
  gi|70607443|ref|YP_256313.1| 193 NAV-YVWIGYEIIqigqteyGTVNYYDKITIYQPNIISASLMINGNNYTPNGLYYDAELVWGGGGNGAPTSFNSLNCTLGL 272
                                   *99.*******999*****999*********************************************************** PP

                    Thermopsin 233 yYlngtnyqpvknaydfGsdTaEtaenv 260
                                   yY+++ +++pv+++y+fG+dTaE+a+nv
  gi|70607443|ref|YP_256313.1| 273 YYISNGSITPVPSLYTFGADTAEAAYNV 300
                                   ***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2664.16
//
Query:       gi|70607444|ref|YP_256314.1|  [L=561]
Description: dihydroxy-acid dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     8e-207  687.9   1.6     9e-207  687.8   1.6    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.8   1.6    5e-211    9e-207       1     517 []      36     554 ..      36     554 .. 0.98

  Alignments for each domain:
  == domain 1  score: 687.8 bits;  conditional E-value: 5e-211
                      ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqllD 81 
                                   kp++++a+++se  pc+ h  +la+ +keg++e g +p+ f+ti v+D i mg+egmrysL+sR+liad+ve+  +a+ +D
  gi|70607444|ref|YP_256314.1|  36 KPLVAVATAWSEAGPCNFHTLSLAHVAKEGAKEGGLTPLAFPTIVVNDNIGMGTEGMRYSLVSRDLIADMVEAQFNAHAFD 116
                                   8******************************************************************************** PP

                      ILVD_EDD  82 alvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGsCs 160
                                   al+ i+gCDK++Pg+lma+arln+P+i+++gG+ e+g +   +l++++v ea+ga+ agki+e+el e+e++a p++G+Cs
  gi|70607444|ref|YP_256314.1| 117 ALIGIGGCDKTTPGILMAMARLNVPSIYIYGGSAEPGFYLgrRLTIEDVHEAIGAFIAGKIDEHELYEIEKRAHPTVGTCS 197
                                   ************************************87445599************************************* PP

                      ILVD_EDD 161 gmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalGGStNavlH 241
                                   gm+TAntm ++ ealG++lpgsas +ats++r  +++e+gk++ +l+e+ +k rdilt eafeNAi+vl+a+GGStNavlH
  gi|70607444|ref|YP_256314.1| 198 GMFTANTMGSMSEALGMALPGSASPTATSSRRIMYVRETGKAVSRLLENGVKSRDILTFEAFENAIAVLMAMGGSTNAVLH 278
                                   ********************************************************************************* PP

                      ILVD_EDD 242 llAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktlaenlee... 319
                                   llAiA eagv+ltlddf+++s+++p++ +lkP g+y m dl+++GGvp v+k+Ll+agll+gdvltvtgkt+++nl+e   
  gi|70607444|ref|YP_256314.1| 279 LLAIAYEAGVKLTLDDFNRISKRTPYIGSLKPGGDYVMADLDEVGGVPLVMKKLLDAGLLNGDVLTVTGKTMKQNLQEyri 359
                                   ****************************************************************************99554 PP

                      ILVD_EDD 320 aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikagdvvvirye 400
                                    +v ++++++++++p++++gg+ +LkG+LapeGav+K++a++  ++kfeg+A+v++see+a++ i+++++k+g+vvvirye
  gi|70607444|ref|YP_256314.1| 360 PNVPHNHIVKDVKNPIKPRGGIVILKGSLAPEGAVIKVAATN--VTKFEGKAKVYNSEEQAFKGIQSNEVKDGEVVVIRYE 438
                                   4559*************************************9..99*******************99************** PP

                      ILVD_EDD 401 GPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevse 481
                                   GPkGgpGmpEml++t+a++g+gl ++va++tDGRfSGa++g+++ghv+PEA++gGpia+vedGD+i id+e+++l++++s+
  gi|70607444|ref|YP_256314.1| 439 GPKGGPGMPEMLRVTAAIVGAGL-SNVAMVTDGRFSGATRGPMVGHVAPEAMVGGPIAIVEDGDVIVIDVENERLDIKLSD 518
                                   ***********************.9******************************************************** PP

                      ILVD_EDD 482 eelaaRraawkp.ekkvktrgllakyaklvssaseGA 517
                                   +e+++R ++w+p e++  ++gllakya+lv + s GA
  gi|70607444|ref|YP_256314.1| 519 AEIKRRLNNWSPpEPRY-KSGLLAKYASLVAQSSMGA 554
                                   ************44444.5****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3694.22
//
Query:       gi|70607445|ref|YP_256315.1|  [L=66]
Description: hypothetical protein Saci_1716 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   12.4   0.2      0.049   12.3   0.2    1.0  1  DHC_N1    Dynein heavy chain, N-terminal region 1
      0.088   13.1   0.2       0.13   12.6   0.2    1.3  1  Nif11     Nif11 domain


Domain annotation for each model (and alignments):
>> DHC_N1  Dynein heavy chain, N-terminal region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   5.5e-06     0.049      57      99 ..       4      44 ..       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-06
                        DHC_N1 57 kkvlkvLkaakssyleafkaldtelkkaleeAkdnvkyLktLe 99
                                  + ++k+L+  ++ y +  k  +++lk+ +e Ak+n++++k Le
  gi|70607445|ref|YP_256315.1|  4 RVIIKILEDRER-YRK-SKMSEADLKRLAELAKENMELMKRLE 44
                                  6899********.444.8999*********************6 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.5e-05      0.13       1      24 [.      21      44 ..      21      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                         Nif11  1 MSeeqlkaFlekvkqDpalreqlk 24
                                  MSe +lk++ e +k++ +l ++l 
  gi|70607445|ref|YP_256315.1| 21 MSEADLKRLAELAKENMELMKRLE 44
                                  ********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 477.66
//
Query:       gi|70607446|ref|YP_256316.1|  [L=186]
Description: hypothetical protein Saci_1717 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1394.55
//
Query:       gi|70607447|ref|YP_256317.1|  [L=260]
Description: hypothetical protein Saci_1718 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-68  230.9   0.0    3.6e-68  229.4   0.0    1.6  1  DLH             Dienelactone hydrolase family
    8.4e-07   28.5   0.0      0.018   14.3   0.0    2.9  3  Hydrolase_4     Serine aminopeptidase, S33
     0.0024   17.7   0.0     0.0036   17.1   0.0    1.2  1  Abhydrolase_2   Phospholipase/Carboxylesterase
  ------ inclusion threshold ------
      0.045   13.5   0.0      0.084   12.6   0.0    1.4  1  Abhydrolase_5   Alpha/beta hydrolase family
      0.097   12.1   0.0          3    7.2   0.0    2.1  2  Peptidase_S9    Prolyl oligopeptidase family
       0.14   11.1   0.0       0.39    9.7   0.0    1.6  2  Chlorophyllase  Chlorophyllase
       0.17   11.8   0.1         15    5.4   0.0    2.3  2  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina


Domain annotation for each model (and alignments):
>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.4   0.0   1.4e-71   3.6e-68       2     216 ..      18     258 ..      17     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 1.4e-71
                           DLH   2 daylatpknakkpvvvviqeifGvndnikdiserlaeeGYvalaPdlYarqa.......................ldpnde 59 
                                   +++la+p+++ k++v+ i+ei+G+n+nikdi+ rla+eGY+a+aP+lY+rq+                        dpn +
  gi|70607447|ref|YP_256317.1|  18 RTFLARPESP-KLAVILIHEIWGLNENIKDIAVRLANEGYLAFAPQLYTRQEdilspsniervmskvwsippekrSDPNVY 97 
                                   799*******.9****************************************99999999999999999999988888999 PP

                           DLH  60 aeaaraldelvskvaeekvlddl.......kaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlsp 133
                                   ++  + ld +++ v+e  vl++        k+ v+++ +  ++  +k++++GfCmGG la++la+evp +d+a++fYG ++
  gi|70607447|ref|YP_256317.1|  98 QQVLSSLDDKGKRVVETLVLNRSkfeeqmiKDLVKTYDYLHSQGFNKIVSMGFCMGGGLAFQLATEVP-LDGAIVFYG-RN 176
                                   9999999999999988888888899**9***************************************8.*********.** PP

                           DLH 134 ekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyneeaaedawervlelfk 214
                                   +++le+++k+k+ +l+l+++eD++i+a+ +++l +a++++++dlelk+Ypga+HaF+nd+ + yn+ea edawerv+++++
  gi|70607447|ref|YP_256317.1| 177 PQPLEAIQKLKGAVLGLYAGEDPPIDAG-LPDLISAMIKYKKDLELKIYPGAYHAFFNDRGRVYNKEASEDAWERVKNFLR 256
                                   ****************************.8**************************************************9 PP

                           DLH 215 qv 216
                                   +v
  gi|70607447|ref|YP_256317.1| 257 RV 258
                                   97 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.13   3.3e+02       2      36 ..      26      60 ..      25      63 .. 0.89
   2 !    9.9   0.0   0.00016       0.4      56     105 ..     124     170 ..     119     175 .. 0.85
   3 !   14.3   0.0   6.9e-06     0.018     187     238 ..     183     235 ..     175     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.13
                   Hydrolase_4  2 epkavvvlvHGlaehsgryaelaeaLaaqGfavya 36
                                  +pk +v+l+H +    +  +++a +La++G+  +a
  gi|70607447|ref|YP_256317.1| 26 SPKLAVILIHEIWGLNENIKDIAVRLANEGYLAFA 60
                                  68899999999999999999***********9887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
                   Hydrolase_4  56 ddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvagli 105
                                   +++++Dl + ++ + ++  + +++ +G  mGG +a++++++ p   +g+i
  gi|70607447|ref|YP_256317.1| 124 EQMIKDLVKTYDYLHSQGFN-KIVSMGFCMGGGLAFQLATEVPL--DGAI 170
                                   799*********99966655.69****************99887..6666 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 6.9e-06
                   Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk.dktlklypglyHellnEp 238
                                    +k++  +l l++++D+ +d +    + + ++ k d +lk+ypg+yH  +n++
  gi|70607447|ref|YP_256317.1| 183 IQKLKGAVLGLYAGEDPPIDAGLPDLISAMIKYKkDLELKIYPGAYHAFFNDR 235
                                   5778888999**********999988888888777****************96 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-06    0.0036      92     201 ..     125     231 ..     100     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHTT.....--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT- CS
                 Abhydrolase_2  92 elidaelkkg.....ipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeD 167
                                   ++i+  +k          ++i+ +GF +G+ la +  l+++ +l g++ f g+ p++ +  ++  + +   ++l ++  eD
  gi|70607447|ref|YP_256317.1| 125 QMIKDLVKTYdylhsQGFNKIVSMGFCMGGGLAFQ--LATEVPLDGAIVFYGRNPQPLEAIQK--LKG---AVLGLYAGED 198
                                   44444444334434477899**********98876..5677899*************999973..333...58******** PP

                                   SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS- CS
                 Abhydrolase_2 168 pvvplalgkaakevlkkllkkvelksyeglaHsi 201
                                   p ++  l  + + ++ k  k+ elk+y+g  H+ 
  gi|70607447|ref|YP_256317.1| 199 PPIDAGLPDLISAMI-KYKKDLELKIYPGAYHAF 231
                                   *******99998765.56667********99986 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.3e-05     0.084      11     143 ..      93     232 ..      87     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                 Abhydrolase_5  11 eaesYaelaeklaksGyevvlvklPlnlavlgknkaeeiikeap.....klekfvvgGhslGGvvasrfaaeeekiegvvf 86 
                                   +++ Y +++++l ++G  vv   l ln + + ++ +++++k ++     + +k v  G  +GG +a ++a+e     ++vf
  gi|70607447|ref|YP_256317.1|  93 DPNVYQQVLSSLDDKGKRVV-ETLVLNRSKFEEQMIKDLVKTYDylhsqGFNKIVSMGFCMGGGLAFQLATEVPLDGAIVF 172
                                   77889999999999998875.667899999999999999998752222256889999*************9988767799* PP

                 Abhydrolase_5  87 lasYPe.kdelselskkvlsivgteDgvlnv..kslekakkflpkdtkvvsieGgnhagf 143
                                   ++  P+  + +++l+  vl +++ eD  ++    +l  a  +  kd ++    G  ha f
  gi|70607447|ref|YP_256317.1| 173 YGRNPQpLEAIQKLKGAVLGLYAGEDPPIDAglPDLISAMIKYKKDLELKIYPGAYHAFF 232
                                   *****987889999999******9997655311344444444555555555556666655 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.031        79      42      82 ..     124     161 ..     117     165 .. 0.82
   2 ?    7.2   0.0    0.0012         3     165     204 ..     208     248 ..     198     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHH CS
                  Peptidase_S9  42 qnefdDfiaaaealakegyvdserlaitGgSyGGyltgaal 82 
                                   ++ ++D+++  ++l ++g+    +++ +G   GG l+  ++
  gi|70607447|ref|YP_256317.1| 124 EQMIKDLVKTYDYLHSQGFN---KIVSMGFCMGGGLAFQLA 161
                                   67799*************95...999999999998776555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0012
                                   HHHHHH--S-SEEEEEETTS-SSTTSSHHHH.HHHHHHHHH CS
                  Peptidase_S9 165 lvaaLqkkgknvlllifpdegHgvgkprakv.eelarllaF 204
                                   l++a+ k +k+++l+i+p++ H + ++r +v ++ a++ a+
  gi|70607447|ref|YP_256317.1| 208 LISAMIKYKKDLELKIYPGAYHAFFNDRGRVyNKEASEDAW 248
                                   67899999**************8888888886666666666 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00015      0.39      49      93 ..      31      79 ..      23      86 .. 0.83
   2 ?   -1.9   0.0      0.52   1.3e+03      61      76 ..     137     152 ..     128     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                Chlorophyllase 49 vlflhGtllsnkfyskllnhiashGfivvaPqlyk....llpPsaqdei 93
                                  v+++h +   n++  ++   +a  G++  aPqly+    +l+Ps+++ +
  gi|70607447|ref|YP_256317.1| 31 VILIHEIWGLNENIKDIAVRLANEGYLAFAPQLYTrqedILSPSNIERV 79
                                  7899******************************822224457777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.52
                Chlorophyllase  61 fyskllnhiashGfiv 76 
                                    +s+ +n i s Gf +
  gi|70607447|ref|YP_256317.1| 137 LHSQGFNKIVSMGFCM 152
                                   4567777777777765 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.017        44       9      44 ..     133     165 ..     131     175 .. 0.79
   2 ?    5.4   0.0     0.006        15     191     209 ..     239     257 ..     236     260 .] 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.017
                                   HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSS CS
                        BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflk 44 
                                    ++yl ++ +   +ki  +G + Gg la+ la+  +
  gi|70607447|ref|YP_256317.1| 133 TYDYLHSQGF---NKIVSMGFCMGGGLAFQLATEVP 165
                                   5778877743...57999**************9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.006
                                   HHHHHHHHHHHHHHHHHHH CS
                        BAAT_C 191 ahakAqedsWkkilkFlkk 209
                                   ++ +A ed+W+++ +Fl++
  gi|70607447|ref|YP_256317.1| 239 YNKEASEDAWERVKNFLRR 257
                                   5789*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1974.45
//
Query:       gi|70607448|ref|YP_256318.1|  [L=39]
Description: hypothetical protein Saci_1719 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 286.39
//
Query:       gi|70607449|ref|YP_256319.1|  [L=221]
Description: hypothetical protein Saci_1720 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-37  130.0   0.2    1.6e-37  129.7   0.2    1.0  1  DUF72     Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.2   9.2e-42   1.6e-37      10     205 ..      19     204 ..      13     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 9.2e-42
                                   HHHHHCCT..-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS.G-.SCHHHHHHHHHH.CHHHCT-EEEE CS
                         DUF72  10 rLeyYarh..fntVEinstFYalpspetvakwaaqtpedFrFavKapraitherne.daeealerflesalepLgeklgpl 87 
                                    L+ Y+r+  fn+VE+n +FY++psp+ v++w++    + r++vK++r ith +   +  e++++f e ++++L  ++  +
  gi|70607449|ref|YP_256319.1|  19 NLDWYFRNtgFNAVELNMSFYRFPSPKLVNSWKKY---NLRWSVKVNRMITHVN-RmKDSELWKKFEE-IFSGL--NVDFY 92 
                                   6999****************************975...79************86.4468899999999.5**99..6999* PP

                                   EEE--TT--S.HHHHHHHHHHTTTS-S.EEEE--BGGGHHHHHHHHHTT-E.EEE..E--SSC--------SSTEEEEEE- CS
                         DUF72  88 lfQlppsfkfdeenlerLeaflaalpl.lavEvRhrswfellellrehgva.vvl..depkkpklpledvttadfvyvRlh 164
                                   lfQlp+sfk+++enler+++f + +   +avE+R+++w+      r+++++ vv+  d   +p  ++ ++  + +vy+R+h
  gi|70607449|ref|YP_256319.1|  93 LFQLPQSFKYSPENLERIKKFEETVGEkMAVEFRDPEWY-----KRDLDLNcVVVsiD---SPIGRYIEISPQGTVYLRMH 165
                                   ***********99********7766655**********8.....34444443333237...567778999999******** PP

                                   -SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCC CS
                         DUF72 165 greeryayrYseeelaewaerikawaaegrevyvffnndae 205
                                   g +++y+y+Ys+eel+++a+++ a++   +++yvffnnd +
  gi|70607449|ref|YP_256319.1| 166 GADNWYQYDYSDEELRDIAKEVLALHP--KKIYVFFNNDLW 204
                                   *98**********************99..89*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1653.37
//
Query:       gi|70607450|ref|YP_256320.1|  [L=148]
Description: hypothetical protein Saci_1721 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-17   62.5   0.0    3.5e-17   62.4   0.0    1.1  1  RVT_3     Reverse transcriptase-like
    1.4e-05   25.3   0.0    2.5e-05   24.5   0.0    1.4  1  RNase_H   RNase H
  ------ inclusion threshold ------
       0.06   13.2   0.0      0.081   12.8   0.0    1.1  1  DUF1465   Protein of unknown function (DUF1465)


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   5.9e-21   3.5e-17       8     122 ..      14     130 ..       5     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 5.9e-21
                         RVT_3   8 kksgaggagvvirdsnGevllag..aek.lqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvkss 85 
                                   +  g+++ g vi  ++G+ + ++  a+k +++ +++ +AE++++++ +++  +l++++  + gDs+ v+++l+g+ kvks 
  gi|70607450|ref|YP_256320.1|  14 NPGGIATYGFVIILEDGNTVKGYglASKpFSKDSTNNVAEYTGIICLMRKMIELKLSNPKIRGDSQLVIRQLRGEYKVKSL 94 
                                   44478899*********998764334555**************************************************** PP

                         RVT_3  86 elanlldeirkllksfesvsvehipReqNrvAdalAk 122
                                   +++ l++++++l++++ ++++e++pRe+N  Ad+l++
  gi|70607450|ref|YP_256320.1|  95 RIKPLYEKALELVRQL-NAELEWVPREENEEADQLSR 130
                                   ****************.9****************987 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.2e-09   2.5e-05       7     140 ..       5     131 ..       2     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.2e-09
                                   EEEEEEECTTTCE..EEEEEE.CTT....E...EEEEEECCCCHHHHHHHHHHHHHHHTT.SCSEEE...EEES-HHHHHH CS
                       RNase_H   7 YtDGsclgnpgeg..gagavl.ykeg..ar...nisapleeaqtnnraELsAvieaLkalksdekvn...iytDSkYvvkg 76 
                                   Y DG c  ++  g  ++g+v+  ++g   +     s+p ++ +tnn aE + +i  ++++ ++ k+    i+ DS+ v+  
  gi|70607450|ref|YP_256320.1|   5 YFDGLCEPKNPGGiaTYGFVIiLEDGntVKgygLASKPFSKDSTNNVAEYTGIICLMRKM-IELKLSnpkIRGDSQLVIRQ 84 
                                   99****9885555569999554666655224567788889**************999975.443333356********992 PP

                                   HHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHH CS
                       RNase_H  77 itqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAke 140
                                   +          ++k +s    +k   l+e++ el+++ + +l+wv+      ++Ne+aD+l + 
  gi|70607450|ref|YP_256320.1|  85 LR--------GEYKVKSLR--IKP--LYEKALELVRQLNAELEWVP----R-EENEEADQLSRV 131
                                   22........234334333..555..777777999**********9....4.79******9875 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05     0.081       4      47 ..      90     133 ..      87     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                   ----TTCHHHHHHHHHHHHHHHHHHTTHHHHHHCTS-HHHHHHH CS
                       DUF1465   4 llaselfkalfregmdLveetaayldgegreeskalsreaalay 47 
                                    ++s ++k l++++++Lv +  a l+   ree +++++ +++ay
  gi|70607450|ref|YP_256320.1|  90 KVKSLRIKPLYEKALELVRQLNAELEWVPREENEEADQLSRVAY 133
                                   5789999***********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.55
# Mc/sec: 803.66
//
Query:       gi|70607451|ref|YP_256321.1|  [L=186]
Description: hypothetical protein Saci_1722 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-16   61.2   0.0    1.3e-16   61.0   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   7.5e-21   1.3e-16       4     142 ..      15     153 ..      11     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 7.5e-21
                                   S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCCC CS
                 Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtdd 84 
                                   +++p +++ t +++++ + +++s+ +++s +P ++++s+ ++ +t++ lk     +in+  ++  +l  ++++ sg +++d
  gi|70607451|ref|YP_256321.1|  15 HPRPTVIIGTLCEDGRVNLMPASWNMPISEEPETIGVSVYKETFTYRCLKFHPYATINVPGPELLDLTYSLGSVSG-KDVD 94 
                                   699*************************************************************************.9*** PP

                                   CCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTT CS
                 Flavin_Reduct  85 ksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadee 142
                                   k + + +++ es + ++p ++ a+a +e ++ +++++g  +lf+ eV++ kv+d+  ++
  gi|70607451|ref|YP_256321.1|  95 KVKKFNVELVESeKINVPGMAKAIAIYETRIYNQIDVGECTLFVFEVLKSKVRDGITNQ 153
                                   ***********9999**************************************995544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1229.46
//
Query:       gi|70607452|ref|YP_256322.1|  [L=310]
Description: hypothetical protein Saci_1723 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-26   92.0  38.4    7.6e-16   58.4  11.9    2.1  2  Na_Ca_ex  Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4  11.9   4.2e-20   7.6e-16       7     148 ..      12     150 ..       6     153 .. 0.81
   2 !   39.8  18.5   2.3e-14   4.1e-10       3     150 ..     169     308 ..     167     309 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.2e-20
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHH CS
                      Na_Ca_ex   7 ilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlia 87 
                                   ++ ++ i +++ +l +++ ei k  ++   + G ++l l nslpE+i+++ a+l+g  ++a+g+++Gs +f+++++iGli 
  gi|70607452|ref|YP_256322.1|  12 LFWIVSIGLTSTLLAKATMEIEK--KLDSGLTGGLILGLINSLPETIIITEAVLSGANEVAVGSITGSLLFIFTFGIGLIS 90 
                                   455666778999999*******8..99999*************************************************** PP

                                   HHHHBTTSSCE..CCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  88 ligslkvdses..lkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvl 148
                                   ++  + ++s++  +  d++   +++ll+ l++++l+l+ f  + +++  +++ll+ Y+ y++ 
  gi|70607452|ref|YP_256322.1|  91 VVYYFRYKSKTiqIGGDIS-SEYTSLLIALVTFTLVLLVF--RSVNYYASILLLIPYVYYVYR 150
                                   **99888877744444443.33444444444444444445..******************985 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 2.3e-14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHT..TTHHHHHHHHHHHHHHHHHT CS
                      Na_Ca_ex   3 fvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaalt..gevdlaignvlGsnifnlll 81 
                                   ++l+ ++ +++ ++++f+vss+ +++++l+i+  vl+ +l+++++ l++ +++++ + +   +vd +i n +G+ + nl+l
  gi|70607452|ref|YP_256322.1| 169 ILLLSIGAMMLFMISNFFVSSLVSLSTVLNIPTVVLASILVPIASELGDGFLALSLLYNsaSNVDTVITNFMGGKLENLTL 249
                                   567778889999**********************************************85455****************** PP

                                   HHHHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
                      Na_Ca_ex  82 viGlialigslkvdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                                   +++++++++++   s+   ld+ +l+ +++l+     ll+++   ++++++ egl+l+ +Y + ++++l
  gi|70607452|ref|YP_256322.1| 250 MLSIPGFYTTVNLVSN--HLDI-ILIPLSVLS-----LLMIIR--DKNIKISEGLALITIYPILILFLL 308
                                   ********77333332..3444.444444444.....345555..4*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2106.16
//
Query:       gi|70607453|ref|YP_256323.1|  [L=493]
Description: trypsin-like serine protease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-32  111.6   0.1    4.7e-32  110.9   0.1    1.4  1  Peptidase_M61    M61 glycyl aminopeptidase
      2e-13   50.7   0.7    5.6e-12   46.1   0.2    2.7  2  Peptidase_M61_N  Peptidase M61 N-terminal domain
    4.2e-06   26.5   0.0      9e-06   25.4   0.0    1.5  1  PDZ_6            PDZ domain
     0.0016   18.7   0.4      0.047   14.0   0.4    2.6  1  PDZ_2            PDZ domain
     0.0025   17.1   0.1     0.0049   16.2   0.1    1.4  1  Peptidase_M9     Collagenase
  ------ inclusion threshold ------
      0.029   14.7   0.2      0.083   13.2   0.0    1.8  2  PDZ              PDZ domain
       0.11   12.4   0.0       0.25   11.3   0.0    1.5  1  Nup35_RRM        Nup53/35/40-type RNA recognition motif


Domain annotation for each model (and alignments):
>> Peptidase_M61  M61 glycyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.1   1.8e-35   4.7e-32       5     116 ..     212     321 ..     208     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.8e-35
                                   HHHHHHHHTTBTTTB-BGGGSS---SS----STHHHHTHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHSGGGGT-- CS
                 Peptidase_M61   5 llaHEyfHsWnvkrirPaelepfdyekenytellwvaEGlTsYygdlllarsgliseeeyleelaktlarlentpgrkvqs 85 
                                   l+aHEyfH  nvk++ P++l   +ye+e+yt+llw+aEG+T+Y+++l+++r+gl ++ee+++++ ++l++l + pg k+ s
  gi|70607453|ref|YP_256323.1| 212 LFAHEYFHRLNVKKLVPKDLN-HNYETEVYTDLLWFAEGFTDYMAHLICLRAGLNTPEEIFRRILQSLHNL-TFPGAKRVS 290
                                   89*****************98.8**********************************************99.89******* PP

                                   HHHHHHTIIIIITT--TTHHHH---TTHHHH CS
                 Peptidase_M61  86 laessfdawiklyrsdensanskvsyYskGa 116
                                   l+e+s +awik+y++den  n+++syY+ G 
  gi|70607453|ref|YP_256323.1| 291 LSEASKTAWIKYYKQDENFLNASISYYDGGL 321
                                   ****************************995 PP

>> Peptidase_M61_N  Peptidase M61 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.2   2.2e-15   5.6e-12      23     166 ..      17     136 ..       9     137 .. 0.87
   2 ?   -2.9   0.0       2.4     6e+03      39      59 ..     374     394 ..     373     404 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.2e-15
               Peptidase_M61_N  23 kkgeltlslPkwiPGsYlirdfaknieglkafdakgkelaveridkntwrvenpkkeveveyrvyafdlsvrtsylddeha 103
                                   + +e  +++P+ +PGsY ir+  +n+ +++            ri+kn++ v++     + +y vya   ++r+++ +++++
  gi|70607453|ref|YP_256323.1|  17 QGKEGVVIFPTYVPGSYVIRELERNVVEIEG----------FRITKNKFYVKE-----NFKYLVYASSRDQREAISTNDYL 82 
                                   56667899********************999..........5899******96.....689******************** PP

               Peptidase_M61_N 104 flngaslflyvegleekpievtlslpkgwkvataLpaaeedagtgtfeaedydeLvDsPvlaG 166
                                   f+n++++f   + +e+  +   ++   +wkvat+L+++++      + a++y+e+ DsP++a+
  gi|70607453|ref|YP_256323.1|  83 FINPPAVFPFQNIYEK--YC--VKIETNWKVATTLQEENG-----YYCADNYHEFADSPIEAS 136
                                   *******986555543..33..455678*********998.....9***************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
               Peptidase_M61_N  39 Ylirdfaknieglkafdakgk 59 
                                   Y+i + +  i +l+++d+++k
  gi|70607453|ref|YP_256323.1| 374 YQIVEAIGRIIDLQFVDKGKK 394
                                   999999*********665544 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.5e-09     9e-06       1      29 [.     404     432 ..     404     444 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.5e-09
                         PDZ_6   1 vVtaVdpgsPAdrAGlrvGDiilsvNGqp 29 
                                   +V+ V+++sPAd AGl + D+i+ v+G++
  gi|70607453|ref|YP_256323.1| 404 RVKFVEENSPADLAGLMPEDQIVGVDGIS 432
                                   6999***********************86 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   1.8e-05     0.047      18      43 ..     405     430 ..     387     457 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                                   EEEE-TTSGGGGT.--TT-EEEEETT CS
                         PDZ_2  18 vvsVkeggPaakaglkagDvilkvdg 43 
                                   v  V+e++Pa+ agl ++D+i+ vdg
  gi|70607453|ref|YP_256323.1| 405 VKFVEENSPADLAGLMPEDQIVGVDG 430
                                   4459*********************9 PP

>> Peptidase_M9  Collagenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.9e-06    0.0049     152     201 ..     204     256 ..     193     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-06
                  Peptidase_M9 152 eeeeefsiynLeHEytHyLdgrydv....egdfaksaeerlvWweEGlAEyvay 201
                                   + ++++si+   HEy H L+ +  v    + ++++++ + l W+ EG+ +y+a+
  gi|70607453|ref|YP_256323.1| 204 WDKKDLSIL-FAHEYFHRLNVKKLVpkdlNHNYETEVYTDLLWFAEGFTDYMAH 256
                                   556667776.57***********9944444445566677899**********97 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.2   1.3e+04      42      51 ..     162     172 ..     143     177 .. 0.48
   2 ?   13.2   0.0   3.2e-05     0.083      29      55 ..     404     430 ..     387     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.2
                                   HT.SSTTEEEE CS
                           PDZ  42 dg.lkvGDkIl 51 
                                   ++ +++ Dk++
  gi|70607453|ref|YP_256323.1| 162 GKiVSEADKVI 172
                                   33333333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.2e-05
                                   EEEEECTTSHHHHHTSSTTEEEEEETT CS
                           PDZ  29 fvsevlpggaaeadglkvGDkIlsvNg 55 
                                    v+ v+++++a+ +gl + D+I++v+g
  gi|70607453|ref|YP_256323.1| 404 RVKFVEENSPADLAGLMPEDQIVGVDG 430
                                   5899****9999999***********9 PP

>> Nup35_RRM  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05      0.25      41      79 ..      45      83 ..      28      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                                  ------------EETTEEEEEBS-HHHHHHHHTTTTEEE CS
                     Nup35_RRM 41 klgkglnpkpiptgenwvkltYksessaskAlqengtil 79
                                   +g +++ ++ + +en+ +l Y+s  +++ A++ n+ ++
  gi|70607453|ref|YP_256323.1| 45 IEGFRITKNKFYVKENFKYLVYASSRDQREAISTNDYLF 83
                                  456689999**************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3059.05
//
Query:       gi|70607454|ref|YP_256324.1|  [L=473]
Description: sugar-proton symporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-42  145.2  25.1    3.3e-42  144.9  25.1    1.0  1  Sugar_tr        Sugar (and other) transporter
      1e-34  120.1  50.3    1.4e-27   96.6  35.3    2.1  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.059   13.1   0.2       0.14   11.8   0.2    1.6  1  PPR_1           PPR repeat
       0.15   12.4   0.1       0.39   11.1   0.1    1.7  1  PPR             PPR repeat


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.9  25.1   7.3e-46   3.3e-42      43     451 ..      41     452 ..      15     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 7.3e-46
                                   H...........HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHH CS
                      Sugar_tr  43 e........ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGig 115
                                   +         +++ +li+si l+G i Gsl +g+l+dr+GRk++l+ +++l+ ig++ +a++    ++ +l+v R++ G g
  gi|70607454|ref|YP_256324.1|  41 AalpyipflNASTASLIASIGLFGYIPGSLGLGYLADRIGRKPVLILTVTLTAIGSLGMALSV---NFPMLAVFRFIEGAG 118
                                   344444444578899************************************************...*************** PP

                                   HHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HH CS
                      Sugar_tr 116 vGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPr 196
                                   +G+  +l+ +y+ E+Ap ++Rg+   +  l+  +   v+a++  +l ++    gwr+ +g+++++a + l+l++ +PE+ r
  gi|70607454|ref|YP_256324.1| 119 IGGDLNLAMVYVTEFAPSAKRGKYANYIYLSGWIAVGVGATIASVLVTSLPGIGWRLAFGIAAIMAFAALVLRVAAPETVR 199
                                   *********************99998877766666666666666665555558**************************** PP

                                   HHHHTT-HHHHHHHHHHHHHCHHHHHHHHH..HHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHH...HHHTTHHH CS
                      Sugar_tr 197 ylvekgkeeeakevlaklrgeedadrelae..ekdsleaeqeeekaswkellssktvrqrlligvvlqif...qqltGina 272
                                   +lv+kgk +ea++ ++ +++++ a  ++    e + ++++    +++w+ +l+++t ++rl+  v  ++f    q+t    
  gi|70607454|ref|YP_256324.1| 200 FLVKKGKIDEAEKLVRSMEETAMARAKVSSlpEPKIIQYNTP--TKTWS-VLGNRTFLKRLVGLVIFWFFiyfVQYTFSTL 277
                                   *****************9988666555555004444555533..45555.5555587777777666666522267777788 PP

                                   HHHHTTTHHHH.SS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHH CS
                      Sugar_tr 273 imyysptifen.lglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasiva 352
                                     yy+  +  +   +++ +l t+      +++ f  + +++++ RR +  +G++g +i +++ +   ++++   +  ++++
  gi|70607454|ref|YP_256324.1| 278 WDYYGLALGITgSTFNQYVLYTGFAALGDTAMAFLLLAFIEKTDRRLITQIGSFGWLIGTIVAA---YFVTRF-DLLGMAL 354
                                   88998765333033444478888888888888888899*********************99997...444444.4789999 PP

                                   HHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHH CS
                      Sugar_tr 353 ivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifv 433
                                   + +++l ++  +++     ++++sE fp+s Rs++ ai+  +  +   +  ll   ++ + g      + a+ +v+++++ 
  gi|70607454|ref|YP_256324.1| 355 TLGFILNAIGGGMSYLAG-YLMSSESFPTSARSTGFAISDGLGHIGGAIGPLLLFPLVASFGPITAWGLEAFPVVIAAVIL 434
                                   999999999999998765.6999******************************9999999994555556677788999999 PP

                                   HHHS--STT--CCCCGGG CS
                      Sugar_tr 434 fffvpetkgrtleeieel 451
                                   +f+vp t+g+ leei+e 
  gi|70607454|ref|YP_256324.1| 435 WFTVPKTVGVRLEEINEN 452
                                   ***************985 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  35.3   3.1e-31   1.4e-27      24     312 ..      36     358 ..      15     358 .. 0.75
   2 !   33.7  21.7     4e-12   1.8e-08      19     187 ..     277     451 ..     271     470 .. 0.81

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 3.1e-31
                         MFS_1  24 aedlg........ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqG 96 
                                     + g        +++s+++l++++  +g++ +sl lG+l+dr+Gr++vl+l+++l+a+g+l ++++ ++++l+v+r++ G
  gi|70607454|ref|YP_256324.1|  36 VGNIGaalpyipfLNASTASLIASIGLFGYIPGSLGLGYLADRIGRKPVLILTVTLTAIGSLGMALSVNFPMLAVFRFIEG 116
                                   22223444455556799*******************************************77777778999********** PP

                         MFS_1  97 lgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpe 174
                                   +g g+ + ++++++++ +p  +rg++  +++++  +++ +g+ ++++l++sl    Wr++f i+ai+++ a+v     l++
  gi|70607454|ref|YP_256324.1| 117 AGIGGDLNLAMVYVTEFAPSAKRGKYANYIYLSGWIAVGVGATIASVLVTSLPgigWRLAFGIAAIMAFAALV-----LRV 192
                                   *************************************************6665599***************55.....344 PP

                         MFS_1 175 epperkrkspkeee............................kgtgpaplvpawkallkdpvlwillialllfffgfsg.l 226
                                    +pe  r+  k+ +                              + ++p ++ w+ l ++ +l   l++l++f+f++++  
  gi|70607454|ref|YP_256324.1| 193 AAPETVRFLVKKGKideaeklvrsmeetamarakvsslpepkIIQYNTPTKT-WSVLGNRTFLK-RLVGLVIFWFFIYFvQ 271
                                   4444444444444445568888888888888777766666555555555555.********886.4444444444444423 PP

                         MFS_1 227 ltllpl..ylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavll 303
                                   +t+++l  y    lg++  ++ + +l+ +++al+  ++a+l+ +++ ++    r+l++ ++ + +++g +++a + + + l
  gi|70607454|ref|YP_256324.1| 272 YTFSTLwdYYGLALGITgsTFNQYVLYTGFAALGDTAMAFLLLAFIEKTD---RRLITQIGSFGWLIGTIVAAYFVTRFDL 349
                                   33333334557777777*97778888899999999999999999999966...5777777777777777777777777888 PP

                         MFS_1 304 llvlvliGf 312
                                   l + +++Gf
  gi|70607454|ref|YP_256324.1| 350 LGMALTLGF 358
                                   888888886 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 4e-12
                         MFS_1  19 lplalaedlgispseigl..lltlyal.gaavaslplGrlsdrfGrrrvlllglllfalglllll.fa...sslw.lllvl 91 
                                   l+ +++ +lgi++s+++   l+t++a+ g  +++++l +++++  rr +  +g +++++g+++++ f+     l  +l ++
  gi|70607454|ref|YP_256324.1| 277 LWDYYGLALGITGSTFNQyvLYTGFAAlGDTAMAFLLLAFIEKTDRRLITQIGSFGWLIGTIVAAyFVtrfDLLGmALTLG 357
                                   3337777788888886665566665543889*************9999************455556764533355458999 PP

                         MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                    +l ++g+g+++ ag+ + ++ fp + r+ ++++  +   +G ++gpll   l++s+g   ++ + a+  ++a+v+  l++
  gi|70607454|ref|YP_256324.1| 358 FILNAIGGGMSYLAGYLMSSESFPTSARSTGFAISDGLGHIGGAIGPLLLFPLVASFGPITAWGLEAFPVVIAAVI--LWF 436
                                   99*************************************************9*********************998..999 PP

                         MFS_1 173 peepperkrkspkee 187
                                   +++++   r +++ e
  gi|70607454|ref|YP_256324.1| 437 TVPKTVGVRLEEINE 451
                                   888777776666555 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   3.2e-05      0.14      19      34 .]     203     218 ..     203     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.2e-05
                                   HTS-HHHHHHHHHHHH CS
                         PPR_1  19 kaGrvdeAfelfdeMe 34 
                                   k+G++deA++l++ Me
  gi|70607454|ref|YP_256324.1| 203 KKGKIDEAEKLVRSME 218
                                   89*************7 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   8.7e-05      0.39      10      28 ..     201     219 ..     198     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                           PPR  10 ycknGkleeAlelfkeMke 28 
                                   ++k+Gk++eA++l + M+e
  gi|70607454|ref|YP_256324.1| 201 LVKKGKIDEAEKLVRSMEE 219
                                   79***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3405.01
//
Query:       gi|70607455|ref|YP_256325.1|  [L=329]
Description: CoA-transferase family III protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-53  182.8   0.0    2.2e-53  181.7   0.0    1.5  1  CoA_transf_3  CoA-transferase family III


Domain annotation for each model (and alignments):
>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.0   1.2e-57   2.2e-53       4     319 ..       8     282 ..       6     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 1.2e-57
                  CoA_transf_3   4 vrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkrLva 84 
                                   v+Vldl+++l G +at+lL dlG  VIkvE+ +kgD +R ++         +f+ +n +K+s++++lk++ gre++ +Lv+
  gi|70607455|ref|YP_256325.1|   8 VTVLDLTRLLPGGVATRLLVDLGFNVIKVEDTEKGDYMRETS-------PEVFNYLNYGKKSISINLKDDRGREIFYELVR 81 
                                   89*************************************985.......478***************************** PP

                  CoA_transf_3  85 kADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvkvgvplgD 165
                                   k+ +vie+fr  v++rl+++y++lr  n +Liy+s++gyG +Gp    p +D++ +a++G+ ++            v+++D
  gi|70607455|ref|YP_256325.1|  82 KSRIVIESFRSDVVKRLKIDYDTLRVLNEKLIYCSITGYGYEGPL--LPNHDINCNAYAGIDKVL----------PVQVAD 150
                                   *******************************************97..699**********98887..........4899** PP

                  CoA_transf_3 166 ivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyrtkdgwvaiaaa 246
                                   i + lla+++il  + + e    G  +dvs++ a+  +   ++++ l++g+      n   + ++y++y+ kdg ++++a 
  gi|70607455|ref|YP_256325.1| 151 IGSSLLAVIGILNKMWRNE----GGFVDVSMAGASKLF---NVINILTEGKSVL---NG--DYPCYNLYESKDGKISLGAL 219
                                   ***************7776....9********998844...3444444554444...34..4599**************** PP

                  CoA_transf_3 247 tdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapvntleevl 319
                                   ++k+w ++++a+gr+el    +f  na          + ++e++++ t++e++e+ ++++vp+ pv++l ev 
  gi|70607455|ref|YP_256325.1| 220 EPKFWVNFLHAVGREEL-INRQFDPNAI---------KDVSEIVKSYTTKELMEIAERYDVPIYPVRRLGEVK 282
                                   ****************8.3455555555.........79******************************9994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2004.39
//
Query:       gi|70607456|ref|YP_256326.1|  [L=272]
Description: hypothetical protein Saci_1727 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-70  235.9   0.0    3.9e-70  235.6   0.0    1.1  1  DUF1028       Family of unknown function (DUF1028)
    1.5e-13   50.8   0.1    3.6e-13   49.6   0.1    1.7  1  PG_binding_2  Putative peptidoglycan binding domain
  ------ inclusion threshold ------
       0.12   12.4   0.1        2.7    8.0   0.0    2.5  2  Gp45_2        Phage gene product 45.2


Domain annotation for each model (and alignments):
>> DUF1028  Family of unknown function (DUF1028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.6   0.0   6.5e-74   3.9e-70       1     193 []       2     200 ..       2     200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.6 bits;  conditional E-value: 6.5e-74
                                   EEEEEEE-TTT--EEEEEEESSS-HHHHHEEEETTTEEEEEESS--HHHHHHHHHHHHTT--HHHHHHHHHHT-TTGGG-E CS
                       DUF1028   1 TfSivardpetgelGvAvaskslaVgalvpfaragvGavatQaltnpelgekglelleagasaeealeallaadegrelRQ 81 
                                   T+Siv++dp+++++Gv vask+laVga+vp+++++vGa+atQal+n e+g+kglelle+g++a++++++l++ad+ +e+RQ
  gi|70607456|ref|YP_256326.1|   2 TYSIVIYDPNEEAWGVGVASKFLAVGAFVPWLKPEVGAIATQALANLEYGKKGLELLEKGYDARSTVNSLTSADQLKEKRQ 82 
                                   9******************************************************************************** PP

                                   EEEEETTS-EEEEE-TTS-S-EEEE.ETTEEEEEES-S-TCHHHHHHHHH.....S-HHHHHHHHHHHHHHT--------E CS
                       DUF1028  82 lavvdakgetaaftGeeclewaghrtgenyavaGNlLageevleamaeafeategepLaerLlaALeaGeaaGGDkrgrqS 162
                                   l+vvd kg+++aftG+ec ++agh+ g+n++v+GN+Lageevleama++ e + g ++ e++l+AL+++e++GGD+rgrqS
  gi|70607456|ref|YP_256326.1|  83 LGVVDSKGNAYAFTGRECYPYAGHIIGNNFTVQGNILAGEEVLEAMAKEAEGR-G-RIYEKILNALKMAESKGGDRRGRQS 161
                                   **************************************************543.3.6************************ PP

                                   EEEEEEE............TTEEEEEEEE--SS-HHHHH CS
                       DUF1028 163 AallVvr........esedeskpyvdLrvddhedpiaeL 193
                                   Aa++Vvr         + ++  +yvd+rvdd+++p+ eL
  gi|70607456|ref|YP_256326.1| 162 AAIIVVRkptksnteFEPSNVGKYVDIRVDDSKEPLVEL 200
                                   *********99988633455789*************997 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   6.1e-17   3.6e-13       2      74 .]     211     264 ..     210     264 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 6.1e-17
                  PG_binding_2   2 llerkpeeervlaedvaeevqaaLsrLGyydgeaggafrealrdALrafiaveNFEnraradgeidrlVlayl 74 
                                   +le    ee+v+++d+ +++++aLs+LGy              ++L+++++++NFE+++++d+ i+++Vl++l
  gi|70607456|ref|YP_256326.1| 211 FLE----EEMVSVYDYLDKINSALSKLGY--------------QDLKSWVEINNFEAKFSGDK-IGKTVLKVL 264
                                   554....59********************..............********************.******997 PP

>> Gp45_2  Phage gene product 45.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00045       2.7      11      36 ..     106     131 ..     104     147 .. 0.83
   2 ?    1.5   0.0     0.049   2.9e+02       7      19 ..     237     249 ..     232     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00045
                        Gp45_2  11 yvlidsFsneEkiltEsqLleAFkaE 36 
                                   +++ ++F+ + +il+   +leA  +E
  gi|70607456|ref|YP_256326.1| 106 HIIGNNFTVQGNILAGEEVLEAMAKE 131
                                   6999**********999999998877 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.049
                        Gp45_2   7 EiKryvlidsFsn 19 
                                   ++K +v i++F  
  gi|70607456|ref|YP_256326.1| 237 DLKSWVEINNFEA 249
                                   689*******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1936.02
//
Query:       gi|70607457|ref|YP_256327.1|  [L=376]
Description: nonspecific lipid-transfer protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-27   94.4   0.0      2e-26   92.9   0.0    1.7  2  Thiolase_N      Thiolase, N-terminal domain
    1.7e-06   27.7   0.1    4.9e-06   26.2   0.1    1.7  2  Thiolase_C      Thiolase, C-terminal domain
    2.2e-05   24.2   0.1    0.00073   19.4   0.2    2.4  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
       0.14   12.9   0.3        5.1    7.9   0.0    2.5  3  Ribosomal_L28e  Ribosomal L28e protein family


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   4.5e-30     2e-26       1     259 [.       2     214 ..       2     215 .. 0.92
   2 ?   -2.4   0.0      0.52   2.3e+03     230     248 ..     223     240 ..     221     241 .. 0.78

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 4.5e-30
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+iv+++ t++gk     ++ s  +L +e++  l++k ++d   v++ + G+  +  +g  +++ a+  +gi ++vp+++v
  gi|70607457|ref|YP_256327.1|   2 VAIVDGSITKFGK-----RKESLLQLISEVGIPLVKKYEIDFVIVSNTYSGELNS-ISG--LNNLATTYLGI-DKVPSIRV 73 
                                   7899999999999.....8888999999999999888888777777777776543.333..67889999***.******** PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenl 162
                                   +++++Sg +a+  a   + ++ a+ v+++G+E+ms+++t++ t+v+++l   +e + +l++p+          +Gl ++++
  gi|70607457|ref|YP_256327.1|  74 DNTSGSGGSALLVAKSLLDSKMANTVLVIGAEKMSEKSTKQVTSVIASLLPREERMAGLTLPS---------LAGLLSKEY 145
                                   ***************************************************************.........9******** PP

                                   HHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTS CS
                    Thiolase_N 163 akkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgn 243
                                    k+y+++Re+ +++Avk+h++++ ++ a+  ++e+              + +e ++s+v a++L  +             +
  gi|70607457|ref|YP_256327.1| 146 MKRYDAPREAFARVAVKNHHNGSLNPYAH-VQKEV--------------SLEEVLKSPVIADPLTLY-------------E 198
                                   *****************************.89988..............99****************.............9 PP

                                   B--BEEEEEEEEEEEH CS
                    Thiolase_N 244 asqisDGaaavllmse 259
                                   + +isDGa a+l+++ 
  gi|70607457|ref|YP_256327.1| 199 FTPISDGACALLMVRS 214
                                   ************9875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.52
                                   -BSSSTTSS-BTTSB--BE CS
                    Thiolase_N 230 kpaFkkeGtvtAgnasqis 248
                                   kp+F k G  tA + s+is
  gi|70607457|ref|YP_256327.1| 223 KPVFIK-GIGTASDTSSIS 240
                                   899996.555799999987 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         1   4.7e+03      49      60 ..     154     165 ..     152     171 .. 0.82
   2 !   26.2   0.1   1.1e-09   4.9e-06      30     109 ..     255     352 ..     230     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                                   -SBHHHHHHHHH CS
                    Thiolase_C  49 EAFaaqaLavak 60 
                                   EAFa +a+++++
  gi|70607457|ref|YP_256327.1| 154 EAFARVAVKNHH 165
                                   9***99999876 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-09
                                   HHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHHH CS
                    Thiolase_C  30 kvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivvt 92 
                                    v+ k+  +ve++d+ E+++  ++  ++ a++l+l +                    +N  GG  + GHP+GasG+ ++  
  gi|70607457|ref|YP_256327.1| 255 GVIAKKTAKVEKVDFAELHDMSTVLEIVQAEELGLLKkgegwkayfdtvteingeMPINTSGGLNSKGHPIGASGVAQAYE 335
                                   578889999**************99*********9999***************9889************************ PP

                                   HHHHHHHCTTSEEEEEE CS
                    Thiolase_C  93 llselkkeggklgvaal 109
                                   +  +l++e g+  v  +
  gi|70607457|ref|YP_256327.1| 336 AFLQLRREAGQRQVKDA 352
                                   ********999887655 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   1.6e-07   0.00073      12      39 ..      82     109 ..      73     120 .. 0.87
   2 ?    2.0   0.0     0.042   1.9e+02      52      66 ..     202     216 ..     191     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-07
                                   HHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                   ACP_syn_III  12 yalsvAdaliesgaakrvLvigaetlsk 39 
                                    al vA++l++s +a++vLvigae++s+
  gi|70607457|ref|YP_256327.1|  82 SALLVAKSLLDSKMANTVLVIGAEKMSE 109
                                   6999**********************97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.042
                                   B-EEEEEEEEEEESS CS
                   ACP_syn_III  52 fGDGAgAvvleasee 66 
                                    +DGA+A+++ +se+
  gi|70607457|ref|YP_256327.1| 202 ISDGACALLMVRSED 216
                                   58*******999864 PP

>> Ribosomal_L28e  Ribosomal L28e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.057   2.6e+02      22      94 ..      43     119 ..      30     132 .. 0.65
   2 ?   -3.0   0.0       2.8   1.2e+04      68      81 ..     150     166 ..     140     183 .. 0.52
   3 ?    7.9   0.0    0.0011       5.1      17      52 ..     231     266 ..     210     284 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                Ribosomal_L28e  22 qtFsrepyNltglhsrkysglanskavtVr....eekkgvvlvtkkkerahkpakawekvklsknsrkalkqiakll 94 
                                   +t+s e + + gl++   + l  +k+  +r    + ++g  l + k+    k a+++  +  +k s+k+ kq+ + +
  gi|70607457|ref|YP_256327.1|  43 NTYSGELNSISGLNNLATTYLGIDKVPSIRvdntSGSGGSALLVAKSLLDSKMANTVLVIGAEKMSEKSTKQVTSVI 119
                                   56788888888888888777777777777764542255555555555445567777777777777777777766654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                Ribosomal_L28e  68 hkpakawekvkls...k 81 
                                     p++a+ +v ++   +
  gi|70607457|ref|YP_256327.1| 150 DAPREAFARVAVKnhhN 166
                                   45555555555553322 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0011
                Ribosomal_L28e  17 rtsnkqtFsrepyNltglhsrkysglanskavtVre 52 
                                    t   ++  +e+ N+ +l+s + +g + +k+++V++
  gi|70607457|ref|YP_256327.1| 231 GTASDTSSISERENILSLNSVRNAGVIAKKTAKVEK 266
                                   444556667899**********************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2589.84
//
Query:       gi|70607458|ref|YP_256328.1|  [L=89]
Description: hypothetical protein Saci_1729 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-05   23.8   0.5      5e-05   23.3   0.5    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0016   18.4   1.8      0.076   13.0   0.1    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0052   16.6   1.4     0.0094   15.8   1.4    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0083   15.0   0.8      0.009   14.8   0.8    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
  ------ inclusion threshold ------
       0.02   14.6   5.2      0.046   13.4   5.2    1.6  1  Rubredoxin_2    Rubredoxin metal binding domain
      0.023   14.6   2.1      0.055   13.4   2.1    1.7  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.023   14.9   1.5      0.053   13.8   0.0    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.028   14.0   1.7        2.3    7.8   0.1    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.028   14.5   5.1      0.078   13.1   5.1    1.8  1  Zn-ribbon_8     Zinc ribbon domain
      0.037   14.1   2.3      0.037   14.1   2.3    1.8  2  DZR             Double zinc ribbon
      0.037   14.2   2.2      0.059   13.5   2.2    1.4  1  Ribosomal_L37e  Ribosomal protein L37e
      0.056   13.3   6.0        1.9    8.4   0.1    2.6  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.092   12.6   0.4       0.11   12.4   0.4    1.1  1  FdhE            Protein involved in formate dehydrogenase for
      0.094   12.7   7.5       0.93    9.5   4.5    2.6  1  zinc_ribbon_4   zinc-ribbon domain
      0.098   12.5   1.4      0.098   12.5   1.4    1.8  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.11   12.7   0.7       0.11   12.7   0.7    1.2  1  DUF2072         Zn-ribbon containing protein
       0.17   11.3   4.2       0.34   10.4   0.3    2.4  2  zf-ribbon_3     zinc-ribbon domain
       0.18   12.5   2.3       0.23   12.1   2.3    1.5  1  zinc-ribbon_6   zinc-ribbon domain
       0.22   11.7   4.1        5.2    7.3   0.1    2.3  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.23   11.2   5.1       0.59    9.9   5.1    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.23   11.1   4.1        1.1    8.9   0.2    2.5  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.24   11.9   2.7        3.2    8.3   0.3    2.4  2  zf-H2C2_2       Zinc-finger double domain
       0.24   11.2   6.7        2.5    7.9   0.2    3.1  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.26   11.4   4.2        2.6    8.2   0.5    2.4  2  UPF0547         Uncharacterised protein family UPF0547
       0.68   10.1   3.2        9.6    6.4   0.2    2.2  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
          2    8.2   7.6        2.5    7.9   0.3    2.5  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        4.4    7.2   9.7        1.1    9.1   0.6    2.6  3  zinc_ribbon_2   zinc-ribbon domain
        5.3    8.2   6.3         18    6.5   0.9    2.5  2  zf-C2H2_4       C2H2-type zinc finger
          6    7.5   9.6       0.85   10.2   1.1    2.6  2  zf-C2H2         Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.5   8.1e-08     5e-05      71     108 ..       3      38 ..       1      41 [. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.1e-08
                                   EEETTTS-EEECHHHHHS-TTTSSS-EEEEESSSEEEE CS
                          HypA  71 vrCreCgkefeleekalrCpkCgsadveivsGeellvk 108
                                   ++C++Cg++f++e+  +rCpkCg++d++ v+ +e +v 
  gi|70607458|ref|YP_256328.1|   3 YTCKRCGYSFSVER--ARCPKCGNSDFSSVEKREGKVV 38 
                                   68*********995..59**********9999987775 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.047        29      38      45 ..       3      10 ..       1      11 [. 0.84
   2 !   13.0   0.1   0.00012     0.076      18      35 ..      16      33 ..      14      42 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.047
                 Zn_Tnp_IS1595 38 fqCkeCrk 45
                                  + Ck+C++
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGY 10
                                  89****98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                 Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktr 35
                                  + +CP+Cg++ + ++++r
  gi|70607458|ref|YP_256328.1| 16 RARCPKCGNSDFSSVEKR 33
                                  678*******99999883 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.4   1.5e-05    0.0094      11      36 ..       2      27 ..       1      28 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                       DUF35_N 11 gqrCpdCGtvqfPPravCphCgsddl 36
                                  +  C+ CG  +   ra Cp+Cg +d+
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCGYSFSVERARCPKCGNSDF 27
                                  567*******99999*******9887 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.8   1.5e-05     0.009     509     531 ..       4      27 ..       1      41 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                   EETT.--..EESSSB-TTT--BE.E CS
                          NRDD 509 vCnecgy..kgeiekCpkCgseeev 531
                                   +C++cgy  + e+ +CpkCg+++ +
  gi|70607458|ref|YP_256328.1|   4 TCKRCGYsfSVERARCPKCGNSD-F 27 
                                   8******87777799*****876.3 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.2   7.5e-05     0.046       1      22 [.       3      24 ..       3      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                  Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCgs 22
                                  Y C++CG++++    rCp Cg 
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVERARCPKCGN 24
                                  99******************97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.1   8.9e-05     0.055       4      31 ..       2      23 ..       2      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-05
                Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhnYrCrrCk 31
                                  +Y+C +Cg    + +s+ r++  C++C+
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCG----YSFSVERAR--CPKCG 23
                                  59999999....9******88..****8 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3       1.3   7.9e+02      57      64 ..       3      10 ..       1      16 [. 0.71
   2 ?   13.8   0.0   8.6e-05     0.053       5      30 ..      16      41 ..      13      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.3
                 zf-LITAF-like 57 hyCpnCga 64
                                  ++C++Cg 
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGY 10
                                  57888875 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.6e-05
                 zf-LITAF-like  5 qvdCpaCqqrvvTsveyksgkltwll 30
                                  +  Cp+C++   +sve++ gk+ + +
  gi|70607458|ref|YP_256328.1| 16 RARCPKCGNSDFSSVEKREGKVVQYW 41
                                  578*****************998855 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.027        17      20      27 ..       3      10 ..       3      16 .. 0.69
   2 ?    7.8   0.1    0.0038       2.3       2      11 ..      18      27 ..      17      38 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.027
                                  EEESSSSB CS
                  TF_Zn_Ribbon 20 lvCtdCGl 27
                                  ++C++CG+
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGY 10
                                  56777774 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                                  EETTTTCEEC CS
                  TF_Zn_Ribbon  2 kCPnCgstnl 11
                                  +CP+Cg++++
  gi|70607458|ref|YP_256328.1| 18 RCPKCGNSDF 27
                                  6999999875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.1   0.00013     0.078       6      35 ..       3      26 ..       2      30 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                   Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.e 35
                                  Y C++Cg  f v +         CP+Cg  +
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVER-------ARCPKCGNsD 26
                                  99*********775.......34****9755 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.3   5.9e-05     0.037      29      49 .]       3      23 ..       2      25 .. 0.87
   2 ?   -1.6   0.0       4.6   2.9e+03       4       6 ..      68      70 ..      62      86 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-05
                           DZR 29 drCpsCgekvdpearfCpeCG 49
                                  ++C +Cg++ + e + Cp+CG
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVERARCPKCG 23
                                  589999999999999999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.6
                           DZR  4 Cge 6 
                                  C++
  gi|70607458|ref|YP_256328.1| 68 CRS 70
                                  222 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.2   9.6e-05     0.059      18      38 ..       4      23 ..       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-05
                Ribosomal_L37e 18 lCrrCgkrsyhvqkktCascG 38
                                  +C+rCg  s+ v++ +C +cG
  gi|70607458|ref|YP_256328.1|  4 TCKRCGY-SFSVERARCPKCG 23
                                  7*****5.9***********9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0044       2.7      28      38 ..       2      12 ..       1      13 [. 0.87
   2 ?    8.4   0.1    0.0031       1.9       2      12 ..      18      28 ..      17      33 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0044
                       TFIIS_C 28 fykCtkCghrW 38
                                  +y+C+ Cg+ +
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCGYSF 12
                                  7*******988 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0031
                       TFIIS_C  2 kCpkCgsreay 12
                                  +CpkCg+ + +
  gi|70607458|ref|YP_256328.1| 18 RCPKCGNSDFS 28
                                  7*****99866 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00017      0.11     196     228 ..       4      33 ..       2      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                   EETTT--EEE--TTS-TTT---SS-EEE----- CS
                          FdhE 196 hCslCeteWhvvRvkCsnCeetkelaylslede 228
                                   +C  C   + v R++C +C++++   + s+e++
  gi|70607458|ref|YP_256328.1|   4 TCKRCGYSFSVERARCPKCGNSD---FSSVEKR 33 
                                   7*******************984...5555555 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.5    0.0015      0.93       1      33 [.       1      24 [.       1      25 [. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                 zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCgh 33
                                  M+ tC++C+  ++++          +rC+kCg+
  gi|70607458|ref|YP_256328.1|  1 MIYTCKRCGYSFSVER---------ARCPKCGN 24
                                  9999********9999.........58888886 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   0.00016     0.098      24      44 ..       3      23 ..       1      26 [. 0.90
   2 ?   -2.0   0.0       5.6   3.5e+03      42      48 ..      67      73 ..      66      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                  EE-HHHHHHHHHTT-B-TTT- CS
                    zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCr 44
                                  ++C++C  ++  ++++Cp C 
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVERARCPKCG 23
                                  69********88********7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.6
                                  TT--B-- CS
                    zf-C3HC4_3 42 iCrrpie 48
                                  +Cr+ ie
  gi|70607458|ref|YP_256328.1| 67 FCRSAIE 73
                                  6998885 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   0.00018      0.11       3      39 ..       4      36 ..       3      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                       DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkFlyvkeeekk 39
                                   C +C+  f+  ++     Cp+CG   F  v+++e k
  gi|70607458|ref|YP_256328.1|  4 TCKRCGYSFSVERA----RCPKCGNSDFSSVEKREGK 36
                                  69999999987766....7***********9998855 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.23   1.4e+02      18      24 ..       4      10 ..       3      12 .. 0.81
   2 ?   10.4   0.3   0.00055      0.34       3      11 ..      17      25 ..      15      29 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.23
                   zf-ribbon_3 18 vCpyCGt 24
                                  +C+ CG+
  gi|70607458|ref|YP_256328.1|  4 TCKRCGY 10
                                  5999997 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00055
                   zf-ribbon_3  3 vrCPnCGap 11
                                   rCP+CG+ 
  gi|70607458|ref|YP_256328.1| 17 ARCPKCGNS 25
                                  59*****86 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.3   0.00038      0.23       1      24 [.       2      25 ..       2      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00038
                 zinc-ribbon_6  1 lfeCeqCgqllffenssClkCgaa 24
                                  +++C++Cg ++  e  +C kCg++
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCGYSFSVERARCPKCGNS 25
                                  59*******************975 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.7     0.029        18      37      44 ..       4      11 ..       1      13 [. 0.85
   2 ?    7.3   0.1    0.0084       5.2       1      12 [.      18      29 ..      18      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.029
                zinc_ribbon_13 37 sCknCgYt 44
                                  +Ck+CgY+
  gi|70607458|ref|YP_256328.1|  4 TCKRCGYS 11
                                  8******6 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0084
                zinc_ribbon_13  1 kCpKCgnteaev 12
                                  +CpKCgn+++++
  gi|70607458|ref|YP_256328.1| 18 RCPKCGNSDFSS 29
                                  5******99876 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.1   0.00096      0.59       1      24 [.       3      23 ..       3      24 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00096
                                  -B-SSS--B----SSS----SSS- CS
                DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpiRCkeCG 24
                                  Y+C +Cg ++s+++    RC +CG
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVERA---RCPKCG 23
                                  9*************9...*****9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2    0.0018       1.1       3      15 ..       3      15 ..       2      18 .. 0.86
   2 ?    3.5   0.5     0.085        52       4      10 ..      18      24 ..      15      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                        zf_UBZ  3 ylCerCgkeipes 15
                                  y+C+rCg +++++
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSVE 15
                                  9******999875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                        zf_UBZ  4 lCerCgk 10
                                   C++Cg 
  gi|70607458|ref|YP_256328.1| 18 RCPKCGN 24
                                  5****96 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3    0.0052       3.2      14      25 ..       2      13 ..       1      13 [. 0.90
   2 ?    3.5   0.1      0.17   1.1e+02      16      21 ..      18      23 ..      15      29 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0052
                     zf-H2C2_2 14 pyeCplCdkaFk 25
                                  +y+C+ C+++F+
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCGYSFS 13
                                  59*********5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                     zf-H2C2_2 16 eCplCd 21
                                   Cp+C+
  gi|70607458|ref|YP_256328.1| 18 RCPKCG 23
                                  6****8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2     0.004       2.5      21      31 ..       2      12 ..       2      14 .. 0.86
   2 ?    4.8   0.2     0.038        23      24      30 ..      19      25 ..      18      26 .. 0.91
   3 ?    0.5   0.1      0.88   5.5e+02      18      24 ..      51      57 ..      50      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.004
                 A2L_zn_ribbon 21 ylvCieCgasf 31
                                  ++ C+ Cg+sf
  gi|70607458|ref|YP_256328.1|  2 IYTCKRCGYSF 12
                                  689******99 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.038
                 A2L_zn_ribbon 24 CieCgas 30
                                  C++Cg+s
  gi|70607458|ref|YP_256328.1| 19 CPKCGNS 25
                                  *****98 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.88
                 A2L_zn_ribbon 18 eqgylvC 24
                                  e++y+ C
  gi|70607458|ref|YP_256328.1| 51 EDSYYLC 57
                                  799**99 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0042       2.6      17      25 ..       5      13 ..       3      14 .. 0.89
   2 ?    4.1   0.2     0.079        49      17      21 ..      19      23 ..      17      26 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                       UPF0547 17 CphCGyvFq 25
                                  C  CGy+F+
  gi|70607458|ref|YP_256328.1|  5 CKRCGYSFS 13
                                  989*****7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.079
                       UPF0547 17 CphCG 21
                                  Cp CG
  gi|70607458|ref|YP_256328.1| 19 CPKCG 23
                                  77776 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.015       9.6      17      28 ..       3      14 ..       1      18 [. 0.81
   2 ?    5.1   0.2      0.04        25      17      31 ..      17      31 ..      13      36 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.015
                      zf-Mss51 17 feCpdCGiptyc 28
                                  ++C++CG++  +
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFSV 14
                                  99*****98765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                      zf-Mss51 17 feCpdCGiptycsee 31
                                    Cp+CG + + s e
  gi|70607458|ref|YP_256328.1| 17 ARCPKCGNSDFSSVE 31
                                  57*****98877766 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.2      0.15        94      22      28 ..       3       9 ..       3       9 .. 0.93
   2 ?    7.9   0.3    0.0041       2.5       6      17 ..      18      29 ..      15      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                       zf-RRN7 22 yyCrrCh 28
                                  y C+rC+
  gi|70607458|ref|YP_256328.1|  3 YTCKRCG 9 
                                  89****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0041
                       zf-RRN7  6 pCgvCgcrsftl 17
                                  +C+ Cg+ +f +
  gi|70607458|ref|YP_256328.1| 18 RCPKCGNSDFSS 29
                                  8******99987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6     0.086        53       2       7 ..       5      10 ..       4      12 .. 0.69
   2 ?    9.1   0.6    0.0018       1.1       1       7 [.      18      24 ..      15      25 .. 0.84
   3 ?   -2.8   0.1       9.6   5.9e+03      15      16 ..      67      68 ..      66      70 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.086
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C++CG+
  gi|70607458|ref|YP_256328.1|  5 CKRCGY 10
                                  777775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +Cp+CG+
  gi|70607458|ref|YP_256328.1| 18 RCPKCGN 24
                                  5999997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.6
                 zinc_ribbon_2 15 FC 16
                                  FC
  gi|70607458|ref|YP_256328.1| 67 FC 68
                                  77 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.9      0.03        18       1      11 [.       3      13 ..       3      17 .. 0.85
   2 ?    4.3   0.4      0.15        94       2      13 ..      18      30 ..      17      33 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.03
                     zf-C2H2_4  1 fkCpiCgksFs 11
                                  ++C+ Cg sFs
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFS 13
                                  89********6 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                     zf-C2H2_4  2 kCpiC.gksFssk 13
                                  +Cp C +  Fss 
  gi|70607458|ref|YP_256328.1| 18 RCPKCgNSDFSSV 30
                                  6****87777765 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1    0.0014      0.85       1      11 [.       3      13 ..       3      16 .. 0.93
   2 ?    3.0   0.2      0.27   1.7e+02       2       7 ..      18      23 ..      18      30 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                                  EEETTTTEEES CS
                       zf-C2H2  1 ykCpdCgksFk 11
                                  y+C+ Cg+sF+
  gi|70607458|ref|YP_256328.1|  3 YTCKRCGYSFS 13
                                  9*********7 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.27
                                  EETTTT CS
                       zf-C2H2  2 kCpdCg 7 
                                  +Cp+Cg
  gi|70607458|ref|YP_256328.1| 18 RCPKCG 23
                                  7****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 589.60
//
Query:       gi|70607459|ref|YP_256329.1|  [L=266]
Description: hypothetical protein Saci_1730 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   22.5   2.7    0.00017   21.8   0.5    2.3  3  DUF4352   Domain of unknown function (DUF4352)
  ------ inclusion threshold ------
      0.024   14.5   2.0      0.024   14.5   2.0    2.1  3  ODV-E18   Occlusion-derived virus envelope protein ODV-E18
      0.095   12.6   1.2       0.18   11.7   1.2    1.4  1  SurA_N_2  SurA N-terminal domain
       0.23   11.6   1.4       0.41   10.8   1.4    1.4  1  YebO      YebO-like protein


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.15   6.7e+02      84      99 ..      31      46 ..      26      53 .. 0.84
   2 !   21.8   0.5   3.9e-08   0.00017      13     108 ..      43     136 ..      35     147 .. 0.78
   3 ?   -0.9   0.1      0.42   1.9e+03      43      54 ..     198     210 ..     178     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                                  --EEEE-TT-EEEEEE CS
                       DUF4352 84 lflgtlnpGkkvtGkl 99
                                   +++t+++G++++Gk+
  gi|70607459|ref|YP_256329.1| 31 SHSSTIQSGGTISGKV 46
                                  5789**********98 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.9e-08
                                   EEEEEEEEEEEEETTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB..--EEEE-T CS
                       DUF4352  13 evtVnsveytksvgkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskadd..lflgtlnp 91 
                                   + +Vn+v  +  +   e  +  +++ f+ v++tv  +g+ ++++ + +f L+++ g +    +++   +    ++ +tl++
  gi|70607459|ref|YP_256329.1|  43 SGKVNNV--IINQA-IEKASNVPDKMFVEVNITVSYNGSGSVNIVPQDFYLTTSRGVYEGSPGEPVFGD-PspFQPTTLKN 119
                                   5578888..55555.3444456889**************************988865555555554444.458******** PP

                                   T-EEEEEEEEEESTT-C CS
                       DUF4352  92 GkkvtGklvFdvpkgkk 108
                                    ++  G ++F  p + +
  gi|70607459|ref|YP_256329.1| 120 ETSANGIVSFLTPSNIS 136
                                   *************9987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.42
                                   EEEEEE.-SSS-E CS
                       DUF4352  43 dvtvkN.kgkeal 54 
                                   +vt+ N + +e++
  gi|70607459|ref|YP_256329.1| 198 NVTIHNlNYNETV 210
                                   5555554433333 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.0   5.3e-06     0.024      25      68 ..       6      48 ..       2      63 .. 0.75
   2 ?   -3.2   0.0       1.8   8.1e+03      59      74 ..     123     138 ..     118     140 .. 0.71
   3 ?   -3.3   0.1       1.9   8.6e+03      41      48 ..     178     185 ..     164     203 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-06
                       ODV-E18 25 sllltilvvlviiil.lvllvqssstGsdssssnannartGfvnP 68
                                  +++  +l+++vii+l l+l+++ +s  s ss+ ++  +  G vn 
  gi|70607459|ref|YP_256329.1|  6 AIFTVVLIIVVIIALsLLLFMNRAS--SHSSTIQSGGTISGKVNN 48
                                  5778899999999994445556666..899998888888888885 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                       ODV-E18  59 nnartGfvnPlnaalr 74 
                                    n  + f+ P n +l 
  gi|70607459|ref|YP_256329.1| 123 ANGIVSFLTPSNISLH 138
                                   5667788888888776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.9
                       ODV-E18  41 vllvqsss 48 
                                   v + ++ss
  gi|70607459|ref|YP_256329.1| 178 VYFTNVSS 185
                                   33333333 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   3.9e-05      0.18      10      53 ..      12      53 ..       1      57 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                      SurA_N_2 10 gllviiiglallaFilgdlfgvgsylfssssnevaeVnGekIsl 53
                                  +++v+ii+l ll+F+  +  ++ s++ +s+ +  ++Vn+  I++
  gi|70607459|ref|YP_256329.1| 12 LIIVVIIALSLLLFM--NRASSHSSTIQSGGTISGKVNNVIINQ 53
                                  234444888888888..55555666677899*******998876 PP

>> YebO  YebO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.4   9.1e-05      0.41       1      25 [.      10      34 ..      10      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                          YebO  1 vvlvivvlvgllvwFFvnRasvrAn 25
                                  vvl+ivv+++l +  F+nRas+  +
  gi|70607459|ref|YP_256329.1| 10 VVLIIVVIIALSLLLFMNRASSHSS 34
                                  6999*****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1682.79
//
Query:       gi|70607460|ref|YP_256330.1|  [L=443]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-21   75.2  47.7      9e-18   64.4  47.7    2.1  1  Sugar_tr  Sugar (and other) transporter
      5e-16   58.6  58.2      5e-16   58.6  58.2    1.7  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.063   13.0   1.2       0.55   10.0   1.2    2.8  1  DUF3094   Protein of unknown function (DUF3094)


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4  47.7   1.5e-21     9e-18       1     440 [.      11     429 ..      11     433 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.5e-21
                                   HHHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                      Sugar_tr   1 valvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslli 81 
                                   v+l a++g +l+ Yd+ + ++++ +      f+  +++ +      ls  +v+i+++++ +G+l++g +gd++GRk++l+i
  gi|70607460|ref|YP_256330.1|  11 VTLAASIGTFLEYYDLLLSATAAGIVWPSLYFNPATKNPTVGL--ALSLSTVGIAFIVRPLGGLIFGQIGDKLGRKSTLII 89 
                                   578899999******9988888777766666666666666665..68999******************************* PP

                                   HHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCH..HHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  82 aavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklR..galvslyqlaitfGilvaa 155
                                   + +l++ig++  ++ + +      s  ++i+ R++ Gig G++ + +  ++ E+A+k+     + +s+ q a+ fGi  ++
  gi|70607460|ref|YP_256330.1|  90 TLLLMFIGTFGLGVLPTYaqigvISAFMIIILRIIQGIGFGGEWGGAVSWMVEFAKKANSspTYWTSFLQGAVLFGISAST 170
                                   ****************8888888778889999***********************999986678999*********98777 PP

                                   HHHHHHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                      Sugar_tr 156 ifglglnktsn.....adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsl 231
                                   +  ++++   +     ++gwr+l+ + +++ +l +++++   ESP +l  k k e +k    +       +++ + ++   
  gi|70607460|ref|YP_256330.1| 171 FGFAIVSALLDrasflSWGWRLLFIVGAIIVVLGALMRYYTSESPLFLELKVKGELSKSPALE-----TLKKYWVSIILLA 246
                                   666666555556999*********************************998855533333222.....2222222222222 PP

                                   HHHHH.....HTTHHHHSH...HHHHHHHHHH...HHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHH. CS
                      Sugar_tr 232 eaeqeeekaswkellssktvrqrlligvvlqi...fqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvai. 308
                                    a        w +     t    +++ +++     f    G+n i+ +s++ f n          +++g+  +v  +++i 
  gi|70607460|ref|YP_256330.1| 247 IAW-------WYM-----T---VTTVLIATPYsiqFASAIGVNTILGLSSQSFMN----------LVIGIGYVVGGLASIv 302
                                   222.......111.....2...112222222200022334555555555555554..........4444444444444432 PP

                                   ..HHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHH CS
                      Sugar_tr 309 ..flvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRska 387
                                      + + + + +l ++ a++++++  ++   +++++ k+  a +v++   +++ a+f   +g++     +E fp++ R+++
  gi|70607460|ref|YP_256330.1| 303 lgVMTKSIRMTRLNVIVAVVCSVLVYLY---FYMISLKE--AYFVILSSAIFYGAVFY-PFGGLA-SWFAESFPTKYRYTG 376
                                   1133445555556777777777776666...56666665..57888888999999999.466665.4457*********** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--S CS
                      Sugar_tr 388 laiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpet 440
                                   + +a+++  l + ++s++ p i   +++ +v  ++   a+ ++i++++   +t
  gi|70607460|ref|YP_256330.1| 377 TGLAYQIGGLLSGIVSTFVPPIILLYTKLPVSQLWIYYALTYTIICVVSALAT 429
                                   ***********************999999999999999999999888877666 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6  58.2   8.4e-20     5e-16       5     351 ..      19     391 ..      15     393 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 8.4e-20
                         MFS_1   5 aflsalarsilgpalpl.alaedlg..ispseigllltlyalga.....avaslplGrlsdrfGrrrvlllglllfalgll 77 
                                   +fl +++  + ++a+ + + +  ++      ++gl+l+l ++g       ++ l++G ++d++Gr+++l+++lll+++g +
  gi|70607460|ref|YP_256330.1|  19 TFLEYYDLLLSATAAGIvWPSLYFNpaTKNPTVGLALSLSTVGIafivrPLGGLIFGQIGDKLGRKSTLIITLLLMFIG-T 98 
                                   55555555555555555555555553333455777777755544333337788999999********************.4 PP

                         MFS_1  78 lll..f...a....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergrai..gllsagfslGailgpllgg..... 142
                                   ++l  +   a    +s +++++lr++qG+g g+ + ++++++++ ++k + +  +  ++l++    ++++g  ++      
  gi|70607460|ref|YP_256330.1|  99 FGLgvLptyAqigvISAFMIIILRIIQGIGFGGEWGGAVSWMVEFAKKANSSPTYwtSFLQG----AVLFGISASTfgfai 175
                                   444454444356678888******************************76655542344444....333333333322221 PP

                         MFS_1 143 ..llasslg.....Wravfyilaivsllafvlfllll.peepperkrkspkeeekgtgpaplvpawkallkdpvl....w. 210
                                     +l++ ++     Wr++f++ ai+ +l++++   ++  e+p   + k + e+     ++p+++ +k+ + +  l    w 
  gi|70607460|ref|YP_256330.1| 176 vsALLDRASflswgWRLLFIVGAIIVVLGALM--RYYtSESPLFLELKVKGEL----SKSPALETLKKYWVSIILlaiaWw 250
                                   22333333355555***************995..5551444445555555555....888888877777777766333332 PP

                         MFS_1 211 .illialllfffgfsg.lltllplylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrlllalllllla 287
                                    + ++++l++ + +s+ + + + +  ++ lgls  +++ ++  ++++++vg  +++++g + + +   r +++  ++++++
  gi|70607460|ref|YP_256330.1| 251 yMTVTTVLIA-TPYSIqFASAIGV--NTILGLSsqSFMNLV--IGIGYVVGGLASIVLGVMTKSIRMTRLNVIVAVVCSVL 326
                                   2222222222.2333344444444..999999986655555..*******************8876666666655555555 PP

                         MFS_1 288 alglallavtssavllllvlvl.iGfglgfvfpsllalasdlappeeagtasglfn.tagslggal 351
                                   + +++++   ++a +++l++++ +G  ++  f+ l+++ ++++p++++ t +gl+  + g l+g++
  gi|70607460|ref|YP_256330.1| 327 VYLYFYMISLKEAYFVILSSAIfYGA-VFYPFGGLASWFAESFPTKYRYTGTGLAYqIGGLLSGIV 391
                                   55555555555555555555551555.33349***********************94444477666 PP

>> DUF3094  Protein of unknown function (DUF3094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.2   9.1e-05      0.55      30      50 ..     189     209 ..     175     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.1e-05
                       DUF3094  30 pWlllvvvlavvigLGllsRl 50 
                                    W+ll++v a++++LG l R 
  gi|70607460|ref|YP_256330.1| 189 GWRLLFIVGAIIVVLGALMRY 209
                                   48**************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2740.10
//
Query:       gi|70607461|ref|YP_256331.1|  [L=412]
Description: phytoene dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-06   25.8   0.0    3.6e-05   23.2   0.0    1.9  1  Amino_oxidase  Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     2e-09   3.6e-05     121     444 ..      68     397 ..       1     405 [. 0.74

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-09
                                   HHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSC CS
                 Amino_oxidase 121 leallqktldeldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggs 201
                                   +e +l+k+l   dl + +  + ++++ +++  d    +++ ++e  +k   +s++f+g   +   + a+++  ++  +g++
  gi|70607461|ref|YP_256331.1|  68 MEKFLYKELKISDLLDSTIINNMNRFPIFNTLDNFNRRYFPNDEFLQKALGFSAVFLG--GSPFNTPAIYAMVNYAIYGKG 146
                                   3333333333555555555555555555555553334444444444444445555555..567****************** PP

                                   CCEETTHTHHHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHH CS
                 Amino_oxidase 202 lllprgGlsqlpealae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekae 280
                                   +++p+gG++ l+  l e  ++ g++++++ +V +++ +++  +   + g+ v++D+ +  ++   +  +l+s    ++ + 
  gi|70607461|ref|YP_256331.1| 147 VFYPEGGFKGLVLKLFEacKRAGVEFKFDFEVDKVQGSNGMLKYVESKGRAVDGDYFIFNMDYHYAD-KLLSS---NDEVY 223
                                   ************************************99999999999*****************999.45554...24444 PP

                                   HHHHSEEEEEEEEEEEESSGG.SGCSTS.E.CE..........CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHH CS
                 Amino_oxidase 281 airnlgfgsvnkvilefdrkf.wednal.g.qg..........vlvseltttlgeafissdfpsrappgkglvllvyvggd 348
                                    +r+  ++s++ v+  ++++   +++     +g             + +++ l + ++++   +++  g +lv lv +++ 
  gi|70607461|ref|YP_256331.1| 224 WMRRKLAPSAILVYAGVEGELkSPHH-ViIiNGdwryhfnsimRGAEPDLNNLSYYVSYTRATDKRIKGDSLVFLVPISAG 303
                                   44444667788888888888833333.243344556566666667777777777777777788888888888888888855 PP

                                   HHHHHTTS-HHHHHHHHHHHHHHHHT..GTSSTCSEEEEEECCT..ETTTSSSEEE.BTTHHHHHHHHHHCHHCSTTEEE. CS
                 Amino_oxidase 349 aaneleslsdeelvqavlrdLrklfg..eevpepkatlvtrWht..dplargsysyvsvgpghedydplakpegdprlffA 425
                                         ++ +e+ v+++++d+++  g  ++v+  + ++  ++    ++++++++  +++  ++  ++p+++++   +++  
  gi|70607461|ref|YP_256331.1| 304 L----FGINPEAYVKRAIQDFKEKTGskFDVKFMRVYTPFDFLVdyNAYRGTAFGISHTLDQTGPFRPPMRNRRWRNVYHV 380
                                   4....456******************886666666688888877668999******************************* PP

                                   SGGGCTTTTTS.HHHHHHHH CS
                 Amino_oxidase 426 Gehtsreypgt.vegAilSG 444
                                   G +t    pg  v+    S+
  gi|70607461|ref|YP_256331.1| 381 GQYTQ---PGIgVPMVTISA 397
                                   *****...998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2486.28
//
Query:       gi|70607462|ref|YP_256332.1|  [L=154]
Description: beta-carotene hydroxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 987.58
//
Query:       gi|70607463|ref|YP_256333.1|  [L=275]
Description: phytoene synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-48  165.5   0.1    1.8e-48  165.3   0.1    1.0  1  SQS_PSY   Squalene/phytoene synthase


Domain annotation for each model (and alignments):
>> SQS_PSY  Squalene/phytoene synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.1     1e-52   1.8e-48       2     263 .]       9     254 ..       8     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 1e-52
                                   XHH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----........------------..---------THHHHHHHHH CS
                       SQS_PSY   2 raasksfylaslllppelRdalgalYafcreaddlvDdvseplqararldwwrdavdavyaedklkpprepvlralaqlir 82 
                                   ++as ++y +s ++pp++R++++ lYaf r+ ddlvD+   p++a++ + ++r ++ + +   ++k++++ vl+ + +l+r
  gi|70607463|ref|YP_256333.1|   9 KRASVTYYNSSVFFPPQVRRDVTKLYAFVRVFDDLVDS--IPQKAKE-FYELRSKYYEQL---DGKDSNDLVLKNFVDLMR 83 
                                   78999********************************9..7899998.9********999...89**************** PP

                                   HHT--HHHHHHHHHHTS--SS-..--SHHHHHHHHHHHHHHHHHHHHHHH-S.S-HHHHHHHHHHHHHHHHHHHHHT---S CS
                       SQS_PSY  83 tyklpkellleliegmeadleftryetlddLeeYcyrvagvVgelclrllgarrsdralaeaarrlGkalQltnilRdvpe 163
                                   +++ +ke++++++++me+dl +  y t+d+L eY y +a vVg +++++l + +++   + +ar lG+a+Q++n++Rdv e
  gi|70607463|ref|YP_256333.1|  84 RKNFDKEWVDAFLDAMESDLKKSVYYTIDELLEYIYGSAEVVGVMMAKILDLPEES---YYYARMLGRAMQYINFIRDVEE 161
                                   ****************************************************5555...9********************* PP

                                   HHHHTT..S-HHHHHHHT--HHHHHHT-.-SHHHHHHHHHHHHHHHHHHHHHHHTGGGS.-HHHHHHHHHHHHHHHHHHHH CS
                       SQS_PSY 164 DaergrvyLPadvlkefgvseedllrkgvrsaelrallrrlaerArelldearellkqlpdrrarpalllavalyrailer 244
                                   D ++gr yLP + + ef+ s  d       s+++ + +r++++r  e+ ++a+++   + + r+  a+++a+ +y  + ++
  gi|70607463|ref|YP_256333.1| 162 DMALGRQYLPFQEMMEFKTSLLDS------SPRFNEFIRFQISRYFEYQKTAEKGYSYI-PFRYLIAIKTAADMYKWTAKK 235
                                   ****************97755433......679**************************.888****************** PP

                                   HHHTTT-TTT------HHH CS
                       SQS_PSY 245 ieaadydvlsrrvklsllr 263
                                   i ++++ + +r++k +++r
  gi|70607463|ref|YP_256333.1| 236 IWNNPQIIKQRKIKPKKRR 254
                                   *****98888999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1885.99
//
Query:       gi|70607464|ref|YP_256334.1|  [L=220]
Description: hypothetical protein Saci_1735 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1600.34
//
Query:       gi|70607465|ref|YP_256335.1|  [L=292]
Description: hypothetical protein Saci_1736 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2308.28
//
Query:       gi|70607466|ref|YP_256336.1|  [L=522]
Description: hypothetical protein Saci_1737 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0046   16.5   2.7       0.31   10.6   0.0    3.8  3  BetaGal_dom3  Beta-galactosidase, domain 3
  ------ inclusion threshold ------
      0.043   13.7   0.5       0.47   10.4   0.4    2.9  2  DUF1533       Protein of unknown function (DUF1533)
      0.075   12.8   8.3       0.37   10.6   1.8    3.5  4  HCV_NS4a      Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> BetaGal_dom3  Beta-galactosidase, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   5.2e-05      0.31      29      67 ..     201     239 ..     198     249 .. 0.82
   2 ?   -0.0   0.0      0.11   6.5e+02      52      76 ..     337     361 ..     315     362 .. 0.84
   3 ?    2.8   0.1     0.015        87      51      70 ..     404     425 ..     395     432 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.2e-05
                  BetaGal_dom3  29 asisgstLaltGDlnatttleviapssvktltwNgkkle 67 
                                    ++++ tL+l+G +  ttt+e   p+  +++++  + l+
  gi|70607466|ref|YP_256336.1| 201 LQLQKVTLNLSGSFSFTTTIESSHPKRYSQVEFHYNGLN 239
                                   467899*************************98655554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                  BetaGal_dom3  52 apssvktltwNgkklettktkyGsl 76 
                                    p+ v+++ + g+++ + +t++G +
  gi|70607466|ref|YP_256336.1| 337 SPKVVTKVMVSGNPVIVVVTNNGVM 361
                                   469999*********9999999975 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.015
                  BetaGal_dom3  51 iap..ssvktltwNgkklettk 70 
                                   ++p   +v+++t+Ngk+ e ++
  gi|70607466|ref|YP_256336.1| 404 VVPqsVNVQNVTINGKSYESQV 425
                                   455336789*******988765 PP

>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.56   3.4e+03      45      55 ..     273     283 ..     271     285 .. 0.87
   2 ?   10.4   0.4   7.9e-05      0.47       7      30 ..     410     433 ..     409     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.56
                       DUF1533  45 tIvIkakGYeD 55 
                                   +I ++a+GY++
  gi|70607466|ref|YP_256336.1| 273 SISFQAQGYFT 283
                                   5999*****86 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 7.9e-05
                       DUF1533   7 aIsevtvNGkklennkyslssigk 30 
                                   ++++vt+NGk++e +  s++ +g 
  gi|70607466|ref|YP_256336.1| 410 NVQNVTINGKSYESQVVSINATGY 433
                                   689****************99985 PP

>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.62   3.7e+03      14      35 ..     246     267 ..     244     278 .. 0.80
   2 ?   10.6   1.8   6.2e-05      0.37      20      45 ..     335     359 ..     333     363 .. 0.80
   3 ?    4.1   0.0    0.0064        38      27      45 ..     379     397 ..     376     403 .. 0.83
   4 ?   -3.2   0.1       1.3   7.6e+03      26      36 ..     411     423 ..     408     435 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.62
                      HCV_NS4a  14 AiyalttGSvvvvtrwsvnGkg 35 
                                   A +a   GS v    w+++ +g
  gi|70607466|ref|YP_256336.1| 246 ATLAYFQGSYVPAMVWTTSTQG 267
                                   7788999999999999999888 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.2e-05
                      HCV_NS4a  20 tGSvvvvtrwsvnGkgppvvvvpdee 45 
                                    GS+ vvt++ v+G++  +vvv  + 
  gi|70607466|ref|YP_256336.1| 335 YGSPKVVTKVMVSGNP-VIVVVTNNG 359
                                   59**************.666666655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0064
                      HCV_NS4a  27 trwsvnGkgppvvvvpdee 45 
                                    + +vnG+g++v+v p   
  gi|70607466|ref|YP_256336.1| 379 VDLDVNGNGQYVLVFPNSS 397
                                   5789**********99875 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.3
                      HCV_NS4a  26 vtrwsvnGkg..p 36 
                                   v ++++nGk   +
  gi|70607466|ref|YP_256336.1| 411 VQNVTINGKSyeS 423
                                   6778899988543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1449  (0.0808188); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3439.21
//
Query:       gi|70607467|ref|YP_256337.1|  [L=468]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-149  498.7   0.0   1.4e-149  498.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.17   11.7   0.0       0.38   10.6   0.0    1.6  1  LPD23     Large polyvalent protein associated domain 23


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  498.6   0.0  1.6e-153  1.4e-149       7     462 .]       3     463 ..       1     463 [. 0.97

  Alignments for each domain:
  == domain 1  score: 498.6 bits;  conditional E-value: 1.6e-153
                                   SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHH CS
                        Aldedh   7 etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaear 87 
                                   etiev++P++ +vi+kv++++++dv+a +++A + f+  ++lp+++R +iL++a d++e++ke+la+l++le+Gkp+++ar
  gi|70607467|ref|YP_256337.1|   3 ETIEVVSPSNLKVIGKVKRMSRDDVRAQIEEADKGFEDISSLPLYKRTAILKRASDIIEREKERLARLLALEAGKPIKDAR 83 
                                   68******************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHH.HSEEEEEEC........TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEE CS
                        Aldedh  88 aeveeaidvlryyaelaek.legevlpss........egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvl 159
                                    ev++a + +r + e+a   leg+   ++        e++  +++rePlGvv+aI P+NfP++ +a+k+apa+a+GN+vv+
  gi|70607467|ref|YP_256337.1|  84 VEVTRASRLFRQAGEEAVFvLEGKNYRVDgyeyppgnENRIVVSQREPLGVVSAILPFNFPVNSFAHKVAPAIAVGNSVVV 164
                                   ****************999899988555445566666999***************************************** PP

                                   EE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---E CS
                        Aldedh 160 KPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGkn 240
                                   KP+ +tplsal +a+++ eagl ++++ vvtg+ +e+g++l +hp++ +v++tGst++g  ia++a +  kr+++ElGG +
  gi|70607467|ref|YP_256337.1| 165 KPSINTPLSALEMAKILVEAGLTEKAIRVVTGYSKEIGDELYTHPSISLVTLTGSTQTGLMIASKAVSLGKRIIMELGGSD 245
                                   ********************************************************************************* PP

                                   EEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHH CS
                        Aldedh 241 plivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekve 321
                                   p+ivledaD+++  +  v++ + +aGQ+C a++r++v e+iy++fv+ + +++k+l+vgdplde+tdvGP+i+++++e+++
  gi|70607467|ref|YP_256337.1| 246 PIIVLEDADIERSSSISVRARYEYAGQNCNAGKRIIVREEIYERFVSSFEKKVKELRVGDPLDENTDVGPVINRESVENLN 326
                                   ********************************************************************************* PP

                                   HHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE CS
                        Aldedh 322 kyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvf 402
                                   +++++ak++g k+ +     ++g+++g+f+  t + + + dm + ++E+FGPV+++i++k++eeai++aN+t+yGL+++vf
  gi|70607467|ref|YP_256337.1| 327 SVIDDAKSKGGKVEIL----NKGPDNGHFFPLTAVLKPSLDMLVTKTEVFGPVAPIIPVKSDEEAIQVANSTDYGLQSAVF 403
                                   ***************4....4899********************************************************* PP

                                   -SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                        Aldedh 403 tkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                   tkd++ra+r++++l++G v iNdst+ + ++lpfgG+k++g+Greg ++ + e+te k v
  gi|70607467|ref|YP_256337.1| 404 TKDVNRALRISKALKFGAVIINDSTRLRWDSLPFGGFKKTGIGREGVRDTMLEMTENKLV 463
                                   *******************************************************99865 PP

>> LPD23  Large polyvalent protein associated domain 23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.2e-05      0.38      10      43 ..     169     202 ..     159     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.2e-05
                         LPD23  10 tadlealaeAkeleaqGedaesIrqeTGWfrgkD 43 
                                   +++l+al+ Ak l ++G + ++Ir  TG+ + + 
  gi|70607467|ref|YP_256337.1| 169 NTPLSALEMAKILVEAGLTEKAIRVVTGYSKEIG 202
                                   8999************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3076.43
//
Query:       gi|70607468|ref|YP_256338.1|  [L=272]
Description: hypothetical protein Saci_1739 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-47  161.6   0.1    4.1e-47  161.3   0.1    1.0  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.3   0.1   2.3e-51   4.1e-47       1     288 [.       2     265 ..       2     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.3 bits;  conditional E-value: 2.3e-51
                                   EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHH.HHHHHHHHHHHHHHH CS
                  Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaal.crgannrvlaeaakr 80 
                                   iD H+H          ++e  +f  e  +++ +  +++ +l ++++ l +++ +gi r v++ +  + ++  r+  ea  +
  gi|70607468|ref|YP_256338.1|   2 IDFHFHA--------PVREFVEFLGEYAEPAFRYFNAKIELKEFKEILDYYEGIGIKRFVVLPIDsTTFLGRRIHNEAVPN 74 
                                   9*****5........57999999999999***************************999999876589************* PP

                                   CTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHH CS
                  Amidohydro_2  81 pdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpspewlfggpq 161
                                   +dr+v+++ v+p   ++a++el++a+++   +Gv+l+p+ +g ++l++    +++e+ + +gl + +htG+s+ +    ++
  gi|70607468|ref|YP_256338.1|  75 DDRVVRFVSVDP-MKPNAVEELKEAIKKFEPVGVKLHPQLQGFHPLDEKAM-KLYEVVNNHGLIIVFHTGTSGIGAGLRSS 153
                                   *******66665.8889**********************************.********************9999999** PP

                                   HHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-G CS
                  Amidohydro_2 162 ettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlieavgp 242
                                   +++++  p +++++a++fP+ kivlaH+G+p  + ++a++++ + pnvy++lsg        ++p++ p al    + + +
  gi|70607468|ref|YP_256338.1| 154 IRLDYGRPIYFDEIAVRFPDIKIVLAHFGWP--WTEEAIAIALHKPNVYLDLSG--------WAPKYVPDALWKNAKRL-K 223
                                   *******************************..*********************........9***************9.* PP

                                   GGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHH CS
                  Amidohydro_2 243 drilfGsDyPhptleaepealalldlvallsdeerekilggNAarl 288
                                   d++lfGsD+P ++++++  +l ++ l    +++++ kil++NA rl
  gi|70607468|ref|YP_256338.1| 224 DKLLFGSDFPLIKPDRWINELSQVNL----DADLKNKILSENAGRL 265
                                   *************************9....*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2162.95
//
Query:       gi|70607469|ref|YP_256339.1|  [L=138]
Description: hypothetical protein Saci_1740 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.084   12.7   0.0      0.096   12.5   0.0    1.3  1  SprT-like  SprT-like family


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.4e-06     0.096      48      91 ..      73     114 ..      22     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-06
                     SprT-like  48 sIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGae 91 
                                    IeL ++ +   se++ +++L+HE+ H+      g   + HG++
  gi|70607469|ref|YP_256339.1|  73 VIELITERYSRLSEEEKIKVLIHEILHIPKGFSGG--LRAHGKH 114
                                   699999999999***************98866666..6777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 989.79
//
Query:       gi|70607470|ref|YP_256340.1|  [L=139]
Description: holliday junction resolvase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-28   98.9   0.1    1.9e-28   98.3   0.1    1.3  1  Hjc        Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.045   13.3   0.0       0.11   12.0   0.0    1.7  2  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.3   0.1   2.1e-32   1.9e-28       2      92 ..       9     102 ..       8     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 2.1e-32
                                   HHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHH..TCEEEEEEE CS
                           Hjc   2 yERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarka..ggelllavk 80 
                                   +ERelv+iLr +gf++vR+++S+++++plpD++A++g+++l+iE+Ks++++++++k +qv kl ef +++   g++l+avk
  gi|70607470|ref|YP_256340.1|   9 AERELVSILRSEGFNAVRIPTSNSSPNPLPDIFATKGNILLAIECKSTWEHKVKVKDRQVIKLFEFLSMFtmEGRALIAVK 89 
                                   7*********************************************************************88899****** PP

                                   E.TTTEEEEEEGG CS
                           Hjc  81 l.qgkewkllvve 92 
                                   + + ++wk+++++
  gi|70607470|ref|YP_256340.1|  90 FkEIHKWKVMEIR 102
                                   *889*****9986 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.3e-05      0.11      16      67 ..      13      60 ..       3      76 .. 0.80
   2 ?   -2.5   0.0       0.4   3.6e+03      36      45 ..     121     130 ..     118     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                     AHJR-like 16 laeqyrekGyevllhPnredlPdfLksYrpDliarkdeeaviiEvksrrssa 67
                                  l + +r +G++ +  P ++  P+ L    pD+ a+k++  ++iE ks   + 
  gi|70607470|ref|YP_256340.1| 13 LVSILRSEGFNAVRIPTSNSSPNPL----PDIFATKGNILLAIECKSTWEHK 60
                                  56667899**************999....9****************987733 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.4
                     AHJR-like  36 lPdfLksYrp 45 
                                   + +fL++Y p
  gi|70607470|ref|YP_256340.1| 121 ISQFLENYIP 130
                                   5689999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1050.46
//
Query:       gi|70607471|ref|YP_256341.1|  [L=697]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-96  322.4   0.0    1.4e-95  320.8   0.0    1.6  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.3e-22   80.2   0.0    4.1e-22   78.6   0.0    1.9  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.8   0.0   1.6e-99   1.4e-95       3     550 .]     135     640 ..     133     640 .. 0.90
   2 ?   -1.4   0.0     0.065   5.8e+02     360     399 ..     644     683 ..     643     689 .. 0.89

  Alignments for each domain:
  == domain 1  score: 320.8 bits;  conditional E-value: 1.6e-99
                                   TT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT- CS
                 Ald_Xan_dh_C2   3 eeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlgl 81 
                                   e++++nv++  ++e+G ve+  +     +e  ++++r++ +++E+ +a ++p  +d+ l v s+ qa   v + + ++lg+
  gi|70607471|ref|YP_256341.1| 135 EDLKSNVVReqTFEFGKVENKGK----SIEINLYWSRSSGNPIEPYGAQVIP--KDDGLIVISNQQAGNVVSNELQKALGV 209
                                   56788888877888898875443....4778*********************..7999**********************9 PP

                                   -GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHH.S-EEEEEEEEEEEEE-TTS-EEEEEEEE CS
                 Ald_Xan_dh_C2  82 penkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmla.tgkrhpfkikykvgadkdGkitaldvdl 161
                                      kv+ +  r GG+FG K   v +  ++ +a++k + p+k++++R+e++la ++++ + k+k+ + +++dGk+ ald++l
  gi|70607471|ref|YP_256341.1| 210 ---KVVHKNARQGGSFGAKFSFVRYLSVLGYASLKYKVPIKWIETRSEHLLAsNSSGPERKFKINAYYSSDGKVNALDIHL 287
                                   ...9**********************************************99345678899******************** PP

                                   EEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHHHH CS
                 Ald_Xan_dh_C2 162 ladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelRrr 242
                                   + d+Ga+ d ++a   + l++l+gpYkipn+r++g++v tN+ p +afRG+G p +++alEr+md++A+ lg++++e+R++
  gi|70607471|ref|YP_256341.1| 288 WEDVGASIDSGQAF--KPLGFLTGPYKIPNIRYTGTLVATNKNPPGAFRGAGTPPHTWALERVMDAIADDLGISRAEIRKI 366
                                   *******9999987..6699999********************************************************** PP

                                   HBCECGCC.SEEET..EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEEEEE CS
                 Ald_Xan_dh_C2 243 Nlikpgeltpygqp..vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqegalvr 321
                                   N+i  +++ py++     dsg+ + ll+ ++++ d+        +++++  + G+g+a+ + ++   +      +++ +v+
  gi|70607471|ref|YP_256341.1| 367 NAI--DTF-PYDTGfaYIDSGNPKGLLELALSRKDI-------FSMRDE--RTGVGIALSTDPS--TP------SGSERVK 427
                                   ***..567.999988778**********99996655.......455545..79***********..22......3466777 PP

                                   E-.TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 322 vn.tdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrerll 401
                                   ++ ++G++++ +g    GqG e + + +a++ Lg+p ed++ +  d +  p + g ++Sr+++ + ++v  A e+l+++ +
  gi|70607471|ref|YP_256341.1| 428 IKvKNGKIVIGLGFGAEGQGNEHTAVYLASKLLGLPTEDITYEALDNTELPTSFGPGGSRMAAFTYGSVSGAVEELKAKTR 508
                                   77679**************************************************************************** PP

                                   HHHHHHCTS-CCCEEEETTEEEET.EEEECHHHHHHHHHHTTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETT CS
                 Ald_Xan_dh_C2 402 kiaaellevspedleledgkvvvk.eksvslaelaaaaylervslsatgfyktldeetgkgppfayfaygaavaeVevDte 481
                                   + a+    v  +++++e+g +v + ++++++ +   +    + + + +g+y            f+++++++ +a+V +  e
  gi|70607471|ref|YP_256341.1| 509 RKAE---AVLGDKVSYENGYFVGEkGGKIKITQFEGEE--VEFTYTLQGKY-----------RFNAYPFACDLAVVRI--E 571
                                   ****...77889999**999999955555555555533..34444444444...........699***********98..5 PP

                                   T--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                 Ald_Xan_dh_C2 482 tgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                    g++k  + v+  D G+ i   +v+ Q+ GG + Gi+lal+E+++yd++G+llt++ladY +Ptaad+P
  gi|70607471|ref|YP_256341.1| 572 DGKIKPIKHVVYIDPGNPIDEDLVKEQVIGGTATGIALALYERYLYDDNGNLLTTNLADYGMPTAADLP 640
                                   9******************************************************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.065
                                   EEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 360 vrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrer 399
                                   v++v++ ++ +p+g++ ++     ++ +Av  A e++ +r
  gi|70607471|ref|YP_256341.1| 644 VNIVPTPSQVTPYGVKGVGEIPVGVAVAAVTSAIEDVIKR 683
                                   8899999999***********************9998876 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   4.6e-26   4.1e-22       2     109 ..      12     117 ..      11     118 .. 0.93
   2 ?   -3.3   0.0       1.3   1.1e+04      49      68 ..     635     654 ..     633     693 .. 0.59

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 4.6e-26
                                   T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.TSSS-EEEESS-SSEESSTT CS
                  Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.siledeedallaedkvrsvg 81 
                                   G++ YvdD++++g+ y+ f+rS+++hA+i++id ++a +    + v+t+kd+ +++ ++g    +  ++ lla +k+ +vg
  gi|70607471|ref|YP_256341.1|  12 GRGGYVDDLEFKGK-YAFFLRSPYPHARILKIDPTDAVNRG--ALVLTGKDIVTKRVESGeREGAGLNTSLLAINKALYVG 89 
                                   8999********99.**********************9998..899**********99998555555578*********** PP

                                   -EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  82 qavaavvAedeetArkAaklvkveYeel 109
                                   q+va+v+A+d + A + a+lv+veYe+l
  gi|70607471|ref|YP_256341.1|  90 QPVALVLADDPYRASDLAELVQVEYEPL 117
                                   **************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                                   EHHHHCCGTECCTTSSS-EE CS
                  Ald_Xan_dh_C  49 takdlpkenkaigsiledee 68 
                                   ta+dlp+++ +i +++++ +
  gi|70607471|ref|YP_256341.1| 635 TAADLPDIEVNIVPTPSQVT 654
                                   67777777777765554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5003.64
//
Query:       gi|70607472|ref|YP_256342.1|  [L=490]
Description: thiamine pyrophosphate enzyme [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-34  118.0   0.0    5.4e-34  117.3   0.0    1.3  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    3.4e-14   52.9   0.0    6.8e-14   51.9   0.0    1.5  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    5.7e-12   45.5   0.0    1.1e-11   44.6   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.0   9.1e-38   5.4e-34       2     170 ..       3     165 ..       2     167 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 9.1e-38
                                   EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                  TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                   t a+ + ++L++   ++++g+pG+++l++l++l ++  ++++la+h ++a++  +gy+  ++++gvv++++gpG+ n ++ 
  gi|70607472|ref|YP_256342.1|   3 TIAQQIYDLLSK-YTNSIYGNPGTTELHFLKYLPNN--MKYYLALHDGVAVGLSEGYYLKSRNLGVVNLHAGPGLSNSFGY 80 
                                   789999999999.789*******************9..******************************************* PP

                                   HHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEH CS
                  TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpk 161
                                   +++A+++++Pll+++g++p+++ +    +++l  + ++l  p +k+ +++++++e+ + + rAirt+l+ + gPv+++lp+
  gi|70607472|ref|YP_256342.1|  81 IYSAYRNKSPLLIIAGQQPSYSSP---EEPMLyyNFSSL--PSVKEYVEIKNSKETIKFMNRAIRTCLTYPYGPVVVSLPY 156
                                   ************************...443445588888..**************************************** PP

                                   HHCC-EEEH CS
                  TPP_enzyme_N 162 dvlleevde 170
                                   d++++  de
  gi|70607472|ref|YP_256342.1| 157 DIIEDISDE 165
                                   ***998776 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   1.1e-17   6.8e-14      24     143 ..     372     476 ..     352     486 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.1e-17
                                   ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTSB CS
                  TPP_enzyme_C  24 sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggkrksgpa 104
                                   s+  g +G++lpa++G + a  + +  +i+GDG+f +  q+++ta r++l ++++++nN+gy + +   +  +++ +++  
  gi|70607472|ref|YP_256342.1| 372 SNRSGLLGWALPAGVGYASA--GGKSLVIMGDGSFNYAPQAIWTASRYDLRVKILIINNSGYEALRS--RAGYKRDFFS-- 446
                                   467899************98..569*************************************98887..4555555554.. PP

                                   B.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH CS
                  TPP_enzyme_C 105 gkdlkpvdfaklaealGakgarvekadveeleealkeal 143
                                       +++++ ++aea+  ++    +   e+ + a+k+ +
  gi|70607472|ref|YP_256342.1| 447 ----PETHPWRIAEAYDFRAK---EF--EDYQLAVKWLM 476
                                   ....45677999999966632...33..55555555555 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.9e-15   1.1e-11       4     127 ..     186     300 ..     183     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-15
                                   HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEE CS
                  TPP_enzyme_M   4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipedhplylgmlglhgskaanealeeaDlvla 83 
                                    +e +k++++++i++G ++ +++as+e+ +l++kl++P+ ++ +  +++  + ++     l  +++++ n+++++ Dlvl+
  gi|70607472|ref|YP_256342.1| 186 TVEKIKSSSQIAIVAGYEIETFDASQEVMHLSNKLNCPIyAEPYLSRSSGIRVNDT----L-PTRASELNKIIRNYDLVLV 261
                                   7899***********************************77777776554333332....2.3569*************** PP

                                   ES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEE CS
                  TPP_enzyme_M  84 lGarfddirttgsepefapeakiihididpaeigknyqvdlaiv 127
                                   lG +++ +   +++ +++   ++i++++d +e+ k+ +   +iv
  gi|70607472|ref|YP_256342.1| 262 LGGELHRVLYMDEDIHWK---NVIQVTSDVNEARKRPW--NTIV 300
                                   *****9977666555774...69**********99865..3555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3075.56
//
Query:       gi|70607473|ref|YP_256343.1|  [L=63]
Description: hypothetical protein Saci_1744 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-10   39.0   9.3    6.9e-10   38.7   9.3    1.1  1  DUF3311   Protein of unknown function (DUF3311)
  ------ inclusion threshold ------
      0.018   14.9   7.6      0.021   14.7   7.6    1.1  1  DctQ      Tripartite ATP-independent periplasmic transporters
      0.053   13.5  10.0       0.06   13.3  10.0    1.0  1  DUF485    Protein of unknown function, DUF485
        2.6    8.1   9.5        3.5    7.7   9.5    1.2  1  DUF997    Protein of unknown function (DUF997)


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   9.3   1.5e-13   6.9e-10       3      51 ..      12      60 ..       9      63 .] 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.5e-13
                       DUF3311  3 llvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrl 51
                                  l++ +++   l+p+y  + p++lGlP fyw+q+  + ++++v++++  +
  gi|70607473|ref|YP_256343.1| 12 LALVFVILYSLLPLYSTTSPTFLGLPMFYWYQMILMPIGAIVFFIVILV 60
                                  555556666799*********************************9876 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   7.6   4.7e-06     0.021      73     123 ..      11      59 ..       2      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-06
                          DctQ  73 allfaavliwagwlevaaalfeettpvlglplwwvy..lvlpigaallalval 123
                                   +l+++ v+++++      ++++++ ++lglp++++y  +++piga+++++v+l
  gi|70607473|ref|YP_256343.1|  11 VLALVFVILYSL----LPLYSTTSPTFLGLPMFYWYqmILMPIGAIVFFIVIL 59 
                                   233333444444....59999999999*****99996677*****99988877 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  10.0   1.3e-05      0.06      17      68 ..       9      60 ..       3      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                        DUF485 17 afpltaiflvvYfgfvllvafapdllatkvgegnitvglllgllqivltfll 68
                                  + +l+++f+++Y +++l ++ +p++l+ +++     + +++g++++++++l+
  gi|70607473|ref|YP_256343.1|  9 VGVLALVFVILYSLLPLYSTTSPTFLGLPMFYWYQMILMPIGAIVFFIVILV 60
                                  56899**************************667777777777777777665 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   9.5   0.00078       3.5      11      63 ..      12      59 ..       3      62 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00078
                        DUF997 11 lltllyflwwllfaYglgskeveey.yilglPlWfflscillpilfivlvillv 63
                                  l++++++l+ ll  Y +         ++lglP+  ++ +il+pi +iv+ i+++
  gi|70607473|ref|YP_256343.1| 12 LALVFVILYSLLPLYSTT------SpTFLGLPMFYWYQMILMPIGAIVFFIVIL 59
                                  222222222233333333......238*****************9999877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 443.29
//
Query:       gi|70607474|ref|YP_256344.1|  [L=526]
Description: hypothetical protein Saci_1745 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-17   60.9  33.6    9.5e-17   60.9  33.6    1.7  2  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
        8.1    6.0  13.5      0.074   12.6   1.3    3.1  2  TM140     TM140 protein family


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.7      0.33     3e+03     239     259 ..       9      28 ..       4      31 .. 0.51
   2 !   60.9  33.6   1.1e-20   9.5e-17       3     406 .]      44     459 ..      42     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.33
                           SSF 239 lkltivlilvligmisiilfa 259
                                   l +++++i++++  + ++++a
  gi|70607474|ref|YP_256344.1|   9 L-SLVIFIVLFAVFVYLGFYA 28 
                                   3.3344444444556677776 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 1.1e-20
                           SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdylskRf 79 
                                   lagr+l+++ +   l+a+   a  f+ ++ +v asG  ++  ++   + + ++ ll+++rl     n+g +T +d+++ Rf
  gi|70607474|ref|YP_256344.1|  44 LAGRKLGPYLMWFLLTADLFTAYTFIAVPSLVLASGPIGFYAAFYSGVTAFIA-LLFMPRLWavsrNKGYVTAADFVKDRF 123
                                   9***********************************87777777666666655.566666665888*************** PP

                           SSF  80 kgkrilvylsalslllvitlklsvdlvgg.aklielalGlny.......etavlllaaltalYtviGGllAvvytdtiqav 152
                                   ++k  l  l a++ +++   +++ ++vg  a+l  l+lGl +        +++l+  +++a ++++ Gl+   +t + + +
  gi|70607474|ref|YP_256344.1| 124 NSKT-LAGLVAVTGVVAELPYIALQIVGMqAALSILLLGLGVsnislvnDLSLLVSFIILAAFVFTSGLRGAALTAVYKDI 203
                                   ****.7777777778889999999999842555556666543111222257999999************************ PP

                           SSF 153 lmlvgalilliivllevGgleslveklkeaapkvvdl....ltpdslkllrdpltalslwlglvlGvagl....philvRf 225
                                   ++l+  ++++i+v l++Gg++++++++++ + +v       ++p  ++ l++ ++  +  + l +G a +    ph +   
  gi|70607474|ref|YP_256344.1| 204 IILATVITVAIYVPLAFGGFSAAFSNAATYSSQVNSAlngvNKPIFYQYLQSTVSNNLAYISLAIGSAFAlylyPHAVNGS 284
                                   *****************************999884442454445555555555555555555555555545555******* PP

                           SSF 226 laakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGl.llavmlAai 305
                                   ++a+++k++  ++  l ++ +l+l+   +  ++   +a+ +    + +++   +a+p L+   +p+++ G+ ll + +  +
  gi|70607474|ref|YP_256344.1| 285 VSADSKKSLKISL-ALQPFYSLILAI--IALFGILVYANTNVLNFIIHAKSGAVAVPALIGYTMPDWFVGVaLLGIFIGGL 362
                                   ****999998775.555665555544..4444445566666655666778889*****************93455555555 PP

                           SSF 306 mstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavil 386
                                   +   + + + a+ ++t+ + k+++++   +   ++ ++++i+     +a++l+ + +    +   +l  +++    l+ + 
  gi|70607474|ref|YP_256344.1| 363 V-PAAIMAIGAANLLTRNIIKELKPNM--SPNTESSLAKWISTAFKFIALALVFTVPAT-YAIQLQLLGGVIILQTLPPLF 439
                                   4.445566789999*********9998..455567788888899999999999999888.6777789999999999***** PP

                           SSF 387 lalfwkrvneqGAlagliiG 406
                                   l+l+ +++n++  +ag ++G
  gi|70607474|ref|YP_256344.1| 440 LGLYTHKLNSHSLIAGWVAG 459
                                   *********99888777666 PP

>> TM140  TM140 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3   8.3e-06     0.074       6      42 ..       8      44 ..       4     112 .. 0.72
   2 ?   -3.6   4.9       0.8   7.1e+03     111     166 ..     158     215 ..     127     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-06
                         TM140  6 kllflgilvlvvvvisllfyallwkaGnlvdlpnlri 42
                                   l++++ +vl +v + l fya  w++G+l +lp+  +
  gi|70607474|ref|YP_256344.1|  8 ILSLVIFIVLFAVFVYLGFYASRWRKGDLSKLPEWAL 44
                                  678889999999999******************8644 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.8
                         TM140 111 avgflaassvllagGlglflsyv..wkWvrlsllGpgflalvlaqallillllaivlf 166
                                       l++s + l   l+l++s++  + +v +s l  + l+ v  +++++  +++++++
  gi|70607474|ref|YP_256344.1| 158 LLLGLGVSNISLVNDLSLLVSFIilAAFVFTSGLRGAALTAVYKDIIILATVITVAIY 215
                                   4444677778888888887777622456666655444444455555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 3127.01
//
Query:       gi|70607475|ref|YP_256345.1|  [L=355]
Description: hypothetical protein Saci_1746 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2306.98
//
Query:       gi|70607476|ref|YP_256346.1|  [L=229]
Description: hypothetical protein Saci_1747 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-77  256.3   9.2    1.1e-76  255.4   9.2    1.4  1  SoxE            Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
       0.14   12.3   3.8       0.11   12.7   2.0    1.7  2  Arch_flagellin  Archaebacterial flagellin
        6.7    7.1  26.3        1.7    9.0   9.3    2.7  3  DUF3446         Early growth response N-terminal domain


Domain annotation for each model (and alignments):
>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.4   9.2   1.8e-80   1.1e-76       1     149 []      54     202 ..      54     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 255.4 bits;  conditional E-value: 1.8e-80
                          SoxE   1 pgkvklpydssnktvfiylvvsssasnlfnfnGtsnGqlkiyiPagwsvlvklvneeslphnlvlvqnntaiPnsleissd 81 
                                   +g+++lpy+s+nktvfiylvvsss+snlfnfnGts+G+lkiy+Pagw+v+v+l+n+eslphn+++vqnnt+iPns++issd
  gi|70607476|ref|YP_256346.1|  54 SGAYALPYNSNNKTVFIYLVVSSSSSNLFNFNGTSDGSLKIYVPAGWNVMVILKNTESLPHNANIVQNNTPIPNSINISSD 134
                                   5899***************************************************************************** PP

                          SoxE  82 GkillivGattsnyavsGissGqsasGlledlsaGtywlacgilGhaesGmWvdlivssnvtvPyaii 149
                                   Gki+l+vG+++sny++sG+ssG++asG+le+++aG+yw+acg++Gha++GmWvdlivss++++Pyaii
  gi|70607476|ref|YP_256346.1| 135 GKIILYVGDGPSNYYSSGVSSGNEASGMLENIPAGYYWIACGLPGHAKNGMWVDLIVSSTISTPYAII 202
                                   ******************************************************************96 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.0   1.8e-05      0.11      11      76 ..       6      75 ..       3      99 .. 0.75
   2 ?   -2.7   0.0      0.95   5.7e+03      82      95 ..     131     144 ..     101     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE....EEE-SSSSSEEEEEEE-- CS
                Arch_flagellin 11 fIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg....dsatngtineitiyvkln 76
                                  +IA ++V  v+ gv++  a+++   ++ t ++s++  ss+ +i+++      + ++n++++++ iy+ ++
  gi|70607476|ref|YP_256346.1|  6 LIAIIVVIIVVLGVVVYLATRIGGTSSGTSQSSSSLSSSSSSISSSLPsgayALPYNSNNKTVFIYLVVS 75
                                  6888888888888888888888777777777777766666666665544576889999999977776544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.95
                                   EEGGG-EEEEEESS CS
                Arch_flagellin  82 idlnkttisvtddg 95 
                                   i  +  +i +++dg
  gi|70607476|ref|YP_256346.1| 131 ISSDGKIILYVGDG 144
                                   33333444455554 PP

>> DUF3446  Early growth response N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   9.3   0.00028       1.7      26      73 ..      18      70 ..       3      83 .. 0.54
   2 ?   -2.7   0.1       1.3   7.7e+03      40      40 ..     149     149 ..     118     163 .. 0.53
   3 ?    6.9   5.4    0.0013       7.7      13      51 ..     183     222 ..     174     227 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00028
                       DUF3446 26 glvgvan.....ppsspsssssssssssssssspslscsvaaqqsselehiYs 73
                                  g+v   +     ++s +s+ssss ssssss ss+  s + a   +s+ + ++ 
  gi|70607476|ref|YP_256346.1| 18 GVVVYLAtriggTSSGTSQSSSSLSSSSSSISSSLPSGAYALPYNSNNKTVFI 70
                                  55433232333234444556666666666666666677776677766666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                       DUF3446  40 s 40 
                                    
  gi|70607476|ref|YP_256346.1| 149 Y 149
                                   1 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0013
                       DUF3446  13 nslwaee.llslvsglvgvanppsspssssssssssssss 51 
                                   n++w +  + s +s    + +++ + +sss+++s sssss
  gi|70607476|ref|YP_256346.1| 183 NGMWVDLiVSSTISTPYAIISNSITLPSSSTTTSTSSSSS 222
                                   5566666444455544444433434333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1591.63
//
Query:       gi|70607477|ref|YP_256347.1|  [L=138]
Description: hypothetical protein Saci_1748 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1017.15
//
Query:       gi|70607478|ref|YP_256348.1|  [L=306]
Description: hypothetical protein Saci_1749 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-20   72.6   1.7    6.5e-20   71.9   1.7    1.4  1  Band_7    SPFH domain / Band 7 family
    1.2e-13   51.2   0.4    4.3e-13   49.5   0.4    1.7  1  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   1.7   7.2e-24   6.5e-20       2     156 ..      42     217 ..      41     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 7.2e-24
                        Band_7   2 iieegevgvvvrfGklsrvlepG.................lhf.ilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtid 64 
                                   i+++ e +vv  +G++ +vl++G                 +++  lP+ + v++vs++ ++++vs     +t D +p+ ++
  gi|70607478|ref|YP_256348.1|  42 IVQPTEQAVVLIQGQIAAVLPAGthniqspqnplsnilskFKYnTLPYDTIVYFVSLTRHEVRVSG--VSQTDDLVPLEYE 120
                                   899********************888888888888888888888888999999*************..888********** PP

                        Band_7  65 vtviyrvpddapklvaav.....eresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevl 140
                                   v v+y+v +++  lv+++      +++++l+n i++++++++ +v+++ +l +++++ +++   +++ l+  l+++Gv ++
  gi|70607478|ref|YP_256348.1| 121 VAVYYKV-SNPGLLVTNIqfasqYFRDGELANYISPIIDQEVSQVLNHVKLVDVFKKFADISTAVTAGLKTFLAEIGVDLI 200
                                   *******.999999999966655556666**************************************************** PP

                        Band_7 141 dvritdidppp.evaqa 156
                                   +vrit++ p + e+++ 
  gi|70607478|ref|YP_256348.1| 201 SVRITKLIPQDpELRRI 217
                                   ******98876666655 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.4   4.8e-17   4.3e-13       1     204 [.      27     219 ..      27     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.8e-17
                      Band_7_1   1 vwrfprydneiknGakLivregqeavfvneGqiaDvfapGtytLttenlPvlstLkgwkyGfesPfkaevYfvntrqftdl 81 
                                   ++r+p  +++i   + +iv+ + +av + +Gqia v   Gt+++++   P+ + L ++ky  + P+ + vYfv+ ++ +  
  gi|70607478|ref|YP_256348.1|  27 IFRYP--KENITSKSLIIVQPTEQAVVLIQGQIAAVLPAGTHNIQSPQNPLSNILSKFKYN-TLPYDTIVYFVSLTRHEVR 104
                                   68999..455999999********************************************7.68**********9876654 PP

                      Band_7_1  82 kwGtknpvilrDpefglvrvrafGtyslrvvdpakllreivGtdgefdteeiseqlkslivtrlsdvlaeskipvldlaak 162
                                     G        D+   lv++    ++  +v++p+ l+++i  + + f+  e+++++  +i +++s+vl++  + ++d+  k
  gi|70607478|ref|YP_256348.1| 105 VSGV----SQTDD---LVPLEYEVAVYYKVSNPGLLVTNIQFASQYFRDGELANYISPIIDQEVSQVLNH--VKLVDVFKK 176
                                   4454....44443...4555555566789***************************************75..7789***** PP

                      Band_7_1 163 seelaeklkealkeelaeyGlelekleien.islpeevekald 204
                                     +++  ++  lk+ lae+G++l ++ i++ i  ++e++++l+
  gi|70607478|ref|YP_256348.1| 177 FADISTAVTAGLKTFLAEIGVDLISVRITKlIPQDPELRRILQ 219
                                   **************************99872455668887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2097.98
//
Query:       gi|70607479|ref|YP_256349.1|  [L=158]
Description: hypothetical protein Saci_1750 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.056   13.5   0.4       0.89    9.7   0.0    2.4  2  TolA_bind_tri  TolA binding protein trimerisation
       0.13   11.4   0.3       0.21   10.8   0.3    1.4  1  PLU-1          PLU-1-like protein


Domain annotation for each model (and alignments):
>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0001      0.89       5      66 ..      48     108 ..      35     110 .. 0.89
   2 ?    4.3   0.6    0.0046        42       7      56 ..     102     150 ..      99     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
                 TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                    ++++E ++++ s+    +++++e+  +e+r+L G i+  q    ++  r + + ++lDe +
  gi|70607479|ref|YP_256349.1|  48 NLSTIESQIAS-SNPFSPILKRIESIISEIRTLIGMIQSSQGGGADIYARYKIQTEQLDEIV 108
                                   57788888888.58899999*********************999999999999999999876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0046
                 TolA_bind_tri   7 arLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQr 56 
                                   ++L++i+++ +  ++ +  q+ +l+  l+ L G i  l    + ++ rQ+
  gi|70607479|ref|YP_256349.1| 102 EQLDEIVKN-DLQMISIADQVYNLSLSLDNLEGIIPLLGQIRQVIISRQK 150
                                   7999***99.69999******************99887777777777777 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   2.3e-05      0.21     231     297 ..      36     111 ..      21     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.3e-05
                         PLU-1 231 klsleeLeallneaqeipvslpslaaleeilkkarewqrkveelikssq.......daaer..ptlseleellkkg 297
                                   + ++++L++ +n+++ i+ ++ s   +++ilk+ + + +++ +li   q       d   r  + +++l+e++k+ 
  gi|70607479|ref|YP_256349.1|  36 QSTIAKLQNTINNLSTIESQIASSNPFSPILKRIESIISEIRTLIGMIQssqgggaDIYARykIQTEQLDEIVKND 111
                                   56899********************************988888865555545888744444567777788777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.37s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 836.72
//
Query:       gi|70607480|ref|YP_256350.1|  [L=94]
Description: hypothetical protein Saci_1751 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0054   17.3   0.5     0.0084   16.7   0.5    1.4  1  MgtE_N       MgtE intracellular N domain
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.017   14.6   0.1    1.0  1  Tam41_Mmp37  Phosphatidate cytidylyltransferase, mitochondria
      0.039   14.3   1.0      0.061   13.6   0.4    1.6  1  PRANC        PRANC domain


Domain annotation for each model (and alignments):
>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   1.4e-06    0.0084      20      92 ..      19      90 ..       7      94 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.4e-06
                                  HHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHHHCS-HHHHHH CS
                        MgtE_N 20 allrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeekveellsaldeeeree 92
                                  ++l++lp+ +  e+  e +     +  +++sde++++l+++l+++    +l+ ++ e+ + +l++++ e+r+ 
  gi|70607480|ref|YP_256350.1| 19 EVLKYLPPVRVKEIVGEHTKTYFWSSRAKISDETIEKLMQNLPPELKLRILDMIESEI-KMVLEQIEDEKRRL 90
                                  6899999999999999999999999999999**************9999999998887.88999998888875 PP

>> Tam41_Mmp37  Phosphatidate cytidylyltransferase, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.8e-06     0.017     201     273 ..      14      88 ..       7      94 .] 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-06
                   Tam41_Mmp37 201 relYkplleelenvellekekekeee..kkleqdlspearaellrkLPkklrskllskyekklskkkkdeeeflk 273
                                   r +Y+++l++l+ v+++e+  e++++   + + ++s e++ +l+++LP +l+ ++l  +e+++++  ++ e+ ++
  gi|70607480|ref|YP_256350.1|  14 RAIYSEVLKYLPPVRVKEIVGEHTKTyfWSSRAKISDETIEKLMQNLPPELKLRILDMIESEIKMVLEQIEDEKR 88 
                                   789***************998777766544558899*********************999999655555544444 PP

>> PRANC  PRANC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4     1e-05     0.061      61      90 ..      48      75 ..      27      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                         PRANC 61 vlnnicskkslWnlLPiEIkykIleyLndk 90
                                  + +++++   l ++LP+E+k  Il++++++
  gi|70607480|ref|YP_256350.1| 48 ISDETIE--KLMQNLPPELKLRILDMIESE 75
                                  3333333..699**************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 666.61
//
Query:       gi|70607481|ref|YP_256351.1|  [L=127]
Description: hypothetical protein Saci_1752 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.067   13.8   0.1       0.37   11.4   0.1    2.0  1  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.1e-05      0.37      37     126 ..      21      91 ..       7      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHH CS
                   Hemerythrin  37 laelldelvdeleaHhaaEEellfPlledrpggravldvlereHdeirelleelrellkgleepsaaafaelleeladllr 117
                                   + ++ d++v+    H ++E++++fPl+       +  +  +++H  i++  + + +  +++e          ++++ + + 
  gi|70607481|ref|YP_256351.1|  21 IMTTHDFVVN---WHAKIEDKYIFPLFG------EKAKPYSNDHLLIERYGNSAIQ-QRNVE---------WIKRYVKIVL 82 
                                   5555555555...6**************......7777777777777766655552.22223.........5666677777 PP

                                   HHHHHHHHT CS
                   Hemerythrin 118 eHiakEesi 126
                                   +H+  Ee+ 
  gi|70607481|ref|YP_256351.1|  83 DHNLNEERN 91 
                                   777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 785.24
//
Query:       gi|70607482|ref|YP_256352.1|  [L=94]
Description: hypothetical protein Saci_1753 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0067   16.2   1.1       0.01   15.6   1.1    1.2  1  Gemini_mov      Geminivirus putative movement protein
  ------ inclusion threshold ------
      0.048   13.7   1.3      0.072   13.2   1.2    1.4  1  LAB_N           Lipid A Biosynthesis N-terminal domain
       0.37    9.2   3.7       0.36    9.3   3.7    1.0  1  Cellulose_synt  Cellulose synthase


Domain annotation for each model (and alignments):
>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.1   1.7e-06      0.01      30      66 ..      40      77 ..      31      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                    Gemini_mov 30 selpwsrvgeiailtlvav.lvlYLlytlvlkDlilvl 66
                                  s+lp+s +++i +l+ v v +++Y+ly +   D++l++
  gi|70607482|ref|YP_256352.1| 40 STLPFSLFVVIFLLIKVGVlGAVYMLYKYTKMDMVLLV 77
                                  789*****999999999873589*************97 PP

>> LAB_N  Lipid A Biosynthesis N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.2   1.2e-05     0.072      39      70 ..      60      90 ..      45      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                         LAB_N 39 GslllliYailrkDpvlilgqslglviyirNl 70
                                  G+ + ++Y + + D+vl++g  ++l++ i Nl
  gi|70607482|ref|YP_256352.1| 60 GA-VYMLYKYTKMDMVLLVGTGISLIVLINNL 90
                                  44.5678************************9 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.7     6e-05      0.36     624     680 ..       4      60 ..       1      92 [. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 6e-05
                Cellulose_synt 624 llippl.tllivnlvavvvgvsrainsayeswgkllGklffafwvlvhlypflkGllG 680
                                   +li pl tl+ +++++ v+g+s+ + ++++  + l   l f+++v++ l     G+lG
  gi|70607482|ref|YP_256352.1|   4 FLIYPLsTLMTLDVLTTVIGLSKGLVEGNPLISGLYSTLPFSLFVVIFLLI-KVGVLG 60 
                                   566665278889**********************************99863.346655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 653.38
//
Query:       gi|70607483|ref|YP_256353.1|  [L=146]
Description: hypothetical protein Saci_1754 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1096.93
//
Query:       gi|70607484|ref|YP_256354.1|  [L=346]
Description: C4-dicarboxylate transporter/malic acid transport protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-37  129.0  35.2    3.3e-37  128.5  35.2    1.2  1  SLAC1     Voltage-dependent anion channel


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.5  35.2   1.8e-41   3.3e-37       3     316 ..      16     333 ..      14     342 .. 0.75

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 1.8e-41
                         SLAC1   3 tpawFaivMGtgilalllkalparglriislilfllalvlfllllvlyllrfilypeavrkelrh....pv.eslflgtfp 78 
                                    p++Fa+vM++gi ++++     +  +++s++l +l+ v++++l+v++++r+++yp++  +el++    p+  s +++t +
  gi|70607484|ref|YP_256354.1|  16 LPSYFASVMAIGIFSIAF-F-L-YNYNVLSYLLSYLSNVIYFALWVITVIRWVYYPRSYLNELKDlgrsPGfLSKVIATNT 93 
                                   59****************.3.1.446679************************************6666666666666666 PP

                         SLAC1  79 mgl.ltil....nglllvlpgewlatlalvllWigvllslltavvvvfllftekeekleeitpawllpvvgllvvallgal 154
                                   +g   +++    ++         + ++ l+ lWi + +++l a+ +      + + ++e ++++w l + +++ v  lg+ 
  gi|70607484|ref|YP_256354.1|  94 IGSeYMLIfkdySL------AYAFFMFGLI-LWIFYQYAVLSAISFNI----NDR-NIEYVNGIWELIPASTQSVVDLGSI 162
                                   66654444222211......1345566666.67666666666554444....333.6************************ PP

                         SLAC1 155 laesqnpslqll.gilvvslllwglGlllalvlfvlylyrlithklppaelrptlfiplGplgqgalallllgkaapk... 231
                                   l +        +  +  +sl+l+++G++ ++v+ +l+l r+++++l p++   +++i  G+++++ala + l   +++   
  gi|70607484|ref|YP_256354.1| 163 LSPF-------HtYLYTLSLILFFIGVAQYIVMTSLILGRIVLKGLKPKDASGSYWIITGAAALSALAGIDLLIYLNEvnl 236
                                   *432.......235789****************************************************999888866666 PP

                         SLAC1 232 ....aaevlkvlalllalflwglglfwllvavlsvls.........lpvrlkfslswWaftFPlgalalatielgka..le 297
                                       +++ l+++ l + ++lw+ g++w+++ + + +          l     +++++W+ +FP+g++a++++ l +   l+
  gi|70607484|ref|YP_256354.1| 237 qsayIGD-LRTIVLTFIILLWSTGTWWIPWLIYMGIWkhvinrvplL----VYDPQFWGAVFPMGMYATSSFLLIRYvnLN 312
                                   6553222.24466666899**********954433335887776655....5*********************96552244 PP

                         SLAC1 298 sea.f.kvlgtillvllvlvw 316
                                    ++ +  ++ ++ +v+lv  +
  gi|70607484|ref|YP_256354.1| 313 IPMlIpDIFILVGSVALVYQT 333
                                   333344555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2359.45
//
Query:       gi|70607485|ref|YP_256355.1|  [L=172]
Description: uracil DNA glycosylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-30  106.2   0.0    1.7e-30  106.1   0.0    1.0  1  UDG             Uracil DNA glycosylase superfamily
  ------ inclusion threshold ------
      0.034   13.9   0.4      0.065   13.0   0.4    1.5  1  Planc_extracel  Planctomycete extracellular


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.0   1.9e-34   1.7e-30      11     152 ..       1     166 [.       1     169 [. 0.91

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1.9e-34
                                   EEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG........CTEEEEESSS....SECGCTTCCCCTCCH CS
                           UDG  11 vivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese........qgvyitnvvkcrppgnrdtptsaeikaca 81 
                                   +ivG aP  + +++tg+ F+g +++n+l k+l+++gl+++++s+        ++vyit vvkc pp+n+  pt  ei++c 
  gi|70607485|ref|YP_256355.1|   1 MIVGLAPAGNgGNRTGRVFTGdESSNNLTKALYDTGLANQPYSVsrddglklNDVYITAVVKCVPPENK--PTTGEIRNCM 79 
                                   9*********9**********9999**************99999***********************99..********** PP

                                   HHHHHHHHHHH.SSEEEEESHHHHHH............HHHHSCESCCCSCT......SEEEEES-SSTTTTTTTTSHHHH CS
                           UDG  82 plleeeiellk.prlivllGktaakall..........geklgklrgklleak.....irvlplphPsplnrnffksnpel 146
                                    +leee + l+  +++v+lGk a+++l+          +   ++ +gk+++       ++++ ++hPsp+n+++ + + e+
  gi|70607485|ref|YP_256355.1|  80 SYLEEETRMLTeAKVYVALGKVAWDSLInlfkskgyelNGDRKFSHGKIVKLVkdgniVYLIGSYHPSPRNVRTRRLTIEM 160
                                   ***********9**************9666888755443344488899999955788****************99999999 PP

                                   HHHHHH CS
                           UDG 147 kaeawe 152
                                   ++e++e
  gi|70607485|ref|YP_256355.1| 161 LEEIFE 166
                                   999886 PP

>> Planc_extracel  Planctomycete extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   7.3e-06     0.065       4      19 ..     147     162 ..     145     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.3e-06
                Planc_extracel   4 rrsrsqrRRLrlEsLE 19 
                                   + ++ + RRL++E+LE
  gi|70607485|ref|YP_256355.1| 147 SPRNVRTRRLTIEMLE 162
                                   568899*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1086.48
//
Query:       gi|70607486|ref|YP_256356.1|  [L=433]
Description: hypothetical protein Saci_1757 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-36  123.7   0.0    1.3e-35  123.0   0.0    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.6e-19   69.8   0.0    3.1e-19   68.9   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
     0.0028   17.9   0.2      0.005   17.1   0.2    1.3  1  Coagulase      Staphylococcus aureus coagulase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   2.2e-39   1.3e-35       1     204 [.      68     425 ..      68     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.2e-39
                                   EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHH CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGaka 80 
                                   l+++H+Dv+p ++ ++w++ pfs+t++d+++y+rGa+d+kg ++a l+a+ ++k +      + +++f+++EE+g+    +
  gi|70607486|ref|YP_256356.1|  68 LVYNHYDVQPVDPLNEWKYdPFSATVKDNYIYARGASDNKGTLMARLMAFSRYKGKL-----NFKFVFEGEEEIGSINLHH 143
                                   689*******88888***********************************9998886.....***********77777788 PP

                                   HHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE.............................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                 Peptidase_M20  81 llegleerekvdavfelhieepgileagklaigvv.............................................. 115
                                   +++  ++r k+da    +i+e+ +l+  k  +++v                                              
  gi|70607486|ref|YP_256356.1| 144 FVDRNKDRLKADA----VIMEGAGLD-TKGRPMIVlgvkglvyveirvrtgerdvhssnapivynpvwrlveilnsiydge 219
                                   8885445566666....567788888.444788888999****************************************** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M20 116 ................................................................................. 115
                                                                                                                    
  gi|70607486|ref|YP_256356.1| 220 kvkikgfydeiepiskdveelldkydvdveelrkslgayalkhkerkevvkalfteptcnidgiysgyigkgsktivpshv 300
                                   ********************************************************************************* PP

                                   ..............................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEE.EESSSBHTHH CS
                                   ..............................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                 Peptidase_M20 116 ..............................kvevelleggapvtln.dsplvkalaeaaeelfgekveli.vsgpggtdar 164
                                                                 kve+ + + ++pv+++   ++++a+ ++a+e++++++ +i  s+ g++ ++
  gi|70607486|ref|YP_256356.1| 301 yvkmdfrlvpkqdpkkifnelvehvkridpKVEIIDMGLEKPVRTSpKTKVARAMISSAKEVYKVEPVVIpNSA-GTQPMG 380
                                   *****************************88*******************************987755554666.9***** PP

                                   HH..TTTEEEEE.EESS.G.GCTTSTTTEEEHHHHHHHHHHHHHH CS
                                   xx..xxxxxxxx.xxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 165 ff..agiptvmi.fgpg.s.glaHspnEyvdledlekgikvlarl 204
                                   +f  +gi  ++  +g g s ++aH+pnE++ +++++k+i+   ++
  gi|70607486|ref|YP_256356.1| 381 IFydLGIDEIVSaIGAGtSsSNAHAPNENITVDNYYKAIEHALKF 425
                                   **999996443336666435******************9976665 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   5.1e-23   3.1e-19       2     107 ..     175     331 ..     174     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.1e-23
                                   EB-EEEEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.................................. CS
                     M20_dimer   2 ghkGlaggkit..vkgkagHsgapgagaNAieklarllaeledeegdia................................ 48 
                                   g kGl+ ++i+  +  +++Hs++   + N+++ l+++l+++ d e+ +                                 
  gi|70607486|ref|YP_256356.1| 175 GVKGLVYVEIRvrTGERDVHSSNAPIVYNPVWRLVEILNSIYDGEKVKIkgfydeiepiskdveelldkydvdveelrksl 255
                                   789999999998899****************************987777******************************** PP

                                   ................TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCST CS
                     M20_dimer  49 .............eerslprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeilekeape 107
                                                 +  + ++t+n+ gi++G+    +k+++p+++++k+d+Rl+p++dp+++ +e++e++++  p+
  gi|70607486|ref|YP_256356.1| 256 gayalkhkerkevVKALFTEPTCNIDGIYSGYigkgSKTIVPSHVYVKMDFRLVPKQDPKKIFNELVEHVKRIDPK 331
                                   ***********************************************************************99887 PP

>> Coagulase  Staphylococcus aureus coagulase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   8.4e-07     0.005     115     210 ..     229     324 ..     212     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.4e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTSGGGS---...HHHHHHHHHHHHHHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHH CS
                     Coagulase 115 eynelskslkdaveefkkevkeiesknkdlksyd...keeekkatdevydlvseidtlvaayygdkqykeeakelrakldl 192
                                   e + +sk +++ ++++  +v+e+++    l +y    ke+ + +     +  ++id ++  y+g+ +      ++ +k+d+
  gi|70607486|ref|YP_256356.1| 229 EIEPISKDVEELLDKYDVDVEELRK---SLGAYAlkhKERKEVVKALFTEPTCNIDGIYSGYIGKGSKTIVPSHVYVKMDF 306
                                   4445666677777777777777765...455554200333344445567899***************************** PP

                                   HH--SSS-----SHHHHH CS
                     Coagulase 193 ilGdednPnritnerikk 210
                                    l  +++P++i ne +++
  gi|70607486|ref|YP_256356.1| 307 RLVPKQDPKKIFNELVEH 324
                                   **************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2760.66
//
Query:       gi|70607487|ref|YP_256357.1|  [L=115]
Description: hypothetical protein Saci_1758 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-09   36.1   0.2    5.6e-09   35.7   0.2    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00014   21.7   0.1    0.00051   20.0   0.1    1.9  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
     0.0065   16.4   0.1     0.0082   16.1   0.1    1.1  1  FdhE           Protein involved in formate dehydrogenase form
  ------ inclusion threshold ------
       0.02   14.6   1.2       0.46   10.3   0.1    3.0  3  zinc_ribbon_5  zinc-ribbon domain
      0.025   15.3   0.1      0.028   15.1   0.1    1.2  1  zinc-ribbon_6  zinc-ribbon domain
      0.029   14.4   0.1      0.039   14.0   0.1    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.036   14.0   0.4       0.22   11.5   0.1    2.2  2  DUF5374        Family of unknown function (DUF5374)
      0.051   13.3   0.4       0.07   12.8   0.4    1.1  1  TackOD1        Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.2   2.5e-12   5.6e-09       7      37 .]      17      47 ..      12      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.5e-12
                       DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddle 37
                                   rL + +C++CG+v+++Pr +C +C s+dl+
  gi|70607487|ref|YP_256357.1| 17 ERLPYIKCTKCGKVFYYPRTFCINCNSTDLQ 47
                                  599999*******************999985 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.3e-07   0.00051      30      64 ..      67     100 ..      49     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                                   EEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                 OB_aCoA_assoc  30 vvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                   ++g+VeL eg r+ +++ +    +  iG  V+++f
  gi|70607487|ref|YP_256357.1|  67 IYGIVELKEGFRLYTNIIDENGKA-DIGVDVEVRF 100
                                   58*****************99765.6*******99 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.7e-06    0.0082     189     218 ..      16      45 ..      12      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.7e-06
                                   ---EEEEEETTT--EEE--TTS-TTT---S CS
                          FdhE 189 aeglRylhCslCeteWhvvRvkCsnCeetk 218
                                   +e+l y++C+ C   + + R+ C+nC++t+
  gi|70607487|ref|YP_256357.1|  16 SERLPYIKCTKCGKVFYYPRTFCINCNSTD 45 
                                   57788*********************9873 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0002      0.46      26      35 ..      22      31 ..      18      32 .. 0.92
   2 ?    0.7   0.2       0.2   4.4e+02       3      18 ..      36      52 ..      35      57 .. 0.65
   3 ?   -0.2   0.0       0.4   8.9e+02      12      24 ..      77      89 ..      75      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                 zinc_ribbon_5 26 VrCakCaevF 35
                                  ++C kC++vF
  gi|70607487|ref|YP_256357.1| 22 IKCTKCGKVF 31
                                  79******** PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                 zinc_ribbon_5  3 irCpdCdtk.Fklvdsk 18
                                  + C +C+++  ++ +s+
  gi|70607487|ref|YP_256357.1| 36 TFCINCNSTdLQVKTSE 52
                                  66888986535666666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.4
                 zinc_ribbon_5 12 FklvdsklKksgk 24
                                  F+l +  + ++gk
  gi|70607487|ref|YP_256357.1| 77 FRLYTNIIDENGK 89
                                  9*****9999997 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.3e-05     0.028       3      24 ..      23      44 ..      21      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                 zinc-ribbon_6  3 eCeqCgqllffenssClkCgaa 24
                                  +C++Cg+ +++  + C +C+++
  gi|70607487|ref|YP_256357.1| 23 KCTKCGKVFYYPRTFCINCNST 44
                                  7******************974 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.039      70     103 ..      21      52 ..       7      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                   EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESS CS
                          HypA  70 kvrCreCgkefeleekalrCpkCgsadveivsGe 103
                                    ++C++Cgk f   ++   C +C+s+d+++++ e
  gi|70607487|ref|YP_256357.1|  21 YIKCTKCGKVFYYPRT--FCINCNSTDLQVKTSE 52 
                                   589******9997643..6*******99998765 PP

>> DUF5374  Family of unknown function (DUF5374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.7e-05      0.22      19      37 ..      36      54 ..      36      57 .. 0.92
   2 ?   -0.4   0.0      0.51   1.1e+03      28      37 ..      95     104 ..      93     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
                       DUF5374 19 rFqIqCtsnkvkVsyPlGk 37
                                  +F I+C s++++V+++ Gk
  gi|70607487|ref|YP_256357.1| 36 TFCINCNSTDLQVKTSEGK 54
                                  699*************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.51
                       DUF5374  28 kvkVsyPlGk 37 
                                   +v+V++  G+
  gi|70607487|ref|YP_256357.1|  95 DVEVRFTVGN 104
                                   6999999886 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   3.1e-05      0.07      74     102 ..      22      50 ..       9      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                       TackOD1  74 rlCpsCksghlnvrevCpkCkSidieeqe 102
                                     C++C       r  C +C+S+d++ ++
  gi|70607487|ref|YP_256357.1|  22 IKCTKCGKVFYYPRTFCINCNSTDLQVKT 50 
                                   57**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 838.87
//
Query:       gi|70607488|ref|YP_256358.1|  [L=382]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.1e-05   22.1   0.1     0.0016   18.1   0.0    2.3  2  Thiolase_C   Thiolase, C-terminal domain
  ------ inclusion threshold ------
      0.013   14.9   0.0       0.02   14.3   0.0    1.2  1  Thiolase_N   Thiolase, N-terminal domain
       0.11   12.4   0.0       0.39   10.6   0.0    1.9  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.045   2.7e+02      27      43 ..      24      40 ..      22      44 .. 0.88
   2 !   18.1   0.0   2.6e-07    0.0016      33      99 ..     263     347 ..     242     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.045
                                  HHHHHHHHHT--GGGES CS
                    Thiolase_C 27 aikkvlkkagltvedid 43
                                  ++ ++l+ agl+ +did
  gi|70607488|ref|YP_256358.1| 24 VVDEALDMAGLEYKDID 40
                                  57899***********9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.6e-07
                                   HHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHHHHHH CS
                    Thiolase_C  33 kkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivvtlls 95 
                                   k a ++++ +d+fE+ + F+  ++  +++++l +                    +N  GG++  G P  +sG  i+  +l 
  gi|70607488|ref|YP_256358.1| 263 KMASFNLNRVDVFELYDSFTITVMLQMEDIGLVEkgkvgkfvesndltykgnIPLNTGGGSLNTGQPAYMSGGVILEEALL 343
                                   457899**************************999*************9997789*******************9999988 PP

                                   HHHH CS
                    Thiolase_C  96 elkk 99 
                                   +l+ 
  gi|70607488|ref|YP_256358.1| 344 QLNG 347
                                   8864 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-06      0.02      25     201 ..      19     190 ..       9     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-06
                                   HHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC....HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHT CS
                    Thiolase_N  25 eLlaealkallekagvdpeevdevivGnvlqagegqn....iarqaalkagipeevpavtvnkvcsSglkavalaaqsiaa 101
                                   +L +e++ ++l+ ag++++++d v       ++ g+      + q++  +gi +  +   ++    S+l+ +++a ++i++
  gi|70607488|ref|YP_256358.1|  19 DLIKEVVDEALDMAGLEYKDIDGVLSTFGRGGFLGNKsfisGSDQLSEYLGI-RARYLDNIQYGGPSALTMIYRAYKAIRS 98 
                                   8999*******************986544444444432212578999999**.9999************************ PP

                                   TSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHH CS
                    Thiolase_N 102 geadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshq 182
                                   gea+ v+++ + ++s+       +  +++ + d+   +++     ++++     ++ a +  k ++ + e+ + + v+   
  gi|70607488|ref|YP_256358.1|  99 GEANTVLCVQGGKISQFRDGLV-T-PQKTDFVDTAFDEFIKVY--TQMSPISDYAMVAYRHSKLFGTTDEQRALVSVSQRY 175
                                   ********99999999877765.2.244444444444444333..555555666777777888888888887777777777 PP

                                   HHHHHHHTTTTTTTBE-EE CS
                    Thiolase_N 183 kaaaaqkagkFkdeivPvk 201
                                   +a ++ ka  Fk    P++
  gi|70607488|ref|YP_256358.1| 176 NAMSNEKAM-FKT---PLT 190
                                   777777776.776...555 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.5e-05      0.39      13      42 ..      88     117 ..      78     132 .. 0.84
   2 ?   -2.6   0.0      0.88   5.3e+03      54      68 ..     214     228 ..     196     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.5e-05
                                   HHHHHHHHHHTTS-SEEEEEEEEEGGGCS- CS
                   ACP_syn_III  13 alsvAdaliesgaakrvLvigaetlskilD 42 
                                    +  A ++i+sg+a++vL + + ++s++ D
  gi|70607488|ref|YP_256358.1|  88 MIYRAYKAIRSGEANTVLCVQGGKISQFRD 117
                                   5667999*******************9877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.88
                                   EEEEEEEEEEESSSS CS
                   ACP_syn_III  54 DGAgAvvleaseeeg 68 
                                   DG  A+++++++ ++
  gi|70607488|ref|YP_256358.1| 214 DGFHAFIVSKKTSKS 228
                                   888899999985443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2752.56
//
Query:       gi|70607489|ref|YP_256359.1|  [L=765]
Description: hypothetical protein Saci_1760 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-24   84.4  16.5    5.9e-15   55.1   3.9    2.3  2  SBP_bac_5      Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.19   11.7   0.9       0.39   10.7   0.9    1.5  1  DAP10          DAP10 membrane protein
       0.88    9.5   2.5          8    6.4   1.1    2.1  2  Protocadherin  Protocadherin


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   3.9   9.9e-19   5.9e-15     155     372 ..      52     285 ..      42     289 .. 0.89
   2 !   34.8   4.8   1.5e-12   8.7e-09       2     146 ..     423     612 ..     422     663 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 9.9e-19
                                   EEEEE-..SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE..EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS- CS
                     SBP_bac_5 155 iefkvi.pdsdaraaalqsGeiddvaepppsdieqlkeakglkv..lyespgggvtylafNtkkppfddkrvRqAlsyAiD 232
                                   i++ +  ++ ++  +al+ G++d+++  + s+i++l++a+  +   l+ +p  ++  +af + ++  ++  +R A++  i+
  gi|70607489|ref|YP_256359.1|  52 IVYTYAySTHTDEFNALLDGKVDFITLTHVSEIQELEKAPYNNTafLAIAPAESFAQVAFAFGNNLTANLYFRYAIASLIN 132
                                   55555435889999******************************************************************* PP

                                   HHHHHHHCT.TTSSEEESSS.STTTSTTCCSCHCCCSHH.......SHHHHHHHHHHHT.T-BCSSTSCEETC.EEEEEEE CS
                     SBP_bac_5 233 reeivkavl.egyatpansl.lppsspgadeeykpayka.......ydpekAkklLkea.Gykdgdggglrek.klkltll 302
                                    + +   vl +g  + ++ + ++ps++ ++ +++++ +        y+++ A  +L+   G++ ++g+++ +  +lklt++
  gi|70607489|ref|YP_256359.1| 133 PQNVTSYVLdNGVLGTDYPFfVSPSLQVYKAWFNSQVESyyeqyqsYNLTRAIMYLERVpGITHVNGQWYYNGqPLKLTFY 213
                                   *********555558888889**************98779*****************855*************9******* PP

                                   EETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH..HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHST CS
                     SBP_bac_5 303 lasgspaekaiaeliqqqlkkiGikvevktvdwa..atylervkdgdfdmillgwgadypdpdnflnpflss 372
                                   +++  ++ k+ a+l+q++ ++i++++   +  +a  +++ ++   +df+m+ +gw+ + p p++ ++ +++s
  gi|70607489|ref|YP_256359.1| 214 YTYPPETLKKFADLLQSSAAAINLTIVPVQETFAalENQIQTPPYNDFNMSTFGWTNIGPFPNSWMDGIYTS 285
                                   *********************998877766655568555578999*******************99999887 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.5e-12
                                   EEESSEEEEE............EEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC....... CS
                     SBP_bac_5   2 vvpaLAesww............evsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee....... 63 
                                   + p++A+sw             +   +g+++t++L ++ ++ DG pltA Dv f+  ++  p+ +++++++  +       
  gi|70607489|ref|YP_256359.1| 423 LMPWVASSWTitspvnmtlpngDKIVNGTILTVNLVHNDTWIDGYPLTAYDVNFTVWYYDLPGMMGTNTFDG-Vhlnytyl 502
                                   679*****55**********9977899***************************977766666555554444.34777889 PP

                                   .............TCTEEEEEEEETTEEEEEESSE.TTTTTTHCHHHHHHHGC..CHTCTCTTTTTGTTTSE-BSSSEEEE CS
                     SBP_bac_5  64 .............dqdikkveavddytvrftlkkp.nalfltllaavpasiak..kaaekeddkdkdtnekpvgtGPYklk 128
                                                 +  +   ++++y+++f+l++  + + + +l+++p+ + +     +  + + ++ +++ +++GPY+++
  gi|70607489|ref|YP_256359.1| 503 sqedfingdlfgtITALVWTNVTNPYQIVFYLNSSsYVNDYLVLSEYPIMPLHaiGPVNVVTLYHSTLAPE-ISSGPYRFV 582
                                   99********9888888888999************555788888888888888864445566655666666.9******** PP

                                   EEETTT.EEEEEE-TTST...........T CS
                     SBP_bac_5 129 efkpgq.kivlernpdYw...........g 146
                                   + + +  +++++ np+Y+            
  gi|70607489|ref|YP_256359.1| 583 SLNEEAkTVTVTYNPYYFrinpsifmqnvT 612
                                   *777553777999****8555555555443 PP

>> DAP10  DAP10 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.9   6.5e-05      0.39      12      56 ..     719     762 ..     714     765 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.5e-05
                         DAP10  12 llpvaaaqtteGscsGcGplslpllaGlvaadavvsllivgvvfv 56 
                                    +p a++ t++ + s   + slpl a +va   vv ++i +vv++
  gi|70607489|ref|YP_256359.1| 719 TVPPATSSTAPPTSSTTTSTSLPLTA-IVAVIVVVIIIIAAVVIL 762
                                   5799*******************977.777777776666666655 PP

>> Protocadherin  Protocadherin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.026   1.5e+02       6      51 ..     295     341 ..     292     344 .. 0.84
   2 ?    6.4   1.1    0.0013         8      32      62 ..     733     763 ..     712     765 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.026
                 Protocadherin   6 tlveelvarsletp.ldqdiagdpdveslskdrlkiliavlaGvvtv 51 
                                   +++++ ++++l++p l q+ia + ++e l +++l ++i v + ++ +
  gi|70607489|ref|YP_256359.1| 295 STIDATLQKALNAPtLAQEIAYTKEAELLLQQQLPYVIYVWSNAIQA 341
                                   679*********96489**********99999999999888777655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                 Protocadherin  32 slskdrlkiliavlaGvvtvilvilivvlvR 62 
                                   s+++  +  l a++a +v+vi++i  vv++R
  gi|70607489|ref|YP_256359.1| 733 STTTSTSLPLTAIVAVIVVVIIIIAAVVILR 763
                                   345555566899*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5030.14
//
Query:       gi|70607490|ref|YP_256360.1|  [L=395]
Description: hypothetical protein Saci_1761 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.7   0.0         13    5.8   0.0    3.2  3  DUF4982   Domain of unknown function (DUF4982)


Domain annotation for each model (and alignments):
>> DUF4982  Domain of unknown function (DUF4982)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.063   1.1e+03      32      53 ..      92     115 ..      78     117 .. 0.83
   2 ?    5.8   0.0   0.00071        13      13      40 ..     137     170 ..     131     176 .. 0.83
   3 ?    3.3   0.0    0.0044        79      38      55 ..     301     319 ..     278     324 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.063
                                   SSS-EEEE.EEB.-SSEEEEEEEE CS
                       DUF4982  32 kdyrltWd.vpy.epGeLkAvayk 53 
                                   +  +l ++  +y + G++  +ay+
  gi|70607490|ref|YP_256360.1|  92 NSSYLFFNlGEYlQDGTIYSIAYN 115
                                   567888998899899*******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00071
                                   SEEEEEETTEEEEEE........E-SSS-EEEEE CS
                       DUF4982  13 deVeLflNGkslGrkkk......kekdyrltWdv 40 
                                   +eV L+ NGk +   k        +++y ++W  
  gi|70607490|ref|YP_256360.1| 137 PEVVLYTNGKAINISKLipdtytPGQAYAASWTG 170
                                   89***********999999888766678888875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0044
                                   EE.EEB-SSEEEEEEEETT CS
                       DUF4982  38 Wd.vpyepGeLkAvayknG 55 
                                   +   +y  G + Av+y ++
  gi|70607490|ref|YP_256360.1| 301 FInLKYSVGIVVAVGYGDD 319
                                   54489***********655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2632.54
//
Query:       gi|70607491|ref|YP_256361.1|  [L=352]
Description: binding-protein-dependent transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-31  107.4  20.2    7.2e-31  107.4  20.2    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   2.1      0.28   5.1e+03      31      41 ..      37      47 ..      19     135 .. 0.61
   2 !  107.4  20.2     4e-35   7.2e-31       2     184 ..     142     350 ..     134     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.28
                  BPD_transp_1 31 Psfvlaillvl 41
                                    ++++ ++++
  gi|70607491|ref|YP_256361.1| 37 FGILVFNFFIF 47
                                  22222222221 PP

  == domain 2  score: 107.4 bits;  conditional E-value: 4e-35
                  BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...........................vilsilghlilp 55 
                                   ++lG+++  +++k++d ++++  i+++ +P f+l+ +l++++                           ++ s  ++l lp
  gi|70607491|ref|YP_256361.1| 142 VVLGLYSISRQGKIGDSVISFTAIMTYFIPAFWLGEILLYILgfylnifptniaqaittsngmalqgftYWVSLMKFLTLP 222
                                   67888888************************************************************************* PP

                  BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                   +++++++s++  ++l+r+++++ + +++v++ ra+G s+++i++k+v +na++p++t +++ +++l+ g v++e +++ pG
  gi|70607491|ref|YP_256361.1| 223 ILFITIISYGVRNILFRNNGVELMGSNFVNYLRARGISDRKILYKHVTRNAIIPVVTRVGIDLAFLFAGVVFIEDIFNIPG 303
                                   ********************************************************************************* PP

                  BPD_transp_1 137 lgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                   lg+ll++a  + d+++   g ++++ ++ ++++l++d+l+ l+dprv+
  gi|70607491|ref|YP_256361.1| 304 LGRLLVNAAANLDVPLLE-GDFYIISLFAIIILLALDLLYPLIDPRVK 350
                                   ******************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2402.23
//
Query:       gi|70607492|ref|YP_256362.1|  [L=475]
Description: oligopeptide transport system permease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-19   69.7  16.6    2.5e-19   69.7  16.6    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
    0.00025   20.9   1.2    0.00025   20.9   1.2    3.6  5  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2     0.099   8.9e+02     154     179 ..      13      38 ..       2      44 .. 0.61
   2 !   69.7  16.6   2.8e-23   2.5e-19       1     181 [.     278     469 ..     278     472 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.099
                  BPD_transp_1 154 snggvlalviavlllnlvadilqrll 179
                                   s++ +++++ ++++l+l+a +l+++ 
  gi|70607492|ref|YP_256362.1|  13 SFVFSIIIIGFFVILSLAAPVLTQYN 38 
                                   44556666666666666666666665 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 2.8e-23
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...vilsilghlilpviillllsaapyvrlirraalrs 78 
                                   g+++G+la+ + ++++d  l  l++++l +P + l+i+l+ +f     +  +    l ++i++lls+++++ +ir + l+ 
  gi|70607492|ref|YP_256362.1| 278 GLVIGLLAG-YVGGFTDLSLNALTDFFLLIPGLPLLIVLISIFdvtGTIVNISKPLLILLIISLLSWPGTAKIIRGQTLSL 357
                                   799******.*********************************9885555666778889********************** PP

                  BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                    ++ ++ea+ralG +r +i++k++lPn++  ++++l++ ++g++ + + l flg +   g +++   lgy + +is     
  gi|70607492|ref|YP_256362.1| 358 KNRTFIEASRALGEGRTRILFKHILPNLMGILFAQLAYDVPGVILAESGLDFLGLGI-SGFPTWGNMLGYATYNISfvngf 437
                                   ******************************************************544.44444444444444444466666 PP

                  BPD_transp_1 155 .....nggvlalviavlllnlvadilqrlldp 181
                                          + + +v++ +++ ++  ++ ++l+p
  gi|70607492|ref|YP_256362.1| 438 awwwvLPPGIGIVLLSMAFYFFGSAMLDALSP 469
                                   65558888888888888888888888877766 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   1.2   2.8e-08   0.00025       6      42 ..       4      45 ..       2      69 .. 0.82
   2 ?   -2.5   0.9      0.59   5.3e+03      17      36 ..     269     288 ..     267     300 .. 0.70
   3 ?   -1.3   0.2      0.25   2.2e+03      24      32 ..     311     319 ..     311     330 .. 0.84
   4 ?   -3.0   0.4      0.87   7.8e+03      24      32 ..     333     341 ..     332     347 .. 0.56
   5 ?   -3.5   0.2       1.2   1.1e+04      24      32 ..     449     457 ..     447     470 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.8e-08
                        OppC_N  6 awrrFkrNklAvvglvilllllliaifaPliaPydp.....q 42
                                  + r +++ k  v++ +i+ +++++++ aP+++ y+      q
  gi|70607492|ref|YP_256362.1|  4 TIRYLFSKKSFVFSIIIIGFFVILSLAAPVLTQYNNpylpsQ 45
                                  5799***************************96654444453 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.59
                        OppC_N  17 vvglvilllllliaifaPli 36 
                                   v++  i+ + l+i ++a ++
  gi|70607492|ref|YP_256362.1| 269 VASVLIIGIGLVIGLLAGYV 288
                                   56666777666677777766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.25
                        OppC_N  24 llllliaif 32 
                                   ll++li+if
  gi|70607492|ref|YP_256362.1| 311 LLIVLISIF 319
                                   689999999 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 0.87
                        OppC_N  24 llllliaif 32 
                                   l+ll+i+++
  gi|70607492|ref|YP_256362.1| 333 LILLIISLL 341
                                   444445444 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 1.2
                        OppC_N  24 llllliaif 32 
                                   ++ll +a++
  gi|70607492|ref|YP_256362.1| 449 IVLLSMAFY 457
                                   566667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3181.00
//
Query:       gi|70607493|ref|YP_256363.1|  [L=328]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-25   88.3   0.0    8.9e-25   87.8   0.0    1.2  1  ABC_tran      ABC transporter
    1.8e-23   82.8   0.1    3.3e-23   82.0   0.1    1.5  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    5.9e-05   22.6   1.2     0.0017   17.8   1.2    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    9.8e-05   22.8   0.0    0.00018   21.9   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0002   21.2   0.0    0.00036   20.3   0.0    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
    0.00029   21.1   0.2     0.0023   18.2   0.2    2.0  1  AAA_22        AAA domain
     0.0028   17.6   0.0     0.0066   16.4   0.0    1.6  1  Rad17         Rad17 P-loop domain
     0.0031   17.5   0.0     0.0058   16.6   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.033   14.1   0.1    1.6  1  RsgA_GTPase   RsgA GTPase
       0.02   15.0   0.0      0.045   13.8   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.023   14.4   0.0      0.051   13.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.024   15.0   0.1       0.07   13.5   0.0    1.9  2  RNA_helicase  RNA helicase
      0.026   13.7   0.5      0.038   13.2   0.5    1.5  1  NB-ARC        NB-ARC domain
      0.037   13.0   0.0      0.067   12.2   0.0    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.067   13.1   1.1       0.19   11.6   0.2    2.1  2  NTPase_1      NTPase
      0.094   12.0   0.0       0.16   11.2   0.0    1.3  1  Septin        Septin
       0.11   12.5   0.2       0.64   10.1   0.1    2.0  2  DUF87         Helicase HerA, central domain
       0.17   11.8   0.0       0.31   10.9   0.0    1.4  1  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   8.9e-28   8.9e-25       2     136 ..      31     187 ..      30     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 8.9e-28
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB-HHHCCHC.....EEEE-SS..--S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx..xxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqeleslrke.....igvlpqe..pqlf 71 
                                   + vsl + + +++++ Ge+G+GKStL+ ++ + l       eGe++++g+++ + +l+ +rk+     i+++pq   + l+
  gi|70607493|ref|YP_256363.1|  31 DSVSLFVDRAKILGVAGESGCGKSTLVTTIFRVLPRnaqiVEGEVKFKGQEILKMDLKTFRKNivwrdIAYIPQAsmDVLD 111
                                   789999********************999988776666669*************888888776222226899999999999 PP

                                   TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  72 peltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   p ++++++              e++e+i+kal+++g +    ++++  p++LSgGq+qrv++a+all +p++++ DE+t
  gi|70607493|ref|YP_256363.1| 112 PVYKIKDQmietilahedvskaEATERIYKALESVGVPP---EKADMFPHELSGGQRQRVVIAMALLLNPSMVVSDEAT 187
                                   99999999********99977777777888888888777...555556******************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.1   3.3e-26   3.3e-23       1      65 []     239     304 ..     239     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 3.3e-26
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE g+++klf++plHPYTkaL++++p+l+ +k+ kl++i+g +p+le+ ++GC+FapRCp a+++C
  gi|70607493|ref|YP_256363.1| 239 VEFGDVEKLFRNPLHPYTKALVDAIPDLRLRKKkKLVSIPGYPPDLENPPKGCRFAPRCPIAMPIC 304
                                   8***************************9888889******************************* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.2   1.7e-06    0.0017      27     207 ..      43     228 ..      23     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                   EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrse...klsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                     + G+ G+GKs l+  i  vL   +a+ +  e   k +++++   +  ++++   +++     +++++ + ++ ++i+ +
  gi|70607493|ref|YP_256363.1|  43 LGVAGESGCGKSTLVTTIFRVLPR-NAQIVEGEvkfKGQEILKMdlKTFRKNIVWRDIAY---IPQASMDVLDPVYKIKDQ 119
                                   567888888888888888777773.44222222111223333332222222222222222...233334444444555555 PP

                                   EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 103 vkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                   ++++   +  + + e+t + + + les+g+ +e       +LSgG+++ v +a+ + +      ++++ De   aLD    
  gi|70607493|ref|YP_256363.1| 120 MIETILAHEDVSKAEAT-ERIYKALESVGVPPEkadmfphELSGGQRQRVVIAMALLL----NPSMVVSDEATTALDVITQ 195
                                   44444444444444333.3455666777766667777777*****9875555544322....3468999************ PP

                                   HHHHHHHH..HHCTTSEEEEE-SSHHHCCC-SC CS
                                   xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 177 kkvaellk..eksknaQfivislreemlekadk 207
                                   +kv +++k  ++s ++ ++ ++++  +l++ + 
  gi|70607493|ref|YP_256363.1| 196 AKVLKIMKdlQESRKFSMMFVTHDLALLANISD 228
                                   ******994444445666777877777766644 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.8e-07   0.00018      25      69 ..      41     101 ..      29     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.8e-07
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggif...lrgkcdql.esa............ipy 69 
                                    ++ + GesG+GKs+lv++++r l ++  i+   ++ k ++  +++            i+y
  gi|70607493|ref|YP_256363.1|  41 KILGVAGESGCGKSTLVTTIFRVLPRNAQIVegeVKFKGQEIlKMDlktfrknivwrdIAY 101
                                   67789****************9888884444544444544444333333333344444333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.7e-07   0.00036       1      94 [.      42     142 ..      42     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.7e-07
                           PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaei......egdsflrldraekdleleerkrakekevsflspeandfdlly 75 
                                   ++gvag+SG+Gk+t+  ++  ++ r++   +e+      + +  + l+ + k++  ++ +   +++++ l+p  +  d++ 
  gi|70607493|ref|YP_256363.1|  42 ILGVAGESGCGKSTLVTTIFRVLPRNAQI-VEGevkfkgQEILKMDLKTFRKNIVWRDIAYIPQASMDVLDPVYKIKDQMI 121
                                   78*****************9999865543.333345644455555666788888888888888888888888888888888 PP

                           PRK  76 evlkelkegkkv..dkpiYsh 94 
                                   e++++ ++  k   + +iY+ 
  gi|70607493|ref|YP_256363.1| 122 ETILAHEDVSKAeaTERIYKA 142
                                   888888776554114567765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   2.3e-06    0.0023       4     126 ..      39     214 ..      37     222 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........................................erpe 41 
                                   +a+il v GesG+GK+tl+ ++++ l++ a++ e                                            +++
  gi|70607493|ref|YP_256363.1|  39 RAKILGVAGESGCGKSTLVTTIFRVLPRNAQIVEgevkfkgqeilkmdlktfrknivwrdiayipqasmdvldpvykIKDQ 119
                                   688999********************9988888899999666666666666555555555555555555555555543333 PP

                        AAA_22  42 vvfvtlpsst.sskdllrellralglelkaerlsseellealeqalrarav.........ielliiDEaqh.lr...seea 108
                                    ++  l+++  s ++  +++ +al++ +     ++ +++ +     ++++v         +++++ DEa   l+   ++++
  gi|70607493|ref|YP_256363.1| 120 MIETILAHEDvSKAEATERIYKALESVGVP--PEKADMFPHELSGGQRQRVviamalllnPSMVVSDEATTaLDvitQAKV 198
                                   332222222224444444444444433333..4445555444444444444455555666666666666666655544666 PP

                        AAA_22 109 leeLrsllnlsrkgvqli 126
                                   l+  ++l++  + ++++ 
  gi|70607493|ref|YP_256363.1| 199 LKIMKDLQE--SRKFSMM 214
                                   666666666..6666555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.7e-06    0.0066      25      92 ..      21      87 ..      15     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                         Rad17 25 kkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdf 92
                                  k k  +vk ++++ +L   + +iL ++G sGCgkst v  + + l  + +     v++k  +  k d+
  gi|70607493|ref|YP_256363.1| 21 KTKTGNVK-AVDSVSLFVDRAKILGVAGESGCGKSTLVTTIFRVLPRNAQIVEGEVKFKGQEILKMDL 87
                                  56666665.5677777777789****************999888877777666677777666655555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.8e-06    0.0058       5      89 ..      46     125 ..      43     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                                   E--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--HHHHH CS
                         AAA_5   5 vGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraesevln 83 
                                    G++G+gKs+l+  + ++l r+ ++v +  + + ++++  +++k   ++ +++d ++     ++++ vlD v ++++++++
  gi|70607493|ref|YP_256363.1|  46 AGESGCGKSTLVTTIFRVLPRNAQIVEGEVKFKGQEILK-MDLKtfRKNIVWRDIAYIP---QASMDVLDPVYKIKDQMIE 122
                                   6***************************99999888763.4443347777777777764...4455566666666665555 PP

                                   HHHHHH CS
                         AAA_5  84 sLlsll 89 
                                   +    l
  gi|70607493|ref|YP_256363.1| 123 TI---L 125
                                   44...4 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.3e-05     0.033      85     120 ..      25      61 ..       6      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                                   TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                    + +++++++  ++  k+  ++G+SG GKStL+ ++ 
  gi|70607493|ref|YP_256363.1|  25 GNVKAVDSVSLFVDRaKILGVAGESGCGKSTLVTTIF 61 
                                   445667777777776699999***********99875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.5e-05     0.045       3      57 ..      44     103 ..      42     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                   EEEESTTSSHHHHHHHHHT....STEEE.SSSTTSSSSEEEEEEEETTEEEEEEECGGCS CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltg....ekaiv.sdkpgtTrdinegrvklkgkeielvDtpGli 57 
                                   +++G +  GKStL+ ++++    ++ iv ++ +++ ++i +  +k+ +k+i++ D++ + 
  gi|70607493|ref|YP_256363.1|  44 GVAGESGCGKSTLVTTIFRvlprNAQIVeGEVKFKGQEILKMDLKTFRKNIVWRDIAYIP 103
                                   799**************9855533456678999999999999999777899999999852 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.1e-05     0.051      19      46 ..      37      64 ..      23      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                        AAA_29 19 idlkgatlltGpsGsGKSTllDAiqalL 46
                                  +d++ +  ++G+sG GKSTl+  i  +L
  gi|70607493|ref|YP_256363.1| 37 VDRAKILGVAGESGCGKSTLVTTIFRVL 64
                                  5555666799**********98777776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-05      0.07       3      64 ..      45     105 ..      43     142 .. 0.78
   2 ?   -2.1   0.0       4.9   4.9e+03      49      92 ..     165     208 ..     158     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                  RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                   + G+sg+GKStl++++ + l ++  ++ +++v +++ e   +d  t  + +v+ D++ +++ 
  gi|70607493|ref|YP_256363.1|  45 VAGESGCGKSTLVTTIFRVLPRNA-QIVEGEVKFKGQEILKMDLKTFRKNIVWRDIAYIPQA 105
                                   67*************998888776.6666888888888888888888888888888777755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.9
                  RNA_helicase  49 gqevvvidDfgqvkdeenpsdlaelirlvsstpyplnmasleek 92 
                                   +q vv+   +  +++    ++ ++ + +++ +++   m++l+e 
  gi|70607493|ref|YP_256363.1| 165 RQRVVIAMALLLNPSMVVSDEATTALDVITQAKVLKIMKDLQES 208
                                   56666666666655443334666666777777777777776664 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   3.8e-05     0.038      19      43 ..      41      63 ..      28     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                  CSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 19 qslvvalvGmgGvGKttlakqilnk 43
                                  +  ++++ G  G+GK+tl++ i++ 
  gi|70607493|ref|YP_256363.1| 41 K--ILGVAGESGCGKSTLVTTIFRV 63
                                  4..99*****************985 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.8e-05     0.067      26      55 ..      37      66 ..      19      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.8e-05
                                  -S-SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
                          MeaB 26 aGraqvvGltGvPGaGkstlvealglelrr 55
                                    ra+ +G+ G  G Gkstlv  +   l r
  gi|70607493|ref|YP_256363.1| 37 VDRAKILGVAGESGCGKSTLVTTIFRVLPR 66
                                  579******************998877765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00019      0.19       3      32 ..      44      73 ..      42      84 .. 0.88
   2 ?   -1.2   0.1       1.7   1.7e+03     124     157 ..     185     218 ..     180     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                  EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                      NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                   + G++G GK+Tlv  + ++l ++   v+G
  gi|70607493|ref|YP_256363.1| 44 GVAGESGCGKSTLVTTIFRVLPRNAQIVEG 73
                                  589******************988888877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                   TTSEEEEE--SS--SHHHHHHHT-TT-EEEE--T CS
                      NTPase_1 124 sekpvlavihrrkdlalveeirerkdvkvfevte 157
                                   + +  l vi ++k l+++++++e+++++++ vt 
  gi|70607493|ref|YP_256363.1| 185 EATTALDVITQAKVLKIMKDLQESRKFSMMFVTH 218
                                   5677888999999999999999999999888876 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.16       9      37 ..      45      73 ..      41      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                  EEEBTTSSCCCCCCTTSSSS--------- CS
                        Septin  9 vvGesglGkttlintlfetdlieeeklee 37
                                  v+Gesg Gk+tl+ t+f+    +++ +e 
  gi|70607493|ref|YP_256363.1| 45 VAGESGCGKSTLVTTIFRVLPRNAQIVEG 73
                                  89***************876666655554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00064      0.64      20      47 ..      41      64 ..      22      83 .. 0.77
   2 ?    0.3   0.0      0.63   6.3e+02     136     180 ..     106     147 ..      94     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00064
                         DUF87 20 klvtrHlAilgsTGsGKSntvavLleel 47
                                  k+    l++ g++G GKS++v  +++ l
  gi|70607493|ref|YP_256363.1| 41 KI----LGVAGESGCGKSTLVTTIFRVL 64
                                  44....89****************9876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.63
                         DUF87 136 klssdepveklleelkkekeelrklknqaiarlldkledllrkgg 180
                                   ++++ +pv+k+++++    e++  + + ++a+  +++++ l++ g
  gi|70607493|ref|YP_256363.1| 106 SMDVLDPVYKIKDQMI---ETILAHEDVSKAEATERIYKALESVG 147
                                   5666677777777777...55555555555555555555555444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00031      0.31       5      24 ..      45      64 ..      41      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                  EEC-TTTCHHHHHHHHHHHH CS
                         NACHT  5 lqGeaGsGKTtLlqklalaw 24
                                  + Ge+G+GK+tL+  + + +
  gi|70607493|ref|YP_256363.1| 45 VAGESGCGKSTLVTTIFRVL 64
                                  78***********9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2062.62
//
Query:       gi|70607494|ref|YP_256364.1|  [L=313]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-29  102.4   0.0    6.6e-29  101.2   0.0    1.6  2  ABC_tran       ABC transporter
    3.2e-17   62.8   0.1    5.4e-17   62.1   0.1    1.4  1  oligo_HPY      Oligopeptide/dipeptide transporter, C-terminal
    2.4e-06   27.6   0.5      0.033   14.0   0.0    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0016   18.0   0.1     0.0027   17.2   0.1    1.3  1  SMC_N          RecF/RecN/SMC N terminal domain
     0.0025   18.1   0.4     0.0077   16.5   0.4    1.9  1  AAA_22         AAA domain
      0.003   18.0   0.1     0.0051   17.2   0.1    1.3  1  AAA_16         AAA ATPase domain
      0.005   16.5   0.0      0.013   15.2   0.0    1.7  1  AAA_29         P-loop containing region of AAA domain
     0.0056   15.9   0.1      0.013   14.7   0.1    1.6  2  NB-ARC         NB-ARC domain
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.033   13.9   0.0    1.3  1  PRK            Phosphoribulokinase / Uridine kinase family
       0.14   12.1   0.1       0.23   11.3   0.1    1.4  1  RsgA_GTPase    RsgA GTPase
       0.15   11.6   0.1        0.3   10.6   0.1    1.5  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
       0.19   10.6   0.0       0.25   10.2   0.0    1.1  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0   4.4e-32   6.6e-29       2     136 ..      22     175 ..      21     176 .. 0.89
   2 ?   -2.1   0.0       3.5   5.2e+03      22      36 ..     257     271 ..     254     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 4.4e-32
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltvr 77 
                                   + v++k+ke e+v++vGe+G+GK+tL +++++l +pt+G++l++gkd+ +   +e++ +rke ++++q+  + ++ +l+v+
  gi|70607494|ref|YP_256364.1|  22 DGVDIKVKEREIVGLVGESGSGKTTLGRTILNLQRPTAGKVLWNGKDVFKlkgKEEKAFRKENQIIFQNpyEAVDIRLKVY 102
                                   7899*******************************************999999****************776777777788 PP

                                   HH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   +                e++e i kal+ +gl+  +++ ++s p++LSgGq qrva+aral+ +p+++++DEp 
  gi|70607494|ref|YP_256364.1| 103 DIvaegirvhgitkskdEEREMILKALKDVGLTP-EEEYANSLPNQLSGGQLQRVAIARALVLDPSFIVADEPV 175
                                   88**********9854333333777888888777.788888999*****************************7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.5
                                   SSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxx RF
                      ABC_tran  22 aGKStLlkllagllk 36 
                                   +G +tL++l  ++++
  gi|70607494|ref|YP_256364.1| 257 SGRTTLFSLTVKEET 271
                                   89*****99877654 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   3.6e-20   5.4e-17       1      65 []     227     292 ..     227     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.6e-20
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerlde..GCpFapRCpfaleeC 65 
                                   +E gp+++++ +plHPYTkaL+++vp +d+  +  + +  ++++ ++  +  GC+++pRCpfa++ C
  gi|70607494|ref|YP_256364.1| 227 IESGPADEVLGNPLHPYTKALISAVPIPDPSGR-TTLFSLTVKEETEPYNgkGCRYYPRCPFAMDVC 292
                                   79*******************************.6666666666666666669************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   6.7e-05       0.1       2      25 ..      34      57 ..      33      95 .. 0.78
   2 !   14.0   0.0   2.2e-05     0.033     219     300 ..     112     209 ..      67     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                   +l+G  gsGK++L +++  l+r 
  gi|70607494|ref|YP_256364.1| 34 VGLVGESGSGKTTLGRTILNLQRP 57
                                  68****************999875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.2e-05
                        AAA_21 219 r..................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllel 281
                                                      +v +  ++ + +  +++lS G+++  a++ al  ++   s+++ DEp + L+ ++ + +l++
  gi|70607494|ref|YP_256364.1| 112 HgitkskdeeremilkalkDVGLTPEEEYANSLPNQLSGGQLQRVAIARALVLDP---SFIVADEPVSMLDMSIRAGVLDI 189
                                   03333333344667777778888999999999999*******9999999999999...*********************99 PP

                        AAA_21 282 l.kelsrngaQviltTHSpl 300
                                   + k+++++g  v++ TH+ +
  gi|70607494|ref|YP_256364.1| 190 FlKLKEERGKSVLMITHDIS 209
                                   98888889*********965 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.8e-06    0.0027      24     212 ..      31     222 ..      18     228 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                                   SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                   +++  +vG+ GSGK+ l   il +   ++ k l   + +d+ + + +++++ + e +i+f+n+ ++       v i+ +v+
  gi|70607494|ref|YP_256364.1|  31 REIVGLVGESGSGKTTLGRTILNLQRPTAGKVLW--NGKDVFKLKGKEEKAFRKENQIIFQNPYEA-------VDIRLKVY 102
                                   567889**********999993322222222222..233444434555555555556666666666.......66666555 PP

                                   TTSEEEEEE....TTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS- CS
                                   xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 105 rkgeseyki....ngkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLD 172
                                         +++    + k+ +++ + + l+++g+++e         +LSgG+ + va+a  + +      ++ + De  + LD
  gi|70607494|ref|YP_256364.1| 103 DIVAEGIRVhgitKSKDEEREMILKALKDVGLTPEeeyanslpnQLSGGQLQRVAIARALVL----DPSFIVADEPVSMLD 179
                                   44443333311114455556778999********9***************999998866544....4579999******** PP

                                   HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCEEEEE CS
                                   xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxx RF
                         SMC_N 173 eknvkkvaellkekskn..aQfivislreemleka.dklvgvt 212
                                    + ++ v +++ + +++    +++i+++  ++  + d+++ ++
  gi|70607494|ref|YP_256364.1| 180 MSIRAGVLDIFLKLKEErgKSVLMITHDISTIGYVaDRIYVMY 222
                                   *999999887665554434778888988777654326666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   5.1e-06    0.0077       4      35 ..      30      59 ..      26     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeaka 35
                                  ++ i+ ++GesG+GKTtl r++l+    ++ a
  gi|70607494|ref|YP_256364.1| 30 EREIVGLVGESGSGKTTLGRTILNLQ--RPTA 59
                                  5677889***************9985..3444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   3.4e-06    0.0051      25      63 ..      32      70 ..      13     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.4e-06
                        AAA_16 25 elvllsGesGvGKsslvrellralekd.........ggiflrgkcdql 63
                                  e+v l+GesG+GK++l r++l  l++          +        d +
  gi|70607494|ref|YP_256364.1| 32 EIVGLVGESGSGKTTLGRTIL-NLQRPtagkvlwngK--------DVF 70
                                  8999*****************.566664444444331........333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.8e-06     0.013      12      38 ..      21      47 ..      19      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.8e-06
                        AAA_29 12 fdghtieidlkgatlltGpsGsGKSTl 38
                                   dg +i++++++++ l+G+sGsGK+Tl
  gi|70607494|ref|YP_256364.1| 21 VDGVDIKVKEREIVGLVGESGSGKTTL 47
                                  57789999999999************9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   8.5e-06     0.013      16      43 ..      29      54 ..      14      62 .. 0.83
   2 ?   -3.2   0.0       2.6   3.8e+03     126     152 ..     194     220 ..     178     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.5e-06
                                  TTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC 16 delqslvvalvGmgGvGKttlakqilnk 43
                                  +e +  +v+lvG  G+GKttl + iln 
  gi|70607494|ref|YP_256364.1| 29 KERE--IVGLVGESGSGKTTLGRTILNL 54
                                  5666..*****************99985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                                   HHCHTTSEEEEEESBCCCCCCS-S-.EE CS
                        NB-ARC 126 parenrlrvllTTRdeevanavsat.se 152
                                   + +e++ +vl+ T d +  ++v+++ + 
  gi|70607494|ref|YP_256364.1| 194 K-EERGKSVLMITHDISTIGYVADRiYV 220
                                   4.66777788888887777777766444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.033       1      84 [.      33     115 ..      33     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                           PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlkel 81 
                                   ++g+ g+SG+Gktt+ r++ ++ +  +   +  +g+ +++l+  e+++  +e++  +++ +++ + + + +d + e ++  
  gi|70607494|ref|YP_256364.1|  33 IVGLVGESGSGKTTLGRTILNLQR-PTAGKVLWNGKDVFKLKGKEEKAFRKENQIIFQNPYEAVDIRLKVYDIVAEGIRVH 112
                                   79*****************99777.44444666888888998888888888888888888888888888888777777666 PP

                           PRK  82 keg 84 
                                   + +
  gi|70607494|ref|YP_256364.1| 113 GIT 115
                                   555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.23      77     121 ..       7      53 ..       1      66 [. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   SEEEE--TTTH.TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  77 yevllvsaktk.egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   ++v++ s +   ++++ +  ++k+ +++ lvG+SG GK+tL  ++l+
  gi|70607494|ref|YP_256364.1|   7 LKVYFKSRDVIvKAVDGVDIKVKErEIVGLVGESGSGKTTLGRTILN 53 
                                   55555554432266777777888878999************888776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0002       0.3       2      34 ..      33      65 ..      32      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEEEES CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklavivN 34
                                  +++l+G  GsGKTtL +++l+ ++     v+ N
  gi|70607494|ref|YP_256364.1| 33 IVGLVGESGSGKTTLGRTILNLQRPTAGKVLWN 65
                                  57899***************8777776666666 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.25       7      73 ..      24      94 ..      18     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                 TrwB_AAD_bind  7 vplpkeretqhilivGttGsGKtqalekllrairargdrai.....vlDltGafvsrfydegkdillnPlDa 73
                                  v +++ +e++ + +vG  GsGKt+  + +l+  r  + +++     v+ l+G+  ++f +e++ i  nP++a
  gi|70607494|ref|YP_256364.1| 24 VDIKV-KEREIVGLVGESGSGKTTLGRTILNLQRPTAGKVLwngkdVFKLKGKEEKAFRKENQIIFQNPYEA 94
                                  55543.5788899*******************99999777666666999**********9997777899875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1974.12
//
Query:       gi|70607495|ref|YP_256365.1|  [L=167]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   14.5   2.3        1.6    8.0   0.1    2.0  2  UbiA      UbiA prenyltransferase family
        1.1    8.1   2.9       0.63    8.9   0.1    1.7  2  MMPL      MMPL family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2   0.00038       3.4      70     105 ..      18      53 ..       7      65 .. 0.67
   2 ?    8.0   0.1   0.00018       1.6     125     246 ..      89     147 ..      69     152 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00038
                          UbiA  70 lifaivllilgllllalllnpltallgllalllyvv 105
                                   ++f+  ++ilg+l++ + + pl+ +++ l+ +l+++
  gi|70607495|ref|YP_256365.1|  18 VVFSSTFVILGFLVAFFSYLPLFTVIVPLSAFLLFF 53 
                                   456777777777777555666666777676666643 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00018
                          UbiA 125 afglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavllla..l 203
                                   a                                                               +  ++l++++++++  +
  gi|70607495|ref|YP_256365.1|  89 A---------------------------------------------------------------V--IILIILGPMILsvF 104
                                   1...............................................................1..23333333333333 PP

                          UbiA 204 lllllalllllylllalllaalallraarlvrrrdakkaakff 246
                                   l  l+    ++++++a +l +++ ++  +lv r+++ k +kf+
  gi|70607495|ref|YP_256365.1| 105 LPPLPWISVTMAFVMAWPLSNVLEFILQQLVERETGGKLRKFY 147
                                   3333333333344444444444444455555555555555555 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.07   6.3e+02     249     272 ..      17      39 ..      10      52 .. 0.53
   2 ?    8.9   0.1     7e-05      0.63     153     196 ..      89     132 ..      76     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.07
                          MMPL 249 kvvtaaGltvaiamlgLvvarlpv 272
                                   +vv+ +++++ + ++++ ++ lp 
  gi|70607495|ref|YP_256365.1|  17 EVVFSSTFVILGFLVAF-FSYLPL 39 
                                   45555555555555543.344443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 7e-05
                          MMPL 153 lvvilviLlivyrSlvaallplltvvvsllaalglvlilalllg 196
                                   +v+il+iL  +  S+  + lp ++v + +++a++l  +l+++l 
  gi|70607495|ref|YP_256365.1|  89 AVIILIILGPMILSVFLPPLPWISVTMAFVMAWPLSNVLEFILQ 132
                                   6899999999*************************888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1120.89
//
Query:       gi|70607496|ref|YP_256366.1|  [L=307]
Description: fumarylacetoacetate (FAA) hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-71  238.7   0.0      7e-71  238.4   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.4   0.0   3.9e-75     7e-71       1     217 [.      96     303 ..      96     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 238.4 bits;  conditional E-value: 3.9e-75
                                   .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHH CS
                 FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeA 81 
                                   ki+  ++ny++h +e +   ++pp+     ep++f+k +++l+g+++p++ P+ s+k+dyE ELav++gk+++ v + ++A
  gi|70607496|ref|YP_256366.1|  96 KIFLLAVNYRAHGQETN---NNPPK-----EPYIFTKFNNTLIGHNQPVLFPRASNKVDYEIELAVIMGKRAKYV-NSSKA 167
                                   578889*********75...77888.....999******************************************.99*** PP

                                   HTTEEEEEEEEEEE-SBGGG---.HH..HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSH CS
                 FAA_hydrolase  82 edaiaGytllnDvsaRdlqaeekapl..gwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifsp 160
                                    d+++Gyt++nD+s Rd q++  +p+   w++gk+ dt++p+Gpwivt+de+++ ++l+l+lrvnge +qd+ ++dmif++
  gi|70607496|ref|YP_256366.1| 168 LDYVFGYTIFNDISFRDKQFPPEIPYgmRWVHGKGLDTAAPMGPWIVTKDEIDNINNLRLKLRVNGEIRQDAYAEDMIFKV 248
                                   ***********************99999***************************************************** PP

                                   HHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE CS
                 FAA_hydrolase 161 aeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                   +++i++ls+g+tL+pGd+i+tGTpsgv    ++ k+lk+gD++e+ei+++G lrn++
  gi|70607496|ref|YP_256366.1| 249 EQIIEYLSNGITLKPGDVISTGTPSGVA--LATGKYLKPGDVMEAEISKIGVLRNNL 303
                                   **************************76..899*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2520.12
//
Query:       gi|70607497|ref|YP_256367.1|  [L=178]
Description: methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-17   62.0   0.0    5.9e-17   61.9   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    6.2e-17   62.0   0.0    8.1e-17   61.7   0.0    1.1  1  Methyltransf_11  Methyltransferase domain
    3.3e-15   56.5   0.0    4.4e-15   56.2   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    7.8e-10   38.5   0.0    1.1e-09   38.0   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.1e-09   36.9   0.0    3.8e-09   36.6   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    8.3e-09   36.1   0.0    1.1e-08   35.7   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    1.3e-06   28.3   0.0    1.8e-06   27.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.8e-05   23.7   0.0    3.8e-05   23.2   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    3.2e-05   23.6   0.0      5e-05   22.9   0.0    1.3  1  MTS              Methyltransferase small domain
      4e-05   23.3   0.0    0.00056   19.6   0.0    1.9  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    8.1e-05   22.1   0.0    0.00011   21.7   0.0    1.1  1  TehB             Tellurite resistance protein TehB
    0.00039   20.6   0.0    0.00066   19.8   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
     0.0007   19.6   0.0    0.00096   19.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00077   19.1   0.0      0.001   18.7   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
    0.00098   18.9   0.0     0.0014   18.3   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
     0.0041   16.9   0.0     0.0048   16.7   0.0    1.1  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.015   15.2   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.019   13.5   0.0      0.023   13.3   0.0    1.0  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.034   14.0   0.0       0.19   11.6   0.0    1.9  1  Methyltransf_8   Hypothetical methyltransferase
      0.036   13.5   0.0       0.43   10.0   0.0    2.0  2  Methyltransf_4   Putative methyltransferase
       0.05   12.9   0.0      0.057   12.7   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
      0.092   12.4   0.0       0.22   11.2   0.0    1.5  2  N6_N4_Mtase      DNA methylase
       0.25   11.0   0.0        1.2    8.8   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   7.6e-20   5.9e-17       3     108 ..      34     136 ..      32     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7.6e-20
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeq.gdieeleklledekfDlilsne 82 
                                    g++vlD GCG G++tf la+++g k+ v+ +D +e+ i+   +++++ g++nv+  +  d   +++    +++D++ls++
  gi|70607497|ref|YP_256367.1|  34 PGMVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTFVsRDLSPIPS----NSIDFVLSKD 110
                                   689***************************************************8665156666994....89******** PP

               Methyltransf_31  83 vlnaladpdkileeiervlkpggill 108
                                   vl+++   ++   ei+rvlkpgg   
  gi|70607497|ref|YP_256367.1| 111 VLCCTVLHKELADEIKRVLKPGGLAF 136
                                   **********************9765 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0     1e-19   8.1e-17       1      96 []      39     137 ..      39     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1e-19
                                   EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CC CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaekl.pfednsfDlvvssevlhhved 76 
                                   Ld GcG G+++  la+++   + v+++D +++++++ ++k ++eg+ +v+  v++  +l p+++ns+D+v+s+ vl+    
  gi|70607497|ref|YP_256367.1|  39 LDHGCGPGYYTFSLARKVgnkGLVYALDSDERQIRILSSKLEREGItNVKTFVSR--DLsPIPSNSIDFVLSKDVLCCTVL 117
                                   899************6666999***********************7643333333..455*******************99 PP

                                   HHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                   ++++ +ei+RvLkpgGl ++
  gi|70607497|ref|YP_256367.1| 118 HKELADEIKRVLKPGGLAFV 137
                                   ****************9875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   5.7e-18   4.4e-15       1      97 []      38     133 ..      38     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 5.7e-18
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEE.EEESBCCGBSSSTTTEEEEEEESTGGGSS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nve.fvqgdaedlpfedgsfDlvvssgalhhls 78 
                                   vLd GcG+G +t+ la+++g k+ v+++D +e+++++  +++e+eg+ nv+ fv  d++ +  +++s+D+v+s  +l+++ 
  gi|70607497|ref|YP_256367.1|  38 VLDHGCGPGYYTFSLARKVGnKGLVYALDSDERQIRILSSKLEREGItNVKtFVSRDLSPI--PSNSIDFVLSKDVLCCTV 116
                                   9******************659************************997772566676655..5899******87777644 PP

                                   HHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  79 dedlekalkeiarvLkpgG 97 
                                      ++++ +ei+rvLkpgG
  gi|70607497|ref|YP_256367.1| 117 --LHKELADEIKRVLKPGG 133
                                   ..346899**********9 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.4e-12   1.1e-09      26     150 ..      13     136 ..       9     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.4e-12
                                   HHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
               Ubie_methyltran  26 vlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                   +lsl   rl  +    ++ vk+g  vlD  +G g ++f+l+++vg+kg v  lD +e  +++   kl++eg +n++  ++ 
  gi|70607497|ref|YP_256367.1|  13 ILSLPLRRLIESEDDFIDYVKPGMVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTFVSR 93 
                                   56677777777777778899*******************************************************998876 PP

                                   TTT-TTS-T-EEEEEEES-GGG-S-HHHHH.HHHHHHEEEEEEEE CS
               Ubie_methyltran 107 aeeLpfeddsfDvvtvsfGlrnvtDklkaL.keayrvlkpGGrlv 150
                                       p   +s D+v  s  +   t  +k L  e+ rvlkpGG  +
  gi|70607497|ref|YP_256367.1|  94 DL-SPIPSNSIDFVL-SKDVLCCTVLHKELaDEIKRVLKPGGLAF 136
                                   54.48999****985.55666666666665279*********755 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   4.8e-12   3.8e-09      18     120 ..      30     140 ..      14     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.8e-12
               Methyltransf_23  18 pklraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlre 90 
                                   ++ ++g+ vLd GcG G ++ +++r+ g    v++ D +++++ i++     + ++++k+ + ++  + p++++d++ + +
  gi|70607497|ref|YP_256367.1|  30 DYVKPGMVVLDHGCGPGyYTFSLARKVGNkgLVYALDSDERQIRILSsklerEGITNVKTFVSRDLSPIPSNSIDFVLSKD 110
                                   5567899**********77888889998856688***********999998855555555554555666************ PP

               Methyltransf_23  91 vlehvpdppellrqiatllkpgGylllsep 120
                                   vl+    + el + i++ lkpgG++++s  
  gi|70607497|ref|YP_256367.1| 111 VLCCTVLHKELADEIKRVLKPGGLAFVSIR 140
                                   **************************9974 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.4e-11   1.1e-08       1      98 [.      39     134 ..      39     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.4e-11
               Methyltransf_12   1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                   L+ GcG G +++ l++k  ++ ++ ++D ++++i   + kl +++    +nv+ ++  +l+  +++s D v++ +vl+++ 
  gi|70607497|ref|YP_256367.1|  39 LDHGCGPGYYTFSLARKVGNKGLVyALDSDERQIRILSSKLEREGI---TNVKTFVSRDLSPIPSNSIDFVLSKDVLCCTV 116
                                   799***************7777776*********777777777775...56666666666666779**************9 PP

               Methyltransf_12  81 direvldnirklLkpgGr 98 
                                     +e+ d+i+++LkpgG 
  gi|70607497|ref|YP_256367.1| 117 LHKELADEIKRVLKPGGL 134
                                   999**************6 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   2.3e-09   1.8e-06      68     131 ..      28      92 ..      21     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.3e-09
                                   HTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES CS
                          PCMT  68 lle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvg 131
                                   +++ +k+g+ vL+ G+G Gy t  lar vg+kg+v +++  ++ ++  + +l++++++nv++ v+
  gi|70607497|ref|YP_256367.1|  28 FIDyVKPGMVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTFVS 92 
                                   566689***********************************99999999***********98776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.8e-08   3.8e-05     158     259 ..      31     138 ..      23     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.8e-08
                          PrmA 158 lvkegeevlDvGtGSGiL..aiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk..eekadviva. 232
                                   +vk+g  vlD G+G G    ++a +  +   v+a+D De  +++  + +e+ ++++ k   ++s++l    ++++d +++ 
  gi|70607497|ref|YP_256367.1|  31 YVKPGMVVLDHGCGPGYYtfSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNvKT--FVSRDLSPipSNSIDFVLSk 109
                                   7999************7611555544455579**********************99544..45555552334677777763 PP

                          PrmA 233 NILaevl..ielaedikklvkeggllilS 259
                                    +L   +   ela++ik+++k+ggl+ +S
  gi|70607497|ref|YP_256367.1| 110 DVLCCTVlhKELADEIKRVLKPGGLAFVS 138
                                   45554431248*************99877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   6.4e-08     5e-05      34     103 ..      37     108 ..      28     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.4e-08
                                   EEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE CS
                           MTS  34 kvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivs 103
                                    vlD GcG G+ + +la++  +   v ++d d r +++    le++++  v+++ s  l+ ++ +++d+++s
  gi|70607497|ref|YP_256367.1|  37 VVLDHGCGPGYYTFSLARKVGNKGlVYALDSDERQIRILSSKLEREGITnVKTFVSRDLSPIPSNSIDFVLS 108
                                   59*****************99988899*********************9999999999999999******97 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.1e-07   0.00056      10      72 ..      36      99 ..      31     115 .. 0.85
   2 ?    2.0   0.0      0.18   1.4e+02     108     133 ..     109     134 ..     105     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.1e-07
                                  -EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEE.EES-CTCCH CS
               Methyltr_RsmB-F 10 etilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntiv.leaDarkid 72
                                    +lD  ++PG  T  +a  + nkg v+A+d +++ ++ + + l+r g+tn++  ++ D++ i+
  gi|70607497|ref|YP_256367.1| 36 MVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTfVSRDLSPIP 99
                                  579***********************************************98641566666554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHCCCEEEEEE CS
               Methyltr_RsmB-F 108 kdiaqlaklqkellsaaidllkkgGv 133
                                   kd+  ++ l kel + +  +lk+gG 
  gi|70607497|ref|YP_256367.1| 109 KDVLCCTVLHKELADEIKRVLKPGGL 134
                                   79999999*********9999*9996 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.4e-07   0.00011      26     129 ..      29     134 ..      20     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.4e-07
                                   CCCS-S-E.EEEES-TTSHHHHHHHHT.T-E..EEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEE CS
                          TehB  26 vkivkpgk.vldlgcgqgrnslylsll.gyd..vtawdknensiafleeikekenlknistalydineaklderydfilst 102
                                   ++ vkpg  vld gcg g  ++ l+ + g +  v a+d +e  i  l +  e+e ++n++t +    +   ++  df+ls 
  gi|70607497|ref|YP_256367.1|  29 IDYVKPGMvVLDHGCGPGYYTFSLARKvGNKglVYALDSDERQIRILSSKLEREGITNVKTFVSRDLSPIPSNSIDFVLSK 109
                                   67899996369********9999986424435599**************************87654455568899*****9 PP

                                   SSGGGS-GGGHHHHHHHHHHTEEEEEE CS
                          TehB 103 vvlmfleaeripsiienmqectkvggy 129
                                    vl         ++ +++++  k+gg 
  gi|70607497|ref|YP_256367.1| 110 DVLCCTVL--HKELADEIKRVLKPGGL 134
                                   99865332..23455666666777765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.5e-07   0.00066      14      58 ..      26      77 ..      20     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.5e-07
                                  HHH.T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......H CS
                          FtsJ 14 ekf.klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......a 58
                                  + f + +kpg+ v+D g++PG ++  l++++g+kg v+a+D  +       +
  gi|70607497|ref|YP_256367.1| 26 DDFiDYVKPGMVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERqirilsS 77
                                  44426789*********************************97763344431 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00096      25      65 ..      34      73 ..      19     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
               Methyltransf_32 25 galtvvDvGaGkgYLsfvlalkekeyklkvvgidakeelve 65
                                  + + v+D+G+G gY +f la  ++ +k  v+++d+ e+ ++
  gi|70607497|ref|YP_256367.1| 34 PGMVVLDHGCGPGYYTFSLAR-KVGNKGLVYALDSDERQIR 73
                                  557899***************.7789********9987664 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.3e-06     0.001       9     103 ..      30     130 ..      25     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                          MetW   9 elikpgsrvldlGcGdGellellkeekqvdg..rGleldeegva....ecvakGlsviqgdldkdlenfedksfdyvvlsq 83 
                                   +++kpg  vld GcG G     l+ + + +g  + l+ de+ +     +    G++ ++  + +dl+  +++s d+v+ + 
  gi|70607497|ref|YP_256367.1|  30 DYVKPGMVVLDHGCGPGYYTFSLARKVGNKGlvYALDSDERQIRilssKLEREGITNVKTFVSRDLSPIPSNSIDFVLSKD 110
                                   689**************998888665444443356788888886222133456**************************** PP

                          MetW  84 tlqatrnpkevldellrigr 103
                                    l  t   ke+ de+ r+ +
  gi|70607497|ref|YP_256367.1| 111 VLCCTVLHKELADEIKRVLK 130
                                   *****999999999999866 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-06    0.0014      38     101 ..      32      95 ..      28     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                         GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDv 101
                                   +kpG vv++ G G g  + ++ar v+ +G +++++  e++++    ++++++++++ t   rD+
  gi|70607497|ref|YP_256367.1|  32 VKPGMVVLDHGCGPGYYTFSLARKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTFVSRDL 95 
                                   89***************************************************99999999996 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.2e-06    0.0048      89     163 ..      23      98 ..      18     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-06
                                   HHHHHHHTT--TT-EEEETT-TTTCCHHHCC.HHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
                        Met_10  89 aErerlaklveegevVvdvfAGiGpfaipia.kyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                                   +     +  v++g vV+d   G G+++ ++a k +++  v+a d + + ++ l + +++  + +v + +  D   +
  gi|70607497|ref|YP_256367.1|  23 ESEDDFIDYVKPGMVVLDHGCGPGYYTFSLArKVGNKGLVYALDSDERQIRILSSKLEREGITNVKTFVSRDLSPI 98 
                                   555667889*****************999873468999******************99999988877777776655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     2e-05     0.015       9      86 ..      29     106 ..      26     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
               Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtv 86 
                                   +++v++g +v+D G+  gy ++ l+++ g+   v+a D  e  ++   +++e++g++ ++++ +s  l+++ ++++d v
  gi|70607497|ref|YP_256367.1|  29 IDYVKPGMVVLDHGCGPGYYTFSLARKvGNKGLVYALDSDERQIRILSSKLEREGIT-NVKTFVSRDLSPIPSNSIDFV 106
                                   6899********************97725666799********************96.699999*99**9988889876 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.023     119     217 ..      36     137 ..      20     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
               Methyltransf_29 119 rtvlDvGCgvasfgayllsrdvltlsla.pkDeheaqvqf...aLeR.gvpailavlgtkrlpyPsrsfdlihCsrCridw 194
                                    +vlD GCg   ++   l r+v    l    D+ e q+ +    LeR g+  + + ++    p Ps+s d++      +  
  gi|70607497|ref|YP_256367.1|  36 MVVLDHGCGPGYYTFS-LARKVGNKGLVyALDSDERQIRIlssKLEReGITNVKTFVSRDLSPIPSNSIDFVLSK-DVLCC 114
                                   589******9877655.566665554431458888888763336**96677777777777779*******98644.33444 PP

               Methyltransf_29 195 teedgilllevdRvlRpgGyfvl 217
                                   t     l  e++Rvl+pgG   +
  gi|70607497|ref|YP_256367.1| 115 TVLHKELADEIKRVLKPGGLAFV 137
                                   445556889**********7554 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.19     109     157 ..      91     138 ..      15     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                   EES-TTS-S--TT-EEEEEEES---SS-HHH.HHHHHHHHEEEEEEEEEE CS
                Methyltransf_8 109 vacdlakvPledesvdvavfclslmgtnlad.flkeanrvlkvGGllkva 157
                                   v+ dl+ +P   +s+d ++    l  t l++    e++rvlk+GGl +v+
  gi|70607497|ref|YP_256367.1|  91 VSRDLSPIP--SNSIDFVLSKDVLCCTVLHKeLADEIKRVLKPGGLAFVS 138
                                   445555555..56888776555555555443144699********99875 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00055      0.43       3      56 ..      36      90 ..      34     104 .. 0.89
   2 ?    1.3   0.0      0.27   2.1e+02      94     112 ..     116     134 ..     115     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                                  EEEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEE CS
                Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlril 56
                                   vvl+ GcG G  +  lA k  +k ++ +++  ++ ++ + +k e+++++N++ +
  gi|70607497|ref|YP_256367.1| 36 MVVLDHGCGPGYYTFSLARKVGNKgLVYALDSDERQIRILSSKLEREGITNVKTF 90
                                  5899***************998773677************************976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.27
                                   TTSHHHHHHHHHHEEEEEE CS
                Methyltransf_4  94 llqpellkelarvLkkgGv 112
                                   +l++el +e++rvLk+gG+
  gi|70607497|ref|YP_256367.1| 116 VLHKELADEIKRVLKPGGL 134
                                   5789999***********7 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.4e-05     0.057      60     133 ..      32     108 ..      29     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                                   --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES..-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.--SEEEE CS
                          CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTl..Skeqaklakkrvdeldlerkvevklldyedlde.kvdrvvs 133
                                   +kpGm +Ld GcG G+ +   +++ + k +   l   + q +    +++++++++ ++    d   ++   +d v s
  gi|70607497|ref|YP_256367.1|  32 VKPGMVVLDHGCGPGYYTFSLARKVGNKGLVYALdsDERQIRILSSKLEREGITNVKTFVSRDLSPIPSnSIDFVLS 108
                                   79*******************99988886555552034466677777777777776666666666655545555555 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.6   2.8e+03     188     215 ..      31      59 ..      30      77 .. 0.71
   2 ?   11.2   0.0   0.00028      0.22      35      71 ..     118     154 ..     112     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.6
                                   HS-TT-EEEETT-TTTH.HHHHHHHTT-E CS
                   N6_N4_Mtase 188 stkkgdivlDpFaGSGt.Tavaakelgrk 215
                                   + k+g +vlD  +G G+ T   a++ g k
  gi|70607497|ref|YP_256367.1|  31 YVKPGMVVLDHGCGPGYyTFSLARKVGNK 59 
                                   57899999999888884377777776665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00028
                                   HHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHH CS
                   N6_N4_Mtase  35 lekvlkevrrvLkddgsifiniddseikkelkalade 71 
                                   +++ ++e++rvLk++g +f++i +    +++ + a+e
  gi|70607497|ref|YP_256367.1| 118 HKELADEIKRVLKPGGLAFVSIRKGFGPDPRNISAKE 154
                                   68899****************9877666555555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0015       1.2      78     127 ..      61     108 ..      49     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                   -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                       UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                    +y++D+d+r ++   +++e+ g+++  +f++ d   ++ ++ ++d +++
  gi|70607497|ref|YP_256367.1|  61 LVYALDSDERQIRILSSKLEREGITNVKTFVSRDLSPIP-SN-SIDFVLS 108
                                   389**********************************99.55.8999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1321.93
//
Query:       gi|70607498|ref|YP_256368.1|  [L=661]
Description: membrane associated phosphoesterase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-73  245.8   0.3    9.7e-73  245.4   0.3    1.2  1  Phosphoesterase  Phosphoesterase family


Domain annotation for each model (and alignments):
>> Phosphoesterase  Phosphoesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.4   0.3   5.4e-77   9.7e-73       1     356 []      32     345 ..      32     345 .. 0.88

  Alignments for each domain:
  == domain 1  score: 245.4 bits;  conditional E-value: 5.4e-77
               Phosphoesterase   1 ikhvViivqENrsfdhlfGtlkgvrgiddasplaqqdGvkkqalnkaevsapfsldtakg.lsaqvvvedpehsfqaiqeq 80 
                                   ikhv+ii++EN+sfd+ fG ++ + g+++         ++++  +++++     l + k   +  +v+ dp++ +  ++++
  gi|70607498|ref|YP_256368.1|  32 IKHVIIIFMENHSFDNFFGVYP-TGGVNES--------LSNELTKPNNLLGLPVLSQLKPvPNGTYVTVDPNEGYIPYHQD 103
                                   89********************.4446522........3334466777765555555555345568999************ PP

               Phosphoesterase  81 wnggrndkfvaaaeselvmgyfkredipvlwelaqeftlcDryFssvlggtepNrlflisgtsdpsGteggpsladpkktv 161
                                   wngg++d+f++ +++ + + y++ +++  lw+l +e+ l+D+yFs v++ + pN+l+l++++s        p ++d  + +
  gi|70607498|ref|YP_256368.1| 104 WNGGKMDGFLQGSGP-QGLTYYTVSQLAPLWDLTEEYGLADNYFSPVMSESAPNHLYLYTAYS--------PVIDDYGPPP 175
                                   ***************.***********************************************........9988889999 PP

               Phosphoesterase 162 lkgftqktigerLsekgvswaiYqealdnlakskvapfnyyvrklkklearrkalkqlglaakqlekfkkdvkngkLPqvs 242
                                     +f++ ti+ +Ls+ gvsw+ Y  ++   ++++        +++ +++++ +++ +++        f+++++ng+LP+vs
  gi|70607498|ref|YP_256368.1| 176 YIPFNE-TIFAELSQYGVSWGYYIFNA-SDWGQS------DLKYFSGVKDYLNHVGSWST-------FIDQLNNGTLPSVS 241
                                   999986.66777**********99888.222222......23456677777788777776.......************** PP

               Phosphoesterase 243 fikpngandeHpgadvaagdklikevlealtsspqwaktllivtyDEngGfyDhVappvapvsdpdglkGdpyglgvrvPl 323
                                   +i p  + d+ p a+v +g+ ++  +++a+++sp+w++t++++t+DE gG+yDhV+ppv +     g     ++lg rvPl
  gi|70607498|ref|YP_256368.1| 242 WILPSPTTDMGPPANVLQGEMWLLYIVNAVMRSPEWNSTAIFITFDEAGGYYDHVPPPVFQ-----G-----QQLGERVPL 312
                                   **********************************************************776.....3.....59******* PP

               Phosphoesterase 324 lviSpyakkgtvdhelfdhtSvlrfiekrfglp 356
                                   +viSpy+k+ +v+++l+ h+S+++fi++++glp
  gi|70607498|ref|YP_256368.1| 313 IVISPYSKEDYVSNTLLTHASLIAFIDYNWGLP 345
                                   *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4736.42
//
Query:       gi|70607499|ref|YP_256369.1|  [L=231]
Description: phenylacetic acid catabolic protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-21   74.8   0.0    7.1e-21   74.5   0.0    1.0  1  PaaA_PaaC  Phenylacetic acid catabolic protein
  ------ inclusion threshold ------
      0.042   13.5   0.0      0.083   12.6   0.0    1.5  1  MiaE_2     tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
       0.11   12.6   0.0        0.2   11.7   0.0    1.4  1  MOEP19     KH-like RNA-binding domain


Domain annotation for each model (and alignments):
>> PaaA_PaaC  Phenylacetic acid catabolic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   1.2e-24   7.1e-21       5     192 ..       7     187 ..       3     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.2e-24
                                   .........HHHHHHHHHHHHHHHHHHHHHHTTTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS.-HHHHHHC- CS
                     PaaA_PaaC   5 kdwmpeeyrkalirlllqlAdselilaqresewigrAPsLeediallnivlDelGharllysaaeelegkgkdeddlaflr 85 
                                   +d   ee +++l++l+  +Ads+l +    s w+   P++   +  +  v Del ha  + ++ e+  g++ +  +l +lr
  gi|70607499|ref|YP_256369.1|   7 SDIKDEELKTELLDLIFVIADSKLAIVEQTSPWLVNSPTVDSRLFTARFVADELNHAWQMSRMIEDF-GEKDKVKELQELR 86 
                                   56677888999********************************************************.7666777777776 PP

                                   -CCC----CGGGS---SHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSHHHHH CS
                     PaaA_PaaC  86 degefknsllvelpngdwadtivrqflvdaaaiilleaLkrssygplaaiaakvlkEesyHlrhgeewvlrLgdGteeskr 166
                                       ++ +  ++lp  +w d+++  f++d +++il+++L++++y+pl++ a+ ++k  +yH   +e+ ++rL   + e+++
  gi|70607499|ref|YP_256369.1|  87 LG--LHRLEPFNLPLFTWEDAVAFVFVIDSYNVILMNSLMDCEYEPLSKLAKSIVKDDEYHTMFSENEIIRL---SRENRN 162
                                   64..566788*************************************************************8...579*** PP

                                   HHHHHHHHHGGGGGGGG---HHHHHH CS
                     PaaA_PaaC 167 rvqeAlnrlwpyvlelfgpddaeeal 192
                                   ++q Aln + p ++++ ++  +  +l
  gi|70607499|ref|YP_256369.1| 163 KIQGALNFWLPRLNDVYEHMRKL-RL 187
                                   ***********999988776554.44 PP

>> MiaE_2  tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05     0.083       6     160 ..      17     175 ..      12     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHCC-SSSTTHHHHHHHHHHHHHHHHHHHHHHHHTT--.HHHHHGGGHHHHHHHHHTT- CS
                        MiaE_2   6 avvdllgalayGelsaferlaedarlaPtladraalaklaaaefrhyelledrlaeiGve.aeeamePfvaavddfhkrta 85 
                                    + dl+ ++a  +l+  e+ +     +Pt+  r   a++ a e++h  +++  +++ G++   + ++ +   +  ++    
  gi|70607499|ref|YP_256369.1|  17 ELLDLIFVIADSKLAIVEQTSPWLVNSPTVDSRLFTARFVADELNHAWQMSRMIEDFGEKdKVKELQELRLGLHRLEPFNL 97 
                                   5789******************************************************85145667778888888887777 PP

                                   -S.SHHHHHHHHHHHHHHHHHHHHHHCCCS-HHHHHHHHHH.S--HHHHHHHHHH.HHHHHHH-TTHHHHHHHHHHHH CS
                        MiaE_2  86 Pa.dwleslvkayvgdsvaadfyrevaeyldadtrelvlav.lddtghaevaeek.vraaladdprladrlalwgrrl 160
                                   P   w +++   +v+ds    +   + +       +l +++ +dd+ h+ + e++ +r + ++ +++++ l +w  rl
  gi|70607499|ref|YP_256369.1|  98 PLfTWEDAVAFVFVIDSYNVILMNSLMDCEYEPLSKLAKSIvKDDEYHTMFSENEiIRLSRENRNKIQGALNFWLPRL 175
                                   753788889999999999998888877766555666666551566668888876625777778888999999998776 PP

>> MOEP19  KH-like RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.3e-05       0.2      18      81 ..      13      76 ..       4      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                        MOEP19 18 yleawlleaiFGpdgeripeiEqvsqtllevkaldseglaeilifGrprykkrvkkmllslAew 81
                                  +l+++ll++iF   ++++  +Eq+s  l++  ++ds+  +  ++ ++ ++  ++ +m+   +e 
  gi|70607499|ref|YP_256369.1| 13 ELKTELLDLIFVIADSKLAIVEQTSPWLVNSPTVDSRLFTARFVADELNHAWQMSRMIEDFGEK 76
                                  58899*******************************************9999999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1567.49
//
Query:       gi|70607500|ref|YP_256370.1|  [L=256]
Description: phenylacetic acid catabolic protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-29  101.5   0.0    5.1e-29  101.2   0.0    1.0  1  PaaA_PaaC  Phenylacetic acid catabolic protein
  ------ inclusion threshold ------
       0.24   10.6   0.0       0.42    9.8   0.0    1.3  1  DS         Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> PaaA_PaaC  Phenylacetic acid catabolic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0   5.7e-33   5.1e-29       8     227 ..      31     249 ..      25     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 5.7e-33
                                   ......HHHHHHHHHHHHHHHHHHHHHHTTTTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS.-HHHHHHC--CC CS
                     PaaA_PaaC   8 mpeeyrkalirlllqlAdselilaqresewigrAPsLeediallnivlDelGharllysaaeelegkgkdeddlaflrdeg 88 
                                    p+e+ + l++ll+  +d+e+ +      w+ +APsL e ++++ i+ De+ h+  + ++++e    g+   ++a+++ + 
  gi|70607500|ref|YP_256370.1|  31 LPQEAVEVLLKLLSVQGDTEFASIEQHLYWLFHAPSLTERVTIARIMADEMRHGWQIIQVLKEF---GEPGKRIAEELLAT 108
                                   67888999********************************************************...65566666666666 PP

                                   C----CG..GGS---SHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSHHHHHH CS
                     PaaA_PaaC  89 efknsll..velpngdwadtivrqflvdaaaiilleaLkrssygplaaiaakvlkEesyHlrhgeewvlrLgdGteeskrr 167
                                   ++  ++l  +++p + w dti+  fl+d++ + +l a ++ss gpl++i   +l+Ee++H + g++ + rL ++   +++ 
  gi|70607500|ref|YP_256370.1| 109 RMGKHRLdaFNMPFNLWEDTIAFTFLIDRVGLYQLMAFEDSSFGPLSRIIPTMLMEEEFHINFGYTGIKRLVESG--KRDI 187
                                   665544333***************************************************************976..6889 PP

                                   HHHHHHHHGGGGGGGG---HHH...HHHHHTTSS--GGGGHHHHHHHHHHHHHHTT-----S- CS
                     PaaA_PaaC 168 vqeAlnrlwpyvlelfgpddae...ealaekgkavdndeLrqkfeakvvpvleeagltlPdep 227
                                   +q+ +n+++p  l++fg++ +     a +++ k  +n+e+r+ ++++v++ +  +gl+lPd p
  gi|70607500|ref|YP_256370.1| 188 AQKLINKWYPRGLDMFGHSRSRtieLAYKYGLKKWSNEEMRKMYMKDVEELVSPLGLELPD-P 249
                                   9*****************99988778999999****************************9.3 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   4.7e-05      0.42       5      57 ..     140     194 ..     137     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.7e-05
                            DS   5 syekigfqatslgeaidilnkmrkdekctiflglts..nlissGlreiiadlvke 57 
                                    y+ ++f+ +s+g   +i+  m  +e+ +i +g+t+   l+ sG r+i ++l+++
  gi|70607500|ref|YP_256370.1| 140 LYQLMAFEDSSFGPLSRIIPTMLMEEEFHINFGYTGikRLVESGKRDIAQKLINK 194
                                   58899*******************************6679************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1920.40
//
Query:       gi|70607501|ref|YP_256371.1|  [L=267]
Description: 3-hydroxybutyryl-CoA dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-55  188.1   0.0    1.9e-55  187.9   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.9e-30  106.5   0.0    1.1e-28  100.7   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.0   2.1e-59   1.9e-55       2     250 ..      15     266 ..      14     267 .] 0.96

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 2.1e-59
                                   EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHH CS
                         ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlelw 81 
                                    e+gv  +klnrP ++Na + e+l El + + + + d +v+++v+t+  +++F+aG d++e+  ++++   l+++  +e +
  gi|70607501|ref|YP_256371.1|  15 VEDGVGIVKLNRP-PANAHNLEMLRELDNIIVESRFDDNVKVIVITSnTPRFFSAGFDINEIKDKSPEYIGLSSQYSKEVM 94 
                                   5789*********.****************************************************999999999999*** PP

                                   HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTE..EE-GGG.GGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EE CS
                         ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnas..fglnel.klGlipgaggtqilarkvGkskAeeilllgkki 159
                                    ++++  k +ia +nG+++gGGlela+acDi+ +a++ +   g +e+ +l lipg ggtq+lar+vG+skA +++ +gk +
  gi|70607501|ref|YP_256371.1|  95 LRMMSTRKLIIASINGHCMGGGLELAMACDIRFIANDDNikLGMPEVsNLALIPGEGGTQFLARIVGRSKAIYLMTTGKTL 175
                                   *******************************987754442388888538******************************** PP

                                   EHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHH CS
                         ECH_1 160 saqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaf 240
                                   +++ea + Glv++ v  e+l  e++  a+k+a+ + +a+ ++k a+n+ l+  l +++++e++++++  +++d keG  af
  gi|70607501|ref|YP_256371.1| 176 TPKEAYELGLVERLVEPEKLYTETMDFARKVASGPAKAVGFAKLAVNEGLDIPLYTAFALEREMQNQALASEDAKEGARAF 256
                                   ********************************************************************************* PP

                                   HTCSH----- CS
                         ECH_1 241 lEkrkpefed 250
                                    Ekrkp f++
  gi|70607501|ref|YP_256371.1| 257 FEKRKPVFRG 266
                                   ********87 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   1.3e-32   1.1e-28       1     178 [.      19     196 ..      19     214 .. 0.88
   2 !    4.1   0.0    0.0031        28     271     309 ..     221     258 ..     203     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.3e-32
                                   .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                         ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                   vg+++Lnrp a Na +lem+r+l++++ e + dd+vk++v+++++++ f+AG D++++ ++  e    + + +++e  +  
  gi|70607501|ref|YP_256371.1|  19 VGIVKLNRPPA-NAHNLEMLRELDNIIVESRFDDNVKVIVITSNTPRFFSAGFDINEIKDKSPEYIGLS-SQYSKE--VML 95 
                                   5899*****87.************************************************999975443.333443..566 PP

                                   HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-..TT-EEE--GG.GGT----TTHHHHHHCSST.THHHHHHHH---B- CS
                         ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvt..ertvfAmPEt.aIGlfPDvGgsyfLsrlpg.elGlylalTGarlk 158
                                   ++ + +k ++a ++G +mGgG+ l++ + +r +   ++ ++ mPE+ ++ l+P  Gg+ fL+r+ g + + yl  TG++l+
  gi|70607501|ref|YP_256371.1|  96 RMMSTRKLIIASINGHCMGGGLELAMACDIRFIAndDNIKLGMPEVsNLALIPGEGGTQFLARIVGrSKAIYLMTTGKTLT 176
                                   788899*************************766234679*****856***************977578************ PP

                                   HHHHHHTTS--EE--GGGHH CS
                         ECH_2 159 gadalaaglathyvpsekle 178
                                    ++a+++gl + +v+ ekl 
  gi|70607501|ref|YP_256371.1| 177 PKEAYELGLVERLVEPEKLY 196
                                   **************999885 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0031
                                   HHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTT CS
                         ECH_2 271 lrrgrklsslaevlrmElrlalrllaekDfveGvrallv 309
                                   +++g +   l ++++ E ++ +++la++D  eG ra + 
  gi|70607501|ref|YP_256371.1| 221 VNEGLDIP-LYTAFALEREMQNQALASEDAKEGARAFFE 258
                                   55666665.8999**********************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1873.98
//
Query:       gi|70607502|ref|YP_256372.1|  [L=428]
Description: hypothetical protein Saci_1773 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-22   79.5   0.2    1.2e-21   77.1   0.0    2.3  3  AAA_14        AAA domain
    4.2e-08   33.4   0.1    6.3e-08   32.8   0.1    1.4  1  DUF4143       Domain of unknown function (DUF4143)
      0.004   16.9   0.0       0.02   14.6   0.0    1.9  2  AAA_24        AAA domain
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.29   11.5   0.0    1.6  1  AAA           ATPase family associated with various cellular 
       0.13   11.7   0.0       0.23   10.9   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.15   11.4   0.0       0.23   10.8   0.0    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0     4e-25   1.2e-21       4     130 ..      36     162 ..      34     163 .. 0.90
   2 ?   -1.4   0.0      0.74   2.2e+03      21      58 ..     165     197 ..     161     218 .. 0.61
   3 ?   -3.1   0.0       2.4   7.2e+03      63      75 ..     390     402 ..     379     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4e-25
                        AAA_14   4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewek 81 
                                    +++ G+R+vGKTt+lk+ i e l   +++++ l++++d+ rd +   +  l++++++++++ ++ y+flDEi  v++w  
  gi|70607502|ref|YP_256372.1|  36 NILLLGPRQVGKTTFLKTTIMEVLeseANPKKALFFSCDSMRDMEDLIE--LIHEYRNLINP-NNGYIFLDEITFVKDWNV 113
                                   57899***************9999******************9876654..99999999888.999*************** PP

                        AAA_14  82 alkslvdeg..knldvivtGSnskllskeiatslagrva.eielyplsfaEf 130
                                    l +l++ g  ++  v+vtGS s+ l+k   ++l gr   ++  ypl+f+ +
  gi|70607502|ref|YP_256372.1| 114 GLLHLFNAGyfRDSIVYVTGSTSMYLMK---ETLPGRPLkKLVFYPLDFRTY 162
                                   *******8878999************99...6888887637999*****976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.74
                        AAA_14  21 qlikellvkkesilyinldderdkkladpekllelile 58 
                                    ++++++ + ++i  +nl++  +k+++    ll +++e
  gi|70607502|ref|YP_256372.1| 165 VFFQNKI-NVDRINLFNLKESYEKAKD----LLPYLQE 197
                                   5666666.7777888888775554433....2333333 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
                        AAA_14  63 ekktylflDEiqe 75 
                                   ++ ++l lDEi +
  gi|70607502|ref|YP_256372.1| 390 SEGYILSLDEIGM 402
                                   4678899999965 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.1   2.1e-11   6.3e-08      23     122 .]     291     380 ..     167     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.1e-11
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  23 rlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEv 103
                                   r+++    +n   + ++  K+yf+D++++  +   ++     + e + +++E +V ++L +   + g ++ y  +k+g+Ev
  gi|70607502|ref|YP_256372.1| 291 RVFRK--IENGHFNNKSFKKVYFIDPFIYRVMKMYTRGIGDISREELPRVVEGIVGEHLAR---EYGREVGYTFTKSGKEV 366
                                   33333..7999999**************998666665543334499***************...4477888888888**** PP

                                   xxxxxxxxxxxxxxxxxxx RF
                       DUF4143 104 DfvielkggkivpiEvKss 122
                                   Dfv+++     v++EvK++
  gi|70607502|ref|YP_256372.1| 367 DFVVRN-----VGVEVKYG 380
                                   ****74.....799***96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.6e-06      0.02       4      36 ..      36      77 ..      34     111 .. 0.86
   2 ?   -0.5   0.0      0.29   8.5e+02      67     109 ..     242     285 ..     171     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.6e-06
                        AAA_24  4 kiliyGpsgiGKTtlakel..........gpkplfidtekGlk 36
                                  +il+ Gp  +GKTt++k+           ++k+lf+ ++  ++
  gi|70607502|ref|YP_256372.1| 36 NILLLGPRQVGKTTFLKTTimevleseanPKKALFFSCDS-MR 77
                                  799****************999999999999999999997.44 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                        AAA_24  67 ktlviDtideleelclaevirqnekaesk.edkgdgkGygelae 109
                                   + ++iD i+e+ +     + +++ ++++   + +++k y el+e
  gi|70607502|ref|YP_256372.1| 242 ERIFIDIIGEIIDSLGSRISENTIAKKTSiGSHNTVKSYLELGE 285
                                   56899999999999988886666554333377888888877776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.8e-05      0.29       1      67 [.      37     105 ..      37     109 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-05
                                   EEEESSTTSSHHHHHHHHHHHH.....T.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETG CS
                           AAA   1 vllyGppGtGKTllakavakel.....g.vefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEi 67 
                                   +ll Gp  +GKT++ k  + e+     +  + l +s+ +++       ++++ el+ e ++    +   +f+DEi
  gi|70607502|ref|YP_256372.1|  37 ILLLGPRQVGKTTFLKTTIMEVleseaNpKKALFFSCDSMR------DMEDLIELIHEYRNLInpNNGYIFLDEI 105
                                   69**************9999964433313445555555555......2233333333333333444599999998 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.8e-05      0.23      33      85 ..      34      86 ..      30     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.8e-05
                         AAA_7 33 kkpvllvGptGtGKtviikd.llkkldkekylsltinfsaqtsanqlqdiiesk 85
                                  + ++ll Gp  +GKt+ +k+ +++ l+ ++ ++++  f ++ s +++ d+ie  
  gi|70607502|ref|YP_256372.1| 34 RENILLLGPRQVGKTTFLKTtIMEVLE-SEANPKKALFFSCDSMRDMEDLIELI 86
                                  5789****************6666666.77777777777788888888888754 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.9e-05      0.23      39      64 ..      27      59 ..       5      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.9e-05
                                  -........SEEEE--TTSSHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE 39 a.......shllvaGatgsGKStalntLilSla 64
                                  +        ++l++G  + GK+t+l+t i+ ++
  gi|70607502|ref|YP_256372.1| 27 PyrippirENILLLGPRQVGKTTFLKTTIMEVL 59
                                  344445668******************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2805.05
//
Query:       gi|70607503|ref|YP_256373.1|  [L=526]
Description: acetyl-coenzyme A synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-84  283.2   0.0    3.3e-84  282.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    4.7e-23   81.9   1.5    9.2e-23   81.0   1.5    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.9   0.0   3.7e-88   3.3e-84      10     422 ..      24     426 ..      16     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 282.9 bits;  conditional E-value: 3.7e-88
                                   TSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHH CS
                   AMP-binding  10 dkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayil 90 
                                   +++a+++  +++ +TYr l +++nr++++L++  +++++r ++++  sp ++ ++++++k+Ga ++p+n+ + +++  + l
  gi|70607503|ref|YP_256373.1|  24 GRPAIYY--KDEIWTYRRLIDEINRVGNALKK-FLEREQRLLMISYDSPYFISVFYGAMKIGAFPIPVNTFTIPDDHIFYL 101
                                   799**99..99********************9.89********************************************** PP

                                   HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.........-TSCCCS-BTTSEE CS
                   AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.........kpeeeeelkpddla 162
                                   eds+akvl+  v+ e  ++l+++   + +  + +++  ++ +  e+l+++ +++++           ++  +++++pd++a
  gi|70607503|ref|YP_256373.1| 102 EDSKAKVLV--VEPEIWDRLASKLNGRTEELKYVMILPGGHR--EQLHISPHPAKVMLyedivphesTDLNPAKTSPDEPA 178
                                   *********..8888867777666654444444444434433..4577777766665246788888944466789****** PP

                                   EEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                   AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpk 243
                                   + +YTSG+TG+PK +++ h+ ++  + ++ +++  k++e+d+++s   l++++gl  + ++a+ +Ga+vvl+p+  +  pk
  gi|70607503|ref|YP_256373.1| 179 FGLYTSGSTGHPKCAVHLHKDIIVVLNTY-VKNVLKINENDKLFSASKLFFAYGLGNSSYFAFGNGASVVLMPERVE--PK 256
                                   **********************9998886.78889999***********************************7777..99 PP

                                   HHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC CS
                   AMP-binding 244 lllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvv 324
                                   ++l++i+++k+t++++vP++++ ll+ ++ k    ++dlss+rl++++gepl+ ++ +++++++  e+l+g G TE++++ 
  gi|70607503|ref|YP_256373.1| 257 RVLHYIQTYKPTIFFAVPTIYNSLLNVEEWK----KYDLSSIRLCVSAGEPLPGKIYEEWKKRYVVEILDGIGSTEALHIY 333
                                   9*************************54444....46*******************************************9 PP

                                   EECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCC.EEEEEEEEEE CS
                   AMP-binding 325 tvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegr.wlrTGDlgrl 404
                                   +  + +++ ++++ +Gk++pg evkivDe+ g+ v+ ge G l+v+g +v++ Yl k e t++ +    + w+r+GD  ++
  gi|70607503|ref|YP_256373.1| 334 I-SNFPGE-SRPNCTGKVVPGYEVKIVDEN-GNQVKAGEIGDLYVKGDSVAMYYLHKYEDTRKNMQ---GyWFRSGDKFYF 408
                                   7.444444.468899**************9.999*******************************7...44********** PP

                                   ETTSEEEEEEECCCEEEE CS
                   AMP-binding 405 dedGyleivgRkkdlikl 422
                                   d++Gyl+++gR++d+ik 
  gi|70607503|ref|YP_256373.1| 409 DDNGYLYYIGRSDDMIKA 426
                                   ****************96 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   1.5     1e-26   9.2e-23       1      76 []     435     513 ..     435     513 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1e-26
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evEs++++h+aV eaaVvG++dev    +vafVv+k+g+ea   lee +k++++ +l++y+ pk+++fv+elpkt++GK
  gi|70607503|ref|YP_256373.1| 435 EVESVILTHEAVLEAAVVGIKDEVGLTKVVAFVVPKQGYEAnekLEEGIKEYLKGKLPSYKIPKQIRFVNELPKTATGK 513
                                   8***********************************99533356**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3166.17
//
Query:       gi|70607504|ref|YP_256374.1|  [L=262]
Description: phenylacetic acid degradation operon negative regulatory protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-32  111.5   0.1    3.3e-32  110.7   0.1    1.4  1  PaaX_C         PaaX-like protein C-terminal domain
    3.8e-16   59.1   0.1    6.2e-16   58.4   0.1    1.3  1  PaaX           PaaX-like protein
     0.0068   16.2   0.0      0.028   14.2   0.0    1.9  2  LexA_DNA_bind  LexA DNA binding domain
  ------ inclusion threshold ------
      0.027   14.5   0.1      0.083   12.9   0.1    1.7  2  DUF4313        Domain of unknown function (DUF4313)
       0.05   13.8   1.2       0.22   11.7   0.0    2.8  5  CRISPR_Cas2    CRISPR associated protein Cas2
      0.089   12.9   0.4       0.24   11.5   0.4    1.7  1  LZ3wCH         Leucine zipper with capping helix domain
       0.13   11.9   0.0        0.7    9.6   0.0    2.1  2  GntR           Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> PaaX_C  PaaX-like protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.1   1.3e-35   3.3e-32       3      98 ..     165     257 ..     163     258 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.3e-35
                        PaaX_C   3 elveelWdldelaakYeeflaeyrpllkellekeelapeeaFlvrtlllheyrkllfrDPgLPeellpedWpGaaarelfr 83 
                                   e v+++Wdl+e+++kY+ef++++ ++++++++   l+p+eaF++r++l+heyrk+l++DP+LP++llp++W G++a+elf+
  gi|70607504|ref|YP_256374.1| 165 EIVRKCWDLKEVEEKYKEFVNQWGKVMENISS---LKPNEAFITRIRLVHEYRKFLHIDPNLPKDLLPPNWVGYEAYELFQ 242
                                   679**********************9988887...899******************************************* PP

                        PaaX_C  84 elyrelaeaaerfle 98 
                                   +l+++l++++++f++
  gi|70607504|ref|YP_256374.1| 243 KLRNKLSTLSDQFFK 257
                                   *************97 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   2.4e-19   6.2e-16       3      60 ..       4      61 ..       2      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.4e-19
                          PaaX  3 rSlivtlygdyveprggaiwlgsLirllaelGiseslvRaalsRlakaGwlvrekegr 60
                                  + l++t+ygdy+ ++g++i ++sLi+++ e+G+ e+++Ra+l+Rl ++G+++  +  r
  gi|70607504|ref|YP_256374.1|  4 QTLFFTIYGDYIINYGNSITVRSLIKIMREFGFTEGAIRAGLFRLRQKGLVDMIDRRR 61
                                  6799**********************************************99887765 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.1e-05     0.028      28      61 ..      27      59 ..      14      61 .. 0.91
   2 ?   -1.7   0.0      0.98   2.5e+03      39      48 ..     128     137 ..     125     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                 LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyierdpg 61
                                     i+r++g++   a+   L +L++KG++++ + 
  gi|70607504|ref|YP_256374.1| 27 LIKIMREFGFT-EGAIRAGLFRLRQKGLVDMIDR 59
                                  557********.99****************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.98
                                   .HHHHHHHHH CS
                 LexA_DNA_bind  39 SpsaveehLk 48 
                                   Sp++vee L 
  gi|70607504|ref|YP_256374.1| 128 SPNPVEESLT 137
                                   9******997 PP

>> DUF4313  Domain of unknown function (DUF4313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   4.9e+03      42      62 ..     123     143 ..     120     147 .. 0.81
   2 ?   12.9   0.1   3.3e-05     0.083      21     100 ..     181     259 ..     173     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                       DUF4313  42 neayidtnnlskdvleflken 62 
                                   + ++i+ n + + + +f++e 
  gi|70607504|ref|YP_256374.1| 123 QSTWISPNPVEESLTKFINEL 143
                                   567899899999999999876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.3e-05
                       DUF4313  21 edgleefgdltVnlpgvslepneayidtnnlskdvleflken.klgevlgetakSGyceYpevaFdlerlkeldpkgvkey 100
                                   ++ ++++g++  n+  +sl+pnea+i+   l ++  +fl+   +l + l   +  Gy +Y+ ++  +++l+ l ++ +k +
  gi|70607504|ref|YP_256374.1| 181 KEFVNQWGKVMENI--SSLKPNEAFITRIRLVHEYRKFLHIDpNLPKDLLPPNWVGYEAYELFQKLRNKLSTLSDQFFKSV 259
                                   445599********..**********************98652566554445589*********9999*999999887765 PP

>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.3   1.4e+04      17      29 ..      25      37 ..      22      37 .. 0.78
   2 ?   -2.5   0.0       2.4   6.1e+03      40      54 ..      64      78 ..      61      85 .. 0.50
   3 ?   11.7   0.0   8.5e-05      0.22       2      54 ..      91     145 ..      90     158 .. 0.85
   4 ?   -2.8   0.0         3   7.8e+03      44      48 ..     186     190 ..     172     210 .. 0.54
   5 ?   -2.5   0.1       2.3     6e+03      47      55 ..     243     251 ..     237     261 .. 0.39

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.3
                                  HHHHHHHHHTTEE CS
                   CRISPR_Cas2 17 rkvakilkkyGfq 29
                                  r + ki++++Gf+
  gi|70607504|ref|YP_256374.1| 25 RSLIKIMREFGFT 37
                                  6678999999985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                  ESHHHHHHHHHHHHH CS
                   CRISPR_Cas2 40 lseaqleklkkrlkk 54
                                  lsea l +l++ +k+
  gi|70607504|ref|YP_256374.1| 64 LSEAGLYRLQEGMKR 78
                                  444444444444444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 8.5e-05
                                   EEEEEEEC.HCHHHHHHHHHHHHHHTTEEEEETTEEEE.EESHHHHHHHHHHHHH CS
                   CRISPR_Cas2   2 lvlvvYDi.kedrkrrrkvakilkkyGfqrvQySVFeg.elseaqleklkkrlkk 54 
                                   + +vvY i +++r  r +++k+lk  Gf  +  S  +  +  e+ l k +++lk+
  gi|70607504|ref|YP_256374.1|  91 WRIVVYNIpESNRSVRDEMRKTLKWLGFGYLAQSTWISpNPVEESLTKFINELKD 145
                                   789*****9999****************999999999888778888888888876 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 3
                                   HHHHH CS
                   CRISPR_Cas2  44 qlekl 48 
                                   q+ k+
  gi|70607504|ref|YP_256374.1| 186 QWGKV 190
                                   33333 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 2.3
                                   HHHHHHHHH CS
                   CRISPR_Cas2  47 klkkrlkki 55 
                                   kl+++l+ +
  gi|70607504|ref|YP_256374.1| 243 KLRNKLSTL 251
                                   333333222 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   9.5e-05      0.24       5      28 ..     172     198 ..     169     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                        LZ3wCH   5 ekkkatkkakeaanrWtd...nifdik 28 
                                   ++k++++k+ke +n+W +   ni ++k
  gi|70607504|ref|YP_256374.1| 172 DLKEVEEKYKEFVNQWGKvmeNISSLK 198
                                   689***************999998876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00027       0.7      29      61 ..      29      61 ..      16      64 .. 0.89
   2 ?   -1.0   0.0      0.54   1.4e+03      30      47 ..     121     138 ..     119     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                          GntR 29 eLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                  +++ efg++   +R  L rL ++glv   ++r 
  gi|70607504|ref|YP_256374.1| 29 KIMREFGFTEGAIRAGLFRLRQKGLVDMIDRRR 61
                                  6899**********************9999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                                   HHHHHTS-HHHHHHHHHH CS
                          GntR  30 LaaefgVsrttvReALrr 47 
                                   La+   +s ++v e+L +
  gi|70607504|ref|YP_256374.1| 121 LAQSTWISPNPVEESLTK 138
                                   777788999*****9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1537.28
//
Query:       gi|70607505|ref|YP_256375.1|  [L=117]
Description: hypothetical protein Saci_1776 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0046   15.9   8.4     0.0046   15.9   8.4    1.5  1  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt
  ------ inclusion threshold ------
        3.3    7.7   9.2         11    6.0   8.7    2.1  1  Caveolin   Caveolin


Domain annotation for each model (and alignments):
>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   8.4   5.1e-07    0.0046     280     346 ..      24      90 ..      21     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-07
                     LptF_LptG 280 laclvfaliaaplglvkrrggrglrlliaillfvlyyvllslgkalaengvlppilaawlpnilfll 346
                                   l+++ ++l+++plgl +r+++ ++++l++++  ++ y+l  lg+ l  ++++  il+   + +++l 
  gi|70607505|ref|YP_256375.1|  24 LYPFTAILVGIPLGLLSRKYSAISGFLVGFIASLSLYLLYPLGNVLQLADKVGGILGLNGVVVVLLY 90 
                                   7899******************************************999887666655555555443 PP

>> Caveolin  Caveolin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   8.7    0.0012        11      49     101 ..      18      75 ..       2     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0012
                      Caveolin  49 vfevvkvliYrlltallaiPlal.......ilgilfallsalhiwlvvPlvklllielkl 101
                                   +fe   +++Y + ++l++iPl l       i+g+l++++++l+ +l+ Pl ++l+++ k+
  gi|70607505|ref|YP_256375.1|  18 IFE--LFVLYPFTAILVGIPLGLlsrkysaISGFLVGFIASLSLYLLYPLGNVLQLADKV 75 
                                   343..47899999*******965333333378********************99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 800.33
//
Query:       gi|70607506|ref|YP_256376.1|  [L=817]
Description: penicillin amidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.5e-152  508.1   0.0   6.8e-152  507.8   0.0    1.0  1  Penicil_amidase  Penicillin amidase
  ------ inclusion threshold ------
       0.12   13.2   0.1       0.27   12.1   0.1    1.5  1  DUF2553          Protein of unknown function (DUF2553)


Domain annotation for each model (and alignments):
>> Penicil_amidase  Penicillin amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.8   0.0  7.6e-156  6.8e-152       2     664 ..      44     800 ..      43     804 .. 0.91

  Alignments for each domain:
  == domain 1  score: 507.8 bits;  conditional E-value: 7.6e-156
                                   EEEEEEGGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHHTS.. CS
               Penicil_amidase   2 VeirrDewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaelaal.l 81 
                                   V+i++D++g++hIyA+n +dl++a Gy  A++rl+qme++ ++a G+l++++G++ l+sD++++ +g++++a  + +   +
  gi|70607506|ref|YP_256376.1|  44 VNIYVDNNGIAHIYADNLHDLLLAEGYYEASQRLFQMEFFGLLAMGNLSSWVGSRGLSSDIAMHLIGIPQNANMSTNYIrE 124
                                   99**********************************************************************999755554 PP

                                   .....HHHHHHHHHHHHHHHHH-..-ST-HH.HHHH---....S.........SS-.XXXXXX.....XXX.XXXXXXXX. CS
               Penicil_amidase  82 d.petralleaYaaGvNaylaelkakalPlefallgykpepWtpvdslavakvmaldlagnleeelararalaaklgdekv 161
                                   + p+ +++l ++++GvN+y+++l  ++lPlef++lg+kp++W p+ sla+ ++ma++l++++++ela a  l a ++ ++v
  gi|70607506|ref|YP_256376.1| 125 NyPTVYSYLVDFSEGVNDYISTLSYRNLPLEFKFLGVKPYNWAPIYSLAFGEYMAWSLTSGFSDELASAL-LYAYFNFSEV 204
                                   42555******************9777*******************************99********98.8888888888 PP

                                   ................................................................................. CS
               Penicil_amidase 162 aelfp..p......................................................................... 167
                                   +e+ p  p                                                                         
  gi|70607506|ref|YP_256376.1| 205 NEINPyyPhfidgnltvmpgdgtvngynltsqgispsylwsldwyqswatgltkqqlislvplmkyallnisdpyvdftap 285
                                   888664326777888888899999999999999999999999999999999999999999999999999999999999999 PP

                                   ..X-EEEEE-TTTBTTSS-EEEEE-EEESSGGG--EEEEEEETTEEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-SEEEE CS
               Penicil_amidase 168 ..gSNnwvvsgerTasGkpllanDPHlglsapslwyqahlqapgldviGaslpGlPgvliGhnediAWglTnagadvqdly 246
                                     +SN+wv++++ +++G p+lanDPHl+l  ps+w+  +l + g++v+G+ l+G+PgvliGh+ +  WglT+ +   ++ y
  gi|70607506|ref|YP_256376.1| 286 ilASNSWVITSNFSSQG-PILANDPHLPLLYPSVWIPLQLVGGGFNVTGWGLVGIPGVLIGHTPYTVWGLTTPEGSSSNAY 365
                                   999************99.*************************************************************** PP

                                   EEEEETTEEEEEEETTEEEE-EEEEEEEEEE-TT.EEEEEEEEETTEEEE-.......TB--EEEEG-TTHHHHHHHHHT- CS
               Penicil_amidase 247 aeklnpddptrylydgkwepmetrtetikvkggddsvtltvreTrhGPvvsd..gkavalrwtalepgdrsldallalnra 325
                                   +e++n  + t+y +dgkw pm++++ t+   g     t tv++T++GP+v++  ++ ++l wta ++ + ++ a+l l++ 
  gi|70607506|ref|YP_256376.1| 366 VERVN--G-TYYYFDGKWYPMQEYNYTLM--G----KTYTVYYTNNGPLVARegNYGISLYWTAMKEPILTVIAILLLDNS 437
                                   ***99..4.56769*************43..3....358*************77777************************ PP

                                   -SHHHHHHHHHHH---SEEEEEEETT--EEEE--S--B---...............TT--EEETT-GGGS--TB--GGGS- CS
               Penicil_amidase 326 rnvaefraalkdlaapaqnvvyADreGnigyqaagrvPvrp............aaddgllpvpGsdsayeWtgyipfeelP 394
                                   ++++++ +a+k++  p+qn+ + +r+ ++gy++ag +P+ +            +    ++p++G++s++e  gy+pf+ lP
  gi|70607506|ref|YP_256376.1| 438 TSFNDLINAAKYWVIPPQNIAMISRN-HAGYIVAGSYPLINetlpngktvlviG---ARTPLNGTTSKFEPVGYVPFKYLP 514
                                   *************************9.**************7776654433322...456********************* PP

                                   EEEE..SSEEEESSS----S..........--T-HHHHHHHHHH..SS...-B-HHHHHHHHHT-BBTHHHHHHHHH.... CS
               Penicil_amidase 395 qvvnPargyivtaNnrvlpddypa.algsdwappyRarrirelLeekaagkkvtledmaalqtdtrsllaerllpll..al 472
                                   qv++P+rgy++  N+ +   +yp+ ++g++w+++ Ra+ i+++L   + +k v+++dm++lq++++++ a++l+pll  a+
  gi|70607506|ref|YP_256376.1| 515 QVFDPSRGYAFAPNQPTAWINYPYpFIGGYWSSGGRAEDIYHYL---KYQKSVDVSDMMSLQSNVTDYWASQLTPLLlkAI 592
                                   ****************99999***999999**************...45577***********************998633 PP

                                   ..-..GGGHHHHHHHHH-.SB-STT-THHHHHHHHHHHHTT....................................---T CS
               Penicil_amidase 473 .eaaeaeaaaaldlLraWdgrmdadsaaaalfaawlaalvralfedelg..........rlaealeklle....da.sfww 537
                                    + +++ +a+a+++L++W+++  ++++a++++  ++a++v+  ++  l+             +++++l+     d+ s w+
  gi|70607506|ref|YP_256376.1| 593 gNGNTTIEAQAVQYLKSWNYTFYQGEVAPTIYTYIVAEMVNMSMARILDnyglgiigisGIPYVVPDLIYialnDPtSIWV 673
                                   64455556779********************************999999999******95567888888866644467777 PP

                                   TSTTT-SESHH.HHHHHHHHHHHHHHHST-T-B.....HHHHEEEE.E............EE---B-GGG........... CS
               Penicil_amidase 538 ddptttpktrdelllaalaealaeleaaglgadpakwrwgklhrlelrhplg...fnrg.lpvgGgeetvnatsysara.. 612
                                   +       + ++l+++a+a+a++ l+++ lg+++++w+wgk+h+le+  pl    +++g +p+ G+ +t+ ++s+ + +  
  gi|70607506|ref|YP_256376.1| 674 NG------NFNSLVQNAFAKAISLLQQE-LGTNVSGWNWGKVHFLEIYDPLQlsqLSIGpIPIFGDPHTLAVGSTPYVPtv 747
                                   66......7899*************999.79********************9***99*************99999887799 PP

                                   ..EEEEEEE-EEEEEE--T.S.EEEEETT-S-S-TTSTTSSHHHHHHHTT--EE CS
               Penicil_amidase 613 ..frvtrgpsyrmvvdladrdkaravlpgGqsgnpgsphyaDqlelwaegeylp 664
                                      +vt g+s+r+v+  +     +++ pgG s+ +++++ ++ql+lw++ +y++
  gi|70607506|ref|YP_256376.1| 748 plPYVTVGSSLRFVACIN-SSLFYGIFPGGPSEGIFNQYSQNQLPLWLNFRYVS 800
                                   ***************666.456*****************************986 PP

>> DUF2553  Protein of unknown function (DUF2553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     3e-05      0.27      15      55 ..      41      81 ..      32      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                       DUF2553 15 ngeleLYldnekiGevkeesenqyelkegysqeeekiykke 55
                                  +g++++Y+dn+ i ++   + + + l+egy +  ++++++e
  gi|70607506|ref|YP_256376.1| 41 QGNVNIYVDNNGIAHIYADNLHDLLLAEGYYEASQRLFQME 81
                                  699*************88999*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (817 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4964.28
//
Query:       gi|70607507|ref|YP_256377.1|  [L=557]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-39  134.6   0.0    5.1e-39  133.9   0.0    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.9e-13   50.4   0.0    3.5e-13   49.6   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      3e-08   34.0   0.0    5.4e-08   33.2   0.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    3.7e-06   27.0   0.0      1e-05   25.6   0.0    1.7  2  AidB_N         Adaptive response protein AidB N-terminal doma


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9   0.0   1.1e-42   5.1e-39       1     149 [.     275     434 ..     275     435 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.1e-42
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   ++G++++ etl+++R+a+a +alglar+a+ ea+ ya++rkafgkpli+h+lvr+ l +m++ +e++ +l+++ ++ +++ 
  gi|70607507|ref|YP_256377.1| 275 NQGIYYTVETLTVSRIANAFGALGLARKAYLEAYYYAQKRKAFGKPLIEHPLVRRDLLDMEVYIEGTMALALKSVSEFQKS 355
                                   79******************************************************************************* PP

                                   ---...........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpd...........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                   +++           r  +++aK++++++  +v++ am+l+Gg G+l+e p+erl+r+a++++i+eG+s+iq +++ ++l
  gi|70607507|ref|YP_256377.1| 356 WMStppynenynyaRLLTHIAKNMTADMSAYVTKMAMELHGGIGFLREFPIERLHREALITPIWEGPSNIQALDMLEAL 434
                                   ************************************************************************9998875 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   7.7e-17   3.5e-13       1      95 [.     165     264 ..     165     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 7.7e-17
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEE.EEEEEETTTT-SEEEEEEE.TS-------EEEEEEE..GG....GEEE CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnG.eKiwitnaaiatlalvlar.tekpdrarglslflvprdap....gvsv 75 
                                   a+++TE q+Gsd+ ++  +a++ dg+ + lnG +K + + a+ a++alv ar ++ p++a+gl lfl p+ ++    ++ +
  gi|70607507|ref|YP_256377.1| 165 ATWFTEVQGGSDLGANLVEAYK-DGNTWKLNGiTKYFASDAGLAHYALVTARpKGAPSGAKGLGLFLAPKLDSsgrrNFLI 244
                                   5789*************98843.4446*************************7666669**********44444677**** PP

                                   -----BSS-TTS-EEEEEEE CS
                 Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfe 95 
                                   rr++ek ++ ++ptge++f+
  gi|70607507|ref|YP_256377.1| 245 RRLKEKSATISVPTGEVEFH 264
                                   ******************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.2e-11   5.4e-08       4     125 ..     293     415 ..     290     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.2e-11
                                   HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---...-HHHHH CS
                 Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkev...tvedra 81 
                                   a  alG+Ar a+ e+  +a++r+   +g++l ++p +   l +++  ++   al ++ +++ ++      ++       r+
  gi|70607507|ref|YP_256377.1| 293 AFGALGLARKAYLEAYYYAQKRKA--FGKPLIEHPLVRRDLLDMEVYIEGTMALALKSVSEFQKSWMSTPPYnenYNYARL 371
                                   5669********************..***********************************88875554444110334567 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHH CS
                 Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDaha 125
                                      +a+ +++++++ ++++++e++Gg + + e p++Rl R+a +
  gi|70607507|ref|YP_256377.1| 372 LTHIAKNMTADMSAYVTKMAMELHGGIGFLREFPIERLHREALI 415
                                   77788***********************************9966 PP

>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.2e-09     1e-05       9     145 ..      19     150 ..      14     158 .. 0.82
   2 ?   -3.6   0.0       2.1   9.3e+03      22      50 ..     491     519 ..     483     522 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.2e-09
                        AidB_N   9 vnlfasdpaLqeavaregaaeaaeelaalGellgsaevlelarlanr.npPrlrthDrfGrRiDevefhpayhalmaaav. 87 
                                    n f+ d+++q++++      a  +l+ lGe +g  e+le  +  ++  +P+   +   G+R+Dev  +p  + ++++ + 
  gi|70607507|ref|YP_256377.1|  19 KNHFTIDKPFQQLLKYFRG--AVPDLTPLGEFAGG-ELLEISDYIDKgAHPKHIMWSIDGQRVDEVWISPMQRLVLERLLk 96 
                                   799************8765..578***********.88887776655278********************99987776651 PP

                        AidB_N  88 eaglhasaweearegahvaraallyllaqveaGhlCPltmThAavpaL.kaepalaeew 145
                                   e++++a++++    g + +++a +yl+++  +G++C lt T+  + +L k   a ++++
  gi|70607507|ref|YP_256377.1|  97 EYHVNAYPYK---GGDWFQHFASIYLISD--PGIACILTVTNQTAYTLyKYGDAYQRTL 150
                                   4566677776...899***********86..**********998888856666666555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.1
                        AidB_N  22 varegaaeaaeelaalGellgsaevlela 50 
                                   ++  g+a a+  l + Ge+lgs++++  +
  gi|70607507|ref|YP_256377.1| 491 LNTLGNAVATVLLLHAGESLGSSRLRTVG 519
                                   55556666667778888888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3719.14
//
Query:       gi|70607508|ref|YP_256378.1|  [L=513]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-82  277.0   0.0    2.6e-82  276.7   0.0    1.0  1  AMP-binding    AMP-binding enzyme
      1e-17   64.8   0.0    1.8e-17   64.1   0.0    1.4  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.7   0.0   2.9e-86   2.6e-82       8     422 ..      18     411 ..      11     412 .. 0.89

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 2.9e-86
                                   STTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHH CS
                   AMP-binding   8 tpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelay 88 
                                   tp+   +v+  +++ +TY+e++erv +lA+ L +lG+kkg++++++ +n+ ++v +l+a + +G+v+ p+n +l++e++ +
  gi|70607508|ref|YP_256378.1|  18 TPNVE-IVY--GDNIYTYKEVYERVVKLANSLHNLGIKKGTTIGVADWNTNRFVELLYASALLGCVIYPVNIRLPPEQIIW 95 
                                   45545.558..8999****************************************************************** PP

                                   HHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE-- CS
                   AMP-binding  89 iledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSG 169
                                    ++ ++++ l+  ++++      ea +k+ ++++v++ld ++ + + e  +++++ ek      +  +k  d++ i++TSG
  gi|70607508|ref|YP_256378.1|  96 TIKFANVEWLF--ISRDF-----EALSKVFDSSKVVYLDGNNGQISYEDLISKGAMEK-----VNYDVKGGDPYSILFTSG 164
                                   ***********..66555.....66777777889999998877666666666655543.....44568************* PP

                                   SSSS-EEEEEEHHHHHHHHHHHH....HHHC...SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                   AMP-binding 170 TTGkPKGVmlshrnlvanvaslk....letr...fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpk 243
                                   TTGkPK+Vm++h+ +++ + s+     l  +    kl+++dv++ + p++h  ++  + ++a + Ga+ vl  k+++   k
  gi|70607508|ref|YP_256378.1| 165 TTGKPKAVMYTHEKVIHGALSIVhqlgL--YnspAKLSSNDVIMPFIPFYHLWSW-GSAFIASYLGAKYVLTGKFDP---K 239
                                   ******************9999777443..343556777****************.***************998876...5 PP

                                   HHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC CS
                   AMP-binding 244 lllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvv 324
                                   + ++li+++++t i++vP++++++l+sg  +      +l++++  l+gg++++ ++++ +++ + + ++ +YG T ++++ 
  gi|70607508|ref|YP_256378.1| 240 TAIQLIKRENATWINAVPTMIQMILSSG--E------QLPGVKA-LIGGQAIPYNVAKSISDAGLK-FSTIYGGTDMLAIS 310
                                   569***********************84..4......89****9.68****************887.*************9 PP

                                   EE.....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEE CS
                   AMP-binding 325 tv.....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGD 400
                                   +      ++ ++d  +l ++  p+p vevk++ ++ g +   +e Gel+vr p++   Y+++pe+t++a+d e++w++TGD
  gi|70607508|ref|YP_256378.1| 311 ISiipgkFQVNDDIDYLRTTTHPVPFVEVKVIKPD-GTEASYNEIGELYVRAPWLPGSYYNNPEETQRAYD-ENGWFKTGD 389
                                   5558999777788889******************9.88889*****************************9.767****** PP

                                   EEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 401 lgrldedGyleivgRkkdlikl 422
                                   l+ ++e+G l+iv+R+kd+ik+
  gi|70607508|ref|YP_256378.1| 390 LAIITEEGGLRIVDRLKDVIKS 411
                                   ********************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0     2e-21   1.8e-17       2      76 .]     421     500 ..     420     500 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 2e-21
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------....HHHHHHHHHHH.HT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea....leeeLkahvrk.elgpyavpkkvvfvdelpktrsGK 76 
                                   +Es++++ paV+++aV G pd+++Ge+++a+V lk+g++     + e L++ v+k ++ +++ p+k+vfvd +p+t +GK
  gi|70607508|ref|YP_256378.1| 421 LESIISEIPAVEQVAVLGYPDQKWGERPMAVVKLKPGQRTdqkeILEYLRDAVNKgRINKWWLPDKIVFVDNMPLTSTGK 500
                                   6**********************************996331234555555555336***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3325.53
//
Query:       gi|70607509|ref|YP_256379.1|  [L=201]
Description: pyrrolidone-carboxylate peptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-51  175.1   0.0    2.1e-51  175.0   0.0    1.0  1  Peptidase_C15  Pyroglutamyl peptidase


Domain annotation for each model (and alignments):
>> Peptidase_C15  Pyroglutamyl peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.0   1.2e-55   2.1e-51       1     198 [.       1     197 [.       1     201 [] 0.96

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 1.2e-55
                                   -EEEEEEE---TT-S--HHHHHHHHHTT-EETTEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT--SEEEE-E CS
                 Peptidase_C15   1 mkvLvtGfdPfgkekinPaleavkeLdgaeiaeativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrsaitverv 81 
                                   m vL+ Gf+Pf + + nP++ +v++L+g+ i++++i+  ++P+v+ k ++++ ++i + +p+++l iG a+Gr++it+e++
  gi|70607509|ref|YP_256379.1|   1 MTVLLFGFEPFSEYSENPSEIIVRNLNGNVIEGHKIIGVILPVVYDKLEEMVTQSIRRYQPNLILGIGLAPGRTKITPEKI 81 
                                   789****************************************************************************** PP

                                   EES-BE-SS--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHHHHHHHS--SEE CS
                 Peptidase_C15  82 ainldDaripDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvlylldkklpevra 162
                                   ain + +ripDn g    ++ i+ + +   fs+lPv ++v+ lk + +P+++s +aG ++Cn +++ vl  ++ k+  +r+
  gi|70607509|ref|YP_256379.1|  82 AINYKYSRIPDNMGVTYKGQRIDMNEPDGIFSNLPVEELVEYLKSKNIPSEISLSAGSYICNMTMFLVL--REAKGIGARG 160
                                   ******************************************************************986..5778999*** PP

                                   EEEEE-B-GGGTHH.HHHT-B--HHHHHHHHHHHHHH CS
                 Peptidase_C15 163 GfihiPylpeqvid.kpetpslsldkevagvkaaiea 198
                                   GfihiP+  + +i+ k +++ +sldk  ++++ ai+ 
  gi|70607509|ref|YP_256379.1| 161 GFIHIPCHEKCAIEsKRDMAFMSLDKMQEAINLAIQF 197
                                   **********99972567799*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1323.79
//
Query:       gi|70607510|ref|YP_256380.1|  [L=400]
Description: amidohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-44  153.1   0.0    1.4e-44  152.9   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    1.3e-12   48.0   0.0    1.7e-08   34.4   0.0    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.9   0.0   1.5e-48   1.4e-44       1     343 [.      49     390 ..      49     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 152.9 bits;  conditional E-value: 1.5e-48
                                   EEEE-EEEEEEECETTECSSS.GHHHHH.STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHT.SSSEEE CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.tledwl.vppetaaealesgiktalksGtttvadmgattstgiealleaaee.lplglr 78 
                                   +++PGlIDaH+H++   ++++  +++w  v++ ++a  + + ++t+l+sG+ttv+d g +    + +l +  ++  ++g+r
  gi|70607510|ref|YP_256380.1|  49 LIMPGLIDAHLHFF---GVEEdNVLSWNiVNEIDVAIRSTRDMETLLRSGFTTVRDLGSK---VAVRLDRLQRRgEIIGPR 123
                                   58***********8...555676666666******************************7...66666666666799**** PP

                                   EEEESSEGGS.........................GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                  Amidohydro_1  79 ilggkvsldr.........................gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                   ++++++sl+                          + +e++ka+r+++++g a +ik+ ++g+++   + +  p+f  +el
  gi|70607510|ref|YP_256380.1| 124 VIASGYSLAItggnddpkelpldfaqsisysfycdSPYECRKAVRKAIRQG-ATVIKVYSSGAFS--QGGRILPGFALDEL 201
                                   ***************************************************.8**********98..55566899999*** PP

                                   HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCE CS
                  Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagv 215
                                   k++++e ++++l va Ha + ++ + +++ a+++tiehg  l+        +++++i ++g+++ pt a++   ++   +v
  gi|70607510|ref|YP_256380.1| 202 KAIVEESHRAGLLVASHAYGKEALM-NSIMAGVDTIEHGLGLDE-------ETAQMIKERGICYIPTLATY---QIPFESV 271
                                   ********************99999.******************.......999*************4444...2222333 PP

                                   E...HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCG...GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                  Amidohydro_1 216 a...hcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnsl...nlleelrlalklqrgllyedeegglslkealrmaT 290
                                   +      ++++i r   e+++ a++ G+k+++gtD ++s + +   n     + a++l+r          +s  +alr++T
  gi|70607510|ref|YP_256380.1| 272 NpeaKMYREEMIRRHFNEDMKIAVEHGLKIATGTDYVGSKKRPhgqN----YIEAVLLSR---------YMSNIDALRAST 339
                                   36778899***********************************5544....444444444.........5*********** PP

                                   HHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGkl 343
                                     + ++lgl ++vG i +G++ADl++v +d+la++++l+++  +  v+++Gk+
  gi|70607510|ref|YP_256380.1| 340 SVASECLGL-RNVGYIRAGFKADLIAVRGDPLASLEELSPSH-IMYVVKDGKI 390
                                   *********.6***************************9965.9999999986 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   1.7e-05      0.15       9      41 ..      49      78 ..      48     100 .. 0.74
   2 !   34.4   0.0   1.9e-12   1.7e-08     257     471 ..     193     390 ..     166     392 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
                  Amidohydro_3  9 lvlPGFvDsHtHlagggvnl.rllrlpdarvtsl 41
                                  l +PG++D+H+H +g+     ++l+++   v+ +
  gi|70607510|ref|YP_256380.1| 49 LIMPGLIDAHLHFFGVE--EdNVLSWNI--VNEI 78
                                  579*********88864..446666666..5555 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.9e-12
                  Amidohydro_3 257 wpdfedealaelvaaadergldvaihaigdaavd.dvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqp 336
                                    p f  ++l+++v++ + +gl va ha+g +a++  +            + ++ ++eh+ g++e++++ +++ +++    +
  gi|70607510|ref|YP_256380.1| 193 LPGFALDELKAIVEESHRAGLLVASHAYGKEALMnSI------------MAGVDTIEHGLGLDEETAQMIKERGICYIPTL 261
                                   56778889**************************333............33333788888887777777777777654443 PP

                  Amidohydro_3 337 vfnf........edelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeels 409
                                   ++          e +++ ++    r++  + +k   ++g+k+a g+D  +    +  r ++ +        e +  ++ +s
  gi|70607510|ref|YP_256380.1| 262 ATYQipfesvnpEAKMYREEM--IRRHFNEDMKIAVEHGLKIATGTDYVG----SKKRPHGQNYI------EAVLLSRYMS 330
                                   333345555655555555554..789999******************222....22222222221......3345778899 PP

                  Amidohydro_3 410 leealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvrltvvdGrv 471
                                     +al++ T+ + + lgl+   G +++G++ADl+  + dpl+  ++ l    + ++v+dG++
  gi|70607510|ref|YP_256380.1| 331 NIDALRASTSVASECLGLRNV-GYIRAGFKADLIAVRGDPLASLEE-LSPSHIMYVVKDGKI 390
                                   99******************9.***************999999965.88888********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2776.15
//
Query:       gi|70607512|ref|YP_256381.1|  [L=492]
Description: sugar-related transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-39  134.4  25.4      7e-39  133.9  25.4    1.1  1  Sugar_tr      Sugar (and other) transporter
      3e-29  102.0  92.9    1.8e-25   89.6  53.2    3.5  2  MFS_1         Major Facilitator Superfamily
     0.0015   16.9  14.9      0.024   12.9   3.0    3.0  2  OATP          Organic Anion Transporter Polypeptide (OATP) fa
  ------ inclusion threshold ------
       0.01   15.7   0.0       0.01   15.7   0.0    4.0  4  DUF485        Protein of unknown function, DUF485
       0.24   10.6   1.4       0.56    9.3   0.7    2.0  2  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.9  25.4   1.9e-42     7e-39      10     448 ..      37     490 ..      27     492 .] 0.80

  Alignments for each domain:
  == domain 1  score: 133.9 bits;  conditional E-value: 1.9e-42
                                   HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                      Sugar_tr  10 llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfviga 90 
                                   l   Yd++ i++   ++++  ++  s+ +s++    +l+g  v + l+G +iGsl++++++d++GR+  l+i+ +++  g+
  gi|70607512|ref|YP_256381.1|  37 LFTFYDIFDINVSFIQTAVTIFHV-SSPSSPQIP--LLLGPAVLLNLIGYVIGSLVLSPVSDIIGRRRMLMITMIITGLGS 114
                                   44569******9999999555555.555556665..8******************************************** PP

                                   HHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-..... CS
                      Sugar_tr  91 vlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn..... 166
                                   + + + +    +  ++++R ++GigvG+  ++v +yi+E+Ap++ R + +sl  l+ t+G  +++++gl l +  +     
  gi|70607512|ref|YP_256381.1| 115 LYNTFVN---DYLNFVMARTITGIGVGADLAIVNTYIGEVAPTNGRAKYTSLVFLFSTLGATLGIWLGLLLTTPPApfplg 192
                                   *******...89999999*****************************************************999999**** PP

                                   ............TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHC....HHHHHHHHHHHHHH CS
                      Sugar_tr 167 ............adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrge....edadrelaeekdsl 231
                                                +gwr++ g+ +++al+ l+l++ lPESPr+l+++++ +ea++++  ++++     ++ ++l + ++ +
  gi|70607512|ref|YP_256381.1| 193 lpfalglsgffaVNGWRVMYGIGALLALVGLLLRFSLPESPRWLISRNRISEAEKIVNMMEDKatkkLKQLPSLPKVITPY 273
                                   ***********999********************************************96666444344455666777777 PP

                                   HHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH.HHHHHHHHHHHHHHHHHH.HHH CS
                      Sugar_tr 232 eaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks.llvtiivgvvnfvatfva.ifl 310
                                     e+ +   ++k+++s+ ++ +r++i + +++f  +t +     + ++++ +lg+ ++ + + + +g + f+ +    + +
  gi|70607512|ref|YP_256381.1| 274 LSEMLSYADTLKTIFSNSQYVKRFVILFTMWLFGYMTVYTLAAGL-TSVLASLGYPPPeAGIIAAMGSIGFILVPLTtFAV 353
                                   77777669999******99**************999987766665.788899******64444455666666666653456 PP

                                   HHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHH CS
                      Sugar_tr 311 vdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaia 391
                                    dr+ R+    +++++ ++  +++   al++++      +v+ ++ ++ +  f+  w p+ +   +E fp++ Rs++ a++
  gi|70607512|ref|YP_256381.1| 354 GDRLERKVWTAISVIFTFLGGLLI---ALAGTNV-----VVSFIGSIILFYGFN-LWVPISYAWTAESFPTRARSTGFALC 425
                                   699999955555555544444444...4555555.....333333333335555.6************************* PP

                                   HHHHHHHHHHHHHHHHHHHCHHH........T-HHHHHHHHHHHHHHHHHHHHS--STT--CCCC CS
                      Sugar_tr 392 vavnwlanflisllfpiiteaig........ggyvflvfaglavlfiifvfffvpetkgrtleei 448
                                     +  +   +  +++  + +++         +  vf++ +++ ++++++       t+++ l+ei
  gi|70607512|ref|YP_256381.1| 426 DGIGHVGGGIGLIIIASFISSLLssgvttglAVEVFVIIGVFQLISTLIAISSGHKTANKRLDEI 490
                                   99998888777666665555554455565555677777777777777777777777777777776 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6  53.2     5e-29   1.8e-25       3     352 ..      34     436 ..      24     436 .. 0.81
   2 !   26.5  31.7     8e-10   2.9e-06       7     168 ..     306     475 ..     299     486 .. 0.83

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 5e-29
                         MFS_1   3 laaflsalarsilgpalplalaedlgispse.......igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgl 76 
                                   +++++++++++ +++++ ++  + +++s  +       +g ++ l  +g++++sl+l+++sd +Grrr+l++++++++lg+
  gi|70607512|ref|YP_256381.1|  34 IGFLFTFYDIFDINVSFIQTAVTIFHVSSPSspqipllLGPAVLLNLIGYVIGSLVLSPVSDIIGRRRMLMITMIITGLGS 114
                                   444455555555777777777778885555556655555559999***********************************7 PP

                         MFS_1  77 llllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg....... 149
                                   l+ +f  + +  ++ +r ++G+g ga +++++++i +++p + r+++++l+ +++ lGa lg  lg ll++          
  gi|70607512|ref|YP_256381.1| 115 LYNTF-VNDYlNFVMARTITGIGVGADLAIVNTYIGEVAPTNGRAKYTSLVFLFSTLGATLGIWLGLLLTTPPApfplglp 194
                                   77778.555548*******************************************************99955558999999 PP

                         MFS_1 150 .............Wravfyilaivsllafvlfllllpeepperkrkspkeee...................kgtgpaplvp 198
                                                Wr+++ i a+++l++++   l +  ++++r+  s  + +                         p +p
  gi|70607512|ref|YP_256381.1| 195 falglsgffavngWRVMYGIGALLALVGLL---LRFSLPESPRWLISRNRISeaekivnmmedkatkklkqL-----PSLP 267
                                   9999999999999**************977...777777777777766555577999999988877555331.....2222 PP

                         MFS_1 199 ...............awkallkdpvlw....illialllfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                                   +k ++++ +      il++++l++ + +++l + l++     lg++   +ag ++a+++ +g+il
  gi|70607512|ref|YP_256381.1| 268 kvitpylsemlsyadTLKTIFSNSQYVkrfvILFTMWLFGYMTVYTLAAGLTSV-LASLGYP-PPEAG-IIAAMGSIGFIL 345
                                   555677778888888888888888663334568888888888888899999996.99*****.56666.577777777788 PP

                         MFS_1 261 allagrls.drlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfvfpsllalasdlappeeagtasg 339
                                    +l+++ + drl r+  + +++++++l+ l++al+++    v++ ++++++ f g+ + +p++ a++++++p++++ t ++
  gi|70607512|ref|YP_256381.1| 346 VPLTTFAVgDRLERKVWTAISVIFTFLGGLLIALAGTN--VVVSFIGSIIL-FyGFNLWVPISYAWTAESFPTRARSTGFA 423
                                   899999999*****999999999999999999999999..44444444444.44888889********************* PP

                         MFS_1 340 lfntagslggalg 352
                                   l   +g++gg +g
  gi|70607512|ref|YP_256381.1| 424 LCDGIGHVGGGIG 436
                                   *********9987 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 8e-10
                         MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslw 86 
                                   + +++ ++l++ l+  +  +lg+ p e+g+++++ ++g+++  l + +++dr+ r+ +  +++++++lg+ll+++a +++ 
  gi|70607512|ref|YP_256381.1| 306 FGYMTVYTLAAGLT-SVLASLGYPPPEAGIIAAMGSIGFILVPLTTFAVGDRLERKVWTAISVIFTFLGGLLIALAgTNVV 385
                                   44555555666666.88899*********************************8888************777777779988 PP

                         MFS_1  87 .lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslg.......Wravfyila 158
                                     ++ + +l   +  + +p+++a++a+ fp + r+ +++l  +   +G  +g  +++++++s+l+          vf+i++
  gi|70607512|ref|YP_256381.1| 386 vSFIGSIILFYGF-NLWVPISYAWTAESFPTRARSTGFALCDGIGHVGGGIGlIIIASFISSLLSsgvttglAVEVFVIIG 465
                                   6666666666665.79************************************77778888888888887776556699999 PP

                         MFS_1 159 ivsllafvlf 168
                                   ++ l++ +++
  gi|70607512|ref|YP_256381.1| 466 VFQLISTLIA 475
                                   9988887754 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   1.9   4.2e-05      0.15     134     193 ..     125     184 ..     104     294 .. 0.73
   2 !   12.9   3.0   6.7e-06     0.024       2      86 ..     297     380 ..     296     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.2e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                    f++a ++ GiG  +  ++  +Yi + + ++  + y ++++ +++lG  lG  lG ll+ 
  gi|70607512|ref|YP_256381.1| 125 NFVMARTITGIGVGADLAIVNTYIGEVAPTNGRAKYTSLVFLFSTLGATLGIWLGLLLTT 184
                                   79*****************************************************98876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.7e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP   2 flvllsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsll 82 
                                   f++l+ +  +  ++v+++    +t++    ++p  + g+ia++  ig il+ l    +g+r  r  w +i+++++ lg ll
  gi|70607512|ref|YP_256381.1| 297 FVILFTMWLFGYMTVYTL-AAGLTSVLASLGYPPPEAGIIAAMGSIGFILVPLTTFAVGDRLERKVWTAISVIFTFLGGLL 376
                                   666776666666666665.55678888899*********************999999************************ PP

                                   xxxx RF
                          OATP  83 lalP 86 
                                   +al 
  gi|70607512|ref|YP_256381.1| 377 IALA 380
                                   *985 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.92   3.3e+03      51      61 ..     172     182 ..     160     204 .. 0.65
   2 ?   -3.2   5.5       2.4   8.7e+03      19      42 ..     296     319 ..     288     353 .. 0.59
   3 ?   -1.4   0.3      0.66   2.4e+03      33      58 ..     348     372 ..     331     391 .. 0.59
   4 ?   15.7   0.0   2.9e-06      0.01      29      83 ..     435     490 ..     416     491 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.92
                        DUF485  51 itvglllgllq 61 
                                    t+g++lgll+
  gi|70607512|ref|YP_256381.1| 172 ATLGIWLGLLL 182
                                   35555555543 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                        DUF485  19 pltaiflvvYfgfvllvafapdll 42 
                                    ++++f ++ fg++ + ++a +l 
  gi|70607512|ref|YP_256381.1| 296 RFVILFTMWLFGYMTVYTLAAGLT 319
                                   455666666666666655554443 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.66
                        DUF485  33 llvafapdllatkvgegnitvglllg 58 
                                   l++    d l++kv+  +i+v + + 
  gi|70607512|ref|YP_256381.1| 348 LTTFAVGDRLERKVW-TAISVIFTFL 372
                                   333334567777777.5566655443 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 2.9e-06
                        DUF485  29 fgfvllvafapdllatkvgeg.nitvglllgllqivltflltglYvrrAnrefDpl 83 
                                   +g++++++f  +ll+  v+ g ++ v +++g++q+++t +++    + An+++D+ 
  gi|70607512|ref|YP_256381.1| 435 IGLIIIASFISSLLSSGVTTGlAVEVFVIIGVFQLISTLIAISSGHKTANKRLDEI 490
                                   589**************************************************985 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7   0.00016      0.56     102     173 ..     268     342 ..     261     393 .. 0.81
   2 ?    1.9   0.7     0.029   1.1e+02      27      91 ..     294     383 ..     291     476 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                                   XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX CS
                  Bac_export_2 102 kalkpklsk.lnplkglkrifslrslvellksllkvvlvgavaylvlkseleellalaeldle..aalelllsll 173
                                   k ++p ls+ l+ +  lk ifs ++ v+ +  l+ + l+g++++++l + l ++la + +++    ++++++s+ 
  gi|70607512|ref|YP_256381.1| 268 KVITPYLSEmLSYADTLKTIFSNSQYVKRFVILFTMWLFGYMTVYTLAAGLTSVLASLGYPPPeaGIIAAMGSIG 342
                                   677777776589999**********************************99999988877766222333333333 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.029
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..............................XXXXXXXXXXXXXXXX CS
                  Bac_export_2  27 lssalvllaglllllllgpslveelaellrevlsa..............................lelllelllallllll 77 
                                   ++ +++l++++l+ ++++ +l++ l+++l+++                                      + +++++ +++
  gi|70607512|ref|YP_256381.1| 294 VKRFVILFTMWLFGYMTVYTLAAGLTSVLASLG-YpppeagiiaamgsigfilvplttfavgdrlE----RKVWTAISVIF 369
                                   555666666666666666666666666555533.25887777777777777776666655533332....33333333333 PP

                                   XXXXXXXXXXXXXX CS
                  Bac_export_2  78 plllvlllaallan 91 
                                   ++l  ll+a + +n
  gi|70607512|ref|YP_256381.1| 370 TFLGGLLIALAGTN 383
                                   33322222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 3511.67
//
Query:       gi|70607511|ref|YP_256382.1|  [L=138]
Description: hypothetical protein Saci_1783 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 926.78
//
Query:       gi|70607513|ref|YP_256383.1|  [L=516]
Description: hypothetical protein Saci_1784 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-18   66.6  32.5    1.5e-17   63.9  32.5    2.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    3.7e-07   30.3   3.6    3.7e-07   30.3   3.6    2.6  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.7e-05   23.4  24.7    3.7e-05   23.4  24.7    3.4  3  ABC2_membrane_5  ABC-2 family transporter protein
    0.00013   22.0  15.7    0.00013   22.0  15.7    2.8  3  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.13   12.3   8.5        1.1    9.3   1.7    3.0  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.89    8.6  45.0        4.1    6.4  44.9    2.0  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9  32.5   4.9e-21   1.5e-17      76     286 ..     287     514 ..       4     516 .] 0.76

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 4.9e-21
               ABC2_membrane_2  76 v.................vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iaval 138
                                   +                   +++++++p++ + +++ ++a+ +++g lk+lL++Pv+R+++ +   i+g++ +l+  +v  
  gi|70607513|ref|YP_256383.1| 287 RfypygyvtdyvitttyaQLLPFSFIFPIMMLYLSYAIFAKPRDSGALKFLLARPVTRRDVFINRYISGVLTALIiAIVFS 367
                                   04444444555445544456899************************************************9666444444 PP

               ABC2_membrane_2 139 latvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvael 219
                                   l++    + i l+ g  ++l  +l + ++ ++++l v+f++l++l+ ++++ss   + ++++lf+++ i ++i+++ ++  
  gi|70607513|ref|YP_256383.1| 368 LVS---LVTIELIIGARIPLIPILPISLS-LFVGL-VAFFSLTYLFPTFIKSSGGYLGISIFLFLLFTIGYSIIGAILGLY 443
                                   555...55688889999999988766543.33444.358************************************665544 PP

               ABC2_membrane_2 220 lagpavpqeindflsllsptsayntllneilagsdlna......lgstatnllilllllavllvlgyvlFkrk 286
                                    +   +  + +  l +++p   ++++   + +  +           + +  +l+++l++av+l+lgy +F++ 
  gi|70607513|ref|YP_256383.1| 444 TN-LGI-VKAQYVLGYFNPLGIFQFGEYYVDKLIGAGLvsdasgVVILPLVVLSSVLWIAVPLILGYMRFRKV 514
                                   44.444.588999***********99988888776444778999999***********************996 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   3.6   1.2e-10   3.7e-07       2      61 ..      59     131 ..      58     149 .. 0.80
   2 ?   -1.2   0.3      0.82   2.5e+03      18      47 ..     262     290 ..     252     310 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.2e-10
               CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtg.............tvastttdadGafrlrglppgtysvtvsapGyat 61 
                                   i G+V d sg+pi+ga+V+v+++++              ++++ttt+++G f  + +p gt++  v++ G   
  gi|70607513|ref|YP_256383.1|  59 IIGYVFDNSGKPISGASVVVFSEAEVaqannglgfrpvnETSQTTTNSSGMFITSVVPNGTITCNVTYGGKTV 131
                                   77*******************86642445566777776689************999999********998654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.82
               CarboxypepD_reg  18 tVtvtnadtgtvastttdadGafrlrglpp 47 
                                    V++ n +++t+++ t  ++G+f ++   p
  gi|70607513|ref|YP_256383.1| 262 VVEILN-SSSTNTGNTGSSSGSFGFSRFYP 290
                                   566664.55556666666778887776555 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.11   3.2e+02     146     167 ..      13      37 ..       2      60 .. 0.45
   2 ?    0.0   0.1      0.18   5.3e+02     111     156 ..      96     141 ..      72     192 .. 0.75
   3 !   23.4  24.7   1.3e-08   3.7e-05      29     167 ..     298     438 ..     292     501 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
               ABC2_membrane_5 146 gri...vliiiifgiifllvaifsl 167
                                   +r+   +l+i++++i+++l  ++++
  gi|70607513|ref|YP_256383.1|  13 IRLsvvILLIVSVLIAVGLGYLVKS 37 
                                   4432212222222233333223332 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.18
               ABC2_membrane_5 111 vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifg 156
                                   v+  +  +++  g +i++++   ++++   +g +++++++++i+ +
  gi|70607513|ref|YP_256383.1|  96 VNETSQTTTNSSGMFITSVVPNGTITCNVTYGGKTVTLISFLISSV 141
                                   5555666677777777788888888888888888888888777765 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1.3e-08
               ABC2_membrane_5  29 liflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllllii.avlik 108
                                   +i++++  ll fs+++++++ +l   ++++ + s+  k+ll  Pvtr+++ + +Y+++++  li  ++++l++++ ++li 
  gi|70607513|ref|YP_256383.1| 298 VITTTYAQLLPFSFIFPIMMLYLSYAIFAKPRDSGALKFLLARPVTRRDVFINRYISGVLTALIIAIVFSLVSLVtIELII 378
                                   45555666688999999999999*************************************998888888888765466666 PP

               ABC2_membrane_5 109 gn.vtisevllsiliglvialiflaiv..lPlyfkfgvekgrivliiiifgiif.llvaifsl 167
                                   g  + + ++l  +l  +v  ++f++++  +P ++k +   g ++ i i++++ f ++++i+  
  gi|70607513|ref|YP_256383.1| 379 GArIPLIPILPISLSLFVGLVAFFSLTylFPTFIKSS---GGYLGISIFLFLLFtIGYSIIGA 438
                                   6567777877777777776666655550156666655...44444444444333355555543 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.33   9.8e+02      19      33 ..      17      31 ..       5      55 .. 0.47
   2 !   22.0  15.7   4.2e-08   0.00013      50     177 ..     303     429 ..     281     432 .. 0.76
   3 ?    0.3   0.4      0.19   5.8e+02     103     148 ..     420     465 ..     417     467 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
               ABC2_membrane_4 19 vlaallvpllallyf 33
                                  v+++l+v +l+ +  
  gi|70607513|ref|YP_256383.1| 17 VVILLIVSVLIAVGL 31
                                  222222222222222 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.2e-08
               ABC2_membrane_4  50 svfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfs 130
                                   +++ + + +++p+++  ++  ++ + ++++ lk Ll +Pv+r+ +++  +i  +l+++++ +v+ l+++++  l+ ++++ 
  gi|70607513|ref|YP_256383.1| 303 YAQLLPFSFIFPIMMLYLSYAIFAKPRDSGALKFLLARPVTRRDVFINRYISGVLTALIIAIVFSLVSLVTIELIIGARIP 383
                                   455566789*******************************************99999999999999999988888888887 PP

               ABC2_membrane_4 131 vklvlellkkclelgllvffavlpiialvllkk.syvlpliltlvyti 177
                                     ++l +   +l +gl+ f ++l  ++ +++k+ +  l++ + l++ +
  gi|70607513|ref|YP_256383.1| 384 LIPILPISL-SLFVGLVAF-FSLTYLFPTFIKSsGGYLGISIFLFLLF 429
                                   666666433.455555444.4554555565554145777777777665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.19
               ABC2_membrane_4 103 lllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllv 148
                                    + ++l++l+t   +++ a+l  ++++ + +  ++l  +  lg++ 
  gi|70607513|ref|YP_256383.1| 420 GISIFLFLLFTIGYSIIGAILGLYTNLGIVKAQYVLGYFNPLGIFQ 465
                                   4556677777777777777777778888888778887777777765 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0031       9.3       2      24 ..      60      81 ..      59      90 .. 0.77
   2 ?    9.3   1.7   0.00037       1.1      24      71 ..      98     145 ..      96     157 .. 0.82
   3 ?   -3.1   0.1       2.7   8.2e+03      23      40 ..     270     287 ..     258     295 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0031
               CarbopepD_reg_2  2 sGtVvdketkeplpgatVyvkgt 24
                                   G V+d++ ++p+ ga+V+v + 
  gi|70607513|ref|YP_256383.1| 60 IGYVFDNS-GKPISGASVVVFSE 81
                                  599**976.68*******99655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00037
               CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                    + +t+T+++G F  + +p+g+ t +v+y G +   ++  +s+ +t+d
  gi|70607513|ref|YP_256383.1|  98 ETSQTTTNSSGMFITSVVPNGTITCNVTYGGKTVTLISFLISSVTTTD 145
                                   5778*************************9998887777777666665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.7
               CarbopepD_reg_2  23 gtkkgtvTdenGnFelkn 40 
                                   +t++g +  ++G+F +++
  gi|70607513|ref|YP_256383.1| 270 STNTGNTGSSSGSFGFSR 287
                                   578888888999998765 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  44.9    0.0014       4.1       4     290 ..      18     439 ..      14     506 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
               ABC2_membrane_3   4 liitlllPiilvlllglifsnsve..ddentpi...........avvdedn......sslsqqlv................ 49 
                                   +i+ +++++i v+l++l+ s+ ++  +  n+++           +v d+++      s      v                
  gi|70607513|ref|YP_256383.1|  18 VILLIVSVLIAVGLGYLVKSSLSStnNLGNINVvattsgdkiigYVFDNSGkpisgaS------Vvvfseaevaqannglg 92 
                                   5556666666666666665533333456666655444444445444444444332220......23355555555555555 PP

               ABC2_membrane_3  50 ................................................................................. 49 
                                                                                                                    
  gi|70607513|ref|YP_256383.1|  93 frpvnetsqtttnssgmfitsvvpngtitcnvtyggktvtlisflissvtttdyalssgtvtyssyssysgetrsrgglvv 173
                                   555555555555555555555555555555554444444444444444444444444444444444444444444444444 PP

               ABC2_membrane_3  50 ....ealeaspsvelvyevdseeeakkalkngdidgilvipkgfskdll................................ 94 
                                       +                                           +                                
  gi|70607513|ref|YP_256383.1| 174 gtseT-------------------------------------------Mystpssivasyavtgnkelivasnvygsnlkl 211
                                   44433...........................................044444444444444444444444443333334 PP

               ABC2_membrane_3  95 .........kgesatvtvlinssnlnsskailnalnsllqqlnasalv.............lqseatstsaninvestqle 153
                                            ++ + +++ l n+  l+ + ++++++n++   +++++ +             ++ +++s+s ++++  +  +
  gi|70607513|ref|YP_256383.1| 212 yvgfmnsmpSNVTLNISSLPNYVKLTYVGTVNSYINTYDIGNLNAN-GsyivveilnssstNTGNTGSSSGSFGFSRFYPY 291
                                   4443333225555566666666666666888899888433322222.2244444444433333344444444444444444 PP

               ABC2_membrane_3 154 eelsnvasf.....lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.. 227
                                    + ++++ +     l+++ +i++i++ +++ a  +++ + s++++++l  +v++   ++ ++++ +l +l++++++ l+  
  gi|70607513|ref|YP_256383.1| 292 GYVTDYVITttyaqLLPFSFIFPIMMLYLSYA-IFAKPRDSGALKFLLARPVTRRDVFINRYISGVLTALIIAIVFSLVsl 371
                                   44444433366566777777777777777666.48*********************9999999999999999999887431 PP

               ABC2_membrane_3 228 .....afglgipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpl 290
                                        ++g  ip   ++ + l +++++ a+ +l+yl+ +++k+s+   ++ ++++ll+ + + +++ +
  gi|70607513|ref|YP_256383.1| 372 vtielIIGARIPLIPILPISLSLFVGLVAFFSLTYLFPTFIKSSGGYLGISIFLFLLFTIGYSIIGAI 439
                                   22233555478888888888************************999988888888666666666543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3244.46
//
Query:       gi|70607514|ref|YP_256384.1|  [L=533]
Description: hypothetical protein Saci_1785 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-20   72.5   0.1    1.9e-19   69.9   0.0    2.3  3  B12-binding  B12 binding domain
    1.6e-15   57.8   0.0      4e-15   56.6   0.0    1.7  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.088   12.9   0.1       0.25   11.5   0.1    1.8  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   3.1e-23   1.9e-19       8     120 ..      20     134 ..      13     135 .. 0.94
   2 ?   -1.3   0.0      0.35   2.1e+03      23      46 ..     297     320 ..     291     327 .. 0.81
   3 ?   -2.3   0.0      0.71   4.3e+03      41      62 ..     364     384 ..     329     385 .. 0.67

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.1e-23
                   B12-binding   8 vggdlhplGlavlaaalrd.agfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirprvkv 84 
                                   +g+   plGl +la+ lr+  ++++++++++++     d+++ +++ +p++vg++++ t++++  ++l++ +k++ ++  +
  gi|70607514|ref|YP_256384.1|  20 FGFMPTPLGLLQLAGDLRAvGNWDIKVVDMEADSlsvSDVISLAKSYDPEIVGITLHATASHNISTQLAKGIKQELNDSLI 100
                                   5666689************669***********9*********************************************** PP

                   B12-binding  85 vvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   ++GG+h+++ p ++l+  +g+d+vv+geg+ ++ ++
  gi|70607514|ref|YP_256384.1| 101 IAGGHHATFVPSQMLA--EGFDIVVLGEGDLTMMEI 134
                                   ***************7..8***********999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                   B12-binding  23 alrdagfeVqllganvenedivaa 46 
                                     +dag +V +lg++   ++++++
  gi|70607514|ref|YP_256384.1| 297 LASDAGLRVAFLGIESGSQETLKK 320
                                   67899********99988777765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.71
                   B12-binding  41 edivaairaekpdvvglSallt 62 
                                    ++ +++++  +d v +S+ +t
  gi|70607514|ref|YP_256384.1| 364 IKFSRKLADVGADGVQFSI-YT 384
                                   5667788888888888888.65 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.0   6.6e-19     4e-15       2     166 ..     202     366 ..     201     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 6.6e-19
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   ++ rgC+++C fC+++ t  ++ ++r++s  +il+e++e+ ++ g + ++++ +  +++p+  +  +  ++  +++++i +
  gi|70607514|ref|YP_256384.1| 202 ETARGCPYACDFCSVTPT--WGNKWRNKSNSRILKEIEEI-KKLGYNWIFFVDDIFIVWPNRSQREKLFREMIDRKLTINF 279
                                   789**************8..********************.6998888888888777776555444444444334444444 PP

                                   EECSSCHG.....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                   xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd.....eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGende 158
                                   +t     d     +  +++  ++g+ +  lg+e+++ e +lk+m++g  + + ++a++ l+e+g+ +   +++g p e+ +
  gi|70607514|ref|YP_256384.1| 280 ITQIRA-DvtarnPQLIKLASDAGLRVAFLGIESGSQE-TLKKMHKGLAIPDSVKAVKVLHENGVIVFLGMMLGAPYESLK 358
                                   444444.23667799***********************.99999999*******************999999999999999 PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                   Radical_SAM 159 eleellel 166
                                   ++ +++++
  gi|70607514|ref|YP_256384.1| 359 DMIATIKF 366
                                   99999887 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.1e-05      0.25       7      43 ..     206     241 ..     201     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                       Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkk 43 
                                   gC+ +C +C  + tw +++ +++++++l++i  + kk
  gi|70607514|ref|YP_256384.1| 206 GCPYACDFCSVTPTWGNKWRNKSNSRILKEIE-EIKK 241
                                   9**************************96654.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3486.36
//
Query:       gi|70607515|ref|YP_256385.1|  [L=95]
Description: hypothetical protein Saci_1786 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.017   14.9   8.4      0.021   14.6   8.4    1.2  1  7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
      0.018   14.8   4.4      0.018   14.8   4.4    1.8  2  PGG          Domain of unknown function
      0.023   14.6   0.0      0.052   13.4   0.0    1.6  1  DUF2633      Protein of unknown function (DUF2633)
       0.58   10.1   8.2      0.076   13.0   3.7    1.7  2  DUF2678      Protein of unknown function (DUF2678)
        5.3    7.3   8.8        0.9    9.8   1.3    2.6  3  MHYT         Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   8.4   5.9e-06     0.021       1      77 [.       5      83 ..       5      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                   7TM-7TMR_HD  1 wlsllgllllvlllllilllflrrfrkelrernkkllllslllllvlllskl....vvlissiesiiylvplaavalLlsl 77
                                  w++ ++l+++ +++ ++++l ++  rke+  + + +lll+++lll+ +++ +    ++ ++   + +y++p  a+a++ ++
  gi|70607515|ref|YP_256385.1|  5 WYIHISLAIVSAIFSILIFLEFKSLRKEFHGKLSGVLLLISVLLLFESVVNAvafsMWSYG--HDPVYVYPSMAIAIVSTS 83
                                  78999*********************************99999999999999555555555..899999999999887665 PP

>> PGG  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   4.4   5.1e-06     0.018      53     114 ..       2      64 ..       1      65 [. 0.91
   2 ?   -0.0   0.7      0.21   7.5e+02      61      74 ..      76      88 ..      69      95 .] 0.45

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                           PGG  53 fkvFvisnaiAlvaSlvvvvlll.isslvedeakslpkklrvllvllvlsllsllvaFaagly 114
                                   f++++i  ++A+v+++ +++++l ++sl ++++ +l   l ++ vll+++ ++ +vaF + +y
  gi|70607515|ref|YP_256385.1|   2 FELWYIHISLAIVSAIFSILIFLeFKSLRKEFHGKLSGVLLLISVLLLFESVVNAVAFSMWSY 64 
                                   8999*******************555669999**************************98665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                           PGG 61 aiAlvaSlvvvvll 74
                                  aiA+v+  +v++l+
  gi|70607515|ref|YP_256385.1| 76 AIAIVST-SVIILF 88
                                  3443333.333333 PP

>> DUF2633  Protein of unknown function (DUF2633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.052       2      28 ..      30      56 ..      29      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                       DUF2633  2 RrRfntrlTrivLliSFLflFGRllYs 28
                                  R+ f ++l  ++LliS L+lF  ++ +
  gi|70607515|ref|YP_256385.1| 30 RKEFHGKLSGVLLLISVLLLFESVVNA 56
                                  889******************988866 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.32   1.2e+03      70      80 ..      13      23 ..       4      44 .. 0.55
   2 ?   13.0   3.7   2.1e-05     0.076      37      82 ..      44      91 ..      30      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                       DUF2678 70 lisssvivlif 80
                                  ++s+   +lif
  gi|70607515|ref|YP_256385.1| 13 IVSAIFSILIF 23
                                  22222223333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.1e-05
                       DUF2678 37 ltsllvlvtvvssfvfps..lppkplniffavcillisssvivlifwy 82
                                  ++ ll++++vv ++ f        p+ ++ ++ i ++s+svi+l ++y
  gi|70607515|ref|YP_256385.1| 44 ISVLLLFESVVNAVAFSMwsYGHDPVYVYPSMAIAIVSTSVIILFYYY 91
                                  4567788999999998751156799*********************99 PP

>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.07   2.5e+02      32      52 ..       9      29 ..       2      36 .. 0.64
   2 ?    0.4   0.2      0.21   7.4e+02      28      37 ..      42      51 ..      32      63 .. 0.48
   3 ?    9.8   1.3   0.00025       0.9      14      44 ..      56      87 ..      54      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.07
                          MHYT 32 lliaivasvlAlalavrrrdt 52
                                  + +aiv++++ ++++   ++ 
  gi|70607515|ref|YP_256385.1|  9 ISLAIVSAIFSILIFLEFKSL 29
                                  446777777777766555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                          MHYT 28 talSlliaiv 37
                                   ++S+l+ + 
  gi|70607515|ref|YP_256385.1| 42 LLISVLLLFE 51
                                  4555433332 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00025
                          MHYT 14 Aftlpg.pigydpaltalSlliaivasvlAla 44
                                  A+ +++   g+dp ++  S++iaiv+  + ++
  gi|70607515|ref|YP_256385.1| 56 AVAFSMwSYGHDPVYVYPSMAIAIVSTSVIIL 87
                                  6677777899***************9977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 643.22
//
Query:       gi|70607516|ref|YP_256386.1|  [L=99]
Description: hypothetical protein Saci_1787 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-11   42.0   0.8    7.5e-11   41.7   0.2    1.5  2  HTH_5     Bacterial regulatory protein, arsR family
     0.0011   18.9   0.6      0.002   18.0   0.4    1.5  1  HTH_45    Winged helix-turn-helix
     0.0022   17.9   0.2     0.0051   16.7   0.0    1.7  2  HTH_11    HTH domain
     0.0023   17.8   0.0     0.0044   16.9   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0052   16.3   1.7     0.0056   16.2   0.1    1.9  2  HTH_24    Winged helix-turn-helix DNA-binding
     0.0065   16.0   0.1      0.012   15.1   0.1    1.4  1  GerE      Bacterial regulatory proteins, luxR family
     0.0069   16.8   0.3     0.0098   16.3   0.0    1.5  2  HTH_40    Helix-turn-helix domain
     0.0098   15.9   0.0      0.016   15.2   0.0    1.4  1  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.048   13.8   0.0      0.093   12.9   0.0    1.5  1  HTH_28    Helix-turn-helix domain
      0.059   12.3   0.1      0.064   12.2   0.1    1.1  1  TnsD      Tn7-like transposition protein D
      0.061   13.4   0.5       0.19   11.8   0.1    1.9  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
       0.09   13.0   2.0       0.12   12.6   2.0    1.2  1  MSV199    MSV199 domain


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.7     1e+04       6      11 ..      11      16 ..      10      17 .. 0.78
   2 !   41.7   0.2     5e-14   7.5e-11       2      45 ..      24      67 ..      23      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.7
                                  HHHHHH CS
                         HTH_5  6 kILklL 11
                                  kILk+L
  gi|70607516|ref|YP_256386.1| 11 KILKFL 16
                                  799888 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 5e-14
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  +tRl+I+klL+ ++l + ++ae+l+l+  tv hHL +L+e ++V
  gi|70607516|ref|YP_256386.1| 24 KTRLEIVKLLEFNSLNANQIAEKLNLNYKTVIHHLEVLMENRIV 67
                                  79****************************************99 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   1.4e-06     0.002      10      56 ..      28      74 ..      23      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekY 56
                                  +I + ++ ++ +  +i  k nL+yk++   L+ L+e+ ++ k+++ Y
  gi|70607516|ref|YP_256386.1| 28 EIVKLLEFNSLNANQIAEKLNLNYKTVIHHLEVLMENRIVVKEGDGY 74
                                  555666677889999*************************9988777 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.2   3.2e+03       3       9 ..      10      16 ..       6      20 .. 0.61
   2 !   16.7   0.0   3.4e-06    0.0051       3      54 ..      27      74 ..      25      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.2
                        HTH_11  3 lqilelL 9 
                                  ++il++L
  gi|70607516|ref|YP_256386.1| 10 KKILKFL 16
                                  4555555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.4e-06
                        HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGY 54
                                  l i++lL e ++ ++++++Ae+Ln+  +tv  +++ L e   +I+ + g GY
  gi|70607516|ref|YP_256386.1| 27 LEIVKLL-EFNS-LNANQIAEKLNLNYKTVIHHLEVLMEN--RIVVKEGDGY 74
                                  6788888.5555.************************888..4666666677 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     3e-06    0.0044      16      55 ..      31      70 ..      29      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  +Ll+  +++a++iae+l++ + +v   L+ L++  +V +e
  gi|70607516|ref|YP_256386.1| 31 KLLEFNSLNANQIAEKLNLNYKTVIHHLEVLMENRIVVKE 70
                                  79******************************99888777 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       1.6   2.4e+03       4      12 ..       8      16 ..       6      16 .. 0.75
   2 !   16.2   0.1   3.7e-06    0.0056      17      47 ..      37      67 ..      24      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                        HTH_24  4 tdrkILelL 12
                                    +kIL+ L
  gi|70607516|ref|YP_256386.1|  8 QIKKILKFL 16
                                  678999876 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.7e-06
                        HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +++ +++Ae+l+l   tv  +l+ L+e+ ++
  gi|70607516|ref|YP_256386.1| 37 SLNANQIAEKLNLNYKTVIHHLEVLMENRIV 67
                                  68899*********************98776 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     8e-06     0.012      20      43 ..      40      63 ..      35      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8e-06
                                  HHHHHHHHTS-HHHHHHHHHHHHH CS
                          GerE 20 nkeIAeelniSekTVkvhksnimk 43
                                   ++IAe+ln+ +kTV  h++ +m+
  gi|70607516|ref|YP_256386.1| 40 ANQIAEKLNLNYKTVIHHLEVLME 63
                                  58****************998885 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.3   9.4e+03      53      61 ..       5      13 ..       2      16 .. 0.54
   2 !   16.3   0.0   6.6e-06    0.0098      11      39 ..      36      64 ..      25      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.3
                        HTH_40 53 eekeIeeai 61
                                  e+k+I++++
  gi|70607516|ref|YP_256386.1|  5 ERKQIKKIL 13
                                  455555544 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.6e-06
                        HTH_40 11 eglsieeIAkerglkesTIegHLaeliee 39
                                  ++l+  +IA++ +l+ +T++ HL  l+e+
  gi|70607516|ref|YP_256386.1| 36 NSLNANQIAEKLNLNYKTVIHHLEVLMEN 64
                                  678999*****************999988 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.016      11      59 ..      25      72 ..      22      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                        HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                  +R++i ++L +   l a+++ae l l  +t+ +HL+vL e  +v  ++ 
  gi|70607516|ref|YP_256386.1| 25 TRLEIVKLL-EFNSLNANQIAEKLNLNYKTVIHHLEVLMENRIVVKEGD 72
                                  899999999.999*************************99999877765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05     0.093       2      29 ..      26      54 ..      25      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                        HTH_28  2 Rleiiklla.aGhsvreaArelgisrrtv 29
                                  Rlei+kll  +  +++++A++l++++ tv
  gi|70607516|ref|YP_256386.1| 26 RLEIVKLLEfNSLNANQIAEKLNLNYKTV 54
                                  9********8888**************98 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.3e-05     0.064     175     226 ..      13      64 ..       1      73 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                          TnsD 175 yrisrikkfGivweerlkeLveeeglslkeiAkelgvdiktVlryakklgll 226
                                    ++  + + G +++ ++ +L+e ++l+ ++iA+ l+++ ktV+ +++ l+++
  gi|70607516|ref|YP_256386.1|  13 LKFLFFSSRGGKTRLEIVKLLEFNSLNANQIAEKLNLNYKTVIHHLEVLMEN 64 
                                   44445556688889999999999**********************9988876 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5   2.2e+03      41      51 ..       6      16 ..       5      18 .. 0.78
   2 ?   11.8   0.1   0.00013      0.19      22      57 ..      32      67 ..      29      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                  HHHHHHHHHHH CS
                         HTH_9 41 ldqVkksLvvL 51
                                  ++q+kk+L  L
  gi|70607516|ref|YP_256386.1|  6 RKQIKKILKFL 16
                                  68999999655 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                                  HHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9 22 LlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  Ll+ + l ++++++k++L+ + V + L vL+ +r+V
  gi|70607516|ref|YP_256386.1| 32 LLEFNSLNANQIAEKLNLNYKTVIHHLEVLMENRIV 67
                                  78889999**************************98 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.0   7.9e-05      0.12      27      96 ..       2      69 ..       1      71 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                        MSV199 27 dkkdvlitneiLeflgyeGeykkqkkkfkklLkrnnieykelkykdeeielypslkeeikllkknaiaqk 96
                                  ++k++   ++iL+fl ++ +  k + ++ klL+ n+++ +++   ++   +y+++++ ++ l +n i+ k
  gi|70607516|ref|YP_256386.1|  2 NNKERKQIKKILKFLFFSSRGGKTRLEIVKLLEFNSLNANQIA--EKLNLNYKTVIHHLEVLMENRIVVK 69
                                  5566666689********************************9..566789***********99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 768.74
//
Query:       gi|70607517|ref|YP_256387.1|  [L=772]
Description: hypothetical protein Saci_1788 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (772 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1521  (0.0848346); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.84u 0.26s 00:00:01.10 Elapsed: 00:00:00.42
# Mc/sec: 5501.83
//
Query:       gi|70607518|ref|YP_256388.1|  [L=411]
Description: hypothetical protein Saci_1789 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.2e-30  103.9  42.5    2.1e-24   86.1  23.4    2.3  2  MFS_1      Major Facilitator Superfamily
    0.00022   19.8   2.0    0.00031   19.3   2.0    1.1  1  MFS_3      Transmembrane secretion effector
     0.0064   15.3  23.8      0.064   12.0   3.5    2.9  3  LacY_symp  LacY proton/sugar symporter
  ------ inclusion threshold ------
       0.19   12.3   0.0       0.58   10.7   0.0    1.7  2  HEV_ORF1   Hepatitis E virus ORF-2 (Putative capsid protein)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1  23.4   4.6e-28   2.1e-24      10     348 ..      20     355 ..      11     360 .. 0.84
   2 !   31.6  11.2   1.8e-11   8.1e-08       4     183 ..     226     404 ..     223     408 .. 0.87

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 4.6e-28
                         MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf.......a. 82 
                                   la+++ ++++  ++    g++  ++g+l+++ a+   ++sl++++ +d++Gr+++lll+  ++ ++l++llf       a 
  gi|70607518|ref|YP_256388.1|  20 LAAGFMSVIIG-IYYLYIGLNIIQVGILFAIGAFINPLFSLLFSVNADKYGRKPFLLLSTSFLPISLVILLFtryfpllAl 99 
                                   44444555555.444577999*********************************************777777333343325 PP

                         MFS_1  83 .sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    + l  + +++ ++ G  +++++p+  a++a+ ++kee ++ ++l+++ +  + + g++l+g+      +r +f++  ++s
  gi|70607518|ref|YP_256388.1| 100 sAALGgFGIAGGLIGGGIGAIVAPIQTAILAEKTKKEELTKIYSLFTTISTYSGAAGAVLAGIND----YRILFLLGILLS 176
                                   5666667788888999999*******************************************998....************ PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeee....kgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqev 237
                                   +l+f+   +++p+++++++  ++k+ e    +    ++ ++  +   +++ +   + ++ l++++   +++ ++p+ + + 
  gi|70607518|ref|YP_256388.1| 177 ALSFI---FVIPVSEKKSSDLKEKPVEintnS----KNSRN--GDNNRNRDIIkKFTYTGLFNGLSQGLIVPFIPIVFEKF 248
                                   *****...9************99999643331....22222..33333333333578888888888888*******99*** PP

                         MFS_1 238 lglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvf 318
                                   ++l+   ++g++++l+++v+a l ll+ +l  rlg  r ++ + l+ ++++l + +l      +l++l + +++ + ++  
  gi|70607518|ref|YP_256388.1| 249 YNLP-QAEIGYIVSLSGIVSASLILLTPKLNERLGFVRLIIYTRLVSTILTLVFPFLRYD---LLAALDYTIFTSFRAISL 325
                                   ****.8******************************999999999999999999999999...555556666777888889 PP

                         MFS_1 319 psllalasdlappeeagtasglfntagslg 348
                                   p+ +al+++l++ ++++t sg ++ta+ l+
  gi|70607518|ref|YP_256388.1| 326 PAQQALMMSLVSSNRRATTSGTNQTARLLS 355
                                   *************************99887 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.8e-11
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfas 83 
                                   ++++++l+ +++ p++p+   + +++  +eig +++l ++++a ++l++  l +r+G  r ++ + l++++l+l+++++  
  gi|70607518|ref|YP_256388.1| 226 TGLFNGLSQGLIVPFIPIVFEKFYNLPQAEIGYIVSLSGIVSASLILLTPKLNERLGFVRlIIYTRLVSTILTLVFPFL-R 305
                                   578999***********9888889*********************************8885666777777777555553.3 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                      l ++   +   + ++++pa +al+  +++ ++r+   g  +++  l+ +   ll+g+l+ sl+   +f ++ +   + 
  gi|70607518|ref|YP_256388.1| 306 YDLLAALDYTIFTSFRAISLPAQQALMMSLVSSNRRATTSGTNQTARLLSLASSTLLSGFLL-SLSVIFPFTLAFFTNSFN 385
                                   3446777777777788**********************************************.889889999999999999 PP

                         MFS_1 165 fvlfllllpeepperkrks 183
                                   ++l + +++  p +r++k+
  gi|70607518|ref|YP_256388.1| 386 LWLYYKFFWNVPEAREKKR 404
                                   9999999999999998875 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.0   6.9e-08   0.00031      53     305 ..      49     305 ..      30     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-08
                         MFS_3  53 aatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwllla.ltllig.iG...aalndPaWqAsv 128
                                    ++    l+s+l  + aD++ r+ +ll   ++l ++ v+l  + ++ ll+ ++ l+ + +  g iG    a+ +P   A++
  gi|70607518|ref|YP_256388.1|  49 IGAFINPLFSLLFSVNADKYGRKPFLLLSTSFLPISLVILLFTRYFPLLALSAALGgFGIAGGlIGggiGAIVAPIQTAIL 129
                                   555555699**************************************99998877525554432221235999******** PP

                         MFS_3 129 gelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevrksslprEkllealra 209
                                    e  k++++ +   L +     + ++G  l+G+    +  +l   + als++++i +  +   + +++++  ++  +  r+
  gi|70607518|ref|YP_256388.1| 130 AEKTKKEELTKIYSLFTTISTYSGAAGAVLAGINDYRILFLLGILLSALSFIFVIPVSEKKSSDLKEKPVEINTNSKNSRN 210
                                   *****************9999************9999999999999***********999999999999999999999888 PP

                         MFS_3 210 glRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvlla 290
                                   g    +    ik+    +   gls   ++  +P+v  +  +   +  G++++  G+      ll+++L erl+  rl+ ++
  gi|70607518|ref|YP_256388.1| 211 GDN-NRNRDIIKKFTYTGLFNGLSQGLIVPFIPIVFEKFYNLPQAEIGYIVSLSGIVSASLILLTPKLNERLGFVRLIIYT 290
                                   865.556667888888888889*****************9999999****999888777778889*************999 PP

                         MFS_3 291 avalAlvllslalas 305
                                    ++  +  l+  + +
  gi|70607518|ref|YP_256388.1| 291 RLVSTILTLVFPFLR 305
                                   998888877766655 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.025   1.1e+02     350     378 ..      10      38 ..       5      42 .. 0.86
   2 !   11.2   8.0   2.6e-05      0.12      39     177 ..      37     176 ..      35     208 .. 0.71
   3 !   12.0   3.5   1.4e-05     0.064      22      99 ..     233     312 ..     213     389 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.025
                     LacY_symp 350 fligfqlskqlaivllstlaGklydkvGf 378
                                    l+g ++s++la+ ++s+++G+ y  +G 
  gi|70607518|ref|YP_256388.1|  10 LLMGSRVSRSLAAGFMSVIIGIYYLYIGL 38 
                                   367999******************99886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.6e-05
                     LacY_symp  39 glsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepllqlnilvGa..lvGgvflGlv 117
                                   gl   ++Gi+f++  ++  lf  lf +  dk G k  ll + s+l + +  +l   + pll l   +G   + Gg+  G +
  gi|70607518|ref|YP_256388.1|  37 GLNIIQVGILFAIGAFINPLFSLLFSVNADKYGRKPFLLLSTSFLPISLVILLFTRYFPLLALSAALGGfgIAGGLIGGGI 117
                                   5666789**************************************99999999999*******999985337788765555 PP

                     LacY_symp 118 ysagagaieayi.ekvsras.kfeyGkarvfGclGyalcaslaGilfsidpslvfwlasgfa 177
                                    +  a++  a + ek  ++  +  y     + +   a +a+laGi    d ++ f l+ + +
  gi|70607518|ref|YP_256388.1| 118 GAIVAPIQTAILaEKTKKEElTKIYSLFTTISTYSGAAGAVLAGIN---DYRILFLLGILLS 176
                                   5555555555441444333212235666666666667777777773...5566666665544 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.4e-05
                     LacY_symp  22 imsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwv..islllvlfapfliyvfepll 99 
                                     +++ p++p+ +++  +l ++e+G + s   ++s ++  l   ++++lG+ + ++++  +s++l l+ pfl y     l
  gi|70607518|ref|YP_256388.1| 233 SQGLIVPFIPIVFEKFYNLPQAEIGYIVSLSGIVSASLILLTPKLNERLGFVRLIIYTrlVSTILTLVFPFLRYDLLAAL 312
                                   367899**************************************************976689*********999665555 PP

>> HEV_ORF1  Hepatitis E virus ORF-2 (Putative capsid protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.58      17      67 ..      85     135 ..      72     145 .. 0.88
   2 ?   -2.7   0.0       1.9   8.3e+03      49      71 ..     171     192 ..     142     197 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                      HEV_ORF1  17 cfclccprhrpvsrlaaavggaaavpavvsgvtglilspsqspifiqptps 67 
                                    + l   r+ p+  l+aa+gg      ++ g  g i++p q+ i+ + t  
  gi|70607518|ref|YP_256388.1|  85 LVILLFTRYFPLLALSAALGGFGIAGGLIGGGIGAIVAPIQTAILAEKTKK 135
                                   566778999***********************************9988865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                      HEV_ORF1  49 tglilspsqspifiqptpsppms 71 
                                    g+ l  + s if+ p      s
  gi|70607518|ref|YP_256388.1| 171 LGI-LLSALSFIFVIPVSEKKSS 192
                                   233.3345677787777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2571.01
//
Query:       gi|70607519|ref|YP_256389.1|  [L=136]
Description: hypothetical protein Saci_1790 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-09   36.5   0.3    6.4e-09   36.4   0.3    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.3   3.6e-13   6.4e-09       2     118 ..       3     120 ..       2     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.6e-13
                                   EE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                           PIN   2 vlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeia 78 
                                   v+D+sv+i+++ +ee ++ a +l  ++     +l  + +   E++++l++  +  + ++elv    +l++++i   +  ++
  gi|70607519|ref|YP_256389.1|   3 VVDASVVIKWYTKEEYSDDANRLKRAYseglVDLKAPCILPFEVINGLKY--TYNLGEEELVIISKILDDFQITYYSFFDT 81 
                                   8**********5555555555555544544999999**************..99*************************** PP

                                   HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                           PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                   ee+  ++ kyg++++D   + + k  g   ++t+De++ r
  gi|70607519|ref|YP_256389.1|  82 EEIITFSMKYGITIYDSAYITLGKTLGE-EVYTADEKLLR 120
                                   ****************************.566****9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 927.31
//
Query:       gi|70607520|ref|YP_256390.1|  [L=88]
Description: hypothetical protein Saci_1791 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.27   11.2   0.3       0.27   11.2   0.3    2.6  3  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   1.5e-05      0.27       2      17 ..       4      19 ..       3      20 .. 0.93
   2 ?    1.8   0.3     0.014   2.6e+02      26      34 ..      25      33 ..      22      38 .. 0.82
   3 ?   -2.3   0.1      0.27   4.9e+03      33      37 ..      78      82 ..      72      84 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                                  EEEEEEHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdel 17
                                  +++r+d+el+e+ d+l
  gi|70607520|ref|YP_256390.1|  4 ITVRIDDELKEKMDQL 19
                                  9************998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.014
                                  HHHHHHHHH CS
                         RHH_1 26 SelIReAlr 34
                                  Se+IR+ + 
  gi|70607520|ref|YP_256390.1| 25 SEVIRRSII 33
                                  9****9885 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.27
                                  HHHHH CS
                         RHH_1 33 lreyl 37
                                  +re++
  gi|70607520|ref|YP_256390.1| 78 IREWR 82
                                  45554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1511  (0.0842769); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.31s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 580.72
//
Query:       gi|70607521|ref|YP_256391.1|  [L=304]
Description: 3-ketoacyl-ACP reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-65  220.9   0.0      2e-65  220.6   0.0    1.1  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    1.1e-53  181.6   0.0    1.4e-53  181.3   0.0    1.1  1  adh_short      short chain dehydrogenase
    1.1e-08   35.2   0.0    2.4e-08   34.1   0.0    1.5  2  KR             KR domain
    5.2e-08   32.6   0.0    6.2e-07   29.1   0.0    2.0  1  DUF1776        Fungal family of unknown function (DUF1776)
     0.0018   17.8   0.1     0.0046   16.4   0.1    1.7  1  Epimerase      NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.026   13.9   0.5      0.037   13.4   0.1    1.6  2  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
      0.055   13.3   0.1       0.19   11.6   0.0    1.8  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.13   12.2   0.0        3.1    7.7   0.0    2.6  3  AAA_31         AAA domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.6   0.0   9.1e-69     2e-65       1     234 []       9     247 ..       9     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 220.6 bits;  conditional E-value: 9.1e-69
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                   G a+gIG+ i  +l ++G++vv++d++eea   r+e++++e   + ++++DV++e++v++l++ev +++g++D+l+nnagi
  gi|70607521|ref|YP_256391.1|   9 GGAKGIGASISYTLGKRGYSVVIADVDEEAgLYRLEQFHKENIDSlFVRTDVSSETDVKNLMDEVYKRYGRIDVLINNAGI 89 
                                   6689**************************99*******99777747********************************** PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC....CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeg....gsivnlssvgaervvpnynaygaaKaalealtrylA 156
                                     +   +++e + ee+++++d+nl++++l++k+++++mk++    g i+n++s++a ++ pn++ y+a+K++++alt++lA
  gi|70607521|ref|YP_256391.1|  90 GFS-GRSIEEQTLEEWRKIIDTNLTGTWLCSKYVINYMKRNkergGVIINIASTRALQSEPNTEPYSASKGGIVALTHSLA 169
                                   **9.99999***************************999888899************************************ PP

                                   HHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                  adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                   v+l +++iRv avspg+i+T  ++  +++++l +  ++++  +r+g pe++ +++lfL+sdeas+i+G ++v+DgG+t
  gi|70607521|ref|YP_256391.1| 170 VSLSKYNIRVIAVSPGWIDTSRWQYPPKESRLTNLDHKQHLTRRVGIPEDISSIVLFLVSDEASWISGVNFVIDGGMT 247
                                   ****************************************************************************98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.3   0.0   6.2e-57   1.4e-53       1     187 [.       3     192 ..       3     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.3 bits;  conditional E-value: 6.2e-57
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEE CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvL 81 
                                   kv++vtG+++GIG  i+++l k+G++vv++d  ee+    ++++++e+ + l++++Dv+++++v++l++++ k++g++dvL
  gi|70607521|ref|YP_256391.1|   3 KVAIVTGGAKGIGASISYTLGKRGYSVVIADVDEEAGLYRLEQFHKENIDSLFVRTDVSSETDVKNLMDEVYKRYGRIDVL 83 
                                   89******************************************************************************* PP

                                   EE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH..HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                     adh_short  82 vnNAGi.tgsgpfselseeewervievNltgvflltravlpaml..kqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                   +nNAGi    ++++e + eew+++i++Nltg+ l+++ v+++m+  k+++G I+n++S+ ++++ +++ +YsAsK+++++l
  gi|70607521|ref|YP_256391.1|  84 INNAGIgFSGRSIEEQTLEEWRKIIDTNLTGTWLCSKYVINYMKrnKERGGVIINIASTRALQSEPNTEPYSASKGGIVAL 164
                                   ******76678899999***************************9999********************************* PP

                                   HHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                     adh_short 160 trslakelaptgirvnavaPGlvdTdma 187
                                   t+sla  l++++irv+av PG +dT   
  gi|70607521|ref|YP_256391.1| 165 THSLAVSLSKYNIRVIAVSPGWIDTSRW 192
                                   ************************9865 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.1e-11   2.4e-08       4     151 ..       6     156 ..       4     181 .. 0.83
   2 ?   -3.2   0.0         3   6.7e+03      55      79 ..     276     300 ..     269     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.1e-11
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---E CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikG 84 
                                   ++tGG+ g+G +++ +l ++g + ++    +    e+   +++++++ +++  +v+ Dvs++++v++l++e+ ++ ++i  
  gi|70607521|ref|YP_256391.1|   6 IVTGGAKGIGASISYTLGKRGYSVVIADVDE----EAGLYRLEQFHKENIDSLFVRTDVSSETDVKNLMDEVYKRYGRIDV 82 
                                   8********************9877654443....55566899999999999***************************** PP

                                   EEE----.-----TTT--HHHHHHHHTTTTHHHHHHHHHTTT......S--SEEEEEEEHHHHH--TT-HHHHH CS
                            KR  85 vihaAgv.lrdklleemtaedleqvlapKvkGawnLhelled......esldffvlfSSiagllgsagqanYaa 151
                                    i+ Ag+ +  + +ee+t e++++++   ++G+w   +++ +      e+  +++ ++S  +l  ++    Y+a
  gi|70607521|ref|YP_256391.1|  83 LINNAGIgFSGRSIEEQTLEEWRKIIDTNLTGTWLCSKYVINymkrnkERGGVIINIASTRALQSEPNTEPYSA 156
                                   ******9456889*********************9888776555544455566666666666666666666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                   EEE----TT-HHHHHHHHHHHHHHS CS
                            KR  55 vevvaaDvsdkdavealleeikaee 79 
                                   +++v+   sdkd+v++ll+++ ++ 
  gi|70607521|ref|YP_256391.1| 276 IKLVEKAKSDKDSVKRLLNSLVRDR 300
                                   5666666688999999998887665 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.8e-10   6.2e-07      19     217 ..      17     203 ..       4     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.8e-10
                       DUF1776  19 sialDLerrGFiVfvtvesaeeeklvesed..redIrplsvdddpssieasleefaqslesphvalpgakphvlrLkgvil 97 
                                   si++ L +rG+ V++   ++e + l + e+  +e+I++l v + + s e+ +++ + ++ ++          + r   +i 
  gi|70607521|ref|YP_256391.1|  17 SISYTLGKRGYSVVIADVDEE-AGLYRLEQfhKENIDSLFVRT-DVSSETDVKNLMDEVYKR----------YGRIDVLIN 85 
                                   78999********99998888.5666666645667*******9.899999999999999976..........668888888 PP

                       DUF1776  98 vPslsyptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalf 178
                                        ++   ie+ +l++w++ + ++l  ++l ++  ++ ++  +k++  +i+  +s  +  + p+  p +   + + al+
  gi|70607521|ref|YP_256391.1|  86 NAGIGFSGRSIEEQTLEEWRKIIDTNLTGTWLCSKYVINYMKR-NKERGGVIINIASTRALQSEPNTEPYSASKGGIVALT 165
                                   8888897778********************************6.66999999999999888899***************** PP

                       DUF1776 179 evLkrelrphnidvtqikLGnldlangsqsnskiasvag 217
                                   ++L+ +l+++ni v+ +  G +d + + q+ +k +++++
  gi|70607521|ref|YP_256391.1| 166 HSLAVSLSKYNIRVIAVSPGWIDTS-RWQYPPKESRLTN 203
                                   ***********************99.7777666666655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.1e-06    0.0046       2      96 ..       6     116 ..       5     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHH....H.T-SEEEE CS
                     Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfke....e.qpdavih 70 
                                   +VtG++  iG+ +   l ++gy v+  d +++a+   +++          +v+ d+  ++++++l++e    + ++d+ i+
  gi|70607521|ref|YP_256391.1|   6 IVTGGAKGIGASISYTLGKRGYSVVIADVDEEAGLYRLEQ-FhkenidsLFVRTDVSSETDVKNLMDEvykrYgRIDVLIN 85 
                                   8*****************************7766655444.35899999999999999997776666522225789***** PP

                                   --S---HHHHHHSHH.....HHHHHHTHHHH CS
                     Epimerase  71 lAavggvaassedpa.....dfieknlqgtl 96 
                                    A++g  ++s+e+++     ++i++nl gt+
  gi|70607521|ref|YP_256391.1|  86 NAGIGFSGRSIEEQTleewrKIIDTNLTGTW 116
                                   *******999987643223367777777775 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.6e-05     0.037       1     106 [.       6     115 ..       6     165 .. 0.78
   2 ?   -3.8   0.0       2.9   6.5e+03      30      72 ..     253     294 ..     239     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.....T- CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.....qp 76 
                                   ++TG+a  iG+ +   L ++gy v++  + +++  + r+e+  k++      +  +++ D++ ++ +++l++ev     ++
  gi|70607521|ref|YP_256391.1|   6 IVTGGAKGIGASISYTLGKRGYSVVI-ADVDEEAGLYRLEQFHKEN-----IDSLFVRTDVSSETDVKNLMDEVykrygRI 80 
                                   59**********************75.6677777889999987643.....2567*****************998888889 PP

                                   SEEEE--S---HHHHTTSH.....HHHHHHHTHHH CS
                 GDP_Man_Dehyd  77 devynLAAqshVdvsfekP.....eytaevnvlGt 106
                                   d  +n A+  + ++s+e+       + +++n++Gt
  gi|70607521|ref|YP_256391.1|  81 DVLINNAGIGFSGRSIEEQtleewRKIIDTNLTGT 115
                                   99999888888888886531111135566666666 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.9
                                   EESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHH CS
                 GDP_Man_Dehyd  30 rsssfntgriehlakdpkeeleenlklhkgDltDssslerlla 72 
                                   +++++  ++++ l +d++ +    +kl++   +D++s++rll+
  gi|70607521|ref|YP_256391.1| 253 LDENVIRDSLSILLDDEELS-GLLIKLVEKAKSDKDSVKRLLN 294
                                   45555556666666665432.3367888888888888888876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.5e-05      0.19       2      66 ..       4      72 ..       3      82 .. 0.73
   2 ?   -1.4   0.0      0.84   1.9e+03      22      65 ..     245     294 ..     238     298 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                                  EEEE--SC..CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-.HHHHCCCHHC CS
                       3HCDH_N  2 vaviGaGt..mGagiaavfasagleVvlvdiseealekalekiek.sleklvekgklk.eeeveaalar 66
                                  va++  G   +Ga+i + + ++g++Vv+ d++eea    le+ +k ++++l  +  ++ e +v++++++
  gi|70607521|ref|YP_256391.1|  4 VAIVTGGAkgIGASISYTLGKRGYSVVIADVDEEAGLYRLEQFHKeNIDSLFVRTDVSsETDVKNLMDE 72
                                  77775554339********************99886555555544388887777766646666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.84
                                   T-EEEEE-S-HHHHHHHHHHHHH......HHHCCTTTTSS-HHHHCCCHH CS
                       3HCDH_N  22 gleVvlvdiseealekalekiek......sleklvekgklkeeeveaala 65 
                                   g++V+++  +e+ ++++l+ + +       l klvek k ++++v+++l+
  gi|70607521|ref|YP_256391.1| 245 GMTVRMIYLDENVIRDSLSILLDdeelsgLLIKLVEKAKSDKDSVKRLLN 294
                                   66777777766666665543333232333666777777777766666655 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0014       3.1      21      84 ..      17      83 ..       9     116 .. 0.74
   2 ?    0.3   0.0      0.25   5.5e+02       9      36 ..     157     182 ..     154     189 .. 0.80
   3 ?   -0.2   0.0      0.37   8.3e+02      69     113 ..     253     295 ..     197     302 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                        AAA_31 21 nlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiik..tkvenldli 84
                                   ++++l k+g+ v + D+D  a +    +++k++i++ ++++ + +e+++k+++ +  +++ ++d++
  gi|70607521|ref|YP_256391.1| 17 SISYTLGKRGYSVVIADVDEEAGLYRLEQFHKENIDSLFVRTDVsSETDVKNLMDEvyKRYGRIDVL 83
                                  689***********************9999****999999986546666666554200233444555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                        AAA_31   9 qKGGvGKTTtsvnlaaalaklgkkvLlv 36 
                                    KGG+   T    la++l+k++ +v+ v
  gi|70607521|ref|YP_256391.1| 157 SKGGIVALT--HSLAVSLSKYNIRVIAV 182
                                   688876555..56899999***999987 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.37
                        AAA_31  69 ikeaiiktkvenldlipssidLaeaeielvelekk.eeilkellek 113
                                   ++e +i    ++l+++  + +L+++ i+lve+ k+ ++ +k+ll++
  gi|70607521|ref|YP_256391.1| 253 LDENVI---RDSLSILLDDEELSGLLIKLVEKAKSdKDSVKRLLNS 295
                                   334444...4556888889999999999998887734556777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2134.62
//
Query:       gi|70607522|ref|YP_256392.1|  [L=89]
Description: hypothetical protein Saci_1793 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-17   62.6   3.2    2.9e-17   62.4   3.2    1.0  1  HTH_45          Winged helix-turn-helix
    0.00056   19.7   0.7    0.00065   19.5   0.7    1.2  1  DUF4364         Domain of unknown function (DUF4364)
     0.0079   15.7   0.2       0.01   15.3   0.2    1.4  1  PI-TkoII_IV     DNA polymerase II intein Domain IV
  ------ inclusion threshold ------
      0.025   15.1   0.1      0.038   14.5   0.1    1.3  1  HTH_27          Winged helix DNA-binding domain
      0.051   13.4   0.4      0.054   13.3   0.4    1.1  1  DUF4393         Domain of unknown function (DUF4393)
      0.062   13.0   0.0      0.079   12.7   0.0    1.2  1  Ribosomal_S19e  Ribosomal protein S19e
      0.075   13.6   0.0       0.25   11.9   0.0    1.7  2  AAA_assoc_C     C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   3.2   1.1e-20   2.9e-17       2      74 ..       8      82 ..       7      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.1e-20
                        HTH_45  2 RskleIiadILeais..egeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkelee 74
                                  Rsk+eI++ IL++++  e e kkT++my + L+y++++kY++ + + gl++ +ke Y+lT+ G++ le ++++  
  gi|70607522|ref|YP_256392.1|  8 RSKIEIMYTILKVLResETEVKKTHLMYLVGLNYDVFSKYISRIEKLGLVRVNKEGYSLTDSGKRELEMIENYLT 82
                                  **************94456779**********************************************9999865 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.7   2.5e-07   0.00065      28      80 ..      36      84 ..       9      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                       DUF4364 28 neytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenripks 80
                                     +nY  +++++s +++ gl+++    nk+ y++T++Gk+ le++en +  +
  gi|70607522|ref|YP_256392.1| 36 LVGLNYDVFSKYISRIEKLGLVRV----NKEGYSLTDSGKRELEMIENYLTIE 84
                                  44689******************7....899*****************99765 PP

>> PI-TkoII_IV  DNA polymerase II intein Domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.9e-06      0.01      61      87 ..      43      69 ..       6      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-06
                                  THHHHHHHHHHCTSEEE-SSSEEES-H CS
                   PI-TkoII_IV 61 tarrylkhleklGyvklkkrGyevldw 87
                                   +++y+  +eklG+v+++k Gy ++d 
  gi|70607522|ref|YP_256392.1| 43 VFSKYISRIEKLGLVRVNKEGYSLTDS 69
                                  6899******************99985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.5e-05     0.038       7      68 .]      16      70 ..      12      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                        HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   +L ++r+ + ++k++ l+  + +++  +s+ +++ ++ GLv r  +e       ++lTd+G
  gi|70607522|ref|YP_256392.1| 16 TILKVLRESETEVKKTHLMYLVGLNYDVFSKYISRIEKLGLV-RVNKE------GYSLTDSG 70
                                  589999************************************.66666......68888887 PP

>> DUF4393  Domain of unknown function (DUF4393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   2.1e-05     0.054     113     157 ..      37      84 ..       3      88 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                       DUF4393 113 vlenpekvkasldnLerlgLiklsekqk.lteekv..yeelenskiie 157
                                   v  n+++++++++ +e+lgL++++++ + lt+      e +en+  ie
  gi|70607522|ref|YP_256392.1|  37 VGLNYDVFSKYISRIEKLGLVRVNKEGYsLTDSGKreLEMIENYLTIE 84 
                                   22356888****************998867775544455556555555 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.1e-05     0.079      96     132 ..      44      79 ..      29      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                   TSSS--SSS---SS-HHHHHTHHHHH--SS--S--XX CS
                Ribosomal_S19e  96 irkilqqLeklglvkkekkkgrrltkkGqrlldriae 132
                                     k +  +eklglv+ + k+g  lt++G+r l+ i +
  gi|70607522|ref|YP_256392.1|  44 FSKYISRIEKLGLVRVN-KEGYSLTDSGKRELEMIEN 79 
                                   56778999******666.67************98865 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.66   1.7e+03      63      79 ..      11      27 ..       4      36 .. 0.70
   2 ?   11.9   0.0   9.7e-05      0.25       7      44 ..      37      74 ..      31      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.66
                   AAA_assoc_C 63 vplaaairrvLderenk 79
                                  + ++ +i +vL+e+e++
  gi|70607522|ref|YP_256392.1| 11 IEIMYTILKVLRESETE 27
                                  56677778888887764 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.7e-05
                   AAA_assoc_C  7 lelevddLlpiveaaelLglveveegdielTelGrkfv 44
                                  ++l+ d   + +   e Lglv+v++    lT+ G++ +
  gi|70607522|ref|YP_256392.1| 37 VGLNYDVFSKYISRIEKLGLVRVNKEGYSLTDSGKREL 74
                                  67889999999***********************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 598.24
//
Query:       gi|70607523|ref|YP_256393.1|  [L=237]
Description: hypothetical protein Saci_1794 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.29   11.4   4.7        1.6    9.0   0.1    2.6  2  DIM       DIM protein


Domain annotation for each model (and alignments):
>> DIM  DIM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.2    0.0067   1.2e+02       4      27 ..      11      32 ..       8      35 .. 0.74
   2 ?    9.0   0.1   8.9e-05       1.6      19      30 ..     158     171 ..     156     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0067
                           DIM  4 LsLlaflllllalaaanal.pGkVi 27
                                  +s+ a   lll +++ +a  +G V+
  gi|70607523|ref|YP_256393.1| 11 ISV-AA--LLLSMLVYQAFvAGFVV 32
                                  455.33..4458******9999998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 8.9e-05
                           DIM  19 anal..pGkViING 30 
                                   ++++  pG+V ING
  gi|70607523|ref|YP_256393.1| 158 VDPTntPGTVMING 171
                                   678888*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1697.45
//
Query:       gi|70607524|ref|YP_256394.1|  [L=368]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-05   23.4   0.4     0.0001   22.2   0.4    1.6  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.4   5.6e-09    0.0001       4      68 ..      50     126 ..      49     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.6e-09
                                   SSTTCCTXXTTXEEEEECTS...---TTSEEEEEETTCE......-EEEEEEE.EETTEEEEE.SST.T.STEEEEC CS
                 Peptidase_S24   4 GdSMeptlldGdlilVdkfs...epkrGdivvfrlpgee......eayiKrvi.glpgdrvllasnn.e.ypplyin 68 
                                   G SM p l++Gd+ +  +++   ++ +G ivv+++p+         ++i++vi  lp++++ ++  n +  +++y +
  gi|70607524|ref|YP_256394.1|  50 GYSMFPYLKPGDVAITIPEPvagKITNGSIVVIKDPDYGvlpgypPYIIHQVInVLPNGSFVTKGINdNfVDQIYMP 126
                                   67***************9999***********************9********888999999887776778888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2867.80
//
Query:       gi|70607525|ref|YP_256395.1|  [L=293]
Description: hypothetical protein Saci_1796 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0086   15.5  13.0     0.0066   15.9   5.8    2.8  2  DUF5305   Family of unknown function (DUF5305)
  ------ inclusion threshold ------
       0.03   14.0   0.3      0.063   12.9   0.3    1.5  1  DUF2026   Protein of unknown function (DUF2026)
       0.07   13.4   0.0       0.16   12.2   0.0    1.5  1  DRE2_N    Fe-S cluster assembly protein DRE2 N-terminus


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.7     0.073   4.4e+02      22      77 ..      37      92 ..      31      96 .. 0.77
   2 !   15.9   5.8   1.1e-06    0.0066      26     219 .]     115     287 ..     109     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.073
                       DUF5305 22 isesvsinlseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsr 77
                                  +++++ in s + +  +ei++   +s+ t++l+v+ + + ++++  ++++ ++t+ 
  gi|70607525|ref|YP_256395.1| 37 YQTTFYINDSILFNNKTEINTNSMFSSLTKSLVVNGYFYTTANSYTGNFTVNETIV 92
                                  66777778788888889999999999999999999999999966666666666655 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.1e-06
                       DUF5305  26 vsinlseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsrlpiplteqtyeikkdetd..eengeitet 104
                                   ++ n++  +    +i+++l++    +  ++ l+++v++ i   s +   + r ++++ ++ty+i+ ++++    +g+ +++
  gi|70607525|ref|YP_256395.1| 115 FTPNFTYAQSLFYQIDKQLRIPI--NYYSIRLNISVNAVIMYPSGNVPLNFRDSLTIQNGTYNISVNYNNdsFASGSFYKE 193
                                   55677788888999999999999..66788889999999999999999999999999999*****9999955567888888 PP

                       DUF5305 105 vtvkespslaegilliilgllaliglvvlirriiftsskaekyelelekilkeYdewIvkgslppdlgdekvievdsledL 185
                                   ++v+e+ ++ +  +++ +++l +i+l +l+ r+  +        l++++++++    I+  + p++ +   vie+   ed 
  gi|70607525|ref|YP_256395.1| 194 ISVEEETGYNY-SYFYGAAFLVIIALSILFIRM--S--------LNIQNVINK--NSISGSKPPMNAS---VIEIRKAEDF 258
                                   88888888877.444444444444444444442..2........333333332..3555555555553...7777777777 PP

                       DUF5305 186 vdvaielnepvlydeeedeegkFvvvddevvYvY 219
                                   +++ + +ne  + +++      +++++d++vY Y
  gi|70607525|ref|YP_256395.1| 259 LKLIKQYNEKAVKCDN-----DYYITHDNIVYLY 287
                                   7777777777776666.....4677777777766 PP

>> DUF2026  Protein of unknown function (DUF2026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   1.1e-05     0.063       4      53 ..      36      85 ..      33      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHHHHHHH---EEEEEEEE CS
                       DUF2026  4 DYqRiyrvinsvlksenadtakaslffsvagaaiLkehykieakplaGla 53
                                   Yq  + +  s+l ++++++++ s+f s++ + +++ ++ + a+ ++G  
  gi|70607525|ref|YP_256395.1| 36 KYQTTFYINDSILFNNKTEINTNSMFSSLTKSLVVNGYFYTTANSYTGNF 85
                                  69999****************************************99965 PP

>> DRE2_N  Fe-S cluster assembly protein DRE2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05      0.16      46      98 ..      32      85 ..      25      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                                  --SSS--SEEEE---.....SS-S----HHHHHHHHTT--TT--EE---H....HH CS
                        DRE2_N 46 LpastYdlvllltde...eeeeeelliprkliqkivkaLkpgGklkgqdgkakeaq 98
                                  L + +Y +  +++d    +++ +e+++ +++++ + k+L  +G +++  ++ ++++
  gi|70607525|ref|YP_256395.1| 32 LANTKYQTTFYINDSilfNNK-TEINT-NSMFSSLTKSLVVNGYFYTTANSYTGNF 85
                                  8899************96444.68888.9******************999877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2065.98
//
Query:       gi|70607526|ref|YP_256396.1|  [L=156]
Description: hypothetical protein Saci_1797 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.01   15.7   0.2      0.017   15.0   0.2    1.4  1  DUF2721         Protein of unknown function (DUF2721)
      0.029   13.2   3.5      0.034   12.9   3.5    1.0  1  DUF2207         Predicted membrane protein (DUF2207)
      0.052   13.6   1.5       0.47   10.6   1.5    2.2  1  Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
      0.064   13.7   0.0      0.089   13.2   0.0    1.2  1  Peptidase_M61   M61 glycyl aminopeptidase
       0.14   12.0   0.1       0.21   11.4   0.1    1.3  1  IclR            Bacterial transcriptional regulator
       0.17   12.0   0.2       0.21   11.7   0.2    1.2  1  zf-CRD          Cysteine rich domain with multizinc binding r


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   5.6e-06     0.017      26      86 ..      59     115 ..      52     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.6e-06
                       DUF2721  26 adrirqLedeleelaeeeeedeelakeiknlrrRarlirrailllvlsallvvlvvlllfl 86 
                                   ++r+  +++el+++ ++     +  ke++n +rRa+l+  a+   +++++l+ ++++l + 
  gi|70607526|ref|YP_256396.1|  59 IKRLDPIKRELDDIRQK----VNNIKEVENASRRAKLCYTALNYSMITLILTFTISILFYT 115
                                   56666666666644444....566899*********************9998887776655 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.5   1.2e-05     0.034     316     429 ..      29     141 ..       3     150 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                       DUF2207 316 dpyEkalldlLfdkseegks..lkeikkyakkskkkakkfkkalkkwksavkk.kergyfdkkgkkklkklsalglgliil 393
                                   +++ ++ll+ + +++++ k   +kei ++  k   + + +k++l++++++v++ ke +  +++ k  ++ l++  + li+ 
  gi|70607526|ref|YP_256396.1|  29 NSEVNDLLEEILTYITSLKGrqWKEIYETTIK---RLDPIKRELDDIRQKVNNiKEVENASRRAKLCYTALNYSMITLILT 106
                                   44445555555555555522468888888777...9*****************5444444444444444444444444444 PP

                       DUF2207 394 glilillallllvlllvfllilllillliaiivlll 429
                                   ++i il+  +++ + ++ +l+l ++  +i+++ +l+
  gi|70607526|ref|YP_256396.1| 107 FTISILFYTIFMDY-IYSFLFLEIVETIIIFLEILY 141
                                   44444444444444.333333333333333333333 PP

>> Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.5   0.00016      0.47      32      70 ..      42      81 ..      24      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                Myb_DNA-bind_5 32 atnkaKsraWeeiaervna.lgsveRtaeelkkkwedlkr 70
                                  + +  K r W+ei e   + l +++R+++++++k +++k+
  gi|70607526|ref|YP_256396.1| 42 YITSLKGRQWKEIYETTIKrLDPIKRELDDIRQKVNNIKE 81
                                  556788999****99988879999************9996 PP

>> Peptidase_M61  M61 glycyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     3e-05     0.089      51     101 ..      19      69 ..      14      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                                   HHHHHTTSS-HHHHHHHHHHHHHHHHHSGGGGT--HHHHHHTIIIIITT-- CS
                 Peptidase_M61  51 lllarsgliseeeyleelaktlarlentpgrkvqslaessfdawiklyrsd 101
                                   +l+  s+l+s++e+ + l++ l+ +++ +gr+++++ e++++    ++r+ 
  gi|70607526|ref|YP_256396.1|  19 FLISLSKLMSNSEVNDLLEEILTYITSLKGRQWKEIYETTIKRLDPIKREL 69 
                                   5677899**********************************9777776663 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.9e-05      0.21      37      70 ..      46      79 ..      31      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                                  HHHHT---SSTTS--SHHHHHHHHHHHHHHTSEE CS
                          IclR 37 lerlelkrlterTitdpeeLleeLakvReqGyav 70
                                  l+ +++k++ e+Ti+  + +++eL+ +R++   +
  gi|70607526|ref|YP_256396.1| 46 LKGRQWKEIYETTIKRLDPIKRELDDIRQKVNNI 79
                                  6779************************986555 PP

>> zf-CRD  Cysteine rich domain with multizinc binding regions
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     7e-05      0.21      85     159 .]      33     111 ..       7     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                        zf-CRD  85 neveqkilkdylaekgltlqdvlkevlekld..kgelkrtrkklnlseak..itsdtvlCseCaekvfsellykyrisi 159
                                   n+   +il+   + kg+++++++++ +++ld  k+el+++r+k+n  +     +++  lC+   +  +  l+ ++ isi
  gi|70607526|ref|YP_256396.1|  33 NDLLEEILTYITSLKGRQWKEIYETTIKRLDpiKRELDDIRQKVNNIKEVenASRRAKLCYTALNYSMITLILTFTISI 111
                                   55666788888888****************9556668888877775533233478888899888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1808  (0.100842); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1025.80
//
Query:       gi|70607527|ref|YP_256397.1|  [L=293]
Description: hypothetical protein Saci_1798 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0091   15.5   7.9      0.062   12.8   7.9    2.2  1  LysE             LysE type translocator
  ------ inclusion threshold ------
      0.025   14.5  15.0      0.015   15.3   8.4    2.5  3  DsbD_2           Cytochrome C biogenesis protein transmembran


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   7.9   6.9e-06     0.062      16      76 ..      49     108 ..      44     236 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-06
                          LysE  16 kqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvl 76 
                                   k++ k g+k+g+l+ lg +i  a+l ++g lGla++ +++      +  + g++ +  g  
  gi|70607527|ref|YP_256397.1|  49 KYSTKGGMKAGFLFSLGFTIQRAFLTTIGFLGLAAIYNQYNL-DGPVYAVVGIVMAIAGSY 108
                                   78999*********************************6543.333333333333444444 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.7    0.0085        76     122     195 ..      24     104 ..      20     106 .. 0.63
   2 ?   15.3   8.4   1.6e-06     0.015      67     190 ..      88     227 ..      74     236 .. 0.68
   3 ?   -0.4   0.2      0.11   9.5e+02      40      56 ..     219     236 ..     202     291 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0085
                        DsbD_2 122 lllGllnGllpCglvys.alllalasgsaleGalvmlaFgLG.Tlp.alllfglllgll....skklrkkllrlagvllil 195
                                   l+lG+l+G+ p    ++ ++ +a+ + s  +G+ + ++F+LG T+  a+l++  +lgl+    + +l   +  ++g+++++
  gi|70607527|ref|YP_256397.1|  24 LILGMLHGVTPDEHTWPiTFSYAIGKYSTKGGMKAGFLFSLGfTIQrAFLTTIGFLGLAaiynQYNLDGPVYAVVGIVMAI 104
                                   789999999999887761577999999**************9443312333322222222222335556666666666655 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-06
                        DsbD_2  67 eglrallgvllgllllllglkll.lkkkllklerlgkllsrllkklakklkslasalllGllnGllpCgl.vysalllala 145
                                     l + +  ++g+++++ g ++l +k  +l +++l k  +++ ++ + k    +  ++ Gl+ G+ + +     +++la+ 
  gi|70607527|ref|YP_256397.1|  88 YNLDGPVYAVVGIVMAIAGSYILkGKYIHLPIDALFKSKQHTEEAGKVKDIPIKMTIVHGLVAGFGFGAYaTIITFVLAPQ 168
                                   356777788888888888999984444566777776544444333333225677889999999999987768899999*** PP

                        DsbD_2 146 sgsaleGalvmlaFgLGTlpalllfglllgll..............skklrkkllrlag 190
                                     s+++  l  l+FgLGT+++ ++fg+++g +               +k+  ++l   g
  gi|70607527|ref|YP_256397.1| 169 LPSVVYAPLPGLFFGLGTMVMQIIFGMIFGNIlrlkkmteeqlsfiARKTAGRVLYYGG 227
                                   *****************************998555544444444443344444444445 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.11
                        DsbD_2  40 lGRilsYallGal.vgll 56 
                                   +GR+l Y  l  l vgll
  gi|70607527|ref|YP_256397.1| 219 AGRVLYYGGLVFLiVGLL 236
                                   455555543332202222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1940.00
//
Query:       gi|70607528|ref|YP_256398.1|  [L=305]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-28  100.4   0.0    2.1e-28   99.5   0.0    1.4  1  ABC_tran      ABC transporter
    1.6e-15   57.7   2.6    1.3e-08   35.0   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.2e-05   24.5   0.0    3.7e-05   23.7   0.0    1.3  1  Rad17         Rad17 P-loop domain
    2.5e-05   23.9   0.3    9.3e-05   22.1   0.2    1.9  2  AAA_29        P-loop containing region of AAA domain
    0.00013   21.8   0.3     0.0056   16.4   0.4    2.4  2  AAA_15        AAA ATPase domain
    0.00084   19.9   0.1     0.0016   19.0   0.0    1.6  2  AAA_23        AAA domain
    0.00094   19.5   0.4       0.02   15.2   0.1    2.3  2  AAA_22        AAA domain
     0.0057   16.1   0.1       0.29   10.5   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.042   13.6   0.0    1.7  1  AAA_30        AAA domain
      0.022   14.7   0.1       0.04   13.8   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
      0.036   14.3   0.2      0.093   13.0   0.1    1.7  1  AAA_28        AAA domain
      0.055   14.0   0.0       0.14   12.7   0.0    1.7  1  AAA_18        AAA domain
      0.063   13.7   0.1       0.17   12.3   0.1    1.9  1  AAA           ATPase family associated with various cellular 
      0.084   12.6   0.1       0.91    9.2   0.0    2.3  3  IstB_IS21     IstB-like ATP binding protein
      0.094   13.1   0.0       0.16   12.3   0.0    1.5  1  AAA_16        AAA ATPase domain
        0.1   12.6   0.1       0.21   11.6   0.1    1.6  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.13   11.9   0.2       0.28   10.9   0.1    1.6  2  AAA_24        AAA domain
       0.18   11.4   0.1       0.35   10.5   0.1    1.4  1  SRP54         SRP54-type protein, GTPase domain
       0.21   11.0   0.1       0.33   10.3   0.1    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.5   0.0   2.2e-31   2.1e-28       1     136 [.      17     161 ..      17     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 2.2e-31
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-.TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlf.peltvren. 79 
                                   l+nvs+k+++ ++ a+vG+nGaGK+tL+k+l+ l  p +G+ l++g ++ + e++++r++ig ++  ++lf ++lt+ en 
  gi|70607528|ref|YP_256398.1|  17 LDNVSFKIENKSIGALVGPNGAGKTTLIKILSTLIIPSSGDALVNGYSVVK-EEKKVRESIGLMTVSERLFyYRLTALENl 96 
                                   79*******************************************999999.8999999**999988666526899***** PP

                                   ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               ++++++ ++l+ +gl+e+++ +      ++S G+++++alaral+++p++lllDEpt
  gi|70607528|ref|YP_256398.1|  97 iffaslqnlslsDARRRAMEMLELVGLSEWANLPY----MKFSTGMQRKLALARALITDPPVLLLDEPT 161
                                   *********99888888************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.6   1.1e-07   9.9e-05       3      22 ..      31      50 ..      29      78 .. 0.82
   2 !   35.0   0.0   1.4e-11   1.3e-08     231     297 ..     128     190 ..     124     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.1e-07
                        AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                  +l+GpNg+GK++L+++l+ l
  gi|70607528|ref|YP_256398.1| 31 ALVGPNGAGKTTLIKILSTL 50
                                  79***************877 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.4e-11
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTH 297
                                   +lp+ ++S G++r lal+ al+ ++   ++ll+DEp +gL+P   r + +l+ ++ ++    ++lt+H
  gi|70607528|ref|YP_256398.1| 128 NLPYMKFSTGMQRKLALARALITDP---PVLLLDEPTLGLDPLSARMFRDLVrRIGKE--KTILLTSH 190
                                   68999****************9999...**************6665555666433444..669****9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.9e-08   3.7e-05      31     124 ..      13     117 ..       6     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.9e-08
                         Rad17  31 vkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrf........ 102
                                   v ++l+  + + ++k i  + GP G gk+t +k+Ls    ++  +  +n+ s+ + + ++ +  gl+ + +r+        
  gi|70607528|ref|YP_256398.1|  13 VINALDNVSFKIENKSIGALVGPNGAGKTTLIKILSTLIIPSSGDaLVNGYSVVKEEKKVRESIGLMTVSERLfyyrltal 93 
                                   5567888888888899*9*******************99988765168******************999999778898887 PP

                         Rad17 103 ..lsqiesfkeleLkdakylklqk 124
                                     l   +s ++l L da+   +++
  gi|70607528|ref|YP_256398.1|  94 enLIFFASLQNLSLSDARRRAMEM 117
                                   766677888888888888888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   9.9e-08   9.3e-05      13      50 ..      18      55 ..      14      64 .. 0.87
   2 ?   -1.3   0.0         2   1.9e+03      15      36 ..     201     221 ..     196     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.9e-08
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  d+ +++i+ k++  l+Gp+G+GK+Tl+  +++l++p++
  gi|70607528|ref|YP_256398.1| 18 DNVSFKIENKSIGALVGPNGAGKTTLIKILSTLIIPSS 55
                                  677899998889***********************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                        AAA_29  15 htieidlkgatlltGpsGsGKS 36 
                                   +ti ++ kg +l+ G+ +s KS
  gi|70607528|ref|YP_256398.1| 201 KTILLK-KGKVLVEGDRESLKS 221
                                   566666.6679*****999888 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4     6e-06    0.0056      19      50 ..      22      54 ..      16      77 .. 0.72
   2 ?    1.8   0.0      0.17   1.6e+02     322     364 ..     150     190 ..     127     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
                        AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                   +++++ +  l+G+N++GK++++++l  ++  +
  gi|70607528|ref|YP_256398.1| 22 FKIENKsIGALVGPNGAGKTTLIKILSTLIIPS 54
                                  444444499*****************9887665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   +++ +ll++EP + L p   +++ +l +++ +++   +++t+H
  gi|70607528|ref|YP_256398.1| 150 TDPPVLLLDEPTLGLDPLSARMFRDLVRRIGKEKT--ILLTSH 190
                                   456899**************************995..999999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06    0.0016      14      41 ..      21      49 ..       6     147 .. 0.84
   2 ?   -2.1   0.0       4.8   4.5e+03     160     174 ..     193     207 ..     158     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                        AAA_23 14 eidF.skgltlItGpNGaGKTTildAikl 41
                                  ++   +k + +++GpNGaGKTT++  +  
  gi|70607528|ref|YP_256398.1| 21 SFKIeNKSIGALVGPNGAGKTTLIKILST 49
                                  333367788899************88765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                        AAA_23 160 keleeledekkllek 174
                                   k++eel+++  ll+k
  gi|70607528|ref|YP_256398.1| 193 KDIEELSEKTILLKK 207
                                   444444444444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.1e-05      0.02       4      25 ..      26      47 ..      23      56 .. 0.90
   2 ?    1.5   0.0      0.35   3.3e+02      86     115 ..     145     178 ..     106     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                  +++i++++G+ G+GKTtl++ l
  gi|70607528|ref|YP_256398.1| 26 NKSIGALVGPNGAGKTTLIKIL 47
                                  799***************9966 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.35
                        AAA_22  86 lrarav....ielliiDEaqh.lr..seealeeLrsl 115
                                   +r   +    +++l++DE    l+  s++++++L+++
  gi|70607528|ref|YP_256398.1| 145 AR---AlitdPPVLLLDEPTLgLDplSARMFRDLVRR 178
                                   23...23447889999998888877779999888443 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0003      0.29      23      42 ..      26      45 ..      15      54 .. 0.84
   2 ?    3.2   0.0     0.053        50     149     205 ..     142     198 ..     134     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                                  TSSEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 23 sksftaivGpNGSGKsnlld 42
                                  +ks+ a+vGpNG+GK+ l+ 
  gi|70607528|ref|YP_256398.1| 26 NKSIGALVGPNGAGKTTLIK 45
                                  467899**********9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.053
                                   HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                   L +A   +   p+ llDe    LD    + + +l+++  k+  ++ +s+  + +e+ 
  gi|70607528|ref|YP_256398.1| 142 LALARALITDPPVLLLDEPTLGLDPLSARMFRDLVRRIGKEKTILLTSHYMKDIEEL 198
                                   456666677889***********************************9988777765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.5e-05     0.042      18      50 ..      27      60 ..      21     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaa.ggrvi 50
                                  + + +l+Gp G+GKtt++k l  ++  + g  ++
  gi|70607528|ref|YP_256398.1| 27 KSIGALVGPNGAGKTTLIKILSTLIIPSsGDALV 60
                                  457899**************97766555354433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.3e-05      0.04      89     120 ..      16      48 ..       5      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-05
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinall 120
                                   +l++++ ++++ ++ +lvG+ G+GK+tLi+ l 
  gi|70607528|ref|YP_256398.1|  16 ALDNVSFKIENkSIGALVGPNGAGKTTLIKILS 48 
                                   678888899987899**************9886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   9.8e-05     0.093       3      29 ..      31      68 ..      30      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-05
                        AAA_28  3 vitGgestGKTtlleaLa........ar...gypvvpE 29
                                  +++G+ ++GKTtl++ L+        +    gy+vv+E
  gi|70607528|ref|YP_256398.1| 31 ALVGPNGAGKTTLIKILStliipssgDAlvnGYSVVKE 68
                                  689***************66665544115778888865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.14       3      22 ..      32      51 ..      31     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                        AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                  l G+ G+GKttl k Ls + 
  gi|70607528|ref|YP_256398.1| 32 LVGPNGAGKTTLIKILSTLI 51
                                  89**************9884 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018      0.17       3      21 ..      32      50 ..      31     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                  EESSTTSSHHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavake 21
                                  l+Gp G GKT+l+k + + 
  gi|70607528|ref|YP_256398.1| 32 LVGPNGAGKTTLIKILSTL 50
                                  89************99876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00096      0.91      31      66 ..      10      46 ..       2      59 .. 0.82
   2 ?   -2.9   0.0       5.1   4.9e+03      78     120 ..      85     129 ..      79     142 .. 0.60
   3 ?    0.2   0.0      0.56   5.3e+02     102     148 ..     145     190 ..     135     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00096
                     IstB_IS21 31 dkrkvkeLatlsf.iekkenivllGpsGvGKshlaia 66
                                  + r +++L + sf ie+k   +l+Gp G+GK+ l   
  gi|70607528|ref|YP_256398.1| 10 KGRVINALDNVSFkIENKSIGALVGPNGAGKTTLIKI 46
                                  568899999999967777778***********98665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.1
                     IstB_IS21  78 vlfvrvedLveelkrarrd.gklaralkrllkv.dllilDdlgll 120
                                    +++r+++L + +  a  +  +l+ a +r +++ +l+ l +++ l
  gi|70607528|ref|YP_256398.1|  85 LFYYRLTALENLIFFASLQnLSLSDARRRAMEMlELVGLSEWANL 129
                                   567777777776666654314555444444433366666666655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.56
                     IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsn 148
                                   a + ++ + +l+lD+  lg   ld  +a+++ +++ +  + ++i++ts 
  gi|70607528|ref|YP_256398.1| 145 ARALITDPPVLLLDEptLG---LDPLSARMFRDLVRRIGKEKTILLTSH 190
                                   4455667789999993344...555555555556665556677777775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.16      25      52 ..      28      61 ..      11     188 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                        AAA_16 25 elvllsGesGvGKsslvrellralekd......g 52
                                  ++  l+G+ G GK++l++ l + +  +      +
  gi|70607528|ref|YP_256398.1| 28 SIGALVGPNGAGKTTLIKILSTLIIPSsgdalvN 61
                                  67789************99998777775444442 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022      0.21      19      59 ..      27      63 ..       9     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                  TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEE CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeY 59
                                  +++ +L G+ GaGKTtl++ l   +    + S   +lv+ Y
  gi|70607528|ref|YP_256398.1| 27 KSIGALVGPNGAGKTTLIKILSTLI----IPSSGDALVNGY 63
                                  55679*************9886654....455555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00029      0.28       5      29 ..      30      52 ..      26      69 .. 0.85
   2 ?   -2.9   0.0       4.8   4.6e+03     123     140 ..     181     200 ..     169     231 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                        AAA_24  5 iliyGpsgiGKTtlakelgpkplfi 29
                                   +++Gp+g+GKTtl+k l  ++l+i
  gi|70607528|ref|YP_256398.1| 30 GALVGPNGAGKTTLIKIL--STLII 52
                                  589*************99..66666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                        AAA_24 123 k..nvifiahektrkdedpe 140
                                   k  ++ +++h  ++  e  e
  gi|70607528|ref|YP_256398.1| 181 KekTILLTSHYMKDIEELSE 200
                                   34477777777666555554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00038      0.35       4      24 ..      30      50 ..      27      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                  EEEEESTTSSHHHHHHHHHHH CS
                         SRP54  4 illvGlqGaGKTttlaKLaal 24
                                   +lvG++GaGKTt +  L+ l
  gi|70607528|ref|YP_256398.1| 30 GALVGPNGAGKTTLIKILSTL 50
                                  579**********99877765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00035      0.33      27      55 ..      32      60 ..      28      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                  Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeeal 55
                                  lvGp G+GKt l+k l++l+ p s +  +
  gi|70607528|ref|YP_256398.1| 32 LVGPNGAGKTTLIKILSTLIIPSSGDALV 60
                                  89****************99888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2136.57
//
Query:       gi|70607529|ref|YP_256399.1|  [L=270]
Description: ABC-2 type transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-15   54.6  26.2    2.2e-14   53.4  26.2    1.6  1  ABC2_membrane    ABC-2 type transporter
    0.00013   21.2  26.9    0.00013   21.2  26.9    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.074   12.9   2.8        1.3    8.9   1.6    2.9  2  LapA_dom         Lipopolysaccharide assembly protein A domain
        0.8    9.8   4.0       0.58   10.3   0.9    2.2  2  DUF3742          Protein of unknown function (DUF3742)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4  26.2   4.9e-18   2.2e-14      13     210 .]      23     224 ..      12     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 4.9e-18
                 ABC2_membrane  13 qrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferer.......gvlerel 86 
                                     +r+ +++ ++ ++ p+++  ++gt  gn+   e g+   + ++f+++ laf++  s++++++++r       g++e   
  gi|70607529|ref|YP_256399.1|  23 VSYRTQTILTVLGWVLPVFTYYFVGTSLGNTLVAEIGV--KNYVAFFTIGLAFQGYVSSVISTISQRlrneqlyGTIEYYV 101
                                   345555566699*****************855333333..33333333333333333333333333222222215555555 PP

                 ABC2_membrane  87 vsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllisalapsfedasqlas 166
                                    s++  +  ++l ++l+ l+++++ a+++l+i y l g ++  +++  + +l+l+++ ++++g++ +a+++  ++++ ++ 
  gi|70607529|ref|YP_256399.1| 102 ISRT-GTLGFLLYSALWGLLLNTVNAVVILTIGYAL-GANYHiNIISTITILFLLIISTLGIGMIAGAVTMITKQGNPISL 180
                                   5666.7888999999********************9.88887678************************************ PP

                 ABC2_membrane 167 lvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                   ++ ++++ll+G ++pi+++p ++++i+y  Plt+a+e+lr++++
  gi|70607529|ref|YP_256399.1| 181 FFNTFTNLLGGTVFPITALPIVVRYISYGIPLTWALEGLRGSML 224
                                   ****************************************9985 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2  26.9   2.9e-08   0.00013     159     340 ..      60     247 ..      55     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.9e-08
               ABC2_membrane_3 159 vasflvgliliilifitasfiavsiv....eEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgi 233
                                   v+++++++ + +++  ++s++++ i     +E   +++e  ++s   +l ++l + l+ +l+  + +++il +  a+g   
  gi|70607529|ref|YP_256399.1|  60 VKNYVAFFTIGLAFQGYVSSVISTISqrlrNEQLYGTIEYYVISRTGTLGFLLYSALWGLLLNTVNAVVILTIgyALG--A 138
                                   566666666666666666655555533333899999********************************9999844666..7 PP

               ABC2_membrane_3 234 pfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgl 313
                                   ++  n+++++  ++l +++++ +g+  ++++  ++ ++ + ++++ ++ ++ g +fp+ +lp  +++i++ iP+++  +gl
  gi|70607529|ref|YP_256399.1| 139 NYHiNIISTITILFLLIISTLGIGMIAGAVTMITKQGNPISLFFNTFTNLLGGTVFPITALPIVVRYISYGIPLTWALEGL 219
                                   7778******************************************55555555588************************ PP

               ABC2_membrane_3 314 lrlitgd.plweillsliilalfavvyl 340
                                      + ++ p+ ++l  + il++f v+++
  gi|70607529|ref|YP_256399.1| 220 RGSMLQNtPITSMLNIVEILLIFDVIVV 247
                                   *998555377777766666666666655 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.054   2.4e+02      24      52 ..      64      93 ..      63      98 .. 0.82
   2 ?    8.9   1.6   0.00029       1.3      19      40 ..     151     172 ..     142     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.054
                      LapA_dom 24 lvafgiGa.llgwllslwsylrlrrelrrl 52
                                  +++f iG+ + g++ s++s + +r+++ +l
  gi|70607529|ref|YP_256399.1| 64 VAFFTIGLaFQGYVSSVISTISQRLRNEQL 93
                                  679999996778888889999999998776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00029
                      LapA_dom  19 LsllllvafgiGallgwllslw 40 
                                   L ll++ ++giG+++g ++++ 
  gi|70607529|ref|YP_256399.1| 151 LFLLIISTLGIGMIAGAVTMIT 172
                                   89******************97 PP

>> DUF3742  Protein of unknown function (DUF3742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.29   1.3e+03      54      67 ..      55      68 ..      28      92 .. 0.77
   2 ?   10.3   0.9   0.00013      0.58      51      81 ..     102     132 ..      96     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                       DUF3742 54 lavlGvllyvafWl 67
                                  +a +Gv  yvaf +
  gi|70607529|ref|YP_256399.1| 55 VAEIGVKNYVAFFT 68
                                  46689999999874 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                       DUF3742  51 vvklavlGvllyvafWlalllvvvvlvawaa 81 
                                   + +   lG lly+a W +ll  v  +v++++
  gi|70607529|ref|YP_256399.1| 102 ISRTGTLGFLLYSALWGLLLNTVNAVVILTI 132
                                   667788***********99766666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1781.05
//
Query:       gi|70607530|ref|YP_256400.1|  [L=130]
Description: hypothetical protein Saci_1801 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 910.98
//
Query:       gi|70607531|ref|YP_256401.1|  [L=641]
Description: 4Fe-4S binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-07   29.6   7.4    8.7e-07   29.0   7.4    1.3  1  Fer4_10   4Fe-4S dicluster domain
    2.8e-05   24.0  10.1      0.021   14.9   0.7    2.4  2  Fer4_6    4Fe-4S binding domain
    4.7e-05   23.9   7.8    4.7e-05   23.9   7.8    1.9  1  Fer4_7    4Fe-4S dicluster domain
     0.0014   18.3  11.9      0.067   13.0   0.5    3.0  2  Fer4      4Fe-4S binding domain
     0.0028   17.8   5.8     0.0028   17.8   5.8    1.8  2  Fer4_9    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.028   14.5   1.8      0.028   14.5   1.8    1.7  2  Fer4_11   4Fe-4S dicluster domain
       0.12   12.1   5.9      0.088   12.6   1.5    2.2  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.13   12.4   8.0       0.45   10.7   8.0    1.8  1  Fer4_21   4Fe-4S dicluster domain
       0.21   12.6   7.3        2.2    9.3   0.1    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
       0.27   11.4  14.2       0.12   12.5   2.3    2.7  2  Fer4_2    4Fe-4S binding domain
       0.41   11.7  11.8        2.3    9.4   4.8    2.6  2  Fer4_3    4Fe-4S binding domain
       0.74   10.4   9.4         66    4.2   9.5    2.4  2  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   7.4   5.8e-10   8.7e-07       3      56 .]     568     619 ..     566     619 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.8e-10
                       Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   v+d++ C++C+  +C kaCP+     ++    + +++ + k+++C+g+g C+eaCP
  gi|70607531|ref|YP_256401.1| 568 VKDPELCVKCEtkACSKACPV----GNTDLPGNFIKKGEFKSSRCIGVGDCAEACP 619
                                   789*******9999*******....89999999999999****************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.9   5.4e-05     0.081       5      22 ..     570     589 ..     568     591 .. 0.89
   2 !   14.9   0.7   1.4e-05     0.021       3      23 ..     602     622 ..     602     623 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                        Fer4_6   5 dpdkCigCgd..CvrvCPeg 22 
                                   dp++C+ C+   C ++CP g
  gi|70607531|ref|YP_256401.1| 570 DPELCVKCETkaCSKACPVG 589
                                   9*******7779******86 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.4e-05
                        Fer4_6   3 eidpdkCigCgdCvrvCPega 23 
                                   e++ ++Cig gdC+ +CP++ 
  gi|70607531|ref|YP_256401.1| 602 EFKSSRCIGVGDCAEACPYDN 622
                                   6999**************975 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   7.8   3.1e-08   4.7e-05       2      51 ..     574     621 ..     573     622 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                        Fer4_7   2 CigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   C++C  +aC +aCpv+  +l+    +k     e+++++C+g g C+++CP++
  gi|70607531|ref|YP_256401.1| 574 CVKCetKACSKACPVGNTDLPGNFIKK----GEFKSSRCIGVGDCAEACPYD 621
                                   ****555*************9986555....5******************86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   5.1    0.0018       2.8       2      21 ..     568     589 ..     567     590 .. 0.87
   2 !   13.0   0.5   4.5e-05     0.067       6      23 ..     606     623 ..     602     624 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                                   EEETTTSSS-..THHHHHSTTT CS
                          Fer4   2 videekCigC..GaCvevCPvg 21 
                                   v d+e+C++C  +aC ++CPvg
  gi|70607531|ref|YP_256401.1| 568 VKDPELCVKCetKACSKACPVG 589
                                   68********5558******98 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.5e-05
                                   TTSSS-THHHHHSTTTEE CS
                          Fer4   6 ekCigCGaCvevCPvgAI 23 
                                   ++Cig G C+e+CP++ I
  gi|70607531|ref|YP_256401.1| 606 SRCIGVGDCAEACPYDNI 623
                                   89*************976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       9.7   1.5e+04       8      17 ..     440     449 ..     438     459 .. 0.69
   2 !   17.8   5.8   1.9e-06    0.0028       2      49 ..     574     621 ..     573     623 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.7
                        Fer4_9   8 CveaCpagvv 17 
                                   C   C a ++
  gi|70607531|ref|YP_256401.1| 440 CSVTCTAPTM 449
                                   7777876655 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.9e-06
                        Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   C++C +  C +aCp g +     +++++  +++ ++Cig g+C+eaCp +
  gi|70607531|ref|YP_256401.1| 574 CVKCETkaCSKACPVGNTDLP--GNFIKKGEFKSSRCIGVGDCAEACPYD 621
                                   ****6444******9876443..3333334444468************97 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       4.8   7.1e+03      81      98 ..     435     452 ..     434     453 .. 0.82
   2 ?   14.5   1.8   1.9e-05     0.028       6      61 ..     570     625 ..     567     637 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                       Fer4_11  81 Gllpacvescptgalnfg 98 
                                   G   +c+ +c++ +++ g
  gi|70607531|ref|YP_256401.1| 435 GSRQICSVTCTAPTMYQG 452
                                   566789999*99999877 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.9e-05
                       Fer4_11   6 lpeqCrhCleppCvasapse......aivkdeetGaVlldektkkeevrevveacPykivrk 61 
                                    pe C +C++++C +++p++       ++k+       ++++++  +v +++eacPy+ ++ 
  gi|70607531|ref|YP_256401.1| 570 DPELCVKCETKACSKACPVGntdlpgNFIKKG-----EFKSSRC-IGVGDCAEACPYDNIMF 625
                                   599***************98555444444444.....4667777.5***********86543 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.5   5.9e-05     0.088      19      47 ..     569     599 ..     564     605 .. 0.76
   2 ?    1.3   0.2      0.19   2.8e+02      21      40 ..     605     622 ..     599     640 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                                   HHHTT----TT-HHHHCSTT--.-HH.HHHH CS
                       Fer4_20  19 eeAsRClqCkkapcvkgCPvei.dip.efik 47 
                                   ++ + C++C+++ c+k+CPv + d p +fik
  gi|70607531|ref|YP_256401.1| 569 KDPELCVKCETKACSKACPVGNtDLPgNFIK 599
                                   56677***************75255524665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.19
                                   HTT----TT-HHHHCSTT-- CS
                       Fer4_20  21 AsRClqCkkapcvkgCPvei 40 
                                   +sRC+      c ++CP ++
  gi|70607531|ref|YP_256401.1| 605 SSRCIGV--GDCAEACPYDN 622
                                   6899987..78******875 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   8.0    0.0003      0.45       4      55 ..     570     622 ..     567     625 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                       Fer4_21   4 dedkCigCg..kCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPved 55 
                                   d++ C++C+   C +aC+ + ++ + ++  ++ +  +++C+G   C++ CP ++
  gi|70607531|ref|YP_256401.1| 570 DPELCVKCEtkACSKACPVGNTD-LPGNFIKKGEFKSSRCIGVGDCAEACPYDN 622
                                   7899****7336******76665.5555556668899**************755 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   4.6     0.055        82       2      26 ..     574     604 ..     573     610 .. 0.69
   2 ?    9.3   0.1    0.0015       2.2       1      20 [.     607     626 ..     607     639 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.055
                       Fer4_16   2 CgtCgk..CaevCPtnaikek....kekeie 26 
                                   C++C+   C ++CP++  + +    k+ e++
  gi|70607531|ref|YP_256401.1| 574 CVKCETkaCSKACPVGNTDLPgnfiKKGEFK 604
                                   99997556*******9988774444444455 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   rC++ g Cae+CP + i   
  gi|70607531|ref|YP_256401.1| 607 RCIGVGDCAEACPYDNIMFY 626
                                   699999*******9999766 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.3     8e-05      0.12       5      21 ..     569     587 ..     565     588 .. 0.87
   2 ?    7.9   0.2    0.0024       3.6       5      22 .]     603     620 ..     599     620 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                        Fer4_2   5 vdtdrCigCg..aCvsaCP 21 
                                    d++ C+ C+  aC +aCP
  gi|70607531|ref|YP_256401.1| 569 KDPELCVKCEtkACSKACP 587
                                   69*******667******* PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0024
                        Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                   + + rCig g C  aCP+
  gi|70607531|ref|YP_256401.1| 603 FKSSRCIGVGDCAEACPY 620
                                   778899999********5 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.8    0.0015       2.3       1      14 [.     574     589 ..     574     590 .. 0.93
   2 ?    6.0   0.6     0.018        26       1      14 [.     608     621 ..     607     622 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                        Fer4_3   1 CtgCg..aCvevCPvg 14 
                                   C+ C+  aC ++CPvg
  gi|70607531|ref|YP_256401.1| 574 CVKCEtkACSKACPVG 589
                                   99**9889******98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+g g C e+CP++
  gi|70607531|ref|YP_256401.1| 608 CIGVGDCAEACPYD 621
                                   444478******85 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   3.8      0.48   7.2e+02      45      58 ..     573     588 ..     565     591 .. 0.66
   2 ?    4.2   9.5     0.044        66      39      59 ..     601     621 ..     573     622 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.48
                       Fer4_17  45 lCieC..geCerkCPq 58 
                                   lC++C  + C+++CP 
  gi|70607531|ref|YP_256401.1| 573 LCVKCetKACSKACPV 588
                                   6666633357777774 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.044
                       Fer4_17  39 keekaslCieCgeCerkCPqg 59 
                                    e k s+Ci+ g C+++CP++
  gi|70607531|ref|YP_256401.1| 601 GEFKSSRCIGVGDCAEACPYD 621
                                   235889*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4024.55
//
Query:       gi|70607532|ref|YP_256402.1|  [L=236]
Description: hypothetical protein Saci_1803 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-51  174.4   2.7    2.7e-51  174.2   2.7    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.2   2.7   1.5e-55   2.7e-51       1     200 [.       4     203 ..       4     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.2 bits;  conditional E-value: 1.5e-55
                                   EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------------EEEEEEES.SS-EEEEE--SSSEE CS
                         AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet....gllkalkrlltgeslfllkftakissgtvllapklpgt 77 
                                   +++lg++ ++l+v+L++ge  ya +G +v+ s++v+++t    g+l+++kr+ltg ++f+++f +   +g+v+l+  +pg+
  gi|70607532|ref|YP_256402.1|   4 YQILGDDLQYLKVELAQGEGFYADAGHMVMKSSTVNLQTkmrgGILSGMKRALTGGTFFVTEFYG---PGEVMLSGIFPGK 81 
                                   89**************************************************************5...5************ PP

                                   EEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGG CS
                         AIM24  78 ivtlelgggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpg 157
                                   iv++++  + +++++ + fL a+++ve+d ++  +l +g++ggeglfl +++G G+++l++yG++y ++l++ge+++v+ +
  gi|70607532|ref|YP_256402.1|  82 IVQVQV--QGSILAEAHTFLGAENTVEYDATMA-RLtTGILGGEGLFLARFKGYGNLFLHAYGGLYVKDLAPGETIQVEAS 159
                                   *****9..447**********************.5779******************************************* PP

                                   GEEEEETTEEEEEEEETT---STTTTS-E.EEEEEEEEEEEEES CS
                         AIM24 158 hlvafsgslkfdiervgglkrrligGegl.flkltGpgtvllqs 200
                                   hl+af+++++++++ vggl++ ++  egl f+++tGpg+v+l +
  gi|70607532|ref|YP_256402.1| 160 HLMAFQEGMNYSVQLVGGLRSIFFAHEGLfFVTITGPGRVWLHT 203
                                   ******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1843.57
//
Query:       gi|70607533|ref|YP_256403.1|  [L=112]
Description: hypothetical protein Saci_1804 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-38  131.5   0.7    1.5e-38  131.4   0.7    1.0  1  DUF2173   Uncharacterized conserved protein (DUF2173)


Domain annotation for each model (and alignments):
>> DUF2173  Uncharacterized conserved protein (DUF2173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.4   0.7   8.2e-43   1.5e-38       1     106 []       4     108 ..       4     108 .. 0.99

  Alignments for each domain:
  == domain 1  score: 131.4 bits;  conditional E-value: 8.2e-43
                       DUF2173   1 klkkLmklpGvvAagefsddGelveykGeldeeeaemlakmcaantrmvkmqadglealtgkkGwepvnGwavrgaelsvc 81 
                                   kl+kLm+l+G+++ag++++dG+l ey+G+l++e aem+akm aant m +++a+++++++g+k w+p+ Gwav+++e++vc
  gi|70607533|ref|YP_256403.1|   4 KLNKLMQLRGALVAGHYANDGKLIEYEGQLPKELAEMVAKMVAANTLMGTVEAESFSKISGMK-WTPFLGWAVAAGEYAVC 83 
                                   599************************************************************.***************** PP

                       DUF2173  82 vvgnsavfvenaeadlneilkalae 106
                                   v+gn++vfv+ aead+n+i+k+l+e
  gi|70607533|ref|YP_256403.1|  84 VMGNYGVFVKLAEADFNQIFKTLRE 108
                                   **********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 848.07
//
Query:       gi|70607534|ref|YP_256404.1|  [L=296]
Description: hypothetical protein Saci_1805 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-24   85.5   3.1    3.5e-24   85.5   3.1    1.5  2  MS_channel   Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.093   12.6   0.0       0.17   11.8   0.0    1.4  1  Haemagg_act  haemagglutination activity domain
       0.82    9.5  12.0        1.6    8.6   1.6    2.2  2  DUF2975      Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   2.2       2.1   1.2e+04       6      25 ..      10      29 ..       5      34 .. 0.44
   2 !   85.5   3.1   5.9e-28   3.5e-24       3     193 ..      88     282 ..      86     290 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 2.1
                                  HHHHHHHHHHHHHTTT--SC CS
                    MS_channel  6 iliivvgilivlsllgvnvs 25
                                   +ii++++  v   l+v +s
  gi|70607534|ref|YP_256404.1| 10 AIIILLVVGFVVYILHVVIS 29
                                  44444444444444444444 PP

  == domain 2  score: 85.5 bits;  conditional E-value: 5.9e-28
                                   HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS......SEEEEEE CS
                    MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig......dieGtVe 77 
                                   i+ ++++++ il++ls lgvn++    + +++g+a+gla++++ sn+++Gi+++ +++++ GD v ++       i+G+Ve
  gi|70607534|ref|YP_256404.1|  88 IVDLILYTLLILAILSALGVNLTGAAIGGAVGGVAIGLAAQTVASNVLSGILVTSSRTVRPGDSVILQswiwspPIIGEVE 168
                                   677899*************************************************************************** PP

                                   EE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEE CS
                    MS_channel  78 diglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellv 158
                                    +++++t +rt +g++v +Pns+++ +++  +++ +++  +++  ++t+++dv+ ++++l+++k +l+ + + +++  ++v
  gi|70607534|ref|YP_256404.1| 169 RVSILFTEVRTNTGNLVKVPNSAFLGNTV--FTKLEDGGVLTYPYQLTVNADVS-ANQLLDRVKGILEDEFKKENSLVPDV 246
                                   *************************8887..666689999************55.99999999999999999999999998 PP

                                   EEEEE-SSSEEEEEEEEEET....TTHHHHHHHHHH CS
                    MS_channel 159 vldefgdsslnfevrvfvkt.vvpeeylsvqseinl 193
                                    +      +  f vr+ v++  +++ y ++ +++++
  gi|70607534|ref|YP_256404.1| 247 TFYSKNGATNIFLVRIKVTEiSKLNGYIDIVNKAFD 282
                                   888887777778888777774556666666665555 PP

>> Haemagg_act  haemagglutination activity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.9e-05      0.17      46      84 ..     242     279 ..     210     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                                   -TTEEEEEE-SSSTTSEEEEEE-SSS-EEEECEEEEEEC CS
                   Haemagg_act  46 peggvvlfnaqngaasvilnrVtggspSkIqGaievlga 84 
                                      +v +++ +nga+++ l r+  ++ Sk++G+i+++++
  gi|70607534|ref|YP_256404.1| 242 LVPDVTFYS-KNGATNIFLVRIKVTEISKLNGYIDIVNK 279
                                   445555555.89999999*****************8764 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.6   0.00027       1.6      59     107 ..       8      57 ..       4      58 .. 0.92
   2 ?    6.5   4.6    0.0012       7.4      30     114 ..      53     136 ..      51     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00027
                       DUF2975  59 Lrriglaliaaalllaagivalallae.lelapgvvllllgvafaslvig 107
                                   +r+i+ +l++  +++++ +v+  ++a+   lap+  ++ lgv  a ++ig
  gi|70607534|ref|YP_256404.1|   8 IRAIIILLVVGFVVYILHVVISGFVAQnQTLAPYARDIELGVDAALVGIG 57 
                                   7999**********************************999999988876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0012
                       DUF2975  30 afvvalvqlwkLlrsirkgevFspanvrrLrriglaliaaalllaagivalallaelelap.gvvllllgvafaslvigll 109
                                    + ++ ++++++++++ +g + s+     Lr i+l++ ++  +l+++++  al  +  l +  +   ++gva++ ++  + 
  gi|70607534|ref|YP_256404.1|  53 LVGIGGYIIIRIIKYVIEGYILSRTDNTGLRSISLIVDLILYTLLILAILSALGVN--LTGaAIGGAVGGVAIGLAAQTVA 131
                                   6778889**************************99888886666665555555555..22212222333444444444444 PP

                       DUF2975 110 vlvla 114
                                   + vl+
  gi|70607534|ref|YP_256404.1| 132 SNVLS 136
                                   44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2153.53
//
Query:       gi|70607535|ref|YP_256405.1|  [L=370]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-20   72.5  36.7    8.7e-12   44.6  19.4    2.4  2  MFS_1     Major Facilitator Superfamily
    3.3e-20   72.4  22.2    4.7e-17   62.0  11.9    2.2  2  Sugar_tr  Sugar (and other) transporter
    3.5e-07   29.1  21.1    0.00017   20.3   5.8    2.7  2  MFS_2     MFS/sugar transport protein
  ------ inclusion threshold ------
      0.022   14.3   9.2       0.61    9.7   1.2    3.1  2  FGFR3_TM  Fibroblast growth factor receptor 3 transmembrane d


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6  19.4     2e-15   8.7e-12       4     207 ..      14     205 ..      10     231 .. 0.73
   2 !   31.7  11.9   1.6e-11   7.2e-08      16     148 ..     222     345 ..     208     369 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2e-15
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa. 82 
                                   + +l + + + +++++++   + + +s  +  l++tl ++g + +s+++G+++d++Grr  ++l++++ +l+ +l+l+ + 
  gi|70607535|ref|YP_256405.1|  14 GSLLLTVSEWYTFFLVSQ--VSFFVLSLYVGILIYTLGFIGRVSGSILFGYIGDKMGRRHSIILSAVMIILStSLILI-Sp 91 
                                   555555555555555554..22355555556679999****************************9999999455555.65 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslg....Wravfyila 158
                                   s+l +l+++r lqGl  g+ + a+ +++a+ +   + r + ++l ++++ lG+il   ++ l++s ++    W +  ++  
  gi|70607535|ref|YP_256405.1|  92 SNLLFLVIARTLQGLSLGGEWGAASTILAESYLNsNYRVFILSLNQLSVPLGIILS-TFSILVLSIINkvedWNLFLLLPI 171
                                   7777**************************9999899****************999.666666668888989*99999999 PP

                         MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdp 207
                                   ++s +++     +    +++++  s++++            w+a++ d 
  gi|70607535|ref|YP_256405.1| 172 LLSSISLF---TFKDLGETKSPSTSKIPL------------WEAIRDDW 205
                                   99999833...444444444444444444............55555555 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1.6e-11
                         MFS_1  16 gpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlq 95 
                                   + ++++   +e+  +s+sei++++ + +++++++++++G+l++ fG +rv+l g++++++g++l+l   +   + ++ +  
  gi|70607535|ref|YP_256405.1| 222 YYIFTSyVFSES--LSVSEISTIVLIATITQLFTMPLFGYLANSFGVKRVILSGIVIYVIGATLFL--YN---ITLAELTL 295
                                   344444355666..89*********************************************77777..78...66777777 PP

                         MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllassl 148
                                   ++  +al++   +l++d+f+ + r +++   + +++l++ilg  ++ ++la ++
  gi|70607535|ref|YP_256405.1| 296 SVSNSALYSPQSSLFVDLFKSKYRVSGT---NFSYQLASILGgSMVPSVLA-LY 345
                                   78889999***********998776666...66666666666444444444.22 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0  11.9     1e-20   4.7e-17      19     186 ..      13     179 ..      10     189 .. 0.89
   2 !   16.0   2.6   9.7e-07    0.0043      36      93 ..     227     284 ..     206     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1e-20
                                   GGGTHHHHHHHHTSTT--SHHHHHH...HHH.HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTT CS
                      Sugar_tr  19 igafltllkfaknfglsksksskeessvlsg.livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakg 98 
                                   ig+ l   + ++ f+l +++s     s+++g li  + ++G++ Gs+++g++gd++GR+ s++ +av+ + ++ l+ +++ 
  gi|70607535|ref|YP_256405.1|  13 IGSLLLTVSEWYTFFLVSQVSFFVL-SLYVGiLIYTLGFIGRVSGSILFGYIGDKMGRRHSIILSAVMIILSTSLILISP- 91 
                                   7777888888888888888888885.4554416677789*****************************************. PP

                                   TSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS.-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCH CS
                      Sugar_tr  99 knsvevlivgRvlvGigvGlasvlvPmyisEiA.pkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglql 178
                                    +++  l+++R l G+++G++ + +++ ++E     ++R ++ sl+ql++ +Gi++++++ l+l+ +++ + w ++l l +
  gi|70607535|ref|YP_256405.1|  92 -SNLLFLVIARTLQGLSLGGEWGAASTILAESYlNSNYRVFILSLNQLSVPLGIILSTFSILVLSIINKVEDWNLFLLLPI 171
                                   .78****************************87699*********************************99*********9 PP

                                   HHHHHHHH CS
                      Sugar_tr 179 vpalllli 186
                                   +++ + l+
  gi|70607535|ref|YP_256405.1| 172 LLSSISLF 179
                                   99966554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.7e-07
                                   -SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  36 ksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlq 93 
                                   +++ s+  s + ++ iv i+ + ++++  ++g+l++ fG k ++l ++v++viga l 
  gi|70607535|ref|YP_256405.1| 227 SYVFSESLSVSEISTIVLIATITQLFTMPLFGYLANSFGVKRVILSGIVIYVIGATLF 284
                                   22222233778899****************************************9885 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   5.8   3.8e-08   0.00017     262     342 ..      44     122 ..       4     130 .. 0.80
   2 !   14.5   7.2   2.1e-06    0.0096     170     308 ..     162     286 ..     125     343 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-08
                         MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladv 342
                                     ++++ +i+ + g++l+ ++  ++g++++++l+a++ i+ + l+l+  psnll+++++ ++ g+++g+ + ++  +la++
  gi|70607535|ref|YP_256405.1|  44 L-IYTLGFIGRVSGSILFGYIGDKMGRRHSIILSAVMIILSTSLILIS-PSNLLFLVIARTLQGLSLGGEWGAASTILAES 122
                                   3.44568****************************9999999999999.*******************9999988888876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.1e-06
                         MFS_2 170 gylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYy 250
                                    + +f+l+  lL+ ++ ++     k+      + k ++++k++l+e++++  +n     +ll++ +++     ++  + Y+
  gi|70607535|ref|YP_256405.1| 162 DWNLFLLLPILLSSISLFTF----KDL----GETKSPSTSKIPLWEAIRDDWKN-----ILLAIGVKISESSNYYIFTSYV 229
                                   55555555555554444443....222....23456667777777777776666.....2222222333333444455566 PP

                         MFS_2 251 ltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvll 308
                                   +   l + s++s++ l++ti +l ++pl+ +la  +g k+++l+g+++++++ +l+l 
  gi|70607535|ref|YP_256405.1| 230 FSESL-SVSEISTIVLIATITQLFTMPLFGYLANSFGVKRVILSGIVIYVIGATLFLY 286
                                   66665.457899999999**********************************999875 PP

>> FGFR3_TM  Fibroblast growth factor receptor 3 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.2   0.00014      0.61       3      15 ..      38      50 ..      38      51 .. 0.90
   2 ?    7.6   1.5    0.0006       2.7       7      18 ..     273     284 ..     272     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                      FGFR3_TM  3 svYaeILIYctGf 15
                                  s Y++ILIY  Gf
  gi|70607535|ref|YP_256405.1| 38 SLYVGILIYTLGF 50
                                  57**********9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0006
                      FGFR3_TM   7 eILIYctGffLi 18 
                                   +I+IY++G+ L+
  gi|70607535|ref|YP_256405.1| 273 GIVIYVIGATLF 284
                                   8********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2449.97
//
Query:       gi|70607536|ref|YP_256406.1|  [L=223]
Description: hypothetical protein Saci_1807 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-26   92.3   0.1    4.5e-26   92.1   0.1    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0015   18.1   0.0     0.0025   17.4   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.054   12.9   0.0    1.5  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.1   7.6e-30   4.5e-26       5     197 .]      21     214 ..      17     214 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 7.6e-30
                                   SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCH CS
                   Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfme 85 
                                   +v ++lie+++g+iL+D+Gt++  ++++ e+ +lg+ ++dv++v+ TH+H DHiG +++l++  + +++  +  + +++ e
  gi|70607536|ref|YP_256406.1|  21 FVKVFLIETKEGLILVDSGTPGNGKKIVTEITRLGKSLDDVKYVVFTHSHGDHIGSAHELKDILPDAKFGIESSGVSYLQE 101
                                   6779***************************************************************************** PP

                                   HHHHHHHHCCHH........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                   Lactamase_B  86 eaddaasrkgll........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetg 158
                                   ++ + ++ +++l        +++ ++  ++++ + +  ++  +++++++ +pgh+++++++++++ + +++GD+l   ++g
  gi|70607536|ref|YP_256406.1| 102 GKIRNPVLHSSLqkflfglaRPFIVRGFKGTKVDLELKDGKLVEGVEIMKTPGHTSDSISIYLPEIGSVIVGDMLQGTKRG 182
                                   *******************99999999999999999999999**********************************99999 PP

                                   CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                   +  +           d e++ +s++++++lk+++++ +H
  gi|70607536|ref|YP_256406.1| 183 LKYP-------NIYEDFEELKRSVERIKKLKPKMVYVSH 214
                                   9998.......999999********************99 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.1e-07    0.0025      24      51 ..      54      81 ..      34     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.1e-07
                                  SS--..SEEEEE-SS--HHHHGGGGCCC CS
                 Lactamase_B_2 24 lrdelppidaVllthaHyDHlaglltlr 51
                                  l ++l++++ V++th+H DH+  +  l+
  gi|70607536|ref|YP_256406.1| 54 LGKSLDDVKYVVFTHSHGDHIGSAHELK 81
                                  678999***************6555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-06     0.054       2      51 ..      27      76 ..      26      87 .. 0.89
   2 ?   -3.0   0.0       0.7   4.2e+03      97     117 ..     186     206 ..     164     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-06
                 Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGa 51
                                  +e  +  iL+D G+ ++  ++ + +  l k +++v  ++++h+  +h+G+
  gi|70607536|ref|YP_256406.1| 27 IETKEGLILVDSGTPGNGKKIVTEITRLGKSLDDVKYVVFTHSHGDHIGS 76
                                  6667778********99999999999***********************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.7
                 Lactamase_B_6  97 dseeleledideafdkiktlk 117
                                    +   ++e+ +++ ++ik+lk
  gi|70607536|ref|YP_256406.1| 186 PNIYEDFEELKRSVERIKKLK 206
                                   333446678888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1435.89
//
Query:       gi|70607537|ref|YP_256407.1|  [L=427]
Description: hypothetical protein Saci_1808 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3257.68
//
Query:       gi|70607538|ref|YP_256408.1|  [L=327]
Description: hypothetical protein Saci_1809 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-19   69.9  12.8    2.3e-19   69.9  12.8    2.0  3  CbiQ        Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3      0.21   3.7e+03      60      69 ..      17      26 ..       8      45 .. 0.64
   2 !   69.9  12.8   1.3e-23   2.3e-19       2     217 ..      51     286 ..      50     287 .. 0.77
   3 ?   -3.2   0.6      0.28   5.1e+03      60      71 ..     303     314 ..     291     322 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.21
                                  CHCHHHHHHH CS
                          CbiQ 60 pllflllgll 69
                                   +l++++gl+
  gi|70607538|ref|YP_256408.1| 17 SWLVFFFGLI 26
                                  4666666665 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 1.3e-23
                                   SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---...HHHHHHHCCCHCHHHHHHHHHHE...... CS
                          CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp...rvlaqalilpllflllgllillf...... 73 
                                   +svl +++p +kli ++++++a++l  ++ ++ i++ ++lll+   + p   +++a +l +   + +++   + +      
  gi|70607538|ref|YP_256408.1|  51 ESVLYKISPLTKLILVISTTIAVSLTIWWFGA-ILALIYLLLFSTLNNPgkkILYAGFLTFSTSLGVVSSFSFYTpyyilt 130
                                   688999*************************9.777777777777766656644444444333333333333333566666 PP

                                   ................EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHH CS
                          CbiQ  74 .........qlittegefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillL 145
                                                 ++ fv++g +  ++t e l +g  +a+R+++ ++  lll++TT+p +++  le+++ Pl+++++l++
  gi|70607538|ref|YP_256408.1| 131 qaigtdtlhVIWYWPSYFVYMGYQ-PGLTLEALYYGFQVAFRFIAPMLSGLLLIITTTPSDVLRYLEKVKFPLVFIFALTV 210
                                   344444444222234444444444.5555555************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHTTTTS....SHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHTTS-SS.....S CS
                          CbiQ 146 ayRfiflLleevqrikqAqklRlgds..klgirrslrslgkl..iaalflralkraervalAmeaRGYtgseerth 217
                                   a R i+ +++++++i + q++R++ +    ++r  +  lg l  i++ ++ ++++a  +a+A ++RG++ +++rt+
  gi|70607538|ref|YP_256408.1| 211 AMRSIPRIFDTLDTIVKLQMMRGLGYgkPKALRPFYLLLGGLygIVPTLIFLMRQAKYTAIAADTRGFNAMPKRTY 286
                                   **************************8656666678888888666899*********************9887776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.28
                                   CHCHHHHHHHHH CS
                          CbiQ  60 pllflllgllil 71 
                                     l+ ++++++l
  gi|70607538|ref|YP_256408.1| 303 TVLLYIITAILL 314
                                   222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2292.47
//
Query:       gi|70607539|ref|YP_256409.1|  [L=525]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-48  163.1   0.0    9.3e-23   81.3   0.0    2.2  2  ABC_tran         ABC transporter
    1.8e-17   64.2   0.0      2e-05   24.6   0.0    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.7e-12   46.6   0.0    5.2e-06   27.1   0.0    2.4  2  AAA_23           AAA domain
    3.2e-11   43.1   2.6    6.5e-05   22.5   0.3    3.8  2  SMC_N            RecF/RecN/SMC N terminal domain
    1.3e-09   37.6   0.6    0.00011   21.8   0.1    2.5  2  AAA_29           P-loop containing region of AAA domain
    2.7e-07   31.1   0.0    0.00069   20.0   0.0    2.4  2  AAA_16           AAA ATPase domain
    1.1e-06   28.6   0.0     0.0002   21.2   0.0    3.2  3  AAA_15           AAA ATPase domain
    1.4e-06   28.6   0.7       0.16   12.2   0.5    3.3  2  AAA_22           AAA domain
    1.6e-06   27.9   0.3      0.018   14.7   0.0    2.8  2  AAA_30           AAA domain
    2.8e-06   27.3   1.1      0.065   13.1   0.1    2.7  2  RsgA_GTPase      RsgA GTPase
      1e-05   25.5   2.5       0.13   12.1   0.1    3.2  3  NTPase_1         NTPase
    1.1e-05   25.1   0.1       0.12   11.9   0.0    3.1  3  AAA_25           AAA domain
    4.9e-05   23.3   0.2       0.34   10.8   0.1    2.5  2  NACHT            NACHT domain
    7.3e-05   22.6   0.2       0.52   10.0   0.0    3.2  3  IstB_IS21        IstB-like ATP binding protein
    0.00011   21.7   0.3      0.011   15.2   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00027   20.8   1.0       0.13   12.1   0.1    3.2  3  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0003   20.3   2.3       0.29   10.6   0.0    3.2  3  AAA_7            P-loop containing dynein motor region
    0.00068   19.4   0.6       0.43   10.3   0.1    3.4  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
    0.00077   20.0   2.2          1    9.9   0.0    3.5  2  AAA_18           AAA domain
    0.00095   18.6   0.1       0.77    9.1   0.1    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0016   18.5   3.5          1    9.4   0.4    3.1  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0021   17.5   0.2       0.24   10.7   0.0    2.8  3  ATPase           KaiC
     0.0026   17.5   3.0        1.5    8.5   0.1    3.0  2  AAA_24           AAA domain
     0.0034   16.5   1.4       0.68    8.9   0.2    2.6  2  T2SSE            Type II/IV secretion system protein
     0.0038   17.6   0.5       0.35   11.3   0.0    2.9  2  AAA              ATPase family associated with various cellul
     0.0041   17.5   0.5        2.7    8.4   0.0    2.7  2  RNA_helicase     RNA helicase
     0.0043   16.7   0.3      0.046   13.3   0.1    2.4  2  AAA_27           AAA domain
     0.0051   17.0   0.2        1.8    8.7   0.0    2.5  2  AAA_33           AAA domain
      0.006   16.6   0.2       0.66   10.0   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0064   15.4   0.4        1.1    8.0   0.1    2.2  2  DLIC             Dynein light intermediate chain (DLIC)
     0.0076   16.2   0.3        4.3    7.2   0.0    3.0  3  Rad17            Rad17 P-loop domain
      0.009   16.2   0.1       0.66   10.2   0.0    3.2  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.015   14.5   0.1        1.5    7.9   0.0    2.3  2  NB-ARC           NB-ARC domain
      0.016   15.3   1.3        1.6    8.8   0.2    2.9  2  DUF87            Helicase HerA, central domain
      0.029   12.3   0.3        2.8    5.8   0.1    2.1  2  Herpes_Helicase  Helicase
      0.032   13.9   1.1       0.24   11.0   0.2    2.3  2  SRP54            SRP54-type protein, GTPase domain
      0.034   13.9   4.1        4.7    6.9   0.1    3.1  3  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.039   13.6   0.0        2.5    7.7   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.043   13.6   1.9        6.3    6.5   0.1    2.6  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.049   14.0   3.6         18    5.7   0.1    3.7  4  AAA_19           AAA domain
      0.061   12.1   4.0        1.9    7.2   0.1    3.4  4  ABC_ATPase       Predicted ATPase of the ABC class
      0.061   12.7   1.1         14    5.0   0.0    3.3  4  TniB             Bacterial TniB protein
      0.065   12.5   1.6        7.8    5.7   0.0    2.6  2  Zeta_toxin       Zeta toxin
      0.067   12.3   0.1        1.2    8.2   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
      0.071   12.4   1.9        4.9    6.4   0.1    2.4  2  ATP_bind_2       P-loop ATPase protein family
      0.072   12.8   0.1       0.77    9.4   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.073   13.1   0.5        7.6    6.5   0.1    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
      0.083   12.1   0.7          7    5.8   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.11   12.4   0.9        1.8    8.4   0.1    2.5  2  APS_kinase       Adenylylsulphate kinase
       0.17   11.4   1.9         11    5.6   0.2    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.18   12.1   5.4        1.1    9.5   0.2    2.5  2  AAA_28           AAA domain
       0.53    8.9   1.5          5    5.7   0.0    2.8  4  AAA_13           AAA domain
        1.4    8.7   3.3        9.3    6.0   0.2    2.9  2  DEAD             DEAD/DEAH box helicase
        2.7    8.0   5.4        8.4    6.5   0.9    2.7  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   8.3e-25   2.8e-22       7     137 .]      27     172 ..      24     172 .. 0.85
   2 !   81.3   0.0   2.8e-25   9.3e-23       3     137 .]     302     448 ..     300     448 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 8.3e-25
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.. RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.. 79 
                                    +++ge v i+G++G+GKStL++++ g          +Ge+ + gk++k+++l++l+  +g++ q+ ++   ++tv+e+  
  gi|70607539|ref|YP_256409.1|  27 FIEKGESVLITGRSGSGKSTLVSCINGIIPHmtsgdLKGEVYVLGKSIKDTPLSKLSTVVGTVLQDpESQVVNYTVEEEva 107
                                   589************************9988877778899999***********************7556677789999** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              +  e++++ ++  g+++l  +     +++LSgG+ qr +la +l  +p++l+lDEpt+
  gi|70607539|ref|YP_256409.1| 108 fgpenlnfppeQIVERVKESMEIAGISHLWGRE----TTTLSGGELQRTVLASVLTMRPEVLILDEPTS 172
                                   **9999995555555555555555666655555....5*****************************96 PP

  == domain 2  score: 81.3 bits;  conditional E-value: 2.8e-25
                                   EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vre 78 
                                   + sl+l ege+vai+G+nGaGK+t lk+lag l+       G+i+++g++l +++     k + ++pq   l   ++ vr+
  gi|70607539|ref|YP_256409.1| 302 DFSLDLWEGELVAIMGKNGAGKTTALKALAGILDTseysITGSIKYQGEELINKPVWYRGKYMIYMPQSFDLMLVTNqVRK 382
                                   6799*****************************99888889************9***************444444433777 PP

                                   H...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   +           +++e  ek+++++gl e +d+      + LS G+++rva+a +l++  k++l+DEpt+
  gi|70607539|ref|YP_256409.1| 383 EieyslkkrkvkNYREISEKYMREFGLFEYRDRDP----TLLSMGERRRVAMASVLASGVKIMLMDEPTS 448
                                   7999988766654444599**********999998....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0024      0.79       3      22 ..      35      54 ..      33     101 .. 0.84
   2 !    9.5   0.0    0.0023      0.77     237     287 ..     144     191 ..     138     199 .. 0.82
   3 !   24.6   0.0   6.1e-08     2e-05       2      89 ..     313     401 ..     312     415 .. 0.85
   4 !   16.7   0.0   1.5e-05     0.005     229     299 ..     412     479 ..     383     482 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0024
                        AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                  +++G+ gsGKS+L  ++ ++
  gi|70607539|ref|YP_256409.1| 35 LITGRSGSGKSTLVSCINGI 54
                                  79***************887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                        AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                   lS G ++   +l+++l  ++   +l++DEp ++++P+ +  ++  lk+l+ 
  gi|70607539|ref|YP_256409.1| 144 LSGGELQR-TVLASVLTMRP--EVLILDEPTSNIDPEGTNQIFSTLKDLRG 191
                                   67788888.89999999998..9*************988888888877765 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 6.1e-08
                        AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersq 82 
                                    ++ G+Ng+GK++ L+al ++ ++  +++ + ++ +g   i k  ++   y + +p  f +  ++++ vr + ++ l+++ 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSEYSITGSIKYQGEELINKPVWYRGKYMIYMPQSFDLM-LVTNQVRKEIEYSLKKRK 392
                                   6899********************999999999999999*****************999999.999999999999999999 PP

                        AAA_21  83 v..eeklss 89 
                                   v  ++ +s+
  gi|70607539|ref|YP_256409.1| 393 VknYREISE 401
                                   944333333 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 1.5e-05
                        AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                   +++++++ lS+G +r  a+++ l++     ++ l DEp +g +++   +l + l++l+++g  v+++TH+ 
  gi|70607539|ref|YP_256409.1| 412 YRDRDPTLLSMGERRRVAMASVLASGV---KIMLMDEPTSGQDYSNKMSLGKELRQLTDKGYTVVVVTHDS 479
                                   467788999***************988...9**************************************96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-05     0.006      22      48 ..      34      60 ..      18     126 .. 0.85
   2 !   27.1   0.0   1.6e-08   5.2e-06      15      85 ..     301     394 ..     288     465 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-05
                        AAA_23 22 tlItGpNGaGKTTildAiklaLygetp 48
                                  +lItG  G+GK+T++ +i  +  + t+
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCINGIIPHMTS 60
                                  79****************987766665 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.6e-08
                        AAA_23  15 idF.....skgltlItGpNGaGKTTildAiklaL.ygetprlsrks............grgfeksdveiese......... 68 
                                   +dF     +  l++I G+NGaGKTT l A+  +L + e + +++ +            +    +       +         
  gi|70607539|ref|YP_256409.1| 301 VDFsldlwEGELVAIMGKNGAGKTTALKALAGILdTSEYSITGSIKyqgeelinkpvwY----R-------Gkymiympqs 370
                                   56666669999***********************9999998888885443333322220....2.......1233333344 PP

                        AAA_23  69 .......gkvkayveltfenkdgr 85 
                                          ++v++ +e ++++ + +
  gi|70607539|ref|YP_256409.1| 371 fdlmlvtNQVRKEIEYSLKKRKVK 394
                                   445555444444444444333332 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.6e-05    0.0085      27     201 ..      34     204 ..      24     220 .. 0.72
   2 !   22.5   0.3     2e-07   6.5e-05      23     212 ..     309     493 ..     293     499 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-05
                                   EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                     i+G+ GSGKs l+  i  ++ + ++  l+ e +  ++ k  +++  s  +  v  ++++++++++  + e ++    ++
  gi|70607539|ref|YP_256409.1|  34 VLITGRSGSGKSTLVSCINGIIPHMTSGDLKGEVY--VLGKsiKDTPLSKLSTVVGTVLQDPESQVVNYTVEEEVAFGPEN 112
                                   5799**************99999888888887754..33333233444444555566667777774443334444444444 PP

                                   TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                    +    +i ++  ++ e++ + +  g + ++LSgGe + + la +     ++p+ l +lDe  +++D + ++++ + lk  
  gi|70607539|ref|YP_256409.1| 113 LNFPPEQIVERVKESMEIAGISHLWGRETTTLSGGELQRTVLASV---LTMRPEVL-ILDEPTSNIDPEGTNQIFSTLKDL 189
                                   444455666677777777777777777888******999999866...56678765.89********************** PP

                                   CTTSEEEEE-SSHHH CS
                                   xxxxxxxxxxxxxxx RF
                         SMC_N 187 sknaQfivislreem 201
                                   + +  +i++ ++ e 
  gi|70607539|ref|YP_256409.1| 190 RGQKTLIIVEHKVER 204
                                   *99999999998654 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2e-07
                                   TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH..CCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                         SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrse..klsdlihkskekasvkkaeveitfdnedkk.lkiekeevsis 100
                                   + ++ ai+G+NG+GK+  l A+  +L +++++   s   + ++li+k    +   +++  i++ ++ +  l++++ + +i 
  gi|70607539|ref|YP_256409.1| 309 EGELVAIMGKNGAGKTTALKALAGILDTSEYSITGSIkyQGEELINK----PVWYRGKYMIYMPQSFDLmLVTNQVRKEI- 384
                                   556889********************988874444431145678887....55666666665433333312223333333. PP

                                   EEEETTSEEEEEETTEEE-H.HHHHH.......HHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 101 rrvkrkgeseykingkevtk.kevse.......llesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                            ey +++++v++ +e+se       l+e  + +++lLS Ge+  va+a ++A        ++l+De  +  D 
  gi|70607539|ref|YP_256409.1| 385 ---------EYSLKKRKVKNyREISEkymrefgLFEYRDRDPTLLSMGERRRVAMASVLAS----GVKIMLMDEPTSGQDY 452
                                   .........3444444444334443210000115666666778**************9985....5679************ PP

                                   HHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCEEEEE CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxxx RF
                         SMC_N 174 knvkkvaellkekskn.aQfivislreemleka.dklvgvt 212
                                   +n   + + l++ +++   ++v++++++++ +  d+l+ ++
  gi|70607539|ref|YP_256409.1| 453 SNKMSLGKELRQLTDKgYTVVVVTHDSKFVYDFaDRLIVIS 493
                                   ***********99988789999***9998765437777665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.4e-07   0.00011      22      40 ..      30      49 ..      22      57 .. 0.81
   2 !   13.6   0.1   0.00013     0.042      23      47 ..     310     335 ..     297     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-07
                        AAA_29 22 kg.atlltGpsGsGKSTllD 40
                                  kg ++l+tG+sGsGKSTl+ 
  gi|70607539|ref|YP_256409.1| 30 KGeSVLITGRSGSGKSTLVS 49
                                  4559**************95 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00013
                        AAA_29  23 g.atlltGpsGsGKSTllDAiqalLv 47 
                                   g  + ++G++G+GK+T l A++ +L 
  gi|70607539|ref|YP_256409.1| 310 GeLVAIMGKNGAGKTTALKALAGILD 335
                                   34789***************998885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.1e-06   0.00069      23      88 ..      30      92 ..      22     198 .. 0.49
   2 !    8.7   0.0    0.0062       2.1      24      51 ..     310     337 ..     298     415 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqalareellrqllde 88
                                   +e+vl++G sG+GKs+lv ++   +         g +++ gk  +    +p+s l       +++  +l++
  gi|70607539|ref|YP_256409.1| 30 KGESVLITGRSGSGKSTLVSCINGIIPHMtsgdlkGEVYVLGKSIKD---TPLSKLS------TVVGTVLQD 92
                                  4589*****************99655544666665333344444444...4543333......333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0062
                        AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                   +elv + G  G GK++ +++l+  l ++
  gi|70607539|ref|YP_256409.1| 310 GELVAIMGKNGAGKTTALKALAGILDTS 337
                                   4899****************99777766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.71   2.4e+02      26      44 ..      34      52 ..      24      78 .. 0.86
   2 !   21.2   0.0     6e-07    0.0002      13      84 ..     299     377 ..     292     415 .. 0.62
   3 ?    1.5   0.0      0.58   1.9e+02     325     369 .]     439     482 ..     432     482 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.71
                        AAA_15 26 tvliGkNnsGKSsileald 44
                                   ++ G+ +sGKS+++  ++
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCIN 52
                                  5677**********99885 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 6e-07
                        AAA_15  13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef......... 83 
                                   ++ d+++dl e  l  + GkN++GK+++l+al  +l+++e+           +++++ ++  +k+++ + ++         
  gi|70607539|ref|YP_256409.1| 299 QIVDFSLDLWEGeLVAIMGKNGAGKTTALKALAGILDTSEYSI-------TGSIKYQGEELINKPVWYRGKYmiympqsfd 372
                                   5667888887778************************995554.......3445555555555555555555444444334 PP

                        AAA_15  84 ....a 84 
                                        
  gi|70607539|ref|YP_256409.1| 373 lmlvT 377
                                   43331 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.58
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                   +i l++EP   + ++++++l k l+ l +++   v++ TH + ++
  gi|70607539|ref|YP_256409.1| 439 KIMLMDEPTSGQDYSNKMSLGKELRQLTDKGY-TVVVVTHDSKFV 482
                                   58999**************************8.9******99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.5   0.00048      0.16       5     115 ..      31     189 ..      28     206 .. 0.53
   2 !   11.5   0.0   0.00084      0.28       7      38 ..     312     353 ..     309     445 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00048
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee................................erpevvfvtlpsst.. 51 
                                     ++++tG sG+GK+tl+  +    +                                       ++++vv +t+ ++   
  gi|70607539|ref|YP_256409.1|  31 GESVLITGRSGSGKSTLVSCINGIIPHMT---SgdlkgevyvlgksikdtplsklstvvgtvlqdPESQVVNYTVEEEVaf 108
                                   56899************988777665333...1333555555555555555544444444444443333332222222222 PP

                        AAA_22  52 sskdllrellralglelka..............erlsseellealeqalraravielliiDEaqh.lr...seealeeLrs 114
                                   ++++l     +++++ +++               +ls  el +++   + + +  e+li+DE    ++   +++++++L++
  gi|70607539|ref|YP_256409.1| 109 GPENLNFPPEQIVERVKESmeiagishlwgretTTLSGGELQRTVLASVLTMRP-EVLILDEPTSnIDpegTNQIFSTLKD 188
                                   333333333333333222255566667666655555555666666666665555.77777776655544433555666555 PP

                        AAA_22 115 l 115
                                   l
  gi|70607539|ref|YP_256409.1| 189 L 189
                                   5 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00084
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..........e 38 
                                   +++++G  G+GKTt l+ l+  ld  ++  +           
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAGILDTSEYSITgsikyqgeelI 353
                                   689****************99998777666566666444441 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0011      0.36      13      45 ..      26      58 ..      20     198 .. 0.78
   2 !   14.7   0.0   5.5e-05     0.018      19      51 ..     311     343 ..     297     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                        AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaa 45
                                  l  ++   +++tG+ G+GK+t+++ ++ ++ + 
  gi|70607539|ref|YP_256409.1| 26 LFIEKGESVLITGRSGSGKSTLVSCINGIIPHM 58
                                  5555556899*************9998877655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.5e-05
                        AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvig 51 
                                    ++++ G  G+GKttalkal+ +++++++++ g
  gi|70607539|ref|YP_256409.1| 311 ELVAIMGKNGAGKTTALKALAGILDTSEYSITG 343
                                   48899******************9999988865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00042      0.14      98     121 ..      30      53 ..      14      72 .. 0.83
   2 !   13.1   0.1    0.0002     0.065      78     126 ..     289     337 ..     260     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00042
                                   TTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                   k++ +++ G SG GKStL+  +++
  gi|70607539|ref|YP_256409.1|  30 KGESVLITGRSGSGKSTLVSCING 53 
                                   45788999**********988776 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0002
                                   EEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  78 evllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                   + l +++k+k+ ++   +l+++++++++G+ G+GK+t ++al++ l+++
  gi|70607539|ref|YP_256409.1| 289 ANLRINVKEKQIVDFSLDLWEGELVAIMGKNGAGKTTALKALAGILDTS 337
                                   4556777777777777888999********************9975554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00062      0.21       2      20 ..      34      52 ..      33      60 .. 0.87
   2 !   12.1   0.1    0.0004      0.13       2      34 ..     313     345 ..     312     352 .. 0.91
   3 ?   -0.9   0.0       4.1   1.4e+03     114     144 ..     458     489 ..     426     499 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00062
                                  EEEE--TTSSHHHHHHHHH CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvl 20
                                  v+iTG++G+GK+Tlv+ + 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCIN 52
                                  89*************8775 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0004
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfy 34 
                                   v+i G+ G GKtT +k ++  l+ s+++++G +
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSEYSITGSI 345
                                   6899**************************976 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.1
                                   HHHHHHHHHTTTSEEEEE--SS-.-SHHHHHH CS
                      NTPase_1 114 fkeaveevLksekpvlavihrrk.dlalveei 144
                                   + ++++++ +++  v++v h +k   ++ +++
  gi|70607539|ref|YP_256409.1| 458 LGKELRQLTDKGYTVVVVTHDSKfVYDFADRL 489
                                   56788999999999999999987655666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00036      0.12      28      51 ..      26      49 ..      14      54 .. 0.86
   2 !    8.8   0.0    0.0034       1.1      32      54 ..     309     331 ..     292     336 .. 0.88
   3 ?   -0.4   0.0       2.1   7.1e+02     169     191 ..     459     480 ..     447     481 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                        AAA_25 28 gllpagelallaGapgtGKttlal 51
                                   ++ +ge +l++G++g+GK+tl++
  gi|70607539|ref|YP_256409.1| 26 LFIEKGESVLITGRSGSGKSTLVS 49
                                  5899******************87 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0034
                        AAA_25  32 agelallaGapgtGKttlaldla 54 
                                   +gel++++G  g+GKtt++  la
  gi|70607539|ref|YP_256409.1| 309 EGELVAIMGKNGAGKTTALKALA 331
                                   8****************987776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.1
                        AAA_25 169 vealeriarrtgaavllvhHvgK 191
                                    + l+++ + +g +v++v H +K
  gi|70607539|ref|YP_256409.1| 459 GKELRQL-TDKGYTVVVVTHDSK 480
                                   5678888.7999********887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0014      0.46       3      20 ..      34      51 ..      32     168 .. 0.85
   2 !   10.8   0.1     0.001      0.34       2      25 ..     312     335 ..     311     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                  EEEEC-TTTCHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkl 20
                                  v+++G++GsGK+tL+  +
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCI 51
                                  89************9644 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.001
                                   CEEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   2 lvilqGeaGsGKTtLlqklalawa 25 
                                   lv++ G++G GKTt l+ la  + 
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAGILD 335
                                   799**************9997665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0016      0.52      43      65 ..      27      49 ..      20      53 .. 0.87
   2 ?    5.4   0.0     0.042        14     106     146 ..     159     198 ..     142     204 .. 0.81
   3 ?    3.2   0.0      0.19        64      46      68 ..     309     331 ..     269     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                     IstB_IS21 43 fiekkenivllGpsGvGKshlai 65
                                  fiek e+++++G sG GKs l  
  gi|70607539|ref|YP_256409.1| 27 FIEKGESVLITGRSGSGKSTLVS 49
                                  9******************9865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.042
                     IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiit 146
                                    +++++lilD+  + ++d + ++++f  +++  +++++ii 
  gi|70607539|ref|YP_256409.1| 159 TMRPEVLILDEP-TSNIDPEGTNQIFSTLKDLRGQKTLIIV 198
                                   3577*******6.689**************99999888875 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.19
                     IstB_IS21  46 kkenivllGpsGvGKshlaialg 68 
                                   + e ++++G  G+GK+    al+
  gi|70607539|ref|YP_256409.1| 309 EGELVAIMGKNGAGKTTALKALA 331
                                   56889***********8777776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.2e-05     0.011      23      53 ..      32      62 ..      23      81 .. 0.88
   2 ?    3.9   0.1     0.089        30      26      48 ..     314     336 ..     309     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                  Mg_chelatase 23 HnlllvGppGsGKtmlakrlpsllpplseee 53
                                   ++l++G +GsGK+ l +++++++p++++ +
  gi|70607539|ref|YP_256409.1| 32 ESVLITGRSGSGKSTLVSCINGIIPHMTSGD 62
                                  5799**********************99865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.089
                  Mg_chelatase  26 llvGppGsGKtmlakrlpsllpp 48 
                                    ++G  G+GKt   k+l+++l  
  gi|70607539|ref|YP_256409.1| 314 AIMGKNGAGKTTALKALAGILDT 336
                                   579*****************965 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.076        25       2      18 ..      34      50 ..      33      67 .. 0.71
   2 !   12.1   0.1    0.0004      0.13       2      37 ..     313     349 ..     312     355 .. 0.88
   3 ?    0.4   0.0       1.7   5.7e+02      18      37 ..     460     479 ..     449     486 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.076
                          MobB  2 lgivgksgsGKTtLlek 18
                                  + i+g+sgsGK tL++ 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSC 50
                                  5699**********863 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0004
                          MobB   2 lgivgksgsGKTtLleklipelkarglrv.gtiKhah 37 
                                   ++i+gk+g+GKTt l+ l  +l  +++++ g iK + 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSEYSItGSIKYQG 349
                                   789************************9856888765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.7
                          MobB  18 klipelkarglrvgtiKhah 37 
                                   k +++l+++g++v ++ h++
  gi|70607539|ref|YP_256409.1| 460 KELRQLTDKGYTVVVVTHDS 479
                                   55789************986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00088      0.29      27      51 ..      25      49 ..      21      66 .. 0.88
   2 ?    6.1   0.0     0.022       7.3      34      64 ..     311     341 ..     293     347 .. 0.88
   3 ?    1.5   0.1      0.55   1.8e+02      68     102 ..     370     404 ..     360     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00088
                         AAA_7 27 elllknkkpvllvGptGtGKtviik 51
                                  el+++++ +vl++G +G+GK+++++
  gi|70607539|ref|YP_256409.1| 25 ELFIEKGESVLITGRSGSGKSTLVS 49
                                  67899*****************986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                         AAA_7  34 kpvllvGptGtGKtviikdllkkldkekyls 64 
                                     v ++G+ G GKt+ +k l   ld+++y++
  gi|70607539|ref|YP_256409.1| 311 ELVAIMGKNGAGKTTALKALAGILDTSEYSI 341
                                   568899***************9999999876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.55
                         AAA_7  68 nfsaqtsanqlqdiiesklekrrkgvygPpggkkl 102
                                   +f  +   nq+++ ie +l+kr+ ++y    +k +
  gi|70607539|ref|YP_256409.1| 370 SFDLMLVTNQVRKEIEYSLKKRKVKNYREISEKYM 404
                                   677778899****************9987777765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.065        22       3      23 ..      33      53 ..      31      60 .. 0.88
   2 ?   -0.7   0.0       3.1     1e+03     105     128 ..     118     141 ..     114     153 .. 0.79
   3 !   10.3   0.1    0.0013      0.43       4      45 ..     313     357 ..     311     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.065
                     PduV-EutP  3 killiGkvgsGKttLtqalkg 23
                                   +l+ G++gsGK tL   ++g
  gi|70607539|ref|YP_256409.1| 33 SVLITGRSGSGKSTLVSCING 53
                                  58999**********988876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.1
                     PduV-EutP 105 eenieaveelLksaGaekifevsa 128
                                   e+ +e v+e ++ aG+++++  ++
  gi|70607539|ref|YP_256409.1| 118 EQIVERVKESMEIAGISHLWGRET 141
                                   566899**********99876555 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0013
                     PduV-EutP   4 illiGkvgsGKttLtqalkg..eelkYkktqaiefs.deviDtPG 45 
                                   + ++Gk g+GKtt  +al g  ++ +Y+ t +i+++ +e+i  P 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGilDTSEYSITGSIKYQgEELINKPV 357
                                   678****************98878899999999987345577774 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4     0.016       5.5       1      15 [.      34      48 ..      34      71 .. 0.92
   2 !    9.9   0.0     0.003         1       1      20 [.     313     332 ..     313     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                        AAA_18  1 IlltGtpGvGKttla 15
                                  +l+tG +G+GK+tl 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLV 48
                                  79***********96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.003
                        AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                   ++++G+ G+GKtt  k+L+ 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAG 332
                                   689***************75 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0023      0.77      36      56 ..      29      48 ..      21      57 .. 0.83
   2 !    7.1   0.0     0.009         3      38      59 ..     310     330 ..     275     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0023
                                  GGS-.SEEEE--TTSSHHHHH CS
                  FtsK_SpoIIIE 36 kkmashllvaGatgsGKStal 56
                                   k +  +l+ G++gsGKSt +
  gi|70607539|ref|YP_256409.1| 29 EKGE-SVLITGRSGSGKSTLV 48
                                  5555.79************87 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.009
                                   S-.SEEEE--TTSSHHHHHHHH CS
                  FtsK_SpoIIIE  38 mashllvaGatgsGKStalntL 59 
                                    +  + ++G  g GK+tal++L
  gi|70607539|ref|YP_256409.1| 310 GE-LVAIMGKNGAGKTTALKAL 330
                                   33.678**************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0055       1.8       2      19 ..      34      51 ..      33      67 .. 0.86
   2 !    9.4   0.4    0.0031         1       2      22 ..     313     337 ..     312     499 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0055
                                  EEEEESTTSSHHHHHHHH CS
                      MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                  v+i Gr+ +GKStL++ +
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCI 51
                                  89************9876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0031
                                   EEEEESTTSSHHHHHHHHHT....S CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg....e 22 
                                   vai+G+  +GK+t ++al g    +
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGildtS 337
                                   89****************9844331 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00071      0.24       9      36 ..      24      48 ..      17      52 .. 0.87
   2 ?    3.4   0.0      0.12        41      17      34 ..     308     325 ..     299     331 .. 0.89
   3 ?   -2.8   0.0       9.9   3.3e+03      69      86 ..     457     474 ..     436     480 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                        ATPase  9 DeilkgGipegrvvlitGepGtGKtifa 36
                                  De++   i +g++vlitG +G+GK++++
  gi|70607539|ref|YP_256409.1| 24 DELF---IEKGESVLITGRSGSGKSTLV 48
                                  6777...899***************986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                        ATPase  17 pegrvvlitGepGtGKti 34 
                                    eg+ v i+G+ G+GKt+
  gi|70607539|ref|YP_256409.1| 308 WEGELVAIMGKNGAGKTT 325
                                   68999************7 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 9.9
                        ATPase  69 slGwdlekleeegklaii 86 
                                   slG +l++l ++g  +++
  gi|70607539|ref|YP_256409.1| 457 SLGKELRQLTDKGYTVVV 474
                                   455555555555544444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0058       1.9       3      22 ..      32      51 ..      30      59 .. 0.86
   2 !    8.5   0.1    0.0045       1.5       5      22 ..     313     330 ..     310     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0058
                        AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                   ++li+G sg+GK+tl++ +
  gi|70607539|ref|YP_256409.1| 32 ESVLITGRSGSGKSTLVSCI 51
                                  579*************9865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   ++i+G++g+GKTt +k l
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKAL 330
                                   78************9987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2     0.002      0.68     128     154 ..      30      56 ..      22      61 .. 0.82
   2 ?    5.6   0.0     0.021       7.1     130     159 ..     311     340 ..     278     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                         T2SSE 128 erglilvsGgTgsGKttllyallkein 154
                                   +  ++l++G  gsGK+tl+  +  +i+
  gi|70607539|ref|YP_256409.1|  30 KGESVLITGRSGSGKSTLVSCINGIIP 56 
                                   45789*************998877776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                         T2SSE 130 glilvsGgTgsGKttllyallkeinksder 159
                                    l+ + G  g GKtt l al  ++++s+  
  gi|70607539|ref|YP_256409.1| 311 ELVAIMGKNGAGKTTALKALAGILDTSEYS 340
                                   56678899***************9998655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.34   1.1e+02       1      18 [.      34      51 ..      34      77 .. 0.89
   2 !   11.3   0.0     0.001      0.35       2      37 ..     314     355 ..     313     400 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.34
                                  EEEESSTTSSHHHHHHHH CS
                           AAA  1 vllyGppGtGKTllakav 18
                                  vl++G  G GK++l++ +
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCI 51
                                  799***********9876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.001
                                   EEESSTTSSHHHHHHHHHHHHTHE......EEEEETTTCSSS CS
                           AAA   2 llyGppGtGKTllakavakelgve......fleisgsellsk 37 
                                    ++G  G GKT++ ka+a  l+++       ++ +g el++k
  gi|70607539|ref|YP_256409.1| 314 AIMGKNGAGKTTALKALAGILDTSeysitgSIKYQGEELINK 355
                                   578*****************9755222223456666666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0     0.008       2.7       1      37 [.      34      70 ..      34      80 .. 0.72
   2 ?    6.5   0.1     0.032        11       2      23 ..     314     335 ..     313     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.008
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl.klkkkdsvysr 37
                                  ++++G+sg GKStl+   ++ +  ++   + k++vy+ 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSC-INGIIPHMtSGDLKGEVYVL 70
                                  6799**********998.55555444355556777764 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.032
                  RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                                    + G++g GK+t+ k La  l 
  gi|70607539|ref|YP_256409.1| 314 AIMGKNGAGKTTALKALAGILD 335
                                   689*************875554 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.5   4.9e+02      29      47 ..      34      52 ..      25      58 .. 0.85
   2 !   13.3   0.1   0.00014     0.046      16      49 ..     302     333 ..     296     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                        AAA_27 29 hliyGpNEAGKstalrAis 47
                                   li G   +GKst+++ i+
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCIN 52
                                  5899**********99886 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00014
                        AAA_27  16 drsldfsaeeadlhliyGpNEAGKstalrAisdl 49 
                                   d sld+   e +l  i+G N AGK+tal+A+  +
  gi|70607539|ref|YP_256409.1| 302 DFSLDLW--EGELVAIMGKNGAGKTTALKALAGI 333
                                   5556665..788999***************9866 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.038        12       2      16 ..      34      48 ..      34      55 .. 0.90
   2 !    8.7   0.0    0.0054       1.8       1      21 [.     312     332 ..     312     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.038
                        AAA_33  2 vllvGlpGsGKstla 16
                                  vl+ G +GsGKstl+
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLV 48
                                  6789*********97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0054
                        AAA_33   1 lvllvGlpGsGKstlaerllk 21 
                                   lv + G +G+GK+t ++ l+ 
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAG 332
                                   68899************9964 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.15        49      19      39 ..      31      51 ..      20      62 .. 0.80
   2 !   10.0   0.0     0.002      0.66       8      45 ..     301     336 ..     292     345 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                                  TEEEEEEESTTSSHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                  g+ +l++G  G+GK+tlv  +
  gi|70607539|ref|YP_256409.1| 31 GESVLITGRSGSGKSTLVSCI 51
                                  6679*************9765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                                   HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                          TsaE   8 ealgkklakalgdvilLeGdLGaGKTtlvrglakalgv 45 
                                    ++  +l +  g+++++ G+ GaGKTt  ++la  l+ 
  gi|70607539|ref|YP_256409.1| 301 VDFSLDLWE--GELVAIMGKNGAGKTTALKALAGILDT 336
                                   444445545..889*****************9987765 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0034       1.1      25      50 ..      31      56 ..      25      83 .. 0.86
   2 ?    5.4   0.0     0.021         7      24      51 ..     309     336 ..     299     343 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                          DLIC 25 gksvlvlGedgsGkttliaklqGvee 50
                                  g svl+ G +gsGk+tl++ + G+  
  gi|70607539|ref|YP_256409.1| 31 GESVLITGRSGSGKSTLVSCINGIIP 56
                                  789********************854 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                          DLIC  24 sgksvlvlGedgsGkttliaklqGveee 51 
                                    g  v ++G++g+Gktt +  l G+ ++
  gi|70607539|ref|YP_256409.1| 309 EGELVAIMGKNGAGKTTALKALAGILDT 336
                                   567799****************999765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.052        17      46      65 ..      32      51 ..      20      62 .. 0.81
   2 ?   -1.3   0.0       5.5   1.8e+03     124     140 ..     184     200 ..     175     204 .. 0.80
   3 ?    7.2   0.0     0.013       4.3      45      71 ..     310     336 ..     291     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.052
                         Rad17 46 riLLisGPsGCgkstvvkvL 65
                                  + +Li+G sG gkst v  +
  gi|70607539|ref|YP_256409.1| 32 ESVLITGRSGSGKSTLVSCI 51
                                  5689***********99765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.5
                         Rad17 124 klGddlrtdkklilved 140
                                      +dlr++k li+ve 
  gi|70607539|ref|YP_256409.1| 184 STLKDLRGQKTLIIVEH 200
                                   45689*********995 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.013
                         Rad17  45 kriLLisGPsGCgkstvvkvLskelgi 71 
                                    +++ i G  G gk+t++k L+ +l +
  gi|70607539|ref|YP_256409.1| 310 GELVAIMGKNGAGKTTALKALAGILDT 336
                                   568889****************98865 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0     0.002      0.66      28      89 ..     139     187 ..     123     188 .. 0.78
   2 ?    0.4   0.0       2.4   7.9e+02      62      77 ..     436     451 ..     379     462 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.002
                       SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   r+++tlSGGe q ++         ++++       ++++++LDE  s++D+e +++++++l+
  gi|70607539|ref|YP_256409.1| 139 RETTTLSGGELQRTVLA-------SVLTM------RPEVLILDEPTSNIDPEGTNQIFSTLK 187
                                   77888888888665533.......33444......6899*****************999987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.4
                       SbcCD_C  62 palrlvfLDEAFsklD 77 
                                   + ++++++DE  s+ D
  gi|70607539|ref|YP_256409.1| 436 SGVKIMLMDEPTSGQD 451
                                   2455666666666555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0045       1.5      22      41 ..      33      52 ..      23     103 .. 0.87
   2 ?    4.3   0.0     0.057        19      22      39 ..     312     329 ..     298     405 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0045
                                  EEEEEESTTSSHHHHHHHHC CS
                        NB-ARC 22 vvalvGmgGvGKttlakqil 41
                                   v + G+ G+GK+tl++ i+
  gi|70607539|ref|YP_256409.1| 33 SVLITGRSGSGKSTLVSCIN 52
                                  4789***********99886 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.057
                                   EEEEEESTTSSHHHHHHH CS
                        NB-ARC  22 vvalvGmgGvGKttlakq 39 
                                   +va++G+ G GKtt +k 
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKA 329
                                   79************7765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0047       1.6      25      43 ..      33      51 ..      26      55 .. 0.90
   2 ?    4.0   0.0      0.14        46      26      43 ..     313     330 ..     293     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0047
                         DUF87 25 HlAilgsTGsGKSntvavL 43
                                  +++i g++GsGKS++v+ +
  gi|70607539|ref|YP_256409.1| 33 SVLITGRSGSGKSTLVSCI 51
                                  6899************976 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.14
                         DUF87  26 lAilgsTGsGKSntvavL 43 
                                   +Ai+g+ G+GK++  + L
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKAL 330
                                   8************99887 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0083       2.8      62      81 ..      34      53 ..      30      64 .. 0.87
   2 ?    4.5   0.0      0.02       6.5      60      85 ..     311     336 ..     261     354 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0083
               Herpes_Helicase 62 ylitGtAGaGkstsiqalae 81
                                   litG  G+Gkst +++++ 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCING 53
                                  69***************986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.02
               Herpes_Helicase  60 saylitGtAGaGkstsiqalaenldC 85 
                                   +   i G  GaGk+t+++ala  ld 
  gi|70607539|ref|YP_256409.1| 311 ELVAIMGKNGAGKTTALKALAGILDT 336
                                   456799***************99985 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.3   4.5e+02       4      19 ..      34      49 ..      32      56 .. 0.86
   2 ?   11.0   0.2   0.00072      0.24       4      31 ..     313     340 ..     311     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.3
                                  EEEEESTTSSHHHHHH CS
                         SRP54  4 illvGlqGaGKTttla 19
                                  +l+ G  G+GK t ++
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVS 49
                                  799**********876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00072
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkkegkk 31 
                                   ++++G +GaGKTt+l  La +l +++++
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSEYS 340
                                   7899***************999988776 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.023       7.5       1      21 [.      36      56 ..      36      61 .. 0.85
   2 ?    6.9   0.1     0.014       4.7       1      25 [.     315     339 ..     315     342 .. 0.88
   3 ?   -0.0   0.0       1.9   6.2e+02     110     138 ..     457     485 ..     433     493 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                    ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                  ++G  GsGK+t+v+ ++ i++
  gi|70607539|ref|YP_256409.1| 36 ITGRSGSGKSTLVSCINGIIP 56
                                  6899*********99887776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgr 25 
                                   ++G  G+GKtt  +al+ il+++++
  gi|70607539|ref|YP_256409.1| 315 IMGKNGAGKTTALKALAGILDTSEY 339
                                   79***************99998865 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.9
                    ATP_bind_1 110 slakiveeLesefalvvvyLvDsqrltdp 138
                                   sl k +++L+ ++ +vvv+  Ds+++ d 
  gi|70607539|ref|YP_256409.1| 457 SLGKELRQLTDKGYTVVVVTHDSKFVYDF 485
                                   34444778888999*********999884 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.12        41      11      34 ..      28      51 ..      21     131 .. 0.89
   2 ?    7.7   0.0    0.0076       2.5       4      54 ..     300     350 ..     298     480 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                  EBTT-EEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqsl 34
                                  i +G+ +li g +g Gk+++++ +
  gi|70607539|ref|YP_256409.1| 28 IEKGESVLITGRSGSGKSTLVSCI 51
                                  679****************98554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0076
                                   HHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   4 vlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergn 54 
                                   ++D  + + +G+ ++i+g++g Gkt+ +++l+   ++++++i   i  +g+
  gi|70607539|ref|YP_256409.1| 300 IVDFSLDLWEGELVAIMGKNGAGKTTALKALAGILDTSEYSITGSIKYQGE 350
                                   6788889999******************99998877776777777443333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.019       6.3       4      24 ..      36      56 ..      34      76 .. 0.85
   2 ?    6.1   0.2     0.025       8.5       2      27 ..     313     338 ..     312     430 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.019
                           PRK  4 vagsSGaGkttvarklekifg 24
                                  ++g SG+Gk+t+   ++ i+ 
  gi|70607539|ref|YP_256409.1| 36 ITGRSGSGKSTLVSCINGIIP 56
                                  9***********999988876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.025
                           PRK   2 IgvagsSGaGkttvarklekifgrek 27 
                                   +++ g+ GaGktt  ++l  i+   +
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSE 338
                                   79****************99998554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.054        18      10      33 ..      31      54 ..      25      73 .. 0.81
   2 ?    1.7   0.0      0.91     3e+02      99     134 ..     157     197 ..     114     199 .. 0.71
   3 ?   -1.0   0.0       6.1     2e+03      66     115 ..     230     302 ..     217     309 .. 0.61
   4 ?    4.4   0.4      0.13        44      10      34 ..     310     334 ..     297     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.054
                        AAA_19 10 ekvllvtaGpGtGKTrvlkhival 33
                                   + +l+t+  G+GK++++ +i  +
  gi|70607539|ref|YP_256409.1| 31 GESVLITGRSGSGKSTLVSCINGI 54
                                  56799***********99887655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.91
                        AAA_19  99 klqeee.llivDE.fqdvd.elqyrLlkallgek..kklll 134
                                    l+ +  +li DE ++++d e  ++++++l++ +  k+l++
  gi|70607539|ref|YP_256409.1| 157 VLTMRPeVLILDEpTSNIDpEGTNQIFSTLKDLRgqKTLII 197
                                   44444449*****7799**9999**9999986554233555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 6.1
                        AAA_19  66 gaeatTiHrlal...................ldfddlltealelle....eaeeekklqeee.llivDEfqdvd 115
                                   ++ a+T+H+ ++                    ++++l+ +    le    ++ e+k l  ++  + v E q vd
  gi|70607539|ref|YP_256409.1| 230 LEGAETLHSAGVevpeyfiyakkfgvkspdlDTVKKLIVQNNVKLEhpkrRTPENKIL-TANlRINVKEKQIVD 302
                                   4458999998888888888888888777775223333323333333555333444444.444477777777776 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.13
                        AAA_19  10 ekvllvtaGpGtGKTrvlkhivall 34 
                                    +++++++  G GKT+ lk+   +l
  gi|70607539|ref|YP_256409.1| 310 GELVAIMGKNGAGKTTALKALAGIL 334
                                   67899*************9877665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0057       1.9     240     272 ..      26      58 ..      16      72 .. 0.80
   2 ?   -1.8   0.0         3     1e+03     324     380 ..     145     212 ..     140     222 .. 0.56
   3 ?    3.8   0.0     0.061        20     244     265 ..     309     331 ..     288     336 .. 0.85
   4 ?   -0.8   0.1       1.5     5e+02     376     412 ..     458     493 ..     428     498 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0057
                                   EEE-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE- CS
                    ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAlekGvynhv 272
                                   + i kG  +lI+G+   GKsTL++ ++ G+ +h+
  gi|70607539|ref|YP_256409.1|  26 LFIEKGeSVLITGRSGSGKSTLVSCIN-GIIPHM 58 
                                   6688888899**************996.666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS.....-HHHH-...--HHHHH...HS-GGG--B--HHHCH CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts.....AtNlmi...rDermqe...lvskekepitplvdrv 380
                                   SG   q   ++  l ++ ++l++DE ts      tN ++   +D r q+   +v+++ e + p+vdrv
  gi|70607539|ref|YP_256409.1| 145 SGGELQRTVLASVLTMRPEVLILDEPTSnidpeGTNQIFstlKDLRGQKtliIVEHKVERVLPFVDRV 212
                                   66667777777788888888888887762222235544322244444432224555666666666665 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.061
                                   SS.EEEEEE-TTSSHHHHHHHHH CS
                    ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAle 265
                                   +G +++I+G +  GK+T L+Al+
  gi|70607539|ref|YP_256409.1| 309 EGeLVAIMGKNGAGKTTALKALA 331
                                   566899***************96 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.5
                                   HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                    ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                   l + +r+l ++ g ++++v+  s+   d Ad+ i++ 
  gi|70607539|ref|YP_256409.1| 458 LGKELRQL-TDKGYTVVVVTHDSKFVYDFADRLIVIS 493
                                   44556666.6777788888888888888888877765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.093        31      36      53 ..      32      49 ..      26      74 .. 0.88
   2 ?    5.0   0.0     0.042        14      96     151 ..     138     191 ..     129     209 .. 0.77
   3 ?   -1.1   0.0       3.2   1.1e+03      38      53 ..     313     328 ..     311     335 .. 0.87
   4 ?   -1.9   0.0       5.8   1.9e+03     109     130 ..     427     448 ..     418     475 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.093
                          TniB 36 pnlllvGdsnnGKtmive 53
                                  +++l+ G+s  GK+++v+
  gi|70607539|ref|YP_256409.1| 32 ESVLITGRSGSGKSTLVS 49
                                  689************996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                          TniB  96 aplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgn 151
                                    +  ++ +  +l++ vl+   +++++vLi+DE  + +    +  ++++ +lk L  
  gi|70607539|ref|YP_256409.1| 138 GRETTTLSGGELQRTVLASVLTMRPEVLILDEPTSNI--DPEGTNQIFSTLKDLRG 191
                                   555556667799999*****************88777..45555667777877765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.2
                          TniB  38 lllvGdsnnGKtmive 53 
                                   + ++G+   GKt+ ++
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALK 328
                                   5799********9987 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.8
                          TniB 109 qqvlrllrelkvrvLiiDEihn 130
                                   + +++   + +v+++++DE  +
  gi|70607539|ref|YP_256409.1| 427 RVAMASVLASGVKIMLMDEPTS 448
                                   5566667788999999999655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.023       7.8      17      36 ..      32      51 ..      27      59 .. 0.86
   2 ?    5.2   0.2     0.034        11      18      40 ..     312     334 ..     310     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.023
                    Zeta_toxin 17 klillgGqpGAGKselaell 36
                                   ++l+ G +G+GKs+l + +
  gi|70607539|ref|YP_256409.1| 32 ESVLITGRSGSGKSTLVSCI 51
                                  579************98866 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.034
                    Zeta_toxin  18 lillgGqpGAGKselaellkdel 40 
                                   l+ + G  GAGK++++++l+  l
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAGIL 334
                                   567789**********9998766 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0036       1.2      53      73 ..      31      51 ..      25     100 .. 0.79
   2 ?    1.6   0.0      0.39   1.3e+02      56      74 ..     313     331 ..     287     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                        DUF815 53 annvLLwGarGtGKSslvkal 73
                                   + vL++G  G+GKS+lv  +
  gi|70607539|ref|YP_256409.1| 31 GESVLITGRSGSGKSTLVSCI 51
                                  678*************99765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.39
                        DUF815  56 vLLwGarGtGKSslvkall 74 
                                   v ++G+ G+GK + +kal 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALA 331
                                   6689*************97 PP

>> ATP_bind_2  P-loop ATPase protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.043        14       4      20 ..      34      50 ..      32      55 .. 0.84
   2 ?    6.4   0.1     0.015       4.9       2      22 ..     311     331 ..     311     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.043
                                  EEEEESTTSSHHHHHHH CS
                    ATP_bind_2  4 vivsGlsGaGksvalra 20
                                  v+++G+sG+Gks+ + +
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSC 50
                                  89**********98765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                                   EEEEEEESTTSSHHHHHHHHH CS
                    ATP_bind_2   2 elvivsGlsGaGksvalrale 22 
                                   elv + G+ GaGk++al+al 
  gi|70607539|ref|YP_256409.1| 311 ELVAIMGKNGAGKTTALKALA 331
                                   5899**************995 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0023      0.77      19      42 ..      28      51 ..      20      64 .. 0.83
   2 ?    0.3   0.0       1.5   4.8e+02      25      41 ..     313     329 ..     298     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0023
                                  CTSSS-EEEECSTTSSHHHHHHHH CS
               Sigma54_activat 19 aktdlsvlitGesGtGKellarai 42
                                  +++  svlitG sG+GK++l ++i
  gi|70607539|ref|YP_256409.1| 28 IEKGESVLITGRSGSGKSTLVSCI 51
                                  556689************999887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                                   EEEECSTTSSHHHHHHH CS
               Sigma54_activat  25 vlitGesGtGKellara 41 
                                   v i+G++G+GK++  +a
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKA 329
                                   789********987665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.023       7.6       2      19 ..      34      51 ..      33      72 .. 0.88
   2 ?    3.6   0.0      0.19        62       4      39 ..     315     350 ..     313     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                                  EEEE--SSSSHHHHHHHG CS
                         AAA_5  2 vlLvGppGtgKselaerl 19
                                  vl+ G +G+gKs+l+  +
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSCI 51
                                  99************9766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                                   EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HH CS
                         AAA_5   4 LvGppGtgKselaerlaaalnreveyvqltrdttee 39 
                                   + G+ G gK++  + la  l ++   + ++ +++ e
  gi|70607539|ref|YP_256409.1| 315 IMGKNGAGKTTALKALAGILDTSEYSITGSIKYQGE 350
                                   78****************996665555555555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.042        14       4      20 ..      34      50 ..      31      73 .. 0.82
   2 ?    5.8   0.0     0.021         7       3      75 ..     312     408 ..     310     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.042
                       DUF2075  4 vlVtGvaGtGKtvvlln 20
                                  vl+tG++G+GK+ + + 
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVSC 50
                                  89**********98765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                       DUF2075   3 vvlVtGvaGtGKtvvllnllaeledde.....................eertavylsvNhplvl...vlrealakkeekkk 59 
                                   +v + G+ G+GKt  l +l+  l ++e                     ++++ +y+ ++ +l+l    +r++++++ +k+k
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAGILDTSEysitgsikyqgeelinkpvwyRGKYMIYMPQSFDLMLvtnQVRKEIEYSLKKRK 392
                                   67899********99999998883333566677777777888888888899999999888888743457888888886666 PP

                       DUF2075  60 kkeafeklssfinnls 75 
                                    k+  e +++++ ++ 
  gi|70607539|ref|YP_256409.1| 393 VKNYREISEKYMREFG 408
                                   6666666666666555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0055       1.8       2      23 ..      31      52 ..      30      70 .. 0.85
   2 ?    1.9   0.1      0.56   1.9e+02       4      32 ..     312     340 ..     309     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0055
                                  -EEEEEESSTTSSHHHHHHHHH CS
                    APS_kinase  2 gvvvwltGlsgsGKstianale 23
                                  g  v++tG sgsGKst+   ++
  gi|70607539|ref|YP_256409.1| 31 GESVLITGRSGSGKSTLVSCIN 52
                                  66799***********987665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.56
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT-- CS
                    APS_kinase   4 vvwltGlsgsGKstianalekkLvekgis 32 
                                    v + G  g+GK+t  +al+  L ++ +s
  gi|70607539|ref|YP_256409.1| 312 LVAIMGKNGAGKTTALKALAGILDTSEYS 340
                                   67889*********999999988877665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.033        11       3      18 ..      34      49 ..      32      65 .. 0.88
   2 ?    5.0   0.1     0.048        16       3      21 ..     313     331 ..     311     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.033
                                  EEEEESTTCCHHHHHH CS
                          cobW  3 tvltGflGsGKTtLln 18
                                  +++tG  GsGK+tL++
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVS 49
                                  689***********96 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.048
                                   EEEEESTTCCHHHHHHHHH CS
                          cobW   3 tvltGflGsGKTtLlnhll 21 
                                   + + G  G+GKTt l++l 
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALA 331
                                   5689999********9886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.9      0.15        48       2      17 ..      34      49 ..      33      54 .. 0.90
   2 ?    9.5   0.2    0.0033       1.1       2      20 ..     313     331 ..     312     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                        AAA_28  2 ivitGgestGKTtlle 17
                                  + itG +++GK+tl++
  gi|70607539|ref|YP_256409.1| 34 VLITGRSGSGKSTLVS 49
                                  78************96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0033
                        AAA_28   2 ivitGgestGKTtlleaLa 20 
                                   ++i+G  ++GKTt l+aLa
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALA 331
                                   89****************9 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.72   2.4e+02      20      39 ..      35      54 ..      32      75 .. 0.84
   2 ?   -1.8   0.0       2.6   8.7e+02     527     570 ..     162     201 ..     156     204 .. 0.82
   3 ?    5.7   0.0     0.015         5      21      40 ..     315     334 ..     311     369 .. 0.75
   4 ?   -3.2   0.0         7   2.3e+03     528     575 ..     439     483 ..     434     489 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.72
                        AAA_13 20 liYGwNGaGKTtLSrllrsl 39
                                  li G+ G+GK+tL + ++ +
  gi|70607539|ref|YP_256409.1| 35 LITGRSGSGKSTLVSCINGI 54
                                  67799********9988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.6
                        AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                    ++ ++D P S  D +  + +fs +k+        k l+i  H 
  gi|70607539|ref|YP_256409.1| 162 PEVLILDEPTSNIDPEGTNQIFSTLKDLR----GQKTLIIVEHK 201
                                   6899*********************9984....66666666665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.015
                        AAA_13  21 iYGwNGaGKTtLSrllrsle 40 
                                   i G+NGaGKTt  ++l+ + 
  gi|70607539|ref|YP_256409.1| 315 IMGKNGAGKTTALKALAGIL 334
                                   78*********988888763 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 7
                        AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffk 575
                                   ki  +D P S  D    ++    +++ +   +k   + + TH  +f  
  gi|70607539|ref|YP_256409.1| 439 KIMLMDEPTSGQDYSNKMSLGKELRQLT---DKGYTVVVVTHDSKFVY 483
                                   6888999999999999999999999999...67777999999999975 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.028       9.3      11      32 ..      28      49 ..      20     198 .. 0.87
   2 ?    2.6   0.2      0.31     1e+02      13      31 ..     309     327 ..     298     466 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
                                  HHTTCEEEEEESTTSSHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 11 ilgggdvlvaaeTGsGKTlafl 32
                                  i +g++vl+ ++ GsGK++  +
  gi|70607539|ref|YP_256409.1| 28 IEKGESVLITGRSGSGKSTLVS 49
                                  44899************87654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                                   TTCEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          DEAD  13 gggdvlvaaeTGsGKTlaf 31 
                                   +g+ v + ++ G+GKT+a 
  gi|70607539|ref|YP_256409.1| 309 EGELVAIMGKNGAGKTTAL 327
                                   688899999*******993 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.39   1.3e+02       4      16 ..      36      48 ..      34      51 .. 0.84
   2 ?    6.5   0.9     0.025       8.4       2      30 ..     313     341 ..     312     343 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.39
                                  EESSTTSSHHHHH CS
                                  xxxxxxxxxxxxx RF
                          CbiA  4 astkGGvGKTtla 16
                                  + + +G+GK+tl+
  gi|70607539|ref|YP_256409.1| 36 ITGRSGSGKSTLV 48
                                  6799*******96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.025
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   2 aiastkGGvGKTtlaanLaralarrglrV 30 
                                   +++ +k G+GKTt + +La +l   ++ +
  gi|70607539|ref|YP_256409.1| 313 VAIMGKNGAGKTTALKALAGILDTSEYSI 341
                                   5677999**************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.51
# Mc/sec: 3125.20
//
Query:       gi|70607540|ref|YP_256410.1|  [L=238]
Description: hypothetical protein Saci_1811 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1439.26
//
Query:       gi|70607541|ref|YP_256411.1|  [L=77]
Description: hypothetical protein Saci_1812 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0025   18.1   2.1     0.0025   18.1   2.1    2.2  3  M              M protein repeat
     0.0042   17.8   1.0      0.014   16.2   1.0    1.7  1  PSK_trans_fac  Rv0623-like transcription factor
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.018   14.6   0.0    2.2  3  LEM            LEM domain
      0.026   13.5   0.2      0.026   13.5   0.2    1.1  1  Vps53_N        Vps53-like, N-terminal
       0.04   14.0   0.3      0.045   13.8   0.3    1.1  1  YpjP           YpjP-like protein
      0.073   13.5   0.1        1.1    9.7   0.2    2.0  2  Propep_M14     Carboxypeptidase activation peptide
       0.16   11.8   1.3       0.35   10.8   1.2    1.6  1  UvrB           Ultra-violet resistance protein B
       0.18   12.7   2.2        9.4    7.1   0.0    2.0  2  Histone_HNS    H-NS histone family


Domain annotation for each model (and alignments):
>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1         8   1.8e+04       9      12 ..      16      19 ..      15      20 .. 0.46
   2 ?   -0.5   0.1       1.4   3.1e+03       4       9 ..      34      39 ..      33      41 .. 0.70
   3 !   18.1   2.1   1.1e-06    0.0025       2      20 ..      44      62 ..      44      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8
                             M  9 elqe 12
                                  el+e
  gi|70607541|ref|YP_256411.1| 16 ELKE 19
                                  4444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                             M  4 keLEae 9 
                                  k+LE e
  gi|70607541|ref|YP_256411.1| 34 KALEEE 39
                                  778877 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.1e-06
                             M  2 akkeLEaelqeLeeelqaL 20
                                  a +eLE+el++L+e+ q++
  gi|70607541|ref|YP_256411.1| 44 AIQELEKELKDLKEKSQIS 62
                                  579**************98 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.0   6.1e-06     0.014       9      63 ..      12      63 ..       9      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.1e-06
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHTS- CS
                 PSK_trans_fac  9 everlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaaka 63
                                  +v r  +eL++  g     ++r+Alee+ +r+   + ++l ++l++l ++ ++ +
  gi|70607541|ref|YP_256411.1| 12 KVPRELKELMDKYGIKPGPVIRKALEEEVRRR---AIQELEKELKDLKEKSQISD 63
                                  6777889999999999999***********98...67889999999988888722 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.9e-06     0.018       9      25 ..      16      32 ..      15      34 .. 0.92
   2 ?   -1.1   0.7      0.64   1.4e+03       9      16 ..      47      54 ..      46      58 .. 0.75
   3 ?   -2.8   0.0       2.2   4.9e+03       4      10 ..      60      66 ..      59      70 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                           LEM  9 eLreeLkkyGvspGPIt 25
                                  eL+e + kyG++pGP+ 
  gi|70607541|ref|YP_256411.1| 16 ELKELMDKYGIKPGPVI 32
                                  9**************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.64
                           LEM  9 eLreeLkk 16
                                  eL +eLk 
  gi|70607541|ref|YP_256411.1| 47 ELEKELKD 54
                                  88888886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.2
                           LEM  4 sLsDeeL 10
                                  + sDe+ 
  gi|70607541|ref|YP_256411.1| 60 QISDEDV 66
                                  6688875 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.2e-05     0.026      56      93 ..      33      72 ..      10      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                       Vps53_N 56 kealeea..qkaieelfqkikeikdkaekseemvkeitrd 93
                                  ++alee    +ai+el++++k++k+k++ s+e v  + r+
  gi|70607541|ref|YP_256411.1| 33 RKALEEEvrRRAIQELEKELKDLKEKSQISDEDVARLIRE 72
                                  56666532268***********************999886 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     2e-05     0.045      11      59 ..      17      67 ..       8      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                          YpjP 11 leeaeeqsllKlGkkiaekiedefeeeilpkieevieellekv..eeekle 59
                                  l+e  ++  +K G+ i++ +e+e++ + + ++e+++++l ek   ++e+++
  gi|70607541|ref|YP_256411.1| 17 LKELMDKYGIKPGPVIRKALEEEVRRRAIQELEKELKDLKEKSqiSDEDVA 67
                                  567778888999**************************9887622455544 PP

>> Propep_M14  Carboxypeptidase activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.14   3.1e+02      45      59 ..      14      28 ..       4      34 .. 0.78
   2 ?    9.7   0.2   0.00049       1.1      40      72 ..      40      72 ..      39      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                    Propep_M14 45 ledfeelLeslgisy 59
                                    +++el++++gi++
  gi|70607541|ref|YP_256411.1| 14 PRELKELMDKYGIKP 28
                                  57899*******997 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00049
                    Propep_M14 40 VppekledfeelLeslgisyevlieDvqklide 72
                                  V+ +  +++e+ L++l+ + ++ +eDv +li e
  gi|70607541|ref|YP_256411.1| 40 VRRRAIQELEKELKDLKEKSQISDEDVARLIRE 72
                                  6677899***********************975 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2   0.00015      0.35      10      25 ..      32      47 ..      24      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                  HHHHHHHHHHHHHHHH CS
                          UvrB 10 MkkAideTerRReiQe 25
                                  ++kA++e  rRR+iQe
  gi|70607541|ref|YP_256411.1| 32 IRKALEEEVRRRAIQE 47
                                  79*************7 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0042       9.4      23      50 ..      12      39 ..       8      44 .. 0.78
   2 ?    6.2   2.4    0.0083        19      11      50 ..      35      74 ..      31      77 .] 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0042
                                  XXXXXXXXXXXXXX----SSS-----EE CS
                   Histone_HNS 23 ealaeirelaaeyGltleelaaeakkak 50
                                  ++  e++el+++yG+++  + ++a +++
  gi|70607541|ref|YP_256411.1| 12 KVPRELKELMDKYGIKPGPVIRKALEEE 39
                                  567899**********999988865554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0083
                                  XXXXXXXXXXXXXXXXXXXXXXXXXX----SSS-----EE CS
                   Histone_HNS 11 kqeealeaeerkealaeirelaaeyGltleelaaeakkak 50
                                  + ee+ ++++++e+ +e+++l ++  ++ e++a+  ++ +
  gi|70607541|ref|YP_256411.1| 35 ALEEEVRRRAIQELEKELKDLKEKSQISDEDVARLIREDR 74
                                  3344478899999999999999999999999987765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2147  (0.11975); expected 358.6 (0.02)
Passed bias filter:                     1126  (0.0628033); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 530.88
//
Query:       gi|70607542|ref|YP_256412.1|  [L=140]
Description: hypothetical protein Saci_1813 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   20.0   0.7     0.0012   19.3   0.7    1.4  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.7   6.9e-08    0.0012      29     119 ..      16     118 ..       4     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.9e-08
                                   SEEEEEHHHHHHHHHHHHS........SCHCHHHHHHHHHHHHHHHTSEEEE.....BCHHHHHHHHHHHHHHHSBHHHHH CS
                           PIN  29 eelvtsalvlaEllyvlar........rkskrekaaelvelllllsalkilp.....idaeiaeeaaeialkygllpnDal 96 
                                    + ++s+l+  E+l+ + +         ++k +   + ++ + +++ +k+++       ++  ee+ ++alk +l+++Da 
  gi|70607542|ref|YP_256412.1|  16 KRGIVSPLTNGETLNLALYecisaiwkEYRKLKVISRDLAGKYIRAIIKVMSiipvnSISGSEEEVFDLALKEDLTIYDAS 96 
                                   45566666666666666666666666666666666666666666777766664444456788899999************* PP

                                   HHHHHHHHT-EEE.ESSTHHHHH CS
                           PIN  97 iaAtAkehgikliatfDedfrrv 119
                                    + +A+  ++ l+ t D+ +r+ 
  gi|70607542|ref|YP_256412.1|  97 YLLVAINKNLMLV-TDDKVLRDR 118
                                   *************.****98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 898.31
//
Query:       gi|70607543|ref|YP_256413.1|  [L=130]
Description: carboxymuconolactone decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-24   84.4   0.0    5.3e-24   84.1   0.0    1.1  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0     3e-28   5.3e-24       3      85 .]      37     119 ..      35     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 3e-28
                                   HHHHHHHHHHHHCC.GSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHHHHHH CS
                           CMD   3 llraltalrealla.reggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaaraAlaa 82 
                                   l++++t++ ++ ++ r+  Ld+k+r+Li++a+++a+++ ++++ H+++Al++G+++eei+e+l +  +y+g+paa++A+++
  gi|70607543|ref|YP_256413.1|  37 LQDLITEHVWGNIWsRPV-LDRKTRSLITVAMLIALNRPNELRIHIKGALRNGCSKEEIRELLIHSTVYCGFPAAVDAFKI 116
                                   78999*********8877.*********************99*************************************** PP

                                   HHH CS
                           CMD  83 aee 85 
                                   aee
  gi|70607543|ref|YP_256413.1| 117 AEE 119
                                   *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 951.80
//
Query:       gi|70607544|ref|YP_256414.1|  [L=101]
Description: hypothetical protein Saci_1815 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 734.78
//
Query:       gi|70607545|ref|YP_256415.1|  [L=558]
Description: glycosyl hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-44  151.8   0.3    1.3e-40  139.6   0.2    2.9  2  Glyco_hydro_15   Glycosyl hydrolases family 15
    0.00078   19.9   0.0     0.0037   17.7   0.0    2.1  2  TPR_19           Tetratricopeptide repeat
     0.0037   17.7   0.1      0.021   15.4   0.1    2.3  2  TPR_4            Tetratricopeptide repeat
     0.0072   16.4   0.7      0.046   13.8   0.1    2.5  3  TPR_2            Tetratricopeptide repeat
     0.0092   14.9   0.1        2.9    6.7   0.0    2.3  2  Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.043   14.0   0.0    1.9  2  TPR_8            Tetratricopeptide repeat
      0.042   14.5   0.1       0.11   13.2   0.1    1.8  1  TPR_6            Tetratricopeptide repeat
      0.046   13.9   0.0       0.19   12.0   0.0    1.9  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      0.084   12.2   0.0        3.7    6.8   0.0    2.1  2  TPR_MalT         MalT-like TPR region
       0.11   12.4   0.1       0.24   11.4   0.1    1.6  1  TPR_10           Tetratricopeptide repeat
       0.12   13.3   0.2       0.35   11.8   0.0    1.8  1  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.2     8e-44   1.3e-40      10     360 ..     205     503 ..     198     516 .. 0.92
   2 !    8.4   0.0   0.00048      0.78     413     446 ..     516     549 ..     502     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 8e-44
                                   CBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHH CS
                Glyco_hydro_15  10 nvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglle 81 
                                   +v+ l+ l+++p +G  iA+ +ts+p         DYr++WvRDs+++ +a++  gy  e+r+  + +   ++ + + ll+
  gi|70607545|ref|YP_256415.1| 205 SVGVLLGLIYSP-SGSSIAAATTSLPeavgdsrnwDYRFVWVRDSSMISEALLYSGYVVEARRILNFMLALVNFTAKPLLH 284
                                   6777888999**.****************************************999************************* PP

                                   HHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHH..HCTTHCHCCCCHHHHTHHHHHH CS
                Glyco_hydro_15  82 amvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqm..tasglqiistldevafvqnlvd 160
                                     +  +g   +  e + +   ++++++++ +++vG+ +  ++QlD+ ++ + a++++  ++s+  ++++ +    ++ + d
  gi|70607545|ref|YP_256415.1| 285 PLYAVDGS-DPPPEIEIP---WLSGYMNSRPVRVGNAAASQIQLDIEGFLVDAIYKYykYTSDRVFVEENWDK--IKYIGD 359
                                   *******7.99999****...************************************8889999999999999..****** PP

                                   HHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCE CS
                Glyco_hydro_15 161 YieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfnty 241
                                   ++ +++   d g+WE +++ +++++s+v+m++Al++  ++++              kdei +++       r +++ ++ +
  gi|70607545|ref|YP_256415.1| 360 WVSKNWMLKDAGMWEDRGDPKHYTHSKVMMWVALDRIEKIMNVKI---------HEKDEIKEWV------MRNCVK-DGSF 424
                                   ***********************************9999987654.........479*******......555666.5666 PP

                                   CECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS--SBT CS
                Glyco_hydro_15 242 lildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvrRys 322
                                   ++  +s            +++da+ll lp + f+   d          p +l++++ i+d+l  +gf         v+Rys
  gi|70607545|ref|YP_256415.1| 425 VRSSDS------------NDVDANLLTLPLYDFIDVKD----------PIFLKTLKRIEDELYVDGF---------VKRYS 474
                                   666666............6*******************..........*******************.........9**** PP

                                   T--CGSSSBSCT--BHHHHHHHHHHHHHHHHHHHHHTE CS
                Glyco_hydro_15 323 edvkpdklglsGrpyylctlwtvetlldelyekagkgr 360
                                   +d+    +g++ +p+ l+t+w     l+++y + g+ +
  gi|70607545|ref|YP_256415.1| 475 QDF----MGEAKHPFALATIW-----LARVYIRLGRKE 503
                                   **9....79************.....888888888754 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00048
                                   S-TTS---SEE-TTT--EESSTT-HHHHHHHHHH CS
                Glyco_hydro_15 413 dnslgvLteevdvylgeliraqpllfsealllri 446
                                   +  l ++ e++dv+  e++++ p++f++a+ll +
  gi|70607545|ref|YP_256415.1| 516 SGTLYLIGEHIDVENMEYTGNYPQAFVHAQLLLA 549
                                   66667899**********************9965 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.3e-06    0.0037      24      53 ..     485     514 ..     470     517 .. 0.84
   2 ?   -1.9   0.0       3.2   5.1e+03      22      41 ..     535     553 ..     529     554 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
                        TPR_19  24 naearllLAeallalgqldeAealLdalpe 53 
                                    a a ++LA++++ lg+ + A++lLd++++
  gi|70607545|ref|YP_256415.1| 485 FALATIWLARVYIRLGRKERAMELLDKVLK 514
                                   6678899*******************9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.2
                        TPR_19  22 pknaearllLAeallalgql 41 
                                    +++ a    A++llal+++
  gi|70607545|ref|YP_256415.1| 535 GNYPQAFV-HAQLLLALKEV 553
                                   56777777.89999999886 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.1   6.6e+03      14      24 ..     258     268 ..     253     269 .. 0.76
   2 !   15.4   0.1   1.3e-05     0.021       2      25 ..     487     510 ..     486     511 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.1
                         TPR_4  14 lGdldeArall 24 
                                    G   eAr++l
  gi|70607545|ref|YP_256415.1| 258 SGYVVEARRIL 268
                                   68889***997 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                         TPR_4   2 rallaLArallalGdldeAralle 25 
                                    a+++LAr++ +lG+ ++A +ll+
  gi|70607545|ref|YP_256415.1| 487 LATIWLARVYIRLGRKERAMELLD 510
                                   799******************997 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         7   1.1e+04       8      22 ..     252     266 ..     250     268 .. 0.80
   2 !   13.8   0.1   2.8e-05     0.046       5      29 ..     490     514 ..     486     514 .. 0.91
   3 ?   -0.5   0.0       1.1   1.8e+03      12      30 ..     532     550 ..     530     552 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
                         TPR_2   8 GlayyklgdyeeAle 22 
                                    +a++++g   eA++
  gi|70607545|ref|YP_256415.1| 252 SEALLYSGYVVEARR 266
                                   578999999999986 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.8e-05
                         TPR_2   5 ynlGlayyklgdyeeAleafekAle 29 
                                    +l+++y++lg+ e+A e+++k+l+
  gi|70607545|ref|YP_256415.1| 490 IWLARVYIRLGRKERAMELLDKVLK 514
                                   68********************997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.1
                         TPR_2  12 yklgdyeeAleafekAlel 30 
                                   ++ g+y +A  + +  l+l
  gi|70607545|ref|YP_256415.1| 532 EYTGNYPQAFVHAQLLLAL 550
                                   589******9999888887 PP

>> Glyco_hydro_125  Metal-independent alpha-mannosidase (GH125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0028       4.6      38     151 ..     242     353 ..     237     413 .. 0.80
   2 !    6.7   0.0    0.0018       2.9     301     396 ..     436     531 ..     422     546 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0028
                                   SEEHHHHH..HHHGGGGGGTTTSGGGHHHHHHHHHHHHHHHHH-TT-.SEE-..SS...SS---SS..--BS-TT.....E CS
               Glyco_hydro_125  38 amWlRDsa..nqlasYlpllkedeklaslirgvinlqaryilispYa.naFqppeesglkkteneaaqkdkvepeydeelv 115
                                     W+RDs+  ++   Y  ++ e +++ + + +++n  a+ +l+  Ya +   pp+e +++  +  ++     +p       
  gi|70607545|ref|YP_256415.1| 242 FVWVRDSSmiSEALLYSGYVVEARRILNFMLALVNFTAKPLLHPLYAvDGSDPPPEIEIPWLSGYMN----SRPV-RVGNA 317
                                   57*****93346778999****************************944566777777766555332....2333.44566 PP

                                   EE----HHHHHHHHHHHHHHHHHH---TT--HHHHH CS
               Glyco_hydro_125 116 feckyelDSlaaflqlsseyyeatgdleffeekwvk 151
                                      + +lD     +   ++yy+ t+d  f+ee+w k
  gi|70607545|ref|YP_256415.1| 318 AASQIQLDIEGFLVDAIYKYYKYTSDRVFVEENWDK 353
                                   77889999999999****************999965 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0018
                                   -STTHHHHTSS-TT-HHHHHHHHHHTST.TSTTEEE-SS-EEE--TTS..-TTEEEHHHHHHHHHT---HHHHHHHHHHHH CS
               Glyco_hydro_125 301 sLLslpllgyvkkddevYqnTrkfvlsk.anpYflkGkalsgiGgphv..glgkaWpmalivqaltsdddeeiaellklll 378
                                   +LL+lpl+++++++d+++ +T k + ++     f+k  + + +G +     l ++W   + ++      +e  +ell+++l
  gi|70607545|ref|YP_256415.1| 436 NLLTLPLYDFIDVKDPIFLKTLKRIEDElYVDGFVKRYSQDFMGEAKHpfALATIWLARVYIRL---GRKERAMELLDKVL 513
                                   59*********************99776544555555555555544331145566644433333...23556677888888 PP

                                   HTSTTSSS--SEEETTEE CS
               Glyco_hydro_125 379 kstaglglvhEsvnvdne 396
                                   k +  l l+ E ++v+n 
  gi|70607545|ref|YP_256415.1| 514 KPSGTLYLIGEHIDVENM 531
                                   888888888888877764 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.6   9.1e+03       6      16 ..     209     219 ..     208     224 .. 0.77
   2 ?   14.0   0.0   2.7e-05     0.043       6      29 ..     491     514 ..     489     514 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.6
                                   HHHHHHHHTT- CS
                         TPR_8   6 nlgsiylklgd 16 
                                   +lg+iy+  g 
  gi|70607545|ref|YP_256415.1| 209 LLGLIYSPSGS 219
                                   79****98776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                   +l+++y+ lg++e A+e + k+l+
  gi|70607545|ref|YP_256415.1| 491 WLARVYIRLGRKERAMELLDKVLK 514
                                   69*******************996 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.8e-05      0.11       5      28 ..     491     514 ..     488     514 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                                   +la+ y++lg++++A+e+l++++k
  gi|70607545|ref|YP_256415.1| 491 WLARVYIRLGRKERAMELLDKVLK 514
                                   79*******************986 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.19      24      61 ..     487     521 ..     463     525 .. 0.81
   2 ?   -1.7   0.0       2.1   3.4e+03      59      71 ..     540     552 ..     530     554 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHH CS
                        ANAPC3  24 edayllAlclylngqykrAyellrkaklnskslgcryl 61 
                                    ++ +lA ++ ++g+ +rA+ell+k     k  g +yl
  gi|70607545|ref|YP_256415.1| 487 LATIWLARVYIRLGRKERAMELLDKV---LKPSGTLYL 521
                                   5688*********************9...344455666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHTT- CS
                        ANAPC3  59 rylfAqcllkLkk 71 
                                   ++++Aq ll+Lk+
  gi|70607545|ref|YP_256415.1| 540 AFVHAQLLLALKE 552
                                   5666777776665 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.033        54      33     110 ..     197     275 ..     194     286 .. 0.92
   2 ?    6.8   0.0    0.0023       3.7     243     278 ..     489     524 ..     478     529 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.033
                      TPR_MalT  33 eddllariaatavlGeasllqG.dleaAlqalqeaeklarqadslhvallallqqaeilvaqGrLheAletyeqalqla 110
                                   ++d  +r+ +  +lG ++   G   +aA+ +l ea+  +r+ d+  v++     ++e l   G+  eA ++ +  l+l+
  gi|70607545|ref|YP_256415.1| 197 SNDEVWRTSVGVLLGLIYSPSGsSIAAATTSLPEAVGDSRNWDYRFVWVRDSSMISEALLYSGYVVEARRILNFMLALV 275
                                   67789*****************999**********************************************99999887 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                      TPR_MalT 243 lrnlarvllalgrydeAlellerLlkaaeelgrvrs 278
                                    + larv++ lgr ++A+ell++ lk +  l ++++
  gi|70607545|ref|YP_256415.1| 489 TIWLARVYIRLGRKERAMELLDKVLKPSGTLYLIGE 524
                                   5679******************99988766665555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00014      0.24       7      29 ..     491     513 ..     486     514 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                        TPR_10   7 NLanalrqrgrydeAealleeal 29 
                                    La+++ ++gr ++A++ll+++l
  gi|70607545|ref|YP_256415.1| 491 WLARVYIRLGRKERAMELLDKVL 513
                                   7*******************998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.35       4      29 ..     489     514 ..     486     518 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                        TPR_14   4 llalaeallalGdpdeAiallrrala 29 
                                   +  la+++ +lG+ ++A++ll+++l+
  gi|70607545|ref|YP_256415.1| 489 TIWLARVYIRLGRKERAMELLDKVLK 514
                                   5679******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3995.47
//
Query:       gi|70607546|ref|YP_256416.1|  [L=207]
Description: hypothetical protein Saci_1817 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     9e-106  352.2  21.3     1e-105  352.0  21.3    1.0  1  OFeT_1    Ferrous iron uptake permease, iron-lead transporter
  ------ inclusion threshold ------
      0.014   15.8   0.4      0.071   13.5   0.0    2.2  2  DUF2681   Protein of unknown function (DUF2681)
      0.089   12.8   5.3      0.091   12.8   0.0    2.9  3  DUF3185   Protein of unknown function (DUF3185)
       0.12   12.5   0.5       0.12   12.5   0.5    3.4  4  DUF4229   Protein of unknown function (DUF4229)
       0.47    9.5   4.9       0.21   10.6   0.3    2.0  2  Frizzled  Frizzled/Smoothened family membrane region
        1.1    9.4   5.5        2.4    8.3   5.0    1.9  1  DUF4079   Protein of unknown function (DUF4079)


Domain annotation for each model (and alignments):
>> OFeT_1  Ferrous iron uptake permease, iron-lead transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.0  21.3  3.4e-109    1e-105       1     207 []       1     206 [.       1     206 [. 1.00

  Alignments for each domain:
  == domain 1  score: 352.0 bits;  conditional E-value: 3.4e-109
                        OFeT_1   1 mdlgvllaalgisllelseagavaaiyqgiyknlkpflyavaGvlivliptftlGkyivllpldyvllvaavilfyfGyrl 81 
                                   md++vlla+lgis+lelsea+ava+i+qgiykn+kpflya+aG+livl+p+ftlG+yivllp++yvllvaavil+yfGy+l
  gi|70607546|ref|YP_256416.1|   1 MDFSVLLASLGISILELSEASAVAVIFQGIYKNSKPFLYAIAGILIVLVPVFTLGQYIVLLPINYVLLVAAVILAYFGYKL 81 
                                   9******************************************************************************** PP

                        OFeT_1  82 lrsarryfkgikkkkkeeeeeglavvfvvsavealeaalvilalipqsyssallGtllasilvvaltavlkdqiarirlph 162
                                   lrsarr+fkg+kkk+ ee+eeg+++vfvvsa+ealea+lvilalipqs+ssallGt +a+i+v+alt++l++qi++ir+ph
  gi|70607546|ref|YP_256416.1|  82 LRSARRSFKGSKKKH-EEKEEGIMTVFVVSATEALEAGLVILALIPQSFSSALLGTGIAVIIVIALTIALRSQIMKIRVPH 161
                                   ************999.9**************************************************************** PP

                        OFeT_1 163 lkfvlsallfslgtlfilevllditelvlllffliylgvnyliik 207
                                   lkfvlsallf+l+tlf++e+l+di+e++l+lff+iylgvnyl+ik
  gi|70607546|ref|YP_256416.1| 162 LKFVLSALLFGLATLFVAEALVDIDEVFLPLFFVIYLGVNYLVIK 206
                                   *******************************************98 PP

>> DUF2681  Protein of unknown function (DUF2681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.071       4      40 ..      63     100 ..      60     112 .. 0.82
   2 ?   -0.6   0.1      0.62   1.8e+03       7      25 ..     134     152 ..     129     163 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                       DUF2681   4 lallvgliaavlllvaylswqlkkar.kknaklqaekq 40 
                                   ++ ++ ++a++l++++y+ +++++   k  +k+ +ek+
  gi|70607546|ref|YP_256416.1|  63 INYVLLVAAVILAYFGYKLLRSARRSfKGSKKKHEEKE 100
                                   78899*****************9988666666666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.62
                       DUF2681   7 lvgliaavlllvaylswql 25 
                                   l++ ia+++++++ + +++
  gi|70607546|ref|YP_256416.1| 134 LGTGIAVIIVIALTIALRS 152
                                   4455566666665555554 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.098   2.9e+02      24      57 ..      18      52 ..       5      54 .. 0.72
   2 ?   12.8   0.0     3e-05     0.091       5      27 ..      65      87 ..      63      95 .. 0.87
   3 ?   -2.3   0.5       1.6   4.8e+03       8      54 ..     134     142 ..     128     147 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.098
                       DUF3185 24 SlgsqvseaftGstt.dktlllligGgvaaivGlv 57
                                  S +s+v+  f+G ++  k  l+ i+G+  ++v ++
  gi|70607546|ref|YP_256416.1| 18 SEASAVAVIFQGIYKnSKPFLYAIAGILIVLVPVF 52
                                  45677777788877757888999999999988766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3e-05
                       DUF3185  5 iiLlvaGivLlvfGynasdSlgs 27
                                   +Llva ++L++fGy+  +S+  
  gi|70607546|ref|YP_256416.1| 65 YVLLVAAVILAYFGYKLLRSARR 87
                                  59*************99999865 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                       DUF3185   8 lvaGivLlvfGynasdSlgsqvseaftGsttdktlllligGgvaaiv 54 
                                   l  Gi+                                      +i+
  gi|70607546|ref|YP_256416.1| 134 LGTGIA--------------------------------------VII 142
                                   444443......................................333 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   3.9e-05      0.12      13      57 ..      43      89 ..      37      98 .. 0.70
   2 ?   -0.5   1.8      0.46   1.4e+03      28      42 ..     132     149 ..     104     152 .. 0.61
   3 ?    2.8   2.9     0.042   1.3e+02       8      43 ..     138     173 ..     135     179 .. 0.86
   4 ?   -1.2   0.1      0.74   2.2e+03      11      24 ..     189     202 ..     187     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                       DUF4229 13 vltavillvarliglp.....vpllvaallAlvvalplSmvllkklRdra 57
                                  ++++v++ v  l         +p+ +++l+A+v+ +  ++ ll++ R+ +
  gi|70607546|ref|YP_256416.1| 43 GILIVLVPVFTL---GqyivlLPINYVLLVAAVILAYFGYKLLRSARRSF 89
                                  222222222222...224466899999********************976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.46
                       DUF4229  28 p...vpllvaallAlvva 42 
                                   +    ++ v++++Al +a
  gi|70607546|ref|YP_256416.1| 132 AllgTGIAVIIVIALTIA 149
                                   334456666666666666 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.042
                       DUF4229   8 laLfvvltavillvarliglpvpllvaallAlvval 43 
                                   +a+++v+++ i+l  +++ ++vp l  +l Al+  l
  gi|70607546|ref|YP_256416.1| 138 IAVIIVIALTIALRSQIMKIRVPHLKFVLSALLFGL 173
                                   578999999999999999999999999999998765 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.74
                       DUF4229  11 fvvltavillvarl 24 
                                   f+ l++vi+l ++ 
  gi|70607546|ref|YP_256416.1| 189 FLPLFFVIYLGVNY 202
                                   67778888776644 PP

>> Frizzled  Frizzled/Smoothened family membrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3     7e-05      0.21     183     255 ..      55     127 ..      40     140 .. 0.72
   2 ?    1.1   0.4     0.055   1.6e+02      16      56 ..     165     205 ..     152     207 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7e-05
                      Frizzled 183 lrgfvlaPllvylliGllflla.gfvslfrirkvlkkqgkkatekleklmirigifsvlytvpaliviacliye 255
                                    ++ vl+P+  +ll+++++l+  g+  l + r+++k ++kk +e+ e+ ++ + + s+   + a +vi  li +
  gi|70607546|ref|YP_256416.1|  55 GQYIVLLPINYVLLVAAVILAYfGYKLLRSARRSFKGSKKK-HEEKEEGIMTVFVVSATEALEAGLVILALIPQ 127
                                   56889****99999988777651566666689999999866.66666667777777888888887777776665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.055
                      Frizzled  16 lwsilclvstlftvlTFlidssrfkYPerpiiflslCyllv 56 
                                   ++s+l + ++++ v+  l+d +    P   +i+l + yl++
  gi|70607546|ref|YP_256416.1| 165 VLSALLFGLATLFVAEALVDIDEVFLPLFFVIYLGVNYLVI 205
                                   45555555555667777888888888888888888888876 PP

>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.0   0.00081       2.4       6     131 ..      62     181 ..      28     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00081
                       DUF4079   6 PvlmvllvfpllgavaylGwqtrqr.rlqskaerkekipkkvrdeHvklgslllllvvlgaigglvllylrrgklfpssHl 85 
                                   P+  vllv++++ a  y+G+++ ++ r +      + ++kk +++   +  + ++ ++ ++ +glv l l   + f s  l
  gi|70607546|ref|YP_256416.1|  62 PINYVLLVAAVILA--YFGYKLLRSaRRSF-----KGSKKKHEEKEEGIMTVFVVSATEALEAGLVILALI-PQSFSSALL 134
                                   77778888888877..99977766502222.....233455555655666666666666666666666555.55899**** PP

                       DUF4079  86 yaGlavvvLlalsaalvpeiqkgks.taRtlHialnvlalllfawqa 131
                                    +G+av++ +al +al  +i k +   ++ +  al + ++ lf++ a
  gi|70607546|ref|YP_256416.1| 135 GTGIAVIIVIALTIALRSQIMKIRVpHLKFVLSALLFGLATLFVAEA 181
                                   ********************998877777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1392.98
//
Query:       gi|70607547|ref|YP_256417.1|  [L=379]
Description: hypothetical protein Saci_1818 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-21   77.2  53.2    2.2e-12   46.6  26.7    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6  26.7   1.3e-16   2.2e-12       1     267 [.      12     256 ..      12     261 .. 0.79
   2 !   34.4  25.1     6e-13   1.1e-08      40     170 ..     245     375 ..     238     379 .] 0.82

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.3e-16
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   ++++af++ l++  + +++p+     +g+    +g++ +l + +  ++s+++G  +d++Gr+r+++lg  l +l   l+ f
  gi|70607547|ref|YP_256417.1|  12 IAFSAFFADLGYQSAVASFPIVFVLIFGAPFYMYGIAEALNYGLGTLMSYIGGIAGDKYGRKRIVILGNSLIILV-SLMGF 91 
                                   6899*****************999****************9999*******************************.55556 PP

                         MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfyilaiv 160
                                    +  +   l++ +l  ++  +  p   a++a++++++er+ a+g+l +   +Ga+l   +l  +l+    +r++ +   ++
  gi|70607547|ref|YP_256417.1|  92 -ARDYiQALLFFMLGWWFRNFRSPPRRAMMAEVTSPDERAEAFGILHSIDIAGALLSiTILTLVLY----FRLSLLSYLPF 167
                                   .788845666666666667**************************************566666666....99999999999 PP

                         MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls 241
                                   ++l +v+  +l+   +  +  +++  +    ++         + +++v+w ++i+   fffg+s++++ +p++  ++  ++
  gi|70607547|ref|YP_256417.1| 168 TALPLVISTILVSIVKAGHLQNNGSSK----AK-------VTVTNKRVFWGIIIST--FFFGYSQYSFGFPIL--TTTEIT 233
                                   999988888888888888888888888....33.......3455588886444444..445999999999995..555555 PP

                         MFS_1 242 glllaglllallalvgailallagrl 267
                                   g  ++g  +  ++++ a ++ l+g+l
  gi|70607547|ref|YP_256417.1| 234 GKEYLG--IISYGIFLA-GSSLFGYL 256
                                   334444..222222222.23355555 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 6e-13
                         MFS_1  40 lyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpagaaliadwfpke 117
                                   ++ +g++++ +++G    +f   r + +lg+ll+a+ +l ++f+   +++ l+ l +l+G++ +++ +   ++i+++++++
  gi|70607547|ref|YP_256417.1| 245 IFLAGSSLFGYLFGI--SKFRELRaLAFLGYLLSAFVSLGFAFIsgYGITSLYTLSFLMGIAVASAETFEPTVISKLTNEQ 323
                                   444455555555554..49987777************77777864666777****************************** PP

                         MFS_1 118 ergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                     g+a+g+lsag s+G+ lg  + g+l+ +l+++++++++ + sl+af+++l+
  gi|70607547|ref|YP_256417.1| 324 AYGSAMGYLSAGRSVGIFLGNTIMGFLY-QLSYSYAYVFAFFTSLIAFLIILV 375
                                   ****************************.888888988888888888885333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2757.77
//
Query:       gi|70607548|ref|YP_256418.1|  [L=271]
Description: hypothetical protein Saci_1819 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-15   58.0  42.2      8e-12   45.5  17.2    2.5  2  EamA             EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  17.0   1.4e-07    0.0026       6     109 ..       6     110 ..       3     129 .. 0.79
   2 !   45.5  17.2   4.4e-16     8e-12       3     135 ..     138     266 ..     136     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-07
                          EamA   6 lallaalfwaiyfvlskillrkvspltltfvrfliagilllii..allkegklaklslkdwlll.lllgllgtvlafllff 83 
                                   l++ + + +++++++ k   +++ p  +t +rfl+ag++ll+i  a  k+g++++ + +++ l  l+l  l   l ++lf+
  gi|70607548|ref|YP_256418.1|   6 LLFFGGVAFGTAAIFVKF--CSITPPYITLFRFLFAGLVLLLIgrAIRKQGNNKNSHNNPISLRkLVLPSLFLSLHMVLFV 84 
                                   667888999*******98..6999999**************9965555555556666666666677777788888889999 PP

                          EamA  84 yalkktsasnaslitslePvftlils 109
                                    ++  t+ +  ++++s++P+f++i+ 
  gi|70607548|ref|YP_256418.1|  85 FSVFLTTIAASTILVSTSPIFAMIFK 110
                                   9999********************85 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 4.4e-16
                          EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllff 83 
                                   g l+a+++al++a+y+ +  ++  +++ +t+t   ++i++++++++++++   +  ++l+ + ++l l +++t+++++  +
  gi|70607548|ref|YP_256418.1| 138 GNLMAVISALSFALYTYFLSKI--QYDFFTVTPRIYIISSAFMVPVLPFFSMGN--FNLETLMAILGLVFIPTIIGHGSVI 214
                                   889***************9887..9********9********************..************************* PP

                          EamA  84 yalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                   y+ +k++ s ++ + ++ePv++++l+++l+ + ++l +++g vl l+++++ 
  gi|70607548|ref|YP_256418.1| 215 YSANKVPISLVTSAELIEPVVATLLAFILFSQVPSLEEIVGGVLTLISLFFA 266
                                   ************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1873.93
//
Query:       gi|70607549|ref|YP_256419.1|  [L=403]
Description: Mn2+ and Fe2+ transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-32  112.8  18.1    2.2e-32  112.4  18.1    1.1  1  Nramp     Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
        9.7    6.5  17.7        0.4   11.0   3.5    3.5  2  YwiC      YwiC-like protein


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4  18.1   2.4e-36   2.2e-32       7     357 ..      32     375 ..      28     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 2.4e-36
                         Nramp   7 aGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAialnllf 87 
                                    G+q+G  L w +ll  l ++++qe + r+  vTgkgl e+ir ++++k++i++ + ++ + ++t + e +G+Ai+ +l+ 
  gi|70607549|ref|YP_256419.1|  32 TGQQYGLGLTWFVLLLALPLFVVQETAGRISAVTGKGLGEIIRTYYSRKLAIVATLPIFSIDVFTYISEYVGIAIGSYLIG 112
                                   69**************************************************************************99996 PP

                         Nramp  88 gipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpgkeslllavgi.l 167
                                    ip ++g l + ++ ll+++  +++y+k E+++i++ ++++ls   +++++ p+ +++  +   P +++++ +l+ ++i +
  gi|70607549|ref|YP_256419.1| 113 -IPPTLGLLSFFLFHLLVIL--TRKYEKTERALIIVSFILVLS---SIIVTIPKASNLDLS---PYFSTSNDFLTYLAInI 184
                                   .******9999999999999..9********988766666333...444455555554433...9999966666666666* PP

                         Nramp 168 Gatvmp.hnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAavlysggkdv..esledaaeaL 245
                                   Ga+v+p  +l +++s +  + ++ d s+k+ +l+  + +ti++++ +      ++iv+A+v+ +g ++v  ++  ++ ++L
  gi|70607549|ref|YP_256419.1| 185 GAVVTPpCMLIYQASATSVKYNKLDISTKD-KLSWVTKETILGALTT-----ELIIVFAEVVGTGLGKVdpTNTIQLSSVL 259
                                   ****97367888888888888666556666.8999999998877655.....45688888888665555227778888888 PP

                         Nramp 246 epllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafv.....palivilligaelelvk 321
                                   +   +  +  ++F++ +++aG++++++++l++++ + ++lg  +s++++  + ++l+++     pal+++ l++++    +
  gi|70607549|ref|YP_256419.1| 260 SSFSS--ILPFVFGVLIMSAGFLALVVVSLSSAWGVLEALGRGSSKDNKYNMRDVLTIYgleslPALLIVYLSSQNYA--E 336
                                   88765..899*************************************9999999999983333355666666666655..5 PP

                         Nramp 322 llvlsq...vllslllPfaliplllltsskklMGefkns 357
                                   +l ++    +l  ++  f++ +l +++ss+++MG+++ s
  gi|70607549|ref|YP_256419.1| 337 ILQFATtllALAPIVFTFTASLLGMIISSRRIMGNYAYS 375
                                   55555522266678999999****************977 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   6.4      0.29   2.6e+03      69     114 ..     103     148 ..       6     159 .. 0.53
   2 ?   11.0   3.5   4.5e-05       0.4      12      99 ..     265     354 ..     263     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                          YwiC  69 llllllalllqpallwwallflplvavavyeakrkreRsllndlat 114
                                   ++++  +l+  p  l ++  fl  ++v +  +++k+eR+l+     
  gi|70607549|ref|YP_256419.1| 103 GIAIGSYLIGIPPTLGLLSFFLFHLLVILTRKYEKTERALIIVSFI 148
                                   2233334455566777777777777777777777777777644444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.5e-05
                          YwiC  12 lvPlllGlllagpvwahlll.lvawlvgYlaffplllllkarrrarylkplliYgavallllllalllqpa...llwwall 88 
                                   ++P+++G+l+   +  +l+l +v   +++ + ++l+   +++++  ++  l+iYg+ +l +ll+++l ++    +l +a  
  gi|70607549|ref|YP_256419.1| 265 ILPFVFGVLIM--SAGFLALvVVSLSSAWGVLEALGRGSSKDNKYNMRDVLTIYGLESLPALLIVYLSSQNyaeILQFATT 343
                                   79*******88..4555554045556799999***************************9999998887542136666666 PP

                          YwiC  89 flplvavavye 99 
                                   +l+l+ + + +
  gi|70607549|ref|YP_256419.1| 344 LLALAPIVFTF 354
                                   66666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3148.46
//
Query:       gi|70607550|ref|YP_256420.1|  [L=196]
Description: DNA protection protein DPS [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-24   85.0   0.4    5.9e-24   84.6   0.4    1.1  1  Ferritin      Ferritin-like domain
  ------ inclusion threshold ------
      0.041   14.6   0.1        1.4    9.7   0.0    2.1  2  DUF4439       Domain of unknown function (DUF4439)
      0.049   14.0   0.2      0.093   13.1   0.2    1.5  1  Rubrerythrin  Rubrerythrin
      0.071   13.3   0.0       0.12   12.6   0.0    1.4  1  Ferritin_2    Ferritin-like domain
       0.09   12.5   0.0       0.29   10.9   0.0    1.7  2  COQ7          Ubiquinone biosynthesis protein COQ7


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.4   1.7e-27   5.9e-24       1     136 [.      32     172 ..      32     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.7e-27
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......C-SS CS
                      Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......ieap 75 
                                   i++L ++ a+e+t +y+y  +  ++ g + egl+e  ++   e r h++ + +ri +lGg+ + + +e+++       + p
  gi|70607550|ref|YP_256420.1|  32 IDKLVKATAAEFTTYYYYTILRMHLTGLDGEGLKEIAEDARLEDRLHFELMTQRIYELGGSLPRDIREVADisacadAYLP 112
                                   68999**************************************************************99998888854445 PP

                                   SSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  76 kefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleall 136
                                   +++++++e+l+ +le+e++++++ +e+++l+  + Dp t+d+++ +l+e+ ehe+++ +ll
  gi|70607550|ref|YP_256420.1| 113 QNWKDPKEILKVLLEAEQCAIRTWKEVCDLTYGK-DPRTYDLAQRILQEEIEHEAWFIELL 172
                                   55******************************96.*********************97776 PP

>> DUF4439  Domain of unknown function (DUF4439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.041   1.5e+02       2      32 ..      35      65 ..      34      85 .. 0.81
   2 ?    9.7   0.0   0.00038       1.4      55     103 ..     102     150 ..      96     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.041
                       DUF4439  2 lqaalaaEhaavYgYgvvsarldgarraaar 32
                                  l++a aaE  + Y Y +++ +l+g + +  +
  gi|70607550|ref|YP_256420.1| 35 LVKATAAEFTTYYYYTILRMHLTGLDGEGLK 65
                                  68999****************9987666554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
                       DUF4439  55 tppaaeaaYelpfevtdaasaarlaaelEedlaaayaalv.aaddadlRs 103
                                   +  a + aY lp++ +d+++ ++++ e+E+ ++++++++   +  +d R+
  gi|70607550|ref|YP_256420.1| 102 DISACADAY-LPQNWKDPKEILKVLLEAEQCAIRTWKEVCdLTYGKDPRT 150
                                   666778888.779*************************994444444454 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.6e-05     0.093       3     136 ..      35     171 ..      33     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SS....BBS-------TT CS
                  Rubrerythrin   3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevke....kvreyaeakpkf 78 
                                   L kA a+E++ + +Y++l  ++     + ++e+ e+   e r H +++ + + +l ++l  +++e     +   a+ ++ +
  gi|70607550|ref|YP_256420.1|  35 LVKATAAEFTTYYYYTILRMHLTgLDGEGLKEIAEDARLEDRLHFELMTQRIYELGGSLPRDIREvadiSACADAYLPQNW 115
                                   899********************8888999999999999999998888888877777766444331111345667777788 PP

                                   GGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  79 lttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                   +  ++ L+ ++e + ++ ++  ++    +   +++++ +l +++ ++E +He  + +l
  gi|70607550|ref|YP_256420.1| 116 KDPKEILKVLLEAEQCAIRTWKEVCDLTYG--KDPRTYDLAQRILQEEIEHEAWFIEL 171
                                   777777777777777777777666666666..67999999***********9988665 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.2e-05      0.12       9     135 ..      38     173 ..      30     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                    Ferritin_2   9 AlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale..Gaaa.........vakptfdfafdp 78 
                                   A ++E++   +Yt          ++l  +  +e+ae+++ + + H e++++ +   G++          +++++  +  ++
  gi|70607550|ref|YP_256420.1|  38 ATAAEFTTYYYYTILRMHL----TGLDGEGLKEIAEDARLEDRLHFELMTQRIYelGGSLprdirevadISACADAYLPQN 114
                                   5556665555555444432....3444455688999999999999999999998886665344444333344444558899 PP

                    Ferritin_2  79 fadeksflalaavlEdvgvsAYlgaaplls..nkelltaaasIlsvEArHaavirtllg 135
                                    +d+k++l++    E+ +++  + +  l    ++    +a +Il+ E +H a++ +ll+
  gi|70607550|ref|YP_256420.1| 115 WKDPKEILKVLLEAEQCAIRTWKEVCDLTYgkDPRTYDLAQRILQEEIEHEAWFIELLY 173
                                   99999999999999999999999998865533777999999999999999999988886 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.42   1.5e+03      13      58 ..      42      88 ..      33      92 .. 0.69
   2 ?   10.9   0.0   8.1e-05      0.29       4      58 ..     120     174 ..     118     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.42
                          COQ7 13 ElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeellke 58
                                  E+   + Y+   + l   + + lk++ +++  + + H++++ +++ e
  gi|70607550|ref|YP_256420.1| 42 EFTTYYYYTILRMHLtGLDGEGLKEIAEDARLEDRLHFELMTQRIYE 88
                                  55555666665555633444558888888888888899998888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.1e-05
                          COQ7   4 rllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellke 58 
                                   ++l+v    E +A + +k   +    kdp++ +l +++l++E eH a+f ell  
  gi|70607550|ref|YP_256420.1| 120 EILKVLLEAEQCAIRTWKEVCDLTYGKDPRTYDLAQRILQEEIEHEAWFIELLYA 174
                                   56777777899**************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1426.25
//
Query:       gi|70607551|ref|YP_256421.1|  [L=110]
Description: Rieske (2Fe-2S) protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-13   49.3   0.0    4.2e-13   49.1   0.0    1.2  1  Rieske    Rieske [2Fe-2S] domain
       0.01   15.8   0.0      0.013   15.4   0.0    1.3  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   4.7e-17   4.2e-13      10      83 ..       9      82 ..       3     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.7e-17
                                  GC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHH CS
                        Rieske 10 dvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPapr 83
                                  +v+eg+++++++ g++l++++  +ge++++s  C+H+g  l+ g   ++++++C +Hg  y+  +G+++ +P  +
  gi|70607551|ref|YP_256421.1|  9 NVKEGETKKIEIDGKDLLIVN-IRGELKCFSRWCPHKGGDLAYGDFIGGNQIKCHLHGYIYNlDTGNAVYIPYRD 82
                                  799******************.6******************995555888*******************999765 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-06     0.013      11     103 ..      10     107 ..       2     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-06
                                   S-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS........ CS
                      Rieske_2  11 lvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle........ 83 
                                   + +++ +   +dgk+ +++ + ++e+   + ++p +    l+ G   d  g   +++ l++ +++L+tG+ +         
  gi|70607551|ref|YP_256421.1|  10 VKEGETKKIEIDGKDLLIVNI-RGELKCFSRWCPHK-GGDLAYG---DFIGGNQIKCHLHGYIYNLDTGNAVYipyrdgyg 85 
                                   555555666666666666666.66666666666664.3333333...233445899************************* PP

                                   ..-TTSB-BEE-EEESTSEEEE CS
                      Rieske_2  84 ..deevslkvypvrvedgkvev 103
                                     +++ +l+vy+v  +dg++ +
  gi|70607551|ref|YP_256421.1|  86 kwKDTLNLEVYRVVNKDGEICI 107
                                   **99***************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 789.72
//
Query:       gi|70607552|ref|YP_256422.1|  [L=141]
Description: thioredoxin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-24   83.5   0.0    1.2e-23   83.1   0.0    1.1  1  Thioredoxin    Thioredoxin
    1.9e-07   31.5   0.1    1.6e-05   25.3   0.1    2.3  1  Thioredoxin_2  Thioredoxin-like domain
    9.1e-05   22.7   0.0     0.0012   19.2   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
    0.00011   21.9   0.0    0.00019   21.1   0.0    1.5  1  Redoxin        Redoxin
     0.0015   18.3   0.0     0.0022   17.8   0.0    1.2  1  Thioredoxin_9  Thioredoxin
     0.0022   18.0   0.0     0.0055   16.7   0.0    1.8  2  Thioredoxin_3  Thioredoxin domain
     0.0031   17.4   0.0      0.018   15.0   0.0    1.8  2  AhpC-TSA       AhpC/TSA family
  ------ inclusion threshold ------
      0.026   13.9   0.0      0.038   13.3   0.0    1.3  1  OST3_OST6      OST3 / OST6 family, transporter family
       0.16   11.8   0.0       0.28   11.0   0.0    1.3  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   5.8e-27   1.2e-23       2     102 ..      38     136 ..      37     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 5.8e-27
                                   EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                   Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                   +++lt++nF+e +++  k  +v+F+A+wC++C  l+P +e+l++++k  v + k++vd+ +++a+ y+v ++Pt++lf++g
  gi|70607552|ref|YP_256422.1|  38 IHHLTDKNFNEFLSS-FKVSVVDFWAEWCPPCHLLSPIIEELSKDYK-GVGFGKLNVDQYPEIATSYGVISLPTVLLFHEG 116
                                   6789**********9.9******************************.9******************************** PP

                                   EEEEEEESS-HHHHHHHHHH CS
                   Thioredoxin  83 kevkkyegarekeklaaflk 102
                                   k v+ + ga ++e ++++l+
  gi|70607552|ref|YP_256422.1| 117 KPVDYVLGAVPREVIEHKLR 136
                                   ************99998876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.1   8.1e-09   1.6e-05       6     108 ..      54     134 ..      50     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.1e-09
                 Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                   k  +v+f++++Cp C++l   ++el +   ++       + + +   ++++ +             e a +ygv ++Pt++
  gi|70607552|ref|YP_256422.1|  54 KVSVVDFWAEWCPPCHLLSPIIEELsK---DY-------KGVGFGKLNVDQYP-------------EIATSYGVISLPTVL 111
                                   5679*******************9922...22.......22334455555555.............5679*********65 PP

                 Thioredoxin_2  86 .fldgkeivarlpGyvpaeeleal 108
                                    f +gk +v+ + G+vp+e +e+ 
  gi|70607552|ref|YP_256422.1| 112 lFHEGK-PVDYVLGAVPREVIEHK 134
                                   388888.***********988765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.9e-07    0.0012       2      31 ..      54      83 ..      52      95 .. 0.88
   2 ?    1.2   0.0      0.24   4.8e+02      73      89 ..      97     113 ..      85     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.9e-07
                                  SEEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                 Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklk 31
                                  kv ++ f+a+wcppc    p + el++++k
  gi|70607552|ref|YP_256422.1| 54 KVSVVDFWAEWCPPCHLLSPIIEELSKDYK 83
                                  7889************************98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.24
                                   HHTT-S--TT-SEEEEE CS
                 Thioredoxin_8  73 klkkkynvkaiPtlvvl 89 
                                   +++  y+v ++Pt+++ 
  gi|70607552|ref|YP_256422.1|  97 EIATSYGVISLPTVLLF 113
                                   78889********9986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   9.7e-08   0.00019      29      66 ..      54      90 ..      28     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.7e-08
                                  SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEE CS
                       Redoxin 29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvv 66
                                  k+ vv f++  +cP+C    p +e+l++ +k  g+ ++
  gi|70607552|ref|YP_256422.1| 54 KVSVVDFWAE-WCPPCHLLSPIIEELSKDYKGVGFGKL 90
                                  7889******.******************998888764 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06    0.0022      45     123 ..      57     132 ..      35     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                   EEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEESS-HHHHH CS
                 Thioredoxin_9  45 ilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwgerPaevqe 123
                                   ++ + ++wC+ +    P+++++++  +++ +  l  d+++e+  +y   g  + Pt++++ e+  +  v+g  P+ev e
  gi|70607552|ref|YP_256422.1|  57 VVDFWAEWCPPCHLLSPIIEELSKDYKGVGFGKLNVDQYPEIATSY---GVISLPTVLLFHEGKPVDYVLGAVPREVIE 132
                                   5556789***************************************...99***********9888889**99999865 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   2.5e+03      28      49 ..      35      57 ..      20      59 .. 0.65
   2 !   16.7   0.0   2.8e-06    0.0055       9      55 ..      64     112 ..      52     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                                  TCECEEECCTTHHHH.HHCT-SS CS
                 Thioredoxin_3 28 gikaevekvtdfeei.ekygVms 49
                                  g k++    ++f+e+ ++++V  
  gi|70607552|ref|YP_256422.1| 35 GGKIHHLTDKNFNEFlSSFKVSV 57
                                  56666666788888888888865 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.8e-06
                                   SSTTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEEEC CS
                 Thioredoxin_3   9 gCakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPalvi 55 
                                    C+ C+ l+ +++e+ ++  g+ +   +v +++ei  +ygV+s P++++
  gi|70607552|ref|YP_256422.1|  64 WCPPCHLLSPIIEELSKDYkGVGFGKLNVDQYPEIaTSYGVISLPTVLL 112
                                   4*****************977999**********************954 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.9e-06     0.018      19      59 ..      45      86 ..      31      94 .. 0.78
   2 ?    0.3   0.0      0.31   6.2e+02      89     117 ..      93     115 ..      89     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
                                  ECHHH.TT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTT CS
                      AhpC-TSA 19 slsdy.kg.kpvvlffypkdwcpvCttelpalaklyeefkerg 59
                                  +++++ +  k+ v+ f+++ wcp+C    p +++l +++k  g
  gi|70607552|ref|YP_256422.1| 45 NFNEFlSSfKVSVVDFWAE-WCPPCHLLSPIIEELSKDYKGVG 86
                                  556664335999*******.******99999999998888555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
                                   -TTSHHHHHTT-EETTTTECSCEEEEE-T CS
                      AhpC-TSA  89 Deegkvakaygvlkeekglalratfvidk 117
                                   D+  ++a++ygv+       l+++ ++ +
  gi|70607552|ref|YP_256422.1|  93 DQYPEIATSYGVI------SLPTVLLFHE 115
                                   7777999999999......7777776655 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.038      15     105 ..      40     116 ..      26     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                     OST3_OST6  15 klndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglns 95 
                                   +l+d+n++e+l+ +   s vv + a      C +C+ + p +e ++k ++           F+k+++d+ +++  ++g+ s
  gi|70607552|ref|YP_256422.1|  40 HLTDKNFNEFLS-SFKVS-VVDFWA----EWCPPCHLLSPIIEELSKDYKGV--------GFGKLNVDQYPEIATSYGVIS 106
                                   566666666664.22222.222333....35999999999999999988766........6******************** PP

                     OST3_OST6  96 aPhlllfppk 105
                                   +P +llf+  
  gi|70607552|ref|YP_256422.1| 107 LPTVLLFHEG 116
                                   *******983 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.28     136     203 ..      60     117 ..      52     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                          TraF 136 Fyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks 203
                                   F ++ cp c+ ++pi++++ ++y g      +vd+ p   ++           +gv + P+++l+++ +
  gi|70607552|ref|YP_256422.1|  60 FWAEWCPPCHLLSPIIEELSKDYkGVGFGKLNVDQYPE--IAT---------SYGVISLPTVLLFHEGK 117
                                   77788******************999999999999987..666.........9***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 971.83
//
Query:       gi|70607553|ref|YP_256423.1|  [L=195]
Description: hypothetical protein Saci_1824 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-62  208.7   6.4      6e-62  208.2   6.4    1.1  1  Endonuc_Holl    Endonuclease related to archaeal Holliday jun
     0.0056   16.6   2.7     0.0056   16.6   2.7    1.9  2  PIN_8           PIN like domain
  ------ inclusion threshold ------
      0.021   14.9   2.1      0.038   14.0   2.1    1.5  1  eIF3_p135       Translation initiation factor eIF3 subunit 13
      0.026   13.4   2.7      0.042   12.6   2.7    1.2  1  O-antigen_lig   O-antigen ligase like membrane protein
      0.033   14.3   2.7        2.8    8.2   1.2    2.3  2  Death           Death domain
      0.055   12.8   0.8       0.16   11.2   1.0    1.8  2  DUF929          Domain of unknown function (DUF929)
      0.063   11.6   0.3      0.079   11.2   0.3    1.1  1  OATP            Organic Anion Transporter Polypeptide (OATP) 
       0.11   12.6   0.2       0.31   11.2   0.0    1.8  1  HTH_48          HTH domain in Mos1 transposase
       0.12   13.4   0.7       0.12   13.4   0.7    2.0  3  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
       0.12   13.3   0.2       0.21   12.5   0.2    1.4  1  EphA2_TM        Ephrin type-A receptor 2 transmembrane domain
       0.44   10.0   1.8       0.56    9.7   1.8    1.1  1  UCH             Ubiquitin carboxyl-terminal hydrolase
        3.4    8.0  12.0        0.2   12.0   6.5    1.7  2  Phage_Gp23      Protein gp23 (Bacteriophage A118)


Domain annotation for each model (and alignments):
>> Endonuc_Holl  Endonuclease related to archaeal Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   6.4     4e-65     6e-62       1     160 [.      14     173 ..      14     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 4e-65
                  Endonuc_Holl   1 ilvlvilvlllkiskiqkklekkarelfeewkkeeaeeleklkeaeallkkeaevkleewkkkeekeiRedaikksksvil 81 
                                   i+vl+i++++++i+kiq++ +++a+e+f++w++++++el++++  e++++++++++le+w+ ++e+eiR+da++ks++++l
  gi|70607553|ref|YP_256423.1|  14 IIVLIIISYSRRINKIQEESKRQAQEMFSQWTQQHSNELRTQI--EQSVEMKYKAMLEQWTIQKESEIRKDAVTKSINTLL 92 
                                   7899***************************************..************************************ PP

                  Endonuc_Holl  82 gkvtEeliPlf..pefsynpkDaRflGtPvDlvvFdGLsegeveeivfvEvKtGkssslseReravrdaieakrvsyevlr 160
                                   gk++Ee++P+f  +++s++pkD+R+lG+PvD+v+F+GLs+++  ei+f+E+KtGkss+l+eRer++rdai akrv+yev++
  gi|70607553|ref|YP_256423.1|  93 GKISEEFAPIFiaQKYSISPKDFRHLGSPVDFVAFKGLSDESEPEIIFFEIKTGKSSALTERERKIRDAIVAKRVKYEVIN 173
                                   ***************************************9999************************************98 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.7   3.7e-06    0.0056      63     147 ..      23     100 ..      18     109 .. 0.82
   2 ?    0.4   0.2      0.33     5e+02      74     110 ..     156     192 ..     134     195 .] 0.56

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                         PIN_8  63 ekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedpilkkleellegkig 143
                                   ++ ++k++++ +++ +e++++w ++ + +   lr ++++++e   +++   le+++ + ++++++d + k +++ll+ ki+
  gi|70607553|ref|YP_256423.1|  23 SRRINKIQEESKRQAQEMFSQWTQQHSNE---LRTQIEQSVEMKYKAM---LEQWTIQKESEIRKDAVTKSINTLLG-KIS 96 
                                   56778999999999999999999998876...8888888887666666...79999999999999*********965.898 PP

                         PIN_8 144 eals 147
                                   e++ 
  gi|70607553|ref|YP_256423.1|  97 EEFA 100
                                   8875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                         PIN_8  74 ekkleealkkwakkkaldteelrkelkkqleelkeel 110
                                    k +++++ k+ k++ ++ + l ++ k++++e  +++
  gi|70607553|ref|YP_256423.1| 156 RKIRDAIVAKRVKYEVINLNSLVEDAKRKISEEIDKV 192
                                   3333445556666666665555555555555555444 PP

>> eIF3_p135  Translation initiation factor eIF3 subunit 135
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.1   2.5e-05     0.038     105     159 ..      30      86 ..      20     110 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                     eIF3_p135 105 kkkkkkknkkkesewtkltpeslweqiekevkarfryeleedsiee..elkkislLR 159
                                   ++++k+++++  s+wt+  +++l++qie+ v+ +++  le+ +i++  e++k ++ +
  gi|70607553|ref|YP_256423.1|  30 QEESKRQAQEMFSQWTQQHSNELRTQIEQSVEMKYKAMLEQWTIQKesEIRKDAVTK 86 
                                   23334444445899**********************999887777666555544444 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   2.8e-05     0.042     248     332 ..       6      90 ..       2      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                 O-antigen_lig 248 llaiillvligillaiypyspiyrrkelkekeieiksekkeeeeikneikeny.kseglk.eavleqyeyandkqfsqell 326
                                   +l+i+l+++i+  l+i++ys+ +++++ ++k+++++   + +++  ne+  +  +s ++k +a+leq +++++ ++ ++  
  gi|70607553|ref|YP_256423.1|   6 ILSIFLMIIIV--LIIISYSRRINKIQEESKRQAQEMFSQWTQQHSNELRTQIeQSVEMKyKAMLEQWTIQKESEIRKDAV 84 
                                   45555555444..5888888888888888888888888887777777766554156677799*********9999998877 PP

                 O-antigen_lig 327 keeves 332
                                    +++ +
  gi|70607553|ref|YP_256423.1|  85 TKSINT 90 
                                   766644 PP

>> Death  Death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2    0.0019       2.8      28      60 ..      23      51 ..      19      56 .. 0.83
   2 ?    6.2   0.0    0.0079        12      36      82 ..      53     104 ..      50     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                  HHHHHHHHHHSSSTHHHHHHHHHHHHHHHHTTT CS
                         Death 28 seeeidriekennslrsqsyalLqlWedregen 60
                                  s++ i+ i++e+   + q+++++  W++++ ++
  gi|70607553|ref|YP_256423.1| 23 SRR-INKIQEES---KRQAQEMFSQWTQQHSNE 51
                                  555.99999999...*************99654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0079
                                   HHSS.STHHHHHHHHHHHHHHHHT....TTCSHHHHHHHHHHTTHHHHHHHH CS
                         Death  36 eken.nslrsqsyalLqlWedreg....enatvgtLleaLrklgrddaaekl 82 
                                   +++  +s   + +a+L  W++++     ++a +++  + L k+  ++a  ++
  gi|70607553|ref|YP_256423.1|  53 RTQIeQSVEMKYKAMLEQWTIQKEseirKDAVTKSINTLLGKISEEFAPIFI 104
                                   555566788999*********9877887777777777888877777766555 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00011      0.16       3      56 ..       5      54 ..       4     122 .. 0.84
   2 ?   -0.4   0.0       0.4   5.9e+02     202     215 ..     102     115 ..      53     163 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        DUF929  3 liviaiivliivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdlas 56
                                  li+ +++ +iiv+i++ + + i  n++ +  ++ +a+e++s + ++  +++l  
  gi|70607553|ref|YP_256423.1|  5 LILSIFLMIIIVLIIISYSRRI--NKI-QEESKRQAQEMFS-QWTQQHSNELRT 54
                                  6788888888888888887777..333.3456667888888.888888777765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                        DUF929 202 tyilvgysinPsll 215
                                    +i+  ysi+P+++
  gi|70607553|ref|YP_256423.1| 102 IFIAQKYSISPKDF 115
                                   34444445555554 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   5.3e-05     0.079     217     285 ..       3      69 ..       3     121 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 217 lgflilgvllllaaiplffFPkelpkkkeerakkkseeesaekkeekkkkeksksseeeelkslkdfpk 285
                                   +g +++ +l+++++++++++ ++++k +ee++++++e+ s+ +++++++ +++ +++     + k +++
  gi|70607553|ref|YP_256423.1|   3 IGLILSIFLMIIIVLIIISYSRRINKIQEESKRQAQEMFSQWTQQHSNELRTQIEQS--VEMKYKAMLE 69 
                                   689999*****************9988888888887766542444444444444444..3334444333 PP

>> HTH_48  HTH domain in Mos1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.31       7      36 ..     138     169 ..     137     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                        HTH_48   7 ciLyefkkgksa..aeahrkickvygedvlse 36 
                                   +i++e+k+gks+  +e  rki++++    +++
  gi|70607553|ref|YP_256423.1| 138 IIFFEIKTGKSSalTERERKIRDAIVAKRVKY 169
                                   8***********9999*****99998776666 PP

>> HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   7.8e-05      0.12       5      58 ..      27      78 ..      23      97 .. 0.80
   2 ?   -2.2   0.0       5.9   8.8e+03      46      58 ..     157     168 ..     145     182 .. 0.65
   3 ?   -1.7   0.1       4.2   6.2e+03      10      24 ..     180     194 ..     172     195 .] 0.52

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                HK97-gp10_like  5 kkleklserevekaikkalkkaAkevldkakkrtpsvdtggdLrdsitvqgkvk 58
                                  +k+++ s+r+++++  +++++  +e+++++ + ++  ++ + + +++t+q++ +
  gi|70607553|ref|YP_256423.1| 27 NKIQEESKRQAQEMFSQWTQQHSNELRTQIEQSVE-MKY-KAMLEQWTIQKESE 78
                                  6777778899*************************.999.*********33222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.9
                HK97-gp10_like  46 dLrdsitvqgkvk 58 
                                   ++rd i+  ++vk
  gi|70607553|ref|YP_256423.1| 157 KIRDAIVA-KRVK 168
                                   46666666.5444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.2
                HK97-gp10_like  10 lserevekaikkalk 24 
                                    ++r+++++i+k++k
  gi|70607553|ref|YP_256423.1| 180 DAKRKISEEIDKVTK 194
                                   333456666666655 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00014      0.21       7      55 ..       6      54 ..       1      70 [. 0.42

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                      EphA2_TM  7 aglvllvilvilvlvlvrrrsknrkqksdl..k.......skeekkeeensgkk.glkt 55
                                  +  ++l+i+++l+++ ++rr ++ +++s++  +       +          +++ +l+t
  gi|70607553|ref|YP_256423.1|  6 ILSIFLMIIIVLIIISYSRRINKIQEESKRqaQemfsqwtQ----------QHSnELRT 54
                                  33344444444444444333333333333222122222221..........11123443 PP

>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.8   0.00037      0.56      87     194 ..      36     184 ..      24     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                                   HHSGGGTSSSTCEHHHHHHHHHHHHHHHHCCHCCCHHH..HHHCCCTTSHHHHHH-EEEEE.................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.................... RF
                           UCH  87 klaksfsgykqqDaqEflaflLdqlhedlnrevaeekw..kkhlkrndslitdlfegqlks.................... 145
                                   + +++fs+++qq ++E+ +++ ++++ + ++    e+w  +k+++  ++ +t+  ++ l +                    
  gi|70607553|ref|YP_256423.1|  36 QAQEMFSQWTQQHSNELRTQIEQSVEMKYKAM--LEQWtiQKESEIRKDAVTKSINTLLGKiseefapifiaqkysispkd 114
                                   55677999************999999999994..4444458888888888888877777777789**************** PP

                                   ..............EEEEEEB-SEEEEEEESEEETEE...EEE--SEEB--S....EEE-GGGBSS-BTT CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx....xxxxxxxxxxxxxx RF
                           UCH 146 ..............klklkrlPeiLiihlkRfsynss...ksKlntkvefpe....eldlssylaeekkk 194
                                                  l+ ++ Pei+++++k  + +     ++K+++ +  ++     ++l+s++++ k+k
  gi|70607553|ref|YP_256423.1| 115 frhlgspvdfvafkGLSDESEPEIIFFEIKTGKSSALterERKIRDAIVAKRvkyeVINLNSLVEDAKRK 184
                                   *********999998888999*****99998888555667899999999997777788888888766665 PP

>> Phage_Gp23  Protein gp23 (Bacteriophage A118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   6.5   0.00013       0.2      22     109 ..       5      92 ..       3      99 .. 0.87
   2 ?   -1.9   0.2       2.7     4e+03      84      84 ..     171     171 ..     142     194 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                    Phage_Gp23  22 lsvvlflillivtkriwddrkilkiemkeerekkeekrekkekeskeekdktissvdkskrlldkqndliksekkaidels 102
                                   l + +fl+++iv   i   r+i ki+    r+ +e   +  ++ s+e + ++  sv+ + + +  q  + k+ +   d ++
  gi|70607553|ref|YP_256423.1|   5 LILSIFLMIIIVLIIISYSRRINKIQEESKRQAQEMFSQWTQQHSNELRTQIEQSVEMKYKAMLEQWTIQKESEIRKDAVT 85 
                                   567789999999999999********999****************************999999999999998888888888 PP

                    Phage_Gp23 103 kslvkla 109
                                   ks+  l 
  gi|70607553|ref|YP_256423.1|  86 KSINTLL 92 
                                   8877664 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                    Phage_Gp23  84 l 84 
                                   +
  gi|70607553|ref|YP_256423.1| 171 V 171
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2914  (0.16253); expected 358.6 (0.02)
Passed bias filter:                     1135  (0.0633053); expected 358.6 (0.02)
Passed Vit filter:                       157  (0.00875676); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1289.70
//
Query:       gi|70607554|ref|YP_256424.1|  [L=170]
Description: hypothetical protein Saci_1825 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-11   44.6   0.0      2e-11   44.3   0.0    1.1  1  DUF4382         Domain of unknown function (DUF4382)


Domain annotation for each model (and alignments):
>> DUF4382  Domain of unknown function (DUF4382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   1.1e-15     2e-11       2      87 ..      31     127 ..      30     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.1e-15
                       DUF4382   2 GtvslslsDaPvddfeevvvtiskvelkpadgeesdggwveldeeevdepqtvdLlelqggkatllaelelpaGeYsqirl 82 
                                   G++++++ D Pv +  ++++tis++ +++a+++++++ w++++    + + tv L +    ++t la+++lp GeY++i++
  gi|70607554|ref|YP_256424.1|  31 GNLNIYVQDPPVTSTLKIYLTISSIMIHKANSTSNSTAWITIS----NRTMTVLL-T---YNMTFLASAKLPPGEYNEIFI 103
                                   99******************************999999****9....67777766.3...4699***************** PP

                       DUF4382  83 vlsd...................d 87 
                                    +s+                   +
  gi|70607554|ref|YP_256424.1| 104 QVSSveasigtvnvsvilpssvfK 127
                                   ***888888766443333333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1207.63
//
Query:       gi|70607555|ref|YP_256425.1|  [L=218]
Description: hypothetical protein Saci_1826 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1484.50
//
Query:       gi|70607556|ref|YP_256426.1|  [L=401]
Description: group 1 glycosyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-23   81.8   0.0    7.1e-23   81.0   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-08   35.4   0.0    1.8e-08   34.9   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00012   22.4   0.0    0.00019   21.8   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.19   11.4   0.0       0.41   10.3   0.0    1.5  1  IL11             Interleukin 11


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   1.6e-26   7.1e-23       6     171 ..     205     373 ..     201     374 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.6e-26
                                   HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..........STTHHHHHHHHHHHCTTCGGGE CS
               Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.........ngeeekelkklaeelelsdnvif 77 
                                   + k g+ e+k+++  ++r+++ K++  +ika++l k  ++ +++l  +G         ++ +++ +++  +   +  ++ +
  gi|70607556|ref|YP_256426.1| 205 MSKFGISEDKPLVTQISRFDYAKDPLGVIKAYKLAK--RHVDLQLAYVGspatddpegEKVYNEVIRESRDDKDI--HILM 281
                                   6788999**************************765..49*************9876666666666666666666..8888 PP

                                   EECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
               Glycos_transf_1  78 lgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                   l   s+ ++ ++ +++ ++ ++si+EgfG+++ EAm  ++pvi  n+gg++ +v +g+tG+lv ++  + +a + + l ++
  gi|70607556|ref|YP_256426.1| 282 LPPYSDLEINAFQSASTVVMQKSIKEGFGLTVSEAMWKNKPVIGGNTGGIPLQVINGVTGFLVNSP--QGAAHYTIYLTRN 360
                                   888888899999999************************************************999..99*********** PP

                                   HHHHHHHHHHHHH CS
               Glycos_transf_1 159 eelrerlgenark 171
                                    + r+ +g nar+
  gi|70607556|ref|YP_256426.1| 361 AKVRHTMGTNARE 373
                                   ***********97 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     4e-12   1.8e-08       3     132 ..     216     358 ..     214     360 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4e-12
                                   EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---...........HHHHHHHT.T-T.TEEEE---TH..HHHHH CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp..rp.......eeleelaa.gleerveftGfved..laell 70 
                                    +  ++r+ +  k    +++a +l +++ d++l  vG+ p  ++       +e+ ++ + + + ++ ++   +d  ++++ 
  gi|70607556|ref|YP_256426.1| 216 LVTQISRF-DYAKDPLGVIKAYKLAKRHvDLQLAYVGS-PatDDpegekvyNEVIRESRdDKDIHILMLPPYSDleINAFQ 294
                                   56677888.556888889999999996667*******4.333223454333222222222212235555555665477777 PP

                                   HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--.TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv.gengllvppgdpealaeailrLl 132
                                   +a++v+   s  egfgl++ Eam   +pv+  ++ggi  +v+ g++g+lv+  +p+  a   + L 
  gi|70607556|ref|YP_256426.1| 295 SASTVVMQKSikEGFGLTVSEAMWKNKPVIGGNTGGIpLQVInGVTGFLVN--SPQGAAHYTIYLT 358
                                   7777777777*99**********************9835566********8..8888888777775 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.2e-08   0.00019       6      90 ..     304     388 ..     290     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.2e-08
               Glyco_trans_1_2   6 srsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                   s +e++ l ++Ea+  + +++   + g++  + +g +++l+ +++ +a    yl +n + r+ ++++are+v++++  ++ 
  gi|70607556|ref|YP_256426.1| 304 SIKEGFGLTVSEAMWKNKPVIGGNTGGIPLQVINGVTGFLVNSPQGAAHYTIYLTRNAKVRHTMGTNAREHVRRNFLITRE 384
                                   5569999********************************************************************988777 PP

               Glyco_trans_1_2  87 aeql 90 
                                   ++++
  gi|70607556|ref|YP_256426.1| 385 LRDY 388
                                   6665 PP

>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.2e-05      0.41      40      65 ..      10      35 ..       2      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.2e-05
                          IL11 40 vehrlksLPalsnsasdlsslevkst 65
                                  +eh+l+sL +++++ +dls l v+st
  gi|70607556|ref|YP_256426.1| 10 GEHELDSLFKIAERIKDLSILHVNST 35
                                  67*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2519.38
//
Query:       gi|70607557|ref|YP_256427.1|  [L=432]
Description: transporter protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-17   61.9  50.4    1.1e-16   60.5  50.4    1.7  1  AA_permease    Amino acid permease
    3.7e-15   55.7  54.7    4.8e-15   55.3  54.7    1.1  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
       0.26   11.4   1.9         11    6.2   0.0    3.1  2  PspB           Phage shock protein B


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5  50.4   1.9e-20   1.1e-16       2     429 ..      20     397 ..      19     421 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.9e-20
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++i+ gg  + + ++  g v  +  + +++ a+++a++v+++ +l +++++  ++++gg+ytya  +l  +lG  +G++y
  gi|70607557|ref|YP_256427.1|  20 LFFISFGGQAPFISLLTFGTVMIALVGTAGVFAMIIATLVVLFNGLVVYYLSKRFKRGGGYYTYAVYSLTTRLGLETGWSY 100
                                   6788999999977777777777777666889************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillag 163
                                    ++ i + +  +t+ ++++ ++   t  + + + ++++ vv ++i l gv+v+++  +i++li + ai+++ i +      
  gi|70607557|ref|YP_256427.1| 101 ILYAISYGGTLVTGGAYVLYYI---TGWN-QTILALIVSVVASAIVLSGVRVSAKYAMIMSLIEMGAIVILSIYFL----Y 173
                                   **************99999999...7777.789999*******************888888888888888777772....2 PP

                   AA_permease 164 gkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvirit 244
                                     + ++      ++++     n+p++            +s+  + +   tG++++a +++E+ d +ksi ka + v+i  +
  gi|70607557|ref|YP_256427.1| 174 SSGWHF------YNPV-----NFPSK-----------LASAVLFGLGIPTGYGSIAPLGEEA-DTRKSIGKAAILVLIFGG 231
                                   222333......4444.....59999...........7777777777779********9996.78***********99999 PP

                   AA_permease 245 ifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP 325
                                    +  l+++++g+++ + +   l            ++  s +++  +++ ++ l   +  ++s++ + sR++ ++++d ++P
  gi|70607557|ref|YP_256427.1| 232 GLASLFFYSLGAINFTGN---LV----------DYLLASFSIIGTVFLSFLALNDGILGGVSYILANSRTVKAMSEDLIFP 299
                                   999998888888865555...33..........33344667778888888899999999********************** PP

                   AA_permease 326 kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgf 406
                                   k+l+k+ k+ +Pl + ++ +i+   +l la  + ++  +f  l a+++l ++++++++++s++  R a +  +++i+el +
  gi|70607557|ref|YP_256427.1| 300 KFLSKSVKN-RPLISEIFIAIVFITILTLAVHYIGLYDTFVTLGALAGLGNIFIHTSANISLI--RLASRRPRKHIDELMV 377
                                   *****9986.7*****999999888888899999999**************************..8887788888999876 PP

                   AA_permease 407 kaallplgvilvlaaliiillil 429
                                    +   + + i+ ++++++++ ++
  gi|70607557|ref|YP_256427.1| 378 GI---IATIISLWVLVSSLFSVN 397
                                   54...445555555555555554 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3  54.7     8e-19   4.8e-15       1     411 [.      15     400 ..      15     413 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 8e-19
                 AA_permease_2   1 lsllsafalvigsv...igsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkva 77 
                                   l+++++f++++g     i s  ++ + ++a +g+a ++  +ia+l++ l  +lv   ls +++r gG y+y+ +    +++
  gi|70607557|ref|YP_256427.1|  15 LTFVDLFFISFGGQapfI-SLLTFGTvMIALVGTAGVFAMIIATLVV-LFNGLVVYYLSKRFKRGGGYYTYAVYSLTTRLG 93 
                                   6899*******9966754.444444447999**************99.678888888**99******************** PP

                 AA_permease_2  78 flsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                     ++w++ + ++    ++l+ +++y l+ +      + w + ++a ++ ++  +i + g++ sak+++i+ ++ +     i
  gi|70607557|ref|YP_256427.1|  94 LETGWSYILYAIS-YGGTLVTGGAYVLYYI------TGWNQTILALIVSVVASAIVLSGVRVSAKYAMIMSLIEMG-A--I 164
                                   ******9765555.5578899999999976......4567888899*****************************5.5..5 PP

                 AA_permease_2 159 liilglitvdgggfsslstetdtffpn.gwpgvllgllivlwsfdGfesaanvseevkk.kdvpkaifigllivlvlyllv 237
                                   +i+  +++ + g++      +   fp+   + vl+gl+i     +G+ s+a   ee+ + k + ka++++l++ ++l  l+
  gi|70607557|ref|YP_256427.1| 165 VILSIYFLYSSGWHF----YNPVNFPSkLASAVLFGLGI----PTGYGSIAPLGEEADTrKSIGKAAILVLIFGGGLASLF 237
                                   555555555666665....23334555455556666664....58***********887589*****99999999999988 PP

                 AA_permease_2 238 niaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvnkf 318
                                       ++ ++  +++  +nl++++ +     ++ ++++++++l+    ++++ ++++++sr++ a+++d ++P+f++k+ k+
  gi|70607557|ref|YP_256427.1| 238 ----FYSLGAINFT--GNLVDYLLAS----FSIIGTVFLSFLALNDGILGGVSYILANSRTVKAMSEDLIFPKFLSKSVKN 308
                                   ....5544444444..5654333333....4346688888888888888999**************************988 PP

                 AA_permease_2 319 gspiraiiltaivslillllfllas....saaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfl 395
                                    +p+ + i++aiv  i  +l+l++     ++ + +l +++ lg+i++ + + i+++ l  +rp+ k +   +v+ii+++++
  gi|70607557|ref|YP_256427.1| 309 -RPLISEIFIAIVF-IT-ILTLAVHyiglYDTFVTLGALAGLGNIFIHTSANISLIRLASRRPR-KHIDELMVGIIATIIS 385
                                   .7777777777763.33.3344333344799******************************998.5566678999999999 PP

                 AA_permease_2 396 lfllvalffppkgpat 411
                                   l++lv   f  ++p +
  gi|70607557|ref|YP_256427.1| 386 LWVLVSSLFS-VNPYV 400
                                   9999888774.45444 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0018        11       8      30 ..      52      74 ..      47      79 .. 0.86
   2 ?    2.5   0.8     0.026   1.6e+02       6      26 ..     312     332 ..     308     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0018
                          PspB  8 pliifvlfVapiWLiLHYrskkk 30
                                   +ii +l+V++ +L+ +Y sk+ 
  gi|70607557|ref|YP_256427.1| 52 AMIIATLVVLFNGLVVYYLSKRF 74
                                  579999**************975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                          PspB   6 avpliifvlfVapiWLiLHYr 26 
                                   +  + i ++f+ ++ L  HY+
  gi|70607557|ref|YP_256427.1| 312 ISEIFIAIVFITILTLAVHYI 332
                                   566889999999999*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2786.85
//
Query:       gi|70607558|ref|YP_256428.1|  [L=112]
Description: hypothetical protein Saci_1829 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-05   24.4   0.4    7.1e-05   22.8   0.4    1.9  1  DUF2250   Uncharacterized protein conserved in archaea (DUF22
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.038   14.3   0.0    1.4  1  DUF2513   Hypothetical protein (DUF2513)


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.4   7.9e-09   7.1e-05       7      89 ..       5     102 ..       1     106 [. 0.69

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.9e-09
                       DUF2250   7 delalkvlkhlkkanvdYaksiakel........eipleevrellkkLeelGLlervegktikrteaklKk.....ksev. 73 
                                   ++l+ k+l h+ k ++d +  +a++l        + +  e++  +kkL+e+GLl+ ++g+  +      K+     ++e+ 
  gi|70607558|ref|YP_256428.1|   5 TDLMKKILIHIYKYGPDNSWYMARRLlgesgytpKFDEDEIEINCKKLKEMGLLTVYNGSLKRSVTSSVKPwlkvkAKETg 85 
                                   567788999999999999888888764444444467889****************99986554444444441111122221 PP

                       DUF2250  74 .hkhHtYYrltreGell 89 
                                    + +  YY+lt++G  +
  gi|70607558|ref|YP_256428.1|  86 aKPKGVYYDLTKKGRKI 102
                                   145678********875 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.3e-06     0.038       5      66 ..       6      76 ..       5     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-06
                       DUF2513  5 dlvRdiLltleeletkeeslddeeekls..aidgyskeeiiyhlkllaeagLieaekkkakss.......i 66
                                  dl ++iL+++ ++  +++++ + +   +    ++++++ei   +k+l e gL+ +++ + k s       +
  gi|70607558|ref|YP_256428.1|  6 DLMKKILIHIYKYGPDNSWYMARRLLGEsgYTPKFDEDEIEINCKKLKEMGLLTVYNGSLKRSvtssvkpW 76
                                  899*******999999988888654444799************************9999888854444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 743.09
//
Query:       gi|70607559|ref|YP_256429.1|  [L=203]
Description: hypothetical protein Saci_1830 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-15   55.3   0.0    1.6e-11   43.9   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    3.3e-13   49.9   0.1    3.2e-11   43.4   0.0    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    5.2e-09   37.0   0.0    4.5e-08   34.0   0.0    1.8  2  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.021   13.5   0.0      0.035   12.8   0.0    1.4  1  Ndr            Ndr family
       0.15   11.7   0.0       0.23   11.1   0.0    1.2  1  FSH1           Serine hydrolase (FSH1)


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   4.6e-15   1.6e-11       7     110 ..      29     125 ..      27     138 .. 0.87
   2 !   10.0   0.0   0.00011      0.38     186     220 ..     133     168 ..     126     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.6e-15
                   Hydrolase_4   7 vvlvHG..laehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                   v+l+HG  ++ + ++  ++ +  a++Gf  + +D  G+G+s  +rg+++s++d++ D+   ++       + + fllG Sm
  gi|70607559|ref|YP_256429.1|  29 VILFHGsrFNAYTWKETNTLDSVAKAGFRAISVDFPGYGKS--ERGKFTSLSDFIYDFIFSLSL------N-KPFLLGASM 100
                                   788888667888899999***********************..9*************9655433......2.46******* PP

                   Hydrolase_4  86 GGliallyllrypdkvaglilsaPa 110
                                   GG  +l+y   +p++++glil++++
  gi|70607559|ref|YP_256429.1| 101 GGEAVLSYSVYHPKDIKGLILVGAV 125
                                   **********************986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                   Hydrolase_4 186 raakit.lPllllhGeaDkvvdpeasrelyerlgsk 220
                                     ++++ +P+ll+ G++D++ ++e+ + ++++++ +
  gi|70607559|ref|YP_256429.1| 133 LLTNLEgVPILLIWGKKDRISSEENYKLIMNSVKTT 168
                                   44555569**************99999888888765 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   8.9e-15   3.2e-11       2     106 ..      28     124 ..      27     132 .. 0.94
   2 !    5.0   0.0    0.0044        16     199     236 ..     132     164 ..     125     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 8.9e-15
                                   EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETH CS
                 Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSm 82 
                                   +++++hG   +++ w e    +  ak+gf+ i +D +G+g+S++++ +        s+ d+++ +  +l + k+ l+G Sm
  gi|70607559|ref|YP_256429.1|  28 PVILFHGSRFNAYTWKETNTLDSVAKAGFRAISVDFPGYGKSERGKFT--------SLSDFIYDFIFSLSLNKPFLLGASM 100
                                   899****999999999999999************************74........6************************ PP

                                   HHHHHHHHHHHHGGGEEEEEEESE CS
                 Abhydrolase_1  83 GGmialayaaeyperVkalvllga 106
                                   GG  +l y   +p+ +k+l+l+ga
  gi|70607559|ref|YP_256429.1| 101 GGEAVLSYSVYHPKDIKGLILVGA 124
                                   ***********************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0044
                                   HHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHC CS
                 Abhydrolase_1 199 klllrlrelknvlaptlvisgtsDplvppkaledlaql 236
                                   kll +l++     +p+l+i+g +D++ +++++  + + 
  gi|70607559|ref|YP_256429.1| 132 KLLTNLEG-----VPILLIWGKKDRISSEENYKLIMNS 164
                                   55555555.....4*************99776665555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.2e-11   4.5e-08       1      95 [.      29     124 ..      29     137 .. 0.84
   2 ?    1.1   0.0      0.14   4.9e+02     166     218 ..     137     188 ..     128     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.2e-11
                                   EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT..TTSEEEEEETCHHHHH CS
                 Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaagggpvvlvGHSlGGala 79 
                                   v+l HG+ ++a+ W  +  L   + ag++ +++D+pG+G s++  ++   l d+  +++ +l    ++++l+G S+GG  +
  gi|70607559|ref|YP_256429.1|  29 VILFHGSRFNAYTWKeTNTLDSVAKAGFRAISVDFPGYGKSERGKFTS--LSDFiYDFIFSLS--LNKPFLLGASMGGEAV 105
                                   799***********6588999999999999*********888888888..9***988888885..99**********9877 PP

                                   HHHHHCC....EE.EEES- CS
                 Abhydrolase_6  80 laaapla..lvvg.vlldp 95 
                                   l +  +   ++ g +l+ +
  gi|70607559|ref|YP_256429.1| 106 LSYSVYHpkDIKGlILVGA 124
                                   7744444657777777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.14
                                   HTT-TTGCEEECTT-CHHHHCHHCCCH.STTEEET.CE...SSS-HHHHSHHHHH CS
                 Abhydrolase_6 166 wadlpvpllvlggeDplvprllerlla.qagarlp.vvlpgaGHlphleepdeva 218
                                   ++++p +l ++g++D++  +    +   ++++++   v  g+ H+ +l++p+ ++
  gi|70607559|ref|YP_256429.1| 137 LEGVPILL-IWGKKDRISSEE--NYKLiMNSVKTThFVQIGNNHACYLDDPTTFN 188
                                   55555555.546999988866..44554355555535555999955555998776 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-06     0.035      84     134 ..      76     126 ..      58     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-06
                                   HHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES--- CS
                           Ndr  84 dladqllavldhfklksviglGvgaGAyilarfalkhperveglvLinits 134
                                   +l+d +   +  ++l++   lG+  G   ++ +++ hp+ ++gl+L+ + +
  gi|70607559|ref|YP_256429.1|  76 SLSDFIYDFIFSLSLNKPFLLGASMGGEAVLSYSVYHPKDIKGLILVGAVG 126
                                   68888888999999*********************************8776 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.4e-05      0.23     133     200 ..     114     177 ..      94     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.4e-05
                          FSH1 133 pslkfailvsGfkleepkyeeyyeedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpggH 200
                                   +++k +ilv +  +  +kye++  ++   +p+L + G++D + +ee+ + +++++k  +++++    H
  gi|70607559|ref|YP_256429.1| 114 KDIKGLILVGAVGV--KKYEKLL-TNLEGVPILLIWGKKDRISSEENYKLIMNSVKT-THFVQIGNNH 177
                                   45677777777777..4688888.44448***************9999999999998.8888777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1503.91
//
Query:       gi|70607560|ref|YP_256430.1|  [L=207]
Description: hypothetical protein Saci_1831 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-69  229.5  16.5      2e-37  127.2   4.3    2.0  2  DUF2250          Uncharacterized protein conserved in archaea
    1.7e-05   24.6   1.0     0.0018   18.0   0.1    2.2  2  DUF4423          Domain of unknown function (DUF4423)
    0.00042   20.1   1.6          1    9.3   0.1    2.9  3  DUF3116          Protein of unknown function (DUF3116)
     0.0018   18.2   0.7       0.68    9.9   0.1    2.3  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
      0.002   18.0   0.8      0.052   13.4   0.0    3.0  2  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.036   14.2   0.4      0.096   12.8   0.1    1.9  2  FUR              Ferric uptake regulator family
      0.045   13.5   2.4          7    6.5   0.1    2.8  3  DUF501           Protein of unknown function (DUF501)
      0.089   12.8   1.2       0.41   10.7   0.0    2.7  2  Cdc6_C           CDC6, C terminal winged helix domain
       0.16   12.5   8.5       0.58   10.7   0.2    3.7  4  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.2   4.3     1e-40     2e-37       2      93 .]       6      97 ..       5      97 .. 0.98
   2 !  108.5   4.4   6.7e-35   1.3e-31       2      93 .]     108     199 ..     107     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.2 bits;  conditional E-value: 1e-40
                       DUF2250  2 eeleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYYrltr 84
                                  +e+ +d++ l+vl+hlk+anvdY+ksi+ +++ipl+ev ++l+kLe+lGL+erv+g+t+k+teak+K+++evhkhHtYYrltr
  gi|70607560|ref|YP_256430.1|  6 KEVLKDKRLLEVLRHLKRANVDYGKSIMLNTKIPLTEVLDVLDKLESLGLIERVTGATLKNTEAKFKLSQEVHKHHTYYRLTR 88
                                  678899***************************************************************************** PP

                       DUF2250 85 eGelllrel 93
                                  +G++llr+l
  gi|70607560|ref|YP_256430.1| 89 DGDHLLRRL 97
                                  *******86 PP

  == domain 2  score: 108.5 bits;  conditional E-value: 6.7e-35
                       DUF2250   2 eeleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYYrl 82 
                                   e +++de+ lk+l++++++++d+a++++k l++plee++ ++++Le++GL+e++++k+ik++e+++K+k+e+++hH+YY+l
  gi|70607560|ref|YP_256430.1| 108 EIVKDDEVGLKLLYYAEELHSDHALTYSKLLRKPLEEITPKIEELERMGLMEEKNSKVIKFRERRAKPKKETRTHHKYYGL 188
                                   56899**************************************************************************** PP

                       DUF2250  83 treGelllrel 93 
                                   tr Gell+rel
  gi|70607560|ref|YP_256430.1| 189 TRLGELLVREL 199
                                   *********96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   9.2e-07    0.0018      45      91 ..      33      79 ..      17      82 .. 0.94
   2 !    5.5   0.1    0.0064        13      44      90 ..     136     180 ..     128     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.2e-07
                       DUF4423 45 rlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevks 91
                                  +l+ ki+  ev + l+ L++lgl+++    +++ te++++ s+ev +
  gi|70607560|ref|YP_256430.1| 33 MLNTKIPLTEVLDVLDKLESLGLIERVTGATLKNTEAKFKLSQEVHK 79
                                  78999***********************************9999865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0064
                       DUF4423  44 krlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevk 90 
                                   k lr   + ee+   +e L+++gl ++++++ ++  e+  + ++e++
  gi|70607560|ref|YP_256430.1| 136 KLLR--KPLEEITPKIEELERMGLMEEKNSKVIKFRERRAKPKKETR 180
                                   5666..677899999***************99999888888777765 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.6   3.2e+03      41      61 ..      40      60 ..      16      77 .. 0.68
   2 !    9.3   0.1   0.00051         1      61      84 ..      75      98 ..      68      99 .. 0.85
   3 !    9.2   0.2   0.00055       1.1      61      84 ..     177     200 ..     157     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                       DUF3116 41 kneLLytvYWLElkgyilRke 61
                                   +e+L ++  LE+ g i R  
  gi|70607560|ref|YP_256430.1| 40 LTEVLDVLDKLESLGLIERVT 60
                                  466666666677777777754 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00051
                       DUF3116 61 eekannkkrYelTekGellykelk 84
                                  +e+ +++++Y+lT +G+ l+++l 
  gi|70607560|ref|YP_256430.1| 75 QEVHKHHTYYRLTRDGDHLLRRLD 98
                                  4456899**************996 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00055
                       DUF3116  61 eekannkkrYelTekGellykelk 84 
                                   +e+++++k+Y lT  Gell +elk
  gi|70607560|ref|YP_256430.1| 177 KETRTHHKYYGLTRLGELLVRELK 200
                                   5667899***************98 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0027       5.4      58     103 ..      31      76 ..      20      92 .. 0.68
   2 !    9.9   0.1   0.00034      0.68      50     103 ..     125     178 ..      92     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0027
               Phage_rep_org_N  58 mlalifnreletvrlaLkvlkdlelieisedkvikiknwekhqnie 103
                                    + l ++ +l +v  +L+ l++l+lie +   ++k ++ +   ++e
  gi|70607560|ref|YP_256430.1|  31 SIMLNTKIPLTEVLDVLDKLESLGLIERVTGATLKNTEAKFKLSQE 76 
                                   455667789999****************955555544433333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00034
               Phage_rep_org_N  50 enipytaemlalifnreletvrlaLkvlkdlelieisedkvikiknwekhqnie 103
                                   e   + a + + +++++le++   ++ l+ ++l+e +++kvik+ +      +e
  gi|70607560|ref|YP_256430.1| 125 ELHSDHALTYSKLLRKPLEEITPKIEELERMGLMEEKNSKVIKFRERRAKPKKE 178
                                   344556778899*******************************99866555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   2.6e-05     0.052      27      58 ..      31      62 ..      14      84 .. 0.87
   2 ?    1.4   0.1      0.15   2.9e+02      43      63 ..     149     169 ..     138     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                  HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   i  ++++p + v +vL +Le+ Gl+er+ g 
  gi|70607560|ref|YP_256430.1| 31 SIMLNTKIPLTEVLDVLDKLESLGLIERVTGA 62
                                  5667889*********************9876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.15
                                   HHHHHHCTSEEEESSTTTEEE CS
                          TrmB  43 LrsLedkGlVerekgrpklYr 63 
                                   +++Le++Gl e + ++  ++r
  gi|70607560|ref|YP_256430.1| 149 IEELERMGLMEEKNSKVIKFR 169
                                   689********9998866654 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.8e-05     0.096      35      81 ..      33      82 ..      12     120 .. 0.79
   2 ?   -1.3   0.0       1.2   2.3e+03      82     105 ..     158     181 ..     148     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
                                  HTTTT--HHHHHHHHHHHHHTTSEEEEE...ETTSEEEEEESSSSSEEEE CS
                           FUR 35 eedpeislaTVYrtLklleeaglvkele...fedgesryelakkehhdhl 81
                                    + +i l+ V  +L+ le++gl+++++   ++++e++++l+++ h +h 
  gi|70607560|ref|YP_256430.1| 33 MLNTKIPLTEVLDVLDKLESLGLIERVTgatLKNTEAKFKLSQEVHKHHT 82
                                  557789999999************998622266899******97666664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                   EETTT--EEEE--HHHHHHHHHHH CS
                           FUR  82 icekCgkviefkddeiekiqeeia 105
                                   ++ek +kvi+f++   +  +e++ 
  gi|70607560|ref|YP_256430.1| 158 MEEKNSKVIKFRERRAKPKKETRT 181
                                   556666677776665554444444 PP

>> DUF501  Protein of unknown function (DUF501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0076        15      41      80 ..      45      85 ..      38     104 .. 0.68
   2 ?    1.1   0.1      0.15   3.1e+02      43      69 ..      94     120 ..      79     143 .. 0.67
   3 ?    6.5   0.1    0.0035         7      38      79 ..     144     189 ..     137     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0076
                        DUF501 41 kavsrLEaeglvkaleek.laedeelaqalekahaeyaakR 80
                                     ++LE+ gl+++++ + l++ e+ ++  +++h+++   R
  gi|70607560|ref|YP_256430.1| 45 DVLDKLESLGLIERVTGAtLKNTEAKFKLSQEVHKHHTYYR 85
                                  56799**********97746666555555555555554444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                        DUF501  43 vsrLEaeglvkaleeklaedeelaqal 69 
                                     rL ++++++a++e++++de   + l
  gi|70607560|ref|YP_256430.1|  94 LRRLDEKDIIDAYAEIVKDDEVGLKLL 120
                                   679999***********9998544433 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0035
                        DUF501  38 elvkavsrLEaeglvkaleekl....aedeelaqalekahaeyaak 79 
                                   e++ ++++LE+ gl+++ + k+    ++ ++ +++ ++ h+ y  +
  gi|70607560|ref|YP_256430.1| 144 EITPKIEELERMGLMEEKNSKVikfrERRAKPKKETRTHHKYYGLT 189
                                   78899***************99777544555555566666666555 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.41      39      60 ..      40      61 ..      33      81 .. 0.78
   2 ?   -1.0   0.1      0.88   1.8e+03      46      60 ..     149     163 ..     142     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                  HHHHHHHHHHHHHTTSEEEEEE CS
                        Cdc6_C 39 qrevsdllseLemlgileleks 60
                                   +ev+d+l++Le+lg++e+ ++
  gi|70607560|ref|YP_256430.1| 40 LTEVLDVLDKLESLGLIERVTG 61
                                  589***************9876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.88
                                   HHHHHHTTSEEEEEE CS
                        Cdc6_C  46 lseLemlgileleks 60 
                                   + eLe +g+ e ++s
  gi|70607560|ref|YP_256430.1| 149 IEELERMGLMEEKNS 163
                                   666777776665544 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00029      0.58       8      54 ..      17      62 ..      13      69 .. 0.80
   2 ?   -2.1   0.0       2.8   5.6e+03      15      45 ..      93     100 ..      80     107 .. 0.55
   3 ?    5.1   0.1     0.016        32      39      53 ..     149     163 ..     144     181 .. 0.88
   4 ?   -0.6   0.3         1     2e+03      39      49 ..     196     206 ..     191     207 .] 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                        HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                  vL++++ r + +  + ++  +++  + +  +l+kL+  GL+er + +
  gi|70607560|ref|YP_256430.1| 17 VLRHLK-RANVDYGKSIMLNTKIPLTEVLDVLDKLESLGLIERVTGA 62
                                  566666.33444448899999********************998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                        HTH_27  15 rrrrkkladlcgrlnvedshisyslkkLtek 45 
                                                           l++L ek
  gi|70607560|ref|YP_256430.1|  93 L-----------------------LRRLDEK 100
                                   2.......................3333333 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.016
                        HTH_27  39 lkkLtekGLvertgd 53 
                                   +++L+++GL+e++ +
  gi|70607560|ref|YP_256430.1| 149 IEELERMGLMEEKNS 163
                                   899*******87765 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1
                        HTH_27  39 lkkLtekGLve 49 
                                   +++L ++G++e
  gi|70607560|ref|YP_256430.1| 196 VRELKRRGVLE 206
                                   89******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1488.29
//
Query:       gi|70607561|ref|YP_256431.1|  [L=203]
Description: hypothetical protein Saci_1832 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-07   29.9   0.4    1.2e-06   29.1   0.4    1.3  1  CxxCxxCC    Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.043   13.9   0.1    1.5  1  Sigma70_r3  Sigma-70 region 3


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.4   1.3e-10   1.2e-06       2      78 ..      59     140 ..      58     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-10
                      CxxCxxCC   2 CkeC.gaCCk.elkvklteedlerlkaaev....aeeeeeskkiak...adgrCvfldeetklCkiYeeRpkicrlfpas. 72 
                                   C++C g+CC    ++ + e d++++  +      + ++++s    +    + +C++ ++    C i++ +p +c  fp+s 
  gi|70607561|ref|YP_256431.1|  59 CERCgGKCCDyGFGIPVYEFDYKEIVNKLGgakgISDKRDSV---NfriLERPCPYKRGW--ACGIHSFKPYACLSFPFSt 134
                                   ****9****987888999999888854433000033444444...35559******9999..8****************95 PP

                      CxxCxxCC  73 ekeell 78 
                                   e+e+ +
  gi|70607561|ref|YP_256431.1| 135 EDEQKE 140
                                   334433 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.8e-06     0.043       6      30 ..     169     193 ..     164     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHSSXXXHHHHHHHH CS
                    Sigma70_r3   6 ikraqreLeqelgrePtpeEiAeeL 30 
                                   +k++++ L+ +lgr+P+p E+ eeL
  gi|70607561|ref|YP_256431.1| 169 VKKIIDDLTKRLGRQPSPRELYEEL 193
                                   89******************98888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1467.65
//
Query:       gi|70607562|ref|YP_256432.1|  [L=191]
Description: hypothetical protein Saci_1833 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1411.70
//
Query:       gi|70607563|ref|YP_256433.1|  [L=120]
Description: hypothetical protein Saci_1834 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   18.3   0.0     0.0031   17.9   0.0    1.2  1  DrsE      DsrE/DsrF-like family
  ------ inclusion threshold ------
       0.18   11.1   0.0        0.3   10.4   0.0    1.3  1  DUF4141   Domain of unknown function (DUF4141)


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.4e-07    0.0031       2     114 ..       3     117 ..       2     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-07
                                   EEEEEE-S-TTTBSHHHHHHHHHHHH.HTTT..-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHH CS
                          DrsE   2 kvfilvtggpygseaarealelalaa.aalg..hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgq 79 
                                   k++++v + p + +++  a ++   a  +++   +v+v f g G++++       ++ +k l++++++++++g  l +Cg 
  gi|70607563|ref|YP_256433.1|   3 KILFVVMNDPTNLADSIKAAHVLHYAvELKEkgNDVYVYFDGLGTKIPIT-----ESPYKGLKPAYEKAMKEGLILGACGY 78 
                                   667777777776666655555444442444466*****************.....66689********************* PP

                                   HHHHTT--GGGE-..T-..-EEEE-HHHHHHHHHH-SEE CS
                          DrsE  80 aakargldededl..gv..gvevsglgelaelqnegdrv 114
                                   +a   +l   ++l  ++          +l +l+++g+++
  gi|70607563|ref|YP_256433.1|  79 CASPPHLNIRDKLpnTIklIGDEDHHYALTDLVDKGYQI 117
                                   **9888887775532112122222233566666666666 PP

>> DUF4141  Domain of unknown function (DUF4141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.3e-05       0.3      21      32 ..       8      19 ..       2      22 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.3e-05
                       DUF4141 21 VVtDPgNLAqgI 32
                                  V  DP+NLA +I
  gi|70607563|ref|YP_256433.1|  8 VMNDPTNLADSI 19
                                  456********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 917.83
//
Query:       gi|70607564|ref|YP_256434.1|  [L=426]
Description: proline/betaine transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-28   99.6  56.6    1.7e-16   60.1  27.4    2.8  2  MFS_1       Major Facilitator Superfamily
      2e-27   96.2  39.2    7.7e-19   67.9  13.8    2.0  2  Sugar_tr    Sugar (and other) transporter
    1.5e-10   40.2  14.0    1.5e-10   40.2  14.0    2.5  2  MFS_2       MFS/sugar transport protein
  ------ inclusion threshold ------
      0.024   14.6   0.4      0.024   14.6   0.4    2.5  3  TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-me
       0.64   10.0   4.4        1.3    9.0   0.1    3.1  2  PsbI        Photosystem II reaction centre I protein (PSII 4.
        0.9    7.7  11.0        1.5    7.0   5.5    2.5  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1  27.4   5.8e-20   1.7e-16      12     240 ..      22     264 ..      11     266 .. 0.70
   2 !   44.1  26.9   4.2e-15   1.2e-11       2     174 ..     236     413 ..     235     418 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 5.8e-20
                         MFS_1  12 rsilgpalplalaedlgispseigl.....lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa..ss 84 
                                   + i+g++  ++ +  + ++ s ++l     ++++ ++g  ++++++G+l+d++Gr+ +l+l+++l++l++l+   ++  +s
  gi|70607564|ref|YP_256434.1|  22 FLIFGFISGILAKLFFPSTNSLVSLldtlaVFATGFAGRPIGAIIFGHLGDKIGRKYTLILTMTLMGLSSLFTGlLPgyAS 102
                                   4444444443333334456666777333334555666669*****************************555553423433 PP

                         MFS_1  85 ....lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wra 152
                                        + ll  lr+lqG+  g+ f +g++l a+ + +++r++++g+++++ + G++l+ +l  l++s  +        Wr 
  gi|70607564|ref|YP_256434.1| 103 igilAPlLLTTLRILQGVSLGGEFGGGITLSAEFAEPSKRAFYVGIAQMAQGTGPLLATGLIFLFSSFMStqeynsigWRI 183
                                   3333455699************************************************99999999888899999****** PP

                         MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllf.ffgfsglltllpl 232
                                   +f+i a+++++++++   l   e p  k+++++ +     + pl++a+++ +k+     l ++++++ +++++++ ++  +
  gi|70607564|ref|YP_256434.1| 184 LFVIGALIAVIGVII--RLKISESPVFKKVRETGK---ISKIPLAEAFRHHWKKIL---LGLGFIVGgTTMTYATGVFASS 256
                                   ************664..444444444444444444...244444444444444442...2222222213344558888888 PP

                         MFS_1 233 ylqevlgl 240
                                   yl  v g 
  gi|70607564|ref|YP_256434.1| 257 YLENVIGV 264
                                   99888876 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 4.2e-15
                         MFS_1   2 llaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    l++++ +++++ ++ ++ + +l +  g+   e++l+l++ ++ + +a++++G+l+dr+Gr++++++++++++++ +++ f
  gi|70607564|ref|YP_256434.1| 236 GLGFIVGGTTMTYATGVFASsYLENVIGVPTKEVSLILVIGYIIQTIAIFLFGYLADRIGRKPLMITTAAGLVIF-VYPYF 315
                                   578899999999999999999******************************************************.77775 PP

                         MFS_1  82 ...asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigl.lsagfslGailgpllggllasslgWravfyil 157
                                      +++ +  +l++ ++ ++ ++a+++a a++++++fp + r  a+++ + +g+++    +p ++ +l+ + g+ ++ +  
  gi|70607564|ref|YP_256434.1| 316 yllSTGAFsNILLAQLIYSIVGSASTAAYATALTEMFPTSVRYTALSFdYHVGVAVFGGTTPFIATYLIYATGYKLAPVYW 396
                                   4443454546**************************************6677999999*******************9999 PP

                         MFS_1 158 aivsllafvlfllllpe 174
                                   +i+++++ +++++l+ e
  gi|70607564|ref|YP_256434.1| 397 GIAGMIVTLIAYILYKE 413
                                   99999999999999876 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9  13.8   2.6e-22   7.7e-19       3     197 ..       9     208 ..       7     219 .. 0.88
   2 !   35.1  16.9   2.2e-12   6.6e-09     255     450 ..     233     424 ..     209     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 2.6e-22
                                   HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                      Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                   + a++g   + Yd+ + g+++ +l+++++   ++ +s      +++ ++++  ++G+ iG++++g lgd++GRk++l+ + 
  gi|70607564|ref|YP_256434.1|   9 IAASIGIAFEFYDFLIFGFISGILAKLFFPSTNSLVSL-----LDTLAVFATGFAGRPIGAIIFGHLGDKIGRKYTLILTM 84 
                                   45666668889999999999999995555444444443.....35799********************************* PP

                                   HHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  84 vlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifgl 159
                                   +l+  +++ +++ +g+      +  +l++ R+l G+++G++ +   ++ +E+A +++R + v++ q+a  +G l+a+++ +
  gi|70607564|ref|YP_256434.1|  85 TLMGLSSLFTGLLPGYasigiLAPLLLTTLRILQGVSLGGEFGGGITLSAEFAEPSKRAFYVGIAQMAQGTGPLLATGLIF 165
                                   **************9966666666667777**************************************************9 PP

                                   HHHTSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                      Sugar_tr 160 glnktsn.....adgwrillglqlvpallllilllflPESPry 197
                                    ++ + +     + gwril+ + +++a++ +i++l + ESP +
  gi|70607564|ref|YP_256434.1| 166 LFSSFMStqeynSIGWRILFVIGALIAVIGVIIRLKISESPVF 208
                                   99888777999******************************98 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 2.2e-12
                                   HHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 255 lligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvi 333
                                   +l+g++  ++    +++   + s+++ + +g+ ++   l+ +i ++++++a+f   +l dr+GR++l+++ aag  i+   
  gi|70607564|ref|YP_256434.1| 233 ILLGLGFIVGGTTMTYATGVFASSYLENVIGVPTKevSLILVIGYIIQTIAIFLFGYLADRIGRKPLMITTAAGLVIFVYP 313
                                   55555544444444555555556666666777777555555555566666666666****************999998888 PP

                                   HH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHH.HHHHHHHHHHHHHHCHH CS
                      Sugar_tr 334 lgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnw.lanflisllfpiiteai 413
                                   +   ++ll+++  a s+++++  +++ ++ +++ +      ++E+fp+svR++al++ + v + ++   + ++ +++  a 
  gi|70607564|ref|YP_256434.1| 314 Y---FYLLSTG--AFSNILLAQ-LIYSIVGSASTAAYA-TALTEMFPTSVRYTALSFDYHVGVaVFGGTTPFIATYLIYAT 387
                                   8...6999999..688887765.567777777877777.5669****************9986478999999999999999 PP

                                   HT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                      Sugar_tr 414 gggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                   g     +++++  ++++++ ++ + et g  +e +++
  gi|70607564|ref|YP_256434.1| 388 GYKLAPVYWGIAGMIVTLIAYILYKETLGTMFEGQQK 424
                                   9666677777777889999*************99876 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   2.6    0.0026       7.6     262     321 ..      50     109 ..      17     126 .. 0.75
   2 !   40.2  14.0   5.2e-14   1.5e-10     130     347 ..     140     360 ..     130     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
                         MFS_2 262 svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvll 321
                                    +++++ +++  +g++++  l  ++g+k t +l ++l+ + ++++ ll+ +  +  l+ l
  gi|70607564|ref|YP_256434.1|  50 LAVFATGFAGRPIGAIIFGHLGDKIGRKYTLILTMTLMGLSSLFTGLLPGYASIGILAPL 109
                                   445556677778****************99999999999999999999444444333333 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 5.2e-14
                         MFS_2 130 deRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkek 210
                                   + R    ++ ++++  g +la+ l+fl+  + ++ + +  g++i+ +i+al++++gvii  l   e+  ++k ++t++ +k
  gi|70607564|ref|YP_256434.1| 140 SKRAFYVGIAQMAQGTGPLLATGLIFLFSSFMSTQEYNSIGWRILFVIGALIAVIGVIIR-LKISESPVFKKVRETGKISK 219
                                   56666678899999999***********999999777888*******************9.66677767799999****** PP

                         MFS_2 211 lslleqlkevfrnraflillllfllaalalgvlnglll.Yyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkk 289
                                   ++l e++++  ++   ++l l+f++  ++++   g ++  yl+ v+g   +++s++l++ +i ++++i+l+ +la r+g+k
  gi|70607564|ref|YP_256434.1| 220 IPLAEAFRHHWKK---ILLGLGFIVGGTTMTYATGVFAsSYLENVIGvPTKEVSLILVIGYIIQTIAIFLFGYLADRIGRK 297
                                   ********99999...6666667776666666666554279**************************************99 PP

                         MFS_2 290 .ntyllgalltivllvlvlll...qpsnlllflvll.viagfgvgvaallpwsmladvvDyge 347
                                     ++  +a l+i+ +  ++ll     sn+ll+ +++ ++++ ++++ a++++ m++++v y +
  gi|70607564|ref|YP_256434.1| 298 pLMITTAAGLVIFVYPYFYLLstgAFSNILLAQLIYsIVGSASTAAYATALTEMFPTSVRYTA 360
                                   566666777777777788888887566666666655155566778899999999999998876 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         3     9e+03       6      13 ..      96     103 ..      95     112 .. 0.66
   2 ?   -3.8   0.4       4.4   1.3e+04      20      25 ..     306     311 ..     305     312 .. 0.86
   3 ?   14.6   0.4     8e-06     0.024       3      28 ..     388     412 ..     386     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                    TNFR_16_TM   6 lIPiYcSI 13 
                                   l+P Y SI
  gi|70607564|ref|YP_256434.1|  96 LLPGYASI 103
                                   67888886 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.4
                    TNFR_16_TM  20 gLlaYv 25 
                                   gL+++v
  gi|70607564|ref|YP_256434.1| 306 GLVIFV 311
                                   899998 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8e-06
                    TNFR_16_TM   3 sdnlIPiYcSILaaVvvgLlaYvifK 28 
                                   +++l P+Y  I a ++v+L+aY+ +K
  gi|70607564|ref|YP_256434.1| 388 GYKLAPVYWGI-AGMIVTLIAYILYK 412
                                   78999*****9.66899********9 PP

>> PsbI  Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.5      0.28   8.2e+02      19      26 ..      23      30 ..      15      30 .. 0.81
   2 ?    9.0   0.1   0.00045       1.3       6      31 ..     272     297 ..     271     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.28
                          PsbI 19 FvFGfLsn 26
                                   +FGf+s+
  gi|70607564|ref|YP_256434.1| 23 LIFGFISG 30
                                  59****96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00045
                          PsbI   6 ivVyivViffvslFvFGfLsnDPsRN 31 
                                   i+V   +i  +++F+FG+L+   +R 
  gi|70607564|ref|YP_256434.1| 272 ILVIGYIIQTIAIFLFGYLADRIGRK 297
                                   5677789999*********8766665 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2    0.0059        18     153     193 ..     129     169 ..     113     199 .. 0.80
   2 ?    7.0   5.5   0.00049       1.5       7      88 ..     238     315 ..     233     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0059
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 153 GisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                   Gi+   +++++++ ++y+gi+++++  Gp l+  l  l+ +
  gi|70607564|ref|YP_256434.1| 129 GITLSAEFAEPSKRAFYVGIAQMAQGTGPLLATGLIFLFSS 169
                                   77888899*********************998666554444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00049
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP   7 sllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggr.ghrPrwigigallmalgslllalP 86 
                                   ++++   +m+++  + + + +E   + p++++ li+++  i ++++i + +Y+++r g++P +i ++      g ++++ P
  gi|70607564|ref|YP_256434.1| 238 GFIVGGTTMTYATGVFASSYLENVIGVPTKEVSLILVIGYIIQTIAIFLFGYLADRiGRKPLMITTA-----AGLVIFVYP 313
                                   55555667888888888899************************************88999998543.....344444444 PP

                                   xx RF
                          OATP  87 hf 88 
                                   +f
  gi|70607564|ref|YP_256434.1| 314 YF 315
                                   44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2796.05
//
Query:       gi|70607565|ref|YP_256435.1|  [L=410]
Description: amidohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-53  182.2   0.1    2.1e-53  181.9   0.1    1.1  1  Amidohydro_1  Amidohydrolase family
    1.1e-20   74.6   0.2      1e-12   48.3   0.0    2.1  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.059   12.8   0.0    1.9  2  AP_endonuc_2  Xylose isomerase-like TIM barrel
       0.15   11.5   0.6       0.49    9.8   0.2    2.0  3  Urocanase_C   Urocanase C-terminal domain


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.1   4.7e-57   2.1e-53       1     343 [.      49     399 ..      49     399 .. 0.92

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 4.7e-57
                                   EEEE-EEEEEEECETTECSSS.GHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHT.SSSEEEE CS
                  Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.tledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaee.lplglri 79 
                                   +vlPGlIDaH+Hl++  ++g   l+++++ pe+    + ++++++l +G+ttv+d+g+   +   al++a+ e ++ g+ i
  gi|70607565|ref|YP_256435.1|  49 FVLPGLIDAHIHLSG--IKGGsLLKTMFERPEYRVLRASKWLERLLLAGFTTVRDCGE---YVSLALKRAVQEgIIRGPNI 124
                                   79***********64..45667888999******************************...377777779999******** PP

                                   EEESSEGGS..........................GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                  Amidohydro_1  80 lggkvsldr..........................gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                   ++++ ++++                          g++++ +a r+ l++g  ++ik++a+g+v ++ + +e p++s+ee+
  gi|70607565|ref|YP_256435.1| 125 IAAGRPITQtfghgeinhdiplefshkvgfsefcdGTESCIHAARKVLRDG-SDFIKVFATGGVLSQRDKPENPQLSYEEI 204
                                   ***************************************************.7**************************** PP

                                   HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH....HHHHHHHHHH CS
                  Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt....eaellkerlk 211
                                   k++++ea+k +++va+Ha+++ g++  a++a+++tiehgt+l++       d++kl++ +gv ltpt    e+++  +++k
  gi|70607565|ref|YP_256435.1| 205 KAIVNEAHKVGTYVAAHAHGDAGAK-IAVEAGVKTIEHGTLLKD-------DTLKLMVNRGVSLTPTltiqEVIY--RYGK 275
                                   ******************9999997.99999999**********.......**************9998555555..9*** PP

                                   HHCEE..HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT.....TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHH CS
                  Amidohydro_1 212 eagva..hcpfsnsilrsgrealrkaldeGvkvglgtDga.....asgnslnlleelrlalklqrgllyedeegglslkea 285
                                   ++gv    +++  ++ +   + ++ka + Gv ++ gtD       + ++ ++ + el l++          e+ggl++kea
  gi|70607565|ref|YP_256435.1| 276 QIGVDewGLQKIFEVRERVADVVKKAKEYGVLMISGTDLGfetglGDIDMGKNWYELVLLV----------ERGGLTPKEA 346
                                   *******99*****************************33575554444444455555555..........89******** PP

                                   HHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEE CS
                  Amidohydro_1 286 lrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGkl 343
                                   l  aT+n   alg+  ++G i+ G+d Dlvv+++++l+++  ++k   v++v ++G++
  gi|70607565|ref|YP_256435.1| 347 LITATYNSSLALGI--NAGFIDIGRDGDLVVINGNPLENIYDVTK---VTHVLKAGRV 399
                                   **************..***************************99...9999999975 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   5.3e-09   2.4e-05       1      37 [.      41      80 ..      41      91 .. 0.75
   2 !   48.3   0.0   2.2e-16     1e-12     231     471 ..     176     399 ..     160     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5.3e-09
                  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg..vnl.rllrlpdar 37
                                  e+iDa+ ++vlPG++D+H+Hl g +  + l +++  p++r
  gi|70607565|ref|YP_256435.1| 41 EEIDARDMFVLPGLIDAHIHLSGIKggSLLkTMFERPEYR 80
                                  68******************97755336666666666555 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.2e-16
                  Amidohydro_3 231 igavklfadgvlgsrtalltepyftgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrl 311
                                    + +k+fa g   s+   + +p       +++e+++++v++a+++g  va ha+gda +          a + g++   ++
  gi|70607565|ref|YP_256435.1| 176 SDFIKVFATGGVLSQRDKPENP------QLSYEEIKAIVNEAHKVGTYVAAHAHGDAGAK--------IAVEAGVK---TI 239
                                   4566666666666666666665......559999************************99........23344555...9* PP

                  Amidohydro_3 312 ehaegvtesqiervaalqvaagvqpvfnf..........edelldsrlgperargstpvkellnagvkvalgsDapvgpfd 382
                                   eh++ + +++++ +   +v     +               de+  +++ + r r  + vk  ++ gv ++ g+D     + 
  gi|70607565|ref|YP_256435.1| 240 EHGTLLKDDTLKLMVNRGVSLTPTLTIQEviyrygkqigVDEWGLQKIFEVRERVADVVKKAKEYGVLMISGTD-----LG 315
                                   ******99999999999998777755555778999999988888899999999999******************.....77 PP

                  Amidohydro_3 383 pwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaearvr 463
                                      ++g+ +m+k++ +  +l ++  l+  eal + T ++  alg     G + +G d+Dlvv++ +pl+   +    ++v 
  gi|70607565|ref|YP_256435.1| 316 FETGLGDIDMGKNWYELVLLVERGGLTPKEALITATYNSSLALGINA--GFIDIGRDGDLVVINGNPLENIYD---VTKVT 391
                                   77899*********999******************************..***************887754433...34499 PP

                  Amidohydro_3 464 ltvvdGrv 471
                                   +++++Grv
  gi|70607565|ref|YP_256435.1| 392 HVLKAGRV 399
                                   99999997 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05     0.059      50     137 ..     139     228 ..     124     244 .. 0.81
   2 ?   -1.2   0.0      0.26   1.1e+03     109     125 ..     290     306 ..     278     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                   CCCHSTCTHCHTTCS..HHHHHHHHHHHHHHHHHH...TBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTS CS
                  AP_endonuc_2  50 ftrfgypdederear..reesvdalkraielaaaL...GapllvlhpGtagagpkgseeeawerlaeslneladyaekegv 125
                                    +++  p+e   +++    e+ d ++++i +a+++   G +++ +++   g ++ ++++e+ ++ +e +++++ +a+k+g 
  gi|70607565|ref|YP_256435.1| 139 EINHDIPLE--FSHKvgFSEFCDGTESCIHAARKVlrdGSDFIKVFAT-GGVLSQRDKPENPQLSYEEIKAIVNEAHKVGT 216
                                   444444444..3333477888899999999999999999999988865.589***************************** PP

                                   EEEEE--TTTTS CS
                  AP_endonuc_2 126 klalEtlagsgv 137
                                    +a++ +  +g+
  gi|70607565|ref|YP_256435.1| 217 YVAAHAHGDAGA 228
                                   *******99886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.26
                                   HHHHHHHHHHHHHHHTS CS
                  AP_endonuc_2 109 laeslneladyaekegv 125
                                   ++e++ +++++a+++gv
  gi|70607565|ref|YP_256435.1| 290 VRERVADVVKKAKEYGV 306
                                   45555566666666664 PP

>> Urocanase_C  Urocanase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.99   4.4e+03      70      89 ..     106     125 ..     100     128 .. 0.77
   2 ?   -2.6   0.0      0.72   3.2e+03     158     172 ..     159     173 ..     149     186 .. 0.56
   3 ?    9.8   0.2   0.00011      0.49     122     173 ..     205     256 ..     199     261 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHSSSSS-EEE CS
                   Urocanase_C  70 ialafnelvregeikapvvl 89 
                                   ++la+ ++v+eg i++p ++
  gi|70607565|ref|YP_256435.1| 106 VSLALKRAVQEGIIRGPNII 125
                                   56788888999998888665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.72
                                   -SSHHHHHHHHHHHH CS
                   Urocanase_C 158 dGteeaeerlervlt 172
                                   dGte+  + +++vl+
  gi|70607565|ref|YP_256435.1| 159 DGTESCIHAARKVLR 173
                                   444444444444443 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHT-SEEEEEESTTT-TTS-EEEEEEEEE-SSHHHHHHHHHHHHH CS
                   Urocanase_C 122 lnallnaargatwvslhnGGgvgiGesinagfvvvldGteeaeerlervlta 173
                                   + ++ +a +  t+v+ h  G  g   +++ag++++  Gt  +++ l+ +++ 
  gi|70607565|ref|YP_256435.1| 205 KAIVNEAHKVGTYVAAHAHGDAGAKIAVEAGVKTIEHGTLLKDDTLKLMVNR 256
                                   56777888899*********************************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2401.89
//
Query:       gi|70607566|ref|YP_256436.1|  [L=362]
Description: aspartate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-54  183.6   0.0    7.4e-54  183.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    6.7e-13   48.3   0.0    1.1e-12   47.6   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    3.5e-08   32.4   0.0    3.7e-08   32.3   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.3e-06   27.6   0.1    1.7e-06   27.2   0.1    1.2  1  Alliinase_C      Allinase
    0.00016   21.1   0.0    0.00026   20.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00071   18.9   0.0     0.0014   18.0   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.17   10.6   0.1       0.33    9.6   0.1    1.6  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3   0.0   2.9e-57   7.4e-54      39     360 ..      43     347 ..      39     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 2.9e-57
                                   ST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEE CS
                 Aminotran_1_2  39 eygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvr 119
                                   eyg+++g   l+e +   ++      +  +++v+v++G  +++ + i  l + pgd +lv  p+y ++   l+    ++ +
  gi|70607566|ref|YP_256436.1|  43 EYGHTKGKIRLRELISNMYS------TASSDNVIVTNGGAEANYITILSL-IKPGDHVLVEMPNYMQIPGLLKGLNTKIDY 116
                                   7*******************......677779999999999999888888.88**************************** PP

                                   EEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHT CS
                 Aminotran_1_2 120 yplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgslda 200
                                   + l++e++f++dle++ e++++       tk i++++p+NPtG +++  ++++++++a+ ++ +++ De+Y g + +    
  gi|70607566|ref|YP_256436.1| 117 FWLKDENGFRIDLEEINEKVTK------DTKAIVITNPNNPTGMALSDSDIKAIVEIAEDNKTWIIADEVYRGSEHDGN-- 189
                                   **********************......99**********************************************943.. PP

                                   HHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 201 vatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrq 279
                                       ++v+ +++ + ++s+sK +Gl+G+R+G+++g+ ++v+ + +++    +  s + q++++++l + +    +l+++ +
  gi|70607566|ref|YP_256436.1| 190 -VRPSFVDVYDKAISTNSMSKVYGLPGIRIGWVVGSREIVDKMWSVKDYTSIspSVISQEIALQVLMNRE----KLQARSR 265
                                   .239*******************************************9888789999***********99....799**** PP

                                   HHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHH CS
                 Aminotran_1_2 280 rlqkrrkelrdeLael.glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleel 359
                                    ++++ ++l++eL +  + k++ ++++++ +  ++ ++  ++s++L e++ v+v pg++f++pg lRi + + ++e+l+e+
  gi|70607566|ref|YP_256436.1| 266 DIANKNMRLFEELMRNvDMKWVRPNATVLAFPKTPVKDTYKFSEELFEKYSVLVNPGECFEMPGYLRIGLGSKNAEYLREA 346
                                   ****9999999998889*****************************************************88999999988 PP

                                   H CS
                 Aminotran_1_2 360 v 360
                                   +
  gi|70607566|ref|YP_256436.1| 347 L 347
                                   7 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   4.3e-16   1.1e-12      48     224 ..      53     234 ..      45     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 4.3e-16
                                   HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE CS
                   Aminotran_5  48 arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld 128
                                    re + +++ ++s++++i+t G++ea+ + +lsl   +kpgd+++v   ++       + l   t+++  +++ +++ ++d
  gi|70607566|ref|YP_256436.1|  53 LRELISNMYSTASSDNVIVTNGGAEANYITILSL---IKPGDHVLVEMPNYMQIPGLLKGL--NTKIDYFWLKDENGFRID 128
                                   6999******************************...********9876665544333444..3556666777777789** PP

                                   GGGHHHH--TTEEEEEEESBETTTTE.B..--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEE.....EEETTT CS
                   Aminotran_5 129 ldelekllnektklvaithvsnvtGt.i..qpveeigklakkkgalvlvDaaqavghipidvkklgvDfl.....afsghK 201
                                   l+e++++++++tk++ it  +n tG+ +   ++++i+++a +++ ++++D +     +  +v+   vD++     + s  K
  gi|70607566|ref|YP_256436.1| 129 LEEINEKVTKDTKAIVITNPNNPTGMaLsdSDIKAIVEIAEDNKTWIIADEVYRGSEHDGNVRPSFVDVYdkaisTNSMSK 209
                                   *************************9633368************************************986633345668* PP

                                   TTSSTT-..EEEEEEHHHHHTS..S CS
                   Aminotran_5 202 llgPtGi..Gvlyvrkelleklepl 224
                                   ++g +Gi  G +++++e+  k+  +
  gi|70607566|ref|YP_256436.1| 210 VYGLPGIriGWVVGSREIVDKMWSV 234
                                   ******5449999999999999444 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.4e-11   3.7e-08      59     176 ..      55     181 ..      41     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.4e-11
                                   HHHHHHHT-...SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHH CS
               Cys_Met_Meta_PP  59 eriaaLegg...eaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleeleka 133
                                   e i++++++   +++++++ G  A   +il+l+k Gd+++v+   Y     llk + +k+       +     dlee++++
  gi|70607566|ref|YP_256436.1|  55 ELISNMYSTassDNVIVTNGGAEANYITILSLIKPGDHVLVEMPNYMQIPGLLKGLNTKIDYFWLKDENgfrIDLEEINEK 135
                                   5555555443337899************************************99999997655444443344799****** PP

                                   CCTTEEEEEEESS-TTT...T----HHHHHHHHHHTT-EEEEEGTT CS
               Cys_Met_Meta_PP 134 ikentklvylEtptnpl...lkvvDiekiaklakkagvlvvvDntf 176
                                   +++ tk++ +  p np+   l+  Di++i+++a ++++ ++ D ++
  gi|70607566|ref|YP_256436.1| 136 VTKDTKAIVITNPNNPTgmaLSDSDIKAIVEIAEDNKTWIIADEVY 181
                                   ****************853356689*****************9876 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   6.5e-10   1.7e-06     138     274 ..     140     292 ..      68     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.5e-10
                                   -EEEEEESS-TTT--.--....----...-TT-EEEEEE-TT-STTTS---S-B.....--SEEEEEHHHHHS-GGG-EEE CS
                   Alliinase_C 138 efielvtsPnnPdgl.lr....eavv...kgseakviyDlayYWPhytpitska.....dedimLftlskltGhaGsrlGW 205
                                       ++t PnnP g+ l     +a+v   +++++ +i D +y   ++    +++     d+ i+  ++sk+ G  G+r+GW
  gi|70607566|ref|YP_256436.1| 140 TKAIVITNPNNPTGMaLSdsdiKAIVeiaEDNKTWIIADEVYRGSEHDGNVRPSfvdvyDKAISTNSMSKVYGLPGIRIGW 220
                                   3344789*****88633322223455566888999*******9887754444332222288899***************** PP

                                   EEES-HHHHHHHHHHHHHHHSS--HHHHHHHHHHH...HHHHHHTT--STTT.SHHHHHHHHHHHHHHHHHHH CS
                   Alliinase_C 206 alvkdkevakklveyieknsiGvskesqlrvlkil...kvvlaeiktekgte.dlfefgyeklkerWeklkev 274
                                    +v  +e+ +k+ +    +si  s  sq  +l++l   ++++a+ +   +++ +lfe  ++++  +W + ++ 
  gi|70607566|ref|YP_256436.1| 221 -VVGSREIVDKMWSVKDYTSISPSVISQEIALQVLmnrEKLQARSRDIANKNmRLFEELMRNVDMKWVRPNAT 292
                                   .68999*****98766666666555555555554411156666655544444488988889999999876655 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     1e-07   0.00026      37     144 ..      65     178 ..      46     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1e-07
                                   T-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EE.EEE-B-TTTSSB-GGGCGGG--TTEEEEE CS
               DegT_DnrJ_EryC1  37 gvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakp.vfvDvdpdtynidpaaieaaitertkaIl 116
                                    ++++i ++ G +A+ +++  l ++pgd V+v   +++        l+ k   f   d++ + id ++i++++t+ tkaI+
  gi|70607566|ref|YP_256436.1|  65 SSDNVIVTNGGAEANYITILSL-IKPGDHVLVEMPNYMQIPGLLKGLNTKIdYFWLKDENGFRIDLEEINEKVTKDTKAIV 144
                                   5778999999999999999876.8999*****999**999999999999873566678999******************** PP

                                   EB-...GGGB--...-HHHHHHHHHHCT-EEEEE CS
               DegT_DnrJ_EryC1 117 pVh...lyGqva...dmdalkaiaakhglkvieD 144
                                   + +     G +    d++a+ +ia++ + ++i D
  gi|70607566|ref|YP_256436.1| 145 ITNpnnPTGMALsdsDIKAIVEIAEDNKTWIIAD 178
                                   8873333344323349****************99 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.3e-07    0.0014      35     166 ..      54     177 ..      41     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.3e-07
                                   HHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSST.THHHHCC--EEEEE-EBTTTBE-HHHH CS
               Beta_elim_lyase  35 nrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdet.gaiaelagvklrdlknkeaGkmdlekl 114
                                   ++L  ++   +  + ++ +  G  An i +  l+++g+ v+v+ p+ +      ++++    +    lk ++   +dle++
  gi|70607566|ref|YP_256436.1|  54 RELISNMYSTASSDNVIVTNGGAEANYITILSLIKPGDHVLVEMPNYMQIPGLlKGLN--TKIDYFWLKDENGFRIDLEEI 132
                                   3334444445556778888899***********************9888776554443..556667788888679****** PP

                                   HHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEE CS
               Beta_elim_lyase 115 eaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhl 166
                                   ++++++      ++k+i++t+ nn   G ++s   ++++ +ia++++  ++ 
  gi|70607566|ref|YP_256436.1| 133 NEKVTK------DTKAIVITNPNNP-TGMALSDSDIKAIVEIAEDNKTWIIA 177
                                   ****99......489*********5.9****************998876655 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00013      0.33      72     114 ..      54      98 ..      34     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                                   HHHHHHHCT-SEE..EEESSHHHHHHHHHHHHH--TTEEEEEESS CS
                      OKR_DC_1  72 qkyaarvfgadks..yfvvnGTsssnkvvlnavltpgdlvlvdRN 114
                                    +++++++ ++ s   +v+nG + +n + + ++++pgd vlv+  
  gi|70607566|ref|YP_256436.1|  54 RELISNMYSTASSdnVIVTNGGAEANYITILSLIKPGDHVLVEMP 98 
                                   5778888876655337899**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2539.25
//
Query:       gi|70607567|ref|YP_256437.1|  [L=685]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.2e-118  394.6   0.0    1.5e-90  304.2   0.0    2.1  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
      2e-15   57.1   0.2    8.3e-15   55.1   0.0    2.0  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.2   0.0   1.7e-94   1.5e-90       1     401 [.     132     518 ..     132     537 .. 0.90
   2 !   88.1   0.5     5e-29   4.5e-25     466     550 .]     544     628 ..     532     628 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.2 bits;  conditional E-value: 1.7e-94
                                   STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevl 79 
                                   +h+++++n+     ++ G+  +  ++ad+vv+++++ +r+  +++E+++ ++++  +++ l+vy+stqap+ vr+ + e+l
  gi|70607567|ref|YP_256437.1| 132 IHDDLKNNISIdqVLQGGNL-SLKSSADVVVSRKIKQHRIVSNPMEPKGFICWW--DNDVLNVYVSTQAPFGVRNDLREAL 209
                                   57877777766633444555.77889**99************************..69*********************** PP

                                   T--GGGEEEE-.SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-E.EEEEEEEEEEEE-TTS-EEEEE CS
                 Ald_Xan_dh_C2  80 glpenkvrviv.prvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgk.rhpfkikykvgadkdGkitald 158
                                   g+p++k++v + p+vGGGFG+K+  +p++vla +a++k+grpVk++++R+e +++t++ ++   +++k+ a+++G+i++++
  gi|70607567|ref|YP_256437.1| 210 GIPPEKIKVYSpPNVGGGFGNKSGGYPEYVLASIASLKLGRPVKWIETRSEILVNTQSlGRGEVSDMKLYATNKGEILGIE 290
                                   *********9989****************************************997654899999**************** PP

                                   EEEEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHH CS
                 Ald_Xan_dh_C2 159 vdlladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldple 238
                                    +++a+ Gay    + +++  ++s ++gpYk++  ++++  v+tNtpp + +RG+G+p+a+++ E+l+++lAeelg+dp+e
  gi|70607567|ref|YP_256437.1| 291 GTVIANIGAYnHGINFFTPLFVASLSNGPYKLKFTSIRAISVFTNTPPMGFYRGAGRPEAALIHETLVEDLAEELGIDPIE 371
                                   **********44666667777888888****************************************************** PP

                                   HHHHHBCE.CGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEE CS
                 Ald_Xan_dh_C2 239 lRrrNlik.pgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqega 318
                                   lRr+Nl+  +g +tp g +  d  +++++l +++  +    r+a+  e  +    +G++l++++e + +++       ega
  gi|70607567|ref|YP_256437.1| 372 LRRKNLVDnTGYITPLGAK-LDPAGYQDVLSRAEVYY----RKAK--EVHK---DKGVSLVIFTEIVRTSP------GEGA 436
                                   *******6378889****9.7**********987754....3222..2222...37***********6665......579* PP

                                   EEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 319 lvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrer 399
                                   +v+v+ dG+v+ ++g+ ++Gq   t++ ++a+e+Lg++ e++++++g+td+v++g+g+++Sr+ +++g+Av  A ++l ++
  gi|70607567|ref|YP_256437.1| 437 RVEVK-DGKVHFYLGLGPHGQAYSTTFKKLASETLGISEENIEIITGNTDTVKEGIGSFGSRAGTIGGSAVIAAGKELLKK 516
                                   ****7.**************************************************************************9 PP

                                   HH CS
                 Ald_Xan_dh_C2 400 ll 401
                                   l 
  gi|70607567|ref|YP_256437.1| 517 LN 518
                                   96 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 5e-29
                                   BEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----G CS
                 Ald_Xan_dh_C2 466 yfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPta 546
                                    fa ga+va+V+vD etg  kv ++++v+DvG+++N++ +egQi GG+ qG+ ++lmE ++yde+G +l +s ad+ +Pta
  gi|70607567|ref|YP_256437.1| 544 IFAPGAHVAVVDVDKETGFAKVIDYYAVDDVGRVLNKEEIEGQIVGGMLQGVSQVLMEAMRYDERGIPLCSSIADCGVPTA 624
                                   6899***************************************************************************** PP

                                   GGS- CS
                 Ald_Xan_dh_C2 547 adiP 550
                                   ++ P
  gi|70607567|ref|YP_256437.1| 625 MESP 628
                                   *987 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   9.2e-19   8.3e-15       1     109 [.      10     117 ..      10     118 .. 0.87
   2 ?   -1.4   0.0      0.33   2.9e+03      26      54 ..     547     575 ..     534     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 9.2e-19
                                   TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT....TSSS-EEEESS-SSEE CS
                  Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig....siledeedallaedkv 77 
                                   tG+ +Y+dDi+ ++ +yl +vrS++a++ i+s+      +   V+  +t++d+++  +a +    + ++  +  +la+ kv
  gi|70607567|ref|YP_256437.1|  10 TGKSTYIDDISPKNVVYLHVVRSSIARGVIKSVS-----KPSNVLLALTWDDIKSFMSARLfpglAGAQVARMPVLANGKV 85 
                                   89*********99999****************97.....55668889999999998888777654333333467******* PP

                                   SSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  78 rsvgqavaavvAedeetArkAaklvkveYeel 109
                                   ++vgq+v a v +d++ A++ a+ v+++Yee 
  gi|70607567|ref|YP_256437.1|  86 NFVGQPVLAFVVDDRYKAEDVAEEVSIDYEEM 117
                                   ******************************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.33
                                   SSEEEEEEE-HHHHCSTTEEEEEEHHHHC CS
                  Ald_Xan_dh_C  26 ahAkivsidvsaalalpGVvavitakdlp 54 
                                   + A++  +dv++     +V++++  +d+ 
  gi|70607567|ref|YP_256437.1| 547 PGAHVAVVDVDKETGFAKVIDYYAVDDVG 575
                                   45777777888888888888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 4149.31
//
Query:       gi|70607568|ref|YP_256438.1|  [L=552]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-38  131.3  12.8    4.1e-38  131.3  12.8    2.0  2  CitMHS         Citrate transporter
    1.1e-13   51.1  33.4    4.1e-10   39.3  11.4    2.5  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    3.5e-11   42.8   0.7    3.2e-07   30.1   0.0    2.7  2  TrkA_C         TrkA-C domain


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3  12.8   6.9e-42   4.1e-38       3     283 ..      19     491 ..      17     502 .. 0.80
   2 ?    2.2   2.7     0.014        86     111     168 ..     489     550 ..     487     551 .. 0.86

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 6.9e-42
                                   xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS   3 llileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllv 79 
                                   lli +++r d+v ++ lv+l     ++ ++al  +a+p++++l+ +mii++ le++G+ ++ ++ + ++ ++k  +++ l 
  gi|70607568|ref|YP_256438.1|  19 LLISKRIRFDIVGIVSLVVLiligGISVNQALINLANPAVVVLGSLMIISKTLEKSGFLESFGELISSRLKNKYVIFATLL 99 
                                   678888999999998888888878888888******************************************988****** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                        CitMHS  80 lltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll....... 153
                                   ++tal s+f+s ++ ++++ip+++ + kr +++p  +lipl++ a +gg  t+iGt             pnl+l       
  gi|70607568|ref|YP_256438.1| 100 AITALSSGFMSDVALTAVLIPVFFYVSKRFNDSPSKYLIPLSFTAILGGRYTIIGTT------------PNLILdqlwfek 168
                                   *****************************7777777*********************............************ PP

                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx RF
                        CitMHS 154 ..............lalllvgllplvllfmfgvalalpvnap....................kvkkqkaiieaiarsllpv 200
                                                 l +++vgll++++++       lp n                      +                  
  gi|70607568|ref|YP_256438.1| 169 egkflslfqfapigLSVVAVGLLAMIVIV-----RVLPSNLTragnvedfkisnylveakveD-----------------G 227
                                   ***********999999999999999999.....33444433444445555555555544440.................1 PP

                                   ................................................................................. RF
                        CitMHS 201 ................................................................................. 200
                                                                                                                    
  gi|70607568|ref|YP_256438.1| 228 eligksvkyleklgvkildiyprrisfgprtilkgdllllqvspdklsvltsiqglklapsseevkgedlyellipsgsea 308
                                   555555555555666666667777777777777777777777777777788888888888888888888888888888888 PP

                                   ................................................................................. RF
                        CitMHS 201 ................................................................................. 200
                                                                                                                    
  gi|70607568|ref|YP_256438.1| 309 vgktladleldfvygvrvlgisgkfirgklsritltpgvillvqgkeesitkmmnnlglvplykrtvkifnvkrgvlalss 389
                                   888888888888888888888888888888888888887777777777778777777777888888888888877777777 PP

                                   ........xxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 201 ........atillla.......................ykkveWsvlllfaGvfllvgaleqtGilealadllgaggplva 250
                                                 +                       y+++eW +l++++  + +++al  tG+l+++  ++  g+p+v 
  gi|70607568|ref|YP_256438.1| 390 lglsialsL-----LginiaeafliglipvavmeyreiYRNIEWTILVFVGTYISMGDALASTGLLTHIP-FI--GNPIV- 461
                                   666555550.....1555555555566688899************************************6.66..34655. PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 251 lalvlgliallsafisnvavaalmapialgmap 283
                                      +++++all +f+sn+a+a+++ p+al+m  
  gi|70607568|ref|YP_256438.1| 462 ---LFFITALLANFVSNTAAAVILGPVALTMNN 491
                                   ...499************************876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.014
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxx RF
                        CitMHS 111 klppl.lliplalaaniggaltpiGtpttraaarpglslpnlll................lalllvgllplvllf 168
                                   +++pl +l+++a++++    +tp+                nll+                + l++vgl++l++l+
  gi|70607568|ref|YP_256438.1| 489 MNNPLlALTIVAMGSSCTF-ITPFSHQ------------ANLLVseaggyrvrdflmagsIMLIVVGLVTLLFLG 550
                                   4455548888999999998.*******............999999999999999999999999999999999987 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3  11.4   6.8e-14   4.1e-10     291     461 ..      25     196 ..       3     203 .. 0.79
   2 !   17.0  14.0   3.9e-07    0.0024     253     461 ..     356     548 ..     337     551 .. 0.68

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.8e-14
                 Na_sulph_symp 291 idattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslf 371
                                   i   +v+iv lv+l+l+  ++ +     + a   +++lg+l+ ++k le+sg++e +g+ +++ l+    + +i++ l+++
  gi|70607568|ref|YP_256438.1|  25 IRFDIVGIVSLVVLILIGGISVN-QALINLANPAVVVLGSLMIISKTLEKSGFLESFGELISSRLK---NKYVIFATLLAI 101
                                   45568999999999999988877.344556677899**************************9999...778888888888 PP

                 Na_sulph_symp 372 vlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfllpyatgpnpiv....fga..gylkvkdywrl 446
                                    ++   f S +A+ta+l+p++  v++      p    ++l ++  l+g  + ++t pn i+    f    ++l+  +++ +
  gi|70607568|ref|YP_256438.1| 102 TALSSGFMSDVALTAVLIPVFFYVSKRFNDS-PSKYLIPLSFTAILGGRYTIIGTTPNLILdqlwFEKegKFLSLFQFAPI 181
                                   99999***********************666.777789********************99633224332135677777888 PP

                 Na_sulph_symp 447 Gfilsiigllillll 461
                                   G+ +  +gll ++++
  gi|70607568|ref|YP_256438.1| 182 GLSVVAVGLLAMIVI 196
                                   876666666555554 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.9e-07
                 Na_sulph_symp 253 avaktelkelG..pltarekallilfvlllllWifgeslnidattvaivvlvillllr.............vldWkDivkq 318
                                   + +++ +++lG  pl +r  ++  +  ++l l   g s+ ++   +           +             v+++ +i + 
  gi|70607568|ref|YP_256438.1| 356 ESITKMMNNLGlvPLYKRTVKIFNVKRGVLALSSLGLSIALSLLGI-----------NiaeafliglipvaVMEYREIYR- 424
                                   5555555555544555555555555555555555554444333322...........0222222223335599**97766. PP

                 Na_sulph_symp 319 ktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqai 399
                                   +  W +l++ g+ i++   l  +gl         t+       +   i+l+ + ++   f S+tA  ++l p+ l++ + +
  gi|70607568|ref|YP_256438.1| 425 NIEWTILVFVGTYISMGDALASTGL--------LTHIP----FIGNPIVLFFITALLANFVSNTAAAVILGPVALTMNNPL 493
                                   589*********************4........44444....444455566666777899************999887766 PP

                 Na_sulph_symp 400 pgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillll 461
                                          +al+++   s  +f++p++  +n +v  ag   v+d+  +G i+ i+  l+ ll+
  gi|70607568|ref|YP_256438.1| 494 -------LALTIVAMGSSCTFITPFSHQANLLVSEAGGYRVRDFLMAGSIMLIVVGLVTLLF 548
                                   .......5566666666666*****************************9999887777765 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   6.5e-05      0.39       2      69 ..     220     281 ..     219     282 .. 0.81
   2 !   30.1   0.0   5.3e-11   3.2e-07       1      69 [.     297     365 ..     297     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.5e-05
                                   EEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   ve +v  +  l+Gk++k   l++ gv ++ i  + + i+ ++ t+L +GD+ll+ +sp+ l+ l++++
  gi|70607568|ref|YP_256438.1| 220 VEAKVE-DGELIGKSVKY--LEKLGVKILDIY-P-RRISFGPRTIL-KGDLLLLQVSPDKLSVLTSIQ 281
                                   677886.556********..**99*******7.3.44666666655.7************99999887 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 5.3e-11
                                   CEEEEEE--GGGTTSBHHHHTHHHH.S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C   1 lvevtvpagsplvGktlkelnlrar.gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   l+e+ +p+gs  vGktl++l l    gv+v++i  + ++    +  +L++G +llv g+ +++ ++ + l
  gi|70607568|ref|YP_256438.1| 297 LYELLIPSGSEAVGKTLADLELDFVyGVRVLGISGK-FIRGKLSRITLTPGVILLVQGKEESITKMMNNL 365
                                   6899******************999********855.8888899******************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3402.57
//
Query:       gi|70607569|ref|YP_256439.1|  [L=185]
Description: hypothetical protein Saci_1840 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.02   14.8   8.3      0.029   14.3   8.3    1.4  1  DsbD_2        Cytochrome C biogenesis protein transmembrane r


Domain annotation for each model (and alignments):
>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   8.3   1.6e-06     0.029      77     195 ..      52     171 ..      12     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-06
                        DsbD_2  77 lgllllllglklllkkkllklerlgkllsrllkklakkl.kslasalllGllnGllp.CglvysalllalasgsaleGalv 155
                                   ++ l ll+++ +l  + l +  ++g l+s ll + + k  + + ++  +Gll G l   +  + +l+lalas+s+++ +l+
  gi|70607569|ref|YP_256439.1|  52 AIPLSLLSLVTILEFPLLITSYSIGLLVSGLLLYGTVKGkELEIEPKRFGLLQGALViSPSKLIVLILALASESIFYAVLI 132
                                   333334444444433334444555566666554444433244456777899998776378899****************** PP

                        DsbD_2 156 mlaFgLGTlpalllfglllgllskklrkkllrlagvllil 195
                                   +l+F +  ++++++f+ll +l+ k++ k ++ ++++  i+
  gi|70607569|ref|YP_256439.1| 133 LLVFIVTSIISFMIFSLL-NLIPKRFDKIVNIVISLGSII 171
                                   ***************976.555566665555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1253.79
//
Query:       gi|70607570|ref|YP_256440.1|  [L=515]
Description: hypothetical protein Saci_1841 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-32  110.9  47.0      8e-32  110.5  47.0    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
    4.7e-14   52.6   3.1    1.3e-07   31.9   0.6    2.7  2  CBS             CBS domain
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.023   14.7   0.0    1.6  1  Tfb5            Transcription factor TFIIH complex subunit Tf
       0.18   12.0   1.2         12    6.1   0.1    2.3  2  HGTP_anticodon  Anticodon binding domain
       0.68   10.1  35.0       0.56   10.4   3.4    4.3  4  DUF5518         Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5  47.0   2.2e-35     8e-32       5     379 ..      13     364 ..      10     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 2.2e-35
                                   HHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHH CS
                Na_H_Exchanger   5 illallvgl...larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksilll 82 
                                   i+ ++l+++   +++rl+l + vg i++G++lG  + +li+ + ++++++s lg+++llFlaG e    e  k   + l  
  gi|70607570|ref|YP_256440.1|  13 IM-LILSKIaeqVFSRLGLIPFVGSIFVGIVLGEGVTNLIQVN-TIISFISSLGIVFLLFLAGAEEINTEY-KISNKLLFT 90 
                                   44.4444445868*****************************9.*******************98555554.445689999 PP

                                   HHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHH CS
                Na_H_Exchanger  83 allgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavll 163
                                    +++++++++li l+l+  +   +++ + l++ + l +t+++ ++++l ++g+ ++++g  l+  + l ++++v+l++++ 
  gi|70607570|ref|YP_256440.1|  91 TIIQIILPFILIFLILHE-V---LDIPDYLALIVPLIMTSAGPLTRLLIDLGISRNEVGANLFYQATLVEIISVILFSIFS 167
                                   99*********9899997.3...5*******************************************************99 PP

                                   HHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHH CS
                Na_H_Exchanger 164 alakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgafla 244
                                   ++          lll+ l+++++++++l+lg +i  +l++i+ ++ + re+e++ ++ l+l++ +lae + + ++++a+++
  gi|70607570|ref|YP_256440.1| 168 QFN-------KNLLLITLEIVLIFLLILILGPFITKVLEKIEGYI-KVREVEFASIISLVLIIGFLAEFFNFNSAIAALFL 240
                                   996.......7899******************************8.*********************************** PP

                                   HHHHH.HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHH CS
                Na_H_Exchanger 245 Glvls.eyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslre 324
                                   G +l    + + +l ekl+ f +g+f+plfFv++Gl +    +  +l+ l + +++++++l+++++a+f+  +   +++++
  gi|70607570|ref|YP_256440.1| 241 GFLLRgYFKDRPDLLEKLHGFTYGFFEPLFFVSIGLFFV--KI--NLQILVIGFILFLSVLISKFIAGFISGK---ITRND 314
                                   *****88888889***********************999..44..38888888888888899********996...99*** PP

                                   HHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
                Na_H_Exchanger 325 aliigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                                    ++ g+g +++g v + l++++ ++g+++   y+ +++++ +  l       pll
  gi|70607570|ref|YP_256440.1| 315 PITNGLGTSTKGGVDVSLLISALTAGIITPIEYSYTTLAISLASL-----AIPLL 364
                                   *****************************9998888888877777.....44444 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.6   3.7e-11   1.3e-07       9      54 ..     394     439 ..     385     442 .. 0.89
   2 !   20.4   0.1   1.5e-07   0.00053      11      56 ..     459     504 ..     449     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.7e-11
                                   CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                    v+v+ d tl+ea+ ++ ekgv++l VVde+ +++G++t + ll+ 
  gi|70607570|ref|YP_256440.1| 394 TVFVSCDNTLREAILKINEKGVRALVVVDEEMRVIGLITVKTLLEI 439
                                   479999***********9999****889**************9985 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.5e-07
                                   EEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  11 tvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    +++d  +++al+++re++   + V+d+  +l G + +r llr+l+
  gi|70607570|ref|YP_256440.1| 459 IIDEDYKVSDALRKFRESETPVIAVIDKRRRLKGTLYERELLRFLM 504
                                   6899***********99777677777******************98 PP

>> Tfb5  Transcription factor TFIIH complex subunit Tfb5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.4e-06     0.023       2      27 ..     389     414 ..     388     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.4e-06
                          Tfb5   2 vkaikGvLveCDpaikqlilkldeqe 27 
                                   v+++  v+v+CD + ++ ilk++e+ 
  gi|70607570|ref|YP_256440.1| 389 VNVTSTVFVSCDNTLREAILKINEKG 414
                                   899999******************85 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.014        52      38      72 ..     400     434 ..     390     449 .. 0.81
   2 ?    6.1   0.1    0.0034        12      32      69 ..     457     494 ..     446     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                                   SSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEE CS
                HGTP_anticodon  38 nesigkkireadllgipfavvvGekelekgtvtvr 72 
                                   +++++++i + +++g++  vvv+e+    g +tv+
  gi|70607570|ref|YP_256440.1| 400 DNTLREAILKINEKGVRALVVVDEEMRVIGLITVK 434
                                   678999999**************986434776666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                                   EEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEE CS
                HGTP_anticodon  32 velddsnesigkkireadllgipfavvvGekelekgtv 69 
                                   +e+ d+++++  ++r+ ++  +p++ v++++   kgt+
  gi|70607570|ref|YP_256440.1| 457 AEIIDEDYKVSDALRKFRESETPVIAVIDKRRRLKGTL 494
                                   6788999***********************98777775 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.5    0.0019       6.9      28     101 ..      29     105 ..       8     111 .. 0.72
   2 ?    1.3   2.5       0.1   3.6e+02      66     104 ..     157     195 ..     149     205 .. 0.48
   3 ?   10.4   3.4   0.00016      0.56      10      90 ..     218     295 ..     208     299 .. 0.70
   4 ?    5.9   6.8    0.0037        13      12      95 ..     286     361 ..     274     370 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0019
                       DUF5518  28 llgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlll...glvaaigglagfvallvalllvvllllv 101
                                    l ++vg++ +G + g+++ +   + +++ +i ++ ++ ll+++++    +  +i + ++f++++ ++l ++l++l+
  gi|70607570|ref|YP_256440.1|  29 GLIPFVGSIFVGIVLGEGVTNLIQVNTIISFISSLGIVFLLFLAGAeeiNTEYKISNKLLFTTIIQIILPFILIFLI 105
                                   3567*******************************999999999987764445556666666666666666455544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                       DUF5518  66 vlllvlllglvaaig.glagfvallvalllvvllllvvll 104
                                   +++++l++ +++ +  +l+++++ +v+++l++l+l  +++
  gi|70607570|ref|YP_256440.1| 157 IISVILFS-IFSQFNkNLLLITLEIVLIFLLILILGPFIT 195
                                   33344442.4444440444455555555555444444444 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00016
                       DUF5518  10 vaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaaigglagfvallv 90 
                                   + +++++l+  +  +++ +++l++g l+ Gy+  +      ++G+  G++  + ++ + l+++   +++   ++gf+++l 
  gi|70607570|ref|YP_256440.1| 218 LVLIIGFLAE-FFNFNSAIAALFLGFLLRGYFKDRPDLLEKLHGFTYGFFEPLFFVSIGLFFVK--INLQILVIGFILFLS 295
                                   3344455555.999*************************************9998666666662..233333333333322 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0037
                       DUF5518  12 ivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipv.lvlllvlllglvaaigglagfvallva 91 
                                   +v++++l+      + l++ +++G+++G ++++   d   +G+ +   g++ v l+++++++ g+++ i  + +++a+++a
  gi|70607570|ref|YP_256440.1| 286 LVIGFILF-----LSVLISKFIAGFISGKITRN---DPITNGLGTSTKGGVDVsLLISALTA-GIITPIEYSYTTLAISLA 357
                                   34444444.....66677778888888866654...78999*********999544444444.566666665555555555 PP

                       DUF5518  92 lllv 95 
                                   +l++
  gi|70607570|ref|YP_256440.1| 358 SLAI 361
                                   5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3552.73
//
Query:       gi|70607571|ref|YP_256441.1|  [L=269]
Description: hypothetical protein Saci_1842 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-30  104.9   5.3    1.5e-30  104.9   5.3    2.2  3  PDDEXK_10        PD-(D/E)XK nuclease superfamily
    9.4e-22   77.0   8.5    1.7e-19   69.8   8.1    3.0  1  DUF3782          Protein of unknown function (DUF3782)
  ------ inclusion threshold ------
      0.053   13.0   3.9      0.073   12.5   3.9    1.2  1  MIF4G_like_2     MIF4G like
      0.089   12.9   3.6       0.33   11.1   0.1    3.0  3  DUF4143          Domain of unknown function (DUF4143)
       0.14   12.3   3.3       0.57   10.3   3.3    1.9  1  SEEK1            Psoriasis susceptibility 1 candidate 1
       0.37   10.9   6.2        1.6    8.9   4.2    2.1  2  DUF1779          TATA-box binding
        1.3    9.2   6.3         22    5.2   5.8    2.6  2  Ribonucleas_3_3  Ribonuclease-III-like
        2.9    9.4  14.9    5.6e+02    2.4   0.2    7.1  7  Toxin_36         Conantokin-G mollusc-toxin
        5.3    7.1   6.2        7.9    6.5   1.2    2.6  3  SelB-wing_1      Elongation factor SelB, winged helix


Domain annotation for each model (and alignments):
>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.7   3.5e+03      27      32 ..      93      98 ..      74     116 .. 0.57
   2 ?   -1.7   0.1       1.4   2.8e+03      30      34 ..     114     118 ..      93     139 .. 0.58
   3 !  104.9   5.3   7.5e-34   1.5e-30       1      74 []     188     261 ..     188     261 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                     PDDEXK_10 27 Dlavik 32
                                  Dl+++ 
  gi|70607571|ref|YP_256441.1| 93 DLQKMA 98
                                  333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                     PDDEXK_10  30 vikrk 34 
                                   ++  k
  gi|70607571|ref|YP_256441.1| 114 KMATK 118
                                   33333 PP

  == domain 3  score: 104.9 bits;  conditional E-value: 7.5e-34
                     PDDEXK_10   1 sevelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                   s+ve+Dvv+k+gkvi++Ei+s ++rgD+ vi +kke+Yekakgvkvd++iv+t++i+dr+p+rvka Ae+lgi+
  gi|70607571|ref|YP_256441.1| 188 SDVEIDVVLKNGKVIMIEISSGIRRGDVGVILKKKEFYEKAKGVKVDEVIVITSIIEDRDPDRVKARAESLGIK 261
                                   79**********************************************************************97 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   8.1   8.3e-23   1.7e-19       1      78 []     110     187 ..      58     187 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 8.3e-23
                       DUF3782   1 eelekleee....eeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgvkVekwlyyDkeGeVygy 77 
                                   e+l+k++++    +++tkedl++lek   +l ++i+ +GaRWG+ +E++fR+g+ e+L+++ g++ +++l+yD++G+Vyg+
  gi|70607571|ref|YP_256441.1| 110 EDLQKMATKedlqKMATKEDLQKLEK---RLITMINGIGARWGVKNEDSFRQGVVELLSDV-GFTANRELLYDNTGYVYGD 186
                                   56778877788888999999998888...********************************.******************9 PP

                       DUF3782  78 P 78 
                                   P
  gi|70607571|ref|YP_256441.1| 187 P 187
                                   8 PP

>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.9   3.7e-05     0.073     154     237 ..      59     154 ..      32     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                  MIF4G_like_2 154 krtlskvnkrvkkvrqeleelkkkeeee....kakeeed............keeeeeleraeekleaaqkeqkelflivfe 218
                                   + tl+k     ++ +++l+++ +ke+ +    k    ed             +++e+l+++  k + ++ + ke ++ +++
  gi|70607571|ref|YP_256441.1|  59 FDTLRKELEGKMATKEDLQKMATKEDLQkmatK----EDlqkmatkedlqkMATKEDLQKMATKEDLQKMATKEDLQKLEK 135
                                   556666665555566666555555444433221....113344455568888899************************** PP

                  MIF4G_like_2 219 rlveilsesleeletsgse 237
                                   rl+++++++  + ++++++
  gi|70607571|ref|YP_256441.1| 136 RLITMINGIGARWGVKNED 154
                                   *******997666666555 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.1   6.2e+03      19      31 ..      31      41 ..       5      54 .. 0.57
   2 ?    1.4   0.6      0.17   3.3e+02       2      19 ..     119     140 ..      73     176 .. 0.60
   3 ?   11.1   0.1   0.00016      0.33      93     121 ..     182     208 ..     171     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                                  xxxxxxxxxxxxx RF
                       DUF4143 19 glverlppwsesp 31
                                   +++rl pw   +
  gi|70607571|ref|YP_256441.1| 31 QVLSRLTPW--QN 41
                                  456677777..33 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                                   xxxxxxxxxxxxxxxxx....x RF
                       DUF4143   2 rDirklagvrdpeelrk....g 19 
                                   +D++k+a ++d+++l+k    +
  gi|70607571|ref|YP_256441.1| 119 EDLQKMATKEDLQKLEKrlitM 140
                                   3444444444444444444440 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00016
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  93 yyyrdkngaEvDfvielkggkivpiEvKs 121
                                   y y d +  E+D+v++  +gk++ iE+ s
  gi|70607571|ref|YP_256441.1| 182 YVYGDPSDVEIDVVLK--NGKVIMIEISS 208
                                   77888899*******6..78*******87 PP

>> SEEK1  Psoriasis susceptibility 1 candidate 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3   0.00029      0.57      41      84 ..      77     121 ..      36     135 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                         SEEK1  41 ddlatlepanhfwhagdlqamiske.fhlaatqddcrkvktqedi 84 
                                   +++at e  +++    dlq m +ke ++  at++d +k  t+ed+
  gi|70607571|ref|YP_256441.1|  77 QKMATKEDLQKMATKEDLQKMATKEdLQKMATKEDLQKMATKEDL 121
                                   344444444444444455555444423444555555555555544 PP

>> DUF1779  TATA-box binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.4     0.011        21       3      68 ..      38     102 ..      36     110 .. 0.87
   2 ?    8.9   4.2   0.00078       1.6       9     110 ..      73     172 ..      69     198 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                                   EEEEEEEEEE---H..HHHHHHHHHHHHHEEEEE--SS.EEEEEEEEEETTTTEEEEEEEEEE..S CS
                       DUF1779   3 eWsvlakenlsvvelkklaeqlakelkaeektekkesedeekitgikvegkndsdekvsivatkte 68 
                                    W++la+++ + + l+k+++ ++++l++e + +  ++ed +k+++++  +k +++e ++++atk++
  gi|70607571|ref|YP_256441.1|  38 PWQNLATKT-DLENLRKDIDIKFDTLRKELEGKMATKEDLQKMATKEDLQKMATKEDLQKMATKED 102
                                   6******98.9******************8888899999999999999999**********99554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00078
                                   EEEE---H..HHHHHHHHHHHHHEEEEE--SS.EEEEEEEEEETTTTEEEEEEEEEE..SS-SS--EEEEEEEEE.-S-HH CS
                       DUF1779   9 kenlsvvelkklaeqlakelkaeektekkesedeekitgikvegkndsdekvsivatktekkkdeetyllyevkg.lsswd 88 
                                   ke l+   +k++++++a + +++   +  ++ed +k+++++  +k +++e ++++atk++ +k e+  +++  +g + +w+
  gi|70607571|ref|YP_256441.1|  73 KEDLQKMATKEDLQKMATKEDLQ---KMATKEDLQKMATKEDLQKMATKEDLQKMATKEDLQKLEKRLITMI-NGiGARWG 149
                                   45555555555555555554444...5677888899999999999************666555544444444.47899*** PP

                                   H.....HHHHHHHHHHHH.HSS- CS
                       DUF1779  89 eeeleelkekvektlkkl.fsek 110
                                    ++++++++ v + l+++ f+ +
  gi|70607571|ref|YP_256441.1| 150 VKNEDSFRQGVVELLSDVgFTAN 172
                                   ***********999988734455 PP

>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   5.8     0.011        22      48      79 ..      86     117 ..      48     144 .. 0.55
   2 ?   -2.2   0.0       2.2   4.3e+03      59      80 ..     218     239 ..     204     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
               Ribonucleas_3_3  48 degeltklraslvseeslaeiAkelgLgkvlr 79 
                                   ++ +  ++++++ ++e l+++A + +L+k+  
  gi|70607571|ref|YP_256441.1|  86 QKMATKEDLQKMATKEDLQKMATKEDLQKMAT 117
                                   22233333333333444444444433333332 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
               Ribonucleas_3_3  59 lvseeslaeiAkelgLgkvlrl 80 
                                   +++++++ e Ak ++ ++v+ +
  gi|70607571|ref|YP_256441.1| 218 ILKKKEFYEKAKGVKVDEVIVI 239
                                   7788888888888888888877 PP

>> Toxin_36  Conantokin-G mollusc-toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         9   1.8e+04       3       7 ..       5       9 ..       5      12 .. 0.77
   2 ?    2.2   0.0      0.32   6.4e+02       3       9 ..      74      80 ..      73      82 .. 0.87
   3 ?    2.2   0.0      0.31   6.2e+02       3       9 ..      83      89 ..      81      91 .. 0.88
   4 ?    2.3   0.1       0.3     6e+02       3       9 ..      92      98 ..      90     101 .. 0.88
   5 ?    2.2   0.0      0.32   6.4e+02       3       9 ..     101     107 ..     100     109 .. 0.87
   6 ?    2.2   0.0      0.32   6.4e+02       3       9 ..     110     116 ..     109     118 .. 0.87
   7 ?    2.4   0.2      0.28   5.6e+02       3       9 ..     119     125 ..     118     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 9
                      Toxin_36 3 EElqk 7
                                 EE+ k
  gi|70607571|ref|YP_256441.1| 5 EEIKK 9
                                 89888 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                      Toxin_36  3 EElqkMa 9 
                                  E lqkMa
  gi|70607571|ref|YP_256441.1| 74 EDLQKMA 80
                                  89****8 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.31
                      Toxin_36  3 EElqkMa 9 
                                  E lqkMa
  gi|70607571|ref|YP_256441.1| 83 EDLQKMA 89
                                  89****8 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.3
                      Toxin_36  3 EElqkMa 9 
                                  E lqkMa
  gi|70607571|ref|YP_256441.1| 92 EDLQKMA 98
                                  89****8 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.32
                      Toxin_36   3 EElqkMa 9  
                                   E lqkMa
  gi|70607571|ref|YP_256441.1| 101 EDLQKMA 107
                                   89****8 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.32
                      Toxin_36   3 EElqkMa 9  
                                   E lqkMa
  gi|70607571|ref|YP_256441.1| 110 EDLQKMA 116
                                   89****8 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.28
                      Toxin_36   3 EElqkMa 9  
                                   E lqkMa
  gi|70607571|ref|YP_256441.1| 119 EDLQKMA 125
                                   7899998 PP

>> SelB-wing_1  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   5.1e+03      20      29 ..      39      48 ..      36      54 .. 0.80
   2 ?    5.9   2.5    0.0063        13      19      57 ..      75     113 ..      67     117 .. 0.80
   3 ?    6.5   1.2     0.004       7.9      19      56 ..      93     130 ..      90     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                   SelB-wing_1 20 WqeaaaraaL 29
                                  Wq+ a++  L
  gi|70607571|ref|YP_256441.1| 39 WQNLATKTDL 48
                                  9999998876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0063
                   SelB-wing_1  19 dWqeaaaraaLsleetrkLLqdmaaaGqltLLavendLy 57 
                                   d q  a++  L    t+  Lq+ma    l  +a   dL 
  gi|70607571|ref|YP_256441.1|  75 DLQKMATKEDLQKMATKEDLQKMATKEDLQKMATKEDLQ 113
                                   678888888888888888888888888888888888875 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.004
                   SelB-wing_1  19 dWqeaaaraaLsleetrkLLqdmaaaGqltLLavendL 56 
                                   d q  a++  L    t+  Lq+ma    l  +a   dL
  gi|70607571|ref|YP_256441.1|  93 DLQKMATKEDLQKMATKEDLQKMATKEDLQKMATKEDL 130
                                   67888888888888999999999988888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1679  (0.0936472); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2150.10
//
Query:       gi|70607572|ref|YP_256442.1|  [L=115]
Description: hypothetical protein Saci_1843 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-05   24.7   0.1    3.4e-05   24.1   0.1    1.2  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.9e-09   3.4e-05     104     135 ..      14      46 ..       2      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.9e-09
                       Cyclase 104 eky.rnpglseeaaewlaekgvkavGvDtlsvD 135
                                   + y   pgl+ ++a wl+ek+v++v+ Dt++v+
  gi|70607572|ref|YP_256442.1|  14 AGYtPAPGLGLDTAIWLHEKRVAGVASDTWGVE 46 
                                   345555*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 768.21
//
Query:       gi|70607573|ref|YP_256443.1|  [L=178]
Description: hypothetical protein Saci_1844 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   22.6   0.0    0.00012   22.4   0.0    1.2  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   6.6e-09   0.00012      17      57 ..     105     172 ..      26     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.6e-09
                       Cyclase  17 p........islsehtGTHlDapgHfae....k................tidelpleelvgpavvldvs 57 
                                   +        i ++ ++ T++Da++H++     +                +i +++ +++vg++v+ld+ 
  gi|70607573|ref|YP_256443.1| 105 KdisyaddiIIMPLQCATQWDALSHIFFegkmWngydaslvnssgalknDIAKVK-DKVVGRGVLLDFP 172
                                   0344445558999************944443313444444444555555668888.***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1251.74
//
Query:       gi|70607574|ref|YP_256444.1|  [L=146]
Description: hypothetical protein Saci_1845 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1022.12
//
Query:       gi|70607575|ref|YP_256445.1|  [L=1064]
Description: hypothetical protein Saci_1846 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      9e-78  261.3  25.8      9e-78  261.3  25.8    6.1  6  Thermopsin  Thermopsin
  ------ inclusion threshold ------
      0.085   12.8   3.9        3.1    7.8   0.1    4.1  3  KSHV_K1     Glycoprotein K1 of Kaposi's sarcoma-associated he


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3  25.8     1e-81     9e-78       2     260 .]      61     314 ..      60     314 .. 0.96
   2 ?   -1.6   2.4      0.16   1.5e+03     103     198 ..     342     462 ..     337     468 .. 0.59
   3 ?   -2.3   4.0      0.28   2.5e+03     112     213 ..     468     573 ..     456     610 .. 0.72
   4 ?   -3.1   7.3      0.47   4.3e+03     130     160 ..     677     705 ..     660     794 .. 0.57
   5 ?   -4.2   4.4       1.1   9.5e+03     131     198 ..     903     984 ..     858    1022 .. 0.61
   6 ?   -1.9   0.3       0.2   1.8e+03     114     165 ..     983    1034 ..     964    1042 .. 0.72

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 1e-81
                    Thermopsin   2 lvnvlslyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvtggktysyw 82 
                                   +++v+sl++sepaPmGi+dyG+++n+    +y+++t++++G++n++ ls++++s      +s+QLN++l+++ +g ty++w
  gi|70607575|ref|YP_256445.1|  61 YISVYSLHYSEPAPMGITDYGLSPNG----SYILTTTQWMGVINLYGLSTNTTS------VSFQLNLNLHYYLNGYTYDLW 131
                                   6789**********************....8*****************987665......99******************* PP

                    Thermopsin  83 vQnVvsfnttekqltfidNiWNftspsanlsnsaisGnGtvy.asskgefYyayatey.....lelslPltlkLvinvslt 157
                                   vQ+V+ f+t++++++++dNiWNf+sp+a ++++  +GnG++y  s+ +++Yyay+ +       +l+lP+t++L++nvs++
  gi|70607575|ref|YP_256445.1| 132 VQDVAFFDTQDNNIQILDNIWNFSSPHAYITSV--QGNGNIYsYSKLNTTYYAYEASGypgspATLTLPATVYLLVNVSTN 210
                                   ******************************766..*******888999999999998889999****************** PP

                    Thermopsin 158 sngvpevsFgYsid.ggvvtYDnvtinstgkasa.eilvngssltpsgllyDaeLvlgGpgngekttfnslnatlsLyYln 236
                                   s g+p+++F+Y+ d +g++ YD+vt+++++++s+ ++lv+g+++++ g+++D+e+v++Gpg+g++t+++s++++l+L Y+n
  gi|70607575|ref|YP_256445.1| 211 SLGEPVIYFYYN-DgYGWILYDTVTVTNAQGSSQvYFLVDGFQYNGYGTFWDSEMVFAGPGGGSTTYVYSSEVYLELLYWN 290
                                   ************.66****************9999********************************************** PP

                    Thermopsin 237 gtnyqpvknaydfGsdTaEtaenv 260
                                   g+n+q+v+nay+fGsdT+E+aenv
  gi|70607575|ref|YP_256445.1| 291 GHNFQEVENAYNFGSDTGESAENV 314
                                   ***********************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.16
                    Thermopsin 103 WNftspsanlsnsai.sGnGtvy.......asskgefYyayatey..lelslPltlkLvinvsltsngvpevsFgYsid.. 171
                                   WN+ s +    n+ + sG  tvy       +ss+ + +y  + e   + + +P ++ ++ n +l+ +g++  + g ++   
  gi|70607575|ref|YP_256445.1| 342 WNYDSVTILEINTPVqSGYATVYnfsipfsDSSNIQDFYFTGGEFilTLFPMPYSILVYQNGQLAYEGYSPGDTGLNVVnt 422
                                   666665443333333367777777777766666777777777776433334455555555555555555555555554455 PP

                    Thermopsin 172 ..............ggvvtYDnvtinstgkasaeilvngss 198
                                                 ++ ++YD+v+  + +   a+i+vn+s+
  gi|70607575|ref|YP_256445.1| 423 erfalnlssgfiklYTNQSYDEVINIIGE-GPAYIYVNSSN 462
                                   66666666777777888899998654444.44688888765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.28
                    Thermopsin 112 lsnsai..sGnGtvy..asskgefYyayateylelslPltlkLvinvsltsngvpevsFgYsid.ggvvtYDnvtinstgk 187
                                   ls++ +  +G G+v      ++  +y ++   ++++l   ++L  + s++ ++++ v+F+ ++  +++ t    t++++++
  gi|70607575|ref|YP_256445.1| 468 LSQEYLnlNGDGSVNlrIYPQSPGFYTVT---VTVNLLNGYYLRATFSVYVQAISSVKFNINVVgSQLPTSPVLTLQFPNG 545
                                   44444333888898855444555555544...5588888899999999999999******998876666777778888888 PP

                    Thermopsin 188 asaeilvng..ssltpsgllyDaeLvlg 213
                                   + ++++v++  + + p g+ y+   ++g
  gi|70607575|ref|YP_256445.1| 546 TISTLTVSPgeTLYLPVGTTYNLQQIIG 573
                                   8888888752234667777777666664 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 0.47
                    Thermopsin 130 efYyayateylelslPltlkLvinvsltsng 160
                                    fYy+  + y+++++P+t++ +in +++   
  gi|70607575|ref|YP_256445.1| 677 AFYYN--EYYVTVKTPVTVYAYINGTKNTLS 705
                                   33333..444788888888888887554332 PP

  == domain 5  score: -4.2 bits;  conditional E-value: 1.1
                    Thermopsin 131 fYyayateylelslPltlkLv.invsltsngv..pevsFgYsid...........ggvvtYDnvtinstgkasaeilvngs 197
                                   +Yy    + ++++  ++ +L+ +n+s +++g   ++++++Y ++           + +++   +t+++++ ++  +++ng+
  gi|70607575|ref|YP_256445.1| 903 QYYINVISPIPVKALVNGTLTsLNSSWVNSGTkiQVINYTYYVSnnerlvptlipSNLTVTSPITVEIKTVTQYLVTINGN 983
                                   445445555555555555554355555555541134555555555555555555433333334444444444434445554 PP

                    Thermopsin 198 s 198
                                   s
  gi|70607575|ref|YP_256445.1| 984 S 984
                                   4 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 0.2
                    Thermopsin  114 nsaisGnGtvyasskgefYyayateylelslPltlkLvinvsltsngvpevs 165 
                                    ns+ + nG+ +  + +  +y  ++ + +++++   +Lv+n  l++n  ++++
  gi|70607575|ref|YP_256445.1|  983 NSSWHNNGSTIVLNANIPFYMTGKYIGTYNVSPGAELVVNRPLVENLTETIN 1034
                                    3445677777767777778888888888888888888888888888777766 PP

>> KSHV_K1  Glycoprotein K1 of Kaposi's sarcoma-associated herpes virus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0073        66       5      23 ..     772     790 ..     768     807 .. 0.74
   2 ?    7.8   0.1   0.00035       3.1       1      22 [.     842     863 ..     842     883 .. 0.84
   3 ?   -2.7   0.1      0.65   5.8e+03       8      22 ..     922     936 ..     917     946 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0073
                       KSHV_K1   5 cpsntslptswycndtrll 23 
                                     +n +l t wy n t++ 
  gi|70607575|ref|YP_256445.1| 772 NGTNVTLTTGWYNNGTKIQ 790
                                   56899**********9863 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00035
                       KSHV_K1   1 ytltcpsntslptswycndtrl 22 
                                   y++    ntsl t wy n t++
  gi|70607575|ref|YP_256445.1| 842 YAIVNGENTSLTTGWYNNGTKI 863
                                   5666778************986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.65
                       KSHV_K1   8 ntslptswycndtrl 22 
                                    tsl +sw    t++
  gi|70607575|ref|YP_256445.1| 922 LTSLNSSWVNSGTKI 936
                                   589999998877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1064 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 6877.16
//
Query:       gi|70607576|ref|YP_256446.1|  [L=247]
Description: glutamine amidotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-08   32.9   0.0      1e-07   32.2   0.0    1.3  1  GATase_6  Glutamine amidotransferase domain
     0.0001   21.3   0.0    0.00014   20.9   0.0    1.3  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.2e-11     1e-07      13     123 ..      72     179 ..      51     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.2e-11
                      GATase_6  13 e..valaHvRlaivglaeeega.qPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelGeev 88 
                                   +  +a+ H+R a+ g++  ++  +P+  ++++g + l+hNG++++ + l +e++ +        +D+e+ l+ +    ++ 
  gi|70607576|ref|YP_256446.1|  72 QemIAVFHARQASAGNPIGSQFsHPYleVNQNGSIFLAHNGSVDKER-LLKEVSMNSE----YVVDSELALKFI----SRF 143
                                   14599***************99************************6.5556665344....45********99....455 PP

                      GATase_6  89 lerlrGmfafaiwdkrentlila.rdrlgvkplyya 123
                                    +  +G+     ++k++ +l+l+   rlg++ lyy 
  gi|70607576|ref|YP_256446.1| 144 KDLYEGVEVLKGYTKSALNLFLVnISRLGEAELYYL 179
                                   556677777777999999999999999999999997 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.6e-08   0.00014      29     172 ..      34     174 ..       1     180 [. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.6e-08
                      GATase_4  29 tdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGe.vklenthpFvRelwgrewifAHn 108
                                    ++h+dGwG+      ++      +p  e +l   ++++     ++v H R+a+ G+ +  + +hp+    ++ ++ +AHn
  gi|70607576|ref|YP_256446.1|  34 NSSHKDGWGFVIVTRDKIIHYRSGRPIFEDTLPIKLNDQ---EMIAVFHARQASAGNpIGSQFSHPYLEVNQNGSIFLAHN 111
                                   5689*****999997777788888999999988878884...5689**********8467889****************** PP

                      GATase_4 109 Gdlke..ykpklegrfePvGsTDsElafCelleelasrfekaepsaeeleralaelakeiaelGvf 172
                                   G++++  + +  e +++     DsEla+  ++++++  +e  e  ++  ++al+ ++ +i++lG++
  gi|70607576|ref|YP_256446.1| 112 GSVDKerLLK--EVSMNSEYVVDSELALK-FISRFKDLYEGVEVLKGYTKSALNLFLVNISRLGEA 174
                                   ***6623333..33444444579999984.456677777667777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1603.71
//
Query:       gi|70607577|ref|YP_256447.1|  [L=404]
Description: proline/betaine transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.1  47.7    1.4e-22   80.1  47.7    2.1  2  MFS_1     Major Facilitator Superfamily
    9.6e-20   70.9  38.4    4.1e-15   55.6  15.1    2.7  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1  47.7   1.6e-26   1.4e-22      30     347 ..      38     351 ..       6     356 .. 0.79
   2 ?   -1.2   7.0     0.081   7.3e+02      34      81 ..     344     387 ..     340     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.6e-26
                         MFS_1  30 spseigllltlyalga....avaslplGrlsdrfGrrrvlllglllfalg.lllllf.a.......sslwlllvlrvlqGl 97 
                                    ++ + l++tl  +++     ++ +++G+++d++Grr  +l+++l+++l+ +l +++ +       +s+ ll vlr+lqG+
  gi|70607577|ref|YP_256447.1|  38 PKQLALLAATLPIIFTiisrPLGGFLFGYIGDKLGRRASMLITVLGYSLSiGLTAFLpTylqigilASI-LLSVLRILQGI 117
                                   444444455665555511134555666666********************4444443313343443333.5********** PP

                         MFS_1  98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.......Wravfyilaivsllafvlflll 171
                                   + g+ ++++ ++  + + k +rg   gl++ag+ +G+++   l  +las +g       Wr +f i  i +lla++   + 
  gi|70607577|ref|YP_256447.1| 118 FIGGDVAGSFTISMESVVK-RRGILSGLMQAGVLVGFVIVDSLFTYLASIYGkaffttyWRIIFGIGMIPALLAVL---IR 194
                                   *****************99.********************9999*****************************977...99 PP

                         MFS_1 172 lpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllal 252
                                   +  ++pe + k + +        pl+  +         w  li++++f++++++  ++lp++  +v++l+   + g ++  
  gi|70607577|ref|YP_256447.1| 195 FKMSEPEMWLKVKGKN-------PLSG-IMD----V--WQPLIVMIGFWMAIYAGPQFLPVLYGTVMKLN-PAYYGQIILY 260
                                   999*******998777.......4444.222....2..5689*******************88*******.89******** PP

                         MFS_1 253 lalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappee 333
                                   + ++g++++llag+lsd +gr+   +++ ++++++ ++l++  ++  + ll+   +l+Gf + ++++++ a++++ +  + 
  gi|70607577|ref|YP_256447.1| 261 MNVIGIPAMLLAGFLSDYVGRKLLGIIGSVIGIIGGALLYFHLPS--TYLLADYTFLFGFLVNLASSISPAYLAERF--KT 337
                                   ********************9888888888888888888888888..45555589999*******************..66 PP

                         MFS_1 334 agtasglfntagsl 347
                                     +a+g+ + ++++
  gi|70607577|ref|YP_256447.1| 338 FSRATGVGTAYNGA 351
                                   77777766655554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.081
                         MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   +g+++ + ++ a++++l+++ ls+ +    v+++++ +fa+g +++++
  gi|70607577|ref|YP_256447.1| 344 VGTAYNGAFIIAGWTQLIISLLSQSI---NVFIATFSIFAIG-WIIAI 387
                                   56677778889999999999999987...7777777777777.66663 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6  15.1   4.5e-19   4.1e-15       5     203 ..      11     209 ..       7     213 .. 0.84
   2 !   19.6  15.4   3.8e-08   0.00034      47     188 ..     253     390 ..     224     398 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.5e-19
                                   HHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                      Sugar_tr   5 aalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavl 85 
                                   a+++ ++ gYd+g +  ++++l++++  ++    +   +     +l   ++++ + +G++++g++gd++GR+ s+li+++ 
  gi|70607577|ref|YP_256447.1|  11 AYISWVMDGYDLGAVVITSSILGQLFYPKQLALLA---A-----TLPIIFTIISRPLGGFLFGYIGDKLGRRASMLITVLG 83 
                                   45555899999999999999999666666665554...3.....5778888999*************************** PP

                                   HHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  86 fvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl 161
                                   ++ ++ l+a+ + +      +  +l v R+l Gi++G+  +  + +is  +  k Rg+l +l q ++ +G+++   + + l
  gi|70607577|ref|YP_256447.1|  84 YSLSIGLTAFLPTYlqigiLASILLSVLRILQGIFIGGDVA-GSFTISMESVVKRRGILSGLMQAGVLVGFVIVDSLFTYL 163
                                   ************8877766666667777*********9765.56788888999******************9886555555 PP

                                   .HTSS-...TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT- CS
                      Sugar_tr 162 .nktsn...adgwrillglqlvpallllilllflPESPrylvekgk 203
                                    + +++   ++ wri +g+ ++pall +++++ + E   +l  kgk
  gi|70607577|ref|YP_256447.1| 164 aSIYGKaffTTYWRIIFGIGMIPALLAVLIRFKMSEPEMWLKVKGK 209
                                   2555558**********************************99987 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.8e-08
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                   ++g i   ++v++i   l+ag+l+d++GRk   +i++v+ +ig++l ++     s+++l+   +l G+ v las ++P y+
  gi|70607577|ref|YP_256447.1| 253 YYGQIILYMNVIGIPAMLLAGFLSDYVGRKLLGIIGSVIGIIGGALLYFHL--PSTYLLADYTFLFGFLVNLASSISPAYL 331
                                   56889999****************************************988..89************************** PP

                                   HTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 128 sEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpallllill 188
                                   +E  ++  R + v+   +a+   +++a ++ l+++  s+  + +  ++ + ++  ++ +++l
  gi|70607577|ref|YP_256447.1| 332 AERFKTFSRATGVG---TAYNGAFIIAGWTQLIISLLSQsINVFIATFSIFAIGWIIAIVGL 390
                                   **999988855433...345555666666666665555521122222222222223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2866.02
//
Query:       gi|70607578|ref|YP_256448.1|  [L=491]
Description: beta-galactosidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-62  211.2   4.0      2e-54  184.7   1.4    2.8  2  Glyco_hydro_1  Glycosyl hydrolase family 1
    7.5e-05   22.3   0.3    0.00016   21.2   0.3    1.5  1  Cellulase      Cellulase (glycosyl hydrolase family 5)


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   6.2e-10   5.5e-06       4      88 ..       3      91 ..       1     101 [. 0.84
   2 !  184.7   1.4   2.2e-58     2e-54      90     452 ..     123     472 ..     119     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.2e-10
                                  GS-TT-EEEEE--HHHHH--TTSTT---BHHHHHHHHGGGSTTS--.-SSTT-...HHHHHHHHHHHHHHTT-SEEEEE--HH CS
                 Glyco_hydro_1  4 tfpedFlwgaataayqiEGawnedGkgesiwDtftetpgkvlegsn.gdvacd...sYhrykeDvallkelgvkayrfSisWp 82
                                  +fp++F +g + + +q E ++      +s w ++ + +++++++   gd+  +   ++  yk+  +  +++g++a+r+ + W+
  gi|70607578|ref|YP_256448.1|  3 SFPKGFKFGWSQSGFQSEMGTPGSEDPNSDWHVWVHDRENIVSQVVsGDLPENgpgYWGNYKRFHDEAEKIGLNAVRINVEWS 85
                                  6********************999999*********999888776656664432227888888888899************** PP

                                  HHSTTS CS
                 Glyco_hydro_1 83 RilPkG 88
                                  Ri+P++
  gi|70607578|ref|YP_256448.1| 86 RIFPRP 91
                                  ****97 PP

  == domain 2  score: 184.7 bits;  conditional E-value: 2.2e-58
                                   T---HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH.H....-......GGG-SHHHHHHHHHHHHHHHHHTTT--E CS
                 Glyco_hydro_1  90 geinekGlayYerLidelleagieplvTlyHwdlPqaLqd.e....G......gwenrsiidafkeyaevvfkrfgdkvkl 159
                                   +  n++ l++Y+++++ l ++g + ++ +yHw lP +L+d      G      gw n +++ +f +++++v  ++ d    
  gi|70607578|ref|YP_256448.1| 123 NYANHEALSHYRQILEDLRNRGFHIVLNMYHWTLPIWLHDpIrvrrGdftgptGWLNSRTVYEFARFSAYVAWKLDDLASE 203
                                   567999********************************9852455543333558999************************ PP

                                   EEEEE-HHHHHHHHHT..SS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSSHHHHHHH CS
                 Glyco_hydro_1 160 wlTfnEpnvvallgyl..tgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplseseedkeaa 238
                                   ++T+nEpnvv  +gy    + f+P+  +++ +  a+ n++ ahara++++k+v +  ++gi+++ ++ +pl ++   +ea+
  gi|70607578|ref|YP_256448.1| 204 YATMNEPNVVWGAGYAfpRAGFPPNYLSFRLSEIAKWNIIQAHARAYDAIKSVSK-KSVGIIYANTSYYPLRPQD--NEAV 281
                                   ***********9999733589*****************************99865.579***********98765..5566 PP

                                   HHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...-S.TT---SSGG CS
                 Glyco_hydro_1 239 eraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseeas.lskteekkl 318
                                   e a++++   f+d ++kG+  +e ++          +     e l++  d++g+nyYt+++v+++es   + + + ++ + 
  gi|70607578|ref|YP_256448.1| 282 EIAERLNRWSFFDSIIKGEITSEGQN----------V----REDLRNRLDWIGVNYYTRTVVTKAESGYLTlPGYGDRCER 348
                                   6666666555********86654332..........2....356899**************99999655441456666666 PP

                                   GGG-SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH--HHHHHHHHHHHHHHHHHHHTT-- CS
                 Glyco_hydro_1 319 eeevdpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveDdkRidYlkehlnevkkaiedgvd 399
                                   ++    +lp++d gw+  pegl+++l    ++Y+ lp+y+ eNG+++          D++R +Yl +h+ +v++a+++gvd
  gi|70607578|ref|YP_256448.1| 349 NSLSLANLPTSDFGWEFFPEGLYDVLLKYWNRYG-LPLYVMENGIADDA--------DYQRPYYLVSHIYQVHRALNEGVD 420
                                   7777899***************************.**********9766........99********************** PP

                                   EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH-SS CS
                 Glyco_hydro_1 400 lkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviekng 452
                                   ++gY+ wsl Dn+ew++g+s+rfGl+ vd + t++ + + Sa  y+e+ ++ng
  gi|70607578|ref|YP_256448.1| 421 VRGYLHWSLADNYEWSSGFSMRFGLLKVD-YLTKRLYWRPSALVYREITRSNG 472
                                   *****************************.8899999************9997 PP

>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   1.8e-08   0.00016      17     169 ..      60     265 ..      41     291 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-08
                                   TSCGGSHHHHHHHHHHHT-SEEEEEEECTGGT...............TSSTTT..................GCTHHHHHHH CS
                     Cellulase  17 wgnpyttkalidevkdagfntvRlpvswgelv...............enapdy..................kvdenslerv 64 
                                   wgn    k ++de+ + g n+vR++v w +++               e                         ++++l+ +
  gi|70607578|ref|YP_256448.1|  60 WGN---YKRFHDEAEKIGLNAVRINVEWSRIFprplpkpemqtgtdkE----NspvisvdlnesklremdnYANHEALSHY 133
                                   665...799*******************77776666655555554431....03445555555555555544666****** PP

                                   HHHHHHHHHTT-EEEEEEESS..TTT......CSSSSTTTTHHH.........HHHHHHHHHHHHHHHHTTTTTTEEEESS CS
                     Cellulase  65 eevvkyakenglyvildiHse..egw......ltkadgnssedt.........aeeffkklwtqiAerykkndevvifelm 128
                                    ++++   ++g++++l++ +   + w      +        ++t         +   f+ + + +A ++  +d    + +m
  gi|70607578|ref|YP_256448.1| 134 RQILEDLRNRGFHIVLNMYHWtlPIWlhdpirV-----RRGDFTgptgwlnsrTVYEFARFSAYVAWKL--DDLASEYATM 207
                                   ******************996564444333331.....2222223333333333333677777888888..6666778999 PP

                                   SS--STTCT......................CCTCHHHTTHHHHHHHHHHHHHHHHTTS..SEEE CS
                     Cellulase 129 NEPhgnntg......................aewtseeadevkayaeeaikaIRavgpn..rlii 169
                                   NEP+ +  g                      a+w      ++ +++ +a++aI++v ++   +i 
  gi|70607578|ref|YP_256448.1| 208 NEPNVV-WGagyafpragfppnylsfrlseiAKW------NIIQAHARAYDAIKSVSKKsvGIIY 265
                                   ***995.445899999999999999999999889......77778899*******9999644443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3369.02
//
Query:       gi|70607579|ref|YP_256449.1|  [L=359]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00044   19.8   2.8    0.00087   18.9   0.4    2.9  2  DUF1648   Protein of unknown function (DUF1648)


Domain annotation for each model (and alignments):
>> DUF1648  Protein of unknown function (DUF1648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   4.9e-08   0.00087       1      38 [.     140     177 ..     140     188 .. 0.83
   2 ?   -1.4   0.1      0.11     2e+03      34      47 ..     332     344 ..     331     351 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.9e-08
                       DUF1648   1 lllllplvvglllypkLPdqiPtHfnasGepDgygsK.l 38 
                                   +l+l+++++gl++y+k+P ++  H +  G +  y++K +
  gi|70607579|ref|YP_256449.1| 140 ILALITFLIGLVYYNKIPSEVIFHIGPGGSV-EYAPKtP 177
                                   689***********************99977.5777744 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                       DUF1648  34 ygsKlfalfllPll 47 
                                   +g+K  a++ll ++
  gi|70607579|ref|YP_256449.1| 332 FGNK-KAILLLSVI 344
                                   6777.777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2476.24
//
Query:       gi|70607580|ref|YP_256450.1|  [L=121]
Description: regulatory protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-18   63.8   0.0    1.2e-17   63.3   0.0    1.3  1  GntR           Bacterial regulatory proteins, gntR family
    3.1e-05   23.6   0.0    0.00042   20.0   0.0    2.1  2  HTH_41         Helix-turn-helix domain
    3.3e-05   23.8   0.0      6e-05   22.9   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
     0.0032   17.3   0.4      0.012   15.5   0.2    1.9  2  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
       0.04   13.6   0.0      0.083   12.6   0.0    1.6  1  DUF4423        Domain of unknown function (DUF4423)
      0.058   13.4   0.0        1.2    9.1   0.0    2.3  2  HTH_36         Helix-turn-helix domain
      0.077   13.1   0.3        1.7    8.8   0.0    2.6  3  ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
      0.081   12.9   0.0       0.16   11.9   0.0    1.5  1  MarR           MarR family
       0.12   13.0   0.1       0.27   11.9   0.0    1.6  2  RPA_C          Replication protein A C terminal


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0   6.2e-21   1.2e-17       2      60 ..      16      74 ..      15      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 6.2e-21
                                  HHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                          GntR  2 yeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                  y+q+++++ e+I +gel+pGdkLPs reLa+++gV+  tv++A++ L+ eg ++++++r
  gi|70607580|ref|YP_256450.1| 16 YKQIADQIIELIAKGELKPGDKLPSIRELASMLGVNMLTVNKAYNYLVDEGFIVVQKRR 74
                                  99*****************************************************9997 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.14   2.8e+02      32      43 ..      20      31 ..      17      32 .. 0.86
   2 !   20.0   0.0   2.1e-07   0.00042       1      41 [.      33      73 ..      33      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                        HTH_41 32 ddkaislerrGr 43
                                  +d++i+l+++G 
  gi|70607580|ref|YP_256450.1| 20 ADQIIELIAKGE 31
                                  6899******96 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.1e-07
                        HTH_41  1 kvGdRlktIeelakeleLSvGlvQkALklLeddkaislerr 41
                                  k Gd+l++I ela+ l++   +v kA + L+d++ i +++r
  gi|70607580|ref|YP_256450.1| 33 KPGDKLPSIRELASMLGVNMLTVNKAYNYLVDEGFIVVQKR 73
                                  56**********************************99876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     3e-08     6e-05      22      60 ..      39      78 ..      17      82 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3e-08
                                  HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES CS
                     HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rgrriril 60
                                   + +elAsmlG++  tv+++ + L +eg i  ++rr +++
  gi|70607580|ref|YP_256450.1| 39 PSIRELASMLGVNMLTVNKAYNYLVDEGFIVvQKRRYVVK 78
                                  4779***************************654557776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   5.9e-06     0.012      25      60 ..      41      76 ..      39      98 .. 0.88
   2 ?   -0.3   0.0      0.52     1e+03      14      37 ..      95     116 ..      88     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                  HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                          TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                  ++e+a++lgv   +v+++ + L+d G++ ++k+r+ 
  gi|70607580|ref|YP_256450.1| 41 IRELASMLGVNMLTVNKAYNYLVDEGFIVVQKRRYV 76
                                  689****************************99854 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.52
                                   CHHHHHHCCCHHCHHCCCTTSSCH CS
                          TrmB  14 YlaLlklgpatadeiaeelgvprs 37 
                                   Y aL    +++ dei +e+++  s
  gi|70607580|ref|YP_256450.1|  95 YRALA--SNMSKDEIVNEINRVVS 116
                                   44444..45566677777766555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05     0.083      36      89 ..      38      81 ..      22     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
                       DUF4423 36 kadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssev 89
                                   ++++ela +l+  ++   v+ka ++L++ g++  ++  +y++ +       ev
  gi|70607580|ref|YP_256450.1| 38 LPSIRELASMLG--VNMLTVNKAYNYLVDEGFIVVQKR-RYVVKS-------EV 81
                                  46899*******..**********************98.888766.......44 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00063       1.2      25      55 .]      38      68 ..      33      68 .. 0.92
   2 ?    1.8   0.0      0.12   2.4e+02      32      48 ..      97     113 ..      95     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00063
                        HTH_36 25 fpsqetlakrlglsknTvsraikeLeqlGyi 55
                                   ps + la+ lg++  Tv +a + L++ G+i
  gi|70607580|ref|YP_256450.1| 38 LPSIRELASMLGVNMLTVNKAYNYLVDEGFI 68
                                  59************************99987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                        HTH_36  32 akrlglsknTvsraike 48 
                                   a ++++sk+ +++ i+ 
  gi|70607580|ref|YP_256450.1|  97 ALASNMSKDEIVNEINR 113
                                   56899******999986 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00084       1.7      56      78 ..      15      37 ..      12      39 .. 0.91
   2 ?   -1.5   0.0       1.3   2.6e+03      30      43 ..      54      67 ..      42      70 .. 0.71
   3 ?    1.2   0.1       0.2   3.9e+02      52      74 ..      90     112 ..      87     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00084
                                  HHHHTHHHHHHHHHTTSSSTTSE CS
                 ClpB_D2-small 56 iqreiedplaeeilsgelkegdt 78
                                  i ++i d++ e+i++gelk+gd+
  gi|70607580|ref|YP_256450.1| 15 IYKQIADQIIELIAKGELKPGDK 37
                                  89******************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                  EHHHHHHHHHHHTS CS
                 ClpB_D2-small 30 vtdealdalaekgy 43
                                    ++a ++l+++g+
  gi|70607580|ref|YP_256450.1| 54 TVNKAYNYLVDEGF 67
                                  55678899999887 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.2
                                   HHHHHHHHTHHHHHHHHHTTSSS CS
                 ClpB_D2-small  52 Lrriiqreiedplaeeilsgelk 74 
                                   Lr ii r +   +++  + +e++
  gi|70607580|ref|YP_256450.1|  90 LRVIIYRALASNMSKDEIVNEIN 112
                                   78889999999998877777665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     8e-05      0.16      19      51 ..      40      72 ..      36      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8e-05
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlieRsk 51
                                  s+ eLa++lgv+  tv ++   L+++G+i  +k
  gi|70607580|ref|YP_256450.1| 40 SIRELASMLGVNMLTVNKAYNYLVDEGFIVVQK 72
                                  789**************************8776 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.27      49      97 ..      18      68 ..       7      69 .. 0.79
   2 ?   -2.5   0.0       4.2   8.4e+03      51      58 ..     104     111 ..      93     118 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHHH...SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                         RPA_C 49 alaqqvlnlikq..speseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                  + a+q+++li +     +++  +++e+a  l++++ +v++a ++L++eG i
  gi|70607580|ref|YP_256450.1| 18 QIADQIIELIAKgeLKPGDKLPSIRELASMLGVNMLTVNKAYNYLVDEGFI 68
                                  5667777777776333344445899************************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                   HHHHHHHH CS
                         RPA_C  51 aqqvlnli 58 
                                   +++++n i
  gi|70607580|ref|YP_256450.1| 104 KDEIVNEI 111
                                   23333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 881.33
//
Query:       gi|70607581|ref|YP_256451.1|  [L=311]
Description: hypothetical protein Saci_1852 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-18   64.9   2.3    1.8e-17   64.0   2.3    1.4  1  Glyco_hydro_12  Glycosyl hydrolase family 12


Domain annotation for each model (and alignments):
>> Glyco_hydro_12  Glycosyl hydrolase family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   2.3     1e-21   1.8e-17       5     213 ..      69     311 .]      65     311 .] 0.77

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1e-21
                                   EEE--TTEEEEEEEEEEEE-SSEEEEEEEEEEEEESSG.....B--EEEEE-BGG.....GTB--TT----EEGGGEEEEE CS
                Glyco_hydro_12   5 vennlWgskegsgsvavkvdgekitssgasahtswkek.....gypevygGeksv.....ksysnsgvalpvkvssvssip 75 
                                   v+  lW+ k   g + ++  g+ +  + +  + +  ++     gyp v +G++ +     ++   s   lpvkv s+  + 
  gi|70607581|ref|YP_256451.1|  69 VSPFLWNLKTALGYTNLTYRGNTLVVNVNFTNFEKINSnlqvdGYPGVMYGQEDWfpfagRTLMPSCFVLPVKVISLPNFN 149
                                   66779****************9999888877766655556677***********944443455667889************ PP

                                   EEEEEEEE.-TT--EEEEEEEEEESSTT-S.--TT-EEEEEEEE.EES---SSEEEE....EEEETTE....EEEEEE... CS
                Glyco_hydro_12  76 tevsfsid.dtnvkanvaydlflaaeknqv.tsigdvElmiWlarygniqPiGekie....tavvgGe....tWelwlG.. 144
                                   +++s++i+ +  +  +++yd++l++++n++  +  dvE+miWl++ +++     k +     + v+G      ++++    
  gi|70607581|ref|YP_256451.1| 150 STLSYKINdNRGIIDDFSYDIWLTQNPNTTyIQFPDVEIMIWLYHNETLSDYFVKAGvmsvNIMVNGTviqdDFTVYILph 230
                                   *******97778999**************877889*********9999998877777555578889989999677775444 PP

                                   ....EESSSEEE....EEEESS--EEEEEEHHHHHHHHH.-SS---GGGSEE-EEEEE--B..--TT-...EEEEEEEEEE CS
                Glyco_hydro_12 145 ....aeaeqdvl....sFvakspikgysfDvkdFldalt.sargldaedlylislqiGtEpftgspet...lkvenfsasv 213
                                        ++   ++       a + +  +s  +kd +++++ +   l+++++yl ++q+G+E+    ++    +++ n+++++
  gi|70607581|ref|YP_256451.1| 231 tgssNGWIGVYYisqlELSAGNITVPMSTLIKDSFNYIRgVFPDLQTSAYYLNAIQVGMEFNDINGVVnvgYTLYNWTITI 311
                                   445322222222110033344444778899*******98678899****************65444446789999**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2005.10
//
Query:       gi|70607582|ref|YP_256452.1|  [L=972]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.008   16.6   3.5        1.1    9.8   0.0    4.1  4  MG2            MG2 domain
  ------ inclusion threshold ------
      0.011   15.4   5.4      0.014   15.0   0.1    2.8  2  DUF2140        Uncharacterized protein conserved in bacteria 
      0.018   15.5   3.7      0.018   15.5   3.7    2.0  2  MGC-24         Multi-glycosylated core protein 24 (MGC-24), s
      0.033   14.1   4.3       0.11   12.4   4.3    1.9  1  TMEM154        TMEM154 protein family
      0.045   13.5   1.4      0.094   12.5   0.2    2.0  2  DUF4448        Protein of unknown function (DUF4448)
       0.63    9.7   5.5       0.11   12.1   0.2    2.3  2  SBF            Sodium Bile acid symporter family
        1.7    9.4   9.4       0.94   10.2   4.4    2.9  3  DUF3823_C      Domain of unknown function (DUF3823_C)
          2    8.8   8.8      0.036   14.4   1.7    1.6  2  DUF5383        Family of unknown function (DUF5383)
        7.4    6.9   7.2        1.5    9.0   2.5    2.2  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.047        94      65      96 .]      81     112 ..      52     112 .. 0.71
   2 ?    0.1   0.0      0.58   1.2e+03      24      66 ..     525     567 ..     516     590 .. 0.74
   3 !    9.8   0.0   0.00055       1.1      28      94 ..     629     699 ..     614     700 .. 0.82
   4 ?   -1.6   0.4       1.9   3.9e+03      34      54 ..     904     927 ..     880     949 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.047
                                   EE--TT--SEEEEEEEEECSTTT-EEEEEEEE CS
                           MG2  65 falpeaaklGeysvelsadsaeeslssgsfrV 96 
                                    a+ + ++ G+y++++ + + +++ +s+s+ V
  gi|70607582|ref|YP_256452.1|  81 TATHAYSENGTYTIVATTHQSDGQNASASVTV 112
                                   356778899*******8888888888888876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.58
                                   ESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE CS
                           MG2  24 rdetlqglaklplkltirdpdgkevkelplatdetggaesefa 66 
                                    + +l  l+++ +++ + +++g   ++l+l+  ++++a ++++
  gi|70607582|ref|YP_256452.1| 525 GTLSLYSLTRTYVSVAFINSNGIILQQLSLRLHANSTATVTIP 567
                                   45556667779999999************99999988888775 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00055
                                   CSB---EEEEEEEE-TTSSEEEEEEEEE-CTTE.....EEEEEE--TT--SEEEEEEEEECSTTT-EEEEEE CS
                           MG2  28 lqglaklplkltirdpdgkevkelplatdetgg.....aesefalpeaaklGeysvelsadsaeeslssgsf 94 
                                   ++++++ ++ +++ +p g++v e+ ++t+ +g+     +++ + l+++ + G+y++e+ +d+  +s+++ sf
  gi|70607582|ref|YP_256452.1| 629 GKAIPDSEVDIKLINPYGETVIEKLVNTSPSGLynttlISFPLSLNSTFPYGTYKIEV-NDGLVSSYTNISF 699
                                   67888999*************999999999998555446677899999**********.6666666666666 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.9
                                   EEEEEEEE-TTSSEEEEEEE...E CS
                           MG2  34 lplkltirdpdgkevkelpl...a 54 
                                   +++++t ++++ +++ ++++   +
  gi|70607582|ref|YP_256452.1| 904 TNTSITQTNTHTNTTTSTTIsssT 927
                                   444555555555555555543222 PP

>> DUF2140  Uncharacterized protein conserved in bacteria (DUF2140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   6.8e-06     0.014      63     127 ..     568     633 ..     549     643 .. 0.82
   2 ?    0.3   2.0      0.21   4.2e+02      18      79 ..     889     952 ..     883     960 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                       DUF2140  63 ylkkkqkdeklkykvel.ddevvlegeikvlgqkvplkltfePevlenGnvvLkakslsvGslnlP 127
                                    l++ +k+ +  y v + ++ ++l+g+ k+ +q++ + l++ P+++ nGnv    ++l +    +P
  gi|70607582|ref|YP_256452.1| 568 SLSETDKNGNGVYGVMIyASTLYLTGTQKLYNQQIYIPLHVPPTIKLNGNVFNPGEKLLLSGKAIP 633
                                   578889999999**************************************9766666655555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                       DUF2140  18 vavvlvrvfapseeste...kssekekkseaeftitttkkqlnalinkylkkkqkdeklkykvel 79 
                                    a++  +++++++++t+   ++++++++ +++ ti+++  +l++  n+   + +++++++y++++
  gi|70607582|ref|YP_256452.1| 889 SAFMQETIYTEENNQTNtsiTQTNTHTNTTTSTTISSST-DLTSQTNSSTFQGSHSKTFSYNIYI 952
                                   455556666666666655444444444555555565555.5555555555577788889999987 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.8       2.9   5.7e+03      72      94 ..      92     114 ..      71     137 .. 0.45
   2 ?   15.5   3.7   9.1e-06     0.018      56     123 ..     900     965 ..     874     971 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.9
                        MGC-24  72 kpsstttstsvatsgttnttvtp 94 
                                     + +tt +s   +++++ tvt+
  gi|70607582|ref|YP_256452.1|  92 YTIVATTHQSDGQNASASVTVTL 114
                                   22222222222222222222222 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.1e-06
                        MGC-24  56 skstpkptnstaktttkpsstttstsvatsgttnttvtptsqparkstFDaAsFiGGivLvLgvqAvi 123
                                   +++  ++ +s+++t+t+  +tt++t ++++  t++t + t q ++++tF    +i G+ Lv+ +   i
  gi|70607582|ref|YP_256452.1| 900 ENN-QTN-TSITQTNTHTNTTTSTTISSSTDLTSQTNSSTFQGSHSKTFSYNIYIIGVALVVVIVLLI 965
                                   111.222.233333333333333333335555778888899999****************98775555 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.3   5.3e-05      0.11       8      79 ..     904     968 ..     889     972 .] 0.39

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                       TMEM154   8 gdtaletatleeesadatsaasteseslkqeeakeslssaelsnesdqlel..vlmiiiPlvllillllvviil 79 
                                   ++t++     +++++++ +++st + s  ++++  +++s  ++   ++     + +i + lv++i+ll++  +l
  gi|70607582|ref|YP_256452.1| 904 TNTSI-----TQTNTHTNTTTST-TISSSTDLT-SQTNSSTFQGSHSKTFSynIYIIGVALVVVIVLLIA--LL 968
                                   11111.....1111111122222.111112222.334444444444443332355555666666665554..44 PP

>> DUF4448  Protein of unknown function (DUF4448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.2   2.4e+03      95     141 ..      74     120 ..      61     145 .. 0.56
   2 ?   12.5   0.2   4.7e-05     0.094      88     177 ..     866     968 ..     859     971 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                       DUF4448  95 tvdeewlkgkkser....vtivlvslqpdnvkdeveikkGpkVsltkkedl 141
                                   +v+ +w++  + +      tiv ++ q+d     ++ +   +V+lt++  +
  gi|70607582|ref|YP_256452.1|  74 NVSTSWFTATHAYSengtYTIVATTHQSD----GQNASASVTVTLTSPYYN 120
                                   56666776644333222233344444444....556667777777766554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.7e-05
                       DUF4448  88 sdGfypltvdeewlkgkkservtivlvslqpdnvkd............eveikkGpkVsltkkedlk...kledkeseegk 153
                                     G ++l+v+ +wl+++   +vt v + +q++ +++            ++++++    +++++ dl+   + ++ + +++k
  gi|70607582|ref|YP_256452.1| 866 MSGNMALNVSLNWLNSE--GKVTFVSAFMQETIYTEennqtntsitqtNTHTNTTTSTTISSSTDLTsqtNSSTFQGSHSK 944
                                   57889999999999998..45666666666665554455555667777444444444444444444466877889999999 PP

                       DUF4448 154 kaekyalaialPvvvvvlvlglig 177
                                   + + ++ +i++ +vvv+++l+ ++
  gi|70607582|ref|YP_256452.1| 945 TFSYNIYIIGVALVVVIVLLIALL 968
                                   99999999****999999988765 PP

>> SBF  Sodium Bile acid symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   5.7e-05      0.11      45     127 ..     703     782 ..     689     793 .. 0.85
   2 ?   -1.8   1.3       1.1   2.1e+03      85     130 ..     866     913 ..     862     969 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                           SBF  45 mfilakillrdlklepelavGlilvglapggamsnvwtylakGdlelsvvlvalstllailltPlllyllaksleqttlkv 125
                                   m++l         l+++ +  + l g+ + +++s +  y++kGd  + v+ v  st  +++ tP + + ++++ ++ t++v
  gi|70607582|ref|YP_256452.1| 703 MYALTF---VEQGLPQNSMWSVTLNGSTRTTNSSSITFYVTKGDYYYLVSNVSYSTNYTVGYTPQVQKGYIELDNNSTVRV 780
                                   555555...234589999***********************************************9999998887777777 PP

                           SBF 126 pi 127
                                    +
  gi|70607582|ref|YP_256452.1| 781 LF 782
                                   65 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                           SBF  85 akGdlelsvvlvalstllaillt.Pl.llyllaksleqttlkvpieei 130
                                   + G+++l v+l  l++  ++ ++ ++    +++++++qt++ ++  ++
  gi|70607582|ref|YP_256452.1| 866 MSGNMALNVSLNWLNSEGKVTFVsAFmQETIYTEENNQTNTSITQTNT 913
                                   678999999999999998888884332334555555555554444443 PP

>> DUF3823_C  Domain of unknown function (DUF3823_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   2.3e+03       2      36 ..      93     126 ..      89     132 .. 0.77
   2 ?   -3.5   0.1       8.5   1.7e+04      59      85 ..     724     746 ..     714     747 .. 0.52
   3 ?   10.2   4.4   0.00047      0.94      13      77 ..     868     930 ..     857     948 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                   EEEEEEEEEETTEEEEEEEEEESS--...-EEEEE CS
                     DUF3823_C   2 riknveiskeggkltakfkvtrivtnepenieevq 36 
                                   +i +   + +g++  a+++vt + + + ++i++++
  gi|70607582|ref|YP_256452.1|  93 TIVATTHQSDGQNASASVTVTLTSPYY-NPISKAS 126
                                   666777789999999999999877765.5777776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.5
                                   ---EE-TT-HHHHHHHH.....HT-EE CS
                     DUF3823_C  59 sdeadlatevtleinlpeadksgrkyF 85 
                                   + ++  +++ ++++ +     +g++y+
  gi|70607582|ref|YP_256452.1| 724 NGSTRTTNSSSITFYV----TKGDYYY 746
                                   3334444455555555....4577777 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00047
                                   TEEEEEEEEEESS--...-EEEEEEEEESSS--SS-SGGGG-STT----EE-TT-HHHHHHHH.. CS
                     DUF3823_C  13 gkltakfkvtrivtnepenieevqlfvsktsfvdntnarstklsgasdeadlatevtleinlpea 77 
                                   g++ ++++++  ++++  +++ v+ f++ t +   +n+++t++++++  ++ +t++t+++++  +
  gi|70607582|ref|YP_256452.1| 868 GNMALNVSLNWLNSEG--KVTFVSAFMQETIYTEENNQTNTSITQTNTHTNTTTSTTISSSTDLT 930
                                   6788889999999997..*****************999999999997778888888887775544 PP

>> DUF5383  Family of unknown function (DUF5383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.8         9   1.8e+04      99     110 ..       7      16 ..       4      28 .. 0.41
   2 ?   14.4   1.7   1.8e-05     0.036      41     114 ..     899     969 ..     885     970 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 9
                       DUF5383  99 pillillivlli 110
                                    i++  li+l++
  gi|70607582|ref|YP_256452.1|   7 LIIY--LILLIL 16 
                                   2222..222222 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.8e-05
                       DUF5383  41 kkekeeaeelkesLfassekesntiaakakelgLfseekesvkqsateqeseeksnlLpillillivllivvll 114
                                   +++++++ ++ +   ++++++++t++  +++ +L+s+ + s+ q ++ ++ + ++  + ++l+++ivlli++ll
  gi|70607582|ref|YP_256452.1| 899 EENNQTNTSITQ---TNTHTNTTTSTTISSSTDLTSQTNSSTFQGSHSKTFSYNIYIIGVALVVVIVLLIALLL 969
                                   344444444444...3444478889999*************999999999988888888888999999888886 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.3   2.7e+03      85     106 ..     122     143 ..     106     144 .. 0.84
   2 ?    9.0   2.5   0.00077       1.5       9      84 ..     898     971 ..     891     972 .] 0.56

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                                   HSXXXXXXXXXXXXXXXXXXXX CS
                 Glycophorin_A  85 liKKssvdvkplespDedvPLs 106
                                   + K s ++++p   p ++ P+s
  gi|70607582|ref|YP_256452.1| 122 ISKASPPVIQPDAEPSNKYPIS 143
                                   67999***********999987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00077
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXX.XXXXSSSSSSS-TTHHHHHHHHHHHHHHHHHHHHHHHHT CS
                 Glycophorin_A   9 sttgdkskasvtastpsahevseltirtev..aaeqeetgereqlvhdFselvitliifgvmAgvigtillisYlirR 84 
                                   ++ +++ ++s+t ++   ++++ +ti + +  + + +++  + +  + Fs       i+gv A v+ ++lli+ l+rR
  gi|70607582|ref|YP_256452.1| 898 TEENNQTNTSITQTNTHTNTTTSTTISSSTdlTSQTNSSTFQGSHSKTFSYN---IYIIGV-ALVVVIVLLIALLLRR 971
                                   5566777777666655555444444444440044444434444445555543...235565.7888899999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (972 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 6671.19
//
Query:       gi|70607583|ref|YP_256453.1|  [L=277]
Description: outer surface protein A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2056.65
//
Query:       gi|70607584|ref|YP_256454.1|  [L=331]
Description: hypothetical protein Saci_1855 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-86  289.1  43.6      4e-86  288.9  43.6    1.0  1  DUF973    Protein of unknown function (DUF973)
  ------ inclusion threshold ------
        3.2    8.0  45.9      0.077   13.3  12.7    2.6  3  DUF996    Protein of unknown function (DUF996)
        9.5    5.4  21.6         24    4.1  21.6    1.6  1  DUF3273   Protein of unknown function (DUF3273)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.9  43.6   6.7e-90     4e-86       1     310 []       7     330 ..       7     330 .. 0.97

  Alignments for each domain:
  == domain 1  score: 288.9 bits;  conditional E-value: 6.7e-90
                        DUF973   1 eiegleklregslfliiasllaliliilvlvvlftaissglsqliqssasilssvlllliaaii..liiiasvllilgllk 79 
                                   +i++++++r +++++i++s+l++++++ +++++f+             as  +  + l+i++ii  l++ +s+++i++l++
  gi|70607584|ref|YP_256454.1|   7 DIMEVSRIRVAMILFIVSSILTVVSLFGSFSYIFSL------------ASSSVLNVPLIISVIIsgLAVGGSIIYIISLIM 75 
                                   6899***************************99992............3334567889999999999************** PP

                        DUF973  80 irsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsll...............slilslillgviilligiilal 145
                                   +r+gf++L+++grdvgiG++g++++lig+ii+i+++ilaiv+++               ++ ls + +++ii+li+ ++++
  gi|70607584|ref|YP_256454.1|  76 MRRGFKRLREYGRDVGIGSAGSLVVLIGSIISIVSYILAIVIFVifltsasyslnistyYTLLSGLGASYIIYLISLLIVV 156
                                   ****************************************998899************9999******************* PP

                        DUF973 146 iGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsklr.............sttsqvpvlqv 213
                                   iGqillg++fyklG+vYn+++++igGili+i+   ilsfIG+il++ig+gn+lsklr             ++++q+p +++
  gi|70607584|ref|YP_256454.1| 157 IGQILLGIGFYKLGSVYNDSTTEIGGILIAIY---ILSFIGAILAVIGTGNILSKLRagfvpqpksysysQYPTQYPGYPP 234
                                   ********************************...********************************************** PP

                        DUF973 214 pstpqqvqisqvgqGtlrsnGtanltvysqvqvqIlsAsiegtnysttsinPntLkvGnNsitinFntvlnLvpgstYtir 294
                                   p++p qv+++ + q++++snG+a ++v++++qv+ +sA+i+gtn+sttsi+Pn+L++G+N++tinFnt+lnL+ g tY+ir
  gi|70607584|ref|YP_256454.1| 235 PNVP-QVPMQPAVQNAIKSNGVAIVSVFTNYQVAAVSAQILGTNFSTTSISPNVLNPGTNVLTINFNTPLNLTVGITYVIR 314
                                   ****.**************************************************************************** PP

                        DUF973 295 LlLsngqtidvevtyq 310
                                   + Lsn+++idv+++yq
  gi|70607584|ref|YP_256454.1| 315 ISLSNNTFIDVNAVYQ 330
                                   ***************8 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  12.7   1.3e-05     0.077      30     123 ..      15     109 ..       6     109 .. 0.81
   2 ?    6.1  25.7    0.0021        13      29     130 ..     100     207 ..      94     209 .. 0.89
   3 ?   -2.8   0.1       1.2   7.2e+03      88      88 ..     271     271 ..     246     315 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                        DUF996  30 liafilsiialvvailalllvlgalatalelpgleeaaslilllllvl.iiayvlliisavflkksyellgkrtgvklFet 109
                                    +a+il i++ +++++ l +++  +++  ++  l+  + +i++++  l +   +++iis +++++ +++l ++       +
  gi|70607584|ref|YP_256454.1|  15 RVAMILFIVSSILTVVSLFGSFSYIFSLASSSVLNV-PLIISVIISGLaVGGSIIYIISLIMMRRGFKRLREYGRDVGIGS 94 
                                   578999999999999999999999999888887776.5478888877767788*******************976555555 PP

                        DUF996 110 ag.llyfiGaiLtiv 123
                                   ag l+++iG+i++iv
  gi|70607584|ref|YP_256454.1|  95 AGsLVVLIGSIISIV 109
                                   55166789****997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0021
                        DUF996  29 aliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgkrtgvklFet 109
                                   +li  i+si+++++ai+++++ l+++   l++   ++ +s+++ + ++++i +++++i  ++l   +++lg+ ++ ++ e+
  gi|70607584|ref|YP_256454.1| 100 VLIGSIISIVSYILAIVIFVIFLTSASYSLNISTYYTLLSGLGASYIIYLISLLIVVIGQILLGIGFYKLGSVYNDSTTEI 180
                                   588999********999999999999999999999999999999999999999**************************** PP

                        DUF996 110 aglly......fiGaiLtivlvGliil 130
                                   +g+l+      fiGaiL+++  G i++
  gi|70607584|ref|YP_256454.1| 181 GGILIaiyilsFIGAILAVIGTGNILS 207
                                   **9764444447899999999998875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.2
                        DUF996  88 a 88 
                                   a
  gi|70607584|ref|YP_256454.1| 271 A 271
                                   1 PP

>> DUF3273  Protein of unknown function (DUF3273)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  21.6     0.004        24      36     196 ..      19     191 ..      11     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.004
                       DUF3273  36 llflvsissggkglf.aldlvklaeevkvgsaptlvvslliglyllGtlllmvfqvllaDdssiaRGY.......raGsKi 108
                                   +lf+vs + +   lf ++++++   +++v + p ++  +++gl + G+++ +++ +++    +  R Y        aGs +
  gi|70607584|ref|YP_256454.1|  19 ILFIVSSILTVVSLFgSFSYIFSLASSSVLNVPLIISVIISGLAVGGSIIYIISLIMMRRGFKRLREYgrdvgigSAGSLV 99 
                                   33344444444445524666666777788888998888899999999999999999999998888888544444459**** PP

                       DUF3273 109 LklatlldlvssiLslvtllsa.....skyyekkwleelqeggsewilfvfgrlldsfalllyglavfllEvYhdeGagel 184
                                   + +++++ +vs iL +v+++       ++ + + +++ l + g++ i++ ++ l+  ++ +l+g++++ l    ++ + e+
  gi|70607584|ref|YP_256454.1| 100 VLIGSIISIVSYILAIVIFVIFltsasYSLNISTYYTLLSGLGASYIIYLISLLIVVIGQILLGIGFYKLGSVYNDSTTEI 180
                                   ***********9998765432222222333456788999999**************************9986667778887 PP

                       DUF3273 185 lgylnlvlfvla 196
                                    g l + +++l+
  gi|70607584|ref|YP_256454.1| 181 GGILIA-IYILS 191
                                   775543.33444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1386  (0.0773049); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2286.43
//
Query:       gi|70607585|ref|YP_256455.1|  [L=389]
Description: hypothetical protein Saci_1856 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-97  325.9  56.4    4.3e-97  324.9  56.4    1.4  1  DUF973    Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.9  56.4  2.4e-101   4.3e-97       1     310 []       4     388 ..       4     388 .. 0.96

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 2.4e-101
                        DUF973   1 eiegleklregslfliiasllaliliilvlvvlft....aissgl.......sqliqssasilssvlllliaaii..liii 68 
                                   ei+g+eklregslf++i  ll+lili+l++v+++t    a++ gl       +qli+ssasi+++v+ll+++aii  lii+
  gi|70607585|ref|YP_256455.1|   4 EISGMEKLREGSLFYAI--LLILILILLPIVFVGTtfagATVLGLfqqpfssGQLITSSASIVVGVALLPLGAIIsgLIIL 82 
                                   89***************..999********99999888877777799999*9***************************** PP

                        DUF973  69 asvllilgllkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsll..slilslillgviilligiilaliG 147
                                   +sv+l++++++ir +++i+ss ++dv++G+++lt+ilig iii+ig++l+++s++  +li++li+lg+ii  +g+i+++iG
  gi|70607585|ref|YP_256455.1|  83 FSVFLMFYRNSIRGFYAIISSGKSDVKGGVYSLTMILIGGIIIVIGIALLLSSVFspNLIQVLIDLGAIIGGTGFIITSIG 163
                                   *******************************************************999*********************** PP

                        DUF973 148 qillglsfyklGevYnnglikigGiliiipvi........................d............ilsfIGyilsyi 192
                                   +i+lgl++++lG+vY+ng i+++G++i+i+++                        +            ++s+IGy+l++i
  gi|70607585|ref|YP_256455.1| 164 FIILGLDYSNLGRVYSNGGINVSGRMISIAHVlflasfgvilvtsptfttiinginNlttnllgifigvLMSSIGYALDII 244
                                   *********************************999999999988888777766651556677777888************ PP

                        DUF973 193 glgnvlsklrsttsqvpvlqvpstp......qqvqisqvgq....................GtlrsnGtanltvysqvqvq 247
                                   g+ +++s+lr+++++vpv+qv+s+p      qq++i+qv+q                    Gtl+++Gtanl+vysq+++q
  gi|70607585|ref|YP_256455.1| 245 GFLKLYSNLRVSSVSVPVSQVSSMPqqnvvvQQTNIPQVKQqdnisqpnqqtvteqppqnsGTLNRDGTANLIVYSQYPLQ 325
                                   ***************************9*999************************************************* PP

                        DUF973 248 IlsAsiegtnysttsinPntLkvGnNsitinFntvlnLvpgstYtirLlLsngqtidvevtyq 310
                                   IlsAs++g++++t+++nPn+LkvG+N++t+nF+t+l+L+++++Yti+L+Lsngq+++vevty+
  gi|70607585|ref|YP_256455.1| 326 ILSASLSGVGVITNDVNPNQLKVGVNYVTVNFRTPLSLSQEEKYTISLALSNGQIMSVEVTYK 388
                                   **************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 2430.62
//
Query:       gi|70607586|ref|YP_256456.1|  [L=481]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-164  547.3   0.1   2.7e-164  547.1   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.1   0.1  1.5e-168  2.7e-164       9     460 ..      22     468 ..      13     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 547.1 bits;  conditional E-value: 1.5e-168
                                   EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHHHH CS
                        Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaearae 89 
                                     +++P++++++a+++ +++ed+++a+++A eafk+w++l+a++R+e+L k+ + +++++ +l++++  e G ++++a +e
  gi|70607586|ref|YP_256456.1|  22 KVKTSPIDNSPLAEIAVGDREDAKRAIDSAYEAFKGWSSLTAMKRSEYLLKLEETIRANEGDLINTLIVEGGGTYKKAWGE 102
                                   55789**************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHH CS
                        Aldedh  90 veeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPaeetplsa 169
                                   v  + + +r +ae+a++ +ge++ps seg  ++++r+P GvvgaItPWN+Pl+++++k+a+ la GNtvvlK ++etp++ 
  gi|70607586|ref|YP_256456.1| 103 VVFTERLVRNAAEMARHFKGETIPSdSEGIISMTFRKPKGVVGAITPWNYPLSISMKKVAHSLAIGNTVVLKLSSETPIIG 183
                                   *************************77****************************************************** PP

                                   HHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHH CS
                        Aldedh 170 lllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDl 250
                                   +++ael+++aglPkgv+nvvtg+gs vg+++v++++v +v+ftG+t++gr+ia++a+++lk vtlElGG +plivl+daD+
  gi|70607586|ref|YP_256456.1| 184 VKIAELVQRAGLPKGVVNVVTGPGSAVGDEIVTNKRVSHVTFTGETNTGREIASKAGHSLKTVTLELGGSDPLIVLDDADV 264
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTT CS
                        Aldedh 251 dkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvekyveeakeeg 331
                                   + av+ +v+gaf+++GQ+C++ +r++v e++y++fv+k+ve++++lkvgdp+d++ + GPlis++q+e++ ++ e+ +++g
  gi|70607586|ref|YP_256456.1| 265 NLAVKIAVFGAFFHQGQICTSSKRIIVSEKVYEAFVKKFVERVSQLKVGDPRDRTIEQGPLISKRQVESMIEFYEDSVKRG 345
                                   ********************************************************************************* PP

                                   SEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHH CS
                        Aldedh 332 aklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagvftkdleraerv 412
                                    k+++Gg      + +g+++ Ptv+++v+++ ri++eE+FGP+ +v+++kd+eeaie+aNdteyGL+a+v+t++++ra+++
  gi|70607586|ref|YP_256456.1| 346 GKIMTGG------KWDGNYFYPTVVTDVDRNFRIMKEEVFGPIRPVLRVKDDEEAIEVANDTEYGLSAAVVTRNVTRAFKF 420
                                   *******......679***************************************************************** PP

                                   HHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEE CS
                        Aldedh 413 aerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevk 460
                                   +e++e G+v+iNd t  +++++pfgG+k+Sg+Gregg+++++e t  +
  gi|70607586|ref|YP_256456.1| 421 VEQIESGMVHINDVTMLEESHIPFGGIKASGIGREGGEYSFRETTYER 468
                                   *****************************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3204.98
//
Query:       gi|70607587|ref|YP_256457.1|  [L=462]
Description: cytochrome b558/566 subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-30  104.5   0.0    1.5e-29  103.7   0.0    1.4  1  EB_dh     Ethylbenzene dehydrogenase


Domain annotation for each model (and alignments):
>> EB_dh  Ethylbenzene dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   8.6e-34   1.5e-29       3     249 .]      57     402 ..      55     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 8.6e-34
                                   HHHTS-EEEEE-EE--GGGG--S-----EEEEEEEE-SSEEEEEEEEE----............................. CS
                         EB_dh   3 dWskappveislsgqklvipvpgkeevkpvtVkAaydgeniyfrleWkdptk............................. 54 
                                    Ws++p+++isl+ ++++ + p+++ + ++ VkAa++g+ i+++ eW++p++                             
  gi|70607587|ref|YP_256457.1|  57 YWSQIPWTNISLT-ANIPMA-PTSGLTHYLLVKAAWNGSWIFILEEWQAPEPafnawstavagiypnasgpglfrmieltp 135
                                   6*********975.778888.8************************************99999999999999999999999 PP

                                   ........................................................................-S--STT-. CS
                         EB_dh  55 .................................................................salpsevgegkedde. 69 
                                                                                                    +               
  gi|70607587|ref|YP_256457.1| 136 gttyslernytnyvsiingkeetgrivfnysgitlpapnnteitvmsngtillwhsprpvedllyNDG-----------Mf 205
                                   99999999999999999999999888888888888888888777777777777776555555554434...........14 PP

                                   ..........---EEEEEEES...............STT--GGG..............T-BTTB-EEEEEEETT-SS-EEE CS
                         EB_dh  70 ..........yedkvAvmfdddqaGcwg...tchegarglpgapakeeatgsky....mgtagsfvdlwqWkagrseplgl 133
                                             y+d+ A+m++    G+ +   + ++++ + pg+  +    + k+    ++++g  +++w W +g++     
  gi|70607587|ref|YP_256457.1| 206 ygyyvnstwyYPDRAAIMWYL---GSGVptkDDMNIGGKYPGQQFDGI--TFKDaggsLAQSGGSANIWMWVSGATW---- 277
                                   4555555555***********...777755788888888888774433..333345557999999***********8.... PP

                                   EESSTTSEE-GGGGG..........................................................---EEEEE CS
                         EB_dh 134 vddgyvleerqndkgktnytynvenekdepaamf.skegfradd.enesvpfdp....ewkegdt........advkaeak 200
                                           + + d+ ++  +++ e  +    ++   ++gf+    +n++  +      +w++           + + ++ak
  gi|70607587|ref|YP_256457.1| 278 -------NNSTYDPAFKSNIWQNESLT-GLSYVDsGNHGFAVPLyTNNTNMYEVdtagIWYTPVAseglngslFFIWTGAK 350
                                   .......44444455444444322222.222333566666666664444444444455555544466777778******** PP

                                   EETTEEEEEEEEES---TTS.....---TTEEEEEEEEEE-GGGT--TT-SE CS
                         EB_dh 201 ykdGkWtVelvRpLkagnpldv...alepgkvydvafAvwdgkagershhks 249
                                   y++G W+Ve+ RpL  + +++    +++ gk+y+vafAvw+g  ge+  +ks
  gi|70607587|ref|YP_256457.1| 351 YENGSWVVEFARPLSVPLDYQPfmpNITVGKTYYVAFAVWQGRLGETLFDKS 402
                                   *****************99977778*****************9999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3068.58
//
Query:       gi|70607588|ref|YP_256458.1|  [L=310]
Description: cytochrome b558/566 subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1941.47
//
Query:       gi|70607589|ref|YP_256459.1|  [L=325]
Description: hypothetical protein Saci_1860 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.3   0.1    1.7e-07   31.1   0.1    2.1  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   9.3e-12   1.7e-07      19      87 ..     152     263 ..     143     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 9.3e-12
                                   EEETTEEEEEEE-T...........TS-EEEEESC-TTTT-BC................................GGSEEE CS
                        Rieske  19 vkvggeplvvlrde...........dgevyAlsdvCtHrgapl................................segkid 56 
                                   v++  +++v++++            +++++A+s +C+H+g+++                                 + +  
  gi|70607589|ref|YP_256459.1| 152 VEINPTKVVIPQTGktydfpggvgpNKSIVAYSAICQHLGCTPpyihfyppnyvnsgqltasepdqltaaallaaRQAN-- 230
                                   556777777777546677777777789999************9999************999888888777776522222.. PP

                                   TT.EEE-TTT--EEE..TTSBEEE-TTHHHEEE CS
                        Rieske  57 ekgvleCpcHgwayd..adGkvikgPaprplat 87 
                                       ++C cHg++yd  + ++v++gP+ rpl+ 
  gi|70607589|ref|YP_256459.1| 231 VPALIHCDCHGSTYDpyHGASVLTGPTVRPLPA 263
                                   3348***********98899999******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2212.39
//
Query:       gi|70607590|ref|YP_256460.1|  [L=537]
Description: cytochrome b [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-55  185.8   6.4      6e-55  185.8   6.4    3.6  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    5.4e-23   81.8  15.6    5.4e-23   81.8  15.6    2.6  2  Cytochrome_B     Cytochrome b/b6/petB
    2.6e-05   24.5   1.6    2.6e-05   24.5   1.6    3.7  5  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
  ------ inclusion threshold ------
      0.026   14.7   1.7      0.026   14.7   1.7    3.2  4  DUF4079          Protein of unknown function (DUF4079)


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3     0.047   2.1e+02      25      78 ..      32      85 ..      23      89 .. 0.85
   2 !  185.8   6.4   1.3e-58     6e-55       1     169 []      90     275 ..      90     279 .. 0.86
   3 ?   -4.0   5.5       2.9   1.3e+04      64      64 ..     401     401 ..     337     507 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.047
               Cytochrom_B_N_2 25 elnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvel 78
                                  ++n+++G l+    + + + G +L   + + ++ + ++ ii++vP+ + +l + 
  gi|70607590|ref|YP_256460.1| 32 NVNYWLGSLVAAAFIYTVVSGLILLLYYNAEAGYSSTEFIIQKVPYGSVILYSH 85
                                  5799*****************************************955555555 PP

  == domain 2  score: 185.8 bits;  conditional E-value: 1.3e-58
               Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfG 81 
                                   y+miil+y+Hm+r++f GaYkkpRel WiiGv++l+ltl+++flGysL++d+l+++a++vg+giissvP   ++ + +lfG
  gi|70607590|ref|YP_256460.1|  90 YAMIILAYIHMFRNYFAGAYKKPRELLWIIGVIMLVLTLGTAFLGYSLIGDALATSAVDVGEGIISSVPG-LSIFIPILFG 169
                                   79********************************************************************.56669***** PP

               Cytochrom_B_N_2  82 gelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknvvg..........eplvpvnavkmlllflvl. 151
                                   ++  g   + r++a+Hi +++al+++l+++h++++e++g++psr+ ++   +          +p++p+n+v+m++l++++ 
  gi|70607590|ref|YP_256460.1| 170 NYDAGY--YGRVLAWHI-IFVALIGLLFIFHFFMAEHYGIMPSRKVKDRAPAvyareewqkfNPWWPRNFVYMMSLVFLTw 247
                                   ***954..59*******.************************98555544335577777888***********94444333 PP

               Cytochrom_B_N_2 152 .valli.........alalinPvpllgp 169
                                    ++lli         ++ ++nP+ +++p
  gi|70607590|ref|YP_256460.1| 248 gFILLIpnalaylngLPQQLNPFLNPQP 275
                                   5999999966555555557777776665 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.9
               Cytochrom_B_N_2  64 i 64 
                                   i
  gi|70607590|ref|YP_256460.1| 401 I 401
                                   2 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8  15.6   1.2e-26   5.4e-23      11     187 ..      32     203 ..      25     205 .. 0.92
   2 ?   -0.5   2.4      0.21   9.3e+02      67     142 ..     315     388 ..     288     395 .. 0.74

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.2e-26
                  Cytochrome_B  11 siiynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglk 91 
                                   ++ y lGsl+   ++  +++G++l +yy+++    ++s ++i++ v +G +i + h +ga  +++l y+h+fr ++ g++k
  gi|70607590|ref|YP_256460.1|  32 NVNYWLGSLVAAAFIYTVVSGLILLLYYNAE--AGYSSTEFIIQKVPYGSVILYSHLYGAYAMIILAYIHMFRNYFAGAYK 110
                                   56799***********************976..57999******************************************* PP

                  Cytochrome_B  92 ktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffslhfllPf 172
                                   k+rel W+iGvi+l+l++ taf+Gy+L  d ++  av v  +++s++P + +++  +l+g    d     r+ + h+++  
  gi|70607590|ref|YP_256460.1| 111 KPRELLWIIGVIMLVLTLGTAFLGYSLIGDALATSAVDVGEGIISSVPGLSIFI-PILFGNY--DAGYYGRVLAWHIIFVA 188
                                   ************************************************997765.6788876..55567899****99999 PP

                  Cytochrome_B 173 lllillllhllllhk 187
                                   l+ +l + h+++  +
  gi|70607590|ref|YP_256460.1| 189 LIGLLFIFHFFMAEH 203
                                   9*********99766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.21
                  Cytochrome_B  67 angasllflllylhifrglllgglkktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviG 142
                                    +   ll+l+l+  i r+  l    k+r+l    G++++  +i t++ G   p   +s     ++   +++i ++G
  gi|70607590|ref|YP_256460.1| 315 GVIIPLLYLILVPFIDRSPHL--DLKKRRLFTAFGILMVTYLIQTTIFGDLTPGVEISIIQQIIVYLPPAVITLVG 388
                                   455668899999999999888..55666777788999999999999999999999888877777766666666666 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.96   4.3e+03      59      75 ..     108     124 ..      77     140 .. 0.49
   2 ?   -1.2   0.0      0.55   2.5e+03      66      90 ..     188     212 ..     171     220 .. 0.74
   3 !   24.5   1.6   5.7e-09   2.6e-05       9      99 ..     285     377 ..     276     379 .. 0.82
   4 ?   -2.1   0.3       1.1   4.8e+03      71      81 ..     423     433 ..     399     455 .. 0.53
   5 ?   -2.4   0.0       1.4   6.1e+03      64      79 ..     480     495 ..     467     514 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.96
                                   TT-.HHHHHHHHHHHHH CS
                 Cytochrom_B_C  59 ryrkplakvllallvvs 75 
                                   +y+kp   ++++ +++ 
  gi|70607590|ref|YP_256460.1| 108 AYKKPRELLWIIGVIML 124
                                   33322222222222222 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.55
                                   HHHHHHHHHHHHHHHHHHTS-SSCC CS
                 Cytochrom_B_C  66 kvllallvvsfvvLgylGvqppeev 90 
                                    ++ +l++++f++   +G++p ++v
  gi|70607590|ref|YP_256460.1| 188 ALIGLLFIFHFFMAEHYGIMPSRKV 212
                                   3444568888888888888887765 PP

  == domain 3  score: 24.5 bits;  conditional E-value: 5.7e-09
                                   TT-..---GGGHHHHHHHHCSSSHHHHH.HHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS- CS
                 Cytochrom_B_C   9 ahI..aPeWYflpfYaiLraipakllGv.vamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqp 86 
                                   ahI  +P W+fl+ Y+i   +++ l+ + + +++ ++ l+l+p++drs+    ++r  l++++ +l+v+ ++  +++G   
  gi|70607590|ref|YP_256460.1| 285 AHIttYPPWFFLFLYKIADFTNDVLIFLfIGVIIPLLYLILVPFIDRSPHLDLKKR-RLFTAFGILMVTYLIQTTIFGDLT 364
                                   677558************99976664331344556789999***************.899999999999999999***999 PP

                                   SSCCHHHHHHHHH CS
                 Cytochrom_B_C  87 peevavllsqiat 99 
                                   p   + +++qi++
  gi|70607590|ref|YP_256460.1| 365 PGVEISIIQQIIV 377
                                   9888888888865 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHH CS
                 Cytochrom_B_C  71 llvvsfvvLgy 81 
                                   ++vvs  +L++
  gi|70607590|ref|YP_256460.1| 423 TFVVSPSLLTI 433
                                   33333333332 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHH CS
                 Cytochrom_B_C  64 lakvllallvvsfvvL 79 
                                   +a++l+ +l++  vvL
  gi|70607590|ref|YP_256460.1| 480 IAEILISILFILSVVL 495
                                   4444444433333333 PP

>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.7   5.7e-06     0.026      51     137 ..      35     137 ..      25     140 .. 0.83
   2 ?   -1.3   0.1      0.49   2.2e+03      58     130 ..     181     197 ..     175     260 .. 0.60
   3 ?   -2.5   0.1       1.1   5.1e+03      98     128 ..     322     355 ..     303     361 .. 0.51
   4 ?    0.0   0.1      0.19   8.5e+02      36      69 ..     463     496 ..     406     532 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                       DUF4079  51 vklgslllllvvlgaigglvlly.................lrrgklfpssHlyaGlavvvLlalsaalvpeiqkgkstaRt 114
                                   + lgsl+ + ++  ++ gl+ll+                 + +g+ +  sHly + a+++L  + ++        k + R+
  gi|70607590|ref|YP_256460.1|  35 YWLGSLVAAAFIYTVVSGLILLLyynaeagysstefiiqkVPYGSVILYSHLYGAYAMIILAYIHMFRNYFAGAYK-KPRE 114
                                   6677777777777777777777799************99999999***********99999999887666555555.59** PP

                       DUF4079 115 lHialnvlalllfawqaitGlri 137
                                   l  +++v++l+l ++ a+ G ++
  gi|70607590|ref|YP_256460.1| 115 LLWIIGVIMLVLTLGTAFLGYSL 137
                                   *******************9876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.49
                       DUF4079  58 lllvvlgaigglvllylrrgklfpssHlyaGlavvvLlalsaalvpeiqkgkstaRtlHialnvlalllfawq 130
                                    + ++++a++gl++ +                                                        +
  gi|70607590|ref|YP_256460.1| 181 AWHIIFVALIGLLFIF--------------------------------------------------------H 197
                                   4445555555554444........................................................2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                       DUF4079  98 saalvpeiqkgks...taRtlHialnvlalllfa 128
                                    ++lvp i ++ +   + R+l +a ++l++  ++
  gi|70607590|ref|YP_256460.1| 322 YLILVPFIDRSPHldlKKRRLFTAFGILMVTYLI 355
                                   3344444443332213456666666666665555 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.19
                       DUF4079  36 aerkekipkkvrdeHvklgslllllvvlgaiggl 69 
                                   + +  + +++ r+   k++++l++++++++++  
  gi|70607590|ref|YP_256460.1| 463 DAKAVLEKPENRELKKKIAEILISILFILSVVLA 496
                                   3444455677777788888888877777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 3771.55
//
Query:       gi|70607591|ref|YP_256461.1|  [L=97]
Description: hypothetical protein Saci_1862 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.5   0.0    2.2e-14   53.3   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase
    0.00031   19.7   0.8      0.053   12.4   0.2    2.1  2  SOR       Sulphur oxygenase reductase


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   2.4e-18   2.2e-14       1      75 [.       1      75 [.       1      78 [. 0.95

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.4e-18
                                  CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHH CS
                           ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaa 75
                                  m+ v  ++++k+g++++f+++f e+v+ l  +  G +++ l+rs edp+e+++++eW++ ++++++  s+ +k +
  gi|70607591|ref|YP_256461.1|  1 MINVGFYYKIKKGHEKEFEEKFLEIVKILKTTNSGLIEAKLYRSVEDPTEYLMYTEWKDLDSFRNFILSEGYKNT 75
                                  889999*********************9999**********************************9999988875 PP

>> SOR  Sulphur oxygenase reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   5.9e-06     0.053     164     195 ..       8      40 ..       2      46 .. 0.86
   2 !    6.7   0.0   0.00033         3     239     258 ..      44      63 ..      39      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-06
                           SOR 164 htvkeGkekeFeegavetlellke.apGllGym 195
                                   +++k+G+ekeFee+ +e++++lk   +Gl+ + 
  gi|70607591|ref|YP_256461.1|   8 YKIKKGHEKEFEEKFLEIVKILKTtNSGLIEAK 40 
                                   5799*******************9788998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00033
                           SOR 239 aaetPkeylvhveWesleaa 258
                                   + e P+eyl+++eW++l++ 
  gi|70607591|ref|YP_256461.1|  44 SVEDPTEYLMYTEWKDLDSF 63 
                                   5689***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 764.44
//
Query:       gi|70607592|ref|YP_256462.1|  [L=165]
Description: hypothetical protein Saci_1863 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.023   14.9   0.1    1.3  1  DDE_Tnp_1_6  Transposase DDE domain
      0.036   14.0   0.1      0.068   13.1   0.1    1.4  1  DUF4334      Domain of unknown function (DUF4334)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_6  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.6e-06     0.023      25      60 ..     102     142 ..      88     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-06
                   DDE_Tnp_1_6  25 vavyrlkdCrgCplreqCtkk....kkgrqltirpe.lsel 60 
                                   + +++   C+ Cp+++qC        k+  ++i++e  +e+
  gi|70607592|ref|YP_256462.1| 102 NLEFNEYSCTSCPVKNQCVVGmkkvAKENDIKISKEnPREA 142
                                   4468999***********55543365566677766633334 PP

>> DUF4334  Domain of unknown function (DUF4334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.6e-06     0.068      27      58 .]      24      57 ..      22      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-06
                                  EEEEEEETTEEEEEEEETT....-SS-EEEEEEE CS
                       DUF4334 27 DhFRkVdddtvlGamdgkgle..darpyyFvLeR 58
                                  D F + +dd ++ ++++ + +  +++++yF+L R
  gi|70607592|ref|YP_256462.1| 24 DIFQRLSDDKIMKIISSHERQgiSKSYFYFLLDR 57
                                  99***************99845799*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1230.09
//
Query:       gi|70607593|ref|YP_256463.1|  [L=281]
Description: hypothetical protein Saci_1864 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-35  121.5   0.2    3.1e-35  120.9   0.2    1.3  1  Cas6_N       Cas6 N-terminal domain
    9.5e-18   64.6   0.0    1.6e-17   63.9   0.0    1.4  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
  ------ inclusion threshold ------
      0.035   14.6   0.0      0.066   13.7   0.0    1.5  1  Ets          Ets-domain


Domain annotation for each model (and alignments):
>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.2   5.2e-39   3.1e-35       1     113 [.       5     117 ..       5     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 5.2e-39
                                   EEEEEEEEESS-EE--SSTTHHHHHHHHTSSGGGHHHHH---TT-SEEE---BSTTSB--.S------EE-SSSSEEEEEE CS
                        Cas6_N   1 vkatfevtpkrDvilppltSKvskyillslspslsklvesrekyKplrisvlkdngrrly.aegkkkvrlkagerlsfsls 80 
                                   v+a+++v+pk+Dvilp ltSKv+k+il++ ++++ +l+ s++kyK+l+is+l++ngr+ly ++++k++r ++ge+l+f++s
  gi|70607593|ref|YP_256463.1|   5 VSAEIDVIPKHDVILPLLTSKVAKFILSK-NQQIGELIGSKKKYKELSISPLSSNGRFLYaENDGKLLRAMRGEKLHFTFS 84 
                                   57899************************.******************************99999**************** PP

                                   EESSSCCTTTTGSEEEEEETTEEEEEEEEEEEE CS
                        Cas6_N  81 faledvveeivekegvvktvygefsveLkeikv 113
                                   +a+++v+e++++ +g v+t+ygef+v Lk+i++
  gi|70607593|ref|YP_256463.1|  85 VATSEVNEKTFDLDGDVSTSYGEFYVLLKTIYI 117
                                   *******************************98 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   2.6e-21   1.6e-17       1      86 []     134     278 ..     134     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.6e-21
                                   EEEEEEE-EE...............TEEESS--HHHHHHHHHHHHHHHTSS.............................. CS
                   CRISPR_Cas6   1 lrfltPtrfk...............krkgllpsprlvfssllrrwnalaglkgk........................... 39 
                                   lrf++Pt++                + ++l+p+p+l+fs l++ wn++a ++++                           
  gi|70607593|ref|YP_256463.1| 134 LRFESPTLLSnkymvppvfkkkkvrSMNRLIPQPSLIFSFLANLWNSIADERERivkgdlewtpyyigriadvafaeigys 214
                                   79********999999999998887788888********************977887777777777666655555555544 PP

                                   ...EECHHH...........HH.HEEEEEEEE--......HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                   CRISPR_Cas6  40 ...ptveee...........le.gGfvGevkysg......eleelekllrfaeylgvGkktafGlGkv 86 
                                      +    +           ++  GfvG+vky+       +le++e+ll +a+++g+G+++++GlG+v
  gi|70607593|ref|YP_256463.1| 215 lrpV----TviigkdnnqriRQaRGFVGWVKYEVinvnprYLETFERLLGLAKIFGIGRSRGIGLGRV 278
                                   4441....0334444444444444********44445679**************************97 PP

>> Ets  Ets-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.066      26      80 ..      26      83 ..      13      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                           Ets 26 egeFklvdpeevarlWgkrknkpkmnyeklsralRyyy..kk.gilekvkgkrlvYkF 80
                                     F l++++++ +l g +k+ +++++  ls + R+ y  ++ + l+ ++g++l++ F
  gi|70607593|ref|YP_256463.1| 26 VAKFILSKNQQIGELIGSKKKYKELSISPLSSNGRFLYaeNDgKLLRAMRGEKLHFTF 83
                                  5789********************************996444789************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2189.57
//
Query:       gi|70607594|ref|YP_256464.1|  [L=300]
Description: hypothetical protein Saci_1865 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   35.1   0.1    1.6e-08   34.6   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.13   12.1   0.6       0.21   11.4   0.6    1.3  1  Galactosyl_T     Galactosyltransferase
       0.16   11.9   0.0       0.36   10.7   0.0    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.1   2.6e-12   1.6e-08      39     133 ..      10     110 ..       3     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.6e-12
                                   SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH..TTCEEEEEEEE CS
               Glycos_transf_2  39 tDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekd.gadvvlgqrpr 118
                                    D+t e++ee+  ++ ++ vi ++e+     a+n   ++a+ d++l++D+D +pdp+w+ +  ++ ek    +v+ g++ r
  gi|70607594|ref|YP_256464.1|  10 GDRTLEVVEEFK-KYLDIMVIYQNEG-YIEEAMNLIYSNANADLLLTIDDDNIPDPNWVLDHKKFHEKYeMLGVARGKVIR 88 
                                   59*********6.5**********99.****************************************98334556678888 PP

                                   EECCCCCCCHC-SS.......E CS
               Glycos_transf_2 119 ifgetdeiernkrv.......g 133
                                   ++++ ++++  k +       +
  gi|70607594|ref|YP_256464.1|  89 KNQNLNNKKLLKDFakkiiyrQ 110
                                   8888888887777654444442 PP

>> Galactosyl_T  Galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   3.4e-05      0.21      33     131 ..       9      99 ..       2     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                  Galactosyl_T  33 edkkvkelvmeeaklygDivvvdledsYenltlKtltlllwavskvpeaklilkvDdDvyvnpdkLlsllkrelidpsess 113
                                   e++++ e v ee k+y Di+v+  ++ Y +       +++ + s ++ a+l+l +DdD   +p+ +l   k +   ++   
  gi|70607594|ref|YP_256464.1|   9 EGDRTLE-VVEEFKKYLDIMVIYQNEGYIEE------AMNLIYSNAN-ADLLLTIDDDNIPDPNWVLDHKKFHEKYEMLGV 81 
                                   5566677.7899999*************996......5899999999.9**********9999999988777766777788 PP

                  Galactosyl_T 114 vygkvlkegavirkkksk 131
                                     gkv+++++++ +kk  
  gi|70607594|ref|YP_256464.1|  82 ARGKVIRKNQNLNNKKLL 99 
                                   889999998888888754 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.9e-05      0.36      43     121 ..      11      80 ..       2     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.9e-05
               Glyco_tranf_2_3  43 aetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavg 121
                                   + tlev+ee+    ++  +++ v ++n g     +a+n  +++++ dl+l +DdD++ +P+ +     f  ++k++++g
  gi|70607594|ref|YP_256464.1|  11 DRTLEVVEEF----KK-YLDIMVIYQNEG--YIEEAMNLIYSNANADLLLTIDDDNIPDPNWVLDHKKF--HEKYEMLG 80 
                                   5567777774....43.234444445556..4558899999*******************986654444..46666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1920.70
//
Query:       gi|70607595|ref|YP_256465.1|  [L=219]
Description: hypothetical protein Saci_1866 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.21   12.0   4.1          9    6.8   0.2    2.4  2  HRG       Haem-transporter, endosomal/lysosomal, haem-respons


Domain annotation for each model (and alignments):
>> HRG  Haem-transporter, endosomal/lysosomal, haem-responsive gene
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0005         9       5      25 ..      66      86 ..      64     109 .. 0.91
   2 ?    6.2   0.5   0.00078        14       7      28 ..     136     155 ..     132     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0005
                           HRG  5 iaygifgsilglsaflvylvl 25
                                  i +g + + +gl+ f vy++l
  gi|70607595|ref|YP_256465.1| 66 IIVGSILLSIGLVYFGVYIAL 86
                                  88999999***********87 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00078
                           HRG   7 ygifgsilglsaflvylvlaiv 28 
                                   +g +++++ + +f++ l++  +
  gi|70607595|ref|YP_256465.1| 136 FGNLFILMTVLWFIAGLFI--Y 155
                                   7889***********9998..4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1493.92
//
Query:       gi|70607596|ref|YP_256466.1|  [L=269]
Description: hypothetical protein Saci_1867 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-06   26.3  11.9     0.0044   17.5   3.0    2.7  2  DUF16           Protein of unknown function DUF16
    1.5e-05   24.6   5.0    9.2e-05   22.0   5.0    2.0  1  HBM             Helical bimodular sensor domain
    3.3e-05   24.1   9.1     0.0055   16.9   1.5    2.4  2  Fib_alpha       Fibrinogen alpha/beta chain family
    3.5e-05   23.9   4.6    0.00035   20.6   0.2    3.4  3  DUF3782         Protein of unknown function (DUF3782)
    5.9e-05   23.0   6.7    0.00018   21.4   2.9    2.2  2  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
    7.7e-05   22.6  16.4     0.0073   16.3   3.3    3.0  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
    0.00015   21.9   6.6    0.00053   20.2   1.4    2.3  3  DUF948          Bacterial protein of unknown function (DUF948
    0.00021   21.9   7.0      0.065   13.9   1.1    2.6  2  SlyX            SlyX
    0.00043   20.3   8.7      0.006   16.6   5.1    2.3  2  DUF1664         Protein of unknown function (DUF1664)
     0.0005   19.0   1.7    0.00067   18.6   1.7    1.3  1  ALMT            Aluminium activated malate transporter
    0.00052   19.0   9.0    0.00074   18.5   9.0    1.2  1  Spc7            Spc7 kinetochore protein
    0.00092   17.5   5.3     0.0013   17.0   5.3    1.2  1  EzrA            Septation ring formation regulator, EzrA
      0.001   19.5   4.4       0.16   12.5   0.8    2.9  2  NPV_P10         Nucleopolyhedrovirus P10 protein
      0.002   17.7   8.7     0.0031   17.0   8.7    1.2  1  HMMR_N          Hyaluronan mediated motility receptor N-termi
     0.0021   15.7   5.0     0.0025   15.4   5.0    1.1  1  DUF3584         Protein of unknown function (DUF3584)
     0.0024   18.1   9.5       0.19   12.0   1.4    2.4  2  FliJ            Flagellar FliJ protein
     0.0025   17.0   7.5     0.0034   16.5   7.5    1.2  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
     0.0026   17.4   2.4     0.0033   17.0   2.4    1.1  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.003   17.2   8.8     0.0054   16.4   8.5    1.5  1  Lebercilin      Ciliary protein causing Leber congenital amau
     0.0033   17.8   6.7        1.9    8.9   0.3    3.2  3  DUF2383         Domain of unknown function (DUF2383)
     0.0038   17.5   9.2      0.021   15.0   8.0    2.0  1  ATG16           Autophagy protein 16 (ATG16)
     0.0042   15.8   8.8     0.0087   14.8   8.8    1.4  1  AAA_13          AAA domain
     0.0044   17.4   7.3      0.097   13.0   0.8    2.5  2  CC2-LZ          Leucine zipper of domain CC2 of NEMO, NF-kapp
     0.0051   16.0   4.9     0.0091   15.2   4.9    1.3  1  FH2             Formin Homology 2 Domain
     0.0051   16.1   7.1      0.007   15.7   7.1    1.2  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
     0.0058   14.7   2.9     0.0076   14.3   2.9    1.2  1  Prominin        Prominin
      0.006   15.9   4.7     0.0088   15.3   4.7    1.3  1  ISG65-75        Invariant surface glycoprotein
     0.0065   14.5   2.0     0.0067   14.4   2.0    1.1  1  V_ATPase_I      V-type ATPase 116kDa subunit family
     0.0074   16.2   7.0       0.56   10.0   1.3    2.3  2  Spc29           Spindle Pole Component 29
     0.0075   16.0   6.9       0.42   10.4   0.3    2.7  2  DASH_Duo1       DASH complex subunit Duo1
     0.0087   15.4   2.6      0.016   14.5   2.6    1.4  1  CorA            CorA-like Mg2+ transporter protein
     0.0087   15.9   4.2       0.46   10.3   0.3    2.8  2  PhageMin_Tail   Phage-related minor tail protein
     0.0089   15.0   9.9      0.014   14.4   9.9    1.3  1  DUF812          Protein of unknown function (DUF812)
  ------ inclusion threshold ------
      0.011   15.8   8.2      0.011   15.8   8.2    1.8  1  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.011   16.0   8.6        0.4   11.0   4.7    2.5  2  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.012   15.4   7.7       0.12   12.2   7.3    2.1  2  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
      0.014   14.4   4.7      0.024   13.6   4.7    1.6  1  Vps53_N         Vps53-like, N-terminal
      0.014   15.1   2.4      0.021   14.5   2.4    1.3  1  DUF713          Protein of unknown function (DUF713)
      0.014   15.6   3.3        1.2    9.5   1.1    2.5  2  Phasin_2        Phasin protein
      0.015   15.2   2.1      0.081   12.9   0.6    2.2  2  DUF1759         Protein of unknown function (DUF1759)
      0.017   14.4   8.6       0.19   11.0   1.7    2.1  2  FmiP_Thoc5      Fms-interacting protein/Thoc5
      0.017   15.2  10.0      0.037   14.1  10.0    1.6  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
      0.018   14.7   5.6      0.023   14.4   2.2    2.2  2  CCDC85          CCDC85 family
      0.024   14.0   9.2      0.073   12.4   9.2    1.7  1  GAS             Growth-arrest specific micro-tubule binding
      0.024   14.3   6.6       0.11   12.1   6.6    1.9  1  LXG             LXG domain of WXG superfamily
      0.031   14.1   6.9      0.049   13.4   6.9    1.3  1  Mer2            Mer2
      0.036   13.5   9.6      0.061   12.7   9.6    1.3  1  DUF4618         Domain of unknown function (DUF4618)
       0.04   13.0   6.5      0.098   11.7   6.5    1.6  1  APG17           Autophagy protein Apg17
       0.04   13.3   3.0       0.25   10.7   2.7    2.0  1  Helo_like_N     Fungal N-terminal domain of STAND proteins
      0.041   13.0   1.3       0.06   12.4   1.3    1.3  1  FUSC-like       FUSC-like inner membrane protein yccS
      0.044   14.2   5.3          3    8.3   0.8    3.1  2  FlaC_arch       Flagella accessory protein C (FlaC)
      0.046   13.9   4.1        1.2    9.3   1.9    2.2  2  DUF2959         Protein of unknown function (DUF2959)
      0.048   13.6   8.7       0.41   10.6   2.7    2.3  2  PhaP_Bmeg       Polyhydroxyalkanoic acid inclusion protein (P
      0.048   13.7   9.6       0.28   11.3   8.8    2.1  2  ADIP            Afadin- and alpha -actinin-Binding
      0.048   12.6   6.3      0.083   11.8   6.3    1.4  1  IFT57           Intra-flagellar transport protein 57
      0.053   14.2   0.7          1   10.0   0.1    2.5  2  Pinin_SDK_N     pinin/SDK conserved region
      0.055   13.8  11.4          2    8.8   2.9    3.0  2  Csm1_N          Csm1 N-terminal domain
      0.055   13.1   6.2       0.57    9.8   3.7    2.3  2  TEX13           Testis-expressed sequence 13 protein family
       0.06   13.0   9.5          1    8.9   1.3    2.3  2  DUF4795         Domain of unknown function (DUF4795)
       0.06   13.7   0.3       0.09   13.1   0.3    1.4  1  Senescence      Senescence-associated protein
      0.064   13.7   5.9        7.6    7.0   5.7    3.0  2  MitMem_reg      Maintenance of mitochondrial structure and fu
      0.065   11.5   3.3        2.5    6.3   0.5    2.1  2  Fusion_gly      Fusion glycoprotein F0
      0.067   13.3   4.2          3    8.0   2.8    2.5  2  Vps51           Vps51/Vps67
      0.079   12.5   9.4       0.13   11.8   9.4    1.3  1  PspA_IM30       PspA/IM30 family
      0.085   12.2  10.8       0.46    9.8   2.6    2.2  2  Rab5-bind       Rabaptin-like protein
      0.089   12.5   0.3       0.17   11.6   0.2    1.6  1  BAG6            BCL2-associated athanogene 6
      0.091   12.4   2.5       0.16   11.6   1.9    1.6  1  TMP_2           Prophage tail length tape measure protein
      0.092   13.2   6.8       0.15   12.5   6.8    1.4  1  Fez1            Fez1
      0.099   13.2   4.8        3.2    8.4   4.8    2.7  1  Syntaxin-6_N    Syntaxin 6, N-terminal
       0.11   12.8   0.6        1.6    9.1   0.0    2.4  2  Retrotrans_gag  Retrotransposon gag protein
       0.11   11.1   2.5       0.14   10.8   2.5    1.1  1  Peptidase_S46   Peptidase S46
       0.11   13.0  10.5      0.051   14.1   7.2    1.9  1  FlgN            FlgN protein
       0.11   11.3   1.2       0.16   10.8   1.2    1.1  1  Glypican        Glypican
       0.12   11.6   7.3       0.24   10.6   7.0    1.7  2  TMPIT           TMPIT-like protein
       0.12   12.7   2.0        5.1    7.5   0.1    2.8  2  ATG_C           Autophagy-related protein C terminal domain
       0.12   12.0   5.1       0.54    9.9   1.4    2.3  2  RPW8            Arabidopsis broad-spectrum mildew resistance 
       0.12   11.6   0.7        0.2   10.9   0.7    1.5  1  CmlA_N          Diiron non-heme beta-hydroxylase N-terminal d
       0.13   12.2   9.1       0.24   11.3   1.4    2.9  4  Prefoldin       Prefoldin subunit
       0.15   12.3   7.1        1.6    8.9   6.2    2.3  2  SMBP            Small metal-binding protein
       0.15   12.2   7.2        1.8    8.7   1.3    2.8  2  COG5            Golgi transport complex subunit 5
       0.16   10.8   4.2       0.28   10.0   4.2    1.4  1  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
       0.21   11.6   3.5        1.8    8.6   1.1    3.5  2  NEMO            NF-kappa-B essential modulator NEMO
       0.22   11.5   8.7       0.41   10.6   4.0    2.4  2  Cauli_AT        Aphid transmission protein
       0.22   11.7   5.7       0.79    9.9   5.7    1.8  1  CREPT           Cell-cycle alteration and expression-elevated
       0.27   11.2  12.8       0.27   11.2   3.7    2.2  2  JAKMIP_CC3      JAKMIP CC3 domain
       0.29    9.6   2.3       0.76    8.2   2.2    1.7  1  Corona_S2       Coronavirus S2 glycoprotein
       0.32   10.9   5.5       0.99    9.3   3.1    2.5  3  Sec34           Sec34-like family
       0.34   10.6  10.5          1    9.0  10.3    2.0  2  YkyA            Putative cell-wall binding lipoprotein
       0.34    9.5   2.2       0.47    9.0   2.2    1.2  1  Tweety          Tweety
       0.34   10.2   6.2       0.64    9.3   6.2    1.3  1  DUF4407         Domain of unknown function (DUF4407)
       0.37   11.3   9.0        4.4    7.8   2.3    2.3  2  Spectrin        Spectrin repeat
       0.41   10.8   8.4        5.8    7.1   1.2    2.5  2  BRE1            BRE1 E3 ubiquitin ligase
       0.41   10.3   6.2        9.2    6.0   0.6    3.3  3  DUF2312         Uncharacterized protein conserved in bacteria
       0.42    9.3   8.2          1    8.0   8.2    1.5  1  Tektin          Tektin family
       0.52   10.0   5.3       0.64    9.7   2.6    2.0  2  ZapD            Cell division protein
       0.61   10.8   3.9        2.5    8.9   0.3    2.8  2  Occludin_ELL    Occludin homology domain
       0.75    9.9   6.9        3.2    7.9   3.0    2.3  2  COG2            COG (conserved oligomeric Golgi) complex comp
       0.78    9.6   6.7        2.8    7.8   0.5    2.3  2  Sec8_exocyst    Sec8 exocyst complex component specific domai
       0.86    8.8  10.5        3.3    6.9  10.5    1.8  1  HemX            HemX, putative uroporphyrinogen-III C-methylt
       0.92    9.7  10.4        3.9    7.7  10.1    2.2  2  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
       0.94    9.3   4.5        2.4    8.0   0.4    2.3  2  GP41            Retroviral envelope protein
       0.96    9.8   9.0        8.5    6.7   0.6    2.3  2  DUF641          Plant protein of unknown function (DUF641)
        1.3    9.1   9.4        4.7    7.2   8.1    2.3  2  Laminin_II      Laminin Domain II
        1.3    8.7   7.6        3.5    7.3   2.7    2.3  2  Med4            Vitamin-D-receptor interacting Mediator subun
        1.4    9.2   7.1        1.9    8.7   0.6    2.8  3  XhlA            Haemolysin XhlA
        1.4    8.7  10.2        1.9    8.4   7.5    2.2  2  DUF2570         Protein of unknown function (DUF2570)
        1.5    9.1  11.4        9.9    6.4  11.5    2.3  1  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
        1.9    8.9   6.8        7.2    7.1   1.1    3.4  3  LPP             Lipoprotein leucine-zipper
          2    8.7   9.6        1.4    9.2   5.8    1.8  2  zf-C4H2         Zinc finger-containing protein
          2    8.7   5.8         16    5.9   2.5    2.7  2  Rx_N            Rx N-terminal domain
        2.2    8.3   6.9        3.8    7.6   0.5    3.2  3  DUF4298         Domain of unknown function (DUF4298)
        2.2    8.4   6.6        1.3    9.2   0.7    3.1  3  DUF5595         Domain of unknown function (DUF5595)
        2.3    8.4  11.0        9.4    6.4   2.7    2.3  2  Tropomyosin_1   Tropomyosin like
        2.6    8.8   7.8         14    6.4   6.5    2.4  2  DUF2203         Uncharacterized conserved protein (DUF2203)
          5    7.8   6.7         13    6.5   1.1    2.7  2  YabA            Initiation control protein YabA
        5.1    7.3  10.5         11    6.2   3.7    2.8  2  Med9            RNA polymerase II transcription mediator comp


Domain annotation for each model (and alignments):
>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.0   2.8e-05    0.0044      34      91 ..      37      94 ..       5     101 .. 0.59
   2 !   12.0   5.0    0.0014      0.22      41      97 ..      93     149 ..      85     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.8e-05
                                  HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHH CS
                         DUF16 34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelilet 91
                                  +rL++  + ++ l++ i  le++v++qg  ik l++++k+ +e++  ++e+++   e+
  gi|70607596|ref|YP_256466.1| 37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEI 94
                                  4555555556666666666666666666666666666666666655444444443333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0014
                                   HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                         DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkink 97 
                                   + ++ + e i+ l+++v++  e ik l++ +k+ ++++++v +    +   + ++ +
  gi|70607596|ref|YP_256466.1|  93 EILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTN 149
                                   456788999999999999999999999999999999999888866666666666655 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   5.0     6e-07   9.2e-05      43     145 ..       9     111 ..       1     168 [. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6e-07
                                   HHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           HBM  43 aaavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleaevl 123
                                    +++ +  + ++++  k+++++k++  +++L+e ++++ ++++    l++a++++  + ++l+++ ++ +eai +l++ v 
  gi|70607596|ref|YP_256466.1|   9 VKKLLEDPKFISTLASKIYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVK 89 
                                   44444444567888999**************************************************************** PP

                                   CS-S-HHHHHHHHHHHHHHHHH CS
                           HBM 124 qtpeadserlaqlqaiaelkrq 145
                                   q+ e   e ++ +++++e+ +q
  gi|70607596|ref|YP_256466.1|  90 QQGEILREHSEAIKSLQETVKQ 111
                                   *998765555555555544443 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.5   3.6e-05    0.0055      54     129 ..      19      92 ..       6      97 .. 0.78
   2 !   11.1   1.4    0.0022      0.34      88     123 ..     100     135 ..      93     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  54 aeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                   +++l ++i+d l+++   k+  ++ + +  ++l++ i+ l+e + +q  +i+ Lq+++++ ++ i  L+++++q+ 
  gi|70607596|ref|YP_256466.1|  19 ISTLASKIYDRLKDEVVIKR-LEENT-EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQG 92 
                                   55666667777766666655.34444.444678899*************************************985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0022
                                   HCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  88 eeilrlketidaqesnirvLqnvlesneqkiqkLeq 123
                                   e i  l+et++++ + i+ Lq+ +++++++i++  +
  gi|70607596|ref|YP_256466.1| 100 EAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   356677777877778888888888877777777655 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3       4.1   6.4e+02       6      20 ..      56      70 ..      27      86 .. 0.56
   2 ?    3.5   0.8      0.52        80       9      33 ..      91     118 ..      65     119 .. 0.69
   3 !   20.6   0.2   2.3e-06   0.00035       2      74 ..     115     189 ..     100     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 4.1
                       DUF3782  6 leeeeeetkedleel 20
                                  lee  +++   ++ l
  gi|70607596|ref|YP_256466.1| 56 LEEAVRQQGGSIKSL 70
                                  333344444444444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.52
                       DUF3782   9 e...eeetkedleelekeieklertiga 33 
                                   +    +e++e ++ l++ +++++++i+ 
  gi|70607596|ref|YP_256466.1|  91 QgeiLREHSEAIKSLQETVKQHSEAIKG 118
                                   2334777888888888888887777765 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 2.3e-06
                       DUF3782   2 elekleeeeeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv...kVekwlyyDkeGeV 74 
                                    ++ l+e  +++++d++e++k   kl++ ig+   R G   E+++   +ke+Le   g+   kV+  +++D+ G++
  gi|70607596|ref|YP_256466.1| 115 AIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNRAGKGLEKTIMMVYKEALELH-GIdpnKVKHGNIVDTLGII 189
                                   56778999************************************************.**999*********99986 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   2.9   1.2e-06   0.00018      85     175 ..      24     117 ..      14     119 .. 0.90
   2 ?    3.5   0.1      0.37        57     114     146 ..     119     151 ..     117     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-06
                  Bacillus_HBL  85 qsyyktlveavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdskn...Fktdvdeltsilagdsgvisq 162
                                   +++y+ l+  v  k  +e +e++ +Lq++i+  +++v+q+ + +k+l++ +++ s+    ++++v++  +il   s  i+ 
  gi|70607596|ref|YP_256466.1|  24 SKIYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAirgLQEAVKQQGEILREHSEAIKS 104
                                   5789999999999999**************************99999999999987633378999**************** PP

                  Bacillus_HBL 163 lqneiedlqgkik 175
                                   lq+++++  ++ik
  gi|70607596|ref|YP_256466.1| 105 LQETVKQHSEAIK 117
                                   *********9998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.37
                  Bacillus_HBL 114 iqqnqkevkqlikeLkklklklakdsknFktdv 146
                                   +q+  k+  ++ike++kl  kl  +  +F++ +
  gi|70607596|ref|YP_256466.1| 119 LQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNRA 151
                                   556667777788888888888888888888776 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   4.6   0.00063     0.098       4      69 ..      36     101 ..      33     106 .. 0.90
   2 !   16.3   3.3   4.7e-05    0.0073      22      70 ..     103     151 ..      93     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00063
                    TMF_DNA_bd   4 ekklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                    k l+e  e I +L++  + L+   +++  +ik+L++++k++ + i+ l++ ++++ + l e++e 
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEA 101
                                   68899999*******************************************999998888777765 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4.7e-05
                    TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                   + L+ +  +++++ik L++ +k+l ++ike +k + kl+ e+ + ++r+
  gi|70607596|ref|YP_256466.1| 103 KSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNRA 151
                                   4567777777788888888888888777777777777777777777766 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3    0.0014      0.21      26      84 ..      37      95 ..      33     100 .. 0.93
   2 !   20.2   1.4   3.4e-06   0.00053      21      88 ..      67     134 ..      64     135 .. 0.84
   3 !   10.4   0.4     0.004      0.61      21      57 ..     102     138 ..      98     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0014
                        DUF948 26 ktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84
                                  k l+e++++i++l++ + ++ + v++    ++ l+e v++++e++  l eav++ ge +
  gi|70607596|ref|YP_256466.1| 37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEIL 95
                                  6789*************************************************999865 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.4e-06
                        DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                   +++l++t+++ +++i++l++ v++  + +++  + ++ l+e v++++e+++ l eav++l++ ++e++
  gi|70607596|ref|YP_256466.1|  67 IKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   789****************7666666666666666666666***********************9986 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.004
                        DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvn 57 
                                   +++l++t+++ +++i++l++ v++++++++++ + + 
  gi|70607596|ref|YP_256466.1| 102 IKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTI 138
                                   6677777777777777777777777777777666555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.1   0.00042     0.065       2      52 ..      50     100 ..      36     104 .. 0.86
   2 !   11.8   1.2    0.0019      0.29      16      52 ..      99     135 ..      93     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00042
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                   ++ ++ LE+ +  q   i++L+++v ++ + i  lq+ +++  e l+e +e
  gi|70607596|ref|YP_256466.1|  50 QQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSE 100
                                   677888999999999999999999999999999999999998888887766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    ++i++L+++v ++ + i+ lq+ +++l + +ke+++
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   5789****************************99876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.6    0.0022      0.34      71     120 ..      35      84 ..       4      86 .. 0.85
   2 !   16.6   5.1   3.9e-05     0.006      55     121 ..      68     134 ..      66     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0022
                       DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                   v k+l+e++e+++++++ ++ ++e +++ g  ++s++e+v++  + ++ +
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGL 84 
                                   6689************************************9988877655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.9e-05
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   +sl++t ++ s+ i  +++ +++q ei +e +e +++++e +++ +e ++ ++eav++l + +++++
  gi|70607596|ref|YP_256466.1|  68 KSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   688999999999*************************************************999986 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.7   4.3e-06   0.00067     261     356 ..      54     142 ..      14     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.3e-06
                          ALMT 261 vkvggvlrqcaytvealhgcilseiqapeelrkkfkeelqrvslesakvlrelaesvkkmkklsk.veellkevkvaaeeL 340
                                   + + +++rq + ++++l+  +++  +a + l++++k        +++++lre +e++k  ++  k  +e +k ++ a+++L
  gi|70607596|ref|YP_256466.1|  54 MGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVK--------QQGEILREHSEAIKSLQETVKqHSEAIKGLQEAVKQL 126
                                   445566777777777777777666666666655555........55666666666666555444435677889******** PP

                          ALMT 341 qskldskskLlvnsek 356
                                    + +++ skL ++ ++
  gi|70607596|ref|YP_256466.1| 127 SNDIKEVSKLTIKLST 142
                                   *********9987544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   9.0   4.8e-06   0.00074     148     304 ..       9     169 ..       2     175 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.8e-06
                          Spc7 148 legleedkelLekqeeel.dellpele.eekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkela 223
                                   +++l ed + ++   +++ d+l++e++ ++ +e +e +++lq+    le+    +  ++++l+e+++++++ i+ +++ ++
  gi|70607596|ref|YP_256466.1|   9 VKKLLEDPKFISTLASKIyDRLKDEVViKRLEENTEAIRNLQQGIMGLEEavrQQGGSIKSLQETVKQHSEAIRGLQEAVK 89 
                                   556666666666666655455555543256666666677777744444443324567788888888888888888888888 PP

                          Spc7 224 elqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevk.aleeltgwkivslsgstleltyrsele 303
                                   +  e l e +e+i++l+e  +++ e+i+  ++ ++ + + + +evs+l+ +++ ++ ++t+ +  +l ++t+ ++y+++le
  gi|70607596|ref|YP_256466.1|  90 QQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVK-QLSNDIKEVSKLTIKLStEIGSFTNRAGKGL-EKTIMMVYKEALE 168
                                   88888888888888888888888888887777776.4456677777777666524555555555555.4447777777776 PP

                          Spc7 304 v 304
                                   +
  gi|70607596|ref|YP_256466.1| 169 L 169
                                   5 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   5.3   8.7e-06    0.0013      88     206 ..      31     147 ..      18     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.7e-06
                                   T--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHH CS
                          EzrA  88 eelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelek 168
                                   ++ +  +++ + ++++++l++ +  +ee +++    +k l+e  ++++e+i  l+e  ++  + l++++++ ++ +e++++
  gi|70607596|ref|YP_256466.1|  31 KDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQ 111
                                   55666678899999******************************************************************* PP

                                   HHHHH----------------HHHHHHHHHHHHHHHHH CS
                          EzrA 169 qleniekefsefeeltengdyveakeilkkleeeidel 206
                                   + e+i+   ++ ++l  ++d +e+++++ kl++ei ++
  gi|70607596|ref|YP_256466.1| 112 HSEAIKGLQEAVKQL--SNDIKEVSKLTIKLSTEIGSF 147
                                   *99999999999998..5899*********99999876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.7     0.039         6      12      66 ..      45      96 ..       9     111 .. 0.74
   2 !   12.5   0.8     0.001      0.16      10      45 ..     106     141 ..      99     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.039
                       NPV_P10 12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                  +i+++++ +  l+++v +    +   + l+e + + s+++  l+++v++  +iL 
  gi|70607596|ref|YP_256466.1| 45 AIRNLQQGIMGLEEAVRQQGGSI---KSLQETVKQHSEAIRGLQEAVKQQGEILR 96
                                  66666666666666665544444...44777777777777777777777777775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.001
                       NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLd 45 
                                    + +k+ ++ ++ lq++v+++++++++v++l+ kL 
  gi|70607596|ref|YP_256466.1| 106 QETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLS 141
                                   567999999***********************9996 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   8.7     2e-05    0.0031     193     315 ..      34     145 ..      19     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2e-05
                        HMMR_N 193 vtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLee 273
                                   v+ k Lee  +++++L++ ++ le+   ++   ++ l e +++ s++++ l   ++ ++q  e+l e+ + i+sL++++++
  gi|70607596|ref|YP_256466.1|  34 VVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGL---QEAVKQQGEILREHSEAIKSLQETVKQ 111
                                   667889999999*****9999999999999999999999999999999999...99999999*****99999999998887 PP

                        HMMR_N 274 keqelskqvkdlnekckllekekeelvreeeekeqtlsaEle 315
                                    ++     +k l+e +k+l ++ +    e  + + +ls+E++
  gi|70607596|ref|YP_256466.1| 112 HSE----AIKGLQEAVKQLSNDIK----EVSKLTIKLSTEIG 145
                                   776....89999999999988887....34444555666665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   5.0   1.6e-05    0.0025     640     773 ..      39     178 ..       8     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                       DUF3584 640 kravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekka 720
                                    ++ +ea+++l++    le +  ++    + l++ ++++ ++  + lq+  +q++ +++++ +a++ l+e++++++ e  +
  gi|70607596|ref|YP_256466.1|  39 LEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEA-IRGLQEAVKQQGEILREHSEAIKSLQETVKQHS-EAIK 117
                                   456678888888888888888888888888888888777655.467788888888999999*************99.9999 PP

                       DUF3584 721 kwqevvgeldeqlaelkkaieaartq....akarlkeleea....ykreLkskdvDpetvk 773
                                    +qe v +l++ ++e++k   +  t+     ++  k le+     yk+ L+  ++Dp++vk
  gi|70607596|ref|YP_256466.1| 118 GLQEAVKQLSNDIKEVSKLTIKLSTEigsfTNRAGKGLEKTimmvYKEALELHGIDPNKVK 178
                                   9**************9999888887633322333444544322228999999999999996 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.4    0.0012      0.19      34      82 ..      38      81 ..      27      90 .. 0.82
   2 ?    7.9   6.2     0.022       3.4      18      92 ..      78     133 ..      71     144 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0012
                          FliJ 34 qlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82
                                  +l++++     +++rn+q+ i+ l+ea+ qq  +++ +++ v++  e+ 
  gi|70607596|ref|YP_256466.1| 38 RLEENT-----EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAI 81
                                  555555.....8999************************9999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.022
                          FliJ  18 eekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkl 92 
                                    e +  l++                     ++  + ++   eai++++++++q+ ++++  +e+ ++     k +
  gi|70607596|ref|YP_256466.1|  78 SEAIRGLQEA-------------------VKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEV 133
                                   3333333333...................3333444444444444444444444444444444444444444443 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   7.5   2.2e-05    0.0034      58     157 ..      35     140 ..       8     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-05
                         Atg14  58 ledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk.......kRrsdleslqneleerrkk 131
                                     ++++ +++++++l++ i  l+e +++   ++++l++ +++ ++ +++l++++k       +  + ++slq+ +++ + +
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKqqgeilrEHSEAIKSLQETVKQ-HSE 114
                                   55778889999999999999999999999999999999999999999999999997777764444445555555544.456 PP

                         Atg14 132 qiaklqdaikrieqklsslssktles 157
                                    i++lq+a+k+ ++ ++++s++t++ 
  gi|70607596|ref|YP_256466.1| 115 AIKGLQEAVKQLSNDIKEVSKLTIKL 140
                                   67778888888888888888777764 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.4   2.2e-05    0.0033     163     253 ..      38     137 ..       9     185 .. 0.41

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.2e-05
                  Exonuc_VII_L 163 lleekkqrleklasrl..............kspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekk 229
                                   +lee+ + +++l++ +              ks +e +++++++++ l+e +++ + + l++++e++++l+e    ++++++
  gi|70607596|ref|YP_256466.1|  38 RLEENTEAIRNLQQGImgleeavrqqggsiKSLQETVKQHSEAIRGLQEAVKQ-QGEILREHSEAIKSLQE----TVKQHS 113
                                   33333333333333330000000000000033333333333333333333333.22233333333333332....222222 PP

                  Exonuc_VII_L 230 erlkklkerlelleekkerleele 253
                                   e +k l+e +++l++  +++++l+
  gi|70607596|ref|YP_256466.1| 114 EAIKGLQEAVKQLSNDIKEVSKLT 137
                                   222222222222222222222222 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.5   3.5e-05    0.0054       7     102 ..      40     135 ..      34     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-05
                    Lebercilin   7 sarllkikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerele 87 
                                    ++++ i +Lq+ +  l++ +++     k L++  k +++a++ ++++ ++  ++l++h+e ++ l+e ++++ e+ + l+
  gi|70607596|ref|YP_256466.1|  40 EENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQ 120
                                   567788999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                    Lebercilin  88 kklkekeaellrlkd 102
                                   + +k+  ++++++++
  gi|70607596|ref|YP_256466.1| 121 EAVKQLSNDIKEVSK 135
                                   999999999888766 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.84   1.3e+02      20      65 ..      19      64 ..       6      69 .. 0.72
   2 ?    8.5   1.8     0.015       2.4      34      64 ..      68      98 ..      35     102 .. 0.73
   3 ?    8.9   0.3     0.012       1.9      34      72 ..     103     141 ..      96     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.84
                                  HHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT------- CS
                       DUF2383 20 ykeaaekvkdpqlktlleriaeereeaaeeLqseiralggepedgg 65
                                   ++ a k+ d    ++  ++ ee +ea+++Lq+ i  l +  +++g
  gi|70607596|ref|YP_256466.1| 19 ISTLASKIYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQG 64
                                  5666777776666678888889999999999999888887766663 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.015
                                  HHHHHHHHHHHHHHHHHHHHHHHCT------ CS
                       DUF2383 34 tlleriaeereeaaeeLqseiralggepedg 64
                                  + l++ +++++ea++ Lq+ ++++g+  +++
  gi|70607596|ref|YP_256466.1| 68 KSLQETVKQHSEAIRGLQEAVKQQGEILREH 98
                                  45899********************977776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHCT-------------- CS
                       DUF2383  34 tlleriaeereeaaeeLqseiralggepedggslagklh 72 
                                   + l++ +++++ea++ Lq+ +++l  + ++ + l+ kl 
  gi|70607596|ref|YP_256466.1| 103 KSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLS 141
                                   56899*******************999998888887776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   8.0   0.00014     0.021      79     159 ..      49     129 ..      41     152 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 0.00014
                         ATG16  79 leqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                   l+q +  l e + +   s   l++ +++ +e+++ l+e  k++ e l+e ++ +++l++ +k++ e++++++++v++l  +
  gi|70607596|ref|YP_256466.1|  49 LQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSND 129
                                   444444444444444444445666666666666677777777777777777777777777777777777776666666543 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   8.8   5.6e-05    0.0087     338     470 ..      20     147 ..       4     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.6e-05
                        AAA_13 338 kglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkky 418
                                    +l +++ ++ k+ +    le+ ++ i ++++ +  ++e +++    +++l+e +++  ++++      l++++++  + +
  gi|70607596|ref|YP_256466.1|  20 STLASKIYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRG-----LQEAVKQQGEIL 95 
                                   5556666666666666556777777778888888888888888888888888888888888886.....333344444556 PP

                        AAA_13 419 kklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                   ++ ++ai++l++ +k++++++k l+e +k+L + ++++ +   ++ +e+ +f
  gi|70607596|ref|YP_256466.1|  96 REHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSF 147
                                   7777788888888888888888888888888888888777777777776666 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.8   0.00063     0.097      12      65 ..      42      96 ..      31     100 .. 0.87
   2 ?    7.6   3.3      0.03       4.7      20      52 ..      85     117 ..      79     149 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00063
                        CC2-LZ 12 kkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeele.tisvlkaQaevYr 65
                                  + e i +L++ +   eea++++   i+ l+e++k+++e ++   +  k+Q e+ r
  gi|70607596|ref|YP_256466.1| 42 NTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRgLQEAVKQQGEILR 96
                                  47899**********************************9965678899999866 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.03
                        CC2-LZ  20 kaqlqaaeealaakqeeidelkeeikkkeeele 52 
                                   ++++++  e l++++e i+ l+e++k+++e ++
  gi|70607596|ref|YP_256466.1|  85 QEAVKQQGEILREHSEAIKSLQETVKQHSEAIK 117
                                   555555555555555555555555555555332 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   4.9   5.9e-05    0.0091     249     345 ..      35     134 ..      33     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-05
                                   HHHHHHTTSGGGGGHHHHTTTHHHCCTS...-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHH CS
                           FH2 249 lvkiireklpevldfsseLknvkkaakv...nleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeek 326
                                   + k ++e+++ + ++++ +  +++a +    +++sl+++vk+ ++ ++ l++ ++++ +   ++ + +++l+e +k+ +e 
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQqggSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEA 115
                                   667778889999999999998888876522279**************************9999999*************** PP

                                   HHHHHHHHHHHHHHHHHHH CS
                           FH2 327 lkkleeelkeakelvkelv 345
                                   +k l+e  k++ +  ke+ 
  gi|70607596|ref|YP_256466.1| 116 IKGLQEAVKQLSNDIKEVS 134
                                   ************9999986 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   7.1   4.5e-05     0.007      91     235 ..       2     133 ..       1     166 [. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-05
                ALIX_LYPXL_bnd  91 AsesDkivrqklqenkedlelLsgpeeeleaalpssssaaasesveeqirklrsllekldelkaereqllkdlkekaendD 171
                                   AsesD++v++ l++ k   +l s+  + l++ +  +    + e+++e+ir+l++ +  l+e  +++   +k+l+e++++  
  gi|70607596|ref|YP_256466.1|   2 ASESDDMVKKLLEDPKFISTLASKIYDRLKDEVVIK----RLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQH- 77 
                                   899999999999998877777799999999997732....2369999999999999999999999999999999988888. PP

                ALIX_LYPXL_bnd 172 itpklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksd 235
                                     ++ ++ +++  a++++ ++++e+ e +++lqe ++q     +e +k +qea+++++++ k+ 
  gi|70607596|ref|YP_256466.1|  78 --SEAIRGLQE--AVKQQGEILREHSEAIKSLQETVKQ----HSEAIKGLQEAVKQLSNDIKEV 133
                                   ..667777777..5556666666666655555555555....5555555555555555444443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.9   4.9e-05    0.0076     315     413 ..      37     135 ..       6     166 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                      Prominin 315 dqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkip..realdavisd 393
                                   + l++ +e +++l++ +   l+++v+++  ++++++e+vk++ +e ++ l++a+++++e +++++++i+  +e++++ +++
  gi|70607596|ref|YP_256466.1|  37 KRLEENTEAIRNLQQGIM-GLEEAVRQQGGSIKSLQETVKQH-SEAIRGLQEAVKQQGEILREHSEAIKslQETVKQHSEA 115
                                   445555555555555433.46666666677777777777654.45566777777777777777777776666777777777 PP

                      Prominin 394 lenterssktfddvvekyek 413
                                   ++ +++ +k+ ++ +++++k
  gi|70607596|ref|YP_256466.1| 116 IKGLQEAVKQLSNDIKEVSK 135
                                   77777777776666666554 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.7   5.7e-05    0.0088      54     157 ..      55     157 ..      36     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.7e-05
                      ISG65-75  54 yllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaekaskkak 134
                                    l + ++++ ++i++ +e v++++e +++l e  k++g++  + +e +k++ +e+ ++ ++a +  ++a+++  + +k++ 
  gi|70607596|ref|YP_256466.1|  55 GLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSL-QETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   5678899************************************99888775.55556667788888888888888888888 PP

                      ISG65-75 135 eaakkAlGeeleeensnstGLlk 157
                                   + + k   e  + +n+ ++GL k
  gi|70607596|ref|YP_256466.1| 135 KLTIKLSTEIGSFTNRAGKGLEK 157
                                   88877777777777777777766 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   2.0   4.3e-05    0.0067      29     126 ..      36     137 ..      31     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                    V_ATPase_I  29 vrrcdemerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnenleklkkelnelvelk 106
                                   ++r++e ++ +r l++ i  le+av+++  +    +++ +++++ +  l+e +++  e l+e +e  ++l++++++  e+ 
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSiksLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   89****************99999999887776666777778888899999999999999***************9999999 PP

                    V_ATPase_I 107 avlekakefleee.eeeeeee 126
                                   + l++a + l+++ +e ++ +
  gi|70607596|ref|YP_256466.1| 117 KGLQEAVKQLSNDiKEVSKLT 137
                                   999999999987744443333 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0     0.011       1.7     111     165 ..      25      85 ..      19      91 .. 0.78
   2 !   10.0   1.3    0.0036      0.56     124     167 ..      93     136 ..      84     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                         Spc29 111 siyssvkkivelek......klddqkleIkeLkreleqqrtvnseLqekvaeleeevkrla 165
                                   +iy+++k  v +++       + + +  I  L+ ++ qq+ +++ Lqe v++  e ++ l+
  gi|70607596|ref|YP_256466.1|  25 KIYDRLKDEVVIKRleenteAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQ 85 
                                   6888888777777777777788888888888899999999999999999988888876664 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0036
                         Spc29 124 kklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaal 167
                                    +l ++ + Ik+L+  ++q+   ++ Lqe v++l + +k++  l
  gi|70607596|ref|YP_256466.1|  93 EILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   48999*******************************99987665 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3    0.0027      0.42       2      41 ..      39      78 ..      38      82 .. 0.94
   2 ?    7.9   1.3     0.017       2.7       2      43 ..      95     136 ..      89     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0027
                     DASH_Duo1  2 LekEleqLrkinevienviesLkkaksniervketvestn 41
                                  Le+  e +r++ + i +++e+ ++  + i++++etv++ +
  gi|70607596|ref|YP_256466.1| 39 LEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHS 78
                                  89999*******************************9976 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.017
                     DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervketvestntL 43 
                                   L++  e ++++ e++++  e++k  ++ ++++++ ++++++L
  gi|70607596|ref|YP_256466.1|  95 LREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   677788888888888888888888888888888888888887 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   2.6    0.0001     0.016     120     226 ..      39     148 ..       5     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.0001
                          CorA 120 vdrlfellekleeeldeledel.edstkkeilrelaqlrrrlvk.lrralapnrevlkrlla..kaddkllddedkeylrd 196
                                   ++++ e++++l + +  le+ + ++  + + l+e+++ + ++++ l++a++++ e+l ++ +  k+++++++++ +e ++ 
  gi|70607596|ref|YP_256466.1|  39 LEENTEAIRNLQQGIMGLEEAVrQQGGSIKSLQETVKQHSEAIRgLQEAVKQQGEILREHSEaiKSLQETVKQH-SEAIKG 118
                                   56788999999999999999999888888888888888877555379999999999977776755555555544.577999 PP

                          CorA 197 lldelerllemlealrerleslqdtyssll 226
                                   l++ +++l+++++ +++++ +l+ ++ s  
  gi|70607596|ref|YP_256466.1| 119 LQEAVKQLSNDIKEVSKLTIKLSTEIGSFT 148
                                   999999999999999888888888777765 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3     0.003      0.46     142     190 ..      36      91 ..      18      98 .. 0.82
   2 ?    5.6   0.3     0.084        13      90     175 ..     106     190 ..      99     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.003
                 PhageMin_Tail 142 lsrltkeaaealkkl.....Gis.tkdaq.gkmksldeiledlsealkkltda.qra 190
                                   + rl  e +ea+++l     G++ +  +q g +ksl+e+ ++ sea+ +l++a +++
  gi|70607596|ref|YP_256466.1|  36 IKRL-EENTEAIRNLqqgimGLEeAVRQQgGSIKSLQETVKQHSEAIRGLQEAvKQQ 91 
                                   4566.6888888888888889999888998999*****************9995443 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.084
                 PhageMin_Tail  90 atsvedlaealkevgavakaaGlsfeetaaalallaa.agikgseAgtalknllsrltkeaaealkklGistkdaq.gkmk 168
                                   + +v++ +ea+k +  + k++  +++e++ +   l++  g  +++Ag +l + ++      +eal+  Gi+  +++ g++ 
  gi|70607596|ref|YP_256466.1| 106 QETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTeIGSFTNRAGKGLEKTIMMV---YKEALELHGIDPNKVKhGNIV 183
                                   445555566666666666666666666666666666656666677777777777744...555555557777777777777 PP

                 PhageMin_Tail 169 sldeile 175
                                   ++ +i++
  gi|70607596|ref|YP_256466.1| 184 DTLGIID 190
                                   7766665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   9.9   8.8e-05     0.014     326     417 ..      40     135 ..      10     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.8e-05
                        DUF812 326 kkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd....aeeniekLq 402
                                   +++ e +++lq+ i  le+ + +    ik+l++++kq +e+++ ++e  +++ + ++ +  +++ l++      e i+ Lq
  gi|70607596|ref|YP_256466.1|  40 EENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQEtvkqHSEAIKGLQ 120
                                   456678889999999999999999999999999999999999888888888888888888888777654444778888899 PP

                        DUF812 403 alveasaqrlvelak 417
                                   ++v++ +++++e++k
  gi|70607596|ref|YP_256466.1| 121 EAVKQLSNDIKEVSK 135
                                   999999999888775 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   8.2   7.3e-05     0.011       9      80 ..      66     140 ..      59     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.3e-05
                    TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiake...aqqkYerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                    iksl+e  +++ ++++ lqe +++q ei++e   a ++ ++ + +h+e++k lq++ ++l++  +e+++l+ ++
  gi|70607596|ref|YP_256466.1|  66 SIKSLQETVKQHSEAIRGLQEAVKQQGEILREhseAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKL 140
                                   5789999999999999999999999999998622255677889*********************99999998776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5      0.03       4.6      44      83 ..      37      76 ..      20      89 .. 0.56
   2 ?   11.0   4.7    0.0026       0.4      38      88 ..      87     137 ..      65     144 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.03
                       BLOC1_2 44 aslekkleklnekyeelqpylqqidqiekqvteLeeavse 83
                                  + le++ e+++++++ +  + + + q   ++++L+e+v++
  gi|70607596|ref|YP_256466.1| 37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQ 76
                                  4555555555555555555555555555555555555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0026
                       BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                   ++k++ + l++ +e++++++e+++++ + i+ +++ v++L + ++e+ + +
  gi|70607596|ref|YP_256466.1|  87 AVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLT 137
                                   222333335555555555555555555555555555555555555555555 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.3    0.0016      0.25      98     167 ..      35     104 ..       2     107 .. 0.81
   2 ?   12.2   7.3   0.00077      0.12      91     163 ..      63     135 ..      40     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0016
                                   ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqavee 167
                                   + k  ++ +e++ + +q +    e v++ g ++k++ e+v++ ++ ++ ++ a+++q + + e ++a++ 
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKS 104
                                   3577788888888888888888889999999999999999999999999999999999999998888876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00077
                                   HHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  91 iealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                       i+ +q+ +++  e++   ++ v++  e+ +e  ea+k++ e+v++ ++ ++ ++ a++++s+ i+ev++
  gi|70607596|ref|YP_256466.1|  63 QGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   3334445555555555555666666666666666666666666666666666666666666666666666665 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   4.7   0.00016     0.024      17     116 ..      57     138 ..       7     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00016
                       Vps53_N  17 eqslanidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqL 97 
                                   e+++ + +  ik+lqe +k+  + i+ +++a  + ge     l+e  +ai++l + +k+  +  +  +e vk++++dIk+ 
  gi|70607596|ref|YP_256466.1|  57 EEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGE----ILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKE- 132
                                   2222222222234444444444444333333332222....255555555555555555555555555555555555554. PP

                       Vps53_N  98 DiAKknlttsiTtlkrLkm 116
                                                + +L++
  gi|70607596|ref|YP_256466.1| 133 -------------VSKLTI 138
                                   .............444444 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.4   0.00014     0.021      71     167 ..      37     137 ..      10     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00014
                        DUF713  71 edleelqselsnLakkvlsaynkLeeafeklkelsekfedki.FlkvLqksisdvatklleilevldeleldk....ekle 146
                                   + lee ++ ++nL++ ++ + ++++++  ++k+l+e+++ ++  ++ Lq+ + +++++l e  e++++l+++     e ++
  gi|70607596|ref|YP_256466.1|  37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSeAIRGLQEAVKQQGEILREHSEAIKSLQETVkqhsEAIK 117
                                   5678888999**************************998876479**************99966666666554444699** PP

                        DUF713 147 elrelfskldpsdIptTskLr 167
                                    l+e++++l+ +dI ++skL 
  gi|70607596|ref|YP_256466.1| 118 GLQEAVKQLS-NDIKEVSKLT 137
                                   ********96.6899999886 PP

>> Phasin_2  Phasin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.055       8.5      34      69 ..      65      97 ..      34     102 .. 0.52
   2 ?    9.5   1.1    0.0077       1.2      50      94 ..      98     146 ..      85     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.055
                      Phasin_2 34 eaarasleeslaaakallsa.kdpqellelqselaqp 69
                                    ++++ e+  ++ +    a + +qe++++q e +++
  gi|70607596|ref|YP_256466.1| 65 GSIKSLQETVKQHSE----AiRGLQEAVKQQGEILRE 97
                                  333333333333333....224455666666665555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0077
                      Phasin_2  50 llsa.kdpqellelqselaqpa...lekavayarklaelaaktqeeaak 94 
                                    ++a k++qe ++++se ++ +   ++++  + ++++ l+ k+ +e+  
  gi|70607596|ref|YP_256466.1|  98 HSEAiKSLQETVKQHSEAIKGLqeaVKQLSNDIKEVSKLTIKLSTEIGS 146
                                   555559***********975443339999*************9999865 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.042       6.5      62     113 ..      34      88 ..      20      92 .. 0.71
   2 ?   12.9   0.6   0.00053     0.081      48     118 ..      69     139 ..      65     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.042
                       DUF1759  62 aLkkrYdnkrkiirellnelmklpslkee...dasqlrrivdavneivralealg 113
                                   +  kr +++ + ir+l + +m l++  ++   + + l+++v +  e +r+l+++ 
  gi|70607596|ref|YP_256466.1|  34 VVIKRLEENTEAIRNLQQGIMGLEEAVRQqggSIKSLQETVKQHSEAIRGLQEAV 88 
                                   5668888999999999999999999555501155666777777778888888764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00053
                       DUF1759  48 hlalseenYeaaveaLkkrYdnkrkiirellnelmklpslkeedasqlrrivdavneivralealgeeadk 118
                                    l+ + + +  a+  L++   ++ +i+re+ +++ +l+++ ++  + ++ + +av ++   ++++++ + k
  gi|70607596|ref|YP_256466.1|  69 SLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIK 139
                                   56667788899999******************************************999999998877665 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.0     0.013         2      62     148 ..      11      90 ..       3      98 .. 0.58
   2 ?   11.0   1.7    0.0012      0.19     107     155 ..      98     146 ..      93     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                    FmiP_Thoc5  62 eLvpeeeFyeeapeeiskpedtkkeadehelmlaRLewEleqRkelaeqlkeleekkkkleqeieekkkfLssLppkLksl 142
                                   +L+++ +F++++ ++i     ++    + e  ++RLe   e  ++l++ +  lee +++    i++ ++  ++ +++++ l
  gi|70607596|ref|YP_256466.1|  11 KLLEDPKFISTLASKIY----DR---LKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGL 84 
                                   56666666665555551....11...3455666666666666666666666666666666666666666666666666666 PP

                    FmiP_Thoc5 143 kkatkp 148
                                   ++a+k+
  gi|70607596|ref|YP_256466.1|  85 QEAVKQ 90 
                                   666654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0012
                    FmiP_Thoc5 107 laeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealgl 155
                                    +e++k+l+e +k+++++i+  ++  ++L++ +k+++k t +l  ++g 
  gi|70607596|ref|YP_256466.1|  98 HSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGS 146
                                   5789999*******************************99999999884 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  10.0   0.00024     0.037      92     189 ..      36     133 ..       5     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00024
                       UPF0242  92 eelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqi 172
                                    ++ ee+ e  ++l++    le+  +++    + l++++++ +e  + l+e+++++ e l e  e i+++++++++  + i
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   333344444444444444444444444443344677788888888888999999999999999999999999999999999 PP

                       UPF0242 173 eqLeskVrDlnyEiktL 189
                                   + L+  V+ l+  ik  
  gi|70607596|ref|YP_256466.1| 117 KGLQEAVKQLSNDIKEV 133
                                   99999999998888865 PP

>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.8     0.041       6.4       9      62 ..      32      87 ..      25      93 .. 0.79
   2 ?   14.4   2.2   0.00015     0.023      17      77 ..      77     137 ..      68     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.041
                        CCDC85  9 Deellkl..skeelvrrLRraeaekvsllvergrlikevnrrLqqhLleiRelkev 62
                                  De ++k      e +r+L++  +   +++ ++g +ik     ++qh + iR+l+e 
  gi|70607596|ref|YP_256466.1| 32 DEVVIKRleENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEA 87
                                  5555554113457899999999999999*************************984 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00015
                        CCDC85  17 keelvrrLRraeaekvsllvergrlikevnrrLqqhLleiRelkevnqkLqednqelrdlC 77 
                                   + e +r L++a +++ ++l e+++ ik     ++qh + i++l+e  ++L +d +e+ +l 
  gi|70607596|ref|YP_256466.1|  77 HSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLT 137
                                   468899*************************************************998875 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   9.2   0.00047     0.073      39     142 ..      36     136 ..      25     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00047
                           GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekve 119
                                    k+ e+n+  + +++q  + l+e ++++   ++ L++ +k++++   +++ l++ +k++ + l++ ++  ++l++ +++ +
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSE---AIRGLQEAVKQQGEILREHSEAIKSLQETVKQHS 113
                                   47788899999999999999999999999999999999999888...6667777777888888888888888888888888 PP

                           GAS 120 kerdelykkfeaaiqevqqktgl 142
                                   ++++ l++  ++  +++++ ++l
  gi|70607596|ref|YP_256466.1| 114 EAIKGLQEAVKQLSNDIKEVSKL 136
                                   88888888888887777777665 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.6   0.00074      0.11      16     190 ..      36     134 ..      30     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00074
                           LXG  16 kseleelkeqleqlkkaiqklveledslkGkaaeaiknfyadlhlplltslqdlieqyeefLkkikealesvepssngfid 96 
                                   +++lee +e++ +l+++i++l e   + +G + +++++  ++ h + ++ lq+++ q+ e L++++ea++s  +++  + +
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAV-RQQGGSIKSLQETVKQ-HSEAIRGLQEAVKQQGEILREHSEAIKS--LQETVKQH 112
                                   5667777777777777777744444.6677777777777777.7777777777777777777777777777..44444444 PP

                           LXG  97 edfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanles 177
                                   +++++  l+ ++k+++++++                                                             
  gi|70607596|ref|YP_256466.1| 113 SEAIK-GLQEAVKQLSNDIK------------------------------------------------------------- 131
                                   44444.44444444444443............................................................. PP

                           LXG 178 dlkalktyvseLe 190
                                             e++
  gi|70607596|ref|YP_256466.1| 132 ----------EVS 134
                                   ..........333 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.9   0.00032     0.049      56     188 ..      19     150 ..       3     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00032
                          Mer2  56 nskeLlkvisklnellidlkeeesdnskekeikdlikdLsvkienqlskvskavldklkvkkhksntdtksnLte.llekk 135
                                    s+  +k+ ++l++++  +k+ e + + + ++++ i+ L+  + +q   ++ ++++++k++++  ++ ++ + ++ ++ ++
  gi|70607596|ref|YP_256466.1|  19 ISTLASKIYDRLKDEV-VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIK-SLQETVKQHSEAIRGLQEAVKQQgEILRE 97 
                                   4555567789999998.6788899*******************99876665.44555665555555555554444577778 PP

                          Mer2 136 eakileeidkkqtkleksvdttqelllnvnkQledvnevllSlskdlenlstr 188
                                   +++ ++ +++  ++  ++++ +qe +  +++ +++v ++ + ls+++ +  +r
  gi|70607596|ref|YP_256466.1|  98 HSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNR 150
                                   8888899999999*********************************9988776 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   9.6   0.00039     0.061      92     221 ..       4     135 ..       2     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00039
                       DUF4618  92 qlnakvqklqeelnvLstYkDkeYp..vkavqIanlvrqlqqlkdsqq..deldeleelikevleklskkiqkkkekllks 168
                                   + +++v+kl e+ +++st   k Y      v I+ l ++ + +++ qq  + l+e  +     +++l++ +++++e++   
  gi|70607596|ref|YP_256466.1|   4 ESDDMVKKLLEDPKFISTLASKIYDrlKDEVVIKRLEENTEAIRNLQQgiMGLEEAVRQQGGSIKSLQETVKQHSEAIR-G 83 
                                   56889*******************632468*************999984446677777777788888887777777765.4 PP

                       DUF4618 169 laektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqa 221
                                   l ++++k+  e L +++   ++l++ ++++ e i+ l+e +++L +++++ ++
  gi|70607596|ref|YP_256466.1|  84 L-QEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   5.577788899***********************************9998765 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.5   0.00064     0.098      22     324 ..      61     137 ..       2     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00064
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS CS
                         APG17  22 elltsarqeleeavkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrktkveps 102
                                    +                                                                               
  gi|70607596|ref|YP_256466.1|  61 RQQG----------------------------------------------------------------------------- 64 
                                   3333............................................................................. PP

                                   .......STGGGCS--TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH-------STCCHHHHHHHHHHHH CS
                         APG17 103 frpegeektLlDFvdedsveelkealkesidelqaaqkkldssllefdtdlrelkkelsksksksessslipellkelesl 183
                                                                                                                    
  gi|70607596|ref|YP_256466.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   HHHHHHHHHHHHHHHHHHHHH................S-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         APG17 184 eeemAslLesLtnHfDqcvkAvkltegggalrraaaelseeereelleVlekDaaeledVvkelqerleemekakkllsek 264
                                                                                                        ++++ +++++++
  gi|70607596|ref|YP_256466.1|  65 --------------------------------------------------------------------GSIKSLQETVKQH 77 
                                   ....................................................................3345566666666 PP

                                   HHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                         APG17 265 keeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLr 324
                                    e+i+ l++a+k++ e l+e ++++++  +++k+ +e ++  +e  +++ ++++e+++L+
  gi|70607596|ref|YP_256466.1|  78 SEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLT 137
                                   666666666666666666666666666666666666666665555555555555555554 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7    0.0016      0.25      29     117 ..      37     132 ..      19     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0016
                   Helo_like_N  29 ksfrsrdktvreLkeeleaLeev.......LesLeevavaeeeselalLklpllrCgkaCkefeqvikkcskkssksrtsf 102
                                   k++ ++++++r+L++ +  Lee        ++sL+e +v+++++ ++ L+  +++ g++ +e  ++ik++++  +++++++
  gi|70607596|ref|YP_256466.1|  37 KRLEENTEAIRNLQQGIMGLEEAvrqqggsIKSLQE-TVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   455555555555555555554431222222778888.56788888999999999999999999999988888777776666 PP

                   Helo_like_N 103 rDwa.kleymggdind 117
                                   +     ++ +++di++
  gi|70607596|ref|YP_256466.1| 117 KGLQeAVKQLSNDIKE 132
                                   6543134555566665 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   0.00039      0.06     197     260 ..      69     131 ..      32     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00039
                     FUSC-like 197 elreafk.nsdvlfrfqrllelqakaceeiaqaillnkpyqhserleraleeleqslellakqnn 260
                                   +l+e++k +s+ +  +q+ +++q++ ++e ++ai+  ++    +++++a+++l++++++l +  +
  gi|70607596|ref|YP_256466.1|  69 SLQETVKqHSEAIRGLQEAVKQQGEILREHSEAIKSLQETV--KQHSEAIKGLQEAVKQLSNDIK 131
                                   688898879**************************666655..4456788888888877666533 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.062       9.6       5      38 ..      56      89 ..      53      91 .. 0.92
   2 ?    8.3   0.8      0.02         3       2      34 ..     102     134 ..      95     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.062
                     FlaC_arch  5 lEnklsklsteletvkkeneelsksveelkenVk 38
                                  lE+ + +   ++++++++ ++ s+ +  l+e Vk
  gi|70607596|ref|YP_256466.1| 56 LEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVK 89
                                  899999999**********************998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.02
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelk 34 
                                   i++l++ ++++s  ++ +++  ++ls++++e+ 
  gi|70607596|ref|YP_256466.1| 102 IKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   678888888999999999999999999888876 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.22        33     135     170 ..      26      61 ..       5      64 .. 0.88
   2 ?    9.3   1.9    0.0075       1.2      25     169 ..      68     130 ..      61     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.22
                       DUF2959 135 vlaalkdqvlfLKhnlNaqaiaalkgelselekdvs 170
                                   + + lkd+v+  + + N++ai  l++ +  le+ v+
  gi|70607596|ref|YP_256466.1|  26 IYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVR 61 
                                   56789*********************9999999886 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0075
                       DUF2959  25 dsqeeakeqfksALerfkavvefdggeLekeyeklnkeyeesekaaeevrerieaveevaealfkeWeeeldqyssaslrr 105
                                   +s +e+ +q ++A+  ++++v+ +g  L+++ e++++  e+ ++++e+++   eav++ +++                   
  gi|70607596|ref|YP_256466.1|  68 KSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSND------------------- 129
                                   45555566666666666666666666666666666655555555555555555555555554................... PP

                       DUF2959 106 eSeqklketrkkykellkamkkaekkmePvlaalkdqvlfLKhnlNaqaiaalkgelselekdv 169
                                                                                                  +
  gi|70607596|ref|YP_256466.1| 130 ---------------------------------------------------------------I 130
                                   ...............................................................3 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.059       9.1      32      78 ..      32      77 ..      21      83 .. 0.88
   2 ?   10.6   2.7    0.0027      0.41      37      80 ..      86     128 ..      78     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.059
                     PhaP_Bmeg 32 EqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktvenl 78
                                  +++ +k l++  +++++l++++  le+  +q    + + lq+tv++ 
  gi|70607596|ref|YP_256466.1| 32 DEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSI-KSLQETVKQH 77
                                  5678999*************************9999.8889999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0027
                     PhaP_Bmeg  37 kalkqqqdlvkeltkalselekeskqltaeledqlqktvenlrs 80 
                                   +a+kqq ++++e  +a+++l+++ kq    + + lq+ v++l +
  gi|70607596|ref|YP_256466.1|  86 EAVKQQGEILREHSEAIKSLQETVKQHSEAI-KGLQEAVKQLSN 128
                                   5778888888888888888888888876666.556777777743 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6    0.0032       0.5      65     127 ..      25      90 ..      16      96 .. 0.73
   2 ?   11.3   8.8    0.0018      0.28      45     137 ..      36     131 ..      34     145 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0032
                          ADIP  65 leaeierlqskierlktqleq...lerelalvqakerqlekklktleqklknekeelqrlknalqq 127
                                   + ++  +++  i+rl++++e+   l++ +  ++++ rq+  ++k+l++++k+ +e ++ l+ a++q
  gi|70607596|ref|YP_256466.1|  25 KIYDRLKDEVVIKRLEENTEAirnLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQ 90 
                                   555666666677788777665222667777889999999999999999999999888888888877 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0018
                          ADIP  45 lqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                   +++++++ e+  +l++ i  le    ++  +i++l++ ++q    +  +q++ +q+   l++ ++++k+++e ++    a+
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   566666666666666666666666666666666666666666666666666666666666666666666666666555554 PP

                          ADIP 126 qqik...tqyahelk 137
                                   + ++   +q+++++k
  gi|70607596|ref|YP_256466.1| 117 KGLQeavKQLSNDIK 131
                                   332211134444444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.3   0.00054     0.083     224     314 ..      44     137 ..      17     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00054
                         IFT57 224 ahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleel...lqeyreaqeelsevkekykqlsegvs 301
                                   + + ++++   ++ee++ +   ++k l+e +++  e i   ++ + +q e l    +  +++qe++++ +e +k l+e v+
  gi|70607596|ref|YP_256466.1|  44 EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILrehSEAIKSLQETVKQHSEAIKGLQEAVK 124
                                   334444444447788888888889999999999999999988888888554300033466666666666666666777777 PP

                         IFT57 302 eltrelaeiseel 314
                                   +l+++ +e+s+  
  gi|70607596|ref|YP_256466.1| 125 QLSNDIKEVSKLT 137
                                   7666666666555 PP

>> Pinin_SDK_N  pinin/SDK conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       2.1   3.2e+02       5      28 ..      67      90 ..      59      93 .. 0.91
   2 ?   10.0   0.1    0.0068         1       4      41 ..     101     137 ..      99     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.1
                   Pinin_SDK_N  5 vraLqeqlekAkEnLkgvDenikk 28
                                  +++Lqe +++  E+++g+ e +k+
  gi|70607596|ref|YP_256466.1| 67 IKSLQETVKQHSEAIRGLQEAVKQ 90
                                  789***************999985 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0068
                   Pinin_SDK_N   4 avraLqeqlekAkEnLkgvDenikkltGRDPnelrpga 41 
                                   a+++Lqe +++  E++kg+ e +k+l   D +e+ + +
  gi|70607596|ref|YP_256466.1| 101 AIKSLQETVKQHSEAIKGLQEAVKQLS-NDIKEVSKLT 137
                                   89**********************996.4666665555 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.9     0.013         2      12      69 ..      36      93 ..      31      94 .. 0.86
   2 ?    8.6   1.3     0.015       2.3      32      62 ..     105     135 ..      99     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.013
                        Csm1_N 12 qerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkkqeE 69
                                   +rl++   ++ +l +    L+++++++   i+sL+e++++  e ++ l+e  k+q E
  gi|70607596|ref|YP_256466.1| 36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGE 93
                                  56777777777777777788999***************************99999877 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.015
                        Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkelee 62 
                                   L+++++++++ i+ L+e +++l +++ke  +
  gi|70607596|ref|YP_256466.1| 105 LQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   89999******************99999876 PP

>> TEX13  Testis-expressed sequence 13 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.7    0.0037      0.57      63     134 ..      44     114 ..      16     117 .. 0.79
   2 ?    9.1   0.8    0.0061      0.94      81     126 ..      97     141 ..      93     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0037
                         TEX13  63 cawsaLaLgvrvaarqrelqarrvqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlqlaqaalae 134
                                    a   L  g+   +   ++q   ++ Lq+ v++h  a   L   +k+  e   +e++ea   lq + ++ +e
  gi|70607596|ref|YP_256466.1|  44 EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGE-ILREHSEAIKSLQETVKQHSE 114
                                   466666667777777778999**************************999.8899*****99*999887665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0061
                         TEX13  81 lqarrvqkLqdqveehksaaqaLaselkrlreqqemerkeaasqlq 126
                                   ++++ ++ Lq+ v++h  a + L   +k+l + + +e ++ +++l 
  gi|70607596|ref|YP_256466.1|  97 EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSN-DIKEVSKLTIKLS 141
                                   67899*************************99.6666666666665 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.3    0.0068         1       5      57 ..      32      87 ..      23     101 .. 0.67
   2 ?    8.0   2.0     0.012       1.9       6      48 ..      99     141 ..      95     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0068
                       DUF4795  5 saellkklq...eaieklqeelekleekvkelekrledkekklealkkqieelekv 57
                                  +++ +k l+   eai++lq+ +  lee+v++  ++++ +++ ++ + ++i+ l+++
  gi|70607596|ref|YP_256466.1| 32 DEVVIKRLEentEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEA 87
                                  45555555555566777777777777777777777777777777777777777664 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                       DUF4795   6 aellkklqeaieklqeelekleekvkelekrledkekklealk 48 
                                   +e++k lqe++++ +e ++ l+e+vk+l++++++ +k +  l 
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLS 141
                                   6778888888888888888888888888888887776655554 PP

>> Senescence  Senescence-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   0.00058      0.09      21      86 ..      86     158 ..      54     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00058
                    Senescence  21 kgiqkgaeyyiskskps...ekPlefsprtrkalr.kvrkvsgqaakvsaktv...ggvgdaagrvgaavaks 86 
                                   +++++++e ++++s++    ++ ++  ++  k+l+ +v+++s+ +++vs+ t+    ++g+ + r+g+++ k 
  gi|70607596|ref|YP_256466.1|  86 EAVKQQGEILREHSEAIkslQETVKQHSEAIKGLQeAVKQLSNDIKEVSKLTIklsTEIGSFTNRAGKGLEKT 158
                                   67889999999999665333444566666666666699*****999999988877799*********999886 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       8.6   1.3e+03      50      67 ..      34      51 ..      21      64 .. 0.65
   2 ?    7.0   5.7     0.049       7.6      18      53 ..     100     136 ..      31     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 8.6
                    MitMem_reg 50 veegelpvnheilrnlqk 67
                                  v+ ++l+ n+e++rnlq+
  gi|70607596|ref|YP_256466.1| 34 VVIKRLEENTEAIRNLQQ 51
                                  444455556666666664 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.049
                    MitMem_reg  18 as.stlstglnrqyyslkilqerldlikdYlkkveeg 53 
                                   ++ ++l++ ++++ +++k+lqe ++++++ +k+v + 
  gi|70607596|ref|YP_256466.1| 100 EAiKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   1134555555555555555555555555555555533 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.031       4.9     117     159 ..      48      90 ..      42      92 .. 0.81
   2 ?    6.3   0.5     0.016       2.5     117     152 ..      97     132 ..      93     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHTHHSSEEEECHCCSHCEEEEETTHHHHHH CS
                    Fusion_gly 117 knaeeiaklkeslektnkAveklqngvselvlavnalqdyint 159
                                   ++++ i  l e++++   ++++lq++v++   a+++lq+ + +
  gi|70607596|ref|YP_256466.1|  48 NLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQ 90 
                                   4567788999999999999999999999999999999987765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHTHHSSEEEECHCCSHCEEEEET CS
                    Fusion_gly 117 knaeeiaklkeslektnkAveklqngvselvlavna 152
                                   + +e+i++l+e +++  +A++ lq++v++l   +++
  gi|70607596|ref|YP_256466.1|  97 EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKE 132
                                   456788888888888888888888888887666555 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.25        39      57      87 .]      43      73 ..      37      73 .. 0.93
   2 ?    8.0   2.8     0.019         3      20      85 ..      83     148 ..      71     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.25
                         Vps51 57 sdtIrkmksemdkldqklselkqaiskiaet 87
                                  +++Ir++++ +  l++ + +++ +i++++et
  gi|70607596|ref|YP_256466.1| 43 TEAIRNLQQGIMGLEEAVRQQGGSIKSLQET 73
                                  899***********************99986 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.019
                         Vps51  20 tlkellkveasllseiraldselkalVydnYskLisasdtIrkmksemdkldqklselkqaiskia 85 
                                   +l+e  k + ++l+e  +  ++l+++V ++ +      +++++++++++++++ + +l+ +i++++
  gi|70607596|ref|YP_256466.1|  83 GLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFT 148
                                   5788889999999999***********9999999999************************99987 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.4   0.00087      0.13      30     124 ..      44     133 ..      28     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00087
                     PspA_IM30  30 qairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLArealaeikslekqaealetqlaqq 110
                                   +air++q+ +  +++a+ q+ ++ k+l++ +++ +e ++ l++ +k+     + e  re  + iksl+++++++++  + +
  gi|70607596|ref|YP_256466.1|  44 EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQ-----QGEILREHSEAIKSLQETVKQHSEAIKGL 119
                                   69***************************************998864.....667889*********************** PP

                     PspA_IM30 111 rsaveqlrkqleal 124
                                   ++av+ql + +++ 
  gi|70607596|ref|YP_256466.1| 120 QEAVKQLSNDIKEV 133
                                   *******9888764 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6     0.003      0.46     221     277 ..      30      86 ..       7      97 .. 0.83
   2 ?    4.2   6.3      0.15        23     203     278 ..      71     143 ..      67     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.003
                     Rab5-bind 221 vekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqt 277
                                   +  e + k l+e+t+++++lq+ +  lEe +++      +++++v ++ +  + Lq+
  gi|70607596|ref|YP_256466.1|  30 LKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQE 86 
                                   4456677899***********************************999998888886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.15
                     Rab5-bind 203 keelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqtE 278
                                   +e +++ s     l+e   ++++    l+e+++++++lq+++++  e +k l+++  ++ + + e  + + +L tE
  gi|70607596|ref|YP_256466.1|  71 QETVKQHSEAIRGLQEAVKQQGE---ILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTE 143
                                   44444444444444444333333...66777777777777777777777777777777777777766666666666 PP

>> BAG6  BCL2-associated athanogene 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0011      0.17       5      75 ..      74     143 ..      70     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                          BAG6   5 lqelrevqerlePfleryieileedptfeesdntegreeaqrildrvsEalhllshalhalSDlrldLsqp 75 
                                   +++ +e  + l+  +++  eil+e +++ +s  +e+++++   +++  Ea++ ls+ +  +S l ++Ls++
  gi|70607596|ref|YP_256466.1|  74 VKQHSEAIRGLQEAVKQQGEILREHSEAIKSL-QETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTE 143
                                   55555666667777888899*******99999.566888889999***********************975 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9    0.0011      0.16      91     189 ..      71     169 ..      59     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                         TMP_2  91 akearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGqsvdet 171
                                   +++ ++  +a+ ++ +a+ +  + L + +e+i+  ++t+++ +ea++ l ++ k  ++++++v+k +++l+   G+ ++ +
  gi|70607596|ref|YP_256466.1|  71 QETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNRA 151
                                   5666666777777777777777889999************************************************99999 PP

                         TMP_2 172 akelaklakdPvkaaekl 189
                                    k l+k      k a +l
  gi|70607596|ref|YP_256466.1| 152 GKGLEKTIMMVYKEALEL 169
                                   999999877777776665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   6.8   0.00099      0.15      42     147 ..      41     143 ..      23     170 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00099
                          Fez1  42 elrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeaka 122
                                   e ++++++ ++ i+ lee+++++  +++ +++ ++++++    l+e v++  e    lre+ ++ ++ +e+ +++s++ k 
  gi|70607596|ref|YP_256466.1|  41 ENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEI---LREHSEAIKSLQETVKQHSEAIKG 118
                                   555555555566666666666666666555555555554444444433333322...222222222223333334444444 PP

                          Fez1 123 qrqeaeeleelkreverlraeLkee 147
                                    +++ ++l++  +ev +l  +L++e
  gi|70607596|ref|YP_256466.1| 119 LQEAVKQLSNDIKEVSKLTIKLSTE 143
                                   4444445555555555555555444 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.8     0.021       3.2      44      98 ..      68     126 ..      23     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.021
                  Syntaxin-6_N  44 teLrkalrsiewdledLeetv....riveknpskfkidekelsrrrafveevreevkem 98 
                                   + L++++++ ++ ++ L+e+v    +i++++ +  k  +++++++ + ++ ++e vk++
  gi|70607596|ref|YP_256466.1|  68 KSLQETVKQHSEAIRGLQEAVkqqgEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQL 126
                                   45556666666666666666644434666666666666666666666666666666654 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0      0.01       1.6      27      79 ..      25      72 ..       8      90 .. 0.70
   2 ?    1.6   0.1       2.2   3.5e+02      50      83 ..      99     132 ..      87     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.01
                Retrotrans_gag 27 esWkdlkkaflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde 79
                                  ++++ lk+++  + l+     + +e +++l+Qg + ++e+v++    +  l+e
  gi|70607596|ref|YP_256466.1| 25 KIYDRLKDEVVIKRLE-----ENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQE 72
                                  4555566655555555.....55566**************9998777777774 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 2.2
                Retrotrans_gag  50 eeelsslrQgtesvreYvtrfktladqldevlte 83 
                                    e ++sl++  +  +e+++ +++ + ql + ++e
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKE 132
                                   4557788887777778877777777777754444 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.5   0.00088      0.14     283     377 ..      34     127 ..      19     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00088
                                   HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHCT-H.HHHTTHHHHHHHHHHHH CS
                 Peptidase_S46 283 llkeemkkdpeirikyasklagleNylKnliGmlealkkkkvlekkqaeeaalrawlkkdpekkekygkalselealvkek 363
                                   ++ +  ++++e+ ++ ++ + gle +++++ G +++l++  ++++  ++ + l++++k+++e  ++  +a+++l+++vk++
  gi|70607596|ref|YP_256466.1|  34 VVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQE--TVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQH 112
                                   444555666666677777788888888888888888864..5777788888888888888888777778888887777776 PP

                                   HHHHHH.HHHHHHHT CS
                 Peptidase_S46 364 rklaer.salleeae 377
                                   +++ +  + ++++++
  gi|70607596|ref|YP_256466.1| 113 SEAIKGlQEAVKQLS 127
                                   665544123333333 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   7.2   0.00033     0.051       3      71 ..      66     136 ..      54     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00033
                                   .HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                          FlgN   3 lleeLielleeelelleeLlelleeEteaLkag..dieaLeelleekqellekleqleqkrakllaelgls 71 
                                   ++++L e++++  e+++ L+e  +++ e+L++    i++L+e++++  e ++ l+++ +++++ ++e+++ 
  gi|70607596|ref|YP_256466.1|  66 SIKSLQETVKQHSEAIRGLQEAVKQQGEILREHseAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   57899**************************9976799999999999999999999999999999988765 PP

>> Glypican  Glypican
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.2     0.001      0.16     288     403 ..      21     135 ..      16     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                      Glypican 288 lvaeklegpfnienviksievkiseaimalqeNseklskkvfkgCgtpkktqarsersskdeekkkrglktaepeeketta 368
                                   ++a+k++   + e vik +e +  eai +lq+  + l++ v ++ g+ k  q   +++s+     +  +k + +  +e+ +
  gi|70607596|ref|YP_256466.1|  21 TLASKIYDRLKDEVVIKRLEEN-TEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSE 100
                                   6788999999999999999976.79*************************9998888888877777778888888899999 PP

                      Glypican 369 agtkldrlvtelkekLkkvkkfwvsLpdtlCsdek 403
                                   a ++l++ v +  e +k +++   +L + + + +k
  gi|70607596|ref|YP_256466.1| 101 AIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   99999999999999999999988888877766555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.0    0.0016      0.24       8      88 ..      57     136 ..      25     149 .. 0.77
   2 ?    7.9   1.8      0.01       1.6       6      67 ..      97     158 ..      93     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0016
                         TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesl 88 
                                   e+ +++   + k++++++++ s+ +  +++++k+q + l+e ++++k+l+++v ++++e+++ l+e +k+ ++ +kev++l
  gi|70607596|ref|YP_256466.1|  57 EEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETV-KQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   45555555555666777777777777778888888888888888888888886.577888888888888888888888775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.01
                         TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeee 67 
                                   e ++ +k+l+et k+  + ++ l++  +++s++ik+ +k   +l++++ ++++++++  e++
  gi|70607596|ref|YP_256466.1|  97 EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTNRAGKGLEKT 158
                                   56778889999999999999999999999999999999999999999888887766444444 PP

>> ATG_C  Autophagy-related protein C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.3     0.095        15       9      55 ..      78     124 ..      36     126 .. 0.75
   2 ?    7.5   0.1     0.033       5.1       9      42 ..     113     146 ..     106     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.095
                         ATG_C   9 edlreGlqqAysslskglksaaqtilavpsevaeskgakgavkavvr 55 
                                   ++   Glq+A+++  + l++  ++i +++  v+++++a + ++++v+
  gi|70607596|ref|YP_256466.1|  78 SEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVK 124
                                   45567888888888888888888888888888887555555555444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.033
                         ATG_C   9 edlreGlqqAysslskglksaaqtilavpsevae 42 
                                   ++  +Glq+A+++ls+++k++ +  +++ +e+  
  gi|70607596|ref|YP_256466.1| 113 SEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGS 146
                                   66779***************99988888887654 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.36        56      31      74 ..      33      76 ..      18      86 .. 0.84
   2 ?    9.9   1.4    0.0035      0.54      10      81 ..      92     164 ..      87     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.36
                          RPW8 31 ksilkrLestleritPvvkeieklnkeldrpreeieeLkklLek 74
                                  +  +krLe+  e+i+ + + i  l++++ ++   i++L+++ ++
  gi|70607596|ref|YP_256466.1| 33 EVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQ 76
                                  467899*******************9998888999999999876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0035
                          RPW8  10 gaalgellkaileakkksldfksilkrLestleritPvvkeieklnkel.drpreeieeLkklLekaekLVek 81 
                                   g +l+e  +ai+  ++++++ +  +k L++ +++++  +ke+ kl+ +l  +  + +++  k Lek   +V+k
  gi|70607596|ref|YP_256466.1|  92 GEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLsTEIGSFTNRAGKGLEKTIMMVYK 164
                                   6789999**************************************9998666666777777788888888877 PP

>> CmlA_N  Diiron non-heme beta-hydroxylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7    0.0013       0.2      71     134 ..      64     128 ..      30     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                        CmlA_N  71 veevrallektkkeqadllelaeaikeleklLkeeakG.asLeplYaklpeaLkGyvElvydlnn 134
                                      +++l e++k++ ++   l+ea+k+  ++L+e+ +  +sL++  ++  ea+kG+ E v  l+n
  gi|70607596|ref|YP_256466.1|  64 GGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAiKSLQETVKQHSEAIKGLQEAVKQLSN 128
                                   56789999999999999999999999999999987655389999999999999999998887776 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1         2   3.1e+02      90     115 ..      36      61 ..      21      66 .. 0.59
   2 ?    3.8   0.4      0.34        52      77     118 ..      44      85 ..      40      87 .. 0.82
   3 ?    3.7   0.2      0.36        56      82     112 ..      63      93 ..      53      99 .. 0.67
   4 ?   11.3   1.4    0.0015      0.24      76     112 ..      99     135 ..      94     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  90 ekqlekleeeleklkdqittleanla 115
                                    k le+ +e+++ l++ i  le++++
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVR 61 
                                   35666666666666666666665554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  77 eAiellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                   eAi+ l++ +  le+++++   +++ l++++++  ++++ l+
  gi|70607596|ref|YP_256466.1|  44 EAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQ 85 
                                   889999999999999999999999999999998887777665 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.36
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittlea 112
                                       +++l+++++++ e+++ l++++++  +
  gi|70607596|ref|YP_256466.1|  63 QGGSIKSLQETVKQHSEAIRGLQEAVKQQGE 93 
                                   4456778888888888888888887777555 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  76 eeAiellkkkleelekqlekleeeleklkdqittlea 112
                                    eAi+ l++ +++ +++++ l+e++++l++ i+++ +
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   69******************************99865 PP

>> SMBP  Small metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       2.1   3.3e+02      66      87 ..      40      61 ..      23      64 .. 0.78
   2 ?    8.9   6.2     0.011       1.6      26      88 ..      76     132 ..      57     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.1
                                  .-------HHHHHHHHHHHHHH CS
                          SMBP 66 kakeeekehldegikhLeeAIk 87
                                  ++++e+ + l++gi  LeeA++
  gi|70607596|ref|YP_256466.1| 40 EENTEAIRNLQQGIMGLEEAVR 61
                                  4566777788888888888886 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH...-------HHHHHHHHHHHHHHH CS
                          SMBP  26 hlaeAiehaeaAvahgkaghakalveHaeealkhakaaaekakeeekehldegikhLeeAIkh 88 
                                     +eAi+ +++Av+     +  +++ +  ea+k ++++  k++ e+ + l+e++k+L + Ik+
  gi|70607596|ref|YP_256466.1|  76 QHSEAIRGLQEAVK-----QQGEILREHSEAIKSLQET-VKQHSEAIKGLQEAVKQLSNDIKE 132
                                   33455555555554.....3456888888999999999.999999999999999999999987 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.6        93      86     119 ..      25      56 ..      18      62 .. 0.78
   2 ?    8.7   1.3     0.012       1.8      71     117 ..      63     110 ..      53     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.6
                                   XXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHHHH CS
                          COG5  86 asyerlkskvlepyeeaeklqsalkrlhqtldLl 119
                                   + y+rlk +v+   +++e+ ++a+ +l+q  + l
  gi|70607596|ref|YP_256466.1|  25 KIYDRLKDEVVI--KRLEENTEAIRNLQQGIMGL 56 
                                   5699******96..68999999999999876655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.012
                                   XX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHH CS
                          COG5  71 ss.vlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtld 117
                                   ++ + ++l++ +++ s++++ l++ v +  e ++++++a+k+l++t++
  gi|70607596|ref|YP_256466.1|  63 QGgSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVK 110
                                   4448899**************************************986 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.2    0.0018      0.28     173     258 ..      32     124 ..      19     160 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                    Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelkseke.......deelkeeieelekeikelkeklefletlledlkeseesseee 246
                                    e++ +Rlee +e i++l++ +  le+  +++       +e++k+++e+++   + +k++ e+l++  e +k+ +e+ +++
  gi|70607596|ref|YP_256466.1|  32 DEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQggsikslQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQH 112
                                   566666666666666666666666666666665553333333333333333333333333333333333333333322222 PP

                    Fmp27_WPPW 247 eskskelsaast 258
                                   ++  k l++a +
  gi|70607596|ref|YP_256466.1| 113 SEAIKGLQEAVK 124
                                   211111111111 PP

>> NEMO  NF-kappa-B essential modulator NEMO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1         8   1.2e+03      16      31 ..      54      69 ..      39      79 .. 0.55
   2 ?    8.6   1.1     0.012       1.8       6      50 ..      72     116 ..      67     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 8
                          NEMO 16 neLkealkqsNqalke 31
                                    L ea++q+  ++k 
  gi|70607596|ref|YP_256466.1| 54 MGLEEAVRQQGGSIKS 69
                                  5566666666555554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.012
                          NEMO   6 eqlkellteNneLkealkqsNqalkeRlEeLsawqekqkeerefl 50 
                                   e++k+  +  + L+ea+kq+ + l+e  E ++  qe  k   e +
  gi|70607596|ref|YP_256466.1|  72 ETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   5566666666789*****************999999888766654 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3     0.053       8.2     108     160 ..      34      90 ..       3      91 .. 0.73
   2 ?   10.6   4.0    0.0026      0.41      99     161 ..      70     133 ..      65     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.053
                      Cauli_AT 108 klletLkeaqnrikkleeetkklaekivte....kllkeevkdlderlseirdslka 160
                                     ++ L+e  + i++l++ +  l+e +  +    k l+e+vk+  e ++ +++ +k+
  gi|70607596|ref|YP_256466.1|  34 VVIKRLEENTEAIRNLQQGIMGLEEAVRQQggsiKSLQETVKQHSEAIRGLQEAVKQ 90 
                                   456777777778888888877777777654333367899999999999999999996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0026
                      Cauli_AT  99 ggedkekktklletLkeaqnrikkl.eeetkklaekivtekllkeevkdlderlseirdslkai 161
                                    +e  +++++ +  L+ea ++ +++  e+++ +++  +t k+  e +k l+e ++++ +++k++
  gi|70607596|ref|YP_256466.1|  70 LQETVKQHSEAIRGLQEAVKQQGEIlREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEV 133
                                   5556667777777777776655554145555666667777778888888888888888888776 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.7    0.0051      0.79      37     131 ..      36     135 ..      24     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0051
                         CREPT  37 lekik.dkeeaekllkqv...eealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvr 113
                                   +++++ ++e+ ++l++ +   eea+++     k+L++ +++ ++  + l++ +++q e l+++ e +++l+e +++ +++ 
  gi|70607596|ref|YP_256466.1|  36 IKRLEeNTEAIRNLQQGImglEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAI 116
                                   556652344444444443222677777777788999999999999999999999999999999999999999999999999 PP

                         CREPT 114 kelkshiqsLP.dLtelpd 131
                                   k l++ ++ L  d++e+++
  gi|70607596|ref|YP_256466.1| 117 KGLQEAVKQLSnDIKEVSK 135
                                   9999888888435555554 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.7    0.0018      0.27      91     160 ..      20      90 ..       2      94 .. 0.82
   2 ?    5.8   7.4     0.077        12      93     172 ..      70     144 ..      69     151 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0018
                    JAKMIP_CC3  91 alLreklggeldaerelkareqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqe....Lvekikk 160
                                   + L +k+   l  e ++k  e+  + +r+ +  i  Leea +q+G   k ++e    +k++ e    L e +k+
  gi|70607596|ref|YP_256466.1|  20 STLASKIYDRLKDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQE---TVKQHSEairgLQEAVKQ 90 
                                   4566666666778899999999999****************************...469999988888888876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.077
                    JAKMIP_CC3  93 Lreklggeldaerelkareqleselrktksk.ikdLeeaLaqkGqdskwveekQalikrnqeLvekikkleeeeskLkqei 172
                                   L+e++  + +a r l++  + + e+ + +s+ ik L+e+ +q+ +  k+++e        ++L + ik++ +  +kL  ei
  gi|70607596|ref|YP_256466.1|  70 LQETVKQHSEAIRGLQEAVKQQGEILREHSEaIKSLQETVKQHSEAIKGLQE------AVKQLSNDIKEVSKLTIKLSTEI 144
                                   5555555556666666665556665555554356666666666666666666......33556666666666666666666 PP

>> Corona_S2  Coronavirus S2 glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.2    0.0049      0.76     258     318 ..      67     130 ..      34     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                                   HHHHHHHHHHHHSHHHHHHHHHHHHHHHH...HHHHHHHSHHTTSSHSHHHHHHHHSCHHHHHH CS
                     Corona_S2 258 igniseglatvatalakiqdvvnkqgqal...nelvaqlsknfgaissviqdiydrldkieada 318
                                   i  ++e+++  + a+  +q+ v++qg++l   +e +++l++  +  s +i+ + + + +++ d 
  gi|70607596|ref|YP_256466.1|  67 IKSLQETVKQHSEAIRGLQEAVKQQGEILrehSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDI 130
                                   5566888888888888888888888888833334677888888877877777777766666654 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       9.7   1.5e+03      47      69 ..       9      31 ..       3      54 .. 0.71
   2 ?    1.2   0.1         2   3.1e+02      16      47 ..      57      88 ..      33      94 .. 0.43
   3 ?    9.3   3.1    0.0064      0.99      14      72 ..      93     148 ..      70     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 9.7
                         Sec34 47 ceqlleeqkrleelaeeieekLk 69
                                   ++lle+ k +++la +i ++Lk
  gi|70607596|ref|YP_256466.1|  9 VKKLLEDPKFISTLASKIYDRLK 31
                                  56777777777777777777775 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 2
                         Sec34 16 leqtdealeqLeeleekfksvsektsslheac 47
                                   e +++   ++++l+e +k+ se  + l+ea 
  gi|70607596|ref|YP_256466.1| 57 EEAVRQQGGSIKSLQETVKQHSEAIRGLQEAV 88
                                  22233333334444444444444444444443 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0064
                         Sec34  14 elleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                   e+l+   e  e +++l+e +k+ se  + l+ea +ql ++ k++++l+ ++++++  F+
  gi|70607596|ref|YP_256466.1|  93 EILR---EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFT 148
                                   3333...4455666777778888899999999999999999999999999998888876 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.55        85     130     171 ..      22      62 ..       6      76 .. 0.75
   2 ?    9.0  10.3    0.0066         1      12     108 ..      38     135 ..      23     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.55
                          YkyA 130 ldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqFne 171
                                   l  ++Y+ Lk+ e+ +++lee +e+i + ++ ++   e+  +
  gi|70607596|ref|YP_256466.1|  22 LASKIYDRLKD-EVVIKRLEENTEAIRNLQQGIMGLEEAVRQ 62 
                                   56788999999.999999999999998888877776666555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0066
                          YkyA  12 eavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeie 92 
                                    ++e  +++++ q+ +  le+   +   +i +l+ +  ++ ++ +  ++e v+++ e+l +  e+i++ +e +++ +e i+
  gi|70607596|ref|YP_256466.1|  38 RLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQ-ETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIK 117
                                   5566777778888888888888888877776654.5568888888888888888888888888888888888888888888 PP

                          YkyA  93 eiede..elkkeaeelie 108
                                    +++   +l ++++e+ +
  gi|70607596|ref|YP_256466.1| 118 GLQEAvkQLSNDIKEVSK 135
                                   885332245555555544 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.2    0.0031      0.47      87     166 ..      49     128 ..      39     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                        Tweety  87 tndGvlqltyslrkanhtlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselp.flkk 166
                                   +++G++ l +++r+    + +++++v++ +e+++  l+e +++  ei+ ++ + +++l+ + +q +e+++ l+e + +l++
  gi|70607596|ref|YP_256466.1|  49 LQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIR-GLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVkQLSN 128
                                   5678888888888888888888888887777653.5666667777777777777777777666666666666554423322 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   6.2    0.0041      0.64     111     233 ..      33     147 ..      18     161 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0041
                       DUF4407 111 elaeeqqeeakelkeqlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakek 188
                                   e+  ++ ee++e+ ++l++    l++ +++    i++lq+++++ +++++ l+++++                +g++ +e 
  gi|70607596|ref|YP_256466.1|  33 EVVIKRLEENTEAIRNLQQGimgLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVK---------------QQGEILREH 98 
                                   444444444444444444444443333333333333333333333333333333333...............333333333 PP

                       DUF4407 189 kaqldaaqaelaelkakld....atarlaalraelaeleaerakeraas 233
                                    ++++ +q+++++ ++ ++    a ++l+++ +e ++l+ ++++e+ ++
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKglqeAVKQLSNDIKEVSKLTIKLSTEIGSF 147
                                   3333333333333333333433335556666666666665555555555 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.3     0.029       4.4      28      93 ..      38     103 ..      28     105 .. 0.82
   2 ?    6.6   4.3     0.069        11      25      62 ..      90     128 ..      74     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.029
                                   SCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  28 dlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLk 93 
                                   +l++  e++++l++   +le+ +++q + +k+l+e+ ++  ++    +e+++++ e l+e+ e++k
  gi|70607596|ref|YP_256466.1|  38 RLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIK 103
                                   5667889999999999******************99999988888888888888888887776665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.069
                                   CCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  25 ssedl.gkdleevqallkkhkaleaelaaqqervkalne 62 
                                   ++ ++  ++ e++++l+++ k++ + ++  qe vk+l  
  gi|70607596|ref|YP_256466.1|  90 QQGEIlREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSN 128
                                   445555677777777777777777777777777777762 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.5     0.055       8.5      20      91 ..      40     111 ..      33     114 .. 0.88
   2 ?    7.1   1.2     0.037       5.8       1      40 [.     105     144 ..     105     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.055
                          BRE1  20 skkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefvrklke 91 
                                   ++ ++ + +l++ ++ le    ++   +++++   ++    ++ L++ ++++ e+  +  e+ k++++ +k+
  gi|70607596|ref|YP_256466.1|  40 EENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQ 111
                                   556678899999999999999999999999**99******************99999999999998888775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.037
                          BRE1   1 lqkELvklekafeelseqlskkvkeltileekklrleaek 40 
                                   lq  +++ ++a++ l+e+++++ ++++   +  ++l++e+
  gi|70607596|ref|YP_256466.1| 105 LQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEI 144
                                   6777888899999999999999999999999999999997 PP

>> DUF2312  Uncharacterized protein conserved in bacteria (DUF2312)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.059       9.2       8      52 ..      35      79 ..      27     102 .. 0.86
   2 ?    4.8   0.2      0.14        22       3      29 ..     107     133 ..      99     137 .. 0.82
   3 ?    0.4   0.0       3.3   5.1e+02      60      71 ..     156     167 ..     149     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.059
                       DUF2312  8 fieRiErleeEkkaiaedikdvyaeaKseGfdtkvlrkivklrkk 52
                                  +i R+E++ e ++++++ i  + + ++ +G  +k l++ vk  + 
  gi|70607596|ref|YP_256466.1| 35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSE 79
                                  799**********************************99987665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.14
                       DUF2312   3 dqLrqfieRiErleeEkkaiaedikdv 29 
                                   +  +q  e i  l+e  k++++dik+v
  gi|70607596|ref|YP_256466.1| 107 ETVKQHSEAIKGLQEAVKQLSNDIKEV 133
                                   556777788889999999999999998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 3.3
                       DUF2312  60 eeallelYkaAl 71 
                                   e +++++Yk+Al
  gi|70607596|ref|YP_256466.1| 156 EKTIMMVYKEAL 167
                                   467889999988 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   8.2    0.0066         1     251     361 ..      37     144 ..      30     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0066
                        Tektin 251 krieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvkelee 331
                                   kr+ee ++a ++l++    ++e + ++  +i++L++++++ +++++  q  +++     ++   + ea ++L e vk+ +e
  gi|70607596|ref|YP_256466.1|  37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQ---QGEILREHSEAIKSLQETVKQHSE 114
                                   899999**************************************9999865554...55566666677789********** PP

                        Tektin 332 tieaLkeklaeaeaslkaLertrleleedi 361
                                    i+ L+e +++  + +k+  +   +l  +i
  gi|70607596|ref|YP_256466.1| 115 AIKGLQEAVKQLSNDIKEVSKLTIKLSTEI 144
                                   *****************9999999999998 PP

>> ZapD  Cell division protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6    0.0042      0.64      35     105 ..      35     106 ..      30     113 .. 0.91
   2 ?    3.2   0.4      0.43        66      51      92 ..      97     137 ..      95     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0042
                                   HHCCS-HHHHHHHHHHHHHHHHHCTTT-TTS-HHHHHHHHHHHHHHHHHHHH--.STTHHHHC.-HHHHHHH CS
                          ZapD  35 vleRadlksellkeLerqkqkLkalrenpgvdeealeelleeleqalsaLeaaegklgqslke.delLssir 105
                                   v++R +  +e +++L++    L++  +++g + + l+e++++ ++a++ L++a ++ g+ l+e  e ++s++
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREhSEAIKSLQ 106
                                   78899999******************************************************9456676665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.43
                                   HHHHHHHCTTT-TTS-HHHHHHHHHHHHHHHHHHHH--.STT CS
                          ZapD  51 rqkqkLkalrenpgvdeealeelleeleqalsaLeaaegklg 92 
                                   ++++++k+l+e+ +  +ea++ l e ++q+++++++++ kl 
  gi|70607596|ref|YP_256466.1|  97 EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS-KLT 137
                                   56677777777777777777777777777777777776.554 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3         2   3.1e+02      25      48 ..      68      91 ..      35     104 .. 0.62
   2 ?    8.9   0.3     0.016       2.5      25      71 ..     103     149 ..      96     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 2
                  Occludin_ELL 25 kelhaeleevskkfseLerelkel 48
                                  k+l++ +++ s+ ++ L++ +k++
  gi|70607596|ref|YP_256466.1| 68 KSLQETVKQHSEAIRGLQEAVKQQ 91
                                  455566666666666666555554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.016
                  Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                   k+l++ +++ s+ ++ L++ +k+l+++ ke++k++ ++  e  ++++
  gi|70607596|ref|YP_256466.1| 103 KSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFTN 149
                                   789*****************************999998888777665 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.0      0.02       3.2      57     119 ..      46     108 ..      24     112 .. 0.77
   2 ?    7.8   2.6     0.022       3.4      61     124 ..      78     142 ..      76     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.02
                          COG2  57 FvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                     +l +  +gl+e++++   +++++++ v++  e++   +e+v+++ e  +e  e+ ++l+  
  gi|70607596|ref|YP_256466.1|  46 IRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQET 108
                                   556777788999999999999999999999999999999999999988888777777777655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.022
                          COG2  61 SghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllklde 124
                                   S++ +glqe++++    l +  + ++s++e +++++e++++  e+ k+l +   e+ kl +kl++
  gi|70607596|ref|YP_256466.1|  78 SEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIkEVSKLTIKLST 142
                                   67789999999999999999999999999999999999999999988888775467777776665 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.5     0.018       2.8      77     128 ..      35      86 ..      32      97 .. 0.92
   2 ?    3.5   0.9      0.39        61      74     111 ..      98     135 ..      92     145 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.018
                  Sec8_exocyst  77 ilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLda 128
                                   +++ ++e +e +++l++ +   ++++ ++  ++k l+++ ++++e i+ L++
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQE 86 
                                   67889999***************************************99975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.39
                  Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklstkkkeLke 111
                                   +s++++s+qe  ++ se  + l+ea k+ls++ ke ++
  gi|70607596|ref|YP_256466.1|  98 HSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   45555555555555555555555555555555555444 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  10.5     0.021       3.3      32     102 ..      66     129 ..      21     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                          HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                   + ++ +++++q+ +a       ++ ++e  +++ e l++ +e++++l+++++q +++++ lq++++++s+ 
  gi|70607596|ref|YP_256466.1|  66 SIKSLQETVKQHSEA-------IRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSND 129
                                   222222333333333.......4444444444444555555555555555555555555555555555544 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.66     1e+02      83     111 ..      35      63 ..      21      67 .. 0.86
   2 ?    7.7  10.1     0.025       3.9       9     107 ..      41     136 ..      36     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.66
                   TMF_TATA_bd  83 lLellGeksEeveELraDvaDlKemykeq 111
                                   + + l e +E +  L++ +  l e +++q
  gi|70607596|ref|YP_256466.1|  35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQ 63 
                                   55668899999999999999999999998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.025
                   TMF_TATA_bd   9 psvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGe 89 
                                    +++ + +l++ i  lE  +++   ++++l++  ++ +e i  l    e++k++ + l+e ++ +++lqe  ++  e ++ 
  gi|70607596|ref|YP_256466.1|  41 ENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQ---EAVKQQGEILREHSEAIKSLQETVKQHSEAIKG 118
                                   578889999999999999999999999999999998888888887...778888888888888999999999999999999 PP

                   TMF_TATA_bd  90 ksEeveELraDvaDlKem 107
                                    +E v++L +D++++ ++
  gi|70607596|ref|YP_256466.1| 119 LQEAVKQLSNDIKEVSKL 136
                                   999*********998665 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4     0.016       2.4      15      63 ..      26      75 ..      18      82 .. 0.82
   2 ?    2.7   0.4      0.66     1e+02      26      53 ..      87     128 ..      79     152 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.016
                                  HHHHH.HHHHHHHHHHHHHHHHHHHHHHHCHHHH..........HHHHHH CS
                          GP41 15 lvdgl.qrnvlkvleeqqeldkkleaRlsAleevvrvlgedvaslktrmk 63
                                  + d l ++ v+k lee  e +++l++ +  lee vr+ g  ++sl++  k
  gi|70607596|ref|YP_256466.1| 26 IYDRLkDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVK 75
                                  5555644557899999****************************998765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.66
                                   HHHHHHHH..............HHHHHHHHHCHHHH...... CS
                          GP41  26 vleeqqel..............dkkleaRlsAleevvrvlge 53 
                                   ++++q e+               k+  + ++ l+e v++l +
  gi|70607596|ref|YP_256466.1|  87 AVKQQGEIlrehseaikslqetVKQHSEAIKGLQEAVKQLSN 128
                                   555555553333333111111133333333333333333333 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6     0.055       8.5      72     122 ..      31      81 ..       9      86 .. 0.82
   2 ?    6.2   4.2     0.081        13      74     126 ..      82     134 ..      75     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.055
                        DUF641  72 eeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                   +++ + ++++e+ ++++ ++  +  le+ ++++   i++L+e++++ +++ 
  gi|70607596|ref|YP_256466.1|  31 KDEVVIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAI 81 
                                   5666778899999999999999999*************9999999887765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.081
                        DUF641  74 seleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkkle 126
                                   + l+  +++q ++l+ +  ++k+l++ +k+  + i+ L+e ++++++  k+++
  gi|70607596|ref|YP_256466.1|  82 RGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   456778888999****************************9999988777665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       2.1   3.2e+02      67     105 ..      22      63 ..       1      69 [. 0.52
   2 ?    7.2   8.1     0.031       4.7      11      91 ..      66     143 ..      37     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.1
                                   TTTTTGGGHHH...HHHHHHH...HHHHHHHHHHHHHHHHHH CS
                    Laminin_II  67 lapqLldklke...lkqleeassslsdniseikelIaqARka 105
                                   la ++ d+lk    +k lee+ +++ +  + i  l ++ R++
  gi|70607596|ref|YP_256466.1|  22 LASKIYDRLKDevvIKRLEENTEAIRNLQQGIMGLEEAVRQQ 63 
                                   455555555533335666666555433333344444444555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.031
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
                    Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91 
                                   ++k+ +e +++ s+ +  ++e +++  + ++e  e +k++++++++ ++++k L++ + qL + +ke+ +l  +   ls +
  gi|70607596|ref|YP_256466.1|  66 SIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIK---LSTE 143
                                   55556666666666666666666666666666666666666666666666666666666666666666666666...5555 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.4      0.28        43      24      62 ..      39      77 ..      28      92 .. 0.72
   2 ?    7.3   2.7     0.023       3.5      26      63 ..      97     134 ..      82     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.28
                          Med4 24 hqknearilqLraeveslDekikeivksLkeyekeLkav 62
                                   ++n + i++L++ +  l+e +++  +s+k++++ +k+ 
  gi|70607596|ref|YP_256466.1| 39 LEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQH 77
                                  567788888888888888888888777777777777654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.023
                          Med4  26 knearilqLraeveslDekikeivksLkeyekeLkavp 63 
                                   + ++ i++L++ v+++ e ik +++++k++ + +k+v 
  gi|70607596|ref|YP_256466.1|  97 EHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   55689****************************99986 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3       0.3        47       4      43 ..      37      76 ..      33      82 .. 0.84
   2 ?    8.7   0.6     0.013       1.9       6      49 ..      67     110 ..      60     111 .. 0.92
   3 ?    6.4   1.8     0.068        10      12      49 ..      94     131 ..      83     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.3
                          XhlA  4 erlerietkldnleervdkleekaaeaeekiknleedlkk 43
                                  +rle+  + + nl++ +  lee  + +  +ik+l+e++k+
  gi|70607596|ref|YP_256466.1| 37 KRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSLQETVKQ 76
                                  5677777778888889999999999999999999999875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.013
                          XhlA   6 lerietkldnleervdkleekaaeaeekiknleedlkklesnqk 49 
                                   ++ +++ ++ ++e +  l+e    + e + +  e +k+l++++k
  gi|70607596|ref|YP_256466.1|  67 IKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVK 110
                                   678899999****999************************9987 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.068
                          XhlA  12 kldnleervdkleekaaeaeekiknleedlkklesnqk 49 
                                    l +++e ++ l+e    + e ik l+e +k+l + +k
  gi|70607596|ref|YP_256466.1|  94 ILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIK 131
                                   45667777777777777777777777777777776665 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.5       1.6   2.4e+02      49      84 ..      35      70 ..      20      76 .. 0.77
   2 ?    8.4   7.5     0.012       1.9      17      74 ..      73     130 ..      49     143 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.6
                       DUF2570 49 LteqLeqerqavekqqkianelkakveeekeevkti 84
                                  ++++Le +  a+++ q+    l+++v ++   +k++
  gi|70607596|ref|YP_256466.1| 35 VIKRLEENTEAIRNLQQGIMGLEEAVRQQGGSIKSL 70
                                  567888888899998888888888888888888875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.012
                       DUF2570  17 wlwsqsqkidsLraenkaqaqlieeqqkanqrLteqLeqerqavekqqkianelkakv 74 
                                    + + s+ i  L+  +k q ++++e  +a + L+e ++q   a++  q+  ++l + +
  gi|70607596|ref|YP_256466.1|  73 TVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDI 130
                                   3334455555555555555555555555555555555555555555555555555554 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.5     0.064       9.9       4     100 ..      36     133 ..       9     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.064
                                   HHHHHH-HHHHHHHHCCCTCCCHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHH CS
                  Seryl_tRNA_N   4 iklirenpeavkeklkkRgedkadvdell.eldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkee 82 
                                   ik + en+ea+++ ++   + ++ v +   ++ + +++++++ e+++  + ++ ++ g++ +++ e +++l + vk+ +e 
  gi|70607596|ref|YP_256466.1|  36 IKRLEENTEAIRNLQQGIMGLEEAVRQQGgSIKSLQETVKQHSEAIRGLQEAVKQQ-GEILREHsEAIKSLQETVKQHSEA 115
                                   55666666666666655554444444322022333333333333333333333333.333343368899999999999999 PP

                                   HHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  83 lkaleaelkeleaelekl 100
                                   +k l++++k+l+++++++
  gi|70607596|ref|YP_256466.1| 116 IKGLQEAVKQLSNDIKEV 133
                                   999999999999998876 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2         1   1.6e+02       9      32 ..      67      90 ..      56      93 .. 0.84
   2 ?    7.1   1.1     0.047       7.2       3      24 ..     110     131 ..      95     143 .. 0.60
   3 ?    3.8   0.1      0.51        78       2      24 ..     123     145 ..     122     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 1
                           LPP  9 VsqLkskvdqlssdvnsakaaaqa 32
                                  +++L++ v+q s+ +  +++a+++
  gi|70607596|ref|YP_256466.1| 67 IKSLQETVKQHSEAIRGLQEAVKQ 90
                                  678999999999999999998876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.047
                           LPP   3 deLssqVsqLkskvdqlssdvn 24 
                                   ++ s+ ++ L++ v+qls+d++
  gi|70607596|ref|YP_256466.1| 110 KQHSEAIKGLQEAVKQLSNDIK 131
                                   3344445555555555555555 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.51
                           LPP   2 ldeLssqVsqLkskvdqlssdvn 24 
                                   +++Ls+++++ ++   +ls ++ 
  gi|70607596|ref|YP_256466.1| 123 VKQLSNDIKEVSKLTIKLSTEIG 145
                                   68999999988887777777754 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.7     0.043       6.7      30     109 ..      57     137 ..       8     151 .. 0.61
   2 ?    9.2   5.8     0.009       1.4       6      89 ..      68     151 ..      65     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.043
                       zf-C4H2  30 ekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse.lglekle 109
                                   e+ +++    ++ L++  ++H+e +r +++ +++  ++++e  e+ +   e++k+++e +k l+e v +l ++   ++kl 
  gi|70607596|ref|YP_256466.1|  57 EEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDiKEVSKLT 137
                                   333444444455555555666666666666666666666666555555555666666666666666666655544455444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.009
                       zf-C4H2   6 rektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakkly 86 
                                   ++  + +++ ++ ++   ea++++ ++l+e ++ ++ L++  ++H+e ++ +++ +++l + ike  + + k  +++ +++
  gi|70607596|ref|YP_256466.1|  68 KSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEIGSFT 148
                                   444445555566666666777777788888888888888888888888888888888888888887777777766666665 PP

                       zf-C4H2  87 eey 89 
                                   +  
  gi|70607596|ref|YP_256466.1| 149 NRA 151
                                   544 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7      0.48        75       1      27 [.      18      60 ..      18      96 .. 0.58
   2 ?    5.9   2.5       0.1        16       6      70 ..      67     132 ..      63     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.48
                          Rx_N  1 vvsallqkLadllaeea................kllkgvkeel 27
                                  ++s+l +k+ d l++e+                + ++g++e +
  gi|70607596|ref|YP_256466.1| 18 FISTLASKIYDRLKDEVvikrleenteairnlqQGIMGLEEAV 60
                                  6889999999999999988555555544443333333333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.1
                          Rx_N   6 lqkLadllaeeakllkgvkeeleklkdeLesiqavLedaee.rqikdeavkeWlkelrdlaydaeD 70 
                                   ++ L + +++  + ++g++e +++  + L+     ++   e  ++++ea+k   + +++l+ d+  
  gi|70607596|ref|YP_256466.1|  67 IKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQEtVKQHSEAIKGLQEAVKQLSNDIKE 132
                                   677888888888888888888888888888888888877665555777777777777777777755 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       3.5   5.4e+02       7      36 ..      26      57 ..      23      59 .. 0.68
   2 ?    1.6   0.2       1.7   2.6e+02       1      32 [.      67      98 ..      67     101 .. 0.80
   3 ?    7.6   0.5     0.024       3.8       1      35 [.     102     136 ..     102     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 3.5
                                  HHHHHHH..HHHHHHHHHHHHHHTHHHHHHHH CS
                       DUF4298  7 ildeisa..llqqLeealeqwkklqkklakLd 36
                                  i+d++++  +++ Lee+ e +++lq+ +  L+
  gi|70607596|ref|YP_256466.1| 26 IYDRLKDevVIKRLEENTEAIRNLQQGIMGLE 57
                                  55555552246889999999999988776665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1.7
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                       DUF4298  1 ieemekildeisallqqLeealeqwkklqkkl 32
                                  i+++++++++ s++++ L+ea++q  ++ +++
  gi|70607596|ref|YP_256466.1| 67 IKSLQETVKQHSEAIRGLQEAVKQQGEILREH 98
                                  67889999999999999999999877776665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHH CS
                       DUF4298   1 ieemekildeisallqqLeealeqwkklqkklakL 35 
                                   i+++++++++ s++++ L+ea++q+ +  k+++kL
  gi|70607596|ref|YP_256466.1| 102 IKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   7899***************************9999 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       3.8   5.8e+02      41      70 ..      55      84 ..      50      87 .. 0.77
   2 ?    0.1   0.1       5.7   8.8e+02      42      63 ..      70      91 ..      66     102 .. 0.77
   3 ?    9.2   0.7    0.0084       1.3      36      72 ..      99     135 ..      93     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.8
                       DUF5595 41 kLkelynvdeaqlesleeeekrLeeEierl 70
                                   L+e + ++   ++sl+e  k  +e i+ l
  gi|70607596|ref|YP_256466.1| 55 GLEEAVRQQGGSIKSLQETVKQHSEAIRGL 84
                                  688888888889999999888777766655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 5.7
                       DUF5595 42 LkelynvdeaqlesleeeekrL 63
                                  L+e ++++++ ++ l+e  k +
  gi|70607596|ref|YP_256466.1| 70 LQETVKQHSEAIRGLQEAVKQQ 91
                                  7888899999999999877765 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0084
                       DUF5595  36 aeleskLkelynvdeaqlesleeeekrLeeEierlek 72 
                                    e    L+e ++++++ ++ l+e  k L+++i+++ k
  gi|70607596|ref|YP_256466.1|  99 SEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSK 135
                                   55667899************************99876 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.7     0.061       9.4      14      64 ..      37      94 ..      25     101 .. 0.49
   2 ?    5.4   6.5      0.12        19      17      71 ..      82     136 ..      75     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.061
                 Tropomyosin_1 14 ekaeeleekvKeleqenlekeq.......eiksLtkknqqleeevekleeklkeakek 64
                                  ++ ee  e++++l+q  +  e+        iksL++ ++q  e +  l+e++k++ e 
  gi|70607596|ref|YP_256466.1| 37 KRLEENTEAIRNLQQGIMGLEEavrqqggSIKSLQETVKQHSEAIRGLQEAVKQQGEI 94
                                  5555555555555555555555000000055555555555555555555555555444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.12
                 Tropomyosin_1  17 eeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekk 71 
                                     l+e+vK++ +   e+ + iksL++ ++q  e +  l+e++k+  +  +e +k+
  gi|70607596|ref|YP_256466.1|  82 RGLQEAVKQQGEILREHSEAIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   5678999999999999999999999999999999999999999988887776655 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.5     0.094        14      23      80 ..      68     134 ..       9     147 .. 0.59
   2 ?    4.0   0.8       0.5        77      52      82 ..     106     136 ..      97     209 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.094
                       DUF2203  23 ralrkeleeleeeleeakaeaekse.........aaeleaeleeleaeieelveeieelGvevkdle 80 
                                   ++l++ +++ +e+++  +++ ++++          ++l++++++ ++ i+ l e +++l  ++k+++
  gi|70607596|ref|YP_256466.1|  68 KSLQETVKQHSEAIRGLQEAVKQQGeilrehseaIKSLQETVKQHSEAIKGLQEAVKQLSNDIKEVS 134
                                   2222222222222222222222222332222234555556666666666666666666666666555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.5
                       DUF2203  52 eaeleeleaeieelveeieelGvevkdleag 82 
                                   ++++++ ++ i+ l e +++l  ++k+++++
  gi|70607596|ref|YP_256466.1| 106 QETVKQHSEAIKGLQEAVKQLSNDIKEVSKL 136
                                   3333333333333333333333333333222 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.7      0.58        89       4      70 ..      47     113 ..      23     121 .. 0.70
   2 ?    6.5   1.1     0.086        13       4      45 ..     103     144 ..      93     170 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegk 70 
                                   ++l + ++ lee +++   ++++l+e++++  e  + L+   ++  e l+e++++ k+ ++++++  
  gi|70607596|ref|YP_256466.1|  47 RNLQQGIMGLEEAVRQQGGSIKSLQETVKQHSEAIRGLQEAVKQQGEILREHSEAIKSLQETVKQHS 113
                                   5677788888888888888888888888888888777776655555555444443333333333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLelen 45 
                                   k+l +++++ +e ++ l+e +++l ++++e+ +   +L++e 
  gi|70607596|ref|YP_256466.1| 103 KSLQETVKQHSEAIKGLQEAVKQLSNDIKEVSKLTIKLSTEI 144
                                   334445555555555555555555555555555555555554 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.7      0.07        11      34      75 ..      52      97 ..      17     102 .. 0.55
   2 ?    3.8   1.9      0.38        59      39      71 ..      96     128 ..      87     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.07
                          Med9 34 kLkkarelirelpg....idrsveeqeaeieeleeqlakKrelLkk 75
                                   +    e++r+  g    ++++v++  + i+ l+e ++++ e L++
  gi|70607596|ref|YP_256466.1| 52 GIMGLEEAVRQQGGsiksLQETVKQHSEAIRGLQEAVKQQGEILRE 97
                                  2333334444433355557777777777777777777777777765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.38
                          Med9  39 relirelpgidrsveeqeaeieeleeqlakKre 71 
                                   re+ + ++ ++++v++  + i+ l+e +++  +
  gi|70607596|ref|YP_256466.1|  96 REHSEAIKSLQETVKQHSEAIKGLQEAVKQLSN 128
                                   778888888888888888888888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1884  (0.105081); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                       263  (0.014669); expected 17.9 (0.001)
Passed Fwd filter:                       119  (0.00663729); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             116  [number of targets reported over threshold]
# CPU time: 1.12u 0.32s 00:00:01.44 Elapsed: 00:00:00.49
# Mc/sec: 1648.51
//
Query:       gi|70607597|ref|YP_256467.1|  [L=163]
Description: hypothetical protein Saci_1868 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.068   12.7   0.0      0.078   12.5   0.0    1.1  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.4e-06     0.078     115     157 ..      66     120 ..      12     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-06
                                   E............CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSST CS
                                   x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Exo_endo_phos 115 i............ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarp 157
                                                a+  +++ +++++ +  +++ +++ +  g p +++GDfN+++
  gi|70607597|ref|YP_256467.1|  66 FvrgfgigsklkvARIERVYQPICEMSYVIFRESQRGKNSYGVPSLITGDFNVVS 120
                                   1455555566666666999**********************************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1156.11
//
Query:       gi|70607598|ref|YP_256468.1|  [L=716]
Description: membrane bound kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-31  107.1   0.0    2.2e-30  105.9   0.0    1.5  1  Pkinase       Protein kinase domain
    6.3e-14   51.9   0.0    4.7e-13   49.0   0.0    2.3  1  Pkinase_Tyr   Protein tyrosine kinase
    0.00071   19.6   0.0     0.0031   17.5   0.0    2.1  2  Exonuc_VII_S  Exonuclease VII small subunit
  ------ inclusion threshold ------
       0.12   11.7   0.0       0.31   10.4   0.0    1.6  1  Kdo           Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0   4.9e-34   2.2e-30       1     260 [.     400     712 ..     400     713 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 4.9e-34
                                   EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.......HHHHHHHHHHHHHS..CTTB--EEEEEEE... CS
                       Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.......kkvlrEikilkklk..hpnivrlyevfee... 69 
                                   y++++ lGeG+++ V++a+   +g+ +A+K+ k ++ +++ +       +++ +E + l++l+   +n+v++y++f +   
  gi|70607598|ref|YP_256468.1| 400 YKVESVLGEGGTSYVLSAT---SGERFAIKVPKLSQPSSSATklskvtfEELYKESSNLQRLSegVENVVKIYGIFLDinl 477
                                   788999************9...8********99999888777788899999************99**************** PP

                                   .............SSEEEEEEE--TTEBHHHHHHHHSS--HH....HHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEET CS
                       Pkinase  70 .............kdelylvleyveggeladllerkgslsee....eakkiakqilegleylHskgiiHrDlKpeNiLide 133
                                                ++   +v+ey+egg+ladl++++ +++++     +k +a++++++l+y+Hs g +H D+Kp+Ni+++ 
  gi|70607598|ref|YP_256468.1| 478 lrriergevkyylTNPPAIVMEYMEGGTLADLMRNDIVVNSShwgdIVKVVARKVAKALDYIHSSGYVHLDVKPQNIFFSA 558
                                   *******88666666666****************8888777755657889999***************************7 PP

                                   ................TTEEEE-SGTTSEESSSSCSBCTTTSCGGGS-HHHH....TTSCBSHHHHHHHHHHHHHHHHHSS CS
                       Pkinase 134 ................kgelKitDFGlakelessskltsfvgtseYlAPEvl....keneyskkvDvWslGvilyelltgk 194
                                                   ++e+K++D+G ak++ ++        t++Y++   +     +++ ++++Dv++ G ++y+ ltgk
  gi|70607598|ref|YP_256468.1| 559 pvgktggevfdslvkgRNEVKLGDLGSAKRVGERV----SQYTPNYCPVDQVealiVGKGAETTMDVYAFGATIYTALTGK 635
                                   7999999999998877777*************976....8899***99887755567799********************* PP

                                   -STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS............-HHHHHHHHHHT-SSGCCSTTHHHHHT CS
                       Pkinase 195 ppfsgekgkekvekeldqlekilkilgetkeklpeasei............seeakdllkkllkkdpkkRltaeellq 260
                                      +  +    ve+ +++ ++    lg+ k++ ++ +e             ++e+ +++ k  + dp+kR  ++ell+
  gi|70607598|ref|YP_256468.1| 636 AFSP-PEVVGLVEEAVEDYTRGGSPLGKLKLARDRYEEYyfnvlpstltsaPREISEVVIKATHPDPSKRAKVSELLK 712
                                   9998.66777788888887777777777777777777777899999999999*******************9999886 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.1e-16   4.7e-13      41     257 ..     441     712 ..     400     714 .. 0.69

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.1e-16
                                   SHHHHHHHHHHHHHHHTS..-BTTB--EEEEEE..........SSSS........EEEEEE--TTEBHHHHHHHT.CTTTS CS
                   Pkinase_Tyr  41 teeekeelleeakimkkl..khpnivkllgvct..........keep........llivteyvkgGdLlkfLrkk.ekekl 100
                                   ++ + eel++e + +++l    +n+vk++g+ +             +          iv+ey++gG+L + +r++   ++ 
  gi|70607598|ref|YP_256468.1| 441 SKVTFEELYKESSNLQRLseGVENVVKIYGIFLdinllrrierG--EvkyyltnpPAIVMEYMEGGTLADLMRNDiVVNSS 519
                                   23336788889999999965578999999998876666655430..14455555599****************99544556 PP

                                   BHHHHHH.HHHHHHHHHHHHHHTTEEEST-SGGGEEEEE................TTEEEE-STTTHEETTTSSEEEETTS CS
                   Pkinase_Tyr 101 tlkdlls.falqvAkGmeyLeskklvHrdlaarNvLlse................nkvvkisDfGLardiekddeyvkkee 164
                                   +  d+++ +a +vAk+++y++s  +vH d+  +N++ s                 ++ vk++D G a+++   ++ ++ + 
  gi|70607598|ref|YP_256468.1| 520 HWGDIVKvVARKVAKALDYIHSSGYVHLDVKPQNIFFSApvgktggevfdslvkgRNEVKLGDLGSAKRV--GERVSQYTP 598
                                   667777725789**************************9***************999*************..667777778 PP

                                   STSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSS..GT....................TTTS.HHHHHHHHHHTT CS
                   Pkinase_Tyr 165 aklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlge..sp....................ypgl.kneevleklkeg 221
                                   + +pv    +E+l  +k  ++  Dv++fG +++  +t g+  sp                    + +l  +++ +e +  +
  gi|70607598|ref|YP_256468.1| 599 NYCPVDQ--VEALIVGKgAETTMDVYAFGATIYTALT-GKafSPpevvglveeavedytrggspLGKLkLARDRYEEYYFN 676
                                   8888885..56655544489999**********9998.4412336777777777777655554422221222333333334 PP

                                   EES-BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHH CS
                   Pkinase_Tyr 222 krlekpekcpeelyelmkkcweedpeeRptfselve 257
                                      ++ +++p+e+ e++ k  + dp++R++ sel++
  gi|70607598|ref|YP_256468.1| 677 VLPSTLTSAPREISEVVIKATHPDPSKRAKVSELLK 712
                                   445555667777777777777777777777777765 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.9e-07    0.0031      10      41 ..     255     286 ..     250     288 .. 0.92
   2 ?   -3.1   0.0         2   8.8e+03      23      32 ..     647     656 ..     646     656 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.9e-07
                  Exonuc_VII_S  10 eIvekLEsgelsLeeslklyeeGvkLlkeCek 41 
                                   +++++LE++ + +ee+++++ ++++ +k+C++
  gi|70607598|ref|YP_256468.1| 255 AVLAELENQGVGVEEAFNEFVRATRTYKRCNE 286
                                   5789**************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                  Exonuc_VII_S  23 eeslklyeeG 32 
                                   ee+++ y +G
  gi|70607598|ref|YP_256468.1| 647 EEAVEDYTRG 656
                                   9999999998 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.9e-05      0.31      73     154 ..     475     559 ..     471     571 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.9e-05
                           Kdo  73 vavpkpvaagavkvgleyrAlllterlegaqdLedllakwae....laeelkrallkavgrliaklhragvnHadlyakni 149
                                   ++ ++ +  g+vk+ l    ++++e +eg   L+dl+++  +      +   +   ++v+++   +h+ g  H d+ ++ni
  gi|70607598|ref|YP_256468.1| 475 INLLRRIERGEVKYYLTNPPAIVMEYMEGG-TLADLMRNDIVvnssHWGDIVKVVARKVAKALDYIHSSGYVHLDVKPQNI 554
                                   566677777788888888889999999995.47777776444222222334445556666666779*************** PP

                           Kdo 150 llqqe 154
                                   ++ + 
  gi|70607598|ref|YP_256468.1| 555 FFSAP 559
                                   *9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5048.51
//
Query:       gi|70607599|ref|YP_256469.1|  [L=180]
Description: hypothetical protein Saci_1871 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1312.48
//
Query:       gi|70607600|ref|YP_256470.1|  [L=671]
Description: putative ATP-dependent helicase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-06   27.7   0.0    9.2e-05   22.3   0.0    2.5  3  DEAD        DEAD/DEAH box helicase
    0.00021   21.3   0.0     0.0011   19.0   0.0    2.1  1  ResIII      Type III restriction enzyme, res subunit
     0.0087   16.4   0.0      0.029   14.7   0.0    1.9  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.027   14.8   0.0      0.056   13.8   0.0    1.6  1  Phage_ASH   Ash protein family
       0.03   14.4   0.1      0.055   13.5   0.1    1.3  1  DUF1357     Protein of unknown function (DUF1357)
      0.083   11.9   0.0       0.15   11.1   0.0    1.3  1  T2SSE       Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.1e-08   9.2e-05       3      73 ..      23      88 ..      21     119 .. 0.87
   2 ?    2.3   0.0     0.043   1.3e+02      80     171 ..     163     253 ..     154     258 .. 0.69
   3 ?   -3.7   0.0       2.9   8.6e+03      95     114 ..     421     440 ..     408     451 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.1e-08
                                  HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73
                                   Q+e +  + + + +l++a+TGsGKT   ++ +l+++      +g  +  + P+++L+ ++++ lk+ +  
  gi|70607600|ref|YP_256470.1| 23 FQEELLYSLDKYRRILLRAPTGSGKTFTLIVSLLKNL-----GRGMPVTGLYPSKSLVYDQYESLKNTLIR 88
                                  6888888888999*********************999.....567788899**************998765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.043
                                   EEETTSSHHHHHHHHH.TTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                   xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  80 liiggvaardqlskld.ngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                   +++g+++ ++ql ++  +g++ v +    l++l+++ +       ++ +DE + +     +  +n ++  ++   +     
  gi|70607600|ref|YP_256470.1| 163 STLGKSPHSSQLIEMAmKGIRSVNMSKATLVNLFNDFS--RFFNGYFFVDEFHLYNGI-ERSSLNVLVDMVEFYWKYLGTP 240
                                   55667777777777764669999999999999886333..444478999****99998.6666777677665444443355 PP

                                   SEEEEEESSBS.H CS
                                   xxxxxxxxxxx.x RF
                          DEAD 160 rqvivlSATlp.k 171
                                   + +++ SAT++  
  gi|70607600|ref|YP_256470.1| 241 HSIVFSSATPTsM 253
                                   5699999*99855 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.9
                                   HTTCSEEEEEHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          DEAD  95 dngvdivvgtpgrlddllst 114
                                    ++v+i+v   +r +d l++
  gi|70607600|ref|YP_256470.1| 421 TAEVHIFVEANKRAADSLNK 440
                                   46799999999999997742 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.7e-07    0.0011       4     144 ..      20     215 ..      17     251 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-07
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG... CS
                        ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayk 83 
                                   lr+ Qee + +l      ++ +r+l+ ++TG+GKT+++ ++l ++l +      +  l p+ksl+   +e +k++l     
  gi|70607600|ref|YP_256470.1|  20 LRKFQEELLYSL------DKYRRILLRAPTGSGKTFTLiVSLLKNLGR---GMPVTGLYPSKSLVYDQYESLKNTLIRMGF 91 
                                   555555555555......57789**************95555555554...348999999999999999999776665544 PP

                                   ......GEEEESSS-B--.....................-SEEEEEHHHHHHTH........................... CS
                        ResIII  84 e.....igkkvsgdkkka..............kekdstnkkilvttiqsldadseee........................ 121
                                   +      ++k++ ++ ++                              +l++d ++e                        
  gi|70607600|ref|YP_256470.1|  92 SnngdyFMGKIKVEGVDQsegipeeeevklrvV---------------KLTSDTKREvfeslehfipnpkelllvltvpey 157
                                   444555333344333333223322222222221...............222222122222233333333334455555555 PP

                                   ........................................HHHTTT-SEEEEETGGGT CS
                        ResIII 122 ...................................eeeseellrdrfdviiiDEaHrl 144
                                                                       +  ++++r ++ ++++DE H +
  gi|70607600|ref|YP_256470.1| 158 pymflstlgksphssqliemamkgirsvnmskatlVNLFNDFSRFFNGYFFVDEFHLY 215
                                   5555555555444444444444444443332122233333333333337777777755 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.5e-06     0.029      66     111 .]     366     409 ..     358     409 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.5e-06
                                   SSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  66 esdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                   es+v++  ++++ G+dip+++l  + + +   +++iqr GR gR++
  gi|70607600|ref|YP_256470.1| 366 ESKVIVGNNALSFGVDIPDLDLGYITSND--AETLIQRFGRFGRMN 409
                                   678******************98887655..789**********85 PP

>> Phage_ASH  Ash protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.056      30      86 ..     207     267 ..     181     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                     Phage_ASH  30 ffvrsalthkefrnkalss...MVAlagqpsgwPvsavagpanpvratthkeia.vSggsl 86 
                                   ffv++ + +   ++  l+    MV   ++  g P s+v+++a+p + t  k i  +Sg+++
  gi|70607600|ref|YP_256470.1| 207 FFVDEFHLYNGIERSSLNVlvdMVEFYWKYLGTPHSIVFSSATPTSMTFDKVITaQSGQGN 267
                                   5888888887766666665677**************************9987751444333 PP

>> DUF1357  Protein of unknown function (DUF1357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.9e-05     0.055     160     214 ..     407     463 ..     384     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                       DUF1357 160 klrktassnsssvdsvkgnivvkseera..slldsnfvpinftefvqaisntykqrr 214
                                   ++ k+ ssns s  + +  i v +++ra  sl + n   + + ef+q i n y+ r 
  gi|70607600|ref|YP_256470.1| 407 RMNKNISSNSPSESTAEVHIFVEANKRAadSLNKVNGKELTYEEFIQLINNIYQGRV 463
                                   688************************866788899*****************9875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.15     112     150 ..      17      55 ..       4      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                         T2SSE 112 ealkekiaevlrkavrerglilvsGgTgsGKttllyall 150
                                   +    k++e l +++ ++  il+  +TgsGKt +l + l
  gi|70607600|ref|YP_256470.1|  17 GIRLRKFQEELLYSLDKYRRILLRAPTGSGKTFTLIVSL 55 
                                   5555677888888889****************9985443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4085.13
//
Query:       gi|70607601|ref|YP_256471.1|  [L=255]
Description: hypothetical protein Saci_1873 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   12.1   0.1       0.35   11.4   0.1    1.3  1  NPV_P10   Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     2e-05      0.35      10      52 ..     172     215 ..     170     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                       NPV_P10  10 radikavdd.kVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                   r d+k+++d kV+ ++++v+++  n++d +e   k+ + s+ ++
  gi|70607601|ref|YP_256471.1| 172 RVDVKEIQDfKVEKVKDEVTNIPVNIKDAEEFGYKIKSSSKLIE 215
                                   889***9776**********************999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1764.53
//
Query:       gi|70607602|ref|YP_256472.1|  [L=351]
Description: hypothetical protein Saci_1874 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-17   61.3   0.0    9.6e-17   60.9   0.0    1.2  1  Csc2      Csc2 Crispr


Domain annotation for each model (and alignments):
>> Csc2  Csc2 Crispr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   5.4e-21   9.6e-17      91     229 ..     127     270 ..     103     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 5.4e-21
                          Csc2  91 veasckkcpDcilYGfAigdsg..sekskvvtddAfsllayeesveeftlnavfetGtm...sekgeassalnesdhikPe 166
                                   +   c++cp+c+ +GfA+ ++     ks+v  d   + ++ ++sv  +t+nav+++ +    + +g+ + +l     +k +
  gi|70607602|ref|YP_256472.1| 127 MGGLCRECPNCMTFGFAVAEDAkyNLKSRVEGDLFIATTPEQKSVVVRTFNAVDDATKTtfiETEGTRTGSLFRLSLVKGG 207
                                   5678**************98875578***************************98766567799999999*********** PP

                          Csc2 167 vtFpdvvtlkDvtedellYvlgnilrtrrYGAqesRtGkvknellgivfsdgEifsnLeltqa 229
                                   + F   v++kDvt +e+   +  +  t r G +++  Gkvk ++  +++s  E+ s L l ++
  gi|70607602|ref|YP_256472.1| 208 TLFVGKVSMKDVTPAEFSVLVLSLATTARIGGNTTDFGKVKIRIPAVILSPYEMSSGLDLFNS 270
                                   *******************999************************************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2572.58
//
Query:       gi|70607603|ref|YP_256473.1|  [L=862]
Description: hypothetical protein Saci_1875 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    9.0   4.1        4.9    7.3   0.1    3.8  3  MetOD2    Metanogen output domain 2


Domain annotation for each model (and alignments):
>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.57     1e+04       9      31 ..     106     128 ..     102     131 .. 0.70
   2 ?    0.1   0.1     0.048   8.7e+02      65      84 ..     292     311 ..     249     315 .. 0.67
   3 ?    7.3   0.1   0.00027       4.9      23      54 ..     375     404 ..     366     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.57
                        MetOD2   9 verAkkaGvdkeiidEYarLaks 31 
                                     +Akk+  +++ii+  a+L+k+
  gi|70607603|ref|YP_256473.1| 106 DRMAKKEEEARAIITRIAELTKN 128
                                   45777777777788777777775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.048
                        MetOD2  65 nlekkleaqeerlkqikkel 84 
                                   +l+ ++ ++eer+kqi +++
  gi|70607603|ref|YP_256473.1| 292 ELKPEVIDDEERVKQIPNSI 311
                                   35555667777777777766 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00027
                        MetOD2  23 dEYarLaksvevnkrllslLsqtydidddkae 54 
                                   +EY + +ks e   +l+ +L+++y+  ++  +
  gi|70607603|ref|YP_256473.1| 375 KEYVKTFKSEELLEKLIPVLKKLYGQKRE--T 404
                                   69**********************99865..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (862 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 5376.02
//
Query:       gi|70607604|ref|YP_256474.1|  [L=221]
Description: hypothetical protein Saci_1876 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.9   0.3      0.035   14.6   0.1    1.8  2  Syntaxin-6_N  Syntaxin 6, N-terminal
      0.017   14.9   0.1      0.031   14.1   0.1    1.5  1  HTH_38        Helix-turn-helix domain
      0.052   14.0   0.7       0.15   12.5   0.7    1.7  1  DASH_Dad2     DASH complex subunit Dad2
      0.076   12.9   0.4       0.16   11.9   0.4    1.5  1  HTH_5         Bacterial regulatory protein, arsR family
      0.078   12.9   0.0       0.14   12.1   0.0    1.4  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 


Domain annotation for each model (and alignments):
>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         5   1.8e+04      50      62 ..      83      95 ..      76      96 .. 0.67
   2 ?   14.6   0.1   9.8e-06     0.035      32      77 ..     157     203 ..     127     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                  Syntaxin-6_N 50 lrsiewdledLee 62
                                  +++i + l+d++e
  gi|70607604|ref|YP_256474.1| 83 ISQIHEVLRDFDE 95
                                  5667777777776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.8e-06
                  Syntaxin-6_N  32 ss.stseeldetrteLrkalrsiewdledLeetvriveknpskfkid 77 
                                   s+ ++  e++e  + L+k++++i+++l+ + + v+  ek p+ +k++
  gi|70607604|ref|YP_256474.1| 157 SElTQMREIREVASRLNKTVSTISKQLSKISDLVECTEKRPKMCKLN 203
                                   33347899*******************************99988876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.6e-06     0.031      23      41 ..     165     183 ..     147     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.6e-06
                        HTH_38  23 lreIArrLgrspsTIsREl 41 
                                   +re+A rL++  sTIs+ l
  gi|70607604|ref|YP_256474.1| 165 IREVASRLNKTVSTISKQL 183
                                   89**************865 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   4.1e-05      0.15       9      44 ..     157     192 ..     150     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                     DASH_Dad2   9 aELeaLkqlrdlsdslakqleeLeeklstladgtea 44 
                                   +EL++++++r+++++l+k +++++++ls+++d  e+
  gi|70607604|ref|YP_256474.1| 157 SELTQMREIREVASRLNKTVSTISKQLSKISDLVEC 192
                                   79***************************9986665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   4.4e-05      0.16       7      39 ..     152     186 ..     148     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                                   HHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHH CS
                         HTH_5   7 ILklLae..gelcvcelaeelglsqstvShHLkkL 39 
                                   ++ l++e  + + + e a  l+++ st+S +L+k 
  gi|70607604|ref|YP_256474.1| 152 MIELMSEltQMREIREVASRLNKTVSTISKQLSKI 186
                                   67788888778999*******************97 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.14       4      42 ..     153     191 ..     151     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHT CS
                         HTH_1   4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelg 42 
                                   ++l  ++ + + +++ A +L+ + +++s+q+++  ++++
  gi|70607604|ref|YP_256474.1| 153 IELMSELTQMREIREVASRLNKTVSTISKQLSKISDLVE 191
                                   67788889999********************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1450.36
//
Query:       gi|70607605|ref|YP_256475.1|  [L=287]
Description: hypothetical protein Saci_1877 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-12   46.4   0.1    1.4e-11   44.9   0.1    1.8  2  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
    0.00029   21.1   2.6     0.0027   18.0   0.7    2.7  2  Cas6_N       Cas6 N-terminal domain


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.67     6e+03      11      29 ..     104     123 ..      90     136 .. 0.64
   2 !   44.9   0.1   1.6e-15   1.4e-11       1      85 [.     157     281 ..     157     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
                                   TEEESS.--HHHHHHHHHHH CS
                   CRISPR_Cas6  11 krkgll.psprlvfssllrr 29 
                                   ++++ l p+++ v+ sl++ 
  gi|70607605|ref|YP_256475.1| 104 GYDMSLePEVSKVMTSLFSG 123
                                   44444488888888888765 PP

  == domain 2  score: 44.9 bits;  conditional E-value: 1.6e-15
                                   EEEEEEE-EE............TEEESS--HHHHHHH....................HHHHHHHHTSS............E CS
                   CRISPR_Cas6   1 lrfltPtrfk............krkgllpsprlvfss....................llrrwnalaglkgk.........p 40 
                                   ++++tP +fk            k+++ lp p+ +fs+                    ll+ +n+l+++++          p
  gi|70607605|ref|YP_256475.1| 157 VKLITPSMFKdpfekladldrvKYRRYLPFPAFIFSTnvfeifretykrniirlsygLLESHNNLNTVRKVwyyydgkwlP 237
                                   5789****************99999999**********************99999999999*******9556555543333 PP

                                   ECHHHHHHEEEEEEEE......--.HHHECCCHHHHHHHH-SSSTGGGTTT- CS
                   CRISPR_Cas6  41 tveeelegGfvGevky......sg.eleelekllrfaeylgvGkktafGlGk 85 
                                           G+vG++k+      ++ +++ +++++ +a+++gvG+++a+G+G 
  gi|70607605|ref|YP_256475.1| 238 --------GVVGYLKFfvrkglRKeVMNIFREIFIHANIMGVGTGRAAGFGF 281
                                   ........********9986552279*************************5 PP

>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.7     3e-07    0.0027      13      72 ..      22      85 ..      11     141 .. 0.60
   2 ?   -2.7   0.0      0.81   7.3e+03      77      97 ..     189     208 ..     188     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-07
                                  EE--SSTTHHHHHHHHTSSGGGHHHHH---TT..-SEEE---BS.TTSB--.S------EE-SS CS
                        Cas6_N 13 vilppltSKvskyillslspslsklvesreky..Kplrisvlkd.ngrrly.aegkkkvrlkag 72
                                   i    t K  k++l + +p l+++ e ++k   Kp+r++ l d n++ +y ++  +   + ++
  gi|70607605|ref|YP_256475.1| 22 FITNDYTGKFVKTVLINANPDLQEVFEGKKKVqpKPMRVTSLLDeNNEAVYpKHIVNRFEMDHK 85
                                  56677899*******************99986559*******9989999985544444444333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.81
                                   EEEEEESSSCCTTTTGSEEEE CS
                        Cas6_N  77 fslsfaledvveeivekegvv 97 
                                   f++s+   ++++e+ ++ ++ 
  gi|70607605|ref|YP_256475.1| 189 FIFSTNVFEIFRETYKR-NII 208
                                   77888888888886643.344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2279.21
//
Query:       gi|70607606|ref|YP_256476.1|  [L=74]
Description: hypothetical protein Saci_1878 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 615.92
//
Query:       gi|70607607|ref|YP_256477.1|  [L=96]
Description: hypothetical protein Saci_1879 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-15   55.4   0.2    6.9e-15   55.0   0.2    1.2  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.2   3.9e-19   6.9e-15       1      74 [.       1      72 [.       1      74 [. 0.96

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.9e-19
                                  EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHH CS
                   CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfe 74
                                  m+v+v+YDi +d+k r kv+++l++yG+  +  SV+ g+ls +++  + +r+ k+++++ ds+ i+++++  f+
  gi|70607607|ref|YP_256477.1|  1 MYVVVAYDI-SDEKVRGKVRRLLRRYGLSFISRSVYAGRLSWNRALLISERVAKYLEER-DSVVIVPVQNVDFS 72
                                  9********.***********************************************87.*******9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 682.19
//
Query:       gi|70607608|ref|YP_256478.1|  [L=169]
Description: hypothetical protein Saci_1880 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0083   16.1   0.2      0.018   15.0   0.1    1.5  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.17   3.1e+03     116     135 ..      44      64 ..      17      72 .. 0.55
   2 !   15.0   0.1     1e-06     0.018     221     255 .]     132     166 ..     129     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.17
                      PDDEXK_1 116 pvalelefg.gekvrLkGriD 135
                                      le+ f+ g + ++ G  D
  gi|70607608|ref|YP_256478.1|  44 KKTLEIYFNfGDWAKIIGVPD 64 
                                   223444333546777777777 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-06
                      PDDEXK_1 221 llqeleelaeeilagefparpskkCeyCpyksvCr 255
                                   +l+++ +++++i +g+++ r +k C +C yk++C+
  gi|70607608|ref|YP_256478.1| 132 VLDYIADQLQRIVNGRVEGRRNKFCPSCIYKRICP 166
                                   5789999***************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1163.71
//
Query:       gi|70607609|ref|YP_256479.1|  [L=305]
Description: hypothetical protein Saci_1881 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-41  141.4   0.0    3.8e-41  141.1   0.0    1.1  1  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.1   0.0   2.1e-45   3.8e-41       7     256 ..       8     245 ..       3     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.1e-45
                                   EEEEEEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHHHH CS
                      Cas_Cas1   7 gaylrkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepeesgnvelrra 86 
                                   +a++ +kg  l+++    ++ +++  d+e +vi+g+ v l+++++ +l++ +ipv++  ++   +  ++p  ++ v++rr+
  gi|70607609|ref|YP_256479.1|   8 NATIMRKGSDLQMTWSVGKNLTVSSLDLELVVIVGNnVRLTSEVILFLSSLNIPVLVHGKRND-VVLVSPFLNSLVNVRRK 87 
                                   45688999999999988889***********************************99998866.5678899********** PP

                                   HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHHHH CS
                      Cas_Cas1  87 QyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfeafd 167
                                    y ++dd +  l la+k+++gk+  + +v +++   +      +   e++  l+++++++s++eLr +E+e++ka +e+++
  gi|70607609|ref|YP_256479.1|  88 FYTLSDDMK--LYLARKFIKGKILGMINVAKYFMYLT------KVPVEIDLELKQIDNTKSIDELRSVEAEMSKACWEQLR 160
                                   *****9988..**********************9877......666777778899************************** PP

                                   HHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHHCHHHHHH CS
                      Cas_Cas1 168 kllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpllvDrlvls 248
                                   k+l+   +f+gR+ r  +D++N   +++Y+++y+ +++++ a gLdPy G +H + pgr++L +D+ E+f+p+ + + v+ 
  gi|70607609|ref|YP_256479.1| 161 KFLP--PSFTGRKPRN-EDEINRAVDYAYSVIYALCTHSLIASGLDPYGGLMHVEYPGRTALTYDFSEMFKPVAIHS-VIA 237
                                   ***8..5799*****9.9******************************************************65555.555 PP

                                   HHHTTSS- CS
                      Cas_Cas1 249 linkrqlk 256
                                   + +k +lk
  gi|70607609|ref|YP_256479.1| 238 VSRKVKLK 245
                                   55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1961.99
//
Query:       gi|70607610|ref|YP_256480.1|  [L=74]
Description: hypothetical protein Saci_1882 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-05   22.7   4.5    0.00035   21.0   4.0    1.8  1  CcdA           Post-segregation antitoxin CcdA
  ------ inclusion threshold ------
      0.023   14.0   0.6      0.024   13.9   0.6    1.0  1  PPDK_N         Pyruvate phosphate dikinase, PEP/pyruvate bind
      0.025   14.7   0.9      0.034   14.3   0.5    1.5  2  Mrr_N          Mrr N-terminal domain
      0.039   14.7   5.8      0.047   14.4   5.8    1.2  1  PSK_trans_fac  Rv0623-like transcription factor
      0.048   14.2   1.3      0.057   13.9   1.3    1.1  1  YtxH           YtxH-like protein
      0.053   12.7   0.8      0.061   12.5   0.8    1.0  1  NAD_binding_4  Male sterility protein
       0.31   11.1   3.8       0.27   11.3   2.1    1.7  2  DUF4449        Protein of unknown function (DUF4449)


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   4.0   1.3e-07   0.00035       4      52 ..       5      53 ..       3      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                          CcdA  4 vnlsldsdllaqAralgiNlSatleeaLaeevkeekaerwkeenreaie 52
                                  +++ + ++l ++A +lgiNl +++e+aL+e++++++ er +   ++  e
  gi|70607610|ref|YP_256480.1|  5 ISVRVRKELKRRAEELGINLREVVERALEEAIRKKEMERVRTIAKKIQE 53
                                  578899***************************8877775443333333 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   9.2e-06     0.024     240     293 ..      14      64 ..       3      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-06
                        PPDK_N 240 kivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfa 293
                                   k+ ++e +   +  ev e ++ + a++++e+e++++iakki+++++ + + E+a
  gi|70607610|ref|YP_256480.1|  14 KRRAEELG--INLREVVE-RALEEAIRKKEMERVRTIAKKIQENMQGISEEEWA 64 
                                   33333333..34444533.566678****************************9 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   3.2e+03      21      29 ..      11      19 ..       3      32 .. 0.57
   2 ?   14.3   0.5   1.3e-05     0.034      10      46 ..      34      71 ..      25      74 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                         Mrr_N 21 keirervae 29
                                  ke+++r++e
  gi|70607610|ref|YP_256480.1| 11 KELKRRAEE 19
                                  444444433 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                         Mrr_N 10 ealadgsehrlkeirervaerf.glseeeraellpsgk 46
                                  ea+++++ +r++ i ++++e++ g+seee+a+l  +++
  gi|70607610|ref|YP_256480.1| 34 EAIRKKEMERVRTIAKKIQENMqGISEEEWAQLVRESR 71
                                  45566899999*********************986655 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   5.8   1.8e-05     0.047      13      61 ..      12      64 ..       4      74 .] 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX--HHHHHHHHHHHHHT CS
                 PSK_trans_fac 13 lareLarltgeskteAvrrAleerlerlrre....raepllerllallrraaa 61
                                    ++ a+  g ++ e+v+rAlee++++ + e     a++ +e+++ + +++ a
  gi|70607610|ref|YP_256480.1| 12 ELKRRAEELGINLREVVERALEEAIRKKEMErvrtIAKKIQENMQGISEEEWA 64
                                  55556888999***************998774444444444444444443333 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.3   2.2e-05     0.057      26      72 ..       9      60 ..       7      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                          YtxH 26 tRkdlkekaddlkekakelleeakeka.....kekaedlkekvkekadelke 72
                                  +Rk+lk++a++l  ++ e++e+a e a      e++  +++k++e  + ++e
  gi|70607610|ref|YP_256480.1|  9 VRKELKRRAEELGINLREVVERALEEAirkkeMERVRTIAKKIQENMQGISE 60
                                  7***************************988866677777777777666555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   2.4e-05     0.061      27      87 ..       7      69 ..       2      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                                  EEE-SSSHHHHHH...HHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH CS
                 NAD_binding_4 27 llvRaksgesaee...RleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaee 87
                                  + vR++ ++ aee    l +e+ +  l++a++k+  er++ ++  ++e+  G+see++ +l++e
  gi|70607610|ref|YP_256480.1|  7 VRVRKELKRRAEElgiNL-REVVERALEEAIRKKEMERVRTIAKKIQENMQGISEEEWAQLVRE 69
                                  556655555444422234.88999999999999***************************9875 PP

>> DUF4449  Protein of unknown function (DUF4449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.47   1.2e+03      50      66 ..       3      19 ..       2      23 .. 0.78
   2 ?   11.3   2.1    0.0001      0.27      30      67 ..      24      62 ..      19      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.47
                       DUF4449 50 Daelyevkqeaerakee 66
                                  D + ++v++e +r  ee
  gi|70607610|ref|YP_256480.1|  3 DVISVRVRKELKRRAEE 19
                                  67788999999988776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                       DUF4449 30 irpaiqkalekqird.aleklDaelyevkqeaerakeea 67
                                  +r+++++ale++ir+ ++e++ +++ +++++++   ee+
  gi|70607610|ref|YP_256480.1| 24 LREVVERALEEAIRKkEMERVRTIAKKIQENMQGISEEE 62
                                  89***********86269**************9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2223  (0.123989); expected 358.6 (0.02)
Passed bias filter:                      963  (0.0537119); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 542.33
//
Query:       gi|70607611|ref|YP_256481.1|  [L=131]
Description: hypothetical protein Saci_1883 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-05   22.9   0.1    0.00012   22.6   0.1    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   6.6e-09   0.00012      28     116 ..      22     113 ..       6     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.6e-09
                                   S..SEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHH CS
                           PIN  28 l..eelvtsalvlaEllyvlar...rkskrekaaelvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAk 102
                                   +   ++++  l+l+E+ + + +    + +++ a+e+ +l+++ + +++i++  ++ ++e+  ia  +g++ +Da  + +  
  gi|70607611|ref|YP_256481.1|  22 VdlKNIYILHLTLYEVGNAIWKdafLHGRIKNAKEVALLFQQlMGEFNIID--DPPLDEVIGIAISKGITYYDASYVYVSA 100
                                   345899******************988888888888888888899999966..99999999******************** PP

                                   HHT-EEE.ESSTHH CS
                           PIN 103 ehgikliatfDedf 116
                                   +++++l+ ++D+++
  gi|70607611|ref|YP_256481.1| 101 KEKLILV-SNDKEL 113
                                   ****999.***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 929.55
//
Query:       gi|70607612|ref|YP_256482.1|  [L=290]
Description: hypothetical protein Saci_1884 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.1e-105  349.7   0.0   8.4e-105  349.5   0.0    1.0  1  DUF1177   Protein of unknown function (DUF1177)
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.35   11.0   0.0    1.5  1  Oscp1     Organic solute transport protein 1


Domain annotation for each model (and alignments):
>> DUF1177  Protein of unknown function (DUF1177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.5   0.0  9.4e-109  8.4e-105       3     270 ..      28     286 ..      26     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 349.5 bits;  conditional E-value: 9.4e-109
                       DUF1177   3 vegekgstdfvkiliegkeGkskggsaptlgilGrlGgigarperiGlvsDaDGalaalavalkllemkekgdalegdviv 83 
                                    e++ g+++++k+l++g       + ++++++lGrlG+i++r+e +GlvsDaDGa+++l+v+++ll+++ekg +l++dv +
  gi|70607612|ref|YP_256482.1|  28 EEKQLGEVTYIKCLYRG-------RGKDRVEVLGRLGAIQVRQE-KGLVSDADGAIVSLTVLFELLNLREKGVELNVDVSF 100
                                   5788899********99.......56899*************98.9*********************************** PP

                       DUF1177  84 athicpdaptqphePvpfmgspvdlaeankeevdpeldailsiDttkgnriikkrgfaisptvkeGyilkvsedlldiler 164
                                   +t+i+ da+++ph+P++fm ++++l+ea++eevd+e+++ilsiD+tkgnri+k+++fai++++k+Gyilkv+++l+di++r
  gi|70607612|ref|YP_256482.1| 101 VTNISLDAKLIPHRPFNFMVPLIGLDEALREEVDREANLILSIDSTKGNRIAKYDDFAITHVIKDGYILKVKDELVDIYNR 181
                                   ********************************************************************************* PP

                       DUF1177 165 vtgkepvvlplttqDitPygngvyHlnsilqPavatkaPvvgvAittetvvpGcatgashledleeaarfviEvakefgkg 245
                                   vtg+e++++pltt+D+tP++++vyH++++++P++++++P++g+A+++++vvpG+ tg++++e+le+a+rf++Ev+k+++kg
  gi|70607612|ref|YP_256482.1| 182 VTGHEVYFVPLTTGDLTPMEYNVYHISTLVSPWLYSNSPLIGIATVSKQVVPGYVTGVQDVEMLEHASRFCLEVLKYVEKG 262
                                   ********************************************************************************* PP

                       DUF1177 246 kvkfydeeefeelkelyGelkllqt 270
                                     ++y+e+e++elke++Ge++l++ 
  gi|70607612|ref|YP_256482.1| 263 G-TVYEESELKELKEKLGESSLMRL 286
                                   *.9*****************99876 PP

>> Oscp1  Organic solute transport protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.9e-05      0.35      33      68 ..     253     288 ..     240     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                         Oscp1  33 kkfldelfkpqklyskkalktvleklahsSiMrLne 68 
                                    ++l+ + k   +y++++lk++ ekl +sS+MrL +
  gi|70607612|ref|YP_256482.1| 253 LEVLKYVEKGGTVYEESELKELKEKLGESSLMRLKR 288
                                   556677777888**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2044.09
//
Query:       gi|70607613|ref|YP_256483.1|  [L=415]
Description: alkyl-dihydroxyacetonephosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-27   93.5   0.0    1.6e-26   92.7   0.0    1.4  1  FAD_binding_4  FAD binding domain
      5e-07   29.6   0.1    3.5e-06   26.8   0.1    2.1  2  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
  ------ inclusion threshold ------
      0.037   13.3   0.2      0.053   12.8   0.2    1.1  1  HlyE           Haemolysin E (HlyE)


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   2.6e-30   1.6e-26       3     134 ..      49     182 ..      47     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 2.6e-30
                                   EEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC..SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                 FAD_binding_4   3 avvrpeseeevaaalrlaneaglpvlvrGgGssllgqav..atggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                   +vv + +ee++ +a+rl++ +++p+l+rG+G+s++gq++    +++vld+ r++ ++e d  + ++++ + v++ ++ ++l
  gi|70607613|ref|YP_256483.1|  49 GVVMADDEEDIFNAVRLCDTHHIPLLARGAGTSTIGQVLpiSPSTIVLDINRMREVIESD--DSWVRITPSVKVFKALQYL 127
                                   699***********************************99999*******99******99..79***************** PP

                                   HHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGT..EEEEEEEETTSE CS
                 FAD_binding_4  82 aakglllglepgsgipgtvGGaiatnagGygsekyGlirdn..vlglevvladGe 134
                                   +++g  l+++p+s+  +t+GG+ia++ +G gs +yG ++dn  + +++vv ++G+
  gi|70607613|ref|YP_256483.1| 128 RKRGKELRVYPSSFYISTLGGYIAGGDVGIGSFQYGYHFDNggINSVRVVGPTGK 182
                                   ***************************************87779*********98 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.098   5.8e+02       9      49 ..     220     260 ..     219     282 .. 0.84
   2 !   26.8   0.1   5.8e-10   3.5e-06     221     250 .]     384     413 ..     377     413 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.098
                                   EEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHT CS
                 FAD-oxidase_C   9 lvafpsfeaavkavreiaqagiipaalelmdkkaldlveat 49 
                                   lv+f+s+e++ k ++++++ + ++ ++ + dk++l  v+++
  gi|70607613|ref|YP_256483.1| 220 LVTFNSVEEVTKYLVRVRDYKSKIRRITIEDKETLSSVAKD 260
                                   689***************99999999999888888877665 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.8e-10
                                   ------THHHHHHHHHHHH-TT--BSTT-- CS
                 FAD-oxidase_C 221 erekgeeglalmrriKaalDPkgiLNPgkv 250
                                   +r   e  l+lm+++K+++DP++iLNPgk+
  gi|70607613|ref|YP_256483.1| 384 YRVDEESRLNLMKKLKRTIDPNNILNPGKL 413
                                   566678899*******************96 PP

>> HlyE  Haemolysin E (HlyE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   8.9e-06     0.053       5      83 ..     203     277 ..     200     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-06
                                   HHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          HlyE   5 lksldnvlvkykkeldtvvkfqqldeaideldeakldysqvakvklddlktllsdardkyfdavqtvfeWcvsitslla 83 
                                   + s++ + v y+   d+ v f+ ++e  + l +++   s++ +  ++d  tl s a+d+     + v eW v ++s+l+
  gi|70607613|ref|YP_256483.1| 203 ISSAELATVDYEDWKDQLVTFNSVEEVTKYLVRVRDYKSKIRRITIEDKETLSSVAKDRL----DKVGEWNVIVASTLS 277
                                   67889999*************************998889999**************9875....567899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2537.56
//
Query:       gi|70607614|ref|YP_256484.1|  [L=396]
Description: hypothetical protein Saci_1886 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   14.1   0.2      0.085   13.3   0.2    1.4  1  DUF1180   Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.7e-06     0.085      68     127 ..     336     393 ..     316     396 .] 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-06
                       DUF1180  68 gsspragsaadaggslavvpelssntdkpmtlqrallvlvvvsaavivylvvRtvrlrrr 127
                                    s  + +s + ++ s ++ +  +s+ +   t    l + vv++a+v+v+l++ +++  +r
  gi|70607614|ref|YP_256484.1| 336 SSI-NFTSINSSSNSTSMNTSSNSSPSSSTT-TEGLSLYVVITALVVVVLLLLVIKYTKR 393
                                   333.333333444444444433444444445.899********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2543.36
//
Query:       gi|70607615|ref|YP_256485.1|  [L=396]
Description: hypothetical protein Saci_1887 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-17   61.9   8.5    1.7e-08   34.6   0.8    2.2  2  AAA_15        AAA ATPase domain
    5.1e-12   46.2   2.3    2.4e-08   34.2   0.2    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0011   19.5   0.4     0.0011   19.5   0.4    1.8  2  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.069   13.2   0.0    1.4  1  Eryth_link_C  Annelid erythrocruorin linker subunit C-terminu


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   1.6   3.9e-11   1.8e-07       5      84 ..       2     101 ..       1     159 [. 0.68
   2 !   34.6   0.8   3.8e-12   1.7e-08     275     368 ..     253     336 ..     225     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.9e-11
                        AAA_15   5 kikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef.. 83 
                                   ki+i+N + +k++++++s+   v++G N++GK+ i+ + +++ln     +   +++ +   +i+en++ s +i ++++   
  gi|70607615|ref|YP_256485.1|   2 KIRINNIGPIKEADLEFSD-KAVIVGGNATGKTFIAALVYFLLNPLIMVDRPLKYKLELPAKIEENREVSLEIPVNYKDim 81 
                                   6******************.************************9855554445556666667777777777777777665 PP

                        AAA_15  84 ...................a 84 
                                                       
  gi|70607615|ref|YP_256485.1|  82 eenkdligaavkrtltsifG 101
                                   55555555555555555441 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 3.8e-12
                        AAA_15 275 nykgkkneeieik...ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkela 352
                                   ++ ++k+  i  k   ++ e++ + +++G+ +++++ l + +   k        +++iEEPE++LH +aq    +  k+la
  gi|70607615|ref|YP_256485.1| 253 EIEVNKELMI--KvskEGKEVNSSLVSTGIYQFIPVELALQHPLLK--------TVIIEEPEINLHVNAQI---EVAKRLA 320
                                   2333333333..24489999***************99999888888........9***************5...5566788 PP

                        AAA_15 353 ndnktQviitTHSphi 368
                                   +++ ++++itTHS++i
  gi|70607615|ref|YP_256485.1| 321 REKAKKLLITTHSEWI 336
                                   88888********998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   2.9e-05      0.13       2      25 ..      22      45 ..      21     153 .. 0.73
   2 !   34.2   0.2   5.3e-12   2.4e-08     219     298 ..     253     333 ..     178     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                  +v++G N++GK+ +  + ++l   
  gi|70607615|ref|YP_256485.1| 22 AVIVGGNATGKTFIAALVYFLLNP 45
                                  69******************9643 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 5.3e-12
                        AAA_21 219 r.....gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                   +      +++ + + g+e++++ +S G  +++++ +al   l   ++++i+EpE +LH  ++ ++++ l ++++   ++++
  gi|70607615|ref|YP_256485.1| 253 EievnkELMIKVSKEGKEVNSSLVSTGIYQFIPVELALQHPLL--KTVIIEEPEINLHVNAQIEVAKRLAREKA--KKLLI 329
                                   044445678888999************************9999..69*******************99977777..7**** PP

                        AAA_21 295 tTHS 298
                                   tTHS
  gi|70607615|ref|YP_256485.1| 330 TTHS 333
                                   ***9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.4   2.4e-07    0.0011       1      36 [.       2      36 ..       2     152 .. 0.90
   2 ?   -2.1   0.1         1   4.5e+03     143     143 ..     316     316 ..     248     391 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.4e-07
                        AAA_23  1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTil 36
                                  k++i+n++++++ +++Fs++  +I+G N +GKT i 
  gi|70607615|ref|YP_256485.1|  2 KIRINNIGPIKEADLEFSDKA-VIVGGNATGKTFIA 36
                                  79****************887.9*********9664 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                        AAA_23 143 f 143
                                   +
  gi|70607615|ref|YP_256485.1| 316 A 316
                                   1 PP

>> Eryth_link_C  Annelid erythrocruorin linker subunit C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.5e-05     0.069      29      78 ..     241     290 ..     238     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                  Eryth_link_C  29 itsvkrskfFpsrlkvkatvelesekdgeeqesslqvkGvYsfgkrrlil 78 
                                   it +++   F  +++v+ ++ ++++k+g+e++ssl   G+Y+f   +l+l
  gi|70607615|ref|YP_256485.1| 241 ITPNTKFTLFGHEIEVNKELMIKVSKEGKEVNSSLVSTGIYQFIPVELAL 290
                                   77778888999*******************************97666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2801.36
//
Query:       gi|70607616|ref|YP_256486.1|  [L=148]
Description: hypothetical protein Saci_1888 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.9   3.5      0.048   13.6   0.7    2.0  2  DUF327    Protein of unknown function (DUF327)
      0.041   14.1   0.5      0.098   12.9   0.4    1.8  1  DUF3216   Protein of unknown function (DUF3216)
      0.066   13.2   0.2      0.079   12.9   0.2    1.1  1  DUF2461   Conserved hypothetical protein (DUF2461)


Domain annotation for each model (and alignments):
>> DUF327  Protein of unknown function (DUF327)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   8.1e-06     0.048      16      59 ..      41      88 ..      31      95 .. 0.81
   2 ?    0.8   0.1     0.075   4.5e+02      47      74 ..      97     124 ..      90     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-06
                                  XXXX....XXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF327 16 tkkk....ekkkksFsetlekeeeeeseeelkelleeidkqgerLaes 59
                                  ++k+    +++++s++ +l +++e+ +e++lke +++i+ + +r+  +
  gi|70607616|ref|YP_256486.1| 41 ERKRycfeSQNNESYEAILVEIKEKLNEKHLKEAIDQITCSKSRIDAK 88
                                  23334566789*****************************99999876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.075
                                   HHHHHHHHHHHHH--HHHHHHHHHHHHH CS
                        DUF327  47 eeidkqgerLaesrtiedlkkYkklvke 74 
                                   ++ +k+    ++++ +e +k+Yk  + +
  gi|70607616|ref|YP_256486.1|  97 SDCSKAKTAQEDKMLLEAMKQYKIHITN 124
                                   5666666777889999999999988865 PP

>> DUF3216  Protein of unknown function (DUF3216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   1.6e-05     0.098      47      84 ..      55      92 ..      24      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHTTT---HHHHHHHHHHHHHHHHHH----XX CS
                       DUF3216 47 leGlltvlkekydeekvkellekvkakreeleellrkp 84
                                   e +l  +kek +e+++ke ++++ + +  +++++r+ 
  gi|70607616|ref|YP_256486.1| 55 YEAILVEIKEKLNEKHLKEAIDQITCSKSRIDAKIRRA 92
                                  589********************************986 PP

>> DUF2461  Conserved hypothetical protein (DUF2461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.3e-05     0.079     104     198 ..       7     117 ..       1     123 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                       DUF2461 104 sflggGlwapeaatlaklReaid....................enpeelraileekaflklfkelkeealkrapkgfdkdh 164
                                   + +g G+ + + ++l ++ +++d                    +n e ++ail     ++ +++l+e++lk a  +++ ++
  gi|70607616|ref|YP_256486.1|   7 ISVGEGVLCIKYDKLYRIGKSVDalcvtmkvneeerkrycfesQNNESYEAIL-----VEIKEKLNEKHLKEAIDQITCSK 82 
                                   6799999***************9999999999999999999999999999999.....444444899************** PP

                       DUF2461 165 pdiellklksftvskkledeevlspd.lleevaea 198
                                    +i+   ++ f++  +++++++ ++d +l e ++ 
  gi|70607616|ref|YP_256486.1|  83 SRIDAKIRRAFILLSDCSKAKTAQEDkMLLEAMKQ 117
                                   ********************999999855555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1501  (0.0837191); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1086.59
//
Query:       gi|70607617|ref|YP_256487.1|  [L=136]
Description: hypothetical protein Saci_1891 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0016   18.7   0.0     0.0022   18.3   0.0    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.083   13.0   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.4e-07    0.0022      14      57 ..      52      96 ..      38     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-07
                                  TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.HHHEHHHHHH CS
                  NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre.kkeeglekla 57
                                  ++ v+lfG y  G+++ +SD+ llv+++ + ++  + + +l++++
  gi|70607617|ref|YP_256487.1| 52 SKIVILFGTYGIGDYTDDSDVNLLVISRYWLKDHiETFGTLYRIW 96
                                  55699**********************999765554443444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-06     0.083      14      42 ..      53      81 ..      43     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-06
                                  HSTTEEEEEE-S------EEEEEEEESS- CS
                       Polbeta 14 elaylFGSrakgkareeSDiDlavllkek 42
                                  ++++lFG +  g+++++SD+ l v+ +  
  gi|70607617|ref|YP_256487.1| 53 KIVILFGTYGIGDYTDDSDVNLLVISRYW 81
                                  689*********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 979.64
//
Query:       gi|70607618|ref|YP_256488.1|  [L=87]
Description: hypothetical protein Saci_1892 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 699.70
//
Query:       gi|70607619|ref|YP_256489.1|  [L=394]
Description: hypothetical protein Saci_1893 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-23   81.7   0.3    1.2e-22   81.0   0.3    1.4  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.3   6.6e-27   1.2e-22       8     213 .]      15     291 ..       8     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 6.6e-27
                                   EE----.......................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H............. CS
                         RAMPs   8 lhiGdg.........kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd.... 75 
                                   ++iG+          +i   k  +   + +   P IP++S+kG lRs +ek+l++++    ++  +k++ +++ +++    
  gi|70607619|ref|YP_256489.1|  15 TRIGSTgvyfdyasaDIVTYKLPLQDSNEVYYIPAIPATSFKGLLRSTYEKYLRWNNVGYQRREVKKERIKNIINEYsvnh 95 
                                   555555555555555555555566667778899************************99999999988888888888**** PP

                                   ................................................................................. CS
                         RAMPs  76 ................................................................................. 75 
                                                                                                                    
  gi|70607619|ref|YP_256489.1|  96 gdtvkelveemkselrryisgglikntnlpdditeliilylnvtgwnskdacyvtsdldqcvnlsiiedegvrkkkelwlk 176
                                   ********************************************************************************* PP

                                   ........HHHHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEE CS
                         RAMPs  76 ........leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktk 148
                                            ++ ++G+    + +g+v+f D                               +  +++ er+t++ai+r t+
  gi|70607619|ref|YP_256489.1| 177 lmerdqicKVCNVLGSS---GVRGKVKFTDLIA---------------------------VDPFPVYIERSTHIAINRLTG 227
                                   *****************...**********955...........................5679***************** PP

                                   E...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.....HHH---STTTTBTTT-EE CS
                         RAMPs 149 tngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdll....dlhflglGggkplGfGsve 213
                                   t++k  g++ft+e+ip++    +++ +   l +++l+++ + L++l    +   +++Gg+ + G+G +e
  gi|70607619|ref|YP_256489.1| 228 TAEK--GKIFTEEIIPPG---VKFLGFVAVLDNSILNQVREMLRILktkaERGEVWIGGRGTAGYGTFE 291
                                   ****..************...*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3174.49
//
Query:       gi|70607620|ref|YP_256490.1|  [L=111]
Description: hypothetical protein Saci_1894 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.61
# Mc/sec: 548.10
//
Query:       gi|70607621|ref|YP_256491.1|  [L=105]
Description: hypothetical protein Saci_1895 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.078   13.6   0.0       0.18   12.5   0.0    1.6  2  Asp_protease_2  Aspartyl protease


Domain annotation for each model (and alignments):
>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.9e-06      0.18       2      55 ..       4      55 ..       3      78 .. 0.73
   2 ?   -1.1   0.0      0.18   3.2e+03      21      33 ..      81      93 ..      59     102 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-06
                Asp_protease_2  2 pvtinGkpvrfllDTGast.tlispelaeklglkvreseltvrvsgaggevkarl 55
                                  ++++nG  v+f +DTG ++ +l++ +   k+g   ++ +    vs+++g+    +
  gi|70607621|ref|YP_256491.1|  4 DLNLNGINVSFKIDTGFDGeCLLPHDIFSKIGGYEYDGP---PVSLSDGRGYLTR 55
                                  5789*************9748888888899976666654...4555555544444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.18
                Asp_protease_2 21 tlispelaeklgl 33
                                  tl+ +++  klg+
  gi|70607621|ref|YP_256491.1| 81 TLLGERALSKLGI 93
                                  4555555556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 688.71
//
Query:       gi|70607622|ref|YP_256492.1|  [L=228]
Description: hypothetical protein Saci_1896 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-10   40.8   0.4    4.7e-10   39.9   0.4    1.4  1  RAMPs         RAMP superfamily
  ------ inclusion threshold ------
      0.072   13.0   0.1       0.18   11.7   0.0    1.6  1  eIF-5_eIF-2B  Domain found in IF2B/IF5


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.4   5.3e-14   4.7e-10      26     212 ..      31     219 ..      12     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 5.3e-14
                                   ..---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H........................................ CS
                         RAMPs  26 rdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd............................... 75 
                                   +    +PyI +S++kG lRsa+   +    +  ++++s+k   +++ +++                               
  gi|70607622|ref|YP_256492.1|  31 SIFYSYPYINPSTIKGFLRSAAVYGYP---DVSCEILSSKTIISNIDRIKkkihneeqirlsfmcsdiedllenrnsreas 108
                                   566789****************83333...556666666666666666666667777888899999999999999999999 PP

                                   .................HHHHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE-- CS
                         RAMPs  76 .................leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrt 139
                                                     ++++FGn    + +g+++++                                 +++ +t++ +
  gi|70607622|ref|YP_256492.1| 109 vylevlgdiirklkrpcKVCRVFGNG---SVKGKLRIIYQ-------------------------------IRPLNTTEIK 155
                                   99999999999999999*********...******99985...............................7888888888 PP

                                   SSS-EEEEEE.........-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                         RAMPs 140 rvaidrktktngk......kkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                   +++  r+ k n +        + + +  +++++              +e ++ ++ + + +++  ++lG  k++GfG v
  gi|70607622|ref|YP_256492.1| 156 GLKFSREYKENREglsvmmS-KDPIEFTVLCED--------------KECQEVIKRAVSVINDSVVRLGRFKSRGFGIV 219
                                   88888888888887765532.333788899999..............9*****************************98 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     2e-05      0.18      11      53 ..      54      95 ..      48     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                  -SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHH CS
                  eIF-5_eIF-2B 11 ykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkel 53
                                  y  p++++++  + kt+i N+++i k+++ +++  l+++ +++
  gi|70607622|ref|YP_256492.1| 54 YGYPDVSCEILSS-KTIISNIDRIKKKIHNEEQIRLSFMCSDI 95
                                  6678889999999.***********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1455.83
//
Query:       gi|70607623|ref|YP_256493.1|  [L=127]
Description: hypothetical protein Saci_1897 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.11   12.5   0.4       0.21   11.6   0.4    1.4  1  Tachystatin_B  Antimicrobial chitin binding protein tachystat


Domain annotation for each model (and alignments):
>> Tachystatin_B  Antimicrobial chitin binding protein tachystatin B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   1.2e-05      0.21      20      36 ..      38      54 ..      34      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                 Tachystatin_B 20 CfGyyCrrdfPGsifGt 36
                                  C+   C rdf  s+fG 
  gi|70607623|ref|YP_256493.1| 38 CYALLCNRDFDRSVFGS 54
                                  9999************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 890.56
//
Query:       gi|70607624|ref|YP_256494.1|  [L=245]
Description: hypothetical protein Saci_1898 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.7   0.0       0.14   11.8   0.0    1.4  1  DUF5314   Family of unknown function (DUF5314)


Domain annotation for each model (and alignments):
>> DUF5314  Family of unknown function (DUF5314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.7e-06      0.14      14      53 ..     197     236 ..     187     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-06
                       DUF5314  14 sklipikLsgvqnfdiWleklenvvsetsliwaeYvetGd 53 
                                     l ++  +++++f + ++k+   +++++++ +eYv++G 
  gi|70607624|ref|YP_256494.1| 197 VLLCTFRYNESNEFGSFYNKFPGSLDSIEHYTKEYVKAGT 236
                                   55678999******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1781.45
//
Query:       gi|70607625|ref|YP_256495.1|  [L=885]
Description: hypothetical protein Saci_1899 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.3    7.3   6.9        2.1    8.6   0.4    3.0  3  DUF1492   Protein of unknown function (DUF1492)


Domain annotation for each model (and alignments):
>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.83   1.5e+04      20      38 ..      58      76 ..      54      97 .. 0.47
   2 ?    8.6   0.4   0.00012       2.1      15      85 ..     351     419 ..     339     423 .. 0.82
   3 ?    0.9   0.2     0.029   5.3e+02      16      57 ..     617     662 ..     606     675 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.83
                       DUF1492 20 kddvyveLvvakediekkt 38
                                  +d  y e+      i ++ 
  gi|70607625|ref|YP_256495.1| 58 NDSTYYEICDHIASIAEES 76
                                  4555555544444443333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00012
                       DUF1492  15 GkkkkkddvyveLvvakediekktaeaikkklelqrlidklensdsrsvLrmvyidkltvwqvidklnisr 85 
                                    +++k d +   +v    ++ek+  + ik    +++l+++ + +d+  ++++ y   +t ++++dk ++ +
  gi|70607625|ref|YP_256495.1| 351 RTERKSDIIL--VVSELGKVEKDSEDKIKLAEKVNELLKTTDHTDYFRIIKIEYDGSITSDKLCDKCKVRK 419
                                   5556665544..3566789***********************************************98866 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.029
                       DUF1492  16 kkkkkddvyveLvvak...ediekkt.aeaikkklelqrlidklen 57 
                                   k kkkd++ ++ ++ k   +d e++      kk+le+ ++i   +n
  gi|70607625|ref|YP_256495.1| 617 KSKKKDNMLINNIARKtltNDPENEMrLKFFKKRLEFVKMISAENN 662
                                   56889999999998772223444333135689999*9999976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (885 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 6018.87
//
Query:       gi|70607626|ref|YP_256496.1|  [L=236]
Description: hypothetical protein Saci_1900 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-22   80.1   0.6    2.2e-22   79.6   0.6    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.8e-15   57.3   0.1    2.9e-15   56.7   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    1.5e-13   51.3   0.1    3.3e-13   50.1   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
    1.3e-07   31.5   0.0    2.2e-07   30.7   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
    1.5e-07   32.1   0.0    2.8e-07   31.2   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.9e-07   31.0   0.1    1.3e-06   28.3   0.1    1.9  1  Methyltransf_31  Methyltransferase domain
    2.5e-06   27.4   0.0    3.4e-06   27.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0017   17.6   0.0     0.0028   16.9   0.0    1.5  1  Methyltransf_7   SAM dependent carboxyl methyltransferase
     0.0052   16.4   0.0     0.0095   15.5   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.044   13.5   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.05   13.6   0.0      0.076   13.0   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
       0.16   11.5   0.0       0.29   10.6   0.0    1.4  1  TRM13            Methyltransferase TRM13


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.6   1.4e-25   2.2e-22       6     211 ..      19     214 ..      15     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.4e-25
                                   XXXXXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TT..EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHH CS
               Ubie_methyltran   6 eekvkevfesvaskyDlmndvlslgihrlWkkfveklvavkrga..kvlDvagGtgDlafklsdsvgekgkvvvlDinenm 84 
                                   +e+ + +++ + + yD  n+++s+     W++ + k  +   +   ++lDva+G g+l++ + ++++++   v++D+ enm
  gi|70607626|ref|YP_256496.1|  19 NEELQRIYNDLPKFYDRANALISFFKDVEWRATLVKYISYYYPDtrRILDVACGKGELSYVINKMIKAE--TVMVDYAENM 97 
                                   677899**************************888877776655459******************9875..6789****** PP

                                   HHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHH CS
               Ubie_methyltran  85 LkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqa 165
                                   L          ++++ + +q++  +Lpf d+sfD+v  sf l    D+ +++ke+ rv +    + v+ + k  + ++++ 
  gi|70607626|ref|YP_256496.1|  98 LLN--------SFVKTDRVQGSFYKLPFRDESFDCVVSSFALHSADDIGEVVKEMARVSRNC--VGVIAMGKSDNVMYRKY 168
                                   *75........56777889***************************************9975..66777888888899998 PP

                                   HHHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHT CS
               Ubie_methyltran 166 yelyskevlPvlGkllakdldsyryLvesirafPdqetlkelieda 211
                                    + y  ++ P l  l+  +  +y+y+    ++ P +++l+++i + 
  gi|70607626|ref|YP_256496.1| 169 ASFYLSYIQPYLACLVGAKSRDYKYIFYIYQRIPTNNQLRNIISKI 214
                                   8999999*********9999*********************99874 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.1     2e-18   2.9e-15       1      89 [.      67     149 ..      67     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 2e-18
                                   EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                   Ldv+cG+G l+  + k   a++v vD++++ml   ++ +++++     v++++ klpf+d+sfD+vvss++lh  +d  ++
  gi|70607626|ref|YP_256496.1|  67 LDVACGKGELSYVINKMIkAETVMVDYAENML--LNSFVKTDR-----VQGSFYKLPFRDESFDCVVSSFALHSADDIGEV 140
                                   8**************999**************..888888888.....********************************* PP

                                   HHHHHHHEE CS
               Methyltransf_11  81 lkeiaRvLk 89 
                                   +ke+aRv +
  gi|70607626|ref|YP_256496.1| 141 VKEMARVSR 149
                                   ******966 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   2.2e-16   3.3e-13       1      94 [.      66     149 ..      66     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.2e-16
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                   +Ld++cG+G+l+  + k + ka+ ++vD++e+ml +    +    ++ + vqg++ +lpf d+sfD+vvss+alh    +d
  gi|70607626|ref|YP_256496.1|  66 ILDVACGKGELSYVINKMI-KAETVMVDYAENMLLNS---F----VKTDRVQGSFYKLPFRDESFDCVVSSFALHSA--DD 136
                                   8*****************9.7************9753...3....46688*********************999975..59 PP

                                   HHHHHHHHHHHEE CS
               Methyltransf_25  82 lekalkeiarvLk 94 
                                   + +++ke+arv +
  gi|70607626|ref|YP_256496.1| 137 IGEVVKEMARVSR 149
                                   **********965 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.5e-10   2.2e-07       5     106 ..      54     152 ..      49     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.5e-10
                          MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtl 85 
                                   ++i  + ++  r+ld+ cG+Gel +++++  + ++  ++  e+ + ++  k   v qg   k    f+d+sfd vv s +l
  gi|70607626|ref|YP_256496.1|  54 KYISYYYPDTRRILDVACGKGELSYVINKMIKAETVMVDYAENMLLNSFVKTDRV-QGSFYK--LPFRDESFDCVVSSFAL 131
                                   56777889999****************6655555556666677778887776554.555544..469************** PP

                          MetW  86 qatrnpkevldellrigrrai 106
                                    +  +  ev++e+ r++r+++
  gi|70607626|ref|YP_256496.1| 132 HSADDIGEVVKEMARVSRNCV 152
                                   ******************997 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.9e-10   2.8e-07       1      92 [.      67     147 ..      67     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.9e-10
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                   L++ cG G+l+ ++ +  + +e + vD+ ++++    + + k ++ + ++++l  +d     +  sfD vv+s++lh  +d
  gi|70607626|ref|YP_256496.1|  67 LDVACGKGELSYVINKM-IKAETVMVDYAENML---LNSFVKTDRVQGSFYKLPFRD-----E--SFDCVVSSFALHSADD 136
                                   8*******999888666.***************...666666665555566655555.....2..9*************** PP

               Methyltransf_12  82 irevldnirkl 92 
                                   i ev+++++++
  gi|70607626|ref|YP_256496.1| 137 IGEVVKEMARV 147
                                   ******99987 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   8.4e-10   1.3e-06       6     103 ..      65     150 ..      62     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.4e-10
               Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                   r+lD++CG+Gel+++++ +++ kae v +D+ e+++  +  ++           qg++ +l+  + de+fD ++s  +l+ 
  gi|70607626|ref|YP_256496.1|  65 RILDVACGKGELSYVIN-KMI-KAETVMVDYAENMLLNSFVKT--------DRVQGSFYKLP--FRDESFDCVVSSFALHS 133
                                   89***************.766.699999999999998877743........3458*******..***************** PP

               Methyltransf_31  87 ladpdkileeiervlkp 103
                                     d  ++ +e+ rv ++
  gi|70607626|ref|YP_256496.1| 134 ADDIGEVVKEMARVSRN 150
                                   ************99775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.3e-09   3.4e-06      19     107 ..      59     146 ..      16     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.3e-09
               Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdp 98 
                                   + +   r+Ld++cG+G+l+ v+ +  + + ++vD  +++     ++ k   +q    + ++ +++fd++v+++ l++ +d 
  gi|70607626|ref|YP_256496.1|  59 YYPDTRRILDVACGKGELSYVINKMIKaETVMVDYAENMLLN--SFVKTDRVQGSFYKLPFRDESFDCVVSSFALHSADDI 137
                                   245566****************887555*******8875554..33333333333347778999***************** PP

               Methyltransf_23  99 pellrqiat 107
                                    e+++ +a+
  gi|70607626|ref|YP_256496.1| 138 GEVVKEMAR 146
                                   999999987 PP

>> Methyltransf_7  SAM dependent carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.9e-06    0.0028      95     158 ..     107     170 ..      60     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-06
                                   EEES-TTS--S-TT-EEEEEEES-TTB-SS--GGG..TTSTT--TTTSSSSS--H.HHHHHHHH CS
                Methyltransf_7  95 gvPgSFYgRLfPsnslhlvhssysLhWlSqvpeelekkkskalnkgniyisktsppevvkaYae 158
                                    v gSFY+  f ++s + v+ss++Lh  + + e ++++ + + n   + + ++s++ +++ Ya+
  gi|70607626|ref|YP_256496.1| 107 RVQGSFYKLPFRDESFDCVVSSFALHSADDIGEVVKEMARVSRNCVGVIAMGKSDNVMYRKYAS 170
                                   588******************************9977778888877777777777777777776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06    0.0095      31      67 ..      62      97 ..      50     153 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                                  TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHH CS
                           MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarA 67
                                   ++++lD++cG G l+ ++ k+ +  e ++vd   + 
  gi|70607626|ref|YP_256496.1| 62 DTRRILDVACGKGELSYVINKMIKA-ETVMVDYAENM 97
                                  6789***************998776.77788865443 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.044      62     114 ..      49     101 ..      15     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHH CS
                          PCMT  62 valalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveea 114
                                    a+++++++    +  r+L+v +G G l+ v+ +++++++  v +++ +++  ++
  gi|70607626|ref|YP_256496.1|  49 RATLVKYISyyYPDTRRILDVACGKGELSYVINKMIKAET--VMVDYAENMLLNS 101
                                   57778888876677899*********************99..8899998887666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-05     0.076      24      89 ..      61     122 ..      43     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
               Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsi 89 
                                    +  +++Dv++Gkg Ls v++      k + v +d  e++  ++    ++++  f  +l f + s 
  gi|70607626|ref|YP_256496.1|  61 PDTRRILDVACGKGELSYVINK---MIKAETVMVDYAENMLLNSFVKTDRVQGSF-YKLPFRDESF 122
                                   45679*****************...889999999999998888888888888777.6666666665 PP

>> TRM13  Methyltransferase TRM13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00019      0.29      17      44 ..      61      90 ..      49     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00019
                         TRM13 17 ekssayvEfGaGkgelsryvnqaleed..k 44
                                   +++ +++  +Gkgels ++n++++ +   
  gi|70607626|ref|YP_256496.1| 61 PDTRRILDVACGKGELSYVINKMIKAEtvM 90
                                  56678999***************9776331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1923.88
//
Query:       gi|70607627|ref|YP_256497.1|  [L=218]
Description: hypothetical protein Saci_1901 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.004   17.0   0.4       0.28   11.0   0.0    2.1  2  Myelin_PLP  Myelin proteolipid protein (PLP or lipophilin)


Domain annotation for each model (and alignments):
>> Myelin_PLP  Myelin proteolipid protein (PLP or lipophilin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.1    0.0015        27      67     100 ..      22      55 ..      19      82 .. 0.65
   2 !   11.0   0.0   1.6e-05      0.28      22      66 ..     119     162 ..     102     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0015
                    Myelin_PLP  67 klviyglaavffllgilllavgfyttgavkellg 100
                                   k+vi+g+  + +++  l++  +f+ t+a  +++ 
  gi|70607627|ref|YP_256497.1|  22 KYVILGTVLAVVIVVGLVVYFSFFSTSAQAKIIP 55 
                                   5666666666666666666666777776666554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.6e-05
                    Myelin_PLP  22 lcflGvalFcgcghealtgteklletyFsknlqdaelllevieav 66 
                                   ++f+Gv  F  c  ++ ++t+++l  +F  n ++a+  +++ +a+
  gi|70607627|ref|YP_256497.1| 119 VIFSGVVEFLNCNINGQNATVNILTMVFT-NSSEANQEFSIYKAF 162
                                   689*************************9.666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1384.25
//
Query:       gi|70607628|ref|YP_256498.1|  [L=140]
Description: hypothetical protein Saci_1902 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-32  110.2   0.0    8.5e-32  109.9   0.0    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   4.7e-36   8.5e-32      12     114 ..      22     118 ..      14     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 4.7e-36
                                   -EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEEEEEET CS
                          TrmO  12 aeaeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvvklekveg 92 
                                   +  +i++++ey  ee+l+g+e++shl++++++h +   ++  +++  + +g  rvGvfatR+  Rpnpig+svv+l kveg
  gi|70607628|ref|YP_256498.1|  22 SVVKIVVDKEY--EEGLRGIEDYSHLIIVYHLHLS---QFDGNLVRDFHEG-VRVGVFATRTHERPNPIGISVVELLKVEG 96 
                                   45678888999..********************88...4556666677776.89*************************** PP

                                   TEEEEES----TT-EEEEEEE- CS
                          TrmO  93 nvlevsgvDlldgtpvlDiKPY 114
                                   n+l+v g++++dgtpvlDiKPY
  gi|70607628|ref|YP_256498.1|  97 NILQVGGINAVDGTPVLDIKPY 118
                                   ********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1197.12
//
Query:       gi|70607629|ref|YP_256499.1|  [L=375]
Description: hypothetical protein Saci_1903 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-17   61.0  61.1    9.3e-17   61.0  61.1    1.4  1  MFS_1     Major Facilitator Superfamily
    7.9e-12   44.8  18.2    7.9e-12   44.8  18.2    2.3  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0  61.1     1e-20   9.3e-17       1     351 [.      13     335 ..      13     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1e-20
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                   lll++++sala++ ++++lp +l++ +g    ++ + ++l  +g +++ l++G+++d  + r  lll+++lfal   +l+ 
  gi|70607629|ref|YP_256499.1|  13 LLLIFLFSALAIYSISFVLP-TLMQIYG---EAVAFSIALSWIGGGIGGLIMGVFGDLKSKRYALLLSIVLFALP--MLAn 87 
                                   68999***************.9******...88888889999***************987777************..4443 PP

                         MFS_1  81 fa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                   ++  ++ +++++++l G+g  a++ ++++++++++p + rg+  +++++++ lGailg l+ ++++  +   + f+i+ i+
  gi|70607629|ref|YP_256499.1|  88 VVqLNIIVFYIVWFLIGFGVNAVNGISYVYVTELAPSRTRGFIGSIMQGFYFLGAILG-LVTSFIV-KGDIFVYFLIVSIL 166
                                   34477889**************************************************.9999999.9999999******* PP

                         MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlg 239
                                   sll++ l  +++  e + ++++s k               + +lk      ++ ++++++ ++++  l++l+++ l + lg
  gi|70607629|ref|YP_256499.1| 167 SLLSIPL--WVFIPESKWKGNFSFKLP-------------RDMLKVT----VFGSIFSIGSFLYLvpLVSLSFT-LFSFLG 227
                                   ****775..777666666666654333.............6777777....55666666555555444444444.245566 PP

                         MFS_1 240 lsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfps 320
                                       l+++  +  ++++g+i+++++gr+sd +grr   +++ ++ +++++ l+l a+ s++vll+ +++++ +g++ +f+ 
  gi|70607629|ref|YP_256499.1| 228 SR--LYVV--IFSAFILGMISFMVSGRISDTVGRRLSSYIFAGISIVSSITLFLGATLSDPVLLIGSFIVLIVGSS-FFAY 303
                                   66..6666..6666677777788***********************************888888865555444555.5899 PP

                         MFS_1 321 llalasdlappeeagtasglfntags.lggal 351
                                   + +++s+++p +  +t + ++ ++g  +gg +
  gi|70607629|ref|YP_256499.1| 304 FGVWMSEVYPVNFKATGTNITLFLGRlIGGGF 335
                                   99999999999999999999998777466655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8  18.2   8.8e-16   7.9e-12      51     196 ..      45     182 ..      18     184 .. 0.91
   2 ?   -0.1  15.9     0.035   3.2e+02      48     394 ..     231     327 ..     194     374 .. 0.54

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 8.8e-16
                                   HHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS CS
                      Sugar_tr  51 ivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiA 131
                                   + ++  +G+ iG+l++g +gd  +++++ll ++vlf    + +++     ++ v+++  +l+G+gv ++++++ +y+ E+A
  gi|70607629|ref|YP_256499.1|  45 SIALSWIGGGIGGLIMGVFGDLKSKRYALLLSIVLFALPMLANVVQL---NIIVFYIVWFLIGFGVNAVNGISYVYVTELA 122
                                   5666789*********************************9999999...9****************************** PP

                                   -SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HH CS
                      Sugar_tr 132 pkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllflPESPr 196
                                   p + Rg+++s+ q ++ +G +++ ++ +++  ++         + + ++++ll + l++f+PES++
  gi|70607629|ref|YP_256499.1| 123 PSRTRGFIGSIMQGFYFLGAILGLVTSFIVkGDIFV------YFLIVSILSLLSIPLWVFIPESKW 182
                                   ****************99999998888888545554......7899999999************75 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.035
                                   HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                   + +i+s+f++G +i+ +++g ++d++GR+ s  i+a +++++++  ++   + s  vl++g ++v i    + +   +++s
  gi|70607629|ref|YP_256499.1| 231 YVVIFSAFILG-MISFMVSGRISDTVGRRLSSYIFAGISIVSSITLFLGA-TLSDPVLLIGSFIVLIVGSSFFAYFGVWMS 309
                                   33444444444.55555556666666666555555555555555444444.224455555555554444444444445555 PP

                                   TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHH CS
                      Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeake 209
                                   E+ p                                                                             
  gi|70607629|ref|YP_256499.1| 310 EVYP----------------------------------------------------------------------------- 313
                                   5544............................................................................. PP

                                   HHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHH CS
                      Sugar_tr 210 vlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksl 290
                                                                                                                    
  gi|70607629|ref|YP_256499.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHH CS
                      Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvp 371
                                                                                                                    
  gi|70607629|ref|YP_256499.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   HHHHHHHSHTTTHHHHHHHHHHH CS
                      Sugar_tr 372 wvlvsElfpqsvRskalaiavav 394
                                             +++++++ i+ ++
  gi|70607629|ref|YP_256499.1| 314 ---------VNFKATGTNITLFL 327
                                   .........44444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2616.36
//
Query:       gi|70607630|ref|YP_256500.1|  [L=369]
Description: partially protein, partial [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-20   71.1   0.0    2.1e-19   69.7   0.0    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
      5e-14   52.9   0.0    8.8e-14   52.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-08   34.8   0.0     0.0061   16.6   0.0    2.7  3  Glyco_transf_4   Glycosyltransferase Family 4
    0.00053   20.3   0.0    0.00099   19.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0037   17.3   0.1       0.19   11.8   0.0    2.8  3  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
      0.035   14.1   0.0        2.3    8.3   0.0    2.3  2  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.15   11.8   0.0       0.34   10.6   0.0    1.6  1  Glyco_transf_5   Starch synthase catalytic domain
       0.22   12.0   0.0       0.56   10.6   0.0    1.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   3.9e+03      93     108 ..     157     177 ..     147     178 .. 0.63
   2 !   69.7   0.0   9.5e-23   2.1e-19      12     159 ..     198     330 ..     189     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                   ESEEEEEESS.....BSS-HH CS
               Glycos_transf_1  93 adifvlpsis.....EgfGiv 108
                                   + +f+ +s       E++Gi 
  gi|70607630|ref|YP_256500.1| 157 SALFITNSNFtkslyESWGIK 177
                                   555555555455555999997 PP

  == domain 2  score: 69.7 bits;  conditional E-value: 9.5e-23
                                   TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
               Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                   +++++++ ++g   ke +++++ ++++       + vk+   G      + +k+ e+   s n+++lg+v+++ l  l++n
  gi|70607630|ref|YP_256500.1| 198 PSRDYVLAYLGIRGKETNLKVIKELAR-------QGVKIKAFG------KSSKEYEKELSSQNIEILGYVDDNTLVDLYTN 265
                                   555555555555555555554444444.......466666777......3334445556677999**************** PP

                                   ESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
               Glycos_transf_1  93 adifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                   a  ++++ + E+fG  ++E+ma+g+pvi+++ +gp+ +v ++ tG+lv +   e+l+++ +++ +++
  gi|70607630|ref|YP_256500.1| 266 ALFTLFTFTHEPFGYIPVESMACGTPVITYDKQGPKNTVSHNRTGWLVSND--EELVREAIRIWKQG 330
                                   ************************************************988..77777777777666 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   3.9e-17   8.8e-14      21     131 ..     216     326 ..     207     329 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.9e-17
                                   HHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---TH..HHHHHHH-SEEEE--..---SHHHHHHHHTT-EE CS
               Glyco_trans_1_4  21 leavpllrkkdvrlvivGdgprpeeleelaagleerveftGfved..laellaaadvfvaPs..egfglkllEamaaglpv 97 
                                   l+ +++l+++ v++   G++   +e+e++++  ++++e++G+v+d  l +l+ +a  ++++   e fg+  +E+ma+g+pv
  gi|70607630|ref|YP_256500.1| 216 LKVIKELARQGVKIKAFGKS-S-KEYEKELS--SQNIEILGYVDDntLVDLYTNALFTLFTFthEPFGYIPVESMACGTPV 292
                                   667788886679999***65.4.47887665..479*******6567********8888888879**************** PP

                                   EE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHH CS
               Glyco_trans_1_4  98 Vatdvggiaevv..gengllvppgdpealaeailrL 131
                                   ++ d +g++++v  +++g+lv+  + e+l+++ +r+
  gi|70607630|ref|YP_256500.1| 293 ITYDKQGPKNTVshNRTGWLVS--NDEELVREAIRI 326
                                   *******99999999******9..778888887776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0061       3      43 ..      15      54 ..      13      85 .. 0.66
   2 !   15.1   0.0   7.7e-06     0.017     112     169 ..     135     189 ..     124     190 .. 0.88
   3 ?   -1.8   0.0       1.2   2.7e+03      11      26 ..     218     233 ..     215     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                Glyco_transf_4  3 GverhvleLaraLarrGheVtvvtpgddgpleeevelvvrv 43
                                  G+ r +l+++++LarrGh+Vt++tp +      + +++ ++
  gi|70607630|ref|YP_256500.1| 15 GAVRPALTVSKELARRGHDVTILTPYSMLSDFHK-VRIAEI 54
                                  78888999****************9766655555.333333 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.7e-06
                Glyco_transf_4 112 lkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                   +k+ +++l +l+++l+ ++  ++  +i++S++t+  +++ +g++ +  +Vi+++ Dle
  gi|70607630|ref|YP_256500.1| 135 YKFIRGMLVNLEKRLMMQFRENSALFITNSNFTKSLYES-WGIKVD--HVIYPPLDLE 189
                                   566677788999***************************.**8864..88******98 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                Glyco_transf_4  11 LaraLarrGheVtvvt 26 
                                   ++++Lar+G+++  + 
  gi|70607630|ref|YP_256500.1| 218 VIKELARQGVKIKAFG 233
                                   57999***99988774 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.4e-07   0.00099       5      91 ..     272     357 ..     268     358 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.4e-07
               Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydh 85 
                                   +  +e + +  +E +acG++++t d +g+ + ++ ++++ l+++ eel++   +  ++  + ++i ++  +   +e+++++
  gi|70607630|ref|YP_256500.1| 272 TFTHEPFGYIPVESMACGTPVITYDKQGPKNTVSHNRTGWLVSNDEELVREAIRIWKQGYDESSIKNKCLAN-AQEYDVKK 351
                                   555566666778*******************************88888888777777766667777777777.66777777 PP

               Glyco_trans_1_2  86 raeqll 91 
                                    a+++l
  gi|70607630|ref|YP_256500.1| 352 IADEWL 357
                                   777665 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   8.4e-05      0.19      10      53 ..      15      54 ..      14      78 .. 0.78
   2 ?   -1.6   0.0       1.2   2.6e+03     102     134 ..      70     102 ..      54     105 .. 0.76
   3 ?    2.0   0.0     0.089     2e+02      17      50 ..     217     250 ..     202     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
                                  HHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE- CS
               Glyco_transf_28 10 GhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepi 53
                                  G v Pal + keL+++gh+V+ + t+  + +     +++ + +i
  gi|70607630|ref|YP_256500.1| 15 GAVRPALTVSKELARRGHDVT-ILTPYSMLSDF---HKVRIAEI 54
                                  7799*****************.**999887665...44444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                   CCCCCHCCCTTHCCCCCHCTS-ECCCCCCCCC- CS
               Glyco_transf_28 102 paviaaplaripviihEqnaipglanktlsrta 134
                                   p + +  +a i  ++hE  ++  l+  t+s+  
  gi|70607630|ref|YP_256500.1|  70 PLLREWMKALILPYVHEREKSESLVINTSSSLI 102
                                   555566678889999999999888888887765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.089
                                   HHHHHHHCTT-EEEEEEET.CCCHHHHHHCCT-EE CS
               Glyco_transf_28  17 AlakeLkkegheVrylgtk.rgleerlveeaglef 50 
                                    ++keL+++g++++++g++ +++e++l  ++++e+
  gi|70607630|ref|YP_256500.1| 217 KVIKELARQGVKIKAFGKSsKEYEKEL-SSQNIEI 250
                                   578999999999998887515667776.7777765 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.001       2.3      16      56 ..      23      62 ..      12      81 .. 0.68
   2 ?    3.5   0.0      0.03        67      14      47 ..     216     250 ..     203     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
               Glyco_trans_4_2 16 lakeLakrgyeVhvitpkkgakdeleaegihvhrl..kvdrkg 56
                                  + keLa rg++V+++tp  + +d+ +    ++ ++  k++r+g
  gi|70607630|ref|YP_256500.1| 23 VSKELARRGHDVTILTPYSMLSDFHKV---RIAEIkeKIQRSG 62
                                  679**************8886666544...3333311444555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.03
               Glyco_trans_4_2  14 lrlakeLakrgyeVhvitp.kkgakdeleaegihv 47 
                                   l+++keLa +g++++ +    k++++el +++i++
  gi|70607630|ref|YP_256500.1| 216 LKVIKELARQGVKIKAFGKsSKEYEKELSSQNIEI 250
                                   789**************996667799999999987 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00015      0.34      25      58 ..      23      56 ..      18     121 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                Glyco_transf_5 25 LpkaLaklghdvrvilPrygaikeekkeleevae 58
                                   +k+La++ghdv++++P+    + +k ++ e++e
  gi|70607630|ref|YP_256500.1| 23 VSKELARRGHDVTILTPYSMLSDFHKVRIAEIKE 56
                                  589**************98333333323333333 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.56       9      27 ..      22      40 ..      15      85 .. 0.72
   2 ?   -3.0   0.0       3.9   8.7e+03     121     153 ..     148     180 ..     140     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
               Glyco_trans_4_4  9 elaraLaarGheVtvltpa 27
                                   ++++La+rGh+Vt+ltp 
  gi|70607630|ref|YP_256500.1| 22 TVSKELARRGHDVTILTPY 40
                                  56899************73 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.9
               Glyco_trans_4_4 121 alerrllrradavlvvseaeaeelralgvpadr 153
                                   +l +    + ++++++s++   +++ +g+  d+
  gi|70607630|ref|YP_256500.1| 148 RLMMQFRENSALFITNSNFTKSLYESWGIKVDH 180
                                   455566667889999999999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2407.74
//
Query:       gi|70607631|ref|YP_256501.1|  [L=461]
Description: hypothetical protein Saci_1905 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.7   7.4    1.1e-08   34.7   7.4    3.0  3  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.2e-06   28.2  25.9    1.2e-06   28.2  25.9    2.3  2  Polysacc_synt    Polysaccharide biosynthesis protein
    3.4e-05   23.9  13.0    3.4e-05   23.9  13.0    4.1  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3     0.048   2.8e+02     134     157 ..      14      37 ..       3     106 .. 0.67
   2 !   34.7   7.4   1.8e-12   1.1e-08     146     284 ..     166     301 ..     133     306 .. 0.88
   3 ?   -2.1   2.7      0.29   1.7e+03     105     166 ..     332     392 ..     307     428 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.048
               Polysacc_synt_3 134 llglgvwALvigtllssllslvll 157
                                    ++ g++AL++  l++ ++   ++
  gi|70607631|ref|YP_256501.1|  14 TILNGIYALIFFLLAARFTTPEFV 37 
                                   555666666666666555443333 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.8e-12
               Polysacc_synt_3 146 tllssllslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpva 226
                                   +   +ll+++ +wl ++ ++++  ++ ++++l++ gl + +sn++n++a++ d l+  ++l+ ++LG+Y+    ++++p +
  gi|70607631|ref|YP_256501.1| 166 WTSGALLQAIYYWLKLPRKLEF--KTGVASKLIKEGLPIYISNVINFIASQGDRLITVYLLGLYDLGIYQLVTLMSTFPNN 244
                                   4456788888888888887665..888****************************************************** PP

               Polysacc_synt_3 227 eitsviakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvll 284
                                   ++ s i++  +P+ +   + +k++  ++  +lr+  l++ P+av+ +v+++ ++++++
  gi|70607631|ref|YP_256501.1| 245 MLLSLISSL-LPSSAYYLSLNKDMSYMTSLTLRFYVLLSAPTAVISYVLSTVFLTTFF 301
                                   ******996.5777777777799****************************9999887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.29
               Polysacc_synt_3 105 lrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrpr 166
                                   ++ + ++k l ++ ++s v  ++++++l    lg+   +i +++++l+s++ll++++  +  
  gi|70607631|ref|YP_256501.1| 332 ISLKKDYKPLLYVGVISGVEVLVLSLYLI-PRLGILGAAIAQVVNALTSSILLLYICLRQKA 392
                                   55556677777777777666666666664.45666666777777777777766666544444 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2  25.9     2e-10   1.2e-06       9     269 ..      11     256 ..       5     260 .. 0.87
   2 ?   -3.2  16.8       0.7   4.2e+03      83     191 ..     287     390 ..     267     435 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2e-10
                 Polysacc_synt   9 llsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlv 89 
                                   l+ ++++ + a++++ + ar+ +pe +G  a+++ + ++ +++t+l     ++reia +     + +++l  ++l++l   
  gi|70607631|ref|YP_256501.1|  11 LSTTILNGIYALIFFLLAARFTTPEFVGMIATVQLLEVFVSNFTGLLSWYVASREIAYNLN---KDKKLLDDIILTSLGYP 88 
                                   455677777899999999****************************999999999998886...88888888888888777 PP

                 Polysacc_synt  90 llfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaav 170
                                    l++ + ++ af  lp+++vl + +++ +l       ++r+ + gl +++ a +  v+  ++r  +++ a+f  + + +++
  gi|70607631|ref|YP_256501.1|  89 FLAIPFIFLLAF-VLPRYVVLAVPYMFLYL----YGNYQRSVLGGLGKFTEANIGLVIFLTFRWLFSIPAIFFNN-FEIII 163
                                   777777777555.56777777666666666....356889999***************99999999999999888.***** PP

                 Polysacc_synt 171 lgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqll 251
                                   l+ +++al+++i++++ l +k+ +++ +       +l+++++p+ is +++ +  + d+++  +llg +++GiY+++  ++
  gi|70607631|ref|YP_256501.1| 164 LIWTSGALLQAIYYWLKLPRKLEFKTGVA-----SKLIKEGLPIYISNVINFIASQGDRLITVYLLGLYDLGIYQLVTLMS 239
                                   *******************8886666666.....79********************************************* PP

                 Polysacc_synt 252 vaisgllapivtaalfPv 269
                                   + +++ l + ++ +l P 
  gi|70607631|ref|YP_256501.1| 240 TFPNNMLLSLIS-SLLPS 256
                                   ***********9.99995 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.7
                 Polysacc_synt  83 lvllvlvllfllllliaaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflf 163
                                   +++ vl+++fl++++    +    l++ +l+ al+ l   +   + + +   +++ k+++   v++ + +++l+l ++   
  gi|70607631|ref|YP_256501.1| 287 VISYVLSTVFLTTFFH--EYLPGLLVLQLLVVALSAL--SPLLYLSTPIISLKKDYKPLLYVGVISGVEVLVLSLYLIPRL 363
                                   3444555555555555..4444444444444444444..444445555555677777888888888888888999999999 PP

                 Polysacc_synt 164 ldivaavlgavlaalvggivslavlrkk 191
                                   + i++a++++v+ al+++i++l++  + 
  gi|70607631|ref|YP_256501.1| 364 G-ILGAAIAQVVNALTSSILLLYICLRQ 390
                                   9.***************99999987654 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   4.1      0.98   5.8e+03      64     109 ..      15      62 ..       4     110 .. 0.41
   2 !   10.5   8.7   7.7e-05      0.46       4     109 ..     107     222 ..     105     241 .. 0.80
   3 ?   -2.0   5.5      0.57   3.4e+03      86     141 ..     240     297 ..     218     299 .. 0.68
   4 ?   -2.6   6.7      0.89   5.3e+03      64     132 ..     250     318 ..     245     327 .. 0.49
   5 !   23.9  13.0   5.7e-09   3.4e-05       1     102 [.     310     415 ..     308     445 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.98
               Polysacc_synt_C  64 lallvvavlnlyalrrllgikl..ellrrllkpllaalvmgivvylll 109
                                   +   ++a++ + ++ r +   +  ++ +  l  ++++ + g++ ++++
  gi|70607631|ref|YP_256501.1|  15 ILNGIYALIFFLLAARFTTPEFvgMIATVQLLEVFVSNFTGLLSWYVA 62 
                                   333333333333333333333333222222333333333333333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.7e-05
               Polysacc_synt_C   4 ilalsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgi 83 
                                   +la+  +fl+l+ +   s+L glg+  +a + lvi + + ++++++ i + +   +++ ++ + l+ a++ +  l r+l +
  gi|70607631|ref|YP_256501.1| 107 VLAVPYMFLYLYgNYQRSVLGGLGKFTEANIGLVIFLTFRWLFSIPAIFFNNFEIIILIWTSGALLQAIYYWLKLPRKLEF 187
                                   4555566666666999********************************6555555999*********************** PP

               Polysacc_synt_C  84 kl....ellrrllkpllaalvmgiv........vylll 109
                                   k     +l++  l ++++ ++ +i+        v   +
  gi|70607631|ref|YP_256501.1| 188 KTgvasKLIKEGLPIYISNVINFIAsqgdrlitV---Y 222
                                   **99988888888999999999999666663322...3 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.57
               Polysacc_synt_C  86 ellrrllkpllaalvmgivvylllllllgllllaal..alllavlvgalvYlllllll 141
                                   ++ +++l  l+++l+ + + yl l+  ++  ++ +l   +ll++  +++ Y+l +++l
  gi|70607631|ref|YP_256501.1| 240 TFPNNMLLSLISSLLPSSAYYLSLNKDMSYMTSLTLrfYVLLSAPTAVISYVLSTVFL 297
                                   344556677777777777766666666666666655669999999******9988876 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.89
               Polysacc_synt_C  64 lallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgllllaal..alllavlvgal 132
                                   ++ l+ +   +  l++ + +      +l  ++l+++  +++ y l  ++l++++ + l   l+l++lv al
  gi|70607631|ref|YP_256501.1| 250 ISSLLPSSAYYLSLNKDMSYMT--SLTLRFYVLLSAPTAVISYVLSTVFLTTFFHEYLpgLLVLQLLVVAL 318
                                   5555555555666666666655..33333456666666666553444444444433233445555544444 PP

  == domain 5  score: 23.9 bits;  conditional E-value: 5.7e-09
               Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvk.lilnllliplfgivGaaiatvlallvvavlnlyalrrl 80 
                                   vL++l++++  ls    ls+ +++l++  ++l+++ +   v  l+l+l+lip++gi+Gaaia v+  l++++l+ly+  r+
  gi|70607631|ref|YP_256501.1| 310 VLQLLVVALSALSPLLYLSTPIISLKKDYKPLLYVGVISGVEvLVLSLYLIPRLGILGAAIAQVVNALTSSILLLYICLRQ 390
                                   5777777777777776666667777777776666666655551789****************************9999888 PP

               Polysacc_synt_C  81 lgikl..ellrrll.kpllaalvmg 102
                                     + l  +  r+ll  p+ + ++++
  gi|70607631|ref|YP_256501.1| 391 KALVLgsMEKRSLLlLPIPFLAFIS 415
                                   8888887445555444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3237.17
//
Query:       gi|70607632|ref|YP_256502.1|  [L=642]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.068   13.3   0.0    1.3  1  DUF5010_C  DUF5010 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF5010_C  DUF5010 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-06     0.068      19      82 ..     476     539 ..     473     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                     DUF5010_C  19 vtsteaGewlewkeipfkaGavtlkvryattkeaakvrfvidgtagpsvelpaTgglqewetvd 82 
                                   v+s+ aG+  e+ ++ +++G   +    ++t ++  vrf +  ++ + +el +T+g++ ++ + 
  gi|70607632|ref|YP_256502.1| 476 VYSLYAGNKTEFMQLAMESGLKYVVWFNSSTYKNYDVRFAFLSKELSLQELINTTGFNIYKSIG 539
                                   78999***************87777777777***************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 3637.53
//
Query:       gi|70607633|ref|YP_256503.1|  [L=354]
Description: hypothetical protein Saci_1907 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-37  126.9   0.1    1.7e-35  122.1   0.0    2.3  2  Glycos_transf_1  Glycosyl transferases group 1
    7.9e-25   87.8   0.0    1.5e-24   87.0   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      6e-20   71.9   1.1    1.1e-19   71.1   1.1    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    8.3e-06   26.1   0.0    3.8e-05   24.0   0.0    2.0  2  Glyco_trans_1_2  Glycosyl transferases group 1
    4.7e-05   23.9   0.0    0.00046   20.7   0.0    2.0  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
      0.045   13.4   0.4      0.091   12.4   0.4    1.6  1  Glyco_trans_4_5  Glycosyl-transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.035     1e+02       4      39 ..      51      86 ..      48      89 .. 0.86
   2 !  122.1   0.0   5.7e-39   1.7e-35       4     165 ..     167     323 ..     165     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.035
                                  HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHC CS
               Glycos_transf_1  4 kkrkklgknekkkiilsvgrlekeKgvdllikafal 39
                                  ++   + + ++ k+ l  + l++ K++d++ +++a+
  gi|70607633|ref|YP_256503.1| 51 EIDGIKLIHKGNKVTLHFHSLKYAKNYDVVMDSVAH 86
                                  5666778899********************998875 PP

  == domain 2  score: 122.1 bits;  conditional E-value: 5.7e-39
                                   HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSS CS
               Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsre 84 
                                    ++++ g+++ +++il +grl+++K++ ++ik f+ l    + ++kl+i+G + e++   + +++   sdn+i+lg+++++
  gi|70607633|ref|YP_256503.1| 167 HDKFRPGEKSPEPMILWIGRLKRYKNPLHAIKIFKML----KTKAKLIIVG-KGEKDIENQIIQASSSSDNIIYLGRIPED 242
                                   56788888999************************99....578*******.5666777778899999************* PP

                                   SHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
               Glycos_transf_1  85 dleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                   ++++l+++a +++ +s  Eg+G++++EA a+g+p++a+ +g ++e++++g++G+lv+ ++  ++ae+i+ +l+de+  +++
  gi|70607633|ref|YP_256503.1| 243 QKIKLYQSAWVVLSTSFIEGWGMTITEANASGTPAVAYSVGSLPEIIQHGKNGFLVDYEDYTKAAEYIDYILSDENIMKKM 323
                                   ***************************************************************************877776 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   4.9e-28   1.5e-24       2     134 .]     179     316 ..     178     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 4.9e-28
                                   EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHH.T..T-T.TEEEE---.TH.HHHHHHH-SEEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleela.a..gleerveftGfv.ed.laellaaadvfv 77 
                                   p il++Grl +++k+    ++ ++ l+ k ++l+ivG+g+ + ++e+++ +    +++++++G++ ed + +l+++a+v++
  gi|70607633|ref|YP_256503.1| 179 PMILWIGRL-KRYKNPLHAIKIFKMLKTK-AKLIIVGKGE-K-DIENQIiQasSSSDNIIYLGRIpEDqKIKLYQSAWVVL 255
                                   89*******.778**************55.9******994.3.566544334455699*******9556************ PP

                                   E--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    +s  eg+g+++ Ea a+g+p Va +vg ++e++  g+ng+lv+ +d  + ae i  +l+d
  gi|70607633|ref|YP_256503.1| 256 STSfiEGWGMTITEANASGTPAVAYSVGSLPEIIqhGKNGFLVDYEDYTKAAEYIDYILSD 316
                                   ***************************99******************99999999999987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   1.1   3.6e-23   1.1e-19       1     169 [.      16     168 ..      16     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 3.6e-23
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvv..Hah 79 
                                   +GG e++++e++++L ++G+e++ ++ +++ + ++e         +   +l   ++ ++ +++  + +k  ++Dvv   + 
  gi|70607633|ref|YP_256503.1|  16 AGGSEVVIYEVSKRLMENGIEIHWLSENTRLEGRNE---------IDGIKLIHKGNKVTLHFHSLKYAK--NYDVVmdSVA 85 
                                   59************************9999999999.........333444456778888999999999..9****86444 PP

                Glyco_transf_4  80 spaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                   ++++++ ++l  +  + + lV++vH        +  +kpl +++++ler+l ++ +r+iavS++t+ +l++++++++ ki+
  gi|70607633|ref|YP_256503.1|  86 HAVPFF-SYLVNK--RTVALVHHVHQYV---VDYELSKPLAYVVKKLERYL-KKYKRIIAVSHSTKLDLIKLLKIDEHKIE 159
                                   445543.444334..5889999999888...78899999*******99986.***************************** PP

                Glyco_transf_4 161 VipnGvDle 169
                                   Vi+nGvD +
  gi|70607633|ref|YP_256503.1| 160 VIHNGVDHD 168
                                   *******98 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   4.2e+03      50      69 ..     120     139 ..     109     144 .. 0.73
   2 !   24.0   0.0   1.3e-08   3.8e-05       2      89 ..     254     342 ..     251     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
               Glyco_trans_1_2  50 eelaekiryllanpeerrai 69 
                                   + +++k++++l+  +++ a+
  gi|70607633|ref|YP_256503.1| 120 AYVVKKLERYLKKYKRIIAV 139
                                   56788999998877766555 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.3e-08
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                   vL +s  e+  + + Ea a+G++a++ +  +l+e+++ gk ++l++  d   +ae i+y l+++   ++++   ++    +
  gi|70607633|ref|YP_256503.1| 254 VLSTSFIEGWGMTITEANASGTPAVAYSVGSLPEIIQHGKNGFLVDyeDYTKAAEYIDYILSDENIMKKMSLDSYHA-SLK 333
                                   56666668999****************99*************999999****************9999999998888.446 PP

               Glyco_trans_1_2  81 htydhraeq 89 
                                   ++++ +a++
  gi|70607633|ref|YP_256503.1| 334 YDWNIAANK 342
                                   677766665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00046      59     160 .]      64     164 ..      17     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
               Glyco_trans_4_4  59 alralrrllrqrrerpdvvhahspt.aglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvs 137
                                    +  + +l    + ++dvv     +  +++  l   +r + lv+++h+  ++++ s +++ +++ ler+ l+   ++++vs
  gi|70607633|ref|YP_256503.1|  64 VTLHFHSLK--YAKNYDVVMDSVAHaVPFFSYLVN-KRTVALVHHVHQYVVDYElSKPLAYVVKKLERY-LKKYKRIIAVS 140
                                   445555554..67899***9777552577788888.99**********998888677777777888866.79********* PP

               Glyco_trans_4_4 138 eaeaeelra.lgvpadrvvvvpng 160
                                   ++   +l+  l ++ ++++v++ng
  gi|70607633|ref|YP_256503.1| 141 HSTKLDLIKlLKIDEHKIEVIHNG 164
                                   *********888***********8 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   3.1e-05     0.091       5     117 ..       3     117 ..       1     163 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
               Glyco_trans_4_5   5 vllishel....sltGaPlvlmelatlLrsvgaevvvltlskkggllkeladrgikvlea.....kaeelfklalkaDlvv 76 
                                   vl+++h +      +G+ +v++e+ + L + g+e+ +l+ + +   + + +  gik++++      + +++k a + D+v+
  gi|70607633|ref|YP_256503.1|   3 VLVVNHRDifhpYAGGSEVVIYEVSKRLMENGIEIHWLSENTRL--EGRNEIDGIKLIHKgnkvtLHFHSLKYAKNYDVVM 81 
                                   677777762222358999*********************99988..56666679*****9997776667889999***998 PP

               Glyco_trans_4_5  77 lntvvaakwidqlleenkakvlskvlWWihenrreYfdiak 117
                                      + a+ +   l+++ +       +  +h     Y   +k
  gi|70607633|ref|YP_256503.1|  82 DSVAHAVPFFSYLVNKRTVA----LVHHVHQYVVDYE-LSK 117
                                   88888888887777754444....4444455444444.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2578.06
//
Query:       gi|70607634|ref|YP_256504.1|  [L=508]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3680.44
//
Query:       gi|70607635|ref|YP_256505.1|  [L=244]
Description: dolichyl-phosphate beta-glucosyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-20   72.1   0.1    6.5e-20   71.6   0.1    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
      5e-07   29.5   0.0    7.7e-07   28.9   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0008   19.4   0.0     0.0012   18.8   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.023   15.2   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.1   1.5e-23   6.5e-20       1     140 [.       3     131 ..       3     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 1.5e-23
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   svvip+yNee+ + +tl  +l +   +  eiivv Dg  D+t+e+++++     +v++++ +++ Gk+ a+  g+++++ d
  gi|70607635|ref|YP_256505.1|   3 SVVIPAYNEENRIGNTLS-CLGI-WFDSAEIIVVHDGK-DNTPEVVKKF----NGVKLLKSPNRLGKGLAIKIGIENSSVD 76 
                                   8****************9.***9.**************.**********....69*******999**************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHC CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyf 140
                                    il++DaD+  ++d+lek++      +ad+v+ +r++ + ++ ++  +k++ +  rl f
  gi|70607635|ref|YP_256505.1|  77 RILLIDADLPTTRDDLEKVLSV----DADLVITKRRFVNISSERYILHKGFIFLVRLLF 131
                                   ******************9875....567899999999999999999998733333333 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.7e-10   7.7e-07       1     107 [.       3     100 ..       3     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-10
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskae 81 
                                   svvip +++e+r  i +++     ++d   e+ivv dg  +++ e+v+++   +ll + ++      +++ a   G++++ 
  gi|70607635|ref|YP_256505.1|   3 SVVIPAYNEENR--IGNTLSCLGIWFDS-AEIIVVHDGK-DNTPEVVKKFNGVKLLKS-PNR----LGKGLAIKIGIENSS 74 
                                   8***********..*****999999985.7999999996.5569************99.887....8************** PP

               Glyco_tranf_2_2  82 sdlvlFlDaDcfissDkfekilklit 107
                                    d +l +DaD   + D +ek+l++  
  gi|70607635|ref|YP_256505.1|  75 VDRILLIDADLPTTRDDLEKVLSVDA 100
                                   **********************9755 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.7e-07    0.0012       4      98 ..       2      85 ..       1     111 [. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
               Glyco_tranf_2_3  4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealrav 86
                                  l+v++p++nee ++g++l  l     ++ e++vv d++d    ev++     +   +v+++  +++lg   k  a++ ++++ 
  gi|70607635|ref|YP_256505.1|  2 LSVVIPAYNEENRIGNTLSCLGI-WFDSAEIIVVHDGKDNT-PEVVKK----FN--GVKLLKSPNRLG---KGLAIKIGIENS 73
                                  89****************76664.58*******99998876.888876....63..689997777666...777888****** PP

               Glyco_tranf_2_3 87 ksdlvllvDdDt 98
                                  + d +ll+D+D 
  gi|70607635|ref|YP_256505.1| 74 SVDRILLIDADL 85
                                  **********96 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     5e-06     0.023       1      52 [.       9      60 ..       9     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
               Glyco_tranf_2_4  1 rneadiLpeflahhlalgfd.rilvydndstDgtrailkelpevkllhvdksy 52
                                  +ne+++++++l ++  + fd + +++ +d +D+t +++k+   vkll++++  
  gi|70607635|ref|YP_256505.1|  9 YNEENRIGNTLSCLGIW-FDsAEIIVVHDGKDNTPEVVKKFNGVKLLKSPNRL 60
                                  69************887.65245555566677***************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1822.38
//
Query:       gi|70607636|ref|YP_256506.1|  [L=330]
Description: hypothetical protein Saci_1910 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2446.04
//
Query:       gi|70607637|ref|YP_256507.1|  [L=261]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-06   25.5   0.2    1.5e-05   24.9   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.046   13.4   0.2       0.24   11.1   0.1    2.3  2  DUF4325          STAS-like domain of unknown function (DUF432


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.7e-09   1.5e-05      11      99 ..      12      91 ..       3     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-09
                                  TTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE- CS
               Glycos_transf_2 11 ktlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepd 93
                                  k+l+++les++ q +y+dfe+ivv+ g+ +   ++++e+     +++ +r + n  + +a+  + ++++g+  l+lD   +  
  gi|70607637|ref|YP_256507.1| 12 KYLRNVLESIRTQ-TYQDFEVIVVNSGD-ELISDLIREY-----GFKEVREKVN--LLNARYLAHKNSSGEKALVLDETRVLR 85
                                  89***********.**************.5557777777.....8999999977..***************999999888888 PP

                                  TTHHHH CS
               Glycos_transf_2 94 pdwlek 99
                                  +d+le 
  gi|70607637|ref|YP_256507.1| 86 KDTLEI 91
                                  877765 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.42   3.8e+03       2      19 ..      11      31 ..      10      35 .. 0.58
   2 ?   11.1   0.1   2.7e-05      0.24      36      60 ..      38      62 ..      37      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.42
                       DUF4325  2 Gerfrdkilkpllke...gek 19
                                  G+++r+ ++  + +    +e 
  gi|70607637|ref|YP_256507.1| 11 GKYLRNVLESIRTQTyqdFEV 31
                                  777777777766666332444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.7e-05
                       DUF4325 36 deaFgglirefgeeeiskklkiknl 60
                                  de++++lire+g++e+++k+++ n+
  gi|70607637|ref|YP_256507.1| 38 DELISDLIREYGFKEVREKVNLLNA 62
                                  8******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1880.07
//
Query:       gi|70607638|ref|YP_256508.1|  [L=769]
Description: hypothetical protein Saci_1912 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5425.29
//
Query:       gi|70607639|ref|YP_256509.1|  [L=97]
Description: hypothetical protein Saci_1913 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 749.48
//
Query:       gi|70607640|ref|YP_256510.1|  [L=355]
Description: group 1 glycosyl transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-14   53.0   0.1    7.4e-14   51.6   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    7.1e-11   42.7   0.0    1.5e-10   41.6   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
     0.0015   18.6   0.0     0.0039   17.2   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.058   13.4   0.0    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.65   2.9e+03     100     100 ..     174     174 ..     133     208 .. 0.47
   2 !   51.6   0.0   1.7e-17   7.4e-14      80     158 ..     244     321 ..     214     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.65
                                   E CS
               Glycos_transf_1 100 s 100
                                    
  gi|70607640|ref|YP_256510.1| 174 L 174
                                   1 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 1.7e-17
                                   CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
               Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpnnaealaeairklled 158
                                   +v++e+l  l+++a ++++p   E fG  ++E+ma+g+pvia + +ggp+e + + etG+lv ++  +++ e   k+ e 
  gi|70607640|ref|YP_256510.1| 244 RVDEERLRDLYSSALVTLYPVDFEYFGYIPVESMASGTPVIAFKySGGPSESIIHDETGWLVSNE--KEFYEVTLKVYER 321
                                   45699*********************************************************998..6666555555555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   3.3e-14   1.5e-10      55     132 ..     236     319 ..     212     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 3.3e-14
                                   .TEEEE---...THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--..TTSSEE--TT-HHHHHHH CS
               Glyco_trans_1_4  55 erveftGfv...edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvg.giaevv..gengllvppgdpealaea 127
                                   ++ e++G +   e l++l+++a v++ P   e fg+  +E+ma+g+pv+a++ + g++e +   e+g+lv+  +++++ e 
  gi|70607640|ref|YP_256510.1| 236 DGAEYLGDRvdeERLRDLYSSALVTLYPVdfEYFGYIPVESMASGTPVIAFKYSgGPSESIihDETGWLVS--NEKEFYEV 314
                                   57788897767445****************99*******************9964899988888******9..88999988 PP

                                   HHHHH CS
               Glyco_trans_1_4 128 ilrLl 132
                                    l+++
  gi|70607640|ref|YP_256510.1| 315 TLKVY 319
                                   77776 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.6e-07    0.0039      12      57 ..      22      71 ..      14      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.6e-07
               Glyco_trans_4_2 12 htlrlakeLakrgyeVhvitpkkga..kdeleaegihvhrlkvdrkg..p 57
                                   t+++ak+L+k+g++V++++++ +   k+el++++i+v++l+ +r++   
  gi|70607640|ref|YP_256510.1| 22 ATINFAKGLSKHGVKVKIVSLGLEDgiKEELKNNDIEVISLDQPRSVyyD 71
                                  5899*****************544446**************999776444 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.058       2      38 ..      17      60 ..      16     111 .. 0.74
   2 ?   -1.5   0.0      0.49   2.2e+03     131     169 ..     155     191 ..     124     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                Glyco_transf_4  2 GGverhvleLaraLarrGheVtvvtpgddgpleeev.......e 38
                                   G+ r + ++a++L ++G++V +v+ g ++ + ee        +
  gi|70607640|ref|YP_256510.1| 17 DGQSRATINFAKGLSKHGVKVKIVSLGLEDGIKEELknndievI 60
                                  699*************************9999999765543321 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.49
                Glyco_transf_4 131 lrradrviavSeatadelreryg.vppekitVipnGvDle 169
                                   +++ + ++a+S++ a  +   y+ vp     V+++++D++
  gi|70607640|ref|YP_256510.1| 155 VSKYHMLLANSNTSALVVSLFYNrVPQ---GVVYPPIDID 191
                                   566677777777777777776663444...7889988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2605.44
//
Query:       gi|70607641|ref|YP_256511.1|  [L=318]
Description: glycosyl transferase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-13   49.2   0.2    8.9e-13   48.4   0.2    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
    2.6e-09   37.3   0.0    4.2e-09   36.6   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.2   9.9e-17   8.9e-13       1     112 [.       6     110 ..       6     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 9.9e-17
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   sv+i++yN+++ l  +++sll  ++ +d eiivv++   ++  + l++l    p + ++ ++  + ++g l  g+++++g+
  gi|70607641|ref|YP_256511.1|   6 SVIITSYNRKQFLTSLIDSLLIYTKNYDSEIIVVKNFLDERIDSYLDSL----PVINIYSKD--TTLGGKLKDGISRSSGN 80 
                                   8************************************988888888888....666666666..46*************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvv 112
                                   +i+f+ +Dd ++pd+++++++ + + +a++ 
  gi|70607641|ref|YP_256511.1|  81 IIFFVEDDDLFHPDKIPRVLNTFGN-RASIS 110
                                   *********************9998.77554 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   4.7e-13   4.2e-09       1     115 [.       2     107 ..       2     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.7e-13
               Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqe.yprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                   p d++v+++++n+ + l+++++sll ++ + ++e++vv +  d+   + ++     lp +  +++ ++  lg  gk   l+
  gi|70607641|ref|YP_256511.1|   2 PKDFSVIITSYNRKQFLTSLIDSLLIYTkNYDSEIIVVKNFLDERIDSYLDS----LPVI--NIYSKDTTLG--GK---LK 71 
                                   678**********************9975799*************9999987....7885..8887777666..77...66 PP

               Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqff.ltp 115
                                   +++++ ++ ++ +v+dD++ +Pd ++r+l++f +++
  gi|70607641|ref|YP_256511.1|  72 DGISRSSGNIIFFVEDDDLFHPDKIPRVLNTFgNRA 107
                                   *******************************97554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2301.59
//
Query:       gi|70607642|ref|YP_256512.1|  [L=442]
Description: hypothetical protein Saci_1916 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-21   76.3   0.0      4e-21   75.3   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-13   51.6   0.0    1.9e-13   51.0   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   4.5e-25     4e-21       7     168 ..     244     415 ..     240     418 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.5e-25
                                   HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...........STTHHHHHHHHHHHCTTCGGGE CS
               Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..........ngeeekelkklaeelelsdnvif 77 
                                   ++++  +k+ ++++ +rl + Kg   l   + ++k+ + +++kl i+G          n++ ++++ +l+ee +lsd++ +
  gi|70607642|ref|YP_256512.1| 244 FREKRTDKDDYMVFFARLLPLKGTLELPFILSKVKE-IVKEAKLFIVGkfpedirgkkNESFQDYFFNLVEEMGLSDHIVY 323
                                   566677999*************************87.7******************************************* PP

                                   EECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHS CS
               Glycos_transf_1  78 lgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklled 158
                                    g++  ++l  + ++a+++v+ps+ + f +++lE++++g+pv++++++gp+ v++      +v +++++a++++++ l + 
  gi|70607642|ref|YP_256512.1| 324 KGYLTGNELYDVVSKAKCVVYPSHEDTFSLSILESITVGTPVVSYDIPGPKSVFNGLPAVKFVREYDIDAMSKEVANLFKA 404
                                   ******************************************************988877788888************999 PP

                                   H.HHHHHHHHH CS
               Glycos_transf_1 159 e.elrerlgen 168
                                   + e+++++ +n
  gi|70607642|ref|YP_256512.1| 405 GwEDYRKIVYN 415
                                   98888888777 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   2.1e-17   1.9e-13       4     132 ..     255     402 ..     252     404 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.1e-17
                                   EEEES---G..G.GTHHHHHHHHHHHH.HHEEEEEES---........HHHHH....HHT..T-T.TEEEE---..THHHH CS
               Glyco_trans_1_4   4 ilfvGrlee..nvkgvdllleavpllrkkdvrlvivGdgprp......eelee....laa..gleerveftGfv..edlae 68 
                                   ++f+ rl +      + ++l +v+++ k +++l ivG+ p++      e++++    l++  gl++++++ G++  ++l +
  gi|70607642|ref|YP_256512.1| 255 MVFFARLLPlkGTLELPFILSKVKEIVK-EAKLFIVGKFPEDirgkknESFQDyffnLVEemGLSDHIVYKGYLtgNELYD 334
                                   5677777332223345788999988884.49******654223344444444433334547899**********9999*** PP

                                   HHHH-SEEEE--.-.--SHHHHHHHHTT-EEEE-TGGGTTT--.TTSS.EE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  69 llaaadvfvaPs.e.gfglkllEamaaglpvVatdvggiaevv.geng.llvppgdpealaeailrLl 132
                                   ++++a+++v Ps e +f+l++lE+  +g+pvV+ d++g++ v  g  +   v + d +a+ +++++L+
  gi|70607642|ref|YP_256512.1| 335 VVSKAKCVVYPShEdTFSLSILESITVGTPVVSYDIPGPKSVFnGLPAvKFVREYDIDAMSKEVANLF 402
                                   ************9559**********************777778755523667889******999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3008.37
//
Query:       gi|70607643|ref|YP_256513.1|  [L=757]
Description: hypothetical protein Saci_1917 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4959.50
//
Query:       gi|70607644|ref|YP_256514.1|  [L=259]
Description: hypothetical protein Saci_1918 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-10   39.9   0.3    3.9e-05   23.7   0.3    2.2  2  Methyltransf_21  Methyltransferase FkbM domain
    1.7e-06   28.0   0.1      3e-06   27.1   0.1    1.4  1  Met_10           Met-10+ like-protein
    3.4e-05   23.4   0.1      5e-05   22.8   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.032   14.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.047   13.3   0.0      0.075   12.7   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.11   13.0   4.8       0.15   12.6   0.2    3.2  4  HMA              Heavy-metal-associated domain
       0.12   12.0   0.0       0.17   11.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.12   13.1   0.0       0.27   12.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
       0.13   11.8   0.0        0.2   11.2   0.0    1.2  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05     0.021       1      42 [.     122     162 ..     122     182 .. 0.71
   2 !   23.7   0.3     2e-08   3.9e-05      95     172 ..     178     240 ..     165     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
               Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpns....lpkfekl 42 
                                   d+Ga ig  ds +++    ++g + v+a+EP p++    ++++e +
  gi|70607644|ref|YP_256514.1| 122 DIGAAIG--DSPIYFS---LMGAKSVVAVEPDPKKvkymKVNLELN 162
                                   9******..9999885...88999999*******664333333333 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2e-08
               Methyltransf_21  95 ievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefetelfdeirqflrecgyr 172
                                    + + v+l ++le++  + +d+ kiD+EG E  v+ ++ kg+      +i +E+ +       + + + ++lre gy+
  gi|70607644|ref|YP_256514.1| 178 DNEREVRLNTLLEKF--GPFDIAKIDCEGCERRVI-SDIKGIPE----II-IEWDF-------EYRSLAEKLREEGYE 240
                                   567889999****99..9*****************.59999955....45.9**97.......367788888888887 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.5e-09     3e-06     102     154 ..     118     169 ..     111     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.5e-09
                                   -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                        Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                   + V+d+ A iG  +i  +    ak v+a++ +P+ vky+k n++lN++ +v+ 
  gi|70607644|ref|YP_256514.1| 118 KKVLDIGAAIGDSPIYFSL-MGAKSVVAVEPDPKKVKYMKVNLELNDIRNVIV 169
                                   579************9997.66778*************************994 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.5e-08     5e-05     161     220 ..     116     175 ..     106     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                          PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalsee 220
                                   ++++vlD+G+  G   i  +++gak+vvav  D+  vk  k N+elN++++ + v  + +
  gi|70607644|ref|YP_256514.1| 116 REKKVLDIGAAIGDSPIYFSLMGAKSVVAVEPDPKKVKYMKVNLELNDIRNVIVVDKALS 175
                                   6789***********************************************987754433 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-05     0.032      21      62 ..     115     172 ..      99     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
               Methyltransf_23  21 raggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae...............k 62 
                                    + ++vLdiG++ G    +++  g+ sv++v+++p++v+  +               k
  gi|70607644|ref|YP_256514.1| 115 VREKKVLDIGAAIGDSPIYFSLMGAkSVVAVEPDPKKVKYMKvnlelndirnvivvdK 172
                                   5678********************999********98776656666655555554440 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.075       9      73 ..     117     179 ..     112     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                   T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHH CS
               Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73 
                                   e+++lD+ aa G    + + +   ++ vvAv+ + +++k ++ nl+   ++n+iv+   ++ +d+
  gi|70607644|ref|YP_256514.1| 117 EKKVLDIGAAIGDSPIYFSLM--GAKSVVAVEPDPKKVKYMKVNLELNDIRNVIVVDKALSTVDN 179
                                   6789*********99999877..7889***************************99988777765 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.5   1.3e+04      45      60 ..      19      31 ..       9      33 .. 0.65
   2 ?   -0.5   0.1      0.91   1.8e+03      35      49 ..     140     154 ..     135     178 .. 0.62
   3 ?   12.6   0.2   7.4e-05      0.15       2      26 ..     195     219 ..     195     222 .. 0.93
   4 ?   -0.0   0.0      0.63   1.3e+03      43      62 .]     224     240 ..     219     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.5
                           HMA 45 estklrkiieaiekag 60
                                  +    +++ie +++ +
  gi|70607644|ref|YP_256514.1| 19 TI---KRLIELLRQYK 31
                                  33...77888887755 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.91
                           HMA  35 tktvtVegdaestkl 49 
                                   ++ v Ve d+ ++k+
  gi|70607644|ref|YP_256514.1| 140 KSVVAVEPDPKKVKY 154
                                   455556665555444 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 7.4e-05
                           HMA   2 vrvsgmhCagCaakvekvLselpgV 26 
                                   +++  ++C+gC+++v + ++++p++
  gi|70607644|ref|YP_256514.1| 195 FDIAKIDCEGCERRVISDIKGIPEI 219
                                   78999****************9987 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.63
                           HMA  43 daestklrkiieaiekagyk 62 
                                   d e   +r + e++++ gy+
  gi|70607644|ref|YP_256514.1| 224 DFE---YRSLAEKLREEGYE 240
                                   444...499*********96 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.6e-05      0.17      33     116 ..     107     197 ..      94     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-05
                                   HHHHCCC.HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T......TTEEEEES-HHHHCT CS
                 Cons_hypoth95  33 Fnilaae.iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee......etaelkedaleallk 106
                                   Fn  +++ +++++vLD+ a  G   +     gak++v+ve d++ vk +k nle  ++++        +++ ++++ +l++
  gi|70607644|ref|YP_256514.1| 107 FNDYRKAdVREKKVLDIGAAIGDSPIYFSLMGAKSVVAVEPDPKKVKYMKVNLELNDIRNvivvdkALSTVDNEREVRLNT 187
                                   6665555588888888888888888888888*************************9999666665566666666667777 PP

                                   S--SS-EEEE CS
                 Cons_hypoth95 107 lakkkeefdi 116
                                   l +k ++fdi
  gi|70607644|ref|YP_256514.1| 188 LLEKFGPFDI 197
                                   7677777776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.27       1      57 [.     120     176 ..     120     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed 57 
                                   vLd+G+  G+  ++++   g+++v++v+++++ +++++ ++e +++ nv +v + +++
  gi|70607644|ref|YP_256514.1| 120 VLDIGAAIGDSPIYFSLM-GAKSVVAVEPDPKKVKYMKVNLELNDIrNVIVVDKALST 176
                                   9**************977.79*******************988888666655555444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001       0.2      31      96 ..     116     180 ..     108     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveek 96 
                                   +++kvlD+G+ +G   + +  +  + +v++v+ d + ++  k nle n+++  +v   +l++v+++
  gi|70607644|ref|YP_256514.1| 116 REKKVLDIGAAIGDSPIYFSLMGAK-SVVAVEPDPKKVKYMKVNLELNDIRNVIVVDKALSTVDNE 180
                                   6789**********99999887777.8************************999999999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1858.55
//
Query:       gi|70607645|ref|YP_256515.1|  [L=816]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.6e-104  349.7  41.9   3.6e-104  349.2  41.9    1.2  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.2  41.9    2e-108  3.6e-104       2     456 .]      44     493 ..      43     493 .. 0.97

  Alignments for each domain:
  == domain 1  score: 349.2 bits;  conditional E-value: 2e-108
                       DUF2079   2 lasLnstayDlGifdQviwntsqGelfysslsgvl....hlLgqHfapillllaplyalfPsvltLllvqalllslgglpl 78 
                                   l++Ln+++y+l++f Q+++++sqG++fy+++++++    ++L++H+++il++l+ply+ fPs+ltL+lv++l+l+l++l+l
  gi|70607645|ref|YP_256515.1|  44 LYNLNYSSYNLSMFIQELYSASQGKPFYDTINLLFrgipYGLAIHPYLILYILVPLYKAFPSWLTLSLVESLVLTLASLYL 124
                                   799****************************************************************************** PP

                       DUF2079  79 yrlarer.llsrrlalliallYllspvvinptlfdFhpevlaiPllllalllalrrrkwllllvlilllllvredlslvvv 158
                                   y++are+  +s++l+++ ++++l++p++++ +l+ F+ ++++ Pl++la ++++++++w+l++++++llll++e+ +++v+
  gi|70607645|ref|YP_256515.1| 125 YKIAREVlPQSKLLPVISSMIFLFNPLTVASFLSGFQVLSFI-PLFYLASYYYYLTKRWKLFIISTALLLLTSEASYPIVL 204
                                   *******999********************************.************************************** PP

                       DUF2079 159 ilglwlilrerkrrk......iglillllglawvilvtsvliPlfsstksqvfgverysylgsSlleillnlitqpl.lvl 232
                                   +++++li+++++  k      ++ ++l+l+++++++v+ ++ P+f +tk+            +++++ +l+ i+q++ l +
  gi|70607645|ref|YP_256515.1| 205 TYMVLLIIKNKNNNKllsksfFRRNILFLSVIVATIVIALTLPTFLQTKY------------TGTSHSILQDIEQYYsLNY 273
                                   **********555556888899***************************9............9**************9*** PP

                       DUF2079 233 qellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqlslgyqYsllvipflvlaaifglaklsssv 313
                                    ++++++  kl+y+ll+f+++g l l+ sp++Ll+alP++ll+++s y+++++ gy+Y++lv+p+l++a++++l+k++   
  gi|70607645|ref|YP_256515.1| 274 VNYDILN--KLEYWLLVFGSFGALSLF-SPLELLPALPYILLTVMSFYPNYYTPGYYYFFLVLPMLAVALVYTLKKIH--- 348
                                   *******..******************.**************************************************... PP

                       DUF2079 314 elrrikriwsvalvlvlvltlflnparslsflvpdsesp.....vvylstlaqlqas...rellklIpsdasvlatsnLaP 386
                                      +ikr+++valv+vl++ +f+np+ +++f++++s+++     ++ ++t+ + +++   +el++lIp+++s++at++L+P
  gi|70607645|ref|YP_256515.1| 349 ---DIKRVVRVALVFVLLIGVFFNPYIYTTFQSYNSPKIvspgyPPSFNTTLASVNQmyiNELTSLIPPNSSIVATTDLLP 426
                                   ...9**********************************99999977777777777667*********************** PP

                       DUF2079 387 hlan..Rayvylfpeneel......ydleylleevdyvlldvafrgwasrkdrerklidklrnsgrygviaeedgvll 456
                                   +++n  +ayv+++++n +l      + l++l+++++y+l+d            +  + + ++ +g+yg++ae++g+ l
  gi|70607645|ref|YP_256515.1| 427 FVSNsmNAYVLPPYSNVNLnilknlNVLKRLAPTPNYLLID-----------GSFLTPSFNSIEGNYGIYAETNGISL 493
                                   **********************999999*************...........7899*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (816 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 5142.37
//
Query:       gi|70607646|ref|YP_256516.1|  [L=783]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     2e-102  343.4  41.5   2.6e-102  343.0  41.5    1.1  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.0  41.5  1.5e-106  2.6e-102       1     456 []      16     462 ..      16     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 343.0 bits;  conditional E-value: 1.5e-106
                       DUF2079   1 rlasLnstayDlGifdQviwntsqGelfysslsgvl....hlLgqHfapillllaplyalfPsvltLllvqalllslgglp 77 
                                   rl++L+s+a+DlGif+Q++++t++G++fy+s+++++    ++Lg+H+++i+++l+p+y++fPs+ltL+l+q+l++sl++++
  gi|70607646|ref|YP_256516.1|  16 RLYDLYSGAFDLGIFLQELYSTLHGRIFYDSPNFTYygviSGLGIHPYFIMFFLLPIYYFFPSWLTLSLTQSLIISLSSIY 96 
                                   89******************************************************************************* PP

                       DUF2079  78 lyrlarer.lls..rrlalliallYllspvvinptlfdFhpevlaiPllllalllalrrrkwllllvlilllllvredlsl 155
                                   +y++ ++   ++  r+l+l++++lYl++p+ i+ +l+dFh+ev++ Pl++l+++++++ + w+ + ++i++lll +e++++
  gi|70607646|ref|YP_256516.1|  97 VYKIGSTLfKENgfRTLPLIFTILYLFNPLSISGYLYDFHAEVFF-PLFYLGAYYYYLIKAWRRFSTFIIFLLLSMEAAYP 176
                                   ********5555*********************************.*********************************** PP

                       DUF2079 156 vvvilglwlilre..rkrrk......iglillllglawvilvtsvliPlfsstksqvfgverysylgsSlleillnlitqp 228
                                   +v+ ++++li+++  +          ++ ++l+l++++++++++++iP++ ++++ ++++       sS++++l+++it +
  gi|70607646|ref|YP_256516.1| 177 IVILFMIYLIIKSykK---GtkikffLKNTTLFLIFIIISIIMGLTIPHYLNSIFATSSH-------SSTTHYLYSTITYL 247
                                   ************9542...13458899***************************988888.......9************* PP

                       DUF2079 229 llvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqlslgyqYsllvipflvlaaifglakl 309
                                   +l   ++ +++  k  ++l++f+++gflpl+ sp++Ll+alP++++ l+s++ ++ ++gyqY+++++  +++a+++ l++l
  gi|70607646|ref|YP_256516.1| 248 FLKGINYAWSF--KSSFWLMYFASFGFLPLF-SPIELLPALPYIGTSLFSIMLTYSGIGYQYVFIALGPMATASLHSLNTL 325
                                   ***********..******************.************************************************* PP

                       DUF2079 310 sssvelrrikriwsvalvlvlvltlflnparslsflvpdsesp.....vvylstlaqlqas...rellklIpsdasvlats 382
                                          ++  +++valv+vl+++++lnp ++ + + ++s+++     v++++ + +++++   +++++lIp++a+vla++
  gi|70607646|ref|YP_256516.1| 326 L------KRPGVIKVALVIVLFISFLLNPFTYNNLQAMNSPRYygggyVPPFNLSLANSNYeviSNMTSLIPENAVVLASN 400
                                   *......999**************************************999*********9******************** PP

                       DUF2079 383 nLaPhlanRayvylfpeneel.ydleylleevdyvlldvafrgwasrkdrerklidklrnsgrygviaeedgvll 456
                                   nL+P++an+   y+++++  + ++l+y+++ +dy++l+             + ++   + +g+y++ ae++g+ll
  gi|70607646|ref|YP_256516.1| 401 NLFPFVANNLNSYPLYGSLITsSQLKYSPRFPDYIFLS-------------EPELFLSYIRGNYSMLAEANGLLL 462
                                   ********888889999988889***************.............89999999*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (783 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 4749.00
//
Query:       gi|70607647|ref|YP_256517.1|  [L=383]
Description: hypothetical protein Saci_1921 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-20   72.7   0.3    4.7e-20   71.8   0.3    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
      2e-15   57.4   0.0    3.8e-15   56.5   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.9e-11   43.6   0.0    6.3e-11   42.5   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    6.4e-05   23.0   0.0    0.00057   19.9   0.0    2.4  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.028   13.8   0.8       0.54    9.7   0.2    2.8  3  Clathrin-link    Clathrin, heavy-chain linker
      0.083   13.3   0.0       0.17   12.3   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.3   1.6e-23   4.7e-20      13     171 ..     208     358 ..     200     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.6e-23
                                   TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
               Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                    +k++i ++ r ek K+ +l+i+ + +l +  + n+  +i+     +++lk++++   +      + +  +e++ +l++ a
  gi|70607647|ref|YP_256517.1| 208 REKNVIMTILRSEKIKNSELAIRTLNSLAE--KINFSAIIVD-HGVLNTLKDKIKFKYI-----SYSHPTYEEMVKLYNEA 280
                                   5899************************86..6*********.6677888888666555.....45555578999****** PP

                                   SEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
               Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                   ++f+++s+ E+  ++ +EAm++g+pv+++++ g++ +v + e+ l+ k ++ ++l   + ++l+++ l+ rl en+ k
  gi|70607647|ref|YP_256517.1| 281 SVFLITSRLESYSLTTVEAMSCGTPVVTTDNIGMRAYVINRENALVSKHHDEKELLSLVLEVLSNPRLALRLVENGIK 358
                                   ***************************************************************************976 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   1.3e-18   3.8e-15       3     134 .]     212     345 ..     210     345 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.3e-18
                                   EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---..HHHHHHHTT-T.TEEEE---.THHHHHHHH-SEEEE--. CS
               Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgprpeeleelaagleerveftGfv.edlaellaaadvfvaPs. 80 
                                   vi+++ r  e++k+ +l ++ +  l++k ++  +iv  g   + l+++++ + + +++     e++ +l+++a+vf+++s 
  gi|70607647|ref|YP_256517.1| 212 VIMTILRS-EKIKNSELAIRTLNSLAEKiNFSAIIVDHGVL-NTLKDKIK-F-KYISYSHPTyEEMVKLYNEASVFLITSr 288
                                   67777787.799**********9999887899****98865.48998885.4.578888888899***************9 PP

                                   .---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  81 .egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    e+ +l+++Eam++g+pvV+td  g++++v   en+l+ + +d+++l   +l++l++
  gi|70607647|ref|YP_256517.1| 289 lESYSLTTVEAMSCGTPVVTTDNIGMRAYVinRENALVSKHHDEKELLSLVLEVLSN 345
                                   99*******************9889988888545655557889****9999999986 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   2.1e-14   6.3e-11       2      91 ..     283     373 ..     282     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.1e-14
               Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                   +L +sr es +l ++Ea+ cG++++t+d  g++ ++ + + +++ +  d++el+  + ++l+np ++ ++ e++++ ++a 
  gi|70607647|ref|YP_256517.1| 283 FLITSRLESYSLTTVEAMSCGTPVVTTDNIGMRAYVINRENALVSKhhDEKELLSLVLEVLSNPRLALRLVENGIKTAKA- 362
                                   78899******************************99988888877*******************************655. PP

               Glyco_trans_1_2  81 htydhraeqll 91 
                                    ++d+ +e+++
  gi|70607647|ref|YP_256517.1| 363 NDWDNVIERWI 373
                                   5*****99986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.9e-07   0.00057       3      98 ..      15     133 ..      13     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.9e-07
                Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev..........................elvvrvprvplpllkrllrs 57 
                                   G + ++le+a++L rrG++V +vt g +   +++                           +   ++  +++ l+  l+++
  gi|70607647|ref|YP_256517.1|  15 GGNYSILEIANRLLRRGFDVKIVTTGAKVWYYDHNkvpiiypkepkvlkyllsplsfkykmIKEFAGFDYYYALSHLLGID 95 
                                   8999*******************9999888888878889999999999999999988886633344444556777888888 PP

                Glyco_transf_4  58 laflrrlrrllkrekpDvvHahspaalgaallalrrrlgip 98 
                                   + f++r+++++   + D++ ++ + +++++ la ++  +++
  gi|70607647|ref|YP_256517.1|  96 FDFAKRVMEIIP--QSDLLIVNEFKTALWGFLAKWQ-GKVK 133
                                   888999999998..8999999999999999999997.4443 PP

>> Clathrin-link  Clathrin, heavy-chain linker
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.07   2.1e+02      13      20 ..     223     230 ..     219     230 .. 0.87
   2 ?   -2.3   0.1         1     3e+03       8      14 ..     250     256 ..     250     256 .. 0.84
   3 ?    9.7   0.2   0.00018      0.54       8      21 ..     339     352 ..     339     352 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.07
                 Clathrin-link  13 nNpdLALr 20 
                                   +N +LA+r
  gi|70607647|ref|YP_256517.1| 223 KNSELAIR 230
                                   7*****98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1
                 Clathrin-link   8 IlntLnN 14 
                                   +lntL++
  gi|70607647|ref|YP_256517.1| 250 VLNTLKD 256
                                   89***85 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00018
                 Clathrin-link   8 IlntLnNpdLALrl 21 
                                   +l +L+Np LALrl
  gi|70607647|ref|YP_256517.1| 339 VLEVLSNPRLALRL 352
                                   789**********8 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.6e-05      0.17       1     107 [.      14     142 ..      14     191 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaal..................... 60 
                                   +G++  + e+a +L +rG +V ++t+++  + + +++++v+++  + p   + l +   +                     
  gi|70607647|ref|YP_256517.1|  14 TGGNYSILEIANRLLRRGFDVKIVTTGA--KVWYYDHNKVPIIYPKEPKVLKYLLS---Plsfkykmikefagfdyyyals 89 
                                   689999*******************955..55556999999986443322221111...1111222223333333333333 PP

               Glyco_trans_4_4  61 ..........ralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhgll 107
                                              ++ +      ++ d++++++++++l + la+++ +++ +  + +ll
  gi|70607647|ref|YP_256517.1|  90 hllgidfdfaKRVME----IIPQSDLLIVNEFKTALWGFLAKWQGKVKRLAFFPQLL 142
                                   333333221122233....35889999999999999999999888887655554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2478.91
//
Query:       gi|70607648|ref|YP_256518.1|  [L=437]
Description: hypothetical protein Saci_1922 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-18   65.2   1.2    8.4e-18   64.5   0.2    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-11   44.4   0.0    3.6e-11   43.6   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.23   2.1e+03      12      42 ..      67      96 ..      39     109 .. 0.67
   2 !   64.5   0.2   9.3e-22   8.4e-18       9     159 ..     255     396 ..     248     411 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.23
                                  TTT-EEEEEESS-TTTTTHHHHHHHHHCCCC CS
               Glycos_transf_1 12 nekkkiilsvgrlekeKgvdllikafallkk 42
                                   ek++ +l ++ le+  gv+++ ++++ l+ 
  gi|70607648|ref|YP_256518.1| 67 EEKERKYLNLKELER-NGVEVFPEVWKYLEM 96
                                  355566666666665.555555555555544 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 9.3e-22
                                   TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
               Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                   + k+ k++++l+ gr+++ Kg+  lik ++      + nvk+ +aG+ ++ ke+++l  +     n+ +lg  ++++l ++
  gi|70607648|ref|YP_256518.1| 255 S-KKVKENFALYAGRITYLKGIIDLIKIAK------ETNVKIMLAGSFDNHKEMERLFSKFPP--NLVYLGSFMNNELYKI 326
                                   4.4589************************......78*******************888877..9999999999****** PP

                                   HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHHHHSH CS
               Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpn.naealaeairkllede 159
                                   ++n+++++lps++E+f +  +E++a+ +pvia+n + + e+  d +  + ++ + n + +a+ +++l+e++
  gi|70607648|ref|YP_256518.1| 327 ISNSKVTLLPSYKESFSLITMESLALDTPVIAYNLPAINEIYGDIKAVIKIP-VgNYKLMAKTLESLMEKD 396
                                   **********************************************544455.45************9986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0     4e-15   3.6e-11       5     133 ..     264     394 ..     260     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4e-15
                                   EEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE--..- CS
               Glyco_trans_1_4   5 lfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfvaPs..e 81 
                                   l+ Gr+    kg+  l++ +++     v+++++G+ ++++e+e+l +++ ++ +++G    ++l +++++++v+++Ps  e
  gi|70607648|ref|YP_256518.1| 264 LYAGRI-TYLKGIIDLIKIAKETN---VKIMLAGSFDNHKEMERLFSKFPPNLVYLGSFmnNELYKIISNSKVTLLPSykE 340
                                   678888.56688888888777776...99*****7765579997778999**99999887888****************99 PP

                                   --SHHHHHHHHTT-EEEE-TGGGTTT--T..TSSEE--TT-HHHHHHHHHHHHH CS
               Glyco_trans_1_4  82 gfglkllEamaaglpvVatdvggiaevvg..engllvppgdpealaeailrLle 133
                                   +f+l ++E++a+ +pv+a ++++i+e+ g  ++ + +p g+ + +a+ ++ L+e
  gi|70607648|ref|YP_256518.1| 341 SFSLITMESLALDTPVIAYNLPAINEIYGdiKAVIKIPVGNYKLMAKTLESLME 394
                                   **************************885334457889999*****99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3060.10
//
Query:       gi|70607649|ref|YP_256519.1|  [L=369]
Description: hypothetical protein Saci_1923 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-17   64.2   0.0    2.1e-17   63.2   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    1.9e-07   31.6   0.0    4.1e-07   30.5   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   2.4e-21   2.1e-17       8     157 ..     193     335 ..     189     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 2.4e-21
                                   HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHH CS
               Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredlee 88 
                                     +++++++ +l  gr+++eK +d++i+ +++      +++++++aG +++ +e    +  ++  dnv+++ + ++e+++ 
  gi|70607649|ref|YP_256519.1| 193 NVELDNREECVLIFGRINREKKLDVVIEIAKR------SRYRFIVAGAVNKGDESYFNSLRAKSPDNVNIIPNPNEENKDI 267
                                   567788999**********************5......6799*****88888888888899999***************** PP

                                   HHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHH CS
               Glycos_transf_1  89 llknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklle 157
                                   l++++++f+++ ++E+ G+++ EA+++gl+ ++ ++ggp e ++++  ++ +  +++e+++ ai ++++
  gi|70607649|ref|YP_256519.1| 268 LFRKCSVFLQTKRYEHYGLSVAEAISYGLIPVVPKVGGPWEDITEYG-KYGFGYEDIEEAISAIGQVMK 335
                                   *******************************************9999.577777788888888877776 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   4.5e-11   4.1e-07       4     132 ..     203     334 ..     200     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.5e-11
                                   EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.......HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
               Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp..rp...eeleelaagleerveftGfv..edlaellaaadvfv 77 
                                   +l +Gr++ ++k +d+++e +++ r   +r++++G  +  ++   ++l++   +  ++v +      e+++ l+++++vf+
  gi|70607649|ref|YP_256519.1| 203 VLIFGRIN-REKKLDVVIEIAKRSR---YRFIVAGAVNkgDEsyfNSLRA---KSPDNVNIIPNPneENKDILFRKCSVFL 276
                                   7899***5.56***********999...89*****543323323344433...4458899999887566999********* PP

                                   E--..---SHHHHHHHHTT-EEEE-TGGGT.TT--..TTSSEE--TT-HHHHHHHHHHHH CS
               Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdvggi.aevv..gengllvppgdpealaeailrLl 132
                                    +   e  gl++ Ea ++gl  V+ +vgg+ +++   g+ g+  +  d e+ + ai +++
  gi|70607649|ref|YP_256519.1| 277 QTKryEHYGLSVAEAISYGLIPVVPKVGGPwEDITeyGKYGFGYE--DIEEAISAIGQVM 334
                                   ***999*********************996366668888888887..9999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2208.88
//
Query:       gi|70607650|ref|YP_256520.1|  [L=104]
Description: hypothetical protein Saci_1924 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 683.34
//
Query:       gi|70607651|ref|YP_256521.1|  [L=211]
Description: phosphoadenosine phosphosulfate reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-23   81.7   0.1    1.1e-22   80.9   0.1    1.4  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.18   12.1   0.0    1.4  1  DUF2280      Uncharacterized conserved protein (DUF2280)


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.1   1.2e-26   1.1e-22      24     166 ..       3     166 ..       1     174 [. 0.92

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.2e-26
                                   TTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC......................HH CS
                   PAPS_reduct  24 kpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee......................aa 82 
                                   k+v+ + +d   +f+et ef+++++++ g+ + v  +e+ +  k     + s+l +e                      a 
  gi|70607651|ref|YP_256521.1|   3 KEVKAIVIDHFMHFDETWEFIERVKKEWGVSVVVKGNERLKGHKYGDVVKVSELSREdreelqrlgynreefvfalnniAG 83 
                                   6778999************************999999888777777777677777778899****************9999 PP

                                   HHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCCTT- CS
                   PAPS_reduct  83 eriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLydqgf 163
                                   +++ K++plk+a ++l+ dal++G+R de+++ra++ +++ +ed +++ rv+ +l +te+d+w++ l + +p++pLy +g+
  gi|70607651|ref|YP_256521.1|  84 NHLLKTVPLKEAVKDLKIDALIVGVRWDENPARASETFFSPRED-PPHTRVHTILLFTERDIWEFTLGNRLPVHPLYYKGY 163
                                   ********************************************.77********************************** PP

                                   SS- CS
                   PAPS_reduct 164 rsi 166
                                   rs+
  gi|70607651|ref|YP_256521.1| 164 RSL 166
                                   **8 PP

>> DUF2280  Uncharacterized conserved protein (DUF2280)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.18       5      44 ..       2      41 ..       1      86 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                       DUF2280  5 kdevKafivqalAcfdtpsevvkavkeefgvkvsrqqves 44
                                  ++evKa ++ ++  fd   e ++ vk+e+gv+v  +  e+
  gi|70607651|ref|YP_256521.1|  2 NKEVKAIVIDHFMHFDETWEFIERVKKEWGVSVVVKGNER 41
                                  79*****************************998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1479.38
//
Query:       gi|70607652|ref|YP_256522.1|  [L=185]
Description: hypothetical protein Saci_1926 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1253.59
//
Query:       gi|70607653|ref|YP_256523.1|  [L=132]
Description: hypothetical protein Saci_1927 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-12   46.4   1.6    1.2e-11   44.7   1.6    1.7  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00017   21.5   0.2    0.00058   19.8   0.2    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.015   14.8   0.4      0.017   14.6   0.4    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   1.6     2e-15   1.2e-11       1     116 [.      10     113 ..      10     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2e-15
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   sv+i +y ++++l+ +les+  q   +  e+iv+ D    + v     +   +++v vi  +  + +++ + +g+ra+tgd
  gi|70607653|ref|YP_256523.1|  10 SVIINVYKRYQYLPFALESVFTQ-SVKPNEVIVIADDP--DKVP----Y---RDKVYVIESK-DEKYGTKIIEGFRASTGD 79 
                                   8**********************.99999999999999..2222....2...3456666666.66**************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvlgqr 116
                                   +i+fl +Dd +++d+++ + e ++   +dvv+++ 
  gi|70607653|ref|YP_256523.1|  80 LIFFLEDDDLFHKDKVKIVKEIFQS-KKDVVAVHN 113
                                   *****************99999999.888887764 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   9.7e-08   0.00058       4     121 ..       9     112 ..       7     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.7e-08
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgksralneal 83 
                                   ++v++ ++++ ++l   les+ +q+  + ev+v++ d+++   ++            +v  v+ +++   ++   ++ e++
  gi|70607653|ref|YP_256523.1|   9 TSVIINVYKRYQYLPFALESVFTQSVKPNEVIVIAdDPDKVPYRD------------KVY-VIESKDEKYGT---KIIEGF 73 
                                   689999999999999999999999998888888884555555444............555.45667655444...577*** PP

               Glyco_tranf_2_3  84 ravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavg 121
                                   ra ++dl+ +++dD++ ++d +k +  +f   ++v av 
  gi|70607653|ref|YP_256523.1|  74 RASTGDLIFFLEDDDLFHKDKVKIVKEIFqSKKDVVAVH 112
                                   ****************************94444565554 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   2.8e-06     0.017      56     123 ..      54     114 ..      10     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-06
               Glyco_tranf_2_2  56 lvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpv 123
                                   +vy+ + +d+ y+       G+  + +dl++Fl+ D+++  Dk++ + ++ ++kk     d   v  +
  gi|70607653|ref|YP_256523.1|  54 KVYVIESKDEKYGTKI--IEGFRASTGDLIFFLEDDDLFHKDKVKIVKEIFQSKK-----DVVAVHNL 114
                                   5555555566665544..369999*******************988777777664.....33334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 927.47
//
Query:       gi|70607654|ref|YP_256524.1|  [L=174]
Description: hypothetical protein Saci_1928 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00044   20.2   1.0       0.69    9.8   0.1    2.1  2  Thioredoxin_6    Thioredoxin-like domain
    0.00088   18.9   0.5        1.3    8.8   0.1    2.4  2  E3_UbLigase_EDD  E3 ubiquitin ligase EDD
     0.0024   17.5   0.6        1.6    8.2   0.0    2.2  2  RexA             Intracellular sensor of Lambda phage, Abi co
  ------ inclusion threshold ------
       0.13   12.8   0.7       0.94   10.0   0.1    2.1  2  EF-G-binding_N   Elongation factor G-binding protein, N-termi


Domain annotation for each model (and alignments):
>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00018      0.79      77     134 ..      28      83 ..      19     100 .. 0.87
   2 !    9.8   0.1   0.00015      0.69      71     133 ..     110     168 ..      88     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                                   -SEEE-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEE CS
                 Thioredoxin_6  77 plvreltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfalad 134
                                   +lv  +  en +el  +   ++l++++ kdde  +++ ++  +v +++k +inf +a 
  gi|70607654|ref|YP_256524.1|  28 NLVMIIGLENEDELVYDS--NVLVVVRSKDDETVREIARTALEVNAKYKCSINFHVAS 83 
                                   688889999999999999..68999999*************************98775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00015
                                   HHHH---SEEE-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEE CS
                 Thioredoxin_6  71 ieknslplvreltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfala 133
                                   ++++ + l  +++ e+++ +      ++l++++ kdde  +++ ++  +v +++k +inf ++
  gi|70607654|ref|YP_256524.1| 110 FKEKLMKLGNVVSVEYFNGY----DSNVLVVVRSKDDETVREIARTALEVNAKYKCSINFHVV 168
                                   56677777777777777775....34568899999*************************876 PP

>> E3_UbLigase_EDD  E3 ubiquitin ligase EDD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00029       1.3      19      40 ..      51      71 ..      38      74 .. 0.71
   2 !    8.1   0.1   0.00048       2.1      27      40 ..     144     157 ..     131     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00029
               E3_UbLigase_EDD 19 LqgKSRqvIiRELQrtnLdVNl 40
                                   + K  +  +RE+ rt L+VN+
  gi|70607654|ref|YP_256524.1| 51 VRSKD-DETVREIARTALEVNA 71
                                  44444.3469***********6 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00048
               E3_UbLigase_EDD  27 IiRELQrtnLdVNl 40 
                                    +RE+ rt L+VN+
  gi|70607654|ref|YP_256524.1| 144 TVREIARTALEVNA 157
                                   58***********6 PP

>> RexA  Intracellular sensor of Lambda phage, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1   0.00055       2.5      53      82 ..      41      70 ..      13      77 .. 0.80
   2 !    8.2   0.0   0.00035       1.6      51      82 ..     125     156 ..     104     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00055
                          RexA 53 vkvdgntylfiktrdnelvkkinratlkve 82
                                  + +d n+ ++++++d+e v+ i r+ l+v+
  gi|70607654|ref|YP_256524.1| 41 LVYDSNVLVVVRSKDDETVREIARTALEVN 70
                                  458999*******************98875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00035
                          RexA  51 ylvkvdgntylfiktrdnelvkkinratlkve 82 
                                   y   +d n+ ++++++d+e v+ i r+ l+v+
  gi|70607654|ref|YP_256524.1| 125 YFNGYDSNVLVVVRSKDDETVREIARTALEVN 156
                                   7778999********************98875 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00021      0.94      24      72 ..      42     107 ..      35     117 .. 0.84
   2 ?    1.7   0.1     0.087   3.9e+02       7      45 ..     107     149 ..     104     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                EF-G-binding_N  24 vnDkkvveavkalaaekIlel................fpelseeqkelLeqiddik.tkekaeklL 72 
                                   v D++v+ +v++   e ++e+                f  +se++kel++++ + + + e+ +  +
  gi|70607654|ref|YP_256524.1|  42 VYDSNVLVVVRSKDDETVREIartalevnakykcsinFHVASENDKELIKAFLTYRsEGEDCDASF 107
                                   7799999999999999999999999999999999999*****************997777766655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.087
                EF-G-binding_N   7 YnfIkkqveqllna....yrsvnDkkvveavkalaaekIlelf 45 
                                   +n+ k+++++l n+    y +  D++v+ +v++   e ++e+ 
  gi|70607654|ref|YP_256524.1| 107 FNYFKEKLMKLGNVvsveYFNGYDSNVLVVVRSKDDETVREIA 149
                                   6777777777766622224466789999999888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1321.83
//
Query:       gi|70607655|ref|YP_256525.1|  [L=113]
Description: hypothetical protein Saci_1929 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-09   36.9   0.2    3.9e-09   36.7   0.2    1.0  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   2.2e-13   3.9e-09       6     117 ..       2     107 ..       1     108 [. 0.94

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.2e-13
                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHHCCCHH CS
                          HEPN   6 rrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLekayie 86 
                                   ++A+  l++Ae +l+ + ++ ++++++ a+ k + +l +k+g ++p+  d  +L++ lk ++k  ++l+e++ +L + + +
  gi|70607655|ref|YP_256525.1|   2 NKADILLNEAEIDLKFKCFNKSVSASYFAVRKEIEYLAIKLGSTIPRRDD--KLINILKHLGK--DKLAEDVLYLYERRKD 78 
                                   799999**************************************999987..89999998885..9*************** PP

                                   CCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  87 srYpdakeeyteedaeealkdaeevlelvee 117
                                   ++Y+d+    +e  a ++l++a+ v++ v++
  gi|70607655|ref|YP_256525.1|  79 ADYGDTGM--DEGIAINCLNIAKIVITEVRR 107
                                   ******99..****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 828.84
//
Query:       gi|70607656|ref|YP_256526.1|  [L=416]
Description: hypothetical protein Saci_1930 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-29  103.2   1.2    1.6e-29  102.6   0.2    1.9  2  AAA_14    AAA domain
    1.1e-08   35.2   0.3    3.6e-08   33.6   0.3    1.9  1  DUF4143   Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.033   13.3   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
      0.034   14.2   0.0      0.071   13.1   0.0    1.4  1  Mrr_cat   Restriction endonuclease
      0.051   13.5   4.7       0.44   10.4   0.1    3.4  4  ATPase_2  ATPase domain predominantly from Archaea
      0.087   13.1   0.3        0.2   11.9   0.1    1.8  2  AAA_28    AAA domain
      0.089   12.9   0.0       0.78    9.9   0.0    2.4  2  KHA       KHA, dimerisation domain of potassium ion channel
       0.16   12.2   0.1        2.1    8.5   0.0    2.3  2  RTP1_C1   Required for nuclear transport of RNA pol II C-term


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.2   7.3e-33   1.6e-29       3     131 .]      35     164 ..      33     164 .. 0.91
   2 ?   -2.0   0.1       1.5   3.3e+03      14      50 ..     265     300 ..     263     308 .. 0.41

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 7.3e-33
                        AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkla..dpekllelileklkeekktylflDEiqevp 77 
                                    i+++tG Rr GKT+ll+q i+el+    +++++ily++++d r+k ++  d +k+l+++ e+ ++++ +y+flDEiq+++
  gi|70607656|ref|YP_256526.1|  35 YIITVTGGRRNGKTFLLYQTIQELMrsglASQDEILYVDFEDYRLKGSKvdDLDKILTIFVEL-TGKQPKYVFLDEIQNIE 114
                                   589**************************9***************877633566999999997.55699************ PP

                        AAA_14  78 ewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                   +  ++ ++   ++ n++v+++GS+s+l   +ia++l+gr  ++e+yplsf+Efl
  gi|70607656|ref|YP_256526.1| 115 NYGSWFRK---RS-NFRVYLSGSSSSLTPFRIAEELRGRSVNYEIYPLSFKEFL 164
                                   *9998764...44.899************************************7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                        AAA_14  14 GKTtllkqlikellvkkesilyinldderdkkladpe 50 
                                   GK t+++ + + +  +  s+l  ++++ + k++a+p+
  gi|70607656|ref|YP_256526.1| 265 GKETVIELFERAKE-TYFSFLVEEFEKSERKRKANPK 300
                                   55555433322222.1134444444444444444443 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.3   1.6e-11   3.6e-08      14     120 ..     271     365 ..     201     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.6e-11
                                   xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  14 eelrk....glverlppwsespnskkrlrkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekega 90 
                                   e +++    +  + ++ +   + ++kr+ +  Kly++DtG  +a lg + +          + +En+V+ eLl+   + + 
  gi|70607656|ref|YP_256526.1| 271 ELFERaketYFSFLVEEF--EKSERKRKANPKKLYIIDTGYPTA-LGYEFS--------ISHAMENAVFIELLR---RGYR 337
                                   334447777677777778..88899999************9777.444433........3589***********...5578 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  91 klyyyrdkngaEvDfvielkggkivpiEvK 120
                                   +++y+++  ++E+Dfvi+++     +i+v 
  gi|70607656|ref|YP_256526.1| 338 EVFYWKK--KREIDFVIARNFSPTTLIQVT 365
                                   9*****9..69*******998888888886 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.033     116     156 ..      21      61 ..       9      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                         T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                   + i++ ++ ++++ ++i v+Gg   GKt lly  ++e+  s
  gi|70607656|ref|YP_256526.1|  21 NIIKRDISLPLQRDYIITVTGGRRNGKTFLLYQTIQELMRS 61 
                                   5677889999**************************99776 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.071       8      87 ..     322     397 ..     319     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                   CHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEEEEESS CS
                       Mrr_cat   8 eFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadkgifvtts 87 
                                    +e  v   l + Gy+e  +   ++   iD+++ ++ + s ++l+q+    ++v+ +eV++++ a  + ++d++i+ t++
  gi|70607656|ref|YP_256526.1| 322 AMENAVFIELLRRGYRE--VFYWKKKREIDFVIARN-F-SPTTLIQVTYAGDRVEDREVEAIVEAKSELKVDNAIILTWD 397
                                   56777777788899995..555568999*****874.3.48******9999**************************985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0002      0.44      18      65 ..      32      82 ..      26     116 .. 0.75
   2 ?    2.5   0.0      0.05   1.1e+02     154     208 ..     122     174 ..      84     204 .. 0.73
   3 ?    0.3   0.2      0.25   5.6e+02      80     118 ..     258     296 ..     204     308 .. 0.68
   4 ?   -0.5   0.4      0.42   9.5e+02      56      83 ..     276     306 ..     261     392 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                      ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesiskl 65
                                  +++ i+ ++G ++ GKt Ll + i++l  ++    + i y ++++++++  
  gi|70607656|ref|YP_256526.1| 32 QRDYIITVTGGRRNGKTFLLYQTIQELMRSGLasqDEILYVDFEDYRLKGS 82
                                  567899********************9665544457788888888876544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                      ATPase_2 154 kekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflkegfkel 208
                                   k+ + +v + +sS +l+  r+ +  el+gr+  +++ +l +++ l f  +  ++l
  gi|70607656|ref|YP_256526.1| 122 KRSNFRVYLSGSSSSLTPFRIAE--ELRGRSVNYEIYPLSFKEFLRFKGFEYNKL 174
                                   56667777889999998885555..599999999999998888887776655555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.25
                      ATPase_2  80 kalgiavpkaeleeilkeksklvfkaielllekikkkgk 118
                                   k lgi+++k ++ e++++ ++  f+ + + +ek ++k+k
  gi|70607656|ref|YP_256526.1| 258 KGLGIKIGKETVIELFERAKETYFSFLVEEFEKSERKRK 296
                                   444888888888888885555555555555555555544 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.42
                      ATPase_2  56 alreesiskldefieeeeekkklekal.....g 83 
                                   a +++++  ++ef  e++e+k+ ++++      
  gi|70607656|ref|YP_256526.1| 276 AKETYFSFLVEEF--EKSERKRKANPKklyiiD 306
                                   3333344444444..333333333333333340 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.8   6.3e+03       2      16 ..      37      51 ..      37      64 .. 0.83
   2 ?   11.9   0.1   8.8e-05       0.2      62     121 ..     289     348 ..     268     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.8
                        AAA_28  2 ivitGgestGKTtll 16
                                  i +tGg   GKT ll
  gi|70607656|ref|YP_256526.1| 37 ITVTGGRRNGKTFLL 51
                                  678999999999887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.8e-05
                        AAA_28  62 eqleeeaaaaankvlfcDrglldtlaYarayggeaeaeleaaarekrydlvfllppapei 121
                                   e+ e+ ++a+++k++++D+g+++ l Y      + e+++  ++ ++ y+ vf+ +   ei
  gi|70607656|ref|YP_256526.1| 289 EKSERKRKANPKKLYIIDTGYPTALGYEFSISHAMENAVFIELLRRGYREVFYWKKKREI 348
                                   23456677799****************99998887887777777879*****99887776 PP

>> KHA  KHA, dimerisation domain of potassium ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00035      0.78      14      34 ..      42      62 ..      33      90 .. 0.86
   2 ?   -0.3   0.0      0.53   1.2e+03      34      59 ..     382     408 ..     377     409 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00035
                           KHA 14 krseGklvllpdsleeLlkia 34
                                   r++Gk +ll ++++eL++++
  gi|70607656|ref|YP_256526.1| 42 GRRNGKTFLLYQTIQELMRSG 62
                                  489***************976 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.53
                           KHA  34 asekfgiaatrvlted.gAeiddidvi 59 
                                   a++++++    +lt d  +ei  i++i
  gi|70607656|ref|YP_256526.1| 382 AKSELKVDNAIILTWDyEGEINGIKAI 408
                                   78889999999***999*****99988 PP

>> RTP1_C1  Required for nuclear transport of RNA pol II C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00094       2.1      34      72 ..      83     121 ..      49     127 .. 0.80
   2 ?    0.7   0.0      0.26   5.8e+02      64      91 ..     269     296 ..     267     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00094
                       RTP1_C1  34 avldiekilkllleaLkdedsYvYLnaikgLvaLadvfp 72 
                                   +v d++kil++++e   ++ +Yv+L  i+ +++ +++f 
  gi|70607656|ref|YP_256526.1|  83 KVDDLDKILTIFVELTGKQPKYVFLDEIQNIENYGSWFR 121
                                   8999*************************9998777765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                       RTP1_C1  64 LvaLadvfpeevlklLleeyeeenekes 91 
                                   + +L ++ +e+ ++ L+ee+e++++k++
  gi|70607656|ref|YP_256526.1| 269 VIELFERAKETYFSFLVEEFEKSERKRK 296
                                   67899999************77666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2945.34
//
Query:       gi|70607657|ref|YP_256527.1|  [L=138]
Description: hypothetical protein Saci_1931 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1081.13
//
Query:       gi|70607658|ref|YP_256528.1|  [L=61]
Description: hypothetical protein Saci_1932 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-07   30.7   0.9    4.4e-07   30.6   0.9    1.0  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.9   2.4e-11   4.4e-07       2      57 ..       6      61 .]       5      61 .] 0.93

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.4e-11
                  VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLle.kkkkgkkkellelfgilseeeadei 57
                                  tI +sd v+  L+++K+ ++ ++++++ L++ +k+k++++ + +l++il+e++++ei
  gi|70607658|ref|YP_256528.1|  6 TIPVSDTVKVILEREKG-NMNWDEFLLMLVNeYKRKKREEGISDLRKILTEDDIREI 61
                                  89***************.************96677788899************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 438.21
//
Query:       gi|70607659|ref|YP_256529.1|  [L=113]
Description: hypothetical protein Saci_1933 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.081   13.7   0.3       0.11   13.2   0.3    1.3  1  DUF4282   Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   6.4e-06      0.11       3      35 ..      43      75 ..      41      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-06
                       DUF4282  3 sFnrfitpkllkvlYilgivlialvllslivga 35
                                   F++f ++kl k +Y+ +iv+ +lv ++++  +
  gi|70607659|ref|YP_256529.1| 43 YFKKFRSSKLEKPIYYALIVFGLLVSIFGLKVT 75
                                  7**************************887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 836.45
//
Query:       gi|70607660|ref|YP_256530.1|  [L=331]
Description: pyridine nucleotide-disulfide oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-39  135.4   0.7    2.7e-39  135.1   0.7    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      3e-13   50.1   4.2    2.7e-12   47.1   1.3    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.5e-05   24.4   0.2      2e-05   24.0   0.1    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00026   20.7   0.9       0.15   11.6   0.2    3.3  4  DAO            FAD dependent oxidoreductase
     0.0011   18.1   0.0     0.0024   17.1   0.0    1.5  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.018   14.8   0.2        6.7    6.5   0.1    2.5  2  HycI           Hydrogenase maturation protease
       0.11   12.5   0.2         15    5.6   0.0    3.1  3  NAD_binding_9  FAD-NAD(P)-binding
       0.22   10.2   2.6        2.8    6.6   0.4    3.1  3  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   0.7   1.2e-42   2.7e-39       3     293 ..       2     267 ..       1     268 [. 0.90

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 1.2e-42
                                   EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkk 83 
                                   +v++GgG+AG++a  +    + + ++v +++ +++ ++++   ++g +e +++  +         +++lg e  kid++ k
  gi|70607660|ref|YP_256530.1|   2 IVILGGGFAGVSAYNQ----NSEAVVV-DKKDFFLLTPWVIDYVCGLKELEDVTVKY-------KRVVLG-ELRKIDYKGK 69 
                                   89**********9654....5567889.99**********99999999999866654.......356666.777******* PP

                                   EEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  84 kvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiGvElAaalak 163
                                   +v l     ++ ++i ydkl++  G +++++ ++G+ e+++k  +tld+a al++ l + k++v+vGgG++GvElA+    
  gi|70607660|ref|YP_256530.1|  70 RVIL-----DKDREIRYDKLIVSLGHHQNLPRLKGAREYAHKI-ETLDDAVALRKRLEEvKNVVIVGGGATGVELAGN--I 142
                                   ****.....56679**********************9999888.*********************************8..6 PP

                                   HT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 164 lgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstell 244
                                    gk++tl+++ +rll+++    s+++e+ l++ Gv+++l+ s++ei+++g    vv+++g  ++ +l ++a G++  + + 
  gi|70607660|ref|YP_256530.1| 143 RGKNITLIHRKERLLPTMTTGSSKRAEKLLTELGVNLMLKVSAEEITKEG----VVTSNGF-VKSELTIFAGGLKGPQII- 217
                                   799********************************************999....6888888.6************99855. PP

                                   SHCCT-EE.EETTEEE--TTSBES.STTEEE-GGGC..TECCSS--HHHHHHH CS
                                   xxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                   Pyr_redox_2 245 eeklglel.derggivvdeflrtn.vpgiyaiGDva..ggkggpelaqaAvqq 293
                                    ++  +e  +++ +++vd++lr+    +iy +GD+a  +++++p++a +Av +
  gi|70607660|ref|YP_256530.1| 218 -DT--IEHrNKDHRLLVDKYLRSVeFNDIYGAGDCAtfENEDIPMSANTAVIS 267
                                   .44..44437999********9755*************************865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.058   1.3e+02       2      13 ..       2      13 ..       1      31 [. 0.91
   2 !   47.1   1.3   1.2e-15   2.7e-12       1      71 [.     125     193 ..     125     200 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.058
                                  EEEECSSHHHHH CS
                     Pyr_redox  2 vvvvGgGyiglE 13
                                  +v++GgG+ g+ 
  gi|70607660|ref|YP_256530.1|  2 IVILGGGFAGVS 13
                                  89*******985 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1.2e-15
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                   +vv+vGgG +g+ElAg+++  gk++t+++r+++ll+ +    sk+ ++ l+++g++++l+ ++eei++++ 
  gi|70607660|ref|YP_256530.1| 125 NVVIVGGGATGVELAGNIR--GKNITLIHRKERLLPTMTTGSSKRAEKLLTELGVNLMLKVSAEEITKEGV 193
                                   59**************997..677*******************************************8775 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   9.1e-09     2e-05      84     305 .]      37     247 ..       7     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 9.1e-09
                   Pyr_redox_3  84 leYlrevaksfelpiklfeeVe.svkk.edegfevetske.tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhk 161
                                    +Y+  + + +++ +k++  V  ++ k + +g +v  +k+ +++ +k+i++ G   + n+++ +G+ +++    + +++  
  gi|70607660|ref|YP_256530.1|  37 IDYVCGLKELEDVTVKYKRVVLgELRKiDYKGKRVILDKDrEIRYDKLIVSLGH--HQNLPRLKGAREYAHKIETLDDAVA 115
                                   678888888888888888888525666556778888888669***********9..7899999**9987666666666655 PP

                   Pyr_redox_3 162 yag.....qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevke 237
                                   +++     ++vv++Gg+ ++v+ A ++  +g+++t+++r++ +  +       +     +r e+l++e  ++++ + +++e
  gi|70607660|ref|YP_256530.1| 116 LRKrleevKNVVIVGGGATGVELAGNI--RGKNITLIHRKERLLPT-------MTTGSSKRAEKLLTELGVNLMLKVSAEE 187
                                   4432222389**************998..688********976665.......4555567777777774589999999999 PP

                   Pyr_redox_3 238 ikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   i+++ +     t++g  + +++  ++a G k   ++++  +  +++d r ++++   +  +++++ aG
  gi|70607660|ref|YP_256530.1| 188 ITKEGV----VTSNG--FVKSELTIFAGGLKGP-QIID-TIEHRNKDHRLLVDKYLRSVEFNDIYGAG 247
                                   998743....45665..3344566777776654.5565.45556678888888888888888888776 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        26       2      29 ..       2      27 ..       1      31 [. 0.77
   2 ?    1.2   0.0       0.1   2.3e+02     161     225 ..      49     105 ..      40     121 .. 0.66
   3 !   11.6   0.2   6.5e-05      0.15       2      45 ..     126     173 ..     125     191 .. 0.79
   4 ?   -0.7   0.0      0.36   8.1e+02     156     207 ..     172     216 ..     168     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                                  EEEECTSHHHHHHHHHHHHTTEEEEESS CS
                           DAO  2 vviiGGGiiGlstAyeLarrgVtllekg 29
                                  +vi GGG +G+s+  + ++   ++++k+
  gi|70607660|ref|YP_256530.1|  2 IVILGGGFAGVSAYNQNSE--AVVVDKK 27
                                  8**********98766665..5666666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
                                   -EEEESECEEE.EEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEE CS
                           DAO 161 veilegtevtg.leeedgkvwgverttp.gendaadavVnaaGawsdllgllkeldlpispvrgqvl 225
                                   v++ +++ v g l++ d k+++v  +++ +++  +d+++++ G++ + l   ++l    +++r +  
  gi|70607660|ref|YP_256530.1|  49 VTVKYKRVVLGeLRKIDYKGKRVILDKDrEIR--YDKLIVSLGHHQN-L---PRL----KGAREYAH 105
                                   67777778888666666556666534444665..799******9933.2...333....55555554 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6.5e-05
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSS....TTSSGGGSSEEEEE CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdi....agsgaSgrnsgllh 45 
                                   vvi+GGG +G+  A     rg  +tl+ ++++      +g+S r+ +ll+
  gi|70607660|ref|YP_256530.1| 126 VVIVGGGATGVELAGNI--RGknITLIHRKERllptMTTGSSKRAEKLLT 173
                                   9****************..5558*****9966443322688888888876 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.36
                                   HHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH CS
                           DAO 156 aealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll 207
                                   + +lGv++ ++  ++++        gv  +t+ g +++ +  + a G+   ++
  gi|70607660|ref|YP_256530.1| 172 LTELGVNLMLKVSAEEIT-----KEGV--VTSnGFVKS-ELTIFAGGLKGPQI 216
                                   678899999987777773.....3566..444487655.77999999875533 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-06    0.0024     142     231 ..      74     159 ..      46     169 .. 0.82
   2 ?   -3.1   0.0       1.5   3.4e+03     222     257 ..     193     228 ..     174     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                   K_oxygenase 142 geeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklv 222
                                   ++ +e++  +l+++ G + ++P +  + e  +++   +++   +++l++ k++++vG+G ++ e++ ++    + ++++l+
  gi|70607660|ref|YP_256530.1|  74 DKDREIRYDKLIVSLGHHQNLPRLKGAREYAHKIETLDDAVALRKRLEEVKNVVIVGGGATGVELAGNI----RGKNITLI 150
                                   4567888899************9988887777777777777777789***************9987665....44568888 PP

                   K_oxygenase 223 trsealepl 231
                                    r+e+l p 
  gi|70607660|ref|YP_256530.1| 151 HRKERLLPT 159
                                   888887775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                   K_oxygenase 222 vtrsealeplddspfvneifsPeyvdyfyslpeekr 257
                                   v+ s+++ +++ + f+  +  P+ +d + ++++++r
  gi|70607660|ref|YP_256530.1| 193 VVTSNGFVKSELTIFAGGLKGPQIIDTIEHRNKDHR 228
                                   667788888888888888888888888888887777 PP

>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.003       6.7       6      37 ..     115     146 ..     113     151 .. 0.85
   2 ?    5.8   0.0     0.005        11      15      63 ..     202     258 ..     193     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.003
                                   HHHHHEC--TTEEEEEECT-SGGGHHHHCC-S CS
                          HycI   6 kLkrryefkenvtviDgGtqglelvgtleead 37 
                                   +L +r+e+ +nv ++ gG+ g el g ++  +
  gi|70607660|ref|YP_256530.1| 115 ALRKRLEEVKNVVIVGGGATGVELAGNIRGKN 146
                                   68999*******************99998754 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.005
                                   TTEEEEEECT-SGGGHHHHCC..-SEEEEEE....E--SSS-..TT-EEEEECCHHH CS
                          HycI  15 envtviDgGtqglelvgtlee..adkliivD....avdfgle..pGevkiikddevp 63 
                                    ++t++ gG +g++ ++t+e+   d+ + vD     v+f++    G   +++++++p
  gi|70607660|ref|YP_256530.1| 202 SELTIFAGGLKGPQIIDTIEHrnKDHRLLVDkylrSVEFNDIygAGDCATFENEDIP 258
                                   4699*****************988888888843334666544123556677777776 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.3   6.7e+02       1      14 [.       3      16 ..       3      28 .. 0.86
   2 ?    5.6   0.0    0.0066        15     117     155 ..      49      90 ..      34      91 .. 0.71
   3 ?    2.7   0.0      0.05   1.1e+02       1      16 [.     127     142 ..     127     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.3
                 NAD_binding_9  1 aivGaGprGlavle 14
                                  +i G+G++G+++ +
  gi|70607660|ref|YP_256530.1|  3 VILGGGFAGVSAYN 16
                                  699*******9875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0066
                 NAD_binding_9 117 vevhraevv..dleera.dgqavlladgaslaadaVvLAlGh 155
                                   v+v  ++vv  +l++ + +g +v+l++++++++d++++ lGh
  gi|70607660|ref|YP_256530.1|  49 VTVKYKRVVlgELRKIDyKGKRVILDKDREIRYDKLIVSLGH 90 
                                   44444444433677755355699******************9 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.05
                 NAD_binding_9   1 aivGaGprGlavlerL 16 
                                   +ivG+G++G+ ++ ++
  gi|70607660|ref|YP_256530.1| 127 VIVGGGATGVELAGNI 142
                                   79*******9988665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.14   3.1e+02       3      29 ..       2      24 ..       1      30 [. 0.66
   2 ?    0.8   0.0     0.067   1.5e+02     123     165 ..      48      91 ..      36     110 .. 0.67
   3 ?    6.6   0.4    0.0012       2.8       2      35 ..     125     156 ..     124     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.14
                                  EEEE--SHHHHHHHHHHHHTT--EEEE CS
                   HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlll 29
                                  ++++GgG AG+ a     +++++ +++
  gi|70607660|ref|YP_256530.1|  2 IVILGGGFAGVSA----YNQNSEAVVV 24
                                  799****999754....4444445555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.067
                                   T-EEE-S--EE.EEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 123 gvklrletevk.svekeedgkfrvktkseeeleadklvlAtGGl 165
                                   +v++++++ v  +++k + +  rv +++++e++ dkl++++G  
  gi|70607660|ref|YP_256530.1|  48 DVTVKYKRVVLgELRKIDYKGKRVILDKDREIRYDKLIVSLGHH 91 
                                   4445554444314555566668899999************9963 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0012
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                   +v+++GgGa G+  A ++  rgk+++l+ ++++l
  gi|70607660|ref|YP_256530.1| 125 NVVIVGGGATGVELAGNI--RGKNITLIHRKERL 156
                                   79**********999999..89999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2192.07
//
Query:       gi|70607661|ref|YP_256531.1|  [L=549]
Description: pyruvate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-48  162.6   0.1    1.4e-45  154.9   0.0    2.2  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    1.7e-40  138.3   1.5    4.7e-40  136.9   0.1    2.3  2  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    3.7e-29  101.2   0.0    5.9e-29  100.5   0.0    1.3  1  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
     0.0021   17.8   0.0     0.0043   16.8   0.0    1.4  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.19   11.6   0.0    1.6  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.9   0.0     4e-49   1.4e-45       2     167 ..       3     165 ..       2     169 .. 0.98
   2 !    5.4   0.0    0.0035        13      55      99 ..     405     450 ..     399     484 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 4e-49
                                   EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHH CS
                  TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalta 82 
                                   +vae++ ++L++ gv++++g+pG++i pl+da++++ ++ ++++rhE+gaafaA+  a++tg+p++++ tsgpG +++l++
  gi|70607661|ref|YP_256531.1|   3 SVAEVITKVLEESGVQRIYGIPGDSIDPLVDAVRRS-KVSYIQVRHEEGAAFAASVEAKITGRPVACMGTSGPGSIHLLNG 82 
                                   689*********************************.5******************************************* PP

                                   HHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHH CS
                  TPP_enzyme_N  83 laeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdv 163
                                   l++Ak d+ P++++sg++++++ g++++q e++ ++lf +v+ +++ + +p++++ ++rrAir+a  +++g+++++lp d+
  gi|70607661|ref|YP_256531.1|  83 LYDAKMDHAPVIAFSGQVESDMLGHDYFQ-EVNLVKLFDDVAVFNQVLINPDNAEYTVRRAIREA-VTKRGVAHINLPVDI 161
                                   *****************************.***********************************.999************ PP

                                   CC-E CS
                  TPP_enzyme_N 164 llee 167
                                   l++ 
  gi|70607661|ref|YP_256531.1| 162 LRKS 165
                                   9875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0035
                                   HHHHHHHH.TS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE CS
                  TPP_enzyme_N  55 Adgyarat.gkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgd 99 
                                   A+g + at ++++v++     G+t +++ l++Ak+ ++P+ v+  +
  gi|70607661|ref|YP_256531.1| 405 AVGASLATnRERQVIAFVGDGGFTMTMMELITAKKYGLPIKVIIYN 450
                                   889999998889999999999******************9887655 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.21   7.7e+02      54      54 ..      98      98 ..      41     157 .. 0.57
   2 !  136.9   0.1   1.3e-43   4.7e-40       1     152 [.     369     515 ..     369     516 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                                  E CS
                  TPP_enzyme_C 54 G 54
                                  G
  gi|70607661|ref|YP_256531.1| 98 G 98
                                  2 PP

  == domain 2  score: 136.9 bits;  conditional E-value: 1.3e-43
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH.STTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla.kpdrevvaivGDGgflmilqelatavrrnlpitvvvl 80 
                                   d+G++t+w+ar+++++ +++++ s++lg+mG g+p+A+Ga+la +++r+v+a+vGDGgf m+++el+ta +++lpi+v+++
  gi|70607661|ref|YP_256531.1| 369 DTGNVTMWTARHFRASGKQTFVFSSWLGSMGIGVPGAVGASLAtNRERQVIAFVGDGGFTMTMMELITAKKYGLPIKVIIY 449
                                   89****************************************834589********************************* PP

                                   E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                   nN+ +gm++ +qe +g   + g++   l ++df klae++G kg+++e++   e e +++e l+ +g a+++
  gi|70607661|ref|YP_256531.1| 450 NNSKLGMIKFEQEVMGY-PEWGVD---LFNPDFSKLAESMGFKGFKLEEP--GEAESVIEEFLNAEGGAVLD 515
                                   **************996.777877...7888***************9999..***********999999998 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.0   1.7e-32   5.9e-29       3     134 ..     187     310 ..     185     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.7e-32
                                   HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEE CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvla 83 
                                   k+ el++++++pv+++Ggg++  g  e++ ++ae++g Pv+  l+gkg++p+ +p+ +g +gl+g+k+   a+++aDl+++
  gi|70607661|ref|YP_256531.1| 187 KVKELIERSEKPVLMIGGGAR--GLGEQISKFAERIGSPVIYALNGKGILPDLDPKVMGGIGLLGTKPSISAMDKADLLIL 265
                                   7889*****************..********************************************************** PP

                                   ES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHH CS
                  TPP_enzyme_M  84 lGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketl 134
                                   lG+ f  +       +f +++ k+i++di+p++igk+  vd+++   + e+l
  gi|70607661|ref|YP_256531.1| 266 LGTSFPYV-------NFLNRDaKVIQVDINPSNIGKRIDVDISLPIPAEEFL 310
                                   **999664.......45555559******************99977777776 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0043      30      92 ..      32      96 ..      25     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                                  CCCCTTEE.EEEE-S.SHHHHHHHHHHHHCTT-E.EEEEEECCHHHHCCCCHHHHHHTT--EEEE CS
                         POR_N 30 lakgevgdvevvqme.sEigaisaviGAaaaGar.aaTaTSgqGllLmienlglaageelPvviv 92
                                  ++ ++  +v ++q+  +E +a++a + A ++G   a   TSg+G +     l+ a ++++Pv+ +
  gi|70607661|ref|YP_256531.1| 32 VDAVRRSKVSYIQVRhEEGAAFAASVEAKITGRPvACMGTSGPGSIHLLNGLYDAKMDHAPVIAF 96
                                  5555556789999972567788999*******8615678**********************9875 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.2e-05      0.19     114     158 ..     180     224 ..     147     229 .. 0.88
   2 ?   -4.0   0.0       3.2   1.2e+04     129     141 ..     258     270 ..     255     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.2e-05
                                   SS-B-HHHHHHHHHH--S-EEEEE--TT---HHHHTT-SEEB--T CS
               Methyltrn_RNA_4 114 entvsyeelrelleeeekpvlllfGtgwGlaeevlekadyiLepi 158
                                   e +v++++++el+e++ekpvl++ G + Gl e++ + a+ i +p+
  gi|70607661|ref|YP_256531.1| 180 EYSVDFSKVKELIERSEKPVLMIGGGARGLGEQISKFAERIGSPV 224
                                   668999***************************999988887776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.2
                                   --S-EEEEE--TT CS
               Methyltrn_RNA_4 129 eekpvlllfGtgw 141
                                   ++ ++l+l+Gt++
  gi|70607661|ref|YP_256531.1| 258 DKADLLILLGTSF 270
                                   5678999***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 3494.52
//
Query:       gi|70607662|ref|YP_256532.1|  [L=98]
Description: hypothetical protein Saci_1936 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0064   17.2   0.4      0.022   15.5   0.3    2.0  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   1.2e-06     0.022      23      59 ..      46      82 ..      17      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-06
                  VAPB_antitox 23 FsdvIerLlekkkkgkkkellelfgilseeeadeiek 59
                                   +d+I+ Ll+++k+++ + l+++fg+ +  e+ e+ k
  gi|70607662|ref|YP_256532.1| 46 VDDAINYLLKESKVKRPELLDQVFGVAKGVELYEMLK 82
                                  68*************************9999966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 611.13
//
Query:       gi|70607663|ref|YP_256533.1|  [L=131]
Description: hypothetical protein Saci_1937 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-10   40.9   0.0    3.1e-10   40.6   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   1.7e-14   3.1e-10       2     115 ..       6     116 ..       5     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.7e-14
                                   EE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                           PIN   2 vlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                   vlD+ vl+++++g+ k   +   + +   + ++s+l+l E++y+  r  ++ eka+e+v  l+    ++++ ++ ++  ea
  gi|70607663|ref|YP_256533.1|   6 VLDSGVLLSFVEGKYKG--IFNKIKGGeIRPIVSSLSLVETYYITCR-ALGVEKAEEVVSHLISSGLFRVVGVNRKVISEA 83 
                                   89*********888866..3333333369******************.********************************* PP

                                   HHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTH CS
                           PIN  82 aeialkygllpnDaliaAtAkehgikliatfDed 115
                                   ++ + ky +++ D+  +AtAk  + +++ ++ e+
  gi|70607663|ref|YP_256533.1|  84 GKCKCKYPISLTDCTTIATAKVKNTRAL-SREEK 116
                                   *************************999.76654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 985.80
//
Query:       gi|70607664|ref|YP_256534.1|  [L=478]
Description: aldehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.6e-162  540.5   0.0     3e-162  540.3   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.064   12.3   0.0    2.1  1  LuxC      Acyl-CoA reductase (LuxC)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.3   0.0  3.3e-166    3e-162       1     462 []      11     474 ..      11     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 540.3 bits;  conditional E-value: 3.3e-166
                                   EET-SSSEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH- CS
                        Aldedh   1 wvesesetievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletG 80 
                                   w+++++e++  +nPa +++v+ak++  t++d+++ +++A ++f++w+++p ++R++iL ka +l+e++++ela l+tle G
  gi|70607664|ref|YP_256534.1|  11 WIRGSGEEYLDVNPAdKEHVLAKIKLFTKDDLKESLNKALSKFDEWSRTPSPKRGQILLKAGELMEQEAKELALLMTLEEG 91 
                                   888888899999***8899************************************************************** PP

                                   --HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEE CS
                        Aldedh  81 kplaearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlK 160
                                   k+l++++aev+++ + l++y +la k+ g++lps ++++++++ +ePlGvv++ItPWNfPl++++wklapala+GNtvvlK
  gi|70607664|ref|YP_256534.1|  92 KTLKDSMAEVTRSYNLLKFYGALAFKIGGKTLPSsDPDSRIYTLKEPLGVVALITPWNFPLSIPVWKLAPALATGNTVVLK 172
                                   **********************************88********************************************* PP

                                   E-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHH..CTTSEEEEEE--- CS
                        Aldedh 161 PaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaa..knlkrvtlElGGk 239
                                   Pa++tpl +++l+e++ +aglP+gv+n+v+g+g e+g+ +v+++++ +vsftGstevg++i++  +  ++++r++lElGGk
  gi|70607664|ref|YP_256534.1| 173 PATKTPLLVAKLVEILSRAGLPDGVVNLVVGKGGELGDIIVSDENISAVSFTGSTEVGKRIYRLVGdkNRMTRIQLELGGK 253
                                   ****************************************************************665677*********** PP

                                   EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHH CS
                        Aldedh 240 nplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekv 320
                                   n+l v  +a+ld a e +v+gafg +GQ C+a+srl+v++++y +f +kl+e+++k++vg++ d d+d+GP+++e q++k 
  gi|70607664|ref|YP_256534.1| 254 NALYVDRSANLDLASELAVRGAFGLTGQSCTATSRLIVHKDVYGHFKQKLIERVRKWRVGNGTD-DVDMGPVVDEGQFKKD 333
                                   **************************************************************88.**************** PP

                                   HHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESEEEE CS
                        Aldedh 321 ekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLaagv 401
                                    +yve +k eg kl++Gg   +  + kgyf+ePt++++vtp++r+++eEiFGPVl+v+++ ++++ai+++N+ eyG +ag+
  gi|70607664|ref|YP_256534.1| 334 LEYVEIGKREGFKLIYGG---NVIPGKGYFLEPTIFDGVTPESRLFKEEIFGPVLTVTEVGSLDDAISLVNSVEYGHTAGI 411
                                   ******************...7789******************************************************** PP

                                   E-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES..-BSHHHHHHHTEEEEEE CS
                        Aldedh 402 ftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglG..reggkegleeytevktv 462
                                   +++d++ ++r+++++eaG + +N++t+g + ++pfgG+k+Sg    +e+g+e+le+y++ ktv
  gi|70607664|ref|YP_256534.1| 412 VSTDIKAINRFVREVEAGVIKVNKPTVGLELQAPFGGFKNSGATtwKEMGEEALEFYLREKTV 474
                                   *************************99999889*********9999*************9997 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.1e-06     0.064      83     268 ..     132     311 ..     120     441 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-06
                          LuxC  83 syekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksgdtk 162
                                    y    p g+v  +++ N pl +pv+ ++ +l ++n  +lk+    p l+a+l+  l +      +++    v   ++  +
  gi|70607664|ref|YP_256534.1| 132 IYTLKEPLGVVALITPWNFPLsIPVWKLAPALATGNTVVLKPATKTPLLVAKLVEILSRAGLPDGVVN---LV--VGKGGE 207
                                   688889**************8579************************99999998888777533333...23..366778 PP

                          LuxC 163 leeeiv..qnaDvvvawGgeeaikaise....klkpgkqlikfGakvSfavvdkealeeealdkaaeraAkDiivfdQqAC 237
                                   l + iv  +n  +v+  G+ e  k i      k + +   ++ G k  + +vd++a    +ld a+e a      +  q+C
  gi|70607664|ref|YP_256534.1| 208 LGDIIVsdENISAVSFTGSTEVGKRIYRlvgdKNRMTRIQLELGGKNAL-YVDRSA----NLDLASELAVRGAFGLTGQSC 283
                                   8888887777888888888777665544110144455555677888776.678888....888888888888888888888 PP

                          LuxC 238 lspqvvfvekddkieidefaeaLaaaLekra 268
                                    +   + v kd    +  f+++L++  +k  
  gi|70607664|ref|YP_256534.1| 284 TATSRLIVHKD---VYGHFKQKLIERVRKWR 311
                                   88888888877...88888888888777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3503.34
//
Query:       gi|70607665|ref|YP_256535.1|  [L=292]
Description: hypothetical protein Saci_1939 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-26   91.4   0.0    3.5e-25   89.0   0.0    1.9  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.0   1.9e-29   3.5e-25      27     217 ..     111     286 ..      84     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.9e-29
                                   EEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTEEEEEEEEEEE-SBGGG---.HH CS
                 FAA_hydrolase  27 hiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedaiaGytllnDvsaRdlqaeekapl 107
                                    +p+  +ff ++ +  vg+g+ i++++ se    E ELavvi  + +           i+Gyt+l DvsaRdl a +  pl
  gi|70607665|ref|YP_256535.1| 111 VRPE--IFFKATGNRCVGHGEAIVVRSDSEWTLPEPELAVVIDSRGK-----------ILGYTILDDVSARDLEADN--PL 176
                                   3333..6888899***************99999********976655...........56************97666..58 PP

                                   HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEE..TTEEE..EEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES CS
                 FAA_hydrolase 108 gwflgksfdtftpiGpwivtpdeledpedlelrlrv..ngeev..qdsntkdmifspaeliahlsagltLepGdliltGTp 184
                                      ++k + + + +Gp+ivtpde+++p +l++rl +  +g ++  ++ nt++m  +++e+i++l +  +++ G++++tGT 
  gi|70607665|ref|YP_256535.1| 177 YLPQSKIYYGCCAFGPFIVTPDEVGNPYSLDIRLKImrEGRVLfeGSVNTNKMRRKIEEQIQYLLRDNPVPDGTILTTGTA 257
                                   8899**********************999999998877666651245577******************************9 PP

                                   .........S--EE--TT-EEEEEETTTEEEEEEE CS
                 FAA_hydrolase 185 ..sgvgaeeeslkflkdgDeveveieglGelrnrV 217
                                     +g      ++k l++gD+ve++i++lG+l ++V
  gi|70607665|ref|YP_256535.1| 258 iiPG------KDKGLRHGDVVEISITKLGTLLTPV 286
                                   3334......5678****************98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1801.33
//
Query:       gi|70607666|ref|YP_256536.1|  [L=172]
Description: proline iminopeptidase, partial [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00096   18.9   0.0     0.0011   18.7   0.0    1.1  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
       0.06   12.6   0.0      0.088   12.1   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
       0.13   12.3   0.0        0.2   11.8   0.0    1.2  1  Abhydrolase_4  TAP-like protein
       0.18   11.9   0.0       0.33   11.1   0.0    1.5  1  DUF3726        Protein of unknown function (DUF3726)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-07    0.0011     206     256 ..      64     153 ..       9     154 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                                   C........................................THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEE CS
                 Abhydrolase_1 206 e........................................lknvlaptlvisgtsDplvppkaledlaqllpkkrlvvis 246
                                   +                                        lk + +ptl+  g +D ++p ++ e + + ++++rlv ++
  gi|70607666|ref|YP_256536.1|  64 MpeavkrtfeylekrktyeimngpneftiigtikdvdltdqLKRIAVPTLITVGKYDEVTP-NVAELIHKGIRGSRLVLFE 143
                                   13334444444444445555555555555555555555555888999*************8.788888889********** PP

                                   TCSSSHHHHS CS
                 Abhydrolase_1 247 dagHlafleg 256
                                   ++ H+a +e+
  gi|70607666|ref|YP_256536.1| 144 NSSHMAMWEE 153
                                   ********97 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05     0.088     182     237 ..     100     152 ..      55     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                   Hydrolase_4 182 rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                   +l+++ ++i +P+l+  G+ D+v+++  ++ +++ ++    +l l+++  H+ + E
  gi|70607666|ref|YP_256536.1| 100 DLTDQLKRIAVPTLITVGKYDEVTPN-VAELIHKGIR--GSRLVLFENSSHMAMWE 152
                                   5788999*****************95.4445555555..78999999999998866 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.5e-05       0.2      32      77 ..     107     151 ..      95     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                 Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgala 77 
                                   + a+p+L+  +++D +TP   a+ ++k ++g++lv  e++ H a+ 
  gi|70607666|ref|YP_256536.1| 107 RIAVPTLITVGKYDEVTPN-VAELIHKGIRGSRLVLFENSSHMAMW 151
                                   3479**************6.6999******************9875 PP

>> DUF3726  Protein of unknown function (DUF3726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.4e-05      0.33      16      62 ..     111     160 ..     100     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
                       DUF3726  16 GaglswGeaeeaAkmvrwLqmagLdGike..lnnalef.lfnekdvpldi 62 
                                    +  ++G ++e+  +v++L   g+ G +   ++n ++  + +e+++ l++
  gi|70607666|ref|YP_256536.1| 111 PTLITVGKYDEVTPNVAELIHKGIRGSRLvlFENSSHMaMWEEREKYLST 160
                                   566789********************885337776663367888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1230.39
//
Query:       gi|70607667|ref|YP_256537.1|  [L=417]
Description: ISC1913-like transposase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-18   65.3   0.0    5.7e-18   64.6   0.0    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.069   12.4   1.2        0.6    9.3   0.1    2.4  2  DUF3427         Domain of unknown function (DUF3427)
       0.13   12.0   0.1         25    4.7   0.0    2.6  2  DUF3945         Protein of unknown function (DUF3945)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   9.6e-22   5.7e-18       1      69 []     300     372 ..     300     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 9.6e-22
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke....alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f++lk+ + +kake+G++v +vnpayTS+ C+ + +k  +    + ++r+ +C++   +++rDv+A +N+lk+
  gi|70607667|ref|YP_256537.1| 300 FASLKNAIVEKAKEFGVPVLLVNPAYTSSVCPIHECKIIYppdgSSAPRVGVCERGRERWHRDVVALYNLLKK 372
                                   889**********************************99999*****************************96 PP

>> DUF3427  Domain of unknown function (DUF3427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0001       0.6      85     121 ..      14      52 ..       6      78 .. 0.79
   2 ?    1.0   0.2     0.035   2.1e+02      44      85 ..     229     269 ..     197     313 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0001
                       DUF3427  85 yrlseefkkll..eneeFkkfledlielglarykkkyse 121
                                   +++++e+ + l   +ee+k++led i++gl+++ +++ +
  gi|70607667|ref|YP_256537.1|  14 LKVNSEVYARLkeVEEEYKQILEDAIDYGLRNNINSFTK 52 
                                   6788888888854568****************9999887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.035
                       DUF3427  44 vdeetiesalrvLdlsffksaekkkygnipliekeekenkey 85 
                                   ++++++++al+ L+++f k + ++k +++ + e   +e+k +
  gi|70607667|ref|YP_256537.1| 229 TKDRVVRRALKSLKERFKKLDIRRKLAKLIVTEAL-REGKGI 269
                                   67777777777777777766777777666666522.222333 PP

>> DUF3945  Protein of unknown function (DUF3945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0045        27      33      52 ..     187     206 ..     178     211 .. 0.88
   2 ?    4.7   0.0    0.0041        25      41      54 ..     261     274 ..     226     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0045
                       DUF3945  33 vkLteeqkqdLreGkavlle 52 
                                   v+L+e+    L +Gk++l+e
  gi|70607667|ref|YP_256537.1| 187 VDLNEDNVSVLLDGKPLLVE 206
                                   89*****************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0041
                       DUF3945  41 qdLreGkavllegm 54 
                                   ++LreGk + le++
  gi|70607667|ref|YP_256537.1| 261 EALREGKGIILEDL 274
                                   69**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2730.94
//
Query:       gi|70607668|ref|YP_256538.1|  [L=128]
Description: proline iminopeptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-18   67.3   0.0    1.8e-18   67.1   0.0    1.0  1  Abhydrolase_1   alpha/beta hydrolase fold
    3.9e-14   52.5   0.0    4.5e-14   52.3   0.0    1.0  1  Hydrolase_4     Serine aminopeptidase, S33
    2.8e-12   47.7   0.0    3.2e-12   47.5   0.0    1.0  1  Abhydrolase_6   Alpha/beta hydrolase family
    0.00023   21.4   0.0    0.00028   21.1   0.0    1.1  1  Thioesterase    Thioesterase domain
    0.00094   18.9   0.0     0.0011   18.6   0.0    1.2  1  Esterase        Putative esterase
     0.0013   18.6   0.0     0.0014   18.5   0.0    1.2  1  Lipase_3        Lipase (class 3)
     0.0027   17.2   0.0     0.0043   16.5   0.0    1.3  1  Peptidase_S9    Prolyl oligopeptidase family
     0.0044   16.8   0.1     0.0079   15.9   0.1    1.5  1  PGAP1           PGAP1-like protein
     0.0047   16.0   0.1     0.0077   15.3   0.1    1.4  1  DUF1057         Alpha/beta hydrolase of unknown function (DUF
      0.005   16.7   0.0     0.0078   16.0   0.0    1.3  1  Abhydrolase_2   Phospholipase/Carboxylesterase
     0.0065   16.3   0.0     0.0065   16.3   0.0    1.2  1  Abhydrolase_3   alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.022   14.1   0.0    1.2  1  DUF915          Alpha/beta hydrolase of unknown function (DUF
      0.035   13.7   0.0      0.045   13.3   0.0    1.2  1  DLH             Dienelactone hydrolase family
      0.037   12.6   0.0       0.11   11.0   0.0    1.7  2  PAF-AH_p_II     Platelet-activating factor acetylhydrolase, i
      0.043   13.7   0.1       0.11   12.4   0.1    1.7  1  RXLR_WY         RXLR phytopathogen effector protein WY-domain
      0.049   13.2   0.0      0.064   12.8   0.0    1.2  1  LIDHydrolase    Lipid-droplet associated hydrolase
      0.067   12.8   0.0      0.081   12.5   0.0    1.3  1  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
       0.11   11.6   0.1       0.16   11.0   0.1    1.2  1  DUF1749         Protein of unknown function (DUF1749)
       0.11   12.0   0.0       0.12   11.8   0.0    1.2  1  DUF676          Putative serine esterase (DUF676)
       0.16   10.9   0.0       0.17   10.9   0.0    1.1  1  Chlorophyllase  Chlorophyllase
       0.18   11.7   0.0       0.24   11.3   0.0    1.2  1  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina
        0.2   11.2   0.0       0.28   10.7   0.0    1.2  1  DUF2974         Protein of unknown function (DUF2974)


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   2.3e-21   1.8e-18       3     101 ..      30     124 ..      28     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.3e-21
                                   EEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHH CS
                 Abhydrolase_1   3 lvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmG 83 
                                   l+ lhG+pg+s+ + e    + L+k+g  v+ +D+ G+g+S+ +++   + y+ +   + l+ ++ +  +dk++++GhS+G
  gi|70607668|ref|YP_256538.1|  30 LITLHGGPGGSHDYLE--PLSELSKHGVNVLFYDQFGCGRSEEPKEL--SKYTVDYGVEELEELRKQIFNDKVVILGHSYG 106
                                   7889************..999**************************..99****************************** PP

                                   HHHHHHHHHHHGGGEEEE CS
                 Abhydrolase_1  84 GmialayaaeyperVkal 101
                                   G++alaya +y+e+ k++
  gi|70607668|ref|YP_256538.1| 107 GLLALAYAIKYKENLKGC 124
                                   *************99876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   5.5e-17   4.5e-14       3     104 ..      26     124 ..      24     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 5.5e-17
                   Hydrolase_4   3 pkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                    ++ ++ +HG    s  y e   +L ++G++v+ +D+ G Grse +k      +d  v+ l+    +++++  + ++++lG
  gi|70607668|ref|YP_256538.1|  26 SEKKLITLHGGPGGSHDYLEPLSELSKHGVNVLFYDQFGCGRSEePKELSKYTVDYGVEELE----ELRKQIFNDKVVILG 102
                                   5778999************************************8555555555555566665....5566666999***** PP

                   Hydrolase_4  83 hSmGGliallyllrypdkvagl 104
                                   hS GGl+al+y+ +y+++++g 
  gi|70607668|ref|YP_256538.1| 103 HSYGGLLALAYAIKYKENLKGC 124
                                   *****************99986 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   3.9e-15   3.2e-12       2      86 ..      31     114 ..      30     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.9e-15
                                   EEE--GC.....GCHHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHC.HHH.HHHHCCTT....TTSEEEEEETCHHHH CS
                 Abhydrolase_6   2 lllHGagssassWlvapLaallaagvhvlapDlpGhGrsdpppldledl.adl.aalldelaa..gggpvvlvGHSlGGal 78 
                                   + lHG++++++++   pL +l+ +gv vl +D  G+G ++  p +l+ + +d+ ++ l+el++    ++vv++GHS+GG+l
  gi|70607668|ref|YP_256538.1|  31 ITLHGGPGGSHDY-LEPLSELSKHGVNVLFYDQFGCG-RSEEPKELSKYtVDYgVEELEELRKqiFNDKVVILGHSYGGLL 109
                                   679**********.36*********************.56666666663366676666666555668889*********** PP

                                   HHHHHHCC CS
                 Abhydrolase_6  79 alaaapla 86 
                                   ala   +a
  gi|70607668|ref|YP_256538.1| 110 ALA---YA 114
                                   ***...76 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.4e-07   0.00028       2      90 ..      29     120 ..      28     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-07
                                   EEEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTSTSHHHCTTCHHHHHHHHHHHH...HHH-SSSSEEEEEETHHHHH CS
                  Thioesterase   2 pLflfppagGsasvfrslasklsdpvvevlavqlpgrerdepplesieelaaeyaeal...rqiqpegPyalfGhSlGgll 79 
                                   +L+ ++++ G+++ +    s+ls+  v vl++ + g +r+e+p e  +  +++ +e+l   r++   + +++ GhS+Ggll
  gi|70607668|ref|YP_256538.1|  29 KLITLHGGPGGSHDYLEPLSELSKHGVNVLFYDQFGCGRSEEPKELSKYTVDYGVEELeelRKQIFNDKVVILGHSYGGLL 109
                                   68999*****9999988777777777888888888888999999999999999877661115555566999********** PP

                                   HHHHHHHHHHC CS
                  Thioesterase  80 AfevArqLesq 90 
                                   A + A +++++
  gi|70607668|ref|YP_256538.1| 110 ALAYAIKYKEN 120
                                   ***99988876 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0011     114     145 ..      95     126 ..      57     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                   CCCEEEEEETHHHHHHHHHHHCSTTTCCEEEE CS
                      Esterase 114 pdgravaGqSmGGlgALilalkhpdrFgsvss 145
                                    d+ +++G+S GGl AL +a+k+ +  + +s 
  gi|70607668|ref|YP_256538.1|  95 NDKVVILGHSYGGLLALAYAIKYKENLKGCSL 126
                                   33489******************998877765 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-06    0.0014      37      89 ..      57     120 ..      15     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHH...........S-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHHHHT CS
                      Lipase_3  37 sgfleaye...........eslreqvlkelkrllekypeysivvtGHSLGgalAlLaaldlven 89 
                                     f++ ++           + + +   +el++l ++  + ++v+ GHS Gg lAl  a+ ++en
  gi|70607668|ref|YP_256538.1|  57 VLFYDQFGcgrseepkelsKYTVDYGVEELEELRKQIFNDKVVILGHSYGGLLALAYAIKYKEN 120
                                   555555555566666544433344445678888888889****************999999887 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.3e-06    0.0043      52      83 ..      83     115 ..      74     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.3e-06
                                   HHHHHHTT.S--GGGEEEEEETHHHHHHHHHHH CS
                  Peptidase_S9  52 aealakeg.yvdserlaitGgSyGGyltgaaln 83 
                                   +e+l +   ++ +++++i G+SyGG+l++a + 
  gi|70607668|ref|YP_256538.1|  83 VEELEELRkQIFNDKVVILGHSYGGLLALAYAI 115
                                   5566666668889***************99775 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.7e-06    0.0079      90     109 ..      95     114 ..      72     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.7e-06
                         PGAP1  90 ptsviliGHSmGGivaraal 109
                                   + +v+++GHS+GG++a a +
  gi|70607668|ref|YP_256538.1|  95 NDKVVILGHSYGGLLALAYA 114
                                   679*************8755 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   9.4e-06    0.0077      31     125 ..      23     117 ..       6     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.4e-06
                       DUF1057  31 sgsplGtvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylg.qkytnaeRnsyskalleelelk...gkli 107
                                   ++++    ++lhG PG   D+    s+l ++ + ++  +  G    ++ ++  kyt     +y    leel  +   +k++
  gi|70607668|ref|YP_256538.1|  23 KANSEKKLITLHGGPGGSHDYLEPLSELSKHGVNVLFYDQFGCGRSEEPKElSKYT----VDYGVEELEELRKQifnDKVV 99 
                                   567777899******98888888889999999999988888877776655513344....35666666666654555**** PP

                       DUF1057 108 llghsRGcenaLqlavtl 125
                                   +lghs G+  aL  a+++
  gi|70607668|ref|YP_256538.1| 100 ILGHSYGGLLALAYAIKY 117
                                   ************999876 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.5e-06    0.0078      96     133 ..      87     124 ..      68     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-06
                                   HHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEE CS
                 Abhydrolase_2  96 aelkkgipssriiigGFSqGaalalylaltlpkklggi 133
                                   +el k i +++++i G S G+ lal+ a+++++ l+g 
  gi|70607668|ref|YP_256538.1|  87 EELRKQIFNDKVVILGHSYGGLLALAYAIKYKENLKGC 124
                                   355556**************************999985 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     8e-06    0.0065      52     104 ..      82     125 ..      31     128 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8e-06
                                   HHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEE CS
                 Abhydrolase_3  52 alaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqv 104
                                   +++ l+ l++q     + ++++v++G S GG la+a a++ +++    ++g+ 
  gi|70607668|ref|YP_256538.1|  82 GVEELEELRKQ-----IFNDKVVILGHSYGGLLALAYAIKYKEN----LKGCS 125
                                   44445555555.....899*********************9996....55555 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.022      93     127 ..      86     120 ..      70     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                        DUF915  93 lseLkkkYnikkfnavGhSmGglaltsYleeyadd 127
                                   l+eL+k+   +k+ ++GhS Ggl ++ Y+++y+++
  gi|70607668|ref|YP_256538.1|  86 LEELRKQIFNDKVVILGHSYGGLLALAYAIKYKEN 120
                                   678888888899********************976 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.6e-05     0.045      88     129 ..      85     128 .]      66     128 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                           DLH  88 ylksvpev.stkkvgvvGfCmGGalalllaaev.pevdaavafY 129
                                    l++ +++  ++kv++ G   GG lal++a +  + ++++  fY
  gi|70607668|ref|YP_256538.1|  85 ELEELRKQiFNDKVVILGHSYGGLLALAYAIKYkENLKGCSLFY 128
                                   455544431589******************998899***99998 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.44   3.6e+02      34     305 ..      15      29 ..       3      61 .. 0.60
   2 ?   11.0   0.0   0.00013      0.11     217     244 ..      84     112 ..      66     128 .] 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.44
                                   EEEEEEE.S.SSSS-EEESS-SHHHHHHHHHHHTS-HHHHHHH.HHHHTT-EEEEEET--B--SS-EEEEEEE--TT--TT CS
                   PAF-AH_p_II  34 lRlyypldkadedredelWlPkkeyaqGlsevlkasrlllnllfkllvgslrlpvkknellktkekyPlivFsHGLgafRt 114
                                   lR+yy l k                                                                        
  gi|70607668|ref|YP_256538.1|  15 LRIYYKLFK------------------------------------------------------------------------ 23 
                                   445554443........................................................................ PP

                                   TTHHHHHHHHHTT-EEEEE---SS-SSEEEE-SSHHHHHHT.......--EEEE-----GGGHHHHHHHHHHHHHHHHHHH CS
                   PAF-AH_p_II 115 lYsalcielAskGfvvaavEHrDesAaatyvlkdklaaeeeeevvesrekewiklrkvkeeeevklrneqvkqRaqEcska 195
                                                                                                                    
  gi|70607668|ref|YP_256538.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   HHHHHHHHTT-----SS--SS-GGGGTT-EEEEEEEEEEETHHHHHHHHHHHH-TTS-EEEEES---TTS-GGGGGG--S- CS
                   PAF-AH_p_II 196 LkllreinlGepvenvldsdfdlqqlKdnldtskvaviGHsFGgAtvikslsedteFrcaialDaWmlPveeevyskvrqP 276
                                                                                                                    
  gi|70607668|ref|YP_256538.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   EEEEEETTT--HHHHHHHHTT--TTS-EE CS
                   PAF-AH_p_II 277 llfinsekfqtaedikkmkkvvslkkesk 305
                                                           + e+k
  gi|70607668|ref|YP_256538.1|  24 -----------------------ANSEKK 29 
                                   .......................333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                                   -.GGGGTT-EEEEEEEEEEETHHHHHHHH CS
                   PAF-AH_p_II 217 d.lqqlKdnldtskvaviGHsFGgAtvik 244
                                   + l++l+ ++ + kv+++GHs+Gg  +++
  gi|70607668|ref|YP_256538.1|  84 EeLEELRKQIFNDKVVILGHSYGGLLALA 112
                                   35899*******************76653 PP

>> RXLR_WY  RXLR phytopathogen effector protein WY-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014      0.11       3      25 ..      11      33 ..       9      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                  GG-HHHHHHHHHTTS-HHHHHHH CS
                       RXLR_WY  3 afsDldiYyLLlktnSeeeLkiL 25
                                   ++ l iYy L k nSe  L +L
  gi|70607668|ref|YP_256538.1| 11 NILGLRIYYKLFKANSEKKLITL 33
                                  57889****************99 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.8e-05     0.064       4     115 ..      29     125 ..      26     128 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.8e-05
                  LIDHydrolase   4 livlipGNPGlveFYetFlsllseklnpelevlgishaGfeleeeekeakenekvfsLedQiehkedflkellekaksekd 84 
                                    ++ + G PG ++ Y + ls ls+     ++vl + + G   +ee     ++ + ++++  +e  e++ k+++       +
  gi|70607668|ref|YP_256538.1|  29 KLITLHGGPGGSHDYLEPLSELSKH---GVNVLFYDQFGCGRSEEP----KELSKYTVDYGVEELEELRKQIF-------N 95 
                                   5677778888887777777777777...788888888888877777....45555666655555555544444.......6 PP

                  LIDHydrolase  85 vklilvGHSvGaYialevlkrlsersikkvv 115
                                    k++++GHS G  +al  + +++e+  k++ 
  gi|70607668|ref|YP_256538.1|  96 DKVVILGHSYGGLLALAYAIKYKEN-LKGCS 125
                                   89***************99999998.77665 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.9e-05     0.081      55     127 ..      52     122 ..      12     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                                   HTT-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEE CS
                 Peptidase_S15  55 arGYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalk 127
                                   ++G  v+++d  G g Se   +  ++  ++ g++ ++ l+k +  n+kV  +G SY+G ++l+ a + ++ lk
  gi|70607668|ref|YP_256538.1|  52 KHGVNVLFYDQFGCGRSEEPKEL-SKYTVDYGVEELEELRK-QIFNDKVVILGHSYGGLLALAYAIKYKENLK 122
                                   55666666666666666644444.55555555555555555.5789*******************99888887 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0002      0.16      75     128 ..      63     119 ..      57     124 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                       DUF1749  75 wGtgsLkrDaeeieklveYlkktk...sGeekkekvvlmGHstGsqdvlyYltssne 128
                                   +G g  +  +e  +  v+Y  ++      +  ++kvv++GHs G    l Y+ + +e
  gi|70607668|ref|YP_256538.1|  63 FGCGRSEEPKELSKYTVDYGVEELeelRKQIFNDKVVILGHSYGGLLALAYAIKYKE 119
                                   5555544444444446666443332323356789***********999999988766 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.12      60      99 ..      75     117 ..      25     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                        DUF676  60 gerlaeevlevvkkkkdk..nkkiSfvghSlGglia.raaiak 99 
                                    + ++++ +e++++ +++  n k+ ++ghS Ggl a  +ai +
  gi|70607668|ref|YP_256538.1|  75 SKYTVDYGVEELEELRKQifNDKVVILGHSYGGLLAlAYAIKY 117
                                   5555666677778877778888***********9763678875 PP

>> Chlorophyllase  Chlorophyllase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.17     112     146 ..      90     122 ..      26     127 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                Chlorophyllase 112 ptsveanlsklalvGhsrGGktafalalgysselt 146
                                   ++++    +k+ + Ghs GG  a+a a++y  +l+
  gi|70607668|ref|YP_256538.1|  90 RKQIF--NDKVVILGHSYGGLLALAYAIKYKENLK 122
                                   44443..35899******************98876 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.24      18      45 ..      92     119 ..      80     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                   TB--SSEEEEEETHHHHHHHHHHHHSSS CS
                        BAAT_C  18 kvkkdkigllGiSkGgelalllasflkk 45 
                                   ++ +dk+ +lG+S Gg lal+ a+++k+
  gi|70607668|ref|YP_256538.1|  92 QIFNDKVVILGHSYGGLLALAYAIKYKE 119
                                   57789********************993 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.28      81     109 ..      93     121 ..      77     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                       DUF2974  81 esegkiylgGhSkGGnlAvyaamnaeddl 109
                                    +++k+++ GhS GG lA+  a++ +++l
  gi|70607668|ref|YP_256538.1|  93 IFNDKVVILGHSYGGLLALAYAIKYKENL 121
                                   35778*************99988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 982.31
//
Query:       gi|70607669|ref|YP_256539.1|  [L=485]
Description: sugar proton symporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-83  281.5  26.0      2e-83  280.7  26.0    1.3  1  Sugar_tr         Sugar (and other) transporter
    2.1e-22   79.5  35.2    2.1e-22   79.5  35.2    1.9  2  MFS_1            Major Facilitator Superfamily
  ------ inclusion threshold ------
        1.7    9.4   4.3        2.9    8.6   0.0    3.4  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.7  26.0   3.4e-87     2e-83       2     450 ..      25     457 ..      24     459 .. 0.90

  Alignments for each domain:
  == domain 1  score: 280.7 bits;  conditional E-value: 3.4e-87
                                   HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                      Sugar_tr   2 alvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                   +++aa+gg+lfgYdt vig+++ +  + +  +l  ++              +++++Ga+iG+l++++ +dr+GRk+ l++ 
  gi|70607669|ref|YP_256539.1|  25 TVLAAIGGFLFGYDTSVIGTVAVFVPYNFTGFLLGYE-------------IASASLGAAIGALIGYFSTDRYGRKSLLIVD 92 
                                   689*******************999954444444444.............6899**************************9 PP

                                   HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnk 163
                                   a ++  +a+l+a++    +  +++v+R ++Gi++G+ s++++ yi E+Apk+ Rg l  ++q++it+Gil ++ +g ++ +
  gi|70607669|ref|YP_256539.1|  93 AGIYTGAAILTALSV---NDIMFLVMRTIIGIAIGADSAVATSYITEYAPKDRRGSLAIMQQWMITIGILGSYLVGSAVLY 170
                                   99999999*******...77***********************************************************99 PP

                                   SS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHC...HHHHHHHHHHHHHHHHHHH. CS
                      Sugar_tr 164 tsn....adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrge...edadrelaeekdsleaeqee 237
                                   +      ++ wr+ll+l+++p+l+ l+l++++PESPr+l+  gk+e+ k  l++l  +   ++ dr++ e  ++ +++   
  gi|70607669|ref|YP_256539.1| 171 IAPslayTVDWRLLLALAAIPSLIGLVLRFMMPESPRWLLVSGKKEKLKSDLRRLGLQiddSLLDRAASEVRSEVRQS--- 248
                                   9999999***********************************************443333345555555555555555... PP

                                   ....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...........HHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 238 ekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks...........llvtiivgvvnfvatfva 307
                                           ++  t +++++i+++  ifqq tGin+ +yy+pti+enl+l  s           +l++ i+ v+n++at +a
  gi|70607669|ref|YP_256539.1| 249 --------FDIAT-KRAFTIVALWIIFQQITGINVPFYYGPTIIENLHLFSStsnpmysqinsVLASSILAVINTAATYIA 320
                                   ........77755.4555555556689*********************98888899************************* PP

                                   HHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHH CS
                      Sugar_tr 308 iflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskal 388
                                   +  +dr+GRR+l l   +gm+i+ +i g   +l+ ++     ++a++++a fi++fa g+g++ w++ +E f++ vR+  +
  gi|70607669|ref|YP_256539.1| 321 FRYIDRIGRRKLALSAYTGMLIFDLIGG---ILVMQG---VLVGALIAFAGFIIFFAYGVGGTGWLIQAEYFDTPVRGRMA 395
                                   **********************999998...444444...367999*********************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                      Sugar_tr 389 aiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                   ai + + wlanf+i  +fp+++++ig +++ +vf++l ++++   +  +petkg++le i +
  gi|70607669|ref|YP_256539.1| 396 AIIALIDWLANFIIIEVFPVMLSTIGLAGSMFVFTALDAIALGLFYKLLPETKGLSLETIVK 457
                                   **********************************************************9865 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5  35.2   3.5e-26   2.1e-22       2     350 ..      29     407 ..      28     410 .. 0.80
   2 !    7.3  18.6   0.00032       1.9      33     176 ..     299     448 ..     278     468 .. 0.77

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 3.5e-26
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   ++++fl +++ s++g+++  ++   +++++  +g  ++  +lgaa+++l++ + +dr+Gr+++l++ + ++  +++l +++
  gi|70607669|ref|YP_256539.1|  29 AIGGFLFGYDTSVIGTVAV-FV--PYNFTGFLLGYEIASASLGAAIGALIGYFSTDRYGRKSLLIVDAGIYTGAAILTALS 106
                                   7899*************99.66..57788*************************************999999994455566 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.......Wravfyi 156
                                    +  ++lv+r + G++ ga  +++ ++i++++pk++rg+   + + ++ +G++  +l+g++++  +        Wr++  +
  gi|70607669|ref|YP_256539.1| 107 VNDIMFLVMRTIIGIAIGADSAVATSYITEYAPKDRRGSLAIMQQWMITIGILGSYLVGSAVLYIAPslaytvdWRLLLAL 187
                                   8888************************************************9999999977744446889999******* PP

                         MFS_1 157 laivsllafvlfllllpeepperkrkspkeee.....................kgtgpaplvpawkallkdpvlw.illia 215
                                   +ai sl+++v   l ++ ++++r+   + ++e                     ++ +++++++    + +++ +  ++l++
  gi|70607669|ref|YP_256539.1| 188 AAIPSLIGLV---LRFMMPESPRWLLVSGKKEklksdlrrlglqiddslldraASEVRSEVRQ-SFDIATKRAFTiVALWI 264
                                   ********88...55555555555555555555999999999999999888886666666666.55555555442225555 PP

                         MFS_1 216 lllfffgfsglltllplylqevlgls.......glllaglllallalvgailallagrlsdrlgrrrrlllallllllaal 289
                                   ++   +g++  +++ p+++   + +s       + + ++l++++la+++ ++  +a r++dr+grr+  l a+ ++l++ l
  gi|70607669|ref|YP_256539.1| 265 IFQQITGINVPFYYGPTIIENLHLFSstsnpmySQINSVLASSILAVINTAATYIAFRYIDRIGRRKLALSAYTGMLIFDL 345
                                   55555567778999999866666666999****66899999************************9999999999988877 PP

                         MFS_1 290 glallavtssavllllvlvliGfglgfv...fpsllalasdlappeeagtasglfntagslgga 350
                                   +  +l +    vl+ ++++++Gf  +f+    ++ + + ++++ +  +g++++++ ++  l+ +
  gi|70607669|ref|YP_256539.1| 346 IGGILVMQ--GVLVGALIAFAGFIIFFAygvGGTGWLIQAEYFDTPVRGRMAAIIALIDWLANF 407
                                   76666666..444444555555533333345777777778888899999999999887766665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00032
                         MFS_1  33 eigl..lltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa.ss.lw.lllvlrvlqGlgagalfpaga 107
                                   +i+   + ++ a+   +a++++ r +dr+Grr++ l ++++++++ l+ ++++ ++ l  +l+++  +  ++a ++  +g 
  gi|70607669|ref|YP_256539.1| 299 QINSvlASSILAVINTAATYIAFRYIDRIGRRKLALSAYTGMLIFdLIGGILVmQGvLVgALIAFAGFIIFFAYGVGGTGW 379
                                   444422566688899******************************777777545332334566666666666655555666 PP

                         MFS_1 108 aliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                    + a++f  + rgr+ +++++   l+  +   + ++++s +g  +++++++++ ++a+ lf+ llpe++
  gi|70607669|ref|YP_256539.1| 380 LIQAEYFDTPVRGRMAAIIALIDWLANFIIIEVFPVMLSTIGLAGSMFVFTALDAIALGLFYKLLPETK 448
                                   7889***********************999999999999999999999999999999666666665544 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00048       2.9      41      73 ..       8      40 ..       1      42 [. 0.88
   2 ?    0.1   0.2      0.23   1.4e+03      29      67 ..     121     163 ..      96     196 .. 0.72
   3 ?   -1.7   0.2       0.8   4.8e+03      51      64 ..     329     342 ..     303     375 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00048
               NADH-u_ox-rdase 41 aleklsPsvagkamtlagligflggfllayqns 73
                                  +l+k+++s++ + +++ ++++ +ggfl+ y+ s
  gi|70607669|ref|YP_256539.1|  8 ILDKIDRSRVTRLYWIITVLAAIGGFLFGYDTS 40
                                  6789999999999*****************998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
               NADH-u_ox-rdase  29 aaita.afplallaleklsPsvagka.......mtlagligflggfl 67 
                                   +ai a ++ +  +++e ++P+  + +       m    +ig+lg++l
  gi|70607669|ref|YP_256539.1| 121 IAIGAdSAVATSYITE-YAPKDRRGSlaimqqwM---ITIGILGSYL 163
                                   5666644444444444.66666444467763333...4555555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.8
               NADH-u_ox-rdase  51 gkamtlagligflg 64 
                                   ++++ l++++g+l 
  gi|70607669|ref|YP_256539.1| 329 RRKLALSAYTGMLI 342
                                   33355555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3443.78
//
Query:       gi|70607670|ref|YP_256540.1|  [L=186]
Description: hypothetical protein Saci_1944 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-43  146.9  28.4    8.3e-43  146.4  28.4    1.2  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4  28.4   4.6e-47   8.3e-43      14     193 ..       3     172 ..       1     178 [. 0.92

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 4.6e-47
               Gpr1_Fun34_YaaH  14 krkfaNPaPlgllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsyaa 94 
                                   ++k aNPaPlgl++faltt+vls +n+g    + +n+v+gla fyGGl+qllaGi+e+ +gntFg++a+ +YG+Fw  + +
  gi|70607670|ref|YP_256540.1|   3 EQKRANPAPLGLSGFALTTLVLSTYNAGLLT-SGQNAVLGLAAFYGGLAQLLAGILEYRAGNTFGYVAFFTYGAFWEWFFL 82 
                                   6899************************986.5669****************************************87766 PP

               Gpr1_Fun34_YaaH  95 ilipgfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkAggvfg 175
                                     +  fg ++a         + +g +l+++ ift+++++ t++s++ lf++f++l++tf+ll++g+++g++++ +Agg++g
  gi|70607670|ref|YP_256540.1|  83 TSLGIFGGVTA---------TGIGYVLVAFGIFTLVMWFGTFKSNLGLFITFLLLWITFFLLGAGAMMGNNTLFHAGGYIG 154
                                   65555555555.........57*********************************************************** PP

               Gpr1_Fun34_YaaH 176 iiaaflawYnalaglatk 193
                                   i++a++awY++la ++ +
  gi|70607670|ref|YP_256540.1| 155 ILTAIAAWYTGLAIVVAE 172
                                   ************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1190.18
//
Query:       gi|70607671|ref|YP_256541.1|  [L=117]
Description: hypothetical protein Saci_1945 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-07   30.6   0.2    4.7e-07   30.3   0.2    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.14   11.9   0.0    1.1  1  SRA1      Steroid receptor RNA activator (SRA1)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   5.3e-11   4.7e-07      25     118 ..       6     107 ..       2     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 5.3e-11
                                   HHTSSEEEEEHHHHHHHHHHHHS.........SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHH CS
                           PIN  25 leeleelvtsalvlaEllyvlar.........rkskrekaaelvelllllsalkilpidaeiaeeaaeialkygllpnDal 96 
                                   +e  e  v+s ++++E++ v++r          ks+ e  ++++ l l + + ++++++ +++e+  e++ ++++++  a+
  gi|70607671|ref|YP_256541.1|   6 VEVKEPYVVSLISIIEITSVIRRkylelakkgEKSRAEGYIRFLNLTLSHIRNNVVEVTFRDVERGIELMFERDVNLGEAV 86 
                                   5545899************************888889999999999999******************************** PP

                                   HHHHHHHHT-EEE.ESSTHHHH CS
                           PIN  97 iaAtAkehgikliatfDedfrr 118
                                      +Ak+ ++++i + D+d++ 
  gi|70607671|ref|YP_256541.1|  87 NTMVAKRLNLTVI-SSDKDWES 107
                                   *************.*****875 PP

>> SRA1  Steroid receptor RNA activator (SRA1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05      0.14      32     105 ..      36     110 ..      16     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                          SRA1  32 sesepeledvlsvLnqaLeaCrksvkkqvcddvekrLrll.edsWksG.kLslpvrkrmevLsqelqskrWdaaDd 105
                                   +  +   e  ++ Ln +L++ r++v +  + dve+ ++l+ e   + G  +   v kr+++ +   + k W++  d
  gi|70607671|ref|YP_256541.1|  36 KGEKSRAEGYIRFLNLTLSHIRNNVVEVTFRDVERGIELMfERDVNLGeAVNTMVAKRLNLTVI-SSDKDWESLRD 110
                                   455667889999*************************987333445451567788888876554.45677777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 866.19
//
Query:       gi|70607672|ref|YP_256542.1|  [L=90]
Description: hypothetical protein Saci_1946 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.36   11.4   2.8        1.1    9.8   0.1    2.3  2  NTS       N-terminal segments of PfEMP1


Domain annotation for each model (and alignments):
>> NTS  N-terminal segments of PfEMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3     0.023   4.1e+02       8      32 ..       1      24 [.       1      24 [. 0.85
   2 ?    9.8   0.1   6.2e-05       1.1      11      29 ..      71      89 ..      71      90 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.023
                           NTS  8 sIGkkVhdkvkkeaakkYkdeLkGd 32
                                  +IG+k   k+ ++  ++Y+ e kG+
  gi|70607672|ref|YP_256542.1|  1 MIGEKFERKADEK-GRIYIPEYKGK 24
                                  7999999999999.99999888886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.2e-05
                           NTS 11 kkVhdkvkkeaakkYkdeL 29
                                  ++Vh+++++e ak++ ++L
  gi|70607672|ref|YP_256542.1| 71 EDVHKEAENELAKRFLKQL 89
                                  79***********998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 659.86
//
Query:       gi|70607673|ref|YP_256543.1|  [L=74]
Description: hypothetical protein Saci_1947 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.0   0.8      0.032   14.7   0.8    1.2  1  DUF4790   Domain of unknown function (DUF4790)


Domain annotation for each model (and alignments):
>> DUF4790  Domain of unknown function (DUF4790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.8   1.8e-06     0.032       8      51 ..       1      44 [.       1      54 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-06
                       DUF4790  8 lkvpyqvvClerYkeakrkyerqfkrEikklidlqssaldavrl 51
                                  +kv y+++  +r +e+ +ky+ + ++Ei+++i+ +++ l++ ++
  gi|70607673|ref|YP_256543.1|  1 MKVVYSIRIDKRLREEMQKYNIKWREEIENFIARKTEELKEEEI 44
                                  5899****************************999877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1658  (0.0924759); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 509.59
//
Query:       gi|70607674|ref|YP_256544.1|  [L=412]
Description: transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-15   55.4  11.8    4.6e-15   55.4  11.8    2.3  2  Sugar_tr     Sugar (and other) transporter
    4.5e-14   52.1  42.5    4.5e-14   52.1  42.5    1.9  2  MFS_1        Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.18   12.0   0.0    1.3  1  Methylase_S  Type I restriction modification DNA specificity 


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4  11.8   7.8e-19   4.6e-15      45     213 ..      45     210 ..      14     224 .. 0.88
   2 !    2.7  14.6    0.0074        44     291     446 ..     252     402 ..     220     407 .. 0.63

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 7.8e-19
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                   ++l +l+++ + +  iiG  fag+++dr+GRk +l i+ +++vig++  +++    ++ ++++   ++ +++G++ +++  
  gi|70607674|ref|YP_256544.1|  45 KILESLLLAWAPLWLIIGIAFAGPIADRIGRKTTLWITLAIYVIGGIGLIFSF---NYVLVLIFTAIMLFSAGGEMNTIMA 122
                                   5666777777778889*************************************...99999999***************** PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHH CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeee 206
                                    + Ei p++ Rg+++ l   +i +G  v  ++gl ++ +s   +  +l ++ +v a++l+i +l lPES r+l  k+k   
  gi|70607674|ref|YP_256544.1| 123 ATHEIMPQRNRGRIMFLEINFINLGGAVLGGLGLLTQFSSIFFQRLVLGAVIMVAAVVLFITRLELPESVRWLSAKRKMTN 203
                                   **************************999999999887777555667778899999********************99887 PP

                                   HHHHHHH CS
                      Sugar_tr 207 akevlak 213
                                      v+++
  gi|70607674|ref|YP_256544.1| 204 GGSVVKQ 210
                                   7777766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0074
                                   HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHH CS
                      Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvp 371
                                   ++ ++  ++ f++ +v+ fl d ++RR lll++ +g  +++ +l+   +l++a +     v+  ++++ i +f++    + 
  gi|70607674|ref|YP_256544.1| 252 TIIFVADITEFIVGLVVSFLADSLSRRGLLLWSNLGIVVFT-FLT--YYLIPAWK--SDLVIFWALLVAINAFTAVQYLTE 327
                                   234455579999999999999******99999998876655.554..45555553..233444444444555555544455 PP

                                   HHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHH..HHHHHHHHHHHHHHHHS--S.TT--CC CS
                      Sugar_tr 372 wvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvfl..vfaglavlfiifvfffvpet.kgrtle 446
                                       +El ++  R++ +aia +v+  + + i ++f ++  ++++++ f+  ++  + +++ +  ++f +et kg +++
  gi|70607674|ref|YP_256544.1| 328 DTFKAELWSTIRRGTYTAIARVVS--IGLYIPTIFLTLSFSLSQYVLFNlgIWS-IGLFASVLWYIFGFETsKGTSID 402
                                   566788888888888888888887..5678888888888888866666622333.33444444444444441555555 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1  42.5   7.6e-18   4.5e-14       3     342 ..      17     348 ..      15     355 .. 0.73
   2 ?   -3.6   5.0      0.67     4e+03     284     321 ..     351     387 ..     334     399 .. 0.40

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 7.6e-18
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                   ++ f +++    +++ l ++ ++ +++ +   +lll+   l  ++++ ++G+++dr+Gr+ +l+++l+++++g++ l+f+ 
  gi|70607674|ref|YP_256544.1|  17 FVSFSAGMFLESFIFGLESIATNWYTVPKILESLLLAWAPLWLIIGIAFAGPIADRIGRKTTLWITLAIYVIGGIGLIFSF 97 
                                   5666666666666666665555557777777788999999999******************************77777877 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   ++ l+l++ +++ + ag+ + +++a++ ++ p+++rgr + l   +++lG ++  +lg  l+    ++++f+   +++++ 
  gi|70607674|ref|YP_256544.1|  98 NYVLVLIFTAIMLFSAGGEMNTIMAATHEIMPQRNRGRIMFLEINFINLGGAVLGGLGL-LT---QFSSIFFQRLVLGAVI 174
                                   7779999999999999************************99999******99988854.44...3555544333333333 PP

                         MFS_1 165 fv....lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls 241
                                   +v    lf+  l  +++ r+ +++++    t + ++v+  + l kd  +  l+++ +++  + +++ + l +y+   + +s
  gi|70607674|ref|YP_256544.1| 175 MVaavvLFITRLELPESVRWLSAKRKM---TNGGSVVK--QGLDKDTAFK-LFVTTAIA--FANSAGFGLITYVLGPYFFS 247
                                   331112666666888888888888888...34444444..7888888664.44444444..34446666666667777888 PP

                         MFS_1 242 glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt..ssavllllvlvliGfglgfvfps 320
                                      l+g+++ ++ +  +i++l++++l+d l+rr  ll++ l++++++++ ++l ++  s+ v+++++lv i  + ++ + +
  gi|70607674|ref|YP_256544.1| 248 --NLTGTIIFVADITEFIVGLVVSFLADSLSRRGLLLWSNLGIVVFTFLTYYLIPAwkSDLVIFWALLVAINAFTAVQYLT 326
                                   ..88888999999999999******************99999999999999999993333333333444444444444555 PP

                         MFS_1 321 llalasdlappeeagtasglfn 342
                                     ++ ++l ++ ++gt+++++ 
  gi|70607674|ref|YP_256544.1| 327 EDTFKAELWSTIRRGTYTAIAR 348
                                   5555555556677888777766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.67
                         MFS_1 284 lllaalglallavtssavllllvlvliGf.glgfvfpsl 321
                                    + +++  ++l ++   +l+ +vl+ +G+   g++ + l
  gi|70607674|ref|YP_256544.1| 351 SIGLYIPTIFLTLS--FSLSQYVLFNLGIwSIGLFASVL 387
                                   22222222222222..11111123333333333333333 PP

>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.18      33     106 ..     193     268 ..     182     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                   EEE-HH.HCCT..EE-HHHHCCTT---B-.TT-EEEE-SSSTT-EEEESS-BEE-TTEEEEEESTTT--HHHHHHHHH CS
                   Methylase_S  33 pyirag.ilnn..kvvkdglgykkkyilp.kgdilissratiGkvayrdkkyylnqsvivlipknkkkineflylyll 106
                                    +++a+  + n  +vvk+gl+++ +++l+   +i ++ +a +G + y   +y++++  +++i+    +i+ef+  +  
  gi|70607674|ref|YP_256544.1| 193 RWLSAKrKMTNggSVVKQGLDKDTAFKLFvTTAIAFANSAGFGLITYVLGPYFFSNLTGTIIFV--ADITEFIVGLVV 268
                                   5777776666679**************************************************6..577799877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2904.92
//
Query:       gi|70607675|ref|YP_256545.1|  [L=176]
Description: hypothetical protein Saci_1949 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-25   88.5   0.0    4.3e-25   87.9   0.0    1.3  1  PaREP1          Archaeal PaREP1/PaREP8 family
      0.001   19.3   0.1     0.0023   18.1   0.1    1.5  1  DUF29           Domain of unknown function DUF29
  ------ inclusion threshold ------
      0.071   13.2   0.5       0.21   11.7   0.3    1.8  2  ARL2_Bind_BART  The ARF-like 2 binding protein BART


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   7.2e-29   4.3e-25       2     115 .]      19     138 ..      18     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 7.2e-29
                        PaREP1   2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstke.......llkavaklleelg 75 
                                   r+ e++ e++++ ++l++G++r++a+K++ A+ka+++al+  n++kl + + ++++w+ k        + k +++ le+lg
  gi|70607675|ref|YP_256545.1|  19 RVLESLFEVRLSIKMLKDGYSRNSANKIFLAWKAFISALVTLNLDKLGKDE-KQKEWYNKIgfcapttGIKGITQELEDLG 98 
                                   899***************************************999994444.444477777******************** PP

                        PaREP1  76 dkevvdlwklAldLHeyq..fheaklelsdveskeeavkdlv 115
                                   +k++++++++Al LH y+  ++++   +++++skeea++d++
  gi|70607675|ref|YP_256545.1|  99 YKDLSNVTSTALLLHSYAynGIYKG--ITNYSSKEEAIRDII 138
                                   ******************9999999..*************96 PP

>> DUF29  Domain of unknown function DUF29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   3.9e-07    0.0023      28     111 ..      88     171 ..      84     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTHHHHHHHHHHHHHHHHHH-..-GGGG--H....HHHHHHHHH CS
                         DUF29  28 enLieEiedlgrsekrelesrlavllehlLkwqyqpekrsrswrseireqrkeieklledspsLksyleeeleeaYqdArk 108
                                   + + +E+edlg ++ ++++s    l  + +   y+  ++ +s ++ ir   k  + +l++ +s k  +++elee Y+++++
  gi|70607675|ref|YP_256545.1|  88 KGITQELEDLGYKDLSNVTSTALLLHSYAYNGIYKGITNYSSKEEAIRDIIKLTKFILDNITSFKDIWDNELEEEYTKSLN 168
                                   56889***************9888877777777888899***************************************998 PP

                                   HHH CS
                         DUF29 109 las 111
                                   +++
  gi|70607675|ref|YP_256545.1| 169 EFK 171
                                   876 PP

>> ARL2_Bind_BART  The ARF-like 2 binding protein BART
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.47   2.8e+03      44      71 ..      44      71 ..      34      82 .. 0.66
   2 ?   11.7   0.3   3.5e-05      0.21      22      55 ..     140     175 ..     136     176 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.47
                                  HHHHHHHHHHHHHHHHHHHTT-SSS--T CS
                ARL2_Bind_BART 44 tdihkeYkklveklleslleeigismee 71
                                  ++i+  +k ++  l++  l+++g ++++
  gi|70607675|ref|YP_256545.1| 44 NKIFLAWKAFISALVTLNLDKLGKDEKQ 71
                                  5677777777766666555555555444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHTT--..SS-SSTTHHHHHHHHHHHHH CS
                ARL2_Bind_BART  22 vqeFidencivFdd..eeenkleytdihkeYkklve 55 
                                   +++Fi +n + F+d  ++e + eyt+  +e+k+l+ 
  gi|70607675|ref|YP_256545.1| 140 LTKFILDNITSFKDiwDNELEEEYTKSLNEFKELLS 175
                                   689***********76699999***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1077.39
//
Query:       gi|70607676|ref|YP_256546.1|  [L=225]
Description: hypothetical protein Saci_1950 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.4   0.9       0.25   11.2   0.9    1.6  1  Microcin  Colicin E1 (microcin) immunity protein


Domain annotation for each model (and alignments):
>> Microcin  Colicin E1 (microcin) immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   1.4e-05      0.25      19      40 ..      14      34 ..      12      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                      Microcin 19 LcPySkyaiEhialkfikkeFf 40
                                  L+P+S+ a  +++lk+ik e f
  gi|70607676|ref|YP_256546.1| 14 LFPFSVDA-KDFFLKYIKDEKF 34
                                  9*****98.8********8866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1623.26
//
Query:       gi|70607677|ref|YP_256547.1|  [L=82]
Description: hypothetical protein Saci_1951 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 610.18
//
Query:       gi|70607678|ref|YP_256548.1|  [L=82]
Description: hypothetical protein Saci_1952 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.6   0.3      0.094   12.7   0.0    2.1  2  RHH_1     Ribbon-helix-helix protein, copG family
      0.014   15.6   0.1      0.031   14.5   0.1    1.6  2  DUF5388   Family of unknown function (DUF5388)
      0.054   13.2   0.1      0.065   12.9   0.1    1.1  1  TerB_N    TerB N-terminal domain
      0.057   13.6   0.9      0.069   13.4   0.9    1.2  1  ATG16     Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.094       2      29 ..       5      33 ..       4      43 .. 0.88
   2 ?    1.0   0.1     0.099   4.5e+02       5      15 ..      49      59 ..      44      61 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelI 29
                                  ++i+++++++++++++++ +  +++ e++
  gi|70607678|ref|YP_256548.1|  5 ITIKVSDDIYDLIQRMVKLGIaKTKNEAV 33
                                  8*****************99999999987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.099
                                  EEEHHHHHHHH CS
                         RHH_1  5 rldeellerLd 15
                                  rl+ee+ ++++
  gi|70607678|ref|YP_256548.1| 49 RLEEEVERLVE 59
                                  56666555554 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.9e-06     0.031       9      44 ..       4      39 ..       2      55 .. 0.92
   2 ?   -1.0   0.0      0.48   2.2e+03      36      47 ..      52      63 ..      42      78 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.9e-06
                       DUF5388  9 dvnvrvdNHirNklqALaaiGlaksqkeavkklves 44
                                  +++++v+  i   +q ++ +G+ak++ eav+ l+e+
  gi|70607678|ref|YP_256548.1|  4 PITIKVSDDIYDLIQRMVKLGIAKTKNEAVNLLIEY 39
                                  6899***************************99987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.48
                       DUF5388 36 eavkklveslid 47
                                  e v+ lve++++
  gi|70607678|ref|YP_256548.1| 52 EEVERLVEKWLN 63
                                  456666666665 PP

>> TerB_N  TerB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.5e-05     0.065      94     140 ..      13      72 ..      13      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                        TerB_N  94 fygLerrvgvdnpqegyeklielpeiy............eeldrllkeygddy.sfreya 140
                                   +y L++r +  ++++++ + ++l  +y            ee++rl++ +++d   +++++
  gi|70607678|ref|YP_256548.1|  13 IYDLIQRMVKLGIAKTKNEAVNLLIEYgraevermvrleEEVERLVEKWLNDGfPYKGLS 72 
                                   79*************************************************986666655 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   1.5e-05     0.069     153     190 ..      25      63 ..       8      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                         ATG16 153 vqdlqDElsaLqlqlnqaE.eklrklekENkeLveRWmk 190
                                   + + + E + L +++  aE e+  +le+E + Lve+W++
  gi|70607678|ref|YP_256548.1|  25 IAKTKNEAVNLLIEYGRAEvERMVRLEEEVERLVEKWLN 63 
                                   667899*************55556*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 534.38
//
Query:       gi|70607679|ref|YP_256549.1|  [L=139]
Description: hypothetical protein Saci_1953 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-18   66.8   1.8    2.8e-18   66.6   1.8    1.0  1  PIN       PIN domain
    0.00015   22.3   0.9    0.00017   22.1   0.9    1.1  1  PIN_12    PIN domain
     0.0024   18.6   0.3      0.003   18.3   0.3    1.2  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   1.8   4.7e-22   2.8e-18       1     116 [.       5     122 ..       5     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 4.7e-22
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBC.HHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpid.aeiae 79 
                                   +++DT+v++++++ + + e+ar+++ee  ++lvt +++l El  +++r++++  +a++ v+  l   ++++++id  +++e
  gi|70607679|ref|YP_256549.1|   5 CYVDTNVILSFVEQDANYERAREIVEERrGKLVTGEVTLLELSSFYSRKLKDDVLAKASVKYALKVCNVELVEIDfNRLFE 85 
                                   59**********************************************99999999999999999********8835799* PP

                                   HHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                           PIN  80 eaaeialkygllpnDaliaAtAkehgikliatfDedf 116
                                   +a++++ +++l+++D l ++ A   ++++++tfD+d+
  gi|70607679|ref|YP_256549.1|  86 KALQLSPRLKLKTLDVLQVVSASLVKASVFITFDKDI 122
                                   ***********************************97 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.9   2.9e-08   0.00017       2     128 ..       6     133 ..       5     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.9e-08
                        PIN_12   2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkiees..kkle.kalkslsklksakkklnek 79 
                                   ++DTn++l+ f + + +   ++ +e +e+++ kl++ +++l E+ + +++k+++    k++ k   ++ +++  + ++n++
  gi|70607679|ref|YP_256549.1|   6 YVDTNVILS-FVEQDAN--YERAREIVEERRGKLVTGEVTLLELSSFYSRKLKDDvlAKASvKYALKVCNVELVEIDFNRL 83 
                                   69******8.9999888..9999999**************************98878555544444455555555555444 PP

                        PIN_12  80 kkllslkeikkkieek.veeslkkllekleaikvipetndevkkileraf 128
                                    ++  + +   k+++  v +++ + l k ++    +++  ++++i++r++
  gi|70607679|ref|YP_256549.1|  84 FEKALQLSPRLKLKTLdVLQVVSASLVKASVFITFDKDIIAKEEIVNRVL 133
                                   44333333333333220234466666666664444666677778877765 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   5.1e-07     0.003       4      89 ..       7      95 ..       5     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.1e-07
                         PIN_3  4 lDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvaler......kavap 80
                                  +Dtnv+l+ +  ++  +++ ++ +e+++  lv+++ +l El    +r+l ++  ++ +++ a++   v   +      + ++ 
  gi|70607679|ref|YP_256549.1|  7 VDTNVILSFVE-QDANYERAREIVEERRGKLVTGEVTLLELSSFYSRKLKDDVLAKASVKYALKVCNVE--LveidfnRLFEK 86
                                  7*******999.5559**************************999999988888888888866665554..333466644444 PP

                         PIN_3 81 daelrpllk 89
                                    +l+p lk
  gi|70607679|ref|YP_256549.1| 87 ALQLSPRLK 95
                                  444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1052.97
//
Query:       gi|70607680|ref|YP_256550.1|  [L=131]
Description: PIN domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-18   67.0   1.5    2.4e-18   66.8   1.5    1.0  1  PIN       PIN domain
    0.00031   21.0   0.1     0.0041   17.4   0.1    2.0  1  PIN_9     PIN like domain
     0.0049   17.1   0.5      0.011   16.1   0.5    1.8  1  PIN_4     PIN domain
  ------ inclusion threshold ------
      0.065   13.7   0.6       0.11   13.0   0.6    1.5  1  PIN_12    PIN domain
      0.096   12.4   0.0        2.2    8.1   0.0    2.5  3  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   1.5   6.6e-22   2.4e-18       1     121 [.       3     123 ..       3     124 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.6e-22
                                   EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHH CS
                           PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaee 80 
                                   i++DT+vli+ l ++++++++a+++l+++e++v++++v+ El+++l++   + +++ + v ++ + +  +i++ d ++++ 
  gi|70607680|ref|YP_256550.1|   3 ILVDTNVLIYDLvENSKFHKEAEDILDRAETWVIPSVVVHELVWFLRA---NNLERMDYVSAYVESPKAEIVCEDFDVLKN 80 
                                   79**********************************************...****************************** PP

                                   HHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                           PIN  81 aaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvak 121
                                   a ei+l+ +    + nD +i+++A+ ++++l  tfD++++++ak
  gi|70607680|ref|YP_256550.1|  81 AMEIILREKislSRYNDPVILSHAILRKLPLS-TFDRRLSNLAK 123
                                   ********************************.******99986 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.1e-06    0.0041       1      51 [.       3      54 ..       3     131 .] 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                         PIN_9  1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgk 51
                                  +++Dtn+L+     + +  +e+e +l +++  v+p+ v++EL    +a++ +
  gi|70607680|ref|YP_256550.1|  3 ILVDTNVLIYDLVENSKFHKEAEDILdRAETWVIPSVVVHELVWFLRANNLE 54
                                  689***********************777778*********98765444332 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5     3e-06     0.011       2      48 ..       4      58 ..       3     131 .] 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-06
                         PIN_4  2 VlDTnvlLhdpealksf........keehdvviPitVleELdklKkgsserelar 48
                                   +DTnvl++d+    +f        +     viP +V++EL  + + ++++++++
  gi|70607680|ref|YP_256550.1|  4 LVDTNVLIYDLVENSKFhkeaedilDRAETWVIPSVVVHELVWFLRANNLERMDY 58
                                  58*********88888899999999888889**********88877777655554 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.6   3.1e-05      0.11       1      49 [.       3      48 ..       3     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                        PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknr 49
                                  i +DTn+++   ++l e++++ k +e+i ++  + ++p++v++E+   +
  gi|70607680|ref|YP_256550.1|  3 ILVDTNVLI---YDLVENSKFHKEAEDILDRAETWVIPSVVVHELVWFL 48
                                  789******...78888888899999999999999*********86554 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.065   2.3e+02       1      15 [.       1      16 [.       1      32 [. 0.80
   2 ?   -1.9   0.0      0.81   2.9e+03      17      44 ..      53      81 ..      50      84 .. 0.62
   3 ?    8.1   0.0   0.00061       2.2      29      65 ..      89     125 ..      77     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.065
                       DUF5615  1 mklllDenls.prlve 15
                                  mk+l+D n+  ++lve
  gi|70607680|ref|YP_256550.1|  1 MKILVDTNVLiYDLVE 16
                                  9******986555555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.81
                       DUF5615 17 lreaghdvlhvrelgleg.asDeeileyA 44
                                  l++  + + +v + + e  ++D ++l+ A
  gi|70607680|ref|YP_256550.1| 53 LERMDYVSAYVESPKAEIvCEDFDVLKNA 81
                                  55556666667555555357787877766 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00061
                       DUF5615  29 elglegasDeeileyAkeedriivTkDkDFgellllg 65 
                                   +++l++ +D+ il+ A+ +++ + T+D+  ++l++++
  gi|70607680|ref|YP_256550.1|  89 KISLSRYNDPVILSHAILRKLPLSTFDRRLSNLAKRY 125
                                   5778899********************9999997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 993.29
//
Query:       gi|70607681|ref|YP_256551.1|  [L=75]
Description: hypothetical protein Saci_1955 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-15   54.3   0.3    1.2e-14   53.8   0.3    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    1.6e-06   28.4   0.1    1.8e-06   28.3   0.1    1.1  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.017   15.4   0.0      0.024   14.9   0.0    1.3  1  DUF3006         Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.3     2e-18   1.2e-14       1      45 [.       4      48 ..       4      49 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 2e-18
                                  EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHSX CS
                MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplkslp 45
                                  +kv+++++v+iP  vr  lgi+eGd +e++v++dki+ ++++s++
  gi|70607681|ref|YP_256551.1|  4 VKVTRNYQVTIPSSVRNVLGIKEGDILEVYVENDKIVMKKVESKR 48
                                  69***************************************9976 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1     3e-10   1.8e-06       3      48 ..       5      48 ..       3      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3e-10
                PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytilddgkvvisraeeea 48
                                  ++t+ +q tiP svR++L++k+  d ++    ++ k+v+++ e++ 
  gi|70607681|ref|YP_256551.1|  5 KVTRNYQVTIPSSVRNVLGIKE-GDILEVY-VENDKIVMKKVESKR 48
                                  89*******************9.5455555.566678888887765 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     4e-06     0.024      31      63 ..      23      57 ..      11      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                       DUF3006 31 gakeGdvLeie..ddeieldpeetekrkeriqell 63
                                  g+keGd+Le+   +d+i++ + e ++ + +i++l+
  gi|70607681|ref|YP_256551.1| 23 GIKEGDILEVYveNDKIVMKKVESKRPRIKIEKLM 57
                                  69*********95559****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:01.18
# Mc/sec: 192.75
//
Query:       gi|70607682|ref|YP_256552.1|  [L=147]
Description: hypothetical protein Saci_1956 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-10   40.4   0.4    9.3e-10   38.3   0.0    2.2  2  MarR            MarR family
    9.5e-10   38.2   0.1      2e-09   37.2   0.1    1.6  1  MarR_2          MarR family
      5e-09   36.5   0.1    1.2e-08   35.4   0.0    1.7  2  HTH_27          Winged helix DNA-binding domain
    7.1e-06   25.5   0.1    4.1e-05   23.0   0.0    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00013   22.1   0.0    0.00027   21.0   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
    0.00014   22.0   0.0    0.00031   20.9   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00029   20.4   1.1     0.0026   17.4   0.0    2.3  2  GntR            Bacterial regulatory proteins, gntR family
     0.0025   17.8   0.1      0.011   15.8   0.0    2.1  2  HTH_20          Helix-turn-helix domain
     0.0032   17.7   0.1     0.0055   16.9   0.1    1.4  1  PaaX            PaaX-like protein
     0.0065   16.3   0.0      0.014   15.2   0.0    1.6  1  DUF3116         Protein of unknown function (DUF3116)
     0.0071   16.2   0.7      0.026   14.4   0.1    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.025   14.6   0.0    1.5  1  HTH_45          Winged helix-turn-helix
      0.099   12.8   0.0       0.15   12.3   0.0    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
       0.11   12.5   0.0       0.36   10.9   0.0    1.7  2  HTH_54          ParA helix turn helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.6     2e+03       4      14 ..       7      17 ..       4      25 .. 0.68
   2 !   38.3   0.0   7.3e-13   9.3e-10      21      58 ..      53      90 ..      44      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                  HHHHHHHHHHH CS
                          MarR  4 tqfviLrilye 14
                                   +++iLr+l++
  gi|70607682|ref|YP_256552.1|  7 KEIEILRLLST 17
                                  56677777654 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 7.3e-13
                                  HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR 21 seLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                   +La  +gvsks++t ++drLe++G++ R +s++DrR+
  gi|70607682|ref|YP_256552.1| 53 VKLAHTFGVSKSAITYAVDRLERRGYVLRVRSERDRRA 90
                                  49***********************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.1   1.6e-12     2e-09       9      62 .]      40      90 ..      33      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.6e-12
                                  HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                        MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                   +L+a+  +     ++  la ++g+sksa++++++rL+++G+v r+++++D+Ra
  gi|70607682|ref|YP_256552.1| 40 GILNAISKGVN---SPVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSERDRRA 90
                                  56666666654...88889**********************************7 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.4   8.2e+03       5      13 ..       8      16 ..       4      31 .. 0.52
   2 !   35.4   0.0     9e-12   1.2e-08       5      68 .]      38      99 ..      34      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.4
                        HTH_27  5 qalvLhlir 13
                                  ++ +L+l+ 
  gi|70607682|ref|YP_256552.1|  8 EIEILRLLS 16
                                  566666655 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 9e-12
                        HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                  ++ +L+ i    + ++   l+ +  v++s+i y++++L+++G+v r ++e+drr+ ++++Td G
  gi|70607682|ref|YP_256552.1| 38 DVGILNAIS--KGVNSPVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSERDRRAITLQITDQG 99
                                  666666666..444444677888899************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.2   1.6e+03       3      12 ..       6      15 ..       4      17 .. 0.79
   2 !   23.0   0.0   3.2e-08   4.1e-05       4      47 ..      37      79 ..      34      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                        HTH_24  3 etdrkILelL 12
                                   ++++IL+lL
  gi|70607682|ref|YP_256552.1|  6 AKEIEILRLL 15
                                  57899**998 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3.2e-08
                        HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  +d  IL+++ k +  s   LA   g+S+s++++ ++rLe+ G++
  gi|70607682|ref|YP_256552.1| 37 LDVGILNAISK-GVNSPVKLAHTFGVSKSAITYAVDRLERRGYV 79
                                  68889999999.99*****************************8 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.1e-07   0.00027      17      71 ..      52     105 ..      41     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                        HTH_34  17 fvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                   +v+l  + +++++++   ++ Le  gY+ +  + +++ + ++l+iT++G++  k+
  gi|70607682|ref|YP_256552.1|  52 PVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSERDR-RAITLQITDQGKQLLKR 105
                                   678889999********************99999999.9999********98776 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.4e-07   0.00031      19      52 ..      46      79 ..      40      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-07
                                  HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                  +k+v ++ +la   +vs+s ++  + +Le+ Gyv
  gi|70607682|ref|YP_256552.1| 46 SKGVNSPVKLAHTFGVSKSAITYAVDRLERRGYV 79
                                  89999****************************9 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     2e-06    0.0026      29      58 ..      54      83 ..      52      86 .. 0.93
   2 ?    1.3   0.2      0.21   2.7e+02      19      40 ..     116     136 ..      99     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                          GntR 29 eLaaefgVsrttvReALrrLeaeglverrq 58
                                  +La  fgVs++ +  A +rLe++g+v r +
  gi|70607682|ref|YP_256552.1| 54 KLAHTFGVSKSAITYAVDRLERRGYVLRVR 83
                                  69************************9976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                                   -TTSB---HHHHHHHHTS-HHH CS
                          GntR  19 rpGdkLPsereLaaefgVsrtt 40 
                                   r  + L se+eL + + +s+  
  gi|70607682|ref|YP_256552.1| 116 RKLSVL-SEEELNTLLSISTKL 136
                                   556789.999999999999765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.7e-06     0.011      14      61 .]      40      86 ..      36      86 .. 0.86
   2 ?   -1.7   0.1       2.5   3.2e+03      25      30 ..     121     126 ..     101     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                                  HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                  +il a+ +++  ++  la+++++sk+ + y ++ Le+ g+v +vr++r
  gi|70607682|ref|YP_256552.1| 40 GILNAI-SKGVNSPVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSER 86
                                  566677.777778889*************************9999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                                   B-HHHH CS
                        HTH_20  25 ltasel 30 
                                   l+ +el
  gi|70607682|ref|YP_256552.1| 121 LSEEEL 126
                                   344444 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.3e-06    0.0055      26      60 ..      52      86 ..      45      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-06
                          PaaX 26 LirllaelGiseslvRaalsRlakaGwlvrekegr 60
                                   ++l + +G+s s++  a+ Rl+++G + r + +r
  gi|70607682|ref|YP_256552.1| 52 PVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSER 86
                                  58999***********************9999887 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.014      40      84 ..      62     107 ..      49     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                       DUF3116  40 tkneLLytvYWLElkgyilRkeekann.kkrYelTekGellykelk 84 
                                   +k  + y+v  LE +gy+lR +++++    + ++T++G++l+k+++
  gi|70607682|ref|YP_256552.1|  62 SKSAITYAVDRLERRGYVLRVRSERDRrAITLQITDQGKQLLKRIE 107
                                   77778888888*********8887655156899**********997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1     2e-05     0.026      20      58 ..      47      85 ..      41      94 .. 0.87
   2 ?   -0.5   0.1      0.94   1.2e+03      13      31 ..     109     129 ..     107     142 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                  HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  +g  +  ++a+  gv++s +  ++ +Le++G+V r++++
  gi|70607682|ref|YP_256552.1| 47 KGVNSPVKLAHTFGVSKSAITYAVDRLERRGYVLRVRSE 85
                                  566677789************************999876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.94
                                   HCHHHH..HHCCCHHCHHCCC CS
                          TrmB  13 vYlaLl..klgpatadeiaee 31 
                                    Y++L+  kl  ++ +e+   
  gi|70607682|ref|YP_256552.1| 109 LYVTLVrrKLSVLSEEELNTL 129
                                   789999555555555555555 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     2e-05     0.025      10      72 ..      40     109 ..      37     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                        HTH_45  10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkel 72 
                                    IL+ais+g +++ k+      s + +   +d L  +g++       + +  + ++T++G++ll++++el
  gi|70607682|ref|YP_256552.1|  40 GILNAISKGVNSPVKLAHTFGVSKSAITYAVDRLERRGYVlrvrserDRRAITLQITDQGKQLLKRIEEL 109
                                   59*************************************99999986668899**************987 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.15      23      52 ..      54      83 ..      46     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkqs 52
                                   La++++ +++ ++y ++ Le+ g++ ++ 
  gi|70607682|ref|YP_256552.1| 54 KLAHTFGVSKSAITYAVDRLERRGYVLRVR 83
                                  699***********************9875 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.36      32      73 ..      54      93 ..      48      98 .. 0.78
   2 ?   -0.6   0.0       1.1   1.4e+03       8      34 ..      91     119 ..      84     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                        HTH_54 32 alaklpklsrrkvdkavsemeaeGyefekkeagstekYalti 73
                                  +la++ ++s+ ++ +av+ +e +Gy+++ ++       a+t+
  gi|70607682|ref|YP_256552.1| 54 KLAHTFGVSKSAITYAVDRLERRGYVLRVRSERDR--RAITL 93
                                  6788899*******************998854443..34444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                        HTH_54   8 lteqiqkqkkEl..kedeyyqtyskaala 34 
                                   +t qi++q k l  +++e y t  + +l+
  gi|70607682|ref|YP_256552.1|  91 ITLQITDQGKQLlkRIEELYVTLVRRKLS 119
                                   56667666666655566666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 791.34
//
Query:       gi|70607683|ref|YP_256553.1|  [L=567]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-42  143.4  52.3    8.3e-42  143.4  52.3    3.4  2  MFS_1         Major Facilitator Superfamily
    3.7e-08   32.7  25.3    1.1e-07   31.1  11.1    2.5  2  Sugar_tr      Sugar (and other) transporter
    0.00017   20.7   2.4    0.00017   20.7   2.4    2.5  2  PUCC          PUCC protein
     0.0048   15.4   3.6     0.0048   15.4   3.6    2.3  2  MFS_3         Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4  52.3   1.9e-45   8.3e-42       3     349 ..      14     425 ..      12     429 .. 0.83
   2 ?   -4.2  10.8       1.4   6.1e+03       2      55 ..     473     524 ..     428     544 .. 0.60

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 1.9e-45
                         MFS_1   3 laaflsalarsilgpalplalaedlg......ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                   +++++++++ +i++++lp a+ +  +      +s   + ++l +y +++a++ + +Grlsd fGr r++ lg+++f +g  
  gi|70607683|ref|YP_256553.1|  14 IGVLMASINGTITLISLP-AIFRGINinplnpSSFEYLLWILMGYNVVTAALLVTFGRLSDIFGRVRLYNLGFAIFTVG-S 92 
                                   778888899999999999.777777744655555555999***************************************.5 PP

                         MFS_1  78 lll.fa.....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                   +ll ++     ++   l+v+rv+qG+ga++lf+++aa+i+d fp++erg+a+g+ ++++ +G+++g + gg+l+  l+Wr+
  gi|70607683|ref|YP_256553.1|  93 ILLyITpnqgtTGALELIVFRVVQGIGAAFLFSNSAAIITDAFPPNERGKALGINQIAALAGSLIGLVMGGILS-TLNWRY 172
                                   5552434544444556********************************************************99.999*** PP

                         MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeee............................................. 188
                                   vf++  +v+ll+ v    +l  +++      +k                                                
  gi|70607683|ref|YP_256553.1| 173 VFLVSVPVGLLGTVW--SYLKLKETGVISRGEK--Idipgnvtfaaglisillgityglepygssamgwtnpyvitalaig 249
                                   ************882..3333333333333333..23588899999999******************************99 PP

                         MFS_1 189 ..........kgtgpaplvpawkallkdpvlw.....illialllfffgfsg...lltllplylqevlgls...glllagl 248
                                             +++++ p++  +++++ + +l+     il+  ++++ +++ +     ++lpl      g++   + + ag+
  gi|70607683|ref|YP_256553.1| 250 aglliafpfiERKVKYPMFR-LELFKIRGFLMgslsqILFSFAFGGVMIILIillQGIWLPLH-----GYKyedTPFWAGV 324
                                   99999999999999999999.999999998865555444444444444444465566777774.....3333353477776 PP

                         MFS_1 249 llallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdla 329
                                   +   ++l+++i+++++g+lsd++g++ + +++l+++ +a+l+l  l+   +++ +++ ++++G+g+g++ ++ +a++++++
  gi|70607683|ref|YP_256553.1| 325 YTLPMMLGFVIMGPISGALSDKYGAKYISTVGLVIIGTAFLALSTLPYDFNYPEFAVTIFVLGLGSGMFGAPNIAAIMNSV 405
                                   666777777777********************************************************************* PP

                         MFS_1 330 ppeeagtasglfntagslgg 349
                                   p++ +g+asg  +t+++ + 
  gi|70607683|ref|YP_256553.1| 406 PRNSRGAASGMRTTLQNSAQ 425
                                   **************999876 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.4
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrl 55 
                                   l+aafl +  +++++++lp+ l  +  isp +i +l+++y +   +a +++ +l
  gi|70607683|ref|YP_256553.1| 473 LFAAFLGYNPIGTILSLLPSQLLAT--ISPNAIATLTSTYWFPETIAPPFMNAL 524
                                   4555555556666666666533333..677777777777777777777777666 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1  11.1   2.4e-11   1.1e-07      47     188 ..      49     188 ..       7     196 .. 0.87
   2 !    6.9   6.2   0.00053       2.4      40     121 ..     314     395 ..     278     447 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.4e-11
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGigvGlasvlvPm 125
                                   ++ +i+  ++v+ ++  +++g l+d+fGR   +  + ++f +g++l ++++++  +    liv Rv+ Gig+ +    +  
  gi|70607683|ref|YP_256553.1|  49 YLLWILMGYNVVTAALLVTFGRLSDIFGRVRLYNLGFAIFTVGSILLYITPNQgtTGALELIVFRVVQGIGAAFLFSNSAA 129
                                   56788888999999999**********************************9977778889******************** PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    i    p++ Rg+  +++q a  +G l++ ++g +l++  n   wr+ + +++   ll  ++ 
  gi|70607683|ref|YP_256553.1| 130 IITDAFPPNERGKALGINQIAALAGSLIGLVMGGILSTL-N---WRYVFLVSVPVGLLGTVWS 188
                                   *****************************9999888765.5...9****99999999988876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00053
                                   HHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHHHHH CS
                      Sugar_tr  40 skeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGigvGl 118
                                   ++e++  + g+ +  +++G +i + ++g l+d++G k++  ++   ++ig++  a+++    +++  ++v  +++G+g G+
  gi|70607683|ref|YP_256553.1| 314 KYEDTPFWAGVYTLPMMLGFVIMGPISGALSDKYGAKYISTVGL--VIIGTAFLALSTLPydFNYPEFAVTIFVLGLGSGM 392
                                   3344567889999999*********************9877765..5788888888885578*****************98 PP

                                   HHH CS
                      Sugar_tr 119 asv 121
                                   + +
  gi|70607683|ref|YP_256553.1| 393 FGA 395
                                   755 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   4.4      0.02        88      59     147 ..      81     165 ..      51     188 .. 0.66
   2 !   20.7   2.4   3.8e-08   0.00017     251     352 ..     324     430 ..     311     456 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.02
                          PUCC  59 lalglaiaplalivlsgkgeaeaaatwaglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivv 139
                                   + lg+ai +++ i+l    + +++   +g + ++v  ++ G+g+       +A+++d+  ++er k+ g+  +  l g  +
  gi|70607683|ref|YP_256553.1|  81 YNLGFAIFTVGSILLYI--TPNQGT--TGALELIVFRVVQGIGAAFLFSNSAAIITDAFPPNERGKALGINQIAALAGSLI 157
                                   34566666666666665..222222..233333444456677777777788888888888888888888887777777777 PP

                          PUCC 140 saivvgal 147
                                   + ++ g+l
  gi|70607683|ref|YP_256553.1| 158 GLVMGGIL 165
                                   65554443 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.8e-08
                          PUCC 251 lfalGtlvGlllag...lvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldl 328
                                   ++ l  ++G+++ g    +ls + +++ + ++g++++ ++fl+l       n   +++++++lGl+sG+f++  ++++++ 
  gi|70607683|ref|YP_256553.1| 324 VYTLPMMLGFVIMGpisGALSDKYGAKYISTVGLVIIGTAFLALSTLPYDFNYPEFAVTIFVLGLGSGMFGAPNIAAIMNS 404
                                   5666667777776511156888888899999999999999999999999999***************************** PP

                          PUCC 329 aaeeraglalGaWGaaQaia..agla 352
                                   ++++  g a G+    Q  a  a+la
  gi|70607683|ref|YP_256553.1| 405 VPRNSRGAASGMRTTLQNSAqtASLA 430
                                   *******9999988887554114455 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.6   1.1e-06    0.0048      62     174 ..      65     176 ..      59     200 .. 0.87
   2 !    2.5   2.6    0.0084        38      55     155 ..     326     428 ..     322     473 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-06
                         MFS_3  62 silaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAva 142
                                    +  G l+D+f r ++   + ++  ++s+ll ++   g +    l+++ ++ giGaa+      A++ +  + ++  +A  
  gi|70607683|ref|YP_256553.1|  65 LVTFGRLSDIFGRVRLYNLGFAIFTVGSILLYITPNQGTTGALELIVFRVVQGIGAAFLFSNSAAIITDAFPPNERGKALG 145
                                   467799*************************************************************************** PP

                         MFS_3 143 LnsvginiaRsvGPAlgGvlvaavGaalafav 174
                                   +n +       +G  +gG+l +++   ++f v
  gi|70607683|ref|YP_256553.1| 146 INQIAALAGSLIGLVMGGIL-STLNWRYVFLV 176
                                   ****9999999999999986.44555555555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0084
                         MFS_3  55 tLPifl....lsilaGalaDnfdrRkvllavqlllalvsvlltvlaa.lgllspwlllaltlligiGaalndPaWqAsvge 130
                                   tLP++l    +  ++Gal+D++  + +  ++  l+++++++l+++++ +++  p    + ++++g+G+ +      A++ +
  gi|70607683|ref|YP_256553.1| 326 TLPMMLgfviMGPISGALSDKYGAKYISTVG--LVIIGTAFLALSTLpYDFNYPE-FAVTIFVLGLGSGMFGAPNIAAIMN 403
                                   6777663111444688888888876655444..3444555555555415555554.4556788889988877667777778 PP

                         MFS_3 131 lvkrrdvpaAvaLnsvginiaRsvG 155
                                    v+r+   aA  + +   n a ++ 
  gi|70607683|ref|YP_256553.1| 404 SVPRNSRGAASGMRTTLQNSAQTAS 428
                                   8888888888777776666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3105.21
//
Query:       gi|70607684|ref|YP_256554.1|  [L=165]
Description: hypothetical protein Saci_1958 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.5   0.8       0.13   11.8   0.8    1.3  1  Spo7      Spo7-like protein


Domain annotation for each model (and alignments):
>> Spo7  Spo7-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8     7e-06      0.13      36      98 ..      10      73 ..       7      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-06
                          Spo7 36 llLalviafflyalflapredgsgvggsvywvvevvekvll..iggvvTlvLfwlsGeyertivi 98
                                  ++L+++iaf++++lfl  + ++++ + +vy  + +v   l+  ++  +T   +w s ey r +  
  gi|70607684|ref|YP_256554.1| 10 AVLFTLIAFVFFSLFL-MSLQTVNASSNVYSKYVYVDGTLFgkVIYRITHTQVWTSDEYGRVVYF 73
                                  6899************.5555556665666655555555442244558************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 914.54
//
Query:       gi|70607685|ref|YP_256555.1|  [L=227]
Description: hypothetical protein Saci_1959 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1325.30
//
Query:       gi|70607686|ref|YP_256556.1|  [L=255]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1457.28
//
Query:       gi|70607687|ref|YP_256557.1|  [L=284]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-21   76.4   0.0      6e-21   75.4   0.0    1.5  1  ABC_tran     ABC transporter
    1.5e-12   48.0   0.0    2.6e-05   24.2   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      9e-10   38.3   0.1    0.00039   19.9   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    3.7e-05   23.6   0.0     0.0036   17.1   0.0    2.3  2  AAA_15       AAA ATPase domain
    0.00013   22.6   0.1    0.00031   21.3   0.1    2.0  1  AAA_23       AAA domain
    0.00015   21.4   0.0    0.00038   20.2   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00074   19.9   0.0     0.0013   19.1   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0024   17.8   0.0     0.0053   16.7   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
     0.0029   17.3   0.0     0.0043   16.8   0.0    1.4  1  AAA_30       AAA domain
     0.0057   16.6   0.0      0.015   15.2   0.0    1.8  1  NTPase_1     NTPase
     0.0085   15.7   0.0      0.016   14.8   0.0    1.5  1  SRP54        SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.016   15.6   0.0        5.8    7.3   0.0    2.5  2  AAA          ATPase family associated with various cellular a
      0.022   13.6   0.2       0.53    9.0   0.1    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.058   13.2   0.2        6.1    6.5   0.1    2.3  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.066   13.4   0.1        1.4    9.1   0.1    2.2  2  AAA_33       AAA domain
      0.089   13.0   0.1        1.2    9.4   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.15   11.6   0.0       0.28   10.8   0.0    1.3  1  AAA_27       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   5.7e-24     6e-21       1     137 []      17     145 ..      17     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 5.7e-24
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.e 80 
                                   l++vsl+++eg  +a+vG+nGaGKStLl +lag +k  eGe ++ g + ++   ++ ++++++   +  +fp+++vr+  +
  gi|70607687|ref|YP_256557.1|  17 LDDVSLEVREGY-TALVGPNGAGKSTLLGVLAGVYK-YEGECHILGIECRD--SKRIHERVSFSIDT-PVFPDIKVRNIlK 92 
                                   799******995.79********************8.7***********99..78888888877666.899***9999988 PP

                                   HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     e  e+++ +lg +e+ +++     +sLS Gq + v++  al ++++l++lDEpta
  gi|70607687|ref|YP_256557.1|  93 IAEADEEIVYQLGAEEILKKNF----NSLSTGQAKLVSISIALGRDADLYILDEPTA 145
                                   8888999******999888888....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   9.9e-08    0.0001       2      43 ..      29      72 ..      28     108 .. 0.76
   2 !   24.2   0.0   2.5e-08   2.6e-05     220     300 ..     100     174 ..      76     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.9e-08
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggir 43
                                  ++l+GpNg+GKS+LL  l ++  +   +++ g  + +s++ ++r
  gi|70607687|ref|YP_256557.1| 29 TALVGPNGAGKSTLLGVLAGVYKYegECHILGIECRDSKRIHER 72
                                  89****************99887788666666666666655555 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2.5e-08
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                    v++l  +   + ++++lS G+ +l  +  al r++   +l+++DEp ++L+P    r++++l +++++    v++++H  
  gi|70607687|ref|YP_256557.1| 100 IVYQLGAEEILKKNFNSLSTGQAKLVSISIALGRDA---DLYILDEPTANLDPDKRVRFYDVLlRKAKN----VFIASHEL 173
                                   5555555555566899******************99...9********************999555555....******76 PP

                        AAA_21 300 l 300
                                   +
  gi|70607687|ref|YP_256557.1| 174 S 174
                                   5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.2e-06    0.0044      16      41 ..      18      43 ..       3      50 .. 0.82
   2 !   19.9   0.0   3.7e-07   0.00039     130     208 ..     107     182 ..      61     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-06
                                  EEEEEETTSSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 16 ktvilpfsksftaivGpNGSGKsnll 41
                                  + v+l++ ++ ta+vGpNG+GKs ll
  gi|70607687|ref|YP_256557.1| 18 DDVSLEVREGYTALVGPNGAGKSTLL 43
                                  6788999****************987 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.7e-07
                                   TT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                   xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 130 agiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                   ++i k+   +LS G+ +Lv++++ +     + a ly+lDe  a+LD  ++ ++ ++l +k k   +++ s++   +++  +
  gi|70607687|ref|YP_256557.1| 107 EEILKKnfnSLSTGQAKLVSISIAL----GRDADLYILDEPTANLDPDKRVRFYDVLLRKAK--NVFIASHELSEVNNIAS 181
                                   4443323338**********99875....58899*********************9998885..57888988777766544 PP

                                   E CS
                                   x RF
                         SMC_N 208 l 208
                                   +
  gi|70607687|ref|YP_256557.1| 182 N 182
                                   4 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.4e-06    0.0036      14      43 ..      17      46 ..      16      78 .. 0.91
   2 ?    4.3   0.0     0.026        27     280     354 ..      96     165 ..      66     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-06
                        AAA_15 14 lkdveidlseeltvliGkNnsGKSsileal 43
                                  l+dv++++ e +t l+G+N++GKS++l +l
  gi|70607687|ref|YP_256557.1| 17 LDDVSLEVREGYTALVGPNGAGKSTLLGVL 46
                                  678999********************9877 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.026
                        AAA_15 280 kneeieik..ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                    +eei ++   +e l+ n n++ + ++ l+++ i+  ++        ++++++EP a+L p+    +++ l++ a++
  gi|70607687|ref|YP_256557.1|  96 ADEEIVYQlgAEEILKKNFNSLSTGQAKLVSISIALGRDA-------DLYILDEPTANLDPDKRVRFYDVLLRKAKN 165
                                   3344444477777788888888888888888888888888.......99**************99999999887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1     3e-07   0.00031      11      36 ..      18      43 ..       8     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3e-07
                        AAA_23 11 rdqeidFskgltlItGpNGaGKTTil 36
                                  +d++++   g t+++GpNGaGK+T+l
  gi|70607687|ref|YP_256557.1| 18 DDVSLEVREGYTALVGPNGAGKSTLL 43
                                  677888899****************9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.6e-07   0.00038      15      39 ..      20      43 ..      15      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                        AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                   ++e++ +g t l+Gp+G+GKSTll
  gi|70607687|ref|YP_256557.1| 20 VSLEVR-EGYTALVGPNGAGKSTLL 43
                                  555665.569**************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.2e-06    0.0013      23     127 ..      25     163 ..      16     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-06
                        AAA_16  23 rpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesa.........ipy.........salaqalareellrq 84 
                                   r++++ l+G+ G GKs+l+  l+  ++ +g ++ l  +c+++++          +p          + +a+a   ee++ q
  gi|70607687|ref|YP_256557.1|  25 REGYTALVGPNGAGKSTLLGVLAGVYKYEGeCHILGIECRDSKRIhervsfsidTPVfpdikvrniLKIAEAD--EEIVYQ 103
                                   457889*****************99999977999*******95554444444442223333322222233333..244444 PP

                        AAA_16  85 llde....aesaeleawrekleeala...........................avpelagaeasrllellkrll 127
                                   l++e    ++               +                           ++++l+++++ r++++l r +
  gi|70607687|ref|YP_256557.1| 104 LGAEeilkKNF--------------NslstgqaklvsisialgrdadlyildePTANLDPDKRVRFYDVLLRKA 163
                                   44444444333..............2444444455556669999999999999999999999999999998866 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     5e-06    0.0053      87     121 ..      14      48 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
                                   HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinallp 121
                                   k  l++++ ++++  ++lvG+ G+GKStL+ +l++
  gi|70607687|ref|YP_256557.1|  14 KVVLDDVSLEVREGYTALVGPNGAGKSTLLGVLAG 48 
                                   5567888899999*****************99987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.1e-06    0.0043      19      67 ..      27      74 ..      20     164 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.1e-06
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67
                                   +++l+Gp G+GK+t+l++l+ +++ +g + ++l  + + +k++ e + 
  gi|70607687|ref|YP_256557.1| 27 GYTALVGPNGAGKSTLLGVLAGVYKYEG-ECHILGIECRDSKRIHERVS 74
                                  5789*********************997.56666666666666666555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.015       4      51 ..      31      79 ..      28     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
                                  EE--TTSSHHHHHHHHHHHH....GGGEEEEEEEEE-------EEEEEE CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlellkss.gvkvgGfyteevreggrrigFkivd 51
                                  + Gp G GK+Tl+  ++ + k + ++++ G+ +++ ++  +r+ F+i +
  gi|70607687|ref|YP_256557.1| 31 LVGPNGAGKSTLLGVLAGVYKYEgECHILGIECRDSKRIHERVSFSIDT 79
                                  78******************988469*******************9965 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.016       4      41 ..      29      68 ..      26      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-..EEEEEESTSS CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkk..vllvaaDtfR 41
                                  ++lvG++GaGK t l+ La ++k eg+   + + + D  R
  gi|70607687|ref|YP_256557.1| 29 TALVGPNGAGKSTLLGVLAGVYKYEGEChiLGIECRDSKR 68
                                  689********************99654003455666666 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0055       5.8       3      24 ..      31      52 ..      29     122 .. 0.80
   2 ?    5.9   0.0     0.015        16      95     130 ..     202     234 ..     173     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0055
                                  EESSTTSSHHHHHHHHHHHHTH CS
                           AAA  3 lyGppGtGKTllakavakelgv 24
                                  l+Gp G GK++l   +a   + 
  gi|70607687|ref|YP_256557.1| 31 LVGPNGAGKSTLLGVLAGVYKY 52
                                  89**********9999987753 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.015
                                   HTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
                           AAA  95 gvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                                   +        +vi+ tnrp+++ + l r + f   + i
  gi|70607687|ref|YP_256557.1| 202 NKYG----NLVIIKTNRPQEIIKLLGRgNHFGNSVLI 234
                                   3333....499**************999998877665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0005      0.53     241     269 ..      23      50 ..      19      54 .. 0.87
   2 ?    2.5   0.0     0.048        50      66     122 ..     147     203 ..     101     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0005
                                   EE-SSEEEEEE-TTSSHHHHHHHHHHCCS CS
                    ABC_ATPase 241 gipkGvtlIvGggfhGKsTLLeAlekGvy 269
                                    +++G t++vG++  GKsTLL  l +Gvy
  gi|70607687|ref|YP_256557.1|  23 EVREGYTALVGPNGAGKSTLLGVL-AGVY 50 
                                   5899*****************877.5777 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.048
                                   S-HHHHHHHHHHHHHHHHHCC....CTT-SSS--S-EE-----SEE--BSSEEE--E CS
                    ABC_ATPase  66 kskerrvaledfllrklkaelekltsksagsgksgalaidkksqevlersavelsde 122
                                    ++++rv + d+llrk k+ +  + + s  ++ +++l i + ++ v + +  els++
  gi|70607687|ref|YP_256557.1| 147 LDPDKRVRFYDVLLRKAKNVFIASHELSEVNNIASNLVIIRRGKIVFNGTLKELSNK 203
                                   57899****************888888999999999999999999988776666655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0058       6.1       2      23 ..      32      53 ..      31      62 .. 0.84
   2 ?    4.5   0.0     0.025        26      43      99 ..      83     143 ..      76     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0058
                    ATP_bind_1  2 vGpaGsGKttfvgalseilelr 23
                                  vGp G+GK+t+ g l+ +++ +
  gi|70607687|ref|YP_256557.1| 32 VGPNGAGKSTLLGVLAGVYKYE 53
                                  8***********9998777655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                    ATP_bind_1  43 aavdirelitledvmed..lglgpngalvvaleflresldwl.deeleke.eddyllfDtP 99 
                                   +++ +r++++ ++++e+  ++lg    l   ++ l++   +l + ++    ++d++++D P
  gi|70607687|ref|YP_256557.1|  83 PDIKVRNILKIAEADEEivYQLGAEEILKKNFNSLSTGQAKLvSISIALGrDADLYILDEP 143
                                   7899*****************************9999996664555645546699999988 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0013       1.4       4      20 ..      31      47 ..      29      59 .. 0.84
   2 ?    2.2   0.0      0.18   1.9e+02      64      96 ..     128     163 ..      66     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                        AAA_33  4 lvGlpGsGKstlaerll 20
                                  lvG++G+GKstl+  l+
  gi|70607687|ref|YP_256557.1| 31 LVGPNGAGKSTLLGVLA 47
                                  89*********986665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                        AAA_33  64 rkalsagrn.vildat..nlsrrerarflklarrlg 96 
                                    +al + ++ +ild +  nl++++r rf  ++ r  
  gi|70607687|ref|YP_256557.1| 128 SIALGRDADlYILDEPtaNLDPDKRVRFYDVLLRKA 163
                                   344444444689999988999***999988876554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0012       1.2      18      82 ..     102     153 ..      86     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                       SbcCD_C  18 dedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesia 82 
                                    + g+e+ l++++++lS+G++ +l+++ +a++      +      + +l +LDE  ++lD++++ 
  gi|70607687|ref|YP_256557.1| 102 YQLGAEEILKKNFNSLSTGQA-KLVSISIALG------R------DADLYILDEPTANLDPDKRV 153
                                   4558888899**********9.9999999843......3......34677777777777777665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026      0.28      10      44 ..      10      44 ..       2      50 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                        AAA_27 10 ryGk...ftdrsldfsaeeadlhliyGpNEAGKstalr 44
                                  r+Gk   ++d sl+ +   ++ + ++GpN AGKst+l 
  gi|70607687|ref|YP_256557.1| 10 RFGKkvvLDDVSLEVR---EGYTALVGPNGAGKSTLLG 44
                                  6665333455666665...788899**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1695.24
//
Query:       gi|70607688|ref|YP_256558.1|  [L=195]
Description: hypothetical protein Saci_1962 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1264.76
//
Query:       gi|70607689|ref|YP_256559.1|  [L=109]
Description: Rieske-type (2Fe-2S) protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-14   51.9   0.1    5.8e-14   51.8   0.1    1.1  1  Rieske    Rieske [2Fe-2S] domain
    1.7e-09   37.6   0.0      2e-09   37.3   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1   6.5e-18   5.8e-14       2      87 ..       3      95 ..       2      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 6.5e-18
                                  EEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEE.TT.EEE-TTT--EEE.TTSBEEE-TTH CS
                        Rieske  2 wvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkid.ekgvleCpcHgwayd.adGkvikgPap 82
                                  w     ++ +++ ++ +vkv ++ +++ +  +g++yA++ vC+H++++l  g++d ek +++C cH +++d ++G++++ P  
  gi|70607689|ref|YP_256559.1|  3 WKRTISAKALEKAKYASVKVEDKVIFMAN-IKGKLYAMDAVCSHARCIL--GQLDeEKLTVKCFCHHAVFDlNTGNMLEPPYV 82
                                  5666778889999999**99999999999.6*****************9..44533788********************9998 PP

                                  HH........EEE CS
                        Rieske 83 rp........lat 87
                                  +p        l+t
  gi|70607689|ref|YP_256559.1| 83 APdapkeklgLKT 95
                                  8765555555555 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   2.2e-13     2e-09       2     103 ..       3     107 ..       2     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.2e-13
                                   EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEEC.TTCEEEE-TTT--EEETTT-BB CS
                      Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdk.kgelvvasPlykqkfdLktGec 81 
                                   w++ ++ ++l k + + + v++k + ++ + k+++yA+d+++        +r ++g+  +++l+v++  +  +fdL+tG++
  gi|70607689|ref|YP_256559.1|   3 WKRTISAKALEKAKYASVKVEDKVIFMANI-KGKLYAMDAVCSH------ARCILGQLdEEKLTVKCFCHHAVFDLNTGNM 76 
                                   999999****************99999999.9**********99......5899998867899****************** PP

                                   SS.........-TTSB-BEE-EEESTSEEEE CS
                      Rieske_2  82 le.........deevslkvypvrvedgkvev 103
                                   le         +e+  lk+y++r + g +ev
  gi|70607689|ref|YP_256559.1|  77 LEppyvapdapKEKLGLKTYQIRDNSGWIEV 107
                                   *********99999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 727.33
//
Query:       gi|70607690|ref|YP_256560.1|  [L=86]
Description: hypothetical protein Saci_1964 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 654.02
//
Query:       gi|70607691|ref|YP_256561.1|  [L=244]
Description: short chain dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-62  211.4   0.0    1.5e-62  211.2   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    7.6e-54  182.1   0.2    8.8e-54  181.9   0.2    1.0  1  adh_short     short chain dehydrogenase
    4.8e-14   52.7   0.1    6.5e-14   52.2   0.1    1.1  1  KR            KR domain
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.22   11.5   0.0    1.2  1  YdjC          YdjC-like protein


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.2   0.0   3.4e-66   1.5e-62       4     234 .]      11     243 ..       6     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.2 bits;  conditional E-value: 3.4e-66
                                   TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHH..SSEEEEEE---- CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v..lecDVtdeeqvealveevvekf..gklDilvnnagi 79 
                                   sgIG+ +  +la+ G+ v++ d+  + +++++++ e++++e v  l++DVtd ++++a+ +++ +++  +++Dil+nnagi
  gi|70607691|ref|YP_256561.1|  11 SGIGYTTSIKLASLGYGVIMGDIAPNIEEKAKSVREATKNEkVigLHLDVTDWDSCNAFYNKALSSLgiDHVDILINNAGI 91 
                                   8***********************************999666669*********************9888*********** PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    ++  + f++++re++d++++v ly++f+++k++++ ++k + g+i+n+ss+ + ++  +++ y+aaKa+l+++t++lA+e
  gi|70607691|ref|YP_256561.1|  92 LRD--ALFVKMTREQWDQVIKVHLYGAFNMTKQVVEgMIKYQwGRIINMSSI-SWKGNVGQANYSAAKAGLIGFTKTLAKE 169
                                   ***..*******************************8888778*********.5688889999****************** PP

                                   HGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                  adh_short_C2 159 lgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                   lg+++i+vNa+ pg+i+T++++ ++  d++++ + +r+p gr+g+pee+ ++++fL+sdeasyi+G+++ v gG++
  gi|70607691|ref|YP_256561.1| 170 LGKYNITVNAIVPGFIDTPMTAPLP--DKIKKMFLERIPAGRMGRPEEISNIIAFLVSDEASYISGAEIEVTGGFS 243
                                   ************************9..9**********************************************96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.2     2e-57   8.8e-54       2     193 ..       3     196 ..       2     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 2e-57
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHH..SSE CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkkl..gkl 78 
                                    ++vtG++sGIG+ ++ +la+ G+ v++ d+ ++ +ee ak+++e+  ++k++ +++Dvtd+++++a+++ka + l  +++
  gi|70607691|ref|YP_256561.1|   3 YAIVTGGGSGIGYTTSIKLASLGYGVIMGDIAPN-IEEKAKSVREAtkNEKVIGLHLDVTDWDSCNAFYNKALSSLgiDHV 82 
                                   58**************************777765.4444444444446799************************9888** PP

                                   SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHH CS
                     adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagl 159
                                   d+L+nNAGi +++ f +++ e+w++vi+v l g+f++t++v++ m+k ++GrI+n+sS+   +++ g+a YsA+Ka+++g+
  gi|70607691|ref|YP_256561.1|  83 DILINNAGILRDALFVKMTREQWDQVIKVHLYGAFNMTKQVVEGMIKYQWGRIINMSSISW-KGNVGQANYSAAKAGLIGF 162
                                   **********************************************************876.99***************** PP

                                   HHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                     adh_short 160 trslakelaptgirvnavaPGlvdTdmakelrek 193
                                   t++lakel +++i+vna++PG++dT+m+++l +k
  gi|70607691|ref|YP_256561.1| 163 TKTLAKELGKYNITVNAIVPGFIDTPMTAPLPDK 196
                                   ****************************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.1   1.5e-17   6.5e-14       4     160 ..       5     163 ..       3     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.5e-17
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS..S-- CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee..ppi 82 
                                   ++tGG  g+G +++  la+ g    v+++  a++ e++++ ++e ++ + +v  +++Dv+d d+ +a  +++ ++   + +
  gi|70607691|ref|YP_256561.1|   5 IVTGGGSGIGYTTSIKLASLGYG--VIMGDIAPNIEEKAKSVREATK-NEKVIGLHLDVTDWDSCNAFYNKALSSLgiDHV 82 
                                   89*******************87..6688887777777778888776.56888899************999988887999* PP

                                   -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
                            KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDal 159
                                      i+ Ag+lrd+l+ +mt e+++qv++  + Ga n+ + + +     +   ++ +SSi+   g+ gqanY+aa a l ++
  gi|70607691|ref|YP_256561.1|  83 DILINNAGILRDALFVKMTREQWDQVIKVHLYGAFNMTKQVVEgmikYQWGRIINMSSISW-KGNVGQANYSAAKAGLIGF 162
                                   *************************************999888554456666899999975.9***********9876555 PP

                                   H CS
                            KR 160 a 160
                                    
  gi|70607691|ref|YP_256561.1| 163 T 163
                                   5 PP

>> YdjC  YdjC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.9e-05      0.22      39     105 ..      36     136 ..      33     142 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                                   THHHHHH.HHHH-TT...-EEEE-S-----S..........S-TTTSGGGB-TTS-B............CCCH........ CS
                          YdjC  39 aaeeaae.lakeapa...lGlHlnltegkpl..........sppeevpsLvdedGrfas..........lrll........ 87 
                                    +ee a+ +++++++   +GlHl +t++ ++          +  ++v  L+++ G ++                       
  gi|70607691|ref|YP_256561.1|  36 NIEEKAKsVREATKNekvIGLHLDVTDWDSCnafynkalssLGIDHVDILINNAGILRDalfvkmtreqW--Dqvikvhly 114
                                   5566666333333336668********9877677765554444459999999999985555443333330..022233333 PP

                                   ....--HHHHHHHHHHHHHHHG CS
                          YdjC  88 ....asleeverEieaQierfr 105
                                       ++++ ve  i+ Q+ r++
  gi|70607691|ref|YP_256561.1| 115 gafnMTKQVVEGMIKYQWGRII 136
                                   4444444666777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1633.00
//
Query:       gi|70607692|ref|YP_256562.1|  [L=511]
Description: long-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-85  285.9   0.0    5.5e-85  285.5   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-20   74.5   0.8    1.9e-20   73.6   0.8    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    2.8e-05   23.2   0.2    6.7e-05   21.9   0.1    1.6  2  GH3            GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.5   0.0   9.1e-89   5.5e-85       8     421 ..      26     412 ..      20     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 285.5 bits;  conditional E-value: 9.1e-89
                                   STTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHH CS
                   AMP-binding   8 tpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelay 88 
                                     d+va+ +   g++++Yr+l+  vn++++ L   +++kgd+V++ ++n p++++a +ai+k G++v p+np++t++el y
  gi|70607692|ref|YP_256562.1|  26 SSDHVAVSY--FGRKISYRQLNYMVNSVSSSL---DLEKGDVVLLSMQNIPQFIIAEFAIWKRGGIVLPVNPSYTERELDY 101
                                   569****99..9********************...669******************************************* PP

                                   HHHHHTESEEE....E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEE CS
                   AMP-binding  89 iledseakvli....a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlay 163
                                   +++ds+ak++i    +  +d++  +  + e+ +  ++  ++   + +++++e ++k+    ++++     e  +++dd+a+
  gi|70607692|ref|YP_256562.1| 102 LIQDSGAKLMIasceSiSTDKIPvVRTNPETFGPIPSEYSKA-WKLKDCNEELDFKSGG--KQAN--G-HETDVRSDDIAL 176
                                   ***********7654266667776666666666555554443.3334444332332222..2222..3.23369******* PP

                                   EEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHH CS
                   AMP-binding 164 iiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkl 244
                                   ++YTSGTTGkPKGV ++h n+ a+ +++  ++ fk++e+d+ l+i+p++hi+g+i+++  ++lsG+++  + ++++   +l
  gi|70607692|ref|YP_256562.1| 177 LVYTSGTTGKPKGVPITHSNIFAS-STI-YKHWFKFSERDKNLAIAPFFHITGQIFGITSSILSGSEITTFFRFNP---DL 252
                                   ***********************9.665.35559999*******************************99997876...45 PP

                                   HHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSEC CS
                   AMP-binding 245 llelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvv 324
                                    l+++e++k tv+++v +++  +++  + ++      dlss+rl  +gg +++++l  ++++++g  ++ ++GlTEtt  +
  gi|70607692|ref|YP_256562.1| 253 TLRVVEEEKTTVTMAVATAYTSMVNaYKGEE------DLSSMRLWSSGGMAMPRSLEMKWKEKLGSWIYMAWGLTETTSPA 327
                                   69***********************665555......********99********************************** PP

                                   EE........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEE CS
                   AMP-binding 325 tv........lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlr 397
                                   t         lpl+ +  ++ s G p+ ++ev++ ++           Gellvrgp+v +gY++      e+f+  ++wl 
  gi|70607692|ref|YP_256562.1| 328 TLwpypyegdLPLDSEY-NVVSSGIPVYNTEVMVSND-----------GELLVRGPQVVSGYWRM-----EKFK--DGWLP 389
                                   888999***86655554.5568************997...........9**************88.....9998..57*** PP

                                   EEEEEEEETTSEEEEEEECCCEEE CS
                   AMP-binding 398 TGDlgrldedGyleivgRkkdlik 421
                                   TGD+g+++ +G ++i++Rkkd+i+
  gi|70607692|ref|YP_256562.1| 390 TGDIGKIE-NGWVYIIDRKKDVIN 412
                                   *******9.9************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.8   3.2e-24   1.9e-20       1      76 []     422     500 ..     422     500 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 3.2e-24
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evE++l  hpaV+e+aVv v de +Ge++ af+ l+++  + +  l++++++++r++l+py+vpk v fv+e+pkt sGK
  gi|70607692|ref|YP_256562.1| 422 EVEEVLYMHPAVEEVAVVSVVDEYRGETVGAFIKLREQfsE-SdeLKKDIIDFCRQRLAPYKVPKVVNFVKEIPKTPSGK 500
                                   8**********************************877642.246**********************************9 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.1e-08   6.7e-05      62     216 ..     160     309 ..     159     312 .. 0.82
   2 ?   -2.3   0.0      0.24   1.5e+03     393     418 ..     403     428 ..     400     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-08
                                   HHHTTCC.CTSSSS-SEEEEECCEETTEEEEEEESHHHHHHHHHH.HHHHHHHHHHHSTTSEEEEE------EE-TTSSEE CS
                           GH3  62 riakGeqnvLtsepiklfalsSGTtsgksKliPvteeslkelallvlallaallsryvekgkalylllakeerktkgglpv 142
                                   + a+G+++   s+ i l+  +SGTt gk+K +P+t+++    + + ++  +++ +r  + + a  ++ + +     +++  
  gi|70607692|ref|YP_256562.1| 160 KQANGHETDVRSDDIALLVYTSGTT-GKPKGVPITHSNIFASSTI-YKHWFKFSERDKNLAIAPFFHITGQIFGITSSILS 238
                                   578997778899*************.***********99886665.88888888777655556666777777776666666 PP

                                   EEHHHHHHTSCCHHHCCTBSS-HHHHT-S-HHHHHHHHHHHHHHTCCCEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                           GH3 143 gtastsylkseafllkklytsPkevisiedseqslychllcgLlqreevevisavfastllralrlleenweel 216
                                   g+  t +++ ++ l   l ++ +e  +++   ++ y  ++ +   +e+++ +++++ s+ + + r le +w+e+
  gi|70607692|ref|YP_256562.1| 239 GSEITTFFRFNPDL--TLRVVEEEKTTVTMAVATAYTSMVNAYKGEEDLSSMRLWS-SGGMAMPRSLEMKWKEK 309
                                   77777788877775..5678888888899999999********99**********9.999999999*9999997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.24
                                   EEECCTEEE-SSSS-CCHHHHHHHHH CS
                           GH3 393 FvgRknvvlsidgeklteeelqkave 418
                                   ++ Rk+ v+++ g k++ +e+++++ 
  gi|70607692|ref|YP_256562.1| 403 IIDRKKDVINASGFKVMPREVEEVLY 428
                                   789******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3318.12
//
Query:       gi|70607693|ref|YP_256563.1|  [L=372]
Description: mandelate racemase/muconate lactonizing enzyme [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-60  202.9   0.0    6.1e-60  202.5   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    2.3e-16   60.1   0.0      4e-16   59.3   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   0.0   6.8e-64   6.1e-60       4     219 ..     154     364 ..     151     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 6.8e-64
                                   HHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSSSTT CS
                      MR_MLE_C   4 eearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPvppe 84 
                                   ee++  + e+gf+ vK+k+gg +v+ed++r++a+re +  g+++ ++vDan  +d +tA++v+rele+l+++++EEP++  
  gi|70607693|ref|YP_256563.1| 154 EEVKG-YIEKGFTSVKIKIGGLSVQEDMKRLNAIRENF--GNSLNIAVDANNVYDFNTALKVGRELEKLGVMFFEEPIST- 230
                                   67766.5567****************************..6688**********************99***********9. PP

                                   THHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHH CS
                      MR_MLE_C  85 ddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglgla 164
                                   d ++  ael+ ra +ipia+ E + ++ ++r+l++++ vdivq+d+s+ gGite++++ +la+afg+pv+pH   gg++++
  gi|70607693|ref|YP_256563.1| 231 DLPDLSAELT-RAlDIPIAGYETASTLFEYRDLITKRSVDIVQVDASWNGGITEMVRIGNLARAFGLPVVPHYSAGGISFV 310
                                   78********.888**********************************************************9659***** PP

                                   HHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                      MR_MLE_C 165 aslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveldee 219
                                   aslh a  i+ + i ey+l  ++l+e l+ e++++e+G +  pd+pGlG+ lde+
  gi|70607693|ref|YP_256563.1| 311 ASLHSALVID-SPIIEYHLRYNPLRESLAGEAIRYENGEFLPPDKPGLGISLDER 364
                                   *********5.777888888878******************************86 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   4.5e-20     4e-16      26     117 .]      32     128 ..      16     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 4.5e-20
                                   EEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS......CHHHHHHHHHHH CS
                      MR_MLE_N  26 qslvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg......nmsAkaaidmAl 100
                                     +++v + ts+G  G gea ++g     +   +++   pll+g++ +ni +l++++++  +       + s  +++d+Al
  gi|70607693|ref|YP_256563.1|  32 MDVAVVSVVTSNGEIGYGEAIAYG-ILDVVSTTIEKIYRPLLLGEESSNILGLWNKMYKTTFRlgrrgvTISSLSGVDIAL 111
                                   56899*******************.9999999*****************************9999****9*********** PP

                                   HHHHHHHTTSBHHHHTT CS
                      MR_MLE_N 101 wDlkakalnlpladLlG 117
                                   wDl++k l+ p+++LlG
  gi|70607693|ref|YP_256563.1| 112 WDLLGKELGSPVYKLLG 128
                                   ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2542.04
//
Query:       gi|70607694|ref|YP_256564.1|  [L=386]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-05   22.5   0.2    0.00025   20.7   0.0    1.9  2  Thiolase_C  Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.15   2.6e+03      27      43 ..      24      40 ..      21      43 .. 0.86
   2 !   20.7   0.0   1.4e-08   0.00025      29     102 ..     262     353 ..     251     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.15
                                  HHHHHHHHHT--GGGES CS
                    Thiolase_C 27 aikkvlkkagltvedid 43
                                   ++k+l+ a ++++did
  gi|70607694|ref|YP_256564.1| 24 TVSKALDMATVDLKDID 40
                                  57899**********99 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHH CS
                    Thiolase_C  29 kkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivv 91 
                                   ++v + +g+++e id+f + + F+  ++  +++++l +                    vN  GG++ +G P  +sG  i+ 
  gi|70607694|ref|YP_256564.1| 262 PAVESSKGVNLERIDAFQLYDSFTITVMLQMEDIGLTKkgkggefvertdityqgeVPVNTGGGSLNVGQPAFMSGGVILE 342
                                   5555679******************************9****************9888**********************9 PP

                                   HHHHHHHHCTT CS
                    Thiolase_C  92 tllselkkegg 102
                                    ++ +l++  +
  gi|70607694|ref|YP_256564.1| 343 EAILQLNNMAT 353
                                   99988887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2793.22
//
Query:       gi|70607695|ref|YP_256565.1|  [L=114]
Description: hypothetical protein Saci_1969 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-11   41.5   2.1    1.2e-10   41.1   2.1    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    1.2e-05   25.2   0.0    1.7e-05   24.7   0.0    1.3  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    0.00047   20.2   0.1    0.00061   19.8   0.1    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.001   18.8   0.2     0.0011   18.6   0.2    1.1  1  TackOD1         Thaumarchaeal output domain 1
     0.0022   18.1   2.1       0.11   12.6   0.0    2.5  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
  ------ inclusion threshold ------
      0.015   16.0   1.9      0.024   15.4   1.9    1.3  1  zinc_ribbon_15  zinc-ribbon family
      0.017   15.1   0.9      0.021   14.7   0.9    1.1  1  FdhE            Protein involved in formate dehydrogenase for
      0.021   14.1   0.3       0.47    9.8   0.1    2.3  2  zf-TFIIB        Transcription factor zinc-finger
      0.022   14.7   2.3       0.19   11.7   0.0    2.5  2  zinc_ribbon_4   zinc-ribbon domain
      0.079   12.8   2.8        2.9    7.8   0.2    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.32   11.2   2.2       0.94    9.7   0.0    2.2  2  DUF2387         Probable metal-binding protein (DUF2387)
       0.42   10.2   3.1        3.4    7.3   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
        1.1    9.1   5.8         12    5.7   0.3    2.4  2  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   2.1   8.4e-14   1.2e-10       5      37 .]      14      46 ..      11      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 8.4e-14
                       DUF35_N  5 aegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                  +e +L + +C+ CG+ +++Pr +Cp+C+s++le
  gi|70607695|ref|YP_256565.1| 14 REEKLPYLKCTRCGHSFYYPRDYCPKCRSRELE 46
                                  7889999************************98 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.7e-05       4      64 ..      50     101 ..      47     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                                   E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                 OB_aCoA_assoc   4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                   + g G v+s t    ++ ++++ + + +g+VeL+eg r+ +++  +     +iG++Vr+ f
  gi|70607695|ref|YP_256565.1|  50 SRGIGSVFSVT----KF-RDRDNKEVYYGIVELEEGFRLYTNFLVPV----EIGDKVRVKF 101
                                   56789999999....44.556688899*****************664....5*******98 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   4.4e-07   0.00061      65     104 ..      15      52 ..       2      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                                   EEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSS CS
                          HypA  65 eevpvkvrCreCgkefeleekalrCpkCgsadveivsGee 104
                                   ee+   ++C++Cg++f   ++   CpkC s+++e+++ ++
  gi|70607695|ref|YP_256565.1|  15 EEKLPYLKCTRCGHSFYYPRD--YCPKCRSRELEVKESRG 52 
                                   56667799********97755..6**********998775 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   8.2e-07    0.0011      74     103 ..      21      50 ..       2      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.2e-07
                       TackOD1  74 rlCpsCksghlnvrevCpkCkSidieeqel 103
                                     C++C ++    r++CpkC+S ++e +e+
  gi|70607695|ref|YP_256565.1|  21 LKCTRCGHSFYYPRDYCPKCRSRELEVKES 50 
                                   68**********************998875 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.1     0.034        48      36      47 ..      21      32 ..       7      35 .. 0.75
   2 !   12.6   0.0   8.3e-05      0.11       2      31 ..      37      68 ..      36      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.034
                zinc_ribbon_13 36 vsCknCgYtelY 47
                                    C++Cg++  Y
  gi|70607695|ref|YP_256565.1| 21 LKCTRCGHSFYY 32
                                  679999987555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.3e-05
                zinc_ribbon_13  2 CpKCgnteaevkevaatGsgls..kifdvqnk 31
                                  CpKC ++e evke +  Gs +s  k+ d +nk
  gi|70607695|ref|YP_256565.1| 37 CPKCRSRELEVKESRGIGSVFSvtKFRDRDNK 68
                                  *******************9974466666665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.9   1.7e-05     0.024      48      85 ..       3      40 ..       1      41 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                zinc_ribbon_15 48 easkelgkeiekkessekkeCknCgkeveeefkyCpkC 85
                                  e+ k++ +e+ ++e+  + +C +Cg++     +yCpkC
  gi|70607695|ref|YP_256565.1|  3 EEIKKKYQEMFREEKLPYLKCTRCGHSFYYPRDYCPKC 40
                                  55666777777888888********************* PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   1.5e-05     0.021     189     217 ..      15      43 ..      10      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                                   ---EEEEEETTT--EEE--TTS-TTT--- CS
                          FdhE 189 aeglRylhCslCeteWhvvRvkCsnCeet 217
                                   +e+l yl+C+ C + + + R  C +C + 
  gi|70607695|ref|YP_256565.1|  15 EEKLPYLKCTRCGHSFYYPRDYCPKCRSR 43 
                                   57788*********************975 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.08   1.1e+02       1       8 [.      22      29 ..      11      30 .. 0.80
   2 ?    9.8   0.1   0.00034      0.47       1      16 [.      36      52 ..      35      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.08
                      zf-TFIIB  1 kCPkCqde 8 
                                  kC +C+++
  gi|70607695|ref|YP_256565.1| 22 KCTRCGHS 29
                                  67777765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00034
                      zf-TFIIB  1 kCPkCqd.eleesergg 16
                                  +CPkC++ ele  e++g
  gi|70607695|ref|YP_256565.1| 36 YCPKCRSrELEVKESRG 52
                                  79999987898666555 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.19      26      35 ..      21      30 ..      10      31 .. 0.86
   2 ?    2.0   0.6      0.14     2e+02       5       9 ..      37      41 ..      36      43 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                 zinc_ribbon_4 26 vrCskCghvF 35
                                  ++C++Cgh+F
  gi|70607695|ref|YP_256565.1| 21 LKCTRCGHSF 30
                                  79*******9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
                 zinc_ribbon_4  5 CpsCk 9 
                                  Cp+C 
  gi|70607695|ref|YP_256565.1| 37 CPKCR 41
                                  66665 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0021       2.9      28      38 ..      20      30 ..      15      31 .. 0.80
   2 ?    5.1   0.3     0.015        20       3      10 ..      37      44 ..      36      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                       TFIIS_C 28 fykCtkCghrW 38
                                  + kCt Cgh +
  gi|70607695|ref|YP_256565.1| 20 YLKCTRCGHSF 30
                                  789*****987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                       TFIIS_C  3 CpkCgsre 10
                                  CpkC+sre
  gi|70607695|ref|YP_256565.1| 37 CPKCRSRE 44
                                  ******98 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00068      0.94      21      39 ..      11      29 ..       6      35 .. 0.92
   2 ?    0.6   0.5      0.47   6.5e+02      11      16 ..      37      42 ..      34      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00068
                       DUF2387 21 rmweedeveyrECvsCgft 39
                                   m++e++ +y  C+ Cg++
  gi|70607695|ref|YP_256565.1| 11 EMFREEKLPYLKCTRCGHS 29
                                  59***************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.47
                       DUF2387 11 CPrCse 16
                                  CP+C +
  gi|70607695|ref|YP_256565.1| 37 CPKCRS 42
                                  ****87 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.042        57       2      10 ..      22      30 ..      21      36 .. 0.68
   2 ?    7.3   0.1    0.0025       3.4       3      18 ..      37      52 ..      35      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.042
                                  EETTTTCEE CS
                  TF_Zn_Ribbon  2 kCPnCgstn 10
                                  kC  Cg+++
  gi|70607695|ref|YP_256565.1| 22 KCTRCGHSF 30
                                  788888876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
                                  ETTTTCEECHEETSTT CS
                  TF_Zn_Ribbon  3 CPnCgstnlveDperg 18
                                  CP+C s++l++ ++rg
  gi|70607695|ref|YP_256565.1| 37 CPKCRSRELEVKESRG 52
                                  ********99988876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0      0.01        14       1       7 [.      22      28 ..      22      30 .. 0.69
   2 ?    5.7   0.3     0.009        12      15      20 ..      36      41 ..      35      43 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
                 zinc_ribbon_2  1 fCpnCGa 7 
                                  +C++CG+
  gi|70607695|ref|YP_256565.1| 22 KCTRCGH 28
                                  6777775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.009
                 zinc_ribbon_2 15 FCpyCG 20
                                  +Cp+C+
  gi|70607695|ref|YP_256565.1| 36 YCPKCR 41
                                  677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 917.86
//
Query:       gi|70607696|ref|YP_256566.1|  [L=80]
Description: hypothetical protein Saci_1970 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-15   54.1   0.4    1.5e-14   53.5   0.4    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    1.3e-05   25.5   0.2    1.5e-05   25.3   0.2    1.3  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.066   12.8   0.0      0.072   12.7   0.0    1.0  1  PQQ_2           PQQ-like domain


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.4   2.6e-18   1.5e-14       2      43 ..       6      47 ..       5      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.6e-18
                                  EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHH CS
                MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplks 43
                                  +v+++++++iP+ +r++lgir+Gd+++++++gdkiil+++k 
  gi|70607696|ref|YP_256566.1|  6 RVTRNYRITIPATIRQKLGIRVGDKLIVYTEGDKIILVKKKG 47
                                  89*******************************999999985 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   2.6e-09   1.5e-05       1      43 [.       4      45 ..       4      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.6e-09
                PrlF_antitoxin  1 estltergqttiPasvRkaLklkkgrdkiaytilddgkvvisr 43
                                  es++t+ +  tiPa++R+ L++  g+  i+yt   d+ + +++
  gi|70607696|ref|YP_256566.1|  4 ESRVTRNYRITIPATIRQKLGIRVGDKLIVYTE-GDKIILVKK 45
                                  8**********************9877777763.334444444 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.072     108     150 ..      21      65 ..      13      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                         PQQ_2 108 epaelrssaspava..gdtvvvgessgklvaldpkdGkvlWerel 150
                                   +++ +r+ ++ +v+  gd+++++  +g+lv l++k G++  ++e+
  gi|70607696|ref|YP_256566.1|  21 QKLGIRVGDKLIVYteGDKIILVKKKGDLVSLNLKLGRKFTDEEV 65 
                                   67789999999999************************9888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 555.58
//
Query:       gi|70607697|ref|YP_256567.1|  [L=446]
Description: transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-24   84.9  56.5    6.5e-24   84.4  56.5    1.2  1  AA_permease    Amino acid permease
    5.1e-14   51.9  59.8      7e-14   51.5  59.7    1.3  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4  56.5   7.2e-28   6.5e-24       2     429 ..      27     422 ..      26     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 7.2e-28
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   +++ ++gg  +   ++  gvv+    +l + +a++l+++ ++  ++s++e++  + k gg+ytya  +l+++lGf +G++y
  gi|70607697|ref|YP_256567.1|  27 IVFLSIGGQSPFLSILTYGVVALLYAGLFGPIAIILGTLLVLVNGMSVYELSKRFTKEGGYYTYAFYSLSKRLGFETGWMY 107
                                   7888999988866666666655555555889************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillag 163
                                    +++ t+ a  +++ ++++  +  +  ++  w++ + ++ +  ++ ++g+k + +  ++++l+ ii++ a+ +++i  ++g
  gi|70607697|ref|YP_256567.1| 108 ILYSTTYGAGYVFGTAYVLYHV--L-NIN-PWIVTLGVMSISALLGILGIKISTKYAIFATLLEIIMMTALAVLLI-QSTG 183
                                   ******9999999999999887..4.455.59999899999999999999*9999777777777777666666663.3333 PP

                   AA_permease 164 gkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvirit 244
                                                    +++n ++ +       ++++ ++++ + +   tG++++a i+gE+k+ +  i kai+ v++  +
  gi|70607697|ref|YP_256567.1| 184 F----------------HLYNPFSLK------LNLSQLAIAILFGSSIPTGYGSIAPISGETKNARNVISKAIITVILVGG 242
                                   3................334445555......557777777777888889***************************9888 PP

                   AA_permease 245 i.....fYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslak 320
                                   +     +Y +++++  ++++ n+ ++l+          ++   +g+  l +++ a i   +++ ++++l+++sR+++++a 
  gi|70607697|ref|YP_256567.1| 243 LlaafdVYAIGTYVSYFHLSMNNVDILT----------LIRDRLGLLTLVFVLFASINDGIVG-SLAFLTATSRTVFAMAS 312
                                   7222224555555555555555555555..........7788899999988887777777666.579************** PP

                   AA_permease 321 dglaPkvlkkvskrgvPlraillsmiisllal.llaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrs 400
                                   ++ +Pk+++k++ ++ P+ra+lls +i+++++ +  ++  + +++f  +++++ +++l+v+l++++s++r+  ++ ++++ 
  gi|70607697|ref|YP_256567.1| 313 SNFLPKFFAKFESYKGPVRAVLLSVLIYFAIIsVGLYFLRSIFTAFILISSVALFANLFVHLSANFSLIRISIKKVLKRKI 393
                                   *****************************99967777777777888888888899**************998887777776 PP

                   AA_permease 401 ieelgfkaallplgvilvlaaliiillil 429
                                      +g+ +al+     +  +a +  ++++
  gi|70607697|ref|YP_256567.1| 394 QLIVGVASALYTVYELIYSIAGSVPIVVY 422
                                   66788888777554444444443333333 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5  59.7   7.9e-18     7e-14       1     420 [.      22     430 ..      22     439 .. 0.69

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 7.9e-18
                 AA_permease_2   1 lsllsafalvigsv.....igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                   ls+ + ++l+ig       i ++++v+  ++++g    + +++++l++ l  +    Els ++ ++gG y+y+ +  +k++
  gi|70607697|ref|YP_256567.1|  22 LSFTDIVFLSIGGQspflsILTYGVVA--LLYAGLFGPIAIILGTLLV-LVNGMSVYELSKRFTKEGGYYTYAFYSLSKRL 99 
                                   577777888888766776666777777..7777777777778888887.67888889************************ PP

                 AA_permease_2  77 aflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpli 157
                                   +f ++w++ +       ++ + +++y l+ +   l+ n+w++ l   +++ + al+ i+gik+s k++ + ++l i+ +  
  gi|70607697|ref|YP_256567.1| 100 GFETGWMYILYSTT-YGAGYVFGTAYVLYHV---LNINPWIVTL---GVMSISALLGILGIKISTKYAIFATLLEII-M-- 170
                                   ********775555.5456666666666644...4567777776...899999***********************5.4.. PP

                 AA_permease_2 158 iliilglitvdgggfsslstetdtffpn...gwpgvllgllivlwsfdGfesaanvseevkk.kd.vpkaifigllivlvl 233
                                    + +l++++++ +gf+       + f+     +++ ++ l+      +G+ s+a +s e k+ ++ ++kai+ ++l+ ++l
  gi|70607697|ref|YP_256567.1| 171 -MTALAVLLIQSTGFH-----LYNPFSLklnLSQLAIAILF-GSSIPTGYGSIAPISGETKNaRNvISKAIITVILVGGLL 244
                                   .455555666666665.....33333222125555555554.555668**************9876899998888877777 PP

                 AA_permease_2 234 yll..vniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilial..sllgaintavigssrvlealardgvlPr 310
                                     +  ++i  +      +++n+    ++++l  +++g   ++ ++v+++ +  + + + +++++++sr+++a+a  ++lP+
  gi|70607697|ref|YP_256567.1| 245 AAFdvYAIGTYVSYFHLSMNNV----DILTLIRDRLG--LLTLVFVLFASIndG-IVGSLAFLTATSRTVFAMASSNFLPK 318
                                   7774322222222223444443....4689999**99..777777766666644.4466789999**************** PP

                 AA_permease_2 311 ffakvnkfgspiraiiltaivslillllfl..las..saaynfllsvsslgliisyllliigalilrkkrphlkrpgkilv 387
                                   ffak   ++ p+ra+ l++++ ++++ + l  l     +a+ +++sv+ ++++++ l + ++++ + +k ++lkr+   +v
  gi|70607697|ref|YP_256567.1| 319 FFAKFESYKGPVRAVLLSVLIYFAIISVGLyfL-RsiFTAFILISSVALFANLFVHLSANFSLIRISIK-KVLKRKIQLIV 397
                                   ******************999855432222221.12334555555555555555555555555555555.66666666778 PP

                 AA_permease_2 388 aiigalfllfllvalffppkgpatqssliytii 420
                                   +  +al++++ l+  +  ++ ++++  + + ii
  gi|70607697|ref|YP_256567.1| 398 GVASALYTVYELIYSIAGSVPIVVYVFMSWIII 430
                                   888888887777666544444455544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3280.94
//
Query:       gi|70607698|ref|YP_256568.1|  [L=748]
Description: hypothetical protein Saci_1973 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-65  219.5  10.7    8.8e-33  113.6   1.1    2.4  2  MMPL           MMPL family
  ------ inclusion threshold ------
      0.039   14.4   0.0       0.27   11.7   0.0    2.5  1  F1F0-ATPsyn_F  Mitochondrial F1-F0 ATP synthase subunit F of 
        3.1    8.4  16.3      0.049   14.2   2.3    3.7  3  DUF3054        Protein of unknown function (DUF3054)


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   1.1   1.5e-36   8.8e-33       9     329 ..      46     405 ..      39     409 .. 0.80
   2 !  110.5   2.6   1.3e-35     8e-32       4     302 ..     438     733 ..     435     746 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 1.5e-36
                          MMPL   9 svkamdrleaafpe.eadsdkiivvvlaegdealgsaaaeaavdelvdelkkdtkhvgevsdfls................ 72 
                                   s ++   +++ +++ + + d++ivvv+   ++  ++ +a++ +  +   l+k+ + + +v++++s                
  gi|70607698|ref|YP_256568.1|  46 SNSESAIVNKILNGtSYNNDTLIVVVK---ENPFTPYSANQSLSFQNSTLSKNIPYLSSVQSPFSdyinfltavlsgvyhn 123
                                   555566677778885555555566655...8999999999999999999************99656666666666666666 PP

                          MMPL  73 ...................dpd.vaaafvSkDgkaaralvtlegdp......gsteadesvaairaaveearpleglkvev 127
                                                       p  +++  vS+D+++  + +t++ ++      g+t +++++  +++++++     g ++++
  gi|70607698|ref|YP_256568.1| 124 ttlahqysvkyveqnglkgAPSfITSRYVSPDNTTFLLFLTFNKSSgfilpnGETPSQQAYPVVKDIAQKYF---GDNASL 201
                                   666666666666666665566699******************976522222268889999999999999999...99**** PP

                          MMPL 128 tGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgll 207
                                   tG +a++ ++++++++++   ++v +++++++  i++rS    l+ ll + v   + +g  +++l  +l+ ++  +v   l
  gi|70607698|ref|YP_256568.1| 202 TGEGAIAYETQQITSKNAFAFGLVFIILAIAV-GITLRSYKGSLVSLLFISVT--TLIGYfAIFLVGALVTNVDFVVNYTL 279
                                   *********99999999999888877666655.68999999999999876555..5555544678888888888888889* PP

                          MMPL 208 vvlliavGtDYallLvsRyreelaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdv 288
                                   +++l++v tDY +++++R+r+el++g++ ++a+  a  ++g++v+++Gltv i++l  +++ +p + + G+++  +v++++
  gi|70607698|ref|YP_256568.1| 280 TAVLVGVTTDYVVFILARFRQELREGREDKAALEVASSKAGRAVLISGLTVGISLL--SFSLVPNFLSWGLVLFSAVVIST 358
                                   ******************************************************95..667789***************** PP

                          MMPL 289 livlTllPAllvllGraa.la.....kprrkrkkrwWrrlgrlvvrr 329
                                   +++lTllP++l+++G+++  +         ++++ w+ r++ l+vrr
  gi|70607698|ref|YP_256568.1| 359 ALILTLLPSILAITGKRVfTKgglntVTTENLERSWFYRVSDLSVRR 405
                                   *****************744466554333334446668888887776 PP

  == domain 2  score: 110.5 bits;  conditional E-value: 1.3e-35
                          MMPL   4 padaesvkamdrleaafpeeadsdkiivvvlaegdealgs..aaaeaavdelvdelkkdtkhvgevsdflsdpd.....va 77 
                                   p+  +svka++ +e +f    +  +iiv+++ +g++ l+s  +a ++++ ++++e+   t+++ +v  +  + +     ++
  gi|70607698|ref|YP_256568.1| 438 PSSLPSVKALNFIEDKFGA-NELYPIIVLMKVNGSSDLNSnnTALKNQIIATAKEI-LSTPGITKVYGPYVNGQeiannTN 516
                                   66779999*********99.9999**999997777777651156678888888888.677778888888433333544444 PP

                          MMPL  78 aafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilv 158
                                     +    g+ + ++ ++e dp+s+ a+++v+a+r+  +           v+G +  + d++  +++d + +ev++ + +++
  gi|70607698|ref|YP_256568.1| 517 ISAFVVGGSYLLFTAYTEYDPFSSNAIHTVNALRQYHDL---------LVGGLTSSVIDQQAETTQDFTELEVLITLFVAL 588
                                   455556899999999999999999999999988876544.........46******************************* PP

                          MMPL 159 iLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedree 238
                                   i  i ++S   +l+ +  v++s+  a gl  li +++l ++l   ++ +l+v+l++ G DY+++++sR  e ++++ ++ +
  gi|70607698|ref|YP_256568.1| 589 IIGISFKSWKFPLISISGVLISITWATGLlYLISRFVLNQALIYLIPVILFVILMSLGNDYTVFIISRVVEDMQEHGEK-R 668
                                   *****************************9999****************************************999888.6 PP

                          MMPL 239 aviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvll 302
                                   +++ a+ +tg vvt  Gl++a+++ +L+++ +++l+q+G+a  +++l+d+++++T+  PA+l++l
  gi|70607698|ref|YP_256568.1| 669 GIQLAISRTGIVVTSLGLILAASLGALALIPIGFLEQLGIAFIISLLIDTFVIRTIYfPAMLSIL 733
                                   *************************************************************9986 PP

>> F1F0-ATPsyn_F  Mitochondrial F1-F0 ATP synthase subunit F of fungi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.5e-05      0.27      39      68 ..     173     201 ..     170     214 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                 F1F0-ATPsyn_F  39 LPkGpapkakakgllgrykakyfdgknasg 68 
                                   LP+G+ p+++a  +++ + +kyf g+nas 
  gi|70607698|ref|YP_256568.1| 173 LPNGETPSQQAYPVVKDIAQKYF-GDNASL 201
                                   9**********************.****95 PP

>> DUF3054  Protein of unknown function (DUF3054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.3   8.2e-06     0.049      50     105 ..     209     265 ..     199     269 .. 0.79
   2 ?    0.9   1.8      0.11   6.3e+02      31     103 ..     278     360 ..     266     365 .. 0.63
   3 ?   -0.1   0.2      0.22   1.3e+03      58      95 ..     573     610 ..     540     626 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.2e-06
                       DUF3054  50 yearaaskaaralpagvvvwlvavvvGlllRallkggvalsFvlValvvl..avlLlg 105
                                   ye+++ +  ++a+  g+v  ++a++vG++lR++ ++ v+l F+ V+++++  a++L+g
  gi|70607698|ref|YP_256568.1| 209 YETQQIT-SKNAFAFGLVFIILAIAVGITLRSYKGSLVSLLFISVTTLIGyfAIFLVG 265
                                   4333333.6899999*******************************998622556655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                       DUF3054  31 tawPFlvglavgWllvapl.yearaas.k......aaralpagvvvwlvavvvGlllR..allkggvalsFvlValvvlav 101
                                   t++  lvg++  ++++    +++ +++ +        +  +ag +v++++++vG+ l   +l+ + +++  vl ++vv   
  gi|70607698|ref|YP_256568.1| 278 TLTAVLVGVTTDYVVFILArFRQELREgRedkaalEVASSKAGRAVLISGLTVGISLLsfSLVPNFLSWGLVLFSAVVIST 358
                                   666778888887777554453222222223344444456668999999999999988855666666667766666666555 PP

                       DUF3054 102 lL 103
                                   +L
  gi|70607698|ref|YP_256568.1| 359 AL 360
                                   54 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.22
                       DUF3054  58 aaralpagvvvwlvavvvGlllRallkggvalsFvlVa 95 
                                   +  +  +++++++va+++G+ ++++    +++s vl++
  gi|70607698|ref|YP_256568.1| 573 QDFTELEVLITLFVALIIGISFKSWKFPLISISGVLIS 610
                                   33444577888999999999988776555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 5119.23
//
Query:       gi|70607699|ref|YP_256569.1|  [L=301]
Description: hypothetical protein Saci_1974 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2365.22
//
Query:       gi|70607700|ref|YP_256570.1|  [L=286]
Description: modification methylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-42  144.3   0.1    6.1e-42  143.9   0.1    1.1  1  N6_N4_Mtase  DNA methylase
    0.00039   20.2   0.0      0.017   14.8   0.0    2.3  2  UPF0020      Putative RNA methylase family UPF0020
     0.0042   17.0   0.9      0.027   14.4   0.2    2.4  2  SUV3_C       Mitochondrial degradasome RNA helicase subunit C


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.1     1e-45   6.1e-42       2     229 ..      21     243 ..      20     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1e-45
                                   EEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT....HHHHHHHHHTT.-EE CS
                   N6_N4_Mtase   2 dlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk....elkaladeifg.gff 77 
                                    l++t+pPY +       +  + + syeeyl++l+ v ke++rvL d+ +++   +d +i+      +  l++   + gf+
  gi|70607700|ref|YP_256570.1|  21 GLVLTSPPYYNAPF----DFPDLFPSYEEYLNLLRDVGKELYRVLDDGRVAVFVTSDVRIEGvlypIVADLIRIMTDlGFK 97 
                                   589******99987....899****************************************9***95555555555556** PP

                                   EEEEEEEEESSSTTTSTCC.............S-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC- CS
                   N6_N4_Mtase  78 llnvivwkkpnsmpesnkd.............rltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkg 145
                                   ++++i+wkkp+++ + +++             + ++ +E i+vf+k++k+          ++++ek+k++ ++     +k+
  gi|70607700|ref|YP_256570.1|  98 YQERIIWKKPEGYIRISRRsgvliqhpyplyyYPDNVYEDIVVFKKPGKF---------HTTNQEKSKIDVNK----FQKE 165
                                   **********98888888888899999999889999*************9.........77777777777777....8899 PP

                                   B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHH CS
                   N6_N4_Mtase 146 kkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyv 226
                                   k++ ++W+++++ +n+k sk      ++a++P++l+ r++ l++  gd+vlDpFaG+GtT+ +a+ l+r+++G+ei+ e +
  gi|70607700|ref|YP_256570.1| 166 KWYLNVWEITNVLPNNKYSK------FTAPFPEELANRIVTLYSYVGDTVLDPFAGTGTTLYVARILSRNAVGYEIDLELK 240
                                   99****************98......***************************************************9998 PP

                                   HHH CS
                   N6_N4_Mtase 227 ela 229
                                   e +
  gi|70607700|ref|YP_256570.1| 241 EVI 243
                                   866 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.01        61     111     165 ..       8      69 ..       1      80 [. 0.61
   2 !   14.8   0.0   2.8e-06     0.017       9      54 ..     187     231 ..     179     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.01
                                   -GGG--.STTS---EEEE-------.......---HHHHHHHHHHHHHHHHHH-TT..-EEEE CS
                       UPF0020 111 daakLr.lkegevdvivtnpPYGer.......lgskkalekLYseflrelkrvlrgggrlvll 165
                                   d +++   +++++++++t pPY ++         s ++  +L + +++el rvl+  gr ++ 
  gi|70607700|ref|YP_256570.1|   8 DSRNMSeVEDKSIGLVLTSPPYYNApfdfpdlFPSYEEYLNLLRDVGKELYRVLDD-GRVAVF 69 
                                   55556543455999999999997763222222445666677777777777777777.444333 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.8e-06
                                   --SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT-- CS
                       UPF0020   9 papLketLAaalvrlagwkpgepllDPmCGsGtilIEaallgania 54 
                                    ap  e+LA  +v+l  +  g++ lDP+ G+Gt l  a +l++n++
  gi|70607700|ref|YP_256570.1| 187 TAPFPEELANRIVTLYSY-VGDTVLDPFAGTGTTLYVARILSRNAV 231
                                   599999********9876.788999********9988877777776 PP

>> SUV3_C  Mitochondrial degradasome RNA helicase subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13   7.8e+02      21      32 ..      36      47 ..      33      62 .. 0.72
   2 !   14.4   0.2   4.5e-06     0.027      23      48 .]     258     283 ..     255     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                  -------HHHHH CS
                        SUV3_C 21 fpevFpdrelae 32
                                  fp+ Fp+ e+  
  gi|70607700|ref|YP_256570.1| 36 FPDLFPSYEEYL 47
                                  99***9988755 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.5e-06
                                   -----HHHHHHHHHHHHHHHHHHHHT CS
                        SUV3_C  23 evFpdrelaeelkkeveekIeeaLer 48 
                                    vF++r+ a  l++++ ekI+e+Le+
  gi|70607700|ref|YP_256570.1| 258 VVFVERSDAKRLRTKLREKINEKLEK 283
                                   57**********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1832.33
//
Query:       gi|70607701|ref|YP_256571.1|  [L=371]
Description: hypothetical protein Saci_1976 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.032   14.8   0.3         13    6.4   0.2    2.4  2  Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
      0.057   13.4   0.0      0.095   12.6   0.0    1.3  1  DUF2677    Protein of unknown function (DUF2677)
       0.18   12.1   3.1        0.7   10.2   2.8    2.1  2  DUF2524    Protein of unknown function (DUF2524)


Domain annotation for each model (and alignments):
>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0037        22      21      74 ..      77     131 ..      68     136 .. 0.87
   2 ?    6.4   0.2    0.0022        13      45      70 ..     337     362 ..     332     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0037
                                   TTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEE CS
                     Pyr_redox  21 lgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgve 74 
                                    gkkVt++  ++      D+++ ++ + +l  + g+ v+l+  ve+ ++s+ +++
  gi|70607701|ref|YP_256571.1|  77 SGKKVTIIPVMKDEGEEGDRDFIQWDTISLMSLlGVYVILGYYVEASKKSQGKIT 131
                                   589*****9999999999*******999998888***************998844 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0022
                                   HHHHHHHHTTEEEECSEEEEEEEEET CS
                     Pyr_redox  45 ilqeklekngievllntkveeiegse 70 
                                   +l ++ ++n+ +++ln+kv  ++gse
  gi|70607701|ref|YP_256571.1| 337 ELLREAKENNLKIILNQKVIDVKGSE 362
                                   678899****************9986 PP

>> DUF2677  Protein of unknown function (DUF2677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.095      35      81 ..      68     115 ..      61     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                       DUF2677  35 qrlwweiqyssgrltrvlvfhdegeegd.dvhltdthhctscthpyvi 81 
                                    r++  +q+s  ++t + v++degeegd d    dt    s    yvi
  gi|70607701|ref|YP_256571.1|  68 ARVYNTLQFSGKKVTIIPVMKDEGEEGDrDFIQWDTISLMSLLGVYVI 115
                                   588999*********************944445688887777777776 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.8   0.00012       0.7      10      68 ..     161     224 ..     154     231 .. 0.82
   2 ?   -2.2   0.0      0.91   5.4e+03      37      50 ..     302     315 ..     300     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                       DUF2524  10 llqkceqaieeaeeqfeeakrqehyndeeYteAqlkLEeavneLeklaksan.....dqQreqL 68 
                                    ++k+ + ++ a e +e+ ++  +   ++ ++A++k Ee++++Lek+++++      +qQre L
  gi|70607701|ref|YP_256571.1| 161 QVNKIGDLMNMAIEAYERISQRLNVRLKDIQSAKNKAEEVYRDLEKFKNHSRtqsekAQQREVL 224
                                   578999999***********99*************************98776111114566655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.91
                       DUF2524  37 eeYteAqlkLEeav 50 
                                   +eY +A  ++E+++
  gi|70607701|ref|YP_256571.1| 302 YEYGDAYIRIEHIN 315
                                   6999***9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1437  (0.0801495); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2629.39
//
Query:       gi|70607702|ref|YP_256572.1|  [L=143]
Description: hypothetical protein Saci_1977 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-28   99.8   0.8    1.4e-28   99.4   0.8    1.1  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.8   7.9e-33   1.4e-28       1     117 [.       6     133 ..       6     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 7.9e-33
                                   HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT............... CS
                          HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke............ 69 
                                   +e+++rr+ ++l++A+++l++g+yd+a+fh++qa++++ KA+++++ g+    h++r Ll++l k+l+e            
  gi|70607702|ref|YP_256572.1|   6 VERLKRRGLRFLDNAKDDLKNGYYDIAIFHVEQAVQLYTKAVIFELFGKEYTIHGIRGLLSYLTKLLEEngykelsrrive 86 
                                   689****************************************************************99**9999999999 PP

                                   .-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                          HEPN  70 .seelreeleeLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                     +e+r++l  +e+ayi srY+d ++   + +ae+++++ae++++l++e
  gi|70607702|ref|YP_256572.1|  87 fTKENRDTLLGIEEAYISSRYEDIDF--GRYEAESSVQTAESLIKLLDE 133
                                   999999999*****************..9***************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1010.87
//
Query:       gi|70607703|ref|YP_256573.1|  [L=114]
Description: hypothetical protein Saci_1978 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-07   32.2   0.0    1.2e-07   31.9   0.0    1.2  1  NTP_transf_2   Nucleotidyltransferase domain
    4.7e-07   29.8   0.0    6.7e-07   29.3   0.0    1.3  1  Polbeta        Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.076   12.6   0.2       0.13   11.9   0.2    1.3  1  Kelch_1        Kelch motif
       0.08   12.8   0.0      0.086   12.7   0.0    1.1  1  Adenyl_cycl_N  Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.8e-11   1.2e-07       5      69 ..      23      77 ..      19     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.8e-11
                                  HHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTE CS
                  NTP_transf_2  5 leelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellgl 69
                                  +++ k+l ++ kv++fG +a G  +  SDiD+lvv++              + ei + +  ++++
  gi|70607703|ref|YP_256573.1| 23 AKATKDLCSNCKVYVFGGVAEGRVTVLSDIDILVVSEGKLT----------DTEIKEIWINIMKR 77
                                  56666666799***************************943..........44444444444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.5e-10   6.7e-07      15      72 ..      34      88 ..      20     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.5e-10
                                  STTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT.TS CS
                       Polbeta 15 laylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln.ea 72
                                   +y+FG +a+g+ +  SDiD+ v+ + kl+  e  e++ +++++     +D+  l  +a
  gi|70607703|ref|YP_256573.1| 34 KVYVFGGVAEGRVTVLSDIDILVVSEGKLTDTEIKEIWINIMKR----AMDVYSLPfDA 88
                                  59**************************9999999999998887....45665555444 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.8e-05      0.13      10      32 ..      31      55 ..      29      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                  ETTEEEEEEEBCS..SSBEEEEEEE CS
                       Kelch_1 10 vggkiYviGGsdg..gnalssvevy 32
                                   + k+Yv+GG  +   + ls++ ++
  gi|70607703|ref|YP_256573.1| 31 SNCKVYVFGGVAEgrVTVLSDIDIL 55
                                  6789*********999999998776 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.9e-05     0.086      71     157 ..      12      99 ..       3     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                 Adenyl_cycl_N  71 lkelarsaeekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaeelelLekK..leliekwaeelgvevn 149
                                   l++  ++ae   k++ ++ ++   +y+ G ++    +  SD+Di v+ + +l+++e++++      +++  +   +++ v+
  gi|70607703|ref|YP_256573.1|  12 LRRWREYAEIMAKAT-KDLCSNCKVYVFGGVAEGRVTVLSDIDILVVSEGKLTDTEIKEIWINimKRAMDVYSLPFDAPVE 91 
                                   555555555555544.45677788********************************9987433003455666666666666 PP

                 Adenyl_cycl_N 150 fFlideek 157
                                   ++++d+e+
  gi|70607703|ref|YP_256573.1|  92 LHVVDKER 99 
                                   66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 769.37
//
Query:       gi|70607704|ref|YP_256574.1|  [L=410]
Description: hypothetical protein Saci_1979 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-10   39.9   0.0    9.5e-10   38.4   0.0    1.7  2  HTH_20    Helix-turn-helix domain
    2.2e-06   27.5   0.2    1.7e-05   24.5   0.1    2.3  2  HTH_5     Bacterial regulatory protein, arsR family
    0.00048   19.6   4.3    0.00064   19.1   4.3    1.4  1  DUF4097   Putative adhesin
      0.003   17.1   0.2      0.012   15.1   0.2    2.1  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.6   0.2      0.031   14.2   0.2    1.6  1  HTH_45    Winged helix-turn-helix
      0.032   15.3   2.5        6.5    7.9   0.0    3.6  2  PPC       Bacterial pre-peptidase C-terminal domain
       0.15   12.2   0.2        2.6    8.2   0.0    2.4  2  Mrr_N     Mrr N-terminal domain
       0.16   12.5   0.0       0.37   11.3   0.0    1.6  1  HTH_27    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   4.2e-13   9.5e-10       2      56 ..       2      52 ..       2      57 .. 0.93
   2 ?   -2.6   0.0       2.6   5.8e+03      39      49 ..     214     224 ..     203     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.2e-13
                                  HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  +i+eA++++ Rr+il +L  + + ++sel+erl l  + l +HL++L   gLv+ 
  gi|70607704|ref|YP_256574.1|  2 DIFEAVSNEIRRKILNML--ETPKSFSELCERLNLESSALAFHLKKL--DGLVTK 52
                                  69****************..***************************..888875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHH CS
                        HTH_20  39 ntlsyHLrvLe 49 
                                    ++  HLrvL 
  gi|70607704|ref|YP_256574.1| 214 FNIGSHLRVLY 224
                                   56778***996 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   7.8e-09   1.7e-05       2      40 ..      10      47 ..       9      52 .. 0.90
   2 ?    0.0   0.0      0.36     8e+02      32      41 ..     216     225 ..     215     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 7.8e-09
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLr 40
                                  + R+kIL++L+  +++++el+e l+l  s++  HLkkL 
  gi|70607704|ref|YP_256574.1| 10 EIRRKILNMLE-TPKSFSELCERLNLESSALAFHLKKLD 47
                                  78******995.7************************94 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.36
                                   HHHHHHHHHH CS
                         HTH_5  32 vShHLkkLre 41 
                                   +  HL++L++
  gi|70607704|ref|YP_256574.1| 216 IGSHLRVLYD 225
                                   6679999886 PP

>> DUF4097  Putative adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.3   2.9e-07   0.00064      82     215 ..     232     381 ..     104     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.9e-07
                       DUF4097  82 edlqvkassGdlsvek...........atklkaetlelksssGdltlsnvsaktltvksesGdvtiegseakklklqltsG 151
                                   ++l+v+ ++G ++++k             +l   + +++++   l+++   +++l+v+ + G+v+i+g++a++lk++ + G
  gi|70607704|ref|YP_256574.1| 232 DSLSVEIDGGVVKISKgdphlfakcrhDGDLDIYDSSISADGCYLRVTYPDLNQLKVNVDGGKVEINGIKANNLKVNVDGG 312
                                   478888888888888777777777776666777777777777777777777999***********************9999 PP

                       DUF4097 152 dieleslslet....ldltsssGdltlsntkle.gsltitassGdvdlslpeekkaavdassesGdvsl 215
                                    ++l+    +     ld    +Gd++ + t+++  +++i+   G+  +++p+e ++    +++ G  +l
  gi|70607704|ref|YP_256574.1| 313 LVNLNMECKDSvdisLDGGKAEGDVHFKDTTKArLNIDIDGGVGKFGVTVPKEFSIITSSRVSGGVTRL 381
                                   999975444441111555667888999986555158999999999999999888776666555555555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.4e-06     0.012       2      41 ..       9      46 ..       8      47 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                        HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrL 41
                                  +e++rkIL+ L+     s +eL+erl+l +s++  +lk+L
  gi|70607704|ref|YP_256574.1|  9 NEIRRKILNMLET--PKSFSELCERLNLESSALAFHLKKL 46
                                  8999*******99..99**********************9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.4e-05     0.031       6      73 ..      10      75 ..       8      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                        HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlelleklkele 73
                                  eI   IL+++ e  ++ +++  + nL+ + l   L++L   gl+ k+++++Yvl e G++ l+ ++++e
  gi|70607704|ref|YP_256574.1| 10 EIRRKILNML-ETPKSFSELCERLNLESSALAFHLKKL--DGLVtKDENGNYVLSELGKKALSIINTIE 75
                                  788899**99.99************************9..69*9555999*************999987 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0029       6.5       9      38 ..     228     272 ..     223     323 .. 0.82
   2 ?    4.3   0.7     0.039        88      12      39 ..     344     370 ..     317     408 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0029
                                   E-TT-EEEEEES-TT.................SEEEEE-TT..-S CS
                           PPC   9 vpagdsltididggti...............dldLylldsngtsv 38 
                                   ++++dsl+++idgg                 d dL ++ds+ + +
  gi|70607704|ref|YP_256574.1| 228 LKVSDSLSVEIDGGVVkiskgdphlfakcrhDGDLDIYDSSISAD 272
                                   899******************999999999977787777775444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.039
                                   T-EEEEEES-TT..SEEEEE-TT..-SS CS
                           PPC  12 gdsltididggtidldLylldsngtsva 39 
                                     +l+ididgg + + +++++ + + ++
  gi|70607704|ref|YP_256574.1| 344 KARLNIDIDGGVGKFGVTVPKEF-SIIT 370
                                   46799999999998877777777.3333 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0012       2.6      60      85 ..      42      68 ..      38      69 .. 0.90
   2 ?    1.1   0.1      0.19   4.3e+02       4      49 ..     134     184 ..     132     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                         Mrr_N 60 yLkk.agllespkrgvwkiTekGrevl 85
                                  +Lkk  gl++++++g + ++e G+++l
  gi|70607704|ref|YP_256574.1| 42 HLKKlDGLVTKDENGNYVLSELGKKAL 68
                                  788878*******************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.19
                         Mrr_N   4 lmlplLealad....gsehrlkeirervaerf.glseeeraellpsgkqtr 49 
                                   l+ ++Le +++    +s  +lk++++r ++++ ++ e  ++e   sgk+t+
  gi|70607704|ref|YP_256574.1| 134 LLNEVLELVENvitvQSPPNLKDVISRKSKQVmSIEEGSVEEDQRSGKETI 184
                                   566777777777777888889999998888888**************9865 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.37      12      48 ..      16      50 ..      10      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                        HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  +++ + +k+ ++lc+rln+e+s+ +  lkkL   GLv
  gi|70607704|ref|YP_256574.1| 16 LNMLETPKSFSELCERLNLESSALAFHLKKLD--GLV 50
                                  4566788888***************9999996..566 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3044.32
//
Query:       gi|70607705|ref|YP_256575.1|  [L=78]
Description: hypothetical protein Saci_1980 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 601.75
//
Query:       gi|70607706|ref|YP_256576.1|  [L=134]
Description: hypothetical protein Saci_1981 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-11   42.8   1.4    1.1e-10   42.1   1.4    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.4     6e-15   1.1e-10       2     121 ..       3     125 ..       2     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 6e-15
                                   EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEEE.... CS
                           PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkilp.... 72 
                                   ++D+s+l al+ +ee+ + ++k +      ++ ++v+ E+++ + r     +      +++ + ++   +  +++l+    
  gi|70607706|ref|YP_256576.1|   3 IVDASALTALVLKEEGWDDILKFF---TPAHSIEHVVKETMNAIWRmknvkK------LIDDKTAFGMkRVLFELLNertl 74 
                                   79**********************...79*****************666652......44444444443333333331111 PP

                                   ...BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                           PIN  73 ...idaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                         e +e a eia + +l+ +D l +A +++h ++li t+D++ +rva+
  gi|70607706|ref|YP_256576.1|  75 lllNEMEYVENAFEIAMNNNLTFYDSLYIAACLKHSAQLI-TRDDKQARVAE 125
                                   11135566777888888888********************.*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1029.02
//
Query:       gi|70607707|ref|YP_256577.1|  [L=368]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.2       0.64    9.9   0.0    2.1  2  DUF2835   Protein of unknown function (DUF2835)


Domain annotation for each model (and alignments):
>> DUF2835  Protein of unknown function (DUF2835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0     0.097   1.7e+03      32      52 ..     198     218 ..     194     229 .. 0.83
   2 ?    9.9   0.0   3.6e-05      0.64      15      37 ..     324     346 ..     313     352 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.097
                       DUF2835  32 GrrvqlpashlrpfvthdGvr 52 
                                   G  ++l+a +  +f +++G++
  gi|70607707|ref|YP_256577.1| 198 GDLLKLDAVNQIHFADREGIK 218
                                   777899999999999999995 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 3.6e-05
                       DUF2835  15 layYqGaakkvvvraedGrrvql 37 
                                     +Y+ ++ +vv++++dGr++ +
  gi|70607707|ref|YP_256577.1| 324 RGVYSQEVGRVVIITRDGRTIDI 346
                                   569*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2540.54
//
Query:       gi|70607708|ref|YP_256578.1|  [L=124]
Description: hypothetical protein Saci_1983 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.9   0.1      0.014   14.8   0.1    1.1  1  DUF2226   Uncharacterized protein conserved in archaea (DUF22
       0.17   11.8   0.1       0.29   11.0   0.1    1.4  1  BESS      BESS motif


Domain annotation for each model (and alignments):
>> DUF2226  Uncharacterized protein conserved in archaea (DUF2226)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.5e-06     0.014     181     252 ..      34     105 ..      17     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                       DUF2226 181 eelLkKlGikepdeesietiledvfepsdeelaeddleelkekilseivlkvkrmegvvdvlvnlkikveeg 252
                                    e LkK+Gi  +d+ +    ++d+++   +e      ++++ek+++ + +++  ++  v v ++ k  ++++
  gi|70607708|ref|YP_256578.1|  34 IEALKKYGIPDDDYHFAKSFIHDCLRLNPKECIAVIKDDRIEKLIKGLINEIPELKYRVTVTITHKFCMNND 105
                                   588**********************97766654444556666667777777766666666777766666664 PP

>> BESS  BESS motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.3e-05      0.29       1      20 [.      44      63 ..      44      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                          BESS  1 DsDdlFLlSllPtmkrLppl 20
                                  D+D++F +S+ +++ rL+p+
  gi|70607708|ref|YP_256578.1| 44 DDDYHFAKSFIHDCLRLNPK 63
                                  9*************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 812.19
//
Query:       gi|70607709|ref|YP_256579.1|  [L=84]
Description: hypothetical protein Saci_1984 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-06   26.9   0.5      6e-06   26.1   0.5    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0056   16.6   0.1      0.008   16.1   0.1    1.3  1  MraZ            MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.5   6.7e-10     6e-06       6      37 ..      16      52 ..      13      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.7e-10
                                  EEEEEE-CCCHHHC.....CEEC.TCEEEEEECTTCCC CS
                MazE_antitoxin  6 sgavriPkevrfel.....gire.Gdevelevdgdkii 37
                                   g+++iPke+r+        ir+ Gd+++le+++ ++i
  gi|70607709|ref|YP_256579.1| 16 RGRITIPKEIRERIktrmlKIRVeGDKIILEPME-IDI 52
                                  69*****************99999********98.555 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   8.9e-07     0.008       4      30 ..       7      33 ..       5      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.9e-07
                                  TEEEEEB-TTSEEE--CHHHHHTTSCS CS
                          MraZ  4 gatevelDakGRlllPaklreeaklek 30
                                  ++  v +D+ GR+++P++ re +k  +
  gi|70607709|ref|YP_256579.1|  7 ETEIVVMDDRGRITIPKEIRERIKTRM 33
                                  566788***************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 584.85
//
Query:       gi|70607710|ref|YP_256580.1|  [L=128]
Description: hypothetical protein Saci_1985 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-14   52.7   0.1    6.9e-14   52.4   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   3.8e-18   6.9e-14       2     117 ..       5     121 ..       4     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.8e-18
                                   EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHH CS
                           PIN   2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaee 80 
                                   ++D +v++++l  ++ +  +a+ +l++  e +ts+++   ++ vl++++ +++++ e+ ++  + l++l i  +d + +++
  gi|70607710|ref|YP_256580.1|   5 YFDVNVFVYYLtGDRTNGQRAKYWLANTVEKYTSSITPLFVILVLSKVLGRSLRDHEFAKSVVDaLDSLGIEYLDLPPWDK 85 
                                   89**********999999999****999*******************9999**********9999**************** PP

                                   HHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHH CS
                           PIN  81 aaeialkygllpnDaliaAtAkehgikliatfDedfr 117
                                   +  +++ y+l++ D +++AtA e++++l+ ++De+++
  gi|70607710|ref|YP_256580.1|  86 ITGVMKMYKLDLEDSIHVATAVENKLELV-SNDEELK 121
                                   *****************************.****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 940.56
//
Query:       gi|70607711|ref|YP_256581.1|  [L=156]
Description: hypothetical protein Saci_1986 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1154.37
//
Query:       gi|70607712|ref|YP_256582.1|  [L=300]
Description: hypothetical protein Saci_1987 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   39.9   6.3    8.1e-10   38.8   6.3    1.5  1  Cas_DxTHG        CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
      0.026   14.9   0.4         10    6.5   0.0    2.6  2  Minor_capsid_3   Minor capsid protein from bacteriophage
      0.081   11.1   0.1       0.11   10.7   0.1    1.1  1  Nop14            Nop14-like family
        1.4    8.9   5.5       0.13   12.1   0.8    1.7  2  Antimicrobial22  Frog antimicrobial peptide


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   6.3   1.8e-13   8.1e-10     100     359 .]       9     264 ..       2     264 .. 0.62

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.8e-13
                     Cas_DxTHG 100 ifekllek.leen.deiilDiThGfrylPvla...llalaylrnvk.nltikgiyYgafkeeeedPildlteflelsdwlt 174
                                   +f+++  k ++e+ deii+D ThG++y  +++      +a + +vk + +i   +Y a++++ ++ ++ ++   + +  ++
  gi|70607712|ref|YP_256582.1|   9 LFDAINGKdVDEDiDEIIVDTTHGINYFAIMTqlmSRDIASILSVKlKKEIRVRFYNAIPSS-NEEFVIVKVNTDAKPRIR 88 
                                   7888888889999***************9999999777888888886667777899999443.344444666666666666 PP

                     Cas_DxTHG 175 averflktgdaeklaellre...kkekkkek..lkklk.klkeklkkeleefskalelirp..lellekaeklekeivekl 247
                                   ++e   ++g   ++  l+ +          +  l+++k ++      +l+++ + ++l ++  +++++  ++l ++    +
  gi|70607712|ref|YP_256582.1|  89 TLEDISDRGLLIPYNALIYNaplAL-----SqyLQESKiEI-----PSLDSVYDKVNLKNKagKLVVD--YNLREQ----K 153
                                   6677777776666666664432211.....11122222233.....4477777777777754334433..333333....1 PP

                     Cas_DxTHG 248 keeleeiesleeeesakplellldeikkklekflkkqikwclekgliqqaltllreliisl.lle..gedilnkkkrreei 325
                                    ++++ i          +l+lll+ i++ ++     ++++ + ++l++  ++l+ e+  s+ + +  +  ++  kk+ +ei
  gi|70607712|ref|YP_256582.1| 154 AKKRNDI----------YLNLLLKAIEDSFDVH--GEVNLRVLNELTKTVYSLISEVS-SAiISHevSVLLSTVKKKGKEI 221
                                   1223333..........7888999999988888..3377888999***********99.6634446644444555555555 PP

                     Cas_DxTHG 326 ........eeelknlskvekksseekeek........lsniRNdiaHaGl 359
                                           +e +     ++ + ++e   k          +iRN+iaH+Gl
  gi|70607712|ref|YP_256582.1| 222 vckgkvkySEIY----PLTFETEKE---KsekcggklEDEIRNFIAHGGL 264
                                   555544433333....222222222...1234678899**********97 PP

>> Minor_capsid_3  Minor capsid protein from bacteriophage
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0023        10      87     112 ..      62      91 ..      38     106 .. 0.77
   2 ?    5.9   0.1    0.0036        16      71      99 ..     107     135 ..     102     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                Minor_capsid_3  87 e....lpslngsYtfesleitskPflieid 112
                                        +ps+n+ + + ++++ +kP++  ++
  gi|70607712|ref|YP_256582.1|  62 RfynaIPSSNEEFVIVKVNTDAKPRIRTLE 91 
                                   15555*******************986544 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0036
                Minor_capsid_3  71 sqvleelselldeleielpslngsYtfes 99 
                                   +++  +ls++l e +ie+psl++ Y   +
  gi|70607712|ref|YP_256582.1| 107 YNAPLALSQYLQESKIEIPSLDSVYDKVN 135
                                   666778*****************997655 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   2.5e-05      0.11     487     559 ..     152     225 ..     143     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.5e-05
                         Nop14 487 eeNKeklqkflavLlqhiaylasqeeappfailesLvrhlhsLaksfpeeaaeafrekLkemqke.lekklakg 559
                                   ++ K++   +l++Ll+ i++ ++ + + ++++l++L+++++sL  ++++++ ++ +++L ++ k+  ++ ++kg
  gi|70607712|ref|YP_256582.1| 152 QKAKKRNDIYLNLLLKAIEDSFDVHGEVNLRVLNELTKTVYSLISEVSSAIISHEVSVLLSTVKKkGKEIVCKG 225
                                   567999999***************99877*********************999999988777665244445555 PP

>> Antimicrobial22  Frog antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.3       1.8   7.9e+03       8      14 ..     139     145 ..     139     145 .. 0.81
   2 ?   12.1   0.8   2.9e-05      0.13       2      15 ..     210     223 ..     210     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
               Antimicrobial22   8 GaGKkiv 14 
                                   +aGK +v
  gi|70607712|ref|YP_256582.1| 139 KAGKLVV 145
                                   69**887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.9e-05
               Antimicrobial22   2 iLsgvLGaGKkivC 15 
                                   +Ls+v++ GK ivC
  gi|70607712|ref|YP_256582.1| 210 LLSTVKKKGKEIVC 223
                                   7************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2120.33
//
Query:       gi|70607713|ref|YP_256583.1|  [L=333]
Description: hypothetical protein Saci_1988 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2312.90
//
Query:       gi|70607714|ref|YP_256584.1|  [L=582]
Description: hypothetical protein Saci_1989 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-17   62.7   0.0      2e-16   60.2   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
    1.3e-06   28.3   0.0    2.6e-06   27.3   0.0    1.4  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    2.5e-06   28.0   0.0    4.7e-05   23.8   0.0    2.7  2  AAA           ATPase family associated with various cellular 
      8e-05   23.2   0.0    0.00048   20.7   0.0    2.4  2  AAA_18        AAA domain
    0.00056   20.3   0.0     0.0014   19.1   0.0    1.7  1  AAA_16        AAA ATPase domain
    0.00072   19.3   0.0     0.0019   18.0   0.0    1.7  1  IstB_IS21     IstB-like ATP binding protein
    0.00076   19.0   0.0     0.0057   16.2   0.0    2.3  2  AAA_7         P-loop containing dynein motor region
     0.0041   17.5   0.0       0.01   16.2   0.0    1.7  1  RNA_helicase  RNA helicase
     0.0055   17.0   0.0      0.024   14.9   0.0    2.1  2  AAA_22        AAA domain
     0.0064   15.9   0.0      0.013   14.9   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0097   15.8   0.1       0.32   10.8   0.0    2.8  3  AAA_3         ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.054   13.8   0.0       0.12   12.7   0.0    1.5  1  AAA_19        AAA domain
      0.068   12.8   0.0      0.088   12.5   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.12   12.3   0.0       0.36   10.7   0.0    1.8  1  Arch_fla_DE   Archaeal flagella protein
       0.12   12.5   0.0       0.23   11.6   0.0    1.4  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   1.7e-19     2e-16       1     138 []     301     468 ..     301     468 .. 0.85
   2 ?   -2.5   0.0         4   4.8e+03      77      95 ..     560     578 ..     544     581 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.7e-19
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.....G-SE...EEEES CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.....egei...lvlDE 73 
                                   ++lLvGppG+gK+++a+ +a+ l++ +++   ++ +t++dl+g+ +i+n+   +++++l++a+      + e+   ++lDE
  gi|70607714|ref|YP_256584.1| 301 NILLVGPPGVGKTQIAKIIAESLCDDYLMATANALWTRRDLIGGESIRNSSVIWKKGILMEAFLkvpktTEEVlfpVILDE 381
                                   689************************************************************9****9666622257*** PP

                                   GGG--.HHHHHHHHHHHHSSE...EE..-SSSEEE---.........................-EEEEEESS--..-TT-T CS
                         AAA_5  74 verae.sevlnsLlslleerr...llleeggelvkakndd..ller.................frviatanpld.rslnel 130
                                   ++ra+ +++++ + + ++  r   +   +  +lv + ++   + e+                 +r+iat+n  d r l +l
  gi|70607714|ref|YP_256584.1| 382 INRADiDKAFGDFFTTFSSARpeeWV-IP-SWLVEELKYYssFQEElkpllsalhsdkqrlskIRIIATMNLKDlRNLYQL 460
                                   *************9999876522222.22.233333333223444488899****************************** PP

                                   THHHHTT- CS
                         AAA_5 131 spalrsRf 138
                                     al +Rf
  gi|70607714|ref|YP_256584.1| 461 GDALTRRF 468
                                   *******9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4
                                   --HHHHHHHHHHHHSSEEE CS
                         AAA_5  77 aesevlnsLlslleerrll 95 
                                   ++++v+n +  +lee+r  
  gi|70607714|ref|YP_256584.1| 560 VDRKVVNNVKEILEEKRTK 578
                                   5678999999999999876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.1e-09   2.6e-06      35     110 ..     301     380 ..     277     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.1e-09
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvl.....fideihrlsraveevlysamed 110
                                    +ll+GpPG+Gkt +akiia+ l  +  ++++ +l   +dl++   +++++ v+     +++   ++ +++eevl++ + d
  gi|70607714|ref|YP_256584.1| 301 NILLVGPPGVGKTQIAKIIAESLCDDYLMATANALWTRRDLIGG-ESIRNSSVIwkkgiLMEAFLKVPKTTEEVLFPVILD 380
                                   69***************************************984.445555554111115677789999999999998766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.9e-08   4.7e-05       1      35 [.     302     336 ..     302     387 .. 0.73
   2 ?    0.5   0.0      0.61   7.3e+02      86     113 ..     426     453 ..     417     473 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.9e-08
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsell 35 
                                   +ll+GppG+GKT +ak +a++l  ++l   +  l+
  gi|70607714|ref|YP_256584.1| 302 ILLVGPPGVGKTQIAKIIAESLCDDYLMATANALW 336
                                   69*******************97666666655555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.61
                                   HHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                           AAA  86 vnqLlteldgvkkkeskvivigatnrpd 113
                                   ++ Ll++l   k++ sk+ +i++ n  d
  gi|70607714|ref|YP_256584.1| 426 LKPLLSALHSDKQRLSKIRIIATMNLKD 453
                                   4568888999999999999999999854 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.4   4.1e+03      47      64 ..     222     239 ..     144     283 .. 0.62
   2 !   20.7   0.0     4e-07   0.00048       1      39 [.     302     360 ..     302     422 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.4
                        AAA_18  47 deskrldedkldklldal 64 
                                      ++++ + + k ++  
  gi|70607714|ref|YP_256584.1| 222 FLLEKFNNNEVSKTIQFY 239
                                   223333333333333333 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 4e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglll 39 
                                   Ill G+pGvGKt++ak ++++l +                     +++ ++v++++g+l 
  gi|70607714|ref|YP_256584.1| 302 ILLVGPPGVGKTQIAKIIAESL-CddylmatanalwtrrdliggeSIRNSSVIWKKGILM 360
                                   99******************97.5566755555556666666555555555555555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.1e-06    0.0014      25      55 ..     300     331 ..     288     440 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                        AAA_16  25 elvllsGesGvGKsslvrellralekdg.gif 55 
                                   +++ll+G++GvGK+ +++ ++++l++d+ + +
  gi|70607714|ref|YP_256584.1| 300 GNILLVGPPGVGKTQIAKIIAESLCDDYlMAT 331
                                   689************************53322 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.5e-06    0.0019      44      74 ..     296     326 ..     267     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                     IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavra 74 
                                   + k+ ni+l+Gp+GvGK+ +a  ++ + + +
  gi|70607714|ref|YP_256584.1| 296 VLKNGNILLVGPPGVGKTQIAKIIAESLCDD 326
                                   45789*******************9999875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.95   1.1e+03      50      86 ..     219     255 ..     218     262 .. 0.85
   2 !   16.2   0.0   4.7e-06    0.0057      17      66 ..     285     331 ..     272     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.95
                         AAA_7  50 ikd.llkkldkekylsltinfsaqtsanqlqdiieskl 86 
                                   ik+ ll+k++ ++ +s+ti+f +  s+  +q++ e+kl
  gi|70607714|ref|YP_256584.1| 219 IKNfLLEKFN-NNEVSKTIQFYNEISSWLVQKVPEEKL 255
                                   6776788888.8888999*************9999887 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.7e-06
                         AAA_7  17 vdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylslt 66 
                                   +d++ ++y+l+ l  ++ ++llvGp G+GKt i+k + ++l  ++yl++t
  gi|70607714|ref|YP_256584.1| 285 QDNTTIDYMLSVL--KNGNILLVGPPGVGKTQIAKIIAESLC-DDYLMAT 331
                                   5777777777655..67789***************9999998.6666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.4e-06      0.01       1      37 [.     302     338 ..     302     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.4e-06
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysr 37 
                                   i+l+Gp+g+GK+++ak +a++l++++ + +++ +++r
  gi|70607714|ref|YP_256584.1| 302 ILLVGPPGVGKTQIAKIIAESLCDDYLMATANALWTR 338
                                   689*********************9999998888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.024       5      55 ..     299     340 ..     297     385 .. 0.81
   2 ?   -1.9   0.0       3.1   3.7e+03      83      86 ..     461     464 ..     416     518 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                        AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskd 55 
                                    g ++++G++G+GKT  ++ ++e+l         +++++  t++++ +++d
  gi|70607714|ref|YP_256584.1| 299 NGNILLVGPPGVGKTQIAKIIAESL---------CDDYLMATANALWTRRD 340
                                   5789********************9.........55555555555444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                        AAA_22  83 eqal 86 
                                    +al
  gi|70607714|ref|YP_256584.1| 461 GDAL 464
                                   2222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.013      19      47 ..     296     324 ..     279     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                  Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllp 47 
                                   +  + n+llvGppG GKt +ak +++ l+
  gi|70607714|ref|YP_256584.1| 296 VLKNGNILLVGPPGVGKTQIAKIIAESLC 324
                                   555679****************9987665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00027      0.32       2      52 ..     302     359 ..     301     390 .. 0.60
   2 ?    1.4   0.0      0.22   2.6e+02     103     130 ..     442     469 ..     420     470 .. 0.85
   3 ?   -3.2   0.0       5.9     7e+03      16      42 ..     524     550 ..     519     557 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke.......k 52 
                                   +ll g PG++kt+++k +a++l  ++      +     d++G e +++++        
  gi|70607714|ref|YP_256584.1| 302 ILLVGPPGVGKTQIAKIIAESLCDDYLMATANALWTRRDLIGGESIRNSSviwkkgiL 359
                                   7999*****************9888866555555556677776665555434433331 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                         AAA_3 103 pflvlatqnPieqeGtyplpeaqldrfl 130
                                   +  ++at n  + +  y+l +a   rf 
  gi|70607714|ref|YP_256584.1| 442 KIRIIATMNLKDLRNLYQLGDALTRRFS 469
                                   4679*******************99995 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 5.9
                         AAA_3  16 vkalakaldlefkriqftpdllPsdil 42 
                                    k l++   l+  r   t+++ P di+
  gi|70607714|ref|YP_256584.1| 524 SKVLTQLGVLQQLRSSSTSEITPEDIV 550
                                   445555555677788899999999997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001      0.12       8      35 ..     297     324 ..     293     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                        AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallv 35 
                                   lk++++l++++pG GKT++ k i + l 
  gi|70607714|ref|YP_256584.1| 297 LKNGNILLVGPPGVGKTQIAKIIAESLC 324
                                   68999**************999988776 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.3e-05     0.088       4      38 ..     289     323 ..     287     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-05
                                   HHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab   4 vlDalfpivqGqrtlipgafgvGktvisqslskqs 38 
                                   ++D ++++ + +++l++g  gvGkt+i++ +++  
  gi|70607714|ref|YP_256584.1| 289 TIDYMLSVLKNGNILLVGPPGVGKTQIAKIIAESL 323
                                   79**************************9998875 PP

>> Arch_fla_DE  Archaeal flagella protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.36      24      55 ..     221     253 ..     207     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                   Arch_fla_DE  24 efLvervgvenaaealdyYeei.gWiseevree 55 
                                   +fL+e++  +++++++++Y+ei  W+ ++v ee
  gi|70607714|ref|YP_256584.1| 221 NFLLEKFNNNEVSKTIQFYNEIsSWLVQKVPEE 253
                                   69********************55*99998654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.23       2      24 ..     302     324 ..     302     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                        AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                   +llvG+pG+GK++ a+ +++ l 
  gi|70607714|ref|YP_256584.1| 302 ILLVGPPGVGKTQIAKIIAESLC 324
                                   689************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 3657.19
//
Query:       gi|70607715|ref|YP_256585.1|  [L=269]
Description: hypothetical protein Saci_1990 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2153.54
//
Query:       gi|70607716|ref|YP_256586.1|  [L=412]
Description: hypothetical protein Saci_1991 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-29  103.1   0.0    2.4e-29  102.0   0.0    1.6  1  AAA_14       AAA domain
    1.1e-11   45.0   0.3    2.4e-11   43.9   0.2    1.6  2  DUF4143      Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
      0.024   14.9   1.4        3.2    8.1   0.0    3.2  2  DUF1947      Domain of unknown function (DUF1947)
      0.032   14.4   0.2       0.57   10.3   0.0    2.7  3  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
        0.1   11.7   0.7       0.19   10.8   0.7    1.4  1  Poty_PP      Potyviridae polyprotein


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   6.7e-33   2.4e-29       3     131 .]      41     162 ..      40     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 6.7e-33
                        AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..kllelileklkeekktylflDEiqevpewek 81 
                                   +il+i G+Rr+GK+tl+  l+k       ++ y+n+dde+++ ++ ++   l+e+i + +++ + +y+++DEi++v++we 
  gi|70607716|ref|YP_256586.1|  41 NILTILGVRRSGKSTLAVMLLKGI-----KFSYVNFDDESLYGIRAEDlrGLEEAIYQ-VYG-NVEYMVFDEIHNVKGWEL 114
                                   689*************99999665.....5***********99986654355566666.455.899*************** PP

                        AAA_14  82 alkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                   +  +l ++g + +++vtGSnsk+ls e+at+l+gr++++ l+p+sf E+l
  gi|70607716|ref|YP_256586.1| 115 FASRLRESG-K-RLVVTGSNSKMLSGELATHLTGRHSDYVLFPFSFGEYL 162
                                   *********.4.8***********************************97 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   5.5e+03      18      42 ..      89     124 ..      28     129 .. 0.61
   2 !   43.9   0.2   6.6e-15   2.4e-11      18     108 ..     231     347 ..     173     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                   x...........xxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  18 k...........glverlppwsespnskkrlrkspK 42 
                                               ++++++++++  ++ ++rlr+s K
  gi|70607716|ref|YP_256586.1|  89 EaiyqvygnveyMVFDEIHNVKGWELFASRLRESGK 124
                                   044444444444555555555445666666666655 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 6.6e-15
                                   x.......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  18 k.......................................glverlppwsespnskkrlrkspKlyfvDtGLlvallgldk 59 
                                                                           + v+ lp++   +++++rl+ + K+y+vDtGL+  ++  +k
  gi|70607716|ref|YP_256586.1| 231 DfantlisyyssevslsrlaksmgidektvfqwsfgmenaYSVYFLPRY--GEKLRERLTYNKKVYIVDTGLISRVAARKK 309
                                   25556666777777777777788888888889999999999********..*********************999764444 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DUF4143  60 eelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvie 108
                                           ++G+l+En+Va +Llk  e + + lyy +dk  +EvDf  e
  gi|70607716|ref|YP_256586.1| 310 --------DRGRLIENMVALKLLK--ENQLKGLYYIKDK-DYEVDFYDE 347
                                   ........46**************..4445788888885.8*****766 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0009       3.2       4      42 ..     172     209 ..     171     214 .. 0.85
   2 ?    4.3   0.2     0.014        51       3      37 ..     333     368 ..     332     371 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0009
                                   E--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEE CS
                       DUF1947   4 fLSkKeakeileklkekyisislesdkiEieeekkeklY 42 
                                   +LS +e+ ei+++l+++  ++   ++++ +++e+  ++Y
  gi|70607716|ref|YP_256586.1| 172 LLSTRERAEIKNELESYI-DVGGFPESLILGKEQTLTIY 209
                                   69************9988.**999998878887766666 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                   EE--HHHHH.HHHHHHHTTT---TT--..-EEEE-S CS
                       DUF1947   3 HfLSkKeak.eileklkekyisislesdkiEieeek 37 
                                   +++++K+ + +++++++++ i++s  +dk+E  e k
  gi|70607716|ref|YP_256586.1| 333 YYIKDKDYEvDFYDEVNSRLIQVSYATDKVEDREIK 368
                                   57788887658*******************966665 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   4.3e+03      65     108 ..      88     131 ..      85     139 .. 0.77
   2 ?   10.3   0.0   0.00016      0.57      25      47 ..     242     264 ..     218     311 .. 0.79
   3 ?    0.6   0.0      0.16   5.9e+02       7      42 ..     323     359 ..     313     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                   HTTHHHHHHHHHHHHHSSS--HHHHHHHHHHTT--EEEEEEEEE CS
                   HTH_Tnp_1_2  65 eeeraevykaLlrkilkgrssvkAieLylkrrgeltdkkkveak 108
                                   ee   +vy +   ++  +  +vk  eL+  r +e  ++ +v++ 
  gi|70607716|ref|YP_256586.1|  88 EEAIYQVYGNVEYMVFDEIHNVKGWELFASRLRESGKRLVVTGS 131
                                   56667889999999998888999999999998887776666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                   --S-HHHHHHHHTS-HHHHHHHH CS
                   HTH_Tnp_1_2  25 ekltldeiaeevgvsrsTlykWk 47 
                                    +++l+ +a+ +g++++T ++W 
  gi|70607716|ref|YP_256586.1| 242 SEVSLSRLAKSMGIDEKTVFQWS 264
                                   78899*****************7 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.16
                                   HS-HHHHHHHHHHHHHHH--S-HHHHHH.HHTS-HHH CS
                   HTH_Tnp_1_2   7 eLtakQkkaaellvendyekltldeiae.evgvsrsT 42 
                                    L+++Q+k  + + ++dye    de+ +  ++vs +T
  gi|70607716|ref|YP_256586.1| 323 LLKENQLKGLYYIKDKDYEVDFYDEVNSrLIQVSYAT 359
                                   3899999999999999998888888864156777655 PP

>> Poty_PP  Potyviridae polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   5.3e-05      0.19     202     268 ..     304     370 ..     212     375 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                       Poty_PP 202 lrary.akdrveenievLenvr.sqleefsvvsdkdeleellienyeslalvesqsktekfkdlklkgi 268
                                   + ar    +r+ en+  L+ ++ +ql+++  ++dkd++++++ e +  l  v++  +t+k+ d ++kg 
  gi|70607716|ref|YP_256586.1| 304 VAARKkDRGRLIENMVALKLLKeNQLKGLYYIKDKDYEVDFYDEVNSRLIQVSY--ATDKVEDREIKGL 370
                                   3333337789*********99758*****************9888888877777..5566999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3178.42
//
Query:       gi|70607717|ref|YP_256587.1|  [L=126]
Description: hypothetical protein Saci_1992 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-06   27.0   0.1    5.1e-06   25.9   0.1    1.6  1  HTH_24        Winged helix-turn-helix DNA-binding
    4.8e-05   23.1   0.0    8.8e-05   22.2   0.0    1.4  1  HTH_IclR      IclR helix-turn-helix domain
    0.00057   20.4   0.4      0.039   14.5   0.1    2.0  2  DUF2407       DUF2407 ubiquitin-like domain
     0.0014   18.6   0.0     0.0024   17.8   0.0    1.3  1  HTH_45        Winged helix-turn-helix
     0.0051   15.9   0.1     0.0052   15.8   0.1    1.1  1  Topoisom_bac  DNA topoisomerase
     0.0057   16.5   0.0      0.013   15.4   0.0    1.6  2  MarR_2        MarR family
     0.0077   16.3   0.0      0.014   15.4   0.0    1.4  1  HemN_C        HemN C-terminal domain
  ------ inclusion threshold ------
       0.04   14.1   0.1       0.24   11.6   0.1    2.2  2  AbiEi_4       Transcriptional regulator, AbiEi antitoxin
        0.1   12.5   0.2       0.18   11.7   0.2    1.4  1  HTH_23        Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   2.6e-09   5.1e-06       5      47 ..      53      94 ..      53      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.6e-09
                        HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  d +IL+++++ +   ++++ +++g ++st++rr++rL++e ++
  gi|70607717|ref|YP_256587.1| 53 DMEILKAIKE-GYVRIKDITRKIGRPVSTTWRRVNRLVKERYL 94
                                  7789999999.****************************9876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-08   8.8e-05       8      52 .]      56      98 ..      54      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                                  HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                      HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                  iL+a+ e+    +++++ r++g p St+ R ++ Lv+++y+e+dg
  gi|70607717|ref|YP_256587.1| 56 ILKAIKEGYV--RIKDITRKIGRPVSTTWRRVNRLVKERYLEKDG 98
                                  5555555444..69*****************************97 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.027        53      13      52 ..      25      63 ..      22      66 .. 0.84
   2 !   14.5   0.1   1.9e-05     0.039      11      68 ..      67     123 ..      65     126 .] 0.93

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                       DUF2407 13 DleLdipdpntttvagLkqliRerlpaelasrrLrLIyaG 52
                                  D+e++ ++ + + +  L  ++R+ l +  + + L+ I +G
  gi|70607717|ref|YP_256587.1| 25 DIEVEAENQQGVVTRRLSDTVRTDL-EPGDMEILKAIKEG 63
                                  9999999999***************.66666777777766 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.9e-05
                       DUF2407  11 ipDleLdipdpntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslasslklp 68 
                                   i+D++ +i  p +tt   + +l++er   e + + +rL  +G +L + +++++++  +
  gi|70607717|ref|YP_256587.1|  67 IKDITRKIGRPVSTTWRRVNRLVKERY-LEKDGEMFRLTTKGEILVQISDVSREVVFK 123
                                   89************************9.788999****************99998765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.2e-06    0.0024       9      67 ..      54     112 ..      53     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                        HTH_45   9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelle 67 
                                   ++IL+ai+eg  +   i  k     +++ + ++ Lv++ +++k++e+++lT kG+ l++
  gi|70607717|ref|YP_256587.1|  54 MEILKAIKEGYVRIKDITRKIGRPVSTTWRRVNRLVKERYLEKDGEMFRLTTKGEILVQ 112
                                   79****************************************************86654 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.6e-06    0.0052     338     380 ..      63     115 ..      31     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                  Topoisom_bac 338 a.........giGtp.aTraeiieklvergYverkkkslvptelGkalvelle 380
                                             +iG+p +T    +++lv+++Y+e++++ ++ t++G+ lv++ +
  gi|70607717|ref|YP_256587.1|  63 GyvrikditrKIGRPvSTTWRRVNRLVKERYLEKDGEMFRLTTKGEILVQISD 115
                                   45555555669***999*****************99*************9864 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.8   7.5e+03      48      54 ..      34      40 ..      33      44 .. 0.54
   2 !   15.4   0.0   6.5e-06     0.013       2      53 ..      48      96 ..      47      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.8
                                  TTSEEEE CS
                        MarR_2 48 aGLverr 54
                                  +G v+rr
  gi|70607717|ref|YP_256587.1| 34 QGVVTRR 40
                                  4555555 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.5e-06
                                  T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  +l+p +  +L a+  +    +++++++r+ g + s++ r+++rLv+  ++e+
  gi|70607717|ref|YP_256587.1| 48 DLEPGDMEILKAIKEGY---VRIKDITRKIGRPVSTTWRRVNRLVKERYLEK 96
                                  67888888899997776...9****************************986 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.1e-06     0.014      21      64 ..      65     107 ..      60     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                        HemN_C  21 ldlaafeqrfgldleellaaaleklqeqGLLeldggrlrltprG 64 
                                   + +++++ ++g +++ +++  + +l ++++Le dg+ +rlt +G
  gi|70607717|ref|YP_256587.1|  65 VRIKDITRKIGRPVSTTWRR-VNRLVKERYLEKDGEMFRLTTKG 107
                                   77999***************.********************998 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.61   1.2e+03       7      17 ..      30      40 ..      27      40 .. 0.85
   2 ?   11.6   0.1   0.00012      0.24      12      40 ..      63      96 ..      55     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                       AbiEi_4  7 asrqvGlfttr 17
                                  a+ q+G++t+r
  gi|70607717|ref|YP_256587.1| 30 AENQQGVVTRR 40
                                  78899***987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                       AbiEi_4 12 Glfttrelea.aGispsa....lrrLvrkGwLvr 40
                                  G+++ +++++  G++ s+    ++rLv++  L++
  gi|70607717|ref|YP_256587.1| 63 GYVRIKDITRkIGRPVSTtwrrVNRLVKERYLEK 96
                                  9***************888**********99985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2     9e-05      0.18       9      44 ..      55      91 ..      54      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-05
                        HTH_23  9 rillllae.GlsvreIAreLgvsrrTvyrwlkryree 44
                                  +il++ +e   ++++I r+ g++ +T +r ++r ++e
  gi|70607717|ref|YP_256587.1| 55 EILKAIKEgYVRIKDITRKIGRPVSTTWRRVNRLVKE 91
                                  78999999999*******************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 874.41
//
Query:       gi|70607718|ref|YP_256588.1|  [L=177]
Description: hypothetical protein Saci_1993 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-14   54.2  19.5    1.5e-11   43.9   2.0    2.4  2  DUF973           Protein of unknown function (DUF973)
  ------ inclusion threshold ------
        0.5   10.4   3.6       0.23   11.5   1.4    1.5  2  DUF5392          Family of unknown function (DUF5392)
       0.62   10.1  14.7      0.061   13.4   4.5    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.1    8.7   6.5       0.43   10.0   2.1    2.0  2  DUF1129          Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   9.9   1.1e-06    0.0051       3     107 ..      25     113 ..      23     118 .. 0.82
   2 !   43.9   2.0   3.4e-15   1.5e-11     146     204 ..     118     175 ..     113     177 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                        DUF973   3 egleklregslfliiasllaliliilvlvvlftaissglsqliqssasilssvlllliaaii.liiiasvllilgllkirs 82 
                                   ++++klr+g++f ++   + l +++l +v +f                  + + l+  + ii ++++a+ ++ +gl ++ +
  gi|70607718|ref|YP_256588.1|  25 DSIKKLRDGVIFALLGVPIYLLAVFLLIVGIFM-----------------APTSLNSASLIIgISVLAIAIIAIGLTRLYN 88 
                                   6899**********9998888888888876666.................222344566777888999999999******* PP

                        DUF973  83 gfsiLsstgrdvgiGitgltlilig 107
                                   gf  L+ + ++vg G++g++l++i 
  gi|70607718|ref|YP_256588.1|  89 GFVGLTPYMNNVGLGKIGTLLLVIP 113
                                   *******************999985 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 3.4e-15
                        DUF973 146 iGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsklrst 204
                                    + il+g++ y++Ge ++ngl+kigGil +ip + i++++G+ l+y glg++l++ +++
  gi|70607718|ref|YP_256588.1| 118 FATILIGVALYQVGEKFQNGLVKIGGILGAIP-LGITTLVGFLLAYEGLGQLLKEFERK 175
                                   578*****************************.79******************988765 PP

>> DUF5392  Family of unknown function (DUF5392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4   5.1e-05      0.23       8      72 ..      15      82 ..      10      88 .. 0.69
   2 ?   -3.2   0.0       1.8   8.1e+03      70      77 ..     122     129 ..     106     142 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.1e-05
                       DUF5392  8 fikkEldklqeviaPllkKsskysfislPLllvslinlillllkaele.edsliaiil..yal.lgAlG 72
                                   + + +d + + i+  l+  ++++++++P+ l++++ li+ ++ a+++ +   ++i++   a+ + A+G
  gi|70607718|ref|YP_256588.1| 15 IVYNHMDTIYDSIK-KLRDGVIFALLGVPIYLLAVFLLIVGIFMAPTSlNSASLIIGIsvLAIaIIAIG 82
                                  56678999999998.68999******************9877776666222333333300332134555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                       DUF5392  70 AlGlAlfk 77 
                                    +G+Al++
  gi|70607718|ref|YP_256588.1| 122 LIGVALYQ 129
                                   24666655 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.5   1.4e-05     0.061      29      84 ..      26      81 ..      23      88 .. 0.83
   2 ?    2.3   2.6     0.038   1.7e+02      34      86 ..     103     163 ..      99     175 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
               Phage_holin_3_6 29 eakragsgagllgaagvlallalllllvalalalaa.lwlaalivaavllvlagvla 84
                                  + k++  g++++++++ + lla++ll+v++++a  + l  a li+++ +l++a++++
  gi|70607718|ref|YP_256588.1| 26 SIKKLRDGVIFALLGVPIYLLAVFLLIVGIFMAP-TsLNSASLIIGISVLAIAIIAI 81
                                  568999999999****************998766.4488899999999999998875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.038
               Phage_holin_3_6  34 gsgagllgaagvlallalllllvala.............lalaalwlaalivaavllvlagvlalv 86 
                                   g+ + ll++  v+ ++a +l+ val                     l+a+ + ++  +++ +la+ 
  gi|70607718|ref|YP_256588.1| 103 GKIGTLLLVIPVVNAFATILIGVALYqvgekfqnglvkiG----GILGAIPL-GITTLVGFLLAYE 163
                                   6667777777777778888888888544666663333321....23333333.4444444444444 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.1   9.6e-05      0.43     128     196 ..      17      86 ..       5      91 .. 0.78
   2 ?    0.6   0.1     0.072   3.2e+02     176     193 ..     113     130 ..     102     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.6e-05
                       DUF1129 128 vlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpv..Lpplvliiigviafvvryy 196
                                   +  ++ ++    kk r +++  ll + + l++ ++l++ + + p+++N    +  +  ++i++ia+++ ++
  gi|70607718|ref|YP_256588.1|  17 YNHMDTIYD-SIKKLRDGVIFALLGVPIYLLAVFLLIVGIFMAPTSLNSAslIIGISVLAIAIIAIGLTRL 86 
                                   333344443.78999*********************************85335677788899999887665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.072
                       DUF1129 176 pvLpplvliiigviafvv 193
                                   pv++++++i+igv+ + v
  gi|70607718|ref|YP_256588.1| 113 PVVNAFATILIGVALYQV 130
                                   899999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1191.93
//
Query:       gi|70607719|ref|YP_256589.1|  [L=102]
Description: hypothetical protein Saci_1994 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00054   20.5   0.3    0.00062   20.3   0.3    1.1  1  PIN              PIN domain
  ------ inclusion threshold ------
      0.058   12.6   0.5       0.12   11.6   0.2    1.6  2  Glyco_transf_11  Glycosyl transferase family 11


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   6.9e-08   0.00062      40     120 ..       5      93 ..       1      95 [. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.9e-08
                                   HHHHHHHS.........SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.E CS
                           PIN  40 Ellyvlar.........rkskrekaaelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliat 111
                                   E++ v+++          k   +  +e++ l l   + ++++++ ++ ee  +i+ ++++++  a+ a  A++ ++++i +
  gi|70607719|ref|YP_256589.1|   5 EMASVIRNkylellrkgEKAMAKGYIEFLNLVLSQIRNNVVEVTFSDIEEGIKIMFERDVNLSEAINAIIARRLKAIVI-S 84 
                                   666666666666665555577778888999999999*******************************************.* PP

                                   SSTHHHHHH CS
                           PIN 112 fDedfrrva 120
                                   +D+d+ r++
  gi|70607719|ref|YP_256589.1|  85 NDKDWVRLK 93 
                                   ****99986 PP

>> Glyco_transf_11  Glycosyl transferase family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.084   7.5e+02     188     209 ..      28      49 ..       7      65 .. 0.64
   2 ?   11.6   0.2   1.3e-05      0.12     193     220 ..      66      91 ..      58     102 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.084
               Glyco_transf_11 188 aDieYleealdkfrarvssvvf 209
                                   + ie+l+  l ++r++v+ v f
  gi|70607719|ref|YP_256589.1|  28 GYIEFLNLVLSQIRNNVVEVTF 49 
                                   4567777778888877755554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.3e-05
               Glyco_transf_11 193 leealdkfrarvssvvfvvfSddveWck 220
                                   l+ea++ + ar+  ++ +v+S+d +W++
  gi|70607719|ref|YP_256589.1|  66 LSEAINAIIARR--LKAIVISNDKDWVR 91 
                                   89**********..99***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 702.64
//
Query:       gi|70607720|ref|YP_256590.1|  [L=197]
Description: hypothetical protein Saci_1998 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1338.22
//
Query:       gi|70607721|ref|YP_256591.1|  [L=326]
Description: hypothetical protein Saci_1999 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2324.11
//
Query:       gi|70607722|ref|YP_256592.1|  [L=270]
Description: ABC transporter ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-22   80.5   0.0    2.3e-22   80.0   0.0    1.3  1  ABC_tran      ABC transporter
    5.7e-09   36.2   1.0    2.9e-05   24.1   0.4    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      8e-06   25.4   1.1      0.091   12.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    3.4e-05   23.5   0.2    6.2e-05   22.7   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00016   21.5   0.4    0.00026   20.8   0.4    1.4  1  AAA_15        AAA ATPase domain
    0.00023   21.7   0.0    0.00036   21.1   0.0    1.3  1  AAA_23        AAA domain
     0.0017   18.3   0.5     0.0035   17.3   0.2    1.7  2  RsgA_GTPase   RsgA GTPase
     0.0021   17.0   0.1     0.0033   16.3   0.1    1.3  1  DLIC          Dynein light intermediate chain (DLIC)
     0.0029   16.7   0.2     0.0057   15.7   0.2    1.4  1  T2SSE         Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.017   14.3   0.0    1.2  1  PIF1          PIF1-like helicase
      0.015   14.7   0.0      0.022   14.1   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.017   15.5   0.0      0.032   14.6   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.037   13.4   0.2      0.064   12.6   0.2    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.039   13.9   0.0      0.071   13.0   0.0    1.4  1  NACHT         NACHT domain
      0.065   12.4   0.2        0.1   11.7   0.2    1.3  1  G-alpha       G-protein alpha subunit
      0.073   12.8   0.2       0.47   10.2   0.1    2.2  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.076   12.9   0.1       0.28   11.1   0.1    2.0  1  NTPase_1      NTPase
      0.097   12.9   0.2       0.38   11.0   0.2    2.1  1  AAA_22        AAA domain
        0.1   12.3   0.1       0.18   11.5   0.1    1.3  1  IstB_IS21     IstB-like ATP binding protein
       0.11   11.1   0.2       0.17   10.5   0.2    1.2  1  AAA_13        AAA domain
       0.15   12.4   0.1       0.41   11.0   0.0    1.7  2  AAA_19        AAA domain
       0.17   11.4   0.2       0.36   10.4   0.2    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   2.9e-25   2.3e-22       1     137 []      18     155 ..      18     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 2.9e-25
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+nvs+k  eg+ ++++G+nG+GK+tLl++++gll+p++G+++++g +  +  + s+ k +++ +++p++  +++vr+   
  gi|70607722|ref|YP_256592.1|  18 LDNVSFKA-EGKNIVVLGHNGSGKTTLLNIISGLLRPNSGNLTINGIEPYR-HKGSVLKLLSFSFEKPRFELNMKVRDYys 96 
                                   78999996.699999******************************988888.7899999*******************9** PP

                                   .....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        e+++ +e + ++l++k l+++++    + LS Gq q + + +a+++k ++ +lDEp+a
  gi|70607722|ref|YP_256592.1|  97 flkefEDSDCMEFFWEQLDMKSLANSHI----NDLSSGQTQLINMSQAICRKTEIKVLDEPFA 155
                                   **99888889******************....*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.4   3.5e-08   2.9e-05       3      81 ..      31      94 ..      30     111 .. 0.87
   2 !   10.4   0.0   0.00049       0.4     234     297 ..     124     181 ..     113     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.5e-08
                        AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81
                                  v+ G NgsGK++LL ++++l               + ++    ++ + +y  ++++   ++ f  +++r++ ++++ + 
  gi|70607722|ref|YP_256592.1| 31 VVLGHNGSGKTTLLNIISGLL--------------RPNSGNLTINGIEPYRHKGSVLKLLS-FSFEKPRFELNMKVRDY 94
                                  899*****************7..............58899999999999999999999999.99999999999888766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00049
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                   +++lS+G+ +l+ +  a+ r      + ++DEp ++L+P  +  l e l    ++g  +++tTH
  gi|70607722|ref|YP_256592.1| 124 INDLSSGQTQLINMSQAICRKT---EIKVLDEPFAHLDPMKVGLLGEYL---LKRGFEFVITTH 181
                                   6899*********999999855...999***********7777777555...333677999999 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.4   0.00014      0.11      18      45 ..      21      48 ..      12      64 .. 0.81
   2 !   12.2   0.0   0.00011     0.091     134     198 ..     124     182 ..      77     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                  EEEETTSSEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 18 vilpfsksftaivGpNGSGKsnlldAil 45
                                  v+ + + +  +++G+NGSGK+ ll+ i+
  gi|70607722|ref|YP_256592.1| 21 VSFKAEGKNIVVLGHNGSGKTTLLNIIS 48
                                  566667778899**********998775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                                   TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislr 198
                                   ++ LS G+ +L+ ++       ++++ + +lDe  a+LD ++v  + e+l ++   + f+++++ 
  gi|70607722|ref|YP_256592.1| 124 INDLSSGQTQLINMSQA----ICRKTEIKVLDEPFAHLDPMKVGLLGEYLLKRG--FEFVITTHV 182
                                   44799999999988754....5889999**********************9999..999999986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   7.6e-08   6.2e-05      17      55 ..      21      61 ..      14      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.6e-08
                        AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                  ++++ +g ++++ G++GsGK+Tll  i+ lL p++ +++ N
  gi|70607722|ref|YP_256592.1| 21 VSFKAEGkNIVVLGHNGSGKTTLLNIISGLLRPNSgNLTIN 61
                                  677778899************************98655555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   3.1e-07   0.00026      25     126 ..      29     134 ..      16     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-07
                        AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn............kkvikiekedleifeniseskdikIdvefaekekakeye 93 
                                     v+ G+N+sGK+++l+++  +l  + + n             +v+k+ + ++e+     ++ ++k++ ++   ++ ke+e
  gi|70607722|ref|YP_256592.1|  29 NIVVLGHNGSGKTTLLNIISGLLRPN-SGNltingiepyrhkGSVLKLLSFSFEKP---RFELNMKVRDYY---SFLKEFE 102
                                   46888*******************88.44478889999976544555555555555...999999999999...8999999 PP

                        AAA_15  94 ktlkskekkkadlllkkkesdlkktikdkklkl 126
                                   ++  ++  +++  ++k + +++ + + + +++l
  gi|70607722|ref|YP_256592.1| 103 DSDCMEFFWEQL-DMKSLANSHINDLSSGQTQL 134
                                   999999888776.77777776666666666654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.4e-07   0.00036      18      85 ..      26     105 ..      16     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.4e-07
                        AAA_23  18 skgltlItGpNGaGKTTildAiklaLygetprlsrks............grgfeksdveiesegkvkayveltfenkdgr 85 
                                   + +  ++ G+NG+GKTT+l+ i   L   +++l  +               +f  +++++e + kv+ y+++  e +d +
  gi|70607722|ref|YP_256592.1|  26 EGKNIVVLGHNGSGKTTLLNIISGLLRPNSGNLTINGiepyrhkgsvlkLLSFSFEKPRFELNMKVRDYYSFLKEFEDSD 105
                                   44556899**************9998877666655556666666666542244455555555567777777776666654 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   4.3e-06    0.0035      86     122 ..      14      50 ..       6      71 .. 0.84
   2 ?   -2.7   0.0       5.8   4.8e+03      14      28 ..     233     246 ..     217     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.3e-06
                                   THTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  86 tkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                                   ++++l++++ + ++k +v++G+ G GK+tL+n + + 
  gi|70607722|ref|YP_256592.1|  14 KRKALDNVSFKAEGKNIVVLGHNGSGKTTLLNIISGL 50 
                                   4678999999**********************98764 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.8
                                   ES--EEEEEEESTTT CS
                   RsgA_GTPase  14 aNvdqllivvslkep 28 
                                   + v+ +++v s++ +
  gi|70607722|ref|YP_256592.1| 233 SKVQSVMVVKSTE-E 246
                                   5566666666666.2 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.1e-06    0.0033      24      54 ..      26      56 ..      17      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                          DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkG 54
                                   gk+++vlG++gsGkttl+  + G+  ++ G
  gi|70607722|ref|YP_256592.1| 26 EGKNIVVLGHNGSGKTTLLNIISGLLRPNSG 56
                                  59******************99998766655 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     7e-06    0.0057     128     160 ..      26      58 ..      10      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7e-06
                         T2SSE 128 erglilvsGgTgsGKttllyallkeinksderi 160
                                   e ++i+v G  gsGKttll+++   +  ++ ++
  gi|70607722|ref|YP_256592.1|  26 EGKNIVVLGHNGSGKTTLLNIISGLLRPNSGNL 58 
                                   5689******************99998776655 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.1e-05     0.017      10      49 ..      18      54 ..      12      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                  HHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                          PIF1 10 fdaiieavlnekgklfFvtGsgGtgKtflwkallkklrse 49
                                  +d++    ++ +gk++ v G+ G+gKt l++ ++  lr++
  gi|70607722|ref|YP_256592.1| 18 LDNV---SFKAEGKNIVVLGHNGSGKTTLLNIISGLLRPN 54
                                  4444...56799************************9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.022       2      50 ..       8      55 ..       7      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                  Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50
                                  l++v G+++a   +   a G+ n++++G  GsGKt l + +++ll p s
  gi|70607722|ref|YP_256592.1|  8 LTKVLGKRKALDNVSFKAEGK-NIVVLGHNGSGKTTLLNIISGLLRPNS 55
                                  678999999999999998886.9999******************98866 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     4e-05     0.032      22      45 ..      25      48 ..      15      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrell 45
                                   ++ ++++ G+ G+GK++l++ + 
  gi|70607722|ref|YP_256592.1| 25 AEGKNIVVLGHNGSGKTTLLNIIS 48
                                  34489***************8665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   7.9e-05     0.064      35      57 ..      24      45 ..       8      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                                  GGGS-.SEEEE--TTSSHHHHHH CS
                  FtsK_SpoIIIE 35 lkkmashllvaGatgsGKStaln 57
                                   ++   +++v+G  gsGK+t ln
  gi|70607722|ref|YP_256592.1| 24 KAEG-KNIVVLGHNGSGKTTLLN 45
                                  3444.5**************998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.7e-05     0.071       3      23 ..      30      50 ..      28      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.7e-05
                                  EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklala 23
                                  +++ G +GsGKTtLl  +  +
  gi|70607722|ref|YP_256592.1| 30 IVVLGHNGSGKTTLLNIISGL 50
                                  799************977655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00012       0.1      22      49 ..      26      53 ..       9     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                  .EEEEEEEESTTSSHHHHHHHHHHHCS- CS
                       G-alpha 22 revkllllGqseSGKsTilkqlkllykk 49
                                  +  ++++lG+++SGK+T+l+ +  l ++
  gi|70607722|ref|YP_256592.1| 26 EGKNIVVLGHNGSGKTTLLNIISGLLRP 53
                                  3349***************988866555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00058      0.47       2      23 ..      28      49 ..      27      53 .. 0.90
   2 ?   -0.2   0.0       0.9   7.4e+02      44      63 ..     165     184 ..     124     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00058
                     PduV-EutP  2 kkilliGkvgsGKttLtqalkg 23
                                  k+i+++G+ gsGKttL + ++g
  gi|70607722|ref|YP_256592.1| 28 KNIVVLGHNGSGKTTLLNIISG 49
                                  799*************998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.9
                     PduV-EutP  44 PGeylenrklysalivtsae 63 
                                    Geyl +r +  ++++  a+
  gi|70607722|ref|YP_256592.1| 165 LGEYLLKRGFEFVITTHVAD 184
                                   58999999888888765543 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00035      0.28       1      33 [.      29      63 ..      29      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                                  EEEEE--TTSSHHHHHHHHHHHH.....GGGEEEE CS
                      NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkss..gvkvgGf 33
                                  ++++ G+ G+GKtTl++ ++ ll+ +  +++++G+
  gi|70607722|ref|YP_256592.1| 29 NIVVLGHNGSGKTTLLNIISGLLRPNsgNLTINGI 63
                                  58899*****************9855448888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00047      0.38       5      25 ..      27      47 ..      24     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                        AAA_22  5 agilvvtGesGtGKTtllrrl 25
                                   + +vv G+ G+GKTtll+ +
  gi|70607722|ref|YP_256592.1| 27 GKNIVVLGHNGSGKTTLLNII 47
                                  5679*************9865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00022      0.18      36      63 ..      16      43 ..      10      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                     IstB_IS21 36 keLatlsfiekkenivllGpsGvGKshl 63
                                  k+L + sf ++ +niv+lG+ G GK+ l
  gi|70607722|ref|YP_256592.1| 16 KALDNVSFKAEGKNIVVLGHNGSGKTTL 43
                                  5788999******************987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0002      0.17      20      40 ..      31      51 ..      24      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                        AAA_13 20 liYGwNGaGKTtLSrllrsle 40
                                  ++ G NG+GKTtL ++++ l 
  gi|70607722|ref|YP_256592.1| 31 VVLGHNGSGKTTLLNIISGLL 51
                                  577**************9984 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0005      0.41       7      34 ..      24      51 ..      17      61 .. 0.82
   2 ?   -2.3   0.0       6.4   5.2e+03      85     124 ..     129     167 ..     114     177 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                                  +++ k+++v++  G+GKT++l+ i  ll
  gi|70607722|ref|YP_256592.1| 24 KAEGKNIVVLGHNGSGKTTLLNIISGLL 51
                                  78999**************999876555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.4
                        AAA_19  85 tealelleeaeeekklqeee.llivDE.fqdvdelqyrLlka 124
                                   + + +l++    ++ + +++ + + DE f  +d++ + Ll +
  gi|70607722|ref|YP_256592.1| 129 SGQTQLIN---MSQAICRKTeIKVLDEpFAHLDPMKVGLLGE 167
                                   44444433...2233333333556666566666666666665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00044      0.36       3      20 ..      30      47 ..      28      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                                  EEEEESTTCCHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhl 20
                                  +v+ G  GsGKTtLln +
  gi|70607722|ref|YP_256592.1| 30 IVVLGHNGSGKTTLLNII 47
                                  6899***********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1664.85
//
Query:       gi|70607723|ref|YP_256593.1|  [L=139]
Description: hypothetical protein Saci_2001 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 888.94
//
Query:       gi|70607724|ref|YP_256594.1|  [L=106]
Description: hypothetical protein Saci_2002 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 768.71
//
Query:       gi|70607725|ref|YP_256595.1|  [L=88]
Description: hypothetical protein Saci_2003 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0041   17.0   0.1     0.0041   17.0   0.1    2.8  3  RHH_1         Ribbon-helix-helix protein, copG family
     0.0061   16.2   0.3      0.042   13.6   0.0    2.3  2  Fur_reg_FbpA  Fur-regulated basic protein A
     0.0073   16.5   0.2     0.0076   16.4   0.2    1.1  1  RHH_8         Ribbon-Helix-Helix transcriptional regulator fa
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.39   10.9   0.1    1.9  1  DUF5388       Family of unknown function (DUF5388)


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   9.2e-07    0.0041       2      29 ..      13      41 ..      12      46 .. 0.94
   2 ?   -1.1   0.1      0.48   2.1e+03      30      37 ..      56      63 ..      54      65 .. 0.77
   3 ?    1.7   0.3     0.059   2.6e+02       1      18 [.      69      86 ..      69      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.2e-07
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelI 29
                                  v+ir+d e+l+++del+  +  +Sr e++
  gi|70607725|ref|YP_256595.1| 13 VTIRIDTEVLKKIDELITLGIfSSRNEAL 41
                                  8************************9985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                  HHHHHHHH CS
                         RHH_1 30 ReAlreyl 37
                                  Re +r y 
  gi|70607725|ref|YP_256595.1| 56 REIIRKYE 63
                                  78888886 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.059
                                  EEEEEEEHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdela 18
                                  rv++ +d+ l e+L e+ 
  gi|70607725|ref|YP_256595.1| 69 RVEVFIDKPLEELLKERD 86
                                  788889999999999975 PP

>> Fur_reg_FbpA  Fur-regulated basic protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   9.3e-06     0.042       6      24 ..      25      43 ..      23      44 .. 0.92
   2 ?   -0.1   0.2      0.17   7.7e+02      26      33 ..      77      84 ..      75      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                  Fur_reg_FbpA  6 IekLIqsGiykkdgrqLfe 24
                                  I++LI  Gi+++++++L +
  gi|70607725|ref|YP_256595.1| 25 IDELITLGIFSSRNEALNT 43
                                  9****************75 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                  Fur_reg_FbpA 26 TleELerE 33
                                  +leEL +E
  gi|70607725|ref|YP_256595.1| 77 PLEELLKE 84
                                  59999998 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.7e-06    0.0076       3      45 ..      10      52 ..       8      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                         RHH_8  3 tekvtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakh 45
                                   + vti +++  L +iD L+  G +s+R + + t ir  L++ 
  gi|70607725|ref|YP_256595.1| 10 IQTVTIRIDTEVLKKIDELITLGIFSSRNEALNTVIRIGLDEL 52
                                  5679*********************************888754 PP

>> DUF5388  Family of unknown function (DUF5388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.8e-05      0.39      10      50 ..      13      53 ..       7      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.8e-05
                       DUF5388 10 vnvrvdNHirNklqALaaiGlaksqkeavkklveslidsLs 50
                                  v++r+d  +  k+  L  +G+ +s  ea+++++   +d+L+
  gi|70607725|ref|YP_256595.1| 13 VTIRIDTEVLKKIDELITLGIFSSRNEALNTVIRIGLDELK 53
                                  799*******************************9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 571.36
//
Query:       gi|70607726|ref|YP_256596.1|  [L=175]
Description: hypothetical protein Saci_2004 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.61   10.2   2.7         20    5.3   0.6    3.1  3  UvsW      ATP-dependant DNA helicase UvsW


Domain annotation for each model (and alignments):
>> UvsW  ATP-dependant DNA helicase UvsW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.047   8.3e+02       8      21 ..      76      89 ..      74     103 .. 0.82
   2 ?    2.9   0.1    0.0066   1.2e+02       9      28 ..     125     144 ..     121     145 .. 0.84
   3 ?    5.3   0.6    0.0011        20       5      34 ..     145     171 ..     141     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.047
                                  HHHHHHHHHHHHHT CS
                          UvsW  8 dGlvElEklYkkkk 21
                                  +Gl El  lY  kk
  gi|70607726|ref|YP_256596.1| 76 EGLTELFTLYYLKK 89
                                  8999*999886554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0066
                                   HHHHHHHHHHHHTTT..S-- CS
                          UvsW   9 GlvElEklYkkkkKElGael 28 
                                   G++ l k+Y++   El  e+
  gi|70607726|ref|YP_256596.1| 125 GIERLWKYYTRGNDELLDEI 144
                                   9999*******999986665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0011
                                   -SHHHHHHHHHHHHHHTTT..S--TTHHHH CS
                          UvsW   5 tTkdGlvElEklYkkkkKElGaelkdtdDI 34 
                                   +Tk+ l E Ekl ++k K    ++ d  DI
  gi|70607726|ref|YP_256596.1| 145 ETKENLFESEKLVQQKLKI---KIYDLIDI 171
                                   79**************997...77777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1228.85
//
Query:       gi|70607727|ref|YP_256597.1|  [L=132]
Description: hypothetical protein Saci_2005 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-05   22.8   1.6     0.0016   18.2   0.3    2.3  2  HTH_23          Homeodomain-like domain
    0.00039   19.9   0.3     0.0015   18.0   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00043   20.8   0.2       0.04   14.5   0.0    2.2  2  Mga             Mga helix-turn-helix domain
    0.00058   19.7   0.2     0.0014   18.6   0.0    1.7  1  HTH_11          HTH domain
    0.00066   19.7   0.3     0.0011   19.0   0.3    1.5  1  HTH_19          Helix-turn-helix domain
    0.00072   19.6   0.0     0.0018   18.3   0.0    1.7  1  HTH_3           Helix-turn-helix
    0.00079   19.6   0.6     0.0012   19.0   0.4    1.4  1  HTH_Tnp_1_2     Helix-turn-helix of insertion element transpo
    0.00084   19.4   0.1     0.0016   18.5   0.1    1.4  1  HTH_28          Helix-turn-helix domain
     0.0015   18.5   0.6       0.63   10.1   0.0    2.5  2  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0016   18.7   0.4     0.0022   18.2   0.4    1.3  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
     0.0038   17.0   0.0     0.0077   16.0   0.0    1.5  1  TetR_N          Bacterial regulatory proteins, tetR family
     0.0046   16.9   0.1      0.055   13.4   0.0    2.6  3  MarR            MarR family
      0.005   17.1   0.0     0.0086   16.4   0.0    1.4  1  HTH_Tnp_1       Transposase
     0.0055   16.7   0.0      0.011   15.8   0.0    1.6  1  HTH_29          Winged helix-turn helix
     0.0056   16.5   0.0      0.017   15.0   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0094   15.6   0.4      0.011   15.4   0.4    1.2  1  Pox_D3          Chordopoxvirinae D3 protein
  ------ inclusion threshold ------
      0.014   15.3   0.1       0.03   14.2   0.1    1.6  1  P22_Cro         DNA-binding transcriptional regulator Cro
      0.015   15.2   0.0      0.029   14.2   0.0    1.5  1  Phage_AlpA      Prophage CP4-57 regulatory protein (AlpA)
      0.017   15.6   0.3      0.026   15.0   0.3    1.4  1  HTH_40          Helix-turn-helix domain
      0.023   14.4   0.1      0.057   13.2   0.1    1.7  1  MerR            MerR family regulatory protein
      0.031   13.8   0.2      0.069   12.7   0.1    1.7  1  HTH_CodY        CodY helix-turn-helix domain
      0.047   13.5   0.0       0.14   12.0   0.0    1.8  2  HTH_10          HTH DNA binding domain
      0.061   13.4   0.4       0.12   12.5   0.4    1.6  1  MerR_1          MerR HTH family regulatory protein
      0.072   12.8   0.1       0.18   11.5   0.0    1.7  1  Sigma70_r4_2    Sigma-70, region 4
      0.076   13.1   0.5       0.19   11.8   0.4    1.8  1  HTH_7           Helix-turn-helix domain of resolvase
      0.081   12.8   0.0       0.15   11.9   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.11   12.3   0.0        0.2   11.5   0.0    1.4  1  HTH_Tnp_Tc3_1   Tc3 transposase


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   2.4e-06    0.0016      15      38 ..      25      49 ..      19      57 .. 0.86
   2 ?    3.8   0.1      0.08        53       3      24 ..      57      78 ..      55      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-06
                        HTH_23 15 ae.GlsvreIAreLgvsrrTvyrwl 38
                                  +e   +++eIA++ g++r+ +y+w+
  gi|70607727|ref|YP_256597.1| 25 DEyNVNISEIAKKIGITRSAIYHWI 49
                                  4467789*****************6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.08
                        HTH_23  3 sereRlrillllaeGlsvreIA 24
                                   e+++++ l ll e+++vr+I+
  gi|70607727|ref|YP_256597.1| 57 DEENKAKLLDLLYEKDRVRAIS 78
                                  6899***************996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.3e-06    0.0015       7      34 ..      18      45 ..      17      47 .. 0.95
   2 ?   -2.1   0.0       4.3   2.9e+03       7      17 ..      63      73 ..      58      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                        HTH_24  7 kILelLqknprisqreLAerlglSpstv 34
                                  kI ++L+++ + +++e+A+++g+++s++
  gi|70607727|ref|YP_256597.1| 18 KIVNILRDEYNVNISEIAKKIGITRSAI 45
                                  8************************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                        HTH_24  7 kILelLqknpr 17
                                  k+L lL+++ r
  gi|70607727|ref|YP_256597.1| 63 KLLDLLYEKDR 73
                                  89999999877 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.1e-05      0.04      10      60 ..       8      58 ..       1      60 [. 0.88
   2 !    8.2   0.2    0.0057       3.8      11      44 ..      54      87 ..      52     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-05
                                  HHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHHCHC CS
                           Mga 10 qellkeslkyqllkflfeeeevsieelaqelyiSestlkrkikelnklLke 60
                                   ++l++ +  +++  l  e +v+i e+a++  i +s +++ i e+ k++ e
  gi|70607727|ref|YP_256597.1|  8 GKFLTKTDCVKIVNILRDEYNVNISEIAKKIGITRSAIYHWIWEIAKYIDE 58
                                  57888888899999999999****************************976 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0057
                                  HHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--H CS
                           Mga 11 ellkeslkyqllkflfeeeevsieelaqelyiSe 44
                                  +++ e +k +ll++l+e+++v   ++ qel + +
  gi|70607727|ref|YP_256597.1| 54 KYIDEENKAKLLDLLYEKDRVRAISFVQELLVEY 87
                                  789999************************9876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-06    0.0014       4      34 ..      18      47 ..      17      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrr 34
                                  +i+ +L + + +++++e+A++++++r++++ 
  gi|70607727|ref|YP_256597.1| 18 KIVNIL-RDEYNVNISEIAKKIGITRSAIYH 47
                                  688899.88889*****************95 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   1.6e-06    0.0011       5      41 ..      21      57 ..      18      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                        HTH_19  5 keaReelgltqeelaerlgisrskisaiEngkkdvps 41
                                  + +R e++ ++ e+a+++gi+rs i++++ +  ++++
  gi|70607727|ref|YP_256597.1| 21 NILRDEYNVNISEIAKKIGITRSAIYHWIWEIAKYID 57
                                  568*************************877334666 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0018       4      29 ..      23      48 ..      20      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                                  HHHHTTHHHHHHHHHHTSSHHHHHHH CS
                         HTH_3  4 lRkqlglsqeeLAeklGvsrstisri 29
                                  lR++ +  + e+A+k+G++rs+i+++
  gi|70607727|ref|YP_256597.1| 23 LRDEYNVNISEIAKKIGITRSAIYHW 48
                                  79999*******************99 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   1.8e-06    0.0012      20      58 ..      23      61 ..       8      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                  HHHHH--S-HHHHHHHHTS-HHHHHHHH.H-HHHHHHHHH CS
                   HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWk.kkkeFieyvne 58
                                     +y ++ ++eia+++g+ rs +y+W  +  ++i++ n+
  gi|70607727|ref|YP_256597.1| 23 LRDEY-NVNISEIAKKIGITRSAIYHWIwEIAKYIDEENK 61
                                  45788.999*******************99999**99986 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.4e-06    0.0016      13      33 ..      29      49 ..      18      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                        HTH_28 13 hsvreaArelgisrrtvyrWi 33
                                  ++++e+A++ gi+r+ +y Wi
  gi|70607727|ref|YP_256597.1| 29 VNISEIAKKIGITRSAIYHWI 49
                                  599*****************8 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00094      0.63       8      41 ..      17      49 ..      13      55 .. 0.89
   2 ?    6.3   0.2     0.014       9.6       5      19 ..      59      72 ..      56      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00094
                       HTH_Mga  8 lkLlelLteneksltldelakeLglseltlqsdi 41
                                  +k++++L + e   +++e+ak+ g++++++ + i
  gi|70607727|ref|YP_256597.1| 17 VKIVNILRD-EYNVNISEIAKKIGITRSAIYHWI 49
                                  6999*****.999***************997766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                       HTH_Mga  5 krklkLlelLtenek 19
                                  ++k+kLl+lL+e ++
  gi|70607727|ref|YP_256597.1| 59 ENKAKLLDLLYE-KD 72
                                  79**********.55 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   3.3e-06    0.0022      15      75 ..       8      73 ..       3     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-06
                       UPF0122 15 qsLLTekqanylelyyadDl..SlsEiAeefnvsrqavydnikrtekllek.yEekLk..llekyk 75
                                  ++ LT+  +  +     d++   +sEiA +  ++r+a+y  i  + k + +   +kL   l+ek +
  gi|70607727|ref|YP_256597.1|  8 GKFLTKTDCVKIVNILRDEYnvNISEIAKKIGITRSAIYHWIWEIAKYIDEeNKAKLLdlLYEKDR 73
                                  6677777776666666666622579********************999866033344222444444 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-05    0.0077      16      35 ..      28      47 ..      24      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                  T--HHHHHHHHTSSHHHHHH CS
                        TetR_N 16 attvreIAkrAGvskgalYr 35
                                  ++ ++eIAk+ G++++a+Y+
  gi|70607727|ref|YP_256597.1| 28 NVNISEIAKKIGITRSAIYH 47
                                  5899***************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.3e-05     0.055       7      34 ..      18      45 ..      16      51 .. 0.89
   2 ?   -0.4   0.0       1.7   1.1e+03       4      21 ..      60      77 ..      58      89 .. 0.75
   3 ?   -1.8   0.0       4.7   3.1e+03      10      21 ..     108     119 ..     108     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-05
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHH CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstv 34
                                  +i+ il+++ + ++se+akk+g+++s++
  gi|70607727|ref|YP_256597.1| 18 KIVNILRDEYNVNISEIAKKIGITRSAI 45
                                  5778999999****************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                  HHHHHHHHHHHSTTEEHH CS
                          MarR  4 tqfviLrilyeqgplsvs 21
                                  +  ++L +lye++  + +
  gi|70607727|ref|YP_256597.1| 60 NKAKLLDLLYEKDRVRAI 77
                                  567899999999887766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.7
                                   HHHHHSTTEEHH CS
                          MarR  10 rilyeqgplsvs 21 
                                   ri+y++++ ++s
  gi|70607727|ref|YP_256597.1| 108 RIIYTNPNVTIS 119
                                   689999999986 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0086      21      65 ..      26      69 ..      15      77 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                     HTH_Tnp_1 21 epgksvsevArrhgvspnqLykWrrqyregeeaspaefeltalee 65
                                  e  +++se+A++ g+ +++ y+W+ +  + ++++    +l++l  
  gi|70607727|ref|YP_256597.1| 26 EYNVNISEIAKKIGITRSAIYHWIWEIAKYIDEENKA-KLLDLLY 69
                                  57899******************99887666666666.6666655 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.011      13      33 ..      28      49 ..      18      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                        HTH_29 13 s.tvsqiAkllglsrrtvyrwl 33
                                    ++s+iAk  g++r+ +y+w+
  gi|70607727|ref|YP_256597.1| 28 NvNISEIAKKIGITRSAIYHWI 49
                                  249******************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05     0.017       5      34 ..      17      47 ..      16      49 .. 0.93
   2 ?   -2.6   0.0       7.7   5.1e+03       4      14 ..      61      71 ..      59      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHH CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvSh 34
                                  +kI+++L++  +  ++e+a+++g+++s++ h
  gi|70607727|ref|YP_256597.1| 17 VKIVNILRDeYNVNISEIAKKIGITRSAIYH 47
                                  79*******777*****************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.7
                                  HHHHHHHHTTS CS
                         HTH_5  4 RlkILklLaeg 14
                                  + k+L lL e+
  gi|70607727|ref|YP_256597.1| 61 KAKLLDLLYEK 71
                                  66788888764 PP

>> Pox_D3  Chordopoxvirinae D3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   1.6e-05     0.011     160     219 ..      18      78 ..      10     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                        Pox_D3 160 avnslifkaesskLkellekll.seskldkakviaivklkdaddikLvkfcYdrdkFraFv 219
                                   ++ ++++++ + ++ e+ +k+  ++s + ++++ +     + +++kL+  +Y++d+ ra  
  gi|70607727|ref|YP_256597.1|  18 KIVNILRDEYNVNISEIAKKIGiTRSAIYHWIWEIAKYIDEENKAKLLDLLYEKDRVRAIS 78 
                                   577899999************88*******999877777777778*************843 PP

>> P22_Cro  DNA-binding transcriptional regulator Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.6e-05      0.03      12      29 ..      31      48 ..      29      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                                  HHHHHHHHTS-HHHHHHH CS
                       P22_Cro 12 vekvAkalgvtksAVsqW 29
                                  ++ +Ak +g+t sA++ W
  gi|70607727|ref|YP_256597.1| 31 ISEIAKKIGITRSAIYHW 48
                                  5789************** PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-05     0.029       3      24 ..      28      49 ..      26      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                    Phage_AlpA  3 ilrlreVeqktglsrstiYrli 24
                                  ++++ e+++k+g+ rs iY +i
  gi|70607727|ref|YP_256597.1| 28 NVNISEIAKKIGITRSAIYHWI 49
                                  58999****************9 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   3.9e-05     0.026      13      58 ..      29      78 ..      21     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                        HTH_40 13 lsieeIAkerglkesTIegHLaeliee...geeidlerlv.seeeekeIe 58
                                   +i eIAk+ g+++s I+  + e+++    +++ +l +l+ ++++ ++I 
  gi|70607727|ref|YP_256597.1| 29 VNISEIAKKIGITRSAIYHWIWEIAKYideENKAKLLDLLyEKDRVRAIS 78
                                  689*****************999888833234455555542556666664 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.5e-05     0.057       1      19 [.      30      48 ..      30      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                                  EHHHHHHHHTTTHHHHHHH CS
                          MerR  1 tIgevAeltGvsprtLRyY 19
                                  +I+e+A++ G++ +++ ++
  gi|70607727|ref|YP_256597.1| 30 NISEIAKKIGITRSAIYHW 48
                                  69****************9 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0001     0.069       6      21 ..      30      45 ..      25      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                      HTH_CodY  6 taskiaDriGitrsvi 21
                                    s+ia +iGitrs i
  gi|70607727|ref|YP_256597.1| 30 NISEIAKKIGITRSAI 45
                                  579***********98 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021      0.14      24      42 ..      29      47 ..      26      56 .. 0.86
   2 ?   -2.4   0.0       6.5   4.3e+03      15      24 ..      88      97 ..      87     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                        HTH_10 24 vtlkeLAkelGIskstlse 42
                                  v+++e+Ak++GI++s+++ 
  gi|70607727|ref|YP_256597.1| 29 VNISEIAKKIGITRSAIYH 47
                                  899************9976 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                        HTH_10 15 mGYFdyPRrv 24
                                  mG+ +  +r 
  gi|70607727|ref|YP_256597.1| 88 MGFLEKEKRK 97
                                  7888877775 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00018      0.12       2      54 ..      30      85 ..      29     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                  EHHHHHHHHTS-HHHHHHHHHHTT..-S-EE.-TTS-EEEEHHHHHHHHHHHHHHH CS
                        MerR_1  2 sigevakilgvtthtlrywekegl..lkpkr.teggrryYtdedierLklikyLlk 54
                                  +i+e ak++g+t + + +w  e    +  +   +    +Y ++ ++ + ++++Ll 
  gi|70607727|ref|YP_256597.1| 30 NISEIAKKIGITRSAIYHWIWEIAkyIDEENkAKLLDLLYEKDRVRAISFVQELLV 85
                                  79*****************9998888888886666669999999999999999985 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.18      20      47 ..      22      49 ..      22      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                  HHHHTS---HHHHHHHHT--HHHHHHHH CS
                  Sigma70_r4_2 20 llryleglsykEIAellgisegtVksrl 47
                                  +lr++ +  + EIA+++gi+ +++++++
  gi|70607727|ref|YP_256597.1| 22 ILRDEYNVNISEIAKKIGITRSAIYHWI 49
                                  589999999**************99876 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00029      0.19      23      39 ..      30      46 ..      20      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                                  -STTTSSSS---SSSS- CS
                         HTH_7 23 siskIAkevnisRsTvY 39
                                   is+IAk  +i+Rs +Y
  gi|70607727|ref|YP_256597.1| 30 NISEIAKKIGITRSAIY 46
                                  59**************9 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.15      12      31 ..      32      51 ..      29      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                YdaS_antitoxin 12 kaLAealgvsqqaVsqWlkg 31
                                  ++ A+++g++++a++ W++ 
  gi|70607727|ref|YP_256597.1| 32 SEIAKKIGITRSAIYHWIWE 51
                                  689**************985 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031       0.2      18      47 ..      26      55 ..      18      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                  HTT--HHHHHHHHT--HHHHHHHHHSCCCT CS
                 HTH_Tnp_Tc3_1 18 llnvklsEiarklsRsRnCIrryLKdPvkY 47
                                  + nv++sEia+k+   R  I  ++ +  kY
  gi|70607727|ref|YP_256597.1| 26 EYNVNISEIAKKIGITRSAIYHWIWEIAKY 55
                                  78************9999998887665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 922.12
//
Query:       gi|70607728|ref|YP_256598.1|  [L=181]
Description: hypothetical protein Saci_2006 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1304.15
//
Query:       gi|70607729|ref|YP_256599.1|  [L=347]
Description: hypothetical protein Saci_2007 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 2270.90
//
Query:       gi|70607730|ref|YP_256600.1|  [L=270]
Description: hypothetical protein Saci_2008 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.7e-42  142.0   1.2    1.4e-41  141.4   1.2    1.3  1  Cas6_N       Cas6 N-terminal domain
    5.7e-17   62.1   0.1    1.4e-16   60.9   0.1    1.7  2  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
    0.00017   22.2   2.1    0.00044   20.8   0.5    2.1  2  Cas_Cas6     CRISPR associated protein Cas6
     0.0063   16.8   0.2      0.014   15.7   0.2    1.6  1  DUF223       Domain of unknown function DUF223
  ------ inclusion threshold ------
      0.042   14.1   0.9      0.096   12.9   0.1    1.9  2  DUF4883      DOmain of unknown function (DUF4883)


Domain annotation for each model (and alignments):
>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   1.2   3.9e-45   1.4e-41       1     114 []       9     124 ..       9     124 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 3.9e-45
                                   EEEEEEEEESS-EE--SSTTHHHHHHHHTSSGGGHHHHH---TT-SEEE---BS.TTSB--S------EE-SSSSEEEEEE CS
                        Cas6_N   1 vkatfevtpkrDvilppltSKvskyillslspslsklvesrekyKplrisvlkd.ngrrlyaegkkkvrlkagerlsfsls 80 
                                   ++++fe+t+++D+ilpp+tSK+s++il++ls+++skl++++++yKplr++v+kd +gr++ya+g+ k ++++++++sf++s
  gi|70607730|ref|YP_256600.1|   9 FYTSFEITTDHDIILPPFTSKLSRLILVKLSDTYSKLQYQNTSYKPLRVTVIKDpEGRPVYARGRGKSIINGNQSYSFTFS 89 
                                   6899***************************************************************************** PP

                                   EESSSCCTTTTGSEEEEEETTE.EEEEEEEEEEEE CS
                        Cas6_N  81 faledvveeivekegvvktvyg.efsveLkeikvv 114
                                   f++e++++ei+ek +++ ++++ +f+v+Lk+ikvv
  gi|70607730|ref|YP_256600.1|  90 FQDENIFREIMEKVQTTVEAWNtKFQVNLKDIKVV 124
                                   *********************************97 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.5   8.9e+03      18      32 ..      91     105 ..      67     124 .. 0.66
   2 !   60.9   0.1     4e-20   1.4e-16       1      86 []     139     263 ..     139     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                                   -HHHHHHHHHHHHHH CS
                   CRISPR_Cas6  18 sprlvfssllrrwna 32 
                                   + +++f+ +++++++
  gi|70607730|ref|YP_256600.1|  91 QDENIFREIMEKVQT 105
                                   445666666666443 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 4e-20
                                   EEEEEEE-EE..........TEEESS--HHHHHHHHHHHHHHHTSS..................EECHHH..........H CS
                   CRISPR_Cas6   1 lrfltPtrfk..........krkgllpsprlvfssllrrwnalaglkgk...............ptveee..........l 46 
                                   ++fltPt+++          +r++l+p +  ++ s++++wn+ + +k++                                
  gi|70607730|ref|YP_256600.1| 139 MEFLTPTLLQpirpnlkrkdNRFVLFPYVPILLFSIVKHWNQNMDQKIHgvtglktlyymrevdY----RlrpvttyydgK 215
                                   68***************988889999********************9888888877766644440....233333334443 PP

                                   H.HEEEEEEEE.......--HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                   CRISPR_Cas6  47 e.gGfvGevky.......sgeleelekllrfaeylgvGkktafGlGkv 86 
                                   +  Gf+G+  +       s+ +++++kll++a+y+gvGk++a+G+G+v
  gi|70607730|ref|YP_256600.1| 216 PvRGFTGWTVFelrskrnSKITRNVQKLLEYANYFGVGKSRAIGFGEV 263
                                   333********7764432226666777*******************97 PP

>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.066   2.4e+02      85     118 ..      82     116 ..       6     117 .. 0.60
   2 !   20.8   0.5   1.2e-07   0.00044      12     146 .]     113     265 ..     104     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.066
                                   .SS---EEEEE.EEEE......TEEEEEEEEEEEE CS
                      Cas_Cas6  85 keeklsikpdk.kvkkivvkkketyirGylgrfel 118
                                   +  ++ ++++  ++ + ++ k +t+++++  +f++
  gi|70607730|ref|YP_256600.1|  82 QSYSFTFSFQDeNIFREIMEKVQTTVEAWNTKFQV 116
                                   33444444444445555555558888888888875 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.2e-07
                                   TEEEEEEEEEE----S..--TCEE..EEESS-BBEEEEEEETTCCEEEEE.....-T.TSTTHHHHHHHHHHHHHHHHHSS CS
                      Cas_Cas6  12 nnefkveevellkepe..itssevv.fktlSPivvrstkkengkkktyyl.....sp.ddeeFsellkenlkkkykalyge 83 
                                   + ++++++++++++ e  +++s++  +++l+P +++ ++++n k+k   +      p       +  ++n+++k++ ++g 
  gi|70607730|ref|YP_256600.1| 113 KFQVNLKDIKVVDQTEslRSESKLYrMEFLTPTLLQ-PIRPNLKRKDNRFvlfpyVPiLLFSIVKHWNQNMDQKIHGVTGL 192
                                   5678899****9999998444444449*********.4455555555533122224545555566779999***9999998 PP

                                   .......SS---EEEEEEEEE.......TEEEEEEE..EEEEE.........EE-HHHHHHHHHC-SCS-CCCT-S-EEE CS
                      Cas_Cas6  84 e.....keeklsikpdkkvkkivvkkk.etyirGyl..grfel.........egdpellklaydaGlGeknsqGFGmvev 146
                                   +     +e++ +++p +       + + +  +rG++    fel         +  ++ll++a + G+G+ ++ GFG v+v
  gi|70607730|ref|YP_256600.1| 193 KtlyymREVDYRLRPVT-------TYYdGKPVRGFTgwTVFELrskrnskitRNVQKLLEYANYFGVGKSRAIGFGEVNV 265
                                   87776666666666655.......334778999999444899999*99999999**********************9986 PP

>> DUF223  Domain of unknown function DUF223
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2     4e-06     0.014      36      85 ..     118     167 ..      87     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                        DUF223  36 issfvvrsnsesiritkheyrilFmeqTeVtssktretvlfnnltpFdyI 85 
                                    + + v  ++es r+++  yr+ F + T +++  +  + ++n+++ F y+
  gi|70607730|ref|YP_256600.1| 118 LKDIKVVDQTESLRSESKLYRMEFLTPTLLQPIRPNLKRKDNRFVLFPYV 167
                                   56678999****************************************98 PP

>> DUF4883  DOmain of unknown function (DUF4883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         1   3.7e+03      30      62 ..       9      41 ..       3      53 .. 0.70
   2 ?   12.9   0.1   2.7e-05     0.096      63     112 ..      78     127 ..      69     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                       DUF4883 30 lykeievdkeeieiiknflksLkkenfiekekk 62
                                  +y  +e+++++  i+  f ++L++   ++ +++
  gi|70607730|ref|YP_256600.1|  9 FYTSFEITTDHDIILPPFTSKLSRLILVKLSDT 41
                                  788888888888888888888877666644443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.7e-05
                       DUF4883  63 leekpeyklfitfesekyvidvyneklisvypwDgkykkdyidiknipas 112
                                   ++ +++y ++++f++e+ + ++ ++   +v  w  k++ ++ dik +++ 
  gi|70607730|ref|YP_256600.1|  78 INGNQSYSFTFSFQDENIFREIMEKVQTTVEAWNTKFQVNLKDIKVVDQT 127
                                   57899************************************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1971.56
//
Query:       gi|70607731|ref|YP_256601.1|  [L=121]
Description: hypothetical protein Saci_2009 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0012   19.2   1.6     0.0019   18.6   1.6    1.4  1  DUF2919        Protein of unknown function (DUF2919)
  ------ inclusion threshold ------
      0.012   14.5   3.2      0.014   14.3   3.2    1.1  1  AA_permease_2  Amino acid permease
      0.012   15.4   0.8      0.017   14.9   0.8    1.2  1  CbtA           Probable cobalt transporter subunit (CbtA)
       0.18   11.9   1.7       0.22   11.7   0.0    2.0  3  DUF4234        Domain of unknown function (DUF4234)
        5.2    7.3   7.7       0.44   10.7   1.2    2.3  3  COX2_TM        Cytochrome C oxidase subunit II, transmembrane


Domain annotation for each model (and alignments):
>> DUF2919  Protein of unknown function (DUF2919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.6   5.2e-07    0.0019      47     128 ..      38     115 ..       7     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                       DUF2919  47 alfYPdkssfylgLalgvpalllllligrrkkssewleklwragrplllllllvdlllqlyrlalsheafswltaltllll 127
                                   +++YP  +  +l L+lg+ +++l+++++ r  s e l++l ++  ++ +++l+++l+++++++ + ++    + a+ +l++
  gi|70607731|ref|YP_256601.1|  38 NMVYPLDD--ILVLVLGIVGIVLYFAMRSR--SVEGLKRLNNIYLTVFVVALAIKLVWTIIEAPHPDDMADDIPAVIILAV 114
                                   58999555..677899**********9999..679**************************99998887777777766665 PP

                       DUF2919 128 l 128
                                   +
  gi|70607731|ref|YP_256601.1| 115 V 115
                                   5 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   3.2   3.9e-06     0.014      98     165 ..      18      92 ..      10     118 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-06
                 AA_permease_2  98 vaasyllnalgpdlqgn..........twltyliaiaililvalinirgikesakiqnilgilkillpliiliilgli 165
                                   +++s  l ++g+d+  +          ++l+++++i+ ++l +++ +r++ ++++++ni  ++ ++  l+i ++  + 
  gi|70607731|ref|YP_256601.1|  18 LFFSITLLVFGSDIAAEiadnmvypldDILVLVLGIVGIVLYFAMRSRSVEGLKRLNNIYLTVFVV-ALAIKLV--WT 92 
                                   45555555555544444444455555599******************************8777774.4444333..22 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8   4.9e-06     0.017     150     215 ..      47     110 ..      46     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.9e-06
                          CbtA 150 atvalsavalalavflarrlaargwnavlaaavaflvlvavallalPhvveaPqpeaaesgfpaal 215
                                   ++++l++v+++l  ++++r  +    + l  +   + +va+a+ ++ +++eaP+p++++ ++pa +
  gi|70607731|ref|YP_256601.1|  47 LVLVLGIVGIVLYFAMRSRSVE--GLKRLNNIYLTVFVVALAIKLVWTIIEAPHPDDMADDIPAVI 110
                                   6789999999999999998844..45566666667888999999999*********9999999865 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     6e-05      0.22      45      67 ..      17      65 ..       2      68 .. 0.76
   2 ?   -2.2   0.1       1.3   4.6e+03      16      25 ..      76      85 ..      74      96 .. 0.59
   3 ?   -2.2   0.0       1.3   4.8e+03       3      12 ..     106     115 ..     100     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                       DUF4234 45 flllsl..........................itcgiysivwayklgkr 67
                                  fl++s+                          +++gi++iv+++ +++r
  gi|70607731|ref|YP_256601.1| 17 FLFFSItllvfgsdiaaeiadnmvyplddilvLVLGIVGIVLYFAMRSR 65
                                  34466677777888888888888888888888**************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                       DUF4234 16 IYslyWlykl 25
                                  IY  ++++ l
  gi|70607731|ref|YP_256601.1| 76 IYLTVFVVAL 85
                                  4555554433 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.3
                       DUF4234   3 lavvilLsiv 12 
                                   +++vi+L +v
  gi|70607731|ref|YP_256601.1| 106 IPAVIILAVV 115
                                   6678888776 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.81   2.9e+03      19      39 ..       6      27 ..       2      35 .. 0.56
   2 ?   10.7   1.2   0.00012      0.44      16      74 ..      35      94 ..      25      97 .. 0.78
   3 ?   -0.8   0.3      0.48   1.7e+03      74      83 ..     106     115 ..     104     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.81
                       COX2_TM 19 eleelhdyi.lliltlililVl 39
                                  e+e+l   + +++ + i++lV+
  gi|70607731|ref|YP_256601.1|  6 EIEKLVARTrVFLFFSITLLVF 27
                                  5555544431344455666665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                       COX2_TM 16 lmeeleelhdyilliltlililVly.ilvlilvefrrrknkitakylvhgqeiEiiWTii 74
                                  +++++ +  d+il++++ i+ +Vly ++ +  ve  +r n+i  + +v +  i ++WTii
  gi|70607731|ref|YP_256601.1| 35 IADNMVYPLDDILVLVLGIVGIVLYfAMRSRSVEGLKRLNNIYLTVFVVALAIKLVWTII 94
                                  55556666678888888888888772566778888899999999***************8 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.48
                       COX2_TM  74 iPalililia 83 
                                   iPa+i++++ 
  gi|70607731|ref|YP_256601.1| 106 IPAVIILAVV 115
                                   7999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 857.24
//
Query:       gi|70607732|ref|YP_256602.1|  [L=98]
Description: hypothetical protein Saci_2010 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-19   69.1   0.1    3.3e-19   68.8   0.1    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.1   1.8e-23   3.3e-19       1      75 [.       1      78 [.       1      79 [. 0.93

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.8e-23
                                  EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHT.TTC...EEEEEEEETCHHHT CS
                   CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidp.eed...siriykltekqfek 75
                                  ml++v+YDi +d+  r kva++lkk+G+ r+Q+SVF+gel+++++++l + l+ + ++ +e+   +++i+++te+qf++
  gi|70607732|ref|YP_256602.1|  1 MLYVVFYDI-SDDDLRGKVADFLKKKGLVRLQFSVFFGELNSSRVKDLTAGLRLYAKRrSEGerfNVLILPVTETQFKQ 78
                                  99*******.***********************************************84233677***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 652.00
//
Query:       gi|70607733|ref|YP_256603.1|  [L=301]
Description: hypothetical protein Saci_2011 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-63  213.3   0.1    4.6e-63  213.0   0.1    1.0  1  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.0   0.1   2.6e-67   4.6e-63       2     251 ..       9     256 ..       8     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 213.0 bits;  conditional E-value: 2.6e-67
                                   EEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSSTH CS
                      Cas_Cas1   2 yvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.eesgnv 81 
                                   +v ++ga+lr++++ ++++ ++e k +++ ++++siv++++  +s+++++l+ e+g+++vf+++++ ++++l+p + sg++
  gi|70607733|ref|YP_256603.1|   9 FVKDHGAHLRVNKGMIECSVKDEVKWSVSPSELSSIVVISRSAISSEVIKLAYEHGVDLVFFEKYE-PIAKLIPaRYSGSM 88 
                                   6899*************************************************************6.67777777****** PP

                                   HHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHH CS
                      Cas_Cas1  82 elrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaY 162
                                   +l ++Q+ +++ ++     a+++v gkl+nq  +lr+++r++   +l+ + + l+el++++ ++++++e++++E++ ak Y
  gi|70607733|ref|YP_256603.1|  89 RLWLKQMLVVHRKT-MYLYAREFVYGKLHNQMMTLRYYERKY---SLDLKTRVLSELAKSVLALTDVKEIMQVEAQGAKVY 165
                                   **********9988.9999***********************...89999999**************************** PP

                                   HHHHHHHCSCGGS-SS-SSSS-..SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHH CS
                      Cas_Cas1 163 feafdkllkeefefegRsrrpp..kDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpll 241
                                   ++ +++ll++++ f+gR++r    kDp+N+ L+ gY++l + vlsa+ +vgL+PyiGfLH+ r+gr+sL++DLmEefR +l
  gi|70607733|ref|YP_256603.1| 166 WSGVKNLLPKSLGFKGRKKRIElnKDPFNVALNIGYAMLRKLVLSALISVGLNPYIGFLHRVRSGRTSLVFDLMEEFRSPL 246
                                   ********************96559******************************************************** PP

                                   CHHHHHHHHH CS
                      Cas_Cas1 242 vDrlvlslin 251
                                   vDr ++ + +
  gi|70607733|ref|YP_256603.1| 247 VDRKLIGIAR 256
                                   ***8887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2120.31
//
Query:       gi|70607734|ref|YP_256604.1|  [L=133]
Description: hypothetical protein Saci_2012 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-20   71.4   0.1      1e-19   71.2   0.1    1.0  1  Cas_Cas4  Domain of unknown function DUF83
    2.1e-05   24.6   0.1    2.5e-05   24.3   0.1    1.0  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.1   1.1e-23     1e-19      54     161 ..      13     121 ..       4     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.1e-23
                      Cas_Cas4  54 sikiDvvekekeklvvvEvKkskkkeeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeie 134
                                   +++ D++    +   + ++K ++k + ++k+Q+ +Y +l+e+kg+ +keG ++y+k k+ ++v++t+++r+ +e++i++i+
  gi|70607734|ref|YP_256604.1|  13 TGQPDYILAFYHYFSPLDIKAGEKVRLDHKMQVIFYSYLMERKGMLVKEGLIYYVKLKRIVRVKYTNQERRYIESVINKIR 93 
                                   56677777777778889**************************************************************** PP

                      Cas_Cas4 135 eiisse.kppkvkkkkiCkkCayaelCl 161
                                      s   k + v+ +k+C +C + ++C 
  gi|70607734|ref|YP_256604.1|  94 GTESGRrKERIVQPAKKCINCGFLPYCN 121
                                   **9998567778999************6 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   2.8e-09   2.5e-05     129     255 .]      11     121 ..       4     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.8e-09
                      PDDEXK_1 129 rLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvk 209
                                   +L+G+ D +    +++  +D K g   +      +l + +Q+ +Y ++++++  ++ +  ++ ++y++l        +++ 
  gi|70607734|ref|YP_256604.1|  11 DLTGQPDYILAFYHYFSPLDIKAGE--KV-----RLDHKMQVIFYSYLMERKG-MLVK--EGLIYYVKL--------KRIV 73 
                                   59********9999********888..23.....356899***********93.4433..677777777........6666 PP

                      PDDEXK_1 210 kmalteeeleallqeleel..aeeilagefparpskkCeyCpyksvCr 255
                                   ++++t +e++ +++ ++++   e+ +++e  ++p kkC +C + ++C+
  gi|70607734|ref|YP_256604.1|  74 RVKYTNQERRYIESVINKIrgTESGRRKERIVQPAKKCINCGFLPYCN 121
                                   6667777777777777776655666777899999999**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 980.82
//
Query:       gi|70607735|ref|YP_256605.1|  [L=386]
Description: hypothetical protein Saci_2016 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.043   13.9   0.0      0.082   12.9   0.0    1.4  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.6e-06     0.082      68     120 ..      93     144 ..      89     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-06
                   B12-binding  68 vkelvel...lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                   ++el ++   lk  r ++kv+vGG++    +e+ l++ + +d v +ge+e++l+ l
  gi|70607735|ref|YP_256605.1|  93 FQELSRRvsrLKD-RYDFKVIVGGPG---SWEFSLNTPEWVDTVLMGEAEETLPKL 144
                                   5555555553333.3589******98...999999754889************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 2037.85
//
Query:       gi|70607736|ref|YP_256606.1|  [L=158]
Description: phosphohistidine phosphatase/mutase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-14   52.6   0.0    5.1e-12   45.9   0.0    2.0  2  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   2.9e-16   5.1e-12       1      81 [.       4      84 ..       4      87 .. 0.90
   2 !    5.0   0.0   0.00098        17     136     182 ..      99     138 ..      90     151 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 2.9e-16
                                  EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTT..S---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS--- CS
                    His_Phos_1  1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlag..epidaiysSplkRarqTaeliaealglpveldegLrEid 81
                                  l++vRHGe e +++g     +d +L ++G++q++++a  l +    id+ ++S+l Ra+q ae i+++lg +  + e L+E++
  gi|70607736|ref|YP_256606.1|  4 LIIVRHGEAEPQVDG--TDDKDRKLIKKGIKQMKRVASLLDQmdYTIDRYLTSTLMRAYQSAEVILDELGEDQGKIETLNELN 84
                                  799***********7..999**********************55556666********************8888888888865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.00098
                                   HTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE- CS
                    His_Phos_1 136 rhegetvlvVsHggvirallarllglpleelrrleldnaslsvlefd 182
                                     +   +lvV H  ++  l++ l g ++e+      +  +l v+e+d
  gi|70607736|ref|YP_256606.1|  99 LDNI-SILVVGHEPFLSHLIKSLCGGNVEM------KKGALAVVEYD 138
                                   4433.3******************988875......34444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1024.67
//
Query:       gi|70607737|ref|YP_256607.1|  [L=411]
Description: hypothetical protein Saci_2018 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-41  140.2   0.0    1.3e-40  139.6   0.0    1.2  1  Ppx-GppA  Ppx/GppA phosphatase family
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.018   14.0   0.0    1.4  1  DDR       Diol dehydratase reactivase ATPase-like domain


Domain annotation for each model (and alignments):
>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.0   1.5e-44   1.3e-40       8     280 ..      24     287 ..      17     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.5e-44
                                   TEEEEEEEEEEE--CCCCCHCCSSC-HHHHHHHHHHHHHHHHHCCCTTGCCEEEEEEHHHHHSTTHHHHHHHHCCCCSS-E CS
                      Ppx-GppA   8 gllqivarekrkvrLaeglnesgrlqeeaiertisaLkefaellqkfkvenvrvVATsalRdavNadeFlarvkkevglkv 88 
                                   + + i+ ++k+ +rL+eg++e  ++++++++++ ++ k f  +l+k +++ v+ V+Tsa R a N + + +   + +g+k 
  gi|70607737|ref|YP_256607.1|  24 QTFRILGSQKSFLRLGEGVKEGSPISPDRVNEAEKVFKSFRAILNKKGIKDVKLVGTSAFRYASNGNQVAELLSEIIGVKM 104
                                   55899**************************************************************************** PP

                                   EEE-HHHHHHHHHHHHHHHT---SSEEEEEEETTEEEEEEEETTEEEEEEEES--CCHHHHHHSGCCC--HHHHHHHHHHH CS
                      Ppx-GppA  89 eiisgeeEarliylgvvssllekgrglviDiGGGStElvlgeekevsklvSlplGavrlterfltddpltkeeveaarkav 169
                                    +++geeE+++++ gv ++l    +g + D+GGGS+E+v  ++++v++++  +lGa +l+++  ++  l k++ +++    
  gi|70607737|ref|YP_256607.1| 105 RVLTGEEEGEMSAVGVLNTL-PVDSGAMFDLGGGSLEVVYFDSRQVKEVYHFDLGALKLARELKDESELRKRIRSELSV-- 182
                                   ********************.888889**********************************988877777776666655.. PP

                                   HHHCTTTHHHHCCCEHHCCCCCCCHCCHHCHHHHHHCT.SSCEEEHHHHHHHHHHHCTSSCHHHHHSTTS-CCHHCTHHHH CS
                      Ppx-GppA 170 ekeleevkdevkkegewtrlvgtsgtisalaeltelhgekgyeitaeeleeliekllqlkkeeelklagvsdeRadvivag 250
                                      l+++k  +   g  +r+++++    ++ +l++ hg   y i+ +++ ++++ l++l+ ee+ +l g+ +eR   +  +
  gi|70607737|ref|YP_256607.1| 183 ---LKPIKGVLVGSGGNIRAIAKMDARVSAFPLKSIHG---YVIKTKQIGKYSKVLMNLDPEERENLPGIGKERSYTVHTA 257
                                   ...5555544333346**********************...**************************************** PP

                                   HHHHHHHHHHCT-SEEEEES--HHHHHHHH CS
                      Ppx-GppA 251 alilsavlealeieaviisegalrEGvlys 280
                                    ++++++ +al    + is  +lrEGvl++
  gi|70607737|ref|YP_256607.1| 258 SVVIEELGNALDSPTIMISSFGLREGVLME 287
                                   ****************************87 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     2e-06     0.018      97     160 ..      90     154 ..      65     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-06
                           DDR  97 qkiaeeleeelgvkvev..ggvEaemAilGalttPGtekplailDlGaGstDaalieeegevkavh 160
                                   +++ae l+e +gvk +v  g  E em ++G l t  +++  a+ DlG+Gs +  + ++++  +  h
  gi|70607737|ref|YP_256607.1|  90 NQVAELLSEIIGVKMRVltGEEEGEMSAVGVLNTLPVDSG-AMFDLGGGSLEVVYFDSRQVKEVYH 154
                                   6899999999998877721556899*********988876.789*******977777665555545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2783.61
//
Query:       gi|70607738|ref|YP_256608.1|  [L=213]
Description: thymidylate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-28  100.3   0.0    3.3e-28   98.6   0.0    1.7  1  Thymidylate_kin  Thymidylate kinase
    4.7e-05   23.3   0.1    7.7e-05   22.6   0.1    1.5  1  dNK              Deoxynucleoside kinase
      0.004   17.7   0.0      0.011   16.2   0.0    1.8  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.049   14.1   0.1       0.63   10.5   0.0    2.7  2  AAA_17           AAA domain
       0.09   12.5   0.2        6.2    6.5   0.1    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.12   12.5   0.0       0.31   11.2   0.0    1.7  2  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   1.1e-31   3.3e-28       1     185 []       8     200 ..       8     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.1e-31
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                   +EG+DG+GK++qa llk++l+++ + +++t  +++  i + i+e+ + ++ l ++t+ l  a d ++  e++i p lk g+
  gi|70607738|ref|YP_256608.1|   8 FEGIDGSGKSSQASLLKSWLSKRRY-TFITEWNSSEWIHDIIKEAKK-KNLLTPLTFSLIHATDFADRYEKYILPMLKCGF 86 
                                   8***********************9.588888888889999999966.********************************* PP

                                   EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS.............TTTSHHHHH CS
               Thymidylate_kin  82 tvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrde.............ldeeeeeql 149
                                   +vi dRy++  +a +++ +gvd+++v++l  +++ kPd+tf++ v+ evalkRl+  +              +   ee  +
  gi|70607738|ref|YP_256608.1|  87 VVIADRYIYTAYARDSV-RGVDIEWVKKLYSFAV-KPDITFYIRVPSEVALKRLKSSRRqikpteagadvfpNLTPEEGFI 165
                                   ****************8.55*************9.*******************987776899988877773334455567 PP

                                   HHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
               Thymidylate_kin 150 dflrkvrerylelakederiliidasksieevheeI 185
                                   +++ ++ e+y+++a+ +++++++d +k  ++v++eI
  gi|70607738|ref|YP_256608.1| 166 KYQSSIIEVYDRIAE-ENNFVVVDGTKDPRQVQSEI 200
                                   899999********5.*****************998 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   2.6e-08   7.7e-05       1     147 [.       6     145 ..       6     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.6e-08
                                   EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS.......HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSS CS
                           dNK   1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk.......nlLekfYkdpsrwsfalqtyvllsrlkqqlealat 74 
                                   i+ eG  g+GKs+ ++lL+  l  k  +  + +w n  +       +  +k    p  +s+   t +   + k++l +l++
  gi|70607738|ref|YP_256608.1|   6 IAFEGIDGSGKSSQASLLKSWLS-KRRYTFITEW-NSSEwihdiikEAKKKNLLTPLTFSLIHATDFADRYEKYILPMLKC 84 
                                   678999************99995.4444455555.22222332233333344444566666667777777777777778** PP

                                   S-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCC CS
                           dNK  75 kqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgree 147
                                   + vv+++R iy++         +++++  ++++  k+l+++++    kpd+  Y++++ e+ l+r+k   r+ 
  gi|70607738|ref|YP_256608.1|  85 GFVVIADRYIYTAY--------ARDSVRGVDIEWVKKLYSFAV----KPDITFYIRVPSEVALKRLKSSRRQI 145
                                   ***********998........678999999999*******99....7******************9877664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.8e-06     0.011       1     114 [.       6     142 ..       6     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                        AAA_18   1 IlltGtpGvGKttlakeL....skrlgf............gvnlrdvakenglllevdpe..aldeskrldedkldkllda 63 
                                   I+  G+ G+GK++ a  L    skr  +            ++++++  k+n l    +    a+d  +r ++  l  l  +
  gi|70607738|ref|YP_256608.1|   6 IAFEGIDGSGKSSQASLLkswlSKRR-YtfitewnssewiHDIIKEAKKKNLLTPLTFSLihATDFADRYEKYILPMLKCG 85 
                                   7899**************66665553.244777788888777777777777666666666788888888888888888888 PP

                        AAA_18  64 leenss..aleegknlvidghlaeleseaakdikk....vvLtaspeelleRlekRg 114
                                   +  +++   ++      + g+  e+++  + +++k    ++++++ e+ l+Rl+  +
  gi|70607738|ref|YP_256608.1|  86 FVVIADryIYTAYARDSVRGVDIEWVKKLYSFAVKpditFYIRVPSEVALKRLKSSR 142
                                   888777884555555556666666666666666668888**************9865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00021      0.63       2     127 ..      10     143 ..       9     151 .. 0.68
   2 ?   -2.6   0.0       2.3   6.9e+03      63      78 ..     176     189 ..     165     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                   E-TTSSHHHHHHHHH...HHHTEEEE...EHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEE CS
                        AAA_17   2 GgPGsGKgtqceklv...ekygfthl...saGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvl 75 
                                   G+ GsGK+ q++ l+    k  +t++   + ++ + + +k+ +  k+     + +l +  ++ ++ ++ i  +  +   v+
  gi|70607738|ref|YP_256608.1|  10 GIDGSGKSSQASLLKswlSKRRYTFItewNSSEWIHDIIKEAKK-KNLLTPLTFSLIHATDFADRYEKYILPMLkCGFVVI 89 
                                   88899999999998733323355554333778888887777664.233333366777888888888888888753445678 PP

                                   EEE-SEEEETTEEEESSHHHHHH.....HH..SEEEEEE--HHHHHHHHHHHTTST- CS
                        AAA_17  76 vdghprikeqagfldglpkevle.....elkpdaiilleadpeeilerrlkdrtrgr 127
                                    d +  +   ++ + g++ e ++      +kpd+ +++ ++ e+ l+r+++     r
  gi|70607738|ref|YP_256608.1|  90 ADRYIYTAYARDSVRGVDIEWVKklysfAVKPDITFYIRVPSEVALKRLKSS---RR 143
                                   88888888888888888876665244446679**********9888887664...33 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                   HHHHHHHHSSEEEEEE CS
                        AAA_17  63 ekiaeeakkkgvlvdg 78 
                                   ++iaee  ++ v+vdg
  gi|70607738|ref|YP_256608.1| 176 DRIAEE--NNFVVVDG 189
                                   445543..33356665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.008        24       2      76 ..       6      75 ..       5     102 .. 0.66
   2 ?    6.5   0.1    0.0021       6.2     148     178 ..      98     128 ..      79     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.008
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllye 76
                                  I+  g  G+Gk++ a  l++ + +   +      + + +  +  +d+  e +k++    ++f    a df++ ye
  gi|70607738|ref|YP_256608.1|  6 IAFEGIDGSGKSSQASLLKSWLSKRRYT-----FITEWNSSEWIHDIIKEAKKKNLLTPLTFSLIHATDFADRYE 75
                                  7888999***************965555.....444444444444444444444555566666666666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0021
                           PRK 148 lqRDiaeRGrsleavldsil.rrkpdyvnyik 178
                                     RD   RG ++e v++ +  ++kpd + yi+
  gi|70607738|ref|YP_256608.1|  98 YARDS-VRGVDIEWVKKLYSfAVKPDITFYIR 128
                                   56774.6************999********97 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.31       1     129 [.       5     151 ..       5     160 .. 0.61
   2 ?   -0.2   0.0      0.33   9.8e+02     130     130 ..     152     152 ..     120     211 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        AAA_33   1 lvllvGlpGsGKstlaerl...lkklgavllssdt........lrrrlfgtdqqsktdytrvldrlyqilnelarkalsag 70 
                                   l+ + G  GsGKs  a  l   l k+ ++++++ +        ++++ +++  +++t +   ++++ ++ ++++  +l+ g
  gi|70607738|ref|YP_256608.1|   5 LIAFEGIDGSGKSSQASLLkswLSKRRYTFITEWNssewihdiIKEAKKKNLLTPLTFSLIHATDFADRYEKYILPMLKCG 85 
                                   7899*********86654433399999999999885555444333333334444444444334445556678888888889 PP

                        AAA_33  71 rnvildatnlsrrer.......arflklarrlgvp.vrivvvetdeetlkeRlakRaangddrsevp 129
                                   + vi+d    ++ +r        +++k +  + v+ +   +++++ e++ +Rl+   ++  +++e++
  gi|70607738|ref|YP_256608.1|  86 FVVIADRYIYTAYARdsvrgvdIEWVKKLYSFAVKpDITFYIRVPSEVALKRLKSSRRQ-IKPTEAG 151
                                   99998887666555544556653444444444444155588888888888888765543.3455555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                        AAA_33 130 e 130
                                    
  gi|70607738|ref|YP_256608.1| 152 A 152
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1458.55
//
Query:       gi|70607739|ref|YP_256609.1|  [L=210]
Description: thymidylate kinase-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-11   43.6   0.0      3e-11   43.3   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
     0.0013   18.7   0.2      0.081   12.8   0.0    2.2  2  dNK              Deoxynucleoside kinase
     0.0024   18.4   0.0     0.0067   17.0   0.0    1.8  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.019   15.4   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.015   15.1   0.0      0.023   14.5   0.0    1.3  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.018   14.5   0.0      0.033   13.7   0.0    1.5  1  KTI12            Chromatin associated protein KTI12
      0.024   14.5   0.0      0.047   13.6   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.033   14.0   0.0      0.083   12.7   0.0    1.6  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.12   12.6   0.0       0.18   11.9   0.0    1.4  1  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.5e-14     3e-11       1     185 []       9     198 ..       9     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.5e-14
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT- CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgk 81 
                                   iEG+  +GKtt+++ l+++l+++g+ vv+t   +++++   + +++++   +++ t+ l ++ d ++++e+++kp+l++g+
  gi|70607739|ref|YP_256609.1|   9 IEGIMSSGKTTHVQSLRDYLEDRGY-VVTTIGIQSSKLMADAIASVKRDIVFQRRTLFLAYVTDLADQTENLVKPSLDSGF 88 
                                   8***********************9.788887777776555555567799999999************************* PP

                                   EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS.....TTTSHHHHHHHHHHHHH CS
               Thymidylate_kin  82 tvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrde.....ldeeeeeqldflrkvre 157
                                   +vi d y++   a++  +++++ ++v  +   ++ k  l + l  +p + ++R+ kr+      +   e  +l++ + +  
  gi|70607739|ref|YP_256609.1|  89 IVIADGYVLTLEAWAL-TRRLEREWVEGVLSMLP-KASLSISLISPPTEIMRRIIKRKGfldplS---ESVDLNVKEDTFL 164
                                   **********999998.56689999999999988.9999999999*********99998865541...4444444444444 PP

                                   HHHHHHH.TTSTE.....EEEETTS-HHHHHHHH CS
               Thymidylate_kin 158 rylelak.ederi.....liidasksieevheeI 185
                                    y++ +k ++ ++      ++ ++++++ev +eI
  gi|70607739|ref|YP_256609.1| 165 AYKKYVKeFQSHLksispNVLVTKNNVNEVNREI 198
                                   4444444334444000114556677777777665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   4.1e-05     0.081       1      23 [.       7      29 ..       7      38 .. 0.89
   2 ?    4.0   0.1      0.02        39     111     182 ..     111     190 ..      92     208 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                  EEEEESTTSSHHHHHHHHHCCST CS
                           dNK  1 ivveGnIgaGKstlvklLskklg 23
                                  i++eG +++GK+t v+ L++ l+
  gi|70607739|ref|YP_256609.1|  7 IAIEGIMSSGKTTHVQSLRDYLE 29
                                  89****************99886 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.02
                                   HHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT...TS-HHHHHHHHHHHHHHHTS....GGCS.-EEEEETSS CS
                           dNK 111 elldnlleelakpdlliYLkasletclerikkRgreeek...kieldYlekLhekyeewlkk....lnev.pvlvidvee 182
                                   e+ + +l+ l+k +l i L  ++ ++++ri kR+   +     ++l+  e     y++++k+    l+++ p + +  ++
  gi|70607739|ref|YP_256609.1| 111 EWVEGVLSMLPKASLSISLISPPTEIMRRIIKRKGFLDPlseSVDLNVKEDTFLAYKKYVKEfqshLKSIsPNVLVTKNN 190
                                   67788888999999999999*********999987655445544444444444444444444111144445544444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.4e-06    0.0067       1     114 [.       7     144 ..       7     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.ale 72 
                                   I++ G++ +GKtt  + L++ l          g++++++ ++   +  +d     + + l   ++  l d+ e+  + +l+
  gi|70607739|ref|YP_256609.1|   7 IAIEGIMSSGKTTHVQSLRDYLeDRgyvvttiGIQSSKLMADAIASVKRDIV--FQRRTLFLAYVTDLADQTENLVKpSLD 85 
                                   89****************6665333668899999999999998888888888..666666666666666666666667677 PP

                        AAA_18  73 egknlvidghlaeleseaakdikk.................vvLtaspeelleRlekRg 114
                                   +g  ++ dg +  le +a++++                   + L  +p e ++R+ kR+
  gi|70607739|ref|YP_256609.1|  86 SGFIVIADGYVLTLEAWALTRRLErewvegvlsmlpkaslsISLISPPTEIMRRIIKRK 144
                                   77777778888888888777766688888999999999999**************9996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   9.4e-06     0.019      24      91 ..       4      63 ..       1     143 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.4e-06
                        AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaes 91
                                  ++++ + G   +GK++ v++l+++le++ g+++++   q+      s   a+a+ + ++ r++  + ++
  gi|70607739|ref|YP_256609.1|  4 GRIIAIEGIMSSGKTTHVQSLRDYLEDR-GYVVTTIGIQS------SKlMADAI-A-SVKRDIVFQRRT 63
                                  4799999***************988888.77766655555......34466666.4.555555555444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.023       1      97 [.       4     101 ..       4     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                   --EEEEEE-TTSSHHHHHHHHHHHSSS.-EEEEEHHHHHHH.S-GGGGTSTTSEEEETTSEEE-HHHHHHHHHHHHHHHHH CS
                           CPT   1 ariilLnGgsssGKsslaralqevlde.pwlhlgvDafvea.lppkrqdeadglefeteleeigpeldlllaalyeavaam 79 
                                   +rii ++G  ssGK++ ++ l++ l++  ++   +     + + ++  + + ++ f+  +    + +  l++   + v+  
  gi|70607739|ref|YP_256609.1|   4 GRIIAIEGIMSSGKTTHVQSLRDYLEDrGYVVTTIGIQSSKlMADAIASVKRDIVFQ-RRTLFLAYVTDLADQTENLVKPS 83 
                                   79*********************9876257766666666663666777788999888.55556888888999999****** PP

                                   HHTT-EEEEEE--TTTHH CS
                           CPT  80 araGnnvivDdvilekew 97 
                                   ++ G  vi+D ++l+ e+
  gi|70607739|ref|YP_256609.1|  84 LDSGFIVIADGYVLTLEA 101
                                   **********88777653 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.033       4      44 ..       7      47 ..       5      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                  EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TT CS
                         KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiek 44
                                  + + G+ ssGK+t ++ L+++le++++ v+ i  +s ++  
  gi|70607739|ref|YP_256609.1|  7 IAIEGIMSSGKTTHVQSLRDYLEDRGYVVTTIGIQSSKLMA 47
                                  6788999*****************99999988776666333 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.047       1      37 [.       6      42 ..       6      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKhah 37
                                  +++i g   sGKTt ++ l   l++rg+ v ti  ++
  gi|70607739|ref|YP_256609.1|  6 IIAIEGIMSSGKTTHVQSLRDYLEDRGYVVTTIGIQS 42
                                  6889999************************996555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.2e-05     0.083       3      30 ..      11      38 ..       9      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                    ATP_bind_1  3 GpaGsGKttfvgalseilelrgrsvavv 30
                                  G  +sGKtt v++l ++le+rg+ v ++
  gi|70607739|ref|YP_256609.1| 11 GIMSSGKTTHVQSLRDYLEDRGYVVTTI 38
                                  899******************9988876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.2e-05      0.18       2     120 ..       7     145 ..       6     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                        AAA_33   2 vllvGlpGsGKstlaerl...lkklg....avllssdtlrrrlfg.......tdqqsktdytrvldrlyqilnelarkals 68 
                                   + + G   sGK+t +++l   l+ +g    ++ + s +l+    +          q+ t      ++l +++++l++  l 
  gi|70607739|ref|YP_256609.1|   7 IAIEGIMSSGKTTHVQSLrdyLEDRGyvvtTIGIQSSKLMADAIAsvkrdivF--QRRTLFLAYVTDLADQTENLVKPSLD 85 
                                   5678999*********9977677777444333355555555333323222211..12333333445567788899999999 PP

                        AAA_33  69 agrnvildat........nlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                   +g+ vi+d          +++r er+++  +++ l  + + + + +++ ++ +R+ kR+ 
  gi|70607739|ref|YP_256609.1|  86 SGFIVIADGYvltleawaLTRRLEREWVEGVLSMLPKASLSISLISPPTEIMRRIIKRKG 145
                                   *******99844444444333444444444444444445668888888999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      803  (0.0447878); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1371.67
//
Query:       gi|70607740|ref|YP_256610.1|  [L=206]
Description: hypothetical protein Saci_2021 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-06   26.5   2.0     0.0014   18.6   1.5    2.4  1  CHAD      CHAD domain


Domain annotation for each model (and alignments):
>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.5   7.9e-08    0.0014      22     191 ..      22     142 ..       9     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.9e-08
                                   THHHHHHHHHHHHHHHHHHHTTTSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH.HTS-TTTCGGGHHHHHHHH CS
                          CHAD  22 peavHqmRvalRRlRsalrlfapvldkeeaaalekelrwlaraLGeaRDldVllerllsrleerlpaaeqealerllkrle 102
                                    e++H++Rv lR+  +  r+    l  ++  +   +  +l+++LG+ RD d+l                     +++ + +
  gi|70607740|ref|YP_256610.1|  22 QEDIHDARVELRKYLTIARTT-YKL--HNNPECVLRASKLMKRLGKIRDMDILA--------------------CVRSDSR 79 
                                   599*****************9.555..45556666778**************77....................3333333 PP

                                   HHHHHHHHHHHHHHTSHHHHHHHHHHHHHHT--S--TSBHHHHHHHHHHHHHHHH.HHHH--------THHHHHHHHHHHH CS
                          CHAD 103 kerkrararvlaaLdsaryqalldaldallaaerleaepaaaalekrlrkayrklekraakaeadesdeealHelRkaaKr 183
                                   ++ +r+   + + +++    +l     +l              +++r+   yr+l     k      +e ++H++Rk ++ 
  gi|70607740|ref|YP_256610.1|  80 DKLARETVSMFQVMRKYLLPRLYG--SRL-------------LVAERIYNDYRRL-----K------EEVEFHSIRKIVRE 134
                                   332222222222222221111111..112.............2344444555555.....2......24566666666666 PP

                                   HHHHHHHH CS
                          CHAD 184 lRYaaeaf 191
                                   +R  +e +
  gi|70607740|ref|YP_256610.1| 135 VRFLVESL 142
                                   66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1379.76
//
Query:       gi|70607741|ref|YP_256611.1|  [L=209]
Description: ISC1913-like resolvase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-24   86.0   0.1    3.7e-24   85.5   0.1    1.3  1  Resolvase   Resolvase, N terminal domain
    1.9e-13   50.3   0.2    3.9e-13   49.3   0.2    1.6  1  HTH_17      Helix-turn-helix domain
    7.4e-06   25.6   0.3    1.8e-05   24.4   0.1    1.8  2  MerR        MerR family regulatory protein
    5.5e-05   23.2   0.1    0.00011   22.2   0.1    1.6  1  MerR_1      MerR HTH family regulatory protein
    0.00059   19.6   0.0     0.0015   18.3   0.0    1.6  1  HTH_23      Homeodomain-like domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.031   14.3   0.0    1.7  1  HTH_29      Winged helix-turn helix
      0.066   13.3   0.0       0.16   12.2   0.0    1.5  1  HTH_28      Helix-turn-helix domain
      0.078   13.3   0.0        0.3   11.4   0.0    1.8  2  Helicase_C  Helicase conserved C-terminal domain
      0.095   12.5   0.0       0.19   11.6   0.0    1.5  1  Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
       0.12   12.7   0.0       0.22   11.9   0.0    1.5  1  HTH_Tnp_1   Transposase


Domain annotation for each model (and alignments):
>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.1   2.1e-27   3.7e-24       1     134 [.      61     190 ..      61     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.1e-27
                                   EEEEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S... CS
                     Resolvase   1 aigYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRsvr 81 
                                   a++YaRvS+++q+ +l+rQ+e l++y+ ++g+k+v++ +D   SG +++R+ l +l ++++egk+dv+v++  dRL+R  +
  gi|70607741|ref|YP_256611.1|  61 AVIYARVSSSDQKSDLDRQIEYLTNYCLAKGYKVVDTLSDI-SSGLNTKRKNLLKLFQLVKEGKVDVVVITYKDRLTRFGF 140
                                   69***************************************.*************************************** PP

                                   S-HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHHHHHHHCT-T CS
                     Resolvase  82 dlltlleelrekgvslvsldegidtstpmgrlllqilaalaeferelirertk 134
                                   ++l++   +++ gv++ ++    +++++ ++l+ ++l+++  f  +l   r++
  gi|70607741|ref|YP_256611.1| 141 EYLEY--FFQQFGVRVEVVLG-EEPKDAYQELVEDLLSIVTSFAGKLYGIRSH 190
                                   *****..78999999999985.7899999***999999999998887766655 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2   2.2e-16   3.9e-13       1      49 [.       4      53 ..       4      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.2e-16
                        HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleewlek 49
                                  ll ++E+++ Lg+s +t+ r+i++g+++a+k  G+ +rip s++e+ l++
  gi|70607741|ref|YP_256611.1|  4 LLRPKEVCQTLGISYRTLLRWIDQGKIKAVKtEGGIYRIPYSEVERILKN 53
                                  6999**************************997777**********9986 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   9.9e-09   1.8e-05       2      35 ..       7      39 ..       6      42 .. 0.93
   2 ?   -2.5   0.0       2.6   4.7e+03       2       8 ..     203     209 .]     203     209 .] 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.9e-09
                                  HHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSS CS
                          MerR  2 IgevAeltGvsprtLRyYEreGLipppeRtegGy 35
                                   +ev++ +G+s rtL ++ ++G+i ++++tegG 
  gi|70607741|ref|YP_256611.1|  7 PKEVCQTLGISYRTLLRWIDQGKI-KAVKTEGGI 39
                                  69**********************.*******96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                                   HHHHHHH CS
                          MerR   2 IgevAel 8  
                                   Ige++e+
  gi|70607741|ref|YP_256611.1| 203 IGELSEK 209
                                   9***985 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   6.4e-08   0.00011       3      47 ..       7      51 ..       5      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-08
                                  HHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHH CS
                        MerR_1  3 igevakilgvtthtlrywekegllkpkrteggrryYtdedierLk 47
                                   +ev++ lg++++tl  w ++g++k  +tegg ++   +++er+ 
  gi|70607741|ref|YP_256611.1|  7 PKEVCQTLGISYRTLLRWIDQGKIKAVKTEGGIYRIPYSEVERIL 51
                                  58******************************9887777777775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.1e-07    0.0015      18      39 ..       5      26 ..       2      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.1e-07
                        HTH_23 18 lsvreIAreLgvsrrTvyrwlk 39
                                  l+++e+++ Lg+s+rT+ rw+ 
  gi|70607741|ref|YP_256611.1|  5 LRPKEVCQTLGISYRTLLRWID 26
                                  6899****************86 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.031      13      34 ..       5      26 ..       1      41 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                        HTH_29 13 stvsqiAkllglsrrtvyrwlk 34
                                   +++++++ lg+s+rt  rw++
  gi|70607741|ref|YP_256611.1|  5 LRPKEVCQTLGISYRTLLRWID 26
                                  4799****************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.7e-05      0.16      15      34 ..       7      26 ..       3      27 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-05
                        HTH_28 15 vreaArelgisrrtvyrWik 34
                                   +e+++ lgis+rt+ rWi 
  gi|70607741|ref|YP_256611.1|  7 PKEVCQTLGISYRTLLRWID 26
                                  58999*************97 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.21   3.8e+02      40      92 ..      61     117 ..      29     121 .. 0.61
   2 ?   11.4   0.0   0.00017       0.3       2      61 ..     108     172 ..     107     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.21
                                   TSTEEEESTTSTHHHHHHHHHHHH....TTSSSEEEESGGGTSSSTSTTESEEEESS CS
                    Helicase_C  40 gikvavlhgelpqnereeileqfn....kgesdvLiatdvaerGidipkvnlVinfd 92 
                                   ++ +a++ ++ ++++ ++ +e       ++ ++v+ + ++++ G++ ++ nl+  f+
  gi|70607741|ref|YP_256611.1|  61 AVIYARVSSSDQKSDLDRQIEYLTnyclAKGYKVVDTLSDISSGLNTKRKNLLKLFQ 117
                                   344444444434444344444443355667788888889999999988877766655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.....HHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                    Helicase_C   2 kleallellkleeeggkilifvntidrlek.....vklllekkgikvavlhgelpqnereeileq 61 
                                   k + ll+l++l +eg+  +++++++drl +     ++++ +++g++v v+ ge p++  +e +e+
  gi|70607741|ref|YP_256611.1| 108 KRKNLLKLFQLVKEGKVDVVVITYKDRLTRfgfeyLEYFFQQFGVRVEVVLGEEPKDAYQELVED 172
                                   567788888888888888********99778877889999999**********999998888776 PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.19       2      27 ..       3      28 ..       2      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                    Phage_AlpA  2 rilrlreVeqktglsrstiYrlikdg 27
                                  ++lr +eV+q++g+s  t+ r+i +g
  gi|70607741|ref|YP_256611.1|  3 KLLRPKEVCQTLGISYRTLLRWIDQG 28
                                  78********************9876 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.22      27      47 ..       8      28 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                     HTH_Tnp_1 27 sevArrhgvspnqLykWrrqy 47
                                  +ev++ +g+s+ +L +W+ q 
  gi|70607741|ref|YP_256611.1|  8 KEVCQTLGISYRTLLRWIDQG 28
                                  89***************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1448.37
//
Query:       gi|70607742|ref|YP_256612.1|  [L=418]
Description: ISC1913-like transposase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-18   64.7   0.0      1e-17   63.8   0.0    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.06   12.6   0.8       0.65    9.2   0.0    2.3  3  DUF3427         Domain of unknown function (DUF3427)


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.1e-21     1e-17       1      69 []     301     373 ..     301     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.1e-21
                OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke....alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                   f++lk+ + +kake+G++v +vnpayTS+ C+ + +k  +    + ++r+  C++   e++rDv+A +N+lk+
  gi|70607742|ref|YP_256612.1| 301 FASLKNAIVEKAKEFGVPVLLVNPAYTSSVCPIHECKIIYppdgSSAPRVGMCEKGREEWHRDVVALYNLLKK 373
                                   889**********************************99999*****************************96 PP

>> DUF3427  Domain of unknown function (DUF3427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   7.3e-05      0.65      85     121 ..      15      53 ..       7      76 .. 0.83
   2 ?    0.6   0.1     0.031   2.7e+02      39      77 ..     222     263 ..     196     296 .. 0.73
   3 ?   -0.7   0.0     0.079     7e+02      17      64 ..     271     312 ..     247     324 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 7.3e-05
                       DUF3427  85 yrlseefkkll..eneeFkkfledlielglarykkkyse 121
                                   +++++e+ + l   +ee+k++led i++gl+++ k++ +
  gi|70607742|ref|YP_256612.1|  15 LKVNSEVYTRLkeVEEEYKQILEDAIDYGLRNNIKSFTR 53 
                                   6788888888854568****************9998875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.031
                       DUF3427  39 efaek...vdeetiesalrvLdlsffksaekkkygnipliek 77 
                                   +  ++   ++++ +++al+ L+++f k + ++k +++ + e 
  gi|70607742|ref|YP_256612.1| 222 KRISEgrsTKDRDVKRALKSLKERFKKLDIRRKLAKLIVTEA 263
                                   33333566899999*********9998899999988877773 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.079
                       DUF3427  17 lLkeLlknksisieelakelkkefaek.....vdeetiesalrvLdlsffksa 64 
                                   +L+ L k              +++ +      + ++ ++sa++ L++ ++++a
  gi|70607742|ref|YP_256612.1| 271 VLEDLPK-----------NTPEKMVQDikdkqLRDRIYKSAFASLKNAIVEKA 312
                                   3444443...........33322222222224778999999999999888443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      759  (0.0423336); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2767.63
//
Query:       gi|70607743|ref|YP_256613.1|  [L=157]
Description: hypothetical protein Saci_2024 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1206.37
//
Query:       gi|70607744|ref|YP_256614.1|  [L=360]
Description: hypothetical protein Saci_2025 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-21   76.6   0.3    4.4e-21   75.9   0.3    1.3  1  ATPase_2  ATPase domain predominantly from Archaea
    6.1e-09   36.0   0.4    0.00068   19.7   0.0    2.6  3  AAA_14    AAA domain
    1.3e-06   28.7   0.0    2.5e-06   27.8   0.0    1.5  1  AAA_22    AAA domain
    4.5e-05   23.9   0.0    7.7e-05   23.1   0.0    1.4  1  AAA_16    AAA ATPase domain
    0.00058   20.3   0.0     0.0071   16.8   0.0    2.3  1  AAA       ATPase family associated with various cellular acti
     0.0012   18.6   0.0      0.004   17.0   0.0    1.9  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.045   13.8   0.0       0.18   11.9   0.0    2.0  1  ER        Enhancer of rudimentary
      0.056   13.4   0.1       0.17   11.9   0.0    1.8  2  PadR      Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.3     2e-24   4.4e-21       1     232 [.      14     247 ..      14     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 2e-24
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie....eeeekkk 77 
                                   Ff+R++e+++++++ +     i ++ G ++ GK++++k ++++l+   +  i y +lr+ +   + +f +     e+e+kk
  gi|70607744|ref|YP_256614.1|  14 FFNRDEEINRVRSLSSP----ITLVLGLRRTGKSSIIKIALNELSL-PY--I-YLDLRKFEDRAYISFKDllleLEREVKK 86 
                                   9**********998765....*********************9943.33..3.4556665555555554455556777888 PP

                      ATPase_2  78 lekal...........giavpkaeleeilk..eksklvfkaielllekikkkgkk.iiiiiDelqklidlglngaellvke 144
                                   l++++           g  +  +e+   ++   k+     ++++lle +++  k  +ii +De+q li   l+   +l++ 
  gi|70607744|ref|YP_256614.1|  87 LTRKFpslvdflkgvkGVSIAGNEV--RFNwgVKN---RLNFSDLLETLNDWSKDrVIIAFDEAQDLI--NLR-GVNLLYP 159
                                   8888899999998855444444444..44522444...5567777777777666559***********..777.66899** PP

                      ATPase_2 145 LlnliesltkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyr 221
                                   L++ +++    k++++++ +s+  l+ +   + + +s+l gr+   ++++++d e++ +fl++gfke++  +  + e++y+
  gi|70607744|ref|YP_256614.1| 160 LAYTFDN---LKKVRIIMSGSEMRLLYRflgVENPKSPLFGRAMNeVELRPFDHEKSIEFLRRGFKEVN-VEFREYERVYE 236
                                   *******...56788999999999988877677889*******999**********************5.56679****** PP

                      ATPase_2 222 yvGGkPkalve 232
                                    +GG+P+ l +
  gi|70607744|ref|YP_256614.1| 237 ELGGIPGWLTY 247
                                   ******98876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     3e-07   0.00068       2      60 ..      29      84 ..      28     107 .. 0.79
   2 !   14.0   0.0   1.7e-05     0.039      48     126 ..     122     209 ..     104     213 .. 0.70
   3 ?   -3.4   0.0       4.1   9.3e+03      52      59 ..     277     284 ..     253     300 .. 0.47

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
                        AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilekl 60
                                  ++i ++ G+Rr+GK+ ++k  ++el      ++y++l + +d+++  +++ll ++ +++
  gi|70607744|ref|YP_256614.1| 29 SPITLVLGLRRTGKSSIIKIALNELS---LPYIYLDLRKFEDRAYISFKDLLLELEREV 84
                                  57899*************99998877...899999999999988887765554444443 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.7e-05
                        AAA_14  48 dpekllelileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllskeia.....tslagrva 118
                                   ++++lle + +  + +++ ++ +DE+q +      ++   l + +d+ k++++i++GS   ll++ +      + l gr+ 
  gi|70607744|ref|YP_256614.1| 122 NFSDLLETLNDW-S-KDRVIIAFDEAQDLinlrgVNLLYPLAYTFDNLKKVRIIMSGSEMRLLYRFLGvenpkSPLFGRAM 200
                                   444455555554.3.47899*********4444444455588888999**************9875544455566666654 PP

                        AAA_14 119 .eielypls 126
                                    e+el p++
  gi|70607744|ref|YP_256614.1| 201 nEVELRPFD 209
                                   367777776 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 4.1
                        AAA_14  52 llelilek 59 
                                   +++++ ++
  gi|70607744|ref|YP_256614.1| 277 FNNFLSKR 284
                                   22333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.1e-09   2.5e-06       7     131 ..      31     178 ..      25     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.1e-09
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka................ 70 
                                   i++v G   tGK+  ++  l++l         + ++++ +l + ++++ + +++ll +l++e k+                
  gi|70607744|ref|YP_256614.1|  31 ITLVLGLRRTGKSSIIKIALNEL---------SLPYIYLDLRKFEDRAYIsFKDLLLELEREVKKltrkfpslvdflkgvk 102
                                   899********************.........9************999999999999999999999999************ PP

                        AAA_22  71 ................erlsseellealeqalraravielliiDEaqhlr...seealeeL.rsllnlsrkgvqliLvGtp 131
                                                   +rl+ ++lle+l++ +++r     +  DEaq l+     ++l  L  ++ n   k+v++i+ G +
  gi|70607744|ref|YP_256614.1| 103 gvsiagnevrfnwgvkNRLNFSDLLETLNDWSKDRVI---IAFDEAQDLInlrGVNLLYPLaYTFDN--LKKVRIIMSGSE 178
                                   ***********99999999999999999999999855...********9856336666666555566..9*****999986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.4e-08   7.7e-05       2     147 ..      14     148 ..      13     173 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.4e-08
                        AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareell 82 
                                   ++ R+ee+++++s+ +       +++l+ G + +GKss+++ +l++l+  ++++   k+++     +y+ +       +ll
  gi|70607744|ref|YP_256614.1|  14 FFNRDEEINRVRSLSS-------PITLVLGLRRTGKSSIIKIALNELSLPYIYLDLRKFEDR----AYISFK------DLL 77 
                                   6778888877777665.......9**************************988877777777....444444......444 PP

                        AAA_16  83 rqlldeaesaeleawrekleeala..avpelagaea.........srllellkrllallsrderplvlvlDdlqwa 147
                                    +l++e   ++l +    l + l+   + ++ag e            +   l + l+  s+ +r +++ +D++q++
  gi|70607744|ref|YP_256614.1|  78 LELEREV--KKLTRKFPSLVDFLKgvKGVSIAGNEVrfnwgvknrLNF-SDLLETLNDWSK-DR-VIIAFDEAQDL 148
                                   4444441..122222222333333222233333333555556642222.233333333333.44.99999999953 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.2e-06    0.0071       2     115 ..      33     182 ..      32     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS............................................. CS
                           AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk............................................. 37 
                                   l+ G   tGK++++k   +el+ +++ +++ ++ +                                              
  gi|70607744|ref|YP_256614.1|  33 LVLGLRRTGKSSIIKIALNELSLPYIYLDLRKFEDRayisfkdlllelerevkkltrkfpslvdflkgvkgvsiagnevrf 113
                                   6788899***************99999999999866889999999999999999999999999999999999999999998 PP

                                   .STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGS CS
                           AAA  38 .yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkl 115
                                    +  ++  ++++l++++   + + +i+ +DE+  l++ r           vn L++    +++  +kv +i+ + +++ l
  gi|70607744|ref|YP_256614.1| 114 nWGVKNRLNFSDLLETLNDWSkDRVIIAFDEAQDLINLR----------GVNLLYPLAYTFDNL-KKVRIIMSGSEMRLL 182
                                   777777888999998887777445***********9999..........899999999999996.55***9999988776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06     0.004      23      64 ..     309     349 ..     306     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                          TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64 
                                   +ta ei+e  +++ s +Y++L++L+d  ++ + ++ ++ Y++
  gi|70607744|ref|YP_256614.1| 309 KTAVEIHEGREISDSEIYNYLNNLMDSSWIVKDEE-KNEYCP 349
                                   799**************************999854.455555 PP

>> ER  Enhancer of rudimentary
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.8e-05      0.18      54      83 ..     323     352 ..     302     355 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                            ER  54 sdLfefidsladlsaLvleketksylprdk 83 
                                   s++++++++l d s +v ++e ++y p +k
  gi|70607744|ref|YP_256614.1| 323 SEIYNYLNNLMDSSWIVKDEEKNEYCPAEK 352
                                   689************************987 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.3   9.5e+03      34      48 ..      58      72 ..      52      75 .. 0.84
   2 ?   11.9   0.0   7.5e-05      0.17      14      55 ..     307     346 ..     303     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.3
                                  HHHHHHHHHHTTSEE CS
                          PadR 34 lYpaLkrLekeglve 48
                                  +Y  L+++e+  +++
  gi|70607744|ref|YP_256614.1| 58 IYLDLRKFEDRAYIS 72
                                  799999999999986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.5e-05
                                   HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-ST CS
                          PadR  14 eiikeleelsegllelseGslYpaLkrLekeglveseweesg 55 
                                   ei+ ++e + eg +e+s++++Y  L+ L ++ ++++ +e+++
  gi|70607744|ref|YP_256614.1| 307 EIKTAVEIH-EG-REISDSEIYNYLNNLMDSSWIVKDEEKNE 346
                                   677778888.77.9**********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2418.54
//
Query:       gi|70607745|ref|YP_256615.1|  [L=399]
Description: hypothetical protein Saci_2026 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-72  236.6  50.6    2.7e-11   42.9   0.3   10.4 10  TPR_11          TPR repeat
    4.9e-69  223.0  40.0      6e-09   35.3   0.5   10.9 11  TPR_2           Tetratricopeptide repeat
    8.8e-64  208.9  50.8    6.2e-08   32.1   0.6   10.9 11  TPR_1           Tetratricopeptide repeat
    1.4e-51  168.4  33.6    1.5e-05   24.8   0.0   10.5 10  TPR_8           Tetratricopeptide repeat
    1.3e-47  156.8  30.4    1.1e-05   25.5   0.0   11.2 11  TPR_17          Tetratricopeptide repeat
    5.7e-43  145.3   3.7    2.2e-07   31.4   0.5    6.9  7  TPR_16          Tetratricopeptide repeat
    5.1e-39  129.6   1.4     0.0053   17.5   0.1   10.3 10  TPR_14          Tetratricopeptide repeat
    2.8e-34  117.1   0.3      2e-06   27.8   0.0    6.3  6  TPR_9           Tetratricopeptide repeat
    1.6e-28   98.8  16.3    2.6e-07   30.8   0.1    5.1  5  ANAPC3          Anaphase-promoting complex, cyclosome, subuni
    2.4e-26   92.0  16.8    4.9e-07   30.2   0.1    7.0  8  TPR_19          Tetratricopeptide repeat
    2.8e-16   59.6  19.0    0.00024   21.4   0.1    7.4  6  TPR_12          Tetratricopeptide repeat
    1.8e-15   56.4  21.4      0.067   13.9   0.0    9.4  9  TPR_6           Tetratricopeptide repeat
      3e-15   56.1  14.8     0.0001   21.4   0.2    7.0  8  NARP1           NMDA receptor-regulated protein 1
    5.7e-13   49.0   2.2      0.019   15.3   0.0    6.1  7  TPR_20          Tetratricopeptide repeat
    1.3e-10   40.8  17.0       0.32   10.9   0.2    8.9  9  TPR_10          Tetratricopeptide repeat
    1.6e-10   40.2  11.5      0.045   13.8   0.1    9.3 10  TPR_7           Tetratricopeptide repeat
    5.2e-10   39.9   3.0      0.035   14.6   0.1    5.8  7  BTAD            Bacterial transcriptional activator domain
    5.9e-08   32.7   3.8       0.88    9.7   0.1    5.9  6  ANAPC5          Anaphase-promoting complex subunit 5
    6.7e-08   32.5  17.9      0.025   14.6   0.1    7.5  8  Fis1_TPR_C      Fis1 C-terminal tetratricopeptide repeat
      2e-07   31.5   0.4       0.25   11.9   0.0    5.0  6  Syntaxin-6_N    Syntaxin 6, N-terminal
    1.3e-05   25.0   6.6      0.081   12.7   0.0    5.3  6  TOM20_plant     Plant specific mitochondrial import receptor 
    2.5e-05   23.6  11.2        3.7    7.1   0.0    7.6  7  SHNi-TPR        SHNi-TPR
     0.0002   21.5   0.7         33    4.5   0.0    6.3  5  DUF3856         Domain of Unknown Function (DUF3856)
     0.0032   17.2  18.5       0.16   11.7   1.3    4.7  3  YfiO            Outer membrane lipoprotein
     0.0036   16.8   1.9        8.1    5.8   0.0    4.3  4  EST1_DNA_bind   Est1 DNA/RNA binding domain
  ------ inclusion threshold ------
      0.011   15.7  19.6        9.3    6.4   0.1    8.1  9  MIT             MIT (microtubule interacting and transport) d
      0.046   13.4   0.0         10    5.8   0.0    4.0  7  HrpB1_HrpK      Bacterial type III secretion protein (HrpB1_H
      0.052   13.6   2.2         13    5.9   0.0    4.6  5  TFIIA_gamma_N   Transcription initiation factor IIA, gamma su
      0.094   12.4   9.3        2.1    8.0   0.1    4.8  5  PA28_beta       Proteasome activator pa28 beta subunit
       0.17   10.3   2.2        6.5    5.1   0.0    3.4  3  CAS_CSE1        CAS/CSE protein, C-terminus
       0.18   11.7   1.4       0.93    9.4   0.4    2.6  3  Wzy_C_2         Virulence factor membrane-bound polymerase, C
       0.33   10.9  10.2        3.6    7.6   0.2    5.7  6  Gin             Inhibitor of sigma-G Gin
        0.4   11.2   2.6         42    4.7   0.0    4.5  5  Biotin_carb_N   Biotin carboxylase, N-terminal domain
       0.43   10.7  10.9        4.8    7.4   0.0    5.0  4  KN17_SH3        KN17 SH3-like C-terminal domain
        3.2    8.2   9.0         22    5.5   0.2    3.8  4  Streptin-Immun  Lantibiotic streptin immunity protein


Domain annotation for each model (and alignments):
>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.7   2.3e-08   1.2e-05       1      36 [.      31      66 ..      26      72 .. 0.93
   2 !   30.1   0.1   5.6e-10   2.8e-07      10      39 ..      85     114 ..      84     117 .. 0.94
   3 !   23.4   2.6   6.8e-08   3.5e-05       7      40 ..     116     149 ..     115     151 .. 0.89
   4 !   14.6   0.0   3.9e-05      0.02       6      42 .]     149     185 ..     146     185 .. 0.92
   5 !   25.1   0.3     2e-08     1e-05       4      40 ..     181     217 ..     178     219 .. 0.91
   6 !   36.2   0.3   6.7e-12   3.4e-09       1      42 []     212     253 ..     212     253 .. 0.97
   7 !   42.9   0.3   5.3e-14   2.7e-11       3      39 ..     248     284 ..     246     285 .. 0.95
   8 !   30.4   1.3   4.4e-10   2.2e-07      10      40 ..     289     319 ..     288     320 .. 0.95
   9 !   35.3   0.1   1.3e-11   6.9e-09       9      42 .]     322     355 ..     322     355 .. 0.97
  10 !   24.2   0.2   3.9e-08     2e-05       7      27 ..     354     374 ..     350     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.3e-08
                        TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGl 36
                                  G ay+ +++y eAi ++ +A++l+P  a+ +y  +l
  gi|70607745|ref|YP_256615.1| 31 GLAYFNLNNYSEAIREFDEAIRLNPFHADSHYYKAL 66
                                  89******************************8766 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 5.6e-10
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                   ye Ai ++ +A+k+dP+n+e +y  Gla+ 
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNPEYHYQKGLALE 114
                                   99*************************986 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 6.8e-08
                        TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   +G+  eA+ +Y+ A+kl+P n+e yy  + +++ 
  gi|70607745|ref|YP_256615.1| 116 LGRQYEALLEYQDAIKLNPRNPEYYYRKAIILQD 149
                                   68888*********************98887776 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 3.9e-05
                        TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   +q ky +Ai++  +A++l+P+n + y+  +l++  +G
  gi|70607745|ref|YP_256615.1| 149 DQEKYVDAIAEVDTAIRLNPKNSTYYFRKALLLKSMG 185
                                   7999************************999998887 PP

  == domain 5  score: 25.1 bits;  conditional E-value: 2e-08
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   + + Gk++eA+ ++ kA+ l+P+ ae y+  Gl++ +
  gi|70607745|ref|YP_256615.1| 181 LKSMGKLKEALDQLDKAISLNPQVAEYYHQKGLILKE 217
                                   5689****************************99876 PP

  == domain 6  score: 36.2 bits;  conditional E-value: 6.7e-12
                        TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   G ++ e+ +y++ +++Y +A+kl+P+n+e ++  G++yy++G
  gi|70607745|ref|YP_256615.1| 212 GLILKELKRYDDVLKDYDNAIKLSPNNPEYHFRKGVLYYELG 253
                                   789999**********************************99 PP

  == domain 7  score: 42.9 bits;  conditional E-value: 5.3e-14
                        TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                   +yye+Gkye+A+ ++++ ++l+P+n+e +y LGla++
  gi|70607745|ref|YP_256615.1| 248 LYYELGKYEKAVMELEESVRLNPNNPEYHYQLGLALF 284
                                   7**********************************86 PP

  == domain 8  score: 30.4 bits;  conditional E-value: 4.4e-10
                        TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   ye+A+e++ kA+kldP+n+  yy  G+a+ +
  gi|70607745|ref|YP_256615.1| 289 YEDAVEEFDKAVKLDPQNPQYYYYKGNALKA 319
                                   9***************************975 PP

  == domain 9  score: 35.3 bits;  conditional E-value: 1.3e-11
                        TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ky++Ai++Y kA+ l+P+++  +y  G+++  +G
  gi|70607745|ref|YP_256615.1| 322 KYDKAIKEYDKAISLNPNDPLPHYQKGVVLKTLG 355
                                   8****************************99887 PP

  == domain 10  score: 24.2 bits;  conditional E-value: 3.9e-08
                        TPR_11   7 qGkyeeAieaYkkAlkldPdn 27 
                                   +GkyeeAi ++ +A+kl+Pdn
  gi|70607745|ref|YP_256615.1| 354 LGKYEEAIVELDEAIKLNPDN 374
                                   7*******************9 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.5   1.2e-11     6e-09       3      32 ..      26      55 ..      24      57 .. 0.94
   2 ?   -0.3   0.1         3   1.5e+03       1      16 [.      58      73 ..      58      74 .. 0.84
   3 !   11.0   0.1   0.00072      0.37      17      34 .]      85     102 ..      82     102 .. 0.95
   4 !   21.5   1.0   3.1e-07   0.00016       1      34 []     103     136 ..     103     136 .. 0.97
   5 !   20.8   0.1   5.3e-07   0.00027       1      34 []     137     170 ..     137     170 .. 0.97
   6 !   21.3   0.0   3.7e-07   0.00019       3      33 ..     173     203 ..     171     204 .. 0.95
   7 !   23.8   0.3   5.7e-08   2.9e-05       1      34 []     205     238 ..     205     238 .. 0.98
   8 !   27.7   0.0   3.4e-09   1.7e-06       1      34 []     239     272 ..     239     272 .. 0.97
   9 !   24.7   0.0   3.1e-08   1.6e-05       1      34 []     273     306 ..     273     306 .. 0.97
  10 !   31.8   1.7   1.6e-10   8.1e-08       2      34 .]     308     340 ..     307     340 .. 0.96
  11 !   25.8   0.0   1.4e-08     7e-06       4      34 .]     344     374 ..     341     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.2e-11
                         TPR_2  3 alynlGlayyklgdyeeAleafekAleldP 32
                                  +++n+Glay++l++y eA++ f++A++l+P
  gi|70607745|ref|YP_256615.1| 26 YHFNRGLAYFNLNNYSEAIREFDEAIRLNP 55
                                  8****************************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3
                         TPR_2  1 aealynlGlayyklgd 16
                                  a+ +y+ +l++++l++
  gi|70607745|ref|YP_256615.1| 58 ADSHYYKALSLIALQR 73
                                  6789999999999876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00072
                         TPR_2  17 yeeAleafekAleldPnn 34 
                                   ye+A+  f++A+++dP+n
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKN 102
                                   9***************97 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 3.1e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +e++y+ Gla++ lg+  eAl  ++ A++l+P+n
  gi|70607745|ref|YP_256615.1| 103 PEYHYQKGLALEILGRQYEALLEYQDAIKLNPRN 136
                                   699*****************************87 PP

  == domain 5  score: 20.8 bits;  conditional E-value: 5.3e-07
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +e++y+ + ++  + +y +A++  + A++l+P+n
  gi|70607745|ref|YP_256615.1| 137 PEYYYRKAIILQDQEKYVDAIAEVDTAIRLNPKN 170
                                   699*****************************97 PP

  == domain 6  score: 21.3 bits;  conditional E-value: 3.7e-07
                         TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                   ++++ +l++  +g+++eAl+ ++kA++l+P+
  gi|70607745|ref|YP_256615.1| 173 YYFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   89****************************6 PP

  == domain 7  score: 23.8 bits;  conditional E-value: 5.7e-08
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ae++++ Gl++ +l++y++ l++++ A++l Pnn
  gi|70607745|ref|YP_256615.1| 205 AEYYHQKGLILKELKRYDDVLKDYDNAIKLSPNN 238
                                   79*******************************8 PP

  == domain 8  score: 27.7 bits;  conditional E-value: 3.4e-09
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +e++++ G +yy+lg+ye+A+  +e++++l+Pnn
  gi|70607745|ref|YP_256615.1| 239 PEYHFRKGVLYYELGKYEKAVMELEESVRLNPNN 272
                                   699******************************8 PP

  == domain 9  score: 24.7 bits;  conditional E-value: 3.1e-08
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +e++y+lGla+++   ye+A+e f+kA++ldP+n
  gi|70607745|ref|YP_256615.1| 273 PEYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQN 306
                                   699*****************************97 PP

  == domain 10  score: 31.8 bits;  conditional E-value: 1.6e-10
                         TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +++y+ G+a+ +l +y++A++ ++kA++l+Pn+
  gi|70607745|ref|YP_256615.1| 308 QYYYYKGNALKALWKYDKAIKEYDKAISLNPND 340
                                   79*****************************97 PP

  == domain 11  score: 25.8 bits;  conditional E-value: 1.4e-08
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +y+ G ++  lg+yeeA+  +++A++l+P+n
  gi|70607745|ref|YP_256615.1| 344 HYQKGVVLKTLGKYEEAIVELDEAIKLNPDN 374
                                   9****************************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.6   1.2e-10   6.2e-08       3      32 ..      26      55 ..      24      57 .. 0.94
   2 ?   -0.7   0.1       2.9   1.5e+03      23      30 ..      61      68 ..      58      73 .. 0.59
   3 !    8.4   0.2    0.0039         2      17      34 .]      85     102 ..      83     102 .. 0.94
   4 !   17.8   1.2     4e-06     0.002       2      34 .]     104     136 ..     103     136 .. 0.95
   5 !   19.1   0.2   1.6e-06   0.00083       2      34 .]     138     170 ..     137     170 .. 0.96
   6 !   25.3   0.0   1.8e-08   9.3e-06       3      33 ..     173     203 ..     171     204 .. 0.95
   7 !   28.0   1.0   2.5e-09   1.3e-06       1      34 []     205     238 ..     205     238 .. 0.97
   8 !   26.3   0.1   8.4e-09   4.3e-06       2      34 .]     240     272 ..     239     272 .. 0.96
   9 !   26.5   0.0   7.1e-09   3.6e-06       2      34 .]     274     306 ..     273     306 .. 0.96
  10 !   25.9   3.7   1.1e-08   5.6e-06       2      34 .]     308     340 ..     307     340 .. 0.95
  11 !   28.1   0.0   2.2e-09   1.1e-06       4      34 .]     344     374 ..     341     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-10
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1  3 alynlGnayfklgkydeAleyyekALelnP 32
                                   ++n+G+ayf+l++y eA+  +++A++lnP
  gi|70607745|ref|YP_256615.1| 26 YHFNRGLAYFNLNNYSEAIREFDEAIRLNP 55
                                  589*************************** PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                                  HHHHHHHH CS
                         TPR_1 23 yyekALel 30
                                  +y kAL+l
  gi|70607745|ref|YP_256615.1| 61 HYYKALSL 68
                                  56666654 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0039
                                   HHHHHHHHHHHHHHSTTH CS
                         TPR_1  17 ydeAleyyekALelnPnn 34 
                                   y+ A+  +++A++++P+n
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKN 102
                                   999*************98 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 4e-06
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + +y++G+a+  lg+  eAl  y+ A++lnP n
  gi|70607745|ref|YP_256615.1| 104 EYHYQKGLALEILGRQYEALLEYQDAIKLNPRN 136
                                   789****************************87 PP

  == domain 5  score: 19.1 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + +y+++ +++ ++ky +A++  + A++lnP+n
  gi|70607745|ref|YP_256615.1| 138 EYYYRKAIILQDQEKYVDAIAEVDTAIRLNPKN 170
                                   78*****************************98 PP

  == domain 6  score: 25.3 bits;  conditional E-value: 1.8e-08
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    ++++++++ ++gk++eAl+  +kA++lnP+
  gi|70607745|ref|YP_256615.1| 173 YYFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   59****************************6 PP

  == domain 7  score: 28.0 bits;  conditional E-value: 2.5e-09
                                   HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   a+ + ++G+++ +l++yd+ l++y+ A++l Pnn
  gi|70607745|ref|YP_256615.1| 205 AEYYHQKGLILKELKRYDDVLKDYDNAIKLSPNN 238
                                   7899*****************************8 PP

  == domain 8  score: 26.3 bits;  conditional E-value: 8.4e-09
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + ++++G++y++lgky++A+   e+ ++lnPnn
  gi|70607745|ref|YP_256615.1| 240 EYHFRKGVLYYELGKYEKAVMELEESVRLNPNN 272
                                   789*****************************8 PP

  == domain 9  score: 26.5 bits;  conditional E-value: 7.1e-09
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + +y+lG+a+f+  +y++A+e ++kA++l+P+n
  gi|70607745|ref|YP_256615.1| 274 EYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQN 306
                                   789****************************97 PP

  == domain 10  score: 25.9 bits;  conditional E-value: 1.1e-08
                                   HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                   + +y +Gna+  l kyd+A++ y+kA++lnPn+
  gi|70607745|ref|YP_256615.1| 308 QYYYYKGNALKALWKYDKAIKEYDKAISLNPND 340
                                   67*****************************97 PP

  == domain 11  score: 28.1 bits;  conditional E-value: 2.2e-09
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   4 lynlGnayfklgkydeAleyyekALelnPnn 34 
                                   +y++G+++  lgky+eA+   ++A++lnP+n
  gi|70607745|ref|YP_256615.1| 344 HYQKGVVLKTLGKYEEAIVELDEAIKLNPDN 374
                                   8****************************98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.7e-08   2.9e-05       4      34 .]      27      57 ..      25      57 .. 0.94
   2 !    8.3   0.0     0.006       3.1      17      34 .]      85     102 ..      80     102 .. 0.93
   3 !   15.8   0.3   2.3e-05     0.012       2      34 .]     104     136 ..     103     136 .. 0.95
   4 !   10.6   0.1    0.0011      0.55       2      34 .]     138     170 ..     137     170 .. 0.96
   5 !   21.5   0.1   3.3e-07   0.00017       3      33 ..     173     203 ..     171     204 .. 0.95
   6 !   19.6   0.5   1.4e-06   0.00073       1      34 []     205     238 ..     205     238 .. 0.97
   7 !   24.8   0.0     3e-08   1.5e-05       2      34 .]     240     272 ..     239     272 .. 0.95
   8 !   16.4   0.0   1.5e-05    0.0077       2      34 .]     274     306 ..     273     306 .. 0.95
   9 !   20.0   2.0   1.1e-06   0.00054       2      34 .]     308     340 ..     307     340 .. 0.95
  10 !   23.8   0.0     6e-08   3.1e-05       4      34 .]     344     374 ..     343     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.7e-08
                                  HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                                  ++n g++y++l++y eA+  + +a++l+p +
  gi|70607745|ref|YP_256615.1| 27 HFNRGLAYFNLNNYSEAIREFDEAIRLNPFH 57
                                  79***************************75 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.006
                                   HHHHHHHHHHHHHHHHH. CS
                         TPR_8  17 yeeAkeyyekaleldpdn 34 
                                   ye A+  + +a+++dp+n
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKN 102
                                   9***************97 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.3e-05
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   e++y++g++++ lg+  eA   y+ a++l+p n
  gi|70607745|ref|YP_256615.1| 104 EYHYQKGLALEILGRQYEALLEYQDAIKLNPRN 136
                                   789****************************75 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0011
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   e+yy+++ i++++++y  A++    a++l+p+n
  gi|70607745|ref|YP_256615.1| 138 EYYYRKAIILQDQEKYVDAIAEVDTAIRLNPKN 170
                                   79*****************************97 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 3.3e-07
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   +y++++++++++g+++eA   + ka++l+p+
  gi|70607745|ref|YP_256615.1| 173 YYFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   8*****************************7 PP

  == domain 6  score: 19.6 bits;  conditional E-value: 1.4e-06
                                   CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ae+y+++g+i+++l++y+   + y  a++l+p+n
  gi|70607745|ref|YP_256615.1| 205 AEYYHQKGLILKELKRYDDVLKDYDNAIKLSPNN 238
                                   799*****************************97 PP

  == domain 7  score: 24.8 bits;  conditional E-value: 3e-08
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   e+++++g +y +lg+ye+A+  +e+ ++l+p+n
  gi|70607745|ref|YP_256615.1| 240 EYHFRKGVLYYELGKYEKAVMELEESVRLNPNN 272
                                   789****************************97 PP

  == domain 8  score: 16.4 bits;  conditional E-value: 1.5e-05
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   e++y+lg++++    ye A+e + ka++ldp+n
  gi|70607745|ref|YP_256615.1| 274 EYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQN 306
                                   789****************************96 PP

  == domain 9  score: 20.0 bits;  conditional E-value: 1.1e-06
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   ++yy +g++++ l +y++A++ y ka++l+p++
  gi|70607745|ref|YP_256615.1| 308 QYYYYKGNALKALWKYDKAIKEYDKAISLNPND 340
                                   68999**************************96 PP

  == domain 10  score: 23.8 bits;  conditional E-value: 6e-08
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +y++g ++++lg+yeeA+  + +a++l+pdn
  gi|70607745|ref|YP_256615.1| 344 HYQKGVVLKTLGKYEEAIVELDEAIKLNPDN 374
                                   599**************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.075        39      15      33 ..      26      44 ..      15      45 .. 0.85
   2 !   12.4   0.0   0.00031      0.16       2      26 ..      47      71 ..      46      79 .. 0.86
   3 !   17.3   0.0   8.5e-06    0.0044       2      31 ..      92     121 ..      91     123 .. 0.89
   4 !   21.2   0.3   4.9e-07   0.00025       2      33 ..     126     157 ..     125     158 .. 0.96
   5 !   19.3   0.0     2e-06     0.001       4      33 ..     162     191 ..     161     192 .. 0.95
   6 !   12.3   0.0   0.00033      0.17       3      31 ..     195     223 ..     194     226 .. 0.93
   7 !   24.9   0.1   3.3e-08   1.7e-05       2      33 ..     228     259 ..     227     260 .. 0.96
   8 !   14.0   0.0   9.5e-05     0.049       2      32 ..     262     292 ..     261     294 .. 0.85
   9 !   16.3   0.5   1.8e-05    0.0094       2      33 ..     296     327 ..     295     328 .. 0.90
  10 !   25.5   0.0   2.1e-08   1.1e-05       2      33 ..     330     361 ..     329     362 .. 0.97
  11 ?    1.6   0.1       0.9   4.6e+02       3      12 ..     365     374 ..     363     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.075
                        TPR_17 15 aynnLAelllknGdlmtAr 33
                                   ++n++ ++ +++++ +A+
  gi|70607745|ref|YP_256615.1| 26 YHFNRGLAYFNLNNYSEAI 44
                                  589************9997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00031
                        TPR_17  2 ylkaleldPnnadaynnLAelllkn 26
                                  + +a++l+P +ad+++++A  l  +
  gi|70607745|ref|YP_256615.1| 47 FDEAIRLNPFHADSHYYKALSLIAL 71
                                  789****************987655 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 8.5e-06
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                                   + +a+++dP+n++ +++++ +l+ +G+  +
  gi|70607745|ref|YP_256615.1|  92 FDEAIKIDPKNPEYHYQKGLALEILGRQYE 121
                                   789**********************97655 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 4.9e-07
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   y+ a++l+P n++ y+ +A +l  + ++ +A+
  gi|70607745|ref|YP_256615.1| 126 YQDAIKLNPRNPEYYYRKAIILQDQEKYVDAI 157
                                   9****************************997 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 2e-06
                        TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                    a++l+P+n+  y+ +A ll++ G+l++A+
  gi|70607745|ref|YP_256615.1| 162 TAIRLNPKNSTYYFRKALLLKSMGKLKEAL 191
                                   69**************************96 PP

  == domain 6  score: 12.3 bits;  conditional E-value: 0.00033
                        TPR_17   3 lkaleldPnnadaynnLAelllknGdlmt 31 
                                    ka+ l+P  a+ y++++ +l++++++++
  gi|70607745|ref|YP_256615.1| 195 DKAISLNPQVAEYYHQKGLILKELKRYDD 223
                                   69**********************99986 PP

  == domain 7  score: 24.9 bits;  conditional E-value: 3.3e-08
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   y +a++l Pnn++ ++ +++l++++G++++A+
  gi|70607745|ref|YP_256615.1| 228 YDNAIKLSPNNPEYHFRKGVLYYELGKYEKAV 259
                                   99****************************97 PP

  == domain 8  score: 14.0 bits;  conditional E-value: 9.5e-05
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                   ++++++l+Pnn++ +++L+ +l +   +++A
  gi|70607745|ref|YP_256615.1| 262 LEESVRLNPNNPEYHYQLGLALFHVMMYEDA 292
                                   58999***************99877777766 PP

  == domain 9  score: 16.3 bits;  conditional E-value: 1.8e-05
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   + ka++ldP n+  y++++++l+ + ++++A+
  gi|70607745|ref|YP_256615.1| 296 FDKAVKLDPQNPQYYYYKGNALKALWKYDKAI 327
                                   89********************9988888876 PP

  == domain 10  score: 25.5 bits;  conditional E-value: 2.1e-08
                        TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                   y ka+ l+Pn++ ++++++++l+ +G++++A+
  gi|70607745|ref|YP_256615.1| 330 YDKAISLNPNDPLPHYQKGVVLKTLGKYEEAI 361
                                   9*****************************96 PP

  == domain 11  score: 1.6 bits;  conditional E-value: 0.9
                        TPR_17   3 lkaleldPnn 12 
                                    +a++l+P+n
  gi|70607745|ref|YP_256615.1| 365 DEAIKLNPDN 374
                                   68*******9 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.5   4.2e-10   2.2e-07       2      60 ..      29      88 ..      28      89 .. 0.88
   2 !   17.6   0.1   8.5e-06    0.0044      13      68 .]      85     137 ..      82     137 .. 0.94
   3 !   26.2   0.0   1.9e-08   9.5e-06       1      66 [.     141     203 ..     141     205 .. 0.95
   4 !   28.4   0.0   3.7e-09   1.9e-06       3      68 .]     211     273 ..     209     273 .. 0.91
   5 !   30.1   0.0   1.1e-09   5.8e-07       6      68 .]     248     307 ..     248     307 .. 0.98
   6 !   28.3   0.1     4e-09     2e-06      13      68 .]     289     341 ..     277     341 .. 0.93
   7 !   19.8   0.0   1.8e-06   0.00093      12      67 ..     322     374 ..     314     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.2e-10
                        TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq...grlaeAa.alyraa 60
                                  ++++a++++++y +A++ +++a++++   P++a++++++++++ ++   g + + + +ly++a
  gi|70607745|ref|YP_256615.1| 29 NRGLAYFNLNNYSEAIREFDEAIRLN---PFHADSHYYKALSLIALqrsGSVNAGIsDLYERA 88
                                  789***********************...************9998867777777777777776 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8.5e-06
                        TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                   y++A+  +++a+k d   P ++e ++ +g+a+  +gr  eA+  y+ a++  p +p
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKID---PKNPEYHYQKGLALEILGRQYEALLEYQDAIKLNPRNP 137
                                   99*************...99999*******************99999999999876 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 1.9e-08
                        TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   + +a ++ ++ +y dA+a  ++a++++   P +   ++ +++++   g l+eA++++++a+   p+
  gi|70607745|ref|YP_256615.1| 141 YRKAIILQDQEKYVDAIAEVDTAIRLN---PKNSTYYFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   67899**********************...***************************999988876 PP

  == domain 4  score: 28.4 bits;  conditional E-value: 3.7e-09
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraalraapdap 68 
                                   +++++ ++++ydd ++ ++ a+k+    P ++e ++ +g++++++g +++A+ +l ++  r  p++p
  gi|70607745|ref|YP_256615.1| 211 KGLILKELKRYDDVLKDYDNAIKLS---PNNPEYHFRKGVLYYELGKYEKAVmELEESV-RLNPNNP 273
                                   67888999*****************...99999*******************7777775.8998887 PP

  == domain 5  score: 30.1 bits;  conditional E-value: 1.1e-09
                        TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                   +++++g+y++A+  le+ ++++   P ++e ++ lg+a+++   +++A++ +++a++ +p++p
  gi|70607745|ref|YP_256615.1| 248 LYYELGKYEKAVMELEESVRLN---PNNPEYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNP 307
                                   59********************...99999*******************************98 PP

  == domain 6  score: 28.3 bits;  conditional E-value: 4e-09
                        TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                   y+dA++ ++ a+k+d   P++++ ++++g+a+ ++  +++A+  y++a+   p++p
  gi|70607745|ref|YP_256615.1| 289 YEDAVEEFDKAVKLD---PQNPQYYYYKGNALKALWKYDKAIKEYDKAISLNPNDP 341
                                   9**************...*******************************9999997 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 1.8e-06
                        TPR_16  12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                   +yd+A++ ++ a+ ++   P ++  ++ +g+++  +g ++eA+  +++a++  pd+
  gi|70607745|ref|YP_256615.1| 322 KYDKAIKEYDKAISLN---PNDPLPHYQKGVVLKTLGKYEEAIVELDEAIKLNPDN 374
                                   8***************...66666*******************7777777999986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00025      0.13       7      38 ..      30      61 ..      27      69 .. 0.84
   2 ?    7.8   0.0     0.014         7      17      42 ..      85     110 ..      70     112 .. 0.88
   3 !   17.5   0.1     1e-05    0.0053       1      42 [.     103     144 ..     103     146 .. 0.93
   4 !   12.4   0.0   0.00044      0.23       1      42 [.     137     178 ..     137     180 .. 0.93
   5 !   14.3   0.0   0.00011     0.056       8      41 ..     178     211 ..     176     214 .. 0.88
   6 !   11.8   0.0   0.00067      0.34       4      43 ..     208     247 ..     205     248 .. 0.89
   7 !   16.4   0.0   2.2e-05     0.012       9      42 ..     247     280 ..     242     282 .. 0.92
   8 !   15.6   0.0   4.1e-05     0.021       1      42 [.     273     314 ..     273     316 .. 0.93
   9 !   12.9   0.0   0.00031      0.16       4      40 ..     310     346 ..     307     350 .. 0.81
  10 !   15.4   0.0   4.7e-05     0.024       5      36 ..     345     376 ..     341     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00025
                        TPR_14  7 laeallalGdpdeAiallrralalaPddaeaw 38
                                  ++ a+++l ++ eAi+ +++a++l+P +a+ +
  gi|70607745|ref|YP_256615.1| 30 RGLAYFNLNNYSEAIREFDEAIRLNPFHADSH 61
                                  6789**********************666544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                        TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                                   +++Ai  +++a++ +P+++e++++ +
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNPEYHYQKG 110
                                   7899****************998765 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1e-05
                        TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   pe +++ + al+ lG+  eA+  +++a++l+P ++e++++ a
  gi|70607745|ref|YP_256615.1| 103 PEYHYQKGLALEILGRQYEALLEYQDAIKLNPRNPEYYYRKA 144
                                   6778999*******************************9988 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00044
                        TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   pe +++ a +l  ++++ +Aia  + a++l+P++ +++++ a
  gi|70607745|ref|YP_256615.1| 137 PEYYYRKAIILQDQEKYVDAIAEVDTAIRLNPKNSTYYFRKA 178
                                   6789999*******************************9988 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 0.00011
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlll 41 
                                   a +l   G+++eA++ l++a++l+P+ ae++ + 
  gi|70607745|ref|YP_256615.1| 178 ALLLKSMGKLKEALDQLDKAISLNPQVAEYYHQK 211
                                   5678899*********************999776 PP

  == domain 6  score: 11.8 bits;  conditional E-value: 0.00067
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   + + + +l +l ++d+ ++ ++ a++l P+++e++++ + 
  gi|70607745|ref|YP_256615.1| 208 YHQKGLILKELKRYDDVLKDYDNAIKLSPNNPEYHFRKGV 247
                                   567788999**************************99875 PP

  == domain 7  score: 16.4 bits;  conditional E-value: 2.2e-05
                        TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                    ++++lG++++A+  l++ ++l+P+++e++++l+
  gi|70607745|ref|YP_256615.1| 247 VLYYELGKYEKAVMELEESVRLNPNNPEYHYQLG 280
                                   5799**************************9997 PP

  == domain 8  score: 15.6 bits;  conditional E-value: 4.1e-05
                        TPR_14   1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                   pe +++l+ al++   +++A++ +++a++l+P++++++++ +
  gi|70607745|ref|YP_256615.1| 273 PEYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNPQYYYYKG 314
                                   6789*******************************9998865 PP

  == domain 9  score: 12.9 bits;  conditional E-value: 0.00031
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawll 40 
                                   ++  + al al ++d+Ai+ +++a++l+P+d+  +++
  gi|70607745|ref|YP_256615.1| 310 YYYKGNALKALWKYDKAIKEYDKAISLNPNDPLPHYQ 346
                                   56667778888899*****************987766 PP

  == domain 10  score: 15.4 bits;  conditional E-value: 4.7e-05
                        TPR_14   5 lalaeallalGdpdeAiallrralalaPddae 36 
                                   ++ + +l +lG+++eAi  l++a++l+Pd+++
  gi|70607745|ref|YP_256615.1| 345 YQKGVVLKTLGKYEEAIVELDEAIKLNPDNQQ 376
                                   6778899**********************986 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.5e-05     0.018      33      64 ..      28      59 ..      25      70 .. 0.84
   2 !    9.6   0.1     0.002         1      10      64 ..      84     138 ..      79     141 .. 0.90
   3 !   19.1   0.0   2.1e-06    0.0011       4      61 ..     146     203 ..     143     209 .. 0.94
   4 !   27.8   0.0     4e-09     2e-06       7      63 ..     217     273 ..     212     274 .. 0.93
   5 !   16.0   0.0     2e-05      0.01      21      64 ..     265     308 ..     263     311 .. 0.94
   6 !   25.6   0.0     2e-08     1e-05      11      64 ..     323     376 ..     318     391 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.5e-05
                         TPR_9 33 rdRGlllaqlGclsaAladLeaylalapdapd 64
                                  + RGl+++ l+++s+A+++++ +++l+p  +d
  gi|70607745|ref|YP_256615.1| 28 FNRGLAYFNLNNYSEAIREFDEAIRLNPFHAD 59
                                  68*************************94333 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                         TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                    +era+   +  + ++P+ pe ++  Gl+l+ lG+  +Al + + ++ l+p +p+
  gi|70607745|ref|YP_256615.1|  84 LYERAILEFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLEYQDAIKLNPRNPE 138
                                   56777777888899*************************************8875 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 2.1e-06
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                   i++ +e++  a+a v+  + l+P+    ++  +lll  +G l++Al+ L+ +++l+p+
  gi|70607745|ref|YP_256615.1| 146 ILQDQEKYVDAIAEVDTAIRLNPKNSTYYFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   66899**************************************************997 PP

  == domain 4  score: 27.8 bits;  conditional E-value: 4e-09
                         TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                                   + ++++  l+ ++  + l P+ pe ++  G+l+++lG +++A+++Le  ++l+p++p
  gi|70607745|ref|YP_256615.1| 217 ELKRYDDVLKDYDNAIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESVRLNPNNP 273
                                   5689999*******************************************9999876 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 2e-05
                         TPR_9  21 llllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                    + l+P+ pe ++  Gl+l+++  ++ A+++++ ++ l+p++p+
  gi|70607745|ref|YP_256615.1| 265 SVRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNPQ 308
                                   5789*************************************997 PP

  == domain 6  score: 25.6 bits;  conditional E-value: 2e-08
                         TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                   +++a++ ++  + l+P+dp  ++  G++l  lG +++A+ +L+ ++ l+pd+++
  gi|70607745|ref|YP_256615.1| 323 YDKAIKEYDKAISLNPNDPLPHYQKGVVLKTLGKYEEAIVELDEAIKLNPDNQQ 376
                                   7999**********************************************9987 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   7.1e-06    0.0036      27      71 ..      24      73 ..       8      76 .. 0.88
   2 !   20.6   0.4   7.7e-07    0.0004       4      78 ..      84     159 ..      82     163 .. 0.95
   3 !   15.8   0.8   2.4e-05     0.012      23      77 ..     169     226 ..     162     231 .. 0.86
   4 !   28.7   0.1   2.3e-09   1.2e-06      15      81 ..     231     298 ..     225     299 .. 0.93
   5 !   30.8   0.1   5.1e-10   2.6e-07       4      81 ..     288     366 ..     285     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.1e-06
                                  HHH....HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT- CS
                        ANAPC3 27 yll....AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkk 71
                                  yl+    +l+++++++y +A++ +++a +ln+ +  ++y +A +l++L++
  gi|70607745|ref|YP_256615.1| 24 YLYhfnrGLAYFNLNNYSEAIREFDEAiRLNPFHADSHYYKALSLIALQR 73
                                  55556779***************************************986 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 7.7e-07
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                    y+ Ai+ ++ + + ++++pe  y ++l+l  +g+ ++A+  +++a kln++++++ y +A  l +++ky +Aia 
  gi|70607745|ref|YP_256615.1|  84 LYERAILEFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLEYQDAiKLNPRNPEYYYRKAIILQDQEKYVDAIAE 159
                                   6999*********************************************************************985 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.4e-05
                                   HHHHHHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                        ANAPC3  23 pedayll..AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                    +++y++  Al l ++g+ k+A++ l+ka  ln++  ++   ++  l +Lk+y++ ++
  gi|70607745|ref|YP_256615.1| 169 KNSTYYFrkALLLKSMGKLKEALDQLDKAiSLNPQVAEYYHQKGLILKELKRYDDVLK 226
                                   344555455*********************************************9875 PP

  == domain 4  score: 28.7 bits;  conditional E-value: 2.3e-09
                                   HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   + + ++++pe  + ++  +y++g+y++A   l+++ +ln+++++++y ++ +l+    ye+A+  ++k
  gi|70607745|ref|YP_256615.1| 231 AIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESvRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDK 298
                                   556789********************************************************988776 PP

  == domain 5  score: 30.8 bits;  conditional E-value: 5.1e-10
                                   -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                        ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                   +y++A+  ++++++ ++++p+  y+++ +l  + +y++A++ ++ka  ln++++  +y ++ +l  L+kyeeAi  L++
  gi|70607745|ref|YP_256615.1| 288 MYEDAVEEFDKAVKLDPQNPQYYYYKGNALKALWKYDKAIKEYDKAiSLNPNDPLPHYQKGVVLKTLGKYEEAIVELDE 366
                                   799***********************************************************************98876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0029       1.5      14      62 ..      10      63 ..       5      70 .. 0.74
   2 ?    5.4   0.3     0.051        26       7      62 ..      85     140 ..      82     146 .. 0.79
   3 !   15.5   0.7   3.6e-05     0.019      10      62 ..     122     174 ..     118     182 .. 0.89
   4 !   19.7   0.8   1.7e-06   0.00088       3      62 ..     149     209 ..     147     214 .. 0.93
   5 !   25.0   0.0   3.8e-08   1.9e-05       5      62 ..     219     276 ..     215     282 .. 0.95
   6 !   20.8   0.1   7.8e-07    0.0004       5      62 ..     253     310 ..     253     320 .. 0.95
   7 !   12.7   0.3   0.00028      0.14       7      49 ..     289     331 ..     287     332 .. 0.94
   8 !   30.2   0.1   9.6e-10   4.9e-07       6      62 ..     322     378 ..     319     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                        TPR_19 14 leqalqedpknaearllL...AeallalgqldeAealLdalpeedpd..darya 62
                                  + ++ +++p ++   l+      a+++l+++ eA++  d++ + +p   d+ y 
  gi|70607745|ref|YP_256615.1| 10 YDEMGEQNPSQDQGYLYHfnrGLAYFNLNNYSEAIREFDEAIRLNPFhaDSHYY 63
                                  566777777766666643444789******************999986654444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.051
                        TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   y++A+  + +a++ dpkn+e  ++   al  lg+  eA    +++ + +p +++y 
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLEYQDAIKLNPRNPEYY 140
                                   78899999999999999999999888888888888888888888777777776654 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 3.6e-05
                        TPR_19  10 AlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   Al  ++ a++ +p n+e  ++ A++l  +  + +A+a +d++ + +p+++ y 
  gi|70607745|ref|YP_256615.1| 122 ALLEYQDAIKLNPRNPEYYYRKAIILQDQEKYVDAIAEVDTAIRLNPKNSTYY 174
                                   6667888*****************************************85553 PP

  == domain 4  score: 19.7 bits;  conditional E-value: 1.7e-06
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62 
                                   ++++y +A+a    a+  +pkn+    + A +l ++g l+eA + Ld++   +p+  ++y+
  gi|70607745|ref|YP_256615.1| 149 DQEKYVDAIAEVDTAIRLNPKNSTYYFRKALLLKSMGKLKEALDQLDKAISLNPQVaEYYH 209
                                   799****************************************************746666 PP

  == domain 5  score: 25.0 bits;  conditional E-value: 3.8e-08
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   ++y++ l+ + +a++ +p+n+e   +   ++++lg +++A   L++  + +p++++y+
  gi|70607745|ref|YP_256615.1| 219 KRYDDVLKDYDNAIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESVRLNPNNPEYH 276
                                   6899*****************************************************9 PP

  == domain 6  score: 20.8 bits;  conditional E-value: 7.8e-07
                        TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   g+y+ A+  le+    +p+n+e  ++L  al+    +++A +  d++ + dp++++y 
  gi|70607745|ref|YP_256615.1| 253 GKYEKAVMELEESVRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNPQYY 310
                                   89****************************************************9986 PP

  == domain 7  score: 12.7 bits;  conditional E-value: 0.00028
                        TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                   y++A++ + +a + dp+n+   ++  +al al  +d+A++  d
  gi|70607745|ref|YP_256615.1| 289 YEDAVEEFDKAVKLDPQNPQYYYYKGNALKALWKYDKAIKEYD 331
                                   89************************************98765 PP

  == domain 8  score: 30.2 bits;  conditional E-value: 9.6e-10
                        TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62 
                                   +y+ A++ + +a++ +p+++   ++   +l  lg ++eA+  Ld++ + +pd+++y+
  gi|70607745|ref|YP_256615.1| 322 KYDKAIKEYDKAISLNPNDPLPHYQKGVVLKTLGKYEEAIVELDEAIKLNPDNQQYK 378
                                   69**************************************************99996 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4   0.00047      0.24       7      51 ..      27      71 ..      22     101 .. 0.81
   2 ?    2.8   0.4      0.28   1.4e+02      19      66 ..      85     131 ..      75     133 .. 0.74
   3 !   14.3   0.1   7.5e-05     0.038       6      74 ..     140     200 ..     138     203 .. 0.84
   4 !   21.4   0.1   4.6e-07   0.00024       2      74 ..     204     268 ..     203     271 .. 0.93
   5 !    8.8   0.4    0.0038       1.9       7      72 ..     277     334 ..     274     337 .. 0.80
   6 !   10.8   0.1   0.00087      0.45       8      74 ..     312     370 ..     307     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00047
                        TPR_12  7 n.nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnL 51
                                  + n++++++ l +y eA++ +++a+++    + + h++ a +l++L
  gi|70607745|ref|YP_256615.1| 27 HfNRGLAYFNLNNYSEAIREFDEAIRLN-PFHADSHYYKALSLIAL 71
                                  45899999***************99998.77777777777777665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                        TPR_12  19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAle 66 
                                   y+ A+  +++a+ i  +   ++h++   +l  Lgr y+al +y++A++
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKN-PEYHYQKGLALEILGRQYEALLEYQDAIK 131
                                   666777777777777444.46788888888888888888888888876 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 7.5e-05
                        TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   +++ a +l+ +++y +A++  ++a+++      p++   +t+++  + l+  +g+++eAl+ l +a+ +
  gi|70607745|ref|YP_256615.1| 140 YYRKAIILQDQEKYVDAIAEVDTAIRLN-----PKN---STYYFRKALLLKSMGKLKEALDQLDKAISL 200
                                   5678999*****************7777.....665...889999999999999999999999998865 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 4.6e-07
                        TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                   va  +++ +++l +l+ryd+ l+ ++ a+ +      p++p+   + +  g ly++lg+ye+A+  lee++++
  gi|70607745|ref|YP_256615.1| 204 VAEYYHQKGLILKELKRYDDVLKDYDNAIKLS-----PNNPE---YHFRKGVLYYELGKYEKAVMELEESVRL 268
                                   7888999*********************9999.....99988...7************************997 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0038
                        TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                   ++l+++l++   y++A e ++ka+ +      p++p+   +++  g ++ al +y++A++ + +a+
  gi|70607745|ref|YP_256615.1| 277 YQLGLALFHVMMYEDAVEEFDKAVKLD-----PQNPQ---YYYYKGNALKALWKYDKAIKEYDKAI 334
                                   48999******************9988.....77766...58888888877778888888887776 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00087
                        TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                     +++l +l +yd+A++ ++ka+ +      p+ pl     +  g ++  lg+yeeA+  l ea+++
  gi|70607745|ref|YP_256615.1| 312 YKGNALKALWKYDKAIKEYDKAISLN-----PNDPL---PHYQKGVVLKTLGKYEEAIVELDEAIKL 370
                                   57888888889999999999997777.....88877...6889999999999999998888888765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00013     0.067       4      31 ..      28      55 ..      26      57 .. 0.93
   2 ?    2.2   0.0      0.67   3.4e+02       1      32 [.      59     101 ..      59     102 .. 0.77
   3 ?    0.7   0.1         2     1e+03       5      29 ..     115     132 ..     105     136 .. 0.54
   4 ?    7.6   0.2     0.012       6.4       3      32 ..     174     203 ..     173     203 .. 0.93
   5 ?    0.8   0.0       1.9   9.9e+02       6      32 ..     211     237 ..     206     238 .. 0.67
   6 !   12.6   0.0   0.00033      0.17       3      32 ..     242     271 ..     240     272 .. 0.90
   7 !   12.1   0.0   0.00047      0.24       3      32 ..     276     305 ..     274     306 .. 0.93
   8 ?    5.9   0.6     0.045        23       3      32 ..     310     339 ..     308     340 .. 0.86
   9 ?    7.0   0.0      0.02        10       4      33 .]     345     374 ..     344     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6  4 yklalsyrklgdtdkAlealerlikeYP 31
                                  ++++l+y++l+++++A++ +++ i+  P
  gi|70607745|ref|YP_256615.1| 28 FNRGLAYFNLNNYSEAIREFDEAIRLNP 55
                                  89*******99************99887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.67
                                   HHHHHHHHHHHHH...........HHHHHHHHHHHHHHHH-TT CS
                         TPR_6   1 dAlyklalsyrkl...........gdtdkAlealerlikeYPd 32 
                                   d+ y+ als+++l           + +++A+  +++ ik  P+
  gi|70607745|ref|YP_256615.1|  59 DSHYYKALSLIALqrsgsvnagisDLYERAILEFDEAIKIDPK 101
                                   5679999999995488888888877888888888888888776 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   5 klalsyrklgdtdkAlealerlike 29 
                                    l++ y+       Al  +++ ik 
  gi|70607745|ref|YP_256615.1| 115 ILGRQYE-------ALLEYQDAIKL 132
                                   3444444.......55555555555 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +++ al+++++g+  +Al+ l++ i+  P+
  gi|70607745|ref|YP_256615.1| 174 YFRKALLLKSMGKLKEALDQLDKAISLNPQ 203
                                   6999*********************99885 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                    +l +++l+++d+ l+ +++ ik  P+
  gi|70607745|ref|YP_256615.1| 211 KGLILKELKRYDDVLKDYDNAIKLSPN 237
                                   567777777777777777777777666 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 0.00033
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                    ++ + +y++lg+++kA+  le+ ++  P+
  gi|70607745|ref|YP_256615.1| 242 HFRKGVLYYELGKYEKAVMELEESVRLNPN 271
                                   5899******************99999998 PP

  == domain 7  score: 12.1 bits;  conditional E-value: 0.00047
                                   HHHHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrk.lgdtdkAlealerlikeYPd 32 
                                    y+l+l+++  +  +++A+e +++ +k  P+
  gi|70607745|ref|YP_256615.1| 276 HYQLGLALFHvM-MYEDAVEEFDKAVKLDPQ 305
                                   69**********.**************9997 PP

  == domain 8  score: 5.9 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +y+ + ++++l ++dkA++ +++ i+  P+
  gi|70607745|ref|YP_256615.1| 310 YYYKGNALKALWKYDKAIKEYDKAISLNPN 339
                                   6788888888779*************9998 PP

  == domain 9  score: 7.0 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                         TPR_6   4 yklalsyrklgdtdkAlealerlikeYPdS 33 
                                   y+ +  ++ lg++++A+  l++ ik  Pd+
  gi|70607745|ref|YP_256615.1| 345 YQKGVVLKTLGKYEEAIVELDEAIKLNPDN 374
                                   67788888899*****************95 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.031        16     181     234 ..      12      66 ..       1      84 [. 0.64
   2 ?    3.7   0.1     0.046        24     208     250 ..      85     127 ..      80     133 .. 0.83
   3 ?    5.8   0.1     0.011       5.4      50     237 ..     115     148 ..     105     156 .. 0.55
   4 !   21.4   0.2     2e-07    0.0001     204     255 ..     149     200 ..     139     204 .. 0.87
   5 !   15.3   0.1   1.4e-05    0.0071     199     238 ..     178     217 ..     171     231 .. 0.85
   6 !   10.3   0.0   0.00044      0.23     204     255 ..     217     268 ..     204     273 .. 0.88
   7 !   11.6   0.2   0.00019     0.095     204     259 ..     285     340 ..     273     342 .. 0.89
   8 ?    5.3   0.1     0.015       7.7      43      77 ..     346     380 ..     342     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
                                   GSS----SSHHHHHHHH.HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHH CS
                         NARP1 181 edsekepesallwvlyf.lAqhydklgsrekAleyidkaiehtptlvelyltKar 234
                                   e+ e++p +   + + f     y +l+++++A++  d+ai+ +p   + ++ Ka 
  gi|70607745|ref|YP_256615.1|  12 EMGEQNPSQDQGYLYHFnRGLAYFNLNNYSEAIREFDEAIRLNPFHADSHYYKAL 66 
                                   3444444444334444412445667899999************999999999984 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.046
                                   SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                         NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevme 250
                                   +e+A+   d+ai+ +p+  e++++K+  l+  G   +A    +
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLEYQ 127
                                   6899999*******************99988888777765555 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
                                   HTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT-SHHHHTHHHH--HHHHHHHHHHHH CS
                         NARP1  50 kLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprsdaprRlpLdfleGeeFkelvdkYl 130
                                    Lgr+ eA   y                                                                     
  gi|70607745|ref|YP_256615.1| 115 ILGRQYEALLEY--------------------------------------------------------------------- 126
                                   444444444444..................................................................... PP

                                   HHHHHCT-TTHHHHHGGGGGGSCHHHHHHHHHHHHHTTTTTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHH CS
                         NARP1 131 rkaLrkgvPslfanlksLYedkeKvkileelvegyvkslktsgklsesdnedsekepesallwvlyflAqhydklgsrekA 211
                                                                                                                    
  gi|70607745|ref|YP_256615.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                                   HHHHHHHHHH-TT-HHHHHHHHHHHH CS
                         NARP1 212 leyidkaiehtptlvelyltKarilk 237
                                       + ai+ +p   e+y++Ka il+
  gi|70607745|ref|YP_256615.1| 127 ----QDAIKLNPRNPEYYYRKAIILQ 148
                                   ....5555666666666666665554 PP

  == domain 4  score: 21.4 bits;  conditional E-value: 2e-07
                                   HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                     +++  A+  +d+ai+ +p+   +y +Ka +lk +G lk+A + +++a +l
  gi|70607745|ref|YP_256615.1| 149 DQEKYVDAIAEVDTAIRLNPKNSTYYFRKALLLKSMGKLKEALDQLDKAISL 200
                                   4556669*****************************************9887 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH CS
                         NARP1 199 AqhydklgsrekAleyidkaiehtptlvelyltKarilkh 238
                                   A     +g+ ++Al+ +dkai+ +p++ e+y +K+ ilk 
  gi|70607745|ref|YP_256615.1| 178 ALLLKSMGKLKEALDQLDKAISLNPQVAEYYHQKGLILKE 217
                                   6667889999***************************985 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00044
                                   HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                         NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                   +l++++  l+  d+ai+ +p+  e++ +K+ ++   G  +kA+  +ee+ +l
  gi|70607745|ref|YP_256615.1| 217 ELKRYDDVLKDYDNAIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESVRL 268
                                   577899999999*******************************999998665 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00019
                                   HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                         NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                   ++  +e A+e  dka++ +p+  ++y+ K++ lk     +kA++  ++a +l  +D
  gi|70607745|ref|YP_256615.1| 285 HVMMYEDAVEEFDKAVKLDPQNPQYYYYKGNALKALWKYDKAIKEYDKAISLNPND 340
                                   677899*******************************************9998766 PP

  == domain 8  score: 5.3 bits;  conditional E-value: 0.015
                                   HHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHH CS
                         NARP1  43 tkaelllkLgrkeeAeatyeaLlernpenskYyeg 77 
                                   +k+ +l  Lg++eeA   + + ++ np+n++Y  +
  gi|70607745|ref|YP_256615.1| 346 QKGVVLKTLGKYEEAIVELDEAIKLNPDNQQYKIS 380
                                   68889999**********************99755 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       8.9   4.6e+03       6      33 ..      42      69 ..      27      74 .. 0.65
   2 ?    3.4   0.0      0.19        99      10      44 ..      91     125 ..      85     146 .. 0.83
   3 ?    3.0   0.1      0.25   1.3e+02       9      43 ..     124     158 ..     118     160 .. 0.90
   4 !   11.3   0.1   0.00066      0.34       7      52 ..     156     201 ..     150     214 .. 0.87
   5 !    8.1   0.0    0.0066       3.4       9      49 ..     226     266 ..     219     268 .. 0.89
   6 !   15.3   0.0   3.7e-05     0.019       8      52 ..     259     303 ..     256     323 .. 0.89
   7 !    8.5   0.0    0.0047       2.4       6      57 ..     325     376 ..     322     394 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 8.9
                        TPR_20  6 pelaeleaalaanpddldarldlAlall 33
                                  + ++e+++a+  np   d ++  Al l+
  gi|70607745|ref|YP_256615.1| 42 EAIREFDEAIRLNPFHADSHYYKALSLI 69
                                  4566666666667766666666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.19
                        TPR_20  10 eleaalaanpddldarldlAlallaagryeeAleq 44 
                                   e+++a++ +p++ + +++  lal   gr+ eAl +
  gi|70607745|ref|YP_256615.1|  91 EFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLE 125
                                   788999*****************999999999865 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.25
                        TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAle 43 
                                    e ++a++ np + +  +  A  l  +++y +A++
  gi|70607745|ref|YP_256615.1| 124 LEYQDAIKLNPRNPEYYYRKAIILQDQEKYVDAIA 158
                                   578999***************************96 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00066
                        TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                    +ae+++a+  np++    +  Al+l + g+ +eAl+qL + ++ +
  gi|70607745|ref|YP_256615.1| 156 AIAEVDTAIRLNPKNSTYYFRKALLLKSMGKLKEALDQLDKAISLN 201
                                   6899***********************************8877655 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.0066
                        TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                                   ++ ++a++ +p++ + ++    ++++ g+ye+A+ +L e +
  gi|70607745|ref|YP_256615.1| 226 KDYDNAIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESV 266
                                   667889999*************************9998776 PP

  == domain 6  score: 15.3 bits;  conditional E-value: 3.7e-05
                        TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrd 52 
                                   + ele+ +  np++ + +++l lal++   ye+A+e++ + +k d
  gi|70607745|ref|YP_256615.1| 259 VMELEESVRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDKAVKLD 303
                                   6799********************************998888766 PP

  == domain 7  score: 8.5 bits;  conditional E-value: 0.0047
                        TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                   + ++e ++a+  np+d   +++   +l   g+yeeA+ +L e +k + + ++
  gi|70607745|ref|YP_256615.1| 325 KAIKEYDKAISLNPNDPLPHYQKGVVLKTLGKYEEAIVELDEAIKLNPDNQQ 376
                                   56889999**********************************9998877643 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00062      0.32       7      31 ..      29      53 ..      29      54 .. 0.92
   2 ?   -0.6   0.2       2.6   1.3e+03      11      30 ..     112     131 ..     110     133 .. 0.76
   3 ?    0.6   0.1       1.1   5.6e+02       9      30 ..     144     165 ..     140     167 .. 0.87
   4 ?    6.1   0.0     0.021        11       9      31 ..     178     200 ..     178     201 .. 0.90
   5 ?    2.6   0.0      0.26   1.3e+02       1      30 [.     204     233 ..     204     235 .. 0.87
   6 !    9.2   0.0    0.0023       1.2       9      30 ..     246     267 ..     246     269 .. 0.92
   7 ?    0.6   0.0       1.1   5.7e+02       8      30 ..     279     301 ..     278     302 .. 0.83
   8 ?    6.2   0.0     0.019       9.9       9      31 ..     314     336 ..     310     337 .. 0.93
   9 ?    6.6   0.0     0.015       7.5       9      30 ..     348     369 ..     347     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00062
                        TPR_10  7 NLanalrqrgrydeAealleealai 31
                                  N + a++++++y eA + ++ea+++
  gi|70607745|ref|YP_256615.1| 29 NRGLAYFNLNNYSEAIREFDEAIRL 53
                                  6799******************985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.6
                        TPR_10  11 alrqrgrydeAealleeala 30 
                                   al  +gr  eA+  +++a+ 
  gi|70607745|ref|YP_256615.1| 112 ALEILGRQYEALLEYQDAIK 131
                                   55567888899999999986 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   a++l+++ +y +A a  + a++
  gi|70607745|ref|YP_256615.1| 144 AIILQDQEKYVDAIAEVDTAIR 165
                                   899*********9998888876 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.021
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   a +l ++g+++eA++ l++a+++
  gi|70607745|ref|YP_256615.1| 178 ALLLKSMGKLKEALDQLDKAISL 200
                                   678999**************985 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.26
                        TPR_10   1 tAsslnNLanalrqrgrydeAealleeala 30 
                                   +A  ++  + +l +++ryd+ +++++ a+ 
  gi|70607745|ref|YP_256615.1| 204 VAEYYHQKGLILKELKRYDDVLKDYDNAIK 233
                                   57889999***********99999988886 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0023
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   +++++++g+y++A+  lee+++
  gi|70607745|ref|YP_256615.1| 246 GVLYYELGKYEKAVMELEESVR 267
                                   789****************997 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 1.1
                        TPR_10   8 LanalrqrgrydeAealleeala 30 
                                   L+ al+++  y++A++ +++a+ 
  gi|70607745|ref|YP_256615.1| 279 LGLALFHVMMYEDAVEEFDKAVK 301
                                   7888888888999**99999986 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.019
                        TPR_10   9 analrqrgrydeAealleealai 31 
                                   +nal ++ +yd+A + +++a+++
  gi|70607745|ref|YP_256615.1| 314 GNALKALWKYDKAIKEYDKAISL 336
                                   89******************985 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.015
                        TPR_10   9 analrqrgrydeAealleeala 30 
                                   +++l  +g+y+eA   l+ea+ 
  gi|70607745|ref|YP_256615.1| 348 GVVLKTLGKYEEAIVELDEAIK 369
                                   78999***************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   8.7e-05     0.045       3      35 ..      28      58 ..      26      59 .. 0.90
   2 ?   -1.7   0.0       7.7   3.9e+03      21      30 ..      84      94 ..      83     101 .. 0.55
   3 ?    0.4   0.2       1.7   8.7e+02       4      21 ..     115     132 ..     112     133 .. 0.77
   4 ?   -0.3   0.0       2.9   1.5e+03       4      19 ..     142     157 ..     140     168 .. 0.80
   5 ?    1.3   0.0      0.84   4.3e+02       8      31 ..     180     201 ..     174     206 .. 0.60
   6 ?    1.5   0.0      0.75   3.8e+02       4      35 ..     210     239 ..     208     240 .. 0.74
   7 ?    7.3   0.0      0.01       5.3       5      32 ..     245     270 ..     242     274 .. 0.75
   8 ?    3.6   0.0      0.15        78       4      35 ..     278     307 ..     276     308 .. 0.82
   9 ?    5.4   0.0     0.044        22       6      35 ..     314     341 ..     310     342 .. 0.78
  10 ?    2.5   0.0      0.36   1.9e+02       6      20 ..     348     362 ..     344     375 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.7e-05
                         TPR_7  3 lnLarlysrlGdyeeAielyeqsLaltkdpeda 35
                                  +n + +y++l++y+eAi+ + +  a++  p++a
  gi|70607745|ref|YP_256615.1| 28 FNRGLAYFNLNNYSEAIREFDE--AIRLNPFHA 58
                                  68899*****************..999999875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.7
                         TPR_7 21 lyeqsL.altk 30
                                  lye+++ ++++
  gi|70607745|ref|YP_256615.1| 84 LYERAIlEFDE 94
                                  56664444443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.7
                         TPR_7   4 nLarlysrlGdyeeAiel 21 
                                    L+r y++l +y++Ai+l
  gi|70607745|ref|YP_256615.1| 115 ILGRQYEALLEYQDAIKL 132
                                   57777888889****987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.9
                         TPR_7   4 nLarlysrlGdyeeAi 19 
                                   + a + +++ +y +Ai
  gi|70607745|ref|YP_256615.1| 142 RKAIILQDQEKYVDAI 157
                                   5678899999999998 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.84
                         TPR_7   8 lysrlGdyeeAielyeqsLaltkd 31 
                                   l  ++G+ +eA++ + +  a+   
  gi|70607745|ref|YP_256615.1| 180 LLKSMGKLKEALDQLDK--AISLN 201
                                   56667777777766666..55555 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.75
                         TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   + + +  +l +y++ ++ y    a+  +p+++
  gi|70607745|ref|YP_256615.1| 210 QKGLILKELKRYDDVLKDYDN--AIKLSPNNP 239
                                   556777788888888888888..888888876 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.01
                         TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdp 32 
                                    ++ly +lG+ye+A+  +e+   ++  p
  gi|70607745|ref|YP_256615.1| 245 KGVLYYELGKYEKAVMELEE--SVRLNP 270
                                   599***********977776..555555 PP

  == domain 8  score: 3.6 bits;  conditional E-value: 0.15
                         TPR_7   4 nLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   +L+ + + +  ye+A+e + +  a+  dp+++
  gi|70607745|ref|YP_256615.1| 278 QLGLALFHVMMYEDAVEEFDK--AVKLDPQNP 307
                                   677777777789*********..999999875 PP

  == domain 9  score: 5.4 bits;  conditional E-value: 0.044
                         TPR_7   6 arlysrlGdyeeAielyeqsLaltkdpeda 35 
                                   +++  +l +y++Ai+ y +  a+   p+d+
  gi|70607745|ref|YP_256615.1| 314 GNALKALWKYDKAIKEYDK--AISLNPNDP 341
                                   666677778**********..998888875 PP

  == domain 10  score: 2.5 bits;  conditional E-value: 0.36
                         TPR_7   6 arlysrlGdyeeAie 20 
                                   +++   lG+yeeAi 
  gi|70607745|ref|YP_256615.1| 348 GVVLKTLGKYEEAIV 362
                                   6667779******95 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.077        39      67     112 ..      29      77 ..      19      87 .. 0.78
   2 !   12.1   0.0    0.0004       0.2      78     124 ..      85     131 ..      79     133 .. 0.92
   3 ?    0.5   0.0       1.4   7.4e+02      79     120 ..     154     195 ..     147     201 .. 0.75
   4 ?    1.0   0.0         1   5.3e+02      74     121 ..     183     230 ..     160     237 .. 0.72
   5 !   14.6   0.1   6.8e-05     0.035      73     124 ..     250     301 ..     230     305 .. 0.93
   6 ?   -0.9   0.0         4     2e+03     106     136 ..     310     340 ..     308     349 .. 0.79
   7 ?    0.8   0.0       1.2     6e+02      74      95 ..     353     374 ..     346     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                                   HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHH...HHHHHHHHHTT-H CS
                          BTAD  67 alaeaelrlGraeealaelealvaehPlrErlh...rqlmrAlarsGrq 112
                                    +  a + l+ ++ea++e +++++++P++ ++h   ++ + Al rsG  
  gi|70607745|ref|YP_256615.1|  29 NRGLAYFNLNNYSEAIREFDEAIRLNPFHADSHyykALSLIALQRSGSV 77 
                                   5666778999******************999883333457777777765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                   +e+a+ e +++++ +P + ++h q  +Al  +Grq eAL  Y+++ +
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNPEYHYQKGLALEILGRQYEALLEYQDAIK 131
                                   578899999**********************************9865 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                          BTAD  79 eealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                    +a+ae + +++++P + +++    + l  +G+  eAL + +
  gi|70607745|ref|YP_256615.1| 154 VDAIAEVDTAIRLNPKNSTYYFRKALLLKSMGKLKEALDQLD 195
                                   578888888888888888888888888888888888887755 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1
                                   HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
                          BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYer 121
                                   ++G+ +eal++l+++++++P   +++ q  + l  + r  + L+ Y++
  gi|70607745|ref|YP_256615.1| 183 SMGKLKEALDQLDKAISLNPQVAEYYHQKGLILKELKRYDDVLKDYDN 230
                                   577888888888888888887777776666666666666666666665 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 6.8e-05
                                   HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                    +lG++e+a+ ele+ v+++P + ++h ql +Al+++   ++A e ++++++
  gi|70607745|ref|YP_256615.1| 250 YELGKYEKAVMELEESVRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDKAVK 301
                                   589****************************************999998876 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 4
                                   HHHTT-HHHHHHHHHHHHHHHHHHHS----H CS
                          BTAD 106 larsGrqaeALevYerlrrlLaeeLgvepgp 136
                                   +++ G+  +AL +Y+++ +  ++ +++ p  
  gi|70607745|ref|YP_256615.1| 310 YYYKGNALKALWKYDKAIKEYDKAISLNPND 340
                                   6788888899999999888888888887765 PP

  == domain 7  score: 0.8 bits;  conditional E-value: 1.2
                                   HTT-HHHHHHHHHHHHHHSTT- CS
                          BTAD  74 rlGraeealaelealvaehPlr 95 
                                   +lG++eea+ el+++++++P +
  gi|70607745|ref|YP_256615.1| 353 TLGKYEEAIVELDEAIKLNPDN 374
                                   6899999999999999999976 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0017      0.88      24      77 ..       9      60 ..       3      74 .. 0.83
   2 ?   -0.6   0.0       2.9   1.5e+03      57      70 ..      85      98 ..      68     105 .. 0.86
   3 ?    3.2   0.1      0.18        90      44      70 ..     174     200 ..     112     207 .. 0.82
   4 !    8.8   0.0    0.0032       1.6      45      74 ..     243     272 ..     214     292 .. 0.79
   5 ?   -0.9   0.0       3.4   1.8e+03      41      70 ..     276     302 ..     270     307 .. 0.68
   6 ?    5.9   0.0     0.025        13      52      75 ..     352     375 ..     345     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                        ANAPC5 24 yFDyvlsqnessqkksyqyalLnlaslhadfghneeAvkaleeairlArenkDk 77
                                   +D + +qn s+  + y y  +n      +++++ eA++ + eairl   ++D+
  gi|70607745|ref|YP_256615.1|  9 NYDEMGEQNPSQ-DQGYLY-HFNRGLAYFNLNNYSEAIREFDEAIRLNPFHADS 60
                                  688888888888.777777.5899999999****************98888776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
                        ANAPC5 57 neeAvkaleeairl 70
                                  +e A+  + eai++
  gi|70607745|ref|YP_256615.1| 85 YERAILEFDEAIKI 98
                                  799*********98 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.18
                        ANAPC5  44 lLnlaslhadfghneeAvkaleeairl 70 
                                    +  a l  ++g+ +eA++ l  ai+l
  gi|70607745|ref|YP_256615.1| 174 YFRKALLLKSMGKLKEALDQLDKAISL 200
                                   57788999999***********99987 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0032
                        ANAPC5  45 LnlaslhadfghneeAvkaleeairlAren 74 
                                   +   +l +++g++e+Av  lee++rl  +n
  gi|70607745|ref|YP_256615.1| 243 FRKGVLYYELGKYEKAVMELEESVRLNPNN 272
                                   567899*******************97655 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 3.4
                        ANAPC5  41 qyalLnlaslhadfghneeAvkaleeairl 70 
                                   +y  L la +h  +  +e+Av+ +  a++l
  gi|70607745|ref|YP_256615.1| 276 HYQ-LGLALFHVMM--YEDAVEEFDKAVKL 302
                                   543.5667776665..77788888888876 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.025
                        ANAPC5  52 adfghneeAvkaleeairlArenk 75 
                                    ++g++eeA+  l eai+l  +n+
  gi|70607745|ref|YP_256615.1| 352 KTLGKYEEAIVELDEAIKLNPDNQ 375
                                   579***************976665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0012      0.59       3      32 ..      26      55 ..      25      60 .. 0.90
   2 ?    0.2   0.0       1.5   7.9e+02      17      35 ..      85     103 ..      83     112 .. 0.91
   3 ?   -0.6   0.0       2.7   1.4e+03      16      35 ..     152     171 ..     149     184 .. 0.86
   4 ?   -0.8   0.0       3.2   1.7e+03      14      34 ..     218     238 ..     217     243 .. 0.75
   5 ?    3.8   0.2      0.12        62      11      34 ..     249     272 ..     239     274 .. 0.86
   6 !   14.6   0.1     5e-05     0.025       2      36 ..     274     308 ..     273     311 .. 0.97
   7 ?   -0.7   0.2       2.9   1.5e+03       5      33 ..     311     339 ..     308     340 .. 0.68
   8 !    8.6   0.1    0.0036       1.9      14      38 ..     354     378 ..     345     389 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                                  HHHHHHHHHHHHT-HHHHHHHHHHHHHHTT CS
                    Fis1_TPR_C  3 clYylAlGhyklgeYseArryvdalLeiEP 32
                                  +++   l+++ l +YseA r  d  +++ P
  gi|70607745|ref|YP_256615.1| 26 YHFNRGLAYFNLNNYSEAIREFDEAIRLNP 55
                                  678999***************999998887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  17 YseArryvdalLeiEPenr 35 
                                   Y++A    d  ++i+P+n 
  gi|70607745|ref|YP_256615.1|  85 YERAILEFDEAIKIDPKNP 103
                                   999999999*******995 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.7
                                   -HHHHHHHHHHHHHHTTS-H CS
                    Fis1_TPR_C  16 eYseArryvdalLeiEPenr 35 
                                   +Y +A   vd+ +++ P+n+
  gi|70607745|ref|YP_256615.1| 152 KYVDAIAEVDTAIRLNPKNS 171
                                   68889999999999999995 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.2
                                   HT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                                   l++Y++ ++  d  +++ P+n
  gi|70607745|ref|YP_256615.1| 218 LKRYDDVLKDYDNAIKLSPNN 238
                                   677777777778888888887 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.12
                                   HHHHT-HHHHHHHHHHHHHHTTS- CS
                    Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPen 34 
                                   +y lg+Y++A   ++   ++ P+n
  gi|70607745|ref|YP_256615.1| 249 YYELGKYEKAVMELEESVRLNPNN 272
                                   899***********9999999999 PP

  == domain 6  score: 14.6 bits;  conditional E-value: 5e-05
                                   HHHHHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HH CS
                    Fis1_TPR_C   2 eclYylAlGhyklgeYseArryvdalLeiEPenrQ 36 
                                   e++Y+l l+ + +  Y++A +  d   +++P+n Q
  gi|70607745|ref|YP_256615.1| 274 EYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNPQ 308
                                   89*******************************99 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHT-HHHHHHHHHHHHHHTTS CS
                    Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPe 33 
                                   Yy   +   l +Y++A +  d  +++ P+
  gi|70607745|ref|YP_256615.1| 311 YYKGNALKALWKYDKAIKEYDKAISLNPN 339
                                   55555666667788888888887777775 PP

  == domain 8  score: 8.6 bits;  conditional E-value: 0.0036
                                   HT-HHHHHHHHHHHHHHTTS-HHHH CS
                    Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQaq 38 
                                   lg+Y+eA   +d  +++ P+n+Q +
  gi|70607745|ref|YP_256615.1| 354 LGKYEEAIVELDEAIKLNPDNQQYK 378
                                   89*********************76 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       7.8     4e+03      49      65 ..      36      52 ..       3      65 .. 0.73
   2 ?   -0.9   0.0       4.7   2.4e+03      59      73 ..      91     105 ..      82     161 .. 0.60
   3 ?    6.1   0.0     0.031        16      43      95 ..     177     232 ..     151     233 .. 0.75
   4 !    9.2   0.0    0.0034       1.8       4      76 ..     208     279 ..     206     301 .. 0.82
   5 ?    0.5   0.0       1.7   8.8e+02      54      81 ..     290     317 ..     284     335 .. 0.78
   6 !   11.9   0.0    0.0005      0.25       9      92 ..     315     395 ..     303     397 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 7.8
                  Syntaxin-6_N 49 alrsiewdledLeetvr 65
                                  +l++ ++ +++++e++r
  gi|70607745|ref|YP_256615.1| 36 NLNNYSEAIREFDEAIR 52
                                  67788888999999984 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.7
                  Syntaxin-6_N  59 dLeetvriveknpsk 73 
                                   +++e+++i  knp+ 
  gi|70607745|ref|YP_256615.1|  91 EFDEAIKIDPKNPEY 105
                                   666666666666633 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.031
                  Syntaxin-6_N  43 rteLrkalrsiewdledLeetvr...iveknpskfkidekelsrrrafveevreev 95 
                                   +  L k+++++++ l++L+++++    v +  ++ ++  kel+r  +++++  + +
  gi|70607745|ref|YP_256615.1| 177 KALLLKSMGKLKEALDQLDKAISlnpQVAEYYHQKGLILKELKRYDDVLKDYDNAI 232
                                   55688999**************5223333334668888899999888888887776 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0034
                  Syntaxin-6_N   4 fevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpsk.fki 76 
                                   +  k  + k+l++   +++ + +  ++++  +++e++  +  L  +l++ e+ + +Lee+vr   +np+  +++
  gi|70607745|ref|YP_256615.1| 208 YHQKGLILKELKRYDDVLKDYDNAIKLSP--NNPEYHFRKGVLYYELGKYEKAVMELEESVRLNPNNPEYhYQL 279
                                   55666678899999999999976566654..589***************************9999998665655 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 1.7
                  Syntaxin-6_N  54 ewdledLeetvriveknpskfkidekel 81 
                                   e  +e+++++v+   +np+ +  + ++l
  gi|70607745|ref|YP_256615.1| 290 EDAVEEFDKAVKLDPQNPQYYYYKGNAL 317
                                   67899******99999998876665555 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.0005
                  Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafve 89 
                                   +  k+l k  + ++++ +  +++++   +  + ++  + k+l++ e+ + +L+e+++     ++++ki+ +e+++  + ++
  gi|70607745|ref|YP_256615.1| 315 NALKALWKYDKAIKEYDKAISLNPN--DPLPHYQKGVVLKTLGKYEEAIVELDEAIKLNPD-NQQYKISRDEVEKTLEALR 392
                                   5556666666666666554444432..33344455567899***************44433.488********99877776 PP

                  Syntaxin-6_N  90 evr 92 
                                   ++r
  gi|70607745|ref|YP_256615.1| 393 KMR 395
                                   665 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00016     0.081      52     118 ..      41     107 ..      36     121 .. 0.89
   2 ?   -0.4   0.0       1.6     8e+02      51      68 ..     187     204 ..     173     242 .. 0.80
   3 ?    5.4   0.0     0.027        14      49      78 ..     287     316 ..     216     320 .. 0.72
   4 ?    6.1   0.1     0.016       8.1      49      85 ..     287     323 ..     282     353 .. 0.78
   5 ?    2.1   0.1      0.27   1.4e+02      51      69 ..     357     375 ..     342     378 .. 0.81
   6 ?    3.3   0.1      0.12        59      96     124 ..     357     385 ..     351     395 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHH CS
                   TOM20_plant  52 qdaiskleeallidPkkhdalWcignaytsfafltpdeeeakenfekatqffqqavdedPdndlyrk 118
                                   ++ai  ++ea+ ++P   d+ +  + + ++  +  + +   ++ +e+a   f++a++ dP+n  y+ 
  gi|70607745|ref|YP_256615.1|  41 SEAIREFDEAIRLNPFHADSHYYKALSLIALQRSGSVNAGISDLYERAILEFDEAIKIDPKNPEYHY 107
                                   79***********************************************************987653 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHH-TT- CS
                   TOM20_plant  51 iqdaiskleeallidPkk 68 
                                   +++a+ +l++a+ ++P+ 
  gi|70607745|ref|YP_256615.1| 187 LKEALDQLDKAISLNPQV 204
                                   678888888888888864 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.027
                                   HHHHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
                   TOM20_plant  49 qmiqdaiskleeallidPkkhdalWcigna 78 
                                    m +da+  +++a+ +dP+  +  +  gna
  gi|70607745|ref|YP_256615.1| 287 MMYEDAVEEFDKAVKLDPQNPQYYYYKGNA 316
                                   355555555555555555555555555555 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH CS
                   TOM20_plant  49 qmiqdaiskleeallidPkkhdalWcignaytsfafl 85 
                                    m +da+  +++a+ +dP+  +  +  gna  +   +
  gi|70607745|ref|YP_256615.1| 287 MMYEDAVEEFDKAVKLDPQNPQYYYYKGNALKALWKY 323
                                   5778999999999999999999888888887765444 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHHHHH-TT-H CS
                   TOM20_plant  51 iqdaiskleeallidPkkh 69 
                                    ++ai  l+ea+ ++P  +
  gi|70607745|ref|YP_256615.1| 357 YEEAIVELDEAIKLNPDNQ 375
                                   5799999999999999876 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                   TOM20_plant  96 fekatqffqqavdedPdndlyrkslelaa 124
                                   +e a   +++a++ +Pdn++y+ s +  +
  gi|70607745|ref|YP_256615.1| 357 YEEAIVELDEAIKLNPDNQQYKISRDEVE 385
                                   55555566666677777777766666555 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.061        31      15      30 ..      38      53 ..      36      54 .. 0.90
   2 ?   -0.2   0.0       1.4     7e+02      14      29 ..     150     165 ..     146     168 .. 0.85
   3 ?    0.6   0.0      0.79     4e+02      16      30 ..     220     234 ..     217     235 .. 0.90
   4 ?    1.3   0.0      0.47   2.4e+02      15      30 ..     253     268 ..     251     269 .. 0.88
   5 !    7.1   0.0    0.0072       3.7      17      30 ..     289     302 ..     288     305 .. 0.95
   6 ?    3.7   0.0      0.08        41      16      30 ..     322     336 ..     322     337 .. 0.92
   7 ?    4.9   0.0     0.034        18      16      30 ..     356     370 ..     354     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.061
                      SHNi-TPR 15 enFpqAveDlrkaLeL 30
                                  +n+++A+ ++++a+ L
  gi|70607745|ref|YP_256615.1| 38 NNYSEAIREFDEAIRL 53
                                  69**********9866 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                      SHNi-TPR  14 nenFpqAveDlrkaLe 29 
                                   +e++ +A+ + ++a+ 
  gi|70607745|ref|YP_256615.1| 150 QEKYVDAIAEVDTAIR 165
                                   79******99988875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.79
                      SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                   ++++ ++D++ a++L
  gi|70607745|ref|YP_256615.1| 220 RYDDVLKDYDNAIKL 234
                                   79999*******998 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.47
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   ++++ Av +l++++ L
  gi|70607745|ref|YP_256615.1| 253 GKYEKAVMELEESVRL 268
                                   69***********976 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0072
                      SHNi-TPR  17 FpqAveDlrkaLeL 30 
                                   +++Ave+++ka++L
  gi|70607745|ref|YP_256615.1| 289 YEDAVEEFDKAVKL 302
                                   89**********98 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.08
                      SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                   +++ A+++++ka+ L
  gi|70607745|ref|YP_256615.1| 322 KYDKAIKEYDKAISL 336
                                   7999********987 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.034
                      SHNi-TPR  16 nFpqAveDlrkaLeL 30 
                                   ++++A+ +l++a++L
  gi|70607745|ref|YP_256615.1| 356 KYEEAIVELDEAIKL 370
                                   9***********998 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.92   4.7e+02     104     126 ..      28      50 ..       7      56 .. 0.68
   2 ?    4.5   0.0     0.065        33     104     128 ..     107     131 ..     104     164 .. 0.90
   3 ?    1.1   0.0      0.73   3.7e+02     104     127 ..     175     198 ..     171     207 .. 0.87
   4 ?    1.3   0.0      0.64   3.3e+02      68      92 ..     225     249 ..     205     265 .. 0.56
   5 ?    1.1   0.0      0.73   3.7e+02     105     127 ..     312     334 ..     305     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.92
                                   HHHHHHHHHTT-HHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrma 126
                                   f+r+ a+ +l +++ea+++f  a
  gi|70607745|ref|YP_256615.1|  28 FNRGLAYFNLNNYSEAIREFDEA 50 
                                   56666666666666666666554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.065
                                   HHHHHHHHHTT-HHHHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrmage 128
                                   ++++ ale lGr+ eal +++ a  
  gi|70607745|ref|YP_256615.1| 107 YQKGLALEILGRQYEALLEYQDAIK 131
                                   68999*************9998865 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.73
                                   HHHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrmag 127
                                   f++a  l+++G+ +eal+++ +a 
  gi|70607745|ref|YP_256615.1| 175 FRKALLLKSMGKLKEALDQLDKAI 198
                                   789999***********9998875 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.64
                                   TT-HHHHHHHHHHHHHHHHHH--TT CS
                       DUF3856  68 lgrydealesadkalryfnrrGele 92 
                                   l++yd+a++ + +  +y  r+G l 
  gi|70607745|ref|YP_256615.1| 225 LKDYDNAIKLSPNNPEYHFRKGVLY 249
                                   3344444444444444555555555 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.73
                                   HHHHHHHHTT-HHHHHHHHHHHH CS
                       DUF3856 105 sravaleelGrkdealkafrmag 127
                                    ++ al+ l ++d+a+k++ +a 
  gi|70607745|ref|YP_256615.1| 312 YKGNALKALWKYDKAIKEYDKAI 334
                                   57888999999999999888775 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.7    0.0039         2      46      87 ..      28      66 ..       2      97 .. 0.77
   2 !   11.7   1.3   0.00031      0.16     100     175 ..     147     232 ..      85     238 .. 0.76
   3 ?    4.8   3.1      0.04        20      10      77 ..     244     308 ..     235     393 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0039
                                  HHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHHHHHHHHH CS
                          YfiO 46 ldliyAyykdadyaealasaerFlrlyPthknvdyvlYlrgl 87
                                   +   Ay++ ++y+ea+ + ++ +rl+P h +  y    ++l
  gi|70607745|ref|YP_256615.1| 28 FNRGLAYFNLNNYSEAIREFDEAIRLNPFHADSHY---YKAL 66
                                  556679************************99876...3444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00031
                                   TS-THHHHHHHHHHHHHHHHST.TSTT.HHHH..HHHHHHHHHHHHHHHH......HHHHHHHHHT-HHHHHHHHHHHHHH CS
                          YfiO 100 krdpesarqafedfkklvekyP.dseY.aada..kkrltelrerLArhEl......evaefylkreayvaainRvkevlkn 170
                                    +d+e+ ++a+ ++ + ++  P +s+Y  ++a   k + +l+e+L + +       +vae+y +++  +  ++R+  vlk+
  gi|70607745|ref|YP_256615.1| 147 LQDQEKYVDAIAEVDTAIRLNPkNSTYyFRKAllLKSMGKLKEALDQLDKaislnpQVAEYYHQKGLILKELKRYDDVLKD 227
                                   5788999999999999999999535442555522689999999998876422222378*********************** PP

                                   STTSH CS
                          YfiO 171 ypdte 175
                                   y ++ 
  gi|70607745|ref|YP_256615.1| 228 YDNAI 232
                                   *9865 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.04
                                   HHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTT CS
                          YfiO  10 ekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthkn 77 
                                   +kg+  ++ g+y++A+ +le+     P+ p   + +++l  A ++ + y++a+++ ++ ++l P+ ++
  gi|70607745|ref|YP_256615.1| 244 RKGVLYYELGKYEKAVMELEESVRLNPNNP---EYHYQLGLALFHVMMYEDAVEEFDKAVKLDPQNPQ 308
                                   555555555566666666665555555544...23455555556666666666666666666665554 PP

>> EST1_DNA_bind  Est1 DNA/RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.053        27       5      36 ..     126     157 ..     122     160 .. 0.95
   2 ?    5.8   0.0     0.016       8.1       5      26 ..     194     215 ..     190     223 .. 0.87
   3 ?    1.2   0.0      0.41   2.1e+02       5      31 ..     228     254 ..     225     262 .. 0.88
   4 ?    1.0   0.0      0.46   2.4e+02       3      26 ..     328     351 ..     326     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.053
                                   HHHHHHH-TTBHHHHHHHHHHHHHTT-HHHHH CS
                 EST1_DNA_bind   5 YllAaellPsnGepyNQlgviaiysedkldav 36 
                                   Y+ A++l P n e y   ++i  ++e+ +da+
  gi|70607745|ref|YP_256615.1| 126 YQDAIKLNPRNPEYYYRKAIILQDQEKYVDAI 157
                                   9*****************************97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                                   HHHHHHH-TTBHHHHHHHHHHH CS
                 EST1_DNA_bind   5 YllAaellPsnGepyNQlgvia 26 
                                    ++A+ l P + e y+Q g+i 
  gi|70607745|ref|YP_256615.1| 194 LDKAISLNPQVAEYYHQKGLIL 215
                                   589*****************96 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.41
                                   HHHHHHH-TTBHHHHHHHHHHHHHTT- CS
                 EST1_DNA_bind   5 YllAaellPsnGepyNQlgviaiysed 31 
                                   Y+ A++l P+n e +   gv++++ ++
  gi|70607745|ref|YP_256615.1| 228 YDNAIKLSPNNPEYHFRKGVLYYELGK 254
                                   9*********************98776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.46
                                   HHHHHHHHH-TTBHHHHHHHHHHH CS
                 EST1_DNA_bind   3 rYYllAaellPsnGepyNQlgvia 26 
                                   + Y++A+ l P+   p+ Q gv+ 
  gi|70607745|ref|YP_256615.1| 328 KEYDKAISLNPNDPLPHYQKGVVL 351
                                   55*******************986 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.13        68      17      32 ..      37      52 ..      29      59 .. 0.81
   2 ?    2.4   0.0      0.31   1.6e+02      25      44 ..      83     104 ..      82     111 .. 0.86
   3 ?   -0.2   0.2         2     1e+03      17      32 ..     116     131 ..     105     132 .. 0.61
   4 ?    1.1   0.1      0.82   4.2e+02      28      51 ..     188     210 ..     173     226 .. 0.71
   5 ?   -2.3   0.0       9.7     5e+03      15      26 ..     223     234 ..     220     234 .. 0.77
   6 ?   -1.8   0.0       6.8   3.5e+03      18      35 ..     253     263 ..     244     274 .. 0.60
   7 ?    5.0   0.0      0.05        26      26      43 ..     288     307 ..     286     319 .. 0.84
   8 ?    2.9   0.2      0.22   1.2e+02      19      32 ..     322     335 ..     312     341 .. 0.68
   9 ?    6.4   0.1     0.018       9.3      24      58 ..     354     389 ..     346     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.13
                           MIT 17 agnyeeAlelYkeale 32
                                   +ny+eA++ + ea++
  gi|70607745|ref|YP_256615.1| 37 LNNYSEAIREFDEAIR 52
                                  5788888888888876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.31
                           MIT  25 elYkealelLlqalk.e.knee 44 
                                   +lY+ a+  + +a+k   kn+e
  gi|70607745|ref|YP_256615.1|  83 DLYERAILEFDEAIKiDpKNPE 104
                                   69*************7788875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2
                           MIT  17 agnyeeAlelYkeale 32 
                                    g   eAl  Y++a++
  gi|70607745|ref|YP_256615.1| 116 LGRQYEALLEYQDAIK 131
                                   4555677777777765 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.82
                           MIT  28 kealelLlqalkekneerrellre 51 
                                   keal+ L +a++  n++  e +++
  gi|70607745|ref|YP_256615.1| 188 KEALDQLDKAIS-LNPQVAEYYHQ 210
                                   577777777776.34454444444 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 9.7
                           MIT  15 DnagnyeeAlel 26 
                                   D  ++y+ A++l
  gi|70607745|ref|YP_256615.1| 223 DVLKDYDNAIKL 234
                                   677889999875 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 6.8
                           MIT  18 gnyeeAlelYkealelLl 35 
                                   g+ye       +a+  L 
  gi|70607745|ref|YP_256615.1| 253 GKYE-------KAVMELE 263
                                   4555.......5554444 PP

  == domain 7  score: 5.0 bits;  conditional E-value: 0.05
                           MIT  26 lYkealelLlqalk.e.kne 43 
                                   +Y++a+e + +a+k   +n+
  gi|70607745|ref|YP_256615.1| 288 MYEDAVEEFDKAVKlDpQNP 307
                                   79***********9667776 PP

  == domain 8  score: 2.9 bits;  conditional E-value: 0.22
                           MIT  19 nyeeAlelYkeale 32 
                                   +y++A++ Y +a+ 
  gi|70607745|ref|YP_256615.1| 322 KYDKAIKEYDKAIS 335
                                   56677777766664 PP

  == domain 9  score: 6.4 bits;  conditional E-value: 0.018
                           MIT  24 lelYkealelLlqalk.ekneerrellrekieeYle 58 
                                   l +Y+ea+  L +a+k + + ++ +  r ++e+ le
  gi|70607745|ref|YP_256615.1| 354 LGKYEEAIVELDEAIKlNPDNQQYKISRDEVEKTLE 389
                                   668*************66666888888888887765 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.4   1.8e+03      58      89 ..      37      71 ..      29      75 .. 0.62
   2 ?   -0.7   0.0         2     1e+03      39      68 ..     131     160 ..     118     181 .. 0.78
   3 ?    0.8   0.0      0.69   3.5e+02      35      72 ..     162     198 ..     144     214 .. 0.76
   4 ?    0.5   0.0      0.88   4.5e+02      25      65 ..     185     225 ..     173     230 .. 0.82
   5 ?    5.8   0.0      0.02        10      39      72 ..     233     266 ..     208     290 .. 0.81
   6 ?   -2.9   0.0        10   5.1e+03      41      72 ..     337     368 ..     335     378 .. 0.69
   7 ?   -1.7   0.0       4.2   2.1e+03      28      41 ..     382     395 ..     378     398 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.4
                    HrpB1_HrpK 58 rgrweeAlrlLreveaeasg...tpyakaLlAlcL 89
                                   ++++eA+r + e    +++     y kaL  ++L
  gi|70607745|ref|YP_256615.1| 37 LNNYSEAIREFDEAIRLNPFhadSHYYKALSLIAL 71
                                  67899999999998744443001445555555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                    HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlL 68 
                                    L P+++e     +++l  ++++ +A+   
  gi|70607745|ref|YP_256615.1| 131 KLNPRNPEYYYRKAIILQDQEKYVDAIAEV 160
                                   489999999999999999999999998655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.69
                    HrpB1_HrpK  35 dalrvLrPevaeldllegvlliergrweeAlrlLreve 72 
                                    a+ +L P++ +  +  ++ll + g+++eAl  L +  
  gi|70607745|ref|YP_256615.1| 162 TAI-RLNPKNSTYYFRKALLLKSMGKLKEALDQLDKAI 198
                                   344.5899999999999999999999999998887654 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.88
                    HrpB1_HrpK  25 edtedaellLdalrvLrPevaeldllegvlliergrweeAl 65 
                                   ++ ++a + Ld    L P+vae     g++l e +r+++ l
  gi|70607745|ref|YP_256615.1| 185 GKLKEALDQLDKAISLNPQVAEYYHQKGLILKELKRYDDVL 225
                                   5667777778888899*******999999999999999865 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.02
                    HrpB1_HrpK  39 vLrPevaeldllegvlliergrweeAlrlLreve 72 
                                    L+P+++e ++  gvl+ e g++e A+  L+e  
  gi|70607745|ref|YP_256615.1| 233 KLSPNNPEYHFRKGVLYYELGKYEKAVMELEESV 266
                                   69*************************9999854 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 10
                    HrpB1_HrpK  41 rPevaeldllegvlliergrweeAlrlLreve 72 
                                    P+ +  +   gv+l   g++eeA+  L e  
  gi|70607745|ref|YP_256615.1| 337 NPNDPLPHYQKGVVLKTLGKYEEAIVELDEAI 368
                                   56666666667777777888999988888765 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 4.2
                    HrpB1_HrpK  28 edaellLdalrvLr 41 
                                   +++e+ L+alr +r
  gi|70607745|ref|YP_256615.1| 382 DEVEKTLEALRKMR 395
                                   78899999999998 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       8.1   4.2e+03      31      43 ..      84      96 ..      82      97 .. 0.79
   2 ?    5.9   0.0     0.025        13      13      32 ..     186     205 ..     183     207 .. 0.91
   3 ?   -0.2   0.0         2     1e+03      34      43 ..     223     232 ..     209     234 .. 0.64
   4 ?   -1.2   0.0         4   2.1e+03      35      44 ..     292     301 ..     287     305 .. 0.72
   5 ?    2.2   0.0      0.36   1.9e+02      32      45 ..     316     329 ..     313     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 8.1
                 TFIIA_gamma_N 31 lamkVLeqFDksi 43
                                  l ++   +FD++i
  gi|70607745|ref|YP_256615.1| 84 LYERAILEFDEAI 96
                                  77788899**998 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.025
                 TFIIA_gamma_N  13 aLtdaLDeliqegkIspqla 32 
                                    L +aLD+l ++ +++pq+a
  gi|70607745|ref|YP_256615.1| 186 KLKEALDQLDKAISLNPQVA 205
                                   599***************98 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2
                 TFIIA_gamma_N  34 kVLeqFDksi 43 
                                    VL+ +D +i
  gi|70607745|ref|YP_256615.1| 223 DVLKDYDNAI 232
                                   5777777766 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4
                 TFIIA_gamma_N  35 VLeqFDksin 44 
                                     e+FDk+++
  gi|70607745|ref|YP_256615.1| 292 AVEEFDKAVK 301
                                   5678888874 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.36
                 TFIIA_gamma_N  32 amkVLeqFDksine 45 
                                   a+k L ++Dk+i+e
  gi|70607745|ref|YP_256615.1| 316 ALKALWKYDKAIKE 329
                                   789999****9987 PP

>> PA28_beta  Proteasome activator pa28 beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.52   2.7e+02      88     105 ..      33      50 ..      19      59 .. 0.86
   2 ?   -0.3   0.0       1.5   7.5e+02      51      63 ..     150     162 ..     126     191 .. 0.58
   3 ?    8.0   0.1    0.0042       2.1      60     100 ..     192     233 ..     184     244 .. 0.85
   4 ?    4.2   0.4      0.06        31      63      99 ..     297     334 ..     284     340 .. 0.82
   5 ?   -1.7   0.0         4   2.1e+03      91     105 ..     353     367 ..     345     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.52
                     PA28_beta  88 kyphvedyrealeelDek 105
                                    y ++++y+ea++e+De+
  gi|70607745|ref|YP_256615.1|  33 AYFNLNNYSEAIREFDEA 50 
                                   577899**********96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                     PA28_beta  51 Qeevleelsrvee 63 
                                   Qe+ ++ +++v++
  gi|70607745|ref|YP_256615.1| 150 QEKYVDAIAEVDT 162
                                   4444444444433 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0042
                     PA28_beta  60 rveeeaanlldqiskyfleraklvskllkyphv.edyreale 100
                                   +  ++a +l+ q+ +y+ +++ ++++l +y +v +dy +a++
  gi|70607745|ref|YP_256615.1| 192 DQLDKAISLNPQVAEYYHQKGLILKELKRYDDVlKDYDNAIK 233
                                   5557888999********************99846***9997 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.06
                     PA28_beta  63 eeaanlldqiskyfleraklvskllkyp.hvedyreal 99 
                                   ++a +l  q  +y+  ++++++ l ky   +++y +a+
  gi|70607745|ref|YP_256615.1| 297 DKAVKLDPQNPQYYYYKGNALKALWKYDkAIKEYDKAI 334
                                   46778888999***************962699999998 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 4
                     PA28_beta  91 hvedyrealeelDek 105
                                   ++  y+ea+ elDe+
  gi|70607745|ref|YP_256615.1| 353 TLGKYEEAIVELDEA 367
                                   567899999999996 PP

>> CAS_CSE1  CAS/CSE protein, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.073        37      67      94 ..     114     141 ..     105     145 .. 0.82
   2 ?   -0.9   0.1      0.84   4.3e+02      78      95 ..     261     278 ..     255     287 .. 0.81
   3 ?    5.1   0.0     0.013       6.5      81     106 ..     298     323 ..     281     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.073
                      CAS_CSE1  67 pvadvvlqkLieilevvskNPsnPrFny 94 
                                   ++ +   + L e  ++++ NP+nP+++y
  gi|70607745|ref|YP_256615.1| 114 EILGRQYEALLEYQDAIKLNPRNPEYYY 141
                                   555556678899999**********998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.84
                      CAS_CSE1  78 eilevvskNPsnPrFnyY 95 
                                   e+ e v+ NP+nP+++y 
  gi|70607745|ref|YP_256615.1| 261 ELEESVRLNPNNPEYHYQ 278
                                   56678999******9875 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                      CAS_CSE1  81 evvskNPsnPrFnyYlFEalgalvrl 106
                                   ++v+  P+nP+++yY   al al ++
  gi|70607745|ref|YP_256615.1| 298 KAVKLDPQNPQYYYYKGNALKALWKY 323
                                   678999**********9999988775 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4    0.0018      0.93     113     177 ..     140     205 ..     104     213 .. 0.81
   2 ?   -1.0   0.0       2.8   1.4e+03     125     174 ..     220     270 ..     206     282 .. 0.75
   3 ?   -1.6   0.0       4.3   2.2e+03     152     178 ..     350     376 ..     322     381 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                       Wzy_C_2 113 llelgllplspenlaaklalarklihlsPepavie.rlilslallGdedeAeqilararalfpeed 177
                                   + + +++ +++e++ + +a    +i+l P+  +++ r +l+l   G+ +eA+++l++a+ l p+ +
  gi|70607745|ref|YP_256615.1| 140 YYRKAIILQDQEKYVDAIAEVDTAIRLNPKNSTYYfRKALLLKSMGKLKEALDQLDKAISLNPQVA 205
                                   5566677889999999*************998877699********************99888755 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
                       Wzy_C_2 125 nlaaklalarklihlsPepavie.rlilslallGdedeAeqilararalfp 174
                                    ++++l+ + ++i+lsP    ++ r  +++  lG+ ++A + l++   l p
  gi|70607745|ref|YP_256615.1| 220 RYDDVLKDYDNAIKLSPNNPEYHfRKGVLYYELGKYEKAVMELEESVRLNP 270
                                   567777788889999998888775778899999999999877776655555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.3
                       Wzy_C_2 152 slallGdedeAeqilararalfpeeda 178
                                    l  lG+ +eA   l++a++l p++++
  gi|70607745|ref|YP_256615.1| 350 VLKTLGKYEEAIVELDEAIKLNPDNQQ 376
                                   567799999999999999999998876 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.61   3.1e+02      26      39 ..      94     107 ..      93     110 .. 0.84
   2 ?   -0.8   0.1       3.1   1.6e+03      28      39 ..     130     141 ..     127     145 .. 0.81
   3 ?    1.0   0.0      0.83   4.3e+02      28      40 ..     232     244 ..     229     248 .. 0.83
   4 ?    1.1   0.0      0.77     4e+02      26      39 ..     264     277 ..     262     279 .. 0.86
   5 ?    7.6   0.2     0.007       3.6      26      41 ..     298     313 ..     297     318 .. 0.87
   6 ?   -1.3   0.0       4.4   2.3e+03      26      38 ..     366     378 ..     364     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.61
                                   HHHHHS---S---X CS
                           Gin  26 kivntevddpkYef 39 
                                   + +++++++p+Y++
  gi|70607745|ref|YP_256615.1|  94 EAIKIDPKNPEYHY 107
                                   56899*******98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.1
                                   HHHS---S---X CS
                           Gin  28 vntevddpkYef 39 
                                   +++++ +p+Y++
  gi|70607745|ref|YP_256615.1| 130 IKLNPRNPEYYY 141
                                   78999*****87 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.83
                                   HHHS---S---XX CS
                           Gin  28 vntevddpkYefy 40 
                                   +++++++p+Y+f 
  gi|70607745|ref|YP_256615.1| 232 IKLSPNNPEYHFR 244
                                   789*******985 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.77
                                   HHHHHS---S---X CS
                           Gin  26 kivntevddpkYef 39 
                                   + v++++++p+Y++
  gi|70607745|ref|YP_256615.1| 264 ESVRLNPNNPEYHY 277
                                   5599********98 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.007
                                   HHHHHS---S---XXX CS
                           Gin  26 kivntevddpkYefyk 41 
                                   k v++++++p+Y++yk
  gi|70607745|ref|YP_256615.1| 298 KAVKLDPQNPQYYYYK 313
                                   6799***********9 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 4.4
                                   HHHHHS---S--- CS
                           Gin  26 kivntevddpkYe 38 
                                   + +++++d+++Y+
  gi|70607745|ref|YP_256615.1| 366 EAIKLNPDNQQYK 378
                                   66899*******7 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.083        42      36      76 ..      38      78 ..      32      90 .. 0.85
   2 ?   -1.0   0.0       5.1   2.6e+03      40      62 ..      87     109 ..      79     122 .. 0.81
   3 ?    0.7   0.1       1.5   7.5e+02      29      66 ..     144     180 ..     129     215 .. 0.76
   4 ?   -1.6   0.0       7.8     4e+03      31      63 ..     248     280 ..     229     292 .. 0.72
   5 ?    0.8   0.0       1.3   6.9e+02      41      70 ..     292     321 ..     280     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.083
                                  GTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-S CS
                 Biotin_carb_N 36 danslhvreadeavelgpasasesYlniekivkaakesgad 76
                                  ++ s+++re dea++l+p +a++ Y ++ +++++ ++ +++
  gi|70607745|ref|YP_256615.1| 38 NNYSEAIREFDEAIRLNPFHADSHYYKALSLIALQRSGSVN 78
                                  5678999*******************999999887766555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.1
                                   HHHHHSSEEEEEESSTTCCGGG- CS
                 Biotin_carb_N  40 lhvreadeavelgpasasesYln 62 
                                   +++ e dea++++p++++  Y +
  gi|70607745|ref|YP_256615.1|  87 RAILEFDEAIKIDPKNPEYHYQK 109
                                   5677889******9999999876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.5
                                   EEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHH CS
                 Biotin_carb_N  29 vavyseedanslhvreadeavelgpasasesYlnieki 66 
                                     + +++++   ++ e d+a++l+p++ s+ Y + + +
  gi|70607745|ref|YP_256615.1| 144 AIILQDQEKYVDAIAEVDTAIRLNPKN-STYYFRKALL 180
                                   556677788888899999999997554.4455554444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 7.8
                                   EEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-H CS
                 Biotin_carb_N  31 vyseedanslhvreadeavelgpasasesYlni 63 
                                   +y e  +  ++v e +e+v+l+p++++  Y   
  gi|70607745|ref|YP_256615.1| 248 LYYELGKYEKAVMELEESVRLNPNNPEYHYQLG 280
                                   556666677788889999999999998888655 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 1.3
                                   HHHHSSEEEEEESSTTCCGGG-HHHHHHHH CS
                 Biotin_carb_N  41 hvreadeavelgpasasesYlniekivkaa 70 
                                   +v+e d+av+l+p++++  Y + +++ ++ 
  gi|70607745|ref|YP_256615.1| 292 AVEEFDKAVKLDPQNPQYYYYKGNALKALW 321
                                   68899**********999999988876665 PP

>> KN17_SH3  KN17 SH3-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.75   3.8e+02      23      43 ..     104     125 ..      98     132 .. 0.79
   2 ?    7.4   0.0    0.0093       4.8      23      44 ..     138     159 ..     134     166 .. 0.83
   3 ?    3.7   0.1      0.13        66      23      33 ..     206     216 ..     200     230 .. 0.81
   4 ?    1.4   0.0      0.67   3.4e+02      25      46 ..     344     365 ..     343     373 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.75
                      KN17_SH3  23 kyykkKgvvekv.edeyvAevk 43 
                                   +y+++Kg+  ++   +y A ++
  gi|70607745|ref|YP_256615.1| 104 EYHYQKGLALEIlGRQYEALLE 125
                                   6******998885677888776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0093
                      KN17_SH3  23 kyykkKgvvekvedeyvAevkl 44 
                                   +yy++K+++ + +++yv  +  
  gi|70607745|ref|YP_256615.1| 138 EYYYRKAIILQDQEKYVDAIAE 159
                                   7***************977655 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                      KN17_SH3  23 kyykkKgvvek 33 
                                   +yy +Kg++ k
  gi|70607745|ref|YP_256615.1| 206 EYYHQKGLILK 216
                                   5********87 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.67
                      KN17_SH3  25 ykkKgvvekvedeyvAevklld 46 
                                   +++Kgvv k  ++y   +  ld
  gi|70607745|ref|YP_256615.1| 344 HYQKGVVLKTLGKYEEAIVELD 365
                                   689*****99999965555555 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       6.1   3.1e+03      71      85 ..      36      50 ..      34      54 .. 0.78
   2 ?    5.5   0.2     0.043        22      35      88 ..     215     268 ..     189     272 .. 0.84
   3 ?    5.0   0.1     0.062        32      37      87 ..     251     301 ..     244     304 .. 0.77
   4 ?    5.4   0.2     0.048        25      36      74 ..     352     390 ..     346     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.1
                Streptin-Immun 71 kideyeelvrkldkf 85
                                  ++++y e++r +d+ 
  gi|70607745|ref|YP_256615.1| 36 NLNNYSEAIREFDEA 50
                                  578999999998875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.043
                Streptin-Immun  35 trrlakydfsklnltesvtleqiekeieklqnelskkideyeelvrkldkfvkv 88 
                                    + l +yd    +  ++++l   + e +  +  l  ++ +ye++v  l++ v++
  gi|70607745|ref|YP_256615.1| 215 LKELKRYDDVLKDYDNAIKLSPNNPEYHFRKGVLYYELGKYEKAVMELEESVRL 268
                                   578888988888889999999999999999999999999999999999998874 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.062
                Streptin-Immun  37 rlakydfsklnltesvtleqiekeieklqnelskkideyeelvrkldkfvk 87 
                                    l ky+ + + l esv+l+  + e +        ++  ye++v  +dk vk
  gi|70607745|ref|YP_256615.1| 251 ELGKYEKAVMELEESVRLNPNNPEYHYQLGLALFHVMMYEDAVEEFDKAVK 301
                                   588999999999999999988888765444444677888888888877665 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.048
                Streptin-Immun  36 rrlakydfsklnltesvtleqiekeieklqnelskkide 74 
                                   + l ky+ + + l e+++l+  +++ + +++e++k+++ 
  gi|70607745|ref|YP_256615.1| 352 KTLGKYEEAIVELDEAIKLNPDNQQYKISRDEVEKTLEA 390
                                   7899**********************9999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.63
# Mc/sec: 1918.42
//
Query:       gi|70607746|ref|YP_256616.1|  [L=307]
Description: hypothetical protein Saci_2027 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-05   23.4   0.1    0.00019   21.3   0.1    2.0  2  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.031   5.6e+02      95     130 ..      13      47 ..       9      56 .. 0.78
   2 !   21.3   0.1     1e-08   0.00019      67     123 ..      54     108 ..      19     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.031
                                   THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC- CS
               Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernk 130
                                   d l +l+++l+   +dv +  +++ +++t+ ++r+ 
  gi|70607746|ref|YP_256616.1|  13 DSLYPLLRKLKT-WKDVEILLVYKGEVKTKDYNRAI 47 
                                   778888888888.88888888888888888888875 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1e-08
                                   HHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCC CS
               Glycos_transf_2  67 kagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifget 123
                                   +  a+n  +r++ + ++l+ D+D +p++ w+++ v + e++++ +v+    + +g++
  gi|70607746|ref|YP_256616.1|  54 YEEAINIIFRESHSSILLITDDDAIPSDTWIQDHVSFHERNEKIGVA--SGVVEGKK 108
                                   5679************************************8884433..33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2179.15
//
Query:       gi|70607747|ref|YP_256617.1|  [L=355]
Description: nickel transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-88  296.3  13.4    2.1e-88  296.3  13.4    1.5  2  NicO            High-affinity nickel-transport protein
  ------ inclusion threshold ------
       0.38    9.7   5.1       0.23   10.4   0.8    2.6  2  SHR3_chaperone  ER membrane protein SH3
        2.2    8.8   7.0       0.33   11.4   0.8    2.8  3  DUF2231         Predicted membrane protein (DUF2231)


Domain annotation for each model (and alignments):
>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5      0.47   2.8e+03      75     104 ..       4      35 ..       2      42 .. 0.53
   2 !  296.3  13.4   3.6e-92   2.1e-88       2     282 ..      50     341 ..      49     342 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.47
                          NicO  75 gaaigtei.asFll.villlnllllrklrklf 104
                                   ++++++++  +F+l ++ +  l+++ +  ++f
  gi|70607747|ref|YP_256617.1|   4 KNTPFLKLsLFFILeLVITTVLFIWLDTLSSF 35 
                                   56677777444443334444555565555544 PP

  == domain 2  score: 296.3 bits;  conditional E-value: 3.6e-92
                          NicO   2 lvliglsflyGvrHAvdagHgkai...irklmqagktalkrGillslgsslvvvlvavllvvaavlvlrltslsetgaaig 79 
                                   ++l++l++++G+rHAvda+H++ai   +rkl+q++k +  +G+++slg+s++v++++++++++++l+ +++s++ +++++ 
  gi|70607747|ref|YP_256617.1|  50 FALGVLAYVFGLRHAVDADHLAAIdntTRKLVQENKPSTFTGLFFSLGHSTIVIVLSLVIMLSSRLLDNISSIQSISSTLS 130
                                   6899***************************************************************************** PP

                          NicO  80 tei.asFllvilllnllllrklrklfrklerlgrapaaeleaalakrgllsrilgklfrlitkswhmypvgflfglGfdta 159
                                   t+i ++Fl++i++ln l++ +++ +f+++++ g+ ++ +l++ l  rg+++r++gklf+++++++h y +gflfglGfdta
  gi|70607747|ref|YP_256617.1| 131 TLIsGFFLYIIGFLNFLVVLEIYGIFKQVKS-GKLDEGKLNEVLLRRGFMNRFFGKLFKIVDSQYHLYVIGFLFGLGFDTA 210
                                   *****************************99.************************************************* PP

                          NicO 160 teiallaidps..ealkgdsfdsilalpalfavGlrlcdgadivlmfaalnwaflg..grklvyamsitgtsitvalligl 236
                                   te+allai++s   ++++++++  l++p lf++G+ l+d++d+++m+ a++waflg  +rk++y++s+t++si+va+l+g+
  gi|70607747|ref|YP_256617.1| 211 TETALLAISASsaVLFSKVPLWYLLVYPLLFTAGMTLVDTTDGLFMNGAYKWAFLGnpLRKVWYNLSMTLISIIVAFLVGT 291
                                   *********9965679***************************************************************** PP

                          NicO 237 ivtlklvakkfalsgslwaaiisle....leivGavlvllfallllgasl 282
                                   ++ l+l++ +f+ sg +w+ i++++    +e+vG+++++ fal+++ ++l
  gi|70607747|ref|YP_256617.1| 292 LEILGLLQSEFNFSGPFWSLIDTINsdvwWENVGIIIIGSFALAWIFSFL 341
                                   **********************************************9986 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.8   3.9e-05      0.23      61     121 ..      15      75 ..       5     115 .. 0.78
   2 ?   -0.4   0.2     0.078   4.7e+02       8      29 ..     324     345 ..     321     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.9e-05
                SHR3_chaperone  61 rilhiviglgliglliklykpsednllFdgaSLvLyvvgvvvyitnivkglrtvtegawge 121
                                    il  vi+  l   l  l    +++ +F g+S  L+ +gv+ y+  +++++++    a ++
  gi|70607747|ref|YP_256617.1|  15 FILELVITTVLFIWLDTLSSFFNSSIVFRGSSTTLFALGVLAYVFGLRHAVDADHLAAIDN 75 
                                   57888888888888999999999*********************99999987655555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.078
                SHR3_chaperone   8 aliigstsFflGvlfanfpyDy 29 
                                   + ii+  sF l+ +f+ + y +
  gi|70607747|ref|YP_256617.1| 324 VGIIIIGSFALAWIFSFLLYKV 345
                                   5689999*********998866 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.5      0.57   3.4e+03      65      65 ..      82      82 ..      46     144 .. 0.58
   2 ?   -1.5   0.0      0.59   3.5e+03      12      30 ..     131     149 ..     123     153 .. 0.81
   3 ?   11.4   0.8   5.5e-05      0.33       6      60 ..     273     336 ..     269     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                       DUF2231 65 r 65
                                  +
  gi|70607747|ref|YP_256617.1| 82 Q 82
                                  0 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.59
                       DUF2231  12 alvigflaalaGlvellla 30 
                                    l++gf+  ++G++++l++
  gi|70607747|ref|YP_256617.1| 131 TLISGFFLYIIGFLNFLVV 149
                                   5788999999999999876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 5.5e-05
                       DUF2231   6 lwnlvaalvigflaalaGlvelllaepsi............rakktallHavggvlllalivaltvW 60 
                                   ++nl + l+++++a l+G++e+l   +s+            + ++ +++  vg +++ ++++a   W
  gi|70607747|ref|YP_256617.1| 273 WYNLSMTLISIIVAFLVGTLEILGLLQSEfnfsgpfwslidTINSDVWWENVGIIIIGSFALA---W 336
                                   9**********************9977778888888888876777777777766666666666...5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2916.64
//
Query:       gi|70607748|ref|YP_256618.1|  [L=83]
Description: hypothetical protein Saci_2029 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   15.2   0.4      0.042   14.3   0.4    1.7  1  CcdA       Post-segregation antitoxin CcdA
      0.033   14.4   0.0      0.036   14.3   0.0    1.1  1  Eisosome1  Eisosome protein 1
      0.047   13.7   0.1      0.075   13.0   0.1    1.3  1  Mistic     Membrane-integrating protein Mistic


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4     7e-06     0.042      21      43 ..      28      50 ..       2      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-06
                          CcdA 21 iNlSatleeaLaeevkeekaerw 43
                                   N+S++++e+L++e+ ++++ r 
  gi|70607748|ref|YP_256618.1| 28 KNISRVVNELLRKELSRRRKVRS 50
                                  5**************88776553 PP

>> Eisosome1  Eisosome protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-06     0.036      21      82 ..      10      80 ..       1      81 [. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-06
                     Eisosome1 21 ekvyadtgkvspslneewerkakaaaqar.....adkrsene......agkvdiGggkfmdqeevdaiAarrv 82
                                  + vy+    v+ s+++  ++k+ +++ ++      ++r++ +      +  v + g  ++++ee+d+iA++ +
  gi|70607748|ref|YP_256618.1| 10 DDVYEA--IVNLSVKKYGNTKNISRVVNEllrkeLSRRRKVRsnrvsmKVSVRVPGAETLSPEEIDRIAEEEI 80
                                  555555..44444444444444444444434333333333332335457778888**************9876 PP

>> Mistic  Membrane-integrating protein Mistic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.2e-05     0.075      30      68 ..       3      43 ..       1      47 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                  S-SS-SHHHHHHHHHH.HHHHTSS.SS-HHHHHHHHHHHHH CS
                        Mistic 30 kpliefeeevleaiek.AkekYGe.evvnkKiNtivkevLs 68
                                  k ++ f+++v eai +   +kYG+ + +++ +N+++++ Ls
  gi|70607748|ref|YP_256618.1|  3 KTVVTFDDDVYEAIVNlSVKKYGNtKNISRVVNELLRKELS 43
                                  6799********9976489****735688888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 622.77
//
Query:       gi|70607749|ref|YP_256619.1|  [L=133]
Description: PIN domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   54.2   3.6    2.2e-14   54.0   3.6    1.0  1  PIN       PIN domain
     0.0081   15.9   0.1      0.015   15.1   0.1    1.5  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   3.6   2.5e-18   2.2e-14       2     121 ..       8     122 ..       7     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.5e-18
                                   EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHH CS
                           PIN   2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeea 81 
                                   ++DT+vli  + +++  ++ +rkll++l+++++ +++l E++ v +r  +k+  ++ + ++ ++l++  ++ + +e+ +ea
  gi|70607749|ref|YP_256619.1|   8 IVDTNVLIFDFiEDSQYHDVSRKLLNSLDRMLILPNILVEFILVSRR--LKIRDEDIRSKVDEILKNSILVGVKKEDIKEA 86 
                                   89****997777***********************************..7777777777777777777788999******* PP

                                   HHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                           PIN  82 aeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                     ++lk    +nDa+i+++Ak+ ++++i + D+d ++++k
  gi|70607749|ref|YP_256619.1|  87 ISLSLKE---INDAIIVSVAKRLNLPII-SLDRDVKELGK 122
                                   9999975...******************.*******9986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.6e-06     0.015       5      61 ..      66     120 ..      62     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-06
                       DUF5615   5 lDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgel 61 
                                   +De l  ++   ++++  d++   +l+l++++D  i+++Ak+ ++ i++ D+D  el
  gi|70607749|ref|YP_256619.1|  66 VDEILKNSILVGVKKE--DIKEAISLSLKEINDAIIVSVAKRLNLPIISLDRDVKEL 120
                                   5666666666666554..667777999**************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 784.63
//
Query:       gi|70607750|ref|YP_256620.1|  [L=148]
Description: hypothetical protein Saci_2031 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-30  103.5   0.6    8.4e-30  103.4   0.6    1.0  1  COXG      Carbon monoxide dehydrogenase subunit G (CoxG)
     0.0022   17.5   0.1      0.003   17.1   0.1    1.1  1  ParA      NUBPL iron-transfer P-loop NTPase


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.6   9.3e-34   8.4e-30       1     139 [.       5     147 ..       5     148 .] 0.98

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 9.3e-34
                                   EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEE....EEEEEEEEEETTTEEE..EEEE CS
                          COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsf....karvelselekensttieikGk 76 
                                   Gef v+  k++v ef+++p+ + +c+P ++ +e +g +e+++++k++v+ + +++    +a+++++ ++++++  iei G+
  gi|70607750|ref|YP_256620.1|   5 GEFVVNMVKAKVSEFFTEPKMFTECLPSLQGYEIKGdNEISATFKIDVSGFNIPHmstiTANINAKIIKDNEK--IEIVGN 83 
                                   899***************************************************99999*************8..9***** PP

                                   EE-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                          COXG  77 Grgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecisskl 139
                                   Gr+agv+++ ++ +   e ++ t++ wsak+++g l + lG+  i+++a++++n +++ci+s++
  gi|70607750|ref|YP_256620.1|  84 GRSAGVSVKINISLNLYEMQKsTKVIWSAKMDMGLLTKLLGENSIRKIAESNVNYIINCIRSRV 147
                                   **************99999999***************************************987 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.3e-07     0.003      38     106 ..      48     125 ..      37     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-07
                          ParA  38 lDaDiyGpsiprllgvee...ekpeqsekkliPvea...kgikv...mSigfllesedeavvwrGpmkskaikqllkd 106
                                   + +D+ G++ip++  ++    +k+ ++++k+  v +    g++v   +S+++   ++++ v+w + m ++++++ll +
  gi|70607750|ref|YP_256620.1|  48 FKIDVSGFNIPHMSTITAninAKIIKDNEKIEIVGNgrsAGVSVkinISLNLYEMQKSTKVIWSAKMDMGLLTKLLGE 125
                                   569**********9998844333444465666665555655554436899999999*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1009.46
//
Query:       gi|70607751|ref|YP_256621.1|  [L=431]
Description: glycerol-3-phosphate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-48  165.5   0.0    2.7e-48  165.3   0.0    1.0  1  DAO             FAD dependent oxidoreductase
      3e-06   26.7   0.3    6.7e-06   25.6   0.4    1.5  2  FAD_binding_3   FAD binding domain
    3.8e-05   23.8   0.8    0.00011   22.4   0.4    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0002   20.7   0.1    0.00056   19.2   0.1    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00033   19.9   0.4    0.00085   18.5   0.2    1.7  2  FAD_binding_2   FAD binding domain
    0.00045   19.0   0.1    0.00074   18.3   0.1    1.3  1  HI0933_like     HI0933-like protein
      0.001   18.5   0.2      0.023   14.1   0.1    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0054   17.3   2.8      0.015   15.9   0.3    3.1  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.013   15.1   0.3      0.036   13.7   0.1    1.9  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.031   14.6   0.1       0.53   10.6   0.0    2.5  2  LAGLIDADG_3     LAGLIDADG-like domain
      0.043   12.7   0.1      0.065   12.1   0.1    1.2  1  Trp_halogenase  Tryptophan halogenase
      0.059   12.4   2.1       0.31   10.1   0.3    2.3  3  GIDA            Glucose inhibited division protein A
        0.1   11.8   0.1       0.18   11.0   0.1    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.0     2e-51   2.7e-48       2     351 ..       7     360 ..       6     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 2e-51
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTTS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgidid 80 
                                   v++iGGG  Gl+tA++La rg  Vtl+e++ ++gsg+Sgr  gllhsg ry+       + ++e+++e   +++  +++  
  gi|70607751|ref|YP_256621.1|   7 VLVIGGGANGLFTALDLALRGidVTLVERR-DIGSGTSGRFHGLLHSGARYAVTDP---ESAKECIQENNIISKI-APH-A 81 
                                   99****************************.8899**************9777652...5677888888888887.775.5 PP

                                   EEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT CS
                           DAO  81 yrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaalaraaealG 160
                                    r tG l+l+ + e+le ldk l +l+++g++++++d ++v++ ep   ++l+ a+++pd  +v  + l+ ++a +   + 
  gi|70607751|ref|YP_256621.1|  82 IRDTGGLFLGITKEDLEFLDKFLSSLKKLGIEHKIVDNNQVLQEEPYvNKDLKIAIWVPD-KVVYGYDLLSSIAVTGSLNK 161
                                   899******988888***********99******************97669*********.******************** PP

                                   -EEEESECEEEEEEEE..TCEEEEE..EECT.EEEEEEEEEEE--GGGHHHH.HTT..CTTTSEEEEEEEEEEEEEECCTH CS
                           DAO 161 veilegtevtgleeed..gkvwgve..rttp.gendaadavVnaaGawsdll.gll..keldlpispvrgqvlvlkplsek 233
                                   ++i ++ evt++ +++  +k+++v+   t++ + +++ d ++n+ G+w+ ++  ++  +e  +pi p+ g + v+ ++ ++
  gi|70607751|ref|YP_256621.1| 162 ARIMTYNEVTEFIRDGnsIKGVKVFdkITNQmNLIKS-DIIINTSGPWAFKIiTMAglEE--IPILPTAGIMAVFGKKVNN 239
                                   ***********86766455555565975555555445.88********985557774444..5************554443 PP

                                   STGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGG..CGEEEEEEEEEE. CS
                           DAO 234 lvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPql..gdvlrkwaGlrp. 311
                                    v ++        + +++g +++p+  ++ ++G+ta+  +++d++++++ed+  l+++ ++l+P+l   +v r++a +rp 
  gi|70607751|ref|YP_256621.1| 240 AVLNR-------LRPPSDGDIIVPYQ-DTSILGTTATIIEDPDNFTISDEDVKMLIKEGSQLVPELskTRVIRTYASVRPl 312
                                   33333.......8999*********7.76999*****89999999********************7547799********7 PP

                                   E...TTS......SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                           DAO 312 l...pdg......lpligetpgvkglylatGhsghGltlapatGkllae 351
                                   +    dg      + ++++ ++ +g+  +  + g  +t++ ++G+ + +
  gi|70607751|ref|YP_256621.1| 313 MrtsEDGrkasrdFTILDH-EREDGVSGLISIIGGKFTTSRLVGEKVGD 360
                                   2334466788885555555.44666666666677799999999987765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.4   4.8e-09   6.7e-06       1      39 [.       4      42 ..       4      52 .. 0.87
   2 ?   -2.8   0.0         2   2.8e+03      52      66 ..     106     120 ..     102     207 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.8e-09
                                  EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                 FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                  +t+Vl++G+G  Gl +al L+ +G++v+lve+r+  + +
  gi|70607751|ref|YP_256621.1|  4 KTSVLVIGGGANGLFTALDLALRGIDVTLVERRDIGSGT 42
                                  689*****************************9866555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                                   HHHHTT-HHHHHHHS CS
                 FAD_binding_3  52 llrqlGledrilaeg 66 
                                   +l++lG+e++i ++ 
  gi|70607751|ref|YP_256621.1| 106 SLKKLGIEHKIVDNN 120
                                   455666666655544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.4   7.9e-08   0.00011       1      42 [.       9      48 ..       9      66 .. 0.81
   2 ?   -2.9   0.0       6.2   8.5e+03      31      41 ..     344     355 ..     342     373 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-08
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETT CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpg 42
                                  ++G+G+ Gl +A  La +g+dv+l+e+rd  +G  +s +++g
  gi|70607751|ref|YP_256621.1|  9 VIGGGANGLFTALDLALRGIDVTLVERRDIGSG--TSGRFHG 48
                                  8**************************976555..5555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.2
                                   SSGGG-EECE.T CS
                 NAD_binding_8  31 lGGraasyev.p 41 
                                   +GG+ ++ ++ +
  gi|70607751|ref|YP_256621.1| 344 IGGKFTTSRLvG 355
                                   899999888742 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     4e-07   0.00056       2      58 ..       6      77 ..       5     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4e-07
                                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH...........H CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                   Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias...........e 58
                                  +v+viGgG+ Gl +al+la  g++vtlve      gt   ++ ll++ ++ +  d+e a+            
  gi|70607751|ref|YP_256621.1|  6 SVLVIGGGANGLFTALDLALRGIDVTLVErrdiGSGTSGRFHGLLHSGARYAVTDPESAKeciqenniiskI 77
                                  79**************************87776445555556667777777777777777666665333330 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   6.2e-07   0.00085       2      36 ..       7      41 ..       6      64 .. 0.89
   2 ?   -1.7   0.0      0.83   1.1e+03     157     200 ..     163     206 ..     153     241 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.2e-07
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  v+ViG+G+ GL  Al +a +G +v++ve  +  +g
  gi|70607751|ref|YP_256621.1|  7 VLVIGGGANGLFTALDLALRGIDVTLVERRDIGSG 41
                                  9***************************8775444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.83
                                   EEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                 FAD_binding_2 157 dfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                   ++++  e++e+i++++ + G+ v ++ + +   i+++ ++ ++g
  gi|70607751|ref|YP_256621.1| 163 RIMTYNEVTEFIRDGNSIKGVKVFDKITNQMNLIKSDIIINTSG 206
                                   66777789999999999999999988666555555555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   5.3e-07   0.00074       2      32 ..       6      36 ..       5      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.3e-07
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                  +v+viGgGa Gl++A+ +a rg +V+l+e+ 
  gi|70607751|ref|YP_256621.1|  6 SVLVIGGGANGLFTALDLALRGIDVTLVERR 36
                                  699*************************986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   1.7e-05     0.023       2      33 ..       7      38 ..       6      72 .. 0.90
   2 ?    2.6   0.0     0.049        68     101     144 ..     161     206 ..     101     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergv 33
                                  v+V+GGg+ G+  A+  a +G  v Lve+r+ 
  gi|70607751|ref|YP_256621.1|  7 VLVIGGGANGLFTALDLALRGIDVTLVERRDI 38
                                  9****************************986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.049
                  FAD_oxidored 101 gvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                   + ++++  +++e +++g+ i++v+v +k  + +  i+++++i  +g
  gi|70607751|ref|YP_256621.1| 161 KARIMTYNEVTEFIRDGNSIKGVKVFDKItNqMNLIKSDIIINTSG 206
                                   678899999********9*********9976799999999998876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   1.1e-05     0.015       1      32 [.       6      37 ..       6      39 .. 0.96
   2 ?   -2.8   0.0         7   9.6e+03      17      33 ..     106     122 ..     101     133 .. 0.66
   3 ?   -2.3   0.0       4.9   6.7e+03      55      78 ..     162     185 ..     157     188 .. 0.79
   4 ?   -2.3   0.0       4.8   6.7e+03      21      46 ..     263     287 ..     261     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                  +v+v+GgG  gl  A  la  g +Vt+ver+d
  gi|70607751|ref|YP_256621.1|  6 SVLVIGGGANGLFTALDLALRGIDVTLVERRD 37
                                  699***************************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                                   HHHHTTSEEEEEESSSS CS
                     Pyr_redox  17 alaelgkkVtvversdk 33 
                                    l++lg + ++v+++  
  gi|70607751|ref|YP_256621.1| 106 SLKKLGIEHKIVDNNQV 122
                                   56777777777777654 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 4.9
                                   EEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox  55 ievllntkveeiegsedgvesvkl 78 
                                    ++++ ++v+e+  +++ +++vk+
  gi|70607751|ref|YP_256621.1| 162 ARIMTYNEVTEFIRDGNSIKGVKV 185
                                   578888999999988888888887 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.8
                                   TTSEEEEEESSSSSSTTSSHHHHHHH CS
                     Pyr_redox  21 lgkkVtvversdkllrllDeeaskil 46 
                                   lg   t++e  d++    De++  ++
  gi|70607751|ref|YP_256621.1| 263 LGTTATIIEDPDNFT-ISDEDVKMLI 287
                                   677789999999999.7777776555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.6e-05     0.036       1      31 [.       7      37 ..       7      86 .. 0.88
   2 ?   -3.4   0.0       4.7   6.5e+03      39      61 ..     366     388 ..     364     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                  ++++G Ga G + a  La  g dvtl+ r++
  gi|70607751|ref|YP_256621.1|  7 VLVIGGGANGLFTALDLALRGIDVTLVERRD 37
                                  68***************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                                   HCEEEEETTCEEEEEECEEECCH CS
                          ApbA  39 nGlrltseggeeilrppealsae 61 
                                    G+r +s+++e++l  p ++++e
  gi|70607751|ref|YP_256621.1| 366 LGVRAKSKTKETKLISPSEIDFE 388
                                   68899999999999999988887 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.53      27      57 ..      90     120 ..      80     146 .. 0.83
   2 ?    0.9   0.0      0.41   5.7e+02      38      83 .]     356     395 ..     348     395 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                   EEEEES-HHHHHHHHHHHHHCT.HSCEEEEE CS
                   LAGLIDADG_3  27 isltssskelledvqrlLlrlGIestiyekk 57 
                                   + +t  ++e+l+++   L++lGIe++i  ++
  gi|70607751|ref|YP_256621.1|  90 LGITKEDLEFLDKFLSSLKKLGIEHKIVDNN 120
                                   67999**********************9883 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                                   HHHHHHHH.HCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTTTX CS
                   LAGLIDADG_3  38 edvqrlLl.rlGIestiyekkkakgrgvyrlliisgenlkrFlekig 83 
                                   e+v  l + +lG+ ++ ++k  + +     l+  s+ +++++lekig
  gi|70607751|ref|YP_256621.1| 356 EKVGDLVSeKLGVRAKSKTK--ETK-----LISPSEIDFEKYLEKIG 395
                                   55555555566666666666..222.....34458889999999998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.7e-05     0.065       2      40 ..       7      42 ..       6      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                                  EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S CS
                Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvg 40
                                  ++++GGG  G  +A  la  +   ++vtlve  +ig   
  gi|70607751|ref|YP_256621.1|  7 VLVIGGGANGLFTALDLALRG---IDVTLVERRDIGSGT 42
                                  89************9998877...***********9755 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00022      0.31       2      29 ..       7      34 ..       6      59 .. 0.89
   2 ?    1.4   0.1     0.098   1.4e+02     116     156 ..     168     213 ..     154     231 .. 0.74
   3 ?   -2.8   0.0       1.9   2.6e+03      71     125 ..     236     290 ..     216     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                  EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLit 29
                                  v ViGgG  G+  Al +a +G++v+L+ 
  gi|70607751|ref|YP_256621.1|  7 VLVIGGGANGLFTALDLALRGIDVTLVE 34
                                  89************************93 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.098
                                   S-EEEEEECTTEEEEE.....EETTS-EEEECEEEE--TT-BT-EE CS
                          GIDA 116 eeveeliveekkvkgv.....vtedgetikakavviatGtflkgki 156
                                   +ev+e i + +++kgv     +t++ + ik+++++ ++G++    i
  gi|70607751|ref|YP_256621.1| 168 NEVTEFIRDGNSIKGVkvfdkITNQMNLIKSDIIINTSGPWAFKII 213
                                   67888888788888883333346677788999********654444 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.9
                                   EEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECT CS
                          GIDA  71 giqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveelivee 125
                                   +++  +lNr + p+ + + + ++   +  +    +e+ +n +i  e v+ li e 
  gi|70607751|ref|YP_256621.1| 236 KVNNAVLNRLRPPSDGDIIVPYQDTSILGTTATIIEDPDNFTISDEDVKMLIKEG 290
                                   4556778888888888887778888888888888999999999999998886644 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.18       1      33 [.       8      39 ..       4      43 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                  ++iG+G+ Gl +a+ l   g+ d++ +E+  ig
  gi|70607751|ref|YP_256621.1|  8 LVIGGGANGLFTALDLALRGI-DVTLVERRDIG 39
                                  578888888888888888888.68888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2945.37
//
Query:       gi|70607752|ref|YP_256622.1|  [L=497]
Description: glycerol kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-81  272.9   0.0    3.4e-81  272.4   0.0    1.2  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    1.8e-61  207.3   0.3    3.5e-61  206.4   0.2    1.5  2  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
     0.0052   16.3   0.1       0.59    9.6   0.0    2.2  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.4   0.0   5.8e-85   3.4e-81       1     245 []       5     248 ..       5     248 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.4 bits;  conditional E-value: 5.8e-85
                                   EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                        FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                   +++++D Gtts +aiv+d++ ++++ +q e+++++p++g++e++peeiwqa+  ai+k+le+a+i+ ++i  Igi++qre+
  gi|70607752|ref|YP_256622.1|   5 YVIAIDEGTTSARAIVFDKELNILGIGQNEFTQYYPQPGYVEHSPEEIWQAQLLAINKALEKAKIDRNNILSIGITNQRET 85 
                                   89******************************************************************************* PP

                                   EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC....EEEEHH CS
                        FGGY_N  82 lvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie....kfllid 157
                                   +v++D ++ kp+ynai+w+drrta+i + lk+ ++   ++ +tglv +++f++sk+kW+++n p+++ek+e    kf++id
  gi|70607752|ref|YP_256622.1|  86 TVMWDTRTgKPIYNAIVWQDRRTAPITDYLKA-NYLRLIKDRTGLVPDPYFSASKIKWILDNIPNAREKAEkgeiKFGTID 165
                                   *******************************9.8999******************************************** PP

                                   HHHHHHHCT..--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEE CS
                        FGGY_N 158 dyLiwrLtg..qfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpvvggg 236
                                   +yLiw+Lt+  ++vtd++nas++mlfni+klewd+e+l+il ipe++LP +++ssei+g+ ++       l+  +p++g +
  gi|70607752|ref|YP_256622.1| 166 TYLIWKLTNgkAHVTDYSNASRTMLFNIRKLEWDREILEILNIPEAILPDVKPSSEIYGYAEI-------LNSSIPISGDA 239
                                   ********999************************************************9654.......5779******* PP

                                   EHHHHHHHH CS
                        FGGY_N 237 gDqqaaalG 245
                                   gDqqaa++G
  gi|70607752|ref|YP_256622.1| 240 GDQQAALFG 248
                                   ********9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.2     7e+03      48      66 ..     137     155 ..     133     174 .. 0.68
   2 !  206.4   0.2   5.8e-65   3.5e-61       2     197 ..     258     445 ..     257     446 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                        FGGY_C  48 gslvawlldnl.glreeird 66 
                                    s ++w+ldn  ++re+  +
  gi|70607752|ref|YP_256622.1| 137 ASKIKWILDNIpNAREKA-E 155
                                   456799999974443333.3 PP

  == domain 2  score: 206.4 bits;  conditional E-value: 5.8e-65
                        FGGY_C   2 kvslGTssflll.vgtkpvisehglltpva.gedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaa 80 
                                   k+++GT+sf+ll +g++ v s + llt++a g  +  +yalegsi+++g++v+w++d l++   i+ ++e+ e+la     
  gi|70607752|ref|YP_256622.1| 258 KCTYGTGSFILLnTGSNLV-SSNDLLTTIAwGVGKGITYALEGSIFITGAAVQWFRDGLRA---IDVSDEI-EPLA----- 328
                                   8***********6666666.99999999996777788*********************888...******9.****..... PP

                        FGGY_C  81 eavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgsk 161
                                    +v+d+ggv+fvpaf+gl apywdp arg i+g++++tt+ahiarA+le+ a+q++++l  +++dsg+++d l vdGG+sk
  gi|70607752|ref|YP_256622.1| 329 GSVPDNGGVYFVPAFTGLGAPYWDPYARGLIIGITRGTTKAHIARAILESMAYQTMDVLGIMQRDSGIKIDALKVDGGASK 409
                                   ********************************************************************************* PP

                        FGGY_C 162 ndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                   ndllmq++Adil ++V+rpk  e+t +G+A+lA+++
  gi|70607752|ref|YP_256622.1| 410 NDLLMQFQADILKMKVVRPKIMETTSMGVAMLAGLS 445
                                   *********************************986 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   9.9e-05      0.59       3      61 ..       9      73 ..       7     159 .. 0.77
   2 !    4.7   0.1     0.003        18     190     252 ..     371     433 ..     363     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.9e-05
                                  EEE-SSEEEEEEEETTTEEEEEEEE--.......TTS-HHH.........HHHHHHHHHHT--GGG CS
                   BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns.......anlesvrfeaaekvleealtealerageeead 61
                                  iD G+T+ +a+++d++ ++lg g+           ++e +  e+ ++    a+++ale+a+ ++++
  gi|70607752|ref|YP_256622.1|  9 IDEGTTSARAIVFDKELNILGIGQNEFtqyypqpGYVE-HSPEEIWQAQLLAINKALEKAKIDRNN 73
                                  9********************99887733333322222.222333333334555555555555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.003
                                   -HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE-- CS
                   BcrAD_BadFG 190 kaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkinin 252
                                   +a++Il+ ++ + ++ +  +++ sg   d + + GG +kn  +++   + +k ++ + ki ++
  gi|70607752|ref|YP_256622.1| 371 IARAILESMAYQTMDVLGIMQRDSGIKIDALKVDGGASKNDLLMQFQADILKMKVVRPKIMET 433
                                   577888888888888888888999999999**********99999999999999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3407.34
//
Query:       gi|70607753|ref|YP_256623.1|  [L=293]
Description: glycerol uptake facilitator protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-39  135.3   6.9      4e-39  134.7   6.9    1.2  1  MIP       Major intrinsic protein


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   6.9   2.2e-43     4e-39       9     226 ..      11     275 ..       4     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 2.2e-43
                                   HHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSH CS
                           MIP   9 ravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisl 89 
                                    +++AEf++t++l+++g g+++  ++ v++ +   s ++  + +++g++++ ++y+++ iSGaH+NP vTla++v+++++ 
  gi|70607753|ref|YP_256623.1|  11 WRYFAEFVGTFILMLFGDGAVV--ASLVTNGT---SPGYGFIMISWGFGVVLAIYAVGPISGAHINPNVTLAFAVTKRMKW 86 
                                   4689***************666..55554533...45677788889999******************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHCHHH.........................................HHHTTTTSSSSS CS
                           MIP  90 lrailYivaQllGaivaaallklltkgl.........................................esraglfanslk 129
                                   + +i Yi  Q lGa +aa++l ++  +                                           s ++lf+  ++
  gi|70607753|ref|YP_256623.1|  87 RDVIPYILFQTLGAAAAAGILLAWWGSIitkmdppptlyaqvgasffteypnpsfwgqywpkelllpnsASGTSLFS-EVN 166
                                   *************************9999*************************************98666666666.889 PP

                                   TTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHH.HHHHHHHHHST-SSHHHHHHHHHHHTH.... CS
                           MIP 130 pglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllval.iilvgipltGaamNpArslgpavvlnk.... 205
                                   +    + + ++E+++tf+L+l+v+a+td    + + +lap aig+ +++   l+ ++ltG  +N Ars gp ++l+     
  gi|70607753|ref|YP_256623.1| 167 QVFPLWIGAFAELLMTFLLLLIVLAVTDTDSPFFNQSLAPWAIGIGYVMpFLLFEAQLTGGMINEARSWGPMLALYLfgyr 247
                                   99999****************************999*********887725678999************************ PP

                                   .......STTTTHHHHHHHHHHHHHHHH CS
                           MIP 206 .......fedhwvylvGPliGailgalv 226
                                           ++++vy +  +iG+ilgal 
  gi|70607753|ref|YP_256623.1| 248 tgafnfrGQYFFVYGIPDFIGGILGALF 275
                                   ***9987789****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2096.36
//
Query:       gi|70607754|ref|YP_256624.1|  [L=347]
Description: hypothetical protein Saci_2035 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-93  311.0   0.0    9.9e-93  310.7   0.0    1.0  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.7   0.0   5.5e-97   9.9e-93       2     335 ..       8     332 ..       7     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.7 bits;  conditional E-value: 5.5e-97
                                   GHHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH....HHHHHH CS
                        DUF917   2 dlealatGaavLGtGGGGspysgylllrqaleegksvrvvsldelpddalvvvvgamGsptvieeklpsgdelleaveale 82 
                                   d+ +la+G++vLG+GGGG+p+ gy  l+  ++e ++ +++  +e++d+++++ vg mGsp v++ek+p+g+e+ +a+e l+
  gi|70607754|ref|YP_256624.1|   8 DIYHLAIGSSVLGSGGGGNPFLGYEILKTKMKELNKDELYYEQEIADNDFIIGVGGMGSPLVGIEKIPAGTEYFKAYECLS 88 
                                   899*****************************88779******************************************** PP

                                   HHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EEEEEE.---H CS
                        DUF917  83 kllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvvllkkaqsdk 163
                                   k+l+r+++ + s+EiGG+N++v+++a+   + p+vD+D+ GRAfPel++tt ++ gi++tP++++de+gn+v+l++  ++ 
  gi|70607754|ref|YP_256624.1|  89 KFLKREASRITSIEIGGINSVVPFIASLFANKPLVDGDLEGRAFPELYMTTSHFIGINATPMCIVDERGNQVILDS-VDNY 168
                                   ****************************************************************************.6666 PP

                                   HHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--..-SHHHHHHHHHH-EEEEEEEEE---- CS
                        DUF917 164 avErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaeareakdvveailealgggakvlfkGkivdve 244
                                    +E+++R+++v++g+++++a ypm+g+   ++a+ g++sl++ iG+ +++       ++++l++++g + +lf+Gk++dv+
  gi|70607754|ref|YP_256624.1| 169 YAEKIARSITVRFGGRGYIAIYPMNGESYIKSAILGSISLSIDIGKILNNEG-----LDSMLDYVKG-R-ILFHGKVIDVR 242
                                   9************************************************988.....79*******5.5.5*********9 PP

                                   ----------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB-TTTT.TS-EEEEEE---G CS
                        DUF917 245 rrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigteelryGlrVtVlalpase 325
                                   r+   gf+   vti+gl+e+++  +k+ ++NE+ll+e++++++ ++P++I ++d   ++ i+++ ++yG rV V+++p s+
  gi|70607754|ref|YP_256624.1| 243 RTNLPGFNSAIVTIQGLEEYKDYIAKLYVKNEYLLFEVNNNIVSIAPNIINLVD-YRNKIITSDMIKYGIRVRVIGIPVSP 322
                                   9999*************************************************8.5579********************** PP

                                   GGS..SHHHH CS
                        DUF917 326 kwrteeglel 335
                                   kwr+  g e+
  gi|70607754|ref|YP_256624.1| 323 KWREIGGEEI 332
                                   ***8766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2414.46
//
Query:       gi|70607755|ref|YP_256625.1|  [L=514]
Description: hydantoinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-36  125.0   2.7    6.8e-36  123.6   0.1    2.7  4  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.5e-25   90.1   5.6    1.4e-20   73.8   0.1    4.1  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    2.7e-06   26.3   1.0     0.0084   14.7   0.2    2.5  2  MutL            MutL protein
    6.3e-06   25.9   0.6    0.00078   19.0   0.3    2.4  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    4.4e-05   23.9   6.0      0.088   13.2   0.1    3.6  3  FtsA            Cell division protein FtsA
     0.0027   17.2   0.2     0.0027   17.2   0.2    2.3  3  ROK             ROK family


Domain annotation for each model (and alignments):
>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.6   0.1   2.3e-39   6.8e-36       1     177 [.       4     171 ..       4     172 .. 0.97
   2 ?   -0.0   0.0      0.21   6.3e+02       2      14 ..     270     282 ..     269     293 .. 0.82
   3 ?   -2.0   0.0      0.83   2.5e+03     114     152 ..     350     388 ..     345     390 .. 0.85
   4 ?   -3.8   0.0       2.9   8.7e+03     137     152 ..     462     477 ..     445     482 .. 0.56

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 2.3e-39
                    Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg..... 76 
                                   +ig+D+G+T+TDaval++  + + ++K+ +t  + +eg+++a+ ev+++ ++r+++i+++++GTT+ +Na+ + k+     
  gi|70607755|ref|YP_256625.1|   4 KIGVDIGSTHTDAVALEGR-NLIYATKVETT-PDLTEGLLNAITEVIKNLGERKNEIKALMIGTTHGLNAIHQAKRlnrva 82 
                                   69***************88.99*********.99*********************************************** PP

                    Hydant_A_N  77 .ervaLittkgfrdlleigrqnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavv 156
                                     r++L+  +g++ l+e+ +  r+ +            ++v+ v++++e++ge++ plde+++ +++++++ + v+s+a++
  gi|70607755|ref|YP_256625.1|  83 vIRIGLPAGEGVPPLMEWPEGLRSFV------------TSVHLVRGGHEYTGEEILPLDENKIYQIASEINGK-VDSVAIT 150
                                   *********************99999............7899******************************9.******* PP

                    Hydant_A_N 157 llhSylnpehElrvaeiarei 177
                                   +++S +npehE rv++i+ ++
  gi|70607755|ref|YP_256625.1| 151 SIFSIVNPEHENRVKDILLKE 171
                                   *****************9886 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                    Hydant_A_N   2 igIDvGGTfTDav 14 
                                   i  D+GGT T + 
  gi|70607755|ref|YP_256625.1| 270 IVMDIGGTTTNVG 282
                                   789******9875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.83
                    Hydant_A_N 114 eevvevderveadgevlkpldeeevrealkalkaagves 152
                                   ++v  v ++++++g+  + ++++ +   lk+++++ ves
  gi|70607755|ref|YP_256625.1| 350 TDVSMVVKGIKIEGSNPELVRNKYLDGYLKKIYNKMVES 388
                                   567778889999999999999999999999999999887 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 2.9
                    Hydant_A_N 137 evrealkalkaagves 152
                                   ++++ ++++k++ +++
  gi|70607755|ref|YP_256625.1| 462 AIKSLIEEAKKTAISA 477
                                   4455555555555555 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.4     0.001         3      82     252 ..       5     187 ..       3     189 .. 0.61
   2 !   73.8   0.1   4.6e-24   1.4e-20       1     175 [.     191     359 ..     191     366 .. 0.89
   3 !    8.1   0.0   0.00047       1.4     215     287 ..     379     444 ..     370     448 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.001
                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei...................agvkvrlpaldirtvgagGgsilvvdeggklrvg 143
                                   I++D+G+T tD+ +++  +   +++ e+                   ++ k +++al+i t     g+ ++++ ++  rv 
  gi|70607755|ref|YP_256625.1|   5 IGVDIGSTHTDAVALEGRNLIYATKVETtpdltegllnaiteviknlGERKNEIKALMIGT---THGLNAIHQAKRLNRVA 82 
                                   7788888888888888444443444444677777777777777755444444444444443...33333333333333332 PP

                Hydantoinase_A 144 ....pesagadpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevA.egils 219
                                       + +ag  + p+     g +  vT  +lv G   +e ++   ++  +ld+    +++ ++a e+n kv+ vA   i s
  gi|70607755|ref|YP_256625.1|  83 viriGLPAGEGVPPLMEWPEGLRSFVTSVHLVRGG--HE-YT--GEEILPLDE----NKIYQIASEINGKVDSVAiTSIFS 154
                                   11112356666666555555557777777777763..33.55..234455555....456678888999999999446889 PP

                Hydantoinase_A 220 vavenmanavrklsvergldpkeltlvvfGGaG 252
                                   +++ +  n v++++ + g  +  +    +GG G
  gi|70607755|ref|YP_256625.1| 155 IVNPEHENRVKDILLKEGISVPITLSHQIGGIG 187
                                   999999999999999999888887777777766 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 4.6e-24
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgak.arlmvmqsdGglvsadearkkpvetilSGPaa.Gvvgaaatsklagek 79 
                                   r +++++n+ + +i+++ ++ +++ l+k g +  +l++ q dG ++sa+ ++k p+ t+ +GP + ++ ga     l+g +
  gi|70607755|ref|YP_256625.1| 191 RENATILNSLILNIFNNLIQILQSLLHKLGLEnVELYFAQNDGTIASAQFIKKFPIFTV-AGPVSnSIRGAHL---LTGIT 267
                                   7899************************998769***************9999988776.5666537888888...99999 PP

                Hydantoinase_A  80 kvItfDmGGTstDvslikdgevevs.leteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacyrkG 159
                                   ++I++D+GGT+t v ++ +g ++ s +  eiag+++++++ di t+++gGg+i+ + e    ++gpes+g        + G
  gi|70607755|ref|YP_256625.1| 268 DAIVMDIGGTTTNVGVLYKGYPRESaSPVEIAGIRTNFRMPDIYTLALGGGTII-RGE----EIGPESVGFMLTKRGLSWG 343
                                   ******************9998654144688***********************.555....8********9999999*** PP

                Hydantoinase_A 160 gteltvTDanlvLGrl 175
                                   g++ t+TD ++v+  +
  gi|70607755|ref|YP_256625.1| 344 GDTFTTTDVSMVVKGI 359
                                   *********9997655 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00047
                Hydantoinase_A 215 egilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdv 287
                                   ++i++++ve   na++ +     +  ke ++v+  G+G ++ +++    g +k ++p+ a+ ++a+G++l +v
  gi|70607755|ref|YP_256625.1| 379 KKIYNKMVESWENAIDIM-----KTSKEDVIVIGVGGGSIMLPEI--LKGSSKLVIPKNAQYANAIGCTLTKV 444
                                   578899999999999999.....5555555666666677777777..4689999999999*********9987 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   2.8e-06    0.0084       4      58 ..       7      54 ..       5      75 .. 0.82
   2 !    9.5   0.0   0.00011      0.33     245     273 ..     265     293 ..     242     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.8e-06
                          MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklgkt 58
                                  +DiGSt T +++++ +    +l++ ++  Tt    d++eGl +a++e+ ++lg+ 
  gi|70607755|ref|YP_256625.1|  7 VDIGSTHTDAVALEGR----NLIYATKVETTP---DLTEGLLNAITEVIKNLGER 54
                                  8**************5....599999999998...79999999999988887755 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00011
                          MutL 245 glgdllvvDvGGaTTdvhsvaegspekek 273
                                   g+ d++v+D+GG+TT+v    +g p+++ 
  gi|70607755|ref|YP_256625.1| 265 GITDAIVMDIGGTTTNVGVLYKGYPRESA 293
                                   5789*************999999888765 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.3   2.6e-07   0.00078       1      76 [.       5      71 ..       5      84 .. 0.79
   2 !    4.7   0.0    0.0062        19      42     117 ..     206     281 ..     175     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                                  EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCC CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGrat 76
                                  +G+D+GsT t av ++ +  + ++ + ++  l+ ++       l +a+te+++++ge +++i+ + + gt  G++ 
  gi|70607755|ref|YP_256625.1|  5 IGVDIGSTHTDAVALEGRNLIYATKVETTPDLT-EG-------LLNAITEVIKNLGERKNEIKAL-MIGTTHGLNA 71
                                  7***************99996666665555555.34.......569*****************88.5555566655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0062
                                   ....HHHHHHHHHHT--GGGECEE..EEESTTCCCTCTTBSEEE-..HHHHHHHHHHHH-TT--.EEEEEETTEEEE CS
                   BcrAD_BadFG  42 kvleealtealerageeeadieetylvgtgyGratlpekfekeiirseilvhgdGavalypgtr.tvldigGqdskg 117
                                   ++l ++l+ +l ++g+e+ ++      gt+ + ++++ kf+  ++   ++   +Ga++l + t   v+digG+ + +
  gi|70607755|ref|YP_256625.1| 206 NNLIQILQSLLHKLGLENVELYFAQNDGTIASAQFIK-KFPIFTVAGPVSNSIRGAHLLTGITDaIVMDIGGTTTNV 281
                                   5777788888888888888888887788888888888.7887777778888999*********98899****98866 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   2.9e-05     0.088       1      52 [.       5      59 ..       5     238 .. 0.76
   2 !   10.8   0.1   0.00016      0.49       1      28 [.     270     301 ..     270     438 .. 0.87
   3 ?    1.4   0.3      0.15   4.4e+02      39      62 ..     461     484 ..     421     511 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                  EEEEE-SSSEEEEEEETTEEEE...EEEES--HHHHHHHHHHHHT--HHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  1 alvDiGagktdvavaedgalvh...lrvigvggngitkdiakalrtaveeAerik 52
                                  ++vDiG+++td++ +e+ +l++   +++ +   +g+ + i +++++  e   +ik
  gi|70607755|ref|YP_256625.1|  5 IGVDIGSTHTDAVALEGRNLIYatkVETTPDLTEGLLNAITEVIKNLGERKNEIK 59
                                  58*****************999533333333555555555555554444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                                   EEEEE-SSSEEEEEEETTEEEE....EEEES- CS
                                   xxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                          FtsA   1 alvDiGagktdvavaedgalvh....lrvigv 28 
                                   ++ DiG+++t+v v+ +g ++     +++ g+
  gi|70607755|ref|YP_256625.1| 270 IVMDIGGTTTNVGVLYKGYPREsaspVEIAGI 301
                                   589***************99986666444444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.15
                                   HHHT--HHHHHHHHHHH--S--EE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          FtsA  39 kalrtaveeAerikikyGsalaek 62 
                                   +a++  +eeA++ +i+ G+   + 
  gi|70607755|ref|YP_256625.1| 461 IAIKSLIEEAKKTAISAGAIETSI 484
                                   5699999*******9998877633 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     9e-07    0.0027       2      65 ..       5      66 ..       4      79 .. 0.89
   2 ?   -2.2   0.0      0.78   2.3e+03      51     143 ..     397     417 ..     377     436 .. 0.52
   3 ?   -2.4   0.1      0.89   2.6e+03     187     212 ..     453     478 ..     443     485 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9e-07
                                  EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEES CS
                           ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigsp 65
                                  ig+diG t++ +  ++  ++  +  kv ++t+++ e+l +ai e+++++ ++ +e+ a+ ig +
  gi|70607755|ref|YP_256625.1|  5 IGVDIGSTHTDAVALE-GRNLIYATKV-ETTPDLTEGLLNAITEVIKNLGERKNEIKALMIGTT 66
                                  8*********988887.7888888899.78999999999******************9999976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.78
                                   HCCHTEEEEEEEEESSEEETTCCEBSSGGCGCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEES CS
                           ROK  51 erkadeliavgigspGlisdksgkivstpnitwenfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvg 131
                                   + + +++i +g                                                                      
  gi|70607755|ref|YP_256625.1| 397 KTSKEDVIVIG---------------------------------------------------------------------- 407
                                   33333344444...................................................................... PP

                                   SSEEEEEEETTE CS
                           ROK 132 tGvGaGviingk 143
                                     vG+G i+  +
  gi|70607755|ref|YP_256625.1| 408 --VGGGSIMLPE 417
                                   ..4444444333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.89
                                   CHTCCGTTS-HHHHHHHHCTT-HHHH CS
                           ROK 187 raqqkgekleakeiiklaekgdevae 212
                                   +++q+ +++ +k++i+ a+k   +a 
  gi|70607755|ref|YP_256625.1| 453 SYEQTNRDIAIKSLIEEAKKTAISAG 478
                                   47889999999999999999877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3338.57
//
Query:       gi|70607756|ref|YP_256626.1|  [L=358]
Description: hypothetical protein Saci_2037 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.1e-115  383.8   0.1   6.9e-115  383.6   0.1    1.0  1  DUF917    Protein of unknown function (DUF917)


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.6   0.1  3.8e-119  6.9e-115       2     350 .]      10     349 ..       9     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 383.6 bits;  conditional E-value: 3.8e-119
                                   GHHHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH....HHHHHH CS
                        DUF917   2 dlealatGaavLGtGGGGspysgylllrqaleegksvrvvsldelpddalvvvvgamGsptvieeklpsgdelleaveale 82 
                                   d+++l+tGaa+LGtGGGG+py+g l+l++a+e++  v+v++  + ++   vv  ++mG+p v++ek+psgde+ +a++ ++
  gi|70607756|ref|YP_256626.1|  10 DVNNLVTGAAFLGTGGGGDPYIGGLMLKRAIERRGPVEVIRNAKSNNA-QVVGSAMMGAPIVMIEKIPSGDEANKALKIYS 89 
                                   899*****************************8845****99887775.5999**************************** PP

                                   HHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EEEEEE.---H CS
                        DUF917  83 kllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvvllkkaqsdk 163
                                   +++grk++++ +lEiGG+N++++l++a+ lglpv+D+DgmGRAfPelq+ttf+++g++++P+++ de+gnv +++   + +
  gi|70607756|ref|YP_256626.1|  90 EITGRKVEYITPLEIGGVNSTIPLIVASALGLPVLDGDGMGRAFPELQMTTFYFYGVDPSPVIVLDERGNVSVVEG-IDGV 169
                                   ****************************************************************************.8888 PP

                                   HHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--..-SHHHHHHHHHH-EEEEEEEEE---- CS
                        DUF917 164 avErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaeareakdvveailealgggakvlfkGkivdve 244
                                   ++E+++R ++ ++g++a+++ y +t +  +++av  tlslal+iG+ +++ +     ++++l++l+  ak+lfkGk++dv 
  gi|70607756|ref|YP_256626.1| 170 WAEKIARVITLRYGGAAYISLYGTTLNMYNKTAVLDTLSLALHIGELLNQIK-----FNEVLDYLK--AKILFKGKVIDVI 243
                                   ****************************************************.....789******..477********** PP

                                   ----------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB-TTTT.TS-EEEEEE---G CS
                        DUF917 245 rrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigteelryGlrVtVlalpase 325
                                   rr+e+gf++g v+ieg++e+++++lki fqNE+l+a  +++vl++vPDlI+vld  t +pi+t++++yG++V ++++pa+e
  gi|70607756|ref|YP_256626.1| 244 RRIEKGFSRGFVVIEGMEEYSNKSLKIDFQNEFLIATLEDNVLVSVPDLITVLDMFTFKPITTDRIKYGQKVLIIGIPAHE 324
                                   ********************************************************************************* PP

                                   GGS..SHHHH-S-....-....--- CS
                        DUF917 326 kwrteeglelvgPkaFGydleykpl 350
                                   ++rt+e+l+++gP+ FGy+++y+p+
  gi|70607756|ref|YP_256626.1| 325 RLRTKEALKYIGPRVFGYNIDYEPI 349
                                   ***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2404.98
//
Query:       gi|70607757|ref|YP_256627.1|  [L=129]
Description: hypothetical protein Saci_2038 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.1    7.9   4.6        3.4    7.7   0.3    2.2  2  Vma12     Endoplasmic reticulum-based factor for assembly of 


Domain annotation for each model (and alignments):
>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.5     0.013   2.3e+02      78      89 ..      10      21 ..       3      28 .. 0.83
   2 ?    7.7   0.3   0.00019       3.4      78     123 ..      33      79 ..      25      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.013
                         Vma12 78 ilvlNiliSvva 89
                                   lv+N+liS++ 
  gi|70607757|ref|YP_256627.1| 10 YLVVNFLISIAY 21
                                  58*******985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00019
                         Vma12  78 ilvlNiliSvvavffavwialrsartpslpvrvllslvva.llVgvA 123
                                   + + N+   v++ f ++w a+r++r+++ + r   ++ ++ l+V +A
  gi|70607757|ref|YP_256627.1|  33 VKIYNLTYGVLILFLCIWDAIRYLRNNNIEDRTRAGVQFSwLIVSFA 79 
                                   568999********************988887777776662444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 894.56
//
Query:       gi|70607758|ref|YP_256628.1|  [L=455]
Description: pyrimidine transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-19   67.6  46.7    1.2e-18   67.1  46.7    1.1  1  Transp_cyt_pur  Permease for cytosine/purines, uracil, thiami


Domain annotation for each model (and alignments):
>> Transp_cyt_pur  Permease for cytosine/purines, uracil, thiamine, allantoin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1  46.7   6.7e-23   1.2e-18      12     435 ..      30     426 ..      20     431 .. 0.75

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 6.7e-23
                Transp_cyt_pur  12 lnlfsiWlganlnin.twvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpilsRasfGir.gsllpl 90 
                                   +n+f ++ +    i+  w+ galg  +gL + q++++++ g+++++i+  l++ +Ga  Gl++ +l R+  G + g++ ++
  gi|70607758|ref|YP_256628.1|  30 YNMFLVFASVYGAIAvIWAGGALG--YGLTFSQAIIAVLGGTIVLTILGGLAASIGAYSGLSTYVLWRFPLGRWgGKIAGF 108
                                   566655555555554146666666..**********************************************661567777 PP

                Transp_cyt_pur  91 llrv.viaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifw..vvslvivllgvskirkffviaal 168
                                   ll+   + i+w++v +w+      ++ ++if+           +  ++ v+f++ w  ++++v  + g + +  ++ ++++
  gi|70607758|ref|YP_256628.1| 109 LLITvTTGIGWYAVETWLF----GIVMNEIFP-----------NNPFFSVGFAAIWggIIMIVMTYIGYKMLSFLSYFTIP 174
                                   77763567*********85....588899999...........33344555555444466666666666655555555555 PP

                Transp_cyt_pur 169 l.vpvaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryaktkkssvkiqlvavpllftl 248
                                   + + ++a+g++i ++ k + ++v+++a  ++   ++l ++ + ++ +++  +  pD +r++kt+k ++   +  + +l+  
  gi|70607758|ref|YP_256628.1| 175 FhIWLIAIGIAIVIALKGGFSAVMSAAPTSHM--SLLDGISATVGLYSAGTIISPDIARFGKTAKDASVAWVAHIIFLYPF 253
                                   42456669999999999999*****7766663..79*****************************9998777777777777 PP

                Transp_cyt_pur 249 llligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsagldlaallPkkinikrgsliaa 329
                                   l+l g++++ ++ +   +na+  l        +  ++ +l+++ + q  +n + nl+s  l l +l P  + +  +s+i+ 
  gi|70607758|ref|YP_256628.1| 254 LILGGVAMVLVTGTYLVTNAMLEL-------GM--GAGVLLIIVFGQFIIN-TDNLYSGSLSLVNLYP--MRRELASVING 322
                                   777777777777777777776666.......33..3333445556666655.66899***********..*********** PP

                Transp_cyt_pur 330 vialvivpwkllsssskl..ftaflsllavflspvagviiadyfvvrrgylklaalytrr...rgsaYwyrkgvNwravaa 405
                                   vi+++++      + s++  f +f+++l+ +l pv g++iad+f+vr +   +++   r    +g aY+     N + v+a
  gi|70607758|ref|YP_256628.1| 323 VIGTAVAAYVGFTAGSSItpFENFITVLGNILPPVGGIVIADFFIVRSYLKGVKDPHERYkfkPGNAYY---NLNIAGVVA 400
                                   ****9876655555555459***************************9998888766644222555565...999999*** PP

                Transp_cyt_pur 406 yivGiaaglvgvagsvgikvvkgaeklfdl 435
                                     +G+++g++ +    + +++ +a   + l
  gi|70607758|ref|YP_256628.1| 401 LGLGALVGFIVP----YGIPAINALITGFL 426
                                   999999999983....44555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3016.68
//
Query:       gi|70607759|ref|YP_256629.1|  [L=159]
Description: transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-11   44.1   0.8    2.7e-11   43.1   0.8    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.6e-08   32.2   4.3    5.6e-08   32.2   4.3    2.0  3  HTH_24          Winged helix-turn-helix DNA-binding
     0.0018   18.2   0.1     0.0039   17.1   0.1    1.6  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0065   16.4   0.4      0.016   15.1   0.4    1.8  1  HTH_11          HTH domain
     0.0075   16.1   0.5      0.018   14.9   0.5    1.6  1  TFIIE_alpha     TFIIE alpha subunit
  ------ inclusion threshold ------
      0.023   14.4   0.1      0.048   13.4   0.1    1.5  1  HTH_38          Helix-turn-helix domain
      0.081   12.6   0.0       0.28   10.8   0.0    2.0  2  HTH_50          Helix-turn-helix domain
      0.089   13.4   0.4       0.43   11.2   0.1    2.1  3  Mga             Mga helix-turn-helix domain
      0.089   12.7   0.5       0.67    9.9   0.1    2.5  3  MarR            MarR family


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.8   1.4e-14   2.7e-11       1      42 []      13      54 ..      13      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.4e-14
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                  LDe D+kIL++L  +a +s a++A+++GlS +t++ R  rLe
  gi|70607759|ref|YP_256629.1| 13 LDEKDIKILKILNNNANTSDAKIAREIGLSKTTIRMRRLRLE 54
                                  8************************************99987 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   4.3   2.8e-11   5.6e-08       1      47 [.      13      59 ..      13      60 .. 0.96
   2 ?   -2.3   0.0       1.7   3.3e+03      36      47 ..      90     101 ..      89     101 .. 0.84
   3 ?   -3.5   0.0       4.1   8.1e+03       7      15 ..     128     136 ..     125     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.8e-11
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                  lde+d+kIL++L  n+++s + +A+++glS++t++ r  rLe++ ++
  gi|70607759|ref|YP_256629.1| 13 LDEKDIKILKILNNNANTSDAKIAREIGLSKTTIRMRRLRLENKKIL 59
                                  79****************************************99876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                        HTH_24  36 rrlkrLeeeGlI 47 
                                   +++k L +++lI
  gi|70607759|ref|YP_256629.1|  90 TYIKSLLSNELI 101
                                   689999999987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.1
                        HTH_24   7 kILelLqkn 15 
                                   +IL ++  +
  gi|70607759|ref|YP_256629.1| 128 EILTIINHD 136
                                   788888766 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     2e-06    0.0039       1      74 [.      77     148 ..      77     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                   vlv+l+ + +e  ++ ++ l   + + e+    G++d+l++v   d  +l + + + + +++ v +++ +++++
  gi|70607759|ref|YP_256629.1|  77 VLVKLK-NVKELRQTYIKSLLSNELIYEISEYVGEWDLLVRVFHSDPVQLKEEILT-IINHDAVMDYKINFAIR 148
                                   567777.455788888999999999999****************************.99**********99986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   8.3e-06     0.016       4      33 ..      19      47 ..      16      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvr 33
                                  +il++L +++ + s +++A+e+++S++t+r
  gi|70607759|ref|YP_256629.1| 19 KILKIL-NNNANTSDAKIAREIGLSKTTIR 47
                                  8*****.777779****************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   8.9e-06     0.018       6      58 ..       8      60 ..       5      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.9e-06
                                  HHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha  6 vvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                  ++ k  +e+ +++l++L  ++++++  +a+e+++ ++ +r    rL ++++ k
  gi|70607759|ref|YP_256629.1|  8 ILSKYLDEKDIKILKILNNNANTSDAKIAREIGLSKTTIRMRRLRLENKKILK 60
                                  67788899********************************9888888888766 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.4e-05     0.048       4      37 ..      12      46 ..      10      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                        HTH_38  4 hLsleeReeIerll.aeGlslreIArrLgrspsTI 37
                                  +L   +   + +l  +++ s ++IAr++g s++TI
  gi|70607759|ref|YP_256629.1| 12 YLDEKDIKILKILNnNANTSDAKIAREIGLSKTTI 46
                                  5666666556666325788889************* PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.28      24      45 ..      30      52 ..       6      53 .. 0.75
   2 ?   -2.8   0.0       2.5   4.9e+03      32      45 ..      69      82 ..      68      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                        HTH_50 24 pStRklAkrLGvShtai.anklr 45
                                  +S  k+A+  G+S+t+i +++lr
  gi|70607759|ref|YP_256629.1| 30 TSDAKIAREIGLSKTTIrMRRLR 52
                                  67789************777776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                        HTH_50 32 rLGvShtaianklr 45
                                   LGv  + ++ kl+
  gi|70607759|ref|YP_256629.1| 69 NLGVPYADVLVKLK 82
                                  79999999999987 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.43       4      49 ..       4      48 ..       2      66 .. 0.81
   2 ?   -0.7   0.0       1.1   2.3e+03      38      61 ..      68      91 ..      61     107 .. 0.70
   3 ?   -1.2   0.0       1.6   3.3e+03      55      55 ..     105     105 ..      82     134 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                  XTHHHHHHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHH CS
                           Mga  4 sleellqellkeslkyqllkflfeeeevsieelaqelyiSestlkr 49
                                  ++e++l+++l e  ++++lk l +++++s +++a+e  +S++t+  
  gi|70607759|ref|YP_256629.1|  4 KWEDILSKYLDE-KDIKILKILNNNANTSDAKIAREIGLSKTTIRM 48
                                  567788887765.689***************************864 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                                  HHCT--HHHHHHHHHHHHHHCHCC CS
                           Mga 38 qelyiSestlkrkikelnklLkef 61
                                  q+l + ++ +  k+k++++l +++
  gi|70607759|ref|YP_256629.1| 68 QNLGVPYADVLVKLKNVKELRQTY 91
                                  667777777777777777764444 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.6
                                   H CS
                           Mga  55 n 55 
                                    
  gi|70607759|ref|YP_256629.1| 105 S 105
                                   2 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00034      0.67       5      34 ..      17      46 ..      13      59 .. 0.89
   2 ?   -1.1   0.0      0.95   1.9e+03       8      26 ..      77      95 ..      75     102 .. 0.64
   3 ?   -0.8   0.0      0.76   1.5e+03       5      21 ..     110     126 ..     108     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                                  HHHHHHHHHHSTTEEHHHHHHHHTS-HHHH CS
                          MarR  5 qfviLrilyeqgplsvseLakklgvskstv 34
                                   ++iL il ++ + s +++a+ +g+sk+t+
  gi|70607759|ref|YP_256629.1| 17 DIKILKILNNNANTSDAKIAREIGLSKTTI 46
                                  689*************************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.95
                                  HHHHHHHSTTEEHHHHHHH CS
                          MarR  8 iLrilyeqgplsvseLakk 26
                                  +L++l++  +l+++ + + 
  gi|70607759|ref|YP_256629.1| 77 VLVKLKNVKELRQTYIKSL 95
                                  6777777777777655544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.76
                                   HHHHHHHHHHSTTEEHH CS
                          MarR   5 qfviLrilyeqgplsvs 21 
                                   ++++L+ + +++p  ++
  gi|70607759|ref|YP_256629.1| 110 EWDLLVRVFHSDPVQLK 126
                                   89999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 1070.64
//
Query:       gi|70607760|ref|YP_256630.1|  [L=680]
Description: hydantoin utilization protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-94  316.8   0.0    4.8e-94  314.9   0.0    1.9  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    7.4e-51  172.4   0.4    2.8e-50  170.5   0.3    2.0  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
      0.025   14.1   0.0       0.33   10.4   0.0    2.3  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.14   8.5e+02      82     104 ..       4      26 ..       3      42 .. 0.79
   2 !  314.9   0.0     8e-98   4.8e-94       1     290 [.     199     492 ..     199     493 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.14
                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevs 104
                                   I++D+GG  tD+  +++ + e++
  gi|70607760|ref|YP_256630.1|   4 IGIDIGGAFTDLVYYDQSNDEFE 26 
                                   899***********998776654 PP

  == domain 2  score: 314.9 bits;  conditional E-value: 8e-98
                Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkv 81 
                                   rt+t+v+nAy++p++++yl++++k+++krg+k +++ m s+Gg++++d     p+ t++SGP aG++ga a+++la ek++
  gi|70607760|ref|YP_256630.1| 199 RTNTVVLNAYIKPKMNNYLRKLKKEIDKRGFKGKYYAMLSNGGMATFDFTMDFPITTLESGPVAGIIGAIAIGELAHEKNI 279
                                   89******************************************************************************* PP

                Hydantoinase_A  82 ItfDmGGTstDvslikdgevevsletei......agvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgpacy 156
                                   I++D G+T+t++sl+++  +++ +++ i       g++v++p++di +vg gG+si++ de ++l+vgp++ag+ pgpa+y
  gi|70607760|ref|YP_256630.1| 280 IGLDGGSTTTKASLVENLMPNIITDYYIernpysPGYPVKVPTIDIVEVGNGGTSIAWIDEIDNLKVGPRAAGSYPGPAAY 360
                                   ********************************************************************************* PP

                Hydantoinase_A 157 rkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrklsverg 237
                                   ++G te+tvTDa+++ G l+p+++l   +g+ k++++la++a++ +a++++ +v+e+Aegi+++a++n +n++r +sv+rg
  gi|70607760|ref|YP_256630.1| 361 GRGATEPTVTDAYILSGLLNPNELL---GGKLKVRRDLAEKAIKRIADHYKISVDEAAEGIVRLANNNAVNVIRLVSVQRG 438
                                   *************************...***************************************************** PP

                Hydantoinase_A 238 ldpkeltlvvfGGaGaqhaaalaeelgvkkvivppya.gvlsalGmalAdvree 290
                                   +dp++++l+++GG+G+++a+ +aeel++kkvivp  + gv+sa+Gm++Ad+r++
  gi|70607760|ref|YP_256630.1| 439 YDPRDFVLIAYGGSGPMFAPFIAEELDLKKVIVPFVPpGVFSAWGMLVADIRHD 492
                                   ************************************99**************97 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   0.3   4.7e-54   2.8e-50       1     177 [.       3     177 ..       3     178 .. 0.96
   2 ?   -1.5   0.0       0.3   1.8e+03       9      50 ..     368     411 ..     367     434 .. 0.67

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 4.7e-54
                    Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaL 81 
                                   rigID+GG fTD+v++d+ ++e+ ++K+ +t ++++ g+++a++e++     + ++ + +++G T+a+N+++erkg++v+L
  gi|70607760|ref|YP_256630.1|   3 RIGIDIGGAFTDLVYYDQSNDEFEWIKVETTTQDPSIGVIRAVDESK----VDLKNANEIIHGQTLAINTIIERKGAKVGL 79 
                                   79******************************************984....458899************************ PP

                    Hydant_A_N  82 ittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhS 160
                                   ittkgfrd+lei+r nr+d+++ + k  +  v++  + ev+er++  ge+++pl+ ee++  +++l ++gvesiav+l++S
  gi|70607760|ref|YP_256630.1|  80 ITTKGFRDILEIQRANRRDMYNFKYKkpESFVPRYLRREVSERISSSGEIISPLKIEELKIVVNDLVKKGVESIAVSLINS 160
                                   ********************999999555579************************************************* PP

                    Hydant_A_N 161 ylnpehElrvaeiarei 177
                                   y+n +hEl+v+e+++ei
  gi|70607760|ref|YP_256630.1| 161 YVNSAHELKVKELLKEI 177
                                   **************998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                    Hydant_A_N   9 TfTDavaldeke..eevavlKllstpdavaegirealeevlees 50 
                                   T TDa++l++    +e+   Kl   +d ++++i+++ ++ + + 
  gi|70607760|ref|YP_256630.1| 368 TVTDAYILSGLLnpNELLGGKLKVRRDLAEKAIKRIADHYKISV 411
                                   78888888854366777778888888888888888877765443 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.039   2.4e+02       1      20 [.       4      23 ..       4     147 .. 0.84
   2 ?   10.4   0.0   5.6e-05      0.33       1      17 [.     280     296 ..     280     454 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.039
                                  EEEEE-SSEEEEEEEETTTE CS
                   BcrAD_BadFG  1 vGiDgGsTttkavlmdekge 20
                                  +GiD+G+  t  v +d++ +
  gi|70607760|ref|YP_256630.1|  4 IGIDIGGAFTDLVYYDQSND 23
                                  7************9997654 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.6e-05
                                   EEEEE-SSEEEEEEEET CS
                   BcrAD_BadFG   1 vGiDgGsTttkavlmde 17 
                                   +G+DgGsTttka l+++
  gi|70607760|ref|YP_256630.1| 280 IGLDGGSTTTKASLVEN 296
                                   7***********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4298.34
//
Query:       gi|70607761|ref|YP_256631.1|  [L=574]
Description: hypothetical protein Saci_2042 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.2e-158  528.7   0.0   1.6e-158  528.4   0.0    1.1  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.4   0.0  8.6e-163  1.6e-158       1     516 []       2     523 ..       2     523 .. 0.96

  Alignments for each domain:
  == domain 1  score: 528.4 bits;  conditional E-value: 8.6e-163
                Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadg.elvaqaphipvhlgsmseavkavlekfegelkp 80 
                                   D++tle+++n l  + eem  +  rta+Sp+i+e lDf+++++d+ g +lv+qap++p + g +++++++v++k+++e+kp
  gi|70607761|ref|YP_256631.1|   2 DQFTLEIIKNGLIVASEEMFYAFGRTARSPVIYEVLDFAVGITDKYGrGLVVQAPGVPGFSGVLDFTIREVMAKWKDEIKP 82 
                                   899********************************************9***************************99**** PP

                Hydantoinase_B  81 GDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegeleedv 161
                                   GD+++tN Py ggtHl+D+++i+P+f+++ l++f+++++H+++iGG++ Gs+++datei++EGl++p++kl+ eg++++dv
  gi|70607761|ref|YP_256631.1|  83 GDMIATNIPYDGGTHLNDVALIMPMFYKDILLGFIVNKGHWSEIGGMHFGSWTSDATEIYQEGLQLPSIKLFIEGKPNRDV 163
                                   ****************************99*************************************************** PP

                Hydantoinase_B 162 lelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgtyeaedyldd.g 241
                                   +++++an+R+p+ +lgD++Aq+a+++v+ rr+++l+ +yG+d+v +amd++++++er  + +l+elp+g+yeaedy+dd g
  gi|70607761|ref|YP_256631.1| 164 IDIIKANSRMPDATLGDMDAQLASMRVAYRRVQRLVMKYGVDNVLTAMDKLIEDGERLSKLRLKELPKGVYEAEDYIDDdG 244
                                   *****************************************************************************9977 PP

                Hydantoinase_B 242 .....ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnpse 317
                                        + +kv+vti++d+++ Dftg+s+qv+g+iN+pl +t sav  ++++++d+  p N+G+++p+ev++pegs++nps+
  gi|70607761|ref|YP_256631.1| 245 isdnpVYVKVKVTITEDKFIADFTGSSRQVRGPINSPLPATVSAVREIYMAVTDPYAPPNAGYFKPLEVIAPEGSIFNPSR 325
                                   888777999999********************************************************************* PP

                Hydantoinase_B 318 paavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdGasa.vhvh 397
                                   pa++++  +e +  ++d+++kala++++ r++A++  ++ ++++ggv+e+ ge+f+++e+  gG+GA+++ dG+s+ v++ 
  gi|70607761|ref|YP_256631.1| 326 PAPTST-YWESMSYATDLIWKALAPHVNGRLPAGHFLSILATILGGVKED-GEPFAIVEPQPGGWGASNNSDGESGlVASG 404
                                   ****65.6***************************************985.6677************************** PP

                Hydantoinase_B 398 mtntrntdvEilErryPvlverfelrpdsg.GaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGepGargrvv 477
                                    ++t + ++E+ E+r+P+lv+r el+   g G+GkyrGG G+++++ + ++++ +++   r++++ wG++GG +G++++++
  gi|70607761|ref|YP_256631.1| 405 DGETYIASAEVYEKRMPILVDRLELNVSDGtGHGKYRGGFGIIKDYIVMSEQAYLTVSIGRSKYPTWGVEGGMNGTPNYCM 485
                                   *************************876655*******************99***************************88 PP

                Hydantoinase_B 478 lnllvr.geeenlggkatvelkagdvlvietpGGGGyGdp 516
                                   +   +r +e +++++ a++ l +gd + +++ GGGG+G+p
  gi|70607761|ref|YP_256631.1| 486 I--FKRgEEPKRMRKVASLLLYKGDKVSLRSGGGGGWGNP 523
                                   6..2333556666667779*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 4138.69
//
Query:       gi|70607762|ref|YP_256632.1|  [L=253]
Description: hypothetical protein Saci_2043 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-16   60.7   0.1    2.6e-16   60.3   0.1    1.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   1.5e-20   2.6e-16       4     212 ..       9     221 ..       6     222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.5e-20
                                   ESS-..EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H................ CS
                         RAMPs   4 tltP..lhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd....... 75 
                                   ++tP  l++G+        + ++  + ++  +IP++SlkG +R   e +++++++ +++   ++ + q+++k         
  gi|70607762|ref|YP_256632.1|   9 FKTPngLRVGGE-------DTLKPLKYDNDYVIPSTSLKGIFRRVSEMIVNDKDHMEEHPVEDLSRYQNELKQIesclnsn 82 
                                   555544666666.......99999********************************9999999777777777669999999 PP

                                   .................................HHHHHH--S...SS--SEEEEE.......................EEE CS
                         RAMPs  76 .................................leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspkls 123
                                                                     +e++ G+e    +a++++++D+                         
  gi|70607762|ref|YP_256632.1|  83 cfdmrfkkilkskgledsndrkemvrlyllwncPVERLYGSE---YFASALTISDS------------------------- 135
                                   999966666666666666666666666666666666666666...66666666666......................... PP

                                   EEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..................HHHHHHHHHHHHHH.HHH-- CS
                         RAMPs 124 gselrelldhsterrtrvaidrktktngkkkgglftleaipae....rikfsgrirlenlsdeelgallklLdlldlhflg 200
                                         +++    +rt+v idrk+k+n +  g+lft+e++       +  ++   + + +   + +++lk L+++ +   +
  gi|70607762|ref|YP_256632.1| 136 -----VIRQADIVERTHVVIDRKNKKNLE--GHLFTEEILNVYkidvNVVLRDSSQGNSKQAGQSELWLKTLKFMVNVGTF 209
                                   .....679999******************..********************************************99999* PP

                                   -STTTTBTTT-E CS
                         RAMPs 201 lGggkplGfGsv 212
                                   +Gggk++G G++
  gi|70607762|ref|YP_256632.1| 210 VGGGKSRGIGLM 221
                                   **********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1704.58
//
Query:       gi|70607763|ref|YP_256633.1|  [L=313]
Description: hypothetical protein Saci_2044 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   21.2   0.6    0.00041   20.4   0.6    1.5  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.6   2.3e-08   0.00041      31     164 ..      29     169 ..      25     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-08
                                   S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S...SS--SEEEEE.............. CS
                         RAMPs  31 lPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGneeeskiagrvffeDarpvkipgqilees 111
                                   + yIP+++l+Ga+   +e +  +++k+++d y ++++ q+     + ++ F  +  ++++g  f+e +r+++i+++ + ++
  gi|70607763|ref|YP_256633.1|  29 TDYIPATTLRGAIL--AEYY-YQKGKIEEDFYVSPAYPQNS----APSHYFSPA--EGRKGSEFVEESRILSIKNDEINKG 100
                                   78***********9..5545.55788899999998887776....*********..********************98776 PP

                                   ...........................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEE CS
                         RAMPs 112 kqikstpsp..................klsgselrelldhsterrtrvaidrktktngkkkgglftleaip 164
                                   k+     +                   k++ +  +    +s ++  +vaid+   +++    +l+ +e++ 
  gi|70607763|ref|YP_256633.1| 101 KDMREVMNLgidkkprigviikpnekqKSPNETRYIKYTPSSTILMHVAIDKVSASSFH--RMLYAYEYLK 169
                                   66554444466666666666666655433333333333344455555555555555444..5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2136.47
//
Query:       gi|70607764|ref|YP_256634.1|  [L=201]
Description: hypothetical protein Saci_2045 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-10   39.4   0.0    1.3e-09   38.4   0.0    1.4  1  RAMPs         RAMP superfamily
  ------ inclusion threshold ------
      0.064   12.6   0.0        1.3    8.2   0.0    2.0  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.4e-13   1.3e-09       2     202 ..       7     166 ..       6     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.4e-13
                                   EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H............HHHH CS
                         RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd...leea 79 
                                   ++ lt l iG+g       +    + ++ +  IP+SS+kG+lR+a+ + l   ++ +  +   +k   ++ +g+    +++
  gi|70607764|ref|YP_256634.1|   7 IKNLTSLTIGGG------SVIVGTDIPFSELEIPSSSIKGVLRTAVTQFLP--QGFTSCNEVEPKMIRQAHRGKepcDVCQ 79 
                                   778999999999......8888888999999****************8877..444444555556666666666777**** PP

                                   HH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEE CS
                         RAMPs  80 iFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkgglftl 160
                                   +FG + +    g v+f++                                  d +++r  rv+i++kt ++++  g+lf+ 
  gi|70607764|ref|YP_256634.1|  80 LFGYP-DARTEGCVNFMVE-------------------------------TKDLKKYRLMRVSIEDKTQKAKE--GALFSQ 126
                                   *****.99*********96...............................789****************9999..****** PP

                                   EEEESS..............HHHHHHHHHHHHHH.HHH---S CS
                         RAMPs 161 eaipaerikfsgrirlenlsdeelgallklLdlldlhflglG 202
                                   e++ ++       i+++n+ ++ l++ll    +l  ++ +lG
  gi|70607764|ref|YP_256634.1| 127 EVVKPGTEVVVNVIYRDNCGERLLKLLLSSVLAL--RYWRLG 166
                                   ******8888899999999999999999998888..888887 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00015       1.3      16      55 ..      19      60 ..      16      77 .. 0.88
   2 ?    2.5   0.0     0.008        72      27      80 ..     105     163 ..      80     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00015
                                  TECSSS..GHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEE CS
                  Amidohydro_1 16 sllrga..tledwlvppetaaealesgiktalksGtttvadm 55
                                  s+++g+  ++ ++ +p + ++ +l+++++++l  G+t+++++
  gi|70607764|ref|YP_256634.1| 19 SVIVGTdiPFSELEIPSSSIKGVLRTAVTQFLPQGFTSCNEV 60
                                  66777788999****************************986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.008
                                   H......STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEE CS
                  Amidohydro_1  27 l......vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglril 80 
                                   +      +++ + a   + + ++ +k Gt+ v ++++  +++ e+ll+ + + +l lr +
  gi|70607764|ref|YP_256634.1| 105 RlmrvsiEDKTQKAKEGALFSQEVVKPGTEVVVNVIYR-DNCGERLLKLLLSSVLALRYW 163
                                   4445556777777777889999***************5.559999999999888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1528.51
//
Query:       gi|70607765|ref|YP_256635.1|  [L=906]
Description: hypothetical protein Saci_2046 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-07   30.1   2.6    8.1e-07   29.3   0.7    2.3  3  HD        HD domain
  ------ inclusion threshold ------
       0.05   13.1   0.0        0.1   12.1   0.0    1.4  1  HDOD      HDOD domain
      0.082   13.3   1.2        1.7    9.0   0.0    3.4  4  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5     9e+03      87     120 ..      95     118 ..      79     119 .. 0.72
   2 !   29.3   0.7   1.4e-10   8.1e-07      24      93 ..     181     243 ..     161     259 .. 0.86
   3 ?   -2.3   0.0      0.81   4.9e+03      48      74 ..     796     822 ..     785     837 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                                   TTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                            HD  87 ehheswegkkrprglaerqlslearivklaDrla 120
                                   +h   +e           ++++ + + +l+D+l+
  gi|70607765|ref|YP_256635.1|  95 RHKYGKE----------LMITPDLGVKDLMDKLE 118
                                   4444444..........68999999999999997 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.4e-10
                                   HHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHTTCCHHH CS
                            HD  24 drellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld........ledvaklirehheswe 93 
                                   d   l++aaLlHDiGk ++++              H+ +++ il+ev+  +           +e + + +++hh+++ 
  gi|70607765|ref|YP_256635.1| 181 DQSQLRVAALLHDIGKLVNPE-------------HHVRESVDILEEVLRKS--TgelcikggIEKIRDEVLHHHGQIQ 243
                                   56679*************997.............59999999999998777..4468999**************9986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.81
                                   HHHHHCTCCHHHHHHHHHHHHHHHHHH CS
                            HD  48 kkeeefekflaHekvgaeilrevekrl 74 
                                   ++++e   ++++e +g+ +++ev+ + 
  gi|70607765|ref|YP_256635.1| 796 EDFKELVNLYNNEREGRNKVKEVLRPI 822
                                   334444455667777777777776665 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.7e-05       0.1      88     150 ..     154     214 ..     141     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                                   -SS-HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHH CS
                          HDOD  88 egadlkklwehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsllpeeleellekv 150
                                    g+++++l++h + ++lv  ++ +++  ++  ++ +a+LLhdiGklv  + +  e   +le+v
  gi|70607765|ref|YP_256635.1| 154 PGFNFTSLASHLQLTSLVVWAMQQQTYDQS--QLRVAALLHDIGKLVNPEHHVRESVDILEEV 214
                                   478899999999999999999988887766..9*************98777776666666655 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.21   1.3e+03      21      46 ..      18      43 ..      11      47 .. 0.83
   2 ?   -2.9   0.0       1.4   8.2e+03      15      49 ..     187     220 ..     184     239 .. 0.78
   3 ?   -1.3   0.0      0.44   2.6e+03      33      63 ..     225     256 ..     211     274 .. 0.76
   4 ?    9.0   0.0   0.00028       1.7      49      89 ..     662     704 ..     630     713 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                         mCpol 21 deeeleklskevkeaikklkkllkde 46
                                  +e+++++l++++ + i ++++l +++
  gi|70607765|ref|YP_256635.1| 18 EENKVKALREKIINIITQISNLSCEI 43
                                  68899999999999999999987765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                         mCpol  15 alllsndeeeleklskevkeaikklkkllkdelga 49 
                                    + l +d+ +l++  ++v+e+++ l+++l + +  
  gi|70607765|ref|YP_256635.1| 187 VAALLHDIGKLVNPEHHVRESVDILEEVLRKST-G 220
                                   556788889999999999999999999998874.3 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.44
                         mCpol  33 keaikklkkllkdel.gasvifaaGDsilaks 63 
                                   k  i+k+++ + +   + + i + +D++ a+ 
  gi|70607765|ref|YP_256635.1| 225 KGGIEKIRDEVLHHHgQIQTILNMADDVAASH 256
                                   55677887777666657788888888887765 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00028
                         mCpol  49 asvifaaGDsilaksslee..dllvelsrvyqkitgltvSiGv 89 
                                     v++ +GD+i+++s+     + +v l +  q++tg+t+ +Gv
  gi|70607765|ref|YP_256635.1| 662 SGVLYLGGDDIMLMSPSVIaiQFAVRLFKKAQEYTGFTFKVGV 704
                                   5699***********98777888888888899999****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (906 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.89u 0.37s 00:00:01.26 Elapsed: 00:00:00.57
# Mc/sec: 4749.51
//
Query:       gi|70607766|ref|YP_256636.1|  [L=71]
Description: hypothetical protein Saci_2047 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 389.42
//
Query:       gi|70607767|ref|YP_256637.1|  [L=251]
Description: hypothetical protein Saci_2048 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-09   37.1   0.0    6.3e-09   36.2   0.0    1.6  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.5e-13   6.3e-09      21     120 ..      51     160 ..       2     239 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.5e-13
                                   .......---S----HHHHHHHHHHHHH.......HHHH.HHHTT-HHHHH.H.................HHHHHH--S.. CS
                         RAMPs  21 espefrdkgglPyIPGSSlkGalRsale.......kllgsekkekkdeysrkkekqrvkkgd........leeaiFGneee 86 
                                   +  + + ++g+ +IPG ++kG++R+ le        +++   ++   +y++     ++ +++        +++ ++G +  
  gi|70607767|ref|YP_256637.1|  51 IHEFNKYSDGRLVIPGATIKGMVRTRLElsipdscYVVNRQSNYSSPRYIN--IFRPAFRRYyhkfpqvcVVDDLLGTA-- 127
                                   556778899*******************99999986666666666666666..44455555569999999*********.. PP

                                   .SS--SEEEEE....................... CS
                         RAMPs  87 skiagrvffeDarpvkipgqileeskqikstpsp 120
                                    k a+rv+f D++  +++++++  ++  + ++ +
  gi|70607767|ref|YP_256637.1| 128 -KLASRVNFTDFVGSNVKVKKVNINNEDYECAEK 160
                                   .***********9888877776665555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1372.55
//
Query:       gi|70607768|ref|YP_256638.1|  [L=278]
Description: hypothetical protein Saci_2049 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-27   94.6   0.0    1.5e-26   93.8   0.0    1.4  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   8.5e-31   1.5e-26       4     213 .]      23     221 ..      20     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 8.5e-31
                                   ESS-EE----.................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H............... CS
                         RAMPs   4 tltPlhiGdg...kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd...... 75 
                                   +++Pl++G+g    +++e     + +d++g+P+IPGSS+kG++Rsa e++l+s++ + ++   r + + r++ ++      
  gi|70607768|ref|YP_256638.1|  23 VISPLRVGAGksaISPGELARDVVLKDSTGRPVIPGSSWKGVFRSAGERILNSKGVKVCTGIGR-DICLRNYGKYedfqrf 102
                                   89********999999999999**************************************9999.99************** PP

                                   .................HHHHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE-- CS
                         RAMPs  76 .................leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrt 139
                                                    l +++FG     +  g+v+f D+ p++                               ++ +rt
  gi|70607768|ref|YP_256638.1| 103 lksdirqaidtfwkytcLNCKLFGTM---SVSGMVNFLDSLPID------------------------------YKLNVRT 150
                                   **************************...***********9966..............................57899** PP

                                   SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                         RAMPs 140 rvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                    vai r  + ++    +l ++e+++++  kf+++    nl++ + g+ll + + + +   ++Gg k++GfG+v+
  gi|70607768|ref|YP_256638.1| 151 MVAISRTEGASAR--SALVQVEYVEPN-SKFEFKLMGRNLPNYVVGYLLTIMKNIHDGLTQIGGHKTRGFGFVK 221
                                   ******9999998..************.********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1817.51
//
Query:       gi|70607769|ref|YP_256639.1|  [L=128]
Description: hypothetical protein Saci_2052 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.2   0.2        7.8    6.7   0.0    2.2  2  PPR_3     Pentatricopeptide repeat domain


Domain annotation for each model (and alignments):
>> PPR_3  Pentatricopeptide repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00044       7.8      14      48 ..      33      68 ..      29      71 .. 0.85
   2 ?    4.6   0.0    0.0019        33      21      42 ..      74      94 ..      70     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00044
                         PPR_3 14 dvvtYthLLtayanagnk.klalevlermkkkgikP 48
                                  d  t + LLt   n +n  + + +++ +m  + i P
  gi|70607769|ref|YP_256639.1| 33 DASTINNLLTILQNRKNVdEVIAYIIRQMGREEIDP 68
                                  6678899****999999625789*********9999 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0019
                         PPR_3 21 LLtayanagnkklalevlermk 42
                                  LL+a  + ++++ al +l+++k
  gi|70607769|ref|YP_256639.1| 74 LLKA-LQGKDLEKALSILGYVK 94
                                  4555.899*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 884.08
//
Query:       gi|70607770|ref|YP_256640.1|  [L=91]
Description: hypothetical protein Saci_2053 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00067   20.3   0.0     0.0007   20.2   0.0    1.1  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.9e-08    0.0007      46      86 .]      27      70 ..       1      70 [. 0.74

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.9e-08
                                  HH.HEEEEEEEE--..HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                   CRISPR_Cas6 46 le.gGfvGevkysg..eleelekllrfaeylgvGkktafGlGkv 86
                                   e  G++G+++y+   +++ + ++l+   ++gvG+++  G+G+v
  gi|70607770|ref|YP_256640.1| 27 KEiLGLLGKFSYTVleNSQLIYEILEDVIAMGVGSSRRNGFGRV 70
                                  3334********66778888889*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 610.78
//
Query:       gi|70607771|ref|YP_256641.1|  [L=96]
Description: hypothetical protein Saci_2054 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.024   14.4   0.0    1.2  1  DUF5615   Domain of unknown function (DUF5615)
       0.16   11.9   0.1       0.44   10.5   0.0    1.7  2  Cas_csx3  CRISPR-associated protein (Cas_csx3)


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-06     0.024      30      61 ..      30      61 ..       9      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-06
                       DUF5615 30 lglegasDeeileyAkeedriivTkDkDFgel 61
                                  ++ +   D +i  yA++ ++i+vT Dk F  +
  gi|70607771|ref|YP_256641.1| 30 IETPYKYDIAIALYAERLGAIVVTSDKRFPYR 61
                                  556667899******************99765 PP

>> Cas_csx3  CRISPR-associated protein (Cas_csx3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.9e-05      0.44      46      69 ..      34      56 ..      21      65 .. 0.81
   2 ?   -0.9   0.0      0.17   1.5e+03      14      29 ..      62      77 ..      58      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.9e-05
                                  TTTSSEEEEEETTT.EEEEEEESS CS
                      Cas_csx3 46 lhetawiavydprLegavvvasht 69
                                  ++   +ia y  rL ga+vv+s  
  gi|70607771|ref|YP_256641.1| 34 YKYDIAIALYAERL-GAIVVTSDK 56
                                  566778********.*****9975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                                  GT-----.--TTSEEE CS
                      Cas_csx3 14 kklelPeeidlkqgvv 29
                                  kk+ lP++  +++gv+
  gi|70607771|ref|YP_256641.1| 62 KKIVLPQKFVTNSGVI 77
                                  5777888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 636.03
//
Query:       gi|70607772|ref|YP_256642.1|  [L=484]
Description: 3-polyprenyl-4-hydroxybenzoate decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-105  353.4   0.0   1.7e-105  353.2   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.2   0.0  9.6e-110  1.7e-105       1     406 []      19     427 ..      19     427 .. 0.93

  Alignments for each domain:
  == domain 1  score: 353.2 bits;  conditional E-value: 9.6e-110
                                   HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS..-GHHHHHHHH CS
                          UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalgl..ssleeilekl 79 
                                   +e++++ g l+++k   +++lEi++i++ + ++++  llF+++k++ ++++vlt+++  ++rv lal+l  +s  e+++kl
  gi|70607772|ref|YP_256642.1|  19 IERVRELGLLREVK-GASWDLEIGAITDLNAKRRKFTLLFDEIKDYPKGYRVLTGALLDYRRVSLALNLpaNSDIELVKKL 98 
                                   68889999999999.89*************9999**********66679********************997778888888 PP

                                   HHHHHS..-....---EE--GCG-GGGSEE.ECCCCC--HHHS---BSSTTSSS-EEEC.EEEEEE-TTTT-EEEEEEEEE CS
                          UbiD  80 aellepkpp....ippkvvesekapcqeev.vlegddvdLskLPvltlwpgDgGpyitl.glvitrdpetgkrnlgiyRmq 154
                                   +e+l+   +    + p++v+  + p  e+v v  g++vdL k+P ++++++DgG+yi +   v+t+dpe+++ n+g yR++
  gi|70607772|ref|YP_256642.1|  99 RERLAYASKeyanYSPREVS--DSPLLENVdV--GEKVDLFKFPSPKWHEHDGGRYIGTaDAVVTKDPESEWVNVGAYRVM 175
                                   8888864435677******5..689999**66..9**********************66488******************* PP

                                   EEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSE CS
                          UbiD 155 vldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdle 235
                                   ++dkn+l++++ + ++g++h++k++++g +++p+ + +  +  l++ + + +P+g+sE++f Ga+ g++v++ + e ++l+
  gi|70607772|ref|YP_256642.1| 176 LVDKNRLAIFIDSPHHGRIHMEKYLRQG-KKCPIVISFSPPLDLFIFSGMEVPQGVSEYNFSGAVTGKRVDVLRGEDTGLP 255
                                   ****************************.8*************************************************** PP

                                   EETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCS.HHHHCHHHHHHHHHHHH CS
                          UbiD 236 vpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkpp.eedallgkalealflpl 315
                                   +pa++Ei +eG+i+  e+ +EGPfg+++Gyy + r++ pv++V+++++R+dpi+  t++g pp + +++    ++a+++++
  gi|70607772|ref|YP_256642.1| 256 IPAESEIAIEGYITG-ELTDEGPFGEFMGYYAGGRMKNPVIEVKRVYYRNDPILLGTTPGIPPyDYSYFRCPIRSAMIWDM 335
                                   **************8.79*************************************666*****888888888889999*** PP

                                   H.HCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--C CS
                          UbiD 316 l.kkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdp 395
                                   l + ++ +vk v+++e g ++ l+vv+ik++++gh+  ++++l       +  ++vivvDed+d+ dl++v+wa++tr dp
  gi|70607772|ref|YP_256642.1| 336 LeRIGIRDVKGVWAHEVGFSRALVVVAIKQAFAGHQTMLGHILAISPLTSYGGRYVIVVDEDIDPSDLNQVVWALCTRTDP 416
                                   *888999**********************************999555557788**************************** PP

                                   CCCEEEECCCE CS
                          UbiD 396 drDlviiegtr 406
                                   ++ + ++++++
  gi|70607772|ref|YP_256642.1| 417 ANSIEVVKNVP 427
                                   *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3236.53
//
Query:       gi|70607773|ref|YP_256643.1|  [L=316]
Description: hypothetical protein Saci_2056 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-20   73.6   0.0    2.3e-20   73.3   0.0    1.2  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   1.3e-24   2.3e-20      12     135 ..      62     247 ..      40     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.3e-24
                       Cyclase  12 pvw.p.dp..............................islsehtGTHlDapgHfae.k..................tide 41 
                                   pvw +  p                              + +  + +T++Da+gH+ + +                  ++++
  gi|70607773|ref|YP_256643.1|  62 PVWiGrRPtvhlmtkdegtyisgkaeprpgggksaddiVIMHLQGSTQVDALGHYWKdNtlyngfdsrttigglakdDVSK 142
                                   6664442244555666677777777778888888888788999************88732333444444444444445588 PP

                       Cyclase  42 lpleelvgpavvldv.sak.aaa.edyeiitaedleaalakqgveikpgdivlirTgwskrl....edk..ekyrnpgl.. 111
                                   l+ + ++g++v+ldv ++k + + ++ e+i+ +dl ++++++gv+i++ di+l+rTg+ k +    +++  +++++pg+  
  gi|70607773|ref|YP_256643.1| 143 LAERGILGRGVLLDVaRHKgKGSlDKGEMISFSDLLDTAKEEGVKINKHDIILVRTGFLKTFyekgPNEfyKDFSEPGIty 223
                                   999************544442347777899*****************************99998663333456688*9855 PP

                       Cyclase 112 seeaaewlaekgvkavGvDtlsvD 135
                                   ++e ++w+ e+++ a G Dt++ +
  gi|70607773|ref|YP_256643.1| 224 ERELVKWFYENEFIAYGSDTIASE 247
                                   789*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2300.37
//
Query:       gi|70607774|ref|YP_256644.1|  [L=344]
Description: alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  105.5   0.1    2.2e-30  104.8   0.1    1.4  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    1.6e-21   76.7   0.1    2.5e-21   76.0   0.1    1.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.2e-19   71.7   0.0    1.8e-19   71.1   0.0    1.3  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    0.00014   21.4   0.1    0.00022   20.8   0.1    1.2  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.003   17.4   0.0     0.0044   16.8   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0047   17.6   0.0     0.0086   16.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   15.0   0.0      0.057   14.2   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
       0.04   14.0   0.4      0.077   13.1   0.4    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.098   12.6   0.0        0.2   11.6   0.0    1.5  1  ADH_N_2          N-terminal domain of oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.1   1.1e-33   2.2e-30       2     105 ..      26     135 ..      25     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.1e-33
                                   TEEEEEEEEEEE-HHHHHHHTTS.....TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT- CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkgg.....kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkege 77 
                                   g+vl+kv +ag+C++Dl + +g      ++++  lpl++GHEi+Gev+e+g +v+++k+ d+V+++p+i +g+C++Ck ge
  gi|70607774|ref|YP_256644.1|  26 GQVLVKVDYAGVCHTDLSVRSGAifnriSSSKPTLPLVIGHEIAGEVVELGGNVEGFKKSDKVLIDPWIGDGSCHYCKIGE 106
                                   69*******************999999999999************************************************ PP

                                   GGG-TTBEETTTSS-SSSBSEEEEC.GGG CS
                         ADH_N  78 enlCeeakllgvsldGgfaeyvvvp.ekk 105
                                   +++C++ k+lg++++Gg+ eyv+vp  ++
  gi|70607774|ref|YP_256644.1| 107 DQYCDNPKWLGINVNGGYGEYVLVPdYRY 135
                                   ************************94444 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.1   1.2e-24   2.5e-21       1     128 [.     180     305 ..     180     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.2e-24
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   g+G++avq+Aka+    +i+vd+see l+la  lGad+v        +e+++++t g+gvd+++++vGs+ t +++++ll+
  gi|70607774|ref|YP_256644.1| 180 GLGSIAVQIAKAIHGsFIIGVDVSEEGLKLATNLGADYVTSK---VDEEEVRKITTGRGVDAIIDFVGSEFTTSNYYTLLA 257
                                   89*********66555*************************9...569********************************* PP

                                   EEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkealdll 128
                                   + Gr v vG+ +g+ +     +l+    +++G+l g+ r++f e+l+l+
  gi|70607774|ref|YP_256644.1| 258 KLGRYVKVGTYGGGLPhDAGLRLHSMGWQFIGTLTGN-RKDFLEVLELA 305
                                   **********555555245555999************.9***9999986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   9.2e-23   1.8e-19       1     133 []     213     341 ..     213     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 9.2e-23
                                   TT-SEEE.ETTSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG CS
                  ADH_zinc_N_2   1 lGAdevi.dyrtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfs 80 
                                   lGAd v  + ++e++++ t g+gvD+++d vg+e + ++  ++l++ Gr+v +g      +l+  a   + +s  ++f+ +
  gi|70607774|ref|YP_256644.1| 213 LGADYVTsKVDEEEVRKITTGRGVDAIIDFVGSEFTTSNYYTLLAKLGRYVKVGT--YGGGLPHDAG-LRLHSMGWQFIGT 290
                                   8******6666999999***************888889999999888*****996..4556666666.89**********9 PP

                                   ...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                  ADH_zinc_N_2  81 mkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                   ++ + ++d + e+++l e Gk++p +++v++leea++A++ le+g++ G+ Vl
  gi|70607774|ref|YP_256644.1| 291 LTGN-RKD-FLEVLELAENGKIKPMITKVLSLEEANDALDNLEKGKVSGRQVL 341
                                   9999.***.****************************************9887 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.1e-07   0.00022      31     201 ..     169     329 ..     153     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                   Glu_dehyd_C  31 pesalvlGaG.slGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsr..etpvdeipeaseemdlvvEaT 108
                                    +s++++GaG  lG +a+ +     ++++  +++g  d  +  ++l  +lGa Yv+s+  e++v +i  + + +d +++  
  gi|70607774|ref|YP_256644.1| 169 SKSVMIIGAGgGLGSIAVQIA----KAIHGSFIIGV-DVSEEGLKLATNLGADYVTSKvdEEEVRKI-TTGRGVDAIIDFV 243
                                   36899***9725787774443....45777889996.7789999************96336789999.6899********* PP

                   Glu_dehyd_C 109 GsakhafeaiealapnGvaaLlGvpedsevevdgg.elhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtk 188
                                   Gs     +  + la  G  + +G + +  +  d+g +lh+         +G+   nr+ f   ++ L+ +++  ++ ++tk
  gi|70607774|ref|YP_256644.1| 244 GSEFTTSNYYTLLAKLGRYVKVGTYGGG-LPHDAGlRLHSM----GWQFIGTLTGNRKDF---LEVLELAENGKIKPMITK 316
                                   ************************9998.667776255555....44689*********9...56788889999******* PP

                   Glu_dehyd_C 189 vvdldeleeAfed 201
                                   v+ l+e+++A ++
  gi|70607774|ref|YP_256644.1| 317 VLSLEEANDALDN 329
                                   ********99875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.2e-06    0.0044       3      47 ..     170     213 ..     168     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAren 47 
                                   k + ++ +G G G ++ ++a +++ ++ ++G+D see ++lA++ 
  gi|70607774|ref|YP_256644.1| 170 KSVMIIGAGGGLGSIAVQIA-KAIHGSFIIGVDVSEEGLKLATNL 213
                                   5667788999**********.99999****************985 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.3e-06    0.0086       4      94 ..     177     264 ..     174     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                                   ET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHH CS
               Methyltransf_25   4 lGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlek 84 
                                   +G G G ++ ++ak+++ + ++gvD+see l+ a +  + + +  ++ + +++++    + +D+++ + + + ++ +++ +
  gi|70607774|ref|YP_256644.1| 177 AGGGLGSIAVQIAKAIHGSFIIGVDVSEEGLKLATNLGA-DYVTSKVDEEEVRKITTG-RGVDAIIDFVGSE-FTTSNYYT 254
                                   6889999********9559***************99885.457999999999999855.5899999964455.45577888 PP

                                   HHHHHHHHEE CS
               Methyltransf_25  85 alkeiarvLk 94 
                                   +l+++ r +k
  gi|70607774|ref|YP_256644.1| 255 LLAKLGRYVK 264
                                   8888888777 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.9e-05     0.057       4      57 ..     178     231 ..     175     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
               Methyltransf_12   4 GcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnveleald 57 
                                   G+G Gs++  ++++++++ ++gvD+s++ ++ a +  a++   ++++ e++++ 
  gi|70607774|ref|YP_256644.1| 178 GGGLGSIAVQIAKAIHGSFIIGVDVSEEGLKLATNLGADYVTSKVDEEEVRKIT 231
                                   9*****************************666666666665555555555444 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   3.8e-05     0.077       2     100 ..     171     269 ..     170     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEB.SSHHHHHHH..-SEEEE-S-HHH CS
                        DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavt.ddleevlek..advliDFTtpea 79 
                                   +v+++Ga G +G+  v+ +++  +  + ++  ++e    g ++ + lg + +  +v  +++ ++++   +d +iDF   e 
  gi|70607774|ref|YP_256644.1| 171 SVMIIGAGGGLGSIAVQIAKAIHGSFIIGVDVSEE----GLKLATNLGADYVTSKVDeEEVRKITTGrgVDAIIDFVGSEF 247
                                   69******************988877777655554....777777788886666666466777777689********9999 PP

                                   HHHHHHHHHHT.T-EEEE--SS CS
                        DapB_N  80 vlenlklalek.gvklViGTTG 100
                                   + +n+ ++l+k g  + +GT G
  gi|70607774|ref|YP_256644.1| 248 TTSNYYTLLAKlGRYVKVGTYG 269
                                   9999988888746666677755 PP

>> ADH_N_2  N-terminal domain of oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05       0.2      18      71 ..      13      73 ..       8      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
                       ADH_N_2 18 feleeeelpelkdGevlvralylSv...DPymR..grmndaksyve..pvelgdvmrggav 71
                                  ++le+ ++p+++ G+vlv+++y +v   D   R     n+  s  +  p+ +g+ ++g++v
  gi|70607774|ref|YP_256644.1| 13 LRLEDMDVPKVGVGQVLVKVDYAGVchtDLSVRsgAIFNRISSSKPtlPLVIGHEIAGEVV 73
                                  6899******************998555666664222233333333346666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 2166.18
//
Query:       gi|70607775|ref|YP_256645.1|  [L=443]
Description: transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-19   70.1  47.6    1.6e-19   70.1  47.6    2.4  2  MFS_1     Major Facilitator Superfamily
    1.7e-15   56.8  37.3    2.5e-11   43.1  12.3    2.6  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        0.2   11.4   0.7       0.38   10.6   0.7    1.5  1  SHOCT     Short C-terminal domain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1  47.6   2.6e-23   1.6e-19      11     351 ..      28     386 ..      14     387 .. 0.73
   2 !    5.3   5.9    0.0013       7.8     108     175 ..     357     426 ..     356     439 .. 0.75

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.6e-23
                         MFS_1  11 arsilgpalplalaedlg.ispseigllltlyalga......avaslplGrlsdrfGrrrvlllglllfalg.lllllfas 83 
                                   + +++++++p ++++ +  +s +++++++t  ++++      + a+++++r+sd++Gr+r ++ gl++++++ +l +++ +
  gi|70607775|ref|YP_256645.1|  28 DLFTILLVAP-YISSLFFpSSITFLSIAATYAGFATslimrpVGATVFGSRVSDKVGRKRAIFYGLIGLVITsTLQGAL-P 106
                                   4455666666.45444331455555554444333334455668899999***********************6666666.2 PP

                         MFS_1  84 s.......lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg...pllggllasslg.... 149
                                   +        + lll++r++qG++ g+++++++++  + +p++ rg + gl  ++++++++++     l  +l         
  gi|70607775|ref|YP_256645.1| 107 TyqvvgviAPiLLLAVRLIQGVFIGGITAGSHVIGPESVPERYRGIVGGLGFSAAGVAYLIAagwFFLTTIL----Ypgss 183
                                   222333334446******************************999999999998888886662112233333....13344 PP

                         MFS_1 150 .....Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                        Wr++f+   + ++++   +++ ++++++e ++k +k+   +++++pl++++++ + +  +  +l+ ++++++ f+ 
  gi|70607775|ref|YP_256645.1| 184 ylvwgWRVMFFGGLLSLAVL---GFVNYLVPESEVWTKIKKRG--SVVKSPLKEIFSKYRYQLGV--ALLLSIGWGASFYV 257
                                   66644776655544444444...55999999999999999999..88999999988888888866..99999999999999 PP

                         MFS_1 226 lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt.....ssav 301
                                   +   lp++l +v +l+   ++++++ ++++++ i+ l++g +s+ +gr+++ l++ +++l+++  l+l   +         
  gi|70607775|ref|YP_256645.1| 258 TDGILPTFLSSVNKLA-KTEIAIVMIIGSIGMSIGPLIGGEISQIIGRKITSLIGAIIVLAVVGPLFLSLGSlksgdL--- 334
                                   ****************.8*****************************9888888887777777777777777544432... PP

                         MFS_1 302 llll........vlvliGfglgfvfpsllalasdlappeeagtasglfn.tagslggal 351
                                               +l+l+ +g+g    +l++++++ +p++ +gt +g++  t +++gg +
  gi|70607775|ref|YP_256645.1| 335 ---NqiilhsfaILFLVDIGGG----MLMTYLNEIYPASVRGTGVGFTWnTGFAIGGTI 386
                                   ...3122222345555555555....68999999999999******9987888898875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0013
                         MFS_1 108 aliadwfpkeergraigl.lsagfslGailgpllggllasslg...Wrav.fyilaivsllafvlfllllpee 175
                                   +++ +++p + rg ++g+ +++gf++G  +  +++ ++a s+g   ++++ fy l +vs++ +v  + +l+ e
  gi|70607775|ref|YP_256645.1| 357 TYLNEIYPASVRGTGVGFtWNTGFAIGGTIPTIISLAVA-SAGlsaFPSImFYTLIVVSVIILV--GTVLTKE 426
                                   78999***********9879********99999999998.445478555559999999999844..4444433 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1  12.3   4.1e-15   2.5e-11      51     204 ..      59     223 ..      14     240 .. 0.84
   2 !   18.6  16.9   1.1e-07   0.00067      45     195 ..     274     428 ..     247     442 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 4.1e-15
                                   HHHTHHHHHHHHH.HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  51 ivsiflvGaiiGs.lfagllgdrfGRkkslliaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPm 125
                                    ++  l+ + +G+ +f++ ++d++GRk ++  + + +vi + lq+a + +      +  +l++ R++ G+++G++++ + +
  gi|70607775|ref|YP_256645.1|  59 GFATSLIMRPVGAtVFGSRVSDKVGRKRAIFYGLIGLVITSTLQGALPTYqvvgvIAPILLLAVRLIQGVFIGGITAGSHV 139
                                   45555677888882456689****************************8888888888899999***************** PP

                                   HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHT CS
                      Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsn....adgwrillglqlvpallllilllflPESPrylvek 201
                                      E  p+++Rg++++l  +a  +  l+aa+  + +   + +     +gwr++++  l++  +l ++ +++PES  ++ +k
  gi|70607775|ref|YP_256645.1| 140 IGPESVPERYRGIVGGLGFSAAGVAYLIAAGWFFLTtILYPGssylVWGWRVMFFGGLLSLAVLGFVNYLVPESEVWTKIK 220
                                   ****************************9977766635555589999*******99999888888888**********988 PP

                                   T-H CS
                      Sugar_tr 202 gke 204
                                   ++ 
  gi|70607775|ref|YP_256645.1| 221 KRG 223
                                   875 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.1e-07
                                   ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH..HHHHHHHHHHHHH-TTTT.SS-TGGGGGHHHHHHHHHHHHHH CS
                      Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslli..aavlfvigavlqaaakgk.nsvevlivgRvlvGigvGlasvl 122
                                   ++ + +++ i ++G  iG l++g +++++GRk + li  ++vl+v+g +   +   k   + ++i+  + + + v +  ++
  gi|70607775|ref|YP_256645.1| 274 KTEIAIVMIIGSIGMSIGPLIGGEISQIIGRKITSLIgaIIVLAVVGPLFLSLGSLKsGDLNQIILHSFAILFLVDIGGGM 354
                                   456778888889999999999999999999999988865677788887665555544589999999999999999999999 PP

                                   HHHHHHTTS-SCCHHHHHH.HHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---H CS
                      Sugar_tr 123 vPmyisEiApkklRgalvs.lyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESP 195
                                     +y++Ei p+++Rg+ v+  ++++ ++G  + +i+ l+++  + +    i+++  +v ++++l++ ++  E++
  gi|70607775|ref|YP_256645.1| 355 LMTYLNEIYPASVRGTGVGfTWNTGFAIGGTIPTIISLAVASAGLSAFPSIMFYTLIVVSVIILVGTVLTKETK 428
                                   99999999999999986551578999999999999999998888866667999999999999999999988884 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   6.4e-05      0.38      12      27 ..     428     443 .]     427     443 .] 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.4e-05
                         SHOCT  12 rGeIteEEFeakKakL 27 
                                   +G I++EE+e +K+ L
  gi|70607775|ref|YP_256645.1| 428 KGTISKEEYEIQKETL 443
                                   79***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2730.99
//
Query:       gi|70607776|ref|YP_256646.1|  [L=447]
Description: aromatic ring dioxygenase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-17   62.7   0.0    3.7e-17   62.0   0.0    1.3  1  Rieske           Rieske [2Fe-2S] domain
    2.5e-13   50.5   0.0      1e-12   48.5   0.0    1.9  1  Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic 


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   4.2e-21   3.7e-17       1      82 [.      38     120 ..      38     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.2e-21
                                   CEEEEEEGGGC-.TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGG.SEEETT.EEE-TTT--EEETTSBEEE- CS
                        Rieske   1 swvavakesdvp.egdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplse.gkidekgvleCpcHgwaydadGkvikg 79 
                                   +w+ +  +++v  +gd++  ++g + ++v+r edg ++A+ + C+H+g+ l+e +++   ++++Cp+Hgw+y++ G+++++
  gi|70607776|ref|YP_256646.1|  38 NWIFLGFVDEVLnPGDFVVRRIGLNSVIVVRGEDGRIRAFFNACRHMGTELCEaEYG-RASTFTCPYHGWTYNNMGRLVGV 117
                                   58899999999999*************************************998888.667******************** PP

                                   TTH CS
                        Rieske  80 Pap 82 
                                   P +
  gi|70607776|ref|YP_256646.1| 118 PVK 120
                                   976 PP

>> Ring_hydroxyl_A  Ring hydroxylating alpha subunit (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   1.2e-16     1e-12       2     208 ..     158     437 ..     157     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.2e-16
                                   HHHHGGGHHHHH...................ESS-HHHHHHHHHH.CCCCCTTTHHHHHHCS-TTS-...........--E CS
               Ring_hydroxyl_A   2 eellrvaaetld...................ikaNWKlaaEnflE.sYHvpvlHpellrallpeele...........tae 51 
                                    ++l++ +++ld                    ++ WK  a nf E   H+ ++H++ +  ++++  +           +  
  gi|70607776|ref|YP_256646.1| 158 SDYLGETKWYLDiffkasggmkivgkpikfiADFDWKSGASNFAEdRLHTITTHRSVVELGYASPISrfgyvtpglseITA 238
                                   57788888888888888888888888888888999****************************99999****999776333 PP

                                   EEEE-SSSS-EEEEEES-THHHHHHHHHHHHHHHHSHHHHHHHGCHHHHCEEEE.....EEEETTTEEEE..TTTTE.... CS
               Ring_hydroxyl_A  52 aaeyagfgphgsgsyvgqpgdlrlepaaavreldaeaaapelegledeqdrgal.....hftifPnlsillapdhvv.... 123
                                   ++  +  g+    + + +    +  p+   ++ d  +  +++eg+ +eq+   +       tifPnls+ +a+d+      
  gi|70607776|ref|YP_256646.1| 239 CYLNDSLGRPVGAF-GMRFPPEESIPGFFGFYGDHFREHSKPEGVSEEQYKVFQrvshwVGTIFPNLSFFTAADQTDksgk 318
                                   33333333333333.2222333333344444555558888899999999888888887789**************999999 PP

                                   .......EEEEEESSTT-EEEEEEEEEETT..S-HHHHHHHHHHHHHHCS...TTHHHHHHHHHHHHHHTTS......... CS
               Ring_hydroxyl_A 124 .......ifrviPtgpettevelealvppdataseelkeelaavvdrtfg...vveeeDaelceevQqglrs......... 185
                                          i+ + P gp++tev+++++vp+    ++e+++++ +v++ +fg   v e +D++++ ++ + + +         
  gi|70607776|ref|YP_256646.1| 319 pnspvslIRLWQPIGPGKTEVWTWVVVPRV--LPDEIAKRVYEVTTSHFGpsgVAEMDDTAIWRRISKSASGnlarrisql 397
                                   9999999***********************..9***********************************9998888888888 PP

                                   ...................TTTSBSCCC..SCSSHHHHHHHHHH CS
               Ring_hydroxyl_A 186 ...................rgyepgpvl..srqEeavrhFhewv 208
                                                      +g+           E++ r+F +++
  gi|70607776|ref|YP_256646.1| 398 iiggldsvsdlpvlrdwrgPGL-V---RptQFHEDGPRTFWKRW 437
                                   8888877777777755544444.2...12246777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2946.84
//
Query:       gi|70607777|ref|YP_256647.1|  [L=170]
Description: aromatic ring dioxygenase subunit B [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-22   80.3   0.1    1.6e-22   80.1   0.1    1.0  1  Ring_hydroxyl_B  Ring hydroxylating beta subunit
     0.0023   17.7   0.0     0.0034   17.2   0.0    1.3  1  DUF3872          Domain of unknown function, B. Theta Gene de
  ------ inclusion threshold ------
       0.04   13.7   0.0      0.063   13.1   0.0    1.3  1  WVELL            WVELL protein


Domain annotation for each model (and alignments):
>> Ring_hydroxyl_B  Ring hydroxylating beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.1   2.7e-26   1.6e-22       1     139 [.      21     158 ..      21     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 2.7e-26
                                   HHHHHHHTT-HHHHHCTEEEEEEEEEE-B----GGGGGGSBTS-EEEEE-HHHHHHHHHHHTSTT-GG.GSS--EEEEEEE CS
               Ring_hydroxyl_B   1 reAelLDdrdydaWlallaedihYwmpareereererdpqaeesaifdddragLedRvrrietgrswa.enPpsRtrhlvs 80 
                                   +eAe+LD++ y++Wl++l +d +Y +   + ++  + ++ +e+s++ + ++++L++ v+r+  +  wa ++  sR+r++v+
  gi|70607777|ref|YP_256647.1|  21 HEAEILDNEMYREWLEMLGDDFEYLITYVQPEKGAKLKY-TEDSFLMKANKQKLSEMVKRLYHPSGWAlQDSLSRFRRIVG 100
                                   69***********************99988866666665.79*************************956678******** PP

                                   EEEEEE-SSTTEEEEEEEEEEEEEETT.TEEEEEEEEEEEEEEE-SSTEEEEEEEEEES- CS
               Ring_hydroxyl_B  81 nVeveeteadgelevrsnflvlrnrle.rqvdifaGeredvlrrsddsfkiarrtilldn 139
                                   nV+v+e   +++++vrsn+ ++r  ++   + +++Gered l  s++ +++++r ++ld 
  gi|70607777|ref|YP_256647.1| 101 NVRVKEA-LNNTVRVRSNIALFRIEMNeGSQSVITGEREDLLSLSGE-IRLRKRVVVLDS 158
                                   ******5.99*************99986899999********99875.9*********97 PP

>> DUF3872  Domain of unknown function, B. Theta Gene description (DUF3872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.7e-07    0.0034      61     109 ..      41      89 ..      35     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.7e-07
                                   S---EEEEE-SS---EEEETTS-EE-TTS-EE-S-SEEEEEEE---SS- CS
                       DUF3872  61 dteYtirYfqldgkGelkledgtvllpndlyllekekFrLyYtsesees 109
                                   d eY i Y+q++   +lk+++++ l+  +  +l++ + rLy+ s  + +
  gi|70607777|ref|YP_256647.1|  41 DFEYLITYVQPEKGAKLKYTEDSFLMKANKQKLSEMVKRLYHPSGWALQ 89 
                                   568**************************************98865555 PP

>> WVELL  WVELL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.063       3      34 ..      12      43 ..      10      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                         WVELL  3 ferLteeLlekNeklsyaqArtWvElLweDFe 34
                                  + +L e L+++ e l+++  r W+E+L +DFe
  gi|70607777|ref|YP_256647.1| 12 YINLCEFLYHEAEILDNEMYREWLEMLGDDFE 43
                                  5679999************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1262.77
//
Query:       gi|70607778|ref|YP_256648.1|  [L=219]
Description: HTH domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-22   79.7   0.0    3.6e-22   77.9   0.0    1.9  2  HTH_10    HTH DNA binding domain
     0.0003   20.3   0.3      0.038   13.5   0.0    2.9  3  GerE      Bacterial regulatory proteins, luxR family
     0.0072   15.9   0.6       0.14   11.7   0.0    3.1  4  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.045   13.6   0.0        0.4   10.6   0.0    2.4  2  HTH_5     Bacterial regulatory protein, arsR family
       0.12   12.9   0.0       0.21   12.2   0.0    1.5  1  DUF134    Protein of unknown function  DUF134


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.71   2.6e+03      23      35 ..      25      37 ..      22      40 .. 0.58
   2 !   77.9   0.0     1e-25   3.6e-22       1      52 [.     153     204 ..     153     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
                        HTH_10 23 rvtlkeLAkelGI 35
                                    ++ e+A++l++
  gi|70607778|ref|YP_256648.1| 25 YYEVPEIANILNL 37
                                  4555566666665 PP

  == domain 2  score: 77.9 bits;  conditional E-value: 1e-25
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                   LT ++l+vl++A+++GYFdyPR++++keL+++lGIs++t+  hLr+ae+k++
  gi|70607778|ref|YP_256648.1| 153 LTSRELKVLTTALDLGYFDYPRKIKSKELSEILGISEPTFVFHLRNAERKIV 204
                                   9*************************************************98 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.45   1.6e+03      21      30 ..      29      38 ..      26      39 .. 0.81
   2 ?    3.3   0.1     0.016        58       2      13 ..     152     163 ..     151     166 .. 0.85
   3 !   13.5   0.0   1.1e-05     0.038      20      45 ..     178     203 ..     176     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.45
                                  HHHHHHHTS- CS
                          GerE 21 keIAeelniS 30
                                   eIA +ln+ 
  gi|70607778|ref|YP_256648.1| 29 PEIANILNLT 38
                                  59*****986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.016
                                   SS-HHHHHHHHH CS
                          GerE   2 sLskRErevLrl 13 
                                   +L++RE++vL+ 
  gi|70607778|ref|YP_256648.1| 152 NLTSRELKVLTT 163
                                   7*********75 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                          GerE  20 nkeIAeelniSekTVkvhksnimkKL 45 
                                   +ke +e+l+iSe T  +h++n+ +K+
  gi|70607778|ref|YP_256648.1| 178 SKELSEILGISEPTFVFHLRNAERKI 203
                                   79*********************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.27   9.6e+02      22      31 ..      30      39 ..      28      39 .. 0.89
   2 ?   -0.7   0.2       0.3   1.1e+03       3      18 ..      89     104 ..      88     109 .. 0.83
   3 ?   -2.9   0.0       1.5   5.3e+03      34      41 ..     126     133 ..     125     135 .. 0.65
   4 !   11.7   0.0     4e-05      0.14      18      43 ..     176     201 ..     171     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                        HTH_24 22 eLAerlglSp 31
                                  e+A  l+l+p
  gi|70607778|ref|YP_256648.1| 30 EIANILNLTP 39
                                  9*******97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.3
                        HTH_24   3 etdrkILelLqknpri 18 
                                   ++d  I++++ +n +i
  gi|70607778|ref|YP_256648.1|  89 DYDNSIYSIINRNNGI 104
                                   578889******9998 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                        HTH_24  34 vnrrlkrL 41 
                                   vnr +k++
  gi|70607778|ref|YP_256648.1| 126 VNRLIKEF 133
                                   67777776 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 4e-05
                        HTH_24  18 isqreLAerlglSpstvnrrlkrLee 43 
                                   i  +eL+e lg+S +t   +l++ e+
  gi|70607778|ref|YP_256648.1| 176 IKSKELSEILGISEPTFVFHLRNAER 201
                                   889*************9888888776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.34   1.2e+03      18      29 ..      28      39 ..      24      39 .. 0.85
   2 ?   10.6   0.0   0.00011       0.4      18      37 ..     178     197 ..     174     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.34
                                  HHHHHHHHTS-H CS
                         HTH_5 18 vcelaeelglsq 29
                                  v e+a++l+l++
  gi|70607778|ref|YP_256648.1| 28 VPEIANILNLTP 39
                                  679******986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                                   HHHHHHHHTS-HHHHHHHHH CS
                         HTH_5  18 vcelaeelglsqstvShHLk 37 
                                   + el+e+lg+s++t   HL+
  gi|70607778|ref|YP_256648.1| 178 SKELSEILGISEPTFVFHLR 197
                                   68****************98 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.7e-05      0.21      45      83 ..     169     208 ..     125     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                        DUF134  45 lvdy.edlkqeeaaklmGiskatlwrlltearkkiakalv 83 
                                     dy +++k +e ++++Gis++t+   l +a +ki +  +
  gi|70607778|ref|YP_256648.1| 169 YFDYpRKIKSKELSEILGISEPTFVFHLRNAERKIVSNFI 208
                                   4677457999*************99999999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1624.75
//
Query:       gi|70607779|ref|YP_256649.1|  [L=561]
Description: acetyl-coenzyme A synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-85  286.3   0.0    3.9e-85  286.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.6e-23   82.3   0.7    7.2e-23   81.4   0.7    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.0   0.0   4.3e-89   3.9e-85      13     423 .]      59     445 ..      50     445 .. 0.86

  Alignments for each domain:
  == domain 1  score: 286.0 bits;  conditional E-value: 4.3e-89
                                   EEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHH CS
                   AMP-binding  13 alvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayil 90 
                                    l++   +g+ +++T+++l+ ++++++a+L+  Gvk+gdrV++++++ p ++++llai ++Gav+vp+++t+++e+++y +
  gi|70607779|ref|YP_256649.1|  59 GLIWiseKGDIKSYTFHDLEVKASSFGAVLKDSGVKPGDRVVVMSKRVPSLYFSLLAIGMIGAVIVPIYSTFGEEAIRYRV 139
                                   455555678899*******************77************************************************ PP

                                   HHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SS CS
                   AMP-binding  91 edseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTT 171
                                   e+s++kv i  v++ l++k +++ +       + +l+    ++e  ++e++  +         +e + +d+ +i+YTSGTT
  gi|70607779|ref|YP_256649.1| 140 ENSGSKVAI--VHESLADKFRNISG-------IKILK---TSEEGIVNEQNVHN-----T-SYVERSINDPTLILYTSGTT 202
                                   *********..76666555555554.......22333...23333333333222.....2.2336789************* PP

                                   SS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHH CS
                   AMP-binding 172 GkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleliekl 252
                                   G+PKG+ +s++ +++ + s   + +f+++++d+++++ + a+++g+ +++++a l+   +v ++++  +d++ ++  ie+ 
  gi|70607779|ref|YP_256649.1| 203 GRPKGIWHSQDIMTFYYFSG--KYHFDMHAQDKFWHTGDPAWVAGF-AGVWTAWLNSIPIVSYEGK--FDAESWYSNIERV 278
                                   *************9999995..5669999****************9.***************9966..67899******** PP

                                   T-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE..CHCTT CS
                   AMP-binding 253 kvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv..lplee 331
                                   kvt++ ++P++++ l ++g  +   ++ dlss+r++ +gge + p+++r+  ++fg ++++gYG+TEt++ v+   +    
  gi|70607779|ref|YP_256649.1| 279 KVTLMSTAPTAIRLLKKEG-VE-LARKFDLSSIRFIHAGGEYVDPDIIRWSMEVFGVPIHDGYGQTETATYVIAnyVS--- 354
                                   *************995543.33.223349*******************************************642333... PP

                                   TCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEE CS
                   AMP-binding 332 dkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyl 410
                                      k+gs Gkplpgv++ +vDe+ g+p+p++++G l +      ++kg ++++e+ + +f+ + +++ TGD+g++dedGy+
  gi|70607779|ref|YP_256649.1| 355 MPIKIGSMGKPLPGVKALVVDEN-GNPLPPNTKGILALDPDfpAMAKGIWNDEERWKNSFK-N-GYYLTGDMGYIDEDGYF 432
                                   33469*****************9.*************9854449****************8.4.7**************** PP

                                   EEEEECCCEEEET CS
                   AMP-binding 411 eivgRkkdliklr 423
                                   +++gR++d+ik++
  gi|70607779|ref|YP_256649.1| 433 WYLGRADDIIKVS 445
                                   ***********85 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.7   8.1e-27   7.2e-23       1      76 []     453     531 ..     453     531 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 8.1e-27
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+Es++++hpaVae aV+Gv d+++G +++a++vlk++  + +  l++e++ hvr +lg++ vp++v++v+elp t sGK
  gi|70607779|ref|YP_256649.1| 453 EIESVIMTHPAVAESAVIGVEDPIRGFRIKAYIVLKKDysP-SdeLKNEIINHVRVKLGAHVVPREVEIVKELPHTLSGK 531
                                   8**********************************988532.246**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 4138.65
//
Query:       gi|70607780|ref|YP_256650.1|  [L=254]
Description: enoyl-CoA hydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-55  188.5   0.0    1.5e-55  188.3   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.1e-33  116.2   0.0    7.5e-30  104.6   0.0    2.4  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.0   1.6e-59   1.5e-55       2     250 ..       8     253 ..       7     254 .] 0.94

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 1.6e-59
                                   EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHH CS
                         ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlelw 81 
                                   +e+ + ++ ++r e++Na++  ++ E+ + + +le+++ vr++++ G g+kaF++G+d+ e +     +  + + e+   +
  gi|70607780|ref|YP_256650.1|   8 KENRIGKVLIDRQEKMNAITVSMRREIGERILELEKSPDVRVIIVRGlGGKAFSSGGDVSEFLSLT-PETLIDWGED---L 84 
                                   678999**********************************************************74.2333344444...4 PP

                                   HHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                         ECH_1  82 tklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                   +    + kpvia + G+ +g+Glelal cDi+ia   ++fgl+e++lG++p++gg  +l++ +G s+A ++l+lgk+i  q
  gi|70607780|ref|YP_256650.1|  85 SSSERITKPVIASIDGYTFGAGLELALSCDIRIATPRSEFGLPEIRLGMVPASGGITRLVKVLGLSRATYMLMLGKRIDSQ 165
                                   45566789************************************************************************* PP

                                   HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTC CS
                         ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEk 243
                                    a ++G+v ++v +e+l e + e+a++la  sp+al++lk+ l++ +++    + ++e+k f  +  + d+keG++afl k
  gi|70607780|ref|YP_256650.1| 166 LAYQWGIVHEIVDAEKLDERTYEVAKELAGLSPLALKALKKVLHEIADSPMYVGYDIERKTFGLLKYSGDFKEGVEAFLNK 246
                                   ********************************************************************************* PP

                                   SH----- CS
                         ECH_1 244 rkpefed 250
                                   rkp+f++
  gi|70607780|ref|YP_256650.1| 247 RKPKFDG 253
                                   *****87 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0   8.4e-34   7.5e-30       2     179 ..      13     184 ..      12     191 .. 0.92
   2 !   10.0   0.0   4.9e-05      0.44     251     317 ..     188     251 ..     183     254 .] 0.87

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 8.4e-34
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   g + ++r +++Na++ +m r++ e++ e ek+++v++++++g g+kaf++GgDv ++ +   e+  +    + e  +    
  gi|70607780|ref|YP_256650.1|  13 GKVLIDRQEKMNAITVSMRREIGERILELEKSPDVRVIIVRGLGGKAFSSGGDVSEFLSLTPETLID----WGEDLSSS-- 87 
                                   667899*****************************************************99997655....55555544.. PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgada 162
                                    ++++kpv+a +dG++ G G+ l++++ +r++t r+ f  PE+++G++P  Gg   L ++ g + ++y+ + G+r++++ a
  gi|70607780|ref|YP_256650.1|  88 -ERITKPVIASIDGYTFGAGLELALSCDIRIATPRSEFGLPEIRLGMVPASGGITRLVKVLGlSRATYMLMLGKRIDSQLA 167
                                   .4668************************************************999999877699**************** PP

                                   HHTTS--EE--GGGHHH CS
                         ECH_2 163 laaglathyvpseklea 179
                                   ++ g+   +v++ekl++
  gi|70607780|ref|YP_256650.1| 168 YQWGIVHEIVDAEKLDE 184
                                   *************9987 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 4.9e-05
                                   HHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                         ECH_2 251 ktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                   +++++l+  sP++lk+  + l++ ++   +   ++ E +    l  ++Df eGv+a l +  +kPk+
  gi|70607780|ref|YP_256650.1| 188 EVAKELAGLSPLALKALKKVLHEIADSP-MYVGYDIERKTFGLLKYSGDFKEGVEAFLNK--RKPKF 251
                                   67899**********************7.999999999999988889*********9955..46776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1703.84
//
Query:       gi|70607781|ref|YP_256651.1|  [L=758]
Description: aldehyde oxidase and xanthine dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.8e-119  398.3   0.0   5.6e-119  398.1   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    3.9e-21   75.5   0.2    9.4e-21   74.2   0.1    1.8  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.1   0.0  6.2e-123  5.6e-119       1     550 []     135     706 ..     135     706 .. 0.93

  Alignments for each domain:
  == domain 1  score: 398.1 bits;  conditional E-value: 6.2e-123
                                   STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevl 79 
                                   +h+++++n++   ++++Gd+e   +++++vve++++++r ++ +lEt  ++a++  +++++++ys+ q+p++++ l+ ++l
  gi|70607781|ref|YP_256651.1| 135 IHPQVKSNIVLnkTFTYGDFEYESEKSEVVVENRVKFPRYSCSPLETYEVFARY--DGDKYEIYSNFQGPYSIHYLLTKAL 213
                                   6999999*99999999**************************************..69*********************** PP

                                   T--GGGEEEE-.SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEE CS
                 Ald_Xan_dh_C2  80 glpenkvrviv.prvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldv 159
                                   +    +v ++  +++GG+FG K+  +p+ +l+a a++ + rp  ++++R+e+++a++ + + ++ +kv  ++ Gki a+++
  gi|70607781|ref|YP_256651.1| 214 KA---DVLLKGpRDIGGSFGIKSAIYPYMALIASASRVIWRPLLWRETRTEHVIASSAGAERESVVKVYGNRSGKINAIEI 291
                                   85...788887589******************************************************************* PP

                                   EEEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHH CS
                 Ald_Xan_dh_C2 160 dlladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplel 239
                                   + +++ Gay  + +p+ l r +++l+g+Y+i++++v++ +v tNt p++  RG+G+p  + a+E+++d  A+e+++dp+++
  gi|70607781|ref|YP_256651.1| 292 KAIDNLGAYpRPPEPGNLLRNHGNLTGAYDIKSMKVNYMAVLTNTIPTGLNRGYGAPHLYTAIETTIDIFADEIKMDPIDV 372
                                   *********6699******************************************************************** PP

                                   HHHHBCECGCC.S.EEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.........EE CS
                 Ald_Xan_dh_C2 240 RrrNlikpgeltp.ygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgf........tak 311
                                   R++N+ik++ +++  g   y s +  ++l+++ke +  ++++  ++  +a++k++G+g+++++e++g++            
  gi|70607781|ref|YP_256651.1| 373 RMKNVIKDEYYETaSGG-KYRSFSCYKVLRRMKELY--DKLNTDVEMERAKGKRIGVGVSLIIEPSGTNIgyldlareS-- 448
                                   ******99877441344.6***************85..8888888888877899************9999877554431.. PP

                                   TTEE.........EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-S.BTTSSS-.---S-TT-H CS
                 Ald_Xan_dh_C2 312 flnq.........egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvveg.dtdkvpn.gsgtaaSrs 381
                                      +         + ++v ++  G+v+v++ g++ GqG+et++ + ++++Lgv+++dv+v+   dt++    +sgt++Sr 
  gi|70607781|ref|YP_256651.1| 449 ---SdflpkssaqDIVMVYIDLYGKVKVFVNGSNEGQGHETVVSEQVSRRLGVKPQDVDVIYRtDTERPWAvSSGTYSSRF 526
                                   ...15556677657799*******************************************98879999877799******* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET..EEEECHHHHHHHHHH.......TTSSEEEEEEE.. CS
                 Ald_Xan_dh_C2 382 tdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk..eksvslaelaaaayl.......ervslsatgfykt 453
                                   + ++++A  +A + l ++ll +a+ell+v++++l++++gkv++   +ksvsl++l+   ++       ++++l a g+++ 
  gi|70607781|ref|YP_256651.1| 527 APIVMEALNRALDSLEDKLLLAASELLGVQKSSLKIKEGKVTTVteDKSVSLRQLVGIFHWdpvklrnTEQGLVAVGHFQS 607
                                   ******************************************9999***********999989999888899999999998 PP

                                   ..EEEETHCHCSBBEEEEEEEEEEEEETTT--EE.EEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTE CS
                 Ald_Xan_dh_C2 454 .ldeetgkgppfayfaygaavaeVevDtetgevk.vlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGq 532
                                    + ++ ++g+ +++++yg+   +Vev++   e+  ++r++++hD+Gk++N +++egQi G+  qG+   l+  l y+edG 
  gi|70607781|ref|YP_256651.1| 608 pYADNLKEGKINSSISYGCMGQVVEVEIGETEMPfIRRAYVIHDAGKILNEKMAEGQIVGASFQGVEVSLFSSLEYNEDGI 688
                                   9999****************99999998666664399******************************************** PP

                                   ESS-STTTS----GGGS- CS
                 Ald_Xan_dh_C2 533 lltasladYkiPtaadiP 550
                                   +l+++++dY++ ta++ P
  gi|70607781|ref|YP_256651.1| 689 PLSQNFSDYLVLTAMESP 706
                                   ***************987 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.1     1e-24   9.4e-21       2     109 ..      11     120 ..      10     121 .. 0.87
   2 ?   -4.0   0.0         2   1.8e+04      28      60 ..     565     597 ..     562     604 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1e-24
                                   T-SCCGGGC...C-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.TSSS-EEEESS-SSEES CS
                  Ald_Xan_dh_C   2 GeavYvdDi...papgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.siledeedallaedkvr 78 
                                   Ge+ Y+dD+   +++++l++ ++rS++ahA i++id+s+a ++   v+vit  dl +  +    s   + e + +a+dk+ 
  gi|70607781|ref|YP_256651.1|  11 GEGSYIDDMiikEYKNHLHVSILRSPYAHALIKRIDYSDASKAG--VKVITFRDLMNFLSPFPlSLDTKVEYYPIARDKAV 89 
                                   99******844334455699*********************998..99********99888864555555589******** PP

                                   STT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeel 109
                                   ++g++va+v+A+d+++A++A +l++v+Ye+ 
  gi|70607781|ref|YP_256651.1|  90 YYGEPVALVIAKDQYEAEDAKELIQVDYEPI 120
                                   ****************************975 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2
                                   EEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECC CS
                  Ald_Xan_dh_C  28 AkivsidvsaalalpGVvavitakdlpkenkai 60 
                                   +k++ +  +++ +l   v ++ ++ ++ +n++ 
  gi|70607781|ref|YP_256651.1| 565 GKVTTVTEDKSVSLRQLVGIFHWDPVKLRNTEQ 597
                                   788888888888999999999888887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4942.68
//
Query:       gi|70607782|ref|YP_256652.1|  [L=244]
Description: hypothetical protein Saci_2065 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.9    7.6   7.0       0.78    9.9   0.6    2.7  2  DUF962    Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.6   4.3e-05      0.78      13      57 ..       2      46 ..       1      49 [. 0.93
   2 ?    0.6   1.1     0.034     6e+02      70      70 ..     153     153 ..      66     240 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.3e-05
                        DUF962 13 aeHsnpinrllHfigvplilltvlllllraklklllalfvvgyif 57
                                  ++H++ +n +l ++g++  +++++ +     +++++++++++y++
  gi|70607782|ref|YP_256652.1|  2 SSHRKVRNHALYVVGIMSYVVSLIPFYNLNFFRTIILIPILAYTL 46
                                  78*********************999999999***********86 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.034
                        DUF962  70 P 70 
                                   P
  gi|70607782|ref|YP_256652.1| 153 P 153
                                   0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1716.20
//
Query:       gi|70607783|ref|YP_256653.1|  [L=196]
Description: hypothetical protein Saci_2066 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0076   16.2   0.6       0.13   12.2   0.1    2.0  2  PhaP_Bmeg     Polyhydroxyalkanoic acid inclusion protein (Pha
  ------ inclusion threshold ------
       0.02   14.0   0.1      0.026   13.6   0.1    1.2  1  Poty_PP       Potyviridae polyprotein
       0.14   12.0   0.3       0.33   10.8   0.0    1.6  2  eIF3_subunit  Translation initiation factor eIF3 subunit


Domain annotation for each model (and alignments):
>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.017     1e+02      39      98 ..      14      70 ..       3      89 .. 0.76
   2 !   12.2   0.1   2.2e-05      0.13      53     113 ..     100     161 ..      78     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                     PhaP_Bmeg 39 lkqqqdlvkeltkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdkle 98
                                  lk  + l+     als l+k++k l   l d +q+  en+  +  nk e++i+ + +  +
  gi|70607783|ref|YP_256653.1| 14 LKATKSLL--YSYALSLLYKDQKYLDFIL-DFYQDFYENFVINCHNKKEEKISSLVNFDD 70
                                  55555555..5668999999999888755.99********99999999999998876555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
                     PhaP_Bmeg  53 lselekeskqltaeledqlqktvenlrskaGnkvednieE.wtdkleevsakleklalspsK 113
                                   ++++ +e+ ++ +++++ + + +e+++++ G +v+  +     + ++++++k+ +l++ ++ 
  gi|70607783|ref|YP_256653.1| 100 INHVVEEENKWLSNVNGDFEEVMEEVEKDIGEEVHKHYVKsVEELYNDITTKFPILDILQVT 161
                                   56788999**************************9998651566679*****8766654433 PP

>> Poty_PP  Potyviridae polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.4e-06     0.026     113     189 ..      44     123 ..      24     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-06
                       Poty_PP 113 kdlseklaiklaeavk.karskslaaikv.tavnvskiAlklstdeksvgr.tlliveelLveerskleqlkhlvsesvg 189
                                   +d+ e++ i+  +  + k  s +++   v + ++++kiAl+  td+  +g  +++++++  +ee ++l++ +   +e ++
  gi|70607783|ref|YP_256653.1|  44 QDFYENFVINCHNKKEeKISSLVNFDDTVrDHAEIRKIALRAFTDTDRIGEfSIVMINHVVEEENKWLSNVNGDFEEVME 123
                                   4555555555544432133334444444425789***************975899**************99877666655 PP

>> eIF3_subunit  Translation initiation factor eIF3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.34     2e+03     166     181 ..      34      49 ..      21      80 .. 0.58
   2 ?   10.8   0.0   5.5e-05      0.33     144     197 ..     116     167 ..     101     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                  eIF3_subunit 166 hYssfleelirdlaks 181
                                   +Y +f+ ++ +d  ++
  gi|70607783|ref|YP_256653.1|  34 KYLDFILDFYQDFYEN 49 
                                   4444444444443333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.5e-05
                  eIF3_subunit 144 edFeelrkalaekltklekksphYssfleelirdlakslssedikkvassltvl 197
                                    dFee  +++ + + +   ++ hY++ +eel  d++++ +  di +v+ +++ l
  gi|70607783|ref|YP_256653.1| 116 GDFEEVMEEVEKDIGEEV-HK-HYVKSVEELYNDITTKFPILDILQVTPTMNKL 167
                                   69************9988.55.**************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1570.52
//
Query:       gi|70607784|ref|YP_256654.1|  [L=140]
Description: hypothetical protein Saci_2067 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-09   37.0   1.9    1.4e-08   35.4   1.5    1.9  2  Hemerythrin  Hemerythrin HHE cation binding domain


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   1.5     8e-13   1.4e-08       4     131 .]       6     112 ..       3     112 .. 0.94
   2 !    7.7   0.0   0.00028       5.1      40      64 ..      89     113 ..      67     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 8e-13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHHH CS
                   Hemerythrin   4 ealdeeHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHdeir 84 
                                   + l  +H +  +ll++lr+l++         +++++ +  +++ l+ H   EEe+lfP l      + ++ +l ++H ++ 
  gi|70607784|ref|YP_256654.1|   6 QKLINDHVEEDRLLDELRELSNG--------DEMRRKFSIFCRNLKYHIYLEEEILFPKLD---LSDPMVIELMNQHVAMW 75 
                                   56778999999***********9........99****************************...9**************** PP

                                   HHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
                   Hemerythrin  85 elleelrellkgleepsaaafaelleeladllreHiakEesilfpll 131
                                    l+ +++e  +  +          l+ l +ll+ H+a Ee  ++p+l
  gi|70607784|ref|YP_256654.1|  76 NLMAQIEESYDINS----------LKMLSSLLKVHNAIEETNVYPRL 112
                                   *******8888877..........*********************86 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00028
                                   HHHHHHHHHHHHHHHHHHHCHHHHH CS
                   Hemerythrin  40 lldelvdeleaHhaaEEellfPlle 64 
                                    l+ l   l+ H a+EE+ ++P+l 
  gi|70607784|ref|YP_256654.1|  89 SLKMLSSLLKVHNAIEETNVYPRLN 113
                                   4455555566677777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 956.62
//
Query:       gi|70607785|ref|YP_256655.1|  [L=204]
Description: hypothetical protein Saci_2068 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-19   69.6   0.1    2.3e-19   69.0   0.1    1.3  1  DUF2249       Uncharacterized conserved protein (DUF2249)
    5.5e-07   29.2   0.1      2e-06   27.4   0.0    1.9  2  Cupin_2       Cupin domain
    5.1e-05   23.2   0.0    8.3e-05   22.5   0.0    1.4  1  AraC_binding  AraC-like ligand binding domain
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.035   13.8   0.0    1.5  1  Auxin_BP      Auxin binding protein
      0.039   13.6   0.1      0.092   12.3   0.0    1.5  1  Cupin_1       Cupin
      0.055   13.2   0.0        0.1   12.3   0.0    1.4  1  Cupin_6       Cupin
      0.088   12.5   0.0       0.19   11.5   0.0    1.6  1  Cupin_3       Protein of unknown function (DUF861)
       0.15   11.5   0.0       0.41   10.0   0.0    1.7  2  PCO_ADO       PCO_ADO


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.1     1e-22   2.3e-19       1      69 [.       5      74 ..       5      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1e-22
                       DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr.pgffsweylergpgewrvlit 69
                                  +lDvR+++p  rh++I+e+fe+L+pGe++ ++ndh+P++Ll++L++r  ++  +++++e+++g+w ++++
  gi|70607785|ref|YP_256655.1|  5 VLDVRKYSPTVRHSLILEEFERLKPGEGMYIINDHEPVHLLHFLSHRDdFDINAYHAKEEEEGKWIAFLK 74
                                  59*********************************************8878889***********98876 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   2.5e+03      43      49 ..      29      35 ..      22      46 .. 0.52
   2 !   27.4   0.0   8.9e-10     2e-06       4      70 ..     117     180 ..     114     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                                  TTEEEEE CS
                       Cupin_2 43 aGdsvyf 49
                                  +G+ +y+
  gi|70607785|ref|YP_256655.1| 29 PGEGMYI 35
                                  3333332 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 8.9e-10
                                   EEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                       Cupin_2   4 elppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                    ++pG+ +p h  p  d ++ + +G+g++  +++++ +++Gd+v++p+g+  ++  ++  ++++l +
  gi|70607785|ref|YP_256655.1| 117 YFKPGQFIPVHK-PSIDVILLIRKGKGVVVAGDNKYNVKEGDLVIVPRGVKRGVLAET--EMEILHI 180
                                   578999999999.7778************************************99988..7777766 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   3.7e-08   8.3e-05      12      57 ..     120     165 ..     113     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.7e-08
                                   TT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS CS
                  AraC_binding  12 pdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppge 57 
                                   p++  p h ++  vi ++ +G+g +  +++ y++++Gdl+++p+g+
  gi|70607785|ref|YP_256655.1| 120 PGQFIPVHKPSIDVILLIRKGKGVVVAGDNKYNVKEGDLVIVPRGV 165
                                   56666778889999******************************97 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.035      45      84 ..     112     151 ..      88     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                   EEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSS CS
                      Auxin_BP  45 evwlqtlapgsrtpihrhsceevfvvlkgkgtlylassss 84 
                                    v l  + pg+  p+h+ s + ++ + kgkg ++ ++ + 
  gi|70607785|ref|YP_256655.1| 112 AVILAYFKPGQFIPVHKPSIDVILLIRKGKGVVVAGDNKY 151
                                   678999*************************998776543 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05     0.092      32     102 ..     109     172 ..     101     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                                   TEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEE CS
                       Cupin_1  32 gisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqyns 102
                                   +  a+ +++ + g++ P   p+   i+ + +G+g    vv g+     + +++eGd+++vP+g+   + + 
  gi|70607785|ref|YP_256655.1| 109 NTYAVILAYFKPGQFIPVHKPSIDVILLIRKGKGV---VVAGD----NKYNVKEGDLVIVPRGVKRGVLAE 172
                                   556777778455566666677999*********99...55553....2456************96555555 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.5e-05       0.1      36      86 ..     134     182 ..     119     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                       Cupin_6  36 lhvvlrGscwlidpasgepvrLsagdvvllpggephvladspgtaplavie 86 
                                   ++++ +G+  ++ ++  +   +++gd+v++p+g +  +  +++++ l  ++
  gi|70607785|ref|YP_256655.1| 134 ILLIRKGKGVVVAGD--NKYNVKEGDLVIVPRGVKRGVLAETEMEILHIVS 182
                                   578999999999666..67**************887776666654443333 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.4e-05      0.19      31      61 ..     137     166 ..     117     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.4e-05
                                   EEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                       Cupin_3  31 ileGevkvtpeggetvelraGDlvvlpkgls 61 
                                   i +G+  v++ g +++ +++GDlv +p g +
  gi|70607785|ref|YP_256655.1| 137 IRKGKGVVVA-GDNKYNVKEGDLVIVPRGVK 166
                                   5679999998.*****************983 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00019      0.41      21      65 ..      88     131 ..      51     155 .. 0.78
   2 ?   -1.1   0.0      0.47   1.1e+03     134     149 ..     174     189 ..     144     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                       PCO_ADO  21 seaaakskskppvtyltlyetdsfslgvFvlppgaviPLHdHPgM 65 
                                   + +++k+ s++  t ++++ t++ ++ + +++pg+ iP H  P  
  gi|70607785|ref|YP_256655.1|  88 NFDSNKKLSETSFTPIQIFRTNTYAVILAYFKPGQFIPVHK-PSI 131
                                   355667788899999*************************5.555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                       PCO_ADO 134 paaflDilsPPYseee 149
                                      +l i+sPP +e +
  gi|70607785|ref|YP_256655.1| 174 EMEILHIVSPPPNERD 189
                                   4568999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1670.99
//
Query:       gi|70607786|ref|YP_256656.1|  [L=122]
Description: hypothetical protein Saci_2069 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-18   64.2   0.1    1.2e-17   63.9   0.1    1.1  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.055   13.5   0.0      0.092   12.8   0.0    1.3  1  Hyd_WA          Propeller


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.1   1.3e-21   1.2e-17       1      73 [.       9      82 ..       9      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.3e-21
                                  HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT--EEEEE CS
                FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalr.alpgvevveVe 73
                                  k+++++ L++V+DPe+++d+v+lgl++e++i++ g+V++ + +t+p c++ e+i+  +e+ ++ ++   ++ +Ve
  gi|70607786|ref|YP_256656.1|  9 KKKIMEGLKDVYDPEIPIDIVNLGLIYELRISEeGDVYIRVGVTTPYCPVTEDIAYTVEQVIKeTVNA-KSINVE 82
                                  57899**********************************************************55554.666665 PP

>> Hyd_WA  Propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.092       7      22 ..      41      57 ..      33      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                        Hyd_WA  7 vdGqvcfRqGVt.rdrP 22
                                    G v++R GVt + +P
  gi|70607786|ref|YP_256656.1| 41 EEGDVYIRVGVTtPYCP 57
                                  579********879999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 833.43
//
Query:       gi|70607787|ref|YP_256657.1|  [L=356]
Description: hypothetical protein Saci_2070 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2974.52
//
Query:       gi|70607788|ref|YP_256658.1|  [L=115]
Description: hypothetical protein Saci_2071 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.027   14.8   0.0    1.3  1  Aim19     Altered inheritance of mitochondria protein 19


Domain annotation for each model (and alignments):
>> Aim19  Altered inheritance of mitochondria protein 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-06     0.027       9      75 ..      18      98 ..      14     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                         Aim19  9 walsalllaslllsvkksaal..............klsklallkpsklsvllfgaafalggymiydgDlenGsGfltAWSl 75
                                  w+ + +ll++ ++s++  + l               +   + l  s+++v+++ +  ++g+y i +g+ + GsGf  A S+
  gi|70607788|ref|YP_256658.1| 18 WIGTLALLKNKTISKRLGVPLalfeifyytyltavISLLHSDLLFSTFTVFFLITHVTGGSYYIFKGERQYGSGFYNAYSI 98
                                  55566666666666666665566666666665542112334455677888888888899*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 880.20
//
Query:       gi|70607789|ref|YP_256659.1|  [L=217]
Description: hypothetical protein Saci_2072 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.03   14.6   0.0      0.051   13.8   0.0    1.3  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.8e-06     0.051      51     116 ..     144     212 ..     131     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-06
                                   -SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSH.HHHHHHHHH..CCS-SSHHHHHHGCTEEEESSST CS
                 Ribosomal_L13  51 ltgkkleqkvyyrhtgypgglkevtakellekkp.eeilekaVk..gmLpknklgrrrlkrLkvyagee 116
                                   ++  k ++k+  ++ g+ g+l  +  + l++k+    +++++V+  g Lpk  ++rr+ k+L+++++++
  gi|70607789|ref|YP_256659.1| 144 MNRVKGANKFLIKYIGFKGSLMLILTEFLVSKRElGSMVRLTVRynGSLPKSLIERRMSKHLQIFRENA 212
                                   455677899999*********99999999977665999***9965599****99***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1544.23
//
Query:       gi|70607790|ref|YP_256660.1|  [L=378]
Description: hypothetical protein Saci_2073 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-42  144.1  71.1    1.5e-31  109.6  44.4    1.9  2  MFS_1      Major Facilitator Superfamily
    2.7e-05   22.8   6.2    2.7e-05   22.8   6.2    2.1  2  MFS_3      Transmembrane secretion effector
  ------ inclusion threshold ------
       0.32    9.7  33.4       0.65    8.7  16.2    2.2  2  LacY_symp  LacY proton/sugar symporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6  44.4   2.5e-35   1.5e-31       2     352 ..       8     333 ..       7     334 .. 0.87
   2 !   48.1  18.7   1.3e-16   7.5e-13       6     172 ..     204     367 ..     197     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 2.5e-35
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +l++ + +++ si++p +  al + +g+  s+++l + + a++ ++as+ +G ++d +Gr+r + l++l+++++ lll+++
  gi|70607790|ref|YP_256660.1|   8 ALIGGFRSFSGSIIWPYVGFALYKVYGLPLSVVSLFYLVQAVVNVIASISGGIITDYLGRKRSMALSILFSSIA-LLLAYV 87 
                                   67778889999*********9*****************************************************.777767 PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    +++ +++v+ ++q+++  +++ ++ a++ d++++ ++  +a++   +g+++G +lgpl+gg++ + +++r + +i  ++ 
  gi|70607790|ref|YP_256660.1|  88 LNMPlYVMVFILFQSFFNTVYNVSSTAIVGDMYKGtSQLIKAYSRQRVGINAGWALGPLVGGYIFTFFSFRTLLLISSLLV 168
                                   89999******************************99******************************************** PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                   l+ +    ++   ++ + + +          ++++++             +li  +l+f+++ +l + + +y ++ l+++ 
  gi|70607790|ref|YP_256660.1| 169 LIIIP---IVKILPDFKGAGSILNFN----LNKEFLT-------------FLIPTFLTFAIVGQLGFSILTYYNTILHFT- 228
                                   **977...555555555555544333....2333444.............77777777777777888888888*******. PP

                         MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpslla 323
                                    +++g+l+a+ +l++++++ lagrl+    + + + ++++   la+l++a++ +     +++l +v+i+++  +v+p+++a
  gi|70607790|ref|YP_256660.1| 229 EFEVGILFAINGLLIVAFQDLAGRLIGS--KVKLISFGMVMYGLAYLAIAFITNL---YVAMLDVVFITIAEMIVTPISQA 304
                                   9*************************55..3556666666666666666666666...6666689999************* PP

                         MFS_1 324 lasdlappeeagtasglfntagslggalg 352
                                   la+ la ++ +g+++gl++++ +lg+++g
  gi|70607790|ref|YP_256660.1| 305 LANTLANKDTRGKQMGLYSMVTGLGRVIG 333
                                   ***************************99 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 1.3e-16
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfassl 85 
                                   fl+++  + lg+++  ++++ l++++ e+g+l+++ +l+ ++++ ++Grl   +G++  ++ +g+++++l+ l+++f+++l
  gi|70607790|ref|YP_256660.1| 204 FLTFAIVGQLGFSILTYYNTILHFTEFEVGILFAINGLLIVAFQDLAGRL---IGSKVkLISFGMVMYGLAYLAIAFITNL 281
                                   55555555566666558899999999999999999999999999999999...8888889999999999995555576888 PP

                         MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                   ++ ++  v+  +++ +++p+++al+  +++k+ rg+ +gl+s+ ++lG ++g  +++ l+ ++   ++  + + +sl++f 
  gi|70607790|ref|YP_256660.1| 282 YVAMLDVVFITIAEMIVTPISQALANTLANKDTRGKQMGLYSMVTGLGRVIGSSVSSELM-NYYLYYPLGLWGSISLFGFS 361
                                   899999999999999999999999999999999999999999999999999999999999.55566777777777777765 PP

                         MFS_1 167 lfllll 172
                                    ++l++
  gi|70607790|ref|YP_256660.1| 362 SAVLYY 367
                                   333444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   6.2   4.6e-09   2.7e-05      56     185 ..      49     174 ..      36     193 .. 0.82
   2 !    3.9   2.0    0.0024        15     282     362 ..     256     336 ..     230     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 4.6e-09
                         MFS_3  56 LPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvk.rr 135
                                   +  ++ si  G+++D + r++ +    l+   +s+ l +   + l  p  +++++l+ +   ++ + +  A+vg++ k  +
  gi|70607790|ref|YP_256660.1|  49 VVNVIASISGGIITDYLGRKRSMALSILF---SSIALLLA--YVLNMPLYVMVFILFQSFFNTVYNVSSTAIVGDMYKgTS 124
                                   4457889**************99766554...44444333..345568889999999999999*************98357 PP

                         MFS_3 136 dvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylaliva 185
                                   ++ +A   + vgin   + GP +gG + +++   +   + +l  l++i +
  gi|70607790|ref|YP_256660.1| 125 QLIKAYSRQRVGINAGWALGPLVGGYIFTFFSFRTLLLISSLLVLIIIPI 174
                                   899****************************9999999999887777654 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0024
                         MFS_3 282 sserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsll 362
                                   s+ +l++  +v++ l  l++a+ ++l+va+l +++   a +++    ++ + ++  +  +g+ + +Y +v+  g   Gs +
  gi|70607790|ref|YP_256660.1| 256 SKVKLISFGMVMYGLAYLAIAFITNLYVAMLDVVFITIAEMIVTPISQALANTLANKDTRGKQMGLYSMVTGLGRVIGSSV 336
                                   55689999***********************99999999999988889999999999999999999999987777777765 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  16.2   0.00011      0.65      19     181 ..      14     171 ..       2     191 .. 0.82
   2 ?    6.8   9.4    0.0004       2.4       6      99 ..     193     286 ..     187     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00011
                     LacY_symp  19 yffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepll 99 
                                     f  s+++p+    l +v gl  + + + + v  ++ ++     G+i+d lG k+++  ++s+l+  +a +l yv +  l
  gi|70607790|ref|YP_256660.1|  14 RSFSGSIIWPYVGFALYKVYGLPLSVVSLFYLVQAVVNVIASISGGIITDYLGRKRSM--ALSILFSSIALLLAYVLNMPL 92 
                                   55777999*********************************************99987..577788888999999987444 PP

                     LacY_symp 100 qlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfsidpslvfwlasgfalil 180
                                    +   v  ++   f+  vy+  ++ai   + k + +    y + rv    G+al+  + G +f+  +  ++ l s   +++
  gi|70607790|ref|YP_256660.1|  93 YVM--V-FILFQSFFNTVYNVSSTAIVGDMYKGTSQLIKAYSRQRVGINAGWALGPLVGGYIFTFFSFRTLLLISSLLVLI 170
                                   433..3.3566779999********99999999999999************************987766666655544433 PP

                     LacY_symp 181 l 181
                                   +
  gi|70607790|ref|YP_256660.1| 171 I 171
                                   3 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0004
                     LacY_symp   6 ntnfylfalffffyffimsay.fplfpvwlkevlglsktetGivfsvislfsilfqplfG.lisdklGlkkellwvislll 84 
                                   n++f +f +  f+ f i++   f++++ + + +l++++ e+Gi+f+++ l+ + fq l G li  k+ l      v+  l 
  gi|70607790|ref|YP_256660.1| 193 NKEFLTFLIPTFLTFAIVGQLgFSILT-YYNTILHFTEFEVGILFAINGLLIVAFQDLAGrLIGSKVKLISF-GMVMYGLA 271
                                   789*************98755288776.6799**************************99445555544322.12344444 PP

                     LacY_symp  85 vlfapfliyvfepll 99 
                                    l   f+  ++  +l
  gi|70607790|ref|YP_256660.1| 272 YLAIAFITNLYVAML 286
                                   444455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2781.96
//
Query:       gi|70607791|ref|YP_256661.1|  [L=414]
Description: HD domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-11   43.5   0.5    5.9e-11   42.7   0.5    1.5  1  HD        HD domain
  ------ inclusion threshold ------
      0.027   14.1   0.4        0.1   12.2   0.1    2.0  2  MIF4G     MIF4G domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.5   6.6e-15   5.9e-11       1     122 []      51     186 ..      51     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 6.6e-15
                                   HHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHTTTTHHHHTS..HHH...................HHHCTCCHH CS
                            HD   1 rleHsleVaklarrlaedlge....eedrellllaaLlHDiGkgpfgdafekk...................eeefekfla 58 
                                   r+eHsl+V+++a  + ++++        re ++  aL HDiG+ pf+++fe +                   ++e++  + 
  gi|70607791|ref|YP_256661.1|  51 RFEHSLGVYHVADLMFNRIKDvneeTVTRENIRRLALVHDIGHLPFSHTFEFAlkyieymdngiystfrnefFKEVKVAKL 131
                                   79******************9**99999*************************9999998888888876665555888899 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHHH CS
                            HD  59 HekvgaeilrevekrlgldledvaklirehheswegkkrprglaerqlslearivklaDrlaam 122
                                   He vg  ++++  + ++l+ ++    +++  + + +         +++ +++++++++D+l+++
  gi|70607791|ref|YP_256661.1| 132 HELVGIHVIQKCMNNDDLSRWMKRVYVENSEDTKTI---------KAILNSSLDADRLDYLQRD 186
                                   999999999999999977744444444444444444.........4***************986 PP

>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.14   1.3e+03      68      82 ..     127     146 ..     112     166 .. 0.75
   2 ?   12.2   0.1   1.2e-05       0.1      40      93 ..     282     329 ..     254     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.14
                                   H.....HHHHHHHHHHHHHH CS
                         MIF4G  68 q.....qnFrikllnklqee 82 
                                   +     + ++i++++k++ +
  gi|70607791|ref|YP_256661.1| 127 KvaklhELVGIHVIQKCMNN 146
                                   13444458888888888765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHCGGGHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHC-S-HHH CS
                         MIF4G  40 elifekaveepsfsplyarlcgklnsrfqqnFrikllnklqeefekryelenel 93 
                                   + i++k +e+++ s +y+rl  +l++r++   r+k+l++ q +f +     +++
  gi|70607791|ref|YP_256661.1| 282 NFIISKLHEIRDRSETYSRLYETLYKRVK--YRKKVLEYDQANFFSM----AMN 329
                                   679**************************..**************92....222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3403.05
//
Query:       gi|70607792|ref|YP_256662.1|  [L=93]
Description: hypothetical protein Saci_2075 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 593.95
//
Query:       gi|70607793|ref|YP_256663.1|  [L=452]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-31  107.3  21.8    1.1e-30  107.0  21.8    1.1  1  Sugar_tr  Sugar (and other) transporter
    5.3e-21   74.9  49.3    3.9e-20   72.1  30.4    1.8  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.028   13.8   0.4       0.07   12.5   0.4    1.6  1  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0  21.8   1.8e-34   1.1e-30      50     446 ..      62     448 ..      24     452 .] 0.84

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.8e-34
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH.HHHHHT CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv.PmyisE 129
                                    +v+++++Ga++G+l++ l+gd +GR+ +++   +l++ig +l+ +a    ++ ++ + R+++G+gvG + vlv  +   E
  gi|70607793|ref|YP_256663.1|  62 YTVALLFLGAFVGCLLFTLIGDAYGRRTAIVLNMFLLSIGELLIPLAS---NIGLYGLFRFISGLGVGPEAVLVlDIMSTE 139
                                   579*********************************************...9******************9998357778* PP

                                   TS-SCCHH.HHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHH CS
                      Sugar_tr 130 iApkklRg.alvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeake 209
                                   + p+++Rg +l   y la+t  i++a  + +++ +t    gw++l  ++ +  l ++ l++++PESPr+l  kgk eea++
  gi|70607793|ref|YP_256663.1| 140 FFPARIRGrRLALGYTLAWTSPIVIAVLSIFIIPRTFIIPGWQWLYIISGLGILSIIPLRFLIPESPRWLEVKGKFEEAEK 220
                                   *******7268899*******************666665888888888887777789999********************* PP

                                   HHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH. CS
                      Sugar_tr 210 vlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks. 289
                                   +++k ++ ++++       ++++   ++ek+ +++++s+ ++r+r+++     +fq   +   ++ ++ t++ + g++   
  gi|70607793|ref|YP_256663.1| 221 IVSKFEERALKEYGSLPPLSEIKVV-KAEKIPISTIFSK-EYRKRTTMLWIFEFFQTAAY-YGFTSLAVTVLLTKGFTIVs 298
                                   ****998888888888888888887.5568999999999.99*************99988.78899999999999999888 PP

                                   .HHHHHHHHHHHHHHHHHHHHHHH..HS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTT CS
                      Sugar_tr 290 .llvtiivgvvnfvatfvaiflvd..rfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgw 367
                                    l+ ++i+++  f+ +++++f++d  +f R+    + +++m+i+  i g   + ++ +     i+++ +++l     a  +
  gi|70607793|ref|YP_256663.1| 299 tLQYSLIIYTGYFTGSLISVFIIDskKFDRK----WQIVTMIILIGIDG-LIFGYSLNV---PILLTSGFILAN--MANIF 369
                                   89*****************999875578998....88999999999998.455555552...444444444443..34456 PP

                                   THHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CC CS
                      Sugar_tr 368 gpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtle 446
                                      +  + +El+p+++R++a+   + ++ l nf+ ++  p i+ a+g + +fl   ++a+++++ v +  p     + e
  gi|70607793|ref|YP_256663.1| 370 SNAFHQYGAELYPTRIRGFATGAQYSLSRLGNFIWQTYLPKILVAYGPFAMFLAIFIIAIVVALDVGILGPKASQIKVE 448
                                   67788899***************************************88888888888888888777776666655555 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1  30.4   6.5e-24   3.9e-20       2     351 ..      28     403 ..      27     405 .. 0.79
   2 !   16.8  10.9   4.2e-07    0.0025      37     166 ..     306     433 ..     297     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 6.5e-24
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                   +++ f+  ++ +i g+++p  +a  + +  + + +  ++l +lga+v+ l++  ++d +Grr  ++l ++l+++g ll++l
  gi|70607793|ref|YP_256663.1|  28 AIGEFFDLFDLFIGGFVVP-SVAAYYKVGRADAVFyTVALLFLGAFVGCLLFTLIGDAYGRRTAIVLNMFLLSIGeLLIPL 107
                                   6788889999999999999.77777776666666647888***********************************999999 PP

                         MFS_1  81 fasslwlllvlrvlqGlgagalfp.agaaliadwfpkeergraigllsagfslGailgpllggllasslg....Wravfyi 156
                                    as++ l  ++r+++Glg g  +  +  ++ ++ fp + rgr ++l ++ +  ++i+ ++l+ +++        W+++++i
  gi|70607793|ref|YP_256663.1| 108 -ASNIGLYGLFRFISGLGVGPEAVlVLDIMSTEFFPARIRGRRLALGYTLAWTSPIVIAVLSIFIIPRTFiipgWQWLYII 187
                                   .69999*************8876615679999*******************************99955445777****888 PP

                         MFS_1 157 laivsllafvlfllllpeepperkrkspkeee.........................kgtgpaplvpawkallkdpvlw.. 210
                                    ++  l  +    l ++ ++++r+ + + + e                          ++++a+ +p ++ ++++ +    
  gi|70607793|ref|YP_256663.1| 188 SGLGILSIIP---LRFLIPESPRWLEVKGKFEeaekivskfeeralkeygslpplseIKVVKAEKIP-ISTIFSKEYRKrt 264
                                   8877777766...555555555555555555556999999999999988888888876666666666.6677777755344 PP

                         MFS_1 211 .illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdr..lgrrrrlllallllllaa 288
                                    +l+i  ++ +++++g+++l  +    + g++  ++++ ++ +++ + + ++l++ +++d   + r+++++ +++l+ +  
  gi|70607793|ref|YP_256663.1| 265 tMLWIFEFFQTAAYYGFTSLAVTV-LLTKGFT-IVSTLQYSLIIYTGYFTGSLISVFIIDSkkFDRKWQIVTMIILIGIDG 343
                                   556666666667999999999996.9******.788888888888888888888888886645777777777777777777 PP

                         MFS_1 289 lglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                   l++ +  +   ++ll  +++l+ ++  f + ++  + ++l+p++ +g+a+g+  +++ lg ++
  gi|70607793|ref|YP_256663.1| 344 LIFGYSLNV--PILLTSGFILANMANIF-SNAFHQYGAELYPTRIRGFATGAQYSLSRLGNFI 403
                                   777777777..55555566666666665.89999999**********************9987 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.2e-07
                         MFS_1  37 lltlyalgaavaslplGrlsd..rfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfp 115
                                   ++t+y+ g++++++++    d  +f r++ ++++++l ++ +l++ ++ ++++ll + ++ + +a ++  a + + a+++p
  gi|70607793|ref|YP_256663.1| 306 IYTGYFTGSLISVFII----DskKFDRKWQIVTMIILIGIDGLIFGYSLNVPILLTSGFILANMANIFSNAFHQYGAELYP 382
                                   4555555555555555....4439*9999888888888887788888899999999999999999**************** PP

                         MFS_1 116 keergraigllsagfslGailg.pllggllasslgWravfyilaivsllafv 166
                                    + rg+a+g  ++ + lG  +    l  +l+ ++g  a+f+++ i+++++++
  gi|70607793|ref|YP_256663.1| 383 TRIRGFATGAQYSLSRLGNFIWqTYLPKILV-AYGPFAMFLAIFIIAIVVAL 433
                                   *******************999899999999.66655666666666666655 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   1.2e-05      0.07     141     226 ..     221     305 ..     215     326 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                        TMEM43 141 vvakqkgntlepYst.kngdeielleegevsaeemfakeksenklltwllRllGfllmflglllllsplsvlvslipllge 220
                                   +v+k ++  l++Y +  +  ei++++ +++   ++f ke+++ +++ w++ ++    ++  ++l++++   l++ ++++++
  gi|70607793|ref|YP_256663.1| 221 IVSKFEERALKEYGSlPPLSEIKVVKAEKIPISTIFSKEYRKRTTMLWIFEFFQTAAYYGFTSLAVTV--LLTKGFTIVST 299
                                   899999*******99899********************************988755544433333333..24444444443 PP

                        TMEM43 221 lvglgl 226
                                   l    +
  gi|70607793|ref|YP_256663.1| 300 LQYSLI 305
                                   333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3178.51
//
Query:       gi|70607794|ref|YP_256664.1|  [L=559]
Description: hypothetical protein Saci_2077 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-10   40.7   7.8    8.6e-05   22.8   0.9    3.3  3  DUF4352   Domain of unknown function (DUF4352)
  ------ inclusion threshold ------
      0.071   12.4   0.5         10    5.5   0.7    2.8  2  tify      tify domain


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.9   9.5e-09   8.6e-05      26      73 ..      21      68 ..       7     136 .. 0.82
   2 ?   -2.8   0.2       0.8   7.2e+03      45      61 ..     158     174 ..     151     195 .. 0.62
   3 !   20.8   0.0   4.1e-08   0.00037      38     115 ..     299     383 ..     268     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.5e-09
                                  TTS-CEETT-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BE CS
                       DUF4352 26 gkneylqpdaggeflivdvtvkNkgkealtvnssqfkLkdgdgkeyda 73
                                  ++++ l++ + g f+i++ +v+N++ + +t+ +s+f+L++++g  y++
  gi|70607794|ref|YP_256664.1| 21 YSQSELNSLQNGYFVIIKASVTNNEAQNFTLYPSSFELVTNNGSVYSY 68
                                  444444555669********************************9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.8
                                   EEEE-SSS-EEEEGGGE CS
                       DUF4352  45 tvkNkgkealtvnssqf 61 
                                   t++N ++ +l++ns+++
  gi|70607794|ref|YP_256664.1| 158 TFTNDSEVSLSLNSAST 174
                                   55666666666666543 PP

  == domain 3  score: 20.8 bits;  conditional E-value: 4.1e-08
                                   EEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-B....EEESCCCCTTB...--EEEE-TT-EEEEEEEEEESTT-CGEE CS
                       DUF4352  38 eflivdvtvkNkgkealtvnssqfkLkdgdgkeyd....adlsasskadd...lflgtlnpGkkvtGklvFdvpkgkkkle 111
                                   ++l++++++  +g+ ++ +n+ + +L++++g +++    ++  ++ +a +       t+ +G+ ++G+++F++p g+k+l 
  gi|70607794|ref|YP_256664.1| 299 TYLVANLSIMYNGSASVAFNPGNIHLVTNKGIYSNlygpTSPFIYLYAVTnhiPYINTIVNGQIIQGQVAFQIPLGAKPLY 379
                                   8**************************99988876443344555566655888999***********************99 PP

                                   EEE. CS
                       DUF4352 112 Leyq 115
                                   ++y 
  gi|70607794|ref|YP_256664.1| 380 IIYV 383
                                   9985 PP

>> tify  tify domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7    0.0012        10      10      22 ..     252     264 ..     252     265 .. 0.91
   2 ?    3.6   0.0    0.0047        42       5      17 ..     303     315 ..     302     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0012
                          tify  10 FYgGkVvVfDdvp 22 
                                   +Y+G V+Vf +v+
  gi|70607794|ref|YP_256664.1| 252 SYNGNVNVFMNVT 264
                                   6********9997 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0047
                          tify   5 aQLTIFYgGkVvV 17 
                                   a L I+Y+G+  V
  gi|70607794|ref|YP_256664.1| 303 ANLSIMYNGSASV 315
                                   5799*****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3852.92
//
Query:       gi|70607795|ref|YP_256665.1|  [L=220]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   20.6   7.0      0.048   13.0   0.0    2.2  2  YhfC      YhfC intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> YhfC  YhfC intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   4.3   4.1e-05      0.73      20     124 ..      25     124 ..       5     127 .. 0.67
   2 !   13.0   0.0   2.7e-06     0.048     152     219 ..     125     191 ..     122     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 4.1e-05
                          YhfC  20 slkvvglGalvFalfalvlerplhlallkqneatakalsapllfavygaLtAGlfEevgrylalrfllkrksekkdalayG 100
                                   ++   +lG+++   f++++ + + ++  +   +t        +++ yg+LtA +fE    yl l +l+k k + + +l+yG
  gi|70607795|ref|YP_256665.1|  25 KRNAYLLGIAAASYFTAIILKEIIQLSFRSFFITP----TLPTYLSYGILTA-IFEPGFAYLYL-VLTKAKVNGQLGLSYG 99 
                                   44455666665555555444443333222222333....4467888998875.*********88.56667777788***** PP

                          YhfC 101 lGhGGle.aiLvgvlsllnlvllav 124
                                      +  e ai++g+lsl n +ll+v
  gi|70607795|ref|YP_256665.1| 100 SYLAFYEnAIFLGLLSLPNYLLLSV 124
                                   *****************99998874 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-06
                          YhfC 152 altpltillgvlERlaalvvqialsvlvlqavrakrvlllllaillhaliDllaalyqaglvanavve 219
                                   ++++l+ +l +lER+ ++++++++       + +k++ +l +++ +  ++D +aa+yq       v +
  gi|70607795|ref|YP_256665.1| 125 QFSVLSLALYGLERISSFILHLFWGFSSALSASKKNIKYLSVSMPY-GMVDSVAAYYQLSHNISLVST 191
                                   789999***********************************99987.689999****98875555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1510.68
//
Query:       gi|70607796|ref|YP_256666.1|  [L=76]
Description: hypothetical protein Saci_2079 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-08   35.1   2.8    1.6e-08   34.9   2.8    1.2  1  CcdA           Post-segregation antitoxin CcdA
     0.0025   16.0   1.2     0.0029   15.8   1.2    1.1  1  Nup84_Nup100   Nuclear pore protein 84 / 107
  ------ inclusion threshold ------
      0.046   14.6   2.9        0.4   11.5   0.4    2.1  2  Histone_HNS    H-NS histone family
      0.055   13.4   0.3      0.055   13.4   0.3    2.5  3  RHH_1          Ribbon-helix-helix protein, copG family
      0.073   13.8   5.8      0.092   13.5   5.8    1.2  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   2.8   4.3e-12   1.6e-08       4      60 ..       7      63 ..       5      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.3e-12
                          CcdA  4 vnlsldsdllaqAralgiNlSatleeaLaeevkeekaerwkeenreaieelNrfvee 60
                                  v+  + +++l++Ar++giN+S++l  aL+eev+++++e+ k++   a eel++   e
  gi|70607796|ref|YP_256666.1|  7 VSTKVRREVLEKARQYGINVSEVLRNALEEEVRRREEEELKRKLTIAAEELKKVSTE 63
                                  5667889*************************************9999999887655 PP

>> Nup84_Nup100  Nuclear pore protein 84 / 107
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.2     8e-07    0.0029     439     479 ..       9      55 ..       5      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......X CS
                  Nup84_Nup100 439 keeRekqLklakklgldveailkrtvervieeteseyeps......e 479
                                   ++ R+++L+ a+++g++v+++l+   e+ ++  e+e+ ++      e
  gi|70607796|ref|YP_256666.1|   9 TKVRREVLEKARQYGINVSEVLRNALEEEVRRREEEELKRkltiaaE 55 
                                   678*************************9999999655553332220 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00011       0.4      22      55 ..       9      42 ..       5      49 .. 0.79
   2 ?    3.9   0.8     0.026        94       4      33 ..      45      74 ..      42      76 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                  XXXXXXXXXXXXXXX----SSS-----EEEEE.. CS
                   Histone_HNS 22 kealaeirelaaeyGltleelaaeakkakkkkak 55
                                  ++++ e+ e+a++yG++++e++++a +++ ++++
  gi|70607796|ref|YP_256666.1|  9 TKVRREVLEKARQYGINVSEVLRNALEEEVRRRE 42
                                  68999****************9997666655544 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Histone_HNS  4 alieelekqeealeaeerkealaeirelaa 33
                                  +l+++l  ++e+l++ + +e+++ i+e+ +
  gi|70607796|ref|YP_256666.1| 45 ELKRKLTIAAEELKKVSTEEVVDWIKEMRR 74
                                  678889999999999999999999999865 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.5e-05     0.055      16      39 .]      17      40 ..       6      40 .. 0.88
   2 ?    1.3   0.1       0.1   3.7e+02       8      28 ..      44      65 ..      43      66 .. 0.80
   3 ?    0.2   0.0      0.22     8e+02       8      21 ..      63      76 .]      62      76 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                                  HHHHHHTSSHHHHHHHHHHHHHHH CS
                         RHH_1 16 elarrrgrSrSelIReAlreyler 39
                                  e+ar  g ++Se++R Al+e + r
  gi|70607796|ref|YP_256666.1| 17 EKARQYGINVSEVLRNALEEEVRR 40
                                  89******************9875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
                                  HHHHHHHHHHHHHHT.SSHHHH CS
                         RHH_1  8 eellerLdelarrrg.rSrSel 28
                                  eel+++L   a++++ +S  e+
  gi|70607796|ref|YP_256666.1| 44 EELKRKLTIAAEELKkVSTEEV 65
                                  8899999989999888888776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.22
                                  HHHHHHHHHHHHHH CS
                         RHH_1  8 eellerLdelarrr 21
                                  ee+++ + e++r+r
  gi|70607796|ref|YP_256666.1| 63 EEVVDWIKEMRRKR 76
                                  78888899999986 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.8   2.6e-05     0.092       8      56 ..       9      61 ..       7      76 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX--HHHHHHHHH CS
                 PSK_trans_fac  8 peverlareLarltgeskteAvrrAleerlerlrre....raepllerllall 56
                                   +v+r + e ar  g +  e+ r Alee+ +r+++e    +    +e+l+++ 
  gi|70607796|ref|YP_256666.1|  9 TKVRREVLEKARQYGINVSEVLRNALEEEVRRREEEelkrKLTIAAEELKKVS 61
                                  5799999999**********************875555432222333444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2058  (0.114786); expected 358.6 (0.02)
Passed bias filter:                      831  (0.0463495); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 565.77
//
Query:       gi|70607797|ref|YP_256667.1|  [L=122]
Description: hypothetical protein Saci_2080 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-05   24.6   0.6    3.8e-05   24.2   0.6    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.6   2.1e-09   3.8e-05       1     120 [.       3     114 ..       3     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.1e-09
                                   EEE-HHHHHHHH..TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                           PIN   1 ivlDTsvliall..rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79 
                                   +++D+s+++++l   g++  + +        e  t +l+++El +vl + + +++ ++ l +l  lls +++++   ++  
  gi|70607797|ref|YP_256667.1|   3 YLFDSSAIFEALksLGSKAIDVL-------REESTINLAYYELGNVLWKYRNEINVKTVLDALTGLLSLMNVID--VKLDY 74 
                                   67899999999943333333222.......3336899************5555555555555555688888866..77777 PP

                                   HHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                           PIN  80 eaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                   ++++ +  +g++ +Da  ++t ++ +++l+ + D+d+ +++
  gi|70607797|ref|YP_256667.1|  75 QILKESVDKGITYYDAAYLVTSLRMNLTLV-SLDRDLIKYG 114
                                   8888888889********************.*****98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 785.83
//
Query:       gi|70607798|ref|YP_256668.1|  [L=368]
Description: cytochrome P450 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-23   81.9   0.2      4e-19   68.7   0.2    3.0  3  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   4.6e-05      0.83      34     133 ..      18     114 ..       2     133 .. 0.78
   2 !    2.0   0.0    0.0039        71     256     283 ..     192     219 ..     177     227 .. 0.86
   3 !   68.7   0.2   2.2e-23     4e-19     315     445 ..     231     350 ..     200     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 4.6e-05
                                   -SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHHHHHHHHHTSHSTT.T CS
                          p450  34 gpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklRrfltptltsfgkl.s 113
                                   g+i++++  +++  vl++ + + + l   +e  ++  ++    ++ + +  + +l+++++ + +lR+++   +  + kl +
  gi|70607798|ref|YP_256668.1|  18 GNIWQVFSYRYTKEVLNNFSKFSSDLTGYHERLEDL-RNGK--IRFDIPTRYTMLTSDPPLHDELRSMSADIFSPQ-KLqT 94 
                                   666666666666666666666666666665544443.3333..3345788999*********************99.999* PP

                                   HHHHHHHHHHHHHHHHHCCC CS
                          p450 114 leelveeeaedlveklrkka 133
                                   le ++ e ++ l++ ++++ 
  gi|70607798|ref|YP_256668.1|  95 LETFIRETTRSLLDSIDPRE 114
                                   **************998876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.0039
                                   SSSSHHHHHHHHHHHHHHHHHHHHHHHH CS
                          p450 256 sklsdeelaatvlellfaGvdTtsstls 283
                                   s+lsd e    ++ ll+aG +Tt++ +s
  gi|70607798|ref|YP_256668.1| 192 SNLSDIEKLGYIILLLIAGNETTTNLIS 219
                                   5799999999*************98766 PP

  == domain 3  score: 68.7 bits;  conditional E-value: 2.2e-23
                                   HHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCT CS
                          p450 315 yddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgns 395
                                   ++ + +  +  ++i+E+LR++p+v  ++ R++++ v++++ +i++G  v v++ + +rd+evf++ e+F p+R        
  gi|70607798|ref|YP_256668.1| 231 WQRIREENLYLKAIEEALRYSPPVM-RTVRKTKERVKLGDQTIEEGEYVRVWIASANRDEEVFHDGEKFIPDR-------- 302
                                   5555555555578************.999******************************************98........ PP

                                   ESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGE CS
                          p450 396 krksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdppp 445
                                     ++  +l FG G + C+G +lAr+e ++++  + ++F++  + +t++ p
  gi|70607798|ref|YP_256668.1| 303 --NPNPHLSFGSGIHLCLGAPLARLEARIAIEEFSKRFRHIEILDTEKVP 350
                                   ..355689******************************987665555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 2226.21
//
Query:       gi|70607799|ref|YP_256669.1|  [L=297]
Description: ISC1173-like transposase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-87  291.4  41.4    3.2e-86  289.2  41.4    1.8  1  DUF973           Protein of unknown function (DUF973)
      1e-06   29.0  34.9    1.7e-06   28.4  23.9    2.3  2  DUF996           Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.2  41.4   3.6e-90   3.2e-86       1     310 []       6     296 ..       6     296 .. 0.96

  Alignments for each domain:
  == domain 1  score: 289.2 bits;  conditional E-value: 3.6e-90
                        DUF973   1 eiegleklregslfliiasllaliliilvlvvlft...aissgl.....sqliqssasilssvlllliaaiiliiiasvll 73 
                                   e eg+ ++r+++lf+i+a+l++l+++++v++ l+    +iss+l     s++++++ +ils+v+++++ a+i++i+ +v++
  gi|70607799|ref|YP_256669.1|   6 EAEGIARIRSAALFYIVAILITLVAVFAVFIPLIVsisSISSNLsnpnaSSASAAAGGILSAVIGVIVVAVIVSIVILVFI 86 
                                   689*************************99988886667777779999999999999************************ PP

                        DUF973  74 ilgllkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilaliGqillgls 154
                                   il++l++r+gfsiL+++grdvgiG+tg+tlil+gai++ii ++                     +igiil+++Gqillg++
  gi|70607799|ref|YP_256669.1|  87 ILSFLRFRDGFSILQAIGRDVGIGKTGTTLILVGAILLIIPFL--------------------DIIGIILIFVGQILLGIG 147
                                   *****************************************76....................889*************** PP

                        DUF973 155 fyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsklrsttsqvpvlqvpstp.qqvqisqvgqGtlrsnG 234
                                   +y++Ge+Ynn+l+kigGil++ip+idi++fIG+i++y+g+g++         ++  +++p+ p +q++ +q+g+G+lr+nG
  gi|70607799|ref|YP_256669.1| 148 IYRIGEIYNNSLTKIGGILVAIPLIDITAFIGMIMTYVGVGQIQ--------REFGMRPPLPPsSQIPSQQTGSGVLRGNG 220
                                   *******************************************4........67889999999999*************** PP

                        DUF973 235 tanltvysqvqvqIlsAsiegtnysttsinPntLkvGnNsitinFntvlnLvpgstYtirLlLsngqtidvevtyq 310
                                   ta+l++y q+q+q++sA+i+gtny t  i+Pn+L++G+N++t+nFn +lnL+p+s+Y+irL L++g+t+dv+vt+q
  gi|70607799|ref|YP_256669.1| 221 TADLNIYLQTQEQVVSAQILGTNYLTGLIVPNMLQPGFNNLTVNFNVPLNLMPNSIYVIRLNLASGRTLDVNVTFQ 296
                                   **************************************************************************98 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  23.9   1.9e-10   1.7e-06      25     135 .]      13     142 ..       7     142 .. 0.79
   2 !    6.3   3.1    0.0012        11      96     133 ..     149     186 ..     144     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.9e-10
                        DUF996  25 ifsnaliafilsii...alvvailalllvlgalatalelpgleeaas...........lilllllvliiayvlliisavfl 91 
                                   i+s al ++++ +i   a++++++ l++++ ++ + l++p+++ a++           +i++ ++v i+++v++i+s + +
  gi|70607799|ref|YP_256669.1|  13 IRSAALFYIVAILItlvAVFAVFIPLIVSISSISSNLSNPNASSASAaaggilsavigVIVVAVIVSIVILVFIILSFLRF 93 
                                   556666555555552005555588888999999999999999887779******97776666677779999********** PP

                        DUF996  92 kksyellgkr.tgvklFetagllyfiGaiLtiv....lvGliilliaei 135
                                   ++ ++ l+++   v + +t+ +l+++GaiL+i+    ++G+i++++++i
  gi|70607799|ref|YP_256669.1|  94 RDGFSILQAIgRDVGIGKTGTTLILVGAILLIIpfldIIGIILIFVGQI 142
                                   **999998863467788999*************88777*********98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0012
                        DUF996  96 ellgkrtgvklFetagllyfiGaiLtivlvGliillia 133
                                   +++g++++++l +++g+l+ i  i +  ++G+i+ +++
  gi|70607799|ref|YP_256669.1| 149 YRIGEIYNNSLTKIGGILVAIPLIDITAFIGMIMTYVG 186
                                   578999****************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 1761.14
//
Query:       gi|70607800|ref|YP_256670.1|  [L=187]
Description: isochorismatase family protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-29  102.6   0.0    3.3e-29  102.3   0.0    1.1  1  Isochorismatase  Isochorismatase family


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0   1.8e-33   3.3e-29       1     165 [.      18     171 ..      18     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.8e-33
               Isochorismatase   1 talvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelvpe 81 
                                   ++lvv+D+q+ +v    +++ + ++++ ++++l++aar +g+p+++t  ++        +++ + +  +++  +  ++ +e
  gi|70607800|ref|YP_256670.1|  18 SVLVVWDVQDTLV----NSIFNKEEFIVKTKELIEAARSSGVPIVYTMITPY-------PERFQPKVNLRRILNPGDINKE 87 
                                   589**********....***********************************.......4444455555555566667777 PP

               Isochorismatase  82 laplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhdaalkr 162
                                   + p+egdv++ K+++s+f gt+++ +L+  g   iv++Giat+++Ve++ar+a  lG+ +v++++Av++ ++++h+ +l++
  gi|70607800|ref|YP_256670.1|  88 VYPKEGDVILRKNTPSIFVGTNFELMLRHGGYVAIVFTGIATEIGVETSARHAQALGFIPVIAKEAVSSADKQAHERSLAN 168
                                   77779**************************************************************************** PP

               Isochorismatase 163 lkq 165
                                   + +
  gi|70607800|ref|YP_256670.1| 169 MTK 171
                                   *84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1319.67
//
Query:       gi|70607801|ref|YP_256671.1|  [L=474]
Description: membrane transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-60  203.9  53.2    1.3e-58  198.6  46.7    2.0  2  MFS_1     Major Facilitator Superfamily
    1.7e-08   33.8  15.6    1.7e-08   33.8  15.6    2.7  3  Sugar_tr  Sugar (and other) transporter
    3.7e-05   22.3   9.8    3.7e-05   22.3   9.8    2.2  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6  46.7   2.2e-62   1.3e-58       2     352 ..      12     401 ..      11     402 .. 0.93
   2 !    9.5   0.4   6.9e-05      0.41     127     178 ..     420     466 ..     417     474 .] 0.78

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 2.2e-62
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   +l++++sa++ +i+++a+p ++a++l ++ s i +++ +y l+ av++  lGr++d +Gr r++ +g+l+f +g++l+   
  gi|70607801|ref|YP_256671.1|  12 VLGTLMSAIDTTIVLLAIP-TIAQELRADLSIIIWVIIIYLLVIAVFTTQLGRIGDIYGRSRLYNMGFLIFTIGSALCG-- 89 
                                   799****************.******************************************************55555.. PP

                         MFS_1  83 sslw.l.llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                   +sl  + l+++r++qGlga+++ ++++a+iad+fp+++rgra+g+ s+g+++Ga lg +lgg++++ +gWr++fyi+ +++
  gi|70607801|ref|YP_256671.1|  90 ASLSaVdLVAFRAIQGLGAAMMQANSGAIIADIFPPNKRGRAYGYTSIGWNAGATLGIVLGGFITTFIGWRYIFYINVPIG 170
                                   3333234************************************************************************** PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeee..........................................kgtgpaplvpaw 200
                                   +la++l+l ++ ++++++ +                                                 ++++++p+++ +
  gi|70607801|ref|YP_256671.1| 171 ILAILLGLRYIKTNERRKVKLDILGMAfllaslsliaygsadiagagvrslniylisggiillliffllERRQEFPIID-L 250
                                   ******99***9999999999888888****************************************************.* PP

                         MFS_1 201 kallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllal 281
                                   ka++ ++v+ + l+a++l ++g+ ++ + + +ylq  +gls  + a++ll  +++++ i+++++grlsdr+g+r++ +++l
  gi|70607801|ref|YP_256671.1| 251 KAFKGSRVFTYSLLASFLQTTGYLATAFIIIMYLQGIRGLS-PFDASVLLVPGYVLASIVSPFTGRLSDRIGARIPATIGL 330
                                   *********745555555556********************.8************************************** PP

                         MFS_1 282 lllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                   +l+++a+l+++ +++  +++ +++ ++v+ G+g++++fp+ +++++ +ap+   g asgl  t+ ++g++l+
  gi|70607801|ref|YP_256671.1| 331 GLMIIAVLIYLSIGLD-TPLYVVViASVIGGLGSSLFFPANNSAIMANAPRGFYGGASGLSRTLANIGTLLS 401
                                   ****************.555555525555666************************************9986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 6.9e-05
                         MFS_1 127 sagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                                    ++ +   ++g +++++l+   g  ++fy+  +++++a++l    l+ ++ +
  gi|70607801|ref|YP_256671.1| 420 EVFLGTTNLIGGVASSFLI---GLKSAFYVSIGILVVALIL--SALRGKEAR 466
                                   5667777899*********...****************887..555555444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8  15.6   2.8e-12   1.7e-08      48     188 ..      43     177 ..      15     180 .. 0.92
   2 ?   -2.1   0.0      0.22   1.3e+03     253     273 ..     256     276 ..     240     286 .. 0.75
   3 !    5.5  11.6    0.0011       6.7      60     189 ..     307     438 ..     293     457 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.8e-12
                                   HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                   + ++  i+l++ ++    +g +gd++GR   + ++ ++f ig++l++a+    s   l++ R + G+g+ + ++ +   i+
  gi|70607801|ref|YP_256671.1|  43 IIWVIIIYLLVIAVFTTQLGRIGDIYGRSRLYNMGFLIFTIGSALCGASL---SAVDLVAFRAIQGLGAAMMQANSGAIIA 120
                                   566777777777777778899*****************************...889999********************** PP

                                   TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    i p+++Rg+  +++  ++ +G  +++++g ++ ++ +   wr+ +++++ + +l ++l+
  gi|70607801|ref|YP_256671.1| 121 DIFPPNKRGRAYGYTSIGWNAGATLGIVLGGFITTFIG---WRYIFYINVPIGILAILLG 177
                                   ******************************99999999...************9999887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.22
                                   .HHHHHHHHHHHHHHTTHHHH CS
                      Sugar_tr 253 qrlligvvlqifqqltGinai 273
                                    r+++  +l++f q tG+ a 
  gi|70607801|ref|YP_256671.1| 256 SRVFTYSLLASFLQTTGYLAT 276
                                   488999999999999997654 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHH CS
                      Sugar_tr  60 iiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalv 140
                                    i s f+g l+dr+G +    i+  l++i+ ++   +  ++ ++v++++ v+ G+g  l+       i  +Ap    g   
  gi|70607801|ref|YP_256671.1| 307 SIVSPFTGRLSDRIGARIPATIGLGLMIIAVLIYLSIGLDTPLYVVVIASVIGGLGSSLFFPANNSAIMANAPRGFYGGAS 387
                                   455678999***********99999999999988888888***************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHTSS-..TTHHHHHHHCCHHHHHHHHHHGG CS
                      Sugar_tr 141 slyqlaitfGilvaaifglglnktsn..adgwrillglqlvpallllilll 189
                                   +l  +   +G l+++ + l ++ ++   ++ + ++lg + ++  + + +l+
  gi|70607801|ref|YP_256671.1| 388 GLSRTLANIGTLLSYAIVLSVASVTIprEVAFEVFLGTTNLIGGVASSFLI 438
                                   ********************9777666789999999988777777666665 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   9.8   6.2e-09   3.7e-05      50     241 ..      46     234 ..       7     244 .. 0.77
   2 ?    1.6   0.7     0.012        71      63     128 ..     311     374 ..     256     404 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.2e-09
                         MFS_3  50 vqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvge 130
                                   v +   L i +++   G + D++ r ++  ++ l+  ++s+l         ls + l+a+  + g+Gaa+++    A++ +
  gi|70607801|ref|YP_256671.1|  46 VIIIYLLVIAVFTTQLGRIGDIYGRSRLYNMGFLIFTIGSALCGA-----SLSAVDLVAFRAIQGLGAAMMQANSGAIIAD 121
                                   555556677778888899*******99999999998888876543.....35777899*********************** PP

                         MFS_3 131 lvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna.lsylalivallrwkrevrksslprEklleal.ra 209
                                   + + ++   A   +s+g+n   + G  lgG + +++G  + f +n+ +  la+++ l  +k + r +++  + l  a+  a
  gi|70607801|ref|YP_256671.1| 122 IFPPNKRGRAYGYTSIGWNAGATLGIVLGGFITTFIGWRYIFYINVpIGILAILLGLRYIKTNER-RKVKLDILGMAFlLA 201
                                   *********************************************85677777777777776654.556666666664257 PP

                         MFS_3 210 glRftaa.sreikavlvRaalFglsasavlaLL 241
                                   +l   a+ s +i  + vR+   +l +  ++ LL
  gi|70607801|ref|YP_256671.1| 202 SLSLIAYgSADIAGAGVRSLNIYLISGGIILLL 234
                                   777766547788888888888888777777666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.012
                         MFS_3  63 ilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspw.lllaltlligiGaalndPaWqAsv 128
                                    ++G l+D +  R    ++  l++++ vl+     +gl +p  ++++ +++ g+G++l  Pa + ++
  gi|70607801|ref|YP_256671.1| 311 PFTGRLSDRIGARIPATIGLGLMIIA-VLI--YLSIGLDTPLyVVVIASVIGGLGSSLFFPANNSAI 374
                                   45566777766666655555555543.333..33455555541455667778888888888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3111.05
//
Query:       gi|70607802|ref|YP_256672.1|  [L=63]
Description: hypothetical protein Saci_2085 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.004   16.4   2.0     0.0041   16.4   2.0    1.0  1  Fuseless         Fuseless
  ------ inclusion threshold ------
       0.26   11.3   3.0        0.3   11.2   3.0    1.0  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        1.6    8.0   4.4        1.6    8.0   4.4    1.0  1  DUF4220          Domain of unknown function (DUF4220)
        6.9    6.7   8.4        8.2    6.4   3.2    2.2  2  SecE             SecE/Sec61-gamma subunits of protein translo


Domain annotation for each model (and alignments):
>> Fuseless  Fuseless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.0   9.2e-07    0.0041     207     265 ..       3      61 ..       1      63 [] 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.2e-07
                      Fuseless 207 vslliGyvvvlllfllqaplrklskkltgrlllrlvledafllvsfigvvnvWrGlwnl 265
                                   v +li +++ + +++l+ pl+ ls+++ g+ ++ ++++ ++l+++ i  + v rG+ ++
  gi|70607802|ref|YP_256672.1|   3 VAVLITSIIAIFFIILSIPLNLLSSNTIGSSNTSIIMAATYLILASIIFLVVYRGINKM 61 
                                   7899***************************************************9765 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.0   6.6e-05       0.3      41      93 ..       3      60 ..       1      62 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.6e-05
               Phage_holin_3_6 41 gaagvlallalllllval.alala.a...lwlaalivaavllvlagvlalvglkklkk 93
                                  +a ++  ++a++++++ + + +l+     +    +i+aa +l+la +  lv ++ + k
  gi|70607802|ref|YP_256672.1|  3 VAVLITSIIAIFFIILSIpLNLLSsNtigSSNTSIIMAATYLILASIIFLVVYRGINK 60
                                  4444555555555555555455544467888889999********9999999886655 PP

>> DUF4220  Domain of unknown function (DUF4220)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.4   0.00036       1.6     235     287 ..       5      55 ..       1      61 [. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00036
                       DUF4220 235 llltalaalvlfvvllklskvss..sadekevntsnvDviiTyvllvgaillEll 287
                                    l+t+++a+ ++++++ l    +  s++++ ++ +++ ++ Ty++l+++i+l ++
  gi|70607802|ref|YP_256672.1|   5 VLITSIIAIFFIILSIPL----NllSSNTIGSSNTSIIMAATYLILASIIFLVVY 55 
                                   344433333333333332....244567889999999**************9665 PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.2    0.0018       8.2      25      41 ..       1      17 [.       1      25 [. 0.89
   2 ?    3.6   0.2     0.014        64      24      43 ..      34      53 ..      32      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                                  HHHHHHHHHHHHHHHHH CS
                          SecE 25 ttvvVlvfvvimglflf 41
                                  +tv+Vl++++i  +f+ 
  gi|70607802|ref|YP_256672.1|  1 MTVAVLITSIIAIFFII 17
                                  699********999985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                                  HHHHHHHHHHHHHHHHHHHH CS
                          SecE 24 kttvvVlvfvvimglflflv 43
                                  +t+++ +++ +i++ ++flv
  gi|70607802|ref|YP_256672.1| 34 NTSIIMAATYLILASIIFLV 53
                                  56777777778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 434.62
//
Query:       gi|70607803|ref|YP_256673.1|  [L=40]
Description: hypothetical protein Saci_2086 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.37   10.3   3.8       0.22   11.0   2.4    1.4  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   1.3e-05      0.22      15      30 ..       8      23 ..       5      28 .. 0.90
   2 ?   -3.3   0.0      0.36   6.4e+03      10      15 ..      29      34 ..      29      38 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.3e-05
                                  HHHHHHHHHHHHHHHH CS
               ATP1G1_PLM_MAT8 15 lgGLifAglLfivGil 30
                                  + GLif++ +f+vG++
  gi|70607803|ref|YP_256673.1|  8 ILGLIFGATAFMVGFM 23
                                  78************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.36
                                  HCCHHH CS
               ATP1G1_PLM_MAT8 10 yesLrl 15
                                  + s++l
  gi|70607803|ref|YP_256673.1| 29 WDSVKL 34
                                  777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 304.29
//
Query:       gi|70607804|ref|YP_256674.1|  [L=562]
Description: cytochrome b [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-56  189.5   3.0    4.4e-56  189.5   3.0    3.6  5  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    2.2e-23   83.1  10.9    2.2e-23   83.1  10.9    2.2  3  Cytochrome_B     Cytochrome b/b6/petB
    0.00081   19.6   1.9    0.00081   19.6   1.9    3.8  5  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3     0.082   4.9e+02      26      75 ..      34      83 ..      25      90 .. 0.82
   2 !  189.5   3.0   7.4e-60   4.4e-56       1     168 [.      91     288 ..      91     289 .. 0.90
   3 ?   -3.5   0.2       1.5   9.1e+03     106     155 ..     328     338 ..     317     348 .. 0.48
   4 ?    1.1   0.1      0.06   3.6e+02     107     161 ..     398     455 ..     393     468 .. 0.69
   5 ?   -4.0   0.1       2.2   1.3e+04     149     158 ..     508     517 ..     491     529 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.082
               Cytochrom_B_N_2 26 lnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwl 75
                                  +++++G ++      + ++G  L   +  + a + ++ ii+svP+ +  l
  gi|70607804|ref|YP_256674.1| 34 ISYWLGAMVAASFAYTIITGLFLLLYYQPAFAYQSTQTIINSVPYGSVLL 83
                                  67899999999999999999999999999999999999*****9944444 PP

  == domain 2  score: 189.5 bits;  conditional E-value: 7.4e-60
               Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvg.twlvellf 80 
                                   yimi l+y+Hm+r+f++GaYkkpRel+W++Gvlll ltl+++f+GysL++d+l+v+a+++g++++ ++++ g t +v +lf
  gi|70607804|ref|YP_256674.1|  91 YIMILLAYIHMFRNFYKGAYKKPRELQWVTGVLLLALTLGASFFGYSLVSDVLGVNAIDIGDQLLVGTGIPGaTAIVGWLF 171
                                   79**********************************************************************99******* PP

               Cytochrom_B_N_2  81 G.........gelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknvvg...........eplvpvna 141
                                   G         ++l++++l++rl+++Hi ++++ll++l+++h++l e++g+tp + +ek++v            +p++p+n+
  gi|70607804|ref|YP_256674.1| 172 GpggsaalssNPLVRSELFDRLLGWHI-IMVFLLGVLFLFHFMLSERYGMTPAT-REKPKVPsyytkeeqekfNPWWPRNF 250
                                   ***************************.************************76.444333334455555556******** PP

               Cytochrom_B_N_2 142 vkmlllflvl..valli.........alalinPvpllg 168
                                   v+ml+++l++  ++l++         ++++inP+p+++
  gi|70607804|ref|YP_256674.1| 251 VYMLSIVLITwgIILFVpnllaningLPIVINPYPAPQ 288
                                   ***97777665699999999988888888****99876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.5
               Cytochrom_B_N_2 106 lalivahlllvekkgqtpsrrkeknvvgeplvpvnavkmlllflvlvall 155
                                   +al+v+                                        +++l
  gi|70607804|ref|YP_256674.1| 328 IALLVV---------------------------------------GLVIL 338
                                   222222.......................................22222 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.06
               Cytochrom_B_N_2 107 alivahlllv..ekkgqtpsr.rkeknvvgeplvpvnavkmlllflvlvallialali 161
                                   ++i++ ++l+  e+k++t s+ ++++ v + ++ p  ++   +++l+++a l  ++++
  gi|70607804|ref|YP_256674.1| 398 VIIGIIVYLWptERKTKTVSTtATDSRVIKMNITPMEILLGAVGTLSFAATLFNFIQF 455
                                   5556666666557777777766889999999999999998888888776555544433 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 2.2
               Cytochrom_B_N_2 149 lvlvallial 158
                                    +++ +++ l
  gi|70607804|ref|YP_256674.1| 508 GIIALFVVSL 517
                                   3332222222 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1  10.9   3.6e-27   2.2e-23      11     183 ..      33     213 ..      26     219 .. 0.84
   2 ?   -3.0   0.7      0.93   5.5e+03      91     116 ..     353     377 ..     322     380 .. 0.49
   3 ?   -4.0   0.2       1.8   1.1e+04      97     115 ..     504     521 ..     496     529 .. 0.54

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.6e-27
                  Cytochrome_B  11 siiynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglk 91 
                                   +i y lG+++   ++  i+tG++l +yy+p +  a+ s q i++ v +G ++   h +g+ +++ll y+h+fr ++ g++k
  gi|70607804|ref|YP_256674.1|  33 NISYWLGAMVAASFAYTIITGLFLLLYYQPAF--AYQSTQTIINSVPYGSVLLFSHLYGSYIMILLAYIHMFRNFYKGAYK 111
                                   67899************************976..899******************************************** PP

                  Cytochrome_B  92 ktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGs.tlvellwg...svsvddatLtr...... 162
                                   k+rel Wv+Gv+ll l++  +f Gy+L+ d ++  a+ +  +ll    + G  ++v +l+g   s+++++  L r      
  gi|70607804|ref|YP_256674.1| 112 KPRELQWVTGVLLLALTLGASFFGYSLVSDVLGVNAIDIGDQLLVGTGIPGAtAIVGWLFGpggSAALSSNPLVRselfdr 192
                                   *******************************************9999998862699***8544367777776665111111 PP

                  Cytochrome_B 163 ffslhfllPflllillllhll 183
                                   +   h+++ fll +l l h++
  gi|70607804|ref|YP_256674.1| 193 LLGWHIIMVFLLGVLFLFHFM 213
                                   555666666666666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.93
                  Cytochrome_B  91 kktrelvWviGvillllvivtafiGy 116
                                   ++++  +W++   l++ ++  ++ Gy
  gi|70607804|ref|YP_256674.1| 353 TRRKFWTWIM-TTLAVYLVELSVWGY 377
                                   2233334433.345566666666666 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.8
                  Cytochrome_B  97 vWviGvillllvivtafiG 115
                                   + + G+i +l+v++  ++G
  gi|70607804|ref|YP_256674.1| 504 IAFFGII-ALFVVSLVLLG 521
                                   4455543.44444444444 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.4   8.6e+03      48      50 ..      99     101 ..      59     136 .. 0.50
   2 ?   -2.3   0.0      0.89   5.3e+03      68      87 ..     204     223 ..     190     232 .. 0.59
   3 !   19.6   1.9   1.4e-07   0.00081      12      96 ..     300     389 ..     290     394 .. 0.82
   4 ?   -2.9   0.1       1.5   8.7e+03      49      87 ..     407     445 ..     398     459 .. 0.56
   5 !    4.7   0.2    0.0059        35      30      54 ..     505     529 ..     469     555 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                   HHH CS
                 Cytochrom_B_C  48 pwl 50 
                                     +
  gi|70607804|ref|YP_256674.1|  99 IHM 101
                                   222 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHHHHHHHTS-S CS
                 Cytochrom_B_C  68 llallvvsfvvLgylGvqpp 87 
                                   l +l++++f++   +G++p+
  gi|70607804|ref|YP_256674.1| 204 LGVLFLFHFMLSERYGMTPA 223
                                   23345555555555565555 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.4e-07
                                   ---GGGHHHHHHHHCS......SSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS- CS
                 Cytochrom_B_C  12 aPeWYflpfYaiLrai......pakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqp 86 
                                   +P W+fl+ ++++  +         +l + ++++ +vil+llp+ld s+   ++ r ++ ++++++l+v +v L + G  +
  gi|70607804|ref|YP_256674.1| 300 YPPWFFLFLFKLVDFLlpngipITPILTIALLVVGLVILMLLPFLDPSDSLYVTRR-KFWTWIMTTLAVYLVELSVWGYLE 379
                                   699********999974444433788888889999**************9999988.888999999999999999999987 PP

                                   SSCCHHHHHH CS
                 Cytochrom_B_C  87 peevavllsq 96 
                                   p  +  + +q
  gi|70607804|ref|YP_256674.1| 380 PGVPEPTSAQ 389
                                   7666555555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.5
                                   HH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-S CS
                 Cytochrom_B_C  49 wldrskvksiryrkplakvllallvvsfvvLgylGvqpp 87 
                                   w  ++k+k ++   + ++v+ + +    ++Lg +G+ + 
  gi|70607804|ref|YP_256674.1| 407 WPTERKTKTVSTTATDSRVIKMNITPMEILLGAVGTLSF 445
                                   445555555555555555666666666677777777544 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0059
                                   HHHHHHHHHHHHHGGGCHHHH---S CS
                 Cytochrom_B_C  30 kllGvvamgaaivilfllpwldrsk 54 
                                    ++G++a+++  ++l+ l w   s 
  gi|70607804|ref|YP_256674.1| 505 AFFGIIALFVVSLVLLGLMWTLPSV 529
                                   3455555555555555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3877.20
//
Query:       gi|70607805|ref|YP_256675.1|  [L=508]
Description: cytochrome c and quinol oxidase polypeptide I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-72  244.5  64.5    2.4e-72  244.2  64.5    1.1  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.2  64.5   1.3e-76   2.4e-72       2     428 ..      10     447 ..       9     451 .. 0.88

  Alignments for each domain:
  == domain 1  score: 244.2 bits;  conditional E-value: 1.3e-76
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT-H.....HCHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHCTSS-S-H CS
                          COX1   2 igllylilalvlllvggllgllirlqlafpdl.....etynqlrtlHgnlmiflfatpf.ilgfgnylvplllgardlafp 76 
                                   +++ly+i ++++l v g++++ +r+ l++ ++     e y+ ++t+Hg++++++f+ ++ ++++g+ l++  l    + ++
  gi|70607805|ref|YP_256675.1|  10 VVWLYTIGSIFWLGVLGIAAMNLRTFLTYDQNspnvgELYYSALTIHGWAAMIAFVPMAaAAVIGFSLYKSKL---SIIHT 87 
                                   789************************9852233557****************99998866667777777766...77888 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCSS-STTTTTTTC...............SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          COX1  77 rlnalsfwlvvlgvvllllsllgaattgwteYapls..............evdlwllglllvvvssllgainfivtilkrr 143
                                   + +a+ fw   l+ vll ++++g++++gw++Y+pl+               ++l+ +++l++ ++++l  + f++ i+   
  gi|70607805|ref|YP_256675.1|  88 KQMAIFFW---LSNVLLGIAMAGSPDMGWYMYPPLAiesnsqfhaflfytTPQLMGMAYLVMSIAVILQTAAFVTLIADAY 165
                                   8999****...55555555555669***********************996666666666666667777777777777777 PP

                                   HHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SS..SCE-HHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                          COX1 144 apgmtvaklplfvwavlatailillalpvlalalllllldrslgkff..spgdplldqhlfWffgHpeVyililpalgivy 222
                                   a +++ ++l++f+ + +a++i+i+++lp+la+a+l+ +l      ff   p+++ll+++lfWf+gHp+Vy++ +p +g++y
  gi|70607805|ref|YP_256675.1| 166 ATKPKGERLNIFAAYGVAFSIVIAVTLPALAAATLWYTL-----YFFanVPVNNLLWAILFWFYGHPVVYYVPFPLFGALY 241
                                   7777889**************************999553.....3564344****************************** PP

                                   HHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCC.TTS-CHC.H CS
                          COX1 223 yilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatl.wrgsirf.k 301
                                   y++p++agr l+s+k++++++ l++++ + vw+HHl t++lp +l+ +  + +l++a  sgl+v+n+ +t+  + + ++ +
  gi|70607805|ref|YP_256675.1| 242 YYIPQYAGRSLYSEKWARWNIYLLAIGTMGVWVHHLQTWPLPIVLREWVNLSTLILATGSGLTVLNLGLTIfTSRKYDWkD 322
                                   ***********************************************************************6566677955 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH.SB--...HHHHHHH CS
                          COX1 302 tpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpklt.grml...serlakl 378
                                    + + +l++++ fi++G+++++l  +s+n ++hn+y+vv+HfHl++++ +++++ ++++ +l   + g  +   s +++++
  gi|70607805|ref|YP_256675.1| 323 PVGMGALISLIGFILAGAQALVLPENSINPLFHNSYYVVGHFHLMIWTLIIMGYTTVFLDMLRTSFaGFNFsatSSKWMRI 403
                                   5668899999999*************************************************9999885443449999*** PP

                                   HHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHH CS
                          COX1 379 hfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrti 428
                                    ++++++ ++ + ++m ++G+lg+ rr+ +y +       +qp+n++ ++
  gi|70607805|ref|YP_256675.1| 404 GMIWWTAPFMGVGYAMSVAGYLGFLRRMIAY-P-----VIFQPYNLVESF 447
                                   *******************************.3.....589***999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3244.62
//
Query:       gi|70607806|ref|YP_256676.1|  [L=168]
Description: quinol oxidase polypeptide II [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1181.51
//
Query:       gi|70607807|ref|YP_256677.1|  [L=328]
Description: hypothetical protein Saci_2090 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-08   33.8   0.1      9e-08   32.0   0.1    1.9  1  Rieske    Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.23   11.6   0.0    1.2  1  DUF2275   Predicted integral membrane protein (DUF2275)


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1     1e-11     9e-08      32      86 ..     160     254 ..     137     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1e-11
                                   T...........TS-EEEEESC-TTTT-BC..........................GG.SEEETT.EEE-TTT--EEE..T CS
                        Rieske  32 e...........dgevyAlsdvCtHrgapl..........................se.gkidekgvleCpcHgwayd..a 72 
                                               +++++A+s +C+H+g+ +                          +   + +  g ++C cHg++yd  +
  gi|70607807|ref|YP_256677.1| 160 GvtysfpggvgpNKSIVAYSAICQHLGCAPpeihfyppkymkvglptpnylpgvalQAaQQANAPGIIHCDCHGSSYDpyH 240
                                   244444555556899**************9999******************999984445556789************988 PP

                                   TSBEEE-TTHHHEE CS
                        Rieske  73 dGkvikgPaprpla 86 
                                    ++v++gP+ rpl+
  gi|70607807|ref|YP_256677.1| 241 GASVLTGPTVRPLP 254
                                   99999******987 PP

>> DUF2275  Predicted integral membrane protein (DUF2275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.5e-05      0.23      32      95 ..      62     129 ..      60     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                       DUF2275  32 rlkrklalaglivlilAavgfgvvsy.....atiskmdvvrvlkkaglslkaeevqkkvkgldeegLga 95 
                                   r + k  l+g++v+++A+++ ++vsy       +++   + +    g ++ka++++ + + ++   +++
  gi|70607807|ref|YP_256677.1|  62 RAFLKAVLIGIGVAAVASAV-PIVSYlnqpeISLNTFPWIIIVDSSGNPIKASQLKVNNPEILIFQYPM 129
                                   56678889***********9.********9999999999**************9655555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2233.64
//
Query:       gi|70607808|ref|YP_256678.1|  [L=162]
Description: hypothetical protein Saci_2091 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.4   11.3   0.4        0.4   11.3   0.4    2.2  2  OAD_gamma  Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       0.3   5.3e+03      16      28 ..     109     121 ..     105     124 .. 0.63
   2 ?   11.3   0.4   2.2e-05       0.4       6      29 ..     136     159 ..     134     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.3
                     OAD_gamma  16 vvLilLslvislf 28 
                                    +L +Ls+++ +f
  gi|70607808|ref|YP_256678.1| 109 SFLNVLSILFAAF 121
                                   5666777776655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.2e-05
                     OAD_gamma   6 ltllGmgvVFvvLilLslvislfs 29 
                                   l+ +Gmg+VF+v++    +i++++
  gi|70607808|ref|YP_256678.1| 136 LMQMGMGFVFAVITASGCLIYAIK 159
                                   799*********998777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1177.46
//
Query:       gi|70607809|ref|YP_256679.1|  [L=136]
Description: hypothetical protein Saci_2092 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        6.2    6.9  10.4       0.76    9.8   6.0    1.7  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.43   7.7e+03      41      42 ..      27      28 ..      15      39 .. 0.51
   2 ?    9.8   6.0   4.3e-05      0.76      31      88 ..      50     108 ..      47     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.43
               Phage_holin_3_6 41 ga 42
                                  ++
  gi|70607809|ref|YP_256679.1| 27 LL 28
                                  11 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4.3e-05
               Phage_holin_3_6  31 kragsgagllgaagvlallalllllvalalala.alwlaalivaavllvlagvlalvgl 88 
                                   + a+++ g ++ a++++++++++l  a+  ++  ++ l+ l +  + +++ag la+ g+
  gi|70607809|ref|YP_256679.1|  50 SEALILSGHIIFAMLVGFFGVAILAQAIREGIRnIYILSILNMIFIGIAAAGGLAFYGI 108
                                   578899999*******************9999877999999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1029.04
//
Query:       gi|70607810|ref|YP_256680.1|  [L=168]
Description: hypothetical protein Saci_2093 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.035   14.3   0.8      0.096   12.9   0.8    1.8  1  DUF3930          Protein of unknown function (DUF3930)
       0.11   12.5   0.0       0.39   10.8   0.0    1.8  2  FliMN_C          Type III flagellar switch regulator (C-ring)
        3.2    7.9   5.4        1.2    9.2   0.5    2.2  2  TssO             Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> DUF3930  Protein of unknown function (DUF3930)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   1.6e-05     0.096      11      45 ..      40      79 ..      31      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                       DUF3930 11 keefvhedkW..adsvi...kGliifltivGiPytayifi 45
                                  ke+fv   k+    svi    G+iif  i  iPy   +fi
  gi|70607810|ref|YP_256680.1| 40 KEQFVRIGKFflISSVItivTGIIIFAYIYLIPYNGNLFI 79
                                  888888888744467763337***************9999 PP

>> FliMN_C  Type III flagellar switch regulator (C-ring) FliN C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.37   2.2e+03      16      30 ..      87     101 ..      80     103 .. 0.76
   2 ?   10.8   0.0   6.4e-05      0.39      20      37 ..     117     134 ..     114     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.37
                                   EEEEEHHHHHHHHTT CS
                       FliMN_C  16 rtrltlrellnLkvG 30 
                                   + ++ +r +lnL  G
  gi|70607810|ref|YP_256680.1|  87 SLNIRIRAFLNLVGG 101
                                   568999999999766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.4e-05
                                   EHHHHHHHHTTSEEE--T CS
                       FliMN_C  20 tlrellnLkvGdvipLdk 37 
                                    +r+l+nL++Gdv+ L+ 
  gi|70607810|ref|YP_256680.1| 117 RIRQLMNLREGDVVGLEI 134
                                   59************9975 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5   0.00021       1.2       3      40 ..      39      76 ..      38      91 .. 0.90
   2 ?    0.8   0.5      0.08   4.8e+02       3      26 ..     134     157 ..     132     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00021
                          TssO  3 kkErrsgflyflllFlvtvlllflivffffkssplqek 40
                                  +kE++  + +f+l+ +v++++ ++i+f + + +p++ +
  gi|70607810|ref|YP_256680.1| 39 EKEQFVRIGKFFLISSVITIVTGIIIFAYIYLIPYNGN 76
                                  599999*********************99998888765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.08
                          TssO   3 kkErrsgflyflllFlvtvlllfl 26 
                                   ++  +s   +f ++Fl++++ +++
  gi|70607810|ref|YP_256680.1| 134 IRNSISTLSKFNIVFLLLSISMMI 157
                                   566778888999999988887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1167.76
//
Query:       gi|70607811|ref|YP_256681.1|  [L=394]
Description: manganese transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-39  134.5  21.2    5.9e-39  134.1  21.2    1.2  1  Nramp     Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.03   14.3   0.0    1.5  1  PfaD_N    Fatty acid synthase subunit PfaD N-terminal domain


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1  21.2   6.6e-43   5.9e-39       4     357 ..      29     371 ..      26     372 .. 0.87

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 6.6e-43
                         Nramp   4 dlqaGaqfGykLlwvlllstllaillqelsarLGlv.TgkglaelirerlpkkvsillwilaelaiiatdlaeviGaAial 83 
                                    ++ G+++Gy L+++ll+ tl ++++qe + r G v  gkgl  l+re++++k+++ ++i ++l+ ++t + e +G+A++ 
  gi|70607811|ref|YP_256681.1|  29 GVADGQTYGYRLIILLLVLTLPLYIVQEAAGRVGAVnNGKGLGTLLREKFSQKFALTAAIPMFLVDLFTYVVEYVGIAVGS 109
                                   5677******************************99459*****************************************7 PP

                         Nramp  84 nllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvkpdwgevlkglvvPslpgkeslllav 164
                                    ++ g+p++++ +++ v+ l +++  ++ y+k+E+ ++++ ++++++Fi+++fl  ++ ++ l      s ++ ++l+ ++
  gi|70607811|ref|YP_256681.1| 110 LMI-GVPVYISLPLFFVIHLSIVL--TRTYEKMEKTLLGISFFLVIAFIVQAFLRGVSPNQQLLY---FSASK-SFLFFLA 183
                                   666.6*******************..*********************************998776...45666.99***** PP

                         Nramp 165 gilGatvmphnlflhsslvqerkitidrsekeealkyeriDtiialivaflinlailivaAavlysggkdvesledaaeaL 245
                                   + +Ga+vmp ++f+++s ++ + ++  + +k+ ++k ++++t+i+++v+ l ++ai i +         d  + +++  aL
  gi|70607811|ref|YP_256681.1| 184 ANIGAVVMPFMIFYQASATAYKYNNS-ALSKDVKVKWSSMETFIGALVSELLMVAIEISTTGLSS--SIDPLNYREMSYAL 261
                                   ***********************665.4444469**********************998876655..555689******** PP

                         Nramp 246 epllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralafvpalivilligaele..lvkllv 324
                                   + + G  ++ ++F+igL+  Gl+++i+ +l +++ + ++l+ ++  +   l   +++ vpa+i++ +++++    ++++l 
  gi|70607811|ref|YP_256681.1| 262 SAISGI-YSPYVFGIGLICGGLLALIVESLGSAWGTLEALNKHNHRNTTLL--YVFESVPAIIIASIFSQNYDqiVNTVLS 339
                                   *****5.*********************************98888855554..469999***9999999999942223333 PP

                         Nramp 325 lsqvllslllPfaliplllltsskklMGefkns 357
                                   l+  ++ +++ + ++++ ll+ ++k+MG++  s
  gi|70607811|ref|YP_256681.1| 340 LMS-VTPIIVFIPAFFVGLLVGDEKIMGKYSYS 371
                                   332.33333334456778999********9866 PP

>> PfaD_N  Fatty acid synthase subunit PfaD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-06      0.03      19      42 ..      44      68 ..      42      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-06
                                  HT-TTS-EEEEE.TTTCEEEES--B CS
                        PfaD_N 19 LldldkpcYiVr.seggiGvtnegy 42
                                  Ll l  p+YiV+ ++g++G++n+g+
  gi|70607811|ref|YP_256681.1| 44 LLVLTLPLYIVQeAAGRVGAVNNGK 68
                                  78999*****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2594.48
//
Query:       gi|70607812|ref|YP_256682.1|  [L=457]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-51  173.6  22.4    8.1e-51  173.3  22.4    1.0  1  Sugar_tr  Sugar (and other) transporter
    1.8e-22   79.7  35.5    1.8e-22   79.7  35.5    1.9  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
          1    8.8   5.7       0.24   10.9   0.5    2.5  3  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.3  22.4   1.4e-54   8.1e-51       5     448 ..      24     448 ..      20     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 1.4e-54
                                   HHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                      Sugar_tr   5 aalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavl 85 
                                   + +g +  gYd+  ig +l        fg ++++ ++    ++++li++++l G+++G++++g+l+++ GRk  + + +++
  gi|70607812|ref|YP_256682.1|  24 TGMGVFTDGYDLSSIGIVLLTVL--QTFGITRANPDYS---LYVSLITGSALMGSAVGAILFGFLSNK-GRKTFYGVDVAI 98 
                                   55677999********9876655..7889988886443...7**********************9997.************ PP

                                   HHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHH.HHHHHHHHHHHHHHHHHHHHTSS CS
                      Sugar_tr  86 fvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvsl.yqlaitfGilvaaifglglnkts 165
                                   + iga+lqa+        +li+ R+++G+g+G+ +vl+Pm ++E + ++ Rg++  l + l++ fG   +a ++lgl+ ++
  gi|70607812|ref|YP_256682.1|  99 LTIGAILQALVV---DPVQLIIVRFILGLGIGADYVLSPMIMAEHSNARDRGKMLALgFGLFWGFGATTSALLYLGLSSMG 176
                                   ************...99**********************************766554399*****************7776 PP

                                   -..TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH.HHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HT CS
                      Sugar_tr 166 n..adgwrillglqlvpallllilllflPESPryl.vekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswk 243
                                      +  w++ l+  ++pa  +++l+  +PE+ ryl  +kg+ ee   v++ + ge+ +       k+s++ +       + 
  gi|70607812|ref|YP_256682.1| 177 LspQLLWKVVLAAGAIPAASVIYLRRKIPETARYLgRIKGDLEELNSVIKSVTGETYPVNTDLRDKNSFRFY-------LT 250
                                   66999**********************************************888877777777777777777.......77 PP

                                   THHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHH CS
                      Sugar_tr 244 ellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGa 324
                                   +++++      +l ++vl+++   + ++ +++ ++ i ++lg++  + + +i g   +   +va++lvdr+GR+++  +G+
  gi|70607812|ref|YP_256682.1| 251 KFWRQ------FLAACVLWFLFDIVAYAGNLFGPSLIASSLGINSGVFQIMIEGLFVIPGGIVALMLVDRIGRKPMQTIGF 325
                                   88888......9999*******************************99999999999999********************* PP

                                   HHHHHHHHHHH...HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHH..HHHHHSHTTTHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 325 agmaicfvilg.ivalllvakskaasivaivfialfialfalgwgpvpwv..lvsElfpqsvRskalaiavavnwlanfli 402
                                   +gma++++ ++ +  ++l+ +     iva   + l  ++ ++g+g+v +v  l  El+p+++R+++++++va+  +   l+
  gi|70607812|ref|YP_256682.1| 326 FGMALALLGFSlYKSFALSFS----PIVAFLIYGLNNFASQAGPGSVSAVgiLGVELAPTKIRGFVQSLTVASGRIGAALT 402
                                   *******99995555555555....566666666778899999999866522789************************** PP

                                   HHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCC CS
                      Sugar_tr 403 sllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleei 448
                                   +++fp ++  +g+++   +  ++a++++i++++ +petkg++lee 
  gi|70607812|ref|YP_256682.1| 403 AFVFPSLFTEYGEAFAIGFLSAVAIVSAIVTLISIPETKGKSLEET 448
                                   ************999999**************************96 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7  35.5     3e-26   1.8e-22       3     352 ..      26     402 ..      24     403 .. 0.78
   2 !    7.8   4.3   0.00022       1.3     102     175 ..     367     438 ..     360     452 .. 0.66

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3e-26
                         MFS_1   3 laaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                   +++f  +++ s +g++l  ++ +++gi+ +       ++l+++    g+av+++++G+ls++ Gr+ ++ + ++++ +g +
  gi|70607812|ref|YP_256682.1|  26 MGVFTDGYDLSSIGIVLL-TVLQTFGITRANpdyslyVSLITGSALMGSAVGAILFGFLSNK-GRKTFYGVDVAILTIG-A 103
                                   678889999999999999.999****888888877778888888888***************.****************.5 PP

                         MFS_1  78 lll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigl.lsagfslGailgpllggllasslg...... 149
                                   +l  +    +  l+++r++ Glg ga + ++  ++a+ ++ ++rg++++l +++++++Ga   +ll   l+ s g      
  gi|70607812|ref|YP_256682.1| 104 ILQaL-VVDPvQLIIVRFILGLGIGADYVLSPMIMAEHSNARDRGKMLALgFGLFWGFGATTSALLYLGLS-SMGlspqll 182
                                   55534.446667************************************98345599999999988888777.445589999 PP

                         MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeee...............kgtgpaplvpawkallkdpvl...... 209
                                   W +v  + ai ++ +     ++l+++ pe +r  ++ ++                       v+  + l+ ++ +      
  gi|70607812|ref|YP_256682.1| 183 WKVVLAAGAIPAASV-----IYLRRKIPETARYLGRIKGdleelnsviksvtgeT-----YPVN--TDLRDKNSFrfyltk 251
                                   **9999999999998.....44444444444444444433466777776444331.....2222..455555544444444 PP

                         MFS_1 210 .willialllfffgfsg....lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalllll 285
                                    w  ++a+++ +f f +       + p+++ + lg++   ++++ +++ +l++++++++a  l+dr+gr+++ ++++++++
  gi|70607812|ref|YP_256682.1| 252 fWRQFLAACVLWFLFDIvayaGNLFGPSLIASSLGIN---SGVFQIMIEGLFVIPGGIVALMLVDRIGRKPMQTIGFFGMA 329
                                   4855555555556777622335555555566666666...8888999********************************** PP

                         MFS_1 286 laalglallavtssavllllvlvliGf.glgfv.....fpsllalasdlappeeagtasglfntagslggalg 352
                                   la+lg+ l   +  ++  +++++++G+  ++       ++++  l ++lap++ +g++++l+   g +g+al 
  gi|70607812|ref|YP_256682.1| 330 LALLGFSLYKSFALSFSPIVAFLIYGLnNFASQagpgsVSAVGILGVELAPTKIRGFVQSLTVASGRIGAALT 402
                                   ************************888554444777779******************************9985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00022
                         MFS_1 102 lfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                   +++a+++l ++++p + rg++ +l  a+  +Ga+l++ + + l + +g   +  +l +v+++++++   l+  +
  gi|70607812|ref|YP_256682.1| 367 SVSAVGILGVELAPTKIRGFVQSLTVASGRIGAALTAFVFPSLFTEYGEAFAIGFLSAVAIVSAIV--TLISIP 438
                                   5667777888999********************999777777776666333444444444444333..333333 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       0.2   1.2e+03      93     131 ..      40      79 ..      26     110 .. 0.63
   2 ?   10.9   0.5     4e-05      0.24     113     200 ..     116     203 ..      97     207 .. 0.92
   3 ?   -3.3   0.0      0.87   5.2e+03      88     103 ..     421     436 ..     418     443 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.2
                       DUF1129  93 allfgilalfskkkqtasiGl.itlllvalvgGlamvlvy 131
                                    +l  +l+ f+   ++ + +l ++l++ ++++G a   + 
  gi|70607812|ref|YP_256682.1|  40 IVLLTVLQTFGITRANPDYSLyVSLITGSALMGSAVGAIL 79 
                                   4566666666666555553332667777777777665544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4e-05
                       DUF1129 113 litlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNpvLpplvliiigviafvv 193
                                   +i+ ++++l  G+ +vl   ++ ++ +  +r +++   + l+  + + + + + ++l    + p+L + v ++ g+i  ++
  gi|70607812|ref|YP_256682.1| 116 IIVRFILGLGIGADYVLSPMIMAEHSNARDRGKMLALGFGLFWGFGATTSALLYLGLSSMGLSPQLLWKVVLAAGAIPAAS 196
                                   788899******************9************************9999****99********************** PP

                       DUF1129 194 ryylkkk 200
                                    +yl++k
  gi|70607812|ref|YP_256682.1| 197 VIYLRRK 203
                                   ******9 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.87
                       DUF1129  88 llalfallfgilalfs 103
                                   +l+ +a++++i++l+s
  gi|70607812|ref|YP_256682.1| 421 FLSAVAIVSAIVTLIS 436
                                   7788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3018.32
//
Query:       gi|70607813|ref|YP_256683.1|  [L=134]
Description: sulfocyanin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.4e-59  198.2   8.7      5e-59  198.0   8.7    1.0  1  SoxE         Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.24   11.7   0.0    1.5  1  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.0   8.7   5.6e-63     5e-59      16     148 ..       2     131 ..       1     132 [. 0.97

  Alignments for each domain:
  == domain 1  score: 198.0 bits;  conditional E-value: 5.6e-63
                          SoxE  16 fiylvvsssasnlfnfnGtsnGqlkiyiPagwsvlvklvneeslphnlvlvqnntaiPnsleissdGkillivGattsnya 96 
                                   fiylvv+ s+    n+nGtsnGq++iy+Pagw+vlvkl+n++slphn+++v+nnt  Pn+l+is+dGki+l+vGa++++y+
  gi|70607813|ref|YP_256683.1|   2 FIYLVVQGSSL---NYNGTSNGQMRIYVPAGWNVLVKLTNPQSLPHNALIVLNNTVKPNNLNISADGKIMLYVGANATDYY 79 
                                   99999998765...******************************************************************* PP

                          SoxE  97 vsGissGqsasGlledlsaGtywlacgilGhaesGmWvdlivssnvtvPyai 148
                                    +Gi +Gqsa+G+l +++aG+yw+acgi  haesGmWv+l++s++vtvPyai
  gi|70607813|ref|YP_256683.1|  80 GNGIYGGQSAVGVLPNIPAGYYWIACGIYSHAESGMWVVLVASNSVTVPYAI 131
                                   **************************************************98 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.24      21      62 ..      17      57 ..       8      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                   NPCBM_assoc 21 atnvslslslPeGWtvvevspasaaslapGetveatvkVtpp 62
                                  ++n+++++ +P+GW+ v v+ ++ +sl+ ++    + +V+p+
  gi|70607813|ref|YP_256683.1| 17 TSNGQMRIYVPAGWN-VLVKLTNPQSLPHNALIVLNNTVKPN 57
                                  6899***********.77777777788888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1078.25
//
Query:       gi|70607814|ref|YP_256684.1|  [L=361]
Description: hypothetical protein Saci_2097 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-20   73.9  42.8    1.5e-15   57.0  19.3    2.0  2  MFS_1       Major Facilitator Superfamily
     0.0044   15.9  18.6       0.46    9.3   6.9    3.6  2  MFS_1_like  MFS_1 like family
     0.0073   14.7   0.5     0.0073   14.7   0.5    1.6  2  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
      0.051   13.7   2.8       0.54   10.4   0.3    2.7  2  DUF3325     Protein of unknown function (DUF3325)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9  15.5   7.5e-09   3.4e-05       3     180 ..      11     171 ..       9     181 .. 0.85
   2 !   57.0  19.3   3.3e-19   1.5e-15       6     174 ..     190     358 ..     186     361 .] 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.5e-09
                         MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                   ++  + ++++++ +++++ ++  +lg+sp +ig ll++  +  a+ sl l++l+d +Gr+++ +++  ++ l+ +++lf  
  gi|70607814|ref|YP_256684.1|  11 ISSSIFGISMGANTIIMS-LYLLSLGLSPLTIGELLSGSIIIGALISLTLSFLGDMYGRKKFSIISRGISTLS-IFFLF-L 88 
                                   666677778888888888.45589*************************************************.55555.4 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   +++  l+  + q++g+g+l+ + +a  ++ f      r +g+ ++ + l ++ g l+  +l+    +  + +i  +v l++
  gi|70607814|ref|YP_256684.1|  89 GYP--LAYLFYQSWGSGSLIMSLLAEKSESF-----QRLLGVRQSLSILLSVAGSLFPLVLT----YKEILLIEVVVNLIS 158
                                   555..99********8666655555555555.....56************************....*************** PP

                         MFS_1 165 fvlfllllpeepperk 180
                                   ++   ll+p++++ ++
  gi|70607814|ref|YP_256684.1| 159 LL---LLIPVKESYKG 171
                                   88...89999988776 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 3.3e-19
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr..vlllglllfalglllllfass 84 
                                   +l++l++++++p+++l+ +  +g++ s+++ ++++  l+ a+++++   +++++G  +  v+l + ++ +l+ ll+ f s+
  gi|70607814|ref|YP_256684.1| 190 ALIGLGAGLVIPLMSLWFNLRFGVTSSQMSPVFAIAELTLAFSTYFSVIIAEKIGGVKtiVYLHATAIALLF-LLP-F-SP 267
                                   68999*************************************************855524444444444444.444.5.66 PP

                         MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   ++ +  +  v   + + +  p+ +a++ +++p++ergra+g++++++s+  ++gp +gg+    +++ ++f+i + ++ la
  gi|70607814|ref|YP_256684.1| 268 SFiIGSIIFVTRNALMNMTSPVFQAMVLKLVPENERGRANGIVNLMSSIPRAFGPSIGGFYFNIGNYVLPFIITGSLYSLA 348
                                   67688888888888889*********************************************9999*************** PP

                         MFS_1 165 fvlfllllpe 174
                                    vlf+l+++ 
  gi|70607814|ref|YP_256684.1| 349 TVLFFLFFRN 358
                                   **99999864 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   3.8   0.00013      0.59      22      81 ..      27      87 ..      15     179 .. 0.87
   2 !    9.3   6.9    0.0001      0.46      16     172 ..     197     332 ..     194     356 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00013
                    MFS_1_like 22 ltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkk.vvilslllsavlfls 81
                                  +++yl s gl++  ig +++   ++  l ++ +++l D +g++k  +++ ++    ++fl 
  gi|70607814|ref|YP_256684.1| 27 MSLYLLSLGLSPLTIGELLSGSIIIGALISLTLSFLGDMYGRKKFsIISRGISTLSIFFLF 87
                                  789*************************************998853555555555566553 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0001
                    MFS_1_like  16 gsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqees 95 
                                   g ++P ++++++   g++ s+   + +i+ lt  +s  +   +a+++g+ k++v l + + a+lfl    +p         
  gi|70607814|ref|YP_256684.1| 197 GLVIPLMSLWFNlRFGVTSSQMSPVFAIAELTLAFSTYFSVIIAEKIGGVKTIVYLHATAIALLFL----LP--------- 264
                                   567899999999778****************************************99999888888....34......... PP

                    MFS_1_like  96 klevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkel.gedrkd.yGrqrlfGsvGyaifafitGilidhy 172
                                              ++ +f+i  ++ v  +++++ + +++ a++lk + +++r++  G + l +s+  a    i G+ ++  
  gi|70607814|ref|YP_256684.1| 265 -----------FSPSFIIGSIIFVTRNALMNMTSPVFQAMVLKLVpENERGRaNGIVNLMSSIPRAFGPSIGGFYFNIG 332
                                   ...........55566666666666666666666666666666665333333356666666665555555555555555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2      0.36   1.6e+03     267     307 ..      24      65 ..      13      75 .. 0.62
   2 !   14.7   0.5   1.6e-06    0.0073      89     169 ..     254     335 ..     236     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.36
                         MFS_3 267 AilgalllsrLR.erlsserlvllaavalAlvllslalassl 307
                                    i+ +l l  L  + l+  +l++ + +  Al+ l+l++  ++
  gi|70607814|ref|YP_256684.1|  24 TIIMSLYLLSLGlSPLTIGELLSGSIIIGALISLTLSFLGDM 65 
                                   444444444443144666777777777777777777776555 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.6e-06
                         MFS_3  89 svlltvlaalgllspwlllaltlligiGa..alndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavG 167
                                   ++ +++  +l  +sp+ ++++++++   a   +++P +qA+v  lv+ ++   A  +  +   i R+ GP +gG    +  
  gi|70607814|ref|YP_256684.1| 254 ATAIAL-LFLLPFSPSFIIGSIIFVTRNAlmNMTSPVFQAMVLKLVPENERGRANGIVNLMSSIPRAFGPSIGGFYFNIGN 333
                                   333333.3444578999999988776654115678***************************************8766555 PP

                         MFS_3 168 aa 169
                                    +
  gi|70607814|ref|YP_256684.1| 334 YV 335
                                   55 PP

>> DUF3325  Protein of unknown function (DUF3325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.032   1.4e+02      67      95 ..     128     156 ..      97     164 .. 0.81
   2 ?   10.4   0.3   0.00012      0.54      40      90 ..     223     272 ..     209     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.032
                       DUF3325  67 lgllslaAlllvllLayrprlllalalaa 95 
                                    +lls+a+ l  l+L+y+  ll  +++ +
  gi|70607814|ref|YP_256684.1| 128 SILLSVAGSLFPLVLTYKEILLIEVVVNL 156
                                   5799*************987777766655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                       DUF3325  40 laGwlllllslalavaawgwavGlvlwlgllslaAlllvllLayrprllla 90 
                                   +++ l+l++s++ +v   + ++G v  ++ l + A++l +lL+++p ++  
  gi|70607814|ref|YP_256684.1| 223 AIAELTLAFSTYFSVIIAE-KIGGVKTIVYLHATAIALLFLLPFSPSFIIG 272
                                   5677889999999999998.9*************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2255.82
//
Query:       gi|70607815|ref|YP_256685.1|  [L=467]
Description: hypothetical protein Saci_2098 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-07   30.2   5.6    5.6e-07   29.6   5.6    1.3  1  Fer4_10   4Fe-4S dicluster domain
     0.0002   21.5   5.1     0.0002   21.5   5.1    1.9  2  Fer4_9    4Fe-4S dicluster domain
    0.00025   21.5  15.1     0.0017   18.9   8.8    2.5  3  Fer4_7    4Fe-4S dicluster domain
    0.00062   19.7   8.4       0.08   13.0   0.4    2.5  2  Fer4_6    4Fe-4S binding domain
     0.0031   18.4   2.3       0.38   11.7   0.0    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.011   15.8   5.4      0.027   14.6   5.4    1.6  1  Fer4_21   4Fe-4S dicluster domain
      0.077   13.0   0.5       0.16   12.0   0.5    1.5  1  DUF999    Protein of unknown function (DUF999)
        0.1   12.5  10.3      0.067   13.0   0.9    2.9  2  Fer4      4Fe-4S binding domain
       0.16   12.2   2.6       0.32   11.2   2.6    1.4  1  Fer4_18   4Fe-4S dicluster domain
       0.23   11.3   5.0       0.16   11.8   1.9    2.0  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
       0.25   11.9   7.3        0.3   11.7   0.2    2.5  2  Fer4_17   4Fe-4S dicluster domain
       0.53   10.8   8.9        1.6    9.2   0.2    2.7  3  Fer4_8    4Fe-4S dicluster domain
       0.95   10.1   6.3        8.3    7.2   2.0    2.6  2  Fer4_4    4Fe-4S binding domain
          1    9.6  14.2        1.1    9.4   2.5    2.9  2  Fer4_2    4Fe-4S binding domain
        1.2   10.2  12.2        5.3    8.2   0.9    2.7  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   5.6   4.7e-10   5.6e-07       3      56 .]     390     441 ..     388     441 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.7e-10
                       Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   v+d+++C++C+  +C  aCP+      +   a+ +++ + k+ kC+g+g CveaCP
  gi|70607815|ref|YP_256685.1| 390 VKDPQQCLNCKtvDCALACPV----GLTDMRANFIKKGEFKSFKCIGVGDCVEACP 441
                                   789********999*******....777888888999999***************9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.7   3.3e+03       7      28 ..     261     282 ..     260     290 .. 0.72
   2 !   21.5   5.1   1.7e-07    0.0002       1      49 [.     395     443 ..     395     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                        Fer4_9   7 aCveaCpagvvvedaaerkarl 28 
                                    C   C a  + +  +++ +r 
  gi|70607815|ref|YP_256685.1| 261 ICSVTCTAPFMLQGTFQGSMRK 282
                                   5999998888877777776665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.7e-07
                        Fer4_9   1 kCtgCga..CveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                   +C +C++  C  aCp g++ ++ ++ +k + + +   +Cig g+CveaCp++
  gi|70607815|ref|YP_256685.1| 395 QCLNCKTvdCALACPVGLTdMRANFIKKGEFKSF---KCIGVGDCVEACPHD 443
                                   6*****888*********9455555666665554...8************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   3.4    0.0011       1.3      33      51 ..     391     411 ..     363     412 .. 0.82
   2 !   18.9   8.8   1.4e-06    0.0017       1      51 [.     395     443 ..     395     445 .. 0.90
   3 !   14.6   0.4   3.2e-05     0.039       1      22 [.     429     450 ..     429     460 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                        Fer4_7  33 idpekClgCga..CvavCPtg 51 
                                    dp++Cl+C+   C+ +CP+g
  gi|70607815|ref|YP_256685.1| 391 KDPQQCLNCKTvdCALACPVG 411
                                   4899******999******98 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.4e-06
                        Fer4_7   1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                   +C +C+   C+ aCpv+  +++    +k     e+++ kC+g g Cv++CP++
  gi|70607815|ref|YP_256685.1| 395 QCLNCKtvDCALACPVGLTDMRANFIKK----GEFKSFKCIGVGDCVEACPHD 443
                                   5****9999************9986555....5******************86 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 3.2e-05
                        Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                   +Cig g Cv+aCp++ i ++++
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACPHDNIVFHDV 450
                                   7*************99999875 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   2.4   0.00081      0.97       5      22 ..     392     411 ..     390     414 .. 0.92
   2 !   13.0   0.4   6.7e-05      0.08       8      23 ..     429     444 ..     424     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00081
                        Fer4_6   5 dpdkCigCgd..CvrvCPeg 22 
                                   dp+ C+ C    C+ +CP g
  gi|70607815|ref|YP_256685.1| 392 DPQQCLNCKTvdCALACPVG 411
                                   99******999*******87 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.7e-05
                        Fer4_6   8 kCigCgdCvrvCPega 23 
                                   kCig gdCv +CP++ 
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACPHDN 444
                                   8************975 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.7     0.024        28       1      20 [.     395     416 ..     395     427 .. 0.81
   2 !   11.7   0.0   0.00032      0.38       1      20 [.     429     448 ..     429     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.024
                       Fer4_16   1 rCgtCgk..CaevCPtnaikek 20 
                                   +C +C+   Ca +CP++  +++
  gi|70607815|ref|YP_256685.1| 395 QCLNCKTvdCALACPVGLTDMR 416
                                   599999888******9976665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00032
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C++ g C+e+CP++ i   
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACPHDNIVFH 448
                                   59999**********99876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   5.4   2.3e-05     0.027       4      56 ..     392     445 ..     390     448 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                       Fer4_21   4 dedkCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                   d+++C++C+   C++aC+  + + ++ +  ++ +  + +C+G   C++ CP ++ 
  gi|70607815|ref|YP_256685.1| 392 DPQQCLNCKTvdCALACPV-GLTDMRANFIKKGEFKSFKCIGVGDCVEACPHDNI 445
                                   789*****8555******6.455555555566678899*************6544 PP

>> DUF999  Protein of unknown function (DUF999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   0.00013      0.16      84     135 ..     301     355 ..     270     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                        DUF999  84 klrwvlliiwsiiivlaidkkfevkeflsiw...inenrfyseiwgpiaiyvcll 135
                                    ++wv++ +w+ +iv+a+   f+ + ++s      +  +fy+ ++  ++ y  ++
  gi|70607815|ref|YP_256685.1| 301 WYKWVMITVWASLIVFAVLSYFNYEGVISFSvlgNDATKFYASLYFNVIWYFQFM 355
                                   479*****************99998877766222345689999999998887655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.8      0.11   1.3e+02      14      21 ..     404     411 ..     389     412 .. 0.71
   2 ?   13.0   0.9   5.6e-05     0.067       7      23 ..     429     445 ..     426     446 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                                   HHHHSTTT CS
                          Fer4  14 CvevCPvg 21 
                                   C+ +CPvg
  gi|70607815|ref|YP_256685.1| 404 CALACPVG 411
                                   ******97 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.6e-05
                                   TSSS-THHHHHSTTTEE CS
                          Fer4   7 kCigCGaCvevCPvgAI 23 
                                   kCig G Cve+CP++ I
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACPHDNI 445
                                   89999*********977 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.6   0.00027      0.32      56      96 ..     391     441 ..     386     455 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                       Fer4_18  56 kgagdcidces..cvkvcPtgi.d.....irkGl..qleciscllcidacd 96 
                                   k+  +c++c++  c   cP+g+ d     i+kG    ++ci  + c++ac 
  gi|70607815|ref|YP_256685.1| 391 KDPQQCLNCKTvdCALACPVGLtDmranfIKKGEfkSFKCIGVGDCVEACP 441
                                   55678****96559******9756333334456333689***********5 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00013      0.16      18      48 ..     390     422 ..     383     430 .. 0.76
   2 ?   -0.2   0.2      0.69   8.3e+02      29      40 ..     433     444 ..     425     464 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                   HHHHTT----TT-HHHHCSTT---..HHHHHHH CS
                       Fer4_20  18 leeAsRClqCkkapcvkgCPveid..ipefikk 48 
                                   +++ + Cl+Ck+  c  +CPv ++    +fikk
  gi|70607815|ref|YP_256685.1| 390 VKDPQQCLNCKTVDCALACPVGLTdmRANFIKK 422
                                   677899***************864113456665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.69
                                   T-HHHHCSTT-- CS
                       Fer4_20  29 kapcvkgCPvei 40 
                                      cv++CP ++
  gi|70607815|ref|YP_256685.1| 433 VGDCVEACPHDN 444
                                   45799***9875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.3      0.24   2.9e+02      44      60 ..     394     412 ..     386     413 .. 0.76
   2 ?   11.7   0.2   0.00025       0.3      41      59 ..     425     443 ..     413     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
                       Fer4_17  44 slCieCg..eCerkCPqgl 60 
                                   ++C++C+   C+ +CP gl
  gi|70607815|ref|YP_256685.1| 394 QQCLNCKtvDCALACPVGL 412
                                   6899998445999999776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                    k  +Ci+ g C+++CP++
  gi|70607815|ref|YP_256685.1| 425 FKSFKCIGVGDCVEACPHD 443
                                   47889************96 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.8   5.7e+03      11      20 ..     262     273 ..     260     305 .. 0.52
   2 ?    4.2   2.3     0.049        59      49      64 ..     394     411 ..     387     412 .. 0.85
   3 ?    9.2   0.2    0.0013       1.6       3      17 ..     428     446 ..     426     465 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.8
                        Fer4_8  11 CqsaC..pvlrr 20 
                                   C  +C  p++ +
  gi|70607815|ref|YP_256685.1| 262 CSVTCtaPFMLQ 273
                                   888885543333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.049
                        Fer4_8  49 wsCttcga..CtevCpvg 64 
                                   ++C++c+   C+ +Cpvg
  gi|70607815|ref|YP_256685.1| 394 QQCLNCKTvdCALACPVG 411
                                   6899999999******97 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0013
                        Fer4_8   3 ekCieCgaCqsaCp....v 17 
                                   +kCi+ g C +aCp    v
  gi|70607815|ref|YP_256685.1| 428 FKCIGVGDCVEACPhdniV 446
                                   5777777777777744442 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.0    0.0069       8.3       3      17 .]     395     411 ..     393     413 .. 0.88
   2 ?    4.2   0.1     0.064        77       3      15 ..     429     441 ..     427     454 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0069
                        Fer4_4   3 rCigCgs..CvaaCPqg 17 
                                    C++C+   C  aCP+g
  gi|70607815|ref|YP_256685.1| 395 QCLNCKTvdCALACPVG 411
                                   5*****889******85 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.064
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                   +Cig g Cv aCP
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACP 441
                                   6888899*****9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5   0.00095       1.1       5      21 ..     391     409 ..     388     410 .. 0.91
   2 ?    8.5   0.2     0.002       2.3       9      22 .]     429     442 ..     422     442 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00095
                        Fer4_2   5 vdtdrCigCg..aCvsaCP 21 
                                    d++ C++C+   C  aCP
  gi|70607815|ref|YP_256685.1| 391 KDPQQCLNCKtvDCALACP 409
                                   58999************** PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                        Fer4_2   9 rCigCgaCvsaCPa 22 
                                   +Cig g Cv aCP+
  gi|70607815|ref|YP_256685.1| 429 KCIGVGDCVEACPH 442
                                   788889*******7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.4     0.024        29       1      14 [.     396     411 ..     396     411 .. 0.87
   2 ?    8.2   0.9    0.0045       5.3       1      13 [.     430     442 ..     429     444 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                        Fer4_3   1 CtgCg..aCvevCPvg 14 
                                   C++C    C  +CPvg
  gi|70607815|ref|YP_256685.1| 396 CLNCKtvDCALACPVG 411
                                   99**8556******98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0045
                        Fer4_3   1 CtgCgaCvevCPv 13 
                                   C+g g Cve+CP 
  gi|70607815|ref|YP_256685.1| 430 CIGVGDCVEACPH 442
                                   444478******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3460.11
//
Query:       gi|70607816|ref|YP_256686.1|  [L=336]
Description: hypothetical protein Saci_2099 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        4.4    7.8   5.1         12    6.4   5.1    1.7  1  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.1   0.00064        12       3      19 ..      20      36 ..      18      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00064
               FeoB_associated  3 iIVgliiaaavafvirr 19
                                  ++V+lii+aav+fv++ 
  gi|70607816|ref|YP_256686.1| 20 VVVILIIIAAVGFVLYA 36
                                  79************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2287.34
//
Query:       gi|70607817|ref|YP_256687.1|  [L=233]
Description: hypothetical protein Saci_2100 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-17   61.5   0.0    1.1e-16   61.1   0.0    1.1  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.0   6.1e-21   1.1e-16      19     136 ..      54     181 ..      27     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 6.1e-21
               Nitrate_red_del  19 l.....aa.ededllelaaeYtrLFlgp.grrsasPyesvYlsekkgllfgest.....levrefyrqagle.vaeefnep 86 
                                         ++ ++++ +++  eYt LFl + g +++ P es        ll ge+       ++++fy+  gl  + ++f   
  gi|70607817|ref|YP_256687.1|  54 DmfeirKKfKSKSKKDYLIEYTTLFLTGfGNKPLTPVESKRNY----LLIGEGIttfryNDIVRFYTTRGLVmKSRSFMHE 130
                                   255554335999***************99**********9999....88888766677688******************** PP

               Nitrate_red_del  87 pDHlaveLeflahLaereaeaeea.eeaealleaqkafleehllpWlpefa 136
                                   pDH++++L f+++L+++e +  ++  +  +++ +  +f+++h+++W+pe++
  gi|70607817|ref|YP_256687.1| 131 PDHISTILGFMSFLIREEINLSKDnGDISKIVMDEYNFMTTHIMSWVPEWI 181
                                   ***************99999777799**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1616.67
//
Query:       gi|70607818|ref|YP_256688.1|  [L=277]
Description: 4Fe-4S binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-18   66.9   9.0    1.3e-18   66.9   9.0    2.0  2  Fer4_11   4Fe-4S dicluster domain
    4.7e-12   46.3  17.1      2e-05   25.0   5.3    3.1  3  Fer4_7    4Fe-4S dicluster domain
    5.6e-08   32.8  21.0     0.0013   18.9   7.2    3.0  2  Fer4_9    4Fe-4S dicluster domain
    2.9e-07   30.5  21.9    4.4e-05   23.5   9.5    3.3  3  Fer4_10   4Fe-4S dicluster domain
    2.3e-05   24.7  16.9    6.1e-05   23.4   1.0    3.0  2  Fer4_8    4Fe-4S dicluster domain
    7.6e-05   22.4   3.6    7.6e-05   22.4   3.6    4.3  4  Fer4      4Fe-4S binding domain
    0.00017   21.5   2.0    0.00017   21.5   2.0    4.8  5  Fer4_6    4Fe-4S binding domain
    0.00037   20.8  35.0     0.0064   16.9   3.1    4.7  5  Fer4_4    4Fe-4S binding domain
    0.00046   20.1  28.3    0.00052   20.0   1.2    4.5  5  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   16.1  22.1       0.27   11.8   0.3    3.7  3  Fer4_17   4Fe-4S dicluster domain
       0.38   10.9  26.9       0.81    9.9   1.4    3.7  3  Fer4_21   4Fe-4S dicluster domain
        1.3   10.0  23.2        2.8    9.0   0.3    3.8  3  Fer4_16   4Fe-4S double cluster binding domain
        4.8    8.3  39.2       0.12   13.3   7.9    4.3  4  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.3   1.8e+03      54      75 ..      25      46 ..       8      55 .. 0.66
   2 !   66.9   9.0   9.6e-22   1.3e-18       3      95 ..      94     191 ..      92     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                       Fer4_11 54 cPykivrkneetgkvekCdmcl 75
                                  +P+k  ++ +  + ++kC +c+
  gi|70607818|ref|YP_256688.1| 25 LPFKPSKNFAIITDLNKCFGCA 46
                                  5555555555566677888776 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 9.6e-22
                       Fer4_11   3 wlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaG.. 81 
                                   ++ +p +C hC+++pCv ++p++a +k+ e+G+Vl+d +++  +++ ++ +cPy   + +  +g+v+kC+ c+dr      
  gi|70607818|ref|YP_256688.1|  94 VYNIPINCFHCMNAPCVPVCPVGATFKRVEDGIVLVDYNKCI-GCKYCIYGCPYGNRFFDPVQGVVKKCTHCFDRLYDTti 173
                                   566899***********************************7.********************************875411 PP

                       Fer4_11  82 ....llpacvescptgal 95 
                                       + pac++ c+ +a+
  gi|70607818|ref|YP_256688.1| 174 ppeeRIPACIHGCMVQAR 191
                                   111167899999988776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   2.9    0.0056       7.7      31      49 ..      35      53 ..      17      56 .. 0.76
   2 !   25.0   5.3   1.5e-08     2e-05       1      52 []      41     117 ..      41     117 .. 0.67
   3 !   24.6   4.7   2.1e-08   2.8e-05       1      52 []     133     190 ..     133     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0056
                        Fer4_7 31 veidpekClgCgaCvavCP 49
                                  +  d +kC gC  C+  C 
  gi|70607818|ref|YP_256688.1| 35 IITDLNKCFGCAGCQMSCK 53
                                  5567889999999999995 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.5e-08
                        Fer4_7   1 rCigCgaCvaaC................pvkaieldeeenek............gtekveidpekClgCga..CvavCPtg 51 
                                   +C gC  C+  C                p++ +++                   ++ kv+  p +C +C +  Cv vCP+g
  gi|70607818|ref|YP_256688.1|  41 KCFGCAGCQMSCkewntsgmfgplpdlnPYGDLDVM-----FwlrvlnvevgnwPQTKVYNIPINCFHCMNapCVPVCPVG 116
                                   7***********766666666666666644433333.....022222222333344788889********99********9 PP

                        Fer4_7  52 a 52 
                                   a
  gi|70607818|ref|YP_256688.1| 117 A 117
                                   8 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 2.1e-08
                        Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgC...............gaCvavCPtga 52 
                                   +CigC++C   Cp++ + +d++         +++  kC++C                aC+  C ++a
  gi|70607818|ref|YP_256688.1| 133 KCIGCKYCIYGCPYGNRFFDPV---------QGVVKKCTHCfdrlydttippeeriPACIHGCMVQA 190
                                   7******************997.........67899*****88888888888877778999999876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   6.1   1.8e-06    0.0025       1      50 [.      41     117 ..      41     118 .. 0.84
   2 !   18.9   7.2   9.3e-07    0.0013       1      49 [.     133     189 ..     133     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..........................eaCigCga..CveaCpkga 50 
                                   kC gC  C+ +C+ + +++  ++  + +  +++                           +C++C+   Cv +Cp ga
  gi|70607818|ref|YP_256688.1|  41 KCFGCAGCQMSCKEWNTSGMFGPLPDLN-PYGDldvmfwlrvlnvevgnwpqtkvynipINCFHCMNapCVPVCPVGA 117
                                   7***********8888877766666554.44445788999999999999999999999*99**************986 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 9.3e-07
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga...............CveaCpkg 49 
                                   kC+gC++C++ Cp+g    d +++ ++       +C++C +               C++ C  +
  gi|70607818|ref|YP_256688.1| 133 KCIGCKYCIYGCPYGNRFFDPVQGVVK-------KCTHCFDrlydttippeeripaCIHGCMVQ 189
                                   7************************99.......5**************************877 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.2   0.00012      0.17       2      19 ..      35      52 ..      34      71 .. 0.88
   2 !   23.5   9.5   3.2e-08   4.4e-05       4      56 .]      96     145 ..      93     145 .. 0.92
   3 !   17.0   7.9   3.4e-06    0.0046       2      55 ..     127     186 ..     126     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                       Fer4_10  2 vvidddtCirCgkCvkaC 19
                                  ++ d ++C +C+ C+ +C
  gi|70607818|ref|YP_256688.1| 35 IITDLNKCFGCAGCQMSC 52
                                  67899************* PP

  == domain 2  score: 23.5 bits;  conditional E-value: 3.2e-08
                       Fer4_10   4 idddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +  C +C    Cv +CP+     ga+ ++ e++ v +++ kC+gc +C+  CP
  gi|70607818|ref|YP_256688.1|  96 NIPINCFHCMnaPCVPVCPV-----GATFKRVEDGIVLVDYNKCIGCKYCIYGCP 145
                                   55678****9889*******.....*****************************9 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 3.4e-06
                       Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc...............gaCveaC 55 
                                   v +d ++Ci+C+ C   CP+          +   ++v+++v+kCt+c                aC+  C
  gi|70607818|ref|YP_256688.1| 127 VLVDYNKCIGCKYCIYGCPY---------GNRFFDPVQGVVKKCTHCfdrlydttippeeriPACIHGC 186
                                   56899***************.........5666667777788899984444444444433223666655 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.0   4.4e-08   6.1e-05       2      64 ..      39     116 ..      38     117 .. 0.82
   2 ?    4.9   8.8     0.026        35       3      20 ..     132     149 ..     130     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.4e-08
                        Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.............dvqeeqvleeeealwsCttcga..CtevCpvg 64 
                                   l+kC +C  Cq +C  +++++++   +  +  +             +v ++  ++ +++  +C +c++  C+ vCpvg
  gi|70607818|ref|YP_256688.1|  39 LNKCFGCAGCQMSCKEWNTSGMFGPLPDLNPYGdldvmfwlrvlnvEVGNWPQTKVYNIPINCFHCMNapCVPVCPVG 116
                                   79****************99988777777777777567777666666666666666********************97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.026
                        Fer4_8   3 ekCieCgaCqsaCpvlrr 20 
                                   +kCi+C +C   Cp  +r
  gi|70607818|ref|YP_256688.1| 132 NKCIGCKYCIYGCPYGNR 149
                                   79***********97665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   2.4    0.0076        10       2      18 ..      36      52 ..      35      54 .. 0.89
   2 !    6.9   3.5    0.0043       5.9      14      22 ..     109     117 ..     108     118 .. 0.97
   3 !   22.4   3.6   5.5e-08   7.6e-05       2      21 ..     128     147 ..     127     149 .. 0.93
   4 ?   -0.8   0.4       1.2   1.6e+03       7      11 ..     160     164 ..     157     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0076
                                  EEETTTSSS-THHHHHS CS
                          Fer4  2 videekCigCGaCvevC 18
                                  + d +kC gC  C + C
  gi|70607818|ref|YP_256688.1| 36 ITDLNKCFGCAGCQMSC 52
                                  67999*********999 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0043
                                   HHHHSTTTE CS
                          Fer4  14 CvevCPvgA 22 
                                   Cv vCPvgA
  gi|70607818|ref|YP_256688.1| 109 CVPVCPVGA 117
                                   ********9 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 5.5e-08
                                   EEETTTSSS-THHHHHSTTT CS
                          Fer4   2 videekCigCGaCvevCPvg 21 
                                    +d++kCigC++C+  CP+g
  gi|70607818|ref|YP_256688.1| 128 LVDYNKCIGCKYCIYGCPYG 147
                                   59****************98 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.2
                                   TSSS- CS
                          Fer4   7 kCigC 11 
                                   kC++C
  gi|70607818|ref|YP_256688.1| 160 KCTHC 164
                                   9***9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.7     0.064        88       5      21 ..      38      54 ..      35      59 .. 0.88
   2 !    7.2   4.3     0.004       5.5       9      23 ..     101     117 ..      96     118 .. 0.88
   3 !   21.5   2.0   1.2e-07   0.00017       1      22 [.     126     147 ..     126     148 .. 0.93
   4 ?    0.2   0.2      0.66   9.1e+02       8      13 ..     160     165 ..     159     166 .. 0.76
   5 ?   -0.7   0.2       1.3   1.8e+03       8      13 ..     181     187 ..     179     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.064
                        Fer4_6  5 dpdkCigCgdCvrvCPe 21
                                  d +kC gC  C + C e
  gi|70607818|ref|YP_256688.1| 38 DLNKCFGCAGCQMSCKE 54
                                  679999*****999975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.004
                        Fer4_6   9 CigCgd..CvrvCPega 23 
                                   C +C++  Cv vCP ga
  gi|70607818|ref|YP_256688.1| 101 CFHCMNapCVPVCPVGA 117
                                   66899999******998 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.2e-07
                        Fer4_6   1 vveidpdkCigCgdCvrvCPeg 22 
                                   +v +d++kCigC  C+  CP+g
  gi|70607818|ref|YP_256688.1| 126 IVLVDYNKCIGCKYCIYGCPYG 147
                                   5889****************97 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.66
                        Fer4_6   8 kCigCg 13 
                                   kC++C 
  gi|70607818|ref|YP_256688.1| 160 KCTHCF 165
                                   799995 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.3
                        Fer4_6   8 kCi.gCg 13 
                                   +Ci gC+
  gi|70607818|ref|YP_256688.1| 181 ACIhGCM 187
                                   7997798 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.3   0.00012      0.16       2      15 ..      40      53 ..      39      62 .. 0.91
   2 !   10.6   3.1    0.0005       0.7       3      17 .]     100     116 ..      98     117 .. 0.91
   3 !   16.9   3.1   4.7e-06    0.0064       1      17 []     131     147 ..     131     147 .. 0.92
   4 ?    0.6   0.9       0.8   1.1e+03       2       7 ..     159     164 ..     159     164 .. 0.88
   5 ?   -1.7   0.1       4.2   5.8e+03       4       8 ..     182     187 ..     179     188 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  ++C+gC  C  +C+
  gi|70607818|ref|YP_256688.1| 40 NKCFGCAGCQMSCK 53
                                  89***********7 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0005
                        Fer4_4   3 rCigCgs..CvaaCPqg 17 
                                   +C++C+   Cv +CP+g
  gi|70607818|ref|YP_256688.1| 100 NCFHCMNapCVPVCPVG 116
                                   6*****889******86 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 4.7e-06
                        Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                   +++CigC+ C++ CP+g
  gi|70607818|ref|YP_256688.1| 131 YNKCIGCKYCIYGCPYG 147
                                   589************86 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.8
                        Fer4_4   2 erCigC 7  
                                   ++C++C
  gi|70607818|ref|YP_256688.1| 159 KKCTHC 164
                                   58**** PP

  == domain 5  score: -1.7 bits;  conditional E-value: 4.2
                        Fer4_4   4 Ci.gCg 8  
                                   Ci gC+
  gi|70607818|ref|YP_256688.1| 182 CIhGCM 187
                                   665676 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   1.0     0.002       2.7       5      21 ..      37      53 ..      33      54 .. 0.84
   2 !    7.0   3.9    0.0048       6.7       9      21 ..     100     114 ..      93     115 .. 0.82
   3 !   20.0   1.2   3.7e-07   0.00052       3      22 .]     127     146 ..     125     146 .. 0.91
   4 ?    0.7   0.1      0.51     7e+02       8      13 ..     159     164 ..     153     167 .. 0.84
   5 ?   -2.3   0.1       4.4   6.1e+03       9      13 ..     181     186 ..     176     188 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                        Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                   d ++C gC  C+ +C 
  gi|70607818|ref|YP_256688.1| 37 TDLNKCFGCAGCQMSCK 53
                                  6889*****88*****5 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0048
                        Fer4_2   9 rCigCg..aCvsaCP 21 
                                   +C +C   +Cv +CP
  gi|70607818|ref|YP_256688.1| 100 NCFHCMnaPCVPVCP 114
                                   69999777******* PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.7e-07
                        Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                   v vd ++CigC+ C+  CP+
  gi|70607818|ref|YP_256688.1| 127 VLVDYNKCIGCKYCIYGCPY 146
                                   789****************5 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.51
                        Fer4_2   8 drCigC 13 
                                    +C++C
  gi|70607818|ref|YP_256688.1| 159 KKCTHC 164
                                   58***9 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 4.4
                        Fer4_2   9 rCi.gC 13 
                                   +Ci gC
  gi|70607818|ref|YP_256688.1| 181 ACIhGC 186
                                   476456 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00019      0.27      41      57 ..      37      53 ..       3      55 .. 0.64
   2 ?    5.9   1.1     0.014        19       1      20 [.     100     121 ..     100     131 .. 0.80
   3 ?    6.5   8.0    0.0091        13       1      25 [.     133     157 ..     133     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                       Fer4_17 41 ekaslCieCgeCerkCP 57
                                  +  ++C +C +C+++C 
  gi|70607818|ref|YP_256688.1| 37 TDLNKCFGCAGCQMSCK 53
                                  6789************6 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                       Fer4_17   1 rCiqCgy..ClpeCpsyeaydn 20 
                                   +C +C    C+p+Cp ++  + 
  gi|70607818|ref|YP_256688.1| 100 NCFHCMNapCVPVCPVGATFKR 121
                                   699999778******9877655 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0091
                       Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkl 25 
                                   +Ci+C+yC+  Cp++++  +  + +
  gi|70607818|ref|YP_256688.1| 133 KCIGCKYCIYGCPYGNRFFDPVQGV 157
                                   6************988765555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.4   0.00059      0.81       4      20 ..      38      54 ..      34      60 .. 0.83
   2 ?    0.9   5.0      0.37     5e+02      40      53 ..     100     115 ..      90     121 .. 0.73
   3 ?   -2.2   0.1       3.5   4.8e+03      10      15 ..     160     165 ..     155     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00059
                       Fer4_21  4 dedkCigCgkCliaCed 20
                                  d +kC gC  C ++C++
  gi|70607818|ref|YP_256688.1| 38 DLNKCFGCAGCQMSCKE 54
                                  5689***********97 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.37
                       Fer4_21  40 eCvGC..nlCssvCPv 53 
                                   +C  C  + C+ vCPv
  gi|70607818|ref|YP_256688.1| 100 NCFHCmnAPCVPVCPV 115
                                   677773335******9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.5
                       Fer4_21  10 gCgkCl 15 
                                   +C++C+
  gi|70607818|ref|YP_256688.1| 160 KCTHCF 165
                                   355554 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3     0.002       2.8      50      64 ..      38      52 ..      12      55 .. 0.83
   2 ?    6.9   1.2    0.0089        12       2      17 ..     101     118 ..     100     128 .. 0.83
   3 ?    2.2   9.0      0.25   3.5e+02       1      16 [.     133     148 ..     133     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                       Fer4_16 50 kqeaitgCdiCqdvC 64
                                    ++++gC+ Cq+ C
  gi|70607818|ref|YP_256688.1| 38 DLNKCFGCAGCQMSC 52
                                  3489*********** PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0089
                       Fer4_16   2 CgtCgk..CaevCPtnai 17 
                                   C  C +  C+ vCP++a 
  gi|70607818|ref|YP_256688.1| 101 CFHCMNapCVPVCPVGAT 118
                                   99998889*******995 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.25
                       Fer4_16   1 rCgtCgkCaevCPtna 16 
                                   +C++C+ C+  CP + 
  gi|70607818|ref|YP_256688.1| 133 KCIGCKYCIYGCPYGN 148
                                   5************864 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   4.2       3.4   4.7e+03       1      11 [.      42      52 ..      42      55 .. 0.82
   2 ?   13.3   7.9   8.9e-05      0.12       1      15 []     101     117 ..     101     117 .. 0.92
   3 ?    9.3   3.2    0.0017       2.4       1      14 [.     134     147 ..     134     148 .. 0.95
   4 ?    4.2   1.0     0.072     1e+02       1      13 [.     161     188 ..     161     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.4
                        Fer4_3  1 CtgCgaCvevC 11
                                  C gC  C  +C
  gi|70607818|ref|YP_256688.1| 42 CFGCAGCQMSC 52
                                  99997798888 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.9e-05
                        Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                   C +C+  +Cv vCPvgA
  gi|70607818|ref|YP_256688.1| 101 CFHCMnaPCVPVCPVGA 117
                                   9***8778********9 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0017
                        Fer4_3   1 CtgCgaCvevCPvg 14 
                                   C+gC  C   CP+g
  gi|70607818|ref|YP_256688.1| 134 CIGCKYCIYGCPYG 147
                                   ****99******98 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.072
                        Fer4_3   1 CtgCg...............aCvevCPv 13 
                                   Ct+C                aC   C v
  gi|70607818|ref|YP_256688.1| 161 CTHCFdrlydttippeeripACIHGCMV 188
                                   ****778889999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1864.08
//
Query:       gi|70607819|ref|YP_256689.1|  [L=1452]
Description: hypothetical protein Saci_2102 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00032   19.8   0.0       0.85    8.5   0.0    3.2  4  Molybdopterin   Molybdopterin oxidoreductase
  ------ inclusion threshold ------
      0.012   15.4   0.2      0.026   14.4   0.2    1.6  1  TAT_signal      TAT (twin-arginine translocation) pathway sig
       0.19   11.7   0.3       0.39   10.8   0.3    1.5  1  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00014      0.85       1      29 [.     110     138 ..     110     145 .. 0.93
   2 !    6.9   0.0   0.00043       2.5     132     275 ..     256     637 ..     227     685 .. 0.72
   3 ?   -1.0   0.0      0.11   6.6e+02     370     406 ..     806     842 ..     750     854 .. 0.88
   4 ?   -2.4   0.0      0.29   1.8e+03     307     356 ..     922     969 ..     880     975 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00014
                                   B--S-EEECTTTTTSEEEE--HHHHHHHH CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleli 29 
                                   Rl+yP++R + rg Gk+  +  d+A+++ 
  gi|70607819|ref|YP_256689.1| 110 RLRYPLLRAGPRGSGKWIAIDYDTAYDIL 138
                                   9*************************975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00043
                                   HHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHH.CCCCTCHHHHHHEECHHHCCCCCCCEECC CS
                 Molybdopterin 132 rirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilq.elkvdkeflrkytygkeetdmpllvtlee 211
                                   ri+++ ++++ kv  i p+   + +  de+l ++p+td+al+++   v+++  ++v k       +gk  ++ ++l+  + 
  gi|70607819|ref|YP_256689.1| 256 RIIARIRENGGKVLTIAPERFGFYSVSDEHLYVNPATDGALFMGWIRVLVDfHFYVYK-----VSNGKTVLNPITLQQVSP 331
                                   67788999899*******99998899***************99988887752444444.....444555555554444444 PP

                                   S................................................................................ CS
                 Molybdopterin 212 e................................................................................ 212
                                                                                                                    
  gi|70607819|ref|YP_256689.1| 332 Sysgtgqllfqtvapngqvvtlpqfgeipdtanfphideeflryytnlswlvilnpnpqygdpldpsdpnasnntglhvrm 412
                                   455557777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                   ................................................................................. CS
                 Molybdopterin 213 ................................................................................. 212
                                                                                                                    
  gi|70607819|ref|YP_256689.1| 413 pvknslystsqkitattssgstvsftfpaskwleavlgsdgnvysyvdipwqngvmpiltldelpssmisnivqvsyrlrn 493
                                   777777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                   ................................................................................H CS
                 Molybdopterin 213 ................................................................................t 213
                                                                                                                    
  gi|70607819|ref|YP_256689.1| 494 gqmikvpaiqvtvpaspgssntitltvttgfellraelmnydpytspdqtaqygainvsnltgipeytvvrianelavvaF 574
                                   777777777777777777777777777777777777777777777777777777777777777777777777777766666 PP

                                   HHHHHCCHHHHHHHHHHHHHHTSSEEEEECH.HHHTSTTHHHHHHHHHHHHHHCTHCSSTTCE CS
                 Molybdopterin 214 gkkkevvariarelarnaaktagksmiivGa.glnhrqdgdaiyravinLallvgnvgqpgGg 275
                                    k+ +++++ ++ l r   + +g++  i+ + gl  +++g +  + ++ L+l++g+  +pg++
  gi|70607819|ref|YP_256689.1| 575 QKSIQQPVKWVDYLGRYHESITGRPVSIYFMrGLAAHANGFQSAASAYYLVLMLGAWDNPGAD 637
                                   666666777777777766666666666665556666777777777777777777766666665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.11
                                   EEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEE CS
                 Molybdopterin 370 vvldgrltstalyaDiiLPaatwyEkedlytndegrf 406
                                    ++d ++ ++ +  D++ P+ +++E  ++ ++ ++++
  gi|70607819|ref|YP_256689.1| 806 TTIDLFMHENDNVVDLVIPDLSFLEVYGFHSTFDRPT 842
                                   57999999999**************999998877775 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.29
                                   HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTS CS
                 Molybdopterin 307 ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhade 356
                                   ++  f + qpg +    ++ + +  +l+   gk+++y+l+n+ e ++++ 
  gi|70607819|ref|YP_256689.1| 922 GQQIFSQGQPGLIST--GIYILKSGTLIAGYGKNFEYILKNEAEAQTPNP 969
                                   566666666666666..666666778888899********8777666655 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   4.3e-06     0.026       1      20 [.       5      24 ..       5      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                    TAT_signal  1 klSRRdFLKgsAAaaAAaal 20
                                  klSRRdFLK s+ a+ ++a+
  gi|70607819|ref|YP_256689.1|  5 KLSRRDFLKISGFAGLGTAV 24
                                  69*********999988886 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   6.5e-05      0.39       3      48 ..      54     100 ..      52     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.5e-05
                                   EEEEE-SSBTT--EEEEEE.ETTEEEEEEE-TTSTTTTT---HHHHT CS
                Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhv.kdgkivkvegdpdhpvnegrlCvKGrt 48 
                                    v t C  C  +C ++v+  + g  + v g     +n g +C++G++
  gi|70607819|ref|YP_256689.1|  54 IVYTNCFQCLGRCAIQVTRtPEGYPRFVTGTIGWHINDGGVCPRGAA 100
                                   58899************9878888999******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 9296.32
//
Query:       gi|70607820|ref|YP_256690.1|  [L=209]
Description: hypothetical protein Saci_2103 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00099   19.0   0.0     0.0023   17.8   0.0    1.6  1  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0077   16.1   0.0      0.019   14.8   0.0    1.7  2  MarR_2     MarR family
  ------ inclusion threshold ------
       0.08   12.4   0.0      0.098   12.1   0.0    1.2  1  HVSL       Uncharacterised conserved protein
      0.098   12.6   0.0        0.3   11.1   0.0    1.8  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.1e-07    0.0023       6      58 ..       4      56 ..       2      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.1e-07
                                  HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  L  +++ v   L+ + ++t +  ++ +g++ +++ ++ ++L+  GlV+re++r
  gi|70607820|ref|YP_256690.1|  4 LEPNDILVLEELILYIQLTSYRFSKLTGISNATAWRTFNRLVGLGLVKREDKR 56
                                  5678999999***************************************9876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   4.3e-06     0.019       3      62 .]       4      57 ..       2      57 .. 0.92
   2 ?   -2.4   0.0         1   4.6e+03      26      41 ..      65      80 ..      63      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
                                  --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSSS CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkRa 62
                                  l+p +  vL +L       lt     + +g+s +++ r+ +rLv  GLv r+    DkR+
  gi|70607820|ref|YP_256690.1|  4 LEPNDILVLEELILYIQ--LTSYRFSKLTGISNATAWRTFNRLVGLGLVKRE----DKRG 57
                                  67888999999999998..9999999************************99....8885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                  HHHHHHTSSHHHHHHH CS
                        MarR_2 26 elarrlglsksavsri 41
                                  ++  +l+ sk++v r+
  gi|70607820|ref|YP_256690.1| 65 AIILYLNTSKGNVRRR 80
                                  5667788899999886 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.2e-05     0.098     150     206 ..      69     149 ..      13     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                          HVSL 150 p........................endeLkklleavnkvleefglpplykdeaFHiSiawslgepseeekeellseleka 206
                                                            ++++Lk  le v+kvl++++l p+       + ia +l ++++e++ee+++++ + 
  gi|70607820|ref|YP_256690.1|  69 YlntskgnvrrrclsvlkklwnydgDEEKLKYFLEDVDKVLKSMNLSPFVICFNQPVTIATMLYNKQDELREETKEVIANI 149
                                   0555555555555555555677777789**********************888888********99999999888887654 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.6e-05       0.3      20      62 ..      19      63 ..       4      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                                  EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET.EE.EEES-H CS
                     HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglisrg.rr.irildl 62
                                  ++lt    + + G++  t  r++++L   gl++r+ +r + i+ +
  gi|70607820|ref|YP_256690.1| 19 IQLTSYRFSKLTGISNATAWRTFNRLVGLGLVKREdKRgFSITAR 63
                                  6788889999***********************643555877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1337.37
//
Query:       gi|70607821|ref|YP_256691.1|  [L=287]
Description: hypothetical protein Saci_2104 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   13.3   0.1        2.7    8.3   0.0    2.9  3  DUF2999   Protein of unknown function (DUF2999)


Domain annotation for each model (and alignments):
>> DUF2999  Protein of unknown function (DUF2999)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.042   7.6e+02      48      67 ..     102     121 ..      78     127 .. 0.75
   2 ?   -0.1   0.0     0.062   1.1e+03      14      50 ..     190     225 ..     181     230 .. 0.71
   3 ?    8.3   0.0   0.00015       2.7       9      39 ..     230     260 ..     224     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.042
                       DUF2999  48 allalvmtnPalikeaveel 67 
                                    ll  ++ nP ++k av++l
  gi|70607821|ref|YP_256691.1| 102 GLLRGLVLNPIVVKGAVDNL 121
                                   46777778999999999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.062
                       DUF2999  14 sdekiaelfealtenPlaamaliqqlGipqeklqall 50 
                                   s +   el e + en    ++ ++++G+ q+ +++l 
  gi|70607821|ref|YP_256691.1| 190 SSKVYRELGEVVRENE-NNLTYVEDIGMNQDSVKKLK 225
                                   5555566666666665.56889999999999888775 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00015
                       DUF2999   9 kehnvsdekiaelfealtenPlaamaliqql 39 
                                   k   v d++i el + +t+nP+a+   +  l
  gi|70607821|ref|YP_256691.1| 230 KTIIVHDKNILELTKNFTKNPFASPFSVVIL 260
                                   556689****************986555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1919.91
//
Query:       gi|70607822|ref|YP_256692.1|  [L=254]
Description: hypothetical protein Saci_2105 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-19   66.6  13.1      0.017   15.2   0.1    7.1  7  TPR_2         Tetratricopeptide repeat
    9.5e-18   64.5   0.3    9.6e-10   38.8   0.0    4.0  4  TPR_19        Tetratricopeptide repeat
    2.3e-17   63.3   0.0    1.1e-06   29.2   0.0    4.1  4  TPR_16        Tetratricopeptide repeat
    3.7e-16   59.1   7.5    7.2e-05   22.9   0.2    4.0  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    1.1e-13   50.6   8.8      0.023   14.4   1.0    5.8  6  TPR_11        TPR repeat
    1.7e-11   43.3   9.8      0.012   15.8   0.0    6.5  6  TPR_8         Tetratricopeptide repeat
    4.3e-09   36.4   0.3      0.031   15.1   0.1    5.4  6  TPR_14        Tetratricopeptide repeat
    4.6e-09   35.7  14.7       0.51   10.3   0.2    6.4  6  TPR_1         Tetratricopeptide repeat
    5.1e-09   36.2   0.0    5.4e-05   23.3   0.0    3.8  3  TPR_9         Tetratricopeptide repeat
      1e-05   25.5   7.2     0.0018   18.3   3.4    2.9  3  SRP_TPR_like  Putative TPR-like repeat
    2.1e-05   24.7   8.9        2.1    8.7   0.3    5.8  4  TPR_12        Tetratricopeptide repeat
    3.5e-05   24.2   6.6        3.4    8.5   0.0    6.4  7  TPR_6         Tetratricopeptide repeat
    3.9e-05   22.8   0.2     0.0067   15.5   0.0    2.1  2  ChAPs         ChAPs (Chs5p-Arf1p-binding proteins)
    6.2e-05   22.1   1.5     0.0023   16.9   0.5    2.3  2  NARP1         NMDA receptor-regulated protein 1
    0.00011   22.5   0.3        1.8    8.9   0.0    3.9  5  TPR_20        Tetratricopeptide repeat
    0.00014   22.0  15.1        1.5    9.4   0.0    6.7  6  TPR_17        Tetratricopeptide repeat
    0.00014   21.2   0.0        3.4    6.8   0.0    4.2  5  TPR_15        Tetratricopeptide repeat
    0.00039   19.8   0.3          4    7.0   0.0    4.2  4  SHNi-TPR      SHNi-TPR
     0.0059   16.0   0.1         14    4.9   0.0    3.8  4  TPR_MalT      MalT-like TPR region
     0.0064   16.4   0.0        8.4    6.3   0.0    3.4  2  YfdX          YfdX protein
  ------ inclusion threshold ------
      0.014   15.4   0.3       0.43   10.6   0.0    2.7  2  DUF3856       Domain of Unknown Function (DUF3856)
      0.038   14.1   3.6        5.8    7.1   0.0    4.0  4  DUF4363       Domain of unknown function (DUF4363)
      0.041   13.6   0.1       0.29   10.8   0.1    2.2  2  TPR_21        Tetratricopeptide repeat-like domain
      0.072   13.5   0.1        3.1    8.2   0.0    2.7  3  BTAD          Bacterial transcriptional activator domain


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.073        55       7      23 ..      12      28 ..      10      31 .. 0.83
   2 !   15.2   0.1   2.2e-05     0.017       1      32 [.      35      66 ..      35      68 .. 0.93
   3 !   12.0   0.3   0.00025      0.18       4      32 ..      72     100 ..      69     102 .. 0.94
   4 !    9.2   0.0    0.0019       1.4       4      34 .]     106     136 ..     103     136 .. 0.90
   5 !   14.8   0.2   3.1e-05     0.023       6      33 ..     142     169 ..     137     170 .. 0.91
   6 ?    3.6   0.0      0.11        85       4      33 ..     174     203 ..     172     204 .. 0.88
   7 !   11.1   0.0   0.00046      0.34       1      34 []     204     237 ..     204     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.073
                         TPR_2  7 lGlayyklgdyeeAlea 23
                                   ++ ++++gdy eAl+ 
  gi|70607822|ref|YP_256692.1| 12 EAERLIEKGDYPEALNV 28
                                  6788999*******975 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.2e-05
                         TPR_2  1 aealynlGlayyklgdyeeAleafekAleldP 32
                                  +ea+  + +ay+++g+ eeA++ +++ +   P
  gi|70607822|ref|YP_256692.1| 35 PEAYILRSKAYIEMGKSEEAIRELKEGINRFP 66
                                  69************************998877 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00025
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldP 32 
                                   +y+l+l+y++ +d+  Al+  + Al++ P
  gi|70607822|ref|YP_256692.1|  72 YYELALLYFNHNDLVNALDEVNNALSILP 100
                                   9************************9988 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0019
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                   +   +++++++++ye+A + +  +++  P++
  gi|70607822|ref|YP_256692.1| 106 NKLKARILFEMQEYEQAFDVLTYVIKMKPDD 136
                                   56789*********************99986 PP

  == domain 5  score: 14.8 bits;  conditional E-value: 3.1e-05
                         TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                    ++++ y  g++ +Al+  ++Ale++ +
  gi|70607822|ref|YP_256692.1| 142 LRAQCFYLTGKFLDALKEINRALEYNNK 169
                                   69***********************976 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.11
                         TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                                   +   G++y++   y+ Al  f+ ++++ P+
  gi|70607822|ref|YP_256692.1| 174 HTLKGKIYLETHFYKLALSEFKISVSIRPT 203
                                   6678*****************999999887 PP

  == domain 7  score: 11.1 bits;  conditional E-value: 0.00046
                         TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                   ae +y l+ + y  g+   A+ + ekAl+ldPnn
  gi|70607822|ref|YP_256692.1| 204 AENYYLLAFSEYMTGECGNAISDSEKALSLDPNN 237
                                   6889*****************************8 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.8e-06    0.0073       1      57 [.      16      67 ..      16      72 .. 0.89
   2 !   10.1   0.1    0.0012      0.91       3      68 .]      47     112 ..      47     112 .. 0.95
   3 !   38.8   0.0   1.3e-12   9.6e-10       1      68 []     113     180 ..     113     180 .. 0.98
   4 ?    0.7   0.0         1   7.8e+02       8      25 ..     221     238 ..     215     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.8e-06
                        TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                  l++ gdy eAl+ l ++ +     +ea +l  +a++++g  +eA++ L++  + +p 
  gi|70607822|ref|YP_256692.1| 16 LIEKGDYPEALNVLGNL-SL----PEAYILRSKAYIEMGKSEEAIRELKEGINRFPY 67
                                  7899************5.66....9999999******************99888775 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                        TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                   ++g+ +eA++ l++ +   p   +  + LA ++++ ++l  A + ++ ++   p + +y +L+A++
  gi|70607822|ref|YP_256692.1|  47 EMGKSEEAIRELKEGINRFPYAHYMYYELALLYFNHNDLVNALDEVNNALSILPYSYDYNKLKARI 112
                                   68999*************************************************999999999986 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 1.3e-12
                        TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                   l++++ y++A + l+++++ +p++ e rll A++ + +g + +A + +++++e + +d+ +++L++k+
  gi|70607822|ref|YP_256692.1| 113 LFEMQEYEQAFDVLTYVIKMKPDDVESRLLRAQCFYLTGKFLDALKEINRALEYNNKDETLHTLKGKI 180
                                   789**************************************************************997 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1
                        TPR_19   8 aeAlalleqalqedpkna 25 
                                    +A++  e+al+ dp+n 
  gi|70607822|ref|YP_256692.1| 221 GNAISDSEKALSLDPNNN 238
                                   67888889********96 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.15   1.1e+02       4      20 ..      13      29 ..      12      33 .. 0.84
   2 !   21.5   0.0   3.8e-07   0.00028       5      65 ..      43     100 ..      39     103 .. 0.88
   3 !   29.2   0.0   1.4e-09   1.1e-06       3      61 ..     109     164 ..     108     171 .. 0.93
   4 ?    4.2   0.0      0.09        67       3      66 ..     177     236 ..     175     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                        TPR_16  4 araalragdyddAaaal 20
                                  a  +++ gdy++A+++l
  gi|70607822|ref|YP_256692.1| 13 AERLIEKGDYPEALNVL 29
                                  6788999*******998 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.8e-07
                        TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                   +a+++ g+ ++A++ l++ + r+   P a+ ++++l+++++ +++l  A++ ++ al   p
  gi|70607822|ref|YP_256692.1|  43 KAYIEMGKSEEAIRELKEGINRF---PYAHYMYYELALLYFNHNDLVNALDEVNNALSILP 100
                                   799********************...************************66655556666 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 1.4e-09
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                   +ar++++ ++y++A  +l+ ++k+    Pd++e++ll++++++  g + +A+  +++al
  gi|70607822|ref|YP_256692.1| 109 KARILFEMQEYEQAFDVLTYVIKMK---PDDVESRLLRAQCFYLTGKFLDALKEINRAL 164
                                   69***********************...************************7777776 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.09
                        TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                   +++++l+   y  A+  +++ +  +   P +ae ++ll+ + +  g+   A+   ++al  +p+
  gi|70607822|ref|YP_256692.1| 177 KGKIYLETHFYKLALSEFKISVSIR---P-TAENYYLLAFSEYMTGECGNAISDSEKALSLDPN 236
                                   6899999999***************...9.9***************999998444444566665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.018      23      80 ..       6      59 ..       1      61 [. 0.89
   2 !   17.8   2.2   3.9e-06    0.0029      21      79 ..      67     126 ..      63     129 .. 0.92
   3 !   22.9   0.2   9.6e-08   7.2e-05      16      76 ..     130     191 ..     125     197 .. 0.90
   4 ?    4.0   0.0     0.078        58      20      55 ..     201     237 ..     191     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                                  HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                        ANAPC3 23 pedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                  +ed  + A+ l + g+y +A+++l ++    + +++ +l  +++++++k eeAi+ L+
  gi|70607822|ref|YP_256692.1|  6 EEDPIYEAERLIEKGDYPEALNVLGNL----SLPEAYILRSKAYIEMGKSEEAIRELK 59
                                  566666799999***************....999********************9987 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.9e-06
                                   --HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                        ANAPC3  21 espedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                   + ++  y lAl +++ ++   A++ +++a  + + s  +  l+A+ l+++++ye+A ++L
  gi|70607822|ref|YP_256692.1|  67 YAHYMYYELALLYFNHNDLVNALDEVNNAlSILPYSYDYNKLKARILFEMQEYEQAFDVL 126
                                   556667889********************99999999********************998 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 9.6e-08
                                   H.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                        ANAPC3  16 laaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                    ++++++ e+++l A+c+yl+g++  A++ +++a + n+k++  + l+++ +l+ + y+ A+
  gi|70607822|ref|YP_256692.1| 130 IKMKPDDVESRLLRAQCFYLTGKFLDALKEINRAlEYNNKDETLHTLKGKIYLETHFYKLAL 191
                                   4688999**********************************************999888776 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.078
                                   H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC- CS
                        ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnsks 55 
                                   +  +e+ yllA + y +g+   A+   +ka  l++++
  gi|70607822|ref|YP_256692.1| 201 RPTAENYYLLAFSEYMTGECGNAISDSEKAlSLDPNN 237
                                   66789*******************9999997776665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0086       6.5       3      17 ..      15      29 ..      13      32 .. 0.85
   2 !   14.4   1.0   3.1e-05     0.023       3      40 ..      44      81 ..      43      83 .. 0.95
   3 !   13.0   0.0   8.1e-05      0.06       2      42 .]     111     151 ..     110     151 .. 0.94
   4 !   14.4   0.2   3.1e-05     0.023       4      40 ..     147     183 ..     144     184 .. 0.94
   5 ?   -1.7   0.0       3.1   2.3e+03      23      34 ..     200     210 ..     187     218 .. 0.58
   6 ?    4.8   0.0     0.031        23       8      27 ..     218     237 ..     213     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0086
                        TPR_11  3 ayyeqGkyeeAieaY 17
                                   + e+G+y+eA++++
  gi|70607822|ref|YP_256692.1| 15 RLIEKGDYPEALNVL 29
                                  5789********986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.1e-05
                        TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                  ay e Gk eeAi ++k+ ++  P     yy+L+l+y++
  gi|70607822|ref|YP_256692.1| 44 AYIEMGKSEEAIRELKEGINRFPYAHYMYYELALLYFN 81
                                  8***********************************97 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 8.1e-05
                        TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                   ++++e ++ye+A  ++   +k +Pd++e  + +++ +y  G
  gi|70607822|ref|YP_256692.1| 111 RILFEMQEYEQAFDVLTYVIKMKPDDVESRLLRAQCFYLTG 151
                                   799******************************99999776 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 3.1e-05
                        TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                   +y  Gk+ +A+++ ++Al++++++ +++   G++y++
  gi|70607822|ref|YP_256692.1| 147 FYLTGKFLDALKEINRALEYNNKDETLHTLKGKIYLE 183
                                   7889*******************************86 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 3.1
                        TPR_11  23 ldPdnaeayynL 34 
                                   ++P+  + yy L
  gi|70607822|ref|YP_256692.1| 200 IRPTAEN-YYLL 210
                                   5555444.5555 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.031
                        TPR_11   8 GkyeeAieaYkkAlkldPdn 27 
                                   G+  +Ai + +kAl ldP+n
  gi|70607822|ref|YP_256692.1| 218 GECGNAISDSEKALSLDPNN 237
                                   55566777779********9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.012       2      28 ..      36      62 ..      35      66 .. 0.90
   2 ?    4.8   0.1     0.053        39       3      29 ..      71      97 ..      69     100 .. 0.79
   3 !    9.3   0.0     0.002       1.5       7      34 .]     109     136 ..     106     136 .. 0.94
   4 ?    4.2   0.1     0.082        61       2      33 ..     138     169 ..     137     170 .. 0.84
   5 ?   -0.5   0.0       2.7     2e+03       5      25 ..     175     195 ..     172     203 .. 0.64
   6 !    9.6   0.1    0.0015       1.1       4      34 .]     207     237 ..     204     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                  CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                         TPR_8  2 eayynlgsiylklgdyeeAkeyyekal 28
                                  eay + +++y+++g+ eeA+  +++ +
  gi|70607822|ref|YP_256692.1| 36 EAYILRSKAYIEMGKSEEAIRELKEGI 62
                                  89******************9999877 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                                  HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                         TPR_8  3 ayynlgsiylklgdyeeAkeyyekale 29
                                  +yy l+++y++ +d+ +A    + al+
  gi|70607822|ref|YP_256692.1| 71 MYYELALLYFNHNDLVNALDEVNNALS 97
                                  7*********99998777766666665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
                                   HHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   7 lgsiylklgdyeeAkeyyekaleldpdn 34 
                                   +++i++++++ye+A  ++  +++++pd+
  gi|70607822|ref|YP_256692.1| 109 KARILFEMQEYEQAFDVLTYVIKMKPDD 136
                                   89************************86 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.082
                                   CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                   e+ ++ +++   +g++  A + +++ale++ +
  gi|70607822|ref|YP_256692.1| 138 ESRLLRAQCFYLTGKFLDALKEINRALEYNNK 169
                                   56678889999999999999999999999987 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.7
                                   HHHHHHHHHTT-HHHHHHHHH CS
                         TPR_8   5 ynlgsiylklgdyeeAkeyye 25 
                                    ++g+iyl++  y+ A + ++
  gi|70607822|ref|YP_256692.1| 175 TLKGKIYLETHFYKLALSEFK 195
                                   678999988766666666555 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                         TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                   yy+l+     +g+  +A++  ekal+ldp+n
  gi|70607822|ref|YP_256692.1| 207 YYLLAFSEYMTGECGNAISDSEKALSLDPNN 237
                                   5555555555566679*************97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       6.5   4.8e+03       8      24 ..      13      29 ..      11      31 .. 0.74
   2 !   15.1   0.1   4.2e-05     0.031       1      42 [.      35      76 ..      35      78 .. 0.93
   3 ?    5.9   0.0     0.038        28       4      43 ..      72     111 ..      69     112 .. 0.92
   4 ?    5.9   0.0     0.038        28       8      44 .]     110     146 ..     107     146 .. 0.92
   5 !    8.9   0.0    0.0041         3       2      43 ..     138     179 ..     137     180 .. 0.92
   6 ?    0.8   0.0       1.6   1.2e+03      12      39 ..     215     242 ..     204     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 6.5
                        TPR_14  8 aeallalGdpdeAiall 24
                                  ae l + Gd+ eA+++l
  gi|70607822|ref|YP_256692.1| 13 AERLIEKGDYPEALNVL 29
                                  45577788888888876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.2e-05
                        TPR_14  1 peallalaeallalGdpdeAiallrralalaPddaeawllla 42
                                  pea+ ++ +a+ + G+ +eAi+ l++ + ++P     +++la
  gi|70607822|ref|YP_256692.1| 35 PEAYILRSKAYIEMGKSEEAIRELKEGINRFPYAHYMYYELA 76
                                  7999****************************9999999988 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.038
                        TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   +++la ++++  d+  A++  + al+  P + +++ l a+
  gi|70607822|ref|YP_256692.1|  72 YYELALLYFNHNDLVNALDEVNNALSILPYSYDYNKLKAR 111
                                   899**************************99999888887 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.038
                        TPR_14   8 aeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                   a++l++ +++++A ++l  +++  Pdd e +ll aq+
  gi|70607822|ref|YP_256692.1| 110 ARILFEMQEYEQAFDVLTYVIKMKPDDVESRLLRAQC 146
                                   899**************************99999986 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0041
                        TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                   e +l++a+ ++  G++ +A++  +ral+ + +d+++++l ++
  gi|70607822|ref|YP_256692.1| 138 ESRLLRAQCFYLTGKFLDALKEINRALEYNNKDETLHTLKGK 179
                                   678999*****************************9999886 PP

  == domain 6  score: 0.8 bits;  conditional E-value: 1.6
                        TPR_14  12 lalGdpdeAiallrralalaPddaeawl 39 
                                   +  G+   Ai   ++al+l+P++ +++ 
  gi|70607822|ref|YP_256692.1| 215 YMTGECGNAISDSEKALSLDPNNNVIRE 242
                                   555555566666689******9987775 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.85   6.3e+02      13      21 ..      18      26 ..      16      31 .. 0.83
   2 ?    4.9   0.0     0.033        25       9      22 ..      43      56 ..      35      66 .. 0.77
   3 !    9.7   0.6    0.0011      0.79       3      32 ..      71     100 ..      69     102 .. 0.90
   4 !    7.7   0.1    0.0044       3.3       7      34 .]     109     136 ..     105     136 .. 0.91
   5 !   10.3   0.2   0.00068      0.51       6      31 ..     142     167 ..     137     170 .. 0.88
   6 !    7.5   0.1     0.005       3.7       5      34 .]     208     237 ..     204     237 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.85
                                  HTT-HHHHH CS
                         TPR_1 13 klgkydeAl 21
                                  ++g+y eAl
  gi|70607822|ref|YP_256692.1| 18 EKGDYPEAL 26
                                  579999998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.033
                                  HHHHHTT-HHHHHH CS
                         TPR_1  9 nayfklgkydeAle 22
                                   ay ++gk +eA+ 
  gi|70607822|ref|YP_256692.1| 43 KAYIEMGKSEEAIR 56
                                  69**********97 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                         TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                    +y l+++yf+ +++  Al+  + AL++ P
  gi|70607822|ref|YP_256692.1|  71 MYYELALLYFNHNDLVNALDEVNNALSILP 100
                                   59*****************99999998877 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0044
                                   HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                   ++ ++f++++y++A +    +++  P++
  gi|70607822|ref|YP_256692.1| 109 KARILFEMQEYEQAFDVLTYVIKMKPDD 136
                                   7889************999999999986 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00068
                                   HHHHHHHHTT-HHHHHHHHHHHHHHS CS
                         TPR_1   6 nlGnayfklgkydeAleyyekALeln 31 
                                    ++++++  gk+ +Al+  ++ALe n
  gi|70607822|ref|YP_256692.1| 142 LRAQCFYLTGKFLDALKEINRALEYN 167
                                   69**********************88 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.005
                                   HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                         TPR_1   5 ynlGnayfklgkydeAleyyekALelnPnn 34 
                                   y l+   +  g+   A+ + ekAL+l+Pnn
  gi|70607822|ref|YP_256692.1| 208 YLLAFSEYMTGECGNAISDSEKALSLDPNN 237
                                   555555555555556777779********8 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0032       2.4      23      71 ..      63     111 ..      14     113 .. 0.85
   2 !   23.3   0.0   7.2e-08   5.4e-05       4      69 ..     112     177 ..     108     180 .. 0.92
   3 ?   -1.0   0.0       2.6     2e+03      35      62 ..     210     237 ..     196     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                         TPR_9  23 llaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                                     +P +++ +++ +ll++  ++l  Al++ + +l++ p   d   ++a+
  gi|70607822|ref|YP_256692.1|  63 NRFPYAHYMYYELALLYFNHNDLVNALDEVNNALSILPYSYDYNKLKAR 111
                                   557889999*************************999988888877776 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 7.2e-08
                         TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                   i+ + +++e+a  v+  ++ ++Pdd+e r+ R+++ +  G +  Al++ +++l+ + ++++ ++++
  gi|70607822|ref|YP_256692.1| 112 ILFEMQEYEQAFDVLTYVIKMKPDDVESRLLRAQCFYLTGKFLDALKEINRALEYNNKDETLHTLK 177
                                   4478899***********************************************999999998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.6
                         TPR_9  35 RGlllaqlGclsaAladLeaylalapda 62 
                                    ++ ++  G    A+ d e +l+l+p++
  gi|70607822|ref|YP_256692.1| 210 LAFSEYMTGECGNAISDSEKALSLDPNN 237
                                   5666666777778888888888888865 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.4   2.4e-06    0.0018      19     100 ..      40     128 ..      21     138 .. 0.78
   2 !    8.8   0.0    0.0021       1.6      71     101 ..     132     163 ..     127     179 .. 0.73
   3 ?    3.9   0.1      0.07        53      55      92 ..     147     188 ..     143     200 .. 0.47

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                  SRP_TPR_like  19 fkvvaliklekyeeaLkllkkgs...alsedvrfEkaYvlYklkkykkalkilkkvea....eekvkvlksqvlYrlgsye 92 
                                    +  a+i+++k eea++ lk+g      ++ + +E a  ++  + + +al  ++++ +    +   + lk+ +l+ +++ye
  gi|70607822|ref|YP_256692.1|  40 LRSKAYIEMGKSEEAIRELKEGInrfPYAHYMYYELALLYFNHNDLVNALDEVNNALSilpySYDYNKLKARILFEMQEYE 120
                                   57789***************9986666789999********9999999887666554422214589*************** PP

                  SRP_TPR_like  93 kAYklLsk 100
                                   +A+++L+ 
  gi|70607822|ref|YP_256692.1| 121 QAFDVLTY 128
                                   *****954 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                  SRP_TPR_like  71 veaee.kvkvlksqvlYrlgsyekAYklLske 101
                                   ++ ++ +++ l++q++Y  g++ +A k + + 
  gi|70607822|ref|YP_256692.1| 132 MKPDDvESRLLRAQCFYLTGKFLDALKEINRA 163
                                   4555558999***************9888443 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.07
                  SRP_TPR_like  55 lYklkkykkalk....ilkkveaeekvkvlksqvlYrlgsye 92 
                                   +Y + k+ +alk     l+  +++e +++lk +++   ++y+
  gi|70607822|ref|YP_256692.1| 147 FYLTGKFLDALKeinrALEYNNKDETLHTLKGKIYLETHFYK 188
                                   344444444443100023333333455555555555555555 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0062       4.6      44      74 ..      34      64 ..      11      66 .. 0.87
   2 ?    3.2   0.5      0.14   1.1e+02       9      23 ..     109     123 ..      67     135 .. 0.58
   3 !    8.7   0.3    0.0028       2.1      10      73 ..     110     165 ..     101     169 .. 0.75
   4 ?    5.4   0.0     0.029        22       3      32 ..     204     233 ..     202     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0062
                        TPR_12 44 tattlrnLgrlyralgryeeAlelleealai 74
                                  + ++++  + +y ++g+ eeA++ l+e +++
  gi|70607822|ref|YP_256692.1| 34 LPEAYILRSKAYIEMGKSEEAIRELKEGINR 64
                                  567899999**************99998876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                        TPR_12   9 laavlrrlgrydeAl 23 
                                    a +l+++++y++A+
  gi|70607822|ref|YP_256692.1| 109 KARILFEMQEYEQAF 123
                                   344444455555444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0028
                        TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                   a +l+++++y++A++ l  ++ +      pd    ++++   +++++++g++ +Al+  ++al+
  gi|70607822|ref|YP_256692.1| 110 ARILFEMQEYEQAFDVLTYVIKMK-----PD---DVESRLLRAQCFYLTGKFLDALKEINRALE 165
                                   566666666666666666665555.....55...588999999999999999999999999998 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.029
                        TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                                   a  ++ la  ++  g++  A++  ekal +
  gi|70607822|ref|YP_256692.1| 204 AENYYLLAFSEYMTGECGNAISDSEKALSL 233
                                   556778888888888888888888888865 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       3.3   2.4e+03      12      26 ..      18      32 ..      11      33 .. 0.73
   2 !    8.5   0.0    0.0046       3.4       1      31 [.      36      66 ..      36      66 .. 0.89
   3 ?    4.0   0.0      0.13        93       3      20 ..      72      89 ..      70      97 .. 0.86
   4 ?    3.5   0.0      0.18   1.3e+02       7      28 ..     110     131 ..     108     135 .. 0.84
   5 ?    3.2   0.1      0.23   1.7e+02       2      27 ..     139     164 ..     138     167 .. 0.77
   6 ?   -1.0   0.0       4.7   3.5e+03       3      12 ..     186     195 ..     186     197 .. 0.85
   7 ?    1.3   0.0      0.88   6.6e+02       3      32 ..     207     236 ..     205     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.3
                                  HHHHHHHHHHHHHHH CS
                         TPR_6 12 klgdtdkAlealerl 26
                                  + gd+ +Al  l +l
  gi|70607822|ref|YP_256692.1| 18 EKGDYPEALNVLGNL 32
                                  547999999888765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0046
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                         TPR_6  1 dAlyklalsyrklgdtdkAlealerlikeYP 31
                                  +A+ ++ ++y+++g++++A++ l++ i+++P
  gi|70607822|ref|YP_256692.1| 36 EAYILRSKAYIEMGKSEEAIRELKEGINRFP 66
                                  57778889**************999888888 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.13
                                  HHHHHHHHHHHHHHHHHH CS
                         TPR_6  3 lyklalsyrklgdtdkAl 20
                                  +y lal+y++ +d  +Al
  gi|70607822|ref|YP_256692.1| 72 YYELALLYFNHNDLVNAL 89
                                  7*********77988886 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   7 alsyrklgdtdkAlealerlik 28 
                                   a+ +++++++++A + l  +ik
  gi|70607822|ref|YP_256692.1| 110 ARILFEMQEYEQAFDVLTYVIK 131
                                   89999988*****999877765 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                   + +++a++++ +g+  +Al+  +r +
  gi|70607822|ref|YP_256692.1| 139 SRLLRAQCFYLTGKFLDALKEINRAL 164
                                   67899*****9888888887666655 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 4.7
                                   HHHHHHHHHH CS
                         TPR_6   3 lyklalsyrk 12 
                                   +yklals +k
  gi|70607822|ref|YP_256692.1| 186 FYKLALSEFK 195
                                   59****9886 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.88
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                         TPR_6   3 lyklalsyrklgdtdkAlealerlikeYPd 32 
                                   +y+la s +++g+  +A+   e+ ++  P+
  gi|70607822|ref|YP_256692.1| 207 YYLLAFSEYMTGECGNAISDSEKALSLDPN 236
                                   899*****9987777777666666666665 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0     0.009       6.7     245     293 ..      46      94 ..      31     111 .. 0.82
   2 !   15.5   0.0     9e-06    0.0067     182     272 ..     116     209 ..     104     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.009
                                   HHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHT CS
                         ChAPs 245 lskkkeelAlevakravksaPsefktWalLvkvYikledienALltLNs 293
                                   ++  k+e A++  k++++  P +   +++L+  Y + +d+ nAL  +N 
  gi|70607822|ref|YP_256692.1|  46 IEMGKSEEAIRELKEGINRFPYAHYMYYELALLYFNHNDLVNALDEVNN 94 
                                   5556667788888999****************************98874 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9e-06
                                   HT-HHHHHHHHH...HHHTT-GGGHHHHHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHH CS
                         ChAPs 182 tkrydralelle...kLkeeepevvillarvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakr 259
                                    ++y++a ++l    k+k +++e   l a+ + l+ + +da+k +n++le ++kd  l +l+ +  l+ + ++lAl+  k 
  gi|70607822|ref|YP_256692.1| 116 MQEYEQAFDVLTyviKMKPDDVESRLLRAQCFYLTGKFLDALKEINRALEYNNKDETLHTLKGKIYLETHFYKLALSEFKI 196
                                   56778887777722245555567778889999************************************************* PP

                                   HHHH-TT-HHHHH CS
                         ChAPs 260 avksaPsefktWa 272
                                   +v++ P + + + 
  gi|70607822|ref|YP_256692.1| 197 SVSIRPTAENYYL 209
                                   **99998755444 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   3.1e-06    0.0023     182     250 ..      60     127 ..      37     136 .. 0.82
   2 !    7.9   0.1    0.0016       1.2     205     264 ..     116     175 ..     113     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                                   SS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                         NARP1 182 dsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevme 250
                                   +  ++++ a  +++y lA  y ++++  +Al+ +++a++  p + ++   Karil  + + ++A +v+ 
  gi|70607822|ref|YP_256692.1|  60 EGINRFPYA-HYMYYELALLYFNHNDLVNALDEVNNALSILPYSYDYNKLKARILFEMQEYEQAFDVLT 127
                                   445666666.7999******************************************9999999998876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                                   HT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-HHHHH CS
                         NARP1 205 lgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDRyiNs 264
                                   ++++e+A +++   i+ +p  ve  l +a+ +  +G + +A + +++a +  ++D  + +
  gi|70607822|ref|YP_256692.1| 116 MQEYEQAFDVLTYVIKMKPDDVESRLLRAQCFYLTGKFLDALKEINRALEYNNKDETLHT 175
                                   567777888888888888888888888888888888888888888877777777765555 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.4   2.6e+03      29      45 ..      13      29 ..      10      32 .. 0.87
   2 ?    3.6   0.0      0.11        82      23      48 ..      36      61 ..      35      65 .. 0.84
   3 !    7.9   0.0     0.005       3.7       5      46 ..      52      93 ..      48     114 .. 0.79
   4 ?    2.1   0.0      0.34   2.5e+02      28      50 ..     109     131 ..      89     133 .. 0.77
   5 !    8.9   0.0    0.0024       1.8      15      55 ..     130     170 ..     116     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.4
                        TPR_20 29 AlallaagryeeAleqL 45
                                  A+ l+++g+y eAl+ L
  gi|70607822|ref|YP_256692.1| 13 AERLIEKGDYPEALNVL 29
                                  788999********977 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                        TPR_20 23 darldlAlallaagryeeAleqLlei 48
                                  +a +  ++a+++ g+ eeA+ +L e 
  gi|70607822|ref|YP_256692.1| 36 EAYILRSKAYIEMGKSEEAIRELKEG 61
                                  56777899*************99775 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.005
                        TPR_20  5 apelaeleaalaanpddldarldlAlallaagryeeAleqLl 46
                                  ++ ++el++ ++  p  +   ++lAl+++  ++   Al++  
  gi|70607822|ref|YP_256692.1| 52 EEAIRELKEGINRFPYAHYMYYELALLYFNHNDLVNALDEVN 93
                                  67899********************************98753 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.34
                        TPR_20  28 lAlallaagryeeAleqLleilk 50 
                                    A+ l++ ++ye+A++ L  ++k
  gi|70607822|ref|YP_256692.1| 109 KARILFEMQEYEQAFDVLTYVIK 131
                                   58889999*********999887 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0024
                        TPR_20  15 laanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                   ++ +pdd++ rl  A+  +  g+  +Al+++ + l+ + k+
  gi|70607822|ref|YP_256692.1| 130 IKMKPDDVESRLLRAQCFYLTGKFLDALKEINRALEYNNKD 170
                                   6789*************************999988877665 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.088        65      13      33 ..      35      55 ..      18      56 .. 0.80
   2 ?    5.9   0.3     0.026        19       6      33 ..      62      89 ..      57      90 .. 0.78
   3 !    9.4   0.0    0.0019       1.5       5      33 ..     129     157 ..     126     158 .. 0.90
   4 ?    3.9   0.1      0.11        82       3      25 ..     161     183 ..     159     192 .. 0.90
   5 ?   -1.1   0.1       4.4   3.3e+03      13      25 ..     204     216 ..     204     222 .. 0.77
   6 ?    3.2   0.0      0.18   1.4e+02       3      12 ..     228     237 ..     228     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.088
                        TPR_17 13 adaynnLAelllknGdlmtAr 33
                                  ++ay ++ +++ + G++++A+
  gi|70607822|ref|YP_256692.1| 35 PEAYILRSKAYIEMGKSEEAI 55
                                  577888888888****99997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.026
                        TPR_17  6 leldPnnadaynnLAelllknGdlmtAr 33
                                  + + P   + y++LA l+ + +dl  A+
  gi|70607822|ref|YP_256692.1| 62 INRFPYAHYMYYELALLYFNHNDLVNAL 89
                                  5555666677*************98875 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0019
                        TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                   +++  P+++++  ++A++++  G++ +A+
  gi|70607822|ref|YP_256692.1| 129 VIKMKPDDVESRLLRAQCFYLTGKFLDAL 157
                                   68999***************999988876 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.11
                        TPR_17   3 lkaleldPnnadaynnLAelllk 25 
                                    +ale++ ++  +++++++++l+
  gi|70607822|ref|YP_256692.1| 161 NRALEYNNKDETLHTLKGKIYLE 183
                                   69*******************85 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 4.4
                        TPR_17  13 adaynnLAelllk 25 
                                   a+ y++LA   ++
  gi|70607822|ref|YP_256692.1| 204 AENYYLLAFSEYM 216
                                   6789***987665 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 0.18
                        TPR_17   3 lkaleldPnn 12 
                                   +kal ldPnn
  gi|70607822|ref|YP_256692.1| 228 EKALSLDPNN 237
                                   79*******9 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         3   2.3e+03      15      31 ..      13      29 ..       6      34 .. 0.82
   2 ?    4.4   0.0     0.025        19     148     178 ..      37      67 ..      25      80 .. 0.89
   3 ?    2.5   0.0     0.092        69      14      40 ..     108     134 ..      94     139 .. 0.77
   4 ?    0.7   0.0      0.32   2.4e+02     151     182 ..     142     173 ..     135     177 .. 0.79
   5 !    6.8   0.0    0.0045       3.4     145     184 ..     205     242 ..     188     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                        TPR_15 15 atllykqgdvkkAlevL 31
                                  a+ l ++gd+ +Al+vL
  gi|70607822|ref|YP_256692.1| 13 AERLIEKGDYPEALNVL 29
                                  67788999999999999 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.025
                        TPR_15 148 fllaraelyrqegqtdaAlrdyreAlalapd 178
                                    +++r+++y + g++++A+r ++e+++++p 
  gi|70607822|ref|YP_256692.1|  37 AYILRSKAYIEMGKSEEAIRELKEGINRFPY 67 
                                   5789***********************9985 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.092
                        TPR_15  14 l.atllykqgdvkkAlevLkeaaqkaap 40 
                                   l a++l++ +++++A+ vL +++ k +p
  gi|70607822|ref|YP_256692.1| 108 LkARILFEMQEYEQAFDVL-TYVIKMKP 134
                                   469****************.66666644 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.32
                        TPR_15 151 araelyrqegqtdaAlrdyreAlalapdssel 182
                                   +ra+    +g+  +Al+ + +Al+++ ++++l
  gi|70607822|ref|YP_256692.1| 142 LRAQCFYLTGKFLDALKEINRALEYNNKDETL 173
                                   67777777888888888889998888888876 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0045
                        TPR_15 145 saafllaraelyrqegqtdaAlrdyreAlalapdsselra 184
                                   + ++lla +e+   +g+  +A+ d ++Al+l+p+++ +r+
  gi|70607822|ref|YP_256692.1| 205 ENYYLLAFSEY--MTGECGNAISDSEKALSLDPNNNVIRE 242
                                   55667777666..57999****************999987 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.5   1.9e+03       2      12 ..      24      34 ..      21      34 .. 0.72
   2 ?    5.7   0.0     0.013       9.8      15      30 ..     151     166 ..     148     169 .. 0.89
   3 !    7.0   0.0    0.0054         4      10      31 ..     180     201 ..     173     206 .. 0.88
   4 ?    1.4   0.0       0.3   2.2e+02      20      30 ..     223     233 ..     221     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                      SHNi-TPR  2 dvydlLGEisl 12
                                  + ++ LG++sl
  gi|70607822|ref|YP_256692.1| 24 EALNVLGNLSL 34
                                  55677888886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                      SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                   ++F +A+++ ++aLe+
  gi|70607822|ref|YP_256692.1| 151 GKFLDALKEINRALEY 166
                                   79************97 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0054
                      SHNi-TPR  10 islEnenFpqAveDlrkaLeLr 31 
                                   i lE+++++ A+++++ ++ +r
  gi|70607822|ref|YP_256692.1| 180 IYLETHFYKLALSEFKISVSIR 201
                                   679*****************99 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.3
                      SHNi-TPR  20 AveDlrkaLeL 30 
                                   A++D +kaL L
  gi|70607822|ref|YP_256692.1| 223 AISDSEKALSL 233
                                   9********97 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.075        56     279     305 ..      34      60 ..      23      63 .. 0.88
   2 ?    3.6   0.1     0.049        36     116     151 ..      63      98 ..      58     113 .. 0.86
   3 ?    4.9   0.0     0.019        14     278     309 ..     135     166 ..     101     176 .. 0.75
   4 ?   -2.3   0.0       2.9   2.2e+03       8      36 ..     211     239 ..     207     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.075
                      TPR_MalT 279 lieiliLqalalqaqgreeeAlaaLeq 305
                                   l e+ iL++ a+ ++g++eeA+++L++
  gi|70607822|ref|YP_256692.1|  34 LPEAYILRSKAYIEMGKSEEAIRELKE 60 
                                   56789******************9986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.049
                      TPR_MalT 116 qqlplvgfllvlladllyEwndLeeAeqhlqeGiel 151
                                    ++p +  ++ +la l++  ndL  A + +++++ +
  gi|70607822|ref|YP_256692.1|  63 NRFPYAHYMYYELALLYFNHNDLVNALDEVNNALSI 98 
                                   6789999999999**********9999988888776 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                      TPR_MalT 278 slieiliLqalalqaqgreeeAlaaLeqALeL 309
                                   + +e+ +L+a+ ++ +g+  +Al+++ +ALe+
  gi|70607822|ref|YP_256692.1| 135 DDVESRLLRAQCFYLTGKFLDALKEINRALEY 166
                                   567889999*******************9987 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.9
                      TPR_MalT   8 AllaiasgdaeralelArqALallpeddl 36 
                                   A+   ++g+ + a+  +++AL+l p++++
  gi|70607822|ref|YP_256692.1| 211 AFSEYMTGECGNAISDSEKALSLDPNNNV 239
                                   66677889999999999999999998886 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.011       8.4     114     136 ..       7      29 ..       1      33 [. 0.82
   2 ?    5.3   0.0     0.023        17      10      95 ..      44     177 ..      37     180 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHTT-HHHHHHHH CS
                          YfdX 114 paavkkAaelleegkyyeAkeaL 136
                                   ++ +++A +l+e+g+y eA ++L
  gi|70607822|ref|YP_256692.1|   7 EDPIYEAERLIEKGDYPEALNVL 29 
                                   66789999999999999999998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.023
                                   HHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-...............S--SSSS......................... CS
                          YfdX  10 laldqgdtkeAkkllekAqgkleaaladdpklvk...............kapasad......................... 50 
                                   + +++g+++eA+++l++  +++  a  ++ +l                       +                         
  gi|70607822|ref|YP_256692.1|  44 AYIEMGKSEEAIRELKEGINRFPYAHYMYYELALlyfnhndlvnaldevN-----Nalsilpysydynklkarilfemqey 119
                                   56667777777777776666666665555555334444332222222220.....02222222222222222233334444 PP

                                   ...........-EEEEEEEEEEE--..----HHHHHHHHHHHHHHHTT-HHHHHHHHH CS
                          YfdX  51 ...........alvPvdaevividd..ladtpekkaaikkanellkkgdtqaArelLk 95 
                                              ++ P d+e  +     +  t +   a+k++n++l++++++++ ++Lk
  gi|70607822|ref|YP_256692.1| 120 eqafdvltyviKMKPDDVESRLLRAqcFYLTGKFLDALKEINRALEYNNKDETLHTLK 177
                                   4444444433333333333222222225555566666777777777777777777665 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.32   2.4e+02     104     125 ..      39      60 ..      30      65 .. 0.80
   2 ?   10.6   0.0   0.00058      0.43      64     106 ..     146     188 ..     137     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.32
                                   HHHHHHHHHTT-HHHHHHHHHH CS
                       DUF3856 104 fsravaleelGrkdealkafrm 125
                                   + r++a+ e+G+++ea+++++ 
  gi|70607822|ref|YP_256692.1|  39 ILRSKAYIEMGKSEEAIRELKE 60 
                                   5578899999999999988775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                                   HHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHH CS
                       DUF3856  64 alaklgrydealesadkalryfnrrGeleqdeGklWiaavfsr 106
                                    +   g++ +al+ +++al+y n+   l+  +Gk+++ + f +
  gi|70607822|ref|YP_256692.1| 146 CFYLTGKFLDALKEINRALEYNNKDETLHTLKGKIYLETHFYK 188
                                   5666799****************************99876655 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.26   1.9e+02      69      87 ..      12      30 ..       7      34 .. 0.63
   2 ?    7.1   0.0    0.0078       5.8      66      91 ..      38      63 ..      36      68 .. 0.86
   3 ?   -0.1   0.0       1.4     1e+03      77      92 ..      83      98 ..      70     139 .. 0.65
   4 ?    1.8   0.1      0.33   2.5e+02      66      97 ..     156     187 ..     151     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
                       DUF4363 69 klkayietedkeealaela 87
                                  +++ +ie++d++eal  l 
  gi|70607822|ref|YP_256692.1| 12 EAERLIEKGDYPEALNVLG 30
                                  5666777777777766554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0078
                       DUF4363 66 slaklkayietedkeealaelaelkf 91
                                   + + kayie++  eea+ el+e ++
  gi|70607822|ref|YP_256692.1| 38 YILRSKAYIEMGKSEEAIRELKEGIN 63
                                  57899****************98765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.4
                       DUF4363 77 edkeealaelaelkfl 92
                                  +d  +al e++++ ++
  gi|70607822|ref|YP_256692.1| 83 NDLVNALDEVNNALSI 98
                                  3333333333333333 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.33
                       DUF4363  66 slaklkayietedkeealaelaelkfllehik 97 
                                   +l++++  +e+++k+e l +l+  ++l  h++
  gi|70607822|ref|YP_256692.1| 156 ALKEINRALEYNNKDETLHTLKGKIYLETHFY 187
                                   68899999999999999998887766666665 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         5   3.7e+03     123     137 ..      16      30 ..      13      39 .. 0.73
   2 ?   10.8   0.1   0.00039      0.29      57     140 ..      50     130 ..      38     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5
                        TPR_21 123 llaekkydeAlktLe 137
                                   l+++++y eAl+ L 
  gi|70607822|ref|YP_256692.1|  16 LIEKGDYPEALNVLG 30 
                                   678888888888875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                        TPR_21  57 kakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLe 137
                                   k +ea++el++  ++ +Ya++    lA   ++++dl +A  + +++l+  +     +  +l+ ar+l+++++y++A   L+
  gi|70607822|ref|YP_256692.1|  50 KSEEAIRELKEGINRFPYAHYMYYELALLYFNHNDLVNALDEVNNALSILPYS--YDYNKLK-ARILFEMQEYEQAFDVLT 127
                                   578999****************************************9988665..4555666.9999********999997 PP

                        TPR_21 138 akk 140
                                    + 
  gi|70607822|ref|YP_256692.1| 128 YVI 130
                                   553 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0042       3.1      64     117 ..      37      90 ..      11     100 .. 0.87
   2 ?    2.3   0.0      0.28   2.1e+02      73     120 ..     114     161 ..     106     183 .. 0.68
   3 ?   -1.9   0.0       5.7   4.2e+03      72      95 ..     214     237 ..     190     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0042
                                   HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHH CS
                          BTAD  64 alealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALe 117
                                   a+  + +a +++G+ eea++el++ ++  P+   ++ +l + ++  ++   AL 
  gi|70607822|ref|YP_256692.1|  37 AYILRSKAYIEMGKSEEAIRELKEGINRFPYAHYMYYELALLYFNHNDLVNALD 90 
                                   5667788999**********************9999999988888888777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                                   HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                          BTAD  73 lrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                   +++ ++e+a + l+  ++++P + +++ +  ++ + +G+  +AL+  +
  gi|70607822|ref|YP_256692.1| 114 FEMQEYEQAFDVLTYVIKMKPDDVESRLLRAQCFYLTGKFLDALKEIN 161
                                   566677777777777777777777777777777777777777776544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.7
                                   HHHTT-HHHHHHHHHHHHHHSTT- CS
                          BTAD  72 elrlGraeealaelealvaehPlr 95 
                                   e   G+  +a+++ e++++++P +
  gi|70607822|ref|YP_256692.1| 214 EYMTGECGNAISDSEKALSLDPNN 237
                                   445577777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1548.40
//
Query:       gi|70607823|ref|YP_256693.1|  [L=504]
Description: 4Fe-4S binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-10   39.4  12.1    0.00077   20.0   0.4    3.6  3  Fer4_7     4Fe-4S dicluster domain
    1.3e-08   34.8  15.3    0.00028   20.9   0.3    3.8  4  Fer4_10    4Fe-4S dicluster domain
    2.6e-08   33.3  30.0    6.3e-05   22.6   4.1    4.6  5  Fer4       4Fe-4S binding domain
      4e-08   33.0  26.6    0.00049   20.0   5.3    4.0  4  Fer4_6     4Fe-4S binding domain
    1.7e-07   31.2  10.4    1.3e-06   28.4   4.9    2.8  2  Fer4_21    4Fe-4S dicluster domain
    9.9e-06   25.6   4.3    9.9e-06   25.6   4.3    3.5  3  Fer4_9     4Fe-4S dicluster domain
    0.00013   21.8  27.2     0.0019   18.2   3.5    4.6  4  Fer4_2     4Fe-4S binding domain
      0.005   17.3  15.8       0.34   11.4   1.3    3.7  3  Fer4_8     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.019   15.7  13.6        2.5    8.9   8.8    3.5  2  Fer4_15    4Fe-4S single cluster domain
      0.025   15.1   2.7      0.025   15.1   2.7    4.6  4  Fer4_4     4Fe-4S binding domain
      0.094   13.3  17.5        1.6    9.3   0.3    4.3  4  Fer4_17    4Fe-4S dicluster domain
        0.1   12.3   0.0       0.27   10.9   0.0    1.7  1  CRAL_TRIO  CRAL/TRIO domain
       0.17   12.4  11.2        1.7    9.2   0.6    3.5  3  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
       0.33   11.9  13.8       0.78   10.7   3.4    3.7  3  Fer4_16    4Fe-4S double cluster binding domain
        3.4    7.8   7.5         29    4.9   0.0    3.4  3  DUF678     Protein of unknown function (DUF678)


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0065       7.8      33      45 ..     174     186 ..     142     188 .. 0.79
   2 !   20.0   0.4   6.4e-07   0.00077      19      48 ..     356     385 ..     348     388 .. 0.87
   3 !   17.8   1.7   3.1e-06    0.0037       2      43 ..     408     452 ..     407     487 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0065
                        Fer4_7  33 idpekClgCgaCv 45 
                                    dp+kC++Cg C 
  gi|70607823|ref|YP_256693.1| 174 SDPDKCTSCGFCS 186
                                   4789999999885 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.4e-07
                        Fer4_7  19 ldeeenekgtekveidpekClgCgaCvavC 48 
                                   l+ee++ +g+ kv++dp+kC+ Cg+Cv+ C
  gi|70607823|ref|YP_256693.1| 356 LNEEDEIPGVFKVVVDPDKCVLCGVCVRSC 385
                                   5677778899******************** PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.1e-06
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..gt.ekveidpekClgCga 43 
                                   Cig ++Cv++Cp +ai+l  + + k  g+   v     kC +Cg+
  gi|70607823|ref|YP_256693.1| 408 CIGSQRCVRNCPEGAITLVGSVKIKelGNrSVVSATIGKCKYCGK 452
                                   ******************988777744332445567889999975 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.3    0.0066       7.9       3      16 ..     173     186 ..     168     188 .. 0.84
   2 !   15.8   1.1   9.2e-06     0.011       1      19 [.     367     385 ..     367     399 .. 0.86
   3 !   20.9   0.3   2.3e-07   0.00028       3      50 ..     402     452 ..     400     456 .. 0.91
   4 ?   -2.2   0.1       3.8   4.6e+03      38      48 ..     475     485 ..     461     487 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0066
                       Fer4_10   3 vidddtCirCgkCv 16 
                                   v d+d+C+ Cg C 
  gi|70607823|ref|YP_256693.1| 173 VSDPDKCTSCGFCS 186
                                   67899999999995 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.2e-06
                       Fer4_10   1 kvvidddtCirCgkCvkaC 19 
                                   kvv+d+d+C+ Cg Cv++C
  gi|70607823|ref|YP_256693.1| 367 KVVVDPDKCVLCGVCVRSC 385
                                   6899*************** PP

  == domain 3  score: 20.9 bits;  conditional E-value: 2.3e-07
                       Fer4_10   3 vidddtCirCgkCvkaCPadl...tsvgakgeaseeeavrkkvekCtgcga 50 
                                   ++d + Ci+ ++Cv+ CP  +    ++++++e  + ++v+  ++kC  cg+
  gi|70607823|ref|YP_256693.1| 402 YHDLSYCIGSQRCVRNCPEGAitlVGSVKIKELGNRSVVSATIGKCKYCGK 452
                                   67999**************99999999999999999999**********96 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.8
                       Fer4_10  38 vrkkvekCtgc 48 
                                   +++ v+ C +c
  gi|70607823|ref|YP_256693.1| 475 IEDYVDVCNDC 485
                                   45555555555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.8   4.4e-05     0.053       4      15 ..     175     186 ..     173     188 .. 0.90
   2 !   22.6   4.1   5.3e-08   6.3e-05       1      18 [.     368     385 ..     368     389 .. 0.93
   3 !   15.1   0.1   1.3e-05     0.015       2      24 .]     402     424 ..     401     424 .. 0.92
   4 ?   -0.8   1.9       1.3   1.5e+03       7      12 ..     446     451 ..     445     452 .. 0.85
   5 ?   -2.9   0.2         6   7.2e+03       6      12 ..     480     486 ..     479     487 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                   ETTTSSS-THHH CS
                          Fer4   4 deekCigCGaCv 15 
                                   d++kC+ CG C 
  gi|70607823|ref|YP_256693.1| 175 DPDKCTSCGFCS 186
                                   9**********5 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.3e-08
                                   EEEETTTSSS-THHHHHS CS
                          Fer4   1 vvideekCigCGaCvevC 18 
                                   vv+d++kC+ CG Cv  C
  gi|70607823|ref|YP_256693.1| 368 VVVDPDKCVLCGVCVRSC 385
                                   69**************** PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.3e-05
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   + d + Cig  +Cv  CP gAIt
  gi|70607823|ref|YP_256693.1| 402 YHDLSYCIGSQRCVRNCPEGAIT 424
                                   679999****************7 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.3
                                   TSSS-T CS
                          Fer4   7 kCigCG 12 
                                   kC +CG
  gi|70607823|ref|YP_256693.1| 446 KCKYCG 451
                                   9****9 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 6
                                   TTSSS-T CS
                          Fer4   6 ekCigCG 12 
                                   + C  C+
  gi|70607823|ref|YP_256693.1| 480 DVCNDCK 486
                                   6688886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   1.3   0.00048      0.57       5      15 ..     175     185 ..     173     186 .. 0.91
   2 !   20.0   5.3   4.1e-07   0.00049       1      19 [.     367     385 ..     367     387 .. 0.96
   3 !   17.2   0.2   3.3e-06    0.0039       4      24 .]     403     423 ..     401     423 .. 0.91
   4 ?   -2.8   0.9         7   8.3e+03      12      15 ..     482     485 ..     480     486 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                        Fer4_6   5 dpdkCigCgdC 15 
                                   dpdkC++Cg C
  gi|70607823|ref|YP_256693.1| 175 DPDKCTSCGFC 185
                                   9********** PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.1e-07
                        Fer4_6   1 vveidpdkCigCgdCvrvC 19 
                                   +v++dpdkC+ Cg Cvr C
  gi|70607823|ref|YP_256693.1| 367 KVVVDPDKCVLCGVCVRSC 385
                                   69****************9 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.3e-06
                        Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                   +d + Cig  +Cvr+CPegai
  gi|70607823|ref|YP_256693.1| 403 HDLSYCIGSQRCVRNCPEGAI 423
                                   57789***************8 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7
                        Fer4_6  12 CgdC 15 
                                   C+dC
  gi|70607823|ref|YP_256693.1| 482 CNDC 485
                                   5555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.023        27      37      48 ..     175     186 ..     160     195 .. 0.76
   2 !   28.4   4.9   1.1e-09   1.3e-06       2      58 ..     369     424 ..     368     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.023
                       Fer4_21  37 vedeCvGCnlCs 48 
                                     d+C+ C  Cs
  gi|70607823|ref|YP_256693.1| 175 DPDKCTSCGFCS 186
                                   357888888886 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-09
                       Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                   ++d+dkC+ Cg C+ +C+    +  +++++t+l +  + C+G + C+  CP e++i+
  gi|70607823|ref|YP_256693.1| 369 VVDPDKCVLCGVCVRSCQMLVFDIKNTSSSTTLYHDLSYCIGSQRCVRNCP-EGAIT 424
                                   689***************98888778888888899999*************.89998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.042        50      34      42 ..     177     185 ..     143     188 .. 0.72
   2 !   25.6   4.3   8.2e-09   9.9e-06       1      51 []     374     423 ..     374     423 .. 0.85
   3 !    6.9   7.0    0.0058         7       1      41 [.     407     452 ..     407     488 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.042
                        Fer4_9  34 eaCigCgaC 42 
                                   ++C++Cg C
  gi|70607823|ref|YP_256693.1| 177 DKCTSCGFC 185
                                   579999988 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 8.2e-09
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kC+ Cg Cv++C++ v+  ++      l ++  + Cig ++Cv  Cp+gai
  gi|70607823|ref|YP_256693.1| 374 KCVLCGVCVRSCQMLVFDIKNTSSSTTLYHDL-SYCIGSQRCVRNCPEGAI 423
                                   7****************888877766665433.46*************997 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0058
                        Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.....eaCigCga 41 
                                   +C+g ++Cv+ Cp g+++   + ++ +l ++s       +C  Cg+
  gi|70607823|ref|YP_256693.1| 407 YCIGSQRCVRNCPEGAITLVGSVKIKELGNRSVvsatiGKCKYCGK 452
                                   69****************9999999999888879999988999985 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6    0.0001      0.12       5      16 ..     174     185 ..     170     187 .. 0.85
   2 !   18.2   3.5   1.6e-06    0.0019       2      20 ..     367     385 ..     366     386 .. 0.94
   3 !    7.2   0.2    0.0051         6       6      22 .]     404     420 ..     401     420 .. 0.82
   4 ?   -0.0   0.2      0.97   1.2e+03       7      14 ..     479     486 ..     475     487 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                        Fer4_2   5 vdtdrCigCgaC 16 
                                    d+d+C++Cg C
  gi|70607823|ref|YP_256693.1| 174 SDPDKCTSCGFC 185
                                   59********** PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.6e-06
                        Fer4_2   2 pvvvdtdrCigCgaCvsaC 20 
                                   +vvvd+d+C+ Cg Cv +C
  gi|70607823|ref|YP_256693.1| 367 KVVVDPDKCVLCGVCVRSC 385
                                   589***************9 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0051
                        Fer4_2   6 dtdrCigCgaCvsaCPa 22 
                                   d   Cig   Cv +CP+
  gi|70607823|ref|YP_256693.1| 404 DLSYCIGSQRCVRNCPE 420
                                   556699999*******5 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.97
                        Fer4_2   7 tdrCigCg 14 
                                    d C+ C+
  gi|70607823|ref|YP_256693.1| 479 VDVCNDCK 486
                                   589**996 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.035        42       3      12 ..     177     186 ..     175     198 .. 0.86
   2 !   10.1   8.5   0.00073      0.88       3      64 ..     373     421 ..     371     422 .. 0.73
   3 !   11.4   1.3   0.00028      0.34       2      55 ..     405     486 ..     404     487 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.035
                        Fer4_8   3 ekCieCgaCq 12 
                                   +kC+ Cg+C 
  gi|70607823|ref|YP_256693.1| 177 DKCTSCGFCS 186
                                   6899999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00073
                        Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                   +kC+ Cg C  +C       +  +d ++  +            + l +C + ++C+++Cp+g
  gi|70607823|ref|YP_256693.1| 373 DKCVLCGVCVRSCQ------MLVFDIKNTSSS-TTLY------HDLSYCIGSQRCVRNCPEG 421
                                   69***********5......344455555444.2223......3499*************97 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00028
                        Fer4_8   2 lekCieCgaCqsaCp...................vlrrtkkhlldargeaae.................dvqeeqvlee.. 44 
                                   l++Ci+ ++C  +Cp                   v++              +                 +++ ++ l++  
  gi|70607823|ref|YP_256693.1| 405 LSYCIGSQRCVRNCPegaitlvgsvkikelgnrsVVS--------------AtigkckycgkpldsikvKNRVSEILMSsg 471
                                   789***********97776655544333333333111..............122233333333333333333333333366 PP

                        Fer4_8  45 ....eealwsCttcg 55 
                                       e++++ C+ c+
  gi|70607823|ref|YP_256693.1| 472 indiEDYVDVCNDCK 486
                                   666788888888887 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.063        75       4      15 ..     175     186 ..     173     195 .. 0.89
   2 ?    8.9   8.8    0.0021       2.5       1      65 [.     368     424 ..     368     425 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
                       Fer4_15   4 DrdaCigcglCv 15 
                                   D d+C++cg C 
  gi|70607823|ref|YP_256693.1| 175 DPDKCTSCGFCS 186
                                   89*********6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                       Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaa..qeAaraCPvdAIr 65 
                                   VvvD d+C  cg+Cv+ ++ + ++d +  +         +++++  d+  ++  q+ +r+CP++AI+
  gi|70607823|ref|YP_256693.1| 368 VVVDPDKCVLCGVCVRSCQ-MLVFDIKNTS---------SSTTLYHDLSYCIgsQRCVRNCPEGAIT 424
                                   89***************96.7888854444.........2457788888877667888888888886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.7      0.04        48       1      10 [.     176     185 ..     176     186 .. 0.93
   2 ?   15.1   2.7   2.1e-05     0.025       1      14 [.     372     385 ..     372     388 .. 0.92
   3 ?    5.7   0.2     0.021        25       3      16 ..     407     420 ..     405     427 .. 0.87
   4 ?    1.3   0.7      0.52   6.3e+02       2       9 ..     480     487 ..     480     487 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.04
                        Fer4_4   1 qerCigCgsC 10 
                                   +++C+ Cg C
  gi|70607823|ref|YP_256693.1| 176 PDKCTSCGFC 185
                                   69*******9 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                        Fer4_4   1 qerCigCgsCvaaC 14 
                                   +++C+ Cg+Cv++C
  gi|70607823|ref|YP_256693.1| 372 PDKCVLCGVCVRSC 385
                                   69************ PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.021
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                    Cig  +Cv+ CP 
  gi|70607823|ref|YP_256693.1| 407 YCIGSQRCVRNCPE 420
                                   699999*******6 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.52
                        Fer4_4   2 erCigCgs 9  
                                   + C++C++
  gi|70607823|ref|YP_256693.1| 480 DVCNDCKQ 487
                                   57****97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.041        48       1      10 [.     178     187 ..     167     218 .. 0.83
   2 ?    8.1   2.0    0.0033         4      44      58 ..     373     387 ..     348     390 .. 0.80
   3 ?    9.3   0.3    0.0013       1.6      41      59 ..     403     421 ..     388     423 .. 0.79
   4 ?    1.7   6.8      0.32   3.8e+02       2      17 ..     408     423 ..     407     489 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.041
                       Fer4_17   1 rCiqCgyClp 10 
                                   +C++Cg+C  
  gi|70607823|ref|YP_256693.1| 178 KCTSCGFCSG 187
                                   5888888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0033
                       Fer4_17  44 slCieCgeCerkCPq 58 
                                   ++C+ Cg C+r+C +
  gi|70607823|ref|YP_256693.1| 373 DKCVLCGVCVRSCQM 387
                                   689999999999976 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0013
                       Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                   +  s Ci+ ++C+r CP+g
  gi|70607823|ref|YP_256693.1| 403 HDLSYCIGSQRCVRNCPEG 421
                                   6778899999999999986 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.32
                       Fer4_17   2 CiqCgyClpeCpsyea 17 
                                   Ci+++ C+++Cp +++
  gi|70607823|ref|YP_256693.1| 408 CIGSQRCVRNCPEGAI 423
                                   7777777777776555 PP

>> CRAL_TRIO  CRAL/TRIO domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.27      31     111 ..     145     230 ..     128     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                     CRAL_TRIO  31 pkklsleelvralvlvlerllkelee......dgqvegvtvviDlkglslskmlwkpisllkkilkilqdnyperlgkili 105
                                     ++s e+ +++l++++e ++ +++e      + +++++ +   ++ l+++ m++++++++  ++++l+++ p     i++
  gi|70607823|ref|YP_256693.1| 145 AQEISFEREMKYLSSLCELVV-KTPEgpqvsdPDKCTSCGFCSGMSFLGYLEMPNFSTDQVIAFINTLSKYAPTDKPGIVL 224
                                   556778899*********999.777778899899********************999****************88777777 PP

                     CRAL_TRIO 106 vnaPkl 111
                                   + + ++
  gi|70607823|ref|YP_256693.1| 225 ITCNRI 230
                                   777665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.042        50       2      13 ..     175     186 ..     173     189 .. 0.88
   2 ?    9.2   0.6    0.0014       1.7       1      22 [.     370     392 ..     370     402 .. 0.81
   3 ?    4.3   0.2     0.051        61       3      18 ..     405     420 ..     404     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                       Fer4_13   2 DrdtCiacgaCv 13 
                                   D d+C++cg C 
  gi|70607823|ref|YP_256693.1| 175 DPDKCTSCGFCS 186
                                   789********7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                       Fer4_13   1 VDrdtCiacgaCvelaPd.vFee 22 
                                   VD d+C+ cg+Cv  +   vF++
  gi|70607823|ref|YP_256693.1| 370 VDPDKCVLCGVCVRSCQMlVFDI 392
                                   9************9997535655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.051
                       Fer4_13   3 rdtCiacgaCvelaPd 18 
                                    + Ci+ + Cv  +P+
  gi|70607823|ref|YP_256693.1| 405 LSYCIGSQRCVRNCPE 420
                                   567************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.1   1.3e+03      53      60 ..     178     185 ..     146     188 .. 0.75
   2 ?    5.9   0.2     0.021        25       1      12 [.     374     385 ..     351     397 .. 0.81
   3 ?   10.7   3.4   0.00065      0.78       2      29 ..     408     433 ..     407     488 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
                       Fer4_16  53 aitgCdiC 60 
                                   ++t C+ C
  gi|70607823|ref|YP_256693.1| 178 KCTSCGFC 185
                                   55666666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                       Fer4_16   1 rCgtCgkCaevC 12 
                                   +C+ Cg C+ +C
  gi|70607823|ref|YP_256693.1| 374 KCVLCGVCVRSC 385
                                   466677777766 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00065
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare 29 
                                   C++ ++C+  CP++ai+     +++++e
  gi|70607823|ref|YP_256693.1| 408 CIGSQRCVRNCPEGAITLV--GSVKIKE 433
                                   9999*************88..5555444 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.024        29      18      32 ..     172     186 ..     164     200 .. 0.88
   2 ?    3.9   1.8      0.05        59      18      47 ..     368     398 ..     358     415 .. 0.80
   3 ?   -0.8   0.0       1.4   1.7e+03      43      70 ..     428     456 ..     422     459 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                        DUF678  18 tvededdctTCSlCq 32 
                                   +v d+d+ct C  C+
  gi|70607823|ref|YP_256693.1| 172 QVSDPDKCTSCGFCS 186
                                   499***********6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.05
                        DUF678  18 tvededdctTCSlC.qSkLvkvsdvskvsls 47 
                                   +v d+d+c+ C +C  S  + v d++++s s
  gi|70607823|ref|YP_256693.1| 368 VVVDPDKCVLCGVCvRSCQMLVFDIKNTSSS 398
                                   47899*********54666677788777655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.4
                        DUF678  43 kvslsklkvavgkgntl.rCaACgSsLtl 70 
                                    v++++l +    + t+ +C+ Cg  L +
  gi|70607823|ref|YP_256693.1| 428 SVKIKELGNRSVVSATIgKCKYCGKPLDS 456
                                   5677777777444444438****988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3212.50
//
Query:       gi|70607824|ref|YP_256694.1|  [L=180]
Description: hypothetical protein Saci_2107 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00059   20.0   0.0      0.002   18.3   0.0    1.7  2  HAD_2     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.13   2.4e+03     108     124 ..      16      32 ..       8      41 .. 0.75
   2 !   18.3   0.0   1.1e-07     0.002      86     177 ..      46     136 ..      35     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.13
                         HAD_2 108 aveekleqlgiesyFdv 124
                                   +++e l+q++  +yF+v
  gi|70607824|ref|YP_256694.1|  16 NLKEILKQIEGSDYFKV 32 
                                   56777888888888876 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.1e-07
                         HAD_2  86 elLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDie 166
                                   +lLeeL + + ++ i+T+  ++ + e l++++++s+++ +v++edv+    +p+ +e + + +++++    ++  ++  i 
  gi|70607824|ref|YP_256694.1|  46 YLLEEL-SYRGRIFIATNVPSKLAYEILNRFNLDSFITRVVSAEDVGMFTTNPKFFEYLYRMTGIQRGTGYFITSNTLSIN 125
                                   689999.77789***********************************9999999999999999999999999988888888 PP

                         HAD_2 167 aakkagikvia 177
                                    ak    kv++
  gi|70607824|ref|YP_256694.1| 126 NAKSHQFKVVM 136
                                   88888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1316.67
//
Query:       gi|70607825|ref|YP_256695.1|  [L=138]
Description: hypothetical protein Saci_2108 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-34  118.3   1.1    2.8e-34  117.8   1.1    1.2  1  DUF2299        Uncharacterized conserved protein (DUF2299)
  ------ inclusion threshold ------
      0.073   12.7   0.0      0.085   12.5   0.0    1.1  1  Amidoligase_2  Putative amidoligase enzyme


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   1.1   3.1e-38   2.8e-34       1     138 []       6     131 ..       6     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3.1e-38
                                   HHHHHHHHTT-EEEE---TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHH CS
                       DUF2299   1 eikeWLkeeGlkveevpdanaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselk 81 
                                   ei e++ke+G+kv+e +++ ++fh++++pp+ ++ +v++i+p++ s+++vv+m+++v++           + +k++l+e+ 
  gi|70607825|ref|YP_256695.1|   6 EIVEIFKELGMKVKEEKQQGLHFHVSISPPTANSAIVSIIRPTAFSKYYVVTMAIEVDPP----------KLNKKVLREIG 76 
                                   6899*******************************************************9..........9999******* PP

                                   HHHTTTT-EEEEE-TTS--.-EEEEEEEEEGGG--HHHHHHHHHHHHHHHHHHHHHH CS
                       DUF2299  82 rdLlrlcvdfqlipqdeelpqsiqvskeiykdgltknelldavkrvrnakllviwll 138
                                   ++L+rl+v+f ++p+d+  p++iq++k +y+++l+knel+++v+ v+na+++v+++l
  gi|70607825|ref|YP_256695.1|  77 VELARLNVEFYVMPPDK--PTTIQIAKLLYQEDLSKNELINTVTLVKNAGFIVFNIL 131
                                   *****************..9*********************************9875 PP

>> Amidoligase_2  Putative amidoligase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.4e-06     0.085      96     201 ..       6     115 ..       4     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-06
                 Amidoligase_2  96 elvraLreagavgtnas.cglhvHldaevpdleaetlrnllkilalledwleklldvdlarrlnpyckpldeeyver...v 172
                                   e+v++ +e g ++ +++  glh H+++++p+ + ++++ +  ++++++ +++ +++vd+  ++++  +++  e+ +     
  gi|70607825|ref|YP_256695.1|   6 EIVEIFKELGMKVKEEKqQGLHFHVSISPPTANSAIVSIIRPTAFSKYYVVTMAIEVDPPKLNKKVLREIGVELARLnveF 86 
                                   688999999999966669*************98888888888999999999999999997776666677777777765443 PP

                 Amidoligase_2 173 rleasksatldeliddylkrnptrnrald 201
                                   +  +  ++t  ++ + +++   ++n+  +
  gi|70607825|ref|YP_256695.1|  87 YVMPPDKPTTIQIAKLLYQEDLSKNELIN 115
                                   44466666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1076.64
//
Query:       gi|70607826|ref|YP_256696.1|  [L=349]
Description: polysulfide reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   47.3  30.1    7.6e-12   45.5  25.6    2.2  2  NrfD      Polysulphide reductase, NrfD
       0.01   15.9   0.1       0.01   15.9   0.1    2.9  3  DUF1361   Protein of unknown function (DUF1361)
  ------ inclusion threshold ------
      0.052   13.0  23.0      0.015   14.8  19.6    1.8  2  DmsC      DMSO reductase anchor subunit (DmsC)


Domain annotation for each model (and alignments):
>> NrfD  Polysulphide reductase, NrfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5  25.6   1.3e-15   7.6e-12      11     270 ..      28     263 ..      20     281 .. 0.76
   2 !    3.8   0.1    0.0061        37     285     310 ..     297     322 ..     291     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.3e-15
                          NrfD  11 WglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrpe.rflklllyynf... 87 
                                   W++++a +l+++g++ + + + ++l++  +  +    l+ r+  ++  ++ ++ l+   ++lg p   f++     n    
  gi|70607826|ref|YP_256696.1|  28 WDVTVALALYFTGLAGMLMAITSILEFTGRYPS----LVKRNSIFV-FIFAVLSLVAFDIHLGVPIrGFYAPA---NAfaa 100
                                   *************************99988443....344444443.22222234444457787772455444...33233 PP

                          NrfD  88 ..sSimswgvlllslyivvlvlyllvifekdlaakglpalgilaklislaervakilaiialilavllgsytgfllsavls 166
                                     +S+m+ g+ +  + +v++++++++    ++++         + +++       ++ai+ l+  +   +y gf lsa   
  gi|70607826|ref|YP_256696.1| 101 llNSWMARGIEFVGGLLVFSLIFMAI----KVLDV--------KNVVATW-----VFAILGLVAGIFSTTYSGFELSAATG 164
                                   568********999999999999655....22222........2333333.....57888899999999************ PP

                          NrfD 167 rplwnspllpvlFlasaiasGlavlllasllaarfekesedagllkklellvilteagllvilfvglaleggekiealeaa 247
                                    p+wn++ lp lFlas+i+ G a + ++sl+ +++e  ++ + l +kl+ + ++ e++  ++++  + +  + +  a++  
  gi|70607826|ref|YP_256696.1| 165 VPFWNNGGLPALFLASGIVGGSAWSYIISLVTKGEEGIRARR-LTAKLLAYSAVAELATWFLFMANVNFVYVFNEVAYNYM 244
                                   ********************************9975544433.44689999999999999999999999****99999997 PP

                          NrfD 248 lsggfltvlFwlgvvllglaipl 270
                                   +s+    v F+++++llgla ++
  gi|70607826|ref|YP_256696.1| 245 ISA----VTFVIDLALLGLAFVV 263
                                   777....***********98654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0061
                          NrfD 285 vvviasilalvgvlllrfllliagql 310
                                   ++++++ilalv +++ r  +l+agq 
  gi|70607826|ref|YP_256696.1| 297 IILVVAILALVSGFFTREDILFAGQY 322
                                   5799********************95 PP

>> DUF1361  Protein of unknown function (DUF1361)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.7e-06      0.01      67     133 ..      27     105 ..      14     125 .. 0.84
   2 ?   -0.9   0.1      0.23   1.4e+03      68      89 ..     132     153 ..     118     165 .. 0.77
   3 ?   -2.9   4.2      0.96   5.8e+03      32      72 ..     219     256 ..     187     325 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                       DUF1361  67 wldvlllislallglllgflslvivlkvlrkrlkekallkallvaliillLsavGiYlGRflR............lnSw 133
                                    +dv++ + l+++gl  ++++++ +l+ + ++ + +++ ++ ++++++l L a+ i+lG  +R            lnSw
  gi|70607826|ref|YP_256696.1|  27 EWDVTVALALYFTGLAGMLMAITSILEFTGRYPSLVKRNSIFVFIFAVLSLVAFDIHLGVPIRgfyapanafaalLNSW 105
                                   458999999999999999999999999999999988888799*****************99997777777777777777 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                       DUF1361  68 ldvlllislallglllgflslv 89 
                                    +v+   ++a+lgl++g++s +
  gi|70607826|ref|YP_256696.1| 132 KNVVATWVFAILGLVAGIFSTT 153
                                   5677778888999999988875 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.96
                       DUF1361  32 lalvwllflPNa..pYllTDlihlsekessileetslwldvll 72 
                                    ++ w+lf+ N   +Y++ ++ +     s ++     ++d++l
  gi|70607826|ref|YP_256696.1| 219 ELATWFLFMANVnfVYVFNEVAYNY-MISAVT----FVIDLAL 256
                                   4455666665432245555553332.112221....2222222 PP

>> DmsC  DMSO reductase anchor subunit (DmsC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  19.6   2.6e-06     0.015      24     184 ..      44     208 ..      23     275 .. 0.78
   2 ?   -3.0   0.1      0.69   4.1e+03     115     132 ..     295     312 ..     288     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                          DmsC  24 illalllllgknqalprevvlvgmfvlliLlgiGliasilHLGsplRAf....nalnrvgsSwLSrEivagaiffalagli 100
                                   +l+a+  +l+ +  + +  v +  ++++i  +  l+a  +HLG p+R f    na+  + +Sw+ r i + + +  +++++
  gi|70607826|ref|YP_256696.1|  44 MLMAITSILEFTGRY-PSLVKRNSIFVFIFAVLSLVAFDIHLGVPIRGFyapaNAFAALLNSWMARGIEFVGGLLVFSLIF 123
                                   456666666555555.777899999999999*****************97777899999*******998877778889999 PP

                          DmsC 101 wLvavlkklskaleklllivtailgiifvymmamvYasiktvptWhsgyTllaflltvlltGsvllyallqaakva.tvav 180
                                     + vl+        ++ i+  + gi +    +    + + vp W++g     fl   +++Gs  +y+++ ++k +  +  
  gi|70607826|ref|YP_256696.1| 124 MAIKVLDVKNVVATWVFAILGLVAGIFSTTYSGFELSAATGVPFWNNGGLPALFLASGIVGGSAWSYIISLVTKGEeGIRA 204
                                   9999998888888899**********9987777777779******************************987765534444 PP

                          DmsC 181 lalp 184
                                   + l+
  gi|70607826|ref|YP_256696.1| 205 RRLT 208
                                   4444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.69
                          DmsC 115 klllivtailgiifvymm 132
                                   k++ +v ail++++++ +
  gi|70607826|ref|YP_256696.1| 295 KIIILVVAILALVSGFFT 312
                                   566667778888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2565.57
//
Query:       gi|70607827|ref|YP_256697.1|  [L=435]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-17   61.1  38.9    8.5e-17   61.1  38.9    1.4  1  MFS_1        Major Facilitator Superfamily
    9.3e-14   51.1  27.4    1.8e-13   50.2  27.3    1.4  1  Sugar_tr     Sugar (and other) transporter
  ------ inclusion threshold ------
        0.2   11.4   0.1        0.2   11.4   0.1    2.3  3  ISK_Channel  Slow voltage-gated potassium channel


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1  38.9   1.4e-20   8.5e-17       2     343 ..      21     378 ..      20     388 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.4e-20
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdr.fGrrrvlllglllfalg.llll 79 
                                   + ++++ +++++++++++p ++  + +      + l+ l  +l+a++++l+l+++sdr +Gr+ +++++++l+++g +l++
  gi|70607827|ref|YP_256697.1|  21 FASVVVGYFMWGVISSIAP-LIYPSIN------SVLFLLtPTLAALAGNLILSFFSDRkLGRKVTFFITMTLYSVGtILII 94 
                                   6678899999999999999.6655555......4444445999***************9*****************44444 PP

                         MFS_1  80 lfa........ss......lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllas 146
                                   l a        ss      + l++++ +l  +g  + +p+++++ a++ p + r + + l   + ++Ga +++l+g l +s
  gi|70607827|ref|YP_256697.1|  95 L-AsvlsgfntSSlaqfpyILLIVIGIILGEFGVEGEVPIMLSYSAEMMPLNYRDSILILGPNFDNIGATVAALIGYLTYS 174
                                   4.22443444411555442335777888888999**************************************999998884 PP

                         MFS_1 147 slg.Wrav...fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl.....willialll 218
                                   + + ++       ++ai+++++++++ +llpe+ +    k ++ + ++ +++ +++ ++++ ++ ++     +i  +++l+
  gi|70607827|ref|YP_256697.1| 175 LSNsFTIEllaLSLVAILGIIFGIVIRFLLPESVRWLMAKGDISKAEREANKVAKE-IGEINTQTQVkddtsLISRYIFLV 254
                                   44455555112444445555555555555544444444444444436666777777.777777777744433245555555 PP

                         MFS_1 219 fffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtss 299
                                   +  ++++l++ l  +++ ++ +s   ++ +++ ++ l++ +++++a+ l++r++ r + l+++ +++l+ + ++ll +  +
  gi|70607827|ref|YP_256697.1| 255 IIGVTQYLTYGLMAFTVADYYFS-SSQTPFIIFIANLGASVSGFIATVLVRRINTRMFSLISYMGGALSMIPIVLLTMNFN 334
                                   5557777999999999*******.7*****************************999999999999999999999999955 PP

                         MFS_1 300 avllllvlvliGf.glgfvfpsllalasdlappeeagtasglfnt 343
                                     +++ +l++i + ++ f ++  + +   l+p++ +++++gl+ +
  gi|70607827|ref|YP_256697.1| 335 VGIFY-ILLFINMlFSEFSWAVRTLYEPVLMPNNIRAFMIGLVRI 378
                                   55555.6666777699999**********************9875 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2  27.3     3e-17   1.8e-13      44     387 ..      43     372 ..       8     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3e-17
                                   ...HHHHHHHTHHHHHHHHHHHHHHHHHH.TTHHHHHHHHHHHHHHHHHHHH-TTTT..........SS-TGGGGGHHHHH CS
                      Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdr.fGRkkslliaavlfvigavlqaaakgk..........nsvevlivgRvlvG 113
                                    s+ s l++    + a++G l++++++dr +GRk ++ i+ +l+++g++l+++a             + + +liv  +++G
  gi|70607827|ref|YP_256697.1|  43 PSINSVLFLLTPTLAALAGNLILSFFSDRkLGRKVTFFITMTLYSVGTILIILASVLsgfntsslaqFPYILLIVIGIILG 123
                                   567788899999999************9649************************98999999999988888888888888 PP

                                   .HHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-..TTHHHHHHHCCHHHHHHHHHHGGGS CS
                      Sugar_tr 114 .igvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn..adgwrillglqlvpallllilllfl 191
                                    +gv ++  ++  y +E+ p ++R  +  l   +  +G  vaa +g+ +   sn  + +   l  ++++  ++ ++++++l
  gi|70607827|ref|YP_256697.1| 124 eFGVEGEVPIMLSYSAEMMPLNYRDSILILGPNFDNIGATVAALIGYLTYSLSNsfTIELLALSLVAILGIIFGIVIRFLL 204
                                   89***********************************************7777723333333333333333445666799* PP

                                   ---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHH CS
                      Sugar_tr 192 PESPrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGina 272
                                   PES r+l+ kg+ ++a++   k      + +e+ e+ ++++ ++++      +l        r +  v + ++q lt+  +
  gi|70607827|ref|YP_256697.1| 205 PESVRWLMAKGDISKAEREANK------VAKEIGEINTQTQVKDDT------SL------ISRYIFLVIIGVTQYLTYGLM 267
                                   ******************9999......777888888877777443......23......336899999*********999 PP

                                   HHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHH CS
                      Sugar_tr 273 imyysptifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivai 353
                                    +  + + f++    ++  + +i      v+ f+a  lv+r+  R + l++ +g+a+ ++ +    ll+ + +    +++ 
  gi|70607827|ref|YP_256697.1| 268 AFTVADYYFSSSQ--TP-FIIFIANLGASVSGFIATVLVRRINTRMFSLISYMGGALSMIPIV---LLTMNFN---VGIFY 339
                                   9999999999853..44.555666666667777888899*********************994...4444443...44444 PP

                                   HHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHH CS
                      Sugar_tr 354 vfialfialfalgwgpvpwvlvsElfpqsvRska 387
                                   +++++ + + +++w+    ++ + l p+++R++ 
  gi|70607827|ref|YP_256697.1| 340 ILLFINMLFSEFSWAVRT-LYEPVLMPNNIRAFM 372
                                   444444566678887544.555556666666655 PP

>> ISK_Channel  Slow voltage-gated potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.64   3.9e+03      41      61 ..     116     137 ..      98     139 .. 0.69
   2 ?   11.4   0.1   3.3e-05       0.2      25      79 ..     233     288 ..     218     291 .. 0.79
   3 ?   -4.0   0.5       1.9   1.2e+04      38      49 ..     335     346 ..     325     354 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.64
                   ISK_Channel  41 lyillllgffgff.tlGimlsy 61 
                                   + i ++lg fg    + imlsy
  gi|70607827|ref|YP_256697.1| 116 IVIGIILGEFGVEgEVPIMLSY 137
                                   3444677778775247788888 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.3e-05
                   ISK_Channel  25 sssslaarseddklevlyilll.lgffgfftlGimlsyirskklehshdPynvyie 79 
                                   +  + ++ ++d++l   yi+l+ +g+  ++t G+m   +    +  s+ P+ ++i+
  gi|70607827|ref|YP_256697.1| 233 EINTQTQVKDDTSLISRYIFLViIGVTQYLTYGLMAFTVADYYFSSSQTPFIIFIA 288
                                   444555556688898999976527******************************98 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 1.9
                   ISK_Channel  38 levlyillllgf 49 
                                   + + yill++ +
  gi|70607827|ref|YP_256697.1| 335 VGIFYILLFINM 346
                                   567888887653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3050.78
//
Query:       gi|70607828|ref|YP_256698.1|  [L=565]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-42  145.9  69.7    1.5e-27   96.5  19.1    3.4  3  MFS_1     Major Facilitator Superfamily
    1.5e-06   27.4  35.6    1.5e-05   24.1  12.2    3.3  3  Sugar_tr  Sugar (and other) transporter
    0.00011   21.4   3.2    0.00011   21.4   3.2    2.9  3  PUCC      PUCC protein
    0.00043   18.8   1.7    0.00043   18.8   1.7    2.0  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5  19.1   3.3e-31   1.5e-27       3     173 ..      19     193 ..      17     212 .. 0.84
   2 !   62.8  28.2   5.7e-21   2.6e-17     126     350 ..     216     429 ..     208     432 .. 0.83
   3 ?   -1.5   6.6      0.21   9.4e+02     136     167 ..     519     544 ..     432     559 .. 0.77

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 3.3e-31
                         MFS_1   3 laaflsalarsilgpalplalaedlg....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                   +++++++++ si++++lp a+ +  +     s +++ ++l +y +++a + + +G lsd +Gr r++ lg+l+f +g++ll
  gi|70607828|ref|YP_256698.1|  19 IGVLMASINGSITIISLP-AIFRGINvnpfDSFQFLLWILMGYNVVTATFLVSFGKLSDIYGRVRLYNLGFLIFTVGSILL 98 
                                   788899999999999999.7766666223225566999***************************************6666 PP

                         MFS_1  80 lfa...sslwl..llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                   +++    sl +  l+++rv+qG+g+++lf+++aa+i+d fp +erg+a+g+ +++f  G+++g +lgg+l+  ++Wr+vf+
  gi|70607828|ref|YP_256698.1|  99 SITpnqGSLGAleLIIFRVIQGVGGAFLFSNSAAIITDAFPYNERGKALGINQIAFLGGSLIGLILGGILS-VINWRLVFL 178
                                   6654532233357*********************************************************9.99******* PP

                         MFS_1 156 ilaivsllafvlfllllp 173
                                   +  +v++l+ +   + ++
  gi|70607828|ref|YP_256698.1| 179 VSVPVGILGTI---WSYT 193
                                   *********99...5553 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 5.7e-21
                         MFS_1 126 lsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkd 206
                                   + + +s+ ++++++l ++ +s+lgW  +++i+++v  +a++ +++ ++e++++ +           ++ +l++ ++++ + 
  gi|70607828|ref|YP_256698.1| 216 AVGLISILVAVTYGLLPYGSSQLGWGNPYVIAGLVVGFALI-GAFIYVERKVQYPM----------FRLELFK-IRMFAAG 284
                                   455667778888888899999999**************955.44444444444444..........4456678.8999999 PP

                         MFS_1 207 pvl.w..illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallll 284
                                   ++  +  ++ ++ l++++++++  ++lp+     +  +  + ag+++  l+++++ +++++g+lsdr+g++   +l+++++
  gi|70607828|ref|YP_256698.1| 285 NFAsLlrSIAYGGLTIMLVIFLQGIWLPIH-GYSYEET-PFWAGIYMIPLMVGFVSMGPISGWLSDRYGAKLLATLGMVIV 363
                                   9665258999999999*************5.5556555.577775555555555556*************99999999999 PP

                         MFS_1 285 llaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                    +++l+l  l+   s++ ++++++++G+g g++ ++ +a +++++pp+++g+asg   t++++g  
  gi|70607828|ref|YP_256698.1| 364 GVGFLMLTTLPYNFSYPEFAAIIFFMGLGNGMFASPNTASIMNSVPPKYRGAASGMRATIQNIGQT 429
                                   9999999999999**************************************************976 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.21
                         MFS_1 136 lgpllggllasslgWravfyilaivsllafvl 167
                                   ++p +   l+   + r +fyi ai+++la++ 
  gi|70607828|ref|YP_256698.1| 519 IAPSF---LL---SLREAFYISAILCFLAAIA 544
                                   44333...33...68999**********9884 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1  12.2   3.3e-09   1.5e-05      50     188 ..      55     191 ..      25     196 .. 0.90
   2 ?    2.1   0.2     0.015        69     405     443 ..     230     267 ..     212     270 .. 0.74
   3 !   10.4   9.9   4.9e-05      0.22      47     159 ..     324     436 ..     292     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.3e-09
                                   HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGigvGlasvlvPmyis 128
                                   +i+  ++v+ +   + +g+l+d++GR   +  + ++f +g++l  +++++       li+ Rv+ G+g  +    +   i 
  gi|70607828|ref|YP_256698.1|  55 WILMGYNVVTATFLVSFGKLSDIYGRVRLYNLGFLIFTVGSILLSITPNQgsLGALELIIFRVIQGVGGAFLFSNSAAIIT 135
                                   5666677778888899********************************9944445568999*******9999999999999 PP

                                   TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                      Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                      p + Rg+  +++q a   G l++ i+g +l+ + n   wr+ + +++   +l  i+ 
  gi|70607828|ref|YP_256698.1| 136 DAFPYNERGKALGINQIAFLGGSLIGLILGGILSVI-N---WRLVFLVSVPVGILGTIWS 191
                                   999***************************998866.5...9********9999999886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.015
                                   HHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT- CS
                      Sugar_tr 405 lfpiiteaigggyvflvfaglavlfiifvfffvpetkgr 443
                                   l p+  +++g ++  +v agl+v f++++ f ++e k +
  gi|70607828|ref|YP_256698.1| 230 LLPYGSSQLG-WGNPYVIAGLVVGFALIGAFIYVERKVQ 267
                                   4466677777.9999*******************98866 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 4.9e-05
                                   HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                   + g+ +  ++vG +  + ++g+l+dr+G k     + v++ +g ++  + + ++s+  +++  +++G+g G++    +  i
  gi|70607828|ref|YP_256698.1| 324 WAGIYMIPLMVGFVSMGPISGWLSDRYGAKLLATLGMVIVGVGFLMLTTLPYNFSYPEFAAIIFFMGLGNGMFASPNTASI 404
                                   44444444555555556788999999999999999999999999999999988**************************** PP

                                   HTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 128 sEiApkklRgalvslyqlaitfGilvaaifgl 159
                                       p+k+Rga  ++  +   +G+  ++++ +
  gi|70607828|ref|YP_256698.1| 405 MNSVPPKYRGAASGMRATIQNIGQTASITIFF 436
                                   ***************99999999987666554 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.7     0.018        78      26     147 ..      63     168 ..      52     187 .. 0.68
   2 ?   -2.2   0.3      0.35   1.6e+03      53     100 ..     209     258 ..     203     264 .. 0.62
   3 !   21.4   3.2   2.4e-08   0.00011     256     349 ..     335     428 ..     315     456 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.018
                          PUCC  26 lvapfraliGfrSDtkralGwkRvpyiwlGslalalglaiaplalivlsgkgeaeaaatwaglilaavafllvGlgvslsq 106
                                   + a f +++G+ SD ++     Rv+   lG l++++g+ +++++            +  ++g + +++  ++ G+g     
  gi|70607828|ref|YP_256698.1|  63 VTATFLVSFGKLSDIYG-----RVRLYNLGFLIFTVGSILLSITP-----------NQGSLGALELIIFRVIQGVGGAFLF 127
                                   55666666777777666.....66666666666666655444321...........1223444445555567788888888 PP

                          PUCC 107 TallALladlaeeeerpkvvgllyvmlligivvsaivvgal 147
                                      +A+++d+   +er k+ g+  + +l g  ++ i  g+l
  gi|70607828|ref|YP_256698.1| 128 SNSAAIITDAFPYNERGKALGINQIAFLGGSLIGLILGGIL 168
                                   88889999999999999999999888888877776666554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.35
                          PUCC  53 wlGslalalglaiaplaliv..lsgkgeae.aaatwaglilaavafllvGl 100
                                   w G l+la+gl  +++a+ +  l   g+++ +       + ++v f+l+G+
  gi|70607828|ref|YP_256698.1| 209 WVGNLTLAVGLISILVAVTYglLPY-GSSQlGWGNPYVIAGLVVGFALIGA 258
                                   7899999999988888886421444.3333233333344445566777776 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.4e-08
                          PUCC 256 tlvGlllaglvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeragl 336
                                   ++v ++  + +ls + +++ la+lg++++ ++fl+l+      +   ++a ++++Gl++G+fa   ++++++ ++++  g 
  gi|70607828|ref|YP_256698.1| 335 GFVSMGPISGWLSDRYGAKLLATLGMVIVGVGFLMLTTLPYNFSYPEFAAIIFFMGLGNGMFASPNTASIMNSVPPKYRGA 415
                                   344555567899*************************9999999************************************9 PP

                          PUCC 337 alGaWGaaQaiaa 349
                                   a G+   +Q i +
  gi|70607828|ref|YP_256698.1| 416 ASGMRATIQNIGQ 428
                                   9999888888765 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.7   9.7e-08   0.00043      63     191 ..      69     197 ..      61     218 .. 0.87
   2 ?   -2.3   0.9      0.24   1.1e+03      65     141 ..     343     417 ..     330     456 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.7e-08
                         MFS_3  63 ilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaL 143
                                   +  G l+D++ r ++   + l+  ++s+ll ++   g l    l+++ ++ g+G a+      A++ +  + ++  +A  +
  gi|70607828|ref|YP_256698.1|  69 VSFGKLSDIYGRVRLYNLGFLIFTVGSILLSITPNQGSLGALELIIFRVIQGVGGAFLFSNSAAIITDAFPYNERGKALGI 149
                                   45699**************************************************************************** PP

                         MFS_3 144 nsvginiaRsvGPAlgGvlvaavGaalafavna.lsylalivallrwkr 191
                                   n + +     +G  lgG+ ++++   l+f v + +  l  i+  ++ k 
  gi|70607828|ref|YP_256698.1| 150 NQIAFLGGSLIGLILGGI-LSVINWRLVFLVSVpVGILGTIWSYTKLKE 197
                                   *****99999***99997.578888888888763556666666666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.24
                         MFS_3  65 aGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAv 141
                                   +G l+D +  +  lla+  +++++  +l+++++   +s     a+++++g+G  + +    As+ + v+ +   aA 
  gi|70607828|ref|YP_256698.1| 343 SGWLSDRYGAK--LLATLGMVIVGVGFLMLTTLPYNFSYPEFAAIIFFMGLGNGMFASPNTASIMNSVPPKYRGAAS 417
                                   55556655543..4555555555555666665555556666778888999998888777788888777766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 3197.36
//
Query:       gi|70607829|ref|YP_256699.1|  [L=146]
Description: MarR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-11   43.7   0.0    3.2e-11   43.0   0.0    1.5  1  MarR            MarR family
    1.1e-09   38.6   0.1    1.7e-09   38.0   0.1    1.3  1  HTH_27          Winged helix DNA-binding domain
    1.4e-08   34.5   0.0    2.2e-08   33.9   0.0    1.3  1  MarR_2          MarR family
    0.00068   19.8   0.4     0.0056   16.8   0.0    2.1  2  HTH_34          Winged helix DNA-binding domain
     0.0012   18.7   0.1     0.0023   17.7   0.1    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0017   18.2   0.1     0.0031   17.3   0.1    1.5  1  HxlR            HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.029   14.6   0.0    1.7  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.017   14.7   0.1       0.11   12.0   0.0    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   1.4e-14   3.2e-11      16      59 .]      49      92 ..      35      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.4e-14
                                  TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTSE CS
                          MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRev 59
                                  gp  + eLa+k  v+++++t ++d+Le+ Gl++R++s +DrR v
  gi|70607829|ref|YP_256699.1| 49 GPKPMVELANKYLVTQASITSTVDKLEDMGLVRRERSQDDRRLV 92
                                  777888************************************76 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   7.7e-13   1.7e-09       2      68 .]      36     100 ..      35     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 7.7e-13
                        HTH_27   2 trqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   ++++ lvL+ i+  +++k   +l+ ++ v++++i + ++kL+ +GLv r+++  drr +++ +T+kG
  gi|70607829|ref|YP_256699.1|  36 SYLDYLVLRGIK--DGPKPMVELANKYLVTQASITSTVDKLEDMGLVRRERSQDDRRLVLIYITEKG 100
                                   67899*******..****************************************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   9.6e-12   2.2e-08       7      61 ..      39      90 ..      33      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 9.6e-12
                                  HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  ++ vL  + ++p     + ela +  +++++++ ++++L++ GLv+r+++++D+R
  gi|70607829|ref|YP_256699.1| 39 DYLVLRGIKDGPK---PMVELANKYLVTQASITSTVDKLEDMGLVRRERSQDDRR 90
                                  6789999999998...9*************************************9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.21   4.6e+02       2      24 ..       8      30 ..       8      39 .. 0.87
   2 !   16.8   0.0   2.5e-06    0.0056      18      71 ..      54     106 ..      38     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.21
                        HTH_34  2 RlavlsyLasvdeadfvelkeal 24
                                  Rl+v+ + a+v++a  +el ++l
  gi|70607829|ref|YP_256699.1|  8 RLQVIVTIAKVNRAFQRELNKKL 30
                                  8999999*******999998876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.5e-06
                        HTH_34  18 velkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                   vel ++  +t++ + + ++kLe+ g + ++ + +++ +  l+ iT++G+   ++
  gi|70607829|ref|YP_256699.1|  54 VELANKYLVTQASITSTVDKLEDMGLVRRERSQDDR-RLVLIYITEKGKGVMEE 106
                                   678888889***********************9999.9**********976665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     1e-06    0.0023      19      58 ..      47      86 ..      30      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                                  HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  k gp+ + e+a++  v ++++ +++ +Led+GlV+re+++
  gi|70607829|ref|YP_256699.1| 47 KDGPKPMVELANKYLVTQASITSTVDKLEDMGLVRRERSQ 86
                                  8899999******************************987 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.4e-06    0.0031       8      74 ..      40     105 ..      36     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHH CS
                          HxlR   8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslep 74 
                                    l+l+ + +g+k + el++++  ++q  ++++  +Le  gl+ re  +     v   +tekG+ +++
  gi|70607829|ref|YP_256699.1|  40 YLVLRGIKDGPKPMVELANKY-LVTQASITSTVDKLEDMGLVRRERSQDDRRLVLIYITEKGKGVME 105
                                   699*****************9.9**************************99999999*****98865 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.029      27      55 ..      55      83 ..      47      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyveye 55
                                  +la    v  +s++ ++ kLe++G+v  e
  gi|70607829|ref|YP_256699.1| 55 ELANKYLVTQASITSTVDKLEDMGLVRRE 83
                                  677777899*****************765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.11      14      48 .]      47      81 ..      46      81 .. 0.93
   2 ?   -0.9   0.1      0.56   1.2e+03       7       7 ..     117     117 ..     108     127 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                        HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  k++  ++ eLA +  ++++ ++  +++Le++Gl++
  gi|70607829|ref|YP_256699.1| 47 KDGPKPMVELANKYLVTQASITSTVDKLEDMGLVR 81
                                  67788999*************************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.56
                        HTH_24   7 k 7  
                                   +
  gi|70607829|ref|YP_256699.1| 117 E 117
                                   3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 978.42
//
Query:       gi|70607830|ref|YP_256700.1|  [L=396]
Description: drug transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-47  160.6  42.4    1.4e-30  106.4  20.0    2.0  2  MFS_1       Major Facilitator Superfamily
    1.3e-08   33.9  30.4    2.5e-06   26.4  16.7    2.3  2  MFS_2       MFS/sugar transport protein
    1.1e-07   31.1  26.2    0.00013   20.9  12.9    2.1  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
        6.2    6.7   6.9        7.8    6.4   0.0    3.2  3  Flp_Fap     Flp/Fap pilin component


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4  20.0   3.2e-34   1.4e-30       1     228 [.      18     227 ..      18     232 .. 0.81
   2 !   56.5  21.3   4.8e-19   2.2e-15       2     168 ..     209     376 ..     201     396 .] 0.86

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 3.2e-34
                         MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                   l+l+afl + +++i++p+lp +++ +lg++p e++ll+++y+++++v+s+ ++rlsd  Gr+ +l lg+ + ++g l++ +
  gi|70607830|ref|YP_256700.1|  18 LALTAFLDSVGFGIIIPILP-YYSLQLGATPIEYSLLTVTYSIAQLVFSPYISRLSDIRGRKNILTLGIGSEVVGYLIIGL 97 
                                   6899****************.******************************************************555557 PP

                         MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    s+++ lll++r+++G+ + + +p+++++++++ +  + +r ig++s++f++G++ gp++gg+l+  lg+r +f+i+a+++
  gi|70607830|ref|YP_256700.1|  98 -SPYFyLLLLARFITGALT-SNLPVILSYATELGK--DNSRNIGIISGTFGVGFVAGPVIGGVLS-PLGYRNTFLIVAGLA 173
                                   .99999************6.99999*9**999865..7***************************.99************* PP

                         MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdp.vlw.illialllfffgfsgllt 228
                                   +l ++l  ++l++++ ++k    +              +k++++    ++ + li++l+f ++++g+l+
  gi|70607830|ref|YP_256700.1| 174 FLNLIL--VYLLVSNDNKKIAMRQAS------------LKEIFRMSsSFFtLTLIIALSF-AVLQGTLA 227
                                   ***997..444444444444433333............3333333314432233333333.35555544 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 4.8e-19
                         MFS_1   2 llaaflsalarsilgpalplalaed.lgispseigllltlyalgaavaslpl.GrlsdrfGrrrvlllglllfalglllll 80 
                                   + +++++al++++l  +l  ++++  +++ ps+igl+l+l+++++ava+++l  r++ + G r    +gl +++++ ++ll
  gi|70607830|ref|YP_256700.1| 209 FTLTLIIALSFAVLQGTLA-FYGRYfYNWGPSQIGLVLGLVGIVQAVAQFLLvYRIIGKAGERIATTIGLSITFIA-YILL 287
                                   4556666666777666666.44444588************************9999********************.7777 PP

                         MFS_1  81 .fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                    f +s   l +v+ vl ++g g++  ++++l+++  p+  r+ ++g+++++++lG+++g +lg  + + l+  + ++++ +
  gi|70607830|ref|YP_256700.1| 288 sF-PSNQiLAYVSLVLLAMGNGIAQNSILTLLSKTLPPGSRSGGFGFAQSSTALGSLIGFPLGNTMFQVLSPNSEYFLCSA 367
                                   69.777779************************************************************************ PP

                         MFS_1 160 vsllafvlf 168
                                   +s+l++v f
  gi|70607830|ref|YP_256700.1| 368 LSILSIVYF 376
                                   *****8843 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.4   2.4e-06     0.011     226     324 ..      15     112 ..       7     129 .. 0.85
   2 !   26.4  16.7   5.5e-10   2.5e-06     139     335 ..     134     314 ..     131     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-06
                         MFS_2 226 flillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlv 306
                                   +++l+l+++l ++++g+   +l Yy      +  ++s+++++  i++l+++p +++l    g+kn+  lg+ + +v+++++
  gi|70607830|ref|YP_256700.1|  15 LITLALTAFLDSVGFGIIIPILPYYSLQLGATPIEYSLLTVTYSIAQLVFSPYISRLSDIRGRKNILTLGIGSEVVGYLII 95 
                                   7899*********************998877***********************************************999 PP

                         MFS_2 307 lllqpsnlllflvllvia 324
                                    l  p+ +ll+l+ ++ +
  gi|70607830|ref|YP_256700.1|  96 GLS-PYFYLLLLARFITG 112
                                   888.55555544433333 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 5.5e-10
                         MFS_2 139 rsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlke 219
                                   r++  + g++++ ++a+++++   +    + gy+ + li a L++l  i+v+l + ++          +k+       lke
  gi|70607830|ref|YP_256700.1| 134 RNIGIISGTFGVGFVAGPVIGGVLS----PLGYRNTFLIVAGLAFLNLILVYLLVSND----------NKKIAMRQASLKE 200
                                   6666677999999999999888887....9**************************88..........4445555567999 PP

                         MFS_2 220 vfrnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvv.tisallgiplwqplakrlgkkntyllgall 298
                                   +fr+     +++l l+ al+++vl g l++y +y+ +   s++ ++l++v ++ a++ ++l+ ++  + g + ++ +g+++
  gi|70607830|ref|YP_256700.1| 201 IFRMSS--SFFTLTLIIALSFAVLQGTLAFYGRYFYNwGPSQIGLVLGLVgIVQAVAQFLLVYRIIGKAGERIATTIGLSI 279
                                   999955..6788889999999**************************9999****************************** PP

                         MFS_2 299 tivllvlvlllqpsnlllflvllviagfgvgvaallp 335
                                   t++ ++l+ +   sn +l++v lv+  +g g+a+  +
  gi|70607830|ref|YP_256700.1| 280 TFIAYILLSFP--SNQILAYVSLVLLAMGNGIAQNSI 314
                                   *****999887..666666666666666655555444 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   5.4   7.6e-07    0.0034     226     373 ..      14     157 ..       8     159 .. 0.94
   2 !   20.9  12.9     3e-08   0.00013     178     378 ..     161     357 ..     157     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.6e-07
                    MFS_1_like 226 eviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                    +i++ l+a++  + +gii   l  Y  +lga+ +  + l++   +a++++  + ++l ++ G  ++l++++ + ++ +l+
  gi|70607830|ref|YP_256700.1|  14 TLITLALTAFLDSVGFGIIIPILPYYSLQLGATPIEYSLLTVTYSIAQLVFSPYISRLSDIRGRKNILTLGIGSEVVGYLI 94 
                                   5789999999999***********999****************************************************** PP

                    MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll 373
                                   +++   + l+l++ ++ g+ +  l  ++ +y+ ++   + +++ +g++sg+ fg+G   G +iGG+l
  gi|70607830|ref|YP_256700.1|  95 IGLSPYFYLLLLARFITGALTSNL-PVILSYATELG--KDNSRNIGIISGT-FGVGFVAGPVIGGVL 157
                                   ******************988888.89999999774..557899******8.*************96 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3e-08
                    MFS_1_like 178 pysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiie...nFlflYLkel 255
                                   +y+  ++++a+l  + l++v+ l   + ++k++++  + +l++i+++ +   f++ +li+  s+++++   +F+  Y+  +
  gi|70607830|ref|YP_256700.1| 161 GYRNTFLIVAGLAFLNLILVYLLV-SNDNKKIAMR--QASLKEIFRMSSS--FFTLTLIIALSFAVLQgtlAFYGRYF--Y 234
                                   488999999999999999977665.4556677777..4789999999875..77777777777777763336788888..5 PP

                    MFS_1_like 256 gasntllGslv.algvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaav 335
                                   +   + +G ++  +g v  +  f++  +++ k G +   +i+l+++++ ++l+++ +n  l+ +  vL ++  g+   ++ 
  gi|70607830|ref|YP_256700.1| 235 NWGPSQIGLVLgLVGIVQAVAQFLLVYRIIGKAGERIATTIGLSITFIAYILLSFPSNQILAYVSLVLLAMGNGIAQNSIL 315
                                   6666667766625799999999*********************************************************** PP

                    MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlks 378
                                   +  sk  p++ ++ g g+ ++    lG+ +G  +G  +++  s
  gi|70607830|ref|YP_256700.1| 316 TLLSKTLPPGSRSGGFGFAQSS-TALGSLIGFPLGNTMFQVLS 357
                                   *****************98876.89*****9999988888655 PP

>> Flp_Fap  Flp/Fap pilin component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.3       1.7   7.7e+03      18      33 ..      14      29 ..      13      31 .. 0.72
   2 ?    6.4   0.0    0.0017       7.8       6      22 ..      43      59 ..      42      67 .. 0.82
   3 ?    2.7   0.5     0.025   1.1e+02      16      40 ..     294     319 ..     294     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                       Flp_Fap 18 aliAvviiayvttlgt 33
                                  +li++++ a ++ +g 
  gi|70607830|ref|YP_256700.1| 14 TLITLALTAFLDSVGF 29
                                  6888888887777775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                       Flp_Fap  6 sGATAIEYgLIaaliAv 22
                                   GAT IEY L+ +  ++
  gi|70607830|ref|YP_256700.1| 43 LGATPIEYSLLTVTYSI 59
                                  5*********9886655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.025
                       Flp_Fap  16 IaaliAvviiayvttlg.taLktkFt 40 
                                   I+a +++v++a+++ +  +++ t+++
  gi|70607830|ref|YP_256700.1| 294 ILAYVSLVLLAMGNGIAqNSILTLLS 319
                                   899*******9999887677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2940.58
//
Query:       gi|70607831|ref|YP_256701.1|  [L=262]
Description: hypothetical protein Saci_2114 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-19   67.7   4.0    9.2e-14   50.7   0.4    2.3  2  HTH_24         Winged helix-turn-helix DNA-binding
    6.6e-12   45.1   0.8    2.4e-08   33.7   0.1    2.2  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
    1.9e-06   27.7   0.0     0.0033   17.3   0.0    2.3  2  MarR           MarR family
    0.00019   21.3   0.0     0.0055   16.7   0.0    2.2  2  HTH_Crp_2      Crp-like helix-turn-helix domain
    0.00046   20.0   0.0      0.024   14.5   0.0    2.2  2  MarR_2         MarR family
    0.00056   19.7   0.7       0.59   10.0   0.1    3.0  3  TFIIE_alpha    TFIIE alpha subunit
     0.0009   19.1   0.2       0.61   10.0   0.0    2.6  3  HTH_5          Bacterial regulatory protein, arsR family
     0.0015   18.3   0.1       0.56   10.1   0.0    2.7  3  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0043   17.1   0.1      0.072   13.1   0.0    2.8  3  HTH_Mga        M protein trans-acting positive regulator (MGA
  ------ inclusion threshold ------
      0.041   14.0   0.0        5.3    7.3   0.0    2.3  2  HTH_28         Helix-turn-helix domain
      0.064   13.3   0.0        3.9    7.6   0.0    2.6  2  HTH_7          Helix-turn-helix domain of resolvase
      0.076   13.2   0.0        4.2    7.6   0.0    2.6  2  HTH_17         Helix-turn-helix domain
       0.12   12.2   0.1        3.5    7.6   0.0    2.5  3  HTH_23         Homeodomain-like domain
       0.12   11.9   0.0       0.18   11.4   0.0    1.3  1  HEPPP_synt_1   Heptaprenyl diphosphate synthase (HEPPP syntha
       0.12   12.1   0.1        1.7    8.5   0.0    2.3  2  HTH_38         Helix-turn-helix domain
       0.14   12.1   0.0        9.9    6.2   0.0    2.3  2  HTH_37         Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.4   8.2e-17   9.2e-14       1      48 []       1      48 [.       1      48 [. 0.99
   2 !   18.2   0.2   1.2e-06    0.0014       8      41 ..     136     169 ..     131     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.2e-17
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +detdr I+  L +++risq+ LA+ ++l p+ +n r +rL++eG+I+
  gi|70607831|ref|YP_256701.1|  1 MDETDRLIIFNLLRDGRISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  8**********************************************7 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.2e-06
                        HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrL 41 
                                   ++++L +npr  ++e+A +l+  +s v+r + +L
  gi|70607831|ref|YP_256701.1| 136 LIKTLVENPRAEISEIANKLNFKVSKVRRLISEL 169
                                   5799***************************999 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   2.1e-11   2.4e-08       1      41 [.       1      41 [.       1      42 [. 0.99
   2 !   10.0   0.0   0.00052      0.58       8      36 ..     136     164 ..     134     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.1e-11
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                  +De+Dr I+  L +d+Ris  +LA+ ++l+++    R rrL
  gi|70607831|ref|YP_256701.1|  1 MDETDRLIIFNLLRDGRISQNKLAKIINLAPPSLNSRFRRL 41
                                  9***************************************9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00052
                 HTH_AsnC-type   8 ILeaLqedaRisyaeLAervGlSestvlr 36 
                                   +++ L e++R+  +e+A +++   s v+r
  gi|70607831|ref|YP_256701.1| 136 LIKTLVENPRAEISEIANKLNFKVSKVRR 164
                                   7889****************999999887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     3e-06    0.0033       7      48 ..       7      48 ..       2      50 .. 0.93
   2 !    8.0   0.0    0.0024       2.7       7      41 ..     135     169 ..     131     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                  HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  +i+++l + g +s+ +Lak +++ ++++    +rL+++G i+
  gi|70607831|ref|YP_256701.1|  7 LIIFNLLRDGRISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  588899999******************************996 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0024
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHH CS
                          MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrL 41 
                                   +++ +l e++ + +se+a+kl+ + s v r++ +L
  gi|70607831|ref|YP_256701.1| 135 LLIKTLVENPRAEISEIANKLNFKVSKVRRLISEL 169
                                   46678999****************99999988776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.9e-06    0.0055      21      52 ..      17      48 ..       3      56 .. 0.88
   2 ?    2.1   0.0      0.17   1.9e+02      25      46 ..     149     170 ..     137     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-06
                                  EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                     HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis 52
                                  +++q  lA +++l + +++  +++L +eg+i+
  gi|70607831|ref|YP_256701.1| 17 RISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  79*****************************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.17
                                   HHHHHHTTSSHHHHHHHHHHHH CS
                     HTH_Crp_2  25 eelAsmlGltretvsrilseLk 46 
                                    e+A+ l+   + v r++seLk
  gi|70607831|ref|YP_256701.1| 149 SEIANKLNFKVSKVRRLISELK 170
                                   599******************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.1e-05     0.024       6      52 ..       4      48 ..       1      50 [. 0.94
   2 ?    3.3   0.0     0.066        74      13      45 ..     139     169 ..     131     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                  +++ ++++L r ++  ++++ la+  +l +++++ + +rL + G ++
  gi|70607831|ref|YP_256701.1|  4 TDRLIIFNLLRDGR--ISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  78899*******98..****************************996 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.066
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                        MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrL 45 
                                    L  +p+    ++e+a +l+ + s v r++ +L
  gi|70607831|ref|YP_256701.1| 139 TLVENPR--AEISEIANKLNFKVSKVRRLISEL 169
                                   4666666..799****************99887 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0081       9.1      16      58 ..       6      48 ..       1      78 [. 0.87
   2 !   10.0   0.1   0.00052      0.59      16      56 ..     134     174 ..     129     179 .. 0.87
   3 ?   -0.2   0.1      0.81   9.1e+02      56      79 ..     231     255 ..     224     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0081
                                  HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                   l+++ Ll++g ++ + lak +++ ++ l +   rL +++++ 
  gi|70607831|ref|YP_256701.1|  6 RLIIFNLLRDGRISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  68999**********************************9986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00052
                                   HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTS CS
                   TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearl 56 
                                    l ++ L+e+      ++a++l+++  ++r+l+ +L++  +
  gi|70607831|ref|YP_256701.1| 134 LLLIKTLVENPRAEISEIANKLNFKVSKVRRLISELKGFAV 174
                                   5678889999999999********************98666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.81
                                   SEEEEEEEETTTEEEEEE.EEEECC CS
                   TFIIE_alpha  56 lvkykrrrdeekswykyy.wrinye 79 
                                   +++ +rr d++ +++ +y + i+ +
  gi|70607831|ref|YP_256701.1| 231 MIDNVRRIDPDAQVMLVYnYEIKND 255
                                   799999***9999987663777665 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00054      0.61       3      45 ..       5      47 ..       3      48 .. 0.95
   2 ?   -2.7   0.0         5   5.6e+03      16      27 ..     104     115 ..      99     116 .. 0.81
   3 !    6.4   0.0    0.0071         8       5      34 ..     134     164 ..     131     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   Rl I +lL++g  +   la++++l ++ +   +++L ++G++
  gi|70607831|ref|YP_256701.1|  5 DRLIIFNLLRDGRISQNKLAKIINLAPPSLNSRFRRLIDEGVI 47
                                  5999*************************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                                   EEHHHHHHHHTS CS
                         HTH_5  16 lcvcelaeelgl 27 
                                    +v  ++ elg+
  gi|70607831|ref|YP_256701.1| 104 ETVDGISSELGK 115
                                   689999999997 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0071
                                   HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHH CS
                         HTH_5   5 lkILklLaege.lcvcelaeelglsqstvSh 34 
                                   l ++k L e++ + ++e+a++l+   s+v++
  gi|70607831|ref|YP_256701.1| 134 LLLIKTLVENPrAEISEIANKLNFKVSKVRR 164
                                   56789999999999*************9987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.018        20      15      53 ..      10      48 ..       2      67 .. 0.89
   2 ?   -2.3   0.0       3.7   4.2e+03      22      35 ..     103     116 ..     100     117 .. 0.83
   3 !   10.1   0.0    0.0005      0.56      16      47 ..     139     170 ..     135     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                                  HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  + Ll+ g+ + +++a+++++  ++ ++  r+L+d G+++
  gi|70607831|ref|YP_256701.1| 10 FNLLRDGRISQNKLAKIINLAPPSLNSRFRRLIDEGVIR 48
                                  57999999****************************997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                                   CCHHCHHCCCTTSS CS
                          TrmB  22 patadeiaeelgvp 35 
                                   + t+d i++elg p
  gi|70607831|ref|YP_256701.1| 103 KETVDGISSELGKP 116
                                   579999**999987 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0005
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
                          TrmB  16 aLlklgpatadeiaeelgvprskvYevLrsLe 47 
                                   +L+++ +a+++eia++l+   skv + +++L+
  gi|70607831|ref|YP_256701.1| 139 TLVENPRAEISEIANKLNFKVSKVRRLISELK 170
                                   8*************************999986 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.5   2.8e+03      14      39 ..      12      36 ..       4      41 .. 0.73
   2 ?   -0.4   0.0       1.1   1.2e+03      43      55 ..      70      82 ..      69      92 .. 0.90
   3 !   13.1   0.0   6.4e-05     0.072       8      45 ..     134     170 ..     129     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                       HTH_Mga 14 LteneksltldelakeLglseltlqs 39
                                  L+  +++++  +lak  +l   +l+s
  gi|70607831|ref|YP_256701.1| 12 LLR-DGRISQNKLAKIINLAPPSLNS 36
                                  444.5899999999999987766665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                       HTH_Mga 43 eLnelFpeelsiv 55
                                  +L+e+++++++++
  gi|70607831|ref|YP_256701.1| 70 NLREAYSDKIFVK 82
                                  799******9986 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 6.4e-05
                       HTH_Mga   8 lkLlelLteneksltldelakeLglseltlqsdiseLn 45 
                                   l L+ +L e +++ +++e+a++L+   ++++  iseL+
  gi|70607831|ref|YP_256701.1| 134 LLLIKTLVE-NPRAEISEIANKLNFKVSKVRRLISELK 170
                                   6799*****.***************************9 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0047       5.3       2      35 ..       6      40 ..       5      50 .. 0.82
   2 ?    4.5   0.0     0.035        39      15      34 ..     148     167 ..     137     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0047
                        HTH_28  2 RleiikllaaGh.svreaArelgisrrtvyrWikr 35
                                  Rl i  ll +G+ s++ +A++ ++ + ++ +  +r
  gi|70607831|ref|YP_256701.1|  6 RLIIFNLLRDGRiSQNKLAKIINLAPPSLNSRFRR 40
                                  9999********************99999544444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.035
                        HTH_28  15 vreaArelgisrrtvyrWik 34 
                                   ++e+A++l+   + v+r+i+
  gi|70607831|ref|YP_256701.1| 148 ISEIANKLNFKVSKVRRLIS 167
                                   789**************997 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0034       3.9      14      35 ..       9      31 ..       3      34 .. 0.89
   2 ?    2.8   0.0      0.12   1.3e+02      12      32 ..     135     156 ..     127     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0034
                                  GGSSTTTT.--STTTSSSS---S CS
                         HTH_7 14 vvkLleeG.isiskIAkevnisR 35
                                  ++ Ll++G is +k+Ak+ n+++
  gi|70607831|ref|YP_256701.1|  9 IFNLLRDGrISQNKLAKIINLAP 31
                                  5789****************986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                   GGGGSSTTTT.--STTTSSSS- CS
                         HTH_7  12 nrvvkLleeG.isiskIAkevn 32 
                                     +++L+e++   is+IA  +n
  gi|70607831|ref|YP_256701.1| 135 LLIKTLVENPrAEISEIANKLN 156
                                   5789**************8776 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.13   1.4e+02      17      31 ..      37      51 ..      35      62 .. 0.84
   2 ?    7.6   0.0    0.0038       4.2       4      23 ..     148     167 ..     147     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.13
                        HTH_17 17 tvyrlirrgelpaak 31
                                    +rli++g ++ +k
  gi|70607831|ref|YP_256701.1| 37 RFRRLIDEGVIRGFK 51
                                  579********9998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0038
                        HTH_17   4 veEaAelLgvsrstvyrlir 23 
                                   ++E+A+ L+ ++s+v+rli+
  gi|70607831|ref|YP_256701.1| 148 ISEIANKLNFKVSKVRRLIS 167
                                   68****************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.2   2.2e+02       4      36 ..       3      36 ..       1      48 [. 0.80
   2 ?   -3.6   0.0       9.7   1.1e+04      17      27 ..      96     106 ..      95     111 .. 0.70
   3 ?    7.6   0.0    0.0031       3.5      13      44 ..     139     170 ..     131     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                        HTH_23  4 ereRlrillllae.GlsvreIAreLgvsrrTvyr 36
                                  e +Rl i  ll++ ++s+ + A++ +  +  +  
  gi|70607831|ref|YP_256701.1|  3 ETDRLIIFNLLRDgRISQNKLAKIINLAPPSLNS 36
                                  678999999***********99999998887774 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.7
                        HTH_23  17 GlsvreIAreL 27 
                                   G s++eI +  
  gi|70607831|ref|YP_256701.1|  96 GESIEEIKETV 106
                                   88999997765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0031
                        HTH_23  13 llae..GlsvreIAreLgvsrrTvyrwlkryree 44 
                                    l e  ++ ++eIA +L+   + v+r ++    +
  gi|70607831|ref|YP_256701.1| 139 TLVEnpRAEISEIANKLNFKVSKVRRLISEL--K 170
                                   333458999******************9874..4 PP

>> HEPPP_synt_1  Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.18     111     172 ..      89     151 ..      81     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                  HEPPP_synt_1 111 iklYekkeetveellesvkkiesaLlaklaehf.qletwkelieeflllkrLekekeayeegk 172
                                    ++Y  + e++ee++e v+ i s L + ++e++  ++ +k+  + +ll+k L+++  a +++ 
  gi|70607831|ref|YP_256701.1|  89 FNVYGFQGESIEEIKETVDGISSELGKPIMEYIpPQTPIKPKKQYLLLIKTLVENPRAEISEI 151
                                   689******************************667778888888888999988755444333 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0015       1.7       8      34 ..       4      31 ..       1      35 [. 0.90
   2 ?    0.9   0.0      0.36     4e+02      23      40 ..     148     165 ..     142     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                        HTH_38  8 eeReeIerllaeG.lslreIArrLgrsp 34
                                  ++R  I  ll  G  s+ + A++++ +p
  gi|70607831|ref|YP_256701.1|  4 TDRLIIFNLLRDGrISQNKLAKIINLAP 31
                                  79**********************9776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.36
                        HTH_38  23 lreIArrLgrspsTIsRE 40 
                                   ++eIA +L+ + s + R 
  gi|70607831|ref|YP_256701.1| 148 ISEIANKLNFKVSKVRRL 165
                                   679******998877775 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.057        64      25      49 ..      11      35 ..       6      41 .. 0.84
   2 ?    6.2   0.0    0.0088       9.9      13      51 ..     127     165 ..     121     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.057
                                  HHHHHCT--HHHHHHHHT--HHHHH CS
                        HTH_37 25 eliekrelsqseaaqllgiaqPkvs 49
                                   l+++ ++sq ++a++ + a P+++
  gi|70607831|ref|YP_256701.1| 11 NLLRDGRISQNKLAKIINLAPPSLN 35
                                  56777899************99985 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0088
                                   HHHHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHH CS
                        HTH_37  13 lkaKaqlalaiaeliekrelsqseaaqllgiaqPkvsrl 51 
                                   +k K q++l i+ l e  +   se+a++l+ + +kv rl
  gi|70607831|ref|YP_256701.1| 127 IKPKKQYLLLIKTLVENPRAEISEIANKLNFKVSKVRRL 165
                                   677999******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2134.99
//
Query:       gi|70607832|ref|YP_256702.1|  [L=72]
Description: hypothetical protein Saci_2115 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 447.42
//
Query:       gi|70607833|ref|YP_256703.1|  [L=230]
Description: HTH DNA binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-19   68.6   0.4    8.8e-19   67.1   0.1    1.9  2  HTH_10        HTH DNA binding domain
    3.2e-05   23.4   0.0    6.5e-05   22.4   0.0    1.5  1  Sigma70_r4    Sigma-70, region 4
  ------ inclusion threshold ------
      0.019   15.0   0.4       0.12   12.5   0.0    2.4  3  Spo0A_C       Sporulation initiation factor Spo0A C terminal
      0.041   14.3   0.5       0.12   12.8   0.5    1.9  1  DUF2779       Domain of unknown function(DUF2779)
       0.23   11.8   3.6       0.18   12.1   1.5    1.9  2  ATP-synt_E_2  ATP synthase epsilon subunit
          2    8.8   7.1         35    4.8   0.1    3.5  4  Bac_RepA_C    Replication initiator protein A C-terminal doma


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.67     2e+03      36      52 ..      81      97 ..      81      98 .. 0.88
   2 !   67.1   0.1   2.9e-22   8.8e-19       1      52 [.     168     219 ..     168     220 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                        HTH_10 36 skstlsehLrkaeskli 52
                                  sk++l+++ ++ e+ + 
  gi|70607833|ref|YP_256703.1| 81 SKTALLYYFKNFENSIT 97
                                  899*******9999886 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 2.9e-22
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                   LT+ ++++l +Ay+mG+FdyP++++l+eLAk  G++k +l  h+r+a++k++
  gi|70607833|ref|YP_256703.1| 168 LTPTERQILYTAYKMGFFDYPKKTKLEELAKMYGVTKVALDRHIRNAIRKVL 219
                                   9*************************************************96 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.2e-08   6.5e-05       2      47 ..     165     217 ..     164     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-08
                                   HHHS-HHHHHHHHHHH......TTT--.HHHHHHHHTS-HHHHHHHHHHHHHH CS
                    Sigma70_r4   2 LasLpererevlelrf......geglT.leEIgerlgiSrerVrqiekrAlrk 47 
                                   L+sL++ er++l+  +      + + T leE+++++g+++ +  +++++A+rk
  gi|70607833|ref|YP_256703.1| 165 LSSLTPTERQILYTAYkmgffdYPKKTkLEELAKMYGVTKVALDRHIRNAIRK 217
                                   99********************777777*************999999999998 PP

>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.79   2.4e+03      84     102 ..      46      64 ..      30      66 .. 0.71
   2 ?   -2.1   0.1       1.4   4.2e+03      27      41 ..      88     100 ..      67     113 .. 0.52
   3 ?   12.5   0.0   3.9e-05      0.12      26      68 ..     177     219 ..     168     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.79
                       Spo0A_C  84 insekgkPtnsefiallad 102
                                     ++++k + ++fi++l++
  gi|70607833|ref|YP_256703.1|  46 ELYSNTKTQLTDFIDVLSR 64 
                                   3455778889999998876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                       Spo0A_C  27 vledpellesitkel 41 
                                   ++++ e  +sitk +
  gi|70607833|ref|YP_256703.1|  88 YFKNFE--NSITKAM 100
                                   333333..3333333 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 3.9e-05
                       Spo0A_C  26 lvledpellesitkelypevAkkykttpsrVeraIrhaIevaW 68 
                                   ++  ++   ++ +k+  +e+Ak y+ t+ + +r Ir+aI+++ 
  gi|70607833|ref|YP_256703.1| 177 YTAYKMGFFDYPKKTKLEELAKMYGVTKVALDRHIRNAIRKVL 219
                                   5555555666677888899********************9986 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   4.1e-05      0.12      55     102 ..      56     143 ..      28     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                       DUF2779  55 eelieeLikiieke.............gsvvvynksfEksrlkela...........................qlfpeyke 95 
                                   +++i+ L +  +++             ++++ y+k+fE+s+ k ++                           ql  + +e
  gi|70607833|ref|YP_256703.1|  56 TDFIDVLSRKYRNNikiirvdrnksskTALLYYFKNFENSITKAMMnsnaivanltvsdgiedwqvytfnkrdQLETQISE 136
                                   3344444444433355566667777779999***************99999999999999999999888888877788888 PP

                       DUF2779  96 elkqiie 102
                                   elk+i+ 
  gi|70607833|ref|YP_256703.1| 137 ELKKINV 143
                                   8888875 PP

>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.5   5.9e-05      0.18      17      53 ..     127     162 ..     122     164 .. 0.90
   2 ?   -3.7   0.0       5.1   1.5e+04      40      49 ..     190     199 ..     189     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                  ATP-synt_E_2  17 kskLdeKKsElLkkiNmEYEKlLKqRLdeLeklKrkv 53 
                                   +++L+ + sE LkkiN+E E l  +R+ e++++K ++
  gi|70607833|ref|YP_256703.1| 127 RDQLETQISEELKKINVEVENLDFDRV-EMDEVKSEM 162
                                   7899******************99998.799999865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.1
                  ATP-synt_E_2  40 KqRLdeLekl 49 
                                   K +L+eL k+
  gi|70607833|ref|YP_256703.1| 190 KTKLEELAKM 199
                                   5667777665 PP

>> Bac_RepA_C  Replication initiator protein A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.012        35       4      26 ..      40      62 ..      38      69 .. 0.87
   2 ?    4.1   0.7     0.019        57      57      89 ..      64      96 ..      60     109 .. 0.84
   3 ?    1.9   0.0     0.097   2.9e+02      33      61 ..     112     140 ..     104     147 .. 0.79
   4 ?   -2.3   0.0         2   5.9e+03      40      60 ..     200     220 ..     189     228 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                    Bac_RepA_C  4 elvnlLslyantpkklheyigii 26
                                  ++ ++ +ly+nt+++l ++i ++
  gi|70607833|ref|YP_256703.1| 40 SVFEIVELYSNTKTQLTDFIDVL 62
                                  5678999************9876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.019
                    Bac_RepA_C 57 ktLrrffnslrisknkkvknvenYlmrtlknlF 89
                                  ++ r  ++++r++ nk  k+   Y ++ + n  
  gi|70607833|ref|YP_256703.1| 64 RKYRNNIKIIRVDRNKSSKTALLYYFKNFENSI 96
                                  6678999**********9999999999888765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.097
                    Bac_RepA_C  33 vekaervlgvailldeeelqelitktLrr 61 
                                   v    ++ +v+++ ++++l+++i ++L++
  gi|70607833|ref|YP_256703.1| 112 VSDGIEDWQVYTFNKRDQLETQISEELKK 140
                                   55556667899999999******999986 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2
                    Bac_RepA_C  40 lgvailldeeelqelitktLr 60 
                                    gv+ ++ +  + + i k+L 
  gi|70607833|ref|YP_256703.1| 200 YGVTKVALDRHIRNAIRKVLM 220
                                   444444334444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1282.43
//
Query:       gi|70607834|ref|YP_256704.1|  [L=725]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.5e-150  501.6   0.0   3.4e-150  501.1   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    4.8e-15   55.9   0.3    1.2e-13   51.4   0.3    2.5  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
      0.093   13.0   0.0        0.2   11.9   0.0    1.5  1  ATP-synt_DE    ATP synthase, Delta/Epsilon chain, long alpha-


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.1   0.0  5.7e-154  3.4e-150       6     548 ..     131     662 ..     127     663 .. 0.93

  Alignments for each domain:
  == domain 1  score: 501.1 bits;  conditional E-value: 5.7e-154
                                   STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHH.T--G CS
                 Ald_Xan_dh_C2   6 pdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevl.glpe 83 
                                   ++n++   +++ Gd+++ f++a  ++ege+ ++r+ + ++E+++a+a++  ++++ltv+sstq+p+ +++ ++e+l +   
  gi|70607834|ref|YP_256704.1| 131 ESNIVLqdEVNVGDIQSDFKRAYKIIEGELINQRVIPSAMEPRGAFAQF--DGKRLTVWSSTQTPFDLKKSLSEILsEYGV 209
                                   567666688999*************************************..69*********************985689* PP

                                   GGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEEEEEE CS
                 Ald_Xan_dh_C2  84 nkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvdllad 164
                                   n++rvi+p+vGG+FG+K+  +++e+++a+++  t+rp+k+  +R+edm++t++++++++++k+++d++Gk+++++ +l++d
  gi|70607834|ref|YP_256704.1| 210 NDIRVIQPYVGGAFGSKIINYAEEFVVAYLSVVTKRPIKWFNSRTEDMMTTNHGRDMRLRFKAAFDSEGKLLGIEGTLIHD 290
                                   ********************************************************************************* PP

                                   ESST.H...HHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHHH CS
                 Ald_Xan_dh_C2 165 aGay.a...dlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelRr 241
                                    Ga        s  ++++a+  l g Yk++++++++ +v tN++  +a+RG+G+p+a++++Er++   A+elgld++e+R+
  gi|70607834|ref|YP_256704.1| 291 LGAPfEdinRDSFWMTTTAARLLIGRYKVNSLKIRVLGVATNKAFIGAYRGAGRPEATYFIERILTLGARELGLDQYEVRE 371
                                   ***853332445556666666677********************************************************* PP

                                   HHBCECGCC.SEEET.EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEEEEE CS
                 Ald_Xan_dh_C2 242 rNlikpgeltpygqp.vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqegalvr 321
                                   rN++ + ++t   +  +ydsg+++ell+ +k    y+ + +++++ ++++k  G+g+a+v e +++g+       ++a+v+
  gi|70607834|ref|YP_256704.1| 372 RNVMDDVNFTKLPTGlTYDSGKYKELLRIAKPY--YNDLIKRRDSLRSKGKLAGVGVAIVSEIASFGP------YSTAKVK 444
                                   ****9999976555467***********99997..57788888889966688************6555......579**** PP

                                   E-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 322 vntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrerllk 402
                                   v ++G+++v tg+t++GqG  t+++qiaae+++v++++v+v +gdtd + +g  ta+Sr+ +++g+Av++Aa +l+e+llk
  gi|70607834|ref|YP_256704.1| 445 VLPNGRIQVITGTTPHGQGDATAFTQIAAEVFDVDPSNVDVLWGDTDLISDGDLTAGSRTITVGGSAVYEAAVRLKEKLLK 525
                                   ***************************************************999*************************** PP

                                   HHHHHCTS-CCCEEEETTEEEETEEEECHHHHHHHHHHTTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT- CS
                 Ald_Xan_dh_C2 403 iaaellevspedleledgkvvvkeksvslaelaaaaylervslsatgfyktldeetgkgppfayfaygaavaeVevDtetg 483
                                   + +e+++v++e++e+++gk+++++k++sl e+a++ ++++v  ++  +y             ++ +yg++++ VevD++tg
  gi|70607834|ref|YP_256704.1| 526 VVSEKMGVRAEEIEYREGKFIHEDKTMSLWEAARTSMFMGVLPEQDYSY---------VMNLYTSPYGVHMVLVEVDRDTG 597
                                   ************************************9999988888889.........56668999*************** PP

                                   -EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGG CS
                 Ald_Xan_dh_C2 484 evkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaad 548
                                    ++vl++ + +DvG ++Np ++egQ +GG+ qGiG+al+Ee vy++dG+llt++++dY +Pta +
  gi|70607834|ref|YP_256704.1| 598 FTRVLDYKAFDDVGVVVNPLLAEGQTHGGALQGIGQALYEEAVYSQDGNLLTSNFSDYVLPTAVE 662
                                   **************************************************************975 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.3     2e-17   1.2e-13       1     110 []      20     111 ..      20     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2e-17
                                   TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEESSTT CS
                  Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvrsvg 81 
                                   tG+a++v D+++ g+ly+ fvrS++ahAki+s++  +     G    +t +dlpk  + i            a++++ ++g
  gi|70607834|ref|YP_256704.1|  20 TGRATFVYDLDLRGTLYASFVRSQYAHAKIKSVKCPE-----G-SMCFTSHDLPKAITGI------------ARNEAVYQG 82 
                                   8*******************************98754.....4.3568999***994444............677899*** PP

                                   -EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                  Ald_Xan_dh_C  82 qavaavvAedeetArkAaklvkveYeelp 110
                                   q++a+v+ +de+ Ar+ a+ v+veYe+lp
  gi|70607834|ref|YP_256704.1|  83 QPIAVVLTNDEYKARDLAEEVEVEYEPLP 111
                                   **************************986 PP

>> ATP-synt_DE  ATP synthase, Delta/Epsilon chain, long alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05       0.2       3      39 ..     114     152 ..     113     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                   --HHHHHHHHHHHHHHHHH...HHHHSS-HHHHHHHHHHH CS
                   ATP-synt_DE   3 IDverAeeAkerAeerLee...asddnidyarAqaaLrRA 39 
                                   IDve+A   kerA   Le      +d++++   q  ++RA
  gi|70607834|ref|YP_256704.1| 114 IDVEEALSNKERAMSELESnivL-QDEVNVGDIQSDFKRA 152
                                   9*****************99964.5668888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.56
# Mc/sec: 3867.93
//
Query:       gi|70607835|ref|YP_256705.1|  [L=382]
Description: hypothetical protein Saci_2118 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-18   64.5  63.4    5.7e-11   41.9  40.5    1.8  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9  40.5   3.2e-15   5.7e-11       5     352 ..       8     332 ..       6     333 .. 0.81
   2 !   36.3  15.0   1.7e-13     3e-09       2     174 ..     199     375 ..     198     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.2e-15
                         MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa.s 83 
                                   +f++ la+s+++p+++ +   + gi +s++ +++++ + + ++a+++l  ls +  ++++l++g l+ ++  ll++l+a +
  gi|70607835|ref|YP_256705.1|   8 TFFANLASSLTSPFIS-FFVASNGIIGSVLAIATSAGTTFPGIAQYFLINLSIK--AKKLLFWGTLAEGIIwLLIGLLAlT 85 
                                   689999**********.888999****************************999..8***********9995555556655 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                   +  +++vl v+  l +g+ + + + ++ +++    rg++++ +++ + l+ +l+ l+ g++a s    ++ +++ + +l  
  gi|70607835|ref|YP_256705.1|  86 NT-FFVVLYVIITLIMGVTNFGWLLILDKISGT-SRGLVLSQYNLYVYLAGLLATLFTGFVA-SSDINVLRFFFIASGL-- 161
                                   54.59**********999999999999999987.****************************.3344433222222222.. PP

                         MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglll 245
                                        l+++  ++++k + ++e     + ++++p  k +++++    +l+a  lf+f ++++  l+pl  +  ++l+  ++
  gi|70607835|ref|YP_256705.1| 162 -----LYIYGAYVNSKIDIDVEF----KSKSVSP-MKVFKNSKLR-NFLLANSLFTFTWAMAWPLFPLAQVYKFHLD-SFE 230
                                   .....344445556666666666....6666777.6666666633.36666666667***********656666666.6** PP

                         MFS_1 246 aglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalas 326
                                   ++++  ++ l ++il+ ++grl+d+   +r  +++++ ++la++ la++  t ++  +++++++ Gf+ +  ++sl+a++ 
  gi|70607835|ref|YP_256705.1| 231 IAIINVIGNLSTVILQRIVGRLIDK---HRVATMFFSRFALATFPLAYAFST-TPYEIYASSLVSGFTNSA-SVSLTAYIL 306
                                   *************************...788888888888888888888888.779999999999998885.788888888 PP

                         MFS_1 327 dlappeeagtasglfntagslggalg 352
                                   d+   ++  t+++l+n++ +l+++ g
  gi|70607835|ref|YP_256705.1| 307 DVSDYQHKRTIIALYNMLAGLAALGG 332
                                   888889999************99765 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.7e-13
                         MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                   lla  l ++++++++p++pla    ++++  ei ++ ++  l +++++ ++Grl+d++ r  +++++ +++a + l+ +f 
  gi|70607835|ref|YP_256705.1| 199 LLANSLFTFTWAMAWPLFPLAQVYKFHLDSFEIAIINVIGNLSTVILQRIVGRLIDKH-RVATMFFSRFALATFPLAYAF- 277
                                   6888999*************999**********************************9.888999999999999444446. PP

                         MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg........Wrav 153
                                   s+ +  ++++ +++G++  ++  +  a+i d++  +++   i+l+++ ++l+a+ g l+++++   +l+          ++
  gi|70607835|ref|YP_256705.1| 278 STTPyEIYASSLVSGFTN-SASVSLTAYILDVSDYQHKRTIIALYNMLAGLAALGGSLFSSFIFgLLLSyfsnmvttIDVM 357
                                   888989999999999996.66667779999*****************9999999999999977723333444663333333 PP

                         MFS_1 154 fyilaivsllafvlfllllpe 174
                                      ++++ ++a +   l+l++
  gi|70607835|ref|YP_256705.1| 358 LGSIGGLRIIASL---LFLRV 375
                                   4444444444433...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2066.49
//
Query:       gi|70607836|ref|YP_256706.1|  [L=380]
Description: hypothetical protein Saci_2119 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-07   29.2  25.3      0.042   13.9   1.0    4.5  5  TolA_bind_tri    TolA binding protein trimerisation
    1.1e-06   28.6  10.9       0.02   15.0   0.0    5.4  7  MbeD_MobD        MbeD/MobD like
    8.1e-06   25.7  58.7     0.0041   17.1   3.8    5.9  6  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    1.6e-05   24.2  35.3     0.0059   15.7  21.0    3.2  2  TelA             Toxic anion resistance protein (TelA)
    0.00022   21.4  24.7        1.2    9.5   0.3    6.5  7  TetR_C_24        Tetracyclin repressor-like, C-terminal domai
    0.00076   19.8  36.6        1.2    9.5   7.7    5.4  5  Syntaxin_2       Syntaxin-like protein
     0.0016   17.9  15.3        1.9    8.1   0.4    5.6  6  Sigma70_r4       Sigma-70, region 4
     0.0039   17.4  36.3        0.5   10.5  17.3    3.0  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0091   14.9  47.0       0.82    8.5  25.3    2.6  2  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.014   15.0   3.9      0.014   15.0   3.9    3.4  3  Mt_ATP-synt_B    Mitochondrial ATP synthase B chain precursor
      0.025   14.9  10.0      0.025   14.9  10.0    4.2  4  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.031   14.1  42.0       0.48   10.2  14.9    3.0  2  TACC_C           Transforming acidic coiled-coil-containing p
      0.032   14.3   5.6      1e+02    3.1   0.1    4.9  6  YaiA             YaiA protein
      0.042   13.7  57.4       0.26   11.2  15.1    3.4  3  ARGLU            Arginine and glutamate-rich 1
      0.057   13.6  47.6       0.54   10.5  16.0    3.7  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.08   13.3  54.4       0.93    9.9  14.9    3.6  3  DUF4200          Domain of unknown function (DUF4200)
       0.11   12.3  48.1       0.12   12.2  19.5    2.3  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.14   12.1  24.4       0.74    9.7   0.5    4.1  3  DUF1759          Protein of unknown function (DUF1759)
       0.17   12.2  22.5        0.9    9.9   4.5    3.6  1  DUF2935          Domain of unknown function (DUF2935)
       0.18   10.0  42.7        1.2    7.3  15.1    3.0  2  EzrA             Septation ring formation regulator, EzrA
       0.21   11.3  17.1        2.4    7.8   6.3    3.3  4  TMP_2            Prophage tail length tape measure protein
       0.25   11.6  13.7        1.3    9.3   1.7    2.9  2  Vps39_1          Vacuolar sorting protein 39 domain 1
       0.28   10.7  37.9       0.46   10.0  37.9    1.2  1  Filament         Intermediate filament protein
        0.3   11.3  30.0       0.28   11.5   4.7    5.4  4  DUF948           Bacterial protein of unknown function (DUF94
       0.37   11.0  42.0          2    8.6   9.3    3.4  4  ATG16            Autophagy protein 16 (ATG16)
       0.44    9.4  47.7        1.7    7.5  47.7    1.7  1  DUF812           Protein of unknown function (DUF812)
       0.53    9.5  10.8       0.78    8.9   0.9    3.3  3  NanE             Putative N-acetylmannosamine-6-phosphate epi
       0.53    9.8  36.8        2.4    7.7  15.0    2.7  3  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.66    9.6  15.8        1.5    8.4   6.7    2.4  3  CDPS             Cyclodipeptide synthase
        0.7    9.8  11.7    2.5e+02    1.5  11.7    2.9  1  Y_phosphatase3   Tyrosine phosphatase family
       0.72    8.4  42.4          2    6.9  10.6    2.4  2  AAA_13           AAA domain
        1.1    9.4  36.6        0.3   11.2   3.3    4.2  4  DUF148           Domain of unknown function DUF148
        1.3    9.6  30.5         32    5.0   0.6    6.6  6  CcdA             Post-segregation antitoxin CcdA
        1.3    7.0  27.5       0.21    9.6  11.7    2.3  2  Pox_Rap94        RNA polymerase-associated transcription spec
        1.4    8.8   0.0        1.4    8.8   0.0    4.0  5  TusA             Sulfurtransferase TusA
        1.6    8.7   5.2       0.49   10.4   0.7    2.3  2  T2SSF            Type II secretion system (T2SS), protein F
        1.7    9.0  19.3         34    4.9   0.5    5.4  6  YccJ             YccJ-like protein
        1.8    8.3  31.9         13    5.6   9.6    3.5  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
          2    8.8  37.5         12    6.2  30.6    2.4  2  Fez1             Fez1
        2.5    6.3  17.9        6.3    5.0  12.2    2.0  2  SpecificRecomb   Site-specific recombinase
        2.5    6.5   8.0         18    3.7   0.3    2.9  4  Corona_S2        Coronavirus S2 glycoprotein
          4    7.1  47.6        9.1    6.0  16.4    3.3  3  DUF4201          Domain of unknown function (DUF4201)
        4.6    6.0  23.1        7.1    5.3  23.1    1.4  1  ALMT             Aluminium activated malate transporter
        4.6    5.3  41.7      2e+02   -0.1  41.7    2.2  1  HOOK             HOOK protein
        4.9    7.2  45.2        4.3    7.4  16.6    3.5  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
          5    6.6  38.6        3.3    7.2  11.0    3.1  3  MscS_porin       Mechanosensitive ion channel porin domain
        5.4    7.6  28.0        3.6    8.2   4.1    4.6  5  DUF4473          Domain of unknown function (DUF4473)
        5.7    7.1  17.6         10    6.4   2.3    3.7  3  MCD_N            Malonyl-CoA decarboxylase N-terminal domain
        6.8    6.6  19.0         78    3.2   1.3    5.9  6  SfsA             Sugar fermentation stimulation protein RE do
        7.1    7.1  34.1         40    4.7   0.4    6.8  7  SAPIS-gp6        Pathogenicity island protein gp6 in Staphylo
        7.1    6.9  26.4        6.9    6.9   0.6    5.4  6  DUF2584          Protein of unknown function (DUF2584)
        7.8    6.1  47.2        3.8    7.1  20.1    3.4  2  Lebercilin       Ciliary protein causing Leber congenital ama


Domain annotation for each model (and alignments):
>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       5.7     2e+03      48      67 ..      31      50 ..      23      61 .. 0.52
   2 !   13.3   5.2   0.00019     0.065       5      66 ..      76     137 ..      72     144 .. 0.86
   3 !   13.6   3.0   0.00015     0.051       5      55 ..     132     182 ..     128     185 .. 0.92
   4 !   13.2   1.2    0.0002     0.068       5      48 ..     160     203 ..     156     208 .. 0.89
   5 !   13.9   1.0   0.00012     0.042       5      51 ..     188     234 ..     184     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5.7
                 TolA_bind_tri 48 leqleerQrdlYldlDerlr 67
                                  l ++ +  r++ +d D+  +
  gi|70607836|ref|YP_256706.1| 31 LHSISQDFREQQKDYDKKFE 50
                                  44444444444444444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00019
                 TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                    +a+L ++ e ++++++el +q e++ + ++eLR  +Ee++  + +l+++  +  + + e+ 
  gi|70607836|ref|YP_256706.1|  76 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELR 137
                                   689999999**9********************************999999888777776655 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00015
                 TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQ 55 
                                    +a+L ++ e ++++++el +q e++ + ++eLR  +Ee++  + +l+++ 
  gi|70607836|ref|YP_256706.1| 132 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQT 182
                                   6899999**********************************9999998885 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.0002
                 TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyql 48 
                                    +a+L ++ e ++++++el +q e++ + ++eLR  +Ee++  +
  gi|70607836|ref|YP_256706.1| 160 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAI 203
                                   6899999********************************98766 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 0.00012
                 TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                    +a+L ++ e ++++++el +q e++ + ++eLR  +Ee++  + +l
  gi|70607836|ref|YP_256706.1| 188 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRL 234
                                   6899999*********************************9876555 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.26        90       9      33 ..      28      52 ..      21      66 .. 0.83
   2 ?    4.1   0.1      0.14        50      24      63 ..      71     110 ..      56     117 .. 0.78
   3 ?    5.9   0.2     0.041        14      20      63 ..      95     138 ..      92     145 .. 0.85
   4 ?    5.8   0.2     0.045        15      20      63 ..     123     166 ..     120     172 .. 0.85
   5 ?    5.9   0.1     0.039        13      20      63 ..     151     194 ..     147     201 .. 0.85
   6 ?    3.0   0.1      0.32   1.1e+02      21      50 ..     180     209 ..     177     212 .. 0.84
   7 !   15.0   0.0   5.7e-05      0.02      20      68 ..     207     255 ..     202     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.26
                     MbeD_MobD  9 LsAlEqLQqdYeqrlqeWesafael 33
                                  L  l ++ qd+  ++++++  f+e+
  gi|70607836|ref|YP_256706.1| 28 LKELHSISQDFREQQKDYDKKFEEI 52
                                  5668899999999999999999986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                     MbeD_MobD  24 qeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLse 63 
                                   +e   a ael++m e   +    L++q ++ ++ + +L +
  gi|70607836|ref|YP_256706.1|  71 EENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 110
                                   5666788999999999999888999998888877777765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.041
                     MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLse 63 
                                    ++ +e   a ael++m e   +    L++q ++ ++ + +L +
  gi|70607836|ref|YP_256706.1|  95 RKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 138
                                   5788999999*********9999999999999988888887765 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.045
                     MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLse 63 
                                    ++ +e   a ael++m e   +    L++q ++ ++ + +L +
  gi|70607836|ref|YP_256706.1| 123 RKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 166
                                   578899999**********9999999999999988888877765 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.039
                     MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLse 63 
                                    ++ +e   a ael++m e   +    L++q ++ ++ + +L +
  gi|70607836|ref|YP_256706.1| 151 RKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 194
                                   5788999999*********9999999999999988888887765 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.32
                     MbeD_MobD  21 qrlqeWesafaelqrmfeltqrenaaLseq 50 
                                   ++ +e   a ael++m e   +    L++q
  gi|70607836|ref|YP_256706.1| 180 KQTEENTKAIAELRKMTEENTKAIIELRKQ 209
                                   78899999**********999888788777 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 5.7e-05
                     MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                    ++ +e   a ael++m e   +    L + v++L + V  L+e+v+ l
  gi|70607836|ref|YP_256706.1| 207 RKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGL 255
                                   588999999************************************9866 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1     0.056        19      35      71 ..      21      57 ..      13      61 .. 0.68
   2 ?    7.0  10.4     0.017       5.9      22      69 ..      64     111 ..      54     115 .. 0.86
   3 ?    6.9   9.1     0.018       6.2      28      69 ..     112     153 ..     108     156 .. 0.85
   4 !    7.8   6.6    0.0094       3.2      24      65 ..     136     177 ..     134     178 .. 0.85
   5 ?    7.0   9.9     0.017       5.8      24      69 ..     164     209 ..     162     212 .. 0.88
   6 !   17.1   3.8   1.2e-05    0.0041      23      74 .]     205     256 ..     204     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.056
                    TMF_DNA_bd 35 ikkLrkknkelekeikelkkkleklekeleeleerlk 71
                                  +k+L + +kel +  ++  ++ ++++k++ee+ ++l+
  gi|70607836|ref|YP_256706.1| 21 VKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELA 57
                                  6777777777777777777777777777777666654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                    TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                    +L k+  ++ ++i +Lrk  +e++k i el k++e+ +k ++el+++
  gi|70607836|ref|YP_256706.1|  64 GNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKM 111
                                   57888999999*********************************9986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.018
                    TMF_DNA_bd  28 elklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                     ++ ++i +Lrk+ +e++k i+el k +e+ +k + el++ 
  gi|70607836|ref|YP_256706.1| 112 TEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQ 153
                                   567889999**********************99999999875 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0094
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekelee 65 
                                   L+k   ++ ++i +Lrk+ +e++k i+el k +e+ +k + e
  gi|70607836|ref|YP_256706.1| 136 LRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIE 177
                                   67777889999******************9999999887765 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.017
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                   L+k   ++ ++i +Lrk+ +e++k i+el k +e+ +k + el++ 
  gi|70607836|ref|YP_256706.1| 164 LRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQ 209
                                   77777889999**************************999999875 PP

  == domain 6  score: 17.1 bits;  conditional E-value: 1.2e-05
                    TMF_DNA_bd  23 kLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkeae 74 
                                   +L+k+  ++ ++i +Lrk  +e++k i +l+k ++kl+k+++ l+er ++ e
  gi|70607836|ref|YP_256706.1| 205 ELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLE 256
                                   599********************************************98865 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  21.0   1.7e-05    0.0059      53     210 ..      12     172 ..       8     173 .. 0.88
   2 !    7.2  19.7    0.0068       2.3      72     207 ..     118     225 ..     112     231 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                          TelA  53 LvkelkeldpdelkeekklgllplfkkaknkieklfakYekaeeqid...kIvkeLekgqdellkdnaaLdqlyeknleyf 130
                                   +++el+ + +++l+e+ k +l ++ + ++++ +++ +k+e++++++    +I+ +L k+ +e +k +a+L ++ e+n +++
  gi|70607836|ref|YP_256706.1|  12 VREELETFLVKSLAESLK-ELHSISQDFREQQKDYDKKFEEIGKELAglrEITGNLVKSSEENTKAIAELRKMTEENTKAI 91 
                                   578899999999988844.5555669******************9753338****************************** PP

                          TelA 131 keLekyiaaGekkleeldekllpeleakaeas.gdpedaqalrdleealdrleqrvqDLelaravsiQtapqirlvqknnk 210
                                    eL+k+    +k+++el+++++++ +a  e   + +e+++a+ +l+++ ++  + + +L+ +   +   +  +r + + n+
  gi|70607836|ref|YP_256706.1|  92 IELRKQTEENTKAIAELRKMTEENTKAIIELRkQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENT 172
                                   *********************99999987755367789*********************9999999999999998888886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0068
                          TelA  72 gllplfkkaknkieklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekll 152
                                    +++ ++k  ++ +k +a+ +k+ e+  k + eL+k+ +e +k +a+L ++ e+n +++ eL+k+    +k+++el+++++
  gi|70607836|ref|YP_256706.1| 118 AIIE-LRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTE 197
                                   4444.4444445555555555555555555556666666666666666666666666666666666665555666555555 PP

                          TelA 153 peleakaeas.gdpedaqalrdleealdrleqrvqDLelaravsiQtapqirlvqk 207
                                   ++ +a  e   + +e+++a+ +l+++                             +
  gi|70607836|ref|YP_256706.1| 198 ENTKAIIELRkQTEENTKAIAELRKMT----------------------------E 225
                                   555544432213334444444444443............................3 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       2.4   8.4e+02      41      58 ..      35      52 ..       5      58 .. 0.63
   2 !    9.5   0.3    0.0033       1.2      14      58 ..      61     105 ..      55     107 .. 0.82
   3 ?    6.9   0.3     0.021       7.2      31      58 ..     106     133 ..     102     135 .. 0.89
   4 ?    6.9   0.3     0.021       7.2      31      58 ..     134     161 ..     130     163 .. 0.89
   5 ?    7.1   0.3     0.019       6.5      31      58 ..     162     189 ..     158     192 .. 0.89
   6 ?    7.1   0.2     0.019       6.4      31      58 ..     190     217 ..     186     220 .. 0.89
   7 ?    1.2   0.0       1.2   4.3e+02      31      57 ..     218     244 ..     215     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.4
                                  HHHHHHHHHHHHHHHHHH CS
                     TetR_C_24 41 reeiralrreyerllrdl 58
                                   + +r+++++y++ ++++
  gi|70607836|ref|YP_256706.1| 35 SQDFREQQKDYDKKFEEI 52
                                  356788888888888877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0033
                                   HHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  14 ahveviaeereeaavllrelraLspehreeiralrreyerllrdl 58 
                                   +++  ++++ ee +  + elr +++e+ ++i++lr++ e++ +++
  gi|70607836|ref|YP_256706.1|  61 EITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAI 105
                                   555566677777788889*********************998876 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.021
                                   HHGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  31 relraLspehreeiralrreyerllrdl 58 
                                    elr +++e+ ++i++lr++ e++ +++
  gi|70607836|ref|YP_256706.1| 106 AELRKMTEENTKAIIELRKQTEENTKAI 133
                                   699*******************998876 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.021
                                   HHGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  31 relraLspehreeiralrreyerllrdl 58 
                                    elr +++e+ ++i++lr++ e++ +++
  gi|70607836|ref|YP_256706.1| 134 AELRKMTEENTKAIIELRKQTEENTKAI 161
                                   699*******************998876 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.019
                                   HHGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  31 relraLspehreeiralrreyerllrdl 58 
                                    elr +++e+ ++i++lr++ e++ +++
  gi|70607836|ref|YP_256706.1| 162 AELRKMTEENTKAIIELRKQTEENTKAI 189
                                   699*******************998877 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.019
                                   HHGGGS-HHHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  31 relraLspehreeiralrreyerllrdl 58 
                                    elr +++e+ ++i++lr++ e++ +++
  gi|70607836|ref|YP_256706.1| 190 AELRKMTEENTKAIIELRKQTEENTKAI 217
                                   699*******************998877 PP

  == domain 7  score: 1.2 bits;  conditional E-value: 1.2
                                   HHGGGS-HHHHHHHHHHHHHHHHHHHH CS
                     TetR_C_24  31 relraLspehreeiralrreyerllrd 57 
                                    elr +++e+ ++i++l + +++l+++
  gi|70607836|ref|YP_256706.1| 218 AELRKMTEENTKAIIRLTKIVDKLVKS 244
                                   6899999*******9999999988876 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.059        20      75     100 ..      20      45 ..      13      46 .. 0.94
   2 ?    5.3   7.1     0.073        25      10      62 ..      72     125 ..      46     131 .. 0.64
   3 ?    5.2   7.5     0.077        27      11      60 ..     115     165 ..     107     173 .. 0.61
   4 ?    2.6  12.8      0.51   1.8e+02      24      81 ..     142     201 ..     127     217 .. 0.49
   5 !    9.5   7.7    0.0036       1.2      14      81 ..     174     247 ..     170     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.059
                    Syntaxin_2  75 LkkdfkealqeFqkiqrqyaekekqi 100
                                   L+k++ e+l+e+++i ++++e +k++
  gi|70607836|ref|YP_256706.1|  20 LVKSLAESLKELHSISQDFREQQKDY 45 
                                   8999*******************987 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.073
                    Syntaxin_2  10 snvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldns 62 
                                   +n++ + +l+k  + + k   elr++ +e+++ i el k t+e+ k + +l ++
  gi|70607836|ref|YP_256706.1|  72 ENTKAIAELRKMTEENtKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQ 125
                                   445555555555554423566777777777777777777777777666666555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.077
                    Syntaxin_2  11 nvstleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqld 60 
                                   n++ + +l+kq + + k   elr+  +e+++ i el k+t+e+ k +++l 
  gi|70607836|ref|YP_256706.1| 115 NTKAIIELRKQTEENtKAIAELRKMTEENTKAIIELRKQTEENTKAIAELR 165
                                   455556666666555335666666666666666666666666666666654 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.51
                    Syntaxin_2  24 tk.kdteelreklhelieeinelikktnellkklsqldnsssdsqqkl.qkekLkkdfke 81 
                                    + k   elr++ +e+++ i el k t+e+ k + +l ++++ +++ + +  k++++ ++
  gi|70607836|ref|YP_256706.1| 142 ENtKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIaELRKMTEENTK 201
                                   332345555555555555555555555555555555555554442222233333333333 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.0036
                    Syntaxin_2  14 tleklvkqLgtk.kdteelreklhelieeinelikktnellkklsqldnsssds.....qqkl.qkekLkkdfke 81 
                                    + +l+kq + + k   elr+  +e+++ i el k+t+e+ k +++l + ++ +     +  + + +kL+k++++
  gi|70607836|ref|YP_256706.1| 174 AIIELRKQTEENtKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENtkaiiRL-TkIVDKLVKSVSA 247
                                   5555666655553456677777777777777777777777777776666665554332211.1234444444433 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       4.7   1.6e+03      21      30 ..      47      56 ..      39      57 .. 0.81
   2 ?    7.2   0.3      0.01       3.5       7      41 ..      86     120 ..      80     121 .. 0.90
   3 ?    7.1   0.2     0.011       3.8       7      41 ..     114     148 ..     113     149 .. 0.90
   4 ?    7.1   0.2     0.011       3.8       7      41 ..     142     176 ..     141     177 .. 0.90
   5 ?    6.9   0.2     0.012       4.3       7      40 ..     170     203 ..     164     204 .. 0.90
   6 !    8.1   0.4    0.0054       1.9       7      42 ..     198     233 ..     192     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.7
                                  --HHHHHHHH CS
                    Sigma70_r4 21 lTleEIgerl 30
                                    +eEIg++l
  gi|70607836|ref|YP_256706.1| 47 KKFEEIGKEL 56
                                  5689***998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4   7 ererevlelrfgeglTleEIgerlgiSrerVrqie 41 
                                   e+ + ++elr   + + + I+e   +++e  + i+
  gi|70607836|ref|YP_256706.1|  86 ENTKAIIELRKQTEENTKAIAELRKMTEENTKAII 120
                                   67799******9999**************999875 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4   7 ererevlelrfgeglTleEIgerlgiSrerVrqie 41 
                                   e+ + ++elr   + + + I+e   +++e  + i+
  gi|70607836|ref|YP_256706.1| 114 ENTKAIIELRKQTEENTKAIAELRKMTEENTKAII 148
                                   67799******9999**************999875 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                    Sigma70_r4   7 ererevlelrfgeglTleEIgerlgiSrerVrqie 41 
                                   e+ + ++elr   + + + I+e   +++e  + i+
  gi|70607836|ref|YP_256706.1| 142 ENTKAIIELRKQTEENTKAIAELRKMTEENTKAII 176
                                   67799******9999**************999875 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHH CS
                    Sigma70_r4   7 ererevlelrfgeglTleEIgerlgiSrerVrqi 40 
                                   e+ + ++elr   + + + I+e   +++e  + i
  gi|70607836|ref|YP_256706.1| 170 ENTKAIIELRKQTEENTKAIAELRKMTEENTKAI 203
                                   67799******9999**************99877 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0054
                                   HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHH CS
                    Sigma70_r4   7 ererevlelrfgeglTleEIgerlgiSrerVrqiek 42 
                                   e+ + ++elr   + + + I+e   +++e  + i++
  gi|70607836|ref|YP_256706.1| 198 ENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIR 233
                                   67799******9999***************999986 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  16.2     0.011         4      26     123 ..      38     138 ..      15     155 .. 0.48
   2 !   10.5  17.3    0.0015       0.5      26     130 ..     136     243 ..     134     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHCCHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketidaqesn 103
                                   + +++kd++k+ e++ +el+ +++ t +  + ++e ++ ++e  k +++n+++i +++k+ ee    i++l++   ++ + 
  gi|70607836|ref|YP_256706.1|  38 FREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEEntkAIAELRKMTEENTKA 118
                                   445555555555555555555554444433333333333333333333333333333333332111344444444444455 PP

                                   HHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 104 irvLqnvlesneqkiqkLeq 123
                                   i +L++  e+n + i++L++
  gi|70607836|ref|YP_256706.1| 119 IIELRKQTEENTKAIAELRK 138
                                   55555555555555555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0015
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC...CCHHHHHHHCCHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleee...ilrlketidaqesn 103
                                   l k+ ++ +k + +l+++ ee+++   e +++++e ++ + e  k++++n+++i +++k+ ee+   i++l+++  ++ + 
  gi|70607836|ref|YP_256706.1| 136 LRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENtkaIIELRKQTEENTKA 216
                                   7788999999********************9999998888888899999999999999999864333889999999999** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 104 irvLqnvlesneqkiqkLeqdidqker 130
                                   i +L+++ e+n + i +L + +d++ +
  gi|70607836|ref|YP_256706.1| 217 IAELRKMTEENTKAIIRLTKIVDKLVK 243
                                   *******************99998765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5  25.3    0.0024      0.82     149     281 ..      22     157 ..       9     160 .. 0.78
   2 !    8.2  18.6    0.0029         1     172     286 ..     150     263 ..     145     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                          Spc7 149 egleedkelLekqeeeldellpeleeekaeleeeleklqe...aaeelesidkeeLeelreelaelkaeieekkkelaelq 226
                                   ++l e  ++L++  + + e  ++++++++e+ +el+ l+e      + ++ + + ++elr+  +e+ + i e++k+++e +
  gi|70607836|ref|YP_256706.1|  22 KSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREitgNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENT 102
                                   566677777777778888888888888888888888888854433333445788999999999999999999999999999 PP

                          Spc7 227 eqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                   + ++el++  ee ++ + el+++++e  + + e ++++e++ +++ e  k+ ee 
  gi|70607836|ref|YP_256706.1| 103 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEEN 157
                                   9999999999999999999999999999999999999998877776666666555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
                          Spc7 172 leeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                   l+++ +e ++ +++l++    +++ + + + elr++ +e+ + i+e++k+++e ++ + el+++ ee ++ ++el++ ++e
  gi|70607836|ref|YP_256706.1| 150 LRKQTEENTKAIAELRK----MTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEE 226
                                   44444444444444444....555688889999999999999999999999999999999999999999999999988888 PP

                          Spc7 253 aervl.eeckgwse..sevsrlkeevkaleeltgwki 286
                                     + + + +k +++  + vs+l+e+v+ le++ g++ 
  gi|70607836|ref|YP_256706.1| 227 NTKAIiRLTKIVDKlvKSVSALNERVSGLENTFGLMT 263
                                   7665414444443333788899999999999988876 PP

>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   3.9   4.1e-05     0.014      37     105 ..      19      87 ..      11      99 .. 0.89
   2 ?   -0.5  11.2       2.4   8.4e+02      42     112 ..      94     165 ..      89     169 .. 0.85
   3 ?   -1.3  12.8       4.1   1.4e+03      42     116 ..     150     225 ..     149     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHH CS
                 Mt_ATP-synt_B  37 sikefldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaeaferelqa 105
                                    + ++l + +++ +++ +++r+++++  k+  e  k+l  l e+t  l+++s e+++++ae ++ + ++
  gi|70607836|ref|YP_256706.1|  19 FLVKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEEN 87 
                                   5678899999***************************************************99887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHH.HHHHHHH CS
                 Mt_ATP-synt_B  42 ldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaeaferelqa.klareik 112
                                   l k+ e+  +   + r+  ee  k +ie  k++ + ++ + +l +++ e++++++e ++++ ++ k ++e++
  gi|70607836|ref|YP_256706.1|  94 LRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENtKAIAELR 165
                                   6788888889999999999*************************************9998876524556655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHH.HHHHHHHHHHH CS
                 Mt_ATP-synt_B  42 ldkriekiqeelnqsrnlkeealkerieqekklqslveltkslfevskeqvaleaeaferelqa.klareikkkld 116
                                   l k+ e+  +   + r+  ee  k +ie  k++ + ++ + +l +++ e++++++e ++++ ++ k ++e++k+ +
  gi|70607836|ref|YP_256706.1| 150 LRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENtKAIAELRKMTE 225
                                   6678888888899999999*************************************99987765267777777654 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.073        25      31      71 ..      23      63 ..      14      68 .. 0.75
   2 ?    2.4   9.4      0.55   1.9e+02      17      88 ..      69     140 ..      64     142 .. 0.71
   3 ?   -0.2  13.1       3.7   1.3e+03      13      88 ..     124     196 ..     110     198 .. 0.57
   4 ?   14.9  10.0   7.1e-05     0.025      15      95 ..     179     259 ..     165     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.073
                       BLOC1_2 31 aasekykklkdvaaslekkleklnekyeelqpylqqidqie 71
                                  + +e  k+l ++ ++++++ +++++k ee+ + l  + +i 
  gi|70607836|ref|YP_256706.1| 23 SLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREIT 63
                                  45566778888888888888888888888888888777776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.55
                       BLOC1_2  17 atvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                   ++ e+ k + +l + ++e+ k++ +  +++e++ +++ e+ +  +++ + i ++ kq++e ++a++eL +++
  gi|70607836|ref|YP_256706.1|  69 SSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMT 140
                                   566666777777777777777777777777777777777777888888888888888888888888776655 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 3.7
                       BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                   +++e  ++ +  L k+ e+ ++ + +l++++++ +k + +l++     +++ + i ++ kq++e ++a++eL +++
  gi|70607836|ref|YP_256706.1| 124 KQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK---MTEENTKAIIELRKQTEENTKAIAELRKMT 196
                                   3444444444444555555555555555555554444444444...777788888888888888888877776655 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 7.1e-05
                       BLOC1_2  15 leatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                    + t e+ k + +l + ++e+ k++ +  +++e++ +++ e+ +  +++ + i ++ k v++L + vs+L+e ++ LE+ f
  gi|70607836|ref|YP_256706.1| 179 RKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLENTF 259
                                   34455555555555555555555555555555555555556666889999****************************987 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  20.2    0.0047       1.6       2     118 ..      41     161 ..      40     163 .. 0.75
   2 ?   10.2  14.9    0.0014      0.48       8     108 ..     159     255 ..     153     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0047
                        TACC_C   2 sqkdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlla 82 
                                   +qkd d++ e++ +e     e + +l k+ ee +k  +e++k+ +e  k+i +l ++  +++++a +e+ k++ee+ +++ 
  gi|70607836|ref|YP_256706.1|  41 QQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQT-EENTKAIAELRKMTEENTKAII 120
                                   799************9997777788*******************99999999998877.5566889999999999999998 PP

                        TACC_C  83 dln....sveksfsdlfkryekq.kevlegykkneeslkkc 118
                                   +l+    +  k++++l k  e   k  +e  k+ ee  k+ 
  gi|70607836|ref|YP_256706.1| 121 ELRkqteENTKAIAELRKMTEENtKAIIELRKQTEENTKAI 161
                                   88511113456778887776544044455545555555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0014
                        TACC_C   8 aalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsve 88 
                                   +a++++++  ee+ + i el+k+ ee +k  +e++k+ +e  k+i +l ++  +++++a +e+ k++ee+ +++  l+++ 
  gi|70607836|ref|YP_256706.1| 159 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQT-EENTKAIAELRKMTEENTKAIIRLTKI- 237
                                   5677777777788889*****************************9998877.5566899999***99999999999765. PP

                        TACC_C  89 ksfsdlfkryekqkevlegy 108
                                     +++l+k +  + e ++g+
  gi|70607836|ref|YP_256706.1| 238 --VDKLVKSVSALNERVSGL 255
                                   ..556666666665655554 PP

>> YaiA  YaiA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.29     1e+02      18      43 ..      82     107 ..      72     119 .. 0.58
   2 ?    1.8   0.0      0.76   2.6e+02      12      31 ..     118     137 ..     114     145 .. 0.88
   3 ?    2.7   0.1      0.39   1.3e+02      12      31 ..     146     165 ..     129     169 .. 0.55
   4 ?    2.8   0.1      0.37   1.3e+02      13      32 ..     147     166 ..     142     186 .. 0.67
   5 ?    2.9   0.1      0.35   1.2e+02      13      32 ..     175     194 ..     165     212 .. 0.67
   6 ?    1.9   0.0      0.72   2.5e+02      12      31 ..     202     221 ..     198     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.29
                          YaiA  18 kGtagktvtwYeLRaDhPkPdtLise 43 
                                   k t ++t+ + eLR    +    i+e
  gi|70607836|ref|YP_256706.1|  82 KMTEENTKAIIELRKQTEENTKAIAE 107
                                   55555666666655544443333333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.76
                          YaiA  12 kivtvekGtagktvtwYeLR 31 
                                    i++ +k t ++t+ + eLR
  gi|70607836|ref|YP_256706.1| 118 AIIELRKQTEENTKAIAELR 137
                                   589999************99 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.39
                          YaiA  12 kivtvekGtagktvtwYeLR 31 
                                    i++ +k t ++t+ + eLR
  gi|70607836|ref|YP_256706.1| 146 AIIELRKQTEENTKAIAELR 165
                                   34445555555555555554 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.37
                          YaiA  13 ivtvekGtagktvtwYeLRa 32 
                                   i++ +k t ++t+ + eLR 
  gi|70607836|ref|YP_256706.1| 147 IIELRKQTEENTKAIAELRK 166
                                   67777777777777777774 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.35
                          YaiA  13 ivtvekGtagktvtwYeLRa 32 
                                   i++ +k t ++t+ + eLR 
  gi|70607836|ref|YP_256706.1| 175 IIELRKQTEENTKAIAELRK 194
                                   66666777777777777764 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.72
                          YaiA  12 kivtvekGtagktvtwYeLR 31 
                                    i++ +k t ++t+ + eLR
  gi|70607836|ref|YP_256706.1| 202 AIIELRKQTEENTKAIAELR 221
                                   589999**********9999 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  18.1     0.073        25      13     121 ..       5     117 ..       3     118 .. 0.64
   2 ?   11.2  15.1   0.00075      0.26      57     121 ..     110     173 ..     108     175 .. 0.89
   3 ?   10.8  15.8   0.00099      0.34      57     121 ..     166     229 ..     164     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                         ARGLU  13 arRveeavakrVeeelekrkeeieke...verrveearkkmekqveeelerere...aeleeekrkeeeerkkreeleril 87 
                                   ++Rv e v++++e  l k   e  ke   + +  +e++k   k+  ee+ +e +   +   +  +  ee++k   el ++ 
  gi|70607836|ref|YP_256706.1|   5 EKRVREIVREELETFLVKSLAESLKElhsISQDFREQQKDYDKKF-EEIGKELAglrEITGNLVKSSEENTKAIAELRKMT 84 
                                   477888888888777776555555551114444445554444443.334444321103333445556889999******** PP

                         ARGLU  88 eenkrkveeaqrklaEerlaeleekrrlkeerqr 121
                                   een + + e + k+ Ee  + + e r++ ee+++
  gi|70607836|ref|YP_256706.1|  85 EENTKAIIELR-KQTEENTKAIAELRKMTEENTK 117
                                   *******9985.6778889999999999999876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00075
                         ARGLU  57 elerereaeleeekrkeeeerkkreelerileenkrkveeaqrklaEerlaeleekrrlkeerqr 121
                                   ++ +e+ +++ e +++ ee++k   el ++ een + + e + k+ Ee  + + e r++ ee+++
  gi|70607836|ref|YP_256706.1| 110 KMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELR-KQTEENTKAIAELRKMTEENTK 173
                                   57889999******************************9985.6778889999999999999876 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00099
                         ARGLU  57 elerereaeleeekrkeeeerkkreelerileenkrkveeaqrklaEerlaeleekrrlkeerqr 121
                                   ++ +e+ +++ e +++ ee++k   el ++ een + + e + k+ Ee  + + e r++ ee+++
  gi|70607836|ref|YP_256706.1| 166 KMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELR-KQTEENTKAIAELRKMTEENTK 229
                                   57889999******************************9985.6678888999999999999876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   4.2      0.71   2.4e+02      31      96 ..      21      86 ..       4      91 .. 0.60
   2 ?    9.9  19.4    0.0025      0.86      12     103 ..      72     163 ..      62     164 .. 0.90
   3 ?   10.5  16.0    0.0016      0.54      18     103 ..     162     247 ..     156     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.71
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N 31 lleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleae 96
                                  + +l e  +el +  ++++++++   k+++++ k+     e +  l+++++e+ + +++l     ++++e
  gi|70607836|ref|YP_256706.1| 21 VKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELaglrEITGNLVKSSEENTKAIAELR----KMTEE 86
                                  4567777788888888888888888888888777763333334444444444444444444....33333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0025
                                   HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelke 92 
                                   e +k+  + R+  +++ ++++el ++ +e  +++ el++   e +k+I ++ k+ e+ ++ iae +++ ee  ++  el++
  gi|70607836|ref|YP_256706.1|  72 ENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRK 152
                                   45555566788999******************************************************************9 PP

                                   HHHHHHHHHCT CS
                  Seryl_tRNA_N  93 leaelekllla 103
                                    ++e +k++++
  gi|70607836|ref|YP_256706.1| 153 QTEENTKAIAE 163
                                   99998888765 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0016
                                   HCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  18 lkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                                    + R+  +++ ++++el ++ +e  +++ el++   e +k+I ++ k+ e+ ++ iae +++ ee  ++  +l+++ ++l 
  gi|70607836|ref|YP_256706.1| 162 AELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLV 242
                                   45678899******************************************************************9999998 PP

                                   HHHCT CS
                  Seryl_tRNA_N  99 kllla 103
                                   k ++a
  gi|70607836|ref|YP_256706.1| 243 KSVSA 247
                                   77766 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  14.9    0.0027      0.93      13     106 ..      22     115 ..      11     119 .. 0.89
   2 ?    1.2  28.1       1.3   4.5e+02      17     107 ..     103     193 ..      93     194 .. 0.88
   3 ?    8.5  16.0    0.0072       2.5       8     102 ..     164     258 ..     163     260 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0027
                       DUF4200  13 ealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlk 93 
                                   ++l++  +e++ + + +++++++++kk +e+ ++l+ + +      + +++  k ++e rk+++e ++ i +l++++e+  
  gi|70607836|ref|YP_256706.1|  22 KSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENT 102
                                   57888999999999***********************************************************99999999 PP

                       DUF4200  94 seiekleekleey 106
                                   + i++l +  ee 
  gi|70607836|ref|YP_256706.1| 103 KAIAELRKMTEEN 115
                                   8888888776664 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.3
                       DUF4200  17 akkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseie 97 
                                   ++ +e++++ e+++++  el+k+ +e  + ++++ k+ +en +  ++ +k++ee +k++ e  +  ++ ++ i +l+++ e
  gi|70607836|ref|YP_256706.1| 103 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTE 183
                                   4557888999999999999999999999999************************************************** PP

                       DUF4200  98 kleekleeyk 107
                                   ++ ++++e++
  gi|70607836|ref|YP_256706.1| 184 ENTKAIAELR 193
                                   9999999986 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0072
                       DUF4200   8 mfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkae 88 
                                   +++++e+  ++  e++++ e+++++ +el+k  +e  + ++++ k  +en +  a+ +k +ee +k++ + ++ + kl ++
  gi|70607836|ref|YP_256706.1| 164 LRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKS 244
                                   555666666666778888888888888888888888888888888888888888888888888888888888888888888 PP

                       DUF4200  89 ietlkseiekleek 102
                                   +++l+++ + le++
  gi|70607836|ref|YP_256706.1| 245 VSALNERVSGLENT 258
                                   88888888888875 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  19.5   0.00035      0.12      62     179 ..      21     138 ..      17     141 .. 0.96
   2 ?    5.1  21.6     0.051        18      79     189 ..     140     246 ..     138     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00035
                      KASH_CCD  62 aklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhel 142
                                    k+l+e l el  + ++  E+++    + +++ ke   L++   +L    + ++  + el+k ++e +k + eL+kq  e 
  gi|70607836|ref|YP_256706.1|  21 VKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEEN 101
                                   599**************************************999**9999999999999********************** PP

                      KASH_CCD 143 eellaekealleektkqieeLkltieEyssiieeLra 179
                                    + +ae  ++ ee tk i eL+ + eE++++i eLr+
  gi|70607836|ref|YP_256706.1| 102 TKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 138
                                   ***********************************96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.051
                      KASH_CCD  79 leEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkq 159
                                   +eE+ + +   +kq e en   ia++ ++ een+k   e   l+k+++e +k +aeL+k   e  + + e  +  ee tk 
  gi|70607836|ref|YP_256706.1| 140 TEENTKAIIELRKQTE-ENTKAIAELRKMTEENTKAIIE---LRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKA 216
                                   5666666666666665.7778889999999999998886...788888999999999998888888888888888999999 PP

                      KASH_CCD 160 ieeLkltieEyssiieeLraeksrLeeqlq 189
                                   i eL+ + eE++++i  L + + +L + ++
  gi|70607836|ref|YP_256706.1| 217 IAELRKMTEENTKAIIRLTKIVDKLVKSVS 246
                                   999999999999888888888888877665 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   7.3     0.084        29      71     140 ..      81     148 ..      59     156 .. 0.52
   2 ?    4.3   5.6       0.1        36      79     142 ..     145     206 ..     138     214 .. 0.44
   3 ?    9.7   0.5    0.0021      0.74      76     121 ..     212     257 ..     207     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.084
                       DUF1759  71 rkiirellnelmklpslkeedasqlrrivdavneivralealgeeadkydailvsllleKldeevrrkwi 140
                                   rk+ +e  +++ +l++ +ee+++ ++++    +e  +a+ +l ++++  +   + + l+K+ ee  ++ i
  gi|70607836|ref|YP_256706.1|  81 RKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTE--ENTKAIAELRKMTEENTKAII 148
                                   44444555555555555555555555555555555555555554444..333333334555555444444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                       DUF1759  79 nelmklpslkeedasqlrrivdavneivralealgeeadkydailvsllleKldeevrrkwise 142
                                   +++ +l++ +ee+++ ++++    +e  +a+ +l ++++  +   + + l+K+ ee  ++ i+ 
  gi|70607836|ref|YP_256706.1| 145 KAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTE--ENTKAIAELRKMTEENTKAIIEL 206
                                   444455554445554444444444444444444444444..23333333444444444443433 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0021
                       DUF1759  76 ellnelmklpslkeedasqlrrivdavneivralealgeeadkyda 121
                                   e  +++ +l++++ee+++ + r++  v+++v+ + al+e +   + 
  gi|70607836|ref|YP_256706.1| 212 ENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLEN 257
                                   667899*******************************999876655 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.5    0.0026       0.9      30      94 ..      36     103 ..      15     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0026
                       DUF2935  30 kdlikeakefkkeFekllaeavelseglv...rasseleeavakLneealkltreliqFkkellekvl 94 
                                   +d+ ++ k++ k+Fe++ +e   l e +    + s+e+++a+a+L + + + t+++i++ k+++e+ +
  gi|70607836|ref|YP_256706.1|  36 QDFREQQKDYDKKFEEIGKELAGLREITGnlvKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTK 103
                                   56777778888888888877655544433444888888899999999999999999988888888765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  15.1    0.0034       1.2     322     425 ..      24     128 ..       5     135 .. 0.74
   2 ?    6.2   6.9    0.0071       2.4      96     162 ..     189     255 ..     183     270 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0034
                                   HHTTGGG-TTTS-GGGSSTTTS.TTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 322 nkelkeeldrlkqsYeLseeel.eklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeiles 401
                                   + e  +el+ ++q ++ ++++  +k++e+ kel  l++   +l++  ee++ a  el+++ ee ++ + e+ ++ ee  ++
  gi|70607836|ref|YP_256706.1|  24 LAESLKELHSISQDFREQQKDYdKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKA 104
                                   445566777777777666655525688888888888888888888888888888888888888888888888888888888 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 402 lkslrkdEkrAreqldeikkelke 425
                                   +++lrk  ++  + + e++k+ +e
  gi|70607836|ref|YP_256706.1| 105 IAELRKMTEENTKAIIELRKQTEE 128
                                   888888888888888888777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0071
                                   HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHH CS
                          EzrA  96 fkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygea 162
                                   + +++k  +e ++ + e+++++++  ++++el++  e+n ++i  l +  ++l k++ a ++  +  
  gi|70607836|ref|YP_256706.1| 189 IAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGL 255
                                   4445555555556666666666666666666666666666666666666666666665555544444 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.3     0.007       2.4      94     194 ..      59     155 ..      52     164 .. 0.82
   2 ?    5.8   9.3     0.028       9.7      86     194 ..      76     183 ..      75     192 .. 0.78
   3 ?    5.8   9.7     0.029       9.9      86     194 ..     104     211 ..     102     219 .. 0.80
   4 ?    7.7   5.2    0.0075       2.6      85     197 ..     145     256 ..     144     259 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.007
                         TMP_2  94 arefnkaliltGnaaGlTasqLeamaesiaeagg.tqaaaaealaalastGkiggeqlervakaaaelekatGqsvdetak 173
                                   +re++  l+++++   +  ++L +m+e+  +a    ++++ e ++a+a+  k+++e+++ +++  +++e++t     ++++
  gi|70607836|ref|YP_256706.1|  59 LREITGNLVKSSEENTKAIAELRKMTEENTKAIIeLRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENT-----KAIA 134
                                   577788888888888889999999999888888778888999999999999988888888887777777765.....7889 PP

                         TMP_2 174 elaklakdPvkaaeklneqlh 194
                                   el k++++ +ka+ +l +q +
  gi|70607836|ref|YP_256706.1| 135 ELRKMTEENTKAIIELRKQTE 155
                                   9***************99976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.028
                         TMP_2  86 AyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGq 166
                                   A+++ +k ++e +ka+i + +++   ++ ++++ +  +e+++ + + ++++ + +++ +  ++++e+ +ka +el k t +
  gi|70607836|ref|YP_256706.1|  76 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEE 156
                                   666777788888899999988888888888888888888888888888888888888888888888888888888888776 PP

                         TMP_2 167 svdetakelaklakdPvkaaeklneqlh 194
                                   ++ ++++el k++++ +ka+ +l +q +
  gi|70607836|ref|YP_256706.1| 157 NT-KAIAELRKMTEENTKAIIELRKQTE 183
                                   65.5677899999999999999999976 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.029
                         TMP_2  86 AyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatGq 166
                                   A+++ +k ++e +ka+i + +++   ++ ++++ +  +e+++ + + ++++ + +++ +  ++++e+ +ka +el k t +
  gi|70607836|ref|YP_256706.1| 104 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEE 184
                                   777888889999999999999999888888888888888888888888888888888888888888888888888888877 PP

                         TMP_2 167 svdetakelaklakdPvkaaeklneqlh 194
                                   ++ ++++el k++++ +ka+ +l +q +
  gi|70607836|ref|YP_256706.1| 185 NT-KAIAELRKMTEENTKAIIELRKQTE 211
                                   65.567789***********99999976 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0075
                         TMP_2  85 lAyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelekatG 165
                                   +A+ + +k+++e +ka+  + + +   ++ + ++ ++ +e+++ +a+ ++++ + +++    ++q+e+ +ka ael k+t 
  gi|70607836|ref|YP_256706.1| 145 KAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTE 225
                                   577888899999999999999999999999999999999999999999999999999999999999999999999999888 PP

                         TMP_2 166 qsvdetakelaklakdPvkaaeklneqlhfLt 197
                                   +++++++  l k+ ++ vk +++lne++  L+
  gi|70607836|ref|YP_256706.1| 226 ENTKAII-RLTKIVDKLVKSVSALNERVSGLE 256
                                   8876665.699999999999999999988776 PP

>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5    0.0064       2.2      33     103 ..      79     150 ..      60     154 .. 0.77
   2 ?    9.3   1.7    0.0038       1.3      38     106 ..     168     237 ..     153     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0064
                       Vps39_1  33 eeiLkkekkykeLidlYygkklheeALeLlkeladedeedeedsslkgeket.iiqylqklseedldliley 103
                                   e   + e+++k++i+l ++ ++  +A+  l+++ +e+++   +  ++ e++t  i  l+k+ ee+ + i+e+
  gi|70607836|ref|YP_256706.1|  79 ELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTkAIAELRKMTEENTKAIIEL 150
                                   33445688999************************9777777766666665558************999987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0038
                       Vps39_1  38 kekkykeLidlYygkklheeALeLlkeladedeedeedsslkgeket.iiqylqklseedldlileyskw 106
                                    e+++k++i+l ++ ++  +A+  l+++ +e+++   +  ++ e++t  i  l+k+ ee+ + i+ ++k 
  gi|70607836|ref|YP_256706.1| 168 TEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTkAIAELRKMTEENTKAIIRLTKI 237
                                   5788999***********************9777777766666665558***************999886 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  37.9    0.0013      0.46      22     256 ..      23     262 ..      11     269 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                                   XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                      Filament  22 aLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke....lnkr 98 
                                   +L ++ keL++  ++ +e         ++ y k+ ee+ k+l  l +   +l+   ++  +++++lrk  e++    +++r
  gi|70607836|ref|YP_256706.1|  23 SLAESLKELHSISQDFRE--------QQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENtkaiIELR 95 
                                   444444444444444444........4455555555555555555555555555555555555555555555444443444 PP

                                   XXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX..XXXXXXXXXXXXXXXXXXX CS
                      Filament  99 eevE...aelkalrkdldeatlarvdLekkvesLkeelaflkkvheeE...vkelqkqvs..eqvlvevdaarkldLteil 171
                                   +++E   +++++lrk  +e t a ++L k+ e+ ++ +a l+k+ ee    + el+kq +  ++++ e+ +  + + t+++
  gi|70607836|ref|YP_256706.1|  96 KQTEentKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENtkaIIELRKQTEenTKAIAELRK-MTEENTKAI 175
                                   4444111468999*******************************999733355899999876677777774.455679999 PP

                                   XXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 172 keiraqyeelaek..nreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele 250
                                    e+r+q ee  +   + +++ e   + + el+++ e+n++a+ + ++  +e  + i +l+  +++l k+ ++l+++++ le
  gi|70607836|ref|YP_256706.1| 176 IELRKQTEENTKAiaELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLE 256
                                   9******987553113334444445667799***********************************************999 PP

                                   HHHHHH CS
                      Filament 251 erleae 256
                                   +++   
  gi|70607836|ref|YP_256706.1| 257 NTFGLM 262
                                   988665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.29     1e+02      12      69 ..      19      76 ..      17      86 .. 0.68
   2 ?    4.6   1.8      0.11        39      20      57 ..      76     113 ..      73     119 .. 0.81
   3 ?    0.2   9.8       2.7   9.3e+02      22      80 ..     106     164 ..     101     192 .. 0.59
   4 ?   11.5   4.7    0.0008      0.28      19      87 ..     187     255 ..     185     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.29
                        DUF948 12 vLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69
                                  +Lv  l+  l++l ++ + ++++ ++  k+ ++i ke+++l + + +l++  +e +++
  gi|70607836|ref|YP_256706.1| 19 FLVKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKA 76
                                  5677777778888888888888888888888888888777776666666655555444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                        DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvn 57 
                                   ++ +l+k+ +e++++i el+kq+++ +k +++l + ++
  gi|70607836|ref|YP_256706.1|  76 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTE 113
                                   6789999999*********9999999988887766555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.7
                        DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                    +l+k+ +e++++i el+kq+++ +k +++l + ++e ++ + e  ++ ++ t+a+a+l
  gi|70607836|ref|YP_256706.1| 106 AELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAEL 164
                                   56666666666666666666666666666665555554444444444444444444444 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.0008
                        DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                   +++ +l+k+ +e++++i el+kq+++ +k +++l + ++e ++ + + ++ vd+l+++v  l e vs l
  gi|70607836|ref|YP_256706.1| 187 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGL 255
                                   567899**********************************99999999999999999999999999877 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  15.1      0.12        42      68     156 ..      41     136 ..      20     138 .. 0.55
   2 ?    2.6  23.2      0.41   1.4e+02      63     157 ..     102     193 ..      85     194 .. 0.72
   3 ?    2.9  22.1      0.32   1.1e+02      69     157 ..     133     221 ..     121     222 .. 0.84
   4 ?    8.6   9.3    0.0059         2      74     159 ..     180     265 ..     177     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.12
                         ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelq.......kleeklkedeerlaeleaeraaletklkd 141
                                   ++++ ++k ++  ++la lre   +l ks +e+++ + el +  +       +l+++++e+++++ael+++ ++ ++++ +
  gi|70607836|ref|YP_256706.1|  41 QQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEentkaiiELRKQTEENTKAIAELRKMTEENTKAIIE 121
                                   345566667777777777777777777777777766655544333000111145666666666666666666666666666 PP

                         ATG16 142 reeelrekeklvqdl 156
                                   ++++ +e +k++ +l
  gi|70607836|ref|YP_256706.1| 122 LRKQTEENTKAIAEL 136
                                   666666666666555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.41
                         ATG16  63 asasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdre 143
                                   ++     ++ ++ +++ ++++++lr++ +e  k+ +el ++  e ++++ +l+++++e+++++ael+++ ++ ++++ +++
  gi|70607836|ref|YP_256706.1| 102 TK---AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELR 179
                                   11...1334555667777888888888888888888888888888888888888888888888888888888888888888 PP

                         ATG16 144 eelrekeklvqdlq 157
                                   ++ +e +k++ +l+
  gi|70607836|ref|YP_256706.1| 180 KQTEENTKAIAELR 193
                                   88888888888876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.32
                         ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                    ++ ++ +++ ++++++lr++ +e  k+ +el ++  e ++++ +l+++++e+++++ael+++ ++ ++++ +++++ +e 
  gi|70607836|ref|YP_256706.1| 133 IAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEEN 213
                                   334566778888999999**************************************************************9 PP

                         ATG16 150 eklvqdlq 157
                                   +k++ +l+
  gi|70607836|ref|YP_256706.1| 214 TKAIAELR 221
                                   99999987 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0059
                         ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                   +++++ ++++a+lr+  +e  k+  el ++  e ++++++l++ ++e+++++ +l++ + +l + ++ ++e++ ++e++  
  gi|70607836|ref|YP_256706.1| 180 KQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLENTFG 260
                                   567888999999999999999999999999999999******************************999999999998876 PP

                         ATG16 155 dlqDE 159
                                    + +E
  gi|70607836|ref|YP_256706.1| 261 LMTEE 265
                                   66666 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  47.7    0.0048       1.7     253     480 ..      20     246 ..       4     255 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0048
                        DUF812 253 laeqlrkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaeklqftkeelakkaeteeelkkkreeele 333
                                   l+++l +++++ ++ +++  ++++d +++++e++++ ++   +  g  ++++e+        +k+  +   +++++ + + 
  gi|70607836|ref|YP_256706.1|  20 LVKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGL-REITGNLVKSSEE-------NTKAIAELRKMTEENTKAII 92 
                                   3333333333333333344444444455444442222221.1222222222222.......22556677777888888888 PP

                        DUF812 334 elqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlell.pdaeen...iekLqalveasaq 410
                                   el++q ee  + i+el++  +++++ i ++ +++ee+ +  +el k ++ ++k++  l +++een   i++L ++ e++++
  gi|70607836|ref|YP_256706.1|  93 ELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELrKQTEENtkaIAELRKMTEENTK 173
                                   888888888888888888888888888888888888888888888888888887777767777774445688888888888 PP

                        DUF812 411 rlvelakqWekhRvplieeyrelkesksekekeaerklee....ikklrekmkevaeelrqkeellkqLvaele 480
                                    ++el kq e+  +  i+e+r+  e++++   e +++ ee    i++lr+ ++e ++ + +    + +Lv+ + 
  gi|70607836|ref|YP_256706.1| 174 AIIELRKQTEEN-TKAIAELRKMTEENTKAIIELRKQTEEntkaIAELRKMTEENTKAIIRLTKIVDKLVKSVS 246
                                   888888888876.4567888888888877655555555542111444444444444444444444444444444 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7     0.091        31     126     166 ..      69     109 ..       6     135 .. 0.67
   2 ?    2.2   1.0      0.25        85     134     165 ..     133     164 ..     110     191 .. 0.54
   3 ?    8.9   0.9    0.0023      0.78     127     190 ..     182     245 ..     174     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.091
                                   TS-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT- CS
                          NanE 126 eeekaepDfalvkalseaglkviaeGrintPekakkaieiG 166
                                   ++e++   +a +++++e++ k i+e r +t e+ k + e+ 
  gi|70607836|ref|YP_256706.1|  69 SSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELR 109
                                   33334555666777888888888888888888877777654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                                   HHHHHHHHHTT--EEEES---SHHHHHHHHTT CS
                          NanE 134 falvkalseaglkviaeGrintPekakkaiei 165
                                   +a +++++e++ k i+e r +t e+ k + e+
  gi|70607836|ref|YP_256706.1| 133 IAELRKMTEENTKAIIELRKQTEENTKAIAEL 164
                                   33344444555555555555554444444443 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0023
                                   S-.SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT CS
                          NanE 127 eekaepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfveai 190
                                   +e++   +a +++++e++ k i+e r +t e+ k + e+  ++     ai rl++i++k v+++
  gi|70607836|ref|YP_256706.1| 182 TEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSV 245
                                   444556677799***********************************************99987 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  14.8     0.045        16      63     166 ..      25     131 ..       9     142 .. 0.70
   2 ?    0.5  14.8         1   3.6e+02      67     145 ..     114     194 ..     107     201 .. 0.50
   3 ?    7.7  15.0     0.007       2.4      63     159 ..     152     250 ..     141     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                  HAUS-augmin3  63 qedvellevileeeeesleaLeqelqeLqkekalk...lkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraen 140
                                    e+ ++l++i ++ +e+++++ ++++e  ke a +   + +l k     +++  elrk++ee+++a  +l++  ee+++++
  gi|70607836|ref|YP_256706.1|  25 AESLKELHSISQDFREQQKDYDKKFEEIGKELAGLreiTGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAI 105
                                   266777888888888888888888888888876541114455555666777778888888888888888888888888888 PP

                  HAUS-augmin3 141 aetnavLqqlteeakqlaeyfeeaek 166
                                   ae+++  ++ t++  +l ++ ee+ k
  gi|70607836|ref|YP_256706.1| 106 AELRKMTEENTKAIIELRKQTEENTK 131
                                   88888888888877777777776654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1
                  HAUS-augmin3  67 ellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqa...aslqqelrkleeeekeakkklkeaqeelraenaetn 144
                                   e +++i+e  ++++e+  + + eL+k+ +  +k   +L  q+   +++  elrk++ee+++a  +l++  ee+++++ae++
  gi|70607836|ref|YP_256706.1| 114 ENTKAIIEL-RKQTEENTKAIAELRKMTEENTKAIIELRKQTeenTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELR 193
                                   333333333.55555555555555555555555444444444111444456666666666666666666666666666665 PP

                  HAUS-augmin3 145 a 145
                                   +
  gi|70607836|ref|YP_256706.1| 194 K 194
                                   5 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.007
                  HAUS-augmin3  63 qedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqq...elrkleeeekeakkklkeaqeelraen 140
                                   ++++e  ++ ++e+++ +e+  + + eL+k+ +  +k   +L  ++ ++++   elrk +ee+++a  +l++  ee+++++
  gi|70607836|ref|YP_256706.1| 152 KQTEE-NTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKaiiELRKQTEENTKAIAELRKMTEENTKAI 231
                                   33444.455667779999999999999*9999988877777766665555422288999999999999************* PP

                  HAUS-augmin3 141 aetnavLqqlteeakqlae 159
                                    ++++  ++l+++++ l e
  gi|70607836|ref|YP_256706.1| 232 IRLTKIVDKLVKSVSALNE 250
                                   *************999877 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.7    0.0045       1.5      74     155 ..      73     158 ..      46     169 .. 0.72
   2 ?    6.9   7.4     0.013       4.3      74     155 ..     129     214 ..     125     225 .. 0.76
   3 ?    5.6   3.4     0.031        11      75     146 ..     158     233 ..     154     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0045
                                   HHHHHHHHHHHHHHHHHHHHHHT.TTTTCE.EEEECC..CCCC-HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCHH CS
                          CDPS  74 rrkaarelravrarieraleeag.peperv.rvrrls..eflanpaYrelraeveralaedeelreacdemvrqvlerrlk 150
                                   + ka++elr++ +++++a+ e++ +++e++  +++l    +++++a  elr+++e+  ++  elr+  +e +++++e r +
  gi|70607836|ref|YP_256706.1|  73 NTKAIAELRKMTEENTKAIIELRkQTEENTkAIAELRkmTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQ 153
                                   467777777777777777777774333333123344400456778999*****************************9987 PP

                                   HS--- CS
                          CDPS 151 deeap 155
                                    ee++
  gi|70607836|ref|YP_256706.1| 154 TEENT 158
                                   66533 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHT.TTTTCEE.EEECCCC..CC-HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCHH CS
                          CDPS  74 rrkaarelravrarieraleeag.pepervr.vrrlsef..lanpaYrelraeveralaedeelreacdemvrqvlerrlk 150
                                   + ka++elr++ +++++a+ e++ +++e+++ +++l ++  ++++a  elr+++e+  ++  elr+  +e +++++e r +
  gi|70607836|ref|YP_256706.1| 129 NTKAIAELRKMTEENTKAIIELRkQTEENTKaIAELRKMteENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQ 209
                                   579999999999999999999985444443314445444115678999*****************************9987 PP

                                   HS--- CS
                          CDPS 151 deeap 155
                                    ee++
  gi|70607836|ref|YP_256706.1| 210 TEENT 214
                                   66533 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHHHHHHT.TTTTCEE.EEECCCC..CC-HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH CS
                          CDPS  75 rkaarelravrarieraleeag.pepervr.vrrlsef..lanpaYrelraeveralaedeelreacdemvrqvle 146
                                    ka++elr++ +++++a+ e++ +++e+++ +++l ++  ++++a  elr+++e+  ++  elr+  +e ++++++
  gi|70607836|ref|YP_256706.1| 158 TKAIAELRKMTEENTKAIIELRkQTEENTKaIAELRKMteENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIR 233
                                   5777777777777777777777433333221333333311455677788888888888888888877777777665 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  11.7      0.72   2.5e+02      40      90 ..     134     162 ..      60     258 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.72
                Y_phosphatase3  40 adlakLadlgirtviDLRspeEreaeaplegaryvhlpveeaaeeekeeee 90 
                                   a+l+k+++ + +++i LR+++E+++                      ++ +
  gi|70607836|ref|YP_256706.1| 134 AELRKMTEENTKAIIELRKQTEENT----------------------KAIA 162
                                   2222223333333333333333111......................1111 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  39.3    0.0062       2.1     269     465 ..      24     222 ..      15     227 .. 0.84
   2 ?    6.9  10.6    0.0059         2     305     390 ..     171     257 ..     166     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0062
                        AAA_13 269 rkaaLeah..FddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaK 347
                                   ++++L++   ++++f e+q++ +k+ e++ ++ + l e   +++++++e     ++++el++ +e+ ++++ +l+++ e+ 
  gi|70607836|ref|YP_256706.1|  24 LAESLKELhsISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEE---NTKAIAELRKMTEENTKAIIELRKQTEEN 101
                                   55555543227899*****************999887777777776544...56889999999999999999999999999 PP

                        AAA_13 348 rkepfksvel.esvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekai 425
                                    k +++  ++ e+ ++ i ++ k+ +e  + ia+  +++++ +++  e++k+ e     ++el+++ +e +k++ +l k+ 
  gi|70607836|ref|YP_256706.1| 102 TKAIAELRKMtEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTkaIAELRKMTEENTKAIIELRKQT 182
                                   99999977764677777777888888888888888888888888888888888876544788999999999********** PP

                        AAA_13 426 eklekelkeeeaelkkleeeikeLekqlrdekpaaeeink 465
                                   e+++k+++e  + +++  + i eL+kq+++ ++a++e+ k
  gi|70607836|ref|YP_256706.1| 183 EENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 222
                                   ************************************9976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0059
                        AAA_13 305 klkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel.esvkakiesikklvaeineliakhNek 384
                                   + ka+++  ++ ++  ++++el++ +e+ ++++ +l+++ e+  k +++  ++ e+ ++ i +++k+v+++ +++++ Ne+
  gi|70607836|ref|YP_256706.1| 171 NTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMtEENTKAIIRLTKIVDKLVKSVSALNER 251
                                   556778888888888889999999999999999999999999999999988865778888899999999999999999999 PP

                        AAA_13 385 vanlee 390
                                   v+ le+
  gi|70607836|ref|YP_256706.1| 252 VSGLEN 257
                                   998876 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.3   0.00087       0.3      33     108 ..      24      98 ..      10      99 .. 0.84
   2 ?    3.8   8.9      0.18        61      51     108 ..      97     154 ..      88     155 .. 0.77
   3 ?    1.7  15.1      0.78   2.7e+02      19     107 ..     125     209 ..     124     211 .. 0.66
   4 ?    2.3  11.7       0.5   1.7e+02      36      95 ..     167     225 ..     154     239 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00087
                        DUF148  33 vtdeykefeakvkaqkeevkknvtavisnLssvqekleaIldnkslTrkeqkeaieelkkqypkevstlffirkel 108
                                   +++ +ke+++ +++   e +k +++  +++ +  + l++I+ n   + +e ++ai el+k  ++++++++ +rk+ 
  gi|70607836|ref|YP_256706.1|  24 LAESLKELHS-ISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQT 98 
                                   6666666654.5666677788999999*******************************************999985 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.18
                        DUF148  51 vkknvtavisnLs.svqekleaIldnkslTrkeqkeaieelkkqypkevstlffirkel 108
                                     ++ t++i++L    +e+ +aI++ +++T+ e ++ai el+k  ++++++++ +rk+ 
  gi|70607836|ref|YP_256706.1|  97 QTEENTKAIAELRkMTEENTKAIIELRKQTE-ENTKAIAELRKMTEENTKAIIELRKQT 154
                                   4455567788887467788999999999996.66789******9999999999999885 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.78
                        DUF148  19 eieeqleawaekygvtdeykefeakvkaqkeevkknvtavisnLs.svqekleaIldnkslTrkeqkeaieelkkqypkev 98 
                                   ++ee+++a ae   + ++ +e ++ + + +++ ++n+ ++i++L    +e+ +aI++ +++T+ e ++ai el+k  ++++
  gi|70607836|ref|YP_256706.1| 125 QTEENTKAIAE---LRKMTEENTKAIIELRKQTEENT-KAIAELRkMTEENTKAIIELRKQTE-ENTKAIAELRKMTEENT 200
                                   56666666666...44444455555555555555554.5566666367778888998888885.56778999999999999 PP

                        DUF148  99 stlffirke 107
                                   ++++ +rk+
  gi|70607836|ref|YP_256706.1| 201 KAIIELRKQ 209
                                   999888887 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.5
                        DUF148  36 eykefeakvkaqkeevkknvtavisnLs.svqekleaIldnkslTrkeqkeaieelkkqyp 95 
                                   + +e ++ + + +++ ++n t++i++L    +e+ +aI++ +++T+ e ++ai el+k  +
  gi|70607836|ref|YP_256706.1| 167 MTEENTKAIIELRKQTEEN-TKAIAELRkMTEENTKAIIELRKQTE-ENTKAIAELRKMTE 225
                                   2222222222222222222.33333333234444445555555543.33445555555555 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3      0.24        82      44      61 ..      70      87 ..      65      95 .. 0.91
   2 ?    5.0   0.4     0.094        32      41      61 ..      95     115 ..      88     119 .. 0.88
   3 ?    5.0   0.6     0.093        32      41      61 ..     123     143 ..     116     152 .. 0.87
   4 ?    5.0   0.5     0.098        34      41      61 ..     151     171 ..     145     179 .. 0.89
   5 ?    5.0   0.6     0.095        33      41      61 ..     179     199 ..     172     208 .. 0.87
   6 ?    4.9   0.5       0.1        36      41      61 ..     207     227 ..     200     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.24
                          CcdA 44 keenreaieelNrfveeh 61
                                   een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1| 70 SEENTKAIAELRKMTEEN 87
                                  69**************98 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.094
                          CcdA  41 erwkeenreaieelNrfveeh 61 
                                   ++  een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1|  95 RKQTEENTKAIAELRKMTEEN 115
                                   56689**************98 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.093
                          CcdA  41 erwkeenreaieelNrfveeh 61 
                                   ++  een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1| 123 RKQTEENTKAIAELRKMTEEN 143
                                   56689**************98 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.098
                          CcdA  41 erwkeenreaieelNrfveeh 61 
                                   ++  een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1| 151 RKQTEENTKAIAELRKMTEEN 171
                                   56789**************98 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.095
                          CcdA  41 erwkeenreaieelNrfveeh 61 
                                   ++  een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1| 179 RKQTEENTKAIAELRKMTEEN 199
                                   56689**************98 PP

  == domain 6  score: 4.9 bits;  conditional E-value: 0.1
                          CcdA  41 erwkeenreaieelNrfveeh 61 
                                   ++  een +ai+el +++ee+
  gi|70607836|ref|YP_256706.1| 207 RKQTEENTKAIAELRKMTEEN 227
                                   56689**************98 PP

>> Pox_Rap94  RNA polymerase-associated transcription specificity factor, Rap94
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  11.7   0.00062      0.21     562     700 ..      10     158 ..       6     161 .. 0.75
   2 ?    2.4   8.7     0.092        32     625     698 ..     167     240 ..     155     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                     Pox_Rap94 562 silpeelkahy.nrilaelekLlsikrskk..eknydvesk...ievlpleev..kffdsrtiivkalvpl..akevatke 632
                                   +i+ eel++++ + +   l+ L si+++ +  +k+yd + +    e + l+e+  ++ +s++  +ka++ l  ++e +tk 
  gi|70607836|ref|YP_256706.1|  10 EIVREELETFLvKSLAESLKELHSISQDFReqQKDYDKKFEeigKELAGLREItgNLVKSSEENTKAIAELrkMTEENTKA 90 
                                   6999***99872557778999****99866115666654431113445566663335666666777775554355566677 PP

                     Pox_Rap94 633 vvkpaetaeeteeakkefkeltdedlkvlirvndtnateleifitylkieiekkkiiielkklfvrnv 700
                                   +++  +++ee+ +a +e++++t+e++k +i++     ++++   +  k+  e+ k iiel+k  ++n+
  gi|70607836|ref|YP_256706.1|  91 IIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENT 158
                                   888888888888899999******************************************99877765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.092
                     Pox_Rap94 625 akevatkevvkpaetaeeteeakkefkeltdedlkvlirvndtnateleifitylkieiekkkiiielkklfvr 698
                                   ++e +tk +++  +++ee+ +a +e++++t+e++k +i++     ++++   +  k+  e+ k ii l+k++ +
  gi|70607836|ref|YP_256706.1| 167 MTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDK 240
                                   345566777777888888888999999*****************************************999765 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.3       3.1   1.1e+03      20      53 ..      79     112 ..      74     144 .. 0.54
   2 ?   -0.1   0.4       2.4   8.2e+02      18      53 ..     133     168 ..     130     190 .. 0.63
   3 ?   -0.4   0.6       2.9     1e+03      17      52 ..     160     195 ..     147     212 .. 0.70
   4 ?   -0.2   0.2       2.6   8.9e+02      17      52 ..     188     223 ..     186     236 .. 0.65
   5 ?    8.8   0.0     0.004       1.4      33      61 ..     261     287 ..     241     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.1
                                   HHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEE CS
                          TusA  20 alekleegevlevladdpaatediprfakklghe 53 
                                   +l+k+ e+++  ++   ++++e+ ++ a+ ++++
  gi|70607836|ref|YP_256706.1|  79 ELRKMTEENTKAIIELRKQTEENTKAIAELRKMT 112
                                   5555555555555544444544444444444333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
                                   HHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEE CS
                          TusA  18 kkalekleegevlevladdpaatediprfakklghe 53 
                                     +l+k+ e+++  ++   ++++e+ ++ a+ ++++
  gi|70607836|ref|YP_256706.1| 133 IAELRKMTEENTKAIIELRKQTEENTKAIAELRKMT 168
                                   567777777766666666666666666555555544 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.9
                                   HHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTE CS
                          TusA  17 lkkalekleegevlevladdpaatediprfakklgh 52 
                                   +  +l+k+ e+++  ++   ++++e+ ++ a+ +++
  gi|70607836|ref|YP_256706.1| 160 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKM 195
                                   556777777777777766666666666666655554 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.6
                                   HHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTE CS
                          TusA  17 lkkalekleegevlevladdpaatediprfakklgh 52 
                                   +  +l+k+ e+++  ++   ++++e+ ++ a+ +++
  gi|70607836|ref|YP_256706.1| 188 AIAELRKMTEENTKAIIELRKQTEENTKAIAELRKM 223
                                   566788887777777776666666666666665554 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.004
                                   EESSCHHHHHHHHHHHHHTEEEEEEE-GC CS
                          TusA  33 laddpaatediprfakklghelveveeed 61 
                                   l++ +   +d+p+++k++g ++ +v  ++
  gi|70607836|ref|YP_256706.1| 261 LMTEEIIRRDFPAWLKNQGIDVSKV--SG 287
                                   56778889*************9998..54 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0014      0.49      34     105 ..      20      94 ..       7      96 .. 0.91
   2 ?   -0.7   0.1       3.7   1.3e+03      48      87 ..     227     265 ..     171     270 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                   HHHHHHHHHHTTSSHHHHHC...T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         T2SSF  34 elkriarrlraGgslseale...rtpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaallep 105
                                    +k++a+ l++ +s+s+ ++   +  +++f e    l  + e +gnL +  e   + + e r+++ ++ +a++e 
  gi|70607836|ref|YP_256706.1|  20 LVKSLAESLKELHSISQDFReqqKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIEL 94 
                                   5899****************87755559***************************************99999985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.7
                                   HHHHHCT-TT.TS.-HHHHHHHHHHHHHT-HHHHHHHHHHH CS
                         T2SSF  48 lsealertpssef.pelvvqlirageeggnLaevLerlaey 87 
                                     +a+ r +  ++ ++lv +++++ e+ + L+ ++  + e+
  gi|70607836|ref|YP_256706.1| 227 NTKAIIRLT--KIvDKLVKSVSALNERVSGLENTFGLMTEE 265
                                   334444444..333666666666666666666666666555 PP

>> YccJ  YccJ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5      0.11        37       4      34 ..      75     105 ..      72     107 .. 0.86
   2 ?    4.6   0.6      0.12        42       4      34 ..     103     133 ..     100     135 .. 0.86
   3 ?    4.8   0.5      0.11        37       4      34 ..     131     161 ..     128     164 .. 0.86
   4 ?    4.5   0.7      0.13        44       4      34 ..     159     189 ..     156     191 .. 0.86
   5 ?    4.9   0.5     0.098        34       4      34 ..     187     217 ..     184     222 .. 0.87
   6 ?    0.1   0.0       3.1   1.1e+03       4      30 ..     215     241 ..     212     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                          YccJ   4 aeWasvRetsleiaeaifelandDeklaeki 34 
                                   ++ a++R+   e  +ai el ++ e+  + i
  gi|70607836|ref|YP_256706.1|  75 KAIAELRKMTEENTKAIIELRKQTEENTKAI 105
                                   6789*****************9999877766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.12
                          YccJ   4 aeWasvRetsleiaeaifelandDeklaeki 34 
                                   ++ a++R+   e  +ai el ++ e+  + i
  gi|70607836|ref|YP_256706.1| 103 KAIAELRKMTEENTKAIIELRKQTEENTKAI 133
                                   6789*****************9999877766 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.11
                          YccJ   4 aeWasvRetsleiaeaifelandDeklaeki 34 
                                   ++ a++R+   e  +ai el ++ e+  + i
  gi|70607836|ref|YP_256706.1| 131 KAIAELRKMTEENTKAIIELRKQTEENTKAI 161
                                   6789*****************9999887766 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.13
                          YccJ   4 aeWasvRetsleiaeaifelandDeklaeki 34 
                                   ++ a++R+   e  +ai el ++ e+  + i
  gi|70607836|ref|YP_256706.1| 159 KAIAELRKMTEENTKAIIELRKQTEENTKAI 189
                                   6789*****************9999877766 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.098
                          YccJ   4 aeWasvRetsleiaeaifelandDeklaeki 34 
                                   ++ a++R+   e  +ai el ++ e+  + i
  gi|70607836|ref|YP_256706.1| 187 KAIAELRKMTEENTKAIIELRKQTEENTKAI 217
                                   6789*****************9999887776 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 3.1
                          YccJ   4 aeWasvRetsleiaeaifelandDekl 30 
                                   ++ a++R+   e  +ai  l++  +kl
  gi|70607836|ref|YP_256706.1| 215 KAIAELRKMTEENTKAIIRLTKIVDKL 241
                                   677999999999999999988766555 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.3     0.079        27     117     169 ..      36      88 ..       5      91 .. 0.69
   2 ?    2.8  16.1      0.27        92      85     167 ..      81     170 ..      60     175 .. 0.57
   3 ?    2.4  15.8      0.35   1.2e+02      85     166 ..     109     190 ..      90     199 .. 0.49
   4 ?    5.6   9.6     0.037        13      88     155 ..     182     249 ..     167     265 .. 0.48

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 117 eegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                   +   e+ ++  ++++ei ++ a + ++  ++ ++see +++i e  +  ee++
  gi|70607836|ref|YP_256706.1|  36 QDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENT 88 
                                   233344555678899999999999999999999****9999999988888776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHH..............HHHHHHHHHHHHHH.......HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  85 aqaakeiealiieiqkeindsvesleetrqrveegselv.......eetgealkeiveavaevadlvqeiaaaseeqsasi 158
                                    + ++e +++iie+ k++++ ++++ e r+ +ee ++ +       ee ++a++e+ ++++e ++ + e+ + +ee +++i
  gi|70607836|ref|YP_256706.1|  81 RKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIielrkqtEENTKAIAELRKMTEENTKAIIELRKQTEENTKAI 161
                                   334455555556677777666666666666666655544111100044444444445566666666666777777766666 PP

                                   HHHHHHHHH CS
                     MCPsignal 159 eevnqavee 167
                                    e  +  ee
  gi|70607836|ref|YP_256706.1| 162 AELRKMTEE 170
                                   666665555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  85 aqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqav 165
                                    + ++e +++iie+ k++++ ++++ e r+ +ee ++ + e +++ +e ++a+ae+ ++ +e ++a  e+ +  ee ++a+
  gi|70607836|ref|YP_256706.1| 109 RKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAI 189
                                   333444455555666666666666666666666555555444444444444444444444444444444444444433333 PP

                                   H CS
                     MCPsignal 166 e 166
                                   +
  gi|70607836|ref|YP_256706.1| 190 A 190
                                   3 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.037
                                   HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                   ++e +++i+e+ k +++ ++++ e r+++ee ++ ++e ++  +e ++a+ +++++v+ + ++++ + 
  gi|70607836|ref|YP_256706.1| 182 TEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALN 249
                                   33444444444444444455554455555444444444444444444444444444444444443333 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  30.6     0.036        12      12     177 ..      31     208 ..      28     209 .. 0.68
   2 ?    3.5   6.2      0.25        88      40     100 ..     203     263 ..     175     338 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                          Fez1  12 islLKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekl 92 
                                   +  + q  ++ q++  +k +ei +  a lre++ +l ++ ee++++ ++l++ t+e+ +   el+++++e++    +++k+
  gi|70607836|ref|YP_256706.1|  31 LHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKM 111
                                   55677999****************************999999999999999999999999999988866666555555555 PP

                          Fez1  93 eeelkelreelselsleeeeaa............lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqE 161
                                    ee ++   el+++++e+++a+            +  +  k+ ++++++++el++ +e+  +++ e r+++ee++++ ++ 
  gi|70607836|ref|YP_256706.1| 112 TEENTKAIIELRKQTEENTKAIaelrkmteentkAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAEL 192
                                   555555544455544444444423334444333222222223333467778888888888888888888888888888877 PP

                          Fez1 162 RrtWqeeKekVirYqk 177
                                   R++ +e+   +i+ +k
  gi|70607836|ref|YP_256706.1| 193 RKMTEENTKAIIELRK 208
                                   7776666666666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.25
                          Fez1  40 lrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelr 100
                                   + elr++ ee+ ++i el++ +ee t+ + ++ + +++  ++++ l+e+v+ le+ +  + 
  gi|70607836|ref|YP_256706.1| 203 IIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKLVKSVSALNERVSGLENTFGLMT 263
                                   3355566666666666666666666666666666666666666666666666666555554 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   8.1     0.054        19     174     300 ..      43     162 ..       8     171 .. 0.53
   2 ?    5.0  12.2     0.018       6.3     130     261 ..     110     243 ..      99     277 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.054
                SpecificRecomb 174 eeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrkhleenGvsvslvfllerlrqrleRlee 254
                                   +++++ F ++ +el+ l+e   +  +++ee++++ ++lr + ++  +a+ ++rk++een   +    +l++++++    ++
  gi|70607836|ref|YP_256706.1|  43 KDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAI---AELRKMTEE--NTKA 118
                                   445555555555555555555555555555555555555555555555555555555554333...244444443..2344 PP

                SpecificRecomb 255 LldllleeeeeeraralveLlkelveaeaekrsvrellrenielLa 300
                                   +++l +  + ee+ +a++eL k   e++++  ++r+  +en++ +a
  gi|70607836|ref|YP_256706.1| 119 IIELRK--QTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIA 162
                                   555553..44455555555555555555555555555555555555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                SpecificRecomb 130 eeeeeeeeaaeklreellealevls.vqiaalglepelrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlk 209
                                   +++ee+++a  +lr++  e  + ++  +   ++ +++++++ +++ee++++  +l++ +e+ ++a+ +  +++ee++++ +
  gi|70607836|ref|YP_256706.1| 110 KMTEENTKAIIELRKQTEENTKAIAeLRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIA 190
                                   334444444444444444444443313445567778888888888888888888888888888888888888888888888 PP

                SpecificRecomb 210 hlrvlldqcreavdrvrkhleenGvsv.slvfllerlrqrleRleeLldllle 261
                                   +lr + ++  +a+ ++rk++een   + +l  + e  ++ + Rl++++d l++
  gi|70607836|ref|YP_256706.1| 191 ELRKMTEENTKAIIELRKQTEENTKAIaELRKMTEENTKAIIRLTKIVDKLVK 243
                                   88888888888888888888888777634666667777778888888877762 PP

>> Corona_S2  Coronavirus S2 glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.051        18     249     301 ..      82     134 ..      62     139 .. 0.85
   2 ?    3.4   0.4     0.064        22     249     301 ..     110     162 ..      98     165 .. 0.87
   3 ?    3.2   0.9     0.073        25     249     301 ..     138     190 ..     128     210 .. 0.87
   4 ?    1.7   0.1       0.2        71     255     300 ..     214     262 ..     207     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.051
                                   HHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSHHTTSSH CS
                     Corona_S2 249 klaasfnkaigniseglatvatalakiqdvvnkqgqalnelvaqlsknfgais 301
                                   k++++  kai ++++  +  ++a+a+++ + +++++a+ el +q ++n +ai+
  gi|70607836|ref|YP_256706.1|  82 KMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIA 134
                                   55566779999999999999999999999999999999999999999999996 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.064
                                   HHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSHHTTSSH CS
                     Corona_S2 249 klaasfnkaigniseglatvatalakiqdvvnkqgqalnelvaqlsknfgais 301
                                   k++++  kai ++++  +  ++a+a+++ + +++++a+ el +q ++n +ai+
  gi|70607836|ref|YP_256706.1| 110 KMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIA 162
                                   556677899999999999999***************************99996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSHHTTSSH CS
                     Corona_S2 249 klaasfnkaigniseglatvatalakiqdvvnkqgqalnelvaqlsknfgais 301
                                   k++++  kai ++++  +  ++a+a+++ + +++++a+ el +q ++n +ai+
  gi|70607836|ref|YP_256706.1| 138 KMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIA 190
                                   56667789999999999999999999999999999999999999999999997 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHSH...HHHHHHHHHHHHHHHHHHHHHHSHHTTSS CS
                     Corona_S2 255 nkaigniseglatvata...lakiqdvvnkqgqalnelvaqlsknfgai 300
                                    kai+++++  +  ++a   l+ki d + k   alne v+ l++ fg +
  gi|70607836|ref|YP_256706.1| 214 TKAIAELRKMTEENTKAiirLTKIVDKLVKSVSALNERVSGLENTFGLM 262
                                   5777777665555555522266677777778889999999999999866 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   3.3      0.37   1.3e+02      90     125 ..      39      74 ..      13      89 .. 0.44
   2 ?    2.0  22.3      0.43   1.5e+02      51     134 ..      77     160 ..      68     166 .. 0.80
   3 ?    6.0  16.4     0.026       9.1      51     134 ..     161     244 ..     155     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.37
                       DUF4201  90 eselselkkelkekeerlaklrkelykvklerdklr 125
                                   ++++++  k+ +e+ ++la lr+ + ++ +  +   
  gi|70607836|ref|YP_256706.1|  39 REQQKDYDKKFEEIGKELAGLREITGNLVKSSEENT 74 
                                   222222333333333333333333333333333333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.43
                       DUF4201  51 nqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                   +++l+k  ee +k + +l+k+t  + +a+++l++ + ++++   el+k+++e ++ +a+lrk +++  +    lrkq e+ 
  gi|70607836|ref|YP_256706.1|  77 IAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEEN 157
                                   567888888888999999999999999999999999999999999999999999999999999998888888888888876 PP

                       DUF4201 132 kqq 134
                                    + 
  gi|70607836|ref|YP_256706.1| 158 TKA 160
                                   555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.026
                       DUF4201  51 nqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                   +++l+k  ee +k + +l+k+t  + +a+++l++ + ++++   el+k+++e ++ +a+lrk +++  +   +l k  +kl
  gi|70607836|ref|YP_256706.1| 161 IAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLTKIVDKL 241
                                   567888888889999999999999999999999999999999999999999999999999998888888888888877777 PP

                       DUF4201 132 kqq 134
                                    ++
  gi|70607836|ref|YP_256706.1| 242 VKS 244
                                   765 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  23.1     0.021       7.1     289     462 ..      70     252 ..      13     259 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                          ALMT 289 eelrkkfkeelqrvslesakvlrelaesvkkmkklsk.veellkevkvaaeeLqskldskskLlvnsekweaakkkekaee 368
                                   +e + k  +el++++ e+ k++ el +++++ +k      ++ +e  +a+ eL+++ +++ k + +  k +++++k+ +e 
  gi|70607836|ref|YP_256706.1|  70 SEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAeLRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIEL 150
                                   555666667888888888888888888888877776657788888888888888888777765555555444444444443 PP

                          ALMT 369 veekkeeekeseskkeea.....eaveeaeseseksllkeskrslklskkesapaeeslee...kqlskeeelkelelaea 441
                                    ++++e++k   + ++ +     + +e +++++e+++  ++ r+++ ++ +++ + ++++e   k+ ++  +++e +   +
  gi|70607836|ref|YP_256706.1| 151 RKQTEENTKAIAELRKMTeentkAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEentKAIAELRKMTEENTKAI 231
                                   333333333332222222333332333333333333333444444444444433333222212244445555666666777 PP

                          ALMT 442 lslatfaslLielvarldkiv 462
                                   + l  ++  L+  v  l++ v
  gi|70607836|ref|YP_256706.1| 232 IRLTKIVDKLVKSVSALNERV 252
                                   777777777777777766655 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1  41.7      0.57     2e+02     471     641 ..      68     237 ..       4     266 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.57
                          HOOK 471 kqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed....ssllkkkleehleklk 547
                                   k  +++++ ++el ++ e++ + + eL+++   +++ i eL++  ee +ka  e   ++e+     ++l+k  ee  + + 
  gi|70607836|ref|YP_256706.1|  68 KSSEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEEntkaIAELRKMTEENTKAII 148
                                   222333444444444555555555555555555555555555544444444333333333312212234444444555555 PP

                          HOOK 548 evqeelqkkkeqleelepklssnkqkieeleeaLkkkdedlkameerYkkyveKAksViktLdpkqnpaspaevqalknql 628
                                   e+ +++++ ++ + el + +++n++ i el+   k+ +e+ ka+ e  k+  e  k +i  L  ++ ++ ++ +  l++  
  gi|70607836|ref|YP_256706.1| 149 ELRKQTEENTKAIAELRKMTEENTKAIIELR---KQTEENTKAIAELRKMTEENTKAIIE-LRKQT-EENTKAIAELRKMT 224
                                   5555555555555555555555555555554...34555555555555555555555553.33222.22235555666666 PP

                          HOOK 629 aekdkkieslere 641
                                   +e+ k i +l++ 
  gi|70607836|ref|YP_256706.1| 225 EENTKAIIRLTKI 237
                                   6666665555544 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  16.6     0.012       4.3       5     113 ..      23     131 ..      12     139 .. 0.61
   2 ?    2.2  12.6      0.49   1.7e+02      52     111 ..     126     185 ..     120     190 .. 0.72
   3 ?    4.3   9.5      0.11        38      52     105 ..     182     235 ..     176     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                    TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                   sl e +k+l + +++ +++++ + ++ e+  ++++   +   + +   +e++k++++lr+  +e ++ i el+++ e+ ++
  gi|70607836|ref|YP_256706.1|  23 SLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEENTK 103
                                   555555666666666666666666666666666655555444444456667778888888888888888888877777777 PP

                    TPR_MLP1_2  86 eleeseesweeqkeelekelselekrie 113
                                   +++e ++  ee  +++ +  +++e+  +
  gi|70607836|ref|YP_256706.1| 104 AIAELRKMTEENTKAIIELRKQTEENTK 131
                                   7777777777777754444444444333 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.49
                    TPR_MLP1_2  52 haedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekr 111
                                    +e++k++++lr+  +e ++ i el+++ e+ +++++e ++  ee  +++ +  +++e+ 
  gi|70607836|ref|YP_256706.1| 126 TEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEEN 185
                                   456778888888888888888888888888888888888888888777766666665554 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.11
                    TPR_MLP1_2  52 haedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekel 105
                                    +e++k++++lr+  +e ++ i el+++ e+ +++++e ++  ee  +++ +  
  gi|70607836|ref|YP_256706.1| 182 TEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIRLT 235
                                   567899999999999999999999999999999999999998888887654433 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7     0.063        22      18      74 ..      20      77 ..       9      82 .. 0.73
   2 ?    4.7  13.7     0.055        19       4      78 ..      79     151 ..      76     159 .. 0.89
   3 ?    7.2  11.0    0.0096       3.3       4      76 ..     163     233 ..     160     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.063
                    MscS_porin 18 llqdLeqalnlLdki.dkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskei 74
                                  l+++L ++l+ L  i ++++++ +++ k+ ++  kel+ l++ + +l k++ee++k+i
  gi|70607836|ref|YP_256706.1| 20 LVKSLAESLKELHSIsQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEENTKAI 77
                                  6778888888888764678889999999999999999988888888855555555444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.055
                    MscS_porin   4 elekakldeaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilakl 78 
                                   el k   +e++ ka+++  +q+ ++ ++i++ +k +ee  kai +  k+++e ++ +++l+k +ee++k+i++  
  gi|70607836|ref|YP_256706.1|  79 ELRK--MTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELR 151
                                   4444..4599**************************************************999999999998755 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0096
                    MscS_porin   4 elekakldeaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeila 76 
                                   el k   +e++ ka+++  +q+ ++ ++i++ +k +ee  kai +  k+++e ++ +++l+k +ee++k+i++
  gi|70607836|ref|YP_256706.1| 163 ELRK--MTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIR 233
                                   4444..4599**************************************************9999999988876 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.55   1.9e+02      21      66 ..      28      73 ..      25      79 .. 0.77
   2 ?    4.8   2.6      0.12        42      18      58 ..      74     114 ..      73     128 .. 0.73
   3 ?    0.6   7.6       2.4   8.2e+02      19      58 ..     131     170 ..     111     191 .. 0.64
   4 ?    4.5   2.7      0.14        50      18      58 ..     158     198 ..     156     209 .. 0.76
   5 ?    8.2   4.1      0.01       3.6       6      65 ..     187     247 ..     180     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.55
                       DUF4473 21 adglvkiaekfksefakakgdkeaakkafeklkaevdafiktqsee 66
                                   ++l+ i+++f+++ +   + +e+  k ++ l + + + +k+  e+
  gi|70607836|ref|YP_256706.1| 28 LKELHSISQDFREQQKDYDKKFEEIGKELAGLREITGNLVKSSEEN 73
                                  5689999******999998888888777778888888888886655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
                       DUF4473  18 ekaadglvkiaekfksefakakgdkeaakkafeklkaevda 58 
                                   +ka+++l k++e+  + + +  +++e++ ka+++l + +++
  gi|70607836|ref|YP_256706.1|  74 TKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEE 114
                                   58999999999996666666688888888888866665554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.4
                       DUF4473  19 kaadglvkiaekfksefakakgdkeaakkafeklkaevda 58 
                                   ka+++l k++e+  + + +  +++e++ ka+++l + +++
  gi|70607836|ref|YP_256706.1| 131 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEE 170
                                   6777777777775555555566666666666544443333 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.14
                       DUF4473  18 ekaadglvkiaekfksefakakgdkeaakkafeklkaevda 58 
                                   +ka+++l k++e+  + + +  +++e++ ka+++l + +++
  gi|70607836|ref|YP_256706.1| 158 TKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEE 198
                                   589999*******6666666688888888888877666654 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.01
                       DUF4473   6 eakaeLvaaGlsekaadglvkiaekfksefaka...kgdkeaakkafeklkaevdafiktqse 65 
                                   +a aeL++  ++e+  ++++++ ++ ++++++     + +e++ ka+  l++ vd+ +k++s+
  gi|70607836|ref|YP_256706.1| 187 KAIAELRK--MTEENTKAIIELRKQTEENTKAIaelRKMTEENTKAIIRLTKIVDKLVKSVSA 247
                                   46677777..89999999999999988888877899777777777777************996 PP

>> MCD_N  Malonyl-CoA decarboxylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.3     0.029        10      10      71 ..      75     137 ..      53     142 .. 0.67
   2 ?    5.5   0.7     0.053        18      10      58 ..     117     166 ..     112     168 .. 0.73
   3 ?    3.4   6.7      0.25        87      10      55 ..     159     205 ..     126     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.029
                                   HHHHHHCC--.SH.HHHHHHHHHCSBHHHHHHHHHTTSTTHHHHHHHHHHHHHHHTTT-GCHH CS
                         MCD_N  10 kaieayraakgse.kaeeeLrealeprrqeLlrrlnlapgGvkfLVdmRadllallkkekelr 71 
                                   kai++ r+ ++++ ka+ eLr+ +e +   +    ++ ++ +k+++++R++  + +k+  elr
  gi|70607836|ref|YP_256706.1|  75 KAIAELRKMTEENtKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELR 137
                                   566666664433347777777777777766666666667777777777776555555444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.053
                                   HHHHHHCC--.SH.HHHHHHHHHCSBHHHHHHHHHTTSTTHHHHHHHHHH CS
                         MCD_N  10 kaieayraakgse.kaeeeLrealeprrqeLlrrlnlapgGvkfLVdmRa 58 
                                   kai + r++++++ ka++eLr+ +e +   ++   ++ ++ +k++ ++R+
  gi|70607836|ref|YP_256706.1| 117 KAIIELRKQTEENtKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRK 166
                                   45555555444444899999999999999999988889999998888885 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.25
                                   HHHHHHCC--.SH.HHHHHHHHHCSBHHHHHHHHHTTSTTHHHHHHH CS
                         MCD_N  10 kaieayraakgse.kaeeeLrealeprrqeLlrrlnlapgGvkfLVd 55 
                                   kai++ r+ ++++ ka+ eLr+ +e +   +    ++ ++ +k++++
  gi|70607836|ref|YP_256706.1| 159 KAIAELRKMTEENtKAIIELRKQTEENTKAIAELRKMTEENTKAIIE 205
                                   33444444222222444444444444444443333444444444444 PP

>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.9      0.23        81      46      91 ..      75     120 ..      65     128 .. 0.59
   2 ?    3.2   1.3      0.23        78      46      90 ..     103     147 ..      92     156 .. 0.50
   3 ?    2.9   1.2      0.28        96      67      90 ..     152     175 ..     125     184 .. 0.48
   4 ?    2.6   1.1      0.33   1.1e+02      68      90 ..     181     203 ..     154     211 .. 0.51
   5 ?    2.9   0.9      0.27        93      68      91 ..     209     232 ..     182     241 .. 0.58
   6 ?    2.2   0.1      0.45   1.6e+02      26      64 ..     288     326 ..     262     331 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.23
                                   EEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEEE CS
                          SfsA  46 kcyvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyravv 91 
                                   k+  E++ +t e+ +        te  +k + eL ++ +e+ +a++
  gi|70607836|ref|YP_256706.1|  75 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAII 120
                                   4444444444444333333344566667777777777777777765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                                   EEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEE CS
                          SfsA  46 kcyvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyrav 90 
                                   k+  E++ +t e+ +        te  +k + eL ++ +e+ +a+
  gi|70607836|ref|YP_256706.1| 103 KAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAI 147
                                   333333333333322222233345555566666666666666655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.28
                                   S--HHHHHHHHHHHHHHHTT-EEE CS
                          SfsA  67 apteRgqkhleeLaelvkegyrav 90 
                                     te  +k + eL ++ +e+ +a+
  gi|70607836|ref|YP_256706.1| 152 KQTEENTKAIAELRKMTEENTKAI 175
                                   334445555555555555555555 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.33
                                   --HHHHHHHHHHHHHHHTT-EEE CS
                          SfsA  68 pteRgqkhleeLaelvkegyrav 90 
                                    te  +k + eL ++ +e+ +a+
  gi|70607836|ref|YP_256706.1| 181 QTEENTKAIAELRKMTEENTKAI 203
                                   34555566666666666666655 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.27
                                   --HHHHHHHHHHHHHHHTT-EEEE CS
                          SfsA  68 pteRgqkhleeLaelvkegyravv 91 
                                    te  +k + eL ++ +e+ +a++
  gi|70607836|ref|YP_256706.1| 209 QTEENTKAIAELRKMTEENTKAII 232
                                   455566666677777776666665 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.45
                                   ES-EE..TTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE CS
                          SfsA  26 revky..gnsriDfllekeeeekcyvEVKsvtleeggialf 64 
                                   + +k+  +n  +D+ le + ++ ++ EVK +  e++ + +f
  gi|70607836|ref|YP_256706.1| 288 KTIKFgkKNLEFDVFLEYN-NKVYLGEVKATLRERD-VKRF 326
                                   3457755666778888876.5555559998777665.5555 PP

>> SAPIS-gp6  Pathogenicity island protein gp6 in Staphylococcus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       2.4   8.4e+02      39      63 ..      31      51 ..      12      58 .. 0.57
   2 ?    3.7   3.9      0.24        84       7      44 ..      71     107 ..      67     117 .. 0.73
   3 ?    4.7   0.4      0.12        40       8      29 ..     100     121 ..      95     126 .. 0.92
   4 ?    4.7   0.5      0.12        41       8      29 ..     128     149 ..     122     154 .. 0.92
   5 ?    4.7   0.4      0.12        41       8      29 ..     156     177 ..     151     181 .. 0.93
   6 ?    4.6   0.4      0.13        45       8      29 ..     184     205 ..     179     208 .. 0.93
   7 ?    3.7   0.4      0.23        80       8      29 ..     212     233 ..     207     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.4
                     SAPIS-gp6 39 mqeiskElreneqekkkeyqeslqk 63
                                  +  is++ re    ++k+y+++  +
  gi|70607836|ref|YP_256706.1| 31 LHSISQDFRE----QQKDYDKKFEE 51
                                  4445555555....45555544444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.24
                     SAPIS-gp6   7 lentkKvAkalkLneeDknlLieAvdlDiKnnmqeisk 44 
                                    entk +A+  k+ ee+++++ie   +   +n + i++
  gi|70607836|ref|YP_256706.1|  71 EENTKAIAELRKMTEENTKAIIEL-RKQTEENTKAIAE 107
                                   59********************95.4556677776663 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.12
                     SAPIS-gp6   8 entkKvAkalkLneeDknlLie 29 
                                   entk +A+  k+ ee+++++ie
  gi|70607836|ref|YP_256706.1| 100 ENTKAIAELRKMTEENTKAIIE 121
                                   89******************98 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.12
                     SAPIS-gp6   8 entkKvAkalkLneeDknlLie 29 
                                   entk +A+  k+ ee+++++ie
  gi|70607836|ref|YP_256706.1| 128 ENTKAIAELRKMTEENTKAIIE 149
                                   89******************98 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.12
                     SAPIS-gp6   8 entkKvAkalkLneeDknlLie 29 
                                   entk +A+  k+ ee+++++ie
  gi|70607836|ref|YP_256706.1| 156 ENTKAIAELRKMTEENTKAIIE 177
                                   8*******************98 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.13
                     SAPIS-gp6   8 entkKvAkalkLneeDknlLie 29 
                                   entk +A+  k+ ee+++++ie
  gi|70607836|ref|YP_256706.1| 184 ENTKAIAELRKMTEENTKAIIE 205
                                   8*******************98 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.23
                     SAPIS-gp6   8 entkKvAkalkLneeDknlLie 29 
                                   entk +A+  k+ ee+++++i 
  gi|70607836|ref|YP_256706.1| 212 ENTKAIAELRKMTEENTKAIIR 233
                                   89*****************995 PP

>> DUF2584  Protein of unknown function (DUF2584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.9   3.1e+02      43      71 ..      65      93 ..      61      95 .. 0.84
   2 ?    6.9   0.6      0.02       6.9      40      71 ..      90     121 ..      87     123 .. 0.91
   3 ?    6.8   0.4     0.021       7.4      41      71 ..     119     149 ..     117     151 .. 0.91
   4 ?    6.2   0.6     0.034        12      41      71 ..     147     177 ..     144     178 .. 0.91
   5 ?    6.8   0.7     0.022       7.5      40      71 ..     174     205 ..     171     207 .. 0.91
   6 ?    6.1   1.1     0.035        12      40      71 ..     202     233 ..     199     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.9
                                  EEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584 43 evrktkeseksgtaiiekLewennkTtvt 71
                                  +++k+ e+++ + a+ +k++ en k +++
  gi|70607836|ref|YP_256706.1| 65 NLVKSSEENTKAIAELRKMTEENTKAIIE 93
                                  57888899999999******999999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                                   SEEEEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584  40 vplevrktkeseksgtaiiekLewennkTtvt 71 
                                    ++e+rk+ e+++ + a+ +k++ en k +++
  gi|70607836|ref|YP_256706.1|  90 AIIELRKQTEENTKAIAELRKMTEENTKAIIE 121
                                   579***********************999987 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.021
                                   EEEEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584  41 plevrktkeseksgtaiiekLewennkTtvt 71 
                                   ++e+rk+ e+++ + a+ +k++ en k +++
  gi|70607836|ref|YP_256706.1| 119 IIELRKQTEENTKAIAELRKMTEENTKAIIE 149
                                   79***********************999987 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.034
                                   EEEEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584  41 plevrktkeseksgtaiiekLewennkTtvt 71 
                                   ++e+rk+ e+++ + a+ +k++ en k +++
  gi|70607836|ref|YP_256706.1| 147 IIELRKQTEENTKAIAELRKMTEENTKAIIE 177
                                   79**********************9998885 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.022
                                   SEEEEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584  40 vplevrktkeseksgtaiiekLewennkTtvt 71 
                                    ++e+rk+ e+++ + a+ +k++ en k +++
  gi|70607836|ref|YP_256706.1| 174 AIIELRKQTEENTKAIAELRKMTEENTKAIIE 205
                                   579***********************999987 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.035
                                   SEEEEESS----EEEEEEEEEEEEETTEEEEE CS
                       DUF2584  40 vplevrktkeseksgtaiiekLewennkTtvt 71 
                                    ++e+rk+ e+++ + a+ +k++ en k ++ 
  gi|70607836|ref|YP_256706.1| 202 AIIELRKQTEENTKAIAELRKMTEENTKAIIR 233
                                   579*******************9999998875 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  20.1     0.011       3.8      69     191 ..      21     145 ..      17     147 .. 0.85
   2 ?   -0.8  27.6       2.9   9.9e+02      62     186 ..     122     252 ..     122     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                    Lebercilin  69 vrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerklel 149
                                   v+ l e l+++    ++  ++ k+ +++ +++ ++l  l+++      +  ee +k ++el++  ee+++ i eL+++ e 
  gi|70607836|ref|YP_256706.1|  21 VKSLAESLKELHSISQDFREQQKDYDKKFEEIGKELAGLREIT-GNLVKSSEENTKAIAELRKMTEENTKAIIELRKQTEE 100
                                   678999************************************9.5567889999999************************ PP

                    Lebercilin 150 eeksfr...rqlaaekkktkeaqeevkalqeeierlkqklkeKer 191
                                   ++k+ +   ++ +  +k + e+++++++ ++ i +l++  +e ++
  gi|70607836|ref|YP_256706.1| 101 NTKAIAelrKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTK 145
                                   **9865220445555566678888888888888888888877766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.9
                    Lebercilin  62 larhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaer...eeLqkkLeeleakleekeek 139
                                   l++++eE     ++lRk+ e+++++  +l+++ +e  ++  +l+k+ + + +   + r   ee +k ++el++  ee+++ 
  gi|70607836|ref|YP_256706.1| 122 LRKQTEENTKAIAELRKMTEENTKAIIELRKQTEENTKAIAELRKMTEENTKAIIELRkqtEENTKAIAELRKMTEENTKA 202
                                   57889999999999***********9******99999999999999987766655444111666777************** PP

                    Lebercilin 140 ikeLerkleleeksfr...rqlaaekkktkeaqeevkalqeeierlkqkl 186
                                   i eL+++ e ++k+ +   ++ +  +k +  + + v++l + +  l++++
  gi|70607836|ref|YP_256706.1| 203 IIELRKQTEENTKAIAelrKMTEENTKAIIRLTKIVDKLVKSVSALNERV 252
                                   ************98752203444444555667777788888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2420  (0.134977); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                       193  (0.0107647); expected 17.9 (0.001)
Passed Fwd filter:                       131  (0.0073066); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 2.06u 0.46s 00:00:02.52 Elapsed: 00:00:00.75
# Mc/sec: 1529.71
//
Query:       gi|70607837|ref|YP_256707.1|  [L=356]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-30  105.4  35.8    4.1e-30  104.8  35.8    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8  35.8   2.3e-34   4.1e-30       2     267 ..      38     307 ..      37     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.3e-34
                  BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl......lllallvallvgaavglllgll 76 
                                   i  +  + a ++i+A+G a+++ + G+i+l+  +++ +   +++++ ++  +       + +++l++l+++ ++gl++gl+
  gi|70607837|ref|YP_256707.1|  38 ITTIFQYLAEIGIIAIGEAMLM-LCGEIDLSPPALANFVPLITLTIYNSIYQAisptpaIVVSILLSLGLASLIGLMNGLI 117
                                   5567778899************.****************77777777777777799************************* PP

                  BPD_transp_2  77 vlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGra 157
                                   +++ kv++li+t+++l+++ g++l     +++g+  +    + lg +  +l+  +    ++ l ++++++lll++t++G++
  gi|70607837|ref|YP_256707.1| 118 TTKAKVNSLITTVGTLFLFNGIAL----IYSGGYPESFPYFRFLGGTVSILPVPF----IWSLGALVFLILLLHYTKIGVW 190
                                   ************************....445555555566777777777777776....9********************* PP

                  BPD_transp_2 158 lravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGga......gsllgt 231
                                     a+g+n++ a  +G++v+rvk++ f+i + +++l+G+++  +  +i + n+     +++iaa+v+Gg+      gsl+g+
  gi|70607837|ref|YP_256707.1| 191 TIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGAtNFTADVVLEGIAAAVIGGTslvggkGSLVGA 271
                                   *******************************************9999999******************************* PP

                  BPD_transp_2 232 viGaliigvvksllltllgi.ptelarvllgallilv 267
                                   ++G++ i+ + + + ++lgi + e+  +l ga+++++
  gi|70607837|ref|YP_256707.1| 272 FLGSVFISELLN-GFNILGInAYEFDAILGGAIVVVM 307
                                   ************.888888845666677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.55
# Mc/sec: 1951.28
//
Query:       gi|70607838|ref|YP_256708.1|  [L=402]
Description: hypothetical protein Saci_2122 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-46  157.8   0.1    6.1e-46  157.1   0.1    1.3  1  Peripla_BP_4  Periplasmic binding protein domain
    6.5e-05   22.5   0.0     0.0001   21.8   0.0    1.3  1  Peripla_BP_1  Periplasmic binding proteins and sugar binding 


Domain annotation for each model (and alignments):
>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.1   6.8e-50   6.1e-46       1     254 [.      87     350 ..      87     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 6.8e-50
                                   EEEEES-SSTCHHHHHHHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT- CS
                  Peripla_BP_4   1 igvvvkdksnpffsaaregleeaakelgaevtvvgdaendaaeQvaqiedaiakgvdgiivapvdstalapalkkakaaGI 81 
                                   i+++++ ++npff +++ g+++a+  l ++++++g + +d++++v+ +e+ai++g++gi+v++++++a  +  ++a +aGI
  gi|70607838|ref|YP_256708.1|  87 IVFINHVTTNPFFVPTQYGIQDACLLLDCNYQWTGSETSDTTTMVNDMEAAISQGANGIAVSVISPNAFDKPTQDALNAGI 167
                                   789****************************************************************************** PP

                                   EEEEESTTGCTTT-CEE..........EEEC-HHHHHHHHHHHHHHHCTTH.EEEEEETSCCCHHHHHHHHHHHHHHHHH- CS
                  Peripla_BP_4  82 pVvafdsddapsgerla..........yvgfdneaaGelqaeylaeklggkkgkvvilaGspgdpnaeeriegfrkvlkey 152
                                   pV+a+++  +p+++ ++          y+g+  +a+G+l ++ +++ ++++   v+++ ++pg++n + ri+g+ +v++++
  gi|70607838|ref|YP_256708.1| 168 PVFAYNAY-IPTDDPSYsqyhnppylgYIGQSLYASGQLFGQRILNLVPSG-SRVALFIATPGTANIQPRIDGIQSVIEGH 246
                                   ********.666666666666******************************.****************************8 PP

                                   TTCEECCEEESTTTCHHHHHHHHHHHHHTTT.ECEEEESSCCHHHCHHHHHHHTTT.....TSTEEEEEES-HHHHHHHHH CS
                  Peripla_BP_4 153 pgikivaevaganwdaekaqqalealltanp.ldgilaandgmaegalealeaagl.....agkvvvtgqDatpealeaik 227
                                     i +va    ++   ++ q+a+e+++  +p ++g++a+++g ++g+ + l++ g+      g ++  g+D+ p++++ i 
  gi|70607838|ref|YP_256708.1| 247 YTIDVVA----TGALVSDEQSAIESYFNSHPdVKGMFAVDAGSTQGVGNVLREHGIktvsnGGTIAAGGYDLLPATIQNIV 323
                                   8999999....49***************9955************************6666333344*************** PP

                                   TTSSEEEEE--HHHHHHHHHHHHHHHH CS
                  Peripla_BP_4 228 dGtidatvaqdpyelgyaavelavall 254
                                   dG +d+t+ q+py +g   + +++ +l
  gi|70607838|ref|YP_256708.1| 324 DGYLDFTIDQQPYLQGFLPTLAIYLYL 350
                                   ****************99988888765 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.2e-08    0.0001       1     224 [.      84     315 ..      84     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.2e-08
                                   -EEEEEEES-TTSHHHHHHHHHHHHHHHHHTEEEEEEE-SSHHHHH..HHHHHHHHTT-SEEEEE-S-GG.HHHHHHHHHH CS
                  Peripla_BP_1   1 tlklglvlpqldePffldlvkgitkaakehgvdvlllaageeedla..kaidllkakgidgliiatsdts.fdditakaes 78 
                                   t+k+ ++    ++Pff+   +gi+ a   ++ +      +  + +   + ++   ++g++g+ +    ++ fd+ t+ a  
  gi|70607838|ref|YP_256708.1|  84 TWKIVFINHVTTNPFFVPTQYGIQDACLLLDCNYQWTGSETSDTTTmvNDMEAAISQGANGIAVSVISPNaFDKPTQDALN 164
                                   699***********************9999998877655555555577**************9997766669999999999 PP

                                   .T-EEEEESS--B-TTTS-EEEE-HHHHHH.HHHHHHHHHHHHHT..G..........EEEEEE-TTSHHHHHHHHHHHHH CS
                  Peripla_BP_1  79 .gipvialedaidapdgvPcvipddtqage.estqkLiaeghkrp..i..........allegpesaltakervqGflaal 145
                                    gipv a +  i  p + P++    +  +    +q L+a g+  +  i          al+ ++      + r +G    +
  gi|70607838|ref|YP_256708.1| 165 aGIPVFAYNAYI--PTDDPSYSQYHNPPYLgYIGQSLYASGQLFGqrIlnlvpsgsrvALFIATPGTANIQPRIDGIQSVI 243
                                   99***9998875..545788888876666668999999999977777556667777779999999999999********** PP

                                   HHTT-GGGEEEEE-SSSSHHHHHHHHHHHHTT-TT-SEEE-SSHHHHHHHHHHHHHTT.--GGGEEEEEESSGGGHHHH CS
                  Peripla_BP_1 146 aeaGlevkdvhvalgsndiedaaealnelleshPeidaivaindeaalGavlalkkeGrlkikeevdsfiesvvvydgL 224
                                   +++     ++ va+g   + d ++a+++ ++shP+++ + a  + +  G   +l+ +G +k+ ++++    +  +yd L
  gi|70607838|ref|YP_256708.1| 244 EGH---YTIDVVATGA-LVSDEQSAIESYFNSHPDVKGMFAVDAGSTQGVGNVLREHG-IKTVSNGG--TIAAGGYDLL 315
                                   ***...5888888886.688999**************99999999999999*******.88888874..4455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2887.75
//
Query:       gi|70607839|ref|YP_256709.1|  [L=861]
Description: ABC transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-46  157.9  10.2      6e-46  157.3  10.2    1.3  1  ABC_membrane    ABC transporter transmembrane region
    1.7e-34  119.3   0.0    3.6e-34  118.2   0.0    1.6  1  ABC_tran        ABC transporter
    5.6e-30  103.8   0.4    2.9e-29  101.5   0.1    2.3  2  DUF1854         Domain of unknown function (DUF1854)
      7e-06   25.6   0.8     0.0023   17.4   0.0    2.5  2  SMC_N           RecF/RecN/SMC N terminal domain
    1.9e-05   24.0   3.9    1.9e-05   24.0   3.9    2.3  2  ABC_membrane_3  ABC transporter transmembrane region
    6.6e-05   22.9   0.7       0.35   10.6   0.0    2.8  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0022   18.2   0.5      0.066   13.5   0.2    3.3  3  AAA_22          AAA domain
     0.0025   18.0   0.1      0.012   15.8   0.1    2.2  1  DUF87           Helicase HerA, central domain
     0.0038   16.9   0.1     0.0097   15.6   0.1    1.6  1  AAA_29          P-loop containing region of AAA domain
     0.0053   16.5   3.0      0.018   14.8   2.0    2.3  1  AAA_15          AAA ATPase domain
     0.0067   16.9   0.5          1    9.8   0.1    3.2  2  AAA             ATPase family associated with various cellula
  ------ inclusion threshold ------
      0.012   14.6   1.2       0.55    9.1   0.1    2.8  3  AAA_10          AAA-like domain
      0.027   14.9   0.3       0.77   10.2   0.0    2.6  2  RNA_helicase    RNA helicase
      0.029   14.1   2.4      0.044   13.5   0.9    2.2  2  AAA_24          AAA domain
      0.029   14.7   0.0       0.38   11.1   0.0    2.4  2  AAA_16          AAA ATPase domain
      0.031   14.8   0.0      0.091   13.3   0.0    1.9  1  AAA_18          AAA domain
      0.062   13.4   0.1       0.19   11.8   0.1    1.9  1  MMR_HSR1        50S ribosome-binding GTPase
      0.064   13.1   0.1       0.39   10.6   0.0    2.3  2  RsgA_GTPase     RsgA GTPase
       0.11   12.5   0.0       0.66   10.0   0.0    2.4  2  AAA_5           AAA domain (dynein-related subfamily)
       0.12   12.6   0.1       0.83    9.9   0.1    2.4  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.25   11.6   1.6        1.9    8.8   0.9    2.4  2  VirB3           Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3  10.2     7e-49     6e-46       1     273 [.     134     406 ..     134     407 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 7e-49
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklf 81 
                                   +il+  l++++++l+++ p++l+ ++d++l +++++ +   ++ lll+  +   ++++ lq+++ln++g+r++++lr +l+
  gi|70607839|ref|YP_256709.1| 134 MILGATLSLISTGLNLVPPYLLKILIDNVLISNNHSAQLFQLIVLLLITSYTSLALVSSLQTRILNNLGSRIINDLREMLY 214
                                   688999*************************88888867777777777778889999************************ PP

                                   HHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHH CS
                  ABC_membrane  82 kkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsavia 162
                                   +++++ + sf+++ s++++lsrlt+d+ + +++l + l +++++++t++g+ +++f+l++ l+  +l+ +pli+++ + + 
  gi|70607839|ref|YP_256709.1| 215 NHVIKHDYSFIERISPSRILSRLTTDAGNTNWLLVWGLPTLVTNFFTLLGIGVILFTLNPLLATFILIPIPLILFMVVRYR 295
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  ABC_membrane 163 kilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalal 243
                                   k++++l  +++ + a+++s +++++ ++ +V++f +eey+ ++  + l++ ++++++ +++n+l ++++ l+++ls++++ 
  gi|70607839|ref|YP_256709.1| 296 KKSHRLYHRNWRRSADITSRINDTIPNFLVVRSFSKEEYESKRLRNMLDKLYESSVTINRLNSLYWPVIGLVVNLSTVIIW 376
                                   ********************************************************************************* PP

                                   HHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                  ABC_membrane 244 wfGttlvisgelsvgdlvvflslfailfga 273
                                   w+G++ visg + +g +++f+++++++  +
  gi|70607839|ref|YP_256709.1| 377 WVGGHEVISGVIELGVITAFIAYLSQFYSP 406
                                   **************************9877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   0.0   4.2e-37   3.6e-34       1     137 []     468     617 ..     468     617 .. 0.87

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 4.2e-37
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   +kn+++++++gekvaivG++G+GKSt++kll++ ++ ++G+i++ g dlke+++  lr++++++pq+  lf+++ v+ n  
  gi|70607839|ref|YP_256709.1| 468 VKNLNINIRPGEKVAIVGKSGSGKSTIAKLLLRFYDVNKGKITIGGVDLKEIDIDYLRRKVAYVPQDVVLFDTT-VGYNva 547
                                   589********************************************************************999.99999* PP

                                   ..............HHHTCHHHHH.HHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ..............xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..............esdeeiekal.sklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  +    +k++ + ++l+   dt+++++++ LSgGq+qr+++ara++k+p++l++DE+t+
  gi|70607839|ref|YP_256709.1| 548 ygsdnvnevdivraCK---TAKIHdEIVRLPFAYDTILGERGTYLSGGQRQRLSIARAIIKNPDVLIFDEATS 617
                                   9988855555532222...333320334555588*************************************96 PP

>> DUF1854  Domain of unknown function (DUF1854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   1.7e+03     104     126 ..     694     716 ..     666     717 .. 0.83
   2 !  101.5   0.1   3.4e-32   2.9e-29       1     128 [.     734     858 ..     734     860 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                       DUF1854 104 tDsdgnryeipdvkaLDkkSrkl 126
                                    ++dgn  ei d++ L+++S k+
  gi|70607839|ref|YP_256709.1| 694 FSKDGNGKEIHDIRILNPRSTKI 716
                                   56788889999999999999886 PP

  == domain 2  score: 101.5 bits;  conditional E-value: 3.4e-32
                       DUF1854   1 yegvepvrafPisapdeyislvdedgkElaiiedladLdeesrklleeeLarrefvpeIkrIksvsekagpstweveTdrG 81 
                                   y+++ p+ +fPi++p ++i++++ dgkEl+++ed+++Ld+es k+le++L ++++v+++ +I++++ k+++++w++ Td+G
  gi|70607839|ref|YP_256709.1| 734 YRDLIPKALFPITNP-KFIGFYTDDGKELFLLEDYSKLDSESLKVLESALLYNNLVFKVVKINNINIKGDQLEWDLVTDKG 813
                                   8999***********.***************************************************************** PP

                       DUF1854  82 etefvlkneedirrlsskrllitDsdgnryeipdvkaLDkkSrklLe 128
                                     +  + +++++ ++++k +++ D+++n yei +++++Dk+S++lL 
  gi|70607839|ref|YP_256709.1| 814 VSKTFTLGRRNVVVFEKK-VVLIDRNDNLYEI-NMESIDKRSLRLLL 858
                                   ***************999.9999*********.************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.2    0.0083       7.1      27      42 ..     481     496 ..     467     508 .. 0.81
   2 !   17.4   0.0   2.6e-06    0.0023     117     210 ..     552     658 ..     516     665 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0083
                                   EEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                         SMC_N  27 taivGpNGSGKsnlld 42 
                                    aivG+ GSGKs +  
  gi|70607839|ref|YP_256709.1| 481 VAIVGKSGSGKSTIAK 496
                                   68**********9975 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.6e-06
                                   EE-HHHHHHHHHCTT-STT.................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 117 evtkkevsellesagiske.................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                   +v++ ++ +  ++a+i+ e                 +LSgG+++ +++a   Ai  +k   + ++De  ++LD    ++v 
  gi|70607839|ref|YP_256709.1| 552 NVNEVDIVRACKTAKIHDEivrlpfaydtilgergtYLSGGQRQRLSIAR--AI--IKNPDVLIFDEATSNLDVVSEREVY 628
                                   5556666666666666666777777777777777779******9666553..34..45556789***************** PP

                                   HHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 181 ellkeksknaQfivislreemlekadklvg 210
                                   e + e s n  +i i+++ + + +adk++ 
  gi|70607839|ref|YP_256709.1| 629 EAMMEVSRNKTVILITHNIHEVMNADKVIV 658
                                   *************************99875 PP

>> ABC_membrane_3  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   3.9   2.3e-08   1.9e-05       3     168 ..     125     304 ..     123     314 .. 0.83
   2 ?    0.3   0.1       0.4   3.4e+02     128     172 ..     365     410 ..     353     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-08
                ABC_membrane_3   3 tiakkarkrlavtfllvlaenvlllayPlligfaiddllagkvaqlliyalvvlllilig...aarrivDTRay....srI 76 
                                   +i  ++rk +++  +l l+   l l  P+l  + id++l  +   + ++ l+vllli      a+   + TR+     srI
  gi|70607839|ref|YP_256709.1| 125 SISSRYRKTMILGATLSLISTGLNLVPPYLLKILIDNVLISNNHSAQLFQLIVLLLITSYtslALVSSLQTRILnnlgSRI 205
                                   67778888899888999999999********************99999999999887543111445678999975555799 PP

                ABC_membrane_3  77 yaelavevvleqrqqdl......dtSkvaarlalsrelvdFl.EkhlPtlitavvsivgavvmllvlefslglsallilll 150
                                   + +l   ++ + +++d       + S + +rl+      ++l    lPtl+t++++++g  v+l +l+  l+  +l+ + l
  gi|70607839|ref|YP_256709.1| 206 INDLREMLYNHVIKHDYsfieriSPSRILSRLTTDAGNTNWLlVWGLPTLVTNFFTLLGIGVILFTLNPLLATFILIPIPL 286
                                   999999988888877651111115799999*999999899862579*********************************** PP

                ABC_membrane_3 151 lllllprFarrnerlnik 168
                                   +l++++r+ ++++rl+ +
  gi|70607839|ref|YP_256709.1| 287 ILFMVVRYRKKSHRLYHR 304
                                   ***************975 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.4
                ABC_membrane_3 128 gavv.mllvlefslglsallillllllllprFarrnerlnikLNne 172
                                   g vv ++ v++ ++g   ++  ++ l ++++F ++  + ++ +Nn 
  gi|70607839|ref|YP_256709.1| 365 GLVVnLSTVIIWWVGGHEVISGVIELGVITAFIAYLSQFYSPINNL 410
                                   44441456788999***************************99995 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00041      0.35       3      34 ..     482     509 ..     481     574 .. 0.73
   2 !    9.8   0.0   0.00073      0.63     245     300 ..     597     648 ..     587     652 .. 0.81
   3 ?   -3.3   0.2       7.2   6.1e+03      74     126 ..     679     722 ..     675     768 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00041
                        AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltd 34 
                                   +++G+ gsGKS++ ++l  + ++    + +++
  gi|70607839|ref|YP_256709.1| 482 AIVGKSGSGKSTIAKLLLRFYDV----NKGKI 509
                                   79***************776543....22222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00073
                        AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   l ++ a++  +   ++l++DE  ++L+    r+++e + e sr +  vil TH+ +
  gi|70607839|ref|YP_256709.1| 597 LSIARAIIKNP---DVLIFDEATSNLDVVSEREVYEAMMEVSR-NKTVILITHNIH 648
                                   44444444444...9****************************.*********965 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.2
                        AAA_21  74 yglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfs 126
                                   y++++ ++q+         ++e  + +d   +e +d  + ++r ++++  +++
  gi|70607839|ref|YP_256709.1| 679 YFHKIFKDQI---------NEENVFSKDGNGKEIHDIRILNPRSTKITPAERR 722
                                   5555555555.........3333333333333333333333333333333222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.2   2.7e+03      71     126 ..      81     135 ..      40     142 .. 0.67
   2 !   13.5   0.2   7.7e-05     0.066       9      33 ..     482     506 ..     478     651 .. 0.74
   3 ?    0.3   0.1      0.94     8e+02      94     112 ..     609     631 ..     596     686 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.2
                        AAA_22  71 erlsseellealeqalraravielliiDEaqhlrs.eealeeLrsllnl.srkgvqli 126
                                    ++++ee++++l++a+++     + i DE++   s +  +++Lr l+ + sr+  ++i
  gi|70607839|ref|YP_256709.1|  81 FTKRKEEVFKKLAEAFNSGEQ--IEIKDEVDDK-ShKPGVNTLRWLFSIsSRYRKTMI 135
                                   467888888888888888877..8888999986.335555555444444335555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.7e-05
                        AAA_22   9 vvtGesGtGKTtllrrlleqldeea 33 
                                   +++G sG+GK+t ++ ll+ +d  +
  gi|70607839|ref|YP_256709.1| 482 AIVGKSGSGKSTIAKLLLRFYDVNK 506
                                   79*****************998654 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.94
                        AAA_22  94 lliiDEaqh.lr..s.eealeeL 112
                                   +li DEa   l+  s  e++e  
  gi|70607839|ref|YP_256709.1| 609 VLIFDEATSnLDvvSeREVYEAM 631
                                   55555555444443222222222 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.4e-05     0.012      25      45 ..     480     500 ..     470     511 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                         DUF87  25 HlAilgsTGsGKSntvavLle 45 
                                    +Ai+g++GsGKS+ +++Ll+
  gi|70607839|ref|YP_256709.1| 480 KVAIVGKSGSGKSTIAKLLLR 500
                                   69*****************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.1e-05    0.0097      16      38 ..     472     494 ..     467     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        AAA_29  16 tieidlkgatlltGpsGsGKSTl 38 
                                    i+i++ + + ++G+sGsGKST+
  gi|70607839|ref|YP_256709.1| 472 NINIRPGEKVAIVGKSGSGKSTI 494
                                   577888889*************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.0   2.1e-05     0.018      15      55 ..     469     527 ..     467     741 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                        AAA_15  15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.................k 55 
                                   k+  i++ +     ++Gk +sGKS+i+++l  F + ++ k                  k
  gi|70607839|ref|YP_256709.1| 469 KNLNINIRPGeKVAIVGKSGSGKSTIAKLLLRFYDVNKGKItiggvdlkeididylrrK 527
                                   6667777777799*********************9883333666555555544444440 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0012         1       2      98 ..     482     636 ..     481     661 .. 0.71
   2 ?    3.4   0.1      0.11        98      18      84 ..     788     852 ..     781     861 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                                   EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS................................... CS
                           AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk................................... 37 
                                    ++G  G GK+++ak + +            gv++ ei+   l+ k                                   
  gi|70607839|ref|YP_256709.1| 482 AIVGKSGSGKSTIAKLLLRFYdvnkgkitigGVDLKEIDIDYLRRKvayvpqdvvlfdttvgynvaygsdnvnevdivrac 562
                                   579****************97444443333346688888877777788888888888888888888888888888999999 PP

                                   ........................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                           AAA  38 ........................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteld 94 
                                                           +   + ++ r  +++a  k+ p +l++DE+ +                  + ++++ 
  gi|70607839|ref|YP_256709.1| 563 ktakihdeivrlpfaydtilgergTYLSGGQRQRLSIARAIIKN-PDVLIFDEATSNLDVV----------SEREVYEAMM 632
                                   99999999999999999988888855556666666666666666.8999999988776555..........3344444444 PP

                                   HTTT CS
                           AAA  95 gvkk 98 
                                   +v++
  gi|70607839|ref|YP_256709.1| 633 EVSR 636
                                   5544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                                   HHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHH CS
                           AAA  18 vakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeer 84 
                                   v k ++++ ++i+g +l   +   + k ++++f+  +++    ++++++iD  d+l + +    ++ ++r
  gi|70607839|ref|YP_256709.1| 788 VFKVVKINNINIKGDQLE--WDLVTDKGVSKTFTLGRRNVvvfEKKVVLIDRNDNLYEIN---MESIDKR 852
                                   556668888999999999..9999**********9998889*999******999998877...4444444 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00065      0.55      23      54 ..     480     511 ..     469     533 .. 0.87
   2 ?    2.6   0.0     0.059        50     242     289 ..     608     653 ..     598     676 .. 0.88
   3 ?   -1.0   0.1      0.74   6.4e+02      39      63 ..     819     843 ..     792     856 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                        AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkali 54 
                                   +++i+G+ G GKS +akll  +  + +gk+ i
  gi|70607839|ref|YP_256709.1| 480 KVAIVGKSGSGKSTIAKLLLRFYDVNKGKITI 511
                                   569*******************9999999876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.059
                        AAA_10 242 kvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlke 289
                                    v ifDEa +  ++   +++ + ++   R  n  v+l+t++ + v + 
  gi|70607839|ref|YP_256709.1| 608 DVLIFDEATSNLDVVSEREVYEAMMEVSR--NKTVILITHNIHEVMNA 653
                                   689**********************9977..889*******9988654 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.74
                        AAA_10  39 kllvlyisllggkaliiDpkkerek 63 
                                    l   +++++++k+++iD+  + ++
  gi|70607839|ref|YP_256709.1| 819 TLGRRNVVVFEKKVVLIDRNDNLYE 843
                                   4445789999*********999665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0009      0.77       2      81 ..     482     566 ..     481     574 .. 0.71
   2 ?    1.7   0.2      0.38   3.3e+02      48     103 ..     605     658 ..     596     661 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0009
                  RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfw...dgYtgqevvvidDfgqvkdee.nps.dlaelirlv 77 
                                    ++G+sg GKSt+ak L +    + ++++ + v  ++ + d++     Y  q+vv++d     +  + +++  + +++r++
  gi|70607839|ref|YP_256709.1| 482 AIVGKSGSGKSTIAKLLLRFYDVNKGKITIGGVDLKEIDIDYLrrkVAYVPQDVVLFDTTVGYNVAYgSDNvNEVDIVRAC 562
                                   689*************87766655555566666666777777733335777888888877777777777777777777777 PP

                  RNA_helicase  78 sstp 81 
                                   ++++
  gi|70607839|ref|YP_256709.1| 563 KTAK 566
                                   7766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.38
                  RNA_helicase  48 tgqevvvidDfgqvkdee.npsdlaelirlvsstpyplnmasleekgtlftSkvviv 103
                                   ++++v+++d+  ++ d   + + ++ ++++  +++++l + +++e    +++  viv
  gi|70607839|ref|YP_256709.1| 605 KNPDVLIFDEATSNLDVVsEREVYEAMMEVSRNKTVILITHNIHEV---MNADKVIV 658
                                   6899**********99997788999*************99999974...55555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   5.1e-05     0.044       4      59 ..     480     531 ..     478     686 .. 0.84
   2 ?   -3.0   0.0         6   5.1e+03      67      88 ..     831     852 ..     829     853 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                        AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel 59 
                                   k++i+G+sg+GK+t+ak l     f d++kG   + + ++++i  ++ ++ +v+++
  gi|70607839|ref|YP_256709.1| 480 KVAIVGKSGSGKSTIAKLL---LRFYDVNKGKITIGGVDLKEI-DIDYLRRKVAYV 531
                                   89*****************...888899999888888888877.455555555444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6
                        AAA_24  67 ktlviDtideleelclaevirq 88 
                                   k++ iD  d l+e+ ++ ++++
  gi|70607839|ref|YP_256709.1| 831 KVVLIDRNDNLYEINMESIDKR 852
                                   7999999999999999998775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00044      0.38      25      48 ..     479     502 ..     471     535 .. 0.84
   2 ?    0.2   0.0         1   8.5e+02     120     158 ..     744     781 ..     667     784 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                        AAA_16  25 elvllsGesGvGKsslvrellral 48 
                                   e v ++G sG+GKs++++ llr +
  gi|70607839|ref|YP_256709.1| 479 EKVAIVGKSGSGKSTIAKLLLRFY 502
                                   5689***************99855 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1
                        AAA_16 120 lellkrllallsrderplvlvlDdlqwadeaslqllaaL 158
                                     +  +++ +++ d++  +++l+d  ++d++sl++l++ 
  gi|70607839|ref|YP_256709.1| 744 PITNPKFIGFYTDDGK-ELFLLEDYSKLDSESLKVLESA 781
                                   5555678888888777.8999*************99865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.091       1      20 [.     481     500 ..     481     575 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                        AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                   +++ G++G+GK+t+ak L +
  gi|70607839|ref|YP_256709.1| 481 VAIVGKSGSGKSTIAKLLLR 500
                                   689**************933 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00022      0.19       1      22 [.     480     501 ..     480     572 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                   EEEEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltge 22 
                                   +vaivG++ +GKSt+ + l++ 
  gi|70607839|ref|YP_256709.1| 480 KVAIVGKSGSGKSTIAKLLLRF 501
                                   69**************999973 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.2   1.9e+03      16      47 ..     320     351 ..     307     354 .. 0.84
   2 ?   10.6   0.0   0.00046      0.39      93     126 ..     471     505 ..     460     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                                   --EEEEEEESTTTT--HHHHHHHHHHHHHTT- CS
                   RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgi 47 
                                   + + l+v s++++e+++++l  +L  + e+ +
  gi|70607839|ref|YP_256709.1| 320 IPNFLVVRSFSKEEYESKRLRNMLDKLYESSV 351
                                   56789****************99988877766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00046
                                   HHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                   RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                   l+ +++  + +++vG+SG GKSt+ + ll   +++
  gi|70607839|ref|YP_256709.1| 471 LNINIRPgEKVAIVGKSGSGKSTIAKLLLRFYDVN 505
                                   555555557889************99998755555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00077      0.66       2      24 ..     481     505 ..     480     537 .. 0.81
   2 ?   -2.7   0.0       6.3   5.4e+03      49      75 ..     590     616 ..     577     627 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00077
                                   EEEE--SSSSHHHHHHHGGGGB..S CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal..n 24 
                                   v +vG++G+gKs++a+ l++++  n
  gi|70607839|ref|YP_256709.1| 481 VAIVGKSGSGKSTIAKLLLRFYdvN 505
                                   668****************999643 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                                   ........--------G-SEEEEESGG CS
                         AAA_5  49 ngttslvdsplvraaregeilvlDEve 75 
                                   +g+++ + s++   ++++++l++DE +
  gi|70607839|ref|YP_256709.1| 590 SGGQRQRLSIARAIIKNPDVLIFDEAT 616
                                   556666666667677799999999987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.5   2.1e+03      57     110 ..      77     134 ..      56     138 .. 0.64
   2 ?    9.9   0.1   0.00097      0.83       1      40 [.     480     520 ..     480     541 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.5
                                   EEEEEEE-SGGCTTTT-HHHHCTSCEEEEE.EEGHHHH...CHHHHHHHHHHHCSSS- CS
                           Roc  57 klniWDtaGqerfrslhplylreaalailv.ydsrsse...nlkeWlkelkkvagksp 110
                                   +l+ +    +e f++l++ + +++++ i   +d++s++   n  +Wl +++++ +k++
  gi|70607839|ref|YP_256709.1|  77 ELAYFTKRKEEVFKKLAEAFNSGEQIEIKDeVDDKSHKpgvNTLRWLFSISSRYRKTM 134
                                   5555555557889999999999999988742444333222255579988887766655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00097
                                   EEEEESSTTSSHHHHHHCHCT.-CCC-EEETTTTEEEEEEE CS
                           Roc   1 KvvlvGdsgvGKtsllkrfve.dkfsekekstigvdfltke 40 
                                   Kv +vG+sg+GK++++k +++  ++++ + ++ gvd+++ +
  gi|70607839|ref|YP_256709.1| 480 KVAIVGKSGSGKSTIAKLLLRfYDVNKGKITIGGVDLKEID 520
                                   89*************99888733455555555567776544 PP

>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         1   8.7e+02      11      23 ..     131     143 ..     127     195 .. 0.83
   2 ?    8.8   0.9    0.0022       1.9      14      79 ..     248     305 ..     242     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                         VirB3  11 RpamllGvplelv 23 
                                   R++m+lG++l+l+
  gi|70607839|ref|YP_256709.1| 131 RKTMILGATLSLI 143
                                   999****999986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                         VirB3  14 mllGvplelvllnllvsvilflvglslwil.lllvplhlvlrliakrDpqmfrvlllrlktrlrlrn 79 
                                   +++G+p  +  +  l+ + ++l++l+++++ ++l+p+ l+l++++++  +  r++         +rn
  gi|70607839|ref|YP_256709.1| 248 LVWGLPTLVTNFFTLLGIGVILFTLNPLLAtFILIPIPLILFMVVRYRKKSHRLY---------HRN 305
                                   78999988888887777777777777766515666***********999999999.........444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.79u 0.32s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 5426.10
//
Query:       gi|70607840|ref|YP_256710.1|  [L=360]
Description: amidohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-35  123.9   0.6      2e-35  123.0   0.6    1.4  1  Amidohydro_2     Amidohydrolase
  ------ inclusion threshold ------
      0.062   13.7   0.0       0.11   12.8   0.0    1.5  1  Sulfotransfer_3  Sulfotransferase family


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.6   2.2e-39     2e-35       1     291 []      17     335 ..      17     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.2e-39
                                   EEEEEEE..SHHH................CCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHH CS
                  Amidohydro_2   1 iDvHaHllppeaa................irddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaal 65 
                                   iD+HaH++ +++                   + +    ++ ++ + f +  + +   + +    v  a+++ ++   +++ 
  gi|70607840|ref|YP_256710.1|  17 IDYHAHIWKAGESnwlrpelakgwiscfyDYQTALTPDEYKMDFETFKYYGHEKFIEDVMINGYVDVAITQPQYLLYFYKK 97 
                                   89****999999999998888888876653333333334444444555555555555555555677777888888888888 PP

                                   HHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECE.....EEEESSTT........TCCTTTCGGH.. CS
                  Amidohydro_2  66 crgannrvlaeaakrpdrfvggaavvpldpedaaaeleraveelgfkG.....vrlnphvg........gddllgdrld.. 131
                                   ++g ++++ ++a ++p rfv g  ++p+d+e+  ++le+ v ++++k      v+l+++ +                    
  gi|70607840|ref|YP_256710.1|  98 PFGNTEEFGKLAVENPYRFVIGTRFDPRDGEEGKRQLEEDVRKYRVKPwqmrhVKLYTAEWkevdgklsR--------Gwr 170
                                   888888899*****************************************99999999996433322222........134 PP

                                   ......HHHHHHHHHHT-EEE.EE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHH CS
                  Amidohydro_2 132 ......rpifealeelglpvd.ihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellar 205
                                         ++++e  + lg+ ++  h G      ++ ++ + + ++  +++ va  fP+lk+v+ H G p  rl ++ +++ +
  gi|70607840|ref|YP_256710.1| 171 ldskeaYEFLEFSKSLGINIFvAHKG------PTVWPLDKDSFDVKDVDAVASSFPELKFVVTHVGLP--RLDDFCWIATQ 243
                                   4456668************9978977......************************************..*********** PP

                                   HHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH........SSHHHHH CS
                  Amidohydro_2 206 rpnvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval........lsdeere 278
                                    +nvy  l  +   ++++  p++++ ++ +l++++g+dr+l+GsDy ++++++  e++ +++l+++        l+ + ++
  gi|70607840|ref|YP_256710.1| 244 EKNVYGGLAVAS--AFIRKRPKYFASIIGELLFWLGEDRVLWGSDYAIWNPKWLIEDFMKFELPEEikreygveLTLDTKK 322
                                   *****7775543..49***************************************************************** PP

                                   HHHTHHHHHHCTB CS
                  Amidohydro_2 279 kilggNAarlygl 291
                                   k+l+ NA +l+++
  gi|70607840|ref|YP_256710.1| 323 KLLYQNASKLWDI 335
                                   **********985 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.11      74     132 ..     172     228 ..     112     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHTT-BHHHHHHHHHHHTTTSEEEEEESSGGG-HHHHHHHBSSEEEEEEE CS
               Sulfotransfer_3  74 eepeedlqllraalasvilealarvpsyarwlvdKsPshlfrldlllelfPdAkfihlv 132
                                   + +e   +l  +  +s+ ++ ++ +++++ w +dK+ + ++ +d+++  fP+ kf++++
  gi|70607840|ref|YP_256710.1| 172 DSKEAYEFL--EFSKSLGINIFVAHKGPTVWPLDKDSFDVKDVDAVASSFPELKFVVTH 228
                                   222211111..22345556788899999****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2488.42
//
Query:       gi|70607841|ref|YP_256711.1|  [L=124]
Description: hypothetical protein Saci_2125 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   18.9   0.2     0.0015   18.6   0.2    1.2  1  CARD      Caspase recruitment domain
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.25   11.3   0.0    1.5  1  HP1451_C  HP1451 C-terminal domain


Domain annotation for each model (and alignments):
>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   1.6e-07    0.0015      21      70 ..      70     121 ..      53     124 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-07
                                   HHHHHHHTTSS-HHHHHHHHT..SSSHHHHHHHHHHHHHTSCHHHHHHHHHH CS
                          CARD  21 lldyLlekkVLteeeeekika..kttrlskareLldlvqkkgekacqaflea 70 
                                    + ++++++ L+ +e+ek+k   + +r +k ++L+ l ++ + + c+++ ea
  gi|70607841|ref|YP_256711.1|  70 KFHECYSNESLNGDEYEKVKRtfEEKRSNKYGKLVQLSLNINGELCKLIAEA 121
                                   467899*********************************9999999998876 PP

>> HP1451_C  HP1451 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.8e-05      0.25      35      62 ..      33      60 ..      31      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                                  HHHHHHHHHHHH-TTSEEEEEE-TTS-E CS
                      HP1451_C 35 lvkialkkLreefPdkYvsiksnkegek 62
                                  +++i l+++r++ Pd  + +k++++++k
  gi|70607841|ref|YP_256711.1| 33 FLYIMLEEIRNRLPDAIIEVKDHHDSKK 60
                                  789*******************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 817.71
//
Query:       gi|70607842|ref|YP_256712.1|  [L=341]
Description: NAD-dependent alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-30  104.0   0.7    9.7e-30  102.7   0.2    1.9  2  ADH_N            Alcohol dehydrogenase GroES-like domain
      2e-26   92.5   0.2    3.2e-26   91.8   0.2    1.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.1e-12   49.1   0.0    2.2e-12   48.2   0.0    1.5  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    0.00018   21.1   0.3    0.00028   20.4   0.3    1.3  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
     0.0016   18.7   0.5     0.0035   17.6   0.5    1.6  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.039   14.1   0.9      0.073   13.2   0.9    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.045   14.5   0.0       0.11   13.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
      0.052   14.2   2.6        1.4    9.6   2.4    2.5  2  CoA_binding      CoA binding domain
       0.08   12.7   0.2       0.18   11.6   0.2    1.4  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.2   4.9e-33   9.7e-30       3     105 ..      28     133 ..      26     137 .. 0.94
   2 ?   -1.5   0.0       1.1   2.2e+03      34      64 ..     219     244 ..     200     256 .. 0.71

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 4.9e-33
                                   EEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                         ADH_N   3 evlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                   ++++k+k ag+C++Dlhi +g   + ++ klp+++GHE vG+ve  g++v+ l+vGd+V+++p i+c +C+aC++g++ +C
  gi|70607842|ref|YP_256712.1|  28 DIIVKIKGAGVCRTDLHIQEGVwkDIFNPKLPFTIGHENVGVVETKGDNVDWLNVGDQVILHPYITCRRCKACRSGNDMHC 108
                                   79******************98878899***************************************************** PP

                                   TTBEETTTS.S-SSSBSEEEECGGG CS
                         ADH_N  82 eeakllgvs.ldGgfaeyvvvpekk 105
                                   +++k+ g++ +dGg+aey+ +++ +
  gi|70607842|ref|YP_256712.1| 109 PNGKFPGLDgTDGGYAEYLRTSAYS 133
                                   ******************9988655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                   E---EEEEEEEEESTT-CS--TT-EEEE-SE CS
                         ADH_N  34 ilGHEivGeveevgpevkklkvGdrVvvepl 64 
                                   + G E++ ev ++ ++     vG  Vv++++
  gi|70607842|ref|YP_256712.1| 219 VNGKEAIHEVRKITDN-----VGADVVIDFV 244
                                   5566666666666554.....5777777765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.2   1.6e-29   3.2e-26       1     128 [.     180     304 ..     180     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.6e-29
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   g+G++++q+Aka+   ++iavd +e+kl++ak+lGad+++n ke     +++++t+  g+dvv+++vG + t ++a++++k
  gi|70607842|ref|YP_256712.1| 180 GLGHIGIQVAKAITSaRIIAVDLDEDKLKMAKELGADYIVNGKE--AIHEVRKITDNVGADVVIDFVGEHNTPKDAVSMIK 258
                                   89*********76655**************************77..9999*****999*********************** PP

                                   EEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefkealdll 128
                                   +gG+  +vG   g+e   ++ +++ +e+s+lG l+g+  +e++e+++l 
  gi|70607842|ref|YP_256712.1| 259 KGGTYSIVGY--GGEFrDPTVDFISREISVLGNLVGT-YNELSELVQLY 304
                                   *********6..333325777899*************.89999999986 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.1e-15   2.2e-12       1     131 [.     213     337 ..     213     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.1e-15
                                   TT-SEEEETTSTTHH..HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--G CS
                  ADH_zinc_N_2   1 lGAdevidyrtedfe..aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyefl 78 
                                   lGAd +++ ++   e  + t++ g Dvv+d vg +++ +++++++++gG++  +g g    ++++ + +     s+ ++ l
  gi|70607842|ref|YP_256712.1| 213 LGADYIVNGKEAIHEvrKITDNVGADVVIDFVGEHNTPKDAVSMIKKGGTYSIVGyG--GEFRDPTVDF----ISREISVL 287
                                   8******9996655567999999**********99999****999888**9656655..2445455544....33444444 PP

                                   GG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEE CS
                  ADH_zinc_N_2  79 fsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKi 131
                                     +  +   + l el++l+ eGk++++v  +f+l+ea++A++ l +g   G+ 
  gi|70607842|ref|YP_256712.1| 288 GNLVGT-YNE-LSELVQLYVEGKVKVRVK-TFSLDEANKALEELSKGLIPGRG 337
                                   433344.577.*****************7.9*************999777665 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   1.4e-07   0.00028      28     133 ..     166     269 ..     149     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                   Glu_dehyd_C  28 ewepesal.vlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeasee..mdlvv 105
                                   e +p + l ++G G lG + + + +a    ++   +++  d ++ ++++ +elGa Y+ + ++ ++e+ +++ +   d+v+
  gi|70607842|ref|YP_256712.1| 166 ELTPGTFLvIIGVGGLGHIGIQVAKA----ITSARIIA-VDLDEDKLKMAKELGADYIVNGKEAIHEVRKITDNvgADVVI 241
                                   46666655168******999665554....44455555.3678889999*********9999999999988765227**** PP

                   Glu_dehyd_C 106 EaTGsakhafeaiealapnGvaaLlGvp 133
                                   +  G+ +   +a++ ++  G   ++G  
  gi|70607842|ref|YP_256712.1| 242 DFVGEHNTPKDAVSMIKKGGTYSIVGYG 269
                                   ****************999999988855 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   1.7e-06    0.0035       3      46 ..     178     219 ..     174     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
                                   EES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEE CS
                        TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvv 46 
                                   + GlG +G ++a+ ++++   ++++d de++++ ++e g++++v
  gi|70607842|ref|YP_256712.1| 178 VGGLGHIGIQVAKAITSAR--IIAVDLDEDKLKMAKELGADYIV 219
                                   679************9977..9*****************98665 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   3.6e-05     0.073       4      97 ..     177     267 ..     173     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                                   EEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S-HHHHHH CS
                        DapB_N   4 avvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTtpeavle 82 
                                   + vG  G +G +v+ka+++a+ + +   +d+++    +k++g   +   +g +  +++ +++++  adv+iDF   + + +
  gi|70607842|ref|YP_256712.1| 177 G-VGGLGHIGIQVAKAITSARIIAV--DLDEDK-LKMAKELGA--DYIVNGKEAIHEVRKITDNvgADVVIDFVGEHNTPK 251
                                   4.45569***********9443333..344443.345566663..444788899999999999999*******97777766 PP

                                   HHHHHHHT.T-EEEE- CS
                        DapB_N  83 nlklalek.gvklViG 97 
                                    +  +++k g+  ++G
  gi|70607842|ref|YP_256712.1| 252 DAVSMIKKgGTYSIVG 267
                                   6666665546666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.5e-05      0.11       7      87 ..     180     258 ..     176     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                                   TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHH CS
               Methyltransf_25   7 GtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalk 87 
                                   G G++ +++ak++ +a++++vD++e+ l+ a+e  ++  +n +   ++++++   +   D+v+ + + +h +++d+  ++k
  gi|70607842|ref|YP_256712.1| 180 GLGHIGIQVAKAITSARIIAVDLDEDKLKMAKELGADYIVNGKEAIHEVRKITD-NVGADVVIDF-VGEHNTPKDAVSMIK 258
                                   679999******988*******************98877788888888888874.4589999995.547767777776665 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4   0.00071       1.4       7      87 ..     174     261 ..     170     267 .. 0.83
   2 ?    1.9   0.0      0.19   3.7e+02      49      86 ..     292     332 ..     274     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                                   EEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET........TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                   CoA_binding   7 iviGagglgiaglyhfkeklkygikavfgvnprkvgtevl........glpvyksvdeleektevdvavitvPaesaqeav 79 
                                   ++iG+gglg+ g  + k   + +i ++++ +++k+    +        g ++  +v+++ +++++dv + +v + +  + +
  gi|70607842|ref|YP_256712.1| 174 VIIGVGGLGHIGIQVAKAITSARI-IAVDLDEDKLKMAKElgadyivnGKEAIHEVRKITDNVGADVVIDFVGEHNTPKDA 253
                                   79******9888877777777666.67899988666444445***999999999******************999999999 PP

                                   HHHHHTT- CS
                   CoA_binding  80 delveagi 87 
                                   + ++++g 
  gi|70607842|ref|YP_256712.1| 254 VSMIKKGG 261
                                   99999875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                                   EEESCHHHHHHHC..T.TTEEEEES-HHHHHHHHHHHHHTT CS
                   CoA_binding  49 pvyksvdeleekt..e.vdvavitvPaesaqeavdelveag 86 
                                     y++++el++    + v+v v t++ ++a +a +el +  
  gi|70607842|ref|YP_256712.1| 292 GTYNELSELVQLYveGkVKVRVKTFSLDEANKALEELSKGL 332
                                   56888888888888536******************998765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   9.1e-05      0.18      13      47 ..     180     213 ..     175     243 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
               Methyltransf_31  13 GtGeltfelaeelgpkaevvGiDiseeaielAren 47 
                                   G G+++++ a ++++ a+++ +D +e+ ++ A+e 
  gi|70607842|ref|YP_256712.1| 180 GLGHIGIQVA-KAITSARIIAVDLDEDKLKMAKEL 213
                                   77********.99*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2395.69
//
Query:       gi|70607843|ref|YP_256713.1|  [L=412]
Description: transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-24   85.2  39.5    6.3e-24   84.6  39.5    1.2  1  MFS_1     Major Facilitator Superfamily
    4.5e-13   48.9  29.7    9.8e-07   28.0   6.3    2.4  2  Sugar_tr  Sugar (and other) transporter
     0.0031   17.7  16.4     0.0031   17.7  16.4    4.7  5  DUF3792   Protein of unknown function (DUF3792)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6  39.5     1e-27   6.3e-24       5     351 ..      23     364 ..      17     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1e-27
                         MFS_1   5 aflsalarsilgpalplalaedlg..ispseigllltl..yalgaavaslplGrlsdrfGrrr.vlllglllfalglllll 80 
                                   +fl++ a+s+++ +   + +e ++  +  s+ig+ ++l   + + ++++ +lG+lsd++Grr  +++ g+ ++ +++l+++
  gi|70607843|ref|YP_256713.1|  23 TFLVYNASSVIAYTSQNLAQEIFHglYPFSVIGIYTSLvlSYGFRIAGASLLGPLSDKLGRRVaTIIGGIGSSTATALIGF 103
                                   788888888888888878888899998899999977775244456******************777777777777766666 PP

                         MFS_1  81 fa....sslw..lllvlrv.lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                   ++    ++++  +l++l v +qGl++g l ++++++ ++  p+++rg   g+  a ++ +++++ +l+ +     +Wr +f
  gi|70607843|ref|YP_256713.1| 104 LPpytsIGIFsiILYFLLVsIQGLFTGPLSAGVQVIGVENLPERHRGWFSGIGIAVSGTAYLVAVGLSLISG--SNWRFLF 182
                                   53442333332223333337*******************************************977765555..67***** PP

                         MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylq 235
                                   +   i+  ++     ll pe+ + rk k++++      ++ +++   +  +   +  +++ +ll++ +++ + + lp++l 
  gi|70607843|ref|YP_256713.1| 183 WGSLIIVPIS-----LLAPESSRFRKLKEKVKS----PRKIILE---KYGNYLKF--AFLLSLLWASVNFVIGIILPTFLS 249
                                   **********.....788888888888888888....5555555...44444444..89999999999999********** PP

                         MFS_1 236 evlgls..glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfgl 314
                                   +v +++     ++ l+++l+++v+   a+++g ls  +gr+r  l++++l++l++ +++++a  +s   ++l + l++f +
  gi|70607843|ref|YP_256713.1| 250 FVNNFTesEIREVILVYSLVSIVS---AFVGGELSEVFGRKRLSLVGGILGILVSPIYFIIASLNSLYYVILYISLLTFLG 327
                                   ******984477777788888888...999**********************************55555555555588877 PP

                         MFS_1 315 gfvfpsllalasdlappeeagtasglfntagslggal 351
                                   ++  + +lal+++++p++ +gt ++    +g +g+ l
  gi|70607843|ref|YP_256713.1| 328 FLGAGGILALVNESFPTNVRGTGVSMSWNMGFFGATL 364
                                   777899****************999999998888877 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   6.3   1.6e-10   9.8e-07      59     210 ..      67     214 ..      17     224 .. 0.82
   2 !   26.6  15.4   4.3e-10   2.5e-06     290     442 ..     260     406 ..     219     408 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-10
                                   HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SC CS
                      Sugar_tr  59 aiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkk 134
                                   +i+G+ ++g+l+d++GR+ + +i+++ ++ +++l+++ + +     +s+ ++++   + G++ G  s+ v +   E+ p++
  gi|70607843|ref|YP_256713.1|  67 RIAGASLLGPLSDKLGRRVATIIGGIGSSTATALIGFLPPYtsigiFSIILYFLLVSIQGLFTGPLSAGVQVIGVENLPER 147
                                   689**********************************9988999999********************************** PP

                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHH CS
                      Sugar_tr 135 lRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakev 210
                                   +Rg + ++      +    a+ + +gl+ +s+ + wr+l++ +l++      + l++PES r+   k+k +  +++
  gi|70607843|ref|YP_256713.1| 148 HRGWFSGIGIAVSGT----AYLVAVGLSLISG-SNWRFLFWGSLIIV----PISLLAPESSRFRKLKEKVKSPRKI 214
                                   ***988875555444....5666666666666.67******998876....678999******9999998866555 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.3e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHH CS
                      Sugar_tr 290 llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpv 370
                                    +v ++++ v +v+ fv+  l++ fGR++l l+G++ ++++  i+    ++  ++     + +i  i l ++l  lg g++
  gi|70607843|ref|YP_256713.1| 260 REVILVYSLVSIVSAFVGGELSEVFGRKRLSLVGGILGILVSPIYF--IIASLNS----LYYVILYISLLTFLGFLGAGGI 334
                                   67889999******************************99999997..5555555....57788888888888888***** PP

                                   HHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHH.HHHHHHHS--STT CS
                      Sugar_tr 371 pwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlf.iifvfffvpetkg 442
                                   +  lv E fp++vR+++ +++ ++ ++   l++l+     +  +  +++ + a l + + ii v +f +et g
  gi|70607843|ref|YP_256713.1| 335 L-ALVNESFPTNVRGTGVSMSWNMGFFGATLVALTVVSPSSYFNVLPSGEFLALLILGSsIIAVSLFAMETRG 406
                                   *.677********************************999999999999999988886516667788888876 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.8      0.44   2.6e+03      80      97 ..      56      73 ..      11      95 .. 0.47
   2 ?   -3.4   7.5       1.7     1e+04      32      57 ..     105     130 ..      43     141 .. 0.71
   3 ?   -6.6  14.1         3   1.8e+04      58      98 ..     144     187 ..      83     195 .. 0.51
   4 !   17.7  16.4   5.1e-07    0.0031       6     114 ..     228     335 ..     224     336 .. 0.70
   5 ?    0.8   0.9      0.09   5.4e+02      13      54 ..     360     399 ..     353     410 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.44
                       DUF3792 80 lllsllikksgsafslkl 97
                                  +  sl+++ ++ ++ ++l
  gi|70607843|ref|YP_256713.1| 56 IYTSLVLSYGFRIAGASL 73
                                  222222233333334444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                       DUF3792  32 lsekvlsililiililsvfigGflag 57 
                                    + +++ i+++i+++l v i G+++g
  gi|70607843|ref|YP_256713.1| 105 PPYTSIGIFSIILYFLLVSIQGLFTG 130
                                   34566777777777777777777766 PP

  == domain 3  score: -6.6 bits;  conditional E-value: 3
                       DUF3792  58 kkakkkgllnGllvGll..yflillllslli.kksgsafslkll 98 
                                      + +g+++G+ +++    +l+ + lsl++ ++  ++f+++l+
  gi|70607843|ref|YP_256713.1| 144 LPERHRGWFSGIGIAVSgtAYLVAVGLSLISgSNWRFLFWGSLI 187
                                   33578999999988888443333366777773333333333333 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 5.1e-07
                       DUF3792   6 lkgllialvitlilll...ilalllyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflilllls 83 
                                   l +ll+a v ++i ++   +l+++ +ft+ +   + +++++++i+s+f+gG l+    +k+  l G+++G+l   i+++++
  gi|70607843|ref|YP_256713.1| 228 LLSLLWASVNFVIGIIlptFLSFVNNFTESEIREVILVYSLVSIVSAFVGGELSEVFGRKRLSLVGGILGILVSPIYFIIA 308
                                   56666665555555550005555555555555666677778999999*****************************99999 PP

                       DUF3792  84 llikksgsafslkllikllllllagaiGGii 114
                                   +l     s+  + l i+ll  l +   GGi+
  gi|70607843|ref|YP_256713.1| 309 SLN----SLYYVILYISLLTFLGFLGAGGIL 335
                                   998....333444556666666666677776 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.09
                       DUF3792  13 lvitlilllilalllyftsls.ekvlsililiililsvfigGf 54 
                                   + +tl++l +++   yf+ l+  + l +lil ++i++v    +
  gi|70607843|ref|YP_256713.1| 360 FGATLVALTVVSPSSYFNVLPsGEFLALLILGSSIIAVS---L 399
                                   567889999999999999888334444455555555443...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2856.42
//
Query:       gi|70607844|ref|YP_256714.1|  [L=285]
Description: peptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-32  110.9   2.2    1.1e-31  110.5   2.2    1.0  1  Peptidase_S58  Peptidase family S58


Domain annotation for each model (and alignments):
>> Peptidase_S58  Peptidase family S58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   2.2     6e-36   1.1e-31       6     282 ..       7     278 ..       5     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 6e-36
                 Peptidase_S58   6 VaGvrVghatlaegevrtGvTvilprgnlfkekvvAavdvlnGfgkttgtdqleelglle...tpivLtntlsvg.aaadg 82 
                                   V+G+ Vg  t  e+ +++G Tvi+++     +  vA+++ ++G++ t +td+l++ +      ++ivLt+ + +g +a++g
  gi|70607844|ref|YP_256714.1|   7 VEGILVGGYTD-ER-AKSGLTVIVTE-----GDNVAGISQRGGSPATLNTDLLRPGHRQDqsvNAIVLTGRSVFGfRAVQG 80 
                                   99********7.44.9*********8.....4579********************98887788****************** PP

                 Peptidase_S58  83 vvewlleeeee.eearsvvpvVaetnDgvlndiragav...keehvaealaaAaaapvaeGnvGaGtGmiafgl....... 152
                                   vv+ l +++   + a+  +p+V +   ++++d+ + ++   +e+  ++al++ ++ +++ G   aG G +++++       
  gi|70607844|ref|YP_256714.1|  81 VVQELFNKKVGfKIANLRIPIVSA---AAIYDLYENSIlptEEWG-FKALESLST-EIPIGRYWAGKGGTVGKVgglkyak 156
                                   *******87778889999******...999999888762213444.888888855.8************999885555553 PP

                 Peptidase_S58 153 KGGiGtaSrvleegekeytvgalvqaNfggr....edlriagvpvgkelaeeakdgsiivvvatDapLskrqlkrlakraa 229
                                    GG G     l  +++++ vg++v+ N +g+    +   iag +++    +e++ g+++ vv t+a+Ls+ ++ rla+ ++
  gi|70607844|ref|YP_256714.1| 157 PGGQG--YYEL--RKGNVKVGVIVVLNSVGNiydeSGKLIAGNEFT--SVDENTLGTTLGVVITNAKLSNSDACRLASIVE 231
                                   34444..3344..4568**************776633345555554..344559*************************** PP

                 Peptidase_S58 230 lGlartgsp.hsngsGDivlafstaekepeevledeeldelfeaaaeaveeAil 282
                                    G++ +++p   + +GD+v+a++t++ e +        del ++a ea ++A++
  gi|70607844|ref|YP_256714.1| 232 NGFSSVIRPyNLSLDGDTVFAIATNRVEVK-------FDELNAMAYEAARKAVV 278
                                   *********88899**********987754.......78888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1923.12
//
Query:       gi|70607845|ref|YP_256715.1|  [L=430]
Description: sugar transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-22   77.7  68.9    2.3e-19   69.5  38.0    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5  38.0   1.3e-23   2.3e-19      28     351 ..      39     380 ..      12     382 .. 0.74
   2 !   22.0  22.9   3.7e-09   6.6e-05       4     170 ..     246     414 ..     243     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.3e-23
                         MFS_1  28 g.....ispseigllltlyalga......avaslplGrlsdrfGrrrvlllglllfalg.lllllfa..ss....lw.lll 89 
                                         +s ++i+l++t+ +l++      + + +++ +++d++Grr++l +++l+f+++ +  +l++  s+     + l++
  gi|70607845|ref|YP_256715.1|  39 ShlffpVSNQVISLIATFGGLATgaiarpIGSLIFGNFIGDKLGRRSMLTVTILGFSIFgASKGLLPtySQvgilAPiLIY 119
                                   13344499999***9999777664455534444444677**********99999999994433334233223333555699 PP

                         MFS_1  90 vlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.......Wravfyilaivsll 163
                                   ++ +l G++aga + +g +l+ + +p ++r++  +++++gf+ G+ +  l+ + ++ ++        Wr  f+ + + ++l
  gi|70607845|ref|YP_256715.1| 120 LVLFLEGMFAGAEYGGGTSLALENVPIDKRAFIGAFIQSGFGTGYFIISLVYSGIYNLFLndfqtigWRIFFLTCLVPGVL 200
                                   99*******************************************7776666666644445888888************** PP

                         MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls... 241
                                    +v+   l+  e p  +  +++      ++   vp +k l+kd ++  +li+ll+++  +++  +++ +y  +v+ l+   
  gi|70607845|ref|YP_256715.1| 201 TLVI--RLISKETPVFEEMRKR------EEILKVP-IKTLFKDSYIQ-ILIGLLITSGLLYINNATFNIY-PTVMTLNdiq 270
                                   *554..5554444444444444......4467777.99******996.9999999998999988888888.8889999888 PP

                         MFS_1 242 .glllaglllallalvgailallagrlsdrlgr.rrrlllallllllaalglallavtssavllllvlvliGfglgfvfps 320
                                    gl+ +g  +a++ lv++++   +g l++ ++  +r++l+  +l++++   +++++ t++ + +  v+ +  f  +++f++
  gi|70607845|ref|YP_256715.1| 271 gGLVGIG--VAIINLVSLFGVWTGGLLANLISGrKRPMLIYAILFTVSIYPILYFGITNNFTTATTVFSIQAFLEAMIFST 349
                                   8888888..99*****999987777777665550555555555555555566666666555566657777888******** PP

                         MFS_1 321 llalasdlappeeagtasglfntagslggal 351
                                   l +++s+ ++++++ t +g++   g+++g +
  gi|70607845|ref|YP_256715.1| 350 LPSFLSEQFSKKYRTTGVGFTYNGGAIVGGF 380
                                   ********************99999988766 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3.7e-09
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrf.Grrrvlllglllfalglllll.fa 82 
                                   +  l +++ +++++ +p ++++   i++  +g+ +++  l++++++  +G l++ + Gr+r +l+ ++lf ++++ +l f+
  gi|70607845|ref|YP_256715.1| 246 TSGLLYINNATFNI-YP-TVMTLNDIQGGLVGIGVAIINLVSLFGVWTGGLLANLIsGRKRPMLIYAILFTVSIYPILyFG 324
                                   55555555555443.34.3344446999***************************64899999999999999945444575 PP

                         MFS_1  83 .sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    ++ + +   +  +q++ ++++f++  +++++ f+k+ r+ ++g+ + g ++   +   +  ++++++g   +++i+  ++
  gi|70607845|ref|YP_256715.1| 325 iTNNFtTATTVFSIQAFLEAMIFSTLPSFLSEQFSKKYRTTGVGFTYNGGAIVGGFSISIIFAISTYIGLLNSWFINLTIA 405
                                   6555559999999*******************************9999888888888888888888999777777777777 PP

                         MFS_1 162 llafvlfll 170
                                    +a+++++l
  gi|70607845|ref|YP_256715.1| 406 SIAMIIGIL 414
                                   777665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2895.28
//
Query:       gi|70607846|ref|YP_256716.1|  [L=264]
Description: oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-68  230.5   0.1    2.2e-68  230.3   0.1    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.8e-48  164.0   0.8    3.3e-48  163.7   0.8    1.0  1  adh_short        short chain dehydrogenase
    4.5e-13   49.5   0.1    6.5e-13   49.0   0.1    1.2  1  KR               KR domain
    0.00032   20.2   0.0    0.00043   19.8   0.0    1.3  1  DUF1776          Fungal family of unknown function (DUF1776)
     0.0004   20.3   0.0     0.0006   19.7   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0015   19.2   0.0     0.0027   18.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0032   16.8   0.0      0.013   14.9   0.0    1.8  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
  ------ inclusion threshold ------
      0.023   14.2   0.9       0.29   10.5   0.9    2.2  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.3   0.1   9.8e-72   2.2e-68       1     234 []      18     254 ..      18     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 9.8e-72
                                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                   Ga sgIG+aiA+ + e G +vvl+d++ee+ kr+ +  ++ g+ev  ++cD+td +qv++lv+   + +g++D l     i
  gi|70607846|ref|YP_256716.1|  18 GASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGHEVnhMKCDITDLNQVKKLVNFSLSVYGNVDALYVTPSI 98 
                                   899***************************88888888888988778********************************** PP

                                   -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalealtrylAv 157
                                     +  +++++ + e+f+++++vnl++ f+++k++l +mk++   gs+v  ss+++++v p++++y+++Ka++++l++ +A+
  gi|70607846|ref|YP_256716.1|  99 NVR--KSIENYTYEDFEKVINVNLKGNFMVVKEFLSVMKNNkggGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAA 177
                                   999..*******************************99988889************************************* PP

                                   HHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
                  adh_short_C2 158 elgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                                   e+g+++iRvN+++pg+++T+++++ik+ +e  ++  +++ l+r++tpee+a++alfLa +++syitG++++vDgG+t
  gi|70607846|ref|YP_256716.1| 178 EYGKYNIRVNVIAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPASSYITGTVIYVDGGWT 254
                                   ***************************************************************************97 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.7   0.8   1.5e-51   3.3e-48       3     193 ..      14     205 ..      12     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.7 bits;  conditional E-value: 1.5e-51
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                     adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83 
                                   ++v GassGIG+aia+ + ++G kvv+ d+ ee l+++ ++l++ g ++ ++++D+td ++v++lv+   + +g++d+L+ 
  gi|70607846|ref|YP_256716.1|  14 AVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGHEVNHMKCDITDLNQVKKLVNFSLSVYGNVDALYV 94 
                                   89******************************************************************************* PP

                                   ---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHH CS
                     adh_short  84 NAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrsl 163
                                     +i+ ++++++++ e++e+vi+vNl+g f++++++l  m+ ++ +G++v  sS+ g v  +g+++Y+ +Ka++++l++ +
  gi|70607846|ref|YP_256716.1|  95 TPSINVRKSIENYTYEDFEKVINVNLKGNFMVVKEFLSVMKnNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVA 175
                                   *****************************************89999*********************************** PP

                                   HHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                     adh_short 164 akelaptgirvnavaPGlvdTdmakelrek 193
                                   a e+ +++irvn++aPG+vdT+++++++++
  gi|70607846|ref|YP_256716.1| 176 AAEYGKYNIRVNVIAPGVVDTPLTRQIKSD 205
                                   ************************999876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1   2.9e-16   6.5e-13       4     156 ..      15     168 ..      13     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2.9e-16
                                   EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---E CS
                            KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikG 84 
                                   ++ G+  g+G+++a++  e g +  v+ls     +e  k+l ++l+++g ev+ +++D++d ++v++l++   +  +++  
  gi|70607846|ref|YP_256716.1|  15 VVLGASSGIGKAIAEMFSEMGGK--VVLSDI--DEEGLKRLSDSLRSRGHEVNHMKCDITDLNQVKKLVNFSLSVYGNVDA 91 
                                   799****************9988..456666..67888889********************************999***** PP

                                   EEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                            KR  85 vihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaaNafl 156
                                    + +  +   k +e+ t ed+e+v++  +kG   + + + +     +    +vlfSSi g++ ++gq+ Ya + a +
  gi|70607846|ref|YP_256716.1|  92 LYVTPSINVRKSIENYTYEDFEKVINVNLKGNFMVVKEFLSvmknnKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGI 168
                                   *******************************87665544443544577889********************987765 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-07   0.00043      94     201 ..      91     195 ..      58     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-07
                       DUF1776  94 gvilvPslsyptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssal 174
                                   ++ ++Ps +   + ie+ + + +++++n +l   +++++++l+ +++ + +    +v+  si   +  p +++ a++   +
  gi|70607846|ref|YP_256716.1|  91 ALYVTPSINVRKS-IENYTYEDFEKVINVNLKGNFMVVKEFLSVMKN-N-KGGGSVVLFSSIRGTVVEPGQSVYAMTKAGI 168
                                   6668899999999.********************************8.4.44555566679******************** PP

                       DUF1776 175 salfevLkrelrphnidvtqikLGnld 201
                                    +l++v ++e++++ni v  i  G +d
  gi|70607846|ref|YP_256716.1| 169 IQLAKVAAAEYGKYNIRVNVIAPGVVD 195
                                   ******************999888766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.7e-07    0.0006       3      86 ..      15      98 ..      13     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.7e-07
                                  EEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE CS
                       3HCDH_N  3 aviGa.GtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlviE 84
                                   v+Ga   +G+ ia++f + g +Vvl di+ee l++  ++++++ ++ v++ k++  + +++ + ++f+ ++   vda +v  
  gi|70607846|ref|YP_256716.1| 15 VVLGAsSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGHE-VNHMKCDITDLNQVKKLVNFSLSVYGNVDALYVTP 96
                                  577874459*********************************96655.577888899999*******9999998888888765 PP

                                  -S CS
                       3HCDH_N 85 av 86
                                  ++
  gi|70607846|ref|YP_256716.1| 97 SI 98
                                  55 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06    0.0027       1      70 [.      16      84 ..      16     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                  EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70
                                  vL +  G G+ ++++  ++g +kv+  Di+ee l++    ++++g +v+ +++d++dl++ ++ +++ +s
  gi|70607846|ref|YP_256716.1| 16 VLGASSGIGKAIAEMFSEMG-GKVVLSDIDEEGLKRLSDSLRSRGHEVNHMKCDITDLNQVKKLVNFSLS 84
                                  56667899999988888887.*************************************987665555555 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   5.6e-06     0.013      33      73 ..       8      48 ..       4      54 .. 0.86
   2 ?   -1.3   0.0      0.52   1.2e+03      12      39 ..     157     184 ..     150     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.6e-06
                                  --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCH CS
                 THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkdl 73
                                  +++g ++vv+G+s+ +gk++a +++e +  V + +   + l
  gi|70607846|ref|YP_256716.1|  8 SVKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGL 48
                                  789***********************999998887766555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.52
                                   --SS--HHHHHHHHHHHHCT---TT-EE CS
                 THF_DHG_CYH_C  12 eeallpctpkgvvellketgielegkkv 39 
                                    + + + t +g+++l k +  e    ++
  gi|70607846|ref|YP_256716.1| 157 GQSVYAMTKAGIIQLAKVAAAEYGKYNI 184
                                   5667778888888888777666554444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   0.00013      0.29       2      61 ..      15      80 ..      14     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                  EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHH CS
                     Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfk 61
                                  +V+Ga+  iG+a+++ + e g +v+  d ++++ ++ +  d         + +++d+td +++++l++
  gi|70607846|ref|YP_256716.1| 15 VVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLS--DSlrsrghevNHMKCDITDLNQVKKLVN 80
                                  79*******************99888887744444333..333577888899*********9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1641.92
//
Query:       gi|70607847|ref|YP_256717.1|  [L=413]
Description: succinyl-diaminopimelate desuccinylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-37  127.8   0.0    2.3e-36  125.4   0.0    1.8  2  Peptidase_M20  Peptidase family M20/M25/M40
    9.1e-21   73.8   0.0    3.8e-20   71.8   0.0    2.0  2  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.035   13.8   0.0       0.26   11.0   0.0    2.0  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.093   5.6e+02     123     153 ..      26      55 ..      20      86 .. 0.76
   2 !  125.4   0.0   3.9e-40   2.3e-36       1     206 [.      89     406 ..      89     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.093
                                   EEESHEEECCHHHHHHHHHHHHHHHTSCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 123 eggapvtlndsplvkalaeaaeelfgekvel 153
                                     ++p+ ln +++v++l e++++l g+k+e 
  gi|70607847|ref|YP_256717.1|  26 PTENPPGLNYQKIVDKLDEILRDL-GYKTEI 55 
                                   56789999999************8.988443 PP

  == domain 2  score: 125.4 bits;  conditional E-value: 3.9e-40
                                   EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SS.EEEEEEESTTSSTT...T CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...x RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkg.tivllfqpdEEggr...g 76 
                                   ++++H+DvVp++  +gw+  p+s+ ++dGklyGrG++dmk g++a+++ ++ lk+++  p    +  +f+pdEE+ +   +
  gi|70607847|ref|YP_256717.1|  89 AFNGHYDVVPAG--SGWNVsPYSAVVKDGKLYGRGSADMKSGIIAGIYGVELLKRAKSFPSNlQVIQTFVPDEETVGnvnA 167
                                   689*******44..46****************************************987766799999******766699* PP

                                   HHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE......................................... CS
                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                 Peptidase_M20  77 Gakalle.gleerekvdavfelhieepgileagklaigvv......................................... 115
                                   Ga +l+e g+++r kvd+   ++  ep++++      +++                                         
  gi|70607847|ref|YP_256717.1| 168 GAHYLVEkGVLKRGKVDY---VIFTEPTGSD------NICyghrgaiwaivkiygkkshgglpqlgvdavkvsmkiiqely 239
                                   *******888899*****...55999****9......455668899*********************************** PP

                                   ..........................................................................EEEEEEE CS
                                   ..........................................................................xxxxxxx RF
                 Peptidase_M20 116 ..........................................................................kvevell 122
                                                                                                             k++++++
  gi|70607847|ref|YP_256717.1| 240 nsvpeivskyniipevskrpsvlvgtvrcgswmntvadycelsivrrlipeenldevrskiinviekvtmdfkaKYDYDEF 320
                                   *************************************************************************88****99 PP

                                   EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHH CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 123 eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifgpgs.glaHspnEyvdledlekgik 199
                                    + +  t++  +++++++++ ++e+ ++++ l+ s+ g+ d+rf   +gip++  +gpg  ++aH+ +Eyv+++d+ + ik
  gi|70607847|ref|YP_256717.1| 321 YSVETITSDvKNEIYEVMRRKIREVRQREPGLVLSP-GTFDMRFTvkEGIPSI-NYGPGRiEQAHATDEYVEIKDFFDSIK 399
                                   999999******************988789999999.*************988.69***66******************** PP

                                   HHHHHHH CS
                                   xxxxxxx RF
                 Peptidase_M20 200 vlarlle 206
                                   vl  +l+
  gi|70607847|ref|YP_256717.1| 400 VLSLTLL 406
                                   *998775 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.44   2.6e+03      85     107 ..      30      52 ..      23      54 .. 0.85
   2 !   71.8   0.0   6.4e-24   3.8e-20       1     104 [.     199     307 ..     199     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHHHHHHTSCCST CS
                     M20_dimer  85 lpgedpeevleeieeilekeape 107
                                   +pg + +++ +++ eil++++ +
  gi|70607847|ref|YP_256717.1|  30 PPGLNYQKIVDKLDEILRDLGYK 52 
                                   79999999********9998766 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 6.4e-24
                                   SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC..........TCCTCCCCCEECCE-CCCCEESSEE CS
                     M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.....eerslprttlnvtgiegGsaknvipdea 76 
                                   +gh+G++++ +++ gk+ H+g p+ g++A++  +++++el +   +i       ++ ++r+++ v+++++Gs+ n+++d++
  gi|70607847|ref|YP_256717.1| 199 YGHRGAIWAIVKIYGKKSHGGLPQLGVDAVKVSMKIIQELYNSVPEIVskyniIPEVSKRPSVLVGTVRCGSWMNTVADYC 279
                                   79**************************************99965555********************************* PP

                                   EEEEEEEHHHHHHHHHHHHHHHHHHTSC CS
                     M20_dimer  77 eakidiRllpgedpeevleeieeileke 104
                                   e++i +Rl p+e+++ev+ +i +++ek+
  gi|70607847|ref|YP_256717.1| 280 ELSIVRRLIPEENLDEVRSKIINVIEKV 307
                                   *************************997 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.3e-05      0.26       3     101 ..      78     193 ..      76     215 .. 0.82
   2 ?    0.3   0.0     0.079   4.7e+02     112     179 ..     327     395 ..     306     404 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                                   EEEESTTCESEEEEEEEE--B-TTT.............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCS.SEEEEEEEE CS
                 Peptidase_M28   3 iatlegkatdevlllgAHyDsvgvg.............rgp.ifvGAdDnAsgvaalLelarvlaasgsrp.krgvrflff 68 
                                   ++ + g+   + +++++HyD v+ g             +g+    G  D  sg+ a ++ +++l++ +s p + +v+  f+
  gi|70607847|ref|YP_256717.1|  78 VGYI-GNG-GTKIAFNGHYDVVPAGsgwnvspysavvkDGKlYGRGSADMKSGIIAGIYGVELLKRAKSFPsNLQVIQTFV 156
                                   5555.333.46799**********9*****999999886667778********************9776678999****** PP

                                   SSCSG...SSHHHHHHHHHHC..CCTTEEEEEEECS-S CS
                 Peptidase_M28  69 daEEa...gllGSkafakakp..elkkiaavlnlDmvg 101
                                     EE       G++++++ k   ++ k+++v+  + +g
  gi|70607847|ref|YP_256717.1| 157 PDEETvgnVNAGAHYLVE-KGvlKRGKVDYVIFTEPTG 193
                                   *****998999******4.3346777777776665555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.079
                                   HHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE.....CTSSS-TTTTSTTSSG CS
                 Peptidase_M28 112 gdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl.....aetgfpevyHtprDtl 179
                                   +++ ++e+ + +++ +++v +    +p     ++g+ D +  +k+g+p +++     ++  +++ y   +D +
  gi|70607847|ref|YP_256717.1| 327 TSDVKNEIYEVMRRKIREVRQR---EPGLV-LSPGTFDMRFTVKEGIPSINYgpgriEQAHATDEYVEIKDFF 395
                                   3344444444444444444333...33332.2688899************99777765555555565555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2639.55
//
Query:       gi|70607848|ref|YP_256718.1|  [L=407]
Description: allantoate amidohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-32  113.3   0.0    1.5e-32  112.9   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    4.2e-07   29.9   0.0    7.7e-07   29.0   0.0    1.4  1  Peptidase_M28  Peptidase family M28
    5.8e-06   26.2   0.0    1.2e-05   25.2   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
     0.0042   16.1   0.1       0.95    8.4   0.1    2.5  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   3.5e-36   1.5e-32       1     206 [.      74     401 ..      74     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 3.5e-36
                                   EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.....T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.....g 76 
                                   ++gsH+D+Vp     g           Gk++G       +gv+a+le+lr l+++g+++++ti l+ +++EEg+r     +
  gi|70607848|ref|YP_256718.1|  74 AIGSHMDSVP----YG-----------GKYDGF------YGVMAGLEILRGLREHGVRTNHTISLIDFTNEEGSRfkpslM 133
                                   589*******....77...........999999......*********************************999999998 PP

                                   HHHHHHHHHH.T................................TTCESEEEEEEEESSSBTCHSTETEEEE......... CS
                                   xxxxxxxxxx.x................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                 Peptidase_M20  77 Gakallegle.e................................rekvdavfelhieepgileagklaigvv......... 115
                                   G++  ++ ++ +                                 +k+++++elhie++++le+++ +ig+          
  gi|70607848|ref|YP_256718.1| 134 GSGLTTG-VFnReyvysivdkdgitfekalersgflgnesnriiHDKPKFYLELHIEQGPVLEEEGYQIGIPlgivgltvc 213
                                   8866666.443457777788888888899999************99*****************9996666668899***** PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M20 116 ................................................................................. 115
                                                                                                                    
  gi|70607848|ref|YP_256718.1| 214 efkfkgqssqagptpmdrrrdalvgaskfitnirdyarrtsdlratvgivnlkpniynaipgevtltldlrsiekedrera 294
                                   ********************************************************************************* PP

                                   ...............EEEEEEE..EEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTT.EEEEEEESS CS
                                   ...............xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                 Peptidase_M20 116 ...............kvevell..eggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarffagi.ptvmifgpg 178
                                                  k eve+   + ++ v+++ +++v ++++a+ +l g+k+++  s  +g+da+++ ++    mif p+
  gi|70607848|ref|YP_256718.1| 295 lreakrlaeeiadqeKLEVEEKhlWTAEQVKFD-KEVVSVIEKACNQL-GLKYKFLYSW-AGHDAQYMTRVsRVGMIFIPS 372
                                   **************9455554444999999999.*************9.**********.********9995566****** PP

                                   G.GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                   x.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 179 s.glaHspnEyvdledlekgikvlarlle 206
                                     g++Hs +Ey +++d+++g++vla+++e
  gi|70607848|ref|YP_256718.1| 373 HlGISHSKEEYSSDRDMVNGLRVLAKTVE 401
                                   88***********************9986 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   1.7e-10   7.7e-07       1      78 [.      60     135 ..      60     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.7e-10
                                   EEEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSG.....SSH CS
                 Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEa.....gll 76 
                                   N+ia + g++ +  +++g+H+Dsv++       G  D   gv+a Le++r l + g r ++++ ++ f+ EE      +l+
  gi|70607848|ref|YP_256718.1|  60 NIIANIAGEK-EDKIAIGSHMDSVPY---G---GKYDGFYGVMAGLEILRGLREHGVRTNHTISLIDFTNEEGsrfkpSLM 133
                                   9********9.899***********9...3...568********************9***************988888888 PP

                                   HH CS
                 Peptidase_M28  77 GS 78 
                                   GS
  gi|70607848|ref|YP_256718.1| 134 GS 135
                                   87 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.6e-09   1.2e-05       4     107 ..     208     308 ..     205     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.6e-09
                                   -EEEEEEEEEE-B-EEGG.-T.TTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C.CCCEESSEEEEEEE CS
                     M20_dimer   4 kGlaggkitvkgkagHsg.ap.gagaNAieklarllaeledeegdiaeerslprttlnvtgiegGs.aknvipdeaeakid 81 
                                    Gl  ++ ++kg++  +g  p ++ ++A+  ++++++ ++d  ++      ++    +v++++      n+ip+e+++++d
  gi|70607848|ref|YP_256718.1| 208 VGLTVCEFKFKGQSSQAGpTPmDRRRDALVGASKFITNIRDYARR------TSDLRATVGIVNLKPnIYNAIPGEVTLTLD 282
                                   577778899*********855255667***************655......6788888888888776889*********** PP

                                   EEHHHHHHHHHHHHHHHHHHTSCCST CS
                     M20_dimer  82 iRllpgedpeevleeieeilekeape 107
                                   +R   +ed+e++l e + ++e+ a +
  gi|70607848|ref|YP_256718.1| 283 LRSIEKEDRERALREAKRLAEEIADQ 308
                                   *******************9998865 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00021      0.95       1      25 [.      59      82 ..      59      84 .. 0.95
   2 !    5.2   0.0    0.0021       9.3     220     288 ..     325     391 ..     317     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00021
                                  S-EEEEEESSTTSSEEEEEEE--B- CS
                 Peptidase_M42  1 GnliakkkgkekepkvmiaAHmDei 25
                                  Gn+ia++ g eke k++i +HmD +
  gi|70607848|ref|YP_256718.1| 59 GNIIANIAG-EKEDKIAIGSHMDSV 82
                                  9********.999**********87 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0021
                                   CSHHHHHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHH CS
                 Peptidase_M42 220 iyhpklrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddlea 288
                                    +++++++ +++++++ +++y++ ++s  g DA+ +++  + v  + i   +  +Hs+ e  + +d+ +
  gi|70607848|ref|YP_256718.1| 325 KFDKEVVSVIEKACNQLGLKYKF-LYSWAGHDAQYMTRV-SRVGMIFIPSHLGISHSKEEYSSDRDMVN 391
                                   578999*****************.*********999887.55666666666778999999888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.38s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2099.72
//
Query:       gi|70607849|ref|YP_256719.1|  [L=376]
Description: hypothetical protein Saci_2133 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-27   96.0  46.6      2e-27   96.0  46.6    1.3  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        3.3    7.7   4.7       0.74    9.8   0.3    2.2  2  DUF5472   Family of unknown function (DUF5472)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0  46.6   2.3e-31     2e-27       4     353 .]      14     338 ..       9     338 .. 0.85
   2 ?   -4.6   1.0       0.9     8e+03     237     247 ..     350     361 ..     341     373 .. 0.37

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 2.3e-31
                         MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fas 83 
                                   +++l+ l+++++++ ++ +l   l+++p e+g++++ +++g++++s+p+G ++d++G+ + + ++ ++++   l+l+ f  
  gi|70607849|ref|YP_256719.1|  14 MQLLIRLSWGVIALPIS-IL---LNLNPVEVGFVASSFYIGYILFSIPWGLIIDKIGPNKAMATSSAILVPLNLILFlFLR 90 
                                   55666666666544444.55...8888*********************************************555554745 PP

                         MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                   s+ l+++  ++ G+ a+++fp+++ +ia  +++ ++ ++++++l ++  + ++l  ++++++++s  W  +f+++a+ + +
  gi|70607849|ref|YP_256719.1|  91 SYVLIVIIYLMEGIIASSIFPSAMKIIAITYAGsSHLTFYVAILESAGPITILLLGAVSSFILDS--WKFLFLFFAVGFSV 169
                                   5559************************999999*****************************76..99999999999999 PP

                         MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsgll 244
                                   +++     l  + + +++++++++          + ++ l++++ +++ li l    ++++g++t+++++l+  ++++ + 
  gi|70607849|ref|YP_256719.1| 170 LCL-----LSLKLKVNSKSTEVKR----------S-FSVLFNKKIILATLIRLGE-LWATWGTTTWIFSMLVVYRDIP-VT 232
                                   844.....4555555555555555..........4.999*****66522222222.448888****************.89 PP

                         MFS_1 245 laglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllala 325
                                   l++ +l l++l+ +i+ l +  l+  +g ++ +l++l++++l++l+++++ ++    l+++  +l+G++++ ++p+  +++
  gi|70607849|ref|YP_256719.1| 233 LSASFLFLFGLGQLIGILSVESLVAVMGDKNVILINLIGFILVTLLIIITFNP---YLVVAEAFLLGVFSFSYRPPTDSII 310
                                   9999999999999999999**********************************...5556678889**9999********* PP

                         MFS_1 326 sdlappeeagtasglfntagslggalgp 353
                                   ++  ++++agt +g++n +++lg++++p
  gi|70607849|ref|YP_256719.1| 311 MKIGGESRAGTSIGFANAVSQLGTMIAP 338
                                   **************************98 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 0.9
                         MFS_1 237 vlgls..glllag 247
                                    + +s  + l +g
  gi|70607849|ref|YP_256719.1| 350 SFAFSmfA-LDLG 361
                                   33333211.2222 PP

>> DUF5472  Family of unknown function (DUF5472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   8.2e-05      0.74      11      36 ..     154     179 ..     151     196 .. 0.85
   2 ?   -4.2   0.5       1.9   1.7e+04      12      23 ..     217     224 ..     212     226 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.2e-05
                       DUF5472  11 dtwlflwlftafvvavlgllllhyra 36 
                                   d+w fl+lf a   +vl ll l+ + 
  gi|70607849|ref|YP_256719.1| 154 DSWKFLFLFFAVGFSVLCLLSLKLKV 179
                                   89******************998765 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 1.9
                       DUF5472  12 twlflwlftafv 23 
                                   t    w+f+ +v
  gi|70607849|ref|YP_256719.1| 217 T----WIFSMLV 224
                                   4....5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2689.60
//
Query:       gi|70607850|ref|YP_256720.1|  [L=305]
Description: arginase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-78  261.6   0.0    1.1e-77  261.3   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   0.0     6e-82   1.1e-77       3     276 ..      32     296 ..      30     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 6e-82
                                   EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE..SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHH CS
                      Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgv..leelkivdlgdvavtpvdneevleqieeavaeilk 81 
                                   +a+lG+Pfd a+++r+GarfGP a+r++s+ l++   yn+ l++  +++l+ +dlgdv++ p+  e++++ ie+ v++i++
  gi|70607850|ref|YP_256720.1|  32 AAFLGIPFDDAVTYRTGARFGPMAVRQGSRLLRP---YNQFLDTypFDKLNACDLGDVNIIPGYIEDTIKIIEKDVYDIIS 109
                                   799******************************9...788888889*********************************** PP

                                   TTC.EEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STC CS
                      Arginase  82 agk.lpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvd 161
                                   ++k +p + GGDHsi+l+ilra++++yg ++ +ih+D+H+D+++++  g++++hG+++rra+eegllk  +++q+Gir+ +
  gi|70607850|ref|YP_256720.1| 110 SKKlVPFIAGGDHSITLPILRAMHKQYG-KINLIHLDSHYDFWDTY-WGKKYTHGSWLRRALEEGLLK--DVIQAGIRAST 186
                                   966257999******************9.5****************.79******************7..********988 PP

                                   SH..HHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHH CS
                      Arginase 162 ne..eyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallre 240
                                    +  +  +  +lgi+ +t+re++  + k++++ei++      +p+y+S+DiDv+Dpa+aPGtGtpe+gGl++ e+++++r+
  gi|70607850|ref|YP_256720.1| 187 FSkeDLSDKVKLGIKSFTIRELKL-NPKDILKEIESLK----GPTYVSLDIDVVDPAFAPGTGTPEVGGLSSFEIIEFIRQ 262
                                   87546655588***********75.6767888876555....5************************************** PP

                                   HHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHH CS
                      Arginase 241 laeklnlvgaDvvEvnPaldteaeqtarlaarlvre 276
                                    +   +lvg+DvvEv+P++d  +e+t++laa++++e
  gi|70607850|ref|YP_256720.1| 263 WRF-DKLVGFDVVEVSPPYDV-SEITSMLAANIIYE 296
                                   *99.99***************.67**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2089.75
//
Query:       gi|70607851|ref|YP_256721.1|  [L=265]
Description: DNA repair ATPase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-05   23.9  13.7    0.00017   21.7  13.3    2.1  1  DUF1640         Protein of unknown function (DUF1640)
    0.00036   20.4   9.0    0.00036   20.4   9.0    2.0  2  FAM184          Family with sequence similarity 184, A and B
     0.0011   19.1   2.6     0.0024   18.0   2.6    1.7  1  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
     0.0038   16.6   8.5     0.0073   15.7   8.5    1.4  1  IMD             IRSp53/MIM homology domain
     0.0068   16.3   1.3      0.012   15.4   1.3    1.4  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0072   16.6  13.8      0.025   14.9   9.7    3.2  1  Tup_N           Tup N-terminal
     0.0085   14.1   7.1      0.012   13.7   7.1    1.1  1  Prominin        Prominin
  ------ inclusion threshold ------
       0.01   15.9   2.1      0.026   14.6   2.1    1.8  1  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.017   15.2   1.4      0.047   13.7   1.2    1.8  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.028   14.8  10.7      0.023   15.0   8.4    2.1  2  OmpH            Outer membrane protein (OmpH-like)
      0.063   13.6   3.1       0.58   10.5   0.8    2.9  3  Synapsin        Synapsin, N-terminal domain
       0.12   12.1   1.2       0.26   11.1   1.2    1.5  1  Lectin_N        Hepatic lectin, N-terminal domain
       0.12   12.1   0.4        0.3   10.9   0.4    1.6  1  MCPsignal       Methyl-accepting chemotaxis protein (MCP) sig
       0.13   12.9   5.5       0.19   12.4   4.6    1.7  1  AATF-Che1       Apoptosis antagonizing transcription factor
       0.13   12.9   0.6       0.77   10.4   0.6    2.2  1  DUF883          Bacterial protein of unknown function (DUF883
       0.16   12.1  17.3       0.23   11.5  12.7    2.7  2  SPATA1_C        Spermatogenesis-associated C-terminus
       0.24   11.2   4.9        0.4   10.4   4.9    1.4  1  AAA_11          AAA domain
       0.27   11.3  13.2       0.13   12.3   4.3    2.7  2  DUF1664         Protein of unknown function (DUF1664)
       0.27   10.6   6.9       0.44    9.9   6.9    1.3  1  FAM76           FAM76 protein
        0.3   11.2   4.7       0.57   10.3   0.5    3.1  3  Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
       0.31   11.7  10.9       0.21   12.2   1.9    2.9  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.39   10.8   9.0        5.8    7.1   0.0    4.6  4  APC_N_CC        Coiled-coil N-terminus of APC, dimerisation d
       0.44    9.7  13.8       0.68    9.1   4.7    2.2  2  DLP_helical     Dynamin-like helical domain
       0.76    9.8  11.9        1.3    9.0  11.0    1.9  1  Rootletin       Ciliary rootlet component, centrosome cohesio
       0.77   10.3  10.6        1.5    9.4   8.8    2.4  2  DUF2408         Protein of unknown function (DUF2408)
       0.92    9.5  11.0        1.8    8.6   0.7    3.6  4  Sec2p           GDP/GTP exchange factor Sec2p
        1.1    9.1  13.6        3.5    7.5   2.1    3.8  3  DUF919          Nucleopolyhedrovirus protein of unknown funct
        1.3    9.4  11.1         19    5.7   0.7    3.9  2  MutS_IV         MutS family domain IV
        1.4    8.5   8.0        3.5    7.2   2.2    2.7  3  Fzo_mitofusin   fzo-like conserved region
        2.9    8.2   9.7         14    6.0   1.2    3.4  2  Rx_N            Rx N-terminal domain
        3.4    8.1   9.5        2.8    8.4   7.2    2.1  2  DUF1690         Protein of Unknown function (DUF1690)
          5    7.4  11.1        8.3    6.7  10.1    2.1  1  zf-C4H2         Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7  13.3   3.1e-07   0.00017      55     157 ..      64     158 ..      52     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.1e-07
                       DUF1640  55 qkaalselrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgrireelakleakiqelnnki 135
                                   +  +l +lr+e+  +++     + se  kl++e++ +++++++ei kl+++    +n+ +++   e  kl++++++ +++i
  gi|70607851|ref|YP_256721.1|  64 IHEELVKLRQEMNDMRK----DFNSEIIKLRQEMNDMRKDFNSEIIKLRQE----MNDMRKDFNSEIIKLRQEMNDNYKQI 136
                                   44556667777766654....355688899999999999999999999988....99999999999999999999999999 PP

                       DUF1640 136 drevsalrteiEsvKldvikyl 157
                                    r v++l t+iE      +++l
  gi|70607851|ref|YP_256721.1| 137 ARFVENLTTSIEDDAQYYLQWL 158
                                   9999999999996655566665 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   9.0   6.4e-07   0.00036      88     177 ..      59     154 ..       9     177 .. 0.79
   2 ?   -2.8   0.0       7.7   4.3e+03     115     126 ..     210     221 ..     197     249 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-07
                        FAM184  88 lkleaehsqkvvelsreveevkrkFeeklrqfaqlqeqleqekeka.......LeelrkkhreeveeLlkeqeaqsekllk 161
                                   +k ++ h + +v+l +e+++++++F+  + ++ q ++ + ++ ++        ++++rk ++ e+ +L++e +++++++++
  gi|70607851|ref|YP_256721.1|  59 IKFNKIH-EELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEiiklrqeMNDMRKDFNSEIIKLRQEMNDNYKQIAR 138
                                   5555555.4578899999999999999999999999999976665556666668999999999999999999999999999 PP

                        FAM184 162 eqekleekhkaevekl 177
                                     e+l+  ++++ + +
  gi|70607851|ref|YP_256721.1| 139 FVENLTTSIEDDAQYY 154
                                   9998887777776654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.7
                        FAM184 115 klrqfaqlqeql 126
                                   k+++++ ++ +l
  gi|70607851|ref|YP_256721.1| 210 KVEKLKTVKPEL 221
                                   222222222222 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.6   4.2e-06    0.0024      54     129 ..      62     137 ..      15     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-06
                     ApoLp-III  54 deleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakeklakaikqay 129
                                   +++ e l  ++++++ +++++++e   + ++++++++ + s + +l +e + + +++++++ +  +++++  kq+ 
  gi|70607851|ref|YP_256721.1|  62 NKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIA 137
                                   4667777889***************************************************************986 PP

>> IMD  IRSp53/MIM homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   8.5   1.3e-05    0.0073      40     164 ..      17     143 ..      14     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           IMD  40 lqKiaelAlnsrgskelGsvLvrmaerhRsieskLeelvkalhdsLl..npleekveedkkvlnqldkdyakEykkkrael 118
                                   +q+iae+ l++   k+l +       + R i+ +L  + + l ++ +  n++ e++ + ++ +n+++kd++ E  k r+e+
  gi|70607851|ref|YP_256721.1|  17 IQRIAEVVLETVVVKKLDEF----ERQSRFINDNLVLIWEKLAENDIkfNKIHEELVKLRQEMNDMRKDFNSEIIKLRQEM 93 
                                   67777777777777766553....456799999999999999877553389999999999*************97777776 PP

                                   H...H.HHHHHHHHHTTHCCCS-CHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           IMD 119 k...K.kssellklqkKakkgkddlkvqldelledvndkyllleetvkea 164
                                   +   K  +se++kl++  +  ++d + ++ +l +++nd y ++  +v++ 
  gi|70607851|ref|YP_256721.1|  94 NdmrKdFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENL 143
                                   411142479***********************************999864 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.3   2.2e-05     0.012      29     110 ..      62     149 ..      46     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHHHH...HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHH...HHHHCHHCCHHCHCCHCHH CS
                Apolipoprotein  29 drlskeleelrarl...raeleevrarlepyrdevqeqlgqnleelrqrlapyteelre...rlaadaeelqeqlavyaee 103
                                   +++ +el +lr+++   r++ ++   +l + ++++++ +++++ +lrq+++   ++ +    +l++++++  +q+a   e+
  gi|70607851|ref|YP_256721.1|  62 NKIHEELVKLRQEMndmRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSeiiKLRQEMNDNYKQIARFVEN 142
                                   456677777777777777777777777777777777777777777777776666666666777777777777777777777 PP

                                   HHHHHHH CS
                Apolipoprotein 104 lrerler 110
                                   l +++e+
  gi|70607851|ref|YP_256721.1| 143 LTTSIED 149
                                   6666654 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   9.7   4.4e-05     0.025       8      74 ..      63     130 ..      61     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-05
                         Tup_N   8 avkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirq....tlyeLeeahrkikqqYEeeiarLkaeLe 74 
                                    + +E  +l qe++ ++   +++++ i +  qE++ +r+    ++  L ++ +++++ ++ ei +L++e++
  gi|70607851|ref|YP_256721.1|  63 KIHEELVKLRQEMNDMR---KDFNSEIIKLRQEMNDMRKdfnsEIIKLRQEMNDMRKDFNSEIIKLRQEMN 130
                                   46666667777776665...788888888889999998733335789**********************87 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   7.1   2.1e-05     0.012     621     741 ..      42     161 ..       6     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                      Prominin 621 ltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlp...lessvkklkksvk.kldeensdlqesikkl 697
                                   +++ nl  + ekl e   ++    ++++++l +  q+++++ ++++ +   l++++++++k  + ++ +  +++++  k++
  gi|70607851|ref|YP_256721.1|  42 FINDNLVLIWEKLAENDIKF----NKIHEELVKLRQEMNDMRKDFNSEiikLRQEMNDMRKDFNsEIIKLRQEMNDMRKDF 118
                                   44445555555554444444....456666666666666666655555111556666665555424555788888888999 PP

                      Prominin 698 laaveraenflkkngseiinneskklldrileqfeeYidwviee 741
                                    +++ ++ +++++n ++ i+   ++l+++i+   + Y++w ie+
  gi|70607851|ref|YP_256721.1| 119 NSEIIKLRQEMNDNYKQ-IARFVENLTTSIEDDAQYYLQWLIEK 161
                                   999**********9998.577899****************9875 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.1   4.7e-05     0.026      15     106 ..      52     144 ..      43     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-05
                    TPR_MLP1_2  15 eekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqa.lreelnelkaeiaelkaeaesakaeleeseesw 94 
                                   e+ +e + k++k+ e+l k +++++++ +++ +e++k  ++++++++ +++e+ +l++e+++++++ +s   +l ++ +  
  gi|70607851|ref|YP_256721.1|  52 EKLAENDIKFNKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKdFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDN 132
                                   56778888999**************************99999998754899999999999999999998888888888877 PP

                    TPR_MLP1_2  95 eeqkeelekels 106
                                    +q  ++ ++l+
  gi|70607851|ref|YP_256721.1| 133 YKQIARFVENLT 144
                                   777666666654 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0062       3.5      47      95 ..      61     112 ..      34     115 .. 0.63
   2 ?   13.7   1.2   8.5e-05     0.047      25     101 ..      71     147 ..      60     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0062
                  Baculo_PEP_C  47 Lnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                                   +n++ e+l +l +e+++   ++++ + +L + +n + +++++e+  l ++++
  gi|70607851|ref|YP_256721.1|  61 FNKIHEELVKLRQEMNDmrkDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMN 112
                                   4444444444333332222277777777777777777777777766666655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.5e-05
                  Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssv 101
                                   +r     +  + ++ + ++ +++n++ +d++s + +l+++++++ +  ++ + +l ++++ + + +   + nL++s+
  gi|70607851|ref|YP_256721.1|  71 LRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENLTTSI 147
                                   555555566666777778999999999999999999999**********************************9998 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   8.4   4.2e-05     0.023      12      80 ..      70     137 ..      52     165 .. 0.45
   2 ?   -1.5   0.0       5.3     3e+03      90     114 ..     207     230 ..     193     260 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.2e-05
                                   HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH CS
                          OmpH  12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka 80 
                                   +  +e++++++++++++ kl++e+++++k++++++ +l ++++++ +++   e+ k++qe++++++q a
  gi|70607851|ref|YP_256721.1|  70 KLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDM-RKDFNSEIIKLRQEMNDNYKQIA 137
                                   222333333333333333444444444444444444443333333.33333333333333333333322 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                                   HHHHHHHHHHHHHHHHHHHTT-SEE CS
                          OmpH  90 llkpildkinkaikevakekgydlv 114
                                   l+++ ++k++++  e+ k+k++ lv
  gi|70607851|ref|YP_256721.1| 207 LMRK-VEKLKTVKPELFKDKKVILV 230
                                   3332.34444444444444444444 PP

>> Synapsin  Synapsin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.087        49      67      95 ..      63      90 ..      21      91 .. 0.82
   2 ?   10.5   0.8     0.001      0.58      56      94 ..      88     125 ..      65     129 .. 0.57
   3 ?   -1.9   0.0       7.6   4.3e+03      46      56 ..     198     208 ..     157     231 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.087
                      Synapsin 67 sfkpdfvlvrqhvrdaagedyrslllglk 95
                                  + + + v +rq+++d  ++d++s +++l+
  gi|70607851|ref|YP_256721.1| 63 KIHEELVKLRQEMND-MRKDFNSEIIKLR 90
                                  445788999******.9********9985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                      Synapsin  56 kvsrngtkvvrsfkpdfvlvrqhvrdaagedyrslllgl 94 
                                   k +++ + +++ f+ +++ +rq+++d  ++d++s +++l
  gi|70607851|ref|YP_256721.1|  88 KLRQEMNDMRKDFNSEIIKLRQEMND-MRKDFNSEIIKL 125
                                   22233344455566666666666666.666666666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.6
                      Synapsin  46 ysdkglvvdlk 56 
                                    ++k++ ++l+
  gi|70607851|ref|YP_256721.1| 198 RANKSVYMELM 208
                                   33333333333 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   0.00046      0.26      51     116 ..      62     127 ..      58     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                      Lectin_N  51 sqLqreLetLketfsnfssstlaeiqalssqggslsekvtsleaklekkqqdlkadhselllhvkq 116
                                    ++ +eL+ L+++++++ ++ ++ei +l+ + +++ +  +s   kl+++ +d+++d  + +++++q
  gi|70607851|ref|YP_256721.1|  62 NKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQ 127
                                   57899************************************************9998666666655 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00053       0.3      71     160 ..      62     149 ..      55     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00053
                                   HHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHH.HHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  71 aVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgeal.keiveavaevadlvqeiaaa 150
                                     + +E  kL ++  +  k+ ++ ii++ +e+nd  + +++   +  + +   ++ ++++ +ei +  +e++d  ++ia+ 
  gi|70607851|ref|YP_256721.1|  62 NKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEM---NDMRKDFnSEIIKLRQEMNDNYKQIARF 139
                                   556789999************************99988877666655544...4444444157888888888888888888 PP

                                   HHHHHHHHHH CS
                     MCPsignal 151 seeqsasiee 160
                                   +e++++sie+
  gi|70607851|ref|YP_256721.1| 140 VENLTTSIED 149
                                   8888888775 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.6   0.00034      0.19      13      90 ..      49     130 ..      45     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00034
                     AATF-Che1  13 klwDslLelRIklQkaltaanqLp..qpetlkefles....seefeealeeaekalkklleslleLreelleqneikklae 87 
                                    +w++l e  Ik+ k+     +L   +++++k+f ++     +e++++ +++ +++ kl +++ ++r+++  ++ei kl++
  gi|70607851|ref|YP_256721.1|  49 LIWEKLAENDIKFNKIHEELVKLRqeMNDMRKDFNSEiiklRQEMNDMRKDFNSEIIKLRQEMNDMRKDF--NSEIIKLRQ 127
                                   69*******************9996666677777555666655666666666666666666666666666..333444433 PP

                     AATF-Che1  88 ske 90 
                                   + +
  gi|70607851|ref|YP_256721.1| 128 EMN 130
                                   322 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6    0.0014      0.77       3      66 ..      78     141 ..      62     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                        DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaad 66 
                                   ++++++s + +l++ +++  ++ ++e+ +lR++++++ ++  +++ ++++++ ++ k++a+ ++
  gi|70607851|ref|YP_256721.1|  78 MRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVE 141
                                   5566666666666667777778888999999999999999999999999999999999987655 PP

>> SPATA1_C  Spermatogenesis-associated C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  12.7    0.0004      0.23      66     150 ..      44     131 ..      31     133 .. 0.59
   2 ?    1.2   0.4      0.64   3.6e+02      62      82 ..     122     142 ..     118     229 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                      SPATA1_C  66 rqelellykkllaqlkardnkkkek.nvakse.e.lkneliiqiiaaqheidelkrkledakmklvaElk.lRkqaaeelk 142
                                     +l l+++kl  +   + nk +e+  + ++e + +  +   +ii++++e++++++  +   +kl++E++ +Rk  ++e+ 
  gi|70607851|ref|YP_256721.1|  44 NDNLVLIWEKLAEND-IKFNKIHEElVKLRQEmNdMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNdMRKDFNSEII 123
                                   555555555553322.22222222202222222136666777788888888888888888888888888547888888888 PP

                      SPATA1_C 143 aLraelsq 150
                                   +Lr+e+++
  gi|70607851|ref|YP_256721.1| 124 KLRQEMND 131
                                   88888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.64
                      SPATA1_C  62 lkkLrqelellykkllaqlka 82 
                                   + kLrqe++  yk++   ++ 
  gi|70607851|ref|YP_256721.1| 122 IIKLRQEMNDNYKQIARFVEN 142
                                   556677777666666555544 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.9   0.00072       0.4     110     196 ..      66     151 ..      10     153 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00072
                        AAA_11 110 eekvekrlekeekaqlakeiskeleklakelrafeeeeek..eklkkskekskskleqerrklkkerkelskeleeaeesl 188
                                   ee v+ r+e    +++ k+ ++e+ kl++e+++  +++++   kl++++++ +++ + e  kl++e +++ k++ ++ e+l
  gi|70607851|ref|YP_256721.1|  66 EELVKLRQE---MNDMRKDFNSEIIKLRQEMNDMRKDFNSeiIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENL 143
                                   222222222...345555555555555555555555555544466777777777777788888888888888888777777 PP

                        AAA_11 189 eeevldea 196
                                   ++++ d+a
  gi|70607851|ref|YP_256721.1| 144 TTSIEDDA 151
                                   77777766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4    0.0072       4.1      62     121 ..      14      79 ..       3      82 .. 0.81
   2 ?   12.3   4.3   0.00023      0.13      36     118 ..      72     148 ..      68     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0072
                       DUF1664  62 rhLssridr......vdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   r++ +ri++      v kklde ++ s+ i++++  + e+l+e + ++++++e   +l ++++++ 
  gi|70607851|ref|YP_256721.1|  14 REFIQRIAEvvletvVVKKLDEFERQSRFINDNLVLIWEKLAENDIKFNKIHEELVKLRQEMNDMR 79 
                                   5677777662222224699****************************************9999885 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
                       DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   ++ ++d  ++  +++ ++ +++++ +++++s+i ++ ++++   ++ k+ ++e+ ++r++   ++++ +++ + ve+l ++
  gi|70607851|ref|YP_256721.1|  72 RQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMN---DMRKDFNSEIIKLRQE---MNDNYKQIARFVENLTTS 146
                                   7899999999***********************99987655...5667888888888865...456777777778877777 PP

                       DUF1664 117 le 118
                                   +e
  gi|70607851|ref|YP_256721.1| 147 IE 148
                                   65 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.9   0.00078      0.44     214     295 ..      54     139 ..      10     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00078
                         FAM76 214 ssdhlvavtqLkeeiaslkkqle..qkd..qellekdkkitelkaellekekelreklkelekeakekieklekkirellk 290
                                     ++ ++ ++++ee+ +l+++++  +kd  +e+++  +++ +++ +  ++  +lr+ +++++k+++++i kl++++++  k
  gi|70607851|ref|YP_256721.1|  54 LAENDIKFNKIHEELVKLRQEMNdmRKDfnSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYK 134
                                   456667888888898888888863346532579999999999999999999999999999999999999999999999999 PP

                         FAM76 291 evael 295
                                   ++a+ 
  gi|70607851|ref|YP_256721.1| 135 QIARF 139
                                   98875 PP

>> Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5     0.001      0.57      33      75 ..      43      85 ..      22      88 .. 0.80
   2 ?    1.0   0.1      0.82   4.6e+02      47      72 ..      92     118 ..      86     124 .. 0.63
   3 ?   -2.4   0.0       9.2   5.2e+03       6      25 ..     233     252 ..     232     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                Myb_DNA-bind_5 33 tnkaKsraWeeiaervnalgsveRtaeelkkkwedlkrraKkk 75
                                   n+    +We++ae+  +++ ++ ++++l++ ++d++++   +
  gi|70607851|ref|YP_256721.1| 43 INDNLVLIWEKLAENDIKFNKIHEELVKLRQEMNDMRKDFNSE 85
                                  56666679*****************************987655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.82
                Myb_DNA-bind_5  47 rvnalgsv.eRtaeelkkkwedlkrra 72 
                                   ++n +    + ++ +l++ ++d++++ 
  gi|70607851|ref|YP_256721.1|  92 EMNDMRKDfNSEIIKLRQEMNDMRKDF 118
                                   444444444556777888888888765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.2
                Myb_DNA-bind_5   6 seeEkevLvelveknksile 25 
                                   s + +++L++l+++nk  l 
  gi|70607851|ref|YP_256721.1| 233 SLSVTKDLLDLCKENKVYLT 252
                                   55567889999999987665 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.7      0.12        68      46      75 ..      53      82 ..      15      88 .. 0.58
   2 ?   12.2   1.9   0.00038      0.21      23      84 ..      91     152 ..      85     158 .. 0.91
   3 ?   -1.4   0.0       6.4   3.6e+03      46      62 ..     206     222 ..     195     234 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.12
                HIP1_clath_bdg 46 kleeqkeelekLkreleakraelarlkssL 75
                                  kl+e   + +k+++el + r+e++ +++  
  gi|70607851|ref|YP_256721.1| 53 KLAENDIKFNKIHEELVKLRQEMNDMRKDF 82
                                  455555555666666666666665555544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00038
                HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeq 84 
                                   +e++  +k+ + e+ +l++e + + ++ ++e+ kL++e++++ +++ar+ + L++s + ++q
  gi|70607851|ref|YP_256721.1|  91 QEMNDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENLTTSIEDDAQ 152
                                   688999*********************************************99999887776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.4
                HIP1_clath_bdg  46 kleeqkeelekLkrele 62 
                                   +l  + e+l+++k el 
  gi|70607851|ref|YP_256721.1| 206 ELMRKVEKLKTVKPELF 222
                                   33334444444444444 PP

>> APC_N_CC  Coiled-coil N-terminus of APC, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   3.0      0.79   4.4e+02      28      42 ..      83      97 ..      62     117 .. 0.55
   2 ?    7.1   0.0      0.01       5.8      18      33 ..     123     138 ..     115     146 .. 0.83
   3 ?    2.1   0.0      0.38   2.1e+02       2      15 ..     203     216 ..     202     224 .. 0.82
   4 ?   -1.7   0.0       5.6   3.2e+03      25      35 ..     252     262 ..     243     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.79
                      APC_N_CC 28 SshLskLEtetsgmK 42
                                   s + kL +e  +m+
  gi|70607851|ref|YP_256721.1| 83 NSEIIKLRQEMNDMR 97
                                  344455555555543 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                      APC_N_CC  18 thlrrELedNSshLsk 33 
                                    +lr+E++dN  ++ +
  gi|70607851|ref|YP_256721.1| 123 IKLRQEMNDNYKQIAR 138
                                   579********99988 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.38
                      APC_N_CC   2 sYdQLvrQvEaLkk 15 
                                    Y  L+r vE Lk 
  gi|70607851|ref|YP_256721.1| 203 VYMELMRKVEKLKT 216
                                   5889********97 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.6
                      APC_N_CC  25 edNSshLskLE 35 
                                      S  L+kLE
  gi|70607851|ref|YP_256721.1| 252 TTGSRDLTKLE 262
                                   5568899***9 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.4     0.017       9.3      79     128 ..      43      92 ..       2     101 .. 0.49
   2 ?    9.1   4.7    0.0012      0.68      80     168 ..      94     182 ..      88     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                   DLP_helical  79 aeerleelekevekleesakriekelaelkkeieearielreelkayfsd 128
                                   ++++l  + +++++++ ++++i++el +l++e+++ r++ + e+ +++++
  gi|70607851|ref|YP_256721.1|  43 INDNLVLIWEKLAENDIKFNKIHEELVKLRQEMNDMRKDFNSEIIKLRQE 92 
                                   33333333344444444444444444444444444444444444444433 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                   DLP_helical  80 eerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkglsletieeFlereiGdegivvgtkl 160
                                   ++  ++ ++e+ kl++++++++k++++   ++ +  ++ +++++++ ++L ++++  +   ++ ++e+++G++ ++ + ++
  gi|70607851|ref|YP_256721.1|  94 NDMRKDFNSEIIKLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENLTTSIEDDAQYYLQWLIEKKLGYKAEITRLEI 174
                                   556677889999999999999999988888888888888889999***********99999*************9999999 PP

                   DLP_helical 161 eneferql 168
                                    n +e  +
  gi|70607851|ref|YP_256721.1| 175 DNVVEIDI 182
                                   99887554 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  11.0    0.0023       1.3      73     174 ..      30     121 ..       4     152 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                     Rootletin  73 lakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylssehsrllsL 153
                                   ++kL+e  ++s  + +   l  e+l e + + ++++e+l kl+++++ +r++ +++  ++r+e + +++ ++se   +++L
  gi|70607851|ref|YP_256721.1|  30 VKKLDEFERQSRFINDNLVLIWEKLAENDIKFNKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKDFNSE---IIKL 107
                                   45566555555555555555567777777777777777777777777777777766555555555555555444...5555 PP

                     Rootletin 154 Wrevvavrrqfselksaterd 174
                                    +e++ +r+ f+        +
  gi|70607851|ref|YP_256721.1| 108 RQEMNDMRKDFNS-------E 121
                                   5555555555543.......2 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.8    0.0027       1.5       8      94 ..      61     169 ..      54     223 .. 0.62
   2 ?   -0.3   0.1       2.7   1.5e+03      48      87 ..     205     244 ..     185     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
                       DUF2408   8 lepiyekLvsirrsLlslaakskaeeakesee.......vkeelkelkeeLkkieskrde...............egkFks 66 
                                    ++i+e+Lv++r+++  +  + ++e  k ++e       +++e+ +l++e++++ +  ++                 +F++
  gi|70607851|ref|YP_256721.1|  61 FNKIHEELVKLRQEMNDMRKDFNSEIIKLRQEmndmrkdFNSEIIKLRQEMNDMRKDFNSeiiklrqemndnykqIARFVE 141
                                   456677777777777776666666666666654444444555555555555555542222333333334445555677888 PP

                       DUF2408  67 eegkevvekgqavlngLlddcfdlvedl 94 
                                   + ++++++++q  l+ L+++ +    ++
  gi|70607851|ref|YP_256721.1| 142 NLTTSIEDDAQYYLQWLIEKKLGYKAEI 169
                                   8888888888888888888766655555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.7
                       DUF2408  48 keeLkkies.krdeegkFkseegkevvekgqavlngLlddc 87 
                                   +e ++k+e+ k ++ + Fk ++   +v  + +v ++Lld c
  gi|70607851|ref|YP_256721.1| 205 MELMRKVEKlKTVKPELFKDKKV-ILVIFSLSVTKDLLDLC 244
                                   33344444412222334544443.55666666666666666 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.7    0.0033       1.8      56      87 ..      51      82 ..      31      87 .. 0.86
   2 ?    0.2   0.2       1.3   7.4e+02      59      83 ..      93     114 ..      79     127 .. 0.49
   3 ?    6.1   0.1     0.019        10       6      34 ..     123     151 ..     118     155 .. 0.88
   4 ?   -1.8   0.1       5.4     3e+03      52      76 ..     200     224 ..     195     231 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0033
                                  HHHHTTHCHCCCHCTSSSSHHHHCTTTXXXXX CS
                         Sec2p 56 keqLkeketlleslqeqLkeLkevlekmeees 87
                                   e+L+e+++ +++  e+L +L++ +++m ++ 
  gi|70607851|ref|YP_256721.1| 51 WEKLAENDIKFNKIHEELVKLRQEMNDMRKDF 82
                                  589*************************9875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                                   HTTHCHCCCHCTSSSSHHHHCTTTX CS
                         Sec2p  59 LkeketlleslqeqLkeLkevlekm 83 
                                   +++ ++ ++   ++  +L++ +++m
  gi|70607851|ref|YP_256721.1|  93 MNDMRKDFN---SEIIKLRQEMNDM 114
                                   333332222...2233333333333 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Sec2p   6 kkkreeaekekkklekEledLtasLFeeA 34 
                                    k r+e++++ k++ + +e+Lt+s+ ++A
  gi|70607851|ref|YP_256721.1| 123 IKLRQEMNDNYKQIARFVENLTTSIEDDA 151
                                   57899999****************98887 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.4
                                   HHHHHHHHTTHCHCCCHCTSSSSHH CS
                         Sec2p  52 neklkeqLkeketlleslqeqLkeL 76 
                                   n++++ +L  k + l++ + +L + 
  gi|70607851|ref|YP_256721.1| 200 NKSVYMELMRKVEKLKTVKPELFKD 224
                                   5556666666666666666555554 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.1    0.0062       3.5      32      55 ..      60      83 ..      51      88 .. 0.81
   2 ?    3.7   0.4     0.098        55      38      54 ..      84     100 ..      83     101 .. 0.92
   3 ?    4.8   0.4     0.043        24      38      56 ..     102     120 ..     101     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0062
                        DUF919 32 kitKnpkElqdlekklnklRqeFL 55
                                  k  K  +El +l +++n++R++F 
  gi|70607851|ref|YP_256721.1| 60 KFNKIHEELVKLRQEMNDMRKDFN 83
                                  778999*****************5 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.098
                        DUF919  38 kElqdlekklnklRqeF 54 
                                   +E+ +l +++n++R++F
  gi|70607851|ref|YP_256721.1|  84 SEIIKLRQEMNDMRKDF 100
                                   6999************9 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.043
                        DUF919  38 kElqdlekklnklRqeFLn 56 
                                   +E+ +l +++n++R++F +
  gi|70607851|ref|YP_256721.1| 102 SEIIKLRQEMNDMRKDFNS 120
                                   6999*************65 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.7     0.033        19       2      31 ..      64      93 ..      63      98 .. 0.91
   2 ?    5.1   3.4     0.052        29       2      33 ..     100     131 ..      99     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.033
                                  TSHHHHHHHHHHHHHHHHHHHHHCCCCCCC CS
                       MutS_IV  2 fdeeLdelrdrleelekeleeleekerekl 31
                                  ++eeL +lr+ +++++k+++++  k+r++ 
  gi|70607851|ref|YP_256721.1| 64 IHEELVKLRQEMNDMRKDFNSEIIKLRQEM 93
                                  799*******************99999875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.052
                                   TSHHHHHHHHHHHHHHHHHHHHHCCCCCCCT- CS
                       MutS_IV   2 fdeeLdelrdrleelekeleeleekereklgi 33 
                                   f++e+ +lr+ +++++k+++++  k+r++ + 
  gi|70607851|ref|YP_256721.1| 100 FNSEIIKLRQEMNDMRKDFNSEIIKLRQEMND 131
                                   66666677777777777666666666665543 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.1e+03     125     154 ..      27      56 ..      11      64 .. 0.75
   2 ?    7.2   2.2    0.0063       3.5     101     151 ..      66     117 ..      55     120 .. 0.68
   3 ?    6.7   0.5    0.0088       4.9      94     135 ..     106     147 ..     100     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                 Fzo_mitofusin 125 ekeiekleevqkkakllrnkaslleseLek 154
                                   +  ++kl+e +++++ + +   l+ ++L++
  gi|70607851|ref|YP_256721.1|  27 TVVVKKLDEFERQSRFINDNLVLIWEKLAE 56 
                                   445789999999999998888888777765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0063
                 Fzo_mitofusin 101 stfarlcqqvdetekeleeeikelekeieklee.vqkkakllrnkasllese 151
                                   + + +l+q+ + ++k++++ei +l++e++ + +  +++  +lr++ + ++++
  gi|70607851|ref|YP_256721.1|  66 EELVKLRQEMNDMRKDFNSEIIKLRQEMNDMRKdFNSEIIKLRQEMNDMRKD 117
                                   5556777777778888888888888887777542566667777777666665 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0088
                 Fzo_mitofusin  94 qvqqelsstfarlcqqvdetekeleeeikelekeiekleevq 135
                                   +++qe++ + + +++++ + ++e++++ k++ + +e+l + +
  gi|70607851|ref|YP_256721.1| 106 KLRQEMNDMRKDFNSEIIKLRQEMNDNYKQIARFVENLTTSI 147
                                   578999999999999999999999999999999999987654 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.2     0.025        14       9      38 ..      50      79 ..      14      84 .. 0.92
   2 ?    4.9   1.7     0.057        32      13      70 ..      89     149 ..      80     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                          Rx_N  9 LadllaeeakllkgvkeeleklkdeLesiq 38
                                  + ++lae+  ++ +++eel kl++e++ ++
  gi|70607851|ref|YP_256721.1| 50 IWEKLAENDIKFNKIHEELVKLRQEMNDMR 79
                                  568999999*****************9997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.057
                          Rx_N  13 laeea.kllkgvkeeleklkdeLesiqa.vLedaee.rqikdeavkeWlkelrdlaydaeD 70 
                                   l +e   ++k++ +e+ kl++e++ ++  + ++  + rq+ ++  k+  + + +l  ++eD
  gi|70607851|ref|YP_256721.1|  89 LRQEMnDMRKDFNSEIIKLRQEMNDMRKdFNSEIIKlRQEMNDNYKQIARFVENLTTSIED 149
                                   45555578899999*********99987355554445888888888888888888888887 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.2    0.0049       2.8      29     104 ..      53     130 ..      21     150 .. 0.65
   2 ?    0.3   0.2       1.5   8.6e+02      14      24 ..     140     150 ..     118     227 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0049
                       DUF1690  29 qalekliq.erVaeeLkkLraeeeetlkkfeeklekellkde..........adakdelsskalnekieeLrkkleefkkk 98 
                                   + +e+ i+ +++ eeL kLr+e ++ +k+f++++ k  ++ +                    +l+++++++rk ++    k
  gi|70607851|ref|YP_256721.1|  53 KLAENDIKfNKIHEELVKLRQEMNDMRKDFNSEIIKLRQEMNdmrkdfnseiI---------KLRQEMNDMRKDFNSEIIK 124
                                   55666666579*******************99987766655522223333330.........3344444444433333222 PP

                       DUF1690  99 eeeklp 104
                                    +++ +
  gi|70607851|ref|YP_256721.1| 125 LRQEMN 130
                                   222222 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.5
                       DUF1690  14 vsqLessketd 24 
                                   v++L++s e d
  gi|70607851|ref|YP_256721.1| 140 VENLTTSIEDD 150
                                   33333333333 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.1     0.015       8.3      51     117 ..      65     134 ..       9     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                       zf-C4H2  51 veeLrlIhaDinalEsvikeaeeekeksle.kakklyeeykklkeevnelrse..lglekledleeeeee 117
                                    eeL ++++ +n++ + +++   + +++++ + k + +e+ kl++e+n++r++  + + kl++  +++ +
  gi|70607851|ref|YP_256721.1|  65 HEELVKLRQEMNDMRKDFNSEIIKLRQEMNdMRKDFNSEIIKLRQEMNDMRKDfnSEIIKLRQEMNDNYK 134
                                   3666666677777766666555554444430344455677777777777777743344444443333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2266  (0.126387); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 1762.40
//
Query:       gi|70607852|ref|YP_256722.1|  [L=174]
Description: AsnC family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-15   54.0   1.9    1.3e-14   53.4   1.9    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.2e-13   48.4   0.2    9.2e-13   47.8   0.2    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.8e-12   45.4   0.0      1e-11   44.6   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.5e-05   24.7   0.2    3.3e-05   23.6   0.2    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    5.1e-05   23.1   0.1    0.00011   22.1   0.1    1.5  1  MarR            MarR family
    5.6e-05   23.1   0.0    9.5e-05   22.4   0.0    1.4  1  HTH_20          Helix-turn-helix domain
    0.00023   21.0   0.1    0.00061   19.6   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0014   19.0   0.1     0.0046   17.4   0.1    1.9  1  HTH_27          Winged helix DNA-binding domain
     0.0016   18.3   0.0     0.0028   17.5   0.0    1.3  1  MarR_2          MarR family
     0.0018   18.1   0.4     0.0051   16.7   0.3    1.8  2  RuvB_C          RuvB C-terminal winged helix domain
     0.0028   17.6   1.0     0.0047   16.9   0.1    1.8  2  DUF1759         Protein of unknown function (DUF1759)
      0.003   17.9   2.1     0.0039   17.5   0.7    1.8  2  HTH_WhiA        WhiA C-terminal HTH domain
     0.0077   16.3   1.9       0.11   12.6   0.3    2.6  3  DUF2250         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.021   14.7   0.2    1.5  1  TFIIE_alpha     TFIIE alpha subunit
      0.011   15.5   0.0      0.018   14.8   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.015   15.2   2.0      0.019   14.9   0.2    2.0  2  HTH_11          HTH domain
      0.015   14.9   0.3      0.025   14.2   0.3    1.3  1  DDRGK           DDRGK domain
      0.054   13.0   0.0        0.8    9.3   0.0    2.3  2  DUF3400         Domain of unknown function (DUF3400)
      0.072   13.1   0.0       0.11   12.5   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
        0.1   12.8   1.2       0.31   11.3   0.1    2.1  2  HTH_34          Winged helix DNA-binding domain
       0.19   11.6   0.0       0.31   10.9   0.0    1.3  1  HTH_30          PucR C-terminal helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.9   1.6e-17   1.3e-14       1      48 []      25      72 ..      25      72 .. 0.99

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.6e-17
                        HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  lde+d+kIL++Lq+n++ s  + +e+l l++st+ +r+krLe++G+Ik
  gi|70607852|ref|YP_256722.1| 25 LDEIDIKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  7**********************************************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.2   1.1e-15   9.2e-13       1      42 []      25      66 ..      25      66 .. 0.99

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.1e-15
                 HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                  LDeiD+kIL++Lqe+a+ s ++++e++ l  st++ R++rLe
  gi|70607852|ref|YP_256722.1| 25 LDEIDIKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLE 66
                                  8****************************************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.2e-14     1e-11       9      75 .]      97     164 ..      89     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.2e-14
                                   G.TTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                AsnC_trans_reg   9 h.peqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                     ++++ ++  +lae+p V  +y v Gd d+++ ++ ++ e++ +   ekl+s+p+++rt+t iv +t
  gi|70607852|ref|YP_256722.1|  97 YgKDYHLNLGSKLAEIPGVWGVYFVLGDTDFVVMARYKNREEFMKNFLEKLMSMPEIERTSTQIVVKT 164
                                   3568899999**********************************999999***************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   3.9e-08   3.3e-05       5      46 ..      30      72 ..      26      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-08
                                  HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +kILk+L+e  +++  + +e+l+l++st+ +  k+L+ +G+++
  gi|70607852|ref|YP_256722.1| 30 IKILKILQEnAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  69*******899*****************************95 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.2e-07   0.00011       6      48 ..      30      72 ..      26      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                                  HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                  ++iL il e+  +s+ ++ ++l++ kst+   ++rLe +G i+
  gi|70607852|ref|YP_256722.1| 30 IKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  689*************************************995 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-07   9.5e-05      13      56 ..      30      73 ..      25      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-07
                                  HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   +il+ L +++ +++++  e l l+k+t+ y+++ Le+ g++++
  gi|70607852|ref|YP_256722.1| 30 IKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIKG 73
                                  589**************************************985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.2e-07   0.00061       4      53 ..      23      72 ..      22      80 .. 0.95
   2 ?   -2.8   0.0       7.3   6.2e+03      44      55 ..     145     156 ..     142     167 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.2e-07
                                  CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                          TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                  + L e ++k+ + L ++ + + ++ +e+l++p+s++   +++Le+ G+++
  gi|70607852|ref|YP_256722.1| 23 MELDEIDIKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  5799*******************************************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.3
                                   HHHHHCTSEEEE CS
                          TrmB  44 rsLedkGlVere 55 
                                   ++L+++  +er 
  gi|70607852|ref|YP_256722.1| 145 EKLMSMPEIERT 156
                                   555554444433 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.4e-06    0.0046       6      48 ..      30      71 ..      25      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.4e-06
                        HTH_27  6 alvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                  + +L  ++ ++++++l+d +++l++ +s+i+y +k+L+ +G +
  gi|70607852|ref|YP_256722.1| 30 IKILKILQ-ENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGII 71
                                  56788888.999**************************99976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.3e-06    0.0028      15      51 ..      37      71 ..      28      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                                  HCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                        MarR_2 15 grrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                    +     +  +  + l+l+ks++ +++krL+++G +
  gi|70607852|ref|YP_256722.1| 37 QENAK--QSLEDMSEMLKLPKSTIAYRIKRLESQGII 71
                                  55555..6888999*********************98 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   5.9e-06    0.0051       4      42 ..      25      60 ..      22      65 .. 0.91
   2 ?   -3.2   0.0       9.2   7.8e+03      44      55 ..      78      89 ..      76      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                                  --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHH CS
                        RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketied 42
                                  Lde+dik+Lk+l+   ++ + +l+ ++++l+++k+ti  
  gi|70607852|ref|YP_256722.1| 25 LDEIDIKILKILQ---ENAKQSLEDMSEMLKLPKSTIAY 60
                                  9***********9...789******************86 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.2
                                  THHHHHHTTSEE CS
                        RuvB_C 44 iEPyLlkeglIe 55
                                  i Py l + +I 
  gi|70607852|ref|YP_256722.1| 78 IDPYALDQDYIV 89
                                  789988888885 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.8   2.4e+03      93     105 ..      31      43 ..      10      66 .. 0.55
   2 !   16.9   0.1   5.5e-06    0.0047      64     105 ..     130     171 ..     125     174 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.8
                       DUF1759  93 sqlrrivdavnei 105
                                   + l+ + +++ ++
  gi|70607852|ref|YP_256722.1|  31 KILKILQENAKQS 43 
                                   3333333333332 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.5e-06
                       DUF1759  64 kkrYdnkrkiirellnelmklpslkeedasqlrrivdavnei 105
                                     rY n ++ ++++l++lm++p++++ +++ +++++ ++ +i
  gi|70607852|ref|YP_256722.1| 130 MARYKNREEFMKNFLEKLMSMPEIERTSTQIVVKTIKEAPNI 171
                                   57******************************9999988665 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.7   4.5e-06    0.0039      30      81 ..      15      66 ..       7      68 .. 0.81
   2 ?   -1.2   0.0       3.1   2.7e+03      48      73 ..     131     158 ..     126     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                                  HHH.T-GG.GS-HHHHHHHHHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHHH CS
                      HTH_WhiA 30 eek.kgle.klpeklkevaelRlenpdaSLkeLgelleppisKSgvnhrlrklk 81
                                   ek ++++ +l+e   ++ ++  en + SL++++e+l  ++ KS++++r+++l+
  gi|70607852|ref|YP_256722.1| 15 LEKmYYIQmELDEIDIKILKILQENAKQSLEDMSEML--KLPKSTIAYRIKRLE 66
                                  44413344477777788888899**************..9************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                                   HHHH-TTS-HHHHHHTT....T--HHHH CS
                      HTH_WhiA  48 lRlenpdaSLkeLgell..eppisKSgv 73 
                                   +R +n++  +k+  e l   p+i +   
  gi|70607852|ref|YP_256722.1| 131 ARYKNREEFMKNFLEKLmsMPEIERTST 158
                                   5666666666665555545555555544 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.3   0.00013      0.11       4      56 ..      23      75 ..      20      78 .. 0.91
   2 ?   -1.1   0.0       2.4     2e+03      20      38 ..      93     111 ..      78     115 .. 0.66
   3 ?    1.9   0.0      0.28   2.4e+02      29      63 ..     130     164 ..     124     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                       DUF2250  4 leedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                  +e de ++k+lk+l++        ++++l++p++ +   +k+Le+ G+++ + 
  gi|70607852|ref|YP_256722.1| 23 MELDEIDIKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIKGYY 75
                                  6778999*************9***************************99775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.4
                       DUF2250  20 anvdYaksiakeleiplee 38 
                                   + + Y+k +  +l  +l e
  gi|70607852|ref|YP_256722.1|  93 VRAKYGKDYHLNLGSKLAE 111
                                   4456777777666666665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.28
                       DUF2250  29 akeleipleevrellkkLeelGLlervegktikrt 63 
                                   + + + + e +++ l+kL+++  +er + +++ +t
  gi|70607852|ref|YP_256722.1| 130 MARYKNREEFMKNFLEKLMSMPEIERTSTQIVVKT 164
                                   56667777888999***********9998877544 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   2.5e-05     0.021      12      58 ..      26      72 ..      12      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-05
                                  -HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                   TFIIE_alpha 12 geeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                  +e  +++l++L e+++ + ed+++ lk+ +  +   + rL +++++k
  gi|70607852|ref|YP_256722.1| 26 DEIDIKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  456789**************************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.018       7      49 ..      31      72 ..      30      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   iL++l e +   +l ++++ + lpkSt    ++ L+ +G+++
  gi|70607852|ref|YP_256722.1| 31 KILKILQENAKQ-SLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  79*********8.9***********************999875 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   2.2e-05     0.019       4      44 ..      31      70 ..      29      79 .. 0.89
   2 ?   -1.1   0.1       2.2   1.9e+03      28      38 ..     157     167 ..     152     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                  +il++L e+ +  s e+++e L++ ++t+  +Ik+Le++g+
  gi|70607852|ref|YP_256722.1| 31 KILKILQENAK-QSLEDMSEMLKLPKSTIAYRIKRLESQGI 70
                                  8*****77777.6**************************93 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                        HTH_11  28 SrrtvrrdIka 38 
                                   S++ v++ Ik+
  gi|70607852|ref|YP_256722.1| 157 STQIVVKTIKE 167
                                   99999999985 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.9e-05     0.025     103     145 ..      31      73 ..      13      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E CS
                         DDRGK 103 efinyikekKvvlleelavkfklktqevierikeLeeqgsltG 145
                                   ++++ ++e+    le+++  +kl  + ++ rik Le+qg ++G
  gi|70607852|ref|YP_256722.1|  31 KILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIKG 73 
                                   6788888998999****************************99 PP

>> DUF3400  Domain of unknown function (DUF3400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00094       0.8       8      27 ..      82     101 ..      75     109 .. 0.87
   2 ?    1.2   0.0      0.32   2.7e+02      11      35 ..     125     147 ..     123     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00094
                       DUF3400   8 gleadYiVvElArhllGedW 27 
                                    l+ dYiV+   r  +G+d 
  gi|70607852|ref|YP_256722.1|  82 ALDQDYIVITFVRAKYGKDY 101
                                   5889*************996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                       DUF3400  11 adYiVvElArhllGedWmqdfveka 35 
                                   +d++V  +Ar    e+ m++f+ek 
  gi|70607852|ref|YP_256722.1| 125 TDFVV--MARYKNREEFMKNFLEKL 147
                                   78888..899999999999999875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.11      23      53 ..      43      73 ..      21      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                  HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                     HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr 53
                                  + e++++ml l  +t+   +++L+ +g+i+ 
  gi|70607852|ref|YP_256722.1| 43 SLEDMSEMLKLPKSTIAYRIKRLESQGIIKG 73
                                  679**************************94 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.1   9.7e+02      35      49 ..      12      26 ..       6      31 .. 0.80
   2 ?   11.3   0.1   0.00036      0.31       3      45 ..      30      72 ..      28      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
                        HTH_34 35 lkkLekagYievdke 49
                                  + +Lek  Yi+++++
  gi|70607852|ref|YP_256722.1| 12 AYILEKMYYIQMELD 26
                                  5689******99876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00036
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                  +++l +L ++ + + ++++e l++ ++ ++  +k Le++g i+
  gi|70607852|ref|YP_256722.1| 30 IKILKILQENAKQSLEDMSEMLKLPKSTIAYRIKRLESQGIIK 72
                                  689************************************9886 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.31      12      37 ..      41      66 ..      33      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                  TT-HHHHHHHHTS-HHHHHHHHHHHH CS
                        HTH_30 12 ggnisatAkaLhvHrnTlryRLrrie 37
                                   ++++++++ L + + T+ yR++r+e
  gi|70607852|ref|YP_256722.1| 41 KQSLEDMSEMLKLPKSTIAYRIKRLE 66
                                  579999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1208.61
//
Query:       gi|70607853|ref|YP_256723.1|  [L=444]
Description: class-III aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-92  307.9   0.0      1e-91  307.7   0.0    1.0  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.7   0.0   5.6e-96     1e-91      10     406 .]      27     435 ..      20     435 .. 0.95

  Alignments for each domain:
  == domain 1  score: 307.7 bits;  conditional E-value: 5.6e-96
                                   CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEE CS
                   Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkv 90 
                                   +lvi++++G+y +d  g++ylD+ s++  vnlG+ +++v+ka+++q+++l++++ + l+ +  +++++ ll+++pk++ k+
  gi|70607853|ref|YP_256723.1|  27 PLVIKEGKGAYFYDSKGNKYLDFSSQFINVNLGYGNENVIKAIEKQLETLQYIN-PSLGVSIRAEASRALLEVMPKNITKF 106
                                   389***************************************************.************************** PP

                                   EEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTC.TTB.-TSEEEE-TTBGGGTB CS
                   Aminotran_3  91 flansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlf.gpf.lpevvrlkypdeevlk 169
                                   f+ +sG+eA+e+A+K++r       +    ki++   ++HG t g++s+tg+   y++ f +p+ +p+vvr++ p++++++
  gi|70607853|ref|YP_256723.1| 107 FFSTSGTEANEAAIKIIRL-----IKRPSFKILSRYRSYHGSTEGSISLTGD---YRRWFvEPNiMPGVVRFPEPYCFRCP 179
                                   *******************.....3455679*********************...66655245569*************** PP

                                   -HHHHHHHHHHHHHHHH..CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGG CS
                   Aminotran_3 170 eneeeeaalleeleale..kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAle 248
                                    + +  ++ + +++ +    k++++va++ivEpi g  Gv+v+++e++  lr+++ ++dvl+i+DEv+tG Gr G++fA++
  gi|70607853|ref|YP_256723.1| 180 LKLKYPDCGIACANYVDyiIKQEKHVAGIIVEPITGTNGVIVPPKEYMPLLRKIAMENDVLFIADEVMTGWGRVGEWFAVN 260
                                   ***9999999998888777899*********************************************************** PP

                                   GCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS..B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                   Aminotran_3 249 hagvspDlmtlaKaltgG.lplsavlataevmqalapgs..hgsTfgGnplacavalavleiieeekllenaqelgaalke 326
                                    +gv+pD++t+aK+ ++   p+  + + +e+ + ++++   hg+Tf + p+  a++ av+   ++ +ll +++e+g++l +
  gi|70607853|ref|YP_256723.1| 261 LWGVEPDILTTAKGASASyVPIGITGVSKEIGDFFEDNVfaHGHTFEAHPVSLAAIPAVISEYKRVNLLPHVREMGKYLGK 341
                                   ******************99***************777699**************************************** PP

                                   HHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC...............HHHHHHHHHCTEE-EEETTTEEEE---TT--H CS
                   Aminotran_3 327 gLeelqkkyevikevRgkGlmiaielkeeaevke...............keilkkakekGvlilsaGdnvirllppliitd 392
                                   +L+el++++  i++vRg+Gl+ a+el+++ ++++                 ++kka+e Gv +++ G++   ++ppl++++
  gi|70607853|ref|YP_256723.1| 342 RLNELKERHISIGDVRGVGLFWAVELVKDGKNTPfadyndkyegkpillDLLAKKALESGVFVYN-GPSWFIIAPPLVVEK 421
                                   *******************************888**************877899********776.88************* PP

                                   HHHHHHHHHHHHHH CS
                   Aminotran_3 393 eeidelleilkkal 406
                                   e+id+++e+l k++
  gi|70607853|ref|YP_256723.1| 422 EDIDKGVEALDKVI 435
                                   **********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2990.26
//
Query:       gi|70607854|ref|YP_256724.1|  [L=275]
Description: hypothetical protein Saci_2138 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-33  114.4  31.2    1.8e-19   70.3  13.3    2.5  2  EamA             EamA-like transporter family
     0.0015   17.9  14.7     0.0028   17.1  14.6    1.3  1  TPT              Triose-phosphate Transporter family
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.34   10.8   0.0    1.7  1  B_solenoid_ydck  Beta solenoid repeat from YDCK
       0.45   10.3   0.0       0.45   10.3   0.0    2.1  2  Vpu              Vpu protein


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5  10.0     1e-16   4.5e-13      16     134 ..      16     124 ..       3     127 .. 0.86
   2 !   70.3  13.3     4e-23   1.8e-19       2     135 ..     136     266 ..     135     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1e-16
                          EamA  16 iyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnasl 96 
                                   + + ++k ++++ sp+ ++ +r++i+++++l i      ++      d    ++l +l+t++  l +  +lk++s+s+ ++
  gi|70607854|ref|YP_256724.1|  16 LQYYFAKDAITYSSPVVFNLLRYIISSAIFLSIRRRIVFNR------D----VFLLALYTTMSSLTWSLGLKYVSPSESAV 86 
                                   567899******************99999865543333333......2....445558899999***************** PP

                          EamA  97 itslePvftlilsvlllgekltlkqllgivlillGvll 134
                                   +++++P+f++ +++l+l e++t+++ lg+++++lGv l
  gi|70607854|ref|YP_256724.1|  87 LSYTMPLFSIPIAFLILSERPTVIETLGVGIGFLGVTL 124
                                   ************************************98 PP

  == domain 2  score: 70.3 bits;  conditional E-value: 4e-23
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                   lg+ l ++ a+fwa+  v+ ++ lr+ +p+ +++ +f i++++l +++++       ++ + +   +++++lg++l f+l+
  gi|70607854|ref|YP_256724.1| 136 LGATLTIINAVFWALFSVYYRK-LRNEDPIVVNASQFSIGSVILALLLPIDHDVT--INDSFIEGTAYTATLGGALSFFLW 213
                                   68999*****************.7********************99999988888..************************ PP

                          EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                   ++ +k   + +++++++ +P++t+i+ v++++ ++ l+q++gi++i++G++l 
  gi|70607854|ref|YP_256724.1| 214 NMMVKIERVPRVTIFSFSIPILTTIIQVVVFNTSVFLIQIAGIAIIFIGIILS 266
                                   **************************************************996 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  14.6   6.2e-07    0.0028      60     288 ..      48     265 ..      23     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-07
                           TPT  60 isse..flkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasvt 138
                                   i  +  f + ++ lal  t+++++  + l+ v+ S + ++  ++P+F++ ++ l+l e++++   l + +   Gv+l  + 
  gi|70607854|ref|YP_256724.1|  48 IRRRivFNRDVFLLALYTTMSSLTWSLGLKYVSPSESAVLSYTMPLFSIPIAFLILSERPTVIETLGVGIGFLGVTLYGLP 128
                                   4444446678999*******************************************************************9 PP

                           TPT 139 Els.FnligfisAlisnltfslrnifsKkllkklkd..ldalnlfaiitilslllllPvallvegvlktpsllkstkvslk 216
                                    ++ F l+g +  +i  ++ +l +++ +kl ++  d  + +  +f  i+ + l+lllP+   v+      s ++ t     
  gi|70607854|ref|YP_256724.1| 129 LVHgFSLLGATLTIINAVFWALFSVYYRKLRNE--DpiVVNASQF-SIGSVILALLLPIDHDVTI---NDSFIEGT----- 198
                                   9977*************************9888..4435555555.5566668889998655555...33444444..... PP

                           TPT 217 evllllllsgvlfhlynqv.aymvLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiGtavaivGvfl 288
                                     ++  l  ++ f+l n++     + rv+  ++s+      ++  ++ v+vf+++v l+++ G a+  +G++l
  gi|70607854|ref|YP_256724.1| 199 -AYTATLGGALSFFLWNMMvKIERVPRVTIFSFSI-----PILTTIIQVVVFNTSVFLIQIAGIAIIFIGIIL 265
                                   .6888899999999999751444455555555555.....6888889999********************987 PP

>> B_solenoid_ydck  Beta solenoid repeat from YDCK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.7e-05      0.34       6      16 ..     187     197 ..     187     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.7e-05
               B_solenoid_ydck   6 nAtVqhsfVeH 16 
                                   ++t+++sf+e+
  gi|70607854|ref|YP_256724.1| 187 DVTINDSFIEG 197
                                   8*********9 PP

>> Vpu  Vpu protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.9e-05      0.45      14      39 ..     139     164 ..     132     173 .. 0.87
   2 ?   -5.0   4.1         4   1.8e+04      12      12 ..     251     251 ..     227     270 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.9e-05
                           Vpu  14 valiiaivvWtivyreykkikkqkei 39 
                                   ++ ii++v+W++    y+k +++  i
  gi|70607854|ref|YP_256724.1| 139 TLTIINAVFWALFSVYYRKLRNEDPI 164
                                   57899****************99887 PP

  == domain 2  score: -5.0 bits;  conditional E-value: 4
                           Vpu  12 l 12 
                                   +
  gi|70607854|ref|YP_256724.1| 251 I 251
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1726.43
//
Query:       gi|70607855|ref|YP_256725.1|  [L=119]
Description: hypothetical protein Saci_2139 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.034   14.0   0.8       0.31   10.9   0.0    2.5  3  Rad50_zn_hook  Rad50 zinc hook motif
      0.056   13.7   0.1      0.088   13.1   0.1    1.5  1  IF3_N          Translation initiation factor IF-3, N-terminal


Domain annotation for each model (and alignments):
>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.08   7.2e+02       4      16 ..      36      48 ..      33      51 .. 0.78
   2 ?   -0.9   0.6      0.17   1.5e+03      29      51 ..      45      68 ..      42      69 .. 0.67
   3 ?   10.9   0.0   3.5e-05      0.31       6      30 ..      83     107 ..      80     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.08
                                  HHHHHHHHHHHHT CS
                 Rad50_zn_hook  4 eteelnkkieelk 16
                                   t+++ kk++e k
  gi|70607855|ref|YP_256725.1| 36 STKQIVKKALEEK 48
                                  6889999999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                                  E-HHH.HHHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook 29 ldeeh.rseLikelqsklerlpee 51
                                  l+e+  r ++ +  q kl+r +e+
  gi|70607855|ref|YP_256725.1| 45 LEEKTlRFRIKEAVQVKLNRDEEK 68
                                  555556667777777888877775 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 3.5e-05
                                   HHHHHHHHHHTT-SEE-TTT--EE- CS
                 Rad50_zn_hook   6 eelnkkieelkeakgcCPlCgReld 30 
                                   +++ k++ e+k +++ CP Cg e d
  gi|70607855|ref|YP_256725.1|  83 LLYGKRAHEVKYVGHVCPFCGMEVD 107
                                   6899****************97766 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.8e-06     0.088       6      35 ..      18      47 ..       4      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.8e-06
                                  -SSEEEEE-SSS-EEEEEEHHHHHHHHHHH CS
                         IF3_N  6 rarevrlvdedGeqlGvistreAlrlaeek 35
                                  + +e+ lvd +G+ ++ +st+++++ a e+
  gi|70607855|ref|YP_256725.1| 18 EEDEILLVDPKGQHISKVSTKQIVKKALEE 47
                                  5689*********************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 669.05
//
Query:       gi|70607856|ref|YP_256726.1|  [L=315]
Description: parathion hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-82  275.8   0.0    5.3e-82  275.6   0.0    1.0  1  PTE       Phosphotriesterase family


Domain annotation for each model (and alignments):
>> PTE  Phosphotriesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.6   0.0   2.9e-86   5.3e-82       1     297 [.      12     314 ..      12     315 .] 0.96

  Alignments for each domain:
  == domain 1  score: 275.6 bits;  conditional E-value: 2.9e-86
                                   EEGGCTSCEEEEE-SCEE-HHHHCHCCCCC--HHHHHHHHHHHHHHHHHTTEEEEEE---CCCT--HHHHHHHHCCHSSEE CS
                           PTE   1 vetsdlGvtLahehltitldefkqnvpealevedkevaaiieellelkarGvdalveltttglgRdvqtlkrvaeetgvni 81 
                                   +++ ++G tL+hehl +  + ++ + p  ++ ed e+  +++e++ +++ Gv+++v+ t++glgRd+++  +v++etg+n+
  gi|70607856|ref|YP_256726.1|  12 ISPGEMGFTLIHEHLRVFSEPVRYQWPHLYN-EDEELKNAVNEVKTIMSYGVKTIVDPTVMGLGRDIRFSEKVVKETGINV 91 
                                   57889***********************999.999********************************************** PP

                                   EEEECB--CCG--TCCCCS-CHCHHHHHHHHHHT-STTTS--EEEEEEEE-CTBS-HHHHHHHHHHHHHHHHH---EEEEE CS
                           PTE  82 vaatGfYvdatvpeaararsveeltdvlvdeiehGidgteikaGiikeigtsgkltpseekvleavaqahkqtGaPisiht 162
                                   +aatG+Y++++ p   + rs ee+++ l+++i++Gi+gt+ +aG ik +++++++t  +e+ ++a+a a+k t  Pi++h+
  gi|70607856|ref|YP_256726.1|  92 IAATGLYTYTDLPFFFNGRSLEEIAELLIHDIKKGIQGTNNRAGFIKVAADEPGITRDVERAIRAAAIAQKETNVPIITHS 172
                                   ********************************************************************************* PP

                                   GCCTTCHHHHHHHHHHTT--GGGEEETTGGCS--HHHHHHHHHTT-EEEE--TT-TTTS-HHHHHHHHHHHHHTT-GGGEE CS
                           PTE 163 saslragleqlrilqeeGvDlsrvvvghldtktdvkellelidlGaYleyDlfgvdlispdekRirivhalvdrGyedril 243
                                   +a  ++gleq+ril eeGvD  rv +ghl+++++v+++++++d G+++++D++g dl+ p +kR +++ +l+  Gy+dri+
  gi|70607856|ref|YP_256726.1| 173 NAHNGTGLEQQRILMEEGVDPGRVLIGHLGDTDNVDYIKKIADKGSFVGLDRYGLDLFLPIDKRNEVLLKLIKDGYLDRIM 253
                                   ********************************************************************************* PP

                                   E-----SEEC...CCSCCCCCHHTTH....HHHTHHHHHHHTT--HHHHHHHHTHHHHHHH CS
                           PTE 244 lshDittkfr...alkkelvgyaydl....lltdviPklkqrGlteeqldkiLvenPkqil 297
                                   +s+D ++  +   a ++ +   a+++    ++tdviP +k+ G+t+eql++i v nP +++
  gi|70607856|ref|YP_256726.1| 254 VSQDYCCTIDwgiAKPEYKPKLAPKWsmslIFTDVIPSIKRAGVTDEQLHVIFVKNPARLF 314
                                   *******98744334444555678888888*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1741.80
//
Query:       gi|70607857|ref|YP_256727.1|  [L=431]
Description: glutamine synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   8.5e-107  357.1   0.0   1.6e-106  356.2   0.0    1.4  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    2.7e-10   40.0   0.0    4.5e-10   39.3   0.0    1.4  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.2   0.0  1.8e-110  1.6e-106       3     345 .]     106     428 ..     104     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 356.2 bits;  conditional E-value: 1.8e-110
                                   -HHHHHHHHHHHH.HHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHHH CS
                    Gln-synt_C   3 dPRsvlkralarl.aeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiveal 82 
                                   d Rs l+  l++l +eeG++v   +E+EF+l+++ +                    +++++f+ +++   +++++e++++l
  gi|70607857|ref|YP_256727.1| 106 DLRSKLNARLEKLkEEEGYDVRSSFEMEFYLVKDRKP------------------YDDARCFDSSAF-YNNPIISEMIKVL 167
                                   5688899888888578899**************7655..................356889999988.679********** PP

                                   HHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEE CS
                    Gln-synt_C  83 ealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgkn 163
                                   ++ gi++ ++++E+++gQ+E ++ +++ l++aD+vv+fK+++k++A ++g+++ FmpKp+++ +GsgmH+++Slw  +gkn
  gi|70607857|ref|YP_256727.1| 168 TNSGIDIIRVIKEYGPGQYEFDIVHKNSLRSADEVVIFKEITKQIALSKGIEVNFMPKPFNKLPGSGMHLNISLW-REGKN 247
                                   ***************************************************************************.***** PP

                                   SSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-....TSGGCSTEE CS
                    Gln-synt_C 164 lfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa....skekakrvE 240
                                   +f+d++d+y+lsel+++fi+Gll+hakaltal+aptvnSYkRlvpg++aP+++++g++N+s+++Rip+     + + +rvE
  gi|70607857|ref|YP_256727.1| 248 VFYDPKDKYGLSELGYNFIAGLLEHAKALTALVAPTVNSYKRLVPGSWAPTKISYGYNNKSTMIRIPTpyptMESHDRRVE 328
                                   *******************************************************************9999889999**** PP

                                   EECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHHHHHHHHHCSHHHCCSS-HHHHHH CS
                    Gln-synt_C 241 lRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasleeAlealeedellkevlgeeviea 321
                                   +R+pdas+NPYL++ a+l AgldGie++l+pg+pv++++y  ++     ie++P++l+eAl++l++d+ lke +ge+v+++
  gi|70607857|ref|YP_256727.1| 329 YRVPDASSNPYLVILAVLEAGLDGIERGLKPGNPVNENAYLRKD-----IEDIPRNLREALRELDRDNRLKERIGEQVVRE 404
                                   ****************************************9888.....779***************************** PP

                                   HHHHHHHCHHHHHCT--HHHHHHH CS
                    Gln-synt_C 322 ylalkraEleeleeevsdwelery 345
                                   ++++k+aE+ee+e+ v+dwe+e y
  gi|70607857|ref|YP_256727.1| 405 FINIKSAEVEEFESIVTDWEYEVY 428
                                   *********************987 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.0     5e-14   4.5e-10       6      87 ..       5      87 ..       1     103 [. 0.87

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 5e-14
                                  .....------EEEEEEE-TTS-EEEEEEEGGGHHHHHTT-EEE-GGGGG--TTS---TT-S-SSS-.-EEEEE-GGG-EEE- CS
                  Gln-synt_N_2  6 vveqleekqveLieflyvdlaGvtrGkalplasLeekLasGiGltkatlalserdlidevedlgpvG.elrLvpdPasavalp 87
                                  + ++l+  +ve+++f  v l Gv+r k    +++ee +  GiG tka+ ++++ d i +  ++gp   ++ +vpd ++  + p
  gi|70607857|ref|YP_256727.1|  5 IKDKLRSYNVEILRFTWVGLDGVIRSKGAQVSHVEELIRTGIGVTKAMFSFTPMDIISPYGSFGPQDeDVFIVPDLSTLTVFP 87
                                  56789999*********************************************************863699****98877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2794.35
//
Query:       gi|70607858|ref|YP_256728.1|  [L=336]
Description: hypothetical protein Saci_2142 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-32  111.2   0.0      1e-31  110.8   0.0    1.1  1  Amidohydro_2  Amidohydrolase
     0.0015   18.0   0.0      0.002   17.6   0.0    1.2  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.2e-35     1e-31      25     291 .]      49     335 ..      40     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.2e-35
                                   CCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHH CS
                  Amidohydro_2  25 peerlafmkragvdpqlaspeallvlnaaagiaravivaalcrgannrvlaeaakrpdrfvggaavvpldpedaaaelera 105
                                     er + +++ +v ++++  +++++  ++++++++ ++ + +  +   +  e + +   f   ++ + +++e++++   r 
  gi|70607858|ref|YP_256728.1|  49 IKERNRLIRDDPVSYMKFLIDDAKIKAFVIDEGFGSKEMEIPAPYKRLFRIESIINSSLFSLPFDKAIEFFEETLRNKVRE 129
                                   45699999**********************************************************************999 PP

                                   HHHTTECE.....EEEESSTTTCCTTTCGGH..................HHHHHHHHHHT-EEEEE....CHHHCHHHHHH CS
                  Amidohydro_2 106 veelgfkG.....vrlnphvggddllgdrld..................rpifealeelglpvdihtGpspewlfggpqet 163
                                       gfk        ln  +++ ++l+d+l+                  ++++e+++el++p+++htG      +g+++++
  gi|70607858|ref|YP_256728.1| 130 G-YVGFKSiiayrTGLNITCNELKALEDFLSrdedwygekkkgfrdyllCKTMEIAKELDVPLQVHTG------AGDRDIK 203
                                   9.999999988884566666666666555555566999999999999*******************99......******* PP

                                   HHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGG CS
                  Amidohydro_2 164 traiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdr 244
                                   ++ + p +l +v+r++++ kiv+ H G+p  ++r++ ++ + +p+vy++ls       ++ +pl + +al+++ e+++ ++
  gi|70607858|ref|YP_256728.1| 204 LELSRPAYLTNVVRRYEG-KIVFVHSGYP--YHRETAWMSYIFPSVYLDLSQ-----VCPFAPLGALNALEEIMEVAPFNK 276
                                   *****************8.**********..*********************.....8999******************** PP

                                   EEEE--BTSTTSTSCTTHHHHCHHHHH.............SSHHHHHHHHTHHHHHHCTB CS
                  Amidohydro_2 245 ilfGsDyPhptleaepealalldlval.............lsdeerekilggNAarlygl 291
                                   i++GsD + +++ a+ +a   ++++ +               +e r+ il+ NA rly+l
  gi|70607858|ref|YP_256728.1| 277 IMYGSDGFNIPEIAWISAKI-FPRYLDmvlnkmvslgiieEEEEIRQMILSRNASRLYKL 335
                                   ************99999988.4444445779*******999*****************86 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.2e-07     0.002     112     254 ..     176     333 ..     141     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCG.GCCS.......EEEETT--S-HHHHHHHHHT...TEEEEE-GGGG CS
                    TatD_DNase 112 vFeeqlrlAkelklplviHlrkaeedlleilkeaa.eaka.......kvvlHsfsgsaeeakkflkl...gyyislsgllt 181
                                   ++ + +++Akel+ pl++H+++ ++d+   l++ a  +++        v +Hs    ++  ++++++    +y+ ls + +
  gi|70607858|ref|YP_256728.1| 176 LLCKTMEIAKELDVPLQVHTGAGDRDIKLELSRPAyLTNVvrryegkIVFVHS-GYPYHRETAWMSYifpSVYLDLSQVCP 255
                                   567899****************9997766666555444445555552344566.555555555555567788888999999 PP

                                   TTT..THH.HHHHHHHS-GGGEEE---TTSSEECCCTT.SE--GGGHHHHHHHHHH..HHTS-HHHHHHHHHHHHHHHH CS
                    TatD_DNase 182 fkn..ake.lrelvkavpldrlLiETDaPyltpkpyrg.krnepanvayvveklae..lkaltleelaeitaeNakrlf 254
                                   f    a + l e+++  p ++++ ++D  +  p+     ++  p ++  v++k+    + ++++e  + i++ Na rl+
  gi|70607858|ref|YP_256728.1| 256 FAPlgALNaLEEIMEVAPFNKIMYGSDG-FNIPEIAWIsAKIFPRYLDMVLNKMVSlgIIEEEEEIRQMILSRNASRLY 333
                                   97776444588899*************9.88886666669999***********9943344444445557788999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2133.45
//
Query:       gi|70607859|ref|YP_256729.1|  [L=505]
Description: gamma-aminobutyrate metabolism dehydratase/isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-91  304.6   0.1    9.8e-91  304.2   0.1    1.2  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
    1.8e-64  216.6   0.1    2.4e-64  216.1   0.1    1.2  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.043   14.0   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      0.099   12.8   0.0       0.19   12.0   0.0    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.2   0.1   2.2e-94   9.8e-91       1     272 []       5     274 ..       5     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.2 bits;  conditional E-value: 2.2e-94
                                   -HHHHHHHHHH.S---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHHH CS
                        HpaB_N   1 TgeeYlesLrd.kgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDll 80 
                                   Tg++Y++s+ + ++ e+Yv G++V+dvt+hp+++p+v s+++++d+a+d+++k+l +a sp   e++nrf+hi+rs+eDl+
  gi|70607859|ref|YP_256729.1|   5 TGDQYVSSISKrSKVEIYVLGKEVKDVTKHPFLKPSVMSFKATFDAAWDEDTKELGRAWSPYLEEEINRFNHIHRSPEDLA 85 
                                   89*********9999****************************************************************** PP

                                   HHHHHHHHHHHHTTT--S--THHHHHHHHHHHHTGGGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS-TTS-GGG CS
                        HpaB_N  81 kkrkairelarktggclgRcpdydalnalalvaaadvfekegtkeyaenfrkyleyvqendlvlthaitdpkgdRskrpse 161
                                   +k+k++r+l++ktg+c++Rc+++d ln+l +v++    +++g++e +++f +yl+yvq+ndl+l++a+td+kg R+++ps+
  gi|70607859|ref|YP_256729.1|  86 AKVKLLRKLSHKTGACFQRCVGWDSLNTLNIVTKIM--ANKGRTEPRDRFVEYLKYVQKNDLALAGAMTDVKGIRTLKPSQ 164
                                   **********************************95..34566669*********************************** PP

                                   SSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE------.-.S.. CS
                        HpaB_N 162 qedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfed.k.lee 240
                                   q+++++y+rv+e t+dGi+V+Gak+ +Tg+a+++e++vlptram ++edkdyavafa+p+d++G+k++++++ +d + +ee
  gi|70607859|ref|YP_256729.1| 165 QPNKNAYLRVTEVTKDGIYVSGAKANITGVAATEEMVVLPTRAM-GPEDKDYAVAFAIPTDTEGIKIVVGRQINDaRrMEE 244
                                   ********************************************.******************************844778 PP

                                   -TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
                        HpaB_N 241 sefdyplssrfdendalvvfDdVfVPwerVfl 272
                                    e+d      f +++ lv+fD+VfVP++rVfl
  gi|70607859|ref|YP_256729.1| 245 GEIDGLPY--FYNHEGLVIFDNVFVPMNRVFL 274
                                   88986655..999******************6 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.1   0.1   5.4e-68   2.4e-64       2     202 .]     282     477 ..     281     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.1 bits;  conditional E-value: 5.4e-68
                                   HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-EE CS
                          HpaB   2 gklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdpsGvyl 82 
                                   g+lve faa+hrq y+g  +ka+ +d++iG+ a +a+++G+ek++hvq+kl+e+i l+e++y+++iaa+ +a k  +++++
  gi|70607859|ref|YP_256729.1| 282 GTLVEIFAAYHRQGYGG--CKAGLGDVIIGASADLARQIGVEKAPHVQDKLTEMIFLTETMYSAGIAASLNAVKICDNCWW 360
                                   689**************..************************************************************** PP

                                   --HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHHHHHHTSHHH CS
                          HpaB  83 PdlllanaarvlvtrlypriveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllklawdltgsefg 163
                                   ++++ an++++lv+r++++i +++ diaGG++ t+Pse d+knp++++++ +yl+g e+++ae+R+++++l+++++++   
  gi|70607859|ref|YP_256729.1| 361 VNPMHANVTKHLVARFPAQISQLAIDIAGGMVGTAPSEWDLKNPKLKEYIMRYLQGVEDFTAEDRLRMVRLIENVSMG--- 438
                                   ***************************************************************************888... PP

                                   HHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHHHHCH CS
                          HpaB 164 grhelyerhgaGspeaqriaiyrqydleekkelvkkllg 202
                                   +  +++++hgaGsp+aqri+  r ydl+ + e+ kkl+g
  gi|70607859|ref|YP_256729.1| 439 VAFQIESIHGAGSPAAQRIMFSRLYDLDLAREISKKLAG 477
                                   8899********************************996 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.5e-06     0.043      21      75 ..     175     230 ..     151     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.5e-06
                                   EEETT.EEEEEEEEEEEETTTT-SEEEEE.EETS-------EEEEEEE..GGGEEE CS
                 Acyl-CoA_dh_M  21 aerdggeyvlnGeKiwitnaaiatlalvl.artekpdrarglslflvprdapgvsv 75 
                                   +e  +++++++G+K  it++a  + ++vl +r+ +p+ ++    f++p+d++g+++
  gi|70607859|ref|YP_256729.1| 175 TEVTKDGIYVSGAKANITGVAATEEMVVLpTRAMGPEDKDYAVAFAIPTDTEGIKI 230
                                   4444556************99966555551664444424455599*******9976 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.2e-05      0.19      50     114 ..     323     392 ..     289     422 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.2e-05
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHH--------.....HHHHHHHHHHHHHHHHHHHHHHHHHHGGGT CS
                 Acyl-CoA_dh_1  50 hqlvreklaemaaeleaarllvyraaealdagkpd.....raeasmaKlfaselaqevadlamqllGgaG 114
                                    ++v++kl em   +e + ++  +a   + +  ++     ++ a+++K +++++  ++ +la+++ Gg+ 
  gi|70607859|ref|YP_256729.1| 323 APHVQDKLTEMIFLTETMYSAGIAASLNAVKICDNcwwvnPMHANVTKHLVARFPAQISQLAIDIAGGMV 392
                                   5899999999999999888877776666666666666669***************************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3495.47
//
Query:       gi|70607860|ref|YP_256730.1|  [L=332]
Description: thioredoxin reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-30  106.3   0.1    2.3e-30  105.9   0.1    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-25   89.0   0.2    3.4e-22   79.1   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.5e-13   50.4   0.1    3.9e-10   40.1   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.8e-10   38.1   0.2    1.1e-07   31.3   0.0    2.9  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    5.1e-08   32.0   0.0     0.0017   17.2   0.0    3.5  4  HI0933_like     HI0933-like protein
    2.3e-05   24.5   0.2     0.0002   21.5   0.1    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.6e-05   24.0   1.9      0.036   13.6   0.2    3.6  4  DAO             FAD dependent oxidoreductase
    0.00019   20.9   0.2     0.0011   18.4   0.0    2.2  3  FAD_oxidored    FAD dependent oxidoreductase
    0.00036   19.9   1.0      0.031   13.5   0.1    3.4  4  Thi4            Thi4 family
     0.0013   19.1   0.3      0.016   15.7   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
     0.0024   16.4   0.2      0.011   14.1   0.0    1.9  2  FMO-like        Flavin-binding monooxygenase-like
  ------ inclusion threshold ------
       0.04   13.3   0.2       0.25   10.8   0.1    2.0  2  Spermine_synth  Spermine/spermidine synthase domain
      0.051   12.7   1.1        7.5    5.5   0.0    3.1  3  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.1   1.6e-33   2.3e-30       1     290 [.       4     296 ..       4     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 1.6e-33
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE..TTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve..legtclnggcllskallgvaedaeias........evvkklnqgielll 71 
                                   +d++++GgGp Gl a  + +   +  +l++  +e    ++++ + k +  v++ + i++        e+ k ++ +i+  l
  gi|70607860|ref|YP_256730.1|   4 YDIIIVGGGPIGLFATFYSGLRDMSALLIDaqDELGGQLVTIYPEKMVYDVGGYPGILAydlaqnliEQAKMFSPDIR--L 82 
                                   69***************************644222223344455888888888888888*999988877777777766..4 PP

                                   CCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E...EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  72 geevvkidpgkkkvklekkkegdeekiaydklvlAtGs...sprdlgipGvaenvgklvrtldsaealklkllpkrivvvG 149
                                   +e v  i + + ++ + k+  ++++++++++++lA G    +p +lg  G+ e+     r +  + + k++  +kri++vG
  gi|70607860|ref|YP_256730.1|  83 KEWVDWITRTQDNLWVIKT--DKGNEFKAKTILLALGIgriTPSRLGAGGEIEYEN---RGVYYTVKRKKDFEEKRILIVG 158
                                   4348888888888888765..56779***********8344555556666644443...55555555666666689***** PP

                                   -SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE......EEETTSC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx RF
                   Pyr_redox_2 150 gGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle......vvledge 224
                                   gG  +v+ A+ la ++k +tl+++rd++ ra+++++++ ++ a       v++ ++ ke++g+g+k++        +++++
  gi|70607860|ref|YP_256730.1| 159 GGDSAVDWAINLAPVAKSITLIHRRDQF-RAHESSVKQLYNIA------SVHTWHELKEVKGDGSKVTqavifdNRTKEEK 232
                                   ****************************.69999999998766......477889999******95555533456667777 PP

                                   EEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 225 eidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaA 290
                                   ++d+d v++++G + +   +  + gl++ +++ i+v+ +++tn pg+ya+GD+a+++g+p+ a  A
  gi|70607860|ref|YP_256730.1| 233 TLDVDAVIISIGHKGDLGNV-PRWGLNM-KGRDILVNAKMETNLPGVYAAGDIASQEGVPKMALIA 296
                                   7***************8777.9******.*************************999999888766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0011       1.5       1      43 [.       7      50 ..       7      52 .. 0.70
   2 !   79.1   0.0   2.5e-25   3.4e-22      89     305 .]      71     281 ..      62     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.ni.gnsiyrypkem 43
                                  iI+G+GP+Gl a       ++ + l ++ + ++ g+ ++ yp++m
  gi|70607860|ref|YP_256730.1|  7 IIVGGGPIGLFATFYSGLRDM-SALLIDAQdELgGQLVTIYPEKM 50
                                  8*********99888877777.45666666555145555666665 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 2.5e-25
                   Pyr_redox_3  89 evaksfelpiklfeeVesvkk.edegfevetske.tyeAkkviiAtGefd.kPnklnipGeek..lvkhyskvkefhkyag 164
                                   e ak f  +i+l+e V  +++ +d+  +++t+k+ +++Ak++++A G     P +l+  Ge +  +  +y++vk  +++++
  gi|70607860|ref|YP_256730.1|  71 EQAKMFSPDIRLKEWVDWITRtQDNLWVIKTDKGnEFKAKTILLALGIGRiTPSRLGAGGEIEyeNRGVYYTVKRKKDFEE 151
                                   567778889************77889*******88**********99865269****99998633677************* PP

                   Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey 245
                                   ++++++Gg++SavD A++l+   +++t+++r+++ +++es++++    ++   +++  + +++k        ++++  + +
  gi|70607860|ref|YP_256730.1| 152 KRILIVGGGDSAVDWAINLAPVAKSITLIHRRDQFRAHESSVKQL---YNIASVHTWHELKEVKGDG----SKVTQ-AVIF 224
                                   **********************************99998777753...2223333222212234333....34443.3455 PP

                   Pyr_redox_3 246 kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                   + +t+++k+++v d v++ +G k dl  + +  + l+ +gr  l ++++etn+pg++ aG
  gi|70607860|ref|YP_256730.1| 225 DNRTKEEKTLDV-DAVIISIGHKGDLGNVPR--WGLNMKGRDILVNAKMETNLPGVYAAG 281
                                   666777666665.889999*********985..555669999999*************99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0038       5.3       2      35 ..       6      39 ..       5      50 .. 0.81
   2 !   40.1   0.0   2.9e-13   3.9e-10       1      78 [.     153     224 ..     153     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0038
                                  EEEECSSHHHHHHHHHHHHTT.SEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg.kkVtvversdkll 35
                                  +++vGgG igl +A++++ l+  +  +++++d+l 
  gi|70607860|ref|YP_256730.1|  6 IIIVGGGPIGL-FATFYSGLRdMSALLIDAQDELG 39
                                  89********9.99999998834668888888877 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 2.9e-13
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEE CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvkl 78 
                                   ++++vGgG++++++A +la  +k++t+++r+d+++      a +   ++l +    v++ ++++e++g++++  ++v +
  gi|70607860|ref|YP_256730.1| 153 RILIVGGGDSAVDWAINLAPVAKSITLIHRRDQFR------AHESSVKQLYNI-ASVHTWHELKEVKGDGSKvTQAVIF 224
                                   79*********************************......999999999988.89****************6666655 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13   1.9e+02       2      38 ..       3      37 ..       2      39 .. 0.71
   2 !   31.3   0.0   8.2e-11   1.1e-07     132     254 ..      96     210 ..      69     221 .. 0.79
   3 !    4.7   0.0    0.0098        13     299     340 ..     204     245 ..     200     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                   K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerqpe 38
                                   +D+i++G Gp  L +a   +  + +++al ++ q+e
  gi|70607860|ref|YP_256730.1|  3 EYDIIIVGGGPIGL-FATFYSGLR-DMSALLIDAQDE 37
                                  69*********877.455555555.777777777765 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 8.2e-11
                   K_oxygenase 132 lltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllr 212
                                   l+ ++    +++ +e++a++++l+ G  +  P+ l +  + e       y+ +++++ ++kri++vG+G Sa + + +l+ 
  gi|70607860|ref|YP_256730.1|  96 LWVIK----TDKGNEFKAKTILLALGIGRITPSRLGAGGEIEYENRGVYYTVKRKKDFEEKRILIVGGGDSAVDWAINLAP 172
                                   44444....57889*********************98665444444445666666799*********************98 PP

                   K_oxygenase 213 rqkkvelklvtrsealeplddspfvneifsPeyvdyfyslpe 254
                                    +k  +++l+ r++++++ ++s  v+++++ + v+ +++l+e
  gi|70607860|ref|YP_256730.1| 173 VAK--SITLIHRRDQFRAHESS--VKQLYNIASVHTWHELKE 210
                                   776..9***********99988..679999999999999987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0098
                   K_oxygenase 299 pnrevesaeaegkgeveltlrneesgeeetlevdavvlATGY 340
                                   + +e+++++ +g++ ++  + ++ ++ee+tl+vdav+++ G 
  gi|70607860|ref|YP_256730.1| 204 TWHELKEVKGDGSKVTQAVIFDNRTKEEKTLDVDAVIISIGH 245
                                   5689999999*999999999999**************99886 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.2e-06    0.0017       1      38 [.       4      41 ..       4      44 .. 0.93
   2 !    9.6   0.0   0.00024      0.32     109     174 ..      63     130 ..      58     136 .. 0.84
   3 ?   -0.7   0.0      0.31   4.3e+02       2      34 ..     153     185 ..     152     188 .. 0.88
   4 ?   -0.6   0.0      0.31   4.3e+02     138     165 ..     219     246 ..     195     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                  +d+i++GgG+ Gl+a+   + r+ + ll++++++lg  
  gi|70607860|ref|YP_256730.1|  4 YDIIIVGGGPIGLFATFYSGLRDMSALLIDAQDELGGQ 41
                                  589*****************************999965 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---.-SS-G.GGT--S CS
                   HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG.GlSiP.klGstg 174
                                    d+ + l++++k    ++rl++ v  +++++d+   +kt++++e++a++++lA+G G   P +lG+ g
  gi|70607860|ref|YP_256730.1|  63 YDLAQNLIEQAKMFSPDIRLKEWVDWITRTQDNLWVIKTDKGNEFKAKTILLALGiGRITPsRLGAGG 130
                                   5677888899999999999*9999999***************************95554442566655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.31
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                   +++++GgG + +  Ai++a   k+++l+ + ++
  gi|70607860|ref|YP_256730.1| 153 RILIVGGGDSAVDWAINLAPVAKSITLIHRRDQ 185
                                   689****************99999999988766 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.31
                                   ETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 138 eedgkfrvktkseeeleadklvlAtGGl 165
                                   ++  +f  +tk+e++l  d++++++G +
  gi|70607860|ref|YP_256730.1| 219 TQAVIFDNRTKEEKTLDVDAVIISIGHK 246
                                   3444455566788889999999998865 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.4e-07    0.0002       1      48 [.       8      55 ..       8      64 .. 0.94
   2 ?    0.2   0.0      0.66   9.1e+02       1      31 [.     156     186 ..     156     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdyg 48
                                  IvG+G  Gl a  +   ++ + ll++++d lGG++ ++  +++++d+g
  gi|70607860|ref|YP_256730.1|  8 IVGGGPIGLFATFYSGLRDMSALLIDAQDELGGQLVTIYPEKMVYDVG 55
                                  9**********************************9998888888887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.66
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                   IvG+G s+   A  La   ++++l+ +rd++
  gi|70607860|ref|YP_256730.1| 156 IVGGGDSAVDWAINLAPVAKSITLIHRRDQF 186
                                   8999999999999999888899999888876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   2.6e-05     0.036       1      35 [.       5      40 ..       5      43 .. 0.93
   2 ?    4.6   0.0     0.015        21     146     232 ..      63     148 ..      53     155 .. 0.69
   3 ?    2.6   0.0     0.061        84       2      38 ..     154     192 ..     153     195 .. 0.83
   4 ?   -1.1   0.0      0.78   1.1e+03     177     205 ..     216     248 ..     200     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                  d++i+GGG iGl++ ++   r    +l++++d++g g
  gi|70607860|ref|YP_256730.1|  5 DIIIVGGGPIGLFATFYSGLRDmsALLIDAQDELG-G 40
                                  8*****************988789********999.6 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                                   HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEE.EEEEE CS
                           DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpi.spvrg 222
                                   + l++ l ++a+    +i++++ v  + ++++ +w +  +t+ g++++a+++ +a G++ +++  +l       i +  rg
  gi|70607860|ref|YP_256730.1|  63 YDLAQNLIEQAKMFSPDIRLKEWVDWITRTQDNLWVI--KTDkGNEFKAKTILLALGIG-RITpSRLgAGG--EIeYENRG 138
                                   5666677777777777777774444477766789999..777798877799******98.33344444222..333999** PP

                                   EEEEEEECCT CS
                           DAO 223 qvlvlkplse 232
                                    ++++k++++
  gi|70607860|ref|YP_256730.1| 139 VYYTVKRKKD 148
                                   ****977665 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.061
                                   EEEECTSHHHHHHHHHHH.HTT.EEEEESSSSTTSSGGG CS
                           DAO   2 vviiGGGiiGlstAyeLa.rrg.VtllekgdiagsgaSg 38 
                                   ++i+GGG   +  A  La  ++ +tl+ ++d++  + S+
  gi|70607860|ref|YP_256730.1| 154 ILIVGGGDSAVDWAINLApVAKsITLIHRRDQFRAHESS 192
                                   99***************754457*******999876665 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.78
                                   TCEEEEE...EECT.EEE.EEEEEEEE--GGGHH CS
                           DAO 177 gkvwgve...rttp.gen.daadavVnaaGawsd 205
                                    kv++     + t+ + + d +dav+++ G+  d
  gi|70607860|ref|YP_256730.1| 216 SKVTQAVifdNRTKeEKTlD-VDAVIISIGHKGD 248
                                   33333336786666455544.599****998765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.1e-07    0.0011       1      39 [.       5      43 ..       5      79 .. 0.94
   2 ?   -0.4   0.0      0.42   5.8e+02       2      32 ..     154     184 ..     154     186 .. 0.92
   3 ?   -2.9   0.0       2.4   3.3e+03     104     134 ..     202     234 ..     197     240 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.1e-07
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                  D+++vGGgp G+ A   +  ++ + lL++ ++ lGG+l 
  gi|70607860|ref|YP_256730.1|  5 DIIIVGGGPIGLFATFYSGLRDMSALLIDAQDELGGQLV 43
                                  9***********************************986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                   +++vGGg + v  Ai  a   ++  L+++r+
  gi|70607860|ref|YP_256730.1| 154 ILIVGGGDSAVDWAINLAPVAKSITLIHRRD 184
                                   79****************9999999999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.4
                  FAD_oxidored 104 vllntrlvevekegkriesvtveske.g.rkti 134
                                   v ++++l+ev+ +g ++++ ++ +++ + +kt+
  gi|70607860|ref|YP_256730.1| 202 VHTWHELKEVKGDGSKVTQAVIFDNRtKeEKTL 234
                                   678889999999998866555555554546665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   2.2e-05     0.031      17      55 ..       3      40 ..       1      44 [. 0.91
   2 ?    1.6   0.0     0.096   1.3e+02      10      38 ..     144     172 ..     132     184 .. 0.80
   3 ?    0.3   0.0      0.24   3.4e+02     155     176 ..     232     253 ..     210     273 .. 0.81
   4 ?   -2.5   0.0       1.8   2.5e+03     101     120 ..     306     324 ..     295     328 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                  e D++ivG+G+ GL a++y + + d+  ++++++  +GG
  gi|70607860|ref|YP_256730.1|  3 EYDIIIVGGGPIGLFATFYSGLR-DMSALLIDAQDELGG 40
                                  78*******************99.9**999999988888 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.096
                                   HHHHHHTEEEEEEE--SHHHHHHHHHHHH CS
                          Thi4  10 edllkyaesDvvivGaGssGLtaayylak 38 
                                   +   ++ e  ++ivG+G s +  a  la 
  gi|70607860|ref|YP_256730.1| 144 KRKKDFEEKRILIVGGGDSAVDWAINLAP 172
                                   5567899999********99988888775 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.24
                                   EEEEEEEEEE--GSSSTTTTHH CS
                          Thi4 155 lvirakvvvdatGhdgeivavv 176
                                   ++++  +v+ + Gh g++++v 
  gi|70607860|ref|YP_256730.1| 232 KTLDVDAVIISIGHKGDLGNVP 253
                                   57788899999******99985 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.8
                                   HHHHHHHHTSTTEEEEESEE CS
                          Thi4 101 stllskvlqlanvkllnava 120
                                   + ++ k ++ +nv ++ + +
  gi|70607860|ref|YP_256730.1| 306 TSMAKKYID-PNVSIFGGHS 324
                                   234445555.7777776655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.46   6.4e+02       7      20 ..       3      16 ..       1      17 [. 0.81
   2 !   15.7   0.0   1.1e-05     0.016       4      51 ..     148     200 ..     147     274 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.46
                 NAD_binding_7  7 gkkvlvvGgGevAa 20
                                  +  +++vGgG++++
  gi|70607860|ref|YP_256730.1|  3 EYDIIIVGGGPIGL 16
                                  66789******985 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.1e-05
                 NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapev....keele....elvkla 51 
                                   d+++k++l+vGgG+ A   + +l++  + +t++  +     +   e    +l+++a
  gi|70607860|ref|YP_256730.1| 148 DFEEKRILIVGGGDSAVDWAINLAPVAKSITLIHRRDqfraH---EssvkQLYNIA 200
                                   789******************************998543320...24444333322 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   8.3e-06     0.011     176     215 ..     144     183 ..     137     202 .. 0.88
   2 ?   -0.3   0.1       0.2   2.8e+02     306     330 ..     219     245 ..     199     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
                      FMO-like 176 kepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrs 215
                                   k+ + f++kr+l++G G+s+ d a++l+  a+ + l  r+
  gi|70607860|ref|YP_256730.1| 144 KRKKDFEEKRILIVGGGDSAVDWAINLAPVAKSITLIHRR 183
                                   67788***************************99887776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                      FMO-like 306 tetsaifedgtvee...didvvifatGy 330
                                   t +++if++ t+ee   d+d+vi + G+
  gi|70607860|ref|YP_256730.1| 219 T-QAVIFDNRTKEEktlDVDAVIISIGH 245
                                   4.57999999999955568999998886 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.28   3.9e+02      19      61 ..       3      76 ..       1     108 [. 0.67
   2 ?   10.8   0.1   0.00018      0.25      18      57 ..     150     243 ..     140     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.28
                                  T-EEEEESSTT.........................SHHHHHHTTSTT-......SEEEEEES-HHHHHHHHHH CS
                Spermine_synth 19 pkevLiiGGgD.........................Ggvlrevvkhntv......ekitlvdiDqkvidfskkf 61
                                   ++++i+GGg                          Gg+l  +   + v        i   d+ q+ i+  k+f
  gi|70607860|ref|YP_256730.1|  3 EYDIIIVGGGPiglfatfysglrdmsallidaqdelGGQLVTIYPEKMVydvggyPGILAYDLAQNLIEQAKMF 76
                                  68899999997777777777777777777777777766666665555445555554555555555555555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00018
                                   ST-EEEEESSTT......................................................SHHHHHHTTSTT-SE CS
                Spermine_synth  18 npkevLiiGGgD......................................................Ggvlrevvkhntvek 44 
                                   + k++Li+GGgD                                                       +v+  v++ n  ++
  gi|70607860|ref|YP_256730.1| 150 EEKRILIVGGGDsavdwainlapvaksitlihrrdqfrahessvkqlyniasvhtwhelkevkgdgSKVTQAVIFDNRTKE 230
                                   789*********999999999999999999999999999999999999999999999999999986678888888888899 PP

                                   EEEEES-HHHHHH CS
                Spermine_synth  45 itlvdiDqkvidf 57 
                                       d+D  +i++
  gi|70607860|ref|YP_256730.1| 231 EKTLDVDAVIISI 243
                                   9999999998875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0054       7.5       1      39 [.       5      43 ..       5      44 .. 0.93
   2 ?   -0.7   0.0      0.43   5.9e+02       2      37 ..     154     189 ..     153     193 .. 0.90
   3 ?    3.5   0.0     0.023        31     378     402 ..     266     284 ..     257     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0054
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                  D+i++G+G  GL A+     +  + ++++  +e gg+++
  gi|70607860|ref|YP_256730.1|  5 DIIIVGGGPIGLFATFYSGLRDMSALLIDAQDELGGQLV 43
                                  99**************9999999******9999999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.43
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37 
                                   ++++G+G +    A+++a   ++++++   ++f+ +
  gi|70607860|ref|YP_256730.1| 154 ILIVGGGDSAVDWAINLAPVAKSITLIHRRDQFRAH 189
                                   79******************9*99999999998875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.023
                                   BETTSBESTTEEESSBTEEE-STCE CS
                 FAD_binding_2 378 tdengrvldadgqpipGLYAaGeva 402
                                   +++++++      ++pG YAaG  a
  gi|70607860|ref|YP_256730.1| 266 VNAKMET------NLPGVYAAGDIA 284
                                   6677777......*********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2183.99
//
Query:       gi|70607861|ref|YP_256731.1|  [L=363]
Description: alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-29  102.0   1.2    1.6e-29  102.0   1.2    1.9  2  ADH_N            Alcohol dehydrogenase GroES-like domain
    1.7e-27   96.0   0.7    2.7e-27   95.3   0.1    1.7  2  ADH_zinc_N       Zinc-binding dehydrogenase
    8.9e-10   38.4   0.1    1.5e-09   37.7   0.1    1.3  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00012   23.1   0.0    0.00036   21.6   0.0    1.8  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.029   13.7   3.3       0.16   11.2   1.6    2.2  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.052   12.9   0.2      0.098   12.0   0.2    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.079   13.2   0.2       0.15   12.3   0.2    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.22   10.8   1.3       0.42    9.9   1.3    1.4  1  ThiF             ThiF family


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   1.2   7.1e-33   1.6e-29       2     107 ..      26     150 ..      25     152 .. 0.90
   2 ?   -2.6   0.1       2.3   5.1e+03      38      61 ..     257     280 ..     233     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 7.1e-33
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-. CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC. 81 
                                   +ev+i+vka+g+C+sD+ ++ g  +++v++p+i GHEi+G v++vg++v+++k GdrV+  ++++cg+C++C +g enlC 
  gi|70607861|ref|YP_256731.1|  26 NEVMIEVKATGMCHSDVNVFLG--STPVPTPVIAGHEIAGRVVKVGHNVSRVKEGDRVISTFIQPCGKCKNCISGMENLCe 104
                                   89*******************9..7*******************************************************9 PP

                                   ....................TTBEETTTSS-SSSBSEEEECGGGEE CS
                         ADH_N  82 ....................eeakllgvsldGgfaeyvvvpekklv 107
                                                       ++++ + + l Ggfaey +v+e+ l 
  gi|70607861|ref|YP_256731.1| 105 tfasvrlkgtmfdgttrvkyKDGRSIRTFLGGGFAEYSIVHENALT 150
                                   99999998888887777755555555555************98876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                                   EEEEEEEEESTT-CS--TT-EEEE CS
                         ADH_N  38 EivGeveevgpevkklkvGdrVvv 61 
                                   E+ G+ e +  +++++++G +Vv+
  gi|70607861|ref|YP_256731.1| 257 EAGGTQETIQMALEGVRIGGKVVL 280
                                   556666677777778888888875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.4   5.3e+03      62      90 ..     164     192 ..     152     193 .. 0.76
   2 !   95.3   0.1   1.2e-30   2.7e-27       1     128 [.     194     323 ..     194     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                                   EEESSCSHHHHHHHHHCEEEEEEEEECSC CS
                    ADH_zinc_N  62 vfecvGsgatleaalkllkpgGrlvvvGg 90 
                                   v+ c+G+ a    + + ++pg  ++vvG+
  gi|70607861|ref|YP_256731.1| 164 VLGCSGITAYGAISSANVRPGDSVAVVGV 192
                                   66677777777777778888888888885 PP

  == domain 2  score: 95.3 bits;  conditional E-value: 1.2e-30
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   gvGl ++q+++a Ga ++ia   ++ kle+a +lGa+ +in+ke ++v+ +ke+t+g g+d+++e+ G+++t+++al+ ++
  gi|70607861|ref|YP_256731.1| 194 GVGLSVIQMLRAVGAgRIIALGTKKWKLEKALELGATDFINTKESEPVKTLKEMTNG-GPDIIIEAGGTQETIQMALEGVR 273
                                   9*****************************************777**********87.*********************** PP

                                   EEEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGg..gkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                    gG++v++G+   +   ++++++++++ ++i+G  ++++r +++++++l+
  gi|70607861|ref|YP_256731.1| 274 IGGKVVLIGLppTSALIPVRVSMIVRNGITIIGNYGSKPRVDMPKLVELV 323
                                   **********8444444499999***********************9997 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   6.6e-13   1.5e-09      25     200 ..     177     348 ..     159     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 6.6e-13
                   Glu_dehyd_C  25 safewep.esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGat.Yvdsre.tpvdeipease.em 101
                                   s+++ +p +s+ v+G G +GL  + +l+a   g  r+  lg+++    +++   elGat +++++e +pv+++ e+++  +
  gi|70607861|ref|YP_256731.1| 177 SSANVRPgDSVAVVGVGGVGLSVIQMLRA--VGAGRIIALGTKKW---KLEKALELGATdFINTKEsEPVKTLKEMTNgGP 252
                                   555666647999***************97..79999*****8665...555568****97788766268999998764279 PP

                   Glu_dehyd_C 102 dlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpesl 181
                                   d+++Ea G+ + +  a+e ++  G ++L+G+p  s  + v+++     +v +   ++G   ++ r     + +L ++++  
  gi|70607861|ref|YP_256731.1| 253 DIIIEAGGTQETIQMALEGVRIGGKVVLIGLPPTSaLIPVRVSM----IVRNGITIIGNYGSKPRVDMPKLVELVRTKRYD 329
                                   *******************************9876255555544....45556789*******9999999999******** PP

                   Glu_dehyd_C 182 ldelvtkvvdldeleeAfe 200
                                    ++l+t++ +l+e++eA +
  gi|70607861|ref|YP_256731.1| 330 PQKLITGKFKLEEINEAVK 348
                                   ***************9975 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   1.3e+04      38      54 ..     201     216 ..     184     224 .. 0.56
   2 !   21.6   0.0   1.6e-07   0.00036       1     125 [.     227     353 ..     227     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                                   HHHHHEEEEEEEEE--- CS
                  ADH_zinc_N_2  38 aslkvlpggGrlvsigg 54 
                                   + l+++ g Gr++ +g 
  gi|70607861|ref|YP_256731.1| 201 QMLRAV-GAGRIIALGT 216
                                   344444.4588887773 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.6e-07
                                   TT-SEEEETT.STTHH..HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--G CS
                  ADH_zinc_N_2   1 lGAdevidyr.tedfe..aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyefl 78 
                                   lGA+ +i+ + +e ++  ++  ++g D+++++ g++++++ +l+ ++ gG++v ig pp+sa ++ + ++  + ++++   
  gi|70607861|ref|YP_256731.1| 227 LGATDFINTKeSEPVKtlKEMTNGGPDIIIEAGGTQETIQMALEGVRIGGKVVLIGLPPTSALIPVRVSMIVRNGITIIGN 307
                                   8******999899999995555788*******99888889999999888*******9998888888888887788888888 PP

                                   GG...-.-HHHHHHHHHHHHHHH---..-EEEEEEGGGHHHHHHHHHSS CS
                  ADH_zinc_N_2  79 fsmkasaqadileelaalieeGklrp..vvdrvfpleeaaeAhrylesg 125
                                      ++  + d + +l++l+  ++  p   ++  f+lee++eA+++le+g
  gi|70607861|ref|YP_256731.1| 308 YG-SKP-RVD-MPKLVELVRTKRYDPqkLITGKFKLEEINEAVKLLEEG 353
                                   74.333.577.9***********8873357788**************99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.6   7.2e-05      0.16      18      83 ..     171     241 ..     163     256 .. 0.75
   2 ?    2.4   0.0     0.036        80     116     174 ..     245     299 ..     241     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                                   ETTCEETC..B---.EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTC.ECEEHCHHHH CS
                   AlaDh_PNT_C  18 tlaGgvpg..vepa.kvlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslgak.fvevlksqee 83 
                                   t+ G ++   v+p+  v v+G+G +Gl+ i++ +++ga ++ +l +++ +le+  +lga+ f+++++s+  
  gi|70607861|ref|YP_256731.1| 171 TAYGAISSanVRPGdSVAVVGVGGVGLSVIQMLRAVGAgRIIALGTKKWKLEKALELGATdFINTKESEPV 241
                                   555655533377773599*******************9668999999999999999776527777777654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.036
                                   HTS-TTEEEEETTGGGT-SBTT--TBBTTSEEEEETTEEEEEBSTGGGGSHHHHHHHHH CS
                   AlaDh_PNT_C 116 ksMkpgsVivDvAidqGGnvetsrltthgepvveekgvvhygvanlpgavprtasallt 174
                                   k+M +g    D+ i++GG+ et++++ +g  +     vv++g +   + +p+  s++  
  gi|70607861|ref|YP_256731.1| 245 KEMTNGG--PDIIIEAGGTQETIQMALEGVRIGG--KVVLIGLPPTSALIPVRVSMIVR 299
                                   5555555..3999*********999888777755..89999999888888888777655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.4e-05     0.098      36      73 ..     184     222 ..     172     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                   TSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH CS
                  2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee 73 
                                   g  v+++G+G +G +v+++l+a+g+ ++ia  ++k k e
  gi|70607861|ref|YP_256731.1| 184 GDSVAVVGVGGVGLSVIQMLRAVGAgRIIALGTKKWKLE 222
                                   6789********************988888877765444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.6e-05      0.15       1      78 [.     187     260 ..     187     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.SEEEE-SS CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.dlvvnlsp 78 
                                   v ++G G+vG +v+++l + +    +i+  + +k kle++++       ++i    +++ ++L+++ ++g d+++ + +
  gi|70607861|ref|YP_256731.1| 187 VAVVGVGGVGLSVIQMLRAVGAG--RIIALGTKKWKLEKALE---LGATDFINTKESEPVKTLKEMTNGGpDIIIEAGG 260
                                   679****************9987..**************994...56678888888899999****99999**999876 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00019      0.42      20      45 ..     186     211 ..     177     214 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
                                   EEEEE--SHHHHHHHHHHHHHTTTEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  20 kvllvGaGglGsellknLalsGvgkl 45 
                                   +v++vG+Gg+G  ++++L ++G g++
  gi|70607861|ref|YP_256731.1| 186 SVAVVGVGGVGLSVIQMLRAVGAGRI 211
                                   699********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2500.15
//
Query:       gi|70607862|ref|YP_256732.1|  [L=475]
Description: phenylacetyl-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   50.9   0.0    2.4e-13   50.2   0.0    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    0.00044   19.0   0.7     0.0013   17.4   0.7    1.6  1  AMP-binding      AMP-binding enzyme
  ------ inclusion threshold ------
      0.084   12.1   0.0       0.14   11.3   0.0    1.2  1  Glyco_transf_11  Glycosyl transferase family 11


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0     4e-17   2.4e-13       1      96 []     380     472 ..     380     472 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4e-17
                                   TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS-...-EEEEE- CS
               AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvs...vkvelve 78 
                                   G  + P  ie++++ei++++++++i+v+ e e+++l++k+E k++ +d     ea++k++++ l++k+g++   v++e+++
  gi|70607862|ref|YP_256732.1| 380 GKLLLPIYIEDAINEIPDTTGMFNIMVYAE-EMEKLRIKIESKRDRVD-----EAYDKSAKALLANKIGLDendVEIEWIR 454
                                   66789***********************75.9************9877.....59***************6555******* PP

                                   TT-S---------EEE-S CS
               AMP-binding_C_2  79 pgtlprsegKakrviDkR 96 
                                   pg++ ++ +K++ ++D+R
  gi|70607862|ref|YP_256732.1| 455 PGEAVWTGYKLQVFVDQR 472
                                   *****************9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   2.2e-07    0.0013     167     368 ..     128     325 ..      95     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-07
                                   E--SSSS-EEEEEEHHHH....HHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHH..HHHHHHHHTT-EEEE-TTCGCCH CS
                   AMP-binding 167 TSGTTGkPKGVmlshrnl....vanvaslkletrfklkeddvvlsilplahifgli..lelllallsGatvvllpkdaald 241
                                   TSG+TG+P         l     a+++   l    +++++ ++  +l ++  +++   + + ++  +Gat +   ++++++
  gi|70607862|ref|YP_256732.1| 128 TSGSTGMPTFQGWGKLELdyfqEAQARY--LWSFAGVRPGITYANYLNMSGFYSWGppVVETAMWRCGATTIAGGGETFFS 206
                                   8888888854444333332212111122..222244556667777777766666532256677777888888877777777 PP

                                   .HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC..EEEEEEEEGG CS
                   AMP-binding 242 .pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge..evlegYGlTE 319
                                    +++ l  ++ +k+ v+a++P + + + e   ++           +++ll g++  +++ +++ ++ ++    ++++G T 
  gi|70607862|ref|YP_256732.1| 207 wKQRHLLIFKLWKIDVFATTPWLHRLIGEMAIEE-----GWETPFKVLLLHGGAAAENTKKRLFKVHPNaeMAINVWGTTD 282
                                   7788899******************997743333.....23344999999999999999999999999998789******* PP

                                   GSSECEECHCTTTCTSTTS-BEE-.T.TEEE.EEE-TTTSCBEETTSEEEEE CS
                   AMP-binding 320 ttgvvtvlpleedkkklgsvGkpl.p.gvev.kivDeetgepvpdgeeGell 368
                                     ++v  lp + +       G  + + ++e+  ++D++t+epv +ge Gel 
  gi|70607862|ref|YP_256732.1| 283 GHMAVE-LP-NSR-------GELViWeDMEIfDVIDPKTNEPVSEGERGELI 325
                                   *99986.44.333.......333303355542677***************96 PP

>> Glyco_transf_11  Glycosyl transferase family 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.14     192     238 ..     387     433 ..     380     441 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
               Glyco_transf_11 192 YleealdkfrarvssvvfvvfSddveWckkniktssgdvyfagdgsp 238
                                   Y+e+a+++++       ++v+ +++e  + +i+ +++ v +a+d s+
  gi|70607862|ref|YP_256732.1| 387 YIEDAINEIPDTTGMFNIMVYAEEMEKLRIKIESKRDRVDEAYDKSA 433
                                   9*******************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3400.45
//
Query:       gi|70607863|ref|YP_256733.1|  [L=352]
Description: aspartate-semialdehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  106.4   0.0    3.4e-30  105.0   0.0    1.7  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      1e-22   81.1   0.0    1.7e-22   80.4   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
      0.023   14.3   0.1      0.071   12.7   0.0    1.9  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0   5.6e-34   3.4e-30       1     118 [.       6     128 ..       6     131 .. 0.97
   2 ?   -2.3   0.0      0.98   5.9e+03      55      79 ..     198     223 ..     163     233 .. 0.57

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 5.6e-34
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivflalp 75 
                                   k+ai+G tG vG e +r+L++hp+++ ++l+++ +  Gk++ e+v+      +++e+++ +++++d++++++vd+vf+ lp
  gi|70607863|ref|YP_256733.1|   6 KAAILGSTGLVGIEYVRMLANHPYIKPTYLAGRGS-VGKPYGEVVRwqtigqIPKEIANQEIRPTDPKQMDDVDLVFSPLP 85 
                                   689*****************************999.***************99**************************** PP

                                   HHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGG CS
                Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkddavyvlpevnreai 118
                                   ag ++++++++a+ g+kvi++s+d+Rl++d+++++pevn++ +
  gi|70607863|ref|YP_256733.1|  86 AGSAAQVEDEFAKLGFKVISNSPDHRLEPDIPLIIPEVNPHSL 128
                                   ****************************************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.98
                                   BEEE.GGGGGCTT-SEEEE-SCHHHH CS
                Semialdhyde_dh  55 kved.vdeeelkevdivflalpagvs 79 
                                   ++ + +d++ +ke+  v+ ++  +vs
  gi|70607863|ref|YP_256733.1| 198 PLGNeYDAKMVKEMTKVLNSTKRNVS 223
                                   33334555555666666666665555 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   2.8e-26   1.7e-22       1     182 [.     159     331 ..     159     333 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 2.8e-26
                                   HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
               Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                   L P++++ +++++v ++t+qa+SGaG+                    pgv ++++ +N++p+  + +     +++e  k +
  gi|70607863|ref|YP_256733.1| 159 LVPIYQN-FRVQSVFITTMQALSGAGY--------------------PGVASLDVIDNILPLGNEYD-AK--MVKEMTKVL 215
                                   679***6.*******************....................9**************99855.44..69******* PP

                                   HHHHHHCTESC..SEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSHCHHSSH CS
               Semialdhyde_dhC  82 aetkkilefte..kvsatcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvneeedrPtp 148
                                   ++tk  +++++  ++s t +rVP + Gh + v++ +k ++v++ +++e l +             pe+++v  e+ +rP+ 
  gi|70607863|ref|YP_256733.1| 216 NSTKRNVSDESniNISTTTHRVPTIHGHYAVVYVTFK-ENVDLGKIRESLVNFsgepqalklptaPEKVIVLTEQDNRPQV 295
                                   ********99988888********************8.999999999999998899*********999999999******* PP

                                   HHHTTC.....SSSEEEEEEEEETTCTTEEEEEEEEETT CS
               Semialdhyde_dhC 149 aavagg.....tnsvsVGRirkdemgdeglklvvvgDNl 182
                                     ++ +     ++sv VGR+ +   +   + +v++++N 
  gi|70607863|ref|YP_256733.1| 296 YFDR-WlgdppGMSVIVGRLTQVDNN--AIRFVSLIHNS 331
                                   9999.447899*******99998844..5*********5 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.53   3.2e+03       8      24 ..     162     178 ..     157     182 .. 0.83
   2 ?   12.7   0.0   1.2e-05     0.071      63     110 ..     221     268 ..     201     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.53
                                   HHHHHEEEEEEEEEEEE CS
                       Gp_dh_C   8 lndkfgikkglmttvha 24 
                                   + ++f ++++++tt  a
  gi|70607863|ref|YP_256733.1| 162 IYQNFRVQSVFITTMQA 178
                                   778999*******9887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.2e-05
                                   HHSGGGTTTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHH CS
                       Gp_dh_C  63 lVlpelkgkldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaa 110
                                   +V +e +++++++  rVPt+ ++   + v+++++v    + + l + +
  gi|70607863|ref|YP_256733.1| 221 NVSDESNINISTTTHRVPTIHGHYAVVYVTFKENVDLGKIRESLVNFS 268
                                   5778999*****************************999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2757.16
//
Query:       gi|70607864|ref|YP_256734.1|  [L=555]
Description: long-chain-fatty-acid--CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.8e-104  349.7   0.0   2.2e-104  349.4   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      6e-19   68.8   0.2    1.6e-18   67.5   0.2    1.8  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.4   0.0  2.4e-108  2.2e-104       2     422 ..      31     454 ..      30     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 349.4 bits;  conditional E-value: 2.4e-108
                                   HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                   AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                   e +a+++pdk a+++   g+++ Y+ l +++ +++++L  +lG+kkgdrVai++pns++w++a+++il+a+avvvp+np  
  gi|70607864|ref|YP_256734.1|  31 EVSANRYPDKDAIIY--YGTRIKYEKLLSNTLKFSSFLYnELGIKKGDRVAIFMPNSVQWIIAYFGILRANAVVVPINPLI 109
                                   6789***********..99************************************************************** PP

                                   -HHHHHHHHHHHTESEEE.............E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                   AMP-binding  82 taeelayiledseakvli.............a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                    ++el yil+ds++ +++             +  +v +    + ++  ++ ++ k+  ++ ++                  
  gi|70607864|ref|YP_256734.1| 110 AEDELNYILKDSGSVAVVtlssqlpkvmkaiQgtEVRNVISGMFRDYLSSSPEIKVHPLMLKE------------------ 172
                                   ******************444444444333212122122223333333333333333333333.................. PP

                                   S................-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSC.CTTT-EEEESS-T CS
                   AMP-binding 148 e................kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfk.lkeddvvlsilpl 211
                                   +                kp +e++++++d+a+i YTSGTTG PKG++++h  +  +v   +    ++ ++++   l+ lpl
  gi|70607864|ref|YP_256734.1| 173 PeiqgdvikwkesissnKPLPEVSVTSEDIALIPYTSGTTGFPKGCIHTHSTIWPTVIGSA---FWNmVTPSAIGLASLPL 250
                                   144555556666666665777889*****************************99999853...34546678888****** PP

                                   TSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEES CS
                   AMP-binding 212 ahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllgg 292
                                   +h++g++ +l++++++G+t+vl++ +++   ++ l++iek+kvt+++ + +++  ll+ + ++    ++dlssl +v  gg
  gi|70607864|ref|YP_256734.1| 251 FHVTGFVHSLNTPMYVGGTIVLMSIWDR---EAALDAIEKYKVTHWTNISTMVVDLLSTPGIE----KRDLSSLVMVGGGG 324
                                   ************************9988...3347***********************88887....67*******999** PP

                                   S-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETT CS
                   AMP-binding 293 eplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpg 373
                                   +++++++++++r+l+g   +egYGlTEt   ++ ++++++ +kl+  G p  gv++ +vD +tge +p+++eGe++v+ p+
  gi|70607864|ref|YP_256734.1| 325 AAMPEAVAKKLRELTGLDYVEGYGLTETMSQTH-VNPPHR-PKLQCLGIPHFGVDALVVDASTGEVLPPNKEGEIVVKCPS 403
                                   ***************99***************9.775555.788999********************************** PP

                                   S-SEBTT-HHHHHHHEEE.TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 374 vmkgYlkkpeataeafds.egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                   ++kgY++k+e+t+++f++ +g  ++rTGDlg++d++Gy++iv+R k +i++
  gi|70607864|ref|YP_256734.1| 404 LFKGYWRKEEETRKSFITiNGTeYFRTGDLGYMDDEGYFFIVDRVKRMINR 454
                                   *****************863344***********9**************85 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.2   1.7e-22   1.6e-18       1      76 []     463     540 ..     463     540 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.7e-22
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   +vE+ l +hpa+ ea+Vv  pd++ Ge ++a+Vvl+++   + +ee+++++ ++++ +y  p+ v+fvd+lpk  sGK
  gi|70607864|ref|YP_256734.1| 463 KVENKLYQHPAILEACVVSTPDPRVGEEVKAYVVLRPEfRgKVTEEDIIKWSKEHMSAYEYPRVVEFVDSLPKSGSGK 540
                                   69*********************************8765334599********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3708.08
//
Query:       gi|70607865|ref|YP_256735.1|  [L=315]
Description: fumarylacetoacetate (FAA) hydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-57  193.5   0.0    4.6e-57  193.2   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.0   2.6e-61   4.6e-57       2     218 .]     101     314 ..     100     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 2.6e-61
                                   EEEEEEE--SHHHHHTTT....-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HH CS
                 FAA_hydrolase   2 ivcdglnyaehvreagka...aeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsve 79 
                                    v d+l+++ hv+   k    + + ++++ip+   ++ + ++++ g+ +++++P+ s+ ld+E+E+++++ ++  ++ +  
  gi|70607865|ref|YP_256735.1| 101 TVRDFLAFRGHVEASYKRrgqQIPEEWFKIPI---YYKGDPAAFYGHMENVPWPSYSNALDFELEIGAIVYRKGVNI-EKR 177
                                   57899*********999999989999*99999...******************************************.99* PP

                                   HHHTTEEEEEEEEEEE-SBGGG---..HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTS CS
                 FAA_hydrolase  80 eAedaiaGytllnDvsaRdlqaeek.aplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifs 159
                                   +A+d+i+Gyt++nD+saRd+q++e+ + lg+++gk f  +  +Gpwivt+de+++ + l+  ++v+ge+  d++++dm +s
  gi|70607865|ref|YP_256735.1| 178 KARDYILGYTIFNDFSARDIQMREMtCLLGPAKGKDF--ANGLGPWIVTKDEVGEIKGLRAYASVDGEKWCDTKAEDMQWS 256
                                   *************************6666********..****************************************** PP

                                   HHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                 FAA_hydrolase 160 paeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                   ++++i+++s+   ++pGd++++GT+sg  ++ ++ ++l++g  ve+ ie++G l nrV+
  gi|70607865|ref|YP_256735.1| 257 FEDMISYVSQDEYIRPGDIFGSGTISG-CCGLDNGRLLRPGSLVELYIEKIGILVNRVV 314
                                   **************************9.46799************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2295.86
//
Query:       gi|70607866|ref|YP_256736.1|  [L=305]
Description: hypothetical protein Saci_2150 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-25   88.8   0.7    1.7e-24   87.0   0.7    1.8  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.7   9.4e-29   1.7e-24       3     197 .]      23     210 ..      21     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 9.4e-29
                                   CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                   Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                   ++ +n+ +i+g++ v++iD++ts+  ++ ++e  ++ +++k+v+++i+TH H DHi+ ++ l +at + +  ++ ++ ++ 
  gi|70607866|ref|YP_256736.1|  23 WFLSNTGFIVGKDFVVVIDSLTSEKPTKVFKEEMRKIIGDKPVKYLINTHEHGDHIWTNH-LFNATTISHKNCRRTTIEGM 102
                                   6789****************************************************9985.6699999************* PP

                                   CHHHHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTE...EEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCC CS
                   Lactamase_B  84 meeaddaasrkgll...lagvsadkpdvdeeeldgnaggr...ralyvtggpghghghgvveygggkvlftGDallagetg 158
                                   + +++++++ ++     +   ++  p+ ++ e +  ++ +   +   +++g++h+ +++ ++++++kv+ftGD+l++++  
  gi|70607866|ref|YP_256736.1| 103 KSGVNPYEHIFKEVdftG---WKYTPQDVTVESEMSLWVDkdkEIKIIHPGFAHTRSDLFIYFPDEKVVFTGDLLFSPPCT 180
                                   **********99874442...3333333333333333333000344578999***************************** PP

                                   CCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 159 ridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                    + l          +  + y+++l++la l+a+v++pgH
  gi|70607866|ref|YP_256736.1| 181 PFAL---------MGYLQGYIKTLEDLASLDADVYIPGH 210
                                   ****.........************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2323.99
//
Query:       gi|70607867|ref|YP_256737.1|  [L=295]
Description: hypothetical protein Saci_2151 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-17   62.0  15.8    9.4e-17   61.4  15.8    1.2  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4  15.8   5.2e-21   9.4e-17       3     230 ..      12     242 ..      10     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 5.2e-21
                          TauE   3 lagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvd..wrllll.lllgsliGall 79 
                                   +++l+a++  g +G G++ +++P+Ll+ + +p+++ ++  ++ ++ + s+++ +  + +++  + l+++  ++g +iG++l
  gi|70607867|ref|YP_256737.1|  12 IVFLIASIPVGGIGYGFSAVSTPILLIdY-SPKQISPILNFIELFQNSSNVIINSGKYTLKreIILFVVfASPGLAIGSIL 91 
                                   7899999********************88.89998888888888888888887755433431133444404578899**** PP

                          TauE  80 Gallllllpse..llkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllllll 158
                                   G++ll+ l ++   lk+l+ v+l+ l+ll ++  +r + +   +  ++++++++ +l+G l G+++i+g + l+ ++   +
  gi|70607867|ref|YP_256737.1|  92 GSYLLKTLGGTspQLKILIYVILIPLILLQAYGFRR-SFT--LKSWKYLGSIIT-LLIGCLYGVTTISGPP-LALIVN-NQ 166
                                   ******999775579***************996652.222..344445544444.77***********666.444444.38 PP

                          TauE 159 glplkkavatslllilvislagalgyalagavdwpllll...llpgallGallGarlarrlsert.lrrlfallll 230
                                   gl+  + + + +ll +v s +++++y+ +g +++ ++ +     p+++ G+ +G  l++r+  +  +rr+ +++ +
  gi|70607867|ref|YP_256737.1| 167 GLSKEEYRFAISLLRVVESYTTFTSYLTLGIFSPAVIYYsilTSPAIIGGMAIGYFLSSRVRVKEdFRRVAMSFDA 242
                                   9*************************999999988887788677777888899999****9965559999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2072.86
//
Query:       gi|70607868|ref|YP_256738.1|  [L=318]
Description: formamidase/acetamidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-69  234.9   0.0    3.5e-43  147.9   0.0    2.0  2  FmdA_AmdA  Acetamidase/Formamidase family


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   2.1e-28   3.8e-24      14     153 ..       8     149 ..       2     153 .. 0.88
   2 !  147.9   0.0   1.9e-47   3.5e-43     202     371 ..     157     311 ..     151     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2.1e-28
                     FmdA_AmdA  14 klhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAepGDllvveildievlee 94 
                                    +hN+w   +++v +v++g+++ +e++++ dgq++ ++s +d+ ++d++++H+ltgP+ev gAepGD+l ve ld +    
  gi|70607868|ref|YP_256738.1|   8 ITHNKWDNSLQPVLKVSDGDVITLETKEASDGQVTPSSSVQDLLKLDFSRIHPLTGPIEVIGAEPGDALEVEFLDFRN--- 85 
                                   57*************************************************************************875... PP

                     FmdA_AmdA  95 aewGytgifdkenggGfl.kdafpe......aakaiwdlegiyassrq.ipgvrfrglphpGllGta 153
                                   + wG+tg++    g+Gfl ++++++      +a +iw+ ++ ya ++    +v++++ p+pG++G+a
  gi|70607868|ref|YP_256738.1|  86 KGWGWTGVL---PGFGFLaDEQYTSpidvlgPALKIWKADDKYAYAKFgDLEVSVPLHPFPGVIGVA 149
                                   57****998...5*****7666665222222578999999999988765569*************98 PP

  == domain 2  score: 147.9 bits;  conditional E-value: 1.9e-47
                     FmdA_AmdA 202 rtvpprengGnmDiknlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcg.aiemsgvvtlkvevikggmeklgiknpi 281
                                    t+pprengGnmDik+l+ G+k+ylPV+v+Ga lsvGD H +qGDGE+  cg aie    vt+k++++k++    g+++p+
  gi|70607868|ref|YP_256738.1| 157 STIPPRENGGNMDIKHLTIGTKLYLPVFVNGALLSVGDTHLAQGDGEV--CGtAIEGPMEVTIKIRLLKNV----GLSQPV 231
                                   69**********************************************..********************9....****** PP

                     FmdA_AmdA 282 flpeevep.ryseylsfeGisvdesgkqhyldltvAyrnallraieyLkkfGytkeqaylllsvapvegrisgivdiPnvv 361
                                   f+ ++v+  +++ey++f G      ++    dl +A ++a++ +i+ L+k   t  +ay+l s+  v+ r+s++vd+Pn +
  gi|70607868|ref|YP_256738.1| 232 FITKRVKEmEFNEYIAFPG-----IDR----DLWIASKKAVRGIISILSK-YMTPVEAYMLASTV-VNLRVSEVVDVPNWI 301
                                   ****999889*********.....446....99****************4.46899********9.*************** PP

                     FmdA_AmdA 362 atlalPldiF 371
                                   +t++lP d+ 
  gi|70607868|ref|YP_256738.1| 302 VTAYLPKDVL 311
                                   *******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2144.19
//
Query:       gi|70607869|ref|YP_256739.1|  [L=155]
Description: acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-16   59.7   0.0    3.4e-16   59.3   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.8e-16   59.8   0.0    3.5e-16   59.5   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.2e-16   59.5   0.0    4.5e-16   59.0   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.5e-11   44.7   0.0    1.8e-11   44.4   0.0    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    7.7e-10   38.9   0.0    1.5e-09   38.0   0.0    1.5  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    2.5e-07   30.6   0.0      5e-07   29.6   0.0    1.4  1  FR47             FR47-like protein
    0.00079   18.1   0.0     0.0023   16.6   0.0    1.6  2  AstA             Arginine N-succinyltransferase beta subunit
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.014   16.1   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.013   15.0   0.4      0.084   12.3   0.4    2.0  1  Acetyltransf_15  Putative acetyl-transferase
      0.014   15.2   0.0      0.028   14.2   0.0    1.7  2  Acetyltransf_16  GNAT acetyltransferase, Mec-17
      0.018   14.8   0.0      0.021   14.5   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
      0.036   14.2   0.0       0.06   13.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.096   12.3   0.1       0.18   11.5   0.1    1.5  1  CRM1_repeat_2    CRM1 / Exportin repeat 2


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   2.5e-19   3.4e-16      13     112 ..      39     149 ..      17     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.5e-19
               Acetyltransf_10  13 fkefispealrerieegealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                    +e +s +++++ +e+++ +++vae++gkivG++++   ++          i+ ++V+p+yr+qG+gk ++ ++eee+ek+
  gi|70607869|ref|YP_256739.1|  39 LEERVS-KSVDKSLENPDEIIVVAEDNGKIVGTARVvVHERifyfpdreaIIEEFYVHPAYRRQGVGKDIISFIEEELEKR 118
                                   445545.78899999*******************99644448999999999****************************** PP

               Acetyltransf_10  84 gikl.eltvnasp.yavpfYeklGFkavgee 112
                                   gi+l + +  + +  a +fY+k+GF+++ ++
  gi|70607869|ref|YP_256739.1| 119 GIQLlSANFPSRNvIASSFYKKMGFREIHSK 149
                                   ***99999999999************99765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.0   2.5e-19   3.5e-16      17     117 .]      36     143 ..      17     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 2.5e-19
                                   HHHHHHH....HHHHHHSTTCEEEEEEETTEEEEEE......EEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                Acetyltransf_1  17 edaseee....feesfsleaegllvaeedgeliGfi......sllkipdekggvayieslaVspeyrgkGlGsaLlealee 87 
                                   ++  ee+    + +s+++++e ++vae++g+++G++      +++  pd   ++a+ie+++V+p+yr++G+G+  +  +ee
  gi|70607869|ref|YP_256739.1|  36 PENLEERvsksVDKSLENPDEIIVVAEDNGKIVGTArvvvheRIFYFPD---REAIIEEFYVHPAYRRQGVGKDIISFIEE 113
                                   3333333233566667778888888***********5555554444444...89*************************** PP

                                   HHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  88 rareegikkivlaveedndaairlYeklGF 117
                                   +++++gi+ + +   + n+ a  +Y+k+GF
  gi|70607869|ref|YP_256739.1| 114 ELEKRGIQLLSANFPSRNVIASSFYKKMGF 143
                                   *******9987766555********88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   3.2e-19   4.5e-16       2      76 .]      55     145 ..      54     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 3.2e-19
                                   TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEEEEEEEETHH..... CS
                Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLleaae.....kgiileqlelnae..... 63 
                                   ++ + Vaed+gkivG++++++++         a i++++V+p+yr++G+G+ ++ ++e     +gi+l     +a+     
  gi|70607869|ref|YP_256739.1|  55 DEIIVVAEDNGKIVGTARVVVHErifyfpdreAIIEEFYVHPAYRRQGVGKDIISFIEeelekRGIQLL----SANfpsrn 131
                                   56789****************9999999988666666******************83334555776533....22122344 PP

                                   .HHHHHHHHTTEEE CS
                Acetyltransf_7  64 .kaikfYeklGFee 76 
                                     a +fY+k+GF+e
  gi|70607869|ref|YP_256739.1| 132 vIASSFYKKMGFRE 145
                                   68888*******96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.3e-14   1.8e-11       1     135 [.       4     144 ..       4     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.3e-14
                Acetyltransf_4   1 iraateeDakeilaiy.aeyvvntait.....feyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr.a 73 
                                   ir+a++eD k i +     y++n +++     +   ++  e++ k  ++  + + e++  ++++++ivG+a+++ ++ r  
  gi|70607869|ref|YP_256739.1|   4 IRLAKKEDTKTIVDFFsRMYRLNSEFDpllsnP---ENLEERVSKSVDKSlENPDEIIVVAEDNGKIVGTARVV-VHERiF 80 
                                   89*************956679999***554332...222233333333332346788888888**********9.555544 PP

                Acetyltransf_4  74 k...dwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                   +   +++ + ++y+ + + + +g+g+++i ++e+ l + +i+ l a   s n ++  f+k++GF+
  gi|70607869|ref|YP_256739.1|  81 YfpdREAIIEEFYV-HPAYRRQGVGKDIISFIEEELEKRGIQLLSANFPSRNVIASSFYKKMGFR 144
                                   43326777778999.699**********************************************8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.1e-12   1.5e-09       2     127 ..       4     145 ..       3     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.1e-12
                                   EEEE-GGGHHHHHHHHHHHTT----H............HHHHHHHHHHT..TSEEEEEEETTEEEEEEEEEEEE..EEETT CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespl.........e.eireyfrklle..esrvlgaedngelvgqlallple..lnvpG 68 
                                   ir +++ed + +++++++ +  + +           e ++ ++++k le  ++ +++aedng++vg+++++ +e  +++p+
  gi|70607869|ref|YP_256739.1|   4 IRLAKKEDTKTIVDFFSRMYRLNSEFDpllsnpenlEeRVSKSVDKSLEnpDEIIVVAEDNGKIVGTARVVVHEriFYFPD 84 
                                   899***************998877765779998655435555555555554579*************98876662266677 PP

                                   EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--.EEEE--....SSHHHHHTTT-EE CS
                Acetyltransf_9  69 ktlkaagvtgVavapehrgrgvlskLlaraleemreegqp.lsllfP....ssipiYrrfGyei 127
                                   ++   a +    v+p +r++gv ++++    ee++++g++ ls  fP    ++ ++Y+++G++ 
  gi|70607869|ref|YP_256739.1|  85 RE---AIIEEFYVHPAYRRQGVGKDIISFIEEELEKRGIQlLSANFPsrnvIASSFYKKMGFRE 145
                                   66...7899****************************8662799***7777667********86 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   3.6e-10     5e-07      23      83 ..      88     149 ..      81     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.6e-10
                                   SEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEEEEE CS
                          FR47  23 elgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfekieet 83 
                                   ++   +v+p  rr+G g+ +++ + +e+ +rg+++l +     N  ++++y+k+Gf++i  +
  gi|70607869|ref|YP_256739.1|  88 IIEEFYVHPAYRRQGVGKDIISFIEEELEKRGIQLLsANFPSRNVIASSFYKKMGFREIHSK 149
                                   677889**************************99762777889***************9655 PP

>> AstA  Arginine N-succinyltransferase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0023       1      79 [.       1      75 [.       1      77 [. 0.85
   2 ?   -1.6   0.0      0.55   7.5e+02     123     139 ..      89     105 ..      86     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                          AstA  1 MlviRparesDldallelaee...sgvgltsLpadeeaLekkiarsersfakeveepgeesYlfvledtetgevvGtsaiea 79
                                  M+ iR a+++D + ++++ ++       +  L ++ e Le+++++s++   ++   p  ++ + v ed  +g++vGt+ +++
  gi|70607869|ref|YP_256739.1|  1 MVSIRLAKKEDTKTIVDFFSRmyrLNSEFDPLLSNPENLEERVSKSVDKSLEN---P--DEIIVVAED--NGKIVGTARVVV 75
                                  899**************98875667899****************998754433...3..568999998..7*******9875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.55
                          AstA 123 lctlfldpeyrkgglgr 139
                                   +  ++++p+yr++g+g+
  gi|70607869|ref|YP_256739.1|  89 IEEFYVHPAYRRQGVGK 105
                                   66799********9987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.0   9.8e-06     0.014       4     138 .]       4     144 ..       2     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.8e-06
                Acetyltransf_3   4 LrplteeDlealfelrsdpe.vm.rylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedee.. 80 
                                   +r +++eD ++++ ++s+   ++ ++ p   ++e+ ee+++++  +  e+ +   ++ + +++++G++++   e+   +  
  gi|70607869|ref|YP_256739.1|   4 IRLAKKEDTKTIVDFFSRMYrLNsEFDPLLSNPENLEERVSKSVDKSLENPDEIIVVAEDNGKIVGTARVVVHERIFYFpd 84 
                                   6778888988888888876644423666688888888888887666555666656664444446****9996665555566 PP

                Acetyltransf_3  81 ...aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                      +  +++++p+++++G++++  + + e + e+ g++ l a+   +N      ++k+Gf+
  gi|70607869|ref|YP_256739.1|  85 reaIIEEFYVHPAYRRQGVGKDIISFIEEEL-EKRGIQLLSANFPSRNVIASSFYKKMGFR 144
                                   6645556999************999888888.7778***********************96 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   6.1e-05     0.084      75     139 ..      89     146 ..      42     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
               Acetyltransf_15  75 iYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkg 139
                                   i ++yv++ yr++G+ k ++  + +el    + + ++ll+   n       i+ ++Y ++gFr++
  gi|70607869|ref|YP_256739.1|  89 IEEFYVHPAYRRQGVGKDIISFIEEEL----EKRGIQLLSA--N-FPSRNVIASSFYKKMGFREI 146
                                   44789****************997777....4444444432..2.22333578999999999875 PP

>> Acetyltransf_16  GNAT acetyltransferase, Mec-17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   3.5e+03     144     160 ..      11      27 ..       4      30 .. 0.70
   2 ?   14.2   0.0     2e-05     0.028     106     149 ..      89     133 ..      39     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                   --HHHHHHHHHHH---S CS
               Acetyltransf_16 144 PsekllsFlekhynlkk 160
                                    +++++ F+++ y l++
  gi|70607869|ref|YP_256739.1|  11 DTKTIVDFFSRMYRLNS 27 
                                   46677888888888865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2e-05
                                   EEEEEE-GGGTTSSHHHHHHHHHHHHHT--.GGGSEEES--HHHH CS
               Acetyltransf_16 106 vldFyvheseqrkGlGkklfeamlkeekve.pkklaidrPsekll 149
                                   + +Fyvh    r+G+Gk ++ ++ +e + +  + l+ + Ps++++
  gi|70607869|ref|YP_256739.1|  89 IEEFYVHPAYRRQGVGKDIISFIEEELEKRgIQLLSANFPSRNVI 133
                                   558****************99877665444145566777887764 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.5e-05     0.021      37     122 ..      55     145 ..       7     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                          PanZ  37 egalfaarFNdRlLgAvkveledk.......eaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlav 110
                                   ++ +++a  N +  g ++v ++++       ea ++++ V    Rr GVg+ ++  + +++ e +  +l ++++   ++ +
  gi|70607869|ref|YP_256739.1|  55 DEIIVVAEDNGKIVGTARVVVHERifyfpdrEAIIEEFYVHPAYRRQGVGKDIISFIEEEL-EKRGIQLLSANFP-SRNVI 133
                                   4556789999999999998877554444444999*******************97777777.5567777777766.46677 PP

                          PanZ 111 lqaflealgfaa 122
                                   +++f +++gf +
  gi|70607869|ref|YP_256739.1| 134 ASSFYKKMGFRE 145
                                   888888888855 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.3e-05      0.06      22      59 ..      84     121 ..      60     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
               Acetyltransf_CG  22 egvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59 
                                   + + +++  +V++++r++G++k ++  + ++ +++g +
  gi|70607869|ref|YP_256739.1|  84 DREAIIEEFYVHPAYRRQGVGKDIISFIEEELEKRGIQ 121
                                   557899999***************99999988888865 PP

>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.18      19      37 ..      50      68 ..      39      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                 CRM1_repeat_2 19 rMakPeEVliveneeGeiv 37
                                    + P+E+++v +++G+iv
  gi|70607869|ref|YP_256739.1| 50 SLENPDEIIVVAEDNGKIV 68
                                  5678*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1011.83
//
Query:       gi|70607870|ref|YP_256740.1|  [L=427]
Description: NAD-dependent malic enzyme [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-27   96.0   0.2    1.2e-24   87.1   0.2    2.5  1  malic           Malic enzyme, N-terminal domain
    3.7e-23   82.1   0.4    1.9e-22   79.8   0.4    1.9  1  Malic_M         Malic enzyme, NAD binding domain
     0.0022   18.1   0.0     0.0046   17.1   0.0    1.5  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
     0.0081   16.2   0.1       0.13   12.3   0.0    2.2  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.021   15.0   0.0    1.5  1  DUF4031         Protein of unknown function (DUF4031)
      0.021   14.1   0.0      0.043   13.1   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.05   12.3   0.0      0.083   11.6   0.0    1.3  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1   0.2   4.7e-28   1.2e-24       2     182 .]      13     145 ..      12     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 4.7e-28
                                   TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTB CS
                         malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlG 82 
                                   +k+e+ ++ ++++   ++++++YtP+v+e+ +++ ++++k   +++s+ ++                ++vvtdg+r+LGlG
  gi|70607870|ref|YP_256740.1|  13 GKIEIYPKIPITSY--DDFSLIYTPGVAEVSKAIYKDPEKSF-ELTSRWNT----------------IAVVTDGTRVLGLG 74 
                                   57788888888888..9************************9.9*******................9************* PP

                                   S-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHHHHGCTS CS
                         malic  83 dlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavkelfppka 162
                                    +G +a++++m+GK  L++ l+g+d   ++p+ ++v+                             def+++vk+l+ +++
  gi|70607870|ref|YP_256740.1|  75 RIGpTAAMPVMEGKSLLFKYLGGVD---AIPLPINVK---------------------------SADEFISVVKALETSFG 125
                                   *************************...999999999...........................89*************** PP

                                   EEEE-S--CCHHHHHHHHHC CS
                         malic 163 liqfEDfkaknafeileryr 182
                                   +i++ED++++++f+ile+++
  gi|70607870|ref|YP_256740.1| 126 GINLEDIESPKCFYILEKLQ 145
                                   *****************985 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.4   7.6e-26   1.9e-22       2     257 ..     158     388 ..     157     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 7.6e-26
                                   HHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---TTT CS
                       Malic_M   2 qgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekleeek 82 
                                   qgTa   lagl++a+ +t+k  +e+k+v++GaG++ i  a  ++e     G +     +++ ++D+kG l ++re++++  
  gi|70607870|ref|YP_256740.1| 158 QGTAGAILAGLINAMILTNKDPKESKVVLYGAGASNIATARILAE----YGFKL----ENMIMIDSKGPLYSTREDIDHLM 230
                                   9*********************************99987776654....56665....4799***************8877 PP

                                   GGGSBS--SS--S....SHHHHHHHH-.-SEEEE-SSS.SS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHHHT CS
                       Malic_M  83 kpfakkkeelkeakdkltLeevvkkvk.ptvliGlsgv.agafteeivremaksterPiilplSNPtskaEataedvlkwt 161
                                    ++   k el+ +++ ++++e+ +++  ++v+i +s+  ++++++e v  m k+    i+++l NP    E  ++d+ +  
  gi|70607870|ref|YP_256740.1| 231 LHHRW-KYELAVKTNGYEVKEIKDAFSgADVVISASTPgPNVIKKEWVSVMNKN---AIVFALANPIP--EILPQDAKE-- 303
                                   66554.4455555688889998888764799**999962689999*99999776...6********86..899***987.. PP

                                   TT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHHHTT-SS--GGGH CS
                       Malic_M 162 dgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeelkegsllPelsei 242
                                    g+ +va+G          +   ++Q NN++ifP++  gv+ +rak +td+m+ +a+ealae+++++ ++e+ + P+++e 
  gi|70607870|ref|YP_256740.1| 304 AGAKIVATG----------RSDFPNQVNNSLIFPAVFRGVLDSRAKSVTDKMVISASEALAEFARRKGINENYIIPRMDEW 374
                                   589999998..........456799*****************************************************997 PP

                                   HHHHHHHHHHHHHHH CS
                       Malic_M 243 revslkvavavakaa 257
                                   + + ++va a+a +a
  gi|70607870|ref|YP_256740.1| 375 E-AYYEVASAIASKA 388
                                   5.5588888888877 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-06    0.0046      63     112 ..     242     292 ..     237     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                                   HCTT-EE--HHHCTTT-SEEEE-.SSSSSSB-HHHHCCS-TTEEEEE-SST CS
                 AdoHcyase_NAD  63 ameGfevvtleevvkkadivvtt.tGnkdiitlehlkkmkddaivcniGhf 112
                                     +G+ev++++++ + ad+v+++ t   ++i++e ++ m+++aiv  +   
  gi|70607870|ref|YP_256740.1| 242 KTNGYEVKEIKDAFSGADVVISAsTPGPNVIKKEWVSVMNKNAIVFALANP 292
                                   569*****************97637789*****************877655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.13   3.4e+02      10      37 ..     179     206 ..     171     214 .. 0.83
   2 !   12.3   0.0   5.2e-05      0.13      60     114 ..     242     292 ..     230     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                                   .TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                  Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvk 37 
                                    ke+kv+l GaG     +a+ L++ g+k
  gi|70607870|ref|YP_256740.1| 179 PKESKVVLYGAGASNIATARILAEYGFK 206
                                   5789*********999999999988765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                                   T-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS CS
                  Shikimate_DH  60 eiealkleelkellaeadvvisataseepilekeeveealkkrkkplllvDiavP 114
                                   +++  +++e+k++ + advvisa     ++++ke+v+ ++k+     +++ +a+P
  gi|70607870|ref|YP_256740.1| 242 KTNGYEVKEIKDAFSGADVVISASTPGPNVIKKEWVSVMNKN----AIVFALANP 292
                                   34556899****************************988766....788889988 PP

>> DUF4031  Protein of unknown function (DUF4031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.2e-06     0.021      18      74 ..     345     404 ..     336     409 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                       DUF4031  18 lvaDsleELhafAarlGvprrafqr..ktskdHYDvpeerraeavalG.Avevssrelvr 74 
                                   +v    e L +fA+r G++++ +    + ++  Y v+++  ++av+lG A++ +sre  r
  gi|70607870|ref|YP_256740.1| 345 MVISASEALAEFARRKGINENYIIPrmDEWEAYYEVASAIASKAVELGlARNNKSREEFR 404
                                   55566799************98765578899*****************666666777655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05     0.043      27     128 ..     180     290 ..     164     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                                   ---EEEEESTSHHHHHHHHHHHHTT-EEE...EEESSHHHHHHHHHTTTCECEE..........HCHHHHHHHHHHHH-SE CS
                   AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakglgakVt...vlDvrparleqleslgakfvev..........lksqeellaeavkeadv 94 
                                   +++kv+  G+G   ++ +++ ++ g k +   ++D +       e++ + +++              + +++++a + adv
  gi|70607870|ref|YP_256740.1| 180 KESKVVLYGAGASNIATARILAEYGFKLEnmiMIDSKGPLYSTREDIDHLMLHHrwkyelavktNGYEVKEIKDAFSGADV 260
                                   56777778888777777777777776544111456654443333333333232244445554447788899********** PP

                                   EEE---BTTSS---SC-HHHHHTS-TTEEEEETT CS
                   AlaDh_PNT_C  95 vigtvlipGkkaPkLvteemvksMkpgsVivDvA 128
                                   vi++      + P+++++e v+ M++++++  +A
  gi|70607870|ref|YP_256740.1| 261 VISA----STPGPNVIKKEWVSVMNKNAIVFALA 290
                                   **99....4556****************997666 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.3e-05     0.083     259     358 ..     168     274 ..     141     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                                   HHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHH...HHHHHHS.TT...SEEEES.CHHHH CS
                Oxidored_nitro 259 lldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrdde...erlkaeleeg..epeviddadleel 334
                                   l+ a++ + +  ++ +v++yg +   +a ar+l+e+G++   +++ +++ +++   e++   + +   ++e  ++ + +e+
  gi|70607870|ref|YP_256740.1| 168 LINAMILTNKDPKESKVVLYGAGASNIATARILAEYGFKLENMIMIDSKGPLYstrEDIDHLMLHHrwKYELAVKTNGYEV 248
                                   788999999**********************************99999999997777777777777998899999999999 PP

                                   HHHHHHHT.-SEEEE-CC.HHHHHHH CS
                Oxidored_nitro 335 eelikelk.pdlllggsk.eryiaek 358
                                   +e+  + + +d++++ s  + ++ +k
  gi|70607870|ref|YP_256740.1| 249 KEIKDAFSgADVVISASTpGPNVIKK 274
                                   99888875599999888756555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2633.82
//
Query:       gi|70607871|ref|YP_256741.1|  [L=574]
Description: dipeptidyl aminopeptidase/acylaminoacyl-peptidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-38  131.3   0.0    6.6e-38  130.3   0.0    1.4  1  Peptidase_S9   Prolyl oligopeptidase family
    1.5e-08   34.6   1.1    3.4e-06   26.9   0.6    2.3  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.6e-08   34.5   0.6    0.00022   20.9   1.0    2.5  3  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    6.5e-08   32.4   0.4    1.4e-06   28.1   0.4    2.5  1  DLH            Dienelactone hydrolase family
    2.1e-05   23.9   0.5    0.00034   20.0   0.2    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    2.5e-05   25.0   1.6     0.0016   19.1   0.6    2.2  2  Abhydrolase_6  Alpha/beta hydrolase family
    0.00024   20.5   0.7     0.0017   17.7   0.2    2.0  2  LIP            Secretory lipase
  ------ inclusion threshold ------
      0.025   14.5   0.1       0.96    9.3   0.0    2.2  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.056   13.3   0.2        1.5    8.7   0.0    2.7  2  Abhydrolase_3  alpha/beta hydrolase fold
      0.082   12.1   3.7       0.22   10.8   2.6    2.1  2  DUF5050        Domain of unknown function (DUF5050)
       0.17   10.6   0.0       0.22   10.2   0.0    1.2  1  ResB           ResB-like family


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   4.1e-41   6.6e-38      10     187 ..     373     546 ..     365     567 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 4.1e-41
                                   HHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GGG-S CS
                  Peptidase_S9  10 ladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpdlFk 90 
                                   l   Gy vv +n+rGs+gyG +f+    ++ g  ++ D++++ ++++ ++++  e+++++G SyGGy+t+ al+++pd+++
  gi|70607871|ref|YP_256741.1| 373 LLLFGYHVVTPNFRGSTGYGSKFYLMDIGDPGGGDLMDVVKVRDYIVGKKIA--EKVGVMGYSYGGYMTLLALGREPDKWD 451
                                   4467**********************************************98..9************************** PP

                                   EEEEESE---CCCHHCSTTS.THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH CS
                  Peptidase_S9  91 aavaevpvvdvlrydsdtdl.lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLq 170
                                    ++a+++v+d++ ++  +d  + + + e   + +n + +ke+sp+++++n  +++p+++ih+++D+r+ ++  +++v++L 
  gi|70607871|ref|YP_256741.1| 452 FGMAGASVADWIEMYELSDStF-KGFIELLFNGKNLDLMKERSPITYVNN--VKAPVCIIHSQNDSRTFLSPVIRYVQELH 529
                                   *****************99966.55888888889****************..99*************************** PP

                                   --S-SEEEEEETTS-SS CS
                  Peptidase_S9 171 kkgknvlllifpdegHg 187
                                   k+gk +++++ pd+gH 
  gi|70607871|ref|YP_256741.1| 530 KAGKSFEFHVVPDAGHA 546
                                   ****************5 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.6   2.1e-09   3.4e-06       2      97 ..     350     449 ..     349     478 .. 0.81
   2 !    6.0   0.0     0.005       8.2     206     253 ..     485     548 ..     458     552 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.1e-09
                                   EEEEE-STTT.CGGGGTTGHHHHHHHHTTSEEEEEEETTSTT..SSSTTTGB......CHHSHHHHHHHHHHHHHHCTTSS CS
                 Abhydrolase_1   2 vlvilhGlpg.ssdvwaerglapaLakdgfdvillDlrGvgy..Sspapacin.....ddygtasvaddldrildalgddk 74 
                                   ++v++hG+p  + d  ++  + + L + g++v++++ rG+    S++ +   +         +++v ++ d+i+ +   +k
  gi|70607871|ref|YP_256741.1| 350 AVVYVHGGPWgEIDDRWNSIISSLLLF-GYHVVTPNFRGSTGygSKFYL---MdigdpGGGDLMDVVKVRDYIVGKKIAEK 426
                                   79*******659999999888888888.***********8641133333...3355886678999999999********** PP

                                   EEEEEETHHHHHHHHHHHHHGGG CS
                 Abhydrolase_1  75 ltlvGhSmGGmialayaaeyper 97 
                                   + ++G+S+GG + l ++ + p++
  gi|70607871|ref|YP_256741.1| 427 VGVMGYSYGGYMTLLALGREPDK 449
                                   ********************998 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.005
                                   C............THHHHSEEEEEEETTCSSSCH.HHHHHHHHC..HTS..EEEEEEETCSSSHH CS
                 Abhydrolase_1 206 e............lknvlaptlvisgtsDplvpp.kaledlaql..lpk..krlvvisdagHlaf 253
                                   +            ++nv+ap+ +i++++D  +    ++++ ++l    +   + +v++dagH ++
  gi|70607871|ref|YP_256741.1| 485 NldlmkerspityVNNVKAPVCIIHSQNDSRTFLsPVIRYVQELhkA-GksFEFHVVPDAGHADY 548
                                   144445566777799****************9997777777777642.25457789999***887 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.1   3.4e+03     100     131 ..     111     142 ..     106     167 .. 0.72
   2 !   20.9   1.0   1.3e-07   0.00022      53     143 ..     373     466 ..     327     475 .. 0.83
   3 !   10.0   0.0   0.00029      0.48     209     259 ..     483     536 ..     476     546 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                                   EEEEEEEEECHHHHHHHHHCTT--TTEEEEEE CS
                 Peptidase_S15 100 nGkVgmtGiSYlGttqllaaatgvpalkaivp 131
                                   + +V+ +G+S +Gt  +++   + ++l+ + p
  gi|70607871|ref|YP_256741.1| 111 DKNVAFVGSSEDGTYLYVIEGGKLKKLNDVPP 142
                                   6799******9999888776666666655555 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.3e-07
                                   HHHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEE CS
                 Peptidase_S15  53 fvarGYavVvqdvrGtggSeGeftvg.....dsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalka 128
                                   ++  GY+vV  + rG+ g   +f  +     +  +  d+++v d +++++ +  kVg++G SY+G++ lla+ +++++ + 
  gi|70607871|ref|YP_256741.1| 373 LLLFGYHVVTPNFRGSTGYGSKFYLMdigdpGGGDLMDVVKVRDYIVGKKIA-EKVGVMGYSYGGYMTLLALGREPDKWDF 452
                                   66679**********977666666666778889999************9765.69************************** PP

                                   EEEECE-S-TCCCCS CS
                 Peptidase_S15 129 ivpeaaisdlyddyy 143
                                    ++ a+++d+ + +y
  gi|70607871|ref|YP_256741.1| 453 GMAGASVADWIE-MY 466
                                   **********98.33 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00029
                                   -SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..E CS
                 Peptidase_S15 209 gdydafWkdrnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..k 259
                                   g++ +  k+r++ + +++vkapv ++++ nD       +i++ ++l ++g+  +
  gi|70607871|ref|YP_256741.1| 483 GKNLDLMKERSPITYVNNVKAPVCIIHSQNDSRTFlSPVIRYVQELHKAGKsfE 536
                                   566678899**********************87777**********99987552 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.4   8.3e-10   1.4e-06      12     188 ..     347     546 ..     335     552 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8.3e-10
                           DLH  12 kkpvvvviq.eifGvn.dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylk 90 
                                   +  +vv ++   +G   d  + i ++l+  GY +++P++    +     +  ++ ++  ++++    +++d +    +y+ 
  gi|70607871|ref|YP_256741.1| 347 PSTAVVYVHgGPWGEIdDRWNSIISSLLLFGYHVVTPNFRGSTG-----YGSKFYLM-DIGDPG-GGDLMDVV-KVRDYIV 419
                                   44455555524566444888999999999999999999755555.....55666666.555666.44444444.3333443 PP

                           DLH  91 svpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG................................lspekele 138
                                      ++  +kvgv+G+  GG ++ll   ++ ++ d      G                                ++  ++++
  gi|70607871|ref|YP_256741.1| 420 G--KKIAEKVGVMGYSYGGYMTLLALGREpDKWDFG--MAGasvadwiemyelsdstfkgfiellfngknldlMKERSPIT 496
                                   3..35889**************99888773443322..22333455557888********************99999**** PP

                           DLH 139 eaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188
                                   +++++kap+ +++ ++D     + v +  ++l +a++ +e++v p+agHa
  gi|70607871|ref|YP_256741.1| 497 YVNNVKAPVCIIHSQNDSRTFLSPVIRYVQELHKAGKSFEFHVVPDAGHA 546
                                   *************************************************9 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   2.1e-07   0.00034       3     114 ..     347     464 ..     345     482 .. 0.81
   2 ?    1.6   0.0     0.083   1.4e+02     188     232 ..     499     545 ..     487     546 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                   Hydrolase_4   3 pkavvvlvHGl..aehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfdd.y...vdDlaafvekvkeehpelp 77 
                                   p  +vv vHG   +e  +r + ++  L   G++v++ + rG    + k  ++ ++ d     + D+ ++ + ++ ++  ++
  gi|70607871|ref|YP_256741.1| 347 PSTAVVYVHGGpwGEIDDRWNSIISSLLLFGYHVVTPNFRGSTGYGSKF-YLMDIGDpGggdLMDVVKVRDYIVGKKIAEK 426
                                   67799*****65599**************************99985444.444444413222566666779999999999* PP

                   Hydrolase_4  78 lfllGhSmGGliallyllrypdkva.glilsaPalkik 114
                                   + ++G S GG+++ll+l r+pdk++ g+  ++ a +i+
  gi|70607871|ref|YP_256741.1| 427 VGVMGYSYGGYMTLLALGREPDKWDfGMAGASVADWIE 464
                                   *************************9998887776655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.083
                   Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyH 232
                                   +++++P+ ++h+++D  +  ++  +++++l+++    ++++ p + H
  gi|70607871|ref|YP_256741.1| 499 NNVKAPVCIIHSQNDSRTFLSPVIRYVQELHKAgkSFEFHVVPDAGH 545
                                   7899***********99999999888888888733445666676666 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   9.6e-07    0.0016       1      83 [.     351     443 ..     351     461 .. 0.66
   2 ?    4.2   0.0     0.036        59     181     208 ..     514     546 ..     485     556 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.6e-07
                                   EEEE--GC.....G....C.HHHH.HHHHCCTCEEEEE--TTS...TS-........GGCS--HHHCHHH.HHHHCCTT.. CS
                 Abhydrolase_6   1 vlllHGagssassW....l.vapL.aallaagvhvlapDlpGh...Grs........dpppldledladl.aalldelaag 63 
                                   v+ +HG++     W      + ++   ll  g+hv++p ++G    G s        dp   dl d++ + + ++ +    
  gi|70607871|ref|YP_256741.1| 351 VVYVHGGP-----WgeidDrWNSIiSSLLLFGYHVVTPNFRGStgyG-SkfylmdigDPGGGDLMDVVKVrDYIVGKK--I 423
                                   788***99.....97654144455688889999********887334.335555444556666655433333344444..3 PP

                                   TTSEEEEEETCHHHHHHHHH CS
                 Abhydrolase_6  64 ggpvvlvGHSlGGalalaaa 83 
                                   + +v ++G+S+GG++ l+a+
  gi|70607871|ref|YP_256741.1| 424 AEKVGVMGYSYGGYMTLLAL 443
                                   777799********888743 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.036
                                   C.....HHHHCHHCCCHSTTEEET.CE...SSS- CS
                 Abhydrolase_6 181 p.....lvprllerllaqagarlp.vvlpgaGHl 208
                                          v r++++l+  ag+ ++ +v+p+aGH+
  gi|70607871|ref|YP_256741.1| 514 SrtflsPVIRYVQELHK-AGKSFEfHVVPDAGHA 546
                                   24553322277888888.6666666********4 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.1e-06    0.0017      18     135 ..     369     483 ..     365     492 .. 0.80
   2 ?    0.3   0.0      0.22   3.5e+02     215     263 ..     502     549 ..     496     555 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                           LIP  18 livplLkeGyyVvvpDyeGpks......tftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGslAsawAaelq 92 
                                   +i++lL  Gy Vv+p + G  +      +  +g   g   +d ++       + g k + kv+++GYS+G+  +  A    
  gi|70607871|ref|YP_256741.1| 369 IISSLLLFGYHVVTPNFRGSTGygskfyLMDIGDPGGGDLMDVVKVRD---YIVGKKIAEKVGVMGYSYGGYMTLLALGRE 446
                                   7999**************998888887777899999999***998654...555667788***************999887 PP

                           LIP  93 peYAPelelvGaalGgfvanltavaeavdgtvfaGlialalng 135
                                   p+   +  ++    G+ va+  ++ e + +++f G+i l +ng
  gi|70607871|ref|YP_256741.1| 447 PDK-WDFGMA----GASVADWIEMYE-LSDSTFKGFIELLFNG 483
                                   763.355444....556677777766.4556688888888887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
                           LIP 215 qiPvlvyhgvidelipikdakklaknwcdkgiaslefaedlssgHlaet 263
                                   + Pv ++h++ d+   ++ + +  ++  ++g +s+ef+ +  +gH   t
  gi|70607871|ref|YP_256741.1| 502 KAPVCIIHSQNDSRTFLSPVIRYVQELHKAG-KSFEFHVVPDAGHADYT 549
                                   57***********999999999999998888.7*****99999997655 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.071   1.2e+02      22      38 ..     425     441 ..     416     444 .. 0.87
   2 ?    9.3   0.0   0.00059      0.96     108     162 ..     495     546 ..     472     550 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.071
                                   SSEEEEEETHHHHHHHH CS
                        BAAT_C  22 dkigllGiSkGgelall 38 
                                   +k+g++G S Gg ++ll
  gi|70607871|ref|YP_256741.1| 425 EKVGVMGYSYGGYMTLL 441
                                   79***********9987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00059
                                   B--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S- CS
                        BAAT_C 108 lipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHl 162
                                   +  v + k+p+ ++ +++D  +  + ++++ ++ L+kagk+ e +++  p+aGH+
  gi|70607871|ref|YP_256741.1| 495 ITYVNNVKAPVCIIHSQNDSRTFLSPVIRY-VQELHKAGKSFEFHVV--PDAGHA 546
                                   5568889************99999999955.567*************..*****6 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   2.4e+03       1       9 [.     351     359 ..     351     370 .. 0.90
   2 ?    8.7   0.0    0.0009       1.5     135     208 ..     471     546 ..     406     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                   EEEE--STT CS
                 Abhydrolase_3   1 lvyfHGGGf 9  
                                   +vy+HGG +
  gi|70607871|ref|YP_256741.1| 351 VVYVHGGPW 359
                                   79*****98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0009
                                   HHHHHHHHHHSSGGGGG.STTTSGGGC.S-SST---EEEEEETT-..TTHHHHHHHHHHHHHTT--EEEEEETTEETT CS
                 Abhydrolase_3 135 aaldlfwrlylpeadrd.dplasplla.edlsglpptlvvvaefD..plrdegeayaerlraagvevelieyegmvHg 208
                                   ++++ f++l  +++++d     sp+   ++++  +p+ ++  ++D  ++ +  ++y ++l++ag++ e+++++++ H+
  gi|70607871|ref|YP_256741.1| 471 STFKGFIELLFNGKNLDlMKERSPITYvNNVK--APVCIIHSQNDsrTFLSPVIRYVQELHKAGKSFEFHVVPDAGHA 546
                                   55556666666544444333455555534565..67777777777446889999**********************97 PP

>> DUF5050  Domain of unknown function (DUF5050)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.58   9.4e+02      78     120 ..      83     125 ..      74     148 .. 0.44
   2 ?   10.8   2.6   0.00013      0.22     140     255 ..     188     312 ..     175     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                                   EEEEEEETTS---EEEE-S-EEE.EEEETTEEEEEEESSSS-EE CS
                       DUF5050  78 tglyriktdGtertklsddksle.vslvgnwiYYqhydekdglk 120
                                   + +y ++++G+e ++ s  + ++ v+  + ++ ++  +++dg+ 
  gi|70607871|ref|YP_256741.1|  83 HAVYACNLKGEEYEIASPRVRIMsVAYDDKNVAFV-GSSEDGTY 125
                                   33344444444444433332222122223333333.22233332 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                                   --SEEETTEEE....EE-T.TT--EEEEETTTTEEEEEE-S-EEEEEEEETTEEEEEGGGTT-EEEE-SSS---EE-S-S- CS
                       DUF5050 140 eplsvkdgwiY....ytgesedhslykldtdgksiskvseenlyllvvegdyiYyidlsknyaLyrvklsgsekevltedk 216
                                   +p+ +k++++Y    y +  e+  +y++d+++++ ++v   +  + +++   i+y   + +++L+  k +g+e+  l+ + 
  gi|70607871|ref|YP_256741.1| 188 QPYRIKGNKVYlasdYENIGESYWIYTYDLASNTYERVDFPERDIYQYKPVEIFY---DPEDKLIISKRDGRENLFLNGKL 265
                                   6788888888844444444556689999999999999999888898999999999...67888888888888888886666 PP

                                   EEE.......EEEETTEEEEEE-SSS-E..EEEEETTS---EEEEES CS
                       DUF5050 217 vdn.......yNvtgnwiYyqkesdeeka.lyrikldGsekeklaeg 255
                                   +++         v +n+iY++ +s  +++ +yr++++G +  ++ ++
  gi|70607871|ref|YP_256741.1| 266 INTvpgtltgATVIDNYIYFSHSSLVSPHkIYRVDKEGGKVDVVVDN 312
                                   55533333335678999999988876665599999999988877765 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00014      0.22     241     290 ..     180     231 ..     142     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                          ResB 241 kektikVNhPlrykgvriYqss.fgdgg.klelklvllkgksaqelelpgtv 290
                                   ++k+ +VN+P r+kg ++Y++s +++ g +  +  + l++++++++++p+++
  gi|70607871|ref|YP_256741.1| 180 TPKQGSVNQPYRIKGNKVYLASdYENIGeSYWIYTYDLASNTYERVDFPERD 231
                                   567779**************87244444444444444446666667776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3542.94
//
Query:       gi|70607872|ref|YP_256742.1|  [L=152]
Description: hypothetical protein Saci_2158 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1035.87
//
Query:       gi|70607873|ref|YP_256743.1|  [L=248]
Description: hypothetical protein Saci_2160 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0001   22.1  10.2     0.0001   22.1  10.2    1.6  1  YkyA             Putative cell-wall binding lipoprotein
    0.00023   21.2  10.0     0.0014   18.8   5.3    3.3  2  DUF3782          Protein of unknown function (DUF3782)
    0.00083   19.7   6.3        1.4    9.4   5.0    2.9  2  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0022   18.4  14.5     0.0098   16.3   1.8    3.3  2  NBD94            Nucleotide-Binding Domain 94 of RH
     0.0023   18.5   3.5     0.0045   17.5   3.5    1.5  1  FlgN             FlgN protein
     0.0032   17.2   8.6      0.006   16.3   8.6    1.4  1  DUF4201          Domain of unknown function (DUF4201)
     0.0043   17.2   7.6       0.01   16.0   7.6    1.6  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0081   15.3   6.7       0.11   11.6   0.6    2.1  2  RmuC             RmuC family
     0.0096   16.5   8.2      0.022   15.3   8.2    1.6  1  APG6_N           Apg6 coiled-coil region
  ------ inclusion threshold ------
       0.01   15.7   2.2       0.18   11.7   1.4    2.4  2  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
      0.014   14.9   6.8      0.014   14.9   6.8    2.2  2  DegS             Sensor protein DegS
      0.016   15.2   7.8        0.3   11.1   4.8    2.3  2  DUF1664          Protein of unknown function (DUF1664)
      0.019   14.6   0.8      0.025   14.2   0.8    1.3  1  Arfaptin         Arfaptin-like domain
      0.024   14.5   0.6      0.069   13.0   0.5    1.8  2  DUF1465          Protein of unknown function (DUF1465)
      0.035   13.4   5.7      0.056   12.7   5.7    1.3  1  TMPIT            TMPIT-like protein
      0.039   13.8   7.0      0.066   13.0   3.4    2.2  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.07   13.2   7.3       0.12   12.5   7.3    1.3  1  ADIP             Afadin- and alpha -actinin-Binding
      0.073   13.7   7.4       0.26   11.9   7.1    2.0  2  YabA             Initiation control protein YabA
      0.099   12.8   5.6       0.33   11.1   4.4    2.1  2  Nup54            Nucleoporin complex subunit 54
      0.099   13.1   7.9       0.24   11.8   7.9    1.6  1  CENP-H           Centromere protein H (CENP-H)
       0.11   12.8  14.0        1.9    8.9   8.7    3.1  3  CCDC-167         Coiled-coil domain-containing protein 167
       0.12   11.4   5.5       0.18   10.9   5.5    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.15   11.3   7.3      0.065   12.5   5.1    1.5  1  S_4TM            SMODS-associating 4TM effector domain
       0.19   12.0  15.4      0.023   15.0  11.2    1.6  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.19   12.0   0.7       0.62   10.4   0.6    1.9  1  DUF948           Bacterial protein of unknown function (DUF94
        0.2   12.0  12.2       0.46   10.9  12.2    1.5  1  DUF4200          Domain of unknown function (DUF4200)
       0.22   11.4   3.8       0.39   10.6   0.9    1.9  2  Sec34            Sec34-like family
       0.24   11.6   6.9       0.48   10.6   6.9    1.5  1  Fib_alpha        Fibrinogen alpha/beta chain family
        0.3   11.5   3.3       0.77   10.2   3.3    1.7  1  eIF3_N           eIF3 subunit 6 N terminal domain
       0.42   10.6   4.0        1.1    9.2   2.6    2.3  2  Sec20            Sec20
       0.46    9.9   9.7       0.23   10.9   4.5    2.2  2  Flagellar_rod    Paraflagellar rod protein
       0.62   10.0   6.7        2.4    8.1   4.1    2.4  2  DUF4446          Protein of unknown function (DUF4446)
       0.65   10.5   8.4        2.9    8.4   8.4    2.1  1  DUF16            Protein of unknown function DUF16
       0.88    9.7   5.5        2.2    8.4   1.7    2.4  2  NRN1             Neuritin protein family
       0.93   10.2   6.8        3.7    8.3   6.8    2.2  1  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.95    9.9  13.1          1    9.9  10.0    2.3  2  ZapB             Cell division protein ZapB
        1.2    9.0   6.3        1.9    8.4   0.2    2.7  3  FadR_C           FadR C-terminal domain
        1.3    9.3  12.2       0.92    9.8   8.0    2.1  2  OmpH             Outer membrane protein (OmpH-like)
        1.4    8.7   8.1        2.5    8.0   3.4    2.4  2  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
        1.6    9.2  10.8       0.13   12.7   4.7    2.4  1  Snapin_Pallidin  Snapin/Pallidin
        1.8    8.7   9.6          3    8.0   2.4    3.4  2  LPD11            Large polyvalent protein-associated domain 1
          2    8.5   4.8        4.2    7.5   2.9    2.2  2  COG2             COG (conserved oligomeric Golgi) complex com
        2.1    8.6  11.9        1.6    9.0  10.8    1.3  1  zf-C4H2          Zinc finger-containing protein
        2.3    8.5   8.7        1.1    9.5   5.1    2.3  2  DUF4164          Domain of unknown function (DUF4164)
        2.4    7.9  11.0        7.3    6.4  11.0    1.8  1  DUF724           Protein of unknown function (DUF724)
        2.8    8.3   7.0        7.1    7.0   7.0    1.6  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        2.9    8.0  15.2       0.38   10.9  10.1    2.1  2  BRE1             BRE1 E3 ubiquitin ligase
        3.1    8.3   5.7        4.2    7.9   2.5    2.1  2  DUF2115          Uncharacterized protein conserved in archaea
        5.3    6.4  12.9       0.79    9.1   8.5    1.7  2  Cluap1           Clusterin-associated protein-1
        7.5    6.5  14.6        1.3    9.0   3.4    2.5  3  Cauli_AT         Aphid transmission protein
        9.3    6.8   9.7         38    4.8   6.0    2.4  2  Carbpep_Y_N      Carboxypeptidase Y pro-peptide


Domain annotation for each model (and alignments):
>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  10.2   2.9e-07    0.0001      12     130 ..      28     148 ..      20     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.9e-07
                          YkyA  12 eavelE...kefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekike 89 
                                   e v++E   k++ee  +k++el  + + + e+i +++++e ++i++  ++  e++e+++e+ +   esi+++++e++ i+e
  gi|70607873|ref|YP_256743.1|  28 ERVKEElivKKIEELEKKMSELITNSNRIWESI-QATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIRE 107
                                   555555555899********************9.6799******************************************* PP

                          YkyA  90 eieeiedeelkkeaeelieameeryeay..dklykaYkealel 130
                                   e  +i   ++ + ++   +++ +r  +y   ++++ Ykealel
  gi|70607873|ref|YP_256743.1| 108 ENAKIW--KAIERINISFSTFTSRSGHYieRTIMNLYKEALEL 148
                                   ****94..45777777777888888777445677788888876 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9       1.8   6.2e+02       3      16 ..      39      52 ..      23      72 .. 0.51
   2 !   18.8   5.3   3.9e-06    0.0014       3      75 ..      95     169 ..      52     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.8
                       DUF3782  3 lekleeeeeetked 16
                                  +e+le+++ e+   
  gi|70607873|ref|YP_256743.1| 39 IEELEKKMSELITN 52
                                  23333333333333 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.9e-06
                       DUF3782   3 lekleeeeeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv...kVekwlyyDkeGeVy 75 
                                   +++ ++e + ++e+  ++ k+ie+++  +++  +R G + E+++ + +ke+Le   g+   kV   ++ D+eG+V 
  gi|70607873|ref|YP_256743.1|  95 IQATQNEIKGIREENAKIWKAIERINISFSTFTSRSGHYIERTIMNLYKEALELH-GIdssKVTHGVIEDTEGIVH 169
                                   44455556667777777888**********************************9.*99999************96 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   5.0     0.004       1.4       1      38 [.      38      82 ..      38      91 .. 0.80
   2 !    8.7   0.0    0.0063       2.2       7      38 ..      93     136 ..      87     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.004
                     FlaC_arch  1 ridelEnklsklst.......eletvkkeneelsksveelkenVk 38
                                  +i+elE+k+s+l t       +++  ++e++ ++++ +++ e+++
  gi|70607873|ref|YP_256743.1| 38 KIEELEKKMSELITnsnriweSIQATQNEIKAIQEDNKKIWESIE 82
                                  8***********997788888777777777777777777777764 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0063
                     FlaC_arch   7 nklsklsteletvkkeneelsksveelkenV............k 38 
                                   + ++ ++ e++ +++en ++ k +e+++ ++            +
  gi|70607873|ref|YP_256743.1|  93 ESIQATQNEIKGIREENAKIWKAIERINISFstftsrsghyieR 136
                                   56788899*******************97775555555555555 PP

>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.5     0.086        30      48      89 ..      27      68 ..      20      76 .. 0.61
   2 !   16.3   1.8   2.8e-05    0.0098       5      50 ..      79     125 ..      74     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.086
                         NBD94 48 YgrsLikllvqkIdeekkkaenlieeiekyienideikkkls 89
                                  Y+r+  +l+v+kI+e +kk  +li + + + e+i+  +++++
  gi|70607873|ref|YP_256743.1| 27 YERVKEELIVKKIEELEKKMSELITNSNRIWESIQATQNEIK 68
                                  777777777777777666655555555555555555555443 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.8e-05
                         NBD94   5 knivtkidkkkkiyeniekllnEleeiekektsl.eevknielsYgr 50 
                                   + i ++ +++k+i+e i+ + nE++ i +e+  + + ++ i++s+ +
  gi|70607873|ref|YP_256743.1|  79 ESIEKQREETKRIWESIQATQNEIKGIREENAKIwKAIERINISFST 125
                                   567778889******************9999887478*******976 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.5   1.3e-05    0.0045      48     131 ..      33     129 ..      23     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHHHHHHHHHTT--...............SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          FlgN  48 qellekleqleqkrakllaelgls...............aeeatlsellakeedeelkelwqelkelleelkelnelNgrl 113
                                   + +++k+e+le+k+++l+++ +                 ++++++ e ++ +++ee k +w++++++ +e+k + e N+++
  gi|70607873|ref|YP_256743.1|  33 ELIVKKIEELEKKMSELITNSNRIwesiqatqneikaiqEDNKKIWESIE-KQREETKRIWESIQATQNEIKGIREENAKI 112
                                   45567777777777777777777777776444444433555555555555.9**************************997 PP

                                   HHHCCHHHHHHHHHCCHX CS
                          FlgN 114 ieqslefnqrllnllqga 131
                                    + ++e+++ + + ++++
  gi|70607873|ref|YP_256743.1| 113 WK-AIERINISFSTFTSR 129
                                   64.566666666666665 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   8.6   1.7e-05     0.006      53     131 ..      34     112 ..       8     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-05
                       DUF4201  53 alnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                     +kkIee +k++++l  ++++    ++ +++  +++++ +++  ++++++ e+ ++++++++ +++e + +r++n+k+
  gi|70607873|ref|YP_256743.1|  34 LIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKI 112
                                   468*************************************************************************997 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   7.6   2.9e-05      0.01      81     144 ..      50     134 ..      19     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-05
                       UPF0242  81 d.....................eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel 140
                                                         e+ k++ e++e+ +ee+++  e ++a ++e++  +een+++ +  e i   f+ +   +
  gi|70607873|ref|YP_256743.1|  50 ItnsnriwesiqatqneikaiqEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTFTSRS 130
                                   222234444444444333333388899999999999999999999999999999999999999999999988888887766 PP

                       UPF0242 141 eeqL 144
                                      +
  gi|70607873|ref|YP_256743.1| 131 GHYI 134
                                   6555 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   1.5    0.0051       1.8     219     279 ..      23      82 ..      12      83 .. 0.65
   2 !   11.6   0.6   0.00032      0.11     222     281 ..      82     141 ..      75     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0051
                          RmuC 219 wrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkae 279
                                   +++   + + e i+++++el +k++++ ++ +++ ++++ +q++++  +++ +++i +++e
  gi|70607873|ref|YP_256743.1|  23 FNRFYERVKEELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKA-IQEDNKKIWESIE 82 
                                   44444455556677777777777777777777777777777777777.6666666666555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00032
                          RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle.gnilrkaekl 281
                                   e+q++++++i+e +++  ++++++ e+  k+ k++e+++ s+ ++ ++++ + i r++ +l
  gi|70607873|ref|YP_256743.1|  82 EKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTF-TSRSgHYIERTIMNL 141
                                   7999****************************************5.555536666665555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   8.2   6.3e-05     0.022      30     122 ..      25     112 ..      20     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-05
                        APG6_N  30 eflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelql 110
                                   +f +++k+e        +++eele+++++l    ++  e ++++++e ++++++ ++++e  e+  ee +r w++ ++ q 
  gi|70607873|ref|YP_256743.1|  25 RFYERVKEE-----LIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQN 100
                                   556666655.....2335788888888888888888888888888888888888888888888888888888888887777 PP

                        APG6_N 111 elleleeeldsl 122
                                   e +   ee +++
  gi|70607873|ref|YP_256743.1| 101 EIKGIREENAKI 112
                                   777766666554 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00051      0.18      23      63 ..      37      77 ..      30      80 .. 0.91
   2 ?    2.1   0.0      0.49   1.7e+02      43      63 ..      92     112 ..      87     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00051
                        GIT_CC 23 kalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaql 63
                                  k++   e k+ +L+   + + + ++  Q++++ +q++N+++
  gi|70607873|ref|YP_256743.1| 37 KKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKI 77
                                  567889********************************986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.49
                        GIT_CC  43 sdelrlLQskvqkLqaeNaql 63 
                                    + ++  Q++++ + +eNa++
  gi|70607873|ref|YP_256743.1|  92 WESIQATQNEIKGIREENAKI 112
                                   5789999***********986 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.8      0.86     3e+02      31      52 ..      34      55 ..      20      64 .. 0.63
   2 ?   14.9   6.8     4e-05     0.014       5      89 ..      64     148 ..      58     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.86
                          DegS 31 rlkkeleelkeevsevikevdk 52
                                   + k++eel++++se+i++ ++
  gi|70607873|ref|YP_256743.1| 34 LIVKKIEELEKKMSELITNSNR 55
                                  3556666777777777766655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4e-05
                          DegS   5 kktietiekskeeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYee 85 
                                   ++ i++i++  ++i+e  E+ r+e++r+ + ++ +++e++ + +e  k+ k   +     ++  ++  +y e +i++ Y+e
  gi|70607873|ref|YP_256743.1|  64 QNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTFTSRSGHYIERTIMNLYKE 144
                                   6889***************************************************************************** PP

                          DegS  86 akel 89 
                                   a el
  gi|70607873|ref|YP_256743.1| 145 ALEL 148
                                   9876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.8   0.00085       0.3      60     114 ..      30      85 ..      19      91 .. 0.84
   2 ?    7.5   0.4     0.011       3.9      73     116 ..      79     122 ..      75     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00085
                       DUF1664  60 tkrhL.ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                   +k++L  ++i++++kk+ e +  s+ i e +++ ++++++i+ed +++ e +e+  
  gi|70607873|ref|YP_256743.1|  30 VKEELiVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQR 85 
                                   566662589*************************************9999988755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                       DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                   +++++q e +k i e +++ +++++ i+e+  ++ +a+e ++ +
  gi|70607873|ref|YP_256743.1|  79 ESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINIS 122
                                   45667777777777777777777777777777777777666554 PP

>> Arfaptin  Arfaptin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8     7e-05     0.025      24     139 ..      31     141 ..       8     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-05
                                   --....CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H-CCGHHHHHHHHHHHHHHH CS
                      Arfaptin  24 edervitvddeLeaklevlreiketykelvklaknlskallklsqtekelGdvfkdlskrekqealgeaftatgealrlla 104
                                   ++e ++   +eLe+k+ +l      ++ + + +++ ++ +  + + +k++ ++++++ +   ++++ e+++at +  + + 
  gi|70607873|ref|YP_256743.1|  31 KEELIVKKIEELEKKMSELIT---NSNRIWESIQATQNEIKAIQEDNKKIWESIEKQRE--ETKRIWESIQATQNEIKGIR 106
                                   444455555566666555544...46788999999999999999999999999999866..9******************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHH CS
                      Arfaptin 105 kqgeallkalkrfiselntfvnkaieDTllTikky 139
                                   ++++++ ka++r+  + +tf  +  +  + Ti + 
  gi|70607873|ref|YP_256743.1| 107 EENAKIWKAIERINISFSTFTSRSGHYIERTIMNL 141
                                   ********************999766666666555 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5    0.0002     0.069      97     149 ..      35      87 ..      17      92 .. 0.86
   2 ?   -2.0   0.0         8   2.8e+03       8      20 ..     136     148 ..     128     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0002
                                   ---------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXX CS
                       DUF1465  97 daeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqler 149
                                     ++++eL++++ eLi++s+r+ e ++  ++e+++ +e++++  + +++q+e 
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREE 87 
                                   56789******************************999998888888888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8
                                   TTCHHHHHHHHHH CS
                       DUF1465   8 elfkalfregmdL 20 
                                   + + +l++e+++L
  gi|70607873|ref|YP_256743.1| 136 RTIMNLYKEALEL 148
                                   5678999999998 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.7   0.00016     0.056       2      83 ..      44     117 ..      29     143 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                         TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                   ++++el ++ +++ e+ +  +++++ +++ ++k+ ++i+kq+++ k++++s++ +++++k         ++ee +++ k +
  gi|70607873|ref|YP_256743.1|  44 KKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIK--------GIREENAKIWKAI 116
                                   334444444445555555555555555555555555555555555555555555555543........3333333333333 PP

                         TMPIT  83 k 83 
                                   +
  gi|70607873|ref|YP_256743.1| 117 E 117
                                   3 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7      0.04        14     133     169 ..      35      71 ..      24      73 .. 0.86
   2 ?   13.0   3.4   0.00019     0.066      91     161 ..      63     134 ..      57     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 133 iveavaevadlvqeiaaaseeqsasieevnqaveeva 169
                                   iv++++e+++ ++e+ + s+ + +si+ +++ +++++
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQ 71 
                                   9999999999999999999999999999999888876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00019
                                   HHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH CS
                     MCPsignal  91 iealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee.qsasieev 161
                                   +++ i++iq++ ++  es+e+ r++++   e ++ t++++k i e+ a++ + ++ i+ + +   s+s + +
  gi|70607873|ref|YP_256743.1|  63 TQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTfTSRSGHYI 134
                                   456688889**********************************************99887544145555555 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   7.3   0.00034      0.12      54     131 ..      31     108 ..      20     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00034
                          ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                    +e+  ++i++le  ++ l ++ +r  ++ +++++e+++ q++ +++  +++++ + +k+  e++q ++n ++ i+  
  gi|70607873|ref|YP_256743.1|  31 KEELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREE 108
                                   5677788999999*********************************************************99999875 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   7.1   0.00075      0.26       5      76 ..      34     105 ..      30     114 .. 0.87
   2 ?    9.0   0.7    0.0061       2.2       2      44 ..      73     115 ..      72     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00075
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                    +++k+eele++++el ++ +++ e+++++ +e ++++ +n+k+ e +e++++++k+  ++++ ++++++ +
  gi|70607873|ref|YP_256743.1|  34 LIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGI 105
                                   47899*******************************************999999888888888887777666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0061
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLele 44 
                                   d+k++ +++e+  e+++++ e++++ ++e++ + eena++   
  gi|70607873|ref|YP_256743.1|  73 DNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKA 115
                                   788999*******************************998655 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.4   0.00094      0.33      68     136 ..      33     102 ..      24     104 .. 0.89
   2 ?    6.4   0.3     0.026       9.2      39      78 ..      82     120 ..      80     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00094
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS-H.HH.HHHHHHH CS
                         Nup54  68 letsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlndp.aqlkgrvnel 136
                                     + +++e++ k+  el++   r++  ++  ++  +a++++ +++++ +e+  ++ ++  +++++  ne+
  gi|70607873|ref|YP_256743.1|  33 ELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIwESIQATQNEI 102
                                   55789*********************************************99999997358888888887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Nup54  39 kaQqkevaqhrerlkeisdrleeleqkhqletsvrlekak 78 
                                   ++Q++e+++  e +++++++++ ++ ++++++ +++e++ 
  gi|70607873|ref|YP_256743.1|  82 EKQREETKRIWESIQATQNEIKGIR-EENAKIWKAIERIN 120
                                   78***********************.9*******999986 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   7.9   0.00068      0.24       5      77 ..      36     111 ..      33     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00068
                        CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaell.elakekesek..eklkeelekleaelkk 77 
                                   +++++el +++ +l ++++ + e+++ ++ e++++++ n++++++++ + ++ k+ ++  + +++e++ +++e  k
  gi|70607873|ref|YP_256743.1|  36 VKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEkQREETKRIWEsiQATQNEIKGIREENAK 111
                                   68899999999999999*****************************425555555555765566666666655443 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   3.0      0.21        73      21      67 ..      28      76 ..      21      81 .. 0.79
   2 ?    8.9   8.7    0.0054       1.9       2      67 ..      35     111 ..      34     117 .. 0.83
   3 ?    5.5   0.1     0.063        22      49      72 ..     200     223 ..     193     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
                      CCDC-167 21 eaverrlrkeelseeeResle..eEeaslkeqleenekeLksLrkeNrk 67
                                  e+v  +l  ++++e e++  e  +  + + e ++  ++e k +++ N+k
  gi|70607873|ref|YP_256743.1| 28 ERVKEELIVKKIEELEKKMSEliTNSNRIWESIQATQNEIKAIQEDNKK 76
                                  6777788888888887765444488889999999999999999999988 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0054
                      CCDC-167   2 vaseIdkleeklascrerLeaverrlrkeelseee........Resle......eEeaslkeqleenekeLksLrkeNrk 67 
                                   ++++I++le+k++++  + +++  +++ ++ + ++            e      eE + + e ++  ++e k +r+eN k
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAiqednkkiW---EsiekqrEETKRIWESIQATQNEIKGIREENAK 111
                                   799**********9999999998888887776666656665553...34447779***********************99 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.063
                      CCDC-167  49 eqleenekeLksLrkeNrksmlls 72 
                                   eqle  ek L+sL+k+  k++l++
  gi|70607873|ref|YP_256743.1| 200 EQLEIREKILSSLHKKPIKKFLVA 223
                                   7999*****************998 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.5   0.00051      0.18      38     142 ..      39     118 ..      14     170 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                         Atg14  38 keslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdl 118
                                    e+l+kk+++++++ +   +  + i+ +++ ++ ++ +  ++ e +++ ++  ++  ++i+++++++++ +++++      
  gi|70607873|ref|YP_256743.1|  39 IEELEKKMSELITNSN---RIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENA------ 110
                                   2445555555555555...44444444444444444444444444444444444444444444444444444444...... PP

                         Atg14 119 eslqneleerrkkqiaklqdaikr 142
                                                   k+ +ai r
  gi|70607873|ref|YP_256743.1| 111 ----------------KIWKAIER 118
                                   ................33333333 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.1   0.00018     0.065     204     275 ..      47     118 ..      44     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                         S_4TM 204 lpllllalkeyreqresakelerlkeeiesllndaasgkleeeelkeelrklQdeiyqhRkssplipdwlYk 275
                                     l++   + + + +++ +e++ ++e+ +++++++ ++ +e+++++e+++  Q+ei   R+++ +i++ + +
  gi|70607873|ref|YP_256743.1|  47 SELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIER 118
                                   567888889999****************************9999**********************998766 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0  11.2   6.4e-05     0.023      12     104 ..      20     116 ..       6     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-05
                                   HHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHH CS
                  Seryl_tRNA_N  12 eavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkalea 88 
                                   +a+ ++  +R ++++ v+++ el++k+ el++  + + +   + ++eI+ + +++    e +e+ ++e+k + e ++a+++
  gi|70607873|ref|YP_256743.1|  20 DALFNRFYERVKEELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNkkiwESIEKQREETKRIWESIQATQN 100
                                   4444555567699********************98888888888888887777666788********************** PP

                                   HHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  89 elkeleaeleklllai 104
                                   e k +++e  k+  ai
  gi|70607873|ref|YP_256743.1| 101 EIKGIREENAKIWKAI 116
                                   ****999988887766 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6    0.0018      0.62      18      85 ..      36     103 ..      32     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0018
                        DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                   ++ + +l+k ++e+ +  + + + ++++ +e++++ +  +++ e ++++ e+ +++ e+++ + + ++
  gi|70607873|ref|YP_256743.1|  36 VKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIK 103
                                   55566788889999999999999999999999999999999999999999999999999998877765 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  12.2    0.0013      0.46      17     106 ..      30     119 ..      22     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                       DUF4200  17 akkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseie 97 
                                   +k+e i ++ e+l+++  el  + +++ e+++  ++ +k +++  ++  + +e++r+++k+  + i+  ++ei+ +++e++
  gi|70607873|ref|YP_256743.1|  30 VKEELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENA 110
                                   577779*************************************************************************** PP

                       DUF4200  98 kleekleey 106
                                   k  +++e+ 
  gi|70607873|ref|YP_256743.1| 111 KIWKAIERI 119
                                   *99988875 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.4    0.0023      0.82       3      66 ..      37     100 ..      35     127 .. 0.74
   2 ?   10.6   0.9    0.0011      0.39       3      73 ..      58     128 ..      56     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0023
                         Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                   +++e+ e+++ el+++ +++ e+++  +++ k+++e+ +++ e+ e+  ee+kr+ e  ++ ++
  gi|70607873|ref|YP_256743.1|  37 KKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQN 100
                                   5677777888888888888888888888888888888888888888888888777665555444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0011
                         Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                   + ++++++e++++ e+ +++ e++e+ +e+ k++ e+ ++ +++ + + ee+ ++ +  e i+   + F++
  gi|70607873|ref|YP_256743.1|  58 ESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTFTS 128
                                   5689999*******************************************************999999975 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.9    0.0014      0.48      33     121 ..      35     119 ..      23     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                                   CCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                     Fib_alpha  33 vkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                   + k++e+le++++e+  +++ + e ++++++ +++ q+ +k   ++ ++++k+ e e  r+ e+i+a+ ++i+ +++   +
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNK---KIWESIEKQRE-ETKRIWESIQATQNEIKGIREENAK 111
                                   66899999999999999999999999999999988887776...45555555555.8889999**9999999999998888 PP

                                   HHHHHHHH CS
                     Fib_alpha 114 neqkiqkL 121
                                     + i+++
  gi|70607873|ref|YP_256743.1| 112 IWKAIERI 119
                                   87777776 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3    0.0022      0.77      33     112 ..      34     116 ..      18     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0022
                        eIF3_N  33 llkaklell..kkTnmvdyaadlykelegeeevpeelekkreevleeleeleeeaekvlell.edeevvsnlrsdkkqnle 110
                                   l   k+e l  k  ++++    ++++++ +++  +++++ ++++ e +e+ +ee++++ e +   ++ ++ +r++++++ +
  gi|70607873|ref|YP_256743.1|  34 LIVKKIEELekKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIqATQNEIKGIREENAKIWK 114
                                   44445544433446788888999999999999999*************************994456667778888777766 PP

                        eIF3_N 111 fL 112
                                    +
  gi|70607873|ref|YP_256743.1| 115 AI 116
                                   55 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.6    0.0032       1.1       3      57 ..      32      86 ..      30     101 .. 0.87
   2 ?   -0.6   0.0       3.6   1.3e+03      25      61 ..     135     170 ..     107     177 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0032
                         Sec20  3 akqiTeslraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskk 57
                                  ++ i +++ + ++ +s+ + +S+   e+++a  +++++++e+ k++ +++++ ++
  gi|70607873|ref|YP_256743.1| 32 EELIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQRE 86
                                  56788999999*******************************9999999988665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.6
                         Sec20  25 eenleeldastkslekleeeykqvedvlsrskklvkk 61 
                                   e ++++l + + +l+ +++  k +++v++ ++ +v k
  gi|70607873|ref|YP_256743.1| 135 ERTIMNLYKEALELHGIDSS-KVTHGVIEDTEGIVHK 170
                                   56777888888888777665.5667788888877766 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.39   1.4e+02      49      80 ..      19      52 ..      14      59 .. 0.67
   2 ?   10.9   4.5   0.00067      0.23       5      95 ..      58     144 ..      54     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.39
                 Flagellar_rod 49 sdkflqeneeq..qeklvreieelereLqklaee 80
                                  +d+ ++   e+   e +v++ieele+++ +l ++
  gi|70607873|ref|YP_256743.1| 19 MDALFNRFYERvkEELIVKKIEELEKKMSELITN 52
                                  5555555555421345789999999999998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00067
                 Flagellar_rod   5 avidakkrlkeaveeDlekikekreeeaaadekqrkrykaqreesdkflqeneeqqeklvreieelereLqklaeerrelv 85 
                                   + i a ++ ++a++eD +ki e++e+ +++ ++  +  +a ++e    ++ ++e+ +k++++ie+      + + +    +
  gi|70607873|ref|YP_256743.1|  58 ESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNE----IKGIREENAKIWKAIERINISFSTFTSRSGHYI 134
                                   568899999***************99998888877777776665....6678999999******99999999988888888 PP

                 Flagellar_rod  86 edrieaeerE 95 
                                   e+ i +  +E
  gi|70607873|ref|YP_256743.1| 135 ERTIMNLYKE 144
                                   8888766665 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.1    0.0069       2.4      21      80 ..      36      93 ..      19      98 .. 0.86
   2 ?    5.0   0.2     0.064        22      37      79 ..      85     127 ..      76     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0069
                       DUF4446 21 lvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslq 80
                                  + k+++l+kk+++l++  + + + e ++ + +e+++++e+++++ ++ie+ +e+ k+  +
  gi|70607873|ref|YP_256743.1| 36 VKKIEELEKKMSELIT--NSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWE 93
                                  6789999999999998..678899999999999999999999999999999999887665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.064
                       DUF4446  37 gkdgksleellkekleeveelkeeseelekeieeleeklkksl 79 
                                   +++ k + e ++ + +e++ ++ee++++ k ie+++ ++++  
  gi|70607873|ref|YP_256743.1|  85 REETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTFT 127
                                   4578888999999999999999999999999999987776655 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.4    0.0083       2.9      36      97 ..      39     100 ..      20     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0083
                                   HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                         DUF16  36 LkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkink 97 
                                   ++++e+k++ l  + n++ + +++ +++ik ++++ k+  e+++k+ e  + i e++q++++
  gi|70607873|ref|YP_256743.1|  39 IEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQN 100
                                   45666677777777777777788888888888888888888888888888888888887664 PP

>> NRN1  Neuritin protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.7    0.0063       2.2      23      72 ..      39      88 ..      30      91 .. 0.73
   2 ?    4.1   0.3      0.14        50      33      65 ..      85     116 ..      82     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0063
                          NRN1 23 keeedee.eqeletickyWdefhaCaltaladCqeeaaaiWesLrkeskkl 72
                                   ee +++ ++ +++  + W+  +a  ++ +   qe+ ++iWes+ k+ +++
  gi|70607873|ref|YP_256743.1| 39 IEELEKKmSELITNSNRIWESIQAT-QNEIKAIQEDNKKIWESIEKQREET 88
                                  455555524456777899*999875.567899***********98886655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                          NRN1  33 letickyWdefhaCaltaladCqeeaaaiWesL 65 
                                    e+ ++ W+  +a +++ + + +ee a+iW+ +
  gi|70607873|ref|YP_256743.1|  85 REETKRIWESIQA-TQNEIKGIREENAKIWKAI 116
                                   5566777888765.4556788888888888765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.8      0.01       3.7      15      80 ..      39     106 ..       3     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.01
                       DUF2203  15 lkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdle 80 
                                   ++el +++ +l ++ ++++e+++++++e ++ +   ++  +++e+ ++e ++++e i+++  e+k+++
  gi|70607873|ref|YP_256743.1|  39 IEELEKKMSELITNSNRIWESIQATQNEIKAIQedNKKIWESIEKQREETKRIWESIQATQNEIKGIR 106
                                   44444444444444444444555444444433334777788888888889999999999988888875 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  10.0    0.0029         1       6      63 ..      39      96 ..      36     105 .. 0.89
   2 ?    1.9   0.2      0.91   3.2e+02      18      37 ..      93     112 ..      89     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0029
                          ZapB  6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlk 63
                                   e+LE+k +++i++  +  + i++ + e ++ +e n+++ e++e+ +ee + + e ++
  gi|70607873|ref|YP_256743.1| 39 IEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQ 96
                                  599***********99999999999999999999999999999999999888877776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.91
                          ZapB  18 dtitlLqmeieeLkeeneel 37 
                                   + i++ q+ei+  +een++ 
  gi|70607873|ref|YP_256743.1|  93 ESIQATQNEIKGIREENAKI 112
                                   56788888888888888765 PP

>> FadR_C  FadR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0053       1.9     117     158 ..      22      63 ..      13      68 .. 0.90
   2 ?    2.7   0.8       0.3   1.1e+02     131     158 ..      71      98 ..      66     104 .. 0.85
   3 ?   -1.4   0.0       5.3   1.9e+03     137     156 ..      98     117 ..      93     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0053
                        FadR_C 117 lalkfYrelkelceeeeaekvaevvrkygkesgkiWkelkke 158
                                   l  +fY+++ke    ++ e++++ + +  ++s++iW++++++
  gi|70607873|ref|YP_256743.1|  22 LFNRFYERVKEELIVKKIEELEKKMSELITNSNRIWESIQAT 63 
                                   6689*********************************99875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.3
                        FadR_C 131 eeeaekvaevvrkygkesgkiWkelkke 158
                                   +e+++k+ e + k+++e+ +iW++++++
  gi|70607873|ref|YP_256743.1|  71 QEDNKKIWESIEKQREETKRIWESIQAT 98 
                                   677889999**************99865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.3
                        FadR_C 137 vaevvrkygkesgkiWkelk 156
                                    ++ ++  ++e +kiWk+++
  gi|70607873|ref|YP_256743.1|  98 TQNEIKGIREENAKIWKAIE 117
                                   5667888899999***9875 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.0    0.0026      0.92      10      92 ..      35     114 ..      27     124 .. 0.64
   2 ?    1.1   0.1       1.3   4.5e+02      87     114 ..     213     242 ..     189     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0026
                                   HHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          OmpH  10 ileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle.keekeqelqkkeqelqqkqqqkaqelqkkqqe 89 
                                   i+++ +e ++ +++l + ++++ + ++a ++e+++ qe+ +k    +e  e++++e ++  + +q+  q++ + +++++++
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKK---IWEsIEKQREETKRIWESIQA-TQNEIKGIREENAK 111
                                   667777777777777777777777777777777777777752...222266666666666666666.55555666666655 PP

                                   HHH CS
                          OmpH  90 llk 92 
                                   + k
  gi|70607873|ref|YP_256743.1| 112 IWK 114
                                   544 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.3
                                   HHHHHHH..HHHHHHHHHHHHHHHTT-SEE CS
                          OmpH  87 qqellkp..ildkinkaikevakekgydlv 114
                                    ++ +k+  + + i+k ik  a+++g++++
  gi|70607873|ref|YP_256743.1| 213 HKKPIKKflVANSIEKRIKRRAERRGITVI 242
                                   44444442255999999**********998 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.1     0.051        18       6      55 ..      37      89 ..      32      92 .. 0.79
   2 ?    8.0   3.4    0.0071       2.5       6      84 ..      68     150 ..      61     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.051
                          ACCA  6 kpiaeleekieelkklaee...sevdlseeieklekkleklkkeiyknltpwq 55
                                  k+i+ele+k++el + +++   s + +++ei+++++  +k+ ++i k+ ++ +
  gi|70607873|ref|YP_256743.1| 37 KKIEELEKKMSELITNSNRiweSIQATQNEIKAIQEDNKKIWESIEKQREETK 89
                                  89**********87776665645666889999999999999999888776665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0071
                          ACCA   6 kpiaeleekieelkklaeesevdlseeieklekkleklkkeiyknltpwqkvqlaRhpeRpktldyie....alfedfvel 82 
                                   k i+e ++ki e  + ++e++  + e+i++++++++ +++e  k  +++++++++ ++  + + +yie    +l+++  el
  gi|70607873|ref|YP_256743.1|  68 KAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIERINISFSTFTSRSGHYIErtimNLYKEALEL 148
                                   4556666677776666677788899*****************999********9987766666666552222788999999 PP

                          ACCA  83 hG 84 
                                   hG
  gi|70607873|ref|YP_256743.1| 149 HG 150
                                   99 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.7   0.00037      0.13      10      84 ..      34     107 ..      32     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00037
               Snapin_Pallidin  10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                   l++ k++el++k +el+++ +   e+++  ++++k ++e+++ ++ + +++ ++  ++i   +++ ++ ++ +++
  gi|70607873|ref|YP_256743.1|  34 LIVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNK-KIWESIEKQREETKRIWESIQATQNEIKGIRE 107
                                   7889*************************************9.999*****999999999999999999988876 PP

>> LPD11  Large polyvalent protein-associated domain 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.19        67      40      69 .]      18      46 ..       4      46 .. 0.83
   2 ?    8.0   2.4    0.0086         3      24      50 ..      72      97 ..      52     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.19
                         LPD11 40 emkelynslpedeKPewltleqiaeyekrm 69
                                   m +l+n + e  K e l +++i+e+ek+m
  gi|70607873|ref|YP_256743.1| 18 LMDALFNRFYERVK-EELIVKKIEELEKKM 46
                                  5999*******666.557799*******99 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0086
                         LPD11 24 rnekhLwagsveeqieemkelynslpe 50
                                  + +k++w +s+e+q ee k++++s++ 
  gi|70607873|ref|YP_256743.1| 72 EDNKKIW-ESIEKQREETKRIWESIQA 97
                                  567899*.9***************987 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3       1.2   4.3e+02      91     106 ..      38      53 ..      17      69 .. 0.50
   2 ?    7.5   2.9     0.012       4.2      66     118 ..      62     115 ..      42     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                          COG2  91 klsereeeveskleea 106
                                   k++e e+++++ + + 
  gi|70607873|ref|YP_256743.1|  38 KIEELEKKMSELITNS 53 
                                   3333333333333332 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.012
                          COG2  66 glqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellkl 118
                                     q+e++ ++ + +++++ +e+ re+ ++  e +++  +e k ++e++ ++ k+
  gi|70607873|ref|YP_256743.1|  62 ATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIREENaKIWKA 115
                                   578999999*****************9999999999999999999887544444 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  10.8    0.0046       1.6       1      96 [.      38     130 ..      23     177 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0046
                       zf-C4H2   1 aikeirektleleklknklakevealekeekcleeykkel.elLeqEkmaHveeLrlIhaDinalEsvikeaeeekeksle 80 
                                   +i+e+ +k++el + +n++ + ++a+++e k ++e +k++ e +e+ +    ee + I + i+a  + ik  +ee+ k ++
  gi|70607873|ref|YP_256743.1|  38 KIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIwESIEKQR----EETKRIWESIQATQNEIKGIREENAKIWK 114
                                   467777788888888888888888888888877776554414454444....67777888888888888888888888888 PP

                       zf-C4H2  81 kakklyeeykklkeev 96 
                                   +++++   ++   ++ 
  gi|70607873|ref|YP_256743.1| 115 AIERINISFSTFTSRS 130
                                   7777766666555544 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.1    0.0032       1.1      13      72 ..      35     102 ..      28     121 .. 0.83
   2 ?   -1.0   0.1       6.2   2.2e+03      19      31 ..     225     237 ..     222     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0032
                       DUF4164  13 LeaaldsLEkavdrrleaerkr....deleaeiealgedrsRLaeeLdqaearaar....leevnrEv 72 
                                   + +++++LEk + + +++ +      ++ ++ei+a++ed +++ e + +++ +++r    ++++++E+
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIwesiQATQNEIKAIQEDNKKIWESIEKQREETKRiwesIQATQNEI 102
                                   56899*********99999998988899*********************9999987311134555565 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 6.2
                       DUF4164  19 sLEkavdrrleae 31 
                                   s+Ek+++rr e+ 
  gi|70607873|ref|YP_256743.1| 225 SIEKRIKRRAERR 237
                                   6788888888775 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.0     0.021       7.3     107     183 ..      35     125 ..      27     130 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.021
                        DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerqlallk..............ekkeaadkeiarlkseaekleee 173
                                   + +++++lekk++e  ++++++ e+i+ ++++i+ +++ ++ +               e  +a ++ei+ ++ e++k+ ++
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWesiekqreetkriwESIQATQNEIKGIREENAKIWKA 115
                                   455666666666666666666666666666666655555554443333333333344466666666666666666666666 PP

                        DUF724 174 ledveqeFea 183
                                   +e+++ +F++
  gi|70607873|ref|YP_256743.1| 116 IERINISFST 125
                                   6666666655 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.0      0.02       7.1       2      70 ..      38     111 ..      37     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                   Uso1_p115_C   2 kaseleseaaslkdeneklkaelqslskalesleqk.....eakkaaesqakeleaenkklekeleklraelke 70 
                                   k +ele++ ++l + +++   ++q+++++++  ++      e+ ++++++ k++ ++++++++e++ +r+e ++
  gi|70607873|ref|YP_256743.1|  38 KIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDnkkiwESIEKQREETKRIWESIQATQNEIKGIREENAK 111
                                   6799**********************999998888878899999999999999999999999999999998665 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  10.1    0.0011      0.38      23      91 ..      36     104 ..      25     108 .. 0.91
   2 ?   -1.8   0.1       9.4   3.3e+03      54      83 ..     199     228 ..     193     235 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0011
                          BRE1  23 vkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefvrklke 91 
                                   vk+++ le+k++ l ++ ++  + + a++++++a++ ++kk+ ++++K++e  ++  e+  ++++++k 
  gi|70607873|ref|YP_256743.1|  36 VKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKG 104
                                   78999*************************************************999988888888875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.4
                          BRE1  54 kdalenelkkLnkllsKsselieqLkelek 83 
                                   +++le+  k L++l++K  ++    + +ek
  gi|70607873|ref|YP_256743.1| 199 IEQLEIREKILSSLHKKPIKKFLVANSIEK 228
                                   566677777777777775555555555555 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.5     0.012       4.2      29     114 ..      36     126 ..      27     137 .. 0.72
   2 ?    1.4   0.1       1.1     4e+02       8      68 ..     140     200 ..     134     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                       DUF2115  29 ekeikklpekyrkel..seslteylfeaykelknkrsgdkseykeevideeelkeflemleeqceeekeek...eerlrkl 104
                                    k+i++l++k  + +  s+++ e +  + +e+k  ++++k+  ++   ++ee+k+++e ++++ +e k  +    +  + +
  gi|70607873|ref|YP_256743.1|  36 VKKIEELEKKMSELItnSNRIWESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQATQNEIKGIReenAKIWKAI 116
                                   5788888888888762245789999999******66666666677888999999999999998888766542324444555 PP

                       DUF2115 105 yylvslYliF 114
                                    ++ + +++F
  gi|70607873|ref|YP_256743.1| 117 ERINISFSTF 126
                                   5566666666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.1
                       DUF2115   8 ilkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelknkrsgdkse 68 
                                    l kea +++  D  k++  + ++++ + +k rk  ++ + +  +  + e+kn+ ++ ++e
  gi|70607873|ref|YP_256743.1| 140 NLYKEALELHGIDSSKVTHGVIEDTEGIVHKGRKYEIDFYETNGVIYLFEIKNHADEGAIE 200
                                   6889999999999999999999999999999999999999999999999999944433333 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.5    0.0022      0.79     162     219 ..      38      98 ..      11     103 .. 0.75
   2 ?    0.7   0.1      0.78   2.7e+02     174     204 ..      88     118 ..      86     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                        Cluap1 162 eleeiekalkeaikkvk...eelektkkalenlesdeanLeakiekkkqeleraqkrLqsl 219
                                    +ee+ek+++e i++ +   e+++ t+++++ +++d++++ + iek+++e  r  + +q+ 
  gi|70607873|ref|YP_256743.1|  38 KIEELEKKMSELITNSNriwESIQATQNEIKAIQEDNKKIWESIEKQREETKRIWESIQAT 98 
                                   45677777777666544222899****************************9987766665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.78
                        Cluap1 174 ikkvkeelektkkalenlesdeanLeakiek 204
                                   +k++ e+++ t+++++ +++++a++ + ie+
  gi|70607873|ref|YP_256743.1|  88 TKRIWESIQATQNEIKGIREENAKIWKAIER 118
                                   6777889999***********9999999887 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.4    0.0036       1.3     119     161 ..      35      77 ..      25      79 .. 0.91
   2 ?    6.3   1.7     0.023       8.1      91     135 ..      73     117 ..      71     121 .. 0.90
   3 ?   -0.9   0.1       3.9   1.4e+03     111     148 ..     185     221 ..     150     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0036
                      Cauli_AT 119 rikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                    +kk+ee  kk++e i   + + e ++ ++++++ i+++ k+i
  gi|70607873|ref|YP_256743.1|  35 IVKKIEELEKKMSELITNSNRIWESIQATQNEIKAIQEDNKKI 77 
                                   5799***********************************9998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                      Cauli_AT  91 klkkifkeggedkekktklletLkeaqnrikkleeetkklaekiv 135
                                   + kki+++ ++++e++ +  e+++ +qn ik + ee+ k+ + i+
  gi|70607873|ref|YP_256743.1|  73 DNKKIWESIEKQREETKRIWESIQATQNEIKGIREENAKIWKAIE 117
                                   67899999****************************999987765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.9
                      Cauli_AT 111 etLkeaqnrikkleeetkklaekivtekllkeevkdld 148
                                     L e++n+ ++   e+ ++ eki +  l k+ +k++ 
  gi|70607873|ref|YP_256743.1| 185 IYLFEIKNHADEGAIEQLEIREKILS-SLHKKPIKKFL 221
                                   45666777666555555666666654.45566666653 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   6.0      0.11        38      44      87 ..      41      84 ..      26      98 .. 0.79
   2 ?    3.8   0.9      0.22        78      51      84 ..      83     116 ..      79     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                   Carbpep_Y_N 44 klskllee.eekknnvfekiskvlneplkeltseakkiWsemelk 87
                                  +l+k + e   + n ++e+i+   ne +k+++++ kkiW+ +e +
  gi|70607873|ref|YP_256743.1| 41 ELEKKMSElITNSNRIWESIQATQNE-IKAIQEDNKKIWESIEKQ 84
                                  44455555467788899999999888.999999999999988765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.22
                   Carbpep_Y_N  51 e.eekknnvfekiskvlneplkeltseakkiWsem 84 
                                   +  e+++ ++e+i+   ne +k + +e  kiW+ +
  gi|70607873|ref|YP_256743.1|  83 KqREETKRIWESIQATQNE-IKGIREENAKIWKAI 116
                                   4466777788888888777.888888888888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2515  (0.140276); expected 358.6 (0.02)
Passed bias filter:                      930  (0.0518713); expected 358.6 (0.02)
Passed Vit filter:                       192  (0.0107089); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              51  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 1590.62
//
Query:       gi|70607874|ref|YP_256744.1|  [L=286]
Description: hypothetical protein Saci_2161 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-24   84.5  35.9    1.1e-23   83.9  35.9    1.3  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9  35.9     6e-28   1.1e-23      70     330 ..      23     276 ..      13     286 .] 0.78

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6e-28
                       DUF2079  70 llslgglplyrlarerllsrrlalliallYllspvvinptlfd.....Fhpe.vlaiPllllalllalrrrkwllllvlil 144
                                    l ++++ +yr+ + +l     +l+ a+++ll+p++i+ +l+      F      ++Pll+l  ++++++++w++++++++
  gi|70607874|ref|YP_256744.1|  23 SLFISSIFVYRIGKIILRRDSISLISAIIFLLNPSTIFCLLYSpknygFASVgYYFVPLLYLMSYYYYLKKDWKKFTAFTV 103
                                   45679************9*******************99995412222322213467************************ PP

                       DUF2079 145 llllvredlslvvvilglwlilre......rkrrkiglillllglawvilvtsvl.iPlfsstksqvfgverysylgsSll 218
                                    l l++   +l+ +++ ++l++r+        + +++ + + l l+ v+l+++vl iP + +               sSl 
  gi|70607874|ref|YP_256744.1| 104 ALTLTSPLSYLIAITFIVYLLIRNrideksLSWSLLRENKISLVLILVSLIIGVLvIPQTLQHF-------------SSL- 170
                                   ***********************96666553344477777777777777777766578874422.............222. PP

                       DUF2079 219 eillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqlslgyq.Ysllvipfl 298
                                    ++ ++  q++  l ++ ++ + kl y+++lf+ + flp++ sp++L++alP+ll+ l+s+y p++s+gy+ Y++l++p+l
  gi|70607874|ref|YP_256744.1| 171 -LIASIYPQYT-SLNYIYDNVYFKLTYWFILFGVFSFLPIF-SPLELIPALPYLLVGLFSSYIPYYSYGYYpYYFLALPML 248
                                   .2333444555.6999999999*******************.**************************9988********* PP

                       DUF2079 299 vlaaifglaklsssvelrrikriwsvalvlvl 330
                                   ++++i +++ ++      ++  ++s++  +++
  gi|70607874|ref|YP_256744.1| 249 IMGFIRTINLIKD----DKRTMLISYVFIFLF 276
                                   ************3....233333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1959.74
//
Query:       gi|70607875|ref|YP_256745.1|  [L=644]
Description: hypothetical protein Saci_2162 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     3e-108  362.6  37.7     3e-108  362.6  37.7    1.5  2  DUF2079   Predicted membrane protein (DUF2079)
  ------ inclusion threshold ------
      0.015   14.5   0.3      0.024   13.8   0.3    1.2  1  DUF608    Glycosyl-hydrolase family 116, catalytic region


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.6  37.7  3.3e-112    3e-108       1     456 []      32     488 ..      32     488 .. 0.96
   2 ?   -2.8   0.1      0.24   2.1e+03     206     236 ..     587     617 ..     572     624 .. 0.75

  Alignments for each domain:
  == domain 1  score: 362.6 bits;  conditional E-value: 3.3e-112
                       DUF2079   1 rlasLnstayDlGifdQviwntsqGe.lfysslsgvl....hlLgqHfapillllaplyalfPsvltLllvqalllslggl 76 
                                   rl++L+s+a+DlG+f+Q++++t+ G  +fy+ +++++    ++L++H+++il+l++p+y+lfPs+ltL+++q++++s++++
  gi|70607875|ref|YP_256745.1|  32 RLYDLLSGAFDLGLFMQEFYSTIYGGkIFYDAANFLSfgalSGLAIHPYLILFLVIPIYYLFPSWLTLSIIQTVVISISSI 112
                                   799*********************999*********99******************************************* PP

                       DUF2079  77 plyrlarer.lls..rrlalliallYllspvvinptlfdFhpevlaiPllllalllalrrrkwllllvlilllllvredls 154
                                   +lyr+a+ + +++   rl+l++++lYl++p++i+ +lfdFh+e l+ Pl++++++++++r++w++++++i++l+l++e+++
  gi|70607875|ref|YP_256745.1| 113 YLYRIANIVlGNNrnLRLPLILTILYLFNPLIISGLLFDFHAEALF-PLFYMGAFYYYLRKEWKKFTLFIVFLILTMEAAY 192
                                   *********666576789****************************.********************************** PP

                       DUF2079 155 lvvvilglwlilrerkrrk...............iglillllglawvilvtsvliPlfsstksqvfgverysylgsSllei 220
                                   ++v++++++li+r+r r+k               i+ + l++++++v+l+++++iP + st+++v+ +       ++++++
  gi|70607875|ref|YP_256745.1| 193 PIVIFFMIYLIMRNR-RTKeenvkegfsydlatfIRKNKLFIIIIIVTLAVGLTIPKYFSTIFSVSPP-------TGYSSY 265
                                   **************5.4446999****************************************99999.......9***** PP

                       DUF2079 221 llnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqlslgyqYsllvipflvla 301
                                   ++++i++++l   +l++++  k+++l++l++++gflp++ +p++Ll+++P++ll+l+s++ p++++g+qY l+ + ++v+a
  gi|70607875|ref|YP_256745.1| 266 YSSRISSLYLSGISLFWYD--KINFLVILLASFGFLPIF-APTELLPGAPYILLILFSNHVPYFEIGWQYPLIGAGMFVVA 343
                                   *******************..******************.***************************************** PP

                       DUF2079 302 aifglaklsssvelrrikriwsvalvlvlvltlflnparslsflvpdsesp.....vvylstlaqlqas...rellklIps 374
                                   +++++++l       +++ri+ v+++++++l+++lnp+ + +f+ ++s ++      ++ls +++l+++   + +++lIp+
  gi|70607875|ref|YP_256745.1| 344 MVYAISRLI------KNYRIIIVSIFVMFMLSVALNPYLYDNFQPSNSSRIfsggyNPKLSLSTALANYeviSIMTSLIPH 418
                                   *********......99***************************************99*********************** PP

                       DUF2079 375 dasvlatsnLaPhlan..Rayvylfpeneel.ydleylleevdyvlldvafrgwasrkdrerklidklrnsgrygviaeed 452
                                   +a+v+a+snL+P++an  +ay  ++++ +++ y+++yl+++++yvll+              +  + ++ +g+y++iae d
  gi|70607875|ref|YP_256745.1| 419 NAVVIASSNLFPFVANdvNAY--PIYGYFNTsYMITYLPNTPQYVLLS-------------GQSNELTMLKGNYSIIAEGD 484
                                   ****************55555..7777777767***************.............778888999999******** PP

                       DUF2079 453 gvll 456
                                   +++l
  gi|70607875|ref|YP_256745.1| 485 NLIL 488
                                   *997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.24
                       DUF2079 206 gverysylgsSlleillnlitqpllvlqell 236
                                    v +ys + sS l++ +++i+ p+ + +++ 
  gi|70607875|ref|YP_256745.1| 587 KVLNYSIIDSSQLGYGWSIISLPFSIKDYYS 617
                                   345788888999*********9998876665 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.7e-06     0.024     193     264 ..     530     592 ..     515     612 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-06
                        DUF608 193 eeykellekakkvyekkLwnGeYfkydesssesesimadqlaGqwylracglee.ivpkekvksaLktiyeln 264
                                   ++  e+l+  +++y+k+LwnG Y+++             + + q+yl++ + ++ +++ e  +s+L+++ ++ 
  gi|70607875|ref|YP_256745.1| 530 NRQVEILKIYNTSYNKTLWNGPYYNFAM---------G-NYVAQFYLKLGNNSNtTLKVEVFDSTLNKVLNYS 592
                                   455678888999**************94.........2.2334677777665555677777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4089.83
//
Query:       gi|70607876|ref|YP_256746.1|  [L=234]
Description: hypothetical protein Saci_2163 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-06   26.3   5.8    6.7e-06   25.6   5.8    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    0.00036   19.8   1.1    0.00081   18.7   1.1    1.5  1  zf-RanBP        Zn-finger in Ran binding protein and others
     0.0004   20.3   2.6    0.00063   19.7   2.6    1.3  1  DZR             Double zinc ribbon
     0.0015   18.2   0.3     0.0029   17.3   0.3    1.5  1  Gemini_mov      Geminivirus putative movement protein
  ------ inclusion threshold ------
      0.017   14.9   0.1       0.03   14.1   0.1    1.3  1  DUF3094         Protein of unknown function (DUF3094)
      0.058   13.7   0.0      0.071   13.4   0.0    1.1  1  RskA            Anti-sigma-K factor rskA
       0.32   11.0   1.9         24    5.0   0.0    2.6  2  YhfH            YhfH-like protein
       0.57    9.7   4.5       0.94    9.0   4.5    1.4  1  zf-ribbon_3     zinc-ribbon domain
        0.6   10.9   3.9        1.2    9.9   3.9    1.6  1  zinc_ribbon_15  zinc-ribbon family
        3.9    7.4   5.5         56    3.7   5.5    2.2  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        4.2    7.5   6.3         49    4.1   6.3    2.1  1  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   5.8   4.1e-09   6.7e-06       2      22 ..       4      24 ..       3      25 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-09
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                  C +CG+ ++d+ak+C  CG+p
  gi|70607876|ref|YP_256746.1|  4 CQKCGYSNPDDAKYCVACGYP 24
                                  ********************9 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.1     5e-07   0.00081       6      25 ..       3      22 ..       3      24 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5e-07
                                  E-SSS--EEESSSSB-TTT- CS
                      zf-RanBP  6 dCskClvqNfawstkCvaCq 25
                                  +C kC+++N+  + +CvaC+
  gi|70607876|ref|YP_256746.1|  3 NCQKCGYSNPDDAKYCVACG 22
                                  5******************7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.6   3.9e-07   0.00063       1      25 [.       4      28 ..       4      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.9e-07
                           DZR  1 CpqCgeelppdarfCseCgtklkav 25
                                  C++Cg  +p+da++C +Cg + ++ 
  gi|70607876|ref|YP_256746.1|  4 CQKCGYSNPDDAKYCVACGYPFPES 28
                                  *******************997654 PP

>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   1.8e-06    0.0029       8      51 ..      24      70 ..      19      81 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                    Gemini_mov  8 vplspqnalyqkPrvptaapssselpwsrv..g..eiailtlvavlvl 51
                                  +++  ++ + q+P++p++ap+s++ p+  +     ++ai++ + v+++
  gi|70607876|ref|YP_256746.1| 24 PFPESTSEQ-QTPSQPQPAPESPKRPFPLFrvIaaVVAIVIVIGVVAI 70
                                  444455555.9*************999755113113345555555555 PP

>> DUF3094  Protein of unknown function (DUF3094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.8e-05      0.03      25      52 ..      46      73 ..      32      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                       DUF3094 25 RqPFrpWlllvvvlavvigLGllsRlLs 52
                                  ++PF  ++++ +v+a+vi++G+++ lL 
  gi|70607876|ref|YP_256746.1| 46 KRPFPLFRVIAAVVAIVIVIGVVAILLN 73
                                  79********************998885 PP

>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.4e-05     0.071      21      57 ..      30      82 ..      25     144 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                                  ........................XXXXXXXXXXXXXX................ CS
                          RskA 21 aaaaaaaaapppaaapaararr..laaaaAaalllvlg...............q 57
                                  ++++++++++p+++ p+++  +   + aa++a+++v+g               +
  gi|70607876|ref|YP_256746.1| 30 SEQQTPSQPQPAPESPKRPF-PlfRVIAAVVAIVIVIGvvaillntnsvfkstP 82
                                  23333333333333333333.334444444444455664455555544444442 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.8     0.027        44      13      20 ..       1       8 [.       1      10 [. 0.89
   2 ?    5.0   0.0     0.015        24      13      25 ..      15      27 ..      14      30 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                          YhfH 13 kKkCteCG 20
                                  +K C++CG
  gi|70607876|ref|YP_256746.1|  1 MKNCQKCG 8 
                                  69*****9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.015
                          YhfH 13 kKkCteCGkeieE 25
                                  +K C+ CG  + E
  gi|70607876|ref|YP_256746.1| 15 AKYCVACGYPFPE 27
                                  7*******77655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.5   0.00058      0.94       2      26 .]       1      25 [.       1      25 [. 0.94

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00058
                   zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGtkl 26
                                  +++C +CG  +  +d++ C  CG+++
  gi|70607876|ref|YP_256746.1|  1 MKNCQKCGYsN-PDDAKYCVACGYPF 25
                                  799******99.***********985 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.9   0.00075       1.2      66      86 .]       2      22 ..       1      22 [. 0.95

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                  k C++Cg +  ++ kyC  Cg
  gi|70607876|ref|YP_256746.1|  2 KNCQKCGYSNPDDAKYCVACG 22
                                  78******************9 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   5.5     0.034        56       3      34 ..       3      28 ..       1      30 [. 0.65

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                                  BESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                RNA_POL_M_15KD  3 FCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                                   C+kCg   ++  d+ +    C  CgY +p +
  gi|70607876|ref|YP_256746.1|  3 NCQKCG---YSNPDDAKY---CVACGYPFPES 28
                                  577777...666666663...88888888766 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.3      0.03        49       1      25 [.       2      26 ..       2      27 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.03
                       UPF0547  1 KvCPeCeakvPvaaqfCphCGyvFq 25
                                  K+C  C    P +a+ C  CGy F 
  gi|70607876|ref|YP_256746.1|  2 KNCQKCGYSNPDDAKYCVACGYPFP 26
                                  899999999999*****77***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1146  (0.0639188); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1702.60
//
Query:       gi|70607877|ref|YP_256747.1|  [L=214]
Description: 5-amino-6-(5-phosphoribosylamino)uracil reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-49  167.7   0.0    3.1e-49  167.5   0.0    1.0  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.0   1.7e-53   3.1e-49       1     200 []       5     207 ..       5     207 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 1.7e-53
                                   -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEE CS
                        RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvV 81 
                                   py i+++++S+DG+la+++g s+ ++++ ++++ h+lrae+dai+vG +tv++dnpsltv+++kk+  +     ++p+rv+
  gi|70607877|ref|YP_256747.1|   5 PYTIIFSTISIDGRLATKTGYSE-LSCPIDKQRQHQLRAEVDAIMVGGNTVRIDNPSLTVKYAKKK--D-----KDPIRVI 77 
                                   7899*******************.*****************************************6..3.....89***** PP

                                   EETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC....E...SE-HHHHHHHHHHT.T--EEEEEETHHHHHHHHHTT CS
                        RibD_C  82 vdstlrvpldakvltddaptlvatteeadkekveklk....v...rvdlkelleeLker.girsllveGGatLagsllrag 154
                                   v+++l+++ + k+++  +p +v++t++ ++ k  +l+    v     +l +++++L+e  ++r+l++eGG++L++s + ++
  gi|70607877|ref|YP_256747.1|  78 VSKSLNLDVSSKIFSI-PPLTVVYTKSENRSKQYELEkrgvVvrrFNELSDVFSDLYESfNVRRLMIEGGGNLIWSVIHEK 157
                                   ************9997.6999999999999999999999963698778********************************* PP

                                   T-SEEEEEEESCE--TTSBCSSSSST-SS.....EEEEEEEEEEETTEEEE CS
                        RibD_C 155 lvDelrlyiaPkllGgagktlfdgegfka.....lklklvksealgegvvl 200
                                   l+De+r+++ P ++G+ g +l +gegf+      l+l ++k++++g++++l
  gi|70607877|ref|YP_256747.1| 158 LYDEIRVTVSPRIFGN-GVSLAQGEGFQGdesprLRLVDAKICQCGNEIHL 207
                                   ****************.***********9***999999999******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1464.74
//
Query:       gi|70607878|ref|YP_256748.1|  [L=231]
Description: glycerophosphoryl diester phosphodiesterase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-30  107.4   1.6    1.8e-30  106.6   1.6    1.4  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
     0.0032   17.9   0.1      0.023   15.2   0.1    2.2  2  GDPD_2    Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
      0.086   12.2   1.0       0.14   11.5   1.0    1.4  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   1.6   2.9e-34   1.8e-30       1     258 [.       6     218 ..       6     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.9e-34
                                   TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCCS CS
                          GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaql 81 
                                   HRGa+ +  EnT++sf +A  lG+d++E+Dv+l++D +++v+HD+++    ++ +   v++ltl+ l++ +          
  gi|70607878|ref|YP_256748.1|   6 HRGAPLEAKENTIQSFLTAKNLGVDAVELDVHLSSDKKVIVFHDDSVLINSKMVK---VSELTLDRLRKVT---------- 73 
                                   ********************************************99988888877...**********999.......... PP

                                   CCCSSGCCB...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHHHH CS
                          GDPD  82 senrvrlefpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdilk 162
                                       +     +ptleevl+     ++n+ ++i+  s+        i+ +++k+++e+        d+  vi  sf++d++k
  gi|70607878|ref|YP_256748.1|  74 ---GI----EVPTLEEVLE--TVGNFNYVVEIKKSSAFYPS----IEERVAKAIKERE-----LVDNVNVI--SFDFDSIK 134
                                   ...23....36*******9..57777777777765543332....3344445555554.....23566788..******** PP

                                   HHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHH CS
                          GDPD 163 llrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedeeemkr 243
                                   +++e ++k+ +  +++g+ +          ak++kad+l  ++++++e       Vk a+++gl++ ++tvn+   ++  +
  gi|70607878|ref|YP_256748.1| 135 RIKEIEEKISTGIIFVGRINWFLE-----IAKKVKADWLAFYHELATEE-----DVKIAHQSGLKLDAWTVNDL--DQAEQ 203
                                   ****************88887777.....89******************.....9*******************..99999 PP

                                   HHCCC-SEEEES-HH CS
                          GDPD 244 lleagvdgvitDfpd 258
                                   l++ g+d++ tD+p 
  gi|70607878|ref|YP_256748.1| 204 LERSGIDALTTDNPR 218
                                   *************96 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.27   1.6e+03      13      23 ..      21      31 ..      14      32 .. 0.73
   2 !   15.2   0.1   3.8e-06     0.023       1      29 [.     189     217 ..     189     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.27
                        GDPD_2 13 wrelvgaGVdg 23
                                  + ++ ++GVd 
  gi|70607878|ref|YP_256748.1| 21 FLTAKNLGVDA 31
                                  478889***96 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.8e-06
                        GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTDdl 29 
                                   k ++Wt++d ++  +l + G d ++TD++
  gi|70607878|ref|YP_256748.1| 189 KLDAWTVNDLDQAEQLERSGIDALTTDNP 217
                                   579************************98 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.0   2.3e-05      0.14      36     124 ..      24     116 ..       9     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                                   HHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHH..HHHHHHHH---EEE--SS--HHH..HEEE-SSEEEE-G CS
                         eIF-6  36 eeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeel..eklkeslkleverleekltAlGN..vilaNDkvAlvhp 112
                                   +++L+v++ve  ++ s+   ++v   ++ l+ +++v+ +el  ++l++ + +ev +lee l  +GN   ++   k    +p
  gi|70607878|ref|YP_256748.1|  24 AKNLGVDAVELDVHLSSDKKVIVFHDDSVLINSKMVKVSELtlDRLRKVTGIEVPTLEEVLETVGNfnYVVEIKKSSAFYP 104
                                   67999*****************************99988853379****9***************9665666777888899 PP

                                   GGGG.GHHHHHH CS
                         eIF-6 113 dlsketveiiad 124
                                   +++++++++i++
  gi|70607878|ref|YP_256748.1| 105 SIEERVAKAIKE 116
                                   999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1644.62
//
Query:       gi|70607879|ref|YP_256749.1|  [L=116]
Description: hypothetical protein Saci_2166 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-19   68.6   0.0    1.2e-18   67.9   0.0    1.3  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.028   14.6   0.6      0.077   13.2   0.6    1.7  2  DUF3669   Zinc finger protein


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   1.3e-22   1.2e-18       1     122 []       3     108 ..       3     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1.3e-22
                        DUF488   1 slervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferYaae 79 
                                   ++++vyd ++ +dg+r+lv+ R+wP      +++   + d+        wl++l+ps+el +w++ +p +weef++rY +e
  gi|70607879|ref|YP_256749.1|   3 KIKNVYDkPEINDGIRILVE-RTWPA----SVTRG--SIDM--------WLRDLAPSEELITWYNYEPqKWEEFKRRYLEE 68 
                                   699*****************.*****....66665..5788........99**************99989*********** PP

                        DUF488  80 leskeaakealeelkelakkg..vaLlcaekdperchrvvlaeyl 122
                                   l+ +     +++ l   +k +  v++l+ + dp  +++vvl+ey+
  gi|70607879|ref|YP_256749.1|  69 LRYN----PKVKPLLMIVKMTkiVTFLY-SGDPTYNNAVVLKEYI 108
                                   **96....68899999998888555555.56************96 PP

>> DUF3669  Zinc finger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   8.6e-06     0.077      39      63 ..      44      68 ..      35      71 .. 0.87
   2 ?   -1.9   0.0      0.44   3.9e+03      19      32 ..      84      97 ..      76     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.6e-06
                       DUF3669 39 eetavelgpqdeklWevfktrYlek 63
                                  +e++++  + + ++We+fk+rYle 
  gi|70607879|ref|YP_256749.1| 44 SEELITWYNYEPQKWEEFKRRYLEE 68
                                  56788999999************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.44
                       DUF3669 19 iaeavkafwdndpY 32
                                  ++++v  +++ dp 
  gi|70607879|ref|YP_256749.1| 84 MTKIVTFLYSGDPT 97
                                  56788888988883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 886.86
//
Query:       gi|70607880|ref|YP_256750.1|  [L=206]
Description: HTH DNA binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   72.9   0.2    2.9e-20   71.8   0.2    1.6  1  HTH_10          HTH DNA binding domain
    5.1e-06   25.9   0.8    1.2e-05   24.7   0.8    1.6  1  Sigma70_r4      Sigma-70, region 4
     0.0001   21.8   0.7    0.00024   20.6   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.073   13.5   0.0    1.8  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.024   14.5   0.1      0.075   12.9   0.0    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.037   13.8   0.2       0.15   11.9   0.0    2.0  2  HTH_23          Homeodomain-like domain
      0.049   13.8   0.0       0.45   10.7   0.0    2.5  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.054   13.4   0.0       0.11   12.5   0.0    1.4  1  MarR_2          MarR family
      0.069   13.2   0.2         15    5.7   0.0    2.7  2  CIDE-N          CIDE-N domain
      0.095   12.1   0.2       0.98    8.9   0.0    2.4  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.18   11.5   2.2        3.7    7.3   0.1    3.2  3  Sigma70_r4_2    Sigma-70, region 4
       0.18   11.8   3.2       0.66   10.0   0.1    3.0  3  HTH_Mga         M protein trans-acting positive regulator (MG
       0.25   11.1   1.4        2.4    8.0   1.4    2.4  1  LexA_DNA_bind   LexA DNA binding domain
        1.7    8.7   4.9         21    5.2   0.5    3.2  2  RHH_1           Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.2   2.3e-23   2.9e-20       1      51 [.     147     197 ..     147     199 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.3e-23
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                   LT++qle+lkl y+mG+Fd++Rr+t+ eLA++lGI+++tl+e+Lr+a +k 
  gi|70607880|ref|YP_256750.1| 147 LTERQLEILKLSYKMGFFDVDRRITMTELAEKLGIKAPTLEEILRRALRKA 197
                                   9***********************************************995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.8   9.6e-09   1.2e-05       4      47 ..     146     196 ..     145     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 9.6e-09
                                   HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                    Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                   +L+er+ e+l+l++       ++  T+ E++e+lgi   +   i++rAlrk
  gi|70607880|ref|YP_256750.1| 146 QLTERQLEILKLSYkmgffdvDRRITMTELAEKLGIKAPTLEEILRRALRK 196
                                   8************************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       7.1     9e+03       6      14 ..      56      64 ..      53      65 .. 0.64
   2 !   20.6   0.0   1.9e-07   0.00024      15      41 ..     167     193 ..     147     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.1
                        HTH_24  6 rkILelLqk 14
                                   k+L++L++
  gi|70607880|ref|YP_256750.1| 56 EKLLKELKE 64
                                  567777764 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.9e-07
                        HTH_24  15 nprisqreLAerlglSpstvnrrlkrL 41 
                                   + ri+++eLAe+lg+  +t+ + l+r 
  gi|70607880|ref|YP_256750.1| 167 DRRITMTELAEKLGIKAPTLEEILRRA 193
                                   89********************99996 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.7e-05     0.073       8      32 ..     167     191 ..     166     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                        HTH_26   8 drgitkseLargtgisaatlsrlvk 32 
                                   dr+it +eLa+++gi a+tl+ ++ 
  gi|70607880|ref|YP_256750.1| 167 DRRITMTELAEKLGIKAPTLEEILR 191
                                   89******************99875 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.3   6.8e+03      27      37 ..      70      80 ..      67      81 .. 0.76
   2 ?   12.9   0.0   5.8e-05     0.075      15      34 ..     167     186 ..     165     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.3
                 HTH_AsnC-type 27 vGlSestvlrR 37
                                  + +Se+ v+ R
  gi|70607880|ref|YP_256750.1| 70 LRISENSVWIR 80
                                  67899999966 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.8e-05
                 HTH_AsnC-type  15 daRisyaeLAervGlSestv 34 
                                   d Ri+++eLAe++G+ ++t 
  gi|70607880|ref|YP_256750.1| 167 DRRITMTELAEKLGIKAPTL 186
                                   77*************99986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   1.8e+03      24      35 ..      67      78 ..      45      82 .. 0.81
   2 ?   11.9   0.0   0.00012      0.15       8      41 ..     152     193 ..     146     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                        HTH_23 24 AreLgvsrrTvy 35
                                  ++ L +s++ v+
  gi|70607880|ref|YP_256750.1| 67 SKTLRISENSVW 78
                                  578899999887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                        HTH_23   8 lrillllae........GlsvreIAreLgvsrrTvyrwlkry 41 
                                   l+il+l  +        +++ +e A++Lg+   T+  +l+r 
  gi|70607880|ref|YP_256750.1| 152 LEILKLSYKmgffdvdrRITMTELAEKLGIKAPTLEEILRRA 193
                                   55777777444444567*********************9995 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   1.8e+03      24      36 ..      22      34 ..      15      35 .. 0.83
   2 ?   10.7   0.0   0.00035      0.45      23      45 ..     170     192 ..     163     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                                  -HHHHHHHHTS-H CS
                Fe_dep_repress 24 ktkdlaerLnvsp 36
                                   +++l e++nv++
  gi|70607880|ref|YP_256750.1| 22 LVMKLFEEMNVKA 34
                                  678999*****96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                                   B-HHHHHHHHTS-HHHHHHHHHH CS
                Fe_dep_repress  23 vktkdlaerLnvspssVsemlkk 45 
                                   ++ ++lae L++++++  e l++
  gi|70607880|ref|YP_256750.1| 170 ITMTELAEKLGIKAPTLEEILRR 192
                                   6789***************9998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.2e-05      0.11      20      47 ..     168     195 ..     159     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                                   SEEEHHHHHHHHTSSHHHHHHHHHHHHH CS
                        MarR_2  20 rdltvgelarrlglsksavsrilkrLva 47 
                                   r++t++ela++lg++ +++  il+r+ +
  gi|70607880|ref|YP_256750.1| 168 RRITMTELAEKLGIKAPTLEEILRRALR 195
                                   469*********************9865 PP

>> CIDE-N  CIDE-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.023        29      20      52 ..      57      86 ..      45      93 .. 0.80
   2 ?    5.7   0.0     0.012        15       5      32 ..     169     196 ..     167     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                  SSHHHHHHHHHHHCT-S.STT-EEEETTTT-EE CS
                        CIDE-N 20 kslkeLlekgaeklklssseevtlvLeeDGTeV 52
                                  k lkeL+e+ +++l +s   e ++ +   G++V
  gi|70607880|ref|YP_256750.1| 57 KLLKELKERRSKTLRIS---ENSVWIRTEGCQV 86
                                  679*************6...4555556667776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                                   EEEETTSS-EEEEEESSHHHHHHHHHHH CS
                        CIDE-N   5 kvrdvkrekkkgvaakslkeLlekgaek 32 
                                   +++  +  +k g+ a +l+e+l+++ +k
  gi|70607880|ref|YP_256750.1| 169 RITMTELAEKLGIKAPTLEEILRRALRK 196
                                   677788899**************99765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.35   4.5e+02      36      45 ..      69      78 ..      50      78 .. 0.61
   2 ?    8.9   0.0   0.00077      0.98      27      51 ..     169     193 ..     166     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.35
                  HTH_Tnp_ISL3 36 qlgvSwtTVw 45
                                   l++S+++Vw
  gi|70607880|ref|YP_256750.1| 69 TLRISENSVW 78
                                  3566666666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00077
                  HTH_Tnp_ISL3  27 srsvkavArqlgvSwtTVwrildry 51 
                                   ++++++ A+ lg+ + T++ il+r+
  gi|70607880|ref|YP_256750.1| 169 RITMTELAEKLGIKAPTLEEILRRA 193
                                   48********************996 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.83   1.1e+03       6      17 ..      57      68 ..      53      80 .. 0.70
   2 ?    2.1   0.1      0.12   1.6e+02       9      23 ..     145     159 ..     145     163 .. 0.90
   3 ?    7.3   0.1    0.0029       3.7      31      53 ..     174     196 ..     170     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.83
                                  HHHTTS-HHHHH CS
                  Sigma70_r4_2  6 ealaeLperqre 17
                                  ++l eL er+++
  gi|70607880|ref|YP_256750.1| 57 KLLKELKERRSK 68
                                  567777777766 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                   TTS-HHHHHHHHHHH CS
                  Sigma70_r4_2   9 aeLperqreifllry 23 
                                   ++L+erq ei+ l+y
  gi|70607880|ref|YP_256750.1| 145 EQLTERQLEILKLSY 159
                                   69**********998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0029
                                   HHHHHHT--HHHHHHHHHHHHHH CS
                  Sigma70_r4_2  31 EIAellgisegtVksrlsRArkk 53 
                                   E Ae+lgi+  t +  l+RA++k
  gi|70607880|ref|YP_256750.1| 174 ELAEKLGIKAPTLEEILRRALRK 196
                                   99*******************97 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.3   2.9e+03      30      39 ..      52      61 ..      45      64 .. 0.74
   2 ?    0.4   0.1      0.54     7e+02      35      45 ..     118     128 ..     117     133 .. 0.87
   3 ?   10.0   0.1   0.00051      0.66       6      40 ..     150     189 ..     147     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                       HTH_Mga 30 Lglseltlqs 39
                                  L l+e+ l++
  gi|70607880|ref|YP_256750.1| 52 LKLTEKLLKE 61
                                  7788888875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.54
                       HTH_Mga  35 ltlqsdiseLn 45 
                                   l+l+s i+eLn
  gi|70607880|ref|YP_256750.1| 118 LSLKSLIDELN 128
                                   689*******9 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00051
                       HTH_Mga   6 rklkLlel.....LteneksltldelakeLglseltlqsd 40 
                                   r+l++l l     +++ ++++t++ela++Lg+   tl ++
  gi|70607880|ref|YP_256750.1| 150 RQLEILKLsykmgFFDVDRRITMTELAEKLGIKAPTLEEI 189
                                   666666664444467889*************977777665 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.4    0.0019       2.4       2      52 ..     145     195 ..     144     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                                   X---HHHHHHHHHH.HHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHH CS
                 LexA_DNA_bind   2 kkLTerQrevldli.kasieetgypPsireiaralglkSpsaveehLkaLer 52 
                                   ++LTerQ e+l+l  k    +     ++ e+a++lg+k + + ee L++  r
  gi|70607880|ref|YP_256750.1| 145 EQLTERQLEILKLSyKMGFFDVDRRITMTELAEKLGIK-APTLEEILRRALR 195
                                   68*********985144555666667899999999999.5566777766555 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.047        60       3      19 ..      51      67 ..      51      71 .. 0.86
   2 ?    5.2   0.5     0.016        21      24      38 ..     185     199 ..     172     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.047
                                  EEEEEHHHHHHHHHHHH CS
                         RHH_1  3 sirldeellerLdelar 19
                                  +++l e+ll++L e++ 
  gi|70607880|ref|YP_256750.1| 51 TLKLTEKLLKELKERRS 67
                                  6899*********9875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                   SHHHHHHHHHHHHHH CS
                         RHH_1  24 SrSelIReAlreyle 38 
                                   +  e++R+Alr +++
  gi|70607880|ref|YP_256750.1| 185 TLEEILRRALRKAVK 199
                                   668********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1289  (0.0718947); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1538.56
//
Query:       gi|70607881|ref|YP_256751.1|  [L=461]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.2e-111  373.0   0.0   2.6e-111  372.8   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.8   0.0  1.4e-115  2.6e-111       1     451 []      18     442 ..      18     442 .. 0.94

  Alignments for each domain:
  == domain 1  score: 372.8 bits;  conditional E-value: 1.4e-115
                                   HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS- CS
                       Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekD 81 
                                   elv  fl+r++++n+k+n ++ +++++  a+A+++d+ ++ +   +pLhG+P+++KDni +kg++tt+Gs  ++++++++D
  gi|70607881|ref|YP_256751.1|  18 ELVTRFLERVNELNPKVN-AIVTLNDKVMAEAKEMDSLAK-KGICKPLHGIPVTIKDNILTKGIRTTFGSVLFKDFVPDED 96 
                                   799***************.88889************9886.**************************************** PP

                                   -HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHH CS
                       Amidase  82 atvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsf 162
                                   + + erLk+aGa+ilgkTnm+ef+++  t+n++fg t+NPwd++rtpGGSSGGsA+ +A g++p++iG+D+GGSiRiP+sf
  gi|70607881|ref|YP_256751.1|  97 SIISERLKEAGALILGKTNMPEFGLVGITDNPLFGVTKNPWDLTRTPGGSSGGSAVSIALGFSPISIGNDGGGSIRIPSSF 177
                                   ********************************************************************************* PP

                                   CTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEE CS
                       Amidase 163 cglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvv 243
                                   cg++G+KP+  ++++++      +++v Gp++r+v+d++l++r ++g+d +d++s+ +p + +  +e  k++ k +ri++ 
  gi|70607881|ref|YP_256751.1| 178 CGVFGFKPSPHVIPKYPPPNTFRGISVDGPITRYVSDAILTMRILSGPDLRDRRSLTVP-KINFSEELDKNEVKRIRIAYS 257
                                   *********************************************************88.4556667778899******** PP

                                   GGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHH CS
                       Amidase 244 kedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpks 324
                                   +++g+  +d +v++ ve+a+ + +e+G+e ++   p+l+++++++++ +++e+++                  + ++l+++
  gi|70607881|ref|YP_256751.1| 258 RNLGYGVVDSKVEKTVEDAVYRFRELGVETIDEINPELPNLYKALMTKITVEFATF-----------------IYDKLEEW 321
                                   ***************************77777666777778886666666677755.................6899**** PP

                                   HHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGC CS
                       Amidase 325 raellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynl 405
                                    + +++++++  ++  ++ + ++     y k +++ + l+ ++ ++f+++D l++Pt++  a++++e     +       +
  gi|70607881|ref|YP_256751.1| 322 KKVTYKPYLNFLLPYFEKLTYHD-----YVKVDNEVDKLWSKLSNVFQKYDYLITPTVSVVAFKIEEGIGPSEINGQKVGF 397
                                   *****************999988.....899999999******************************98777888899999 PP

                                   CTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
                       Amidase 406 ldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                                    ++ ++++p+nl+g+pa s+p+g  + +lPvG+q+igk++++  +L
  gi|70607881|ref|YP_256751.1| 398 GEWSPFSFPFNLTGQPASSIPVGLVN-NLPVGMQIIGKPYDDFGVL 442
                                   9***********************96.9**************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3420.43
//
Query:       gi|70607882|ref|YP_256752.1|  [L=147]
Description: hypothetical protein Saci_2169 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0057   17.0   0.4     0.0079   16.5   0.4    1.2  1  LTD             Lamin Tail Domain
     0.0071   16.5   0.2     0.0098   16.1   0.2    1.2  1  PCNA_C          Proliferating cell nuclear antigen, C-termina
       0.01   15.0  16.3      0.086   11.9  16.3    1.8  2  DUF973          Protein of unknown function (DUF973)
  ------ inclusion threshold ------
      0.023   12.1   0.1      0.029   11.7   0.1    1.0  1  TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II
      0.024   14.9   1.5      0.037   14.3   1.5    1.3  1  DUF11           Domain of unknown function DUF11
      0.063   13.5   5.5       0.28   11.4   5.5    1.8  1  DUF4330         Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   2.7e-06    0.0079      17      74 ..      57     117 ..      51     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                           LTD  17 gagnnan....efvelyNtsskavdLsgwkledasgeytfpngtgtlaageyvvvwsgsgtt 74 
                                   g+ ++++      v l N+++++v+++  ++++ +   + p+++ +l+ag++ + +   +++
  gi|70607882|ref|YP_256752.1|  57 GTLTGSGsvynLTVTLRNSGTSDVNITSVWIANMKFVPVNPQSS-VLKAGQTQTMTFEIKAN 117
                                   55555445566889*********************556677888.99999988776654444 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   3.3e-06    0.0098      41     113 ..      72     146 ..      64     147 .] 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                                   EEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHH..HHHGGGGGC-SEEEEEEETTSEEEEEE CS
                        PCNA_C  41 vkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYl..aeftkatsLservtlslssevPlvvey 113
                                   ++ s   d+  +s+ ++++k v  + ++++l++ ++ t+tf +k     +ftk +  s ++  +    vP+vv y
  gi|70607882|ref|YP_256752.1|  72 LRNSGTSDVNITSVWIANMKFVPVNPQSSVLKAGQTQTMTFEIKANsnITFTKQSEYSATIYFNTGLGVPVVVTY 146
                                   56677789999******************************98865116799*********************99 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   3.2    0.0018       5.5      88     121 ..       4      37 ..       1      45 [. 0.75
   2 !   11.9  16.3   2.9e-05     0.086     183     309 ..      17     146 ..      16     147 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0018
                        DUF973  88 sstgrdvgiGitgltliligaiiiiigvilaivs 121
                                    +++  +++G   +++ li +ii +i+vi ++++
  gi|70607882|ref|YP_256752.1|   4 DEIKLKTKRGMSDSIIALILTIIGLIAVIAVVLF 37 
                                   5667788899999999999999999998865533 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.9e-05
                        DUF973 183 sfIGyilsyiglgnvlsklrsttsqvpvlqvpstpqqvqisqvgqGtlrsnGta.nltv....ysqvqvqIlsAsiegtny 258
                                   s+I++il++igl  v+       +  +      +p+q +++ +g Gtl ++G++ nltv    + + +v+I+s  i ++++
  gi|70607882|ref|YP_256752.1|  17 SIIALILTIIGLIAVIAV-----VLFTYGLAGTIPRQEPVEVIGGGTLTGSGSVyNLTVtlrnSGTSDVNITSVWIANMKF 92 
                                   689************942.....2233333445567778*************87446662232345789************ PP

                        DUF973 259 sttsinPntLkvGnNs...itinFntvlnLvpgstYtirLlLsngqtidvevty 309
                                   + ++ + ++Lk+G  +    +i+ n++ +++++s Y  +++ + g  + v vty
  gi|70607882|ref|YP_256752.1|  93 VPVNPQSSVLKAGQTQtmtFEIKANSNITFTKQSEYSATIYFNTGLGVPVVVTY 146
                                   *9999999*****875222568888889************************99 PP

>> TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.6e-06     0.029     693     749 ..      64     119 ..      59     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-06
                TRAPPC9-Trs120 693 EkaefkvtLqNPfefeveiesieletegvefe.alkeslvigpkstqkltltgkptes 749
                                    ++++ vtL+N    +v+i+s+ +++  ++f+ + ++s v+++ +tq++t+ +k++++
  gi|70607882|ref|YP_256752.1|  64 SVYNLTVTLRNSGTSDVNITSVWIAN--MKFVpVNPQSSVLKAGQTQTMTFEIKANSN 119
                                   5799********************97..77999********************99875 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   1.2e-05     0.037      13      80 ..      63     118 ..      57     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                         DUF11  13 GdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtr 80 
                                   G   + t+t++N+g+++     +t ++ a++++v+v  +       +s   L+ag++ t++f+++++ 
  gi|70607882|ref|YP_256752.1|  63 GSVYNLTVTLRNSGTSDV---NITSVWIANMKFVPVNPQ-------SS--VLKAGQTQTMTFEIKANS 118
                                   556677899999998766...9999************99.......33..599********9999875 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   5.5   9.3e-05      0.28      22     133 ..      25     121 ..      16     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                       DUF4330  22 ilvilavivgiflkpgtsgsvaqaeaaatkpvevdvvvrglev.peelakvkegektniiirnqPagdveikdvkvlprkv 101
                                   i+ ++avi+++++ +g      ++    ++p  v+v+  g  + + ++++      ++++ rn + +dv+i++v++ + k 
  gi|70607882|ref|YP_256752.1|  25 IIGLIAVIAVVLFTYGLA---GTIPR--QEP--VEVIGGGTLTgSGSVYN------LTVTLRNSGTSDVNITSVWIANMKF 92 
                                   233444444444444444...55543..334..66666666665666666......888889999**************** PP

                       DUF4330 102 vvpqpdGkvkaledepylkdllvtlegkakit 133
                                   v  +p+++v ++ +   ++++++ ++++++it
  gi|70607882|ref|YP_256752.1|  93 VPVNPQSSVLKAGQ---TQTMTFEIKANSNIT 121
                                   *9*******99999...99*******999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.46
# Mc/sec: 962.98
//
Query:       gi|70607883|ref|YP_256753.1|  [L=548]
Description: thermopsin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-61  207.3  17.7    2.8e-61  207.3  17.7    2.6  2  Thermopsin  Thermopsin


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3  17.7   1.6e-65   2.8e-61      13     260 .]      25     278 ..      14     278 .. 0.91
   2 ?    0.7   5.2     0.016   2.9e+02     141     189 ..     335     389 ..     322     432 .. 0.77

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 1.6e-65
                    Thermopsin  13 paPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvtggktysywvQnVvsfntte 93 
                                    aP+Gi++y          + +++t+s+lG++nissl ayns+  +p++aslQLN++lev t ++ty++wvQnV+ f t++
  gi|70607883|ref|YP_256753.1|  25 TAPVGISSY----------SPTVTTTSILGYANISSLLAYNSTFFQPYGASLQLNAILEVDTPSNTYYFWVQNVAGFITSN 95 
                                   699******..........46799********************************************************* PP

                    Thermopsin  94 kqltfidNiWNftspsanlsnsaisGnGtvy....asskgefYyayateylelslPltlkLvinvsltsngvpevsFgYsi 170
                                   ++l f dNiWN t+ ++n++++   G G++      + +++fY a +++++ +++Pl+++++inv+ t +g   v FgY+i
  gi|70607883|ref|YP_256753.1|  96 NTLFFNDNIWNATGMDSNITEV--IGDGNIStcdsCQAPQTFYGASSQQTIYYHFPLSFYMFINVTPTVRGP-LVTFGYVI 173
                                   *******************766..9*****99984444555555555556*********************6.*******9 PP

                    Thermopsin 171 d.......ggvvtYDnvtinstgkasaeilvngssltps.........gllyDaeLvlgGpgngekttfnslnatlsLyYl 235
                                           ++v++YDn++i ++g +sa+i+v+ s+ t           gl  D+eLv+gG +nge+ttf+++++ l++yYl
  gi|70607883|ref|YP_256753.1| 174 LqngkitsPKVQVYDNAIIPVQGAISAQIVVQNSY-TYVynqglysyyGLKKDVELVWGGLSNGEHTTFKEMSSLLAIYYL 253
                                   99******99*****************99998743.33335889999899******************************* PP

                    Thermopsin 236 ngtnyqpvknaydfGsdTaEtaenv 260
                                   ++ ++ +++++y++G dTaE+a+n+
  gi|70607883|ref|YP_256753.1| 254 RNGQWLSFNEIYNYGFDTAESANNL 278
                                   ***********************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.016
                    Thermopsin 141 elslPltlkLvinvsltsngvpevsFgYsid........ggvvtYDnvtinstgkas 189
                                    ++ P++++ + n sl++n       +Ys +        ++ +++D+ +++ + +  
  gi|70607883|ref|YP_256753.1| 335 YINSPISVYFYSNYSLSNNSF--ALLNYSSNqktvrlviNSSTWFDSLQFTPNYTFY 389
                                   5789**********9997777..555555445799****99*******999887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3476.49
//
Query:       gi|70607884|ref|YP_256754.1|  [L=260]
Description: hypothetical protein Saci_2171 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.017   15.1   0.0       0.19   11.7   0.0    2.5  3  DUF4265    Domain of unknown function (DUF4265)
       0.12   12.4   0.3        1.2    9.2   0.1    2.5  3  Pab87_oct  Pab87 octamerisation domain


Domain annotation for each model (and alignments):
>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.1e-05      0.19      25      64 ..      62     102 ..      57     123 .. 0.78
   2 ?   -0.9   0.0      0.17   1.5e+03      71      98 ..     156     183 ..     146     194 .. 0.82
   3 ?   -1.1   0.0      0.21   1.8e+03      47      65 ..     200     218 ..     185     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                       DUF4265  25 vAlgDvvev.dedeerlafervvkesGnstirvlvdekael 64 
                                   + ++Dvve   +d++ + f+ +  + G+stirv++   +e+
  gi|70607884|ref|YP_256754.1|  62 LISDDVVEYnFRDNKGNNFRVTFVAEGKSTIRVVITYFGER 102
                                   5589*****777888888999999**********9988775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.17
                       DUF4265  71 eeLealgceveglsakllavdvpadvdl 98 
                                   + L++l +++  ++ + +a++v   vd+
  gi|70607884|ref|YP_256754.1| 156 SYLSKLTVKSKFTKTQTVAINVGGLVDY 183
                                   5678888889999999999999888887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.21
                       DUF4265  47 kesGnstirvlvdekaelg 65 
                                   + sG   +r+l+ +++ +g
  gi|70607884|ref|YP_256754.1| 200 SGSGGAAFRILFIDNEVKG 218
                                   5678888888877766544 PP

>> Pab87_oct  Pab87 octamerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.026   2.4e+02      39      81 ..      16      53 ..       4      55 .. 0.64
   2 ?    9.2   0.1   0.00014       1.2      31      86 ..      34      90 ..      30     100 .. 0.80
   3 ?   -0.2   0.0      0.12     1e+03      47      80 ..     136     167 ..     130     177 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.026
                     Pab87_oct 39 alkvggkieeeeslpLvPedlegdyaeFytltangerlpvefe 81
                                  +++   ++  ++ lpL+P+ +e++    +t++++ +rl  +fe
  gi|70607884|ref|YP_256754.1| 16 VIQWVKNL--DNVLPLIPNIVESN---GTTVKMKFSRLMLNFE 53
                                  55555444..67799999999998...4566666666666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00014
                     Pab87_oct 31 verkggtLalkvggki.eeeeslpLvPedlegdyaeFytltangerlpvefeikgdd 86
                                  ve +g+t  +k +  + + e+++ + P+ ++ d +e++   ++g++  v f+++g +
  gi|70607884|ref|YP_256754.1| 34 VESNGTTVKMKFSRLMlNFESEFLIEPSLISDDVVEYNFRDNKGNNFRVTFVAEGKS 90
                                  78889999999876551467777888*************************976643 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.12
                     Pab87_oct  47 eeeeslpLvPedlegdyaeFytltangerlpvef 80 
                                    ++++++ +P+d +++  +   l+  +  ++ +f
  gi|70607884|ref|YP_256754.1| 136 GNNNETSTIPNDYSKNLSRLSYLS--KLTVKSKF 167
                                   467889999***999977776666..33344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1716.96
//
Query:       gi|70607885|ref|YP_256755.1|  [L=257]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-19   69.5  21.6    5.9e-19   68.3  21.6    1.6  1  DUF973    Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3  21.6   3.3e-23   5.9e-19      50     200 ..      82     232 ..       8     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 3.3e-23
                        DUF973  50 silssvlllliaaii.liiiasvllil.gllkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsllslils 128
                                   ++  +  +l +++i+ ++ +++ ++++ g++kir+gfs+     ++v+iG  g+ lil+ + + +i++  ++   l++i  
  gi|70607885|ref|YP_256755.1|  82 DKNGNPYGLYFSSIVlITYLVLAFYVVpGIVKIRRGFSNY---PKEVRIGRLGASLILVCILLYMISFGYLV-LSLNYIVP 158
                                   3444566777888885444444444443788******987...99********************9987444.66699999 PP

                        DUF973 129 lillgviilligi..ilaliGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgnvlsk 200
                                    ++++++++ +    +l  iGq+llg+++y+lG+ Y +gl+k+gG li++pv +++ fIGyils +g+++v   
  gi|70607885|ref|YP_256755.1| 159 PVDFSLFAYSFLLitLLYTIGQLLLGIGIYRLGRLYRSGLLKVGGALIAMPVTHFIPFIGYILSRLGMEEVTGY 232
                                   9999999876665347999********************************889***************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1860.23
//
Query:       gi|70607886|ref|YP_256756.1|  [L=185]
Description: hypothetical protein Saci_2175 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.32   11.7   1.1        5.2    7.8   0.0    2.1  2  Bcl-2     Apoptosis regulator proteins, Bcl-2 family


Domain annotation for each model (and alignments):
>> Bcl-2  Apoptosis regulator proteins, Bcl-2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00029       5.2      33      67 ..      62      95 ..      49     112 .. 0.87
   2 ?    2.7   0.2     0.011     2e+02      52      86 ..     139     172 ..     125     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00029
                                  HHHHHHHCCTTS--SCHHHHHHHHHHHHHHHHHHH CS
                         Bcl-2 33 fakvaeelfsdgelnWgrvvalfafagalaerlvr 67
                                  +++ + e+f+ g+++++r++ l+ ++g l+  +v+
  gi|70607886|ref|YP_256756.1| 62 VRRGISEVFK-GKFTFSRILWLIIIGGNLIDAVVS 95
                                  5667889999.58****************988776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHS CS
                         Bcl-2  52 valfafagalaerlvrdglpellrrlvellvdyle 86 
                                    ++ ++ag++++++++    +  + +v +l++y+ 
  gi|70607886|ref|YP_256756.1| 139 YVITTLAGRICVKCKNA-ILAWTSGVVIFLASYIL 172
                                   567899*******9988.55556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1349.37
//
Query:       gi|70607887|ref|YP_256757.1|  [L=247]
Description: hypothetical protein Saci_2176 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 1363.52
//
Query:       gi|70607888|ref|YP_256758.1|  [L=254]
Description: hypothetical protein Saci_2177 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   54.7   0.0    1.8e-14   54.2   0.0    1.2  1  Lactamase_B  Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.014   14.4   0.0      0.021   13.8   0.0    1.2  1  DUF4861      Domain of unknown function (DUF4861)


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0     2e-18   1.8e-14       4     197 .]      31     226 ..      29     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 2e-18
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                   + +n yli+++++ iL D+G+   ++r +++l++  +kp+++  ++++H ++D iG+ + + ++ ++++++ +e+++ +++
  gi|70607888|ref|YP_256758.1|  31 VLTNQYLIVDGDKGILLDPGGYFVFERVFKNLKD-FVKPENIVGLFYSHQDPDVIGAMNLWLDTCPNAKVYISEIWERFIP 110
                                   569**************************96665.69******************************************** PP

                                   HHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHHCCCCCC.. CS
                   Lactamase_B  85 eeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.agetgridl.. 162
                                   + ++ ++s         s++ + +++ + ++     +   v+ +++h+ g +++++   kv f+GD +  + + g+++l  
  gi|70607888|ref|YP_256758.1| 111 HLGMSDPS--------SSERIVKIPDRGMEFKIEKNQVRAVPAHFLHSEGNFHLYDVKSKVYFSGDIGAaIFPKGKWSLyv 183
                                   ***99866........57899999********************************************9666666666699 PP

                                   .........TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                   Lactamase_B 163 ........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                            + +++ r+    + +  +l+++++l++++++p+H
  gi|70607888|ref|YP_256758.1| 184 qnfdehvkYMEWFHRRYLPTRKALDVWLKRVKELDIKIIAPQH 226
                                   *****************************************99 PP

>> DUF4861  Domain of unknown function (DUF4861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.4e-06     0.021     131     154 ..     197     220 ..     196     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-06
                       DUF4861 131 yRvYgdarqgiDifgKrtkelvle 154
                                   +R Y+++r+++D+++Kr+kel ++
  gi|70607888|ref|YP_256758.1| 197 HRRYLPTRKALDVWLKRVKELDIK 220
                                   699*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.36s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1425.48
//
Query:       gi|70607889|ref|YP_256759.1|  [L=200]
Description: hypothetical protein Saci_2180 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.17   12.1   1.8       0.46   10.7   0.6    2.1  3  DUF3124   Protein of unknown function (DUF3124)


Domain annotation for each model (and alignments):
>> DUF3124  Protein of unknown function (DUF3124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.07   1.2e+03      23      42 ..      51      70 ..      39      82 .. 0.78
   2 ?   -0.8   0.0     0.091   1.6e+03      29      42 ..      57      70 ..      50     114 .. 0.61
   3 ?   10.7   0.6   2.6e-05      0.46       6      71 ..     131     194 ..     128     200 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.07
                       DUF3124 23 LtatlsirNtdlkksivits 42
                                  +  t  ir  d++k+i+i+s
  gi|70607889|ref|YP_256759.1| 51 MLFTYKIRKFDKEKEITISS 70
                                  45677899999999999986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.091
                       DUF3124 29 irNtdlkksivits 42
                                  ir  d++k+i+i+s
  gi|70607889|ref|YP_256759.1| 57 IRKFDKEKEITISS 70
                                  55556666665543 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 2.6e-05
                       DUF3124   6 vpvYshiysge.kekklnLtatlsirNtdlkksivitsveYydteGklvreylekpielkplaslel 71 
                                   ++ Ys++++ +  e+k ++t++ls +N + k s+ i  ++Yy    + ++e ++k+++++p++   +
  gi|70607889|ref|YP_256759.1| 131 ISKYSNLFKYDiVEDKESITIILS-HNYNYKYSVLI--ANYYKGLMENIHELADKKCKIEPMEKSIV 194
                                   677999999885678889999999.99999999888..68**********************96554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1236.33
//
Query:       gi|70607890|ref|YP_256760.1|  [L=463]
Description: hypothetical protein Saci_2181 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-28   97.2  54.8    1.1e-27   96.8  54.8    1.1  1  AA_permease    Amino acid permease
    2.3e-25   89.3  57.1      4e-25   88.5  56.5    1.5  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
        1.1    8.6   9.7       0.13   11.6   2.4    2.6  2  SLATT_5        SMODS and SLOG-associating 2TM effector domain
        2.8    8.4   5.6        5.4    7.5   2.7    2.9  2  DUF2583        Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8  54.8   2.5e-31   1.1e-27       2     460 ..      28     455 ..      27     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 2.5e-31
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   vl + ++++ +++  +g+   +++   +g+ la+l+a v i+l +  ++ i+ ++ ++gg+yt+++r lg++++f  +++y
  gi|70607890|ref|YP_256760.1|  28 VLAQGIASAAPAAATIGTLTGAAAFVYGGLPLAVLIALVAILLDATRISIISRYIQSAGGIYTFIERGLGKKVAFIASMSY 108
                                   678899999***************99******************************************************9 PP

                   AA_permease  83 lfswitvlaleltaasili..qfwelvtdlpkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgi 158
                                    ++ ++v+++ + +++ ++  ++ el  +lp  w++   g+   ++ ++i+++g++ + +    ++l   +a i ++i + 
  gi|70607890|ref|YP_256760.1| 109 IVYIFAVIIFVYLIMGLMVptGLQELGLSLP-DWIWipfGLANAAIAVFISYMGIRPSLK----FTLTMSLAEITVLIATS 184
                                   99999999999877666654478899*****.****************************....99999999999999998 PP

                   AA_permease 159 illaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                    l++++ p +         ++++++    p+        ++n   + ++ ++aftG+e v ++++E++dP+ +i k++  +
  gi|70607890|ref|YP_256760.1| 185 LLIFSKVPPDP--------QTFTLAYVPQPQ--------ILNLGLGVSFGILAFTGYETVSVLGEEAQDPKNTITKGVFTA 249
                                   88888888888........455455555566........****************************************** PP

                   AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslak 320
                                    ++++i+Y++++ + +++++ n+ ++    + +  +++ + ++ g ++la +++a+++ + + +a +++ + +Rv+y++++
  gi|70607890|ref|YP_256760.1| 250 ALIVGIVYLIGSEAFTVGWGVNNMSSYFNYLAP--GLIEAYNF-GGPILAIILTALLINSNIACACGFTNAVTRVMYAMSR 327
                                   **********************97776655544..56666555.6678889999999999999****************** PP

                   AA_permease 321 dglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrs 400
                                   dgl+P ++++ +++r+ P+ a l+++i+ ++ ++++sl + ++++f      +++ +li    +++s l + k  ++ +  
  gi|70607890|ref|YP_256760.1| 328 DGLLPsRIGDIHKRRRTPHIAALFTFIFTAVYFVIMSLIFTPANIFIATGVTTTFGFLIAIFTVNISMLIVVKRNNALT-- 406
                                   ***********************************************************99999999997777744444.. PP

                   AA_permease 401 ieelgfkaallplgvilvlaaliiillilalyay.ltvkkgpkdwgaasfaaaylivllfl 460
                                                g il +a++ +i+ ++++ ++ + + ++p+ +g+ + +++ ++  ++l
  gi|70607890|ref|YP_256760.1| 407 ------------IGNILLVAIIETIIGFVFYSQIiTSAINIPVLIGVLTLVLWVVGGAIYL 455
                                   ............4555555555555555555554233445666666666666666666655 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5  56.5   8.8e-29     4e-25       8     403 ..      40     428 ..      32     453 .. 0.72

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 8.8e-29
                 AA_permease_2   8 alvigsvigsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfay 88 
                                   a +ig+++g++ f    ++ g p+++l+ ++a+l+   a ++    +s  + + gGiy++ +++ gkkvaf++++++ + +
  gi|70607890|ref|YP_256760.1|  40 AATIGTLTGAAAF----VYGGLPLAVLIALVAILLD--ATRI--SIISRYIQSAGGIYTFIERGLGKKVAFIASMSYIVYI 112
                                   6677777777777....4355555555555555443..3442..235888********************99999998777 PP

                 AA_permease_2  89 vpvlasilsvaasyl.....lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilgl 164
                                   ++v+  i+++++  l     l+ lg +l ++  +++ ++ a  ++ ++i+++gi+ s k++ ++ ++ i+ +   li++ l
  gi|70607890|ref|YP_256760.1| 113 FAVI--IFVYLIMGLmvptgLQELGLSLPDW--IWIPFGLANAAIAVFISYMGIRPSLKFTLTMSLAEIT-V---LIATSL 185
                                   7755..4444444440122244455588665..55555566666777899*******************6.4...344444 PP

                 AA_permease_2 165 itvdgggfsslstetdtffpngwpgv.llgllivlwsfdGfesaanvseevkk.k.dvpkaifigllivlvlyllvniafl 242
                                   +++++   + ++t t   +p+   ++  lg +  +++f+G+e++++  ee++  k ++ k+ f ++liv+++yl  + af+
  gi|70607890|ref|YP_256760.1| 186 LIFSKVPPD-PQTFTLAYVPQPQILNlGLGVSFGILAFTGYETVSVLGEEAQDpKnTITKGVFTAALIVGIVYLIGSEAFT 265
                                   444332221.111233445554444336677889****************6655527*******************99999 PP

                 AA_permease_2 243 gvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspi 322
                                    + + +++++  n + ++ + + ++gg+++aii+ +l++ s + ++++++ +++rv++a++rdg lP+++ +++ ++ +p 
  gi|70607890|ref|YP_256760.1| 266 VGWGVNNMSSYFNYLAPGLIEAYNFGGPILAIILTALLINSNIACACGFTNAVTRVMYAMSRDGLLPSRIGDIHkRRRTPH 346
                                   9999999987667666788888889999**********************************************99***** PP

                 AA_permease_2 323 raiiltaivslillllfllas..saaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigalfllfllva 401
                                    a  +t+i++ + +++++l+   ++ + +   ++++g++i ++ + i++li+ k+++ l ++g il+++i+  ++ f+++ 
  gi|70607890|ref|YP_256760.1| 347 IAALFTFIFTAVYFVIMSLIFtpANIFIATGVTTTFGFLIAIFTVNISMLIVVKRNNAL-TIGNILLVAIIETIIGFVFYS 426
                                   **********8888887754332555556666677888888888899999999998776.444444444444444444443 PP

                 AA_permease_2 402 lf 403
                                    +
  gi|70607890|ref|YP_256760.1| 427 QI 428
                                   33 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.8      0.11   4.8e+02     162     184 ..      98     121 ..      82     127 .. 0.67
   2 ?   11.6   2.4   2.8e-05      0.13      23      82 ..     339     397 ..     337     402 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                       SLATT_5 162 kklkwfl.rrylivifllylliil 184
                                   kk+ +++ + y+++if++++ ++l
  gi|70607890|ref|YP_256760.1|  98 KKVAFIAsMSYIVYIFAVIIFVYL 121
                                   566666666666666666444433 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.8e-05
                       SLATT_5  23 aeRlrrknklstfslsllSvylivlsllsnkssestinenlldflsiilSilvlvislle 82 
                                   ++R r+ + + +f++++ +vy +++sl+  +  +  i   + + ++++++i+++ is+l+
  gi|70607890|ref|YP_256760.1| 339 HKRRRTPHIAALFTFIFTAVYFVIMSLIF-TPANIFIATGVTTTFGFLIAIFTVNISMLI 397
                                   799*************************9.8999999999999999999***99999986 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.46   2.1e+03      14      30 ..     251     267 ..     239     287 .. 0.67
   2 ?    7.5   2.7    0.0012       5.4       2      62 ..     400     459 ..     399     461 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.46
                       DUF2583  14 mglGlllmvaslaysvl 30 
                                   + +G++ +++s a++v 
  gi|70607890|ref|YP_256760.1| 251 LIVGIVYLIGSEAFTVG 267
                                   34566666666666554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                       DUF2583   2 krkkalllGnvlmglGlllmvaslaysvlnqlpelelpellaeaallgifiGallWlaGar 62 
                                   kr++al +Gn+l++  + ++++ + ys +    ++++p l+   +l+   +G  ++la ar
  gi|70607890|ref|YP_256760.1| 400 KRNNALTIGNILLVAIIETIIGFVFYSQI-ITSAINIPVLIGVLTLVLWVVGGAIYLAIAR 459
                                   9***********98877777666666543.3467999999999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 3223.96
//
Query:       gi|70607891|ref|YP_256761.1|  [L=664]
Description: tyramine oxidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-148  494.8   0.0   2.3e-148  494.5   0.0    1.1  1  Cu_amine_oxid    Copper amine oxidase, enzyme domain
    1.8e-15   57.2   0.0    4.7e-15   55.8   0.0    1.7  2  Cu_amine_oxidN3  Copper amine oxidase, N3 domain
    8.6e-07   29.1   0.1    1.5e-06   28.3   0.1    1.4  1  Cu_amine_oxidN2  Copper amine oxidase, N2 domain


Domain annotation for each model (and alignments):
>> Cu_amine_oxid  Copper amine oxidase, enzyme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.5   0.0  3.9e-152  2.3e-148       1     409 [.     232     644 ..     232     645 .. 0.97

  Alignments for each domain:
  == domain 1  score: 494.5 bits;  conditional E-value: 3.9e-152
                                   .----TT---SEEETTTEEEETTEEEEEEEETTTEEEEEEEEETT....EEEEEEEEEEEEEEEE--SSHHHHH-EEEGGG CS
                 Cu_amine_oxid   1 levvqpeGpsfkvdegnlvewqkWsfrvgfnrreGlvlhdvrykg....rrilyrlslsemvvpYgdprppasrkaafDlg 77 
                                   +e++qp+G+s +v +g++++w +W++r+g+++reGlv++dvry+     r+i+yr+s+ +++vpYgdp+p ++rk+++D+g
  gi|70607891|ref|YP_256761.1| 232 IEILQPQGSSVEV-NGYEIKWYRWRLRIGYTPREGLVIYDVRYNYkgreRQIIYRASVVDLMVPYGDPSPFHYRKMVLDAG 311
                                   5799*********.8****************************998999******************************** PP

                                   T.-SGGG-----TT......TSS-TT.-EEEEEEEEE..TEEEEEEEEEEEEEEE-S-SEEEE-S....EEEE--EEEEEE CS
                 Cu_amine_oxid  78 eyglGklansLelg......cDClge.ityldavladssgepvtiknaiCifEedagilwkHtdfrtgraevtrnreLvvr 151
                                   +yglG+++ +L++g      cDClge i+++d+v a+s+g+pv++k+aiC++Eed +++w+Htd r+g++ev+rnr+Lvv+
  gi|70607891|ref|YP_256761.1| 312 DYGLGNFIVPLKHGngelydCDCLGEgIYHFDVVRASSDGKPVKVKKAICVHEEDFNVIWRHTDLRSGDSEVRRNRRLVVS 392
                                   ************************987999*************************************************** PP

                                   EEEEETTEEEEEEEEE-TTS-EEEEEEEEE----EE-T.....GG--EEETTEE---EEEEEEEEEEE-T.SSEEEEEEEE CS
                 Cu_amine_oxid 152 tiatvgNYdYifdyiFkqdGsievevratGilstaalaeeeeskygtrvapgvlasiHqHlfslrvDldidgeknsvveee 232
                                   ++at++NYdY f ++F+qdGsie+ v++tGi++  a  +++++kygt v+p+v+++iH H f++r+Dldidg+ n+v+e++
  gi|70607891|ref|YP_256761.1| 393 FWATLANYDYGFFWHFYQDGSIELMVKLTGIINDDAAPKGQKRKYGTLVTPEVYGPIHIHWFNIRLDLDIDGQINRVYEVN 473
                                   *************************************999999************************************** PP

                                   E-T..TT.T-...-EEEEEEEEEE--BGGG-EE--.-GG-EEEEEEEEEEE-TTS-EEEEEEE-S----..---SS-TTTT CS
                 Cu_amine_oxid 233 lvpeepelgeenpagnafkvektvletekeaaldldpeknrvlkivnenkknklgepvgYklvpssaasqlllakesslva 313
                                   l+pe  + g+enp gnaf++e+t l++e ea+++++p+++r++kivn +k+n+lgepv+Y+++p++  + +  + ++s+v+
  gi|70607891|ref|YP_256761.1| 474 LKPE--SIGPENPLGNAFYAEETLLKNELEARRHVNPQSGRYWKIVNLKKSNYLGEPVAYRFIPRE--NVACPLPDESFVR 550
                                   ***4..5899******************************************************77..45577889***** PP

                                   TTTGGGG-SEEEEE--TT---S--TTGG-TTS.---GGGG-.S--B-SSEEEEEEEEEEEEE---GGGSS-TTTSEEEEEE CS
                 Cu_amine_oxid 314 kraefakhhlwvtkykdselyaageynnqskgepvglakwvednesieneDlVvWvtlGltHvpraeDfPvmpvetvsflL 394
                                   kr  ++++hlwvt+y+++e+ya+g+y+++  ge  gl+k+ve+n+si+++D+V+W+tlG+ Hv r+eD+Pvmpve+++f+L
  gi|70607891|ref|YP_256761.1| 551 KRGGYINYHLWVTPYDPNERYATGDYPYERIGE--GLPKYVEKNRSIVDKDIVLWYTLGVEHVVRVEDWPVMPVEMAGFML 629
                                   ******************************996..********************************************** PP

                                   EEES-SSS-GGGG-S CS
                 Cu_amine_oxid 395 kPvnFfdenpaldvp 409
                                   +P +Ffdenp++d+p
  gi|70607891|ref|YP_256761.1| 630 RPDGFFDENPCIDLP 644
                                   *************98 PP

>> Cu_amine_oxidN3  Copper amine oxidase, N3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   7.8e-19   4.7e-15       2      94 ..     109     204 ..     108     210 .. 0.93
   2 ?   -3.7   0.0       2.7   1.6e+04       7      45 ..     416     453 ..     414     455 .. 0.71

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7.8e-19
                                   ---HHHHHHHHHHHHTGGGGHHHHHHHH.TTT..T---EEEE--SS-SSST.T--EEEEEEEE--SSS.-GCGSEEE.EEE CS
               Cu_amine_oxidN3   2 pvlleelaeieevikelpqfkealkkrg.ien.ldkvvltpltvgyrgeksegkRllkalvyyrtesa.nlyahPiegLel 79 
                                   p++l+e+ e+e++++++  ++eal+krg + n l+  +++ ++ gy +e++ +kRl+   ++ +++ + n ya+P+ gL +
  gi|70607891|ref|YP_256761.1| 109 PITLDEFGECEKAVRNDKRVQEALQKRGiLPNdLNLLIVDCWSPGYVNEAERNKRLAIGYMWIKKDLKdNNYARPVHGLMP 189
                                   89**************************85556*************************99999998777************ PP

                                   EEE--SSSGGG-EEE CS
               Cu_amine_oxidN3  80 lvDleakkvieitdq 94 
                                    vDl++++v+ i+d 
  gi|70607891|ref|YP_256761.1| 190 WVDLNKMEVVRIDDF 204
                                   ***********9985 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHTGGGGHHHHHHHHTTT.T---EEEE--SS CS
               Cu_amine_oxidN3   7 elaeieevikelpqfkealkkrgienldkvvltpltvgy 45 
                                    +++++ +i+++++ k +  k g + ++  v  p+++ +
  gi|70607891|ref|YP_256761.1| 416 LMVKLTGIINDDAAPKGQKRKYG-TLVTPEVYGPIHIHW 453
                                   57788889999999999988888.445566666666666 PP

>> Cu_amine_oxidN2  Copper amine oxidase, N2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   2.5e-10   1.5e-06       2      83 ..      15      99 ..      14     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.5e-10
                                  HHHHHHHHHHHHCCCCCCCC.TCT-TTSEEEEEEEEE---HHHHHHHHHCH---S-EEEEEEEEETSSS...SEEEEEEEEEE CS
               Cu_amine_oxidN2  2 pLdaltaaeinkvesilkss.aletskknsffeveLeePdKkavlqflekgeppppRkAsvvilfGkqt...kelvvdLatgk 80
                                  pLd+l   ei+ + + ++++  le+ + + f  + L+eP+K  +l++ ++ge+   R+A v     +++   +e++v + + +
  gi|70607891|ref|YP_256761.1| 15 PLDPLDENEIEIAAQVIREKiVLEKGESIKFIAIMLNEPEKDDYLKW-KRGEKSVERQALVKFYNPAEEgkvYEAIVSIESRS 96
                                  9**********8877776551677778********************.************98887666555699999999888 PP

                                  CCS CS
               Cu_amine_oxidN2 81 lls 83
                                  + s
  gi|70607891|ref|YP_256761.1| 97 IVS 99
                                  876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4480.55
//
Query:       gi|70607892|ref|YP_256762.1|  [L=205]
Description: hypothetical protein Saci_2183 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-21   76.2   0.4    2.6e-21   75.2   0.4    1.6  1  HTH_10         HTH DNA binding domain
    8.5e-07   28.4   0.2      2e-06   27.2   0.2    1.6  1  Sigma70_r4     Sigma-70, region 4
    5.5e-05   22.6   0.2    0.00018   21.0   0.2    2.0  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.033   14.1   0.0    1.8  1  MarR           MarR family
      0.028   14.6   0.4      0.078   13.1   0.1    1.9  3  HTH_Tnp_1_2    Helix-turn-helix of insertion element transpos
       0.03   14.6   2.7       0.17   12.2   0.3    2.5  2  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
      0.033   14.0   0.8       0.18   11.6   0.8    2.2  1  LexA_DNA_bind  LexA DNA binding domain
      0.053   13.6   0.1       0.13   12.4   0.1    1.6  1  HTH_3          Helix-turn-helix
      0.056   13.4   0.4        0.2   11.7   0.0    2.0  2  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.066   13.7   0.1       0.19   12.2   0.1    1.8  1  HTH_26         Cro/C1-type HTH DNA-binding domain
      0.071   12.9   0.6        2.4    7.9   0.1    2.7  3  MafB19-deam    MafB19-like deaminase
       0.08   13.0   0.5       0.22   11.6   0.1    1.9  2  HTH_35         Winged helix-turn-helix DNA-binding
      0.085   13.6   0.0       0.24   12.1   0.0    1.8  1  LRR_2          Leucine Rich Repeat
      0.097   12.5   0.3       0.36   10.7   0.1    2.1  2  HTH_23         Homeodomain-like domain
      0.099   12.2   3.1       0.56    9.8   0.8    2.9  2  GerE           Bacterial regulatory proteins, luxR family
       0.11   12.5   0.4        7.7    6.6   0.2    2.5  2  CIDE-N         CIDE-N domain
       0.11   12.2   0.0       0.42   10.4   0.0    2.0  2  HTH_psq        helix-turn-helix, Psq domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.4   2.4e-24   2.6e-21       1      51 [.     146     196 ..     146     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 2.4e-24
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskl 51 
                                   LTd+qle+l+lAy++GYFd++R++++keLA++lGI++stl+e+Lr+a +k 
  gi|70607892|ref|YP_256762.1| 146 LTDRQLEILRLAYKSGYFDVDRKISMKELANKLGIKASTLEEILRRALKKA 196
                                   9***********************************************995 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.9e-09     2e-06       4      47 ..     145     195 ..     144     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.9e-09
                                   HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                    Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrk 47 
                                   +L++r+ e+l+l +       +++ +++E++++lgi  ++   i++rAl+k
  gi|70607892|ref|YP_256762.1| 145 ELTDRQLEILRLAYksgyfdvDRKISMKELANKLGIKASTLEEILRRALKK 195
                                   8************************************************98 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.7e-07   0.00018       2      43 ..     147     194 ..     146     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                        HTH_24   2 detdrkILelLqk......nprisqreLAerlglSpstvnrrlkrLee 43 
                                    + +++IL+l +k      + +is++eLA +lg+  st+ + l+r  +
  gi|70607892|ref|YP_256762.1| 147 TDRQLEILRLAYKsgyfdvDRKISMKELANKLGIKASTLEEILRRALK 194
                                   5778999999999999999************************99776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.2e-05     0.033       1      40 [.     146     191 ..     146     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                   --HHHHHHHHHHHHSTTEEHH......HHHHHHTS-HHHHHHHHHH CS
                          MarR   1 ltltqfviLrilyeqgplsvs......eLakklgvskstvtrvldr 40 
                                   lt  q++iLr+ y +g   v       eLa+klg++ st+ ++l+r
  gi|70607892|ref|YP_256762.1| 146 LTDRQLEILRLAYKSGYFDVDrkismkELANKLGIKASTLEEILRR 191
                                   789999999999999976666666666*************999998 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       6.6     7e+03      20      43 ..      53      76 ..      36      79 .. 0.56
   2 ?   -1.4   0.0       2.4   2.5e+03      84     100 ..     114     130 ..      91     146 .. 0.60
   3 ?   13.1   0.1   7.4e-05     0.078       6      44 ..     144     186 ..     135     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
                                  HHHHH--S-HHHHHHHHTS-HHHH CS
                   HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTl 43
                                  ++ d  k  ++   + + ++++T+
  gi|70607892|ref|YP_256762.1| 53 INDDILKELKRRSLKTLRINENTI 76
                                  444443333333344555666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                                   --HHHHHHHHHHTT--E CS
                   HTH_Tnp_1_2  84 ssvkAieLylkrrgelt 100
                                   ++++A++ +l++ + + 
  gi|70607892|ref|YP_256762.1| 114 PNLSALKQFLEELNSIR 130
                                   46777777776666553 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 7.4e-05
                                   HHS-HHHHHHHHHHHHHHH....--S-HHHHHHHHTS-HHHHH CS
                   HTH_Tnp_1_2   6 deLtakQkkaaellvendy....ekltldeiaeevgvsrsTly 44 
                                    eLt +Q+ +  l  +  y     k +++e+a+++g++ sTl 
  gi|70607892|ref|YP_256762.1| 144 SELTDRQLEILRLAYKSGYfdvdRKISMKELANKLGIKASTLE 186
                                   35************99999999889****************95 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.23   2.4e+02      58      90 ..      23      54 ..      15      67 .. 0.68
   2 ?   12.2   0.3   0.00016      0.17      12      63 ..     140     198 ..     132     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                       UPF0122 58 ekllekyEekLkllekykkreellekikdkllk 90
                                   +++ kyE k ++  + k r ++ ++i   +++
  gi|70607892|ref|YP_256762.1| 23 LDIFRKYEIKAQIT-NVKLRDQVTDHIAFLKIN 54
                                  46777888887764.567777777777655555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                       UPF0122  12 diYqsLLTekqanylelyyadDl.......SlsEiAeefnvsrqavydnikrtekllek 63 
                                   +i +s LT++q + l+l y+  +       S++E+A++  ++ +++ + ++r+ k   k
  gi|70607892|ref|YP_256762.1| 140 EIDESELTDRQLEILRLAYKSGYfdvdrkiSMKELANKLGIKASTLEEILRRALKKAVK 198
                                   5667789******99997654333333344******************99998765555 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   0.00018      0.18       2      53 ..     144     195 ..     143     205 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                   X---HHHHHHHHHH.HHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                 LexA_DNA_bind   2 kkLTerQrevldli.kasieetgypPsireiaralglkSpsaveehLkaLerK 53 
                                   ++LT+rQ e+l+l  k+   +     s++e+a++lg+k +s+ ee L++  +K
  gi|70607892|ref|YP_256762.1| 144 SELTDRQLEILRLAyKSGYFDVDRKISMKELANKLGIK-ASTLEEILRRALKK 195
                                   68**********97255556667778************.99999999876665 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012      0.13       8      31 ..     167     190 ..     165     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                   TTHHHHHHHHHHTSSHHHHHHHHT CS
                         HTH_3   8 lglsqeeLAeklGvsrstisriEn 31 
                                   +++s++eLA klG++ st+  i +
  gi|70607892|ref|YP_256762.1| 167 RKISMKELANKLGIKASTLEEILR 190
                                   78****************987765 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.7   2.8e+03      41      52 ..      57      68 ..      56      79 .. 0.68
   2 ?   11.7   0.0   0.00019       0.2       7      44 ..     153     191 ..     151     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
                                  HHHHHHHTTSEE CS
                     HTH_Crp_2 41 ilseLkreglis 52
                                  il+eLkr+ l +
  gi|70607892|ref|YP_256762.1| 57 ILKELKRRSLKT 68
                                  799999998766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                                   HHHHHCTTTC.EEEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                     HTH_Crp_2   7 Llrlaeragg.eielpltqeelAsmlGltretvsrilse 44 
                                   +lrla+++g   ++ +++++elA+ lG+  +t+  il++
  gi|70607892|ref|YP_256762.1| 153 ILRLAYKSGYfDVDRKISMKELANKLGIKASTLEEILRR 191
                                   588988855478999********************9986 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.19       8      32 ..     166     190 ..     165     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                        HTH_26   8 drgitkseLargtgisaatlsrlvk 32 
                                   dr+i+ +eLa ++gi a+tl+ ++ 
  gi|70607892|ref|YP_256762.1| 166 DRKISMKELANKLGIKASTLEEILR 190
                                   8*******************99876 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.1   1.1e+02      66      84 ..       4      22 ..       2      54 .. 0.88
   2 ?    7.9   0.1    0.0023       2.4      65      94 ..      66      94 ..      39     155 .. 0.75
   3 ?   -1.5   0.0       1.8   1.9e+03      94     135 ..     153     194 ..     149     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
                   MafB19-deam 66 kskrlddatlyvtlepCdm 84
                                  +skr+ ++tl v++ pC++
  gi|70607892|ref|YP_256762.1|  4 ASKRPIEVTLLVDKHPCEV 22
                                  6788999**********86 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
                   MafB19-deam 65 lkskrlddatlyvtlepCdmCagaivqagl 94
                                  lk+ r ++ t+++  + C++C +++  ++l
  gi|70607892|ref|YP_256762.1| 66 LKTLRINENTIWIRTNGCGVC-KLLYHSDL 94
                                  6778899**************.68877776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                   MafB19-deam  94 lkklvygagnpkslnkLkvkekngrvelveddckeilkgffk 135
                                   + +l+y++g+ +   k+++ke  ++  +    ++eil++ +k
  gi|70607892|ref|YP_256762.1| 153 ILRLAYKSGYFDVDRKISMKELANKLGIKASTLEEILRRALK 194
                                   556777788777777777777777776666667777766665 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1         8   8.4e+03       5      15 ..      55      65 ..      54      70 .. 0.76
   2 ?   11.6   0.1   0.00021      0.22      14      42 ..     167     195 ..     165     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8
                        HTH_35  5 adIiAaLrkrg 15
                                  +dI  +L++r 
  gi|70607892|ref|YP_256762.1| 55 DDILKELKRRS 65
                                  58999999985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00021
                        HTH_35  14 rgttLaalsreaglssstlsnaltrpwpk 42 
                                   r++++++l+ ++g++ stl+++l+r   k
  gi|70607892|ref|YP_256762.1| 167 RKISMKELANKLGIKASTLEEILRRALKK 195
                                   899**********************9877 PP

>> LRR_2  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.24       1      22 [.      65      89 ..      65      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                         LRR_2  1 sLKtLhLdsVrf...sdedslekLL 22
                                  sLKtL +  + +   +++++++kLL
  gi|70607892|ref|YP_256762.1| 65 SLKTLRINENTIwirTNGCGVCKLL 89
                                  8********99999**********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.5   2.6e+03      25      35 ..      67      77 ..      57      80 .. 0.79
   2 ?   10.7   0.1   0.00035      0.36       8      41 ..     151     192 ..     145     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                        HTH_23 25 reLgvsrrTvy 35
                                  + L ++++T++
  gi|70607892|ref|YP_256762.1| 67 KTLRINENTIW 77
                                  56888999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                        HTH_23   8 lrillllae........GlsvreIAreLgvsrrTvyrwlkry 41 
                                   l+il+l+ +        ++s +e A +Lg+  +T+  +l+r 
  gi|70607892|ref|YP_256762.1| 151 LEILRLAYKsgyfdvdrKISMKELANKLGIKASTLEEILRRA 192
                                   66888888555555678*********************9995 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.7   2.8e+03      38      49 ..     104     115 ..      95     121 .. 0.64
   2 ?    9.8   0.8   0.00054      0.56       2      44 ..     145     195 ..     144     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                                   HHHHHHHHT-SS CS
                          GerE  38 ksnimkKLnvks 49 
                                   k+ +m KL + +
  gi|70607892|ref|YP_256762.1| 104 KATVMYKLLLPN 115
                                   455666665555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00054
                                   SS-HHHHHHHHHHCT.TS.......-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE   2 sLskRErevLrllae.Gk.......snkeIAeelniSekTVkvhksnimkK 44 
                                    L++R++e+Lrl ++ G+       s+ke A +l+i++ T +  +++++kK
  gi|70607892|ref|YP_256762.1| 145 ELTDRQLEILRLAYKsGYfdvdrkiSMKELANKLGIKASTLEEILRRALKK 195
                                   58999999999988645344444459**************99999999988 PP

>> CIDE-N  CIDE-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.073        77      22      52 ..      58      85 ..      51      95 .. 0.80
   2 ?    6.6   0.2    0.0073       7.7       5      32 ..     168     195 ..     167     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.073
                                  HHHHHHHHHHHCT-S.STT-EEEETTTT-EE CS
                        CIDE-N 22 lkeLlekgaeklklssseevtlvLeeDGTeV 52
                                  lkeL++++ ++l ++   e t+ +   G+ V
  gi|70607892|ref|YP_256762.1| 58 LKELKRRSLKTLRIN---ENTIWIRTNGCGV 85
                                  99************6...5666666667666 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0073
                                   EEEETTSS-EEEEEESSHHHHHHHHHHH CS
                        CIDE-N   5 kvrdvkrekkkgvaakslkeLlekgaek 32 
                                   k+   +  +k g+ a++l+e+l+++ +k
  gi|70607892|ref|YP_256762.1| 168 KISMKELANKLGIKASTLEEILRRALKK 195
                                   5666677899*************99876 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.8   5.1e+03      28      35 ..      71      79 ..      71      82 .. 0.76
   2 ?   10.4   0.0   0.00039      0.42      16      40 ..     168     192 ..     163     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.8
                       HTH_psq 28 iPrsTLw.r 35
                                  i+ +T+w r
  gi|70607892|ref|YP_256762.1| 71 INENTIWiR 79
                                  7889***55 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00039
                       HTH_psq  16 kmSirkAArkYgiPrsTLwrrkrgk 40 
                                   k+S+ ++A+k gi +sTL++ +r+ 
  gi|70607892|ref|YP_256762.1| 168 KISMKELANKLGIKASTLEEILRRA 192
                                   59*******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1488.95
//
Query:       gi|70607893|ref|YP_256763.1|  [L=114]
Description: hypothetical protein Saci_2184 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-27   95.6   0.1    3.8e-27   95.3   0.1    1.1  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
       0.11   12.6   0.2       0.12   12.4   0.2    1.2  1  DUF1940   Domain of unknown function (DUF1940)


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.1   4.2e-31   3.8e-27       1     122 []       3     108 ..       3     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4.2e-31
                        DUF488   1 slervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferYaae 79 
                                   +++rvyd ++ +dgvr+l+D RlwPr    g++k+    d         w+k+++ps+elrkwf+h+p +weef+++Y +e
  gi|70607893|ref|YP_256763.1|   3 KVKRVYDaPESDDGVRILID-RLWPR----GVKKDL--VDI--------WMKDIAPSDELRKWFNHEPeKWEEFKHKYMEE 68 
                                   689*****************.*****....*****7..577........99*****************99*********** PP

                        DUF488  80 leskeaakealeelkelakkg..vaLlcaekdperchrvvlaeyl 122
                                   l+s+     +++ l+e ++++  v++l+a k p  +++vvl+ey+
  gi|70607893|ref|YP_256763.1|  69 LRSN----PKVKVLIEVIRRSenVTFLYATKSPY-NNAVVLKEYI 108
                                   ***6....688888888877779**********8.99******96 PP

>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.4e-05      0.12      59     126 ..      39     108 ..      27     114 .] 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                                   ------HHHHHHHHH-------HHHHHHHT-HH..HHHHHHHHHHHHHHHHHHHHHHTSTTTTTT--HHH CS
                       DUF1940  59 peskLkDeqrkkLnhadevWlDikekmsnGdrr..aayllaaaahlekavaylvrmkedeefkeivkdyl 126
                                   ++   +De rk +nh+ e+W + k+k  +  r     ++l      ++ v++l++ k   +   ++k+y+
  gi|70607893|ref|YP_256763.1|  39 KDIAPSDELRKWFNHEPEKWEEFKHKYMEELRSnpKVKVLIEVIRRSENVTFLYATKSPYNNAVVLKEYI 108
                                   566779*******************965433320123444444455556666666666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 751.47
//
Query:       gi|70607894|ref|YP_256764.1|  [L=262]
Description: hypothetical protein Saci_2185 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-36  124.3   0.0    1.4e-35  123.0   0.0    1.6  1  Aldose_epim  Aldose 1-epimerase
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.49   10.6   0.0    1.8  2  RimM         RimM N-terminal domain


Domain annotation for each model (and alignments):
>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   1.6e-39   1.4e-35       6     298 ..       4     256 ..       1     259 [. 0.87

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 1.6e-39
                                   EETTEEEEEECTCTTEEEEEEETT.STEESB-B-STHHHHHHSC.CSSCEECSS-SEEETTEEEETTEEEECCCCBTTTCE CS
                   Aldose_epim   6 kngaglsakislyGAtllslkvpdkeqrevllgsddaeeylkds.yfgatlgrvanRianGeFeldGkpyqlpqneegknp 85 
                                   k+g + +a+i + GA l s+k ++   ++++l+ ++  + ++++ +  a+l+++anRi++Ge+ +dG++y lp+n+ + n+
  gi|70607894|ref|YP_256764.1|   4 KKG-RAEAEILNKGAYLYSFKING---KDLVLQGNT--DRVTRGgM--AVLIPFANRIKGGEYIFDGIKYELPKNK-EGNA 75 
                                   565.69******************...799999998..67777779..****************************.**** PP

                                   ETBSGGGSB-EEEEEEETTEEEEEEEEEEETCHCSTSEEEEEEEEEEETTEEEEEEEEEEESS.S-EEEEEEEEEEEETSS CS
                   Aldose_epim  86 lHGgargreWeveevkeddgvtvslvlkpdgeegypgdlevrvtytLnednelkieyeatndg.kptpfnltnHtYFnlsg 165
                                   +HG++ ++e++v +++  d v++ + l +d   gyp +l + v y+L +++ +  ++ ++n g k+ p++++ H+YF +s 
  gi|70607894|ref|YP_256764.1|  76 IHGLVLDKEFSVIHKER-DFVILNYLL-ED--KGYPTKLNCLVLYKLFQNG-FMNKIVVQNVGdKRAPLTVGTHPYFVVS- 150
                                   **************995.999999999.55..78***************99.999999999999****************. PP

                                   CTCTGGEEEEEE.EEEEEECTTSGEEEEEEECTTCCCCCCSSEEHCSSETEEEEEEEESSCSEEEEEETTTTEEEEEEEET CS
                   Aldose_epim 166 esidshelqiea.deylevdeeliptgelkdvkgtpfdfrqpkaigedlkglDhayllksklkaviidpdkksgiklevst 245
                                      ++ e+  +   + le  + +iptge+k+vk ++              ++D+++   +     ii+ +  s++k++ ++
  gi|70607894|ref|YP_256764.1| 151 ---SDWEIITQReVRKLESID-NIPTGEIKQVKLSHG-------------EYDDCFIVRG----DIILKSSYSTVKITRRK 210
                                   ...555555554255555555.9********997666.............9********9....789999999******** PP

                                   TSSEEEEEECTTTTSEECCEEESSECTCETCCCECHHHT-EEEHTTTEEEEEE CS
                   Aldose_epim 246 tepalvvytgnflkkylsreglaletqmlpdepnhpefpsivlkpGesysaet 298
                                   + + +++ytg   k      ++a+e+++   +++h++ +  v kp +++++++
  gi|70607894|ref|YP_256764.1| 211 NLNYIQIYTG--VK-----GAVAIEPMSGAPDAFHNKMGIKVIKPAQKHEFSY 256
                                   *********9..33.....5788888888888888888878888888877765 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.69   6.2e+03      38      51 ..     166     179 ..     148     193 .. 0.55
   2 ?   10.6   0.0   5.5e-05      0.49      10      36 ..     220     246 ..     214     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.69
                                   ETTEEEEE-EEEEE CS
                          RimM  38 kkgetreltvesvr 51 
                                   +  ++++ ++++v+
  gi|70607894|ref|YP_256764.1| 166 SIDNIPTGEIKQVK 179
                                   44444445555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.5e-05
                                   TTTTEEEEEE-SSSGGGGGGSSSEEEE CS
                          RimM  10 GlkGevkVkpftdfpealfkygrvlle 36 
                                   G+kG v ++p++  p+a+ ++  + + 
  gi|70607894|ref|YP_256764.1| 220 GVKGAVAIEPMSGAPDAFHNKMGIKVI 246
                                   9*****************999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1725.92
//
Query:       gi|70607895|ref|YP_256765.1|  [L=336]
Description: calcium-gated potassium channel [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-17   63.7   0.3    2.9e-17   63.0   0.3    1.4  1  TrkA_N       TrkA-N domain
      2e-05   24.3   0.4     0.0002   21.1   0.0    2.6  3  TrkA_C       TrkA-C domain
  ------ inclusion threshold ------
      0.013   15.4   8.5      0.026   14.5   8.5    1.5  1  Ion_trans_2  Ion channel


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.3   4.8e-21   2.9e-17       1     114 [.     130     241 ..     130     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 4.8e-21
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilav 80 
                                   +i++G +r   s +++L+e ++ d+vv+ +++e  + l+  g +v+ gd+ +e+ L + gi++a++ i+a++dd +++l++
  gi|70607895|ref|YP_256765.1| 130 VIVLGNSRSVLSAVKKLEElDK-DYVVVTNSQEIYKLLK--GDKVILGDPKNEDNLLSVGINNAESAIIAMDDDSETLLLT 207
                                   799****************767.8*************97..888************************************* PP

                                   HHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEE CS
                        TrkA_N  81 llakelnpkkkiiaraqdpehaellkklgadvvi 114
                                   l ++++np ++i++ ++d++  ++++++gad +i
  gi|70607895|ref|YP_256765.1| 208 LKVQKMNPPLTIVTVVKDSSMMDIMRTAGADIII 241
                                   *******************************998 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.56   3.4e+03      52      64 ..     129     141 ..     126     146 .. 0.74
   2 ?   -0.5   0.0      0.19   1.1e+03      44      64 ..     162     181 ..     154     185 .. 0.73
   3 !   21.1   0.0   3.4e-08    0.0002      16      69 ..     284     335 ..     282     336 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.56
                                   EEEEEEEHHHHHH CS
                        TrkA_C  52 vllvvgspsdlae 64 
                                   +++v+g++ ++  
  gi|70607895|ref|YP_256765.1| 129 HVIVLGNSRSVLS 141
                                   7999999999655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                                   T-B--TT-EEEEEEEHHHHHH CS
                        TrkA_C  44 dtvLeeGDvllvvgspsdlae 64 
                                    ++L +GD++++ g+p++ + 
  gi|70607895|ref|YP_256765.1| 162 IYKLLKGDKVIL-GDPKNEDN 181
                                   568999999998.87777665 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 3.4e-08
                                   BHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C  16 tlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   +lk+  l++ +v+ +ai ++ +  +    dt+ +eG vl+v+g+ps  +e+ +l+
  gi|70607895|ref|YP_256765.1| 284 KLKD--LPN-DVIPIAILKDgKLDPYFEKDTEVKEGQVLFVLGDPSKFKEVNKLI 335
                                   6899..999.*******766477777777*******************9999986 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   8.5   4.3e-06     0.026       3      74 ..      36     105 ..      33     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-06
                                   HHHTCHHHHHHHHT....T---HHHHHHHHHHHHTTS--..--SSTT-----HHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   3 lllvlifgaviysleegwekwsfldalYfsfvtltTiGY..GdivpetdagrlftivyillGlalfalflavlg 74 
                                    ++v i++ +++++    +  ++++a+Y ++ ++tT+G    +i+  + + +lf ++ i++ ++lfa + ++l+
  gi|70607895|ref|YP_256765.1|  36 SIVVYIIALIFVYY----QHLDWISAIYAAVNVITTVGLyaPNIYSMPSQEKLFLTLSIIFSVGLFASIAQTLI 105
                                   35556666666666....667*****************7333455555557****************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2643.53
//
Query:       gi|70607896|ref|YP_256766.1|  [L=209]
Description: hypothetical protein Saci_2187 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-13   51.2   0.0    2.9e-13   50.3   0.0    1.4  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
      0.049   14.2   0.1      0.098   13.3   0.1    1.5  1  VCBS          Repeat domain in Vibrio, Colwellia, Bradyrhizob


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   3.3e-17   2.9e-13     100     262 ..      71     197 ..      67     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 3.3e-17
                                   HHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCT CS
                  Amidohydro_2 100 aeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfP 180
                                    el r++ ++g++G+ lnp  +  dl+ ++     ++ +e+++lp++i+tG                 +p  l +v+  f 
  gi|70607896|ref|YP_256766.1|  71 VELGRQL-DKGIVGIVLNPINHDFDLDKADDV---YQFAEDHDLPLFIYTG-------------RGKGDPSKLTEVLKNFR 134
                                   6999***.**************9999997777...****************.............****************7 PP

                                   TSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTT CS
                  Amidohydro_2 181 nlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepe 261
                                    lk+vl  +G+p   +  + + l +++nvy ++s ++                  +i++++ ++++fGs yP++++++  +
  gi|70607896|ref|YP_256766.1| 135 -LKVVLISLGYP--NYVNEARELLKLNNVYGDISSVP----------------QNVIKTFPREKLIFGSHYPYVPFQEIMD 196
                                   .***********..88888888899999*****9965................57*******************9987665 PP

                                   H CS
                  Amidohydro_2 262 a 262
                                    
  gi|70607896|ref|YP_256766.1| 197 K 197
                                   5 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.098       1      35 [.      92     127 ..      92     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                          VCBS   1 DldgDGrlDlvvan.dgglrvyrnngdGtftdvtkt 35 
                                   D+d D  +D++ +  d+ l +++++g G++ ++  t
  gi|70607896|ref|YP_256766.1|  92 DFDLDKADDVYQFAeDHDLPLFIYTGRGKGDPSKLT 127
                                   9**********98769**********9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1408.98
//
Query:       gi|70607897|ref|YP_256767.1|  [L=314]
Description: ribonucleotide-diphosphate reductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-21   74.9   0.2    1.2e-20   74.1   0.2    1.3  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain
    0.00077   19.9   0.2       0.16   12.4   0.2    2.7  2  Rubrerythrin    Rubrerythrin
     0.0081   15.7   0.0        0.8    9.2   0.0    2.2  2  DUF455          Protein of unknown function (DUF455)


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.2   2.1e-24   1.2e-20      14     222 ..      33     246 ..      27     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 2.1e-24
                                   HHHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBS..SHHHHHHHHHHHHHH CS
                Ribonuc_red_sm  14 elykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevq..ipearafygfqaamE 92 
                                   +ly+   + fW p ++d+skD +dwk kLs+dek+ + ++++++++ +  v+  +++ ++  ++    e   ++  +a++E
  gi|70607897|ref|YP_256767.1|  33 KLYQIGKRLFWDPAKIDFSKDKEDWK-KLSKDEKNYLLNIVSLFMAGEEAVAVDITPLISTMINegRVEDVIYLEQFAFEE 112
                                   578888999****************9.6**************************99999999993334555788999**** PP

                                   HHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHH.....HHHHHHHHCTTTSC..HHHHHHHHHHH.HHHHCCCHHHH CS
                Ribonuc_red_sm  93 niHaesYsllletlvkdekekdelfnaieenpalqkk.....aewikkwyeskkde..ekfaerlvafa.llegilfysgF 165
                                   + Hae++   +++l  +++    +f  +e np +qk        ++  w  + + +  e++a ++  +  ++eg+   sg+
  gi|70607897|ref|YP_256767.1| 113 AKHAEAFRRFCDSLEINDDL--TIF-TTEYNPWYQKIfyeelPSVM--WKLRVD-PspENLAVAVTTYNlYVEGVAAESGY 187
                                   **************843332..222.33333333332100002333..322223.244888888888877*********99 PP

                                   HHHHHHH.HTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHHHHHH CS
                Ribonuc_red_sm 166 aailwlk.krgllpglaeiielilrDeglHtdfagllfkelkeen.elenkeleeevee 222
                                    ++ ++  + +++pgl++ ++li+ De+ H  ++ +l+++l  en e   ++  e++++
  gi|70607897|ref|YP_256767.1| 188 KTFKHIFnSLNIMPGLSKTVNLIATDESRHIAYGTYLITRLIVENgESIYRKAIEQFNK 246
                                   8887654499*******************************999876655555555555 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   2.7e-05      0.16      34      67 ..     104     138 ..      89     150 .. 0.84
   2 !    4.8   0.0     0.006        36      14      56 ..     184     228 ..     178     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSB CS
                  Rubrerythrin  34 lFeelAeeEreHakilnklleklepele.levkek 67 
                                   ++e++A eE++Ha+ ++++ ++le + + +++ ++
  gi|70607897|ref|YP_256767.1| 104 YLEQFAFEEAKHAEAFRRFCDSLEINDDlTIFTTE 138
                                   5799********************99996555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.006
                                   HHHHHHHHHCHH..TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                  Rubrerythrin  14 rrlYkelaekak..egypqiaelFeelAeeEreHakilnkllekl 56 
                                   ++ Yk +   ++  + +p ++++ + +A +E++H +    l+  l
  gi|70607897|ref|YP_256767.1| 184 ESGYKTFKHIFNslNIMPGLSKTVNLIATDESRHIAYGTYLITRL 228
                                   5556666666666568999***************87666666555 PP

>> DUF455  Protein of unknown function (DUF455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0038        23     142     204 ..      66     127 ..      50     155 .. 0.72
   2 !    9.2   0.0   0.00013       0.8     180     219 ..     205     248 ..     189     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0038
                        DUF455 142 kdllarlavvplvlEArGLDvtpalieklraagdeesaeiLevIledEitHVaaGvrWfrylc 204
                                   + ll+ +++     EA  +D+tp  i+ + + g  e +  Le    +E +H +a +r+   l 
  gi|70607897|ref|YP_256767.1|  66 NYLLNIVSLFMAGEEAVAVDITPL-ISTMINEGRVEDVIYLEQFAFEEAKHAEAFRRFCDSLE 127
                                   44566667777778********96.56677789999999************887555544444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00013
                        DUF455 180 eiLevIledEitHVaaGvrWfrylcekegl....dpvetFrelv 219
                                   ++++ I +dE +H+a+G+   ++l  ++g+    +++e+F++lv
  gi|70607897|ref|YP_256767.1| 205 KTVNLIATDESRHIAYGTYLITRLIVENGEsiyrKAIEQFNKLV 248
                                   67899*******************98888855555577777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2129.76
//
Query:       gi|70607898|ref|YP_256768.1|  [L=615]
Description: hypothetical protein Saci_2189 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-42  145.5  52.4      2e-42  145.5  52.4    2.2  2  AA_permease_2  Amino acid permease
    2.3e-28   99.1  53.5    2.3e-28   99.1  53.5    2.2  1  AA_permease    Amino acid permease
     0.0018   18.2   0.6     0.0018   18.2   0.6    5.3  6  DUF3487        Protein of unknown function (DUF3487)
  ------ inclusion threshold ------
        1.4    9.2   5.3        3.1    8.1   0.9    3.7  2  LHC            Antenna complex alpha/beta subunit


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5  52.4   4.5e-46     2e-42       1     403 [.      17     465 ..      17     483 .. 0.77
   2 ?   -4.4  11.6       1.4   6.4e+03     328     406 ..     488     570 ..     472     591 .. 0.68

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 4.5e-46
                 AA_permease_2   1 lsllsafalvigsvigsgifvkn.laas.ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafl 79 
                                   l+l++++ l++g +igs+ +++  +aas +gp+++l+++i+ +++ +  +l+yaEl++a prsgGi+ y ++  g +++++
  gi|70607898|ref|YP_256768.1|  17 LTLIDLVSLALGGIIGSAWLFSAlSAASiAGPSAVLSWVIGGILI-IFIGLAYAELGTAVPRSGGIVRYPHYSHGSYAGYM 96 
                                   56788999********9999988777778***********99998.8999*******99********************** PP

                 AA_permease_2  80 sawfnwfayvpvlasi.lsvaasyllnalgp..dlqgn........twltyliaiaililvalinirgikesakiqnilgi 149
                                    a ++++++v  ++si + ++++yl++ ++p  +l ++        t+  +l+ai+++++++l+n++gik ++k ++ ++i
  gi|70607898|ref|YP_256768.1|  97 LAVLYLISAVT-TPSIeAEAVVEYLAS-ISPlnFL-TTsvngvnvlTVYGILLAICLMVVFFLVNYFGIKALGKTNTGITI 174
                                   *******9988.556615556777755.5666522.223555565566667888*************************** PP

                 AA_permease_2 150 lkillpliiliilglitvdgggfsslstetdtffpngwp.g...vllglli..vlwsfdGfesaanvseevkk..kdvpka 222
                                   +k+++p +++i+l +++ + + f+        f+p+g++ g   v+ ++++  +++++ Gf   + ++ e+k+  +d+ +a
  gi|70607898|ref|YP_256768.1| 175 WKLVVPTVTFILLFFAF-NSKNFT-----SYGFLPTGNSnGlidVFYAIPAsgIVYAYLGFRQPVEYAGEAKNpqRDIGRA 249
                                   ******99999666655.444444.....2348888777543455777766779****************888779***** PP

                 AA_permease_2 223 ifigllivlvlyllvniaflgvvpddei..anlsnlgsv......aalffeavggk.vvaiivvilial.........sll 285
                                   i+i+l+i++++y+l++iaf+g++ + +   ++++n+  +       ++f++ + ++  + +++ ++ +          s  
  gi|70607898|ref|YP_256768.1| 250 IVISLAIAIIIYTLLQIAFIGALDWTSAgiSTPGNWTALtssswaSGPFYNELENSgKALGLALLVYWGyallvdaviSPS 330
                                   *************************77644555553322555554688888887443444443333333333555544778 PP

                 AA_permease_2 286 gaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllli 366
                                   g ++ ++ +++r+++ +a d+++P+ff + nk+++pi ++i t++v +++ll f      + ++ ++ ssl+ ++ y +  
  gi|70607898|ref|YP_256768.1| 331 GTGLVYIGTTTRTFYGIAADRYFPEFFLRLNKYKIPIFSLIATLVVGILFLLPFP-----SWYLFVNFSSLATVFTYVMGG 406
                                   89999999***************************************77766664.....589****************** PP

                 AA_permease_2 367 igalilrkkrphlkrpgk....................i..lvaiigalfllfllvalf 403
                                   ig+  lr++ p+l+rp k                    +   ++i+ +l++lf+lv +f
  gi|70607898|ref|YP_256768.1| 407 IGLQTLRRTAPDLRRPVKlagskviapiatvsamlvayWsgFTTIFYVLTSLFILVPIF 465
                                   *************9944444445555555555544444333555555666666665555 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 1.4
                 AA_permease_2 328 taivslillllfllas..saaynfllsvsslglii..sylll.iigalilrkkrphlkrpgkilvaiigalfllfllvalf 403
                                   +++ + ill  f++++  +++yn++ s  +++l +  + +++ +ig+l +  + +++ + g +l+++i a ++  ++ ++ 
  gi|70607898|ref|YP_256768.1| 488 QLLSN-ILLAYFAYVNilNSSYNLIGSFIMYFLGFlgMSIIPsLIGYLAVNETGRKYIKSGLWLIGLILATYVMSFIGNFG 567
                                   44455.666777777788999999999888876551144444578888888888888889999999999988888887765 PP

                 AA_permease_2 404 fpp 406
                                   + +
  gi|70607898|ref|YP_256768.1| 568 LLS 570
                                   443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1  53.5   5.1e-32   2.3e-28       2     436 ..      22     463 ..      21     480 .. 0.77

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 5.1e-32
                   AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlny 82 
                                   ++  algg+iG + +++  +++s aGp +a+l+++++g+ i++++l+ +e+ t++p+sgg+  y + ++g+ +G++ + +y
  gi|70607898|ref|YP_256768.1|  22 LVSLALGGIIGSAWLFSALSAASIAGP-SAVLSWVIGGILIIFIGLAYAELGTAVPRSGGIVRYPHYSHGSYAGYMLAVLY 101
                                   6889***********************.999************************************************** PP

                   AA_permease  83 lfswitvlaleltaasiliqfwelvtdlpkawvt................gavflvvlliinlvgvkvygeaefi.lalik 146
                                   l+s +t+  +e   a+ +++++ +++ l+  + t                ++ ++vv++++n++g+k+ g++ +  +++ +
  gi|70607898|ref|YP_256768.1| 102 LISAVTTPSIE---AEAVVEYLASISPLN--FLTtsvngvnvltvygillAICLMVVFFLVNYFGIKALGKTNTGiTIWKL 177
                                   *******9999...666666664444444..444456788888999*999889999******************8355666 PP

                   AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv..ivvfaftGielvaiiagEv 225
                                   ++  + fi++++ ++++  ++ g               +lp g   ++ g + +++++++   +v a+ G+   +  agE+
  gi|70607898|ref|YP_256768.1| 178 VVPTVTFILLFFAFNSKNFTSYG---------------FLPTG---NSNG-LIDVFYAIPasGIVYAYLGFRQPVEYAGEA 239
                                   77888898888766666665555...............68888...4444.55555555411457788899999******* PP

                   AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa........aspfvifikesgvs.vlaplinav.. 295
                                   k+P+++i +ai   + + +i+Y+l+ ++ +  +++++ g+ +  + +        ++pf + +++sg + +la l++ +  
  gi|70607898|ref|YP_256768.1| 240 KNPQRDIGRAIVISLAIAIIIYTLLQIAFIGALDWTSAGISTPGNWTaltssswaSGPFYNELENSGKAlGLALLVYWGya 320
                                   ****************************9999***9999988555448999999988988888888765256666654311 PP

                   AA_permease 296 ilt.aals.sanssly..sasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllais 372
                                   +l+ a++s s+ +++y  +++R++y  a d+++P ++ +++k++ P+ +++++++++ l+l    l ++    +  ++++s
  gi|70607898|ref|YP_256768.1| 321 LLVdAVISpSGTGLVYigTTTRTFYGIAADRYFPEFFLRLNKYKIPIFSLIATLVVGILFL----LPFP---SWYLFVNFS 394
                                   333144443455555522678****************************************....3333...467899*** PP

                   AA_permease 373 aliglivwlliilsylrfRkalkyqgrsieelgfk.....aallplgvilvlaaliiillilalyaylt 436
                                    l++++++++  + +  +R++    +r ++++g k     a +  ++v ++  + +i++++++l+++++
  gi|70607898|ref|YP_256768.1| 395 SLATVFTYVMGGIGLQTLRRTAPDLRRPVKLAGSKviapiATVSAMLVAYWSGFTTIFYVLTSLFILVP 463
                                   *********998887777777555555444444331111144455666666666666666666665555 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5      0.12   5.5e+02      27      55 ..      36      64 ..       6      83 .. 0.59
   2 ?    0.2   1.3      0.15   6.7e+02      30      53 ..     133     156 ..     112     184 .. 0.59
   3 ?   -2.8   0.7       1.3   5.8e+03      33      53 ..     250     269 ..     246     281 .. 0.58
   4 !   18.2   0.6   3.9e-07    0.0018      31      81 ..     368     418 ..     363     426 .. 0.94
   5 ?   -1.0   1.1      0.35   1.6e+03      39      67 ..     434     462 ..     421     488 .. 0.56
   6 ?   -3.7   0.9       2.4   1.1e+04      47      60 ..     578     590 ..     549     599 .. 0.46

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                       DUF3487 27 vlaglglvvglvlglllallvgslalipt 55
                                  ++  l+++  +  + +l +++g +++i+ 
  gi|70607898|ref|YP_256768.1| 36 LFSALSAASIAGPSAVLSWVIGGILIIFI 64
                                  33444444555555555555554444433 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                       DUF3487  30 glglvvglvlglllallvgslali 53 
                                   + g+ v  v g+lla+++  + ++
  gi|70607898|ref|YP_256768.1| 133 VNGVNVLTVYGILLAICLMVVFFL 156
                                   333334444444444443332222 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.3
                       DUF3487  33 lvvglvlglllallvgslali 53 
                                   +v+ l++++++ +l++ +a+i
  gi|70607898|ref|YP_256768.1| 250 IVISLAIAIIIYTLLQ-IAFI 269
                                   5555556666655555.4444 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 3.9e-07
                       DUF3487  31 lglvvglvlglllallvgslaliptialllvllvvlvggkllarlKRgkPd 81 
                                   ++l++ lv+g+l++l + s+ l++ +  l+ +++ ++gg  l++l+R  Pd
  gi|70607898|ref|YP_256768.1| 368 FSLIATLVVGILFLLPFPSWYLFVNFSSLATVFTYVMGGIGLQTLRRTAPD 418
                                   78999*******************************************998 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.35
                       DUF3487  39 lglllallvgslaliptialllvllvvlv 67 
                                   ++ + a+lv ++  + ti  +l  l++lv
  gi|70607898|ref|YP_256768.1| 434 IATVSAMLVAYWSGFTTIFYVLTSLFILV 462
                                   44444444444444444444433333332 PP

  == domain 6  score: -3.7 bits;  conditional E-value: 2.4
                       DUF3487  47 vgslaliptialll 60 
                                    +  +l++ i+l+ 
  gi|70607898|ref|YP_256768.1| 578 YD-TILVVIIGLVF 590
                                   22.33444444444 PP

>> LHC  Antenna complex alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9    0.0007       3.1       4      21 ..     174     191 ..     173     192 .. 0.96
   2 ?   -0.0   0.2      0.23   1.1e+03      19      32 ..     581     594 ..     574     597 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0007
                                   HHHH...HHHHHHHHHHH CS
                           LHC   4 iWelvdPhrglvallgff 21 
                                   iW+lv P++++++l+++f
  gi|70607898|ref|YP_256768.1| 174 IWKLVVPTVTFILLFFAF 191
                                   9**************998 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHH CS
                           LHC  19 gffavlAlliHfll 32 
                                     ++ ++l+ H l+
  gi|70607898|ref|YP_256768.1| 581 ILVVIIGLVFHYLA 594
                                   578999*****775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 3890.68
//
Query:       gi|70607899|ref|YP_256769.1|  [L=824]
Description: malate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-43  147.5   0.0      9e-39  133.1   0.0    2.2  2  Malate_synthase  Malate synthase
  ------ inclusion threshold ------
       0.13   12.7   1.7        1.8    9.0   0.1    2.8  2  DUF4413          Domain of unknown function (DUF4413)


Domain annotation for each model (and alignments):
>> Malate_synthase  Malate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0     1e-42     9e-39      23     323 ..      35     371 ..      20     419 .. 0.89
   2 !   12.2   0.0   4.5e-06     0.041     401     499 ..     552     658 ..     539     681 .. 0.77

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1e-42
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHSHHHCCTCCCH-TSS---S-.............................. CS
               Malate_synthase  23 vaelvrdltprrrelLeeRdelqaeidkgelndflketkylreepewktat.............................. 73 
                                   + el  +++++ ++++ +R++  ++ d+ +++ ++++  ++  +++ + +t                              
  gi|70607899|ref|YP_256769.1|  35 IEELSVEFSDEIKRVISKRRKWLESKDSVSSKGSFPSWDEVFVDADGNRRTfreivqgmidnflqrqsslswrlndhvpip 115
                                   678999*****************************9999999999998888899***********************9988 PP

                                   .EECCCCE-TCCCCCCC-C.CHCCCCCCCSSSEEEEESSTTS--.........HHHHHHCCHHCCCHCCTTT-EEEET-TS CS
               Malate_synthase  74 .lhielqdrrveiiGkadr.kmiinalnesaittiaDfEDsvap.........nwenlvkGqlnledavrgrisfrkenkd 143
                                     +  +++   ei+G+  +     n +n+++++ + D ED++ +         +  ++ +   n +    g+      +k+
  gi|70607899|ref|YP_256769.1| 116 nDAHPIKNPGLEITGPWYPlSRAYNQVNTDVTSAMEDEEDASPAwytpygsgkSIADVWDARKNVKLFLSGKAPNPYYEKG 196
                                   8555589999******98636799*****************999999999999888888888899999999999999999* PP

                                   EEEEETTSESSSSEEEEE---TTTEEEEEECTTCEEEHHHHHHHHHHHHHHHHCSCCTTSSEEEEE-S-SSHHHHHHHHHH CS
               Malate_synthase 144 ksYklndglegrsllfvRnrGwhltekhilvdGeeisegilDfgliffhnakelklsrgggpyivlPKmegpqEaalwnev 224
                                   k+Y+ln+  ++ +++f R  G hl +  i++dG+++++ i+ + ++ ++n+  l  + g+g+y++lPK++ p+Ea +  ++
  gi|70607899|ref|YP_256769.1| 197 KTYTLNKPRDKWPTIFHRLPGLHLLDFDITLDGKPVPAIIVSAVIYTLNNYISL-RNAGSGVYFYLPKTQTPEEALIVEKI 276
                                   ******99**********************************************.889*********************** PP

                                   HHHHHHHCTSSTTSCEEEEEE-SHHHHTTHHHHHHCTTTTEEEEEE-CHHHHHHHHHHTCCCCGCB...CGGGGCCSHHHH CS
               Malate_synthase 225 FsraedllglprgtikatvliEtlraslnldeiiyelrdrvaglNcGrlDyifseiktlreagdmvLPdRkavtktapfik 305
                                     r+e+ lglp gt+k ++l E+++a   +  i+   r+r+   N Gr+Dy++s i      +++vLPd +++t+t+p + 
  gi|70607899|ref|YP_256769.1| 277 LRRIEEKLGLPIGTLKLALLYEEVNAGRYFPVILWIFRERLIKSNNGRWDYLGSLIEMWL--QERVLPDPQNITMTSPNMM 355
                                   ********************************************************9665..679**************** PP

                                   HHHHHHHHHHHHTT.CCC CS
               Malate_synthase 306 aYekllvktchkrgvham 323
                                   aY+k +  +     ++a 
  gi|70607899|ref|YP_256769.1| 356 AYQKYNALI--MLLAGAK 371
                                   ***988766..2233333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-06
                                   CS.--BBHHHHHHHHHHHHHHHHHHHHHHCT-SS..EEETT....EEESHHHHHHHHHHHHHHHHTTSC-CCHSHCHHHHH CS
               Malate_synthase 401 ltkipeaeeteeglrnnvqvglqYvvaWlrgvGc..vpiih....LmEDaATaeiSrqqlaqWirhgvvlkeqgvkvslel 475
                                   l  ip++e+t e +++   ++ +Y  + l+g  +  + +++     m D AT +i  + l++ ++ ++v+ ++g    ++l
  gi|70607899|ref|YP_256769.1| 552 LYDIPDGEITPEHVQHAFYMAANYGFQLLNGNLAaaIDDYElkqrFMNDLATYRIFTSWLWSLVNRDAVITKEGYIKAPKL 632
                                   445**************************88766568888888899******************98877666677666666 PP

                                   HHH.HH.HHHCCHHHHHHHCCTTHHH CS
               Malate_synthase 476 mak.lv.deenarleelgkedeayre 499
                                   +++ ++  e++ ++++ +k ++ ++e
  gi|70607899|ref|YP_256769.1| 633 TRDgVIpAENVLKVAKGTKVKDIFEE 658
                                   65423313333344444445555555 PP

>> DUF4413  Domain of unknown function (DUF4413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.037   3.3e+02       8      46 ..     652     688 ..     647     707 .. 0.70
   2 ?    9.0   0.1    0.0002       1.8      39      75 ..     757     794 ..     721     820 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.037
                       DUF4413   8 anlfFneilevkkllkewakseddllskmaekmqekfdk 46 
                                   +++ F+ei++ + + ++++ +e+d+  ++a+++ e+f k
  gi|70607899|ref|YP_256769.1| 652 VKDIFEEIWKLHFDWTNEFYKEQDM--RVANRLAETFGK 688
                                   5789*********999998776663..345555555544 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
                       DUF4413  39 kmqe.kfdkywkksnlllaiaviLDPryKlkyvefalk 75 
                                    m++  + ky+ +s  +l++   LDP+ +lk+++  ++
  gi|70607899|ref|YP_256769.1| 757 LMRQfLYPKYIMNSGKILFVLSPLDPEKRLKVMDSIFS 794
                                   34446789************************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (824 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5094.51
//
Query:       gi|70607900|ref|YP_256770.1|  [L=437]
Description: isocitrate lyase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   4.7e-116  388.4   0.3      9e-63  212.5   0.0    2.1  2  ICL         Isocitrate lyase family
    2.9e-15   56.4   0.0      5e-15   55.6   0.0    1.3  1  PEP_mutase  Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.5   0.0     1e-66     9e-63       6     257 ..      16     255 ..      10     256 .. 0.92
   2 !  176.0   0.3   1.2e-55   1.1e-51     352     526 .]     252     428 ..     250     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 1e-66
                                   HHHHTSGGGGG---SS-HHHHHHH--SS----THHH.HHHHHHHHHHHHHHHT--EEEEB--SHHHHHHHHHH.-S-EEE- CS
                           ICL   6 kkwwsdsrwrktkrvysaedivskrGnlkieyasse.qakklfklleeheaektasktfGaldpvqvtqmaky.ldtiyvs 84 
                                   ++w +d+rw+  kr+y+a d+v+ rG+++iey+ ++  a+kl+kll+++        tfGal   q  +mak  l +iyvs
  gi|70607900|ref|YP_256770.1|  16 QEWSEDPRWKGIKRNYTASDVVKLRGSVRIEYTLARlGAQKLWKLLNTE----PYVATFGALTGSQAVEMAKAgLKAIYVS 92 
                                   4677899*************************9765269*******865....4568***************669****** PP

                                   HHHHHHH--TT----SS-S-S-TTHHHHHHHHHHHHHHHHHHHHHHHHHSS-HHHHTTS--------EEEE-TT-SSSHHH CS
                           ICL  85 GwqssstastsnepspdladypmdtvpnkvehlflaqlfhdrkqkeerlkvkkeereklanvdylrpiiadadtGhGGlta 165
                                   Gwq ++ +  sn+  pdl+ yp ++vpn v  l  a l  d+      ++ ++ +r     vdyl pi+ada++G+GG   
  gi|70607900|ref|YP_256770.1|  93 GWQVAADNNLSNQTYPDLSLYPSNSVPNLVRRLNNALLRADQ------ISWSEGKR----DVDYLLPIVADAEAGFGGPIH 163
                                   **********************************99986664......44444444....69******************* PP

                                   HHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE--GGGEEEES-TT-GG CS
                           ICL 166 vvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvartdseaatlitstidtr 246
                                    + ltk +ie GaaG+h edq ++ kkcGh+ Gkvl+p    i  l a+r++ d+lg+ ++++artd+  a+ ++  id+r
  gi|70607900|ref|YP_256770.1| 164 AFELTKAMIEAGAAGVHFEDQLASEKKCGHLGGKVLIPTGAFIRVLNAARLASDVLGVPTILIARTDALNAAYLSNDIDER 244
                                   ********************************************************************************* PP

                                   GGGGEEEE--T CS
                           ICL 247 dhafilGatnp 257
                                   d af+ G   p
  gi|70607900|ref|YP_256770.1| 245 DTAFLTGKRTP 255
                                   *****998766 PP

  == domain 2  score: 176.0 bits;  conditional E-value: 1.2e-55
                                   S--TT--EEE--SHHHHHHHHHHHTTS-SEEE---SS--HHHHHHHHHHHHTT-TT-EEEEE--SSS-GGGTS-HHHHHSH CS
                           ICL 352 prvreGyyrykGgtqcsvvravafapyadliwmesklpdyaqakefaeGvkakvpeqklaynlspsfnwkkamsadeqety 432
                                    r+ eGyy  kGg++ ++ r++a+apyadl+w+e++ pd+ +ak+fa+ ++a +p ++laynlspsfnwkk m   +  ++
  gi|70607900|ref|YP_256770.1| 252 KRTPEGYYEVKGGIEYTIARGLAYAPYADLLWFETSRPDLDEAKQFADAIHAHFPGKMLAYNLSPSFNWKKFMDDSKIGKF 332
                                   5999***************************************************************************** PP

                                   HHHHHHTTEEEEEETTHHHHHHHHHHHHHHHHHHHHTHHHHH..HHTHHHHHHHT-GGGSHHHHHTHHHHHHHHHHHH--X CS
                           ICL 433 ikrlaklGyvwqfitlaGlhtnalisdkfakdyakrGmkayg..eevqeeeidnGvdvvkhqkwsGaeyidellklvtGGv 511
                                   i+ l+++Gy +qfitlaG h     + ++ak+y ++Gm  y+  +e++ +   +G   v+hq+  G+ey+d +l +++GG 
  gi|70607900|ref|YP_256770.1| 333 IEELGDMGYKFQFITLAGWHLINYHTFTLAKAYKNEGMLGYVrlQELEFQAQREGYTAVSHQREVGTEYFDLVLTIASGGN 413
                                   *****************************************9223444455679*************************** PP

                                   XXXXXXXXXXXX.XXX CS
                           ICL 512 sstaamGkGvte.dqf 526
                                   +st+am kG te +qf
  gi|70607900|ref|YP_256770.1| 414 ASTTAM-KGSTEaEQF 428
                                   ******.555552666 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   5.6e-19     5e-15      25     167 ..      81     277 ..      69     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 5.6e-19
                    PEP_mutase  25 veeagfkalatsSlavaa.....slGvpDgeelpleellaavraiaevvs.................lPlivDledGyges 83 
                                   +++ag ka+ +s+++vaa      + +pD +  p +++ ++vr++ +++                  lP+ +D+e+G+g  
  gi|70607900|ref|YP_256770.1|  81 MAKAGLKAIYVSGWQVAAdnnlsNQTYPDLSLYPSNSVPNLVRRLNNALLradqiswsegkrdvdylLPIVADAEAGFGG- 160
                                   5788*************9444434689999***************99997799**************************9. PP

                    PEP_mutase  84 peevaetvrrliaaGvvgvniEDk.....kknd.aerqlldieefaekiaaaraaaeeag..fvinARtdalll....... 149
                                   p +  e  + +i+aG++gv++ED+     k++  +++ l++   f + ++aar a +  g   +++ARtdal         
  gi|70607900|ref|YP_256770.1| 161 PIHAFELTKAMIEAGAAGVHFEDQlasekKCGHlGGKVLIPTGAFIRVLNAARLASDVLGvpTILIARTDALNAaylsndi 241
                                   88999999****************9985444455777888********************999********9878888888 PP

                    PEP_mutase 150 ..................sagagleeaieRaraYae 167
                                                     + ++g+e +i+R+ aYa 
  gi|70607900|ref|YP_256770.1| 242 derdtafltgkrtpegyyEVKGGIEYTIARGLAYAP 277
                                   888888888888888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2972.95
//
Query:       gi|70607901|ref|YP_256771.1|  [L=146]
Description: hypothetical protein Saci_2192 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-06   27.8   0.0    4.5e-06   27.2   0.0    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.5e-10   4.5e-06       2     119 ..      12     130 ..      11     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.5e-10
                                   EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS....SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                           PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar....rkskrekaaelvelllllsalkilpidaeia 78 
                                   ++DTs l+ +l  +++    + lle+  +++ ++l l El++v+ +      ++   +++++ l  +   ++++p+ + ++
  gi|70607901|ref|YP_256771.1|  12 MVDTSLLLPFLGIKVRGV-DENLLEG-KNVYYPSLMLVELIAVVIKearkLGLGLIPQDAIKGLSYINHTVNLVPMEELDL 90 
                                   79*********8888774.3666666.*******************99654455556666777777789999********* PP

                                   HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                           PIN  79 eeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                     +++i++k + +++Da++++    ++i+l+ t D+ f++ 
  gi|70607901|ref|YP_256771.1|  91 NLVYDIISKGWNDIFDAILYSSHNFTKIPLV-TLDRAFYEF 130
                                   *******************************.******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1034.11
//
Query:       gi|70607902|ref|YP_256772.1|  [L=86]
Description: hypothetical protein Saci_2193 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-12   46.2   0.1    4.4e-12   45.6   0.1    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.039   13.8   0.1       0.07   13.0   0.1    1.4  1  GTP_EFTU_D4     Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   4.9e-16   4.4e-12       2      44 ..      17      59 ..      16      61 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 4.9e-16
                                  EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                  +vG+++a+ iPk++++e+ i+eGd ++++++gdki l+pl+++
  gi|70607902|ref|YP_256772.1| 17 RVGKKYAIYIPKDIVEEMKIKEGDLLMVTREGDKITLVPLRKP 59
                                  89*************************************9976 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.8e-06      0.07      47      85 ..       3      42 ..       2      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-06
                                  EEEEEETTEEESEEETT-EEEEEEESS-T.TTS--TT-EE CS
                   GTP_EFTU_D4 47 ilqiqdkgkkleeakaGqevaisiegkiv.Grqikegdil 85
                                  i++i ++++  ++ + G++ ai i  +iv   +ikegd l
  gi|70607902|ref|YP_256772.1|  3 ISKIYQNDHMAKVLRVGKKYAIYIPKDIVeEMKIKEGDLL 42
                                  789999**********************62579*****88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.50
# Mc/sec: 518.11
//
Query:       gi|70607903|ref|YP_256773.1|  [L=266]
Description: hypothetical protein Saci_2194 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1676.01
//
Query:       gi|70607904|ref|YP_256774.1|  [L=125]
Description: hypothetical protein Saci_2195 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-24   84.0   0.4    8.3e-24   83.7   0.4    1.1  1  PaREP1    Archaeal PaREP1/PaREP8 family


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.4   4.6e-28   8.3e-24       4     115 .]       6     110 ..       3     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 4.6e-28
                        PaREP1   4 eeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvdlwk 84 
                                   ++a ++leeA+ell++Gd++qA+eK+ykA ++ +k+l +  +l+++++  +++ ws ++l+k v +l++  g k+++++w 
  gi|70607904|ref|YP_256774.1|   6 TSADVYLEEADELLSRGDVVQASEKYYKASEESIKILSSVLELEVINKISNEG-WSGELLNKCVFSLSSIFG-KWIIESWG 84 
                                   6899*****************************************99999999.******************.******** PP

                        PaREP1  85 lAldLHeyqfheaklelsdveskeeavkdlv 115
                                   +A+       ++ +++ ++v++++e++ +lv
  gi|70607904|ref|YP_256774.1|  85 SAIA-----LITVNMDSQQVNAYRENILKLV 110
                                   ****.....8999**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 863.53
//
Query:       gi|70607905|ref|YP_256775.1|  [L=372]
Description: mandelate racemase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-55  185.9   0.0    9.5e-55  185.5   0.0    1.1  1  MR_MLE_C      Enolase C-terminal domain-like
    7.1e-10   39.1   0.0    1.2e-09   38.4   0.0    1.3  1  MR_MLE_N      Mandelate racemase / muconate lactonizing enzym
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.043   13.3   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.0   1.6e-58   9.5e-55      12     219 ..     147     364 ..     137     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 1.6e-58
                                   HHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS.......BHHHHHHHHHHHGGGTESEEESSSSTTT CS
                      MR_MLE_C  12 eqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqaw.......dlatAirvareleeldllwlEEPvpped 85 
                                   ++g+++vK+++ ++++++d++ +r++r+++  gd+++++vDanqaw       d+ tA++va+ele++d++wlEEP+ + +
  gi|70607905|ref|YP_256775.1| 147 SKGIDIVKIRFRRNSIKDDLALLREIRKTF--GDSIRVAVDANQAWtftppywDRMTALKVAKELEQYDVEWLEEPLYR-E 224
                                   469*******9999****************..6688*********66666666************99************.5 PP

                                   HHHHHHHHHHHHSSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHH CS
                      MR_MLE_C  86 dleglaelrarasipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaas 166
                                   d+eg+++lr+r++i+i +gE +y++ +f+++++ +a+divq+d+  + Gi e+r +a lae +++++ pH+++ g+g +a+
  gi|70607905|ref|YP_256775.1| 225 DIEGYRWLRERSNIKISGGELEYDLSRFKAFVDSKALDIVQADAVYSNGIRECRVIASLAESHNLEFLPHAWDPGMGWVAN 305
                                   7********555***********************************************************766******* PP

                                   HHHHHTTTTBEEEEEEGGGGH......TSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                      MR_MLE_C 167 lhlaaaipnllileyfldael......leeelleeplevedGrvtvpdgpGlGveldee 219
                                   lhl+a++p++l   + ++ ++      +   ++++ + vedG+  +p+  GlG+e+ +e
  gi|70607905|ref|YP_256775.1| 306 LHLSASLPESLTKYIETPLDPlwwfndVLFAITKNKIIVEDGYAILPEDAGLGLEVSDE 364
                                   ********99888887777778899999999*************************955 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0     2e-13   1.2e-09       3     117 .]       7     117 ..       5     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2e-13
                                   EEEEEEEEEEECEEEETTEEEEEE..EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHH CS
                      MR_MLE_N   3 evvvveeavklrPvqlavttvqkq..slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaql 81 
                                   +v v++++ + +P+q +     +q  ++ l+++e ++Gv+G +   +      t ka +++++ pll++ + + ++ +   
  gi|70607905|ref|YP_256775.1|   7 KVHVLKVPLP-EPIQFSWEPLPHQdyTFSLIELEGENGVKGYSAIELGS----TYKAFINTYVRPLLINLQID-LELIPDR 81 
                                   5667777777.4*****9988766225679************9776655....9***************9986.6788889 PP

                                   HHHHCSSCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                      MR_MLE_N  82 lkravlgnmsAkaaidmAlwDlkakalnlpladLlG 117
                                   + +   +      a+++A+wDl ak+ +lpl+++lG
  gi|70607905|ref|YP_256775.1|  82 FLQIGSWLIQRTGALEVAIWDLIAKSNQLPLYKMLG 117
                                   9999*******************************9 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.2e-06     0.043      85     158 ..     139     214 ..      80     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-06
                                   HHHHHHHHHCT-SEEEES...HHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHH CS
                  His_biosynth  85 ledveelleagadkviig...taavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakklee 158
                                   ++ ++++ + g+d v i     +  ++  l++e+ + fg+ +i va+Da + + ++   w+++t+l++ + +++++ 
  gi|70607905|ref|YP_256775.1| 139 IDLINDYYSKGIDIVKIRfrrNSIKDDLALLREIRKTFGD-SIRVAVDANQAWTFTPPYWDRMTALKVAKELEQYDV 214
                                   55567777777775444311123457899***********.**********99999999999977777666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2263.33
//
Query:       gi|70607906|ref|YP_256776.1|  [L=82]
Description: hypothetical protein Saci_2197 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   13.9   0.0       0.05   13.6   0.0    1.1  1  Lig_C     Ligase Pab1020 C-terminal region


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.8e-06      0.05      49     109 ..      20      80 ..      18      82 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-06
                                   HHHHHHHHHHTT---EEEEEEE-SSHHHHHHHHHHHHCTT--EEEEEEE..TTEEEEE..E CS
                         Lig_C  49 pmvetikkvkeeekvkeefrvrfkdeenieellehLrrlgvkaeveekekedgelvvkfkk 109
                                   p++  ++++k+ ++ +e +++ ++d + +  l+  L+   +++++e+k ke+g + v + k
  gi|70607906|ref|YP_256776.1|  20 PLMIMLTAIKKIQECGEAVEILMNDYDWYVSLKYILQVNDLNLKIEDKGKENGFMKVDVVK 80 
                                   667778888889999****************************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 556.09
//
Query:       gi|70607907|ref|YP_256777.1|  [L=292]
Description: sulfurtransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-41  139.1   0.2    1.5e-20   73.7   0.0    2.2  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   1.2e-21   2.2e-17       3     106 ..      13     121 ..      11     122 .. 0.82
   2 !   73.7   0.0   8.3e-25   1.5e-20       4     105 ..     156     279 ..     155     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.2e-21
                     Rhodanese   3 kelkellekgkvallDvR..ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdgggr. 78 
                                   k++ ++++++kv+++ v   p+ +Y+ +hIpgAv +  ++ l+++  ++     ++e+l+e  gi+n++t+v+y+d ++  
  gi|70607907|ref|YP_256777.1|  13 KWVLDHQKDPKVRIVEVDydPSTAYNVWHIPGAVLIrWREDLRHPVVRDFIEPSQFEKLMESkGINNDTTIVLYGDYNNWf 93 
                                   89***********88888768999************433445555555555566666666669*****************8 PP

                     Rhodanese  79 aaaaaallkklGykn.vsvldGGfkawke 106
                                   a  a +l+k++G+ + v+vl+GG ++w++
  gi|70607907|ref|YP_256777.1|  94 AVYAFWLFKAYGH-DdVRVLNGGRTKWAK 121
                                   888899******5.55***********87 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 8.3e-25
                     Rhodanese   4 elkellekgkva....llDvRppeeY................ekghIpgAvnvskdtlsrakkseapllelpeellel.gi 63 
                                   el ++l+kg++     l+DvR+p e+                  ghIpgA n+++  + +++  e ++ + ++++ e  gi
  gi|70607907|ref|YP_256777.1| 156 ELLQRLNKGEIGkslvLVDVRSPKEFtgevrappeyadeqtqVGGHIPGAANIPWAQAVNPETGEFKSVDELKKIYENaGI 236
                                   5777888887668888*********99999999999999997779*****************************9999*** PP

                     Rhodanese  64 dnkktvvvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                   +++k+v++yc+ g+raa ++  lk+ lGy+ v+v+dG++ +w 
  gi|70607907|ref|YP_256777.1| 237 TPEKEVITYCRIGERAAHTWFVLKYiLGYPAVRVYDGSWAEWG 279
                                   ***************9999*****9***999***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1972.84
//
Query:       gi|70607908|ref|YP_256778.1|  [L=88]
Description: hypothetical protein Saci_2199 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 622.81
//
Query:       gi|70607909|ref|YP_256779.1|  [L=231]
Description: uroporphyrin-III C-methyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-43  147.3   0.0    6.8e-43  147.1   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   0.0   3.8e-47   6.8e-43       1     212 [.       6     204 ..       6     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 3.8e-47
                  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkd 81 
                                   k++++G+GpGdpellT+++l+ l+ advv++d+ ++ + +  +++e          +++ +    e+  e ++++lr +  
  gi|70607909|ref|YP_256779.1|   6 KVIVIGAGPGDPELLTLKGLKYLQVADVVIYDK-LTAQAV-VYARE---------NSVKYMLSSDEDEIEVIRRYLRGYDV 75 
                                   79*******************************.655555.34444.........466777777899999*********** PP

                  TP_methylase  82 VvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallan 160
                                   +v+l+ GDP+v+g+g  l+    a  +gi++eviPGvs++++++a++giplt +g + +v+     ++  +  +++++ + 
  gi|70607909|ref|YP_256779.1|  76 IVRLKNGDPYVFGRGPQLCYNMIA--EGIQCEVIPGVSAVNSVPAYAGIPLTSNGFSDMVTvvSGVTEGGKLFDFSKVPD- 153
                                   *******************99999..9**********************************998888888999****998. PP

                  TP_methylase 161 gdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtleel 212
                                   ++tlv+l+a+++l+e+ + L+ ++ + +++vavve++++ d+rv + +l++l
  gi|70607909|ref|YP_256779.1| 154 KGTLVVLMAGKRLEEVSKGLMSRRSP-LDDVAVVEHGTYVDQRVSVMKLKDL 204
                                   99*********************555.66****************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1627.62
//
Query:       gi|70607910|ref|YP_256780.1|  [L=592]
Description: sulfite reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-37  128.0   0.0    3.9e-35  120.7   0.0    3.1  3  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    3.6e-24   84.4   0.9    9.2e-11   41.4   0.0    4.2  4  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   4.3e-39   3.9e-35       3     157 ..     117     309 ..     115     311 .. 0.81
   2 ?   -2.0   0.0      0.25   2.3e+03     114     136 ..     390     411 ..     385     413 .. 0.87
   3 !    3.9   0.0    0.0039        35       9     122 ..     415     525 ..     406     557 .. 0.64

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 4.3e-39
                                   SSCCCCCCSTCCCTBSS-SS-T..........................HHHHHHHHHHHCTCCCCTSSSS-BEEEEES... CS
                                   xxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       NIR_SIR   3 anlrnvtlcpgaglceeallDt..........................telakaiedelepeygetylPrKfKiavsg... 54 
                                   +n+rn+++cp +  +     ++                          ++  ++++ e   ey+++ lPrKfKi ++g   
  gi|70607910|ref|YP_256780.1| 117 DNVRNTVGCPISSYYGIFNSNGlaskiaryfrlpsnlyiqvfelseeaSSTLREENPEGHYEYADNLLPRKFKIGIAGvmk 197
                                   5666666666666444333333555555555555555555555544444444444477788889999************** PP

                                   .....STCSTSSGGGSSEEEEEEEETTCEE.EEEEEE--B-SSSTC-TCEEEEE...EEEEGGGHHHHHHHHHHHHHHHS- CS
                                   .....xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  55 .....cpnncvaveanDiglvgvkkdekei.gfnilvGGglgrthgakktsarl...gfvpeeevlevveaivevyrdhgd 126
                                          ++c+++++nDig+v+++  +++i  ++++vGGg+g+++g++++sa +   g v e+++l+v++ iv++++d+gd
  gi|70607910|ref|YP_256780.1| 198 igedyYVDDCIEARSNDIGIVPLVSRNGKIeKYQLYVGGGMGENNGYPTFSALAlplGTVSEDDLLKVLDSIVRIQQDWGD 278
                                   ****999***************999999888*********************98*************************** PP

                                   CSSGGG-SHHHHHHHHHHHHHHHHHHHCCTC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 127 rknrkkeRlkylverlGvekFrekveeelgk 157
                                   rknr+++Rlky+v++ G+ ++rek++e++g 
  gi|70607910|ref|YP_256780.1| 279 RKNRHWARLKYVVHKFGIIWMREKIKEYSGV 309
                                   ****************************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHS-CSSGGG-SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR 114 veaivevyrdhgdrknrkkeRlk 136
                                   +e+i++ +  +g r++++++Rl+
  gi|70607910|ref|YP_256780.1| 390 IENILREFG-YGLRNGKHYSRLR 411
                                   688999999.9**********97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0039
                                   CCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEEEEEEEE--B- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR   9 tlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekeigfnilvGGgl 89 
                                   ++c+g+ +c+   +D++ +  ++ dele   g+ +    + i vsgc  +c +   + ig vg   +     + + +GG  
  gi|70607910|ref|YP_256780.1| 415 SACVGFPTCKMSFTDSERFLPKLIDELE---GRGWGNSDVSIGVSGCVAQCSRPALHPIGWVGSGYE----LYMLKIGGDK 488
                                   5799999999999999999999984444...555566789999999999999999999999887663....4446666655 PP

                                   SSSTC-TCEEEEE....EEEEGGGHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                       NIR_SIR  90 grthgakktsarl....gfvpeeevlevveaivevyr 122
                                    r  +    + +       vp+  + +v ea+ ++y+
  gi|70607910|ref|YP_256780.1| 489 ERVGEPLIDYNENviylYQVPASRLADVNEALFQLYE 525
                                   4444443333333334344555556666666666665 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   2.1e-13   1.9e-09       9      68 ..      37     106 ..      31     107 .. 0.85
   2 ?   -3.1   0.0      0.81   7.2e+03      15      32 ..     251     269 ..     249     275 .. 0.63
   3 !   41.4   0.0     1e-14   9.2e-11       7      68 ..     333     396 ..     328     397 .. 0.94
   4 ?   -0.2   0.0       0.1   9.4e+02      49      66 ..     503     520 ..     499     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.1e-13
                  NIR_SIR_ferr   9 yymvrlrvp.nGritaeqlraladia......ekygs...geirlTtrQnlqlhgvpeedleeileeLae 68 
                                   +ym+r+++p +G i++ q+r + dia      ++y       i+lTtrQ +q+h+v++ dl + ++e+ae
  gi|70607910|ref|YP_256780.1|  37 IYMIRVSIPgGGPISSRQWRMFDDIAnkytisDAYTGfnqPSIKLTTRQDIQFHHVKKRDLVNAIREIAE 106
                                   48*******77999************7777774444244589**********************999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.81
                  NIR_SIR_ferr  15 rvpnGritae.qlraladi 32 
                                    +p G ++ + +l+ l  i
  gi|70607910|ref|YP_256780.1| 251 ALPLGTVSEDdLLKVLDSI 269
                                   5778888555366666555 PP

  == domain 3  score: 41.4 bits;  conditional E-value: 1e-14
                  NIR_SIR_ferr   7 kgyymvrlrvpnGri.tae...qlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeLae 68 
                                   k  + ++++v+nGr+ +++    ++  + ia+k+++  + +T++Q+l++  +++ed +ei+++L+e
  gi|70607910|ref|YP_256780.1| 333 K--WVFGIFVENGRLiDNQngrIKSMARYIADKFENLKFFITPNQHLIISEISDEDKHEIENILRE 396
                                   4..79****************99*****************************************98 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.1
                  NIR_SIR_ferr  49 lqlhgvpeedleeileeL 66 
                                   ++l  vp+++l++++e+L
  gi|70607910|ref|YP_256780.1| 503 IYLYQVPASRLADVNEAL 520
                                   8999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3944.75
//
Query:       gi|70607911|ref|YP_256781.1|  [L=239]
Description: phosphoadenosine phosphosulfate reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-46  156.6   0.1    7.5e-46  156.3   0.1    1.1  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.017   15.6   0.0    1.4  1  RsfS            Ribosomal silencing factor during starvation
       0.11   13.0   0.1       0.17   12.3   0.1    1.4  1  Peptidase_S8_N  N-terminal of Subtilase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3   0.1   1.3e-49   7.5e-46       2     174 .]      34     210 ..      33     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 1.3e-49
                                   EEEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHT.T-EEEEEE-SCHHHHHHHHHH-S-THHHC. CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleery.glrlkvyepeeevaekinaekhgsslyee. 80 
                                   +++++s  ++++V+l+++ ++ ++  ++ +dtg+  +et++++del+++y + ++ +y p++e+ e ++    g++l+ + 
  gi|70607911|ref|YP_256781.1|  34 IALACSLQAEDIVILDMMNQVVDKPIIFVIDTGRLNQETYNLIDELRTKYpKTEIRIYFPDKEEVEDMVNRY-GVNLFYKs 113
                                   78999****************999557778********************9999999999998766655544.57777767 PP

                                   .....HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B- CS
                   PAPS_reduct  81 .....aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipyn 156
                                         +++i+Kv+pl++aL++ld  a++tG+Rr+++ +r k++ +e+d+ +   ++++Pl++Wt+e+vw+yi+r+n+pyn
  gi|70607911|ref|YP_256781.1| 114 vefrkLCCEIRKVKPLQRALKGLD--AWITGLRREQNVTRTKIKKIEVDQVNGGIIKINPLADWTWEQVWDYIKRNNLPYN 192
                                   999999******************..******************************************************* PP

                                   CCCCTT-SS--BCTTB-S CS
                   PAPS_reduct 157 pLydqgfrsiGcvpctga 174
                                   +Lyd g++siGc pct+a
  gi|70607911|ref|YP_256781.1| 193 KLYDMGYKSIGCEPCTRA 210
                                   ****************86 PP

>> RsfS  Ribosomal silencing factor during starvation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.8e-06     0.017       7      56 ..      37      86 ..      34     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                                  HHHTT-EEEEEEE-TTTTBSS-SEEEEEEESSHHHHHHHHHHHHHHHHHC CS
                          RsfS  7 ledkkaedivvidlrekkssladymviatakserhlkalaeelekklkee 56
                                  ++  +aediv++d+ ++  +   ++vi t++ ++  ++l++el+ k+ ++
  gi|70607911|ref|YP_256781.1| 37 ACSLQAEDIVILDMMNQVVDKPIIFVIDTGRLNQETYNLIDELRTKYPKT 86
                                  567799**********8888889*********************998554 PP

>> Peptidase_S8_N  N-terminal of Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.9e-05      0.17      31      81 ..      74     126 ..      62     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                Peptidase_S8_N  31 ksldevlaelgavelervfpvdgkfeertrkaGLhlWYd.vkfde.svdlsea 81 
                                   + +de+ +++ ++e++  fp+++++e+   ++G +l Y+ v+f +   +++++
  gi|70607911|ref|YP_256781.1|  74 NLIDELRTKYPKTEIRIYFPDKEEVEDMVNRYGVNLFYKsVEFRKlCCEIRKV 126
                                   568999999*****************************658887744455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1629.47
//
Query:       gi|70607912|ref|YP_256782.1|  [L=411]
Description: sulfate adenylyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-78  263.2   0.0    1.9e-78  262.8   0.0    1.2  1  ATP-sulfurylase  ATP-sulfurylase
    2.3e-41  141.1   0.1    3.7e-41  140.4   0.1    1.3  1  PUA_2            PUA-like domain
    0.00087   18.8   0.4    0.00087   18.8   0.4    1.9  3  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.095   12.4   0.5        1.5    8.6   0.0    2.6  2  DUF309           Domain of unknown function (DUF309)
       0.17   11.3   0.7       0.27   10.7   0.7    1.3  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.0   5.3e-82   1.9e-78       2     211 ..     161     381 ..     160     382 .. 0.95

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 5.3e-82
                                   CCB.-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHHTSE.E.........EEEEEB-SB-STTSTTHHHHHHH CS
               ATP-sulfurylase   2 eyrltPaevreefkekgwdkVvAfqtrnplHraHeellkraleeead.g.........lllhplvgptkpgdvpaevrvra 72 
                                   +++ltP++ re f+++gw+kVvAfqtrn++H++He+l+k a+ + a+ g         +l++ ++g+++ gd+ +e+++ +
  gi|70607912|ref|YP_256782.1| 161 DFWLTPRQHRELFERMGWKKVVAFQTRNVPHTGHEYLMKFAWFA-ANdGlrvdeprtgILVNVVIGEKRIGDYIDEAILLT 240
                                   69*****************************************6.4433455556666*********************** PP

                                   HHHHHHH.HS-GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHH.CTSEE CS
               ATP-sulfurylase  73 yealiee.ylpkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvage.lgiep 151
                                   ++al+++ y+ k++++l+++ ++mryaGprEallhaiir+n+Gcth+++Grdhagvg++Y py+a+e+++k++++ l i+p
  gi|70607912|ref|YP_256782.1| 241 HKALVDAgYISKRVHKLSFTLWDMRYAGPREALLHAIIRTNLGCTHHVFGRDHAGVGNYYSPYEAHEIFSKINEDdLLIKP 321
                                   **********************************************************************988777***** PP

                                   EE---EEEETTTTEEEECCCCGCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHH CS
               ATP-sulfurylase 152 vkfeeavYckkegevasektchkkeevesisgtelrkllregeeipewfsrpevlkvLre 211
                                   v+++e +Yc+k+g++++  +c+++++ +++sg+ +r+++ ++ ++ ++++rpev++vL+e
  gi|70607912|ref|YP_256782.1| 322 VFIRENYYCPKCGTIENDILCDHDSDKQEFSGSLIRSIILDEVRPTKMVMRPEVYDVLME 381
                                   **********************************************************97 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.4   0.1     1e-44   3.7e-41      22     158 ..      16     151 ..       7     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 1e-44
                                   HHHHHTS-EEE--HHHHHHHHHHHTTTTTT-SCC--HHHHHHHHHHSEETTS-E-SS---EEEECCHCHHHTT-SEEEEEE CS
                         PUA_2  22 lkeakelpsielskrelqdlellaeGgfsPLegFmreedyesvleemrLadgllwsiPivLdvseedakklkegdrvaLkd 102
                                    ++ kel+ +e++++ +++++++++G+ sPL+gFm+ e++++v+eemrL +g+lw+iPivLd +e +a+++kegd +  ++
  gi|70607912|ref|YP_256782.1|  16 INDFKELKLVEVKRQLAHEIISISYGFLSPLRGFMNYEEVDNVVEEMRLPNGVLWPIPIVLDLNESEAEEVKEGDVIGFTY 96 
                                   556788999************************************************************************ PP

                                   TTTEEEEEEEEEEEEE-HHHHHHHHHHS---TTSHHHHHHCTS-SEEEEEEEEE-S CS
                         PUA_2 103 kegellAileveeiyeldkeeeaekvfgttdeaHPgvkkvleqgevlvgGkvevle 158
                                     g++lA+++vee++++dk ++aekv++t+d +HPgvk++l+ +e  v+G+v +++
  gi|70607912|ref|YP_256782.1|  97 M-GKPLAVMRVEEKFSYDKGKMAEKVYKTRDVKHPGVKRTLSYKEKFVSGEVYLVN 151
                                   *.**************************************************9986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.3   8.3e+03      28      40 ..      58      70 ..      57      70 .. 0.82
   2 ?   -4.1   0.0       3.4   1.2e+04      28      38 ..     106     116 ..     106     117 .. 0.84
   3 !   18.8   0.4   2.4e-07   0.00087      17      43 .]     325     351 ..     322     351 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.3
                                  EEEECCCCCCCHH CS
                  TF_Zn_Ribbon 28 Vlednsidegpew 40
                                  V+e++   +g+ w
  gi|70607912|ref|YP_256782.1| 58 VVEEMRLPNGVLW 70
                                  9999999888877 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.4
                                   EEEECCCCCCC CS
                  TF_Zn_Ribbon  28 Vlednsidegp 38 
                                   V e +s+d+g+
  gi|70607912|ref|YP_256782.1| 106 VEEKFSYDKGK 116
                                   78999999986 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.4e-07
                                   TTCEEESSSSBEEEECCCCCCCHHHHH CS
                  TF_Zn_Ribbon  17 rgelvCtdCGlVlednsidegpewref 43 
                                   r +++C++CG++  d  +d+ ++++ef
  gi|70607912|ref|YP_256782.1| 325 RENYYCPKCGTIENDILCDHDSDKQEF 351
                                   679**********************98 PP

>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00042       1.5      23      54 ..     261     293 ..     260     298 .. 0.89
   2 ?    1.2   0.2     0.082   2.9e+02      13      20 ..     302     309 ..     296     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00042
                        DUF309  23 lW.keageperkllqglIqlAvAlyhlrrgnvr 54 
                                   lW +++  p++ ll+++I+   +++h+  g+ +
  gi|70607912|ref|YP_256782.1| 261 LWdMRYAGPREALLHAIIRTNLGCTHHVFGRDH 293
                                   799999999*****************9998876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.082
                        DUF309  13 ffeaHEvl 20 
                                   ++eaHE++
  gi|70607912|ref|YP_256782.1| 302 PYEAHEIF 309
                                   7*****97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   7.6e-05      0.27       2      21 ..     327     344 ..     326     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.6e-05
                   zf-ribbon_3   2 tvrCPnCGaplssddnvCpy 21 
                                    ++CP+CG++  + d+ C +
  gi|70607912|ref|YP_256782.1| 327 NYYCPKCGTI--ENDILCDH 344
                                   689******9..88888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 2336.83
//
Query:       gi|70607913|ref|YP_256783.1|  [L=101]
Description: hypothetical protein Saci_2204 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 713.51
//
Query:       gi|70607914|ref|YP_256784.1|  [L=311]
Description: NAD-dependent alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-24   84.2   1.0    9.3e-23   80.2   1.0    2.2  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    9.5e-17   61.2   0.0    1.2e-15   57.6   0.0    2.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.6e-12   48.6   0.1    3.7e-12   47.5   0.0    1.7  2  ADH_zinc_N_2     Zinc-binding dehydrogenase
    1.7e-06   27.7   0.1    2.6e-06   27.1   0.1    1.2  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00066   19.2   0.1     0.0011   18.5   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.031   13.4   0.1      0.047   12.8   0.1    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.053   13.0   0.3       0.17   11.3   0.1    1.8  2  adh_short        short chain dehydrogenase
      0.057   12.9   0.1        0.1   12.1   0.1    1.4  1  Citrate_bind     ATP citrate lyase citrate-binding
      0.057   13.5   0.0       0.13   12.4   0.0    1.6  1  NADH_4Fe-4S      NADH-ubiquinone oxidoreductase-F iron-sulfur
       0.15   11.4   0.2       0.25   10.6   0.2    1.3  1  ThiF             ThiF family
       0.19   10.8   0.2       0.96    8.5   0.2    1.9  1  RmlD_sub_bind    RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   1.0   5.7e-26   9.3e-23       4     109 .]      26     120 ..      23     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 5.7e-26
                                   EEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTB CS
                         ADH_N   4 vlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeea 84 
                                   v+++v+a+giCg Dl ++kg    + klplilGHEivG             +G+ V+v+p+ scg+C++Ck g+enlCe+a
  gi|70607914|ref|YP_256784.1|  26 VVVDVAATGICGRDLVVWKG-GFRNLKLPLILGHEIVGY-----------YKGKPVAVYPNLSCGNCEYCKAGKENLCENA 94 
                                   99******************.6**************995...........679**************************** PP

                                   EETTTS.S-SSSBSEEEECGGGEEEE CS
                         ADH_N  85 kllgvs.ldGgfaeyvvvpekklvkl 109
                                   k++g + + Gg+ e+v++pek+l++l
  gi|70607914|ref|YP_256784.1|  95 KIIGEGeITGGYGEKVIAPEKNLIPL 120
                                   *****99****************985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   7.4e-19   1.2e-15       1     128 [.     161     273 ..     161     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 7.4e-19
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   gvG+++vq++k++G+ ev++  s+    +++k+lGa+ +   k+             e++d+vfe vG  +t++++l++lk
  gi|70607914|ref|YP_256784.1| 161 GVGVHLVQYLKHIGIkEVYGLTSKV---DKLKELGATPITQIKN-------------EKFDAVFELVG-SKTINDSLRSLK 224
                                   8*******************98766...579*****99998844.............68*********.************ PP

                                   EEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdll 128
                                   + G+lv++G ++ge    ++++  ++++ +i+Gs  ++ +ee++ea++++
  gi|70607914|ref|YP_256784.1| 225 KEGTLVLIGNVEGEPItlLRPALTVMRQQKIVGSAAYT-KEEYEEAIRII 273
                                   *********9777666566777688*************.*******9975 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.3   1.5e+04      24      40 ..     129     144 ..     122     168 .. 0.45
   2 !   47.5   0.0   2.2e-15   3.7e-12      16     133 .]     197     308 ..     173     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.3
                                   EEEEES-HHHHH.HHHH CS
                  ADH_zinc_N_2  24 Dvvldtvggealleasl 40 
                                    ++ld v+++ + +a l
  gi|70607914|ref|YP_256784.1| 129 AAALDPVATAIH-SAKL 144
                                   444444443333.2222 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 2.2e-15
                                   HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHH CS
                  ADH_zinc_N_2  16 aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaa 95 
                                   +++++e++D+v+++vg++++  +sl+ l+++G+lv ig     + +ll+pa+    r+ k++      a+  +++ ee  +
  gi|70607914|ref|YP_256784.1| 197 TQIKNEKFDAVFELVGSKTI-NDSLRSLKKEGTLVLIGnVEGEPITLLRPAL-TVMRQQKIVGSA---AY-TKEEYEEAIR 271
                                   5777899*********9999.*******888*******44447888888888.434444444443...56.6777****** PP

                                   HHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                  ADH_zinc_N_2  96 lieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                    i e+k+++  + +++le+++eA+r+l+++  +G+ Vl
  gi|70607914|ref|YP_256784.1| 272 IIGENKIKIIYE-SYELERINEAYRKLANREIFGRAVL 308
                                   *********998.8********************9997 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1   1.6e-09   2.6e-06      30     201 ..     149     296 ..     128     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.6e-09
                   Glu_dehyd_C  30 epesalvlGaG.slGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaTG 109
                                   + +++lv+GaG  +G+  +  l++   g+++vy l        ++d ++elGat +        +i   +e++d v+E  G
  gi|70607914|ref|YP_256784.1| 149 KDSKVLVTGAGgGVGVHLVQYLKH--IGIKEVYGLTS------KVDKLKELGATPI-------TQI--KNEKFDAVFELVG 212
                                   456799***963699999999985..799*9999984......788899****966.......467..5789********* PP

                   Glu_dehyd_C 110 sakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvv 190
                                   s k + ++++ l+ +G  +L+G  e++ + +   +l    v++ + +vGs     +++e+a++ + + +     +++ + +
  gi|70607914|ref|YP_256784.1| 213 S-KTINDSLRSLKKEGTLVLIGNVEGEPITLLRPAL---TVMRQQKIVGSAAYTKEEYEEAIRIIGENKI----KIIYESY 285
                                   7.7899*****************9999888887777...489999******************9998876....5778899 PP

                   Glu_dehyd_C 191 dldeleeAfed 201
                                   +l++++eA+++
  gi|70607914|ref|YP_256784.1| 286 ELERINEAYRK 296
                                   99999999975 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   6.8e-07    0.0011       1      80 [.     153     219 ..     153     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.8e-07
                                   EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHH CS
                     Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaas 80 
                                   +lVtGa G +G +lv++l+  g++ v gl+++ +             +l+ + ++ ++++ k+e++dav+ l + +++++s
  gi|70607914|ref|YP_256784.1| 153 VLVTGAGGGVGVHLVQYLKHIGIKeVYGLTSKVD-------------KLKELGATPITQI-KNEKFDAVFELVGSKTINDS 219
                                   79********************666*******33.............3333344444443.33477777777666666665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.9e-05     0.047       1      64 [.     153     215 ..     153     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvr 64 
                                   vlvtGagG +G +lv+ + +  +k+++ l ++  kl e+  +  +++k++k+++  + ++g+ +
  gi|70607914|ref|YP_256784.1| 153 VLVTGAGGGVGVHLVQYLKHIGIKEVYGLTSKVDKLKELGATPITQIKNEKFDAV-FELVGSKT 215
                                   8****************************99999999999997788888887544.55666544 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.17       2      42 ..     152     193 ..     151     224 .. 0.79
   2 ?   -1.3   0.0      0.75   1.2e+03      20      60 ..     249     289 ..     245     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                   EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHH CS
                     adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevak 42 
                                    vlvtGa++G+G  +++ l   G+k v  + ++ +kl+e+ +
  gi|70607914|ref|YP_256784.1| 152 KVLVTGAGGGVGVHLVQYLKHIGIKEVYgLTSKVDKLKELGA 193
                                   59*********************9988877777777766543 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.75
                                   HHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTS CS
                     adh_short  20 lakeGakvvvvdrseekleevakelkeegakalaiqvDvtd 60 
                                   +++++  v  +++++e+ ee++  ++e++ k+++ ++ ++ 
  gi|70607914|ref|YP_256784.1| 249 VMRQQKIVGSAAYTKEEYEEAIRIIGENKIKIIYESYELER 289
                                   56666666669999999999999999999888887777764 PP

>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.2e-05       0.1       5      47 ..     124     168 ..     121     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                  Citrate_bind   5 keeayiaeldaktga..slKltvlnpkgriwtlvaGGGasvvyaD 47 
                                   + e+y a ld  + a  s Kl+ ln+++++    aGGG+ v ++ 
  gi|70607914|ref|YP_256784.1| 124 EMEKYAAALDPVATAihSAKLANLNKDSKVLVTGAGGGVGVHLVQ 168
                                   568999999977665559*********************997655 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-05      0.13       9      41 ..      71     103 ..      67     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                                   HHHHH--S--HHHHIIIIHHHHHHHHHTBT--- CS
                   NADH_4Fe-4S   9 fyaaesCGkCtpCreGtkrllelleriaagegt 41 
                                   +y + sCG C  C+ G + l e  + i +ge t
  gi|70607914|ref|YP_256784.1|  71 VYPNLSCGNCEYCKAGKENLCENAKIIGEGEIT 103
                                   67788***************9999988888765 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00016      0.25      15      44 ..     146     177 ..     128     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                   HHHT.SEEEEE--S.HHHHHHHHHHHHHTTTE CS
                                   xxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          ThiF  15 kLrd.skvllvGaG.glGsellknLalsGvgk 44 
                                    L++ skvl+ GaG g+G  l+++L  +G+++
  gi|70607914|ref|YP_256784.1| 146 NLNKdSKVLVTGAGgGVGVHLVQYLKHIGIKE 177
                                   34335********737*************987 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2   0.00059      0.96       2      37 ..     152     187 ..     151     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00059
                                   EEEEESTTSHHHHHHHHHCTTTSE.EEEEE-TTT--T CS
                 RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeegl.evlaltreeldl 37 
                                   k+lvtGa+G +G +L++ l++ g+ ev++lt++ +d 
  gi|70607914|ref|YP_256784.1| 152 KVLVTGAGGGVGVHLVQYLKHIGIkEVYGLTSK-VDK 187
                                   79******************9998346666544.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1762.27
//
Query:       gi|70607915|ref|YP_256785.1|  [L=374]
Description: hypothetical protein Saci_2206 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00014   21.8   0.3    0.00048   20.1   0.1    2.0  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.29   11.0   0.0    1.4  1  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.3   1.1e+04      66      74 ..     172     180 ..     163     192 .. 0.58
   2 !   20.1   0.1   5.3e-08   0.00048      20      82 ..     291     358 ..     287     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                                   TSCHHHHCC CS
                Lip_prot_lig_C  66 kidlseyfg 74 
                                   kid++e ++
  gi|70607915|ref|YP_256785.1| 172 KIDVQEMIN 180
                                   333333333 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.3e-08
                                   EEEEETTEEEEEEEEESBSS..SSHCHHHHHHHTTSBSS.HHHHHHHHHTSCHHHHCC..THHHHHHH CS
                Lip_prot_lig_C  20 rldvekgiIkdikiyGDffg..pkdieeleekLigvkye.keaieealekidlseyfg..gieleell 82 
                                   +l  +   Ikdi i+GDf    ++ + ele+kL+gv+++ ke+i+++++++   + f+   ++ e+++
  gi|70607915|ref|YP_256785.1| 291 HLLTDGKEIKDIMISGDFYCspSEYLFELEQKLKGVPLDdKEKISNIVNSMFARKNFEmpMVKGEDIV 358
                                   77778899**********95437778***********9637899999999887777776555556655 PP

>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.29       2     129 ..      54     171 ..      53     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                                   EEEES-HHHHHH..GCGGG--TT-EEEEEEE.SS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH.. CS
                 BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrq.tgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgy 81 
                                   g++++        ++n++e   +g++v+rr  +gG  ++ s kg  +  +++ p++  f+  ++e   +++  a+++a+  
  gi|70607915|ref|YP_256785.1|  54 GYFQDVD-----TEVNLDEARRRGVDVIRRLgVGGGTIYAS-KGSSMAMFMTFPKD-FFT--NMEKAFCQIGSAAVHAY-- 123
                                   5666664.....67899999999999999961566677777.88888888888776.666..78888888899999999.. PP

                                   ....HHTT-TTEEEETTTEEEE....TTEEEEEEEEEEEETTS-EEEEEEEE CS
                 BPL_LplA_LipB  82 rdskpgiegipvfikwpnDlyv....ngrKlaGiavtstrgktlhhivigvg 129
                                      k g +g++       D+ v     +rK++G++ t++    + ++vigvg
  gi|70607915|ref|YP_256785.1| 124 --FKLGVKGAWYD--HIGDVRVgsprAYRKITGFGFTTIEDILVLNMVIGVG 171
                                   ..34588888888..77788889999************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2319.65
//
Query:       gi|70607916|ref|YP_256786.1|  [L=495]
Description: 4-coumarate-CoA ligase 1 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-68  231.1   0.0    2.1e-68  230.8   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    3.7e-08   34.2   0.1    6.7e-08   33.4   0.1    1.4  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.8   0.0   2.4e-72   2.1e-68       3     422 ..      28     416 ..      26     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: 230.8 bits;  conditional E-value: 2.4e-72
                                   HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                   AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                   ++++++ d + lv+  eg+ ++Y+ l++ ++r+A++L+++G+kkgd + +++ n p+ + ++++  ++G+ v+ ++p ++ 
  gi|70607916|ref|YP_256786.1|  28 KSVKEKGDLTLLVF--EGKEFSYSSLYSFAKRFASYLKEHGLKKGDAISLIMSNAPQVIPVFFGSSMLGVRVALIDPLSSG 106
                                   6789999*******..**********************99***************************************** PP

                                   HHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEE CS
                   AMP-binding  84 eelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayi 164
                                   ++l+y+l+ +++k+++  +++e  ++ +e      + +   v + ++l      ++ ++s++++    e+e + ++d+a+ 
  gi|70607916|ref|YP_256786.1| 107 KDLEYQLSLTDPKMIV--TEEEIYKREKE------VMSRYNVFSFNSL------NDLDSSPNVD----EVEINPKEDIAVS 169
                                   ****************..76554222222......2223333443332......3333333232....34457889***** PP

                                   EEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHH CS
                   AMP-binding 165 iYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkll 245
                                   +   G  G+   V ++h  l+++ +  +l +  +++e++++l  lp++hifgl  +ll +++  +++vl+++ ++   ++ 
  gi|70607916|ref|YP_256786.1| 170 MHYAGIIGRTYEVYHTHYGLISSNYVSSLVRAGEIGEENTILISLPISHIFGL-DALLETIMERGKIVLMRRYDP---NRA 246
                                   *****************888766444344445667899**************9.*****************6655...566 PP

                                   HHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECE CS
                   AMP-binding 246 lelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvt 325
                                   l+li+++kvt+++++P v++ +l   ++        +  sl+l+++g++p++p+l++++ + +  +++++YGlTE ++v++
  gi|70607916|ref|YP_256786.1| 247 LDLIREYKVTTWPAPPMVFKEILPnLKK--------EKFSLKLCITGAAPVPPDLQKAYFEELNLPLVQTYGLTEGLIVTY 319
                                   9*********************983422........3346**********************999*************998 PP

                                   ECHCTTTCTSTTS-BEE-TTEEEEEE-TTTS.CBEETTSEEEEEEEETTS-SEBTT-....HHHHHHHEEETCCEEEEEEE CS
                   AMP-binding 326 vlpleedkkklgsvGkplpgvevkivDeetg.epvpdgeeGellvrgpgvmkgYlkk....peataeafdsegrwlrTGDl 401
                                     p   + k+ gsvG plpgv+++ivD etg + vp g+ Gel v++p++mkgY  +     ++ ++a++  ++wl TGD+
  gi|70607916|ref|YP_256786.1| 320 -QP--ANLKVYGSVGIPLPGVKIRIVDKETGtKDVPIGQDGELIVKSPWNMKGYGSHgildIQESSKAIK--DGWLYTGDI 395
                                   .44..455699****************99974689*******************9886664577777776..57******* PP

                                   EEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 402 grldedGyleivgRkkdlikl 422
                                     +d++G l++ g kk  +k 
  gi|70607916|ref|YP_256786.1| 396 FMMDQNGLLYFRGLKKRFLKY 416
                                   *************99988775 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   7.5e-12   6.7e-08       3      69 ..     427     495 .]     425     495 .] 0.90

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 7.5e-12
                                   HHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHHHT-TTTS-SEEEE-S-- CS
                 AMP-binding_C   3 EsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrkelgpyavpkkvvfvdel 69 
                                   E  l +hpaV+ a+V G  d+  G+ + a V lk++ + +  eee++ +v+++++ y++ +k++fvd+l
  gi|70607916|ref|YP_256786.1| 427 ELLLEEHPAVKRAYVDGEWDPEVGHKVFAKVLLKEEyKgKVSEEEIMNFVNDKVAFYKKIRKIIFVDSL 495
                                   77899****************************9764233489***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 3054.92
//
Query:       gi|70607917|ref|YP_256787.1|  [L=657]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-64  217.2   1.1    3.1e-64  216.2   1.1    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    4.2e-52  176.9   0.0    7.6e-52  176.1   0.0    1.4  1  ECH_1            Enoyl-CoA hydratase/isomerase
      1e-44  151.1   0.1    2.4e-23   82.5   0.1    2.6  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    2.3e-35  122.7   0.6    8.8e-35  120.8   0.1    2.1  2  ECH_2            Enoyl-CoA hydratase/isomerase
    0.00064   19.9   0.0     0.0017   18.5   0.0    1.8  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0019   17.5   0.1     0.0035   16.6   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.017   14.5   0.1      0.034   13.5   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.023   14.2   0.0      0.054   13.1   0.0    1.7  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.028   15.0   0.1       0.09   13.4   0.1    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.049   14.3   0.1       0.18   12.5   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
      0.094   12.7   0.1       0.33   10.9   0.0    2.0  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.11   12.0   0.0       0.27   10.7   0.0    1.6  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
       0.12   12.9   0.1        1.2    9.8   0.3    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.21   11.6   1.5       0.72    9.9   0.2    2.4  2  Dimerisation     Dimerisation domain
        2.4    8.5   4.3        7.3    6.9   0.2    3.3  4  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.2   1.1   2.6e-67   3.1e-64       2     179 ..       7     184 ..       6     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.2 bits;  conditional E-value: 2.6e-67
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEE CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlv 82 
                                   v+v+GaGtmG+gia+v+a ag++Vvl+d++e++l++aleki+ slekl ek+++k e+ +++l+ri++t ++ ++ d+d++
  gi|70607917|ref|YP_256787.1|   7 VGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEDILRNALEKIRWSLEKLREKRQIK-ENPNTVLSRIKTTVSFGDFSDVDFI 86 
                                   9*****************************************************9.99*********************** PP

                                   EE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHH CS
                       3HCDH_N  83 iEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvatv 163
                                   iEa++E+ ++Krk+f el++++k+dai+a+nTS+++is lae++ r+e++iglHF+nPp lm+LvE++ g+kT+eet++t+
  gi|70607917|ref|YP_256787.1|  87 IEAAIERSDVKRKIFSELDRVVKKDAIFATNTSTIPISYLAEVTGRQEKFIGLHFMNPPVLMPLVEIIMGNKTAEETLKTT 167
                                   ********************************************************************************* PP

                                   HHHHHHTT-EEEEE.CS CS
                       3HCDH_N 164 velakkigktpvvv.kd 179
                                    +lakki+k  vvv kd
  gi|70607917|ref|YP_256787.1| 168 IDLAKKINKDYVVVkKD 184
                                   **************666 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1   0.0   6.4e-55   7.6e-52       7     250 ..     414     656 ..     409     657 .] 0.89

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 6.4e-55
                                   EEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCH.HHHHHHHH CS
                         ECH_1   7 aviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeev.lelwtkly 85 
                                   a+i++ r +++Nal++++   l++a++k++dd ++ravv+tG ++aF+aG d++ m   +  a + + +e++   l ++l+
  gi|70607917|ref|YP_256787.1| 414 AKITMSRADKLNALNEAMWSGLTEAFKKAKDDSEIRAVVITGEGRAFCAGDDIEMMNYWGSvAGAMEWNEKFsSPLINLLL 494
                                   79*****************************************************988877455555555552468999** PP

                                   HSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHH CS
                         ECH_1  86 tvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealk 166
                                   + pkpvi+avnG a+gGG+el +  Di++a+d+a f+ +e ++G +p+  ++ + +  + +++A++ +l+g+ +sa+ a++
  gi|70607917|ref|YP_256787.1| 495 NYPKPVISAVNGLAFGGGMELNILFDIIVASDDAMFAIPEGLIGALPP-LASSMGVGFISRKIARY-ALTGDWMSAKQAKE 573
                                   ***********************************************5.56778888999999887.589*********** PP

                                   CTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH-- CS
                         ECH_1 167 vGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrkpe 247
                                    Glvd vvp++ql+  ++e++ek  + +p++  ++k a+n   ++ l++   a ++l+  + +++d+keG+ af+E+r+p+
  gi|70607917|ref|YP_256787.1| 574 LGLVDIVVPHDQLEIATVEIVEKAKKIAPLSSMAIKRAVNSIRNSYLQQLQSASQDLL-ILSATEDFKEGMRAFVERRQPK 653
                                   *************************999999999999999876676666666666665.577788**************** PP

                                   --- CS
                         ECH_1 248 fed 250
                                   +++
  gi|70607917|ref|YP_256787.1| 654 YKG 656
                                   *97 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1     2e-26   2.4e-23       1      97 []     187     281 ..     187     281 .. 0.94
   2 !   66.1   0.0   2.8e-21   3.4e-18       6      97 .]     304     395 ..     298     395 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 2e-26
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHH.HHHHHHHTTTH.GGHH-HHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakki.levlaeelger.ayapspllek 79 
                                   GF  nR+ ++++ eav l++eg  s ediDa+ r +lG+pmG++el+d +g+dva+++ le+++++ ge+ +++   +l+k
  gi|70607917|ref|YP_256787.1| 187 GFLINRINGRTFPEAVLLYDEG-YSKEDIDAMSRFRLGMPMGFLELMDFTGIDVAYNAgLEAIKRGEGEPpHFK---VLKK 263
                                   9*********************.********************************9872568888888887777...**** PP

                                   HHHTT--BGGGTBSSSBC CS
                         3HCDH  80 lveagrlgrktgkgfyky 97 
                                   lve+grlg k+gkgfy+y
  gi|70607917|ref|YP_256787.1| 264 LVEEGRLGIKSGKGFYTY 281
                                   ****************98 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 2.8e-21
                                   HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT-- CS
                         3HCDH   6 RvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrl 86 
                                   R++ap +nea +++ + v s++di++ m +g+++p Gp++ +d +g+d ++k le  +e++++++y+p pll+++v++g+l
  gi|70607917|ref|YP_256787.1| 304 RIIAPAVNEAAWILRNDVSSAQDIEKGMVKGMNWPQGPLTFADKYGIDNVLKFLEERYEVTKNEYYKPDPLLTEMVSKGKL 384
                                   9******************************************************************************** PP

                                   BGGGTBSSSBC CS
                         3HCDH  87 grktgkgfyky 97 
                                   g k+g+gf+k+
  gi|70607917|ref|YP_256787.1| 385 GVKSGEGFFKW 395
                                   ********987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.2   2.7e+03     176     241 ..      43     107 ..      28     121 .. 0.57
   2 !  120.8   0.1   7.3e-38   8.8e-35       3     208 ..     415     621 ..     413     653 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                                   GHHHHHHHHHTT..........--------......----SHHHHHHHHHHHT.-S-TT.THHHHHH.T CS
                         ECH_2 176 klealeeaLaelessd..eeaveevleelaeeaeeeeeeselaekreaidrlfsadsve.eiveaLeka 241
                                   +le+++ +L++l++++  +e+ ++vl++++++++      ++++    i++++++++v+ +i+++L++ 
  gi|70607917|ref|YP_256787.1|  43 ALEKIRWSLEKLREKRqiKENPNTVLSRIKTTVS----FGDFSDVDFIIEAAIERSDVKrKIFSELDRV 107
                                   4556666666665554555666666666554433....3555555567777776665532677777653 PP

  == domain 2  score: 120.8 bits;  conditional E-value: 7.3e-38
                                   EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH..HHH CS
                         ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk..lny 81 
                                    it+ r ++lNaL+ +m + l+ea+k+ ++d+e+++vv++g+g +afCAG D++++    +   + e   ++e+++  l +
  gi|70607917|ref|YP_256787.1| 415 KITMSRADKLNALNEAMWSGLTEAFKKAKDDSEIRAVVITGEG-RAFCAGDDIEMMNYWGSVAGAME---WNEKFSspLIN 491
                                   69***************************************88.************99988876664...5555543399* PP

                                   HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHHH CS
                         ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgada 162
                                   l+ +ypkpv++ ++G++ GgG+ l +   + v++++++fA+PE  IG  P  + s+    ++ ++++y alTG+ +++++a
  gi|70607917|ref|YP_256787.1| 492 LLLNYPKPVISAVNGLAFGGGMELNILFDIIVASDDAMFAIPEGLIGALPPLASSMGVGFISRKIARY-ALTGDWMSAKQA 571
                                   *******************************************************************9.9*********** PP

                                   HHTTS--EE--GGGHHHHHHHHHTT............--------..... CS
                         ECH_2 163 laaglathyvpseklealeeaLaelessd....eeaveevleelaeeaee 208
                                    ++gl + +vp+++le  + ++ e  ++     + a+++++++++++  +
  gi|70607917|ref|YP_256787.1| 572 KELGLVDIVVPHDQLEIATVEIVEKAKKIaplsSMAIKRAVNSIRNSYLQ 621
                                   ***************99998888864443677744444544444443333 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0017       1      94 [.       6     123 ..       6     147 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..........EEE-SSHHHHHHHC............SEE CS
                 NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..........akaaesieelvasl............dvv 59 
                                   ++g++G G+MG+ +a+ ++ ag++v++ +++++ +++++++            ++ e+++ +++++            d++
  gi|70607917|ref|YP_256787.1|   6 RVGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEDILRNALEKIrwsleklrekRQIKENPNTVLSRIkttvsfgdfsdvDFI 86 
                                   58******************************9999999886677777666633333333333333333333444444666 PP

                                   EE-SSSHHHHHHHHHS.HCCC--TT-EEEE.-S---H CS
                 NAD_binding_2  60 itmvkagkavdevieg.llealkkgdilid.gstssp 94 
                                   i    + ++v+  i++ l + +kk++i+   +st+ +
  gi|70607917|ref|YP_256787.1|  87 IEAAIERSDVKRKIFSeLDRVVKKDAIFATnTSTIPI 123
                                   6555555555555555466666666666541344444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     3e-06    0.0035     144     211 ..       6      73 ..       2      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidg 211
                                   r+ vvG+G  G  +A + a +g +v+l + ++ +lr+  ++++  le+ +ek+ ++   +t+  +i+ 
  gi|70607917|ref|YP_256787.1|   6 RVGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEDILRNALEKIRWSLEKLREKRQIKENPNTVLSRIKT 73 
                                   789*****************************************************999999998874 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.9e-05     0.034      37      70 ..       5      38 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                  SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                  2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                  ++vG++G+G +G+ +a++++  g++v+ +d++++
  gi|70607917|ref|YP_256787.1|  5 SRVGVVGAGTMGHGIAEVVAIAGFNVVLTDVNED 38
                                  68****************************9866 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.5e-05     0.054       2      36 ..       6      40 ..       5     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekv 36
                                  ++ v+G+G +G   a v+a +g++v++ D++e   
  gi|70607917|ref|YP_256787.1|  6 RVGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEDIL 40
                                  899****************************9755 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.5e-05      0.09       1      49 [.       6      50 ..       6      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvk 49
                                  ++g++GaG mg+++a+ ++ ag    ++v++ + n++ ++ + e++  +
  gi|70607917|ref|YP_256787.1|  6 RVGVVGAGTMGHGIAEVVAIAG---FNVVLT-DVNEDILRNALEKIRWS 50
                                  69********************...999955.88888888888877644 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.18      12      95 ..      21     115 ..       9     116 .. 0.71
   2 ?   -2.8   0.0       8.8   1.1e+04      48      73 ..     611     638 ..     584     649 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                   HHHHHTTSEEEEEES-HHHHHHH.......HHHCCHHT-..........EEEETTEECCCT.SS-T.T-EEEEEEES-CCC CS
               Methyltransf_11  12 ealakrgarvvgvDlskemlkla.......kekaseegl..........kvefvvadaekl.pfed.nsfDlvvssevlhh 73 
                                   e +a +g +vv +D+++  l+ a               +          + + v ++++++  f d + +D+++   +++ 
  gi|70607917|ref|YP_256787.1|  21 EVVAIAGFNVVLTDVNEDILRNAlekirwsL-------EklrekrqikeNPNTVLSRIKTTvSFGDfSDVDFII-EAAIER 93 
                                   3333445899999999999988844444441.......3333333345666779999*98659***77899985.668*** PP

                                   -CCHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  74 vedpekalkeiaRvLkpgGllv 95 
                                    +  +k+++e+ Rv+k++ +++
  gi|70607917|ref|YP_256787.1|  94 SDVKRKIFSELDRVVKKDAIFA 115
                                   *****************99875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.8
                                   TTEECCC..T.SS-TT-EEEEEEES-CCC CS
               Methyltransf_11  48 vvadaek..l.pfednsfDlvvssevlhh 73 
                                    v ++++  l +++++s Dl ++s   + 
  gi|70607917|ref|YP_256787.1| 611 AVNSIRNsyLqQLQSASQDLLILSA-TED 638
                                   2222222222257777777777663.444 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.33       2      33 ..       7      42 ..       6     119 .. 0.83
   2 ?   -2.9   0.0         5   5.9e+03      51      68 ..     158     175 ..     145     183 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                  EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....H CS
                NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvree....e 33
                                  ++v+GaG  G  +A v+a +g +v+l   +e    +
  gi|70607917|ref|YP_256787.1|  7 VGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEdilrN 42
                                  89************************9999955553 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5
                                   ----TTEEEES-HHHHHT CS
                NAD_Gly3P_dh_N  51 iklpenlvattdlaealk 68 
                                    + +e+l+ t dla+ ++
  gi|70607917|ref|YP_256787.1| 158 KTAEETLKTTIDLAKKIN 175
                                   344455555555555555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.27       5      38 ..      14      48 ..       8      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                                  SHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHH CS
                  adh_short_C2  5 gIGraiAkalaeeGaevvltdlneea.kkrveela 38
                                   +G++iA+ +a +G +vvltd+ne+  ++++e++ 
  gi|70607917|ref|YP_256787.1| 14 TMGHGIAEVVAIAGFNVVLTDVNEDIlRNALEKIR 48
                                  69***********************9888877765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00099       1.2       1      69 [.       6      74 ..       6      83 .. 0.90
   2 ?   -0.6   0.0       1.7   2.1e+03      53      70 ..     235     252 ..     227     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00099
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69
                                  +v vvG+G+ g   A++ a  g +V + + ++ +lr+  e+++  l++  ek+ i+   nt++ +i+++
  gi|70607917|ref|YP_256787.1|  6 RVGVVGAGTMGHGIAEVVAIAGFNVVLTDVNEDILRNALEKIRWSLEKLREKRQIKENPNTVLSRIKTT 74
                                  688********************************888888887777777888*********9999976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.7
                                   TTEEEECSEEEEEEEEET CS
                     Pyr_redox  53 ngievllntkveeiegse 70 
                                    gi+v +n+ +e+i+  e
  gi|70607917|ref|YP_256787.1| 235 TGIDVAYNAGLEAIKRGE 252
                                   59***********99554 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.3   1.6e+03       7      22 ..     513     529 ..     512     548 .. 0.65
   2 ?    9.9   0.2    0.0006      0.72       1      45 [.     566     610 ..     566     611 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                  Dimerisation   7 iELgl.ldiiakaggkp 22 
                                   +EL++ +dii+++ +++
  gi|70607917|ref|YP_256787.1| 513 MELNIlFDIIVASDDAM 529
                                   6888637***9997533 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0006
                  Dimerisation   1 mvLKaAiELglldiiakaggkplspsEiaskLptknpeapvlldR 45 
                                   m+ K A ELgl di + +    +++ Ei++k +++ p  ++ ++R
  gi|70607917|ref|YP_256787.1| 566 MSAKQAKELGLVDIVVPHDQLEIATVEIVEKAKKIAPLSSMAIKR 610
                                   77799*************6688*********99987777777766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2    0.0061       7.3       3      39 ..       9      45 ..       7      49 .. 0.87
   2 ?    0.6   0.0      0.55   6.6e+02      38      64 ..      69      95 ..      51      96 .. 0.80
   3 ?   -2.6   0.0       5.5   6.5e+03      42      57 ..     151     166 ..     150     181 .. 0.79
   4 ?   -1.1   0.0       1.9   2.2e+03      64      89 ..     575     600 ..     564     627 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0061
                                  EES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH CS
                        TrkA_N  3 iiGlGrvGrslaeeLseggkdvvvidkdeerveelre 39
                                  ++G+G++G  +ae +  +g +vv+ d +e+ ++++ e
  gi|70607917|ref|YP_256787.1|  9 VVGAGTMGHGIAEVVAIAGFNVVLTDVNEDILRNALE 45
                                  9**************996646********99988765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                                  HHTTSEEEES-TTSHHHHHHTTGGGES CS
                        TrkA_N 38 reeglevvvgdatdeevLeeagiekad 64
                                  ++ +++v  gd +d +++ ea ie+ d
  gi|70607917|ref|YP_256787.1| 69 SRIKTTVSFGDFSDVDFIIEAAIERSD 95
                                  456688999**************9977 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.5
                                   SEEEES-TTSHHHHHH CS
                        TrkA_N  42 levvvgdatdeevLee 57 
                                   +e++ g+ t ee+L+ 
  gi|70607917|ref|YP_256787.1| 151 VEIIMGNKTAEETLKT 166
                                   5688888888888874 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.9
                                   SEEEE-SSSHHHHHHHHHHHHHHTSS CS
                        TrkA_N  64 daviaatgddeanilavllakelnpk 89 
                                    +v +++++d+  i++v+++ +  + 
  gi|70607917|ref|YP_256787.1| 575 GLVDIVVPHDQLEIATVEIVEKAKKI 600
                                   56668888998888887777653332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4134.64
//
Query:       gi|70607918|ref|YP_256788.1|  [L=395]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-25   90.4   0.0      2e-25   89.7   0.0    1.4  1  Thiolase_N      Thiolase, N-terminal domain
    8.2e-09   35.2   0.1    2.4e-06   27.2   0.0    2.8  2  Thiolase_C      Thiolase, C-terminal domain
      1e-07   31.9   5.6      5e-07   29.5   0.9    2.7  3  ketoacyl-synt   Beta-ketoacyl synthase, N-terminal domain
    4.3e-07   29.7   0.2      2e-05   24.3   0.1    2.4  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
     0.0013   18.1   0.0     0.0025   17.2   0.0    1.4  1  FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protei
  ------ inclusion threshold ------
      0.067   11.9   0.2       0.17   10.6   0.1    1.7  2  SpoVAD          Stage V sporulation protein AD (SpoVAD)


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   6.6e-29     2e-25       1     260 []       4     223 ..       4     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 6.6e-29
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+iv++  t++g       d++ +eL  ea+k++le+a++++++++  +vGn     ++   a ++    ++  +  +++v
  gi|70607918|ref|YP_256788.1|   4 VAIVGTGHTKFGV----RTDVNLQELTWEAVKQALEEANLEQKDIEMFVVGNAGGWSSEPLSAIAIGEYCNL-APKGTMRV 79 
                                   799********99....99*********************************99888888888888888899.88899*** PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSE..EEEEHHHHHHTEETTTTSEHHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgde..kakdllipdgladafneehmGltae 160
                                   + +c+ g +a+  a q+i++gea+v++++GvE+m ++p+ ++++++ ++       +  +l+ p            +l a 
  gi|70607918|ref|YP_256788.1|  80 EAACATGSAAIRIAYQAIKSGEAKVALVIGVEQMNQSPHPVAVEMMGRAGNYFWefENFGLTFPG---------YYALYAT 151
                                   ******************************************99996655555500555566666.........7789999 PP

                                   HHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BT CS
                    Thiolase_N 161 nlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtA 241
                                   +  +ky++  e++ ++Avk+h  ++ ++ a  F+++i              + +++++s+v+a +L+ +            
  gi|70607918|ref|YP_256788.1| 152 RRMAKYGMKEEDLGSVAVKNHYYGSYNPYAT-FQKQI--------------KMEDYLKSRVVAYPLKLY------------ 205
                                   9999**************************9.***99..............89****************............ PP

                                   TSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 242 gnasqisDGaaavllmses 260
                                    +a++i+DGaaa++l+se+
  gi|70607918|ref|YP_256788.1| 206 -DACPITDGAAALILASEE 223
                                   .***************986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0063        19      25      50 ..      27      52 ..      10      64 .. 0.85
   2 !   27.2   0.0   8.1e-10   2.4e-06      26     114 ..     261     371 ..     243     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0063
                                  HHHHHHHHHHHT--GGGESEEEE--S CS
                    Thiolase_C 25 ayaikkvlkkagltvedidlfEinEA 50
                                    a+k++l++a l+ +di++f +  A
  gi|70607918|ref|YP_256788.1| 27 WEAVKQALEEANLEQKDIEMFVVGNA 52
                                  5799****************987665 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 8.1e-10
                                   HHHHHHHHHHT--GGG....ESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTT CS
                    Thiolase_C  26 yaikkvlkkagltved....idlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGa 84 
                                    a++++ k+a ++ +d     d+ ++++ F+   +++ ++l++++                    vNv GG  a GHP+Ga
  gi|70607918|ref|YP_256788.1| 261 VATEEAYKRAKIDFSDawryFDVADVHDCFTIAEIMAYEDLGFAKrgeghlmarngetyiggkIPVNVDGGLKAKGHPIGA 341
                                   57778888888887774444699*********************99***************87789*************** PP

                                   HHHHHHHHHHHHHHHCTTSEEEEEEEETTT CS
                    Thiolase_C  85 sGaRivvtllselkkeggklgvaalCiggg 114
                                   +G+ ++v+++++l  + +k + a + +g g
  gi|70607918|ref|YP_256788.1| 342 TGVSMAVSITRQLLYRAHKGTQADIRNGMG 371
                                   ***********9998877766666666665 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.011        34      88     124 ..      22      58 ..      16      77 .. 0.82
   2 !   29.5   0.9   1.7e-10     5e-07     169     212 ..      77     120 ..      74     131 .. 0.84
   3 ?   -3.2   0.0       1.7   5.1e+03     114     126 ..     341     353 ..     328     377 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESST CS
                 ketoacyl-synt  88 qqrllleaawealedagltpeeldgsrvgvfiGvgag 124
                                    q l  ea+++ale+a+l++++++   vg+  G +++
  gi|70607918|ref|YP_256788.1|  22 LQELTWEAVKQALEEANLEQKDIEMFVVGNAGGWSSE 58 
                                   588999**************99998889988888776 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.7e-10
                                   EEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHH CS
                 ketoacyl-synt 169 vtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeava 212
                                   + v++AC+++ +a+  a+q+++sgea+val+ Gve + +    +
  gi|70607918|ref|YP_256788.1|  77 MRVEAACATGSAAIRIAYQAIKSGEAKVALVIGVEQMNQSPHPV 120
                                   679********************************987655444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                                   GEEEEEEESSTHH CS
                 ketoacyl-synt 114 rvgvfiGvgagdy 126
                                   ++gv ++v++  +
  gi|70607918|ref|YP_256788.1| 341 ATGVSMAVSITRQ 353
                                   3666666666643 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   6.7e-09     2e-05       3      38 ..      79     114 ..      77     119 .. 0.94
   2 ?    2.8   0.0     0.036   1.1e+02      53      65 ..     211     223 ..     203     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.7e-09
                                   EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                   ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                                   ++aaC++  +a+ +A ++i+sg+ak +Lvig e++ 
  gi|70607918|ref|YP_256788.1|  79 VEAACATGSAAIRIAYQAIKSGEAKVALVIGVEQMN 114
                                   689******************************986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.036
                                   -EEEEEEEEEEES CS
                   ACP_syn_III  53 GDGAgAvvlease 65 
                                    DGA+A++l  +e
  gi|70607918|ref|YP_256788.1| 211 TDGAAALILASEE 223
                                   6********9874 PP

>> FAE1_CUT1_RppA  FAE1/Type III polyketide synthase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.3e-07    0.0025      84     178 ..      23     116 ..      11     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-07
                FAE1_CUT1_RppA  84 eevlfgavdellaktkvspkdidilvv.ncslfsptPslsamvvnryklredvksynLsgmGCsAglisidlaknllqvhk 163
                                   +e+  +av++ l++++++ kdi+++vv n++ +s++P lsa+ +  y       ++ + +  C+ g  +i +a + ++  +
  gi|70607918|ref|YP_256788.1|  23 QELTWEAVKQALEEANLEQKDIEMFVVgNAGGWSSEP-LSAIAIGEYCNLAPKGTMRVEA-ACATGSAAIRIAYQAIKSGE 101
                                   6778899****************99886888899988.9999999997666666777766.8******************* PP

                FAE1_CUT1_RppA 164 ntlalvvstEnitln 178
                                    ++alv+ +E+++++
  gi|70607918|ref|YP_256788.1| 102 AKVALVIGVEQMNQS 116
                                   ***********9875 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.7e-05      0.17      52     130 ..      23     107 ..      18     123 .. 0.72
   2 ?   -3.4   0.0         1   3.1e+03     162     180 ..     212     230 ..     199     242 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHHHHHHHTT--GGG-SEEEEEES...SGGGHHHHHHHHHH---...EEEB--GGGHHHHHHHHHHHHHHTTS-S CS
                        SpoVAD  52 sklleeavkkalkkanlkkedidfllaGDL...lnqlisssfaarelkiP...flglygaCstsaeslalaallvdggfak 126
                                   ++l  eavk+al++anl+++di++++ G+        +s+    +  ++     + + +aC+t + ++ +a  ++++g ak
  gi|70607918|ref|YP_256788.1|  23 QELTWEAVKQALEEANLEQKDIEMFVVGNAggwSSEPLSAIAIGEYCNLApkgTMRVEAACATGSAAIRIAYQAIKSGEAK 103
                                   568889*******************97764111444444444444444431123455688999888898888888888888 PP

                                   EEEE CS
                        SpoVAD 127 rvla 130
                                    +l+
  gi|70607918|ref|YP_256788.1| 104 VALV 107
                                   7765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                                   -EEEEEEEESS--SEEEEE CS
                        SpoVAD 162 tgagavllakegegpkita 180
                                    ga+a++la+e+   kit 
  gi|70607918|ref|YP_256788.1| 212 DGAAALILASEEVARKITD 230
                                   3555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3096.44
//
Query:       gi|70607919|ref|YP_256789.1|  [L=180]
Description: hypothetical protein Saci_2210 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-13   50.4   0.0    2.5e-13   49.8   0.0    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.8e-11   43.7   0.2    2.7e-11   43.1   0.2    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.018   15.2   3.5      0.035   14.2   0.8    2.2  2  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
       0.13   11.7   0.0       0.16   11.5   0.0    1.1  1  SRAP           SOS response associated peptidase (SRAP)
       0.38   10.6   1.6       0.42   10.5   0.1    1.8  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   6.9e-17   2.5e-13       2      63 ..     103     163 ..     102     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 6.9e-17
                                   EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE CS
                 OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVrav 63 
                                   velsg+G++ ++t++  +p +f  ++ y+vg+ +L eg+ ++a++ + dp ++++Gm+V++ 
  gi|70607919|ref|YP_256789.1| 103 VELSGEGELLTYTIITVKPLSFMHYQDYIVGIARLKEGINVLAWVNE-DPKNIQVGMKVKLS 163
                                   9********************************************96.5788*******986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.2   7.6e-15   2.7e-11       3      32 ..      67      97 ..      65     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.6e-15
                       DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphC.g 32
                                   + +g+L+g++Cp+CGt +fPP+  C+ C +
  gi|70607919|ref|YP_256789.1| 67 YLNQGKLIGTKCPKCGTIYFPPQDDCTSCrL 97
                                  5789*************************55 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.13   4.6e+02      22      32 ..      30      40 ..      30      42 .. 0.80
   2 ?   14.2   0.8   9.9e-06     0.035       5      39 ..      66      95 ..      66      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.13
                 Auto_anti-p27 22 gvPLmrdrkgg 32
                                  g+P+mr++k++
  gi|70607919|ref|YP_256789.1| 30 GMPIMREPKTN 40
                                  79****99644 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 9.9e-06
                 Auto_anti-p27  5 elLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaC 39
                                  e+L +G ++ ++ Cp+Cg++ +  +   +  C +C
  gi|70607919|ref|YP_256789.1| 66 EYLNQG-KLIGTKCPKCGTIYFPPQ--DD--CTSC 95
                                  577777.899************943..35..7777 PP

>> SRAP  SOS response associated peptidase (SRAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05      0.16      91     162 ..      41     122 ..      34     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                          SRAP  91 kplfrsalkk.kRcvvpad...GFYEWkkkgk...ek.....qPyfikrkdgkllalAGLydvweeegeeeklytytiiTt 159
                                   +pl+ ++    +R v+p+     F+E  ++gk   +k     + yf  + d +   l GL  v   +g e +l tytiiT+
  gi|70607919|ref|YP_256789.1|  41 NPLWVDVRDLtQRYVIPIGkiyKFFEYLNQGKligTKcpkcgTIYFPPQDDCTSCRLSGLTTVE-LSG-EGELLTYTIITV 119
                                   566666666558888887522268888434433333411132445555555599******9876.666.689********9 PP

                          SRAP 160 ean 162
                                   ++ 
  gi|70607919|ref|YP_256789.1| 120 KPL 122
                                   864 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00012      0.42       8      25 ..      70      87 ..      67      91 .. 0.75
   2 ?   -1.0   0.1      0.46   1.6e+03      16      21 ..      92      97 ..      86      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                     zf-C2H2_3  8 qksfgasqCkeCgMvYnp 25
                                  q +   ++C++Cg +Y p
  gi|70607919|ref|YP_256789.1| 70 QGKLIGTKCPKCGTIYFP 87
                                  44555579********98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.46
                     zf-C2H2_3 16 CkeCgM 21
                                  C+ C +
  gi|70607919|ref|YP_256789.1| 92 CTSCRL 97
                                  ****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1351.69
//
Query:       gi|70607920|ref|YP_256790.1|  [L=555]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-85  287.3   0.0    1.9e-85  287.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.3e-22   79.2   0.0    7.6e-22   78.1   0.0    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.0   0.0   2.1e-89   1.9e-85      16     422 ..      36     449 ..      21     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: 287.0 bits;  conditional E-value: 2.1e-89
                                   E....CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHH CS
                   AMP-binding  16 d....sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayile 91 
                                   d    +ge + l Y+ + +rv+++A++L+ +l+vk+ d+V+i+ +n ++++ +++ + ++G+v+  ln +l + +l yi++
  gi|70607920|ref|YP_256790.1|  36 DrrlqGGELHILNYGKVLDRVRSMANALEkELDVKPSDVVGIIDWNDHRFFESYFSVPSIGGVLLELNFRLHPSDLVYIVK 116
                                   3555567778899****************9*************************************************** PP

                                   HHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.........-TSCCCS-BTTSEE CS
                   AMP-binding  92 dseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae.........kpeeeeelkpddla 162
                                   +++ak l+  +d+ l l  l+++ +k+ + + ++v+++++l++ e+lk+++ ++++ +          +++ ee+++++ a
  gi|70607920|ref|YP_256790.1| 117 HTKAKGLF--IDDSLlL--LAQILSKEYKFDFIVVMSDKSLEEIEPLKGMSLASKVYGyeelvkshsPNRRFEEVNEKSAA 193
                                   ********..7777732..45556666677889999999999999999999888765267899999955578899****** PP

                                   EEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHH CS
                   AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpk 243
                                   y  +TSGTTG PKGV +shr++v  + ++     ++++++d++l+++p++h+ g+    ++a ++G++ +++ +  +  p+
  gi|70607920|ref|YP_256790.1| 194 YAAFTSGTTGLPKGVFYSHRSVVLHAMTV----AHDMRPTDTLLQVVPMFHANGW-GTPFAAAMQGCRQIYPGRP-T--PE 266
                                   **********************9998886....3557899***************.*************996633.4..67 PP

                                   HHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSE CS
                   AMP-binding 244 lllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgv 323
                                    l ++i ++kvt +a+vP+++  ll+  ++ +    + dl++l++  +gg+ ++++l+ ++ + + e v++gYG TEt++v
  gi|70607920|ref|YP_256790.1| 267 SLTDYILNYKVTRTAAVPTIIIELLKrLEKMD---PKPDLKGLKI-SMGGQEPPSKLVSELAKYGVE-VYQGYGATETSPV 342
                                   899*********************99664444...4569*****9.57****************876.************* PP

                                   CEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETC CS
                   AMP-binding 324 vtv.........lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpeataeafdseg 393
                                   v+v         lp  edk  + ++G ++ gvevk+vD+ t++++p dg++ Ge+++rgp++++ Y+++  +t+++f+ ++
  gi|70607920|ref|YP_256790.1| 343 VSVgfskseidnLP-AEDKFLKMKQGLIVFGVEVKVVDPITNQELPwDGKSvGEIWIRGPWITREYYND-PRTSQSFT-PD 420
                                   *88899999*9555.777788899**********************877778***************99.7899***9.76 PP

                                   CEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 394 rwlrTGDlgrldedGyleivgRkkdlikl 422
                                   +w r+GD+g++d+ Gy+++v+R+kd+ik+
  gi|70607920|ref|YP_256790.1| 421 GWWRSGDVGVVDPLGYIRLVDRLKDVIKS 449
                                   7**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.1   0.0   8.5e-26   7.6e-22       2      76 .]     459     538 ..     458     538 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 8.5e-26
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---....HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea....leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   +E+ l++hp V+ea VvGvp++++Ge+++a+Vvlk++  + +    +++ L +h+ k+++++  p+++vfvde+pkt +GK
  gi|70607920|ref|YP_256790.1| 459 LENFLMAHPYVREASVVGVPHPKWGERPLAIVVLKSDyeN-LpkdeVKKSLLDHLSKKFAKWQLPDDIVFVDEIPKTSTGK 538
                                   7*********************************977541.14457**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4168.86
//
Query:       gi|70607921|ref|YP_256791.1|  [L=330]
Description: ribonucleotide-diphosphate reductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-16   59.4   0.0      6e-16   58.7   0.0    1.2  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain
     0.0058   16.2   0.0        3.5    7.1   0.0    2.2  2  DUF455          Protein of unknown function (DUF455)
  ------ inclusion threshold ------
      0.065   12.1   0.0        0.1   11.5   0.0    1.3  1  Cu_amine_oxid   Copper amine oxidase, enzyme domain
      0.066   12.5   0.6        2.8    7.1   0.0    2.4  3  AurF            P-aminobenzoate N-oxygenase AurF
       0.11   12.8   1.8       0.72   10.3   0.1    2.8  3  Rubrerythrin    Rubrerythrin


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   1.7e-19     6e-16      20     218 ..      41     244 ..      34     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.7e-19
                                   HCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHC...HHHCHHCCBSSHHHHHHHHHHHHHHHHHHH CS
                Ribonuc_red_sm  20 eanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnen...lverllsevqipearafygfqaamEniHae 97 
                                   e+  Wt+ e+d+skD +dwk kL++ +++  k + + + + +  v+     l  + ++e+   e+ ++++ +a +E+ H+ 
  gi|70607921|ref|YP_256791.1|  41 EKFRWTAYELDFSKDREDWK-KLKPSDRTQNKIISSYFLAGEECVARDilpL-ANAMEELGLIEEALYLTQFARDEANHTV 119
                                   6778***************9.6************************994433.47789999******************** PP

                                   HHHHHHHHHT.-HHHHHHHHCHHHH-HHHHH.HHHHH....HHHHCTTTSCHHHHHHHHHHH.HHHHCCCHHHHHHHHHHH CS
                Ribonuc_red_sm  98 sYsllletlvkdekekdelfnaieenpalqk.kaewi....kkwyeskkdeekfaerlvafa.llegilfysgFaailwlk 172
                                   ++   +e+++ +++    +++ + +n+ +++   e+i     ++y++  ++e++++++v +  + egil   g++  +   
  gi|70607921|ref|YP_256791.1| 120 AFRKWFESVG-ETE---GIYDFTYKNEPYRRlFYEIIptdmRRLYNDP-SPENIVRAVVSYNfVAEGILAETGYYGYVKGY 195
                                   **********.444...4555443333333303333322324556543.3599999999999789*********9999988 PP

                                   HTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHH CS
                Ribonuc_red_sm 173 krgl..lpglaeiielilrDeglHtdfagllfkelkeen.elenkelee 218
                                   ++ l  lpgl+++++li+rDe+ H +f+++++  +   + +   +e++ 
  gi|70607921|ref|YP_256791.1| 196 EKILpaLPGLYKMVKLITRDEARHISFGAYVAALMISMHgDSVLNEFNR 244
                                   887788*************************999877766555555555 PP

>> DUF455  Protein of unknown function (DUF455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0012       4.2     169     230 ..      94     159 ..      87     165 .. 0.73
   2 !    7.1   0.0   0.00097       3.5     180     224 ..     207     251 ..     204     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                        DUF455 169 klraagdeesaeiLevIledEitHVaaGvrWfrylcekegl....dpvetFrelvreyfrgklkgp 230
                                    +++ g  e a  L+   +dE +H  a ++Wf+ + e eg      + e +r+l  e  ++++++ 
  gi|70607921|ref|YP_256791.1|  94 AMEELGLIEEALYLTQFARDEANHTVAFRKWFESVGETEGIydftYKNEPYRRLFYEIIPTDMRRL 159
                                   56666667788899999*******************999984444335666666666665555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00097
                        DUF455 180 eiLevIledEitHVaaGvrWfrylcekegldpvetFrelvreyfr 224
                                   ++++ I +dE +H+++G      + + +g +  ++F++   +  +
  gi|70607921|ref|YP_256791.1| 207 KMVKLITRDEARHISFGAYVAALMISMHGDSVLNEFNRYFGQLTQ 251
                                   78999*************999999999999999999887766655 PP

>> Cu_amine_oxid  Copper amine oxidase, enzyme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05       0.1      15      75 ..     114     174 ..     108     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                                   T.TTEEEETTEEEEEEEETTTEEEEEEEEETT...EEEEEEEEEEEEEEEE--SSHHHHH-EEEG CS
                 Cu_amine_oxid  15 e.gnlvewqkWsfrvgfnrreGlvlhdvrykg...rrilyrlslsemvvpYgdprppasrkaafD 75 
                                   e +++v + kW  +vg  ++eG  ++d +yk+   rr++y++   +m   Y dp+p+   +a++ 
  gi|70607921|ref|YP_256791.1| 114 EaNHTVAFRKWFESVG--ETEG--IYDFTYKNepyRRLFYEIIPTDMRRLYNDPSPENIVRAVVS 174
                                   4478888888844444..5566..79******9***********************988777665 PP

>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00079       2.8     102     148 ..     103     148 ..      81     158 .. 0.79
   2 ?    3.3   0.0     0.011        41     193     202 ..     213     222 ..     202     250 .. 0.86
   3 ?   -3.9   0.2       1.8   6.3e+03     200     217 ..     293     310 ..     293     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00079
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH--S---HHHHHHHHHHHH-- CS
                          AurF 102 evryalteiaDEcrHslMfaeaverigadvpgmyrvrrllrelakll 148
                                   e+ y+++ + DE++H++ f +  e +g  + g y ++  +++  +l+
  gi|70607921|ref|YP_256791.1| 103 EALYLTQFARDEANHTVAFRKWFESVG-ETEGIYDFTYKNEPYRRLF 148
                                   77899**********************.6666666666655555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                                   HHHHHHHHHH CS
                          AurF 193 vaEEarHisf 202
                                    ++EarHisf
  gi|70607921|ref|YP_256791.1| 213 TRDEARHISF 222
                                   68*******9 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHS-HH CS
                          AurF 200 isfareelrrrvprlsra 217
                                   +sfa  ++++r++ ++ra
  gi|70607921|ref|YP_256791.1| 293 MSFATRMFQQRYAVIERA 310
                                   689999999999888776 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0002      0.72      32      64 ..     104     137 ..      89     158 .. 0.75
   2 ?    0.1   0.0      0.28     1e+03      16      48 ..     191     222 ..     176     249 .. 0.75
   3 ?   -1.1   0.1      0.64   2.3e+03      75     112 ..     279     316 ..     257     330 .] 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B. CS
                  Rubrerythrin  32 aelFeelAeeEreHakilnklleklepele.lev 64 
                                   a ++ ++A++E+ H   ++k++e++ +++   ++
  gi|70607921|ref|YP_256791.1| 104 ALYLTQFARDEANHTVAFRKWFESVGETEGiYDF 137
                                   556899******************9999983333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                                   HHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  16 lYkelaekakegypqiaelFeelAeeEreHaki 48 
                                   + k +++ +   +p + ++ + + ++E++H  +
  gi|70607921|ref|YP_256791.1| 191 YVKGYEKILP-ALPGLYKMVKLITRDEARHISF 222
                                   5555666666.7788888889999999999765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.64
                                   --TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTS CS
                  Rubrerythrin  75 kpkflttaknLeeaiegayaeeeemyrfyeelaekegn 112
                                   ++ f++ ++  ++++  a+ + ++ y + e++ +++ +
  gi|70607921|ref|YP_256791.1| 279 YKYFVESEEGFQDVMSFATRMFQQRYAVIERAVKMRPE 316
                                   44455555566677777777777777777777765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2318.28
//
Query:       gi|70607922|ref|YP_256792.1|  [L=314]
Description: alpha/beta hydrolase fold protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-27   95.2   0.5    3.4e-17   62.9   0.1    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.4e-15   56.0   0.0    5.3e-15   55.3   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    1.1e-12   49.0   0.0    1.6e-12   48.5   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
    0.00032   20.2   0.4       0.16   11.5   0.0    2.5  2  Peptidase_S9   Prolyl oligopeptidase family
     0.0035   17.0   0.0     0.0073   16.0   0.0    1.6  1  FSH1           Serine hydrolase (FSH1)
  ------ inclusion threshold ------
      0.015   15.1   0.0        5.3    6.8   0.0    2.2  2  Abhydrolase_5  Alpha/beta hydrolase family
      0.033   13.9   0.1       0.14   11.9   0.0    1.9  2  PGAP1          PGAP1-like protein
      0.065   13.3   0.0      0.099   12.8   0.0    1.3  1  Abhydrolase_4  TAP-like protein
       0.13   12.4   0.0       0.19   11.8   0.0    1.2  1  Thioesterase   Thioesterase domain
       0.16   11.9   1.3       0.27   11.1   1.3    1.3  1  TAT_signal     TAT (twin-arginine translocation) pathway sign
       0.22   10.6   0.0       0.33   10.0   0.0    1.2  1  DUF2048        Abhydrolase domain containing 18


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.1   2.1e-20   3.4e-17       2     110 ..      64     172 ..      63     197 .. 0.86
   2 !   30.8   0.0   1.3e-10   2.1e-07     188     253 ..     232     298 ..     207     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2.1e-20
                                   EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH.HH..HHHCTTSSEEEEE CS
                 Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld.ri..ldalgddkltlvG 79 
                                   +l+++ G++g++++ +++ ++++La  +++vi++D rG g+S +    + +d  t ++  +    i  l+ lg  +l+++G
  gi|70607922|ref|YP_256792.1|  64 PLIMIMGYLGNLES-WGPIIINGLAS-QYEVIIFDNRGTGRSGTVGQDPLHDALTYTIPLYASdTIglLNYLGYSNLNVLG 142
                                   89**********96.7889******9.***************99999888555555555555555566************* PP

                                   ETHHHHHHHHHHHHHGGGEEEEEEESECSSC CS
                 Abhydrolase_1  80 hSmGGmialayaaeyperVkalvllgaidpa 110
                                   +SmGG++a + a +yp++V++lvll++ +p+
  gi|70607922|ref|YP_256792.1| 143 WSMGGFVAQQIAIDYPSYVNKLVLLCT-APN 172
                                   ***************************.443 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.3e-10
                                   HHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS.EEEEEEETCSSSHH CS
                 Abhydrolase_1 188 sieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpk.krlvvisdagHlaf 253
                                   + +  ++t   + +++ ++l+n++aptlvi+g+sD l pp+++ +la+ +p+ ++++  +dagH ++
  gi|70607922|ref|YP_256792.1| 232 YTSVLKQTNALATFNSVGQLQNITAPTLVIGGDSDLLLPPQNSQYLAENIPNaQLYIFSPDAGHGLI 298
                                   4455555555555555566999******************************788888889999765 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   3.3e-18   5.3e-15      30     232 ..      88     295 ..      84     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 3.3e-18
                   Hydrolase_4  30 qGfavyalDhrGhGrse......gkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvagl 104
                                     ++v+++D+rG Grs+       + +    +  y  D   +++ +      ++l +lG SmGG++a++++ +yp+ v++l
  gi|70607922|ref|YP_256792.1|  88 SQYEVIIFDNRGTGRSGtvgqdpLHDALTYTIPLYASDTIGLLNYLG----YSNLNVLGWSMGGFVAQQIAIDYPSYVNKL 164
                                   579*************8887776666777777888888888887777....66899************************* PP

                   Hydrolase_4 105 ilsaPalkikaklk.appllklllkllgkllpklqv....snnlkadslsrdpevvaayeadplvhgkitvrlllelldam 180
                                   +l ++a +i  + + ++p   ++  +++   p+++v    +  + +d+l+ +p+v + y    l +  i+   +l+ ++a+
  gi|70607922|ref|YP_256792.1| 165 VLLCTAPNIYLYPPkVSPQSIITGFTAS--DPTVTVetiiPYLVPSDWLQAHPDVAK-YVLFTLEKYPISYTSVLKQTNAL 242
                                   *999888887663333333333333333..344444556688899999999998765.99999999999999999999998 PP

                   Hydrolase_4 181 krlee..raakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                   ++ ++  + ++it+P+l++ G++D + +p++s+ l+e+++   + +   p + H
  gi|70607922|ref|YP_256792.1| 243 ATFNSvgQLQNITAPTLVIGGDSDLLLPPQNSQYLAENIPN-AQLYIFSPDAGH 295
                                   8876533788999**************************96.333344455555 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   9.9e-16   1.6e-12      20     218 ..      83     306 ..      66     308 .. 0.59

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 9.9e-16
                                   HHHHCCTCEEEEE--TTSTS-GGCS.......--HHH...CHHHHHHHCCTT..TTSEEEEEETCHHHHHHH.HHHCC... CS
                 Abhydrolase_6  20 aallaagvhvlapDlpGhGrsdppp.......ldled...ladlaalldelaagggpvvlvGHSlGGalala.aapla.lv 88 
                                    + la++++v+++D +G+Grs +         l+++    + d   ll+ l  g+ +  ++G+S+GG++a++ a +++  v
  gi|70607922|ref|YP_256792.1|  83 INGLASQYEVIIFDNRGTGRSGTVGqdplhdaLTYTIplyASDTIGLLNYL--GYSNLNVLGWSMGGFVAQQiAIDYPsYV 161
                                   5667999999*********77554411111112222222223335566666..69999**************444444955 PP

                                   EE.EEES-.....----TTTS----TTHHHHHH.........TT-CCCCHCCHS-HSCCCCHHH.C....CCCHCHCCCGH CS
                 Abhydrolase_6  89 vg.vlldppp...talpagllaaalelllalla.........llrllawlsreplprlfladed.a....daawrarlarl 151
                                    + vll++ p   + +p   ++ +++ + a  +          l++  wl+        ++d++ +     + +   ++ +
  gi|70607922|ref|YP_256792.1| 162 NKlVLLCTAPniyLYPPKVSPQSIITGFTASDPtvtvetiipYLVPSDWLQ-------AHPDVAkYvlftLEKYPISYTSV 235
                                   556999995533222222223333333332222111111111222233332.......11122221222334455555555 PP

                                   HHHCCHHC.HTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH..STTEEETCE...SSS.-HHHHSHHHHH CS
                 Abhydrolase_6 152 aallaglg.llpaaawadlpvpllvl.ggeDplvprllerlla..qagarlpvvlpgaGH.lphleepdeva 218
                                   ++++++l  ++++  +  +++p+lv+ g++D l+p+   ++la  ++ a+l +  p+aGH l+++  p++++
  gi|70607922|ref|YP_256792.1| 236 LKQTNALAtFNSVGQLQNITAPTLVIgGDSDLLLPPQNSQYLAenIPNAQLYIFSPDAGHgLIYQ-YPTQFI 306
                                   55555555366799*********999669999***999999998888888868888****66666.998886 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.4    0.0037       6.1      59      84 ..     131     156 ..      86     161 .. 0.74
   2 !   11.5   0.0   9.6e-05      0.16     115     188 ..     232     297 ..     208     313 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0037
                                   TS--GGGEEEEEETHHHHHHHHHHHH CS
                  Peptidase_S9  59 gyvdserlaitGgSyGGyltgaalnq 84 
                                   +y   ++l + G+S GG+++  ++ +
  gi|70607922|ref|YP_256792.1| 131 NYLGYSNLNVLGWSMGGFVAQQIAID 156
                                   577789999*********99888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.6e-05
                                   CCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SST CS
                  Peptidase_S9 115 ymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgv 188
                                   y+      ++ +   +++++ +l+n  +++p+L+i G+ D   pp+++  l+++  ++    l+   pd+gHg+
  gi|70607922|ref|YP_256792.1| 232 YTS---VLKQTNALATFNSVGQLQN--ITAPTLVIGGDSDLLLPPQNSQYLAENIPNA---QLYIFSPDAGHGL 297
                                   333...3345666778899999999..*********************9998887764...4677789999975 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.5e-06    0.0073     155     196 ..     246     289 ..     137     297 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.5e-06
                          FSH1 155 y...eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkH 196
                                       + ++i+ ptL + G++D + ++++s++Lae++ n ++++ +
  gi|70607922|ref|YP_256792.1| 246 NsvgQLQNITAPTLVIGGDSDLLLPPQNSQYLAENIPN-AQLYIF 289
                                   233577899***************************99.666554 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0032       5.3      57      92 ..     136     172 ..     123     198 .. 0.88
   2 ?    6.2   0.0     0.005       8.1      86     138 ..     241     293 ..     226     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0032
                 Abhydrolase_5  57 ekfvvgGhslGGvvasrfaaee.ekiegvvflasYPe 92 
                                    ++ v G s+GG va ++a +  + ++ +v+l + P+
  gi|70607922|ref|YP_256792.1| 136 SNLNVLGWSMGGFVAQQIAIDYpSYVNKLVLLCTAPN 172
                                   678899**************985699****9998885 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.005
                 Abhydrolase_5  86 flasYPekdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGg 138
                                    la++ + ++l++ + ++l i g++D +l+ ++ +  ++ +p+   +++    
  gi|70607922|ref|YP_256792.1| 241 ALATFNSVGQLQNITAPTLVIGGDSDLLLPPQNSQYLAENIPNAQLYIFSPDA 293
                                   6899999999************************9999999988877765555 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   1.8e+03       3      23 ..      61      81 ..      60     106 .. 0.81
   2 ?   11.9   0.0   8.5e-05      0.14      91     123 ..     136     165 ..     107     178 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                         PGAP1  3 sGipVlFvpGnagsykqvrsl 23
                                  sG+p +++ G  g+++ +  +
  gi|70607922|ref|YP_256792.1| 61 SGEPLIMIMGYLGNLESWGPI 81
                                  799**********99998654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.5e-05
                         PGAP1  91 tsviliGHSmGGivaraalt.lknyikqsvntil 123
                                   +++ ++G SmGG+va+ +++ +++y+++    ++
  gi|70607922|ref|YP_256792.1| 136 SNLNVLGWSMGGFVAQQIAIdYPSYVNK----LV 165
                                   66789**********9765515666444....33 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.099      32      91 ..     253     313 ..     235     314 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                 Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalggavl.vtvegeGHgalaagntCvdkavdaYL 91 
                                   + +ap+L++++  D   P++  + la+++++a+l +   ++GHg + ++ t   ++v+++L
  gi|70607922|ref|YP_256792.1| 253 NITAPTLVIGGDSDLLLPPQNSQYLAENIPNAQLyIFSPDAGHGLIYQYPTQFINLVTSFL 313
                                   3368***************************9873667788***98877666666666665 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.19      68      84 ..     138     154 ..     125     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   EEEEEETHHHHHHHHHH CS
                  Thioesterase  68 yalfGhSlGgllAfevA 84 
                                   +++ G+S+Gg++A+++A
  gi|70607922|ref|YP_256792.1| 138 LNVLGWSMGGFVAQQIA 154
                                   689***********998 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   0.00017      0.27       2      21 ..       1      20 [.       1      22 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                    TAT_signal  2 lSRRdFLKgsAAaaAAaalg 21
                                  ++RRd +K  +A+a A+al+
  gi|70607922|ref|YP_256792.1|  1 MNRRDAIKILGAGAIAGALA 20
                                  89************999998 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0002      0.33     171     209 ..     131     169 ..     118     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                       DUF2048 171 ereGyGplgltGlSmGGhmaslaasnwpkplvlvpclsw 209
                                   +  Gy +l + G SmGG+ a+  a  +p  +  + +l  
  gi|70607922|ref|YP_256792.1| 131 NYLGYSNLNVLGWSMGGFVAQQIAIDYPSYVNKLVLLCT 169
                                   556*********************999988886666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2001.72
//
Query:       gi|70607923|ref|YP_256793.1|  [L=502]
Description: S-rich protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   18.3   5.1     0.0023   17.9   5.1    1.2  1  RIFIN     Rifin
  ------ inclusion threshold ------
      0.014   14.4   1.5      0.022   13.8   1.5    1.3  1  Pex24p    Integral peroxisomal membrane peroxin
       0.03   13.9   2.5      0.047   13.2   2.5    1.3  1  Stevor    Subtelomeric Variable Open Reading frame
       0.38   11.2   7.2       0.62   10.5   7.2    1.3  1  DUF1180   Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.1   5.1e-07    0.0023     182     304 ..     380     501 ..     324     502 .] 0.57

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.1e-07
                         RIFIN 182 atnyknvtslvkaikeeyeescllklkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaeataeae 262
                                    + y++ +sl+  ++e    +  +  ++++++ t +++++++++ s++++++++++ ++++ ++ +++ +++ ++ ++++ 
  gi|70607923|ref|YP_256793.1| 380 YSAYTEGSSLIINVYEI---KYGVIPTSTTSQSTPTSTSNTSTSISTTSVSQTTSSNQATTSSQVSTSLSQVGESSSTSVS 457
                                   24455555555555554...3333334444444455555555555566666666666666666666666666666666666 PP

                         RIFIN 263 kae..taaveattaslqtaiiasivaivvIvLimvIIYLiLRYr 304
                                   ++e   + +++  ++++ +i   i++++v+v+i+vI+ L+L  r
  gi|70607923|ref|YP_256793.1| 458 STEplSSGLSQPQTTSSPSISPFIIVVIVVVIIIVIVVLLLVRR 501
                                   65532333444444455556556666666666666666666544 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   4.8e-06     0.022      86     172 ..     411     499 ..     362     502 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-06
                        Pex24p  86 rksslik....keesknestsegptldea.....skeivlnLrdlqnkmedllnpidalekflkelagfkdenlstllflt 157
                                   ++s++++    +++s +++ts       +     s+++ + L ++    ++ ++  + l++ l++ ++++ +++s +++++
  gi|70607923|ref|YP_256793.1| 411 PTSTSNTstsiSTTSVSQTTS-------SnqattSSQVSTSLSQVGESSSTSVSSTEPLSSGLSQPQTTSSPSISPFIIVV 484
                                   222222233332222222333.......12334489*******************************************99 PP

                        Pex24p 158 llltpililllsrli 172
                                   +++++i++++++ l+
  gi|70607923|ref|YP_256793.1| 485 IVVVIIIVIVVLLLV 499
                                   999998888886655 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.5   1.1e-05     0.047     182     259 ..     421     500 ..     389     502 .] 0.48

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                        Stevor 182 lsaealkklass.lsilnlfsesslesalk....aavsaaaasdlagtaasaassafepygiaalvllilavvliiLYiwl 257
                                   +s++++++++ss  ++++   ++sl+++ +    + +s++ +s+  ++  +++s  + p+ i+++v++i++v++++L +  
  gi|70607923|ref|YP_256793.1| 421 ISTTSVSQTTSSnQATTSSQVSTSLSQVGEssstSVSSTEPLSSGLSQPQTTSSPSISPFIIVVIVVVIIIVIVVLLLV-- 499
                                   1111111111110111111112222222112111344445555555556677777888888888888887777777643.. PP

                        Stevor 258 yr 259
                                    r
  gi|70607923|ref|YP_256793.1| 500 -R 500
                                   .4 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.2   0.00014      0.62      34     123 ..     407     500 ..     392     502 .] 0.46

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                       DUF1180  34 eaepPlppgataaespgkataieaksaqaaeggngsspragsaadaggslavvpelssntdkpmtlqr....allvlvvvs 110
                                   + + P++ ++t++     +++  ++s+qa  +++ s++ +   + +++s +    lss  ++p+t        ++++v+v 
  gi|70607923|ref|YP_256793.1| 407 SQSTPTSTSNTSTSISTTSVSQTTSSNQATTSSQVSTSLSQVGESSSTSVSSTEPLSSGLSQPQTTSSpsisPFIIVVIVV 487
                                   222444444555543444444344444444444444433333333334333333466666666664331111466666666 PP

                       DUF1180 111 aavivylvvRtvr 123
                                    ++iv+ v+  vr
  gi|70607923|ref|YP_256793.1| 488 VIIIVIVVLLLVR 500
                                   6666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2024  (0.11289); expected 358.6 (0.02)
Passed bias filter:                      836  (0.0466284); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.86u 0.39s 00:00:01.25 Elapsed: 00:00:00.57
# Mc/sec: 2667.21
//
Query:       gi|70607924|ref|YP_256794.1|  [L=879]
Description: hypothetical protein Saci_2215 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.5   0.0         37    4.8   0.0    3.2  2  DUF4376   Domain of unknown function (DUF4376)


Domain annotation for each model (and alignments):
>> DUF4376  Domain of unknown function (DUF4376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0021        37      49      87 ..     298     347 ..     258     360 .. 0.74
   2 ?    3.7   0.0    0.0043        77      56      95 ..     372     411 ..     368     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0021
                       DUF4376  49 e..........aWtladntvvtLtadqlialgqavaq.hkqaifdrerel 87 
                                   +          ++  a+ ++++L+   l++++q ++   +q i+ + +  
  gi|70607924|ref|YP_256794.1| 298 TlnlektniinTFVGASKSFIKLDHSTLMNVVQNISSsTAQVIYSNLQNA 347
                                   122334456779***********************987889999886655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0043
                       DUF4376  56 ntvvtLtadqlialgqavaqhkqaifdrerelkaaieaae 95 
                                   n+++tL +  l a+ + ++  +q i+     lk+ +   +
  gi|70607924|ref|YP_256794.1| 372 NSQITLENSNLSAVNTVIQNSVQNIYSSGVNLKNTVISGS 411
                                   899*************************999999886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (879 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.82u 0.33s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 4769.07
//
Query:       gi|70607925|ref|YP_256795.1|  [L=205]
Description: hypothetical protein Saci_2216 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   17.5   0.0     0.0075   16.7   0.0    1.4  1  SCP2      SCP-2 sterol transfer family
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.056   13.3   0.0    1.3  1  TFCD_C    Tubulin folding cofactor D C terminal


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   8.4e-07    0.0075      53      87 ..     141     175 ..     104     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.4e-07
                                   S-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEE CS
                          SCP2  53 kadvtlslsledllelaegklnpqkafmqgkLkie 87 
                                   +adv+l ++++d+++++egkl+++ a++ g +ki+
  gi|70607925|ref|YP_256795.1| 141 SADVILEARYQDWVKIIEGKLDASLALLGGIIKIK 175
                                   79****************************99997 PP

>> TFCD_C  Tubulin folding cofactor D C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-06     0.056      77     108 ..      49      80 ..       8     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-06
                        TFCD_C  77 peyresvleGlvvSvGglteslvkassqaLle 108
                                   ++ r++v++G+ +S G l+e+l++ +++ L  
  gi|70607925|ref|YP_256795.1|  49 ENVRAAVVKGVAISLGVLNEDLIRQATELLSP 80 
                                   5689***********************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.38s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1104.69
//
Query:       gi|70607926|ref|YP_256796.1|  [L=399]
Description: acyl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-42  143.3   3.4    9.8e-42  142.7   3.4    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.8e-33  115.6   1.7    2.7e-32  111.8   0.0    2.7  3  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.2e-26   91.4   0.0    6.1e-26   90.5   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.3e-19   70.8   2.9    2.6e-19   69.8   2.9    1.5  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.014   15.7   0.1       0.22   11.8   0.0    2.6  3  PucR           Purine catabolism regulatory protein-like fami
      0.069   12.8   0.1       0.18   11.4   0.1    1.7  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   3.4   3.3e-45   9.8e-42       4     147 ..     244     389 ..     241     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 3.3e-45
                                   HHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-------- CS
                 Acyl-CoA_dh_1   4 frvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd 84 
                                   f++am+t++++R++va +alg+a++ale + +y+ +r afg pl+ +q v+ek+ae  +e+ aarll+y aa+++d+ k d
  gi|70607926|ref|YP_256796.1| 244 FKYAMTTFDVSRVGVAGQALGVAQAALEKMTNYSVQRSAFGSPLLGFQMVQEKIAETLTEVNAARLLTYWAASLIDQRKVD 324
                                   89******************************************************************************* PP

                                   ..HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                 Acyl-CoA_dh_1  85 ..raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                      ++asmaK+fa+e+a+++a +a+ ++Gg+G++++++verl+rd+ v+ i+eG+++iq++++ +
  gi|70607926|ref|YP_256796.1| 325 egIVAASMAKYFATEVAERAAIRAITVHGGYGVATSTGVERLLRDVEVMKIYEGANDIQKLVVLK 389
                                   999*********************************************************99876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.0     9e-36   2.7e-32       1     113 []      16     127 ..      16     127 .. 0.96
   2 ?    2.2   0.0     0.092   2.7e+02      40      86 ..     221     267 ..     199     280 .. 0.79
   3 ?   -2.0   0.1       1.9   5.6e+03      14      24 ..     335     345 ..     323     394 .. 0.58

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 9e-36
                                   THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHH CS
                 Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglall 81 
                                   +e +e +r++vref+e+ +ap +++ ++eg++p+++++k++elGl+gi+vp+eygG+ +d+l + i++ee++r++ ++ + 
  gi|70607926|ref|YP_256796.1|  16 SENHELFRKAVREFMERDVAPIVEKGEKEGKVPENVLEKAKELGLFGISVPQEYGGQSGDMLMSTIAVEEMSRVWPSFTAR 96 
                                   689*************************9*************************************************998 PP

                                   HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasge 113
                                   + v++ l + +il fG+eeq+++y+ ++a+g+
  gi|70607926|ref|YP_256796.1|  97 VTVGN-LFMTPILLFGSEEQRKKYVTPVARGD 127
                                   88988.55579*******************96 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.092
                                   HHHTTCTSTTS-.GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHH CS
                 Acyl-CoA_dh_N  40 laelGllgitvp.eeygGagldyleaaivaeelaradaglalllgvhs 86 
                                    ael +  ++vp e   G +++++ +a+ +  ++r+++++++ lgv +
  gi|70607926|ref|YP_256796.1| 221 TAELAFEEVYVPqENLVGEEGSAFKYAMTTFDVSRVGVAGQA-LGVAQ 267
                                   5777777888994555699999**************999665.55544 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.9
                                   HHHHHTHHHHH CS
                 Acyl-CoA_dh_N  14 faeeelaphaa 24 
                                   ++++e+a++aa
  gi|70607926|ref|YP_256796.1| 335 YFATEVAERAA 345
                                   44444444332 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0     2e-29   6.1e-26       1      97 []     131     229 ..     131     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2e-29
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---...----EEEEEEE..GGGEEE.-- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd...rarglslflvprdapgvsv.rr 77 
                                   afa TEpqaGsdva++++ta++ dg +yvln +Ki+itn++ia++++v art  p+   r +g+s+f+v+r ++gv+v +r
  gi|70607926|ref|YP_256796.1| 131 AFANTEPQAGSDVAGIQSTAKKVDG-GYVLNARKIFITNGGIADYYVVTARTSPPEpnaRWKGISMFIVEREWKGVKVlNR 210
                                   799***************5555555.9************************6555567899*****************888 PP

                                   ---BSS-TTS-EEEEEEE.. CS
                 Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                   i e+lGlr  +t+el fe+v
  gi|70607926|ref|YP_256796.1| 211 I-ETLGLRASNTAELAFEEV 229
                                   8.68*************986 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   2.9   8.5e-23   2.6e-19       2     133 ..     257     380 ..     256     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 8.5e-23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   g+a +alG+A+aal++++ +  +r+   +g +l  ++++q ++ae  ++++AAr+l++ aa+     ++++k    e    
  gi|70607926|ref|YP_256796.1| 257 GVAGQALGVAQAALEKMTNYSVQRSA--FGSPLLGFQMVQEKIAETLTEVNAARLLTYWAASL----IDQRKV--DEGIVA 329
                                   6899**********************..***********************************....666555..356688 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                   a++a+ +a+e a +a+ +++ ++Gg++++++  ++Rl+RD++++++++++n
  gi|70607926|ref|YP_256796.1| 330 ASMAKYFATEVAERAAIRAITVHGGYGVATSTGVERLLRDVEVMKIYEGAN 380
                                   9**********************************************9876 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.5e-05      0.22      51     103 ..      14      68 ..       8      72 .. 0.87
   2 ?    0.5   0.0      0.24   7.1e+02      37      80 ..      95     137 ..      75     153 .. 0.78
   3 ?   -3.0   0.0       2.8   8.5e+03      17      33 ..     360     376 ..     346     386 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.5e-05
                          PucR  51 alkddpealaelvrelaeagvaaLviklgr..eipeelieaadelglPlielpee 103
                                    +++++e +++ vre  e++va +v k ++  ++pe+++e a+elgl  i++p+e
  gi|70607926|ref|YP_256796.1|  14 KVSENHELFRKAVREFMERDVAPIVEKGEKegKVPENVLEKAKELGLFGISVPQE 68 
                                   45679999****************99997458**************988888876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                          PucR  37 ellrggeLllttglalkddpealaelvrelaeagvaaLviklgr 80 
                                   + ++ g+L++t  l +  ++e+ +++v  +a+ + +a + ++++
  gi|70607926|ref|YP_256796.1|  95 ARVTVGNLFMTPILLFG-SEEQRKKYVTPVARGDKVAAFANTEP 137
                                   66778999999999998.89999*****9999988888877764 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.8
                          PucR  17 kagldrpVrwvhvlevp 33 
                                   + g++r  r v v+ + 
  gi|70607926|ref|YP_256796.1| 360 STGVERLLRDVEVMKIY 376
                                   45555555555555544 PP

>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   6.2e-05      0.18     132     269 ..     118     235 ..     110     237 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                                   HHHHHHHHHT--EEEEES--SS-TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TT.SG CS
                        HpaB_N 132 kyleyvqendlvlthaitdpkgdRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkee.dk 211
                                   ky++ v++ d v + a t+p+     +  +           ++ d G v +  k+++T++ +ad+ +v    ++ +++   
  gi|70607926|ref|YP_256796.1| 118 KYVTPVARGDKVAAFANTEPQAGSDVAGIQ--------STAKKVDGGYVLNARKIFITNGGIADYYVVTARTSPPEPNaRW 190
                                   566666666666666666666554433333........234566889999999***************9985553444266 PP

                                   GG-EEEEEETT-TTEEEEE-------S..-TTT-TTTTT----EEEEEEEEEEEEGGG CS
                        HpaB_N 212 dyavafavpvdapGlklicresfedkleesefdyplssrfdendalvvfDdVfVPwer 269
                                   +   +f+v+ +++G+k++ r ++   l               n+a + f++V VP e+
  gi|70607926|ref|YP_256796.1| 191 KGISMFIVEREWKGVKVLNRIETLG-L---------R---ASNTAELAFEEVYVPQEN 235
                                   77899*************9988765.2.........1...235666777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2783.70
//
Query:       gi|70607927|ref|YP_256797.1|  [L=639]
Description: 3-hydroxybutyryl-CoA [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-64  215.4   1.5    8.6e-64  214.7   1.5    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    2.9e-53  180.8   0.0      2e-52  178.0   0.0    2.0  2  ECH_1            Enoyl-CoA hydratase/isomerase
    1.2e-34  118.7   0.0    9.1e-24   83.9   0.0    2.5  2  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    9.7e-34  117.3   0.0    2.1e-30  106.4   0.0    2.8  3  ECH_2            Enoyl-CoA hydratase/isomerase
      8e-07   29.2   0.1    1.8e-06   28.0   0.1    1.6  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    1.1e-05   25.8   0.3    3.9e-05   24.1   0.3    2.0  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    2.6e-05   24.5   0.1    5.2e-05   23.5   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00024   20.7   1.0     0.0011   18.6   0.4    2.3  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0011   19.2   0.2     0.0028   17.9   0.2    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0015   17.8   0.1     0.0025   17.1   0.1    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0053   16.1   0.4      0.011   15.1   0.4    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0097   16.5   0.6       0.06   13.9   0.6    2.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.026   15.0   0.1    1.6  1  NAD_binding_7    Putative NAD(P)-binding
      0.018   15.3   0.3       0.09   13.0   0.3    2.2  1  TrkA_N           TrkA-N domain
      0.057   13.5   0.1       0.15   12.1   0.1    1.7  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
       0.82    9.9   2.7         25    5.1   0.1    3.4  3  Spore_YtfJ       Sporulation protein YtfJ (Spore_YtfJ)


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7   1.5   7.7e-67   8.6e-64       1     179 [.       2     181 ..       2     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 7.7e-67
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-S CS
                       3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dad 80 
                                   kv viG+G mG+gia+v+a  + eV+lvdi++e+l+ka +ki++sl++l+++g+++ ee e++l+ri+ + +leeav dad
  gi|70607927|ref|YP_256797.1|   2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEILDKAISKIRESLDRLKKRGSIE-EEPEDILKRITKSINLEEAVkDAD 81 
                                   699****************************************************9.99********************** PP

                                   EEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHH CS
                       3HCDH_N  81 lviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetva 161
                                   lviEav+E ++lK+++f++l++ +kpdaila+nTS+++ise+++ +++++rv+g+HFfnPp lm+LvE+++g++Ts+e+v+
  gi|70607927|ref|YP_256797.1|  82 LVIEAVPEIVDLKQNIFKRLDQFTKPDAILATNTSNIRISEISKFVNKKDRVVGMHFFNPPVLMQLVEIIKGPDTSPEVVQ 162
                                   ********************************************************************************* PP

                                   HHHHHHHHTT-EEEEE.CS CS
                       3HCDH_N 162 tvvelakkigktpvvv.kd 179
                                   +++e++k+igktpv v kd
  gi|70607927|ref|YP_256797.1| 163 KLYEITKQIGKTPVIVnKD 181
                                   ****************776 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.35   3.9e+02     156     204 ..      68     117 ..      63     126 .. 0.84
   2 !  178.0   0.0   1.7e-55     2e-52       3     250 ..     395     638 ..     393     639 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                                   T-EEEHHHH.HHCTSSSEEESG.GGHHHHHHHHHHHHHHSCHHHHHHHHHH CS
                         ECH_1 156 gkkisaqea.lkvGlvdkvvpe.eqlleealelaeklaekspaalrqlkea 204
                                   +k+i+ +ea +++ lv ++vpe  +l+++  +++ +   k+ a+l++ +++
  gi|70607927|ref|YP_256797.1|  68 TKSINLEEAvKDADLVIEAVPEiVDLKQNIFKRLDQFT-KPDAILATNTSN 117
                                   78889999845689********99************99.888888776665 PP

  == domain 2  score: 178.0 bits;  conditional E-value: 1.7e-55
                                   ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                         ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                   e  va +klnrP ++N ++ +ll+El   l +l +d+s+ ++ +tG ++ F+ Ga+l +    + ++ +l+  + +  +++
  gi|70607927|ref|YP_256797.1| 395 EGKVAIVKLNRP-KLNLINYTLLDELDRLLTELWNDRSINVILITGEGQNFSGGAELSAPITDQVQFLELV-RKGERTFKR 473
                                   6789********.************************************************9875665555.567899*** PP

                                   HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHH CS
                         ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqea 164
                                   l+++pk+via v+G+a+gGG+el + cD++ia +na+fg +e+ lGl+p+ ggtq+l++ +G s+A++++l++++isa+ea
  gi|70607927|ref|YP_256797.1| 474 LTEIPKIVIAFVKGYALGGGFELSSYCDLRIATENAVFGFPETGLGLVPAWGGTQRLPKLIGISRAMYLILTAQRISAKEA 554
                                   ********************************************************************************* PP

                                   HHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCS CS
                         ECH_1 165 lkvGlvdkvvpeeqlleealelaeklaekspaalrqlkea.lnakledalaeqleaeaklfestfskddikeGlqaflEkr 244
                                   l+ Glv+k+v +e   +eale a+ l e +  + ++l +  +n+ +e     +le+e+     +f ++d keG+ af  kr
  gi|70607927|ref|YP_256797.1| 555 LEYGLVNKIVKDE---NEALEFAKDLSERIAPISAMLAKRlINRGSEVPIDVGLEMESIAGGLLFTTEDLKEGIVAFFSKR 632
                                   **********996...688999999998887777777665157777799999***************************** PP

                                   H----- CS
                         ECH_1 245 kpefed 250
                                   kpef++
  gi|70607927|ref|YP_256797.1| 633 KPEFKG 638
                                   ****97 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   8.2e-27   9.1e-24       1      97 []     184     277 ..     184     277 .. 0.96
   2 !   32.3   0.0   1.1e-10   1.2e-07       5      76 ..     295     366 ..     294     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 8.2e-27
                                   TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHH CS
                         3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklv 81 
                                   GF+vnR+ a+    ++ ++++g +++e++Da +r  lGlpmGp+el+d+vgld++ + le++a+e + + y ++  ++++v
  gi|70607927|ref|YP_256797.1| 184 GFIVNRINAAESLFICLVLQKG-INYEEVDAYFRS-LGLPMGPYELMDYVGLDIVAHSLEYFAKEISPE-YGKCTKIKEMV 261
                                   9*********************.************.************************888887766.666******** PP

                                   HTT--BGGGTBSSSBC CS
                         3HCDH  82 eagrlgrktgkgfyky 97 
                                   ++g lgrk+g+gfy++
  gi|70607927|ref|YP_256797.1| 262 NNGLLGRKSGRGFYDW 277
                                   **************97 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.1e-10
                                   HHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HH CS
                         3HCDH   5 nRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspl 76 
                                   n +la  +nea +l+e++va+p di++a++lg++ p Gp++++  ++l+ +k+ le + +e+g + ++p++ 
  gi|70607927|ref|YP_256797.1| 295 NDLLAIDINEASKLLEDNVATPNDIETAVKLGMNRPFGPITVAKSADLNDVKSRLERISSEYGITIFQPTDS 366
                                   66778889**********************************************999999999998886654 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.85   9.5e+02     169     240 ..      33     103 ..      20     121 .. 0.61
   2 !  106.4   0.0   1.9e-33   2.1e-30       2     176 ..     399     568 ..     398     581 .. 0.92
   3 !    9.2   0.0    0.0007      0.79     251     317 ..     572     636 ..     565     639 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.85
                                   -EE--GGGHHHHHHHHHTT..........--------......----SHHHHHHHHHHHT.-S-TTTHHHHHH. CS
                         ECH_2 169 thyvpseklealeeaLaelessd..eeaveevleelaeeaeeeeeeselaekreaidrlfsadsveeiveaLek 240
                                   + +++ +++++++e+L +l+++   ee+ e++l++++++ + ee  ++     ea+ +++  d  ++i+++L++
  gi|70607927|ref|YP_256797.1|  33 DEILD-KAISKIRESLDRLKKRGsiEEEPEDILKRITKSINLEEAVKDADLVIEAVPEIV--DLKQNIFKRLDQ 103
                                   54444.457888888888877667888889999988877776554333333344444444..334667777765 PP

  == domain 2  score: 106.4 bits;  conditional E-value: 1.9e-33
                                   EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHH CS
                         ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyl 82 
                                   ++++Lnrpk lN ++++++++l++ l+e  +d ++++++++g+g + f+ G  + a  +++ +      e++r+  +  ++
  gi|70607927|ref|YP_256797.1| 399 AIVKLNRPK-LNLINYTLLDELDRLLTELWNDRSINVILITGEG-QNFSGGAELSAPITDQVQF----LELVRKGERTFKR 473
                                   6899****6.********************************88.99*****999887776663....46999999***** PP

                                   HHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHH CS
                         ECH_2  83 iatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgada 162
                                   + ++pk v+a++ G+++GgG  ls  + +r++te++vf  PEt++Gl+P  Gg+  L++l g + ++yl lT++r+++++a
  gi|70607927|ref|YP_256797.1| 474 LTEIPKIVIAFVKGYALGGGFELSSYCDLRIATENAVFGFPETGLGLVPAWGGTQRLPKLIGiSRAMYLILTAQRISAKEA 554
                                   ************************************************************88799**************** PP

                                   HHTTS--EE--GGG CS
                         ECH_2 163 laaglathyvpsek 176
                                   l+ gl +++v++e+
  gi|70607927|ref|YP_256797.1| 555 LEYGLVNKIVKDEN 568
                                   **********9875 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0007
                                   HHHHHH.HHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                         ECH_2 251 ktletl.kkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                   + ++ l ++ +P+s+ ++ ++++rg++   ++  l+mE  +   l++++D+ eG+ a + ++  kP++
  gi|70607927|ref|YP_256797.1| 572 EFAKDLsERIAPISAMLAKRLINRGSEVP-IDVGLEMESIAGGLLFTTEDLKEGIVAFFSKR--KPEF 636
                                   33444404669*****************7.*************************9987554..5555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.6e-09   1.8e-06       1     142 [.       2     163 ..       2     170 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.6e-09
                                   -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H....HHHHHHHHHSSBTTTBTT...-.....---TTEEEES-HHHHHTT CS
                NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree....elieeineehenvkyLpg...i.....klpenlvattdlaealkg 69 
                                   k+ v+G+G  G  +A v+a   +ev+l   ++    +   +i++ +e  + L++   i     ++ + ++ + +l+ea+k+
  gi|70607927|ref|YP_256797.1|   2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDeildK---AISKIRESLDRLKKrgsIeeepeDILKRITKSINLEEAVKD 79 
                                   799**************************99954542...35555555555544222211111466789999********* PP

                                   --EEEE---HHH..HHHHHHHHCCC--TT-EEEE.........---SEET.TTEEHHHHHHHHH-S--EEEEESS--HHHH CS
                NAD_Gly3P_dh_N  70 adiivlvvPsqa..lrevlkklkgllkkkailvs.........liKGieegtlkllsevieeelkeekvavlsGpslAeEv 139
                                   ad+++ +vP  +   ++++k+l++++k++ail+          ++K ++++   +  +  +  + ++ v ++ Gp    Ev
  gi|70607927|ref|YP_256797.1|  80 ADLVIEAVPEIVdlKQNIFKRLDQFTKPDAILATntsniriseISKFVNKKDRVVGMHFFNPPVLMQLVEIIKGPDTSPEV 160
                                   *********854327899**********99999944444444445544444444444444444445558888888888888 PP

                                   HTT CS
                NAD_Gly3P_dh_N 140 akg 142
                                   +++
  gi|70607927|ref|YP_256797.1| 161 VQK 163
                                   876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   3.5e-08   3.9e-05       1      53 [.       2      53 ..       2      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.5e-08
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHH..HHHHHHT CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskil..qeklekn 53
                                  kvvv+G+G  g   A+++a ++++Vt+v+ +d++l   D+++ski    ++l+k+
  gi|70607927|ref|YP_256797.1|  2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEIL---DKAISKIResLDRLKKR 53
                                  79*********************************...99999985336677766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   4.6e-08   5.2e-05       2     118 ..       3     145 ..       2     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.6e-08
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......................EEE-SSHHHHHHHCSEE CS
                 NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.......................akaaesieelvasldvv 59 
                                   + +iG G+MG+ +a+ ++  + +v++++ + e +++++++                        ++   ++ee+v+++d+v
  gi|70607927|ref|YP_256797.1|   3 VVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEILDKAISKIresldrlkkrgsieeepedilkrITKSINLEEAVKDADLV 83 
                                   779****************************9999999996788999999*9*********98777777888********* PP

                                   EE-SSSHHHHHHHHHS.HCCC--TT-EEE.E-S---HHHHHH.HHHHHHHTT-EEEEEEEES CS
                 NAD_binding_2  60 itmvkagkavdevieg.llealkkgdili.dgstsspedtre.lakelkekglkfldaPVSG 118
                                   i  v++  + ++ i++ l +  k+++il  ++s++ +++  + ++k+ +  g++f++ PV  
  gi|70607927|ref|YP_256797.1|  84 IEAVPEIVDLKQNIFKrLDQFTKPDAILAtNTSNIRISEISKfVNKKDRVVGMHFFNPPVLM 145
                                   ****************5555556666554235566665544414444555678888888865 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.4   9.7e-07    0.0011       1      85 [.       1      88 [.       1      96 [. 0.79
   2 ?   -1.0   0.0         1   1.1e+03      93     148 ..     338     388 ..     326     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.7e-07
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HH....HHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SE CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDidee....kvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadv 79
                                  mk++viG+G +G   a v+a   +ev++vDi +e    +++k++++   +  +g  e   + +  +r++ + ++e+av++ad+
  gi|70607927|ref|YP_256797.1|  1 MKVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEildkAISKIRESLDRLKKRGSIEEEPEDI-LKRITKSINLEEAVKDADL 82
                                  89*****************************97622215666666666666666544444444.4899999999999999999 PP

                                  EEE--- CS
                UDPG_MGDP_dh_N 80 ifiaVg 85
                                  ++ aV+
  gi|70607927|ref|YP_256797.1| 83 VIEAVP 88
                                  998887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                                   TCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEE CS
                UDPG_MGDP_dh_N  93 kaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfd 148
                                   k+aDl+ v+s +++i+   +++ + + + T  ++t +  +k++le ++k+++++f+
  gi|70607927|ref|YP_256797.1| 338 KSADLNDVKSRLERIS---SEYGITIFQPTDSIKTGK--LKELLEGEKKEEKKEFE 388
                                   5667777666665555...578899999999999998..88888877777766665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   2.5e-06    0.0028       1      83 [.       3      93 ..       3      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-06
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..........TTTCEEEEE--..T.TTHHHHHHHHHTTS CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..........lgvrfeaiald..a.enyeavLaallkeg 70
                                  v++iG+G +G+++ae++a  ++   e+t++d ++e l+++++k+             ++e +  d  +   ++  L++++k++
  gi|70607927|ref|YP_256797.1|  3 VVVIGSGEMGHGIAEVMAIYKN---EVTLVDIKDEILDKAISKIresldrlkkrG--SIEEEPEDilKrITKSINLEEAVKDA 80
                                  89*****************987...6***************999**999988552..33333322002022333488999999 PP

                                  SEEEE-SSGGGHH CS
               Sacchrp_dh_NADP 71 dlvvnlsppissl 83
                                  dlv+ ++p i +l
  gi|70607927|ref|YP_256797.1| 81 DLVIEAVPEIVDL 93
                                  ******9998665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.2e-06    0.0025     144     196 ..       2      53 ..       1     105 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke 196
                                   ++vv+G+G  G  +A ++a ++ evtlv+  d++l +  +++++ l ++l+k+
  gi|70607927|ref|YP_256797.1|   2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEILDKAISKIRESL-DRLKKR 53 
                                   79********************************944444444443.445554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   9.5e-06     0.011      30      99 ..       2      87 ..       1      91 [. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-06
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE................HCHHHHHHHHHHHH-SEE CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev................lksqeellaeavkeadvv 95
                                  kv+viG G  G   +++ +  + +Vt++D++ + l +  s + ++ ++                 +  ++ +l+eavk+ad+v
  gi|70607927|ref|YP_256797.1|  2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEILDKAISkIRES-LDRlkkrgsieeepedilkRITKSINLEEAVKDADLV 83
                                  8********************************999988845555.6667999**********99888999************ PP

                                  EE-- CS
                   AlaDh_PNT_C 96 igtv 99
                                  i +v
  gi|70607927|ref|YP_256797.1| 84 IEAV 87
                                  *987 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.6   5.3e-05      0.06       1      70 [.       2      88 ..       2      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.3e-05
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....................-EEECECHHHHHHH- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....................vkvtavdneeaaeea 62
                                  k+ +iG+G+mg+++a+ ++      +e++++ + + e ++++ +++                      + +++ + eea+++a
  gi|70607927|ref|YP_256797.1|  2 KVVVIGSGEMGHGIAEVMAIYK---NEVTLV-DIKDEILDKAISKIResldrlkkrgsieeepedilkRITKSINLEEAVKDA 80
                                  6899************999998...888866.66666666666666666668889999*********7444455899****** PP

                                  SEEEE-S- CS
                 F420_oxidored 63 dvvvlavk 70
                                  d v+ av+
  gi|70607927|ref|YP_256797.1| 81 DLVIEAVP 88
                                  ****9998 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.3e-05     0.026       9      71 ..       2      89 ..       1     107 [. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee..........................lekdlegadlv 65
                                  kv+v+G Ge++   ++ ++ ++ +vt+v+ +  e+l++ ++ ++e                           le+ +++adlv
  gi|70607927|ref|YP_256797.1|  2 KVVVIGSGEMGHGIAEVMAIYKNEVTLVDIK-DEILDKAISKIRESldrlkkrgsieeepedilkritksinLEEAVKDADLV 83
                                  79**************************999.5555644443333323333333555555556666555555577799***** PP

                 NAD_binding_7 66 iaatdd 71
                                  i a+++
  gi|70607927|ref|YP_256797.1| 84 IEAVPE 89
                                  998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3     8e-05      0.09       1      38 [.       3      40 ..       3      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelr 38
                                  +++iG G++G  +ae +  ++++v+++d ++e ++++ 
  gi|70607927|ref|YP_256797.1|  3 VVVIGSGEMGHGIAEVMAIYKNEVTLVDIKDEILDKAI 40
                                  79***************996667********9998875 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00014      0.15       4      97 ..       2     105 ..       1     110 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                   EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TT......SSH-HHHHHHHHHHHHHHT......-EEEEESSCHHHHTT- CS
                        OTCace   4 kiafvGdkknnvanslikllarlgmdvvlvaPkg......lepdkevleeakknakksg......gsititedleeavkga 72 
                                   k++ +G   + + ++ ++++a+++ +v+lv  k+      +++  e l+++kk  + ++      ++it + +leeavk+a
  gi|70607927|ref|YP_256797.1|   2 KVVVIGS--GEMGHGIAEVMAIYKNEVTLVDIKDeildkaISKIRESLDRLKKRGSIEEepedilKRITKSINLEEAVKDA 80 
                                   8999994..59**********************998544444466667776665544433456678899999********* PP

                                   SEEEE--SSETTCCGGHHHHHHHHC CS
                        OTCace  73 Dvvytdvwvsmgeekereerlkklk 97 
                                   D v+  v   +  +++ ++rl +++
  gi|70607927|ref|YP_256797.1|  81 DLVIEAVPEIVDLKQNIFKRLDQFT 105
                                   ***9988776666777777777765 PP

>> Spore_YtfJ  Sporulation protein YtfJ (Spore_YtfJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.022        25      50      79 ..      18      47 ..       9      48 .. 0.89
   2 ?    0.4   0.1      0.67   7.5e+02      58      80 .]      68      92 ..      63      92 .. 0.86
   3 ?    1.9   0.0      0.22   2.4e+02      46      74 ..     106     136 ..     105     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                    Spore_YtfJ 50 fLvikkgevkllpvkkssldklidlvpdvv 79
                                  ++ i k+ev+l+ +k++ ldk+i+++ + +
  gi|70607927|ref|YP_256797.1| 18 VMAIYKNEVTLVDIKDEILDKAISKIRESL 47
                                  578999********88********998866 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.67
                    Spore_YtfJ 58 vkllpvkk..ssldklidlvpdvvd 80
                                  +k +++++  +++d +i++vp++vd
  gi|70607927|ref|YP_256797.1| 68 TKSINLEEavKDADLVIEAVPEIVD 92
                                  678899889999***********96 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.22
                    Spore_YtfJ  46 tPvAfLvikkgevkllpvkk..ssldklidl 74 
                                   +P+A+L  +  ++++ +++k  ++ d+++ +
  gi|70607927|ref|YP_256797.1| 106 KPDAILATNTSNIRISEISKfvNKKDRVVGM 136
                                   79****************9999998988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 3613.08
//
Query:       gi|70607928|ref|YP_256798.1|  [L=164]
Description: hypothetical protein Saci_2219 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.4   0.0      0.065   13.7   0.0    1.5  1  SCP2      SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-06     0.065      55      87 ..     102     134 ..      59     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-06
                                   SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEEE CS
                          SCP2  55 dvtlslsledllelaegklnpqkafmqgkLkie 87 
                                     +l ++++++l++++gkl+ + a++ g +ki+
  gi|70607928|ref|YP_256798.1| 102 SLILEAPYDTWLKIIQGKLDVTVALLGGSIKIK 134
                                   47899***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1088.55
//
Query:       gi|70607929|ref|YP_256799.1|  [L=345]
Description: ribonucleotide-diphosphate reductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-18   64.6   1.6    1.3e-17   64.2   1.6    1.1  1  Ribonuc_red_sm   Ribonucleotide reductase, small chain
     0.0088   15.8   0.1      0.079   12.7   0.0    2.3  3  Haem_oxygenas_2  Iron-containing redox enzyme
  ------ inclusion threshold ------
      0.033   14.6   1.2       0.84   10.0   0.5    2.4  2  Rubrerythrin     Rubrerythrin


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   1.6   2.2e-21   1.3e-17      14     239 ..      33     260 ..      28     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.2e-21
                                   HHHHHHHCT---GGGS-..GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCH..HCCBSSHHHHHHHHHHHH CS
                Ribonuc_red_sm  14 elykkleanfWtpeevd..lskDlkdwkekLsedekefikkvlaflalldtivnenlverl..lsevqipearafygfqaa 90 
                                    l+ k ++ fW p +++  +++D +dw+ ++se e+e+ + + + +++ +  v+  l+e +  l+e+   e+ +f++ +  
  gi|70607929|ref|YP_256799.1|  33 RLWAKSNELFWSPLQFKelIQQDKQDWE-TMSESEREISEYIATAFSAGEEAVSRYLAELViaLDELGYTEEVLFLNQFQQ 112
                                   5899************9989*******9.5**************************887762258999************* PP

                                   HHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTT.SCHHHHHHHHHHH.HHHHCCCHHHHHHHH CS
                Ribonuc_red_sm  91 mEniHaesYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskk.deekfaerlvafa.llegilfysgFaail 169
                                   +E+ H++++   ++++++d++++++  +   ++ +l   a     +  +++ ++e++++  + ++  +egi    gF++  
  gi|70607929|ref|YP_256799.1| 113 EETRHTDAFRRWMDSIGMDKDTEKWTTEINPSYYELFYVALPSAAYGVKANpSPESILRFTATYMfSIEGIAAETGFYFWR 193
                                   **********************999999999999999999888777666665667777766666668************** PP

                                   HHHHTTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                Ribonuc_red_sm 170 wlkkrgl.lpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikeavelEkefitdal 239
                                   ++ +rg  l+g++ei++ ++ De+ H+ f+ +l + l  e    ++ l +++ e++  a  l  ++i  ++
  gi|70607929|ref|YP_256799.1| 194 TMWERGRhLKGIYEIVKRVAADESRHLAFGTYLTTMLIGE----DQSLYDKFLEYFNYAGGLAVRLIGTIV 260
                                   **988888*****************************999....777787777777776666555555555 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.24   1.4e+03      98     127 ..      74     102 ..      43     110 .. 0.62
   2 !   12.7   0.0   1.3e-05     0.079      50      78 ..     106     145 ..      73     168 .. 0.72
   3 ?   -0.8   0.0      0.19   1.2e+03       9      27 ..     269     287 ..     264     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.24
               Haem_oxygenas_2  98 llGallalEllvsletlklaeelrelglde 127
                                   + ++ ++ E+++ ++++ l+ +l elg +e
  gi|70607929|ref|YP_256799.1|  74 ATAFSAGEEAVS-RYLAELVIALDELGYTE 102
                                   344555555555.88888888888888874 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.3e-05
               Haem_oxygenas_2  50 n..........HvelyrrllkalGldeeplealpel.pet 78 
                                              H+  +rr++ ++G+d+++++ ++e+ p+ 
  gi|70607929|ref|YP_256799.1| 106 FlnqfqqeetrHTDAFRRWMDSIGMDKDTEKWTTEInPSY 145
                                   14444444444*******************9999995544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.19
               Haem_oxygenas_2   9 pyklvfgdwlalvhsrltd 27 
                                   pyk+++g+++ +v++ +  
  gi|70607929|ref|YP_256799.1| 269 PYKEKWGRYFEWVYKENGL 287
                                   9***********9998874 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00014      0.84       2      61 ..      72     133 ..      50     151 .. 0.62
   2 ?    2.7   0.0     0.025   1.5e+02      24      48 ..     199     222 ..     182     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHHHHHH.HHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH CS
                  Rubrerythrin   2 iLekAiagEssarrlYke.laekak.egypqiaelFeelAeeEreHakilnklleklepele 61 
                                    +++A+++ ++a ++Y + l   ++  gy++   +++++ +eE +H + ++++++++  +++
  gi|70607929|ref|YP_256799.1|  72 YIATAFSAGEEAVSRYLAeLVIALDeLGYTEEVLFLNQFQQEETRHTDAFRRWMDSIGMDKD 133
                                   44556655555555554313333343333333334566666677777777777776666666 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.025
                                   HHTT-HHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  24 akegypqiaelFeelAeeEreHaki 48 
                                    +  ++ i e+ +++A++E++H ++
  gi|70607929|ref|YP_256799.1| 199 GR-HLKGIYEIVKRVAADESRHLAF 222
                                   44.5667888888899999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2512.83
//
Query:       gi|70607930|ref|YP_256800.1|  [L=223]
Description: hypothetical protein Saci_2221 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-05   23.5  22.9    3.3e-05   23.1  22.9    1.1  1  DUF973    Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1  22.9   1.9e-09   3.3e-05       4     202 ..      32     216 ..      29     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.9e-09
                        DUF973   4 gleklregslfliiasllaliliilvlvvlftaissglsqliqssasilssvlllliaaiiliiiasvllilgllkirsgf 84 
                                   gl ++++ sl++ i s++++i+ +l  ++ ++a  + l          + + ++ li  +i+++i+ +l   +++ +  g+
  gi|70607930|ref|YP_256800.1|  32 GLLSIKRFSLLYTI-SFFVIIAGLLGTLTSIPAFPTPL---------FFIIPVVSLI-FVIITAIGFLLGTASINVLSIGL 101
                                   67788888999999.55555555555555655444444.........2223333444.455588999999999999***** PP

                        DUF973  85 siLsstgrdvgiGitgltli..ligaiiiiigvilaivsllslilslillgviilligiilaliGqillglsfyklGevYn 163
                                    iL ++++d +   +   ++  l+  i +++ +il +++l ++   ++ + ++i+ i+i +++iG i  ++++ klG++Y+
  gi|70607930|ref|YP_256800.1| 102 TILGKIKKDYNSRLVEFSILtpLVTGIGLLVFLILGLLGLNPVPVLELNIVMAIIGIAIAVFFIGMIAAAIKMWKLGKRYE 182
                                   *********99877655544236666666777788888999999999********************************** PP

                        DUF973 164 nglikigGiliiipvidilsfIGyilsyiglgnvlsklr 202
                                   +  ++igGi + +         G il+yi  ++  +k++
  gi|70607930|ref|YP_256800.1| 183 SWGLRIGGIFLFLL-----PPLGGILTYIFSSRAAKKVK 216
                                   *********87665.....67888888887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1685.39
//
Query:       gi|70607931|ref|YP_256801.1|  [L=95]
Description: hypothetical protein Saci_2222 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 732.87
//
Query:       gi|70607932|ref|YP_256802.1|  [L=141]
Description: hypothetical protein Saci_2223 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-09   37.2   0.0    2.5e-09   37.0   0.0    1.1  1  COXG      Carbon monoxide dehydrogenase subunit G (CoxG)


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.4e-13   2.5e-09      11     137 ..      17     137 ..       8     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.4e-13
                                   HHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE...EEEEEE-SSEEEEEEEEE CS
                          COXG  11 avwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsfkarvelselekenstt.ieikGkGrgagvaidfalvv 90 
                                   + ++f+ d +++  ciP++ s     +e ++k+k+k   l  ++k+++   e+ +e     +    k +ga ++i +  +v
  gi|70607932|ref|YP_256802.1|  17 KTLQFIGDQNNFVGCIPNIVSA----NENTFKAKVKALGLPLTVKGELYKYEISPETLILtVGLRVKTTGAVIDIITRSKV 93 
                                   5679999************999....5555555566666666669999999999999775577888888888888888888 PP

                                   EEEEETTEEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHH CS
                          COXG  91 lveegggtrlswsakvnvggllaslGsrlidsaarklinelfeciss 137
                                     ++   +++ w+ ++n++g l+ l + l++s++++ + +++eci+ 
  gi|70607932|ref|YP_256802.1|  94 KEDG---SQVIWDTQYNIAGPLKILLKPLLESVTEQTVVDTIECIKL 137
                                   7755...**************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1017.03
//
Query:       gi|70607933|ref|YP_256803.1|  [L=352]
Description: alcohol dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-30  104.9   0.3    3.8e-30  104.0   0.3    1.5  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    2.2e-24   85.9   0.0    4.5e-24   84.9   0.0    1.5  1  ADH_zinc_N       Zinc-binding dehydrogenase
    7.3e-07   28.9   0.5    1.3e-06   28.1   0.5    1.3  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    7.7e-07   30.2   0.0    1.3e-06   29.5   0.0    1.3  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
     0.0017   17.7   3.9      0.002   17.5   3.1    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0026   17.2   0.2      0.005   16.2   0.2    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.057   13.7   0.1      0.087   13.1   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.076   13.7   0.1        0.2   12.3   0.1    1.7  1  PglD_N           PglD N-terminal domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.3   1.7e-33   3.8e-30       2     108 ..      26     139 ..      25     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.7e-33
                                   TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSS..EE---EEEEEEEEESTT-CS...--TT-EEEE-SEEE-SSSHHHHTT- CS
                         ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklp..lilGHEivGeveevgpevkk...lkvGdrVvvepliscgeCaaCkege 77 
                                   ge+li+v+++g+C+sD+h +kg+  l   +p  +ilGHEi+G ve++gp+v++   l++Gd V+v+++++cg+C++C +g+
  gi|70607933|ref|YP_256803.1|  26 GEILIRVASTGVCHSDIHHMKGE-LLGFMPPegFILGHEISGWVEDFGPNVTNpygLQKGDPVIVSWIVPCGKCRYCASGK 105
                                   79********************5.555444445************************************************ PP

                                   GGG-TT..BEETTTS.S-SSSBSEEEECGGGEEE CS
                         ADH_N  78 enlCee..akllgvs.ldGgfaeyvvvpekklvk 108
                                   en+C++  +k+ g+  ++Gg+aey+ vpe  +++
  gi|70607933|ref|YP_256803.1| 106 ENYCNNvmMKMPGLIgINGGHAEYTSVPEIAVIP 139
                                   ****66225555554799**********987775 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0     2e-27   4.5e-24       1     129 [.     181     311 ..     181     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2e-27
                                   HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEE CS
                    ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllk 80 
                                   gvG+aa+qlA  +G   +iavd+ ++kl+++k+lGa++++n++++d+v +i e+  +eg+d+v+e+   +  l+ a+++++
  gi|70607933|ref|YP_256803.1| 181 GVGSAAIQLASVMGLyPIIAVDVVDSKLAKVKELGATHTVNPNKEDPVGKITEIL-PEGADIVYETKP-NPDLQIAFNVVN 259
                                   9**************99*************************444**********.9***********.************ PP

                                   EEEEEEECSCTSSEEE.EEHHH..HHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                    ADH_zinc_N  81 pgGrlvvvGggkgeee.fdlrn..lllkeksilGsllgslreefkealdlla 129
                                   + G++vv G+g   ++ ++l+   ++ + ++++Gsl++++r +++e+++++a
  gi|70607933|ref|YP_256803.1| 260 KSGTMVVTGLGNATSStINLMTnlFVGRGLKVVGSLGYRPRIDLPELVRMVA 311
                                   *********94444445555554366*********************99987 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.5   5.7e-10   1.3e-06      29     203 ..     169     338 ..     150     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.7e-10
                   Glu_dehyd_C  29 wepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvd..sretpvdeipeas.eemdlvvE 106
                                      +s++v+G+G +G  a ++l++  +gl     + + d  d ++  v+elGat     ++e+pv +i+e+  e  d+v+E
  gi|70607933|ref|YP_256803.1| 169 SAGQSVVVIGTGGVGSAA-IQLAS-VMGLY---PIIAVDVVDSKLAKVKELGATHTVnpNKEDPVGKITEILpEGADIVYE 244
                                   45689**********988.45543.35554...444456677888899*****9964226899*****99853889***** PP

                   Glu_dehyd_C 107 aTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvt 187
                                   +  ++   + a + ++  G ++ +G+ + ++  ++   + + +v +   +vGs   + r     + ++ a  +  +++lvt
  gi|70607933|ref|YP_256803.1| 245 TKPNPDLQI-AFNVVNKSGTMVVTGLGNATSSTINL--MTNLFVGRGLKVVGSLGYRPRIDLPELVRMVASGKLDVKKLVT 322
                                   998887665.78999***********9988777654..66778889999*****98877555555555555555689**** PP

                   Glu_dehyd_C 188 kvvdldeleeAfeddd 203
                                   +v+  de+++A+e+ +
  gi|70607933|ref|YP_256803.1| 323 HVYRPDEINTAYENLE 338
                                   ************9755 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.8e-10   1.3e-06       1     125 [.     214     340 ..     214     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.8e-10
                                   TT-SEEEETTSTTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE-- CS
                  ADH_zinc_N_2   1 lGAdevidyrtedfe...aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyef 77 
                                   lGA++ ++  +ed +   +++ +eg D+v++t  +++l + +++v+++ G++v+ g g  +s++++  ++   gr++k++ 
  gi|70607933|ref|YP_256803.1| 214 LGATHTVNPNKEDPVgkiTEILPEGADIVYETKPNPDL-QIAFNVVNKSGTMVVTGlGNATSSTINLMTNLFVGRGLKVVG 293
                                   8******9997777778866669*********99**99.88999**777**999998888777776666655555555555 PP

                                   GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS CS
                  ADH_zinc_N_2  78 lfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesg 125
                                    +  ++  + d l el++++++Gk  ++  v++v+  +e+++A++ le+g
  gi|70607933|ref|YP_256803.1| 294 SLGYRP--RID-LPELVRMVASGKldVKKLVTHVYRPDEINTAYENLEKG 340
                                   553344..466.************555678999***************99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.1   8.8e-07     0.002      28      76 ..     171     219 ..     152     245 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-07
                                   --EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTCECE CS
                   AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslgakfve 76 
                                      v+viG G +G +Ai+ a+ +g   + ++Dv  ++l ++++lga+  +
  gi|70607933|ref|YP_256803.1| 171 GQSVVVIGTGGVGSAAIQLASVMGLyPIIAVDVVDSKLAKVKELGAT-HT 219
                                   3469********************7369999************9998.33 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   2.2e-06     0.005      35      81 ..     170     217 ..     159     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                                   TTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCE CS
                  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgve 81 
                                   +g+ v +iG+G +G+a++++++ +g+  +ia+d+  +k ++++elg++
  gi|70607933|ref|YP_256803.1| 170 AGQSVVVIGTGGVGSAAIQLASVMGLyPIIAVDVVDSKLAKVKELGAT 217
                                   7999*********************999******99987788888774 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.9e-05     0.087       1      73 [.     174     242 ..     174     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.SEE CS
               Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.dlv 73 
                                   v++iG G+vG+a+++l +  + +   i+ +d  ++kl+++++  lg   +++  ++e++   ++++l eg d+v
  gi|70607933|ref|YP_256803.1| 174 VVVIGTGGVGSAAIQLASVMGLY--PIIAVDVVDSKLAKVKE--LGA-THTVNPNKEDPVGKITEILPEGaDIV 242
                                   89*******************99..89999999999999975..343.44444455554444555555555665 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.8e-05       0.2       2      40 ..     174     215 ..     173     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
                        PglD_N   2 ivIiGaGGhgkvvadiieangeyeiig..flDdnk.kteveg 40 
                                   +v+iG GG g   ++++  +g y ii+  ++D++  k ++ g
  gi|70607933|ref|YP_256803.1| 174 VVVIGTGGVGSAAIQLASVMGLYPIIAvdVVDSKLaKVKELG 215
                                   89**********************998667888741344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2438.56
//
Query:       gi|70607934|ref|YP_256804.1|  [L=541]
Description: medium-chain-fatty-acid-CoA ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-92  310.9   0.0    1.4e-92  310.5   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.6e-18   65.5   0.0    1.2e-17   64.6   0.0    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.5   0.0   1.5e-96   1.4e-92       9     422 ..      24     436 ..      17     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 310.5 bits;  conditional E-value: 1.5e-96
                                   TTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHH CS
                   AMP-binding   9 pdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayi 89 
                                   p +  ++   + +++T++ + e ++ lA++L+++Gvkkgd V+++ + +  ++ +++a+ ++Gav+ ++n ++++e +   
  gi|70607934|ref|YP_256804.1|  24 PTREIVYT--DKRRYTFKKFAESAKILANALKKIGVKKGDIVGVIDWDTDVYMHLYYAVPMIGAVLHTVNLRYPPELIIKT 102
                                   66666655..89********************************************************************* PP

                                   HHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.......-TSCCCS-BTTSEEE CS
                   AMP-binding  90 ledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae.......kpeeeeelkpddlay 163
                                   + ++e k +i  + ++l+  +++++   +   +  ++++d+ +k     +++  + ++        +p +ee lk+d +a+
  gi|70607934|ref|YP_256804.1| 103 MLHAEDKWVI--IRDDLIGLVEDIKNFNPN--IRFIIYNDDKEKI--KVDDKTIDFWDLlqgepkyDP-DEEGLKEDMMAT 176
                                   **********..555554444444443333..3333333232211..222222233321334455445.6678******** PP

                                   EEEE--SSSS-EEEEEEHHHHHHHHHHHH.HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH CS
                   AMP-binding 164 iiYTSGTTGkPKGVmlshrnlvanvaslk.letr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaald 241
                                   ++YTSGTTG+PKGV  +hr lv  + ++  +++    +l+ +dvv+s +p++h+ ++  + ++al+sG + vl+   +   
  gi|70607934|ref|YP_256804.1| 177 LMYTSGTTGNPKGVWFTHRDLVLHAMAMGtISRAppVELTTRDVVMSLVPMFHVHSW-GFPYVALASGLKYVLPGVYN--- 253
                                   *********************99999987655556555777****************.***************77444... PP

                                   HHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSS CS
                   AMP-binding 242 pklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttg 322
                                   p++ l+li++++vt+ a vP++l ++l++++++ ++k   l+ ++++ +gge+l++ l+r++r+ +++ ++ gYGlTEt++
  gi|70607934|ref|YP_256804.1| 254 PATQLKLIANEGVTFSAMVPTILFMILAQPDID-DYK-PYLKNWKVA-IGGEALPEGLARKAREYGIK-LYSGYGLTETCP 330
                                   55669***********************99998.333.357778875.7****************997.************ PP

                                   ECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCC CS
                   AMP-binding 323 vvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegr 394
                                   v+tv         +++e++ + + s+G p+pgv+++ivDee g+ vp+g+ Ge++vr p++++ Y+k+pe+ta+ +   g+
  gi|70607934|ref|YP_256804.1| 331 VLTVayhnsivesFDEEKKFEIQLSAGVPIPGVKLRIVDEE-GKDVPRGKIGEIVVRAPWTTREYYKDPEKTAQLWR--GG 408
                                   **777899999*988888889999****************9.********************************997..57 PP

                                   EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                   AMP-binding 395 wlrTGDlgrldedGyleivgRkkdlikl 422
                                   wl+TGDlg++de Gyl++v+R kd ik+
  gi|70607934|ref|YP_256804.1| 409 WLHTGDLGYIDEYGYLHLVDREKDAIKS 436
                                   **************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.0   1.4e-21   1.2e-17       2      76 .]     446     523 ..     445     523 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 1.4e-21
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--..HHHHHHHHHHH.HT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea..leeeLkahvrk.elgpyavpkkvvfvdelpktrsGK 76 
                                   +E +++ hp Vae+aVvG+++e++Ge++vaf+v++ g+ ++  +++ L+++v++ ++ +++ p+++ +v+++pkt + K
  gi|70607934|ref|YP_256804.1| 446 LETVISLHPSVAEVAVVGIRHEKWGERPVAFIVPN-GQfDEveMRKFLMKKVEEgKIQKWWIPDRFFVVEDIPKTSTMK 523
                                   699*******************************5.7554457999999999656********************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3767.36
//
Query:       gi|70607935|ref|YP_256805.1|  [L=136]
Description: hypothetical protein Saci_2226 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-18   66.1   0.2    2.9e-18   66.0   0.2    1.0  1  COXG      Carbon monoxide dehydrogenase subunit G (CoxG)
  ------ inclusion threshold ------
      0.026   14.6   0.4      0.033   14.2   0.4    1.2  1  DUF4595   Domain of unknown function (DUF4595) with porin-lik
       0.11   12.6   0.0       0.21   11.7   0.0    1.5  1  P2        P2 response regulator binding domain


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.2   4.9e-22   2.9e-18       1     139 [.       7     134 ..       7     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 4.9e-22
                                   EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEEE-SS CS
                          COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsfkarvelselekensttieikGkGrgag 81 
                                   G+f+v+  ++++++f  ++ ++ +ciP   ++    +++k+k+++ vG +k+++ +++   ++ +++ ++  ++++G+g++
  gi|70607935|ref|YP_256805.1|   7 GKFKVKD-PAKAVQFASNYSNFISCIPTARDI----KDKKFKLDATVGAMKVTVDGELIDYKITENG-YVATVQIRGPGVT 81 
                                   7899987.88999*******************....99**************999999989998888.568999****999 PP

                                   EEEEEEEEEEEEEETTEEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                          COXG  82 vaidfalvvlveegggtrlswsakvnvggllaslGsrlidsaarklinelfecisskl 139
                                   ++  ++ ++        ++ w+a+++ +g ++ + + l+d+ ++ + n+++eci++kl
  gi|70607935|ref|YP_256805.1|  82 TTTTTKSTLNG-----DEVTWEAEYKNEGSMVAMLGNLLDTSVQTMMNQTAECIKNKL 134
                                   99888877766.....68**************************************98 PP

>> DUF4595  Domain of unknown function (DUF4595) with porin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   5.6e-06     0.033      44     100 ..      54     119 ..      33     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-06
                       DUF4595  44 tvtdedgnvvtytLnekgyvtscer............selakstrtynFsYdsdgqLvkieesesgget 100
                                   t    dg+ ++y ++e+gyv+ ++             s+l ++++t++ +Y ++g +v + ++  +++ 
  gi|70607935|ref|YP_256805.1|  54 T---VDGELIDYKITENGYVATVQIrgpgvttttttkSTLNGDEVTWEAEYKNEGSMVAMLGNLLDTSV 119
                                   3...3688888888999998888878888888888899999*****************99888777555 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.5e-05      0.21      24      78 ..      19      74 ..      16      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.5e-05
                                  HHHHHTTEEEEEES-HHHHHTT-SSSEEEEEEE.ESS-HHHHHHHHHTSSS-SEEE CS
                            P2 24 kaLeelgeiiksiPsvedieeekfdegfevvll.tkeskeeikealasiseiesve 78
                                  +  +++++ i++iP++ di+++kf+ + +v     + + e i  ++ +   + +v+
  gi|70607935|ref|YP_256805.1| 19 QFASNYSNFISCIPTARDIKDKKFKLDATVGAMkVTVDGELIDYKITENGYVATVQ 74
                                  556788999***************99999987535777777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1054.27
//
Query:       gi|70607936|ref|YP_256806.1|  [L=155]
Description: hypothetical protein Saci_2227 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-34  116.2   0.0    9.7e-34  116.0   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    8.7e-21   74.2   0.0    9.9e-21   74.0   0.0    1.0  1  Redoxin     Redoxin
  ------ inclusion threshold ------
      0.043   13.3   0.0      0.046   13.2   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
      0.048   13.6   0.0        0.2   11.6   0.0    1.9  1  SCO1-SenC   SCO1/SenC
      0.084   12.2   0.0       0.11   11.8   0.0    1.2  1  FPV060      Viral CC-type chemokine
       0.11   12.6   0.0       0.19   11.9   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   3.2e-37   9.7e-34       1     123 [.       4     125 ..       4     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 3.2e-37
                                   TTSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                   +g+kap fe+ +  ge +sl+d+ g   +vl+fypkd++p+Ctte++a++++++ +k  ++ vigvs+d+  shkkf++k+
  gi|70607936|ref|YP_256806.1|   4 IGEKAPIFEAVTDSGERISLADFIGkYNIVLYFYPKDDTPGCTTEACAFRDNWDSLKGFDAMVIGVSSDDTNSHKKFKQKY 84 
                                   89*********************8834599*************************************************** PP

                                   H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  81 slnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                   +l+f l+sD+++k+ + y++      l+ r tfvidk+g+ir+
  gi|70607936|ref|YP_256806.1|  85 NLPFILVSDPDKKIREMYNAK--GFILPARITFVIDKKGVIRH 125
                                   *********************..56799999***********8 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   3.3e-24   9.9e-21       2     147 .]       4     144 ..       3     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.3e-24
                                   TTSBB---ECCEETTCEEEEEHHHHTTSE.EEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkk.vvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefw 80 
                                    g+kaP f+   +++ g+ +sl++f gk  +v++f+p  ++P C++e++ + ++ + l k  +  v++v++d+ +  k+f 
  gi|70607936|ref|YP_256806.1|   4 IGEKAPIFEA--VTDSGERISLADFIGKYnIVLYFYPKDDTPGCTTEACaFRDNWDSL-KGFDAMVIGVSSDDTNSHKKFK 81 
                                   5899**9996..67**********999977*******************666777777.77777778888888888***** PP

                                   HHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHT.STTSHHHHH CS
                       Redoxin  81 gkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepet.eesnaeavl 147
                                    k++l+f+++sD+++++ ++++++       g  l ++ ++vid++g+++++++ +++++  +++a ++l
  gi|70607936|ref|YP_256806.1|  82 QKYNLPFILVSDPDKKIREMYNAK-------GfiLPARITFVIDKKGVIRHIYNSQMNPGnHVNEALKAL 144
                                   **********************77.......445688889******************878888877665 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.046      65     179 ..      27     131 ..       1     146 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                        DUF899  65 egrsqLivyhfmfgpdaeegCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdf 145
                                    g+ ++++y   f p+     pgC++ a ++  +   L+  d +++ vs   +++ +++k++    + +vs+ +++  + +
  gi|70607936|ref|YP_256806.1|  27 IGKYNIVLY---FYPK--DDTPGCTTEACAFRDNWDSLKGFDAMVIGVSSDDTNSHKKFKQKYNLPFILVSDPDKKIREMY 102
                                   555555554...3333..34589999999999999*******************************************999 PP

                        DUF899 146 nvsleeeqaseelpglsvflrdd.grvfhtYstya 179
                                   n++         lp+  +f+ d+ g ++h Y ++ 
  gi|70607936|ref|YP_256806.1| 103 NAK------GFILPARITFVIDKkGVIRHIYNSQM 131
                                   973......35688889999888899****99865 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.5e-05       0.2       4     102 ..      11     104 ..       8     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
                     SCO1-SenC   4 FelvdqdgeavteedlegkpslvffgFthCpd.vCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafd 83 
                                   Fe v+ +ge+++ +d+ gk+ +v +++ +  +  C+t+    ++  d l+     +++++i v    D+ +  k++ ++++
  gi|70607936|ref|YP_256806.1|  11 FEAVTDSGERISLADFIGKYNIVLYFYPKDDTpGCTTEACAFRDNWDSLK----GFDAMVIGVS--SDDTNSHKKFKQKYN 85 
                                   99********************9999987655245555555555555544....4466666663..566667788888888 PP

                     SCO1-SenC  84 priigltGskeeiakaake 102
                                     +i ++++ ++i++++++
  gi|70607936|ref|YP_256806.1|  86 LPFILVSDPDKKIREMYNA 104
                                   8888888888888887765 PP

>> FPV060  Viral CC-type chemokine
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.11      95     124 ..      42      73 ..      23      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                        FPV060  95 drgctgeccdlrenvdslrannp..lgccndy 124
                                     gct e+c +r+n dsl+  +   +g+  d 
  gi|70607936|ref|YP_256806.1|  42 TPGCTTEACAFRDNWDSLKGFDAmvIGVSSDD 73 
                                   459***************98765114555555 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.2e-05      0.19      12      82 ..      60     149 ..      52     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                    AhpC-TSA_2  12 agvklvaig..igdp.sakkFvkltgfpfelyvDpsaklyqalglk..............rglklkl..aplslqkalenl 73 
                                   +g++ ++ig   +d  s kkF +  + pf l+ Dp++k+ +  + k              +g   ++  ++++  + ++++
  gi|70607936|ref|YP_256806.1|  60 KGFDAMVIGvsSDDTnSHKKFKQKYNLPFILVSDPDKKIREMYNAKgfilparitfvidkKGVIRHIynSQMNPGNHVNEA 140
                                   56665555522667766*********************9888888877788888888877444444421233344457777 PP

                    AhpC-TSA_2  74 lkrlkeigi 82 
                                   lk lk+i++
  gi|70607936|ref|YP_256806.1| 141 LKALKQIKS 149
                                   777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1116.28
//
Query:       gi|70607937|ref|YP_256807.1|  [L=188]
Description: indolepyruvate oxidoreductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-35  121.5   0.3    4.6e-35  121.3   0.3    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.3   2.6e-39   4.6e-35       1     175 [.      12     180 ..      12     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.6e-39
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                   GGqG++t+gk++a+a  ++  +v+ ++++g ++rGg++++hvri+d   +p i+ g+ad+lv+l+a+++ ++l+++ ++++
  gi|70607937|ref|YP_256807.1|  12 GGQGIITMGKMIAEAGNYCNVKVLVAETHGLAQRGGAVNVHVRIGDV-NSPLIPLGGADYLVGLEATEVLRNLNYCSKNTV 91 
                                   9********************************************97.899****************************** PP

                                   EEEECTCGTT-CCHHHCTS-HHHHHHH.T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH CS
                           POR  82 iiynseelkpdelkkakeeerelkerl.gvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkrfpkk 161
                                   i++n+  l p   k +++e re+ +rl g++v  ++a +ia+++g+ ++a+N+++lG+l+ ++ ++    eea  k+++  
  gi|70607937|ref|YP_256807.1|  92 IVLNNYVLRPVLPKVRLLEIREVLDRLkGLNVHLINAYEIAEKAGN-TKAVNAALLGYLYSIGAFKGLLTEEAFYKSLK-- 169
                                   *****************9999999888**************88666.***************99999999999999999.. PP

                                   .HHHHHHHHHHHHH CS
                           POR 162 keviekNlkafrag 175
                                      +e N+kaf+ +
  gi|70607937|ref|YP_256807.1| 170 ---YESNVKAFQSA 180
                                   ...89******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1371.83
//
Query:       gi|70607938|ref|YP_256808.1|  [L=611]
Description: indolepyruvate ferredoxin oxidoreductase alpha [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.1   0.0    2.1e-20   73.0   0.0    1.6  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.4e-13   51.1   0.1    6.7e-13   48.9   0.0    1.9  2  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.5e-10   39.4   0.6    7.7e-06   25.6   0.0    2.2  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    2.4e-09   36.6  15.2    2.6e-07   30.2   5.9    2.7  2  Fer4             4Fe-4S binding domain
    5.4e-09   36.5   4.6    1.3e-05   25.6   0.3    2.5  2  Fer4_7           4Fe-4S dicluster domain
      9e-07   28.7  22.7    2.1e-05   24.4   5.2    3.0  3  Fer4_6           4Fe-4S binding domain
      2e-06   27.9  10.3    4.2e-06   26.8  10.3    1.6  1  Fer4_9           4Fe-4S dicluster domain
    2.1e-06   27.8  12.0    4.4e-06   26.7  12.0    1.6  1  Fer4_10          4Fe-4S dicluster domain
    4.4e-06   26.5  18.8    0.00033   20.6   3.1    2.9  3  Fer4_2           4Fe-4S binding domain
    4.6e-05   23.5  12.8    7.9e-05   22.7  12.1    1.8  2  Fer4_21          4Fe-4S dicluster domain
    0.00022   22.1   7.5     0.0023   18.8   1.2    2.7  2  Fer4_16          4Fe-4S double cluster binding domain
    0.00055   19.8   0.1     0.0027   17.6   0.0    2.2  2  Transketolase_C  Transketolase, C-terminal domain
     0.0011   19.3  12.6     0.0082   16.6   3.9    2.5  2  Fer4_4           4Fe-4S binding domain
      0.006   17.4   6.7      0.006   17.4   6.7    2.5  1  Fer4_3           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.012   16.1   9.9      0.066   13.8   1.7    2.6  4  Fer4_17          4Fe-4S dicluster domain
      0.014   15.8  11.2       0.07   13.6   2.7    2.6  2  Fer4_8           4Fe-4S dicluster domain
      0.074   12.0   0.0       0.13   11.2   0.0    1.3  1  Glyco_transf_90  Glycosyl transferase family 90
       0.11   13.3   5.7        0.3   11.9   0.6    2.6  2  Fer4_22          4Fe-4S dicluster domain
       0.13   12.8  11.4        1.4    9.5   2.5    2.7  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
        0.4   11.4  13.0          1   10.1   2.6    3.0  2  Fer4_15          4Fe-4S single cluster domain
        1.4    9.1   8.1       0.28   11.4   2.6    2.0  2  Fer4_18          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   2.5e-23   2.1e-20       1     152 [.     387     522 ..     387     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 2.5e-23
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   diGc+tl      ++ +p + ++    + mG ++++A G+ +a  ++  vai+GD++f+++ ++ la+av+++ p++++vl
  gi|70607938|ref|YP_256808.1| 387 DIGCYTL------GLLPPFEEQD--SSTDMGSSVGIANGVYRAT-GNIPVAIIGDSTFFHSgMSGLANAVYNKTPLVLLVL 458
                                   899***9......8899988888..789**************84.669********************************* PP

                                   E-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EE.....EESSH.HHHHHHHHHHHHCSSSEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.ga.....rvekadveeleealkealekkgpalie 152
                                   +N++++mtg+q++p  +             +d+ ++a++lG++ +       + +++v+ l ea+++  ++k+pa+i 
  gi|70607938|ref|YP_256808.1| 459 DNRSTAMTGQQPSPSKE-------------IDIGEVAKGLGVRfVKyfdpfEM-NSSVKSLTEAIEWVKKNKEPAVII 522
                                   ***********999876.............66666666666664444444322.334788899999999*******96 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   7.9e-16   6.7e-13       3     201 ..      21     208 ..      19     233 .. 0.82
   2 ?   -0.6   0.0         1   8.9e+02      77     103 ..     441     468 ..     436     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 7.9e-16
                                   HHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHH CS
                         POR_N   3 aiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaa 83 
                                    +a gv v+a+YP TPs+ei+e+++++ ++++v         +E  a++++ GAa+ Ga a+T+    Gl  + + l+  +
  gi|70607938|ref|YP_256808.1|  21 SLASGVSVAAGYPGTPSTEILETIQKHSRNVYV-----EWSANEKVAFETAYGAAINGAYALTTMKHVGLNVAADPLMSSS 96 
                                   577899**********************99996.....56789***********************************999 PP

                                   HTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEEEE CS
                         POR_N  84 geelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshevek 164
                                    + +   +v+v    ps  +s +++q   ++ +   + v+ + + q a++l ++Af+l+ kv+ Pvi  +  +++sh + +
  gi|70607938|ref|YP_256808.1|  97 YTGVEGAFVIVSADDPSM-WSSQNEQDNRYYGLHGLIPVIEPYDPQSAYNLMIEAFKLSAKVKHPVIFRT-TTRISHVRAP 175
                                   999999999999899999.***********************************************9776.67777***** PP

                                   EEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTS CS
                         POR_N 165 velpdeedelklikekleeyerkeyaldpekpiargt 201
                                   v + +     + i  k   +++k+y l pe+     +
  gi|70607938|ref|YP_256808.1| 176 VSIKPPI---NPIYGKVT-KNPKKYVLVPENARRNRM 208
                                   *998876...23333332.223344566655544444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                   CCHHHHHHTT--EEEEEE.EEE-STTBE CS
                         POR_N  77 enlglaageelPvvivvv.aRalpstgl 103
                                     l  a+ +++P+v+ v  +R+ ++tg+
  gi|70607938|ref|YP_256808.1| 441 SGLANAVYNKTPLVLLVLdNRSTAMTGQ 468
                                   567889999***99765439***99997 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.4   0.00019      0.16       5      70 ..      15      87 ..      12     108 .. 0.68
   2 !   25.6   0.0     9e-09   7.7e-06      50     157 ..     410     521 ..     404     529 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                  HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHH......HHHHHHTS-EEEEE CS
                  TPP_enzyme_N  5 ealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAd......gyaratgkpgvvlv 70
                                  ea++ a  a gv ++ g+pG+ ++++l+ ++++  ++ v  + +E +a   A       +ya  t k + ++v
  gi|70607938|ref|YP_256808.1| 15 EAIALASLASGVSVAAGYPGTPSTEILETIQKHSrNVYVEWSANEKVAFETAYgaaingAYALTTMKHVGLNV 87
                                  5666666677***********************9766666788998887776622224445555555444555 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9e-09
                                   HHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHC....CCS CS
                  TPP_enzyme_N  50 gaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg..qgvlqqeldqlalfr....pvt 124
                                   + +++A g++ratg++ v++    + + +++ +la+A ++++Pl++l+ d+ ++     q+ + +e+d+ ++++     ++
  gi|70607938|ref|YP_256808.1| 410 SSVGIANGVYRATGNIPVAIIGDSTFFHSGMSGLANAVYNKTPLVLLVLDNRSTAMTgqQPSPSKEIDIGEVAKglgvRFV 490
                                   6789***********9999999999************************988777766888999999*****885555667 PP

                                   SEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                  TPP_enzyme_N 125 kyaervtspeelpealrrAirtalsgrpgPvyl 157
                                   ky++  +  ++ ++ l +Ai+   ++++ P+++
  gi|70607938|ref|YP_256808.1| 491 KYFDPFEMNSS-VKSLTEAIEWV-KKNKEPAVI 521
                                   77666666555.44455666666.666666665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.9   0.00028      0.24       2      16 ..     544     558 ..     543     559 .. 0.91
   2 !   30.2   5.9     3e-10   2.6e-07       2      24 .]     574     596 ..     573     596 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                   EEETTTSSS-THHHH CS
                          Fer4   2 videekCigCGaCve 16 
                                   v+d+ kC+gC +C++
  gi|70607938|ref|YP_256808.1| 544 VVDMAKCTGCTICYD 558
                                   89***********97 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 3e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                   +id   CigCGaCv vCP+ AI+
  gi|70607938|ref|YP_256808.1| 574 EIDVYNCIGCGACVPVCPFKAIS 596
                                   699999***************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.4   0.00026      0.23      24      49 ..     536     563 ..     505     566 .. 0.64
   2 !   25.6   0.3   1.6e-08   1.3e-05       2      20 ..     580     598 ..     567     608 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00026
                        Fer4_7  24 nekgtekveidpekClgCgaCva..vCP 49 
                                   ++++ +k+++d+ kC+gC+ C +  +CP
  gi|70607938|ref|YP_256808.1| 536 DDNKLPKAVVDMAKCTGCTICYDyfTCP 563
                                   22355899*************9877787 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 1.6e-08
                        Fer4_7   2 CigCgaCvaaCpvkaield 20 
                                   CigCgaCv++Cp kai+++
  gi|70607938|ref|YP_256808.1| 580 CIGCGACVPVCPFKAISIK 598
                                   8888888888888887776 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4         5   4.3e+03       6      12 ..     355     361 ..     355     361 .. 0.86
   2 !   15.1   3.4   2.1e-05     0.018       1      21 [.     542     564 ..     542     567 .. 0.83
   3 !   24.4   5.2   2.4e-08   2.1e-05       1      24 []     572     595 ..     572     595 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5
                        Fer4_6   6 pdkCigC 12 
                                   p +C gC
  gi|70607938|ref|YP_256808.1| 355 PALCPGC 361
                                   679**** PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.1e-05
                        Fer4_6   1 vveidpdkCigCgdCvrv..CPe 21 
                                   ++++d  kC+gC  C++   CP+
  gi|70607938|ref|YP_256808.1| 542 KAVVDMAKCTGCTICYDYftCPA 564
                                   689************65555*98 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 2.4e-08
                        Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                   ++eid  +CigCg+Cv vCP++ai
  gi|70607938|ref|YP_256808.1| 572 KAEIDVYNCIGCGACVPVCPFKAI 595
                                   6899*****************998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8  10.3     5e-09   4.2e-06       1      51 []     549     595 ..     549     595 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5e-09
                        Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                   kCtgC+ C +   Cpa + ++d++++++ +      +CigCgaCv +Cp +ai
  gi|70607938|ref|YP_256808.1| 549 KCTGCTICYDYftCPAIIPRKDKKAEIDVY------NCIGCGACVPVCPFKAI 595
                                   7*******65445**************999......7************9887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7  12.0   5.2e-09   4.4e-06       2      56 .]     543     591 ..     542     591 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.2e-09
                       Fer4_10   2 vvidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   +v+d  +C++C+ C +   CPa         +  ++++ +++v++C+gcgaCv +CP
  gi|70607938|ref|YP_256808.1| 543 AVVDMAKCTGCTICYDyfTCPA--------IIPRKDKKAEIDVYNCIGCGACVPVCP 591
                                   7899************666***........6666777778899*************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       6.3   5.4e+03       6      13 ..     354     361 ..     350     363 .. 0.70
   2 !   15.0   3.4   2.2e-05     0.019       2      22 .]     542     564 ..     541     564 .. 0.85
   3 !   20.6   3.1   3.9e-07   0.00033       3      21 ..     573     591 ..     571     592 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.3
                        Fer4_2   6 dtdrCigC 13 
                                    ++ C gC
  gi|70607938|ref|YP_256808.1| 354 PPALCPGC 361
                                   56778888 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.2e-05
                        Fer4_2   2 pvvvdtdrCigCgaCvsa..CPa 22 
                                   ++vvd ++C+gC +C++   CPa
  gi|70607938|ref|YP_256808.1| 542 KAVVDMAKCTGCTICYDYftCPA 564
                                   689************85556**8 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 3.9e-07
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +++d  +CigCgaCv +CP
  gi|70607938|ref|YP_256808.1| 573 AEIDVYNCIGCGACVPVCP 591
                                   6789999************ PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.6   0.00074      0.63      18      52 ..     527     563 ..     524     568 .. 0.70
   2 !   22.7  12.1   9.3e-08   7.9e-05       1      57 [.     543     595 ..     543     597 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
                       Fer4_21  18 CedtshqaieidaktvlkvvedeCvGCnlCss..vCP 52 
                                   C    ++ i+ ++  ++ v   +C+GC++C++   CP
  gi|70607938|ref|YP_256808.1| 527 CALLVTDVIDDNKLPKAVVDMAKCTGCTICYDyfTCP 563
                                   5555566676555566677789********8633688 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 9.3e-08
                       Fer4_21   1 AridedkCigCgkCl..iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                   A++d +kC gC+ C+   +C+     ai   +++++++   +C+GC  C+ vCP  ++i
  gi|70607938|ref|YP_256808.1| 543 AVVDMAKCTGCTICYdyFTCP-----AIIPRKDKKAEIDVYNCIGCGACVPVCPF-KAI 595
                                   899***********7336788.....898889999999999*************7.776 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.027        23      53      65 ..     549     563 ..     507     577 .. 0.68
   2 !   18.8   1.2   2.6e-06    0.0023       1      20 [.     579     598 ..     579     607 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                       Fer4_16  53 aitgCdiCqd..vCP 65 
                                   ++tgC iC d  +CP
  gi|70607938|ref|YP_256808.1| 549 KCTGCTICYDyfTCP 563
                                   566666665422344 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.6e-06
                       Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                   +C++Cg+C+ vCP +ai+ k
  gi|70607938|ref|YP_256808.1| 579 NCIGCGACVPVCPFKAISIK 598
                                   6***************9865 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.9   4.1e+03      54      86 ..      40      73 ..      36     103 .. 0.68
   2 !   17.6   0.0   3.1e-06    0.0027       8      73 ..     230     292 ..     225     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.9
                                  HHHHHHHHSEEEEEE.EEESTTSHHHHHHHHHHH CS
               Transketolase_C 54 ilesvkktgrlvvve.eavkrgGigsevaaalae 86
                                  ile ++k+ r v ve  a++ ++++++  aa++ 
  gi|70607938|ref|YP_256808.1| 40 ILETIQKHSRNVYVEwSANEKVAFETAYGAAING 73
                                  5667778888777774566677777777777766 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.1e-06
                                   TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEEST CS
               Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkr 73 
                                    g++ +++a G   +++ +A++eL   +i+a ++ + t  p+  ++il++v + +r+++vee  ++
  gi|70607938|ref|YP_256808.1| 230 NGSKDLIIASGISYSFVKDAMNEL---NIRANLLRISTPVPIPSKLILKAVSEAERVLIVEEVEPI 292
                                   577779******************...6**********************************8765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   1.5    0.0093       7.9       3      15 ..     549     563 ..     547     574 .. 0.90
   2 !   16.6   3.9   9.6e-06    0.0082       3      16 ..     579     592 ..     577     593 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0093
                        Fer4_4   3 rCigCgsCvaa..CP 15 
                                   +C+gC  C+++  CP
  gi|70607938|ref|YP_256808.1| 549 KCTGCTICYDYftCP 563
                                   8**********9999 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9.6e-06
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   +CigCg+Cv +CP+
  gi|70607938|ref|YP_256808.1| 579 NCIGCGACVPVCPF 592
                                   7************8 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.7     7e-06     0.006       1      15 []     580     594 ..     580     594 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-06
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+gCgaCv vCP +A
  gi|70607938|ref|YP_256808.1| 580 CIGCGACVPVCPFKA 594
                                   ************998 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.6     0.033        29      42      58 ..     546     564 ..     510     567 .. 0.60
   2 ?    5.1   1.3      0.04        34       1      21 [.     549     571 ..     549     578 .. 0.78
   3 ?   13.6   1.6   8.5e-05     0.073       1      14 [.     579     592 ..     566     595 .. 0.67
   4 ?   13.8   1.7   7.8e-05     0.066       1      16 [.     579     594 ..     579     605 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                       Fer4_17  42 kaslCieCgeCe..rkCPq 58 
                                    + +C++C  C     CP+
  gi|70607938|ref|YP_256808.1| 546 DMAKCTGCTICYdyFTCPA 564
                                   6778888888875556775 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.04
                       Fer4_17   1 rCiqCgyClp..eCpsyeaydne 21 
                                   +C++C  C +   Cp  + ++++
  gi|70607938|ref|YP_256808.1| 549 KCTGCTICYDyfTCPAIIPRKDK 571
                                   69999999998889987766655 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.5e-05
                       Fer4_17   1 rCiqCgyClpeCps 14 
                                   +Ci+Cg+C+p+Cp+
  gi|70607938|ref|YP_256808.1| 579 NCIGCGACVPVCPF 592
                                   46666666666664 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 7.8e-05
                       Fer4_17   1 rCiqCgyClpeCpsye 16 
                                   +Ci+Cg+C+p+Cp+ +
  gi|70607938|ref|YP_256808.1| 579 NCIGCGACVPVCPFKA 594
                                   699*********9865 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.3     0.012       9.8       2      21 ..     547     568 ..     546     577 .. 0.76
   2 ?   13.6   2.7   8.2e-05      0.07       2      17 ..     577     592 ..     576     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                        Fer4_8   2 lekCieCgaCq..saCpvlrrt 21 
                                   + kC++C  C    +Cp++  +
  gi|70607938|ref|YP_256808.1| 547 MAKCTGCTICYdyFTCPAIIPR 568
                                   789********6667*977555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.2e-05
                        Fer4_8   2 lekCieCgaCqsaCpv 17 
                                   +++Ci+CgaC   Cp+
  gi|70607938|ref|YP_256808.1| 577 VYNCIGCGACVPVCPF 592
                                   6789999999999985 PP

>> Glyco_transf_90  Glycosyl transferase family 90
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.13     260     299 ..     491     530 ..     486     538 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
               Glyco_transf_90 260 ehYvPikskdklrdlkeavdwgnahdekaqeiaeegseFi 299
                                   + + P++ ++++++l ea++w+++++e a  ia+++   +
  gi|70607938|ref|YP_256808.1| 491 KYFDPFEMNSSVKSLTEAIEWVKKNKEPAVIIAKRACALL 530
                                   45569*****************************997655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4      0.21   1.8e+02      76      91 ..     544     559 ..     524     566 .. 0.76
   2 ?   11.9   0.6   0.00035       0.3      74      94 ..     572     592 ..     567     594 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.21
                       Fer4_22  76 kfgesgCvGCgRCiea 91 
                                    +++ +C+GC  C + 
  gi|70607938|ref|YP_256808.1| 544 VVDMAKCTGCTICYDY 559
                                   45889999**999863 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00035
                       Fer4_22  74 kekfgesgCvGCgRCieacpv 94 
                                   k++++ + C+GCg C+ +cp 
  gi|70607938|ref|YP_256808.1| 572 KAEIDVYNCIGCGACVPVCPF 592
                                   56789999***********96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.7    0.0067       5.8       1      19 [.     545     565 ..     545     574 .. 0.78
   2 ?    9.5   2.5    0.0016       1.4       1      17 [.     575     591 ..     575     592 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0067
                       Fer4_13   1 VDrdtCiacgaCve..laPdv 19 
                                   VD  +C++c++C++  ++P +
  gi|70607938|ref|YP_256808.1| 545 VDMAKCTGCTICYDyfTCPAI 565
                                   899*********974467766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                       Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                   +D  +Ci+cgaCv ++P
  gi|70607938|ref|YP_256808.1| 575 IDVYNCIGCGACVPVCP 591
                                   57779***********9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.2     0.011       9.3       2      31 ..     544     574 ..     543     577 .. 0.73
   2 ?   10.1   2.6    0.0012         1       3      19 ..     575     591 ..     573     601 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                       Fer4_15   2 vvDrdaCigcglCvaea..pevfeldedglas 31 
                                   vvD  +C+gc  C++    p ++  + d +a+
  gi|70607938|ref|YP_256808.1| 544 VVDMAKCTGCTICYDYFtcPAIIPRK-DKKAE 574
                                   69***********9974337666665.55555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                       Fer4_15   3 vDrdaCigcglCvaeap 19 
                                   +D  +Cigcg+Cv ++p
  gi|70607938|ref|YP_256808.1| 575 IDVYNCIGCGACVPVCP 591
                                   8999************8 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.9     0.024        20      48      72 ..     567     591 ..     532     592 .. 0.58
   2 ?   11.4   2.6   0.00033      0.28      49      74 ..     568     593 ..     562     601 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.024
                       Fer4_18  48 kekeerkekgagdcidcescvkvcP 72 
                                    +k++++e ++ +ci c++cv vcP
  gi|70607938|ref|YP_256808.1| 567 PRKDKKAEIDVYNCIGCGACVPVCP 591
                                   3345555555556666666666665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                       Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                   +k++++e ++ +ci c++cv vcP +
  gi|70607938|ref|YP_256808.1| 568 RKDKKAEIDVYNCIGCGACVPVCPFK 593
                                   57788888999*************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4167.71
//
Query:       gi|70607939|ref|YP_256809.1|  [L=144]
Description: hypothetical protein Saci_2230 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-11   43.0   0.0    4.7e-11   42.3   0.0    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    3.7e-05   23.6   0.0    5.4e-05   23.1   0.0    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
      0.027   14.5   0.1      0.041   13.9   0.1    1.4  1  DZR            Double zinc ribbon
      0.041   13.8   2.4       0.93    9.5   0.2    2.4  2  zf-dskA_traR   Prokaryotic dksA/traR C4-type zinc finger
       0.65   10.1   3.4         21    5.2   0.2    2.7  3  zinc_ribbon_6  Zinc-ribbon


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.3e-14   4.7e-11       1      33 [.      36      68 ..      36      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.3e-14
                       DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgs 33
                                  +++++e+++vg++C++CG+v+ PPr +C  C+ 
  gi|70607939|ref|YP_256809.1| 36 FQGLKENKIVGSKCKKCGKVYLPPRIYCEDCFT 68
                                  689****************************95 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.5e-08   5.4e-05       7      62 ..      80     132 ..      73     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                                   G-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEEEES..TT-B-EE CS
                 OB_aCoA_assoc   7 rGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvdpdevriGmrVra 62 
                                    + + sft+++++ +g++ ++P+++g+ ++ +  + ++++l g +    + G r r+
  gi|70607939|ref|YP_256809.1|  80 DAYLDSFTTIYQNDDGQKLTEPVHIGLLRFKGvNGGLFCYLEGTP----KKGGRIRV 132
                                   789*****************************4222666666555....56666665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.2e-05     0.041       1      26 [.      49      74 ..      49     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                           DZR  1 CpqCgeelppdarfCseCgtklkava 26
                                  C++Cg+   p  ++C++C tk++++ 
  gi|70607939|ref|YP_256809.1| 49 CKKCGKVYLPPRIYCEDCFTKIEEYV 74
                                  *********************98765 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.013        45       2      10 ..      44      53 ..      43      54 .. 0.85
   2 ?    9.5   0.2   0.00026      0.93      20      35 ..      56      71 ..      55      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                  zf-dskA_traR  2 iygs.CeeCG 10
                                  i gs C +CG
  gi|70607939|ref|YP_256809.1| 44 IVGSkCKKCG 53
                                  78999***** PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00026
                  zf-dskA_traR 20 alPgarlCveCqekae 35
                                   lP +++C +C++k+e
  gi|70607939|ref|YP_256809.1| 56 YLPPRIYCEDCFTKIE 71
                                  5799**********98 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2    0.0058        21      44      54 ..      43      53 ..      38      55 .. 0.88
   2 ?    4.3   0.3     0.011        41      29      39 ..      60      70 ..      58      78 .. 0.82
   3 ?   -0.3   0.0      0.32   1.1e+03      19      45 ..      78     104 ..      67     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0058
                 zinc_ribbon_6 44 hvlglkCkeCg 54
                                  +++g kCk+Cg
  gi|70607939|ref|YP_256809.1| 43 KIVGSKCKKCG 53
                                  689*******7 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                 zinc_ribbon_6 29 kilCnDCekks 39
                                  +i+C+DC +k 
  gi|70607939|ref|YP_256809.1| 60 RIYCEDCFTKI 70
                                  69*****8775 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.32
                 zinc_ribbon_6  19 mpeeyknkkvkilCnDCekksevkfhv 45 
                                   + + y ++ ++i+ nD ++k + + h+
  gi|70607939|ref|YP_256809.1|  78 LDDAYLDSFTTIYQNDDGQKLTEPVHI 104
                                   667888899999999999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1074.93
//
Query:       gi|70607940|ref|YP_256810.1|  [L=165]
Description: hypothetical protein Saci_2231 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-08   33.0   0.2    7.2e-08   32.2   0.2    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00014   21.7   0.3    0.00021   21.2   0.3    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
       0.24   11.7   0.5       0.24   11.7   0.5    1.6  2  zf-C6H2        zf-MYND-like zinc finger, mRNA-binding
        1.5    8.9   4.3        3.3    7.8   4.3    1.6  1  ADK_lid        Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.2   1.6e-11   7.2e-08       3      34 ..      38      69 ..      36      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.6e-11
                       DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                  +++eg+++g++C +CG+ ++PP  +C  C++ 
  gi|70607940|ref|YP_256810.1| 38 GLKEGKILGRKCVKCGKIYVPPKMYCDECFRP 69
                                  79***************************975 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   4.7e-08   0.00021       1      65 []      73     147 ..      73     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-08
                                   EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-.TT.........-EE-EEEEEEES......TT-B-EEE-S CS
                 OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeL.degvr......imarlvgvdpdevr....iGmrVravfr 65 
                                   wve+ ++G v++++    + ++++ ++P  vgv++L +  +r      i++rl+   ++ vr    iG rV+av+r
  gi|70607940|ref|YP_256810.1|  73 WVEVMDEGYVMTAVASFISWTREKISEPELVGVIRLlPSNPRdfvypgIFHRLCVSYEE-VRnmsvIGKRVKAVWR 147
                                   9*************888888***************7366999************66655.555555*********7 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   5.3e-05      0.24      14      35 ..      48      68 ..      41      74 .. 0.90
   2 ?   -3.7   0.1       3.6   1.6e+04      32      35 ..     160     163 ..     158     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                       zf-C6H2 14 qCptClklgikesfFCsqeCFk 35
                                  +C++C k  ++ +++C+ eCF+
  gi|70607940|ref|YP_256810.1| 48 KCVKCGKIYVPPKMYCD-ECFR 68
                                  8***************7.7**8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.6
                       zf-C6H2  32 eCFk 35 
                                   +CFk
  gi|70607940|ref|YP_256810.1| 160 QCFK 163
                                   6887 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.3   0.00074       3.3       2      27 ..      47      66 ..      47      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00074
                                  EE-TTT--EEETTTB--SSTTB-TTT CS
                       ADK_lid  2 rvCpkCGrsYhvvfnpPkveglCDkC 27
                                  r C kCG++Y     pPk  + CD+C
  gi|70607940|ref|YP_256810.1| 47 RKCVKCGKIYV----PPK--MYCDEC 66
                                  67*********....885..*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1177.76
//
Query:       gi|70607941|ref|YP_256811.1|  [L=392]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-13   50.2   0.3    4.5e-12   45.9   0.3    2.4  1  Thiolase_N   Thiolase, N-terminal domain
    0.00099   18.8   0.0       0.99    9.1   0.0    2.5  2  Thiolase_C   Thiolase, C-terminal domain
  ------ inclusion threshold ------
        0.1   12.5   0.1        2.6    7.9   0.0    2.3  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.3   7.5e-16   4.5e-12       1     260 []      11     229 ..      11     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 7.5e-16
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHH.HHHHTTS-TTSEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarq.aalkagipeevpavt 80 
                                   v++++a +t++ +        + +e++ ea +++le+ag++ ++++ v++G    a++g n++ + +++ +g     p+++
  gi|70607941|ref|YP_256811.1|  11 VAVIGAGMTQFRR----RILETPQEIAWEASSKALEEAGLELKDIECVVIGSAPDAFDGVNLKGEyLSHGSGG-IRKPSSR 86 
                                   799*********9....5667899*************************************666515555554.7999*** PP

                                   EEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHH CS
                    Thiolase_N  81 vnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaen 161
                                   v    + g++a ++++  +a+g ++ v+++  E+ms a    ++ +     + d ++++ l p+ ++        ++   +
  gi|70607941|ref|YP_256811.1|  87 VFVGGATGVMAAITGWYHVASGMCNTVLVVAEEKMSPARPHPQSVF---RYIWDPILEKPLNPNLIW------IFAMEMHR 158
                                   ************************************8766555232...234455666666666222......4588899* PP

                                   HHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTT CS
                    Thiolase_N 162 lakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAg 242
                                   + ++y+i +ee + + vk++++aa+++ a+ +  +i              + d+ ++sev + +++ l             
  gi|70607941|ref|YP_256811.1| 159 YMATYGIKKEEIALVSVKNKRNAANNPYAQ-LGGNI--------------TVDDVLNSEVLVWPVQLL------------- 211
                                   ******************************.88878..............899***************............. PP

                                   SB--BEEEEEEEEEEEHH CS
                    Thiolase_N 243 nasqisDGaaavllmses 260
                                   + s++sDG aa++++se+
  gi|70607941|ref|YP_256811.1| 212 DISPVSDGGAAMVMASED 229
                                   **************9986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0007       4.2      26      48 ..      35      57 ..      25      72 .. 0.80
   2 !    9.1   0.0   0.00017      0.99      27     107 ..     267     367 ..     258     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0007
                                  HHHHHHHHHHT--GGGESEEEE- CS
                    Thiolase_C 26 yaikkvlkkagltvedidlfEin 48
                                   a++k+l++agl+++di+++ i 
  gi|70607941|ref|YP_256811.1| 35 EASSKALEEAGLELKDIECVVIG 57
                                  5899*************998664 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHH CS
                    Thiolase_C  27 aikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGa 87 
                                   a++++ k ag++   +++d++E  + F  + L  ++ l +++                        GG + +G P+ a+G 
  gi|70607941|ref|YP_256811.1| 267 AARMAYKMAGIEnpYKELDVIEPYDPFDYKELHHIEGLRIAKrgeapkllkegvfdidgdIPSSPSGGLLGVGNPIAAAGL 347
                                   777888889988667999999999999999999999999999999999999999999986556789*************** PP

                                   HHHHHHHHHHHHCTTSEEEE CS
                    Thiolase_C  88 Rivvtllselkkeggklgva 107
                                     v+++  +lk   gk+ v 
  gi|70607941|ref|YP_256811.1| 348 MKVISIYWQLKGTAGKMQVK 367
                                   **********9999888775 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00044       2.6      12      38 ..      96     122 ..      90     126 .. 0.82
   2 ?    1.7   0.0      0.04   2.4e+02      52      64 ..     216     228 ..     213     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00044
                                   HHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                   ACP_syn_III  12 yalsvAdaliesgaakrvLvigaetls 38 
                                   +a  +    ++sg++++vLv++ e++s
  gi|70607941|ref|YP_256811.1|  96 MAAITGWYHVASGMCNTVLVVAEEKMS 122
                                   55556667899**************99 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.04
                                   B-EEEEEEEEEEE CS
                   ACP_syn_III  52 fGDGAgAvvleas 64 
                                   ++DG++A+v+  +
  gi|70607941|ref|YP_256811.1| 216 VSDGGAAMVMASE 228
                                   58*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2710.77
//
Query:       gi|70607942|ref|YP_256812.1|  [L=382]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2457.47
//
Query:       gi|70607943|ref|YP_256813.1|  [L=374]
Description: isovaleryl-CoA dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-41  142.3   0.0    2.3e-41  141.5   0.0    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    6.5e-23   80.8   0.0    1.4e-22   79.7   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    6.2e-16   59.1   0.0    1.7e-15   57.7   0.0    1.8  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.4e-13   50.0   0.0    3.8e-12   46.6   0.0    2.3  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.0   5.2e-45   2.3e-41       1     147 [.     214     361 ..     214     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 5.2e-45
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                   ++G++ + + l+++Rla+   ++gla++al+eal++a +r+afg +l ++q +++ +a+  ++l+++++   ++ ++++++
  gi|70607943|ref|YP_256813.1| 214 NRGWDMVNTVLEVGRLAISGISIGLAESALQEALSWALNREAFGSKLYSFQGIKWYIADSITKLTSVKSFMKEVSKKFEEN 294
                                   89******************************************************************************* PP

                                   ---.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                 Acyl-CoA_dh_1  82 kpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    ++ ++ asm+Kl+  e+a++v+dl +q++Gg+Gy++++++er+yrd+r++rigeGt+e+qr ii++
  gi|70607943|ref|YP_256813.1| 295 SNTkGVYASMLKLLSGEVANQVVDLSLQIFGGMGYAKGTKIERIYRDVRLMRIGEGTDEVQRHIISK 361
                                   9999*************************************************************87 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   3.1e-26   1.4e-22       1      97 []     111     202 ..     111     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 3.1e-26
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-----B CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrrieek 81 
                                   +falTEp++Gsdv s+kt  aer +ge+v++G+K+wit++ +a+l++++art +  r+++ls+fl+pr++  ++ r+i e 
  gi|70607943|ref|YP_256813.1| 111 SFALTEPTGGSDVGSMKT-YAERRNGEWVISGRKMWITQGIYADLFITVART-GS-RRGELSVFLLPRSNC-IESRKI-EV 186
                                   69****************.8888888*************************3.33.47*********7665.999999.69 PP

                                   SS-TTS-EEEEEEE.. CS
                 Acyl-CoA_dh_M  82 lGlrglptgelvfedv 97 
                                   +G rg+ t+e+vf ++
  gi|70607943|ref|YP_256813.1| 187 MGNRGTGTSEVVFREC 202
                                   *************876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   3.8e-19   1.7e-15       3     112 ..       3     106 ..       1     107 [. 0.93

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.8e-19
                                   HHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHH CS
                 Acyl-CoA_dh_N   3 eqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllg 83 
                                   e   l  ++ref+++e+++ a+++d+e+ +pr++++kl+elG+l   vp +    +l+y +++i +ee+a+++ ++al+  
  gi|70607943|ref|YP_256813.1|   3 ETTILVNSLREFLRREVEKIAEKVDREDYYPRDIVEKLGELGYL---VPLQ---NNLSYYDMVISLEEMAKVSGSVALIAD 77 
                                   56678899***********************************8...5544...4699*********************** PP

                                   HHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                 Acyl-CoA_dh_N  84 vhsslvapailrfGteeqkrryLpklasg 112
                                   ++  lv++++  f++e qk+++L ++ +g
  gi|70607943|ref|YP_256813.1|  78 AQGELVGEMLRLFANESQKKQFLDPISRG 106
                                   **************************998 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.15   6.8e+02      48      76 ..       5      33 ..       2      40 .. 0.82
   2 !   46.6   0.0   8.4e-16   3.8e-12       2     128 ..     230     347 ..     229     353 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                                  HHHHHHHHHHHHHHHHHHHHHHHTT---- CS
                 Acyl-CoA_dh_2 48 aarldAAralleraaaraealaaagkevt 76
                                  +  ++++r++l+r ++++ +++++++ ++
  gi|70607943|ref|YP_256813.1|  5 TILVNSLREFLRREVEKIAEKVDREDYYP 33
                                  6668899***************9998875 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 8.4e-16
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                    i+ + +G+A++al+e++++a +r    +g kl  ++ ++  +a++ ++l + + +++++ ++        +e++ ++   
  gi|70607943|ref|YP_256813.1| 230 AISGISIGLAESALQEALSWALNREA--FGSKLYSFQGIKWYIADSITKLTSVKSFMKEVSKK-------FEENSNTKGVY 301
                                   678899********************..*****************************999988.......33444568889 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCT CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaa 128
                                   a++ ++l  e a ++vd   +++Gg++++k  +++R++RD++ +++
  gi|70607943|ref|YP_256813.1| 302 ASMLKLLSGEVANQVVDLSLQIFGGMGYAKGTKIERIYRDVRLMRI 347
                                   *****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2633.52
//
Query:       gi|70607944|ref|YP_256814.1|  [L=619]
Description: acyl-CoA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-73  246.4   0.0    4.9e-73  246.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    3.2e-14   53.7   0.3    9.3e-14   52.2   0.1    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
    1.4e-13   50.6   0.4    2.9e-13   49.5   0.4    1.6  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.1   0.0   8.2e-77   4.9e-73       4     421 ..      68     502 ..      65     504 .. 0.88

  Alignments for each domain:
  == domain 1  score: 246.1 bits;  conditional E-value: 8.2e-77
                                   HHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS CS
                   AMP-binding   4 qaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptl 81 
                                   +   ++dkva+++   + e +t++Y +l+++vn++  +L++lGv+kgd V +l p  pe v+  la+ ++Gav+v  + +l
  gi|70607944|ref|YP_256814.1|  68 HIPSRKDKVAFYWaneRFETKTVSYLDLYNEVNKATYVLQELGVRKGDSVSLLFPSIPEAVFFSLAVHRLGAVLVIHYVGL 148
                                   556789*****88999999************************************************************** PP

                                   -HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.... CS
                   AMP-binding  82 taeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae.... 148
                                   + e+lay l+d+++kv++          ++  ++ ++kll+ + +   vk+v+v++++ +++e +++ +   e++++    
  gi|70607944|ref|YP_256814.1| 149 SHETLAYRLNDCGSKVMVvaskgirngNEIRIKDfVDKLLDSHTT--PVKSVLVVSRGYSDFEVKQNRDIVYEDVKPkgkv 227
                                   ********************9998755155556667888888774..5888999999999988888888777777734564 PP

                                   -TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT- CS
                   AMP-binding 149 kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGa 229
                                     +++ee++++++ +i YTSGTTGkPKG  +sh+ ++  + ++ ++   + ++++v++++  l + +  +++l+++ + G 
  gi|70607944|ref|YP_256814.1| 228 Y-VRPEEVESNEPGTIYYTSGTTGKPKGLFHSHAGYTIGLNWA-FRALLNPQDNEVWWTVSELGWPVWPMANLYTIPVMGI 306
                                   2.356689*************************9999997775.4544443458899999*****99988*********** PP

                                   EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC. CS
                   AMP-binding 230 tvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfge. 309
                                   t vl++++   + +l+ ++ie+++v+++++  + l  l + g+++  +k+ d ssl+++l  gepl+  ++ ++ + +++ 
  gi|70607944|ref|YP_256814.1| 307 TGVLFEGFIGYKRDLFSRVIERFNVNYVWSSTTTLYTLKSLGEES--VKSGDTSSLKIILNTGEPLNVGAWNWLTENMPHv 385
                                   *********98889************************8876666..6788****************************** PP

                                   EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETT.S-SEBTT-H..H CS
                   AMP-binding 310 evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpg.vmkgYlkkp..e 383
                                   ++ ++Y++TE ++ +++    l   e   k+gs+G ++pg+   +vD++ g+p+p++++G ++v+  +  +   +++p  e
  gi|70607944|ref|YP_256814.1| 386 KIGDAYWMTEHLIPIACtpygL--GEIPYKPGSAGIVFPGTYFTVVDDD-GKPLPPKQKGYIVVKPLNpATAKMWNDPtyE 463
                                   ************9996668653..3334579*****************9.***************6653556679987778 PP

                                   HHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                   AMP-binding 384 ataeafdse.grwlrTGDlgrldedGyleivgRkkdlik 421
                                   + +++++s  ++++ TGD g++dedGyl+++gR++d+i 
  gi|70607944|ref|YP_256814.1| 464 KIKDKYWSRfPGYFYTGDYGYVDEDGYLFVLGRADDVIR 502
                                   889999974668*************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   1.5e+04      32      64 ..     165     198 ..     163     203 .. 0.60
   2 !   52.2   0.1   1.6e-17   9.3e-14       1      76 []     512     582 ..     512     582 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                                   EEEE---...---HHHHHHHHHHHHT-TTTS-SEEE CS
                 AMP-binding_C  32 fVvlkdg...sealeeeLkahvrkelgpyavpkkvv 64 
                                   +Vv ++g       e  +k++v k l ++ +p k v
  gi|70607944|ref|YP_256814.1| 165 MVVASKGirnG--NEIRIKDFVDKLLDSHTTPVKSV 198
                                   55654453221..35788888888888888887444 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 1.6e-17
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   evEs++ + p+Vae aVvG ++      +vafVv+k+g+ ++  l++e+k ++r   g     +kv+f+++lpkt+sGK
  gi|70607944|ref|YP_256814.1| 512 EVESIIGTYPQVAETAVVGTTNS-----IVAFVVPKQGVnPDdvLRNEIKNYCRNS-GY--IVDKVIFLKRLPKTKSGK 582
                                   8*****************99999.....********99532358*********766.55..59***************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.4   4.8e-17   2.9e-13       2      55 .]      12      64 ..      11      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.8e-17
                                  HHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                        ACAS_N  2 kelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                  k++ k++++dp +FW++  + ++W+k+++++++g ++p+ kWF+ G++Ni+yN+
  gi|70607944|ref|YP_256814.1| 12 KSMSKYAMDDPTSFWRDKTEYITWFKKPESIVEG-QAPYDKWFVRGTTNISYNA 64
                                  68999*****************************.******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4243.40
//
Query:       gi|70607945|ref|YP_256815.1|  [L=246]
Description: hypothetical protein Saci_2236 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-10   39.5   0.0    5.4e-10   38.9   0.0    1.3  1  HTH_IclR       IclR helix-turn-helix domain
    4.2e-07   29.8   0.9    7.6e-07   28.9   0.2    1.7  2  TrmB           Sugar-specific transcriptional regulator TrmB
    1.1e-06   28.1   0.3    2.4e-06   27.0   0.3    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    2.8e-06   27.7   0.2      6e-06   26.7   0.2    1.5  1  HTH_27         Winged helix DNA-binding domain
    8.9e-06   25.5   0.0      2e-05   24.4   0.0    1.5  1  MarR_2         MarR family
    2.4e-05   24.3   0.0    3.9e-05   23.6   0.0    1.3  1  HTH_20         Helix-turn-helix domain
    0.00046   20.0   0.0    0.00082   19.2   0.0    1.4  1  HTH_5          Bacterial regulatory protein, arsR family
     0.0014   18.7   0.0     0.0028   17.8   0.0    1.5  1  HTH_28         Helix-turn-helix domain
     0.0033   17.4   0.0     0.0095   15.9   0.0    1.8  2  HTH_36         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.029   14.2   0.0    1.4  1  HTH_23         Homeodomain-like domain
      0.029   14.4   0.5      0.085   12.8   0.1    2.0  2  HTH_45         Winged helix-turn-helix
      0.062   13.4   0.3      0.094   12.8   0.3    1.3  1  DUF2250        Uncharacterized protein conserved in archaea (
      0.081   12.3   0.1       0.12   11.8   0.1    1.2  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
      0.093   12.3   0.2        0.2   11.2   0.2    1.5  1  Sigma70_r4     Sigma-70, region 4
       0.12   12.2   0.1       0.29   11.0   0.1    1.6  1  Phage_AlpA     Prophage CP4-57 regulatory protein (AlpA)
       0.12   12.4   0.1       0.22   11.6   0.1    1.4  1  HTH_29         Winged helix-turn helix
       0.12   12.2   0.3       0.52   10.2   0.3    2.1  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.15   12.2   0.4       0.15   12.2   0.4    1.6  2  AbiEi_4        Transcriptional regulator, AbiEi antitoxin


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.5e-13   5.4e-10       7      49 ..     189     229 ..     185     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.5e-13
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                   +iL+a+  ++    l+e+ r tglpkSt +R ++ Lv+lGyve
  gi|70607945|ref|YP_256815.1| 189 MILEAIKMGGNN--LTEIMRLTGLPKSTIYRRIRKLVRLGYVE 229
                                   799999999996..****************************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.7   4.7e+03      39      58 ..      56      75 ..      54      85 .. 0.72
   2 !   28.9   0.2   7.6e-10   7.6e-07      19      64 ..     195     241 ..     183     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.7
                                  HHHHHHHHHHCTSEEEESST CS
                          TrmB 39 vYevLrsLedkGlVerekgr 58
                                  +Y v +  + kG++++++ +
  gi|70607945|ref|YP_256815.1| 56 IYVVYNTVLPKGVINVVENN 75
                                  67777777778888777655 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 7.6e-10
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE CS
                          TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYra 64 
                                   k g  + +ei + +g+p+s++Y+ +r+L++ G+Ve +++r + +Y++
  gi|70607945|ref|YP_256815.1| 195 KMGGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVEEIRERgKVRYSV 241
                                   6789999*******************************996667765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.3   2.4e-09   2.4e-06       1      48 []     183     229 ..     183     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.4e-09
                        HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   lde d  ILe+++  ++ + +e+ + +gl++st+ rr+++L++ G+++
  gi|70607945|ref|YP_256815.1| 183 LDERDTMILEAIKM-GGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVE 229
                                   7999999***9999.*******************************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.2     6e-09     6e-06       4      63 ..     186     240 ..     183     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 6e-09
                        HTH_27   4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvr 63 
                                    + ++L+ i+  ++++ l+++++ + + +s+i   ++kL++ G+ve+    ++r+ +r++
  gi|70607945|ref|YP_256815.1| 186 RDTMILEAIK--MGGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVEEI---RERGKVRYS 240
                                   6889******..*********************************877...667889987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     2e-08     2e-05       8      54 ..     188     231 ..     183     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2e-08
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                    ++L a+  ++    + +e+ r +gl+ks++ r++++Lv+ G+ve+ 
  gi|70607945|ref|YP_256815.1| 188 TMILEAIKMGGN---NLTEIMRLTGLPKSTIYRRIRKLVRLGYVEEI 231
                                   678899988887...99***************************986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.9e-08   3.9e-05      27      60 ..     201     234 ..     189     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-08
                                   HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  27 aselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                   ++e++++ +l+k+t+++++r+L++ g+ve  re+
  gi|70607945|ref|YP_256815.1| 201 LTEIMRLTGLPKSTIYRRIRKLVRLGYVEEIRER 234
                                   79******************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.3e-07   0.00082       7      46 ..     190     229 ..     188     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.3e-07
                                   HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                   IL +   g    +e+++ +gl++st+ +  +kL  +G+Ve
  gi|70607945|ref|YP_256815.1| 190 ILEAIKMGGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVE 229
                                   5555555666779**************************8 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.8e-06    0.0028       6      38 ..     190     224 ..     186     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                        HTH_28   6 iklla.aGh.svreaArelgisrrtvyrWikryee 38 
                                   i++++  G+ + +e++r+ g+  +t+yr i+++  
  gi|70607945|ref|YP_256815.1| 190 ILEAIkMGGnNLTEIMRLTGLPKSTIYRRIRKLVR 224
                                   5555525666*********************9765 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.4   8.4e+03      22      33 ..     174     185 ..     171     186 .. 0.73
   2 !   15.9   0.0   9.5e-06    0.0095      30      55 .]     203     228 ..     189     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.4
                        HTH_36  22 ggcfpsqetlak 33 
                                   ++++ s+etl +
  gi|70607945|ref|YP_256815.1| 174 EEVNLSNETLDE 185
                                   568899999965 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.5e-06
                        HTH_36  30 tlakrlglsknTvsraikeLeqlGyi 55 
                                    +++++gl k+T++r i++L++lGy+
  gi|70607945|ref|YP_256815.1| 203 EIMRLTGLPKSTIYRRIRKLVRLGYV 228
                                   68999********************6 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.9e-05     0.029       4      41 ..     183     222 ..     180     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                        HTH_23   4 ereRlrillllae..GlsvreIAreLgvsrrTvyrwlkry 41 
                                    +eR  ++l + +  G + +eI r+ g +++T+yr +++ 
  gi|70607945|ref|YP_256815.1| 183 LDERDTMILEAIKmgGNNLTEIMRLTGLPKSTIYRRIRKL 222
                                   677888899999999*******************887775 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.7   3.6e+03      12      37 ..      89     114 ..      85     116 .. 0.69
   2 ?   12.8   0.1   8.6e-05     0.085      11      50 ..     190     233 ..     188     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                        HTH_45  12 LeaisegeakkTkimykanLsyklln 37 
                                   L++is + ++ T +    nL++k+++
  gi|70607945|ref|YP_256815.1|  89 LNYISPQPSSFTVVNNLYNLTFKNVS 114
                                   66666667777777777788888876 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-05
                        HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli....k 50 
                                   ILeai+ g+++ T+im    L  +++ + + +Lv  g++    +
  gi|70607945|ref|YP_256815.1| 190 ILEAIKMGGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVeeirE 233
                                   9*************************************944433 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   9.5e-05     0.094       7      68 ..     184     245 ..     178     246 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                       DUF2250   7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve.gktikrteaklK 68 
                                   de++ ++l+ +k ++ +    i++ + +p++ + + ++kL +lG +e+   +  ++++ +k K
  gi|70607945|ref|YP_256815.1| 184 DERDTMILEAIK-MGGNNLTEIMRLTGLPKSTIYRRIRKLVRLGYVEEIReRGKVRYSVKKEK 245
                                   566777777766.555556789*************************9874678888888877 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.12      57     136 ..     155     232 ..     143     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   SEECCC.STTSCECEE--CCCHHHHH.TSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                 RNA_pol_Rpc34  57 llvllknsndeLvyravsreeAkkkt.slsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvk 136
                                   l++l + +n e+v +  ++ee + ++ +l+e + +++++I+  Gn+     +i + ++L+ks + + ++ L+  +y+ +++
  gi|70607945|ref|YP_256815.1| 155 LVRLFRRRNVEIVTQGAEDEEVNLSNeTLDERDTMILEAIKMGGNN---LTEIMRLTGLPKSTIYRRIRKLVRLGYVEEIR 232
                                   6777777888888888888888866526778888***********7...789************************99987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2    0.0002       0.2       4      44 ..     182     222 ..     181     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                   HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHH CS
                    Sigma70_r4   4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekrA 44 
                                   +L+er+ ++le     g +l EI +  g++++++ +++++ 
  gi|70607945|ref|YP_256815.1| 182 TLDERDTMILEAIKMGGNNLTEIMRLTGLPKSTIYRRIRKL 222
                                   8*************9999****************9999985 PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00029      0.29       6      25 ..     201     220 ..     200     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                    Phage_AlpA   6 lreVeqktglsrstiYrlik 25 
                                   l+e++  tgl +stiYr i+
  gi|70607945|ref|YP_256815.1| 201 LTEIMRLTGLPKSTIYRRIR 220
                                   899**************887 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022      0.22       3      40 ..     189     226 ..     188     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                        HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40 
                                   ++l +++ G+ +  +i++l+gl ++t+yr ++  +  G
  gi|70607945|ref|YP_256815.1| 189 MILEAIKMGGNNLTEIMRLTGLPKSTIYRRIRKLVRLG 226
                                   67889999988*****************9888776665 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00052      0.52      19      41 ..     200     222 ..     183     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00052
                 HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrL 41 
                                     +e+ + +Gl  st+ rR+r+L
  gi|70607945|ref|YP_256815.1| 200 NLTEIMRLTGLPKSTIYRRIRKL 222
                                   56888899**************9 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       7.9   7.8e+03       3      14 ..     155     167 ..     154     168 .. 0.61
   2 ?   12.2   0.4   0.00015      0.15      17      44 ..     202     235 ..     200     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.9
                       AbiEi_4   3 lpelasrqv.Glf 14 
                                   l++l++r++  ++
  gi|70607945|ref|YP_256815.1| 155 LVRLFRRRNvEIV 167
                                   5667777665665 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00015
                       AbiEi_4  17 relea.aGispsa....lrrLvrkGwLvrlr.rG 44 
                                   +e+++  G++ s+    +r+Lvr G ++ +r rG
  gi|70607945|ref|YP_256815.1| 202 TEIMRlTGLPKSTiyrrIRKLVRLGYVEEIReRG 235
                                   6889999****999*****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1594.65
//
Query:       gi|70607946|ref|YP_256816.1|  [L=165]
Description: hypothetical protein Saci_2237 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.4   11.5   3.1        8.2    7.2   0.7    2.3  2  Big_9     Bacterial Ig domain


Domain annotation for each model (and alignments):
>> Big_9  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0025        46      54      72 ..      67      85 ..      28      95 .. 0.77
   2 ?    7.2   0.7   0.00046       8.2      43      86 ..      94     137 ..      87     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0025
                         Big_9 54 panGtvtinadgtltytpn 72
                                    n t+ +na+gt++++  
  gi|70607946|ref|YP_256816.1| 67 KLNTTLIVNANGTYVFQLL 85
                                  56889**********9875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00046
                         Big_9  43 vtsltvtlvtapanGtvtinadgtltytpnagfsgtdsftYtvs 86 
                                   ++s++vtl+ +++  t+++++d +     +  ++  ++++Ytvs
  gi|70607946|ref|YP_256816.1|  94 FSSFNVTLNISGKVVTLSLDNDHQALNLTTGKYNVVVTLSYTVS 137
                                   5688999999999*******999988888999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 867.00
//
Query:       gi|70607947|ref|YP_256817.1|  [L=202]
Description: hypothetical protein Saci_2238 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0078   17.1   0.8      0.017   16.0   0.4    1.8  2  Pilin_N       Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
       0.02   14.5   0.8      0.031   13.9   0.8    1.3  1  CD34_antigen  CD34/Podocalyxin family
      0.051   13.6   0.2        1.7    8.7   0.1    2.0  2  DUF237        Domain of unknown function (DUF237)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   2.8e-06     0.017      10      69 ..       8      83 ..       7      95 .. 0.72
   2 ?   -2.6   0.0       1.9   1.1e+04      66      74 ..     136     144 ..     116     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                       Pilin_N 10 iLmvaitvIlaAviaafvlglasneekapqasi.................evkidssastgkna..........vslehkgGd 65
                                  i+++ +t+++ A+++  v  l   +++ p+a+                  +      ++    +           ++++++G+
  gi|70607947|ref|YP_256817.1|  8 IILLIVTILVNAFLGIQVYYL-IHQSSHPNAQTplnvsdlqivsqssssqN------TT----SsnnmqtssmsTTVNNNSGQ 79
                                  78999****************.88899999998888887776654332211......11....12234566777999999999 PP

                       Pilin_N 66 sidt 69
                                  + + 
  gi|70607947|ref|YP_256817.1| 80 TYNY 83
                                  8764 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                       Pilin_N  66 sidtkdlki 74 
                                   +id kd+k+
  gi|70607947|ref|YP_256817.1| 136 TIDSKDVKV 144
                                   233344444 PP

>> CD34_antigen  CD34/Podocalyxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   5.2e-06     0.031     104     177 ..       4      76 ..       1      83 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-06
                  CD34_antigen 104 skkllialvtsglllaiLlvagyYgclhrRlskskagerLg.EelqyvEngyhdnptlsvaedtssemqeKasvn 177
                                    ++l+i+l+++ l+ a+L++  yY  l    s   a+  L   +lq+v +++  ++t s+ + + s+m    + n
  gi|70607947|ref|YP_256817.1|   4 QTLLIILLIVTILVNAFLGIQVYY--LIHQSSHPNAQTPLNvSDLQIVSQSSSSQNTTSSNNMQTSSMSTTVNNN 76 
                                   57899999999999**********..777777777777785489*****99999999999887777777664444 PP

>> DUF237  Domain of unknown function (DUF237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00028       1.7       8      65 ..      36      92 ..      31     109 .. 0.86
   2 ?    3.1   0.0     0.015        92      93     124 ..     124     156 ..     115     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00028
                        DUF237  8 kaniklklkkvkvkgkkedeekvwiapesikwnkekggiekrktkpykfkfeveleye 65
                                  +a++ l++ ++++  +++++ +  +++++++  +   +++++  + y++++ v++ ++
  gi|70607947|ref|YP_256817.1| 36 NAQTPLNVSDLQIVSQSSSS-QNTTSSNNMQTSSMSTTVNNNSGQTYNYSLTVKFTLH 92
                                  56777788888888888777.7888999999999999****************99765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.015
                        DUF237  93 lkfvvdGevpswivgkkdypgslfqFedq.dkL 124
                                   + +++d + ++ ++++kd++ +l+ + +  ++L
  gi|70607947|ref|YP_256817.1| 124 VSLNLDHTAQNITIDSKDVKVTLYIYAETnQQL 156
                                   5678888999999*************9994444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1900  (0.105974); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.36s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1115.13
//
Query:       gi|70607948|ref|YP_256818.1|  [L=256]
Description: hypothetical protein Saci_2239 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   17.9   6.8     0.0014   17.9   6.8    2.5  3  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   3.7   0.00083        15     253     296 ..       8      51 ..       5      80 .. 0.89
   2 !   17.9   6.8   8.1e-08    0.0014     182     262 ..     103     189 ..      91     209 .. 0.86
   3 ?   -3.5   0.1      0.26   4.7e+03      81      97 ..     236     252 ..     232     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.00083
                           Zip 253 altaplGiliGilvrs..isessgaeivsgillalsaGtflYvalv 296
                                   al+ ++G  ++i+  s  i ++  ++  +++l  l+aG++ Y+al 
  gi|70607948|ref|YP_256818.1|   8 ALGFLAGGTVAIG--SigITKTNISKTKTAYLSVLAAGILAYIALD 51 
                                   6777889999999..4459999**********************95 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 8.1e-08
                           Zip 182 lkvraiilllglilHsfidGLAlG...vssssstgislfiAvllHelpeelglgai..Llkaglsrkkav.llnllfalta 256
                                         il  +l++H++ +G+A++   +   ++++i+ +iA  +H++ e++++ ++  L+++++ +   v +l+l+ +l +
  gi|70607948|ref|YP_256818.1| 103 THNTPVILAAALGFHNIGEGFAIAaalLGGAVASAITFTIAFGVHNATEGVAIASPgkLVRSKWLNLRNVvVLSLIAGLPT 183
                                   555567899***************998889999********************9744499999999888889********* PP

                           Zip 257 plGili 262
                                   +lG+ i
  gi|70607948|ref|YP_256818.1| 184 MLGASI 189
                                   **9876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.26
                           Zip  81 lvllGflllllvekllt 97 
                                   +++lG+ + + +e+l+t
  gi|70607948|ref|YP_256818.1| 236 WFFLGIAIAYGLESLVT 252
                                   67777888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1710.03
//
Query:       gi|70607949|ref|YP_256819.1|  [L=155]
Description: hypothetical protein Saci_2240 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-29  102.5   0.0    2.4e-29  102.4   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.0   1.3e-33   2.4e-29       1     153 [.       9     152 ..       9     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 1.3e-33
                                   HTTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SC CS
                 Flavin_Reduct   1 mrrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgpr 81 
                                   mr+++ +va+vtt +  ++  g+t+++f slsl+Ppl++fs ++ +   + ++e++ fvin++   +e+l d f+    + 
  gi|70607949|ref|YP_256819.1|   9 MRNFPLGVAIVTT-NWNGRYIGMTINTFNSLSLNPPLIMFSADRIKGNDKPFRESNGFVINFVD--NEKLLDIFAF---KD 83 
                                   9************.8888889******************************************5..59********...44 PP

                                   CCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEEE CS
                 Flavin_Reduct  82 tddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrryag 153
                                    +++  f g++ +e++tg+p+   ++a+le++  + +++gdh ++igeV + k+ ++ d +pL+y+rr y +
  gi|70607949|ref|YP_256819.1|  84 VKER--FDGIEVQEGKTGSPIFPQSYAYLEARKYQIHDVGDHSIIIGEVIDGKIFKE-DFSPLVYFRRAYWK 152
                                   4555..99************************************************9.669*******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1098.79
//
Query:       gi|70607950|ref|YP_256820.1|  [L=258]
Description: hypothetical protein Saci_2241 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-35  120.8   0.0    5.9e-35  120.7   0.0    1.0  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio
     0.0019   17.4   0.0     0.0048   16.1   0.0    1.7  1  Memo      Memo-like protein


Domain annotation for each model (and alignments):
>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   6.6e-39   5.9e-35       3     272 ..       6     256 ..       4     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 6.6e-39
                          LigB   3 lllsHvppilaavdgkeqealrekvikgyesireriaek.sPdtiivvsphhlt..dvnpvfvlgvaeefeaiddfg...k 77 
                                   +++sH++p+++ ++    ++ ++   + ++ ++++i++k  P+t+i+ sph+ +  + n++  +  ++  + i+d+    k
  gi|70607950|ref|YP_256820.1|   6 YFISHGSPMILVEE----NP-WK---GHLADLGKEIKNKyDPETVIISSPHFFSwgEGNYT--VISKD-LKCIQDYFgfpK 75 
                                   89*******77777....33.44...567899**********************6656644..44444.47777765699* PP

                          LigB  78 flprleyelkgnpeLaekiaealkksgidlavesnsmklDHGtlvPLelmlpdeakvpvikvslntvaypllsferlykLG 158
                                    l++  y++++++eLa++++++   s+  l+v  ++ +lDHG+++PL++m+p e k +v+++s+ +      s++r+y+LG
  gi|70607950|ref|YP_256820.1|  76 ELYEFCYQAENDVELASELIKE---SNGMLKV-EEKWGLDHGAWIPLYYMFP-EDKPKVVPISISS-----ASPRRHYELG 146
                                   ****************977655...4445677.899****************.789**********.....89******** PP

                          LigB 159 eAlrkaveeldknvlilgsGglsHqlegdeaakadaqtlllneefdeelldllkegrveelckmskeelsaaa.gheeeel 238
                                     +rk  e+l ++ l++++G+ +H+l  +  +      ++ +++fd  l+ l++eg++e++++m+ +++++ + + +e+ l
  gi|70607950|ref|YP_256820.1| 147 SIIRKVSEKLGRRTLFIATGSPTHRLDLLYFN-----LKPRATKFDVLLIKLINEGKFEDILDMDSKYPKEYSsATPEGDL 222
                                   **************************999955.....5669***************************988651556**** PP

                          LigB 239 vplvvalGalsgdkaelrkelvsyeglpavsavf 272
                                   ++l+ +lG +   ka++    +  +g+++ sa f
  gi|70607950|ref|YP_256820.1| 223 KTLHTLLGFVRPTKAKVLGYDIPWAGVSMLSALF 256
                                   **********998999988888888888888877 PP

>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.3e-07    0.0048      98     183 ..      87     171 ..      83     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-07
                          Memo  98 DeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqseetakevgealakvikdes..nlvii 176
                                   D el+ eL+k+++ ++  e +   +H   ++   L ++++e k k+vPi +s+ s+ ++ e+g+++ kv ++     l+i+
  gi|70607950|ref|YP_256820.1|  87 DVELASELIKESNGMLKVEEKWGLDHGAWIP---LYYMFPEDKPKVVPISISSASPRRHYELGSIIRKVSEKLGrrTLFIA 164
                                   6677777777766666666666666765554...5678888899***************************9988899999 PP

                          Memo 177 SsDlsHy 183
                                       +H 
  gi|70607950|ref|YP_256820.1| 165 TGSPTHR 171
                                   8776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1943.25
//
Query:       gi|70607951|ref|YP_256821.1|  [L=106]
Description: hypothetical protein Saci_2242 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-57  192.7   4.0    1.3e-57  192.6   4.0    1.0  1  Ta0938    Ta0938
  ------ inclusion threshold ------
       0.74   10.0   3.3       0.47   10.6   0.4    1.9  2  YHS       YHS domain


Domain annotation for each model (and alignments):
>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   4.0   1.4e-61   1.3e-57       1     104 [.       1     104 [.       1     105 [. 0.99

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 1.4e-61
                                   .EEE-SSS---SGGGS-SS---S---SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHHHS---EE---TTT-S--EEE CS
                        Ta0938   1 mkivvngkeagtkekgcalcgatwgdyyeevdgeklffccdicakefvnllnevkkrtglskideleingnyykgrnveak 81 
                                   mki+vng++agtke+gcalcg+twgdyyee+dgeklffccdica efvn+l+evkkrtg+++idel+ingny++gr++++k
  gi|70607951|ref|YP_256821.1|   1 MKITVNGRTAGTKETGCALCGGTWGDYYEEIDGEKLFFCCDICALEFVNMLREVKKRTGWDRIDELVINGNYSSGRTCVSK 81 
                                   9******************************************************************************** PP

                                   E-----TT-SS-----HHHHHTT CS
                        Ta0938  82 sgekelkfyvkfnddaeieefke 104
                                   +g++e+kfyv+fn+da++e+f+e
  gi|70607951|ref|YP_256821.1|  82 RGGREYKFYVRFNEDAGVETFRE 104
                                   *********************98 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   5.3e-05      0.47      18      37 ..      28      47 ..      21      49 .. 0.85
   2 ?   -0.7   0.1      0.17   1.6e+03      20      28 ..      81      89 ..      78      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                           YHS 18 kseYkGkeYyFcSegCkdkF 37
                                  + e +G + +Fc++ C  +F
  gi|70607951|ref|YP_256821.1| 28 YEEIDGEKLFFCCDICALEF 47
                                  55668***********9888 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                           YHS 20 eYkGkeYyF 28
                                  +++G+eY F
  gi|70607951|ref|YP_256821.1| 81 KRGGREYKF 89
                                  689****88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 856.50
//
Query:       gi|70607952|ref|YP_256822.1|  [L=304]
Description: hypothetical protein Saci_2243 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-48  163.8   0.1    6.4e-48  163.4   0.1    1.1  1  TENA_THI-4       TENA/THI-4/PQQC family
    3.6e-30  103.6   1.2    1.1e-29  102.0   1.1    1.9  2  zf-C2H2_9        C2H2 type zinc-finger (1 copy)
    2.4e-16   60.0   0.2    4.6e-16   59.1   0.1    1.5  2  Haem_oxygenas_2  Iron-containing redox enzyme


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.1   1.1e-51   6.4e-48       1     206 [.      68     286 ..      68     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 1.1e-51
                                   HHHCHHHHHHHHC..SHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHH.HHHHC-SSHHHHHHHHHHHHHHHHCH... CS
                    TENA_THI-4   1 haqlrpiwkeyin..HpFvkalakGtlpreqfqayviqdylylknfvrvla.iilskssdlevrrelesrivdhdgee... 75 
                                   + + r+i+++y +  HpF+ a++++t  r ++ +yvi+++++lkn+v+vl+ i++ +++d  +++ele++ v+++g+    
  gi|70607952|ref|YP_256822.1|  68 WIRKRFIERFYGEnpHPFISAMQNPT--RGVLLGYVIEHQHFLKNWVKVLSaIVFKTDKDDVMEYELENIKVEFIGYGvrp 146
                                   56889*********************..***********************5666667899999*************99** PP

                                   ..HHHHHHHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHH.....S-TSC CS
                    TENA_THI-4  76 ..ielhlrlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklr.....alegp 149
                                     +el+lr++e+lG++re++++  p+p t+++++++ ++a++ +++e++ a++++++v+++++++++ k++     +l+++
  gi|70607952|ref|YP_256822.1| 147 shYELLLRMGESLGMPREKILSMTPLPSTRNAINFWRRVAETRTWLETMLAMHSLELVADRSLRQYGAKVHyfnpeILSSD 227
                                   ********************************************************************************* PP

                                   HHHHHHHHHCSHHHHHHHHHHHHHHHHHHHTSHHHH.HHHHHHHHHHHHHHHHHHH.HH CS
                    TENA_THI-4 150 eyyewvkeyaseefraaveeakrllerllakvsdeq.leelqeiflkalefetsfl.tm 206
                                    y++ vk++++e+++a+v++a ++l+ + +++++    e++q i+l++++++ ++l ++
  gi|70607952|ref|YP_256822.1| 228 RYPQEVKDFLREGYEADVSHASEALKLGEKYAEELGlKEQAQIIVLRSFDAFSKYLlAR 286
                                   **********************************9977788999***********9554 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   1.1   1.9e-33   1.1e-29       1      59 []       1      60 [.       1      60 [. 0.99
   2 ?   -2.7   0.0      0.94   5.6e+03       4      19 ..     172     187 ..     169     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 1.9e-33
                                  --B-TTT--B-SSHHHHHHHH.HHHTSSS--HHHHHHHHHT-SS---HHHHHHHHHHHHH CS
                     zf-C2H2_9  1 mplCPvCevkfnswkdlseHi.lsaasksdaeHvmWLNRniskkrlskdELekklekffs 59
                                  mplCP+Ce+kf++w dl+ Hi l+a+sksd++HvmWLNRn+s++r++++EL+++le+ffs
  gi|70607952|ref|YP_256822.1|  1 MPLCPSCEMKFETWGDLAGHIeLMANSKSDPSHVMWLNRNLSYERMNREELKVSLENFFS 60
                                  9**********************************************************7 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.94
                                   -TTT--B-SSHHHHHH CS
                     zf-C2H2_9   4 CPvCevkfnswkdlse 19 
                                    P+ ++ +n w++++e
  gi|70607952|ref|YP_256822.1| 172 LPSTRNAINFWRRVAE 187
                                   5889999999*99986 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.66     4e+03      11      34 ..      27      50 ..      21      58 .. 0.58
   2 !   59.1   0.1   7.6e-20   4.6e-16       3     172 ..     100     274 ..      98     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.66
               Haem_oxygenas_2 11 klvfgdwlalvhsrltdrevkral 34
                                  ++ ++  ++++ ++l ++++ r+ 
  gi|70607952|ref|YP_256822.1| 27 SKSDPSHVMWLNRNLSYERMNREE 50
                                  455666666666666655555554 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 7.6e-20
               Haem_oxygenas_2   3 flrqrapyklvfgdwlalvhsrltdrevkrallenls.EElGdgdlernHvelyrrllkalGldeeplealpelpetlali 82 
                                   +++++ ++ ++++++l++++ ++++++v  + len+  E  G g     H el+ r+ ++lG+ +e +   ++lp+t+++i
  gi|70607952|ref|YP_256822.1| 100 YVIEHQHFLKNWVKVLSAIVFKTDKDDVMEYELENIKvEFIGYGVRPS-HYELLLRMGESLGMPREKILSMTPLPSTRNAI 179
                                   8999*****************************************665.******************************** PP

               Haem_oxygenas_2  83 nlfeavalsrrllgallGallalEllvsletlklaee........lrelgldeeapeyfdlHvtiDnaHaamaleaviell 155
                                   n++++va +r++l  +l++ + lEl++ + ++++ ++        l   + ++e  +++++  ++D  Ha +al ++ e++
  gi|70607952|ref|YP_256822.1| 180 NFWRRVAETRTWLETMLAM-HSLELVADRSLRQYGAKvhyfnpeiLSSDRYPQEVKDFLREGYEADVSHASEAL-KLGEKY 258
                                   *************988988.66*****6666666666666777766667777788*******************.998888 PP

               Haem_oxygenas_2 156 ateepeeqedvlegawr 172
                                   a+e   ++e++   ++r
  gi|70607952|ref|YP_256822.1| 259 AEEL-GLKEQAQIIVLR 274
                                   8876.666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2109.14
//
Query:       gi|70607953|ref|YP_256823.1|  [L=279]
Description: amidohydrolase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-26   92.5   0.0    4.6e-26   92.3   0.0    1.0  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.059   12.7   0.0    1.6  1  Amidohydro_1  Amidohydrolase family
       0.22   10.9   0.0        1.1    8.6   0.0    1.9  1  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0   7.7e-30   4.6e-26       1     290 [.       4     276 ..       4     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 7.7e-30
                                   EEEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHH......HHH CS
                  Amidohydro_2   1 iDvHaHllppeaairddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaalcrgannr......vla 75 
                                   iD+H+H +              ++  ++   +k+ag+  +  s++ +l++++ a i++ vi a  +r+++n       ++ 
  gi|70607953|ref|YP_256823.1|   4 IDAHTHAW-----------F--REFLPQNFSSKNAGYEFKPPSLQQVLKEMDSANIDYIVIIAYPARELWNIdesiaiQAI 71 
                                   9*****76...........3..4455568999999*************************999888777766666666667 PP

                                   HHHHHCTTCB...ECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH.......HHHHHHHHHHT-EEE CS
                  Amidohydro_2  76 eaakrpdrfv...ggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrld.......rpifealeelglpvd 146
                                   +++k +++++   gg+  + l +e++   l ++  e+g+ G++l+p +   +++ +r +          ++ +e+++lpv 
  gi|70607953|ref|YP_256823.1|  72 DFLKPYGERFsvvGGIEPNKLTVEETKYWLGKQY-EKGVAGFKLHPVHSWVKPNAYREEegglkqlEIMYQFAEDHNLPVI 151
                                   7777776655233455555555666666666666.999999999999999999999999999999888999********** PP

                                   EE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCH CS
                  Amidohydro_2 147 ihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspl 227
                                   ihtG     +  + +++  + +p ++++v ++fP+lkiv+aH+G+p +++++a +l++ r+n+y+++s         ++p+
  gi|70607953|ref|YP_256823.1| 152 IHTG-----TSMFLRARNKYGDPIYIDDVSVDFPRLKIVMAHMGRP-NWVPTAFQLCRIRRNIYAEISS--------IPPK 218
                                   **99.....66888888889**************************.********************99........8999 PP

                                   HCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHCT CS
                  Amidohydro_2 228 adppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarlyg 290
                                    +  +l r+ e+   ++ ++GsDy  p ++   e l+++     l  e +e+i+ +N++ ly+
  gi|70607953|ref|YP_256823.1| 219 KILDYLPRIEEIS--NKTIYGSDYGGPGTKGLAENLKEFLS---LNIEGKEDIADKNPRSLYK 276
                                   ********99998..***********999887777777765...699**************96 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.8e-06     0.059       5     249 ..       2     241 ..       1     267 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-06
                                   -EEEEEEECETTECSSSGHHHHH........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH....HHHHHHHHHHT. CS
                  Amidohydro_1   5 GlIDaHvHleqsllrgatledwl........vppetaaealesgiktalksGtttvadmgattst....giealleaaee. 72 
                                   G IDaH+H+ ++++        l        +  e+    l++++k++ ++ + ++  + + + +      e ++ +a + 
  gi|70607953|ref|YP_256823.1|   2 GYIDAHTHAWFREF--------LpqnfssknAGYEFKPPSLQQVLKEMDSANIDYIVIIAYPARElwniD-ESIAIQAIDf 73 
                                   88999999965544........344443443555555556889999999999999999999777788742.3333333332 PP

                                   .SSSEEEEEEESSEGGS.....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                  Amidohydro_1  73 .lplglrilggkvsldr.....gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlp 147
                                     p g r+ + ++          ++et   + ++ ++g+a +++ + ++ vk+  + +e  +++  +l+ + + a++++lp
  gi|70607953|ref|YP_256823.1|  74 lKPYGERFSVVGG---IepnklTVEETKYWLGKQYEKGVAGFKLHPVHSWVKPNAYREEEGGLK--QLEIMYQFAEDHNLP 149
                                   4444555544333...13446888899999999999**********999***999999999999..77779999******* PP

                                   EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HHHHHHHHHHHHHHCEE..HHHHHHHH CS
                  Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt..pteaellkerlkeagva..hcpfsnsi 224
                                   v iH+ +t+ +   a++++g      ++ +v  s+++++  k+++ah+  +   pt       +++ +++    ++  +si
  gi|70607953|ref|YP_256823.1| 150 VIIHT-GTSMFL-RARNKYG---DPIYIDDV--SVDFPRL-KIVMAHMGRPNwvPT-------AFQLCRIRrnIYAEISSI 215
                                   *****.667777.7888888...33345666..7889999.999999988887666.......222344444466777777 PP

                                   SEHHHHHHHHHHHH.TSCEEEEEECT CS
                  Amidohydro_1 225 lrsgrealrkalde.GvkvglgtDga 249
                                     +++ +  + ++e + k ++g+D  
  gi|70607953|ref|YP_256823.1| 216 PPKKILDYLPRIEEiSNKTIYGSDYG 241
                                   77777777777777777777777755 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00018       1.1       1     133 [.       4     156 ..       4     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                                   EEEEE-TTSCCC...............TTTHHHHHHHHHHTTEEEEEEE-SSG.......GGHH.HHHHHHTT.TTTEEEE CS
                    TatD_DNase   1 iDaHcHldskef...............eedreeileraeeagvaavvvvgtss.......kdsk.avlelakkypnkvyav 58 
                                   iDaH+H  ++ef                 + +++l++++ a++ ++v +           +++  ++++  k y ++  +v
  gi|70607953|ref|YP_256823.1|   4 IDAHTHAWFREFlpqnfssknagyefkPPSLQQVLKEMDSANIDYIVIIAYPArelwnidESIAiQAIDFLKPYGERFSVV 84 
                                   788888888877666665544444443334888888888888888887666665444443222235566666688888888 PP

                                   E---GGGGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET....-CCCCCGH...HHHHHHHHHHHHHHHHTTEEEEEEEE CS
                    TatD_DNase  59 lGiHPnevdeasedlleelkelanvkhskvvaiGeiGLDy....ysreestk...eaqeevFeeqlrlAkelklplviHlr 132
                                    Gi Pn+++   e++  +l +     ++   ++   G  +    ++++++     e   + +e + + A++++lp++iH++
  gi|70607953|ref|YP_256823.1|  85 GGIEPNKLTV--EETKYWLGKQ---YEK---GV--AGFKLhpvhSWVKPNAYreeEGGLKQLEIMYQFAEDHNLPVIIHTG 155
                                   8888888883..4444566444...122...33..4555533322333222211122234555567889**********97 PP

                                   S CS
                    TatD_DNase 133 k 133
                                    
  gi|70607953|ref|YP_256823.1| 156 T 156
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1970.52
//
Query:       gi|70607954|ref|YP_256824.1|  [L=270]
Description: hypothetical protein Saci_2245 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-28  100.2   0.1    3.1e-28   99.4   0.0    1.4  2  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.21   3.8e+03       1       7 [.       7      13 ..       7      41 .. 0.75
   2 !   99.4   0.0   1.8e-32   3.1e-28      97     289 ..      91     268 ..      59     270 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.21
                                  EEEEEEE CS
                  Amidohydro_2  1 iDvHaHl 7 
                                  iD+H+H+
  gi|70607954|ref|YP_256824.1|  7 IDAHVHY 13
                                  8999993 PP

  == domain 2  score: 99.4 bits;  conditional E-value: 1.8e-32
                                   HHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH.......HHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHH CS
                  Amidohydro_2  97 daaaeleraveelgfkGvrlnphvggddllgdrld.......rpifealeelglpvdihtGpspewlfggpqettraiqpl 170
                                   ++ +ele++  +lg+ G++l+p ++g +++g+r +         i+e +++++lpv+ihtG     +    + +  +++p 
  gi|70607954|ref|YP_256824.1|  91 NVKEELEKQY-SLGIIGIKLHPPHHGFKPNGYREEegglkslLYIYEFAQDHDLPVMIHTG-----TSIEGATRNKYSDPI 165
                                   4889******.************************************************99.....55666667789**** PP

                                   HHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--B CS
                  Amidohydro_2 171 llsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdrilfGsDy 251
                                   l+++v+ +fP+lk+++aH+G+p  ++ +a ++++ ++nvy+++s         ++p  + ++l  l+ +  p+++++GsD+
  gi|70607954|ref|YP_256824.1| 166 LIDDVVKDFPKLKVIIAHAGRP-IWYTTAFYMAKYFDNVYLEISS--------IPPRNILKYLPNLLTI--PEKVIYGSDF 235
                                   **********************.********************99........6788999999988765..8********* PP

                                   TSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHC CS
                  Amidohydro_2 252 PhptleaepealalldlvallsdeerekilggNAarly 289
                                   P   +++  e+ ++++ v        ++il++N  rl 
  gi|70607954|ref|YP_256824.1| 236 PAYVGQDLAEYAHQIYEVV-----KDRRILRDNILRLI 268
                                   *****99999999999654.....44677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1827.03
//
Query:       gi|70607955|ref|YP_256825.1|  [L=459]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-49  168.4   0.0    1.9e-49  167.7   0.0    1.3  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    1.1e-20   73.4   0.3    2.4e-20   72.3   0.3    1.6  1  Fer2_2         [2Fe-2S] binding domain
    1.8e-07   31.0   0.6    4.9e-07   29.6   0.1    2.0  2  Fer2           2Fe-2S iron-sulfur cluster binding domain
      2e-07   31.1   0.2    1.2e-06   28.6   0.0    2.3  2  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai
    4.3e-06   26.7   0.2    1.8e-05   24.7   0.3    2.0  2  Fer2_3         2Fe-2S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.0   5.2e-53   1.9e-49       2     170 ..       5     170 ..       4     171 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 5.2e-53
                                   EEEEEE-SSHHHHHHHHHHCTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHHHH CS
                 FAD_binding_5   2 kfeylrpasleealallaaepdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaaeal 82 
                                   +f+y+rp++l++al+ll+++++a+++aGg++l+++mk++++++++l+d+++++elk+++ +e++l+iG+++t++e+a++ +
  gi|70607955|ref|YP_256825.1|   5 QFKYYRPSNLQQALDLLKENEGARPLAGGQSLVPMMKLRIINVDTLVDLNDLDELKYVKLEEDKLRIGSLLTHNEIATNHI 85 
                                   799****************************************************************************** PP

                                   HHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-EE CS
                 FAD_binding_5  83 vrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktalepgeli 163
                                   +r+ryp+l++a + iA+ q+Rn++TiGG++a+a+p+++++p+L +l+ +v l s    r++++e+f+  p++tal +ge+i
  gi|70607955|ref|YP_256825.1|  86 IRQRYPSLAKASWVIADLQVRNKGTIGGSIAHADPSGNYFPVLFTLEGKVILSS---GRSINIEDFYLFPYTTALSHGEII 163
                                   ****************************************************76...79********************** PP

                                   EEEEEE- CS
                 FAD_binding_5 164 taveiPa 170
                                   +++eiP 
  gi|70607955|ref|YP_256825.1| 164 KEIEIPV 170
                                   ******6 PP

>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.3   6.6e-24   2.4e-20       1      75 [.     374     443 ..     374     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 6.6e-24
                        Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                   T+ gl+++ +    vq af+++ a+qCGyCt Gf+m++++ l++ +p+ +e+ ++ a+ +n+CRCtgY +i++A 
  gi|70607955|ref|YP_256825.1| 374 TIKGLKTK-Q---LVQDAFLRNYAMQCGYCTHGFMMTVYDYLTNVDPDADEDLMKYAI-KNICRCTGYVNIIRAT 443
                                   89999966.5...8*******************************7777755555555.6*************96 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.1   1.1e+04      42      48 ..     192     198 ..     192     205 .. 0.75
   2 !   29.6   0.1   1.4e-10   4.9e-07       2      52 ..     308     356 ..     307     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.1
                                   TTEEEEE CS
                          Fer2  42 tClvevl 48 
                                   tClv v+
  gi|70607955|ref|YP_256825.1| 192 TCLVAVN 198
                                   8**9998 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.4e-10
                                   ETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE CS
                          Fer2   2 tidgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev 52 
                                   t++g+e+ ++v +++ +l d++++ng ++++ +C +g+Cg+C+v v+ g+ 
  gi|70607955|ref|YP_256825.1| 308 TVNGEEIPLNV-EPRILLIDFLRQNGFTEVKRGCDEGKCGACTVLVD-GKA 356
                                   899**999*98.67777***************************877.433 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   3.4e-10   1.2e-06       3     100 ..     180     280 ..     179     282 .. 0.81
   2 ?   -2.5   0.0       1.6   5.9e+03      17      28 ..     360     371 ..     345     387 .. 0.53

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.4e-10
                                   EEEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSH....HHHHHHHHH..HHTTCHH CS
                 CO_deh_flav_C   3 yklsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplse....elleeaaka..leeelsp 77 
                                   + + +r +  ++++ +A+++el+ed+++ + +ia+ggv ++pv  + +     G++++e    + l+ +a+   +e++ ++
  gi|70607955|ref|YP_256825.1| 180 FNVVKRGGASYPTCLVAVNLELSEDRVVVSSKIAIGGVFEKPVLIRDL---FLGEKVDEirrrADLDSIAEKiiAERDEKV 257
                                   6788999************************************98764...555555542113556666665223578899 PP

                                   HTCTTC-HHHHHHHHHHHHHHHH CS
                 CO_deh_flav_C  78 asdprasaeYRrslavsllfrfl 100
                                   + d++as+ YR +l+++ll + l
  gi|70607955|ref|YP_256825.1| 258 INDIHASKSYRLKLTRNLLVKTL 280
                                   99*****************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                   EEEEEEEEETTC CS
                 CO_deh_flav_C  17 naAfrveleedg 28 
                                   + Af++++++++
  gi|70607955|ref|YP_256825.1| 360 CNAFAIQFSGKN 371
                                   224444444444 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.3   8.4e+03      13      41 ..     172     200 ..     167     205 .. 0.78
   2 !   24.7   0.3   4.9e-09   1.8e-05      49      99 ..     337     386 ..     329     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                        Fer2_3  13 rgkqkvqeyeveaeeedtvldaLlkikee 41 
                                   ++++++ +++v ++ + +   +L  ++ e
  gi|70607955|ref|YP_256825.1| 172 KNSEYWLNFNVVKRGGASYPTCLVAVNLE 200
                                   56788999999999999988888888765 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 4.9e-09
                        Fer2_3  49 rasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirD 99 
                                   ++ C eg CG+c+v ++Gk    C+a   ++  ++  ++++ l++ ++++D
  gi|70607955|ref|YP_256825.1| 337 KRGCDEGKCGACTVLVDGKAIKSCNAFAIQFSGKN-IVTIKGLKTKQLVQD 386
                                   579****************************9876.79*****99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3264.05
//
Query:       gi|70607956|ref|YP_256826.1|  [L=775]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-125  419.7   0.0   1.9e-125  419.4   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.2e-11   44.9   0.0    2.3e-11   44.0   0.0    1.5  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.4   0.0  2.2e-129  1.9e-125       1     549 [.     138     708 ..     138     709 .. 0.91

  Alignments for each domain:
  == domain 1  score: 419.4 bits;  conditional E-value: 2.2e-129
                                   STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevl 79 
                                   vhee+++n++   k+++Gd+ +af+e+++v+++ef++ +++  +lE  ++la+    +++l++ ++ q+p+    +++++l
  gi|70607956|ref|YP_256826.1| 138 VHEELGSNIAVnrKMSYGDMVRAFSESPVVIKNEFKVTKHSALPLEGYGVLAYK---TDTLNIVANFQGPMLEAYFISRAL 215
                                   6999999999999999*************************************9...89********************** PP

                                   T--GGGEEEE-.SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEE CS
                 Ald_Xan_dh_C2  80 glpenkvrviv.prvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldv 159
                                   g++ n +++ + +++GG+FG+K+  +p+ ++aa+a+   ++pV+++++R+e++l++++  + + +++++ dk+Gki++++ 
  gi|70607956|ref|YP_256826.1| 216 GISLNWIKLSTpRDIGGSFGVKYSLYPYMTIAAAASILSNHPVRWIESRTESFLYSSSSGDREGYVEIASDKEGKIKGIRY 296
                                   ***********778******************************************************************* PP

                                   EEEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHH CS
                 Ald_Xan_dh_C2 160 dlladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplel 239
                                    ++ d+Gay  + +p+ l r++++l+g+Y+++n++v+ +vv tN+ p++  R++G+pq +falE+++d+lAeelg++p+e+
  gi|70607956|ref|YP_256826.1| 297 AFFEDVGAYpRPPEPGALFRVHGNLNGAYDVRNIEVNHTVVLTNKSPTGLNRAYGAPQFYFALETTIDKLAEELGISPIEI 377
                                   *********669********************************************************************* PP

                                   HHHHBCEC......GCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S... CS
                 Ald_Xan_dh_C2 240 RrrNlikp......geltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgf... 308
                                   R+rN+i++       ++  y++p   +y  +d+ ++l+ l+e++   +    +++        Gig++++ e++g++    
  gi|70607956|ref|YP_256826.1| 378 RKRNVITEfnkrinSDY-FYETPtggLYPRQDYIRVLKLLEEEY--SK----IKREP----LTGIGVSLFLEPSGTNLgyv 447
                                   ******87322222222.46666677888999999999988875..32....33333....57***********9999887 PP

                                   ......EETTEE..........EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-S.BTTSSS-. CS
                 Ald_Xan_dh_C2 309 .....takflnq..........egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvveg.dtdkvpn. 372
                                        +     +          +   +++n dGs++v++ gt+ G G+et+ a+++a+e+g+++++v+v++  dt+     
  gi|70607956|ref|YP_256826.1| 448 dlaleG-----SkrrhkhsasgDYIIMSLNFDGSISVFINGTNEGLGHETVTAEVVAKEFGIDVSRVKVENRvDTSLPWTi 523
                                   765551.....13344567766679***********************************************677665557 PP

                                   ---S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH....TTSSEE CS
                 Ald_Xan_dh_C2 373 gsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl....ervsls 446
                                   +sg+++Sr + ++ + v+kA+++l+++l ++a++   +++e++ +e+gk+++k   +ksv+l++la+a ++    +  sls
  gi|70607956|ref|YP_256826.1| 524 ASGSYSSRFAPIVITGVLKACNELKDKLSDVAKR--FLETEEVYYENGKFYAKkdsTKSVDLKTLASAFHWdpysNPGSLS 602
                                   889******************************5..56678899*********9988999*******88887877888*** PP

                                   EEEEE......EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT-- CS
                 Ald_Xan_dh_C2 447 atgfykt...ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEe 524
                                     +fy+     + e  k ++   ++  a++a+V +D+ t +vkv++++i+hDvG+++ +++ e Q++G++ +Gi++ l+E+
  gi|70607956|ref|YP_256826.1| 603 VVSFYNSpylAPPEGDKINSSLGYSIQAHLAVVRIDPITYDVKVEKYIIIHDVGRILKRELLESQMYGSLLHGIAMSLYER 683
                                   *****999886667777777789999******************************************************* PP

                                   -EEETTTEESS-STTTS----GGGS CS
                 Ald_Xan_dh_C2 525 lvydedGqlltasladYkiPtaadi 549
                                   l yde+G++l ++++ Y+ Pt++++
  gi|70607956|ref|YP_256826.1| 684 LAYDENGNPLITTFDAYETPTFSEM 708
                                   **********************997 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   2.6e-15   2.3e-11       2     109 ..      14     122 ..      13     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.6e-15
                                   T-SCCGGGCC-TTTE.EEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT..TSSS-EEEESS-SSEESS CS
                  Ald_Xan_dh_C   2 GeavYvdDipapgal.ylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig..siledeedallaedkvrs 79 
                                   G   +++Dip p  + ++a+ rS+ +h+ i+++dvs+  ++ G++   t ++l k  k+     +  + + ++ a+dkvr+
  gi|70607956|ref|YP_256826.1|  14 GSSEFINDIPNPSGTlFMAIYRSNLPHGVIKKVDVSEVFNHGGIAY--TNQELLKVIKNPFplGVDLPIKYYAVAKDKVRF 92 
                                   777899******9999*************************99863..444444444444424556666689********* PP

                                   TT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                  Ald_Xan_dh_C  80 vgqavaavvAedeetArkAaklvkveYeel 109
                                   vg+++a+v+A+d + A + ++ v+ve ++l
  gi|70607956|ref|YP_256826.1|  93 VGEPIAIVLARDLYKAVDLLDYVNVEVDPL 122
                                   *************************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 5281.47
//
Query:       gi|70607957|ref|YP_256827.1|  [L=85]
Description: hypothetical protein Saci_2248 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 556.60
//
Query:       gi|70607958|ref|YP_256828.1|  [L=336]
Description: molybdopterin oxidoreductase, iron-sulfur binding subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-13   49.7   1.2    4.5e-13   49.2   1.2    1.2  1  Fer4_11   4Fe-4S dicluster domain
    1.7e-11   43.4  18.4    1.2e-07   31.2   3.0    4.0  4  Fer4      4Fe-4S binding domain
    3.4e-09   36.4  15.9    5.3e-07   29.4   2.1    3.5  3  Fer4_6    4Fe-4S binding domain
    8.7e-08   32.6  22.4      6e-06   26.8   9.0    3.0  3  Fer4_7    4Fe-4S dicluster domain
    2.6e-07   30.7  16.3    0.00012   22.2   6.2    2.3  2  Fer4_9    4Fe-4S dicluster domain
    9.9e-06   25.6  18.6    0.00019   21.5   2.4    2.3  2  Fer4_21   4Fe-4S dicluster domain
    1.1e-05   25.2   1.5    1.1e-05   25.2   1.5    3.1  3  Fer4_2    4Fe-4S binding domain
    1.9e-05   24.6   8.5    1.9e-05   24.6   8.5    2.2  2  Fer4_10   4Fe-4S dicluster domain
    4.3e-05   24.3  11.9       0.44   11.5   0.2    3.8  3  Fer4_16   4Fe-4S double cluster binding domain
    0.00071   19.1   8.1     0.0054   16.3   7.9    2.1  1  DmsC      DMSO reductase anchor subunit (DmsC)
     0.0012   19.7  18.1      0.042   14.8   2.5    3.2  3  Fer4_3    4Fe-4S binding domain
     0.0014   18.9   2.9     0.0014   18.9   2.9    2.8  3  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.12   12.4   5.8       0.16   12.0   0.1    3.0  2  DUF997    Protein of unknown function (DUF997)
       0.47   10.9   9.8       0.48   10.9   2.6    2.4  2  Fer4_8    4Fe-4S dicluster domain
          1   10.0  10.1       0.19   12.3   3.2    2.9  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        2.1    9.0  10.7       0.51   10.9   2.7    2.7  4  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.2     4e-16   4.5e-13      20      99 ..       2      77 ..       1      78 [. 0.92

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 4e-16
                       Fer4_11 20 asapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllpacvescptgalnfgd 99
                                  +++p++ai+k+e  G+V + e+++  ++  ++ acPy++ + +  +g ++kC++c++r+ +Gl p cve+cptgal+fg+
  gi|70607958|ref|YP_256828.1|  2 NVCPANAITKNE-MGIVRIIEDNCI-GCGFCTWACPYEALKITP-SGIMSKCHLCYNRIGSGL-PYCVEACPTGALTFGW 77
                                  789*******99.9**********7.**************9965.678************885.9*************96 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.2    0.0053       5.9      15      24 .]       1      10 [.       1      10 [. 0.88
   2 !   31.2   3.0   1.1e-10   1.2e-07       2      24 .]      18      40 ..      17      40 .. 0.93
   3 ?   -0.0   0.1       0.8   8.9e+02       6      12 ..      48      54 ..      46      55 .. 0.71
   4 !   14.6   0.3   1.9e-05     0.021      13      24 .]      63      74 ..      63      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0053
                                  HHHSTTTEEE CS
                          Fer4 15 vevCPvgAIt 24
                                  ++vCP +AIt
  gi|70607958|ref|YP_256828.1|  1 MNVCPANAIT 10
                                  58*******7 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.1e-10
                                  EEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  2 videekCigCGaCvevCPvgAIt 24
                                   i+e+ CigCG C  +CP++A++
  gi|70607958|ref|YP_256828.1| 18 RIIEDNCIGCGFCTWACPYEALK 40
                                  799******************85 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.8
                                  TTSSS-T CS
                          Fer4  6 ekCigCG 12
                                  +kC  C 
  gi|70607958|ref|YP_256828.1| 48 SKCHLCY 54
                                  7888885 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 1.9e-05
                                  HHHHHSTTTEEE CS
                          Fer4 13 aCvevCPvgAIt 24
                                  +Cve+CP+gA+t
  gi|70607958|ref|YP_256828.1| 63 YCVEACPTGALT 74
                                  5*********86 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.054        60      16      24 .]       1       9 [.       1       9 [. 0.88
   2 !   29.4   2.1   4.8e-10   5.3e-07       1      24 []      16      39 ..      16      39 .. 0.95
   3 !   11.2   1.5   0.00027       0.3       7      24 .]      48      73 ..      46      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.054
                        Fer4_6 16 vrvCPegai 24
                                  ++vCP++ai
  gi|70607958|ref|YP_256828.1|  1 MNVCPANAI 9 
                                  579*****8 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 4.8e-10
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +v+i +d+CigCg C+ +CP+ a+
  gi|70607958|ref|YP_256828.1| 16 IVRIIEDNCIGCGFCTWACPYEAL 39
                                  699******************996 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00027
                        Fer4_6  7 dkCigCgd........CvrvCPegai 24
                                  +kC  C++        Cv +CP+ga+
  gi|70607958|ref|YP_256828.1| 48 SKCHLCYNrigsglpyCVEACPTGAL 73
                                  7899887778888899********97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   5.5   1.1e-06    0.0012      10      52 .]       2      38 ..       1      38 [. 0.90
   2 !   26.8   9.0   5.3e-09     6e-06       2      52 .]      24      72 ..      23      72 .. 0.86
   3 !   10.4   1.0   0.00068      0.76       7      20 ..      63      76 ..      49     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                        Fer4_7 10 aaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  ++Cp++ai+ +e         v+i +++C+gCg C  +CP++a
  gi|70607958|ref|YP_256828.1|  2 NVCPANAITKNEM------GIVRIIEDNCIGCGFCTWACPYEA 38
                                  79*******9884......799******************986 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.3e-09
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCga........CvavCPtga 52
                                  CigCg+C+ aCp++a++++++          + ++kC  C++        Cv++CPtga
  gi|70607958|ref|YP_256828.1| 24 CIGCGFCTWACPYEALKITPS----------GIMSKCHLCYNrigsglpyCVEACPTGA 72
                                  ******************997..........6899***997555555577*******98 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00068
                        Fer4_7  7 aCvaaCpvkaield 20
                                  +Cv+aCp++a+++ 
  gi|70607958|ref|YP_256828.1| 63 YCVEACPTGALTFG 76
                                  89999999999976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.4   1.5e-07   0.00017       9      50 ..       1      38 [.       1      39 [. 0.89
   2 !   22.2   6.2     1e-07   0.00012       1      50 [.      23      72 ..      23      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-07
                        Fer4_9  9 veaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                  +++Cpa+++++ + +  + ++     +CigCg C+ aCp +a
  gi|70607958|ref|YP_256828.1|  1 MNVCPANAITKNEMGIVRIIED----NCIGCGFCTWACPYEA 38
                                  579*******999999988865....7************986 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1e-07
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga........CveaCpkga 50
                                  +C+gCg C+ aCp+++ +   ++ + +        C+ C          CveaCp+ga
  gi|70607958|ref|YP_256828.1| 23 NCIGCGFCTWACPYEALKITPSGIMSK--------CHLCYNrigsglpyCVEACPTGA 72
                                  6******************99998866........999999999************97 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.4   1.7e-07   0.00019      17      56 ..       3      38 ..       1      41 [. 0.84
   2 !   17.4   8.4   3.3e-06    0.0037       2      57 ..      18      73 ..      17      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                       Fer4_21 17 aCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedc 56
                                  +C+    +ai++++  +++++ed+C+GC  C+  CP  ++
  gi|70607958|ref|YP_256828.1|  3 VCP---ANAITKNEMGIVRIIEDNCIGCGFCTWACPY-EA 38
                                  566...589999999999******************6.55 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.3e-06
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvl....kvvedeCvGCnlCssvCPvedci 57
                                  ri ed+CigCg C+ aC+   ++a++i+++ ++       +    G   C++ CP+ +++
  gi|70607958|ref|YP_256828.1| 18 RIIEDNCIGCGFCTWACP---YEALKITPSGIMskchLCYNRIGSGLPYCVEACPT-GAL 73
                                  6889**************...8999888776542111334666677788******6.665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.8   3.1e+03      18      22 .]       2       6 ..       1       6 [. 0.83
   2 !   25.2   1.5     1e-08   1.1e-05       4      22 .]      18      36 ..      15      36 .. 0.88
   3 ?    3.8   1.8     0.064        72      15      22 .]      63      70 ..      48      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                        Fer4_2 18 saCPa 22
                                  ++CPa
  gi|70607958|ref|YP_256828.1|  2 NVCPA 6 
                                  69**8 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1e-08
                        Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                   + +d+CigCg C++aCP+
  gi|70607958|ref|YP_256828.1| 18 RIIEDNCIGCGFCTWACPY 36
                                  5789**************5 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.064
                        Fer4_2 15 aCvsaCPa 22
                                   Cv aCP+
  gi|70607958|ref|YP_256828.1| 63 YCVEACPT 70
                                  6******7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   6.2   8.9e-05     0.099      16      56 .]       1      35 [.       1      35 [. 0.84
   2 !   24.6   8.5   1.7e-08   1.9e-05       2      56 .]      17      69 ..      16      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                       Fer4_10 16 vkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +++CPa      +   ++e + vr+  ++C+gcg C+ aCP
  gi|70607958|ref|YP_256828.1|  1 MNVCPA------NAITKNEMGIVRIIEDNCIGCGFCTWACP 35
                                  789999......67777777888889999999999999999 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.7e-08
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc....g....aCveaCP 56
                                  v+i +d Ci+Cg C+ aCP+          +  + + ++ ++kC+ c    g    +CveaCP
  gi|70607958|ref|YP_256828.1| 17 VRIIEDNCIGCGFCTWACPY----------EALKITPSGIMSKCHLCynriGsglpYCVEACP 69
                                  67899**************9..........8888999999*******666615678******9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.037        42      10      21 ..       2      13 ..       1      22 [. 0.81
   2 !   10.2   4.4     0.001       1.1       1      20 [.      23      42 ..      23      57 .. 0.84
   3 !   11.5   0.2   0.00039      0.44       7      30 ..      63      86 ..      62     128 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.037
                       Fer4_16 10 evCPtnaikekk 21
                                  +vCP+nai++++
  gi|70607958|ref|YP_256828.1|  2 NVCPANAITKNE 13
                                  79******9984 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++Cg C+ +CP +a+k +
  gi|70607958|ref|YP_256828.1| 23 NCIGCGFCTWACPYEALKIT 42
                                  6***************9855 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00039
                       Fer4_16  7 kCaevCPtnaikekkekeiearec 30
                                   C+e+CPt+a++    ++ +a+ +
  gi|70607958|ref|YP_256828.1| 63 YCVEACPTGALTFGWIEKGDANVN 86
                                  5**********9774444444432 PP

>> DmsC  DMSO reductase anchor subunit (DmsC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   7.9   4.8e-06    0.0054      50     175 ..     150     257 ..     144     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                          DmsC  50 lliLlgiGliasilHLGsplRAfnalnrvgsSwLSrEivagaiffalagliwLvavlkklskaleklllivtailgiifvy 130
                                    liL  + l+ s+ H  +  R ++ +  +++SwLSrE+ +++i    + l++L+  +++l       +   ++i   + v 
  gi|70607958|ref|YP_256828.1| 150 GLILPLVSLLLSVNHAKRFDRFYRVIYNLKTSWLSREVLFSSI----SVLFYLISFFNQL-------FYYPAVIFLGLGVL 219
                                   56777788999********************************....8999999876654.......44444444445555 PP

                          DmsC 131 mmamvYasiktvptWhsgyTllaflltvlltGsvllyallqaakv 175
                                   +  m+Y  +k  p W++  T ++f   ++      ++ l  ++ +
  gi|70607958|ref|YP_256828.1| 220 SSIMIYI-LKARPSWYNPDTPVSFIGSIF------TTSLPLLFYL 257
                                   6678999.9999****9999999964444......3333333333 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.63     7e+02       8      15 .]       1       8 [.       1       8 [. 0.85
   2 !   11.8   3.3   0.00033      0.37       1      15 []      24      38 ..      24      38 .. 0.94
   3 !   14.8   2.5   3.7e-05     0.042       1      15 []      50      72 ..      50      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.63
                        Fer4_3  8 vevCPvgA 15
                                  ++vCP +A
  gi|70607958|ref|YP_256828.1|  1 MNVCPANA 8 
                                  68***987 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00033
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gCg C  +CP+ A
  gi|70607958|ref|YP_256828.1| 24 CIGCGFCTWACPYEA 38
                                  ************976 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.7e-05
                        Fer4_3  1 CtgCg........aCvevCPvgA 15
                                  C+ C+         Cve+CP+gA
  gi|70607958|ref|YP_256828.1| 50 CHLCYnrigsglpYCVEACPTGA 72
                                  999*8888888766********9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       8.5   9.6e+03      12      16 ..       2       6 ..       1       7 [. 0.73
   2 !   18.9   2.9   1.3e-06    0.0014       2      16 ..      22      36 ..      21      37 .. 0.92
   3 ?    3.0   2.0      0.16   1.8e+02      10      17 .]      64      71 ..      47      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.5
                        Fer4_4 12 aaCPq 16
                                  ++CP 
  gi|70607958|ref|YP_256828.1|  2 NVCPA 6 
                                  68996 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-06
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++CigCg C+ aCP+
  gi|70607958|ref|YP_256828.1| 22 DNCIGCGFCTWACPY 36
                                  89************8 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                        Fer4_4 10 CvaaCPqg 17
                                  Cv aCP+g
  gi|70607958|ref|YP_256828.1| 64 CVEACPTG 71
                                  ******86 PP

>> DUF997  Protein of unknown function (DUF997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.16      22      61 ..     125     163 ..     122     170 .. 0.81
   2 ?    0.5   2.1      0.56   6.3e+02       3      27 ..     184     208 ..     183     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                        DUF997  22 lfaYglgskeveeyyilglPlWfflscillpilfivlvil 61 
                                   l+a++++s+    y+i+ lP W +++ il  ++ ++l + 
  gi|70607958|ref|YP_256828.1| 125 LLAFTIASELALGYSIFKLPYWNLVGLILP-LVSLLLSVN 163
                                   5799**********************8875.666666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.56
                        DUF997   3 nkEalltllltllyflwwllfaYgl 27 
                                    +E+l++ + +l+y++ ++   + +
  gi|70607958|ref|YP_256828.1| 184 SREVLFSSISVLFYLISFFNQLFYY 208
                                   5899999999999998887766654 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.6   0.00043      0.48       3      17 ..      22      36 ..      21      44 .. 0.86
   2 ?    4.3   0.5     0.051        57      47      64 ..      46      71 ..      36      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                        Fer4_8  3 ekCieCgaCqsaCpv 17
                                  ++Ci+Cg+C+ aCp 
  gi|70607958|ref|YP_256828.1| 22 DNCIGCGFCTWACPY 36
                                  58***********94 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.051
                        Fer4_8 47 alwsCttcga........CtevCpvg 64
                                  ++ +C+ c +        C+e+Cp+g
  gi|70607958|ref|YP_256828.1| 46 IMSKCHLCYNrigsglpyCVEACPTG 71
                                  67889999999999999999999986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.9e+03      49      57 ..       2      10 ..       1      11 [. 0.83
   2 ?   12.3   3.2   0.00017      0.19       2      17 ..      21      35 ..      20      55 .. 0.87
   3 ?    0.2   0.1         1   1.2e+03      48      55 ..      65      72 ..      63      75 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                       Fer4_13 49 daCPvesIg 57
                                  + CP ++I+
  gi|70607958|ref|YP_256828.1|  2 NVCPANAIT 10
                                  67******7 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                       Fer4_13  2 DrdtCiacgaCvelaP 17
                                  + d+Ci+cg C +++P
  gi|70607958|ref|YP_256828.1| 21 E-DNCIGCGFCTWACP 35
                                  5.9************* PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                       Fer4_13 48 adaCPves 55
                                  ++aCP+ +
  gi|70607958|ref|YP_256828.1| 65 VEACPTGA 72
                                  46777766 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.7   0.00045      0.51      45      59 ..      23      37 ..       1      39 [. 0.75
   2 ?    7.7   5.9    0.0047       5.3       1      16 [.      23      38 ..      23      56 .. 0.74
   3 ?   -0.3   1.9       1.5   1.6e+03       7      14 ..      63      70 ..      42      72 .. 0.70
   4 ?    1.3   1.4      0.46   5.2e+02       7      16 ..      63      72 ..      49     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                       Fer4_17 45 lCieCgeCerkCPqg 59
                                  +Ci+Cg C+ +CP++
  gi|70607958|ref|YP_256828.1| 23 NCIGCGFCTWACPYE 37
                                  566666666666664 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                       Fer4_17  1 rCiqCgyClpeCpsye 16
                                  +Ci+Cg+C+ +Cp+ +
  gi|70607958|ref|YP_256828.1| 23 NCIGCGFCTWACPYEA 38
                                  5888888888888754 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                       Fer4_17  7 yClpeCps 14
                                  yC+++Cp+
  gi|70607958|ref|YP_256828.1| 63 YCVEACPT 70
                                  56666665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.46
                       Fer4_17  7 yClpeCpsye 16
                                  yC+++Cp+++
  gi|70607958|ref|YP_256828.1| 63 YCVEACPTGA 72
                                  7888898755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2598.57
//
Query:       gi|70607959|ref|YP_256829.1|  [L=187]
Description: pyruvate/ketoisovalerate oxidoreductase common gamma subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-35  121.1   0.1    8.8e-35  120.4   0.1    1.3  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.1   4.9e-39   8.8e-35       1     176 [.      10     174 ..      10     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 4.9e-39
                                   CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH...HHGGGEEE CS
                           POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls...ehldglkp 78 
                                   GGqGvvta+++la+aa +  +y ++++ yg+e+rG+  +++ risd++i+ + +++e+d++v+ld ++l+   +++ glk 
  gi|70607959|ref|YP_256829.1|  10 GGQGVVTASHLLAEAAGYDNLYSSSFPIYGAERRGAEIEAYCRISDSQIRVTSPIQEPDYVVVLDGSLLHlsnNVYRGLKS 90 
                                   9*********************************************999999999**************8889******** PP

                                   EEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHTS-H.HHHHHHHH CS
                           POR  79 ggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallglpl.ealeeaik 155
                                   +++i++n +     e+k +k            ++++v+atk+a e+g      +++N++mlG l++l+g+p  e+le+ai+
  gi|70607959|ref|YP_256829.1|  91 NSVILANYGS----EIKTDK------------KIITVNATKVASELGLIrsgWPMVNVIMLGSLIKLTGMPSiESLEKAIR 155
                                   ********74....444444............3689*********99989999****************5555******** PP

                                   CCS-CH.HHHHHHHHHHHHHH CS
                           POR 156 krfpkkkeviekNlkafragy 176
                                   ++f +k  ++e N+k +r+ y
  gi|70607959|ref|YP_256829.1| 156 DEFDDK--LAEINMKGVRKMY 174
                                   ****95..*******999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1349.16
//
Query:       gi|70607960|ref|YP_256830.1|  [L=88]
Description: pyruvate synthase delta chain [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-15   56.8  14.3    1.2e-08   34.4   4.2    2.1  2  Fer4      4Fe-4S binding domain
    1.3e-12   47.2  13.2    2.8e-06   27.2   3.5    2.1  2  Fer4_6    4Fe-4S binding domain
    9.2e-12   44.9   9.2    1.3e-11   44.4   9.2    1.2  1  Fer4_21   4Fe-4S dicluster domain
    3.9e-10   39.7  21.6    3.3e-07   30.3  11.8    2.1  2  Fer4_10   4Fe-4S dicluster domain
    5.6e-10   38.7  12.2    8.3e-05   22.5   1.7    2.1  2  Fer4_2    4Fe-4S binding domain
    5.6e-10   39.6  23.1    2.2e-08   34.6  12.9    1.7  2  Fer4_7    4Fe-4S dicluster domain
    1.1e-08   35.1  10.6    1.4e-08   34.7  10.6    1.2  1  Fer4_9    4Fe-4S dicluster domain
    4.5e-08   33.9  10.1    0.00055   20.8   2.2    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
      6e-07   29.5  13.3    0.00072   19.9   1.7    2.2  2  Fer4_4    4Fe-4S binding domain
    2.2e-06   28.1   7.9    0.00093   19.7   0.5    2.2  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    4.7e-05   24.0  10.4      0.077   13.7   0.4    3.0  3  Fer4_15   4Fe-4S single cluster domain
    0.00011   22.6   7.2      0.039   14.5   0.3    2.1  2  Fer4_17   4Fe-4S dicluster domain
    0.00017   22.0  13.3      0.069   13.6   2.3    2.1  2  Fer4_8    4Fe-4S dicluster domain
     0.0012   19.6   9.2       0.22   12.4   2.4    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0025   18.6  18.7      0.082   13.9   7.2    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.57   10.4  11.1         13    6.0   3.3    2.0  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   2.4   8.9e-10   9.9e-07       1      23 [.      31      53 ..      31      54 .. 0.90
   2 !   34.4   4.2     1e-11   1.2e-08       1      24 []      60      83 ..      60      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.9e-10
                                  EEEETTTSSS-THHHHHSTTTEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                  +v+d +kCigC+aC + CP   I
  gi|70607960|ref|YP_256830.1| 31 PVVDLSKCIGCKACFMFCPESTI 53
                                  69*****************8665 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1e-11
                                  EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                  v++d+e C gCG C +vCPv AI+
  gi|70607960|ref|YP_256830.1| 60 VTVDYEYCKGCGVCSNVCPVKAIS 83
                                  689*******************96 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   2.2   6.9e-09   7.7e-06       1      22 [.      30      51 ..      30      53 .. 0.92
   2 !   27.2   3.5   2.5e-09   2.8e-06       1      24 []      59      82 ..      59      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 6.9e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPeg 22
                                  ++++d +kCigC +C++ CPe 
  gi|70607960|ref|YP_256830.1| 30 KPVVDLSKCIGCKACFMFCPES 51
                                  69******************96 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.5e-09
                        Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                  +v++d++ C gCg C +vCP +ai
  gi|70607960|ref|YP_256830.1| 59 KVTVDYEYCKGCGVCSNVCPVKAI 82
                                  79*******************998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   9.2   1.2e-14   1.3e-11       2      59 .]      32      84 ..      31      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.2e-14
                       Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                  ++d +kCigC+ C++ C++     i  ++  +++v  + C GC +Cs+vCPv ++i+m
  gi|70607960|ref|YP_256830.1| 32 VVDLSKCIGCKACFMFCPE---STIVPKG-GKVTVDYEYCKGCGVCSNVCPV-KAISM 84
                                  58899*************7...5565554.456999***************9.99998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3  11.8   2.9e-10   3.3e-07       2      56 .]      31      78 ..      30      78 .. 0.92
   2 !   20.7   2.2     3e-07   0.00034       2      23 ..      60      81 ..      59      88 .] 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.9e-10
                       Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +v+d ++Ci+C++C  +CP        + +  ++++v +++e C gcg C  +CP
  gi|70607960|ref|YP_256830.1| 31 PVVDLSKCIGCKACFMFCPE-------STIVPKGGKVTVDYEYCKGCGVCSNVCP 78
                                  6899****************.......888888888889***************9 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3e-07
                       Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                  v +d + C +Cg C ++CP+++
  gi|70607960|ref|YP_256830.1| 60 VTVDYEYCKGCGVCSNVCPVKA 81
                                  78899**************954 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   1.7   7.4e-08   8.3e-05       2      22 .]      30      50 ..      29      50 .. 0.93
   2 !   21.8   3.1   1.2e-07   0.00013       2      21 ..      59      78 ..      58      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.4e-08
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                  ++vvd  +CigC+aC   CP+
  gi|70607960|ref|YP_256830.1| 30 KPVVDLSKCIGCKACFMFCPE 50
                                  589*****************5 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.2e-07
                        Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                  +v vd + C gCg C ++CP
  gi|70607960|ref|YP_256830.1| 59 KVTVDYEYCKGCGVCSNVCP 78
                                  6889**************** PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.5   8.8e-06    0.0099      30      50 ..      30      50 ..      14      52 .. 0.74
   2 !   34.6  12.9     2e-11   2.2e-08       1      52 []      37      81 ..      37      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.8e-06
                        Fer4_7 30 kveidpekClgCgaCvavCPt 50
                                  k+++d +kC+gC+aC   CP 
  gi|70607960|ref|YP_256830.1| 30 KPVVDLSKCIGCKACFMFCPE 50
                                  556777778888888877774 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2e-11
                        Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                  +CigC+aC   Cp ++i  +         kv++d+e+C gCg+C +vCP++a
  gi|70607960|ref|YP_256830.1| 37 KCIGCKACFMFCPESTIVPKG-------GKVTVDYEYCKGCGVCSNVCPVKA 81
                                  7************99999854.......69*******************987 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7  10.6   1.3e-11   1.4e-08       1      51 []      37      82 ..      37      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.3e-11
                        Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                  kC+gC+aC   Cp  ++v++ ++ ++ ++      C gCg C ++Cp +ai
  gi|70607960|ref|YP_256830.1| 37 KCIGCKACFMFCPESTIVPKGGKVTVDYEY-----CKGCGVCSNVCPVKAI 82
                                  7**************************964.....************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.2   3.1e-06    0.0035       1      20 [.      37      56 ..      37      65 .. 0.86
   2 !   20.8   2.2   4.9e-07   0.00055       2      20 ..      67      85 ..      66      88 .] 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.1e-06
                       Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                  +C++C++C + CP++ i  k
  gi|70607960|ref|YP_256830.1| 37 KCIGCKACFMFCPESTIVPK 56
                                  6****************987 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.9e-07
                       Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                  C++Cg C +vCP++ai++ 
  gi|70607960|ref|YP_256830.1| 67 CKGCGVCSNVCPVKAISMV 85
                                  ****************986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.7   6.5e-07   0.00072       2      15 ..      36      49 ..      35      58 .. 0.91
   2 !   15.1   4.3   2.2e-05     0.025       2      16 ..      65      79 ..      64      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.5e-07
                        Fer4_4  2 erCigCgsCvaaCP 15
                                  ++CigC++C  +CP
  gi|70607960|ref|YP_256830.1| 36 SKCIGCKACFMFCP 49
                                  69************ PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  e C gCg+C ++CP+
  gi|70607960|ref|YP_256830.1| 65 EYCKGCGVCSNVCPV 79
                                  89************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.5   8.3e-07   0.00093       1      18 [.      33      50 ..      33      60 .. 0.94
   2 !   12.2   1.8   0.00018       0.2       1      17 [.      62      78 ..      62      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.3e-07
                       Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                  VD ++Ci+c+aC +++P+
  gi|70607960|ref|YP_256830.1| 33 VDLSKCIGCKACFMFCPE 50
                                  899**************8 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00018
                       Fer4_13  1 VDrdtCiacgaCvelaP 17
                                  VD + C +cg+C +++P
  gi|70607960|ref|YP_256830.1| 62 VDYEYCKGCGVCSNVCP 78
                                  8999************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.4   6.9e-05     0.077       2      20 ..      32      50 ..      32      58 .. 0.92
   2 !   11.7   3.8   0.00029      0.33       1      19 [.      60      78 ..      60      79 .. 0.95
   3 ?    5.3   0.1      0.03        34      58      65 ..      76      83 ..      74      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                       Fer4_15  2 vvDrdaCigcglCvaeape 20
                                  vvD ++Cigc +C   +pe
  gi|70607960|ref|YP_256830.1| 32 VVDLSKCIGCKACFMFCPE 50
                                  69*************9997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00029
                       Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                  V+vD + C gcg+C  ++p
  gi|70607960|ref|YP_256830.1| 60 VTVDYEYCKGCGVCSNVCP 78
                                  89*************9998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.03
                       Fer4_15 58 aCPvdAIr 65
                                  +CPv+AI+
  gi|70607960|ref|YP_256830.1| 76 VCPVKAIS 83
                                  8******8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   3.5e-05     0.039      43      58 ..      35      50 ..      15      52 .. 0.87
   2 !   11.5   1.8    0.0003      0.33       2      14 ..      67      79 ..      63      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-05
                       Fer4_17 43 aslCieCgeCerkCPq 58
                                   s+Ci+C+ C + CP+
  gi|70607960|ref|YP_256830.1| 35 LSKCIGCKACFMFCPE 50
                                  57999*****999997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0003
                       Fer4_17  2 CiqCgyClpeCps 14
                                  C +Cg C ++Cp 
  gi|70607960|ref|YP_256830.1| 67 CKGCGVCSNVCPV 79
                                  7777777777775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   2.3   6.1e-05     0.069       2      63 ..      35      50 ..       5      52 .. 0.65
   2 !   12.8  14.1   0.00011      0.12       1      64 [.      34      80 ..      34      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                        Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                                  l+kCi+C aC+  C                                              p+
  gi|70607960|ref|YP_256830.1| 35 LSKCIGCKACFMFC----------------------------------------------PE 50
                                  45555555555555..............................................54 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_8  1 elekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                  +l+kCi+C aC+  Cp      +    ++g++    ++ ++       ++C +cg C++vCpv+
  gi|70607960|ref|YP_256830.1| 34 DLSKCIGCKACFMFCP------ESTIVPKGGK----VTVDY-------EYCKGCGVCSNVCPVK 80
                                  589************9......4445566662....33444.......89************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.6   0.00034      0.38      78      94 ..      34      50 ..      23      53 .. 0.75
   2 !   12.4   2.4    0.0002      0.22      77      95 ..      62      80 ..      56      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                       Fer4_22 78 gesgCvGCgRCieacpv 94
                                  + s+C+GC  C + cp+
  gi|70607960|ref|YP_256830.1| 34 DLSKCIGCKACFMFCPE 50
                                  66778888888888876 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0002
                       Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                  ++ + C GCg C+++cpvk
  gi|70607960|ref|YP_256830.1| 62 VDYEYCKGCGVCSNVCPVK 80
                                  57889***********986 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.7   0.00088      0.98       1      13 [.      38      50 ..      38      51 .. 0.94
   2 !   13.9   7.2   7.3e-05     0.082       1      15 []      67      81 ..      67      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00088
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C+gC aC+  CP+
  gi|70607960|ref|YP_256830.1| 38 CIGCKACFMFCPE 50
                                  ************6 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.3e-05
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C gCg C +vCPv+A
  gi|70607960|ref|YP_256830.1| 67 CKGCGVCSNVCPVKA 81
                                  9************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  10.5     0.031        35      58      95 ..      35      77 ..      22      77 .. 0.81
   2 ?    6.0   3.3     0.012        13      59      74 ..      65      80 ..      54      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.031
                       Fer4_18 58 agdcidcescvkvcPtgidirkGlqle.....ciscllcidac 95
                                   ++ci c++c   cP    + kG ++      c  c+ c + c
  gi|70607960|ref|YP_256830.1| 35 LSKCIGCKACFMFCPESTIVPKGGKVTvdyeyCKGCGVCSNVC 77
                                  578*************999999976533344588999998887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                       Fer4_18 59 gdcidcescvkvcPtg 74
                                    c  c++c +vcP++
  gi|70607960|ref|YP_256830.1| 65 EYCKGCGVCSNVCPVK 80
                                  5699**********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 687.08
//
Query:       gi|70607961|ref|YP_256831.1|  [L=397]
Description: pyruvate synthase alpha chain [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-68  229.9   0.2      4e-68  229.6   0.2    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.5e-27   94.1   0.1    1.2e-26   92.9   0.1    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    0.00013   21.8   0.0    0.00029   20.7   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    0.00073   19.2   0.1     0.0019   17.8   0.2    1.7  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.6   0.2     9e-72     4e-68       2     228 ..      15     236 ..      14     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.6 bits;  conditional E-value: 9e-72
                                   HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgla 82 
                                   a++ a+v  + +YPITP+++i+e+lae+ a+ge+ ++e+v++esE++a++a  GAa+aG ra+TaT++qGll+m+e+++++
  gi|70607961|ref|YP_256831.1|  15 AVKLARVGLTGIYPITPQTSIIEKLAEMKAQGEI-QTEIVRVESEHSAMAATYGAALAGIRAFTATASQGLLYMHEMVWWV 94 
                                   5677889999***********************9.79******************************************** PP

                                   HHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH.HE CS
                         POR_N  83 ageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgfllshe 161
                                   ag+++Pvv+vv +Ra+ ++ ++i+++++D+   rd+g+i+ +++n qea dl+++Af+++e+  v +Pv+v +Dgf+lsh+
  gi|70607961|ref|YP_256831.1|  95 AGSRVPVVMVVGTRAVGAP-WNIWNEHTDFTSERDSGWIMAFASNPQEALDLTIQAFRISEDerVFLPVMVGMDGFILSHT 174
                                   *******************.*****************************************99999*************** PP

                                   EEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHH CS
                         POR_N 162 vekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvvee 228
                                     +v +pd+e     i++ l+++++  y +dpe p+ +g  ++p+ +++ re+ + a ++ e ++++
  gi|70607961|ref|YP_256831.1| 175 KTNVLIPDQE----QIDDYLPPRRQ-PYVIDPEDPVEIGNMFPPEGYMKLRESIHLALKNSEDIIRQ 236
                                   **********....88888877755.569****************************9999998876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.1   2.7e-30   1.2e-26       1      99 [.     263     359 ..     263     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.7e-30
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   A++++v mG++ag+a +a+d lRe+gik+G+lr+r+lrP  e+e++e l+++k v+vldr++sfg  G+l+ evk+ + + 
  gi|70607961|ref|YP_256831.1| 263 ADYAVVLMGAWAGDAMEAIDVLREKGIKIGMLRVRYLRPWSEKEIRENLEGKKGVLVLDRSTSFGRGGPLYIEVKSTIRDT 343
                                   9******************************************************************************99 PP

                                   TSEEEEEE--GGG----H CS
                       PFOR_II  82 kvkvvnfvaglgGrditv 99 
                                     +v ++v glgG ++  
  gi|70607961|ref|YP_256831.1| 344 --EVKDIVTGLGGVTVGK 359
                                   ..***********99865 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.6e-08   0.00029       9      70 ..     262     323 ..     257     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.6e-08
                                   TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
               Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                     d ++v +G+    a+eA++ L+++gi++  + +r ++p+ ++ i+e ++ ++ ++v++  
  gi|70607961|ref|YP_256831.1| 262 DADYAVVLMGAWAGDAMEAIDVLREKGIKIGMLRVRYLRPWSEKEIRENLEGKKGVLVLDRS 323
                                   567889999**************************************888877777766544 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   4.3e-07    0.0019      13     102 ..      18     110 ..       6     162 .. 0.80
   2 ?   -2.8   0.0      0.94   4.2e+03     150     167 ..     327     344 ..     324     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-07
                                   HCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT CS
                  TPP_enzyme_N  13 algvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdr 90 
                                    ++v    ++p +  ++++++l+e +   +i++  +r E    ++A  y  a   + ++ +t+  G++ +   +   + +r
  gi|70607961|ref|YP_256831.1|  18 LARVGLTGIYPITPQTSIIEKLAEMKaqgEIQTEIVRVESEHSAMAATYGAALAGIRAFTATASQGLLYMHEMVWWVAGSR 98 
                                   55555555555555566666666655556999999999999999999999999889999999999**************** PP

                                   --EEEEEEE--C CS
                  TPP_enzyme_N  91 iPllvlsgdrpt 102
                                   +P+++++g r++
  gi|70607961|ref|YP_256831.1|  99 VPVVMVVGTRAV 110
                                   ********9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.94
                                   SS--EEEEEEEHHHCC-E CS
                  TPP_enzyme_N 150 grpgPvylelpkdvllee 167
                                   gr gP y+e+   + + e
  gi|70607961|ref|YP_256831.1| 327 GRGGPLYIEVKSTIRDTE 344
                                   789******988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2933.85
//
Query:       gi|70607962|ref|YP_256832.1|  [L=296]
Description: pyruvate ferredoxin oxidoreductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-23   83.6   0.2    1.9e-23   82.9   0.2    1.3  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    0.00025   20.1   0.3    0.00038   19.5   0.3    1.2  1  E1_dh           Dehydrogenase E1 component
    0.00053   19.3   0.3     0.0011   18.2   0.3    1.6  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.084   13.1   0.1       0.36   11.0   0.0    2.0  2  CGGC            CGGC domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.2   4.3e-27   1.9e-23       2     153 .]      48     204 ..      47     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.3e-27
                                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH...ST.TSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGakla...kp.drevvaivGDGgflmi.lqelatavrrnlpit 76 
                                   +Gc+++     ++ + p++ ++ + +  ++  g +aA+G+++a   k  d +vv+ +GDGg+++i +  l+ a++rn +i+
  gi|70607962|ref|YP_256832.1|  48 AGCSSI-----IQGNAPYNSYNlPVVNIAFAAGPAAASGLARAykqKGkDVNVVVWAGDGGTADIgFASLSGAAERNEDII 123
                                   588888.....44455666666699*****************744322368****************************** PP

                                   EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   +v+++Ne+y++ ggq   ++p g+ ++++p+gk+++++++  l+ ++ ++ +a+ ++ ++ +  ++lk+a e +g+ +i+v
  gi|70607962|ref|YP_256832.1| 124 YVCVDNEAYMNSGGQrsgSTPLGAITSTTPEGKKENKKNLPFLMVSHNVPyVATASVGYPHDYIQKLKRAKEIDGFRYIHV 204
                                   **************************************************999**************************97 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   8.5e-08   0.00038      99     162 ..      68     130 ..      52     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.5e-08
                                   E-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEES CS
                         E1_dh  99 gngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNk 162
                                    n+  +a +  + G+a+a k++gk++ ++++ GDg++++ + +++l  aa  +  +i+v++ N+
  gi|70607962|ref|YP_256832.1|  68 VNIAFAAGPAAASGLARAYKQKGKDVNVVVWAGDGGTAD-IGFASLSGAAERNEDIIYVCVDNE 130
                                   5777788866777***********************987.56789999999*********9997 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   2.5e-07    0.0011     118     182 ..      77     148 ..      73     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-07
                DXP_synthase_N 118 saalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk........nvGal 182
                                   +aa Gla+a ++kg++ +vv   GDg+ t+ + f +l  ++e +++++ +  dNe  +++        ++Ga+
  gi|70607962|ref|YP_256832.1|  77 AAASGLARAYKQKGKDVNVVVWAGDGG-TADIGFASLSGAAERNEDIIYVCVDNEAYMNSggqrsgstPLGAI 148
                                   5899**********************9.999***********************9766554444444455555 PP

>> CGGC  CGGC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-05      0.36      37      74 ..      14      51 ..       7      70 .. 0.82
   2 ?   -1.7   0.0      0.74   3.3e+03      43      60 ..     246     263 ..     234     278 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                          CGGC 37 velvgfvtCggCpgkkvveklkelkkegvdvihlssCi 74
                                    + g + C gCp++ +++ l +   +++ v++++ C 
  gi|70607962|ref|YP_256832.1| 14 SLISGTAACPGCPENMAMRMLGMGLGKDTVVVVVAGCS 51
                                  5578999****************9*************5 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.74
                          CGGC  43 vtCggCpgkkvveklkel 60 
                                    +C  C +k+  + +k++
  gi|70607962|ref|YP_256832.1| 246 QECLHCLDKRTRRPIKDF 263
                                   566667666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2134.69
//
Query:       gi|70607963|ref|YP_256833.1|  [L=290]
Description: aldose reductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-60  205.2   0.1    7.2e-59  199.4   0.1    2.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   0.1     4e-63   7.2e-59       2     292 ..      15     270 ..      14     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 4e-63
                                   EEEE-SSS-ST.TS-HHHHHHH.....HHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTT CS
                  Aldo_ket_red   2 lglGtwqlgskeeiskeealel.....lrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaei 77 
                                   + +Gtw++g++ ++  ++a +      ++ra+e Gi+++DtAe+Yg+g++eel+Gea+k   ++r++++i++Kv      +
  gi|70607963|ref|YP_256833.1|  15 MAFGTWRIGGG-FWRASHARDGewtasIKRAIELGITTIDTAEMYGNGHAEELVGEAIKG--FERDKLFIVSKV------W 86 
                                   68********8.555554444444567*********************************..************......* PP

                                   SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--E CS
                  Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvki 157
                                   +s+ s e + +s ++s +rLgt ++Dl+llH p +++p ++e+++a+e lv+ G ir +G+Snf+   ++ka +  kk+++
  gi|70607963|ref|YP_256833.1|  87 PSHASYEKVLKSAKASSQRLGT-HIDLYLLHAPSRTVP-LCETISAFERLVDDGIIRFFGLSNFDSSGIQKAmSCCKKYEV 165
                                   *********************6.***************.**************************9999999999****** PP

                                   EEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHH CS
                  Aldo_ket_red 158 vavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselake 238
                                   va+q++++ll++ +e+  l +++++g+  +ay+pl +G+lt                             ++e l+e++k+
  gi|70607963|ref|YP_256833.1| 166 VAIQNHFSLLSRKDENDALLFARNNGLMYMAYTPLENGILT-----------------------------RNEFLNEIGKK 217
                                   **********99999**************************.............................6788******* PP

                                   TT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 239 hgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                   ++++ +q+al++ + +  + ++i++as+++++e+n++a+e++ls e++++++++
  gi|70607963|ref|YP_256833.1| 218 YNKTASQVALNWYI-SVDNLVPIVKASTPAHVEENAQAMEWRLSREDWEAINNH 270
                                   **************.69999*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2194.11
//
Query:       gi|70607964|ref|YP_256834.1|  [L=530]
Description: acetolactate synthase isozyme I large subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-43  146.8   0.0    8.7e-42  142.6   0.0    2.3  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.2e-34  117.5   0.4    6.3e-33  113.7   0.1    2.5  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.9e-22   78.2   0.0    1.2e-21   76.9   0.0    1.7  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6   0.0   1.4e-45   8.7e-42       3     170 ..       5     177 ..       3     179 .. 0.96
   2 ?    1.6   0.0     0.032   1.9e+02      67     147 ..     415     506 ..     393     518 .. 0.66

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 1.4e-45
                                   HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                  TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                   +ae+l++ +++ ++  vfg+ G++ l+l++++++     ++++ + r E g a++Ad yar++ ++gv++  +gpG+tn l
  gi|70607964|ref|YP_256834.1|   5 TAEILIDSISS-QISDVFGIAGTHGLSLFEEIRKKTekgELKYFMPRLEYGGAIMADYYARVKENVGVFISVNGPGFTNSL 84 
                                   68899999999.9**********************999******************************************* PP

                                   HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T....-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                  TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqel....dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                   t+laeA+++++Pl+++s +++ ++r+++ l+  +     ql+l+r+vtk+++r++s++e+++++++A+r+al++++gPvy+
  gi|70607964|ref|YP_256834.1|  85 TGLAEAYSEGSPLVLISLNKEFKYRNDKQLH-DMgyydAQLQLARQVTKASFRIYSASEAQSTMEKAFRIALEDKMGPVYV 164
                                   ******************************9.6669978****************************************** PP

                                   EEEHHHCC-EEEH CS
                  TPP_enzyme_N 158 elpkdvlleevde 170
                                   e+p dvl++ +d 
  gi|70607964|ref|YP_256834.1| 165 EVPVDVLEDSTDI 177
                                   ********99985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.032
                                   EEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH.........S..TC--T..-CCHHHCCCSSEEEE-SSGGGH CS
                  TPP_enzyme_N  67 vvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg.........qgvlqqel..dqlalfrpvtkyaervtspeel 136
                                   vv      G+  +++ l++A   ++  l +  + ++++           +++  +++  d +++++ +   +++v+++++l
  gi|70607964|ref|YP_256834.1| 415 VVSIIGDAGFQACFNELITAVEYKVNFLTVLVQDNVQHFLrmnqmmkhgKPFATDVFpiDYTKVVEGIGVKVFEVEKKDDL 495
                                   55555566666666666666666666655554444444444665665542222222244888889999999********** PP

                                   HHHHHHHHHHH CS
                  TPP_enzyme_N 137 pealrrAirta 147
                                   +++ ++Ai  +
  gi|70607964|ref|YP_256834.1| 496 KRITEEAINSS 506
                                   *******9987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.047   2.8e+02     126     153 .]     141     166 ..      74     166 .. 0.62
   2 !  113.7   0.1   1.1e-36   6.3e-33       1     152 [.     368     514 ..     368     515 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.047
                                   EESSH.HHHHHHHHHHHH.CSSSEEEEEE CS
                  TPP_enzyme_C 126 rvekadveeleealkeal.ekkgpaliev 153
                                   + e +  + +e+a++ al +k gp+++ev
  gi|70607964|ref|YP_256834.1| 141 S-EAQ--STMEKAFRIALeDKMGPVYVEV 166
                                   2.233..5677777777788889999987 PP

  == domain 2  score: 113.7 bits;  conditional E-value: 1.1e-36
                                   ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE CS
                  TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvln 81 
                                   d+G+++++a  + kv+r +sy+++ ++ +mG ++pa+iGak+a p+revv+i+GD gf+ +++el+tav++++++++v+++
  gi|70607964|ref|YP_256834.1| 368 DAGTNQVMAMDM-KVYRHNSYFNPLIFNAMGSAIPAGIGAKIASPEREVVSIIGDAGFQACFNELITAVEYKVNFLTVLVQ 447
                                   89****988888.9******************************************************************* PP

                                   -SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH..CSSSEEEEE CS
                  TPP_enzyme_C  82 NegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal..ekkgpalie 152
                                   +++  + +++q++++gk ++++      p+d+ k++e++G+k++ vek+  ++l+++ +ea+  + k p+l+ 
  gi|70607964|ref|YP_256834.1| 448 DNVQHFLRMNQMMKHGKPFATD----VFPIDYTKVVEGIGVKVFEVEKK--DDLKRITEEAInsSYKYPTLLR 514
                                   ****************999885....579********************..***********87777788775 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0     2e-25   1.2e-21       1     136 [.     197     319 ..     197     320 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2e-25
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEE CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlv 81 
                                   +++a++ +++ ++p++l+G g++    +  + + +eklgiPvv t++gkg+ipe+hply+g +  +     +e+    D++
  gi|70607964|ref|YP_256834.1| 197 LKEAVDFINSCSKPILLLGYGAS----RSNVLKYVEKLGIPVVVTVRGKGAIPENHPLYAGNIFEM-----SEV--PGDCL 266
                                   589********************....778999**************************9965543.....343..68*** PP

                                   EEES-SSSTCCCTTTTT.TTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                  TPP_enzyme_M  82 lalGarfddirttgsep.efapeakiihididpaeigknyqvdlaivgdvketlea 136
                                   +a+G+ f+      +++ + +p+  i+h+d+d + +++++++d++i + + ++le+
  gi|70607964|ref|YP_256834.1| 267 IAIGTSFNS-LEMWNWTtKLPPK--ILHVDVDVSVFNNSVKTDVEIKASAEAFLEQ 319
                                   ********9.5666788566665..*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3360.95
//
Query:       gi|70607965|ref|YP_256835.1|  [L=187]
Description: hypothetical protein Saci_2256 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-65  218.9  21.7    3.7e-65  218.7  21.7    1.0  1  DUF1404   Protein of unknown function (DUF1404)


Domain annotation for each model (and alignments):
>> DUF1404  Protein of unknown function (DUF1404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.7  21.7   2.1e-69   3.7e-65       1     168 [.      16     183 ..      16     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.7 bits;  conditional E-value: 2.1e-69
                       DUF1404   1 ilglvLivisvnPlteelefknevvymlshyalviggiligykllklkkillliglilavlwhlPlfFelgaaslsvrile 81 
                                   i++++L+++s+nP+te+lef+ ++vym+shya++++g++igyk++k+ +i+l++gli+avlwh P+fF+lgaa+l +ril 
  gi|70607965|ref|YP_256835.1|  16 IIPIALLILSFNPYTESLEFSLPAVYMASHYAVYFSGLYIGYKYFKGGYISLILGLIPAVLWHSPYFFSLGAAMLDYRILL 96 
                                   69******************************************************************************* PP

                       DUF1404  82 elslllgGlllGssikalskvvkitllalwmlgdtvlsillilgsslYsnevypfspYstsqlvetgvvmfvvmnvilvyv 162
                                   e++ll+gG+llGssi+++++++kitllalwmlgd++l+il+i +++lYsn +ypfspY++s+l+ +g++mfv+mnv+l+yv
  gi|70607965|ref|YP_256835.1|  97 EITLLFGGVLLGSSINSMRLQIKITLLALWMLGDSILAILFITSTPLYSNLAYPFSPYTPSSLPLAGILMFVIMNVFLIYV 177
                                   ********************************************************************************* PP

                       DUF1404 163 llkllk 168
                                   + k++k
  gi|70607965|ref|YP_256835.1| 178 ISKFMK 183
                                   ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1348.68
//
Query:       gi|70607966|ref|YP_256836.1|  [L=241]
Description: hypothetical protein Saci_2257 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1664.20
//
Query:       gi|70607967|ref|YP_256837.1|  [L=148]
Description: hypothetical protein Saci_2258 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        4.3    8.3  16.9       0.57   11.2   2.5    2.9  3  PIG-Y          Phosphatidylinositol N-acetylglucosaminyltrans
          9    6.3  12.4        1.4    8.9   3.1    2.4  2  Phage_holin_8  Putative phage holin


Domain annotation for each model (and alignments):
>> PIG-Y  Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.9    0.0027        24      47      64 ..      15      32 ..      11      33 .. 0.91
   2 ?   11.2   2.5   6.3e-05      0.57       5      59 ..      57     112 ..      54     115 .. 0.65
   3 ?   -0.7   0.4      0.31   2.8e+03       4      17 ..     132     145 ..     112     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0027
                         PIG-Y 47 vpllipvtlvfvianWvG 64
                                  ++++++v+ +fv + WvG
  gi|70607967|ref|YP_256837.1| 15 IWWVVTVVAFFVAFEWVG 32
                                  788999***********9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.3e-05
                         PIG-Y   5 lltsvllfivgmyavlfskl.lrlgeaplsppvladd...ryYcylvpllipvtlvfvi 59 
                                    l++ ++f+++m +++f ++ +  + ap++++++++    +yY + +++ +++++v+ +
  gi|70607967|ref|YP_256837.1|  57 YLAAGIVFAIFMGSIVFLAVrF--R-APSTTTEVKRIstvTYYYIALVMDLIAGVVITY 112
                                   5778899*********877733..3.355555534333346777777776666666655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.31
                         PIG-Y   4 llltsvllfivgmy 17 
                                   ++++s++ +i+ my
  gi|70607967|ref|YP_256837.1| 132 FVFGSIIYLIYKMY 145
                                   45555555555555 PP

>> Phage_holin_8  Putative phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   2.9     0.025   2.2e+02      26      45 ..      57      76 ..      37     104 .. 0.68
   2 ?    8.9   3.1   0.00015       1.4      14      44 ..     104     134 ..      92     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.025
                 Phage_holin_8 26 gidadvvlGAfaGavlfVvs 45
                                   + a++v+  f G+++f + 
  gi|70607967|ref|YP_256837.1| 57 YLAAGIVFAIFMGSIVFLAV 76
                                  456899*********99874 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                 Phage_holin_8  14 avtgvglagllpgidadvvlGAfaGavlfVv 44 
                                    ++gv++  l+  i ++ ++GA+a a +fV 
  gi|70607967|ref|YP_256837.1| 104 LIAGVVITYLMMTISYEFLIGALASADVFVF 134
                                   589**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 952.63
//
Query:       gi|70607968|ref|YP_256838.1|  [L=146]
Description: cytochrome c oxidase subunit II [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-13   49.9   0.2    2.4e-12   46.8   0.0    2.1  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
    2.5e-06   27.5   0.0    3.4e-06   27.1   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.067   12.9   0.2       0.11   12.2   0.2    1.3  1  DUF2436       Domain of unknown function (DUF2436)


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.053   3.1e+02       3      19 ..      50      66 ..      48      71 .. 0.84
   2 !   46.8   0.0   4.1e-16   2.4e-12      46     114 ..      71     139 ..      65     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.053
                          COX2  3 ikaiGhqwywsyeytdf 19
                                  ik i  q+ w++ y++ 
  gi|70607968|ref|YP_256838.1| 50 IKVIAFQYAWEFVYPNG 66
                                  8999**********985 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 4.1e-16
                          COX2  46 nrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmp 114
                                   +++vl  +++  l + ++dv+h+f +p lg k +a+pG +    ++++ +G++   c+e+cG  h +m 
  gi|70607968|ref|YP_256838.1|  71 DKLVLKANQTYLLEIQSKDVIHAFYIPQLGFKFEAIPGYVYDFYIVVKTPGTYDIWCAEFCGPGHYTMK 139
                                   57899999999******************************************************9985 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.6e-10   3.4e-06      27     104 .]      63     144 ..      29     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.6e-10
                  Cupredoxin_1  27 vkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd.mhm...d.akGkl 102
                                   + +g+ + +k+ +ka++   l+i+ kd   + f++++lg++ +  pg  + + i  ++pG+Y++ c  ++    + +kG+l
  gi|70607968|ref|YP_256838.1|  63 YPNGTTTIDKLVLKANQTYLLEIQSKD-VIHAFYIPQLGFKFEAIPGYVYDFYIVVKTPGTYDIWCAeFCGpghYtMKGTL 142
                                   456788899********9999999887.469*********************************9977555565679**** PP

                  Cupredoxin_1 103 iV 104
                                   iV
  gi|70607968|ref|YP_256838.1| 143 IV 144
                                   *9 PP

>> DUF2436  Domain of unknown function (DUF2436)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.8e-05      0.11      76     129 ..      76     129 ..      60     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                       DUF2436  76 eanfeytlPanadpsvsteniivdgtakvviPaGvydycitnPepadakiwiag 129
                                   +an  y+l  ++  ++ +  i   g     iP+ vyd+ i   +p+   iw a 
  gi|70607968|ref|YP_256838.1|  76 KANQTYLLEIQSKDVIHAFYIPQLGFKFEAIPGYVYDFYIVVKTPGTYDIWCAE 129
                                   555666666666666666666666666678*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.46
# Mc/sec: 957.83
//
Query:       gi|70607969|ref|YP_256839.1|  [L=506]
Description: cytochrome b [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-28   97.8   6.2    6.8e-28   97.8   6.2    2.4  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    3.3e-22   79.2  12.2    3.3e-22   79.2  12.2    2.2  2  Cytochrome_B     Cytochrome b/b6/petB
     0.0013   19.0   1.9     0.0013   19.0   1.9    3.3  3  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
  ------ inclusion threshold ------
        1.3    9.0   4.7       0.55   10.2   1.9    1.8  2  Neur_chan_memb   Neurotransmitter-gated ion-channel transmemb


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   6.2   1.5e-31   6.8e-28       1     161 [.      94     273 ..      94     298 .. 0.76
   2 ?   -0.7   0.4      0.28   1.3e+03      67      90 ..     366     389 ..     361     460 .. 0.76

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.5e-31
               Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfG 81 
                                   y+mi +++vH+ r+f +GaY+ pRe+ Wi+G ll  ltl+e++lGysLp++l+s  a++ g ++   +P+   +l++l+  
  gi|70607969|ref|YP_256839.1|  94 YVMIFAMLVHITRNFIVGAYRPPREFMWIVGTLLAGLTLTEAYLGYSLPYNLISWVATTTGLNLFGYMPFNLGYLISLFTI 174
                                   79********************************************************************99888876544 PP

               Cytochrom_B_N_2  82 ......gelpg.eallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknvvg..............eplvpvna 141
                                         g + g + l++r++++H  ++ +ll+a++++hl+++ek+g+tp+  + k+  +               ++  + +
  gi|70607969|ref|YP_256839.1| 175 vnpnqpGIMSGvDPLVQRFFVFHW-IVGGLLVAVVGLHLYIFEKHGITPPVSEVKPG-ApelideyqdklksdYRWELQPL 253
                                   4455543333313499********.************************76333322.12344444555556655555555 PP

               Cytochrom_B_N_2 142 vkmlllflvlvallialali 161
                                   ++++ ++++++ l  +++++
  gi|70607969|ref|YP_256839.1| 254 IRSIGMVVMIFLLTFGIIFF 273
                                   55554444443333322222 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
               Cytochrom_B_N_2  67 svPvvgtwlvellfGgelpgeall 90 
                                   +++++  ++v+ ++++e+pg+++ 
  gi|70607969|ref|YP_256839.1| 366 GTGFIIAFIVNTIWAEETPGQEIG 389
                                   567777788888888888777653 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2  12.2   7.3e-26   3.3e-22      12     188 ..      37     218 ..      29     219 .. 0.87
   2 ?   -2.4   0.3      0.76   3.4e+03      99     116 ..     256     273 ..     249     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 7.3e-26
                  Cytochrome_B  12 iiynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglkk 92 
                                   i y lG+ +l  l++ i+tG + a+yytp+    ++s +y++ +v +G l+ s+h +ga +++  +++hi+r +++g++  
  gi|70607969|ref|YP_256839.1|  37 IDYWLGGFVLASLIFEIITGALTALYYTPS--DPYTSTTYLISQVPYGALLFSLHSWGAYVMIFAMLVHITRNFIVGAYRP 115
                                   56899***********************96..7899********************************************* PP

                  Cytochrome_B  93 trelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPv.iGstlvel..lw....gsvsvddatLtrffsl 166
                                   +re +W++G +l+ l++++a++Gy+Lp++ +s+ a+t   nl   +P+ +G  +  +  +     g +s  d  ++rff++
  gi|70607969|ref|YP_256839.1| 116 PREFMWIVGTLLAGLTLTEAYLGYSLPYNLISWVATTTGLNLFGYMPFnLGYLISLFtiVNpnqpGIMSGVDPLVQRFFVF 196
                                   ***********************************************84565433221122222233455567789***** PP

                  Cytochrome_B 167 hfllPflllillllhllllhkt 188
                                   h+++  ll++++ lhl ++ k+
  gi|70607969|ref|YP_256839.1| 197 HWIVGGLLVAVVGLHLYIFEKH 218
                                   ****************998776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.76
                  Cytochrome_B  99 viGvillllvivtafiGy 116
                                    iG++++++++++++i +
  gi|70607969|ref|YP_256839.1| 256 SIGMVVMIFLLTFGIIFF 273
                                   578888888887777644 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5     0.087   3.9e+02      39      97 ..      92     152 ..      69     158 .. 0.68
   2 ?   -3.0   0.3         2     9e+03      33      41 ..     258     266 ..     249     280 .. 0.51
   3 !   19.0   1.9   2.9e-07    0.0013      12      99 ..     307     396 ..     297     414 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.087
                                   HHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHH..HHHHTS-SSCCHHHHHHH CS
                 Cytochrom_B_C  39 aaivilfllpwldrskvksiryrkplakvllallvvsfvvL..gylGvqppeevavllsqi 97 
                                   +a v++f++ +  +++    +yr+p   ++++  +++ ++L  +ylG + p +++ +++ +
  gi|70607969|ref|YP_256839.1|  92 GAYVMIFAMLVHITRNFIVGAYRPPREFMWIVGTLLAGLTLteAYLGYSLPYNLISWVATT 152
                                   5566666666666667778899988777766655555555512588888887777776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                                   HHHHHHHHH CS
                 Cytochrom_B_C  33 Gvvamgaai 41 
                                   G+v+m++ +
  gi|70607969|ref|YP_256839.1| 258 GMVVMIFLL 266
                                   333332211 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 2.9e-07
                                   ---GGGHHHHHHHHCSSSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHH...HHHHHHHHHHHHHHHHTS-SSC CS
                 Cytochrom_B_C  12 aPeWYflpfYaiLraipakllGvvamgaaivilfllpwldrskvksiryrkplakv...llallvvsfvvLgylGvqppee 89 
                                    P WYfl++Y   +ai+   + + ++++ +++ +l+p++d    +  + ++ l  +   l + ++++f+v ++ + + p +
  gi|70607969|ref|YP_256839.1| 307 LPDWYFLFIYFFYKAIDPSSASI-IFLGWVAVTVLFPFIDAYVFRHKAPHPGLRPAavsLGTGFIIAFIVNTIWAEETPGQ 386
                                   59**************7776655.567778888899999988777766665444441104555999999999999888877 PP

                                   CHHHHHHHHH CS
                 Cytochrom_B_C  90 vavllsqiat 99 
                                    + +++ ++ 
  gi|70607969|ref|YP_256839.1| 387 EIGTIGLVVD 396
                                   6666666554 PP

>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.9   8.4e+03      50      76 ..     183     209 ..     171     219 .. 0.74
   2 ?   10.2   1.9   0.00012      0.55      23      80 ..     438     503 ..     435     506 .] 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                                   HHHHS-STTHHHHHHHHHHHHHHHHHH CS
                Neur_chan_memb  50 tSlvipLigkYLlftmvfvtlsivetv 76 
                                   +S v pL+ ++++f  ++  l + ++ 
  gi|70607969|ref|YP_256839.1| 183 MSGVDPLVQRFFVFHWIVGGLLVAVVG 209
                                   578889999999999998888776655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                                   TTHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHS-.STTHHHHHHHHHHHHHHHHHHHHHH CS
                Neur_chan_memb  23 gekvtLgIsvlLslTvfllli.......teilPktSlvip.LigkYLlftmvfvtlsivetvfVln 80 
                                   +ek +L+   +Ls+  f+l +       + ++P tSl+   +ig+Y+   m++  lsi   v++ +
  gi|70607969|ref|YP_256839.1| 438 PEKRVLSGALVLSMNLFILGTliyslyqALTIPMTSLANQfIIGQYIGLSMIMFSLSIFLNVVIGY 503
                                   6777777777888877765322222222669******9763789***************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3442.84
//
Query:       gi|70607970|ref|YP_256840.1|  [L=250]
Description: Rieske domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-13   48.1   0.0    1.4e-12   47.4   0.0    1.3  1  Rieske      Rieske [2Fe-2S] domain
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.35   10.8   0.0    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.6e-16   1.4e-12      33      87 ..     130     196 ..     101     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.6e-16
                                   TS-EEEEESC-TTTT-BC.........GG.SEEETT.EEE-TTT--EEE..TTSBEEE-TTHHHEEE CS
                        Rieske  33 dgevyAlsdvCtHrgapl.........se.gkidekgvleCpcHgwayd..adGkvikgPaprplat 87 
                                   +g+++A+sdvC H+g++l         s+ g   ++  l+CpcHg+ y     G v+ gPaprpl++
  gi|70607970|ref|YP_256840.1| 130 NGTIFAFSDVCVHLGCQLpaqvivsseSDpGLYAKGADLHCPCHGSIYAlkDGGVVVSGPAPRPLPI 196
                                   89****************9999999876667778999*************777788899*****986 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.9e-05      0.35       2      22 ..       1      21 [.       1      24 [. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.9e-05
                    TAT_signal  2 lSRRdFLKgsAAaaAAaalgg 22
                                  ++RR+FL+  + ++AA a++ 
  gi|70607970|ref|YP_256840.1|  1 MDRRTFLRLYLLVGAAIAVAP 21
                                  79****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1905.61
//
Query:       gi|70607971|ref|YP_256841.1|  [L=204]
Description: sulfocyanin, blue copper protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-73  244.0   7.2    5.3e-73  243.4   7.2    1.3  1  SoxE          Sulfocyanin (SoxE) domain
  ------ inclusion threshold ------
      0.017   14.9   0.1        1.5    8.5   0.0    2.3  2  Cu-oxidase_2  Multicopper oxidase
      0.043   14.2   0.0      0.089   13.2   0.0    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
       0.08   13.1   4.3         25    5.1   1.2    3.4  3  DUF2749       Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4   7.2   1.2e-76   5.3e-73       1     149 []      54     203 ..      54     203 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 1.2e-76
                          SoxE   1 pgkvklpydssnktvfiylvvsssas.nlfnfnGtsnGqlkiyiPagwsvlvklvneeslphnlvlvqnntaiPnsleiss 80 
                                   p+k+++py+ssnktvf+++vv+ss++ n+fnfnGts+G+l+iyiPag++v+vk++n+eslphnlvl+qn+t++P+s+eiss
  gi|70607971|ref|YP_256841.1|  54 PSKISIPYSSSNKTVFLTIVVESSSNvNQFNFNGTSSGSLVIYIPAGSTVIVKFINQESLPHNLVLLQNSTPTPQSPEISS 134
                                   799*********************999****************************************************** PP

                          SoxE  81 dGkillivGattsnyavsGissGqsasGlledlsaGtywlacgilGhaesGmWvdlivssnvtvPyaii 149
                                   dGki+ ivGattsny+v+Gis+G+sa+G+++++saG+y+l+cgilGha+sGmW++l++s+nvt+Pya+i
  gi|70607971|ref|YP_256841.1| 135 DGKIIDIVGATTSNYDVNGISGGASAEGVWGPISAGDYMLVCGILGHAASGMWAVLVASNNVTAPYAVI 203
                                   *******************************************************************96 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0062        28      24      56 ..      84     116 ..      48     117 .. 0.76
   2 ?    8.5   0.0   0.00034       1.5     109     134 ..     168     193 ..     144     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0062
                                   ETCCTTTSSEEEEEETTEEEEEEEEE-SSS-EE CS
                  Cu-oxidase_2  24 ngeefsentnvitlpkgevveiviqnntklpHP 56 
                                   n + +s +  vi +p g++v++ + n+++lpH 
  gi|70607971|ref|YP_256841.1|  84 NFNGTSSGSLVIYIPAGSTVIVKFINQESLPHN 116
                                   44555678999999*************999995 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00034
                                   S-EEEEEEESSHHHHHTT-EEEEEEE CS
                  Cu-oxidase_2 109 npGvwllHCHilwHldqGmalqfvvr 134
                                    +G ++l C il H+ +Gm +++v +
  gi|70607971|ref|YP_256841.1| 168 SAGDYMLVCGILGHAASGMWAVLVAS 193
                                   579*****************999876 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.089      20      96 ..      96     190 ..      71     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                   EEETTEE..EEEEEESSSSBEEEEET.............TSSTTTGGGTTSCTTC............EEEEBSTTEEEEEE CS
                   Copper-bind  20 tvkkgek..vtfvnlavmgHNvvldk.............dgvpagvdkdkvkaed............etkliggGekdsvt 73 
                                    + +g++  v+f+n+++ +HN+vl +             d             ++            + + i+gG + +  
  gi|70607971|ref|YP_256841.1|  96 YIPAGSTviVKFINQESLPHNLVLLQnstptpqspeissD-------------GKiidivgattsnyDVNGISGGASAEGV 163
                                   5666666225899***********9955555555544441.............3333333333332222235566666655 PP

                                   EE..SSEEEEEEET.T.TTTTTSEEEE CS
                   Copper-bind  74 fd..eagtYkffCs.P.HaaagMkgkv 96 
                                        ag+Y  +C    Haa gM + +
  gi|70607971|ref|YP_256841.1| 164 WGpiSAGDYMLVCGiLgHAASGMWAVL 190
                                   557888889999997459999997765 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.2    0.0056        25       6      35 ..      19      48 ..      14      55 .. 0.63
   2 ?    4.8   0.0    0.0071        32       9      41 ..      93     136 ..      92     154 .. 0.75
   3 ?    1.7   0.2     0.067     3e+02      13      29 ..     179     195 ..     172     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0056
                       DUF2749  6 lIvlviavaagagtilwlvvqpragtsgsg 35
                                  ++v++iava+g       v+ +  ++s+s 
  gi|70607971|ref|YP_256841.1| 19 ILVVIIAVAVGVYVYNQYVMLSSPSASSST 48
                                  567777788777666655665555555544 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0071
                       DUF2749   9 lviavaagagtilwlvvqpr...........agtsgsgeaqReh 41 
                                   lvi + ag++ i+  + q             ++t+ s+e + + 
  gi|70607971|ref|YP_256841.1|  93 LVIYIPAGSTVIVKFINQESlphnlvllqnsTPTPQSPEISSDG 136
                                   68888889999888866665788888888889999999987665 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.067
                       DUF2749  13 vaagagtilwlvvqpra 29 
                                   ++ +a+++++++v+++ 
  gi|70607971|ref|YP_256841.1| 179 LGHAASGMWAVLVASNN 195
                                   67899999***999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1514.23
//
Query:       gi|70607972|ref|YP_256842.1|  [L=788]
Description: quinol oxidase polypeptide I/III [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.1e-124  415.7  56.8   2.1e-124  415.7  56.8    2.9  2  COX1      Cytochrome C and Quinol oxidase polypeptide I
    2.6e-17   63.5  15.5    2.6e-17   63.5  15.5    2.5  3  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7  56.8  2.4e-128  2.1e-124       2     432 .]      19     458 ..      18     458 .. 0.97
   2 ?  -16.0  22.8         2   1.8e+04     119     206 ..     690     771 ..     544     788 .] 0.42

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 2.4e-128
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT..-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHHH CS
                          COX1   2 igllylilalvlllvggllgllirlqlafp..dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprlna 80 
                                   +g +y++l++v+l++g + ++lir ql f   ++  y+ ++tlHg+ mif++++p+ +gf+nylvp+++ga+dl++p++na
  gi|70607972|ref|YP_256842.1|  19 VGQMYIVLGIVALIIGSVNAALIRDQLSFNnlNAVDYYDAVTLHGIFMIFFVVMPLSTGFANYLVPRMIGAHDLYWPKINA 99 
                                   789************************997667799********************************************* PP

                                   HHHHHHHHHHHHHHHHHH.CSS-STTTTTTTC..........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCG CS
                          COX1  81 lsfwlvvlgvvllllsll.gaattgwteYapls.........evdlwllglllvvvssllgainfivtilkrrapgmtvak 151
                                   lsfw++v +v+l+++s l ga++ gw++Yapls         +++l++++l+l+++ss+l+++nf++ti k+++  ++  k
  gi|70607972|ref|YP_256842.1| 100 LSFWMLVPAVILAAISPLlGAVDLGWYMYAPLSvettvnyglGTNLIQIALILSGLSSTLTGVNFVMTITKMKKV-PY-LK 178
                                   ************7777666****************************************************9943.44.56 PP

                                   S-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC...E-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                          COX1 152 lplfvwavlatailillalpvlalalllllldrslg.kffsp...gdplldqhlfWffgHpeVyililpalgivyyilpkf 228
                                   +plfvw++++tail+++a+p l+++l++ +l+r +g  ff+    g+p+l+q lfWffgHpeVyililpa+g+v+++lpk+
  gi|70607972|ref|YP_256842.1| 179 MPLFVWGFFTTAILMIIAMPSLTAGLVFAYLERLWGtPFFDSalgGSPVLWQQLFWFFGHPEVYILILPAMGLVSELLPKM 259
                                   ****************************************8889************************************* PP

                                   HTSCCCTHHHHHHHHHHHHHHC.CCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCCTTS-CHCHHHHHHHH CS
                          COX1 229 agrplfsyklsvlafililfls.flvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatlwrgsirfktpmlffl 308
                                   a+r++f+y++++l+ i+i+fls + vw+HH+ft   ++ ++++ s+++++ia+Psg+kv+nw+atl++g+ir+ktp++ ++
  gi|70607972|ref|YP_256842.1| 260 ARREIFGYTAIALSSIAIAFLSaLGVWMHHMFTAIDNTLVQIVSSATTMAIAIPSGVKVLNWTATLYGGEIRYKTPTILLI 340
                                   **********************889******************************************************** PP

                                   HHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHHHHHHHHHHHHHHH CS
                          COX1 309 gfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserlaklhfwllfiGlvl 389
                                    f+v+f++gG+tGv+  l++++y + +ty+vv+HfH++++ a++++l++a++y++p + g++++  l+k+  +ll++G++l
  gi|70607972|ref|YP_256842.1| 341 SFIVMFLLGGITGVFFPLVPIDYALNGTYFVVGHFHYMVY-AILYALLGALFYYFPFWSGKWYNDDLGKTGAILLVAGTFL 420
                                   **************************************99.8999************************************ PP

                                   HHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                          COX1 390 mflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                   +++ m i+G+lgmprr+a  +s     p ++p+++++++g+vl
  gi|70607972|ref|YP_256842.1| 421 TATGMSIAGILGMPRRYAVIPS-----PIYDPFQFMASVGAVL 458
                                   ******************7644.....89***********986 PP

  == domain 2  score: -16.0 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHHHHHH......HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSCE CS
                          COX1 119 lglllvvvssllgainfivtilk......rrapgmtvaklplfvwavlatailillalpvlalalllllldrslgkffspg 193
                                   lgll + ++ ++    +  +i++         +       +   ++++++++ ++ ++++l +   ++l    + k f p+
  gi|70607972|ref|YP_256842.1| 690 LGLLTMAMGLTF----LGGQIYEfthyihFIPQ-----DSAASSFFFATVSLHGFHVIMGLVIWAFMML---RIRKGFIPY 758
                                   222222111111....11111111000011111.....1111111122222222222222222222212...111222233 PP

                                   -HHHHHHHHHHHH CS
                          COX1 194 dplldqhlfWffg 206
                                   ++ +++++ W f+
  gi|70607972|ref|YP_256842.1| 759 AGSVAATYYWHFV 771
                                   3333333333333 PP

>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1       1.3   1.2e+04     194     211 ..      55      72 ..      47      85 .. 0.74
   2 ?   -4.3   2.7       1.4   1.3e+04     160     173 ..     336     349 ..     269     398 .. 0.47
   3 !   63.5  15.5   2.9e-21   2.6e-17      75     255 ..     608     784 ..     594     786 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHHHHHH CS
                          COX3 194 fylatGlhglhviigtil 211
                                   +y a  lhg+ +i   ++
  gi|70607972|ref|YP_256842.1|  55 YYDAVTLHGIFMIFFVVM 72 
                                   677788888888765544 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHH CS
                          COX3 160 llltillavlftll 173
                                   ++l i ++v+f+l 
  gi|70607972|ref|YP_256842.1| 336 TILLISFIVMFLLG 349
                                   33333334444433 PP

  == domain 3  score: 63.5 bits;  conditional E-value: 2.9e-21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBHHH CS
                          COX3  75 GlklGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegnrkk 155
                                     +  ++ fi++ev+lf ++    +   +sP+++    +    + av+ + +P + t+illss +    a+  + +gn k 
  gi|70607972|ref|YP_256842.1| 608 DARSAVLWFILAEVILFGSFIG-GYAFIMSPVTNP-LSYVNNIVPAVEVFPLPAIMTAILLSSSIPAHIAYEYFKKGNVKM 686
                                   56778999********988664.455677887653.3444555789999*****************99999999******* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHH-S.S-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSSB-HHHHHH CS
                          COX3 156 alkgllltillavlftllqaveyleas.ftisdgvyGsvfylatGlhglhviigtillavallrllkyhltknhhlGfeaa 235
                                     +  llt+++++ f++ q +e+++   f   d++  s f+++  lhg+hvi+g ++ a+ +lr+ k  + +    G  aa
  gi|70607972|ref|YP_256842.1| 687 FRNLGLLTMAMGLTFLGGQIYEFTHYIhFIPQDSAASSFFFATVSLHGFHVIMGLVIWAFMMLRIRKGFIPY---AGSVAA 764
                                   99999******************9875155578888888888889*********************998875...68999* PP

                                   HHHHHHHHHHHHHHHHHTTT CS
                          COX3 236 ilywhfvdvvwlflyvsvyw 255
                                    +ywhfvd vw+ ++ ++y 
  gi|70607972|ref|YP_256842.1| 765 TYYWHFVDAVWVVVFSTFYL 784
                                   ***************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5678.28
//
Query:       gi|70607973|ref|YP_256843.1|  [L=185]
Description: hypothetical protein Saci_2264 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-54  183.1  24.8      4e-54  182.8  24.8    1.0  1  DUF1404    Protein of unknown function (DUF1404)
     0.0012   18.3  12.7     0.0012   18.3  12.7    2.0  2  Caa3_CtaG  Cytochrome c oxidase caa3 assembly factor (Caa3_Ct


Domain annotation for each model (and alignments):
>> DUF1404  Protein of unknown function (DUF1404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8  24.8   4.5e-58     4e-54       1     168 [.       9     175 ..       9     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 4.5e-58
                       DUF1404   1 ilglvLivisvnPlteelefknevvymlshyalviggiligykllkl.....kkillliglilavlwhlPlfFelgaasls 76 
                                   i++++Li+i++nP+te++++ n++ yml+hy+l+++gil++y+++++     k+i+l+ig++lav+wh+P+fF+lg+++l+
  gi|70607973|ref|YP_256843.1|   9 IISVFLIIITINPYTETYMSINPIPYMLAHYSLYASGILLAYFVYDRlkplnKYISLVIGIFLAVTWHIPFFFNLGVYNLW 89 
                                   689*******************************************99***99999************************* PP

                       DUF1404  77 vrileelslllgGlllGssikalskvvkitllalwmlgdtvlsillilgsslYsnevypfspYstsqlvetgvvmfvvmnv 157
                                   +r++eelsl++gG+++G+sik ls++++++llalwm++dt+ls ll++  slY++       Y+t++l+++gv+mf++mn+
  gi|70607973|ref|YP_256843.1|  90 IRLIEELSLFIGGYFMGHSIKGLSRNFNLFLLALWMIADTYLSALLMIYPSLYTTL------YNTQSLQYLGVIMFLMMNT 164
                                   ******************************************************85......99***************** PP

                       DUF1404 158 ilvyvllkllk 168
                                   ++vy+ll+++ 
  gi|70607973|ref|YP_256843.1| 165 LVVYLLLQYVI 175
                                   *******9975 PP

>> Caa3_CtaG  Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3     0.027   2.4e+02     109     148 ..      13      52 ..       4      63 .. 0.55
   2 !   18.3  12.7   1.4e-07    0.0012     101     228 ..      62     175 ..      57     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.027
                     Caa3_CtaG 109 allyllylpplfdaalrsealhalmhlhfllaGllfwwpv 148
                                   +l+++   p   +++  +++ + l h ++ ++G+l+ + v
  gi|70607973|ref|YP_256843.1|  13 FLIIITINPYTETYMSINPIPYMLAHYSLYASGILLAYFV 52 
                                   2222223333333444566667777777777777766655 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-07
                     Caa3_CtaG 101 lvalllfvallyllylpplfdaalrsealhalmhlhfllaGllfwwpvlgpdpeprrlspllrllylfaamvlhaflgall 181
                                    + l++ ++l + +++p +f++ + + ++  +++l++++ G+++  ++ g       ls    l++l + m++++ l+all
  gi|70607973|ref|YP_256843.1|  62 YISLVIGIFLAVTWHIPFFFNLGVYNLWIRLIEELSLFIGGYFMGHSIKG-------LSRNFNLFLLALWMIADTYLSALL 135
                                   57788999999*********************************999988.......455688****************** PP

                     Caa3_CtaG 182 mfastvlypayylaswgsplaDqqlGGlimwvlgelvyllvllalfv 228
                                   m  +++  + y      +  +  q  G+im ++     + +ll  ++
  gi|70607973|ref|YP_256843.1| 136 MIYPSLYTTLY------NT-QSLQYLGVIMFLMMNTLVVYLLLQYVI 175
                                   ***99888888......44.444555566666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1306.77
//
Query:       gi|70607974|ref|YP_256844.1|  [L=135]
Description: hypothetical protein Saci_2265 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1055.10
//
Query:       gi|70607975|ref|YP_256845.1|  [L=78]
Description: hypothetical protein Saci_2266 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00012   21.6   0.1    0.00013   21.5   0.1    1.0  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
     0.0017   18.5   0.1     0.0021   18.2   0.1    1.1  1  HTH_34         Winged helix DNA-binding domain
     0.0043   16.9   0.6     0.0049   16.7   0.6    1.1  1  HxlR           HxlR-like helix-turn-helix
     0.0066   15.3   0.3     0.0067   15.3   0.3    1.1  1  HTH_micro      HTH-like
     0.0066   16.3   0.3     0.0075   16.1   0.3    1.1  1  TFIIE_alpha    TFIIE alpha subunit
     0.0077   16.1   1.2      0.017   15.0   1.2    1.6  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.055   13.4   0.0      0.062   13.2   0.0    1.1  1  MarR_2         MarR family
      0.077   12.6   0.2       0.12   12.0   0.2    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
       0.11   12.4   0.7       0.16   11.9   0.7    1.1  1  HTH_11         HTH domain
       0.12   12.9   0.1       0.13   12.8   0.1    1.1  1  HTH_27         Winged helix DNA-binding domain
       0.12   12.3   0.1       0.15   12.0   0.1    1.2  1  HTH_43         Winged helix-turn helix


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   8.1e-08   0.00013      83     149 ..       3      67 ..       1      70 [. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.1e-08
                                   TSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEESS CS
                 RNA_pol_Rpc34  83 slsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYlla 149
                                   +l+ + +lV++i  e  ++    r++k+ ++L+   +   Lk+L  kk ik++ ++     ++Yl  
  gi|70607975|ref|YP_256845.1|   3 NLPPSAKLVLKILME--RRSLRFRELKEETQLPTRTLYYALKLLKEKKVIKAMPCLDDTRERVYLVV 67 
                                   677777888888876..777889*****************************************975 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.3e-06    0.0021       5      47 ..      11      53 ..      10      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                        HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                                  vl +L++ ++  f+elke++++ +  L+  lk L++++ i+ +
  gi|70607975|ref|YP_256845.1| 11 VLKILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIKAM 53
                                  799*********************************9998865 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6     3e-06    0.0049       9      55 ..      10      56 ..       8      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                                  HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES CS
                          HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevyp 55
                                  l+l  l++  + Rf elk++  ++++++L   L+ L+++++i++ +  
  gi|70607975|ref|YP_256845.1| 10 LVLKILMErRSLRFRELKEET-QLPTRTLYYALKLLKEKKVIKAMPCL 56
                                  788888886899********9.9*******************987765 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   4.1e-06    0.0067     100     137 ..      14      51 ..       9      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.1e-06
                     HTH_micro 100 lvkakdyvkaaelraklnidpKklfYvikkLakkglie 137
                                   ++  ++     el+++ ++ +++l+Y++k L++k++i+
  gi|70607975|ref|YP_256845.1|  14 ILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIK 51 
                                   56667888999**************************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.3   4.6e-06    0.0075      14      66 ..       7      59 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                  HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETT CS
                   TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdee 66
                                  +a+lvl++L+e+  +   +l++e+++    l  +L  L+e++++k     d+ 
  gi|70607975|ref|YP_256845.1|  7 SAKLVLKILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIKAMPCLDDT 59
                                  6899****************************************987777654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2   1.1e-05     0.017      13      54 ..      11      52 ..       7      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                  HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                          TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                  v + L+++ +++ +e+ ee+ +p  + Y +L+ L++k +++ 
  gi|70607975|ref|YP_256845.1| 11 VLKILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIKA 52
                                  678899******************************988875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.8e-05     0.062       3      61 ..       4      60 ..       2      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                  --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  l+p+   vL  L  r    l+ +el ++++l+  ++ ++lk L ++  +   p+++D R
  gi|70607975|ref|YP_256845.1|  4 LPPSAKLVLKILMERRS--LRFRELKEETQLPTRTLYYALKLLKEKKVIKAMPCLDDTR 60
                                  56777778888888877..*******************************999999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.3e-05      0.12       8      48 .]      11      51 ..       6      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.3e-05
                        HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +L++L++  ++  reL e++ l+  t+ + lk L+e+ +Ik
  gi|70607975|ref|YP_256845.1| 11 VLKILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIK 51
                                  89*************************************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   9.9e-05      0.16       4      42 ..      10      47 ..       8      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                   +l++L+e r+ +   eL+ee+ + +rt +  +k L+e+
  gi|70607975|ref|YP_256845.1| 10 LVLKILMERRS-LRFRELKEETQLPTRTLYYALKLLKEK 47
                                  57999*99998.************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     8e-05      0.13       7      62 ..      10      64 ..       4      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-05
                        HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                                  lvL  ++ +rr  + ++l + +++   +  y+lk L ek +++ +++  d re+ +
  gi|70607975|ref|YP_256845.1| 10 LVLKILM-ERRSLRFRELKEETQLPTRTLYYALKLLKEKKVIKAMPCLDDTRERVY 64
                                  4566666.9999999***************************99999999998755 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   9.1e-05      0.15       9      49 ..       9      49 ..       7      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                                  HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT- CS
                        HTH_43  9 rlylaylideeeanvpklieltgmPRRtlqDtlkalaeldi 49
                                  +l l  l+++++    +l e t++P Rtl  +lk l+e ++
  gi|70607975|ref|YP_256845.1|  9 KLVLKILMERRSLRFRELKEETQLPTRTLYYALKLLKEKKV 49
                                  7889999999999********************99998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 580.27
//
Query:       gi|70607976|ref|YP_256846.1|  [L=141]
Description: hypothetical protein Saci_2267 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-12   46.3   0.0    8.2e-12   45.6   0.0    1.3  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   4.6e-16   8.2e-12       5     105 ..      23     108 ..      19     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 4.6e-16
                     Rhodanese   5 lkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaal 85 
                                   ++el +kg+v ++D+R+p+eYe+ hIpgA+ +             p+ ++   l +l   + k++v++c++++r   ++ +
  gi|70607976|ref|YP_256846.1|  23 VRELYKKGEVTIVDIRNPWEYEDHHIPGAILI-------------PMEYCDILLPKL---ETKQIVLVCEHANR--TTWLI 85 
                                   55666999999*********************.............888888777777...999***********..44444 PP

                     Rhodanese  86 lkk....lGyknvsvldGGfkawk 105
                                     k     G k+v+++ GG++ w 
  gi|70607976|ref|YP_256846.1|  86 NSKpelfEG-KTVYNMLGGMELWM 108
                                   443445689.99**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1015.14
//
Query:       gi|70607977|ref|YP_256847.1|  [L=464]
Description: hypothetical protein Saci_2268 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.3   0.0       0.12   12.4   0.0    1.4  1  Ste5_C    Protein kinase Fus3-binding


Domain annotation for each model (and alignments):
>> Ste5_C  Protein kinase Fus3-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.5e-06      0.12      87     149 ..     180     243 ..     145     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-06
                        Ste5_C  87 ikfspkwlknelypeeikknigivvvSnssmeegkSiLlmdykafaslgr.rrpnelkikvGyl 149
                                   +   +++  n l+++++ ++i iv v ++ +ee +  Ll +yk f+++      n+++ kvG l
  gi|70607977|ref|YP_256847.1| 180 VDVAISNSLNDLFTKGVFQDIKIVPVVDAPLEELRTKLLENYKVFSEKYSfEMENDIQPKVGTL 243
                                   44556666789999*******************************9875525678888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3549.08
//
Query:       gi|70607978|ref|YP_256848.1|  [L=281]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-51  173.1   0.0    6.2e-51  172.5   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
      5e-26   90.9   0.0    9.9e-26   89.9   0.0    1.5  1  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai


Domain annotation for each model (and alignments):
>> FAD_binding_5  FAD binding domain in molybdopterin dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.0   6.9e-55   6.2e-51       2     170 ..       5     173 ..       4     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 6.9e-55
                                   EEEEEE-SSHHHHHHHHHHCTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHHHH CS
                 FAD_binding_5   2 kfeylrpasleealallaaepdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaaeal 82 
                                   +f+y+r++sl+eal++l+ +++++++aGg++l++++k++v++p+ ++di++++el++++ + +g+ iGA+++++++ ++++
  gi|70607978|ref|YP_256848.1|   5 EFSYVRAESLQEALKFLEGNDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELNYVKTSLNGVSIGALTRYHDILSNDI 85 
                                   799****************************************************************************** PP

                                   HHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-EE CS
                 FAD_binding_5  83 vrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktalepgeli 163
                                   v++++p +++a ++i+++q+Rn++TiGG + +a+p+sD++++L al+A++ l sa+g r+v++ +f+kgp +t+ ++gel+
  gi|70607978|ref|YP_256848.1|  86 VKSKVPLMHHATRTIGDMQVRNMGTIGGAISNADPASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDTNKGELV 166
                                   ********************************************************************************* PP

                                   EEEEEE- CS
                 FAD_binding_5 164 taveiPa 170
                                   t++e+P 
  gi|70607978|ref|YP_256848.1| 167 TQIEVPV 173
                                   ******6 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0   1.1e-29   9.9e-26       3     103 .]     181     280 ..     179     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.1e-29
                                   E.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHTCTT CS
                 CO_deh_flav_C   3 y.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspasdpr 82 
                                   y k+ rr++ d+a++++A++++l+++ +ied+++a+ggv+++p ra ++e+ +iGk+l+++l++++a+ ++++++p sd r
  gi|70607978|ref|YP_256848.1| 181 YkKVVRRAG-DYALASVALAIKLKGN-EIEDIKLAYGGVHDKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPPSDHR 259
                                   989999999.*************988.****************************************************** PP

                                   C-HHHHHHHHHHHHHHHHHHH CS
                 CO_deh_flav_C  83 asaeYRrslavsllfrfllea 103
                                   +s  YRr+++++l++++++e+
  gi|70607978|ref|YP_256848.1| 260 GSSWYRREVVKVLTMKAFKEV 280
                                   ******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2106.44
//
Query:       gi|70607979|ref|YP_256849.1|  [L=163]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-29  101.7   0.1    1.6e-29  101.7   0.1    1.9  2  Fer2_2          [2Fe-2S] binding domain
    4.7e-05   23.3   2.7    0.00012   21.9   0.4    2.2  2  Fer2            2Fe-2S iron-sulfur cluster binding domain
    0.00036   20.5   2.2    0.00036   20.5   2.2    1.5  1  Fer2_3          2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.78    9.8   0.0    2.0  2  Gly_rich_SFCGS  Glycine-rich SFCGS


Domain annotation for each model (and alignments):
>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5      0.25   1.1e+03      22      32 ..      48      58 ..      44      76 .. 0.80
   2 !  101.7   0.1   3.6e-33   1.6e-29       1      75 [.      82     154 ..      82     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.25
                        Fer2_2 22 egasqCGyCtp 32
                                  ++ + CG Ct 
  gi|70607979|ref|YP_256849.1| 48 CDTTTCGACTV 58
                                  56789999994 PP

  == domain 2  score: 101.7 bits;  conditional E-value: 3.6e-33
                        Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                   T+egl+++ ++lhp+qeaf ++ a+qCG+Ct+G++m+++ +l+e+ p+pteee+r+ + gn+CRCtgY++iv+Av
  gi|70607979|ref|YP_256849.1|  82 TIEGLSSD-SKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEH-PNPTEEEVRDGIHGNICRCTGYQNIVKAV 154
                                   9*****88.78*********************************9.99999***********************8 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.4   2.7e-08   0.00012       3      56 ..      16      72 ..      14      83 .. 0.75
   2 ?    1.3   0.1     0.074   3.3e+02      39      62 ..     106     132 ..     103     145 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.7e-08
                                  TTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTT...S CS
                          Fer2  3 idgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsd...e 56
                                  ++g ++e  v  ++t+l d+ ++  g ++++++C   +Cg+C+v ++ ++v+s+   +
  gi|70607979|ref|YP_256849.1| 16 VNGVWYEKYV-SPRTLLVDFIRDeLGLTGTKVGCDTTTCGACTVIMNGKSVKSCtvlA 72
                                  6666666555.56777999999879*******************99977775553443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.074
                                   SSSTTEEEEEESCE..CTT.SSSSTHH CS
                          Fer2  39 gCgtClvevlegev..qsd.etelege 62 
                                   +Cg C++ +   ++   ++ +  +e+e
  gi|70607979|ref|YP_256849.1| 106 QCGFCTAGMIMQTYffLKEhPNPTEEE 132
                                   59***9988888878533343333333 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.2     8e-08   0.00036      50      91 ..      46      86 ..      35     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8e-08
                        Fer2_3 50 asCregiCGscavainGkptlaCtatikdlakqkseielepl 91
                                    C  + CG+c+v +nGk+   Ct    + +  +  +++e l
  gi|70607979|ref|YP_256849.1| 46 VGCDTTTCGACTVIMNGKSVKSCTVLAAQADGAE-ITTIEGL 86
                                  68**********************9999877654.4556555 PP

>> Gly_rich_SFCGS  Glycine-rich SFCGS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.092   4.1e+02       5      33 ..      35      64 ..      31      71 .. 0.82
   2 ?    9.8   0.0   0.00017      0.78      19      64 ..      73     117 ..      61     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.092
                Gly_rich_SFCGS  5 igdrlg.kgqkvakgveaaggkaivipgla 33
                                  i d lg  g kv+    ++g+ +++++g +
  gi|70607979|ref|YP_256849.1| 35 IRDELGlTGTKVGCDTTTCGACTVIMNGKS 64
                                  677888569999999999999999999865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00017
                Gly_rich_SFCGS  19 veaaggkaivipglaadlklgdvmkkeeadlgisfcgsggagalta 64 
                                   ++a g++++ i+gl++d kl  + +  + ++ +  cg   ag ++ 
  gi|70607979|ref|YP_256849.1|  73 AQADGAEITTIEGLSSDSKLHPIQEAFKDNFALQ-CGFCTAGMIMQ 117
                                   567899****************998877777664.77777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1180.27
//
Query:       gi|70607980|ref|YP_256850.1|  [L=748]
Description: carbon monoxide dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-154  515.8   0.0   1.5e-154  515.5   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    2.7e-23   82.4   0.0    8.4e-23   80.8   0.0    1.9  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a


Domain annotation for each model (and alignments):
>> Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.5   0.0  1.6e-158  1.5e-154       1     550 []     151     684 ..     151     684 .. 0.95

  Alignments for each domain:
  == domain 1  score: 515.5 bits;  conditional E-value: 1.6e-158
                                   STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevl 79 
                                   vh+e+++nv +   ++ Gd+e+af++ad vv+ e  ++r  ++++E++++l v+  ++++l v+ stq+ph+ r+  a+++
  gi|70607980|ref|YP_256850.1| 151 VHDELKTNVSYkiPFKAGDIEKAFSQADKVVKVEAINERLIPNPMEPRGILSVY--DGNSLSVWYSTQVPHFARSEFARIF 229
                                   69999999999677778*************************************..69*********************** PP

                                   T--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEE CS
                 Ald_Xan_dh_C2  80 glpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvd 160
                                   g+pe k+rv +p+vGG+FG+K++ +++e+++ + +  ++rpV+++ +R+e+mla+  r+++ ++ +v+++kdG++++++ +
  gi|70607980|ref|YP_256850.1| 230 GIPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLASEARSNV-FTGEVAVKKDGTVLGIKGK 309
                                   ******************************************************9999886.589**************** PP

                                   EEEEESSTHHHCHCCHCCTTGGGT.TTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHH CS
                 Ald_Xan_dh_C2 161 lladaGayadlspavleralshld.gpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelR 240
                                   ll d Gay +l+ ++  +++  +  gpYk++++++e+++vyt tpp t++RG+ +p+a++++Er+m  +A+elgld + +R
  gi|70607980|ref|YP_256850.1| 310 LLLDLGAYLTLTAGIQPTIIPVMIpGPYKVRDLEIESTAVYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIR 390
                                   ********99999998766655544******************************************************** PP

                                   HHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEE CS
                 Ald_Xan_dh_C2 241 rrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqega 318
                                   +rNli   +l py++p    yd+gd+ ++++ + ++++y+e+r+  ++ ++++ ++G+gla++ e +++g+       e  
  gi|70607980|ref|YP_256850.1| 391 ERNLID--QL-PYTNPfglRYDTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP------WEYG 462
                                   *****5..56.777777777******************************77899************6665......5799 PP

                                   EEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHH CS
                 Ald_Xan_dh_C2 319 lvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrer 399
                                   +++v+++G+v+v tg+t++GqG+et++aqi+a++L++p+e++rvv+gdtd v  + gt++Srs +++g+A++k ae++ ++
  gi|70607980|ref|YP_256850.1| 463 EIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVEGSFGTYGSRSLTIGGSAALKVAERVLDK 543
                                   ********************************************************************************* PP

                                   HHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHHTTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEE CS
                 Ald_Xan_dh_C2 400 llkiaaellevspedleledgkvvvk...eksvslaelaaaaylervslsatgfyktldeetgkgppfayfaygaavaeVe 477
                                   ++++aa++++++ +++++e+++++vk   +k+ s++e+a+ a ++++++ ++ +y        +++   +f+yg++va+Ve
  gi|70607980|ref|YP_256850.1| 544 MKRAAASYFNADVQEIRYENEEFSVKndpSKKASWDEIASLA-TTKEPIVEKIYY--------END--VTFPYGVHVAVVE 613
                                   **************************9999999*******88.567779999999........244..59*********** PP

                                   EETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                 Ald_Xan_dh_C2 478 vDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                   vD + g  +v ++ + +D+Gk+iNpa++e Qi+GG vqG+G+al+E+ +++e+Gq l+ ++adY +Pta ++P
  gi|70607980|ref|YP_256850.1| 614 VD-DLGMARVVEYRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAIINENGQ-LSVTYADYYVPTAVEAP 684
                                   **.78**************************************************.8999*********9988 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   9.4e-27   8.4e-23       1     110 []      18     136 ..      18     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 9.4e-27
                                   TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.........TSSS-EEEESS CS
                  Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.........siledeedall 72 
                                   tG+ +Y+dDi++p   y+ fvrS+++hA i++id+++al+++G+vav+++kd++   k +          s ++ +e++++
  gi|70607980|ref|YP_256850.1|  18 TGRSNYIDDIKIPSL-YAGFVRSPYPHAIIKRIDATDALKVNGIVAVFSGKDINPMLKGGVgvlsayvnpSLFRFKERKAF 97 
                                   89**********976.*************************************9876666557776666634444444555 PP

                                   .-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                  Ald_Xan_dh_C  73 .aedkvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                     ++kv++vg++va+v+ +d+++ r+A++ v+veYe+l+
  gi|70607980|ref|YP_256850.1|  98 pEDNKVKYVGEPVAIVIGQDKYAVRDAIDRVNVEYEQLK 136
                                   15679*******************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5222.04
//
Query:       gi|70607981|ref|YP_256851.1|  [L=144]
Description: rubrerythrin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-26   92.5   3.3    5.1e-26   91.7   3.3    1.4  1  Rubrerythrin     Rubrerythrin
    3.7e-11   43.1   1.8    4.4e-05   23.4   0.0    2.1  2  Ferritin         Ferritin-like domain
     0.0077   15.1   0.0        0.1   11.4   0.0    1.9  2  FA_desaturase_2  Fatty acid desaturase
  ------ inclusion threshold ------
      0.037   13.8   1.0        6.3    6.6   0.1    2.0  2  COQ7             Ubiquinone biosynthesis protein COQ7
       0.11   12.3   0.0        3.7    7.3   0.0    2.1  2  MOR2-PAG1_C      Cell morphogenesis C-terminal
       0.25   11.5   2.3         12    6.1   0.3    2.1  2  Ferritin_2       Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   3.3   1.7e-29   5.1e-26       1     136 [.      11     136 ..      11     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 1.7e-29
                                   HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGG CS
                  Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflt 80 
                                   e+L  A+ gE +a r+Y ++a+ a+ egyp++a+l++ +Ae E  Ha  + + +++   +              +++ + t
  gi|70607981|ref|YP_256851.1|  11 ENLRHAFMGEAMANRRYLFFAKTADeEGYPELAQLMRSIAEGETAHAFGHLDYIKQGGIGDP-----------ATDKPIRT 80 
                                   89******************************************************777766...........67888899 PP

                                   HHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin  81 taknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                    ++ L++ai+g+++e ++my+ y++ a++eg+e+++++f++la+aEk+H+e++ k+
  gi|70607981|ref|YP_256851.1|  81 LEEMLQSAIAGETYEWTQMYPGYAKQAREEGFEDVAEWFETLARAEKSHAEKFTKA 136
                                   999**************************************************987 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.5e-08   4.4e-05       3      93 ..      12      93 ..      10      95 .. 0.90
   2 !   21.9   0.9   4.4e-08   0.00013       3      60 ..      84     142 ..      83     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.5e-08
                                  HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCSSHHHHH CS
                      Ferritin  3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefgsveevl 85
                                   L++++  e  a   yl +a  ++++g+++la++++  ae e+ ha   +++i++ G    +++a+ ++i       ++ee+l
  gi|70607981|ref|YP_256851.1| 12 NLRHAFMGEAMANRRYLFFAKTADEEGYPELAQLMRSIAEGETAHAFGHLDYIKQGGI---GDPATDKPI------RTLEEML 85
                                  5666666777777789***************************************997...999999999......9****** PP

                                  HHHHHHHH CS
                      Ferritin 86 eaalehek 93
                                  + a++ e+
  gi|70607981|ref|YP_256851.1| 86 QSAIAGET 93
                                  ***99986 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 4.4e-08
                                   HHHHHHHHH.HHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                      Ferritin   3 aLneqlade.ltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGg 60 
                                    L++++a e ++  + y  +a  ++++g+e++ae+f++ a  e  ha+k+ + +  l g
  gi|70607981|ref|YP_256851.1|  84 MLQSAIAGEtYEWTQMYPGYAKQAREEGFEDVAEWFETLARAEKSHAEKFTKALELLKG 142
                                   5888888887788899**********************************998877765 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   3.4e-05       0.1     173     229 ..      31      89 ..      16     100 .. 0.88
   2 ?    1.8   0.0     0.029        86     173     207 ..     104     138 ..      97     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
               FA_desaturase_2 173 aklakeagdellakicgaiaadEkrHeaaYtrvvekllevdp..deavlaladmmrkki 229
                                   ak+a+e+g + la++++ ia+ E+ H+    + +++    dp  d+ +++l++m+++ i
  gi|70607981|ref|YP_256851.1|  31 AKTADEEGYPELAQLMRSIAEGETAHAFGHLDYIKQGGIGDPatDKPIRTLEEMLQSAI 89 
                                   899***************************99999865555533889999999999877 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.029
               FA_desaturase_2 173 aklakeagdellakicgaiaadEkrHeaaYtrvve 207
                                   ak+a+e+g e +a+  +++a  Ek H+  +t+ +e
  gi|70607981|ref|YP_256851.1| 104 AKQAREEGFEDVAEWFETLARAEKSHAEKFTKALE 138
                                   89999999999***************999998765 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0021       6.3       5      49 ..      12      57 ..       8      69 .. 0.87
   2 ?    6.4   0.1    0.0023       6.9       2      57 ..      81     138 ..      80     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                          COQ7  5 llRvdhaGElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHl 49
                                   lR    GE  A++ Y   + ++ ++ +pel +l+++++e E+ H 
  gi|70607981|ref|YP_256851.1| 12 NLRHAFMGEAMANRRYLFFAKTAdEEGYPELAQLMRSIAEGETAHA 57
                                  6777888*******9999999998999****************996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0023
                          COQ7   2 ldrllRvdhaGElg.AvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeellk 57 
                                   l+++l+   aGE+   +++Y g +  + ++  +++ + ++  ++ Ek+H ++f + l+
  gi|70607981|ref|YP_256851.1|  81 LEEMLQSAIAGETYeWTQMYPGYAKQArEEGFEDVAEWFETLARAEKSHAEKFTKALE 138
                                   567888888888641578999999888556667799*****************99875 PP

>> MOR2-PAG1_C  Cell morphogenesis C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0012       3.7     130     158 ..      30      58 ..      12      66 .. 0.86
   2 ?    3.3   0.0     0.022        65     129     163 ..     102     136 ..      77     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                   MOR2-PAG1_C 130 laalaeekglenLarvltsyakgrfrtkd 158
                                   +a++a+e+g+++La++++s+a+g++ ++ 
  gi|70607981|ref|YP_256851.1|  30 FAKTADEEGYPELAQLMRSIAEGETAHAF 58 
                                   5899******************9988665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.022
                   MOR2-PAG1_C 129 nlaalaeekglenLarvltsyakgrfrtkddflkq 163
                                     a+ a+e+g+e++a+ ++++a+++ +++++f+k 
  gi|70607981|ref|YP_256851.1| 102 GYAKQAREEGFEDVAEWFETLARAEKSHAEKFTKA 136
                                   5578899********************99999985 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2    0.0056        17       6      60 ..      13      67 ..       8      95 .. 0.66
   2 ?    6.1   0.3    0.0039        12      34      63 ..     110     142 ..      80     144 .] 0.67

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0056
                    Ferritin_2  6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaa 60
                                  L  A   E +++  Y   +++a+++    l + +r +ae   +h  +H++++k+ 
  gi|70607981|ref|YP_256851.1| 13 LRHAFMGEAMANRRYLFFAKTADEEGYPELAQLMRSIAEGETAHAFGHLDYIKQG 67
                                  5566666777777777777766555566666677777777777777777777664 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                    Ferritin_2  34 lldaevrevaeeiakheeaHveflkaale...G 63 
                                      ++v e +e++a  e++H+e +++ale   G
  gi|70607981|ref|YP_256851.1| 110 EGFEDVAEWFETLARAEKSHAEKFTKALEllkG 142
                                   3345688999*****************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 962.37
//
Query:       gi|70607982|ref|YP_256852.1|  [L=397]
Description: hypothetical protein Saci_2273 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-19   67.6   2.4    8.7e-11   41.9   0.0    3.1  4  CCG            Cysteine-rich domain
    3.9e-05   24.2   5.6    0.00013   22.5   5.6    2.0  1  Fer4_7         4Fe-4S dicluster domain
    9.8e-05   22.8   7.6    0.00059   20.3   7.6    2.3  1  Fer4_17        4Fe-4S dicluster domain
    0.00014   21.9   5.1    0.00033   20.7   5.1    1.6  1  Fer4_9         4Fe-4S dicluster domain
     0.0015   18.9  13.0      0.017   15.6   1.6    2.5  2  Fer4_4         4Fe-4S binding domain
      0.003   18.0  10.9      0.045   14.2  11.4    2.4  2  Fer4_8         4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   15.0  13.3       0.27   11.1   2.6    2.5  2  Fer4           4Fe-4S binding domain
      0.063   14.2   5.8        3.9    8.5   1.0    2.7  2  Fer4_16        4Fe-4S double cluster binding domain
       0.14   12.3  10.3       0.13   12.4   1.0    2.5  2  Fer4_2         4Fe-4S binding domain
       0.19   12.0   0.3         40    4.5   0.1    2.9  3  ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal doma
       0.32   11.1  14.4       0.47   10.6   2.6    2.5  2  Fer4_6         4Fe-4S binding domain
       0.42   10.8  12.9        1.6    8.9   2.4    2.5  2  Fer4_10        4Fe-4S dicluster domain
        1.1    9.5  13.0         23    5.2   2.9    2.3  1  Fer4_21        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       7.8   1.1e+04      75      82 ..      26      33 ..      22      36 .. 0.77
   2 ?   -3.2   1.0       7.6     1e+04      53      81 ..      51      74 ..      29      77 .. 0.55
   3 !   41.9   0.0   6.3e-14   8.7e-11       1      85 []     172     256 ..     172     256 .. 0.94
   4 !   24.7   0.0   1.5e-08   2.1e-05       2      83 ..     296     374 ..     295     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.8
                           CCG 75 tacpgCll 82
                                  t c gC +
  gi|70607982|ref|YP_256852.1| 26 TVCHGCRM 33
                                  78899987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.6
                           CCG 53 laealakrnvetaeetgadaivtacpgCl 81
                                  + ++l+k  ++ + +     +++ c +C+
  gi|70607982|ref|YP_256852.1| 51 KEQDLNKLTLDDLFD-----VASKCFHCK 74
                                  444444444444444.....455566665 PP

  == domain 3  score: 41.9 bits;  conditional E-value: 6.3e-14
                           CCG   1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaee..tgadaivtacpg 79 
                                   va+f++C l+++   + ++ l ++ + lg+e+ ++ +  CCGa+   +g  ++ ++ a++n++ +ee   +   iv++ p+
  gi|70607982|ref|YP_256852.1| 172 VALFTTC-LVDNFFTDIGEDLIEVYNSLGIEVIIP-NFLCCGAPMLDAGDVNRLKKNAEHNMKLIEElvNKGYDIVVPIPT 250
                                   799****.***************************.9******************************6525666******* PP

                           CCG  80 Cllqlk 85 
                                   C l++k
  gi|70607982|ref|YP_256852.1| 251 CALMIK 256
                                   ***996 PP

  == domain 4  score: 24.7 bits;  conditional E-value: 1.5e-08
                           CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.laealakrnvetaeetgadaivtacpgCl 81 
                                    y+++Ch    +y +v+    +ll+ lg+++e+  ++ C G  gg   ++  +a++++ +++e++++ +ad+ +t+cp   
  gi|70607982|ref|YP_256852.1| 296 YYHPPCH---LKYLQVGLPGPRLLRTLGAKVEIS-NKGCSGIDGGWGLRNYdTARRVGSKMMESFKQSKADVFMTECPLAG 372
                                   59****5...56888888888999********99.9*********9999988*************************9766 PP

                           CCG  82 lq 83 
                                   lq
  gi|70607982|ref|YP_256852.1| 373 LQ 374
                                   66 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   5.6   9.5e-08   0.00013       2      50 ..      28      82 ..      27      83 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.5e-08
                        Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgt......ekveidpekClgCgaCvavCPt 50
                                  C gC+ Cv++C +  + +++ +++++       +++  +++kC +C+ C   CP+
  gi|70607982|ref|YP_256852.1| 28 CHGCRMCVNYCDSFPVLFKKIDSKEQDlnkltlDDLFDVASKCFHCKLCYVNCPY 82
                                  ***********977666665433332232222244444568*************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   7.6   4.3e-07   0.00059       2      58 ..      28      82 ..      27      83 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.3e-07
                       Fer4_17  2 CiqCgyClpeCpsyea....ydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                  C++C++C++ C s+      +d++++ l ++++l +       ++as+C +C++C   CP+
  gi|70607982|ref|YP_256852.1| 28 CHGCRMCVNYCDSFPVlfkkIDSKEQDL-NKLTLDD-----LFDVASKCFHCKLCYVNCPY 82
                                  ************9776433244444433.3433332.....2479***************7 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   5.1   2.4e-07   0.00033       2      48 ..      28      82 ..      27      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.4e-07
                        Fer4_9  2 CtgCgaCveaC...pagvvvedaaerkarlraase.....eaCigCgaCveaCpk 48
                                  C gC+ Cv+ C   p    + d++e+  +    ++     ++C++C+ C+  Cp 
  gi|70607982|ref|YP_256852.1| 28 CHGCRMCVNYCdsfPVLFKKIDSKEQDLNKLTLDDlfdvaSKCFHCKLCYVNCPY 82
                                  ***********998888888888877777666666899999************95 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   4.1    0.0034       4.7       4      14 ..      28      38 ..      24      40 .. 0.92
   2 !   15.6   1.6   1.2e-05     0.017       2      16 ..      68      82 ..      67      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                        Fer4_4  4 CigCgsCvaaC 14
                                  C gC+ Cv++C
  gi|70607982|ref|YP_256852.1| 28 CHGCRMCVNYC 38
                                  *********** PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  ++C++C+ C+  CP+
  gi|70607982|ref|YP_256852.1| 68 SKCFHCKLCYVNCPY 82
                                  68************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  11.4   3.3e-05     0.045       3      62 ..      26      81 ..      24      83 .. 0.82
   2 !   12.4   3.0   0.00012      0.17       2      19 ..      67      84 ..      66     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                        Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                    C++C +C + C ++    k + +++++ ++   ++      + + +C +c+ C ++Cp
  gi|70607982|ref|YP_256852.1| 26 TVCHGCRMCVNYCDSFPVLFKKIDSKEQDLNKLTLDDLF----DVASKCFHCKLCYVNCP 81
                                  57************9999998888888887773334444....789*************9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                        Fer4_8  2 lekCieCgaCqsaCpvlr 19
                                  ++kC +C +C  +Cp + 
  gi|70607982|ref|YP_256852.1| 67 ASKCFHCKLCYVNCPYVP 84
                                  589***********9765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.2    0.0011       1.5       7      18 ..      27      38 ..      24      40 .. 0.91
   2 ?   11.1   2.6   0.00019      0.27       6      20 ..      68      82 ..      65      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                  TSSS-THHHHHS CS
                          Fer4  7 kCigCGaCvevC 18
                                   C gC  Cv+ C
  gi|70607982|ref|YP_256852.1| 27 VCHGCRMCVNYC 38
                                  6*********** PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                  TTSSS-THHHHHSTT CS
                          Fer4  6 ekCigCGaCvevCPv 20
                                  +kC +C++C+  CP+
  gi|70607982|ref|YP_256852.1| 68 SKCFHCKLCYVNCPY 82
                                  8*************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.0    0.0028       3.9      50      64 ..      24      38 ..      12      40 .. 0.77
   2 ?    7.2   0.3     0.007       9.6      53      65 ..      69      81 ..      45      83 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0028
                       Fer4_16 50 kqeaitgCdiCqdvC 64
                                  +++ ++gC++C++ C
  gi|70607982|ref|YP_256852.1| 24 QATVCHGCRMCVNYC 38
                                  356799999999999 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.007
                       Fer4_16 53 aitgCdiCqdvCP 65
                                  +++ C+ C   CP
  gi|70607982|ref|YP_256852.1| 69 KCFHCKLCYVNCP 81
                                  5555555555555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.5     0.049        68       9      20 ..      27      38 ..      22      42 .. 0.90
   2 ?   12.4   1.0   9.2e-05      0.13       7      22 .]      67      82 ..      62      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.049
                        Fer4_2  9 rCigCgaCvsaC 20
                                   C gC+ Cv+ C
  gi|70607982|ref|YP_256852.1| 27 VCHGCRMCVNYC 38
                                  5889*******9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.2e-05
                        Fer4_2  7 tdrCigCgaCvsaCPa 22
                                  + +C +C+ C+ +CP+
  gi|70607982|ref|YP_256852.1| 67 ASKCFHCKLCYVNCPY 82
                                  679************5 PP

>> ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.061        84      46      93 ..     128     175 ..     123     191 .. 0.86
   2 ?    4.5   0.1     0.029        40      71     124 ..     239     292 ..     222     294 .. 0.85
   3 ?   -0.4   0.0      0.99   1.4e+03      43      58 ..     349     364 ..     345     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.061
                 ATP-synt_ab_C  46 lvelLkQkqysplsveeqviilyaatngllddipvekvkefekelley 93 
                                   lv+ L Qk  + l +++ + +l + ++gl ++++ +k+++ ++++  +
  gi|70607982|ref|YP_256852.1| 128 LVKHLMQKGKEVLGLHKDAPTLPVSEKGLKEKVKPKKIENPKAKVALF 175
                                   67889*********************************9988887655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.029
                 ATP-synt_ab_C  71 tngllddipvekvkefekelleyleeekkeileeieekkklsdeleeklkeaik 124
                                   ++g+   +p+   + + ke++++l+++ ++++++ie  +kl++e + +l++ ++
  gi|70607982|ref|YP_256852.1| 239 NKGYDIVVPIPTCALMIKEYHRVLDKKVPKVYDSIEYLQKLKNEGKIELNAKFD 292
                                   556666678888888999**************************9999987665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.99
                 ATP-synt_ab_C  43 GerlvelLkQkqyspl 58 
                                   G++++e +kQ++   +
  gi|70607982|ref|YP_256852.1| 349 GSKMMESFKQSKADVF 364
                                   999*******987765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.1     0.016        21       9      19 ..      28      38 ..      24      40 .. 0.92
   2 ?   10.6   2.6   0.00034      0.47       6      21 ..      67      82 ..      64      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                        Fer4_6  9 CigCgdCvrvC 19
                                  C gC+ Cv+ C
  gi|70607982|ref|YP_256852.1| 28 CHGCRMCVNYC 38
                                  *********99 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                        Fer4_6  6 pdkCigCgdCvrvCPe 21
                                  ++kC +C  C+++CP+
  gi|70607982|ref|YP_256852.1| 67 ASKCFHCKLCYVNCPY 82
                                  68999**********7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  12.1    0.0024       3.3       4      56 .]      23      81 ..      20      81 .. 0.77
   2 ?    8.9   2.4    0.0012       1.6       6      21 ..      67      82 ..      62      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                       Fer4_10  4 idddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                  +++  C +C+ Cv+ C  d         +s+++   +   +   ++ +kC +c  C+  CP
  gi|70607982|ref|YP_256852.1| 23 RQATVCHGCRMCVNYC--DSfpvlfkkiDSKEQDLNKLTLDDLFDVASKCFHCKLCYVNCP 81
                                  67889***********..666899998644444444555555556899************9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                       Fer4_10  6 ddtCirCgkCvkaCPa 21
                                  +++C +C+ C   CP+
  gi|70607982|ref|YP_256852.1| 67 ASKCFHCKLCYVNCPY 82
                                  579************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.9     0.016        23      39      51 ..      26      38 ..      14      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                       Fer4_21 39 deCvGCnlCssvC 51
                                    C GC +C++ C
  gi|70607982|ref|YP_256852.1| 26 TVCHGCRMCVNYC 38
                                  5699999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2822.25
//
Query:       gi|70607983|ref|YP_256853.1|  [L=158]
Description: hypothetical protein Saci_2274 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-44  151.5   0.0    2.9e-44  151.3   0.0    1.0  1  DUF3501   Protein of unknown function (DUF3501)
  ------ inclusion threshold ------
       0.13   12.8   0.1        0.3   11.6   0.1    1.6  1  COMP      Cartilage oligomeric matrix protein


Domain annotation for each model (and alignments):
>> DUF3501  Protein of unknown function (DUF3501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.3   0.0   3.2e-48   2.9e-44      34     186 ..       2     148 ..       1     149 [. 0.99

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 3.2e-48
                                   EETTTEEEEE--HHHHHHHHHHHHHHHT--SHHHHHHHHHHHGGGS--SSEEEEEEEE--SSHHHHHHHHHHCTTGGGCEE CS
                       DUF3501  34 elgehltllFEnreTvlyQiqEmlrieritdeeeiqeeleaYneLlPdgselkatlfieiedederreelaklvgieesvf 114
                                   +lg++l+llFEnr+Tv +QiqEm++++++ ++e+i +e+++Y++LlP++++lkatl+i+ +d ++++ ++++l gi+++v+
  gi|70607983|ref|YP_256853.1|   2 SLGDRLSLLFENRDTVAHQIQEMIYLDKLYKKEDILREIQVYSTLLPCNGKLKATLYIHAYDFKDLDWVFDNLGGIYNEVY 82 
                                   79******************************************************************************* PP

                                   EEETTS-EE-EE-TTS-HHHS--SEEEEEEE--HHHHHHHHTT--EEEEEEETTCEEEEE--HHHHHHHHTT CS
                       DUF3501 115 levggekvkaiaeedlereektssVhylrfelteeqiaalkegakvelgvdhpaykeeaklpeevresLakd 186
                                   l+vg++ +++++e ++e+ +++s+V+yl f+l+ e+      ++++el+v h++yk+++kl+++++e+L+kd
  gi|70607983|ref|YP_256853.1|  83 LKVGSKLIQGEPEGGREQGREFSTVQYLIFDLQGEK------STDMELQVLHKNYKYTVKLDKKLAEDLIKD 148
                                   ***********************************7......89**************************99 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.3e-05       0.3       9      34 ..       2      27 ..       1      30 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
                          COMP  9 qLseltqllkeLreelrqQvkEisfL 34
                                  +L + ++ll e r+ +++Q++E+ +L
  gi|70607983|ref|YP_256853.1|  2 SLGDRLSLLFENRDTVAHQIQEMIYL 27
                                  577788999999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1102.12
//
Query:       gi|70607984|ref|YP_256854.1|  [L=170]
Description: membrane protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   53.1   2.2    5.7e-14   52.1   2.2    1.5  1  CorA      CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
       0.19   11.9   1.1       0.28   11.3   0.2    1.7  2  MetOD2    Metanogen output domain 2


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   2.2   6.4e-18   5.7e-14     146     292 .]      31     166 ..       2     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.4e-18
                          CorA 146 kkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                   +++ +++++++ +   ++ +  +++ +++  +l+k++ k ld       ++++d+   +++ +e+l  r + l ++y + +
  gi|70607984|ref|YP_256854.1|  31 TDGNVKSTSEINQVRSEIITLYSDSSALY--YLSKKLSKFLD-------KEVEDDCLFAYDRAEILITRESELYNIYLTEI 102
                                   44444444444444444444444444444..33323333333.......568999999*********************** PP

                          CorA 227 serlNrvmkvLTvltaiflPlTlitGiyGmNfkglP.elewsygypfvlllglmallailllfwfkr 292
                                   ++ lN v+k+LT+++ iflP T +++i+   f+ lP +l+++y   f l l+l +ll i+l++++++
  gi|70607984|ref|YP_256854.1| 103 QNDLNIVIKKLTSISFIFLPITAVASILAISFNDLPsNLNSPY---FGLSLVLLVLLGIALTIYLRK 166
                                   ************************************6666666...8889**************997 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   3.1e-05      0.28      25      60 ..      10      42 ..       4      70 .. 0.72
   2 ?   -1.9   0.0      0.43   3.8e+03      44      65 ..      93     112 ..      73     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
                        MetOD2 25 YarLaksvevnkrllslLsqtydidddkaevseeie 60
                                  Y+  ++++evnk+l slL+++ d + +     +ei+
  gi|70607984|ref|YP_256854.1| 10 YELGTRRIEVNKKLESLLKNITDGNVK---STSEIN 42
                                  666789***************999933...333333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.43
                        MetOD2  44 qtydidddkaevseeieaalkn 65 
                                   ++y+i     e+++++++ +k 
  gi|70607984|ref|YP_256854.1|  93 ELYNIYL--TEIQNDLNIVIKK 112
                                   4455552..3555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1251.36
//
Query:       gi|70607985|ref|YP_256855.1|  [L=341]
Description: AIR synthase-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-15   57.6   0.0    2.7e-15   56.8   0.0    1.4  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.8e-11   44.6   0.0    3.3e-11   43.7   0.0    1.3  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
       0.13   12.2   0.4       0.29   11.1   0.4    1.5  1  GA-like   GA-like domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   4.5e-19   2.7e-15       1     153 [.     157     312 ..     157     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.5e-19
                                   STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT...TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHH CS
                        AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds...avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalae 78 
                                   ++Gd +i+t++  + +++++   +   + ++  s    +   +++  + +++  +++  +  +++ +hD T+GG+ gal+e
  gi|70607985|ref|YP_256855.1| 157 RVGDDVIMTKGPAIEAVALLTNLHPEYFRQRTSSkelFEDAYNLYWQMSCWKDGLIASKI--GIHLMHDATEGGVYGALNE 235
                                   689999999998888888777777666666665566666688999999999999988886..******************* PP

                                   HHHTTTEEEEEECG....THHHHHHHH..HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                        AIRS_C  79 mapasgvgaeidld....kvpifdele..splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsv 153
                                   +a+  +  ++i++d    ++ +++      +++++ s ++G ++++ ++ e+  ++++l + g+ ea+vIG++  +e++++
  gi|70607985|ref|YP_256855.1| 236 IAKVTNKMIKIYEDrlfiRPSVREI-TriVEIDPWSSISEGTMIIVSDKGEE--IKRELIRNGI-EAEVIGKIDSGEGVEL 312
                                   **************88864444433.24899**********99888888888..**********.8********9998876 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   5.5e-15   3.3e-11       5      87 ..      47     137 ..      28     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 5.5e-15
                                   EEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEE CS
                          AIRS   5 vvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgG 76 
                                   +vv+td    pv++ p  +    ++ av+  +sD+++ G  P ++l  l+lp      +++++  g++ea++e+gv +vgG
  gi|70607985|ref|YP_256855.1|  47 LVVKTD----PVFIVPQLGfrkSAWFAVHILASDVMTSGIPPQYALIDLNLPpsikddEFQDMWVGMHEAMKEIGVMVVGG 123
                                   589999....8888776666999********************99************************************ PP

                                   EEEEESS...EEEE CS
                          AIRS  77 dtsfsne...ptis 87 
                                   +t ++++   p+i 
  gi|70607985|ref|YP_256855.1| 124 HTGVYEGtdyPMIG 137
                                   ****9887776554 PP

>> GA-like  GA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   4.9e-05      0.29      13      43 ..     285     314 ..     284     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                       GA-like  13 eaAkaeLkaaGitsdfyiekIdkAkTvEgVk 43 
                                   e+ k eL  +Gi + + i kId+   vE V 
  gi|70607985|ref|YP_256855.1| 285 EEIKRELIRNGI-EAEVIGKIDSGEGVELVG 314
                                   56799*******.***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2510.14
//
Query:       gi|70607986|ref|YP_256856.1|  [L=1281]
Description: hypothetical protein Saci_2277 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-25   89.5   0.2    5.7e-25   88.3   0.2    1.7  1  Pro-kuma_activ  Pro-kumamolisin, activation domain
    4.9e-09   36.8   2.1    4.9e-09   36.8   2.1    6.8  7  Big_7           Bacterial Ig domain
    0.00027   20.4   0.3      0.001   18.5   0.3    2.0  1  TcfC            E-set like domain
     0.0053   17.2   0.3        1.7    9.2   0.0    4.0  4  MG2             MG2 domain


Domain annotation for each model (and alignments):
>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.2   1.3e-28   5.7e-25       2     127 ..      40     162 ..      39     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 1.3e-28
                Pro-kuma_activ   2 gwtkrgraasstllpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhs 82 
                                   g++++g+++s+ +++++++++ +n++ l+ +++++s+p+sp y+++lt+++v++lf+p+++ +++++++L+ssg+++ + +
  gi|70607986|ref|YP_256856.1|  40 GFNEVGTLPSNYHVEFTVYIPLKNIDLLYYYVNQISNPSSPLYQHFLTQAQVEKLFYPTDQ-FNEILSYLKSSGFNIVY-T 118
                                   678899******************************************************9.*****************.9 PP

                Pro-kuma_activ  83 dtkgwiafsatvaqverllktsfeaYshkkgssslarcde.yslPe 127
                                   +  ++i++++tv+qve++l++++ + +  +gs s+++  + +++ +
  gi|70607986|ref|YP_256856.1| 119 AADSVIVATGTVKQVENYLGVQYVMMN--NGSVSYYTIYGtPKVDN 162
                                   99*************************..89999999877677765 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.8      0.53   2.4e+03      19      53 ..     113     153 ..     106     172 .. 0.72
   2 ?    0.2   0.6      0.29   1.3e+03      12      63 ..     590     652 ..     580     667 .. 0.56
   3 ?   -1.8   1.3       1.2   5.5e+03      29      59 ..     696     728 ..     671     745 .. 0.57
   4 ?   -3.0   0.4       2.9   1.3e+04      34      56 ..     910     940 ..     906     949 .. 0.48
   5 ?    2.6   0.4     0.054   2.4e+02      36      62 ..     997    1023 ..     996    1030 .. 0.83
   6 !   36.8   2.1   1.1e-12   4.9e-09       1      70 []    1130    1195 ..    1130    1195 .. 0.88
   7 ?   -0.8   0.0      0.62   2.8e+03      27      50 ..    1224    1248 ..    1217    1260 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.53
                                   EEEEEEEE-S.....S-EEEEEEEETTEE..EEEE-SSSEE CS
                         Big_7  19 vtisasAsdd.....ggvskVefyvdgtl.glgtdtsapys 53 
                                   ++i  +A d+     g+v++Ve y++ +   +++ + ++y+
  gi|70607986|ref|YP_256856.1| 113 FNIVYTAADSvivatGTVKQVENYLGVQYvMMNNGSVSYYT 153
                                   678888888888888999****9998766334444445554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.29
                                   --EB.TSEEEEEEEEE-SS-E......EEEEEEETTEE.....EEEE-SSSEEEEEE--...S CS
                         Big_7  12 atvs.ggtvtisasAsddggv......skVefyvdgtl.g...lgtdtsapysltwtttalta 63 
                                   +t+  g+t t+ a+ + + +v      + V   ++g++ +   +++++ + ++ ++t ++ ++
  gi|70607986|ref|YP_256856.1| 590 STFMpGETMTVVANITINRTVvssgsfNAVLEDLYGNVtNiplTYNSSLGLWTGQFTLPSTAN 652
                                   566666666666666666333211111444333445543355555555566666666655555 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                                   S-EEEEEEEETTEE.EEEE-S...SSEEEEEE-- CS
                         Big_7  29 ggvskVefyvdgtlglgtdts...apysltwttt 59 
                                   + v+ V+  ++g++   t+ +   + ys+++t +
  gi|70607986|ref|YP_256856.1| 696 NPVQAVVTDINGNP-APTNFTveaSVYSYNITDN 728
                                   45666777777777.3333222224444444433 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.9
                                   EEEEET.....TEE....EEEE-SSSEEEEE CS
                         Big_7  34 Vefyvd.....gtl.g..lgtdtsapysltw 56 
                                   V +y++     gt+ +  +++ t +p +++ 
  gi|70607986|ref|YP_256856.1| 910 VYVYANitypnGTPvKygMYSATVYPMTFSS 940
                                   5666662222233322455555555555543 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.054
                                    EEETTEE.EEEE-SSSEEEEEE--.... CS
                         Big_7   36 fyvdgtlglgtdtsapysltwttta.lt 62  
                                    +++dg++ +++d s+ y++ +t+ + ++
  gi|70607986|ref|YP_256856.1|  997 VSADGVP-TTNDLSSAYTFYVTPYTlME 1023
                                    689****.**************987333 PP

  == domain 6  score: 36.8 bits;  conditional E-value: 1.1e-12
                                    XEEEEEE--TT--EBTSEEEEEEEEE-SS-EEEEEEEETTEE.EEEE-S.SSEEEEEE--...SEEEEEEE CS
                         Big_7    1 PtvtitsPangatvsggtvtisasAsddggvskVefyvdgtlglgtdts.apysltwtttaltagthtltV 70  
                                    Pt++i  P  +  ++ gtv+i  ++s + +vs+V +y+d++l l+t +  +++s++++tt++++gt+tltV
  gi|70607986|ref|YP_256856.1| 1130 PTIQINVPLGN--LT-GTVNIGITVSGS-QVSQVSLYLDNQL-LTTFSGsGTFSYQLDTTKYPDGTYTLTV 1195
                                    77777777664..55.89*********9.*************.88885549*******************9 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 0.62
                                    -SS-EEEEEEEETTEE..EEEE-SS CS
                         Big_7   27 ddggvskVefyvdgtl.glgtdtsa 50  
                                     ++++++V   ++++l  ++++ ++
  gi|70607986|ref|YP_256856.1| 1224 AHSEIQSVSSTLNNNLqSVSSTLDS 1248
                                    5699***********9554444444 PP

>> TcfC  E-set like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.3e-07     0.001       5      66 ..    1149    1211 ..    1147    1212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-07
                          TcfC    5 lvvflpragrveiyRdgqLlstqnvnaG.nqeidtssLPsGiYeveirvyengqvvrteqqkf 66  
                                    ++v  ++ ++v +y d+qLl t++ +     ++dt++ P G+Y+++++  ++ ++++++++ +
  gi|70607986|ref|YP_256856.1| 1149 ITVSGSQVSQVSLYLDNQLLTTFSGSGTfSYQLDTTKYPDGTYTLTVVAQQTTGLFNKTSTYV 1211
                                    57788999***************987552569****************999999998887655 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.1   4.7e+02      12      80 ..     593     659 ..     587     676 .. 0.67
   2 !    9.2   0.0   0.00038       1.7      32      84 ..     818     870 ..     800     880 .. 0.85
   3 ?   -0.1   0.0       0.3   1.3e+03      14      75 ..     907     976 ..     901     981 .. 0.60
   4 ?   -0.6   0.1      0.42   1.9e+03      54      86 ..    1170    1201 ..    1153    1213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.1
                                   -TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEE CS
                           MG2  12 rPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvel 80 
                                    Pget  + a +  ++     + ++ ++++d  g++++     +++ g+  ++f+lp++a  G  sv++
  gi|70607986|ref|YP_256856.1| 593 MPGETMTVVANITINRTVVS-SGSFNAVLEDLYGNVTNIPLTYNSSLGLWTGQFTLPSTA-NGILSVVV 659
                                   67777666666644444333.34788888888888776555577788899******9987.57777777 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00038
                                   --EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECS CS
                           MG2  32 aklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsads 84 
                                   ++  +k+++++++g++v++  ++ +  g + + +++pe+   G y++ l a+ 
  gi|70607986|ref|YP_256856.1| 818 QGITIKAELVNQQGEVVSQGLVTYSPLGQYYGYIPVPENLNAGLYTILLFASY 870
                                   4478899****************************************994433 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.3
                                   T-EEEEEEEEESTTCSB---.......EEEEEEEE-TTSSEEEEEEE.EE-CTTEEEEEEE--TT--SEE CS
                           MG2  14 getVslkallrdetlqglak.......lplkltirdpdgkevkelpl.atdetggaesefalpeaaklGe 75 
                                   g+tV++ a +  +++++++        +p++++ + ++     + pl  + + ++ e++f++p+a++lG+
  gi|70607986|ref|YP_256856.1| 907 GQTVYVYANITYPNGTPVKYgmysatvYPMTFSSSYSNISANVNIPLfYNPSIQLWEGNFTIPSASSLGN 976
                                   6666666666666666666656555444444444444444444444444444456889999999999986 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.42
                                    EE-CTTEEEEEEE--TT--SEEEEEEEEECSTT CS
                           MG2   54 atdetggaesefalpeaaklGeysvelsadsae 86  
                                    + + +g++++++++ +  + G+y++++ a++++
  gi|70607986|ref|YP_256856.1| 1170 TFSGSGTFSYQLDTTK-YPDGTYTLTVVAQQTT 1201
                                    4555566666666554.4789999999444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 8415.46
//
Query:       gi|70607987|ref|YP_256857.1|  [L=175]
Description: intracellular proteinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-52  176.7   0.0    3.4e-52  176.6   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0048   16.7   0.0     0.0059   16.4   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.028   14.2   0.0      0.033   13.9   0.0    1.2  1  Peptidase_C26  Peptidase C26
       0.15   11.7   0.0        0.2   11.3   0.0    1.3  1  ThiJ_like      ThiJ/PfpI family-like


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   7.7e-56   3.4e-52       1     164 [.       4     167 ..       4     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 7.7e-56
                                   EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS.TSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTS CS
                     DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvd.keevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperlren 80 
                                   kkvl+++++++ed+E+ +p+ +  ++g+k +v+ ++ k +v+g++G++v  d++++dv++++y alv+pGGr  pe++r++
  gi|70607987|ref|YP_256857.1|   4 KKVLFVIGEEFEDIEFLYPYYRVIEEGFKPVVAWKEaKAKVTGKHGYSVISDVAFKDVRPEDYLALVIPGGRG-PENIRNS 83 
                                   79*******************************999899*********************************9.******* PP

                                   HHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGGHHHHHHH CS
                     DJ-1_PfpI  81 ekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpgaaiefale 161
                                   e++  l+++f++ +k+vaaIC+gpq+L++a+v+kgr++Tsy ++kd++ +ag +y+d+ vvvd+nl++sr+pg+++ fa +
  gi|70607987|ref|YP_256857.1|  84 EELKVLTRRFFDLKKPVAAICHGPQVLISANVVKGRKLTSYGSIKDDVIAAGGQYLDEAVVVDDNLISSRHPGDLPYFAAS 164
                                   ********************************************************************************9 PP

                                   HHH CS
                     DJ-1_PfpI 162 lle 164
                                   l++
  gi|70607987|ref|YP_256857.1| 165 LIK 167
                                   997 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-06    0.0059      39      87 ..      62     113 ..      24     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-06
                                   THHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                        GATase  39 llknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                     +++ +++++gG g  +    e+   +++++++ k+P+  IC G Q+l+ +
  gi|70607987|ref|YP_256857.1|  62 RPEDYLALVIPGGRGPENirnSEELKVLTRRFFDLKKPVAAICHGPQVLISA 113
                                   3568999*****98888877888888999999****************9876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.4e-06     0.033      68     119 ..      59     114 ..      19     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.4e-06
                 Peptidase_C26  68 qdvePslygeepsekeeeadpeRdalela.LiraalergvPilgiCrGlqll...n 119
                                   +dv+P+ y +   +     ++ R++ el+ L r+  + ++P+ +iC G q+l   n
  gi|70607987|ref|YP_256857.1|  59 KDVRPEDYLALVIPGGRGPENIRNSEELKvLTRRFFDLKKPVAAICHGPQVLisaN 114
                                   589999999999999999999999999963678999**************994444 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.4e-05       0.2      83     143 ..      64     115 ..      20     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                     ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakp 143
                                   e+y ++ +pGG+++   ++ +se l+ l + ++       + +k ++aic+g  +l  a+ 
  gi|70607987|ref|YP_256857.1|  64 EDYLALVIPGGRGPE--NIRNSEELKVLTRRFF-------DLKKPVAAICHGPQVLISANV 115
                                   68999********96..5889999*99999999.......56899*******999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1272.50
//
Query:       gi|70607988|ref|YP_256858.1|  [L=316]
Description: hypothetical protein Saci_2279 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2445.70
//
Query:       gi|70607989|ref|YP_256859.1|  [L=173]
Description: hypothetical protein Saci_2280 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1360.44
//
Query:       gi|70607990|ref|YP_256860.1|  [L=540]
Description: acetolactate synthase catalytic subunit [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-39  135.3   0.0    2.7e-39  134.5   0.0    1.3  1  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
      5e-18   65.3   0.3    1.3e-16   60.7   0.0    2.4  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
      9e-05   22.2   0.0     0.0021   17.8   0.0    2.4  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.11   11.7   0.0        1.6    7.9   0.0    2.2  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.0   5.9e-43   2.7e-39       3     169 ..       4     179 ..       2     181 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 5.9e-43
                                   HHHHHHHHHHH.CT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   3 vaealvraLka.lgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   +a+++++ Lk+  gv+++f+v G+++ +++++ ++     +++++ hE +a++aA gy+ + gk gv++v++ pG++nal+
  gi|70607990|ref|YP_256860.1|   4 GAKIFLENLKElGGVDKIFIVSGTDYAAFIEEKAKDGaLPEFIVVPHEITATAAAMGYS-LGGKTGVAAVHTIPGTLNALG 83 
                                   7899999****558*********************99999******************5.669****************** PP

                                   HHHHHHHHT--EEEEEEE--CCCHH........S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg........qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                    +++A+++riPl+v++g++p++++g         +++q++ dq  ++r++ k+ ++++++e++pea++r i+ a s+++gP
  gi|70607990|ref|YP_256860.1|  84 IIVDAYTSRIPLIVIAGRSPYTEEGhegsrnlrIHWTQEARDQGTVVRQWIKWDFEIRKVEQIPEAIARGIQLAYSEPRGP 164
                                   **************************************888**************************************** PP

                                   EEEEEEHHHCC-EEE CS
                  TPP_enzyme_N 155 vylelpkdvlleevd 169
                                   vy+++p++v  e+++
  gi|70607990|ref|YP_256860.1| 165 VYITIPREVSVEKTQ 179
                                   ********9888775 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.037   1.7e+02      25      42 ..      54      71 ..      45      97 .. 0.85
   2 !   60.7   0.0   2.9e-20   1.3e-16      19     153 .]     397     534 ..     388     534 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.037
                                  TTTS-TTTHHHHHHHHHH CS
                  TPP_enzyme_C 25 gglgtmGyglpaAiGakl 42
                                  ++ ++mGy+l++ +G+++
  gi|70607990|ref|YP_256860.1| 54 ATAAAMGYSLGGKTGVAA 71
                                  47899**********997 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 2.9e-20
                                   SEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-.SEEEEEEE-SBCCCHHHH...HHH CS
                  TPP_enzyme_C  19 rsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnl.pitvvvlnNegygmtggq...qep 94 
                                   ++y+++  +g++G++l+a+ G +la  +++v+a+vGDG+f++    ++  avr    ++tv++++N+g+ +         p
  gi|70607990|ref|YP_256860.1| 397 GQYFSDPAFGHLGWSLGASFGFSLA-TNKKVIATVGDGSFIFGvPDAFYYAVRSYGgDVTVIIYDNGGWLASAEAtahVYP 476
                                   6899999*****************8.477**************999******96445************999999555445 PP

                                   HTCCTTTTSBB..BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  95 fggkrksgpagk.dlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   +g+ rk ++++  d+k  ++ + ++a+G    ++e+   +ele  lkea+ ++g ++++v
  gi|70607990|ref|YP_256860.1| 477 EGEARKRQNYPGaDFKRYNIGEGVRAYGGFYKVIEEV--SELEYSLKEAILNRGLSVLQV 534
                                   5555555555446799999999999998876687777..***********999*999986 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.6e-07    0.0021       1      47 [.     198     244 ..     198     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.6e-07
                                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGG CS
                  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlm 47 
                                   i+ a  ++++++rp+il     +r++  +e++++++++giPvv+   
  gi|70607990|ref|YP_256860.1| 198 IRTAQRMIEESERPIILTWRAGRRKEWFDEMKKFVDNTGIPVVHYIG 244
                                   567889*************************************8765 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.037   1.7e+02     159     198 ..     260     299 ..     253     351 .. 0.80
   2 ?    7.9   0.0   0.00036       1.6     111     172 ..     406     462 ..     399     474 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.037
                DXP_synthase_N 159 elkkkllvilNdNemsisknvGalskylskllsskayekl 198
                                    ++++l++++ +    i k+vG +++ + ++  +++y+ +
  gi|70607990|ref|YP_256860.1| 260 ITNSDLVIVVENEVPWIPKKVGKINAKVIRVDVDPSYSYI 299
                                   568899999988888999********99999999988765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00036
                DXP_synthase_N 111 gHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNe 172
                                   gH + s+ a+ G++ a++     kkv+a +GDg++  G+       + +   ++ vi+ dN 
  gi|70607990|ref|YP_256860.1| 406 GHLGWSLGASFGFSLATN-----KKVIATVGDGSFIFGVPDAFYYAVRSYGGDVTVIIYDNG 462
                                   788888888888888876.....68*************874444445667889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3857.63
//
Query:       gi|70607991|ref|YP_256861.1|  [L=444]
Description: transporter protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-32  110.8  31.6    3.5e-24   85.5  11.4    2.0  2  Sugar_tr  Sugar (and other) transporter
    9.1e-26   90.6  63.7      1e-19   70.7  30.0    2.1  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5  11.4   3.9e-28   3.5e-24       7     197 ..      16     214 ..      10     226 .. 0.86
   2 !   32.6  11.5   4.4e-12     4e-08     245     446 ..     231     435 ..     215     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 3.9e-28
                                   HHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                      Sugar_tr   7 lgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlf 86 
                                   + g +l  Yd+ +++a +  +++       +         v++ l ++++l+G+ +Gs ++g +gd++GR+ +l+i+++ f
  gi|70607991|ref|YP_256861.1|  16 FLGfMLDAYDLLFVSALTPYIEKNLVPPGLTGLV--G-YFVTLALGLGLTLIGRPLGSAIFGNFGDVWGRRRTLMITIIGF 93 
                                   4453667788888888888877544443333332..2.246799999********************************** PP

                                   HHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr  87 vigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgln 162
                                   ++ ++l+++ + +      +  +++v R++ Gi+vG+++++   ++ E+Ap k+Rg + ++ q a ++G  ++a++ + + 
  gi|70607991|ref|YP_256861.1|  94 SVFSALIGLLPTYaaigiAASILYAVLRFIEGIFVGGEYAVGHPFAIEYAPSKWRGLVSGIAQGAFSWGTAIGAGIVYLFI 174
                                   ********9998888888888999999*****************************************************5 PP

                                   TSS-.....TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                      Sugar_tr 163 ktsn.....adgwrillglqlvpallllilllflPESPry 197
                                    + +     + gwr+ ++  l+pa + +i+++++PE+P +
  gi|70607991|ref|YP_256861.1| 175 SVLGdkamsDYGWRLVFFTGLIPAAVAFIIRYLVPETPVF 214
                                   55555999999***************************98 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4.4e-12
                                   HHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHH CS
                      Sugar_tr 245 llssktvrqrlligvvlqifqqltGinaimyysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllll 322
                                   l++    ++ +l+++vl+ + +++   +++ +++ i+ ++gls++   l+ ++  ++  ++at+ + + +d +GR++ +l+
  gi|70607991|ref|YP_256861.1| 231 LFRPP-TLYTFLNVFVLMTGLFFSS-YSLFDFATGILTKAGLSTQeasLYYSLAGVFAAIAATLWG-LSSDFIGRKKAFLI 308
                                   44444.4788999999999999998.78999**************885555544444444444444.99************ PP

                                   HHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHH CS
                      Sugar_tr 323 GaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflis 403
                                    a++ +i+++      l+++a++    +++  + +l   l ++ wg vp v++sE f ++ R+++  + + + ++++  + 
  gi|70607991|ref|YP_256861.1| 309 AAIVTIILATPSF--YLWYNAAKANDVGLLFLGSFLIGWLTQWPWGLVP-VYLSERFITKRRASGVGFGYSSGVFISAWMP 386
                                   *****99999996..67777775444455555667777889999*****.999******************9999888777 PP

                                   HHHHHHHCHHH......T-HHHHHHHHHHHHHHHHHHHHS--STT--CC CS
                      Sugar_tr 404 llfpiiteaig......ggyvflvfaglavlfiifvfffvpetkgrtle 446
                                   +    +            ++v ++f +la++ + +  +  pet  ++l+
  gi|70607991|ref|YP_256861.1| 387 IYSIPLSAYFAgieggdPWFVAAFFLILAAVIYGIAALIGPETRTVDLY 435
                                   655444444335667888999999*******************998886 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7  30.0   1.1e-23     1e-19      33     233 ..      54     257 ..      12     268 .. 0.79
   2 !   25.1  27.4   8.2e-10   7.3e-06      23     171 ..     264     423 ..     254     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 1.1e-23
                         MFS_1  33 eigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllf...a....sslwlllvlrvlqGlgagalfpa 105
                                   ++ l l+l  +g  ++s ++G ++d +Grrr+l++++++f+++ +l++l+   a    + + l +vlr++ G++ g+ +++
  gi|70607991|ref|YP_256861.1|  54 TLALGLGLTLIGRPLGSAIFGNFGDVWGRRRTLMITIIGFSVFsALIGLLptyAaigiAASILYAVLRFIEGIFVGGEYAV 134
                                   234455557777799999*************************77777754443567544458****************** PP

                         MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wravfyilaivsllafvlfllllpeeppe 178
                                   g+ ++ +++p + rg++ g+++++fs G+++g+++  l++s lg        Wr+vf+   i +++af++   l+pe+p+ 
  gi|70607991|ref|YP_256861.1| 135 GHPFAIEYAPSKWRGLVSGIAQGAFSWGTAIGAGIVYLFISVLGdkamsdygWRLVFFTGLIPAAVAFII-RYLVPETPVF 214
                                   *******************************************************************995.7777999999 PP

                         MFS_1 179 rkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                   rk  s++++    ++ p+++    l+++p     l+++l +f+ ++gl++ + ++
  gi|70607991|ref|YP_256861.1| 215 RKALSERKL----ERIPFFS----LFRPP----TLYTFLNVFVLMTGLFFSSYSL 257
                                   999999999....6666666....*****....9999999988888877776664 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 8.2e-10
                         MFS_1  23 laedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf.....a..sslw.lllvlrvlq 95 
                                   + +  g+s +e++l ++l +++aa+a+ ++G  sd +Gr++ +l++++++++  + ++f     a  ++   ll+++ +l 
  gi|70607991|ref|YP_256861.1| 264 ILTKAGLSTQEASLYYSLAGVFAAIAATLWGLSSDFIGRKKAFLIAAIVTIIL-ATPSFylwynAakANDVgLLFLGSFLI 343
                                   3455599**********************************777777777777.444432346735988888********* PP

                         MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailg....pllggllasslg......Wravfyilaivsllafv 166
                                   G+ + + + ++ +++++ f  ++r++++g+ +++  + ++       +l++++a   g      W ++ ++l +++++ ++
  gi|70607991|ref|YP_256861.1| 344 GWLTQWPWGLVPVYLSERFITKRRASGVGFGYSSGVFISAWMpiysIPLSAYFA---GieggdpWFVAAFFLILAAVIYGI 421
                                   ******************************999555555555000255666666...333457765554444444444444 PP

                         MFS_1 167 lflll 171
                                      + 
  gi|70607991|ref|YP_256861.1| 422 ---AA 423
                                   ...22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3120.88
//
Query:       gi|70607992|ref|YP_256862.1|  [L=190]
Description: TenA family transcription regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-15   56.7   0.2    2.7e-14   53.5   0.2    2.4  1  TENA_THI-4  TENA/THI-4/PQQC family


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.2   1.5e-18   2.7e-14       2     152 ..       7     144 ..       6     190 .] 0.81

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.5e-18
                                   HHCHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHH CS
                    TENA_THI-4   2 aqlrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrl 82 
                                   ++l  +++++ nHpF+ +  +G lp  ++  +  q++++++   r+lai++s+++  ++  +++  +++ d+e ++ +++ 
  gi|70607992|ref|YP_256862.1|   7 QELSNLNEKILNHPFILRAESGDLPLSKLELFYDQQWYIVNYDLRSLAIMVSRANQQDEL-DFFLSTLQGDYEGLKILREV 86 
                                   677889999***************************************************.***********999999887 PP

                                   HHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHH CS
                    TENA_THI-4  83 aealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyy 152
                                   a+         ++++p+p++ +y++yl +la++g+  e ++al+++l v++e  +rl+  +r   g+ + 
  gi|70607992|ref|YP_256862.1|  87 AK---------KTYSPLPTAISYTHYLSWLANYGNSGEQAVALTVNLPVWAENCRRLANAFR---GKADV 144
                                   75.........469*******************************************98888...33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1301.44
//
Query:       gi|70607993|ref|YP_256863.1|  [L=155]
Description: N-acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-12   47.5   0.0    2.3e-12   47.2   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    6.5e-09   36.6   0.0    9.2e-09   36.1   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    8.9e-08   32.1   0.0    1.1e-07   31.9   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.4e-07   31.1   0.0    4.8e-07   30.1   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.9e-06   27.7   0.0    3.2e-06   27.0   0.0    1.4  1  FR47             FR47-like protein
    0.00083   19.4   0.2      0.054   13.6   0.2    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0075   16.0   0.4      0.013   15.3   0.4    1.4  1  SinI             Anti-repressor SinI
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.046   13.3   0.0    1.3  1  GNAT_acetyltran  GNAT acetyltransferase
      0.082   13.0   0.1       0.23   11.6   0.1    1.7  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.12   12.5   0.0       0.33   11.1   0.0    1.7  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.3e-15   2.3e-12      12     117 .]      34     130 ..      15     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.3e-15
                                   THHHHHHHHHHH..HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHH CS
                Acetyltransf_1  12 ffppnedaseee..feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerar 90 
                                   +f  ++ ++ ++   ++     + +++v+e+ g++i+  s++k+ +          l+V+peyr  GlG++L+ al+ +a+
  gi|70607993|ref|YP_256863.1|  34 YFHLYKPTEDDAkrIADC---LDHRTIVVEYQGKIIAEGSIYKDGE--------FALVVHPEYRQLGLGTKLVLALISEAK 103
                                   344444444444222233...33378889***************99........99************************* PP

                                   HTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  91 eegikkivlaveedndaairlYeklGF 117
                                   + gi k+ +++ + n+++i+  +klGF
  gi|70607993|ref|YP_256863.1| 104 KMGISKVRFYTLPENTPMIKIGRKLGF 130
                                   *********************988999 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   5.1e-12   9.2e-09       2     138 .]       5     131 ..       4     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.1e-12
                Acetyltransf_3   2 LlLrplteeDlealfelrs...dpe.vmrylpepltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeed 78 
                                   ++Lr +++eD +++++l+s   d++   ry+   ++ e+  +++++++      +  + ++ + ++++i   +++   ++ 
  gi|70607993|ref|YP_256863.1|   5 ITLRIARKEDWQQIYQLYSsltDEDlYLRYFHLYKPTEDDAKRIADCL------DHRTIVV-EYQGKIIAEGSIY---KD- 74 
                                   7899999*******9985544488877788544455555556666555......3344666.5445489999999...23. PP

                Acetyltransf_3  79 eeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                     +e+ ++++p++++ G++t  v al+  a +++g+++++  + +eN+ +i++ +klGf+
  gi|70607993|ref|YP_256863.1|  75 --GEFALVVHPEYRQLGLGTKLVLALISEA-KKMGISKVRFYTLPENTPMIKIGRKLGFN 131
                                   ..9**********9****************.9999************************6 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     6e-11   1.1e-07      25     109 ..      47     133 ..      20     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 6e-11
               Acetyltransf_10  25 ri.eegealllvaeeggkivGvielrdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnaspyavpfYe 102
                                   ri +  ++ ++v+e +gki+  ++++++++ + l+V+peyr+ G+g++L+ a+++ea+k+gi++   +t+ +++  +++ +
  gi|70607993|ref|YP_256863.1|  47 RIaDCLDHRTIVVEYQGKIIAEGSIYKDGEFA-LVVHPEYRQLGLGTKLVLALISEAKKMGISKvrFYTLPENTPMIKIGR 126
                                   4435668999**********999996666665.78****************************997788999999999999 PP

               Acetyltransf_10 103 klGFkav 109
                                   klGF + 
  gi|70607993|ref|YP_256863.1| 127 KLGFNVK 133
                                   9999876 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.7e-10   4.8e-07       3      69 ..      54     113 ..      52     132 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.7e-10
                                   EEEEEEEETTEEEEEEEEEEESTCTEEEEE-GGGTTSSHHHHHHHH....TT.SEEEEEEEEETHHHHHHHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslldaeitrlaVdpeyrgkGiGraLlea....ae.kgiileqlelnaekaikfY 69 
                                   ++++V+e +gki+ + +++ +   +  l+V+peyr  G+G++L+ a    a+  gi            ++fY
  gi|70607993|ref|YP_256863.1|  54 HRTIVVEYQGKIIAEGSIYKD--GEFALVVHPEYRQLGLGTKLVLAliseAKkMGISK----------VRFY 113
                                   67899********88777776..4666****************976344311344321..........2222 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   1.8e-09   3.2e-06      25      80 ..      77     133 ..      57     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.8e-09
                                   EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47  25 galqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                   +al v+pe r+ Glg++lv al+ e  + g+ +v  ++ ++Ntp i++  klGf++ 
  gi|70607993|ref|YP_256863.1|  77 FALVVHPEYRQLGLGTKLVLALISEAKKMGIsKVRFYTLPENTPMIKIGRKLGFNVK 133
                                   6899************************9972577999****************875 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2     3e-05     0.054       2     108 ..       7     108 ..       6     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                                   EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT.SEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE CS
                Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrkllee.srvlgaedngelvgqlallplelnvpGktlkaagvtgVav 81 
                                   +r +++ed++++++l +    de+ +l ++   ++++ ++ +r+  + d+ ++v     ++ ++   G+++k +  +   v
  gi|70607993|ref|YP_256863.1|   7 LRIARKEDWQQIYQLYSSLT-DEDLYL-RYFHLYKPTEDDaKRIADCLDHRTIV---VEYQGKIIAEGSIYKDGEFAL-VV 81 
                                   57788888888888887544.444443.23334444444423566666666665...445556777788888666655.59 PP

                                   -CCGTTS-HHHHHHHHHHHHHHHTT-- CS
                Acetyltransf_9  82 apehrgrgvlskLlaraleemreegqp 108
                                   +pe+r+ g+ +kL+ +++ e++++g++
  gi|70607993|ref|YP_256863.1|  82 HPEYRQLGLGTKLVLALISEAKKMGIS 108
                                   *********************999876 PP

>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   7.4e-06     0.013       7      19 ..      97     109 ..      96     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-06
                                   HHHHHHHHHT--S CS
                          SinI   7 eLikEAkesGlsk 19 
                                   +Li EAk++G+sk
  gi|70607993|ref|YP_256863.1|  97 ALISEAKKMGISK 109
                                   7***********9 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.6e-05     0.046     161     236 ..      58     132 ..      55     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
               GNAT_acetyltran 161 vilkngeivsgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrgl.yPsWDaa..neaSvaLaekLGYef 236
                                   v+ ++g+i+++ s   +y++g e     +++yr+ gL t++  ali+e+ k g+   ++ +   n++ +++ +kLG++ 
  gi|70607993|ref|YP_256863.1|  58 VVEYQGKIIAEGS---IYKDG-EFALVVHPEYRQLGLGTKLVLALISEAKKMGIsKVRFYTLpeNTPMIKIGRKLGFNV 132
                                   6677777777754...34443.556678*************************84467767678999999999999976 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.23       1     137 [.       7     133 ..       7     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                Acetyltransf_4   1 iraateeDakeilaiyaeyvvntaitfeyev..ssveefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkae 79 
                                   +r+a++eD ++i ++y+     + +  +y +  +  e+ +k++++   +  +   v+++++i++   +       k   +e
  gi|70607993|ref|YP_256863.1|   7 LRIARKEDWQQIYQLYSS-LTDEDLYLRYFHlyKPTEDDAKRIADC--LDHRTIVVEYQGKIIAEGSIY------K--DGE 76 
                                   689999999999999975.344455555555435566667999998..888899999999999877665......2..356 PP

                Acetyltransf_4  80 lsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelv 137
                                       + +   ++ glg +l+ al+  +k+++i +    +  +n++ i++  +lGF++ 
  gi|70607993|ref|YP_256863.1|  77 FALVV-HPEYRQLGLGTKLVLALISEAKKMGISKVRFYTLPENTPMIKIGRKLGFNVK 133
                                   66666.46799********************************************975 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.4   9.7e+03      28      42 ..      53      67 ..      45      69 .. 0.67
   2 ?   11.1   0.0   0.00019      0.33      31      58 ..      80     107 ..      72     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.4
               Acetyltransf_CG 28 thTeVpeelrGkGiA 42
                                  +h  +  e++Gk iA
  gi|70607993|ref|YP_256863.1| 53 DHRTIVVEYQGKIIA 67
                                  455555667777666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
               Acetyltransf_CG  31 eVpeelrGkGiAkkLvkaalddareegl 58 
                                   +V++e+r  G++ kLv a + +a++ g 
  gi|70607993|ref|YP_256863.1|  80 VVHPEYRQLGLGTKLVLALISEAKKMGI 107
                                   79**********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1049.33
//
Query:       gi|70607994|ref|YP_256864.1|  [L=247]
Description: enoyl-CoA hydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-48  165.9   0.0    1.1e-48  165.7   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
      2e-26   93.3   0.0      2e-23   83.4   0.0    2.1  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.0   1.2e-52   1.1e-48       3     250 ..       6     246 ..       4     247 .] 0.96

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.2e-52
                                   ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                         ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                   ++g a +k++rPe++Nal+ ++++++i  l kl+ d++v+ v+LtG ++ F+ Gadl em+e     +a+lk +++   ++
  gi|70607994|ref|YP_256864.1|   6 KDGYAIVKFDRPEKLNALNLKTRNDMISILRKLNADPTVKSVILTGEGRGFCVGADLSEMVE---DIYADLKYTFQPIIKE 83 
                                   678899********************************************************...58************** PP

                                   HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHH CS
                         ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqea 164
                                   +++ +k  i+a+nG ++g+ l ++l +D++i  ++ +f  ++ ++Gl+ + g+  +la+ vG +    +l+lg +++a++a
  gi|70607994|ref|YP_256864.1|  84 IRNPNKLYISAINGVVAGACLGIVLSTDFRISRKDVKFVTAFQRIGLTSDTGVAYFLAKLVGVKS-YDLLILGGEFTAEDA 163
                                   **************************************************************975.689999********* PP

                                   HHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
                         ECH_1 165 lkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                                   +k+Glv+  ++e+ l + a++la+++   + + +++ k+ +n+ l +     le ea l++++ +++d+keG+q+f+Ekr+
  gi|70607994|ref|YP_256864.1| 164 EKWGLVK--ISEDPL-SDAVKLAQRISAGPFLTYVAGKKMVNKILFEDMDDFLEYEALLQSELGKTEDFKEGVQSFIEKRE 241
                                   ******8..566665.779********9999***********9999*********************************** PP

                                   ----- CS
                         ECH_1 246 pefed 250
                                   p++++
  gi|70607994|ref|YP_256864.1| 242 PKYKG 246
                                   ***97 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   2.2e-27     2e-23       3     168 ..      11     169 ..       9     174 .. 0.90
   2 !    8.1   0.0   0.00019       1.7     265     318 ..     194     245 ..     172     247 .] 0.76

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.2e-27
                                   EEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHH CS
                         ECH_2   3 vitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyli 83 
                                   +++++rp++lNaL+l+  +++ ++l++ ++d++vk v+l+g+g ++fC G D+ +++e++ ++ k     f+    + + i
  gi|70607994|ref|YP_256864.1|  11 IVKFDRPEKLNALNLKTRNDMISILRKLNADPTVKSVILTGEG-RGFCVGADLSEMVEDIYADLKY---TFQ---PIIKEI 84 
                                   7899*************************************88.***************9995433...233...356677 PP

                                   HC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHHHHH CS
                         ECH_2  84 atypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgadala 164
                                    + +k +++ ++G+v G  +G+ +++ fr+  ++ +f     +IGl+ D G+ yfL++l g     l + G +++++da +
  gi|70607994|ref|YP_256864.1|  85 RNPNKLYISAINGVVAGACLGIVLSTDFRISRKDVKFVTAFQRIGLTSDTGVAYFLAKLVGVKSYDLLILGGEFTAEDAEK 165
                                   777888*****************************************************9988888888888899999888 PP

                                   TTS- CS
                         ECH_2 165 agla 168
                                    gl 
  gi|70607994|ref|YP_256864.1| 166 WGLV 169
                                   8875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                         ECH_2 265 kvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                    v+ +++ +    +++++ l+ E  l ++l +++Df eGv++  ++k ++Pk+k
  gi|70607994|ref|YP_256864.1| 194 YVAGKKMVNKILFEDMDDFLEYEALLQSELGKTEDFKEGVQSF-IEK-REPKYK 245
                                   45555555555556899***********************986.666.678876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1567.14
//
Query:       gi|70607995|ref|YP_256865.1|  [L=256]
Description: enoyl-CoA hydratase/isomerase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-82  277.1   0.2    1.3e-82  276.9   0.2    1.0  1  ECH_1           Enoyl-CoA hydratase/isomerase
    9.7e-39  133.8   0.7    4.6e-35  121.7   0.1    2.0  2  ECH_2           Enoyl-CoA hydratase/isomerase
    0.00023   21.1   0.2      0.002   18.1   0.1    2.2  2  Peptidase_S49   Peptidase family S49
  ------ inclusion threshold ------
      0.068   13.1   1.7        1.9    8.4   0.6    3.2  2  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.9   0.2     3e-86   1.3e-82       3     250 ..      12     256 .]      10     256 .] 0.98

  Alignments for each domain:
  == domain 1  score: 276.9 bits;  conditional E-value: 3e-86
                                   ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHH CS
                         ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwtk 83 
                                    + +  iklnrP+ +Na++ +++++l++al +le++  v++v++tG +kaF+aGad+kem+      ++++ +    lw+k
  gi|70607995|ref|YP_256865.1|  12 DKKIGIIKLNRPDRLNAINFKMVDDLVNALDELEKS-PVKVVIITGEGKAFSAGADVKEMVDT--PLKEIVLKGHMPLWEK 89 
                                   567999******************************.8************************7..7888999999****** PP

                                   HHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHH CS
                         ECH_1  84 lytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqea 164
                                   ++  +kpviaavnG a+gGGlela+acDi+ia+++a+fg++e++lG+ipgaggtq+l+r+vGk  A++++l+g+ isa+ea
  gi|70607995|ref|YP_256865.1|  90 MRAFKKPVIAAVNGVAAGGGLELAMACDIIIASESAKFGQPEINLGIIPGAGGTQRLTRTVGKYNAMKMVLTGELISAKEA 170
                                   ********************************************************************************* PP

                                   HHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
                         ECH_1 165 lkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                                   +++Glv kvvp+  l +ea+ la+++a+k+  +l  +kea+n++le +l+++l++e+++f+   ++++ keG++aflEkrk
  gi|70607995|ref|YP_256865.1| 171 KDMGLVVKVVPDGSLIDEAIRLANEIASKPLFSLILAKEAVNRALETNLQQGLDIERRNFYVALASEEAKEGMKAFLEKRK 251
                                   ********************************************************************************* PP

                                   ----- CS
                         ECH_1 246 pefed 250
                                   p++e+
  gi|70607995|ref|YP_256865.1| 252 PRWEE 256
                                   ***96 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.1     1e-38   4.6e-35       1     177 [.      15     185 ..      15     195 .. 0.93
   2 !   11.3   0.0   3.8e-05      0.17     251     318 ..     191     255 ..     187     256 .] 0.90

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 1e-38
                                   .EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                         ECH_2   1 vgvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                   +g+i+Lnrp+ lNa++ +mv++l +al+e ek++ vk+v+++g+g kaf+AG Dv++++++  ++      + +    l  
  gi|70607995|ref|YP_256865.1|  15 IGIIKLNRPDRLNAINFKMVDDLVNALDELEKSP-VKVVIITGEG-KAFSAGADVKEMVDTPLKEI-----VLKGHMPLWE 88 
                                   589***************************9887.9*******88.**************999944.....789999**** PP

                                   HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHH CS
                         ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgad 161
                                    +  ++kpv+a ++G++ GgG+ l++ + + +++e+++f  PE+++G++P  Gg+  L+r+ g   ++ + lTG+ +++++
  gi|70607995|ref|YP_256865.1|  89 KMRAFKKPVIAAVNGVAAGGGLELAMACDIIIASESAKFGQPEINLGIIPGAGGTQRLTRTVGkYNAMKMVLTGELISAKE 169
                                   ************************************************************977355889************ PP

                                   HHHTTS--EE--GGGH CS
                         ECH_2 162 alaaglathyvpsekl 177
                                   a  +gl  ++vp+ +l
  gi|70607995|ref|YP_256865.1| 170 AKDMGLVVKVVPDGSL 185
                                   *********9998876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                         ECH_2 251 ktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                   + +++++++  +sl ++ e+++r+ +++ l++ l+ E r    +la+++  eG +a l +  +kP+W+
  gi|70607995|ref|YP_256865.1| 191 RLANEIASKPLFSLILAKEAVNRALETN-LQQGLDIERRNFYVALASEEAKEGMKAFLEK--RKPRWE 255
                                   567788999999***************5.***************************9854..68***7 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   4.4e-07     0.002       4      38 ..      92     126 ..      89     130 .. 0.90
   2 ?    0.2   0.0      0.14   6.3e+02     113     139 ..     155     181 ..     148     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                                   HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-E CS
                 Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpsti 38 
                                   + kkPv+a +++vaa gg  la+a+d i+a+ s+ 
  gi|70607995|ref|YP_256865.1|  92 AFKKPVIAAVNGVAAGGGLELAMACDIIIASESAK 126
                                   569***************************99875 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                                   HHHCHHCCHEEEHHHHHHTTSSSEETS CS
                 Peptidase_S49 113 qvdkiAegrvltgqqAlklgLvdelgt 139
                                   +++ + +g+  ++++A++ gLv ++  
  gi|70607995|ref|YP_256865.1| 155 AMKMVLTGELISAKEAKDMGLVVKVVP 181
                                   56667788999999*******988754 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.6   0.00043       1.9       9      38 ..     183     221 ..     179     230 .. 0.77
   2 ?   -0.5   0.0      0.27   1.2e+03      29      41 ..     240     252 ..     236     256 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00043
                                   XXXXXXXXXXXX.XXXX........XXXXXXXXXX---- CS
                VapB_antitoxin   9 DeLlaeAirltg.lktK........rEaVnlALreLiqr 38 
                                    +L++eAirl++ ++ K        +EaVn AL++ +q 
  gi|70607995|ref|YP_256865.1| 183 GSLIDEAIRLANeIASKplfslilaKEAVNRALETNLQQ 221
                                   57899999988877776666666669*******986665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.27
                                   XXXXXX------- CS
                VapB_antitoxin  29 nlALreLiqrrkr 41 
                                   ++++++++++rk 
  gi|70607995|ref|YP_256865.1| 240 KEGMKAFLEKRKP 252
                                   5899*****9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1771.70
//
Query:       gi|70607996|ref|YP_256866.1|  [L=423]
Description: pyridine nucleotide-disulfide oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-58  198.8   0.0    1.3e-58  198.6   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.1e-19   69.8   0.1    9.2e-17   61.4   0.2    3.2  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.3e-13   49.6   0.0      8e-13   48.8   0.0    1.5  1  Reductase_C    Reductase C-terminal
    7.7e-11   41.8   0.9      2e-10   40.4   0.3    2.1  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00032   19.9   0.0       0.16   11.1   0.0    2.3  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    0.00039   19.6   0.4      0.061   12.4   0.0    3.1  3  Lycopene_cycl  Lycopene cyclase protein
    0.00092   18.9   1.2        1.6    8.3   0.0    3.3  3  DAO            FAD dependent oxidoreductase
    0.00094   18.0   0.5        1.3    7.7   0.0    3.0  4  HI0933_like    HI0933-like protein
     0.0021   18.1   2.2         30    4.6   0.0    4.1  4  NAD_binding_9  FAD-NAD(P)-binding
      0.005   16.1   0.0        1.4    8.1   0.0    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0056   16.1   0.0      0.094   12.1   0.0    2.1  2  ThiF           ThiF family
     0.0065   16.6   0.1       0.28   11.2   0.0    2.5  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
  ------ inclusion threshold ------
      0.011   16.0   0.3        0.5   10.6   0.0    2.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.024   13.8   2.8        5.8    5.9   0.1    3.8  4  GIDA           Glucose inhibited division protein A
      0.054   13.7   0.1        3.7    7.8   0.0    2.5  2  TrkA_N         TrkA-N domain
       0.14   11.5   0.0       0.29   10.5   0.0    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   0.0   1.2e-61   1.3e-58       2     294 .]      22     316 ..      21     316 .. 0.93

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 1.2e-61
                                   SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHCCTCE CS
                                   xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielllgeevv 76 
                                   ++v+iG+G+AG++a +++ +   +a++tlv ++  +++++++lsk++ ++++d++ +     e    ++ +++++l+++v 
  gi|70607996|ref|YP_256866.1|  22 KYVIIGSGIAGYHALKEMLNidPKANITLVTSDSSLPYDRPPLSKEYMRSERDRDSLFfekpE--FYQRDNLKVMLNTTVE 100
                                   79******************977*******************************988897431..333445999***9999 PP

                                   EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiGvE 156
                                   ++  ++k ++l     + ++++ +dkl++ tG++pr+lgi+G++ n+++ +rtl +a+ +k++l+  k+ v+vG+G+iGvE
  gi|70607996|ref|YP_256866.1| 101 RLNVKEKFLTL-----STGQTLNFDKLLITTGGKPRKLGIHGENLNGVHYLRTLSDADSIKEDLKHgKKPVIVGAGFIGVE 176
                                   99999977777.....5688*********************************************999************* PP

                                   HHHHHHHHT-EEEEEESSSSSS.TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 157 lAaalaklgkevtlveardrll.raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvvav 235
                                   +Aa l++lg e +++e  + +    +d+++s+++++++e++Gv++ l++ vke++g ++ +  v+++ g++i+ ++v+vav
  gi|70607996|ref|YP_256866.1| 177 VAASLRSLGFEPVVIEVKPFIWsTFVDEKVSEMVRKYFENKGVTFLLNEGVKEFEGSQR-VNsVITSGGKKIESSMVLVAV 256
                                   ***********999********9999********************************8.656****************** PP

                                   -EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 236 GvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                   G++p+ e++ ++l++    ++gi+vde+l+   ++iy++GDva       g+++++e++ +A  +G
  gi|70607996|ref|YP_256866.1| 257 GISPNVEIA-NELQV----NNGILVDEHLKA-KEDIYVAGDVAnildpvsGKRRRIEHWNNAYYTG 316
                                   ******998.55444....89********77.9*****************************8766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.44     5e+02       2      30 ..      23      53 ..      22      71 .. 0.80
   2 ?    2.7   0.0      0.17   1.9e+02      52      71 ..      88     107 ..      83     114 .. 0.83
   3 !   61.4   0.2   8.2e-20   9.2e-17       3      79 ..     166     242 ..     164     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.44
                                  EEEECSSHHHHHHHHHHHHTT..SEEEEEES CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvver 30
                                   v++G+G  g  + +++ ++   +++t+v  
  gi|70607996|ref|YP_256866.1| 23 YVIIGSGIAGYHALKEMLNIDpkANITLVTS 53
                                  69********999999988875566777765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.17
                                   HTTEEEECSEEEEEEEEETT CS
                     Pyr_redox  52 kngievllntkveeiegsed 71 
                                   + + +v+lnt+ve+++ +e+
  gi|70607996|ref|YP_256866.1|  88 RDNLKVMLNTTVERLNVKEK 107
                                   5589***********98876 PP

  == domain 3  score: 61.4 bits;  conditional E-value: 8.2e-20
                                   EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                     Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                   v+vG+G+ig+E+A+ l+ lg +  v+e ++ +     De++s+++++++e++g+++lln+ v+e+egs++ v+sv ++
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSLGFEPVVIEVKPFIWsTFVDEKVSEMVRKYFENKGVTFLLNEGVKEFEGSQR-VNSVITS 242
                                   9********************************************************************9.9999875 PP

>> Reductase_C  Reductase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   7.1e-16     8e-13       2      84 ..     336     421 ..     335     422 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 7.1e-16
                                   EEEEETTEEEEEEE--TT--EEEEEEETTTTEEEEEEEETTEEEEEEEES-.HHHHHHHHHHTTTT----..HHHHH-TTS CS
                   Reductase_C   2 fWSDqydlklQiaGlatgadevvvRgdpeerafsvfylrdgrlvaveavnr.prdlmaarrliaagasvd..paalaDpav 79 
                                   +WSD +dl+++  G +tg+d++v+Rg+ +++++ v+y+++g +++ +a+nr  ++l a+ +li++++ ++   ++l D+++
  gi|70607996|ref|YP_256866.1| 336 VWSDIFDLHIESGGETTGYDDYVMRGNFDKKSLNVIYVKGGLVIGYVAFNRdMSELEAINKLIQDKVDIKskVDKLKDESF 416
                                   6**************************999********************9889***********997651167999**** PP

                                   -HHH. CS
                   Reductase_C  80 dLkkl 84 
                                   d++kl
  gi|70607996|ref|YP_256866.1| 417 DIRKL 421
                                   ***97 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.3   1.8e-13     2e-10      91     276 ..      86     267 ..      82     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.8e-13
                   Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskv.kefhkya.....gq 165
                                    ++ +l+++l+++Ve+++ +++  +++t  +t++ +k++i tG   kP+kl+i+Ge+ + +hy    ++++ ++     g+
  gi|70607996|ref|YP_256866.1|  86 YQRDNLKVMLNTTVERLNVKEKFLTLST-GQTLNFDKLLITTGG--KPRKLGIHGENLNGVHYLRTlSDADSIKedlkhGK 163
                                   57889*************9988777776.6799**********8..***********999999655345544432222489 PP

                   Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeyk 246
                                   k v++G++  +v++A  l + g e  v+  +  i +  + ++ +++ ++++ +e+    + +++l n+ vke + +++   
  gi|70607996|ref|YP_256866.1| 164 KPVIVGAGFIGVEVAASLRSLGFEPVVIEVKPFIWS--TFVDEKVSEMVRKYFEN----KGVTFLLNEGVKEFEGSQRVNS 238
                                   9**********************9888888875433..34566666666666665....559*************999999 PP

                   Pyr_redox_3 247 vktedgkkvevkddvvlatGykpdlsflkk 276
                                   v t+ gkk+e+ + v++a+G +p++++ ++
  gi|70607996|ref|YP_256866.1| 239 VITSGGKKIES-SMVLVAVGISPNVEIANE 267
                                   99****99987.778999*******99875 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00014      0.16     192     254 ..      21      84 ..      12     102 .. 0.79
   2 !    7.1   0.0    0.0023       2.6     122     212 ..     102     183 ..      85     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                   K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvneifsPeyv..dyfyslpe 254
                                    + +++GsG  + + ++++l+  +k++++lvt+ ++  p d  p+ +e++ +e+   + f+++pe
  gi|70607996|ref|YP_256866.1|  21 SKYVIIGSGIAGYHALKEMLNIDPKANITLVTSDSS-LPYDRPPLSKEYMRSERDrdSLFFEKPE 84 
                                   5668***************************98766.59**********9887641145666666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0023
                   K_oxygenase 122 vepdeeeeeelltveskdaegeeeelearnlvlgvGtep.kiPevleklegkervvHsseylerkeellakkriaVvGsGq 201
                                   ++++e+     lt++      + ++l+  +l++++G++p k+  + e+l+g + +   s++ + ke+l+++k+ ++vG+G 
  gi|70607996|ref|YP_256866.1| 102 LNVKEK----FLTLS------TGQTLNFDKLLITTGGKPrKLGIHGENLNGVHYLRTLSDADSIKEDLKHGKKPVIVGAGF 172
                                   333332....34444......478899999*****988735778888888878888888888888889************* PP

                   K_oxygenase 202 Saaeifedllr 212
                                    + e++  l +
  gi|70607996|ref|YP_256866.1| 173 IGVEVAASLRS 183
                                   *****998865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.15   1.6e+02       3      36 ..      24      57 ..      23      65 .. 0.83
   2 ?    2.0   0.1     0.079        88       3      34 ..     166     195 ..     165     201 .. 0.84
   3 !   12.4   0.0   5.4e-05     0.061      88     161 ..     205     277 ..     196     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.15
                 Lycopene_cycl  3 vviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  v+iG+G Ag    +++ +  p+ +++l+ +  sl
  gi|70607996|ref|YP_256866.1| 24 VIIGSGIAGYHALKEMLNIDPKANITLVTSDSSL 57
                                  8*********999999899999999999544444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.079
                 Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieasp 34 
                                   v++GaG  g+ +Aa l     g + v+ie  p
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASL--RSLGFEPVVIEVKP 195
                                   89**************..88888888887665 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 5.4e-05
                 Lycopene_cycl  88 rlkeellerlvengvkll.eakvesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyGveve 161
                                   +  e++ + + ++gv++l +  v++ e ++    +v+++gg+ki++++v++a g  s++ + +  lQ+  G++v 
  gi|70607996|ref|YP_256866.1| 205 KVSEMVRKYFENKGVTFLlNEGVKEFEGSQR-VNSVITSGGKKIESSMVLVAVG-ISPNVEIANELQVNNGILVD 277
                                   5566666666688888752777888888888.788999****************.9999999999******9996 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.14   1.5e+02       2      15 ..      23      36 ..      22      58 .. 0.71
   2 !    5.5   0.5    0.0099        11       3      26 ..     166     191 ..     165     200 .. 0.81
   3 !    8.3   0.0    0.0014       1.6     152     206 ..     210     263 ..     199     285 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                                  EEEECTSHHHHHHH CS
                           DAO  2 vviiGGGiiGlstA 15
                                   viiG+Gi+G  + 
  gi|70607996|ref|YP_256866.1| 23 YVIIGSGIAGYHAL 36
                                  79********7665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0099
                                   EEECTSHHHHHHHHHHHHTT..EEEE CS
                           DAO   3 viiGGGiiGlstAyeLarrg..Vtll 26 
                                   vi+G+G iG+ +A  L   g   +++
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSLGfePVVI 191
                                   8***************4447885555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0014
                                   HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHH.H CS
                           DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsd.l 206
                                   +++ +e++Gv++l+++ v+++e  + +v  v   t+ g +  ++   v +a G+  + +
  gi|70607996|ref|YP_256866.1| 210 VRKYFENKGVTFLLNEGVKEFEG-SQRVNSV--ITSgGKK--IESsmVLVAVGISPNvE 263
                                   45669****************54.4678888..7786776..45556******876654 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8   2.1e+03       2      15 ..      22      35 ..      21      47 .. 0.83
   2 !    7.7   0.0    0.0011       1.3     121     165 ..      88     129 ..      84     140 .. 0.83
   3 ?   -1.4   0.0      0.63     7e+02       4      31 ..     166     193 ..     163     197 .. 0.88
   4 !    6.8   0.0    0.0021       2.4     109     163 ..     204     257 ..     199     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                                  SEEEE--SHHHHHH CS
                   HI0933_like  2 dviviGgGaAGlma 15
                                  + ++iG G AG  a
  gi|70607996|ref|YP_256866.1| 22 KYVIIGSGIAGYHA 35
                                  579*******9766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                                   HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                   HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                   + + k++l+t+v++++  ++++++++t  +++l+ dkl+++tGG+
  gi|70607996|ref|YP_256866.1|  88 RDNLKVMLNTTVERLNV-KEKFLTLST--GQTLNFDKLLITTGGK 129
                                   56889999*******66.455466666..9**************8 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.63
                                   EEE--SHHHHHHHHHHHHTT--EEEE-S CS
                   HI0933_like   4 iviGgGaAGlmaAisaakrgkrVlllek 31 
                                   +++G+G  G+  A+s+++ g + +++e 
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSLGFEPVVIEV 193
                                   8***************999999999986 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                   e++ ++  k  +++gv++ l++ vk++e ++    +v t++++++e++ +++A+G
  gi|70607996|ref|YP_256866.1| 204 EKVSEMVRKYFENKGVTFLLNEGVKEFEGSQRV-NSVITSGGKKIESSMVLVAVG 257
                                   5788999999*****************887766.555555*************98 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.027        30       1      31 [.      24      51 ..      24      72 .. 0.75
   2 ?    3.6   0.0     0.052        58     121     154 ..      96     127 ..      84     129 .. 0.77
   3 ?    3.8   0.5     0.046        52       1      19 [.     166     184 ..     166     194 .. 0.81
   4 ?    2.4   0.0      0.12   1.4e+02      97     154 ..     199     257 ..     196     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlf 31
                                  +i+G G++G  +l+++l+      + +itl+
  gi|70607996|ref|YP_256866.1| 24 VIIGSGIAGYHALKEMLNID---PKANITLV 51
                                  7****************994...44555544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.052
                 NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlG 154
                                   +++v++l+ +++   ++l++g++l +d++ +++G
  gi|70607996|ref|YP_256866.1|  96 NTTVERLNVKEK--FLTLSTGQTLNFDKLLITTG 127
                                   555666665543..6899***************9 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.046
                 NAD_binding_9   1 aivGaGprGlavlerLlar 19 
                                   +ivGaG+ G+ v++ L + 
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSL 184
                                   7************999765 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.12
                 NAD_binding_9  97 GrYlrdlfeellarlpegvtvevh.raevvdleeradgqavlladgaslaadaVvLAlG 154
                                   + ++++ ++e+++++ e+  v+++ ++ v + e +++   v++++g++++   V +A+G
  gi|70607996|ref|YP_256866.1| 199 STFVDEKVSEMVRKYFENKGVTFLlNEGVKEFEGSQRVNSVITSGGKKIESSMVLVAVG 257
                                   5677778888888887777888864778888888888889******************9 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0013       1.4      28      50 ..      20      42 ..      13      57 .. 0.81
   2 !    5.5   0.0    0.0082       9.2      30      61 ..     164     195 ..     157     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                                  --EEEEESTSHHHHHHHHHHHHT CS
                   AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakgl 50
                                   +k ++iG G+aG +A++   ++
  gi|70607996|ref|YP_256866.1| 20 TSKYVIIGSGIAGYHALKEMLNI 42
                                  5799************9977666 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0082
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                   k +++G+G  G++ +a  ++lg + +v++v+p
  gi|70607996|ref|YP_256866.1| 164 KPVIVGAGFIGVEVAASLRSLGFEPVVIEVKP 195
                                   569*******************9999998876 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.14   1.6e+02      18      50 ..      20      53 ..       8      55 .. 0.85
   2 !   12.1   0.0   8.4e-05     0.094      14      44 ..     157     188 ..     143     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
                                  TSEEEEE--SHHHHHHHHHHHHHTTT.EEEEEES CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          ThiF 18 dskvllvGaGglGsellknLalsGvg.kltlvDn 50
                                  +sk++++G G  G  +lk++  +  + ++tlv  
  gi|70607996|ref|YP_256866.1| 20 TSKYVIIGSGIAGYHALKEMLNIDPKaNITLVTS 53
                                  589****************999999668998855 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.4e-05
                                   HHHHT.SEEEEE--SHHHHHHHHHHHHHTTTE CS
                                   xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  14 ekLrd.skvllvGaGglGsellknLalsGvgk 44 
                                   e L++ +k ++vGaG +G e++  L  +G++ 
  gi|70607996|ref|YP_256866.1| 157 EDLKHgKKPVIVGAGFIGVEVAASLRSLGFEP 188
                                   45555799*********************975 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00025      0.28      21      57 ..     160     196 ..     147     202 .. 0.90
   2 ?    2.3   0.0      0.14   1.6e+02      85     139 ..     351     412 ..     347     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                   -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HH CS
                 AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPi 57 
                                     Gk+ v++G G +G   aasl++lG   +v ev P 
  gi|70607996|ref|YP_256866.1| 160 KHGKKPVIVGAGFIGVEVAASLRSLGFEPVVIEVKPF 196
                                   579*******************************995 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                                   -SSSSSSB-HHHHCCS-TTEEEEE....-SSTTTTBTHHHHHTT...T-EEEEEETTEEEEE CS
                 AdoHcyase_NAD  85 ttGnkdiitlehlkkmkddaivcn....iGhfdseidvaalean...alkkeevkpqvdrvt 139
                                   ttG +d +++ +++k   ++i       iG+   + d+++lea     ++k+++k++vd+++
  gi|70607996|ref|YP_256866.1| 351 TTGYDDYVMRGNFDKKSLNVIYVKgglvIGYVAFNRDMSELEAInklIQDKVDIKSKVDKLK 412
                                   788888888888888877777643334488888888888887762224678899****9875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.17   1.9e+02       1      10 [.      25      34 ..      25      51 .. 0.86
   2 ?   10.6   0.0   0.00044       0.5       1      27 [.     167     193 ..     167     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                                  EE--SHHHHH CS
                 NAD_binding_8  1 IvGaGlsGlv 10
                                  I+G+G++G  
  gi|70607996|ref|YP_256866.1| 25 IIGSGIAGYH 34
                                  9*******65 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00044
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllek 27 
                                   IvGaG+ G   A+ L+  gf+ +++e 
  gi|70607996|ref|YP_256866.1| 167 IVGAGFIGVEVAASLRSLGFEPVVIEV 193
                                   9*********************99996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.4   4.4e+02       3      14 ..      24      35 ..      22      53 .. 0.86
   2 ?    2.0   0.0     0.076        85     108     150 ..      88     128 ..      72     155 .. 0.83
   3 ?    2.5   0.3     0.054        61       3      25 ..     166     188 ..     164     197 .. 0.86
   4 ?    5.9   0.1    0.0051       5.8      95     150 ..     204     258 ..     195     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.4
                                  EEE-SSHHHHHH CS
                          GIDA  3 iViGgGhAGceA 14
                                  ++iG G AG+ A
  gi|70607996|ref|YP_256866.1| 24 VIIGSGIAGYHA 35
                                  89*******998 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.076
                                   STTEEEE.ES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 108 epnleii.eeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    +nl+++ + +ve+l+v   k k +++++g+t++ ++  i+tG 
  gi|70607996|ref|YP_256866.1|  88 RDNLKVMlNTTVERLNV---KEKFLTLSTGQTLNFDKLLITTGG 128
                                   56777763678999988...6678999****************7 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.054
                                   EEE-SSHHHHHHHHHHHHTT--E CS
                          GIDA   3 iViGgGhAGceAAlaaarlGakv 25 
                                   +++G+G  G+e A+ +  lG++ 
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSLGFEP 188
                                   79*************99999875 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0051
                                   HHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA  95 elyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   e++s+ v+++ en+    +++e v+e +  +++v+ v+t+ g++i+++ v +a G 
  gi|70607996|ref|YP_256866.1| 204 EKVSEMVRKYFENKGVTFLLNEGVKEFEG-SQRVNSVITSGGKKIESSMVLVAVGI 258
                                   67899999999998888899999999955.9***********************97 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.075        84       1      31 [.      23      55 ..      23      57 .. 0.86
   2 ?    7.8   0.0    0.0033       3.7       2      31 ..     166     195 ..     165     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.075
                                  EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSH CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkde 31
                                  ++iiG G  G++ ++e+ + +   +++++ +d 
  gi|70607996|ref|YP_256866.1| 23 YVIIGSGIAGYHALKEMLNiDPkANITLVTSDS 55
                                  79****************976566699998886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0033
                                   EEES-SHHHHHHHHHHHH.TTEEEEEEESSH CS
                        TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkde 31 
                                   +i+G+G +G ++a  L++ g +  vvi+ ++
  gi|70607996|ref|YP_256866.1| 166 VIVGAGFIGVEVAASLRSlGFE-PVVIEVKP 195
                                   8*****************7775.78888766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00026      0.29      34      67 ..     160     193 ..     142     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                   GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                  2-Hacid_dh_C  34 lsgktvGiiGlGrIGqavakrlkafgmkviaydr 67 
                                    +gk+  i+G+G IG +va  l+++g++ +++++
  gi|70607996|ref|YP_256866.1| 160 KHGKKPVIVGAGFIGVEVAASLRSLGFEPVVIEV 193
                                   479999******************9998666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2620.79
//
Query:       gi|70607997|ref|YP_256867.1|  [L=386]
Description: acetyl-CoA acetyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-21   76.2   0.4    5.1e-20   71.9   0.4    2.1  1  Thiolase_N       Thiolase, N-terminal domain
      8e-10   38.4   0.2    1.2e-08   34.6   0.0    2.6  3  Thiolase_C       Thiolase, C-terminal domain
    2.7e-06   27.1   4.5    0.00088   18.9   2.6    2.5  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.062   13.2   0.7       0.13   12.1   0.7    1.5  1  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
        1.2    9.2   7.3        6.3    6.8   0.0    3.7  5  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.4   1.4e-23   5.1e-20       1     260 []       4     223 ..       4     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.4e-23
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v++++   +++gk      d+s++eL+ e +k++ e+agv++++v+ vi+G  +  g +  +   +a  +g+  +vp ++v
  gi|70607997|ref|YP_256867.1|   4 VAVIGVGHSKFGK----RDDVSIQELAWESIKEAFEDAGVTQKDVNTVILGSTAYRGVELYPGPIVAEYSGLTGKVP-MRV 79 
                                   5667777777777....99*****************************************************77777.79* PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGltae 160
                                   + +c+ gl+a  +a   +a+g a++++a+Gv +m++++t++s +v    g  + +    +++ p+           +l a 
  gi|70607997|ref|YP_256867.1|  80 EAMCATGLAAALTAYSLVASGLAEIAMAVGVDKMTEVDTSTSLAVGgrGGNYQWEYHFYGTTFPT---------YYALYAT 151
                                   *************************************9998855433255555566667888888.........7899999 PP

                                   HHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BT CS
                    Thiolase_N 161 nlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtA 241
                                   +  + ++ + e+ + + vk h+ +a+++ka+ F++ +              + +e ++s+v   +++ l            
  gi|70607997|ref|YP_256867.1| 152 RHMAVFGTTEEQMALVSVKAHKYGASNPKAH-FQKPV--------------TVEEVLKSRVISWPIKLL------------ 205
                                   99*****************************.***55..............778999999999999999............ PP

                                   TSB--BEEEEEEEEEEEHH CS
                    Thiolase_N 242 gnasqisDGaaavllmses 260
                                    +a++isDG+a+ +++se+
  gi|70607997|ref|YP_256867.1| 206 -DACPISDGSATAIFASEE 223
                                   .999999999999999985 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   5.1e+02      27      45 ..      29      47 ..      11      60 .. 0.81
   2 ?   -2.5   0.0       1.1   3.9e+03       5      55 ..     167     218 ..     163     227 .. 0.61
   3 !   34.6   0.0   3.5e-12   1.2e-08       8     102 ..     243     356 ..     238     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                                  HHHHHHHHHT--GGGESEE CS
                    Thiolase_C 27 aikkvlkkagltvedidlf 45
                                   ik++ ++ag+t +d++ +
  gi|70607997|ref|YP_256867.1| 29 SIKEAFEDAGVTQKDVNTV 47
                                  6888999999999999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                                   EEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--..GGGESEEEE--SBHHHH CS
                    Thiolase_C   5 akirsyaevgvdpeilglgPayaikkvlkkaglt..vedidlfEinEAFaaqa 55 
                                   + ++++++ + +p+     P+  +++vlk   ++  ++ +d+  i +  a+ +
  gi|70607997|ref|YP_256867.1| 167 VSVKAHKYGASNPKAHFQKPVT-VEEVLKSRVISwpIKLLDACPISDGSATAI 218
                                   5677788888888887778875.456666654332255566655555555555 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 3.5e-12
                                   EEEEEEE--GGGGGG.HHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGB CS
                    Thiolase_C   8 rsyaevgvdpeilgl.gPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekv 69 
                                   ++ya+v+   e lg+ + + a++ + k a +t ++i++  +++AF+   ++  ++l++ +                    v
  gi|70607997|ref|YP_256867.1| 243 NDYAYVARRGEWLGFkATTLAAQDAYKMADITPNSIEVATVHDAFTIAEIMGYEDLGFVEkgkggkfieegqsekggkVGV 323
                                   578899999999987245789*************************************999************99987779 PP

                                   STT--HHHH-B-TTTHHHHHHHHHHHHHHHCTT CS
                    Thiolase_C  70 NvnGGaialGHPlGasGaRivvtllselkkegg 102
                                   N+ GG  + GHPlGa+G  ++  ++++l++e g
  gi|70607997|ref|YP_256867.1| 324 NLFGGLKSKGHPLGATGLSMIYEITKQLREEAG 356
                                   ****************************99876 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00084         3      88     121 ..      22      51 ..      14      62 .. 0.83
   2 !   18.9   2.6   2.5e-07   0.00088     158     213 ..      65     121 ..      60     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00084
                                   HHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEE CS
                 ketoacyl-synt  88 qqrllleaawealedagltpeeldgsrvgvfiGv 121
                                    q l+ e  +ea+edag+t++++++    v++G+
  gi|70607997|ref|YP_256867.1|  22 IQELAWESIKEAFEDAGVTQKDVNT----VILGS 51 
                                   5899****************99876....44444 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.5e-07
                                   HHHHHT--SS.EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHH CS
                 ketoacyl-synt 158 isyalglrGp.svtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavag 213
                                   ++   gl+G   + v++ C+++l+a   a++ + sg a++a a Gv+ +++  +  +
  gi|70607997|ref|YP_256867.1|  65 VAEYSGLTGKvPMRVEAMCATGLAAALTAYSLVASGLAEIAMAVGVDKMTEVDTSTS 121
                                   56667888851589********99999999******************999877666 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   3.7e-05      0.13       3      42 ..      79     117 ..      77     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                                   EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS- CS
                   ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilD 42 
                                   ++a C++ ++a  +A +l++sg a+ ++ +g +++++ +D
  gi|70607997|ref|YP_256867.1|  79 VEAMCATGLAAALTAYSLVASGLAEIAMAVGVDKMTE-VD 117
                                   6899*******************************98.55 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        56      29      47 ..      26      47 ..       2      55 .. 0.72
   2 ?   -4.2   0.4       4.6   1.7e+04      89     100 ..      94     105 ..      80     109 .. 0.64
   3 ?   -2.0   0.0      0.99   3.5e+03      66      85 ..     154     171 ..     150     177 .. 0.76
   4 ?    6.8   0.0    0.0018       6.3      25      52 ..     259     286 ..     246     291 .. 0.88
   5 ?   -0.1   0.0      0.26   9.2e+02      88     108 ..     333     353 ..     327     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                  H...HHHHHHHHT--GGGEEEE CS
               Ketoacyl-synt_C 29 a...iekalaeagvdpedvdyv 47
                                  a   i++a+++agv+ +dv+ v
  gi|70607997|ref|YP_256867.1| 26 AwesIKEAFEDAGVTQKDVNTV 47
                                  34449**************988 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4.6
                                   B-GGGHHHHHHH CS
               Ketoacyl-synt_C  89 HleaAaGvaeli 100
                                    ++ A+G+ae++
  gi|70607997|ref|YP_256867.1|  94 YSLVASGLAEIA 105
                                   456677777765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.99
                                   HHHHGGGGGSCTSEEE-THH CS
               Ketoacyl-synt_C  66 kkvfgekarkqplavgSvKs 85 
                                    +vfg+++  +++a+ SvK+
  gi|70607997|ref|YP_256867.1| 154 MAVFGTTE--EQMALVSVKA 171
                                   56788877..5699999997 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0018
                                   HHHHHHHHHHHHHT--GGGEEEEE-SS- CS
               Ketoacyl-synt_C  25 aqaraiekalaeagvdpedvdyveahgt 52 
                                   a   a ++a+++a+++p+++++   h++
  gi|70607997|ref|YP_256867.1| 259 ATTLAAQDAYKMADITPNSIEVATVHDA 286
                                   5567899****************99986 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.26
                                   -B-GGGHHHHHHHHHHHHHHH CS
               Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalkh 108
                                   GH ++A G+  +  + ++l++
  gi|70607997|ref|YP_256867.1| 333 GHPLGATGLSMIYEITKQLRE 353
                                   9********999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2661.61
//
Query:       gi|70607998|ref|YP_256868.1|  [L=136]
Description: hypothetical protein Saci_2289 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-11   42.2   0.0    1.3e-10   41.4   0.0    1.4  1  4HBT         Thioesterase superfamily
      3e-05   24.2   0.0    4.4e-05   23.6   0.0    1.3  1  DUF4442      Domain of unknown function (DUF4442)
     0.0058   16.9   0.0     0.0071   16.6   0.0    1.1  1  4HBT_3       Thioesterase-like superfamily
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.089   12.8   0.0    2.0  3  INCA1        INCA1
      0.053   12.8   0.0       0.06   12.6   0.0    1.2  1  Acyl-ACP_TE  Acyl-ACP thioesterase


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   3.7e-14   1.3e-10       1      78 [.      38     111 ..      38     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 3.7e-14
                                   TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                          4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                   +G vhg  ++al+D+a  ++ +    +    v++++ idf+r+++lg+++ +e+  +  grt+  +++ v++edg+ +
  gi|70607998|ref|YP_256868.1|  38 HGGVHGSFIFALADTAFEYISNFSRNS----VALHMDIDFRRQATLGEKIIAEGFEESKGRTTSLYRIVVKNEDGKII 111
                                   688****************99999985....*******************************************9865 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   4.4e-05      19     127 ..      12     115 ..       3     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                                   G--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S---S-EEEEEE-T CS
                       DUF4442  19 vgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlakatgdltavaele 99 
                                   ++++ ee++ g+++v+++ r ++ N  g+vH+  i++la++a+  + + +  ++ + +   m++d+ ++at + + +ae  
  gi|70607998|ref|YP_256868.1|  12 LHLKLEEIREGYVKVSAEVREENLNIHGGVHGSFIFALADTAFEYISNFS--RNSVAL--HMDIDFRRQATLGEKIIAEGF 88 
                                   67889**************************************9987554..444444..799******999999999988 PP

                                   TS-TT--EEEEEEEEEEETTE.EEEEEE CS
                       DUF4442 100 pedvgekeelvvevevrdekgeevvrae 127
                                   +e  g++ +   ++ v++e+g+ +++++
  gi|70607998|ref|YP_256868.1|  89 EESKGRT-TSLYRIVVKNEDGKIIAHVT 115
                                   8887744.44457778888888777765 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     2e-06    0.0071       8      88 ..      38     123 ..      30     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-06
                                   TTC.-HHHHHHHHHHHHHHT.......-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEET.TEEEEEE CS
                        4HBT_3   8 ggagyGGyvlAlalraaqrtv......pdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqg.grpifta 79 
                                    g+++G ++ Ala  a +             +  ++ ++F r++  g ++i +  +   Gr++s++++ +  + g+ i+++
  gi|70607998|ref|YP_256868.1|  38 HGGVHGSFIFALADTAFE--YisnfsrN--SVaLHMDIDFRRQATLGeKIIAEGFEESKGRTTSLYRIVVKNEdGKIIAHV 114
                                   333466666666666666..03344432..34569***********************************88659*****9 PP

                                   EEEEE---T CS
                        4HBT_3  80 tasfgraes 88 
                                   ta    ++s
  gi|70607998|ref|YP_256868.1| 115 TALAYHLDS 123
                                   998877776 PP

>> INCA1  INCA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.53   1.9e+03      85     102 ..      14      31 ..       9      36 .. 0.84
   2 ?   -1.9   0.0       0.8   2.9e+03     103     121 ..      64      82 ..      61      99 .. 0.75
   3 ?   12.8   0.0   2.5e-05     0.089      90     122 ..     103     135 ..      84     136 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.53
                         INCA1  85 pklagmqqGpgsiparvr 102
                                    kl+ +++G ++++a vr
  gi|70607998|ref|YP_256868.1|  14 LKLEEIREGYVKVSAEVR 31 
                                   578899999999999999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.8
                         INCA1 103 avtyhledlrrrqriinel 121
                                   +v+ h++   rrq ++ e+
  gi|70607998|ref|YP_256868.1|  64 SVALHMDIDFRRQATLGEK 82 
                                   5788888666788887775 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.5e-05
                         INCA1  90 mqqGpgsiparvravtyhledlrrrqriinelk 122
                                   +++  g+i a+v a++yhl+ ++r q+   e k
  gi|70607998|ref|YP_256868.1| 103 VKNEDGKIIAHVTALAYHLDSVKREQSNKGENK 135
                                   477889*******************98766665 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05      0.06      57     119 ..      65     127 ..      13     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                   Acyl-ACP_TE  57 vvakyeieierlpefgdkveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrr 119
                                   v  +++i+  r   +g+k+  e   es+++     +  v++e+g+ i++++++  ++d  +r 
  gi|70607998|ref|YP_256868.1|  65 VALHMDIDFRRQATLGEKIIAEGFEESKGRTTSLYRIVVKNEDGKIIAHVTALAYHLDSVKRE 127
                                   567899**********************************************99999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1014.65
//
Query:       gi|70607999|ref|YP_256869.1|  [L=428]
Description: phenylacetate-coenzyme A ligase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   57.8   0.6    2.6e-15   56.5   0.6    1.7  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    2.4e-13   49.5   0.0    3.3e-13   49.0   0.0    1.2  1  AMP-binding      AMP-binding enzyme
    1.3e-05   24.3   0.3      0.087   11.7   0.1    2.1  2  GH3              GH3 auxin-responsive promoter


Domain annotation for each model (and alignments):
>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.6   4.4e-19   2.6e-15       1      93 [.     341     425 ..     341     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 4.4e-19
                                   TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT- CS
               AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelvepgt 81 
                                   Gv+++Ps+i+ vl++++e++ eYq+v +r+g+  ++ +k Ev++         ++l++ki ++++++  v++++e+++ g+
  gi|70607999|ref|YP_256869.1| 341 GVKIYPSAINLVLMKYSEIA-EYQVVFDRRGNEHKMILKLEVENPS-------NELKHKIVEEIRTVAFVTPEIEFIKVGS 413
                                   9******************8.9**********************95.......68************************** PP

                                   S---------EE CS
               AMP-binding_C_2  82 lprsegKakrvi 93 
                                   lpr egK+krvi
  gi|70607999|ref|YP_256869.1| 414 LPRFEGKSKRVI 425
                                   ***********7 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   5.6e-17   3.3e-13     160     370 ..      88     294 ..      22     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 5.6e-17
                                   SEEEEEEE--SSSS-EEEEEEHHHH...HHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTC CS
                   AMP-binding 160 dlayiiYTSGTTGkPKGVmlshrnl...vanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkd 237
                                    ++ +  TSGTTG P    ++++ +   ++ va   + ++ +++++d ++ i  +   +g i    +a   G +v+ ++  
  gi|70607999|ref|YP_256869.1|  88 KVVRFHMTSGTTGIPTVNAYTTNDIevwSNLVAR--CLKTANVNKNDIMMNIYGYGLFTGGIGLQQGAEKIGVKVIPWSAG 166
                                   5566667**************9988754444444..445677889***********99999999999********999966 PP

                                   GCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC..EEEEEE CS
                   AMP-binding 238 aaldpklllelieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllggeplspellrffralfge..evlegY 315
                                    +   + ++++i+++k+tvi+g+P+    ++e   +k    +      lrl++ g+e++ +e+l+++++ +       e+Y
  gi|70607999|ref|YP_256869.1| 167 RT---EGMVKAIKDFKATVITGTPSYELVVAET--IKkLGIDP-TTLNLRLAIPGAEAMTSEMLKRIESELALkeGAREIY 241
                                   54...3468***************965555443..33121221.2334999888***************998887689*** PP

                                   EEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEE CS
                   AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvr 370
                                   G TE+ g  +  +++ d     + G  ++  +  ++ivD+etge + +geeGel++ 
  gi|70607999|ref|YP_256869.1| 242 GFTEAMGPGVSQECPYD----DHKGMHIWtdHFIAEIVDPETGEVLDEGEEGELVIT 294
                                   ********984444444....3345544334999*********************96 PP

>> GH3  GH3 auxin-responsive promoter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   2.9e-05      0.17       6     110 ..      14     122 ..      12     154 .. 0.73
   2 !   11.7   0.1   1.5e-05     0.087     354     460 ..     283     387 ..     263     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.9e-05
                                   HHTHHHHHHHHHHHHHHH.CTTSHHHHHC....TT.....HCHHHHHHHS--BEHHHHHHHHHHHHTTCC.CT.SSSS-SE CS
                           GH3   6 tknaaevqeevLkeiLkr.nanteylkkf.efssi.....ksaedFkkkvPivtYedlepyieriakGeqnvL.tsepikl 78 
                                   +++++e+q++ L+++++   +n+ y +k+ + ++i     k++ed  +k+P +t e+l++  +    G + +    e++++
  gi|70607999|ref|YP_256869.1|  14 KNDIKEIQQKRLRRLINYvYENSPYYRKLfQQRRIspediKTVED-LRKLPFTTKEELRD--KAYPYGGEFLAvPFEKVVR 91 
                                   6789999*****999986268899998872444448877788888.6779*********9..455556552331559**** PP

                                   EEEECCEETTEEEEEEESHHHHHHHHHH.HHH CS
                           GH3  79 falsSGTtsgksKliPvteeslkelallvlal 110
                                   f ++SGTt g + +  +t++  + +++lv++ 
  gi|70607999|ref|YP_256869.1|  92 FHMTSGTT-GIPTVNAYTTNDIEVWSNLVARC 122
                                   ********.99988888888888877764333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.5e-05
                                   S-TTSEEEEEEESTT....S-SSEEECEEEEEEEEETTEE..EEEEE.ECCTEEE-SSSS-CCHHHHHHHHH.HHHHHTT- CS
                           GH3 354 vevGkeYelvvTtfa....GLyRYrigDvvrvtgfynkaP..rleFv.gRknvvlsidgeklteeelqkaveeaakeltgl 427
                                   +  G+e elv+Tt +     L RYr+ D+ ++t+    +P  ++ ++ gR + v+  +g k+  + +  ++  +       
  gi|70607999|ref|YP_256869.1| 283 LDEGEEGELVITTLSkeavPLIRYRTRDITKITESDDDIPypKISIIkGRIDDVIFYKGVKIYPSAINLVLM-KY-----S 357
                                   6789999******7644447******************98778887548**************999999999.33.....4 PP

                                   EEEEEEEEE.ESS.SSSEEEEEEEEECS..... CS
                           GH3 428 elvdftsfapdtsesepghyvlflElkkkeepe 460
                                   e++++ ++  d    ++ + +l lE+++ +++e
  gi|70607999|ref|YP_256869.1| 358 EIAEYQVVF-DRR-GNEHKMILKLEVEN-PSNE 387
                                   578899966.555.66667777777764.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2894.07
//
Query:       gi|70608000|ref|YP_256870.1|  [L=127]
Description: hypothetical protein Saci_2291 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-14   51.9   0.1    8.8e-14   51.3   0.1    1.4  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.8e-12   46.9   0.0    2.9e-12   46.2   0.0    1.3  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0034   17.2   0.3       0.33   10.9   0.0    2.2  2  TFIIS_C        Transcription factor S-II (TFIIS)
     0.0037   17.4   0.0     0.0055   16.8   0.0    1.3  1  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.039   13.6   0.2      0.052   13.2   0.2    1.1  1  TackOD1        Thaumarchaeal output domain 1


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   2.4e-17   8.8e-14       1      64 [.      58     116 ..      58     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.4e-17
                                   EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                 OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                   wvel+g+G+++++++v ++p+gf++++ yv+g+V+L e v +ma++ g ++    +G +V++ +
  gi|70608000|ref|YP_256870.1|  58 WVELQGEGELMTYSIVSQKPQGFEKYPDYVIGIVRLGE-VSVMAWIKGRPR----VGSKVKIST 116
                                   **************************************.99*******995....9***99865 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   8.1e-16   2.9e-12       2      37 .]      22      57 ..      21      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 8.1e-16
                       DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsddle 37
                                  + ++eg++v++rC +C +v+fPP+  C++Cgsd +e
  gi|70608000|ref|YP_256870.1| 22 EKLKEGKVVATRCVACNSVYFPPQKDCSNCGSDKME 57
                                  689******************************987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0095        34      23      37 ..      26      40 ..      24      41 .. 0.86
   2 !   10.9   0.0   9.1e-05      0.33       2      17 ..      47      62 ..      46      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0095
                       TFIIS_C 23 EpmtvfykCtkCghr 37
                                  E+ +v  +C++C+  
  gi|70608000|ref|YP_256870.1| 26 EGKVVATRCVACNSV 40
                                  8889999*****976 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 9.1e-05
                       TFIIS_C  2 kCpkCgsreayffqlQ 17
                                   C +Cgs+++ +++lQ
  gi|70608000|ref|YP_256870.1| 47 DCSNCGSDKMEWVELQ 62
                                  6**************9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-06    0.0055       5      44 ..      28      66 ..      24      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                  NOB1_Zn_bind  5 kswvlrChaCfkvtkdmtkkFCpkCGnktLkrvavsvden 44
                                  k   +rC aC +v+   +k  C++CG++ ++ v+++ + +
  gi|70608000|ref|YP_256870.1| 28 KVVATRCVACNSVYFPPQKD-CSNCGSDKMEWVELQGEGE 66
                                  55679*********998887.********99888765555 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.4e-05     0.052      73      99 ..      31      57 ..      13      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                       TackOD1 73 irlCpsCksghlnvrevCpkCkSidie 99
                                     C  C+s  +  ++ C++C+S ++e
  gi|70608000|ref|YP_256870.1| 31 ATRCVACNSVYFPPQKDCSNCGSDKME 57
                                  568********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 862.63
//
Query:       gi|70608001|ref|YP_256871.1|  [L=342]
Description: hypothetical protein Saci_2292 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-05   25.0   0.2    6.2e-05   23.4   0.1    1.9  2  Rubrerythrin     Rubrerythrin
    0.00067   18.6   0.1        0.4    9.5   0.1    2.2  2  FA_desaturase_2  Fatty acid desaturase
    0.00069   19.0   1.5      0.001   18.4   0.0    2.0  2  AurF             P-aminobenzoate N-oxygenase AurF
  ------ inclusion threshold ------
      0.011   15.0   0.4      0.015   14.6   0.4    1.2  1  DUF4932          Domain of unknown function (DUF4932)


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   4.8e+03     112     130 ..     102     120 ..      91     122 .. 0.69
   2 !   23.4   0.1   1.4e-08   6.2e-05       8      73 ..     184     247 ..     176     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                                   SHHHHHHHHHHHHHHHHHH CS
                  Rubrerythrin 112 neeakklfkklaeaEkkHe 130
                                   +  ++ ++ ++  +E++H 
  gi|70608001|ref|YP_256871.1| 102 DTAVRGILTTITWDENRHN 120
                                   4556677888888888885 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS---- CS
                  Rubrerythrin   8 agEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyae 73 
                                    gE  a+ +++++ ++ak  +++ +++F+ +A +E +H ++   ++ +  p+ + ++k+ v ++  
  gi|70608001|ref|YP_256871.1| 184 MGEAAATTVFTSMGKNAK--NEEFSKIFKNTAVDETRHYAFTHLIMTQNAPNMNEDRKKLVTKQIR 247
                                   58****************..****************************999999666666666555 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00051       2.3     163     209 ..      84     130 ..      48     137 .. 0.83
   2 !    9.5   0.1   8.9e-05       0.4     155     208 ..     177     229 ..     167     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00051
               FA_desaturase_2 163 rATkvsHrntaklakeagdellakicgaiaadEkrHeaaYtrvvekl 209
                                    AT v    + k  +++ d+++  i+++i+ dE+rH+      ++++
  gi|70608001|ref|YP_256871.1|  84 HATPVFAYAVVKSFEHHLDTAVRGILTTITWDENRHNLVCGLAIKNA 130
                                   67888778888999999*******************98766655555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 8.9e-05
               FA_desaturase_2 155 fvYtsf..QErATkvsHrntaklakeagdellakicgaiaadEkrHeaaYtrvvek 208
                                   +++tsf   E A +     ++k ak   +e  +ki ++ a dE+rH+a+ + ++++
  gi|70608001|ref|YP_256871.1| 177 VLFTSFmmGEAAATTVFTSMGKNAK---NEEFSKIFKNTAVDETRHYAFTHLIMTQ 229
                                   5667763347777777788888865...5899***************997777654 PP

>> AurF  P-aminobenzoate N-oxygenase AurF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   1.2      0.96   4.3e+03       6      29 ..      33      55 ..      31      67 .. 0.83
   2 !   18.4   0.0   2.3e-07     0.001     105     254 ..     108     277 ..      93     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.96
                                  HHHHHHHHHHHHH-T---...... CS
                          AurF  6 evlerllessarrsfdplvdiDwd 29
                                  e + +l + +++ ++d+  +iDw 
  gi|70608001|ref|YP_256871.1| 33 ERAWQLYRRAKKEQWDED-NIDWR 55
                                  556689999999999999.99996 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.3e-07
                                   HHHHHHHHHHHHHHHHHHHHHHHH................--...S---HHHHHHHHHHHH--SHHHHHHHHHHHHHHHHH CS
                          AurF 105 yalteiaDEcrHslMfaeaverig................ad...vpgmyrvrrllrelakllktiarglvffaavlvgEe 166
                                   +++t   DE+rH l +  a++                   a+       +   r+ ++ + + k++a   v f+  ++gE 
  gi|70608001|ref|YP_256871.1| 108 ILTTITWDENRHNLVCGLAIKNAMegfplnfkpqddlekkAMlnvQWVWWNGSRYWKAYLDAYKKYA-LDVLFTSFMMGEA 187
                                   4445556888888888888877666888888887766654113322222223444455555555555.5566666777776 PP

                                   HHHHHHHHHHT-SSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHS--HHHHHHHHH. CS
                          AurF 167 iidalqrelmrdeelqPlvrrvmriHvaEEarHisfareelrrrvprlsraerallrlllalalrafasslvnppvyala. 246
                                       +  ++ ++ + +   +++++  +++E rH  f + +++++ p++++ +++l+ + +  +  ++    ++pp+++++ 
  gi|70608001|ref|YP_256871.1| 188 AATTVFTSMGKNAKNEE-FSKIFKNTAVDETRHYAFTHLIMTQNAPNMNEDRKKLVTKQIRAGFVFLSLITYKPPKEFWKl 267
                                   66666666555554433.5667777799********************************999999999999999999986 PP

                                   ..T-TTHHHH CS
                          AurF 247 ..gldpaeav 254
                                      + + +++
  gi|70608001|ref|YP_256871.1| 268 ppWFLEVHQR 277
                                   5544444444 PP

>> DUF4932  Domain of unknown function (DUF4932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   3.4e-06     0.015      63     172 ..     119     227 ..      81     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-06
                       DUF4932  63 ydavegaaakieikefevkLspqsDlekkskldnrwteeeleefvrllkefyreskFkdFytanaelykdvlenlkkalek 143
                                    + v g+a+k  +++f ++ +pq+Dlekk +l+ +w+  +   + ++  ++y++ + +  +t+     +++++ +  ++ k
  gi|70608001|ref|YP_256871.1| 119 HNLVCGLAIKNAMEGFPLNFKPQDDLEKKAMLNVQWVWWNGSRYWKAYLDAYKKYALDVLFTSFMMGEAAATTVF-TSMGK 198
                                   5667799999999*************************9999999999999999999999999999999999999.99999 PP

                       DUF4932 144 qdviteleefyGakvankivvvsllnllg 172
                                   +++ +e+ + + ++   ++    ++ l+ 
  gi|70608001|ref|YP_256871.1| 199 NAKNEEFSKIFKNTAVDETRHYAFTHLIM 227
                                   99999999998887766665445555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2502.47
//
Query:       gi|70608002|ref|YP_256872.1|  [L=280]
Description: 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-39  136.0   0.0    1.8e-39  135.7   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.0   9.8e-44   1.8e-39       2     217 ..      52     277 ..      51     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 9.8e-44
                                   EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHH CS
                 FAA_hydrolase   2 ivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAe 82 
                                   i+c+ +n+ + +    k  e ++     ++p+ff+k +s +vg gd + +P++   +  EvE++++i  +lr++ +  + +
  gi|70608002|ref|YP_256872.1|  52 IFCVLVNSYKMLGASSKQ-EGKEM---LGTPKFFIKLPSIVVGNGDIVYAPKS--GIRPEVEIGIIIKEKLRNI-NSGKIQ 125
                                   899999999999998655.44444...55566********************9..8999***************.99**** PP

                                   TTEEEEEEEEEEE-.............SBGGG---.HH....HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTE CS
                 FAA_hydrolase  83 daiaGytllnDvsa.............Rdlqaeekapl....gwflgksfdtftpiGpwivtpdeledpedlelrlrvnge 146
                                   d+i+Gyt++nDv+a             Rd  +   +++      f++k++dtf+++G +i+tpde++  + l++  +++++
  gi|70608002|ref|YP_256872.1| 126 DYILGYTVFNDVTApgeaskdwyyarrRDPNDGVVKRMivrgAHFRNKNRDTFAVLGSIITTPDEVK-LDRLRMMSIYDNK 205
                                   *************************996665555544456658899********************5.79*********** PP

                                   EEEEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-E.EEEEETTTEEEEEEE CS
                 FAA_hydrolase 147 evqdsntkdmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDe.veveieglGelrnrV 217
                                   ++qds+t++ ifsp+e+i +ls +lt++  ++i+tGT+  +gae++s++ l++  + +ev++e +G+l n+V
  gi|70608002|ref|YP_256872.1| 206 VIQDSTTDEFIFSPEEIIRELSTILTIPQLSVITTGTVGYSGAEDTSEYKLEAKSTtMEVHVERIGSLVNPV 277
                                   **************************************4335899********9998*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.33s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1686.40
//
Query:       gi|70608003|ref|YP_256873.1|  [L=490]
Description: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-84  281.6   0.0      1e-83  281.2   0.0    1.1  1  HpaB_N    4-hydroxyphenylacetate 3-hydroxylase N terminal
    1.9e-52  177.3   0.0    3.1e-52  176.6   0.0    1.2  1  HpaB      4-hydroxyphenylacetate 3-hydroxylase C terminal


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.2   0.0   1.1e-87     1e-83       2     271 ..       5     271 ..       4     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.2 bits;  conditional E-value: 1.1e-87
                                   HHHHHHHHHH.S---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHHHH CS
                        HpaB_N   2 geeYlesLrd.kgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDllk 81 
                                   geeY++sL++ ++ evY++GekVed+++h+af+  +++va++Ydl++++e    l++++++ ge+++++f  prskeDl k
  gi|70608003|ref|YP_256873.1|   5 GEEYIKSLKEgNHGEVYYNGEKVEDIVNHHAFKIPIKTVAKYYDLHWEDE---ALRVYNRDVGEDTSISFFRPRSKEDLKK 82 
                                   89*********9999*********************************87...899************************* PP

                                   HHHHHHHHHHHTTT--S--THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS-TTS-GGG CS
                        HpaB_N  82 krkairelarktggclgRcpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkgdRskrpse 161
                                    r  ++ + ++ +g++gR+pdy +++ ++++a+a d+f k   ++  en+ +++++++++dl++thai+ p  dRs++ps+
  gi|70608003|ref|YP_256873.1|  83 MRVGLNRIYDNYYGFFGRSPDYLNIWSMVFYAHAeDYFGKVFGSKIMENVINIYKEATKKDLFYTHAIVAPMYDRSRPPSQ 163
                                   ********************************************************************************* PP

                                   SSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE-------S..-T CS
                        HpaB_N 162 qedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklicresfedkleese 242
                                   +edp+++++vv+et++G++VrGa ++ T++++a+ ++ lp    ++++d +ya++f++p +++G+k+i r+ f  +++  e
  gi|70608003|ref|YP_256873.1| 164 WEDPYIQIGVVKETNEGVIVRGAAMICTAGPYAEMLWYLPNI--RRDSDPRYAIFFSIPGNSKGVKFITRRGFYPRENLGE 242
                                   *****************************************4..4799***************************755799 PP

                                   TT-TTTTT----EEEEEEEEEEEEGGGEE CS
                        HpaB_N 243 fdyplssrfdendalvvfDdVfVPwerVf 271
                                   f+yp+ssrf+e+da++v+D+V++Pw+r++
  gi|70608003|ref|YP_256873.1| 243 FEYPISSRFEESDAILVLDNVLIPWDRII 271
                                   ***************************96 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   3.4e-56   3.1e-52       4     198 ..     283     476 ..     281     482 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 3.4e-56
                                   HHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-EE-- CS
                          HpaB   4 lveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdpsGvylPd 84 
                                   +++++++  +++++ +i+++  l+f++Gla+++ae+ Gi++f +vqeklge+++++ l +a+liaae ++e   +++y+P+
  gi|70608003|ref|YP_256873.1| 283 MWHTVQLRTWFNWHFAIQHYSRLKFYAGLAMAIAESVGINNFINVQEKLGEILIYLTLNEAALIAAEENGEYL-PNIYRPN 362
                                   7899999******************************************************************.99***** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT----HHH.HHST.THHHHHHHT-BTT.B-HHHHHHHHHHHHHHHTSHHHH CS
                          HpaB  85 lllanaarvlvtrlypriveilqdiaGGglitlPsead.fknpeigpllekylrgsegvsaeeRvkllklawdltgsefgg 164
                                   + +  +a ++ +r++pr+ eil+ i++G  i +P   + f+npe +++lekyl++++ ++a eRvkl++l+wd++gse g+
  gi|70608003|ref|YP_256873.1| 363 PYISITASHFNMRALPRVDEILRLISAGSSIPIPAGIRdFENPEERAMLEKYLASKG-LPALERVKLFNLLWDVIGSESGM 442
                                   ************************************999*****************9.*********************** PP

                                   HHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHH CS
                          HpaB 165 rhelyerhgaGspeaqriaiyrqydleekkelvk 198
                                   r+e+y+r+  G+p   ++++y +  +++k e+vk
  gi|70608003|ref|YP_256873.1| 443 RYEQYDRFSRGDPTIRWAQMYTEVFKDRKREYVK 476
                                   *********************9999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3174.73
//
Query:       gi|70608004|ref|YP_256874.1|  [L=313]
Description: catechol 2,3-dioxygenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-23   82.7   0.7    6.7e-11   42.5   0.1    2.3  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.4e-06   28.6   0.0       0.49   10.7   0.0    3.5  3  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0014   18.7   0.3      0.079   13.1   0.0    3.1  4  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.035   14.5   0.1      0.096   13.1   0.1    1.8  1  Pfk_N         Phosphofructokinase N-terminal domain yeast
       0.14   12.9   0.0        1.5    9.6   0.0    2.2  2  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   2.8e-13   9.9e-10       2     123 ..       7     106 ..       6     111 .. 0.87
   2 !   42.5   0.1   1.9e-14   6.7e-11      12     128 .]     148     255 ..     135     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 2.8e-13
                                   EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEE CS
                    Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafial 82 
                                   + hv ++v d++ksl FY++ LGf+ ++k +         +  + ++g+h++lvl +a+s++++            af+++
  gi|70608004|ref|YP_256874.1|   7 LSHVCVRVIDMDKSLFFYRDLLGFHETEKNG------DYVYLRGYEEGQHHSLVLKRAESPGLSYI----------AFRVR 71 
                                   78*****************************......666666778899************98886..........55555 PP

                                   EHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTS CS
                    Glyoxalase  83 dvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdG 123
                                      +v+k+ ++l++ g+k  +  ++ + +a++   f D +G
  gi|70608004|ref|YP_256874.1|  72 ---NVDKMREKLEASGLKTRKFEEKGVDNAII---FSDTGG 106
                                   ...556699*********99999999999999...999988 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 1.9e-14
                                   HHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHH CS
                    Glyoxalase  12 leksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkald 92 
                                    e  ++FY+  LGf  ++ +    ++++ +  +++ +g++++l++  +  + + ++        h+   + d  dv++a d
  gi|70608004|ref|YP_256874.1| 148 FENEIKFYQS-LGFYETEIFL--DKEGKKMVSWLTKSGDSHNLAISKSSRKTPGFH--------HFTYYVHDLRDVIRAAD 217
                                   46679*****.**********..888999999**************9999999987........***************** PP

                                   HHHHTT..GEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                    Glyoxalase  93 rlkeag..vkvvaepgrhyfgalysfyfrDpdGillei 128
                                   ++++a     + ++pgrh+ ++++++y rDp+G +le+
  gi|70608004|ref|YP_256874.1| 218 IMASAElwDYIERGPGRHGVTQGVYIYLRDPNGGRLEF 255
                                   *****97779***********************99997 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.011        41       2      27 ..       9      34 ..       8      59 .. 0.80
   2 !   10.7   0.0   0.00014      0.49      64      93 ..      58      87 ..      46     101 .. 0.84
   3 !    9.5   0.0   0.00032       1.1      60      86 ..     190     216 ..     137     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                  EEEEE-S-HHHHHHHHHH.TT-EESS CS
                  Glyoxalase_4  2 QigivVeDleaavarfsallGvgpwq 27
                                  ++++ V D+++ + ++ +llG+++++
  gi|70608004|ref|YP_256874.1|  9 HVCVRVIDMDKSLFFYRDLLGFHETE 34
                                  999999***************98764 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                                  HTS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
                  Glyoxalase_4 64 ehgeglhhlaywvddldaavarleeqGfev 93
                                  +  +gl ++a++v+++d+  ++le+ G++ 
  gi|70608004|ref|YP_256874.1| 58 AESPGLSYIAFRVRNVDKMREKLEASGLKT 87
                                  3789***********************984 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00032
                                   -THHHTS-EEEEEEEEES-HHHHHHHH CS
                  Glyoxalase_4  60 eflaehgeglhhlaywvddldaavarl 86 
                                   +   ++ +g+hh+ y v dl  +++++
  gi|70608004|ref|YP_256874.1| 190 SKSSRKTPGFHHFTYYVHDLRDVIRAA 216
                                   4556799************99888765 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.047   1.7e+02       1      28 [.       7      34 ..       7      52 .. 0.82
   2 !   13.1   0.0   2.2e-05     0.079      60     109 ..      46      90 ..      24     140 .. 0.75
   3 ?   -1.9   0.0      0.88   3.1e+03       3      25 ..     138     161 ..     136     182 .. 0.76
   4 ?   -0.6   0.1      0.35   1.2e+03       1      16 [.     199     214 ..     199     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.047
                  Glyoxalase_3  1 lDHvvlavpdleeaaarfarrlGftvtp 28
                                  l Hv + v d+++    +++ lGf+ t+
  gi|70608004|ref|YP_256874.1|  7 LSHVCVRVIDMDKSLFFYRDLLGFHETE 34
                                  67****************9*****9873 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.2e-05
                  Glyoxalase_3  60 aperprlfgldrlakgeglhtlalrtddidataarlraaGvdeagrrvrp 109
                                   ++++++++ l+r+ + +gl+ +a+r++++d+++++l+a G++    +++ 
  gi|70608004|ref|YP_256874.1|  46 EEGQHHSLVLKRA-ESPGLSYIAFRVRNVDKMREKLEASGLK----TRKF 90 
                                   4455566677785.57************************75....2233 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.88
                  Glyoxalase_3   3 Hvvlavp.dleeaaarfarrlGft 25 
                                   Hv l+v+ +  e   +f++ lGf 
  gi|70608004|ref|YP_256874.1| 138 HVNLMVDsNVFENEIKFYQSLGFY 161
                                   899999987777777788999995 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.35
                  Glyoxalase_3   1 lDHvvlavpdleeaaa 16 
                                   ++H +++v+dl + ++
  gi|70608004|ref|YP_256874.1| 199 FHHFTYYVHDLRDVIR 214
                                   79*********98765 PP

>> Pfk_N  Phosphofructokinase N-terminal domain yeast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.7e-05     0.096      12      51 ..     144     184 ..     135     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                         Pfk_N  12 keekyeelikfYkklGfkvvksy.skeantkselkGvstds 51 
                                   +++ +e+ ikfY++lGf  + ++ +ke ++  +    s ds
  gi|70608004|ref|YP_256874.1| 144 DSNVFENEIKFYQSLGFYETEIFlDKEGKKMVSWLTKSGDS 184
                                   6778*****************99445444555554444444 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00043       1.5       2      90 ..      10      94 ..       9     109 .. 0.70
   2 ?    1.0   0.0       0.2   7.2e+02      41     102 ..     181     251 ..     140     256 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00043
                  Glyoxalase_6  2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpepaknrvHldlavedldaevarlvalGArvl 84
                                  v++ + d+++   F++++lg+  ++++   +    +g +++++ +l+++r++ p+     + ++v ++d+  ++l+a G ++ 
  gi|70608004|ref|YP_256874.1| 10 VCVRVIDMDKSLFFYRDLLGFHETEKN--GDYVYLRGYEEGQHHSLVLKRAESPGL--SYIAFRVRNVDKMREKLEASGLKTR 88
                                  778888999999**********99999..333344455556667777777777655..6888899999888888888886665 PP

                  Glyoxalase_6 85 reprdg 90
                                  + +++g
  gi|70608004|ref|YP_256874.1| 89 KFEEKG 94
                                  555554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.2
                  Glyoxalase_6  41 aedaatllfqrvpepaknrvHldlavedldaevarlvalGArvlreprdgthgr.........vlaDPeGn 102
                                    +d+  l++ +  ++     H+   v dl+  ++++  +   +l +  ++++gr          l+DP G 
  gi|70608004|ref|YP_256874.1| 181 SGDSHNLAISKSSRKTPGFHHFTYYVHDLRDVIRAADIMASAELWDYIERGPGRhgvtqgvyiYLRDPNGG 251
                                   34444555555555333346777777777655544433333333333333333445566667777888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1951.58
//
Query:       gi|70608005|ref|YP_256875.1|  [L=210]
Description: HTH DNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-20   71.0   0.1    9.8e-20   70.1   0.1    1.5  1  HTH_10       HTH DNA binding domain
  ------ inclusion threshold ------
      0.016   14.8   0.1        1.2    8.7   0.0    3.0  3  HTH_24       Winged helix-turn-helix DNA-binding
      0.021   15.0   0.2        1.6    8.9   0.0    2.4  2  DUF1492      Protein of unknown function (DUF1492)
      0.035   14.0   0.0        0.1   12.5   0.0    1.7  1  Homeodomain  Homeodomain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   2.2e-23   9.8e-20       1      53 []     151     203 ..     151     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.2e-23
                        HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                   L++ q++vlk+A+e+GY dyPR+++++ LA++l+Isk t+++hLr+ae+kl+e
  gi|70608005|ref|YP_256875.1| 151 LSPSQVRVLKAAFEYGYLDYPREANADILAEKLNISKVTFLYHLRSAEKKLVE 203
                                   7889***********************************************85 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.03   1.3e+02       3      15 ..      60      72 ..      58      73 .. 0.85
   2 ?   -1.5   0.0      0.41   1.9e+03      31      44 ..     119     132 ..     118     133 .. 0.81
   3 ?    8.7   0.0   0.00027       1.2      23      44 ..     179     200 ..     171     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.03
                        HTH_24  3 etdrkILelLqkn 15
                                   +d+ IL++Lq n
  gi|70608005|ref|YP_256875.1| 60 AKDKGILRVLQVN 72
                                  5799******977 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                        HTH_24  31 pstvnrrlkrLeee 44 
                                   +++vn+ +++L++ 
  gi|70608005|ref|YP_256875.1| 119 STAVNEIVDQLKSY 132
                                   689*****999875 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00027
                        HTH_24  23 LAerlglSpstvnrrlkrLeee 44 
                                   LAe+l++S+ t +++l+  e++
  gi|70608005|ref|YP_256875.1| 179 LAEKLNISKVTFLYHLRSAEKK 200
                                   9****************99986 PP

>> DUF1492  Protein of unknown function (DUF1492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.016        73      51      85 ..      53      87 ..      48      94 .. 0.85
   2 ?    8.9   0.0   0.00036       1.6      72      99 ..     174     201 ..     161     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.016
                       DUF1492 51 lidklensdsrsvLrmvyidkltvwqvidklnisr 85
                                   + k++ ++ + +Lr+  +++   +  +d ln  r
  gi|70608005|ref|YP_256875.1| 53 ELSKMKRAKDKGILRVLQVNQFDSDIYVDFLNTYR 87
                                  567899999*************9999999998766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00036
                       DUF1492  72 ltvwqvidklnisrstyyrllrvavkeL 99 
                                    +++ + +klnis+ t+   lr a+k+L
  gi|70608005|ref|YP_256875.1| 174 ANADILAEKLNISKVTFLYHLRSAEKKL 201
                                   55667789*****************987 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.3e-05       0.1       8      41 ..     152     187 ..     150     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                                   -HHHHHHHHHHHHH..SSS-SHHHHHHHHHHHTS-H CS
                   Homeodomain   8 tkeqleeLeklFee..nrypsaeereeLAkklgLee 41 
                                   +++q+++L+++Fe     yp ++    LA+kl++++
  gi|70608005|ref|YP_256875.1| 152 SPSQVRVLKAAFEYgyLDYPREANADILAEKLNISK 187
                                   799**********667******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1434.72
//
Query:       gi|70608006|ref|YP_256876.1|  [L=293]
Description: pirin-related protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-36  122.1   0.1    3.6e-35  120.2   0.0    1.9  2  Pirin     Pirin
    6.2e-24   84.4   0.0    1.4e-23   83.2   0.0    1.6  2  Pirin_C   Pirin C-terminal cupin domain


Domain annotation for each model (and alignments):
>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0     4e-39   3.6e-35       2     108 .]      20     132 ..      19     132 .. 0.96
   2 ?   -1.3   0.0      0.24   2.2e+03      49      63 ..     200     214 ..     181     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 4e-39
                                   EEECCGTCC.TTCCEECTCEECCEEESS.S.ETTEEEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEE CS
                         Pirin   2 vrvrralgkaaelqsvdpFlfldefdpaelevgeedvigagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwm 82 
                                   v+++r++g++++++ +dpFl+ld f+++++     d++ agfp+hphrg+etvt+l++G+veh+Ds+Gnkgvi+pG+ qwm
  gi|70608006|ref|YP_256876.1|  20 VKLYRVFGGMHTVEYTDPFLLLDFFGSSNP----SDYL-AGFPWHPHRGIETVTLLYKGKVEHQDSEGNKGVIYPGQSQWM 95 
                                   78899*********************9999....599*.****************************************** PP

                                   E-TT-EEEEEEE-SS...........SS-EEEEEEEE CS
                         Pirin  83 tAgsGivhsEmneee...........eesleglqlWv 108
                                   tAgsGi+h+Em+++             e++ glqlWv
  gi|70608006|ref|YP_256876.1|  96 TAGSGIFHQEMPRPLegteiarynqkPEDMYGLQLWV 132
                                   *************999999****999999*******8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
                                   BSEEEEEEEECSEEE CS
                         Pirin  49 rgletvtylleGeve 63 
                                   +g  ++ y+++G+++
  gi|70608006|ref|YP_256876.1| 200 NGYTVLVYVVDGKIK 214
                                   567788999999986 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.94   8.4e+03      22      44 ..      66      83 ..      60     104 .. 0.53
   2 !   83.2   0.0   1.6e-27   1.4e-23       6     103 ..     190     282 ..     185     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.94
                                  EEEEEEES-EEESSTTEEE-TTE CS
                       Pirin_C 22 aavyvleGelevggerseieeeq 44
                                  ++ + ++G++e ++++     ++
  gi|70608006|ref|YP_256876.1| 66 TVTLLYKGKVEHQDSE-----GN 83
                                  5555566666644443.....33 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 1.6e-27
                                   E-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEEEE----S--EEETTEEE CS
                       Pirin_C   6 leagaelelplpegleaavyvleGelevggerseieeeqlavlg.dgdslvvkaeekgarvlLlaGePlgepvvqyGpfVm 85 
                                   l+   e+++p+++g++++vyv++G+++  ++   i+ ++l++++ +gd++ ++ +    r++L++G+Pl+epv++yGp+Vm
  gi|70608006|ref|YP_256876.1| 190 LD--GEVKIPVKNGYTVLVYVVDGKIKTVNTP-YIDSGNLIIFDrEGDEVDLSGN---GRFILISGRPLNEPVYWYGPIVM 264
                                   44..56778899**************988885.9**********99999999987...9********************** PP

                                   SSHHHHHHHHHHHHTT-T CS
                       Pirin_C  86 ntkeeieqafedyregrf 103
                                   n++e+i +a +d r+g+f
  gi|70608006|ref|YP_256876.1| 265 NSEEQILEALNDLRNGTF 282
                                   *****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1800.55
//
Query:       gi|70608007|ref|YP_256877.1|  [L=606]
Description: acetyl-coenzyme A synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-63  214.6   0.0    2.4e-63  214.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      2e-18   67.1   0.0    4.3e-18   66.1   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    8.1e-10   38.5   0.8    8.1e-10   38.5   0.8    2.4  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.2   0.0     4e-67   2.4e-63      16     423 .]      93     489 ..      81     489 .. 0.82

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 4e-67
                                   E...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                   AMP-binding  16 d...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                   +   +ge +tlTY+++  ++++++++L++  +kkgdr++i+lp+ pe + ++l+i +aG++vvpl +++++e ++  leds
  gi|70608007|ref|YP_256877.1|  93 WmneRGESKTLTYNQVLYESKAVSSWLKR-RYKKGDRIGIYLPMIPEIIPIFLGIIRAGMIVVPLFSGFGKEPIRVRLEDS 172
                                   35567899********************8.8************************************************** PP

                                   TESEEE..E.TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTTSEEEEEEE--SS CS
                   AMP-binding  94 eakvli..a.tvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpddlayiiYTSGTT 171
                                   e+k+++  + t+ +   +++++++  ++ +  +iv+++++ +k +    +e ++ +    +  e+++++d+++iiYTSGTT
  gi|70608007|ref|YP_256877.1| 173 EMKAIFttDlTTRK--DKEINPTENLEDFQVDKIVVERGGKAKVNYISYDEVKKTA---GDGLEKTESEDPLMIIYTSGTT 248
                                   ******54243333..3444455554455555666776665555444444433333...23566899************** PP

                                   SS-EEEEEEHHHH.HHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHH CS
                   AMP-binding 172 GkPKGVmlshrnl.vanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleliek 251
                                   GkPKG+++ h  + + ++a++  + +f++k+++ + +i +l +++g  + +++ +l  ++++l+++ + +d  ++ ++ e+
  gi|70608007|ref|YP_256877.1| 249 GKPKGCVHVHMGFpIKAAADI--YFQFDMKNGELLTWITDLGWMMGP-WLIFGGILLRGQIGLYEGYPGFD--QISHFTED 324
                                   **********66625555554..334778889999999********7.99999999999********9977..57789999 PP

                                   HT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.EEEEEEEEGGGSSECEECHCT CS
                   AMP-binding 252 lkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffralfge.evlegYGlTEttgvvtvlple 330
                                   +k+ ++ +  ++++ +   +g+            +rl+   gep+ pe +  +++l  + ++++  G TE +g +   +  
  gi|70608007|ref|YP_256877.1| 325 FKPGILGLSASLVRSFKGrEGK----------LQVRLAGNTGEPIDPESWNYLYRLIDHnPIINYSGGTEISGGIL-GNYV 394
                                   99****9999999999442322..........23898888**************9998899**************6.3334 PP

                                   TTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEET.CC.EEEEEEEEEEETT CS
                   AMP-binding 331 edkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkgYlkkpeataeafdse.gr.wlrTGDlgrlded 407
                                    ++ k++s   p pg+++ + De+ g++  +++eGel+v +   g+++g+++++++  e+++s  ++ w++ GDl+++d  
  gi|70608007|ref|YP_256877.1| 395 IKEIKASSFNGPSPGTKADVFDES-GKRASPNTEGELVVLSVwpGMTRGFWRDEKRYLETYWSRwDNvWVH-GDLAYYDSH 473
                                   4444577888899**********9.88899********9985449*****************756665777.********* PP

                                   SEEEEEEECCCEEEET CS
                   AMP-binding 408 GyleivgRkkdliklr 423
                                   Gy++ivgR++d+ik++
  gi|70608007|ref|YP_256877.1| 474 GYFYIVGRSDDTIKVS 489
                                   **************85 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   7.1e-22   4.3e-18       1      76 []     497     570 ..     497     570 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 7.1e-22
                                   HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                 AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                   e+Es++++h++V e a+vG+pd++kGe +++f v k++ +   e+eL+ ++ ++lg+   p+++ +v+elpktr+ K
  gi|70608007|ref|YP_256877.1| 497 EIESVINAHQKVLESACVGIPDPLKGEKIICFTVTKEEiN---ENELINFAQDKLGKAFSPDRIFLVKELPKTRNAK 570
                                   8**********************************86643...6*******************************98 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.8   1.4e-13   8.1e-10      12      52 ..      36      80 ..      33      83 .. 0.92
   2 ?   -2.0   0.8      0.57   3.4e+03      14      26 ..     442     456 ..     440     467 .. 0.68

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.4e-13
                                  HHHHHHHHHCC...S--SB--S-SECSTTTC.T-EESTT-EE-HH CS
                        ACAS_N 12 peaFWaeqake...ldWekpfdkvldgskgp.fikWFeGGklNic 52
                                  +eaFW++  k+   l++ekp++k+ld skg+ ++kWF++Gk+Ni+
  gi|70608007|ref|YP_256877.1| 36 NEAFWDDFVKNvlsLKFEKPYTKTLDLSKGKqWAKWFVDGKINIA 80
                                  69********776799*************999***********98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.57
                                   HHHHHHHCC..S--S CS
                        ACAS_N  14 aFWaeqake..ldWe 26 
                                   +FW++  +    +W+
  gi|70608007|ref|YP_256877.1| 442 GFWRDEKRYleTYWS 456
                                   799999986224554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 3503.40
//
Query:       gi|70608008|ref|YP_256878.1|  [L=91]
Description: pterin-4-alpha-carbinolamine dehydratase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-30  104.3   0.0      3e-30  104.2   0.0    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
        0.1   12.4   0.1       0.14   11.9   0.1    1.2  1  DUF1965    Domain of unknown function (DUF1965)


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   3.3e-34     3e-30       2      91 .]       2      90 ..       1      90 [. 0.96

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 3.3e-34
                     Pterin_4a  2 klseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenDfkl 84
                                  kl+e+ei+++l e +gW+  e+++l+++fkfk+f e ++fv +++ +a+e++Hhpd++v yn+v ++l+Th+ gg+te+Df+l
  gi|70608008|ref|YP_256878.1|  2 KLDENEIKRRLGEIEGWSY-ENNKLKKTFKFKNFYESVEFVRKIQPIADEMDHHPDLCVYYNRVVLELSTHSEGGVTEKDFEL 83
                                  799********888****8.7779*********************************************************** PP

                     Pterin_4a 85 Aakidel 91
                                  A+ki+++
  gi|70608008|ref|YP_256878.1| 84 AKKINKI 90
                                  ****986 PP

>> DUF1965  Domain of unknown function (DUF1965)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.6e-05      0.14      25      53 ..      15      43 ..      10      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                                  EEEEEETTEEESSHHHHHHHHTSTT---- CS
                       DUF1965 25 vlGwlyngifYetteeFRaaikspgfkkl 53
                                  ++Gw y+++  + t +F++ ++s +f++ 
  gi|70608008|ref|YP_256878.1| 15 IEGWSYENNKLKKTFKFKNFYESVEFVRK 43
                                  89************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 671.30
//
Query:       gi|70608009|ref|YP_256879.1|  [L=550]
Description: flavin oxidoreductase/NADH oxidase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-58  199.0   0.0    1.9e-58  198.4   0.0    1.2  1  Oxidored_FMN    NADH:flavin oxidoreductase / NADH oxidase fam
      3e-09   37.0   0.0      8e-09   35.6   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.6e-09   34.9   0.0    1.8e-08   34.0   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      2e-08   34.6   0.5    5.2e-07   30.1   0.3    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.1e-05   23.7   0.0    0.00045   19.9   0.0    2.3  2  DAO             FAD dependent oxidoreductase
    0.00064   18.9   0.0      0.018   14.1   0.0    2.7  3  Dus             Dihydrouridine synthase (Dus)
     0.0025   16.6   0.1      0.029   13.1   0.2    2.0  2  HI0933_like     HI0933-like protein
     0.0033   16.7   0.2     0.0049   16.2   0.2    1.2  1  FAD_binding_3   FAD binding domain
     0.0034   17.3   0.0     0.0059   16.5   0.0    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0039   16.5   0.0     0.0064   15.8   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0054   16.0   0.0     0.0098   15.2   0.0    1.3  1  Thi4            Thi4 family
     0.0054   16.2   0.0      0.048   13.1   0.0    2.2  2  BtpA            BtpA family
     0.0068   15.5   0.0       0.01   14.9   0.0    1.2  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.019   14.2   0.0    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.028   13.7   0.0      0.047   13.0   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
      0.034   14.1   0.0       0.11   12.5   0.0    1.9  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.18   11.1   0.0        0.3   10.4   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
        0.2   10.7   0.1        0.3   10.1   0.1    1.2  1  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   1.9e-61   1.9e-58       2     338 ..       3     317 ..       2     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 1.9e-61
                                   CCS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSCCC-.SCTTSEE-SSGGGHHH CS
                  Oxidored_FMN   2 LFkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnpksg.gfdnapgiwdeeqiee 81 
                                   L +P+ki +++LknR+vm+pm    ++++g  +++  + y+ +r++   +l+ite++ vn++   g +n+ g++++e i++
  gi|70608009|ref|YP_256879.1|   3 LLEPFKIADVELKNRVVMSPMITNFGTPEG-YPTETHIRYFVRRSS--LGLLITEYTYVNKTDArGSPNELGLYTDEFIPK 80 
                                   789******************999999999.7888**********9..9**********987555**************** PP

                                   HHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHHHHHHHHH CS
                  Oxidored_FMN  82 wrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefveAAkrai 162
                                   ++ lteavh+++ k++vql h Gr+  +  l     +sp +p++++        +v  +e+tk++i+ +i++fv+AA+ra 
  gi|70608009|ref|YP_256879.1|  81 FARLTEAVHNHDTKIFVQLVHVGRKTRKA-LIW--GNSPVAPSNIPLI-----DPV--REMTKDDINRVIDDFVKAAERAE 151
                                   *************************9333.333..4589988888776.....789..*********************** PP

                                   HTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSSEEEEEECE--STTS--HHHHHHH CS
                  Oxidored_FMN 163 eAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeervgyRlSpedvvekgldfaetaqk 243
                                   + gfDg+e hga+GYL+ qFlsp +nkr Dey    ++ ++Fl e++++Vk++v+   vg R+S+ + ++++    et   
  gi|70608009|ref|YP_256879.1| 152 KSGFDGIELHGAHGYLIAQFLSPATNKREDEY----RDGVKFLEEIIKEVKRVVSI-PVGLRISATE-FDPQGLNPET--- 223
                                   *******************************9....56699***********9874.4******976.6666667788... PP

                                   HHHHCHCCEEEEEEETT-SSSSSTTS-TTTT.HHHCCTTHHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEEST CS
                  Oxidored_FMN 244 ivllkelekrlkdgkklalvhaaeprkrgag.svrteqekntefvkevwkkplitvgriadeekaaeivaegeadLvamgR 323
                                   +  +++  ++l+d+ +l+          +++  ++ ++ ++++ ++++  k l+ +g+i   ++a+++++  +a    ++R
  gi|70608009|ref|YP_256879.1| 224 VGKIAKRVENLLDYLHLSAGRDGPLGGSSSFyYKEPSYLEEAKVIRNQFGKTLLVAGSILTVDDAEKVLEFADAA--VLAR 302
                                   556666666666666666543333222233312333455788*******************99777777765555..579* PP

                                   HHHH-TTHHHHHHCC CS
                  Oxidored_FMN 324 efladpdlveklkkg 338
                                   ++ladpd++ k+k g
  gi|70608009|ref|YP_256879.1| 303 QILADPDWLIKVKDG 317
                                   ************987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   8.1e-12     8e-09       1      41 [.     362     402 ..     362     414 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 8.1e-12
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECET CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevp 41 
                                   IvG+G++Gl +A+ Lak+gf+v l+ek ++lGG++  y++p
  gi|70608009|ref|YP_256879.1| 362 IVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQLNEYKDP 402
                                   9**********************************999874 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.8e-11   1.8e-08     137     230 ..     352     463 ..     334     468 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.8e-11
                                   CCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS...TTS-........HHHHHHHHHHHHHTTEEEEESCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx........xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgkevtlveardrll...rald........kelsaaleealekeGvevklgtsv 206
                                   +l + +  +++vGgG++G+E+A +lak g ev l e  ++l    ++++         +l +++e++l++ Gv+v+l++ +
  gi|70608009|ref|YP_256879.1| 352 ELRKGEGEVNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGgqlNEYKdpfkkasfIKLLEYYEKELKRLGVKVYLNSYI 432
                                   444455789************************999999888766444422222211345579****************** PP

                                   EEEEETTE.....EEE...EEETTSCEEEESE CS
                                   xxxxxxxx.....xxx...xxxxxxxxxxxxx RF
                   Pyr_redox_2 207 keidgnge.....kle...vvledgeeidadl 230
                                   k idg++      + +   +++ +ge+i +d 
  gi|70608009|ref|YP_256879.1| 433 KSIDGHTIfavpsQ-RqpiYQEYKGEVILVDS 463
                                   ****9998766532.23556666666666665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.3   5.2e-10   5.2e-07       2      69 ..     360     438 ..     359     441 .. 0.79
   2 ?   -2.8   0.0        10     1e+04      34      58 ..     487     511 ..     482     519 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.2e-10
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSH...........HHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                     Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDe...........easkilqeklekngievllntkveeiegs 69 
                                   v +vGgG++glE+A +la+ g +V++ e  +kl  +l+e           ++ ++ +++l+++g++v+ln+ +++i+g+
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQLNEykdpfkkasfiKLLEYYEKELKRLGVKVYLNSYIKSIDGH 438
                                   569*******************************77776222222222112334558999999*************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 10
                                   SSTTSSHHHHHHHHHHHHHTTEEEE CS
                     Pyr_redox  34 llrllDeeaskilqeklekngievl 58 
                                   l ++lD+  + +l+ek ++ g++ +
  gi|70608009|ref|YP_256879.1| 487 LFKGLDRNRGYLLEEKYKEIGVREW 511
                                   4478899999999999999999755 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.5e-07   0.00045       2      35 ..     360     394 ..     359     397 .. 0.93
   2 ?    1.1   0.0      0.24   2.4e+02     147     182 ..     410     440 ..     407     461 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.5e-07
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35 
                                   v i+GGG++Gl  A+ La+rg  V l+ek++ +g g
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGfeVKLYEKDSKLG-G 394
                                   569***************************9998.6 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                                   HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEE CS
                           DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgv 182
                                   kl+ ++ +++++lGv++++++ +++++     ++++
  gi|70608009|ref|YP_256879.1| 410 KLLEYYEKELKRLGVKVYLNSYIKSID-----GHTI 440
                                   688899999***********9999993.....3344 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   1.3e+03       9      30 ..      35      55 ..      33      62 .. 0.87
   2 !    5.2   0.0    0.0096       9.5     129     186 ..     132     205 ..     120     207 .. 0.77
   3 !   14.1   0.0   1.8e-05     0.018     110     223 ..     190     311 ..     186     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                  S-HHHHHHHHHTT-SSEEEEEE CS
                           Dus  9 tdlpfRelvrefgataLvvtem 30
                                  t+ ++R++vr+ + + L++te 
  gi|70608009|ref|YP_256879.1| 35 TETHIRYFVRRSSLG-LLITEY 55
                                  7899***********.999985 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0096
                                   EESESSTTTC.HHHHHHHHHHCT-SEEEEESS..............ECCCTT-C..G--CHHHHHHHHH-SS-E CS
                           Dus 129 irigiddeeenalelakiveaaGaqaltvHgR..............traqnyeg..tadweaIkevkqavsipv 186
                                   ++  i+   ++ +++a+++e++G + + +Hg                r+++y+   +   e Ikevk+ vsipv
  gi|70608009|ref|YP_256879.1| 132 TKDDINRVIDDFVKAAERAEKSGFDGIELHGAhgyliaqflspatnKREDEYRDgvKFLEEIIKEVKRVVSIPV 205
                                   55555556678899*****************9999******999655556666644444467899999999998 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHCCSSS-EEEEEESE.SS...TTTC.HHHHHHHHHHCT-SEEEEE.SS......ECCCTT-CG--CHHHHHHH CS
                           Dus 110 vaqivkavvkaveiPvtvkirig.id...deeenalelakiveaaGaqaltvH.gR......traqnyegtadweaIkevk 179
                                   +++i+k+v++ v+iPv ++i+    d    + e+  ++ak+ve+   + l +  gR      +    y+++ ++e+ k ++
  gi|70608009|ref|YP_256879.1| 190 LEEIIKEVKRVVSIPVGLRISATeFDpqgLNPETVGKIAKRVENL-LDYLHLSaGRdgplggSSSFYYKEPSYLEEAKVIR 269
                                   7899**************998651563333345555666666665.4444443478*9999666666667*********** PP

                                   HH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHH CS
                           Dus 180 qavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlf 223
                                   +++  ++++ G I +++da+++le   ad+ + +r  l +P  +
  gi|70608009|ref|YP_256879.1| 270 NQFGKTLLVAGSILTVDDAEKVLEF--ADAAVLARQILADPDWL 311
                                   *************************..**************554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   2.9e-05     0.029       3      37 ..     360     394 ..     358     397 .. 0.92
   2 ?    1.1   0.0      0.12   1.2e+02     110     146 ..     410     444 ..     403     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                                   EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                   HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                   v ++GgG  Gl  A  +akrg +V l+ek +klg 
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGG 394
                                   789*****************************996 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEE CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvk 146
                                   ++++ ++kelk+ gvk++l++ +ks+  + + +f v 
  gi|70608009|ref|YP_256879.1| 410 KLLEYYEKELKRLGVKVYLNSYIKSI--DGHTIFAVP 444
                                   679999*******************9..555555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   4.9e-06    0.0049       3      35 ..     359     391 ..     357     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                   +V IVG+G +Gl  a++L+++G +v l ek s+
  gi|70608009|ref|YP_256879.1| 359 EVNIVGGGVTGLEMARVLAKRGFEVKLYEKDSK 391
                                   799**********************99999875 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.9e-06    0.0059       2      33 ..     360     391 ..     359     431 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdisee 33 
                                   v ++G G+ G ++a v+a++g+eV+l++ +++
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDSK 391
                                   89*************************98765 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.5e-06    0.0064      29      81 ..     358     415 ..     353     487 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.5e-06
                                   -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.....TTTCECEEHCHH CS
                   AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.....lgakfvevlksq 81 
                                   ++v ++GgGv Gl+ +++ ++ g +V++++++++   ql++      +a+f+++l+  
  gi|70608009|ref|YP_256879.1| 358 GEVNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQLNEykdpfKKASFIKLLEYY 415
                                   7899******************************999999944443344555554444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.9e-06    0.0098      17      55 ..     357     394 ..     353     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.9e-06
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                   e +v ivG+G +GL  a++lak+ +++v + e+   +GG
  gi|70608009|ref|YP_256879.1| 357 EGEVNIVGGGVTGLEMARVLAKR-GFEVKLYEKDSKLGG 394
                                   56899******************.*********999998 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   4.8e-05     0.048      20      87 ..     132     209 ..     124     214 .. 0.72
   2 ?   -0.1   0.0      0.53   5.2e+02     190     230 ..     263     304 ..     257     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                          BtpA  20 ykanleevidkAvkeakaleegGvDavilen...y....gdaPflke.vd..petvaamtvivkevksdvsiplGvnv 87 
                                    k++++ vid  vk a+  e++G+D++ l     y    +  P  ++  d  +  v  +  i+kevk+ vsip+G+ +
  gi|70608009|ref|YP_256879.1| 132 TKDDINRVIDDFVKAAERAEKSGFDGIELHGahgYliaqFLSPATNKrEDeyRDGVKFLEEIIKEVKRVVSIPVGLRI 209
                                   5789**********************976531112111133344333133113469999****************865 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.53
                          BtpA 190 eelklaketvk.vkvlvgsGvseenlekllsiadGvivgtsi 230
                                   ee k++++    +  ++gs  + +++ek+l++ad  +++ +i
  gi|70608009|ref|YP_256879.1| 263 EEAKVIRNQFGkTLLVAGSILTVDDAEKVLEFADAAVLARQI 304
                                   55556655555588899999999999*******999998776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05      0.01       2      32 ..     360     390 ..     359     408 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkl 32 
                                   v+++GgG  G+e A  +a++G++v+L+ ++ 
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDS 390
                                   99*************************5543 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.019     165     241 ..     358     438 ..     351     481 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                   Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke.....ekikvlfnaevkeike 240
                                    +v ++Gg+ ++ ++A  l+++g eV+++ ++s++  + ++++   k     +l e++++     + +kv+ n+ +k+i+ 
  gi|70608009|ref|YP_256879.1| 358 GEVNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQLNEYKDPFKKASFIKLLEYYEKelkrlG-VKVYLNSYIKSIDG 437
                                   5799******************************99999999998888888788777777675533.99999999999986 PP

                   Pyr_redox_3 241 k 241
                                   +
  gi|70608009|ref|YP_256879.1| 438 H 438
                                   5 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.047       2      35 ..     368     401 ..     367     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEE CS
                 Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrs 35 
                                   +GL  Ar L+ +Gf+V ++E ++ +GG ++ +++
  gi|70608009|ref|YP_256879.1| 368 TGLEMARVLAKRGFEVKLYEKDSKLGGQLNEYKD 401
                                   8**************************9887765 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.11       2      43 ..     360     401 ..     359     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSS CS
                NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehe 43 
                                   + ++G+G  G  +A+vla++g ev+l+ ++++l  ++ne + 
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQLNEYKD 401
                                   889*****************************9999998765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003       0.3       2      38 ..     360     396 ..     359     399 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38 
                                   v +vGGg+ G+  A   a++G +v L e++  lGG+l
  gi|70608009|ref|YP_256879.1| 360 VNIVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQL 396
                                   78*********************************97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00031       0.3       4      38 ..     362     396 ..     359     397 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                                   EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
                 FAD_binding_2   4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38 
                                   ++G+G+ GL  A  +a++G +v + ek ++ gg++
  gi|70608009|ref|YP_256879.1| 362 IVGGGVTGLEMARVLAKRGFEVKLYEKDSKLGGQL 396
                                   9*****************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3869.96
//
Query:       gi|70608010|ref|YP_256880.1|  [L=1007]
Description: tricorn protease [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-24   84.6   0.0      1e-23   83.1   0.0    1.9  1  Tricorn_PDZ    Tricorn protease PDZ domain
    6.4e-23   80.6   2.6      2e-22   79.0   2.6    1.9  1  Tricorn_C1     Tricorn protease C1 domain
    6.6e-22   77.8   0.0    1.3e-21   76.8   0.0    1.6  1  Peptidase_S41  Peptidase family S41
    1.4e-12   47.2  14.2    2.4e-05   24.1   1.2    5.8  6  PD40           WD40-like Beta Propeller Repeat
     0.0001   21.2   0.3       0.16   10.7   0.0    4.2  3  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
      0.009   16.3   0.0      0.038   14.3   0.0    2.1  1  PDZ_2          PDZ domain


Domain annotation for each model (and alignments):
>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   0.0   3.4e-27     1e-23       1      88 []     709     795 ..     709     795 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 3.4e-27
                                   -B-SEEEEEET..TEEEEEEE-BS-TTSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-S CS
                   Tricorn_PDZ   1 GlLGadleldk..gayriakilpGdswdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvkrk 79 
                                   G LGa++++d+  ++++i ki++Gd+++e +rSPL++pGv+++eGd+i+++dge+v+k  +i++++++k++  + L+v ++
  gi|70608010|ref|YP_256880.1| 709 GGLGAEFNYDEqrECFKIVKIYSGDPTNEGERSPLKDPGVELNEGDCIYSIDGEKVRK-GSINSHFINKDQ--AILEVLTS 786
                                   89********54699*****************************************98.7**********9..99****** PP

                                   TT-EEEEEE CS
                   Tricorn_PDZ  80 dgkarrvvv 88 
                                   dgk+r+v v
  gi|70608010|ref|YP_256880.1| 787 DGKNRTVSV 795
                                   ******987 PP

>> Tricorn_C1  Tricorn protease C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   2.6   6.7e-26     2e-22       1      69 [.     630     697 ..     630     698 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 6.7e-26
                                   HHHHHHHHHHHHHHHHHHSS-HH.HHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--S---EE- CS
                    Tricorn_C1   1 eaEwaqmfdeawrllrdkFydpd.mhgvDWeavkerYepllprvatrdeladllsemlgeLntsHvyvsg 69 
                                   e+Ew+qm+ e+w+l++++++ ++ ++   W++v+++Ye+ll+rv+tr+el+d+l+em+ge +tsH+y+++
  gi|70608010|ref|YP_256880.1| 630 EKEWRQMLFETWKLMKENYWSAEkLQ--GWDSVLDKYEKLLDRVSTRYELSDVLKEMQGETKTSHSYETP 697
                                   58*******************95255..799************************************875 PP

>> Peptidase_S41  Peptidase family S41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   4.5e-25   1.3e-21       1     166 []     824     979 ..     824     979 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 4.5e-25
                                   EEEEEEES-BCCTHHHHHHHHHHHHHH.TTSSEEEEE-TTB-EBEHHHHHHHHHCCSSSSEEEEEECTTSEEEEEEHTCSS CS
                 Peptidase_S41   1 kiGyiripsfsektkeelakalkelkk.knvkglilDlRnNgGGlldeavelaslflddglivstrgrdgkkkkkskteka 80 
                                   k+Gy+++p++    ++ +a++++ + +    +gli+D+R+N+GG ++ ++    l+ ++g+ v+++g++            
  gi|70608010|ref|YP_256880.1| 824 KLGYVHVPDM---MYQGFAEFFRLFISeFYRQGLIVDVRFNRGGFISGLILQRLLLRREGYDVPRNGERIPFP-------- 893
                                   68********...6677777777666645599*******************************9998888877........ PP

                                   -STT-BSSEEEEEE-TTBBTHHHHHHHHHHHTTSEEEEES-.-SB-EEEEEEEE-TTSSEEEEEEEEEEETTSBC.TTTTS CS
                 Peptidase_S41  81 seevqykgplvvLvnegsaSaseifagalkdngratlvGer.tfGkgtvqsvvelndgsalkltiakyltpdgrs.iekkG 159
                                     + +  + +v ++ne+  S+++if++++k++++++l+G+r ++G  +++    l d+++++ +   ++  + +  ie+ G
  gi|70608010|ref|YP_256880.1| 894 --YLSSPKVIVAVTNENAGSDGDIFSYLFKKYKIGILIGRRtWGGVIGISPRHLLVDKTVVTQPEFAAIFDEVGLgIENYG 972
                                   ..45699**********************************66666666666666999999988766665555555***** PP

                                   ---SEE- CS
                 Peptidase_S41 160 vePdiev 166
                                   v+Pdiev
  gi|70608010|ref|YP_256880.1| 973 VDPDIEV 979
                                   *****97 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.1e-06    0.0032       3      26 ..      30      53 ..      28      54 .. 0.92
   2 ?   -1.2   0.0      0.74   2.2e+03      22      37 ..     192     206 ..     191     207 .. 0.86
   3 !    4.9   0.0    0.0086        26      17      27 ..     230     240 ..     228     246 .. 0.89
   4 !    5.2   0.0    0.0071        21      16      29 ..     364     377 ..     356     377 .. 0.78
   5 ?   -2.9   0.2       2.5   7.4e+03       7      23 ..     397     413 ..     395     414 .. 0.85
   6 !   24.1   1.2     8e-09   2.4e-05       3      35 ..     437     470 ..     435     474 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-06
                                  E--SSSS.EEEEEE-TTSSEEEEE CS
                          PD40  3 rltntpgnegaPsfSPDGkrlaFs 26
                                  r+t+ +g  + P +SPDGkr+aF+
  gi|70608010|ref|YP_256880.1| 30 RVTTDTGVSIKPKISPDGKRIAFT 53
                                  789999999**************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.74
                                   EEEEEEECT.TCEEEE CS
                          PD40  22 rlaFsSdRgsGkpdIy 37 
                                   r +F Sd +   +++y
  gi|70608010|ref|YP_256880.1| 192 RVYFLSDHE-SVSNLY 206
                                   78*****99.999998 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0086
                                   -TTSSEEEEEE CS
                          PD40  17 SPDGkrlaFsS 27 
                                   S DGkr++F +
  gi|70608010|ref|YP_256880.1| 230 SSDGKRIVFQR 240
                                   99*******76 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0071
                                   E-TTSSEEEEEEEC CS
                          PD40  16 fSPDGkrlaFsSdR 29 
                                    SPDGk+l +s +R
  gi|70608010|ref|YP_256880.1| 364 ASPDGKKLLISNNR 377
                                   6*******998665 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 2.5
                                   SSS.EEEEEE-TTSSEE CS
                          PD40   7 tpgnegaPsfSPDGkrl 23 
                                   + g++ ++ + P G ++
  gi|70608010|ref|YP_256880.1| 397 SYGIIREFDWHPTGEWF 413
                                   678999999***99885 PP

  == domain 6  score: 24.1 bits;  conditional E-value: 8e-09
                                   E--SSSS.EEEEEE-TTSSEEEEEEECT..TCEE CS
                          PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRg.sGkpd 35 
                                   r+t+  + +++Psf+PDGk l+F S R+ + ++d
  gi|70608010|ref|YP_256880.1| 437 RVTSPYAFDFSPSFDPDGKFLYFLSARTlDPSSD 470
                                   78888999*******************9877777 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   5.4e-05      0.16      22      95 ..      15      88 ..      10      99 .. 0.85
   2 ?    1.6   0.1     0.032        96     294     343 ..     191     236 ..     189     254 .. 0.63
   3 ?    2.9   0.0     0.012        37       3      60 ..     367     416 ..     358     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.4e-05
                                  TTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEETTEEEEESTTTSEEEECES-S...TTTEEESB--HHH CS
                       DPPIV_N 22 taeyyiydletneveelspgeeklqlakwSPagdklafvrnnnLyvrelatgkeiqlTsdg...sagifnGvadWvy 95
                                   +++++  l++ +  +++ +++    +k+SP+g+++af+    L++r+ ++g  + +++dg     ++fn  ++Wv+
  gi|70608010|ref|YP_256880.1| 15 DDDVWLMSLKDMRPIRVTTDTGVSIKPKISPDGKRIAFTT---LWLRSGKQGADVFIVEDGrskRVTYFNRPTTWVA 88
                                  578999999999999999999*****************96...9*****99**********8655556677777774 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.032
                                   TEEEEEESSSETTEBEEEEEESSCTTEEEESSTTTSEE.EEEEE-TTSSEE CS
                       DPPIV_N 294 dlvyFtatkdsPlerhlYsvslesggeltrltdeegdh.ysasfspsgkyy 343
                                   d+vyF +  +s   ++lYsv+++ g++l +  +++ +  y    s++gk++
  gi|70608010|ref|YP_256880.1| 191 DRVYFLSDHES--VSNLYSVDMQ-GENLLK--HTNFSDyYCRNASSDGKRI 236
                                   78999998887..7889999998.444333..2233332344444444444 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.012
                                   TSSEEEEEECEEEESSSEETTEEEEEETTTEECEEEETT.TT.BSEEEEESSTTEEEEE CS
                       DPPIV_N   3 dgkflllatnaeknwRhsytaeyyiydletneveelspg.eeklqlakwSPagdklafv 60 
                                   dgk+ll+          + + e+++ydle+++ + + ++  + +  ++w P+g+++++ 
  gi|70608010|ref|YP_256880.1| 367 DGKKLLI---------SNNRLELWLYDLESKKEKLIDKSsYGIIREFDWHPTGEWFSYA 416
                                   5555555.........2335578999999988888888888999999********9996 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.3e-05     0.038       1      74 [.     709     802 ..     709     807 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                   ....XX------..-EEEEEE-TTSGGGGT.--T..........T-EEEEETTB--..........SSHHHHHHHHHTS-T CS
                         PDZ_2   1 pylGvsvsdeedtggvlvvsVkeggPaakaglka..........gDvilkvdgkkv..........ksledlislllkkkp 61 
                                   ++lG+++  +e+ +   +v++++g+P ++    +          gD i+++dg kv          ++++ + + l +  +
  gi|70608010|ref|YP_256880.1| 709 GGLGAEFNYDEQRECFKIVKIYSGDPTNEGERSPlkdpgvelneGDCIYSIDGEKVrkgsinshfiNKDQAILEVLTSDGK 789
                                   57999999999999999999999999887765557779999999************7776666666666666699999999 PP

                                   T-EEEEEEEETTE CS
                         PDZ_2  62 GdtVkltvlRdgk 74 
                                   ++tV+++++ d k
  gi|70608010|ref|YP_256880.1| 790 NRTVSVRLMKDEK 802
                                   9999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1007 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 6128.06
//
Query:       gi|70608011|ref|YP_256881.1|  [L=275]
Description: ATP binding transporter [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-24   85.6   0.1    9.2e-24   84.5   0.0    1.6  2  ABC_tran     ABC transporter
    4.3e-13   49.8   0.0    1.6e-08   34.7   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00035   20.1   0.3       0.24   10.8   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0022   18.4   0.2      0.008   16.6   0.0    2.0  3  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.018   14.8   0.3      0.035   13.9   0.3    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.022   15.3   0.3      0.027   15.0   0.2    1.6  1  AAA_23       AAA domain
      0.022   14.5   0.0        1.5    8.5   0.2    2.3  2  AAA_15       AAA ATPase domain
      0.032   14.2   0.1        0.1   12.5   0.0    1.8  2  Rad17        Rad17 P-loop domain
      0.032   13.4   0.5       0.16   11.2   0.0    2.0  2  NB-ARC       NB-ARC domain
      0.036   14.5   0.0       0.05   14.0   0.0    1.3  1  AAA_16       AAA ATPase domain
      0.037   13.9   0.5      0.073   13.0   0.1    1.7  2  RsgA_GTPase  RsgA GTPase
      0.045   14.1   0.1      0.083   13.2   0.1    1.4  1  DUF4959      Domain of unknown function (DUF4959)
       0.06   12.0   0.1      0.087   11.5   0.1    1.2  1  AAA_13       AAA domain
      0.069   13.4   0.0       0.75   10.1   0.0    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.095   12.8   1.0       0.37   10.8   0.2    2.0  2  DUF87        Helicase HerA, central domain
       0.13   12.6   0.1       0.32   11.3   0.1    1.8  2  AAA_22       AAA domain
       0.13   12.2   0.2       0.53   10.2   0.1    2.0  2  NACHT        NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   8.7e-27   9.2e-24       2     136 ..      19     160 ..      18     161 .. 0.92
   2 ?   -2.0   0.0       4.6   4.9e+03      39      48 ..     229     238 ..     177     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8.7e-27
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                   +n+++k  + +++ ++G+nGaGK+tL+++l+ +l pt+G+ +++g d+ + e +++rk i+ +pqe++    ++ +e+   
  gi|70608011|ref|YP_256881.1|  19 DNLNFKS-NVKVLSVLGRNGAGKTTLVRILSTQLLPTSGTARINGLDIVK-EAKKVRKLISSIPQEARPVGMSSPYEHllm 97 
                                   5666663.457899***********************************9.9**************999999999999*** PP

                                   ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             e++e   k l+ +gl e++d++      +LSgG+k+++ +a+a++++++l++lDEpt
  gi|70608011|ref|YP_256881.1|  98 yltargmsisEAREISRKTLKDIGLWEVRDKPT----DELSGGMKRKIFVAMAIASNAELIFLDEPT 160
                                   ***9999975555558999999*****999999....*****************************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.6
                                   EEEEEETTCE CS
                                   xxxxxxxxxx RF
                      ABC_tran  39 eGeilldgkd 48 
                                    Gei++ + +
  gi|70608011|ref|YP_256881.1| 229 TGEIKVGKMK 238
                                   3444444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   5.9e-05     0.062       4      20 ..      32      48 ..      29      88 .. 0.80
   2 !   34.7   0.0   1.5e-11   1.6e-08     235     298 ..     131     188 ..     105     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                        AAA_21  4 liGpNgsGKSnLLdald 20
                                  + G+Ng+GK++L ++l+
  gi|70608011|ref|YP_256881.1| 32 VLGRNGAGKTTLVRILS 48
                                  68**************5 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.5e-11
                        AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                   +elS G+kr ++++ a+++ +    l+++DEp  gL+P   ++++ +lke+   +++++ltTH 
  gi|70608011|ref|YP_256881.1| 131 DELSGGMKRKIFVAMAIASNA---ELIFLDEPTVGLDPYSRTEVWSILKEA---DSKLVLTTHY 188
                                   578*******99999999999...9***********************999...56*******5 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.2    0.0024       2.5      18      41 ..      21      44 ..       6      52 .. 0.72
   2 !   10.8   0.0   0.00023      0.24     136     209 ..     132     200 ..      59     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0024
                                  EEEETTSSEEEEEESTTSSHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 18 vilpfsksftaivGpNGSGKsnll 41
                                     + + ++ +++G+NG+GK+ l+
  gi|70608011|ref|YP_256881.1| 21 LNFKSNVKVLSVLGRNGAGKTTLV 44
                                  444445566789*********987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka.dklv 209
                                   +LSgG k  + +a+ +A    + a l +lDe    LD   +++v ++lke+   + ++ +++  e  e+  d++v
  gi|70608011|ref|YP_256881.1| 132 ELSGGMKRKIFVAMAIA----SNAELIFLDEPTVGLDPYSRTEVWSILKEAD--SKLVLTTHYMEEAEELsDEIV 200
                                   89999999888887766....56789************************99..777777776665555425555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.6e-06     0.008       3      57 ..      32      83 ..      30      93 .. 0.79
   2 ?   -2.5   0.0       6.1   6.5e+03      54      66 ..     148     158 ..     125     159 .. 0.63
   3 ?   -2.7   0.0         7   7.3e+03      23      27 ..     196     200 ..     173     226 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.6e-06
                                  EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                           AAA  3 lyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfkeakeka 57
                                  + G  G GKT+l++ + ++l   +   +i+g +++     + +kk+r+l++++ ++a
  gi|70608011|ref|YP_256881.1| 32 VLGRNGAGKTTLVRILSTQLlpTSGTARINGLDIV-----KEAKKVRKLISSIPQEA 83
                                  6799***************9666889*********.....55666666666554444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.1
                                   HHTSTSEEEEEET CS
                           AAA  54 kekakpsilfiDE 66 
                                    +  +   +f+DE
  gi|70608011|ref|YP_256881.1| 148 AS--NAELIFLDE 158
                                   22..247888888 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7
                                   THEEE CS
                           AAA  23 gvefl 27 
                                   + e++
  gi|70608011|ref|YP_256881.1| 196 SDEIV 200
                                   22222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   3.3e-05     0.035      24      55 ..      29      61 ..      14      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                        AAA_29 24 atlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                  +  + G++G+GK+Tl+  +++ L+p++ ++r N
  gi|70608011|ref|YP_256881.1| 29 VLSVLGRNGAGKTTLVRILSTQLLPTSgTARIN 61
                                  57899***********99999999988666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   2.6e-05     0.027      15      41 ..      21      49 ..       9     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                        AAA_23 15 idF..skgltlItGpNGaGKTTildAikl 41
                                  ++F  + ++  + G NGaGKTT+++ +  
  gi|70608011|ref|YP_256881.1| 21 LNFksNVKVLSVLGRNGAGKTTLVRILST 49
                                  4553255778889**********998765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0014       1.5      19      44 ..      21      48 ..      16      83 .. 0.83
   2 ?    3.9   0.0     0.035        37     288     364 ..     124     187 ..      64     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                        AAA_15 19 idlsee..ltvliGkNnsGKSsileald 44
                                  ++++++  +  + G+N++GK++++++l 
  gi|70608011|ref|YP_256881.1| 21 LNFKSNvkVLSVLGRNGAGKTTLVRILS 48
                                  6777776667788***********9995 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                        AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   +  + p ++ + G++r +++++ i+++ +          ++++EP + L p   ++++  lke+  d+  ++++tTH
  gi|70608011|ref|YP_256881.1| 124 EVRDKPTDELSGGMKRKIFVAMAIASNAEL---------IFLDEPTVGLDPYSRTEVWSILKEA--DS--KLVLTTH 187
                                   556678899999**********99999999.........*********9999999999888875..22..6788888 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05       0.1      43     112 ..      26      95 ..      12     124 .. 0.75
   2 ?   -1.3   0.0       1.7   1.8e+03      47      68 ..     199     220 ..     176     247 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                         Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgi.klrewlnpvslkepdnqksdfkgltekesrflsqiesfkel 112
                                   +  ++L + G  G gk+t v++Ls +l + +    +n++ + +   ++  + + + +e r + +   ++ l
  gi|70608011|ref|YP_256881.1|  26 N-VKVLSVLGRNGAGKTTLVRILSTQLLPtSGTARINGLDIVKEAKKVRKLISSIPQEARPVGMSSPYEHL 95 
                                   3.569999****************98876156788999998888888887777777777665555555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                         Rad17  47 iLLisGPsGCgkstvvkvLske 68 
                                   i+Li      +k tv   Lsk 
  gi|70608011|ref|YP_256881.1| 199 IVLIHKGKLISKGTVEDLLSKF 220
                                   5555555555555555555553 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.16       9      38 ..      18      45 ..      13      56 .. 0.83
   2 ?   -0.1   0.1      0.41   4.4e+02      92     170 ..     137     219 ..     105     237 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                  HHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                        NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlak 38
                                   ++L  k +++  v+++ G+ G GKttl++
  gi|70608011|ref|YP_256881.1| 18 LDNLNFKSNVK--VLSVLGRNGAGKTTLVR 45
                                  56666678888..***************86 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                                   HHHHHHHHCCCT..TEEEEEEEE-SHHH.H.....HHHHCHTTSEEEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHH CS
                        NB-ARC  92 lkrklvrlLltk..rfllvlDDVweeed.wdkigvvlparenrlrvllTTRdeevanavsat.sekievelLekdeawell 168
                                   +krk++ ++       l+ lD      d + ++ v    +e  ++ +lTT  +e a++ s++    ++ +l++k    +ll
  gi|70608011|ref|YP_256881.1| 137 MKRKIFVAMAIAsnAELIFLDEPTVGLDpYSRTEVWSILKEADSKLVLTTHYMEEAEELSDEiVLIHKGKLISKGTVEDLL 217
                                   566666555433325555566533333335555555555678888888888888888888876666666666666666666 PP

                                   HH CS
                        NB-ARC 169 en 170
                                   ++
  gi|70608011|ref|YP_256881.1| 218 SK 219
                                   55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.7e-05      0.05      25      87 ..      28      81 ..      15     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                        AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlld 87
                                   ++ + G  G GK++lvr l ++l  +   ++r +  +         + +a + ++l+  + +
  gi|70608011|ref|YP_256881.1| 28 KVLSVLGRNGAGKTTLVRILSTQLLPT-SGTARINGLDI--------VKEAKKVRKLISSIPQ 81
                                  6789******************99998.33333333332........3333333344444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.9e-05     0.073      87     122 ..      15      50 ..       3      82 .. 0.83
   2 ?   -3.2   0.0       6.4   6.7e+03      49      67 ..     198     215 ..     175     230 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                                   HTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                   RsgA_GTPase  87 kegleelkellkdktsvlvGqSGvGKStLinallpe 122
                                   +++l++l+ + + k+  ++G  G+GK+tL+  l  +
  gi|70608011|ref|YP_256881.1|  15 TKALDNLNFKSNVKVLSVLGRNGAGKTTLVRILSTQ 50 
                                   56788899999999999*************999877 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.4
                                   EEEEEE-GGG--HHHHHHH CS
                   RsgA_GTPase  49 pvivlnKiDlleeeeelee 67 
                                    ++++ K  l+++ + +e+
  gi|70608011|ref|YP_256881.1| 198 EIVLIHKGKLISKGT-VED 215
                                   344455555555554.443 PP

>> DUF4959  Domain of unknown function (DUF4959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.9e-05     0.083      60      97 ..     212     249 ..     205     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                       DUF4959  60 erevkaSvykdsltveGFgdtkeyevklyavsrseneS 97 
                                   ++e   S++kd+++veG g++k  ++k++ v+r+e e 
  gi|70608011|ref|YP_256881.1| 212 TVEDLLSKFKDKVRVEGTGEIKVGKMKISYVDRKEAET 249
                                   577889****************************9876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.2e-05     0.087      22      39 ..      33      50 ..      21      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                        AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                   G+NGaGKTtL r+l+ +
  gi|70608011|ref|YP_256881.1| 33 LGRNGAGKTTLVRILSTQ 50
                                  6*************9875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00072      0.75      27      89 ..     127     176 ..     108     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00072
                       SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                   ++ + +lSGG k++++      a+a +         + +l+fLDE   +lD+ s++++ ++l+
  gi|70608011|ref|YP_256881.1| 127 DKPTDELSGGMKRKIF-----VAMAIAS--------NAELIFLDEPTVGLDPYSRTEVWSILK 176
                                   5666777777773332.....2222222........3479**************999999886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00035      0.37      26      49 ..      30      53 ..      26      68 .. 0.87
   2 ?    0.1   0.0      0.69   7.3e+02     115     152 ..     190     229 ..     163     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                         DUF87 26 lAilgsTGsGKSntvavLleelle 49
                                  l +lg+ G+GK+++v++L  +ll 
  gi|70608011|ref|YP_256881.1| 30 LSVLGRNGAGKTTLVRILSTQLLP 53
                                  579****************99984 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                         DUF87 115 avqrsvleealdqakakeekeklssdepveklleelk...k 152
                                   ++ +++ +e++  +k ++++ k ++++++ k++++++   +
  gi|70608011|ref|YP_256881.1| 190 EEAEELSDEIVLIHK-GKLISKGTVEDLLSKFKDKVRvegT 229
                                   445556666666555.7888899999999998888885552 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0003      0.32       6      30 ..      28      52 ..      24     158 .. 0.81
   2 ?   -1.5   0.0       2.7   2.8e+03      41      41 ..     198     198 ..     146     239 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                        AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                                  ++l v G  G+GKTtl+r l  ql 
  gi|70608011|ref|YP_256881.1| 28 KVLSVLGRNGAGKTTLVRILSTQLL 52
                                  578899************9999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                        AAA_22  41 e 41 
                                   e
  gi|70608011|ref|YP_256881.1| 198 E 198
                                   1 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0005      0.53       2      23 ..      29      50 ..      28      58 .. 0.86
   2 ?   -1.1   0.0       1.5   1.6e+03     119     164 ..      70     118 ..      60     119 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                                  CEEEEC-TTTCHHHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                  ++ + G++G GKTtL++ l ++
  gi|70608011|ref|YP_256881.1| 29 VLSVLGRNGAGKTTLVRILSTQ 50
                                  56799***********988765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                                   T--EEEEEEECCCHHH..HCTTSSCE...EEEE--TCCHHHHHHHHCTT CS
                         NACHT 119 peasllltvrpralrd..leeqleea.ivlevegfsesrrkqlvrkyfs 164
                                   ++++ l+++ p+  r   + +  e+   +l  +g+s s+++++ rk+++
  gi|70608011|ref|YP_256881.1|  70 KKVRKLISSIPQEARPvgMSSPYEHLlMYLTARGMSISEAREISRKTLK 118
                                   5566666666666655333333333377788888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1887.82
//
Query:       gi|70608012|ref|YP_256882.1|  [L=249]
Description: hypothetical protein Saci_2303 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-05   23.9  26.4    2.4e-05   23.9  26.4    1.5  2  ABC2_membrane    ABC-2 type transporter
    0.00066   18.9  34.1    0.00066   18.9  34.1    1.9  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.029   15.1   7.1      0.029   15.1   7.1    1.9  2  Tmemb_14         Transmembrane proteins 14C


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9  26.4     4e-09   2.4e-05      21     193 ..      30     194 ..       9     209 .. 0.77
   2 ?   -3.5   0.1      0.96   5.7e+03     107     120 ..     223     237 ..     214     242 .. 0.45

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4e-09
                 ABC2_membrane  21 gllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakv 101
                                     ++ +i+pl  ++++ +v  +      g++++g l+ +v  +++s+l+   ++   e ++ + + ++ + ++ +y+l+ +
  gi|70608012|ref|YP_256882.1|  30 V-VTYMITPLAELFLIYVVTRG---ALIGYAIMGGLVAIVAGNGISFLADF-AFLRLETKIQDLLVATEV-TPTEYILGLM 104
                                   3.55566666666666666662...33444569999999999**7777777.555566677777777777.********** PP

                 ABC2_membrane 102 lvelpvsllqalifll..ivyflvgldlsrfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffi 180
                                   l++l++s+  ++++++  + y lv++    ++ ++l+l+l++l++ss+g+li+++ p+++    l+s++ ++l++l ++f+
  gi|70608012|ref|YP_256882.1| 105 LSNLIFSIPGIALYIVlaVLYRLVNILN--ILPIVLVLVLLLLTTSSIGFLIGSFIPHIRYSWGLGSILSILLTVLPPVFY 183
                                   *******966666666215555655544..7************************************************** PP

                 ABC2_membrane 181 pidsmpkwlqwia 193
                                   p+  +pk   +++
  gi|70608012|ref|YP_256882.1| 184 PYFLIPKT--AFY 194
                                   **999843..233 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.96
                 ABC2_membrane 107 vsllqalifll.ivy 120
                                   ++ ++ li+ + i+y
  gi|70608012|ref|YP_256882.1| 223 YGSIALLIVETvIFY 237
                                   333333333332333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   6.6      0.15   8.7e+02     215     263 ..      27      74 ..      10      78 .. 0.80
   2 !   18.9  34.1   1.1e-07   0.00066     162     342 ..      56     239 ..      54     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
               ABC2_membrane_3 215 lvyllqlllilll.afglgipfgnlglllllfllfglayialgyllsslf 263
                                   ++y+++++++ l  +f   i +   g+l+ + +++gl++i+ g  +s+l 
  gi|70608012|ref|YP_256882.1|  27 TIYVVTYMITPLAeLFL--IYVVTRGALIGYAIMGGLVAIVAGNGISFLA 74 
                                   46666666666655555..7777889*********************995 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-07
               ABC2_membrane_3 162 flvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afglgipfgnlgll 241
                                    ++g +++i++  ++sf+a +     e++i  l++ + v+p++y+l+ +l+ ++ ++  ++l+++l ++ + +++ n++ +
  gi|70608012|ref|YP_256882.1|  56 AIMGGLVAIVAGNGISFLADFAFLRLETKIQDLLVATEVTPTEYILGLMLSNLIFSIPGIALYIVLaVLYRLVNILNILPI 136
                                   5677778888888888888777777899*************************************87777699999***** PP

               ABC2_membrane_3 242 lllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli....t 318
                                   +l+++l +l+++++g+l++s++   +   +l +i+++ll ++  +++p   +p+++ ++ + iP++  ++ l +l      
  gi|70608012|ref|YP_256882.1| 137 VLVLVLLLLTTSSIGFLIGSFIPHIRYSWGLGSILSILLTVLPPVFYPYFLIPKTAFYAIFPIPTTLGAMILQDLTglihL 217
                                   ************************************************99*************************866652 PP

               ABC2_membrane_3 319 gdplweil.lsliilalfavvylll 342
                                       +++l  s+++l++++v++  l
  gi|70608012|ref|YP_256882.1| 218 ---SSNVLyGSIALLIVETVIFYYL 239
                                   ...356777************9876 PP

>> Tmemb_14  Transmembrane proteins 14C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   7.1   4.8e-06     0.029       9      89 ..      46     147 ..      40     154 .. 0.92
   2 ?   -2.7   0.1       1.7     1e+04      53      53 ..     226     226 ..     200     244 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-06
                      Tmemb_14   9 llavGGilgYlkagSvpSLiaGlllGallllagyllsknkkakelsl.....................vislvlllvmgkr 68 
                                   +++ G ++gY+  g +++++aG ++++l+ +a  +l+++ ++  +++                     +i+l ++l+ ++r
  gi|70608012|ref|YP_256882.1|  46 VVTRGALIGYAIMGGLVAIVAGNGISFLADFAFLRLETKIQDLLVATevtpteyilglmlsnlifsipGIALYIVLAVLYR 126
                                   67889**************************9999988888877777889999999************************* PP

                      Tmemb_14  69 llktrkfmpaglvavlsalml 89 
                                   l++   ++p++lv+vl +l++
  gi|70608012|ref|YP_256882.1| 127 LVNILNILPIVLVLVLLLLTT 147
                                   *************98877665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                      Tmemb_14  53 l 53 
                                   +
  gi|70608012|ref|YP_256882.1| 226 I 226
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1586.61
//
Query:       gi|70608013|ref|YP_256883.1|  [L=276]
Description: hypothetical protein Saci_2304 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-16   59.2  28.9    2.2e-15   56.7  28.9    1.9  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00027   21.0  20.4    0.00027   21.0  20.4    2.4  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.029   13.5  41.9     0.0048   16.0  37.8    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7  28.9   3.7e-19   2.2e-15      83     288 .]      66     271 ..       4     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3.7e-19
               ABC2_membrane_2  83 vlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledlll 163
                                   +l+ ++a+ +++ + ++E+e+gT+ + L+kP++R + ++ K++g++ +   ++v+++  v+l+l+++  l  v ++ +++ 
  gi|70608013|ref|YP_256883.1|  66 LLLHFLAISIASGSMSEEYEQGTVDFFLTKPITRLQFYIQKWLGSFSL---LVVIYVLMVILSLFLSYTLFGVQEYLEYFW 143
                                   567788******************************************...888888888889999887777777777777 PP

               ABC2_membrane_2 164 lvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlyg..vaellagpavp..........qeindf 232
                                   + + sv++  l vf+ +++ +  ++r s+ +  ++ + ++   ++++++l+   ++++ +++  +          +++  +
  gi|70608013|ref|YP_256883.1| 144 ITIISVIFSSL-VFFCISFSVGEILRRSSLSFIISSFTLIGSILVSDVLLFIsfLTNNTSYE--SiatylpswgsTQLPFI 221
                                   77777766665.58*****************9999999999988888877653233444433..25588888888888888 PP

               ABC2_membrane_2 233 lsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrkDl 288
                                   l+  sp s++++ ++ ++  +       ++  +l++++++++++v++++lF r+D+
  gi|70608013|ref|YP_256883.1| 222 LLSSSPLSNITQFIDMFPIQG------NAWVAVLSIVVYTLIPFVISLYLFSRRDI 271
                                   888888888888888888888......69*************************96 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  20.4   4.5e-08   0.00027      10     177 ..      15     182 ..      13     184 .. 0.70
   2 ?   -3.6   5.9       1.6   9.5e+03     111     142 ..     178     210 ..     170     268 .. 0.44

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-08
               ABC2_membrane_4  10 krskivwllvlaallvpllallyfnllgk....tgldpaefyslsvfgftll....lllplilgiiasylifrEeqndtlk 82 
                                   +r+ iv+++++ +  +++ + l+ +l+ +    t+l p   y+++ +g+  l    lll ++ + ias ++++E++++t+ 
  gi|70608013|ref|YP_256883.1|  15 RRKVIVLITISFI--FEIAVYLALYLVPSqtvrTYLIPIYPYTWA-IGT--LlpqdLLLHFLAISIASGSMSEEYEQGTVD 90 
                                   5555555555544..454443443334430011444445555553.222..22345999999999**************** PP

               ABC2_membrane_4  83 nLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvl.lk 162
                                     lt P++r ++++ K +  + l v++++    ++v+++l++ ++ f v+  le ++++++ ++++ +++  i + v  + 
  gi|70608013|ref|YP_256883.1|  91 FFLTKPITRLQFYIQKWLGSFSLLVVIYV----LMVILSLFLSYTLFGVQEYLEYFWITIISVIFSSLVFFCISFSVGeIL 167
                                   *****************999887777765....577888899999999999999999888888888877777766443377 PP

               ABC2_membrane_4 163 ksyvlpliltlvyti 177
                                   + + l+ i++ +  i
  gi|70608013|ref|YP_256883.1| 168 RRSSLSFIISSFTLI 182
                                   788888888777655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.6
               ABC2_membrane_4 111 lvtflitvlfallsgfvgfsvklvl.ellkkcl 142
                                    +t++ ++l++ ++ f++f ++ +  e++  +l
  gi|70608013|ref|YP_256883.1| 178 SFTLIGSILVSDVLLFISFLTNNTSyESIATYL 210
                                   455555555555555555444332202333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.16   9.8e+02     270     309 ..      19      54 ..      14      70 .. 0.56
   2 ?   16.0  37.8   8.1e-07    0.0048     171     342 ..      68     257 ..      35     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.16
               ABC2_membrane_3 270 qilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                   ++li+i +++ ++++++l++++  + +++  +++iP++ +
  gi|70608013|ref|YP_256883.1|  19 IVLITISFIFEIAVYLALYLVP--SQTVR--TYLIPIYPY 54 
                                   3444444443455555555443..33333..555555555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.1e-07
               ABC2_membrane_3 171 lifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.......afglgipfg..nlglll 242
                                   l f+ +s+++ s+ eE e+++  + l+ ++++lq+++ k lg+f + +++++l+++l       +fg  ++ +   +++++
  gi|70608013|ref|YP_256883.1|  68 LHFLAISIASGSMSEEYEQGTVDFFLTKPITRLQFYIQKWLGSFSLLVVIYVLMVILslflsytLFG--VQEYleYFWITI 146
                                   44556666778899***************************************99964434555555..666673445566 PP

               ABC2_membrane_3 243 llfllfglayialgyllsslfknsetaqilifivil...llsgffgglfpledlpsalkwifsiiPffapglgllrlitgd 320
                                   + +++ +l++ ++++ ++ + ++s+  +i+ +++++   l s +++++ +l   +++   i+ ++P++  +++ + l++  
  gi|70608013|ref|YP_256883.1| 147 ISVIFSSLVFFCISFSVGEILRRSSLSFIISSFTLIgsiLVSDVLLFISFLT-NNTSYESIATYLPSWGSTQLPFILLSSS 226
                                   888888******************9999888888776554444444443332.3666777777777777777777777544 PP

               ABC2_membrane_3 321 plwe.........illsliilalfavvylll 342
                                   pl++         i  + ++ +l++vvy+l+
  gi|70608013|ref|YP_256883.1| 227 PLSNitqfidmfpIQGNAWVAVLSIVVYTLI 257
                                   4444555555555667777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1875.75
//
Query:       gi|70608014|ref|YP_256884.1|  [L=294]
Description: copper transport ATP-binding protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-27   96.2   0.0    7.2e-27   94.6   0.0    1.7  2  ABC_tran   ABC transporter
    8.1e-07   29.1   0.4      0.015   15.1   0.2    2.3  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00017   22.3   0.4    0.00053   20.7   0.4    1.9  1  DUF4162    Domain of unknown function (DUF4162)
     0.0068   16.1   0.0      0.015   15.0   0.0    1.5  1  AAA_29     P-loop containing region of AAA domain
      0.007   16.4   0.1      0.016   15.2   0.1    1.5  1  TsaE       Threonylcarbamoyl adenosine biosynthesis protein T
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.019   15.3   0.0    1.5  1  AAA_16     AAA ATPase domain
      0.011   16.1   0.2       0.07   13.6   0.2    2.3  1  AAA        ATPase family associated with various cellular act
      0.018   14.7   0.1      0.027   14.2   0.1    1.4  1  AAA_30     AAA domain
      0.037   14.5   3.3      0.064   13.7   0.1    2.1  2  AAA_23     AAA domain
      0.042   13.7   3.0       0.51   10.2   0.1    2.8  3  NTPase_1   NTPase
      0.074   12.0   0.0       0.16   10.9   0.0    1.5  1  MeaB       Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.11   12.8   0.4       0.29   11.4   0.4    1.8  1  RelA_SpoT  Region found in RelA / SpoT proteins
       0.13   12.4   0.0       0.45   10.7   0.0    1.8  2  AAA_33     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   5.2e-30   7.2e-27       1     135 [.      17     154 ..      17     155 .. 0.95
   2 ?   -1.3   0.0       2.2     3e+03      54      96 ..     190     242 ..     167     268 .. 0.61

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 5.2e-30
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l+n sl++ +ge+v ++G+nGaGK+t++++++ l +p  G+i++ gkd  +   +s+ +++g++++ p+l p lt r+   
  gi|70608014|ref|YP_256884.1|  17 LNNFSLTITRGEIVTLLGPNGAGKTTFVRIVLALIRPSGGKIEIFGKDPFK--DKSVFSRLGYVQELPNLPPFLTGRQVll 95 
                                   79*******************************************777777..6999999**************99999** PP

                                   .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                   .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                          ++++e++++l  +g++e +d+ +    s++S+G+ qr+a+a+all +p++l++DEp
  gi|70608014|ref|YP_256884.1|  96 lsanikgARKDEVDELLGVIGMVENADKQI----SKYSKGMVQRIAIAEALLGNPEILIMDEP 154
                                   ****99999999************999998....****************************9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                   HHHCCHCEEEE-SS--S-TTSBHHHH...........HHHTCHHHHHHHSTTGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxx RF
                      ABC_tran  54 leslrkeigvlpqepqlfpeltvren...........esdeeiekalsklglke 96 
                                    ++   ++  + + +++f+++t +e            e+d++++++l+kl+ +e
  gi|70608014|ref|YP_256884.1| 190 VKKIADRLILINKGNKMFEGST-EELikkflgirviiEADNNAKEILDKLSYVE 242
                                   4444445555555555555552.2225566777777777777777777776555 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.1e-05     0.015       2      40 ..      30      62 ..      29      79 .. 0.70
   2 !   12.2   0.0   8.2e-05      0.11     234     300 ..     125     188 ..      68     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                        AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40
                                    l GpNg+GK+++ ++   l      +++++ +   +g
  gi|70608014|ref|YP_256884.1| 30 VTLLGPNGAGKTTFVRIVLAL------IRPSGGKIEIFG 62
                                  5799*************9665......444444444444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.2e-05
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellkelsrngaQviltTHSpl 300
                                   +++ S G+ + +a++ all  +    +l+ DEp  g++P     +r+ll   ++l++ g+ +++t+H+ +
  gi|70608014|ref|YP_256884.1| 125 ISKYSKGMVQRIAIAEALLGNP---EILIMDEPNIGIDPifnLNVRSLL---NKLKKSGTLILMTSHDLE 188
                                   5566999988889999999888...9*************8777778888...6666666779*****976 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.4   3.8e-07   0.00053       1      67 [.     209     278 ..     209     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.8e-07
                                   E-HHHHHTTS-SSEEEEE..-------..--.-EEEE-TTS-EEEEE-------------.----EEEEEE CS
                       DUF4162   1 GtleeiKrsygknrieve..adaeelleepg.veeveeeggelelkledeeaanellkal.tsgveirsFe 67 
                                   G+ ee+ +++ + r+ +e  ++a+e+l+  + vee + +g+++ +kl++ +++++llk+l  +gv+++sF 
  gi|70608014|ref|YP_256884.1| 209 GSTEELIKKFLGIRVIIEadNNAKEILDKLSyVEEYTADGEKYYVKLRE-DKREDLLKELvLNGVRVKSFY 278
                                   788899999999999999766688888888879999*999********8.69********88*******96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.015      16      49 ..      21      54 ..      13      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                  +++i++ +++ l Gp+G+GK+T++  + al+ p+
  gi|70608014|ref|YP_256884.1| 21 SLTITRGEIVTLLGPNGAGKTTFVRIVLALIRPS 54
                                  567776669999***********97777777665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.2e-05     0.016      18      41 ..      22      49 ..       4      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                  H....TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE 18 l....gdvilLeGdLGaGKTtlvrglak 41
                                  l    g++++L G+ GaGKTt+vr +++
  gi|70608014|ref|YP_256884.1| 22 LtitrGEIVTLLGPNGAGKTTFVRIVLA 49
                                  03345788****************8875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.4e-05     0.019      22      54 ..      25      57 ..      15     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                        AAA_16 22 grpelvllsGesGvGKsslvrellralekdggi 54
                                   r+e+v l G+ G GK++ vr +l  ++ +gg 
  gi|70608014|ref|YP_256884.1| 25 TRGEIVTLLGPNGAGKTTFVRIVLALIRPSGGK 57
                                  4569********************888877544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   5.1e-05      0.07       2      66 ..      31     153 ..      30     196 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                                   EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS........................................ CS
                           AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellsk........................................ 37 
                                    l Gp G GKT++++ v   +     +   +ei g++ +++                                        
  gi|70608014|ref|YP_256884.1|  31 TLLGPNGAGKTTFVRIVLALIrpsggK---IEIFGKDPFKDksvfsrlgyvqelpnlppfltgrqvlllsanikgarkdev 108
                                   699**************9987332221...333333333112333333333333333333333333333333333344466 PP

                                   ........STTHHHHHHHHHHHHH.HHTS.......TSEEEEEET CS
                           AAA  38 ........yvgesekkirelfkea.keka.......kpsilfiDE 66 
                                           +v+++ k+i+++ k + ++ a       +p il++DE
  gi|70608014|ref|YP_256884.1| 109 dellgvigMVENADKQISKYSKGMvQRIAiaeallgNPEILIMDE 153
                                   677777765555555555444442122223344456677777777 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-05     0.027      15      52 ..      25      61 ..      19     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                        AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                  t g  +++l Gp G+GKtt ++ + ++++ +gg++ ++
  gi|70608014|ref|YP_256884.1| 25 TRG-EIVTLLGPNGAGKTTFVRIVLALIRPSGGKIEIF 61
                                  444.5999*********************999887665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.7e-05     0.064      20      37 ..      28      45 ..       9      80 .. 0.83
   2 ?    1.5   0.7      0.25   3.5e+02     128     176 ..     173     243 ..      91     269 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                        AAA_23 20 gltlItGpNGaGKTTild 37
                                   ++ + GpNGaGKTT+++
  gi|70608014|ref|YP_256884.1| 28 EIVTLLGPNGAGKTTFVR 45
                                  467889*********986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.25
                        AAA_23 128 kkiilnlilflgqer................feefel..kdkkerleelekeleeledekkllekl....e 176
                                    k++ +lil+   +                 +++fe   ++  ++   ++  +e  ++ k+ l+kl    e
  gi|70608014|ref|YP_256884.1| 173 LKKSGTLILMTSHDLeevkkiadrlilinkgNKMFEGstEELIKKFLGIRVIIEADNNAKEILDKLsyveE 243
                                   44444444444444322222222222222221233322333333444444444444444444444422231 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00037      0.51       2      30 ..      30      58 ..      29      67 .. 0.88
   2 ?    2.3   0.1       0.1   1.4e+02      90     142 ..     139     195 ..     115     214 .. 0.77
   3 ?   -0.0   0.0      0.52   7.2e+02      49      84 ..     252     286 ..     224     294 .] 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
                                  EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                  v + Gp G GKtT+v+ vl l++ sg k+
  gi|70608014|ref|YP_256884.1| 30 VTLLGPNGAGKTTFVRIVLALIRPSGGKI 58
                                  5677****************999888766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.1
                                   HHHH.HHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHH CS
                      NTPase_1  90 rkal.seadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalve 142
                                    +al  +++++++DE  iG    +  ++++ ++++ ks++ +l++ h  +  +++ +
  gi|70608014|ref|YP_256884.1| 139 AEALlGNPEILIMDEpnIGIDPIFNLNVRSLLNKLKKSGTLILMTSHDLEeVKKIAD 195
                                   344447889999999999999999999999999999999999999998754334444 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.52
                                   EEET.T--EEEEEETT---SSEETTEEE-HHHHHHH CS
                      NTPase_1  49 ivdlasgeegiLarveakreprvgkyvvdvesfeel 84 
                                   +v+l +++++ L ++   +++rv+++++d +++e+ 
  gi|70608014|ref|YP_256884.1| 252 YVKLREDKREDLLKELVLNGVRVKSFYLD-NDIERA 286
                                   45666667777777777777777777776.455555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.16      18      70 ..      16      68 ..       7      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                  HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                          MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                  +l++ + +  r + v l G  GaGk t+v  + + +r  G ++ +   DP   
  gi|70608014|ref|YP_256884.1| 16 VLNNFSLTITRGEIVTLLGPNGAGKTTFVRIVLALIRPSGGKIEIFGKDPFKD 68
                                  66777777889999********************************9999665 PP

>> RelA_SpoT  Region found in RelA / SpoT proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00021      0.29      21      67 ..     209     256 ..     165     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                   CCCCCCSSTSEEEEEEESSHHHHHHHHHHHHT-SSSEEEEEEETST.S CS
                     RelA_SpoT  21 eekfeeitDligiRvivefkddvyevlelikklwdvkpkrfkdyia.e 67 
                                    ++ e i+  +giRvi+e  ++ +e+l+ ++  ++++ + +k y++ +
  gi|70608014|ref|YP_256884.1| 209 GSTEELIKKFLGIRVIIEADNNAKEILDKLSYVEEYTADGEKYYVKlR 256
                                   4567889999*****************************999998742 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00032      0.45       2      20 ..      30      48 ..      29      73 .. 0.89
   2 ?   -1.7   0.0       2.2     3e+03      81     114 ..     256     289 ..     248     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                        AAA_33  2 vllvGlpGsGKstlaerll 20
                                  v l G++G+GK+t+++ +l
  gi|70608014|ref|YP_256884.1| 30 VTLLGPNGAGKTTFVRIVL 48
                                  7789**********99765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                        AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlkeR 114
                                   ++++r+++lk +   gv+v+  +++ d e + eR
  gi|70608014|ref|YP_256884.1| 256 REDKREDLLKELVLNGVRVKSFYLDNDIERAYER 289
                                   6788999999988999999999999988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1993.40
//
Query:       gi|70608015|ref|YP_256885.1|  [L=621]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-58  198.1   0.0    3.1e-58  197.3   0.0    1.4  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
      2e-34  119.2   1.1    5.5e-34  117.8   0.4    2.0  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
      5e-11   42.8   0.5    7.2e-10   39.1   0.0    2.9  3  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.6e-08   33.0   0.1    1.4e-07   31.5   0.1    1.8  1  Transketolase_C  Transketolase, C-terminal domain
    0.00034   20.3   0.4     0.0027   17.3   0.5    2.3  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   0.0   8.7e-62   3.1e-58       2     225 ..     236     477 ..     235     484 .. 0.88

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 8.7e-62
                                   HHHHCTEEEEEE--BTTTCC..HHHHHCHCCCCCTT......EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHH CS
                         POR_N   2 aaiaagvdviaaYPITPsse..iaeelaellakgev......gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllL 74 
                                   ++ia+g++++++YPITP+s+  ++ e+++ +++         g v+vvq+e+E++ai+++iGAa++Gar+ TaTSg+G++L
  gi|70608015|ref|YP_256885.1| 236 GKIAGGLRFQSYYPITPASDesVYIEANQNVDMIVEgnelrkGGVVVVQAEDELAAINMAIGAALTGARTSTATSGPGFSL 316
                                   7899****************999999999998877678899977************************************* PP

                                   CCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                         POR_N  75 mienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                   m e l +a+++e+Pvv+++++R+ pstgl++r  q Dl +a+     +++ iv+as+++ e+f++ ++A+nlAe++++Pvi
  gi|70608015|ref|YP_256885.1| 317 MAEGLSWAGMNEVPVVVTYYMRGAPSTGLPTRSGQADLKFALnaghgEFPRIVIASGDHHEIFWDSIWALNLAERYQTPVI 397
                                   ********************************************************************************* PP

                                   EEEEHHHH.HEEEEEEC-SGG.GS.....-----SBXXXXXXXX...SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHH CS
                         POR_N 151 vlfDgfllshevekvelpdeedel.....klikekleeyerkey...aldpekpiargtaanpdtglehrekgneaedaae 223
                                   +++++ l+ ++++ ++  + + ++     kl+k+  ++ +r+++   +++p+   + g+    +tg+eh+e+g+++e++++
  gi|70608015|ref|YP_256885.1| 398 HIIEKALA-NAYSLIDEDSIKGQIkidrgKLVKQVGDRFNRFQPsddGISPRV--FLGQSSIFYTGDEHNEEGHITENSLN 475
                                   ********.99999988777644401111556666666666666766666665..5699999***************9665 PP

                                   HH CS
                         POR_N 224 kv 225
                                     
  gi|70608015|ref|YP_256885.1| 476 RT 477
                                   43 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.4   1.5e-37   5.5e-34       2     176 ..       7     206 ..       4     207 .. 0.96
   2 ?   -1.7   0.0      0.74   2.7e+03      75      88 ..     274     287 ..     266     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 1.5e-37
                                   TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEE CS
                           POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggii 82 
                                   G Gv t ++++++a+araGyy ++nrey s+i+G+hsy++v ++++ +v+si+  + ++l  +daetl++h+++++   ++
  gi|70608015|ref|YP_256885.1|   7 GLGVDTSANVFSNAIARAGYYLFGNREYYSNIKGRHSYFEVVFDEK-PVRSIS-SYTNILATFDAETLFQHFTEVT--DFV 83 
                                   88********************************************.9*****.*********************9..99* PP

                                   EEECTCGTT-CCHHHCTS-HHHHHHH.......................T-EEEEE-HHHHHHHCCC.........CCHHH CS
                           POR  83 iynseelkpdelkkakeeerelkerl.......................gvrvygvdatkiakeiggn........eraaN 132
                                   iy + + ++++++  k++e+e++e+                        g++v+++d+ +i+k+i+ +        era+N
  gi|70608015|ref|YP_256885.1|  84 IYGT-DYATTNIDMVKSMEPEMAEQIkqllsenkmgytikdvitylknkGIKVIELDYLDILKKIAAElkvqvsvvERAKN 163
                                   **99.679************99998899******************************999997777777779999***** PP

                                   HHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                           POR 133 tvmlGalaallglplealeeaikkrfpkkkeviekNlkafragy 176
                                   ++++Ga+++llglp++ le  i+  f++   ++++N+ a++ gy
  gi|70608015|ref|YP_256885.1| 164 MAAVGASIGLLGLPFDILENTISSIFRND-LFVKMNVMAAKIGY 206
                                   ***************************97.8************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.74
                                   GEEEEEEEEEECTC CS
                           POR  75 glkpggiiiynsee 88 
                                   +l++gg++++++e+
  gi|70608015|ref|YP_256885.1| 274 ELRKGGVVVVQAED 287
                                   799******99965 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.22     8e+02      13      29 ..     119     135 ..      98     139 .. 0.88
   2 ?   -3.3   0.1       3.3   1.2e+04      49      66 ..     148     166 ..     142     171 .. 0.59
   3 !   39.1   0.0     2e-13   7.2e-10       1     102 []     506     600 ..     506     600 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHTT--E CS
                       PFOR_II  13 gtaksavdelReegikv 29 
                                    t+k+++  l+++gikv
  gi|70608015|ref|YP_256885.1| 119 YTIKDVITYLKNKGIKV 135
                                   57899999999999998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                                   STT-S.EEEEEE-S--TT- CS
                       PFOR_II  49 lkkvk.kvvvldrnisfgs 66 
                                   ++++k +v v++r+ ++ +
  gi|70608015|ref|YP_256885.1| 148 AAELKvQVSVVERAKNMAA 166
                                   4444425778888876655 PP

  == domain 3  score: 39.1 bits;  conditional E-value: 2e-13
                                   -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                       PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                   A++v+++ Gs  g + +a+ el ++gik+ +++++++ P+P++ +k+ll++++k+v ++ n++     + + ev a  ++ 
  gi|70608015|ref|YP_256885.1| 506 ADIVLITWGSPKGAILDAMSELEKDGIKTMMVQVKMFNPYPTKLVKKLLEGKSKIVAVENNYQ-----AQGAEVLAEKTG- 580
                                   9*************************************************************4.....444555555433. PP

                                   TSEEEEEE--GGG----HHHH CS
                       PFOR_II  82 kvkvvnfvaglgGrditvedi 102
                                    + + n+v +  Gr it e+i
  gi|70608015|ref|YP_256885.1| 581 -IFATNYVLKWSGRPITREEI 600
                                   .36778888888888887775 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   3.8e-11   1.4e-07       9      76 ..     505     572 ..     498     585 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.8e-11
                                   TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSH CS
               Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGi 76 
                                     d++l+++Gs     l+A+ eLek+gi++  v +  ++p  +++++++++ + ++v ve++++  G 
  gi|70608015|ref|YP_256885.1| 505 DADIVLITWGSPKGAILDAMSELEKDGIKTMMVQVKMFNPYPTKLVKKLLEGKSKIVAVENNYQAQGA 572
                                   679************************************************************96664 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   7.7e-07    0.0027      33     103 ..     274     341 ..     261     362 .. 0.82
   2 ?   -1.2   0.0      0.38   1.4e+03      82     127 ..     385     435 ..     381     443 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.7e-07
                                   CHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CC CS
                  TPP_enzyme_N  33 alseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrpts 103
                                   +l++  g+ vv+a +E +a+++A g a          +tsgpG+  +  +l  A  + +P++v    r++ 
  gi|70608015|ref|YP_256885.1| 274 ELRKG-GVVVVQAEDELAAINMAIGAALTGA--RTSTATSGPGFSLMAEGLSWAGMNEVPVVVTYYMRGAP 341
                                   44555.7999****************98875..4567789**********************987666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                                   HHHHHHHHT--EEEEEEE--CCCHH...S..TC--T..-CCHHHCCCSSEE CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg...qgvlqqel..dqlalfrpvtkya 127
                                   al  A + ++P++++   + +   +   ++ +++++  d  +l+++v   +
  gi|70608015|ref|YP_256885.1| 385 ALNLAERYQTPVIHIIEKALANAYSlidEDSIKGQIkiDRGKLVKQVGDRF 435
                                   6777999999**999776655555555555555555557777777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 4461.45
//
Query:       gi|70608016|ref|YP_256886.1|  [L=303]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-31  108.9   0.2      3e-31  108.3   0.2    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      9e-25   86.6   0.3      2e-24   85.5   0.3    1.6  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.2   3.4e-35     3e-31       2     153 .]      43     192 ..      42     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 3.4e-35
                                   SSHHHHHHHHHHTTSSSSEEEC...ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt...sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvv 78 
                                   iGc+            ++++++    g+++ +G++l++A+G+kla+p+ ev++ vGDG+ l i + ++++  rrn++it++
  gi|70608016|ref|YP_256886.1|  43 IGCSGK----------MPHFVNlpvGGVHTLHGRALAFATGIKLANPSLEVIVNVGDGDGLGIgMGHFVHLGRRNIDITLI 113
                                   566666..........67777777678****************************************************** PP

                                   EEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  79 vlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   v++N++yg+t+gq   +  +g k+ks p++++ + v++ ++a ++G +  ar   +dv +l+e++k+a+++kg+a+i+v
  gi|70608016|ref|YP_256886.1| 114 VHDNGVYGLTKGQaapTLERGIKTKSLPKPNINDAVNPLAVALSAGYTfIARAYAYDVIHLKEVIKRAIKHKGSAIIDV 192
                                   *************999889999**************************888999***********************98 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.3   2.2e-28     2e-24       1      62 [.     196     268 ..     196     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.2e-28
                                   XTTTXSSSXSXXXXX-EEEGGGS.T---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHH CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerle 62 
                                   C+t+N++nT +wY++rvykl++d ++Dp +         +ekAl k++e+g+kip+G+fY+ e +pt+eerle
  gi|70608016|ref|YP_256886.1| 196 CPTYNDINTKEWYDKRVYKLDKDpTWDPVVrkeeekqskFEKALLKSMEFGEKIPIGVFYEnELVPTFEERLE 268
                                   ***********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2327.68
//
Query:       gi|70608017|ref|YP_256887.1|  [L=111]
Description: hypothetical protein Saci_2308 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.5   0.4     0.0021   18.0   0.4    1.2  1  TBPIP           TBPIP/Hop2 winged helix domain
  ------ inclusion threshold ------
      0.043   13.7   1.3      0.083   12.8   0.2    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.095   13.0   0.0       0.17   12.1   0.0    1.5  1  preATP-grasp_3  pre ATP-grasp 3 domain
       0.14   11.9   0.2       0.16   11.7   0.2    1.2  1  DUF2785         Protein of unknown function (DUF2785)
       0.39   10.4   2.3          2    8.1   1.5    2.4  2  STAS            STAS domain


Domain annotation for each model (and alignments):
>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.4   5.9e-07    0.0021       3      50 ..      52      97 ..      50     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.9e-07
                         TBPIP  3 eelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiie 50
                                  ++++l++l+e  +P+ v+++ + l +  + + + kaL eL++egk++e
  gi|70608017|ref|YP_256887.1| 52 KQVILDLLKE--KPMDVKEIHSILTNLASDEKIRKALYELAEEGKVVE 97
                                  6788888876..8********************************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.42   1.5e+03      20      34 ..      19      33 ..       9      36 .. 0.70
   2 ?   12.8   0.2   2.3e-05     0.083      12      61 ..      53     104 ..      48     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.42
                                  HCCCHHCHHCCCTTS CS
                          TrmB 20 lgpatadeiaeelgv 34
                                  ++ ++ +ei e+l+v
  gi|70608017|ref|YP_256887.1| 19 KEDKKRKEIEEKLEV 33
                                  556666777777776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.3e-05
                                   CHCHHHHHHCCCHHCHHCCCTT..SSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                          TrmB  12 kvYlaLlklgpatadeiaeelg..vprskvYevLrsLedkGlVerekgrpkl 61 
                                   +v l Llk++p++++ei+++l    +  k+ ++L +L + G V   k+++k+
  gi|70608017|ref|YP_256887.1|  53 QVILDLLKEKPMDVKEIHSILTnlASDEKIRKALYELAEEGKVVEDKKTRKF 104
                                   56789***************97445889*************99998888765 PP

>> preATP-grasp_3  pre ATP-grasp 3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.9e-05      0.17      27      54 ..      24      51 ..      17      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                preATP-grasp_3 27 eedvdetfrrlaaeaDaVlvIAPEtdgi 54
                                  +++  e ++ + ++ D+++vIAPE d++
  gi|70608017|ref|YP_256887.1| 24 RKEIEEKLEVVYDDDDLTVVIAPEEDEL 51
                                  56777888889999**********9987 PP

>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   4.5e-05      0.16     108     153 ..      41      86 ..      16     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                       DUF2785 108 svlaadEdeRlatailalleknkleeetllawleelrqelakkepl 153
                                   +v++a E+++l ++il ll+++ ++ +++++ l +l+ + + +++l
  gi|70608017|ref|YP_256887.1|  41 TVVIAPEEDELKQVILDLLKEKPMDVKEIHSILTNLASDEKIRKAL 86 
                                   899********************************97655555544 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.5   0.00055         2      11      61 ..       2      64 ..       1      87 [. 0.82
   2 ?   -0.9   0.0      0.34   1.2e+03      23      51 ..      78     105 ..      71     110 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00055
                                  EEEEEEEEESHHHHHHHHHHHHHHHHCCC....................-SEEEEEEEEEEEE CS
                          STAS 11 lilrldgpidfanaesfkeklkravgeeperve............kkeslkslildlsavsfi 61
                                  li+ ++g ++  +++ +ke+ kr++ ee+++v             ++++lk +ildl +   +
  gi|70608017|ref|YP_256887.1|  2 LIINMEGVVYMSSVGVIKEDKKRKEIEEKLEVVyddddltvviapEEDELKQVILDLLKEKPM 64
                                  688888889999999999999998888888888899999999999999999999998655555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHCCC........-SEE CS
                          STAS  23 naesfkeklkravgeepervekkeslksl 51 
                                   + e++++ l++ ++e++  ve+k+  k++
  gi|70608017|ref|YP_256887.1|  78 SDEKIRKALYELAEEGK-VVEDKKTRKFM 105
                                   56778888888888874.44455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1238  (0.0690501); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 777.21
//
Query:       gi|70608018|ref|YP_256888.1|  [L=115]
Description: hypothetical protein Saci_2309 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 829.26
//
Query:       gi|70608019|ref|YP_256889.1|  [L=236]
Description: hypothetical protein Saci_2310 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-20   72.2   0.0    4.5e-20   71.9   0.0    1.0  1  RmlD_sub_bind  RmlD substrate binding domain
    5.5e-05   22.7   0.0    7.6e-05   22.3   0.0    1.2  1  Epimerase      NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0     5e-24   4.5e-20      45     230 ..      30     205 ..      20     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 5e-24
                                   HHHHHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHH CS
                 RmlD_sub_bind  45 ellkeakpdvvvnaAAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvY 125
                                   +++ke +pdvv+++      D+a s +++a ++n   + ++A+ a+++g++ +++St   FdG+k   Y+e++++ Pln+Y
  gi|70608019|ref|YP_256889.1|  30 RVIKE-RPDVVIHT-YEIPYDEANSSKALAWNINTWHAINIARSANKIGITNVYLSTFLLFDGKKG-YYSETSTPTPLNYY 107
                                   45555.9******7.56789*******************************************965.5************* PP

                                   HHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG CS
                 RmlD_sub_bind 126 GrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekel 206
                                   G tKl GE  +  +  ++li+R + v + + ++ +  + +   ++  +k     + sP   ++ +e+++ l++k ++    
  gi|70608019|ref|YP_256889.1| 108 GLTKLVGESGIM-SLGNYLIIRLGLVTSFNYHSIAYYLYKASLKKRIIKCNTNFYVSPITLNEASEITAGLIKKGIK---- 183
                                   ***********9.7789*********999999999999999999999999999999999999999999999999886.... PP

                                   -EEEE---BS-EEHHHHHHHHHHH CS
                 RmlD_sub_bind 207 agvyHlanegetswlefArailke 230
                                    gv  +a+++  s +e+ r i ++
  gi|70608019|ref|YP_256889.1| 184 -GVVNVAGKR-RSMFEVCRDIGES 205
                                   .777666666.5666666666555 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   8.5e-09   7.6e-05      55     152 ..      27     117 ..      19     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.5e-09
                                   HHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS- CS
                     Epimerase  55 alerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgp 135
                                   a +r++ke +pd+vih   +   +a+s++ a  +++n+  + n++  a+k g+   ++ls+  ++  ++    +et   + 
  gi|70608019|ref|YP_256889.1|  27 AGDRVIKE-RPDVVIHTYEIPYDEANSSK-ALAWNINTWHAINIARSANKIGI-TNVYLSTFLLFDGKKGY-YSET---ST 100
                                   56789996.********777777777776.555********************.99******999977773.3333...46 PP

                                   ---SSHHHHHHHHHHHH CS
                     Epimerase 136 lkpnspYaaaKlagekl 152
                                     p + Y+++Kl ge+ 
  gi|70608019|ref|YP_256889.1| 101 PTPLNYYGLTKLVGESG 117
                                   78***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1870.46
//
Query:       gi|70608020|ref|YP_256890.1|  [L=116]
Description: hypothetical protein Saci_2311 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 834.36
//
Query:       gi|70608021|ref|YP_256891.1|  [L=350]
Description: tRNA and rRNA cytosine-C5-methylase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-31  108.3   0.1    1.3e-30  106.5   0.1    1.9  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00074   19.3   0.2     0.0016   18.2   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.099   12.2   0.0       0.16   11.5   0.0    1.3  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   0.1   2.2e-34   1.3e-30       3     199 ..     169     348 ..     167     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 2.2e-34
                                   HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--..SEEEEES-CTCCHHHHCC..EE CS
               Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt..ntivleaDarkidkvlggelfD 81 
                                   +L+p+++++ilDl++aPG K + i++l +nk++++  d++keRl++     k++gv+   + +l +D +       ++++ 
  gi|70608021|ref|YP_256891.1| 169 ALKPEPNDHILDLASAPGIKVSQIMQLTENKAKLIVADVDKERLEKERLLFKKFGVNvdRLELLLVDSSSL---AIKRKVN 246
                                   79******************************************988888887777644788888998887...44568** PP

                                   EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEE CS
               Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162
                                   ++LlDaPCs+ g+i  +p + lr + + + ++a +q++ll+ a   +k g  ++Y+TCs+ +eE e  +++   +r+    
  gi|70608021|ref|YP_256891.1| 247 KVLLDAPCSSSGAIWNEPTILLRLTREKVLHYADQQRKLLNNA---VKLGDEVIYATCSMFMEEGELIVNDYTTQRP---- 320
                                   ****************************************976...789********************99988883.... PP

                                   ESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEE CS
               Methyltr_RsmB-F 163 vetelsepkglklgeeagtlrllPhtenkdgffiakl 199
                                    ++      gl+++++    r++P  ++++gffi+kl
  gi|70608021|ref|YP_256891.1| 321 LSF------GLDVKNGV---RFVPYLHDTEGFFITKL 348
                                   223......55555555...89************998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       0.6   3.6e+03      55      84 ..     107     136 ..      88     162 .. 0.58
   2 !   18.2   0.0   2.8e-07    0.0016       3     115 ..     174     318 ..     172     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.6
               Methyltransf_31  55 nveFeqgdiee.leklledekfDlilsnevl 84 
                                   +v+  ++d e+ +++ l+d+ +D+  +n++ 
  gi|70608021|ref|YP_256891.1| 107 RVNTLIADEEKvIKN-LNDKGVDVEKDNDIP 136
                                   666666666665554.566666665554444 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 2.8e-07
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklledekfDlilsn 81 
                                    + ++lDl+++ G ++ ++ ++   ka+++  D ++e +e+ r   +k g++  ++e+   d  +l   ++ +k++ +l +
  gi|70608021|ref|YP_256891.1| 174 PNDHILDLASAPGIKVSQIMQLTENKAKLIVADVDKERLEKERLLFKKFGVNvdRLELLLVDSSSLA--IK-RKVNKVLLD 251
                                   6889****************98888*************************9888***********99..88.899999999 PP

               Methyltransf_31  82 ................................evl..naladpdkileeiervlkpggilliedprll 115
                                                                     l  na++  d+++   ++ + ++g+l+++d+ ++
  gi|70608021|ref|YP_256891.1| 252 apcsssgaiwneptillrltrekvlhyadqqrK-LlnNAVKLGDEVIYATCSMFMEEGELIVNDYTTQ 318
                                   888888888888888888888755555555533.1589999999999999999999999999998755 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.7e-05      0.16      17     106 ..     160     253 ..     145     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                                   -HHHHHHHHHCHCCTCSEEEEET-TTSH.HHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTS CS
                           MTS  17 DkGsklLletlpkelsgkvlDlGcGaGv.lgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleev 93 
                                   Dk+s   +e+l+ e ++++lDl++  G+ ++  ++  +++a++ + dvd++ le  +  +++ +++   +e++  d  + +
  gi|70608021|ref|YP_256891.1| 160 DKASMAVVEALKPEPNDHILDLASAPGIkVSQIMQLTENKAKLIVADVDKERLEKERLLFKKFGVNvdrLELLLVDSSSLA 240
                                   9**************************856777777778888***********9999999888887666677777776666 PP

                                   TTS-EEEEEE--- CS
                           MTS  94 eekkfdlivsNPP 106
                                    ++k++ ++   P
  gi|70608021|ref|YP_256891.1| 241 IKRKVNKVLLDAP 253
                                   6677777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2491.04
//
Query:       gi|70608022|ref|YP_256892.1|  [L=105]
Description: transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-18   65.2   0.1    4.3e-18   64.9   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix
      5e-06   26.3   0.0    6.6e-06   25.9   0.0    1.2  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00076   19.4   0.2     0.0012   18.7   0.2    1.5  1  HTH_45    Winged helix-turn-helix
    0.00092   18.7   0.2     0.0014   18.1   0.2    1.4  1  RepL      Firmicute plasmid replication protein (RepL)
     0.0018   18.4   0.0     0.0023   18.1   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain
     0.0075   16.2   0.1      0.011   15.7   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.039   13.5   0.0    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.028   14.3   0.0      0.042   13.8   0.0    1.2  1  MarR      MarR family
      0.037   14.5   0.0      0.051   14.1   0.0    1.3  1  HTH_27    Winged helix DNA-binding domain
      0.068   13.1   0.0      0.094   12.6   0.0    1.2  1  MarR_2    MarR family
       0.14   12.2   0.0       0.18   11.9   0.0    1.2  1  HTH_20    Helix-turn-helix domain
       0.16   12.0   0.0       0.21   11.6   0.0    1.2  1  HTH_43    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.1   2.9e-21   4.3e-18       1      84 [.      22     104 ..      22     105 .] 0.96

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 2.9e-21
                                   HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                          HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkk 81 
                                   lig+  kl++l+ l++  k f+el r   k+  k+L+++L+ Le++g++ r+v+   P +v+Y+lt+kG +l+ +++el k
  gi|70608022|ref|YP_256892.1|  22 LIGSENKLIVLYYLFDEGKGFNELIRLT-KLNSKTLSKTLKDLEESGIVYRKVIGDRPFRVKYELTDKGVKLKGIFEELRK 101
                                   6888999******************987.**************************************************** PP

                                   HHH CS
                          HxlR  82 wge 84 
                                   w++
  gi|70608022|ref|YP_256892.1| 102 WIS 104
                                   *97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.4e-09   6.6e-06       2      46 ..      26      70 ..      25      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.4e-09
                                  HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  +++l +L++L ++ + + el + ++l+  t+S  Lk L+e+G+V+
  gi|70608022|ref|YP_256892.1| 26 ENKLIVLYYLFDEGKGFNELIRLTKLNSKTLSKTLKDLEESGIVY 70
                                  7899****************************************6 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   8.3e-07    0.0012      25      74 ..      45     101 ..      29     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.3e-07
                        HTH_45  25 imykanLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkelee 74 
                                   ++    L+ k+l+k L+ L e g++       +    kY+lT+kG +l   ++el++
  gi|70608022|ref|YP_256892.1|  45 LIRLTKLNSKTLSKTLKDLEESGIVyrkvigdRPFRVKYELTDKGVKLKGIFEELRK 101
                                   5566789*****************9988888666899***********999998887 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   9.3e-07    0.0014      37     111 ..       7      75 ..       2      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.3e-07
                          RepL  37 nFvkvwienliatldliGn.kktrlvyylidnlnsnntliatnRelaeetgislktvsetlkileeanilkkkanG 111
                                   n +   +  +i+++ liG  +k+ ++yyl+d+ +  n li         t +  kt s+tlk lee++i+ +k  G
  gi|70608022|ref|YP_256892.1|   7 NMKSDEVCPVIKAIRLIGSeNKLIVLYYLFDEGKGFNELIRL-------TKLNSKTLSKTLKDLEESGIVYRKVIG 75 
                                   5555556678999****9725778889*******99999964.......667889***************999755 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0023       3      67 ..      29      91 ..      28     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                        HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                  l vl yL + +   f+el   +++++  Ls+ lk Le+ g i+++k   ++  r  +++T++G +
  gi|70608022|ref|YP_256892.1| 29 LIVLYYLFD-EGKGFNELIRLTKLNSKTLSKTLKDLEESG-IVYRKVIGDRPFRVKYELTDKGVK 91
                                  556666665.5668**************************.88999*****999*********75 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   7.1e-06     0.011      27      70 ..      49      90 ..      39      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.1e-06
                                  CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCC CS
                          PadR 27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGr 70
                                  ++l+  +l ++Lk+Le++g+v ++    g++p r  Y+lTd+G 
  gi|70608022|ref|YP_256892.1| 49 TKLNSKTLSKTLKDLEESGIVYRKVI--GDRPFRVKYELTDKGV 90
                                  56666778899**********98855..68************95 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.039      21      47 ..      43      69 ..      37      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                        HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                  +eL + + l + t+++ lk Lee+G++
  gi|70608022|ref|YP_256892.1| 43 NELIRLTKLNSKTLSKTLKDLEESGIV 69
                                  799***********************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.8e-05     0.042      22      50 ..      44      72 ..      30      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                          MarR 22 eLakklgvskstvtrvldrLekkGlieRs 50
                                  eL +  ++++ t++++l+ Le+ G ++R+
  gi|70608022|ref|YP_256892.1| 44 ELIRLTKLNSKTLSKTLKDLEESGIVYRK 72
                                  677778999******************96 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.4e-05     0.051      16      68 .]      37      89 ..      25      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                        HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre..krvrlTdkG 68
                                  +++k   +l++ +++++ + s+ lk L+e G v   ++   +r+  + ++lTdkG
  gi|70608022|ref|YP_256892.1| 37 DEGKGFNELIRLTKLNSKTLSKTLKDLEESGIV--YRKVIGDRPfrVKYELTDKG 89
                                  55555689*************************..33445578866778999999 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.094      10      54 ..      31      72 ..      27      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  vL++L +++      +el r ++l   ++s++lk+L++ G v r+
  gi|70608022|ref|YP_256892.1| 31 VLYYLFDEGK---GFNELIRLTKLNSKTLSKTLKDLEESGIVYRK 72
                                  6777777776...689**************************885 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.18      25      54 ..      40      69 ..      18      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                  B-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                        HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLv 54
                                    ++el ++  l  +tls+ L+ Lee g+v
  gi|70608022|ref|YP_256892.1| 40 KGFNELIRLTKLNSKTLSKTLKDLEESGIV 69
                                  556788899999****************98 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.21       9      71 ..      28      89 ..      25     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-S--EEEEEE-T CS
                        HTH_43  9 rlylaylideeeanvpklieltgmPRRtlqDtlkalaeldielefvqegernnaGyyrisdWG 71
                                  +l + y + +e +   +li+lt++  +tl  tlk l+e +i  + +  g r  + +y+++d G
  gi|70608022|ref|YP_256892.1| 28 KLIVLYYLFDEGKGFNELIRLTKLNSKTLSKTLKDLEESGIVYR-KVIGDRPFRVKYELTDKG 89
                                  6777887778888999*************************988.446999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 810.68
//
Query:       gi|70608023|ref|YP_256893.1|  [L=166]
Description: hypothetical protein Saci_2314 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0041   16.5   2.5       0.13   11.7   0.3    2.4  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
  ------ inclusion threshold ------
      0.036   14.3   1.0      0.064   13.5   1.0    1.4  1  DUF3040          Protein of unknown function (DUF3040)
      0.058   13.2   2.9          1    9.2   0.8    2.3  2  PKD              PKD domain
       0.71   10.2   6.0        0.6   10.4   3.4    2.0  2  DUF11            Domain of unknown function DUF11
        4.6    7.3   9.3         30    4.7   9.1    2.2  2  BACON            Putative binding domain, N-terminal


Domain annotation for each model (and alignments):
>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   3.7e-05      0.13       4      33 ..       9      39 ..       6      40 .. 0.88
   2 !    5.4   0.1    0.0034        12      21      36 ..      40      55 ..      38      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                                  SGCHHHHCCHH.HHHHHHHHHHHHHHHHHHH CS
               ATP1G1_PLM_MAT8  4 dpFyYDyesLr.lgGLifAglLfivGiliil 33
                                  +++ YD   +r l G i+A +L i+G++i++
  gi|70608023|ref|YP_256893.1|  9 SRYRYDKRRIRaLSGAIVALILVIAGVIIAT 39
                                  67889999999669***************86 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0034
                                  HHHHHHHHHHHHHCCH CS
               ATP1G1_PLM_MAT8 21 AglLfivGiliilSkk 36
                                  A++Lf+ G++ ++S++
  gi|70608023|ref|YP_256893.1| 40 AVVLFAFGLIPAISNQ 55
                                  9***********9986 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.0   1.8e-05     0.064      40      76 ..      12      49 ..       3      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                       DUF3040 40 slrrlavlavllfvaGllllvlG.vaaaavvlgvvGfv 76
                                  +  +++++a+ +++++l+l+++G ++a avvl ++G++
  gi|70608023|ref|YP_256893.1| 12 RYDKRRIRALSGAIVALILVIAGvIIATAVVLFAFGLI 49
                                  34455899999************555555666666654 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.015        53      53      70 ..      71      88 ..      68      89 .. 0.90
   2 ?    9.2   0.8   0.00029         1      37      68 ..     127     158 ..     119     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.015
                                  SEEEEEEEEEE-SS-EEE CS
                           PKD 53 pGeYeVtvtasnavgsat 70
                                   G+Y++  t+ n++++ +
  gi|70608023|ref|YP_256893.1| 71 SGQYNIIITVRNTASNFN 88
                                  59************9976 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00029
                                   -EEEEETTEEEEEE-SSEEEEEEEEEE-SS-E CS
                           PKD  37 vvqvlseptvthtYlspGeYeVtvtasnavgs 68 
                                   + +++  pt +++++s  +Y++tv  sn +g+
  gi|70608023|ref|YP_256893.1| 127 TLTITATPTSSIVFSSGQTYTATVYFSNGLGA 158
                                   56789999********************9997 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.4   0.00017       0.6      16      81 ..      74     137 ..      57     148 .. 0.77
   2 ?   -0.1   0.2      0.33   1.2e+03      11      29 ..     141     159 ..     136     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                         DUF11  16 vtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrt 81 
                                    + ++tv+Nt  as  +v vt +  ag ++  ++  + t++ +  ++++ +g++ tl++t+++t +
  gi|70608023|ref|YP_256893.1|  74 YNIIITVRNT--ASNFNVSVTSINIAGISFTINKINNITYNPNNPMEQVGPGKTETLTITATPTSS 137
                                   4445677776..44557****9877777777777777778777777****************9976 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.33
                         DUF11  11 rpGdtvtytltvtNtgpas 29 
                                    +G+t t t+ ++N  +a+
  gi|70608023|ref|YP_256893.1| 141 SSGQTYTATVYFSNGLGAP 159
                                   6899999999999988776 PP

>> BACON  Putative binding domain, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.4       0.2   7.2e+02      12      25 ..      78      92 ..      69     103 .. 0.68
   2 ?    4.7   9.1    0.0084        30      18      47 ..     118     160 ..      78     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                         BACON 12 ltv.spastltvtva 25
                                  +tv ++as+++v+v+
  gi|70608023|ref|YP_256893.1| 78 ITVrNTASNFNVSVT 92
                                  455422225555554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0084
                         BACON  18 s........tltvtvaaNt.....sgeeRtatitvtagsgegt 47 
                                   +        tlt+t+++++     sg+++tat++++ g g  t
  gi|70608023|ref|YP_256893.1| 118 EqvgpgkteTLTITATPTSsivfsSGQTYTATVYFSNGLGAPT 160
                                   144444567**********777655777********9877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1440  (0.0803168); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1236.07
//
Query:       gi|70608024|ref|YP_256894.1|  [L=527]
Description: hypothetical protein Saci_2316 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.0   3.4      0.054   13.7   0.3    3.0  2  DUF3211   Protein of unknown function (DUF3211)
      0.045   13.5   0.1       0.13   12.1   0.1    1.7  1  SpoVIF    Stage VI sporulation protein F


Domain annotation for each model (and alignments):
>> DUF3211  Protein of unknown function (DUF3211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3     6e-06     0.054      47     121 ..      98     169 ..      62     178 .. 0.73
   2 ?   -1.0   0.2      0.21   1.9e+03      99     126 ..     442     473 ..     426     477 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-06
                                   EEEETTEEEEEEEEEEEETTEEEEEEEETTE....EEEEEEEEETTEEEEEEEES-HHHHHHHHHHHHHHHHHHH CS
                       DUF3211  47 egefllveieikgtvyvsntevkyvfevskgeekgsGkieisveeekikleleyegelekliskllskrikkfek 121
                                   +  +++  + + g v   n  + y + ++        k++i+v++++++++l+y+g++ + ++ +ls  i+k+ +
  gi|70608024|ref|YP_256894.1|  98 SFTLSTRYFAMIGDVLYKNRTLIYLMIIDGR---EYAKLYITVKNRRVTFNLDYKGPKLSELKDYLSTSISKLRR 169
                                   2234555677888888888999999987655...788**********************************9976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.21
                                   EES-HHHHHHH....HHHHHHHHHHHHHHHHH CS
                       DUF3211  99 eyegeleklis....kllskrikkfeknldek 126
                                   eye ++++l      +++sk  + +ek+lde+
  gi|70608024|ref|YP_256894.1| 442 EYETWIKSLDPmflkTIVSKVYEMSEKTLDEE 473
                                   77888777544100155666666677777764 PP

>> SpoVIF  Stage VI sporulation protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.4e-05      0.13      33      65 ..     455     487 ..     451     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                        SpoVIF  33 lRqlikqvsklankpvskekedkivkaivndkv 65 
                                   l+ ++++v ++  k +++ek d++vk i ++  
  gi|70608024|ref|YP_256894.1| 455 LKTIVSKVYEMSEKTLDEEKIDNLVKLIGKNAS 487
                                   799*************************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      811  (0.045234); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 3365.56
//
Query:       gi|70608025|ref|YP_256895.1|  [L=560]
Description: type II/IV secretion system protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-44  150.9   0.0    6.1e-44  150.1   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
    0.00096   19.7   0.0     0.0021   18.6   0.0    1.5  1  ABC_tran       ABC transporter
      0.003   17.3   0.1      0.088   12.5   0.0    2.3  2  PCMT           Protein-L-isoaspartate(D-aspartate) O-methyltr
     0.0049   17.3   0.0      0.011   16.1   0.0    1.5  1  AAA_16         AAA ATPase domain
     0.0068   15.4   0.0      0.011   14.7   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.027   14.2   0.1    1.5  1  AAA_29         P-loop containing region of AAA domain
      0.022   15.0   0.0      0.061   13.6   0.0    1.7  1  AAA_22         AAA domain
      0.023   14.0   0.0      0.047   13.0   0.0    1.4  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.024   14.7   0.0      0.048   13.7   0.0    1.5  1  MMR_HSR1       50S ribosome-binding GTPase
      0.026   14.0   0.1      0.049   13.2   0.1    1.3  1  AAA_7          P-loop containing dynein motor region
      0.046   13.6   0.1       0.12   12.2   0.0    1.7  2  RsgA_GTPase    RsgA GTPase
      0.061   12.9   0.1      0.098   12.2   0.1    1.3  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.074   12.3   0.0       0.12   11.6   0.0    1.3  1  Septin         Septin
      0.079   12.6   0.4       0.15   11.7   0.4    1.4  1  SRP54          SRP54-type protein, GTPase domain
      0.085   12.9   0.2        0.2   11.7   0.1    1.7  1  DUF87          Helicase HerA, central domain
        0.1   12.7   0.1       0.23   11.5   0.1    1.6  1  Dynamin_N      Dynamin family
       0.13   12.7   0.3       0.28   11.6   0.3    1.5  1  AAA_23         AAA domain
       0.13   12.8   0.0       0.37   11.3   0.0    1.7  1  AAA_18         AAA domain
       0.21   11.9   0.2       0.55   10.6   0.2    1.8  1  AAA_19         AAA domain
       0.22   11.8   0.0       0.37   11.0   0.0    1.3  1  AAA_28         AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.0   6.8e-47   6.1e-44       7     245 ..     168     423 ..     163     445 .. 0.83

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 6.8e-47
                         T2SSE   7 allddekvsdihvekper.vkvrervdg...........ielreveelekaalerlisriaalakldiseerplqdarlpe 75 
                                   +ll+d+kv di v+  +  + v  r  +           +++ + e   ++ l++++ r  +l++++is  +p+ d+ lp 
  gi|70608025|ref|YP_256895.1| 168 PLLADYKVEDISVNGLNVpIYVYHRDYEyiptniifqkrMSVLNEEVDGEEFLNQITMRYISLSGRSISIASPISDGMLP- 247
                                   5666666667766666666666433333333333211112222222223567899999999*******************. PP

                         T2SSE  76 kgvrlrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                    g r+ +     v +  +++viR+ s++ +t+ +l++++  ++++ + l +a+  +++++v G+Tg GKtt+l+all+ ++
  gi|70608025|ref|YP_256895.1| 248 AGDRIAATYGREVSAkgTSFVIRRFSESPITVLHLIKQGVISADLVAYLWYAIDLKMSFMVIGTTGAGKTTVLNALLNLVK 328
                                   8888877765544443599************************************************************** PP

                         T2SSE 155 ksderivtvEDpvEiqleganqvqlnak......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgsls 229
                                   ++  +iv +ED  E++l+ +n vql ++       +++t+ dll+ +LR rPD+i vGEiR++e++ + +A++TGH g  +
  gi|70608025|ref|YP_256895.1| 329 DT-MKIVSIEDIPELKLARDNWVQLYTRpvfgalGKEITLMDLLKLSLRYRPDIITVGEIRGEESYVLFQALSTGHGG-AT 407
                                   99.******************************999****************************************99.** PP

                         T2SSE 230 TlHansaagalerLeq 245
                                   T Ha ++ +a++rL +
  gi|70608025|ref|YP_256895.1| 408 TFHAYDPESAIKRLMN 423
                                   **************86 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06    0.0021      14      46 ..     306     338 ..     298     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldg 46 
                                     ++G +GaGK+t+l++l++l+k+t+  + +++
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNALLNLVKDTMKIVSIED 338
                                   5689********************999997774 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.15   1.4e+02     154     168 ..      50      64 ..      47      72 .. 0.84
   2 !   12.5   0.0   9.9e-05     0.088      55     112 ..     282     344 ..     263     355 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                                   S--HHHHHTEEEEEE CS
                          PCMT 154 eiPealidQLkeGGr 168
                                   +iP++l+dQL++ G+
  gi|70608025|ref|YP_256895.1|  50 QIPKELVDQLNNSGI 64 
                                   8**********9986 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.9e-05
                                   EE--HHHHHHHHHHTT..--TT-EEEEES-.TTSHHHHH..HHHHHCTTCEEEEEESBHHHHH CS
                          PCMT  55 tiSaphmvalalelle..lkkgarvLevGs.GsGyltav..larlvgekgrvvsierikelve 112
                                    i +  + a ++ +l   ++ +++ + +G+ G+G  t++  l +lv++++++vsie i+el  
  gi|70608025|ref|YP_256895.1| 282 LIKQGVISADLVAYLWyaIDLKMSFMVIGTtGAGKTTVLnaLLNLVKDTMKIVSIEDIPELKL 344
                                   455556666666777666888899999995489988876225589***************975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05     0.011      26     123 ..     305     399 ..     301     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                        AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeala 106
                                   + +++G  G GK++++++ll+ ++++  i+  ++  +l  +++++ ++q+ +r  ++ +l+ e +  +l   + + +  + 
  gi|70608025|ref|YP_256895.1| 305 SFMVIGTTGAGKTTVLNALLNLVKDTMKIVSIEDIPEL--KLARDNWVQLYTR-PVFGALGKEITLMDLLKLSLRYRPDII 382
                                   5689****************655555444444444444..4777889999966.999999999665555555555555555 PP

                        AAA_16 107 avpelagaeasrllell 123
                                    v+e++g+e+  l+++l
  gi|70608025|ref|YP_256895.1| 383 TVGEIRGEESYVLFQAL 399
                                   56667777666666555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.2e-05     0.011      16      42 ..     304     330 ..     294     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                 TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairar 42 
                                   + ++++GttG+GKt++l++ll+ ++  
  gi|70608025|ref|YP_256895.1| 304 MSFMVIGTTGAGKTTVLNALLNLVKDT 330
                                   5789*****************998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     3e-05     0.027      19      45 ..     300     326 ..     296     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                        AAA_29  19 idlkgatlltGpsGsGKSTllDAiqal 45 
                                   idlk +++++G++G+GK+T+l A+  l
  gi|70608025|ref|YP_256895.1| 300 IDLKMSFMVIGTTGAGKTTVLNALLNL 326
                                   45555799***************9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.8e-05     0.061       7      29 ..     305     327 ..     301     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleql 29 
                                   + +v+G +G+GKTt+l+ ll+  
  gi|70608025|ref|YP_256895.1| 305 SFMVIGTTGAGKTTVLNALLNLV 327
                                   679****************9975 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05     0.047      42      60 ..     306     324 ..     290     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                                   EEEE--TTSSHHHHHHHHH CS
                  FtsK_SpoIIIE  42 llvaGatgsGKStalntLi 60 
                                    +v+G+tg GK+t+ln+L+
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNALL 324
                                   59***************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-05     0.048       2      22 ..     306     329 ..     305     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-05
                                   EEEEESTTSSHHHHHHHHHT...S CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltg...e 22 
                                   ++++G + +GK+t++nal++   +
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNALLNlvkD 329
                                   589***************984431 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.4e-05     0.049      30      67 ..     300     336 ..     287     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                         AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekylslti 67 
                                   ++ k++++++G+tG GKt++++ ll+ ++ +++++++i
  gi|70608025|ref|YP_256895.1| 300 IDLKMSFMVIGTTGAGKTTVLNALLNLVK-DTMKIVSI 336
                                   667899*****************999887.77766655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.12     102     128 ..     306     332 ..     283     339 .. 0.77
   2 ?   -3.0   0.0       6.6   5.9e+03       6      38 ..     523     555 ..     520     558 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EEEECSTTSSHHHHHHHHCTT-----S CS
                   RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktg 128
                                    +++G +G+GK+t++nall+  +  ++
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNALLNLVKDTMK 332
                                   4679**************985444433 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                                   -EETTTT.EES--EEEEEEESTTTT--HHHHHHH CS
                   RsgA_GTPase   6 nelvrpk.vaNvdqllivvslkepelslnlldrf 38 
                                   + l rp+    v + +++ s+k p+   + ++r+
  gi|70608025|ref|YP_256895.1| 523 QILDRPDaYVFVKKYIVLYSIK-PDEAIKEVQRM 555
                                   5666776457789999999999.88888888886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011     0.098       4      31 ..     307     334 ..     304     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                   EEEESTTCCHHHHHHHHHCT--SS-EEE CS
                          cobW   4 vltGflGsGKTtLlnhllenraglklav 31 
                                   ++ G  G+GKTt+ln+ll+  ++    v
  gi|70608025|ref|YP_256895.1| 307 MVIGTTGAGKTTVLNALLNLVKDTMKIV 334
                                   68899*************6655554444 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.12       4      27 ..     303     326 ..     300     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                   EEEEEEEEBTTSSCCCCCCTTSSS CS
                        Septin   4 eftlmvvGesglGkttlintlfet 27 
                                   ++  mv+G+ g Gktt++n+l++ 
  gi|70608025|ref|YP_256895.1| 303 KMSFMVIGTTGAGKTTVLNALLNL 326
                                   6889*****************975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00016      0.15       3      31 ..     305     333 ..     303     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                         SRP54   3 villvGlqGaGKTttlaKLaallkkegkk 31 
                                    ++++G++GaGKTt l  L +l+k+  k 
  gi|70608025|ref|YP_256895.1| 305 SFMVIGTTGAGKTTVLNALLNLVKDTMKI 333
                                   589****************9999887655 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00023       0.2      22      48 ..     302     328 ..     288     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                         DUF87  22 vtrHlAilgsTGsGKSntvavLleell 48 
                                   +++++ ++g+TG+GK++    Ll+ + 
  gi|70608025|ref|YP_256895.1| 302 LKMSFMVIGTTGAGKTTVLNALLNLVK 328
                                   578999**************9998655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00025      0.23       2      19 ..     307     324 ..     306     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                   EEEEBTTTTHHHHHHHHH CS
                     Dynamin_N   2 avvGsqSsGKSSvlnaLl 19 
                                   +v+G++ +GK++vlnaLl
  gi|70608025|ref|YP_256895.1| 307 MVIGTTGAGKTTVLNALL 324
                                   69***************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00032      0.28      22      39 ..     306     323 ..     300     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                        AAA_23  22 tlItGpNGaGKTTildAi 39 
                                   + ++G +GaGKTT+l+A+
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNAL 323
                                   6789*************8 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00041      0.37       2      21 ..     307     326 ..     307     380 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                        AAA_18   2 lltGtpGvGKttlakeLskr 21 
                                   ++ Gt G+GKtt+ ++L ++
  gi|70608025|ref|YP_256895.1| 307 MVIGTTGAGKTTVLNALLNL 326
                                   589*************9544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00061      0.55      13      39 ..     306     332 ..     299     462 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
                        AAA_19  13 llvtaGpGtGKTrvlkhivallvelgg 39 
                                   ++v++  G GKT+vl++ ++l++++ +
  gi|70608025|ref|YP_256895.1| 306 FMVIGTTGAGKTTVLNALLNLVKDTMK 332
                                   689***************999988764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00041      0.37       3      21 ..     307     325 ..     305     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                        AAA_28   3 vitGgestGKTtlleaLaa 21 
                                   +++G+ ++GKTt+l+aL +
  gi|70608025|ref|YP_256895.1| 307 MVIGTTGAGKTTVLNALLN 325
                                   79**************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3853.39
//
Query:       gi|70608026|ref|YP_256896.1|  [L=611]
Description: hypothetical protein Saci_2318 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-14   52.7   4.2    1.1e-08   35.1   0.6    4.7  6  T2SSF            Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.26   10.9   0.0    1.5  2  Anemone_cytotox  Sea anemone cytotoxic protein
        4.8    6.4   8.3       0.14   11.5   1.0    2.1  2  DUF4407          Domain of unknown function (DUF4407)
        5.7    6.7   4.4        1.8    8.3   0.5    2.1  2  DUF4448          Protein of unknown function (DUF4448)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   4.2       3.6   1.6e+04     107     122 ..      56      71 ..      49      78 .. 0.47
   2 ?   -4.3   2.8       3.7   1.7e+04     106     117 ..      95     106 ..      86     112 .. 0.57
   3 !   35.1   0.6   2.5e-12   1.1e-08       1     124 [.     134     262 ..     134     263 .. 0.94
   4 ?   -1.4   0.5      0.47   2.1e+03     106     122 ..     320     336 ..     295     336 .. 0.80
   5 !   27.4   0.2   5.7e-10   2.5e-06       1     121 [.     392     516 ..     392     519 .. 0.87
   6 ?   -5.2   1.9         4   1.8e+04     106     115 ..     582     591 ..     574     595 .. 0.41

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3.6
                                   XXXXXXXXXXXXXXXX CS
                         T2SSF 107 lllvvallvllillai 122
                                   l+l+++++++l++++i
  gi|70608026|ref|YP_256896.1|  56 LFLILLVCIVLAVMFI 71 
                                   3334444444444333 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 3.7
                                   XXXXXXXXXXXX CS
                         T2SSF 106 llllvvallvll 117
                                   l++l++++++++
  gi|70608026|ref|YP_256896.1|  95 LVMLFLGVIIPP 106
                                   455555555555 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 2.5e-12
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT- CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggn 76 
                                   f++++++ l++G+++v  ++ l  ++ +  +++++ ++ rr+++ + s+++al      +p + f +++ ++++a+++g +
  gi|70608026|ref|YP_256896.1| 134 FATLFVIFLKSGLSPVLLFRKLEGSKAFSFVQDIVVYVNRRVQYLSeSIEQALLkamdINPGKLFNDFMLAYVTAIRTGAP 214
                                   788999****************************************9777777766667777899**************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                   + e++e+  ++l +++ l+++l++ +l+ +++ +v++l ++ ++++l+
  gi|70608026|ref|YP_256896.1| 215 VIETMEAKLKDLSKQFSLAANLASDRLQGVAESYVVWLSSGYIMLYLV 262
                                   ********************************************9987 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.47
                                   XXXXXXXXXXXXXXXXX CS
                         T2SSF 106 llllvvallvllillai 122
                                    ++l+++l+v+++++++
  gi|70608026|ref|YP_256896.1| 320 YISLPIGLVVAFLIMIF 336
                                   47788888888888875 PP

  == domain 5  score: 27.4 bits;  conditional E-value: 5.7e-10
                                   HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS.-HHHHHHHHHHHHHT- CS
                         T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssef.pelvvqlirageeggn 76 
                                   fl+ ++  l aG++++ ++++l + +e g+++e+l+++   l+ G++l  al+    + + +   +  +++l+ ++e g+ 
  gi|70608026|ref|YP_256896.1| 392 FLNAISEGLLAGLTFESIVTRLKDAQEMGKFREVLRKVDGYLKLGYPLTIALKrgadSIN-EFTsRIALYTLSDMIEIGSM 471
                                   7888899999*******************************************6554332.4556888999********** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXX CS
                         T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllilla 121
                                    ++  ++la++++ ++  rr+ + +    +++ + ++lv+li  +
  gi|70608026|ref|YP_256896.1| 472 TPDNVRALADQINSQLVVRREYQGKVKPLIATPYAGVLVSLIATF 516
                                   ********************9999999888888888888777654 PP

  == domain 6  score: -5.2 bits;  conditional E-value: 4
                                   XXXXXXXXXX CS
                         T2SSF 106 llllvvallv 115
                                   +l++vv+l +
  gi|70608026|ref|YP_256896.1| 582 ILMIVVTLTI 591
                                   2222222222 PP

>> Anemone_cytotox  Sea anemone cytotoxic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.9e-05      0.26      19      71 ..     112     163 ..     106     167 .. 0.86
   2 ?   -4.0   0.0       2.2     1e+04      70      86 ..     526     542 ..     524     544 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                                   HHHHHT-SSSSEEEEEEEEESSS-EEEEEEEECCSBSSS-S-SEE-TTEEEEE CS
               Anemone_cytotox  19 kvleelgkvdrkiavgvdnesgktwtalntyfrsgtsdvvlpekvenskally 71 
                                    +l+   k+d ki  gvd es    t +  + +sg s v+l +k+e ska+ +
  gi|70608026|ref|YP_256896.1| 112 SILDISQKID-KIKNGVDAESFSFATLFVIFLKSGLSPVLLFRKLEGSKAFSF 163
                                   5676666665.899***********************************9865 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.2
                                   EEEEESSSSSSS-SEEE CS
               Anemone_cytotox  70 lysgrkskgpvatgavg 86 
                                   l sg    gp+atg v+
  gi|70608026|ref|YP_256896.1| 526 LNSGIAVYGPIATGLVS 542
                                   566677789*****987 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.2      0.81   3.6e+03      17      43 ..      57      83 ..      44     105 .. 0.58
   2 ?   11.5   1.0   3.1e-05      0.14      44     107 ..     316     378 ..     275     387 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.81
                       DUF4407 17 GavvlltallAalsgayAlytvlkspl 43
                                    ++l+  +lA ++ ++Al  +l+   
  gi|70608026|ref|YP_256896.1| 57 FLILLVCIVLAVMFISFALIIFLRFYR 83
                                  445556666666666666665555444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.1e-05
                       DUF4407  44 l....lallvGllwgllIfnlDRfivssikkrakkrrelalalpRlllAvligvvisepleLkiFeke 107
                                   +    ++l++Gl+++ lI+ ++ +iv  i     +    ++ ++ + +A+lig++i+     + ++ke
  gi|70608026|ref|YP_256896.1| 316 YkifyISLPIGLVVAFLIMIFEHQIVYFI-----TLSGGLQNVFPVSIALLIGLLIASAPPAFFYQKE 378
                                   0445699********************99.....7777777777799*********986655555555 PP

>> DUF4448  Protein of unknown function (DUF4448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.72   3.2e+03     160     177 ..      62      79 ..      44      83 .. 0.67
   2 ?    8.3   0.5    0.0004       1.8     148     179 ..     307     338 ..     271     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.72
                       DUF4448 160 laialPvvvvvlvlglig 177
                                   + i+l v+++ ++l++++
  gi|70608026|ref|YP_256896.1|  62 VCIVLAVMFISFALIIFL 79 
                                   556666666666655554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0004
                       DUF4448 148 eseegkkaekyalaialPvvvvvlvlgligfv 179
                                   + +e++++  ++ +i+lP+ +vv++l++i+ +
  gi|70608026|ref|YP_256896.1| 307 KFPETQSSAYKIFYISLPIGLVVAFLIMIFEH 338
                                   45778888899*****************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 3923.47
//
Query:       gi|70608027|ref|YP_256897.1|  [L=156]
Description: hypothetical protein Saci_2319 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0034   17.6   2.8       0.93    9.8   1.7    3.0  2  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
  ------ inclusion threshold ------
      0.034   13.9   0.0      0.047   13.4   0.0    1.3  1  BppU_N         BppU N-terminal domain
      0.035   14.6   0.3       0.15   12.6   0.3    1.9  2  Cadherin-like  Cadherin-like beta sandwich domain
       0.08   13.3   4.9      0.096   13.0   4.9    1.1  1  MacB_PCD       MacB-like periplasmic core domain
       0.14   12.5   3.4       0.18   12.0   2.7    1.7  1  CARDB          CARDB
       0.16   12.0   2.2       0.25   11.3   2.2    1.5  1  DUF2393        Protein of unknown function (DUF2393)
       0.16   12.3   1.3       0.79   10.0   1.3    2.0  1  DUF4352        Domain of unknown function (DUF4352)
       0.28   10.8   1.0       0.49   10.0   1.0    1.3  1  Baculo_11_kDa  Baculovirus 11 kDa family


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.7   0.00041      0.93       8      64 ..      75     126 ..      67     131 .. 0.86
   2 ?    4.9   0.0     0.014        31       2      22 ..     131     151 ..     130     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00041
                   NPCBM_assoc   8 tltltvtndgtaaatnvslslsl.PeGWtvvevspasaaslapGetveatvkVtppag 64 
                                   ++t+tv+n+gt++++  s+++ + P + +       +a+s+++G+t+  t++Vtp +g
  gi|70608027|ref|YP_256897.1|  75 NITITVKNTGTTSISVTSININGqPFNIN------GTAPSIPAGRTQPITFEVTPASG 126
                                   57899999999999999999998787766......7899****************887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.014
                   NPCBM_assoc   2 epGetvtltltvtndgtaaat 22 
                                   +pG++ t t++++n+ +a+at
  gi|70608027|ref|YP_256897.1| 131 SPGASYTATIYFSNGQGAPAT 151
                                   79*****************98 PP

>> BppU_N  BppU N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.047      15      53 ..      72     109 ..      50     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                        BppU_N  15 kvisqgiqfrsgDtgtaklni.kltkngspldLtgltarl 53 
                                    +  ++i++++++tgt  + + +++ ng+p+++ g  + +
  gi|70608027|ref|YP_256897.1|  72 TI--YNITITVKNTGTTSISVtSININGQPFNINGTAPSI 109
                                   34..99***************667*********9977765 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.11   2.6e+02      70      88 ..      61      79 ..      52      81 .. 0.77
   2 ?   12.6   0.3   6.5e-05      0.15      28      87 ..      75     140 ..      60     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                 Cadherin-like 70 ikvtaedgsttrtYtltvt 88
                                  i+   + gs+++ Y++t+t
  gi|70608027|ref|YP_256897.1| 61 ITNSTASGSSRTIYNITIT 79
                                  4445567788999***997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                 Cadherin-like  28 svtitatae....dsvatvtvngvaveegstetkdvsLneGrnk.ieikvtaedg....sttrtYtltv 87 
                                   ++tit++       sv+++ +ng++ +    + ++ s+  Gr++ i+ +vt + g    s   +Yt t+
  gi|70608027|ref|YP_256897.1|  75 NITITVKNTgttsISVTSININGQPFN---INGTAPSIPAGRTQpITFEVTPASGkpnfSPGASYTATI 140
                                   455555555444489999999999999...4555666666***********998866665567777776 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.9   4.3e-05     0.096       2     105 ..      24     126 ..      23     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                      MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrrevpveavapvv...tvrggg 79 
                                   +l + G++i++a+v   ++l+ g++++ + q+ ++g+   +t +++sg+s +  ++ ++     v++   ++   t  + +
  gi|70608027|ref|YP_256897.1|  24 ILVIAGVIIAIAVVLFAFGLIPGISNQGSIQVLGSGT---ITNSTASGSSRTIYNI-TI----TVKNTGTTSisvT--SIN 94 
                                   689**********************999999987775...5555433344344445.32....2333222211111..111 PP

                      MacB_PCD  80 sgeeevtvvgvdpdyfk......vfglklaeG 105
                                    +++  +++g++p+ +        f +++a+G
  gi|70608027|ref|YP_256897.1|  95 INGQPFNINGTAPSIPAgrtqpiTFEVTPASG 126
                                   11344788998876665444444455555556 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.7   8.2e-05      0.18       9      72 ..      62     124 ..      52     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-05
                                   EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.EEEEESEE-CTEEEEEEEEEE-S CS
                         CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.gtvtvpsLaagesttvsftwtte 72 
                                   t + ++ + ++ ++it+tvkN+Gt +   t++   ++g+    + t ps+ ag +  ++f +t++
  gi|70608027|ref|YP_256897.1|  62 TNSTASGSSRTIYNITITVKNTGTTSISVTSI--NINGQPFnINGTAPSIPAGRTQPITFEVTPA 124
                                   5566777888999***********99766655..5666665444556888888888888888876 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.2   0.00011      0.25      19      94 ..      31     108 ..       6     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                       DUF2393  19 lfliflsllilflapfvvhliidkylkkaeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnk...k 94 
                                   ++ i + l+ + l p +++    ++l   ++t+++++ ++  + + +++t++N+G   i    ++i+  +++ n+   +
  gi|70608027|ref|YP_256897.1|  31 IIAIAVVLFAFGLIPGISNQGSIQVLGSGTITNSTASGSSR-TIYNITITVKNTGTTSISVTSININGQPFNINGtapS 108
                                   34467777778888******************999998765.6899**************9999999999888875552 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3   0.00035      0.79      37      60 ..      71      94 ..      53     156 .] 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00035
                                  SEEEEEEEEEEE-SSS-EEEEGGG CS
                       DUF4352 37 geflivdvtvkNkgkealtvnssq 60
                                   + + +++tvkN+g  +++v s++
  gi|70608027|ref|YP_256897.1| 71 RTIYNITITVKNTGTTSISVTSIN 94
                                  577889**************9987 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.0   0.00022      0.49      36      60 ..      23      48 ..      18      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                 Baculo_11_kDa 36 FvLvicglvvfvvivlfil.Llvvil 60
                                   +Lvi+g+++ + +vlf   L+  i+
  gi|70608027|ref|YP_256897.1| 23 LILVIAGVIIAIAVVLFAFgLIPGIS 48
                                  58***************542555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1477  (0.0823805); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1030.10
//
Query:       gi|70608028|ref|YP_256898.1|  [L=712]
Description: hypothetical protein Saci_2320 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-96  321.5   2.8    4.3e-92  309.1   1.1    2.2  2  Glu_synthase     Conserved region in glutamate synthase
      4e-16   59.3   0.1    1.5e-06   27.9   0.0    3.2  3  Glu_syn_central  Glutamate synthase central domain
    2.3e-07   30.2  11.2    1.4e-05   24.3   5.8    3.2  3  FMN_dh           FMN-dependent dehydrogenase
     0.0011   18.4   3.6     0.0022   17.4   3.6    1.5  1  NMO              Nitronate monooxygenase
  ------ inclusion threshold ------
      0.036   13.1   9.9      0.015   14.3   6.7    1.8  2  IMPDH            IMP dehydrogenase / GMP reductase domain
      0.041   13.1   0.3      0.087   12.0   0.3    1.5  1  NanE             Putative N-acetylmannosamine-6-phosphate epi
       0.14   11.3   2.6       0.32   10.2   2.6    1.6  1  DHO_dh           Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.1   1.1   1.7e-95   4.3e-92      57     367 ..      72     377 ..      37     378 .. 0.92
   2 !   11.8   0.0   3.7e-05     0.094     252     307 ..     585     641 ..     577     647 .. 0.87

  Alignments for each domain:
  == domain 1  score: 309.1 bits;  conditional E-value: 1.7e-95
                                   GS--HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--HHHHHH-SE CS
                  Glu_synthase  57 evepalkikkriltsamSyGalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvteeyLnnaka 137
                                   +v     ++ ++  + mSyGals + ++a+a +++   t + tGEGG+++e  k  k +  +Q as+rFGv+ ++L++++ 
  gi|70608028|ref|YP_256898.1|  72 SV-AGIPVSAPLYLGDMSYGALSGNPNIAIARVADITETLAGTGEGGLHPEVGKS-KRI-FVQWASARFGVDIDVLMKGAG 149
                                   33.33678999*************************************9986665.555.6******************** PP

                                   EEEE---TTSTTS--EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHH CS
                  Glu_synthase 138 leikiaQGakpgeGgqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakvsvKlvaeagvet 218
                                   + iki+QGakpg+Gg+lpg+Kv+  i+ +R+i+ g d+iSPaphhdiysiedl q ie+Lke++  ++v+vK++a + +  
  gi|70608028|ref|YP_256898.1| 150 IVIKIGQGAKPGIGGHLPGSKVTDPISLTRRIPVGIDAISPAPHHDIYSIEDLGQRIEALKEAT-GKPVFVKVAATNYIPY 229
                                   ****************************************************************.9*************** PP

                                   HHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SE CS
                  Glu_synthase 219 iaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAda 299
                                   i +g+a+ +ad + idG+  GTGA+p++++++ G+P+ela+a  d++lk++g+rd+ ++ia+G++  ++d +k +alGAd 
  gi|70608028|ref|YP_256898.1| 230 IVSGIARMGADGVIIDGHGAGTGATPTVIRDNLGIPIELAVAISDKVLKAQGMRDNFTVIAAGRIANATDAAKLIALGADV 310
                                   ********************************************************************************* PP

                                   EE-SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHHHHHHHT- CS
                  Glu_synthase 300 vgigtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevrellaalgi 367
                                   v++gt+alia+gC+m+++Ch ++Cp+ ++ + +  r   + e   + ++n+++ ++ e++++l +lg+
  gi|70608028|ref|YP_256898.1| 311 VSVGTGALIAMGCVMVHKCHIGSCPTALTNKIDGTR-MFETEFGVKVLTNFVRGFSLELANILDNLGM 377
                                   ****************************99999998.88999999*******************9997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.7e-05
                                   ---HHHHHHHHHHHHHHTT-GGG-EEEE.ESS--SHHHHHHHHHHT-SEEE-SHHHH CS
                  Glu_synthase 252 GlPlelalaevdqtlkeeglrdrvslia.dGglktgadvvkalalGAdavgigtaal 307
                                   G  le+ ++ vd++lke g+r+r ++ a + +l+ + d +k + lGAd+v ++ + l
  gi|70608028|ref|YP_256898.1| 585 GEDLEIVISDVDTKLKELGVRRRFDILAkSSKLRDSGDAFKLVGLGADSVIMSHKIL 641
                                   6678999*****************98873679******************9987765 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1     2e-05     0.051     162     218 ..     257     312 ..     227     381 .. 0.89
   2 !   27.9   0.0   5.9e-10   1.5e-06      14      78 ..     425     487 ..     419     510 .. 0.91
   3 !   14.5   0.0   7.3e-06     0.019     173     266 ..     590     682 ..     576     685 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                   -STTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEE CS
               Glu_syn_central 162 vseervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavn 218
                                   v ++++ ip  Lav+  ++ L ++g+r ++ + + +g + +  ++a l+++Gad v 
  gi|70608028|ref|YP_256898.1| 257 VIRDNLGIPIELAVAISDKVLKAQGMRDNFTV-IAAGRIANATDAAKLIALGADVVS 312
                                   5568899**********************986.579******************985 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 5.9e-10
                                   HHTHHHHHHHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG-B--EEE CS
               Glu_syn_central  14 elllepmakegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvmsletll 78 
                                   + +l++++++g   i smG+ +p  v  ekp  + d+++   AqVT P+iDp RE++ +s   + 
  gi|70608028|ref|YP_256898.1| 425 KAYLHELINKGDPVITSMGSTSPPDV--EKPARILDWIRSDGAQVTRPSIDPYREDIDTSFYLNH 487
                                   6689999*****************98..99***************************99987665 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 7.3e-06
                                   HHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEE.EHHHHHHHHHHHTTTS-.----HHHHHHHHHHHH CS
               Glu_syn_central 173 LavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavn.Pylaletieklveegal.aeeeleknyrkavekG 251
                                   ++++ v+++L + g+r+++ ++ +s+++r+  ++  l+g+Gad v   + +l++    + eg+  + ++++ n++ +++k 
  gi|70608028|ref|YP_256898.1| 590 IVISDVDTKLKELGVRRRFDILAKSSKLRDSGDAFKLVGLGADSVImSHKILDV---AIGEGSRsSLKDKAFNLVAGFKKE 667
                                   6899**************************************988503333333...344444412233336777777777 PP

                                   HHHHHHHTT--BHHH CS
               Glu_syn_central 252 llKimskmGistlqS 266
                                   +       G+  +qS
  gi|70608028|ref|YP_256898.1| 668 IALLAGAAGVYSVQS 682
                                   766666666666665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0058        15      31      89 ..      50     109 ..      44     118 .. 0.78
   2 !   24.3   5.8   5.4e-09   1.4e-05     207     308 ..     205     322 ..     198     328 .. 0.79
   3 ?    2.5   0.1     0.023        60     269     304 ..     605     641 ..     562     685 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0058
                                   GGEEE---..SSSS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS CS
                        FMN_dh  31 erirlrpr..vlrdvskvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagi 89 
                                   +ri+++++   + d  +  +st++ G ++s+P++++ +++  l   + ++a+ar a  +++
  gi|70608028|ref|YP_256898.1|  50 DRIHFKKEntLISDSPSSAISTSVAGIPVSAPLYLGDMSYGALSG-NPNIAIARVADITET 109
                                   66666543215567777799********************99986.888999998876655 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 5.4e-09
                                   HHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.........TSSTT---HHHCHHHHHHHH....... CS
                        FMN_dh 207 dikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG.........RqldgapatidvLpeiveav......g 269
                                    i+ l+e+t  p+ vK       +  +  ++++G+dg+++  HG+         R  d    +i+   +i ++v      +
  gi|70608028|ref|YP_256898.1| 205 RIEALKEATGKPVFVKVAatnYIPYIVSGIARMGADGVIIDGHGAgtgatptviR--DNLGIPIELAVAISDKVlkaqgmR 283
                                   5888999999999999873333356788899*************98999998555..445555666666655443333336 PP

                                   .SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHH CS
                        FMN_dh 270 grievlvDgGirrGsDvlkAlalGAdavllGRpflygla 308
                                   ++++v++ g i + +D++k +alGAd+v +G  +l ++ 
  gi|70608028|ref|YP_256898.1| 284 DNFTVIAAGRIANATDAAKLIALGADVVSVGTGALIAMG 322
                                   79*****************************99998865 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.023
                                   ..SS-EEE.ESS--SHHHHHHHHHTT-SEEEESHHHH CS
                        FMN_dh 269 ggrievlv.DgGirrGsDvlkAlalGAdavllGRpfl 304
                                   ++r+++l+ ++  r   D++k + lGAd v++  ++l
  gi|70608028|ref|YP_256898.1| 605 RRRFDILAkSSKLRDSGDAFKLVGLGADSVIMSHKIL 641
                                   45677776245589999*************9988776 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.6   8.6e-07    0.0022     152     231 ..     234     323 ..     200     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.6e-07
                           NMO 152 vearGaDalivqGpeaG.GhqG...tpevgd.....kglfaLvpqvldavd....iPviAaGGiidrrgvaaaLalGAsgv 219
                                   ++++GaD +i++G  aG G ++       ++     +  +a+ ++vl+a        viAaG i ++ + a  +alGA  v
  gi|70608028|ref|YP_256898.1| 234 IARMGADGVIIDGHGAGtGATPtviR---DNlgipiELAVAISDKVLKAQGmrdnFTVIAAGRIANATDAAKLIALGADVV 311
                                   6789**********999788884441...334456567788999999998889999************************* PP

                           NMO 220 qigtrfLltkes 231
                                    +gt  L++  +
  gi|70608028|ref|YP_256898.1| 312 SVGTGALIAMGC 323
                                   ****99998766 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   6.7   5.7e-06     0.015     160     237 ..     232     315 ..     199     322 .. 0.75
   2 ?   -1.5   0.1      0.37   9.4e+02     217     237 ..     618     638 ..     609     673 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-06
                                   HHHHHTT-SEEEE.-SS-STTBH.HHHHCSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHHTT-SEEE CS
                                   xxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 160 kaLieagadavkv.GiGpGsiCt.trvvagvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAlaaGadavm 234
                                   + ++++gad+v + G G+G   t t +   +G+p   Ava   ++ k +g     +via G i +  d +k +a+Gad+v 
  gi|70608028|ref|YP_256898.1| 232 SGIARMGADGVIIdGHGAGTGATpTVIRDNLGIPIELAVAISDKVLKAQGmrdnFTVIAAGRIANATDAAKLIALGADVVS 312
                                   56788999999988788887776244456788888877777777666665444589***********************99 PP

                                   ESC CS
                                   xxx RF
                         IMPDH 235 lGs 237
                                   +G 
  gi|70608028|ref|YP_256898.1| 313 VGT 315
                                   985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.37
                                   -SHHHHHHHHHTT-SEEEESC CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 217 kysgdivkAlaaGadavmlGs 237
                                   + sgd  k + +Gad+v++ +
  gi|70608028|ref|YP_256898.1| 618 RDSGDAFKLVGLGADSVIMSH 638
                                   789999999999999999865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   3.4e-05     0.087     141     174 ..     282     315 ..     270     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                                   HHTT--EEEES---SHHHHHHHHTT--SEEEE-H CS
                          NanE 141 seaglkviaeGrintPekakkaieiGvdavvvGs 174
                                   + ++++via Gri     a+k i +G+d+v vG+
  gi|70608028|ref|YP_256898.1| 282 MRDNFTVIAAGRIANATDAAKLIALGADVVSVGT 315
                                   457899**************************95 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.6   0.00012      0.32     239     286 ..     280     328 ..     198     332 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                                   HHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH.HHHHGTCHHHH CS
                        DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAslvqvyta.lvfegpkiakk 286
                                   + ++++  +I+ G i  + Da   i  GA +v v+t+ l+  g ++++k
  gi|70608028|ref|YP_256898.1| 280 QGMRDNFTVIAAGRIANATDAAKLIALGADVVSVGTGaLIAMGCVMVHK 328
                                   45667899****************************6256667777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 5045.86
//
Query:       gi|70608029|ref|YP_256899.1|  [L=659]
Description: glutamine amidotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-23   81.0   9.7    1.5e-22   80.1   9.7    1.4  1  GXGXG     GXGXG motif
    2.3e-07   31.1   0.0    4.6e-06   26.9   0.0    2.3  1  GATase_6  Glutamine amidotransferase domain
    3.5e-06   26.0   0.0    0.00051   18.9   0.0    2.2  1  GATase_2  Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.013   15.4   0.0       0.13   12.2   0.0    2.2  1  GATase_7  Glutamine amidotransferase domain
      0.091   12.9   1.5         16    5.8   0.2    2.9  2  DUF3091   Protein of unknown function (DUF3091)


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   9.7   4.3e-26   1.5e-22      13     163 ..     391     543 ..     370     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 4.3e-26
                                   HHHHHHHHHHTTT---....-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB- CS
                         GXGXG  13 ilsneiakrygeeglpe...dtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeenii 90 
                                   +++n+ ++ry+  ++++   ++ +i+l+G  G+ ++  + +  ++ + G+  d +G++++gGk+vi++++           
  gi|70608029|ref|YP_256899.1| 391 TVANVTGHRYIGINFKRlgvHNARINLYGIVGNVFANLN-EDNEFYVYGNVSDDCGDTMHGGKVVIYGDA----------- 459
                                   677777788877655543337889************999.999***************************........... PP

                                   S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B......-SSBTTT--EEE CS
                         GXGXG  91 vGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt......grnfaaGmsgGi 159
                                     +v+++  ++G++f++g+ag+R+++++     + + +v++g   d+++eYm+GGv+vvLg+       g+++++Gm gG 
  gi|70608029|ref|YP_256899.1| 460 -RDVLAQTFQNGRIFVKGNAGNRVGIQMreykdRRPYLVIGGFvDDYLGEYMAGGVIVVLGTNvkgepvGNYVGSGMVGGR 539
                                   .69*************************99999999******9899***************99999999************ PP

                                   EEEE CS
                         GXGXG 160 ayvl 163
                                   +y++
  gi|70608029|ref|YP_256899.1| 540 IYIR 543
                                   **98 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.3e-09   4.6e-06      11     134 .]     157     309 ..     146     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.3e-09
                      GATase_6  11 edevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall......... 81 
                                   e++++laH+R  ++         +Pf  ++ ++++vhNG+i+ +++  e l++ +g +    +D+ev++ l+         
  gi|70608029|ref|YP_256899.1| 157 EGDLWLAHTRQPTNSPGHFPYWsHPF--STFNVAIVHNGDISSFGANLEFLKE-RGWEGFVGTDSEVIAFLFeellsegfs 234
                                   67799*****9999987555556888..****************955555555.55554559**********777776666 PP

                      GATase_6  82 ............eelG.......eevl.erlrG.mfafaiwdk.rentlilardrlgvkplyyavdesglafase 134
                                               ++l             +rl+G   a+  +d+ +   li ++dr   +p ++++de++ ++ase
  gi|70608029|ref|YP_256899.1| 235 ieevvkimvnpsRRLNvidpsldYTYRnARLDGpFTAVIGYDSgDDLYLIAIADRAKFRPAIVGEDENYYYVASE 309
                                   666655555555222244444422222459999556667799966666666699999999999999999999998 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.4e-07   0.00051     164     401 ..     122     340 ..     100     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.4e-07
                                   -BTTBEEEEEESSEEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSS...S--GGGSSS-S....SEEEEE--TT CS
                      GATase_2 164 aekefYicslssrtivYkglltseqlkefykdlkdeelesalalvHsRfstnt...fPsWelaqPlR....llaHnGEint 237
                                   + ++  i s+ s   v+kg+  ++++++ y     e+le  l l H+R  tn    fP W+  +P+      + HnG+i  
  gi|70608029|ref|YP_256899.1| 122 EGRRGRIYSIGSSLSVFKGVGYPKDISKMYD---VEKLEGDLWLAHTRQPTNSpghFPYWS--HPFStfnvAIVHNGDISS 197
                                   555666789999999**************94...57899*************755599996..55541112689******* PP

                                   HHHHHHHHHHHCTT--BT-HH.HHHTC--S--TTS-HHHHHHHHHHHHHHTT--HHHHHHHHS----TT-GGGTHHHHHHH CS
                      GATase_2 238 lrGnknwmkareaelksellgdelekllPivneegsDsasldnvlellvlsgrslaealmlliPeawennksldkekkafy 318
                                      n ++ k r  e                    g Ds+ +   +e l+ +g s++e + +++ ++ ++ + +d+++   y
  gi|70608029|ref|YP_256899.1| 198 FGANLEFLKERGWE----G-------------FVGTDSEVIAFLFEELLSEGFSIEEVVKIMVNPS-RRLNVIDPSLD--Y 258
                                   **999998776532....2.............2367888888999999999999999999998665.45566777765..5 PP

                                   HHHTTT-----SS..EEEEEE..-SSEEEEEE-TT--S--EEEEETT--EEEESS.TTSS---GGGEEEEEE--TT-EEEE CS
                      GATase_2 319 eyasalmepWDGP..alivft..dGkvvgavLDRnGLRPaRylvtkddlvvlasE.vGvldleeeevvekgrlqPGrmllv 394
                                    y  a     DGP  a+i +   d  ++ a+ DR   RPa  +  ++++ ++asE   + +++++   + + l+PG+ ++ 
  gi|70608029|ref|YP_256899.1| 259 TYRNAR---LDGPftAVIGYDsgDDLYLIAIADRAKFRPAI-VGEDENYYYVASEeNEIREISPNA--RVWTLEPGSYFMA 333
                                   555544...47774334444411445788999999999985.445555666666515677777764..5578889988888 PP

                                   ETTTTEE CS
                      GATase_2 395 dleegri 401
                                    l++g i
  gi|70608029|ref|YP_256899.1| 334 SLNRGII 340
                                   8887766 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05      0.13      22     121 ..     185     313 ..     171     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                      GATase_7  22 grlvivfnGeiyNykelreeLeakghrfrtksDtevllallea............................ewgeealerl 74 
                                    +++iv+nG i  +    e L+++g +    +D+ev++ l+e+                               +    rl
  gi|70608029|ref|YP_256899.1| 185 FNVAIVHNGDISSFGANLEFLKERGWEGFVGTDSEVIAFLFEEllsegfsieevvkimvnpsrrlnvidpsLDYTYRNARL 265
                                   4699**********************************9*99999999999999999999999999998765555666899 PP

                      GATase_7  75 nGmfAfai.wdeeek.rlllaRDrlGikPLyygedkgdallfaSelkal 121
                                   +G f  +i +d+ ++  l+++ Dr  ++P ++ged+ + +++aSe + +
  gi|70608029|ref|YP_256899.1| 266 DGPFTAVIgYDSGDDlYLIAIADRAKFRPAIVGEDE-NYYYVASEENEI 313
                                   999977772454444466778999999999999996.799999997765 PP

>> DUF3091  Protein of unknown function (DUF3091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0071        26      75      98 ..     577     600 ..     573     602 .. 0.89
   2 ?    5.8   0.2    0.0043        16       1      28 [.     631     658 ..     631     659 .] 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0071
                       DUF3091  75 nvfklkkkyllkvkenlensvkkr 98 
                                   ++ +lk ky+++v+ +l++ +k++
  gi|70608029|ref|YP_256899.1| 577 EFSSLKDKYYIEVMDSLKDKAKEY 600
                                   5789****************9986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0043
                       DUF3091   1 idklkeeiekdYpnfsrevleeikrlke 28 
                                   i+++++++ +dY ++ +e +  ik +++
  gi|70608029|ref|YP_256899.1| 631 IKEFSQDMGRDYTEYLKEKFTVIKSRSK 658
                                   799******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4239.64
//
Query:       gi|70608030|ref|YP_256900.1|  [L=275]
Description: hypothetical protein Saci_2322 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.025   14.6   0.0    1.4  1  CbiG_N    Cobalamin synthesis G N-terminal


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.4e-06     0.025      33      79 ..      48      93 ..      36      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-06
                                  TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXX CS
                        CbiG_N 33 KktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTt 79
                                  K ++ +V+ v e+g++vi++      g   +A+ i++++g++ ++T+
  gi|70608030|ref|YP_256900.1| 48 KFANKPVILVTENGEYVIPVNREE-SGVSLIASLISDMIGGNLILTS 93
                                  77889***************9999.*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1885.22
//
Query:       gi|70608031|ref|YP_256901.1|  [L=268]
Description: vitamin B12 transport protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-13   51.2   0.0    1.7e-13   50.7   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   9.2e-18   1.7e-13       1     202 [.      22     213 ..      22     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 9.2e-18
                                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHHH CS
                  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellks 81 
                                   i+sl+p+ te+l++lG  +kv ++d+++++p++a+     + ++g+++ +++  l +lkPD+v+   g  + + + +l + 
  gi|70608031|ref|YP_256901.1|  22 IISLDPAATETLFMLGFGEKVIATDAFSYRPSEAK----RKLKIGSYTHVNLNLLEELKPDIVFTTMGA-QKELTRKLIDR 97 
                                   89********************************9....99**********************999999.999******** PP

                                   HS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTH CS
                  Peripla_BP_2  82 giptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigd 162
                                   + +++       ++ + +++  +  +++  + +++l++ +   l   +  +++  pk+++ f     gg++  g  + ++d
  gi|70608031|ref|YP_256901.1|  98 NFNVYPLGVATSVSRILNNVILVSLVVNAHNVGRELYQSLLLYLMGYRRLTNKR-PKIYVEFD---LGGPISCGYATHVSD 174
                                   ****999999888**************************999999998888888.55555554...5567999999***** PP

                                   HHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH CS
                  Peripla_BP_2 163 lldalgieniaaeskkseyeeisaEqilasdpdvifvsgr 202
                                    ++ +g+eni+++  +++y + +   + +++pd+i++ ++
  gi|70608031|ref|YP_256901.1| 175 AINLVGGENIFDDI-SDAYFTPNDNDVIERNPDLIVYEPK 213
                                   **************.*********************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2055.98
//
Query:       gi|70608032|ref|YP_256902.1|  [L=171]
Description: hypothetical protein Saci_2324 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   15.4   2.3      0.023   14.6   2.3    1.4  1  Haemagg_act  haemagglutination activity domain
      0.044   13.6   2.5      0.062   13.1   2.5    1.2  1  PilS         PilS N terminal


Domain annotation for each model (and alignments):
>> Haemagg_act  haemagglutination activity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.3   2.5e-06     0.023      47     102 ..      33      85 ..      22      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-06
                                   TTEEEEEE-SSSTTSEEEEEE-SSS-EEEECEEEEEE..CSCEEEEE-TT-EEEECCE CS
                   Haemagg_act  47 eggvvlfnaqngaasvilnrVtggspSkIqGaievlg..akanlflaNpnGiifggna 102
                                   +++ +l+   + +++++l  Vt ++ S+    iev+   ++ n++++Np G+  ++ +
  gi|70608032|ref|YP_256902.1|  33 SNQYILNI--PPNTTLVLKNVTLDQNSY---SIEVITnySNTNVIIVNPDGVAYNNTG 85 
                                   34444444..999*************98...455554459************999876 PP

>> PilS  PilS N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.5   6.9e-06     0.062      24      84 ..      54     120 ..      42     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-06
                          PilS  24 gsagYdakavatlialkvv...Ptsmtk..kgdtlvN.swgGkvtvspastsganntftityenvpe 84 
                                    +++Y+ + +++  + +v+   P+ +    +g +++N ++ G++t+  +++s+ + t+ ++y  +p 
  gi|70608032|ref|YP_256902.1|  54 DQNSYSIEVITNYSNTNVIivnPDGVAYnnTGYIIYNpQYPGNYTIKLGNPSDSQITVRVNYAVLPS 120
                                   567775555555555554433344444422666999978***********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1287.42
//
Query:       gi|70608033|ref|YP_256903.1|  [L=523]
Description: putative alpha-isopropylmalate/homocitrate synthase family transferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-51  175.7   0.1    2.1e-51  175.0   0.1    1.3  1  HMGL-like     HMGL-like
    1.9e-22   79.6   0.8      4e-21   75.3   0.1    2.6  2  LeuA_dimer    LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.046   13.2   0.0       0.59    9.5   0.0    2.3  2  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.1   3.5e-55   2.1e-51       2     264 .]       6     278 ..       5     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 3.5e-55
                                   -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT.-B..--EE-SSHHHHHH. CS
                     HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavk.karilalvrarekdika. 80 
                                   v+++dttLRDG q+++ ++++++k++ia  Lde+gvd+iE g p++ ++d e+ ++i+k    kari a    r+k   a 
  gi|70608033|ref|YP_256903.1|   6 VEVLDTTLRDGAQTANISFTLNDKIRIALLLDELGVDYIEGGWPSSNPKDEEFFKEIKKYKLtKARIAAFGSTRKKESTAk 86 
                                   7889******************************************************97650556888877777665441 PP

                                   ...HHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTB...S--HHHHHHHHHHH CS
                     HMGL-like  81 ...avealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledas...rtdleflaevveaa 155
                                        +++ +a +++  +f     lh+  +lk++ ee ++++ + v++ +s+g +v++ +e +    + + e++++ v++a
  gi|70608033|ref|YP_256903.1|  87 edqSLNSIIKADVDVGVLFGKSWSLHVTDVLKISLEENLDIIYDSVNYLKSHGLRVVYDAEHFYqgyKENREYALKAVKTA 167
                                   1115668999*****99***************************************99999886222578899******** PP

                                   HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BH CS
                     HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGnaal 236
                                   eeaGa+ i + Dt G + P+e++++ + ++++vk  v++ +H Hnd G Avant+++v aGa++v gt+nG+Ger+Gna+l
  gi|70608033|ref|YP_256903.1| 168 EEAGADVIVLCDTNGGTLPHEVYNITKDVVNHVK--VKIGLHMHNDSGGAVANTVMGVVAGARHVQGTINGIGERTGNADL 246
                                   **********************************..********************************************* PP

                                   HHHHHHHHHTT....-B----HHHHHHHHHHH CS
                     HMGL-like 237 eelvaalealg....vdtgldlqklrsiaalv 264
                                    +++ ++  +     ++ +  l+kl +++++v
  gi|70608033|ref|YP_256903.1| 247 IQVIPNIMLKLglnsLKGNESLKKLKEVSRVV 278
                                   99998765444467777778888888888776 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.028   1.7e+02      79     106 ..     157     184 ..     148     198 .. 0.84
   2 !   75.3   0.1   6.8e-25     4e-21       8     132 ..     384     509 ..     377     510 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.028
                                   EEEEEE--TT-TT--EEEEEEEE--GGG CS
                    LeuA_dimer  79 ldYsvhaitegtdaqaevrVelevddgk 106
                                    +Y ++a++  ++a a+v V + +++g+
  gi|70608033|ref|YP_256903.1| 157 REYALKAVKTAEEAGADVIVLCDTNGGT 184
                                   58********************965554 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 6.8e-25
                                   XXXXXXXXXXXX--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH......T-EEEEEE CS
                    LeuA_dimer   8 ealvkdelleaeerlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv......dikLldYs 82 
                                     ++ + l+  ++ +k+e ++v+++++ l+ a vk++      + + aeG+Gpv++++ Alrkal++      ++kL+dY+
  gi|70608033|ref|YP_256903.1| 384 VLVALRDLGMYRDLIKVEYWKVMNEKE-LAIAIVKVNG-----QLEVAEGVGPVHSVDIALRKALQKvypqinKVKLTDYR 458
                                   55666777788899*********9986.8888888877.....3589********************99977777****** PP

                                   EE--TT-TT--EEEEEEEE--GGGE.EEEEEEESSHHHHHHHHHHHHHHHH CS
                    LeuA_dimer  83 vhaitegtdaqaevrVelevddgkk.vsgvGvdsdiveASlkAlisalnrl 132
                                   v   +e +++++ vrV++e++dg+k +++ Gv+++++eAS+ Ali++l+++
  gi|70608033|ref|YP_256903.1| 459 VILPGEIKNTESVVRVTIEFTDGEKnWRTEGVSTSVIEASVIALIDGLDYY 509
                                   ********************996666*********************9987 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.036   2.1e+02       5      55 ..      37      80 ..      34     139 .. 0.69
   2 ?    9.5   0.0   9.9e-05      0.59      37     136 ..     135     213 ..     131     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.036
                                  HHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHST CS
                  AP_endonuc_2  5 aeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgy 55
                                   e+G+d++E  +++  p +       +e+ k ++++ l+ a + +f+    
  gi|70608033|ref|YP_256903.1| 37 DELGVDYIEGGWPSSNPKD-------EEFFKEIKKYKLTKARIAAFGSTRK 80
                                  689*******999999999.......7999999999998776666665554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.9e-05
                                   HHHTTSEEEEEEECCCHSTCTHC...HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHH CS
                  AP_endonuc_2  37 ldelglriaslslftrfgypded...erearreesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaesln 114
                                   l+++glr           y+ e+     +++    ++++ +a+++a++ Ga+++vl+     +    +  +    +++  +
  gi|70608033|ref|YP_256903.1| 135 LKSHGLR---------VVYDAEHfyqGYKEN----REYALKAVKTAEEAGADVIVLC-----D---TNGGTLPHEVYNITK 194
                                   6777777.........444444433334556....9*********************.....2...222233345555555 PP

                                   HHHHHHHHHTSEEEEE--TTTT CS
                  AP_endonuc_2 115 eladyaekegvklalEtlagsg 136
                                   +++ +   + vk++l+ ++ sg
  gi|70608033|ref|YP_256903.1| 195 DVVNH---VKVKIGLHMHNDSG 213
                                   55555...34677777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3817.31
//
Query:       gi|70608034|ref|YP_256904.1|  [L=296]
Description: prenyltransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-38  132.3  20.1    2.2e-38  132.0  20.1    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.23   11.5   0.0       0.23   11.5   0.0    2.9  2  DUF2752   Protein of unknown function (DUF2752)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0  20.1   2.5e-42   2.2e-38       2     236 ..      31     269 ..      30     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 2.5e-42
                          UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgll 82 
                                   l+ a++g++la +  p++++l+l+++ ++++++a+++ ++++DreiDa ++rt+ RPlv+G+i+++ea+++++++li  ++
  gi|70608034|ref|YP_256904.1|  31 LPMAYMGAFLAIREIPPIQVLILMFFSLFFLRTAGMTNDNLADREIDAMNPRTKSRPLVTGKITVREAKLLITISLIGFFI 111
                                   778999*************************************************************************** PP

                          UbiA  83 llalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaa....vtgsl....sllalllalavfll 155
                                    + +l+n+++++++ ++ l++  Y+  ++Kr+t++++  ++   gl+++ g++a    ++ s+    +  ++l+ + + ++
  gi|70608034|ref|YP_256904.1| 112 TA-YLINLYALIFAPIVALIVMSYP--YMKRYTAFANYHLASIQGLAVFSGAVAslglYAKSFtqlvTGIPWLFVISTVFW 189
                                   99.**********************..****************99999988888666633333566699999999999*** PP

                          UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlvr 235
                                   +++++l+n+++d + D+k g+++++v+lG++a ++  l  l+ vll++  +  +   l++++++a++l +l++ +a++  +
  gi|70608034|ref|YP_256904.1| 190 AVGFDLYNHIPDADFDKKMGLHSFAVLLGDRALMFAgLNQLISVLLAL--FGDIQFNLGIIAYIATILHGLIMGYAYYSAT 268
                                   **********************************96522223333322..3444455555666666666666666665554 PP

                          UbiA 236 r 236
                                   r
  gi|70608034|ref|YP_256904.1| 269 R 269
                                   4 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.2      0.29   2.6e+03      27      48 ..     109     130 ..     105     131 .. 0.83
   2 ?   11.5   0.0   2.6e-05      0.23      19      46 ..     263     290 ..     260     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.29
                       DUF2752  27 dfaaAfrynplgvlllplllll 48 
                                    f +A   n+ +++++p+++l+
  gi|70608034|ref|YP_256904.1| 109 FFITAYLINLYALIFAPIVALI 130
                                   5788999999999999999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.6e-05
                       DUF2752  19 avhallhgdfaaAfrynplgvlllplll 46 
                                   a ++ ++g+f +Af+yn+   ++l + +
  gi|70608034|ref|YP_256904.1| 263 AYYSATRGNFGRAFYYNIYSSIVLGIGI 290
                                   678999***********99887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1820.34
//
Query:       gi|70608035|ref|YP_256905.1|  [L=273]
Description: hypothetical protein Saci_2328 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-29  101.1   7.3    4.8e-22   78.8   1.9    2.1  2  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like
    1.6e-09   38.0   1.7    0.00015   22.1   0.0    2.2  2  AIG2_2    AIG2-like family
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.25   11.5   0.0    1.6  2  SF3b10    Splicing factor 3B subunit 10 (SF3b10)


Domain annotation for each model (and alignments):
>> GGACT  Gamma-glutamyl cyclotransferase, AIG2-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   1.9   8.1e-26   4.8e-22       1     120 [.      12     130 ..      12     131 .. 0.87
   2 !   25.6   0.3   2.4e-09   1.4e-05      25     112 ..     163     252 ..     141     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 8.1e-26
                                   EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHHCT....TTTT CS
                         GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlydlggkypalvpgdgekVkGelyevddeelarLDelE...peeps 78 
                                   +FvYG+L+ g++  + +l+++rf+++g   ++gy++ydl g+yp++v+gd   V+Ge+ye++de l+ LDe+E   +++++
  gi|70608035|ref|YP_256905.1|  12 IFVYGSLRFGFELNH-FLKNSRFVGLGL--VEGYKMYDL-GSYPGVVRGDSV-VHGEVYEINDELLNVLDEVEdyrGSPDD 87 
                                   7*********88887.888889998887..********8.79*****98888.**********************9999** PP

                                   SEEEEEEEEEC.TTS-EE...EEEEEEETT..GGGCCS-S-SS-- CS
                         GGACT  79 eYereevkvevledgeqv...eawvYvyageeeegdrliesgdWr 120
                                   +Y+re+v+v + +d++++   ++++Yvy++ + +g++ i +gd++
  gi|70608035|ref|YP_256905.1|  88 LYIREKVRVYF-DDKRKYyldNVYIYVYNQ-DITGRDVIVDGDYS 130
                                   *****777777.6777767999******66.77777778888886 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 2.4e-09
                                   EEEEEECCTBEEEE....ET.TT.EEEETTSSE.EEEEEEEE-HHHHHHHHHCT.TTTTSEEEEEEEEEC..TTS-EEEEE CS
                         GGACT  25 esgpatlkgyrlyd...lgg.ky.palvpgdgekVkGelyevddeelarLDelEpeepseYereevkvev.ledgeqveaw 99 
                                   +  p +l++y+++      + +y  +l++ ++++V G+l+ + ++el+ LD  E ++   Y+re    +v +++g+++ a 
  gi|70608035|ref|YP_256905.1| 163 KKIPVYLPDYKIVFnveC-KwGYcANLTKYENGRVCGYLLMILEDELNLLDSAE-KHLVRYIRE--VFKVyDNNGKEYYAC 239
                                   456778889998866542.236745566555557********************.99*******..5555568******** PP

                                   EEEETT..GGGCC CS
                         GGACT 100 vYvyageeeegdr 112
                                   +Yv+++ + e+++
  gi|70608035|ref|YP_256905.1| 240 AYVAPNISGEHNP 252
                                   ****774433333 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6     4e-06     0.024       2      66 ..      60     133 ..      59     141 .. 0.70
   2 !   22.1   0.0   2.5e-08   0.00015       1      75 [.     195     269 ..     195     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                        AIG2_2   2 VfGvlweidlenlkdLDkqE...gvedgiyrpievrVstatgee.vlaraYvlsnqpetk.....PsetYlkvl 66 
                                   V G ++ei+ e l+ LD+ E   g++d +y++ +vrV   ++++  l  +Y+++ +++       ++ +Y k +
  gi|70608035|ref|YP_256905.1|  60 VHGEVYEINDELLNVLDEVEdyrGSPDDLYIREKVRVYFDDKRKyYLDNVYIYVYNQDITgrdviVDGDYSKYV 133
                                   899**************99966679************8855544355555554444332212333666776665 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.5e-08
                        AIG2_2   1 eVfGvlweidlenlkdLDkqEgvedgiyrpievrVstatgeevlaraYvlsnqpe.tkPsetYlkvlvkGAeesgl 75 
                                   +V G l  i + +l+ LD+ E+ ++  y++   +V +++g+e  a aYv+ n     +P+++Y   +++G + + +
  gi|70608035|ref|YP_256905.1| 195 RVCGYLLMILEDELNLLDSAEK-HLVRYIREVFKVYDNNGKEYYACAYVAPNISGeHNPTDEYKRYILEGLKGHCI 269
                                   5889999999************.999**************************655499***********9776665 PP

>> SF3b10  Splicing factor 3B subunit 10 (SF3b10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.0         3   1.8e+04      14      20 ..      31      37 ..      29      38 .. 0.86
   2 ?   11.5   0.0   4.3e-05      0.25      38      73 ..     129     164 ..     121     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                                  XXXXXXX CS
                        SF3b10 14 skYvGtG 20
                                  s++vG+G
  gi|70608035|ref|YP_256905.1| 31 SRFVGLG 37
                                  89***99 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.3e-05
                                   HHHHHH-HHHHHHHHHHHT--HHHHHHHHHHCTSST CS
                        SF3b10  38 yaSlvgHsalleYfaiaeneskarvrlellekmlqp 73 
                                   y+ +vg sa+ +Yfa aen++ + ++ + + k++++
  gi|70608035|ref|YP_256905.1| 129 YSKYVGTSAIFNYFAYAENTNDEILKARGVTKIFKK 164
                                   899*************************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1836.04
//
Query:       gi|70608036|ref|YP_256906.1|  [L=96]
Description: hypothetical protein Saci_2329 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.2   0.1       0.25   11.3   0.1    1.5  1  DUF2672   Protein of unknown function (DUF2672)


Domain annotation for each model (and alignments):
>> DUF2672  Protein of unknown function (DUF2672)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   1.4e-05      0.25       4      25 ..      61      82 ..      57      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.4e-05
                       DUF2672  4 kklktikasfiksffikdides 25
                                   klk +kas ik    +d+des
  gi|70608036|ref|YP_256906.1| 61 EKLKILKASVIKGEESRDLDES 82
                                  59*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 675.70
//
Query:       gi|70608037|ref|YP_256907.1|  [L=120]
Description: hypothetical protein Saci_2330 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-16   58.3   3.5      2e-15   56.9   3.5    1.7  1  NfeD             NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
      0.049   12.7   0.6      0.058   12.5   0.6    1.1  1  FUSC-like        FUSC-like inner membrane protein yccS


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   3.5   2.3e-19     2e-15       6      84 .]      34     114 ..       7     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.3e-19
                                   XXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSSEEEE CS
                          NfeD   6 svlllvllrplllkklkkkekktnaealiGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVveveGltliVe 83 
                                   s++l+ +l   +++ + +++ + n  ++ Gk+g++++di  g +G v ++Ge+W+a+s+++i+kg++V V++++ l+liV+
  gi|70608037|ref|YP_256907.1|  34 SLALVGFLLYRVVNVIWTTR-RRNLYTYEGKIGRAVDDIspGkEGYVLIEGEYWRAISNEPISKGDEVIVIGMQNLKLIVK 113
                                   44444222222222222212.256669************99668************************************9 PP

                                   E CS
                          NfeD  84 p 84 
                                   +
  gi|70608037|ref|YP_256907.1| 114 K 114
                                   8 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   6.5e-06     0.058      54      94 ..      11      52 ..       4      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-06
                     FUSC-like 54 tLlvaiytmlgasqep.eiwqqplllllGalwYgllsllwsl 94
                                  +++v+i++++  +q+   i   p l l+G l+Y +++++w  
  gi|70608037|ref|YP_256907.1| 11 IIVVVILALILTGQYAnPIVAIPSLALVGFLLYRVVNVIWTT 52
                                  6899**********9989**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 872.99
//
Query:       gi|70608038|ref|YP_256908.1|  [L=434]
Description: thermopsin-like protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-22   78.3   9.7    6.1e-22   78.3   9.7    1.8  3  Thermopsin  Thermopsin


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   9.7   3.4e-26   6.1e-22      19     259 ..      29     249 ..      16     250 .. 0.78
   2 ?   -3.7   0.0      0.35   6.3e+03     222     243 ..     286     308 ..     283     324 .. 0.64
   3 ?   -3.1   0.4      0.24   4.4e+03     124     151 ..     325     352 ..     299     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 3.4e-26
                    Thermopsin  19 adyGiknnsgkltpysyntssvlGevnisslsaynsssn.....spesaslQLNvvlevvtggktysywvQnVv...sfnt 91 
                                    +y+i+ +    +  +y+t++vlGe+nissl+  ns  +        +aslQLN+++       +  yw Q+V+   ++n+
  gi|70608038|ref|YP_256908.1|  29 NSYPIGVSFF-PLFSIYQTQEVLGEINISSLYIGNSYLSngqylTTGNASLQLNAMI-------NGIYWAQDVIlfsQINK 101
                                   4555555543.345689**************99998877677877888*********.......5669******4444455 PP

                    Thermopsin  92 tekqltfidNiWNftspsanlsnsaisGnGtvyasskgefYyayateylelslPltlkLvinvsltsngvpevsFgYsidg 172
                                   t  +++++ N+WN+ +p +nl+ s  +G  t y ++ g + y  +++ + +++P+++kL++  + t      ++FgY i+g
  gi|70608038|ref|YP_256908.1| 102 TAFNASLVVNVWNLLGP-FNLNLS--KGIETTY-QNLGVILYT-GPS-YIVKTPVQIKLFMIINST-----SLYFGYYING 171
                                   55569*********998.466556..7888899.444444444.566.66999***9999998555.....689****996 PP

                    Thermopsin 173 gvvtYDnvtinstgkasaeilvngssltpsgllyDaeLvlgGpgngekttfnslnatlsLyYlngtnyqpvknaydfGsdT 253
                                   +   + +  +  tg    ++ + g   +  gl+ D eLv+gGpg+g++++  +  a  +Ly+  g++++ v++a + G dT
  gi|70608038|ref|YP_256908.1| 172 HSGIFYQ--LPLTG----SFRIGG--FSAIGLPNDLELVFGGPGGGSSVQLIT-TANANLYFKDGNSLTVVPSALSTGLDT 243
                                   4444432..33444....789999..67899****************999875.466789999****************** PP

                    Thermopsin 254 aEtaen 259
                                   aEt+ +
  gi|70608038|ref|YP_256908.1| 244 AETVIG 249
                                   ***965 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.35
                    Thermopsin 222 tfnslnatlsLyYlngtn.yqpv 243
                                   + n+++++  L+Y n+   +q+v
  gi|70608038|ref|YP_256908.1| 286 NSNNSSISVRLMYDNKPImWQKV 308
                                   45667777777775555434443 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.24
                    Thermopsin 124 yasskgefYyayateylelslPltlkLv 151
                                   +++++g+ Y++ +++ + + +P +++L 
  gi|70608038|ref|YP_256908.1| 325 TTDNSGYAYFNTSPSLYVIYYPGNFTLS 352
                                   3555666666666666777777666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2946.97
//
Query:       gi|70608039|ref|YP_256909.1|  [L=258]
Description: hypothetical protein Saci_2332 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-35  120.8   5.3    8.1e-35  120.4   5.3    1.1  1  Band_7         SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.016   14.9   0.7      0.057   13.1   0.4    1.9  2  Band_7_1       SPFH domain-Band 7 family
      0.095   13.0   0.2       0.69   10.2   0.1    2.2  2  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi
       0.11   13.3   1.7       0.23   12.2   0.2    2.0  2  LptE           Lipopolysaccharide-assembly


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   5.3   1.8e-38   8.1e-35       2     177 ..      28     197 ..      27     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.8e-38
                        Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaav 82 
                                   +i e +++v+ r G+  rv++pG+   +Pf+++ +vv++r++t+dv+  +t++tkD++ vtid++++y+v  d+ k +++v
  gi|70608039|ref|YP_256909.1|  28 VIAEWQRAVILRLGRAIRVKGPGIITLIPFVDRPIVVDLRIVTVDVPA-QTTVTKDNVTVTIDAVLYYKV-VDPMKTILSV 106
                                   57889*******************************************.*********************.********** PP

                        Band_7  83 eresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaa 163
                                       an++  + ++++ +lr +i++m+l+e+l +ree++++l+  l e  +++G+ v++v+++di++++e+ +a+a+ ++a
  gi|70608039|ref|YP_256909.1| 107 ----ANYNYAVLNLAQTSLRDIIGQMELDEILVKREEINKRLQLILDEITEGWGIKVTQVTVRDIRLSQELLSAIAEQAKA 183
                                   ....***************************************************************************** PP

                        Band_7 164 eaeaqaeiaraeae 177
                                   e+ ++a++  +e+e
  gi|70608039|ref|YP_256909.1| 184 ERIRRAKVISSEGE 197
                                   *******9999988 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.27   1.2e+03      18      44 ..      28      54 ..      25      70 .. 0.84
   2 ?   13.1   0.4   1.3e-05     0.057     142     209 ..     118     183 ..      95     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.27
                      Band_7_1 18 ivregqeavfvneGqiaDvfapGtytL 44
                                  ++ e q+av ++ G+   v +pG  tL
  gi|70608039|ref|YP_256909.1| 28 VIAEWQRAVILRLGRAIRVKGPGIITL 54
                                  677889********9999999998887 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                      Band_7_1 142 vtrlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                   +t+l d++++ ++   ++  k ee+ ++l+  l+e  +  G++++++++++i l +e+  a+ ++a++
  gi|70608039|ref|YP_256909.1| 118 QTSLRDIIGQMEL--DEILVKREEINKRLQLILDEITEGWGIKVTQVTVRDIRLSQELLSAIAEQAKA 183
                                   5566666666554..455678999******9999999*************************999876 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00016      0.69      18      50 ..     130     163 ..     121     171 .. 0.90
   2 ?   -0.5   0.0      0.35   1.6e+03      22      50 ..     211     240 ..     204     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                 SpoU_sub_bind  18 iekllvtegradkrleellklakkr.gikvelvd 50 
                                   ++++lv++++ +krl+ +l+++++  gikv +v+
  gi|70608039|ref|YP_256909.1| 130 LDEILVKREEINKRLQLILDEITEGwGIKVTQVT 163
                                   899****************************997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                 SpoU_sub_bind  22 lvteg.radkrleellklakkrgikvelvd 50 
                                   +v++  +   r+ e+l+++ +rg  v+ v+
  gi|70608039|ref|YP_256909.1| 211 YVSNPvALQIRFLEMLTDISQRGNMVIVVP 240
                                   555555666789999999999999888886 PP

>> LptE  Lipopolysaccharide-assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   5.2e-05      0.23      41     106 ..      52     127 ..      27     128 .. 0.75
   2 ?    0.1   0.1       0.3   1.3e+03      89     102 ..     171     185 ..     140     220 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.2e-05
                                   S.......-SSEEEEEEEEEE..TTSCEEEEEEEEEEEEEEEETTS....SSCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                          LptE  41 d.......adavlegeitsytl.edgtaseyrltltvqvrltdakd....adsllakeaeedalrraaeqladqivrr 106
                                             +v+  +i+++++  ++t++  ++t+t+++ l+   +    + ++l++++ + a+ ++a++  ++i+ +
  gi|70608039|ref|YP_256909.1|  52 ItlipfvdRPIVVDLRIVTVDVpAQTTVTKDNVTVTIDAVLYY--KvvdpMKTILSVANYNYAVLNLAQTSLRDIIGQ 127
                                   14555655455668899999999999999************99..555679999*****************9999865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHH.HHH CS
                          LptE  89 edalrraaeql.adq 102
                                   +++l+ +aeq+ a++
  gi|70608039|ref|YP_256909.1| 171 QELLSAIAEQAkAER 185
                                   222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      764  (0.0426125); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1690.12
//
Query:       gi|70608040|ref|YP_256910.1|  [L=430]
Description: hypothetical protein Saci_2334 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-20   73.5   2.3    2.4e-20   73.5   2.3    3.1  3  ATPase_2  ATPase domain predominantly from Archaea
    9.7e-15   54.8   1.8      9e-14   51.7   2.3    2.4  2  DUF234    Archaea bacterial proteins of unknown function
    3.2e-08   33.7   1.7    3.3e-08   33.6   0.2    1.8  2  AAA_14    AAA domain
    8.3e-05   23.0   0.0    0.00014   22.2   0.0    1.4  1  AAA_16    AAA ATPase domain
      0.006   16.3   0.0      0.039   13.7   0.0    2.2  2  AAA_24    AAA domain
  ------ inclusion threshold ------
      0.025   14.8   0.1        1.2    9.5   0.1    2.7  1  AAA_22    AAA domain
       0.12   11.8   0.1        1.2    8.5   0.0    2.2  2  TniB      Bacterial TniB protein
       0.12   12.6   0.0       0.24   11.6   0.0    1.5  1  DUF3474   Domain of unknown function (DUF3474)


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   2.3   1.1e-23   2.4e-20       1     233 []       3     192 ..       3     192 .. 0.87
   2 ?   -1.6   0.2      0.91     2e+03     143     143 ..     289     289 ..     202     363 .. 0.62
   3 ?   -1.7   0.7         1   2.3e+03     189     189 ..     354     354 ..     257     419 .. 0.62

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.1e-23
                      ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81 
                                   F+dRe+el+ ++e l++++ e ++iYG++++GKt+L+ e+i+         +yy a +++++  l +f          +++
  gi|70608040|ref|YP_256910.1|   3 FIDRERELEAIRERLNSDKLELILIYGRRRIGKTSLVLEAIKGY-----PSVYYLATEGRNN--LAKF----------KQT 66 
                                   99***************************************866.....7799988887764..4444..........334 PP

                      ATPase_2  82 lgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvvi 162
                                   +  ++p+           k v++ +e+++ ++++k    +++iDe+++li    ++++   + ++++i++ ++ +++ +++
  gi|70608040|ref|YP_256910.1|  67 AERVFPNI----------KFVKEDWESMFFALRDK----VVVIDEFPYLI----REDKAISSIFQKIIDEVLAGTKTKIIL 129
                                   44456664..........5599*************....9**********....888999999****************** PP

                      ATPase_2 163 clsSeglfiervyneselegrhky.ilvddldketalnflkegfkeleel..skedfeeiyryvGGkPkalvel 233
                                   ++sS + + + ++++s+l+gr++  +lv+ l++           kel+ l    ++  +i+ + GG P++l ++
  gi|70608040|ref|YP_256910.1| 130 LGSSISTMSDILSYKSPLYGRRTAsMLVNELKF-----------KELRRLgfDLNEAIKIFGFAGGVPYYLTKV 192
                                   ***********************999*****44...........444333336678999***********9886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.91
                      ATPase_2 143 k 143
                                   k
  gi|70608040|ref|YP_256910.1| 289 K 289
                                   1 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1
                      ATPase_2 189 v 189
                                   +
  gi|70608040|ref|YP_256910.1| 354 I 354
                                   1 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.7   8.3e+03      79      91 ..     152     164 ..     148     169 .. 0.78
   2 !   51.7   2.3     4e-17     9e-14       1      95 [.     296     374 ..     296     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.7
                        DUF234  79 ekkalfgEvKwkn 91 
                                   + ++l+ E K+k+
  gi|70608040|ref|YP_256910.1| 152 TASMLVNELKFKE 164
                                   5679999***998 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 4e-17
                        DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivaldeeekk 81 
                                   wfrf ypn seie+g     +e  ++e+ney+g  FEe++ ++l+e+        r++kvGr+W+k+ eiDi+  d++   
  gi|70608040|ref|YP_256910.1| 296 WFRFTYPNLSEIEEGI----FEISEREYNEYLGRIFEEVAVQYLKERY-------RLNKVGRHWYKDVEIDIL--DKDL-- 361
                                   **************97....4556899******************654.......478*************97..4444.. PP

                        DUF234  82 alfgEvKwknseke 95 
                                    l+gE+Kw++ + +
  gi|70608040|ref|YP_256910.1| 362 KLAGECKWSE-KVN 374
                                   489******9.444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.2   1.5e-11   3.3e-08       4     130 ..      24     165 ..      21     166 .. 0.69
   2 ?   -3.1   0.1       3.3   7.4e+03      20      42 ..     401     421 ..     397     426 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.5e-11
                        AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.....kllelileklke........ekktylflD 71 
                                   +++i G Rr+GKT l+ + ik +     s+ y++ +  ++ ++ +++      ++++++    e         +++++++D
  gi|70608040|ref|YP_256910.1|  24 LILIYGRRRIGKTSLVLEAIKGYP----SVYYLATEGRNNLAKFKQTaervfPNIKFVK----EdwesmffaLRDKVVVID 96 
                                   689*****************8888....9999999998885544332223332223333....2334466778999***** PP

                        AAA_14  72 Eiqevpewekalkslvd.......egknldvivtGSnskllsk..eiatslagrva.eielyplsfaEf 130
                                   E  ++ +  ka+ s+++        g++ ++i+ GS+ + +s     ++ l gr + ++ ++ l+f+E+
  gi|70608040|ref|YP_256910.1|  97 EFPYLIREDKAISSIFQkiidevlAGTKTKIILLGSSISTMSDilSYKSPLYGRRTaSMLVNELKFKEL 165
                                   *9999555555555555444354445789********99998833445777776653788899999985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                        AAA_14  20 kqlikellvkkesilyinldder 42 
                                   k ++k+   ++e++ yi+l++ +
  gi|70608040|ref|YP_256910.1| 401 KSFYKKD--ESEEVEYIDLEKLK 421
                                   4444444..48888899988754 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.4e-08   0.00014       3      63 ..       4      59 ..       3     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-08
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  + Re+ele++++ l+   s+  el+l++G + +GK+slv e+ + +    +++l+++ + +
  gi|70608040|ref|YP_256910.1|  4 IDRERELEAIRERLN---SDKLELILIYGRRRIGKTSLVLEAIKGYP--SVYYLATEGRNN 59
                                  569999988888665...7778*****************77665333..356655555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.8e-05     0.039       5      48 ..      25      80 ..      23     150 .. 0.74
   2 ?   -0.3   0.0      0.33   7.5e+02     147     174 ..     198     225 ..     186     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                        AAA_24  5 iliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdie............s 48
                                  iliyG   iGKT+l++e+    p++ ++ te+   + + +kf++               
  gi|70608040|ref|YP_256910.1| 25 ILIYGRRRIGKTSLVLEAikgYPSVYYLATEG---RNNLAKFKQTAervfpnikfvkeD 80
                                  89*****************9999*******99...455555553333333322233331 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.33
                        AAA_24 147 rlepklgkktanelkeevDlvlranlkr 174
                                    ++ ++ kk+   +k evD++lr + ++
  gi|70608040|ref|YP_256910.1| 198 DWINTELKKVDSFIKDEVDFLLRYEFQE 225
                                   4555566777888888888888876653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00052       1.2       7     130 ..      24     132 ..      18     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00052
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                   +++++G   +GKT l+ +  + +          p+v++    + ++++++ +   r +         + + + e  e  + 
  gi|70608040|ref|YP_256910.1|  24 LILIYGRRRIGKTSLVLEAIKGY----------PSVYYLATEGRNNLAKFKQTAERVFP--------NIKFVKEDWESMFF 86 
                                   68899999999999999998886..........45444444444466666444444444........45556677777777 PP

                        AAA_22  88 aravielliiDEaqhlr.seealeeL..rsllnl.srkgvqliLvGt 130
                                   a ++ ++++iDE+ +l+ +++a++ +  +++ ++ + +++++iL G 
  gi|70608040|ref|YP_256910.1|  87 ALRD-KVVVIDEFPYLIrEDKAISSIfqKIIDEVlAGTKTKIILLGS 132
                                   7778.899999999987667777777655555558899999999886 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00052       1.2      21      57 ..       8      44 ..       5      61 .. 0.86
   2 ?    0.6   0.0      0.14   3.2e+02     113     133 ..      83     103 ..      60     133 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00052
                          TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57
                                  ++Le++ e+ ++++ + +l++G+  +GKt++v +  +
  gi|70608040|ref|YP_256910.1|  8 RELEAIRERLNSDKLELILIYGRRRIGKTSLVLEAIK 44
                                  5799999999********************9976555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
                          TniB 113 rllrelkvrvLiiDEihnlla 133
                                   +++ +l+ +v++iDE+  l++
  gi|70608040|ref|YP_256910.1|  83 SMFFALRDKVVVIDEFPYLIR 103
                                   5677888899*****987765 PP

>> DUF3474  Domain of unknown function (DUF3474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.24     108     131 ..      72      95 ..      60      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                       DUF3474 108 PkhCWvkdpWrsmsyvvrDvvvvf 131
                                   P   +vk+ W+sm + +rD vvv+
  gi|70608040|ref|YP_256910.1|  72 PNIKFVKEDWESMFFALRDKVVVI 95 
                                   66779***************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3093.45
//
Query:       gi|70608041|ref|YP_256911.1|  [L=369]
Description: thiamine biosynthesis protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-46  156.7   0.0    8.2e-46  156.1   0.0    1.3  1  ThiI      Thiamine biosynthesis protein (ThiI)
    1.8e-15   57.3   0.7    1.8e-15   57.3   0.7    1.8  2  THUMP     THUMP domain
    2.9e-06   26.9   0.0    0.00093   18.8   0.0    2.5  2  QueC      Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.0   1.4e-49   8.2e-46       1     196 [.     164     354 ..     164     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 1.4e-49
                          ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeile 81 
                                   g+ gk+++L SgG+DSpVa+++l+kRG+r  l+ ++     ++ +++ v k +++l +++++ +++++ ++  +v +++++
  gi|70608041|ref|YP_256911.1| 164 GSTGKTVVLFSGGFDSPVATWMLMKRGVRPILLNFE---LGGKVQRDLVLKEVDVLKQWSSNNDINVYFINGLDVTSKLVN 241
                                   789***************************999995...6777788889999999*****999************999997 PP

                          ThiI  82 kvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkeigty 162
                                    +++ l+i+llkr m+  A  +a++ +a ++ tGesL+qV+Sqt+ Nl v++  ++l+++rPLig+dKeeii++ ++igt+
  gi|70608041|ref|YP_256911.1| 242 -AEPSLRILLLKRIMYNTARVLANKLRAYSITTGESLSQVSSQTMINLYVTEYDIDLPVFRPLIGFDKEEIIQMSRKIGTF 321
                                   .57789*************************************************************************** PP

                          ThiI 163 eisiekedkCsvlakhPttkakleevekaeeklk 196
                                   e s + +++C v++++  +k++l++v ++e k++
  gi|70608041|ref|YP_256911.1| 322 EYSSKLPEYC-VISNKSIVKSQLDKVLEEERKIE 354
                                   **********.6788899***********99987 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.7     3e-19   1.8e-15      41     140 ..      55     150 ..      11     154 .. 0.86
   2 ?   -2.4   0.1      0.78   4.7e+03      51      71 ..     344     364 ..     327     367 .. 0.61

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3e-19
                                   HHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE- CS
                         THUMP  41 kealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVd 121
                                   +++l+k++gi++ + v e  + +++di +++k  ++   +++  +FaV+vkr+g+h +f+s++++re+G a+   ++l Vd
  gi|70608041|ref|YP_256911.1|  55 YSKLSKVFGISKYFEVYEFSFSSIQDIVNFVKDRFNQTVKGK--KFAVKVKRVGNH-SFNSMDVAREIGNALYP-YSLGVD 131
                                   56788888******************************9998..************.***************99.999*** PP

                                   SSS-SEEEEEEEETTEEEE CS
                         THUMP 122 lenPdivvrveiikdkayi 140
                                   lenPd+ +++ +++d  y+
  gi|70608041|ref|YP_256911.1| 132 LENPDVKINLILRQDYGYV 150
                                   *********9988886555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.78
                                   CEEEEEEEEEESSHHHHHHHH CS
                         THUMP  51 qrvipvcevceadledileaa 71 
                                   ++v+ +++ +e + e+++++a
  gi|70608041|ref|YP_256911.1| 344 DKVLEEERKIEINYEELIKKA 364
                                   445555555555555555555 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-07   0.00093       1      43 [.     168     210 ..     168     247 .. 0.72
   2 !    5.7   0.0    0.0016       9.3     149     175 ..     294     320 ..     252     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-07
                                   EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHH CS
                          QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkelea 43 
                                   k vvl+SGG DS +++++ +k+g + ++l+f+ g + +++l  
  gi|70608041|ref|YP_256911.1| 168 KTVVLFSGGFDSPVATWMLMKRGVRPILLNFELGGKVQRDLVL 210
                                   689******************************9886655432 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0016
                                   TS--EEE-TTTT--HHHHHHHHHHTTH CS
                          QueC 149 dkkieieaPlidlsKaeivklgkelgv 175
                                   d ++ +  Pli ++K+ei++++ ++g 
  gi|70608041|ref|YP_256911.1| 294 DIDLPVFRPLIGFDKEEIIQMSRKIGT 320
                                   44567889****************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2336.40
//
Query:       gi|70608042|ref|YP_256912.1|  [L=345]
Description: myo-inositol-1-phosphate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   73.6   0.1    3.6e-20   72.2   0.0    1.8  2  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
    0.00013   21.5   0.1    0.00036   20.0   0.0    1.7  2  NAD_binding_5   Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.087   13.7   0.1       0.85   10.5   0.1    2.2  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   7.8e+03      69      80 ..      69      80 ..      46      88 .. 0.70
   2 !   72.2   0.0     6e-24   3.6e-20       1     108 [.     181     284 ..     181     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                                  .EEEEE-GGGTT CS
                Inos-1-P_synth 69 evvikYvpylgD 80
                                  +vv kYv++ gD
  gi|70608042|ref|YP_256912.1| 69 NVVPKYVDVRGD 80
                                  345588888888 PP

  == domain 2  score: 72.2 bits;  conditional E-value: 6e-24
                                   SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEEEE-GGGTTE CS
                Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvikYvpylgDs 81 
                                   G T l++ L+e+l+++g++v ++++++i Gn+++++  e++r++ Kk  Ks+++++ ++ +e+         +Yv++lgD+
  gi|70608042|ref|YP_256912.1| 181 GGTSLHTGLIEFLKSKGVQVLRTYQVDIAGNTEVLVTLEDWRKDLKKGIKSNFISKHIDGAEVVA----GTTDYVEFLGDR 257
                                   89*********************************************************988654....456********* PP

                                   EEEEEEEEEEEGGGEEEEEEEEEEEEH CS
                Inos-1-P_synth  82 KvaldeieseiflggkntielkleceD 108
                                   +v+++ +e+ +  g++++i+++l+ +D
  gi|70608042|ref|YP_256912.1| 258 RVSYIVVEGLYSFGIPVRIDVSLKSQD 284
                                   *************************99 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.32   1.9e+03       6      26 ..       7      26 ..       5      31 .. 0.84
   2 !   20.0   0.0   6.1e-08   0.00036     203     300 ..     131     324 ..      95     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.32
                                  xxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5  6 vGlgGnngtTlvagvlankkg 26
                                  +G+ Gn+++ lv ++ ++k+g
  gi|70608042|ref|YP_256912.1|  7 LGV-GNVASALVQALEMVKQG 26
                                  688.**********9999987 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 6.1e-08
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                 NAD_binding_5 203 ispstiyavAailegvpyingsPqntlvpglvelAekkgvfiaGdDfKt................................ 251
                                   + +s  ya  a+++g+++in +P  +lv+      ++kg++i GdD+ +                                
  gi|70608042|ref|YP_256912.1| 131 VKASEYYAEEALKAGSAFINATPT-SLVNQFSSAYKEKGIPIFGDDLLSqiggtslhtglieflkskgvqvlrtyqvdiag 210
                                   678999*****************6.56899999999********************************************* PP

                                   ............................................................................xxxxx RF
                 NAD_binding_5 252 ............................................................................lLAaP 256
                                                                                                                  aP
  gi|70608042|ref|YP_256912.1| 211 ntevlvtledwrkdlkkgiksnfiskhidgaevvagttdyveflgdrrvsyivveglysfgipvridvslksqdapNAVAP 291
                                   ***************************************************************************966679 PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 NAD_binding_5 257 lilDLvllveLaqrvevkkekkkefkklesvlsllsyflKaPlv 300
                                   l+ DL++++ +++  +v            s+ ++++y++K P v
  gi|70608042|ref|YP_256912.1| 292 LV-DLIRIAKMLKESRVG----------GSIPEVSGYYFKKPPV 324
                                   86.**********99999..........7888999999988854 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00014      0.85       1      88 [.       2     147 ..       2     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                   EEEEEETTSHHHHHHHHHHHHTTTTE................EEEEEECSSHHHHHHH......HHHTTHEEESS...... CS
                  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle................evvalldpdaeraeav......aesfgveaysd...... 53 
                                   +r ai G+G+++s  +++l   +++e                evva++d+d+ +           +  +v+ y d      
  gi|70608042|ref|YP_256912.1|   2 IRTAILGVGNVASALVQALEMVKQGEkiqgcltslpykpdeiEVVAAFDIDKRKVGYKlreaifQKPNVVPKYVDvrgdvv 82 
                                   5889*********99999999999998899999999999999999999999876532234444577777778888999999 PP

                                   ...........................HHHHHTCTTESEEEE-S-G...GGHHHHHHHHHHTT-E CS
                  GFO_IDH_MocA  54 ...........................leelladpeidavivatpn...gtheelakaaleagkh 88 
                                                              ++++l+d+++d+vi   p+   +  e +a++al+ag +
  gi|70608042|ref|YP_256912.1|  83 vkkgvvldslegileriielsdekesdISQVLKDEKVDVVINLLPTgvvKASEYYAEEALKAGSA 147
                                   99999999999999999999999999999999999999999999997766688888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2208.75
//
Query:       gi|70608043|ref|YP_256913.1|  [L=461]
Description: NADH dehydrogenase subunit N [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-42  145.4  32.4    1.9e-42  145.4  32.4    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.8     0.075   1.3e+03     211     251 ..      44      85 ..      16     112 .. 0.57
   2 !  145.4  32.4   1.1e-46   1.9e-42       1     291 [.     118     409 ..     118     411 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.075
               Proton_antipo_M 211 fkallFllagsviye.rektrdirayggLakkmPilalvllv 251
                                   ++++lF   g  +y   +++ ++++ g++     ++a++l+v
  gi|70608043|ref|YP_256913.1|  44 LSFTLFFSLGYYNYGvFNNALYLTKFGYFIAISSLIATILVV 85 
                                   344444444444333333444444444444444444444444 PP

  == domain 2  score: 145.4 bits;  conditional E-value: 1.1e-46
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslel 81 
                                   a+++l ++ ++ + + ++y+++ l+ k+ +s+eA++k+++++ll+s+++++g++ + ++ +tl+++ ++++      ++ +
  gi|70608043|ref|YP_256913.1| 118 AYNVLVIFASWAIASAATYVIAMLK-KDYQSVEAGVKYLVMGLLSSSLMIIGLAFFVTAGNTLYLDPVISY------QPLI 191
                                   789****************998887.555******************************************......99** PP

               Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.......vssneisqlllilai 155
                                   +l ++++ +++l+K++++p++ Wlp++y  a      +++++   +g+  l+++l  l+       v + ++ +l+ i+++
  gi|70608043|ref|YP_256913.1| 192 VLSIIFFSIAFLFKIGAFPFQGWLPEVYSLADRFSVGFVSSVGKIVGIEPLLVILYYLIqdnsssqVIYLTVVILFSIISV 272
                                   ****************************999999999998887777775444443333335522222233344567899** PP

               Proton_antipo_M 156 ismllgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyerektrdir 233
                                   +s+++g++ a +  d  ++lAySsi ++G+m+i++a+   + ++++++++++ll++++ +a+lF+   s + + + + +++
  gi|70608043|ref|YP_256913.1| 273 LSLIFGNISAFSRKDFAQILAYSSITQVGFMVIGIAMlpvNMNIAISGLMVYLLSYSIAQAGLFVSL-SHVEKITGSSYFE 352
                                   ***********************************9988889999********************99.5558888****** PP

               Proton_antipo_M 234 ayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasv 291
                                   + +g++  +++la  +++lllsl G+Pp +gF++k+ +Le++++  +++++ + + s+
  gi|70608043|ref|YP_256913.1| 353 SFRGMSSGDRVLAFSMTILLLSLLGIPPILGFWAKLFVLESSFSQPWLTIIGF-INSA 409
                                   ********************************************999999988.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3141.89
//
Query:       gi|70608044|ref|YP_256914.1|  [L=1141]
Description: membrane linked NADH-ubiquinone oxidoreductase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-74  250.9  84.9      9e-45  153.1  29.4    4.8  5  Proton_antipo_M  Proton-conducting membrane transporter
    2.3e-08   34.0  19.4    8.7e-06   25.7   3.7    5.0  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1  29.4     1e-48     9e-45       2     279 ..     123     408 ..     122     428 .. 0.87
   2 ?   -5.6   4.6         2   1.8e+04     119     180 ..     533     593 ..     451     597 .. 0.65
   3 !   14.2   0.1   2.1e-06     0.018       1      31 [.     622     652 ..     622     656 .. 0.92
   4 !  106.5  25.8   1.6e-34   1.4e-30      32     286 ..     672     948 ..     662     955 .. 0.84
   5 ?   -3.6   0.3      0.57   5.1e+03     182     210 ..     978    1004 ..     972    1018 .. 0.53

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 1e-48
               Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslell 82 
                                    +Ll ly++lE+ l+ ++lLi l+++  ++ + sl +f+ t +g ++ L +i++l   tgt+++     +l++    +  l
  gi|70608044|ref|YP_256914.1| 123 INLLELYIFLEIALITSFLLILLYGYG-DRRRISLMYFIWTHVGTILTLTSIVVLGLTTGTMDIYSSYGVLNNYSVINYSL 202
                                   69**********************999.88899*******************************99999977777777788 PP

               Proton_antipo_M  83 lllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgsl 163
                                   l++++ ++g+lvK a + ++ Wlp a+ eaPtp+s+ll+  +v +g++ ++  + l+  s  +++ +++  a+i+m++g+l
  gi|70608044|ref|YP_256914.1| 203 LIFVIGVIGMLVKGAIAGFNIWLPYAHGEAPTPISILLSPNMVGLGIFTVMIYFYLFP-SLSWLAPIFIGWAVITMIYGGL 282
                                   8888889*******************************999**********9999999.99******************** PP

               Proton_antipo_M 164 valaqtdiKrllAySsishlGymlialavatqy...........gveaaiihllthalfkallFllagsviyerektrdir 233
                                    a+aq d Kr lAySs+s++Gyml++++v+ +            gv a+i+  ++h++ ka lF+ ag++i e  ++r+i+
  gi|70608044|ref|YP_256914.1| 283 NAMAQKDFKRFLAYSSVSQMGYMLLGASVGFFVglkssvlslplGVIASILIYVSHGFGKAILFASAGAAITEL-EERNID 362
                                   **************************99944431111122222266778888899************9998776.89**** PP

               Proton_antipo_M 234 ayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavs 279
                                   ++ggL+   P    + +++ll + GlPp  g++s++l+L ++ +  
  gi|70608044|ref|YP_256914.1| 363 KLGGLYLISPAHTGLSFIGLLNILGLPPSVGLVSEILLLLSVGQLA 408
                                   *************************************997765432 PP

  == domain 2  score: -5.6 bits;  conditional E-value: 2
               Proton_antipo_M 119 llAatlvkagvlllirlllllavssneisqlllilaiismllgslvalaqtdiKrllAySsi 180
                                   l+ ++ + ++vl lir +    ++  e +  +   ++ s ll ++++++ + +   +A  si
  gi|70608044|ref|YP_256914.1| 533 LI-GISLILAVLNLIRSIHAPLFYPSETYTTFSYFSFSSSLLQAILGVFVSGLSFFIALYSI 593
                                   44.56667777777776665555666666666666777777777766666666666665555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.1e-06
               Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpks 31 
                                   +n+Lll+  g+E+++l++y Li +w +++++
  gi|70608044|ref|YP_256914.1| 622 SNNLLLFLAGWEGTSLASYGLISYWLDDNER 652
                                   79***********************998876 PP

  == domain 4  score: 106.5 bits;  conditional E-value: 1.6e-34
               Proton_antipo_M  32 leAslklflltllgsliLLlgilllynltg..tlefeelskal......elglnslelllllllllvgllvKsaqvplhlW 104
                                   +++++ +++ t+l+++ L +g+ +l+ lt+  + +f +++++        l+++ + + l+l+++++g + Ksaq+pl +W
  gi|70608044|ref|YP_256914.1| 672 TNSGIRAMIFTRLADVGLAIGLGYLLFLTSlgNPYFGNMALFDgvfrviPLVYALPYAWLILFFIMIGGIGKSAQFPLTQW 752
                                   6899***************998765555443388888888887888888999***************************** PP

               Proton_antipo_M 105 lpdayveaPtpvsall.Aatlvkagvlllirllllla...vssneisqlllilaiismllgslvalaqtdiKrllAySsis 181
                                   l  a + +Ptpvsal+ Aat+v++g++l + l ++l      +  +s +++ +++ +++++s+ ala ++ K +lAyS+  
  gi|70608044|ref|YP_256914.1| 753 LLTA-MTGPTPVSALIhAATMVNLGAILTFFLYPFLVypsPQTTLLSAIMMGVSLFTAIYTSTNALASNEQKVILAYSTAD 832
                                   ****.***********************998888777656677778999999***************************** PP

               Proton_antipo_M 182 hlGymlialav.........atqy...gveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvll 250
                                   ++ +m++  ++         +++y   g+   ++++l+h+  kallF+ agsvi+ + + r+    ++L+k+ P ++++ l
  gi|70608044|ref|YP_256914.1| 833 QISLMILSSSTgaflasvfnNSVYltaGILVGLVQMLAHGTYKALLFMNAGSVIHFT-ENRYTGVFRSLYKRLPSIFILQL 912
                                   *****986654222222222333311133444689******************9988.88999****************** PP

               Proton_antipo_M 251 vlllslaGlPptagFlskfliLeaavavslillvla 286
                                   +++l la +Pp+ gF++  +i   + +++li l ++
  gi|70608044|ref|YP_256914.1| 913 IGALNLASIPPLVGFWAHNAIGDLVSDAGLIYLYIL 948
                                   *****************9998877777777776665 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 0.57
               Proton_antipo_M  182 hlGymlialavatqygveaaiihllthal 210 
                                    h+G+ ++ +a   + +++++++ +l + +
  gi|70608044|ref|YP_256914.1|  978 HIGLTMVTAAS--ILALASIVLGVLYYFF 1004
                                    56665555555..3433333333333333 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   7.7e-07    0.0069      13      46 ..      59      92 ..      53     110 .. 0.87
   2 ?   -2.8   0.1      0.76   6.9e+03      44      57 ..     285     297 ..     284     298 .. 0.74
   3 !   25.7   3.7   9.7e-10   8.7e-06      14      56 ..     566     608 ..     558     612 .. 0.85
   4 ?   -1.2   0.7      0.24   2.2e+03      22      40 ..     794     812 ..     786     814 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.7e-07
               Proton_antipo_N 13 eigfllDklsalmllvvtfvsllvhlYSigYMad 46
                                  ++gf ++ l + +++++ +v+l+   YS  YM++
  gi|70608044|ref|YP_256914.1| 59 NFGFTVNDLNLGFVITILIVTLVTAYYSQRYMQK 92
                                  79******************************75 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.76
               Proton_antipo_N  44 MaddegyqRFfayl 57 
                                   Ma  + ++RF ay 
  gi|70608044|ref|YP_256914.1| 285 MA-QKDFKRFLAYS 297
                                   55.3469*****95 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 9.7e-10
               Proton_antipo_N  14 igfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                   ++f  + l a+  ++v+++s+++ lYSigYM++d   +R+  +
  gi|70608044|ref|YP_256914.1| 566 FSFSSSLLQAILGVFVSGLSFFIALYSIGYMKEDHVLRRYWGF 608
                                   6788888999************************877777544 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.24
               Proton_antipo_N  22 salmllvvtfvsllvhlYS 40 
                                   + l  ++  +vsl+  +Y+
  gi|70608044|ref|YP_256914.1| 794 TTLLSAIMMGVSLFTAIYT 812
                                   5556667778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.87u 0.31s 00:00:01.18 Elapsed: 00:00:00.49
# Mc/sec: 7067.57
//
Query:       gi|70608045|ref|YP_256915.1|  [L=94]
Description: membrane linked NAD(P)H-quinone oxidoreductase chain 4L [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-10   40.5   8.8    1.9e-10   40.3   8.8    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
    0.00094   19.2   5.1     0.0013   18.8   5.1    1.2  1  TspO_MBR     TspO/MBR family
  ------ inclusion threshold ------
          3    7.8   7.4          2    8.3   0.4    2.3  2  CoatB        Bacteriophage coat protein B


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   8.8   3.2e-14   1.9e-10       3     101 ..       8      94 .]       6      94 .] 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3.2e-14
                                   HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHH CS
                   Oxidored_q2   3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetav 83 
                                   l+++++l++i++yg+l ++n+++++++ e++ na +l+++ ++++t             +  lp ++ L+ai  ++ e++v
  gi|70608045|ref|YP_256915.1|   8 LMVSVVLIGISVYGFLNSKNIVRIFLSSEILVNASILIVFSVSSLT------------NQVYLPIYFSLFAIGMALVEIVV 76 
                                   5899*****************************************9............5889******************* PP

                                   HHHHHHHHHHHSSS-BCC CS
                   Oxidored_q2  84 gLallvrlyreygtddvq 101
                                   + a ++  y+++g+++v+
  gi|70608045|ref|YP_256915.1|  77 AFAAIFLYYKNKGSLEVE 94 
                                   ***************996 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   5.1   2.1e-07    0.0013      45     102 ..      10      85 ..       3      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-07
                                   HHHHHHHHHHHHHHHH..................HHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHH CS
                      TspO_MBR  45 vlyilmgvaaylvwka..................lalyavqlvlnllwsplffglkspvlalvdivallglvvali 102
                                   v  +l+g++ y  +++                  l+++ v+ + n ++ p++f l  +++alv+iv+ ++++++ +
  gi|70608045|ref|YP_256915.1|  10 VSVVLIGISVYGFLNSknivriflsseilvnasiLIVFSVSSLTNQVYLPIYFSLFAIGMALVEIVVAFAAIFLYY 85 
                                   566788888888777788999999999999999977*******************************999988776 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4   0.00033         2      23      42 ..       4      23 ..       2      24 .. 0.90
   2 ?    2.3   1.7     0.025   1.5e+02      24      41 ..      66      84 ..      65      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00033
                         CoatB 23 aaiGaaVLvvlVgvavfkWv 42
                                  + iG  V vvl+g+ v+ ++
  gi|70608045|ref|YP_256915.1|  4 GYIGLMVSVVLIGISVYGFL 23
                                  68***************875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                         CoatB 24 aiGaaVLvvlVg.vavfkW 41
                                  aiG a   ++V+ +a+f +
  gi|70608045|ref|YP_256915.1| 66 AIGMALVEIVVAfAAIFLY 84
                                  6898876655542777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 724.25
//
Query:       gi|70608046|ref|YP_256916.1|  [L=168]
Description: hypothetical protein Saci_2341 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-13   51.2  19.4      1e-13   51.2  19.4    1.4  2  Oxidored_q3    NADH-ubiquinone/plastoquinone oxidoreductase c
  ------ inclusion threshold ------
          7    6.5  30.0         51    3.7  30.0    2.2  1  7TMR-DISM_7TM  7TM diverse intracellular signalling


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3      0.59   5.3e+03      15      24 ..      10      19 ..       4      21 .. 0.50
   2 !   51.2  19.4   1.1e-17     1e-13       1     144 []      22     163 ..      22     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.59
                                  HHHHHHHHHH CS
                   Oxidored_q3 15 alfLilsfvg 24
                                  a+ L++s+++
  gi|70608046|ref|YP_256916.1| 10 AFLLLFSVFA 19
                                  3444444444 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 1.1e-17
                                   HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHT...T-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHH CS
                   Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfill...gaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslala 78 
                                   ++ll++ +kn++ysa++L l+ v+va+++ ll    ++F+++l++++YvG  +v++  +++ +  ++ e +e++  ++ ++
  gi|70608046|ref|YP_256916.1|  22 SSLLIVRQKNVFYSAVALGLLGVSVAVIIALLnpiAYSFYSALHLILYVGSAIVFLSVSLVVF--RGLEVKERRVAWASIL 100
                                   5899****************************55559***************99999999996..7788888888888888 PP

                                   HHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
                   Oxidored_q3  79 alligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                                   +++++l++++ ++l++ e   ++ ++ +a+v ++++ +++l+++y++p++++ + L ++li a+ l
  gi|70608046|ref|YP_256916.1| 101 GFITALVVFFAFILTFVE---NTPTPLQAQVFTLSTFANTLLSDYWFPILILVIALATTLIEALSL 163
                                   888888888887777765...34455677888*****************************99865 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  30.0    0.0057        51      72     188 ..      10     141 ..       3     165 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0057
                 7TMR-DISM_7TM  72 tlllllilfll.Farsflelkkkp....rllklllllavllsllllllpllpyteslslaqllallvillllligikaw.. 145
                                   ++lll+ +f++  +  + +   k+     +   ll+++v+  ++++ll+ + y++++ l ++l++  ++++l ++++++  
  gi|70608046|ref|YP_256916.1|  10 AFLLLFSVFAIaSSLLIVRQ--KNvfysAVALGLLGVSVA--VIIALLNPIAYSFYSALHLILYVGSAIVFLSVSLVVFrg 86 
                                   33444434444333333444..433323333333334433..555555555777777777788888888888888888888 PP

                 7TMR-DISM_7TM 146 ..rkgnkparyfliawlllligvlidils.........llgllpsn.ffteyllq 188
                                     +k ++ a+  +++++  l+ ++ +il+           ++++ + f  + l+ 
  gi|70608046|ref|YP_256916.1|  87 leVKERRVAWASILGFITALVVFFAFILTfventptplQAQVFTLStFANTLLSD 141
                                   9**************************9943333333222244444222224444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1340  (0.0747392); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1149.18
//
Query:       gi|70608047|ref|YP_256917.1|  [L=165]
Description: NADH dehydrogenase subunit I [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-15   53.8  13.5    3.8e-09   36.0   3.7    2.5  2  Fer4      4Fe-4S binding domain
      3e-12   46.5  19.5    1.7e-08   34.5  10.4    2.1  2  Fer4_21   4Fe-4S dicluster domain
    9.4e-11   41.7  15.8    9.9e-08   32.0   9.0    1.8  2  Fer4_10   4Fe-4S dicluster domain
    3.8e-10   40.2   9.2      7e-10   39.3   9.2    1.5  1  Fer4_7    4Fe-4S dicluster domain
    1.7e-09   38.5   4.3    0.00039   21.3   0.1    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
    1.2e-08   35.0   6.9    1.9e-08   34.3   6.9    1.4  1  Fer4_9    4Fe-4S dicluster domain
    2.2e-08   33.8  14.9    0.00034   20.6   3.1    2.5  2  Fer4_6    4Fe-4S binding domain
      8e-07   28.8  10.5     0.0041   17.1   2.9    2.4  2  Fer4_2    4Fe-4S binding domain
    3.1e-05   24.1   9.4      0.018   15.5   1.8    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00022   22.0  16.5      0.031   15.2   4.9    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00055   20.4   6.7       0.18   12.4   0.7    2.4  3  Fer4_17   4Fe-4S dicluster domain
    0.00058   20.3   8.3      0.027   14.9   0.6    2.2  2  Fer4_8    4Fe-4S dicluster domain
     0.0033   18.1   5.5       0.44   11.3   0.5    2.5  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.072   13.6  10.2        0.5   11.0   2.3    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.17   12.1  11.0      0.094   12.9   1.7    2.3  2  Fer4_18   4Fe-4S dicluster domain
        1.2   10.0  11.9        6.9    7.6   2.2    2.3  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   2.2     4e-08   4.5e-05       5      23 ..      59      77 ..      55      78 .. 0.89
   2 !   36.0   3.7   3.4e-12   3.8e-09       1      24 []      88     111 ..      88     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                                  TTTSSS-THHHHHSTTTEE CS
                          Fer4  5 eekCigCGaCvevCPvgAI 23
                                  ++ CigC +C+ +CP +A 
  gi|70608047|ref|YP_256917.1| 59 KDICIGCTLCALICPADAM 77
                                  799**************97 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3.4e-12
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                          Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                   +vi++ +C++CG Cv+vCPv+A++
  gi|70608047|ref|YP_256917.1|  88 PVINYGRCVFCGFCVDVCPVDALR 111
                                   69********************85 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.6   2.9e-08   3.2e-05      33      59 .]      54      79 ..      41      79 .. 0.82
   2 !   34.5  10.4   1.5e-11   1.7e-08       5      56 ..      59     109 ..      55     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.9e-08
                       Fer4_21 33 vlkvvedeCvGCnlCssvCPvedciem 59
                                  ++++ +d C+GC+lC+ +CP  d+++m
  gi|70608047|ref|YP_256917.1| 54 MIRLYKDICIGCTLCALICPA-DAMKM 79
                                  677889**************5.99988 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.5e-11
                       Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPvedc 56 
                                   +d CigC++C++ C+  +++  + ++k +l+v+   +Cv C  C++vCPv d+
  gi|70608047|ref|YP_256917.1|  59 KDICIGCTLCALICPADAMKMTTEAGK-KLPVInYGRCVFCGFCVDVCPV-DA 109
                                   789************755555554444.55665278*************9.55 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   9.0   8.9e-11   9.9e-08       3      56 .]      56     106 ..      54     106 .. 0.80
   2 !   20.5   0.5   3.5e-07   0.00039       2      24 ..      88     116 ..      87     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8.9e-11
                       Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   ++ +d Ci+C+ C   CPa      +   + +++   +++++C +cg Cv++CP
  gi|70608047|ref|YP_256917.1|  56 RLYKDICIGCTLCALICPA---DAMKMTTEAGKKLPVINYGRCVFCGFCVDVCP 106
                                   56689**************...4444445555555666***************9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.5e-07
                       Fer4_10   2 vvidddtCirCgkCvkaCPadl......t 24 
                                   +vi+  +C+ Cg Cv++CP+d+      +
  gi|70608047|ref|YP_256917.1|  88 PVINYGRCVFCGFCVDVCPVDAlretrvH 116
                                   589999**************766554440 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   9.2   6.3e-13     7e-10       2      52 .]      62     109 ..      61     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.3e-13
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                   CigC  C+  Cp++a++++ e   +g++ ++i++ +C++Cg Cv+vCP++a
  gi|70608047|ref|YP_256917.1|  62 CIGCTLCALICPADAMKMTTE---AGKKLPVINYGRCVFCGFCVDVCPVDA 109
                                   ******************997...577779*******************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.1   3.1e-06    0.0035       2      22 ..      62      82 ..      61      92 .. 0.86
   2 !   21.3   0.1   3.4e-07   0.00039       1      21 [.      94     115 ..      94     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.1e-06
                       Fer4_16  2 CgtCgkCaevCPtnaikekke 22
                                  C++C+ Ca +CP++a+k+++e
  gi|70608047|ref|YP_256917.1| 62 CIGCTLCALICPADAMKMTTE 82
                                  *****************9844 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.4e-07
                       Fer4_16   1 rCgtCgkCaevCPtnaikek.k 21 
                                   rC+ Cg C++vCP++a++e+  
  gi|70608047|ref|YP_256917.1|  94 RCVFCGFCVDVCPVDALRETrV 115
                                   6*****************9832 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   6.9   1.7e-11   1.9e-08       2      50 ..      62     109 ..      61     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.7e-11
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                   C+gC+ C   Cpa+++++   ++k    + ++ +C++Cg Cv++Cp +a
  gi|70608047|ref|YP_256917.1|  62 CIGCTLCALICPADAMKMTTEAGKKLPVI-NYGRCVFCGFCVDVCPVDA 109
                                   ****************7666655554433.4457************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   4.1   1.2e-06    0.0014       7      23 ..      60      76 ..      59      77 .. 0.92
   2 !   20.6   3.1     3e-07   0.00034       2      24 .]      88     110 ..      87     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.2e-06
                        Fer4_6  7 dkCigCgdCvrvCPega 23
                                  d CigC  C+ +CP++a
  gi|70608047|ref|YP_256917.1| 60 DICIGCTLCALICPADA 76
                                  89*************98 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 3e-07
                        Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                   ++i++ +C+ Cg Cv+vCP +a+
  gi|70608047|ref|YP_256917.1|  88 PVINYGRCVFCGFCVDVCPVDAL 110
                                   89*****************9996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   8.2e-06    0.0091       7      22 .]      59      74 ..      54      74 .. 0.91
   2 !   17.1   2.9   3.7e-06    0.0041       3      21 ..      88     106 ..      86     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.2e-06
                        Fer4_2  7 tdrCigCgaCvsaCPa 22
                                   d+CigC  C   CPa
  gi|70608047|ref|YP_256917.1| 59 KDICIGCTLCALICPA 74
                                  699************8 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.7e-06
                        Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                   +v++  rC+ Cg Cv++CP
  gi|70608047|ref|YP_256917.1|  88 PVINYGRCVFCGFCVDVCP 106
                                   899**************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.0    0.0001      0.11       2      16 ..      60      74 ..      59      80 .. 0.89
   2 !   15.5   1.8   1.6e-05     0.018       3      16 ..      94     107 ..      92     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                        Fer4_4  2 erCigCgsCvaaCPq 16
                                  + CigC  C  +CP 
  gi|70608047|ref|YP_256917.1| 60 DICIGCTLCALICPA 74
                                  67************5 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                        Fer4_4   3 rCigCgsCvaaCPq 16 
                                   rC+ Cg Cv++CP+
  gi|70608047|ref|YP_256917.1|  94 RCVFCGFCVDVCPV 107
                                   9************6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   3.7   0.00018       0.2       1      15 []      62      76 ..      62      76 .. 0.95
   2 !   15.2   4.9   2.8e-05     0.031       1      15 []      95     109 ..      95     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                        Fer4_3  1 CtgCgaCvevCPvgA 15
                                  C+gC +C   CP +A
  gi|70608047|ref|YP_256917.1| 62 CIGCTLCALICPADA 76
                                  ************887 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.8e-05
                        Fer4_3   1 CtgCgaCvevCPvgA 15 
                                   C+ Cg Cv+vCPv+A
  gi|70608047|ref|YP_256917.1|  95 CVFCGFCVDVCPVDA 109
                                   *************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.9   0.00051      0.57      43      59 ..      59      75 ..      27      77 .. 0.79
   2 !   11.6   0.7   0.00028      0.32      42      58 ..      91     107 ..      74     109 .. 0.67
   3 !   12.4   0.7   0.00016      0.18       1      19 [.      94     112 ..      94     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                       Fer4_17 43 aslCieCgeCerkCPqg 59
                                   + Ci+C +C+  CP++
  gi|70608047|ref|YP_256917.1| 59 KDICIGCTLCALICPAD 75
                                  56799999999999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00028
                       Fer4_17  42 kaslCieCgeCerkCPq 58 
                                   + ++C+ Cg C+ +CP 
  gi|70608047|ref|YP_256917.1|  91 NYGRCVFCGFCVDVCPV 107
                                   55677777777777774 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00016
                       Fer4_17   1 rCiqCgyClpeCpsyeayd 19 
                                   rC  Cg+C+++Cp  + ++
  gi|70608047|ref|YP_256917.1|  94 RCVFCGFCVDVCPVDALRE 112
                                   6999999999999855544 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.6    0.0011       1.3       5      17 ..      62      74 ..      59      94 .. 0.78
   2 !   14.9   0.6   2.4e-05     0.027       4      22 ..      94     114 ..      91     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                        Fer4_8  5 CieCgaCqsaCpv 17
                                  Ci+C +C   Cp+
  gi|70608047|ref|YP_256917.1| 62 CIGCTLCALICPA 74
                                  ***********93 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.4e-05
                        Fer4_8   4 kCieCgaCqsaCp..vlrrtk 22 
                                   +C+ Cg+C + Cp  +lr+t+
  gi|70608047|ref|YP_256917.1|  94 RCVFCGFCVDVCPvdALRETR 114
                                   799999999999955444444 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.5   0.00039      0.44       5      19 ..      59      73 ..      55      86 .. 0.85
   2 !    9.0   0.5    0.0021       2.3       3      19 ..      90     106 ..      89     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                       Fer4_15  5 rdaCigcglCvaeap 19
                                  +d Cigc lC+  +p
  gi|70608047|ref|YP_256917.1| 59 KDICIGCTLCALICP 73
                                  799**********98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
                       Fer4_15   3 vDrdaCigcglCvaeap 19 
                                   ++  +C  cg Cv+++p
  gi|70608047|ref|YP_256917.1|  90 INYGRCVFCGFCVDVCP 106
                                   66679***********8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.3   0.00044       0.5       4      17 ..      60      73 ..      59      84 .. 0.91
   2 ?    6.9   1.2    0.0082       9.1       2      17 ..      91     106 ..      90     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                       Fer4_13  4 dtCiacgaCvelaP 17
                                  d Ci+c++C+ ++P
  gi|70608047|ref|YP_256917.1| 60 DICIGCTLCALICP 73
                                  67************ PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0082
                       Fer4_13   2 DrdtCiacgaCvelaP 17 
                                   +  +C+ cg Cv+++P
  gi|70608047|ref|YP_256917.1|  91 NYGRCVFCGFCVDVCP 106
                                   5568***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.7     0.012        13      61      92 ..      62      96 ..      56      96 .. 0.81
   2 ?   12.9   1.7   8.4e-05     0.094      57      74 ..      91     108 ..      75     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                       Fer4_18 61 cidcescvkvcP...tgidirkGlqleciscllci 92
                                  ci c  c  +cP   +++    G +l  i+ ++c+
  gi|70608047|ref|YP_256917.1| 62 CIGCTLCALICPadaMKMTTEAGKKLPVINYGRCV 96
                                  ************33335677889999999999997 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.4e-05
                       Fer4_18  57 gagdcidcescvkvcPtg 74 
                                   + g c+ c++cv+vcP++
  gi|70608047|ref|YP_256917.1|  91 NYGRCVFCGFCVDVCPVD 108
                                   6789************85 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.3    0.0073       8.2      81      94 ..      61      74 ..      51      76 .. 0.68
   2 ?    6.9   2.4    0.0099        11       2      14 ..      62      74 ..      61      89 .. 0.78
   3 ?    7.6   2.2    0.0061       6.9      78      94 ..      91     107 ..      76     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0073
                       Fer4_22 81 gCvGCgRCieacpv 94
                                   C+GC  C   cp+
  gi|70608047|ref|YP_256917.1| 61 ICIGCTLCALICPA 74
                                  56666666666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0099
                       Fer4_22  2 ClsCgaCtlvCpt 14
                                  C++C+ C+l+Cp+
  gi|70608047|ref|YP_256917.1| 62 CIGCTLCALICPA 74
                                  8888888888886 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0061
                       Fer4_22  78 gesgCvGCgRCieacpv 94 
                                   +   Cv Cg C+++cpv
  gi|70608047|ref|YP_256917.1|  91 NYGRCVFCGFCVDVCPV 107
                                   56679999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1217.13
//
Query:       gi|70608048|ref|YP_256918.1|  [L=352]
Description: NADH dehydrogenase subunit H [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-77  259.8  29.1    3.8e-77  259.5  29.1    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.5  29.1   2.1e-81   3.8e-77       8     297 ..      26     342 ..      19     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 259.5 bits;  conditional E-value: 2.1e-81
                                   HHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT..TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS CS
                        NADHdh   8 vvlllvvalltlleRkvlAriqdRlGPnrvGpl..GllqplaDalKlllKediipkkadkllfllapvlalilallafavi 86 
                                   ++++++++l++++eRk++A +q+R+GP +v+++  G+lq++aDa++l + e i+p++++ +lf l p+ +l++++l +avi
  gi|70608048|ref|YP_256918.1|  26 IFTVIILLLTIWFERKIAAIVQMRVGPLYVSKRvgGILQLVADAIRLAFSEIIVPRDVNAVLFGLVPIAVLVFSILPLAVI 106
                                   34566666***********************8667********************************************** PP

                                   -SS..S.......................SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHH CS
                        NADHdh  87 Pfg..e.......................vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEva 142
                                   Pf+  +                       v   +n++++l+l ++++ +++ill +w +n+++a++Ga+R+a   +sy+v 
  gi|70608048|ref|YP_256918.1| 107 PFSaiPasgsilssyfhafydpsigkgvfVGFFVNYNMILALGILAIVPVFILLQAWVTNNRFAIVGAVREALLSVSYDVL 187
                                   ***652677888888888888888888544444499********************************************* PP

                                   HHHHHHHHHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHH CS
                        NADHdh 143 lglsllavvllagslslseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalffla 223
                                   +++s++a+++ +++l++ ++ve+   i  +++++la+++f+i +++ t+r+PF+++eaesELv G+ tEYsg+ f l + +
  gi|70608048|ref|YP_256918.1| 188 IVISVVAIAIEYHTLDMAKVVETG--IPGAIANPLAAFVFFIGMIMGTGRFPFEIVEAESELVIGPATEYSGFLFILSMGG 266
                                   ********************9965..4558899************************************************ PP

                                   HHHHHHHHHHHHHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                        NADHdh 224 eyanmvlvsalavllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                   +y++++++s +++ lFl Gwl pf+   g+l++ +K +++l++ +++r+++ R+R+dq++k++wk++lp+a+a+l+l
  gi|70608048|ref|YP_256918.1| 267 SYIETFALSYIFSNLFLNGWL-PFGgllGALMVSIKSIIVLWFSVFLRSVYGRYRIDQALKISWKYILPIAFASLIL 342
                                   ********************6.677799**********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2408.59
//
Query:       gi|70608049|ref|YP_256919.1|  [L=400]
Description: NADH dehydrogenase subunit D [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-94  316.2   0.0      2e-94  315.7   0.0    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.018   14.0   0.1       0.07   12.0   0.1    1.9  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.7   0.0   2.2e-98     2e-94       2     271 .]     131     400 .]     131     400 .] 0.96

  Alignments for each domain:
  == domain 1  score: 315.7 bits;  conditional E-value: 2.2e-98
                                   TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSS CS
                Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkg 82 
                                   lG+ t f++ f +Re ++++l+++tGaR+t+syi++GGv+rDl++ + e+i++++ + +kk++++ k+l++n+ +++R+++
  gi|70608049|ref|YP_256919.1| 131 LGHSTGFMWGFGDREVWVEILQAITGARVTNSYIIPGGVRRDLTPAIKEMIEKAIVYQRKKIQDWYKILVNNPNIRARLEN 211
                                   69******************************************************************************* PP

                                   SS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S- CS
                Complex1_49kDa  83 vgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegp 163
                                   vgv+ske+a+++g++Gp+lRasGv yD+Rk epY aYd++df++p+ +egD+y+R+lvr+eEm+qS++I+eq+++++p+g+
  gi|70608049|ref|YP_256919.1| 212 VGVMSKENAIKWGAVGPNLRASGVYYDVRKIEPYGAYDKVDFEIPMYKEGDAYARTLVRFEEMEQSMRILEQVIKQIPDGN 292
                                   ********************************************************************************* PP

                                   SB---TTTS---GGGGGT-HHHH.HHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTH CS
                Complex1_49kDa 164 vlaedkkvalpkkeevkksmeal.ihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqal 243
                                   +l+++   ++p+  ++kk +e      f  +   f+ pkge++++vEa++Gel +y++sdgs kpyrl++ +ps+  + ++
  gi|70608049|ref|YP_256919.1| 293 ILSDRFFKQIPP-VRLKKWWEGQrRVVFPGYYASFRPPKGEAISRVEAGRGELAYYIISDGSPKPYRLRMITPSYRLIYVF 372
                                   ***998887777.4445555443033599999************************************************* PP

                                   HHHTTTS-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 244 eellkgellaDvvailgsldivlgevDR 271
                                   +el+kg++ aD+vai+gsld++ +e+DR
  gi|70608049|ref|YP_256919.1| 373 KELCKGARYADLVAIYGSLDYFPPEADR 400
                                   ***************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.8e-06      0.07      34      67 ..      88     121 ..      57     124 .. 0.91
   2 ?   -1.7   0.0      0.11   9.7e+02     419     449 ..     329     357 ..     312     365 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.8e-06
                                   HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHH CS
                  NiFeSe_Hases  34 svravedAlgikipknarlirnliaaalllhdhi 67 
                                    ++ave+ l++++p+ a+++r+l+a ++ + +h+
  gi|70608049|ref|YP_256919.1|  88 YIMAVEKILNVDVPERAQYLRTLVAEVNRIASHL 121
                                   589**************************99997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.11
                                   -SEEEEEEEEEETTEEEEEEEEEETTEEEEE CS
                  NiFeSe_Hases 419 pkeakGvglveapRGaLsHwikikdgkienY 449
                                   pk  + +  vea RG L+ +i i+dg  + Y
  gi|70608049|ref|YP_256919.1| 329 PK-GEAISRVEAGRGELAYYI-ISDGSPKPY 357
                                   34.7888999********998.666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2591.41
//
Query:       gi|70608050|ref|YP_256920.1|  [L=164]
Description: NADH dehydrogenase subunit C [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-34  117.4   0.0    6.9e-34  117.1   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.0   3.8e-38   6.9e-34       2     120 ..      34     155 ..      33     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 3.8e-38
                                   E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.....-EEEEEE....-S-BEE--TTT-STH CS
                Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllslekn....erirvkvevdeeepevpSvtdlfpga 77 
                                    v+++++le+a++lk+    gfd++  +t++D++ +e+fevvyh++s+++     + + ++ +++ ++p++pS+ ++++++
  gi|70608050|ref|YP_256920.1|  34 IVDKSQILEIANYLKQ---IGFDHVKAVTGIDYPeTEEFEVVYHISSYSDLalakVIVALREKTSYKDPVFPSLFKVWESV 111
                                   699************9...*************9999************6553433333333333557************** PP

                                   HHHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-.TTSTTS---- CS
                Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillpedfegh.PLRkdfplsg 120
                                      ERE+y+m+Givfeghp+lrr++l+edfeg  PLRk+++l++
  gi|70608050|ref|YP_256920.1| 112 WTGERETYEMLGIVFEGHPELRRMFLDEDFEGVyPLRKSYKLKQ 155
                                   ******************************8866*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 870.86
//
Query:       gi|70608051|ref|YP_256921.1|  [L=129]
Description: NADH dehydrogenase subunit A [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-07   30.5   3.4    3.3e-07   30.4   2.7    1.4  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch
     0.0026   17.7   4.5     0.0026   17.7   4.5    1.3  1  YqhR         Conserved membrane protein YqhR


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   2.7   3.7e-11   3.3e-07      14      92 ..      34     116 ..      22     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.7e-11
                                   ----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHH.....HHHHHHHHHHHHHHHH CS
                   Oxidored_q4  14 kkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfg.....liemllFllillvglv 89 
                                    ++n+ k s +E+G  p+ge rl f++++y + l++   +  vv+lf  a +++ +  ++     li +l+ +++l   l+
  gi|70608051|ref|YP_256921.1|  34 GQYNPVKVSRFEAGNIPFGEGRLWFPLQYYGYLLIYTSIEPIVVILFSLAQAYYYT-STTlftnlLIIALVSIALLYPVLY 113
                                   368899******************************************99998744.344011334455555555555555 PP

                                   HHH CS
                   Oxidored_q4  90 Yew 92 
                                   Y++
  gi|70608051|ref|YP_256921.1| 114 YAI 116
                                   555 PP

>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.5   2.9e-07    0.0026      24      96 ..      49     119 ..      31     127 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-07
                          YqhR  24 iGfvGGvlWsllaylaylfnfsevspnlilepwvlgdWkkkalGtvisivligvvsigvallyyvllkkiksl 96 
                                   i f  G lW  l y  yl+ +++++p +++    +  + ++    ++ +++i++vsi+  lly vl+  ik++
  gi|70608051|ref|YP_256921.1|  49 IPFGEGRLWFPLQYYGYLLIYTSIEPIVVILFSLAQAYYYTSTTLFTNLLIIALVSIA--LLYPVLYYAIKQI 119
                                   5677899*******************7665555555677778889999******9985..5555554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 877.00
//
Query:       gi|70608052|ref|YP_256922.1|  [L=260]
Description: thymidylate synthase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-64  214.9   0.2    9.5e-64  214.7   0.2    1.1  1  Thy1      Thymidylate synthase complementing protein


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.7   0.2   5.3e-68   9.5e-64       1     187 [.       4     193 ..       4     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 214.7 bits;  conditional E-value: 5.3e-68
                                   EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH...S.GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTS CS
                          Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele..e.eekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHRia 77 
                                   kL++y+ d e++va aa+++ +++ + + +e  + ++++e++i++ ++hg +s+leh+++tf ieg+Sr++++qlvrHRia
  gi|70608052|ref|YP_256922.1|   4 KLVSYSkDGERIVAIAAKMSRSRK-GWDYHEkeMtDDEIETWIRDSITHGYWSVLEHSVYTFSIEGISRVASHQLVRHRIA 83 
                                   699*****************9554.555544444568999***************************************** PP

                                   EEEE--TTTSGCCCTC..BS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHH CS
                          Thy1  78 sfsqqSqRYvesskea..fvippeieqkeeleelyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLl 156
                                   s++q S R+ +  ++    ++pp+ie+  + +e++++a+++a++++++lle+gv++EdaryvLP++++t++vvtmN+r+L+
  gi|70608052|ref|YP_256922.1|  84 SYTQMSHRFAKPVDKYykPITPPSIEK--RGKEVVDKAYQDAYNYFYQLLEKGVPEEDARYVLPNGVNTNIVVTMNARELY 162
                                   **********99775233457777774..5679999********************************************* PP

                                   HHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
                          Thy1 157 hflelracsrAqwEirelaeemleelkkvaP 187
                                   +f+ lr+csrAqwEir++a++ml+e+k+v+P
  gi|70608052|ref|YP_256922.1| 163 NFFGLRLCSRAQWEIRAIAWKMLDEVKRVHP 193
                                   ******************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1971.53
//
Query:       gi|70608053|ref|YP_256923.1|  [L=111]
Description: hypothetical protein Saci_2348 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-34  118.3   2.4    1.6e-34  118.1   2.4    1.0  1  DUF2175          Uncharacterized protein conserved in archaea
    2.9e-05   24.3   2.8      0.048   14.0   0.3    2.1  2  Ca_bind_SSO6904  Calcium binding protein SSO6904
     0.0022   18.4   1.1      0.019   15.4   0.0    2.1  2  Vps39_2          Vacuolar sorting protein 39 domain 2
     0.0062   16.4   1.2     0.0099   15.8   1.3    1.3  1  DUF1825          Domain of unknown function (DUF1825)
  ------ inclusion threshold ------
      0.044   13.4   0.4      0.059   13.0   0.4    1.2  1  DUF3231          Protein of unknown function (DUF3231)
       0.09   13.3   1.1       0.14   12.7   1.0    1.4  1  FliG_N           FliG N-terminal domain
       0.11   12.9   0.2       0.19   12.1   0.1    1.5  2  GFA              Glutathione-dependent formaldehyde-activatin


Domain annotation for each model (and alignments):
>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   2.4   6.2e-38   1.6e-34       1      98 []       6     105 ..       6     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 6.2e-38
                       DUF2175   1 kkwkCyiCgkeivegekFTft.kkgvvHyeClvekarkklkes..edaaaLleleevlneeivklkelervaedeevkkvl 78 
                                   +kw+C +Cgk i+++e+FTf+ +k+vvHy+C++eka++++k +   ++++L++le++ln+++v++++l++v++ ee+kkvl
  gi|70608053|ref|YP_256923.1|   6 TKWNCGLCGKPIYWDELFTFMsNKAVVHYTCFKEKASSTSKVDkdVMKVILDSLEDELNKIVVYKQRLSKVND-EEIKKVL 85 
                                   69***********************************999988668899**********************99.******* PP

                       DUF2175  79 eqkrkelEkaaakltkklek 98 
                                   +q++k++Ek+aa +t+ +ek
  gi|70608053|ref|YP_256923.1|  86 DQTEKDAEKNAALFTRLVEK 105
                                   ****************9986 PP

>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   0.00011      0.28       9      39 ..      37      67 ..      29      73 .. 0.83
   2 !   14.0   0.3   1.9e-05     0.048      15      50 ..      72     107 ..      66     111 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                  HHHHHHHT--S-HHHHHHHHHHHHHHHHHSS CS
               Ca_bind_SSO6904  9 fvklrkfkgkvdveevekileeieedlrksn 39
                                  f++     +kvd+++++ il+ +e++l+k  
  gi|70608053|ref|YP_256923.1| 37 FKEKASSTSKVDKDVMKVILDSLEDELNKIV 67
                                  777777889******************9965 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.9e-05
                                   HT--S-HHHHHHHHHHHHHHHHHSS-HHHHHHHHHH CS
               Ca_bind_SSO6904  15 fkgkvdveevekileeieedlrksnnikssiifvya 50 
                                     +kv+ ee++k+l++ e+d++k  ++ + ++   +
  gi|70608053|ref|YP_256923.1|  72 RLSKVNDEEIKKVLDQTEKDAEKNAALFTRLVEKMS 107
                                   458********************9999988876555 PP

>> Vps39_2  Vacuolar sorting protein 39 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.2e-06     0.019      80     108 ..       9      38 ..       5      39 .. 0.91
   2 ?    2.0   0.2      0.11   2.8e+02      25      63 ..      55      95 ..      42     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.2e-06
                       Vps39_2  80 vCavCkkrlge.svfvvyPngsvvHlgCak 108
                                    C +C k +   + f  + n+ vvH++C+k
  gi|70608053|ref|YP_256923.1|   9 NCGLCGKPIYWdELFTFMSNKAVVHYTCFK 38 
                                   7********998****************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                       Vps39_2 25 plkdlesflekal..rnslekkreeqvvkklrkaeklsvee 63
                                   l +le+ l+k +  +++l+k + e++ k l + ek   ++
  gi|70608053|ref|YP_256923.1| 55 ILDSLEDELNKIVvyKQRLSKVNDEEIKKVLDQTEKDAEKN 95
                                  45555555555432266677777777777777777765555 PP

>> DUF1825  Domain of unknown function (DUF1825)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.3   3.9e-06    0.0099      28      96 ..      42     110 ..      21     111 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.9e-06
                       DUF1825  28 skygkfdreGkkifiekleelleryrilmkrlelsddflakmtvkqlktqlgqfgitpqqmfdqlnktl 96 
                                   s+ +k d++  k+ ++ le+ l+++ ++++rl   +d+  k ++ q +++ ++ +  ++++++++ + l
  gi|70608053|ref|YP_256923.1|  42 SSTSKVDKDVMKVILDSLEDELNKIVVYKQRLSKVNDEEIKKVLDQTEKDAEKNAALFTRLVEKMSNVL 110
                                   667899**********************************************99999999999999876 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   2.3e-05     0.059      20      70 ..      54     104 ..      42     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                       DUF3231  20 slwssyianslgialitgFlqvaedkeikelleralelsnkhikelkelLk 70 
                                    + +s++++  +i+++++ l++++d+eik++l ++ + ++k+ + +++l +
  gi|70608053|ref|YP_256923.1|  54 VILDSLEDELNKIVVYKQRLSKVNDEEIKKVLDQTEKDAEKNAALFTRLVE 104
                                   577889999999*****************************9999998876 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   5.4e-05      0.14      24      79 ..      56     110 ..      41     111 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                   HTTSXHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHHHCCCCHHCHHHHHHHHHH CS
                        FliG_N  24 lkhLdeeeiekltkeiaslksvskeeveaVleefleeleaqeylseggeeyarelL 79 
                                   l  L e+e+ k++    +l +v+ ee+++Vl++  +++e++++l++   e + ++L
  gi|70608053|ref|YP_256923.1|  56 LDSL-EDELNKIVVYKQRLSKVNDEEIKKVLDQTEKDAEKNAALFTRLVEKMSNVL 110
                                   5555.57899999999***************************9998888887776 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.4e-05      0.19      46      83 ..       4      43 ..       1      56 [. 0.84
   2 ?   -2.4   0.0       2.5   6.4e+03      23      42 ..      69      89 ..      63      98 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                           GFA 46 kvtrsfCpeCgsplyse..esaapevvivrvGtlddpekl 83
                                  + t++ C  Cg p+y++   + +++ ++v++ ++ +++  
  gi|70608053|ref|YP_256923.1|  4 PQTKWNCGLCGKPIYWDelFTFMSNKAVVHYTCFKEKASS 43
                                  678899**********988899************998444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.5
                           GFA 23 kaealelleg.elkeykktad 42
                                   +++l+ ++  e+k++ ++++
  gi|70608053|ref|YP_256923.1| 69 YKQRLSKVNDeEIKKVLDQTE 89
                                  444454444445555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1998  (0.11144); expected 358.6 (0.02)
Passed bias filter:                      847  (0.0472419); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 874.00
//
Query:       gi|70608054|ref|YP_256924.1|  [L=382]
Description: hypothetical protein Saci_2349 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.4   0.8      0.093   12.2   0.1    2.6  2  C5-epim_C       D-glucuronyl C5-epimerase C-terminus
  ------ inclusion threshold ------
      0.015   15.7   0.6       0.24   11.9   0.1    2.6  2  Thioredoxin_2   Thioredoxin-like domain
       0.14   11.6   0.9        2.3    7.6   0.2    2.1  1  Glyco_hydro_76  Glycosyl hydrolase family 76


Domain annotation for each model (and alignments):
>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   1.6e-05     0.093      30      63 ..     224     257 ..     222     268 .. 0.88
   2 !    3.9   0.0    0.0055        33      29      61 ..     283     315 ..     266     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                     C5-epim_C  30 aqgqaisvllrAYeltgdekYlkaakkalksfki 63 
                                   +q+ + ++llr Y+ t d+kYl++a k++ ++k 
  gi|70608054|ref|YP_256924.1| 224 DQALVGQALLRVYKKTWDQKYLDLAMKVYTYIKD 257
                                   57788889********************998875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0055
                     C5-epim_C  29 maqgqaisvllrAYeltgdekYlkaakkalksf 61 
                                   +++ + ++ l++ + + +de Yl  akka++++
  gi|70608054|ref|YP_256924.1| 283 ISNSETAIFLSQLWSVNNDETYLLEAKKAMEAS 315
                                   566777888999999**************9865 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     4e-05      0.24       6      40 ..      10      44 ..       8      65 .. 0.79
   2 ?    0.8   0.0      0.11   6.3e+02      26      72 ..     267     314 ..     265     341 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                 Thioredoxin_2  6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllf 40
                                  k ++++f++++C +C+ l++++ +l   +++++l 
  gi|70608054|ref|YP_256924.1| 10 KLIAFFFETENCTNCEDLYNKILKLTISQKYYFLR 44
                                  56788999*****************7777776654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                 Thioredoxin_2  26 elkelddvtvrvllfplkpsfepka.vaiwcakekkkafkdieenvel 72 
                                   ++k+ld+vt+  ++ p+++s  +++  ++w  ++ ++ + + ++ +e 
  gi|70608054|ref|YP_256924.1| 267 DIKPLDEVTKEEFYEPISNSETAIFlSQLWSVNNDETYLLEAKKAMEA 314
                                   78999******9999966665554415788888777555554444443 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00038       2.3     161     191 ..     230     259 ..     223     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHHHH--CHHHHHHHHHHHHHHHHSC CS
                Glyco_hydro_76 161 qlaarLarytgnetYlewAekvwdWvedvgl 191
                                   q+ +r ++ t +++Yl+ A kv+ +++d +l
  gi|70608054|ref|YP_256924.1| 230 QALLRVYKKTWDQKYLDLAMKVYTYIKD-NL 259
                                   56689*********************99.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2626.55
//
Query:       gi|70608055|ref|YP_256925.1|  [L=229]
Description: hypothetical protein Saci_2350 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-29  102.8   0.0    1.7e-29  102.3   0.0    1.2  1  DUF364    Putative heavy-metal chelation
      5e-14   52.3   0.0    8.1e-14   51.6   0.0    1.3  1  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0   1.9e-33   1.7e-29       6     147 .]      91     228 ..      87     228 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.9e-33
                        DUF364   6 leikkgkkVvvVGyfapvlkklkekgaeltvlelnpnlleeeegdlpdeaaeellpeadvviitGstLvngtlerllelak 86 
                                   +++ +g+k++v+Gy  p    + +++ ++t++++++  ++  ++++ +++++++ + +d  +i+Gs+Lv g++e++l++++
  gi|70608055|ref|YP_256925.1|  91 IDVLEGNKLCVFGYS-P--GTVTNRFVSVTIYDFWNPPQRSFDNVTVKPFSSFTSETCDSTVIFGSALVAGNIEKILASIS 168
                                   56799********55.8..45557899****************************************************** PP

                        DUF364  87 kaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeGggtkhlkrkgakkivk 147
                                    +++++l G+s++++p +l++yG+d+i++v+ +d+ k+lr+++eGg +khl+r+++k +vk
  gi|70608055|ref|YP_256925.1| 169 -TDHLILSGISSVYAPITLKKYGFDYIGKVIAVDKIKALRVVCEGGLAKHLSRFTKKIYVK 228
                                   .*******************************************************99885 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   9.1e-18   8.1e-14       1      73 [.       2      79 ..       2      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 9.1e-18
                       DUF4213  1 yeelieaapedltVedvviGlnwtlVelsdggaGlAyt.......eagklvgkparelaelllswnplersvGlAaiNAl 73
                                  ++el +++ ++++V + +iG+ +t V+lsdg++G+++t        +g++ g +a  l+e l+ ++p+ersv +A++N++
  gi|70608055|ref|YP_256925.1|  2 IDELRHSL-KGKKVVNNCIGVAYTSVMLSDGSLGISHTitegensLCGEVFGNDAVSLVESLK-NSPIERSVSVAILNSV 79
                                  68999999.******************************99999888889*************.**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1717.45
//
Query:       gi|70608056|ref|YP_256926.1|  [L=159]
Description: ParR family transcriptional regulator [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-17   61.9   0.1    6.7e-17   61.2   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family
    0.00027   21.5   2.0     0.0021   18.7   0.1    2.3  2  RTP       Replication terminator protein
    0.00071   19.3   0.6     0.0023   17.7   0.2    2.0  2  DUF1495   Winged helix DNA-binding domain (DUF1495)
     0.0047   15.8   0.4     0.0052   15.6   0.4    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
     0.0049   16.6   0.1      0.012   15.3   0.0    1.7  2  DUF4364   Domain of unknown function (DUF4364)
     0.0091   15.9   0.0      0.028   14.3   0.0    2.0  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0098   16.0   0.1      0.025   14.7   0.1    1.7  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.14   12.1   1.3       0.48   10.3   0.1    2.5  3  HTH_5     Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1     3e-20   6.7e-17       1      74 [.      20      88 ..      20      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 3e-20
                                  HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                          PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                  +L+ l+e+p+y yeiik +e+  eg++++s Gs+Yp+L++L ++g++  ++++      +k+Y lTd+G ++++
  gi|70608056|ref|YP_256926.1| 20 VLSSLAEKPMYLYEIIKSIETKAEGFYRPSTGSIYPVLRSLARDGYIIIQERD-----GKKIYSLTDKGVKKVE 88
                                  799***********************************************998.....69*********98876 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   9.3e-07    0.0021       8     101 ..      14      99 ..      10     109 .. 0.82
   2 ?    2.2   0.2      0.12   2.7e+02      94     112 ..     131     149 ..     118     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.3e-07
                                   HHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHH CS
                           RTP   8 AFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkek 88 
                                     l+l ++  +++k++y ++++ ++ ++   + y+P+   iy  l+ l  dg++  +++       +   iYsltd+G  k
  gi|70608056|ref|YP_256926.1|  14 GTLRLLVLSSLAEKPMYLYEIIKSIETKAEGF-YRPSTGSIYPVLRSLARDGYIIIQERD-----GK--KIYSLTDKGVKK 86 
                                   568999*****************998876555.*******************98644322.....22..3799*****999 PP

                                   HHHHHHHHHHHHH CS
                           RTP  89 aklykkqvkidld 101
                                   ++  k ++   + 
  gi|70608056|ref|YP_256926.1|  87 VEEIKIEIESLFT 99 
                                   9999887776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHH CS
                           RTP  94 kqvkidldrckkllekalk 112
                                   +q+ +dl++c+ l+e a+k
  gi|70608056|ref|YP_256926.1| 131 NQLITDLEKCMALVEEAIK 149
                                   57889**********9998 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2     1e-06    0.0023      15      89 ..      18      89 ..       3      90 .. 0.77
   2 ?   -2.4   0.0         2   4.4e+03       6      22 ..     121     137 ..     118     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                       DUF1495 15 llyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYklteeGieivev 89
                                  ll L s  ++  +l+ei++++++k +        +g  y   +sL   G +   +e++g k+Y+lt++G + ve+
  gi|70608056|ref|YP_256926.1| 18 LLVLSSLAEKPMYLYEIIKSIETKAEGFYRP--STGSIYPVLRSLARDGYI-IIQERDGKKIYSLTDKGVKKVEE 89
                                  3445567788999999999999988766554..45678*************.589**************998875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                       DUF1495   6 nkSkvRkkvllyLysiy 22 
                                   n+ k+ +kvl  L+   
  gi|70608056|ref|YP_256926.1| 121 NRKKIDDKVLNQLITDL 137
                                   55666667776666443 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   2.3e-06    0.0052     280     364 ..      57     141 ..      30     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                       DUF2207 280 lldLavkgyitieeekkkkkkgkd........tltilkkndeeldpyEkalldlLfdkseegkslkeikkyakkskkkakk 352
                                   l +La+ gyi i+e + kk  + +        +++i +++  + dp  ++++dlLf+          +  +++ +k + k 
  gi|70608056|ref|YP_256926.1|  57 LRSLARDGYIIIQERDGKKIYSLTdkgvkkveEIKIEIESLFTRDPLKRRVIDLLFNIG--------LTVHINRKKIDDKV 129
                                   568*************9997666689999998778888888888************443........33333333334444 PP

                       DUF2207 353 fkkalkkwksav 364
                                   +++ ++++++ +
  gi|70608056|ref|YP_256926.1| 130 LNQLITDLEKCM 141
                                   444444443322 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06     0.012      39      79 ..      56      96 ..      52     114 .. 0.90
   2 ?   -2.3   0.0       1.5   3.3e+03      39      43 ..     133     137 ..     117     157 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                       DUF4364 39 alseLvesglieeeekenktlykiTekGketlelfenripk 79
                                  +l  L  +g+i  +e+++k++y++T+kG + +e+++ +i +
  gi|70608056|ref|YP_256926.1| 56 VLRSLARDGYIIIQERDGKKIYSLTDKGVKKVEEIKIEIES 96
                                  6899*****************************99988876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                       DUF4364  39 alseL 43 
                                    +++L
  gi|70608056|ref|YP_256926.1| 133 LITDL 137
                                   22222 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.2e-05     0.028      37      66 ..      51      81 ..      24      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                  HCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
                          TrmB 37 skvYevLrsLedkGlVerekgr.pklYravd 66
                                   ++Y vLrsL + G++ ++++  +k+Y+ +d
  gi|70608056|ref|YP_256926.1| 51 GSIYPVLRSLARDGYIIIQERDgKKIYSLTD 81
                                  58*****************977799998766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.1e-05     0.025       2      78 ..      17      96 ..      16      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                        HTH_34  2 RlavlsyLasvdeadfvelkea.......leatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLk 77
                                  Rl vls+La++    ++ +k+         + ++g ++  l+ L   gYi ++    +     ++++T++G ++ ++ + +++
  gi|70608056|ref|YP_256926.1| 17 RLLVLSSLAEKPMYLYEIIKSIetkaegfYRPSTGSIYPVLRSLARDGYIIIQERDGK----KIYSLTDKGVKKVEEIKIEIE 95
                                  6777777777777766666653211111134589****************99755444....5**********9999887777 PP

                        HTH_34 78 s 78
                                  s
  gi|70608056|ref|YP_256926.1| 96 S 96
                                  6 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00021      0.48       4      24 ..      17      37 ..      15      40 .. 0.90
   2 ?   -1.7   0.0       1.2   2.8e+03       1      13 [.     101     113 ..     101     118 .. 0.81
   3 ?   -2.9   0.0       2.9   6.6e+03      12      20 ..     150     158 ..     149     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                                  HHHHHHHHTTSSEEHHHHHHH CS
                         HTH_5  4 RlkILklLaegelcvcelaee 24
                                  Rl +L++Lae++++  e+ + 
  gi|70608056|ref|YP_256926.1| 17 RLLVLSSLAEKPMYLYEIIKS 37
                                  9*****************876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                   SHHHHHHHHHHTT CS
                         HTH_5   1 dptRlkILklLae 13 
                                   dp +++++ lL +
  gi|70608056|ref|YP_256926.1| 101 DPLKRRVIDLLFN 113
                                   7899999999976 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.9
                                   TTSSEEHHH CS
                         HTH_5  12 aegelcvce 20 
                                   ++ge++v++
  gi|70608056|ref|YP_256926.1| 150 SKGEKTVTQ 158
                                   579999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1091.00
//
Query:       gi|70608057|ref|YP_256927.1|  [L=184]
Description: hypothetical protein Saci_2353 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-52  175.1   0.0    9.7e-52  174.9   0.0    1.0  1  ThiP_synth  Thiamine-phosphate synthase


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.9   0.0   5.4e-56   9.7e-52       2     164 ..      11     176 ..      10     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.9 bits;  conditional E-value: 5.4e-56
                                   HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT-- CS
                    ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevr 82 
                                   l++a+++++++e+ + liPev++N++y+l++Ak+i+Dvaa+pGR++++ +rv+++ +p+fgas+h+arv+l+ mk+d+e r
  gi|70608057|ref|YP_256927.1|  11 LKEAVDKFASNEKSYLLIPEVKTNLGYSLSNAKDISDVAAIPGRLTVAFNRVIYCLPPSFGASDHIARVILTSMKYDSEKR 91 
                                   89******************************************************************************* PP

                                   EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESSHHH CS
                    ThiP_synth  83 aainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkdaee 158
                                   +ain++y ++i+++l +   +v+ f+r+eep e     ++tm+ +v+ a+++l ++p++i+d G++GkEp i+v+ +d+++
  gi|70608057|ref|YP_256927.1|  92 SAINLKYYREIVDNLPND--QVFIFSRREEPAEQktkeRKTMNYMVELAFNTLkRIPNYIVDLGDFGKEPGIFVIDNDPMK 170
                                   ***************998..9************99999***************99************************** PP

                                   HHHHHH CS
                    ThiP_synth 159 vvekvl 164
                                   vvek l
  gi|70608057|ref|YP_256927.1| 171 VVEKSL 176
                                   ***965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1380.25
//
Query:       gi|70608058|ref|YP_256928.1|  [L=475]
Description: hypothetical protein Saci_2354 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-09   35.8  10.0    7.2e-09   35.8  10.0    3.4  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.3e-07   31.8  25.6    1.3e-07   31.8  25.6    2.0  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    1.3e-07   31.7   1.1     0.0056   16.9   0.7    2.5  2  XhlA             Haemolysin XhlA
    1.7e-07   31.2   8.6    1.7e-07   31.2   8.6    4.8  1  Big_1            Bacterial Ig-like domain (group 1)
    3.1e-06   27.5   4.1    4.9e-06   26.9   4.1    1.2  1  ATG16            Autophagy protein 16 (ATG16)
    3.4e-06   27.1   3.7      0.014   15.4   0.1    2.4  2  DUF1664          Protein of unknown function (DUF1664)
      8e-06   26.1  14.0      0.009   16.3   4.8    3.0  3  DUF5082          Domain of unknown function (DUF5082)
    8.5e-06   26.1   5.2      0.002   18.5   0.3    3.9  3  MG2              MG2 domain
    8.9e-06   24.8   4.1    1.9e-05   23.7   4.0    1.5  1  Spc7             Spc7 kinetochore protein
    1.2e-05   25.9   0.9       0.01   16.5   0.0    2.5  3  SlyX             SlyX
    1.8e-05   24.6  10.0      0.015   15.3   3.0    2.3  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    2.4e-05   24.3   1.0    0.00013   21.9   0.5    2.3  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    3.2e-05   23.8   0.8      0.052   13.5   0.5    2.4  2  Prefoldin_2      Prefoldin subunit
    3.3e-05   24.2   6.2     0.0045   17.3   1.2    3.1  2  FlaC_arch        Flagella accessory protein C (FlaC)
    4.4e-05   23.5   5.3    0.00016   21.7   5.5    1.7  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    6.1e-05   23.2  11.4    6.1e-05   23.2  11.4    4.1  2  Invasin_D3       Invasin, domain 3
    6.8e-05   23.0  10.1    0.00053   20.1   1.1    2.2  2  ADIP             Afadin- and alpha -actinin-Binding
    7.1e-05   22.7   5.0    0.00014   21.7   5.0    1.4  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    7.4e-05   21.8   0.9    9.9e-05   21.4   0.9    1.1  1  DUF812           Protein of unknown function (DUF812)
    0.00011   22.6   5.4       0.13   12.7   3.3    2.3  2  ZapB             Cell division protein ZapB
    0.00013   22.2   8.8       0.11   12.8   3.7    2.5  2  BLOC1_2          Biogenesis of lysosome-related organelles co
    0.00014   21.9   4.8    0.00024   21.2   4.8    1.3  1  Nup54            Nucleoporin complex subunit 54
    0.00018   21.3   6.2       0.42   10.3   0.1    3.6  3  DUF4988          Domain of unknown function
    0.00019   19.8   2.5    0.00019   19.8   2.5    1.4  1  EzrA             Septation ring formation regulator, EzrA
    0.00019   21.4   9.1      0.043   13.7   3.0    3.9  3  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
    0.00021   19.6   3.6    0.00028   19.2   3.6    1.1  1  HOOK             HOOK protein
    0.00026   21.4  13.0      0.025   15.1   1.0    2.5  2  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0003   21.0   3.1      0.068   13.5   0.6    2.5  2  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
     0.0003   19.5   1.2    0.00047   18.9   1.2    1.2  1  FapA             Flagellar Assembly Protein A
    0.00034   21.1   0.5    0.00099   19.6   0.5    1.7  1  APG6_N           Apg6 coiled-coil region
    0.00035   20.0   2.6     0.0005   19.5   2.6    1.1  1  FAM76            FAM76 protein
    0.00035   20.8   2.6       0.12   12.8   0.7    2.6  2  CLZ              C-terminal leucine zipper domain of cyclic n
    0.00036   19.3   2.7    0.00051   18.8   2.7    1.1  1  AAA_13           AAA domain
    0.00041   20.3   4.9        0.1   12.5   0.8    3.2  3  Prefoldin        Prefoldin subunit
    0.00044   20.6   2.4    0.00044   20.6   2.4    2.2  2  Snapin_Pallidin  Snapin/Pallidin
    0.00048   19.2   6.1    0.00071   18.7   6.1    1.1  1  IFT57            Intra-flagellar transport protein 57
    0.00051   20.0   5.1    0.00051   20.0   5.1    3.3  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00057   19.4   7.1    0.00084   18.9   7.1    1.1  1  Golgin_A5        Golgin subfamily A member 5
    0.00058   19.0   6.0     0.0013   17.9   6.0    1.5  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0006   19.5   6.8    0.00089   18.9   6.8    1.2  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
    0.00067   19.2   4.1     0.0016   18.0   4.1    1.5  1  HMMR_N           Hyaluronan mediated motility receptor N-term
    0.00077   18.8   8.7     0.0044   16.4   6.6    2.1  2  DUF3450          Protein of unknown function (DUF3450)
    0.00096   18.8   2.4     0.0016   18.1   2.4    1.3  1  Filament         Intermediate filament protein
    0.00098   18.5   1.8     0.0017   17.7   1.8    1.3  1  GAS              Growth-arrest specific micro-tubule binding
     0.0012   19.0   0.7     0.0021   18.2   0.7    1.4  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0012   18.9   6.3      0.031   14.4   1.3    2.7  2  TolA_bind_tri    TolA binding protein trimerisation
     0.0012   17.2   2.0     0.0016   16.8   2.0    1.1  1  Cast             RIM-binding protein of the cytomatrix active
     0.0012   17.2   9.4     0.0025   16.2   9.4    1.5  1  Gp58             gp58-like protein
     0.0014   18.9   0.5     0.0014   18.9   0.5    2.5  1  SpaA             Prealbumin-like fold domain
     0.0016   18.6   2.7     0.0029   17.8   2.7    1.4  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0017   18.5  11.7      0.032   14.4   7.6    2.3  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.002   16.4   7.8     0.0028   16.0   7.8    1.1  1  FPP              Filament-like plant protein, long coiled-coi
     0.0021   18.1   6.9      0.011   15.7   3.6    2.0  2  BRE1             BRE1 E3 ubiquitin ligase
     0.0021   18.3   0.0        0.1   12.9   0.0    2.3  3  ABC_tran_CTD     ABC transporter C-terminal domain
     0.0023   17.3   1.2     0.0049   16.2   1.2    1.6  1  TMPIT            TMPIT-like protein
     0.0026   17.4   6.4       0.15   11.7   2.8    2.1  2  DUF4795          Domain of unknown function (DUF4795)
     0.0027   17.7   1.6     0.0057   16.7   0.8    1.7  2  DHR10            Designed helical repeat protein 10 domain
     0.0034   16.8  11.1      0.012   15.1   3.8    2.6  2  FliD_C           Flagellar hook-associated protein 2 C-termin
     0.0034   17.6   4.4       0.03   14.5   4.6    2.2  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0041   16.5   1.7     0.0063   15.9   1.7    1.2  1  Rab5-bind        Rabaptin-like protein
     0.0044   17.1   5.0      0.058   13.5   0.6    2.9  2  DUF2730          Protein of unknown function (DUF2730)
     0.0045   17.5   4.6      0.063   13.8   2.8    2.2  2  DUF16            Protein of unknown function DUF16
     0.0046   16.7   6.0        1.5    8.6   0.1    3.4  3  DivIC            Septum formation initiator
     0.0047   17.2   9.4        2.1    8.6   0.4    3.1  2  Spc24            Spc24 subunit of Ndc80
     0.0049   16.5   1.7     0.0093   15.7   1.7    1.4  1  Lebercilin       Ciliary protein causing Leber congenital ama
      0.005   17.2   2.6      0.013   15.9   2.6    1.7  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
     0.0051   16.8   9.5      0.012   15.6   9.5    1.7  1  Laminin_II       Laminin Domain II
     0.0054   16.3   3.6     0.0087   15.7   3.6    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0059   15.4   2.3     0.0081   14.9   2.3    1.1  1  WEMBL            Weak chloroplast movement under blue light
     0.0061   16.4   2.0      0.009   15.9   2.0    1.2  1  DUF724           Protein of unknown function (DUF724)
     0.0062   16.4  14.0      0.022   14.6   7.9    2.3  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
     0.0064   16.3   0.2       0.27   11.1   0.0    2.5  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
     0.0065   16.7   3.5       0.13   12.5   0.1    2.2  3  FliJ             Flagellar FliJ protein
     0.0067   14.3   1.6     0.0091   13.9   1.6    1.0  1  Myosin_tail_1    Myosin tail
     0.0079   16.3   2.5       0.65   10.1   1.6    2.2  2  Tropomyosin_1    Tropomyosin like
      0.008   15.0   3.0      0.013   14.3   3.0    1.2  1  HlyD_2           HlyD family secretion protein
     0.0087   16.1   6.7      0.011   15.8   1.2    2.0  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0089   15.6   1.5       0.35   10.4   0.9    2.0  2  PspA_IM30        PspA/IM30 family
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.023   15.0   0.2    1.4  1  DUF4164          Domain of unknown function (DUF4164)
      0.014   15.8   0.8      0.029   14.7   0.8    1.6  1  V-SNARE          Vesicle transport v-SNARE protein N-terminus
      0.015   15.3   4.1      0.059   13.4   1.0    2.6  2  DUF2205          Short coiled-coil protein
      0.015   14.8   0.5      0.026   14.0   0.5    1.4  1  DegS             Sensor protein DegS
      0.015   14.7   5.1        1.8    7.9   0.1    2.2  2  DUF4618          Domain of unknown function (DUF4618)
      0.017   13.9   4.2       0.17   10.6   2.0    1.9  1  Tektin           Tektin family
      0.017   14.9   1.6       0.17   11.7   0.8    2.1  2  Phage_GP20       Phage minor structural protein GP20
      0.017   12.6   3.1      0.023   12.2   3.1    1.0  1  DUF3584          Protein of unknown function (DUF3584)
      0.019   14.2   2.7      0.031   13.5   2.7    1.3  1  HAP1_N           HAP1 N-terminal conserved region
       0.02   13.9   2.0      0.043   12.9   1.6    1.6  2  Filo_VP35        Filoviridae VP35
      0.022   14.1  11.5        1.1    8.5  11.5    2.2  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
      0.023   14.3  22.8       0.18   11.3   9.8    2.2  2  MscS_porin       Mechanosensitive ion channel porin domain
      0.024   14.8   7.0          1    9.5   7.0    2.3  1  RasGAP_C         RasGAP C-terminus
      0.025   14.5  18.1       0.17   11.7   1.4    3.7  4  GIT_CC           GIT coiled-coil Rho guanine nucleotide excha
      0.026   13.9   6.0      0.059   12.7   6.0    1.5  1  Dynamitin        Dynamitin
      0.029   14.5   2.1      0.077   13.1   0.8    2.0  2  DivIVA           DivIVA protein
      0.031   14.4   9.8        4.1    7.5   3.3    3.5  3  Vps51            Vps51/Vps67
      0.032   14.4   1.1      0.032   14.4   1.1    3.6  2  MG4              Macroglobulin domain MG4
      0.033   13.6   6.7       0.17   11.3   2.8    2.2  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
      0.033   14.5   6.1        2.4    8.5   0.2    3.2  3  Csm1_N           Csm1 N-terminal domain
      0.033   14.9   1.0      0.072   13.8   0.5    1.6  1  DUF4472          Domain of unknown function (DUF4472)
      0.033   13.8   3.2      0.051   13.2   3.2    1.3  1  GCP_N_terminal   Gamma tubulin complex component N-terminal
      0.036   13.8   1.1       0.13   12.0   0.8    1.6  1  DUF4201          Domain of unknown function (DUF4201)
      0.037   14.2  13.5       0.15   12.2  13.5    1.9  1  COG5             Golgi transport complex subunit 5
       0.04   14.1   3.7       0.87    9.8   3.7    2.1  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.041   13.6   0.6       0.13   12.0   0.6    1.7  1  DUF713           Protein of unknown function (DUF713)
      0.041   14.0   2.4        1.2    9.2   0.6    2.2  1  Med9             RNA polymerase II transcription mediator com
      0.045   12.6   1.2      0.063   12.1   1.2    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
       0.05   13.4   0.6        2.2    8.2   0.2    3.1  2  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma
      0.052   13.3  10.4       0.14   11.8  10.4    1.6  1  Laminin_I        Laminin Domain I
      0.056   12.3   4.3       0.16   10.8   3.4    1.9  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.056   12.6   6.1      0.081   12.0   6.1    1.1  1  DUF4686          Domain of unknown function (DUF4686)
      0.057   12.7   7.3       0.18   11.1   2.8    2.1  2  DUF4763          Domain of unknown function (DUF4763)
      0.059   13.8   0.2        1.8    9.0   0.2    2.2  2  DUF4200          Domain of unknown function (DUF4200)
       0.06   13.3   1.8       0.24   11.3   1.1    1.9  2  Ax_dynein_light  Axonemal dynein light chain
      0.062   12.9   3.1       0.49   10.0   0.5    2.3  2  DUF2968          Protein of unknown function (DUF2968)
      0.065   13.6   0.2        0.2   12.0   0.1    1.8  1  DUF4198          Domain of unknown function (DUF4198)
      0.066   12.8   3.5       0.27   10.8   1.3    2.0  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.067   11.7   2.9       0.11   11.1   2.9    1.2  1  Macoilin         Macoilin family
      0.071   13.4   5.2      0.066   13.5   2.7    2.2  3  KxDL             Uncharacterized conserved protein
      0.074   13.5   1.0       0.12   12.8   1.0    1.3  1  Fez1             Fez1
      0.078   13.2   5.9        2.1    8.6   0.3    3.3  4  WXG100           Proteins of 100 residues with WXG
      0.096   11.9   2.3       0.19   10.9   1.5    1.6  1  Taxilin          Myosin-like coiled-coil protein
      0.098   11.2   8.1       0.15   10.5   8.1    1.2  1  Herpes_UL6       Herpesvirus UL6 like
        0.1   12.0   5.7       0.21   10.9   5.7    1.4  1  SF-assemblin     SF-assemblin/beta giardin
        0.1   13.0  18.7        5.4    7.5   1.0    4.1  4  LPP              Lipoprotein leucine-zipper
       0.11   13.1   2.8        1.7    9.4   1.1    2.4  2  YabA             Initiation control protein YabA
       0.12   11.7   6.4       0.05   12.9   1.4    2.4  1  DUF4407          Domain of unknown function (DUF4407)
       0.12   13.5   1.4       0.25   12.5   1.4    1.5  1  SOGA             Protein SOGA
       0.12   11.6  12.6      0.058   12.7   3.7    2.6  3  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.13   12.5   3.0       0.25   11.5   3.0    1.4  1  Uds1             Up-regulated During Septation
       0.13   12.4   8.6       0.22   11.6   8.6    1.4  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.13   11.9   8.6       0.48   10.1   4.1    2.2  2  LXG              LXG domain of WXG superfamily
       0.13   12.4  12.1        1.8    8.7   0.6    3.4  3  MbeD_MobD        MbeD/MobD like
       0.13   12.4   1.9       0.26   11.5   1.9    1.4  1  SesA             N-terminal domain on NACHT_NTPase and P-loop
       0.14   12.4   2.5        0.8    9.9   2.5    2.0  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
       0.14   12.0   0.6       0.24   11.1   0.6    1.4  1  TACC_C           Transforming acidic coiled-coil-containing p
       0.16   12.3   3.1        1.3    9.4   1.3    2.7  3  TSC22            TSC-22/dip/bun family
       0.16   11.1   4.4        1.5    7.9   2.0    2.1  2  RmuC             RmuC family
       0.18   11.2   5.3          1    8.7   2.5    1.9  2  Cluap1           Clusterin-associated protein-1
       0.19   11.6   1.3       0.73    9.7   1.3    1.8  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
        0.2   11.8   5.0        3.8    7.7   0.9    2.7  3  bZIP_1           bZIP transcription factor
       0.21   12.1   5.4        3.1    8.3   0.5    3.8  2  DUF4140          N-terminal domain of unknown function (DUF41
       0.21   12.1   6.0        1.4    9.5   6.0    2.1  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.23   11.7   0.1       0.23   11.7   0.1    3.8  2  DUF948           Bacterial protein of unknown function (DUF94
       0.24   11.9   4.4        1.9    8.9   0.2    2.8  2  MtrB             Tetrahydromethanopterin S-methyltransferase 
       0.24    9.7   5.7       0.49    8.7   0.4    1.7  2  MAD              Mitotic checkpoint protein
       0.24   11.5   3.2         13    6.0   1.6    2.9  2  Swi5             Swi5
       0.25   11.1   4.1       0.64    9.8   3.2    1.9  2  Nsp1_C           Nsp1-like C-terminal region
       0.28   11.4   3.1        5.5    7.2   1.5    2.3  2  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.28   11.6   7.3        1.5    9.2   7.2    2.1  1  CENP-H           Centromere protein H (CENP-H)
        0.3   11.4   2.7        2.7    8.3   1.3    2.1  2  DUF641           Plant protein of unknown function (DUF641)
       0.31   10.1   6.3       0.52    9.4   6.3    1.3  1  APG17            Autophagy protein Apg17
       0.31   10.6   7.8        1.5    8.4   7.5    2.3  1  Fzo_mitofusin    fzo-like conserved region
       0.32   11.1   6.9        5.8    7.0   3.5    2.3  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.32   11.2   3.5          1    9.5   2.4    2.0  2  GCN5L1           GCN5-like protein 1 (GCN5L1)
       0.32   11.6   7.2       0.52   10.9   3.2    2.3  2  BST2             Bone marrow stromal antigen 2
       0.35   10.4   4.8        0.5    9.8   4.8    1.1  1  Leu_zip          Leucine zipper
       0.37   10.6  10.4        2.6    7.9   2.9    3.3  3  DASH_Dam1        DASH complex subunit Dam1
        0.4   10.1   2.5       0.67    9.3   2.1    1.4  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
        0.4   10.9   2.0        1.6    8.9   1.0    1.9  2  Cnn_1N           Centrosomin N-terminal motif 1
       0.46   10.3   4.1         15    5.4   4.1    2.7  1  CdvA             CdvA-like coiled-coil domain
       0.49   10.2   6.6        3.9    7.2   6.6    2.0  1  SKA1             Spindle and kinetochore-associated protein 1
       0.54   10.1   5.8        1.5    8.7   5.5    1.7  1  STAT_alpha       STAT protein, all-alpha domain
       0.56   10.4   4.9        1.1    9.5   3.1    1.7  2  CREPT            Cell-cycle alteration and expression-elevate
        0.6    9.8   4.5       0.99    9.1   4.5    1.3  1  BAR_3            BAR domain of APPL family
       0.64   10.3   2.8        2.3    8.5   0.9    2.0  2  THOC7            Tho complex subunit 7
       0.65    9.9  11.3        2.1    8.2   7.0    2.2  2  Sec34            Sec34-like family
       0.66    9.0   4.5          1    8.4   4.5    1.2  1  AIP3             Actin interacting protein 3
       0.77    9.8   6.0        4.8    7.2   2.3    2.3  2  Sec2p            GDP/GTP exchange factor Sec2p
       0.77    9.0   8.3      0.093   12.0   3.6    1.9  1  CorA             CorA-like Mg2+ transporter protein
       0.93    9.4   6.4         20    5.1   2.7    2.4  3  CK2S             Casein Kinase 2 substrate
        1.2    7.0  11.5          3    5.7  11.4    1.4  1  Prominin         Prominin
        1.2    9.5   7.9        3.4    8.1   1.7    2.5  2  H-kinase_dim     Signal transducing histidine kinase, homodim
        1.3    9.0   6.9        4.7    7.1   4.8    2.0  2  Wtap             WTAP/Mum2p family
        1.6    8.6   5.8        8.9    6.3   5.8    1.9  1  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        1.7    9.3   9.2        1.2    9.8   6.6    2.0  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        1.9    8.6   4.6        5.4    7.2   1.1    2.4  2  TRPM_tetra       Tetramerisation domain of TRPM
        2.1    7.0   9.7        1.8    7.2   4.3    1.6  2  Vps52            Vps52 / Sac2 family
        2.3    7.7   7.7         10    5.6   7.7    1.8  1  TBK1_CCD1        TANK-binding kinase 1 coiled-coil domain 1
        2.3    8.6  17.0         16    5.9  15.2    2.3  2  Syntaxin_2       Syntaxin-like protein
        2.6    7.5  14.7       0.13   11.7   3.8    3.4  2  DUF4349          Domain of unknown function (DUF4349)
        2.8    8.2   5.6        2.7    8.2   3.7    1.8  1  Cortex-I_coil    Cortexillin I, coiled coil
        2.8    7.0  11.5         35    3.4  11.5    2.0  1  CCDC144C         CCDC144C protein coiled-coil region
        3.2    8.2   9.9    1.1e+02    3.4   7.5    3.3  2  DUF4094          Domain of unknown function (DUF4094)
        3.9    7.0   7.5        8.4    5.9   7.1    1.6  1  Vps5             Vps5 C terminal like
          4    5.5   6.0        5.1    5.2   6.0    1.1  1  Nop14            Nop14-like family
        4.1    7.6   6.9         15    5.8   4.7    2.6  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        4.3    7.8   7.4         39    4.8   3.7    2.8  2  DASH_Dad2        DASH complex subunit Dad2
        4.7    7.9   8.2         20    5.9   8.2    1.9  1  AATF-Che1        Apoptosis antagonizing transcription factor
        7.4    6.7   7.8        3.6    7.7   3.1    2.1  2  End3             Actin cytoskeleton-regulatory complex protei
        9.8    6.0  15.9         58    3.5  10.3    2.8  1  GP41             Retroviral envelope protein


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8  10.0   7.7e-11   7.2e-09       1      81 [.     130     216 ..     130     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.7e-11
               CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgt...vastttdadGafrlrglpp....gtysvtvsapGyatatreevtltagqt 74 
                                   ti+ +V+++ g p+agatV ++n+ +g+   va+ tt+++G  +++ l      +t+++++s +Gya +t  +v++t  q+
  gi|70608058|ref|YP_256928.1| 130 TITATVVNQEGSPLAGATVQLYNTTSGSntlVATQTTNSQGVATFTVLSFpgvtQTFKLVASLQGYAASTA-SVSITGQQN 209
                                   7999*******************876643348999******9888876434588****************8.5****9999 PP

               CarboxypepD_reg  75 ttlditL 81 
                                   + ++itL
  gi|70608058|ref|YP_256928.1| 210 ASVTITL 216
                                   9*****9 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  25.6   1.4e-09   1.3e-07      24     118 ..     350     445 ..     334     464 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.4e-09
                  Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssv 101
                                    i ++  +i ++l++++++++tq+++l+++l+sl++ + t l+++l+ L++++ +l+    +l+++L++l+ ++++L+ss+
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNI-TNLEKTVNNLQTQISTLNSSLSSLSQRI-TSLQNTLASLNSTISSLSgtaSSLSSQLNALQGKISSLNSSI 428
                                   576666677.9**********************88876.57****************9999******************** PP

                  Baculo_PEP_C 102 tNinstLnnllqalnnl 118
                                   tN+   Ln+l + +n+l
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLNSLQSKVNSL 445
                                   *************9998 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.7   5.9e-05    0.0056       3      48 ..     355     400 ..     353     409 .. 0.92
   2 !   12.9   0.0     0.001     0.098      16      67 .]     410     461 ..     404     461 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.9e-05
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                    ++++ +e+ ++nl++++++l+   +   ++i +l+++l++l s++
  gi|70608058|ref|YP_256928.1| 355 VQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTI 400
                                   689***************************************9997 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.001
                          XhlA  16 leervdkleekaaeaeekiknleedlkklesnqkWlirtiiGalisaviyli 67 
                                   l+++++ l+ k +   ++i nl  +l++l+s ++ l  ++ G++i+++i+li
  gi|70608058|ref|YP_256928.1| 410 LSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTPLVYGGIIAGIIGLI 461
                                   6778999999***************************************997 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   8.6   1.8e-09   1.7e-07       6      53 ..     128     177 ..     127     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-09
                         Big_1   6 tntltatvkDangnpvagatVtfsvsg.gals.assgtTdanGkatvtlt 53 
                                   t+t+tatv++++g p+agatV +  +  g+++  +++tT+++G+at+t+ 
  gi|70608058|ref|YP_256928.1| 128 TSTITATVVNQEGSPLAGATVQLYNTTsGSNTlVATQTTNSQGVATFTVL 177
                                   68********************97666655556***************85 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   4.1   5.2e-08   4.9e-06      68     177 ..     336     445 ..     307     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.2e-08
                         ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                   s +++++  +  ++++++l +  ++l k+ + l++++ +ln++l+ l +++++ +++la+l++++++l+   +++  +l+ 
  gi|70608058|ref|YP_256928.1| 336 SVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNA 416
                                   344445555556788999999999999999999999999999999999999999999999999999999999999999999 PP

                         ATG16 149 keklvqdlqDElsaLqlqlnqaEeklrkl 177
                                   ++  +  l   ++ L  qln++ +k + l
  gi|70608058|ref|YP_256928.1| 417 LQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   99999999999999999999999998876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.4   0.00036     0.034      75     122 ..     337     384 ..     332     386 .. 0.93
   2 !   15.4   0.1   0.00015     0.014      63     123 ..     381     441 ..     380     449 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00036
                       DUF1664  75 ldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                   +++++++++ +++e++++ ++++++++ v+++++ +++l+s+l+++++
  gi|70608058|ref|YP_256928.1| 337 VQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQ 384
                                   788999**************************************9986 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 0.00015
                       DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                    Ls+ri +++++l + + ++++++   ++++++l++++ +++s+++ +++l ++l+++++k
  gi|70608058|ref|YP_256928.1| 381 SLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSK 441
                                   5888999999999999999999999999999999999999999999999999998888775 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   4.8   9.6e-05     0.009      75     122 ..     336     383 ..     319     384 .. 0.78
   2 !   12.3   2.2    0.0017      0.16       4      55 ..     385     436 ..     377     440 .. 0.48
   3 ?    9.5   0.2     0.012       1.1      92     121 ..     416     445 ..     414     447 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-05
                       DUF5082  75 lessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                     ++ q+ +  + + i+++ + I++Le++++++q+ ++tl+s+l+sl+
  gi|70608058|ref|YP_256928.1| 336 SVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLS 383
                                   456667778888888899999999999999999999999999999886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0017
                       DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpln 55 
                                   +i++lq+  a+l s+i++l+   + L +   +l+++ +sl +++++l+++ln
  gi|70608058|ref|YP_256928.1| 385 RITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLN 436
                                   4444444444444444444444444444444444444444444444444444 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.012
                       DUF5082  92 aieeEIerLenqiseaqgvldtlqsqlnsl 121
                                   a++ +I+ L ++i++++g l++lqs++nsl
  gi|70608058|ref|YP_256928.1| 416 ALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   566778888888888888888888888777 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.2e-05     0.002      29      96 .]      53     122 ..      38     123 .. 0.77
   2 ?    4.6   0.1      0.49        46      19      64 ..     131     175 ..     128     205 .. 0.85
   3 ?    2.6   0.0       1.9   1.8e+02      28      58 ..     262     292 ..     253     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-05
                                   SB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE-....-TT--SEEEEEEEEECSTTT-EEEEEEEE CS
                           MG2  29 qglaklplkltirdpdgkevkelplatdetggaesefal....peaaklGeysvelsadsaeeslssgsfrV 96 
                                   q  +++ ++l+++dp+g++v++   +t+++gg   ++a+    p  +  G+y+v+l  + ++++++s+s++V
  gi|70608058|ref|YP_256928.1|  53 QSQPNALVTLYVYDPKGNVVYNNVYQTNSSGGLTATIATfgstPGFTTVGTYTVSL--SVQGTTSESASVNV 122
                                   55566779************************99988752222777889*******..66666666666655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.49
                                   EEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEE CS
                           MG2  19 lkallrdetlqglaklplkltirdpdgkevkelplatdetggaese 64 
                                   ++a + ++++++la++ ++l+ +++++++   ++ +t+++g+a ++
  gi|70608058|ref|YP_256928.1| 131 ITATVVNQEGSPLAGATVQLYNTTSGSNTLVATQ-TTNSQGVATFT 175
                                   5677889*****************9999999888.88888887765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 1.9
                                   CSB---EEEEEEEE-TTSSEEEEEEEEE-CT CS
                           MG2  28 lqglaklplkltirdpdgkevkelplatdet 58 
                                   +q ++ +p++++++ p+g ++ + ++ t+ +
  gi|70608058|ref|YP_256928.1| 262 GQRVTTAPVSAQVYYPNGTQTVKASVITSGK 292
                                   6778889**************9999865544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   4.0   2.1e-07   1.9e-05     142     232 ..     352     445 ..     330     449 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-07
                          Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekk 219
                                   ++l +n+++le+  ++L+ q + l++ l +l+++ ++l+++l++l++   +l+    + + +L++l+ ++++l++ i +++
  gi|70608058|ref|YP_256928.1| 352 SSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGtasSLSSQLNALQGKISSLNSSITNLS 432
                                   344555555555555555555555555555555555555555555554444333332446677777777777777777777 PP

                          Spc7 220 kelaelqeqleel 232
                                    +l++lq+++++l
  gi|70608058|ref|YP_256928.1| 433 GQLNSLQSKVNSL 445
                                   7777777766655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.8     0.005      0.47      17      52 ..     356     391 ..     342     393 .. 0.75
   2 !   16.1   0.2   0.00014     0.013       3      53 ..     356     406 ..     354     412 .. 0.86
   3 !   16.5   0.0   0.00011      0.01       2      56 ..     383     437 ..     382     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                   + i  L ++v + q qi+ l   l  l +r+ +l++
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQN 391
                                   567778888888888888888888888888877765 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                   + +++LE  +  ++ +i +Ln  +    q+i+ lq  l+ l+  +++l+ +
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGT 406
                                   679999999999999999999999999999999999999999998888765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                          SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                    +r++ L+  la +  ti +L+ +      q+ +lq ++  l+  + +l+ + ++
  gi|70608058|ref|YP_256928.1| 383 SQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNS 437
                                   6899999999999999999999999999999999999999999999998888765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   3.0   0.00016     0.015      32      72 ..     348     388 ..     341     390 .. 0.92
   2 !   13.5   0.8   0.00058     0.055      24      70 ..     389     435 ..     386     441 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.00016
                    TMF_DNA_bd  32 nntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                   n+ i++L + + +lek++++l+ ++++l+++l++l++r ++
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITS 388
                                   789**********************************9765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00058
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                   L+ +   ln ti++L  +++ l ++++ l+ k+++l++++++l+  l
  gi|70608058|ref|YP_256928.1| 389 LQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQL 435
                                   77888899999999999999999999999999999999999997665 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.5   1.4e-06   0.00013      23      62 ..     138     180 ..     127     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-06
                          bMG3  23 dsgkPvagaeVrlld...kkgevlaegtTDaqGvarfaallar 62 
                                   ++g P+aga+V+l++    ++ ++a++tT++qGva+f+ l+  
  gi|70608058|ref|YP_256928.1| 138 QEGSPLAGATVQLYNttsGSNTLVATQTTNSQGVATFTVLSFP 180
                                   5799**********96556899***************998555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.5   0.00055     0.052      64     101 ..     358     395 ..     346     399 .. 0.86
   2 ?    8.9   0.0     0.015       1.4      59     104 ..     395     440 ..     392     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   +++Le++ ++l+++i+tl+++l++l ++++ l+++l +
  gi|70608058|ref|YP_256928.1| 358 ITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLAS 395
                                   57899999999999999999999999999999998875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.015
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                   Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                                   +++++++ L  ++ +l+ ++++l+ ++++l+  +++l  +l++++ 
  gi|70608058|ref|YP_256928.1| 395 SLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   5677888889999999999999999999999999999998888765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.2   4.8e-05    0.0045       2      38 ..     358     394 ..     357     398 .. 0.93
   2 ?    9.5   0.6     0.013       1.2       1      39 [.     385     423 ..     385     449 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.8e-05
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                   i +lE+ +++l+t+++t+ +++++ls+ ++ l+ +  
  gi|70608058|ref|YP_256928.1| 358 ITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLA 394
                                   789*****************************99875 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.013
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkd 39 
                                   ri +l+n l +l ++++++  + ++ls++++ l+ ++  
  gi|70608058|ref|YP_256928.1| 385 RITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISS 423
                                   666777777777777777777777777777666655543 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   5.5   1.7e-06   0.00016      14     111 ..     339     436 ..     331     446 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-06
                CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqe 94 
                                   +++  +++++  + +L +++ ++e+  +++ ++  t    +++l + i  l+++l  l++ +++l+    +L  +l+  q 
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQG 419
                                   566677888999********************************************************************* PP

                CENP-F_leu_zip  95 rvseLeslnsslenlle 111
                                   ++s+L+s+   l+ +l+
  gi|70608058|ref|YP_256928.1| 420 KISSLNSSITNLSGQLN 436
                                   ******99888887776 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.9       0.1       9.9      23      93 ..      59     122 ..      52     126 .. 0.51
   2 !   23.2  11.4   6.5e-07   6.1e-05      21      94 ..     128     205 ..     127     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.1
                    Invasin_D3  23 tltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLt......a.ttagtatitptvnG.vaiaatatvtl 93 
                                   ++t+ + D +gn v ++  + +++  g             tat+       + tt+gt+t++ +v+G +  +++a+v++
  gi|70608058|ref|YP_256928.1|  59 LVTLYVYDPKGNVVYNNVYQTNSS-GG------------LTATIAtfgstpGfTTVGTYTVSLSVQGtT--SESASVNV 122
                                   566666666666666654444433.33............222221111111557888888888888833..44444432 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 6.5e-07
                    Invasin_D3  21 tstltvtlkDangnpvsgltvtfsttsag...tlsavtdngdGtytatLta..ttagtatitptvnGvaiaatatvtlt 94 
                                   tst+t+t+ +++g p++g+tv++  t +g    + + t+n++G+ t t+ +    + t ++ ++++G  +a+ta+v++t
  gi|70608058|ref|YP_256928.1| 128 TSTITATVVNQEGSPLAGATVQLYNTTSGsntLVATQTTNSQGVATFTVLSfpGVTQTFKLVASLQG-YAASTASVSIT 205
                                   89**********************88677674444677999**********95559***********.55777777766 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   5.3   0.00012     0.012      47     114 ..     336     403 ..     330     407 .. 0.88
   2 !   20.1   1.1   5.6e-06   0.00053      57     119 ..     381     443 ..     378     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 0.00012
                          ADIP  47 ardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklkne 114
                                   + + +++ + ++n++i++l   i++l+++++ l+tq + l + l+++ ++ ++l+ +l++l++++ ++
  gi|70608058|ref|YP_256928.1| 336 SVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   56789999999999999999999999999999999999999999999999999999999999988765 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.6e-06
                          ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelq 119
                                   sl+++i +l++++++l+s+i++l+   ++l ++l ++q k  +l+ ++++l+ +l++++ +++
  gi|70608058|ref|YP_256928.1| 381 SLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   79999***********************************************99999987776 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   5.0   1.5e-06   0.00014      52     162 ..     334     444 ..     327     449 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-06
                      KASH_CCD  52 lkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkek 132
                                   l+s+Q   + + l+++E+  l +++++le   ++l++q + l+    sL+++i+sLq+ +  l + ++ l      L+++ 
  gi|70608058|ref|YP_256928.1| 334 LMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQL 414
                                   566666666666667777777777777777777777777777777777777777777777777777777777777777777 PP

                      KASH_CCD 133 aeLkkqlheleellaekealleektkqiee 162
                                   + L+ ++ +l++ +++    l+  + ++++
  gi|70608058|ref|YP_256928.1| 415 NALQGKISSLNSSITNLSGQLNSLQSKVNS 444
                                   777777666666665555555555555554 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.9   1.1e-06   9.9e-05     316     423 ..     335     439 ..     278     444 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-06
                        DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaee 396
                                    +++ +++l++  ++e+++l ++i +le+++++l+ +i++l+ss++ +++ ++ ++++ + l++++     t++ l    +
  gi|70608058|ref|YP_256928.1| 335 MSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSL---SS 412
                                   5677888899999999999999999999999999999999999999999999999999999999999999999988...78 PP

                        DUF812 397 niekLqalveasaqrlvelakqWekhR 423
                                   ++++Lq  + + ++++ +l+ q ++ +
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   999*****************9998765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   3.3    0.0014      0.13       4      65 ..     341     403 ..     338     407 .. 0.88
   2 ?    9.7   0.0     0.012       1.2       5      37 ..     413     445 ..     409     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0014
                          ZapB   4 elLeqLEsk.iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                   ++L+ L +k i++++++it L + +  L+ + ++l++    l++ +  l+++ +++++ +++L
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKeISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   56666644449****************************************999999988876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.012
                          ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneel 37 
                                   +L+ L+ ki+++   it L+ ++  L+ ++++l
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   899**************************9998 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   3.7    0.0012      0.11      45      95 ..     336     386 ..     308     387 .. 0.74
   2 !   12.7   0.3    0.0012      0.12      33      95 ..     383     442 ..     380     443 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0012
                       BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   s++++ +     ++e+++++q+i ++ek+v+ L++ +s L++  ++L +++
  gi|70608058|ref|YP_256928.1| 336 SVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRI 386
                                   4444444444455899*************************9999998876 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0012
                       BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   s+++++l++ +asl+++++ l+    + +++ +q+++++ ++++L + +  L     +L++k+
  gi|70608058|ref|YP_256928.1| 383 SQRITSLQNTLASLNSTISSLSG---TASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   68899999999999999999999...7777788999999**************9999999998 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   4.8   2.6e-06   0.00024      39     138 ..     338     440 ..     334     447 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.6e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHH CS
                         Nup54  39 kaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletl 119
                                   +a q+  a+ ++ ++++ +++++le k   ++++++ ++ +    ls+R+++l + l  l+s  ++l+    +l+++l++l
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLE-KTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNAL 417
                                   66777888999999999********.9999******************************999999999999999999999 PP

                                   HHHHS-H....HH.HHHHHHHHH CS
                         Nup54 120 eaqlndp....aqlkgrvnelwa 138
                                   + ++++     + l+g++n l +
  gi|70608058|ref|YP_256928.1| 418 QGKISSLnssiTNLSGQLNSLQS 440
                                   99988522223444555555444 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.7     0.038       3.6       3      30 ..     349     376 ..     347     381 .. 0.73
   2 !   10.3   0.1    0.0045      0.42       1      30 [.     375     404 ..     375     413 .. 0.89
   3 ?    6.6   0.1     0.061       5.8       1      29 [.     417     445 ..     408     457 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.038
                       DUF4988   3 ddvndlkdrvaaleeqvkelndniealk 30 
                                   +++++l + ++ le++v++l+++i++l+
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLN 376
                                   5778888888888888888888888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0045
                       DUF4988   1 leddvndlkdrvaaleeqvkelndniealk 30 
                                   l++ +++l +r+++l++++ +ln+ i++l+
  gi|70608058|ref|YP_256928.1| 375 LNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   567899*********************997 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.061
                       DUF4988   1 leddvndlkdrvaaleeqvkelndnieal 29 
                                   l+ ++++l++ ++ l  q+++l++++++l
  gi|70608058|ref|YP_256928.1| 417 LQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   33344444444444444444444444444 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.5     2e-06   0.00019     312     432 ..     309     430 ..     303     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-06
                                   SHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHH.HHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHH CS
                          EzrA 312 keklehlekqnkelkeeldrlkqsYeLseeeleklre.lekelkelekdyeeleekleekkvaYSelqeeleeleekleei 391
                                   ++++ +l    + ++++ + l+ +Y +s +  ++l+  ++ke+++l +++ +le+ +++ ++  S+l++ l +l+++++ +
  gi|70608058|ref|YP_256928.1| 309 QNYVFQLLIVANYTTSSGQTLSTKYLMSVQANQNLQAlVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSL 389
                                   5556666666677777788999999999999888876269***************************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS CS
                          EzrA 392 eekqeeileslkslrkdEkrAreqldeikkelkeikrkiek 432
                                   ++ + +++ +++sl    +    ql+ ++ ++++++++i +
  gi|70608058|ref|YP_256928.1| 390 QNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITN 430
                                   *********************************99999876 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.34        32      23      94 ..      47     123 ..      32     126 .. 0.70
   2 !   13.7   3.0   0.00046     0.043      22     157 ..     129     402 ..     122     405 .. 0.68
   3 ?    4.4   0.1      0.34        32     113     167 ..     407     461 ..     401     474 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.34
                   EMP24_GP25L  23 lltgsyqvtdggaaldvdlsvkdpdgngerlvkkkdresegdfsftak...........esgeykvCfdnsfstksskkvs 92 
                                   +l++s+q +    +  v l+v+  d++g++++++  + ++ +   ta+           + g+y+v ++ + +t+ s++v+
  gi|70608058|ref|YP_256928.1|  47 QLVLSIQSQP---NALVTLYVY--DPKGNVVYNNVYQTNS-SGGLTATiatfgstpgftTVGTYTVSLSVQGTTSESASVN 121
                                   4444444443...457999999..7777999998666555.4444444447888899999999999999999999999998 PP

                   EMP24_GP25L  93 fd 94 
                                   ++
  gi|70608058|ref|YP_256928.1| 122 VQ 123
                                   87 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00046
                   EMP24_GP25L  22 tlltgsyqvtdggaaldvdlsvkdpdgngerlvkkkdresegdfsftak................................ 70 
                                   +++t+++  ++g++  +  ++++++ +  ++lv ++ + s+g  +ft++                                
  gi|70608058|ref|YP_256928.1| 129 STITATVVNQEGSPLAGATVQLYNTTSGSNTLVATQTTNSQGVATFTVLsfpgvtqtfklvaslqgyaastasvsitgqqn 209
                                   566666666666655566666666666666777776777777777777667777777777777777777777777777777 PP

                   EMP24_GP25L  71 ................................................................................. 70 
                                                                                                                    
  gi|70608058|ref|YP_256928.1| 210 asvtitlvpavvtiapmyviqngtvigsgpslssivvyqglpayilaqvsfagqrvttapvsaqvyypngtqtvkasvits 290
                                   777777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                   EMP24_GP25L  71 ..esgeykvCfdnsfstkss................kkvsfdievgseasd....................ykdsakkekl 113
                                       g y++ + ++  + +                 +                                  ++ s   + +
  gi|70608058|ref|YP_256928.1| 291 gkYAGMYNITIMPPTESVQNyvfqllivanyttssgQ-------------TlstkylmsvqanqnlqalvnKEISSLVQNI 358
                                   7777888887777777665544444433333333331.............0333444444444455556546667779*** PP

                   EMP24_GP25L 114 etleselkkleekldsikreqkylrereerlrdtnestnsrvvw 157
                                   ++le+++++l+++++ + + + +l +r ++l++t+ s+ns +  
  gi|70608058|ref|YP_256928.1| 359 TNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISS 402
                                   ***************************************98865 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.34
                   EMP24_GP25L 113 letleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlv 167
                                    ++l s+l+ l+ k++s+ + ++ l  + ++l+  ++s++  v    i+ ++ l+
  gi|70608058|ref|YP_256928.1| 407 ASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTPLVYGGIIAGIIGLI 461
                                   4556666666666666666666666666666666666666666666555555544 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.6     3e-06   0.00028     477     569 ..     348     444 ..     325     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3e-06
                          HOOK 477 eekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed....ssllkkkleehleklkevqeel 553
                                   ++++++l + + + ++++n+L+t+  + n  +++L++++  lq++l++ +s   +    +s+l ++l++++ k++++++ +
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSlsgtASSLSSQLNALQGKISSLNSSI 428
                                   45577777888888888888888888888888888888888888888777765554444788999999999********** PP

                          HOOK 554 qkkkeqleelepklss 569
                                   ++ + ql++l++k++s
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLNSLQSKVNS 444
                                   *********9999987 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   7.6   0.00062     0.058       3      66 ..     341     401 ..     338     408 .. 0.87
   2 !   15.1   1.0   0.00026     0.025       2      62 ..     388     446 ..     388     450 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00062
                       NPV_P10   3 qniLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   qn   ++ ++i+ + + ++ l++ v+++q+++ +   ln+ L ++s+ +++l++++ + +++ +
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQIST---LNSSLSSLSQRITSLQNTLASLNSTIS 401
                                   67777888999999999************98877...999*************99999888765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 0.00026
                       NPV_P10   2 S.qniLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                   S qn L    + i+ ++   ++l++q++ +q ++     ln+ + ++s qL++l++kv++ +
  gi|70608058|ref|YP_256928.1| 388 SlQNTLASLNSTISSLSGTASSLSSQLNALQGKISS---LNSSITNLSGQLNSLQSKVNSLT 446
                                   66999**************************97666...*******************9875 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.6   0.00072     0.068      42      81 ..     340     379 ..     326     382 .. 0.83
   2 ?    7.5   0.1     0.052       4.9      30      82 ..     389     443 ..     379     444 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00072
                  Lzipper-MIP1  42 llslstllpkkakellkeiallEeevvkLEqkllsLyrkl 81 
                                     +l++l+ k++  l ++i  lE++v +L+ ++++L+ +l
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSL 379
                                   457788999***************************9887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.052
                  Lzipper-MIP1  30 Lekal..ssssdgsllslstllpkkakellkeiallEeevvkLEqkllsLyrklf 82 
                                   L+++l   +s  +sl+ + ++l ++ + l   i+ l   + +L  +l+sL+ k++
  gi|70608058|ref|YP_256928.1| 389 LQNTLasLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   555554322223455566668999**************************99875 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.2     5e-06   0.00047     325     411 ..     344     431 ..     311     456 .. 0.46

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5e-06
                          FapA 325 eievgldepelkeklkeleeeleeleeeleklkkkikklpklka..ekqlesekkeqlkklletkeklkeeleeleeelke 403
                                   +  v+ +  +l +++++le+ +++l+ ++ +l++++++l++ ++   ++  +   +++ +l  t  +l+++l++l+ ++ +
  gi|70608058|ref|YP_256928.1| 344 QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQ-RItsLQNTLASLNSTISSLSGTASSLSSQLNALQGKISS 423
                                   33333333333333333333333333333333333333333.111122223333444555555555555555555555555 PP

                          FapA 404 lkeelesk 411
                                   l++++ + 
  gi|70608058|ref|YP_256928.1| 424 LNSSITNL 431
                                   55555554 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5     1e-05   0.00099      14     105 ..     347     435 ..     321     446 .. 0.47

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-05
                        APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                   ++k+++++ + + ++e+  ++l+++ ++ +   ++l +l +++  l+++ ++l + +  l  + ++l ++l+al+ + + l
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLN---SSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSL 424
                                   333444444444444444444444433333...344444444444444444444444444444444444444444444444 PP

                        APG6_N  95 eeeeerfwrey 105
                                   +   ++   + 
  gi|70608058|ref|YP_256928.1| 425 NSSITNLSGQL 435
                                   44444444444 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.6   5.3e-06    0.0005     195     296 ..     332     432 ..     304     439 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.3e-06
                         FAM76 195 klaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeak 275
                                   k   + ++n++ ++ ++++ s  + ++t+L++++++l+ q+++ +++l++  + it+l+  l + ++++ + l+ + ++ +
  gi|70608058|ref|YP_256928.1| 332 KYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTI-SSLSGTASSLS 411
                                   344455666677789999*****************************************9998887766.56889999999 PP

                         FAM76 276 ekieklekkirellkevaels 296
                                   +++++l+ ki++l   +++ls
  gi|70608058|ref|YP_256928.1| 412 SQLNALQGKISSLNSSITNLS 432
                                   999*******99999888876 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.7    0.0012      0.12      26      68 ..     351     389 ..     339     395 .. 0.70
   2 ?    7.3   0.0     0.066       6.2      25      62 ..     406     443 ..     394     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0012
                           CLZ  26 qkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkL 68 
                                     +l +++++Le+++++Lqt++  L + +    + L qRit L
  gi|70608058|ref|YP_256928.1| 351 ISSLVQNITNLEKTVNNLQTQISTLNSSL----SSLSQRITSL 389
                                   55677788888888888888887765544....4466666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.066
                           CLZ  25 eqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                   ++ +l ++++ L++++ +L+  +  L ++++s q+k +
  gi|70608058|ref|YP_256928.1| 406 TASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   55677777888888888888888888888888887765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.7   5.4e-06   0.00051     367     465 ..     340     440 ..     319     448 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.4e-06
                        AAA_13 367 ikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleee 445
                                    ++l+a +n+ i++  + ++nle+ ++++++++      +++l + ++ +++++++l+ +i++l   ++  +++l++l+++
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNssLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGK 420
                                   333444455555555555555555555555555543212455555555566666666666666666666666666666666 PP

                        AAA_13 446 ikeLekqlrdekpaaeeink 465
                                   i+ L  ++++     + + +
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLSGQLNSLQS 440
                                   66665555555444444433 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.8    0.0011       0.1      80     119 ..     345     384 ..     341     385 .. 0.91
   2 !   10.3   0.4    0.0052      0.49       2      34 ..     369     401 ..     368     415 .. 0.84
   3 ?    5.8   0.0      0.13        12      11     102 ..     413     437 ..     403     448 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   +l++k++++l +++++le+ ++ l++qi tl+  l+ l+q
  gi|70608058|ref|YP_256928.1| 345 ALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQ 384
                                   67899**************************999998876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0052
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                     Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkk 34 
                                   + ++++l+++l++l+++i++l++tl+ l++ + 
  gi|70608058|ref|YP_256928.1| 369 QTQISTLNSSLSSLSQRITSLQNTLASLNSTIS 401
                                   679999999999999999999999999998765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHH CS
                     Prefoldin  11 elaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelek 91 
                                   +l++l+ +i++l++++ +l                                                              
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNL-------------------------------------------------------------- 431
                                   3333333333333333332.............................................................. PP

                                   HHHHHHHHHHH CS
                     Prefoldin  92 qlekleeelek 102
                                          +l+ 
  gi|70608058|ref|YP_256928.1| 432 -----SGQLNS 437
                                   .....222222 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.3     0.046       4.3      40      90 .]     340     390 ..     331     390 .. 0.68
   2 !   20.6   2.4   4.7e-06   0.00044       8      89 ..     365     445 ..     362     446 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.046
               Snapin_Pallidin  40 nekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekLq 90 
                                   n++L+ l + + +++++++ +  k ++n++ ++s+ln++l++l +R++ Lq
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQ 390
                                   555554444444667777777777777777777777777777777777775 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.7e-06
               Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                   ++ l+ ++ +l+++l++l q  + L+++l +ln+ + +l+ +++ ++ ++l+  + K++++   +++l+ +l++l+ +++ 
  gi|70608058|ref|YP_256928.1| 365 VNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTAS-SLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNS 444
                                   57899999********************************9999.999******************************998 PP

               Snapin_Pallidin  89 L 89 
                                   L
  gi|70608058|ref|YP_256928.1| 445 L 445
                                   7 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   6.1   7.5e-06   0.00071     244     332 ..     340     432 ..     326     446 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-06
                         IFT57 244 ksqlkkl.hedisktlekiesrEkylns...qleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqe 320
                                   +++l+ l  ++is  +++i++ Ek +n+   q+++l + +++++++++++++ +  l++++s+l+ + +++s +l++++ +
  gi|70608058|ref|YP_256928.1| 340 NQNLQALvNKEISSLVQNITNLEKTVNNlqtQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGK 420
                                   455555415678888888888888876433378888888888888888888888888888888888888888888888888 PP

                         IFT57 321 meergssmtDgs 332
                                   + + +ss+t+ s
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLS 432
                                   888888888754 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2         2   1.9e+02      43      65 ..     101     123 ..      98     133 .. 0.87
   2 !   20.0   5.1   5.5e-06   0.00051       4      79 ..     134     219 ..     131     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 2
               CarbopepD_reg_2  43 agkytLvvsyvGyktqekkvtvs 65 
                                    g+yt+  s+ G ++++ +v+v+
  gi|70608058|ref|YP_256928.1| 101 VGTYTVSLSVQGTTSESASVNVQ 123
                                   699***************99986 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.5e-06
               CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtkkgtv.......TdenG..nFelknlpa..gkytLvvsyvGyktqekkvtvskektldvn 73 
                                   tVv++e + pl+gatV++ +t+ g         T+++G  +F++ + p   ++++Lv+s  Gy   + +v+++++++ +v+
  gi|70608058|ref|YP_256928.1| 134 TVVNQE-GSPLAGATVQLYNTTSGSNtlvatqtTNSQGvaTFTVLSFPGvtQTFKLVASLQGYAASTASVSITGQQNASVT 213
                                   677765.68*********9998654322333449****55577777775446789************************99 PP

               CarbopepD_reg_2  74 illkee 79 
                                   i+l ++
  gi|70608058|ref|YP_256928.1| 214 ITLVPA 219
                                   998766 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   7.1   8.9e-06   0.00084     130     218 ..     347     431 ..     317     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.9e-06
                     Golgin_A5 130 lvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLtesLiqKQtvlEalsteknslvlQLeRleqqikev 210
                                   + ++ ++l+++i++ ek +++l+ q++t    +ss s l++R+ +L ++L     ++ +ls   +sl  QL+ l+ +i+++
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTL---NSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSL 424
                                   44556799999**************9875...456788******************************************* PP

                     Golgin_A5 211 qseaengt 218
                                   +s+ +n  
  gi|70608058|ref|YP_256928.1| 425 NSSITN-L 431
                                   *99877.2 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   6.0   1.4e-05    0.0013      39     153 ..     327     441 ..     309     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-05
                         Atg14  39 eslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdl 118
                                   ++l +k+   ++ ++  +   +++i ++ +++ +l +++  l+ ++++l+ +ls+l ++i   +++la+l+++++    ++
  gi|70608058|ref|YP_256928.1| 327 QTLSTKYLMSVQANQnLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTA 407
                                   566666666666666233456788999999999999999999999999999999999999999999999999999999999 PP

                         Atg14 119 eslqneleerrkkqiaklqdaikrieqklsslssk 153
                                   +sl+++l++ +  +i++l ++i + + +l+sl+sk
  gi|70608058|ref|YP_256928.1| 408 SSLSSQLNALQG-KISSLNSSITNLSGQLNSLQSK 441
                                   999999988765.4677777777777777776665 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   6.8   9.5e-06   0.00089      64     155 ..     349     443 ..     324     449 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.5e-06
                  HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetn 144
                                   ++ ++l + + ++e+++++L++++++L +   ++ +r   Lq + asl+++ ++l+ + ++ + +l+ +q ++++ n+ ++
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSIT 429
                                   444555556667788889999999999999999999999999999999999999999999999999999988888888777 PP

                  HAUS-augmin3 145 av...Lqqlteeak 155
                                   ++   L++l+++++
  gi|70608058|ref|YP_256928.1| 430 NLsgqLNSLQSKVN 443
                                   75111444444444 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.1   1.7e-05    0.0016      64     163 ..     329     425 ..     316     446 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.7e-05
                        HMMR_N  64 ksqkkdkskltkekkkqkeLEkeiRsLvqergeqdkrlqaleeelkkveakLlaavrektslsanvasLekqlaelkrane 144
                                    s k    ++ ++++ q    kei sLvq+ ++ +k +++l+ ++  +++ L+ + +  tsl+ + asL+   + l+ +  
  gi|70608058|ref|YP_256928.1| 329 LSTKYL-MSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTAS 408
                                   444555.55666667777889************************************************998888877776 PP

                        HMMR_N 145 lLksKvsedgtkKklnsLs 163
                                    L s + +   + k++sL 
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNA--LQGKISSLN 425
                                   66666543..345555555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   6.6   4.7e-05    0.0044      15     102 ..     327     414 ..     312     416 .. 0.81
   2 ?    8.2   0.2     0.014       1.4      33      84 ..     394     445 ..     389     449 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-05
                       DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                   ++  ++ l   ++ ++ +a ++k+i++l ++ ++l++ +++l+++++ l+   + l++ ++s+++++asl+  i++++ ++
  gi|70608058|ref|YP_256928.1| 327 QTLSTKYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTA 407
                                   444455556666777788889999999999999999999999999999999999999999999999999999999999999 PP

                       DUF3450  96 relvpll 102
                                   ++l+  l
  gi|70608058|ref|YP_256928.1| 408 SSLSSQL 414
                                   9887766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.014
                       DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                   a+ ++ i++l+  +++l+++++al+ +++sl+    +l+ +++s++++++sl
  gi|70608058|ref|YP_256928.1| 394 ASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   4455666666667777777777777777777777777777777777776666 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.4   1.7e-05    0.0016     186     279 ..     340     436 ..     327     446 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHH CS
                      Filament 186 reeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaele...erleaeleklqek 263
                                   ++++++  ++ ++ l +++++ ++++++ +++i+ l+ ++ sl+  + sl+++ asl+++++ l      l+++l+ lq k
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSgtaSSLSSQLNALQGK 420
                                   556677777888899999999999999999999999999999999999999999999988766541115678899999999 PP

                                   HHHHHHHHHHHHHHHH CS
                      Filament 264 lseleeelaeireema 279
                                   +s+l++ ++++  +++
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLSGQLN 436
                                   9999999988776655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.8   1.8e-05    0.0017      23     119 ..     339     439 ..     332     447 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-05
                           GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknl....karlkelek 99 
                                    N +l+    +ei  l ++ +  ek +++++++ + l+  L  + + +  L++ l+  ++  +sl  +     ++l+ l+ 
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTasslSSQLNALQG 419
                                   455555555566666666666666666666666666666666666666666666666665555554330000233333333 PP

                           GAS 100 elkdlkwehevleqrfekve 119
                                   ++++l  +  +l+ ++++++
  gi|70608058|ref|YP_256928.1| 420 KISSLNSSITNLSGQLNSLQ 439
                                   34444444444433333333 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.7   2.2e-05    0.0021      70     182 ..     339     445 ..     296     449 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-05
                       UPF0242  70 leekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                    +++ + l++  ++++   +++ +l++  ++L+ +++  ++ l  l ++  +Lq  l      ++ l+  +         +
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVN--KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTA----SSLSSQ 413
                                   2222222333..34666667777777777777777777777777777777777766666555554444332....233445 PP

                       UPF0242 151 lqeyqetieeqrsvlekrqdqieqLeskVrDl 182
                                   l+ +q +i+++ s++ +   q + L+skV+ l
  gi|70608058|ref|YP_256928.1| 414 LNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   66666666666666666666666666666544 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   3.5    0.0015      0.14       2      52 ..     368     418 ..     347     418 .. 0.93
   2 !   14.4   1.3   0.00033     0.031       1      58 [.     381     438 ..     381     446 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0015
                 TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqle 52 
                                   l++++++L+  l++ sq ++ lq+ l +l++ +++L G    l+ ql+ l+
  gi|70608058|ref|YP_256928.1| 368 LQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   6889999999999999***********************999999999875 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00033
                 TolA_bind_tri   1 sledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdl 58 
                                   sl +r+++L + l++ ++++  l    ++l+++l+ L+G+i  l+  + +l  + + l
  gi|70608058|ref|YP_256928.1| 381 SLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSL 438
                                   5778888888888888877777777777777777777777777766666665554444 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.0   1.7e-05    0.0016     322     418 ..     347     443 ..     322     450 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-05
                          Cast 322 ckqHievLkesltAkeqRAaiLqtevdalrlrleekeqlLnkktkqlqdlteekstlageirdlkdmldvkeRkvnvlqkk 402
                                     + i  L   +t  e+  + Lqt + +l+  l    q ++  ++ l +l++  s+l+g  + l   l+  + k+  l++ 
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSS 427
                                   355677777778888888888888888888888888888888888888888888888888888888888888888888888 PP

                          Cast 403 ienLqeqlrdkdkqla 418
                                   i nL+ ql   + +++
  gi|70608058|ref|YP_256928.1| 428 ITNLSGQLNSLQSKVN 443
                                   8888888876555544 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   9.4   2.6e-05    0.0025     238     319 ..     338     422 ..     292     452 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.6e-05
                          Gp58 238 rsnqGmrveleskisGlqs...tqqstakqisqeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpn 315
                                   ++nq ++  ++ +is l       + t ++++ +i+  ++++s ++q + s+q+ l + ++  ssL+ t + l s++++ +
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQnitNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   234444444444444432101012334444555555555555555555555555555555555555555555555555444 PP

                          Gp58 316 skle 319
                                   +k++
  gi|70608058|ref|YP_256928.1| 419 GKIS 422
                                   4332 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.5   1.5e-05    0.0014       2      51 ..     139     177 ..     138     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-05
                                   CCCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEE CS
                          SpaA   2 tgkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegL 51 
                                   +g pLaGa+ +ly+++             ++t v+t tt+++G atf+ L
  gi|70608058|ref|YP_256928.1| 139 EGSPLAGATVQLYNTT-----------SGSNTLVATQTTNSQGVATFTVL 177
                                   689*************...........456899**************966 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.7     3e-05    0.0029      18     107 ..     346     431 ..     333     445 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3e-05
                                   HCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  18 lkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                                   l ++ e +++v+ +  l++   +lq+++  l++   +ls+ I ++ +     ++l   +++l+   + l+ +l++l+ ++ 
  gi|70608058|ref|YP_256928.1| 346 LVNK-EISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNT---LASLNSTISSLSGTASSLSSQLNALQGKIS 422
                                   5556.6899************************************975...688999999999999999999999999999 PP

                                   HHHCTS--- CS
                  Seryl_tRNA_N  99 klllaiPNi 107
                                   +l ++i N+
  gi|70608058|ref|YP_256928.1| 423 SLNSSITNL 431
                                   999999997 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   7.6   0.00034     0.032      65     128 ..     333     396 ..     305     399 .. 0.76
   2 ?    6.3   0.1      0.11        10      94     130 ..     404     440 ..     394     449 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00034
                                   HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  65 lrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                   +    + +++ + +++k  ++l ++i++l++t+++  ++i  L + l+s++q+i+ L++  +++
  gi|70608058|ref|YP_256928.1| 333 YLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASL 396
                                   333333344347788888888888*********************************9988766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.11
                                   HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  94 ketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                     t ++  s++++Lq+ ++s++++i++L  + +++++
  gi|70608058|ref|YP_256928.1| 404 SGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   4444555567777777777777777777666555554 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   7.8   2.9e-05    0.0028     681     785 ..     337     446 ..     306     448 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.9e-05
                           FPP 681 gsnesk.....keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcm 756
                                    + +++     ++e  +l +++++l+ + +nl++++++ +++l sl  +++   ++la+l+s ++sl    s + +ql+  
  gi|70608058|ref|YP_256928.1| 337 VQANQNlqalvNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNAL 417
                                   222222445557888899999999999999*************************************************** PP

                           FPP 757 kesyesletrateleaelnelkqkieaLe 785
                                   +   +sl++  t+l  +ln+l++k+++L+
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNSSITNLSGQLNSLQSKVNSLT 446
                                   ************************99985 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.6   0.00012     0.011      20      92 ..     331     403 ..     325     405 .. 0.90
   2 ?    7.8   0.1     0.037       3.5       1      42 [.     389     430 ..     389     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 0.00012
                          BRE1  20 skkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefvrklkel 92 
                                    k ++++++ ++ ++ +++e++   q + ++++  ++l++++ +Ln++ls  s+ i+ L+++ +++++ +++l
  gi|70608058|ref|YP_256928.1| 331 TKYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   566788999999999999*******************************************999999988876 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.037
                          BRE1   1 lqkELvklekafeelseqlskkvkeltileekklrleaekak 42 
                                   lq+ L +l+  +  ls ++s++ ++l +l+ k++ l++ ++ 
  gi|70608058|ref|YP_256928.1| 389 LQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITN 430
                                   799999999999999999999999999999999999998876 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0    0.0011       0.1       8      55 ..     349     398 ..     343     404 .. 0.64
   2 ?    9.2   0.0     0.015       1.4      10      58 ..     379     429 ..     374     438 .. 0.83
   3 ?    2.2   0.0       2.3   2.1e+02       9      33 ..     413     437 ..     408     447 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0011
                  ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleelea 55 
                                   +e+  l + I  LE+   +l+++++  +   s   ++++ l++ l+ l++
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSlSSLsQRITSLQNTLASLNS 398
                                   77888888888888888888888886552211112555555555555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.015
                  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLe 58 
                                   l  l ++I +L++ +a+l+  +++ + ++ +   +l++l+ ++  l++ + 
  gi|70608058|ref|YP_256928.1| 379 LSSLSQRITSLQNTLASLNSTISSLSGTASSlsSQLNALQGKISSLNSSIT 429
                                   678999****************99998866667889999888888887765 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 2.3
                  ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaelad 33 
                                   +l +l  +I +L   i++l  +l++
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNS 437
                                   4666777777777777777777764 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   5.2e-05    0.0049       2      90 ..     349     436 ..     327     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-05
                         TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                   +e+++l +++ +le+t +++++++ +l+++ s++s++i++ ++ l +l+s++++l+ ++ ++ +++++ l+ ++++ ++++
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTA-SSLSSQLNALQGKISSLNSSI 428
                                   67788888888888888888888888888888888888888888888888888888775.577778888888888888887 PP

                         TMPIT  83 kevesllp 90 
                                    +++  l 
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLN 436
                                   77666554 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.8    0.0016      0.15       9      55 ..     358     404 ..     335     408 .. 0.68
   2 !   10.5   0.2    0.0035      0.33       7      55 ..     391     439 ..     387     448 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0016
                       DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieele 55 
                                   +++l++++ +lq++++ l+++ ++l++r+  ++  l +l + i+ l 
  gi|70608058|ref|YP_256928.1| 358 ITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   66677777788888888888888888888888877777777777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0035
                       DUF4795   7 ellkklqeaieklqeelekleekvkelekrledkekklealkkqieele 55 
                                   ++l  l+++i+ l+   ++l+++ + l+++++ + +++  l  q++ l+
  gi|70608058|ref|YP_256928.1| 391 NTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   3445555555555555555555555555555555555555555555554 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.0    0.0016      0.15      40     100 ..     332     392 ..     329     398 .. 0.87
   2 !   16.7   0.8     6e-05    0.0057       9      97 ..     356     445 ..     348     446 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0016
                         DHR10  40 klleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                   k l  ++a+++ +  ++k++++l ++++++e++++ l+++++ l+  l++  ++++ l+++
  gi|70608058|ref|YP_256928.1| 332 KYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNT 392
                                   6677888999999999999999999999999999999999999999999999999999875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6e-05
                         DHR10   9 eelaelErkarelqakidalqvvekdlrsciklleeieaelakleea.kkklkelrdaleekeielrelerkeerlqrqle 88 
                                   +++++lE+  ++lq++i +l+     l++ i+ l+   a l+++ ++ + ++++l+ +l+ ++ + + l++ ++ l  ql+
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSlSGTASSLSSQLNALQGKISSLNSSITNLSGQLN 436
                                   78999999************9999999999999999999998876651567899999999999999999999999999999 PP

                         DHR10  89 naeeklerl 97 
                                   + + k + l
  gi|70608058|ref|YP_256928.1| 437 SLQSKVNSL 445
                                   999998765 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   3.8   0.00012     0.012     161     230 ..     322     392 ..     156     402 .. 0.73
   2 ?    5.9   1.6     0.079       7.5     174     217 ..     400     442 ..     387     449 .. 0.41

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 0.00012
                                   SS.......SXSHHH.HHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                        FliD_C 161 tsqektvtsdsglat.rlenllksyvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaa 230
                                   t+++ ++ s++ l++ + ++ l+ +v+ + ++l ++++nl+k++++l+++i +l+++l++l +r+++  ++
  gi|70608058|ref|YP_256928.1| 322 TTSSGQTLSTKYLMSvQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNT 392
                                   45566777777777548999****************************************88887654444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCH CS
                        FliD_C 174 atrlenllksyvkssngtlqtasknltkqikdldkkiedldkrl 217
                                   +++l++ ++s+++   ++lq+++++l+  i++l+ + ++l++++
  gi|70608058|ref|YP_256928.1| 400 ISSLSGTASSLSSQL-NALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   222333333333222.4444444444444444444444444443 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   4.6   0.00032      0.03      11      81 ..     362     436 ..     330     446 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00032
                   TMF_TATA_bd  11 vqlverlsseirrlEgElaslkeelerleaerdeareeivklm....keneelkelkkeleelekeleelqerye 81 
                                    ++v++l+++i  l + l+sl +++++l++   ++++ i +l+    + + +l++l++++++l++++++l+ +++
  gi|70608058|ref|YP_256928.1| 362 EKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSgtasSLSSQLNALQGKISSLNSSITNLSGQLN 436
                                   456777777777777777777777777777777777777777633334455666666666666666666655544 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.7   6.7e-05    0.0063     142     245 ..     340     443 ..     320     449 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.7e-05
                     Rab5-bind 142 veeLqelvlklrEeliesRtakdHlEekLkaEillLkeqiqaEkalkEnlEetlqleierlkeelasisslkveleeikve 222
                                    ++Lq lv k    l++  t  + + ++L+  i  L   + +  +    l +tl+   + + +  ++ ssl  +l+ ++  
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGK 420
                                   344555555555555555555555555555555555555544444444444444444444444444444444444444444 PP

                     Rab5-bind 223 keslekslaektrqldklqtiks 245
                                     sl++s ++ + ql++lq+ ++
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLSGQLNSLQSKVN 443
                                   44555555555555555554444 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.6   0.00062     0.058      33      91 ..     349     405 ..     328     413 .. 0.89
   2 !   10.9   0.1     0.004      0.38      35      94 ..     379     436 ..     377     451 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00062
                       DUF2730  33 edleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                   +++++l++++++ +k +++l+t++++L   + l++L+  ++ l+  l  l+ ++++ls 
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLN--SSLSSLSQRITSLQNTLASLNSTISSLSG 405
                                   6899999*******************95..67999999999999999999999999975 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.004
                       DUF2730  35 leklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvd 94 
                                   l++l + +++ ++ l++l++++++L  +   ++L+ +l+ l+g+++ l+ ++++ls q++
  gi|70608058|ref|YP_256928.1| 379 LSSLSQRITSLQNTLASLNSTISSLSGT--ASSLSSQLNALQGKISSLNSSITNLSGQLN 436
                                   6789999999999999999999999755..467777888888888888888887776654 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   2.8   0.00067     0.063      33      94 ..     340     402 ..     318     405 .. 0.71
   2 ?    2.7   0.0       1.9   1.8e+02      42      72 ..     413     443 ..     405     450 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00067
                                   HHHHHH.HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHH CS
                         DUF16  33 kqrLkk.ieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqk 94 
                                   +q+L+  +++++++l ++i +le++v++++ +i+ l+      ++++ ++++tl ++  t+ +
  gi|70608058|ref|YP_256928.1| 340 NQNLQAlVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISS 402
                                   445544245567777777777777777777777777777777777777777777777777765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 1.9
                                   HHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DUF16  42 kvdklgeqinkleqkvekqgekikelkveqk 72 
                                   ++++l+ +i+ l+  ++++  +++ l+ +++
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   3334444444444444444444444444433 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.1      0.12        11      25      51 ..     343     369 ..     326     377 .. 0.66
   2 ?    8.6   0.1     0.016       1.5      19      51 ..     365     397 ..     363     404 .. 0.87
   3 ?    5.8   0.0      0.13        12      19      52 ..     407     440 ..     398     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                         DivIC  25 eiaalqaelaklkaeneeLeaevkdLk 51 
                                     a  ++e+ +l + + +Le+ v++L+
  gi|70608058|ref|YP_256928.1| 343 LQALVNKEISSLVQNITNLEKTVNNLQ 369
                                   334446778888888888888888884 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                         DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                   +  l+ +i +l+  l +l++++ +L+  ++ L+
  gi|70608058|ref|YP_256928.1| 365 VNNLQTQISTLNSSLSSLSQRITSLQNTLASLN 397
                                   667899********************9999995 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                    ++l ++++alq ++ +l+  + +L  +++ L+s
  gi|70608058|ref|YP_256928.1| 407 ASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   5677888888888888888888888888888853 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.5      0.04       3.7      15      47 ..     353     385 ..     340     423 .. 0.53
   2 ?    8.6   0.4     0.023       2.1       3      37 ..     411     445 ..     408     447 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.04
                         Spc24  15 dleselesleselaelkeeleeleeeseekese 47 
                                   +l +++++le++ ++l++++ +l+++ ++ +++
  gi|70608058|ref|YP_256928.1| 353 SLVQNITNLEKTVNNLQTQISTLNSSLSSLSQR 385
                                   444444444444444444444444433331111 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.023
                         Spc24   3 dnekfriakelsdleselesleselaelkeeleel 37 
                                    +++ +++ ++s+l+s++++l+ +l++l+++++ l
  gi|70608058|ref|YP_256928.1| 411 SSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   55666677778888888888888888888877765 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.7   9.8e-05    0.0093      11     110 ..     349     448 ..     331     451 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.8e-05
                    Lebercilin  11 lkikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklk 91 
                                   ++i +L +++++l++ +++l++   +L+      +++++ +++t a+L + +++ +     l  +l  +q k ++l++++ 
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSIT 429
                                   466677777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                    Lebercilin  92 ekeaellrlkdklkklkkL 110
                                   +   +l++l++k++ l  L
  gi|70608058|ref|YP_256928.1| 430 NLSGQLNSLQSKVNSLTPL 448
                                   7777777777777777655 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.6   0.00014     0.013       5      73 ..     360     426 ..     356     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 0.00014
                   Uso1_p115_C   5 eleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeeke 73 
                                   +le+++++l+++ ++l+++l+sls++++sl+++  +++ +s  ++l+ ++++l+++l +l+ +++  ++
  gi|70608058|ref|YP_256928.1| 360 NLEKTVNNLQTQISTLNSSLSSLSQRITSLQNT--LASLNSTISSLSGTASSLSSQLNALQGKISSLNS 426
                                   689******************************..8888888889999999999999999888776554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   9.5   0.00013     0.012       4      94 ..     350     437 ..     339     449 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 0.00013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                    +++  + +++ ++ +++l+++++ ++++ls++ + +   ++ + ++n +i + +   + L  +++ L  k+++l+    +
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITN 430
                                   445555666667777777777777777777777777777777777777777777777777777777777777777666555 PP

                                   ...HHHHHHH CS
                    Laminin_II  85 ssslsdnise 94 
                                      ls +++ 
  gi|70608058|ref|YP_256928.1| 431 ---LSGQLNS 437
                                   ...5554444 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   3.6   9.2e-05    0.0087     151     261 ..     338     447 ..     303     450 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.2e-05
                  Exonuc_VII_L 151 elerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk...ekleek 228
                                   +++++l+  +++ +++  q++++l++++++ ++++++ +++l++l++r+++ l+++l++ ++++++l+ + +   ++l++ 
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITS-LQNTLASLNSTISSLSGTASslsSQLNAL 417
                                   345566666666666666666666666666666666666666666666666.66666555555555553321122333334 PP

                  Exonuc_VII_L 229 kerlkklkerle.lleekkerleeleeklealsp 261
                                   + ++++l    + ++++ + +l++l++k+++l p
  gi|70608058|ref|YP_256928.1| 418 QGKISSL----NsSITNLSGQLNSLQSKVNSLTP 447
                                   4333333....13566777777777788877777 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.3   8.6e-05    0.0081     292     390 ..     341     439 ..     316     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.6e-05
                         WEMBL 292 kealasarkELeevkaniekakdevklLkvaaasLrseLekekaeLaslrqregmasiavssLeaelsrtkselelvqake 372
                                   ++  a   kE+  + +ni + ++ v+ L+   ++L+s L+   ++++sl+++ +    ++ssL    s+  s+l+++q k 
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKI 421
                                   333456789*****************************************998888899*********************9 PP

                         WEMBL 373 kearekmvelpkeLqeAa 390
                                      +  +++l  +L++ +
  gi|70608058|ref|YP_256928.1| 422 SSLNSSITNLSGQLNSLQ 439
                                   999999999999998755 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.0   9.5e-05     0.009      67     146 ..     348     428 ..     328     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.5e-05
                        DUF724  67 rseleslkeslaeLekhGFdVkalqsrln.kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                   ++e++sl +++++Lek   + ++  s ln  L sl ++ t+l++++  l++ i+  +   ++l+++++ l+ ki+ l+   
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNsSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   467999999999999999999999999962577899999999999999999999999999999999999999999887654 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   7.9   0.00023     0.022     111     175 ..     336     401 ..     305     404 .. 0.74
   2 ?    5.3   0.3      0.17        16     101     136 ..     408     443 ..     403     446 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00023
                  Bacillus_HBL 111 qee.iqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                   + +  q+ q+ v++ i  L +  ++l+k ++n++t++++l+s l++ s  i  lqn++++l+++i+
  gi|70608058|ref|YP_256928.1| 336 SVQaNQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTIS 401
                                   3331355678889999999999999***************************************98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.17
                  Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklkla 136
                                    +l+++l++Lq +i + + ++++l+++L++l++k++
  gi|70608058|ref|YP_256928.1| 408 SSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   567788888888888888888888888888887765 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4      0.15        14      21      60 ..     345     384 ..     337     389 .. 0.85
   2 !   11.1   0.0    0.0029      0.27       2      59 ..     375     432 ..     374     436 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.15
                 TRAF_BIRC3_bd  21 sVLnrEverssttieaverqrrldqekieaLekKvrqLer 60 
                                   +  n+E+ +   +i ++e+  ++ q  i +L+  + +L  
  gi|70608058|ref|YP_256928.1| 345 ALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQ 384
                                   6789**************************9998888854 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0029
                 TRAF_BIRC3_bd   2 lekklsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqLe 59 
                                   l+  ls L ++++   n  + Ln  + + s t+  ++ q ++ q ki +L+  + +L 
  gi|70608058|ref|YP_256928.1| 375 LNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLS 432
                                   5677899*********************************************999985 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7      0.36        34      47      81 ..     337     371 ..     308     381 .. 0.62
   2 !   10.7   1.7    0.0049      0.47       8      74 ..     338     399 ..     332     403 .. 0.80
   3 !   12.5   0.1    0.0014      0.13       6      76 ..     378     443 ..     374     446 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.36
                          FliJ  47 lrnyqafisaldeaiaqqkqelaqaekqvekaree 81 
                                    ++ q+  + ++++i+++ q+++++ek v++ + +
  gi|70608058|ref|YP_256928.1| 337 VQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQ 371
                                   44445555555566666666666666666665554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0049
                          FliJ   8 aeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekq 74 
                                   ++ q+ ++  ++++ +l q++ +++k  ++ +      ++ ++++ +s+l ++i++++++la ++  
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQ-----TQISTLNSSLSSLSQRITSLQNTLASLNST 399
                                   45566666667889999999999999999999.....999999999999999999999999988765 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0014
                          FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqve 76 
                                    L +  +++++ ++ l++l++++++++  +s+ +     ++l ++q  is+l++ i+ +  +l+ ++ +v+
  gi|70608058|ref|YP_256928.1| 378 SLSSLSQRITSLQNTLASLNSTISSLSGTASSLS-----SQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   5777889999999999999999999999999999.....**************************999987 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.6   9.7e-05    0.0091     357     977 ..     342     443 ..     330     447 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-05
                 Myosin_tail_1 357 aleelseqleqakrskaslekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvsk 437
                                    l                                                                               
  gi|70608058|ref|YP_256928.1| 342 NL------------------------------------------------------------------------------- 343
                                   33............................................................................... PP

                 Myosin_tail_1 438 lqaelesvsslleeaegksiklskdvsslesqlqDtqellqeetrqkLalssrlrqleeeknalkeqleeeeeakknvekq 518
                                                                                                                    
  gi|70608058|ref|YP_256928.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                 Myosin_tail_1 519 lstlqaqlsdlkkkleeeasavealeeakkrlqrelealtqrleekaaaydklektkkRlqqeldDllvdldkqrqlvsnl 599
                                                                                                                    
  gi|70608058|ref|YP_256928.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                 Myosin_tail_1 600 ekkqkkfDqlLaeekaisaklaeeRdraeaeaReketkalslaraleeakdakeelerankalraeledLvsskddvGknv 680
                                                                                                                    
  gi|70608058|ref|YP_256928.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                 Myosin_tail_1 681 heLerskraleqqveelktqleeLeDeLqatedakLRLevnlqalkaqfeRdlqardeqgeekrrqlvkqvreleaeleee 761
                                                                                                                    
  gi|70608058|ref|YP_256928.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                 Myosin_tail_1 762 rkqraqavaakkkleldlkeleaqidaankgrdealkqlkklqaqlkdlqReleearasrdeilaqakesekklksleael 842
                                                                                                                    
  gi|70608058|ref|YP_256928.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                 Myosin_tail_1 843 lqlqedlaaaerakrqveqerDeladeiasgaskksalldekRrleariaqleeeleeeqsnvellndrlrkatlqveqlt 923
                                                                     ++++  e   l + i++le  +++ q+++ +ln  l  +++++ +l+
  gi|70608058|ref|YP_256928.1| 344 ----------------------------------QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQ 390
                                   ..................................33334444444444455555555555555555555555555555555 PP

                 Myosin_tail_1 924 aeLsaeRsasqksesarqqlerqnkelkakLqelegavkskykssiaaleakia 977
                                   + L++  s+     ++ + l  q   l+ k++ l++++   +  ++ +l +k++
  gi|70608058|ref|YP_256928.1| 391 NTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSIT-NLSGQLNSLQSKVN 443
                                   555555555445555555555555555555554444442.33344444444444 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   1.6    0.0069      0.65      30      73 ..     344     387 ..     327     397 .. 0.79
   2 ?    5.6   0.0      0.17        16      18      64 ..     395     441 ..     379     447 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0069
                 Tropomyosin_1  30 nlekeqeiksLtkknqqleeevekleeklkeakekaeesekkkt 73 
                                   +   ++ei+sL + + +le+ v++l++++++ ++++++ +++ t
  gi|70608058|ref|YP_256928.1| 344 QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRIT 387
                                   3445789***********************99999887766654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.17
                 Tropomyosin_1  18 eleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakek 64 
                                    l++ + +l  ++ +  ++++ L+ k++ l++ + +l+ +l+  ++k
  gi|70608058|ref|YP_256928.1| 395 SLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSK 441
                                   33344444444444555555555666666666555555555555554 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   3.0   0.00013     0.013     111     214 ..     340     444 ..     318     453 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00013
                        HlyD_2 111 nerikeienneaieniekdiekldreInvlekdik..esiknedikkieelKeelnalldkKkllygskslsgkdleqlkk 189
                                   n++++ + n+e i+++ ++i +l++ +n l+++i+  +s  +  +++i +l + l++l    ++l g++s   ++l++l+ 
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKE-ISSLVQNITNLEKTVNNLQTQIStlNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQG 419
                                   34444444444.444455555555555555555552233344556789999999999999999999999999999999999 PP

                        HlyD_2 190 kkkeienklesskevikakesGvls 214
                                   k + +++ + + +  +++ +s v s
  gi|70608058|ref|YP_256928.1| 420 KISSLNSSITNLSGQLNSLQSKVNS 444
                                   9999999999988888887776655 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.2     0.036       3.4      50      92 ..     348     391 ..     327     399 .. 0.66
   2 !   15.8   1.2   0.00011     0.011      58     126 ..     371     442 ..     370     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.036
                    TPR_MLP1_2  50 vkh.aedvkelqalreelnelkaeiaelkaeaesakaeleesee 92 
                                   +k  ++ v+++++l + +n+l+++i++l++++ s+++ +   ++
  gi|70608058|ref|YP_256928.1| 348 NKEiSSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQN 391
                                   44325667777777777777777777777777777766655554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 0.00011
                    TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakae...leeseesweeqkeelekelselekriedlneqNklLhdQl 126
                                   ++++l++ l++l ++i++l++ + s++++   l+   +s+++q ++l+ ++s+l++ i++l+ q + L ++ 
  gi|70608058|ref|YP_256928.1| 371 QISTLNSSLSSLSQRITSLQNTLASLNSTissLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   7899999************9988887765111666789*************************988888766 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.9    0.0037      0.35      73     132 ..     338     397 ..     329     404 .. 0.65
   2 ?    8.1   0.0     0.019       1.8      91     144 ..     384     437 ..     380     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0037
                     PspA_IM30  73 kAkaALtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelk 132
                                   +A + L++  ++ +  +++ i +lek++++l+tq + ++s+   l + ++ l   ++ l 
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLN 397
                                   455555555555566666777777777777777777777777777777777766666554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.019
                     PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkareka 144
                                   ++i sl+++++ l+   + +  ++  l  ql+al  ki+ l + ++ l  ++++
  gi|70608058|ref|YP_256928.1| 384 QRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNS 437
                                   789999999999999999999999999999999999999999999988777665 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   0.00024     0.023       4      87 ..     359     446 ..     339     447 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 0.00024
                       DUF4164   4 keleaaltrLeaaldsLEka...vdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaai 80 
                                   ++le+  ++L++ + +L ++   + +r+++ +++ ++l+++i+ l    s L  +L + + + ++l++    +s++L+++ 
  gi|70608058|ref|YP_256928.1| 359 TNLEKTVNNLQTQISTLNSSlssLSQRITSLQNTlASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   57888999999999999976222578999999988********************************************** PP

                       DUF4164  81 etiravL 87 
                                    ++++++
  gi|70608058|ref|YP_256928.1| 440 SKVNSLT 446
                                   ***9975 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.8   0.00031     0.029       3      77 ..     363     435 ..     341     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00031
                       V-SNARE   3 ellaeiksklarlsslageerkaalreiekkldeaeelldqMelEvrnlpsserasykaklreykselkklkkel 77 
                                   +++++++ ++++l+s+  ++ ++ +  +++ l ++++ +++++  +++l+ s+ +++++k+ + +s + +l  +l
  gi|70608058|ref|YP_256928.1| 363 KTVNNLQTQISTLNSS-LSSLSQRITSLQNTLASLNSTISSLSGTASSLS-SQLNALQGKISSLNSSITNLSGQL 435
                                   5677777777777766.46999***************************8.******************998887 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.0   0.00062     0.059      19      44 ..     366     391 ..     348     404 .. 0.83
   2 ?    7.7   0.8     0.036       3.4      21      65 ..     382     426 ..     382     446 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00062
                       DUF2205  19 erLqqqakeLqssLqaLaervdeVke 44 
                                   ++Lq+q+ +L+ssL +L++r+ + ++
  gi|70608058|ref|YP_256928.1| 366 NNLQTQISTLNSSLSSLSQRITSLQN 391
                                   689******************98876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.036
                       DUF2205  21 LqqqakeLqssLqaLaervdeVkeehdKLesenrfLqqYIgdLms 65 
                                   L+q++ +Lq++L +L   + +       L s+   Lq  I++L s
  gi|70608058|ref|YP_256928.1| 382 LSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNS 426
                                   789********************9999999999999999999833 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   0.00028     0.026      78     152 ..     357     431 ..     317     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00028
                          DegS  78 eikeaYeeakelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledl 152
                                   +i +  +++++lq++++ l +  ++l +r  +l+++L +l++ti      +s++++ ln L+g+++++++++++l
  gi|70608058|ref|YP_256928.1| 357 NITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNL 431
                                   455556778999999999999999999999999999999999999999999999999999999999999999876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.7      0.03       2.9     188     221 ..     344     377 ..     315     394 .. 0.51
   2 ?    7.9   0.1     0.019       1.8      63     108 ..     394     439 ..     377     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.03
                       DUF4618 188 nqvlkkeiekfrefieeleeeipeLkaeveqLqa 221
                                   ++ ++kei    ++i +le+ +++L+ ++ +L+ 
  gi|70608058|ref|YP_256928.1| 344 QALVNKEISSLVQNITNLEKTVNNLQTQISTLNS 377
                                   2222344444444444444444444444444443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.019
                       DUF4618  63 kqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLs 108
                                     l++  + L  +++ ++++l+ L+ ++  ln+ +++l+ +ln L+
  gi|70608058|ref|YP_256928.1| 394 ASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   3477778888888999999999999999999999999999998886 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.0    0.0018      0.17     321     367 ..     353     399 ..     341     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0018
                        Tektin 321 rLveEvkeleetieaLkeklaeaeaslkaLertrleleediavKans 367
                                   +Lv+++++le+t+++L+ +++  ++sl++L ++ ++l++ +a  + +
  gi|70608058|ref|YP_256928.1| 353 SLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNST 399
                                   68889999999999999999999999999999998888887766665 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.8    0.0018      0.17       9      70 ..     340     398 ..     331     403 .. 0.79
   2 ?    2.0   0.0       1.8   1.7e+02      25      65 ..     405     442 ..     397     447 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0018
                    Phage_GP20   9 aengkditkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkaka 70 
                                   ++n + + +++++++ ++ ++l++++++ ++q+++L  +     +L + i++lq++++  ++
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSS---LSSLSQRITSLQNTLASLNS 398
                                   444455558889999999999999999999999999777...99999999999999887655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1.8
                    Phage_GP20  25 eerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqakn 65 
                                       +l +ql++ +++++ L  +    ++L  q+++lq k+
  gi|70608058|ref|YP_256928.1| 405 GTASSLSSQLNALQGKISSLNSS---ITNLSGQLNSLQSKV 442
                                   55556666666666666666554...666666666666654 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.1   0.00025     0.023     817     918 ..     340     443 ..     327     447 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                       DUF3584 817 rpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllskl..aelkldadaeqaege 895
                                   +++l++ v++  s++ +   +l++  ++++++++ l++ +++l +++  l+++l  l++ +s l   + +l+ + + ++g+
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLsgTASSLSSQLNALQGK 420
                                   444444443333333333344555555666666666777777777777777777777777777754455666677777777 PP

                       DUF3584 896 laerlaaleelkrkrerlsedvk 918
                                   ++  ++ +++l  ++++l+ +v+
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLSGQLNSLQSKVN 443
                                   77777777777666666666665 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.7   0.00033     0.031     214     305 ..     347     438 ..     329     446 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00033
                        HAP1_N 214 anqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegm 294
                                   +n++i++l +++++ + ++++ q +is+L + + +l q++ +l+     l++ +++   + ++L + L+ lq k +  ++ 
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSS 427
                                   467777777777777777777777777777777777777777777777777777777777777777777777776666655 PP

                        HAP1_N 295 Lheaqeevkel 305
                                   +++   ++ +l
  gi|70608058|ref|YP_256928.1| 428 ITNLSGQLNSL 438
                                   55555555444 PP

>> Filo_VP35  Filoviridae VP35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.6   0.00046     0.043      72     125 ..     361     415 ..     332     429 .. 0.75
   2 ?   -0.6   0.0       5.8   5.5e+02      72     110 ..     410     448 ..     402     451 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH.HHHHHHHHHHHHHHHH CS
                     Filo_VP35  72 ladllivvnrqiidiestlseletrvtelerqlheikp.vldmaktlealskvla 125
                                   l + +  ++ qi+  +s+ls l +r+t+l++ l  ++  +  ++ t ++ls  l 
  gi|70608058|ref|YP_256928.1| 361 LEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNStISSLSGTASSLSSQLN 415
                                   4444566789***********************7765414556667777666555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH CS
                     Filo_VP35  72 ladllivvnrqiidiestlseletrvtelerqlheikpv 110
                                   l++ l +++ +i++ +s++++l  ++++l+ +++ ++p+
  gi|70608058|ref|YP_256928.1| 410 LSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTPL 448
                                   556666777777788888888888888887777777774 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  11.5     0.011       1.1      27      97 ..     369     443 ..     311     447 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.011
                          HemX  27 qqqvqeltaevaelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqls 97 
                                   q q ++l+++ ++l+q++++l+++la+    ++++  + + l+++l++l++k+++l++++++l+ ql++lq++++
  gi|70608058|ref|YP_256928.1| 369 QTQISTLNSSLSSLSQRITSLQNTLASlnstISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   223333333335555555555555544555555566666666666666666666666666666666666666666 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.2     0.012       1.2     171     211 ..     336     376 ..     328     380 .. 0.91
   2 ?   11.3   9.8     0.002      0.18      77     141 ..     376     440 ..     374     448 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.012
                    MscS_porin 171 ellsnnnrqeLlklqrdllklriqqleqelqaLqellnekR 211
                                   + + n+n+q+L +++   l + i++le+ +++Lq+++++ +
  gi|70608058|ref|YP_256928.1| 336 SVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLN 376
                                   5789*********************************9876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.002
                    MscS_porin  77 klsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaa 141
                                   + sl+ L qr+++ ++ l++l++++++l   + +l+++++ +q ++++ +  ++ ++ +Lns++ 
  gi|70608058|ref|YP_256928.1| 376 NSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   57999*******************************************************99854 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   7.0     0.011         1      23      86 ..     339     406 ..     329     449 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                      RasGAP_C  23 rennyqelln....eIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleq 86 
                                    + n+q l+n    ++ + i+n+++  ++ + ++++l++ l++Ls++   l++ l+s+++ i++   +
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNkeisSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGT 406
                                   55666666653222467788888888888888888888888888888888888888888887765444 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   6.6       1.8   1.7e+02      31      61 ..     350     380 ..     336     390 .. 0.58
   2 ?    6.9   5.3     0.062       5.8      16      58 ..     356     398 ..     354     406 .. 0.85
   3 ?   11.7   1.4    0.0018      0.17      21      59 ..     389     427 ..     387     432 .. 0.90
   4 ?    9.8   2.5    0.0077      0.72      24      57 ..     413     446 ..     410     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 1.8
                        GIT_CC  31 kiqqLlkvNtslsdelrlLQskvqkLqaeNa 61 
                                    i  L +  t+l++ ++ LQ ++ +L++  +
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQISTLNSSLS 380
                                   4445555555555555555555555554333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.062
                        GIT_CC  16 eeylelKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqa 58 
                                   ++  +l k + +   +i  L  + +sls+ ++ LQ+ + +L++
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNS 398
                                   666677888999999999999999*************999987 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0018
                        GIT_CC  21 lKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqae 59 
                                   l + la  +++i  L    +sls +l+ LQ k+ +L++ 
  gi|70608058|ref|YP_256928.1| 389 LQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSS 427
                                   56899*******************************975 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0077
                        GIT_CC  24 alaaseakiqqLlkvNtslsdelrlLQskvqkLq 57 
                                   +l a   ki  L  + t+ls +l+ LQskv++L 
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNSLQSKVNSLT 446
                                   7888999************************996 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.0   0.00063     0.059     205     301 ..     353     445 ..     307     449 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00063
                     Dynamitin 205 qqlakiaelekRLaeLEklvGlssesldelsanlkprplletlsrLeaklslL.qtahLDaierRlksllaeldelaekre 284
                                   +  ++i++lek +++L + + + ++sl++ls+    ++l +tl +L++++s L  t    +++++l++l +++ +l+ + +
  gi|70608058|ref|YP_256928.1| 353 SLVQNITNLEKTVNNLQTQISTLNSSLSSLSQR--ITSLQNTLASLNSTISSLsGT--ASSLSSQLNALQGKISSLNSSIT 429
                                   233333333333333333333333333333333..344444444444444444211..12344444444444444444444 PP

                     Dynamitin 285 aiekadaegqekKIneL 301
                                   +++ +     ++K+n+L
  gi|70608058|ref|YP_256928.1| 430 NLSGQLNS-LQSKVNSL 445
                                   44333333.44444444 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   0.00081     0.077      23      75 ..     347     399 ..     343     411 .. 0.78
   2 ?    0.1   0.0       8.2   7.8e+02      36      67 ..     409     440 ..     394     446 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00081
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  23 VdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqet 75 
                                   V++ + ++++++ +l k +++l++++++l+++l++ +++ ++L++tl +  +t
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNST 399
                                   56666777888888888999999999999999999999999999988766555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 8.2
                                   HHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXX CS
                        DivIVA  36 allkeneelkekvkeleeklkeykeleetLkk 67 
                                   +l ++ ++l+ k++ l++++ + + + ++L+ 
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   44555556666666666666666666666554 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.3     0.044       4.1      46      86 ..     347     377 ..     338     399 .. 0.55
   2 ?    7.1   0.3     0.059       5.6      55      86 ..     395     426 ..     388     427 .. 0.88
   3 ?    4.5   0.1      0.39        37      59      84 ..     420     445 ..     416     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.044
                         Vps51  46 VydnYskLisasdtIrkmksemdkldqklselkqaiskiae 86 
                                   V           ++I+++ +++++l++++++l+  is +++
  gi|70608058|ref|YP_256928.1| 347 VN----------KEISSLVQNITNLEKTVNNLQTQISTLNS 377
                                   44..........44444444444444444444444443332 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.059
                         Vps51  55 sasdtIrkmksemdkldqklselkqaiskiae 86 
                                   s ++tI+++++  ++l+++l+ l+  is++++
  gi|70608058|ref|YP_256928.1| 395 SLNSTISSLSGTASSLSSQLNALQGKISSLNS 426
                                   6789********************99998875 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.39
                         Vps51  59 tIrkmksemdkldqklselkqaiski 84 
                                   +I++++s++++l+ +l++l++ ++++
  gi|70608058|ref|YP_256928.1| 420 KISSLNSSITNLSGQLNSLQSKVNSL 445
                                   69999999999999999999999876 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   0.00034     0.032      17      63 ..     130     177 ..     125     211 .. 0.79
   2 ?    1.4   1.1       3.8   3.6e+02      44      92 ..     341     389 ..     321     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00034
                           MG4  17 sikVlvkdpdgspaknvpVkiealk.seteekeslttdedGtakfsin 63 
                                   +i+  v++++gsp+++ +V++  +   + +   ++tt+++G+a f++ 
  gi|70608058|ref|YP_256928.1| 130 TITATVVNQEGSPLAGATVQLYNTTsGSNTLVATQTTNSQGVATFTVL 177
                                   67889****************994423456677889*********874 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 3.8
                           MG4  44 teekeslttdedGtakfsintpedaksltitvktkdpslpeenqatael 92 
                                   ++ +  + ++ + +++ + n++++ ++l+ ++ t  +sl+  +q  ++l
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSL 389
                                   44444445566889999********************999998887766 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.8    0.0018      0.17      22      74 ..     349     400 ..     335     404 .. 0.86
   2 ?    4.7   0.3      0.18        17      24      74 ..     396     442 ..     392     448 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0018
                   Helo_like_N  22 ksLyetvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpl 74 
                                   k + + v++  + +ktv++L+++++ L++ L+sL++ ++++ +++la+L+  +
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQ-RITSLQNTLASLNSTI 400
                                   56778999999*************************.7789999999998766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.18
                   Helo_like_N  24 LyetvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpl 74 
                                   L +t++s+     t   L ++l+aL++ ++sL++ ++++ + +l++L+  +
  gi|70608058|ref|YP_256928.1| 396 LNSTISSLS---GTASSLSSQLNALQGKISSLNS-SITNLSGQLNSLQSKV 442
                                   444554443...4556778888888888888888.6667777777777665 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9       0.2        19      28      53 ..     350     375 ..     335     381 .. 0.52
   2 ?    8.5   0.2     0.026       2.4      30      60 ..     373     403 ..     365     409 .. 0.86
   3 ?    3.6   0.1      0.91        86      31      65 ..     409     443 ..     406     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.2
                        Csm1_N  28 ENsvLsqkletkdqeiesLkeqlael 53 
                                   E s L q++ + ++ +++L+ q+ +l
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQISTL 375
                                   33344444444444444444444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.026
                        Csm1_N  30 svLsqkletkdqeiesLkeqlaeleekvkel 60 
                                   s+L+  l++ +q+i sL+++la+l++ +++l
  gi|70608058|ref|YP_256928.1| 373 STLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   7899999******************998876 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.91
                        Csm1_N  31 vLsqkletkdqeiesLkeqlaeleekvkeleerrk 65 
                                    Ls +l+  + +i+sL   + +l  ++++l+++ +
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   57788888888888888888888888888887654 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   0.00076     0.072      20     103 ..     362     445 ..     347     447 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00076
                       DUF4472  20 nklreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkq 100
                                   +k   ++++++  l++ + +l +r+++l+ + + +++ i+sl+     l ++ ++l+ + ++l++++ +l+ ++++ ++k 
  gi|70608058|ref|YP_256928.1| 362 EKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   4667788999999******************************************************99999999999987 PP

                       DUF4472 101 qel 103
                                   + l
  gi|70608058|ref|YP_256928.1| 443 NSL 445
                                   665 PP

>> GCP_N_terminal  Gamma tubulin complex component N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.2   0.00054     0.051      71     154 ..     338     425 ..     300     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00054
                GCP_N_terminal  71 lvlqalaaaldeelteyyrliaqlEsqlledsesi....ltLlrlevwlqetllllrvLanlveevekanlkggallsllh 147
                                   + +q+l+a +++e+++ ++ i++lE+ +++ +++i     +L++l+ ++ + + +l  L++ +++   + +     l++l+
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQIstlnSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   6799****************************999****************************999966665666666666 PP

                GCP_N_terminal 148 eaaqhgd 154
                                    + ++ +
  gi|70608058|ref|YP_256928.1| 419 GKISSLN 425
                                   6555444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8    0.0014      0.13      48     125 ..     362     439 ..     355     446 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0014
                       DUF4201  48 qienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklr 125
                                   +  +++l+++I   n  L+ l++++t+   +l+ l    + l+ + s l ++l+ ++ ++ +l  +++++  + + l+
  gi|70608058|ref|YP_256928.1| 362 EKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   555666666666666666666666666666666666666655555555555555555555555555544444433333 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  13.5    0.0016      0.15      15     112 ..     352     445 ..     327     449 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0016
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TT CS
                          COG5  15 nallkatnnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskv 95 
                                   ++l+++  n ++t   l+t++++ln+ ++ l +r+++l    +++L +  s+++sls++ s+l s+l++L+  ++ l+s +
  gi|70608058|ref|YP_256928.1| 352 SSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSL----QNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   45667889999999999999999999999998888766....567888899999999999999999999999999999999 PP

                                   HHHHHHHHHHHHHHHHH CS
                          COG5  96 lepyeeaeklqsalkrl 112
                                   ++   ++++lqs+ ++l
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLNSLQSKVNSL 445
                                   99999999999988776 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.7    0.0093      0.87      59     140 ..     340     421 ..     326     447 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0093
                 Jnk-SapK_ap_N  59 leqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklher 139
                                   +++L+   ++e +   +   +le++ ++++ + ++l++ +++l +++  l+  + +++  +s+l+ + ++l+++ ++l+ +
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGK 420
                                   555555555555555555556666666666666666666666666666666666666666666666666666666665554 PP

                 Jnk-SapK_ap_N 140 e 140
                                    
  gi|70608058|ref|YP_256928.1| 421 I 421
                                   4 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6    0.0014      0.13      59     141 ..     359     441 ..     341     449 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0014
                        DUF713  59 kksdkeekklekedleelqselsnLakkvlsaynkLeeafeklkelsekfed.kiFlkvLqksisdvatklleilevldel 138
                                    + +k  ++l+ ++ ++l+s ls+L++ ++s++n+L     ++++ls + +   + l  Lq +is++ + + ++  +l++l
  gi|70608058|ref|YP_256928.1| 359 TNLEKTVNNLQ-TQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSlSSQLNALQGKISSLNSSITNLSGQLNSL 438
                                   33333333322.345556666666666666666666666666666665554423455556666665555555555554444 PP

                        DUF713 139 eld 141
                                   + +
  gi|70608058|ref|YP_256928.1| 439 QSK 441
                                   433 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6     0.013       1.2      40      79 ..     353     392 ..     348     393 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.013
                          Med9  40 elirelpgidrsveeqeaeieeleeqlakKrelLkkyknr 79 
                                   +l++++ +++++v + + +i +l+ +l    + +++++n+
  gi|70608058|ref|YP_256928.1| 353 SLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNT 392
                                   799********************************99986 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00067     0.063      58     143 ..     348     433 ..     331     446 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00067
                      CALCOCO1  58 ekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELEeDi 138
                                   +ke +   ++ ++l++++++l+ +++ l++ l+++ + +++l++    l+++  +l+   s l+++ ++ + +i  L+  i
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   344444444445555555555555555555555555555555555555555555555555555555555555555555555 PP

                      CALCOCO1 139 ktltq 143
                                     l+ 
  gi|70608058|ref|YP_256928.1| 429 TNLSG 433
                                   55544 PP

>> Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       3.2     3e+02      17      34 ..      57      74 ..      47      82 .. 0.84
   2 ?    8.2   0.2     0.023       2.2      18      64 ..     129     175 ..     127     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 3.2
               Glyco_hydro2_C5 17 lafvtvevvDknGnlvpn 34
                                   a vt+ v D +Gn+v n
  gi|70608058|ref|YP_256928.1| 57 NALVTLYVYDPKGNVVYN 74
                                  5789***********987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.023
               Glyco_hydro2_C5  18 afvtvevvDknGnlvpnadnevtfeveGpGelvgvdngdptslesfk 64 
                                   + +t++vv ++G ++  a+ ++  + +G+ +lv+++  +++ +  f+
  gi|70608058|ref|YP_256928.1| 129 STITATVVNQEGSPLAGATVQLYNTTSGSNTLVATQTTNSQGVATFT 175
                                   689********************************998887766665 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  10.4    0.0015      0.14      25     114 ..     348     437 ..     328     447 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0015
                     Laminin_I  25 tkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekv 105
                                   +ke+++ ++++ + ++ +++l+ ++++L++   +L ++ t        +n  ++  ++ a++L  + ++l+ +i+ +++++
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   456666666666666666666666666666666666666666666666666666666666666666666666666666666 PP

                     Laminin_I 106 atlneneea 114
                                    +l+++ + 
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLNS 437
                                   666663333 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       1.4   1.4e+02     298     333 ..     317     352 ..     316     360 .. 0.90
   2 ?   10.8   3.4    0.0017      0.16     184     245 ..     348     409 ..     335     447 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.4
                    Fmp27_WPPW 298 illrylhqvsqrrgfvyymsrkavkfiedlveeqek 333
                                   i+ +y+++  q  +++y+ms +a + ++ lv+++ +
  gi|70608058|ref|YP_256928.1| 317 IVANYTTSSGQTLSTKYLMSVQANQNLQALVNKEIS 352
                                   6789***************************99876 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0017
                    Fmp27_WPPW 184 eeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse....e 245
                                   +++i++l +++ +le++ ++    l+++i++l++ +++l ++++ l+++l +l+++ +s +    +
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNN----LQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSgtasS 409
                                   55566666666666666666....666666666666666666666666666666665533222221 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   6.1   0.00086     0.081     146     256 ..     337     444 ..     327     447 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00086
                       DUF4686 146 tearilekkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkkl 226
                                   ++a    ++ ++++i  + +n ++l ++++  q +   L+ +   L q++ sl++  a+l+ t s+++        ql+ l
  gi|70608058|ref|YP_256928.1| 337 VQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNAL 417
                                   455556677889999999999999999999999999999999999999999999999999999999999999999999999 PP

                       DUF4686 227 enekrksdehlksnqeLsekLsslqqekea 256
                                   + +++  +    s  +Ls +L slq   ++
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNS---SITNLSGQLNSLQSKVNS 444
                                   998877554...445688888888776655 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   3.2     0.022         2     109     151 ..     351     393 ..     328     398 .. 0.53
   2 ?   11.1   2.8    0.0019      0.18      91     156 ..     375     440 ..     369     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.022
                       DUF4763 109 nhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrl 151
                                    + L+q +++l++  ++ +++++ l++sl+++ +r+ +lq  l
  gi|70608058|ref|YP_256928.1| 351 ISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTL 393
                                   2345555555555555555555555555555555555555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0019
                       DUF4763  91 elelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnelds 156
                                    ++ l+s ++ i  Lq   + L   +++l+    +  ++l++l+ +++++++ + +l+ +ln l+s
  gi|70608058|ref|YP_256928.1| 375 LNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   455566678889999999999999999999999999999999999999999999999999998876 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2     0.019       1.8      55     107 ..     338     390 ..     330     402 .. 0.77
   2 ?    2.3   0.0       2.3   2.2e+02      79     104 ..     418     443 ..     406     448 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.019
                       DUF4200  55 kendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleeyk 107
                                   + n++ +a  +k++ +  +++ + e+ +++l+++i+tl+s ++ l +++ +++
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQ 390
                                   56666666677777778888888999999999999999988888888887776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 2.3
                       DUF4200  79 eaeikklkaeietlkseiekleekle 104
                                   + +i  l+++i++l  +++ l+ k++
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNSSITNLSGQLNSLQSKVN 443
                                   44555566666666666666666655 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1    0.0026      0.24      88     186 ..     318     415 ..     313     416 .. 0.71
   2 ?    0.5   0.0       5.4   5.1e+02     123     151 ..     416     444 ..     407     446 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0026
               Ax_dynein_light  88 vrdelrmtiaayktlyessvaFgmrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkhe 168
                                   v ++     ++++t y  sv+ +   +   +++ s l ++i++Le+++++l+ q+++l++ l++l +r +  +++     +
  gi|70608058|ref|YP_256928.1| 318 VANYTTSSGQTLSTKYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLA-SLN 397
                                   66666666666666777777666566666678888888889999999999999999999999999998877665544.445 PP

               Ax_dynein_light 169 eeieflkksnqqlkeqle 186
                                     i  l  + ++l +ql+
  gi|70608058|ref|YP_256928.1| 398 STISSLSGTASSLSSQLN 415
                                   667777777777777775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 5.4
               Ax_dynein_light 123 elekkikeLeeekeelekqvaelkaklea 151
                                    l+ ki++L++   +l  q+++l++k+++
  gi|70608058|ref|YP_256928.1| 416 ALQGKISSLNSSITNLSGQLNSLQSKVNS 444
                                   56778888888888888888888888765 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.8     0.048       4.5     140     177 ..     341     378 ..     327     381 .. 0.87
   2 ?   10.0   0.5    0.0052      0.49     112     177 ..     362     427 ..     360     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.048
                       DUF2968 140 aerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                   ++ Q+ + ke ++L ++ +++++ +++lq qi++L+  
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSS 378
                                   56788999***************************975 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0052
                       DUF2968 112 erqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                   e+ +++ ++++++L++ l+   q  +++++  +++ +  ++L+   +++ +ql+alq +i++L+  
  gi|70608058|ref|YP_256928.1| 362 EKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSS 427
                                   566666666666666666666666666666666666666666666666666666666666666543 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0022       0.2     158     199 ..     137     176 ..     128     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0022
                       DUF4198 158 lldGkPlagaeveveyggtryrdapdeikv..ktdadGvvtftl 199
                                     +G Plaga+v++       ++      +  +t+++Gv+tft+
  gi|70608058|ref|YP_256928.1| 137 NQEGSPLAGATVQLYNTTS-GSNTLV---AtqTTNSQGVATFTV 176
                                   469**********954432.222222...124**********98 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3    0.0029      0.27      79     136 ..     347     404 ..     326     408 .. 0.83
   2 ?    2.8   0.0      0.82        77      86     130 ..     403     447 ..     399     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0029
                 PI3K_P85_iSH2  79 qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLq 136
                                    ++Ei++l +n+ +l++ +++l+ + + L+ +l +  ++  +l+  + +l++ + +L+
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   3899***************************************999999999998885 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.82
                 PI3K_P85_iSH2  86 lqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkp 130
                                   l+   + l s+l+ l+ + ++L+ ++ +   +  +l+ ++n+l p
  gi|70608058|ref|YP_256928.1| 403 LSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTP 447
                                   566677888889999999999999999998888888888888887 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.9    0.0011      0.11     375     456 ..     357     444 ..     289     447 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                      Macoilin 375 ssaalkdaaen......slpnnqlskkdalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendl 449
                                   + ++l+++++n      +l ++  s  + ++ L+++++ L++ +++   t + l s++++l+++  sl s++++l  + ++
  gi|70608058|ref|YP_256928.1| 357 NITNLEKTVNNlqtqisTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNS 437
                                   111222222222222212222222344445566666666666666666666666666666666666666666666666666 PP

                      Macoilin 450 lqtklhe 456
                                   lq+k+++
  gi|70608058|ref|YP_256928.1| 438 LQSKVNS 444
                                   6666665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.3      0.65        61      33      78 ..     341     386 ..     327     390 .. 0.67
   2 ?   13.5   2.7    0.0007     0.066      14      79 ..     365     429 ..     350     433 .. 0.88
   3 ?    7.9   0.2      0.04       3.8      20      75 ..     391     446 ..     388     448 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.65
                          KxDL  33 lelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                   ++l+al++++ ++l +++ +  k++++++ ++ ++++ ++sl +++
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRI 386
                                   4666666666666666666666666666666666666666666655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0007
                          KxDL  14 ilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                   +  lQ+q+s +ln++   L++ ++ +q+ la+l++ + +   +++++ ++L+ ++ ki+sl++ ++
  gi|70608058|ref|YP_256928.1| 365 VNNLQTQIS-TLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSIT 429
                                   557899998.69**************************************************9875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.04
                          KxDL  20 qtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslk 75 
                                   +t++ ln++   L+     ++++l+ l+ ++ +    + ++  +L+s+++k++sl+
  gi|70608058|ref|YP_256928.1| 391 NTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLT 446
                                   68888888888888888888888888888888888888888888888888888875 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0    0.0013      0.12      30     113 ..     348     431 ..     331     448 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0013
                          Fez1  30 lseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselslee 110
                                    +ei +l  ++ +l++++++ +++i++l++sl++ ++ +  ++n l+  +s+ + l+ ++++l+++l+ l+ ++s+l+++ 
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   456667777777777777777777777777777777777777777777777777777777777777777766666655443 PP

                          Fez1 111 eea 113
                                   ++ 
  gi|70608058|ref|YP_256928.1| 429 TNL 431
                                   333 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2       2.2   2.1e+02      48      80 ..     339     371 ..     335     377 .. 0.67
   2 ?    6.2   0.7      0.13        12       2      37 ..     368     403 ..     347     409 .. 0.63
   3 ?    8.6   0.3     0.022       2.1       5      39 ..     392     426 ..     388     434 .. 0.87
   4 ?    6.2   0.2      0.12        12       6      37 ..     414     445 ..     409     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  48 afqaefeewkqaaqklvdaLeeisealkqaana 80 
                                   a q+ ++ +++++  lv++ +++++++++  ++
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNITNLEKTVNNLQTQ 371
                                   556666677777777777777777777776655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.13
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                   ++++ + l ++ +++++  ++l++ l++l++++++l
  gi|70608058|ref|YP_256928.1| 368 LQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   344444455555555555555555555555555555 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.022
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                        WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                   + + l +++++++++a++l+++l++l++++++l+s
  gi|70608058|ref|YP_256928.1| 392 TLASLNSTISSLSGTASSLSSQLNALQGKISSLNS 426
                                   66778999***********************9966 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100   6 peelrqaaarfqkqaeeledelqrlkaevdal 37 
                                    ++l+ ++++++++ ++l+++l++l+++v++l
  gi|70608058|ref|YP_256928.1| 414 LNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   5689999999*******************998 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.5     0.002      0.19     182     249 ..     343     410 ..     324     435 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.002
                       Taxilin 182 eqekkkrekeyllkeakeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekm 249
                                    q   ++e + l++++++l+k+v++l+ + + l + l+  +++   +q+tLa  n+++++       +
  gi|70608058|ref|YP_256928.1| 343 LQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSL 410
                                   44455666667777777777777777777777777777777777777777777777766555444444 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.1    0.0016      0.15     362     464 ..     339     441 ..     309     446 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                    Herpes_UL6 362 vsnsvikcleeqineqfdtiekLkkenelllkklkelekeLerlreeakk.eakarevdlltsstdaslenlpessalskl 441
                                    +++    +++ i +++++i++L+k+ + l++++++l++ L+ l ++ +  +   ++ + + ss + + ++l  ss+l+ l
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSlQNTLASLNSTISSLSGTASSL--SSQLNAL 417
                                   333444445555555555555555555555555555555555554444433333333333333333333333..3444444 PP

                    Herpes_UL6 442 kk.vidtsksvdddesvaNSFfsq 464
                                   +  +  + +s+++ +  +NS +s+
  gi|70608058|ref|YP_256928.1| 418 QGkISSLNSSITNLSGQLNSLQSK 441
                                   443444444444444444444443 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.7    0.0023      0.21      59     139 ..     338     423 ..     329     444 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0023
                  SF-assemblin  59 esdkdiqeefkkeikklqekik......eevddlalelkkaveelnekinnveanvenekakrrdaieklakelvkelnel 133
                                   + ++++q  ++kei  l ++i       +++++    l++++ +l ++i+ ++  +    ++ ++++   a +l  +ln l
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITnlektvNNLQTQISTLNSSLSSLSQRITSLQNTLA-SLNSTISSLSGTASSLSSQLNAL 417
                                   567889999999988877655411111145566666778888888888888877665.45677888888899999999999 PP

                  SF-assemblin 134 eaaide 139
                                   +  i  
  gi|70608058|ref|YP_256928.1| 418 QGKISS 423
                                   998876 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.7      0.39        37       8      31 ..     350     373 ..     345     378 .. 0.60
   2 ?    3.8   7.6      0.79        74       2      28 ..     365     391 ..     357     419 .. 0.76
   3 ?    7.5   1.0     0.057       5.4       4      24 ..     409     429 ..     406     431 .. 0.88
   4 ?    7.1   1.9     0.076       7.2       2      26 ..     421     445 ..     420     449 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.39
                           LPP   8 qVsqLkskvdqlssdvnsakaaaq 31 
                                   ++s+L +++ +l++ vn++++++ 
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQIS 373
                                   566666666666666666666554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.79
                           LPP   2 ldeLssqVsqLkskvdqlssdvnsaka 28 
                                   +++L +q+s+L+s  ++ls+ ++s+++
  gi|70608058|ref|YP_256928.1| 365 VNNLQTQISTLNSSLSSLSQRITSLQN 391
                                   566677777777777777776666665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.057
                           LPP   4 eLssqVsqLkskvdqlssdvn 24 
                                    Lssq+++L+ k+++l+s ++
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSIT 429
                                   79**************99876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.076
                           LPP   2 ldeLssqVsqLkskvdqlssdvnsa 26 
                                   ++ L+s + +L+ + ++l+s+vns+
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLSGQLNSLQSKVNSL 445
                                   6666666666666666666666665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1     0.018       1.7       5      52 ..     353     400 ..     347     416 .. 0.75
   2 ?    3.6   0.0       1.1     1e+02      13      43 ..     410     440 ..     395     449 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                   +l++++++le+++++l++++++l+++l++l ++ ++L+    +l +++
  gi|70608058|ref|YP_256928.1| 353 SLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTI 400
                                   577888888888888888888888888888888888887766666655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  13 leeqleelleeleelkeelaelleenaeLel 43 
                                   l++ql++l+ ++++l++++++l  + ++L+ 
  gi|70608058|ref|YP_256928.1| 410 LSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   3444444444444444444444333333333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   0.00053      0.05     111     217 ..     342     440 ..     335     447 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00053
                       DUF4407 111 elaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq 191
                                    l++  ++e+++l ++++ +l++++++l++qi+ l++ ++++++r++ l++++++  +     +++   G    a +  +q
  gi|70608058|ref|YP_256928.1| 342 NLQALVNKEISSLVQNIT-NLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNS-----TISSLSGT---ASSLSSQ 413
                                   444455555555555555.588888888888888888888888888888888885433.....33333333...5556667 PP

                       DUF4407 192 ldaaqaelaelkakld.atarlaalra 217
                                   l+a+q ++ +l+++++  + +l++l++
  gi|70608058|ref|YP_256928.1| 414 LNALQGKISSLNSSITnLSGQLNSLQS 440
                                   777777777666665543344444444 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4    0.0026      0.25      11      90 ..     346     440 ..     337     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0026
                          SOGA  11 fveeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeee...............eassdsskeaelkeeLklarl 76 
                                   +v+ E + l +++++le+  ++l+++++ + s l++ ++ +++ +               +ass ss+ ++l+ ++ +   
  gi|70608058|ref|YP_256928.1| 346 LVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQntlaslnstisslsgTASSLSSQLNALQGKISSLNS 426
                                   788888889999***************999999998888777665677888888888776666667777788888888888 PP

                          SOGA  77 qineLsgkvvkLqv 90 
                                    i++Lsg++  Lq 
  gi|70608058|ref|YP_256928.1| 427 SITNLSGQLNSLQS 440
                                   88888888888886 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       7.6   7.1e+02     263     298 ..     106     142 ..     103     180 .. 0.73
   2 ?   12.7   3.7   0.00061     0.058     108     172 ..     348     412 ..     340     414 .. 0.88
   3 ?    5.7   0.4     0.082       7.7     106     142 ..     409     445 ..     406     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 7.6
                    FmiP_Thoc5 263 vqLtiklkdsk.lkltfeYlpklnvvtVrvkltakak 298
                                   v+L+++ + s+  +++++Y+p    +t++v  ++++ 
  gi|70608058|ref|YP_256928.1| 106 VSLSVQGTTSEsASVNVQYVPLTSTITATVVNQEGSP 142
                                   67777766333599************99997664444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00061
                    FmiP_Thoc5 108 aeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkqhelaslLPk 172
                                   ++++++l ++ ++le+++++ + ++s L++ L+sl++ ++ lq+ l   +++ ++ + +as L++
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSS 412
                                   6788999999999*******************************998777788888888888876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.082
                    FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLksl 142
                                   +l++ql++l+ k ++l++ i++   +L+sL++k++sl
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   5889999999999999999999999999999999887 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.0    0.0026      0.25      14     118 ..     342     441 ..     335     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0026
                          Uds1  14 efeiLsleeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaes 94 
                                   + + L  +e+ +l ++++ Le+ +++l++++   + l ++  sLs++  +s++++  ++ +s+ +s + +     ++l+++
  gi|70608058|ref|YP_256928.1| 342 NLQALVNKEISSLVQNITNLEKTVNNLQTQI---STLNSSLSSLSQRI-TSLQNT-LASLNSTISSLSGTASSLSSQLNAL 417
                                   5667777888888888888888888888884...44555555555555.333332.3334566666667888889999999 PP

                          Uds1  95 erkvdelaselekleeraaevrrr 118
                                   + k+  l+s + +l+ ++++++ +
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNSSITNLSGQLNSLQSK 441
                                   999999999999999999998876 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   8.6    0.0024      0.22       4      92 ..     347     436 ..     335     446 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0024
                         Mod_r   4 SkeeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83 
                                    ++e+  l+++   le+ v++l  ++ +l++++++l + + sl +   sl+ ++  l+   ++  ++l++l+ +   +++ 
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLqTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSS 427
                                   456777777777777777777777777777777777777777777777777777777777777777777777766666666 PP

                         Mod_r  84 ldellqkfs 92 
                                     +l+ +++
  gi|70608058|ref|YP_256928.1| 428 ITNLSGQLN 436
                                   666665554 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.1    0.0051      0.48     145     197 ..     352     404 ..     316     409 .. 0.80
   2 ?    4.9   0.2       0.2        19      11      39 ..     406     434 ..     400     448 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0051
                           LXG 145 dslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtskgk 197
                                   +sl + + ++++t+++l++    ++s+l++l + +++l++++++L++++s+ +
  gi|70608058|ref|YP_256928.1| 352 SSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   56667788889999999999999999999999999999999999999999865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.2
                           LXG  11 aieqlkseleelkeqleqlkkaiqklvel 39 
                                    +++l+s+l+ l+ ++++l+++i++l++ 
  gi|70608058|ref|YP_256928.1| 406 TASSLSSQLNALQGKISSLNSSITNLSGQ 434
                                   56778888888888888888888886654 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.9      0.12        12      35      68 ..     342     375 ..     335     384 .. 0.67
   2 ?    3.5   1.1      0.84        79      39      69 ..     374     404 ..     368     405 .. 0.69
   3 ?    8.7   0.6     0.019       1.8      39      69 ..     410     446 ..     405     447 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.12
                     MbeD_MobD  35 rmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                   ++  l ++e + L + +t+L + V++L  q++ l
  gi|70608058|ref|YP_256928.1| 342 NLQALVNKEISSLVQNITNLEKTVNNLQTQISTL 375
                                   4555666777777777777777777777776654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.84
                     MbeD_MobD  39 ltqrenaaLseqvtgLsqQVesLseqvrRls 69 
                                     +  ++ Ls+++t L     sL+ +++ ls
  gi|70608058|ref|YP_256928.1| 374 TLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   4445566788888888888888888887776 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.019
                     MbeD_MobD  39 ltqrena......aLseqvtgLsqQVesLseqvrRls 69 
                                   l ++ na       L+  +t+Ls Q +sL  +v+ l+
  gi|70608058|ref|YP_256928.1| 410 LSSQLNAlqgkisSLNSSITNLSGQLNSLQSKVNSLT 446
                                   555555555555599******************9887 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.9    0.0027      0.26       1      77 [.     351     432 ..     351     447 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0027
                          SesA   1 isstiaiveaaiklydaikd.ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa....ikpvlesckekatkl 76 
                                   iss+++ ++ + k+++++++ i++l  +++  ++r+  +q+tL + +s+++s +   ++ s+    ++  + s ++ +t+l
  gi|70608058|ref|YP_256928.1| 351 ISSLVQNITNLEKTVNNLQTqISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSqlnaLQGKISSLNSSITNL 431
                                   8999**************999***************************999988777766655556444444444444444 PP

                          SesA  77 e 77 
                                   +
  gi|70608058|ref|YP_256928.1| 432 S 432
                                   3 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.5    0.0085       0.8      26      82 ..     357     413 ..     338     449 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0085
                        CENP-Q  26 dfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaeare 82 
                                   ++++l +  ++l++q s+++ sl+ L + i  ++++l++   ++ +L  +a+++ ++
  gi|70608058|ref|YP_256928.1| 357 NITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQ 413
                                   344445555566677777777777777777777777777777777777666666655 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6    0.0026      0.24      27     126 ..     329     428 ..     308     446 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0026
                        TACC_C  27 lkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevleg 107
                                   l+ k+  + + nq+++ +v++  + + q i++ +k+ ++ + +i+ + +  + l++ ++s++ +++ l + +  +  + + 
  gi|70608058|ref|YP_256928.1| 329 LSTKYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASS 409
                                   555555555555555555555555555555555555556666666655555555555555555555555555555555555 PP

                        TACC_C 108 ykkneeslkkcaeeylarv 126
                                   + ++ ++l+ +++ + + +
  gi|70608058|ref|YP_256928.1| 410 LSSQLNALQGKISSLNSSI 428
                                   5555555555555544444 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.3     0.013       1.3      12      46 ..     347     381 ..     343     394 .. 0.86
   2 ?    0.9   0.1       5.9   5.6e+02      48      48 ..     413     413 ..     372     440 .. 0.54
   3 ?    1.0   0.0       5.8   5.5e+02      17      38 ..     422     443 ..     413     449 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.013
                         TSC22  12 VrEeVevLkekIkeLeernseleeENslLkalasp 46 
                                   V+ e+  L ++I++Le+++++l+++ s+L + +s+
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSS 381
                                   7889999*********************9988775 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 5.9
                         TSC22  48 q 48 
                                   q
  gi|70608058|ref|YP_256928.1| 413 Q 413
                                   2 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 5.8
                         TSC22  17 evLkekIkeLeernseleeENs 38 
                                     L + I++L  + + l++  +
  gi|70608058|ref|YP_256928.1| 422 SSLNSSITNLSGQLNSLQSKVN 443
                                   4566667777777666666544 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.0     0.016       1.5     222     280 ..     338     395 ..     327     406 .. 0.64
   2 ?    5.7   0.1     0.076       7.2     229     281 ..     387     438 ..     380     455 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                          RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaek 280
                                   +a ++ ++ + +++++l +++ ++++++++l+++++++++s+ ++ +++  ++++++ +
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSL-SQRITSLQNTLAS 395
                                   444444556777888888888888888888888888888888884.4444444444433 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.076
                          RmuC 229 eeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaekl 281
                                   + ++++l++l + ++++  + ++l ++l+ +q ++ +  ++   n++ ++++l
  gi|70608058|ref|YP_256928.1| 387 TSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISS-LNSSITNLSGQLNSL 438
                                   4444455555555555555555555555555555544.333333333333333 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.5     0.011         1     169     221 ..     346     391 ..     318     403 .. 0.54
   2 ?    7.3   5.1     0.029       2.7     116     179 ..     355     419 ..     338     446 .. 0.42

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.011
                        Cluap1 169 alkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqs 221
                                           v++e++++ ++++nle++ +nL+++i   ++ l   ++r+ slq+
  gi|70608058|ref|YP_256928.1| 346 L-------VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQN 391
                                   3.......344444444444444444444444444444444444444444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.029
                        Cluap1 116 ssklsdl.kaarqlaseitekgasLydlLekevelreartkalsrqleleeiekalkeaikkvke 179
                                    +++++l k++ +l ++i +  +sL +l ++ ++l+++  +  s+  +l+   ++l++++++++ 
  gi|70608058|ref|YP_256928.1| 355 VQNITNLeKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQG 419
                                   22222221222333333333333333333333334444444444444444444444444444444 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3    0.0078      0.73      49     123 ..     354     425 ..     335     446 .. 0.36

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0078
                                   HHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHH CS
                Apolipoprotein  49 vrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyv 123
                                   +++++++ ++   ++l+ ++  l++ l+++++++  +l+  +  l  ++++   +  ++l++ + al+ +++ + 
  gi|70608058|ref|YP_256928.1| 354 LVQNITN-LEKTVNNLQTQISTLNSSLSSLSQRI-TSLQNTLASLNSTISS-LSGTASSLSSQLNALQGKISSLN 425
                                   4444432.22222333333333333333333333.1222222222222222.22233333333333333333333 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9      0.04       3.8      27      61 ..     357     391 ..     341     394 .. 0.87
   2 ?    4.9   0.1       0.3        29      29      63 ..     380     414 ..     376     415 .. 0.89
   3 ?    3.9   0.1      0.62        59      30      63 ..     409     442 ..     405     443 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.04
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                    i +Le+ v  L+++ ++L s l++l+  + +L++
  gi|70608058|ref|YP_256928.1| 357 NITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQN 391
                                   57899999999999999999999999999988865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                   + L++r   L++  +sL s++++l+ + ++L s++
  gi|70608058|ref|YP_256928.1| 380 SSLSQRITSLQNTLASLNSTISSLSGTASSLSSQL 414
                                   6899********************99999998876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.62
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  30 eLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    L+++  aL+++ +sL s + +l+ + ++L+skv
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   6788888999999999999999999999998886 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.5     0.033       3.1      69      94 ..     360     385 ..     324     417 .. 0.55
   2 ?    4.4   0.0      0.55        52      67      92 ..     407     432 ..     383     445 .. 0.43

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.033
                       DUF4140  69 alraeleeledelaaledelaaaear 94 
                                    l++++++l+++++ l+++l+++++r
  gi|70608058|ref|YP_256928.1| 360 NLEKTVNNLQTQISTLNSSLSSLSQR 385
                                   22222222222222222222222222 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.55
                       DUF4140  67 lkalraeleeledelaaledelaaae 92 
                                    ++l ++l++l+ +++ l++++++++
  gi|70608058|ref|YP_256928.1| 407 ASSLSSQLNALQGKISSLNSSITNLS 432
                                   23333333333333333333333333 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.0     0.015       1.4       6      83 ..     347     423 ..     317     446 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.015
                  Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsr 83 
                                   v++e+ + ++++++l ++ ++l+++ s+  s+ ++l++  t L+++l s++ +++ L  t + +++   + +  + ++s+
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTlnSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSS---QLNALQGKISS 423
                                   677888888888888888888887777765567778888888888888888888888877744433...34443444444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.4     0.018       1.7      17      58 ..     354     395 ..     350     402 .. 0.82
   2 ?   11.7   0.1    0.0025      0.23      21      80 ..     386     445 ..     379     450 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.018
                        DUF948  17 livvllklkktldeaaatieelekqvdpilkevedllakvne 58 
                                   l+  + +l+kt+++++++i +l++ + ++++ ++ l ++   
  gi|70608058|ref|YP_256928.1| 354 LVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLAS 395
                                   67889999***************9999999999888776655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0025
                        DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadl 80 
                                   + +l++tl ++++ti +l   + +++ ++++l  k+  l + +++ + ++++l ++v+ l
  gi|70608058|ref|YP_256928.1| 386 ITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   456677777777777777777777777777777777776666666666666666555544 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2      0.02       1.9      24      67 ..     344     387 ..     328     398 .. 0.84
   2 ?    3.3   0.8       1.2   1.1e+02      31      91 ..     414     469 ..     389     471 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.02
                          MtrB  24 edvvllsldpvleeidkLekiaddlvnsLdpetallesypgRek 67 
                                   + +v  +++ + ++i++Lek++++l ++++  ++ l+s  +R  
  gi|70608058|ref|YP_256928.1| 344 QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRIT 387
                                   55777889999***************************999955 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 1.2
                          MtrB  31 ldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGfivglviaal 91 
                                   l+ ++ +i  L++   +l     ++ + l+s  +    lv++G++ ++  G+iv++v ++l
  gi|70608058|ref|YP_256928.1| 414 LNALQGKISSLNSSITNLS----GQLNSLQSKVNSLTPLVYGGIIAGI-IGLIVAIVAIVL 469
                                   3333333444433333333....3333333333334456677766665.478877777665 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.0      0.23        22     179     218 ..     338     377 ..     319     381 .. 0.58
   2 ?    8.7   0.4    0.0052      0.49     280     339 ..     381     440 ..     374     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.23
                           MAD 179 iqsqeddslivknskselaripelekelerlreenkklne 218
                                    ++q+ ++l+ k++ s ++ i +lek +++l+ +++ ln+
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNS 377
                                   3345555555566666666666666666666666666655 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0052
                           MAD 280 alsrkieqLqqeeivlkeeksslesslkqlekaqreleqelaqllkkiedlkkkrkehke 339
                                    ls++i  Lq++ ++l++  ssl   +++l ++ + l+ ++++l++ i++l  +++  ++
  gi|70608058|ref|YP_256928.1| 381 SLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQS 440
                                   588888889988888888888888888888888888888888888888888777766554 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.6      0.14        13      16      44 ..     362     390 ..     347     425 .. 0.58
   2 ?    3.8   0.1      0.63        60       2      27 ..     418     443 ..     396     448 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                          Swi5  16 ekelaelkeelkekkdpeetvkrhIklLh 44 
                                   ek +++l+ +    + +   +++ I+ L+
  gi|70608058|ref|YP_256928.1| 362 EKTVNNLQTQISTLNSSLSSLSQRITSLQ 390
                                   33333333333333333333333333333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.63
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Swi5   2 eaeikeleeqleelekelaelkeelk 27 
                                   + +i++l++ +++l  +l++l+++ +
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNSSITNLSGQLNSLQSKVN 443
                                   44566666666666666666666554 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.0     0.013       1.2      57     110 ..     349     402 ..     324     414 .. 0.69
   2 ?    9.8   3.2    0.0067      0.64      17     104 ..     358     445 ..     344     450 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.013
                        Nsp1_C  57 ekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskles 110
                                   ++Is+L +++ + e++ n++  +++ ++s+ + L++ ++++ + l +l+s++ s
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISS 402
                                   566666666666666666666666666666666666666666666666665544 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0067
                        Nsp1_C  17 nktldelinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdny 97 
                                     +l+  +n+ +t++++ ++  ++ ++++++  ++L + ++ Is+L   + +  ++ n++  +++ ++s+ ++L+  L+++
  gi|70608058|ref|YP_256928.1| 358 ITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSL 438
                                   346788888888888888888888888888888888888888888888887777777777777777777777777777777 PP

                        Nsp1_C  98 Ekeleel 104
                                    +++++l
  gi|70608058|ref|YP_256928.1| 439 QSKVNSL 445
                                   7777665 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.5     0.059       5.5       5      53 ..     349     397 ..     340     407 .. 0.50
   2 ?    3.9   0.0      0.66        62      38      68 ..     403     433 ..     395     445 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.059
                      JIP_LZII   5 kevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslq 53 
                                   ke+ +L++  t+L +t n L ++   L + +  L+++ ++L++ l sl+
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLN 397
                                   4555555555555555555544444444444444444444444444444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.66
                      JIP_LZII  38 LtsereiLreEleslqkakerlesrikelEe 68 
                                   L+   ++L++ l++lq   ++l+s+i++l  
  gi|70608058|ref|YP_256928.1| 403 LSGTASSLSSQLNALQGKISSLNSSITNLSG 433
                                   6666667777777777777777777766644 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.2     0.016       1.5       8      83 ..     351     429 ..     343     445 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.016
                        CENP-H   8 rdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrqrwr 83 
                                   +  l++++ +l++ +++lq ++++++ +  +l+++  +l ++l+ l++  +s +   + l+++l++l+ ++    + ++
  gi|70608058|ref|YP_256928.1| 351 ISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSgtaSSLSSQLNALQGKISSLNSSIT 429
                                   5555556666666666666666666666666666666666666555555555555554455555555555544444444 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.3     0.028       2.7      65     123 ..     338     394 ..     319     404 .. 0.69
   2 ?    2.5   0.0       1.9   1.8e+02      87     122 ..     407     442 ..     391     446 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.028
                        DUF641  65 kkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                   ++++  + ++ +++ei  + + +  +e+tv++l++++++ +s +++L ++++++++   
  gi|70608058|ref|YP_256928.1| 338 QANQ--NLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLA 394
                                   3332..45667777777777777888888888888888888888888777777666544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.9
                        DUF641  87 lktyeitvkkleaelkakdseieeLkekLeeaeksn 122
                                     ++   +++l+ ++++ +s i++L  +L++++++ 
  gi|70608058|ref|YP_256928.1| 407 ASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   344445556666666666666666666666666554 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.3    0.0056      0.52     120     193 ..     360     437 ..     317     447 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0056
                                   TTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH....-------STCCHHHHHHHHHHHHHHHHHHHHHH CS
                         APG17 120 sveelkealkesidelqaaqkkldssllefdtdlrelkkel....sksksksessslipellkelesleeemAslLes 193
                                   + e+  ++l++ i+ l++  ++l++++++++++l++l++++     + +s s++ + ++  +++l+s  +++   L+s
  gi|70608058|ref|YP_256928.1| 360 NLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTIsslsGTASSLSSQLNALQGKISSLNSSITNLSGQLNS 437
                                   222222333333444444444444444444444444444444433111222244444444444444444444444444 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.5     0.016       1.5      76     156 ..     339     418 ..     315     449 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.016
                 Fzo_mitofusin  76 atekLrlivsltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                   a++ L++ v+   +++ + +  +l++t+++l++q+ + +++l++  +++++  ++l++++++   l   as+l+s+L++ +
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNI-TNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   67777877777666665444.578888888888888888888888888888888888888888899999999999988765 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.5     0.061       5.8      44     109 ..     341     410 ..     331     418 .. 0.65
   2 ?    6.4   0.3     0.097       9.2      59      94 ..     409     444 ..     402     453 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.061
                          COG2  44 kellelvnedyadFv....slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakel 109
                                   ++l  lvn+++   v    +l +    lq+++++++s+l+++ ++++s+++ l+   ++++s    a++l
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVqnitNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSL 410
                                   5566666666655551111444555677888888888888888888888888888888877766666555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.097
                          COG2  59 slSghLvglqeeleevesplaaarkkvesvreklse 94 
                                   slS++L  lq +++ ++s+++++  +++s+++k++ 
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNS 444
                                   577777777777777777777777777777777765 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.4     0.011         1      30      85 ..     339     394 ..     320     399 .. 0.75
   2 ?    1.7   0.0       2.9   2.7e+02      32      84 ..     391     442 ..     380     447 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                        GCN5L1  30 ltealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsalk 85 
                                    +++l   +n++++ + +n  +lek + +lq+++++++   ++  + + s+++ l 
  gi|70608058|ref|YP_256928.1| 339 ANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLA 394
                                   45667777888888888888888888888888888888888888887777777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 2.9
                        GCN5L1  32 ealvdklnsgvaeayanqkklekeakalqanvakfakqtdqWlalvesfnsal 84 
                                   ++ + +lns ++ +   +  l +++ alq +++ ++   ++     +s++s++
  gi|70608058|ref|YP_256928.1| 391 NT-LASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKV 442
                                   33.35677777777777777777777777777777777666666666666655 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.8      0.91        86      58      87 ..     355     384 ..     323     388 .. 0.63
   2 ?   10.9   3.2    0.0055      0.52      22      89 ..     368     435 ..     362     444 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.91
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2  58 kaqsqkqqakvqelqgeikkLnqkLqdaea 87 
                                   + +  + ++ v++lq +i +Ln +L   ++
  gi|70608058|ref|YP_256928.1| 355 VQNITNLEKTVNNLQTQISTLNSSLSSLSQ 384
                                   333344456778888888888888877665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0055
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          BST2  22 LerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                                   L+ q+   + sl +  + +++ ++t+ +L++ +      +    ++++ lqg+i +Ln ++ + + ++
  gi|70608058|ref|YP_256928.1| 368 LQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQL 435
                                   55566666666666666666666666666666666666666666666666666666666666655444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.8    0.0053       0.5     126     219 ..     342     436 ..     318     446 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0053
                       Leu_zip 126 GgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldle 205
                                      +L++kei+ L ++ ++L++ +++l +q+ ++ +  s l++ + +lq++l + +++ +  s + s+l+++l++l+ +++
  gi|70608058|ref|YP_256928.1| 342 NLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISsLSGTASSLSSQLNALQGKIS 422
                                   446788888888888888888888888888888888888888888888888888766655355566777788888777777 PP

                       Leu_zip 206 ktleektasaksle 219
                                   +  ++ t+ + +l+
  gi|70608058|ref|YP_256928.1| 423 SLNSSITNLSGQLN 436
                                   76666655554443 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.3     0.054       5.1      10      39 ..     349     382 ..     341     384 .. 0.66
   2 ?    7.9   2.9     0.028       2.6       2      43 ..     376     417 ..     368     419 .. 0.80
   3 ?    3.0   0.1      0.97        91       2      29 ..     418     445 ..     417     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.054
                     DASH_Dam1  10 DsletLdknledL....qqihesLsdfNeSFasf 39 
                                   ++++ L +n+++L    ++++ ++s++N S++s+
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLektvNNLQTQISTLNSSLSSL 382
                                   5666666666666222234566788999999997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.028
                     DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsdfNeSFasfLYGL 43 
                                     ++++L+  ++ L++ l  L+++  sLs+   S++s L +L
  gi|70608058|ref|YP_256928.1| 376 NSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNAL 417
                                   457888888888888888888888888888888888888766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.97
                     DASH_Dam1   2 epafaeLaDsletLdknledLqqihesL 29 
                                   + ++++L+ s+++L+ +l+ Lq+  +sL
  gi|70608058|ref|YP_256928.1| 418 QGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   6788999999999999999998876666 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.1    0.0071      0.67     116     193 ..     335     414 ..     320     437 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0071
                          Not3 116 pkekekeearewlkdaideLneqvekleaeieklsskkkkkkk..skekarveeleklierhkfhieklelllrllenee 193
                                      ++++++++ +++ i++L +++ +le+ +++l+++ ++ ++  s+ ++r+++l++++ + +  i++l+     l+ + 
  gi|70608058|ref|YP_256928.1| 335 MSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSslSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQL 414
                                   55677888999999999999999999999999999998777643455556888888888888888888877776665543 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.0     0.017       1.6      27      72 ..     340     385 ..     337     386 .. 0.91
   2 ?    8.9   0.5     0.018       1.7       7      69 ..     356     417 ..     353     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.017
                        Cnn_1N  27 eerleklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                   +++l++l ++++ +l+++ ++l+ +v +lq ++ +++ +l +++++
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQR 385
                                   789999999****************************999988775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.018
                        Cnn_1N   7 eqidkLkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllrea 69 
                                   ++i +L+K   +L+ +i +L++ l  ls+  +++l +++  l  ++ sl  +  ++  +l+ +
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQ-RITSLQNTLASLNSTISSLSGTASSLSSQLNAL 417
                                   67899999999999999999999999999.777777777777777777766666666665554 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.1      0.16        15      45     108 ..     347     410 ..     329     444 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.16
                          CdvA  45 lkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeeikkllekl 108
                                   ++k++++l ++i++lek++ nl+ +  +   + ++  + i+++++ l s+++ +++++ + + l
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSL 410
                                   4445555555555555555555444444444444444444444444444444444444444444 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.6     0.042       3.9      15      64 ..     355     404 ..     329     449 .. 0.45

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.042
                                   .........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SKA1  15 nqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieasl 64 
                                    q+ + l+++++++++++s+l+++l++l +++ + ++++ +l++ i    
  gi|70608058|ref|YP_256928.1| 355 VQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   22222223333333333333333333333333333333333333332222 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.5     0.016       1.5      11      94 ..     347     429 ..     336     446 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.016
                    STAT_alpha  11 lrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklkellnlleslqe 91 
                                   +++++  ++q+i +Le++   ++ q+++l++   ++ ++  ++l++  ++l++++++L+ +  +l ++l++l ++++sl +
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSS-LSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNS 426
                                   35667777777777777777777777777776.333444444455666666665555555555555555555555555554 PP

                    STAT_alpha  92 kll 94 
                                   +++
  gi|70608058|ref|YP_256928.1| 427 SIT 429
                                   443 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.1     0.011       1.1      45     123 ..     325     403 ..     299     417 .. 0.74
   2 ?    8.1   5.2     0.031       2.9      35     123 ..     341     431 ..     327     449 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                         CREPT  45 eaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                   ++++l+++   ++++ ++  +  ++e++   +  ++le+ ++++++++++ ++ l++l +++  +++  ++l+s+i+sL
  gi|70608058|ref|YP_256928.1| 325 SGQTLSTKYLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSL 403
                                   5566666666667777777777777777777777778888888888888888888888888888888888888888777 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.031
                         CREPT  35 sllekikdke..eaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvr 113
                                   + l+ + +ke  +  + +++ e+ ++ l+   + L++ l+  ++  + l++ l++++++++    ++++l ++l+ ++ + 
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEisSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKI 421
                                   333333333211222223333344444444444444444444444444444444445555555555555555555555555 PP

                         CREPT 114 kelkshiqsL 123
                                   ++l+s i +L
  gi|70608058|ref|YP_256928.1| 422 SSLNSSITNL 431
                                   5555555554 PP

>> BAR_3  BAR domain of APPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.5     0.011      0.99      20      98 ..     347     425 ..     339     445 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.011
                         BAR_3  20 vEaeleelekklkkllKlckrlieagkaysaaqkqfaqsLrelkkeskgdeetdesLkkfsellqelenehtilldqaq 98 
                                   v +e++ l +++ +l K +++l +   ++++  ++++q++ +l+    + + t++sL   +++l+   n  +  + +++
  gi|70608058|ref|YP_256928.1| 347 VNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLN 425
                                   6789999999999999999999999999999999999999999999977777776666555555544444333333333 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.3     0.077       7.2      52     100 ..     333     381 ..     328     385 .. 0.92
   2 ?    8.5   0.9     0.025       2.3      10      93 ..     360     437 ..     346     444 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.077
                         THOC7  52 felsierlqllakanerereryeaekeeieseieavreeieelkaqLee 100
                                   + +s++  q+l++   +e+ ++ ++  ++e++  +++++i+ l+++L+ 
  gi|70608058|ref|YP_256928.1| 333 YLMSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSS 381
                                   567999***************************************9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.025
                         THOC7  10 nveerplkrltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavree 90 
                                   n  e+++++l+ ++++l +s      ++l q   +l+  +a+++++i  l   a++ + + + ++ + + ++s+i ++  +
  gi|70608058|ref|YP_256928.1| 360 N-LEKTVNNLQTQISTLNSS-----LSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQ 434
                                   2.344555555555554444.....45555555555555555555555555555555555555555555555555555444 PP

                         THOC7  91 iee 93 
                                     +
  gi|70608058|ref|YP_256928.1| 435 LNS 437
                                   444 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.0     0.022       2.1       4      69 ..     350     415 ..     333     416 .. 0.85
   2 ?    6.7   0.5     0.067       6.3       9      50 ..     404     445 ..     397     449 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.022
                         Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                   +++s  +++++l + ++++++q+++l+++ +s s++ +sl+++  +l +  ++l+ +a +++++L+
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLN 415
                                   556667788888899999999999999999999999999999999999999999999999988886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.067
                         Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslheaceql 50 
                                   + +  +l +q+++++ ++++l+++ ++ s + +sl+++ ++l
  gi|70608058|ref|YP_256928.1| 404 SGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   445566777777777777777777777777777777776665 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.5     0.011         1      72     173 ..     338     439 ..     308     449 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.011
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXX CS
                          AIP3  72 epldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlys 152
                                   ++ ++++  ++++++sl +++++l++++++ ++++++++++ ++ +++ +s +++ ++l++ +++++     L++  +  +
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   333444455555555555555555555555555555555555554444444444444444444444444444444444444 PP

                                   XXXXXXXXXXXXXXXXXXXXX CS
                          AIP3 153 efkseikeslselrekakkvk 173
                                    + s++++s+++l+ ++++++
  gi|70608058|ref|YP_256928.1| 419 GKISSLNSSITNLSGQLNSLQ 439
                                   444444444444444444444 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.3      0.05       4.8      44      86 ..     343     385 ..     335     403 .. 0.66
   2 ?    3.7   0.1      0.64        60      46      82 ..     408     444 ..     396     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.05
                                   HHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXX CS
                         Sec2p  44 ekealekkneklkeqLkeketlleslqeqLkeLkevlekmeee 86 
                                    ++ ++k+ ++l +++++ e+ +++lq+q ++L + l++++++
  gi|70608058|ref|YP_256928.1| 343 LQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQR 385
                                   4555666667777777777777777777777777776666654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.64
                                   HHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTT CS
                         Sec2p  46 ealekkneklkeqLkeketlleslqeqLkeLkevlek 82 
                                    +l  + + l+ +++  ++ + +l+ qL++L++++++
  gi|70608058|ref|YP_256928.1| 408 SSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNS 444
                                   5566666777777777777777777777777766654 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.6   0.00098     0.093     125     224 ..     349     444 ..     304     449 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00098
                          CorA 125 ellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldeler 203
                                   ++++ l +++  le+++   + +   + ++l+ l +r++ l+  la +  ++ + l+ + ++ l++    +l+ l+ ++++
  gi|70608058|ref|YP_256928.1| 349 KEISSLVQNITNLEKTVnnLQTQISTLNSSLSSLSQRITSLQNTLASLNSTI-SSLS-GTASSLSS----QLNALQGKISS 423
                                   2233333333333333332222223333333333334444444444444444.2222.23333332....35666666666 PP

                          CorA 204 llemlealrerleslqdtyss 224
                                   l   +++l+ +l+slq+  +s
  gi|70608058|ref|YP_256928.1| 424 LNSSITNLSGQLNSLQSKVNS 444
                                   666666666666666666665 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.6       1.2   1.1e+02      58      92 ..     344     378 ..     302     387 .. 0.62
   2 ?    5.1   2.7      0.21        20      23      92 ..     351     413 ..     331     417 .. 0.44
   3 ?    4.9   0.2      0.24        22      15      49 ..     413     447 ..     405     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.2
                          CK2S  58 erLrekqlealeevlakLrekleelqkvrdslekl 92 
                                   ++L+ k +++l + +++L+++++ lq   ++l++ 
  gi|70608058|ref|YP_256928.1| 344 QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSS 378
                                   25666666666666666666666666555555444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.21
                          CK2S  23 seslleslsnlaeqlqalqnvklygtplrdfpdlqerLrekqlealeevlakLrekleelqkvrdslekl 92 
                                    +sl+++ +nl +  + lq + ++    ++++ l +      + +l++ la+L++++++l + ++sl+++
  gi|70608058|ref|YP_256928.1| 351 ISSLVQNITNLEKTVNNLQTQIST--LNSSLSSLSQ-----RITSLQNTLASLNSTISSLSGTASSLSSQ 413
                                   333333333333333333333322..1122222222.....22345555555555555555555555555 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.24
                          CK2S  15 kWkellseseslleslsnlaeqlqalqnvklygtp 49 
                                     ++l+ + +sl +s +nl  ql++lq   ++ tp
  gi|70608058|ref|YP_256928.1| 413 QLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTP 447
                                   567899999999999********999988776555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  11.4     0.032         3     583     694 ..     329     442 ..     319     449 .. 0.39

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.032
                      Prominin 583 lsnlelLteeerkdLeklresglski.hsslyleqlckkltkvnletlaekleelanelsngkknlkqslkneaqdlraiq 662
                                   ls+ +l++ +++++L++l + ++s++ +  + le++ ++  +++++tl ++l +l++++++  +n   sl+++ ++l+   
  gi|70608058|ref|YP_256928.1| 329 LSTKYLMSVQANQNLQALVNKEISSLvQNITNLEKTVNN-LQTQISTLNSSLSSLSQRITSL-QNTLASLNSTISSLSGTA 407
                                   555555666666666666665555431222223333333.2334444444444444444333.222222222222222222 PP

                      Prominin 663 qelvlp...lessvkklkksvkkldeensdlqesi 694
                                   + l  +   l+ ++++l++s+++l+ + ++lq+++
  gi|70608058|ref|YP_256928.1| 408 SSLSSQlnaLQGKISSLNSSITNLSGQLNSLQSKV 442
                                   22221111133333333444444444444444443 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.7     0.036       3.4      26      66 ..     352     393 ..     347     396 .. 0.87
   2 ?    4.7   0.5      0.43        41      38      67 ..     414     443 ..     392     445 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.036
                  H-kinase_dim  26 arLnqsleefr.fenglkasvtelksslqnlgrisgeLQegv 66 
                                   ++L q +++++ ++n+l+++ + l+ssl++l++ ++ LQ+  
  gi|70608058|ref|YP_256928.1| 352 SSLVQNITNLEkTVNNLQTQISTLNSSLSSLSQRITSLQNTL 393
                                   6788888888867889999********************875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.43
                  H-kinase_dim  38 englkasvtelksslqnlgrisgeLQegvm 67 
                                    n l+   + l+ss++nl+   + LQ++v 
  gi|70608058|ref|YP_256928.1| 414 LNALQGKISSLNSSITNLSGQLNSLQSKVN 443
                                   3344466777****************9985 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.8      0.05       4.7      87     156 .]     325     393 ..     318     414 .. 0.73
   2 ?    6.5   4.4      0.08       7.5      52     146 ..     348     439 ..     344     446 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.05
                          Wtap  87 tGkrLmakcrvLeqENeELgkvleegrvakLeselalqkkfveelkkaleeleelleeleeevevlqstl 156
                                   +G+ L +k  +  q N++L ++l + ++++L +++  ++k+v+ l+++ + l+  l++l++ +  lq+tl
  gi|70608058|ref|YP_256928.1| 325 SGQTLSTKYLMSVQANQNL-QALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTL 393
                                   4777777777777778888.44555677888888888888888888888888888888877777777775 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.08
                          Wtap  52 nlvfsrlrkeleeaenkleeaqeeLqalkftpdsqtGkrLmakcrvLeqENeELgkvle..egrvakLeselalqkkfvee 130
                                   n ++s l +++ + e+ +++ q ++++l+ +       +L +++  L++  + L  +++  +g  ++L+s+l++++  +  
  gi|70608058|ref|YP_256928.1| 348 NKEISSLVQNITNLEKTVNNLQTQISTLNSSLS-----SLSQRITSLQNTLASLNSTISslSGTASSLSSQLNALQGKISS 423
                                   445555555555555555544444444433322.....3555555555555555555542235555555555555555555 PP

                          Wtap 131 lkkaleeleelleele 146
                                   l+++ ++l   l++l+
  gi|70608058|ref|YP_256928.1| 424 LNSSITNLSGQLNSLQ 439
                                   5555555555555544 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.8     0.094       8.9      36     139 ..     335     434 ..     319     447 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.094
                      MIP-T3_C  36 laessakkeravsaseiekLresiQkltksvnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplk 116
                                   +  +++++ +a++++ei++L ++i +l k vn L  ++   +  + s+ + +++ +++  + +  +    +   ++ + l 
  gi|70608058|ref|YP_256928.1| 335 MSVQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTI----SSLSGTASSLS 411
                                   335667888888888888888888888888888888888888888887777766665544333322....22233333444 PP

                      MIP-T3_C 117 aqlaeleeaIkdqkekisnvrak 139
                                    ql+ l+ +I+  ++ i n+  +
  gi|70608058|ref|YP_256928.1| 412 SQLNALQGKISSLNSSITNLSGQ 434
                                   45555555555554444444443 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.6     0.013       1.2      16      93 ..     338     418 ..     327     424 .. 0.62
   2 ?    2.1   0.2       3.1   2.9e+02      66      95 ..     412     441 ..     403     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.013
                HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlk...eeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                   ++ ++ q  v++e + l +++ +l+   ++ + +++  ++ l +L + +++ ++ la+l+s+++s   + + lssql+aLq
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALVNKEISSLVQNITNLEktvNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQ 418
                                   334444444555555554444333300034455555666777778888888888888888888888888888888988888 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 3.1
                HIP1_clath_bdg  66 aelarlkssLesseqsgeqlssqlaaLqaE 95 
                                    +l+ l++ ++s + s ++ls ql++Lq+ 
  gi|70608058|ref|YP_256928.1| 412 SQLNALQGKISSLNSSITNLSGQLNSLQSK 441
                                   567888889999999999999999999875 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.1     0.057       5.4      17      54 ..     364     401 ..     354     403 .. 0.82
   2 ?    2.1   0.1       2.2   2.1e+02      15      43 ..     411     439 ..     407     445 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.057
                    TRPM_tetra  17 kveevneKenlikaSLqsldfrLgkLedlsaltvdtLk 54 
                                    v+ ++   ++ ++SL+sl +r+  L++  a   +t +
  gi|70608058|ref|YP_256928.1| 364 TVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTIS 401
                                   567777888999***************99888888765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 2.2
                    TRPM_tetra  15 smkveevneKenlikaSLqsldfrLgkLe 43 
                                   s +++ ++ K ++ ++S+++l  +L  L+
  gi|70608058|ref|YP_256928.1| 411 SSQLNALQGKISSLNSSITNLSGQLNSLQ 439
                                   567788889999*************9998 PP

>> Vps52  Vps52 / Sac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.1     0.023       2.2      14      80 ..     363     429 ..     348     434 .. 0.79
   2 ?    7.2   4.3     0.019       1.8      13      82 ..     383     452 ..     373     463 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.023
                         Vps52  14 eniaslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvd 80 
                                   + +++l+ qi+ ++s l+ l + +++ q+ l s+ s i+ l+    +l+++L+  + + + l + + 
  gi|70608058|ref|YP_256928.1| 363 KTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSIT 429
                                   3456777888999999999999999999999999999999999999999999999988888877765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                         Vps52  13 seniaslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvddl 82 
                                   s+ i+sl+n +a+++s ++ l    ++  s+l+ +   i+ l+   ++l+ +L+  +++   l++lv + 
  gi|70608058|ref|YP_256928.1| 383 SQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTPLVYGG 452
                                   4556666666666666666666666666666666666666666666666666666666666666666555 PP

>> TBK1_CCD1  TANK-binding kinase 1 coiled-coil domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.7      0.11        10      33     124 ..     340     432 ..     329     451 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.11
                     TBK1_CCD1  33 lllvqelmrkgvrwliellkedvnkllhkktevelkceiceetlekaekllevlmqanlepsElde.iselhkkllrlsss 112
                                      +q l++k +  l++ + +  + + + +t+++   +  ++ +++ ++l + l   n+++s l+  +s l+++l+ l+ +
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGtASSLSSQLNALQGK 420
                                   444566666666666665555443334445555555555555566666666666666666655543355555555555555 PP

                     TBK1_CCD1 113 lerieeslqeik 124
                                    +++++s+ ++ 
  gi|70608058|ref|YP_256928.1| 421 ISSLNSSITNLS 432
                                   555555555554 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.6      0.18        17      32      70 ..     344     386 ..     323     395 .. 0.55
   2 ?    5.9  15.2      0.17        16       4      95 ..     350     444 ..     347     448 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.18
                    Syntaxin_2  32 r....eklhelieeinelikktnellkklsqldnsssdsqqkl 70 
                                   +    +++ +l+++i++l k++n+l  ++s+l  s+s+ +q++
  gi|70608058|ref|YP_256928.1| 344 QalvnKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRI 386
                                   3333355555666666666666665555555555554444444 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.17
                    Syntaxin_2   4 nlqkinsnvstleklvkqLgtk.....kdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdf 79 
                                   +++++ +n+++lek v+ L+t+          l +++ +l++ +  l +++++l    s+l+ +++  q   + + L++++
  gi|70608058|ref|YP_256928.1| 350 EISSLVQNITNLEKTVNNLQTQistlnSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQG--KISSLNSSI 428
                                   5666666666666666666666222222345555666666666665555555555555555555543343..447899999 PP

                    Syntaxin_2  80 kealqeFqkiqrqyae 95 
                                   +++  +++++q ++++
  gi|70608058|ref|YP_256928.1| 429 TNLSGQLNSLQSKVNS 444
                                   9999999999998876 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       3.1   2.9e+02      22      54 ..     184     216 ..     168     221 .. 0.84
   2 ?   11.7   3.8    0.0014      0.13      62     147 ..     352     443 ..     348     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.1
                       DUF4349  22 airelveeagGyvesssersgtegdersasltl 54 
                                   +  +lv++++Gy +s+ + s t+++++s ++tl
  gi|70608058|ref|YP_256928.1| 184 QTFKLVASLQGYAASTASVSITGQQNASVTITL 216
                                   5568999**********8888888888888886 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0014
                       DUF4349  62 dafldelael.gkvtsrstsaeDVTeqyvDleaRlkaleasedrllallek.ak...sv.edlleiereLsevqaeiesle 136
                                   +++++++ +l ++v + +t+ + + +++  l +R+++l+ + ++l + ++  ++   s+ + l +++ ++s+ ++ i +l 
  gi|70608058|ref|YP_256928.1| 352 SSLVQNITNLeKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSlSGtasSLsSQLNALQGKISSLNSSITNLS 432
                                   566667766546777889999999999999***************9998765552223324677899************** PP

                       DUF4349 137 gqlryLdnqva 147
                                   gql++L+++v+
  gi|70608058|ref|YP_256928.1| 433 GQLNSLQSKVN 443
                                   ******99986 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.7     0.029       2.7       6      69 ..     374     437 ..     369     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.029
                                   XXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   6 rleasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleaklde 69 
                                    l++s ++l++++++l+n+l s   +   l      l s l++l+++    +  + +l  +l+ 
  gi|70608058|ref|YP_256928.1| 374 TLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKISSLNSSITNLSGQLNS 437
                                   6889999999999999999999998888888888888888888888888888888888777765 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  11.5      0.38        35      60     163 ..     338     445 ..     329     448 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.38
                      CCDC144C  60 qyngqLnvl.kaentmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdlelalqr...erdewlrlqdkln 136
                                   q n+ L++l + e + l + + +  ++ + l++ +  + s L++  q +   q +   l+ +      +     +  + l+
  gi|70608058|ref|YP_256928.1| 338 QANQNLQALvNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSlsgTASSLSSQLNALQ 418
                                   556666665234556666666666666666666666666666665555555555555444444330003333333334445 PP

                      CCDC144C 137 fdvsnlkdknevLsqqLskaeskansL 163
                                     +s+l+ ++  Ls qL   +sk+nsL
  gi|70608058|ref|YP_256928.1| 419 GKISSLNSSITNLSGQLNSLQSKVNSL 445
                                   667777777777777777777777776 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   7.5       1.1   1.1e+02      51      83 ..     340     373 ..     315     418 .. 0.73
   2 ?    1.2   0.1       5.2   4.9e+02      62      84 ..     415     437 ..     404     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 1.1
                       DUF4094  51 esr.skdilg.evskthkaiqtLdktissLemeLa 83 
                                   +++ +  +++ e+s   + i++L+kt+ +L+++++
  gi|70608058|ref|YP_256928.1| 340 NQNlQ-ALVNkEISSLVQNITNLEKTVNNLQTQIS 373
                                   22223.34444777777888888888888887765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 5.2
                       DUF4094  62 skthkaiqtLdktissLemeLaa 84 
                                   +  +  i++L+ +i +L  +L +
  gi|70608058|ref|YP_256928.1| 415 NALQGKISSLNSSITNLSGQLNS 437
                                   45566788999999999888765 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.1     0.089       8.4      32      97 ..     357     424 ..     344     464 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.089
                          Vps5  32 eldslesqLkkLykaiellvsqrkelasataelakslesLas..lelskslsralsqlaeveerikel 97 
                                   ++++le++  +L++ i++l+s+ + l++ +  l ++l+sL s  ++ls + s++ sql  ++ +i++l
  gi|70608058|ref|YP_256928.1| 357 NITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNStiSSLSGTASSLSSQLNALQGKISSL 424
                                   33444444444444444444444444444444444444443311233344444444555555555444 PP

>> Nop14  Nop14-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.0     0.054       5.1     638     771 ..     310     438 ..     282     450 .. 0.43

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.054
                         Nop14 638 nfllnlllllapkkskk...kvpgvfpvkevkpsellelkeleekskkekkqrklslsdllkeesskeeseqlklsllsta 715
                                   n++++ll+++  + s+    ++++ ++v+ +   +  +l+ l +k+ ++  q+         + +++ ++ q+++s+l+  
  gi|70608058|ref|YP_256928.1| 310 NYVFQLLIVANYTTSSGqtlSTKYLMSVQAN---Q--NLQALVNKEISSLVQNIT-------NLEKTVNNLQTQISTLNSS 378
                                   4555544444433333212222222222221...1..111111111111111222.......2334444555555555555 PP

                         Nop14 716 lsllek.faelyseksafveifepilkllkklklkkkklp...eelqekleellaklerl 771
                                   ls l++ ++ l +++ ++ ++++ ++ + ++l+++ + l+   ++l++++++l+ +l++l
  gi|70608058|ref|YP_256928.1| 379 LSSLSQrITSLQNTLASLNSTISSLSGTASSLSSQLNALQgkiSSLNSSITNLSGQLNSL 438
                                   554444233344555555555555555555554333333322233333444444444433 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3       2.6   2.5e+02      22      57 ..     340     375 ..     336     383 .. 0.55
   2 ?    5.8   4.7      0.16        15       2      55 ..     369     422 ..     361     445 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.6
                   Cep57_CLD_2  22 heeelkrLnkERdsalrqLgvAyeelneLkaeveal 57 
                                   ++ + + +nkE +s ++ + +   ++n+L+ +  +l
  gi|70608058|ref|YP_256928.1| 340 NQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTL 375
                                   555555555566666666666555555555555444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.16
                   Cep57_CLD_2   2 eaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaeve 55 
                                    ++++tL   L+sl++++ + + +l++Ln+  +s     ++  + ln L+ +  
  gi|70608058|ref|YP_256928.1| 369 QTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLSGTASSLSSQLNALQGKIS 422
                                   567778888888888888888877777777555555555555555555544443 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   3.7      0.41        39      12      60 ..     356     404 ..     340     415 .. 0.60
   2 ?    4.7   1.1      0.43        40      14      42 ..     400     428 ..     384     440 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.41
                     DASH_Dad2  12 eaLkqlrdlsdslakqleeLeeklstladgteavasVlanWqnvlrais 60 
                                   +++ +l++  ++l++q+++L+  ls l++  ++ ++ la+ ++ + + s
  gi|70608058|ref|YP_256928.1| 356 QNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNSTISSLS 404
                                   4455555555666666666666666666655555555555555555544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.43
                     DASH_Dad2  14 LkqlrdlsdslakqleeLeeklstladgt 42 
                                   +  l+  ++sl++ql++L+ k+s l++  
  gi|70608058|ref|YP_256928.1| 400 ISSLSGTASSLSSQLNALQGKISSLNSSI 428
                                   4567888899*************999765 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   8.2      0.21        20      34      87 ..     353     411 ..     334     448 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.21
                     AATF-Che1  34 qLpqpetlkeflesseefeealeeaekalkklleslleLreelleqne.ikkla......e 87 
                                   +L q  ++ ++ ++ ++++++++++ ++l++l + +++L+++l   n+ i++l+      +
  gi|70608058|ref|YP_256928.1| 353 SLVQ--NITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQNTLASLNStISSLSgtasslS 411
                                   3333..3444444478999999999999999999999999999888886666543322210 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.1     0.038       3.6     150     199 .]     341     390 ..     332     392 .. 0.85
   2 ?    1.3   0.2       3.5   3.3e+02     162     194 ..     409     441 ..     390     446 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.038
                          End3 150 eqlreleegegkskeknlksvkedietveeqVegLesylssrkeeLeqLk 199
                                   ++l+ l ++e +s  +n++++++ ++++++q+++L+s lss ++ +++L+
  gi|70608058|ref|YP_256928.1| 341 QNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLNSSLSSLSQRITSLQ 390
                                   5677888888877779********************99999888887775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 3.5
                          End3 162 skeknlksvkedietveeqVegLesylssrkee 194
                                   s +++l+ ++  i+++++ +++L   l+s +++
  gi|70608058|ref|YP_256928.1| 409 SLSSQLNALQGKISSLNSSITNLSGQLNSLQSK 441
                                   333445555555555555555555555544444 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5  10.3      0.62        58      27     169 ..     337     470 ..     327     474 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.62
                                   HHHHHHHHHHHHHHHHCHHHH..........HHHHHHHHS..TTSCCHH.HHHCHHH..HH..HHHHHHHHHHHHHHHHHH CS
                          GP41  27 leeqqeldkkleaRlsAleevvrvlgedvaslktrmklqChanykliCv.tkvPynasdsWdkvkksLegiWnntevsydl 106
                                   +++ q+l+  ++  +s l + + +l + v++l+t+ ++   ++   +    +   n+  s + +  sL         s + 
  gi|70608058|ref|YP_256928.1| 337 VQANQNLQALVNKEISSLVQNITNLEKTVNNLQTQISTLN-SSLSSLSQrITSLQNTLASLNSTISSL---------SGTA 407
                                   5555555555555566665555666666666666655443.122222210222223333333333333.........4445 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH..HHHHHHHHHCHHHHHHHHHHHX CS
                          GP41 107 aelhnliediqnqqektldeldkldklaqslanwfkllnslWvkyivvilvglrivlivlsll 169
                                   + l+++++  q +       + +l++ ++sl +++++l +l    i+++++gl ++++ ++l+
  gi|70608058|ref|YP_256928.1| 408 SSLSSQLNALQGKISSLNSSITNLSGQLNSLQSKVNSLTPLVYGGIIAGIIGLIVAIVAIVLV 470
                                   55666666666655555556677888888999*******996666********9999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2185  (0.12187); expected 358.6 (0.02)
Passed bias filter:                     1020  (0.0568911); expected 358.6 (0.02)
Passed Vit filter:                       373  (0.0208043); expected 17.9 (0.001)
Passed Fwd filter:                       207  (0.0115455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             190  [number of targets reported over threshold]
# CPU time: 1.58u 0.40s 00:00:01.98 Elapsed: 00:00:00.58
# Mc/sec: 2459.43
//
Query:       gi|70608059|ref|YP_256929.1|  [L=1424]
Description: hypothetical protein Saci_2355 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.81u 0.26s 00:00:01.07 Elapsed: 00:00:00.46
# Mc/sec: 9331.70
//
Query:       gi|70608060|ref|YP_256930.1|  [L=646]
Description: hypothetical protein Saci_2356 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.4   7.2     0.0026   17.7   7.2    1.3  1  RIFIN     Rifin
     0.0029   17.5  13.6     0.0029   17.5  13.6    2.4  3  TMEM154   TMEM154 protein family
     0.0049   16.9  31.3     0.0049   16.9  31.3    3.6  3  Mucin     Mucin-like glycoprotein
  ------ inclusion threshold ------
      0.039   14.8   0.6       0.18   12.6   0.6    2.3  1  Filamin   Filamin/ABP280 repeat
      0.087   13.4   2.0       0.18   12.4   0.5    2.3  2  Renin_r   Renin receptor-like protein
       0.14   12.5   1.8         14    6.1   0.0    3.9  4  DUF5334   Family of unknown function (DUF5334)
       0.14   12.8   0.5        1.5    9.5   0.1    2.7  2  YtkA      YtkA-like
       0.23   11.9   1.1       0.47   10.8   1.1    1.4  1  DUF5383   Family of unknown function (DUF5383)
        1.1    8.8   9.1       0.19   11.2   3.7    2.2  2  Stevor    Subtelomeric Variable Open Reading frame
        2.7    8.4   8.0        1.2    9.5   5.3    1.7  2  DUF1180   Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   7.2   1.5e-06    0.0026     182     301 ..     523     644 ..     450     646 .] 0.37

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                         RIFIN 182 atnyknvtslvkaikeeyeescll.....klkkskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaea 257
                                   + ny+ v + +++ + + +    +      +++++  + + +   ++ +s+++++++++++ +++  ++ ++++++++++ 
  gi|70608060|ref|YP_256930.1| 523 NGNYSVVFKPTNTGTYNLTL---VanyngVSNRTMIEFYTHQLPVTTGTSTSTSTTTSTTTSTTTSSTSSTTTSSATTTTS 600
                                   33333332222222222221...1222221122222222223333333333333333333333334444444444555555 PP

                         RIFIN 258 taeaekaetaaveattaslqtaiiasivaivvIvLimvIIYLiL 301
                                   t++++++  +  ++ ++s+  ++i  i++++++++i+ II Li 
  gi|70608060|ref|YP_256930.1| 601 TSTITTTPQSSSTKPSTSSGFPVIPVIIVVIIVIVIVAIILLIR 644
                                   66666666666666666666666665555555555555565553 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2         3   5.4e+03       4      36 ..      90     122 ..      75     136 .. 0.61
   2 ?   -1.7   0.4       1.3   2.4e+03      36      70 ..     414     463 ..     381     464 .. 0.50
   3 !   17.5  13.6   1.6e-06    0.0029       5      80 ..     569     642 ..     560     646 .] 0.54

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                       TMEM154   4 seksgdtaletatleeesadatsaasteseslk 36 
                                   s+ +++ +l+ +  ++ s ++++   t+s   +
  gi|70608060|ref|YP_256930.1|  90 SSLYTTLTLPPYSYKPISLQLSTGLHTISANSE 122
                                   455677777777777777777665555333222 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                       TMEM154  36 k.........qeeakeslssaelsnesdqlel......vlmiiiPlvlli 70 
                                   +           +a+  ls+  + n  +q el      +++ i P+v+l+
  gi|70608060|ref|YP_256930.1| 414 QlpqgtqveiYVKANGYLSNSTVLNVTQQGELtiylkpIVVSITPSVVLV 463
                                   13333222222234444444445555555555667777788888888875 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.6e-06
                       TMEM154   5 eksgdtaletatleeesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiiiPlvllillllvviili 80 
                                   + s++t+++t+t +++s+++++++s+ + +  +++   + +s  +++  ++   v+ +ii  v++i++++v iil 
  gi|70608060|ref|YP_256930.1| 569 STSTSTTTSTTTSTTTSSTSSTTTSSATTTTSTSTITTTPQSSSTKPSTSSGFPVIPVII--VVIIVIVIVAIILL 642
                                   566777777777777777777777776666665544444455555555555544544444..23333333333332 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.3   8.9        10   1.8e+04      11      79 ..      13      81 ..       6     136 .. 0.64
   2 ?    0.9   1.4      0.23   4.1e+02      49      92 ..     371     408 ..     342     436 .. 0.50
   3 !   16.9  31.3   2.7e-06    0.0049      24      98 ..     543     617 ..     506     623 .. 0.84

  Alignments for each domain:
  == domain 1  score: -6.3 bits;  conditional E-value: 10
                         Mucin 11 LvlaLcCCasvCvtangeGqsdaa.vveaaegqskltttttttkppttttttttasttittkttkatttt 79
                                  ++l L C  +   t++    ++++ +  +    +++     +  ppt +  ttt+ +t t    ++ +t 
  gi|70608060|ref|YP_256930.1| 13 ILLSL-CLNTFLFTSQTTAGNQTTnSNAGVYIAPNNLLNPLASSPPTIPVFTTTNQATFTFYVINSRSTQ 81
                                  55555.4444444444422222220222222334444445556677777777776666655544444443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                         Mucin  49 ttttkppttttttttasttittkttkattttttttttttateaP 92 
                                   ttt+      ++ + + + i+  t    + tt++  tt  t++ 
  gi|70608060|ref|YP_256930.1| 371 TTTL------KVVSVNGSPIQGATIDVYNMTTKSLITTLQTNST 408
                                   2223......3333222223333333333333332222222221 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.7e-06
                         Mucin  24 tangeGqsdaavveaaegqskltttttttkppttttttttasttittkttkattttttttttttateaPsdavtt 98 
                                    an +G s+ + +e  + q   tt t t +++tt+ttt+t++++++++tt ++tttt+t+t tt++++ s++ +t
  gi|70608060|ref|YP_256930.1| 543 VANYNGVSNRTMIEFYTHQLPVTTGTSTSTSTTTSTTTSTTTSSTSSTTTSSATTTTSTSTITTTPQSSSTKPST 617
                                   588899***********9*99999999999999999999888887777888888888888888888877654433 PP

>> Filamin  Filamin/ABP280 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6    0.0001      0.18      22      93 ..     418     545 ..     348     552 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                                   -EEEEEEESSSTSCCCSTTS......EEEEE...................ESSTS.......................... CS
                       Filamin  22 sltFtvytkdakgeksevgg....delqvriv.................tgsphgaatk...................... 59 
                                    +++++y+k   g+ s +++    ++ +++i+                 t        +                      
  gi|70608060|ref|YP_256930.1| 418 GTQVEIYVKAN-GYLSNSTVlnvtQQGELTIYlkpivvsitpsvvlvngT--------Qtslvltktgyelaknitvgsti 489
                                   45555555533.55555544333222223333444444444444443331........03333334444444445555555 PP

                                   .......................EEEEEEEE-SSSEEEEEE--SSSCEEEEEEEET CS
                       Filamin  60 ...........s...........svkievvdnedgtytvsYtpeepgtyrvsvkld 93 
                                              +              + v+  ++g y v ++p+  gty++++  +
  gi|70608060|ref|YP_256930.1| 490 efnftvkvsgmVmnnvsvtayinGNMVTVESLGNGNYSVVFKPTNTGTYNLTLVAN 545
                                   554444444330444433333332234699999****************9987655 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.4   4.3e+03      34      55 ..     508     530 ..     465     535 .. 0.58
   2 ?   12.4   0.5    0.0001      0.18      15      72 ..     583     642 ..     565     645 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                       Renin_r  34 kdkke.kklnlakkyssdYpaiF 55 
                                   +++ + + + +++  + +Y+++F
  gi|70608060|ref|YP_256930.1| 508 TAYINgNMVTVESLGNGNYSVVF 530
                                   33333234455555566666666 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0001
                       Renin_r  15 aeekikkrkkrsileakeakdkke..kklnlakkyssdYpaiFniiLwlvvvlvlaliai 72 
                                   +++++++ +++s+++++++++ ++  ++   + + ss +p+i  ii+ ++v++++a+i++
  gi|70608060|ref|YP_256930.1| 583 TTSSTSSTTTSSATTTTSTSTITTtpQSSSTKPSTSSGFPVIPVIIVVIIVIVIVAIILL 642
                                   1112222222222222222222222347888899999**********9999999999875 PP

>> DUF5334  Family of unknown function (DUF5334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.5   6.3e+03      24      55 ..      57      88 ..      48      94 .. 0.80
   2 ?    1.2   0.0      0.26   4.7e+02      42      59 ..     115     132 ..     110     143 .. 0.80
   3 ?    6.1   0.0    0.0078        14       9      38 ..     372     401 ..     369     408 .. 0.79
   4 ?    1.0   0.1      0.29   5.2e+02      22      48 ..     417     443 ..     405     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                       DUF5334 24 dtvdvydydtdetetvlveevtrnarTvElvV 55
                                   t+ v+   ++ t+t  v + +    T+ + V
  gi|70608060|ref|YP_256930.1| 57 PTIPVFTTTNQATFTFYVINSRSTQATIPVYV 88
                                  57889999999999999999888888888877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                       DUF5334  42 eevtrnarTvElvVrdsd 59 
                                   ++++ n+ Tv + V + +
  gi|70608060|ref|YP_256930.1| 115 HTISANSETVNVNVTTVQ 132
                                   678999999999998876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0078
                       DUF5334   9 tdlVEvetdrlpskGdtvdvydydtdetet 38 
                                   t l  v+++  p +G t+dvy+  t+   t
  gi|70608060|ref|YP_256930.1| 372 TTLKVVSVNGSPIQGATIDVYNMTTKSLIT 401
                                   555567778889***********9987655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.29
                       DUF5334  22 kGdtvdvydydtdetetvlveevtrna 48 
                                   +G +v++y   ++   + +v +vt+ +
  gi|70608060|ref|YP_256930.1| 417 QGTQVEIYVKANGYLSNSTVLNVTQQG 443
                                   799********************9876 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.82   1.5e+03      11      42 ..     361     391 ..     354     397 .. 0.65
   2 ?    9.5   0.1   0.00084       1.5      50      85 ..     498     542 ..     450     543 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.82
                          YtkA  11 lvspeepkagentivvtvtqggkpVedadvkv 42 
                                   l+++++++   +t++v v+ +g+p+++a+++v
  gi|70608060|ref|YP_256930.1| 361 LSESSKISLVTTTLKV-VSVNGSPIQGATIDV 391
                                   5555444444444444.5567*******9887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00084
                          YtkA  50 eGmeemttkv.........elkesedGvYeaevnfsmeGtWqvql 85 
                                   +Gm ++++ v         +++  ++G Y++  + +  Gt++++l
  gi|70608060|ref|YP_256930.1| 498 SGMVMNNVSVtayingnmvTVESLGNGNYSVVFKPTNTGTYNLTL 542
                                   55554444444555555449999*******************997 PP

>> DUF5383  Family of unknown function (DUF5383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   0.00026      0.47      58     118 ..     581     641 ..     563     644 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                       DUF5383  58 sekesntiaakakelgLfseekesvkqsateqeseeksnlLpillillivllivvllivli 118
                                   s+++s t++ + +++  +++  +++++    +++ + s+  p++ ++++v++++v++++++
  gi|70608060|ref|YP_256930.1| 581 STTTSSTSSTTTSSATTTTSTSTITTTPQSSSTKPSTSSGFPVIPVIIVVIIVIVIVAIIL 641
                                   2334445555555555555555555555555555566777777777777766666665553 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.38   6.9e+02     156     200 ..     465     511 ..     431     545 .. 0.64
   2 ?   11.2   3.7   0.00011      0.19     185     261 ..     570     646 .]     540     646 .] 0.43

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                        Stevor 156 csvgsvlltliglaaakaaavaa..kvalsaealkklasslsilnlf 200
                                    + +s++lt  g  +ak+ +v +  +  ++ ++   +++ +s++  +
  gi|70608060|ref|YP_256930.1| 465 GTQTSLVLTKTGYELAKNITVGStiEFNFTVKVSGMVMNNVSVTAYI 511
                                   46789999999999999988887432233333333444444444333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                        Stevor 185 ealkklasslsilnlfsesslesalkaavsaaaasdlagta..asaassafepygiaalvllilavvliiLYiwlyrRR 261
                                   +++++++s+++ +   s+ss +++  +a++++ +s +++t   +s+  s+   + +  +++++++v++i+  i l rRR
  gi|70608060|ref|YP_256930.1| 570 TSTSTTTSTTTSTTTSSTSSTTTS--SATTTTSTSTITTTPqsSSTKPSTSSGFPVIPVIIVVIIVIVIVAIILLIRRR 646
                                   222222333222222222222221..22222222222222211233333444444444444455555555555566665 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.1   5.5e+03      10      41 ..      14      60 ..       8      84 .. 0.47
   2 ?    9.5   5.3   0.00069       1.2      46     127 ..     567     645 ..     551     646 .] 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.1
                       DUF1180 10 LLlllLaasaadasralspaasspeae.................pPlpp 41
                                  LL+l L+ +   +s+ +++ +++++++                 pP+ p
  gi|70608060|ref|YP_256930.1| 14 LLSLCLN-TFLFTSQ-TTAGNQTTNSNagvyiapnnllnplassPPTIP 60
                                  5555552.2222222.222222233333455544555544444455555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00069
                       DUF1180  46 aespgkataieaksaqaaeggngsspragsaadaggslavvpelssntdkpmtlqrallvlvvvsaavivylvvRtvrlrr 126
                                   + s     ++ ++++++  +++ ss++++sa+ ++++ ++ +  +s++ kp t    + v+ v+  ++iv+ +v ++ l r
  gi|70608060|ref|YP_256930.1| 567 GTSTST--STTTSTTTSTTTSSTSSTTTSSATTTTSTSTITTTPQSSSTKPST-SSGFPVIPVIIVVIIVIVIVAIILLIR 644
                                   333333..334455677777888887888887777777777777999999999.888988888888888888877766544 PP

                       DUF1180 127 r 127
                                   r
  gi|70608060|ref|YP_256930.1| 645 R 645
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2168  (0.120921); expected 358.6 (0.02)
Passed bias filter:                      804  (0.0448435); expected 358.6 (0.02)
Passed Vit filter:                       160  (0.00892409); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.94u 0.33s 00:00:01.27 Elapsed: 00:00:00.50
# Mc/sec: 3920.99
//
Query:       gi|70608061|ref|YP_256931.1|  [L=140]
Description: hypothetical protein Saci_2357 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-31  107.4   2.2    4.4e-31  107.2   2.2    1.0  1  PaREP1    Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.048   13.3   0.1    1.5  1  GT-D      Glycosyltransferase GT-D fold


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   2.2     5e-35   4.4e-31       4     114 ..      25     133 ..      22     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 5e-35
                        PaREP1   4 eeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvdlwk 84 
                                   ++ae++l+e++e+l  Gdl+qA+eK+ykA+++++k+la+k++ ++l+  ++ +rw+ ++l+ av++l+  l++k+++d+wk
  gi|70608061|ref|YP_256931.1|  25 TAAEVYLREGDEFLGLGDLVQASEKYYKAAEEAIKLLAIKHQIPVLKDLRKIDRWRADLLFLAVKQLS--LYYKDLSDIWK 103
                                   579*****************************************************************..999******** PP

                        PaREP1  85 lAldLHeyqfheaklelsdveskeeavkdl 114
                                   +A+ LH+++fhe +l++++   ++++vk+l
  gi|70608061|ref|YP_256931.1| 104 SAWILHVEGFHETRLNRHELLFYVNHVKKL 133
                                   ***************************997 PP

>> GT-D  Glycosyltransferase GT-D fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.3e-06     0.048     100     146 ..      89     138 ..      11     140 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-06
                          GT-D 100 sksekifeklkkiwkdkdiliveG.eksrlgvgndLf..dnaksierila 146
                                   ++ + ++++l  iwk+  il veG +++rl+    Lf  + +k+++ri+a
  gi|70608061|ref|YP_256931.1|  89 KQLSLYYKDLSDIWKSAWILHVEGfHETRLNRHELLFyvNHVKKLSRIIA 138
                                   456789******************6689**99999985568999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1032.49
//
Query:       gi|70608062|ref|YP_256932.1|  [L=232]
Description: HTH DNA-binding domain-containing protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-09   35.8   0.0    1.4e-08   34.7   0.0    1.6  1  HTH_3        Helix-turn-helix
    8.7e-06   25.7   0.0    1.7e-05   24.7   0.0    1.5  1  HTH_19       Helix-turn-helix domain
    8.1e-05   22.9   0.0    0.00013   22.3   0.0    1.3  1  HTH_31       Helix-turn-helix domain
  ------ inclusion threshold ------
       0.15   12.2   0.0        0.3   11.2   0.0    1.5  1  GP3_package  DNA-packaging protein gp3


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.1e-12   1.4e-08       2      44 ..      27      69 ..      26      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.1e-12
                                  HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                         HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                  +++R+    sq eLA++lG+s+s i+++E+G+r+P +e +k+ 
  gi|70608062|ref|YP_256932.1| 27 RKWRDIFHVSQGELARYLGISQSVIADYEKGRRKPGVEFVKRF 69
                                  777888889*****************************99986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.8e-09   1.7e-05       5      62 ..      27      84 ..      23      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.8e-09
                        HTH_19  5 keaReelgltqeelaerlgisrskisaiEngkkdvpsaell.lkiaealgidleyllqg 62
                                  ++ R  +  +q ela+ lgis+s i+ +E+g++ +p+ e + ++++ +++id+e+  + 
  gi|70608062|ref|YP_256932.1| 27 RKWRDIFHVSQGELARYLGISQSVIADYEKGRR-KPGVEFVkRFVLALVNIDIERGYNV 84
                                  677899999************************.*******667777889999987776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.9e-08   0.00013      14      51 ..      34      70 ..      23      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.9e-08
                        HTH_31 14 GLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                   +sq e+A+ lg+s+s + ++E Grr  p  +++ +++
  gi|70608062|ref|YP_256932.1| 34 HVSQGELARYLGISQSVIADYEKGRR-KPGVEFVKRFV 70
                                  589***********************.6****999986 PP

>> GP3_package  DNA-packaging protein gp3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.7e-05       0.3      48      78 ..      40      71 ..      25      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                                  HHHHHT--HHHHHHHGG..S.HHHHHHHHHHH CS
                   GP3_package 48 LalyLgisrstlkeyekrkr.efsetierikq 78
                                  La+yLgis+s + +yek  r    e ++r   
  gi|70608062|ref|YP_256932.1| 40 LARYLGISQSVIADYEKGRRkPGVEFVKRFVL 71
                                  9****************988666677766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1792.56
//
Query:       gi|70608063|ref|YP_256933.1|  [L=116]
Description: nascent polypeptide-associated complex protein [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-09   37.0   0.6    2.4e-09   37.0   0.6    2.2  3  NAC            NAC domain
     0.0079   16.2   0.6      0.012   15.6   0.6    1.3  1  HOIP-UBA       HOIP UBA domain pair
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.066   13.0   0.0    1.3  1  UBA_4          UBA-like domain
      0.061   12.4   0.6      0.064   12.3   0.6    1.1  1  Pannexin_like  Pannexin-like TM region of LRRC8
      0.062   13.0   0.0       0.17   11.7   0.0    1.8  2  CUE            CUE domain
       0.12   12.1   1.4       0.19   11.5   1.4    1.4  1  PvlArgDC       Pyruvoyl-dependent arginine decarboxylase (Pvl


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.6   7.9e-13   2.4e-09       1      57 []       6      64 ..       6      64 .. 0.92
   2 ?   -2.2   0.2       1.4   4.2e+03      20      33 ..      69      81 ..      68      84 .. 0.70
   3 ?   -1.0   0.0      0.61   1.8e+03       1      11 [.      89      99 ..      89     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 7.9e-13
                           NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaeek 57
                                  +k+++   + lgl  +++ ++ +Vti+  d k+lv+dnP V    ++g++++ v+G+a+e+
  gi|70608063|ref|YP_256933.1|  6 PKQMKDLERMLGLktEQL-NAVKVTIELQD-KILVIDNPVVVkmLAQGQEVFSVMGSAREE 64
                                  79***********96666.9**********.***********777788**********996 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                           NAC 20 eeVtirksdgkvlv 33
                                  ++V i+ +d   ++
  gi|70608063|ref|YP_256933.1| 69 QKVEIKEED-VKFI 81
                                  578899888.5555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.61
                           NAC  1 ekKlrkalkkl 11
                                  ek++r+al k 
  gi|70608063|ref|YP_256933.1| 89 EKEAREALEKS 99
                                  8999***9985 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6     4e-06     0.012      67      94 ..      70     108 ..      45     115 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                      HOIP-UBA  67 e...........nevgklsraEakealleagGdvekAvk 94 
                                   +            e    s++Ea+eal +++Gd+ kA+ 
  gi|70608063|ref|YP_256933.1|  70 KveikeedvkfiMEQTGKSEKEAREALEKSNGDIAKAIL 108
                                   234555666666455556888888888888888888875 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.066      11      33 ..      85     107 ..      80     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                         UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                   TG +e +Ar+ Le +n+d+  Ai
  gi|70608063|ref|YP_256933.1|  85 TGKSEKEAREALEKSNGDIAKAI 107
                                   8889***************9998 PP

>> Pannexin_like  Pannexin-like TM region of LRRC8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   2.1e-05     0.064     201     253 ..      56     107 ..      17     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                 Pannexin_like 201 ssesssseesseeesallkkkssvkskaekkvvekkssvsvLdkkegeqAkal 253
                                   s+   s++e+s+++++   k+++vk+ +e++   +k++ ++L+k++g  Aka+
  gi|70608063|ref|YP_256933.1|  56 SV-MGSAREESKQQQKVEIKEEDVKFIMEQTGKSEKEAREALEKSNGDIAKAI 107
                                   33.34455555566666777889999999999999*****************8 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.94   2.8e+03      16      27 ..      74      85 ..      72      89 .. 0.69
   2 ?   11.7   0.0   5.5e-05      0.17      19      41 ..      91     113 ..      88     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.94
                                  -HHHHHHHHHHC CS
                           CUE 16 deevIravLras 27
                                   ee++++  +++
  gi|70608063|ref|YP_256933.1| 74 KEEDVKFIMEQT 85
                                  589999999554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.5e-05
                                   HHHHHHHHCTTTHHHHHHHHHHC CS
                           CUE  19 vIravLrasngnvEatinaLLeg 41 
                                     r +L+ sng++  +i aL eg
  gi|70608063|ref|YP_256933.1|  91 EAREALEKSNGDIAKAILALTEG 113
                                   56899****************98 PP

>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4   6.3e-05      0.19      31     128 ..      21     109 ..      18     116 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                      PvlArgDC  31 enfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrliaaavgvaipkdekkgGyiaEysgfgeseeea 111
                                   e++N vkv+  l  +  ++  + ++k l +G+ v+ vm++a+ + +++     v +     e+   +i+E +g  +se+ea
  gi|70608063|ref|YP_256933.1|  21 EQLNAVKVTIELQDKILVIDNPVVVKMLAQGQEVFSVMGSAREESKQQ---QKVEIK----EEDVKFIMEQTG--KSEKEA 92 
                                   566777777777777788999999***************999877775...334443....446789999999..678888 PP

                      PvlArgDC 112 eeeaeelaaemlattrg 128
                                   +e+ e+   ++ ++++ 
  gi|70608063|ref|YP_256933.1|  93 REALEKSNGDIAKAILA 109
                                   88888876666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1818  (0.1014); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 796.69
//
Query:       gi|70608064|ref|YP_256934.1|  [L=422]
Description: hypothetical protein Saci_2362 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-16   59.3   0.0    1.3e-15   57.6   0.0    1.9  2  Beta-Casp        Beta-Casp domain
    1.1e-14   54.1   0.1      2e-14   53.2   0.1    1.5  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    2.1e-10   40.3   0.0      3e-09   36.6   0.0    2.2  2  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    7.6e-09   35.4   0.0    1.6e-08   34.4   0.0    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
    7.6e-06   26.1   0.1    0.00027   21.0   0.1    2.6  2  Lactamase_B      Metallo-beta-lactamase superfamily
     0.0002   20.6   0.0    0.00039   19.6   0.0    1.4  1  PDEase_II        cAMP phosphodiesterases class-II
     0.0017   18.3   0.0     0.0032   17.4   0.0    1.4  1  Lactamase_B_3    Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.035   13.3   0.1      0.081   12.1   0.0    1.6  2  Beta_lactamase3  Putative beta-lactamase-like family
       0.13   12.6   0.1       0.25   11.6   0.1    1.5  1  DUF223           Domain of unknown function DUF223


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   3.8e+03      34      41 ..     122     129 ..      85     230 .. 0.65
   2 !   57.6   0.0   6.5e-19   1.3e-15       2     110 .]     233     342 ..     232     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                                   HHHHGGGG CS
                     Beta-Casp  34 atevYkey 41 
                                   ++++Y+e+
  gi|70608064|ref|YP_256934.1| 122 TVNYYQEF 129
                                   33344433 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 6.5e-19
                                   HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG........E-SHH.....HHHH..HHHS-SSEEEEES-T CS
                     Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae........veaks.lewmeskkeelnsskgpkvilassg 73 
                                   qe+l lL + +        ++p+y+d+ +++++te+  +++e        ++a++   +++  +++ +  kg   i++s g
  gi|70608064|ref|YP_256934.1| 233 QEILALLADKK-------FDYPVYYDG-MVKEITELMIQNPEfinnydalKRAHKfYRYVNGWNDRNKAIKGEGAIVSSAG 305
                                   55555555444.......458******.********888888999999885555555555544332245678899****** PP

                                   TSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  74 mlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                   ml+gG++++++kk++e prn v+lv+yqae+T+gr+l
  gi|70608064|ref|YP_256934.1| 306 MLKGGPAVYYFKKIAESPRNGVFLVSYQAENTPGRRL 342
                                   ***********************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.1     1e-17     2e-14       4      62 .]     355     414 ..     352     414 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1e-17
                         RMMBL   4 vkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                                   +kar + +dfS Ha+k++lle+i++ k+   vilvHG++ + sala+ +ke+ g+dv +P
  gi|70608064|ref|YP_256934.1| 355 LKARFQIFDFSSHAGKSQLLEMIKSSKKLEkVILVHGDPSSSSALANEIKEKIGVDVEVP 414
                                   7999999********************9999**************************998 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.5e-12     3e-09       6     168 ..      26     171 ..      21     187 .. 0.84
   2 ?    1.0   0.0      0.12   2.4e+02      24      64 ..     371     408 ..     361     414 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.5e-12
                 Lactamase_B_6   6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldl 86 
                                   +  i+lD G++  +   ++   +l+++ ++v   ++sh+ l+h+G+++ ly+     +  + pv++t+ ++ + +++l d 
  gi|70608064|ref|YP_256934.1|  26 DSAIILDYGVNFDQ--NDNPNLPLQETPNRVKGFVVSHSHLDHVGSLP-LYQ-----ISGSYPVFGTMMTKLITELMLKDF 98 
                                   56799*****9653..3456678999*******************986.332.....34578*************999999 PP

                 Lactamase_B_6  87 yaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhake 167
                                    + +g+  p+     e  ++++ +d+++t+ Y Q++e+ +      +   naGh +G ++ k+++  ++ivY  d n    
  gi|70608064|ref|YP_256934.1|  99 LKLSGARLPF-----EWMEVKRTMDNFRTVNYYQEFEIDT----FKVELGNAGHIPGSSMIKVKTDKHNIVYTGDTNVINT 170
                                   9988887666.....45699***************98875....667778***********************99997665 PP

                 Lactamase_B_6 168 s 168
                                   +
  gi|70608064|ref|YP_256934.1| 171 K 171
                                   5 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                 Lactamase_B_6  24 salkelekviptvdliLLshatlehlGayallyakfkskll 64 
                                   s+l e+ k  ++++ ++L h +++  +a+a   +++k+k++
  gi|70608064|ref|YP_256934.1| 371 SQLLEMIKSSKKLEKVILVHGDPSSSSALA---NEIKEKIG 408
                                   455667778899***************964...55555555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   7.8e-12   1.6e-08       3     168 ..      29     195 ..      28     217 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 7.8e-12
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...........HCCT CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla...........vlea 72 
                                   i++D g ++ q+ ++ l P  l ++++++++ +++h+H DH+ g l l ++++ ++p+++++++                a
  gi|70608064|ref|YP_256934.1|  29 IILDYGVNFDQNDNPNL-P--LQETPNRVKGFVVSHSHLDHV-GSLPLYQISG-SYPVFGTMMTKLitelmlkdflkLSGA 104
                                   67788888888888888.6..569999***************.8888888665.489999977766333433333322223 PP

                                   TCGHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..... CS
                 Lactamase_B_2  73 nfvylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip..... 147
                                   +++++++e++    n+++++  ++fe++   +++++  a h  g              +++++++++y+gDt+ i      
  gi|70608064|ref|YP_256934.1| 105 RLPFEWMEVKrTMDNFRTVNYYQEFEID--TFKVELGNAGHIPGS---------SMIKVKTDKHNIVYTGDTNVINtklvg 174
                                   4444444444444455555555555554..334444444444333.........4445559************99964444 PP

                                   HHHH..HHHCT-SEEEEE-S-SS CS
                 Lactamase_B_2 148 eeig..erlggadllllditaye 168
                                   +  +  + l +ad+l+++ t+ +
  gi|70608064|ref|YP_256934.1| 175 P--AdlNFLSDADVLVIESTYGK 195
                                   2..04479999999999988654 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.4e-07   0.00027      14     155 ..      25     169 ..      17     189 .. 0.73
   2 ?   -2.4   0.0       2.1   4.1e+03      97     124 ..     294     344 ..     271     346 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                   TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEET...CCEHHHHCCHCHHHHHHH CS
                   Lactamase_B  14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvg...avaeeapalfmeeaddaa 91 
                                   ++++i+ D G+  ++++       l   p++v+  +++H+HlDH+G l+       +pv+   + +++++ ++++ ++ + 
  gi|70608064|ref|YP_256934.1|  25 GDSAIILDYGVNFDQNDNPN--LPLQETPNRVKGFVVSHSHLDHVGSLPLYQISGSYPVFgtmMTKLITELMLKDFLKLSG 103
                                   67777777777777777774..6788999********************99977777766111445555555555555555 PP

                                   HHCCHH..TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                   Lactamase_B  92 srkgll..lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                    r + +      + d+  ++   ++++ +  +      g+ +g++ + v  +  ++++tGD+  ++
  gi|70608064|ref|YP_256934.1| 104 ARLPFEwmEVKRTMDNFRTVNYYQEFEIDTFKVELGNAGHIPGSSMIKVKTDKHNIVYTGDTNVIN 169
                                   555555875555566666666667777778888888899999999999999999999999987665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                                   H.......................TTCHCGCCEEEEETTTEECCCTEEEEE CS
                   Lactamase_B  97 l.......................lagvsadkpdvdeeeldgnaggrraly 124
                                   +                       ++++s+++ ++    +++n++grr+l+
  gi|70608064|ref|YP_256934.1| 294 IkgegaivssagmlkggpavyyfkKIAESPRNGVFLVSYQAENTPGRRLLE 344
                                   444444444444444555666666667788888888888888888888775 PP

>> PDEase_II  cAMP phosphodiesterases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     2e-07   0.00039      66      97 ..      39      70 ..      28      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                                  HHS-HHHHHHHHHHTEEEEE-S---GGGTHHH CS
                     PDEase_II 66 esereikktyeiknniksylItHsHLDHvsgl 97
                                  ++ ++ +  +e  n++k + ++HsHLDHv++l
  gi|70608064|ref|YP_256934.1| 39 QNDNPNLPLQETPNRVKGFVVSHSHLDHVGSL 70
                                  567888889999******************98 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-06    0.0032       6     133 ..      16     188 ..      15     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                 Lactamase_B_3   6 ghnsflletagarilvDPf.......kanlgyeppaeeaDlvlisqaledHahletlkql..................... 58 
                                   g +++ +++++  i++D++       ++nl +++ + ++   ++s+++ dH    +l q+                     
  gi|70608064|ref|YP_256934.1|  16 GRAAIEVSKGDSAIILDYGvnfdqndNPNLPLQETPNRVKGFVVSHSHLDHVGSLPLYQIsgsypvfgtmmtklitelmlk 96 
                                   66788888899********99988754488999999************************777777776666666666666 PP

                 Lactamase_B_3  59 ....................aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahels 119
                                                        +n+++++  +++e++     +++ +  +  g+ +g  ++  ++ d+++i++ G++    +
  gi|70608064|ref|YP_256934.1|  97 dflklsgarlpfewmevkrtMDNFRTVNYYQEFEID-----TFKVEL-GNAGHIPG-SSMIKVKTDKHNIVYTGDTNVINT 170
                                   666666666664444443333333333334444433.....333333.22344444.588889999*********998644 PP

                 Lactamase_B_3 120 s....eelkelgrvDvvl 133
                                   +    ++l+ l ++Dv++
  gi|70608064|ref|YP_256934.1| 171 KlvgpADLNFLSDADVLV 188
                                   311114556777777765 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05     0.081     120     175 ..     109     163 ..      80     185 .. 0.89
   2 ?   -3.4   0.0       2.3   4.6e+03      26      58 ..     348     380 ..     347     392 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
               Beta_lactamase3 120 eeidierlkrnvkfiryneliyfddltieakaagtflGWvnyllevekkkilayis 175
                                   e ++++r+  n + ++y + +++d++++e   ag   G ++ +++++k++ + y+ 
  gi|70608064|ref|YP_256934.1| 109 EWMEVKRTMDNFRTVNYYQEFEIDTFKVELGNAGHIPGSSMIKVKTDKHN-IVYTG 163
                                   56799*******************************************99.66664 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
               Beta_lactamase3  26 fdypseiygknfrlgtfekrkkklk.leiikvka 58 
                                   fd  s ++   f++ +f+++ +k + le+ik  +
  gi|70608064|ref|YP_256934.1| 348 FDEYSPMLKARFQIFDFSSHAGKSQlLEMIK-SS 380
                                   5556666666667777666654433134555.33 PP

>> DUF223  Domain of unknown function DUF223
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.25      30      91 ..     132     194 ..     111     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        DUF223  30 egewktissfvvrsnsesiritkheyrilFmeqTeVtssktretvlfnnltpFdy.Iveetvd 91 
                                      + +  ++++ + s  i++++ ++ i+++ +T+V ++k +    +n l ++d+ ++e t+ 
  gi|70608064|ref|YP_256934.1| 132 DTFKVELGNAGHIPGSSMIKVKTDKHNIVYTGDTNVINTKLVGPADLNFLSDADVlVIESTYG 194
                                   555666778899999***************************************945666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2815.30
//
Query:       gi|70608065|ref|YP_256935.1|  [L=387]
Description: threonyl-tRNA synthetase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-49  166.4   0.1    5.5e-49  165.7   0.1    1.4  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    1.3e-15   57.3   0.3    3.8e-15   55.8   0.3    1.8  1  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.1   6.2e-53   5.5e-49       1     137 []       1     134 [.       1     134 [. 0.99

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 6.2e-53
                                   -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE-ST CS
                   tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypyaH 81 
                                   m +Lliha++++++ k+ka++e+ee +  + + e++lv+F++vEk+D+e   k++e+avkei kv++ vka+++++ypyaH
  gi|70608065|ref|YP_256935.1|   1 MIILLIHASKFSFSIKDKAIREPEEPTIPSLEKENVLVAFTTVEKGDDE---KIIERAVKEIGKVFSDVKASSIIIYPYAH 78 
                                   89***********************************************...9**************************** PP

                                   S-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                   tRNA-Thr_ED  82 LssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                   Ls++l++p++a++il++lee+ k+ ++ev+raPFGwyk+f i+c+GhpL+els++i
  gi|70608065|ref|YP_256935.1|  79 LSDNLEKPDIAIKILRQLEEETKKVTMEVSRAPFGWYKQFYINCYGHPLSELSKRI 134
                                   ******************************************************87 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.3   4.3e-19   3.8e-15       1      92 [.     276     361 ..     276     362 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.3e-19
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   qv ++p+++   ++++ a k+a+ ++a    v++dd n+++g ki++a + +ipf+v +Ge+e+++g++t++ r++ eq++
  gi|70608065|ref|YP_256935.1| 276 QVRILPVKS---DYLQDAFKIASYIKAR---VDVDDINDNLGSKIARAGKEWIPFVVLLGEREVKTGSLTIKLREKNEQRS 350
                                   89*******...99*********99966...9************************************************* PP

                                   EETTHHHHHHH CS
                HGTP_anticodon  82 vsldelveklk 92 
                                    ++del e++k
  gi|70608065|ref|YP_256935.1| 351 YTIDELNEEIK 361
                                   *******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2476.15
//
Query:       gi|70608066|ref|YP_256936.1|  [L=590]
Description: glucosamine--fructose-6-phosphate aminotransferase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-48  162.5   1.4    1.1e-25   90.0   0.1    2.4  2  SIS       SIS domain
    1.5e-20   73.8   0.0    3.3e-20   72.7   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
    1.3e-17   63.8   0.0    3.6e-17   62.4   0.0    1.8  1  GATase_7  Glutamine amidotransferase domain
    2.7e-06   27.5   0.1      0.002   18.1   0.0    3.2  3  SIS_2     SIS domain
     0.0017   17.3   0.0     0.0032   16.4   0.0    1.4  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.1   3.1e-29   1.1e-25       3     128 ..     291     412 ..     289     415 .. 0.92
   2 !   71.4   0.1   1.7e-23     6e-20       1     129 [.     448     571 ..     448     573 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 3.1e-29
                                   CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE CS
                           SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergaki 83 
                                    ++ ri+v+GaGtsy+++++++l l +  g++++   ase  ++    +++ddl+++is+sget dl++a+++ ke ga+i
  gi|70608066|ref|YP_256936.1| 291 KSSGRIVVVGAGTSYHAGLYFSLLL-SREGMNSFPLIASE-YYN--FKAKKDDLIFAISQSGETLDLLQAVRKFKEEGARI 367
                                   6788*********************.77888888888888.444..6799******************************* PP

                                   EEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHH CS
                           SIS  84 iaITdskgsplareadlalyinaepetlvastksltaqlaaldal 128
                                   +++T+  +s+lare+ +++y++a+pe+ va+tk++ +ql++l ++
  gi|70608066|ref|YP_256936.1| 368 VSLTNVIESALARESNYKIYMRAGPEISVAATKTFITQLISLLFI 412
                                   ****************************************99876 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 1.7e-23
                                   HHCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTT CS
                           SIS   1 lLakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakerg 80 
                                   +L+k+ +iy+lG+G s ++a+e+alk++e++++++e+++a+e khg+++l+d++ ++++i   ge  dl++++  ++k+rg
  gi|70608066|ref|YP_256936.1| 448 ELSKKTSIYYLGRGMSLPLAMEGALKIKEVAYVHAEAYPAGESKHGPISLVDKGFPIVAIN-DGEITDLLRNNViEMKARG 527
                                   589999*******************************************************.5555555555555****** PP

                                   SEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                           SIS  81 akiiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                   ak  +I  +k+     e+d+ +y+ +      a+  s+++ql+a++a +
  gi|70608066|ref|YP_256936.1| 528 AKAYVISANKK---ISESDVEIYLDSIQFP--ALSISVVLQLIAYYASV 571
                                   ******95554...6678899999999999..9999*********9987 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.0   9.1e-24   3.3e-20      11     133 ..      67     195 ..      51     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 9.1e-24
                      GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllalleelG...... 85 
                                   ++ + l+H+R+a++g +++  a+P +  +g+++++hNG+i+nykelreel+   g+ f+s++Dte++ +l+ee+       
  gi|70608066|ref|YP_256936.1|  67 SGYIFLGHTRWATHGPPTDYNAHPHVDCSGKIAVIHNGTIKNYKELREELQT-LGHVFKSDTDTEIIPHLIEEFMkrgmda 146
                                   34499************77777******************************.******************5554333556 PP

                      GATase_6  86 ....eevlerlrGmfafaiwdkrentlila.rdrlgvkplyyavdesglafas 133
                                          +++l+G +a+ ++ + e+++++a rd     pl+++  e+  ++as
  gi|70608066|ref|YP_256936.1| 147 ysafRNSIKTLEGSYAVLAVIHGEKRIFFAkRD----NPLVIGLGEKENYIAS 195
                                   556666667*************99999999555....4777776666666666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0     1e-20   3.6e-17      12     122 ..      87     201 ..      74     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1e-20
                      GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAf.ai 82 
                                   +a P v + +g++++++nG+i NykelreeL++ gh f++++Dte++ +l+e+            ++ ++ l+G++A+ a+
  gi|70608066|ref|YP_256936.1|  87 NAHPHV-DCSGKIAVIHNGTIKNYKELREELQTLGHVFKSDTDTEIIPHLIEEfmkrgmdaySAFRNSIKTLEGSYAVlAV 166
                                   567888.5799************************************************9999999***********7356 PP

                      GATase_7  83 wdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                   ++ e++ +++ RD     PL +g  + ++ ++aS + a+l
  gi|70608066|ref|YP_256936.1| 167 IHGEKRIFFAKRD----NPLVIGLGE-KENYIASDIPAFL 201
                                   6788888889999....7*******6.799*****99986 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.11   4.1e+02      24      46 ..     282     304 ..     259     312 .. 0.75
   2 !   18.1   0.0   5.7e-07     0.002      98     137 ..     332     371 ..     313     372 .. 0.89
   3 ?    4.2   0.0     0.011        41      18      67 ..     435     484 ..     425     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHTT--EEEEESGGG CS
                         SIS_2  24 aaeliadslenggkvlvfGsGhS 46 
                                   +++ i + +++ g+++v G+G S
  gi|70608066|ref|YP_256936.1| 282 LIDKIIAEMKSSGRIVVVGAGTS 304
                                   467788889999*********98 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 5.7e-07
                                   HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                         SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                   ++++k+ D+++ iS+sG+   +++a++++ke g++++ lt
  gi|70608066|ref|YP_256936.1| 332 NFKAKKDDLIFAISQSGETLDLLQAVRKFKEEGARIVSLT 371
                                   4589**********************************99 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE- CS
                         SIS_2  18 aeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferia 67 
                                    +++e  a+li + l+++  ++ +G G S  la+e a ++  +a +++ a
  gi|70608066|ref|YP_256936.1| 435 ISSVEGYAKLIGEELSKKTSIYYLGRGMSLPLAMEGALKIKEVAYVHAEA 484
                                   67889999***************************999998888887755 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.9e-07    0.0032      68     160 ..      65     158 ..      31     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.9e-07
                      GATase_4  68 piksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpklegrfePvG.....sTDsElafCelleelas 143
                                   ++   +++ H R at+G  ++ n+hp v   +  ++   HnG++k+yk+ + ++ + +G     +TD+E  + +l+ee+ +
  gi|70608066|ref|YP_256936.1|  65 EMSGYIFLGHTRWATHGPPTDYNAHPHVDCSG--KIAVIHNGTIKNYKELR-EELQTLGhvfksDTDTEI-IPHLIEEFMK 141
                                   466778999*****************997544..45667*******99877.355555533333688885.5788888888 PP

                      GATase_4 144 rfekaepsaeelerala 160
                                   r  +a ++ ++  ++l+
  gi|70608066|ref|YP_256936.1| 142 RGMDAYSAFRNSIKTLE 158
                                   88776666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3896.21
//
Query:       gi|70608067|ref|YP_256937.1|  [L=314]
Description: mevalonate kinase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-11   41.9   0.2      3e-10   40.3   0.1    1.9  2  GHMP_kinases_C  GHMP kinases C terminal
    4.9e-09   36.3   1.2    6.6e-09   35.9   0.1    1.8  2  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.079   13.2   3.9        1.8    8.8   0.4    3.0  4  DUF2666         Protein of unknown function (DUF2666)


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   6.9e+03      28      43 ..      62      77 ..      59      86 .. 0.75
   2 !   40.3   0.1   5.1e-14     3e-10       4      79 ..     224     295 ..     221     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                GHMP_kinases_C 28 vvgilppeleelleal 43
                                  ++++++++++++l  +
  gi|70608067|ref|YP_256937.1| 62 EYKVENENVKRVLAYI 77
                                  6788999999998766 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 5.1e-14
                GHMP_kinases_C   4 alergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                   a+ ++d ++lgel++ ++   l+  +gi  p+++++++ ++ +G+ g k+sG GgG++v++   + ++ae ++ a+
  gi|70608067|ref|YP_256937.1| 224 AIAKNDEDELGELMYINHG--LLFSIGITVPVIDQIVSTARIAGVKGCKVSGGGGGGAVVCT--KSEQAEFLIKAM 295
                                   7889***************..8*******************************777777665..588888888777 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   1.1e-12   6.6e-09       2      66 .]      92     158 ..      91     158 .. 0.93
   2 ?   -2.3   0.1      0.92   5.5e+03      13      19 ..     273     279 ..     254     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-12
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDvaasvyGg 66 
                                   i i+s + ++ GLG SA ++v++v A   llg +l +e  ak++ e+e  +q g  s++D  + ++Gg
  gi|70608067|ref|YP_256937.1|  92 IDIESPVDPSVGLGTSAGVVVGMVSAYSTLLGHKLsREqiAKISHEIELRVQ-GLASIMDTHTETFGG 158
                                   7899***99*************************963369********9999.*********999998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.92
                                   SSCHHHH CS
                GHMP_kinases_N  13 GLGSSAA 19 
                                   G G+++A
  gi|70608067|ref|YP_256937.1| 273 GGGGGGA 279
                                   2233333 PP

>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.15   9.2e+02     101     128 ..      38      65 ..      28      67 .. 0.82
   2 ?    3.9   0.1    0.0098        58      24      42 ..      64      82 ..      54      96 .. 0.83
   3 ?   -2.1   0.0      0.69   4.1e+03      53      70 ..     149     166 ..     129     180 .. 0.60
   4 ?    8.8   0.4    0.0003       1.8      54     123 ..     184     253 ..     167     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                                   --HHHHHHHHHHHHHTTT--SS--HHHH CS
                       DUF2666 101 gkeilkvilarivLerlGiktkveskll 128
                                    ke ++ +++   Le  G+k++++  ++
  gi|70608067|ref|YP_256937.1|  38 IKESERFYVTSNTLELTGVKVDLHEYKV 65 
                                   5889999999999**99*9999876555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0098
                                  TS-HHHHHHHHHHHHHHHH CS
                       DUF2666 24 ktedleiarlLasieetvs 42
                                  k e+ ++ r+La i et++
  gi|70608067|ref|YP_256937.1| 64 KVENENVKRVLAYITETIN 82
                                  778999***********97 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.69
                                   HHHHHHHTTT--S--S.. CS
                       DUF2666  53 lekleeiadeikkkkkgr 70 
                                   ++  +e+++++  +kkg 
  gi|70608067|ref|YP_256937.1| 149 MDTHTETFGGFILVKKGG 166
                                   344456666776666654 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0003
                                   HHHHHHTTT--S--S....HHHHHHHHHHHHT-.............---HHHHHHHHHHHHHTTT--SS- CS
                       DUF2666  54 ekleeiadeikkkkkgrvkeedisevleklkspattkklnkitdskegkeilkvilarivLerlGiktkv 123
                                   +++  +ad +k++kk +    ++ e + ++ +  tt+  n+i +++e +  + +++++ +L  +Gi++ v
  gi|70608067|ref|YP_256937.1| 184 RRIATTADMLKRVKKLKESKPQLFESVLNVIEQVTTEAKNAIAKNDEDELGELMYINHGLLFSIGITVPV 253
                                   678999*********5555555655555555555888899***99999999999************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2013.15
//
Query:       gi|70608068|ref|YP_256938.1|  [L=356]
Description: hypothetical protein Saci_2366 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-16   59.6   0.4    9.6e-15   54.8   0.4    2.1  1  NTP_transferase  Nucleotidyl transferase
    2.1e-13   49.4   8.1    1.2e-06   28.0   2.1    4.8  5  Hexapep          Bacterial transferase hexapeptide (six repea
      1e-12   48.7   0.0    1.7e-12   48.0   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0026   16.8   3.5      0.021   13.8   3.3    2.2  1  Fucokinase       L-fucokinase
     0.0047   16.7   0.0     0.0071   16.2   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
     0.0063   16.3   6.8        4.6    7.1   0.2    3.9  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.039   13.1   2.7      0.071   12.3   0.2    2.1  2  CofC             Guanylyl transferase CofC like


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.4   3.8e-18   9.6e-15       2     196 ..       3     181 ..       2     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 3.8e-18
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a+ILaGG+G+ L P t +++k  + +lgk  ++ + +s l ++gi++ +vv+t++ + l+e++l++ +   v+ +++ +  
  gi|70608068|ref|YP_256938.1|   3 AIILAGGKGEGLLPYTERVQKETINILGK-MILSYSISGLKKAGINDFVVVTTDRGKKLIEDELEKLN---VSFEVINQ-H 78 
                                   8****************************.***********************************886...66777766.4 PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-.CTTSEEEEECTTS.BEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpvee.ateyGvieadeeg.rve 160
                                   ++g+ +A++ ++e  +d++    +++  gD++  +  y ++v+ +  ++++  +++ +vpv++  + yG++++  eg +v 
  gi|70608068|ref|YP_256938.1|  79 REGISGAIKDGLEKSDDDN----IVIAFGDIVAPEeFYVNLVNAFSVSGSE--IVIPLVPVSKgIQTYGLAKITTEGlEVV 153
                                   67*******9999999888....8999999999886789999999999995..44444444431578******96665775 PP

                                   EEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHH CS
               NTP_transferase 161 rfvEKPkeakaselassGiYvfnsevllflakdlee 196
                                   +        + s+la +G Y+ ++e ++  +++l++
  gi|70608068|ref|YP_256938.1| 154 K--------EGSTLALAGAYIIKNETFEDFIDYLNQ 181
                                   3........346777777777777777777665554 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.5     3e-05     0.077       2      35 ..     217     250 ..     216     251 .. 0.77
   2 !   28.0   2.1   4.7e-10   1.2e-06       2      35 ..     235     268 ..     228     269 .. 0.77
   3 !   22.4   0.0   2.7e-08   6.9e-05       2      34 ..     253     285 ..     252     289 .. 0.93
   4 !   14.0   0.1   1.2e-05     0.031       3      27 ..     289     318 ..     287     321 .. 0.63
   5 ?   -1.4   0.0      0.88   2.3e+03      12      22 ..     346     356 .]     337     356 .] 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   tvI s + I + a+ig  V+I +n++I  ++v++
  gi|70608068|ref|YP_256938.1| 217 TVISSSSEISKTAIIGKKVIIDNNAVIDDYAVVK 250
                                   6777888888888888888888888888888876 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 4.7e-10
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                   ++I +n++I+ +av+ g++ IG+n++Ig+++ ++
  gi|70608068|ref|YP_256938.1| 235 VIIDNNAVIDDYAVVKGPAYIGENAYIGNFSLVR 268
                                   34555555555*******************9986 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 2.7e-08
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                       Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                   + IG+n++Ig+f+ +++   + +++k+ga++ i
  gi|70608068|ref|YP_256938.1| 253 AYIGENAYIGNFSLVRDYSSVERGAKVGAYCEI 285
                                   78***************************9998 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   EEETTEEE-T.....TEEEETTEEE-TTEE CS
                       Hexapep   3 vIGsnvlIgp.....faviggnVkIGdnvk 27 
                                    I  ++ Ig+     +++ig+n kIG+nv+
  gi|70608068|ref|YP_256938.1| 289 SIQPGAEIGSksyltYSIIGSNSKIGSNVI 318
                                   677788888844444666666666666665 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.88
                                   TTEEEETTEEE CS
                       Hexapep  12 pfaviggnVkI 22 
                                   +++++++++kI
  gi|70608068|ref|YP_256938.1| 346 HGSILRPGTKI 356
                                   45666666665 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   6.5e-16   1.7e-12       1     122 [.       3     130 ..       3     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 6.5e-16
                                   EEEEEESS-TTT....TT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTSS-SHH CS
                  NTP_transf_3   1 aviLAGGrSsRm....gg.dKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededpgkgpl 73 
                                   a+iLAGG++  +     +  K  +++ gk +l +++  l++ag+++ vvv+ d   + ++++l++l+v++ +  ++ +g++
  gi|70608068|ref|YP_256938.1|   3 AIILAGGKGEGLlpytERvQKETINILGKMILSYSISGLKKAGINDFVVVTTDrgkKLIEDELEKLNVSFEVINQHREGIS 83 
                                   79********996654347*******************************988555589**********95555689**** PP

                                   HHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEE CS
                  NTP_transf_3  74 aslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpt 122
                                   ++++ +l+++ d+d ++++ +D++  ++e++  l++a+  sg+++v+p 
  gi|70608068|ref|YP_256938.1|  84 GAIKDGLEKS-DDDNIVIAFGDIVA-PEEFYVNLVNAFSVSGSEIVIPL 130
                                   ********98.9***********87.99*****************9986 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.3   8.1e-06     0.021     271     312 ..     280     321 ..     170     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.1e-06
                    Fucokinase 271 kesavvinSvlessvsvgegsviehsslkgnvsigsnsivsg 312
                                    + + +++S +++++++g +s++ +s +++n +igsn i s+
  gi|70608068|ref|YP_256938.1| 280 GAYCEIVHSSIQPGAEIGSKSYLTYSIIGSNSKIGSNVIMSS 321
                                   567889999999999999999999999999999999999986 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.8e-06    0.0071      44     120 ..      59     135 ..      38     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                                   HHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEE CS
               Glycos_transf_2  44 eileelak.edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprif 120
                                   +++e+  +  +  + vi + +  G +ga+  gl++++ d i++   D + ++++   lv+a+   g  +v++ +p+++
  gi|70608068|ref|YP_256938.1|  59 KLIEDELEkLNVSFEVINQHRE-GISGAIKDGLEKSDDDNIVIAFGDIVAPEEFYVNLVNAFSVSGSEIVIPLVPVSK 135
                                   4444433336888999999966.****************999999************************999888776 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.2    0.0018       4.6      18      33 ..     229     244 ..     218     245 .. 0.82
   2 !    4.9   0.1    0.0087        22       1      16 [.     252     267 ..     252     286 .. 0.70
   3 !    5.3   0.9    0.0063        16      19      31 ..     306     318 ..     271     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                                   EEE-TT-EE-TT-EE- CS
                     Hexapep_2  18 vslGdncvvgaGvvit 33 
                                    ++G++++++++ vi+
  gi|70608068|ref|YP_256938.1| 229 AIIGKKVIIDNNAVID 244
                                   589***********97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0087
                                   .EEE-TT-EE-TT-EE CS
                     Hexapep_2   1 pviIGdnCliGanagi 16 
                                   p  IG+n  iG ++ +
  gi|70608068|ref|YP_256938.1| 252 PAYIGENAYIGNFSLV 267
                                   6789999999998876 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0063
                                   EE-TT-EE-TT-E CS
                     Hexapep_2  19 slGdncvvgaGvv 31 
                                   ++G n+++g++v+
  gi|70608068|ref|YP_256938.1| 306 IIGSNSKIGSNVI 318
                                   4666666666664 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.8e-05     0.071      40      99 ..      40     106 ..      20     144 .. 0.72
   2 ?    0.6   0.2       0.1   2.6e+02      36      78 ..     203     242 ..     200     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                          CofC  40 alkr...ldvlvvsed..eevleyaldelgv..evvkekekdlntavekafeeieekeviiipsdiP 99 
                                    lk+    d +vv+ d  ++++e +l++l+v  ev++++ +++ +a++  +e+ ++++++i   di 
  gi|70608068|ref|YP_256938.1|  40 GLKKagiNDFVVVTTDrgKKLIEDELEKLNVsfEVINQHREGISGAIKDGLEKSDDDNIVIAFGDIV 106
                                   34332423556665442389999999988764489*****************************995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                          CofC  36 dvidalkrldvlvvsedeevleyaldelgvevvkek.ekdlnta 78 
                                   d+i+al+     ++s+ e v+ +  +  +  ++ +k   d n+ 
  gi|70608068|ref|YP_256938.1| 203 DIIGALEA----LLSKHETVISSSSEISKTAIIGKKvIIDNNAV 242
                                   99999999....89999999999999999999988844444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2491.64
//
Query:       gi|70608069|ref|YP_256939.1|  [L=115]
Description: hypothetical protein Saci_2367 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 810.76
//
Query:       gi|70608070|ref|YP_256940.1|  [L=259]
Description: hypothetical protein Saci_2368 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.082   12.8   1.0       0.23   11.3   1.0    1.8  1  T6PP_N    Trehalose-6-phosphate phosphatase N-terminal helica


Domain annotation for each model (and alignments):
>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.0   1.3e-05      0.23      54      90 ..     139     175 ..      82     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                        T6PP_N  54 vlelrtteeekvrldikdEieeLekDlkFLefiqsde 90 
                                   +++l  +++++++ldikd +e++  D +F+e+++s++
  gi|70608070|ref|YP_256940.1| 139 IIDLVDKRKAEISLDIKDILEDIAYDSEFMEKLKSSK 175
                                   4444445899**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1686.91
//
Query:       gi|70608071|ref|YP_256941.1|  [L=354]
Description: aspartate-semialdehyde dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-31  107.6   0.0    5.2e-30  104.4   0.0    2.4  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    1.4e-22   80.7   0.1      2e-22   80.1   0.1    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
      0.054   13.1   0.1       0.33   10.5   0.1    2.1  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   8.8e-34   5.2e-30       1     119 [.       6     129 ..       6     131 .. 0.98
   2 ?    0.4   0.0      0.14   8.4e+02      63      67 ..     207     211 ..     159     244 .. 0.48

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 8.8e-34
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEEE-SC CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivflalp 75 
                                   k+ai+G tG vG e +r+L++hp++++++l+++ +  Gk++ e+v+      +++e+++++++++d++ +++vd+vf+ lp
  gi|70608071|ref|YP_256941.1|   6 KAAILGSTGLVGIEYVRMLANHPYIKVAYLAGKGS-VGKPYGEVVRwqtigqIPKEVANMEIKPTDPKLMDDVDLVFSPLP 85 
                                   689**************************999998.********************************************* PP

                                   HHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                   ag++ ++++++a++g+kvi+ s+d+R+++d+++ +pe+n+++i 
  gi|70608071|ref|YP_256941.1|  86 AGAAGPVEEEFAKHGFKVISDSPDHRFEPDIPLLIPEINPHTIT 129
                                   *****************************************985 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                   GCTT- CS
                Semialdhyde_dh  63 elkev 67 
                                    +kev
  gi|70608071|ref|YP_256941.1| 207 LIKEV 211
                                   22222 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.1   3.4e-26     2e-22       1     183 [.     159     333 ..     159     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 3.4e-26
                                   HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
               Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                   L+P++++ +++++v ++t+qavSG G+                    pgv +++i +N+  +  +  d+    ++e  + +
  gi|70608071|ref|YP_256941.1| 159 LAPIYQN-FKVDSVFITTMQAVSGEGY--------------------PGVASLDIIDNIKVLGEN-YDNK--LIKEVHRVL 215
                                   89****6.*******************....................9*****************.5566..6******** PP

                                   HHHHHHCTESC.SEE..EEEEEESBSSEEEEEEEEEES..SSHHHHHHHHHHHHCS.........TTEEEEESSHCHHSSH CS
               Semialdhyde_dhC  82 aetkkilefte.kvs..atcvrVPvlrGhseavtiklk..lkdveveeveellaaa.........pevkvvvneeedrPtp 148
                                    etk  ++++  +v+  at +rV+ + Gh e +++ +k  ++ ++v+e++++++ +         p++ ++  +e  rP+ 
  gi|70608071|ref|YP_256941.1| 216 SETKRNVNDSGnDVTlsATTHRVATIHGHYEIIYVTFKedVNVEKVREAMDNFKGEpqnlklptaPSKPIILTNEDSRPQV 296
                                   **********9877677********************9776677777777777777*********9999999999****** PP

                                   HHHTTC....SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
               Semialdhyde_dhC 149 aavagg....tnsvsVGRirkdemgdeglklvvvgDNll 183
                                     ++      ++sv VGR+ + +++   + + ++++N++
  gi|70608071|ref|YP_256941.1| 297 YFDRWAgeipGMSVVVGRLSQVNRRA--IRFASLIHNTV 333
                                   9988547799*************877..*********98 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.14   8.5e+02       7      26 ..     161     180 ..     156     183 .. 0.84
   2 ?   10.5   0.1   5.5e-05      0.33      70     109 ..     229     268 ..     206     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                   HHHHHHEEEEEEEEEEEECT CS
                       Gp_dh_C   7 vlndkfgikkglmttvhayt 26 
                                    + ++f+++++++tt  a+ 
  gi|70608071|ref|YP_256941.1| 161 PIYQNFKVDSVFITTMQAVS 180
                                   6889***********99875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.5e-05
                                   TTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHH CS
                       Gp_dh_C  70 gkldglAvrVPtpnvsvvdlvvelekevtveevnaalkea 109
                                   + l+++  rV t+ ++   + v+++++v+ve v +a+++ 
  gi|70608071|ref|YP_256941.1| 229 VTLSATTHRVATIHGHYEIIYVTFKEDVNVEKVREAMDNF 268
                                   46889999****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2388.47
//
Query:       gi|70608072|ref|YP_256942.1|  [L=245]
Description: hypothetical protein Saci_2371 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-18   65.9   0.0    8.6e-18   64.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    6.2e-15   55.6   0.0    3.5e-14   53.2   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
    1.2e-12   47.8   0.0    1.7e-12   47.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.6e-11   44.3   0.0    2.3e-11   43.8   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    3.5e-10   40.5   0.0    6.5e-10   39.6   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    2.9e-09   36.6   0.0    4.9e-09   35.9   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.6e-06   27.7   0.1    2.6e-06   27.0   0.1    1.3  1  TehB             Tellurite resistance protein TehB
      2e-05   24.2   0.3     0.0092   15.5   0.1    2.4  2  CheR             CheR methyltransferase, SAM binding domain
    7.7e-05   22.3   0.0    0.00013   21.6   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00018   21.2   0.0    0.00032   20.4   0.0    1.4  1  NodS             Nodulation protein S (NodS)
    0.00026   20.8   0.0       0.14   11.8   0.0    2.4  2  N6_N4_Mtase      DNA methylase
    0.00092   18.6   0.0     0.0016   17.8   0.0    1.4  2  CMAS             Mycolic acid cyclopropane synthetase
     0.0025   17.8   0.0     0.0037   17.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0041   16.4   0.0      0.076   12.2   0.0    2.5  2  N2227            N2227-like protein
     0.0047   16.5   0.1     0.0071   15.9   0.1    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.017   14.8   0.1    1.3  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
      0.027   14.3   0.0        0.7    9.7   0.0    2.3  2  DUF268           Caenorhabditis protein of unknown function, 
      0.036   14.3   0.1        0.1   12.9   0.0    1.7  2  TrkA_N           TrkA-N domain
      0.066   13.1   0.0       0.14   12.1   0.0    1.5  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   9.1e-21   8.6e-18       1      97 []      46     138 ..      46     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 9.1e-21
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEEST.GGGSSH CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssga.lhhlsd 79 
                                   +Ld+ cG Gr++ +l k    ++v g+Dise+m+++a+er++    + +f++gd+++l+ +  ++fD+++ +++ l ++++
  gi|70608072|ref|YP_256942.1|  46 ILDVPCGIGRVSYYLTKLN--YNVSGIDISEKMINTAKERVK----KGNFIKGDMRHLStLIRDKFDIILNIFNsLGYYEE 120
                                   8***************994..********************5....679*********845788********999****** PP

                                   HHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                   ed  ++l+e++ vLk+gG
  gi|70608072|ref|YP_256942.1| 121 EDDLRILNEFRAVLKQGG 138
                                   *****************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   3.8e-17   3.5e-14       1      96 []      47     142 ..      47     142 .. 0.92
   2 ?   -0.3   0.0       1.8   1.7e+03      80      93 ..     204     217 ..     195     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.8e-17
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES.-CCC-..CCH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvsse.vlhhv..edp 77 
                                   Ldv cG Gr++ +l+k  ++v g+D+s++m+++ake++++ +    f+++d+++l  +  ++fD+++  + +l +   ed 
  gi|70608072|ref|YP_256942.1|  47 LDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKERVKKGN----FIKGDMRHLsTLIRDKFDIILNIFnSLGYYeeEDD 123
                                   899************999********************9987....7*******9779999*****98775666668899* PP

                                   HHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  78 ekalkeiaRvLkpgGllvi 96 
                                    ++l+e++ vLk+gGll++
  gi|70608072|ref|YP_256942.1| 124 LRILNEFRAVLKQGGLLIV 142
                                   ****************996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                                   HHHHHHHHEEEEEE CS
               Methyltransf_11  80 alkeiaRvLkpgGl 93 
                                    l ei+R+L + G+
  gi|70608072|ref|YP_256942.1| 204 SLHEIVRLLTKSGF 217
                                   589******99996 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   1.8e-15   1.7e-12       5     113 ..      44     146 ..      41     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.8e-15
               Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils.nevl 84 
                                    ++lD+ CG G+ ++ l  +l  + +v GiDise++i+ A+e+ +       +F +gd+ +l++l+  +kfD+il  ++ l
  gi|70608072|ref|YP_256942.1|  44 RNILDVPCGIGRVSYYLT-KL--NYNVSGIDISEKMINTAKERVK-----KGNFIKGDMRHLSTLIR-DKFDIILNiFNSL 115
                                   589***************.55..46799**************966.....55667********8666.8****76514666 PP

               Methyltransf_31  85 ..naladpdkileeiervlkpggilliedpr 113
                                     +   d   il+e   vlk+gg l+++  +
  gi|70608072|ref|YP_256942.1| 116 gyYEEEDDLRILNEFRAVLKQGGLLIVNLEN 146
                                   88999*********************99777 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   2.5e-14   2.3e-11       7     164 ..      26     221 ..      20     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2.5e-14
               Methyltransf_23   7 eelsdklerllpk.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqg.. 81 
                                   e++++ ++++++k +    ++Ld+ cG G+++ +l +  ++v g+D+s+++++ a+   k     k +f         g  
  gi|70608072|ref|YP_256942.1|  26 EKWAKWIDEVVKKyKIDARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKervK-----KGNFIK-------Gdm 94 
                                   7899999999976589999**********************************9854432.....333311.......123 PP

               Methyltransf_23  82 .........kfdlIvlr.evlehvp..dppellrqiatllkpgGylllseplasl.......................... 124
                                            kfd+I ++ ++l+  +  d  + l+ +++ lk gG+l++   +++                           
  gi|70608072|ref|YP_256942.1|  95 rhlstlirdKFDIILNIfNSLGYYEeeDDLRILNEFRAVLKQGGLLIVNLENRDYaiynkpevvhsyvppyviidkndfdp 175
                                   344446666*****9862578888766789*********************99999************************* PP

               Methyltransf_23 125 .....kedrllldwlylvpagrhi.sffsarslkelleeaGlevve 164
                                        k +r++l+ + + ++ + + +++s +++ +ll ++G+e++e
  gi|70608072|ref|YP_256942.1| 176 fssrlKVTRSYLKDGKEIERITFSqRLYSLHEIVRLLTKSGFEILE 221
                                   9999889999999888877777779*******************97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   6.9e-13   6.5e-10       1      99 []      47     140 ..      47     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 6.9e-13
               Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv.asnvlhhl. 79 
                                   L++ cG G+++ +l +   + ++ g+Dis+++i+ ake+ +k +     +++ + ++l+ l   ++fD+++ ++n l +  
  gi|70608072|ref|YP_256942.1|  47 LDVPCGIGRVSYYLTKL--NYNVSGIDISEKMINTAKERVKKGN-----FIKGDMRHLSTLIR-DKFDIILnIFNSLGYYe 119
                                   89***************..**************99999988877.....55555555444333.4******666******9 PP

               Methyltransf_12  80 .kdirevldnirklLkpgGrl 99 
                                    +d  ++l+++r++Lk+gG l
  gi|70608072|ref|YP_256942.1| 120 eEDDLRILNEFRAVLKQGGLL 140
                                   88888**************86 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   5.2e-12   4.9e-09      32     151 ..      25     142 ..       7     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.2e-12
                                   HHHHHHHHHHH--S-..-TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT- CS
               Ubie_methyltran  32 hrlWkkfveklvavk..rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeL 110
                                    ++W k + ++v +    ++++lDv +G g +++ l++    +++v ++Di+e+m++++++++k+       f++++  +L
  gi|70608072|ref|YP_256942.1|  25 GEKWAKWIDEVVKKYkiDARNILDVPCGIGRVSYYLTKL---NYNVSGIDISEKMINTAKERVKKGN-----FIKGDMRHL 97 
                                   46788877777665411466****************986...689******************9986.....566666666 PP

                                   TT.S-T-EEEEE.E..ES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
               Ubie_methyltran 111 pf.eddsfDvvt.v..sfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                        d fD++  +  s G     D l+ L+e + vlk GG l+v
  gi|70608072|ref|YP_256942.1|  98 STlIRDKFDIILnIfnSLGYYEEEDDLRILNEFRAVLKQGGLLIV 142
                                   54156888886422338899*********************8865 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   2.7e-09   2.6e-06      27     129 ..      40     139 ..      23     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.7e-09
                                   CCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEES.SGG CS
                          TehB  27 kivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstv.vlm 106
                                   k ++   +ld+ cg gr s yl+ l y+v+ +d  e+ i+  +e  +k n+   +  + ++ +  + +++d+il     l 
  gi|70608072|ref|YP_256942.1|  40 K-IDARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKERVKKGNFI--KGDMRHLST-LIRDKFDIILNIFnSLG 116
                                   4.466789*********************************99999999875..777777755.58899999998762466 PP

                                   GS-GGGHHHHHHHHHHTEEEEEE CS
                          TehB 107 fleaeripsiienmqectkvggy 129
                                   + e+e   +i+++++   k gg 
  gi|70608072|ref|YP_256942.1| 117 YYEEEDDLRILNEFRAVLKQGGL 139
                                   78888888888888888888884 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0036       3.4      61      84 ..      61      84 ..      26      99 .. 0.82
   2 !   15.5   0.1   9.8e-06    0.0092     126     173 ..      93     142 ..      84     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                                  SSS-EEEEEEESSCHHHHHHHHTE CS
                          CheR 61 aklkvkilAtDidlkvlekAkagv 84
                                   kl++++ ++Di++k++++Ak+ v
  gi|70608072|ref|YP_256942.1| 61 TKLNYNVSGIDISEKMINTAKERV 84
                                  456799**************9865 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.8e-06
                                   -TTT.-SGGG--EEEEE.E-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
                          CheR 126 nlle.kksvlgklDvif.crnvliYfdeetqekvlerfaeklkpgglLll 173
                                   ++ + +  + +k+D+i+   n l Y +ee+  ++l++f+  lk+gglL++
  gi|70608072|ref|YP_256942.1|  93 DMRHlSTLIRDKFDIILnIFNSLGYYEEEDDLRILNEFRAVLKQGGLLIV 142
                                   555656677899***98357****************************97 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00013      31     137 ..      42     142 ..      32     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---STTT CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPfhag 110
                                    ++++lD+ cG+G ++  l k + +  v  +d++ + ++ ake +++ ++  +++++   l+++  +kfd+i+    f + 
  gi|70608072|ref|YP_256942.1|  42 DARNILDVPCGIGRVSYYLTKLNYN--VSGIDISEKMINTAKERVKKGNFIkGDMRH---LSTLIRDKFDIILN--IFNSL 115
                                   5789*****************9988..9***************99987652244444...34444588998875..36666 PP

                                   CHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                           MTS 111 katelavaeeliaeAkeaLkegGeLli 137
                                      e++   ++++e +++Lk+gG L++
  gi|70608072|ref|YP_256942.1| 116 GYYEEEDDLRILNEFRAVLKQGGLLIV 142
                                   667777778888888888888876554 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.4e-07   0.00032      43     141 ..      42     139 ..      25     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.4e-07
                          NodS  43 siadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfst..dekfdliv.vaevlyyie 120
                                   ++ ++l+v c  G ++  l+ +  +++ +d+ e+ i+ a+ervk+    ++i+ d++++st   +kfd+i+ + + l y e
  gi|70608072|ref|YP_256942.1|  42 DARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKERVKK---GNFIKGDMRHLSTliRDKFDIILnIFNSLGYYE 119
                                   56799***************************************9...578889999999755799***974567787778 PP

                          NodS 121 dvaelraavrnlvsllapdgq 141
                                   +  +lr  ++++  +l+ +g 
  gi|70608072|ref|YP_256942.1| 120 EEDDLRI-LNEFRAVLKQGGL 139
                                   8777773.4555555555555 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00015      0.14     180     231 .]      31      82 ..       4      82 .. 0.91
   2 !    6.8   0.0    0.0053         5      37     114 ..     125     218 ..     119     240 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                   N6_N4_Mtase 180 llerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelaek 231
                                    + +++k +  +  ++lD  +G G    +  +l+ +  Gi+i+e+ +++a++
  gi|70608072|ref|YP_256942.1|  31 WIDEVVKKYKIDARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKE 82 
                                   567788888899999********************************99986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0053
                                   HHHHHHHHHEEEEEEEEEEE-CCCHHT............HHHHHHHHHTT-EEEEEEEEEEES........SSTTTSTCCS CS
                   N6_N4_Mtase  37 kvlkevrrvLkddgsifiniddseikk............elkaladeifggffllnvivwkkp........nsmpesnkdr 97 
                                   ++l+e r vLk++g +++n   + ++             + +++ +++f+ f  +  ++   +        + ++ s+  r
  gi|70608072|ref|YP_256942.1| 125 RILNEFRAVLKQGGLLIVNLENRDYAIynkpevvhsyvpPYVIIDKNDFDPFSSRLKVTR--SylkdgkeiERITFSQ--R 201
                                   5799***************98888776666666666665333333333331211111111..1112233322333333..6 PP

                                   -B--EEEEEEEESSTT- CS
                   N6_N4_Mtase  98 ltsthEyilvfsknkky 114
                                   l s hE + +++k++ +
  gi|70608072|ref|YP_256942.1| 202 LYSLHEIVRLLTKSGFE 218
                                   77777777777777665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.7e-06    0.0016      52     164 ..      33     142 ..      25     167 .. 0.74
   2 ?   -3.4   0.0         5   4.8e+03     194     215 ..     201     222 ..     184     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-06
                                   HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEE CS
                          CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvv 132
                                   d +++k ++++  ++Ld+ cG G +  +  +  + +v g+ +S++  ++ak+rv++ ++ +    +l+    +++k+d + 
  gi|70608072|ref|YP_256942.1|  33 DEVVKKYKIDA-RNILDVPCGIGRVSYYLTKL-NYNVSGIDISEKMINTAKERVKKGNFIKGDMRHLST--LIRDKFDIIL 109
                                   66667777764.689*********99887666.9*********************98876554444443..3667888775 PP

                                   EES-GGGTSG...GGHHHHHHHHHHHS-TT-EEEE CS
                          CMAS 133 svgafehvgk...enydtffkklkkllkedGllll 164
                                      +f+ +g+   e   +  +++  +lk++Gll++
  gi|70608072|ref|YP_256942.1| 110 N--IFNSLGYyeeEDDLRILNEFRAVLKQGGLLIV 142
                                   4..45555541113444567777778888887765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5
                                   ---BHHHHHHHHHHTT-EEEEE CS
                          CMAS 194 elpsieeieeeiseagftvvdv 215
                                   +l s++ei++  ++ gf++++v
  gi|70608072|ref|YP_256942.1| 201 RLYSLHEIVRLLTKSGFEILEV 222
                                   5777888888888888888775 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.9e-06    0.0037       7      82 ..      26      94 ..      21     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
               Methyltransf_32  7 erlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrl 82
                                  e+ a+ +++++k++  + +a +++Dv +G g  s  l      ++++v gid++e+++++a++r +k +  ++ ++
  gi|70608072|ref|YP_256942.1| 26 EKWAKWIDEVVKKY--KIDARNILDVPCGIGRVSYYLTK----LNYNVSGIDISEKMINTAKERVKKGN-FIKGDM 94
                                  67899999999995..88899**********99999999....79******************999866.444455 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   8.1e-05     0.076      58      92 ..      43      77 ..      22      82 .. 0.76
   2 ?    1.6   0.0      0.13   1.2e+02     230     266 ..     167     203 ..      92     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.1e-05
                                  T-EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                         N2227 58 kvkilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                    +il   +G+Gr+++ l++++y+v+g+++s  m+
  gi|70608072|ref|YP_256942.1| 43 ARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMI 77
                                  34566555***********************9886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                                   HHHHS-EEEEEEEEEEEE-SS-STT--S---EEEEEE CS
                         N2227 230 lakkvgfkvlkeekeiesgYltnkesmlqlkYklvff 266
                                   +++k +f   +++ ++   Yl++ +++   +++   +
  gi|70608072|ref|YP_256942.1| 167 IIDKNDFDPFSSRLKVTRSYLKDGKEIERITFSQRLY 203
                                   4555555555555555555555555555544444443 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.5e-06    0.0071      53     160 ..      40     143 ..      26     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-06
               Methyltransf_PK  53 krevkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPe.egrYdliWiqW.c 131
                                   k + + +ld+ +GiGrv+   L+kl  +v  ++  ek++++ake++     k g+++   +++ +   ++++d+i + +  
  gi|70608072|ref|YP_256942.1|  40 KIDARNILDVPCGIGRVSY-YLTKLNYNVSGIDISEKMINTAKERV-----KKGNFIKGDMRHLSTLiRDKFDIILNIFnS 114
                                   5567789**********96.68999999**************9555.....55999999999987765899**99876527 PP

               Methyltransf_PK 132 vghLtDedlvaflkrckkalkpnGlivvk 160
                                   +g   +ed +  l+     lk++Gl++v 
  gi|70608072|ref|YP_256942.1| 115 LGYYEEEDDLRILNEFRAVLKQGGLLIVN 143
                                   899999999***************99885 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.8e-05     0.017       7      65 ..      27      93 ..      26     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                                  TTHHHHHCCS-....--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH......S CS
               MethyltransfD12  7 kllpeIkelipkd..kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn......n 65
                                  k +++I e+++k   +++ + ++ +G g V++++ k +++v   Di e+ in +k  +k+      +
  gi|70608072|ref|YP_256942.1| 27 KWAKWIDEVVKKYkiDARNILDVPCGIGRVSYYLTKLNYNVSGIDISEKMINTAKERVKKgnfikgD 93
                                  6689*******999*****************************************988874433331 PP

>> DUF268  Caenorhabditis protein of unknown function, DUF268
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00074       0.7      88     119 ..     122     152 ..     108     165 .. 0.82
   2 ?    2.1   0.0      0.16   1.5e+02     122     157 ..     200     237 ..     192     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00074
                        DUF268  88 GdlrellkikCvlkkGgllflglPlGtdaiqy 119
                                    dlr l   + vlk+Ggll ++l    d  +y
  gi|70608072|ref|YP_256942.1| 122 DDLRILNEFRAVLKQGGLLIVNLENR-DYAIY 152
                                   69******************998653.44444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                        DUF268 122 hriyGsirlamll..aGfewlatfsgesekpieltskr 157
                                   +r+y    +  ll  +Gfe+l+  sg s k++e+t  +
  gi|70608072|ref|YP_256942.1| 200 QRLYSLHEIVRLLtkSGFEILEVLSGYSWKRFEVTDPQ 237
                                   5666654444443227**************99998766 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011       0.1       4      56 ..      51     101 ..      51     111 .. 0.82
   2 ?   -2.8   0.0       7.8   7.4e+03      22      30 ..     163     171 ..     140     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   ES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT..SEEEES-TTSHHHHH CS
                        TrkA_N   4 iGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg..levvvgdatdeevLe 56 
                                   +G Grv +     L++ ++ +v++id +e+ +++++e+    ++++gd  + ++L 
  gi|70608072|ref|YP_256942.1|  51 CGIGRVSYY----LTKlNY-NVSGIDISEKMINTAKERVkkGNFIKGDMRHLSTLI 101
                                   566666555....555577.5**************99997788*******999985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.8
                                   EEEEEEESS CS
                        TrkA_N  22 kdvvvidkd 30 
                                   +++v+idk+
  gi|70608072|ref|YP_256942.1| 163 PPYVIIDKN 171
                                   568899887 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.14      15      63 ..      43      89 ..      30     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
               Methyltransf_18 15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagl 63
                                   ++++D+ +  g +++yl+k +   +v  +Di+e+ +++ake ++k ++
  gi|70608072|ref|YP_256942.1| 43 ARNILDVPCGIGRVSYYLTKLNY--NVSGIDISEKMINTAKERVKKGNF 89
                                  4589**************97665..59999***************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1655.03
//
Query:       gi|70608073|ref|YP_256943.1|  [L=308]
Description: ornithine cyclodeaminase/mu-crystallin [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-42  145.1   0.2    2.7e-42  144.8   0.2    1.1  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    6.1e-05   23.1   0.0    0.00011   22.3   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0043   16.4   0.0     0.0079   15.6   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.24   11.2   0.0    1.4  1  Ssl1             Ssl1-like


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.2   6.1e-46   2.7e-42       5     317 ..       3     301 ..       1     302 [. 0.90

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 6.1e-46
                                   EE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSE CS
               OCD_Mu_crystall   5 vltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptv 85 
                                   vl + ++ee+l  + +++av+eaf  ++s +v +p r +l vk       +mp+y     +l+vK+vn+ p+nk++ +p+v
  gi|70608073|ref|YP_256943.1|   3 VLNKTQLEEILDAETAVNAVKEAFSLYSSRRVVQPQRQVLSVKG--NWWGIMPSYTDL--SLAVKIVNVIPSNKERNIPSV 79 
                                   77888999999999*****************************9..999*******99..********************* PP

                                   EEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHH.HS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHH CS
               OCD_Mu_crystall  86 talvvLndpetGvplalmdatlltalRTaAvsavaaky.LarkdasvlaiiGaGvqaetqlealkavldikevriydrdee 165
                                   +++v+L++p+tG  la++d+ +lta+RT  +s ++a   +  +   +l+iiGaG+ a+ +l+     +++ +v i +r+++
  gi|70608073|ref|YP_256943.1|  80 QGVVILMSPDTGETLAILDGLVLTAIRTSSASILSAELaMNTRTIGTLGIIGAGTEARYHLKLGLSYFKVGRVLISARRNH 160
                                   **********************************9985245667789****************************999865 PP

                                   HHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCE.EEE. CS
               OCD_Mu_crystall 166 aaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkrad.ifv. 244
                                          +l + ef  +a++  e++  +ad++  +T + +p++  +++    hi  +ga  p+ +e+ddd +++ + ++v 
  gi|70608073|ref|YP_256943.1| 161 -------YLLAKEFGAEAVE-LEKVLREADVIFSTTSSSSPVILGKYLRDDFHISSIGAHTPESREIDDDTIRKIEtYMVd 233
                                   .......3444477778775.7889*******************************************9987776516666 PP

                                   SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHC.TSS-..-STTSEEEEE----HHHHHHHHHHHHHHHCCC CS
               OCD_Mu_crystall 245 dseaqareeGeiqvaiekgvlaedakvaelgevia.GkkpGRtsdeeitlfdsvGlaveDvaaaklvyeraeek 317
                                   + ea a+e G+  ++++ gvl++ +kv e+gevi+ G        +   lf+ vG+a eD  +a ++y  a++k
  gi|70608073|ref|YP_256943.1| 234 SVEAVANETGDYIQPVNSGVLRK-EKVIEIGEVINrGLNV-----KRPSLFKTVGIASEDNLTAYMAYKVALKK 301
                                   778999************99876.5678******725554.....5567*******************988765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.5e-08   0.00011      15      93 ..     127     198 ..     114     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-08
                                   EEEES-SHHHHHHHHH.HHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HH CS
                  Shikimate_DH  15 vlliGaGemaelvakh.LlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepileke 93 
                                     +iGaG  a+  +k  L+  +v +v++  R       la+e+++e        el+++l+eadv++s t+s++p++  +
  gi|70608073|ref|YP_256943.1| 127 LGIIGAGTEARYHLKLgLSYFKVGRVLISARRN--HYLLAKEFGAE------AVELEKVLREADVIFSTTSSSSPVILGK 198
                                   579****99999988549999*******99965..578*****777......45677889***************99765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-06    0.0079      37      99 ..     125     188 ..      92     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                                   SEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                  2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                    t+GiiG+G  ++   k+    f++  + ++ ++++   ++e g+e v+le++l+e+D+++ ++
  gi|70608073|ref|YP_256943.1| 125 GTLGIIGAGTEARYHLKLGLsYFKVGRVLISARRNHYLLAKEFGAEAVELEKVLREADVIFSTT 188
                                   599*********999988544999955555555565667999******************8765 PP

>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.3e-05      0.24      84     146 ..      56     121 ..      41     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHHHHSSS-TTSEEEEEEEE-S..S----SS-HHHHHHHHHHTT-EEEEEE.ESS--HHHH CS
                          Ssl1  84 naLelalasLkkvpshasrevliifss..lstcDPgdiyetidelkkekirvsvig.Lsaevavck 146
                                     L+la++ ++ +ps  +r++  + +   l++ D g+   ++d l+ + ir s  + Lsae+a+ +
  gi|70608073|ref|YP_256943.1|  56 TDLSLAVKIVNVIPSNKERNIPSVQGVviLMSPDTGETLAILDGLVLTAIRTSSASiLSAELAMNT 121
                                   5699*****************99988633678899****************98766489*998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2069.74
//
Query:       gi|70608074|ref|YP_256944.1|  [L=202]
Description: hypothetical protein Saci_2373 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-45  154.9   0.0    2.4e-45  154.6   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
  ------ inclusion threshold ------
       0.23   11.4   1.6        1.2    9.2   0.7    2.4  2  Mistic           Membrane-integrating protein Mistic


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0   2.6e-49   2.4e-45       2     163 ..      31     184 ..      30     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 2.6e-49
                                   XXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S CS
               Cob_adeno_trans   2 yTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkk 82 
                                   yT +GD+G+T+l +g +v Kd+  v a+G++Delns +g++++l+     ++ke+Le +q ++f+l +e+a       + +
  gi|70608074|ref|YP_256944.1|  31 YTGSGDSGKTRLPSGGEVWKDEDLVVALGDLDELNSSLGVVISLY----PDIKEVLEAVQFDIFELSSEIAG-----FEMN 102
                                   9*****************************************776....589******************94.....4568 PP

                                   --HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHHH CS
               Cob_adeno_trans  83 iteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvlar 162
                                   ++ee+v+++ek i+e++++l+p+k+f+lpgg+ a+++lh+ R++cRraER++v+l +++ +++   kylNRLS lLf+la 
  gi|70608074|ref|YP_256944.1| 103 FDEEKVKHVEKLIEEYSKTLEPIKNFVLPGGHIASSSLHLSRAICRRAERSIVRLLKTNrAKQIHEKYLNRLSTLLFILAL 183
                                   99999**************************************************997755566669************98 PP

                                   H CS
               Cob_adeno_trans 163 v 163
                                   +
  gi|70608074|ref|YP_256944.1| 184 Y 184
                                   7 PP

>> Mistic  Membrane-integrating protein Mistic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7   0.00013       1.2       9      56 ..      61     109 ..      58     126 .. 0.79
   2 ?   -3.1   0.0      0.87   7.8e+03      20      32 ..     181     193 ..     176     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                                   HHTTTHHHHHHHHH--SSS-SS-SS-SHH.HHHHHHHHHHHHTSSSS-H CS
                        Mistic   9 iDkmnegldafieLYNeseedkpliefee.evleaiekAkekYGeevvn 56 
                                   +D++n +l ++i LY + +e  + ++f+  e  ++i      + ee+v+
  gi|70608074|ref|YP_256944.1|  61 LDELNSSLGVVISLYPDIKEVLEAVQFDIfELSSEIAGFEMNFDEEKVK 109
                                   8*************************99536667777666666666664 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.87
                                   HHH--SSS-SS-S CS
                        Mistic  20 ieLYNeseedkpl 32 
                                   + LY + ++++p 
  gi|70608074|ref|YP_256944.1| 181 LALYVNKKTNNPN 193
                                   5677777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1416.14
//
Query:       gi|70608075|ref|YP_256945.1|  [L=1074]
Description: hypothetical protein Saci_2374 [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-06   25.6   0.4    1.3e-05   24.6   0.4    1.4  1  Peptidase_S8    Subtilase family
     0.0016   18.8   0.0     0.0061   16.9   0.0    2.0  2  Pro-kuma_activ  Pro-kumamolisin, activation domain
  ------ inclusion threshold ------
      0.068   13.0   0.1       0.14   12.0   0.1    1.4  1  Alph_Pro_TM     Putative transmembrane protein (Alph_Pro_TM)


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.4   2.2e-09   1.3e-05      80     265 ..     250     454 ..     238     462 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-09
                                   SSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-SEEEE-EE......SCETTCHHCHHHHHH...HHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxx...xxxxxx RF
                  Peptidase_S8  80 gekngvapgakilsvkvldtsggsmetgteliraieeaaedkvdvinmslg......estslpktgrsieal...ainrav 151
                                   ++++ +ap+a i  + v + ++      +e++++i ++++  v v++ s+g       + +lp ++     l   +++++ 
  gi|70608075|ref|YP_256945.1| 250 EYAHSIAPSAGIV-LYVANSNLAL----PEILANIVQDNQ--VAVLSQSFGipeiyfLTGELPLSY-----LqsiMYEYWL 318
                                   5666677777776.4444444433....567777777766..888888888665555233333322.....0233777777 PP

                                   .CC.T-EEEEE--SS-T-HHEEE-TTCEEC..TTTSTTCEEEEEES..................TTSSB-TT--B-TT... CS
                                   xxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx..................xxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 152 nkk.gvlvviSaGNngktgsslqagspvgt..pstsknvitvgayt..................tegkiapfSsrGpssdg 211
                                    +  g+ +v+S+G  g tg ++  + +++   p++   v++vg+++                          S+ G ss  
  gi|70608075|ref|YP_256945.1| 319 GEAlGITFVASSGDAGATGYNFYLSPMGSQlvPASIPYVLAVGGTSlfasynqtyqtawsgqsiL-----GSSTGGYSSLF 394
                                   6667************9999554444444478*****************9977777777444442.....33333333333 PP

                                   ....-EEEE-S-CCCCCCCCCHHHTTTHH.............EEEE-SHHHCHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 212 klkpdivapGgnivstwsrqsnnsaglss.............yqsmsGTSmAsPnaagaaAlllsal 265
                                   +  +  +  G   v+++   +       +             +  + GTS AsP ++g++Al  + +
  gi|70608075|ref|YP_256945.1| 395 PSPYYQSLSGFRKVPDVAALA-------DpytgvkvvyvnneTVIVGGTSVASPIVSGILALTVQVK 454
                                   333333333333333333333.......0223333466667799******************99865 PP

>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     1e-06    0.0061      15     105 ..      37     114 ..      27     130 .. 0.93
   2 ?   -3.6   0.0         2   1.2e+04      49      92 ..     157     200 ..     155     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1e-06
                Pro-kuma_activ  15 lpvrigLkqnnlekledflmdvsdpkspnygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtkgwiafsatva 95 
                                   ++v+i+++++nle l+ ++++         +k l+++e+ +lf ps++ i+++ + L+++gi+ +    t ++i+f+a+  
  gi|70608075|ref|YP_256945.1|  37 VSVSIVVPPKNLELLQIYIQQ---------HKVLNEDELYSLFIPSNK-ISQLVDLLKDNGIQPNV---TLNVISFQASPY 104
                                   7899************99988.........8*****************.***************99...************ PP

                Pro-kuma_activ  96 qverllktsf 105
                                    ve+l+k ++
  gi|70608075|ref|YP_256945.1| 105 LVEKLFKGQY 114
                                   ******9876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                Pro-kuma_activ  49 taeevaelfapseeaidaV..rnwLessgiaasrhsdtkgwiafsa 92 
                                   t+e+++ +  +++ +i +    ++L ++gi+ +    + g+++f++
  gi|70608075|ref|YP_256945.1| 157 TQEQLQGYSISTPNDIRTAynVSYLLDNGITGKG--VNIGILVFDG 200
                                   6666666666666666554225799999999888..7777777765 PP

>> Alph_Pro_TM  Putative transmembrane protein (Alph_Pro_TM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.3e-05      0.14     129     170 ..     761     802 ..     756     838 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                   Alph_Pro_TM 129 eraglYreeeggvefldgtlfraevalPanvpeGkytvevyl 170
                                   +   +Y+++ ++v +++++ +  ++++P n+  G ytve+++
  gi|70608075|ref|YP_256945.1| 761 NGLTYYSTNVNAVPISSSSYYISKIQVPLNLSSGYYTVEAIA 802
                                   55679**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1074 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 6769.02
//
Query:       gi|70608076|ref|YP_256946.1|  [L=411]
Description: isocitrate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.1e-104  350.4   0.1   1.3e-104  350.1   0.1    1.0  1  Iso_dh      Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
      0.061   13.3   0.0       0.13   12.2   0.0    1.5  1  P22_Tail-4  P22 tail accessory factor
        0.4   11.0   0.1        0.4   11.0   0.1    2.2  3  Dodecin     Dodecin


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.1   0.1  2.2e-108  1.3e-104       2     347 ..      29     403 ..      28     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 350.1 bits;  conditional E-value: 2.2e-108
                                   EEEEEESTTHHHHHHHHHHHHHHHHHHHT...-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSS CS
                        Iso_dh   2 iallegdgiGpevveaalkvlkaakekag...lelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekev 79 
                                   i  +egdgiGpe++++a++v+++a+eka+   +e+++ ev++G++a + tg+ +p+et +++ +++vvl+g+++tp +k+ 
  gi|70608076|ref|YP_256946.1|  29 ILYIEGDGIGPEITNSAIRVVNKAVEKAYkssREIKWLEVYAGEKANKITGDRFPKETQDMLLKYRVVLKGPLETPIGKGW 109
                                   7789**********************9998999************************************************ PP

                                   SHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET..............TG. CS
                        Iso_dh  80 rpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg..............si. 145
                                   ++ n  +a+r +ldl+an+rpvk++  ++ +splk+  +e+vd++i+Re+t+++Y+g+e  +++              +  
  gi|70608076|ref|YP_256946.1| 110 KSIN--VAIRLMLDLYANIRPVKYI--EGLESPLKH--PEKVDMIIFRENTDDLYRGIEFPYDSeeakkirkflreelKVd 184
                                   ****..*******************..7999****8..9********************99988899**********9545 PP

                                   .GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC.................TT CS
                        Iso_dh 146 fteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee.................ey 208
                                    ++++++++k++s+  ++ri r+a+++Al++ +kkvt+++K+nv+k +e  +r++++eva +                   
  gi|70608076|ref|YP_256946.1| 185 IEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEgSFREWAYEVALNeyrdkivteeeinrgvnSE 265
                                   7999*******************************************************9999***************999 PP

                                   TTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S- CS
                        Iso_dh 209 pdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaN 289
                                   ++++l+++++D++++q++ +p+++d+i+++N++GD++SD+a al+G +G+l +a++g +  ++fEa+HG+ap++agk++aN
  gi|70608076|ref|YP_256946.1| 266 GKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIG-DTGGMFEAIHGTAPKYAGKNVAN 345
                                   9********************************************************.789******************** PP

                                   THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS.TCCCHHHHHHHH CS
                        Iso_dh 290 piavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea.akevstsefgda 347
                                   p++ i S +lmL + +g++eaA+ iekA+++++++++vT+D+a+    + + t+e++d 
  gi|70608076|ref|YP_256946.1| 346 PTGIIKSCELMLYF-MGWSEAARLIEKAINESIKQKKVTQDIARYLgITPLGTKEYTDT 403
                                   **************.*****************************9989999****9996 PP

>> P22_Tail-4  P22 tail accessory factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05      0.13      58     117 ..     174     233 ..     147     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                   EES-SSSSSSSSSSEE---STTHHHHHHHHHHHSTGGGTS---HHHHHHHHHHHHHHTHH CS
                    P22_Tail-4  58 ykfaadeeepaedddsGlsrkavsaviynLalrilsdyaleptakviatakagkeaLlkd 117
                                    kf  +e +++ +dd G+  k +s    + + r++ +yal+ + k ++  ++g  + +++
  gi|70608076|ref|YP_256946.1| 174 RKFLREELKVDIEDDTGIGLKVMSKFKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTE 233
                                   68999999************************************9999888887666665 PP

>> Dodecin  Dodecin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.7e-05       0.4      19      39 ..      49      69 ..      42      73 .. 0.90
   2 ?   -3.2   0.0       1.8   1.1e+04      29      48 ..     169     188 ..     167     189 .. 0.76
   3 ?   -3.6   0.1       2.3   1.4e+04      15      25 ..     369     379 ..     365     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                                  HHHHHHHHHHH-SSEEEEEEE CS
                       Dodecin 19 iqnAiaeAsktlrnirwveVk 39
                                  +++A+++A k+ r+i+w eV 
  gi|70608076|ref|YP_256946.1| 49 VNKAVEKAYKSSREIKWLEVY 69
                                  799****************95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                                   H-SSEEEEEEEEEEEEECTT CS
                       Dodecin  29 tlrnirwveVketrahvedg 48 
                                     ++ir +  +e+++++ed+
  gi|70608076|ref|YP_256946.1| 169 EAKKIRKFLREELKVDIEDD 188
                                   56778888888999999986 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHH CS
                       Dodecin  15 wedAiqnAiae 25 
                                   +e+Ai++ i++
  gi|70608076|ref|YP_256946.1| 369 IEKAINESIKQ 379
                                   57777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2651.41
//
[ok]
